Multiple sequence alignment - TraesCS5D01G427700

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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 TraesCS5D01G427700 chr5D 100.000 5843 0 0 1 5843 485813823 485819665 0.000000e+00 10791.0
1 TraesCS5D01G427700 chr5D 98.655 1710 22 1 3058 4766 255541400 255539691 0.000000e+00 3029.0
2 TraesCS5D01G427700 chr5D 98.364 1712 26 2 3057 4767 426438230 426439940 0.000000e+00 3005.0
3 TraesCS5D01G427700 chr5D 84.899 841 90 18 1 819 38058517 38057692 0.000000e+00 815.0
4 TraesCS5D01G427700 chr5D 90.499 621 50 3 1 620 18154562 18153950 0.000000e+00 811.0
5 TraesCS5D01G427700 chr5D 97.273 220 6 0 5624 5843 133843814 133844033 1.990000e-99 374.0
6 TraesCS5D01G427700 chr5D 88.288 111 10 3 1348 1456 438777892 438778001 4.750000e-26 130.0
7 TraesCS5D01G427700 chr5D 94.937 79 3 1 1047 1125 485814815 485814892 7.950000e-24 122.0
8 TraesCS5D01G427700 chr5D 94.937 79 3 1 993 1070 485814869 485814947 7.950000e-24 122.0
9 TraesCS5D01G427700 chr3D 96.636 3062 85 10 1 3057 585812871 585809823 0.000000e+00 5068.0
10 TraesCS5D01G427700 chr3D 96.853 858 21 5 4768 5623 585809827 585808974 0.000000e+00 1430.0
11 TraesCS5D01G427700 chr3D 96.501 686 24 0 4939 5624 464891699 464891014 0.000000e+00 1134.0
12 TraesCS5D01G427700 chr3D 95.484 310 11 1 1386 1695 464896474 464896168 5.260000e-135 492.0
13 TraesCS5D01G427700 chr3D 97.273 220 5 1 5624 5843 411337915 411337697 7.150000e-99 372.0
14 TraesCS5D01G427700 chr3D 88.073 109 10 3 993 1099 585811828 585811721 6.150000e-25 126.0
15 TraesCS5D01G427700 chr3D 93.590 78 4 1 1048 1125 585811881 585811805 1.330000e-21 115.0
16 TraesCS5D01G427700 chr4D 92.760 3094 157 32 4 3057 160052420 160049354 0.000000e+00 4410.0
17 TraesCS5D01G427700 chr4D 97.520 2137 44 6 924 3057 132568974 132571104 0.000000e+00 3644.0
18 TraesCS5D01G427700 chr4D 98.424 1713 24 3 3057 4768 30132065 30133775 0.000000e+00 3011.0
19 TraesCS5D01G427700 chr4D 97.555 859 18 2 4768 5623 132571100 132571958 0.000000e+00 1467.0
20 TraesCS5D01G427700 chr4D 93.981 515 11 6 3 517 132567960 132568454 0.000000e+00 761.0
21 TraesCS5D01G427700 chr4D 95.253 316 14 1 5310 5624 490868575 490868260 3.140000e-137 499.0
22 TraesCS5D01G427700 chr4D 96.907 291 5 2 599 885 132568693 132568983 8.800000e-133 484.0
23 TraesCS5D01G427700 chr4D 96.833 221 6 1 5624 5843 131058843 131058623 9.250000e-98 368.0
24 TraesCS5D01G427700 chr4D 91.603 131 6 4 2932 3057 503878544 503878414 6.020000e-40 176.0
25 TraesCS5D01G427700 chr4D 96.203 79 2 1 1047 1125 132569044 132569121 1.710000e-25 128.0
26 TraesCS5D01G427700 chr4D 97.333 75 2 0 993 1067 160051364 160051290 1.710000e-25 128.0
27 TraesCS5D01G427700 chr4D 94.937 79 3 1 993 1070 132569098 132569176 7.950000e-24 122.0
28 TraesCS5D01G427700 chr4D 93.671 79 4 1 1047 1125 160051418 160051341 3.700000e-22 117.0
29 TraesCS5D01G427700 chr6D 98.831 1711 19 1 3058 4767 382043377 382041667 0.000000e+00 3048.0
30 TraesCS5D01G427700 chr6D 98.364 1711 27 1 3058 4767 382050244 382048534 0.000000e+00 3003.0
31 TraesCS5D01G427700 chr6D 90.000 370 28 7 5261 5623 83693825 83693458 2.470000e-128 470.0
32 TraesCS5D01G427700 chr6D 87.037 108 12 1 1249 1356 64662052 64662157 2.860000e-23 121.0
33 TraesCS5D01G427700 chr2D 98.258 1722 28 2 3051 4771 641510502 641508782 0.000000e+00 3013.0
34 TraesCS5D01G427700 chr2D 98.364 1712 26 2 3057 4767 201865102 201866812 0.000000e+00 3005.0
35 TraesCS5D01G427700 chr2D 91.977 349 24 4 5280 5625 21140364 21140017 2.450000e-133 486.0
36 TraesCS5D01G427700 chr2D 97.273 220 6 0 5624 5843 449496699 449496918 1.990000e-99 374.0
37 TraesCS5D01G427700 chr1D 98.307 1713 25 4 3058 4768 438219185 438220895 0.000000e+00 3000.0
38 TraesCS5D01G427700 chr1D 98.305 1711 28 1 3058 4767 473922841 473924551 0.000000e+00 2998.0
39 TraesCS5D01G427700 chr1D 86.445 782 75 18 1 760 418785330 418784558 0.000000e+00 828.0
40 TraesCS5D01G427700 chr3B 96.242 1570 50 4 1489 3057 41694890 41696451 0.000000e+00 2564.0
41 TraesCS5D01G427700 chr3B 95.799 1571 56 7 1489 3057 185804886 185806448 0.000000e+00 2527.0
42 TraesCS5D01G427700 chr2A 96.181 1571 49 4 1489 3057 690513700 690515261 0.000000e+00 2558.0
43 TraesCS5D01G427700 chr2A 90.951 873 54 13 4768 5623 690515257 690516121 0.000000e+00 1151.0
44 TraesCS5D01G427700 chr2A 92.350 366 24 2 918 1279 668841238 668840873 8.680000e-143 518.0
45 TraesCS5D01G427700 chr2A 83.896 385 53 5 1 377 687816238 687815855 5.570000e-95 359.0
46 TraesCS5D01G427700 chr2A 88.333 60 4 3 671 727 687922903 687922844 1.050000e-07 69.4
47 TraesCS5D01G427700 chr7D 95.517 1316 50 5 630 1941 455878192 455876882 0.000000e+00 2095.0
48 TraesCS5D01G427700 chr7D 97.067 1125 31 2 1933 3057 455874991 455873869 0.000000e+00 1893.0
49 TraesCS5D01G427700 chr7D 95.693 859 31 5 4768 5623 455873873 455873018 0.000000e+00 1376.0
50 TraesCS5D01G427700 chr7D 95.761 519 20 2 1 519 455879173 455878657 0.000000e+00 835.0
51 TraesCS5D01G427700 chr7D 96.429 252 9 0 2806 3057 573287789 573287538 3.260000e-112 416.0
