Multiple sequence alignment - TraesCS2D01G471400

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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 TraesCS2D01G471400 chr2D 100.000 3128 0 0 1 3128 575360303 575357176 0.000000e+00 5777.0
1 TraesCS2D01G471400 chr2D 79.482 463 55 22 370 820 140713570 140713136 3.050000e-75 292.0
2 TraesCS2D01G471400 chr2A 94.749 2552 113 8 5 2541 713544556 713542011 0.000000e+00 3951.0
3 TraesCS2D01G471400 chr2A 91.204 432 31 3 2703 3128 713541967 713541537 5.820000e-162 580.0
4 TraesCS2D01G471400 chr2B 92.493 2491 137 13 2 2459 691453902 691451429 0.000000e+00 3518.0
5 TraesCS2D01G471400 chr2B 90.909 418 30 4 2715 3126 691451090 691450675 3.520000e-154 555.0
6 TraesCS2D01G471400 chr2B 91.282 195 9 3 2557 2749 691451279 691451091 3.090000e-65 259.0
7 TraesCS2D01G471400 chr6A 87.983 1190 128 8 947 2128 617686204 617687386 0.000000e+00 1391.0
8 TraesCS2D01G471400 chr6A 82.031 128 10 4 712 839 617685961 617686075 2.570000e-16 97.1
9 TraesCS2D01G471400 chr6D 87.376 1212 129 11 947 2135 472306494 472305284 0.000000e+00 1369.0
10 TraesCS2D01G471400 chr6D 78.543 508 52 29 370 857 472307068 472306598 6.600000e-72 281.0
11 TraesCS2D01G471400 chr6B 87.380 1149 130 8 989 2131 716976748 716975609 0.000000e+00 1304.0
12 TraesCS2D01G471400 chr1D 77.949 585 65 31 273 820 432956219 432955662 1.090000e-79 307.0
13 TraesCS2D01G471400 chr7D 86.007 293 29 8 538 825 24431643 24431928 1.410000e-78 303.0
14 TraesCS2D01G471400 chr7D 79.437 462 58 18 370 820 26614501 26614936 3.050000e-75 292.0
15 TraesCS2D01G471400 chr7D 82.192 365 38 13 464 820 73007823 73007478 3.950000e-74 289.0
16 TraesCS2D01G471400 chr7D 81.096 365 41 14 464 820 190196569 190196225 1.850000e-67 267.0
17 TraesCS2D01G471400 chrUn 81.918 365 39 13 464 820 96713174 96713519 1.840000e-72 283.0
18 TraesCS2D01G471400 chr5D 83.486 327 28 13 500 820 149768358 149768664 6.600000e-72 281.0
19 TraesCS2D01G471400 chr4D 81.644 365 40 13 464 820 21034736 21035081 8.540000e-71 278.0
20 TraesCS2D01G471400 chr5B 85.088 114 13 3 719 831 674553243 674553133 2.550000e-21 113.0


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 TraesCS2D01G471400 chr2D 575357176 575360303 3127 True 5777.00 5777 100.000000 1 3128 1 chr2D.!!$R2 3127
1 TraesCS2D01G471400 chr2A 713541537 713544556 3019 True 2265.50 3951 92.976500 5 3128 2 chr2A.!!$R1 3123
