Multiple sequence alignment - TraesCS1D01G213000

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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 TraesCS1D01G213000 chr1D 100.000 7308 0 0 1 7308 298566874 298574181 0.000000e+00 13496.0
1 TraesCS1D01G213000 chr1D 84.914 928 86 27 4277 5158 216402865 216403784 0.000000e+00 889.0
2 TraesCS1D01G213000 chr1D 98.551 345 5 0 3605 3949 333497998 333498342 1.740000e-170 610.0
3 TraesCS1D01G213000 chr1D 79.762 168 29 4 7019 7185 298619773 298619936 4.630000e-22 117.0
4 TraesCS1D01G213000 chr1D 92.500 80 5 1 1690 1768 413217231 413217310 5.990000e-21 113.0
5 TraesCS1D01G213000 chr1D 90.476 84 5 3 1683 1763 141706064 141705981 2.790000e-19 108.0
6 TraesCS1D01G213000 chr1B 95.931 6193 148 34 1 6137 401617303 401623447 0.000000e+00 9945.0
7 TraesCS1D01G213000 chr1B 88.447 1030 78 13 3997 4986 623198533 623197505 0.000000e+00 1205.0
8 TraesCS1D01G213000 chr1B 97.487 597 11 2 6129 6722 401623598 401624193 0.000000e+00 1016.0
9 TraesCS1D01G213000 chr1B 96.089 179 6 1 7131 7308 401624447 401624625 2.580000e-74 291.0
10 TraesCS1D01G213000 chr1B 93.413 167 11 0 6886 7052 401624282 401624448 1.570000e-61 248.0
11 TraesCS1D01G213000 chr1B 79.762 168 29 4 7019 7185 402050756 402050919 4.630000e-22 117.0
12 TraesCS1D01G213000 chr1B 100.000 33 0 0 5659 5691 386519907 386519939 2.200000e-05 62.1
13 TraesCS1D01G213000 chr1B 94.444 36 2 0 6720 6755 401624223 401624258 1.000000e-03 56.5
14 TraesCS1D01G213000 chr1A 96.788 1619 40 5 1979 3596 372237794 372239401 0.000000e+00 2691.0
15 TraesCS1D01G213000 chr1A 92.211 1900 95 28 110 1989 372235597 372237463 0.000000e+00 2639.0
16 TraesCS1D01G213000 chr1A 96.176 1569 40 10 5158 6722 372239432 372240984 0.000000e+00 2547.0
17 TraesCS1D01G213000 chr1A 81.341 1238 151 37 3996 5161 22645889 22644660 0.000000e+00 933.0
18 TraesCS1D01G213000 chr1A 95.745 423 18 0 6886 7308 372241073 372241495 0.000000e+00 682.0
19 TraesCS1D01G213000 chr1A 92.308 91 4 3 1680 1768 545330974 545330885 7.700000e-25 126.0
20 TraesCS1D01G213000 chr1A 80.357 168 28 4 7019 7185 372467577 372467740 9.960000e-24 122.0
21 TraesCS1D01G213000 chr1A 98.039 51 1 0 3949 3999 372239385 372239435 1.010000e-13 89.8
22 TraesCS1D01G213000 chr1A 92.683 41 2 1 6720 6760 372241014 372241053 2.850000e-04 58.4
23 TraesCS1D01G213000 chr3B 88.245 1191 100 22 3998 5161 561043492 561042315 0.000000e+00 1387.0
24 TraesCS1D01G213000 chr3B 89.242 1069 74 11 3998 5026 20557171 20556104 0.000000e+00 1299.0
25 TraesCS1D01G213000 chr3B 86.693 1022 100 23 3996 4986 64792298 64793314 0.000000e+00 1101.0
26 TraesCS1D01G213000 chr3B 89.855 69 5 1 3269 3337 24008678 24008744 3.630000e-13 87.9
27 TraesCS1D01G213000 chr6D 87.419 1232 85 20 3996 5160 115650842 115649614 0.000000e+00 1352.0
28 TraesCS1D01G213000 chr6D 87.952 249 20 8 5923 6169 399036897 399037137 1.200000e-72 285.0
29 TraesCS1D01G213000 chr6D 95.192 104 5 0 6773 6876 458198883 458198986 1.630000e-36 165.0
30 TraesCS1D01G213000 chr6D 95.192 104 5 0 6773 6876 458222394 458222497 1.630000e-36 165.0
31 TraesCS1D01G213000 chr6D 95.455 88 2 2 1683 1768 155601958 155602045 9.890000e-29 139.0
32 TraesCS1D01G213000 chr6D 96.250 80 2 1 1690 1768 13067120 13067041 5.950000e-26 130.0
33 TraesCS1D01G213000 chr6D 92.771 83 2 3 1690 1768 24823341 24823423 4.630000e-22 117.0
34 TraesCS1D01G213000 chr6D 91.667 84 5 2 1686 1768 458975446 458975364 1.670000e-21 115.0
35 TraesCS1D01G213000 chr6D 92.208 77 4 2 1686 1760 220939552 220939476 2.790000e-19 108.0
36 TraesCS1D01G213000 chr6D 83.168 101 15 2 1677 1775 263008884 263008784 2.810000e-14 91.6
37 TraesCS1D01G213000 chr5B 86.337 1215 114 17 3996 5163 512935841 512934632 0.000000e+00 1277.0
38 TraesCS1D01G213000 chr5B 89.355 310 26 4 4854 5158 407220620 407220313 4.140000e-102 383.0
39 TraesCS1D01G213000 chr5B 95.238 105 5 0 6773 6877 484894699 484894595 4.540000e-37 167.0
40 TraesCS1D01G213000 chr5B 97.222 36 1 0 5659 5694 462886780 462886815 2.200000e-05 62.1
41 TraesCS1D01G213000 chr6B 85.372 1210 112 25 3998 5150 688659384 688658183 0.000000e+00 1194.0
42 TraesCS1D01G213000 chr6B 89.609 818 82 2 3996 4812 648515553 648514738 0.000000e+00 1037.0
43 TraesCS1D01G213000 chr6B 94.444 108 6 0 6773 6880 272401649 272401756 4.540000e-37 167.0
44 TraesCS1D01G213000 chr6B 95.455 88 2 2 1683 1768 278674610 278674697 9.890000e-29 139.0
45 TraesCS1D01G213000 chr6A 85.631 1204 96 33 3998 5158 493845569 493844400 0.000000e+00 1194.0
46 TraesCS1D01G213000 chr6A 94.444 108 6 0 6773 6880 99210576 99210469 4.540000e-37 167.0
47 TraesCS1D01G213000 chr6A 95.455 88 2 2 1683 1768 209391338 209391425 9.890000e-29 139.0
48 TraesCS1D01G213000 chr6A 97.500 80 1 1 1690 1768 14351067 14350988 1.280000e-27 135.0
49 TraesCS1D01G213000 chr6A 91.765 85 5 2 1686 1768 302776513 302776597 4.630000e-22 117.0
50 TraesCS1D01G213000 chr6A 100.000 36 0 0 5659 5694 39440923 39440958 4.730000e-07 67.6
51 TraesCS1D01G213000 chr2A 85.173 1214 115 29 3996 5161 495940851 495942047 0.000000e+00 1184.0