52 TraesCS5D01G427700 chr7D 85.514 214 22 7 388 596 567632124 567631915 1.280000e-51 215.0
53 TraesCS5D01G427700 chr2B 97.410 1004 23 2 1743 2744 771210615 771211617 0.000000e+00 1707.0
54 TraesCS5D01G427700 chr2B 90.367 872 65 12 4768 5623 44182194 44181326 0.000000e+00 1127.0
55 TraesCS5D01G427700 chr2B 93.773 273 10 4 2785 3057 771211615 771211880 2.540000e-108 403.0
56 TraesCS5D01G427700 chr4B 97.211 1004 25 2 1743 2744 633813832 633814834 0.000000e+00 1696.0
57 TraesCS5D01G427700 chr4B 86.432 199 10 7 2864 3057 156169292 156169106 9.930000e-48 202.0
58 TraesCS5D01G427700 chr5B 91.170 872 57 13 4768 5623 24167075 24166208 0.000000e+00 1166.0
59 TraesCS5D01G427700 chr5B 90.711 872 61 13 4768 5623 577990933 577991800 0.000000e+00 1144.0
60 TraesCS5D01G427700 chr5B 96.528 144 5 0 1489 1632 24168488 24168345 7.570000e-59 239.0
61 TraesCS5D01G427700 chr5B 97.802 91 2 0 2702 2792 16247336 16247246 2.180000e-34 158.0
62 TraesCS5D01G427700 chr5B 87.500 96 10 2 1348 1442 533748687 533748781 6.190000e-20 110.0
63 TraesCS5D01G427700 chr7B 90.711 872 61 13 4768 5623 60829076 60828209 0.000000e+00 1144.0
64 TraesCS5D01G427700 chr7B 97.260 219 6 0 5624 5842 648732290 648732072 7.150000e-99 372.0
65 TraesCS5D01G427700 chr7B 97.802 91 2 0 2702 2792 277068181 277068091 2.180000e-34 158.0
66 TraesCS5D01G427700 chr1B 88.546 908 68 15 1 879 110634729 110635629 0.000000e+00 1068.0
67 TraesCS5D01G427700 chr1B 90.960 354 26 6 5278 5626 659088391 659088039 6.850000e-129 472.0
68 TraesCS5D01G427700 chr1B 91.159 328 25 3 1124 1448 110636315 110636641 5.370000e-120 442.0
69 TraesCS5D01G427700 chr1B 96.970 66 2 0 1454 1519 110636672 110636737 1.720000e-20 111.0
70 TraesCS5D01G427700 chr1A 92.623 366 23 2 918 1279 5798199 5798564 1.870000e-144 523.0
71 TraesCS5D01G427700 chr1A 92.350 366 23 3 918 1279 467570183 467569819 3.120000e-142 516.0
72 TraesCS5D01G427700 chr1A 88.073 109 10 3 993 1099 467570055 467569948 6.150000e-25 126.0
73 TraesCS5D01G427700 chr1A 90.426 94 6 3 993 1084 5798328 5798420 2.860000e-23 121.0
74 TraesCS5D01G427700 chr6A 86.207 493 41 9 345 816 306371507 306371993 5.220000e-140 508.0
75 TraesCS5D01G427700 chr6A 89.119 386 32 8 5245 5623 243927464 243927846 6.850000e-129 472.0
76 TraesCS5D01G427700 chr6A 97.273 220 6 0 5624 5843 210413580 210413799 1.990000e-99 374.0
77 TraesCS5D01G427700 chr4A 97.260 219 6 0 5624 5842 571355824 571356042 7.150000e-99 372.0
78 TraesCS5D01G427700 chrUn 97.248 218 6 0 5624 5841 198439012 198439229 2.570000e-98 370.0
79 TraesCS5D01G427700 chrUn 97.248 218 6 0 5624 5841 409434798 409435015 2.570000e-98 370.0
80 TraesCS5D01G427700 chr5A 88.462 104 10 2 1348 1450 554286308 554286410 2.210000e-24 124.0


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 TraesCS5D01G427700 chr5D 485813823 485819665 5842 False 10791.000000 10791 100.000000 1 5843 1 chr5D.!!$F4 5842
1 TraesCS5D01G427700 chr5D 255539691 255541400 1709 True 3029.000000 3029 98.655000 3058 4766 1 chr5D.!!$R3 1708
2 TraesCS5D01G427700 chr5D 426438230 426439940 1710 False 3005.000000 3005 98.364000 3057 4767 1 chr5D.!!$F2 1710
3 TraesCS5D01G427700 chr5D 38057692 38058517 825 True 815.000000 815 84.899000 1 819 1 chr5D.!!$R2 818
4 TraesCS5D01G427700 chr5D 18153950 18154562 612 True 811.000000 811 90.499000 1 620 1 chr5D.!!$R1 619
5 TraesCS5D01G427700 chr3D 585808974 585812871 3897 True 1684.750000 5068 93.788000 1 5623 4 chr3D.!!$R4 5622
6 TraesCS5D01G427700 chr3D 464891014 464891699 685 True 1134.000000 1134 96.501000 4939 5624 1 chr3D.!!$R2 685
7 TraesCS5D01G427700 chr4D 30132065 30133775 1710 False 3011.000000 3011 98.424000 3057 4768 1 chr4D.!!$F1 1711
8 TraesCS5D01G427700 chr4D 160049354 160052420 3066 True 1551.666667 4410 94.588000 4 3057 3 chr4D.!!$R4 3053
9 TraesCS5D01G427700 chr4D 132567960 132571958 3998 False 1101.000000 3644 96.183833 3 5623 6 chr4D.!!$F2 5620
10 TraesCS5D01G427700 chr6D 382041667 382043377 1710 True 3048.000000 3048 98.831000 3058 4767 1 chr6D.!!$R2 1709
11 TraesCS5D01G427700 chr6D 382048534 382050244 1710 True 3003.000000 3003 98.364000 3058 4767 1 chr6D.!!$R3 1709
12 TraesCS5D01G427700 chr2D 641508782 641510502 1720 True 3013.000000 3013 98.258000 3051 4771 1 chr2D.!!$R2 1720
13 TraesCS5D01G427700 chr2D 201865102 201866812 1710 False 3005.000000 3005 98.364000 3057 4767 1 chr2D.!!$F1 1710
14 TraesCS5D01G427700 chr1D 438219185 438220895 1710 False 3000.000000 3000 98.307000 3058 4768 1 chr1D.!!$F1 1710
15 TraesCS5D01G427700 chr1D 473922841 473924551 1710 False 2998.000000 2998 98.305000 3058 4767 1 chr1D.!!$F2 1709
16 TraesCS5D01G427700 chr1D 418784558 418785330 772 True 828.000000 828 86.445000 1 760 1 chr1D.!!$R1 759
17 TraesCS5D01G427700 chr3B 41694890 41696451 1561 False 2564.000000 2564 96.242000 1489 3057 1 chr3B.!!$F1 1568
18 TraesCS5D01G427700 chr3B 185804886 185806448 1562 False 2527.000000 2527 95.799000 1489 3057 1 chr3B.!!$F2 1568
19 TraesCS5D01G427700 chr2A 690513700 690516121 2421 False 1854.500000 2558 93.566000 1489 5623 2 chr2A.!!$F1 4134
