Multiple sequence alignment - TraesCS4B01G268500

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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 TraesCS4B01G268500 chr4B 100.000 3820 0 0 1 3820 543063533 543067352 0.000000e+00 7055
1 TraesCS4B01G268500 chr4B 90.710 549 39 3 1 537 513414857 513415405 0.000000e+00 721
2 TraesCS4B01G268500 chr4B 87.548 522 62 2 1 519 540223354 540222833 5.460000e-168 601
3 TraesCS4B01G268500 chr4B 85.612 278 17 8 569 823 3852875 3852598 1.750000e-68 270
4 TraesCS4B01G268500 chr7A 96.032 1008 31 1 2822 3820 616255983 616256990 0.000000e+00 1631
5 TraesCS4B01G268500 chr7A 84.665 313 16 13 569 850 637271979 637271668 2.250000e-72 283
6 TraesCS4B01G268500 chr7B 95.933 1008 32 1 2822 3820 557211657 557212664 0.000000e+00 1626
7 TraesCS4B01G268500 chr7B 84.557 531 74 6 10 537 649789018 649789543 1.570000e-143 520
8 TraesCS4B01G268500 chr7B 89.614 337 10 9 539 850 557209332 557209668 4.600000e-109 405
9 TraesCS4B01G268500 chr7B 92.473 186 13 1 534 719 269882767 269882583 8.140000e-67 265
10 TraesCS4B01G268500 chr4A 95.933 1008 30 3 2822 3820 629596903 629595898 0.000000e+00 1624
11 TraesCS4B01G268500 chr4A 94.940 1008 41 2 2822 3820 24454599 24455605 0.000000e+00 1570
12 TraesCS4B01G268500 chr4A 94.147 1008 50 1 2822 3820 423964161 423965168 0.000000e+00 1526
13 TraesCS4B01G268500 chr4A 89.869 533 46 6 1071 1600 220151423 220151950 0.000000e+00 678
14 TraesCS4B01G268500 chr4A 87.873 536 57 5 1068 1600 229713380 229713910 1.170000e-174 623
15 TraesCS4B01G268500 chr4A 83.871 310 22 12 569 850 24452363 24452672 1.750000e-68 270
16 TraesCS4B01G268500 chr4A 83.871 310 22 12 569 850 321984579 321984270 1.750000e-68 270
17 TraesCS4B01G268500 chr5A 95.833 1008 33 1 2822 3820 564380458 564379451 0.000000e+00 1620
18 TraesCS4B01G268500 chr5A 94.040 302 9 5 2822 3114 618020900 618020599 2.090000e-122 449
19 TraesCS4B01G268500 chr3A 95.536 1008 36 1 2822 3820 144011695 144012702 0.000000e+00 1604
20 TraesCS4B01G268500 chr3A 91.800 561 39 4 2267 2826 744665218 744664664 0.000000e+00 774
21 TraesCS4B01G268500 chr3A 84.780 749 59 25 882 1598 744666552 744665827 0.000000e+00 701
22 TraesCS4B01G268500 chr3A 84.602 565 42 24 2280 2827 744614415 744613879 1.570000e-143 520
23 TraesCS4B01G268500 chr3A 81.997 611 86 9 1651 2242 744665806 744665201 7.370000e-137 497
24 TraesCS4B01G268500 chr3A 83.186 565 59 20 2270 2827 744469188 744468653 5.740000e-133 484
25 TraesCS4B01G268500 chr3B 95.455 1012 33 3 2822 3820 536044859 536045870 0.000000e+00 1602
26 TraesCS4B01G268500 chr3B 86.803 538 64 7 5 539 490227640 490228173 9.140000e-166 593
27 TraesCS4B01G268500 chr2A 95.238 1008 38 2 2822 3820 643992455 643993461 0.000000e+00 1587
28 TraesCS4B01G268500 chr2A 85.256 312 16 10 569 850 643963362 643963673 1.040000e-75 294
29 TraesCS4B01G268500 chr5B 94.345 1008 48 1 2822 3820 260670781 260669774 0.000000e+00 1537
30 TraesCS4B01G268500 chr6D 93.127 1004 44 14 2822 3820 234438005 234438988 0.000000e+00 1448
