Multiple sequence alignment - TraesCS3B01G179300

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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 TraesCS3B01G179300 chr3B 100.000 6845 0 0 1 6845 187345078 187351922 0.000000e+00 12641.0
1 TraesCS3B01G179300 chr3B 87.774 319 23 9 2095 2400 187346857 187347172 6.530000e-95 359.0
2 TraesCS3B01G179300 chr3B 87.774 319 23 9 1780 2095 187347172 187347477 6.530000e-95 359.0
3 TraesCS3B01G179300 chr3B 100.000 32 0 0 2397 2428 187347274 187347305 7.410000e-05 60.2
4 TraesCS3B01G179300 chr3B 100.000 32 0 0 2197 2228 187347474 187347505 7.410000e-05 60.2
5 TraesCS3B01G179300 chr3D 93.854 2701 127 19 2221 4894 130928113 130930801 0.000000e+00 4032.0
6 TraesCS3B01G179300 chr3D 90.246 1179 51 31 659 1776 130926912 130928087 0.000000e+00 1482.0
7 TraesCS3B01G179300 chr3D 91.501 1059 59 15 4941 5993 130930798 130931831 0.000000e+00 1428.0
8 TraesCS3B01G179300 chr3D 81.235 405 35 16 6029 6431 130931903 130932268 8.690000e-74 289.0
9 TraesCS3B01G179300 chr3D 87.000 200 7 8 6591 6790 130932401 130932581 2.500000e-49 207.0
10 TraesCS3B01G179300 chr3D 82.439 205 22 8 1897 2095 130928092 130928288 4.250000e-37 167.0
11 TraesCS3B01G179300 chr3A 92.408 1989 135 13 2221 4201 142891378 142893358 0.000000e+00 2822.0
12 TraesCS3B01G179300 chr3A 89.910 1229 63 27 5191 6366 142894201 142895421 0.000000e+00 1526.0
13 TraesCS3B01G179300 chr3A 87.649 1174 56 38 675 1776 142890196 142891352 0.000000e+00 1282.0
14 TraesCS3B01G179300 chr3A 97.420 659 17 0 1 659 237050646 237049988 0.000000e+00 1123.0
15 TraesCS3B01G179300 chr3A 89.320 618 42 18 4213 4814 142893344 142893953 0.000000e+00 754.0
16 TraesCS3B01G179300 chr3A 86.434 258 18 11 6591 6845 142896187 142896430 4.070000e-67 267.0
17 TraesCS3B01G179300 chr3A 81.159 207 26 11 1897 2095 142891357 142891558 3.310000e-33 154.0
18 TraesCS3B01G179300 chr3A 100.000 30 0 0 2198 2227 142891556 142891585 1.000000e-03 56.5
19 TraesCS3B01G179300 chr7B 97.428 661 15 2 1 660 212067243 212066584 0.000000e+00 1125.0
20 TraesCS3B01G179300 chr7B 97.420 659 15 2 1 658 102650245 102649588 0.000000e+00 1122.0
21 TraesCS3B01G179300 chr7B 97.006 668 17 3 1 666 618537337 618538003 0.000000e+00 1120.0
22 TraesCS3B01G179300 chr7B 91.935 124 9 1 1774 1896 115517982 115517859 9.130000e-39 172.0
23 TraesCS3B01G179300 chr5B 97.281 662 18 0 1 662 351471982 351472643 0.000000e+00 1123.0
24 TraesCS3B01G179300 chr5B 97.134 663 15 4 1 661 471297357 471298017 0.000000e+00 1116.0
25 TraesCS3B01G179300 chr5B 94.783 115 5 1 1780 1894 73989869 73989982 1.960000e-40 178.0
26 TraesCS3B01G179300 chr4B 97.281 662 16 2 1 661 655788610 655787950 0.000000e+00 1122.0
27 TraesCS3B01G179300 chr4B 92.500 120 9 0 1775 1894 143310084 143309965 9.130000e-39 172.0
28 TraesCS3B01G179300 chr7A 97.277 661 16 2 1 660 497721897 497722556 0.000000e+00 1120.0
29 TraesCS3B01G179300 chr5A 97.273 660 18 0 1 660 591471416 591470757 0.000000e+00 1120.0
30 TraesCS3B01G179300 chr1A 87.975 158 19 0 4546 4703 155695569 155695726 3.260000e-43 187.0
31 TraesCS3B01G179300 chr2A 96.429 112 4 0 2092 2203 758757138 758757249 1.170000e-42 185.0
32 TraesCS3B01G179300 chr6D 94.872 117 6 0 2086 2202 308219404 308219520 4.220000e-42 183.0
33 TraesCS3B01G179300 chr6D 96.330 109 4 0 2092 2200 128989374 128989266 5.450000e-41 180.0
34 TraesCS3B01G179300 chr6D 92.437 119 9 0 1777 1895 329858593 329858711 3.280000e-38 171.0
35 TraesCS3B01G179300 chr6B 94.118 119 7 0 2090 2208 460495299 460495417 1.520000e-41 182.0
36 TraesCS3B01G179300 chr5D 95.575 113 5 0 2090 2202 94343226 94343114 1.520000e-41 182.0
37 TraesCS3B01G179300 chr5D 96.330 109 4 0 2092 2200 399581790 399581682 5.450000e-41 180.0
38 TraesCS3B01G179300 chr1D 87.342 158 20 0 4546 4703 137438765 137438608 1.520000e-41 182.0
39 TraesCS3B01G179300 chr4D 96.330 109 4 0 2092 2200 29093476 29093368 5.450000e-41 180.0
40 TraesCS3B01G179300 chr4D 94.783 115 6 0 2086 2200 333227484 333227598 5.450000e-41 180.0
41 TraesCS3B01G179300 chr4A 94.783 115 6 0 2086 2200 44009065 44009179 5.450000e-41 180.0
42 TraesCS3B01G179300 chr1B 92.562 121 8 1 1780 1899 156585484 156585604 9.130000e-39 172.0
43 TraesCS3B01G179300 chr1B 86.076 158 22 0 4546 4703 209131386 209131229 3.280000e-38 171.0
44 TraesCS3B01G179300 chr1B 90.076 131 12 1 1771 1900 413494712 413494582 1.180000e-37 169.0
45 TraesCS3B01G179300 chr1B 89.147 129 13 1 1770 1897 522116617 522116489 7.110000e-35 159.0
46 TraesCS3B01G179300 chr2D 92.437 119 9 0 1777 1895 305940138 305940256 3.280000e-38 171.0
47 TraesCS3B01G179300 chr2D 86.713 143 18 1 1764 1906 630017937 630017796 2.560000e-34 158.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G179300 chr3B 187345078 187351922 6844 False 12641.000000 12641 100.000000 1 6845 1 chr3B.!!$F1 6844
