Multiple sequence alignment - TraesCS3B01G017500

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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 TraesCS3B01G017500 chr3B 100.000 5228 0 0 435 5662 7191956 7186729 0.000000e+00 9655.0
1 TraesCS3B01G017500 chr3B 91.882 271 17 3 546 816 228792889 228792624 1.930000e-99 374.0
2 TraesCS3B01G017500 chr3B 100.000 132 0 0 1 132 7192390 7192259 1.580000e-60 244.0
3 TraesCS3B01G017500 chr3B 85.811 148 4 9 1 132 228793473 228793327 2.130000e-29 141.0
4 TraesCS3B01G017500 chr3A 92.989 2011 81 23 825 2781 14048915 14046911 0.000000e+00 2878.0
5 TraesCS3B01G017500 chr3A 88.708 1780 88 48 3475 5187 14046643 14044910 0.000000e+00 2069.0
6 TraesCS3B01G017500 chr3A 98.077 364 6 1 5300 5662 14044782 14044419 2.880000e-177 632.0
7 TraesCS3B01G017500 chr3A 95.367 259 11 1 2828 3086 14046904 14046647 1.470000e-110 411.0
8 TraesCS3B01G017500 chr3A 87.879 132 5 4 1 132 14049278 14049158 1.640000e-30 145.0
9 TraesCS3B01G017500 chr3A 86.364 88 8 1 435 522 14049077 14048994 6.040000e-15 93.5
10 TraesCS3B01G017500 chr3A 97.222 36 1 0 788 823 14048993 14048958 1.700000e-05 62.1
11 TraesCS3B01G017500 chr3D 93.114 1946 73 23 885 2781 6333312 6335245 0.000000e+00 2795.0
12 TraesCS3B01G017500 chr3D 89.151 1272 76 28 3423 4676 6335882 6337109 0.000000e+00 1528.0
13 TraesCS3B01G017500 chr3D 94.527 603 28 3 2828 3425 6335252 6335854 0.000000e+00 926.0
14 TraesCS3B01G017500 chr3D 87.730 815 41 24 4889 5662 6337326 6338122 0.000000e+00 896.0
15 TraesCS3B01G017500 chr3D 90.136 294 9 8 491 776 6333004 6333285 1.160000e-96 364.0
16 TraesCS3B01G017500 chr3D 87.603 121 6 2 12 132 6332733 6332844 1.280000e-26 132.0
17 TraesCS3B01G017500 chr2A 85.857 502 47 6 831 1312 173514642 173514145 3.910000e-141 512.0
18 TraesCS3B01G017500 chr2A 88.208 424 29 6 909 1312 572844757 572845179 2.370000e-133 486.0
19 TraesCS3B01G017500 chr2A 88.073 327 27 2 5336 5662 131682809 131683123 1.490000e-100 377.0
20 TraesCS3B01G017500 chr2A 90.688 247 23 0 5410 5656 603523791 603524037 4.230000e-86 329.0
21 TraesCS3B01G017500 chr2A 95.349 43 2 0 791 833 173514703 173514661 1.020000e-07 69.4
22 TraesCS3B01G017500 chr6A 85.600 500 48 9 833 1312 511525975 511526470 2.350000e-138 503.0
23 TraesCS3B01G017500 chr7A 87.972 424 30 6 909 1312 606193524 606193946 1.100000e-131 481.0
24 TraesCS3B01G017500 chrUn 87.736 424 31 6 909 1312 122647061 122647483 5.130000e-130 475.0
25 TraesCS3B01G017500 chrUn 76.667 180 31 9 791 966 122646862 122647034 7.810000e-14 89.8
26 TraesCS3B01G017500 chr1A 82.812 512 57 13 825 1312 462343872 462344376 4.050000e-116 429.0
27 TraesCS3B01G017500 chr1A 84.158 303 22 13 435 722 378972513 378972804 2.600000e-68 270.0
28 TraesCS3B01G017500 chr1A 82.700 237 16 9 435 656 378940000 378940226 2.690000e-43 187.0
29 TraesCS3B01G017500 chr4D 82.197 528 61 12 810 1312 79009173 79009692 1.890000e-114 424.0
30 TraesCS3B01G017500 chr2B 88.991 327 24 2 5336 5662 178338313 178338627 1.480000e-105 394.0
31 TraesCS3B01G017500 chr2B 89.879 247 25 0 5410 5656 541687086 541687332 9.150000e-83 318.0
32 TraesCS3B01G017500 chr2D 88.685 327 25 2 5336 5662 125324414 125324728 6.880000e-104 388.0
33 TraesCS3B01G017500 chr2D 90.688 247 23 0 5410 5656 460648989 460649235 4.230000e-86 329.0
34 TraesCS3B01G017500 chr5B 91.822 269 17 3 548 816 474945085 474945348 2.490000e-98 370.0
35 TraesCS3B01G017500 chr5B 86.486 148 3 11 1 132 474944498 474944644 4.570000e-31 147.0
36 TraesCS3B01G017500 chr1D 88.068 176 16 5 5380 5551 385812581 385812407 2.670000e-48 204.0
37 TraesCS3B01G017500 chr1D 86.607 112 15 0 5551 5662 476558359 476558470 2.140000e-24 124.0
38 TraesCS3B01G017500 chr5A 81.522 276 18 11 435 681 551711117 551711388 4.480000e-46 196.0
39 TraesCS3B01G017500 chr5A 83.221 149 7 10 1 132 551710888 551711035 2.770000e-23 121.0


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 TraesCS3B01G017500 chr3B 7186729 7192390 5661 True 4949.500000 9655 100.000000 1 5662 2 chr3B.!!$R1 5661
1 TraesCS3B01G017500 chr3B 228792624 228793473 849 True 257.500000 374 88.846500 1 816 2 chr3B.!!$R2 815
2 TraesCS3B01G017500 chr3A 14044419 14049278 4859 True 898.657143 2878 92.372286 1 5662 7 chr3A.!!$R1 5661
3 TraesCS3B01G017500 chr3D 6332733 6338122 5389 False 1106.833333 2795 90.376833 12 5662 6 chr3D.!!$F1 5650
4 TraesCS3B01G017500 chr2A 173514145 173514703 558 True 290.700000 512 90.603000 791 1312 2 chr2A.!!$R1 521