31 TraesCS4B01G268500 chr6D 93.258 178 10 1 539 716 193649493 193649668 1.050000e-65 261
32 TraesCS4B01G268500 chr3D 83.695 1429 138 45 873 2242 610431370 610429978 0.000000e+00 1260
33 TraesCS4B01G268500 chr3D 91.950 559 38 5 2269 2826 610429993 610429441 0.000000e+00 776
34 TraesCS4B01G268500 chr3D 84.220 564 63 17 2269 2826 610375772 610375229 3.380000e-145 525
35 TraesCS4B01G268500 chr3D 83.619 525 49 17 2274 2790 610420012 610419517 3.480000e-125 459
36 TraesCS4B01G268500 chr3D 92.135 178 13 1 539 716 602255816 602255992 2.280000e-62 250
37 TraesCS4B01G268500 chrUn 85.545 927 85 29 877 1764 43093306 43094222 0.000000e+00 924
38 TraesCS4B01G268500 chrUn 85.545 927 85 29 877 1764 43261252 43260336 0.000000e+00 924
39 TraesCS4B01G268500 chrUn 85.545 927 85 29 877 1764 262840162 262841078 0.000000e+00 924
40 TraesCS4B01G268500 chrUn 85.545 927 85 29 877 1764 293232129 293233045 0.000000e+00 924
41 TraesCS4B01G268500 chrUn 94.474 561 28 1 2267 2827 43094612 43095169 0.000000e+00 861
42 TraesCS4B01G268500 chrUn 94.474 561 28 1 2267 2827 43259946 43259389 0.000000e+00 861
43 TraesCS4B01G268500 chrUn 94.474 561 28 1 2267 2827 262841468 262842025 0.000000e+00 861
44 TraesCS4B01G268500 chrUn 94.474 561 28 1 2267 2827 293233435 293233992 0.000000e+00 861
45 TraesCS4B01G268500 chrUn 86.803 538 64 4 5 536 114984558 114984022 9.140000e-166 593
46 TraesCS4B01G268500 chrUn 94.314 299 8 5 2822 3111 271829337 271829635 2.090000e-122 449
47 TraesCS4B01G268500 chrUn 94.040 302 9 5 2822 3114 272968948 272968647 2.090000e-122 449
48 TraesCS4B01G268500 chrUn 81.492 362 44 14 1885 2242 43094287 43094629 3.760000e-70 276
49 TraesCS4B01G268500 chrUn 81.492 362 44 14 1885 2242 43260271 43259929 3.760000e-70 276
50 TraesCS4B01G268500 chrUn 81.492 362 44 14 1885 2242 262841143 262841485 3.760000e-70 276
51 TraesCS4B01G268500 chrUn 81.492 362 44 14 1885 2242 293233110 293233452 3.760000e-70 276
52 TraesCS4B01G268500 chr1D 84.050 953 88 35 1146 2072 459697850 459696936 0.000000e+00 859
53 TraesCS4B01G268500 chr1D 83.962 954 86 28 1146 2072 44743489 44744402 0.000000e+00 852
54 TraesCS4B01G268500 chr1D 85.874 538 71 3 1 537 361289696 361289163 5.540000e-158 568
55 TraesCS4B01G268500 chr5D 83.874 955 86 39 1146 2072 430276349 430275435 0.000000e+00 848
56 TraesCS4B01G268500 chr5D 91.713 181 15 0 539 719 507362987 507362807 6.330000e-63 252
57 TraesCS4B01G268500 chr1A 87.616 541 59 5 1066 1603 89966991 89966456 4.190000e-174 621
58 TraesCS4B01G268500 chr1A 84.615 312 18 16 569 850 572834992 572834681 2.250000e-72 283
59 TraesCS4B01G268500 chr1A 77.470 506 90 15 1734 2229 31795729 31796220 8.080000e-72 281
60 TraesCS4B01G268500 chr1B 87.242 533 65 1 5 537 518727967 518727438 4.220000e-169 604
61 TraesCS4B01G268500 chr1B 94.286 175 9 1 539 713 550931080 550931253 2.260000e-67 267
62 TraesCS4B01G268500 chr2D 85.122 531 73 3 5 534 556140033 556140558 4.340000e-149 538
63 TraesCS4B01G268500 chr2D 82.397 534 88 4 6 537 543996166 543996695 9.670000e-126 460