2 TraesCS2D01G471400 chr2B 691450675 691453902 3227 True 1444.00 3518 91.561333 2 3126 3 chr2B.!!$R1 3124
3 TraesCS2D01G471400 chr6A 617685961 617687386 1425 False 744.05 1391 85.007000 712 2128 2 chr6A.!!$F1 1416
4 TraesCS2D01G471400 chr6D 472305284 472307068 1784 True 825.00 1369 82.959500 370 2135 2 chr6D.!!$R1 1765
5 TraesCS2D01G471400 chr6B 716975609 716976748 1139 True 1304.00 1304 87.380000 989 2131 1 chr6B.!!$R1 1142
6 TraesCS2D01G471400 chr1D 432955662 432956219 557 True 307.00 307 77.949000 273 820 1 chr1D.!!$R1 547

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
448 477 0.738389 GTATGGTTGTTCATGGCGGG 59.262 55.000 0.0 0.0 0.0 6.13 F
726 784 1.307430 GGGGAGGAAGAGGAGGCTT 60.307 63.158 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2125 0.325933 CTCCCTCAATGACAGCCACA 59.674 55.0 0.0 0.0 0.00 4.17 R
2643 2911 0.613012 AAACATCCAGCCTTCTGCCC 60.613 55.0 0.0 0.0 42.71 5.36 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
60 62 2.432628 GCGGCTGCACGACTTACT 60.433 61.111 14.08 0.00 42.15 2.24
96 98 4.020662 TGGAATTTACAAGGGAATTGGTGC 60.021 41.667 0.00 0.00 43.68 5.01
127 129 3.368116 GCTGTATACTGACAGGAAACGGT 60.368 47.826 13.44 0.00 45.85 4.83
143 145 5.106830 GGAAACGGTTAACCAGACATGTAAG 60.107 44.000 24.14 6.39 35.14 2.34
155 157 1.877443 ACATGTAAGTTGTCCGGTTGC 59.123 47.619 0.00 0.00 0.00 4.17
192 194 3.498397 GTGTGCATACTACAAAGCTGTGT 59.502 43.478 15.35 15.35 36.96 3.72
233 235 5.947228 ACCACACACAATTTATCACTGAG 57.053 39.130 0.00 0.00 0.00 3.35
263 265 5.784750 TGAGCGAAAACATCAGTTCATAG 57.215 39.130 0.00 0.00 36.84 2.23
282 284 5.716228 TCATAGAGGCAATTGTGAACCAAAT 59.284 36.000 7.40 0.00 36.44 2.32
318 326 4.274459 GCCAATACTAAATGACAGAGCAGG 59.726 45.833 0.00 0.00 0.00 4.85
320 328 2.409948 ACTAAATGACAGAGCAGGGC 57.590 50.000 0.00 0.00 0.00 5.19
409 435 4.332543 TCAGTACCATTCGAATTCACATGC 59.667 41.667 8.21 0.00 0.00 4.06
422 448 5.680594 ATTCACATGCCCAAACAATACAT 57.319 34.783 0.00 0.00 0.00 2.29
448 477 0.738389 GTATGGTTGTTCATGGCGGG 59.262 55.000 0.00 0.00 0.00 6.13
609 662 2.978010 CCCACGCCGCAGAACTTT 60.978 61.111 0.00 0.00 0.00 2.66
647 700 3.428664 TGCCACCCATCCCATCCC 61.429 66.667 0.00 0.00 0.00 3.85
648 701 3.428664 GCCACCCATCCCATCCCA 61.429 66.667 0.00 0.00 0.00 4.37
649 702 2.929483 CCACCCATCCCATCCCAG 59.071 66.667 0.00 0.00 0.00 4.45