1 TraesCS3B01G179300 chr3B 187346857 187347505 648 False 209.600000 359 93.887000 1780 2428 4 chr3B.!!$F2 648
2 TraesCS3B01G179300 chr3D 130926912 130932581 5669 False 1267.500000 4032 87.712500 659 6790 6 chr3D.!!$F1 6131
3 TraesCS3B01G179300 chr3A 237049988 237050646 658 True 1123.000000 1123 97.420000 1 659 1 chr3A.!!$R1 658
4 TraesCS3B01G179300 chr3A 142890196 142896430 6234 False 980.214286 2822 89.554286 675 6845 7 chr3A.!!$F1 6170
5 TraesCS3B01G179300 chr7B 212066584 212067243 659 True 1125.000000 1125 97.428000 1 660 1 chr7B.!!$R3 659
6 TraesCS3B01G179300 chr7B 102649588 102650245 657 True 1122.000000 1122 97.420000 1 658 1 chr7B.!!$R1 657
7 TraesCS3B01G179300 chr7B 618537337 618538003 666 False 1120.000000 1120 97.006000 1 666 1 chr7B.!!$F1 665
8 TraesCS3B01G179300 chr5B 351471982 351472643 661 False 1123.000000 1123 97.281000 1 662 1 chr5B.!!$F2 661
9 TraesCS3B01G179300 chr5B 471297357 471298017 660 False 1116.000000 1116 97.134000 1 661 1 chr5B.!!$F3 660
10 TraesCS3B01G179300 chr4B 655787950 655788610 660 True 1122.000000 1122 97.281000 1 661 1 chr4B.!!$R2 660
11 TraesCS3B01G179300 chr7A 497721897 497722556 659 False 1120.000000 1120 97.277000 1 660 1 chr7A.!!$F1 659
12 TraesCS3B01G179300 chr5A 591470757 591471416 659 True 1120.000000 1120 97.273000 1 660 1 chr5A.!!$R1 659

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
433 434 0.400815 TATCCACTTACCGGGGCCAT 60.401 55.0 6.32 0.00 0.00 4.40 F
981 1029 0.603569 AGCAGCAGTACGTAGCAAGT 59.396 50.0 9.22 0.00 0.00 3.16 F
2659 2766 0.107017 CACCACCCCCTGATCATGTC 60.107 60.0 0.00 0.00 0.00 3.06 F
2759 2866 0.758734 CTCAGGTGGTGGTGAGAACA 59.241 55.0 0.00 0.00 42.49 3.18 F
2878 2985 1.201429 ATCTTCTCGGGCAAGGTGGT 61.201 55.0 0.00 0.00 0.00 4.16 F
4420 4551 0.250295 TGCTTTCCGGGACAGTGAAG 60.250 55.0 11.62 6.56 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1806 0.038744 ACCCATCTTGAAGGCACCAG 59.961 55.000 0.00 0.0 0.00 4.00 R
2830 2937 1.062587 GAGAATTCATTGGTCGCCACG 59.937 52.381 8.44 0.0 30.78 4.94 R
3483 3612 1.331756 GGTGGCGATAAAGCTGACATG 59.668 52.381 0.00 0.0 37.29 3.21 R
4397 4528 1.407258 CACTGTCCCGGAAAGCAAAAA 59.593 47.619 0.73 0.0 0.00 1.94 R
4860 5009 1.708551 CCTTAGGGGGTGTTTGGAAGA 59.291 52.381 0.00 0.0 0.00 2.87 R
5997 6176 0.103390 TTGCGTCGAGTTGGTCAAGA 59.897 50.000 0.00 0.0 0.00 3.02 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
340 341 0.616111 GAGAGAGAGTGGGGAGGCAA 60.616 60.000 0.00 0.00 0.00 4.52
433 434 0.400815 TATCCACTTACCGGGGCCAT 60.401 55.000 6.32 0.00 0.00 4.40
490 491 4.643387 GCAGGTCAACGGGCAGGT 62.643 66.667 0.00 0.00 0.00 4.00
588 589 3.375922 GTCACCGAAAAAGGTCAGAAACA 59.624 43.478 0.00 0.00 43.89 2.83
629 630 4.705023 AGGTCAAATCGGGATTTACTTTGG 59.295 41.667 6.34 0.00 38.84 3.28
700 702 1.003851 TTCCTCGCGCTTTTATTCCG 58.996 50.000 5.56 0.00 0.00 4.30
706 708 1.993369 GCGCTTTTATTCCGCAGCCT 61.993 55.000 0.00 0.00 46.32 4.58
711 714 3.750373 TTATTCCGCAGCCTCCCGC 62.750 63.158 0.00 0.00 37.98 6.13
778 792 0.991920 ACCCACCACACCATTAGAGG 59.008 55.000 0.00 0.00 0.00 3.69
882 924 3.125573 GCGGAAAGCGGGACCTTC 61.126 66.667 0.00 0.00 35.41 3.46
883 925 2.663196 CGGAAAGCGGGACCTTCT 59.337 61.111 0.00 0.00 0.00 2.85
906 949 2.678336 CCCTTTTCGCTTATCTTTCGCT 59.322 45.455 0.00 0.00 0.00 4.93
981 1029 0.603569 AGCAGCAGTACGTAGCAAGT 59.396 50.000 9.22 0.00 0.00 3.16
989 1037 4.665897 GCAGTACGTAGCAAGTAAGCAAAC 60.666 45.833 0.00 0.00 36.85 2.93
990 1038 4.684703 CAGTACGTAGCAAGTAAGCAAACT 59.315 41.667 0.00 0.00 36.85 2.66
1594 1687 6.039941 GGAGCAGATACAGTACAGTACAGATT 59.960 42.308 13.37 0.00 0.00 2.40
1680 1773 3.488048 GCAAATGTGCGTTGGCTTA 57.512 47.368 0.00 0.00 41.93 3.09
1713 1806 7.042254 ACAAGTATGACTTACGTTCCAGTTTTC 60.042 37.037 0.00 0.00 36.03 2.29
1769 1862 3.372206 GCTATTATGGCGTCATGGACATC 59.628 47.826 13.98 0.00 36.85 3.06
1776 1869 3.376859 TGGCGTCATGGACATCAAAATAC 59.623 43.478 0.00 0.00 32.09 1.89
1777 1870 3.627577 GGCGTCATGGACATCAAAATACT 59.372 43.478 0.00 0.00 32.09 2.12
1778 1871 4.496341 GGCGTCATGGACATCAAAATACTG 60.496 45.833 0.00 0.00 32.09 2.74
2449 2555 3.680458 CCTCCTTTTCGAAGTGAGTTAGC 59.320 47.826 15.23 0.00 0.00 3.09
2465 2571 6.758886 GTGAGTTAGCAACTTAGTATCAGCAT 59.241 38.462 3.56 0.00 43.03 3.79
2540 2647 2.493278 AGATTTTGCAACAGGGAATCCG 59.507 45.455 14.34 0.00 38.33 4.18
2567 2674 9.569167 TTTGTAATTGTTATTGTTCAACACGAA 57.431 25.926 0.00 0.00 35.70 3.85
2659 2766 0.107017 CACCACCCCCTGATCATGTC 60.107 60.000 0.00 0.00 0.00 3.06
2684 2791 6.070951 TGAAGATGAATTCACATCCTTCCT 57.929 37.500 23.87 7.08 45.20 3.36
2691 2798 6.180472 TGAATTCACATCCTTCCTCTAAACC 58.820 40.000 3.38 0.00 0.00 3.27
2695 2802 1.209504 CATCCTTCCTCTAAACCGCCA 59.790 52.381 0.00 0.00 0.00 5.69
