Multiple sequence alignment - TraesCS5B01G194700

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 TraesCS5B01G194700 chr5B 100.000 6369 0 0 1 6369 351480479 351486847 0.000000e+00 11762.0
1 TraesCS5B01G194700 chr5B 96.875 64 2 0 4386 4449 351484927 351484864 2.430000e-19 108.0
2 TraesCS5B01G194700 chr5B 81.679 131 13 6 3668 3787 638841114 638840984 1.460000e-16 99.0
3 TraesCS5B01G194700 chr5B 93.478 46 3 0 3668 3713 32461229 32461274 1.150000e-07 69.4
4 TraesCS5B01G194700 chr5B 93.333 45 3 0 3669 3713 32596520 32596564 4.120000e-07 67.6
5 TraesCS5B01G194700 chr5D 94.059 3636 150 28 63 3641 306197188 306200814 0.000000e+00 5457.0
6 TraesCS5B01G194700 chr5D 95.373 1664 43 12 3843 5491 306200944 306202588 0.000000e+00 2615.0
7 TraesCS5B01G194700 chr5D 84.631 501 74 3 5870 6369 306204717 306205215 4.440000e-136 496.0
8 TraesCS5B01G194700 chr5D 82.192 146 16 5 3639 3784 541589685 541589820 4.030000e-22 117.0
9 TraesCS5B01G194700 chr5D 95.556 45 2 0 5530 5574 306202586 306202630 8.860000e-09 73.1
10 TraesCS5B01G194700 chr5D 100.000 35 0 0 4386 4420 306201551 306201517 1.480000e-06 65.8
11 TraesCS5B01G194700 chr5A 94.061 2812 133 16 80 2866 391522324 391519522 0.000000e+00 4237.0
12 TraesCS5B01G194700 chr5A 95.525 1475 51 7 2925 4387 391519421 391517950 0.000000e+00 2344.0
13 TraesCS5B01G194700 chr5A 96.048 1164 32 4 4416 5574 391517949 391516795 0.000000e+00 1882.0
14 TraesCS5B01G194700 chr5A 90.931 408 30 3 842 1249 391526773 391526373 5.620000e-150 542.0
15 TraesCS5B01G194700 chr5A 84.921 504 72 3 5870 6369 391515218 391514715 2.050000e-139 507.0
16 TraesCS5B01G194700 chr5A 85.246 122 7 6 3674 3784 671955980 671956101 1.450000e-21 115.0
17 TraesCS5B01G194700 chr5A 85.000 80 10 2 3709 3787 277726577 277726499 5.290000e-11 80.5
18 TraesCS5B01G194700 chr1A 86.466 133 8 5 3665 3787 201861434 201861302 3.100000e-28 137.0
19 TraesCS5B01G194700 chr1D 85.185 135 10 5 3663 3787 127221827 127221693 5.180000e-26 130.0
20 TraesCS5B01G194700 chr7D 85.714 126 8 5 3665 3790 632329423 632329308 2.410000e-24 124.0
21 TraesCS5B01G194700 chr7D 82.222 90 15 1 6058 6147 629865794 629865882 6.850000e-10 76.8
22 TraesCS5B01G194700 chr7D 91.304 46 2 2 4418 4462 631996644 631996600 1.920000e-05 62.1
23 TraesCS5B01G194700 chr2D 81.507 146 17 5 3639 3784 535728518 535728653 1.880000e-20 111.0
24 TraesCS5B01G194700 chr3A 96.923 65 2 0 3658 3722 722208876 722208940 6.750000e-20 110.0
25 TraesCS5B01G194700 chr3A 82.000 150 8 7 3658 3788 722209288 722209437 6.750000e-20 110.0
26 TraesCS5B01G194700 chr3A 100.000 32 0 0 4386 4417 730177224 730177193 6.900000e-05 60.2
27 TraesCS5B01G194700 chr3B 81.452 124 13 2 3661 3784 754148964 754149077 6.800000e-15 93.5
28 TraesCS5B01G194700 chr3B 89.231 65 5 1 4386 4448 33043541 33043477 5.290000e-11 80.5
29 TraesCS5B01G194700 chr6D 86.585 82 9 2 3709 3789 126435214 126435294 8.790000e-14 89.8
30 TraesCS5B01G194700 chr6D 95.000 40 1 1 4379 4417 395533085 395533124 1.920000e-05 62.1
31 TraesCS5B01G194700 chr3D 84.146 82 11 2 3709 3789 479627477 479627397 1.900000e-10 78.7
32 TraesCS5B01G194700 chr7B 97.500 40 1 0 4417 4456 628465802 628465841 1.150000e-07 69.4
33 TraesCS5B01G194700 chr7B 80.952 84 12 3 3704 3784 726155743 726155825 5.330000e-06 63.9
34 TraesCS5B01G194700 chr7B 100.000 33 0 0 4418 4450 588889178 588889146 1.920000e-05 62.1
35 TraesCS5B01G194700 chr7A 97.500 40 1 0 4417 4456 661165471 661165510 1.150000e-07 69.4
36 TraesCS5B01G194700 chrUn 92.857 42 2 1 4375 4415 379674900 379674859 6.900000e-05 60.2
37 TraesCS5B01G194700 chr6B 92.857 42 2 1 4375 4415 699839234 699839193 6.900000e-05 60.2
38 TraesCS5B01G194700 chr6B 92.857 42 2 1 4375 4415 699879141 699879100 6.900000e-05 60.2
39 TraesCS5B01G194700 chr4A 100.000 32 0 0 4420 4451 674618656 674618625 6.900000e-05 60.2


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 TraesCS5B01G194700 chr5B 351480479 351486847 6368 False 11762.000 11762 100.00000 1 6369 1 chr5B.!!$F3 6368
1 TraesCS5B01G194700 chr5D 306197188 306205215 8027 False 2160.275 5457 92.40475 63 6369 4 chr5D.!!$F2 6306
2 TraesCS5B01G194700 chr5A 391514715 391522324 7609 True 2242.500 4237 92.63875 80 6369 4 chr5A.!!$R3 6289