20 TraesCS5D01G427700 chr7D 455873018 455879173 6155 True 1549.750000 2095 96.009500 1 5623 4 chr7D.!!$R3 5622
21 TraesCS5D01G427700 chr2B 44181326 44182194 868 True 1127.000000 1127 90.367000 4768 5623 1 chr2B.!!$R1 855
22 TraesCS5D01G427700 chr2B 771210615 771211880 1265 False 1055.000000 1707 95.591500 1743 3057 2 chr2B.!!$F1 1314
23 TraesCS5D01G427700 chr4B 633813832 633814834 1002 False 1696.000000 1696 97.211000 1743 2744 1 chr4B.!!$F1 1001
24 TraesCS5D01G427700 chr5B 577990933 577991800 867 False 1144.000000 1144 90.711000 4768 5623 1 chr5B.!!$F2 855
25 TraesCS5D01G427700 chr5B 24166208 24168488 2280 True 702.500000 1166 93.849000 1489 5623 2 chr5B.!!$R2 4134
26 TraesCS5D01G427700 chr7B 60828209 60829076 867 True 1144.000000 1144 90.711000 4768 5623 1 chr7B.!!$R1 855
27 TraesCS5D01G427700 chr1B 110634729 110636737 2008 False 540.333333 1068 92.225000 1 1519 3 chr1B.!!$F1 1518

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
559 564 1.824852 GGACATTTTCCATCCACACCC 59.175 52.381 0.0 0.0 45.1 4.61 F
1329 2241 0.541764 GACCCCAACAATCCCAAGCA 60.542 55.000 0.0 0.0 0.0 3.91 F
3147 5993 0.399949 AGGGGAGAGTGTTGTCCACA 60.400 55.000 0.0 0.0 42.6 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 5151 0.459489 AGCAAAAACAAGCAGCCGAA 59.541 45.000 0.0 0.0 0.00 4.30 R
3283 6129 1.667154 CTCGGCTGGATCGGAGTTCA 61.667 60.000 0.0 0.0 0.00 3.18 R
4856 7703 3.132925 GCATTCAAAAAGCAGAAGCCAA 58.867 40.909 0.0 0.0 43.56 4.52 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
247 250 7.903995 TTGTTCAAAGAAAATGCAAACTTCT 57.096 28.000 0.00 0.00 0.00 2.85
427 431 9.287373 TGGTCATAATGTCGTACACATATACTA 57.713 33.333 10.16 2.46 45.77 1.82
496 501 4.368391 GATGCTCGCGGATCCAAT 57.632 55.556 13.41 0.00 32.39 3.16
559 564 1.824852 GGACATTTTCCATCCACACCC 59.175 52.381 0.00 0.00 45.10 4.61
887 1796 2.852075 TCCCACCCCTGCGTTTCT 60.852 61.111 0.00 0.00 0.00 2.52
890 1799 2.030562 CACCCCTGCGTTTCTCGT 59.969 61.111 0.00 0.00 42.13 4.18
1180 2092 4.630069 CCCAGTATCATCTCGTTTCGTTTT 59.370 41.667 0.00 0.00 0.00 2.43
1243 2155 1.134367 CGTCGGCTTCTGATCCTGTTA 59.866 52.381 0.00 0.00 0.00 2.41
1245 2157 2.427453 GTCGGCTTCTGATCCTGTTAGA 59.573 50.000 0.00 0.00 0.00 2.10
1297 2209 1.213013 GCTCGCGGTGAAGAAGAGA 59.787 57.895 6.13 0.00 0.00 3.10
1329 2241 0.541764 GACCCCAACAATCCCAAGCA 60.542 55.000 0.00 0.00 0.00 3.91
1330 2242 0.831711 ACCCCAACAATCCCAAGCAC 60.832 55.000 0.00 0.00 0.00 4.40
1400 2312 1.668151 AAAGAGAAGCACCCGACGC 60.668 57.895 0.00 0.00 0.00 5.19
1522 2462 7.176515 TGGCCAATGTATATGATTGTATTCACC 59.823 37.037 0.61 0.00 0.00 4.02
1766 2706 4.454678 TGAATCTGTTGCTCTTCTTGTGT 58.545 39.130 0.00 0.00 0.00 3.72
2046 4891 3.358775 CTCTCTGTTACTGCTCGATTCG 58.641 50.000 0.00 0.00 0.00 3.34
2071 4916 3.885901 GCTGGTCACTTCCTTCTTTCTTT 59.114 43.478 0.00 0.00 0.00 2.52
2072 4917 4.261363 GCTGGTCACTTCCTTCTTTCTTTG 60.261 45.833 0.00 0.00 0.00 2.77
2216 5061 3.776616 GCTGATCTACTGCCTTGCT 57.223 52.632 0.00 0.00 37.46 3.91
2224 5069 4.292186 TCTACTGCCTTGCTCTCAATTT 57.708 40.909 0.00 0.00 0.00 1.82
2305 5151 2.040412 CAGTCAGTAGGAGGGGCTTTTT 59.960 50.000 0.00 0.00 0.00 1.94
2367 5213 6.613271 TCTCTGGTTATAAGGATTTCAGAGCT 59.387 38.462 11.28 0.00 43.54 4.09
2694 5540 9.109393 TGTTGCTTTTGTTCAGTATATATCTCC 57.891 33.333 0.00 0.00 0.00 3.71
2855 5701 4.140536 TGTACATCTGTTTGCATGTTCCA 58.859 39.130 0.00 0.00 34.92 3.53
2928 5774 5.804639 AGTATGAGCACTCAACCATTGTAA 58.195 37.500 4.14 0.00 43.58 2.41
2930 5776 4.829064 TGAGCACTCAACCATTGTAAAC 57.171 40.909 0.00 0.00 36.53 2.01
3067 5913 1.077663 AGCATCCTTGTGTTGGGGAAT 59.922 47.619 0.00 0.00 32.53 3.01
3076 5922 5.357032 CCTTGTGTTGGGGAATGTAGTAATC 59.643 44.000 0.00 0.00 0.00 1.75
3147 5993 0.399949 AGGGGAGAGTGTTGTCCACA 60.400 55.000 0.00 0.00 42.60 4.17
3283 6129 0.965866 TCAGCTCGATGACGTCCCTT 60.966 55.000 14.12 0.00 40.69 3.95
3924 6770 7.855409 TCAAAACTCAATAAAACTGTCATCGTG 59.145 33.333 0.00 0.00 0.00 4.35
4041 6887 6.354213 CCCATATTGGCTCCCACATATTCTAT 60.354 42.308 0.00 0.00 35.79 1.98
4529 7376 4.926238 GTCAAGTCAATCACGTCATTCTCT 59.074 41.667 0.00 0.00 0.00 3.10
4826 7673 4.816990 GCTCGAAGGAGGCAGTAC 57.183 61.111 0.00 0.00 40.80 2.73
4856 7703 3.461085 ACCTCCTGATGGATATTGCTTGT 59.539 43.478 0.00 0.00 42.29 3.16
5308 8158 2.742856 GCCCATTTAGCCAATCAAAGCC 60.743 50.000 0.00 0.00 0.00 4.35
5391 8243 2.753966 CGGGCTGATTCTTGTGCCG 61.754 63.158 0.00 0.00 45.75 5.69
5624 8492 8.774586 ACAAGTTGACATATTTCTTGTAGTGAC 58.225 33.333 10.54 0.00 44.11 3.67
5625 8493 7.907214 AGTTGACATATTTCTTGTAGTGACC 57.093 36.000 0.00 0.00 0.00 4.02
5626 8494 7.680730 AGTTGACATATTTCTTGTAGTGACCT 58.319 34.615 0.00 0.00 0.00 3.85
5627 8495 7.819900 AGTTGACATATTTCTTGTAGTGACCTC 59.180 37.037 0.00 0.00 0.00 3.85
5628 8496 7.482169 TGACATATTTCTTGTAGTGACCTCT 57.518 36.000 0.00 0.00 0.00 3.69
5629 8497 8.589701 TGACATATTTCTTGTAGTGACCTCTA 57.410 34.615 0.00 0.00 0.00 2.43
5630 8498 8.687242 TGACATATTTCTTGTAGTGACCTCTAG 58.313 37.037 0.00 0.00 0.00 2.43
