Multiple sequence alignment - TraesCS7D01G260900

Loading Multiple Alignment...

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 TraesCS7D01G260900 chr7D 100.000 4863 0 0 506 5368 236685938 236690800 0.000000e+00 8981.0
1 TraesCS7D01G260900 chr7D 85.214 886 109 18 3513 4387 58483003 58483877 0.000000e+00 891.0
2 TraesCS7D01G260900 chr7D 93.110 566 33 3 4808 5368 529776138 529776702 0.000000e+00 824.0
3 TraesCS7D01G260900 chr7D 92.933 566 33 6 4808 5368 612340628 612340065 0.000000e+00 817.0
4 TraesCS7D01G260900 chr7D 100.000 227 0 0 1 227 236685433 236685659 2.310000e-113 420.0
5 TraesCS7D01G260900 chr7D 87.903 248 21 2 2313 2551 58482339 58482586 3.160000e-72 283.0
6 TraesCS7D01G260900 chr7D 91.892 148 11 1 2084 2231 58482085 58482231 7.050000e-49 206.0
7 TraesCS7D01G260900 chr7D 90.210 143 14 0 4680 4822 567561804 567561946 2.550000e-43 187.0
8 TraesCS7D01G260900 chr7D 86.391 169 20 3 613 779 129361358 129361191 1.190000e-41 182.0
9 TraesCS7D01G260900 chr7D 89.583 96 10 0 1906 2001 58481681 58481776 7.300000e-24 122.0
10 TraesCS7D01G260900 chr7D 90.805 87 8 0 2669 2755 58482584 58482670 3.400000e-22 117.0
11 TraesCS7D01G260900 chr7D 100.000 32 0 0 775 806 413850353 413850322 5.810000e-05 60.2
12 TraesCS7D01G260900 chr7A 92.005 2514 135 36 2086 4581 251838123 251840588 0.000000e+00 3469.0
13 TraesCS7D01G260900 chr7A 93.097 565 34 4 4808 5368 519528060 519528623 0.000000e+00 822.0
14 TraesCS7D01G260900 chr7A 90.619 501 22 5 868 1367 251835636 251836112 4.530000e-180 641.0
15 TraesCS7D01G260900 chr7A 87.026 501 39 9 1575 2063 251836686 251837172 4.730000e-150 542.0
16 TraesCS7D01G260900 chr7A 87.097 248 23 2 2313 2551 62825638 62825885 6.850000e-69 272.0
17 TraesCS7D01G260900 chr7A 82.154 325 31 19 1907 2231 62825245 62825542 2.480000e-63 254.0
18 TraesCS7D01G260900 chr7A 96.610 59 2 0 4619 4677 251840878 251840936 1.230000e-16 99.0
19 TraesCS7D01G260900 chr7B 92.318 1510 49 21 1197 2671 213393486 213394963 0.000000e+00 2084.0
20 TraesCS7D01G260900 chr7B 90.412 1189 84 10 3483 4649 213417565 213418745 0.000000e+00 1537.0
21 TraesCS7D01G260900 chr7B 89.651 831 61 11 2665 3482 213416669 213417487 0.000000e+00 1035.0
22 TraesCS7D01G260900 chr7B 93.824 680 39 2 530 1209 213384266 213384942 0.000000e+00 1020.0
23 TraesCS7D01G260900 chr7B 88.596 228 25 1 1 227 213383857 213384084 5.300000e-70 276.0
24 TraesCS7D01G260900 chr7B 88.393 224 20 5 1 222 237372654 237372435 1.150000e-66 265.0
25 TraesCS7D01G260900 chr5A 85.714 945 100 20 3505 4436 680088029 680088951 0.000000e+00 965.0
26 TraesCS7D01G260900 chr5A 80.428 654 87 27 1906 2554 680086581 680087198 1.360000e-125 460.0
27 TraesCS7D01G260900 chr5A 79.713 488 61 20 897 1365 680085110 680085578 8.680000e-83 318.0
28 TraesCS7D01G260900 chr5A 89.520 229 20 4 3155 3380 680087720 680087947 2.450000e-73 287.0
29 TraesCS7D01G260900 chr5A 92.157 153 9 2 2885 3037 680087483 680087632 4.210000e-51 213.0
30 TraesCS7D01G260900 chr5A 93.878 98 6 0 2660 2757 680087287 680087384 1.200000e-31 148.0
31 TraesCS7D01G260900 chr5A 96.970 33 1 0 774 806 617900432 617900464 7.510000e-04 56.5
32 TraesCS7D01G260900 chr4B 85.441 941 106 19 3505 4436 642100758 642101676 0.000000e+00 950.0
33 TraesCS7D01G260900 chr4B 82.522 452 42 19 2313 2757 642099702 642100123 3.950000e-96 363.0
34 TraesCS7D01G260900 chr4B 81.235 421 52 17 885 1289 642097853 642098262 1.120000e-81 315.0
35 TraesCS7D01G260900 chr4B 87.907 215 25 1 4 217 361390988 361390774 8.930000e-63 252.0
36 TraesCS7D01G260900 chr4B 91.503 153 10 2 2885 3037 642100220 642100369 1.960000e-49 207.0
37 TraesCS7D01G260900 chr4B 92.199 141 11 0 2095 2235 642099457 642099597 3.280000e-47 200.0
38 TraesCS7D01G260900 chr4B 86.982 169 19 3 612 779 426615733 426615567 2.550000e-43 187.0
