Multiple sequence alignment - TraesCS4D01G173000

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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 TraesCS4D01G173000 chr4D 100.000 6765 0 0 1 6765 300859656 300852892 0.000000e+00 12493.0
1 TraesCS4D01G173000 chr4D 87.923 207 18 2 4931 5130 300854651 300854445 3.150000e-58 237.0
2 TraesCS4D01G173000 chr4D 87.923 207 18 2 5006 5212 300854726 300854527 3.150000e-58 237.0
3 TraesCS4D01G173000 chr3D 97.418 2324 43 6 2002 4310 27686682 27684361 0.000000e+00 3943.0
4 TraesCS4D01G173000 chr3D 90.226 1678 142 11 2029 3690 28338988 28337317 0.000000e+00 2170.0
5 TraesCS4D01G173000 chr3D 87.824 1700 173 23 2276 3957 461332170 461330487 0.000000e+00 1962.0
6 TraesCS4D01G173000 chr3D 88.814 590 61 4 3724 4310 28337011 28336424 0.000000e+00 719.0
7 TraesCS4D01G173000 chr3D 87.583 451 52 4 270 719 30499560 30500007 2.800000e-143 520.0
8 TraesCS4D01G173000 chr3D 76.667 210 27 14 2116 2307 597176033 597176238 5.580000e-16 97.1
9 TraesCS4D01G173000 chr7D 97.074 2324 52 5 2001 4310 629939802 629937481 0.000000e+00 3901.0
10 TraesCS4D01G173000 chr7D 86.580 1997 219 24 1994 3957 108364893 108366873 0.000000e+00 2158.0
11 TraesCS4D01G173000 chr7D 86.480 1997 221 24 1994 3957 108343224 108345204 0.000000e+00 2146.0
12 TraesCS4D01G173000 chr7D 86.056 2008 209 35 2002 3957 591021999 591020011 0.000000e+00 2091.0
13 TraesCS4D01G173000 chr7D 95.700 721 27 4 1 719 135937038 135936320 0.000000e+00 1157.0
14 TraesCS4D01G173000 chr7D 96.093 691 26 1 1 690 4599710 4599020 0.000000e+00 1125.0
15 TraesCS4D01G173000 chr7D 85.455 990 111 23 3331 4306 78898890 78899860 0.000000e+00 1000.0
16 TraesCS4D01G173000 chr7D 80.958 793 127 21 3438 4219 68933633 68934412 2.090000e-169 606.0
17 TraesCS4D01G173000 chr7D 80.452 752 113 23 1981 2716 523193985 523193252 1.660000e-150 544.0
18 TraesCS4D01G173000 chr4B 93.872 2464 118 21 4311 6765 374214785 374212346 0.000000e+00 3683.0
19 TraesCS4D01G173000 chr4B 96.394 1248 28 7 723 1953 374216516 374215269 0.000000e+00 2039.0
20 TraesCS4D01G173000 chr4B 83.575 207 20 6 5006 5212 374214179 374213987 1.500000e-41 182.0
21 TraesCS4D01G173000 chr4B 96.610 59 2 0 1943 2001 374214835 374214777 1.550000e-16 99.0
22 TraesCS4D01G173000 chr7B 92.854 2337 121 23 2002 4308 668210654 668212974 0.000000e+00 3349.0
23 TraesCS4D01G173000 chr4A 91.479 2441 154 20 4311 6733 182058452 182060856 0.000000e+00 3306.0
24 TraesCS4D01G173000 chr4A 92.201 1295 47 20 722 2001 182057205 182058460 0.000000e+00 1783.0
25 TraesCS4D01G173000 chr4A 95.146 721 32 3 1 720 589487868 589487150 0.000000e+00 1134.0
26 TraesCS4D01G173000 chr4A 85.854 205 22 4 4930 5127 182059130 182059334 1.910000e-50 211.0
27 TraesCS4D01G173000 chr4A 87.402 127 9 2 4930 5049 182059212 182059338 9.150000e-29 139.0
28 TraesCS4D01G173000 chr7A 92.518 2339 114 23 2002 4313 106770336 106768032 0.000000e+00 3293.0
29 TraesCS4D01G173000 chr6D 95.923 1202 34 12 3113 4311 465349853 465348664 0.000000e+00 1934.0
30 TraesCS4D01G173000 chr6D 94.688 753 25 4 2000 2740 465350597 465349848 0.000000e+00 1155.0
31 TraesCS4D01G173000 chr6D 93.013 687 32 7 3629 4314 142754150 142753479 0.000000e+00 989.0