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
490 524 0.029834 GATCAATGATGTGTGGCGGC 59.970 55.0 0.00 0.00 0.0 6.53 F
957 1014 0.178894 AAGCAAAGCCATTCCCCCTT 60.179 50.0 0.00 0.00 0.0 3.95 F
2282 2339 0.035317 AGACAATGAAGCGCCTCACA 59.965 50.0 11.63 3.27 0.0 3.58 F
3030 3173 0.478072 ACCCTGCCACTTGTTGATCA 59.522 50.0 0.00 0.00 0.0 2.92 F
3735 3891 0.589223 CTAGTCGATCGGTCAGGCTC 59.411 60.0 16.41 0.00 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1682 0.681887 CCATGTTGATGGCCTGCTCA 60.682 55.000 3.32 1.21 43.00 4.26 R
2793 2850 1.701847 ACCATAGCCCATCAGGATCAC 59.298 52.381 0.00 0.00 38.24 3.06 R
3652 3798 0.179230 CGTCGACTAGTCACGTGACC 60.179 60.000 38.00 24.41 45.85 4.02 R
4624 4872 1.064758 TGCCAAGTTGTCTTCTGTGGT 60.065 47.619 1.45 0.00 0.00 4.16 R
5627 5907 0.174617 GCAAGAAGAGAGACGGAGGG 59.825 60.000 0.00 0.00 0.00 4.30 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
25 26 7.826260 TTGAAAGAAGGTGACAAAAATTGAC 57.174 32.000 0.00 0.00 0.00 3.18
26 27 6.033341 TGAAAGAAGGTGACAAAAATTGACG 58.967 36.000 0.00 0.00 0.00 4.35
27 28 5.828299 AAGAAGGTGACAAAAATTGACGA 57.172 34.783 0.00 0.00 0.00 4.20
28 29 5.424121 AGAAGGTGACAAAAATTGACGAG 57.576 39.130 0.00 0.00 0.00 4.18
29 30 4.881850 AGAAGGTGACAAAAATTGACGAGT 59.118 37.500 0.00 0.00 0.00 4.18
30 31 5.357032 AGAAGGTGACAAAAATTGACGAGTT 59.643 36.000 0.00 0.00 0.00 3.01
31 32 6.540914 AGAAGGTGACAAAAATTGACGAGTTA 59.459 34.615 0.00 0.00 0.00 2.24
32 33 6.300354 AGGTGACAAAAATTGACGAGTTAG 57.700 37.500 0.00 0.00 0.00 2.34
33 34 6.053005 AGGTGACAAAAATTGACGAGTTAGA 58.947 36.000 0.00 0.00 0.00 2.10
34 35 6.540914 AGGTGACAAAAATTGACGAGTTAGAA 59.459 34.615 0.00 0.00 0.00 2.10
35 36 6.851330 GGTGACAAAAATTGACGAGTTAGAAG 59.149 38.462 0.00 0.00 0.00 2.85
36 37 6.851330 GTGACAAAAATTGACGAGTTAGAAGG 59.149 38.462 0.00 0.00 0.00 3.46
37 38 6.764085 TGACAAAAATTGACGAGTTAGAAGGA 59.236 34.615 0.00 0.00 0.00 3.36
38 39 7.281324 TGACAAAAATTGACGAGTTAGAAGGAA 59.719 33.333 0.00 0.00 0.00 3.36
39 40 8.166422 ACAAAAATTGACGAGTTAGAAGGAAT 57.834 30.769 0.00 0.00 0.00 3.01
40 41 9.280174 ACAAAAATTGACGAGTTAGAAGGAATA 57.720 29.630 0.00 0.00 0.00 1.75
41 42 9.543018 CAAAAATTGACGAGTTAGAAGGAATAC 57.457 33.333 0.00 0.00 0.00 1.89
42 43 8.842358 AAAATTGACGAGTTAGAAGGAATACA 57.158 30.769 0.00 0.00 0.00 2.29
43 44 9.449719 AAAATTGACGAGTTAGAAGGAATACAT 57.550 29.630 0.00 0.00 0.00 2.29
44 45 9.449719 AAATTGACGAGTTAGAAGGAATACATT 57.550 29.630 0.00 0.00 0.00 2.71
103 104 7.328737 ACTCGCAAATATTGGAAGTCGATATAC 59.671 37.037 0.00 0.00 32.59 1.47
125 126 1.745489 GCGGTAGCAACCTCCCAAG 60.745 63.158 0.00 0.00 44.35 3.61
139 140 3.217626 CTCCCAAGAGCTTCAACAACTT 58.782 45.455 0.00 0.00 32.13 2.66
158 159 6.494146 ACAACTTAGTAGTCTAGCACCTCTTT 59.506 38.462 0.00 0.00 31.99 2.52
159 160 7.015389 ACAACTTAGTAGTCTAGCACCTCTTTT 59.985 37.037 0.00 0.00 31.99 2.27
183 188 5.007385 AGAGACAAAGTTGTTCACGTAGT 57.993 39.130 0.00 0.00 42.21 2.73
189 194 6.905578 ACAAAGTTGTTCACGTAGTTTTCTT 58.094 32.000 0.00 0.00 36.80 2.52
191 196 8.505625 ACAAAGTTGTTCACGTAGTTTTCTTTA 58.494 29.630 0.00 0.00 36.80 1.85
208 213 8.344831 GTTTTCTTTAGCCTTACGGTTTTTCTA 58.655 33.333 0.00 0.00 0.00 2.10
236 241 6.404623 GCCACTGTTGTGCATTCTATTTCATA 60.405 38.462 0.00 0.00 42.54 2.15
237 242 6.968904 CCACTGTTGTGCATTCTATTTCATAC 59.031 38.462 0.00 0.00 42.54 2.39
246 251 8.725148 GTGCATTCTATTTCATACCTATCCAAG 58.275 37.037 0.00 0.00 0.00 3.61
279 307 6.808829 TCTGAAGATGTGCTTTCATTTTGTT 58.191 32.000 0.00 0.00 36.83 2.83
321 349 7.421530 TGTAGACTTACAATCAGTGAAAAGC 57.578 36.000 0.00 0.00 36.86 3.51
490 524 0.029834 GATCAATGATGTGTGGCGGC 59.970 55.000 0.00 0.00 0.00 6.53
493 527 1.023502 CAATGATGTGTGGCGGCATA 58.976 50.000 17.19 10.42 0.00 3.14
496 530 0.744057 TGATGTGTGGCGGCATAGTG 60.744 55.000 17.19 0.00 0.00 2.74
501 535 0.391927 TGTGGCGGCATAGTGTAACC 60.392 55.000 17.19 0.00 37.80 2.85
590 626 6.341316 TGACAAGTTAGAGGAATACATGAGC 58.659 40.000 0.00 0.00 0.00 4.26
593 629 3.961408 AGTTAGAGGAATACATGAGCGGT 59.039 43.478 0.00 0.00 0.00 5.68
631 667 9.813080 GCGATTTACTTACCATTCATCTTATTC 57.187 33.333 0.00 0.00 0.00 1.75
662 699 6.330278 ACGACATCGAAGACATTTAAGATCA 58.670 36.000 8.54 0.00 42.51 2.92
737 774 9.864034 GTGAATATGATAAGGTTAACAATGTCG 57.136 33.333 8.10 0.00 0.00 4.35