39 TraesCS7D01G260900 chr4B 100.000 30 0 0 775 804 533296321 533296292 7.510000e-04 56.5
40 TraesCS7D01G260900 chr4A 86.505 867 87 19 3513 4366 674909032 674909881 0.000000e+00 926.0
41 TraesCS7D01G260900 chr4A 83.452 701 96 15 4680 5368 715592731 715592039 7.580000e-178 634.0
42 TraesCS7D01G260900 chr4A 87.097 248 23 2 2313 2551 674908368 674908615 6.850000e-69 272.0
43 TraesCS7D01G260900 chr4A 82.154 325 30 17 1907 2231 674907964 674908260 2.480000e-63 254.0
44 TraesCS7D01G260900 chr4A 78.481 316 41 14 1916 2231 674918467 674918755 1.190000e-41 182.0
45 TraesCS7D01G260900 chr4A 91.954 87 7 0 2669 2755 674908613 674908699 7.300000e-24 122.0
46 TraesCS7D01G260900 chr4D 89.569 719 67 6 3722 4436 499305252 499305966 0.000000e+00 905.0
47 TraesCS7D01G260900 chr4D 80.506 672 84 32 2095 2757 499303671 499304304 6.290000e-129 472.0
48 TraesCS7D01G260900 chr4D 85.329 334 34 8 885 1205 499302419 499302750 1.110000e-86 331.0
49 TraesCS7D01G260900 chr4D 91.630 227 16 3 3155 3380 499304642 499304866 1.450000e-80 311.0
50 TraesCS7D01G260900 chr4D 88.235 221 23 3 1 219 369960062 369959843 1.480000e-65 261.0
51 TraesCS7D01G260900 chr4D 92.157 153 12 0 2885 3037 499304402 499304554 3.260000e-52 217.0
52 TraesCS7D01G260900 chr4D 90.345 145 13 1 4679 4822 479451453 479451597 7.100000e-44 189.0
53 TraesCS7D01G260900 chr4D 85.526 152 21 1 3499 3649 499304941 499305092 2.000000e-34 158.0
54 TraesCS7D01G260900 chr1D 90.605 628 56 1 3753 4377 467519431 467518804 0.000000e+00 830.0
55 TraesCS7D01G260900 chr1D 92.908 564 36 4 4808 5368 257845629 257846191 0.000000e+00 817.0
56 TraesCS7D01G260900 chr1D 81.278 673 76 31 1907 2555 467521082 467520436 2.890000e-137 499.0
57 TraesCS7D01G260900 chr1D 86.391 169 18 5 614 779 60913326 60913160 4.270000e-41 180.0
58 TraesCS7D01G260900 chr1D 90.385 104 10 0 1700 1803 467521273 467521170 2.610000e-28 137.0
59 TraesCS7D01G260900 chr1D 100.000 30 0 0 775 804 166398317 166398288 7.510000e-04 56.5
60 TraesCS7D01G260900 chr3D 93.238 562 30 4 4814 5368 593208989 593208429 0.000000e+00 821.0
61 TraesCS7D01G260900 chr3D 88.341 223 25 1 1 222 525720775 525720997 3.190000e-67 267.0
62 TraesCS7D01G260900 chr3D 90.000 150 14 1 4677 4825 22038479 22038330 5.490000e-45 193.0
63 TraesCS7D01G260900 chr3D 85.455 165 20 4 614 775 13101723 13101886 9.250000e-38 169.0
64 TraesCS7D01G260900 chr3D 86.538 104 7 3 512 615 98924938 98925034 2.040000e-19 108.0
65 TraesCS7D01G260900 chr6D 93.178 557 36 2 4814 5368 38805526 38804970 0.000000e+00 817.0
66 TraesCS7D01G260900 chr6D 86.425 221 29 1 4 223 35700437 35700217 1.930000e-59 241.0
67 TraesCS7D01G260900 chr5D 92.870 561 34 2 4808 5368 11025520 11026074 0.000000e+00 809.0
68 TraesCS7D01G260900 chr5D 90.066 151 13 2 4673 4822 556147216 556147365 1.530000e-45 195.0
69 TraesCS7D01G260900 chr5D 100.000 32 0 0 775 806 202067308 202067339 5.810000e-05 60.2
70 TraesCS7D01G260900 chr1B 89.857 631 61 1 3753 4380 645347796 645347166 0.000000e+00 808.0
71 TraesCS7D01G260900 chr1B 84.143 700 89 19 4679 5368 67711102 67711789 0.000000e+00 658.0
72 TraesCS7D01G260900 chr1B 87.215 219 27 1 1 218 40203145 40203363 1.150000e-61 248.0
73 TraesCS7D01G260900 chr1B 79.832 357 44 14 1906 2244 645349552 645349206 8.990000e-58 235.0
74 TraesCS7D01G260900 chr1B 86.667 165 20 2 612 775 311519852 311520015 1.190000e-41 182.0
75 TraesCS7D01G260900 chr1B 93.103 87 6 0 2668 2754 645348794 645348708 1.570000e-25 128.0
76 TraesCS7D01G260900 chr1B 100.000 31 0 0 775 805 264417460 264417430 2.090000e-04 58.4
77 TraesCS7D01G260900 chr1A 80.781 666 73 36 1907 2555 560467629 560468256 2.260000e-128 470.0
78 TraesCS7D01G260900 chr1A 82.119 302 40 8 891 1182 560466143 560466440 4.150000e-61 246.0