32 TraesCS4D01G173000 chr6D 93.525 139 9 0 2003 2141 142842020 142841882 2.470000e-49 207.0
33 TraesCS4D01G173000 chr3A 96.667 720 21 3 1 719 200680778 200681495 0.000000e+00 1194.0
34 TraesCS4D01G173000 chr5D 96.111 720 25 3 1 719 477397769 477398486 0.000000e+00 1171.0
35 TraesCS4D01G173000 chr1D 96.111 720 25 3 1 719 405081962 405082679 0.000000e+00 1171.0
36 TraesCS4D01G173000 chr1D 90.244 41 4 0 4847 4887 471437262 471437302 3.000000e-03 54.7
37 TraesCS4D01G173000 chr5B 91.292 689 33 10 1 687 709010165 709010828 0.000000e+00 915.0
38 TraesCS4D01G173000 chr5B 79.585 289 40 8 2109 2381 21169221 21169506 8.960000e-44 189.0
39 TraesCS4D01G173000 chr6A 87.551 731 65 10 1 719 11475116 11475832 0.000000e+00 822.0
40 TraesCS4D01G173000 chr6B 91.182 567 41 7 156 720 612268497 612269056 0.000000e+00 761.0
41 TraesCS4D01G173000 chr6B 95.652 115 4 1 1 114 612220639 612220753 4.170000e-42 183.0
42 TraesCS4D01G173000 chr5A 85.406 603 60 20 125 719 709526835 709527417 9.710000e-168 601.0
43 TraesCS4D01G173000 chr2B 87.838 74 7 2 4859 4931 5084895 5084823 1.210000e-12 86.1
44 TraesCS4D01G173000 chr2B 87.302 63 6 2 1421 1482 58091462 58091401 3.380000e-08 71.3
45 TraesCS4D01G173000 chr2B 87.302 63 6 2 1421 1482 58237001 58236940 3.380000e-08 71.3
46 TraesCS4D01G173000 chr2B 87.302 63 6 2 1421 1482 58311310 58311249 3.380000e-08 71.3
47 TraesCS4D01G173000 chr2B 91.489 47 4 0 1436 1482 58345078 58345124 1.570000e-06 65.8
48 TraesCS4D01G173000 chr2B 91.667 48 2 2 1436 1482 58537069 58537115 1.570000e-06 65.8
49 TraesCS4D01G173000 chr2D 80.342 117 17 5 4348 4459 532496827 532496942 4.350000e-12 84.2
50 TraesCS4D01G173000 chr2D 87.302 63 6 2 1421 1482 35315542 35315603 3.380000e-08 71.3
51 TraesCS4D01G173000 chr2D 91.667 48 2 2 1436 1482 35241716 35241670 1.570000e-06 65.8


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 TraesCS4D01G173000 chr4D 300852892 300859656 6764 True 12493.00 12493 100.00000 1 6765 1 chr4D.!!$R1 6764
1 TraesCS4D01G173000 chr3D 27684361 27686682 2321 True 3943.00 3943 97.41800 2002 4310 1 chr3D.!!$R1 2308
2 TraesCS4D01G173000 chr3D 461330487 461332170 1683 True 1962.00 1962 87.82400 2276 3957 1 chr3D.!!$R2 1681
3 TraesCS4D01G173000 chr3D 28336424 28338988 2564 True 1444.50 2170 89.52000 2029 4310 2 chr3D.!!$R3 2281
4 TraesCS4D01G173000 chr7D 629937481 629939802 2321 True 3901.00 3901 97.07400 2001 4310 1 chr7D.!!$R5 2309
5 TraesCS4D01G173000 chr7D 108364893 108366873 1980 False 2158.00 2158 86.58000 1994 3957 1 chr7D.!!$F4 1963
6 TraesCS4D01G173000 chr7D 108343224 108345204 1980 False 2146.00 2146 86.48000 1994 3957 1 chr7D.!!$F3 1963
7 TraesCS4D01G173000 chr7D 591020011 591021999 1988 True 2091.00 2091 86.05600 2002 3957 1 chr7D.!!$R4 1955
8 TraesCS4D01G173000 chr7D 135936320 135937038 718 True 1157.00 1157 95.70000 1 719 1 chr7D.!!$R2 718
9 TraesCS4D01G173000 chr7D 4599020 4599710 690 True 1125.00 1125 96.09300 1 690 1 chr7D.!!$R1 689
10 TraesCS4D01G173000 chr7D 78898890 78899860 970 False 1000.00 1000 85.45500 3331 4306 1 chr7D.!!$F2 975
11 TraesCS4D01G173000 chr7D 68933633 68934412 779 False 606.00 606 80.95800 3438 4219 1 chr7D.!!$F1 781
