Multiple sequence alignment - TraesCS2D01G168800

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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 TraesCS2D01G168800 chr2D 100.000 3110 0 0 1 3110 112867190 112864081 0.000000e+00 5744
1 TraesCS2D01G168800 chr2D 77.492 311 48 15 475 766 2508184 2507877 1.920000e-37 167
2 TraesCS2D01G168800 chr2A 90.310 3189 147 47 1 3110 114302504 114299399 0.000000e+00 4028
3 TraesCS2D01G168800 chr2A 79.408 777 142 10 5 766 684904804 684904031 1.640000e-147 532
4 TraesCS2D01G168800 chr2B 95.073 2253 88 11 1 2248 163233378 163231144 0.000000e+00 3524
5 TraesCS2D01G168800 chr2B 88.778 900 25 18 2253 3110 163230707 163229842 0.000000e+00 1033
6 TraesCS2D01G168800 chr4A 78.851 766 135 19 19 766 437498789 437499545 2.790000e-135 492
7 TraesCS2D01G168800 chr4A 81.974 233 40 2 10 241 477793683 477793452 2.450000e-46 196
8 TraesCS2D01G168800 chr4D 77.966 708 121 28 66 766 488461627 488462306 8.030000e-111 411
9 TraesCS2D01G168800 chr4D 76.056 497 99 18 7 497 98574777 98575259 1.110000e-59 241
10 TraesCS2D01G168800 chr6D 76.608 684 130 22 91 766 457477492 457478153 1.770000e-92 350
11 TraesCS2D01G168800 chr5D 73.538 975 195 50 1157 2095 456751303 456752250 2.330000e-81 313
12 TraesCS2D01G168800 chr5D 76.112 427 78 6 1 417 118220671 118221083 5.260000e-48 202
13 TraesCS2D01G168800 chr5B 72.970 973 204 48 1157 2095 558686569 558687516 5.080000e-73 285
14 TraesCS2D01G168800 chr5B 72.543 692 151 27 93 766 160119141 160118471 4.090000e-44 189
15 TraesCS2D01G168800 chr5A 72.951 976 199 51 1157 2095 574784847 574785794 2.360000e-71 279
16 TraesCS2D01G168800 chrUn 74.095 525 122 13 94 610 343636834 343637352 1.460000e-48 204
17 TraesCS2D01G168800 chrUn 73.905 525 120 15 94 610 269401652 269401137 8.800000e-46 195
18 TraesCS2D01G168800 chrUn 73.944 426 98 12 94 511 370803770 370803350 3.210000e-35 159
19 TraesCS2D01G168800 chr4B 73.497 449 97 18 348 779 71337626 71337183 1.930000e-32 150
20 TraesCS2D01G168800 chr7D 78.894 199 37 5 422 618 65579129 65578934 2.520000e-26 130


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 TraesCS2D01G168800 chr2D 112864081 112867190 3109 True 5744.0 5744 100.0000 1 3110 1 chr2D.!!$R2 3109
1 TraesCS2D01G168800 chr2A 114299399 114302504 3105 True 4028.0 4028 90.3100 1 3110 1 chr2A.!!$R1 3109
2 TraesCS2D01G168800 chr2A 684904031 684904804 773 True 532.0 532 79.4080 5 766 1 chr2A.!!$R2 761
3 TraesCS2D01G168800 chr2B 163229842 163233378 3536 True 2278.5 3524 91.9255 1 3110 2 chr2B.!!$R1 3109
