Multiple sequence alignment - TraesCS1D01G056100

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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 TraesCS1D01G056100 chr1D 100.000 9045 0 0 1 9045 37212832 37221876 0.000000e+00 16704.0
1 TraesCS1D01G056100 chr1B 95.760 7831 198 53 1267 9008 56996515 57004300 0.000000e+00 12499.0
2 TraesCS1D01G056100 chr1B 93.679 617 28 4 645 1253 56993857 56994470 0.000000e+00 913.0
3 TraesCS1D01G056100 chr1B 80.041 486 65 17 7838 8319 56497560 56497103 1.880000e-86 331.0
4 TraesCS1D01G056100 chr1B 88.256 281 28 4 5514 5790 677050214 677050493 1.880000e-86 331.0
5 TraesCS1D01G056100 chr1B 91.964 112 8 1 7078 7189 56498301 56498191 1.220000e-33 156.0
6 TraesCS1D01G056100 chr1A 97.120 4930 94 17 3668 8566 36565015 36569927 0.000000e+00 8274.0
7 TraesCS1D01G056100 chr1A 96.868 1820 44 8 1267 3084 36562618 36564426 0.000000e+00 3033.0
8 TraesCS1D01G056100 chr1A 98.720 547 7 0 3124 3670 36564423 36564969 0.000000e+00 972.0
9 TraesCS1D01G056100 chr1A 89.402 736 45 18 545 1254 36561575 36562303 0.000000e+00 896.0
10 TraesCS1D01G056100 chr1A 94.033 486 16 4 8565 9039 36594887 36595370 0.000000e+00 725.0
11 TraesCS1D01G056100 chr1A 86.441 413 42 9 2720 3123 63851501 63851094 3.000000e-119 440.0
12 TraesCS1D01G056100 chr1A 89.161 286 29 2 5514 5798 450480784 450480500 1.120000e-93 355.0
13 TraesCS1D01G056100 chr1A 91.765 170 13 1 6224 6393 257239657 257239489 1.520000e-57 235.0
14 TraesCS1D01G056100 chr1A 85.652 230 23 4 5800 6022 450480312 450480086 5.460000e-57 233.0
15 TraesCS1D01G056100 chr1A 86.022 186 19 1 5843 6021 257239848 257239663 9.270000e-45 193.0
16 TraesCS1D01G056100 chr1A 97.727 88 1 1 602 689 553707398 553707484 5.660000e-32 150.0
17 TraesCS1D01G056100 chr5D 91.618 513 32 7 1 507 334053085 334053592 0.000000e+00 699.0
18 TraesCS1D01G056100 chr5D 87.923 414 29 8 2722 3122 346885340 346885745 1.380000e-127 468.0
19 TraesCS1D01G056100 chr5D 87.470 415 33 8 2721 3122 397013862 397013454 2.300000e-125 460.0
20 TraesCS1D01G056100 chr5D 83.810 420 41 12 2720 3125 288573593 288573999 3.080000e-99 374.0
21 TraesCS1D01G056100 chr5D 94.444 162 6 3 349 507 334054383 334054222 7.010000e-61 246.0
22 TraesCS1D01G056100 chr5D 91.250 80 7 0 2141 2220 117743205 117743284 9.600000e-20 110.0
23 TraesCS1D01G056100 chr5D 85.965 57 8 0 465 521 24812498 24812442 2.730000e-05 62.1
24 TraesCS1D01G056100 chr6B 90.172 407 32 4 1 404 301578904 301578503 2.890000e-144 523.0
25 TraesCS1D01G056100 chr6B 88.612 281 27 4 5514 5790 704259502 704259781 4.050000e-88 337.0
