Multiple sequence alignment - TraesCS3D01G045400

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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 TraesCS3D01G045400 chr3D 100.000 5389 0 0 1 5389 17373378 17378766 0.000000e+00 9952.0
1 TraesCS3D01G045400 chr3D 88.715 2109 186 31 2625 4709 17515372 17513292 0.000000e+00 2529.0
2 TraesCS3D01G045400 chr3D 83.751 1797 225 44 2625 4387 17643994 17642231 0.000000e+00 1639.0
3 TraesCS3D01G045400 chr3D 87.896 1421 128 31 2994 4387 11354285 11355688 0.000000e+00 1631.0
4 TraesCS3D01G045400 chr3D 78.723 2397 287 90 22 2300 17646350 17644059 0.000000e+00 1395.0
5 TraesCS3D01G045400 chr3D 84.868 1249 132 33 858 2057 17516952 17515712 0.000000e+00 1206.0
6 TraesCS3D01G045400 chr3D 82.011 567 79 14 173 739 11351526 11352069 1.370000e-125 460.0
7 TraesCS3D01G045400 chr3D 79.204 553 64 24 1850 2384 11353197 11353716 2.400000e-88 337.0
8 TraesCS3D01G045400 chr3D 78.673 211 28 12 2650 2854 11354002 11354201 2.040000e-24 124.0
9 TraesCS3D01G045400 chr3D 89.011 91 10 0 4707 4797 11355572 11355662 4.410000e-21 113.0
10 TraesCS3D01G045400 chr3D 87.302 63 4 3 5029 5087 17626278 17626216 9.690000e-08 69.4
11 TraesCS3D01G045400 chr3D 96.774 31 1 0 4812 4842 153800132 153800162 1.000000e-02 52.8
12 TraesCS3D01G045400 chr3A 89.307 4779 354 70 1 4691 19475794 19471085 0.000000e+00 5849.0
13 TraesCS3D01G045400 chr3A 85.607 4002 359 111 858 4706 19371143 19375080 0.000000e+00 3999.0
14 TraesCS3D01G045400 chr3A 84.563 1898 219 43 2538 4387 25934372 25932501 0.000000e+00 1814.0
15 TraesCS3D01G045400 chr3A 92.157 969 76 0 3419 4387 19306923 19307891 0.000000e+00 1369.0
16 TraesCS3D01G045400 chr3A 85.515 718 97 7 1028 1739 26396035 26396751 0.000000e+00 743.0
17 TraesCS3D01G045400 chr3A 86.128 656 86 5 1083 1736 26469246 26469898 0.000000e+00 702.0
18 TraesCS3D01G045400 chr3A 80.579 829 118 28 2538 3349 19306011 19306813 2.780000e-167 599.0
19 TraesCS3D01G045400 chr3A 85.267 543 57 13 44 585 19303440 19303960 6.140000e-149 538.0
20 TraesCS3D01G045400 chr3A 82.937 463 53 9 309 757 25937407 25936957 1.410000e-105 394.0
21 TraesCS3D01G045400 chr3A 79.245 583 90 19 24 588 26448361 26448930 1.420000e-100 377.0
22 TraesCS3D01G045400 chr3A 82.353 323 49 6 265 586 26419665 26419980 1.910000e-69 274.0
23 TraesCS3D01G045400 chr3A 83.128 243 25 5 1828 2059 25935299 25935062 1.970000e-49 207.0
24 TraesCS3D01G045400 chr3A 89.116 147 8 2 4675 4813 19470854 19470708 5.550000e-40 176.0
25 TraesCS3D01G045400 chr3A 80.303 264 24 15 1849 2094 19305136 19305389 2.000000e-39 174.0
26 TraesCS3D01G045400 chr3B 89.080 2097 200 22 2630 4706 27518183 27520270 0.000000e+00 2577.0
27 TraesCS3D01G045400 chr3B 92.673 1788 85 22 3436 5198 24943724 24945490 0.000000e+00 2534.0
28 TraesCS3D01G045400 chr3B 92.084 1377 77 19 1023 2378 24941531 24942896 0.000000e+00 1910.0
29 TraesCS3D01G045400 chr3B 82.916 1399 146 36 983 2324 27516703 27518065 0.000000e+00 1173.0
30 TraesCS3D01G045400 chr3B 85.801 993 108 14 1 980 24940580 24941552 0.000000e+00 1022.0
31 TraesCS3D01G045400 chr3B 85.307 701 100 3 1037 1736 30231887 30232585 0.000000e+00 721.0
32 TraesCS3D01G045400 chr3B 82.413 779 65 30 2580 3339 24942935 24943660 9.920000e-172 614.0
33 TraesCS3D01G045400 chr3B 86.313 358 45 4 1083 1438 29622823 29623178 2.350000e-103 387.0
34 TraesCS3D01G045400 chr3B 81.971 416 61 12 178 586 30506686 30507094 1.860000e-89 340.0
35 TraesCS3D01G045400 chr3B 76.047 597 116 19 2 581 29730424 29731010 8.830000e-73 285.0
36 TraesCS3D01G045400 chrUn 88.810 1269 123 13 3124 4387 354553079 354551825 0.000000e+00 1539.0
37 TraesCS3D01G045400 chrUn 82.759 754 95 15 1 739 37954501 37955234 1.640000e-179 640.0
38 TraesCS3D01G045400 chrUn 82.695 757 96 15 1 742 340707431 340706695 1.640000e-179 640.0
39 TraesCS3D01G045400 chr6D 78.620 594 102 20 39 621 2051337 2050758 2.370000e-98 370.0
40 TraesCS3D01G045400 chr4A 93.989 183 9 1 5209 5389 273660314 273660496 5.320000e-70 276.0
41 TraesCS3D01G045400 chr4A 96.970 33 1 0 4813 4845 179466088 179466056 7.540000e-04 56.5
42 TraesCS3D01G045400 chr7A 92.899 169 12 0 5208 5376 134712440 134712608 4.170000e-61 246.0
43 TraesCS3D01G045400 chr2A 100.000 31 0 0 4812 4842 610726481 610726511 2.100000e-04 58.4
44 TraesCS3D01G045400 chr1B 100.000 31 0 0 4812 4842 181573342 181573372 2.100000e-04 58.4
45 TraesCS3D01G045400 chr1A 100.000 31 0 0 4812 4842 454685793 454685823 2.100000e-04 58.4
46 TraesCS3D01G045400 chr5B 96.970 33 1 0 4813 4845 211385031 211384999 7.540000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G045400 chr3D 17373378 17378766 5388 False 9952.0 9952 100.000000 1 5389 1 chr3D.!!$F1 5388
1 TraesCS3D01G045400 chr3D 17513292 17516952 3660 True 1867.5 2529 86.791500 858 4709 2 chr3D.!!$R2 3851