64 TraesCS4B01G268500 chr2D 92.135 178 13 1 539 716 185749929 185750105 2.280000e-62 250
65 TraesCS4B01G268500 chr2B 84.074 540 82 4 1 538 253826027 253825490 5.660000e-143 518
66 TraesCS4B01G268500 chr2B 85.246 305 22 8 569 850 63521049 63520745 3.730000e-75 292
67 TraesCS4B01G268500 chr2B 83.333 258 15 5 571 823 683654336 683654570 2.990000e-51 213
68 TraesCS4B01G268500 chr7D 93.750 176 11 0 539 714 620200457 620200282 8.140000e-67 265
69 TraesCS4B01G268500 chr6A 91.713 181 15 0 539 719 203891160 203890980 6.330000e-63 252


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 TraesCS4B01G268500 chr4B 543063533 543067352 3819 False 7055.000000 7055 100.000000 1 3820 1 chr4B.!!$F2 3819
1 TraesCS4B01G268500 chr4B 513414857 513415405 548 False 721.000000 721 90.710000 1 537 1 chr4B.!!$F1 536
2 TraesCS4B01G268500 chr4B 540222833 540223354 521 True 601.000000 601 87.548000 1 519 1 chr4B.!!$R2 518
3 TraesCS4B01G268500 chr7A 616255983 616256990 1007 False 1631.000000 1631 96.032000 2822 3820 1 chr7A.!!$F1 998
4 TraesCS4B01G268500 chr7B 557209332 557212664 3332 False 1015.500000 1626 92.773500 539 3820 2 chr7B.!!$F2 3281
5 TraesCS4B01G268500 chr7B 649789018 649789543 525 False 520.000000 520 84.557000 10 537 1 chr7B.!!$F1 527
6 TraesCS4B01G268500 chr4A 629595898 629596903 1005 True 1624.000000 1624 95.933000 2822 3820 1 chr4A.!!$R2 998
7 TraesCS4B01G268500 chr4A 423964161 423965168 1007 False 1526.000000 1526 94.147000 2822 3820 1 chr4A.!!$F3 998
8 TraesCS4B01G268500 chr4A 24452363 24455605 3242 False 920.000000 1570 89.405500 569 3820 2 chr4A.!!$F4 3251
9 TraesCS4B01G268500 chr4A 220151423 220151950 527 False 678.000000 678 89.869000 1071 1600 1 chr4A.!!$F1 529
10 TraesCS4B01G268500 chr4A 229713380 229713910 530 False 623.000000 623 87.873000 1068 1600 1 chr4A.!!$F2 532
11 TraesCS4B01G268500 chr5A 564379451 564380458 1007 True 1620.000000 1620 95.833000 2822 3820 1 chr5A.!!$R1 998
12 TraesCS4B01G268500 chr3A 144011695 144012702 1007 False 1604.000000 1604 95.536000 2822 3820 1 chr3A.!!$F1 998
13 TraesCS4B01G268500 chr3A 744664664 744666552 1888 True 657.333333 774 86.192333 882 2826 3 chr3A.!!$R3 1944
14 TraesCS4B01G268500 chr3A 744613879 744614415 536 True 520.000000 520 84.602000 2280 2827 1 chr3A.!!$R2 547
15 TraesCS4B01G268500 chr3A 744468653 744469188 535 True 484.000000 484 83.186000 2270 2827 1 chr3A.!!$R1 557
16 TraesCS4B01G268500 chr3B 536044859 536045870 1011 False 1602.000000 1602 95.455000 2822 3820 1 chr3B.!!$F2 998
17 TraesCS4B01G268500 chr3B 490227640 490228173 533 False 593.000000 593 86.803000 5 539 1 chr3B.!!$F1 534
18 TraesCS4B01G268500 chr2A 643992455 643993461 1006 False 1587.000000 1587 95.238000 2822 3820 1 chr2A.!!$F2 998
19 TraesCS4B01G268500 chr5B 260669774 260670781 1007 True 1537.000000 1537 94.345000 2822 3820 1 chr5B.!!$R1 998
20 TraesCS4B01G268500 chr6D 234438005 234438988 983 False 1448.000000 1448 93.127000 2822 3820 1 chr6D.!!$F2 998
21 TraesCS4B01G268500 chr3D 610429441 610431370 1929 True 1018.000000 1260 87.822500 873 2826 2 chr3D.!!$R3 1953