5 TraesCS3B01G017500 chrUn 122646862 122647483 621 False 282.400000 475 82.201500 791 1312 2 chrUn.!!$F1 521
6 TraesCS3B01G017500 chr1A 462343872 462344376 504 False 429.000000 429 82.812000 825 1312 1 chr1A.!!$F3 487
7 TraesCS3B01G017500 chr4D 79009173 79009692 519 False 424.000000 424 82.197000 810 1312 1 chr4D.!!$F1 502
8 TraesCS3B01G017500 chr5B 474944498 474945348 850 False 258.500000 370 89.154000 1 816 2 chr5B.!!$F1 815

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
522 563 1.767681 TGAGGCCTGCCAATTTGTTTT 59.232 42.857 12.00 0.0 38.92 2.43 F
1046 1455 0.321653 AATGTCGGTGCTCTTCCCAC 60.322 55.000 0.00 0.0 0.00 4.61 F
1244 1673 0.463833 GCGGAATAGGTGGACAAGGG 60.464 60.000 0.00 0.0 0.00 3.95 F
2818 3277 0.482887 AACAAGCTAAACCTGGGCCT 59.517 50.000 4.53 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2301 0.529378 ACGGTGCTACTAAAGGACGG 59.471 55.0 3.33 3.33 46.95 4.79 R
2823 3282 0.107848 CGCGGAGTCATTTACCCCTT 60.108 55.0 0.00 0.00 0.00 3.95 R
2825 3284 0.392060 AACGCGGAGTCATTTACCCC 60.392 55.0 12.47 0.00 0.00 4.95 R
4746 5273 0.103026 CTTCCGCTCGACCATCATCA 59.897 55.0 0.00 0.00 0.00 3.07 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
84 104 4.753662 AGCCCGTCTACCTCGCCA 62.754 66.667 0.00 0.00 0.00 5.69
85 105 4.509737 GCCCGTCTACCTCGCCAC 62.510 72.222 0.00 0.00 0.00 5.01
86 106 3.834799 CCCGTCTACCTCGCCACC 61.835 72.222 0.00 0.00 0.00 4.61
483 509 2.740055 CTGCTGAGTGCGTGACCC 60.740 66.667 0.00 0.00 46.63 4.46
484 510 3.231889 CTGCTGAGTGCGTGACCCT 62.232 63.158 0.00 0.00 46.63 4.34
485 511 2.031163 GCTGAGTGCGTGACCCTT 59.969 61.111 0.00 0.00 0.00 3.95
522 563 1.767681 TGAGGCCTGCCAATTTGTTTT 59.232 42.857 12.00 0.00 38.92 2.43
523 564 2.172293 TGAGGCCTGCCAATTTGTTTTT 59.828 40.909 12.00 0.00 38.92 1.94
524 565 2.549329 GAGGCCTGCCAATTTGTTTTTG 59.451 45.455 12.00 0.00 38.92 2.44
525 566 2.092484 AGGCCTGCCAATTTGTTTTTGT 60.092 40.909 3.11 0.00 38.92 2.83
526 567 2.687425 GGCCTGCCAATTTGTTTTTGTT 59.313 40.909 2.58 0.00 35.81 2.83
527 568 3.130164 GGCCTGCCAATTTGTTTTTGTTT 59.870 39.130 2.58 0.00 35.81 2.83
536 577 7.621102 CCAATTTGTTTTTGTTTCTACAGAGC 58.379 34.615 0.00 0.00 35.28 4.09
588 866 9.128107 CACTTATGTGGATATTGTTTTGTGAAC 57.872 33.333 0.80 0.00 40.33 3.18
589 867 9.077885 ACTTATGTGGATATTGTTTTGTGAACT 57.922 29.630 0.00 0.00 0.00 3.01
590 868 9.912634 CTTATGTGGATATTGTTTTGTGAACTT 57.087 29.630 0.00 0.00 0.00 2.66
697 983 5.119743 GTCTAGGTGGTCAAAACGATTACAC 59.880 44.000 0.00 0.00 0.00 2.90
728 1014 9.685828 TGTATAAACTTTTCATTGTTTGTAGCC 57.314 29.630 0.00 0.00 37.06 3.93
752 1038 8.836413 GCCACTATGCTCATATTTAAGTTTGTA 58.164 33.333 0.00 0.00 0.00 2.41
819 1105 6.577427 GTGTTGTAAAACTATTGCTGTACTGC 59.423 38.462 17.07 17.07 0.00 4.40
834 1141 6.150976 TGCTGTACTGCTTTATTTATGTGCTT 59.849 34.615 23.07 0.00 0.00 3.91
842 1149 9.357652 CTGCTTTATTTATGTGCTTAAATGTGT 57.642 29.630 11.12 0.00 34.47 3.72
896 1204 6.121590 TGCTGGAATTCATTTGTATGAGCTA 58.878 36.000 7.93 0.00 41.60 3.32
1032 1441 2.079925 GTGCAGGAGACTCCAAATGTC 58.920 52.381 23.60 9.69 39.61 3.06
1046 1455 0.321653 AATGTCGGTGCTCTTCCCAC 60.322 55.000 0.00 0.00 0.00 4.61
1105 1514 1.001487 CTGCGTTGATGTTGAAAGGCA 60.001 47.619 3.21 3.21 42.86 4.75
1117 1526 2.643933 GAAAGGCATTTCAGAGGTGC 57.356 50.000 18.39 1.43 43.64 5.01
1222 1631 6.108015 GGTTATGACGTGTCTATTACCCAAA 58.892 40.000 0.00 0.00 0.00 3.28
1244 1673 0.463833 GCGGAATAGGTGGACAAGGG 60.464 60.000 0.00 0.00 0.00 3.95
1272 1704 8.005976 TGTCTATTTAAAGGTTTTAAGTGGGGT 58.994 33.333 0.00 0.00 0.00 4.95
1288 1720 2.922955 TGGGGTACTTTGGGATGATGAA 59.077 45.455 0.00 0.00 0.00 2.57
1371 1803 1.389609 CGACCCTAGCCCATACACGT 61.390 60.000 0.00 0.00 0.00 4.49
1381 1813 1.535437 CCCATACACGTCTCGCTTACC 60.535 57.143 0.00 0.00 0.00 2.85
1404 1837 1.228521 CCATGGCCAAGTCACCACA 60.229 57.895 10.96 0.00 39.19 4.17
1730 2177 3.718815 GCTACTACTAGATTGGTGGCAC 58.281 50.000 9.70 9.70 36.45 5.01
1804 2252 5.713792 TCAGGTAAGTGTCTTCAGAGAAG 57.286 43.478 0.39 0.39 32.66 2.85
1814 2262 5.347364 GTGTCTTCAGAGAAGAAATTCTCCG 59.653 44.000 10.72 4.92 46.53 4.63
1853 2301 3.118629 TGTCATGAAGAGGAGGTATGTGC 60.119 47.826 0.00 0.00 0.00 4.57
1866 2314 3.383825 AGGTATGTGCCGTCCTTTAGTAG 59.616 47.826 0.00 0.00 0.00 2.57
2006 2454 6.017109 GGAGAAGCTCAAAACATGTAACAAGA 60.017 38.462 0.00 0.00 31.08 3.02
2029 2477 1.227999 TGCTAGTTGAACTGTGCCGC 61.228 55.000 17.72 9.40 31.33 6.53
2226 2678 2.500098 TGATAAGGCTCAACTTAGCGGT 59.500 45.455 0.00 0.00 43.74 5.68
2315 2767 4.820897 TGTCTGTCATAACTGTTAGCCTG 58.179 43.478 6.40 0.35 0.00 4.85