12 TraesCS4D01G173000 chr7D 523193252 523193985 733 True 544.00 544 80.45200 1981 2716 1 chr7D.!!$R3 735
13 TraesCS4D01G173000 chr4B 374212346 374216516 4170 True 1500.75 3683 92.61275 723 6765 4 chr4B.!!$R1 6042
14 TraesCS4D01G173000 chr7B 668210654 668212974 2320 False 3349.00 3349 92.85400 2002 4308 1 chr7B.!!$F1 2306
15 TraesCS4D01G173000 chr4A 182057205 182060856 3651 False 1359.75 3306 89.23400 722 6733 4 chr4A.!!$F1 6011
16 TraesCS4D01G173000 chr4A 589487150 589487868 718 True 1134.00 1134 95.14600 1 720 1 chr4A.!!$R1 719
17 TraesCS4D01G173000 chr7A 106768032 106770336 2304 True 3293.00 3293 92.51800 2002 4313 1 chr7A.!!$R1 2311
18 TraesCS4D01G173000 chr6D 465348664 465350597 1933 True 1544.50 1934 95.30550 2000 4311 2 chr6D.!!$R3 2311
19 TraesCS4D01G173000 chr6D 142753479 142754150 671 True 989.00 989 93.01300 3629 4314 1 chr6D.!!$R1 685
20 TraesCS4D01G173000 chr3A 200680778 200681495 717 False 1194.00 1194 96.66700 1 719 1 chr3A.!!$F1 718
21 TraesCS4D01G173000 chr5D 477397769 477398486 717 False 1171.00 1171 96.11100 1 719 1 chr5D.!!$F1 718
22 TraesCS4D01G173000 chr1D 405081962 405082679 717 False 1171.00 1171 96.11100 1 719 1 chr1D.!!$F1 718
23 TraesCS4D01G173000 chr5B 709010165 709010828 663 False 915.00 915 91.29200 1 687 1 chr5B.!!$F2 686
24 TraesCS4D01G173000 chr6A 11475116 11475832 716 False 822.00 822 87.55100 1 719 1 chr6A.!!$F1 718
25 TraesCS4D01G173000 chr6B 612268497 612269056 559 False 761.00 761 91.18200 156 720 1 chr6B.!!$F2 564
26 TraesCS4D01G173000 chr5A 709526835 709527417 582 False 601.00 601 85.40600 125 719 1 chr5A.!!$F1 594

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
487 503 0.618458 GGGCTCCACCTGTCATAACA 59.382 55.000 0.00 0.0 39.10 2.41 F
1916 1960 2.017049 AGGACAGATTGCATTAACCGC 58.983 47.619 0.00 0.0 0.00 5.68 F
2865 3771 0.035056 ACTAGTCATGGCAGGCAACC 60.035 55.000 0.00 0.0 37.17 3.77 F
2868 3774 0.698238 AGTCATGGCAGGCAACCTAA 59.302 50.000 0.00 0.0 29.64 2.69 F
3057 3965 0.760567 TCCAGTGCACTCACCAGACT 60.761 55.000 18.64 0.0 44.16 3.24 F
3062 3970 1.067495 GTGCACTCACCAGACTACTCC 60.067 57.143 10.32 0.0 37.24 3.85 F
4487 6083 1.545428 GCCTTGCGGATTATGGGATGA 60.545 52.381 0.00 0.0 0.00 2.92 F
4576 6172 1.967319 AAGACACGCAAACCTCATGT 58.033 45.000 0.00 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1996 2484 0.173708 CCTCTAGCCACGTCCTTGTC 59.826 60.000 0.00 0.0 0.00 3.18 R
3039 3947 0.969149 TAGTCTGGTGAGTGCACTGG 59.031 55.000 27.27 8.9 44.52 4.00 R
4716 6316 0.179034 CTAGCATGTCCCCTCAAGGC 60.179 60.000 0.00 0.0 0.00 4.35 R
4717 6317 1.500474 TCTAGCATGTCCCCTCAAGG 58.500 55.000 0.00 0.0 0.00 3.61 R
4718 6318 2.702478 TCATCTAGCATGTCCCCTCAAG 59.298 50.000 0.00 0.0 0.00 3.02 R
4852 6452 8.931385 AAAACATCATATATTTTGGTGCAGAC 57.069 30.769 0.00 0.0 0.00 3.51 R
5500 7108 0.888736 CCATTTGCACCTCGGTCACA 60.889 55.000 0.00 0.0 0.00 3.58 R
6539 8160 0.179020 CTTGTGGAGAAGTGGTGGCA 60.179 55.000 0.00 0.0 0.00 4.92 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
39 40 4.208686 GGTCCTTCTCGGCGCGAT 62.209 66.667 12.10 0.00 34.61 4.58
123 131 4.161295 CGGCGAGGGGATGAGCAA 62.161 66.667 0.00 0.00 0.00 3.91
261 276 3.041469 GCAGCAGGGCCTAGAGCTT 62.041 63.158 13.76 0.00 43.05 3.74