2 TraesCS3D01G045400 chr3D 17642231 17646350 4119 True 1517.0 1639 81.237000 22 4387 2 chr3D.!!$R3 4365
3 TraesCS3D01G045400 chr3D 11351526 11355688 4162 False 533.0 1631 83.359000 173 4797 5 chr3D.!!$F3 4624
4 TraesCS3D01G045400 chr3A 19371143 19375080 3937 False 3999.0 3999 85.607000 858 4706 1 chr3A.!!$F1 3848
5 TraesCS3D01G045400 chr3A 19470708 19475794 5086 True 3012.5 5849 89.211500 1 4813 2 chr3A.!!$R1 4812
6 TraesCS3D01G045400 chr3A 25932501 25937407 4906 True 805.0 1814 83.542667 309 4387 3 chr3A.!!$R2 4078
7 TraesCS3D01G045400 chr3A 26396035 26396751 716 False 743.0 743 85.515000 1028 1739 1 chr3A.!!$F2 711
8 TraesCS3D01G045400 chr3A 26469246 26469898 652 False 702.0 702 86.128000 1083 1736 1 chr3A.!!$F5 653
9 TraesCS3D01G045400 chr3A 19303440 19307891 4451 False 670.0 1369 84.576500 44 4387 4 chr3A.!!$F6 4343
10 TraesCS3D01G045400 chr3A 26448361 26448930 569 False 377.0 377 79.245000 24 588 1 chr3A.!!$F4 564
11 TraesCS3D01G045400 chr3B 27516703 27520270 3567 False 1875.0 2577 85.998000 983 4706 2 chr3B.!!$F6 3723
12 TraesCS3D01G045400 chr3B 24940580 24945490 4910 False 1520.0 2534 88.242750 1 5198 4 chr3B.!!$F5 5197
13 TraesCS3D01G045400 chr3B 30231887 30232585 698 False 721.0 721 85.307000 1037 1736 1 chr3B.!!$F3 699
14 TraesCS3D01G045400 chr3B 29730424 29731010 586 False 285.0 285 76.047000 2 581 1 chr3B.!!$F2 579
15 TraesCS3D01G045400 chrUn 354551825 354553079 1254 True 1539.0 1539 88.810000 3124 4387 1 chrUn.!!$R2 1263
16 TraesCS3D01G045400 chrUn 37954501 37955234 733 False 640.0 640 82.759000 1 739 1 chrUn.!!$F1 738
17 TraesCS3D01G045400 chrUn 340706695 340707431 736 True 640.0 640 82.695000 1 742 1 chrUn.!!$R1 741
18 TraesCS3D01G045400 chr6D 2050758 2051337 579 True 370.0 370 78.620000 39 621 1 chr6D.!!$R1 582

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
363 391 0.394938 TTCTACAACTGCGCCAGGAA 59.605 50.000 4.18 0.0 35.51 3.36 F
680 732 1.074405 ACAATCTGGCCTCAGCTTCAA 59.926 47.619 3.32 0.0 40.69 2.69 F
968 1542 1.202268 CGTTAACTAGTCCTCGCCAGG 60.202 57.143 3.71 0.0 42.01 4.45 F
1395 2005 1.372997 GCTGCTCGTCCTCGACAAA 60.373 57.895 0.00 0.0 41.35 2.83 F
3133 4682 1.333791 GCACCAACGAAAGAGGAAACG 60.334 52.381 0.00 0.0 34.71 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 3198 0.163788 CGCATCGATCGGGCAATTAC 59.836 55.0 24.94 4.54 0.00 1.89 R
2175 3209 0.597637 AAGTAAGCGCATCGATCGGG 60.598 55.0 16.41 9.28 0.00 5.14 R
2435 3772 0.610232 AAGCTAGCTTGGTGCCTTGG 60.610 55.0 28.83 0.00 44.23 3.61 R
3147 4696 0.716108 CCACTTCGCATCAACTCGTC 59.284 55.0 0.00 0.00 0.00 4.20 R
4778 6669 0.603569 CGAGTGGCTAGTTGACTGGT 59.396 55.0 0.00 0.00 0.00 4.00 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
75 88 3.423154 CGTCTCAGCCCCGTTTGC 61.423 66.667 0.00 0.00 0.00 3.68
80 93 3.508840 CAGCCCCGTTTGCGATCC 61.509 66.667 0.00 0.00 41.33 3.36
154 170 2.042831 CGACGACGTCCCCTACCTT 61.043 63.158 21.63 0.00 34.56 3.50
163 179 2.425392 CGTCCCCTACCTTGGGTACTAT 60.425 54.545 0.00 0.00 45.70 2.12
170 186 0.464036 CCTTGGGTACTATGAGCGCA 59.536 55.000 11.47 0.00 0.00 6.09
324 352 1.115467 CCTCCGTTCTACATGAGCCT 58.885 55.000 0.00 0.00 0.00 4.58
363 391 0.394938 TTCTACAACTGCGCCAGGAA 59.605 50.000 4.18 0.00 35.51 3.36
680 732 1.074405 ACAATCTGGCCTCAGCTTCAA 59.926 47.619 3.32 0.00 40.69 2.69
688 744 5.309020 TCTGGCCTCAGCTTCAATTATCTAT 59.691 40.000 3.32 0.00 40.69 1.98
689 745 5.311265 TGGCCTCAGCTTCAATTATCTATG 58.689 41.667 3.32 0.00 39.73 2.23
855 920 8.664798 GGGACACTAATTAAAAATTGGAAATGC 58.335 33.333 3.17 0.00 0.00 3.56
884 949 1.445871 TAGCGCGTTGACTCTGACTA 58.554 50.000 8.43 0.00 0.00 2.59
968 1542 1.202268 CGTTAACTAGTCCTCGCCAGG 60.202 57.143 3.71 0.00 42.01 4.45
973 1547 3.278072 TAGTCCTCGCCAGGTCCGT 62.278 63.158 0.00 0.00 41.28 4.69
1113 1708 1.813513 AGAAATGCGGTGACCTGAAG 58.186 50.000 0.00 0.00 0.00 3.02
1208 1806 1.744741 GCAGCCAAGCTCTCCTCAC 60.745 63.158 0.00 0.00 36.40 3.51
1368 1978 1.798223 CCGTTCGTCATCAGCAAGAAA 59.202 47.619 0.00 0.00 0.00 2.52
1395 2005 1.372997 GCTGCTCGTCCTCGACAAA 60.373 57.895 0.00 0.00 41.35 2.83
1506 2148 4.629523 GAACCGGGCGTTGTCCCA 62.630 66.667 6.32 0.00 46.92 4.37
1554 2196 3.370231 CTTGGTTTTCCGGGCGGG 61.370 66.667 0.00 4.42 44.36 6.13
1768 2427 4.202441 CCACCATGAATTTCCCTAGTCAG 58.798 47.826 0.00 0.00 0.00 3.51
1772 2435 6.316390 CACCATGAATTTCCCTAGTCAGTAAC 59.684 42.308 0.00 0.00 0.00 2.50
1793 2456 9.425577 AGTAACTAGTTCTTTGATCAAGCTAAC 57.574 33.333 12.39 13.27 31.70 2.34
1896 2668 4.064388 TCTGACATTGAATCGCTGTCAAA 58.936 39.130 15.33 3.82 46.13 2.69
1954 2746 5.104193 AGGAGGAACATAGAATGCTGATTGT 60.104 40.000 0.00 0.00 0.00 2.71
2098 3108 4.692625 CCTATGGATTCCTAGTCAAATGCG 59.307 45.833 3.95 0.00 0.00 4.73
2168 3198 3.007635 GGTTCCAAACAGACTATTCCCG 58.992 50.000 0.00 0.00 0.00 5.14
