Multiple sequence alignment - TraesCS4D01G166200

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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 TraesCS4D01G166200 chr4D 100.000 7996 0 0 1 7996 280175022 280183017 0.000000e+00 14766.0
1 TraesCS4D01G166200 chr4D 94.668 4782 168 43 2893 7643 108630465 108625740 0.000000e+00 7337.0
2 TraesCS4D01G166200 chr4D 94.340 848 24 12 1 827 302347474 302346630 0.000000e+00 1279.0
3 TraesCS4D01G166200 chr4D 96.255 721 26 1 990 1709 108631178 108630458 0.000000e+00 1181.0
4 TraesCS4D01G166200 chr4D 94.554 202 11 0 7795 7996 108610301 108610100 6.020000e-81 313.0
5 TraesCS4D01G166200 chr4D 81.271 299 37 13 7524 7814 256642437 256642724 2.900000e-54 224.0
6 TraesCS4D01G166200 chr4D 93.458 107 7 0 4685 4791 259497365 259497259 8.310000e-35 159.0
7 TraesCS4D01G166200 chr4D 91.667 60 5 0 938 997 108632464 108632405 5.140000e-12 84.2
8 TraesCS4D01G166200 chr4D 100.000 35 0 0 7291 7325 280182277 280182311 1.860000e-06 65.8
9 TraesCS4D01G166200 chr4D 100.000 35 0 0 7256 7290 280182312 280182346 1.860000e-06 65.8
10 TraesCS4D01G166200 chr4A 96.447 4222 124 18 3050 7259 467682575 467686782 0.000000e+00 6942.0
11 TraesCS4D01G166200 chr4A 96.489 712 20 4 999 1706 467681554 467682264 0.000000e+00 1171.0
12 TraesCS4D01G166200 chr4A 88.105 765 78 8 1706 2467 405552457 405551703 0.000000e+00 896.0
13 TraesCS4D01G166200 chr4A 84.830 501 57 8 7319 7813 467749005 467749492 3.350000e-133 486.0
14 TraesCS4D01G166200 chr4A 92.195 205 16 0 7792 7996 467749502 467749706 2.820000e-74 291.0
15 TraesCS4D01G166200 chr4A 98.561 139 2 0 2893 3031 467682260 467682398 6.200000e-61 246.0
16 TraesCS4D01G166200 chr4A 90.000 120 11 1 4676 4795 590945700 590945818 3.860000e-33 154.0
17 TraesCS4D01G166200 chr6B 95.135 2631 87 21 4800 7416 69444500 69441897 0.000000e+00 4111.0
18 TraesCS4D01G166200 chr6B 92.435 846 39 13 1 827 79274491 79273652 0.000000e+00 1184.0
19 TraesCS4D01G166200 chr6B 92.737 716 18 10 1017 1709 69446910 69446206 0.000000e+00 1003.0
20 TraesCS4D01G166200 chr6B 96.769 588 10 4 3387 3967 69445529 69444944 0.000000e+00 972.0
21 TraesCS4D01G166200 chr6B 98.618 434 6 0 4019 4452 69444944 69444511 0.000000e+00 769.0
22 TraesCS4D01G166200 chr6B 90.019 531 18 11 2893 3390 69446213 69445685 0.000000e+00 654.0
23 TraesCS4D01G166200 chr6B 88.685 327 34 3 4789 5114 377933308 377933632 5.820000e-106 396.0
24 TraesCS4D01G166200 chr6B 83.108 444 26 10 7481 7883 69441895 69441460 7.630000e-95 359.0
25 TraesCS4D01G166200 chr6B 92.222 90 7 0 938 1027 69448371 69448282 2.340000e-25 128.0
26 TraesCS4D01G166200 chr3A 92.137 1170 74 9 1740 2893 662416780 662417947 0.000000e+00 1635.0
27 TraesCS4D01G166200 chr3A 87.234 329 36 4 4788 5114 264032029 264031705 3.520000e-98 370.0
28 TraesCS4D01G166200 chr3A 92.045 264 18 3 4332 4594 664692847 664693108 1.270000e-97 368.0
29 TraesCS4D01G166200 chr3A 92.661 109 8 0 4685 4793 503822393 503822285 2.990000e-34 158.0
30 TraesCS4D01G166200 chr5D 88.411 1208 116 12 1702 2891 216018749 216019950 0.000000e+00 1434.0
31 TraesCS4D01G166200 chr5D 93.839 844 31 11 1 827 391047116 391047955 0.000000e+00 1251.0
32 TraesCS4D01G166200 chr5D 81.601 1212 186 24 1707 2893 543654193 543655392 0.000000e+00 968.0
33 TraesCS4D01G166200 chr5D 89.535 258 25 2 5130 5386 201664577 201664321 7.740000e-85 326.0
34 TraesCS4D01G166200 chr5D 89.375 160 14 2 5622 5779 215301982 215302140 1.760000e-46 198.0
35 TraesCS4D01G166200 chr5D 93.519 108 7 0 4684 4791 371860609 371860716 2.310000e-35 161.0
36 TraesCS4D01G166200 chr6D 87.262 1209 128 10 1702 2893 83206710 83207909 0.000000e+00 1356.0
37 TraesCS4D01G166200 chr6D 88.450 329 33 5 4788 5114 276144719 276144394 7.520000e-105 392.0
38 TraesCS4D01G166200 chr6D 91.288 264 20 3 4332 4594 423215391 423215652 2.740000e-94 357.0
39 TraesCS4D01G166200 chr6D 87.938 257 29 2 5128 5383 175718544 175718289 1.300000e-77 302.0
40 TraesCS4D01G166200 chr6D 90.777 206 18 1 7792 7996 361546319 361546524 2.840000e-69 274.0
41 TraesCS4D01G166200 chr6D 90.476 147 14 0 5630 5776 386931496 386931642 2.280000e-45 195.0
42 TraesCS4D01G166200 chr6D 92.661 109 8 0 4683 4791 302113642 302113750 2.990000e-34 158.0
43 TraesCS4D01G166200 chr4B 87.292 1204 132 10 1706 2893 562551031 562549833 0.000000e+00 1356.0
44 TraesCS4D01G166200 chr4B 93.197 441 19 6 396 827 45203464 45203026 8.750000e-179 638.0
45 TraesCS4D01G166200 chr7D 94.681 846 21 9 1 827 635162657 635161817 0.000000e+00 1291.0
46 TraesCS4D01G166200 chr7D 93.288 730 26 11 119 827 633938101 633938828 0.000000e+00 1055.0
47 TraesCS4D01G166200 chr7D 85.747 884 106 10 2027 2893 500158832 500159712 0.000000e+00 917.0
48 TraesCS4D01G166200 chr7D 90.132 152 15 0 5626 5777 156796841 156796992 1.760000e-46 198.0
49 TraesCS4D01G166200 chr7D 89.103 156 16 1 5627 5781 379326469 379326314 8.190000e-45 193.0