2371 2823 3.696051 GACTGGTATTGTCATTGGCACAT 59.304 43.478 0.00 0.00 34.40 3.21
2442 2894 4.836125 AAAGAAAGCGCAAGAAGAATGA 57.164 36.364 11.47 0.00 43.02 2.57
2446 2898 1.527034 AGCGCAAGAAGAATGAAGCA 58.473 45.000 11.47 0.00 43.02 3.91
2623 3082 8.635765 AGTTCTTTCACCATTTTCATAAGCTA 57.364 30.769 0.00 0.00 0.00 3.32
2699 3158 6.917217 CAGATGGAACTCTACTGGAAATTC 57.083 41.667 0.00 0.00 0.00 2.17
2763 3222 4.461198 AGAACAAACCATTCCGAGTTCTT 58.539 39.130 0.00 0.00 41.90 2.52
2766 3225 4.065789 ACAAACCATTCCGAGTTCTTCTC 58.934 43.478 0.00 0.00 39.62 2.87
2778 3237 5.326200 GAGTTCTTCTCGAGGGATAACAA 57.674 43.478 13.56 0.00 33.25 2.83
2779 3238 5.331876 AGTTCTTCTCGAGGGATAACAAG 57.668 43.478 13.56 7.01 0.00 3.16
2780 3239 5.017490 AGTTCTTCTCGAGGGATAACAAGA 58.983 41.667 13.56 9.36 0.00 3.02
2781 3240 4.985538 TCTTCTCGAGGGATAACAAGAC 57.014 45.455 13.56 0.00 0.00 3.01
2782 3241 4.341487 TCTTCTCGAGGGATAACAAGACA 58.659 43.478 13.56 0.00 0.00 3.41
2784 3243 3.024547 TCTCGAGGGATAACAAGACAGG 58.975 50.000 13.56 0.00 0.00 4.00
2785 3244 3.024547 CTCGAGGGATAACAAGACAGGA 58.975 50.000 3.91 0.00 0.00 3.86
2787 3246 2.496070 CGAGGGATAACAAGACAGGACA 59.504 50.000 0.00 0.00 0.00 4.02
2788 3247 3.056107 CGAGGGATAACAAGACAGGACAA 60.056 47.826 0.00 0.00 0.00 3.18
2789 3248 4.383118 CGAGGGATAACAAGACAGGACAAT 60.383 45.833 0.00 0.00 0.00 2.71
2790 3249 5.501156 GAGGGATAACAAGACAGGACAATT 58.499 41.667 0.00 0.00 0.00 2.32
2791 3250 5.892348 AGGGATAACAAGACAGGACAATTT 58.108 37.500 0.00 0.00 0.00 1.82
2792 3251 5.711976 AGGGATAACAAGACAGGACAATTTG 59.288 40.000 0.00 0.00 0.00 2.32
2793 3252 5.402398 GGATAACAAGACAGGACAATTTGC 58.598 41.667 0.00 0.00 0.00 3.68
2794 3253 3.354089 AACAAGACAGGACAATTTGCG 57.646 42.857 0.00 0.00 0.00 4.85
2795 3254 2.571212 ACAAGACAGGACAATTTGCGA 58.429 42.857 0.00 0.00 0.00 5.10
2796 3255 2.948979 ACAAGACAGGACAATTTGCGAA 59.051 40.909 0.00 0.00 0.00 4.70
2797 3256 3.003689 ACAAGACAGGACAATTTGCGAAG 59.996 43.478 0.00 0.00 0.00 3.79
2798 3257 2.154462 AGACAGGACAATTTGCGAAGG 58.846 47.619 0.00 0.00 0.00 3.46
2799 3258 2.151202 GACAGGACAATTTGCGAAGGA 58.849 47.619 0.00 0.00 0.00 3.36
2800 3259 2.552315 GACAGGACAATTTGCGAAGGAA 59.448 45.455 0.00 0.00 34.77 3.36
2801 3260 2.293399 ACAGGACAATTTGCGAAGGAAC 59.707 45.455 0.00 0.00 37.77 3.62
2802 3261 2.293122 CAGGACAATTTGCGAAGGAACA 59.707 45.455 0.00 0.00 37.77 3.18
2803 3262 2.955660 AGGACAATTTGCGAAGGAACAA 59.044 40.909 0.00 0.00 37.77 2.83
2804 3263 3.004734 AGGACAATTTGCGAAGGAACAAG 59.995 43.478 0.00 0.00 37.77 3.16
2805 3264 2.726241 GACAATTTGCGAAGGAACAAGC 59.274 45.455 0.00 0.00 37.77 4.01
2806 3265 2.362077 ACAATTTGCGAAGGAACAAGCT 59.638 40.909 0.00 0.00 37.77 3.74
2807 3266 3.568007 ACAATTTGCGAAGGAACAAGCTA 59.432 39.130 0.00 0.00 37.77 3.32
2808 3267 4.037446 ACAATTTGCGAAGGAACAAGCTAA 59.963 37.500 0.00 0.00 37.77 3.09
2809 3268 4.846779 ATTTGCGAAGGAACAAGCTAAA 57.153 36.364 0.00 0.00 37.77 1.85
2810 3269 3.619233 TTGCGAAGGAACAAGCTAAAC 57.381 42.857 0.00 0.00 28.51 2.01
2811 3270 1.877443 TGCGAAGGAACAAGCTAAACC 59.123 47.619 0.00 0.00 0.00 3.27
2812 3271 2.152016 GCGAAGGAACAAGCTAAACCT 58.848 47.619 0.00 0.00 0.00 3.50
2813 3272 2.095718 GCGAAGGAACAAGCTAAACCTG 60.096 50.000 0.00 0.00 0.00 4.00
2814 3273 2.484264 CGAAGGAACAAGCTAAACCTGG 59.516 50.000 0.00 0.00 0.00 4.45
2815 3274 2.586648 AGGAACAAGCTAAACCTGGG 57.413 50.000 0.00 0.00 0.00 4.45
2816 3275 0.888619 GGAACAAGCTAAACCTGGGC 59.111 55.000 0.00 0.00 0.00 5.36
2817 3276 0.888619 GAACAAGCTAAACCTGGGCC 59.111 55.000 0.00 0.00 0.00 5.80
2818 3277 0.482887 AACAAGCTAAACCTGGGCCT 59.517 50.000 4.53 0.00 0.00 5.19
2819 3278 0.482887 ACAAGCTAAACCTGGGCCTT 59.517 50.000 4.53 0.00 0.00 4.35
2820 3279 1.133167 ACAAGCTAAACCTGGGCCTTT 60.133 47.619 4.53 0.00 0.00 3.11
2821 3280 1.970640 CAAGCTAAACCTGGGCCTTTT 59.029 47.619 4.53 4.33 0.00 2.27
2822 3281 1.632589 AGCTAAACCTGGGCCTTTTG 58.367 50.000 4.53 0.00 0.00 2.44
2823 3282 1.146982 AGCTAAACCTGGGCCTTTTGA 59.853 47.619 4.53 0.00 0.00 2.69
2824 3283 1.967779 GCTAAACCTGGGCCTTTTGAA 59.032 47.619 4.53 0.00 0.00 2.69
2825 3284 2.029020 GCTAAACCTGGGCCTTTTGAAG 60.029 50.000 4.53 0.00 0.00 3.02
2930 3389 4.275689 TCACAACACCATCTGCAAAGTTAG 59.724 41.667 0.00 0.00 0.00 2.34
2951 3410 8.671921 AGTTAGTTAGCAATGTTGAGAATGATG 58.328 33.333 0.00 0.00 0.00 3.07
2952 3411 8.668353 GTTAGTTAGCAATGTTGAGAATGATGA 58.332 33.333 0.00 0.00 0.00 2.92
2964 3423 4.344968 TGAGAATGATGACACGGATATGGT 59.655 41.667 0.00 0.00 0.00 3.55