388 403 4.767255 GACTGGGCGCCCACTGAG 62.767 72.222 44.23 34.30 41.89 3.35
427 442 4.568152 CACAGGAGGTGTTTGGTAAAAG 57.432 45.455 0.00 0.00 42.75 2.27
472 488 2.032681 GAAGAACGGCTGTGGGCT 59.967 61.111 0.00 0.00 41.46 5.19
487 503 0.618458 GGGCTCCACCTGTCATAACA 59.382 55.000 0.00 0.00 39.10 2.41
589 605 4.981674 ACGTGTTTAAATCGTCTAAACCGA 59.018 37.500 19.98 0.00 38.11 4.69
687 705 2.448582 TTCTGTGGGACGGCAACCT 61.449 57.895 0.00 0.00 0.00 3.50
847 875 5.707066 AGTCAATGCTCCCTTTAGATCTT 57.293 39.130 0.00 0.00 0.00 2.40
1317 1360 5.863965 TCATTTTGTGAGTGACATGAGGTA 58.136 37.500 0.00 0.00 33.40 3.08
1543 1586 3.331889 AGCCTCTTTTCCTCCATTCAGAA 59.668 43.478 0.00 0.00 0.00 3.02
1598 1642 2.143122 TCAACCAAAGCTAGCGTTGAG 58.857 47.619 35.34 27.59 39.61 3.02
1859 1903 6.380274 CAGGTAGTAATTCTTGACCACTAGGA 59.620 42.308 0.00 0.00 38.69 2.94
1860 1904 7.070074 CAGGTAGTAATTCTTGACCACTAGGAT 59.930 40.741 0.00 0.00 38.69 3.24
1873 1917 7.918076 TGACCACTAGGATGTTTCTATTTTCT 58.082 34.615 0.00 0.00 38.69 2.52
1902 1946 5.057819 TGCGAGTCTTCTATACTAGGACAG 58.942 45.833 0.00 0.00 0.00 3.51
1903 1947 5.163332 TGCGAGTCTTCTATACTAGGACAGA 60.163 44.000 0.00 0.00 0.00 3.41
1916 1960 2.017049 AGGACAGATTGCATTAACCGC 58.983 47.619 0.00 0.00 0.00 5.68
1933 1977 2.798847 ACCGCGTACTCAAAAGTTCTTC 59.201 45.455 4.92 0.00 36.92 2.87
1934 1978 2.157085 CCGCGTACTCAAAAGTTCTTCC 59.843 50.000 4.92 0.00 36.92 3.46
2038 2526 1.929038 GCACGAGCGTCAGTTGTTAGA 60.929 52.381 0.00 0.00 0.00 2.10
2045 2533 3.057456 AGCGTCAGTTGTTAGAATCGAGT 60.057 43.478 0.00 0.00 0.00 4.18
2158 2649 8.831550 GGTCCAAAATGTTTAAAATACTGCAAA 58.168 29.630 0.00 0.00 0.00 3.68
2189 2680 4.545823 AAGCGTCAAAATTCAGTTTCGA 57.454 36.364 0.00 0.00 0.00 3.71
2238 2729 9.213799 ACAAGTTCTTCAAAACTAGATCTCATC 57.786 33.333 0.00 0.00 38.52 2.92
2495 3008 4.189231 GCCTATCGTGGATGTTTAGTTGT 58.811 43.478 0.00 0.00 0.00 3.32
2764 3670 2.774439 AAGTTGTCCGTCAATGTTGC 57.226 45.000 0.00 0.00 38.38 4.17
2765 3671 0.951558 AGTTGTCCGTCAATGTTGCC 59.048 50.000 0.00 0.00 38.38 4.52
2774 3680 1.069049 GTCAATGTTGCCAAGTTGCCT 59.931 47.619 0.00 0.00 0.00 4.75
2775 3681 2.295909 GTCAATGTTGCCAAGTTGCCTA 59.704 45.455 0.00 0.00 0.00 3.93
2793 3699 9.057089 AGTTGCCTATATATGAAACTAAGTTGC 57.943 33.333 9.10 0.00 0.00 4.17
2802 3708 5.744666 TGAAACTAAGTTGCTTACCACAC 57.255 39.130 0.00 0.00 0.00 3.82
2803 3709 5.433526 TGAAACTAAGTTGCTTACCACACT 58.566 37.500 0.00 0.00 0.00 3.55
2809 3715 5.652994 AAGTTGCTTACCACACTGAAAAA 57.347 34.783 0.00 0.00 0.00 1.94
2850 3756 7.768807 AGGATAATGTTAGGCTACTCACTAG 57.231 40.000 0.00 0.00 0.00 2.57
2865 3771 0.035056 ACTAGTCATGGCAGGCAACC 60.035 55.000 0.00 0.00 37.17 3.77
2868 3774 0.698238 AGTCATGGCAGGCAACCTAA 59.302 50.000 0.00 0.00 29.64 2.69
2871 3777 1.565759 TCATGGCAGGCAACCTAAGAT 59.434 47.619 0.00 0.00 29.64 2.40
2872 3778 2.777114 TCATGGCAGGCAACCTAAGATA 59.223 45.455 0.00 0.00 29.64 1.98
2873 3779 3.144506 CATGGCAGGCAACCTAAGATAG 58.855 50.000 0.00 0.00 29.64 2.08
2874 3780 1.134098 TGGCAGGCAACCTAAGATAGC 60.134 52.381 0.00 0.00 29.64 2.97
2875 3781 1.221414 GCAGGCAACCTAAGATAGCG 58.779 55.000 0.00 0.00 29.64 4.26