50 TraesCS4D01G166200 chr3D 94.543 843 22 10 1 827 457396009 457395175 0.000000e+00 1280.0
51 TraesCS4D01G166200 chr3D 93.118 465 14 7 1 451 896359 895899 0.000000e+00 665.0
52 TraesCS4D01G166200 chr3D 92.661 109 8 0 4685 4793 379826241 379826349 2.990000e-34 158.0
53 TraesCS4D01G166200 chr5B 85.866 1224 132 15 1704 2893 659093238 659092022 0.000000e+00 1264.0
54 TraesCS4D01G166200 chr7A 85.112 1209 155 10 1701 2893 183842924 183844123 0.000000e+00 1212.0
55 TraesCS4D01G166200 chr7A 93.026 846 30 12 1 829 24423815 24422982 0.000000e+00 1208.0
56 TraesCS4D01G166200 chr7A 89.449 853 54 21 1 827 16929983 16929141 0.000000e+00 1044.0
57 TraesCS4D01G166200 chr7A 91.698 265 17 4 4331 4594 515737512 515737772 5.900000e-96 363.0
58 TraesCS4D01G166200 chr7A 89.542 153 16 0 5624 5776 462978739 462978587 2.280000e-45 195.0
59 TraesCS4D01G166200 chr6A 83.951 1215 166 14 1705 2893 30205106 30203895 0.000000e+00 1136.0
60 TraesCS4D01G166200 chr6A 88.073 327 34 5 4789 5114 294645366 294645688 4.530000e-102 383.0
61 TraesCS4D01G166200 chr6A 88.350 206 23 1 7792 7996 502737135 502737340 6.200000e-61 246.0
62 TraesCS4D01G166200 chrUn 92.032 753 44 3 2042 2778 108750267 108749515 0.000000e+00 1044.0
63 TraesCS4D01G166200 chr2B 94.178 584 24 5 1 579 594259794 594260372 0.000000e+00 881.0
64 TraesCS4D01G166200 chr2B 87.156 327 36 4 4790 5114 333042515 333042837 4.560000e-97 366.0
65 TraesCS4D01G166200 chr2B 90.272 257 22 3 5128 5383 234367961 234367707 4.620000e-87 333.0
66 TraesCS4D01G166200 chr7B 92.105 266 18 3 4331 4595 173229520 173229783 9.800000e-99 372.0
67 TraesCS4D01G166200 chr7B 88.119 202 24 0 7795 7996 592178257 592178056 2.880000e-59 241.0
68 TraesCS4D01G166200 chr7B 80.198 303 39 12 7523 7813 478729999 478729706 2.920000e-49 207.0
69 TraesCS4D01G166200 chr7B 77.586 290 52 10 7524 7809 177877080 177877360 6.420000e-36 163.0
70 TraesCS4D01G166200 chr7B 91.304 115 10 0 4677 4791 357651476 357651590 2.990000e-34 158.0
71 TraesCS4D01G166200 chr3B 86.930 329 35 6 4788 5114 299132981 299133303 5.900000e-96 363.0
72 TraesCS4D01G166200 chr3B 80.872 298 41 7 7523 7813 472664095 472664383 3.760000e-53 220.0
73 TraesCS4D01G166200 chr1D 91.635 263 19 3 4332 4593 100462103 100461843 2.120000e-95 361.0
74 TraesCS4D01G166200 chr1D 75.594 463 92 13 7536 7988 286193883 286193432 8.130000e-50 209.0
75 TraesCS4D01G166200 chr1D 84.848 198 29 1 7791 7988 288080388 288080584 1.760000e-46 198.0
76 TraesCS4D01G166200 chr2D 91.603 262 17 5 4331 4590 74146852 74147110 2.740000e-94 357.0
77 TraesCS4D01G166200 chr2D 88.417 259 22 6 5128 5383 633320460 633320713 1.010000e-78 305.0
78 TraesCS4D01G166200 chr2D 87.938 257 29 2 5128 5383 177460083 177459828 1.300000e-77 302.0
79 TraesCS4D01G166200 chr2D 88.235 153 16 2 7791 7942 379295631 379295782 1.770000e-41 182.0
80 TraesCS4D01G166200 chr2D 83.696 184 29 1 7524 7706 345514134 345513951 1.070000e-38 172.0
81 TraesCS4D01G166200 chr5A 90.977 266 21 3 4331 4595 535518763 535518500 9.870000e-94 355.0
82 TraesCS4D01G166200 chr5A 91.667 60 4 1 3696 3755 642914198 642914140 1.850000e-11 82.4
83 TraesCS4D01G166200 chr2A 88.372 258 27 3 5128 5383 190317508 190317252 2.800000e-79 307.0
84 TraesCS4D01G166200 chr2A 89.655 203 21 0 7792 7994 381506526 381506728 7.960000e-65 259.0
85 TraesCS4D01G166200 chr2A 89.542 153 14 1 5624 5776 329688022 329688172 8.190000e-45 193.0
86 TraesCS4D01G166200 chr1A 77.413 487 57 24 7524 7972 13900713 13901184 2.880000e-59 241.0
87 TraesCS4D01G166200 chr1B 78.947 304 43 12 7520 7813 616137287 616137579 3.810000e-43 187.0
88 TraesCS4D01G166200 chr1B 76.589 299 50 11 7524 7813 242238112 242237825 6.470000e-31 147.0


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 TraesCS4D01G166200 chr4D 280175022 280183017 7995 False 4965.866667 14766 100.000000 1 7996 3 chr4D.!!$F2 7995
1 TraesCS4D01G166200 chr4D 108625740 108632464 6724 True 2867.400000 7337 94.196667 938 7643 3 chr4D.!!$R4 6705
2 TraesCS4D01G166200 chr4D 302346630 302347474 844 True 1279.000000 1279 94.340000 1 827 1 chr4D.!!$R3 826
3 TraesCS4D01G166200 chr4A 467681554 467686782 5228 False 2786.333333 6942 97.165667 999 7259 3 chr4A.!!$F2 6260
4 TraesCS4D01G166200 chr4A 405551703 405552457 754 True 896.000000 896 88.105000 1706 2467 1 chr4A.!!$R1 761
5 TraesCS4D01G166200 chr4A 467749005 467749706 701 False 388.500000 486 88.512500 7319 7996 2 chr4A.!!$F3 677
6 TraesCS4D01G166200 chr6B 79273652 79274491 839 True 1184.000000 1184 92.435000 1 827 1 chr6B.!!$R1 826
7 TraesCS4D01G166200 chr6B 69441460 69448371 6911 True 1142.285714 4111 92.658286 938 7883 7 chr6B.!!$R2 6945
8 TraesCS4D01G166200 chr3A 662416780 662417947 1167 False 1635.000000 1635 92.137000 1740 2893 1 chr3A.!!$F1 1153
9 TraesCS4D01G166200 chr5D 216018749 216019950 1201 False 1434.000000 1434 88.411000 1702 2891 1 chr5D.!!$F2 1189
10 TraesCS4D01G166200 chr5D 391047116 391047955 839 False 1251.000000 1251 93.839000 1 827 1 chr5D.!!$F4 826