5631 8499 8.824756 ACATATTTCTTGTAGTGACCTCTAGA 57.175 34.615 0.00 0.00 0.00 2.43
5632 8500 8.688151 ACATATTTCTTGTAGTGACCTCTAGAC 58.312 37.037 0.00 0.00 0.00 2.59
5633 8501 8.687242 CATATTTCTTGTAGTGACCTCTAGACA 58.313 37.037 0.00 0.00 0.00 3.41
5634 8502 5.961396 TTCTTGTAGTGACCTCTAGACAC 57.039 43.478 4.24 4.24 35.15 3.67
5635 8503 4.981812 TCTTGTAGTGACCTCTAGACACA 58.018 43.478 12.88 0.86 37.05 3.72
5636 8504 4.760715 TCTTGTAGTGACCTCTAGACACAC 59.239 45.833 12.88 11.21 37.05 3.82
5637 8505 4.094830 TGTAGTGACCTCTAGACACACA 57.905 45.455 12.88 11.48 37.05 3.72
5638 8506 4.466827 TGTAGTGACCTCTAGACACACAA 58.533 43.478 12.88 0.00 37.05 3.33
5639 8507 4.519350 TGTAGTGACCTCTAGACACACAAG 59.481 45.833 12.88 0.00 37.05 3.16
5640 8508 3.567397 AGTGACCTCTAGACACACAAGT 58.433 45.455 12.88 0.00 37.05 3.16
5641 8509 3.961408 AGTGACCTCTAGACACACAAGTT 59.039 43.478 12.88 0.00 37.05 2.66
5642 8510 4.051922 GTGACCTCTAGACACACAAGTTG 58.948 47.826 0.00 0.00 35.06 3.16
5643 8511 3.958147 TGACCTCTAGACACACAAGTTGA 59.042 43.478 10.54 0.00 0.00 3.18
5644 8512 4.588951 TGACCTCTAGACACACAAGTTGAT 59.411 41.667 10.54 0.00 0.00 2.57
5645 8513 5.140747 ACCTCTAGACACACAAGTTGATC 57.859 43.478 10.54 1.78 0.00 2.92
5646 8514 4.835615 ACCTCTAGACACACAAGTTGATCT 59.164 41.667 10.54 9.01 0.00 2.75
5647 8515 5.167121 CCTCTAGACACACAAGTTGATCTG 58.833 45.833 10.54 0.00 0.00 2.90
5648 8516 5.279206 CCTCTAGACACACAAGTTGATCTGT 60.279 44.000 10.54 7.16 0.00 3.41
5649 8517 6.161855 TCTAGACACACAAGTTGATCTGTT 57.838 37.500 10.54 0.00 0.00 3.16
5650 8518 5.985530 TCTAGACACACAAGTTGATCTGTTG 59.014 40.000 10.54 0.00 0.00 3.33
5651 8519 4.769688 AGACACACAAGTTGATCTGTTGA 58.230 39.130 10.54 0.00 0.00 3.18
5652 8520 5.371526 AGACACACAAGTTGATCTGTTGAT 58.628 37.500 10.54 0.00 35.26 2.57
5653 8521 5.468072 AGACACACAAGTTGATCTGTTGATC 59.532 40.000 10.54 2.06 46.89 2.92
5654 8522 5.371526 ACACACAAGTTGATCTGTTGATCT 58.628 37.500 10.54 0.00 46.84 2.75
5655 8523 5.468072 ACACACAAGTTGATCTGTTGATCTC 59.532 40.000 10.54 2.12 46.84 2.75
5656 8524 5.699915 CACACAAGTTGATCTGTTGATCTCT 59.300 40.000 10.54 3.97 46.84 3.10
5657 8525 5.931146 ACACAAGTTGATCTGTTGATCTCTC 59.069 40.000 10.54 0.00 46.84 3.20
5658 8526 5.350914 CACAAGTTGATCTGTTGATCTCTCC 59.649 44.000 10.54 0.00 46.84 3.71
5659 8527 4.751767 AGTTGATCTGTTGATCTCTCCC 57.248 45.455 7.42 0.00 46.84 4.30
5660 8528 4.099633 AGTTGATCTGTTGATCTCTCCCA 58.900 43.478 7.42 0.00 46.84 4.37
5661 8529 4.161942 AGTTGATCTGTTGATCTCTCCCAG 59.838 45.833 7.42 0.00 46.84 4.45
5662 8530 2.433604 TGATCTGTTGATCTCTCCCAGC 59.566 50.000 7.42 0.00 46.84 4.85
5663 8531 1.198713 TCTGTTGATCTCTCCCAGCC 58.801 55.000 0.00 0.00 0.00 4.85
5664 8532 0.179089 CTGTTGATCTCTCCCAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
5665 8533 0.904865 TGTTGATCTCTCCCAGCCGT 60.905 55.000 0.00 0.00 0.00 5.68
5666 8534 0.460987 GTTGATCTCTCCCAGCCGTG 60.461 60.000 0.00 0.00 0.00 4.94
5667 8535 0.904865 TTGATCTCTCCCAGCCGTGT 60.905 55.000 0.00 0.00 0.00 4.49
5668 8536 1.142748 GATCTCTCCCAGCCGTGTG 59.857 63.158 0.00 0.00 0.00 3.82
5669 8537 2.914777 GATCTCTCCCAGCCGTGTGC 62.915 65.000 0.00 0.00 41.71 4.57
5693 8561 3.922426 CCCCCTCCAACATATTGCA 57.078 52.632 0.00 0.00 34.17 4.08
5694 8562 1.402787 CCCCCTCCAACATATTGCAC 58.597 55.000 0.00 0.00 34.17 4.57
5695 8563 1.402787 CCCCTCCAACATATTGCACC 58.597 55.000 0.00 0.00 34.17 5.01
5696 8564 1.063717 CCCCTCCAACATATTGCACCT 60.064 52.381 0.00 0.00 34.17 4.00
5697 8565 2.301346 CCCTCCAACATATTGCACCTC 58.699 52.381 0.00 0.00 34.17 3.85
5698 8566 1.942657 CCTCCAACATATTGCACCTCG 59.057 52.381 0.00 0.00 34.17 4.63
5699 8567 1.942657 CTCCAACATATTGCACCTCGG 59.057 52.381 0.00 0.00 34.17 4.63
5700 8568 1.280710 TCCAACATATTGCACCTCGGT 59.719 47.619 0.00 0.00 34.17 4.69
5701 8569 1.670811 CCAACATATTGCACCTCGGTC 59.329 52.381 0.00 0.00 34.17 4.79
5702 8570 2.355197 CAACATATTGCACCTCGGTCA 58.645 47.619 0.00 0.00 0.00 4.02
5703 8571 2.945008 CAACATATTGCACCTCGGTCAT 59.055 45.455 0.00 0.00 0.00 3.06
5704 8572 4.126437 CAACATATTGCACCTCGGTCATA 58.874 43.478 0.00 0.00 0.00 2.15
5705 8573 4.623932 ACATATTGCACCTCGGTCATAT 57.376 40.909 0.00 0.00 0.00 1.78
5706 8574 4.569943 ACATATTGCACCTCGGTCATATC 58.430 43.478 0.00 0.00 0.00 1.63
5707 8575 2.154854 ATTGCACCTCGGTCATATCG 57.845 50.000 0.00 0.00 0.00 2.92
5708 8576 0.821517 TTGCACCTCGGTCATATCGT 59.178 50.000 0.00 0.00 0.00 3.73
5709 8577 1.682740 TGCACCTCGGTCATATCGTA 58.317 50.000 0.00 0.00 0.00 3.43
5710 8578 1.607148 TGCACCTCGGTCATATCGTAG 59.393 52.381 0.00 0.00 0.00 3.51
5711 8579 1.666311 GCACCTCGGTCATATCGTAGC 60.666 57.143 0.00 0.00 0.00 3.58
5712 8580 0.873054 ACCTCGGTCATATCGTAGCG 59.127 55.000 0.00 0.00 37.92 4.26
5713 8581 0.168348 CCTCGGTCATATCGTAGCGG 59.832 60.000 0.00 0.00 37.22 5.52
5714 8582 0.873054 CTCGGTCATATCGTAGCGGT 59.127 55.000 0.00 0.00 37.22 5.68
5715 8583 0.589708 TCGGTCATATCGTAGCGGTG 59.410 55.000 0.00 0.00 37.22 4.94
5716 8584 1.002250 CGGTCATATCGTAGCGGTGC 61.002 60.000 0.00 0.00 33.22 5.01
5717 8585 0.314302 GGTCATATCGTAGCGGTGCT 59.686 55.000 0.00 0.00 43.41 4.40