22 TraesCS4B01G268500 chr3D 610375229 610375772 543 True 525.000000 525 84.220000 2269 2826 1 chr3D.!!$R1 557
23 TraesCS4B01G268500 chrUn 43093306 43095169 1863 False 687.000000 924 87.170333 877 2827 3 chrUn.!!$F2 1950
24 TraesCS4B01G268500 chrUn 43259389 43261252 1863 True 687.000000 924 87.170333 877 2827 3 chrUn.!!$R3 1950
25 TraesCS4B01G268500 chrUn 262840162 262842025 1863 False 687.000000 924 87.170333 877 2827 3 chrUn.!!$F3 1950
26 TraesCS4B01G268500 chrUn 293232129 293233992 1863 False 687.000000 924 87.170333 877 2827 3 chrUn.!!$F4 1950
27 TraesCS4B01G268500 chrUn 114984022 114984558 536 True 593.000000 593 86.803000 5 536 1 chrUn.!!$R1 531
28 TraesCS4B01G268500 chr1D 459696936 459697850 914 True 859.000000 859 84.050000 1146 2072 1 chr1D.!!$R2 926
29 TraesCS4B01G268500 chr1D 44743489 44744402 913 False 852.000000 852 83.962000 1146 2072 1 chr1D.!!$F1 926
30 TraesCS4B01G268500 chr1D 361289163 361289696 533 True 568.000000 568 85.874000 1 537 1 chr1D.!!$R1 536
31 TraesCS4B01G268500 chr5D 430275435 430276349 914 True 848.000000 848 83.874000 1146 2072 1 chr5D.!!$R1 926
32 TraesCS4B01G268500 chr1A 89966456 89966991 535 True 621.000000 621 87.616000 1066 1603 1 chr1A.!!$R1 537
33 TraesCS4B01G268500 chr1B 518727438 518727967 529 True 604.000000 604 87.242000 5 537 1 chr1B.!!$R1 532
34 TraesCS4B01G268500 chr2D 556140033 556140558 525 False 538.000000 538 85.122000 5 534 1 chr2D.!!$F3 529
35 TraesCS4B01G268500 chr2D 543996166 543996695 529 False 460.000000 460 82.397000 6 537 1 chr2D.!!$F2 531
36 TraesCS4B01G268500 chr2B 253825490 253826027 537 True 518.000000 518 84.074000 1 538 1 chr2B.!!$R2 537

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
420 433 0.328258 GCTTGTTCCTTGGCTAGGGA 59.672 55.000 15.05 3.05 44.86 4.20 F
1586 2334 0.742281 CTTGGTCATCAGCTGGTCCG 60.742 60.000 15.13 0.00 0.00 4.79 F
2006 3234 1.000394 TCGCAAACAAGACGGATCAGA 60.000 47.619 0.00 0.00 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 3595 0.251354 AGAAGCGATGATGGTGCAGT 59.749 50.000 0.0 0.0 0.0 4.40 R
2540 3790 1.376424 CCAACCTCGCTGCTGATGT 60.376 57.895 0.0 0.0 0.0 3.06 R
3538 5098 2.351447 CCGAGTAGTTGAAGAGCACGAA 60.351 50.000 0.0 0.0 0.0 3.85 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
78 79 2.457743 TTTGCCAGGTCCGCATACGT 62.458 55.000 0.00 0.00 35.83 3.57
103 104 2.693074 TGTAGCGCTCCATAACTGATCA 59.307 45.455 16.34 0.00 0.00 2.92
120 121 2.586258 TCAAGAGGAGCATACTTCGC 57.414 50.000 0.00 0.00 0.00 4.70
245 246 0.773644 TGCTTCCAAGGCCTTCTTCT 59.226 50.000 17.29 0.00 32.41 2.85
420 433 0.328258 GCTTGTTCCTTGGCTAGGGA 59.672 55.000 15.05 3.05 44.86 4.20
445 458 2.636412 CGCTCGAAGGGTCTCCACA 61.636 63.158 0.00 0.00 34.83 4.17
470 483 1.129917 AGCTCTATCTGCAGCCACAT 58.870 50.000 9.47 0.00 36.17 3.21
491 504 9.310716 CCACATCATGTTATAGATACTAGCATG 57.689 37.037 0.00 0.00 38.44 4.06
511 527 7.444629 GCATGATGCTCCTCTTAATATTTGA 57.555 36.000 10.72 0.00 40.96 2.69
564 581 8.038944 CACTACTAGGGAAAAGCTTATACACAA 58.961 37.037 0.00 0.00 0.00 3.33