52 TraesCS1D01G213000 chr2A 88.543 995 81 16 4029 4992 729126443 729127435 0.000000e+00 1175.0
53 TraesCS1D01G213000 chr2A 92.157 51 3 1 7247 7296 669558094 669558144 3.660000e-08 71.3
54 TraesCS1D01G213000 chr2B 80.963 935 110 24 4277 5164 705053295 705052382 0.000000e+00 678.0
55 TraesCS1D01G213000 chr2B 96.944 360 8 2 3594 3950 280493559 280493200 1.050000e-167 601.0
56 TraesCS1D01G213000 chr2B 89.474 152 11 3 6015 6166 543512237 543512091 3.480000e-43 187.0
57 TraesCS1D01G213000 chr2B 79.856 278 38 11 5892 6164 543512515 543512251 3.480000e-43 187.0
58 TraesCS1D01G213000 chr2B 93.519 108 7 0 6779 6886 55924685 55924578 2.110000e-35 161.0
59 TraesCS1D01G213000 chr2B 86.861 137 15 3 6023 6159 543513104 543512971 4.570000e-32 150.0
60 TraesCS1D01G213000 chr2B 92.553 94 5 2 1685 1776 52408856 52408763 4.600000e-27 134.0
61 TraesCS1D01G213000 chr2D 98.841 345 4 0 3605 3949 402239429 402239085 3.750000e-172 616.0
62 TraesCS1D01G213000 chr2D 98.551 345 5 0 3605 3949 370058033 370058377 1.740000e-170 610.0
63 TraesCS1D01G213000 chr2D 94.231 52 3 0 7245 7296 523738250 523738301 6.080000e-11 80.5
64 TraesCS1D01G213000 chr7D 98.555 346 5 0 3605 3950 429475523 429475868 4.850000e-171 612.0
65 TraesCS1D01G213000 chr7D 98.551 345 5 0 3605 3949 554582108 554581764 1.740000e-170 610.0
66 TraesCS1D01G213000 chr3A 98.551 345 5 0 3605 3949 631289696 631290040 1.740000e-170 610.0
67 TraesCS1D01G213000 chr3A 94.595 111 6 0 6773 6883 28893737 28893627 9.750000e-39 172.0
68 TraesCS1D01G213000 chr3A 89.157 83 7 1 3267 3349 20003240 20003160 1.300000e-17 102.0
69 TraesCS1D01G213000 chr3A 95.122 41 2 0 5659 5699 507310449 507310489 1.700000e-06 65.8
70 TraesCS1D01G213000 chr3D 95.989 374 14 1 3605 3978 526277903 526278275 2.250000e-169 606.0
71 TraesCS1D01G213000 chr3D 88.793 232 21 4 5933 6163 132924532 132924305 5.580000e-71 279.0
72 TraesCS1D01G213000 chr3D 95.192 104 5 0 6773 6876 610203711 610203814 1.630000e-36 165.0
73 TraesCS1D01G213000 chr3D 87.209 86 9 1 3264 3349 16619102 16619185 6.030000e-16 97.1
74 TraesCS1D01G213000 chr5D 89.969 319 26 4 4848 5161 72545803 72545486 2.450000e-109 407.0
75 TraesCS1D01G213000 chr5D 92.473 93 4 2 1685 1774 541806265 541806173 5.950000e-26 130.0
76 TraesCS1D01G213000 chr5D 97.143 35 1 0 3303 3337 399980718 399980752 7.920000e-05 60.2
77 TraesCS1D01G213000 chr7B 83.916 286 38 6 5879 6161 634627784 634628064 4.350000e-67 267.0
78 TraesCS1D01G213000 chr7B 92.391 92 3 4 1686 1773 13801939 13801848 2.140000e-25 128.0
79 TraesCS1D01G213000 chr5A 82.609 276 36 8 5892 6165 609951665 609951930 4.410000e-57 233.0
80 TraesCS1D01G213000 chr7A 86.559 186 24 1 5890 6074 669275038 669275223 3.460000e-48 204.0
81 TraesCS1D01G213000 chrUn 95.192 104 5 0 6773 6876 362324364 362324467 1.630000e-36 165.0
82 TraesCS1D01G213000 chrUn 88.889 99 8 3 1679 1775 341187269 341187366 1.290000e-22 119.0
83 TraesCS1D01G213000 chrUn 88.750 80 6 3 1681 1758 288819309 288819387 2.170000e-15 95.3
84 TraesCS1D01G213000 chrUn 86.207 87 10 2 1685 1769 84439923 84439837 7.810000e-15 93.5
85 TraesCS1D01G213000 chrUn 87.500 80 9 1 1690 1768 37371580 37371501 2.810000e-14 91.6
86 TraesCS1D01G213000 chrUn 86.250 80 10 1 1690 1768 37004629 37004708 1.310000e-12 86.1
87 TraesCS1D01G213000 chrUn 86.250 80 10 1 1690 1768 329135091 329135012 1.310000e-12 86.1
88 TraesCS1D01G213000 chrUn 86.250 80 10 1 1690 1768 332577060 332576981 1.310000e-12 86.1
89 TraesCS1D01G213000 chrUn 85.000 80 11 1 1690 1768 196711377 196711298 6.080000e-11 80.5
90 TraesCS1D01G213000 chrUn 88.889 54 3 3 5639 5691 110464771 110464822 6.120000e-06 63.9
91 TraesCS1D01G213000 chr4D 93.258 89 3 3 1682 1768 10243321 10243408 2.140000e-25 128.0
92 TraesCS1D01G213000 chr4D 91.667 84 5 2 1686 1767 234413566 234413483 1.670000e-21 115.0
93 TraesCS1D01G213000 chr4B 94.118 85 3 2 1686 1768 270831755 270831671 2.140000e-25 128.0
94 TraesCS1D01G213000 chr4B 92.135 89 4 3 1682 1768 19727398 19727485 9.960000e-24 122.0
95 TraesCS1D01G213000 chr4B 89.091 55 3 3 5639 5692 660491527 660491579 1.700000e-06 65.8
96 TraesCS1D01G213000 chr4A 97.436 39 1 0 5659 5697 338747797 338747759 4.730000e-07 67.6


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 TraesCS1D01G213000 chr1D 298566874 298574181 7307 False 13496.0 13496 100.000000 1 7308 1 chr1D.!!$F2 7307
1 TraesCS1D01G213000 chr1D 216402865 216403784 919 False 889.0 889 84.914000 4277 5158 1 chr1D.!!$F1 881
2 TraesCS1D01G213000 chr1B 401617303 401624625 7322 False 2311.3 9945 95.472800 1 7308 5 chr1B.!!$F3 7307
3 TraesCS1D01G213000 chr1B 623197505 623198533 1028 True 1205.0 1205 88.447000 3997 4986 1 chr1B.!!$R1 989
4 TraesCS1D01G213000 chr1A 372235597 372241495 5898 False 1451.2 2691 95.273667 110 7308 6 chr1A.!!$F2 7198
5 TraesCS1D01G213000 chr1A 22644660 22645889 1229 True 933.0 933 81.341000 3996 5161 1 chr1A.!!$R1 1165
6 TraesCS1D01G213000 chr3B 561042315 561043492 1177 True 1387.0 1387 88.245000 3998 5161 1 chr3B.!!$R2 1163
7 TraesCS1D01G213000 chr3B 20556104 20557171 1067 True 1299.0 1299 89.242000 3998 5026 1 chr3B.!!$R1 1028