11 TraesCS4D01G166200 chr5D 543654193 543655392 1199 False 968.000000 968 81.601000 1707 2893 1 chr5D.!!$F5 1186
12 TraesCS4D01G166200 chr6D 83206710 83207909 1199 False 1356.000000 1356 87.262000 1702 2893 1 chr6D.!!$F1 1191
13 TraesCS4D01G166200 chr4B 562549833 562551031 1198 True 1356.000000 1356 87.292000 1706 2893 1 chr4B.!!$R2 1187
14 TraesCS4D01G166200 chr7D 635161817 635162657 840 True 1291.000000 1291 94.681000 1 827 1 chr7D.!!$R2 826
15 TraesCS4D01G166200 chr7D 633938101 633938828 727 False 1055.000000 1055 93.288000 119 827 1 chr7D.!!$F3 708
16 TraesCS4D01G166200 chr7D 500158832 500159712 880 False 917.000000 917 85.747000 2027 2893 1 chr7D.!!$F2 866
17 TraesCS4D01G166200 chr3D 457395175 457396009 834 True 1280.000000 1280 94.543000 1 827 1 chr3D.!!$R2 826
18 TraesCS4D01G166200 chr5B 659092022 659093238 1216 True 1264.000000 1264 85.866000 1704 2893 1 chr5B.!!$R1 1189
19 TraesCS4D01G166200 chr7A 183842924 183844123 1199 False 1212.000000 1212 85.112000 1701 2893 1 chr7A.!!$F1 1192
20 TraesCS4D01G166200 chr7A 24422982 24423815 833 True 1208.000000 1208 93.026000 1 829 1 chr7A.!!$R2 828
21 TraesCS4D01G166200 chr7A 16929141 16929983 842 True 1044.000000 1044 89.449000 1 827 1 chr7A.!!$R1 826
22 TraesCS4D01G166200 chr6A 30203895 30205106 1211 True 1136.000000 1136 83.951000 1705 2893 1 chr6A.!!$R1 1188
23 TraesCS4D01G166200 chrUn 108749515 108750267 752 True 1044.000000 1044 92.032000 2042 2778 1 chrUn.!!$R1 736
24 TraesCS4D01G166200 chr2B 594259794 594260372 578 False 881.000000 881 94.178000 1 579 1 chr2B.!!$F2 578


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
775 826 0.171903 TCGACCGGGATTTCGACTTC 59.828 55.000 10.52 0.0 39.29 3.01 F
982 1034 0.388520 CGTCTGACTGATGGCACGAA 60.389 55.000 6.21 0.0 0.00 3.85 F
1820 4544 0.398948 CAAATAAGGGCTGGGGGCAT 60.399 55.000 0.00 0.0 44.01 4.40 F
2194 4925 0.466555 CACCAACAACCTCCCGGAAA 60.467 55.000 0.73 0.0 0.00 3.13 F
2784 5533 0.258194 GGACCCTCCCGTTCTAGAGA 59.742 60.000 0.00 0.0 31.43 3.10 F
2803 5552 1.973281 CGAATGCCAGTGGTTGCCT 60.973 57.895 11.74 0.0 0.00 4.75 F
2901 5650 2.582636 AGGAGGGCAATATGTTTCACCT 59.417 45.455 0.00 0.0 0.00 4.00 F
3379 6317 2.627699 TCCAGAAATGTTTGAGGTTGCC 59.372 45.455 0.00 0.0 0.00 4.52 F
4584 7689 3.695830 ATGCAGACTAAAAAGGACCGA 57.304 42.857 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 4925 0.035458 CTCGGTTCCTTTGGAGCTGT 59.965 55.000 0.00 0.00 39.75 4.40 R
2750 5499 1.337118 GGTCCCAGTTTTGGCAATCA 58.663 50.000 0.00 0.00 43.58 2.57 R
2784 5533 3.354678 GCAACCACTGGCATTCGT 58.645 55.556 0.00 0.00 0.00 3.85 R
3043 5799 6.885922 ACGGCAGGATAATAATATAGGGAAC 58.114 40.000 0.00 0.00 0.00 3.62 R
4681 7786 1.043816 ATGGATCGCAGGGAGTACTG 58.956 55.000 0.00 0.00 41.41 2.74 R
5058 8163 2.157668 CCTTGCTGCTACAAAGTGTACG 59.842 50.000 0.00 0.00 0.00 3.67 R
5448 8554 5.001232 TCTATAAACAGGTTGTGGCACTTC 58.999 41.667 19.83 11.22 0.00 3.01 R
5620 8730 1.254954 AGTGAACGGAGGGAGTACAC 58.745 55.000 0.00 0.00 0.00 2.90 R
7131 10266 1.169661 AAGAACATCCAAACCGCGCA 61.170 50.000 8.75 0.00 0.00 6.09 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
90 93 7.696035 CGCGGCAAATATATGATAGCATTTTTA 59.304 33.333 0.00 0.00 35.94 1.52
426 454 8.168626 GTGAACTTCTTTCAAAATTGTTGAACC 58.831 33.333 1.34 0.00 46.09 3.62
446 475 7.367285 TGAACCTTTTCTAAATCCGTGATTTG 58.633 34.615 17.09 10.14 41.55 2.32
739 790 3.528532 GTTCGATTTAGACCGGGATTGT 58.471 45.455 6.32 0.00 0.00 2.71
775 826 0.171903 TCGACCGGGATTTCGACTTC 59.828 55.000 10.52 0.00 39.29 3.01
808 860 3.596214 GCCGAACCTCTACAAATTCAGA 58.404 45.455 0.00 0.00 0.00 3.27
870 922 6.658188 TTTTTACAATCCGGGTTCAAGATT 57.342 33.333 0.00 0.00 0.00 2.40
871 923 5.890424 TTTACAATCCGGGTTCAAGATTC 57.110 39.130 0.00 0.00 0.00 2.52
872 924 3.721087 ACAATCCGGGTTCAAGATTCT 57.279 42.857 0.00 0.00 0.00 2.40
873 925 3.347216 ACAATCCGGGTTCAAGATTCTG 58.653 45.455 0.00 0.00 0.00 3.02
874 926 2.684881 CAATCCGGGTTCAAGATTCTGG 59.315 50.000 0.00 0.00 0.00 3.86
875 927 1.651737 TCCGGGTTCAAGATTCTGGA 58.348 50.000 0.00 0.00 32.73 3.86
876 928 1.982226 TCCGGGTTCAAGATTCTGGAA 59.018 47.619 0.00 0.00 32.28 3.53
877 929 2.373836 TCCGGGTTCAAGATTCTGGAAA 59.626 45.455 5.03 0.00 32.28 3.13
878 930 3.153919 CCGGGTTCAAGATTCTGGAAAA 58.846 45.455 5.03 0.00 0.00 2.29
879 931 3.572255 CCGGGTTCAAGATTCTGGAAAAA 59.428 43.478 5.03 0.00 0.00 1.94
896 948 2.181954 AAAAGCTGAGTGGAGAGCTG 57.818 50.000 0.00 0.00 44.97 4.24
897 949 1.346062 AAAGCTGAGTGGAGAGCTGA 58.654 50.000 0.00 0.00 44.97 4.26
898 950 1.570803 AAGCTGAGTGGAGAGCTGAT 58.429 50.000 0.00 0.00 44.97 2.90
899 951 1.570803 AGCTGAGTGGAGAGCTGATT 58.429 50.000 0.00 0.00 44.03 2.57
900 952 1.481772 AGCTGAGTGGAGAGCTGATTC 59.518 52.381 0.00 0.00 44.03 2.52
901 953 1.481772 GCTGAGTGGAGAGCTGATTCT 59.518 52.381 0.00 0.00 32.12 2.40
902 954 2.481795 GCTGAGTGGAGAGCTGATTCTC 60.482 54.545 0.00 0.00 42.31 2.87