4 TraesCS2D01G168800 chr4A 437498789 437499545 756 False 492.0 492 78.8510 19 766 1 chr4A.!!$F1 747
5 TraesCS2D01G168800 chr4D 488461627 488462306 679 False 411.0 411 77.9660 66 766 1 chr4D.!!$F2 700
6 TraesCS2D01G168800 chr6D 457477492 457478153 661 False 350.0 350 76.6080 91 766 1 chr6D.!!$F1 675
7 TraesCS2D01G168800 chr5D 456751303 456752250 947 False 313.0 313 73.5380 1157 2095 1 chr5D.!!$F2 938
8 TraesCS2D01G168800 chr5B 558686569 558687516 947 False 285.0 285 72.9700 1157 2095 1 chr5B.!!$F1 938
9 TraesCS2D01G168800 chr5A 574784847 574785794 947 False 279.0 279 72.9510 1157 2095 1 chr5A.!!$F1 938
10 TraesCS2D01G168800 chrUn 343636834 343637352 518 False 204.0 204 74.0950 94 610 1 chrUn.!!$F1 516

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
620 641 0.393944 GTTTAGGTGTGCTAGGGGCC 60.394 60.0 0.0 0.0 40.92 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2910 0.037326 TAGCTGTCGCACAAGGAAGG 60.037 55.0 0.0 0.0 39.1 3.46 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
207 208 1.563879 CATGGATGTTAGGGTGGTGGA 59.436 52.381 0.00 0.00 0.00 4.02
254 257 0.882484 TTCGGCAGACAACATTGCGA 60.882 50.000 0.00 0.00 41.17 5.10
431 439 1.131420 GCTGCTGAGCGAAAACTCG 59.869 57.895 0.00 0.00 39.68 4.18
439 447 2.736995 CGAAAACTCGGCGCCTCA 60.737 61.111 26.68 10.09 0.00 3.86
522 539 4.988716 TCCGTGACAGGGCTCCGT 62.989 66.667 9.40 0.00 0.00 4.69
541 558 2.034001 CGTGTGAAGACCTTTGTTCGTC 60.034 50.000 0.00 0.00 0.00 4.20
578 595 0.706729 GACGCTTTACACGGTTCTCG 59.293 55.000 0.00 0.00 45.88 4.04
618 639 1.209747 GGAGTTTAGGTGTGCTAGGGG 59.790 57.143 0.00 0.00 0.00 4.79
619 640 0.618981 AGTTTAGGTGTGCTAGGGGC 59.381 55.000 0.00 0.00 42.22 5.80
620 641 0.393944 GTTTAGGTGTGCTAGGGGCC 60.394 60.000 0.00 0.00 40.92 5.80
621 642 0.549169 TTTAGGTGTGCTAGGGGCCT 60.549 55.000 0.84 0.00 40.92 5.19
644 665 1.525619 GGCGTAGTGTTGTGTTGTCTC 59.474 52.381 0.00 0.00 0.00 3.36
1380 1443 2.110213 AACTCCAACCGCTTCGCA 59.890 55.556 0.00 0.00 0.00 5.10
1815 1887 3.177884 AACCAGCTCCAGGGCACA 61.178 61.111 0.00 0.00 34.17 4.57
2122 2269 3.379240 CAGCACTAGTGGAGATCATTCG 58.621 50.000 23.95 0.00 0.00 3.34
2142 2289 1.067364 GTTTGGTGGTGTAAAACGGGG 59.933 52.381 0.00 0.00 0.00 5.73
2143 2290 1.108132 TTGGTGGTGTAAAACGGGGC 61.108 55.000 0.00 0.00 0.00 5.80
2249 2832 9.857656 AATGGAATTTGTAGACATACATGATCT 57.142 29.630 0.00 0.00 41.49 2.75
2250 2833 8.893219 TGGAATTTGTAGACATACATGATCTC 57.107 34.615 0.00 0.00 41.49 2.75
2251 2834 8.485392 TGGAATTTGTAGACATACATGATCTCA 58.515 33.333 0.00 0.00 41.49 3.27
2320 2910 3.686726 GGCTGTCCGATGATTATTCCATC 59.313 47.826 0.00 0.00 37.60 3.51