648 669 7.315890 GTTTTTAACCCTCGCTACTACTAAGA 58.684 38.462 0.00 0.00 0.00 2.10
653 674 3.140623 CCTCGCTACTACTAAGAGGTCC 58.859 54.545 1.91 0.00 42.48 4.46
658 679 4.064388 GCTACTACTAAGAGGTCCCTACG 58.936 52.174 0.00 0.00 0.00 3.51
716 737 2.503920 ATAAACCCGCGCTACTACTG 57.496 50.000 5.56 0.00 0.00 2.74
719 740 1.664321 AACCCGCGCTACTACTGAGG 61.664 60.000 5.56 0.00 0.00 3.86
721 742 2.119655 CCGCGCTACTACTGAGGGT 61.120 63.158 5.56 0.00 0.00 4.34
864 922 4.785453 CTCCAACCCAGCCGCCTC 62.785 72.222 0.00 0.00 0.00 4.70
905 963 1.065345 TCGATCCGCCCCAATTAAACA 60.065 47.619 0.00 0.00 0.00 2.83
944 1002 2.829592 GGCCGCAGCTATAACCCT 59.170 61.111 0.00 0.00 39.73 4.34
978 1055 2.975799 GGCCGGCGACACAAAGAA 60.976 61.111 22.54 0.00 0.00 2.52
979 1056 2.556287 GCCGGCGACACAAAGAAG 59.444 61.111 12.58 0.00 0.00 2.85
980 1057 2.556287 CCGGCGACACAAAGAAGC 59.444 61.111 9.30 0.00 0.00 3.86
981 1058 2.250939 CCGGCGACACAAAGAAGCA 61.251 57.895 9.30 0.00 0.00 3.91
982 1059 1.205064 CGGCGACACAAAGAAGCAG 59.795 57.895 0.00 0.00 0.00 4.24
983 1060 1.081840 GGCGACACAAAGAAGCAGC 60.082 57.895 0.00 0.00 0.00 5.25
1026 1103 2.434359 GTGAAGCGCGCCTACCTT 60.434 61.111 30.33 15.78 0.00 3.50
1110 1225 4.576463 AGTTCATCGCTGGATTTATTGACC 59.424 41.667 0.00 0.00 0.00 4.02
1232 1355 4.127040 CTCCAGCTCGCGCAGACT 62.127 66.667 8.75 0.00 39.10 3.24
1296 1431 4.442375 TTCTCTCGATCTGTTCAGTTCC 57.558 45.455 0.00 0.00 0.00 3.62
1500 1919 3.646976 CCGCGAGCATGCCTGATG 61.647 66.667 15.66 0.46 34.84 3.07
1512 1931 0.813821 GCCTGATGCTCTGTTTTCCC 59.186 55.000 0.00 0.00 36.87 3.97
1533 2031 3.390135 CTGCTCTGTTTTCTTGTACGGA 58.610 45.455 0.00 0.00 0.00 4.69
1543 2041 2.333926 TCTTGTACGGATTTGCAGACG 58.666 47.619 0.00 0.00 0.00 4.18
1586 2334 0.742281 CTTGGTCATCAGCTGGTCCG 60.742 60.000 15.13 0.00 0.00 4.79
1603 2601 2.360165 GTCCGTCACCGAGGTATGTATT 59.640 50.000 0.00 0.00 35.63 1.89
1609 2607 3.770388 TCACCGAGGTATGTATTCACCAA 59.230 43.478 0.00 0.00 37.28 3.67
1628 2837 2.810274 CAATCACCACTGACTTCACTGG 59.190 50.000 3.98 3.98 36.36 4.00
1690 2899 9.612620 CAGTTCTAAAAATGAAGTGTGTTATCC 57.387 33.333 0.00 0.00 39.01 2.59
1694 2903 4.685169 AAATGAAGTGTGTTATCCAGCG 57.315 40.909 0.00 0.00 0.00 5.18
1726 2935 4.868171 CCGCTGTTGCTGTTAGAATAACTA 59.132 41.667 1.76 0.00 36.97 2.24
1752 2961 4.707030 TGTGCTCCTGAAATAATGCAAG 57.293 40.909 0.00 0.00 32.10 4.01
1755 2964 2.428171 GCTCCTGAAATAATGCAAGGCA 59.572 45.455 0.00 0.00 44.86 4.75
1757 2966 4.442472 GCTCCTGAAATAATGCAAGGCAAT 60.442 41.667 0.00 0.00 43.62 3.56
1767 2976 7.724305 ATAATGCAAGGCAATGATGATTTTC 57.276 32.000 0.00 0.00 43.62 2.29
1806 3020 7.014134 TGCCAAGTTGAATTTCAAGATACTTGA 59.986 33.333 27.63 15.37 40.91 3.02
1821 3035 7.441890 AGATACTTGAGATAGGTGTATCACG 57.558 40.000 12.10 0.00 40.84 4.35
1833 3047 9.476059 GATAGGTGTATCACGCAAAATTGCTGT 62.476 40.741 15.44 11.85 41.96 4.40
1868 3095 9.465199 TCACTATACTGTTAGTATTACACCACA 57.535 33.333 6.78 0.00 38.17 4.17
1872 3099 6.869206 ACTGTTAGTATTACACCACAGGAT 57.131 37.500 17.47 3.13 40.78 3.24