2973 3432 1.670811 CACGGATATGGTGGCTTCAAC 59.329 52.381 0.00 0.00 0.00 3.18
2990 3449 6.074835 GGCTTCAACGAAGAAAAACATTTCTC 60.075 38.462 7.90 0.00 41.71 2.87
3086 3545 1.228245 ATGTGGTTGAGTGCGGCTT 60.228 52.632 0.00 0.00 0.00 4.35
3099 3558 1.271934 TGCGGCTTATGTTGTTTGCAT 59.728 42.857 0.00 0.00 0.00 3.96
3165 3625 6.463995 TTCAGGAATGCACTGTTAGTTTTT 57.536 33.333 0.00 0.00 37.25 1.94
3193 3653 5.819901 GCTAGAACTGTCATCTATTTTGGCT 59.180 40.000 0.00 0.00 0.00 4.75
3199 3659 6.917533 ACTGTCATCTATTTTGGCTGAAAAG 58.082 36.000 0.00 0.00 36.97 2.27
3204 3664 2.845363 ATTTTGGCTGAAAAGGCTGG 57.155 45.000 0.00 0.00 36.97 4.85
3210 3670 0.752658 GCTGAAAAGGCTGGTTTGGT 59.247 50.000 0.00 0.00 0.00 3.67
3219 3679 5.968676 AAGGCTGGTTTGGTATGTAGATA 57.031 39.130 0.00 0.00 0.00 1.98
3222 3682 7.626999 AGGCTGGTTTGGTATGTAGATATTA 57.373 36.000 0.00 0.00 0.00 0.98
3296 3756 6.655930 ACTAGAACAAAGTAACCAGGACAAA 58.344 36.000 0.00 0.00 0.00 2.83
3387 3851 7.125053 AGAGAGGTGGGATTAGTTCTTTCTAAG 59.875 40.741 0.00 0.00 34.12 2.18
3405 3869 8.621532 TTTCTAAGTTGATTGTGTAGCTTCAT 57.378 30.769 0.00 0.00 0.00 2.57
3436 3930 9.630098 AATTGCTTAGATGATACAACAAGTTTG 57.370 29.630 0.00 0.00 0.00 2.93
3441 3935 6.005583 AGATGATACAACAAGTTTGTGCTG 57.994 37.500 0.00 0.00 41.31 4.41
3473 3967 8.608185 TTTCATAAGGAGGGCATAAATTTTCT 57.392 30.769 0.00 0.00 0.00 2.52
3512 4012 9.102757 CATACAACATACAGCACTATCTTTCTT 57.897 33.333 0.00 0.00 0.00 2.52
3513 4013 7.986085 ACAACATACAGCACTATCTTTCTTT 57.014 32.000 0.00 0.00 0.00 2.52
3515 4015 9.672673 ACAACATACAGCACTATCTTTCTTTAT 57.327 29.630 0.00 0.00 0.00 1.40
3523 4023 7.658982 CAGCACTATCTTTCTTTATGCTATCCA 59.341 37.037 0.00 0.00 39.83 3.41
3538 4038 7.621428 ATGCTATCCATTTCCGAAATCTATG 57.379 36.000 3.23 0.00 0.00 2.23
3571 4072 5.458015 GGGTCAACCAAATTCTAGTTTTCG 58.542 41.667 0.89 0.00 39.85 3.46
3614 4115 1.261989 TTACAGATAACGCGTGCGAC 58.738 50.000 22.32 5.11 42.83 5.19
3662 4163 6.148480 TGTTTCAAAACCTTGTTTCATTGGTG 59.852 34.615 3.33 0.00 38.11 4.17
3697 4198 5.697473 TTATGTCTAGAGGAGATGCGAAG 57.303 43.478 0.00 0.00 36.29 3.79
3724 4225 2.644992 CAGGCACCGAAACCAAGC 59.355 61.111 0.00 0.00 0.00 4.01
3832 4337 2.711542 ACATTTCCTCCATTCACCGTC 58.288 47.619 0.00 0.00 0.00 4.79
3851 4356 7.064609 TCACCGTCAAATCTTGATATGTTTCTC 59.935 37.037 0.00 0.00 42.47 2.87
3856 4361 9.766277 GTCAAATCTTGATATGTTTCTCTTGTC 57.234 33.333 0.00 0.00 42.47 3.18
3935 4441 5.949952 TGCTTCCTCCTCCCTTTTTAATTAC 59.050 40.000 0.00 0.00 0.00 1.89
3936 4442 6.188407 GCTTCCTCCTCCCTTTTTAATTACT 58.812 40.000 0.00 0.00 0.00 2.24
3937 4443 7.037153 TGCTTCCTCCTCCCTTTTTAATTACTA 60.037 37.037 0.00 0.00 0.00 1.82
3986 4492 5.500234 TGGGTTTCCATATCTTCAGACAAG 58.500 41.667 0.00 0.00 38.32 3.16
4007 4513 5.453567 AGTACTTTGGCAAGGATTTGTTC 57.546 39.130 16.87 1.31 36.65 3.18
4008 4514 4.892934 AGTACTTTGGCAAGGATTTGTTCA 59.107 37.500 16.87 0.00 36.65 3.18
4113 4619 3.244181 GGAGGAAGCAATGGAAGCAAAAA 60.244 43.478 0.00 0.00 0.00 1.94
4121 4627 5.181811 AGCAATGGAAGCAAAAATAAAAGCC 59.818 36.000 0.00 0.00 0.00 4.35
4185 4694 7.327214 AGTTGAATCAGAGATAGACAAGGAAC 58.673 38.462 0.00 0.00 0.00 3.62
4201 4710 4.090761 AGGAACATGAAGTTGAAGCTGA 57.909 40.909 0.00 0.00 41.51 4.26
4208 4717 3.668447 TGAAGTTGAAGCTGATCCAGAC 58.332 45.455 0.00 0.00 32.44 3.51
4238 4747 5.819991 TCTAAGGATGCTGAAAAGATTGGT 58.180 37.500 0.00 0.00 0.00 3.67
4287 4796 5.300792 GGTAAAAGTGGGATTTGTGTGAAGA 59.699 40.000 0.00 0.00 0.00 2.87
4304 4813 3.181454 TGAAGACTGGTGAGAAGGGAAAC 60.181 47.826 0.00 0.00 0.00 2.78
4308 4817 0.250295 TGGTGAGAAGGGAAACAGCG 60.250 55.000 0.00 0.00 34.18 5.18
4309 4818 1.578206 GGTGAGAAGGGAAACAGCGC 61.578 60.000 0.00 0.00 0.00 5.92
4361 4870 0.597637 AGGCAGAAGTTGACGACACG 60.598 55.000 0.00 0.00 40.94 4.49
4372 4881 1.000607 TGACGACACGAGGAAGAAAGG 60.001 52.381 0.00 0.00 0.00 3.11
4374 4883 1.684983 ACGACACGAGGAAGAAAGGAA 59.315 47.619 0.00 0.00 0.00 3.36
4375 4884 2.101917 ACGACACGAGGAAGAAAGGAAA 59.898 45.455 0.00 0.00 0.00 3.13
4376 4885 2.475487 CGACACGAGGAAGAAAGGAAAC 59.525 50.000 0.00 0.00 0.00 2.78
4377 4886 3.463944 GACACGAGGAAGAAAGGAAACA 58.536 45.455 0.00 0.00 0.00 2.83
4378 4887 3.467803 ACACGAGGAAGAAAGGAAACAG 58.532 45.455 0.00 0.00 0.00 3.16
4379 4888 3.118371 ACACGAGGAAGAAAGGAAACAGT 60.118 43.478 0.00 0.00 0.00 3.55
4380 4889 3.248602 CACGAGGAAGAAAGGAAACAGTG 59.751 47.826 0.00 0.00 0.00 3.66
4381 4890 3.134081 ACGAGGAAGAAAGGAAACAGTGA 59.866 43.478 0.00 0.00 0.00 3.41
4382 4891 4.202367 ACGAGGAAGAAAGGAAACAGTGAT 60.202 41.667 0.00 0.00 0.00 3.06