79 TraesCS7D01G260900 chr2D 88.789 223 24 1 1 222 466679552 466679774 6.850000e-69 272.0
80 TraesCS7D01G260900 chr2D 86.726 226 23 7 1 222 400290893 400290671 1.490000e-60 244.0
81 TraesCS7D01G260900 chr2D 86.667 165 18 4 614 775 201747257 201747420 4.270000e-41 180.0
82 TraesCS7D01G260900 chr6B 89.349 169 15 3 612 779 518433699 518433865 5.450000e-50 209.0
83 TraesCS7D01G260900 chr6B 89.933 149 13 2 4676 4822 659334919 659335067 1.970000e-44 191.0
84 TraesCS7D01G260900 chr6B 100.000 30 0 0 775 804 203296336 203296307 7.510000e-04 56.5
85 TraesCS7D01G260900 chrUn 86.792 159 21 0 4685 4843 366102781 366102939 1.540000e-40 178.0
86 TraesCS7D01G260900 chr2B 86.061 165 22 1 4680 4843 150329902 150330066 5.530000e-40 176.0
87 TraesCS7D01G260900 chr6A 85.207 169 20 5 614 779 203685212 203685378 9.250000e-38 169.0
88 TraesCS7D01G260900 chr5B 96.970 33 1 0 773 805 422666765 422666733 7.510000e-04 56.5


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 TraesCS7D01G260900 chr7D 236685433 236690800 5367 False 4700.500000 8981 100.000000 1 5368 2 chr7D.!!$F4 5367
1 TraesCS7D01G260900 chr7D 529776138 529776702 564 False 824.000000 824 93.110000 4808 5368 1 chr7D.!!$F1 560
2 TraesCS7D01G260900 chr7D 612340065 612340628 563 True 817.000000 817 92.933000 4808 5368 1 chr7D.!!$R3 560
3 TraesCS7D01G260900 chr7D 58481681 58483877 2196 False 323.800000 891 89.079400 1906 4387 5 chr7D.!!$F3 2481
4 TraesCS7D01G260900 chr7A 251835636 251840936 5300 False 1187.750000 3469 91.565000 868 4677 4 chr7A.!!$F3 3809
5 TraesCS7D01G260900 chr7A 519528060 519528623 563 False 822.000000 822 93.097000 4808 5368 1 chr7A.!!$F1 560
6 TraesCS7D01G260900 chr7A 62825245 62825885 640 False 263.000000 272 84.625500 1907 2551 2 chr7A.!!$F2 644
7 TraesCS7D01G260900 chr7B 213393486 213394963 1477 False 2084.000000 2084 92.318000 1197 2671 1 chr7B.!!$F1 1474
8 TraesCS7D01G260900 chr7B 213416669 213418745 2076 False 1286.000000 1537 90.031500 2665 4649 2 chr7B.!!$F3 1984
9 TraesCS7D01G260900 chr7B 213383857 213384942 1085 False 648.000000 1020 91.210000 1 1209 2 chr7B.!!$F2 1208
10 TraesCS7D01G260900 chr5A 680085110 680088951 3841 False 398.500000 965 86.901667 897 4436 6 chr5A.!!$F2 3539
11 TraesCS7D01G260900 chr4B 642097853 642101676 3823 False 407.000000 950 86.580000 885 4436 5 chr4B.!!$F1 3551
12 TraesCS7D01G260900 chr4A 715592039 715592731 692 True 634.000000 634 83.452000 4680 5368 1 chr4A.!!$R1 688
13 TraesCS7D01G260900 chr4A 674907964 674909881 1917 False 393.500000 926 86.927500 1907 4366 4 chr4A.!!$F2 2459
14 TraesCS7D01G260900 chr4D 499302419 499305966 3547 False 399.000000 905 87.452833 885 4436 6 chr4D.!!$F2 3551
15 TraesCS7D01G260900 chr1D 257845629 257846191 562 False 817.000000 817 92.908000 4808 5368 1 chr1D.!!$F1 560
16 TraesCS7D01G260900 chr1D 467518804 467521273 2469 True 488.666667 830 87.422667 1700 4377 3 chr1D.!!$R3 2677
17 TraesCS7D01G260900 chr3D 593208429 593208989 560 True 821.000000 821 93.238000 4814 5368 1 chr3D.!!$R2 554
18 TraesCS7D01G260900 chr6D 38804970 38805526 556 True 817.000000 817 93.178000 4814 5368 1 chr6D.!!$R2 554
19 TraesCS7D01G260900 chr5D 11025520 11026074 554 False 809.000000 809 92.870000 4808 5368 1 chr5D.!!$F1 560
20 TraesCS7D01G260900 chr1B 67711102 67711789 687 False 658.000000 658 84.143000 4679 5368 1 chr1B.!!$F2 689
21 TraesCS7D01G260900 chr1B 645347166 645349552 2386 True 390.333333 808 87.597333 1906 4380 3 chr1B.!!$R2 2474
22 TraesCS7D01G260900 chr1A 560466143 560468256 2113 False 358.000000 470 81.450000 891 2555 2 chr1A.!!$F1 1664

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
731 740 0.462375 ATTATACCGTCGTGCTGCCA 59.538 50.0 0.00 0.0 0.00 4.92 F
963 989 0.826715 CAGTAGCAGCCTAGGAGCAA 59.173 55.0 23.49 0.0 34.23 3.91 F