2876 3782 1.473434 GCAGGCAACCTAAGATAGCGT 60.473 52.381 0.00 0.00 29.64 5.07
2888 3794 3.225177 AGATAGCGTTAGGCTACCTCA 57.775 47.619 8.86 0.00 45.50 3.86
2889 3795 3.563223 AGATAGCGTTAGGCTACCTCAA 58.437 45.455 8.86 0.00 45.50 3.02
2917 3823 9.819267 AAGTAAGTTTCCTATAGCACTATCAAC 57.181 33.333 0.00 0.00 0.00 3.18
2929 3835 5.809001 AGCACTATCAACTTGGAGATGAAA 58.191 37.500 0.00 0.00 30.72 2.69
2930 3836 5.879223 AGCACTATCAACTTGGAGATGAAAG 59.121 40.000 0.00 0.00 30.72 2.62
2932 3838 6.150140 GCACTATCAACTTGGAGATGAAAGTT 59.850 38.462 0.00 0.00 45.22 2.66
2951 3857 8.726988 TGAAAGTTGTTATGGTAGAATACTTGC 58.273 33.333 0.00 0.00 42.51 4.01
2956 3864 6.346096 TGTTATGGTAGAATACTTGCTGGTC 58.654 40.000 0.00 0.00 42.51 4.02
2992 3900 4.456280 TGAGATTGTTATGCACTCGAGT 57.544 40.909 13.58 13.58 32.72 4.18
2995 3903 1.438651 TTGTTATGCACTCGAGTGGC 58.561 50.000 38.72 30.86 45.72 5.01
3039 3947 6.040054 AGTTTTGGGGTGTGTTTATACAACTC 59.960 38.462 0.00 0.00 39.25 3.01
3040 3948 4.023726 TGGGGTGTGTTTATACAACTCC 57.976 45.455 9.18 9.18 37.98 3.85
3057 3965 0.760567 TCCAGTGCACTCACCAGACT 60.761 55.000 18.64 0.00 44.16 3.24
3062 3970 1.067495 GTGCACTCACCAGACTACTCC 60.067 57.143 10.32 0.00 37.24 3.85
3067 3975 2.158445 ACTCACCAGACTACTCCTGTGT 60.158 50.000 0.00 0.00 0.00 3.72
3071 3979 3.827302 CACCAGACTACTCCTGTGTACTT 59.173 47.826 0.00 0.00 0.00 2.24
3078 3986 7.002879 AGACTACTCCTGTGTACTTTGAGTTA 58.997 38.462 11.30 1.66 37.47 2.24
3087 3995 9.175312 CCTGTGTACTTTGAGTTAGTATCTAGA 57.825 37.037 0.00 0.00 31.31 2.43
3282 4574 8.735692 TGTGTGCTTTTCATCATTATATCTGA 57.264 30.769 0.00 0.00 0.00 3.27
3507 4820 5.248705 AGACTACCCCAGAAAAGGTAAGAAG 59.751 44.000 0.00 0.00 38.15 2.85
3881 5470 9.330063 AGATGAATTCATTAATACACACGATGT 57.670 29.630 21.57 0.00 40.06 3.06
3935 5524 4.144297 AGCACTGAAGTTGCCTCATTTAA 58.856 39.130 0.00 0.00 0.00 1.52
4074 5666 9.026074 CGGTTTGAAAGTTATAGCTTTTTGAAA 57.974 29.630 14.79 11.40 38.64 2.69
4313 5909 7.340232 AGCTGCACTTTTAATCATTCAGGATTA 59.660 33.333 1.02 0.00 38.41 1.75
4432 6028 9.513906 TGAGAATTGGAACTGAAAATACATACA 57.486 29.630 0.00 0.00 0.00 2.29
4461 6057 3.249080 TGTTTTGTTAGCGAGTAGTTGCC 59.751 43.478 6.14 0.00 32.75 4.52
4463 6059 3.396260 TTGTTAGCGAGTAGTTGCCTT 57.604 42.857 6.14 0.00 32.75 4.35
4487 6083 1.545428 GCCTTGCGGATTATGGGATGA 60.545 52.381 0.00 0.00 0.00 2.92
4495 6091 2.613977 GGATTATGGGATGAGCGACCTG 60.614 54.545 0.00 0.00 0.00 4.00
4576 6172 1.967319 AAGACACGCAAACCTCATGT 58.033 45.000 0.00 0.00 0.00 3.21
4577 6173 1.967319 AGACACGCAAACCTCATGTT 58.033 45.000 0.00 0.00 39.43 2.71
4590 6186 5.083533 ACCTCATGTTTGTTCTTGCAAAA 57.916 34.783 0.00 0.00 39.65 2.44
4641 6241 7.593825 AGAAGTAGCATAACAAAATGTCAACC 58.406 34.615 0.00 0.00 0.00 3.77
4711 6311 4.616604 CGTGCATGGTTTGATCTTTGATGT 60.617 41.667 0.00 0.00 0.00 3.06
4712 6312 5.232463 GTGCATGGTTTGATCTTTGATGTT 58.768 37.500 0.00 0.00 0.00 2.71
4713 6313 5.119588 GTGCATGGTTTGATCTTTGATGTTG 59.880 40.000 0.00 0.00 0.00 3.33
4714 6314 5.010820 TGCATGGTTTGATCTTTGATGTTGA 59.989 36.000 0.00 0.00 0.00 3.18
4715 6315 5.575606 GCATGGTTTGATCTTTGATGTTGAG 59.424 40.000 0.00 0.00 0.00 3.02
4716 6316 5.710513 TGGTTTGATCTTTGATGTTGAGG 57.289 39.130 0.00 0.00 0.00 3.86