2169 3199 3.558533 GGTTCCAAACAGACTATTCCCGT 60.559 47.826 0.00 0.00 0.00 5.28
2170 3200 4.322953 GGTTCCAAACAGACTATTCCCGTA 60.323 45.833 0.00 0.00 0.00 4.02
2174 3208 5.878116 TCCAAACAGACTATTCCCGTAATTG 59.122 40.000 0.00 0.00 0.00 2.32
2175 3209 5.448632 CCAAACAGACTATTCCCGTAATTGC 60.449 44.000 0.00 0.00 0.00 3.56
2245 3388 5.375417 TGTGGAAGTCAATGTTATTGCAG 57.625 39.130 0.00 0.00 0.00 4.41
2271 3418 7.704899 GCTGTTTGTTGTTGAATTAGTTAGGTT 59.295 33.333 0.00 0.00 0.00 3.50
2274 3421 9.673454 GTTTGTTGTTGAATTAGTTAGGTTAGG 57.327 33.333 0.00 0.00 0.00 2.69
2275 3422 7.989416 TGTTGTTGAATTAGTTAGGTTAGGG 57.011 36.000 0.00 0.00 0.00 3.53
2282 3429 7.623630 TGAATTAGTTAGGTTAGGGGTGTAAC 58.376 38.462 0.00 0.00 32.90 2.50
2301 3448 2.912771 ACGTTGAATTGGACACTGTGA 58.087 42.857 15.86 0.00 0.00 3.58
2306 3453 4.241590 TGAATTGGACACTGTGATTTGC 57.758 40.909 15.86 0.00 0.00 3.68
2315 3525 3.004734 ACACTGTGATTTGCTTAAGTGGC 59.995 43.478 15.86 0.00 39.42 5.01
2471 3850 7.796054 AGCTAGCTTCAATGGAACTATCTAAA 58.204 34.615 12.68 0.00 0.00 1.85
2472 3851 8.267894 AGCTAGCTTCAATGGAACTATCTAAAA 58.732 33.333 12.68 0.00 0.00 1.52
2604 4024 3.759581 AGTGTCATGATTGTGGCTTCTT 58.240 40.909 0.00 0.00 0.00 2.52
2641 4063 4.460263 TCCATATATGTTGCCACCTTCAC 58.540 43.478 11.73 0.00 0.00 3.18
2643 4065 5.368230 TCCATATATGTTGCCACCTTCACTA 59.632 40.000 11.73 0.00 0.00 2.74
2725 4155 5.102953 TCAACTTATGTAGAAGCTGGCAT 57.897 39.130 0.00 0.00 0.00 4.40
2737 4167 5.933617 AGAAGCTGGCATAGTTATCATGAA 58.066 37.500 0.00 0.00 0.00 2.57
2740 4174 7.340232 AGAAGCTGGCATAGTTATCATGAAAAA 59.660 33.333 0.00 0.00 0.00 1.94
2785 4219 7.646314 AGTTCTTCTCATTTGTCAAGTGATTG 58.354 34.615 10.82 1.87 0.00 2.67
2786 4220 7.500227 AGTTCTTCTCATTTGTCAAGTGATTGA 59.500 33.333 10.82 4.04 0.00 2.57
2807 4241 9.495754 GATTGATTACTCATACTTCTTGTTTGC 57.504 33.333 0.00 0.00 0.00 3.68
2823 4257 5.351233 TGTTTGCTACTTCATAAACCGTG 57.649 39.130 0.00 0.00 33.33 4.94
2832 4299 9.221775 GCTACTTCATAAACCGTGAAAATATTG 57.778 33.333 0.00 0.00 35.36 1.90
2926 4420 2.030262 GCTGCTCGGCCCATCTAG 59.970 66.667 0.00 0.00 0.00 2.43
2941 4435 4.404715 CCCATCTAGTCCTTCGGTTCTTAA 59.595 45.833 0.00 0.00 0.00 1.85
2958 4453 7.362574 CGGTTCTTAATTCCTTGCTCCAAATTA 60.363 37.037 0.00 0.00 0.00 1.40
2984 4505 4.889995 GCATAATATGGAGAATAAGGGGGC 59.110 45.833 2.13 0.00 0.00 5.80
3078 4615 2.213499 CAGTTGGATCATTAGGCGGTC 58.787 52.381 0.00 0.00 0.00 4.79
3133 4682 1.333791 GCACCAACGAAAGAGGAAACG 60.334 52.381 0.00 0.00 34.71 3.60
3155 4704 1.989165 GCTGTAGCTTCAGACGAGTTG 59.011 52.381 23.06 0.00 37.61 3.16
3278 4827 2.770164 TTAGTGCTTCAAGGGAGCTC 57.230 50.000 4.71 4.71 0.00 4.09
3340 4893 2.017782 TGTTTGCCAAACTCGCTTGTA 58.982 42.857 20.11 0.00 41.90 2.41
3352 4914 7.860872 CCAAACTCGCTTGTAAATCTTAACTTT 59.139 33.333 0.00 0.00 0.00 2.66
3353 4915 8.682016 CAAACTCGCTTGTAAATCTTAACTTTG 58.318 33.333 0.00 0.00 0.00 2.77
3354 4916 6.899114 ACTCGCTTGTAAATCTTAACTTTGG 58.101 36.000 0.00 0.00 0.00 3.28
3357 4919 7.357303 TCGCTTGTAAATCTTAACTTTGGAAC 58.643 34.615 0.00 0.00 0.00 3.62
3358 4920 7.012515 TCGCTTGTAAATCTTAACTTTGGAACA 59.987 33.333 0.00 0.00 0.00 3.18
3359 4921 7.323656 CGCTTGTAAATCTTAACTTTGGAACAG 59.676 37.037 0.00 0.00 42.39 3.16
3360 4922 8.135529 GCTTGTAAATCTTAACTTTGGAACAGT 58.864 33.333 0.00 0.00 42.39 3.55
3386 4980 4.022068 AGAGCTCTGTTCTCAAGTCTCAAG 60.022 45.833 17.42 0.00 33.15 3.02
3390 4984 4.938080 TCTGTTCTCAAGTCTCAAGTGTC 58.062 43.478 0.00 0.00 0.00 3.67
3391 4985 4.402474 TCTGTTCTCAAGTCTCAAGTGTCA 59.598 41.667 0.00 0.00 0.00 3.58
3473 5079 4.883021 ACTCAAGGATGGGAGAGTAGTA 57.117 45.455 0.00 0.00 39.40 1.82
3524 5130 0.670854 GACGGGTTGAGCAGTTCCTC 60.671 60.000 0.00 0.00 0.00 3.71
3591 5197 0.313987 CCTATATGGCTGCACGTCGA 59.686 55.000 0.00 0.00 0.00 4.20
4016 5622 1.276859 TGGACATGAGCAGGAGCCAT 61.277 55.000 0.00 0.00 43.56 4.40
4391 6000 1.813513 ATGCTAGCGGGTTATGATGC 58.186 50.000 10.77 0.00 0.00 3.91
4500 6117 8.630917 TCATCTTACTAATAAGTACAGGCTCAC 58.369 37.037 0.00 0.00 37.94 3.51
4577 6194 3.199946 TGTACTAGGAGCAAATTCCAGGG 59.800 47.826 0.00 0.00 39.84 4.45
4616 6252 5.416947 ACATATAGTCGGTTCAAGTTGACC 58.583 41.667 4.68 9.42 31.75 4.02
4620 6256 2.943033 AGTCGGTTCAAGTTGACCAAAG 59.057 45.455 18.54 4.97 31.75 2.77
4726 6609 1.222115 GAAAGAGGACGCGCACTTGT 61.222 55.000 5.73 0.00 0.00 3.16
4731 6622 2.248431 GACGCGCACTTGTTCACC 59.752 61.111 5.73 0.00 0.00 4.02
4755 6646 1.576421 CCTGCAGTTTTCGCCTGAC 59.424 57.895 13.81 0.00 31.38 3.51
4778 6669 7.072328 TGACTTGGTCATCCATAGATTCCATAA 59.928 37.037 0.00 0.00 43.91 1.90
4790 6681 7.875041 CCATAGATTCCATAACCAGTCAACTAG 59.125 40.741 0.00 0.00 0.00 2.57
4822 6738 5.627499 AGCGTCAAATGCTGAAAAGAATA 57.373 34.783 0.00 0.00 39.36 1.75
4835 6751 0.846693 AAGAATATTGCCGAGGCCCT 59.153 50.000 12.05 1.24 41.09 5.19