8 TraesCS1D01G213000 chr3B 64792298 64793314 1016 False 1101.0 1101 86.693000 3996 4986 1 chr3B.!!$F2 990
9 TraesCS1D01G213000 chr6D 115649614 115650842 1228 True 1352.0 1352 87.419000 3996 5160 1 chr6D.!!$R2 1164
10 TraesCS1D01G213000 chr5B 512934632 512935841 1209 True 1277.0 1277 86.337000 3996 5163 1 chr5B.!!$R3 1167
11 TraesCS1D01G213000 chr6B 688658183 688659384 1201 True 1194.0 1194 85.372000 3998 5150 1 chr6B.!!$R2 1152
12 TraesCS1D01G213000 chr6B 648514738 648515553 815 True 1037.0 1037 89.609000 3996 4812 1 chr6B.!!$R1 816
13 TraesCS1D01G213000 chr6A 493844400 493845569 1169 True 1194.0 1194 85.631000 3998 5158 1 chr6A.!!$R3 1160
14 TraesCS1D01G213000 chr2A 495940851 495942047 1196 False 1184.0 1184 85.173000 3996 5161 1 chr2A.!!$F1 1165
15 TraesCS1D01G213000 chr2A 729126443 729127435 992 False 1175.0 1175 88.543000 4029 4992 1 chr2A.!!$F3 963
16 TraesCS1D01G213000 chr2B 705052382 705053295 913 True 678.0 678 80.963000 4277 5164 1 chr2B.!!$R4 887

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
147 148 0.036022 GCTGGAGCTGGGATATCCAC 59.964 60.000 23.27 12.86 41.46 4.02 F
152 153 0.398522 AGCTGGGATATCCACCGTCA 60.399 55.000 23.27 10.38 41.46 4.35 F
886 896 0.694783 TGGACCACAACCCTACACCA 60.695 55.000 0.00 0.00 0.00 4.17 F
1152 1162 0.756070 AGCCCGTAAGCTAGGAGACC 60.756 60.000 4.55 0.00 42.70 3.85 F
1505 1525 0.800300 GAGGTCTGAGCTTCTTCGCG 60.800 60.000 11.11 0.00 34.40 5.87 F
2658 3022 0.942252 CATGTCACGCCATCATCAGG 59.058 55.000 0.00 0.00 0.00 3.86 F
4053 4417 1.263776 CAAAACGCGTTTGCAGTTCA 58.736 45.000 35.31 0.00 40.25 3.18 F
5001 5497 2.196925 AAATGCACCGCGAACCCAA 61.197 52.632 8.23 0.00 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1469 0.389948 GCCTCGTACTGTCCAACCAG 60.390 60.000 0.00 0.00 38.45 4.00 R
1520 1540 0.950836 CCTTGTCATTCACAACGGCA 59.049 50.000 0.00 0.00 40.29 5.69 R
2658 3022 2.206576 ATGGAGGAAAGGAGTTGTGC 57.793 50.000 0.00 0.00 0.00 4.57 R
3118 3482 3.059325 GTGATCTGACAGAACAAGCACAC 60.059 47.826 16.14 10.40 28.60 3.82 R
3472 3836 0.171455 TTGCACCACAAAACGACACC 59.829 50.000 0.00 0.00 34.56 4.16 R
4382 4790 0.035056 CCGCCAAGGAGAAGGACAAT 60.035 55.000 0.00 0.00 45.00 2.71 R
5910 6428 0.755327 ACAAGGTTCCCACAGCAACC 60.755 55.000 0.00 0.00 42.26 3.77 R
6579 7257 1.368579 GCAAAGTGCATGCCTGGTT 59.631 52.632 16.68 0.96 44.26 3.67 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
147 148 0.036022 GCTGGAGCTGGGATATCCAC 59.964 60.000 23.27 12.86 41.46 4.02
152 153 0.398522 AGCTGGGATATCCACCGTCA 60.399 55.000 23.27 10.38 41.46 4.35
160 161 2.526888 TATCCACCGTCAGAGACCTT 57.473 50.000 0.00 0.00 0.00 3.50
580 586 9.773328 ATTTGACGTGTATTACATGATTTCTTG 57.227 29.630 20.25 0.00 37.29 3.02
581 587 8.541133 TTGACGTGTATTACATGATTTCTTGA 57.459 30.769 20.25 0.00 37.29 3.02
582 588 8.716646 TGACGTGTATTACATGATTTCTTGAT 57.283 30.769 20.25 0.00 37.29 2.57
789 799 2.178521 CGTAGGTCGCTGAACGCT 59.821 61.111 0.00 0.00 43.23 5.07
799 809 0.802607 GCTGAACGCTCCCGACTAAG 60.803 60.000 0.00 0.00 38.29 2.18
886 896 0.694783 TGGACCACAACCCTACACCA 60.695 55.000 0.00 0.00 0.00 4.17
1152 1162 0.756070 AGCCCGTAAGCTAGGAGACC 60.756 60.000 4.55 0.00 42.70 3.85
1229 1240 2.666317 GTTCCATTTCGGATTGGGGAT 58.334 47.619 4.80 0.00 45.80 3.85
1334 1345 3.089784 CGCACATCGGCAAGGTAC 58.910 61.111 0.00 0.00 33.78 3.34
1369 1389 2.739996 CCCCTCCCTACTGCTGCAG 61.740 68.421 27.02 27.02 37.52 4.41
1449 1469 9.438291 CTATATCGGTTTGATTTTGATGTGTTC 57.562 33.333 0.00 0.00 38.57 3.18
1505 1525 0.800300 GAGGTCTGAGCTTCTTCGCG 60.800 60.000 11.11 0.00 34.40 5.87
1572 1592 3.679389 CCTTATGTGAGTTTCCAGTGCT 58.321 45.455 0.00 0.00 0.00 4.40
1581 1601 1.461127 GTTTCCAGTGCTACTGCTTCG 59.539 52.381 9.88 0.00 44.63 3.79
1598 1618 3.424962 GCTTCGTACTGCCTTGTGATTTC 60.425 47.826 0.00 0.00 0.00 2.17
1880 1902 9.747898 TTCCAATTGTTAATTTTAGGCTAGAGA 57.252 29.630 4.43 0.00 0.00 3.10
2015 2378 2.113860 TGTTGTTGCATCTAGGCTCC 57.886 50.000 0.00 0.00 34.04 4.70
2119 2482 8.201554 TGTCTAGTGCATGATCTAAATTGTTC 57.798 34.615 0.00 0.00 0.00 3.18
2292 2656 6.718593 TCTTATGTATCTATGGGGGCATTT 57.281 37.500 0.00 0.00 0.00 2.32
2532 2896 5.367060 ACCCACTTAAACAATTTTTGGGCTA 59.633 36.000 3.59 0.00 45.35 3.93
2658 3022 0.942252 CATGTCACGCCATCATCAGG 59.058 55.000 0.00 0.00 0.00 3.86
2698 3062 5.874261 CCATTTGGTTGATTTAAGCGGAAAT 59.126 36.000 0.00 0.00 39.62 2.17
2988 3352 3.134127 GATTGCAGGTGCCCGGTC 61.134 66.667 0.00 0.00 41.18 4.79
3396 3760 8.792633 GCCTTATAAACAATGGTTAGCATATCA 58.207 33.333 0.00 0.00 35.82 2.15
3849 4213 5.995282 CGCTCAAATGGGTTTCATACCTATA 59.005 40.000 0.00 0.00 46.51 1.31
3899 4263 1.501582 AGCCTATCACAACCCTCCTC 58.498 55.000 0.00 0.00 0.00 3.71
4053 4417 1.263776 CAAAACGCGTTTGCAGTTCA 58.736 45.000 35.31 0.00 40.25 3.18
4169 4537 4.465632 TGCAACCGTAGTAGTTCATCAT 57.534 40.909 0.00 0.00 0.00 2.45
4384 4792 3.204827 GATGCGCCGCCACTCATT 61.205 61.111 6.63 0.00 0.00 2.57
4662 5072 4.430765 TCGCGCCGGAAGAGGAAC 62.431 66.667 5.05 0.00 0.00 3.62
5001 5497 2.196925 AAATGCACCGCGAACCCAA 61.197 52.632 8.23 0.00 0.00 4.12
5009 5505 3.399330 CACCGCGAACCCAAAGATATAT 58.601 45.455 8.23 0.00 0.00 0.86