4717 6317 4.022068 TGGTTTGATCTTTGATGTTGAGGC 60.022 41.667 0.00 0.00 0.00 4.70
4718 6318 4.488879 GTTTGATCTTTGATGTTGAGGCC 58.511 43.478 0.00 0.00 0.00 5.19
4909 6509 7.018826 TCACTTTGAACTACAAAAACGACTTG 58.981 34.615 0.00 0.00 45.97 3.16
5289 6897 7.042335 ACGGTGAGAGAATTAATTTAGTGGAG 58.958 38.462 1.43 0.00 0.00 3.86
5777 7385 9.627395 CCGTTCTCAACTAATATAATCTACCTG 57.373 37.037 0.00 0.00 0.00 4.00
5796 7404 2.226330 TGGTGGTTCTGTTGTGTATGC 58.774 47.619 0.00 0.00 0.00 3.14
5895 7503 9.771534 AGCTTAACTTTTTGTTGGCATTTATAA 57.228 25.926 0.00 0.00 39.55 0.98
6023 7635 4.696877 CCAGTCTTTGCATCAAGTGATACA 59.303 41.667 0.00 0.00 32.63 2.29
6024 7636 5.356190 CCAGTCTTTGCATCAAGTGATACAT 59.644 40.000 0.00 0.00 32.63 2.29
6211 7827 1.738099 GTGCCTGCACTAGACACCG 60.738 63.158 14.77 0.00 43.12 4.94
6226 7842 3.838903 AGACACCGGAATATCCCTTATCC 59.161 47.826 9.46 0.00 31.13 2.59
6272 7891 9.256477 CCGCTTACAAATCAAGTGATTAGTATA 57.744 33.333 6.95 0.00 43.41 1.47
6467 8087 0.108138 CCCGTCACAACCCTCTGATC 60.108 60.000 0.00 0.00 0.00 2.92
6471 8091 3.491619 CCGTCACAACCCTCTGATCATAG 60.492 52.174 0.00 0.00 0.00 2.23
6479 8100 5.965033 ACCCTCTGATCATAGACACAAAT 57.035 39.130 9.58 0.00 0.00 2.32
6503 8124 5.865013 TGTATAAATCACACACACCACTACG 59.135 40.000 0.00 0.00 0.00 3.51
6514 8135 6.261381 ACACACACCACTACGATAAAAACATT 59.739 34.615 0.00 0.00 0.00 2.71
6523 8144 5.526010 ACGATAAAAACATTGTCGAGGTC 57.474 39.130 13.02 0.00 36.28 3.85
6581 8202 0.033504 GTGACTCCGCTTCACCTTGA 59.966 55.000 0.00 0.00 37.93 3.02
6586 8207 1.118965 TCCGCTTCACCTTGAGACCA 61.119 55.000 0.00 0.00 0.00 4.02
6621 8242 2.616330 CGCAAAGGCCGCAAGAAGA 61.616 57.895 0.00 0.00 43.02 2.87
6640 8261 3.542648 AGACACATGCAGATCAATCAGG 58.457 45.455 0.00 0.00 0.00 3.86
6687 8308 2.761208 GGATCCGGGATTGATCTACGAT 59.239 50.000 11.57 0.00 38.89 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
358 373 4.864334 CAGTCGCCCCCTCATGCC 62.864 72.222 0.00 0.00 0.00 4.40
427 442 3.432890 CCTCTCTGTATCTTCCTTTGGCC 60.433 52.174 0.00 0.00 0.00 5.36
487 503 6.594937 TGTTTAGTTTGACCGTTAAGTTGACT 59.405 34.615 0.00 0.00 0.00 3.41
847 875 0.543277 GAGTGTGGATGCCATCTCCA 59.457 55.000 4.41 0.00 40.49 3.86
951 979 0.260230 AGTCTGCCCTCTAGCTAGCA 59.740 55.000 18.83 10.36 0.00 3.49
1297 1340 5.029807 TGTACCTCATGTCACTCACAAAA 57.970 39.130 0.00 0.00 38.97 2.44
1317 1360 1.153369 CGATCCATCGCAACCCTGT 60.153 57.895 0.00 0.00 43.84 4.00
1383 1426 2.203182 TCCAGGGTGAGGTTCGGT 59.797 61.111 0.00 0.00 0.00 4.69
1582 1626 1.197721 CCAACTCAACGCTAGCTTTGG 59.802 52.381 27.74 21.30 0.00 3.28
1598 1642 1.299850 GCAACGCTCAAACCCCAAC 60.300 57.895 0.00 0.00 0.00 3.77
1873 1917 8.155510 TCCTAGTATAGAAGACTCGCAAGATTA 58.844 37.037 0.00 0.00 44.69 1.75
1902 1946 2.605818 TGAGTACGCGGTTAATGCAATC 59.394 45.455 12.47 0.00 0.00 2.67
1903 1947 2.623535 TGAGTACGCGGTTAATGCAAT 58.376 42.857 12.47 0.00 0.00 3.56
1916 1960 2.735134 CCGGGAAGAACTTTTGAGTACG 59.265 50.000 0.00 0.00 0.00 3.67
1996 2484 0.173708 CCTCTAGCCACGTCCTTGTC 59.826 60.000 0.00 0.00 0.00 3.18
1998 2486 1.517832 CCCTCTAGCCACGTCCTTG 59.482 63.158 0.00 0.00 0.00 3.61
2038 2526 8.506168 TTCCATATTTAGAAAAGCACTCGATT 57.494 30.769 0.00 0.00 0.00 3.34