742 779 7.359262 TGATAAGGTTAACAATGTCGTCAAG 57.641 36.000 8.10 0.00 0.00 3.02
807 854 0.601311 ATTTAGATCTGAGGCGCCGC 60.601 55.000 24.58 24.58 0.00 6.53
955 1012 0.615827 AGAAGCAAAGCCATTCCCCC 60.616 55.000 0.00 0.00 0.00 5.40
956 1013 0.615827 GAAGCAAAGCCATTCCCCCT 60.616 55.000 0.00 0.00 0.00 4.79
957 1014 0.178894 AAGCAAAGCCATTCCCCCTT 60.179 50.000 0.00 0.00 0.00 3.95
958 1015 0.615827 AGCAAAGCCATTCCCCCTTC 60.616 55.000 0.00 0.00 0.00 3.46
959 1016 1.948721 GCAAAGCCATTCCCCCTTCG 61.949 60.000 0.00 0.00 0.00 3.79
1259 1316 2.126307 CAGGCCTCTGACGACGTG 60.126 66.667 4.58 0.00 43.49 4.49
1478 1535 3.431486 GCTCTTTCCTCAACGATCCAGAT 60.431 47.826 0.00 0.00 0.00 2.90
1568 1625 2.654079 CCTCCTTCAGAGCAGCCGT 61.654 63.158 0.00 0.00 41.74 5.68
1625 1682 4.699522 GCCAACGACCTCCGCCTT 62.700 66.667 0.00 0.00 43.32 4.35
1712 1769 3.329542 GAGTGATGCGCCTTCCCCA 62.330 63.158 4.18 0.00 0.00 4.96
1862 1919 2.919856 ACCGAGAGCACTGCTGGT 60.920 61.111 8.69 7.00 39.88 4.00
1871 1928 1.447217 CACTGCTGGTGTGGTCTCA 59.553 57.895 0.00 0.00 40.79 3.27
1877 1934 0.603707 CTGGTGTGGTCTCATGCGTT 60.604 55.000 0.00 0.00 0.00 4.84
1898 1955 1.048601 AGAACACATGGTCACGGTCT 58.951 50.000 0.00 0.00 33.22 3.85
2282 2339 0.035317 AGACAATGAAGCGCCTCACA 59.965 50.000 11.63 3.27 0.00 3.58
2366 2423 4.219070 CAGAAACTGGAAATGGAGAATGCA 59.781 41.667 0.00 0.00 44.23 3.96
2718 2775 2.581246 TCCTACTAGGAGAGGTTGCTGA 59.419 50.000 2.52 0.00 40.06 4.26
2731 2788 7.187824 AGAGGTTGCTGAGTTTAGATCATTA 57.812 36.000 0.00 0.00 0.00 1.90
2732 2789 7.624549 AGAGGTTGCTGAGTTTAGATCATTAA 58.375 34.615 0.00 0.00 0.00 1.40
2773 2830 1.751351 ACTACGCTTCATGCTCAGCTA 59.249 47.619 0.00 0.00 40.11 3.32
2855 2915 6.099125 ACAACTGGTGGTAAAAGCCTAATTTT 59.901 34.615 0.00 0.00 36.40 1.82
2929 3072 4.265893 TGTTGTTCCAGAGTTAGCACAAA 58.734 39.130 0.00 0.00 0.00 2.83
2974 3117 3.529533 AGCACAGAGTCAGTGATTATGC 58.470 45.455 18.91 9.76 39.30 3.14
3030 3173 0.478072 ACCCTGCCACTTGTTGATCA 59.522 50.000 0.00 0.00 0.00 2.92
3119 3262 4.868171 TCAGCGTTCATCCATAACTGTAAC 59.132 41.667 0.00 0.00 0.00 2.50
3170 3313 1.334384 TGCTGCGAGGGCCAGTATTA 61.334 55.000 6.18 0.00 38.85 0.98
3258 3401 4.391830 TCGTCATCCTGAAAAATAGTGTGC 59.608 41.667 0.00 0.00 0.00 4.57
3261 3404 4.458989 TCATCCTGAAAAATAGTGTGCACC 59.541 41.667 15.69 5.76 0.00 5.01
3332 3475 5.448225 CGTGCTATGCATTTTGATCTTCTGT 60.448 40.000 3.54 0.00 41.91 3.41
3334 3477 5.416639 TGCTATGCATTTTGATCTTCTGTGT 59.583 36.000 3.54 0.00 31.71 3.72
3377 3521 3.559069 CAGATTGCCAGGTAACCATGAT 58.441 45.455 0.00 0.00 37.17 2.45
3425 3569 4.645535 TCCCTCAGTTTCTGTTCTGAATG 58.354 43.478 0.00 0.00 39.67 2.67
3437 3581 6.902341 TCTGTTCTGAATGTAATTGCTTGTC 58.098 36.000 0.00 0.00 36.07 3.18
3659 3805 1.099689 CCACTGTTTTTGGGTCACGT 58.900 50.000 0.00 0.00 0.00 4.49
3692 3838 3.357079 CGCACTGCCAGGGTTGAC 61.357 66.667 0.00 0.00 0.00 3.18
3704 3850 2.928416 GGTTGACTCAAACCCCTCG 58.072 57.895 0.00 0.00 43.31 4.63
3735 3891 0.589223 CTAGTCGATCGGTCAGGCTC 59.411 60.000 16.41 0.00 0.00 4.70
3799 3956 6.285224 TCGAAGACCATGTTTTAACTCAGAA 58.715 36.000 0.00 0.00 0.00 3.02
3845 4083 8.220755 ACTGTAAATTGTTGCTTCTTTCTACA 57.779 30.769 0.00 0.00 0.00 2.74
3941 4181 1.079819 CCTGCGTTCTCGTCCACAT 60.080 57.895 0.00 0.00 39.49 3.21
3945 4189 1.337728 TGCGTTCTCGTCCACATCATT 60.338 47.619 0.00 0.00 39.49 2.57
3948 4192 4.202070 TGCGTTCTCGTCCACATCATTATA 60.202 41.667 0.00 0.00 39.49 0.98
3951 4195 6.073765 GCGTTCTCGTCCACATCATTATAAAT 60.074 38.462 0.00 0.00 39.49 1.40
4004 4248 7.437793 AATAAAAATGTGCCACCATCTTTTG 57.562 32.000 0.00 0.00 0.00 2.44
4100 4348 4.574421 TCGCACCAGTTATCCATTGTAATG 59.426 41.667 0.00 0.00 36.17 1.90
4407 4655 4.405756 ACTCCCTCCGATCCATATTAGT 57.594 45.455 0.00 0.00 0.00 2.24
4408 4656 4.753186 ACTCCCTCCGATCCATATTAGTT 58.247 43.478 0.00 0.00 0.00 2.24
4409 4657 4.528596 ACTCCCTCCGATCCATATTAGTTG 59.471 45.833 0.00 0.00 0.00 3.16
4410 4658 4.489737 TCCCTCCGATCCATATTAGTTGT 58.510 43.478 0.00 0.00 0.00 3.32
4411 4659 4.527038 TCCCTCCGATCCATATTAGTTGTC 59.473 45.833 0.00 0.00 0.00 3.18
4412 4660 4.486090 CCTCCGATCCATATTAGTTGTCG 58.514 47.826 0.00 0.00 0.00 4.35
4413 4661 3.909430 TCCGATCCATATTAGTTGTCGC 58.091 45.455 0.00 0.00 0.00 5.19
4435 4683 4.984785 GCTGATCAGCGACAACTAATATGA 59.015 41.667 30.64 0.00 45.29 2.15