2210 4922 0.107945 CTTCTCCTTCGCCCTCTTGG 60.108 60.0 0.00 0.0 37.09 3.61 F
3130 6081 0.251634 GGAAGTGAGCTGGAAGAGGG 59.748 60.0 0.00 0.0 34.07 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 3414 0.947244 CCGAGCTGCATATTGGAACC 59.053 55.0 1.02 0.00 0.0 3.62 R
2823 5763 0.886490 CGGGAAGAAACTGCTGCTGT 60.886 55.0 6.33 6.33 0.0 4.40 R
3544 6634 0.028110 GACATCAAAGAATCCGCCGC 59.972 55.0 0.00 0.00 0.0 6.53 R
4459 7708 0.192566 AAGAACCCCCTTTTTCCCCC 59.807 55.0 0.00 0.00 0.0 5.40 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
40 41 4.221041 TGAGTTATGTATGTTGGTGACCGA 59.779 41.667 0.00 0.00 0.00 4.69
43 44 6.880484 AGTTATGTATGTTGGTGACCGAATA 58.120 36.000 0.00 0.00 0.00 1.75
50 51 4.390264 TGTTGGTGACCGAATATTGTTCA 58.610 39.130 0.00 0.00 0.00 3.18
56 57 4.567159 GTGACCGAATATTGTTCAGAGTCC 59.433 45.833 0.00 0.00 0.00 3.85
57 58 4.221924 TGACCGAATATTGTTCAGAGTCCA 59.778 41.667 0.00 0.00 0.00 4.02
77 79 4.835056 TCCAGATAAGATCACGGACATGAT 59.165 41.667 0.00 0.00 42.15 2.45
78 80 4.928020 CCAGATAAGATCACGGACATGATG 59.072 45.833 0.00 0.00 39.48 3.07
89 91 1.487976 GGACATGATGAGGAGCTCCAA 59.512 52.381 33.90 21.99 38.89 3.53
95 97 1.680207 GATGAGGAGCTCCAAAATGGC 59.320 52.381 33.90 12.62 37.47 4.40
104 106 1.208844 TCCAAAATGGCCCGGAGGTA 61.209 55.000 0.73 0.00 41.35 3.08
107 109 5.489547 TCCAAAATGGCCCGGAGGTAAAT 62.490 47.826 0.73 0.00 41.35 1.40
141 143 6.054860 AGGATGATAATATTTGGTCTCCGG 57.945 41.667 0.00 0.00 0.00 5.14
152 154 0.886563 GGTCTCCGGAAGAGTTTCGA 59.113 55.000 5.23 0.00 43.71 3.71
171 173 7.643764 AGTTTCGAAATGCACCGAATAATTATG 59.356 33.333 14.69 0.00 43.14 1.90
172 174 5.996219 TCGAAATGCACCGAATAATTATGG 58.004 37.500 0.00 0.00 0.00 2.74
173 175 5.049060 TCGAAATGCACCGAATAATTATGGG 60.049 40.000 12.18 12.18 0.00 4.00
535 537 2.044946 CGCCAAGAAGGAAGGGGG 60.045 66.667 0.00 0.00 41.22 5.40
537 539 1.304617 GCCAAGAAGGAAGGGGGAG 59.695 63.158 0.00 0.00 41.22 4.30
655 664 1.213430 CTCTCCCTCTAGTCCGTCCTT 59.787 57.143 0.00 0.00 0.00 3.36
701 710 2.640184 AGCCCTGCGGAATAGTTTTAC 58.360 47.619 0.00 0.00 0.00 2.01
702 711 1.674441 GCCCTGCGGAATAGTTTTACC 59.326 52.381 0.00 0.00 0.00 2.85
703 712 2.942306 GCCCTGCGGAATAGTTTTACCA 60.942 50.000 0.00 0.00 0.00 3.25
707 716 4.035208 CCTGCGGAATAGTTTTACCATCAC 59.965 45.833 0.00 0.00 0.00 3.06
713 722 5.820947 GGAATAGTTTTACCATCACCGTCAT 59.179 40.000 0.00 0.00 0.00 3.06
714 723 6.317893 GGAATAGTTTTACCATCACCGTCATT 59.682 38.462 0.00 0.00 0.00 2.57
726 735 1.126079 CCGTCATTATACCGTCGTGC 58.874 55.000 0.00 0.00 0.00 5.34
731 740 0.462375 ATTATACCGTCGTGCTGCCA 59.538 50.000 0.00 0.00 0.00 4.92
744 753 2.093764 GTGCTGCCAGAACTCATCTACT 60.094 50.000 0.00 0.00 36.32 2.57
754 763 4.951094 AGAACTCATCTACTACTTCGCCTT 59.049 41.667 0.00 0.00 36.32 4.35
778 787 1.410517 TGCTGGATCGAGAAGGCTAAG 59.589 52.381 9.17 0.00 0.00 2.18
782 791 4.794655 GCTGGATCGAGAAGGCTAAGTTAG 60.795 50.000 9.17 5.47 0.00 2.34
802 811 2.582636 AGAGTATCCAAACAGGGCCATT 59.417 45.455 6.18 0.00 38.24 3.16
803 812 2.689983 GAGTATCCAAACAGGGCCATTG 59.310 50.000 6.18 8.04 38.24 2.82
805 814 2.028561 ATCCAAACAGGGCCATTGTT 57.971 45.000 16.62 16.62 40.30 2.83
938 947 2.047844 CGGACACTCACCAGCCTG 60.048 66.667 0.00 0.00 0.00 4.85
939 948 2.348998 GGACACTCACCAGCCTGG 59.651 66.667 9.83 9.83 45.02 4.45
963 989 0.826715 CAGTAGCAGCCTAGGAGCAA 59.173 55.000 23.49 0.00 34.23 3.91
1697 3204 3.755905 TGCAACTCAAACTGTTGAACTGA 59.244 39.130 9.24 0.00 45.27 3.41
1787 3294 2.363795 ATCGCCGTCTTCTCCCCA 60.364 61.111 0.00 0.00 0.00 4.96
1897 3414 4.094590 GCTGTTGAATCTCCTCTGACATTG 59.905 45.833 0.00 0.00 0.00 2.82
1898 3415 4.582869 TGTTGAATCTCCTCTGACATTGG 58.417 43.478 0.00 0.00 0.00 3.16
2063 4524 1.889105 GCACATCGCCATGGTCGAT 60.889 57.895 27.55 27.55 46.27 3.59