5718 8586 1.269621 GGTCATATCGTAGCGGTGCTT 60.270 52.381 0.00 0.00 40.44 3.91
5719 8587 2.030540 GGTCATATCGTAGCGGTGCTTA 60.031 50.000 0.00 0.00 40.44 3.09
5720 8588 3.235195 GTCATATCGTAGCGGTGCTTAG 58.765 50.000 0.00 0.00 40.44 2.18
5721 8589 2.228103 TCATATCGTAGCGGTGCTTAGG 59.772 50.000 0.00 0.00 40.44 2.69
5722 8590 0.313043 TATCGTAGCGGTGCTTAGGC 59.687 55.000 0.00 0.00 40.44 3.93
5723 8591 2.679132 ATCGTAGCGGTGCTTAGGCG 62.679 60.000 0.00 0.00 40.44 5.52
5724 8592 2.493030 GTAGCGGTGCTTAGGCGA 59.507 61.111 0.00 0.00 40.44 5.54
5725 8593 1.153706 GTAGCGGTGCTTAGGCGAA 60.154 57.895 0.00 0.00 40.44 4.70
5726 8594 1.141019 TAGCGGTGCTTAGGCGAAG 59.859 57.895 2.68 2.68 40.44 3.79
5739 8607 2.499205 CGAAGCCCTGCATCGGTA 59.501 61.111 5.86 0.00 44.27 4.02
5740 8608 1.592669 CGAAGCCCTGCATCGGTAG 60.593 63.158 5.86 0.00 44.27 3.18
5741 8609 1.889573 GAAGCCCTGCATCGGTAGC 60.890 63.158 2.20 0.00 0.00 3.58
5742 8610 2.593468 GAAGCCCTGCATCGGTAGCA 62.593 60.000 2.20 0.00 40.19 3.49
5743 8611 2.124736 GCCCTGCATCGGTAGCAA 60.125 61.111 2.20 0.00 42.17 3.91
5744 8612 2.472909 GCCCTGCATCGGTAGCAAC 61.473 63.158 2.20 0.00 42.17 4.17
5745 8613 1.078497 CCCTGCATCGGTAGCAACA 60.078 57.895 0.00 0.00 42.17 3.33
5746 8614 0.464373 CCCTGCATCGGTAGCAACAT 60.464 55.000 0.00 0.00 42.17 2.71
5747 8615 0.940126 CCTGCATCGGTAGCAACATC 59.060 55.000 0.00 0.00 42.17 3.06
5748 8616 1.655484 CTGCATCGGTAGCAACATCA 58.345 50.000 0.00 0.00 42.17 3.07
5749 8617 2.216046 CTGCATCGGTAGCAACATCAT 58.784 47.619 0.00 0.00 42.17 2.45
5750 8618 2.212652 TGCATCGGTAGCAACATCATC 58.787 47.619 0.00 0.00 39.39 2.92
5751 8619 2.212652 GCATCGGTAGCAACATCATCA 58.787 47.619 0.00 0.00 0.00 3.07
5752 8620 2.032549 GCATCGGTAGCAACATCATCAC 60.033 50.000 0.00 0.00 0.00 3.06
5753 8621 2.309528 TCGGTAGCAACATCATCACC 57.690 50.000 0.00 0.00 0.00 4.02
5754 8622 0.930310 CGGTAGCAACATCATCACCG 59.070 55.000 0.00 0.00 42.41 4.94
5755 8623 1.739035 CGGTAGCAACATCATCACCGT 60.739 52.381 2.91 0.00 42.93 4.83
5756 8624 1.933853 GGTAGCAACATCATCACCGTC 59.066 52.381 0.00 0.00 0.00 4.79
5757 8625 2.616960 GTAGCAACATCATCACCGTCA 58.383 47.619 0.00 0.00 0.00 4.35
5758 8626 2.408271 AGCAACATCATCACCGTCAT 57.592 45.000 0.00 0.00 0.00 3.06
5759 8627 2.283298 AGCAACATCATCACCGTCATC 58.717 47.619 0.00 0.00 0.00 2.92
5760 8628 2.009051 GCAACATCATCACCGTCATCA 58.991 47.619 0.00 0.00 0.00 3.07
5761 8629 2.223112 GCAACATCATCACCGTCATCAC 60.223 50.000 0.00 0.00 0.00 3.06
5762 8630 1.926561 ACATCATCACCGTCATCACG 58.073 50.000 0.00 0.00 46.29 4.35
5763 8631 0.578683 CATCATCACCGTCATCACGC 59.421 55.000 0.00 0.00 45.29 5.34
5764 8632 0.530650 ATCATCACCGTCATCACGCC 60.531 55.000 0.00 0.00 45.29 5.68
5765 8633 2.202743 ATCACCGTCATCACGCCG 60.203 61.111 0.00 0.00 45.29 6.46
5766 8634 3.001902 ATCACCGTCATCACGCCGT 62.002 57.895 0.00 0.00 45.29 5.68
5767 8635 2.884087 ATCACCGTCATCACGCCGTC 62.884 60.000 0.00 0.00 45.29 4.79
5768 8636 4.771356 ACCGTCATCACGCCGTCG 62.771 66.667 0.00 0.00 45.29 5.12
5782 8650 3.843985 GTCGTGCTGACGGAACTC 58.156 61.111 0.00 0.00 46.11 3.01
5783 8651 1.286260 GTCGTGCTGACGGAACTCT 59.714 57.895 0.00 0.00 46.11 3.24
5784 8652 0.729816 GTCGTGCTGACGGAACTCTC 60.730 60.000 0.00 0.00 46.11 3.20
5785 8653 1.444553 CGTGCTGACGGAACTCTCC 60.445 63.158 0.00 0.00 42.18 3.71
5786 8654 1.079750 GTGCTGACGGAACTCTCCC 60.080 63.158 0.00 0.00 38.71 4.30
5787 8655 1.533033 TGCTGACGGAACTCTCCCA 60.533 57.895 0.00 0.00 38.71 4.37
5788 8656 0.904865 TGCTGACGGAACTCTCCCAT 60.905 55.000 0.00 0.00 38.71 4.00
5789 8657 0.460987 GCTGACGGAACTCTCCCATG 60.461 60.000 0.00 0.00 38.71 3.66
5790 8658 1.186200 CTGACGGAACTCTCCCATGA 58.814 55.000 0.00 0.00 38.71 3.07
5791 8659 1.550524 CTGACGGAACTCTCCCATGAA 59.449 52.381 0.00 0.00 38.71 2.57
5792 8660 1.550524 TGACGGAACTCTCCCATGAAG 59.449 52.381 0.00 0.00 38.71 3.02
5793 8661 0.250513 ACGGAACTCTCCCATGAAGC 59.749 55.000 0.00 0.00 38.71 3.86
5794 8662 0.539051 CGGAACTCTCCCATGAAGCT 59.461 55.000 0.00 0.00 38.71 3.74
5795 8663 1.472376 CGGAACTCTCCCATGAAGCTC 60.472 57.143 0.00 0.00 38.71 4.09
5796 8664 1.836802 GGAACTCTCCCATGAAGCTCT 59.163 52.381 0.00 0.00 35.42 4.09
5797 8665 2.419851 GGAACTCTCCCATGAAGCTCTG 60.420 54.545 0.00 0.00 35.42 3.35
5798 8666 0.540923 ACTCTCCCATGAAGCTCTGC 59.459 55.000 0.00 0.00 0.00 4.26
5799 8667 0.831966 CTCTCCCATGAAGCTCTGCT 59.168 55.000 0.00 0.00 42.56 4.24
5800 8668 0.540454 TCTCCCATGAAGCTCTGCTG 59.460 55.000 0.00 0.00 39.62 4.41
5801 8669 0.464013 CTCCCATGAAGCTCTGCTGG 60.464 60.000 0.00 0.00 39.62 4.85
5802 8670 0.911045 TCCCATGAAGCTCTGCTGGA 60.911 55.000 0.00 0.00 39.62 3.86
5803 8671 0.183014 CCCATGAAGCTCTGCTGGAT 59.817 55.000 0.00 0.00 39.62 3.41
5804 8672 1.595466 CCATGAAGCTCTGCTGGATC 58.405 55.000 0.00 0.00 39.62 3.36
5805 8673 1.218763 CATGAAGCTCTGCTGGATCG 58.781 55.000 0.00 0.00 39.62 3.69
5806 8674 0.106335 ATGAAGCTCTGCTGGATCGG 59.894 55.000 0.00 0.00 39.62 4.18
5807 8675 0.972471 TGAAGCTCTGCTGGATCGGA 60.972 55.000 0.00 0.00 39.62 4.55
5808 8676 0.249405 GAAGCTCTGCTGGATCGGAG 60.249 60.000 0.00 0.00 39.62 4.63