2746 2853 1.697432 TCGGGTTCACATTTCTCAGGT 59.303 47.619 0.00 0.00 0.00 4.00
2749 2856 2.489073 GGGTTCACATTTCTCAGGTGGT 60.489 50.000 0.00 0.00 33.45 4.16
2759 2866 0.758734 CTCAGGTGGTGGTGAGAACA 59.241 55.000 0.00 0.00 42.49 3.18
2830 2937 6.612306 CACTTTTACTTATGAAGAGTTGGCC 58.388 40.000 0.00 0.00 0.00 5.36
2878 2985 1.201429 ATCTTCTCGGGCAAGGTGGT 61.201 55.000 0.00 0.00 0.00 4.16
2884 2991 2.866726 CGGGCAAGGTGGTTTTGGG 61.867 63.158 0.00 0.00 0.00 4.12
2899 3006 3.618690 TTTGGGTTTGTTCACAAAGGG 57.381 42.857 5.33 0.00 45.36 3.95
3025 3132 6.327154 ACATCATAAACATCTCGTGACGTTA 58.673 36.000 4.40 0.00 27.83 3.18
3126 3233 5.684704 ACATGGTATGGTTTCTCACTATGG 58.315 41.667 0.00 0.00 35.05 2.74
3157 3264 8.092521 TCATGATTGTTTCTTCTCTTTCAGAC 57.907 34.615 0.00 0.00 0.00 3.51
3192 3299 4.866508 TGTCCGAGAAAGTGAACTATGT 57.133 40.909 0.00 0.00 0.00 2.29
3257 3365 5.887214 TCCTAGCTATTGCCAGTTTATCA 57.113 39.130 0.00 0.00 40.80 2.15
3261 3369 7.878127 TCCTAGCTATTGCCAGTTTATCATTAC 59.122 37.037 0.00 0.00 40.80 1.89
3269 3395 4.399303 GCCAGTTTATCATTACCAGTTGCT 59.601 41.667 0.00 0.00 0.00 3.91
3281 3407 3.820557 ACCAGTTGCTGTATGAGTTGTT 58.179 40.909 0.00 0.00 0.00 2.83
3390 3519 4.553429 CCTTGTTCGCGTAAATTGACAATC 59.447 41.667 5.77 0.00 0.00 2.67
3392 3521 6.401688 CCTTGTTCGCGTAAATTGACAATCTA 60.402 38.462 5.77 0.00 0.00 1.98
3394 3523 6.301108 TGTTCGCGTAAATTGACAATCTAAC 58.699 36.000 5.77 0.00 0.00 2.34
3400 3529 7.412129 CGCGTAAATTGACAATCTAACCAGTTA 60.412 37.037 0.05 0.00 0.00 2.24
3443 3572 3.672808 CCATGACTGCAAGAGAGTTTCT 58.327 45.455 0.00 0.00 37.43 2.52
3445 3574 4.153835 CCATGACTGCAAGAGAGTTTCTTC 59.846 45.833 0.00 0.00 44.34 2.87
3476 3605 4.535526 AATAAGCACAACCAAACCCATC 57.464 40.909 0.00 0.00 0.00 3.51
3477 3606 2.086610 AAGCACAACCAAACCCATCT 57.913 45.000 0.00 0.00 0.00 2.90
3483 3612 3.004734 CACAACCAAACCCATCTCAGAAC 59.995 47.826 0.00 0.00 0.00 3.01
3486 3615 3.424703 ACCAAACCCATCTCAGAACATG 58.575 45.455 0.00 0.00 0.00 3.21
3511 3640 3.440522 AGCTTTATCGCCACCTTTTCTTC 59.559 43.478 0.00 0.00 0.00 2.87
3529 3658 9.813080 CTTTTCTTCAGTCTTTAATAACTTCCG 57.187 33.333 0.00 0.00 0.00 4.30
3656 3785 4.492955 GCTCTGAAGCTCCTGTCG 57.507 61.111 0.00 0.00 45.55 4.35
3725 3854 9.423061 GCATTTGTTAATGTCTTCAGGTTATTT 57.577 29.630 0.00 0.00 42.56 1.40
3854 3984 3.193691 AGCTCACACACACATACCTACTC 59.806 47.826 0.00 0.00 0.00 2.59
4014 4144 6.584184 CAGATGTGAAGCTAAGGTATGATACG 59.416 42.308 0.00 0.00 0.00 3.06
4118 4249 8.324163 AGTGTAGTGTAAAATCTTGAATGTCC 57.676 34.615 0.00 0.00 0.00 4.02
4204 4335 9.643693 ACCAATCATCATGAAACATAGTTTTTC 57.356 29.630 0.00 0.00 34.16 2.29
4420 4551 0.250295 TGCTTTCCGGGACAGTGAAG 60.250 55.000 11.62 6.56 0.00 3.02
4544 4680 3.267031 CCCTGATAGTCTTGGTTTTCCCT 59.733 47.826 0.00 0.00 39.73 4.20
4722 4858 5.585820 AGTTAAATTTGTTGTCCACCGTT 57.414 34.783 0.00 0.00 0.00 4.44
4734 4870 2.230750 GTCCACCGTTCTGTAACTAGCT 59.769 50.000 0.00 0.00 33.15 3.32
4811 4960 8.410912 GGAGTATTTCTTGGTAAAGTTTTGTGT 58.589 33.333 0.00 0.00 34.78 3.72
4821 4970 9.760077 TTGGTAAAGTTTTGTGTTTACTTCAAA 57.240 25.926 0.00 0.00 38.60 2.69
4849 4998 7.731054 TGACTTAAATGCCAAAACTTTACCAT 58.269 30.769 0.00 0.00 0.00 3.55
4854 5003 9.566432 TTAAATGCCAAAACTTTACCATGAAAT 57.434 25.926 0.00 0.00 0.00 2.17
4860 5009 7.606073 GCCAAAACTTTACCATGAAATACCATT 59.394 33.333 0.00 0.00 0.00 3.16
4949 5098 7.951347 ATTCCAATTATATCATTGAGGGCTC 57.049 36.000 10.59 0.00 36.39 4.70
4965 5114 3.770388 AGGGCTCTCTTGGACTACTTAAC 59.230 47.826 0.00 0.00 0.00 2.01
4976 5125 7.876068 TCTTGGACTACTTAACTAACAACCATG 59.124 37.037 0.00 0.00 0.00 3.66
5018 5167 6.403878 AGTTACTTGCTATTCCTCGCTAAAA 58.596 36.000 0.00 0.00 0.00 1.52
5041 5190 5.914898 TGGACTCGATTTTCTCTGTATGA 57.085 39.130 0.00 0.00 0.00 2.15
5070 5219 4.888326 TGGCCTTTGCACTTCATATTTT 57.112 36.364 3.32 0.00 40.13 1.82
5119 5269 7.093509 ACAGTGTTTACCATCTTCCAACTTTTT 60.094 33.333 0.00 0.00 0.00 1.94
5125 5275 4.248058 CCATCTTCCAACTTTTTGATGCC 58.752 43.478 0.00 0.00 34.24 4.40
5174 5324 4.073293 TCTGTCTGTCCCTTTCTTTGTC 57.927 45.455 0.00 0.00 0.00 3.18
5178 5328 4.580167 TGTCTGTCCCTTTCTTTGTCAATG 59.420 41.667 0.00 0.00 0.00 2.82
5181 5331 5.299279 TCTGTCCCTTTCTTTGTCAATGTTC 59.701 40.000 0.00 0.00 0.00 3.18
5182 5332 4.952957 TGTCCCTTTCTTTGTCAATGTTCA 59.047 37.500 0.00 0.00 0.00 3.18
5184 5334 5.748630 GTCCCTTTCTTTGTCAATGTTCAAC 59.251 40.000 0.00 0.00 0.00 3.18
5185 5335 5.049828 CCCTTTCTTTGTCAATGTTCAACC 58.950 41.667 0.00 0.00 0.00 3.77
5200 5350 7.781324 ATGTTCAACCCATCTATTTGAGTTT 57.219 32.000 0.00 0.00 31.11 2.66
5205 5355 7.174413 TCAACCCATCTATTTGAGTTTGATCA 58.826 34.615 0.00 0.00 0.00 2.92
5219 5373 5.504853 AGTTTGATCATCTTCCTTTCTCCC 58.495 41.667 0.00 0.00 0.00 4.30
5299 5453 2.037381 GGATCCCCACTTAGGAATCGAC 59.963 54.545 0.00 0.00 41.22 4.20