4383 4892 4.153117 CGAGGAAGAAAGGAAACAGTGATG 59.847 45.833 0.00 0.00 0.00 3.07
4384 4893 4.401925 AGGAAGAAAGGAAACAGTGATGG 58.598 43.478 0.00 0.00 0.00 3.51
4385 4894 4.141158 AGGAAGAAAGGAAACAGTGATGGT 60.141 41.667 0.00 0.00 0.00 3.55
4389 4898 5.906073 AGAAAGGAAACAGTGATGGTTTTG 58.094 37.500 0.00 0.00 38.50 2.44
4413 4922 0.453390 GGATTGCGAGGCTGAAAAGG 59.547 55.000 0.00 0.00 0.00 3.11
4424 4933 2.463876 GCTGAAAAGGTTGTGCAGAAC 58.536 47.619 17.97 17.97 0.00 3.01
4455 4964 4.379813 GCGATGGTGGCATAGAAATATTGG 60.380 45.833 0.00 0.00 0.00 3.16
4477 4986 3.127721 GGAGATGGTAAAGCTGAAACTGC 59.872 47.826 0.00 0.00 0.00 4.40
4525 5037 4.013050 GGAGGTTCTGGAGAAAAAGATGG 58.987 47.826 0.00 0.00 35.58 3.51
4550 5077 0.392729 CTGAAGAAGGCAGGGCTGAG 60.393 60.000 0.00 0.00 0.00 3.35
4553 5080 0.998145 AAGAAGGCAGGGCTGAGAAT 59.002 50.000 0.00 0.00 0.00 2.40
4650 5177 4.786425 AGATGTCAAATCTAAGGAAGCCC 58.214 43.478 0.00 0.00 0.00 5.19
4676 5203 2.840651 CAATTAGATCGCCCTATCCCCT 59.159 50.000 0.00 0.00 0.00 4.79
4721 5248 5.425196 AAACAAAATAGATGCCAGGCAAT 57.575 34.783 20.84 13.17 43.62 3.56
4739 5266 4.752101 GGCAATATGATTACTGAAGCGAGT 59.248 41.667 0.00 0.00 0.00 4.18
4770 5297 0.105039 ATGGTCGAGCGGAAGATTCC 59.895 55.000 10.46 1.23 44.05 3.01
4801 5337 4.520492 CCAAAACTGATGTAGGTTGAAGCT 59.480 41.667 1.39 1.39 36.16 3.74
4802 5338 5.455392 CAAAACTGATGTAGGTTGAAGCTG 58.545 41.667 7.22 0.00 36.16 4.24
4807 5343 4.905429 TGATGTAGGTTGAAGCTGCTTTA 58.095 39.130 17.10 9.82 0.00 1.85
4833 5369 3.684788 ACGATGTGAAAACTGATGTAGGC 59.315 43.478 0.00 0.00 0.00 3.93
4918 5527 3.314541 TCGACCTTCCTTGTTTAGCTC 57.685 47.619 0.00 0.00 0.00 4.09
5040 5664 1.741706 GATTGGTCTGACATGGCAGTG 59.258 52.381 27.68 4.78 37.20 3.66
5053 5677 1.626654 GGCAGTGATCGACGGTTGTG 61.627 60.000 0.00 0.00 0.00 3.33
5054 5678 1.626654 GCAGTGATCGACGGTTGTGG 61.627 60.000 0.00 0.00 0.00 4.17
5084 5708 1.368641 GTGGCACATGCTTATCGACA 58.631 50.000 13.86 0.00 44.52 4.35
5199 5861 2.107366 CCTCTCCCTCCTCTTCTTGTC 58.893 57.143 0.00 0.00 0.00 3.18
5209 5871 0.179086 TCTTCTTGTCGCACTGCACA 60.179 50.000 1.11 2.31 0.00 4.57
5210 5872 0.870393 CTTCTTGTCGCACTGCACAT 59.130 50.000 1.11 0.00 0.00 3.21
5211 5873 2.068519 CTTCTTGTCGCACTGCACATA 58.931 47.619 1.11 0.00 0.00 2.29
5213 5875 2.698803 TCTTGTCGCACTGCACATAAT 58.301 42.857 1.11 0.00 0.00 1.28
5214 5876 3.855858 TCTTGTCGCACTGCACATAATA 58.144 40.909 1.11 0.00 0.00 0.98
5215 5877 3.865164 TCTTGTCGCACTGCACATAATAG 59.135 43.478 1.11 0.60 0.00 1.73
5224 5886 5.220739 GCACTGCACATAATAGTCTCCAAAG 60.221 44.000 0.00 0.00 0.00 2.77
5230 5892 7.828717 TGCACATAATAGTCTCCAAAGATTGAA 59.171 33.333 0.00 0.00 33.08 2.69
5262 5931 4.353383 AGTGTCCTTCCTTCCAGTTAAC 57.647 45.455 0.00 0.00 0.00 2.01
5268 5937 5.412904 GTCCTTCCTTCCAGTTAACTTCATG 59.587 44.000 5.07 0.00 0.00 3.07
5269 5938 4.156739 CCTTCCTTCCAGTTAACTTCATGC 59.843 45.833 5.07 0.00 0.00 4.06
5270 5939 4.640771 TCCTTCCAGTTAACTTCATGCT 57.359 40.909 5.07 0.00 0.00 3.79
5271 5940 4.579869 TCCTTCCAGTTAACTTCATGCTC 58.420 43.478 5.07 0.00 0.00 4.26
5272 5941 3.691609 CCTTCCAGTTAACTTCATGCTCC 59.308 47.826 5.07 0.00 0.00 4.70
5326 6006 4.498241 TCTTGATTTGAGACACAGATCGG 58.502 43.478 0.00 0.00 41.25 4.18
5442 6123 3.803082 CTGCCCATCGCCAACGTG 61.803 66.667 0.00 0.00 41.18 4.49
5649 6330 3.507290 GAGGACTACGTCGACCCC 58.493 66.667 10.58 3.88 32.65 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 4.753662 TGGCGAGGTAGACGGGCT 62.754 66.667 0.00 0.00 0.00 5.19
68 69 4.509737 GTGGCGAGGTAGACGGGC 62.510 72.222 0.00 0.00 0.00 6.13
86 106 4.697756 TTGAAGACCAGGGCGGCG 62.698 66.667 0.51 0.51 39.03 6.46
472 498 1.981256 AAAATCAAGGGTCACGCACT 58.019 45.000 0.00 0.00 0.00 4.40
483 509 5.717119 CCTCATCCCTTGTCAAAAATCAAG 58.283 41.667 0.00 0.00 40.19 3.02
484 510 4.021192 GCCTCATCCCTTGTCAAAAATCAA 60.021 41.667 0.00 0.00 0.00 2.57
485 511 3.511146 GCCTCATCCCTTGTCAAAAATCA 59.489 43.478 0.00 0.00 0.00 2.57
522 563 0.685097 AGGGCGCTCTGTAGAAACAA 59.315 50.000 10.28 0.00 34.49 2.83
523 564 0.685097 AAGGGCGCTCTGTAGAAACA 59.315 50.000 12.52 0.00 0.00 2.83
524 565 1.079503 CAAGGGCGCTCTGTAGAAAC 58.920 55.000 12.52 0.00 0.00 2.78
525 566 0.685097 ACAAGGGCGCTCTGTAGAAA 59.315 50.000 12.52 0.00 0.00 2.52
526 567 0.685097 AACAAGGGCGCTCTGTAGAA 59.315 50.000 12.52 0.00 0.00 2.10
527 568 0.037326 CAACAAGGGCGCTCTGTAGA 60.037 55.000 12.52 0.00 0.00 2.59
536 577 2.480419 CTCTCTGTAAACAACAAGGGCG 59.520 50.000 0.00 0.00 37.74 6.13
640 922 4.038402 ACAAGGGAACAGAGAAGCAAATTG 59.962 41.667 0.00 0.00 0.00 2.32