2072 4533 1.293924 CCATGGTCGATCTGAACTGC 58.706 55.000 2.57 0.00 34.43 4.40
2209 4921 0.610687 ACTTCTCCTTCGCCCTCTTG 59.389 55.000 0.00 0.00 0.00 3.02
2210 4922 0.107945 CTTCTCCTTCGCCCTCTTGG 60.108 60.000 0.00 0.00 37.09 3.61
2610 5436 7.039784 GGCTAGATAGATAGATCACATCATCCC 60.040 44.444 9.30 5.00 0.00 3.85
2788 5728 3.926821 TTGCCAAACCGATTTAAGGAC 57.073 42.857 0.00 0.00 0.00 3.85
2797 5737 7.544217 CCAAACCGATTTAAGGACTTAATTTGG 59.456 37.037 20.81 20.81 40.21 3.28
3015 5966 1.020861 TGCAGCGCATCATCGTCTTT 61.021 50.000 11.47 0.00 31.71 2.52
3080 6031 4.606457 AGACGAGCAGCATGAAAAATAC 57.394 40.909 0.00 0.00 39.69 1.89
3086 6037 3.133362 AGCAGCATGAAAAATACATGGGG 59.867 43.478 0.00 0.00 43.39 4.96
3130 6081 0.251634 GGAAGTGAGCTGGAAGAGGG 59.748 60.000 0.00 0.00 34.07 4.30
3157 6117 1.135527 TCTTACGGACGCTACATTGGG 59.864 52.381 0.00 0.00 0.00 4.12
3329 6295 1.301716 CCAGTGGGACCAGTTCACG 60.302 63.158 0.00 0.00 36.60 4.35
3395 6361 4.725490 CAAGGTATGGTTTGGGGGTATAG 58.275 47.826 0.00 0.00 0.00 1.31
3397 6363 4.648309 AGGTATGGTTTGGGGGTATAGAA 58.352 43.478 0.00 0.00 0.00 2.10
3398 6364 4.414514 AGGTATGGTTTGGGGGTATAGAAC 59.585 45.833 0.00 0.00 0.00 3.01
3418 6431 9.761504 ATAGAACTATAGATACATCATGCATGC 57.238 33.333 22.25 11.82 35.65 4.06
3430 6443 2.857186 ATGCATGCCATGACCGTATA 57.143 45.000 16.68 0.00 31.48 1.47
3431 6444 2.857186 TGCATGCCATGACCGTATAT 57.143 45.000 16.68 0.00 0.00 0.86
3441 6454 4.486090 CATGACCGTATATAGCAGTGTCC 58.514 47.826 0.00 0.00 0.00 4.02
3465 6478 2.861147 AGAACTGCCAGGGAACTTAC 57.139 50.000 0.00 0.00 40.21 2.34
3475 6488 4.098196 GCCAGGGAACTTACTACAGAGTAG 59.902 50.000 2.79 2.79 39.36 2.57
3500 6590 6.936968 ACTCCTACTTGTTATCCTTGTCTT 57.063 37.500 0.00 0.00 0.00 3.01
3501 6591 6.702329 ACTCCTACTTGTTATCCTTGTCTTG 58.298 40.000 0.00 0.00 0.00 3.02
3502 6592 6.270231 ACTCCTACTTGTTATCCTTGTCTTGT 59.730 38.462 0.00 0.00 0.00 3.16
3503 6593 6.464222 TCCTACTTGTTATCCTTGTCTTGTG 58.536 40.000 0.00 0.00 0.00 3.33
3542 6632 0.616111 ACGAGAGAGACTGGCCCAAT 60.616 55.000 0.00 0.00 0.00 3.16
3544 6634 1.339610 CGAGAGAGACTGGCCCAATAG 59.660 57.143 0.00 0.00 0.00 1.73
3557 6647 1.308998 CCAATAGCGGCGGATTCTTT 58.691 50.000 9.78 0.00 0.00 2.52
3702 6829 2.137523 CTGCAAAGTTCATGGCAAACC 58.862 47.619 0.00 0.00 35.59 3.27
3903 7146 4.435436 TCATCTTCGCGGCGCACT 62.435 61.111 32.61 7.78 0.00 4.40
4064 7310 1.112315 CCTGCCCGCTCTATCAGAGT 61.112 60.000 5.17 0.00 44.12 3.24
4118 7364 1.202758 GGCACCATGAACGGGATCATA 60.203 52.381 0.00 0.00 37.96 2.15
4271 7517 2.668556 CGAGTACAAGAAGAGCAGCGAA 60.669 50.000 0.00 0.00 0.00 4.70
4412 7659 2.095768 TCTGTGCAATAAAACTGCTCGC 60.096 45.455 0.00 0.00 40.59 5.03
4447 7694 4.203226 TGTGTGCTAATGAAGTGTGGAAA 58.797 39.130 0.00 0.00 0.00 3.13
4458 7707 5.890334 TGAAGTGTGGAAAGCTAGTTTTTG 58.110 37.500 6.00 0.00 0.00 2.44
4459 7708 4.918810 AGTGTGGAAAGCTAGTTTTTGG 57.081 40.909 6.00 0.00 0.00 3.28
4460 7709 3.636764 AGTGTGGAAAGCTAGTTTTTGGG 59.363 43.478 6.00 0.00 0.00 4.12
4461 7710 2.962421 TGTGGAAAGCTAGTTTTTGGGG 59.038 45.455 6.00 0.00 0.00 4.96
4476 7725 4.553144 GGGGGAAAAAGGGGGTTC 57.447 61.111 0.00 0.00 0.00 3.62
4478 7727 0.192566 GGGGGAAAAAGGGGGTTCTT 59.807 55.000 0.00 0.00 0.00 2.52
4480 7729 1.254026 GGGAAAAAGGGGGTTCTTCG 58.746 55.000 0.00 0.00 0.00 3.79
4481 7730 1.202964 GGGAAAAAGGGGGTTCTTCGA 60.203 52.381 0.00 0.00 0.00 3.71
4492 7741 3.323243 GGGTTCTTCGACGATTTGAGAA 58.677 45.455 0.00 1.68 0.00 2.87
4496 7745 2.094182 TCTTCGACGATTTGAGAAGGGG 60.094 50.000 0.00 0.00 40.16 4.79
4535 7784 2.025155 CCAGTACCTATGCTCGACACT 58.975 52.381 0.00 0.00 0.00 3.55
4553 7802 0.256752 CTGATGGATGCAACCCAGGA 59.743 55.000 10.94 1.95 37.08 3.86
4568 7817 2.107031 CCCAGGATTACATGCAGATCCA 59.893 50.000 19.09 0.00 41.43 3.41
4576 7825 0.032130 CATGCAGATCCAAGCCATGC 59.968 55.000 0.00 0.00 37.40 4.06