5304 5458 3.430929 CCCCACTTAGGAATCGACTTCAG 60.431 52.174 0.00 0.00 41.22 3.02
5398 5552 4.392940 GCATGAGCCAGGTACATTTCTAT 58.607 43.478 0.00 0.00 33.58 1.98
5402 5556 4.038763 TGAGCCAGGTACATTTCTATACCG 59.961 45.833 0.00 0.00 44.80 4.02
5405 5559 4.281688 GCCAGGTACATTTCTATACCGGTA 59.718 45.833 18.46 18.46 44.80 4.02
5452 5606 2.734606 TCGTCGACACAAATTCATCACC 59.265 45.455 17.16 0.00 0.00 4.02
5487 5641 5.416326 ACCTCATCGCTATTGTATCCTAGAC 59.584 44.000 0.00 0.00 0.00 2.59
5492 5646 4.456222 TCGCTATTGTATCCTAGACAGAGC 59.544 45.833 0.00 0.68 35.68 4.09
5504 5658 4.647399 CCTAGACAGAGCTAAGCTAACCTT 59.353 45.833 0.00 0.00 39.88 3.50
5763 5923 4.057428 GTCCAGAGCAGCGACGGT 62.057 66.667 0.00 0.00 0.00 4.83
5768 5928 2.951745 GAGCAGCGACGGTCATCG 60.952 66.667 9.10 0.00 45.09 3.84
5798 5958 0.903236 GAGGTGGAGTTGGGGACTAC 59.097 60.000 0.00 0.00 39.19 2.73
5799 5959 0.546988 AGGTGGAGTTGGGGACTACC 60.547 60.000 0.00 0.00 38.56 3.18
5830 5993 3.800863 GCGACGTCGAGAGCCAGA 61.801 66.667 39.74 0.00 43.02 3.86
5845 6008 3.047115 AGCCAGACTTCCATGAGATGAT 58.953 45.455 0.00 0.00 0.00 2.45
5846 6009 3.139850 GCCAGACTTCCATGAGATGATG 58.860 50.000 0.00 0.00 0.00 3.07
5847 6010 3.181457 GCCAGACTTCCATGAGATGATGA 60.181 47.826 0.00 0.00 0.00 2.92
5848 6011 4.378774 CCAGACTTCCATGAGATGATGAC 58.621 47.826 0.00 0.00 0.00 3.06
5884 6047 3.591023 GTTGGAGAGAGTTAACCTCAGC 58.409 50.000 19.72 13.42 43.12 4.26
5889 6055 4.429108 GAGAGAGTTAACCTCAGCACATC 58.571 47.826 19.72 8.76 43.12 3.06
5890 6056 3.834813 AGAGAGTTAACCTCAGCACATCA 59.165 43.478 19.72 0.00 43.12 3.07
5891 6057 4.469227 AGAGAGTTAACCTCAGCACATCAT 59.531 41.667 19.72 1.21 43.12 2.45
5932 6098 3.067742 GCTGAATTCACATAAGCTGCCAT 59.932 43.478 3.38 0.00 0.00 4.40
5995 6174 8.458573 TGTTGAGACATATGGTAGTTTTGTTT 57.541 30.769 7.80 0.00 0.00 2.83
5997 6176 8.349983 GTTGAGACATATGGTAGTTTTGTTTGT 58.650 33.333 7.80 0.00 0.00 2.83
5999 6178 7.936847 TGAGACATATGGTAGTTTTGTTTGTCT 59.063 33.333 7.80 0.00 42.74 3.41
6000 6179 8.691661 AGACATATGGTAGTTTTGTTTGTCTT 57.308 30.769 7.80 0.00 38.41 3.01
6001 6180 8.567948 AGACATATGGTAGTTTTGTTTGTCTTG 58.432 33.333 7.80 0.00 38.41 3.02
6002 6181 8.458573 ACATATGGTAGTTTTGTTTGTCTTGA 57.541 30.769 7.80 0.00 0.00 3.02
6003 6182 8.349983 ACATATGGTAGTTTTGTTTGTCTTGAC 58.650 33.333 7.80 0.00 0.00 3.18
6004 6183 5.570234 TGGTAGTTTTGTTTGTCTTGACC 57.430 39.130 0.00 0.00 0.00 4.02
6006 6185 5.477291 TGGTAGTTTTGTTTGTCTTGACCAA 59.523 36.000 0.00 0.00 30.55 3.67
6007 6186 5.803461 GGTAGTTTTGTTTGTCTTGACCAAC 59.197 40.000 9.80 9.80 0.00 3.77
6009 6188 5.709966 AGTTTTGTTTGTCTTGACCAACTC 58.290 37.500 15.45 6.84 0.00 3.01
6010 6189 4.349663 TTTGTTTGTCTTGACCAACTCG 57.650 40.909 15.45 0.00 0.00 4.18
6011 6190 3.254470 TGTTTGTCTTGACCAACTCGA 57.746 42.857 15.45 0.00 0.00 4.04
6012 6191 2.933906 TGTTTGTCTTGACCAACTCGAC 59.066 45.455 15.45 0.00 0.00 4.20
6025 6227 3.181530 CCAACTCGACGCAATTCTACTTG 60.182 47.826 0.00 0.00 0.00 3.16
6037 6239 6.258230 CAATTCTACTTGCATTTCCAGTGA 57.742 37.500 0.00 0.00 0.00 3.41
6038 6240 6.320171 CAATTCTACTTGCATTTCCAGTGAG 58.680 40.000 0.00 0.00 0.00 3.51
6039 6241 4.890158 TCTACTTGCATTTCCAGTGAGA 57.110 40.909 0.00 0.00 0.00 3.27
6041 6243 5.181009 TCTACTTGCATTTCCAGTGAGATG 58.819 41.667 0.00 0.00 36.44 2.90
6043 6245 3.911989 GCATTTCCAGTGAGATGCG 57.088 52.632 8.77 0.00 45.59 4.73
6044 6246 1.089920 GCATTTCCAGTGAGATGCGT 58.910 50.000 8.77 0.00 45.59 5.24
6045 6247 1.202110 GCATTTCCAGTGAGATGCGTG 60.202 52.381 8.77 0.00 45.59 5.34
6046 6248 2.349590 CATTTCCAGTGAGATGCGTGA 58.650 47.619 0.00 0.00 0.00 4.35
6048 6250 2.299993 TTCCAGTGAGATGCGTGATC 57.700 50.000 0.00 0.00 0.00 2.92
6049 6251 1.185315 TCCAGTGAGATGCGTGATCA 58.815 50.000 0.00 0.00 32.86 2.92
6050 6252 1.758862 TCCAGTGAGATGCGTGATCAT 59.241 47.619 0.00 0.00 32.86 2.45
6063 6275 2.615447 CGTGATCATTACATTGGCTGCT 59.385 45.455 0.00 0.00 0.00 4.24
6077 6290 1.739562 CTGCTGGCCGTCTGAACTC 60.740 63.158 0.00 0.00 0.00 3.01
6124 6337 1.009829 GGCTAACGAGATGCTGTTGG 58.990 55.000 0.00 0.00 0.00 3.77
6125 6338 1.405526 GGCTAACGAGATGCTGTTGGA 60.406 52.381 0.00 0.00 0.00 3.53
6131 6344 2.234661 ACGAGATGCTGTTGGATTCAGA 59.765 45.455 0.00 0.00 35.20 3.27
6133 6346 2.613133 GAGATGCTGTTGGATTCAGAGC 59.387 50.000 0.93 0.93 35.20 4.09
6153 6366 2.114616 CAAGAGCCAGGGAGATACAGT 58.885 52.381 0.00 0.00 0.00 3.55
6325 6552 4.867047 AGTAGCATTCAGAATCTGTTGACG 59.133 41.667 10.36 0.00 32.61 4.35
6376 6603 2.302260 TGAGTTTCAACGGCATTTCCA 58.698 42.857 0.00 0.00 34.01 3.53
6378 6605 3.320541 TGAGTTTCAACGGCATTTCCATT 59.679 39.130 0.00 0.00 34.01 3.16
6379 6606 4.520874 TGAGTTTCAACGGCATTTCCATTA 59.479 37.500 0.00 0.00 34.01 1.90
6380 6607 5.059404 AGTTTCAACGGCATTTCCATTAG 57.941 39.130 0.00 0.00 34.01 1.73
