Multiple sequence alignment - TraesCS4D01G262100

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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 TraesCS4D01G262100 chr4D 100.000 3230 0 0 1 3230 433219399 433222628 0.000000e+00 5965.0
1 TraesCS4D01G262100 chr4D 94.224 554 31 1 2678 3230 417792945 417792392 0.000000e+00 845.0
2 TraesCS4D01G262100 chr4D 93.321 554 36 1 2678 3230 401355468 401356021 0.000000e+00 817.0
3 TraesCS4D01G262100 chr4D 83.105 876 115 25 1229 2098 379154977 379155825 0.000000e+00 767.0
4 TraesCS4D01G262100 chr4D 93.243 222 13 1 2057 2278 433368616 433368835 3.110000e-85 326.0
5 TraesCS4D01G262100 chr4D 90.909 44 4 0 2354 2397 433368879 433368922 3.480000e-05 60.2
6 TraesCS4D01G262100 chr4B 96.420 2486 79 7 1 2479 531244549 531247031 0.000000e+00 4089.0
7 TraesCS4D01G262100 chr4B 81.847 931 131 26 1229 2152 465742029 465742928 0.000000e+00 749.0
8 TraesCS4D01G262100 chr4B 94.475 181 9 1 2468 2647 531248641 531248821 8.830000e-71 278.0
9 TraesCS4D01G262100 chr4A 93.004 2087 81 23 556 2612 34668793 34670844 0.000000e+00 2985.0
10 TraesCS4D01G262100 chr4A 93.714 525 29 4 1 523 34667688 34668210 0.000000e+00 784.0
11 TraesCS4D01G262100 chr4A 82.230 906 126 27 1229 2127 85893142 85892265 0.000000e+00 749.0
12 TraesCS4D01G262100 chr4A 88.435 294 28 4 2354 2643 34746674 34746965 1.840000e-92 350.0
13 TraesCS4D01G262100 chr4A 90.749 227 19 2 5 230 34656612 34656837 5.240000e-78 302.0
14 TraesCS4D01G262100 chr4A 80.357 224 19 12 2054 2253 34745764 34745986 2.600000e-31 147.0
15 TraesCS4D01G262100 chr1D 93.682 554 33 2 2678 3230 352247465 352248017 0.000000e+00 828.0
16 TraesCS4D01G262100 chr1D 93.345 556 32 4 2678 3230 273260596 273261149 0.000000e+00 817.0
17 TraesCS4D01G262100 chr1D 92.613 555 40 1 2677 3230 410164505 410165059 0.000000e+00 797.0
18 TraesCS4D01G262100 chr1D 92.280 557 38 2 2675 3230 145381697 145382249 0.000000e+00 785.0
19 TraesCS4D01G262100 chr1D 100.000 31 0 0 2419 2449 73055788 73055818 1.250000e-04 58.4
20 TraesCS4D01G262100 chr5D 93.309 553 31 2 2677 3228 69172744 69172197 0.000000e+00 811.0
21 TraesCS4D01G262100 chr2D 92.935 552 36 2 2678 3228 236042888 236042339 0.000000e+00 800.0
22 TraesCS4D01G262100 chr3D 92.419 554 40 2 2678 3230 91834407 91834959 0.000000e+00 789.0


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 TraesCS4D01G262100 chr4D 433219399 433222628 3229 False 5965.0 5965 100.0000 1 3230 1 chr4D.!!$F3 3229