26 TraesCS1D01G056100 chr6B 92.523 107 6 2 398 502 301570042 301569936 1.570000e-32 152.0
27 TraesCS1D01G056100 chr6B 88.750 80 8 1 2141 2220 625888594 625888672 7.480000e-16 97.1
28 TraesCS1D01G056100 chr6B 95.556 45 2 0 8825 8869 370509378 370509422 1.260000e-08 73.1
29 TraesCS1D01G056100 chrUn 89.024 410 26 7 2722 3118 332817118 332816715 2.930000e-134 490.0
30 TraesCS1D01G056100 chrUn 89.024 410 26 7 2722 3118 332825494 332825091 2.930000e-134 490.0
31 TraesCS1D01G056100 chrUn 89.024 410 26 7 2719 3115 343435909 343436312 2.930000e-134 490.0
32 TraesCS1D01G056100 chrUn 91.333 300 22 4 6541 6837 11128557 11128855 3.040000e-109 407.0
33 TraesCS1D01G056100 chr3B 89.136 405 28 6 2724 3115 562780842 562781243 2.930000e-134 490.0
34 TraesCS1D01G056100 chr3B 86.769 325 32 6 6224 6539 818388185 818387863 1.440000e-92 351.0
35 TraesCS1D01G056100 chr3B 88.194 288 27 5 5514 5795 10018910 10018624 4.050000e-88 337.0
36 TraesCS1D01G056100 chr3B 94.737 95 4 1 593 687 479988580 479988673 7.320000e-31 147.0
37 TraesCS1D01G056100 chr3B 94.737 95 2 3 588 681 147187463 147187555 2.630000e-30 145.0
38 TraesCS1D01G056100 chr3B 89.412 85 8 1 2137 2220 782841611 782841695 1.240000e-18 106.0
39 TraesCS1D01G056100 chr3B 85.149 101 13 2 8826 8926 765921570 765921472 1.610000e-17 102.0
40 TraesCS1D01G056100 chr5B 88.698 407 29 6 2722 3115 507805723 507806125 1.770000e-131 481.0
41 TraesCS1D01G056100 chr5B 92.500 80 6 0 2141 2220 129325333 129325254 2.060000e-21 115.0
42 TraesCS1D01G056100 chr5B 100.000 33 0 0 465 497 526653679 526653711 2.730000e-05 62.1
43 TraesCS1D01G056100 chr7D 86.571 417 32 14 2722 3122 618495075 618495483 1.080000e-118 438.0
44 TraesCS1D01G056100 chr7D 95.652 46 2 0 8824 8869 534215528 534215573 3.500000e-09 75.0
45 TraesCS1D01G056100 chr7D 93.478 46 3 0 8824 8869 284165783 284165738 1.630000e-07 69.4
46 TraesCS1D01G056100 chr2D 91.262 309 23 4 6545 6850 402074484 402074177 1.400000e-112 418.0
47 TraesCS1D01G056100 chr2D 97.959 49 1 0 2172 2220 282927681 282927633 1.620000e-12 86.1
48 TraesCS1D01G056100 chr2D 83.133 83 14 0 8824 8906 394460447 394460365 9.740000e-10 76.8
49 TraesCS1D01G056100 chr2D 94.872 39 2 0 7226 7264 15596796 15596834 2.730000e-05 62.1
50 TraesCS1D01G056100 chr3D 85.926 405 26 10 2723 3115 454906819 454907204 3.930000e-108 403.0
51 TraesCS1D01G056100 chr3D 91.216 296 23 3 6544 6837 365709246 365709540 5.090000e-107 399.0
52 TraesCS1D01G056100 chr3D 94.681 94 5 0 594 687 3302151 3302244 7.320000e-31 147.0