5012 5508 4.062293 CCGCGAACCCAAAGATATATTGA 58.938 43.478 8.23 0.00 0.00 2.57
5063 5580 2.769652 TACGGGCCGGGCGAGTATAT 62.770 60.000 31.78 7.28 0.00 0.86
5371 5889 5.793817 TCACTGTCATGCTGTATGTTACTT 58.206 37.500 5.64 0.00 38.01 2.24
5602 6120 5.751509 TGCTTGTTACCTTATGTGCTATACG 59.248 40.000 0.00 0.00 0.00 3.06
5910 6428 0.035439 AACTAGACAATGCCCCACGG 60.035 55.000 0.00 0.00 0.00 4.94
6127 6646 5.549742 TTGTTGCATGGAGAGGAAAATTT 57.450 34.783 0.00 0.00 0.00 1.82
6548 7226 7.277760 GGTACTCTTTGCAAATGTTTTCAAACT 59.722 33.333 13.23 0.00 39.59 2.66
6568 7246 8.621286 TCAAACTAAGTTTTTCCTCTCAATCAC 58.379 33.333 0.00 0.00 33.10 3.06
6621 7300 5.154222 GGCTACTTGTTTTACTGACAATGC 58.846 41.667 0.00 0.00 36.51 3.56
6623 7302 4.223320 ACTTGTTTTACTGACAATGCCG 57.777 40.909 0.00 0.00 36.51 5.69
6722 7407 3.750373 AAGCACGGCGTTCACAGGT 62.750 57.895 11.19 0.38 0.00 4.00
6723 7408 3.712881 GCACGGCGTTCACAGGTC 61.713 66.667 11.19 0.00 0.00 3.85
6724 7409 2.029073 CACGGCGTTCACAGGTCT 59.971 61.111 11.19 0.00 0.00 3.85
6725 7410 1.287815 CACGGCGTTCACAGGTCTA 59.712 57.895 11.19 0.00 0.00 2.59
6755 7472 1.996898 GCACCGAACATGTCATTACGA 59.003 47.619 0.00 0.00 0.00 3.43
6757 7474 3.063452 GCACCGAACATGTCATTACGATT 59.937 43.478 0.00 0.00 0.00 3.34
6758 7475 4.269123 GCACCGAACATGTCATTACGATTA 59.731 41.667 0.00 0.00 0.00 1.75
6760 7477 5.518847 CACCGAACATGTCATTACGATTACT 59.481 40.000 0.00 0.00 0.00 2.24
6761 7478 5.518847 ACCGAACATGTCATTACGATTACTG 59.481 40.000 0.00 0.00 0.00 2.74
6762 7479 5.518847 CCGAACATGTCATTACGATTACTGT 59.481 40.000 0.00 0.00 0.00 3.55
6763 7480 6.693978 CCGAACATGTCATTACGATTACTGTA 59.306 38.462 0.00 0.00 0.00 2.74
6766 7483 9.297586 GAACATGTCATTACGATTACTGTAGAA 57.702 33.333 0.00 0.00 0.00 2.10
6767 7484 8.858003 ACATGTCATTACGATTACTGTAGAAG 57.142 34.615 0.00 0.00 0.00 2.85
6768 7485 8.467598 ACATGTCATTACGATTACTGTAGAAGT 58.532 33.333 0.00 0.00 43.40 3.01
6769 7486 8.746751 CATGTCATTACGATTACTGTAGAAGTG 58.253 37.037 0.00 0.00 40.26 3.16
6770 7487 6.750501 TGTCATTACGATTACTGTAGAAGTGC 59.249 38.462 0.00 0.00 40.26 4.40
6771 7488 6.750501 GTCATTACGATTACTGTAGAAGTGCA 59.249 38.462 0.00 0.00 40.26 4.57
6773 7490 7.815549 TCATTACGATTACTGTAGAAGTGCAAA 59.184 33.333 0.00 0.00 40.26 3.68
6774 7491 7.576750 TTACGATTACTGTAGAAGTGCAAAG 57.423 36.000 0.00 0.00 40.26 2.77
6775 7492 5.779922 ACGATTACTGTAGAAGTGCAAAGA 58.220 37.500 0.00 0.00 40.26 2.52
6776 7493 5.634020 ACGATTACTGTAGAAGTGCAAAGAC 59.366 40.000 0.00 0.00 40.26 3.01
6778 7495 6.311445 CGATTACTGTAGAAGTGCAAAGACAT 59.689 38.462 0.00 0.00 40.26 3.06
6779 7496 7.463383 CGATTACTGTAGAAGTGCAAAGACATC 60.463 40.741 0.00 0.00 40.26 3.06
6780 7497 5.220710 ACTGTAGAAGTGCAAAGACATCT 57.779 39.130 0.00 0.00 37.88 2.90
6781 7498 5.615289 ACTGTAGAAGTGCAAAGACATCTT 58.385 37.500 0.00 0.00 37.88 2.40
6782 7499 5.468072 ACTGTAGAAGTGCAAAGACATCTTG 59.532 40.000 0.00 0.00 37.88 3.02
6783 7500 4.756642 TGTAGAAGTGCAAAGACATCTTGG 59.243 41.667 0.00 0.00 36.12 3.61
6788 7505 2.915738 GCAAAGACATCTTGGCTCTG 57.084 50.000 12.90 0.00 46.72 3.35
6789 7506 2.430465 GCAAAGACATCTTGGCTCTGA 58.570 47.619 12.90 0.00 46.72 3.27
6790 7507 3.015327 GCAAAGACATCTTGGCTCTGAT 58.985 45.455 12.90 0.00 46.72 2.90
6791 7508 4.194640 GCAAAGACATCTTGGCTCTGATA 58.805 43.478 12.90 0.00 46.72 2.15
6792 7509 4.034975 GCAAAGACATCTTGGCTCTGATAC 59.965 45.833 12.90 0.00 46.72 2.24
6793 7510 5.181009 CAAAGACATCTTGGCTCTGATACA 58.819 41.667 0.00 0.00 31.94 2.29
6794 7511 5.426689 AAGACATCTTGGCTCTGATACAA 57.573 39.130 0.00 0.00 31.94 2.41
6795 7512 5.627182 AGACATCTTGGCTCTGATACAAT 57.373 39.130 0.00 0.00 18.29 2.71
6796 7513 5.366460 AGACATCTTGGCTCTGATACAATG 58.634 41.667 0.00 0.00 18.29 2.82
6797 7514 5.104610 AGACATCTTGGCTCTGATACAATGT 60.105 40.000 0.00 0.00 18.29 2.71
6798 7515 6.098838 AGACATCTTGGCTCTGATACAATGTA 59.901 38.462 0.00 0.00 18.29 2.29
6799 7516 6.286758 ACATCTTGGCTCTGATACAATGTAG 58.713 40.000 0.00 0.00 0.00 2.74
6800 7517 6.098838 ACATCTTGGCTCTGATACAATGTAGA 59.901 38.462 0.00 0.00 0.00 2.59
6801 7518 6.544928 TCTTGGCTCTGATACAATGTAGAA 57.455 37.500 0.00 0.00 0.00 2.10
6802 7519 6.577103 TCTTGGCTCTGATACAATGTAGAAG 58.423 40.000 0.00 0.00 0.00 2.85
6803 7520 5.939764 TGGCTCTGATACAATGTAGAAGT 57.060 39.130 0.00 0.00 0.00 3.01
6804 7521 5.664457 TGGCTCTGATACAATGTAGAAGTG 58.336 41.667 0.00 1.81 0.00 3.16
6805 7522 4.509600 GGCTCTGATACAATGTAGAAGTGC 59.490 45.833 16.94 16.94 0.00 4.40
6806 7523 5.111989 GCTCTGATACAATGTAGAAGTGCA 58.888 41.667 18.82 0.00 0.00 4.57
6807 7524 5.757320 GCTCTGATACAATGTAGAAGTGCAT 59.243 40.000 18.82 0.00 0.00 3.96
6808 7525 6.292757 GCTCTGATACAATGTAGAAGTGCATG 60.293 42.308 18.82 0.00 0.00 4.06
6809 7526 5.525012 TCTGATACAATGTAGAAGTGCATGC 59.475 40.000 11.82 11.82 0.00 4.06
6810 7527 5.430886 TGATACAATGTAGAAGTGCATGCT 58.569 37.500 20.33 0.00 0.00 3.79
6811 7528 5.525012 TGATACAATGTAGAAGTGCATGCTC 59.475 40.000 20.33 15.94 0.00 4.26
6812 7529 3.947868 ACAATGTAGAAGTGCATGCTCT 58.052 40.909 20.33 18.23 0.00 4.09
6813 7530 5.089970 ACAATGTAGAAGTGCATGCTCTA 57.910 39.130 21.70 15.62 0.00 2.43
6814 7531 5.114780 ACAATGTAGAAGTGCATGCTCTAG 58.885 41.667 21.70 9.54 0.00 2.43