903 955 2.759535 CTGAGTGGAGAGCTGATTCTCA 59.240 50.000 0.00 0.00 44.34 3.27
904 956 3.168292 TGAGTGGAGAGCTGATTCTCAA 58.832 45.455 0.00 0.00 44.34 3.02
905 957 3.195182 TGAGTGGAGAGCTGATTCTCAAG 59.805 47.826 0.00 0.00 44.34 3.02
906 958 3.439154 AGTGGAGAGCTGATTCTCAAGA 58.561 45.455 0.00 0.00 44.34 3.02
907 959 4.032310 AGTGGAGAGCTGATTCTCAAGAT 58.968 43.478 0.00 0.00 44.34 2.40
908 960 4.470664 AGTGGAGAGCTGATTCTCAAGATT 59.529 41.667 0.00 0.00 44.34 2.40
909 961 5.660417 AGTGGAGAGCTGATTCTCAAGATTA 59.340 40.000 0.00 0.00 44.34 1.75
910 962 5.752955 GTGGAGAGCTGATTCTCAAGATTAC 59.247 44.000 0.00 0.00 44.34 1.89
911 963 5.163364 TGGAGAGCTGATTCTCAAGATTACC 60.163 44.000 0.00 0.00 44.34 2.85
912 964 4.942852 AGAGCTGATTCTCAAGATTACCG 58.057 43.478 0.00 0.00 35.59 4.02
913 965 4.054671 GAGCTGATTCTCAAGATTACCGG 58.945 47.826 0.00 0.00 33.41 5.28
914 966 3.706594 AGCTGATTCTCAAGATTACCGGA 59.293 43.478 9.46 0.00 0.00 5.14
915 967 4.054671 GCTGATTCTCAAGATTACCGGAG 58.945 47.826 9.46 0.00 0.00 4.63
916 968 4.202161 GCTGATTCTCAAGATTACCGGAGA 60.202 45.833 9.46 0.00 34.77 3.71
917 969 5.682471 GCTGATTCTCAAGATTACCGGAGAA 60.682 44.000 9.46 4.13 46.74 2.87
920 972 4.672587 TCTCAAGATTACCGGAGAATGG 57.327 45.455 9.46 0.00 33.73 3.16
921 973 3.388024 TCTCAAGATTACCGGAGAATGGG 59.612 47.826 9.46 0.00 33.73 4.00
922 974 2.158813 TCAAGATTACCGGAGAATGGGC 60.159 50.000 9.46 0.00 0.00 5.36
923 975 1.507140 AGATTACCGGAGAATGGGCA 58.493 50.000 9.46 0.00 0.00 5.36
924 976 1.843851 AGATTACCGGAGAATGGGCAA 59.156 47.619 9.46 0.00 0.00 4.52
925 977 2.241176 AGATTACCGGAGAATGGGCAAA 59.759 45.455 9.46 0.00 0.00 3.68
926 978 2.588464 TTACCGGAGAATGGGCAAAA 57.412 45.000 9.46 0.00 0.00 2.44
927 979 2.588464 TACCGGAGAATGGGCAAAAA 57.412 45.000 9.46 0.00 0.00 1.94
948 1000 1.207791 AACTGGGCCTATGTGGAGAG 58.792 55.000 4.53 0.00 38.35 3.20
982 1034 0.388520 CGTCTGACTGATGGCACGAA 60.389 55.000 6.21 0.00 0.00 3.85
1570 4261 3.728385 AATTACTGAAGCCTGCCTCTT 57.272 42.857 0.00 0.00 0.00 2.85
1698 4390 6.843069 AATAAATGTCAGTTGTTTTGTGCC 57.157 33.333 0.00 0.00 0.00 5.01
1793 4486 5.440610 AGTCAAGACAGGTTCAAGTTCAAT 58.559 37.500 2.72 0.00 0.00 2.57
1809 4533 8.786898 TCAAGTTCAATGAAGTCTCAAATAAGG 58.213 33.333 3.54 0.00 34.49 2.69
1820 4544 0.398948 CAAATAAGGGCTGGGGGCAT 60.399 55.000 0.00 0.00 44.01 4.40
1900 4625 2.356553 GTGGTGGCGACGCTAACA 60.357 61.111 20.72 20.72 41.78 2.41
1975 4700 4.921834 GCTTGCTAAGCGGTCTCT 57.078 55.556 5.35 0.00 45.74 3.10
1984 4711 3.610585 GCTAAGCGGTCTCTATAGCTGTG 60.611 52.174 7.77 0.00 40.17 3.66
1988 4715 2.225491 GCGGTCTCTATAGCTGTGAGAG 59.775 54.545 13.10 12.92 37.50 3.20
2012 4739 4.545610 CCACACATTTTGTAGATTGCGTT 58.454 39.130 0.00 0.00 35.67 4.84
2056 4784 4.497966 CGCGTTCGATGACTAGTTTATTGA 59.502 41.667 0.00 2.01 38.10 2.57
2118 4849 3.468140 GGGGGCACGTCTAGGGTC 61.468 72.222 0.00 0.00 0.00 4.46
2194 4925 0.466555 CACCAACAACCTCCCGGAAA 60.467 55.000 0.73 0.00 0.00 3.13
2518 5265 1.479709 ATACACTCGAGCAGCTCCTT 58.520 50.000 17.16 0.00 0.00 3.36
2784 5533 0.258194 GGACCCTCCCGTTCTAGAGA 59.742 60.000 0.00 0.00 31.43 3.10
2795 5544 2.159366 CGTTCTAGAGACGAATGCCAGT 60.159 50.000 17.21 0.00 0.00 4.00
2803 5552 1.973281 CGAATGCCAGTGGTTGCCT 60.973 57.895 11.74 0.00 0.00 4.75
2901 5650 2.582636 AGGAGGGCAATATGTTTCACCT 59.417 45.455 0.00 0.00 0.00 4.00
3031 5787 3.244840 ACTCCTTTCTGCTTTGCATCTCT 60.245 43.478 0.00 0.00 38.13 3.10
3032 5788 4.019860 ACTCCTTTCTGCTTTGCATCTCTA 60.020 41.667 0.00 0.00 38.13 2.43
3035 5791 4.699257 CCTTTCTGCTTTGCATCTCTAGTT 59.301 41.667 0.00 0.00 38.13 2.24
3036 5792 5.182760 CCTTTCTGCTTTGCATCTCTAGTTT 59.817 40.000 0.00 0.00 38.13 2.66
3037 5793 6.294397 CCTTTCTGCTTTGCATCTCTAGTTTT 60.294 38.462 0.00 0.00 38.13 2.43
3038 5794 5.869753 TCTGCTTTGCATCTCTAGTTTTC 57.130 39.130 0.00 0.00 38.13 2.29
3039 5795 5.555017 TCTGCTTTGCATCTCTAGTTTTCT 58.445 37.500 0.00 0.00 38.13 2.52
3040 5796 6.701340 TCTGCTTTGCATCTCTAGTTTTCTA 58.299 36.000 0.00 0.00 38.13 2.10
3041 5797 7.334090 TCTGCTTTGCATCTCTAGTTTTCTAT 58.666 34.615 0.00 0.00 38.13 1.98
3043 5799 8.654230 TGCTTTGCATCTCTAGTTTTCTATAG 57.346 34.615 0.00 0.00 31.71 1.31
3044 5800 8.260818 TGCTTTGCATCTCTAGTTTTCTATAGT 58.739 33.333 0.00 0.00 31.71 2.12
3379 6317 2.627699 TCCAGAAATGTTTGAGGTTGCC 59.372 45.455 0.00 0.00 0.00 4.52
4411 7516 9.585099 TGCAAAGCTTGACCAAATTTATATTAG 57.415 29.630 0.00 0.00 0.00 1.73
4584 7689 3.695830 ATGCAGACTAAAAAGGACCGA 57.304 42.857 0.00 0.00 0.00 4.69
4681 7786 8.207521 AGCTCTGAGTAGAATGCTAAATTTTC 57.792 34.615 6.53 0.00 33.96 2.29
4798 7903 3.877508 GGATCGGAGGGAGTAATGTTTTG 59.122 47.826 0.00 0.00 0.00 2.44
5058 8163 6.086785 AGTAGTTCCTTCAACACTAGTGTC 57.913 41.667 28.04 13.23 44.13 3.67
5482 8588 9.206870 ACAACCTGTTTATAGATGCAAAATTTG 57.793 29.630 0.57 0.57 0.00 2.32
5620 8730 4.390909 AGCTTTACACCGGTTTCTTTATCG 59.609 41.667 2.97 0.00 0.00 2.92
5722 8832 8.128582 TGTTTGTTCACTCATTTCAGTTCATAC 58.871 33.333 0.00 0.00 0.00 2.39