1 TraesCS4D01G262100 chr4D 417792392 417792945 553 True 845.0 845 94.2240 2678 3230 1 chr4D.!!$R1 552
2 TraesCS4D01G262100 chr4D 401355468 401356021 553 False 817.0 817 93.3210 2678 3230 1 chr4D.!!$F2 552
3 TraesCS4D01G262100 chr4D 379154977 379155825 848 False 767.0 767 83.1050 1229 2098 1 chr4D.!!$F1 869
4 TraesCS4D01G262100 chr4B 531244549 531248821 4272 False 2183.5 4089 95.4475 1 2647 2 chr4B.!!$F2 2646
5 TraesCS4D01G262100 chr4B 465742029 465742928 899 False 749.0 749 81.8470 1229 2152 1 chr4B.!!$F1 923
6 TraesCS4D01G262100 chr4A 34667688 34670844 3156 False 1884.5 2985 93.3590 1 2612 2 chr4A.!!$F2 2611
7 TraesCS4D01G262100 chr4A 85892265 85893142 877 True 749.0 749 82.2300 1229 2127 1 chr4A.!!$R1 898
8 TraesCS4D01G262100 chr4A 34745764 34746965 1201 False 248.5 350 84.3960 2054 2643 2 chr4A.!!$F3 589
9 TraesCS4D01G262100 chr1D 352247465 352248017 552 False 828.0 828 93.6820 2678 3230 1 chr1D.!!$F4 552
10 TraesCS4D01G262100 chr1D 273260596 273261149 553 False 817.0 817 93.3450 2678 3230 1 chr1D.!!$F3 552
11 TraesCS4D01G262100 chr1D 410164505 410165059 554 False 797.0 797 92.6130 2677 3230 1 chr1D.!!$F5 553
12 TraesCS4D01G262100 chr1D 145381697 145382249 552 False 785.0 785 92.2800 2675 3230 1 chr1D.!!$F2 555
13 TraesCS4D01G262100 chr5D 69172197 69172744 547 True 811.0 811 93.3090 2677 3228 1 chr5D.!!$R1 551
14 TraesCS4D01G262100 chr2D 236042339 236042888 549 True 800.0 800 92.9350 2678 3228 1 chr2D.!!$R1 550
15 TraesCS4D01G262100 chr3D 91834407 91834959 552 False 789.0 789 92.4190 2678 3230 1 chr3D.!!$F1 552

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
155 156 0.534203 GTCGGTCTGGTTCCTTGCAA 60.534 55.0 0.00 0.0 0.00 4.08 F
975 1530 2.158066 TGGTACGGGGGATCCATAAGAT 60.158 50.0 15.23 0.0 38.17 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1957 1.033574 CCCTGACGATCTCTACCACC 58.966 60.0 0.0 0.0 0.0 4.61 R
2709 5571 0.326808 TATAACCCGGCCCCTCTTGT 60.327 55.0 0.0 0.0 0.0 3.16 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
66 67 6.940831 TTTGTACACTTTTACTTGTACCCC 57.059 37.500 0.00 0.00 45.05 4.95
78 79 9.841295 TTTTACTTGTACCCCATCTATATGAAC 57.159 33.333 0.00 0.00 34.84 3.18
101 102 4.677584 TCGGCATACCATTTGCATTTTAC 58.322 39.130 0.00 0.00 41.95 2.01
143 144 1.628846 AGTAAATTGCCCAGTCGGTCT 59.371 47.619 0.00 0.00 0.00 3.85
155 156 0.534203 GTCGGTCTGGTTCCTTGCAA 60.534 55.000 0.00 0.00 0.00 4.08