6400 6629 8.077991 CCATTAGTACATGCCAATGTTCTTATG 58.922 37.037 13.19 13.19 44.94 1.90
6444 7268 2.569853 TCGATCTTAGCCCTCAAACCAA 59.430 45.455 0.00 0.00 0.00 3.67
6448 7272 0.955905 TTAGCCCTCAAACCAAACGC 59.044 50.000 0.00 0.00 0.00 4.84
6468 7292 1.397390 CCCCTGCCTGCATTCATTCC 61.397 60.000 0.00 0.00 0.00 3.01
6475 7299 2.626743 GCCTGCATTCATTCCAGCTTAT 59.373 45.455 0.00 0.00 0.00 1.73
6485 7309 4.572389 TCATTCCAGCTTATCTTTCTTCGC 59.428 41.667 0.00 0.00 0.00 4.70
6497 7321 8.547967 TTATCTTTCTTCGCAAAATCTGTAGT 57.452 30.769 0.00 0.00 0.00 2.73
6498 7322 9.647797 TTATCTTTCTTCGCAAAATCTGTAGTA 57.352 29.630 0.00 0.00 0.00 1.82
6500 7324 7.152645 TCTTTCTTCGCAAAATCTGTAGTAGT 58.847 34.615 0.00 0.00 0.00 2.73
6509 7333 6.631016 CAAAATCTGTAGTAGTAGGTGCAGA 58.369 40.000 0.00 3.58 37.38 4.26
6511 7335 5.838531 ATCTGTAGTAGTAGGTGCAGAAC 57.161 43.478 4.85 0.00 36.70 3.01
6520 7344 3.511934 AGTAGGTGCAGAACGAAAGAGAT 59.488 43.478 0.00 0.00 0.00 2.75
6521 7345 3.409026 AGGTGCAGAACGAAAGAGATT 57.591 42.857 0.00 0.00 0.00 2.40
6526 7350 4.923871 GTGCAGAACGAAAGAGATTACAGA 59.076 41.667 0.00 0.00 0.00 3.41
6529 7353 6.975197 TGCAGAACGAAAGAGATTACAGATAG 59.025 38.462 0.00 0.00 0.00 2.08
6537 7361 7.171167 CGAAAGAGATTACAGATAGTAGTCGGA 59.829 40.741 0.00 0.00 42.45 4.55
6538 7362 7.733402 AAGAGATTACAGATAGTAGTCGGAC 57.267 40.000 0.00 0.00 42.45 4.79
6539 7363 7.069877 AGAGATTACAGATAGTAGTCGGACT 57.930 40.000 15.95 15.95 42.45 3.85
6540 7364 7.156673 AGAGATTACAGATAGTAGTCGGACTC 58.843 42.308 15.05 6.70 42.45 3.36
6541 7365 5.927689 AGATTACAGATAGTAGTCGGACTCG 59.072 44.000 15.05 0.20 42.45 4.18
6542 7366 2.836262 ACAGATAGTAGTCGGACTCGG 58.164 52.381 15.05 3.55 36.95 4.63
6543 7367 2.144730 CAGATAGTAGTCGGACTCGGG 58.855 57.143 15.05 0.00 36.95 5.14
6553 7377 0.806102 CGGACTCGGGCAGTACATTG 60.806 60.000 0.00 0.00 35.26 2.82
6554 7378 1.090052 GGACTCGGGCAGTACATTGC 61.090 60.000 0.00 0.00 43.34 3.56
6558 7382 1.078497 CGGGCAGTACATTGCTCCA 60.078 57.895 7.01 0.00 41.62 3.86
6565 7389 4.640201 GGCAGTACATTGCTCCATTCTTTA 59.360 41.667 7.01 0.00 43.57 1.85
6566 7390 5.300286 GGCAGTACATTGCTCCATTCTTTAT 59.700 40.000 7.01 0.00 43.57 1.40
6568 7392 7.308229 GGCAGTACATTGCTCCATTCTTTATAG 60.308 40.741 7.01 0.00 43.57 1.31
6569 7393 7.442364 GCAGTACATTGCTCCATTCTTTATAGA 59.558 37.037 0.00 0.00 40.89 1.98
6570 7394 9.330063 CAGTACATTGCTCCATTCTTTATAGAA 57.670 33.333 0.00 0.00 44.16 2.10
6571 7395 9.905713 AGTACATTGCTCCATTCTTTATAGAAA 57.094 29.630 0.00 0.00 43.32 2.52
6697 7522 6.607600 TGATCAAGCTCATACTTGTAGGTAGT 59.392 38.462 0.00 0.00 45.86 2.73
6809 7640 0.387878 CTGTCTGTCTGTCTGTCGCC 60.388 60.000 0.00 0.00 0.00 5.54
6821 7653 3.994392 TGTCTGTCGCCACTCTAAAAATC 59.006 43.478 0.00 0.00 0.00 2.17
6828 7660 2.997986 GCCACTCTAAAAATCGACGGAA 59.002 45.455 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 8.757877 TGATAATATAGTGCTATGCATGGTGTA 58.242 33.333 10.16 0.10 41.91 2.90
457 458 2.281484 GCTGACGTGGCAAAGGGA 60.281 61.111 0.00 0.00 0.00 4.20
624 625 3.486383 TGTTCTGACCCTTAAGCCAAAG 58.514 45.455 0.00 0.00 0.00 2.77
629 630 6.819397 AAATTACTGTTCTGACCCTTAAGC 57.181 37.500 0.00 0.00 0.00 3.09
677 678 0.733150 ATAAAAGCGCGAGGAAAGGC 59.267 50.000 12.10 0.00 0.00 4.35
706 708 4.798682 GGAAGGAGAGGGGCGGGA 62.799 72.222 0.00 0.00 0.00 5.14
711 714 2.444895 CGGGAGGAAGGAGAGGGG 60.445 72.222 0.00 0.00 0.00 4.79
766 780 1.834263 GAGTGGAGCCTCTAATGGTGT 59.166 52.381 0.00 0.00 0.00 4.16
864 906 4.717313 AAGGTCCCGCTTTCCGCC 62.717 66.667 0.00 0.00 35.03 6.13
876 918 2.186532 AGCGAAAAGGGAAGAAGGTC 57.813 50.000 0.00 0.00 0.00 3.85
882 924 4.728021 GCGAAAGATAAGCGAAAAGGGAAG 60.728 45.833 0.00 0.00 0.00 3.46
883 925 3.126343 GCGAAAGATAAGCGAAAAGGGAA 59.874 43.478 0.00 0.00 0.00 3.97
906 949 1.590147 GAGAAACGGAAGGAGCGGA 59.410 57.895 0.00 0.00 0.00 5.54
961 1007 0.994995 CTTGCTACGTACTGCTGCTG 59.005 55.000 8.13 4.89 0.00 4.41
967 1013 4.684703 AGTTTGCTTACTTGCTACGTACTG 59.315 41.667 0.00 0.00 0.00 2.74
989 1037 0.803768 CGACGACATCAGAAGCCCAG 60.804 60.000 0.00 0.00 0.00 4.45
990 1038 1.215382 CGACGACATCAGAAGCCCA 59.785 57.895 0.00 0.00 0.00 5.36
1074 1159 3.766691 GAGTTGGTAGCGGGCGGA 61.767 66.667 0.00 0.00 0.00 5.54
1594 1687 3.002246 GTGAGACAAAGAACGCACATGAA 59.998 43.478 0.00 0.00 36.95 2.57
1713 1806 0.038744 ACCCATCTTGAAGGCACCAG 59.961 55.000 0.00 0.00 0.00 4.00
1769 1862 3.282885 GAAGGGAGGGAGCAGTATTTTG 58.717 50.000 0.00 0.00 0.00 2.44
2449 2555 9.069078 CACATTTTCAATGCTGATACTAAGTTG 57.931 33.333 0.00 0.00 0.00 3.16
2540 2647 9.011407 TCGTGTTGAACAATAACAATTACAAAC 57.989 29.630 0.00 0.00 39.50 2.93
2567 2674 8.908903 AGAATCGTACTTAAAGATGAGAGTGAT 58.091 33.333 0.00 0.00 0.00 3.06
2684 2791 1.262640 GGAGGAGGTGGCGGTTTAGA 61.263 60.000 0.00 0.00 0.00 2.10
2746 2853 1.415672 GGGGTCTGTTCTCACCACCA 61.416 60.000 0.00 0.00 33.91 4.17