5913 9025 5.556915 ACCTTTCACGATCATCAGGTTAAA 58.443 37.500 0.00 0.00 29.99 1.52
5952 9066 5.397142 GGAATAATCCATGGGCTCATTTC 57.603 43.478 13.02 8.01 45.79 2.17
5963 9077 2.827921 GGGCTCATTTCTGGACATGTTT 59.172 45.455 0.00 0.00 0.00 2.83
5964 9078 3.259123 GGGCTCATTTCTGGACATGTTTT 59.741 43.478 0.00 0.00 0.00 2.43
5965 9079 4.262592 GGGCTCATTTCTGGACATGTTTTT 60.263 41.667 0.00 0.00 0.00 1.94
6029 9143 0.179073 CAGATGGGCCCTACACTTCG 60.179 60.000 25.70 0.00 0.00 3.79
6153 9267 7.042335 ACTAAGCTCTTTTATGCTCGTAACAT 58.958 34.615 0.00 0.00 38.75 2.71
6368 9482 3.540314 AAACCTTTGCTTGCATTGTCA 57.460 38.095 0.00 0.00 0.00 3.58
6450 9564 3.664107 GTTACACATCAGACCTTGCTCA 58.336 45.455 0.00 0.00 0.00 4.26
6526 9642 6.030228 CCGACTGATATGGCTTTTTCTTTTC 58.970 40.000 0.00 0.00 0.00 2.29
6754 9878 1.504900 GCGGGATTTGGAAACGACC 59.495 57.895 0.00 0.00 0.00 4.79
6786 9910 5.109662 TCGAGCATAGTACTATGTGCTTC 57.890 43.478 33.06 24.89 46.98 3.86
6870 9994 3.057806 GGAAACCGGTATGTTTGTCCTTG 60.058 47.826 8.00 0.00 38.51 3.61
6877 10004 4.379082 CGGTATGTTTGTCCTTGTTTAGCC 60.379 45.833 0.00 0.00 0.00 3.93
7053 10180 3.072330 TGAGAAACACAGTAAGGGCATCA 59.928 43.478 0.00 0.00 0.00 3.07
7086 10213 2.484770 GCTCAAACTGCCCGTATCCATA 60.485 50.000 0.00 0.00 0.00 2.74
7117 10244 1.102222 GTCAGGACGGATAGAGGCGT 61.102 60.000 0.00 0.00 0.00 5.68
7127 10262 0.618458 ATAGAGGCGTTTTGAGGGCA 59.382 50.000 0.00 0.00 0.00 5.36
7131 10266 1.600916 GGCGTTTTGAGGGCAGACT 60.601 57.895 0.00 0.00 0.00 3.24
7163 10298 3.243737 GGATGTTCTTTTTCCCGCAAACT 60.244 43.478 0.00 0.00 0.00 2.66
7206 10341 1.067565 GTCTGGATCGCTGTCACTTCA 60.068 52.381 0.00 0.00 0.00 3.02
7255 10390 1.077787 CTATTCCTTGCCCGTGCCA 60.078 57.895 0.00 0.00 36.33 4.92
7276 10411 0.166161 TTCTCGTCTGAAGCGACTCG 59.834 55.000 0.00 0.00 34.47 4.18
7277 10412 0.669625 TCTCGTCTGAAGCGACTCGA 60.670 55.000 1.63 0.00 34.47 4.04
7279 10414 1.859564 CGTCTGAAGCGACTCGACG 60.860 63.158 1.63 12.85 40.92 5.12
7281 10416 0.441533 GTCTGAAGCGACTCGACGTA 59.558 55.000 1.63 0.00 35.59 3.57
7283 10418 1.062148 TCTGAAGCGACTCGACGTATG 59.938 52.381 1.63 0.00 35.59 2.39
7284 10419 0.098200 TGAAGCGACTCGACGTATGG 59.902 55.000 1.63 0.00 35.59 2.74
7285 10420 0.376152 GAAGCGACTCGACGTATGGA 59.624 55.000 1.63 0.00 35.59 3.41
7286 10421 0.098376 AAGCGACTCGACGTATGGAC 59.902 55.000 1.63 0.00 35.59 4.02
7288 10423 1.011463 CGACTCGACGTATGGACCG 60.011 63.158 0.00 0.00 0.00 4.79
7289 10424 1.699656 CGACTCGACGTATGGACCGT 61.700 60.000 0.00 0.00 42.06 4.83
7290 10425 1.290203 GACTCGACGTATGGACCGTA 58.710 55.000 0.00 0.00 38.92 4.02
7291 10426 1.869767 GACTCGACGTATGGACCGTAT 59.130 52.381 0.00 0.00 38.92 3.06
7292 10427 2.289002 GACTCGACGTATGGACCGTATT 59.711 50.000 0.00 0.00 38.92 1.89
7293 10428 2.684881 ACTCGACGTATGGACCGTATTT 59.315 45.455 0.00 0.00 38.92 1.40
7294 10429 3.242870 ACTCGACGTATGGACCGTATTTC 60.243 47.826 0.00 0.00 38.92 2.17
7296 10431 3.002656 TCGACGTATGGACCGTATTTCTC 59.997 47.826 0.00 0.00 38.92 2.87
7297 10432 3.294943 GACGTATGGACCGTATTTCTCG 58.705 50.000 0.00 0.00 38.92 4.04
7298 10433 2.684881 ACGTATGGACCGTATTTCTCGT 59.315 45.455 0.00 0.00 36.65 4.18
7300 10435 3.003068 CGTATGGACCGTATTTCTCGTCT 59.997 47.826 0.00 0.00 0.00 4.18
7303 10438 2.821378 TGGACCGTATTTCTCGTCTGAA 59.179 45.455 0.00 0.00 0.00 3.02
7304 10439 3.119602 TGGACCGTATTTCTCGTCTGAAG 60.120 47.826 0.00 0.00 0.00 3.02
7305 10440 2.853003 GACCGTATTTCTCGTCTGAAGC 59.147 50.000 0.00 0.00 0.00 3.86
7306 10441 1.846782 CCGTATTTCTCGTCTGAAGCG 59.153 52.381 0.00 0.00 0.00 4.68
7307 10442 2.477357 CCGTATTTCTCGTCTGAAGCGA 60.477 50.000 0.00 0.00 36.85 4.93
7308 10443 2.526688 CGTATTTCTCGTCTGAAGCGAC 59.473 50.000 0.00 0.00 34.47 5.19
7311 10446 0.166161 TTCTCGTCTGAAGCGACTCG 59.834 55.000 0.00 0.00 34.47 4.18
7312 10447 0.669625 TCTCGTCTGAAGCGACTCGA 60.670 55.000 1.63 0.00 34.47 4.04
7313 10448 0.519586 CTCGTCTGAAGCGACTCGAC 60.520 60.000 1.63 0.00 34.47 4.20
7314 10449 1.859564 CGTCTGAAGCGACTCGACG 60.860 63.158 1.63 12.85 40.92 5.12
7315 10450 1.207085 GTCTGAAGCGACTCGACGT 59.793 57.895 1.63 0.00 35.59 4.34
7317 10452 1.062294 GTCTGAAGCGACTCGACGTAT 59.938 52.381 1.63 0.00 35.59 3.06
7337 10487 1.891919 GACCGTTGTCTTGCCTGCA 60.892 57.895 0.00 0.00 38.53 4.41
7346 10496 2.629137 TGTCTTGCCTGCATTTGACAAT 59.371 40.909 15.59 0.00 32.57 2.71
7378 10528 2.017049 CAAAACTCTATCCCTTGCCCG 58.983 52.381 0.00 0.00 0.00 6.13
7383 10533 1.053835 TCTATCCCTTGCCCGCATCA 61.054 55.000 0.00 0.00 0.00 3.07
7392 10542 1.754234 GCCCGCATCATTTCCCACT 60.754 57.895 0.00 0.00 0.00 4.00
7432 10582 3.768632 CGTTCTAGAGCGGCACAC 58.231 61.111 20.01 0.00 0.00 3.82
7433 10583 1.213013 CGTTCTAGAGCGGCACACT 59.787 57.895 20.01 1.08 0.00 3.55
7435 10585 1.351153 GTTCTAGAGCGGCACACTTC 58.649 55.000 1.45 0.00 0.00 3.01
7436 10586 0.966179 TTCTAGAGCGGCACACTTCA 59.034 50.000 1.45 0.00 0.00 3.02