2045 2533 6.186957 TGCTCCTTCCATATTTAGAAAAGCA 58.813 36.000 10.00 10.00 37.97 3.91
2189 2680 3.611530 CGCGAGAAACCCAAATGTGAAAT 60.612 43.478 0.00 0.00 0.00 2.17
2410 2919 8.455903 AGAAAATCCATTCATACACATAGTGG 57.544 34.615 1.93 0.00 37.94 4.00
2495 3008 3.133691 GCAACGAGGCATCAATGATAGA 58.866 45.455 0.00 0.00 0.00 1.98
2739 3645 6.200097 GCAACATTGACGGACAACTTTTTAAT 59.800 34.615 0.00 0.00 41.52 1.40
2775 3681 9.899661 TGTGGTAAGCAACTTAGTTTCATATAT 57.100 29.630 0.00 0.00 0.00 0.86
2815 3721 9.759473 AGCCTAACATTATCCTAAATTGCATAT 57.241 29.630 0.00 0.00 0.00 1.78
2823 3729 8.548880 AGTGAGTAGCCTAACATTATCCTAAA 57.451 34.615 0.00 0.00 0.00 1.85
2824 3730 9.298250 CTAGTGAGTAGCCTAACATTATCCTAA 57.702 37.037 0.00 0.00 0.00 2.69
2833 3739 4.645136 CCATGACTAGTGAGTAGCCTAACA 59.355 45.833 0.00 0.00 35.45 2.41
2839 3745 2.223923 CCTGCCATGACTAGTGAGTAGC 60.224 54.545 0.00 0.00 35.45 3.58
2850 3756 1.098050 CTTAGGTTGCCTGCCATGAC 58.902 55.000 0.00 0.00 34.61 3.06
2873 3779 3.072211 ACTTTTTGAGGTAGCCTAACGC 58.928 45.455 0.00 0.00 31.76 4.84
2874 3780 5.930569 ACTTACTTTTTGAGGTAGCCTAACG 59.069 40.000 0.00 0.00 31.76 3.18
2875 3781 7.741027 AACTTACTTTTTGAGGTAGCCTAAC 57.259 36.000 0.00 0.00 31.76 2.34
2876 3782 7.446319 GGAAACTTACTTTTTGAGGTAGCCTAA 59.554 37.037 0.00 0.00 31.76 2.69
2917 3823 6.824305 ACCATAACAACTTTCATCTCCAAG 57.176 37.500 0.00 0.00 0.00 3.61
2929 3835 6.823689 CCAGCAAGTATTCTACCATAACAACT 59.176 38.462 0.00 0.00 0.00 3.16
2930 3836 6.598064 ACCAGCAAGTATTCTACCATAACAAC 59.402 38.462 0.00 0.00 0.00 3.32
2932 3838 6.308015 ACCAGCAAGTATTCTACCATAACA 57.692 37.500 0.00 0.00 0.00 2.41
2947 3853 2.163818 TTTCTACCACGACCAGCAAG 57.836 50.000 0.00 0.00 0.00 4.01
2948 3854 2.158871 AGTTTTCTACCACGACCAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
2949 3855 1.414919 AGTTTTCTACCACGACCAGCA 59.585 47.619 0.00 0.00 0.00 4.41
2950 3856 2.165319 AGTTTTCTACCACGACCAGC 57.835 50.000 0.00 0.00 0.00 4.85
2951 3857 4.124238 TCAAAGTTTTCTACCACGACCAG 58.876 43.478 0.00 0.00 0.00 4.00
2956 3864 6.300354 ACAATCTCAAAGTTTTCTACCACG 57.700 37.500 0.00 0.00 0.00 4.94
3015 3923 6.151663 AGTTGTATAAACACACCCCAAAAC 57.848 37.500 0.00 0.00 34.61 2.43
3039 3947 0.969149 TAGTCTGGTGAGTGCACTGG 59.031 55.000 27.27 8.90 44.52 4.00
3040 3948 1.615883 AGTAGTCTGGTGAGTGCACTG 59.384 52.381 27.27 9.69 44.52 3.66
3057 3965 8.874744 ATACTAACTCAAAGTACACAGGAGTA 57.125 34.615 9.07 5.49 37.82 2.59
3113 4021 5.079643 GCCCCATCAATGGTGAACTTATAT 58.920 41.667 8.19 0.00 46.65 0.86
3282 4574 7.982761 TGCCAGCAAAAATCATTAAAATCTT 57.017 28.000 0.00 0.00 0.00 2.40
3507 4820 4.322567 GGATGGATGGTATGAGAGCTTTC 58.677 47.826 0.00 0.00 0.00 2.62
3935 5524 5.890334 TCTTTTCAAAAGCAACTTCGATGT 58.110 33.333 4.87 0.00 0.00 3.06
4074 5666 8.250332 ACATGCATTAATTCCAGTACGAAAAAT 58.750 29.630 0.00 0.00 0.00 1.82
4301 5897 4.464008 GGGCATTGTCTAATCCTGAATGA 58.536 43.478 0.00 0.00 0.00 2.57
4313 5909 3.737172 GCAACGCGGGCATTGTCT 61.737 61.111 18.37 0.00 0.00 3.41
4431 6027 6.991485 ACTCGCTAACAAAACAATGAATTG 57.009 33.333 1.45 1.45 43.26 2.32
4432 6028 7.871853 ACTACTCGCTAACAAAACAATGAATT 58.128 30.769 0.00 0.00 0.00 2.17
4483 6079 0.388649 ACGTGAACAGGTCGCTCATC 60.389 55.000 0.00 0.00 34.35 2.92