777 1063 3.703001 ACACCAAGTCCCTACAGAATG 57.297 47.619 0.00 0.00 46.00 2.67
848 1156 5.391312 ACAAGAAACCCATTTCAGCATAC 57.609 39.130 2.86 0.00 45.78 2.39
850 1158 5.625197 GCATACAAGAAACCCATTTCAGCAT 60.625 40.000 2.86 0.00 45.78 3.79
861 1169 5.643379 TGAATTCCAGCATACAAGAAACC 57.357 39.130 2.27 0.00 0.00 3.27
866 1174 8.407832 TCATACAAATGAATTCCAGCATACAAG 58.592 33.333 2.27 0.00 39.20 3.16
1032 1441 2.342279 TTCGTGGGAAGAGCACCG 59.658 61.111 0.00 0.00 0.00 4.94
1046 1455 2.983879 ATGACCTTGGGGGCCTTCG 61.984 63.158 0.84 0.00 40.82 3.79
1105 1514 0.962356 CTTGCCGGCACCTCTGAAAT 60.962 55.000 32.95 0.00 0.00 2.17
1222 1631 0.916086 TTGTCCACCTATTCCGCCAT 59.084 50.000 0.00 0.00 0.00 4.40
1244 1673 9.687210 CCCACTTAAAACCTTTAAATAGACAAC 57.313 33.333 0.00 0.00 0.00 3.32
1272 1704 7.340232 CCATCTTCTTTTCATCATCCCAAAGTA 59.660 37.037 0.00 0.00 0.00 2.24
1288 1720 6.665680 TCTCTTCTAGCACTACCATCTTCTTT 59.334 38.462 0.00 0.00 0.00 2.52
1347 1779 0.554305 TATGGGCTAGGGTCGAGTCA 59.446 55.000 0.00 0.00 0.00 3.41
1371 1803 1.689233 ATGGGCCTGGTAAGCGAGA 60.689 57.895 4.53 0.00 0.00 4.04
1404 1837 1.340991 ACTGAACTTGCAACACCCTGT 60.341 47.619 0.00 0.00 0.00 4.00
1538 1981 2.881074 CAAGTACTGACATCCGAGTGG 58.119 52.381 0.00 0.00 0.00 4.00
1804 2252 1.740025 CCCAGCAAGTCGGAGAATTTC 59.260 52.381 0.00 0.00 44.79 2.17
1814 2262 1.200948 GACAAGCAATCCCAGCAAGTC 59.799 52.381 0.00 0.00 33.31 3.01
1853 2301 0.529378 ACGGTGCTACTAAAGGACGG 59.471 55.000 3.33 3.33 46.95 4.79
1866 2314 2.253603 GCTGAATTTCAATCACGGTGC 58.746 47.619 2.51 0.00 0.00 5.01
1966 2414 1.468985 TCTCCAGTAGCTCTGTCTGC 58.531 55.000 10.86 0.00 42.19 4.26
1968 2416 2.099405 GCTTCTCCAGTAGCTCTGTCT 58.901 52.381 10.86 0.00 42.19 3.41
2006 2454 3.623060 CGGCACAGTTCAACTAGCATAAT 59.377 43.478 14.20 0.00 32.23 1.28
2029 2477 3.689347 TGAACCAGGGACATCAAATGAG 58.311 45.455 0.00 0.00 0.00 2.90
2226 2678 3.202818 ACTGATATGCCCAAATCACCTGA 59.797 43.478 0.00 0.00 0.00 3.86
2315 2767 9.962783 CTTAACCTAACATGTAGAGGTATACAC 57.037 37.037 25.28 0.00 42.93 2.90
2442 2894 4.574674 TCACCACCAGATAGATTTGCTT 57.425 40.909 0.00 0.00 0.00 3.91
2623 3082 9.451206 AAATGGGGAAAATAAATATGTGGAGAT 57.549 29.630 0.00 0.00 0.00 2.75
2642 3101 3.323403 TGCAGTAGTTTGGAAAAATGGGG 59.677 43.478 0.00 0.00 0.00 4.96
2696 3155 3.764434 TCTGCTTCCTCTTGACTACGAAT 59.236 43.478 0.00 0.00 0.00 3.34
2699 3158 3.443037 CATCTGCTTCCTCTTGACTACG 58.557 50.000 0.00 0.00 0.00 3.51
2763 3222 3.024547 CCTGTCTTGTTATCCCTCGAGA 58.975 50.000 15.71 0.00 0.00 4.04
2766 3225 2.496070 TGTCCTGTCTTGTTATCCCTCG 59.504 50.000 0.00 0.00 0.00 4.63
2775 3234 2.571212 TCGCAAATTGTCCTGTCTTGT 58.429 42.857 0.00 0.00 0.00 3.16
2778 3237 2.154462 CCTTCGCAAATTGTCCTGTCT 58.846 47.619 0.00 0.00 0.00 3.41
2779 3238 2.151202 TCCTTCGCAAATTGTCCTGTC 58.849 47.619 0.00 0.00 0.00 3.51
2780 3239 2.270352 TCCTTCGCAAATTGTCCTGT 57.730 45.000 0.00 0.00 0.00 4.00
2781 3240 2.293122 TGTTCCTTCGCAAATTGTCCTG 59.707 45.455 0.00 0.00 0.00 3.86
2782 3241 2.582052 TGTTCCTTCGCAAATTGTCCT 58.418 42.857 0.00 0.00 0.00 3.85
2784 3243 2.726241 GCTTGTTCCTTCGCAAATTGTC 59.274 45.455 0.00 0.00 0.00 3.18
2785 3244 2.362077 AGCTTGTTCCTTCGCAAATTGT 59.638 40.909 0.00 0.00 0.00 2.71
2787 3246 4.846779 TTAGCTTGTTCCTTCGCAAATT 57.153 36.364 0.00 0.00 0.00 1.82
2788 3247 4.546570 GTTTAGCTTGTTCCTTCGCAAAT 58.453 39.130 0.00 0.00 0.00 2.32
2789 3248 3.243267 GGTTTAGCTTGTTCCTTCGCAAA 60.243 43.478 0.00 0.00 0.00 3.68
2790 3249 2.292292 GGTTTAGCTTGTTCCTTCGCAA 59.708 45.455 0.00 0.00 0.00 4.85
2791 3250 1.877443 GGTTTAGCTTGTTCCTTCGCA 59.123 47.619 0.00 0.00 0.00 5.10
2792 3251 2.095718 CAGGTTTAGCTTGTTCCTTCGC 60.096 50.000 0.00 0.00 0.00 4.70
2793 3252 2.484264 CCAGGTTTAGCTTGTTCCTTCG 59.516 50.000 0.00 0.00 0.00 3.79
2794 3253 2.820197 CCCAGGTTTAGCTTGTTCCTTC 59.180 50.000 0.00 0.00 0.00 3.46
2795 3254 2.876581 CCCAGGTTTAGCTTGTTCCTT 58.123 47.619 0.00 0.00 0.00 3.36
2796 3255 1.547901 GCCCAGGTTTAGCTTGTTCCT 60.548 52.381 0.00 0.00 0.00 3.36
2797 3256 0.888619 GCCCAGGTTTAGCTTGTTCC 59.111 55.000 0.00 0.00 0.00 3.62
2798 3257 0.888619 GGCCCAGGTTTAGCTTGTTC 59.111 55.000 0.00 0.00 0.00 3.18
2799 3258 0.482887 AGGCCCAGGTTTAGCTTGTT 59.517 50.000 0.00 0.00 0.00 2.83
2800 3259 0.482887 AAGGCCCAGGTTTAGCTTGT 59.517 50.000 0.00 0.00 0.00 3.16
2801 3260 1.632589 AAAGGCCCAGGTTTAGCTTG 58.367 50.000 0.00 0.00 0.00 4.01
2802 3261 1.970640 CAAAAGGCCCAGGTTTAGCTT 59.029 47.619 0.00 0.00 0.00 3.74
2803 3262 1.146982 TCAAAAGGCCCAGGTTTAGCT 59.853 47.619 0.00 0.00 0.00 3.32