7468 10619 1.668294 CCAGAGCAGACGTGACCTT 59.332 57.895 0.00 0.00 0.00 3.50
7477 10628 3.305199 GCAGACGTGACCTTTACTAGTGT 60.305 47.826 5.39 0.00 0.00 3.55
7500 10651 1.376543 CATTGAAGTGGCTCGCTGAT 58.623 50.000 0.00 0.00 0.00 2.90
7561 10712 6.390504 TCCTGACAATGAGTATTAGGGGTAT 58.609 40.000 0.00 0.00 30.78 2.73
7581 10732 5.221283 GGTATGAAAGAGTGGTAGAGCCTAC 60.221 48.000 4.33 4.33 38.35 3.18
7585 10736 4.817874 AAGAGTGGTAGAGCCTACCTAT 57.182 45.455 23.60 15.73 38.39 2.57
7606 10757 0.234884 GCACAAGTGTAACACTCGGC 59.765 55.000 0.00 0.00 44.62 5.54
7706 10874 7.885399 GGGGTATGATTACAGAGAATGCTTAAT 59.115 37.037 0.00 0.00 0.00 1.40
7707 10875 9.289782 GGGTATGATTACAGAGAATGCTTAATT 57.710 33.333 0.00 0.00 0.00 1.40
7733 10901 2.424234 CCTTACTCTGGAGGAGGAGGAG 60.424 59.091 13.46 0.00 44.85 3.69
7734 10902 1.227249 TACTCTGGAGGAGGAGGAGG 58.773 60.000 2.58 0.00 45.83 4.30
7735 10903 0.553862 ACTCTGGAGGAGGAGGAGGA 60.554 60.000 2.58 0.00 45.83 3.71
7760 10928 2.579207 TATATAGAATGCGCCGCCTC 57.421 50.000 6.63 2.98 0.00 4.70
7761 10929 0.608130 ATATAGAATGCGCCGCCTCA 59.392 50.000 6.63 0.00 0.00 3.86
7816 11015 3.612479 AACTACGGCAGTTACAGGTAACG 60.612 47.826 14.64 11.35 45.93 3.18
7877 11076 0.682209 ACCATTGCAGCTCCCATGTC 60.682 55.000 0.00 0.00 0.00 3.06
7922 11121 1.339342 TGATGGTGGTCATGCTGACTG 60.339 52.381 13.59 0.00 46.19 3.51
7932 11131 2.360475 GCTGACTGGAGGGTTGGC 60.360 66.667 0.00 0.00 0.00 4.52
7935 11134 2.047179 GACTGGAGGGTTGGCGTC 60.047 66.667 0.00 0.00 0.00 5.19
7946 11145 1.593209 TTGGCGTCCGAGTGTTGTC 60.593 57.895 0.00 0.00 0.00 3.18
7953 11152 1.733041 CCGAGTGTTGTCGATGCGT 60.733 57.895 0.00 0.00 42.85 5.24
7981 11180 2.945668 GGACTTCCTGTTGTATGCATCC 59.054 50.000 0.19 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 306 9.982291 TGTTCGTGCATATTTTTCTTTACTATC 57.018 29.630 0.00 0.00 0.00 2.08
299 323 8.502161 AAGTGTTCGTGCATATTTTTCTTTAC 57.498 30.769 0.00 0.00 0.00 2.01
426 454 9.243637 TGAAAACAAATCACGGATTTAGAAAAG 57.756 29.630 10.32 2.72 39.82 2.27
739 790 3.181469 GGTCGATTGCACCCTGAACTATA 60.181 47.826 0.00 0.00 0.00 1.31
775 826 1.133869 GTTCGGCGAAATGAACCCG 59.866 57.895 25.48 0.00 38.79 5.28
847 899 6.492087 AGAATCTTGAACCCGGATTGTAAAAA 59.508 34.615 0.73 0.00 30.98 1.94
848 900 6.007703 AGAATCTTGAACCCGGATTGTAAAA 58.992 36.000 0.73 0.00 30.98 1.52
849 901 5.414454 CAGAATCTTGAACCCGGATTGTAAA 59.586 40.000 0.73 0.00 30.98 2.01
850 902 4.941263 CAGAATCTTGAACCCGGATTGTAA 59.059 41.667 0.73 0.00 30.98 2.41
851 903 4.513442 CAGAATCTTGAACCCGGATTGTA 58.487 43.478 0.73 0.00 30.98 2.41
852 904 3.347216 CAGAATCTTGAACCCGGATTGT 58.653 45.455 0.73 0.00 30.98 2.71
853 905 2.684881 CCAGAATCTTGAACCCGGATTG 59.315 50.000 0.73 0.00 30.98 2.67
854 906 2.576191 TCCAGAATCTTGAACCCGGATT 59.424 45.455 0.73 0.00 33.13 3.01
855 907 2.196595 TCCAGAATCTTGAACCCGGAT 58.803 47.619 0.73 0.00 0.00 4.18
856 908 1.651737 TCCAGAATCTTGAACCCGGA 58.348 50.000 0.73 0.00 0.00 5.14
857 909 2.489938 TTCCAGAATCTTGAACCCGG 57.510 50.000 0.00 0.00 0.00 5.73
858 910 4.846779 TTTTTCCAGAATCTTGAACCCG 57.153 40.909 0.00 0.00 0.00 5.28
876 928 2.105477 TCAGCTCTCCACTCAGCTTTTT 59.895 45.455 0.00 0.00 43.80 1.94
877 929 1.696336 TCAGCTCTCCACTCAGCTTTT 59.304 47.619 0.00 0.00 43.80 2.27
878 930 1.346062 TCAGCTCTCCACTCAGCTTT 58.654 50.000 0.00 0.00 43.80 3.51
879 931 1.570803 ATCAGCTCTCCACTCAGCTT 58.429 50.000 0.00 0.00 43.80 3.74
881 933 1.481772 AGAATCAGCTCTCCACTCAGC 59.518 52.381 0.00 0.00 35.73 4.26
882 934 2.759535 TGAGAATCAGCTCTCCACTCAG 59.240 50.000 0.00 0.00 42.56 3.35
883 935 2.812658 TGAGAATCAGCTCTCCACTCA 58.187 47.619 0.00 0.00 42.56 3.41
895 947 6.283694 CATTCTCCGGTAATCTTGAGAATCA 58.716 40.000 0.00 0.00 46.36 2.57
896 948 5.698545 CCATTCTCCGGTAATCTTGAGAATC 59.301 44.000 0.00 0.00 46.36 2.52
898 950 4.141711 CCCATTCTCCGGTAATCTTGAGAA 60.142 45.833 0.00 0.15 45.08 2.87
899 951 3.388024 CCCATTCTCCGGTAATCTTGAGA 59.612 47.826 0.00 0.00 32.28 3.27
900 952 3.733337 CCCATTCTCCGGTAATCTTGAG 58.267 50.000 0.00 0.00 0.00 3.02
901 953 2.158813 GCCCATTCTCCGGTAATCTTGA 60.159 50.000 0.00 0.00 0.00 3.02
902 954 2.222027 GCCCATTCTCCGGTAATCTTG 58.778 52.381 0.00 0.00 0.00 3.02
903 955 1.843851 TGCCCATTCTCCGGTAATCTT 59.156 47.619 0.00 0.00 0.00 2.40
904 956 1.507140 TGCCCATTCTCCGGTAATCT 58.493 50.000 0.00 0.00 0.00 2.40
905 957 2.341846 TTGCCCATTCTCCGGTAATC 57.658 50.000 0.00 0.00 0.00 1.75
906 958 2.818751 TTTGCCCATTCTCCGGTAAT 57.181 45.000 0.00 0.00 0.00 1.89
907 959 2.588464 TTTTGCCCATTCTCCGGTAA 57.412 45.000 0.00 0.00 0.00 2.85
908 960 2.588464 TTTTTGCCCATTCTCCGGTA 57.412 45.000 0.00 0.00 0.00 4.02
909 961 3.448469 TTTTTGCCCATTCTCCGGT 57.552 47.368 0.00 0.00 0.00 5.28
926 978 2.378547 TCTCCACATAGGCCCAGTTTTT 59.621 45.455 0.00 0.00 37.29 1.94
927 979 1.992557 TCTCCACATAGGCCCAGTTTT 59.007 47.619 0.00 0.00 37.29 2.43
928 980 1.561542 CTCTCCACATAGGCCCAGTTT 59.438 52.381 0.00 0.00 37.29 2.66
929 981 1.207791 CTCTCCACATAGGCCCAGTT 58.792 55.000 0.00 0.00 37.29 3.16