4594 4842 8.203485 AGATTGATTTGTAACATGTGTTTGGTT 58.797 29.630 0.00 0.00 39.31 3.67
4608 4856 9.103861 CATGTGTTTGGTTTGTAGGTTAAAATT 57.896 29.630 0.00 0.00 0.00 1.82
4624 4872 9.847224 AGGTTAAAATTAGAGAAGACACAAAGA 57.153 29.630 0.00 0.00 0.00 2.52
4811 5059 1.205417 GAAGTCCATGGGTGCAAATGG 59.795 52.381 13.02 15.15 44.06 3.16
4819 5067 2.258286 GTGCAAATGGGCCGACAC 59.742 61.111 0.00 0.00 0.00 3.67
4834 5082 2.158900 CCGACACTTCCATCAGCCTATT 60.159 50.000 0.00 0.00 0.00 1.73
5019 5267 0.464373 CTCACCAGGTGCTGTGTGTT 60.464 55.000 15.64 0.00 35.62 3.32
5052 5300 2.817423 GCATGAGGAGAAAGGCGCG 61.817 63.158 0.00 0.00 0.00 6.86
5260 5508 5.185249 TCAGCTCCGTCTCATAAGTTTTACT 59.815 40.000 0.00 0.00 0.00 2.24
5366 5620 0.695347 CAGGAGCAGAGGAACCCTTT 59.305 55.000 0.00 0.00 31.76 3.11
5370 5624 1.073923 GAGCAGAGGAACCCTTTGGAA 59.926 52.381 5.80 0.00 36.41 3.53
5457 5713 1.610038 TGCTTGATGTTCTTGCTGGTG 59.390 47.619 0.00 0.00 0.00 4.17
5461 5717 0.038166 GATGTTCTTGCTGGTGGGGA 59.962 55.000 0.00 0.00 0.00 4.81
5464 5720 1.133199 TGTTCTTGCTGGTGGGGAAAT 60.133 47.619 0.00 0.00 0.00 2.17
5519 5775 4.640647 CCTGAGGAAATAGGTTTTGGTAGC 59.359 45.833 0.00 0.00 0.00 3.58
5574 5830 3.007635 ACCGTAAAGCAGGTATTCTTGC 58.992 45.455 0.00 0.00 45.18 4.01
5627 5907 4.636249 CCTGATGAAGGCTACATAACTCC 58.364 47.826 0.00 0.00 39.93 3.85
5629 5909 3.391296 TGATGAAGGCTACATAACTCCCC 59.609 47.826 0.00 0.00 0.00 4.81
5630 5910 3.130734 TGAAGGCTACATAACTCCCCT 57.869 47.619 0.00 0.00 0.00 4.79
5631 5911 3.039011 TGAAGGCTACATAACTCCCCTC 58.961 50.000 0.00 0.00 0.00 4.30
5632 5912 2.104669 AGGCTACATAACTCCCCTCC 57.895 55.000 0.00 0.00 0.00 4.30
5633 5913 0.680061 GGCTACATAACTCCCCTCCG 59.320 60.000 0.00 0.00 0.00 4.63
5634 5914 1.411041 GCTACATAACTCCCCTCCGT 58.589 55.000 0.00 0.00 0.00 4.69
5635 5915 1.340568 GCTACATAACTCCCCTCCGTC 59.659 57.143 0.00 0.00 0.00 4.79
5636 5916 2.946785 CTACATAACTCCCCTCCGTCT 58.053 52.381 0.00 0.00 0.00 4.18
5637 5917 1.777941 ACATAACTCCCCTCCGTCTC 58.222 55.000 0.00 0.00 0.00 3.36
5638 5918 1.288335 ACATAACTCCCCTCCGTCTCT 59.712 52.381 0.00 0.00 0.00 3.10
5639 5919 1.957877 CATAACTCCCCTCCGTCTCTC 59.042 57.143 0.00 0.00 0.00 3.20
5641 5921 0.410270 AACTCCCCTCCGTCTCTCTT 59.590 55.000 0.00 0.00 0.00 2.85
5642 5922 0.033894 ACTCCCCTCCGTCTCTCTTC 60.034 60.000 0.00 0.00 0.00 2.87
5643 5923 0.257616 CTCCCCTCCGTCTCTCTTCT 59.742 60.000 0.00 0.00 0.00 2.85
5644 5924 0.705253 TCCCCTCCGTCTCTCTTCTT 59.295 55.000 0.00 0.00 0.00 2.52
5645 5925 0.820871 CCCCTCCGTCTCTCTTCTTG 59.179 60.000 0.00 0.00 0.00 3.02
5646 5926 0.174617 CCCTCCGTCTCTCTTCTTGC 59.825 60.000 0.00 0.00 0.00 4.01
5648 5928 0.523966 CTCCGTCTCTCTTCTTGCGT 59.476 55.000 0.00 0.00 0.00 5.24
5649 5929 0.522180 TCCGTCTCTCTTCTTGCGTC 59.478 55.000 0.00 0.00 0.00 5.19
5650 5930 0.456995 CCGTCTCTCTTCTTGCGTCC 60.457 60.000 0.00 0.00 0.00 4.79
5651 5931 0.241213 CGTCTCTCTTCTTGCGTCCA 59.759 55.000 0.00 0.00 0.00 4.02
5652 5932 1.704070 GTCTCTCTTCTTGCGTCCAC 58.296 55.000 0.00 0.00 0.00 4.02
5653 5933 1.271102 GTCTCTCTTCTTGCGTCCACT 59.729 52.381 0.00 0.00 0.00 4.00
5656 7730 0.671781 CTCTTCTTGCGTCCACTGGG 60.672 60.000 0.00 0.00 0.00 4.45
5696 7822 4.373116 TGCGAGCGGTTCACCTCC 62.373 66.667 0.00 0.00 0.00 4.30
5722 7848 1.276421 CGTCTTGGACTGGATGGAGTT 59.724 52.381 0.00 0.00 0.00 3.01
5723 7849 2.289694 CGTCTTGGACTGGATGGAGTTT 60.290 50.000 0.00 0.00 0.00 2.66
5744 7870 1.675641 GATGGCCTGCTGTTCCGTT 60.676 57.895 3.32 0.00 0.00 4.44
5760 7886 1.302511 GTTGCCTCCTTCGCTTGGA 60.303 57.895 0.00 0.00 0.00 3.53
5768 7914 2.048222 TTCGCTTGGACGAGCCTG 60.048 61.111 5.99 0.00 44.00 4.85
5769 7915 2.492449 CTTCGCTTGGACGAGCCTGA 62.492 60.000 5.99 0.00 44.00 3.86
5774 7920 0.539051 CTTGGACGAGCCTGAATCCT 59.461 55.000 0.00 0.00 37.63 3.24
5775 7921 1.757118 CTTGGACGAGCCTGAATCCTA 59.243 52.381 0.00 0.00 37.63 2.94
5780 7926 4.200092 GGACGAGCCTGAATCCTAAATTT 58.800 43.478 0.00 0.00 0.00 1.82
5786 7932 3.181472 GCCTGAATCCTAAATTTGGCCTG 60.181 47.826 3.32 0.00 33.66 4.85
5793 7939 0.039035 TAAATTTGGCCTGCTCCGGT 59.961 50.000 3.32 0.00 0.00 5.28
5806 7952 2.202797 CCGGTGTCAGATGCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
5818 7964 1.943730 ATGCCTCGTCCTCCTCCTCT 61.944 60.000 0.00 0.00 0.00 3.69