5809 8677 0.975040 AAGCTCTGCTGGATCGGAGT 60.975 55.000 0.00 0.00 39.62 3.85
5810 8678 0.975040 AGCTCTGCTGGATCGGAGTT 60.975 55.000 0.00 0.00 40.67 3.01
5811 8679 0.529555 GCTCTGCTGGATCGGAGTTC 60.530 60.000 2.12 0.00 40.67 3.01
5812 8680 0.248825 CTCTGCTGGATCGGAGTTCG 60.249 60.000 0.00 0.00 35.32 3.95
5813 8681 1.880340 CTGCTGGATCGGAGTTCGC 60.880 63.158 0.00 0.00 39.05 4.70
5814 8682 2.956964 GCTGGATCGGAGTTCGCG 60.957 66.667 0.00 0.00 39.05 5.87
5815 8683 2.278857 CTGGATCGGAGTTCGCGG 60.279 66.667 6.13 0.00 39.05 6.46
5816 8684 3.774959 CTGGATCGGAGTTCGCGGG 62.775 68.421 6.13 0.00 39.05 6.13
5817 8685 3.524606 GGATCGGAGTTCGCGGGA 61.525 66.667 6.13 0.00 39.05 5.14
5818 8686 2.278661 GATCGGAGTTCGCGGGAC 60.279 66.667 6.13 5.78 39.05 4.46
5833 8701 1.557651 GGGACGTCATCGAGCTAAAC 58.442 55.000 18.91 0.00 40.62 2.01
5834 8702 1.189403 GGACGTCATCGAGCTAAACG 58.811 55.000 18.91 0.00 40.62 3.60
5836 8704 1.578023 GACGTCATCGAGCTAAACGTG 59.422 52.381 11.55 3.80 45.58 4.49
5837 8705 1.068748 ACGTCATCGAGCTAAACGTGT 60.069 47.619 11.09 0.00 44.10 4.49
5838 8706 1.317611 CGTCATCGAGCTAAACGTGTG 59.682 52.381 0.00 0.00 39.71 3.82
5839 8707 1.059264 GTCATCGAGCTAAACGTGTGC 59.941 52.381 0.00 0.00 0.00 4.57
5840 8708 1.067846 TCATCGAGCTAAACGTGTGCT 60.068 47.619 9.46 9.46 40.02 4.40
5841 8709 1.059692 CATCGAGCTAAACGTGTGCTG 59.940 52.381 13.62 7.51 37.16 4.41
5842 8710 0.312729 TCGAGCTAAACGTGTGCTGA 59.687 50.000 13.62 9.24 37.16 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 250 8.635765 AAAGTAAGAAGCATGGAAGACATAAA 57.364 30.769 0.00 0.00 37.84 1.40
427 431 3.843422 TCCCACAAACCAATCAGAATGT 58.157 40.909 0.00 0.00 37.40 2.71
496 501 3.106609 TCAGGTGGGTTTGGGCCA 61.107 61.111 0.00 0.00 0.00 5.36
667 1029 4.785453 GAGAGGTTGGGGGCGCTG 62.785 72.222 7.64 0.00 0.00 5.18
887 1796 3.763897 TGAATCTCTGATGAACTGGACGA 59.236 43.478 0.00 0.00 0.00 4.20
890 1799 6.556974 ATCTTGAATCTCTGATGAACTGGA 57.443 37.500 0.00 0.00 0.00 3.86
1026 1935 4.704833 GCAGCAAGGGAGTCGCCA 62.705 66.667 3.13 0.00 38.95 5.69
1180 2092 1.227823 CAAGCAGAACCACCACGGA 60.228 57.895 0.00 0.00 38.63 4.69
1243 2155 3.271729 CAGAAACAGCATCAGCAGATCT 58.728 45.455 0.00 0.00 45.49 2.75
1245 2157 2.747989 CACAGAAACAGCATCAGCAGAT 59.252 45.455 0.00 0.00 45.49 2.90
1297 2209 2.434774 GGGTCCTTGTCGGCCTTT 59.565 61.111 0.00 0.00 31.82 3.11
1384 2296 4.070552 GGCGTCGGGTGCTTCTCT 62.071 66.667 0.00 0.00 0.00 3.10
1411 2323 0.608640 ACCGAGAAGCTTACCACAGG 59.391 55.000 0.00 0.00 0.00 4.00
1522 2462 4.258702 AGTTGTGGAGTAGCTGTACAAG 57.741 45.455 0.00 0.00 32.54 3.16
1972 4816 0.679505 TGGGACTTCCACTTCTCACG 59.320 55.000 0.00 0.00 41.46 4.35
2071 4916 1.885388 CGACACCGAGCAAACACCA 60.885 57.895 0.00 0.00 38.22 4.17
2072 4917 1.885850 ACGACACCGAGCAAACACC 60.886 57.895 0.00 0.00 39.50 4.16
2213 5058 6.821160 TGATTTATACGACCAAATTGAGAGCA 59.179 34.615 0.00 0.00 0.00 4.26
2305 5151 0.459489 AGCAAAAACAAGCAGCCGAA 59.541 45.000 0.00 0.00 0.00 4.30
2308 5154 1.862827 CTGAAGCAAAAACAAGCAGCC 59.137 47.619 0.00 0.00 0.00 4.85
2367 5213 4.523173 ACCAGAGATTCAGAACAAGTCGTA 59.477 41.667 0.00 0.00 0.00 3.43
2694 5540 5.065218 ACCTATGCTTACAAATCAGAAAGCG 59.935 40.000 0.00 0.00 45.72 4.68
2855 5701 5.889853 ACCAATAGTGATGATCAGTGCAATT 59.110 36.000 12.86 2.40 31.49 2.32
2928 5774 8.900983 ATACAAAACAAATATGCAAACAGGTT 57.099 26.923 0.00 0.00 0.00 3.50
3283 6129 1.667154 CTCGGCTGGATCGGAGTTCA 61.667 60.000 0.00 0.00 0.00 3.18
4041 6887 5.263968 GGTCTGACCGATAAAGATCTTCA 57.736 43.478 11.71 0.00 0.00 3.02
4529 7376 6.241882 TGATTAACGGGATCACCTCATTTA 57.758 37.500 0.00 0.00 36.97 1.40
4856 7703 3.132925 GCATTCAAAAAGCAGAAGCCAA 58.867 40.909 0.00 0.00 43.56 4.52
4952 7799 4.259810 CGCATAACATTAGACAGACCAACG 60.260 45.833 0.00 0.00 0.00 4.10
5391 8243 3.437795 AGCGTGGCAAGCTGATGC 61.438 61.111 26.78 1.52 44.22 3.91
5504 8372 4.508861 GTCAAAAGCTGGTAGTCGTAAACA 59.491 41.667 0.00 0.00 0.00 2.83
5624 8492 5.167121 CAGATCAACTTGTGTGTCTAGAGG 58.833 45.833 0.00 0.00 0.00 3.69
5625 8493 5.777802 ACAGATCAACTTGTGTGTCTAGAG 58.222 41.667 0.00 0.00 0.00 2.43
5626 8494 5.791336 ACAGATCAACTTGTGTGTCTAGA 57.209 39.130 0.00 0.00 0.00 2.43
5627 8495 5.985530 TCAACAGATCAACTTGTGTGTCTAG 59.014 40.000 0.00 0.00 0.00 2.43
5628 8496 5.912892 TCAACAGATCAACTTGTGTGTCTA 58.087 37.500 0.00 0.00 0.00 2.59
5629 8497 4.769688 TCAACAGATCAACTTGTGTGTCT 58.230 39.130 0.00 0.00 0.00 3.41
5630 8498 5.468072 AGATCAACAGATCAACTTGTGTGTC 59.532 40.000 8.06 0.00 40.49 3.67
5631 8499 5.371526 AGATCAACAGATCAACTTGTGTGT 58.628 37.500 8.06 0.00 40.49 3.72
5632 8500 5.699915 AGAGATCAACAGATCAACTTGTGTG 59.300 40.000 8.06 0.00 40.49 3.82
5633 8501 5.862845 AGAGATCAACAGATCAACTTGTGT 58.137 37.500 8.06 0.00 40.49 3.72
5634 8502 5.350914 GGAGAGATCAACAGATCAACTTGTG 59.649 44.000 8.06 0.00 40.49 3.33
5635 8503 5.486526 GGAGAGATCAACAGATCAACTTGT 58.513 41.667 8.06 0.00 40.49 3.16
5636 8504 4.874966 GGGAGAGATCAACAGATCAACTTG 59.125 45.833 8.06 0.00 40.49 3.16
5637 8505 4.533707 TGGGAGAGATCAACAGATCAACTT 59.466 41.667 8.06 0.00 40.49 2.66