2804 3263 1.627864 TCAAAAGGCCCAGGTTTAGC 58.372 50.000 0.00 0.00 0.00 3.09
2805 3264 2.562738 CCTTCAAAAGGCCCAGGTTTAG 59.437 50.000 0.00 0.00 42.78 1.85
2806 3265 2.604139 CCTTCAAAAGGCCCAGGTTTA 58.396 47.619 0.00 0.00 42.78 2.01
2807 3266 1.423584 CCTTCAAAAGGCCCAGGTTT 58.576 50.000 0.00 0.00 42.78 3.27
2808 3267 3.147826 CCTTCAAAAGGCCCAGGTT 57.852 52.632 0.00 0.00 42.78 3.50
2809 3268 4.952482 CCTTCAAAAGGCCCAGGT 57.048 55.556 0.00 0.00 42.78 4.00
2817 3276 4.156008 CGGAGTCATTTACCCCTTCAAAAG 59.844 45.833 0.00 0.00 0.00 2.27
2818 3277 4.076394 CGGAGTCATTTACCCCTTCAAAA 58.924 43.478 0.00 0.00 0.00 2.44
2819 3278 3.681593 CGGAGTCATTTACCCCTTCAAA 58.318 45.455 0.00 0.00 0.00 2.69
2820 3279 2.617021 GCGGAGTCATTTACCCCTTCAA 60.617 50.000 0.00 0.00 0.00 2.69
2821 3280 1.065709 GCGGAGTCATTTACCCCTTCA 60.066 52.381 0.00 0.00 0.00 3.02
2822 3281 1.664873 GCGGAGTCATTTACCCCTTC 58.335 55.000 0.00 0.00 0.00 3.46
2823 3282 0.107848 CGCGGAGTCATTTACCCCTT 60.108 55.000 0.00 0.00 0.00 3.95
2824 3283 1.262640 ACGCGGAGTCATTTACCCCT 61.263 55.000 12.47 0.00 0.00 4.79
2825 3284 0.392060 AACGCGGAGTCATTTACCCC 60.392 55.000 12.47 0.00 0.00 4.95
2826 3285 0.725117 CAACGCGGAGTCATTTACCC 59.275 55.000 12.47 0.00 0.00 3.69
2930 3389 6.744537 GTGTCATCATTCTCAACATTGCTAAC 59.255 38.462 0.00 0.00 0.00 2.34
2951 3410 1.134521 TGAAGCCACCATATCCGTGTC 60.135 52.381 0.11 0.00 0.00 3.67
2952 3411 0.908910 TGAAGCCACCATATCCGTGT 59.091 50.000 0.11 0.00 0.00 4.49
2964 3423 4.647424 ATGTTTTTCTTCGTTGAAGCCA 57.353 36.364 1.69 0.00 39.29 4.75
2990 3449 5.467035 TGGATTGCCTTTTTCTTGGTAAG 57.533 39.130 0.00 0.00 31.89 2.34
3165 3625 8.514594 CCAAAATAGATGACAGTTCTAGCAAAA 58.485 33.333 0.00 0.00 0.00 2.44
3193 3653 3.571590 ACATACCAAACCAGCCTTTTCA 58.428 40.909 0.00 0.00 0.00 2.69
3199 3659 7.221450 TGTAATATCTACATACCAAACCAGCC 58.779 38.462 0.00 0.00 0.00 4.85
3210 3670 7.663905 GCACCACCCAAATGTAATATCTACATA 59.336 37.037 9.51 0.00 37.18 2.29
3219 3679 2.562298 CACTGCACCACCCAAATGTAAT 59.438 45.455 0.00 0.00 0.00 1.89
3222 3682 0.396974 ACACTGCACCACCCAAATGT 60.397 50.000 0.00 0.00 0.00 2.71
3296 3756 5.536161 AGGACATTAGCGCATAATTTGGAAT 59.464 36.000 11.47 0.00 31.40 3.01
3310 3770 9.007901 AGCAATGATCTATAAAAGGACATTAGC 57.992 33.333 0.00 0.00 33.47 3.09
3357 3817 5.346270 AGAACTAATCCCACCTCTCTCTTT 58.654 41.667 0.00 0.00 0.00 2.52
3360 3820 5.423931 AGAAAGAACTAATCCCACCTCTCTC 59.576 44.000 0.00 0.00 0.00 3.20
3362 3822 5.685520 AGAAAGAACTAATCCCACCTCTC 57.314 43.478 0.00 0.00 0.00 3.20
3411 3875 8.796475 ACAAACTTGTTGTATCATCTAAGCAAT 58.204 29.630 0.00 0.00 38.47 3.56
3421 3885 5.299028 ACATCAGCACAAACTTGTTGTATCA 59.701 36.000 0.00 0.00 39.91 2.15
3451 3945 8.260114 ACAAAGAAAATTTATGCCCTCCTTATG 58.740 33.333 0.00 0.00 0.00 1.90
3457 3951 9.750125 CCTATAACAAAGAAAATTTATGCCCTC 57.250 33.333 0.00 0.00 0.00 4.30
3512 4012 9.166173 CATAGATTTCGGAAATGGATAGCATAA 57.834 33.333 19.96 0.00 0.00 1.90
3513 4013 8.321353 ACATAGATTTCGGAAATGGATAGCATA 58.679 33.333 19.96 2.04 0.00 3.14
3514 4014 7.170965 ACATAGATTTCGGAAATGGATAGCAT 58.829 34.615 19.96 0.00 0.00 3.79
3515 4015 6.533730 ACATAGATTTCGGAAATGGATAGCA 58.466 36.000 19.96 0.00 0.00 3.49
3523 4023 6.488006 CCCATCTCAACATAGATTTCGGAAAT 59.512 38.462 15.45 15.45 33.87 2.17
3538 4038 0.404040 TGGTTGACCCCCATCTCAAC 59.596 55.000 0.00 2.53 43.75 3.18
3614 4115 8.472007 ACATATTACAAAGGAGAGACTAGAGG 57.528 38.462 0.00 0.00 0.00 3.69
3662 4163 9.886132 TCCTCTAGACATAATTTTACCTTTCAC 57.114 33.333 0.00 0.00 0.00 3.18
3697 4198 3.455469 GGTGCCTGCTTCCATGGC 61.455 66.667 6.96 0.00 46.26 4.40
3724 4225 2.008329 GCTTGTCTCAGCTCATCCTTG 58.992 52.381 0.00 0.00 36.79 3.61
3851 4356 8.103948 AGTCATCTAAAATTGGTGAAGACAAG 57.896 34.615 10.56 0.00 31.94 3.16
3856 4361 8.359642 TCCAAAAGTCATCTAAAATTGGTGAAG 58.640 33.333 0.00 0.00 37.63 3.02
3935 4441 9.932699 CAGAAAAGATTTGCAGATATCAACTAG 57.067 33.333 5.32 0.00 0.00 2.57
3936 4442 9.671279 TCAGAAAAGATTTGCAGATATCAACTA 57.329 29.630 5.32 0.00 0.00 2.24
3937 4443 8.571461 TCAGAAAAGATTTGCAGATATCAACT 57.429 30.769 5.32 0.00 0.00 3.16
3986 4492 5.195001 TGAACAAATCCTTGCCAAAGTAC 57.805 39.130 0.00 0.00 35.84 2.73
4007 4513 1.734465 CTTACCAGCGGCTTTCTCTTG 59.266 52.381 0.00 0.00 0.00 3.02
4008 4514 1.339151 CCTTACCAGCGGCTTTCTCTT 60.339 52.381 0.00 0.00 0.00 2.85
4066 4572 0.108424 CACTTCCTTCCTCTCAGCCG 60.108 60.000 0.00 0.00 0.00 5.52
4113 4619 1.202348 GGCAGCTTGTTCGGCTTTTAT 59.798 47.619 0.00 0.00 38.03 1.40
4121 4627 1.165907 TGTCCTTGGCAGCTTGTTCG 61.166 55.000 0.00 0.00 0.00 3.95