930 982 0.692419 CCTCTCCACATAGGCCCAGT 60.692 60.000 0.00 0.00 37.29 4.00
931 983 0.692419 ACCTCTCCACATAGGCCCAG 60.692 60.000 0.00 0.00 36.24 4.45
932 984 0.639943 TACCTCTCCACATAGGCCCA 59.360 55.000 0.00 0.00 36.24 5.36
933 985 1.049402 GTACCTCTCCACATAGGCCC 58.951 60.000 0.00 0.00 36.24 5.80
934 986 1.049402 GGTACCTCTCCACATAGGCC 58.951 60.000 4.06 0.00 36.24 5.19
935 987 1.789523 TGGTACCTCTCCACATAGGC 58.210 55.000 14.36 0.00 36.24 3.93
1015 2301 2.438434 CCACAGCCAACCCGGATC 60.438 66.667 0.73 0.00 36.56 3.36
1070 3739 3.537206 ATATCGGGGAGCTTGGCGC 62.537 63.158 0.00 0.00 39.57 6.53
1307 3988 3.075005 CACCCACCTCGACCCGAT 61.075 66.667 0.00 0.00 34.61 4.18
1443 4130 8.455903 AAGAATATAAGCAATTAAGAGCAGCA 57.544 30.769 0.00 0.00 0.00 4.41
1482 4169 4.255301 GTGGATACCAACAATGTACGGAA 58.745 43.478 8.54 0.00 34.18 4.30
1592 4284 8.697507 ATCTTGTTCCTCTCACAAACTAAAAT 57.302 30.769 0.00 0.00 33.74 1.82
1666 4358 1.531149 CTGACATTTATTAGGCGGGCG 59.469 52.381 0.00 0.00 0.00 6.13
1680 4372 3.067180 CAGAGGCACAAAACAACTGACAT 59.933 43.478 0.00 0.00 0.00 3.06
1698 4390 7.445900 GAAAACCCTTTTTCGTAAAACAGAG 57.554 36.000 0.00 0.00 40.90 3.35
1728 4420 8.776470 GGTGCCGTTGCTTTATAAGTAATATAA 58.224 33.333 0.00 0.00 35.57 0.98
1730 4422 6.768861 TGGTGCCGTTGCTTTATAAGTAATAT 59.231 34.615 0.00 0.00 35.57 1.28
1732 4424 4.944930 TGGTGCCGTTGCTTTATAAGTAAT 59.055 37.500 0.00 0.00 35.57 1.89
1734 4426 3.940319 TGGTGCCGTTGCTTTATAAGTA 58.060 40.909 0.00 0.00 38.71 2.24
1735 4427 2.785562 TGGTGCCGTTGCTTTATAAGT 58.214 42.857 0.00 0.00 38.71 2.24
1736 4428 3.758300 CTTGGTGCCGTTGCTTTATAAG 58.242 45.455 0.00 0.00 38.71 1.73
1793 4486 3.308402 CCCAGCCCTTATTTGAGACTTCA 60.308 47.826 0.00 0.00 0.00 3.02
1808 4532 3.677480 TTTGCTATGCCCCCAGCCC 62.677 63.158 0.00 0.00 42.71 5.19
1809 4533 1.685421 TTTTGCTATGCCCCCAGCC 60.685 57.895 0.00 0.00 42.71 4.85
1820 4544 4.762289 ATGTTTGGGGTTTGTTTTGCTA 57.238 36.364 0.00 0.00 0.00 3.49
1882 4607 2.048503 GTTAGCGTCGCCACCACT 60.049 61.111 14.86 0.00 0.00 4.00
1892 4617 0.458543 CTCTGCATCGGTGTTAGCGT 60.459 55.000 0.00 0.00 40.41 5.07
1900 4625 2.290122 CTTCGCTCCTCTGCATCGGT 62.290 60.000 0.00 0.00 0.00 4.69
1975 4700 1.757118 GTGTGGCCTCTCACAGCTATA 59.243 52.381 16.93 0.00 46.72 1.31
1984 4711 3.674997 TCTACAAAATGTGTGGCCTCTC 58.325 45.455 3.32 1.31 41.89 3.20
1988 4715 3.253230 GCAATCTACAAAATGTGTGGCC 58.747 45.455 0.00 0.00 41.89 5.36
2012 4739 1.940883 GATCCCGTGCCGTGTGACTA 61.941 60.000 0.00 0.00 0.00 2.59
2118 4849 1.188871 GGAGATCCTTAGGCTCCCCG 61.189 65.000 12.26 0.00 41.84 5.73
2194 4925 0.035458 CTCGGTTCCTTTGGAGCTGT 59.965 55.000 0.00 0.00 39.75 4.40
2518 5265 2.741985 CGGAGCACGCACAATGGA 60.742 61.111 0.00 0.00 34.82 3.41
2750 5499 1.337118 GGTCCCAGTTTTGGCAATCA 58.663 50.000 0.00 0.00 43.58 2.57
2784 5533 3.354678 GCAACCACTGGCATTCGT 58.645 55.556 0.00 0.00 0.00 3.85
3043 5799 6.885922 ACGGCAGGATAATAATATAGGGAAC 58.114 40.000 0.00 0.00 0.00 3.62
3044 5800 7.504926 AACGGCAGGATAATAATATAGGGAA 57.495 36.000 0.00 0.00 0.00 3.97
3046 5802 7.788026 TGTAACGGCAGGATAATAATATAGGG 58.212 38.462 0.00 0.00 0.00 3.53
3065 5979 6.898189 GTCAAGTAACTGTGAAAACTGTAACG 59.102 38.462 0.00 0.00 0.00 3.18
3415 6512 8.721478 GCATACATAGATGGTCGAACAATTATT 58.279 33.333 7.51 0.00 0.00 1.40
4681 7786 1.043816 ATGGATCGCAGGGAGTACTG 58.956 55.000 0.00 0.00 41.41 2.74
5058 8163 2.157668 CCTTGCTGCTACAAAGTGTACG 59.842 50.000 0.00 0.00 0.00 3.67
5448 8554 5.001232 TCTATAAACAGGTTGTGGCACTTC 58.999 41.667 19.83 11.22 0.00 3.01
5620 8730 1.254954 AGTGAACGGAGGGAGTACAC 58.745 55.000 0.00 0.00 0.00 2.90
6029 9143 6.854496 TTAACAAGTGTGTTCAGGTCATAC 57.146 37.500 0.00 0.00 45.00 2.39
6142 9256 6.112734 AGATAATGACCAAATGTTACGAGCA 58.887 36.000 0.00 0.00 0.00 4.26
6153 9267 9.456147 TCCTTTCGAAATAAGATAATGACCAAA 57.544 29.630 11.70 0.00 0.00 3.28
6188 9302 4.396166 CCACAAGCTTGTCACCTAATAAGG 59.604 45.833 28.97 18.25 43.69 2.69
6258 9372 9.942526 ATTTTTCCTTGGGTAGATTCAATATCT 57.057 29.630 0.00 0.00 0.00 1.98
6526 9642 4.516321 TCATTTGCCATATCAGTCATTCGG 59.484 41.667 0.00 0.00 0.00 4.30
6754 9878 4.568359 AGTACTATGCTCGATTGTTTGCAG 59.432 41.667 0.00 0.00 38.87 4.41
6802 9926 7.125391 TGATATTCTCCCATTTTTAAGCCTGT 58.875 34.615 0.00 0.00 0.00 4.00
6877 10004 2.449464 TCCAAATTCAGCCCATGAGTG 58.551 47.619 0.00 0.00 39.68 3.51
6926 10053 9.832445 AATGACGAAACCTCTATACAATGTAAT 57.168 29.630 0.00 0.00 0.00 1.89
7086 10213 4.457496 CCTGACCGCGCTGTCCAT 62.457 66.667 26.14 0.00 34.25 3.41
7117 10244 2.260869 GCGCAGTCTGCCCTCAAAA 61.261 57.895 19.14 0.00 41.12 2.44
7127 10262 2.034879 CATCCAAACCGCGCAGTCT 61.035 57.895 8.75 0.00 0.00 3.24
7131 10266 1.169661 AAGAACATCCAAACCGCGCA 61.170 50.000 8.75 0.00 0.00 6.09
7140 10275 1.988293 TGCGGGAAAAAGAACATCCA 58.012 45.000 0.00 0.00 34.82 3.41
7163 10298 4.299796 GCCCACCCCTTGCTTCCA 62.300 66.667 0.00 0.00 0.00 3.53