4971 6903 9.176460 TGTTATGATCTCTTGTTTGATGCATTA 57.824 29.630 0.00 0.00 0.00 1.90
5021 6953 7.707464 TGATCCTAAATAAACGAGAATACGCAA 59.293 33.333 0.00 0.00 36.70 4.85
5026 6958 2.157834 AACGAGAATACGCAACACCA 57.842 45.000 0.00 0.00 36.70 4.17
5115 7048 4.202673 ACAAGGCCTCAAAGGAAGGAAATA 60.203 41.667 5.23 0.00 37.67 1.40
5130 7063 6.264067 GGAAGGAAATATTCTCATGGGTCTTG 59.736 42.308 0.00 0.00 0.00 3.02
5166 7099 3.031736 TCCTGATGGGTACAGAGCTAAC 58.968 50.000 0.00 0.00 37.54 2.34
5198 7131 9.739276 AAGGAGAATGAATCTTGTTATGTTGTA 57.261 29.630 0.00 0.00 38.96 2.41
5199 7132 9.739276 AGGAGAATGAATCTTGTTATGTTGTAA 57.261 29.630 0.00 0.00 38.96 2.41
5225 7158 8.510132 AAAATTTAGGGAAACGTTTACAATCG 57.490 30.769 24.13 0.00 0.00 3.34
5226 7159 5.610235 TTTAGGGAAACGTTTACAATCGG 57.390 39.130 24.13 0.00 0.00 4.18
5227 7160 1.808343 AGGGAAACGTTTACAATCGGC 59.192 47.619 24.13 6.23 0.00 5.54
5228 7161 1.536331 GGGAAACGTTTACAATCGGCA 59.464 47.619 24.13 0.00 0.00 5.69
5229 7162 2.577450 GGAAACGTTTACAATCGGCAC 58.423 47.619 18.49 0.00 0.00 5.01
5281 7214 2.360350 CGTGCACTCCCAGCCATT 60.360 61.111 16.19 0.00 0.00 3.16
5282 7215 2.401766 CGTGCACTCCCAGCCATTC 61.402 63.158 16.19 0.00 0.00 2.67
5283 7216 1.303561 GTGCACTCCCAGCCATTCA 60.304 57.895 10.32 0.00 0.00 2.57
5284 7217 0.895100 GTGCACTCCCAGCCATTCAA 60.895 55.000 10.32 0.00 0.00 2.69
5285 7218 0.609957 TGCACTCCCAGCCATTCAAG 60.610 55.000 0.00 0.00 0.00 3.02
5286 7219 1.318158 GCACTCCCAGCCATTCAAGG 61.318 60.000 0.00 0.00 0.00 3.61
5287 7220 0.038744 CACTCCCAGCCATTCAAGGT 59.961 55.000 0.00 0.00 0.00 3.50
5288 7221 0.329596 ACTCCCAGCCATTCAAGGTC 59.670 55.000 0.00 0.00 0.00 3.85
5289 7222 0.622665 CTCCCAGCCATTCAAGGTCT 59.377 55.000 0.00 0.00 0.00 3.85
5290 7223 0.329261 TCCCAGCCATTCAAGGTCTG 59.671 55.000 0.00 0.00 34.59 3.51
5291 7224 0.329261 CCCAGCCATTCAAGGTCTGA 59.671 55.000 0.00 0.00 35.91 3.27
5292 7225 1.457346 CCAGCCATTCAAGGTCTGAC 58.543 55.000 0.00 0.00 35.91 3.51
5293 7226 1.271543 CCAGCCATTCAAGGTCTGACA 60.272 52.381 10.38 0.00 35.91 3.58
5294 7227 1.808945 CAGCCATTCAAGGTCTGACAC 59.191 52.381 10.38 0.00 35.91 3.67
5295 7228 0.798776 GCCATTCAAGGTCTGACACG 59.201 55.000 10.38 0.00 32.21 4.49
5296 7229 1.878102 GCCATTCAAGGTCTGACACGT 60.878 52.381 10.38 0.00 32.21 4.49
5297 7230 2.611971 GCCATTCAAGGTCTGACACGTA 60.612 50.000 10.38 0.00 32.21 3.57
5298 7231 3.659786 CCATTCAAGGTCTGACACGTAA 58.340 45.455 10.38 0.00 32.21 3.18
5299 7232 3.679980 CCATTCAAGGTCTGACACGTAAG 59.320 47.826 10.38 0.00 37.24 2.34
5300 7233 3.380479 TTCAAGGTCTGACACGTAAGG 57.620 47.619 10.38 0.00 35.79 2.69
5322 7255 2.634100 GGGGGCCACCTTATCTTCT 58.366 57.895 20.04 0.00 40.03 2.85
5323 7256 0.183731 GGGGGCCACCTTATCTTCTG 59.816 60.000 20.04 0.00 40.03 3.02
5324 7257 0.919710 GGGGCCACCTTATCTTCTGT 59.080 55.000 4.39 0.00 36.80 3.41
5325 7258 1.134068 GGGGCCACCTTATCTTCTGTC 60.134 57.143 4.39 0.00 36.80 3.51
5326 7259 1.134068 GGGCCACCTTATCTTCTGTCC 60.134 57.143 4.39 0.00 0.00 4.02
5327 7260 1.840635 GGCCACCTTATCTTCTGTCCT 59.159 52.381 0.00 0.00 0.00 3.85
5328 7261 2.158885 GGCCACCTTATCTTCTGTCCTC 60.159 54.545 0.00 0.00 0.00 3.71
5329 7262 2.769095 GCCACCTTATCTTCTGTCCTCT 59.231 50.000 0.00 0.00 0.00 3.69
5330 7263 3.181470 GCCACCTTATCTTCTGTCCTCTC 60.181 52.174 0.00 0.00 0.00 3.20
5331 7264 4.285863 CCACCTTATCTTCTGTCCTCTCT 58.714 47.826 0.00 0.00 0.00 3.10
5332 7265 4.340950 CCACCTTATCTTCTGTCCTCTCTC 59.659 50.000 0.00 0.00 0.00 3.20
5333 7266 5.200483 CACCTTATCTTCTGTCCTCTCTCT 58.800 45.833 0.00 0.00 0.00 3.10
5334 7267 5.299279 CACCTTATCTTCTGTCCTCTCTCTC 59.701 48.000 0.00 0.00 0.00 3.20
5335 7268 5.044476 ACCTTATCTTCTGTCCTCTCTCTCA 60.044 44.000 0.00 0.00 0.00 3.27
5336 7269 5.299279 CCTTATCTTCTGTCCTCTCTCTCAC 59.701 48.000 0.00 0.00 0.00 3.51
5337 7270 3.797559 TCTTCTGTCCTCTCTCTCACA 57.202 47.619 0.00 0.00 0.00 3.58
5338 7271 3.417101 TCTTCTGTCCTCTCTCTCACAC 58.583 50.000 0.00 0.00 0.00 3.82
5339 7272 1.814793 TCTGTCCTCTCTCTCACACG 58.185 55.000 0.00 0.00 0.00 4.49
5340 7273 1.072489 TCTGTCCTCTCTCTCACACGT 59.928 52.381 0.00 0.00 0.00 4.49
5341 7274 1.466950 CTGTCCTCTCTCTCACACGTC 59.533 57.143 0.00 0.00 0.00 4.34
5342 7275 0.806241 GTCCTCTCTCTCACACGTCC 59.194 60.000 0.00 0.00 0.00 4.79
5343 7276 0.400594 TCCTCTCTCTCACACGTCCA 59.599 55.000 0.00 0.00 0.00 4.02
5344 7277 0.523966 CCTCTCTCTCACACGTCCAC 59.476 60.000 0.00 0.00 0.00 4.02
5345 7278 0.523966 CTCTCTCTCACACGTCCACC 59.476 60.000 0.00 0.00 0.00 4.61
5346 7279 0.110678 TCTCTCTCACACGTCCACCT 59.889 55.000 0.00 0.00 0.00 4.00
5347 7280 1.350019 TCTCTCTCACACGTCCACCTA 59.650 52.381 0.00 0.00 0.00 3.08
5348 7281 2.026169 TCTCTCTCACACGTCCACCTAT 60.026 50.000 0.00 0.00 0.00 2.57
5349 7282 2.356382 CTCTCTCACACGTCCACCTATC 59.644 54.545 0.00 0.00 0.00 2.08