1896 3123 1.769465 TGTAACAACAGGGTGGTGCTA 59.231 47.619 0.00 0.00 39.04 3.49
1905 3132 1.774856 AGGGTGGTGCTAAGTCAACTT 59.225 47.619 0.46 0.46 39.85 2.66
1916 3143 5.069119 TGCTAAGTCAACTTGAAGTCAGAGA 59.931 40.000 0.00 0.00 37.40 3.10
1917 3144 6.162777 GCTAAGTCAACTTGAAGTCAGAGAT 58.837 40.000 0.00 0.00 37.40 2.75
1944 3171 7.987458 ACTATTATGTGTGCATTACTTACTGCT 59.013 33.333 0.00 0.00 39.16 4.24
1947 3174 4.133820 TGTGTGCATTACTTACTGCTGTT 58.866 39.130 0.09 0.00 39.16 3.16
1956 3184 7.218204 GCATTACTTACTGCTGTTTATTTTCCG 59.782 37.037 0.09 0.00 35.49 4.30
2006 3234 1.000394 TCGCAAACAAGACGGATCAGA 60.000 47.619 0.00 0.00 0.00 3.27
2012 3240 2.625737 ACAAGACGGATCAGAGCAATG 58.374 47.619 0.00 0.00 0.00 2.82
2093 3330 9.988815 GAAGAGGATAACAGAGAAATTATGCTA 57.011 33.333 0.00 0.00 38.94 3.49
2130 3367 7.973048 TTATCTGTCAAGTCCTATAGGTTGT 57.027 36.000 18.51 1.78 36.34 3.32
2153 3390 2.105477 AGAGTCATGGCATATGGTCCAC 59.895 50.000 0.00 0.00 34.81 4.02
2240 3478 5.489792 TCTGCAGATTTCAGAAACCTAGT 57.510 39.130 13.74 0.00 37.61 2.57
2241 3479 5.869579 TCTGCAGATTTCAGAAACCTAGTT 58.130 37.500 13.74 0.00 37.61 2.24
2242 3480 6.299141 TCTGCAGATTTCAGAAACCTAGTTT 58.701 36.000 13.74 0.00 37.61 2.66
2243 3481 6.772716 TCTGCAGATTTCAGAAACCTAGTTTT 59.227 34.615 13.74 0.00 37.61 2.43
2244 3482 7.285401 TCTGCAGATTTCAGAAACCTAGTTTTT 59.715 33.333 13.74 0.00 37.61 1.94
2357 3595 2.098443 GGCACGAAAGAGTTGTTTGGAA 59.902 45.455 0.00 0.00 0.00 3.53
2455 3705 7.315247 TGTAAGTCAGCGCAACATTAATTAT 57.685 32.000 11.47 0.00 0.00 1.28
2457 3707 8.884726 TGTAAGTCAGCGCAACATTAATTATTA 58.115 29.630 11.47 0.00 0.00 0.98
2458 3708 9.710979 GTAAGTCAGCGCAACATTAATTATTAA 57.289 29.630 11.47 0.00 0.00 1.40
2460 3710 9.450807 AAGTCAGCGCAACATTAATTATTAATC 57.549 29.630 11.47 0.00 33.73 1.75
2626 3876 6.976925 CCTGATGAAATCCATTAAAGCAGTTC 59.023 38.462 0.00 0.00 44.73 3.01
2787 4114 5.193124 TCAATCCTGGTACTCCTAGTCTACA 59.807 44.000 0.00 0.00 34.23 2.74
2827 4373 1.478916 TCCTCGCCGTTGATTCATGTA 59.521 47.619 0.00 0.00 0.00 2.29
2988 4534 7.843490 TGTTTATAGGATGTGTAAGCTGAAC 57.157 36.000 0.00 0.00 0.00 3.18
2991 4537 3.059352 AGGATGTGTAAGCTGAACCAC 57.941 47.619 0.00 0.00 0.00 4.16
3066 4624 5.085920 ACATTTTTCCACAAGATGATGGGA 58.914 37.500 0.00 0.00 36.56 4.37
3187 4747 2.961893 AACATTGACCCCGGCGCTA 61.962 57.895 7.64 0.00 0.00 4.26
3233 4793 2.655090 TCTGATGTCCTTTGTTGGCA 57.345 45.000 0.00 0.00 0.00 4.92
3565 5125 1.544691 TCTTCAACTACTCGGAGGCAC 59.455 52.381 10.23 0.00 0.00 5.01
3634 5194 2.835701 GATTGCGACGCAGGAGGTCA 62.836 60.000 23.18 6.61 40.61 4.02
3659 5219 3.148279 GGAGGACCTCGACGCCAT 61.148 66.667 15.46 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.939103 CGGAAAGATCATGAGGTGGAAC 59.061 50.000 0.09 0.00 0.00 3.62
78 79 0.179084 GTTATGGAGCGCTACAGGCA 60.179 55.000 28.95 12.86 41.91 4.75
80 81 1.409064 TCAGTTATGGAGCGCTACAGG 59.591 52.381 28.95 14.23 0.00 4.00
84 85 3.636764 TCTTGATCAGTTATGGAGCGCTA 59.363 43.478 11.50 0.00 0.00 4.26
88 89 4.630111 CTCCTCTTGATCAGTTATGGAGC 58.370 47.826 14.69 0.00 34.35 4.70