690 743 4.859245 TCAGATCAGAAAGAAATCGTCACG 59.141 41.667 0.00 0.00 0.00 4.35
716 769 1.382695 GACCGGATCAGGGGAGGAA 60.383 63.158 16.73 0.00 35.02 3.36
726 784 1.307430 GGGGAGGAAGAGGAGGCTT 60.307 63.158 0.00 0.00 0.00 4.35
827 894 3.827898 GGAGGACGACGAGCAGGG 61.828 72.222 0.00 0.00 0.00 4.45
1079 1221 3.858989 GCTGCTCTCCTTTCGCGC 61.859 66.667 0.00 0.00 0.00 6.86
1313 1464 2.687200 CATCACCTCCCCGTCCCA 60.687 66.667 0.00 0.00 0.00 4.37
1593 1744 2.746277 GGCTTCCACGCCGACAAT 60.746 61.111 0.00 0.00 40.79 2.71
1597 1748 1.806623 GCTTCCACGCCGACAATATCT 60.807 52.381 0.00 0.00 0.00 1.98
1956 2107 1.918253 GCTGGGATCCACCATCAGT 59.082 57.895 15.23 0.00 40.36 3.41
2118 2269 2.171448 CAGGGTTATCTCCACCTCAAGG 59.829 54.545 0.00 0.00 42.17 3.61
2145 2296 5.046520 GGAGTAGGAAGGTACATTGTCTTGT 60.047 44.000 0.00 0.00 0.00 3.16
2475 2739 5.616488 TCTACTAAACCCGTGCATTTTTC 57.384 39.130 0.00 0.00 0.00 2.29
2479 2743 3.297830 AAACCCGTGCATTTTTCTAGC 57.702 42.857 0.00 0.00 0.00 3.42
2546 2813 9.657121 GTGATATTTTAGATTTCTGTTGCTAGC 57.343 33.333 8.10 8.10 0.00 3.42
2547 2814 9.618890 TGATATTTTAGATTTCTGTTGCTAGCT 57.381 29.630 17.23 0.00 0.00 3.32
2548 2815 9.875675 GATATTTTAGATTTCTGTTGCTAGCTG 57.124 33.333 17.23 3.90 0.00 4.24
2549 2816 7.693969 ATTTTAGATTTCTGTTGCTAGCTGT 57.306 32.000 17.23 0.00 0.00 4.40
2550 2817 6.486253 TTTAGATTTCTGTTGCTAGCTGTG 57.514 37.500 17.23 3.89 0.00 3.66
2551 2818 3.341823 AGATTTCTGTTGCTAGCTGTGG 58.658 45.455 17.23 4.26 0.00 4.17
2552 2819 2.638480 TTTCTGTTGCTAGCTGTGGT 57.362 45.000 17.23 0.00 0.00 4.16
2555 2822 1.001293 TCTGTTGCTAGCTGTGGTCAG 59.999 52.381 17.23 13.73 43.87 3.51
2568 2835 2.289631 TGTGGTCAGTACAATGAGGCAG 60.290 50.000 0.00 0.00 0.00 4.85
2578 2845 5.720041 AGTACAATGAGGCAGTAACTAAGGA 59.280 40.000 0.00 0.00 0.00 3.36
2601 2869 6.267014 GGATGCACTAGTTAGGTGATAGGTTA 59.733 42.308 0.00 0.00 36.89 2.85
2625 2893 0.251297 TGAACCACAAGCATCAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
2638 2906 2.953093 TCAGGGGGTACTGGTAATGA 57.047 50.000 0.00 0.00 38.98 2.57
2639 2907 3.208570 TCAGGGGGTACTGGTAATGAA 57.791 47.619 0.00 0.00 38.98 2.57
2640 2908 3.112263 TCAGGGGGTACTGGTAATGAAG 58.888 50.000 0.00 0.00 38.98 3.02
2641 2909 3.112263 CAGGGGGTACTGGTAATGAAGA 58.888 50.000 0.00 0.00 34.84 2.87
2642 2910 3.134804 CAGGGGGTACTGGTAATGAAGAG 59.865 52.174 0.00 0.00 34.84 2.85