53 TraesCS1D01G056100 chr4D 90.291 309 26 4 6545 6850 311128874 311128567 1.410000e-107 401.0
54 TraesCS1D01G056100 chr4D 91.275 298 19 5 6545 6836 321118978 321119274 5.090000e-107 399.0
55 TraesCS1D01G056100 chr4D 90.667 300 26 2 6543 6840 250268228 250267929 1.830000e-106 398.0
56 TraesCS1D01G056100 chr4D 86.562 320 35 7 196 507 20438179 20437860 6.720000e-91 346.0
57 TraesCS1D01G056100 chr4D 92.500 80 5 1 2141 2220 5677215 5677293 7.420000e-21 113.0
58 TraesCS1D01G056100 chr4D 90.789 76 5 2 2146 2220 361037343 361037269 5.780000e-17 100.0
59 TraesCS1D01G056100 chr4D 94.595 37 2 0 7226 7262 453044672 453044636 3.530000e-04 58.4
60 TraesCS1D01G056100 chr4D 100.000 29 0 0 3982 4010 299319721 299319749 5.000000e-03 54.7
61 TraesCS1D01G056100 chr4A 90.698 301 26 2 6543 6841 253619782 253619482 5.090000e-107 399.0
62 TraesCS1D01G056100 chr6D 90.132 304 26 4 6543 6843 94090884 94091186 8.510000e-105 392.0
63 TraesCS1D01G056100 chr6D 88.462 286 31 2 5514 5798 297538948 297538664 2.420000e-90 344.0
64 TraesCS1D01G056100 chr6D 91.429 210 17 1 6224 6433 297538255 297538047 4.130000e-73 287.0
65 TraesCS1D01G056100 chr6D 85.652 230 19 6 5800 6022 297538482 297538260 7.060000e-56 230.0
66 TraesCS1D01G056100 chr6D 84.416 77 5 4 7182 7258 292299496 292299427 1.630000e-07 69.4
67 TraesCS1D01G056100 chr6D 90.000 40 4 0 7226 7265 332956023 332955984 1.600000e-02 52.8
68 TraesCS1D01G056100 chr2B 84.946 372 33 8 2763 3122 729803137 729803497 1.120000e-93 355.0
69 TraesCS1D01G056100 chr2B 86.364 330 34 8 6224 6544 15163814 15164141 5.200000e-92 350.0
70 TraesCS1D01G056100 chr2B 94.872 39 2 0 7226 7264 27717216 27717254 2.730000e-05 62.1
71 TraesCS1D01G056100 chr3A 87.762 286 30 5 5514 5798 208226929 208227210 6.770000e-86 329.0
72 TraesCS1D01G056100 chr3A 86.087 230 21 5 5800 6022 208227398 208227623 4.220000e-58 237.0
73 TraesCS1D01G056100 chr3A 98.837 86 0 1 602 687 490340058 490340142 1.570000e-32 152.0
74 TraesCS1D01G056100 chr3A 94.845 97 1 3 595 690 38279307 38279400 2.030000e-31 148.0
75 TraesCS1D01G056100 chr3A 90.244 41 4 0 7226 7266 32122382 32122342 5.000000e-03 54.7
76 TraesCS1D01G056100 chr7B 87.413 286 34 2 5514 5798 34206609 34206893 2.440000e-85 327.0
77 TraesCS1D01G056100 chr7B 81.928 83 15 0 8824 8906 364313987 364314069 4.530000e-08 71.3
78 TraesCS1D01G056100 chr7B 96.875 32 1 0 7226 7257 645325258 645325289 5.000000e-03 54.7
79 TraesCS1D01G056100 chr4B 90.566 212 19 1 6224 6435 669692720 669692510 6.920000e-71 279.0
80 TraesCS1D01G056100 chr4B 96.667 90 2 1 593 681 389113855 389113766 2.030000e-31 148.0