5350 7283 2.026169 TCTCTCACACGTCCACCTATCT 60.026 50.000 0.00 0.00 0.00 1.98
5351 7284 2.755655 CTCTCACACGTCCACCTATCTT 59.244 50.000 0.00 0.00 0.00 2.40
5352 7285 3.162666 TCTCACACGTCCACCTATCTTT 58.837 45.455 0.00 0.00 0.00 2.52
5353 7286 3.192844 TCTCACACGTCCACCTATCTTTC 59.807 47.826 0.00 0.00 0.00 2.62
5354 7287 3.162666 TCACACGTCCACCTATCTTTCT 58.837 45.455 0.00 0.00 0.00 2.52
5355 7288 3.192844 TCACACGTCCACCTATCTTTCTC 59.807 47.826 0.00 0.00 0.00 2.87
5356 7289 3.193691 CACACGTCCACCTATCTTTCTCT 59.806 47.826 0.00 0.00 0.00 3.10
5357 7290 3.193691 ACACGTCCACCTATCTTTCTCTG 59.806 47.826 0.00 0.00 0.00 3.35
5358 7291 3.193691 CACGTCCACCTATCTTTCTCTGT 59.806 47.826 0.00 0.00 0.00 3.41
5359 7292 3.833070 ACGTCCACCTATCTTTCTCTGTT 59.167 43.478 0.00 0.00 0.00 3.16
5360 7293 4.082136 ACGTCCACCTATCTTTCTCTGTTC 60.082 45.833 0.00 0.00 0.00 3.18
5361 7294 4.158764 CGTCCACCTATCTTTCTCTGTTCT 59.841 45.833 0.00 0.00 0.00 3.01
5362 7295 5.336849 CGTCCACCTATCTTTCTCTGTTCTT 60.337 44.000 0.00 0.00 0.00 2.52
5363 7296 6.468543 GTCCACCTATCTTTCTCTGTTCTTT 58.531 40.000 0.00 0.00 0.00 2.52
5364 7297 6.937465 GTCCACCTATCTTTCTCTGTTCTTTT 59.063 38.462 0.00 0.00 0.00 2.27
5365 7298 7.118535 GTCCACCTATCTTTCTCTGTTCTTTTC 59.881 40.741 0.00 0.00 0.00 2.29
5366 7299 7.016661 TCCACCTATCTTTCTCTGTTCTTTTCT 59.983 37.037 0.00 0.00 0.00 2.52
5367 7300 7.333174 CCACCTATCTTTCTCTGTTCTTTTCTC 59.667 40.741 0.00 0.00 0.00 2.87
5368 7301 8.093927 CACCTATCTTTCTCTGTTCTTTTCTCT 58.906 37.037 0.00 0.00 0.00 3.10
5369 7302 8.311109 ACCTATCTTTCTCTGTTCTTTTCTCTC 58.689 37.037 0.00 0.00 0.00 3.20
5370 7303 8.531146 CCTATCTTTCTCTGTTCTTTTCTCTCT 58.469 37.037 0.00 0.00 0.00 3.10
5371 7304 9.573133 CTATCTTTCTCTGTTCTTTTCTCTCTC 57.427 37.037 0.00 0.00 0.00 3.20
5372 7305 7.595819 TCTTTCTCTGTTCTTTTCTCTCTCT 57.404 36.000 0.00 0.00 0.00 3.10
5373 7306 7.657336 TCTTTCTCTGTTCTTTTCTCTCTCTC 58.343 38.462 0.00 0.00 0.00 3.20
5374 7307 7.505585 TCTTTCTCTGTTCTTTTCTCTCTCTCT 59.494 37.037 0.00 0.00 0.00 3.10
5375 7308 6.817765 TCTCTGTTCTTTTCTCTCTCTCTC 57.182 41.667 0.00 0.00 0.00 3.20
5376 7309 6.542821 TCTCTGTTCTTTTCTCTCTCTCTCT 58.457 40.000 0.00 0.00 0.00 3.10
5377 7310 6.655003 TCTCTGTTCTTTTCTCTCTCTCTCTC 59.345 42.308 0.00 0.00 0.00 3.20
5378 7311 6.542821 TCTGTTCTTTTCTCTCTCTCTCTCT 58.457 40.000 0.00 0.00 0.00 3.10
5379 7312 6.655003 TCTGTTCTTTTCTCTCTCTCTCTCTC 59.345 42.308 0.00 0.00 0.00 3.20
5380 7313 6.303054 TGTTCTTTTCTCTCTCTCTCTCTCA 58.697 40.000 0.00 0.00 0.00 3.27
5381 7314 6.206634 TGTTCTTTTCTCTCTCTCTCTCTCAC 59.793 42.308 0.00 0.00 0.00 3.51
5382 7315 4.935205 TCTTTTCTCTCTCTCTCTCTCACG 59.065 45.833 0.00 0.00 0.00 4.35
5383 7316 2.309528 TCTCTCTCTCTCTCTCACGC 57.690 55.000 0.00 0.00 0.00 5.34
5384 7317 1.552792 TCTCTCTCTCTCTCTCACGCA 59.447 52.381 0.00 0.00 0.00 5.24
5385 7318 1.665679 CTCTCTCTCTCTCTCACGCAC 59.334 57.143 0.00 0.00 0.00 5.34
5386 7319 0.732571 CTCTCTCTCTCTCACGCACC 59.267 60.000 0.00 0.00 0.00 5.01
5387 7320 0.678366 TCTCTCTCTCTCACGCACCC 60.678 60.000 0.00 0.00 0.00 4.61
5388 7321 0.962855 CTCTCTCTCTCACGCACCCA 60.963 60.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 70 3.423154 CAAACGGGGCTGAGACGC 61.423 66.667 0.00 0.00 0.00 5.19
91 104 2.956964 GCGCATCGGTTCTCCTCG 60.957 66.667 0.30 0.00 0.00 4.63
154 170 1.191535 ACTTGCGCTCATAGTACCCA 58.808 50.000 9.73 0.00 0.00 4.51
163 179 3.642778 GAGCCCGTACTTGCGCTCA 62.643 63.158 9.73 0.00 45.64 4.26
170 186 0.032017 AGGATCTGGAGCCCGTACTT 60.032 55.000 0.91 0.00 37.67 2.24
315 343 1.599047 CGGTTGAGGAGGCTCATGT 59.401 57.895 17.69 0.00 32.91 3.21
324 352 0.902531 GATGAGGTTCCGGTTGAGGA 59.097 55.000 0.00 0.00 38.79 3.71
439 479 3.179265 CTGCCGGACGCGTTGTAG 61.179 66.667 15.53 10.57 42.08 2.74
455 496 1.613785 GGCGTACCCTCTATCGATCCT 60.614 57.143 0.00 0.00 0.00 3.24
463 504 2.420568 CGGCAAGGCGTACCCTCTA 61.421 63.158 7.94 0.00 45.62 2.43
680 732 3.831642 TTGCATGGCCCCATAGATAAT 57.168 42.857 0.00 0.00 34.91 1.28
688 744 2.092538 CCATTAATTTTGCATGGCCCCA 60.093 45.455 0.00 0.00 31.32 4.96
689 745 2.574450 CCATTAATTTTGCATGGCCCC 58.426 47.619 0.00 0.00 31.32 5.80
846 911 4.384247 CGCTATTTTGTTTCGCATTTCCAA 59.616 37.500 0.00 0.00 0.00 3.53
847 912 3.917380 CGCTATTTTGTTTCGCATTTCCA 59.083 39.130 0.00 0.00 0.00 3.53
855 920 2.334454 GTCAACGCGCTATTTTGTTTCG 59.666 45.455 5.73 0.00 0.00 3.46
968 1542 0.741221 GGATGGCTGACTGAACGGAC 60.741 60.000 0.00 0.00 0.00 4.79
973 1547 1.685224 GTGGGGATGGCTGACTGAA 59.315 57.895 0.00 0.00 0.00 3.02
1104 1699 2.496070 CGGGTAACTGATCTTCAGGTCA 59.504 50.000 9.18 0.00 41.32 4.02
1208 1806 2.202932 CCCCGAACATGGAGCGAG 60.203 66.667 0.00 0.00 0.00 5.03
1368 1978 0.603975 GGACGAGCAGCTCCTTGTTT 60.604 55.000 17.16 0.00 29.63 2.83
1395 2005 2.045926 GTCGCCTCCTTGGTGCAT 60.046 61.111 0.00 0.00 45.61 3.96