2643 2911 2.438392 GGGGGTACTGGTAATGAAGAGG 59.562 54.545 0.00 0.00 0.00 3.69
2644 2912 2.438392 GGGGTACTGGTAATGAAGAGGG 59.562 54.545 0.00 0.00 0.00 4.30
2687 2955 2.345991 GCTCAACCCAGGCACGTA 59.654 61.111 0.00 0.00 0.00 3.57
2692 2960 1.078426 AACCCAGGCACGTAGATGC 60.078 57.895 0.00 0.00 45.34 3.91
2965 3300 1.626825 GGACTGGGGCTTAGTACACAA 59.373 52.381 0.00 0.00 0.00 3.33
3068 3403 6.887002 GGAGGAAAATTCAAATAGAGACCAGT 59.113 38.462 0.00 0.00 0.00 4.00
3099 3434 3.042481 AAAAAGTGGAGCCTGGAGC 57.958 52.632 0.00 0.00 44.25 4.70
3110 3445 0.250467 GCCTGGAGCTGTGTTGAGAA 60.250 55.000 0.00 0.00 38.99 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.379977 TGTTGGCGGTTTGGGTTCA 60.380 52.632 0.00 0.00 0.00 3.18
57 58 9.945904 TGTAAATTCCACATGTTATGTACAGTA 57.054 29.630 0.33 0.00 42.70 2.74
60 62 8.735315 CCTTGTAAATTCCACATGTTATGTACA 58.265 33.333 0.00 0.00 42.70 2.90
96 98 5.444663 TGTCAGTATACAGCTATGCTCTG 57.555 43.478 5.50 0.00 36.40 3.35
127 129 4.992319 CGGACAACTTACATGTCTGGTTAA 59.008 41.667 0.00 0.00 45.99 2.01
155 157 1.077501 ACACCAGAATGCATCGGGG 60.078 57.895 0.00 4.95 46.63 5.73
233 235 0.790207 TGTTTTCGCTCATCTGTCGC 59.210 50.000 0.00 0.00 0.00 5.19
263 265 3.187022 GCAATTTGGTTCACAATTGCCTC 59.813 43.478 15.59 0.00 41.90 4.70
299 302 3.455910 TGCCCTGCTCTGTCATTTAGTAT 59.544 43.478 0.00 0.00 0.00 2.12
318 326 0.318445 CAGTTGCTGTTTGCTCTGCC 60.318 55.000 0.00 0.00 43.37 4.85
320 328 3.181493 ACTTTCAGTTGCTGTTTGCTCTG 60.181 43.478 0.00 0.00 43.37 3.35
409 435 2.261345 CGCTGCAATGTATTGTTTGGG 58.739 47.619 0.00 2.70 39.88 4.12
422 448 1.598882 TGAACAACCATACGCTGCAA 58.401 45.000 0.00 0.00 0.00 4.08
448 477 1.751927 CTGGATTGGTCAGCCCAGC 60.752 63.158 0.00 0.00 46.31 4.85
454 483 0.107508 ATGGCGTCTGGATTGGTCAG 60.108 55.000 0.00 0.00 0.00 3.51
647 700 1.725557 GCATGCTCTGACCATGGCTG 61.726 60.000 13.04 9.05 40.24 4.85
648 701 1.453379 GCATGCTCTGACCATGGCT 60.453 57.895 13.04 0.00 40.24 4.75
649 702 1.445716 GAGCATGCTCTGACCATGGC 61.446 60.000 35.26 10.02 40.24 4.40
690 743 0.598680 CCTGATCCGGTCAATCGAGC 60.599 60.000 0.00 0.00 36.14 5.03
716 769 0.612174 TGCGACTGTAAGCCTCCTCT 60.612 55.000 5.47 0.00 37.60 3.69
807 874 2.750637 TGCTCGTCGTCCTCCTCC 60.751 66.667 0.00 0.00 0.00 4.30
808 875 2.766400 CCTGCTCGTCGTCCTCCTC 61.766 68.421 0.00 0.00 0.00 3.71
809 876 2.752238 CCTGCTCGTCGTCCTCCT 60.752 66.667 0.00 0.00 0.00 3.69