2749 2856 1.768684 GCAGGGGTCTGTTCTCACCA 61.769 60.000 0.00 0.00 42.78 4.17
2759 2866 1.779061 AACGGTGATTGCAGGGGTCT 61.779 55.000 0.00 0.00 0.00 3.85
2830 2937 1.062587 GAGAATTCATTGGTCGCCACG 59.937 52.381 8.44 0.00 30.78 4.94
2878 2985 3.307762 CCCCTTTGTGAACAAACCCAAAA 60.308 43.478 4.52 0.00 40.55 2.44
2884 2991 1.480545 AGCACCCCTTTGTGAACAAAC 59.519 47.619 4.52 0.00 40.55 2.93
2927 3034 6.320672 CCACTTCCATCTCTCAATTGCTTAAT 59.679 38.462 0.00 0.00 0.00 1.40
3025 3132 6.265196 TGTCTTCAGAAATGCAATAACCAACT 59.735 34.615 0.00 0.00 0.00 3.16
3157 3264 4.748892 TCTCGGACAAGATTAAAGAGCAG 58.251 43.478 0.00 0.00 0.00 4.24
3257 3365 5.560724 ACAACTCATACAGCAACTGGTAAT 58.439 37.500 0.00 0.00 35.51 1.89
3261 3369 3.058016 CCAACAACTCATACAGCAACTGG 60.058 47.826 0.00 0.00 35.51 4.00
3281 3407 6.503560 AATCACCCGGATATTTACTAACCA 57.496 37.500 0.73 0.00 34.28 3.67
3362 3491 5.063060 GTCAATTTACGCGAACAAGGTCTAT 59.937 40.000 15.93 0.00 0.00 1.98
3363 3492 4.386652 GTCAATTTACGCGAACAAGGTCTA 59.613 41.667 15.93 0.00 0.00 2.59
3376 3505 8.714179 TGTAACTGGTTAGATTGTCAATTTACG 58.286 33.333 0.00 0.00 0.00 3.18
3390 3519 9.398170 CATTTTCTGAACAATGTAACTGGTTAG 57.602 33.333 12.85 0.00 0.00 2.34
3392 3521 8.006298 TCATTTTCTGAACAATGTAACTGGTT 57.994 30.769 17.06 0.00 32.96 3.67
3394 3523 8.870160 TTTCATTTTCTGAACAATGTAACTGG 57.130 30.769 17.06 0.00 43.54 4.00
3400 3529 6.289834 TGGCATTTCATTTTCTGAACAATGT 58.710 32.000 17.06 0.00 43.54 2.71
3421 3550 1.818642 AACTCTCTTGCAGTCATGGC 58.181 50.000 0.00 0.00 0.00 4.40
3443 3572 8.354711 TGGTTGTGCTTATTATTACCATTGAA 57.645 30.769 0.00 0.00 29.78 2.69
3445 3574 8.868916 GTTTGGTTGTGCTTATTATTACCATTG 58.131 33.333 0.00 0.00 34.47 2.82
3476 3605 4.260132 GCGATAAAGCTGACATGTTCTGAG 60.260 45.833 0.00 0.00 0.00 3.35
3477 3606 3.618594 GCGATAAAGCTGACATGTTCTGA 59.381 43.478 0.00 0.00 0.00 3.27
3483 3612 1.331756 GGTGGCGATAAAGCTGACATG 59.668 52.381 0.00 0.00 37.29 3.21
3486 3615 1.739067 AAGGTGGCGATAAAGCTGAC 58.261 50.000 0.00 0.00 37.29 3.51
3511 3640 4.178540 TCGGCGGAAGTTATTAAAGACTG 58.821 43.478 7.21 0.00 0.00 3.51
3529 3658 1.611491 TCCCAGTTTGACAAAATCGGC 59.389 47.619 7.09 0.00 0.00 5.54
3672 3801 5.776744 AGAGAATGCAAACCAAATGAAGAC 58.223 37.500 0.00 0.00 0.00 3.01
3725 3854 3.636764 GCCTTCCTGAAAAAGAGGTGAAA 59.363 43.478 0.00 0.00 31.85 2.69
3854 3984 9.408731 GTGAAAAAGAAAAAGAAAAGCATAACG 57.591 29.630 0.00 0.00 0.00 3.18
4014 4144 9.650371 GTAGAAATGAAACAAAAAGGAAAATGC 57.350 29.630 0.00 0.00 0.00 3.56
4118 4249 7.770801 TCTGAATTTACTCATATCAACCACG 57.229 36.000 0.00 0.00 0.00 4.94
4204 4335 7.490962 TTAACTATGTTTATGATCCCGCAAG 57.509 36.000 0.00 0.00 0.00 4.01
4397 4528 1.407258 CACTGTCCCGGAAAGCAAAAA 59.593 47.619 0.73 0.00 0.00 1.94
4420 4551 7.031372 TCATTTTCAAGCATTTGAGATACTGC 58.969 34.615 0.00 0.00 43.76 4.40
4544 4680 2.976882 ACTCTGGTGCAAGGTACCTAAA 59.023 45.455 16.67 0.33 39.01 1.85
4722 4858 5.012664 TGAATTTGACCCAGCTAGTTACAGA 59.987 40.000 0.00 0.00 0.00 3.41
4734 4870 5.867903 ACAACAAGAATGAATTTGACCCA 57.132 34.783 0.00 0.00 0.00 4.51
4811 4960 9.823647 TGGCATTTAAGTCAAATTTGAAGTAAA 57.176 25.926 25.13 25.13 39.21 2.01
4821 4970 9.051679 GGTAAAGTTTTGGCATTTAAGTCAAAT 57.948 29.630 0.00 0.00 42.08 2.32
4849 4998 5.245075 GGGTGTTTGGAAGAATGGTATTTCA 59.755 40.000 0.00 0.00 0.00 2.69
4854 5003 2.225167 GGGGGTGTTTGGAAGAATGGTA 60.225 50.000 0.00 0.00 0.00 3.25
4860 5009 1.708551 CCTTAGGGGGTGTTTGGAAGA 59.291 52.381 0.00 0.00 0.00 2.87
4933 5082 5.247110 GTCCAAGAGAGCCCTCAATGATATA 59.753 44.000 0.00 0.00 41.87 0.86
4934 5083 4.041444 GTCCAAGAGAGCCCTCAATGATAT 59.959 45.833 0.00 0.00 41.87 1.63
4935 5084 3.389329 GTCCAAGAGAGCCCTCAATGATA 59.611 47.826 0.00 0.00 41.87 2.15
4939 5088 1.963985 AGTCCAAGAGAGCCCTCAAT 58.036 50.000 0.00 0.00 41.87 2.57
4949 5098 7.439381 TGGTTGTTAGTTAAGTAGTCCAAGAG 58.561 38.462 0.00 0.00 0.00 2.85
5018 5167 6.471233 TCATACAGAGAAAATCGAGTCCAT 57.529 37.500 0.00 0.00 0.00 3.41
5041 5190 2.919328 GCAAAGGCCAAGGCACCT 60.919 61.111 13.87 0.00 44.11 4.00
5070 5219 9.135843 CTGTGACAAGAATAAATACAACGAGTA 57.864 33.333 0.00 0.00 37.06 2.59
5094 5243 6.391227 AAAGTTGGAAGATGGTAAACACTG 57.609 37.500 0.00 0.00 0.00 3.66
5119 5269 0.173481 GCACAGAGTACTCGGCATCA 59.827 55.000 21.11 0.00 34.09 3.07
5125 5275 1.813178 TGAAGAGGCACAGAGTACTCG 59.187 52.381 17.07 13.93 35.22 4.18
5174 5324 7.161773 ACTCAAATAGATGGGTTGAACATTG 57.838 36.000 0.00 0.00 26.31 2.82
5178 5328 7.214467 TCAAACTCAAATAGATGGGTTGAAC 57.786 36.000 0.00 0.00 43.10 3.18
5181 5331 7.395190 TGATCAAACTCAAATAGATGGGTTG 57.605 36.000 0.00 0.00 43.10 3.77
5182 5332 8.057623 AGATGATCAAACTCAAATAGATGGGTT 58.942 33.333 0.00 0.00 45.78 4.11
5184 5334 8.461249 AAGATGATCAAACTCAAATAGATGGG 57.539 34.615 0.00 0.00 0.00 4.00
5185 5335 8.566260 GGAAGATGATCAAACTCAAATAGATGG 58.434 37.037 0.00 0.00 0.00 3.51