1768 2427 8.657729 GGTTAGCTTGATCAAAGAACTAGTTAC 58.342 37.037 8.42 2.64 38.24 2.50
1772 2435 5.586643 GGGGTTAGCTTGATCAAAGAACTAG 59.413 44.000 9.88 0.00 38.24 2.57
1793 2456 2.634453 AGCACTTGAAATTTTGAGGGGG 59.366 45.455 0.00 0.00 0.00 5.40
1857 2629 5.856156 TGTCAGATGGCAATGTCAAAATTT 58.144 33.333 0.00 0.00 0.00 1.82
2098 3108 5.922544 AGCATTGCTGACTAATTCAACAAAC 59.077 36.000 11.09 0.00 42.29 2.93
2168 3198 0.163788 CGCATCGATCGGGCAATTAC 59.836 55.000 24.94 4.54 0.00 1.89
2169 3199 1.565156 GCGCATCGATCGGGCAATTA 61.565 55.000 24.94 3.52 41.60 1.40
2170 3200 2.896801 GCGCATCGATCGGGCAATT 61.897 57.895 24.94 0.95 41.60 2.32
2174 3208 2.355837 TAAGCGCATCGATCGGGC 60.356 61.111 16.41 21.00 42.25 6.13
2175 3209 0.597637 AAGTAAGCGCATCGATCGGG 60.598 55.000 16.41 9.28 0.00 5.14
2245 3388 7.200455 ACCTAACTAATTCAACAACAAACAGC 58.800 34.615 0.00 0.00 0.00 4.40
2271 3418 3.327172 TCCAATTCAACGTTACACCCCTA 59.673 43.478 0.00 0.00 0.00 3.53
2272 3419 2.106857 TCCAATTCAACGTTACACCCCT 59.893 45.455 0.00 0.00 0.00 4.79
2273 3420 2.227149 GTCCAATTCAACGTTACACCCC 59.773 50.000 0.00 0.00 0.00 4.95
2274 3421 2.879646 TGTCCAATTCAACGTTACACCC 59.120 45.455 0.00 0.00 0.00 4.61
2275 3422 3.562557 AGTGTCCAATTCAACGTTACACC 59.437 43.478 19.38 6.95 37.13 4.16
2282 3429 4.488126 AATCACAGTGTCCAATTCAACG 57.512 40.909 0.00 0.00 0.00 4.10
2301 3448 6.947464 TCTCTAAGTAGCCACTTAAGCAAAT 58.053 36.000 6.22 0.00 44.64 2.32
2306 3453 5.982516 CAGCATCTCTAAGTAGCCACTTAAG 59.017 44.000 6.22 0.00 44.64 1.85
2435 3772 0.610232 AAGCTAGCTTGGTGCCTTGG 60.610 55.000 28.83 0.00 44.23 3.61
2472 3851 3.194005 TCCAGAAAACGAGCAGAGTTT 57.806 42.857 0.00 0.00 42.86 2.66
2515 3897 6.523893 TGCAGTAAGTCAAAACGTAACAAAAC 59.476 34.615 0.00 0.00 0.00 2.43
2524 3907 7.075121 TCATACATTTGCAGTAAGTCAAAACG 58.925 34.615 0.00 0.00 36.02 3.60
2525 3908 8.795786 TTCATACATTTGCAGTAAGTCAAAAC 57.204 30.769 0.00 0.00 36.02 2.43
2561 3969 7.074653 ACTTAGATCCTAAAAGTGACACCAA 57.925 36.000 0.84 0.00 32.38 3.67
2737 4167 8.706322 ACTTTATGTAGGATGAGTTGGTTTTT 57.294 30.769 0.00 0.00 0.00 1.94
2740 4174 7.690256 AGAACTTTATGTAGGATGAGTTGGTT 58.310 34.615 0.00 0.00 0.00 3.67
2746 4180 9.829507 AATGAGAAGAACTTTATGTAGGATGAG 57.170 33.333 0.00 0.00 0.00 2.90
2785 4219 9.372369 AGTAGCAAACAAGAAGTATGAGTAATC 57.628 33.333 0.00 0.00 0.00 1.75
2786 4220 9.726438 AAGTAGCAAACAAGAAGTATGAGTAAT 57.274 29.630 0.00 0.00 0.00 1.89
2823 4257 9.928236 GCATAAGAAGAGTCTGTCAATATTTTC 57.072 33.333 0.00 0.00 33.05 2.29
2832 4299 3.431486 CCCCTGCATAAGAAGAGTCTGTC 60.431 52.174 0.00 0.00 33.05 3.51
2887 4357 4.937620 GCTTGATAGTTGATTGGACTCACA 59.062 41.667 0.00 0.00 0.00 3.58
2894 4364 3.002042 CGAGCAGCTTGATAGTTGATTGG 59.998 47.826 3.08 0.00 34.82 3.16
2904 4375 2.955022 GATGGGCCGAGCAGCTTGAT 62.955 60.000 11.73 0.00 0.00 2.57
2958 4453 7.421853 GCCCCCTTATTCTCCATATTATGCTAT 60.422 40.741 0.00 0.00 0.00 2.97
2961 4456 4.889995 GCCCCCTTATTCTCCATATTATGC 59.110 45.833 0.00 0.00 0.00 3.14
3078 4615 2.584791 GAACACCGTTAATGCAGCAAG 58.415 47.619 0.00 0.00 0.00 4.01
3091 4634 4.099120 CAAGAGATAGAAGACGAACACCG 58.901 47.826 0.00 0.00 45.44 4.94
3108 4654 1.532868 CCTCTTTCGTTGGTGCAAGAG 59.467 52.381 0.00 0.00 41.31 2.85
3147 4696 0.716108 CCACTTCGCATCAACTCGTC 59.284 55.000 0.00 0.00 0.00 4.20
3278 4827 0.893270 TTCCAAAGCCACCATCACCG 60.893 55.000 0.00 0.00 0.00 4.94
3357 4919 5.537188 ACTTGAGAACAGAGCTCTAAACTG 58.463 41.667 17.75 7.18 37.62 3.16
3358 4920 5.538433 AGACTTGAGAACAGAGCTCTAAACT 59.462 40.000 17.75 14.91 33.57 2.66
3359 4921 5.778862 AGACTTGAGAACAGAGCTCTAAAC 58.221 41.667 17.75 10.27 33.57 2.01
3360 4922 5.536538 TGAGACTTGAGAACAGAGCTCTAAA 59.463 40.000 17.75 3.73 33.57 1.85
3361 4923 5.073428 TGAGACTTGAGAACAGAGCTCTAA 58.927 41.667 17.75 4.98 33.57 2.10
3362 4924 4.657013 TGAGACTTGAGAACAGAGCTCTA 58.343 43.478 17.75 0.00 33.57 2.43
3591 5197 0.616111 AGAAGGTCACGGCTCATCCT 60.616 55.000 0.00 0.00 0.00 3.24
4016 5622 1.951209 TGGCCAGGTTGATCTCACTA 58.049 50.000 0.00 0.00 0.00 2.74
4182 5788 2.278857 CTCCTTGATCGACGGCCG 60.279 66.667 26.86 26.86 40.25 6.13
4391 6000 9.773328 TTATTTCTTCAGAATCAATACAAAGCG 57.227 29.630 0.00 0.00 33.54 4.68
4522 6139 4.603989 TTTGAATCATTGCCAAGCTCAA 57.396 36.364 0.00 0.00 0.00 3.02
4603 6235 4.340950 TCAATCCTTTGGTCAACTTGAACC 59.659 41.667 4.31 4.33 31.76 3.62
4616 6252 8.139989 AGTTCAACTTCTGAATTCAATCCTTTG 58.860 33.333 9.88 9.27 45.74 2.77
4620 6256 7.206981 TCAGTTCAACTTCTGAATTCAATCC 57.793 36.000 9.88 0.00 45.74 3.01
4691 6327 8.808529 CGTCCTCTTTCTAATAACTGTACATTG 58.191 37.037 0.00 0.00 0.00 2.82
4726 6609 2.046023 CTGCAGGCCATCGGTGAA 60.046 61.111 5.01 0.00 0.00 3.18
4731 6622 1.135315 CGAAAACTGCAGGCCATCG 59.865 57.895 19.93 17.26 0.00 3.84
4778 6669 0.603569 CGAGTGGCTAGTTGACTGGT 59.396 55.000 0.00 0.00 0.00 4.00