4609 8096 6.764877 ATATTAACTCATAACGTTGCCTCG 57.235 37.500 11.99 0.00 0.00 4.63
4613 8100 2.230508 ACTCATAACGTTGCCTCGAAGA 59.769 45.455 11.99 0.00 34.70 2.87
4677 8177 3.554934 TGAAACCTGCAATCTGACTGTT 58.445 40.909 0.00 0.00 0.00 3.16
4694 8194 8.857098 TCTGACTGTTACACTAGTAGAAAACAT 58.143 33.333 3.59 2.68 0.00 2.71
4698 8198 6.765403 TGTTACACTAGTAGAAAACATGGCT 58.235 36.000 3.59 0.00 0.00 4.75
4702 8202 6.296026 ACACTAGTAGAAAACATGGCTTTGA 58.704 36.000 3.59 0.00 0.00 2.69
4714 8214 1.549203 GGCTTTGATTCAGGCCAGAA 58.451 50.000 13.54 13.54 43.59 3.02
4718 8218 3.615834 GCTTTGATTCAGGCCAGAAAAGG 60.616 47.826 15.21 7.30 0.00 3.11
4719 8219 2.220653 TGATTCAGGCCAGAAAAGGG 57.779 50.000 15.21 0.00 0.00 3.95
4720 8220 1.428912 TGATTCAGGCCAGAAAAGGGT 59.571 47.619 15.21 0.00 0.00 4.34
4725 8225 4.938575 TCAGGCCAGAAAAGGGTATTAA 57.061 40.909 5.01 0.00 0.00 1.40
4745 8245 0.963225 TCCCGATTCACTCACGAACA 59.037 50.000 0.00 0.00 0.00 3.18
4752 8252 0.757561 TCACTCACGAACAGGGACCA 60.758 55.000 0.00 0.00 0.00 4.02
4754 8254 0.834612 ACTCACGAACAGGGACCAAA 59.165 50.000 0.00 0.00 0.00 3.28
4758 8258 1.057851 ACGAACAGGGACCAAAGGGA 61.058 55.000 0.00 0.00 38.05 4.20
4760 8260 0.771755 GAACAGGGACCAAAGGGAGT 59.228 55.000 0.00 0.00 38.05 3.85
4764 8264 2.196595 CAGGGACCAAAGGGAGTATCA 58.803 52.381 0.00 0.00 36.25 2.15
4765 8265 2.576191 CAGGGACCAAAGGGAGTATCAA 59.424 50.000 0.00 0.00 36.25 2.57
4787 8287 2.514824 GATTCGTGAGGCCAGGGC 60.515 66.667 5.01 4.33 41.06 5.19
4826 8327 1.074072 CATTGGTCCCGGTTGGTGA 59.926 57.895 0.00 0.00 34.77 4.02
4946 8456 0.517316 GCCATCGCTCTGTTTTTCGT 59.483 50.000 0.00 0.00 0.00 3.85
4971 8481 0.320374 CGTGGGAGAGCTTTGTGGTA 59.680 55.000 0.00 0.00 0.00 3.25
4996 8506 5.454966 TCTAGTTCACCTCCTATGCACATA 58.545 41.667 0.00 0.00 0.00 2.29
5072 8585 4.344968 CCTTGTCCAAACTCCATTTTCCTT 59.655 41.667 0.00 0.00 0.00 3.36
5145 8666 2.190841 TCGATCGCCTGTGCCGATA 61.191 57.895 11.09 0.00 44.60 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.504858 ACTCTGAACAATATTCGGTCACC 58.495 43.478 2.65 0.00 0.00 4.02
40 41 9.995003 GATCTTATCTGGACTCTGAACAATATT 57.005 33.333 0.00 0.00 0.00 1.28
43 44 7.271511 GTGATCTTATCTGGACTCTGAACAAT 58.728 38.462 0.00 0.00 0.00 2.71
50 51 3.886505 GTCCGTGATCTTATCTGGACTCT 59.113 47.826 17.36 0.00 44.67 3.24
56 57 5.776744 TCATCATGTCCGTGATCTTATCTG 58.223 41.667 0.00 0.00 36.72 2.90
57 58 5.047448 CCTCATCATGTCCGTGATCTTATCT 60.047 44.000 0.00 0.00 36.72 1.98
77 79 0.323725 GGCCATTTTGGAGCTCCTCA 60.324 55.000 32.28 17.14 40.96 3.86
78 80 1.039785 GGGCCATTTTGGAGCTCCTC 61.040 60.000 32.28 8.73 40.96 3.71
89 91 3.895041 CAATATTTACCTCCGGGCCATTT 59.105 43.478 4.39 0.00 35.63 2.32
95 97 9.375974 TCCTATATATCAATATTTACCTCCGGG 57.624 37.037 0.00 0.00 32.84 5.73
133 135 0.886563 TCGAAACTCTTCCGGAGACC 59.113 55.000 3.34 0.00 44.45 3.85
140 142 2.412847 CGGTGCATTTCGAAACTCTTCC 60.413 50.000 13.81 11.02 0.00 3.46
141 143 2.478894 TCGGTGCATTTCGAAACTCTTC 59.521 45.455 13.81 2.78 32.11 2.87
152 154 6.493115 TGATCCCATAATTATTCGGTGCATTT 59.507 34.615 0.00 0.00 0.00 2.32
171 173 1.407025 GGAACTCCTTTCGGTGATCCC 60.407 57.143 0.00 0.00 38.89 3.85
172 174 1.278127 TGGAACTCCTTTCGGTGATCC 59.722 52.381 0.00 3.62 42.74 3.36
173 175 2.233922 TCTGGAACTCCTTTCGGTGATC 59.766 50.000 0.00 0.00 34.67 2.92
186 188 0.689623 CTCTGTGGCCTTCTGGAACT 59.310 55.000 3.32 0.00 34.57 3.01
192 194 3.054802 CCAATAACTCTCTGTGGCCTTCT 60.055 47.826 3.32 0.00 0.00 2.85
193 195 3.274288 CCAATAACTCTCTGTGGCCTTC 58.726 50.000 3.32 0.00 0.00 3.46
197 199 1.383523 GCCCAATAACTCTCTGTGGC 58.616 55.000 0.00 0.00 0.00 5.01
516 518 3.127533 CCCTTCCTTCTTGGCGCG 61.128 66.667 0.00 0.00 35.26 6.86
628 637 0.263468 ACTAGAGGGAGAGAAGGGCC 59.737 60.000 0.00 0.00 0.00 5.80