5200 5350 3.118112 GCAGGGAGAAAGGAAGATGATCA 60.118 47.826 0.00 0.00 0.00 2.92
5205 5355 1.563410 CCTGCAGGGAGAAAGGAAGAT 59.437 52.381 26.14 0.00 37.23 2.40
5299 5453 3.785486 TGCCATCTCGTTATCACTGAAG 58.215 45.455 0.00 0.00 0.00 3.02
5304 5458 3.179443 TCCTTGCCATCTCGTTATCAC 57.821 47.619 0.00 0.00 0.00 3.06
5398 5552 3.958798 CAAGGGAAGAAGAGATACCGGTA 59.041 47.826 18.46 18.46 0.00 4.02
5402 5556 5.841783 AGGATACAAGGGAAGAAGAGATACC 59.158 44.000 0.00 0.00 41.41 2.73
5405 5559 5.533112 TGAGGATACAAGGGAAGAAGAGAT 58.467 41.667 0.00 0.00 41.41 2.75
5487 5641 4.100808 AGGATCAAGGTTAGCTTAGCTCTG 59.899 45.833 11.09 6.38 40.44 3.35
5492 5646 5.127845 TCACAGAGGATCAAGGTTAGCTTAG 59.872 44.000 0.00 0.00 37.82 2.18
5750 5910 2.492090 GATGACCGTCGCTGCTCT 59.508 61.111 0.00 0.00 0.00 4.09
5763 5923 3.068064 TCCTGCGTCTGCCGATGA 61.068 61.111 0.96 0.00 41.78 2.92
5768 5928 4.767255 CCACCTCCTGCGTCTGCC 62.767 72.222 0.00 0.00 41.78 4.85
5798 5958 2.202492 CGCCGTCGTCTCTCTTGG 60.202 66.667 0.00 0.00 0.00 3.61
5799 5959 1.512310 GTCGCCGTCGTCTCTCTTG 60.512 63.158 0.00 0.00 36.96 3.02
5830 5993 3.117745 TGGGTCATCATCTCATGGAAGT 58.882 45.455 0.00 0.00 0.00 3.01
5845 6008 0.841289 ACGAAAGGGAAAGTGGGTCA 59.159 50.000 0.00 0.00 0.00 4.02
5846 6009 1.607148 CAACGAAAGGGAAAGTGGGTC 59.393 52.381 0.00 0.00 0.00 4.46
5847 6010 1.687563 CAACGAAAGGGAAAGTGGGT 58.312 50.000 0.00 0.00 0.00 4.51
5848 6011 0.958822 CCAACGAAAGGGAAAGTGGG 59.041 55.000 0.00 0.00 0.00 4.61
5884 6047 5.712004 TGCTGTGGATTTACAAATGATGTG 58.288 37.500 0.00 0.00 43.77 3.21
5889 6055 6.140303 AGCTATGCTGTGGATTTACAAATG 57.860 37.500 0.00 0.00 37.57 2.32
5932 6098 0.179059 TTCGTTGCAGCCAAGTCAGA 60.179 50.000 0.00 0.00 0.00 3.27
5963 6134 8.458573 ACTACCATATGTCTCAACAACAAAAA 57.541 30.769 1.24 0.00 39.30 1.94
5971 6142 8.349983 ACAAACAAAACTACCATATGTCTCAAC 58.650 33.333 1.24 0.00 0.00 3.18
5978 6157 7.807907 GGTCAAGACAAACAAAACTACCATATG 59.192 37.037 2.29 0.00 0.00 1.78
5983 6162 5.570234 TGGTCAAGACAAACAAAACTACC 57.430 39.130 2.29 0.00 0.00 3.18
5986 6165 5.619086 CGAGTTGGTCAAGACAAACAAAACT 60.619 40.000 19.55 10.28 45.43 2.66
5987 6166 4.557301 CGAGTTGGTCAAGACAAACAAAAC 59.443 41.667 19.55 9.03 45.43 2.43
5995 6174 0.596600 GCGTCGAGTTGGTCAAGACA 60.597 55.000 0.00 0.00 32.57 3.41
5997 6176 0.103390 TTGCGTCGAGTTGGTCAAGA 59.897 50.000 0.00 0.00 0.00 3.02
5999 6178 1.529438 GAATTGCGTCGAGTTGGTCAA 59.471 47.619 0.00 0.00 0.00 3.18
6000 6179 1.144969 GAATTGCGTCGAGTTGGTCA 58.855 50.000 0.00 0.00 0.00 4.02
6001 6180 1.429463 AGAATTGCGTCGAGTTGGTC 58.571 50.000 0.00 0.00 0.00 4.02
6002 6181 2.029290 AGTAGAATTGCGTCGAGTTGGT 60.029 45.455 0.00 0.00 0.00 3.67
6003 6182 2.607187 AGTAGAATTGCGTCGAGTTGG 58.393 47.619 0.00 0.00 0.00 3.77
6004 6183 3.722082 GCAAGTAGAATTGCGTCGAGTTG 60.722 47.826 0.00 7.65 45.43 3.16
6006 6185 1.993370 GCAAGTAGAATTGCGTCGAGT 59.007 47.619 0.00 0.00 45.43 4.18
6007 6186 2.703190 GCAAGTAGAATTGCGTCGAG 57.297 50.000 0.00 0.00 45.43 4.04
6025 6227 1.089920 ACGCATCTCACTGGAAATGC 58.910 50.000 0.00 0.00 40.81 3.56
6027 6229 2.768253 TCACGCATCTCACTGGAAAT 57.232 45.000 0.00 0.00 0.00 2.17
6034 6236 5.438117 CAATGTAATGATCACGCATCTCAC 58.562 41.667 0.00 0.00 31.92 3.51
6037 6239 3.251729 GCCAATGTAATGATCACGCATCT 59.748 43.478 0.00 0.00 31.92 2.90
6038 6240 3.251729 AGCCAATGTAATGATCACGCATC 59.748 43.478 0.00 0.00 0.00 3.91
6039 6241 3.004002 CAGCCAATGTAATGATCACGCAT 59.996 43.478 0.00 0.00 0.00 4.73
6041 6243 2.855953 GCAGCCAATGTAATGATCACGC 60.856 50.000 0.00 0.00 0.00 5.34
6042 6244 2.615447 AGCAGCCAATGTAATGATCACG 59.385 45.455 0.00 0.00 0.00 4.35
6043 6245 3.243301 CCAGCAGCCAATGTAATGATCAC 60.243 47.826 0.00 0.00 0.00 3.06
6044 6246 2.953648 CCAGCAGCCAATGTAATGATCA 59.046 45.455 0.00 0.00 0.00 2.92
6045 6247 2.288030 GCCAGCAGCCAATGTAATGATC 60.288 50.000 0.00 0.00 34.35 2.92
6046 6248 1.684983 GCCAGCAGCCAATGTAATGAT 59.315 47.619 0.00 0.00 34.35 2.45
6048 6250 3.654178 GCCAGCAGCCAATGTAATG 57.346 52.632 0.00 0.00 34.35 1.90
6077 6290 1.522668 TTCTTCCAAGCATGACACCG 58.477 50.000 0.00 0.00 0.00 4.94
6124 6337 1.666054 CCTGGCTCTTGCTCTGAATC 58.334 55.000 0.00 0.00 39.59 2.52
6125 6338 0.255318 CCCTGGCTCTTGCTCTGAAT 59.745 55.000 0.00 0.00 39.59 2.57
6131 6344 1.127343 GTATCTCCCTGGCTCTTGCT 58.873 55.000 0.00 0.00 39.59 3.91
6133 6346 2.114616 ACTGTATCTCCCTGGCTCTTG 58.885 52.381 0.00 0.00 0.00 3.02
6153 6366 1.134220 GGTCCAACGAATCCATGCCTA 60.134 52.381 0.00 0.00 0.00 3.93
6325 6552 0.603439 TAAACCGACCGGCACCTTTC 60.603 55.000 8.55 0.00 39.32 2.62
6369 6596 6.808829 ACATTGGCATGTACTAATGGAAATG 58.191 36.000 11.97 0.00 42.24 2.32
6370 6597 7.342799 AGAACATTGGCATGTACTAATGGAAAT 59.657 33.333 11.97 0.00 43.34 2.17
6376 6603 7.998383 TCCATAAGAACATTGGCATGTACTAAT 59.002 33.333 0.00 0.00 43.34 1.73