6815 7532 3.170791 TGTAGAAGTGCATGCTCTAGC 57.829 47.619 21.70 16.29 42.50 3.42
6816 7533 2.762887 TGTAGAAGTGCATGCTCTAGCT 59.237 45.455 21.70 21.45 42.66 3.32
6817 7534 3.954258 TGTAGAAGTGCATGCTCTAGCTA 59.046 43.478 21.70 20.57 42.66 3.32
6818 7535 4.402474 TGTAGAAGTGCATGCTCTAGCTAA 59.598 41.667 21.70 13.22 42.66 3.09
6819 7536 4.686191 AGAAGTGCATGCTCTAGCTAAT 57.314 40.909 21.70 5.92 42.66 1.73
6820 7537 4.378774 AGAAGTGCATGCTCTAGCTAATG 58.621 43.478 21.70 0.00 42.66 1.90
6821 7538 2.492012 AGTGCATGCTCTAGCTAATGC 58.508 47.619 20.22 17.52 45.25 3.56
6824 7541 3.265070 GCATGCTCTAGCTAATGCAAC 57.735 47.619 18.86 12.85 44.74 4.17
6825 7542 2.031333 GCATGCTCTAGCTAATGCAACC 60.031 50.000 18.86 11.73 44.74 3.77
6826 7543 3.208594 CATGCTCTAGCTAATGCAACCA 58.791 45.455 19.70 2.30 42.74 3.67
6827 7544 3.348647 TGCTCTAGCTAATGCAACCAA 57.651 42.857 15.29 0.00 42.74 3.67
6828 7545 3.684908 TGCTCTAGCTAATGCAACCAAA 58.315 40.909 15.29 0.00 42.74 3.28
6829 7546 4.078537 TGCTCTAGCTAATGCAACCAAAA 58.921 39.130 15.29 0.00 42.74 2.44
6830 7547 4.156556 TGCTCTAGCTAATGCAACCAAAAG 59.843 41.667 15.29 0.00 42.74 2.27
6831 7548 4.396166 GCTCTAGCTAATGCAACCAAAAGA 59.604 41.667 11.39 0.00 42.74 2.52
6832 7549 5.674820 GCTCTAGCTAATGCAACCAAAAGAC 60.675 44.000 11.39 0.00 42.74 3.01
6833 7550 3.942130 AGCTAATGCAACCAAAAGACC 57.058 42.857 0.00 0.00 42.74 3.85
6834 7551 3.230134 AGCTAATGCAACCAAAAGACCA 58.770 40.909 0.00 0.00 42.74 4.02
6835 7552 3.640967 AGCTAATGCAACCAAAAGACCAA 59.359 39.130 0.00 0.00 42.74 3.67
6836 7553 4.284234 AGCTAATGCAACCAAAAGACCAAT 59.716 37.500 0.00 0.00 42.74 3.16
6837 7554 4.627035 GCTAATGCAACCAAAAGACCAATC 59.373 41.667 0.00 0.00 39.41 2.67
6838 7555 4.961438 AATGCAACCAAAAGACCAATCT 57.039 36.364 0.00 0.00 36.42 2.40
6839 7556 3.731652 TGCAACCAAAAGACCAATCTG 57.268 42.857 0.00 0.00 34.48 2.90
6840 7557 3.295093 TGCAACCAAAAGACCAATCTGA 58.705 40.909 0.00 0.00 34.48 3.27
6841 7558 3.896888 TGCAACCAAAAGACCAATCTGAT 59.103 39.130 0.00 0.00 34.48 2.90
6842 7559 4.240096 GCAACCAAAAGACCAATCTGATG 58.760 43.478 0.00 0.00 34.48 3.07
6843 7560 4.022068 GCAACCAAAAGACCAATCTGATGA 60.022 41.667 0.00 0.00 34.48 2.92
6844 7561 5.509501 GCAACCAAAAGACCAATCTGATGAA 60.510 40.000 0.00 0.00 34.48 2.57
6845 7562 6.514947 CAACCAAAAGACCAATCTGATGAAA 58.485 36.000 0.00 0.00 34.48 2.69
6846 7563 6.336842 ACCAAAAGACCAATCTGATGAAAG 57.663 37.500 0.00 0.00 34.48 2.62
6847 7564 6.070656 ACCAAAAGACCAATCTGATGAAAGA 58.929 36.000 0.00 0.00 34.48 2.52
6848 7565 6.208204 ACCAAAAGACCAATCTGATGAAAGAG 59.792 38.462 0.00 0.00 34.48 2.85
6849 7566 6.432162 CCAAAAGACCAATCTGATGAAAGAGA 59.568 38.462 0.00 0.00 34.48 3.10
6850 7567 7.303998 CAAAAGACCAATCTGATGAAAGAGAC 58.696 38.462 0.00 0.00 34.48 3.36
6851 7568 6.371595 AAGACCAATCTGATGAAAGAGACT 57.628 37.500 0.00 0.00 34.48 3.24
6852 7569 7.487822 AAGACCAATCTGATGAAAGAGACTA 57.512 36.000 0.00 0.00 34.48 2.59
6853 7570 7.111247 AGACCAATCTGATGAAAGAGACTAG 57.889 40.000 0.00 0.00 32.29 2.57
6854 7571 6.098124 AGACCAATCTGATGAAAGAGACTAGG 59.902 42.308 0.00 0.00 32.29 3.02
6855 7572 5.055812 CCAATCTGATGAAAGAGACTAGGC 58.944 45.833 0.00 0.00 0.00 3.93
6856 7573 5.396101 CCAATCTGATGAAAGAGACTAGGCA 60.396 44.000 0.00 0.00 0.00 4.75
6857 7574 4.998671 TCTGATGAAAGAGACTAGGCAG 57.001 45.455 0.00 0.00 0.00 4.85
6858 7575 3.131933 TCTGATGAAAGAGACTAGGCAGC 59.868 47.826 0.00 0.00 0.00 5.25
6859 7576 2.833943 TGATGAAAGAGACTAGGCAGCA 59.166 45.455 0.00 0.00 0.00 4.41
6860 7577 2.751166 TGAAAGAGACTAGGCAGCAC 57.249 50.000 0.00 0.00 0.00 4.40
6861 7578 1.970640 TGAAAGAGACTAGGCAGCACA 59.029 47.619 0.00 0.00 0.00 4.57
6862 7579 2.568956 TGAAAGAGACTAGGCAGCACAT 59.431 45.455 0.00 0.00 0.00 3.21
6863 7580 3.008375 TGAAAGAGACTAGGCAGCACATT 59.992 43.478 0.00 0.00 0.00 2.71
6864 7581 4.222810 TGAAAGAGACTAGGCAGCACATTA 59.777 41.667 0.00 0.00 0.00 1.90
6865 7582 5.104776 TGAAAGAGACTAGGCAGCACATTAT 60.105 40.000 0.00 0.00 0.00 1.28
6866 7583 6.098266 TGAAAGAGACTAGGCAGCACATTATA 59.902 38.462 0.00 0.00 0.00 0.98
6867 7584 5.461032 AGAGACTAGGCAGCACATTATAC 57.539 43.478 0.00 0.00 0.00 1.47
6868 7585 4.022762 AGAGACTAGGCAGCACATTATACG 60.023 45.833 0.00 0.00 0.00 3.06
6869 7586 3.637229 AGACTAGGCAGCACATTATACGT 59.363 43.478 0.00 0.00 0.00 3.57
6870 7587 3.978687 ACTAGGCAGCACATTATACGTC 58.021 45.455 0.00 0.00 0.00 4.34
6871 7588 2.979814 AGGCAGCACATTATACGTCA 57.020 45.000 0.00 0.00 0.00 4.35
6872 7589 3.260475 AGGCAGCACATTATACGTCAA 57.740 42.857 0.00 0.00 0.00 3.18
6873 7590 2.936498 AGGCAGCACATTATACGTCAAC 59.064 45.455 0.00 0.00 0.00 3.18
6874 7591 2.675844 GGCAGCACATTATACGTCAACA 59.324 45.455 0.00 0.00 0.00 3.33
6875 7592 3.242413 GGCAGCACATTATACGTCAACAG 60.242 47.826 0.00 0.00 0.00 3.16
6876 7593 3.370978 GCAGCACATTATACGTCAACAGT 59.629 43.478 0.00 0.00 0.00 3.55
6877 7594 4.142902 GCAGCACATTATACGTCAACAGTT 60.143 41.667 0.00 0.00 0.00 3.16
6878 7595 5.062934 GCAGCACATTATACGTCAACAGTTA 59.937 40.000 0.00 0.00 0.00 2.24
6879 7596 6.466812 CAGCACATTATACGTCAACAGTTAC 58.533 40.000 0.00 0.00 0.00 2.50
6880 7597 6.090223 CAGCACATTATACGTCAACAGTTACA 59.910 38.462 0.00 0.00 0.00 2.41