2324 2914 5.551233 TGTCCGATGATTATTCCATCCTTC 58.449 41.667 0.00 0.00 37.67 3.46
2370 2970 7.252612 TGTTGGTGGAGAGATTATTACTTGA 57.747 36.000 0.00 0.00 0.00 3.02
2373 2973 6.291377 TGGTGGAGAGATTATTACTTGATGC 58.709 40.000 0.00 0.00 0.00 3.91
2565 3189 4.936411 GCATGGTCAAGGATGAGATGATAG 59.064 45.833 0.00 0.00 35.88 2.08
2566 3190 5.512749 GCATGGTCAAGGATGAGATGATAGT 60.513 44.000 0.00 0.00 35.88 2.12
2594 3218 2.270352 TTGCGTTTCCAGTTGGAGAT 57.730 45.000 0.51 0.00 46.36 2.75
2618 3242 3.513680 TCAATGCCATGCAAATCTGAC 57.486 42.857 0.00 0.00 43.62 3.51
2619 3243 2.826725 TCAATGCCATGCAAATCTGACA 59.173 40.909 0.00 0.00 43.62 3.58
2620 3244 3.258622 TCAATGCCATGCAAATCTGACAA 59.741 39.130 0.00 0.00 43.62 3.18
2621 3245 3.520290 ATGCCATGCAAATCTGACAAG 57.480 42.857 0.00 0.00 43.62 3.16
2622 3246 1.546923 TGCCATGCAAATCTGACAAGG 59.453 47.619 0.00 0.00 34.76 3.61
2623 3247 1.820519 GCCATGCAAATCTGACAAGGA 59.179 47.619 0.00 0.00 0.00 3.36
2624 3248 2.429610 GCCATGCAAATCTGACAAGGAT 59.570 45.455 0.00 0.00 0.00 3.24
2625 3249 3.118884 GCCATGCAAATCTGACAAGGATT 60.119 43.478 0.00 0.00 35.25 3.01
2626 3250 7.580168 TGCCATGCAAATCTGACAAGGATTG 62.580 44.000 0.00 0.00 44.23 2.67
2676 3314 7.728847 GGATTGGCCCAAATTGAATAAATAC 57.271 36.000 0.00 0.00 0.00 1.89
2842 3510 5.629435 GTGTGCTAAAACAGGATAAGCAAAC 59.371 40.000 0.59 0.59 44.16 2.93
2843 3511 4.851558 GTGCTAAAACAGGATAAGCAAACG 59.148 41.667 0.00 0.00 44.16 3.60
2844 3512 3.851969 GCTAAAACAGGATAAGCAAACGC 59.148 43.478 0.00 0.00 33.38 4.84
2845 3513 4.614993 GCTAAAACAGGATAAGCAAACGCA 60.615 41.667 0.00 0.00 33.38 5.24
2846 3514 4.314740 AAAACAGGATAAGCAAACGCAA 57.685 36.364 0.00 0.00 0.00 4.85
2847 3515 2.989422 ACAGGATAAGCAAACGCAAC 57.011 45.000 0.00 0.00 0.00 4.17
2848 3516 1.196808 ACAGGATAAGCAAACGCAACG 59.803 47.619 0.00 0.00 0.00 4.10
2849 3517 0.168128 AGGATAAGCAAACGCAACGC 59.832 50.000 0.00 0.00 0.00 4.84
2850 3518 0.168128 GGATAAGCAAACGCAACGCT 59.832 50.000 0.00 0.00 37.68 5.07
2851 3519 1.395608 GGATAAGCAAACGCAACGCTA 59.604 47.619 0.00 0.00 34.11 4.26
2856 3524 0.518559 GCAAACGCAACGCTAGCTAC 60.519 55.000 13.93 0.00 0.00 3.58
2881 3549 0.967380 CCAAATTTCGAGCCAGGCCT 60.967 55.000 8.22 0.00 0.00 5.19
2882 3550 0.171903 CAAATTTCGAGCCAGGCCTG 59.828 55.000 26.87 26.87 0.00 4.85
2898 3566 3.433306 GCCTGGGCCATGTTATGTATA 57.567 47.619 6.72 0.00 34.56 1.47
2901 3571 4.810720 GCCTGGGCCATGTTATGTATACAT 60.811 45.833 21.57 21.57 36.70 2.29
2902 3572 5.572680 GCCTGGGCCATGTTATGTATACATA 60.573 44.000 19.51 19.51 34.93 2.29