689 698 5.180271 TGACGGTGATGGTAAAACTATTCC 58.820 41.667 0.00 0.00 0.00 3.01
701 710 3.314553 GACGGTATAATGACGGTGATGG 58.685 50.000 0.00 0.00 33.47 3.51
702 711 2.977829 CGACGGTATAATGACGGTGATG 59.022 50.000 0.00 0.00 33.47 3.07
703 712 2.620115 ACGACGGTATAATGACGGTGAT 59.380 45.455 0.00 0.00 33.47 3.06
707 716 1.126079 GCACGACGGTATAATGACGG 58.874 55.000 0.00 0.00 0.00 4.79
713 722 0.179121 CTGGCAGCACGACGGTATAA 60.179 55.000 0.00 0.00 0.00 0.98
714 723 1.033202 TCTGGCAGCACGACGGTATA 61.033 55.000 10.34 0.00 0.00 1.47
726 735 5.587289 GAAGTAGTAGATGAGTTCTGGCAG 58.413 45.833 8.58 8.58 35.79 4.85
731 740 4.528920 AGGCGAAGTAGTAGATGAGTTCT 58.471 43.478 0.00 0.00 38.57 3.01
754 763 1.812571 GCCTTCTCGATCCAGCAAAAA 59.187 47.619 0.00 0.00 0.00 1.94
772 781 6.049790 CCTGTTTGGATACTCTAACTTAGCC 58.950 44.000 0.00 0.00 38.35 3.93
778 787 3.054655 TGGCCCTGTTTGGATACTCTAAC 60.055 47.826 0.00 0.00 38.35 2.34
782 791 2.689983 CAATGGCCCTGTTTGGATACTC 59.310 50.000 0.00 0.00 38.35 2.59
839 848 5.704053 CGGTTACCTACCTCAGAAAACAATT 59.296 40.000 0.00 0.00 45.40 2.32
851 860 3.377573 TGGAATAAGCGGTTACCTACCT 58.622 45.455 9.61 0.00 45.40 3.08
938 947 2.691674 CTAGGCTGCTACTGCGCTCC 62.692 65.000 9.73 0.00 43.34 4.70
939 948 1.299773 CTAGGCTGCTACTGCGCTC 60.300 63.158 9.73 0.00 43.34 5.03
1697 3204 3.257873 CAGTGTCTTCATCCTGTCAGAGT 59.742 47.826 0.00 0.00 0.00 3.24
1787 3294 3.914426 AGGTCTTACATGAAATCGGCT 57.086 42.857 0.00 0.00 0.00 5.52
1825 3332 9.408648 ACTGGAATGTTATCGGAATAATCTTTT 57.591 29.630 0.00 0.00 30.28 2.27
1826 3333 8.980481 ACTGGAATGTTATCGGAATAATCTTT 57.020 30.769 0.00 0.00 30.28 2.52
1827 3334 7.385205 CGACTGGAATGTTATCGGAATAATCTT 59.615 37.037 0.00 0.00 30.28 2.40
1828 3335 6.868864 CGACTGGAATGTTATCGGAATAATCT 59.131 38.462 0.00 0.00 30.28 2.40
1839 3346 6.992123 TGAATCTATTGCGACTGGAATGTTAT 59.008 34.615 0.00 0.00 36.73 1.89
1897 3414 0.947244 CCGAGCTGCATATTGGAACC 59.053 55.000 1.02 0.00 0.00 3.62
1898 3415 0.947244 CCCGAGCTGCATATTGGAAC 59.053 55.000 1.02 0.00 0.00 3.62
2035 3564 2.407268 GCGATGTGCATCCATTCCA 58.593 52.632 6.60 0.00 45.45 3.53
2063 4524 1.486310 ACACCAACAGAGCAGTTCAGA 59.514 47.619 0.00 0.00 0.00 3.27
2072 4533 2.487762 ACACAAACACACACCAACAGAG 59.512 45.455 0.00 0.00 0.00 3.35
2610 5436 1.795872 TGGTACGTGAAATCTTGTGCG 59.204 47.619 0.00 0.00 0.00 5.34
2650 5476 5.155278 TCGCCTTAATAAACCAGAGAACA 57.845 39.130 0.00 0.00 0.00 3.18
2815 5755 3.515502 AGAAACTGCTGCTGTATGGAGTA 59.484 43.478 12.66 0.00 36.43 2.59
2816 5756 2.304180 AGAAACTGCTGCTGTATGGAGT 59.696 45.455 12.66 0.00 36.43 3.85
2817 5757 2.983229 AGAAACTGCTGCTGTATGGAG 58.017 47.619 12.66 0.00 37.17 3.86
2818 5758 3.338249 GAAGAAACTGCTGCTGTATGGA 58.662 45.455 12.66 0.00 0.00 3.41
2819 5759 2.421424 GGAAGAAACTGCTGCTGTATGG 59.579 50.000 12.66 0.00 0.00 2.74
2823 5763 0.886490 CGGGAAGAAACTGCTGCTGT 60.886 55.000 6.33 6.33 0.00 4.40
2878 5822 5.995282 AGTACCTGAATGATCACAAACGAAA 59.005 36.000 0.00 0.00 0.00 3.46
3015 5966 2.058705 TGTACCTTTCCCATGTCACCA 58.941 47.619 0.00 0.00 0.00 4.17
3086 6037 4.752879 TACCGAGCGGCAACAGCC 62.753 66.667 9.14 0.00 45.19 4.85
3130 6081 3.310774 TGTAGCGTCCGTAAGAGTGATAC 59.689 47.826 0.00 0.00 43.02 2.24
3395 6361 6.820152 TGGCATGCATGATGTATCTATAGTTC 59.180 38.462 30.64 6.09 34.14 3.01
3397 6363 6.303903 TGGCATGCATGATGTATCTATAGT 57.696 37.500 30.64 0.00 34.14 2.12
3398 6364 6.990349 TCATGGCATGCATGATGTATCTATAG 59.010 38.462 30.64 9.21 34.50 1.31
3418 6431 4.486090 GACACTGCTATATACGGTCATGG 58.514 47.826 0.00 0.00 0.00 3.66
3430 6443 5.078411 CAGTTCTTACTGGACACTGCTAT 57.922 43.478 0.00 0.00 46.52 2.97
3431 6444 4.521130 CAGTTCTTACTGGACACTGCTA 57.479 45.455 0.00 0.00 46.52 3.49
3453 6466 5.262804 ACTACTCTGTAGTAAGTTCCCTGG 58.737 45.833 8.43 0.00 37.75 4.45
3475 6488 7.407393 AGACAAGGATAACAAGTAGGAGTAC 57.593 40.000 0.00 0.00 0.00 2.73