845 921 0.889186 AACAATCTCCACCACGCACC 60.889 55.000 0.00 0.00 0.00 5.01
846 922 0.517316 GAACAATCTCCACCACGCAC 59.483 55.000 0.00 0.00 0.00 5.34
847 923 0.396435 AGAACAATCTCCACCACGCA 59.604 50.000 0.00 0.00 0.00 5.24
890 972 1.362406 GAAGAGTTACTGGCAGCCGC 61.362 60.000 15.89 4.73 37.44 6.53
897 979 4.282195 ACCAGAAGTCTGAAGAGTTACTGG 59.718 45.833 25.53 25.53 46.59 4.00
902 984 4.762289 ACAACCAGAAGTCTGAAGAGTT 57.238 40.909 9.95 0.00 46.59 3.01
1079 1221 0.738389 GACTCTGAGCTTCCTCGAGG 59.262 60.000 26.32 26.32 41.13 4.63
1593 1744 1.229209 GAGGATGGCCGGGGAGATA 60.229 63.158 2.18 0.00 39.96 1.98
1884 2035 4.569180 ATGCCGGGAATCAGCGGG 62.569 66.667 0.00 0.00 0.00 6.13
1974 2125 0.325933 CTCCCTCAATGACAGCCACA 59.674 55.000 0.00 0.00 0.00 4.17
2118 2269 5.046520 AGACAATGTACCTTCCTACTCCAAC 60.047 44.000 0.00 0.00 0.00 3.77
2145 2296 7.575414 AATACACATACACAAACCAGACAAA 57.425 32.000 0.00 0.00 0.00 2.83
2242 2401 6.092955 ACAATTAGAACTGACAACCGACTA 57.907 37.500 0.00 0.00 0.00 2.59
2416 2575 9.581289 TTTAAACTATCCATGAAACAGGAAAGA 57.419 29.630 0.00 0.00 37.48 2.52
2417 2576 9.626045 GTTTAAACTATCCATGAAACAGGAAAG 57.374 33.333 11.18 0.00 37.48 2.62
2419 2578 8.698973 TGTTTAAACTATCCATGAAACAGGAA 57.301 30.769 18.72 0.00 37.48 3.36
2420 2579 8.877864 ATGTTTAAACTATCCATGAAACAGGA 57.122 30.769 18.72 0.00 39.40 3.86
2475 2739 2.093106 AGTAGACACAAGGACGGCTAG 58.907 52.381 0.00 0.00 0.00 3.42
2479 2743 3.572584 GTTACAGTAGACACAAGGACGG 58.427 50.000 0.00 0.00 0.00 4.79
2536 2803 1.270518 ACTGACCACAGCTAGCAACAG 60.271 52.381 18.83 16.69 46.95 3.16
2537 2804 0.758734 ACTGACCACAGCTAGCAACA 59.241 50.000 18.83 6.44 46.95 3.33
2538 2805 2.288825 TGTACTGACCACAGCTAGCAAC 60.289 50.000 18.83 1.97 46.95 4.17
2539 2806 1.967779 TGTACTGACCACAGCTAGCAA 59.032 47.619 18.83 0.00 46.95 3.91
2540 2807 1.627864 TGTACTGACCACAGCTAGCA 58.372 50.000 18.83 0.00 46.95 3.49
2541 2808 2.743636 TTGTACTGACCACAGCTAGC 57.256 50.000 6.62 6.62 46.95 3.42
2542 2809 4.428209 CTCATTGTACTGACCACAGCTAG 58.572 47.826 0.00 0.00 46.95 3.42
2543 2810 3.195610 CCTCATTGTACTGACCACAGCTA 59.804 47.826 0.00 0.00 46.95 3.32
2544 2811 2.027745 CCTCATTGTACTGACCACAGCT 60.028 50.000 0.00 0.00 46.95 4.24
2545 2812 2.350522 CCTCATTGTACTGACCACAGC 58.649 52.381 0.00 0.00 46.95 4.40
2547 2814 1.696884 TGCCTCATTGTACTGACCACA 59.303 47.619 0.00 0.00 0.00 4.17