5638 8506 4.099633 TGGGAGAGATCAACAGATCAACT 58.900 43.478 8.06 6.58 40.49 3.16
5639 8507 4.440880 CTGGGAGAGATCAACAGATCAAC 58.559 47.826 8.06 2.45 40.49 3.18
5640 8508 3.118482 GCTGGGAGAGATCAACAGATCAA 60.118 47.826 8.06 0.00 40.49 2.57
5641 8509 2.433604 GCTGGGAGAGATCAACAGATCA 59.566 50.000 8.06 0.00 40.49 2.92
5642 8510 2.224257 GGCTGGGAGAGATCAACAGATC 60.224 54.545 0.00 0.00 38.74 2.75
5643 8511 1.767681 GGCTGGGAGAGATCAACAGAT 59.232 52.381 0.00 0.00 0.00 2.90
5644 8512 1.198713 GGCTGGGAGAGATCAACAGA 58.801 55.000 0.00 0.00 0.00 3.41
5645 8513 0.179089 CGGCTGGGAGAGATCAACAG 60.179 60.000 0.00 0.00 0.00 3.16
5646 8514 0.904865 ACGGCTGGGAGAGATCAACA 60.905 55.000 0.00 0.00 0.00 3.33
5647 8515 0.460987 CACGGCTGGGAGAGATCAAC 60.461 60.000 0.00 0.00 0.00 3.18
5648 8516 0.904865 ACACGGCTGGGAGAGATCAA 60.905 55.000 0.00 0.00 0.00 2.57
5649 8517 1.305297 ACACGGCTGGGAGAGATCA 60.305 57.895 0.00 0.00 0.00 2.92
5650 8518 1.142748 CACACGGCTGGGAGAGATC 59.857 63.158 0.00 0.00 0.00 2.75
5651 8519 3.023949 GCACACGGCTGGGAGAGAT 62.024 63.158 0.00 0.00 40.25 2.75
5652 8520 3.695606 GCACACGGCTGGGAGAGA 61.696 66.667 0.00 0.00 40.25 3.10
5675 8543 1.402787 GTGCAATATGTTGGAGGGGG 58.597 55.000 4.23 0.00 36.28 5.40
5676 8544 1.063717 AGGTGCAATATGTTGGAGGGG 60.064 52.381 4.23 0.00 36.28 4.79
5677 8545 2.301346 GAGGTGCAATATGTTGGAGGG 58.699 52.381 4.23 0.00 36.28 4.30
5678 8546 1.942657 CGAGGTGCAATATGTTGGAGG 59.057 52.381 4.23 0.00 36.28 4.30
5679 8547 1.942657 CCGAGGTGCAATATGTTGGAG 59.057 52.381 4.23 0.00 36.28 3.86
5680 8548 1.280710 ACCGAGGTGCAATATGTTGGA 59.719 47.619 4.23 0.00 35.83 3.53
5681 8549 1.670811 GACCGAGGTGCAATATGTTGG 59.329 52.381 0.00 0.00 35.83 3.77
5682 8550 2.355197 TGACCGAGGTGCAATATGTTG 58.645 47.619 0.00 0.00 38.39 3.33
5683 8551 2.779755 TGACCGAGGTGCAATATGTT 57.220 45.000 0.00 0.00 0.00 2.71
5684 8552 4.569943 GATATGACCGAGGTGCAATATGT 58.430 43.478 0.00 0.00 0.00 2.29
5685 8553 3.614176 CGATATGACCGAGGTGCAATATG 59.386 47.826 0.00 0.00 0.00 1.78
5686 8554 3.258372 ACGATATGACCGAGGTGCAATAT 59.742 43.478 0.00 0.85 0.00 1.28
5687 8555 2.626266 ACGATATGACCGAGGTGCAATA 59.374 45.455 0.00 0.00 0.00 1.90
5688 8556 1.412710 ACGATATGACCGAGGTGCAAT 59.587 47.619 0.00 0.00 0.00 3.56
5689 8557 0.821517 ACGATATGACCGAGGTGCAA 59.178 50.000 0.00 0.00 0.00 4.08
5690 8558 1.607148 CTACGATATGACCGAGGTGCA 59.393 52.381 0.00 0.00 0.00 4.57
5691 8559 1.666311 GCTACGATATGACCGAGGTGC 60.666 57.143 0.00 0.00 0.00 5.01
5692 8560 1.399855 CGCTACGATATGACCGAGGTG 60.400 57.143 0.00 0.00 0.00 4.00
5693 8561 0.873054 CGCTACGATATGACCGAGGT 59.127 55.000 0.00 0.00 0.00 3.85
5694 8562 0.168348 CCGCTACGATATGACCGAGG 59.832 60.000 0.00 0.00 0.00 4.63
5695 8563 0.873054 ACCGCTACGATATGACCGAG 59.127 55.000 0.00 0.00 0.00 4.63
5696 8564 0.589708 CACCGCTACGATATGACCGA 59.410 55.000 0.00 0.00 0.00 4.69
5697 8565 1.002250 GCACCGCTACGATATGACCG 61.002 60.000 0.00 0.00 0.00 4.79
5698 8566 0.314302 AGCACCGCTACGATATGACC 59.686 55.000 0.00 0.00 36.99 4.02
5699 8567 2.135664 AAGCACCGCTACGATATGAC 57.864 50.000 0.00 0.00 38.25 3.06
5700 8568 2.228103 CCTAAGCACCGCTACGATATGA 59.772 50.000 0.00 0.00 38.25 2.15
5701 8569 2.596452 CCTAAGCACCGCTACGATATG 58.404 52.381 0.00 0.00 38.25 1.78
5702 8570 1.067776 GCCTAAGCACCGCTACGATAT 60.068 52.381 0.00 0.00 38.25 1.63
5703 8571 0.313043 GCCTAAGCACCGCTACGATA 59.687 55.000 0.00 0.00 38.25 2.92
5704 8572 1.067582 GCCTAAGCACCGCTACGAT 59.932 57.895 0.00 0.00 38.25 3.73
5705 8573 2.493030 GCCTAAGCACCGCTACGA 59.507 61.111 0.00 0.00 38.25 3.43
5706 8574 2.877360 TTCGCCTAAGCACCGCTACG 62.877 60.000 0.00 0.00 38.25 3.51
5707 8575 1.146358 CTTCGCCTAAGCACCGCTAC 61.146 60.000 0.00 0.00 38.25 3.58
5708 8576 1.141019 CTTCGCCTAAGCACCGCTA 59.859 57.895 0.00 0.00 38.25 4.26
5709 8577 2.125512 CTTCGCCTAAGCACCGCT 60.126 61.111 0.00 0.00 42.56 5.52
5723 8591 1.889573 GCTACCGATGCAGGGCTTC 60.890 63.158 6.50 0.00 35.02 3.86
5724 8592 2.190578 GCTACCGATGCAGGGCTT 59.809 61.111 6.50 0.00 35.02 4.35
5725 8593 2.669133 TTGCTACCGATGCAGGGCT 61.669 57.895 6.50 0.00 41.71 5.19
5726 8594 2.124736 TTGCTACCGATGCAGGGC 60.125 61.111 6.50 0.00 41.71 5.19
5727 8595 0.464373 ATGTTGCTACCGATGCAGGG 60.464 55.000 5.09 5.09 41.71 4.45
5728 8596 0.940126 GATGTTGCTACCGATGCAGG 59.060 55.000 0.00 0.00 41.71 4.85
5729 8597 1.655484 TGATGTTGCTACCGATGCAG 58.345 50.000 0.00 0.00 41.71 4.41
5730 8598 2.212652 GATGATGTTGCTACCGATGCA 58.787 47.619 0.00 0.00 38.80 3.96
5731 8599 2.032549 GTGATGATGTTGCTACCGATGC 60.033 50.000 0.00 0.00 0.00 3.91
5732 8600 2.545526 GGTGATGATGTTGCTACCGATG 59.454 50.000 0.00 0.00 0.00 3.84
5733 8601 2.838736 GGTGATGATGTTGCTACCGAT 58.161 47.619 0.00 0.00 0.00 4.18
5734 8602 2.309528 GGTGATGATGTTGCTACCGA 57.690 50.000 0.00 0.00 0.00 4.69
5735 8603 0.930310 CGGTGATGATGTTGCTACCG 59.070 55.000 0.00 0.00 43.93 4.02
5736 8604 1.933853 GACGGTGATGATGTTGCTACC 59.066 52.381 0.00 0.00 0.00 3.18
5737 8605 2.616960 TGACGGTGATGATGTTGCTAC 58.383 47.619 0.00 0.00 0.00 3.58