4487 6083 1.591594 CACACGTGAACAGGTCGCT 60.592 57.895 25.01 0.00 34.35 4.93
4495 6091 0.515564 GTATGGGCACACACGTGAAC 59.484 55.000 25.01 7.91 46.80 3.18
4631 6231 2.496899 AGGCTCATCGGTTGACATTT 57.503 45.000 0.00 0.00 0.00 2.32
4641 6241 1.097232 TGCATGGAAAAGGCTCATCG 58.903 50.000 0.00 0.00 36.25 3.84
4711 6311 0.846427 ATGTCCCCTCAAGGCCTCAA 60.846 55.000 5.23 0.00 0.00 3.02
4712 6312 1.229951 ATGTCCCCTCAAGGCCTCA 60.230 57.895 5.23 0.00 0.00 3.86
4713 6313 1.225704 CATGTCCCCTCAAGGCCTC 59.774 63.158 5.23 0.00 0.00 4.70
4714 6314 2.988839 GCATGTCCCCTCAAGGCCT 61.989 63.158 0.00 0.00 0.00 5.19
4715 6315 1.635817 TAGCATGTCCCCTCAAGGCC 61.636 60.000 0.00 0.00 0.00 5.19
4716 6316 0.179034 CTAGCATGTCCCCTCAAGGC 60.179 60.000 0.00 0.00 0.00 4.35
4717 6317 1.500474 TCTAGCATGTCCCCTCAAGG 58.500 55.000 0.00 0.00 0.00 3.61
4718 6318 2.702478 TCATCTAGCATGTCCCCTCAAG 59.298 50.000 0.00 0.00 0.00 3.02
4852 6452 8.931385 AAAACATCATATATTTTGGTGCAGAC 57.069 30.769 0.00 0.00 0.00 3.51
4887 6487 9.498307 AATACAAGTCGTTTTTGTAGTTCAAAG 57.502 29.630 12.18 0.00 45.14 2.77
4909 6509 9.566432 AATCATACTCCCTCTGAATCAAAATAC 57.434 33.333 0.00 0.00 0.00 1.89
5069 6677 7.951530 AAATCATGTGTCTTTTCATTTCCAC 57.048 32.000 0.00 0.00 0.00 4.02
5082 6690 9.976511 ATGATCAAATTCCATAAATCATGTGTC 57.023 29.630 0.00 0.00 33.74 3.67
5175 6783 5.901413 ACTCACCATGATCATACTCCATT 57.099 39.130 8.15 0.00 0.00 3.16
5487 7095 2.011947 CGGTCACATTGTCATCAGCAT 58.988 47.619 0.00 0.00 0.00 3.79
5489 7097 1.662629 CTCGGTCACATTGTCATCAGC 59.337 52.381 0.00 0.00 0.00 4.26
5491 7099 1.623311 ACCTCGGTCACATTGTCATCA 59.377 47.619 0.00 0.00 0.00 3.07
5500 7108 0.888736 CCATTTGCACCTCGGTCACA 60.889 55.000 0.00 0.00 0.00 3.58
5777 7385 1.196808 CGCATACACAACAGAACCACC 59.803 52.381 0.00 0.00 0.00 4.61
5796 7404 3.302365 AATTGGCAAGATTGAACACCG 57.698 42.857 5.96 0.00 0.00 4.94
5856 7464 9.086336 CAAAAAGTTAAGCTGACAATTCTGAAA 57.914 29.630 0.00 0.00 0.00 2.69
6023 7635 8.060689 TGGCATGCAATAAGGATGGTTATATAT 58.939 33.333 21.36 0.00 45.30 0.86
6024 7636 7.409358 TGGCATGCAATAAGGATGGTTATATA 58.591 34.615 21.36 0.00 45.30 0.86
6211 7827 5.731678 AGTGTATGGGGATAAGGGATATTCC 59.268 44.000 0.00 0.00 38.79 3.01
6380 8000 1.865865 TGACAAGTCTTTGCCTCGTC 58.134 50.000 1.53 0.00 37.85 4.20
6471 8091 7.537306 GGTGTGTGTGATTTATACATTTGTGTC 59.463 37.037 0.00 0.00 32.78 3.67
6479 8100 5.865013 CGTAGTGGTGTGTGTGATTTATACA 59.135 40.000 0.00 0.00 0.00 2.29
6503 8124 4.142988 TGCGACCTCGACAATGTTTTTATC 60.143 41.667 0.00 0.00 43.02 1.75
6514 8135 1.374125 CCAACATGCGACCTCGACA 60.374 57.895 0.00 0.00 43.02 4.35
6539 8160 0.179020 CTTGTGGAGAAGTGGTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
6581 8202 0.393944 TCGAGCTATGTCGGTGGTCT 60.394 55.000 0.00 0.00 40.49 3.85
6586 8207 1.432251 CGGTTCGAGCTATGTCGGT 59.568 57.895 0.00 0.00 40.49 4.69
6621 8242 2.022195 GCCTGATTGATCTGCATGTGT 58.978 47.619 0.00 0.00 0.00 3.72
6640 8261 1.589716 GCCCTGTTCCTGACATGTGC 61.590 60.000 1.15 0.00 37.69 4.57
6687 8308 6.127703 CGGTTCTAGTCTTTCATAGTTCTCCA 60.128 42.308 0.00 0.00 0.00 3.86
6742 8363 2.615869 TCATGCGACGATGATGACAAA 58.384 42.857 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.