4790 6681 0.739813 ATTTGACGCTACCGAGTGGC 60.740 55.000 2.95 2.95 42.09 5.01
4822 6738 1.543944 CCAAAAAGGGCCTCGGCAAT 61.544 55.000 6.46 0.00 44.11 3.56
4835 6751 5.108517 GTCATTGTCAAAGAGTGCCAAAAA 58.891 37.500 0.00 0.00 0.00 1.94
4851 6767 5.413309 TGGGAACTTTGTTTTGTCATTGT 57.587 34.783 0.00 0.00 0.00 2.71
4942 6874 9.176460 TGCATCAAACAAGAGATCATAACAATA 57.824 29.630 0.00 0.00 0.00 1.90
4949 6881 7.058525 TCCTAATGCATCAAACAAGAGATCAT 58.941 34.615 0.00 0.00 0.00 2.45
5067 7000 2.596338 AACGGGCCCTTGGTTTCG 60.596 61.111 22.43 6.18 0.00 3.46
5115 7048 3.009916 AGTTGCTCAAGACCCATGAGAAT 59.990 43.478 7.67 0.00 45.74 2.40
5130 7063 4.320788 CCATCAGGAAAGAACAAGTTGCTC 60.321 45.833 1.81 0.00 36.89 4.26
5166 7099 5.251764 ACAAGATTCATTCTCCTTGTCAGG 58.748 41.667 0.00 0.00 43.85 3.86
5199 7132 8.970293 CGATTGTAAACGTTTCCCTAAATTTTT 58.030 29.630 18.42 0.00 0.00 1.94
5200 7133 7.595875 CCGATTGTAAACGTTTCCCTAAATTTT 59.404 33.333 18.42 0.00 0.00 1.82
5201 7134 7.085746 CCGATTGTAAACGTTTCCCTAAATTT 58.914 34.615 18.42 0.00 0.00 1.82
5202 7135 6.614160 CCGATTGTAAACGTTTCCCTAAATT 58.386 36.000 18.42 0.00 0.00 1.82
5203 7136 5.392272 GCCGATTGTAAACGTTTCCCTAAAT 60.392 40.000 18.42 10.85 0.00 1.40
5204 7137 4.083377 GCCGATTGTAAACGTTTCCCTAAA 60.083 41.667 18.42 6.53 0.00 1.85
5205 7138 3.436359 GCCGATTGTAAACGTTTCCCTAA 59.564 43.478 18.42 8.96 0.00 2.69
5206 7139 3.002102 GCCGATTGTAAACGTTTCCCTA 58.998 45.455 18.42 6.99 0.00 3.53
5207 7140 1.808343 GCCGATTGTAAACGTTTCCCT 59.192 47.619 18.42 0.75 0.00 4.20
5208 7141 1.536331 TGCCGATTGTAAACGTTTCCC 59.464 47.619 18.42 10.10 0.00 3.97
5209 7142 2.577450 GTGCCGATTGTAAACGTTTCC 58.423 47.619 18.42 6.75 0.00 3.13
5210 7143 2.227556 CGTGCCGATTGTAAACGTTTC 58.772 47.619 18.42 9.90 0.00 2.78
5211 7144 1.660896 GCGTGCCGATTGTAAACGTTT 60.661 47.619 18.90 18.90 36.65 3.60
5212 7145 0.110554 GCGTGCCGATTGTAAACGTT 60.111 50.000 0.00 0.00 36.65 3.99
5213 7146 1.494189 GCGTGCCGATTGTAAACGT 59.506 52.632 0.00 0.00 36.65 3.99
5214 7147 1.225908 GGCGTGCCGATTGTAAACG 60.226 57.895 0.00 0.00 37.32 3.60
5215 7148 4.757554 GGCGTGCCGATTGTAAAC 57.242 55.556 0.00 0.00 0.00 2.01
5264 7197 2.360350 AATGGCTGGGAGTGCACG 60.360 61.111 12.01 0.00 0.00 5.34
5265 7198 0.895100 TTGAATGGCTGGGAGTGCAC 60.895 55.000 9.40 9.40 0.00 4.57
5266 7199 0.609957 CTTGAATGGCTGGGAGTGCA 60.610 55.000 0.00 0.00 0.00 4.57
5267 7200 1.318158 CCTTGAATGGCTGGGAGTGC 61.318 60.000 0.00 0.00 0.00 4.40
5268 7201 0.038744 ACCTTGAATGGCTGGGAGTG 59.961 55.000 0.00 0.00 0.00 3.51
5269 7202 0.329596 GACCTTGAATGGCTGGGAGT 59.670 55.000 0.00 0.00 0.00 3.85
5270 7203 0.622665 AGACCTTGAATGGCTGGGAG 59.377 55.000 0.00 0.00 0.00 4.30
5271 7204 0.329261 CAGACCTTGAATGGCTGGGA 59.671 55.000 0.00 0.00 31.95 4.37
5272 7205 0.329261 TCAGACCTTGAATGGCTGGG 59.671 55.000 3.46 0.00 34.40 4.45
5273 7206 1.271543 TGTCAGACCTTGAATGGCTGG 60.272 52.381 3.46 0.00 37.61 4.85
5274 7207 1.808945 GTGTCAGACCTTGAATGGCTG 59.191 52.381 0.00 0.00 37.61 4.85
5275 7208 1.609061 CGTGTCAGACCTTGAATGGCT 60.609 52.381 0.00 0.00 37.61 4.75
5276 7209 0.798776 CGTGTCAGACCTTGAATGGC 59.201 55.000 0.00 0.00 37.61 4.40
5277 7210 2.169832 ACGTGTCAGACCTTGAATGG 57.830 50.000 0.00 0.00 37.61 3.16
5278 7211 3.679980 CCTTACGTGTCAGACCTTGAATG 59.320 47.826 0.00 0.00 37.61 2.67
5279 7212 3.306780 CCCTTACGTGTCAGACCTTGAAT 60.307 47.826 0.00 0.00 37.61 2.57
5280 7213 2.036733 CCCTTACGTGTCAGACCTTGAA 59.963 50.000 0.00 0.00 37.61 2.69
5281 7214 1.616865 CCCTTACGTGTCAGACCTTGA 59.383 52.381 0.00 0.00 0.00 3.02
5282 7215 1.343465 ACCCTTACGTGTCAGACCTTG 59.657 52.381 0.00 0.00 0.00 3.61
5283 7216 1.343465 CACCCTTACGTGTCAGACCTT 59.657 52.381 0.00 0.00 0.00 3.50
5284 7217 0.966920 CACCCTTACGTGTCAGACCT 59.033 55.000 0.00 0.00 0.00 3.85
5285 7218 0.037605 CCACCCTTACGTGTCAGACC 60.038 60.000 0.00 0.00 31.47 3.85
5286 7219 0.037605 CCCACCCTTACGTGTCAGAC 60.038 60.000 0.00 0.00 31.47 3.51
5287 7220 1.189524 CCCCACCCTTACGTGTCAGA 61.190 60.000 0.00 0.00 31.47 3.27
5288 7221 1.295423 CCCCACCCTTACGTGTCAG 59.705 63.158 0.00 0.00 31.47 3.51
5289 7222 2.218454 CCCCCACCCTTACGTGTCA 61.218 63.158 0.00 0.00 31.47 3.58
5290 7223 2.666812 CCCCCACCCTTACGTGTC 59.333 66.667 0.00 0.00 31.47 3.67
5304 7237 0.183731 CAGAAGATAAGGTGGCCCCC 59.816 60.000 0.00 0.00 0.00 5.40
5305 7238 0.919710 ACAGAAGATAAGGTGGCCCC 59.080 55.000 0.00 0.03 0.00 5.80
5306 7239 1.134068 GGACAGAAGATAAGGTGGCCC 60.134 57.143 0.00 0.00 31.07 5.80
5307 7240 1.840635 AGGACAGAAGATAAGGTGGCC 59.159 52.381 0.00 0.00 38.52 5.36
5308 7241 2.769095 AGAGGACAGAAGATAAGGTGGC 59.231 50.000 0.00 0.00 0.00 5.01
5309 7242 4.285863 AGAGAGGACAGAAGATAAGGTGG 58.714 47.826 0.00 0.00 0.00 4.61
5310 7243 5.200483 AGAGAGAGGACAGAAGATAAGGTG 58.800 45.833 0.00 0.00 0.00 4.00
5311 7244 5.044476 TGAGAGAGAGGACAGAAGATAAGGT 60.044 44.000 0.00 0.00 0.00 3.50