5738 8606 3.118811 TGATGACGGTGATGATGTTGCTA 60.119 43.478 0.00 0.00 0.00 3.49
5739 8607 2.283298 GATGACGGTGATGATGTTGCT 58.717 47.619 0.00 0.00 0.00 3.91
5740 8608 2.009051 TGATGACGGTGATGATGTTGC 58.991 47.619 0.00 0.00 0.00 4.17
5741 8609 2.029606 CGTGATGACGGTGATGATGTTG 59.970 50.000 0.00 0.00 42.18 3.33
5742 8610 2.270923 CGTGATGACGGTGATGATGTT 58.729 47.619 0.00 0.00 42.18 2.71
5743 8611 1.926561 CGTGATGACGGTGATGATGT 58.073 50.000 0.00 0.00 42.18 3.06
5744 8612 0.578683 GCGTGATGACGGTGATGATG 59.421 55.000 6.88 0.00 46.20 3.07
5745 8613 0.530650 GGCGTGATGACGGTGATGAT 60.531 55.000 6.88 0.00 46.20 2.45
5746 8614 1.153647 GGCGTGATGACGGTGATGA 60.154 57.895 6.88 0.00 46.20 2.92
5747 8615 3.398920 GGCGTGATGACGGTGATG 58.601 61.111 6.88 0.00 46.20 3.07
5767 8635 1.444553 GGAGAGTTCCGTCAGCACG 60.445 63.158 0.00 0.00 46.29 5.34
5768 8636 1.079750 GGGAGAGTTCCGTCAGCAC 60.080 63.158 0.00 0.00 45.04 4.40
5769 8637 0.904865 ATGGGAGAGTTCCGTCAGCA 60.905 55.000 0.00 0.00 45.04 4.41
5770 8638 0.460987 CATGGGAGAGTTCCGTCAGC 60.461 60.000 0.00 0.00 45.04 4.26
5771 8639 1.186200 TCATGGGAGAGTTCCGTCAG 58.814 55.000 0.00 0.00 45.04 3.51
5772 8640 1.550524 CTTCATGGGAGAGTTCCGTCA 59.449 52.381 0.00 0.00 45.04 4.35
5773 8641 1.740718 GCTTCATGGGAGAGTTCCGTC 60.741 57.143 0.00 0.00 45.04 4.79
5774 8642 0.250513 GCTTCATGGGAGAGTTCCGT 59.749 55.000 0.00 0.00 45.04 4.69
5775 8643 0.539051 AGCTTCATGGGAGAGTTCCG 59.461 55.000 0.00 0.00 45.04 4.30
5776 8644 1.836802 AGAGCTTCATGGGAGAGTTCC 59.163 52.381 0.00 0.00 43.23 3.62
5777 8645 2.903798 CAGAGCTTCATGGGAGAGTTC 58.096 52.381 0.00 0.00 0.00 3.01
5778 8646 1.065564 GCAGAGCTTCATGGGAGAGTT 60.066 52.381 0.00 0.00 0.00 3.01
5779 8647 0.540923 GCAGAGCTTCATGGGAGAGT 59.459 55.000 0.00 0.00 0.00 3.24
5780 8648 0.831966 AGCAGAGCTTCATGGGAGAG 59.168 55.000 0.00 0.00 33.89 3.20
5781 8649 0.540454 CAGCAGAGCTTCATGGGAGA 59.460 55.000 0.00 0.00 36.40 3.71
5782 8650 0.464013 CCAGCAGAGCTTCATGGGAG 60.464 60.000 0.00 0.00 36.40 4.30
5783 8651 0.911045 TCCAGCAGAGCTTCATGGGA 60.911 55.000 7.95 1.74 36.40 4.37
5784 8652 0.183014 ATCCAGCAGAGCTTCATGGG 59.817 55.000 7.95 0.00 36.40 4.00
5785 8653 1.595466 GATCCAGCAGAGCTTCATGG 58.405 55.000 0.00 0.00 36.40 3.66
5786 8654 1.218763 CGATCCAGCAGAGCTTCATG 58.781 55.000 0.00 0.00 36.40 3.07
5787 8655 0.106335 CCGATCCAGCAGAGCTTCAT 59.894 55.000 0.00 0.00 36.40 2.57
5788 8656 0.972471 TCCGATCCAGCAGAGCTTCA 60.972 55.000 0.00 0.00 36.40 3.02
5789 8657 0.249405 CTCCGATCCAGCAGAGCTTC 60.249 60.000 0.00 0.00 36.40 3.86
5790 8658 0.975040 ACTCCGATCCAGCAGAGCTT 60.975 55.000 0.00 0.00 36.40 3.74
5791 8659 0.975040 AACTCCGATCCAGCAGAGCT 60.975 55.000 0.00 0.00 40.77 4.09
5792 8660 0.529555 GAACTCCGATCCAGCAGAGC 60.530 60.000 0.00 0.00 0.00 4.09
5793 8661 0.248825 CGAACTCCGATCCAGCAGAG 60.249 60.000 0.00 0.00 41.76 3.35
5794 8662 1.809869 CGAACTCCGATCCAGCAGA 59.190 57.895 0.00 0.00 41.76 4.26
5795 8663 1.880340 GCGAACTCCGATCCAGCAG 60.880 63.158 0.00 0.00 41.76 4.24
5796 8664 2.184322 GCGAACTCCGATCCAGCA 59.816 61.111 0.00 0.00 41.76 4.41
5797 8665 2.956964 CGCGAACTCCGATCCAGC 60.957 66.667 0.00 0.00 41.76 4.85
5798 8666 2.278857 CCGCGAACTCCGATCCAG 60.279 66.667 8.23 0.00 41.76 3.86
5799 8667 3.833645 CCCGCGAACTCCGATCCA 61.834 66.667 8.23 0.00 41.76 3.41
5800 8668 3.524606 TCCCGCGAACTCCGATCC 61.525 66.667 8.23 0.00 41.76 3.36
5801 8669 2.278661 GTCCCGCGAACTCCGATC 60.279 66.667 8.23 0.00 41.76 3.69
5802 8670 4.189188 CGTCCCGCGAACTCCGAT 62.189 66.667 8.23 0.00 44.77 4.18
5805 8673 3.352338 ATGACGTCCCGCGAACTCC 62.352 63.158 14.12 0.65 44.77 3.85
5806 8674 1.872679 GATGACGTCCCGCGAACTC 60.873 63.158 14.12 5.97 44.77 3.01
5807 8675 2.181021 GATGACGTCCCGCGAACT 59.819 61.111 14.12 0.00 44.77 3.01
5808 8676 3.245315 CGATGACGTCCCGCGAAC 61.245 66.667 14.12 4.32 44.77 3.95
5809 8677 3.391160 CTCGATGACGTCCCGCGAA 62.391 63.158 14.12 0.00 44.77 4.70
5810 8678 3.872728 CTCGATGACGTCCCGCGA 61.873 66.667 14.12 17.07 44.77 5.87
5812 8680 2.332362 TTAGCTCGATGACGTCCCGC 62.332 60.000 14.12 8.19 40.69 6.13
5813 8681 0.099968 TTTAGCTCGATGACGTCCCG 59.900 55.000 14.12 16.31 40.69 5.14
5814 8682 1.557651 GTTTAGCTCGATGACGTCCC 58.442 55.000 14.12 3.95 40.69 4.46
5815 8683 1.189403 CGTTTAGCTCGATGACGTCC 58.811 55.000 14.12 0.00 40.69 4.79
5816 8684 1.578023 CACGTTTAGCTCGATGACGTC 59.422 52.381 9.11 9.11 44.11 4.34
5817 8685 1.068748 ACACGTTTAGCTCGATGACGT 60.069 47.619 0.00 4.00 46.50 4.34
5818 8686 1.317611 CACACGTTTAGCTCGATGACG 59.682 52.381 0.00 3.40 39.43 4.35
5819 8687 1.059264 GCACACGTTTAGCTCGATGAC 59.941 52.381 0.00 0.00 0.00 3.06
5820 8688 1.067846 AGCACACGTTTAGCTCGATGA 60.068 47.619 0.00 0.00 32.05 2.92
5821 8689 1.059692 CAGCACACGTTTAGCTCGATG 59.940 52.381 3.38 0.07 36.26 3.84
5822 8690 1.067846 TCAGCACACGTTTAGCTCGAT 60.068 47.619 3.38 0.00 36.26 3.59
5823 8691 0.312729 TCAGCACACGTTTAGCTCGA 59.687 50.000 3.38 3.41 36.26 4.04
5824 8692 2.809181 TCAGCACACGTTTAGCTCG 58.191 52.632 3.38 0.00 36.26 5.03


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

AutoCloner maintained by Alex Coulton.