103 104 2.697751 AGATGCGAAGTATGCTCCTCTT 59.302 45.455 0.00 0.00 28.93 2.85
120 121 1.212616 GCGGATGAAGTTCGGAGATG 58.787 55.000 0.00 0.00 35.04 2.90
245 246 0.603707 CAAGAGAAAGCGGCTGACCA 60.604 55.000 1.81 0.00 34.57 4.02
420 433 0.320508 GACCCTTCGAGCGGAACTTT 60.321 55.000 6.84 0.00 0.00 2.66
430 443 1.533033 TGCTGTGGAGACCCTTCGA 60.533 57.895 0.00 0.00 0.00 3.71
456 469 3.286329 AACATGATGTGGCTGCAGATA 57.714 42.857 20.43 1.30 0.00 1.98
491 504 8.613060 TGTCATCAAATATTAAGAGGAGCATC 57.387 34.615 5.69 0.00 0.00 3.91
511 527 6.486657 CAGGGTATGTATTTTCGGATTGTCAT 59.513 38.462 0.00 0.00 0.00 3.06
719 740 3.501445 CAGTAGTAGCGTGGGTATCTACC 59.499 52.174 0.00 0.00 45.71 3.18
721 742 4.504514 CCTCAGTAGTAGCGTGGGTATCTA 60.505 50.000 0.00 0.00 0.00 1.98
875 933 4.570663 CGGATCGAGGTCGCACCC 62.571 72.222 0.00 0.00 39.75 4.61
927 985 1.598130 CAGGGTTATAGCTGCGGCC 60.598 63.158 15.55 0.00 39.73 6.13
944 1002 2.203056 CGGATCTTGGGCGATGCA 60.203 61.111 0.00 0.00 32.00 3.96
969 1046 0.666913 CTGCTGCTGCTTCTTTGTGT 59.333 50.000 17.00 0.00 40.48 3.72
980 1057 4.754667 TCTCCGCTGCTGCTGCTG 62.755 66.667 25.43 20.27 40.48 4.41
981 1058 4.756458 GTCTCCGCTGCTGCTGCT 62.756 66.667 25.43 0.00 40.48 4.24
983 1060 3.713205 ATCGTCTCCGCTGCTGCTG 62.713 63.158 14.03 7.35 36.97 4.41
1026 1103 2.345991 GCCCAGTTGTAGACGGCA 59.654 61.111 0.00 0.00 35.53 5.69
1064 1141 4.016706 CGGCGTGGGAAGAAGGGT 62.017 66.667 0.00 0.00 0.00 4.34
1104 1219 2.798501 CGCGCACGAATCGGTCAAT 61.799 57.895 8.75 0.00 43.93 2.57
1139 1262 1.890894 GGCGAAGTAGAGCACCTGA 59.109 57.895 0.00 0.00 34.54 3.86
1296 1431 1.489574 GATGCAGAGCTCAGATGTCG 58.510 55.000 17.77 0.00 0.00 4.35
1500 1919 1.163554 CAGAGCAGGGAAAACAGAGC 58.836 55.000 0.00 0.00 0.00 4.09
1512 1931 3.390135 TCCGTACAAGAAAACAGAGCAG 58.610 45.455 0.00 0.00 0.00 4.24
1533 2031 1.202639 TGTGTGTCCTCGTCTGCAAAT 60.203 47.619 0.00 0.00 0.00 2.32
1543 2041 0.976641 TCACCAGGATGTGTGTCCTC 59.023 55.000 0.00 0.00 45.51 3.71
1586 2334 3.131577 TGGTGAATACATACCTCGGTGAC 59.868 47.826 0.00 0.00 37.84 3.67
1603 2601 2.437651 TGAAGTCAGTGGTGATTGGTGA 59.562 45.455 0.00 0.00 34.36 4.02
1671 2880 5.460646 CGCTGGATAACACACTTCATTTTT 58.539 37.500 0.00 0.00 0.00 1.94
1672 2881 4.082787 CCGCTGGATAACACACTTCATTTT 60.083 41.667 0.00 0.00 0.00 1.82
1677 2886 0.727398 GCCGCTGGATAACACACTTC 59.273 55.000 0.00 0.00 0.00 3.01
1680 2889 1.421410 CTCGCCGCTGGATAACACAC 61.421 60.000 0.00 0.00 0.00 3.82
1726 2935 6.465948 TGCATTATTTCAGGAGCACATTTTT 58.534 32.000 0.00 0.00 0.00 1.94
1752 2961 6.751157 TCCATATGTGAAAATCATCATTGCC 58.249 36.000 1.24 0.00 0.00 4.52
1755 2964 9.758651 CAACATCCATATGTGAAAATCATCATT 57.241 29.630 1.24 0.00 45.79 2.57
1757 2966 7.204604 GCAACATCCATATGTGAAAATCATCA 58.795 34.615 1.24 0.00 45.79 3.07
1806 3020 5.220854 GCAATTTTGCGTGATACACCTATCT 60.221 40.000 0.00 0.00 45.11 1.98
1867 3094 2.813754 CCCTGTTGTTACACACATCCTG 59.186 50.000 0.00 0.00 34.43 3.86
1868 3095 2.441750 ACCCTGTTGTTACACACATCCT 59.558 45.455 0.00 0.00 34.43 3.24
1872 3099 1.282447 ACCACCCTGTTGTTACACACA 59.718 47.619 0.00 0.00 0.00 3.72