81 TraesCS1D01G056100 chr4B 91.089 101 8 1 6444 6544 669680665 669680566 1.580000e-27 135.0
82 TraesCS1D01G056100 chr7A 85.660 265 28 2 6289 6544 431763969 431764232 4.160000e-68 270.0
83 TraesCS1D01G056100 chr7A 86.087 230 22 4 5800 6022 61543445 61543219 1.170000e-58 239.0
84 TraesCS1D01G056100 chr6A 87.719 228 20 6 5800 6022 62887955 62887731 9.010000e-65 259.0
85 TraesCS1D01G056100 chr6A 89.423 208 17 2 6230 6433 62887720 62887514 3.240000e-64 257.0
86 TraesCS1D01G056100 chr5A 88.372 215 18 4 6225 6433 512701919 512702132 1.510000e-62 252.0
87 TraesCS1D01G056100 chr5A 87.444 223 21 5 5805 6022 512701695 512701915 5.420000e-62 250.0
88 TraesCS1D01G056100 chr5A 95.833 96 2 2 588 681 650138097 650138192 4.370000e-33 154.0


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 TraesCS1D01G056100 chr1D 37212832 37221876 9044 False 16704.00 16704 100.000000 1 9045 1 chr1D.!!$F1 9044
1 TraesCS1D01G056100 chr1B 56993857 57004300 10443 False 6706.00 12499 94.719500 645 9008 2 chr1B.!!$F2 8363
2 TraesCS1D01G056100 chr1B 56497103 56498301 1198 True 243.50 331 86.002500 7078 8319 2 chr1B.!!$R1 1241
3 TraesCS1D01G056100 chr1A 36561575 36569927 8352 False 3293.75 8274 95.527500 545 8566 4 chr1A.!!$F3 8021
4 TraesCS1D01G056100 chr1A 450480086 450480784 698 True 294.00 355 87.406500 5514 6022 2 chr1A.!!$R3 508
5 TraesCS1D01G056100 chr5D 334053085 334053592 507 False 699.00 699 91.618000 1 507 1 chr5D.!!$F3 506
6 TraesCS1D01G056100 chr6D 297538047 297538948 901 True 287.00 344 88.514333 5514 6433 3 chr6D.!!$R3 919
7 TraesCS1D01G056100 chr3A 208226929 208227623 694 False 283.00 329 86.924500 5514 6022 2 chr3A.!!$F3 508

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
523 530 0.178926 TCGGTGTCTTCCCCCTTGTA 60.179 55.000 0.00 0.0 0.00 2.41 F
1374 3443 0.109597 CGCTGTCTGTTGGAAATGGC 60.110 55.000 0.00 0.0 0.00 4.40 F
1519 3589 1.031571 ACGATTGCGCATCAACCCAT 61.032 50.000 12.75 0.0 42.48 4.00 F
1804 3874 1.070786 GGCGAGGTGTTGGAACTCA 59.929 57.895 0.00 0.0 0.00 3.41 F
2855 4938 0.660488 TGCGTGAACTTCGTGCAAAT 59.340 45.000 5.52 0.0 31.69 2.32 F
2977 5060 2.629002 TTTTTGCCACGAGCTCCTC 58.371 52.632 8.47 0.0 44.23 3.71 F
3093 5180 3.626996 CTGTTCATGCCCGGGCTCA 62.627 63.158 43.34 29.5 42.51 4.26 F
4951 7125 3.726557 TTCAGCATGTCAGGAAGGATT 57.273 42.857 0.00 0.0 37.40 3.01 F
6657 9034 3.006644 TCTCATGCAAGAGCCTAGCTATG 59.993 47.826 14.07 0.0 39.88 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 3872 0.609957 CTGTCCCTGCAATGGCTTGA 60.610 55.000 0.00 0.00 41.91 3.02 R