6881 7598 6.647481 AGCACATTATACGTCAACAGTTACAA 59.353 34.615 0.00 0.00 0.00 2.41
6882 7599 6.735063 GCACATTATACGTCAACAGTTACAAC 59.265 38.462 0.00 0.00 0.00 3.32
6883 7600 7.569774 GCACATTATACGTCAACAGTTACAACA 60.570 37.037 0.00 0.00 0.00 3.33
6884 7601 7.738609 CACATTATACGTCAACAGTTACAACAC 59.261 37.037 0.00 0.00 0.00 3.32
6916 7633 3.753294 AAAGGACCAGTACACAGACAG 57.247 47.619 0.00 0.00 0.00 3.51
6918 7635 2.520069 AGGACCAGTACACAGACAGAG 58.480 52.381 0.00 0.00 0.00 3.35
6919 7636 2.108425 AGGACCAGTACACAGACAGAGA 59.892 50.000 0.00 0.00 0.00 3.10
6920 7637 2.891580 GGACCAGTACACAGACAGAGAA 59.108 50.000 0.00 0.00 0.00 2.87
6951 7668 2.571528 CGCTCAGCACGTATCACTC 58.428 57.895 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.760047 CTGGAGTCGGGGTTGGCG 62.760 72.222 0.00 0.00 0.00 5.69
27 28 3.607370 GACTGGAGTCGGGGTTGGC 62.607 68.421 0.00 0.00 35.12 4.52
30 31 2.995574 CGGACTGGAGTCGGGGTT 60.996 66.667 6.48 0.00 45.65 4.11
125 126 1.846712 GATATCCCAGCTCCAGCCCC 61.847 65.000 0.00 0.00 43.38 5.80
140 141 2.757894 AGGTCTCTGACGGTGGATAT 57.242 50.000 0.00 0.00 32.65 1.63
147 148 0.741915 GCTCCTAAGGTCTCTGACGG 59.258 60.000 0.00 0.00 32.65 4.79
152 153 0.035247 ACGACGCTCCTAAGGTCTCT 60.035 55.000 0.00 0.00 0.00 3.10
182 183 1.416401 TCAACAAGTGAGGTCCTCCAC 59.584 52.381 16.60 13.59 35.89 4.02
421 425 8.776376 TTTTGAAAAGAATATTCTGGCAATCC 57.224 30.769 18.61 5.33 37.65 3.01
453 457 8.545229 AAAAATGTTCGCATATTCCAAAATGA 57.455 26.923 0.00 0.00 36.70 2.57
786 792 1.601430 GGTACTACTTAGTCGGGAGCG 59.399 57.143 0.00 0.00 37.73 5.03
789 799 3.010584 AGTTGGGTACTACTTAGTCGGGA 59.989 47.826 0.00 0.00 37.73 5.14
799 809 6.228258 TGAGAACAAATGAGTTGGGTACTAC 58.772 40.000 0.00 0.00 41.97 2.73
1162 1172 2.681273 AATAGAGAGCGGGGGAGGGG 62.681 65.000 0.00 0.00 0.00 4.79
1334 1345 3.917760 GGAGGGGTCGGATCAGCG 61.918 72.222 0.00 0.00 0.00 5.18
1369 1389 1.076332 GTGGATGCGGTCTTGTGTAC 58.924 55.000 0.00 0.00 0.00 2.90
1449 1469 0.389948 GCCTCGTACTGTCCAACCAG 60.390 60.000 0.00 0.00 38.45 4.00
1520 1540 0.950836 CCTTGTCATTCACAACGGCA 59.049 50.000 0.00 0.00 40.29 5.69
1553 1573 5.237815 CAGTAGCACTGGAAACTCACATAA 58.762 41.667 8.03 0.00 42.35 1.90
1572 1592 1.616865 ACAAGGCAGTACGAAGCAGTA 59.383 47.619 9.58 0.00 0.00 2.74
1598 1618 6.015519 TCTCTAAACAAACAATGGGGATTGTG 60.016 38.462 1.32 0.00 43.29 3.33
1603 1623 4.141135 TGGTCTCTAAACAAACAATGGGGA 60.141 41.667 0.00 0.00 0.00 4.81
2015 2378 5.600484 ACAGTACAAGAATCCTCCCATCTAG 59.400 44.000 0.00 0.00 0.00 2.43
2292 2656 8.698973 TTGATAAGAAAAGAATACCCACAACA 57.301 30.769 0.00 0.00 0.00 3.33
2532 2896 8.946085 TCAAATTAATCAGCGAGTTACTGAATT 58.054 29.630 0.00 0.00 46.63 2.17
2658 3022 2.206576 ATGGAGGAAAGGAGTTGTGC 57.793 50.000 0.00 0.00 0.00 4.57
2698 3062 4.462483 ACTGCACTCTGTTTCCTTGAAAAA 59.538 37.500 0.00 0.00 33.14 1.94
2730 3094 4.045736 GGAACCTTAATTCCTACCCCTCT 58.954 47.826 1.24 0.00 44.24 3.69
3118 3482 3.059325 GTGATCTGACAGAACAAGCACAC 60.059 47.826 16.14 10.40 28.60 3.82
3396 3760 4.019174 CACTTTGATTAGCCCAAGGACAT 58.981 43.478 0.00 0.00 0.00 3.06
3472 3836 0.171455 TTGCACCACAAAACGACACC 59.829 50.000 0.00 0.00 34.56 4.16
3727 4091 2.159747 GGCGAGCCAACGTAAAAACTAG 60.160 50.000 9.58 0.00 35.81 2.57
3730 4094 0.308376 TGGCGAGCCAACGTAAAAAC 59.692 50.000 15.24 0.00 44.12 2.43
3849 4213 4.062991 CAACGTAAAAACTAGCCAGTCCT 58.937 43.478 0.00 0.00 32.29 3.85
3882 4246 1.486211 ACGAGGAGGGTTGTGATAGG 58.514 55.000 0.00 0.00 0.00 2.57
3899 4263 2.748647 CCCAAGCCCGGGTAAACG 60.749 66.667 24.63 6.45 41.83 3.60
4252 4630 2.735772 CGTGAGATCCCCACCCCTG 61.736 68.421 9.45 0.00 0.00 4.45
4382 4790 0.035056 CCGCCAAGGAGAAGGACAAT 60.035 55.000 0.00 0.00 45.00 2.71
4384 4792 3.068881 CCGCCAAGGAGAAGGACA 58.931 61.111 0.00 0.00 45.00 4.02
5063 5580 1.531365 CTGGCCAGAACAAAGCCCA 60.531 57.895 29.88 0.00 46.55 5.36
5371 5889 7.395772 TGGCTATCCAATTGTTCAAGTCAATAA 59.604 33.333 4.43 0.00 39.99 1.40
5910 6428 0.755327 ACAAGGTTCCCACAGCAACC 60.755 55.000 0.00 0.00 42.26 3.77
6127 6646 9.699410 TTAAATAGCTACAACCTAGTACTACCA 57.301 33.333 0.00 0.00 0.00 3.25
6496 7174 6.602179 TCGTCAATTGATCTGAAATCAACAC 58.398 36.000 12.12 0.00 40.37 3.32
6548 7226 8.980481 AAAGAGTGATTGAGAGGAAAAACTTA 57.020 30.769 0.00 0.00 0.00 2.24
6579 7257 1.368579 GCAAAGTGCATGCCTGGTT 59.631 52.632 16.68 0.96 44.26 3.67
6621 7300 6.201044 CAGCTTTACAAGTATCATAGTTCCGG 59.799 42.308 0.00 0.00 0.00 5.14
6623 7302 6.538742 TGCAGCTTTACAAGTATCATAGTTCC 59.461 38.462 0.00 0.00 0.00 3.62
6722 7407 2.027073 CGGTGCTTGCTGCGTTAGA 61.027 57.895 0.00 0.00 46.63 2.10
6723 7408 1.565156 TTCGGTGCTTGCTGCGTTAG 61.565 55.000 0.00 0.00 46.63 2.34
6724 7409 1.595655 TTCGGTGCTTGCTGCGTTA 60.596 52.632 0.00 0.00 46.63 3.18
6725 7410 2.899838 TTCGGTGCTTGCTGCGTT 60.900 55.556 0.00 0.00 46.63 4.84
6755 7472 7.390027 AGATGTCTTTGCACTTCTACAGTAAT 58.610 34.615 0.00 0.00 32.76 1.89
6757 7474 6.346477 AGATGTCTTTGCACTTCTACAGTA 57.654 37.500 0.00 0.00 32.76 2.74
6758 7475 5.220710 AGATGTCTTTGCACTTCTACAGT 57.779 39.130 0.00 0.00 35.35 3.55
6760 7477 4.756642 CCAAGATGTCTTTGCACTTCTACA 59.243 41.667 0.00 0.00 33.11 2.74