5832 7978 1.834378 CCTCTGATGGCGGCTCCTA 60.834 63.158 11.43 0.00 35.26 2.94
5838 7984 2.093537 GATGGCGGCTCCTACTCCTG 62.094 65.000 11.43 0.00 35.26 3.86
5839 7985 4.228567 GGCGGCTCCTACTCCTGC 62.229 72.222 0.00 0.00 0.00 4.85
5841 7987 2.726351 GCGGCTCCTACTCCTGCTT 61.726 63.158 0.00 0.00 0.00 3.91
5843 7989 1.323271 CGGCTCCTACTCCTGCTTCA 61.323 60.000 0.00 0.00 0.00 3.02
5846 8009 0.102120 CTCCTACTCCTGCTTCAGCG 59.898 60.000 0.00 0.00 45.83 5.18
5863 8026 2.947532 CGCCACCTCCTTCTGCTCA 61.948 63.158 0.00 0.00 0.00 4.26
5872 8035 2.031012 TTCTGCTCAGCCCACACG 59.969 61.111 0.00 0.00 0.00 4.49
5888 8075 2.870161 CGTTCTCGTGCTCCGACG 60.870 66.667 0.00 0.00 41.60 5.12
5942 8129 1.442520 GCAATGTGTGCGACGCAAT 60.443 52.632 26.29 12.19 45.10 3.56
5944 8131 1.442520 AATGTGTGCGACGCAATGC 60.443 52.632 26.29 17.22 42.39 3.56
5977 8164 1.201424 TCTCTGTGGCATGCATCTCT 58.799 50.000 21.36 0.00 0.00 3.10
5979 8166 0.906775 TCTGTGGCATGCATCTCTGA 59.093 50.000 21.36 10.24 0.00 3.27
5982 8169 1.832998 TGTGGCATGCATCTCTGACTA 59.167 47.619 21.36 0.00 0.00 2.59
6032 8220 2.359900 CTTGTGGTAGGTGATCTTGCC 58.640 52.381 0.00 0.00 0.00 4.52
6033 8221 1.357137 TGTGGTAGGTGATCTTGCCA 58.643 50.000 0.00 0.00 0.00 4.92
6035 8223 1.003118 GTGGTAGGTGATCTTGCCACA 59.997 52.381 19.63 7.93 43.49 4.17
6038 8226 2.171448 GGTAGGTGATCTTGCCACAGAT 59.829 50.000 0.00 0.00 36.12 2.90
6047 8235 4.432980 TCTTGCCACAGATCATGATGAT 57.567 40.909 14.30 7.81 40.34 2.45
6050 8238 3.893521 TGCCACAGATCATGATGATGTT 58.106 40.909 14.30 0.00 37.20 2.71
6056 8244 3.059120 CAGATCATGATGATGTTGGCGTC 60.059 47.826 14.30 0.00 37.20 5.19
6115 8305 1.468340 GGCAACGACAACGCAAACAC 61.468 55.000 0.00 0.00 43.96 3.32
6123 8313 1.270412 ACAACGCAAACACGAGGGATA 60.270 47.619 0.00 0.00 36.70 2.59
6126 8316 1.006832 CGCAAACACGAGGGATAAGG 58.993 55.000 0.00 0.00 34.06 2.69
6150 8340 4.404098 CGGGGCTAGGGTTGCGTT 62.404 66.667 0.00 0.00 0.00 4.84
6187 8377 1.913762 CTGGACTTGTCCCTCGGGT 60.914 63.158 16.23 0.00 36.47 5.28
6220 8410 1.512926 GGCGATATGAATGCGTCCTT 58.487 50.000 0.00 0.00 0.00 3.36
6237 8427 2.315155 TCCTTAACTAGCTGGAGGAGGT 59.685 50.000 3.17 0.00 32.91 3.85
6249 8439 3.798758 GGAGGTGCCTGTCAGACT 58.201 61.111 0.00 0.00 0.00 3.24
6250 8440 2.977578 GGAGGTGCCTGTCAGACTA 58.022 57.895 0.00 0.00 0.00 2.59
6263 8453 1.689813 TCAGACTAACGGGTTTCAGCA 59.310 47.619 0.00 0.00 0.00 4.41
6265 8455 3.074412 CAGACTAACGGGTTTCAGCATT 58.926 45.455 0.00 0.00 0.00 3.56
6276 8466 3.908081 CAGCATTGGCCCATCCGC 61.908 66.667 0.00 0.00 42.56 5.54
6352 8542 3.181410 TGGATTCGGTATGGGAGATACCT 60.181 47.826 8.79 0.00 41.36 3.08
6355 8545 3.323774 TCGGTATGGGAGATACCTGTT 57.676 47.619 8.79 0.00 41.36 3.16
6360 8550 4.657039 GGTATGGGAGATACCTGTTAACCA 59.343 45.833 2.48 0.00 40.58 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.253750 CGTCAATTTTTGTCACCTTCTTTCAAG 60.254 37.037 0.00 0.00 0.00 3.02
1 2 6.529829 CGTCAATTTTTGTCACCTTCTTTCAA 59.470 34.615 0.00 0.00 0.00 2.69
2 3 6.033341 CGTCAATTTTTGTCACCTTCTTTCA 58.967 36.000 0.00 0.00 0.00 2.69
3 4 6.262601 TCGTCAATTTTTGTCACCTTCTTTC 58.737 36.000 0.00 0.00 0.00 2.62
4 5 6.127730 ACTCGTCAATTTTTGTCACCTTCTTT 60.128 34.615 0.00 0.00 0.00 2.52
5 6 5.357032 ACTCGTCAATTTTTGTCACCTTCTT 59.643 36.000 0.00 0.00 0.00 2.52
6 7 4.881850 ACTCGTCAATTTTTGTCACCTTCT 59.118 37.500 0.00 0.00 0.00 2.85
7 8 5.169836 ACTCGTCAATTTTTGTCACCTTC 57.830 39.130 0.00 0.00 0.00 3.46
8 9 5.576447 AACTCGTCAATTTTTGTCACCTT 57.424 34.783 0.00 0.00 0.00 3.50
9 10 6.053005 TCTAACTCGTCAATTTTTGTCACCT 58.947 36.000 0.00 0.00 0.00 4.00
10 11 6.295039 TCTAACTCGTCAATTTTTGTCACC 57.705 37.500 0.00 0.00 0.00 4.02
11 12 6.851330 CCTTCTAACTCGTCAATTTTTGTCAC 59.149 38.462 0.00 0.00 0.00 3.67
12 13 6.764085 TCCTTCTAACTCGTCAATTTTTGTCA 59.236 34.615 0.00 0.00 0.00 3.58
13 14 7.186021 TCCTTCTAACTCGTCAATTTTTGTC 57.814 36.000 0.00 0.00 0.00 3.18
14 15 7.562454 TTCCTTCTAACTCGTCAATTTTTGT 57.438 32.000 0.00 0.00 0.00 2.83
15 16 9.543018 GTATTCCTTCTAACTCGTCAATTTTTG 57.457 33.333 0.00 0.00 0.00 2.44
16 17 9.280174 TGTATTCCTTCTAACTCGTCAATTTTT 57.720 29.630 0.00 0.00 0.00 1.94
17 18 8.842358 TGTATTCCTTCTAACTCGTCAATTTT 57.158 30.769 0.00 0.00 0.00 1.82
18 19 9.449719 AATGTATTCCTTCTAACTCGTCAATTT 57.550 29.630 0.00 0.00 0.00 1.82