2186 4264 2.168313 CCTTTTGTCCCAAGCAAGTTGT 59.832 45.455 4.48 0.00 33.87 3.32 R
2430 4509 4.594920 TCCTGAAGAACAAGACAGAATCCT 59.405 41.667 0.00 0.00 32.90 3.24 R
3502 5592 5.068636 CCTTGCTGCCATAAACTATCTGAT 58.931 41.667 0.00 0.00 0.00 2.90 R
4037 6208 2.311841 AGTTTATAGGTTTGGCTGGCCT 59.688 45.455 13.05 0.00 36.94 5.19 R
4951 7125 7.048629 TGGCATACACTCTCAAATTTGAAAA 57.951 32.000 20.82 11.56 36.64 2.29 R
5096 7274 4.371855 AATGCATCATCAAGCTGAGTTG 57.628 40.909 0.00 0.00 0.00 3.16 R
6785 9162 3.127721 GCTTAAGGAACTGCCAACTCATC 59.872 47.826 4.29 0.00 40.86 2.92 R
8353 10835 0.951040 CCAGAACTCAGCACCCGAAC 60.951 60.000 0.00 0.00 0.00 3.95 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
42 43 2.126031 GTCTCCCGTCCTTGCGAC 60.126 66.667 0.00 0.00 38.21 5.19
49 50 3.144605 GTCCTTGCGACGTTCGTC 58.855 61.111 14.25 14.25 42.81 4.20
107 109 1.220477 GAGGGAGCAGGAAGTCAGC 59.780 63.158 0.00 0.00 0.00 4.26
117 119 1.079750 GAAGTCAGCTGGGACGGTC 60.080 63.158 15.13 0.00 42.62 4.79
120 122 2.117423 TCAGCTGGGACGGTCAGA 59.883 61.111 15.13 0.00 36.83 3.27
122 124 1.979155 CAGCTGGGACGGTCAGAGA 60.979 63.158 5.57 0.00 36.83 3.10
124 126 1.679305 GCTGGGACGGTCAGAGAGA 60.679 63.158 10.76 0.00 36.83 3.10
129 131 1.546961 GGACGGTCAGAGAGAAGGAA 58.453 55.000 10.76 0.00 0.00 3.36
135 137 1.135228 GTCAGAGAGAAGGAAGACGCC 60.135 57.143 0.00 0.00 0.00 5.68
136 138 0.891373 CAGAGAGAAGGAAGACGCCA 59.109 55.000 0.00 0.00 0.00 5.69
138 140 0.603569 GAGAGAAGGAAGACGCCACA 59.396 55.000 0.00 0.00 0.00 4.17
152 154 2.267351 CCACAGACATGGCGGCAAA 61.267 57.895 18.31 0.00 31.52 3.68
153 155 1.081242 CACAGACATGGCGGCAAAC 60.081 57.895 18.31 10.50 0.00 2.93
192 194 1.070786 GCGGCGATGGGGATTTCTA 59.929 57.895 12.98 0.00 0.00 2.10
196 198 1.614317 GGCGATGGGGATTTCTATGGG 60.614 57.143 0.00 0.00 0.00 4.00
206 208 3.620488 GATTTCTATGGGGCTGTGTTGA 58.380 45.455 0.00 0.00 0.00 3.18
300 303 4.459089 GCACGGCTCAGGGAGGAC 62.459 72.222 0.00 0.00 0.00 3.85
345 349 1.526887 CCACCTGGTCCGCACATAT 59.473 57.895 0.00 0.00 0.00 1.78
347 351 1.140052 CCACCTGGTCCGCACATATAA 59.860 52.381 0.00 0.00 0.00 0.98
404 409 5.992217 GCTGGGTCATTTTTAGATCGATACT 59.008 40.000 0.00 0.00 0.00 2.12
406 411 7.656137 GCTGGGTCATTTTTAGATCGATACTTA 59.344 37.037 0.00 0.00 0.00 2.24
407 412 8.882415 TGGGTCATTTTTAGATCGATACTTAC 57.118 34.615 0.00 0.00 0.00 2.34
517 524 2.480845 CGAATATTCGGTGTCTTCCCC 58.519 52.381 26.61 0.00 46.30 4.81
518 525 2.805657 CGAATATTCGGTGTCTTCCCCC 60.806 54.545 26.61 0.00 46.30 5.40
519 526 2.191981 ATATTCGGTGTCTTCCCCCT 57.808 50.000 0.00 0.00 0.00 4.79