1880 3107 0.843984 ACTTAGCACCACCCTGTTGT 59.156 50.000 0.00 0.00 0.00 3.32
1883 3110 1.136828 TTGACTTAGCACCACCCTGT 58.863 50.000 0.00 0.00 0.00 4.00
1896 3123 7.296628 AGTATCTCTGACTTCAAGTTGACTT 57.703 36.000 4.68 0.00 36.45 3.01
1905 3132 8.138074 GCACACATAATAGTATCTCTGACTTCA 58.862 37.037 0.00 0.00 0.00 3.02
1917 3144 9.256477 GCAGTAAGTAATGCACACATAATAGTA 57.744 33.333 5.92 0.00 45.63 1.82
1930 3157 7.218204 CGGAAAATAAACAGCAGTAAGTAATGC 59.782 37.037 2.62 2.62 46.58 3.56
1944 3171 5.593909 AGGATGCATGATCGGAAAATAAACA 59.406 36.000 2.46 0.00 30.87 2.83
1947 3174 6.533730 ACTAGGATGCATGATCGGAAAATAA 58.466 36.000 2.46 0.00 30.87 1.40
1956 3184 8.462589 TCATAGAGATACTAGGATGCATGATC 57.537 38.462 2.46 0.00 37.05 2.92
1993 3221 2.897436 TCATTGCTCTGATCCGTCTTG 58.103 47.619 0.00 0.00 0.00 3.02
1994 3222 3.464907 CATCATTGCTCTGATCCGTCTT 58.535 45.455 0.00 0.00 33.59 3.01
2022 3250 6.927294 AGTTTCTAGTGTTCTTTTCTGGTG 57.073 37.500 0.00 0.00 0.00 4.17
2107 3344 7.123383 TGACAACCTATAGGACTTGACAGATA 58.877 38.462 26.01 2.73 38.94 1.98
2108 3345 5.958380 TGACAACCTATAGGACTTGACAGAT 59.042 40.000 26.01 4.10 38.94 2.90
2109 3346 5.330233 TGACAACCTATAGGACTTGACAGA 58.670 41.667 26.01 3.68 38.94 3.41
2110 3347 5.419155 TCTGACAACCTATAGGACTTGACAG 59.581 44.000 28.83 28.83 41.04 3.51
2111 3348 5.330233 TCTGACAACCTATAGGACTTGACA 58.670 41.667 26.01 21.65 38.94 3.58
2112 3349 5.419471 ACTCTGACAACCTATAGGACTTGAC 59.581 44.000 26.01 18.67 38.94 3.18
2130 3367 2.369860 GGACCATATGCCATGACTCTGA 59.630 50.000 0.00 0.00 0.00 3.27
2153 3390 3.054276 TGAACGCACTTTAACAAACCG 57.946 42.857 0.00 0.00 0.00 4.44
2203 3441 5.957842 TCTGCAGAATTTACCATTCGTTT 57.042 34.783 15.67 0.00 33.51 3.60
2252 3490 9.244799 GGTTTCTGAAATCGTTTATTTTCTGTT 57.755 29.630 6.06 0.00 37.93 3.16
2253 3491 8.630037 AGGTTTCTGAAATCGTTTATTTTCTGT 58.370 29.630 6.06 0.00 37.93 3.41
2260 3498 9.939802 ACTAACTAGGTTTCTGAAATCGTTTAT 57.060 29.630 6.06 0.00 0.00 1.40
2261 3499 9.768662 AACTAACTAGGTTTCTGAAATCGTTTA 57.231 29.630 6.06 5.45 0.00 2.01
2262 3500 8.672823 AACTAACTAGGTTTCTGAAATCGTTT 57.327 30.769 6.06 4.63 0.00 3.60
2263 3501 9.201127 GTAACTAACTAGGTTTCTGAAATCGTT 57.799 33.333 6.06 8.62 0.00 3.85
2264 3502 8.583296 AGTAACTAACTAGGTTTCTGAAATCGT 58.417 33.333 6.06 4.99 36.36 3.73
2265 3503 8.983307 AGTAACTAACTAGGTTTCTGAAATCG 57.017 34.615 6.06 0.00 36.36 3.34
2275 3513 7.178097 CCCAACACTAGAGTAACTAACTAGGTT 59.822 40.741 0.00 0.00 39.07 3.50
2357 3595 0.251354 AGAAGCGATGATGGTGCAGT 59.749 50.000 0.00 0.00 0.00 4.40
2540 3790 1.376424 CCAACCTCGCTGCTGATGT 60.376 57.895 0.00 0.00 0.00 3.06
2626 3876 9.738832 TTCATACAATTTATCAGTGCATTGATG 57.261 29.630 29.08 18.47 38.25 3.07
3187 4747 4.410099 TGATTCCCACTGCTCTTCAAAAT 58.590 39.130 0.00 0.00 0.00 1.82
3538 5098 2.351447 CCGAGTAGTTGAAGAGCACGAA 60.351 50.000 0.00 0.00 0.00 3.85
3788 5348 5.982890 AACCATCATCAAAAGGTTGGTAG 57.017 39.130 0.00 0.00 42.42 3.18


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

AutoCloner maintained by Alex Coulton.