6378 6605 6.894682 TCCATAAGAACATTGGCATGTACTA 58.105 36.000 0.00 0.00 43.34 1.82
6379 6606 5.754782 TCCATAAGAACATTGGCATGTACT 58.245 37.500 0.00 0.00 43.34 2.73
6380 6607 5.506317 GCTCCATAAGAACATTGGCATGTAC 60.506 44.000 0.00 0.00 43.34 2.90
6400 6629 4.760204 ACACACCTAATGTTTGTTAGCTCC 59.240 41.667 0.00 0.00 40.64 4.70
6425 6654 3.127030 CGTTTGGTTTGAGGGCTAAGATC 59.873 47.826 0.00 0.00 0.00 2.75
6448 7272 1.382146 AATGAATGCAGGCAGGGGG 60.382 57.895 0.00 0.00 0.00 5.40
6468 7292 6.468319 CAGATTTTGCGAAGAAAGATAAGCTG 59.532 38.462 0.00 0.00 0.00 4.24
6475 7299 7.152645 ACTACTACAGATTTTGCGAAGAAAGA 58.847 34.615 0.00 0.00 0.00 2.52
6485 7309 6.631016 TCTGCACCTACTACTACAGATTTTG 58.369 40.000 0.00 0.00 0.00 2.44
6497 7321 4.077108 TCTCTTTCGTTCTGCACCTACTA 58.923 43.478 0.00 0.00 0.00 1.82
6498 7322 2.891580 TCTCTTTCGTTCTGCACCTACT 59.108 45.455 0.00 0.00 0.00 2.57
6500 7324 4.537135 AATCTCTTTCGTTCTGCACCTA 57.463 40.909 0.00 0.00 0.00 3.08
6509 7333 8.336806 CGACTACTATCTGTAATCTCTTTCGTT 58.663 37.037 0.00 0.00 0.00 3.85
6511 7335 7.171167 TCCGACTACTATCTGTAATCTCTTTCG 59.829 40.741 0.00 0.00 0.00 3.46
6520 7344 4.375272 CCGAGTCCGACTACTATCTGTAA 58.625 47.826 0.00 0.00 38.22 2.41
6521 7345 3.244009 CCCGAGTCCGACTACTATCTGTA 60.244 52.174 0.00 0.00 38.22 2.74
6526 7350 0.182061 TGCCCGAGTCCGACTACTAT 59.818 55.000 0.00 0.00 38.22 2.12
6529 7353 0.745845 TACTGCCCGAGTCCGACTAC 60.746 60.000 0.00 0.00 38.22 2.73
6537 7361 0.108138 GAGCAATGTACTGCCCGAGT 60.108 55.000 3.63 0.00 43.73 4.18
6538 7362 0.811616 GGAGCAATGTACTGCCCGAG 60.812 60.000 3.63 0.00 43.73 4.63
6539 7363 1.220749 GGAGCAATGTACTGCCCGA 59.779 57.895 3.63 0.00 43.73 5.14
6540 7364 0.464373 ATGGAGCAATGTACTGCCCG 60.464 55.000 3.63 0.00 43.73 6.13
6541 7365 1.678101 GAATGGAGCAATGTACTGCCC 59.322 52.381 3.63 5.79 43.73 5.36
6542 7366 2.648059 AGAATGGAGCAATGTACTGCC 58.352 47.619 3.63 0.00 43.73 4.85
6543 7367 4.708726 AAAGAATGGAGCAATGTACTGC 57.291 40.909 0.00 0.00 42.97 4.40
6573 7397 0.109723 TGCCCTACTGCCGACTTTTT 59.890 50.000 0.00 0.00 0.00 1.94
6574 7398 0.605589 GTGCCCTACTGCCGACTTTT 60.606 55.000 0.00 0.00 0.00 2.27
6575 7399 1.003718 GTGCCCTACTGCCGACTTT 60.004 57.895 0.00 0.00 0.00 2.66
6576 7400 1.889530 GAGTGCCCTACTGCCGACTT 61.890 60.000 0.00 0.00 40.53 3.01
6577 7401 2.283966 AGTGCCCTACTGCCGACT 60.284 61.111 0.00 0.00 38.49 4.18
6578 7402 2.184579 GAGTGCCCTACTGCCGAC 59.815 66.667 0.00 0.00 40.53 4.79
6579 7403 3.449227 CGAGTGCCCTACTGCCGA 61.449 66.667 0.00 0.00 40.53 5.54
6580 7404 3.417275 CTCGAGTGCCCTACTGCCG 62.417 68.421 3.62 0.00 40.53 5.69
6581 7405 2.052690 TCTCGAGTGCCCTACTGCC 61.053 63.158 13.13 0.00 40.53 4.85
6582 7406 1.139947 GTCTCGAGTGCCCTACTGC 59.860 63.158 13.13 0.00 40.53 4.40
6583 7407 0.171455 GTGTCTCGAGTGCCCTACTG 59.829 60.000 13.13 0.00 40.53 2.74
6584 7408 0.966370 GGTGTCTCGAGTGCCCTACT 60.966 60.000 13.13 0.00 44.02 2.57
6585 7409 1.511768 GGTGTCTCGAGTGCCCTAC 59.488 63.158 13.13 2.33 0.00 3.18
6586 7410 2.044555 CGGTGTCTCGAGTGCCCTA 61.045 63.158 13.13 0.00 0.00 3.53
6587 7411 3.374402 CGGTGTCTCGAGTGCCCT 61.374 66.667 13.13 0.00 0.00 5.19
6588 7412 3.681835 ACGGTGTCTCGAGTGCCC 61.682 66.667 13.13 9.36 0.00 5.36
6589 7413 2.430921 CACGGTGTCTCGAGTGCC 60.431 66.667 13.13 11.78 0.00 5.01
6668 7493 6.988580 CCTACAAGTATGAGCTTGATCATTCA 59.011 38.462 12.05 1.79 46.34 2.57
6669 7494 6.989169 ACCTACAAGTATGAGCTTGATCATTC 59.011 38.462 12.05 2.35 46.34 2.67
6670 7495 6.893583 ACCTACAAGTATGAGCTTGATCATT 58.106 36.000 12.05 0.00 46.34 2.57
6671 7496 6.491714 ACCTACAAGTATGAGCTTGATCAT 57.508 37.500 12.05 6.61 46.34 2.45
6672 7497 5.939764 ACCTACAAGTATGAGCTTGATCA 57.060 39.130 12.05 0.00 46.34 2.92
6673 7498 7.045126 ACTACCTACAAGTATGAGCTTGATC 57.955 40.000 12.05 0.00 46.34 2.92
6674 7499 7.560262 TGTACTACCTACAAGTATGAGCTTGAT 59.440 37.037 12.05 0.00 46.34 2.57
6675 7500 6.888088 TGTACTACCTACAAGTATGAGCTTGA 59.112 38.462 12.05 0.00 46.34 3.02
6677 7502 7.117397 TCTGTACTACCTACAAGTATGAGCTT 58.883 38.462 0.00 0.00 34.80 3.74
6678 7503 6.660800 TCTGTACTACCTACAAGTATGAGCT 58.339 40.000 0.00 0.00 34.80 4.09
6679 7504 6.513720 GCTCTGTACTACCTACAAGTATGAGC 60.514 46.154 17.16 17.16 43.30 4.26
6680 7505 6.016943 GGCTCTGTACTACCTACAAGTATGAG 60.017 46.154 0.00 0.00 34.80 2.90
6717 7542 4.314522 TTGATTGGGACAGGCAGATTTA 57.685 40.909 0.00 0.00 42.39 1.40
6764 7589 7.218204 GCAGTATTGTTTCATTATTTGTCGTCC 59.782 37.037 0.00 0.00 0.00 4.79
6770 7595 9.069078 CAGACAGCAGTATTGTTTCATTATTTG 57.931 33.333 0.00 0.00 0.00 2.32
6775 7600 6.000219 AGACAGACAGCAGTATTGTTTCATT 59.000 36.000 1.32 0.00 0.00 2.57
6821 7653 2.091588 CGGGCGAATTATTATTCCGTCG 59.908 50.000 0.00 0.00 37.46 5.12


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

AutoCloner maintained by Alex Coulton.