520 527 1.961133 TATTCGGTGTCTTCCCCCTT 58.039 50.000 0.00 0.00 0.00 3.95
521 528 0.328258 ATTCGGTGTCTTCCCCCTTG 59.672 55.000 0.00 0.00 0.00 3.61
522 529 1.057851 TTCGGTGTCTTCCCCCTTGT 61.058 55.000 0.00 0.00 0.00 3.16
523 530 0.178926 TCGGTGTCTTCCCCCTTGTA 60.179 55.000 0.00 0.00 0.00 2.41
524 531 0.909623 CGGTGTCTTCCCCCTTGTAT 59.090 55.000 0.00 0.00 0.00 2.29
525 532 2.112998 CGGTGTCTTCCCCCTTGTATA 58.887 52.381 0.00 0.00 0.00 1.47
526 533 2.502538 CGGTGTCTTCCCCCTTGTATAA 59.497 50.000 0.00 0.00 0.00 0.98
527 534 3.135895 CGGTGTCTTCCCCCTTGTATAAT 59.864 47.826 0.00 0.00 0.00 1.28
528 535 4.384868 CGGTGTCTTCCCCCTTGTATAATT 60.385 45.833 0.00 0.00 0.00 1.40
529 536 5.131067 GGTGTCTTCCCCCTTGTATAATTC 58.869 45.833 0.00 0.00 0.00 2.17
530 537 5.339695 GGTGTCTTCCCCCTTGTATAATTCA 60.340 44.000 0.00 0.00 0.00 2.57
531 538 6.365520 GTGTCTTCCCCCTTGTATAATTCAT 58.634 40.000 0.00 0.00 0.00 2.57
532 539 6.833933 GTGTCTTCCCCCTTGTATAATTCATT 59.166 38.462 0.00 0.00 0.00 2.57
533 540 7.996644 GTGTCTTCCCCCTTGTATAATTCATTA 59.003 37.037 0.00 0.00 0.00 1.90
534 541 8.561769 TGTCTTCCCCCTTGTATAATTCATTAA 58.438 33.333 0.00 0.00 0.00 1.40
535 542 9.588096 GTCTTCCCCCTTGTATAATTCATTAAT 57.412 33.333 0.00 0.00 0.00 1.40
536 543 9.807921 TCTTCCCCCTTGTATAATTCATTAATC 57.192 33.333 0.00 0.00 0.00 1.75
537 544 8.630054 TTCCCCCTTGTATAATTCATTAATCG 57.370 34.615 0.00 0.00 0.00 3.34
538 545 7.980032 TCCCCCTTGTATAATTCATTAATCGA 58.020 34.615 0.00 0.00 0.00 3.59
539 546 8.611257 TCCCCCTTGTATAATTCATTAATCGAT 58.389 33.333 0.00 0.00 0.00 3.59
540 547 8.893727 CCCCCTTGTATAATTCATTAATCGATC 58.106 37.037 0.00 0.00 0.00 3.69
541 548 8.604035 CCCCTTGTATAATTCATTAATCGATCG 58.396 37.037 9.36 9.36 0.00 3.69
542 549 9.151471 CCCTTGTATAATTCATTAATCGATCGT 57.849 33.333 15.94 0.00 0.00 3.73
553 560 7.744059 TCATTAATCGATCGTTAAGTTTGCAA 58.256 30.769 15.94 0.00 0.00 4.08
560 567 5.443562 CGATCGTTAAGTTTGCAATGACGTA 60.444 40.000 7.03 4.71 0.00 3.57
589 596 1.072331 GAGACAGGAAGCAAACAGGGA 59.928 52.381 0.00 0.00 0.00 4.20
590 597 1.202818 AGACAGGAAGCAAACAGGGAC 60.203 52.381 0.00 0.00 0.00 4.46
592 599 1.600916 AGGAAGCAAACAGGGACGC 60.601 57.895 0.00 0.00 0.00 5.19
593 600 1.896660 GGAAGCAAACAGGGACGCA 60.897 57.895 0.00 0.00 0.00 5.24
594 601 1.452145 GGAAGCAAACAGGGACGCAA 61.452 55.000 0.00 0.00 0.00 4.85
596 603 0.820871 AAGCAAACAGGGACGCAAAA 59.179 45.000 0.00 0.00 0.00 2.44
682 693 1.872313 CCACCTAGACTACGACGGATC 59.128 57.143 0.00 0.00 0.00 3.36
684 695 2.544686 CACCTAGACTACGACGGATCTG 59.455 54.545 0.00 0.00 0.00 2.90