6761 7478 4.378874 GCCAAGATGTCTTTGCACTTCTAC 60.379 45.833 12.39 0.00 42.26 2.59
6762 7479 3.753272 GCCAAGATGTCTTTGCACTTCTA 59.247 43.478 12.39 0.00 42.26 2.10
6763 7480 2.555757 GCCAAGATGTCTTTGCACTTCT 59.444 45.455 12.39 0.00 42.26 2.85
6766 7483 2.157738 GAGCCAAGATGTCTTTGCACT 58.842 47.619 17.67 2.01 44.30 4.40
6767 7484 2.095364 CAGAGCCAAGATGTCTTTGCAC 60.095 50.000 17.67 12.74 44.30 4.57
6768 7485 2.156917 CAGAGCCAAGATGTCTTTGCA 58.843 47.619 17.67 0.00 44.30 4.08
6769 7486 2.430465 TCAGAGCCAAGATGTCTTTGC 58.570 47.619 9.99 9.99 42.80 3.68
6770 7487 5.181009 TGTATCAGAGCCAAGATGTCTTTG 58.819 41.667 0.00 0.00 33.11 2.77
6771 7488 5.426689 TGTATCAGAGCCAAGATGTCTTT 57.573 39.130 0.00 0.00 33.11 2.52
6773 7490 5.104610 ACATTGTATCAGAGCCAAGATGTCT 60.105 40.000 0.00 0.00 0.00 3.41
6774 7491 5.121811 ACATTGTATCAGAGCCAAGATGTC 58.878 41.667 0.00 0.00 0.00 3.06
6775 7492 5.108187 ACATTGTATCAGAGCCAAGATGT 57.892 39.130 0.00 0.00 0.00 3.06
6776 7493 6.519382 TCTACATTGTATCAGAGCCAAGATG 58.481 40.000 0.00 0.00 0.00 2.90
6778 7495 6.155221 ACTTCTACATTGTATCAGAGCCAAGA 59.845 38.462 0.00 0.00 0.00 3.02
6779 7496 6.257411 CACTTCTACATTGTATCAGAGCCAAG 59.743 42.308 0.00 0.00 0.00 3.61
6780 7497 6.108687 CACTTCTACATTGTATCAGAGCCAA 58.891 40.000 0.00 0.00 0.00 4.52
6781 7498 5.664457 CACTTCTACATTGTATCAGAGCCA 58.336 41.667 0.00 0.00 0.00 4.75
6782 7499 4.509600 GCACTTCTACATTGTATCAGAGCC 59.490 45.833 10.94 0.10 0.00 4.70
6783 7500 5.111989 TGCACTTCTACATTGTATCAGAGC 58.888 41.667 13.41 13.41 0.00 4.09
6784 7501 6.292757 GCATGCACTTCTACATTGTATCAGAG 60.293 42.308 14.21 0.00 0.00 3.35
6785 7502 5.525012 GCATGCACTTCTACATTGTATCAGA 59.475 40.000 14.21 0.00 0.00 3.27
6786 7503 5.526479 AGCATGCACTTCTACATTGTATCAG 59.474 40.000 21.98 0.00 0.00 2.90
6787 7504 5.430886 AGCATGCACTTCTACATTGTATCA 58.569 37.500 21.98 0.00 0.00 2.15
6788 7505 5.757320 AGAGCATGCACTTCTACATTGTATC 59.243 40.000 21.98 2.25 0.00 2.24
6789 7506 5.678583 AGAGCATGCACTTCTACATTGTAT 58.321 37.500 21.98 0.00 0.00 2.29
6790 7507 5.089970 AGAGCATGCACTTCTACATTGTA 57.910 39.130 21.98 0.00 0.00 2.41
6791 7508 3.947868 AGAGCATGCACTTCTACATTGT 58.052 40.909 21.98 0.00 0.00 2.71
6792 7509 4.025061 GCTAGAGCATGCACTTCTACATTG 60.025 45.833 22.83 8.58 41.59 2.82
6793 7510 4.125703 GCTAGAGCATGCACTTCTACATT 58.874 43.478 22.83 0.00 41.59 2.71
6794 7511 3.387374 AGCTAGAGCATGCACTTCTACAT 59.613 43.478 22.83 6.01 45.16 2.29
6795 7512 2.762887 AGCTAGAGCATGCACTTCTACA 59.237 45.455 22.83 3.70 45.16 2.74
6796 7513 3.451141 AGCTAGAGCATGCACTTCTAC 57.549 47.619 22.83 12.85 45.16 2.59
6797 7514 5.536260 CATTAGCTAGAGCATGCACTTCTA 58.464 41.667 22.83 19.12 45.16 2.10
6798 7515 4.378774 CATTAGCTAGAGCATGCACTTCT 58.621 43.478 22.83 20.02 45.16 2.85
6799 7516 3.059051 GCATTAGCTAGAGCATGCACTTC 60.059 47.826 22.83 14.51 44.74 3.01
6800 7517 2.877168 GCATTAGCTAGAGCATGCACTT 59.123 45.455 22.83 7.95 44.74 3.16
6801 7518 2.492012 GCATTAGCTAGAGCATGCACT 58.508 47.619 21.45 21.45 44.74 4.40
6802 7519 2.965477 GCATTAGCTAGAGCATGCAC 57.035 50.000 21.98 14.59 44.74 4.57
6804 7521 2.031333 GGTTGCATTAGCTAGAGCATGC 60.031 50.000 18.96 18.24 45.25 4.06
6805 7522 3.208594 TGGTTGCATTAGCTAGAGCATG 58.791 45.455 18.96 10.10 45.16 4.06
6806 7523 3.565764 TGGTTGCATTAGCTAGAGCAT 57.434 42.857 18.96 0.00 45.16 3.79
6807 7524 3.348647 TTGGTTGCATTAGCTAGAGCA 57.651 42.857 15.62 15.62 45.16 4.26
6808 7525 4.396166 TCTTTTGGTTGCATTAGCTAGAGC 59.604 41.667 11.35 11.35 42.74 4.09
6809 7526 5.163713 GGTCTTTTGGTTGCATTAGCTAGAG 60.164 44.000 0.00 0.00 42.74 2.43
6810 7527 4.700213 GGTCTTTTGGTTGCATTAGCTAGA 59.300 41.667 0.00 0.00 42.74 2.43
6811 7528 4.458989 TGGTCTTTTGGTTGCATTAGCTAG 59.541 41.667 0.00 0.00 42.74 3.42
6812 7529 4.402829 TGGTCTTTTGGTTGCATTAGCTA 58.597 39.130 0.00 0.00 42.74 3.32
6813 7530 3.230134 TGGTCTTTTGGTTGCATTAGCT 58.770 40.909 0.00 0.00 42.74 3.32
6814 7531 3.658757 TGGTCTTTTGGTTGCATTAGC 57.341 42.857 0.00 0.00 42.57 3.09
6815 7532 5.865552 CAGATTGGTCTTTTGGTTGCATTAG 59.134 40.000 0.00 0.00 30.42 1.73
6816 7533 5.538053 TCAGATTGGTCTTTTGGTTGCATTA 59.462 36.000 0.00 0.00 30.42 1.90
6817 7534 4.344679 TCAGATTGGTCTTTTGGTTGCATT 59.655 37.500 0.00 0.00 30.42 3.56
6818 7535 3.896888 TCAGATTGGTCTTTTGGTTGCAT 59.103 39.130 0.00 0.00 30.42 3.96
6819 7536 3.295093 TCAGATTGGTCTTTTGGTTGCA 58.705 40.909 0.00 0.00 30.42 4.08
6820 7537 4.022068 TCATCAGATTGGTCTTTTGGTTGC 60.022 41.667 0.00 0.00 30.42 4.17
6821 7538 5.710513 TCATCAGATTGGTCTTTTGGTTG 57.289 39.130 0.00 0.00 30.42 3.77
6822 7539 6.550854 TCTTTCATCAGATTGGTCTTTTGGTT 59.449 34.615 0.00 0.00 30.42 3.67
6823 7540 6.070656 TCTTTCATCAGATTGGTCTTTTGGT 58.929 36.000 0.00 0.00 30.42 3.67
6824 7541 6.432162 TCTCTTTCATCAGATTGGTCTTTTGG 59.568 38.462 0.00 0.00 30.42 3.28
6825 7542 7.174599 AGTCTCTTTCATCAGATTGGTCTTTTG 59.825 37.037 0.00 0.00 30.42 2.44
6826 7543 7.230027 AGTCTCTTTCATCAGATTGGTCTTTT 58.770 34.615 0.00 0.00 30.42 2.27
6827 7544 6.777782 AGTCTCTTTCATCAGATTGGTCTTT 58.222 36.000 0.00 0.00 30.42 2.52
6828 7545 6.371595 AGTCTCTTTCATCAGATTGGTCTT 57.628 37.500 0.00 0.00 30.42 3.01