7206 10341 2.024414 GAGCCAAGGTTGTCAAACACT 58.976 47.619 2.89 0.00 38.10 3.55
7255 10390 2.729467 CGAGTCGCTTCAGACGAGAAAT 60.729 50.000 0.00 0.00 45.26 2.17
7276 10411 3.242870 ACGAGAAATACGGTCCATACGTC 60.243 47.826 0.00 0.00 44.37 4.34
7279 10414 4.036027 TCAGACGAGAAATACGGTCCATAC 59.964 45.833 0.00 0.00 34.93 2.39
7281 10416 3.021695 TCAGACGAGAAATACGGTCCAT 58.978 45.455 0.00 0.00 34.93 3.41
7283 10418 3.436496 CTTCAGACGAGAAATACGGTCC 58.564 50.000 0.00 0.00 34.93 4.46
7284 10419 2.853003 GCTTCAGACGAGAAATACGGTC 59.147 50.000 0.00 0.00 34.93 4.79
7285 10420 2.731341 CGCTTCAGACGAGAAATACGGT 60.731 50.000 0.00 0.00 34.93 4.83
7286 10421 1.846782 CGCTTCAGACGAGAAATACGG 59.153 52.381 0.00 0.00 34.93 4.02
7288 10423 3.760537 AGTCGCTTCAGACGAGAAATAC 58.239 45.455 0.00 0.00 45.26 1.89
7289 10424 3.485381 CGAGTCGCTTCAGACGAGAAATA 60.485 47.826 0.00 0.00 45.26 1.40
7290 10425 2.729467 CGAGTCGCTTCAGACGAGAAAT 60.729 50.000 0.00 0.00 45.26 2.17
7291 10426 1.399855 CGAGTCGCTTCAGACGAGAAA 60.400 52.381 0.00 0.00 45.26 2.52
7292 10427 0.166161 CGAGTCGCTTCAGACGAGAA 59.834 55.000 0.00 0.00 45.26 2.87
7293 10428 0.669625 TCGAGTCGCTTCAGACGAGA 60.670 55.000 7.92 0.00 45.26 4.04
7294 10429 0.519586 GTCGAGTCGCTTCAGACGAG 60.520 60.000 7.92 0.00 45.26 4.18
7296 10431 1.859564 CGTCGAGTCGCTTCAGACG 60.860 63.158 7.92 7.75 46.32 4.18
7297 10432 0.441533 TACGTCGAGTCGCTTCAGAC 59.558 55.000 7.92 0.00 41.23 3.51
7298 10433 1.062148 CATACGTCGAGTCGCTTCAGA 59.938 52.381 7.92 0.00 0.00 3.27
7300 10435 0.098200 CCATACGTCGAGTCGCTTCA 59.902 55.000 7.92 0.00 0.00 3.02
7303 10438 1.712977 GGTCCATACGTCGAGTCGCT 61.713 60.000 7.92 0.00 0.00 4.93
7304 10439 1.298190 GGTCCATACGTCGAGTCGC 60.298 63.158 7.92 2.09 0.00 5.19
7305 10440 1.011463 CGGTCCATACGTCGAGTCG 60.011 63.158 6.09 6.09 0.00 4.18
7306 10441 0.449388 AACGGTCCATACGTCGAGTC 59.551 55.000 0.00 0.00 44.83 3.36
7307 10442 0.169672 CAACGGTCCATACGTCGAGT 59.830 55.000 0.00 0.00 44.83 4.18
7308 10443 0.169672 ACAACGGTCCATACGTCGAG 59.830 55.000 0.00 0.00 44.83 4.04
7311 10446 1.990563 CAAGACAACGGTCCATACGTC 59.009 52.381 0.00 0.00 45.48 4.34
7312 10447 1.938016 GCAAGACAACGGTCCATACGT 60.938 52.381 0.00 0.00 45.48 3.57
7313 10448 0.719465 GCAAGACAACGGTCCATACG 59.281 55.000 0.00 0.00 45.48 3.06
7314 10449 1.084289 GGCAAGACAACGGTCCATAC 58.916 55.000 0.00 0.00 45.48 2.39
7315 10450 0.981183 AGGCAAGACAACGGTCCATA 59.019 50.000 0.00 0.00 45.48 2.74
7317 10452 1.227823 CAGGCAAGACAACGGTCCA 60.228 57.895 0.00 0.00 45.48 4.02
7337 10487 2.450476 GGTGAGCCAGGATTGTCAAAT 58.550 47.619 0.00 0.00 34.09 2.32
7346 10496 0.110486 GAGTTTTGGGTGAGCCAGGA 59.890 55.000 2.68 0.00 36.17 3.86
7378 10528 2.231964 TGCTTCAAGTGGGAAATGATGC 59.768 45.455 0.00 0.00 41.78 3.91
7383 10533 3.565307 TGAGTTGCTTCAAGTGGGAAAT 58.435 40.909 0.00 0.00 0.00 2.17
7392 10542 4.156556 GGTATGAATGCTGAGTTGCTTCAA 59.843 41.667 0.00 0.00 35.49 2.69
7432 10582 0.458669 GGGCCAGCATCAATGTGAAG 59.541 55.000 4.39 0.00 0.00 3.02
7433 10583 0.251698 TGGGCCAGCATCAATGTGAA 60.252 50.000 0.00 0.00 0.00 3.18
7435 10585 0.681887 TCTGGGCCAGCATCAATGTG 60.682 55.000 29.02 1.79 0.00 3.21
7436 10586 0.395311 CTCTGGGCCAGCATCAATGT 60.395 55.000 29.02 0.00 0.00 2.71
7468 10619 4.759693 CCACTTCAATGCCAACACTAGTAA 59.240 41.667 0.00 0.00 0.00 2.24
7477 10628 1.865788 GCGAGCCACTTCAATGCCAA 61.866 55.000 0.00 0.00 0.00 4.52
7522 10673 0.533491 CAGGATCGTAACCCCGACAA 59.467 55.000 0.00 0.00 40.08 3.18
7561 10712 3.097614 GGTAGGCTCTACCACTCTTTCA 58.902 50.000 20.38 0.00 43.14 2.69
7581 10732 3.674997 AGTGTTACACTTGTGCCATAGG 58.325 45.455 12.76 0.00 42.59 2.57
7585 10736 1.577468 CGAGTGTTACACTTGTGCCA 58.423 50.000 19.59 0.00 45.44 4.92
7606 10757 0.392595 GGGGCCTGAACTCCTAAACG 60.393 60.000 0.84 0.00 0.00 3.60
7638 10789 1.732259 GCACGAGATGTAGGGTTGTTG 59.268 52.381 0.00 0.00 0.00 3.33
7706 10874 4.101856 CCTCCTCCAGAGTAAGGGTTAAA 58.898 47.826 5.74 0.00 41.47 1.52
7707 10875 3.338824 TCCTCCTCCAGAGTAAGGGTTAA 59.661 47.826 11.43 0.00 41.47 2.01
7708 10876 2.931088 TCCTCCTCCAGAGTAAGGGTTA 59.069 50.000 11.43 0.00 41.47 2.85
7709 10877 1.722851 TCCTCCTCCAGAGTAAGGGTT 59.277 52.381 11.43 0.00 41.47 4.11
7710 10878 1.289530 CTCCTCCTCCAGAGTAAGGGT 59.710 57.143 11.43 0.00 41.47 4.34
7716 10884 0.553862 TCCTCCTCCTCCTCCAGAGT 60.554 60.000 0.00 0.00 41.47 3.24
7760 10928 2.738521 CTGGCGACGTGGGAGTTG 60.739 66.667 0.00 0.00 0.00 3.16
7761 10929 4.003788 CCTGGCGACGTGGGAGTT 62.004 66.667 0.00 0.00 0.00 3.01
7877 11076 0.900647 ACAAGGGAGGTGGAGAGACG 60.901 60.000 0.00 0.00 0.00 4.18
7922 11121 4.452733 CTCGGACGCCAACCCTCC 62.453 72.222 0.00 0.00 0.00 4.30
7932 11131 1.674611 GCATCGACAACACTCGGACG 61.675 60.000 0.00 0.00 34.27 4.79
7935 11134 1.674611 GACGCATCGACAACACTCGG 61.675 60.000 0.00 0.00 34.27 4.63
7953 11152 0.679505 CAACAGGAAGTCCACTCGGA 59.320 55.000 0.00 0.00 39.79 4.55



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

AutoCloner maintained by Alex Coulton.