167 168 5.242838 TGGTTCCTTGCAACAAATTAGTAGG 59.757 40.000 0.00 0.00 0.00 3.18
211 213 7.394016 TGGCACTAGACTATGAAAATGAAAGA 58.606 34.615 0.00 0.00 0.00 2.52
212 214 7.334421 TGGCACTAGACTATGAAAATGAAAGAC 59.666 37.037 0.00 0.00 0.00 3.01
407 409 4.766891 CCCAACTACCAATGTCTCACAAAT 59.233 41.667 0.00 0.00 0.00 2.32
459 462 5.779771 AGCAAAATTTTGGATGAAGGACCTA 59.220 36.000 27.60 0.00 38.57 3.08
859 1412 6.142818 AGTCTATCTTTCTTGTCTCCATCG 57.857 41.667 0.00 0.00 0.00 3.84
975 1530 2.158066 TGGTACGGGGGATCCATAAGAT 60.158 50.000 15.23 0.00 38.17 2.40
1111 1666 4.486090 AGATAACATCATCGCCGTATCAC 58.514 43.478 0.00 0.00 0.00 3.06
1124 1680 3.074412 CCGTATCACCATTAGGATTGGC 58.926 50.000 0.00 0.00 37.81 4.52
2090 2649 3.751518 AGGTTTACAGATTCTTGGCGTT 58.248 40.909 0.00 0.00 0.00 4.84
2331 3562 6.382869 AAAGCATATGAGCCACATAACTTC 57.617 37.500 6.97 0.00 43.47 3.01
2344 3575 5.319139 CACATAACTTCGCTGATTGAACAG 58.681 41.667 0.00 0.00 40.43 3.16
2585 5446 5.234329 CCATAACAATGTGGTAGCTAGTTCG 59.766 44.000 0.00 0.00 33.38 3.95
2647 5509 5.683681 TGCTAATTCATGAGCAATCACCTA 58.316 37.500 4.98 0.00 45.47 3.08
2648 5510 6.121590 TGCTAATTCATGAGCAATCACCTAA 58.878 36.000 4.98 0.00 45.47 2.69
2649 5511 6.774170 TGCTAATTCATGAGCAATCACCTAAT 59.226 34.615 4.98 0.00 45.47 1.73
2650 5512 7.286087 TGCTAATTCATGAGCAATCACCTAATT 59.714 33.333 4.98 0.00 45.47 1.40
2651 5513 8.139989 GCTAATTCATGAGCAATCACCTAATTT 58.860 33.333 0.00 0.00 38.62 1.82
2653 5515 8.937634 AATTCATGAGCAATCACCTAATTTTC 57.062 30.769 0.00 0.00 0.00 2.29
2654 5516 7.465353 TTCATGAGCAATCACCTAATTTTCA 57.535 32.000 0.00 0.00 0.00 2.69
2655 5517 7.649533 TCATGAGCAATCACCTAATTTTCAT 57.350 32.000 0.00 0.00 0.00 2.57
2656 5518 7.709947 TCATGAGCAATCACCTAATTTTCATC 58.290 34.615 0.00 0.00 0.00 2.92
2657 5519 6.455360 TGAGCAATCACCTAATTTTCATCC 57.545 37.500 0.00 0.00 0.00 3.51
2658 5520 5.951148 TGAGCAATCACCTAATTTTCATCCA 59.049 36.000 0.00 0.00 0.00 3.41
2659 5521 6.095860 TGAGCAATCACCTAATTTTCATCCAG 59.904 38.462 0.00 0.00 0.00 3.86
2660 5522 5.045872 GCAATCACCTAATTTTCATCCAGC 58.954 41.667 0.00 0.00 0.00 4.85
2661 5523 5.163478 GCAATCACCTAATTTTCATCCAGCT 60.163 40.000 0.00 0.00 0.00 4.24
2662 5524 6.270815 CAATCACCTAATTTTCATCCAGCTG 58.729 40.000 6.78 6.78 0.00 4.24
2663 5525 5.178096 TCACCTAATTTTCATCCAGCTGA 57.822 39.130 17.39 1.21 0.00 4.26
2664 5526 5.569355 TCACCTAATTTTCATCCAGCTGAA 58.431 37.500 17.39 0.00 33.42 3.02