6829 7546 6.098124 CCTAGTCTCTTTCATCAGATTGGTCT 59.902 42.308 0.00 0.00 34.14 3.85
6830 7547 6.279882 CCTAGTCTCTTTCATCAGATTGGTC 58.720 44.000 0.00 0.00 0.00 4.02
6831 7548 5.396213 GCCTAGTCTCTTTCATCAGATTGGT 60.396 44.000 0.00 0.00 0.00 3.67
6832 7549 5.055812 GCCTAGTCTCTTTCATCAGATTGG 58.944 45.833 0.00 0.00 0.00 3.16
6833 7550 5.668471 TGCCTAGTCTCTTTCATCAGATTG 58.332 41.667 0.00 0.00 0.00 2.67
6834 7551 5.684552 GCTGCCTAGTCTCTTTCATCAGATT 60.685 44.000 0.00 0.00 0.00 2.40
6835 7552 4.202243 GCTGCCTAGTCTCTTTCATCAGAT 60.202 45.833 0.00 0.00 0.00 2.90
6836 7553 3.131933 GCTGCCTAGTCTCTTTCATCAGA 59.868 47.826 0.00 0.00 0.00 3.27
6837 7554 3.118847 TGCTGCCTAGTCTCTTTCATCAG 60.119 47.826 0.00 0.00 0.00 2.90
6838 7555 2.833943 TGCTGCCTAGTCTCTTTCATCA 59.166 45.455 0.00 0.00 0.00 3.07
6839 7556 3.194062 GTGCTGCCTAGTCTCTTTCATC 58.806 50.000 0.00 0.00 0.00 2.92
6840 7557 2.568956 TGTGCTGCCTAGTCTCTTTCAT 59.431 45.455 0.00 0.00 0.00 2.57
6841 7558 1.970640 TGTGCTGCCTAGTCTCTTTCA 59.029 47.619 0.00 0.00 0.00 2.69
6842 7559 2.751166 TGTGCTGCCTAGTCTCTTTC 57.249 50.000 0.00 0.00 0.00 2.62
6843 7560 3.710209 AATGTGCTGCCTAGTCTCTTT 57.290 42.857 0.00 0.00 0.00 2.52
6844 7561 5.508153 CGTATAATGTGCTGCCTAGTCTCTT 60.508 44.000 0.00 0.00 0.00 2.85
6845 7562 4.022762 CGTATAATGTGCTGCCTAGTCTCT 60.023 45.833 0.00 0.00 0.00 3.10
6846 7563 4.230657 CGTATAATGTGCTGCCTAGTCTC 58.769 47.826 0.00 0.00 0.00 3.36
6847 7564 3.637229 ACGTATAATGTGCTGCCTAGTCT 59.363 43.478 0.00 0.00 0.00 3.24
6848 7565 3.978687 ACGTATAATGTGCTGCCTAGTC 58.021 45.455 0.00 0.00 0.00 2.59
6849 7566 3.383505 TGACGTATAATGTGCTGCCTAGT 59.616 43.478 0.00 0.00 0.00 2.57
6850 7567 3.977427 TGACGTATAATGTGCTGCCTAG 58.023 45.455 0.00 0.00 0.00 3.02
6851 7568 4.116961 GTTGACGTATAATGTGCTGCCTA 58.883 43.478 0.00 0.00 0.00 3.93
6852 7569 2.936498 GTTGACGTATAATGTGCTGCCT 59.064 45.455 0.00 0.00 0.00 4.75
6853 7570 2.675844 TGTTGACGTATAATGTGCTGCC 59.324 45.455 0.00 0.00 0.00 4.85
6854 7571 3.370978 ACTGTTGACGTATAATGTGCTGC 59.629 43.478 0.00 0.00 0.00 5.25
6855 7572 5.530519 AACTGTTGACGTATAATGTGCTG 57.469 39.130 0.00 0.00 0.00 4.41
6856 7573 6.160684 TGTAACTGTTGACGTATAATGTGCT 58.839 36.000 2.69 0.00 0.00 4.40
6857 7574 6.397831 TGTAACTGTTGACGTATAATGTGC 57.602 37.500 2.69 0.00 0.00 4.57
6858 7575 7.738609 GTGTTGTAACTGTTGACGTATAATGTG 59.261 37.037 2.69 0.00 0.00 3.21
6859 7576 7.358600 CGTGTTGTAACTGTTGACGTATAATGT 60.359 37.037 2.69 0.00 0.00 2.71
6860 7577 6.946037 CGTGTTGTAACTGTTGACGTATAATG 59.054 38.462 2.69 0.00 0.00 1.90
6861 7578 6.862608 TCGTGTTGTAACTGTTGACGTATAAT 59.137 34.615 2.69 0.00 0.00 1.28
6862 7579 6.142161 GTCGTGTTGTAACTGTTGACGTATAA 59.858 38.462 2.69 0.00 0.00 0.98
6863 7580 5.624900 GTCGTGTTGTAACTGTTGACGTATA 59.375 40.000 2.69 0.00 0.00 1.47
6864 7581 4.442073 GTCGTGTTGTAACTGTTGACGTAT 59.558 41.667 2.69 0.00 0.00 3.06
6865 7582 3.790820 GTCGTGTTGTAACTGTTGACGTA 59.209 43.478 2.69 0.00 0.00 3.57
6866 7583 2.599973 GTCGTGTTGTAACTGTTGACGT 59.400 45.455 2.69 0.00 0.00 4.34
6867 7584 2.855963 AGTCGTGTTGTAACTGTTGACG 59.144 45.455 2.69 4.31 0.00 4.35
6868 7585 4.852609 AAGTCGTGTTGTAACTGTTGAC 57.147 40.909 2.69 0.28 0.00 3.18
6869 7586 5.868258 TGTTAAGTCGTGTTGTAACTGTTGA 59.132 36.000 2.69 0.00 0.00 3.18
6870 7587 6.097156 TGTTAAGTCGTGTTGTAACTGTTG 57.903 37.500 2.69 0.00 0.00 3.33
6871 7588 6.913873 ATGTTAAGTCGTGTTGTAACTGTT 57.086 33.333 0.00 0.00 0.00 3.16
6872 7589 6.913873 AATGTTAAGTCGTGTTGTAACTGT 57.086 33.333 0.00 0.00 0.00 3.55
6873 7590 9.365311 CTTTAATGTTAAGTCGTGTTGTAACTG 57.635 33.333 0.00 0.00 0.00 3.16
6874 7591 8.553696 CCTTTAATGTTAAGTCGTGTTGTAACT 58.446 33.333 0.00 0.00 0.00 2.24
6875 7592 8.550376 TCCTTTAATGTTAAGTCGTGTTGTAAC 58.450 33.333 0.00 0.00 0.00 2.50
6876 7593 8.550376 GTCCTTTAATGTTAAGTCGTGTTGTAA 58.450 33.333 0.00 0.00 0.00 2.41
6877 7594 7.171337 GGTCCTTTAATGTTAAGTCGTGTTGTA 59.829 37.037 0.00 0.00 0.00 2.41
6878 7595 6.017687 GGTCCTTTAATGTTAAGTCGTGTTGT 60.018 38.462 0.00 0.00 0.00 3.32
6879 7596 6.017770 TGGTCCTTTAATGTTAAGTCGTGTTG 60.018 38.462 0.00 0.00 0.00 3.33
6880 7597 6.056884 TGGTCCTTTAATGTTAAGTCGTGTT 58.943 36.000 0.00 0.00 0.00 3.32
6881 7598 5.613329 TGGTCCTTTAATGTTAAGTCGTGT 58.387 37.500 0.00 0.00 0.00 4.49
6882 7599 5.699458 ACTGGTCCTTTAATGTTAAGTCGTG 59.301 40.000 0.00 0.00 0.00 4.35
6883 7600 5.861727 ACTGGTCCTTTAATGTTAAGTCGT 58.138 37.500 0.00 0.00 0.00 4.34
6884 7601 6.869913 TGTACTGGTCCTTTAATGTTAAGTCG 59.130 38.462 0.00 0.00 0.00 4.18
6916 7633 5.275464 GCTGAGCGCGAATTTTAATTTTCTC 60.275 40.000 12.10 2.01 0.00 2.87
6918 7635 4.323336 TGCTGAGCGCGAATTTTAATTTTC 59.677 37.500 12.10 0.00 43.27 2.29
6919 7636 4.089923 GTGCTGAGCGCGAATTTTAATTTT 59.910 37.500 12.10 0.00 43.27 1.82
6920 7637 3.608073 GTGCTGAGCGCGAATTTTAATTT 59.392 39.130 12.10 0.00 43.27 1.82
6946 7663 5.312895 TGTTAATTTGCTTGCTAGGAGTGA 58.687 37.500 0.00 0.00 0.00 3.41
6951 7668 4.794169 ACGTTGTTAATTTGCTTGCTAGG 58.206 39.130 0.00 0.00 0.00 3.02
7216 7933 1.375908 GCTGACGAACCTGATGGCA 60.376 57.895 0.00 0.00 36.63 4.92


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

AutoCloner maintained by Alex Coulton.