2903 3573 5.880332 CCTGGGCCATGTTATGTATACATAC 59.120 44.000 22.44 17.46 38.44 2.39
2904 3574 5.483811 TGGGCCATGTTATGTATACATACG 58.516 41.667 22.44 12.44 38.44 3.06
2905 3575 5.012251 TGGGCCATGTTATGTATACATACGT 59.988 40.000 22.44 15.98 38.44 3.57
2906 3576 5.350365 GGGCCATGTTATGTATACATACGTG 59.650 44.000 22.44 23.23 38.44 4.49
2909 3579 7.201522 GGCCATGTTATGTATACATACGTGATG 60.202 40.741 27.63 22.41 38.44 3.07
3023 3699 3.731136 TTGCCGCACAAGACAGAC 58.269 55.556 0.00 0.00 33.24 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.115930 ACCTGCGTCTCCAGTCAGTT 61.116 55.000 0.00 0.00 0.00 3.16
38 39 2.920645 CGACACCTGCGTCTCCAGT 61.921 63.158 0.00 0.00 33.54 4.00
254 257 4.164221 CCCAAGACAGATAGTTACCACCAT 59.836 45.833 0.00 0.00 0.00 3.55
262 265 1.623811 ACACGCCCAAGACAGATAGTT 59.376 47.619 0.00 0.00 0.00 2.24
291 296 1.682684 CACCCACCTCTAGCCGTCT 60.683 63.158 0.00 0.00 0.00 4.18
522 539 2.198406 CGACGAACAAAGGTCTTCACA 58.802 47.619 0.00 0.00 0.00 3.58
567 584 0.526662 CTTAGGAGCGAGAACCGTGT 59.473 55.000 0.00 0.00 41.15 4.49
571 588 1.144276 GCCCTTAGGAGCGAGAACC 59.856 63.158 0.00 0.00 33.47 3.62
578 595 1.810030 CGACAACGCCCTTAGGAGC 60.810 63.158 0.00 0.23 36.16 4.70
618 639 0.739813 CACAACACTACGCCCTAGGC 60.740 60.000 2.05 0.00 46.75 3.93
619 640 0.606604 ACACAACACTACGCCCTAGG 59.393 55.000 0.06 0.06 0.00 3.02
620 641 2.066262 CAACACAACACTACGCCCTAG 58.934 52.381 0.00 0.00 0.00 3.02
621 642 1.413445 ACAACACAACACTACGCCCTA 59.587 47.619 0.00 0.00 0.00 3.53
644 665 3.000177 GCAAAACACTACGCAACCAAAAG 60.000 43.478 0.00 0.00 0.00 2.27
712 770 4.035684 CACGATCGAACGATACAAGATGT 58.964 43.478 24.34 0.00 34.60 3.06
768 826 1.644509 GTTTTCTGGCTTTCCCCCAT 58.355 50.000 0.00 0.00 0.00 4.00
769 827 0.471022 GGTTTTCTGGCTTTCCCCCA 60.471 55.000 0.00 0.00 0.00 4.96
770 828 0.178932 AGGTTTTCTGGCTTTCCCCC 60.179 55.000 0.00 0.00 0.00 5.40
1815 1887 4.101448 GCCATGGACTCCGGCAGT 62.101 66.667 18.40 0.47 45.52 4.40
2114 2258 5.365403 TTTACACCACCAAACGAATGATC 57.635 39.130 0.00 0.00 0.00 2.92
2122 2269 1.067364 CCCCGTTTTACACCACCAAAC 59.933 52.381 0.00 0.00 0.00 2.93
2142 2289 8.394667 TGTATATACGATGATTGAAATCTCGC 57.605 34.615 17.23 7.35 38.46 5.03
2249 2832 8.855110 ACCCGCAAAATAATCAATAATGTATGA 58.145 29.630 0.00 0.00 0.00 2.15
2250 2833 8.914654 CACCCGCAAAATAATCAATAATGTATG 58.085 33.333 0.00 0.00 0.00 2.39
2251 2834 7.598493 GCACCCGCAAAATAATCAATAATGTAT 59.402 33.333 0.00 0.00 38.36 2.29
2320 2910 0.037326 TAGCTGTCGCACAAGGAAGG 60.037 55.000 0.00 0.00 39.10 3.46
2324 2914 0.742281 ATGCTAGCTGTCGCACAAGG 60.742 55.000 17.23 0.00 39.21 3.61