2548 2815 2.289694 ACTGCCTCATTGTACTGACCAC 60.290 50.000 0.00 0.00 0.00 4.16
2549 2816 1.977854 ACTGCCTCATTGTACTGACCA 59.022 47.619 0.00 0.00 0.00 4.02
2550 2817 2.770164 ACTGCCTCATTGTACTGACC 57.230 50.000 0.00 0.00 0.00 4.02
2551 2818 4.822026 AGTTACTGCCTCATTGTACTGAC 58.178 43.478 0.00 0.00 0.00 3.51
2552 2819 6.351033 CCTTAGTTACTGCCTCATTGTACTGA 60.351 42.308 0.00 0.00 0.00 3.41
2555 2822 5.974108 TCCTTAGTTACTGCCTCATTGTAC 58.026 41.667 0.00 0.00 0.00 2.90
2568 2835 6.979238 CACCTAACTAGTGCATCCTTAGTTAC 59.021 42.308 14.07 0.00 33.60 2.50
2578 2845 7.290248 ACATAACCTATCACCTAACTAGTGCAT 59.710 37.037 0.00 0.00 35.14 3.96
2601 2869 3.949754 CCTGATGCTTGTGGTTCATACAT 59.050 43.478 0.00 0.00 0.00 2.29
2617 2885 3.045634 TCATTACCAGTACCCCCTGATG 58.954 50.000 0.00 0.00 34.23 3.07
2625 2893 2.158798 GCCCCTCTTCATTACCAGTACC 60.159 54.545 0.00 0.00 0.00 3.34
2638 2906 2.610519 CCAGCCTTCTGCCCCTCTT 61.611 63.158 0.00 0.00 42.71 2.85
2639 2907 2.854420 ATCCAGCCTTCTGCCCCTCT 62.854 60.000 0.00 0.00 42.71 3.69
2640 2908 2.381941 ATCCAGCCTTCTGCCCCTC 61.382 63.158 0.00 0.00 42.71 4.30
2641 2909 2.286732 ATCCAGCCTTCTGCCCCT 60.287 61.111 0.00 0.00 42.71 4.79
2642 2910 2.123982 CATCCAGCCTTCTGCCCC 60.124 66.667 0.00 0.00 42.71 5.80
2643 2911 0.613012 AAACATCCAGCCTTCTGCCC 60.613 55.000 0.00 0.00 42.71 5.36
2644 2912 1.203287 GAAAACATCCAGCCTTCTGCC 59.797 52.381 0.00 0.00 42.71 4.85
2684 2952 3.579709 ACACTCTTTCACTGCATCTACG 58.420 45.455 0.00 0.00 0.00 3.51
2687 2955 6.017605 CAGTTTTACACTCTTTCACTGCATCT 60.018 38.462 0.00 0.00 30.92 2.90
2692 2960 5.817816 AGGACAGTTTTACACTCTTTCACTG 59.182 40.000 0.00 0.00 36.93 3.66
2775 3106 0.674895 GTTACCTGCTGCTGTCCCAG 60.675 60.000 0.00 0.00 35.93 4.45
2781 3112 2.072298 GACTTCAGTTACCTGCTGCTG 58.928 52.381 0.00 0.00 38.66 4.41
2875 3210 6.127310 CCTGGTTATTAGCACTAGAGACACTT 60.127 42.308 0.00 0.00 0.00 3.16
2965 3300 4.564406 CCTCTGTTTACCTCTGCAATCACT 60.564 45.833 0.00 0.00 0.00 3.41
3016 3351 1.771854 TCACCTCCAACCAGTTGCTAA 59.228 47.619 4.96 0.00 39.16 3.09
3018 3353 0.773644 ATCACCTCCAACCAGTTGCT 59.226 50.000 4.96 0.00 39.16 3.91
3019 3354 1.620822 AATCACCTCCAACCAGTTGC 58.379 50.000 4.96 0.00 39.16 4.17
3093 3428 3.144506 ACATTTCTCAACACAGCTCCAG 58.855 45.455 0.00 0.00 0.00 3.86
3099 3434 4.534168 CTTGCTGACATTTCTCAACACAG 58.466 43.478 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.