125 126 6.528774 GCTAGACTACTAAGTTGTTGAAGCTC 59.471 42.308 0.00 0.00 35.56 4.09
139 140 8.508883 CTCTTAAAAGAGGTGCTAGACTACTA 57.491 38.462 11.22 0.00 46.88 1.82
158 159 7.037438 ACTACGTGAACAACTTTGTCTCTTAA 58.963 34.615 0.00 0.00 41.31 1.85
159 160 6.567050 ACTACGTGAACAACTTTGTCTCTTA 58.433 36.000 0.00 0.00 41.31 2.10
208 213 1.795170 GAATGCACAACAGTGGCGGT 61.795 55.000 0.00 0.00 33.85 5.68
211 216 3.855689 AATAGAATGCACAACAGTGGC 57.144 42.857 0.00 0.00 33.85 5.01
217 222 8.507249 GGATAGGTATGAAATAGAATGCACAAC 58.493 37.037 0.00 0.00 0.00 3.32
236 241 8.884323 TCTTCAGAATATATTGCTTGGATAGGT 58.116 33.333 1.78 0.00 0.00 3.08
237 242 9.902684 ATCTTCAGAATATATTGCTTGGATAGG 57.097 33.333 1.78 0.00 0.00 2.57
246 251 8.347771 TGAAAGCACATCTTCAGAATATATTGC 58.652 33.333 1.78 0.00 32.88 3.56
253 258 7.439381 ACAAAATGAAAGCACATCTTCAGAAT 58.561 30.769 0.00 0.00 32.88 2.40
295 323 8.507249 GCTTTTCACTGATTGTAAGTCTACATT 58.493 33.333 0.00 0.00 37.86 2.71
297 325 6.989759 TGCTTTTCACTGATTGTAAGTCTACA 59.010 34.615 0.00 0.00 36.20 2.74
370 403 2.275134 TGGAGGTGTACGTGTGTAGA 57.725 50.000 0.00 0.00 0.00 2.59
382 415 6.418101 TCTCCTCATTATTCTTTTGGAGGTG 58.582 40.000 0.00 0.00 41.98 4.00
424 457 0.988832 AAGGCGGTAATGAACCCTGA 59.011 50.000 0.00 0.00 46.62 3.86
426 459 1.834188 CAAAGGCGGTAATGAACCCT 58.166 50.000 0.00 0.00 46.62 4.34
587 623 1.291132 GCTAATGGAAGTGACCGCTC 58.709 55.000 0.00 0.00 0.00 5.03
590 626 2.225068 ATCGCTAATGGAAGTGACCG 57.775 50.000 0.00 0.00 38.74 4.79
593 629 6.759827 GGTAAGTAAATCGCTAATGGAAGTGA 59.240 38.462 0.00 0.00 40.12 3.41
631 667 3.565516 TGTCTTCGATGTCGTTCAAGAG 58.434 45.455 2.04 0.00 40.80 2.85
662 699 5.126396 TCTTCGCATCATCGTCTATCAAT 57.874 39.130 0.00 0.00 0.00 2.57
670 707 2.584492 TGTCATCTTCGCATCATCGT 57.416 45.000 0.00 0.00 0.00 3.73
676 713 6.741992 TTCAATTAGTTGTCATCTTCGCAT 57.258 33.333 0.00 0.00 36.69 4.73
718 755 7.117236 GTCTTGACGACATTGTTAACCTTATCA 59.883 37.037 2.48 0.00 42.37 2.15
807 854 0.249868 TGCCACTGACTTCCTTGTCG 60.250 55.000 0.00 0.00 39.64 4.35
955 1012 3.059800 GGAAGAGGAAACAACGAACGAAG 60.060 47.826 0.14 0.00 0.00 3.79
956 1013 2.867975 GGAAGAGGAAACAACGAACGAA 59.132 45.455 0.14 0.00 0.00 3.85
957 1014 2.476821 GGAAGAGGAAACAACGAACGA 58.523 47.619 0.14 0.00 0.00 3.85
958 1015 1.191647 CGGAAGAGGAAACAACGAACG 59.808 52.381 0.00 0.00 0.00 3.95
959 1016 2.207590 ACGGAAGAGGAAACAACGAAC 58.792 47.619 0.00 0.00 0.00 3.95
1196 1253 1.002502 GTTAAGGGCGAGCAGGGTT 60.003 57.895 0.00 0.00 0.00 4.11
1460 1517 2.632377 GCATCTGGATCGTTGAGGAAA 58.368 47.619 0.00 0.00 0.00 3.13
1568 1625 1.987855 GACACGGGAGATGGTGGGA 60.988 63.158 0.00 0.00 38.46 4.37
1625 1682 0.681887 CCATGTTGATGGCCTGCTCA 60.682 55.000 3.32 1.21 43.00 4.26
1862 1919 3.064207 GTTCTTAACGCATGAGACCACA 58.936 45.455 2.50 0.00 0.00 4.17
1877 1934 2.631062 AGACCGTGACCATGTGTTCTTA 59.369 45.455 0.00 0.00 0.00 2.10
2282 2339 2.130272 TCAGCTCATACTCCAGACGT 57.870 50.000 0.00 0.00 0.00 4.34
2366 2423 4.437239 CTTCCATCTCAGCACGTATTTCT 58.563 43.478 0.00 0.00 0.00 2.52
2718 2775 8.790718 CCAATGCAGCTATTAATGATCTAAACT 58.209 33.333 0.00 0.00 0.00 2.66
2731 2788 3.217626 GGTTAGCTCCAATGCAGCTATT 58.782 45.455 6.74 0.00 46.50 1.73
2732 2789 2.173356 TGGTTAGCTCCAATGCAGCTAT 59.827 45.455 6.74 0.00 46.50 2.97
2793 2850 1.701847 ACCATAGCCCATCAGGATCAC 59.298 52.381 0.00 0.00 38.24 3.06
2929 3072 5.815581 TGTTCACTATTAAGCCTGACCATT 58.184 37.500 0.00 0.00 0.00 3.16
2974 3117 1.269723 TCTAGCACCAACAGACGAGTG 59.730 52.381 0.00 0.00 0.00 3.51
3030 3173 5.039920 TGAATGATAGCTACACCAATGCT 57.960 39.130 0.00 0.00 40.43 3.79
3258 3401 2.783135 AGGCTTGTTCTATGTGTGGTG 58.217 47.619 0.00 0.00 0.00 4.17
3261 3404 3.313526 GGCATAGGCTTGTTCTATGTGTG 59.686 47.826 0.00 0.00 43.46 3.82
3332 3475 4.141574 GGACATAGTATAACCAGGCCAACA 60.142 45.833 5.01 0.00 0.00 3.33
3334 3477 3.393278 GGGACATAGTATAACCAGGCCAA 59.607 47.826 5.01 0.00 0.00 4.52
3377 3521 6.206634 GGCGATCTAACATGATTCCCAATTTA 59.793 38.462 0.00 0.00 0.00 1.40
3425 3569 7.561237 TTTGCGAATTTAGACAAGCAATTAC 57.439 32.000 1.48 0.00 42.90 1.89
3554 3698 6.560253 AACAGAACACATCACAAAGGTATC 57.440 37.500 0.00 0.00 0.00 2.24
3652 3798 0.179230 CGTCGACTAGTCACGTGACC 60.179 60.000 38.00 24.41 45.85 4.02