5312 7245 5.299279 GTGAGAGAGAGGACAGAAGATAAGG 59.701 48.000 0.00 0.00 0.00 2.69
5313 7246 5.885352 TGTGAGAGAGAGGACAGAAGATAAG 59.115 44.000 0.00 0.00 0.00 1.73
5314 7247 5.650266 GTGTGAGAGAGAGGACAGAAGATAA 59.350 44.000 0.00 0.00 0.00 1.75
5315 7248 5.189928 GTGTGAGAGAGAGGACAGAAGATA 58.810 45.833 0.00 0.00 0.00 1.98
5316 7249 4.016444 GTGTGAGAGAGAGGACAGAAGAT 58.984 47.826 0.00 0.00 0.00 2.40
5317 7250 3.417101 GTGTGAGAGAGAGGACAGAAGA 58.583 50.000 0.00 0.00 0.00 2.87
5318 7251 2.161410 CGTGTGAGAGAGAGGACAGAAG 59.839 54.545 0.00 0.00 0.00 2.85
5319 7252 2.155279 CGTGTGAGAGAGAGGACAGAA 58.845 52.381 0.00 0.00 0.00 3.02
5320 7253 1.072489 ACGTGTGAGAGAGAGGACAGA 59.928 52.381 0.00 0.00 0.00 3.41
5321 7254 1.466950 GACGTGTGAGAGAGAGGACAG 59.533 57.143 0.00 0.00 0.00 3.51
5322 7255 1.524848 GACGTGTGAGAGAGAGGACA 58.475 55.000 0.00 0.00 0.00 4.02
5323 7256 0.806241 GGACGTGTGAGAGAGAGGAC 59.194 60.000 0.00 0.00 0.00 3.85
5324 7257 0.400594 TGGACGTGTGAGAGAGAGGA 59.599 55.000 0.00 0.00 0.00 3.71
5325 7258 0.523966 GTGGACGTGTGAGAGAGAGG 59.476 60.000 0.00 0.00 0.00 3.69
5326 7259 0.523966 GGTGGACGTGTGAGAGAGAG 59.476 60.000 0.00 0.00 0.00 3.20
5327 7260 0.110678 AGGTGGACGTGTGAGAGAGA 59.889 55.000 0.00 0.00 0.00 3.10
5328 7261 1.822506 TAGGTGGACGTGTGAGAGAG 58.177 55.000 0.00 0.00 0.00 3.20
5329 7262 2.026169 AGATAGGTGGACGTGTGAGAGA 60.026 50.000 0.00 0.00 0.00 3.10
5330 7263 2.370349 AGATAGGTGGACGTGTGAGAG 58.630 52.381 0.00 0.00 0.00 3.20
5331 7264 2.509166 AGATAGGTGGACGTGTGAGA 57.491 50.000 0.00 0.00 0.00 3.27
5332 7265 3.193691 AGAAAGATAGGTGGACGTGTGAG 59.806 47.826 0.00 0.00 0.00 3.51
5333 7266 3.162666 AGAAAGATAGGTGGACGTGTGA 58.837 45.455 0.00 0.00 0.00 3.58
5334 7267 3.193691 AGAGAAAGATAGGTGGACGTGTG 59.806 47.826 0.00 0.00 0.00 3.82
5335 7268 3.193691 CAGAGAAAGATAGGTGGACGTGT 59.806 47.826 0.00 0.00 0.00 4.49
5336 7269 3.193691 ACAGAGAAAGATAGGTGGACGTG 59.806 47.826 0.00 0.00 0.00 4.49
5337 7270 3.432378 ACAGAGAAAGATAGGTGGACGT 58.568 45.455 0.00 0.00 0.00 4.34
5338 7271 4.158764 AGAACAGAGAAAGATAGGTGGACG 59.841 45.833 0.00 0.00 0.00 4.79
5339 7272 5.669164 AGAACAGAGAAAGATAGGTGGAC 57.331 43.478 0.00 0.00 0.00 4.02
5340 7273 6.688073 AAAGAACAGAGAAAGATAGGTGGA 57.312 37.500 0.00 0.00 0.00 4.02
5341 7274 7.164803 AGAAAAGAACAGAGAAAGATAGGTGG 58.835 38.462 0.00 0.00 0.00 4.61
5342 7275 8.093927 AGAGAAAAGAACAGAGAAAGATAGGTG 58.906 37.037 0.00 0.00 0.00 4.00
5343 7276 8.201242 AGAGAAAAGAACAGAGAAAGATAGGT 57.799 34.615 0.00 0.00 0.00 3.08
5344 7277 8.531146 AGAGAGAAAAGAACAGAGAAAGATAGG 58.469 37.037 0.00 0.00 0.00 2.57
5345 7278 9.573133 GAGAGAGAAAAGAACAGAGAAAGATAG 57.427 37.037 0.00 0.00 0.00 2.08
5346 7279 9.308000 AGAGAGAGAAAAGAACAGAGAAAGATA 57.692 33.333 0.00 0.00 0.00 1.98
5347 7280 8.193953 AGAGAGAGAAAAGAACAGAGAAAGAT 57.806 34.615 0.00 0.00 0.00 2.40
5348 7281 7.505585 AGAGAGAGAGAAAAGAACAGAGAAAGA 59.494 37.037 0.00 0.00 0.00 2.52
5349 7282 7.661040 AGAGAGAGAGAAAAGAACAGAGAAAG 58.339 38.462 0.00 0.00 0.00 2.62
5350 7283 7.505585 AGAGAGAGAGAGAAAAGAACAGAGAAA 59.494 37.037 0.00 0.00 0.00 2.52
5351 7284 7.004086 AGAGAGAGAGAGAAAAGAACAGAGAA 58.996 38.462 0.00 0.00 0.00 2.87
5352 7285 6.542821 AGAGAGAGAGAGAAAAGAACAGAGA 58.457 40.000 0.00 0.00 0.00 3.10
5353 7286 6.656693 AGAGAGAGAGAGAGAAAAGAACAGAG 59.343 42.308 0.00 0.00 0.00 3.35
5354 7287 6.542821 AGAGAGAGAGAGAGAAAAGAACAGA 58.457 40.000 0.00 0.00 0.00 3.41
5355 7288 6.430925 TGAGAGAGAGAGAGAGAAAAGAACAG 59.569 42.308 0.00 0.00 0.00 3.16
5356 7289 6.206634 GTGAGAGAGAGAGAGAGAAAAGAACA 59.793 42.308 0.00 0.00 0.00 3.18
5357 7290 6.612306 GTGAGAGAGAGAGAGAGAAAAGAAC 58.388 44.000 0.00 0.00 0.00 3.01
5358 7291 5.411361 CGTGAGAGAGAGAGAGAGAAAAGAA 59.589 44.000 0.00 0.00 0.00 2.52
5359 7292 4.935205 CGTGAGAGAGAGAGAGAGAAAAGA 59.065 45.833 0.00 0.00 0.00 2.52
5360 7293 4.437390 GCGTGAGAGAGAGAGAGAGAAAAG 60.437 50.000 0.00 0.00 0.00 2.27
5361 7294 3.438781 GCGTGAGAGAGAGAGAGAGAAAA 59.561 47.826 0.00 0.00 0.00 2.29
5362 7295 3.006940 GCGTGAGAGAGAGAGAGAGAAA 58.993 50.000 0.00 0.00 0.00 2.52
5363 7296 2.027653 TGCGTGAGAGAGAGAGAGAGAA 60.028 50.000 0.00 0.00 0.00 2.87
5364 7297 1.552792 TGCGTGAGAGAGAGAGAGAGA 59.447 52.381 0.00 0.00 0.00 3.10
5365 7298 1.665679 GTGCGTGAGAGAGAGAGAGAG 59.334 57.143 0.00 0.00 0.00 3.20
5366 7299 1.677518 GGTGCGTGAGAGAGAGAGAGA 60.678 57.143 0.00 0.00 0.00 3.10
5367 7300 0.732571 GGTGCGTGAGAGAGAGAGAG 59.267 60.000 0.00 0.00 0.00 3.20
5368 7301 0.678366 GGGTGCGTGAGAGAGAGAGA 60.678 60.000 0.00 0.00 0.00 3.10
5369 7302 0.962855 TGGGTGCGTGAGAGAGAGAG 60.963 60.000 0.00 0.00 0.00 3.20
5370 7303 1.074951 TGGGTGCGTGAGAGAGAGA 59.925 57.895 0.00 0.00 0.00 3.10
5371 7304 3.686760 TGGGTGCGTGAGAGAGAG 58.313 61.111 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.