2370 2970 2.172293 ACCACCACCAAAAACAATGCAT 59.828 40.909 0.00 0.00 0.00 3.96
2373 2973 2.559440 CCACCACCACCAAAAACAATG 58.441 47.619 0.00 0.00 0.00 2.82
2565 3189 5.796350 ACTGGAAACGCAAATACTATCAC 57.204 39.130 0.00 0.00 0.00 3.06
2566 3190 5.123186 CCAACTGGAAACGCAAATACTATCA 59.877 40.000 0.00 0.00 37.39 2.15
2594 3218 4.160626 TCAGATTTGCATGGCATTGATTCA 59.839 37.500 0.00 0.00 38.76 2.57
2618 3242 4.309933 GCTTTCTTTTCACCCAATCCTTG 58.690 43.478 0.00 0.00 0.00 3.61
2619 3243 3.324846 GGCTTTCTTTTCACCCAATCCTT 59.675 43.478 0.00 0.00 0.00 3.36
2620 3244 2.899900 GGCTTTCTTTTCACCCAATCCT 59.100 45.455 0.00 0.00 0.00 3.24
2621 3245 2.899900 AGGCTTTCTTTTCACCCAATCC 59.100 45.455 0.00 0.00 0.00 3.01
2622 3246 4.158579 CCTAGGCTTTCTTTTCACCCAATC 59.841 45.833 0.00 0.00 0.00 2.67
2623 3247 4.089361 CCTAGGCTTTCTTTTCACCCAAT 58.911 43.478 0.00 0.00 0.00 3.16
2624 3248 3.117284 ACCTAGGCTTTCTTTTCACCCAA 60.117 43.478 9.30 0.00 0.00 4.12
2625 3249 2.445525 ACCTAGGCTTTCTTTTCACCCA 59.554 45.455 9.30 0.00 0.00 4.51
2626 3250 2.820197 CACCTAGGCTTTCTTTTCACCC 59.180 50.000 9.30 0.00 0.00 4.61
2627 3251 2.820197 CCACCTAGGCTTTCTTTTCACC 59.180 50.000 9.30 0.00 0.00 4.02
2628 3252 3.751518 TCCACCTAGGCTTTCTTTTCAC 58.248 45.455 9.30 0.00 37.29 3.18
2629 3253 4.335416 CATCCACCTAGGCTTTCTTTTCA 58.665 43.478 9.30 0.00 37.29 2.69
2630 3254 3.696548 CCATCCACCTAGGCTTTCTTTTC 59.303 47.826 9.30 0.00 37.29 2.29
2631 3255 3.564352 CCCATCCACCTAGGCTTTCTTTT 60.564 47.826 9.30 0.00 37.29 2.27
2632 3256 2.024941 CCCATCCACCTAGGCTTTCTTT 60.025 50.000 9.30 0.00 37.29 2.52
2856 3524 1.068610 TGGCTCGAAATTTGGAAAGCG 60.069 47.619 4.38 0.00 0.00 4.68
2881 3549 5.012251 ACGTATGTATACATAACATGGCCCA 59.988 40.000 23.88 0.81 40.18 5.36
2882 3550 5.350365 CACGTATGTATACATAACATGGCCC 59.650 44.000 23.88 10.41 40.18 5.80
2883 3551 6.160684 TCACGTATGTATACATAACATGGCC 58.839 40.000 23.88 11.03 40.18 5.36
2884 3552 7.674008 GCATCACGTATGTATACATAACATGGC 60.674 40.741 23.88 18.70 40.18 4.40
2885 3553 7.462724 CGCATCACGTATGTATACATAACATGG 60.463 40.741 23.88 14.23 40.18 3.66
2898 3566 1.521457 CTGGGCGCATCACGTATGT 60.521 57.895 10.83 0.00 46.11 2.29
3020 3696 2.048419 TTGCTGCTGCCAGTCTGTCT 62.048 55.000 13.47 0.00 41.26 3.41
3021 3697 1.168407 TTTGCTGCTGCCAGTCTGTC 61.168 55.000 13.47 0.00 41.26 3.51
3022 3698 1.152902 TTTGCTGCTGCCAGTCTGT 60.153 52.632 13.47 0.00 41.26 3.41
3023 3699 1.579932 CTTTGCTGCTGCCAGTCTG 59.420 57.895 13.47 0.00 41.26 3.51


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

AutoCloner maintained by Alex Coulton.