2665 5527 6.009589 TCACCTAATTTTCATCCAGCTGAAA 58.990 36.000 17.39 7.69 41.97 2.69
2666 5528 6.071952 TCACCTAATTTTCATCCAGCTGAAAC 60.072 38.462 17.39 0.00 43.03 2.78
2667 5529 5.774690 ACCTAATTTTCATCCAGCTGAAACA 59.225 36.000 17.39 0.00 43.03 2.83
2668 5530 6.267471 ACCTAATTTTCATCCAGCTGAAACAA 59.733 34.615 17.39 0.00 43.03 2.83
2669 5531 7.038799 ACCTAATTTTCATCCAGCTGAAACAAT 60.039 33.333 17.39 2.77 43.03 2.71
2670 5532 7.820872 CCTAATTTTCATCCAGCTGAAACAATT 59.179 33.333 17.39 13.13 43.03 2.32
2671 5533 7.662604 AATTTTCATCCAGCTGAAACAATTC 57.337 32.000 17.39 0.00 43.03 2.17
2672 5534 4.424061 TTCATCCAGCTGAAACAATTCG 57.576 40.909 17.39 0.00 38.46 3.34
2673 5535 3.411446 TCATCCAGCTGAAACAATTCGT 58.589 40.909 17.39 0.00 38.46 3.85
2732 5595 1.765597 GAGGGGCCGGGTTATACCAG 61.766 65.000 2.18 0.00 41.02 4.00
2771 5634 1.987807 ATGGCGGGTCATAGCAAGCT 61.988 55.000 0.00 0.00 34.54 3.74
2869 5732 2.353406 GCAAGCTTAGTTAGTCACCGGA 60.353 50.000 9.46 0.00 0.00 5.14
2967 5831 1.153349 GGCGAGTTAGGGGCAAGAG 60.153 63.158 0.00 0.00 0.00 2.85
2991 5857 5.197451 ACAAGAGATCGAGAACTAGGTCAT 58.803 41.667 11.14 0.00 0.00 3.06
3091 5959 3.114065 GCCGAACCAGTATAAACTCTCG 58.886 50.000 0.00 0.00 31.97 4.04
3127 5995 5.434408 CCGATTAACCCCTTTAAGCTAACT 58.566 41.667 0.00 0.00 34.45 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.381718 GCCGAGTTCATATAGATGGGGTAC 60.382 50.000 0.00 0.00 33.49 3.34
66 67 5.965922 TGGTATGCCGAGTTCATATAGATG 58.034 41.667 0.00 0.00 37.67 2.90
78 79 3.441496 AAATGCAAATGGTATGCCGAG 57.559 42.857 0.00 0.00 43.16 4.63
101 102 6.909909 ACTTTTAAGGATTGCTTTTAGACGG 58.090 36.000 0.00 0.00 0.00 4.79
143 144 5.242838 CCTACTAATTTGTTGCAAGGAACCA 59.757 40.000 0.00 0.00 0.00 3.67
167 168 4.275443 TGCCATTTTTGCACCTTCAAATTC 59.725 37.500 0.00 0.00 36.04 2.17
211 213 7.068226 ACTCAAAAGCACACCAATTTAACTAGT 59.932 33.333 0.00 0.00 0.00 2.57
212 214 7.425606 ACTCAAAAGCACACCAATTTAACTAG 58.574 34.615 0.00 0.00 0.00 2.57
222 224 4.274147 TCCTTTTACTCAAAAGCACACCA 58.726 39.130 4.66 0.00 46.23 4.17
248 250 9.760660 GCTTGTACAAAGTACATATCTTTCTTG 57.239 33.333 10.03 0.00 33.58 3.02
407 409 2.093658 GGCGATGGACCTTCTGACTTTA 60.094 50.000 5.88 0.00 0.00 1.85
547 550 2.125106 GTAGCACCAGAAGCGGGG 60.125 66.667 0.00 0.00 37.01 5.73
550 553 0.669318 TTTCGGTAGCACCAGAAGCG 60.669 55.000 6.21 0.00 38.47 4.68
859 1412 0.108774 GCCCCTTGTACCTAGCATCC 59.891 60.000 0.00 0.00 0.00 3.51