4185 4694 4.094590 GTCTGGATCAGCTTCAACTTCATG 59.905 45.833 0.00 0.00 0.00 3.07
4201 4710 5.511545 GCATCCTTAGATTTACCGTCTGGAT 60.512 44.000 0.00 0.00 39.21 3.41
4208 4717 6.538742 TCTTTTCAGCATCCTTAGATTTACCG 59.461 38.462 0.00 0.00 0.00 4.02
4238 4747 7.097192 CACCTTCTTCACTACTATTGCTGTTA 58.903 38.462 0.00 0.00 0.00 2.41
4287 4796 1.202818 GCTGTTTCCCTTCTCACCAGT 60.203 52.381 0.00 0.00 0.00 4.00
4316 4825 1.999735 TCTTGTAAATTCTCAGCGGCG 59.000 47.619 0.51 0.51 0.00 6.46
4325 4834 6.515272 TCTGCCTTTCCATCTTGTAAATTC 57.485 37.500 0.00 0.00 0.00 2.17
4361 4870 4.457257 CCATCACTGTTTCCTTTCTTCCTC 59.543 45.833 0.00 0.00 0.00 3.71
4372 4881 3.451141 TGCCAAAACCATCACTGTTTC 57.549 42.857 0.00 0.00 34.97 2.78
4374 4883 2.102925 CCTTGCCAAAACCATCACTGTT 59.897 45.455 0.00 0.00 0.00 3.16
4375 4884 1.688197 CCTTGCCAAAACCATCACTGT 59.312 47.619 0.00 0.00 0.00 3.55
4376 4885 1.962807 TCCTTGCCAAAACCATCACTG 59.037 47.619 0.00 0.00 0.00 3.66
4377 4886 2.380064 TCCTTGCCAAAACCATCACT 57.620 45.000 0.00 0.00 0.00 3.41
4378 4887 3.328505 CAATCCTTGCCAAAACCATCAC 58.671 45.455 0.00 0.00 0.00 3.06
4379 4888 3.681593 CAATCCTTGCCAAAACCATCA 57.318 42.857 0.00 0.00 0.00 3.07
4445 4954 6.774656 CAGCTTTACCATCTCCCAATATTTCT 59.225 38.462 0.00 0.00 0.00 2.52
4455 4964 3.127721 GCAGTTTCAGCTTTACCATCTCC 59.872 47.826 0.00 0.00 0.00 3.71
4477 4986 3.350912 GTGTTACCGCTGCAATTATTCG 58.649 45.455 0.00 0.00 0.00 3.34
4489 5001 0.828677 ACCTCCTATGGTGTTACCGC 59.171 55.000 0.00 0.00 42.58 5.68
4525 5037 0.813210 CCTGCCTTCTTCAGATCCGC 60.813 60.000 0.00 0.00 33.54 5.54
4659 5186 2.091278 CCATAGGGGATAGGGCGATCTA 60.091 54.545 0.00 0.00 40.01 1.98
4664 5191 1.983224 CACCATAGGGGATAGGGCG 59.017 63.158 0.00 0.00 39.01 6.13
4665 5192 0.842467 AGCACCATAGGGGATAGGGC 60.842 60.000 0.00 0.00 39.01 5.19
4676 5203 4.849518 TGCCACATTTAGTTAGCACCATA 58.150 39.130 0.00 0.00 33.28 2.74
4714 5241 4.751600 TCGCTTCAGTAATCATATTGCCTG 59.248 41.667 0.00 0.00 0.00 4.85
4739 5266 1.007387 CGACCATCATCATCCGCGA 60.007 57.895 8.23 0.00 0.00 5.87
4744 5271 0.315251 TCCGCTCGACCATCATCATC 59.685 55.000 0.00 0.00 0.00 2.92
4746 5273 0.103026 CTTCCGCTCGACCATCATCA 59.897 55.000 0.00 0.00 0.00 3.07
4770 5297 1.608590 ACATCAGTTTTGGTGCCTTCG 59.391 47.619 0.00 0.00 39.10 3.79
4778 5305 4.520492 AGCTTCAACCTACATCAGTTTTGG 59.480 41.667 0.00 0.00 0.00 3.28
4779 5306 5.455392 CAGCTTCAACCTACATCAGTTTTG 58.545 41.667 0.00 0.00 0.00 2.44
4781 5308 3.503748 GCAGCTTCAACCTACATCAGTTT 59.496 43.478 0.00 0.00 0.00 2.66
4784 5311 2.983229 AGCAGCTTCAACCTACATCAG 58.017 47.619 0.00 0.00 0.00 2.90
4801 5337 4.759693 AGTTTTCACATCGTCCATAAAGCA 59.240 37.500 0.00 0.00 0.00 3.91
4802 5338 5.088739 CAGTTTTCACATCGTCCATAAAGC 58.911 41.667 0.00 0.00 0.00 3.51
4807 5343 4.326826 ACATCAGTTTTCACATCGTCCAT 58.673 39.130 0.00 0.00 0.00 3.41
4885 5446 3.326747 GAAGGTCGATACAACAAGCACT 58.673 45.455 0.00 0.00 0.00 4.40
4918 5527 4.319839 GCAAGGAAAAGGAAAGACTCTTCG 60.320 45.833 0.00 0.00 0.00 3.79
4978 5591 0.457443 GCCCATTGGAGTAAAGCAGC 59.543 55.000 3.62 0.00 0.00 5.25
5040 5664 1.393539 CACATTCCACAACCGTCGATC 59.606 52.381 0.00 0.00 0.00 3.69
5053 5677 0.537143 TGTGCCACCTGTCACATTCC 60.537 55.000 0.00 0.00 38.18 3.01
5054 5678 3.019964 TGTGCCACCTGTCACATTC 57.980 52.632 0.00 0.00 38.18 2.67
5074 5698 1.278238 CCGTTGGTCTGTCGATAAGC 58.722 55.000 0.00 0.00 0.00 3.09
5084 5708 2.113139 CAACCCAGCCGTTGGTCT 59.887 61.111 0.09 0.00 46.25 3.85
5098 5722 1.941812 CTGTGAACGTGGAGCCAAC 59.058 57.895 0.00 0.00 0.00 3.77
5199 5861 2.797156 GGAGACTATTATGTGCAGTGCG 59.203 50.000 11.20 0.00 0.00 5.34
5211 5873 9.014297 ACGAAAATTCAATCTTTGGAGACTATT 57.986 29.630 0.00 0.00 33.99 1.73
5213 5875 7.979444 ACGAAAATTCAATCTTTGGAGACTA 57.021 32.000 0.00 0.00 33.99 2.59
5214 5876 6.884280 ACGAAAATTCAATCTTTGGAGACT 57.116 33.333 0.00 0.00 33.99 3.24
5215 5877 7.581476 TGTACGAAAATTCAATCTTTGGAGAC 58.419 34.615 0.00 0.00 33.99 3.36
5224 5886 6.899114 AGGACACTTGTACGAAAATTCAATC 58.101 36.000 0.00 0.00 33.01 2.67
5230 5892 4.969484 AGGAAGGACACTTGTACGAAAAT 58.031 39.130 0.00 0.00 36.97 1.82
5272 5941 2.483363 CCACTCTAGCCTGATCAAGCAG 60.483 54.545 18.29 12.73 35.66 4.24
5326 6006 4.247380 CGGCATGGCTCCTCTCCC 62.247 72.222 18.09 0.00 0.00 4.30
5442 6123 0.942962 CCTTCTTCATGATGCGGCTC 59.057 55.000 0.00 0.00 0.00 4.70
5604 6285 2.273449 GTGGTCATGGCCCAGAGG 59.727 66.667 15.27 0.00 31.13 3.69


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

AutoCloner maintained by Alex Coulton.