3692 3838 2.943449 GACTAGTCGAGGGGTTTGAG 57.057 55.000 7.22 0.00 0.00 3.02
3713 3859 1.664873 CCTGACCGATCGACTAGTCA 58.335 55.000 22.37 19.07 37.65 3.41
3725 3881 3.384014 GACGAGTCGAGCCTGACCG 62.384 68.421 21.50 12.13 39.77 4.79
3799 3956 5.418840 CAGTTGACAAATAAGGCCCATAACT 59.581 40.000 0.00 0.00 0.00 2.24
3845 4083 4.280174 CAGCAAAGCAGCCAAGGATATAAT 59.720 41.667 0.00 0.00 34.23 1.28
3851 4089 1.904865 CCAGCAAAGCAGCCAAGGA 60.905 57.895 0.00 0.00 34.23 3.36
3948 4192 8.897872 ATCAATCAAACAGCTGAAAGAAATTT 57.102 26.923 23.35 5.49 34.07 1.82
3951 4195 6.919662 GTGATCAATCAAACAGCTGAAAGAAA 59.080 34.615 23.35 0.48 38.75 2.52
4004 4248 4.566759 TCTCGCTGCAGTATCACAATAAAC 59.433 41.667 16.64 0.00 0.00 2.01
4100 4348 9.755804 ACTTAACAACTGTACTTCTAACCTAAC 57.244 33.333 0.00 0.00 0.00 2.34
4394 4642 4.546570 TCAGCGACAACTAATATGGATCG 58.453 43.478 0.00 0.00 0.00 3.69
4413 4661 7.410193 CGATTCATATTAGTTGTCGCTGATCAG 60.410 40.741 18.84 18.84 0.00 2.90
4510 4758 6.745907 CACATTGAAAGCATAGAAGTGTGATG 59.254 38.462 0.00 0.00 37.26 3.07
4608 4856 4.893524 TCTGTGGTCTTTGTGTCTTCTCTA 59.106 41.667 0.00 0.00 0.00 2.43
4624 4872 1.064758 TGCCAAGTTGTCTTCTGTGGT 60.065 47.619 1.45 0.00 0.00 4.16
4811 5059 2.109126 GCTGATGGAAGTGTCGGCC 61.109 63.158 0.00 0.00 40.12 6.13
4819 5067 2.289320 CCGGAGAATAGGCTGATGGAAG 60.289 54.545 0.00 0.00 0.00 3.46
4834 5082 1.101635 CGGTCAGTCATAGCCGGAGA 61.102 60.000 5.05 0.00 40.45 3.71
5228 5476 4.569761 TGAGACGGAGCTGACATATAAC 57.430 45.455 0.00 0.00 0.00 1.89
5229 5477 6.490381 ACTTATGAGACGGAGCTGACATATAA 59.510 38.462 0.00 0.00 0.00 0.98
5230 5478 6.004574 ACTTATGAGACGGAGCTGACATATA 58.995 40.000 0.00 0.00 0.00 0.86
5231 5479 4.830046 ACTTATGAGACGGAGCTGACATAT 59.170 41.667 0.00 0.00 0.00 1.78
5232 5480 4.207955 ACTTATGAGACGGAGCTGACATA 58.792 43.478 0.00 0.00 0.00 2.29
5233 5481 3.027412 ACTTATGAGACGGAGCTGACAT 58.973 45.455 0.00 0.00 0.00 3.06
5234 5482 2.447443 ACTTATGAGACGGAGCTGACA 58.553 47.619 0.00 0.00 0.00 3.58
5260 5508 2.655090 TCCATGAACAGCTGAACCAA 57.345 45.000 23.35 1.00 0.00 3.67
5366 5620 9.567776 TTTAAGTTCAACTGACTCATATTTCCA 57.432 29.630 0.00 0.00 0.00 3.53
5393 5647 8.939929 CAATAAACTAGAGAACACACACATCAT 58.060 33.333 0.00 0.00 0.00 2.45
5397 5651 6.288294 AGCAATAAACTAGAGAACACACACA 58.712 36.000 0.00 0.00 0.00 3.72
5398 5652 6.787085 AGCAATAAACTAGAGAACACACAC 57.213 37.500 0.00 0.00 0.00 3.82
5457 5713 1.262417 TCTCGCCCAAAAATTTCCCC 58.738 50.000 0.00 0.00 0.00 4.81
5574 5830 4.404654 GGCCAGGCAAAACGCGAG 62.405 66.667 15.93 0.00 43.84 5.03
5607 5887 3.391296 GGGGAGTTATGTAGCCTTCATCA 59.609 47.826 0.00 0.00 0.00 3.07
5624 5904 0.257616 AGAAGAGAGACGGAGGGGAG 59.742 60.000 0.00 0.00 0.00 4.30
5625 5905 0.705253 AAGAAGAGAGACGGAGGGGA 59.295 55.000 0.00 0.00 0.00 4.81
5626 5906 0.820871 CAAGAAGAGAGACGGAGGGG 59.179 60.000 0.00 0.00 0.00 4.79
5627 5907 0.174617 GCAAGAAGAGAGACGGAGGG 59.825 60.000 0.00 0.00 0.00 4.30
5629 5909 0.523966 ACGCAAGAAGAGAGACGGAG 59.476 55.000 0.00 0.00 43.62 4.63
5630 5910 0.522180 GACGCAAGAAGAGAGACGGA 59.478 55.000 0.00 0.00 43.62 4.69
5631 5911 0.456995 GGACGCAAGAAGAGAGACGG 60.457 60.000 0.00 0.00 43.62 4.79
5632 5912 0.241213 TGGACGCAAGAAGAGAGACG 59.759 55.000 0.00 0.00 43.62 4.18
5633 5913 1.271102 AGTGGACGCAAGAAGAGAGAC 59.729 52.381 0.00 0.00 43.62 3.36
5634 5914 1.270826 CAGTGGACGCAAGAAGAGAGA 59.729 52.381 0.00 0.00 43.62 3.10
5635 5915 1.671261 CCAGTGGACGCAAGAAGAGAG 60.671 57.143 1.68 0.00 43.62 3.20
5636 5916 0.318441 CCAGTGGACGCAAGAAGAGA 59.682 55.000 1.68 0.00 43.62 3.10
5637 5917 0.671781 CCCAGTGGACGCAAGAAGAG 60.672 60.000 11.95 0.00 43.62 2.85
5638 5918 1.371183 CCCAGTGGACGCAAGAAGA 59.629 57.895 11.95 0.00 43.62 2.87
5639 5919 1.672356 CCCCAGTGGACGCAAGAAG 60.672 63.158 11.95 0.00 43.62 2.85
5641 5921 1.701031 TTTCCCCAGTGGACGCAAGA 61.701 55.000 11.95 0.00 45.11 3.02
5642 5922 1.228124 TTTCCCCAGTGGACGCAAG 60.228 57.895 11.95 0.00 45.11 4.01
5643 5923 1.527380 GTTTCCCCAGTGGACGCAA 60.527 57.895 11.95 0.00 45.11 4.85
5644 5924 2.112297 GTTTCCCCAGTGGACGCA 59.888 61.111 11.95 0.00 45.11 5.24
5645 5925 3.047877 CGTTTCCCCAGTGGACGC 61.048 66.667 11.95 0.00 45.11 5.19
5646 5926 2.358247 CCGTTTCCCCAGTGGACG 60.358 66.667 11.95 12.51 45.11 4.79
5648 5928 4.323477 CGCCGTTTCCCCAGTGGA 62.323 66.667 11.95 0.00 43.18 4.02