3487 6577 4.574828 ACACACACACAAGACAAGGATAAC 59.425 41.667 0.00 0.00 0.00 1.89
3500 6590 3.201297 CCGCTGCACACACACACA 61.201 61.111 0.00 0.00 0.00 3.72
3501 6591 4.612536 GCCGCTGCACACACACAC 62.613 66.667 0.00 0.00 37.47 3.82
3542 6632 1.134521 ACATCAAAGAATCCGCCGCTA 60.135 47.619 0.00 0.00 0.00 4.26
3544 6634 0.028110 GACATCAAAGAATCCGCCGC 59.972 55.000 0.00 0.00 0.00 6.53
3557 6647 0.608130 CACCGGAGTCCTTGACATCA 59.392 55.000 9.46 0.00 34.60 3.07
3602 6692 1.035139 CGGCCGGGTAGTAGTACATT 58.965 55.000 20.10 0.00 0.00 2.71
3702 6829 8.655970 TCGTCACTCATTTGAAATACAATAGTG 58.344 33.333 0.00 0.00 40.87 2.74
3711 6838 5.047802 AGCCATTTCGTCACTCATTTGAAAT 60.048 36.000 0.00 0.00 39.21 2.17
3903 7146 1.151899 AGGAGTAACCCAGCACCCA 60.152 57.895 0.00 0.00 40.05 4.51
4114 7360 1.378531 GCCTGCCACGACAAATATGA 58.621 50.000 0.00 0.00 0.00 2.15
4118 7364 3.055719 CCGCCTGCCACGACAAAT 61.056 61.111 0.00 0.00 0.00 2.32
4271 7517 1.867363 AGGAATCGTAGACCTTGCCT 58.133 50.000 0.00 0.00 42.51 4.75
4316 7562 3.830464 ATGCACACAGCCGAGCACA 62.830 57.895 0.00 0.00 44.83 4.57
4459 7708 0.192566 AAGAACCCCCTTTTTCCCCC 59.807 55.000 0.00 0.00 0.00 5.40
4460 7709 1.640917 GAAGAACCCCCTTTTTCCCC 58.359 55.000 0.00 0.00 0.00 4.81
4461 7710 1.202964 TCGAAGAACCCCCTTTTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
4469 7718 1.084289 CAAATCGTCGAAGAACCCCC 58.916 55.000 4.85 0.00 39.69 5.40
4476 7725 2.271800 CCCCTTCTCAAATCGTCGAAG 58.728 52.381 0.00 0.00 34.22 3.79
4478 7727 0.535335 CCCCCTTCTCAAATCGTCGA 59.465 55.000 0.00 0.00 0.00 4.20
4480 7729 2.491675 AACCCCCTTCTCAAATCGTC 57.508 50.000 0.00 0.00 0.00 4.20
4481 7730 2.971901 AAACCCCCTTCTCAAATCGT 57.028 45.000 0.00 0.00 0.00 3.73
4535 7784 0.928505 ATCCTGGGTTGCATCCATCA 59.071 50.000 15.63 4.58 33.29 3.07
4553 7802 3.301794 TGGCTTGGATCTGCATGTAAT 57.698 42.857 0.00 0.00 0.00 1.89
4586 7846 6.509656 TCGAGGCAACGTTATGAGTTAATAT 58.490 36.000 0.00 0.00 46.39 1.28
4600 8087 2.561733 TGTATCTCTTCGAGGCAACG 57.438 50.000 0.00 0.00 46.39 4.10
4650 8150 7.443575 ACAGTCAGATTGCAGGTTTCATATATC 59.556 37.037 0.00 0.00 0.00 1.63
4677 8177 7.446769 TCAAAGCCATGTTTTCTACTAGTGTA 58.553 34.615 5.39 0.00 0.00 2.90
4698 8198 2.899256 CCCTTTTCTGGCCTGAATCAAA 59.101 45.455 23.90 14.96 0.00 2.69
4702 8202 4.337264 AATACCCTTTTCTGGCCTGAAT 57.663 40.909 23.90 12.35 0.00 2.57
4714 8214 6.126594 TGAGTGAATCGGGATTAATACCCTTT 60.127 38.462 11.35 4.89 44.72 3.11
4718 8218 4.684703 CGTGAGTGAATCGGGATTAATACC 59.315 45.833 6.65 6.65 0.00 2.73
4719 8219 5.526115 TCGTGAGTGAATCGGGATTAATAC 58.474 41.667 0.00 0.00 0.00 1.89
4720 8220 5.777850 TCGTGAGTGAATCGGGATTAATA 57.222 39.130 0.00 0.00 0.00 0.98
4725 8225 1.548719 TGTTCGTGAGTGAATCGGGAT 59.451 47.619 0.00 0.00 0.00 3.85
4731 8231 1.002087 GGTCCCTGTTCGTGAGTGAAT 59.998 52.381 0.00 0.00 0.00 2.57
4736 8236 1.512926 CTTTGGTCCCTGTTCGTGAG 58.487 55.000 0.00 0.00 0.00 3.51
4745 8245 2.661176 TGATACTCCCTTTGGTCCCT 57.339 50.000 0.00 0.00 0.00 4.20
4758 8258 3.005897 CCTCACGAATCGGGATTGATACT 59.994 47.826 8.46 0.00 39.06 2.12
4760 8260 2.288825 GCCTCACGAATCGGGATTGATA 60.289 50.000 8.46 0.00 39.06 2.15
4764 8264 1.146263 GGCCTCACGAATCGGGATT 59.854 57.895 8.46 0.00 39.06 3.01
4765 8265 2.032860 CTGGCCTCACGAATCGGGAT 62.033 60.000 8.46 0.00 39.06 3.85
4771 8271 4.473520 CGCCCTGGCCTCACGAAT 62.474 66.667 3.32 0.00 37.98 3.34
4826 8327 0.251165 CATTTGGTCCCGGTTCCAGT 60.251 55.000 13.29 5.86 35.05 4.00
4971 8481 3.702045 GTGCATAGGAGGTGAACTAGAGT 59.298 47.826 0.00 0.00 0.00 3.24
4996 8506 1.463674 GGCATTCCATCGAACACCTT 58.536 50.000 0.00 0.00 0.00 3.50
5072 8585 4.258543 CCGCCAAACCTAGACAAATCTTA 58.741 43.478 0.00 0.00 36.29 2.10


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

AutoCloner maintained by Alex Coulton.