975 1530 0.902048 CTCCTCCACCTGCTCACTCA 60.902 60.000 0.00 0.00 0.00 3.41
1111 1666 2.430465 CGGATCAGCCAATCCTAATGG 58.570 52.381 11.94 0.00 42.68 3.16
1401 1957 1.033574 CCCTGACGATCTCTACCACC 58.966 60.000 0.00 0.00 0.00 4.61
1459 2018 1.609635 TACTTCCGCTTGATCCGCCA 61.610 55.000 0.00 0.00 0.00 5.69
1998 2557 3.790437 CTCGCCATGGCACCCTCT 61.790 66.667 34.93 0.00 42.06 3.69
2090 2649 1.768684 GACCTGCCTGTTCTCCACCA 61.769 60.000 0.00 0.00 0.00 4.17
2352 3583 9.317936 CTTTCAGGAAGCTAAAACTTCAAAAAT 57.682 29.630 6.61 0.00 46.48 1.82
2585 5446 0.392461 TAGGTCATTGCTTCACGGGC 60.392 55.000 0.00 0.00 0.00 6.13
2650 5512 4.278170 ACGAATTGTTTCAGCTGGATGAAA 59.722 37.500 15.13 9.51 44.72 2.69
2651 5513 3.820467 ACGAATTGTTTCAGCTGGATGAA 59.180 39.130 15.13 0.88 37.41 2.57
2652 5514 3.411446 ACGAATTGTTTCAGCTGGATGA 58.589 40.909 15.13 0.00 0.00 2.92
2653 5515 3.837213 ACGAATTGTTTCAGCTGGATG 57.163 42.857 15.13 0.00 0.00 3.51
2665 5527 4.681074 ATCCCCAACAAAAACGAATTGT 57.319 36.364 0.00 0.00 42.56 2.71
2666 5528 8.032451 AGTTATATCCCCAACAAAAACGAATTG 58.968 33.333 0.00 0.00 0.00 2.32
2667 5529 8.129496 AGTTATATCCCCAACAAAAACGAATT 57.871 30.769 0.00 0.00 0.00 2.17
2668 5530 7.712204 AGTTATATCCCCAACAAAAACGAAT 57.288 32.000 0.00 0.00 0.00 3.34
2669 5531 8.810990 ATAGTTATATCCCCAACAAAAACGAA 57.189 30.769 0.00 0.00 0.00 3.85
2670 5532 8.679100 CAATAGTTATATCCCCAACAAAAACGA 58.321 33.333 0.00 0.00 0.00 3.85
2671 5533 7.918562 CCAATAGTTATATCCCCAACAAAAACG 59.081 37.037 0.00 0.00 0.00 3.60
2672 5534 8.201464 CCCAATAGTTATATCCCCAACAAAAAC 58.799 37.037 0.00 0.00 0.00 2.43
2673 5535 7.901861 ACCCAATAGTTATATCCCCAACAAAAA 59.098 33.333 0.00 0.00 0.00 1.94
2709 5571 0.326808 TATAACCCGGCCCCTCTTGT 60.327 55.000 0.00 0.00 0.00 3.16
2732 5595 4.024556 CCATCTTCATTGATAAGTCGCCAC 60.025 45.833 0.00 0.00 0.00 5.01
2771 5634 1.002624 GGTCTTGGGCCGTCAATGA 60.003 57.895 0.00 0.00 0.00 2.57
2869 5732 1.134367 CTCATACACATCGTGTCCGGT 59.866 52.381 0.00 0.00 43.92 5.28
2922 5785 3.477530 GTCACCCCTTTATATCACAGGC 58.522 50.000 0.00 0.00 0.00 4.85
2967 5831 4.636648 TGACCTAGTTCTCGATCTCTTGTC 59.363 45.833 0.00 0.00 0.00 3.18
3007 5873 5.250200 TGTATTGCTTGGGTTTCGATTACT 58.750 37.500 0.00 0.00 0.00 2.24
3091 5959 2.745821 GTTAATCGGGACAAAGGACACC 59.254 50.000 0.00 0.00 0.00 4.16
3127 5995 0.739462 CGTGGAGCCATCGCAACTAA 60.739 55.000 0.00 0.00 37.52 2.24


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

AutoCloner maintained by Alex Coulton.