5650 5930 4.636435 ACCGCCGTTTCCCCAGTG 62.636 66.667 0.00 0.00 0.00 3.66
5651 5931 4.636435 CACCGCCGTTTCCCCAGT 62.636 66.667 0.00 0.00 0.00 4.00
5678 7752 3.112709 GAGGTGAACCGCTCGCAC 61.113 66.667 0.00 0.00 42.08 5.34
5679 7753 4.373116 GGAGGTGAACCGCTCGCA 62.373 66.667 3.16 0.00 42.08 5.10
5680 7754 4.373116 TGGAGGTGAACCGCTCGC 62.373 66.667 3.16 0.00 42.08 5.03
5682 7756 2.047179 GGTGGAGGTGAACCGCTC 60.047 66.667 3.16 0.00 42.08 5.03
5683 7757 2.113243 GAAGGTGGAGGTGAACCGCT 62.113 60.000 3.16 0.00 41.61 5.52
5691 7817 0.471211 TCCAAGACGAAGGTGGAGGT 60.471 55.000 0.00 0.00 36.51 3.85
5696 7822 0.679505 TCCAGTCCAAGACGAAGGTG 59.320 55.000 0.00 0.00 37.67 4.00
5722 7848 0.255890 GGAACAGCAGGCCATCCTAA 59.744 55.000 5.01 0.00 41.93 2.69
5723 7849 1.915228 GGAACAGCAGGCCATCCTA 59.085 57.895 5.01 0.00 41.93 2.94
5744 7870 2.347490 GTCCAAGCGAAGGAGGCA 59.653 61.111 0.00 0.00 35.42 4.75
5760 7886 3.947834 CCAAATTTAGGATTCAGGCTCGT 59.052 43.478 0.00 0.00 0.00 4.18
5768 7914 3.068732 GGAGCAGGCCAAATTTAGGATTC 59.931 47.826 5.01 1.22 0.00 2.52
5769 7915 3.033909 GGAGCAGGCCAAATTTAGGATT 58.966 45.455 5.01 0.00 0.00 3.01
5774 7920 0.039035 ACCGGAGCAGGCCAAATTTA 59.961 50.000 9.46 0.00 33.69 1.40
5775 7921 1.228862 ACCGGAGCAGGCCAAATTT 60.229 52.632 9.46 0.00 33.69 1.82
5786 7932 2.512515 GGCATCTGACACCGGAGC 60.513 66.667 9.46 0.00 0.00 4.70
5793 7939 1.323271 GGAGGACGAGGCATCTGACA 61.323 60.000 0.00 0.00 0.00 3.58
5797 7943 1.456705 GGAGGAGGACGAGGCATCT 60.457 63.158 0.00 0.00 0.00 2.90
5806 7952 1.743321 CGCCATCAGAGGAGGAGGAC 61.743 65.000 0.00 0.00 0.00 3.85
5818 7964 2.134287 GGAGTAGGAGCCGCCATCA 61.134 63.158 0.00 0.00 40.02 3.07
5832 7978 3.630013 TGGCGCTGAAGCAGGAGT 61.630 61.111 7.64 0.00 42.21 3.85
5838 7984 3.909086 AAGGAGGTGGCGCTGAAGC 62.909 63.158 7.64 3.13 37.78 3.86
5839 7985 1.743252 GAAGGAGGTGGCGCTGAAG 60.743 63.158 7.64 0.00 0.00 3.02
5841 7987 2.604686 AGAAGGAGGTGGCGCTGA 60.605 61.111 7.64 0.00 0.00 4.26
5843 7989 4.400961 GCAGAAGGAGGTGGCGCT 62.401 66.667 7.64 0.00 0.00 5.92
5846 8009 1.078567 CTGAGCAGAAGGAGGTGGC 60.079 63.158 0.00 0.00 0.00 5.01
5958 8145 1.134491 CAGAGATGCATGCCACAGAGA 60.134 52.381 16.68 0.00 0.00 3.10
5962 8149 0.616891 AGTCAGAGATGCATGCCACA 59.383 50.000 16.68 0.00 0.00 4.17
5968 8155 4.798924 GCGGAAATCTAGTCAGAGATGCAT 60.799 45.833 0.00 0.00 36.28 3.96
5977 8164 0.744874 CTCGGGCGGAAATCTAGTCA 59.255 55.000 0.00 0.00 0.00 3.41
5979 8166 1.614413 GATCTCGGGCGGAAATCTAGT 59.386 52.381 1.47 0.00 0.00 2.57
5982 8169 1.749033 GGATCTCGGGCGGAAATCT 59.251 57.895 8.09 0.00 0.00 2.40
6004 8192 1.556911 CACCTACCACAAGCTCCTGAT 59.443 52.381 0.00 0.00 0.00 2.90
6032 8220 3.303791 CGCCAACATCATCATGATCTGTG 60.304 47.826 17.13 13.06 34.28 3.66
6033 8221 2.876550 CGCCAACATCATCATGATCTGT 59.123 45.455 4.86 9.72 34.28 3.41
6035 8223 3.136763 GACGCCAACATCATCATGATCT 58.863 45.455 4.86 0.00 34.28 2.75
6038 8226 1.289276 CGACGCCAACATCATCATGA 58.711 50.000 0.00 0.00 33.72 3.07
6056 8244 1.933853 CTTTGAATCTAAGGTCCGCCG 59.066 52.381 0.00 0.00 40.50 6.46
6115 8305 0.603569 CGTCCCATCCTTATCCCTCG 59.396 60.000 0.00 0.00 0.00 4.63
6123 8313 1.766461 CTAGCCCCGTCCCATCCTT 60.766 63.158 0.00 0.00 0.00 3.36
6126 8316 3.242291 CCCTAGCCCCGTCCCATC 61.242 72.222 0.00 0.00 0.00 3.51
6150 8340 3.521560 CAGCTATTTAAGTCAGACGGCA 58.478 45.455 0.00 0.00 0.00 5.69
6194 8384 0.388520 CATTCATATCGCCGCTCCGA 60.389 55.000 0.00 0.00 41.98 4.55
6206 8396 5.289595 CAGCTAGTTAAGGACGCATTCATA 58.710 41.667 0.00 0.00 0.00 2.15
6220 8410 1.486211 GCACCTCCTCCAGCTAGTTA 58.514 55.000 0.00 0.00 0.00 2.24
6237 8427 0.830444 ACCCGTTAGTCTGACAGGCA 60.830 55.000 10.23 0.00 0.00 4.75
6241 8431 2.547218 GCTGAAACCCGTTAGTCTGACA 60.547 50.000 10.88 0.00 0.00 3.58
6249 8439 0.885196 GCCAATGCTGAAACCCGTTA 59.115 50.000 0.00 0.00 33.53 3.18
6250 8440 1.665442 GCCAATGCTGAAACCCGTT 59.335 52.632 0.00 0.00 33.53 4.44
6294 8484 1.291877 ACTGAAACTCATGGACGCGC 61.292 55.000 5.73 0.00 0.00 6.86
6303 8493 8.783660 ATGTAGGGAGAATATACTGAAACTCA 57.216 34.615 0.00 0.00 0.00 3.41
6335 8525 3.323774 AACAGGTATCTCCCATACCGA 57.676 47.619 5.35 0.00 46.52 4.69


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

AutoCloner maintained by Alex Coulton.