698 709 2.467880 GGATCTGTGGTGTTCCCTCTA 58.532 52.381 0.00 0.00 0.00 2.43
699 710 2.168728 GGATCTGTGGTGTTCCCTCTAC 59.831 54.545 0.00 0.00 0.00 2.59
707 718 4.036380 GTGGTGTTCCCTCTACAACAAAAG 59.964 45.833 0.00 0.00 44.16 2.27
710 721 5.126545 GGTGTTCCCTCTACAACAAAAGTTT 59.873 40.000 0.00 0.00 34.33 2.66
711 722 6.263344 GTGTTCCCTCTACAACAAAAGTTTC 58.737 40.000 0.00 0.00 34.33 2.78
722 733 9.581099 CTACAACAAAAGTTTCAAGTTGGTTAT 57.419 29.630 22.01 10.99 42.73 1.89
822 844 2.836360 GCCCATGCATCCCCAGTG 60.836 66.667 0.00 0.00 37.47 3.66
876 898 4.761058 TCGCCCTCGCCTTCCTCT 62.761 66.667 0.00 0.00 35.26 3.69
877 899 4.214327 CGCCCTCGCCTTCCTCTC 62.214 72.222 0.00 0.00 0.00 3.20
1253 1283 0.684153 AGCTCAGCTGTCTCCTCTCC 60.684 60.000 14.67 0.00 37.57 3.71
1255 1285 0.324183 CTCAGCTGTCTCCTCTCCCA 60.324 60.000 14.67 0.00 0.00 4.37
1258 1288 3.074999 GCTGTCTCCTCTCCCAGCG 62.075 68.421 0.00 0.00 40.67 5.18
1259 1289 2.363018 TGTCTCCTCTCCCAGCGG 60.363 66.667 0.00 0.00 0.00 5.52
1260 1290 3.151022 GTCTCCTCTCCCAGCGGG 61.151 72.222 7.24 7.24 46.11 6.13
1261 1291 3.673597 TCTCCTCTCCCAGCGGGT 61.674 66.667 12.46 0.00 44.74 5.28
1277 3346 2.114670 GGTCCGGGTGCATCACATG 61.115 63.158 0.00 0.00 35.86 3.21
1374 3443 0.109597 CGCTGTCTGTTGGAAATGGC 60.110 55.000 0.00 0.00 0.00 4.40
1459 3529 9.774742 GTGGAATGAGAAAATTGTAGAATGTAC 57.225 33.333 0.00 0.00 0.00 2.90
1463 3533 8.862325 ATGAGAAAATTGTAGAATGTACACCA 57.138 30.769 0.00 0.00 0.00 4.17
1473 3543 5.178096 AGAATGTACACCATCACCATTGA 57.822 39.130 0.00 0.00 35.73 2.57
1519 3589 1.031571 ACGATTGCGCATCAACCCAT 61.032 50.000 12.75 0.00 42.48 4.00
1527 3597 1.696686 CATCAACCCATCCCCACCA 59.303 57.895 0.00 0.00 0.00 4.17
1718 3788 1.194121 ACCAAAATGCAGCCCTTCCC 61.194 55.000 0.00 0.00 0.00 3.97
1802 3872 1.705997 AAGGGCGAGGTGTTGGAACT 61.706 55.000 0.00 0.00 0.00 3.01
1804 3874 1.070786 GGCGAGGTGTTGGAACTCA 59.929 57.895 0.00 0.00 0.00 3.41
1889 3959 1.376466 GGGCACACTCACTGGTGAT 59.624 57.895 3.80 0.00 39.13 3.06
2186 4264 3.039011 GGGTTTCATCTCTAGCCTACCA 58.961 50.000 0.00 0.00 0.00 3.25
2430 4509 5.551233 AGACAGCAATGAAGCTTACAGTTA 58.449 37.500 0.00 0.00 43.70 2.24
2467 4549 2.196742 TCAGGATAGGATTGCAGGGT 57.803 50.000 0.00 0.00 0.00 4.34
2788 4870 8.842358 ACAGTACCTCGATTTGAAATAGAAAA 57.158 30.769 2.51 0.00 0.00 2.29
2855 4938 0.660488 TGCGTGAACTTCGTGCAAAT 59.340 45.000 5.52 0.00 31.69 2.32
2977 5060 2.629002 TTTTTGCCACGAGCTCCTC 58.371 52.632 8.47 0.00 44.23 3.71
3093 5180 3.626996 CTGTTCATGCCCGGGCTCA 62.627 63.158 43.34 29.50 42.51 4.26
3308 5395 4.362279 GTTCCACGAGTTGTAAGTGTACA 58.638 43.478 0.00 0.00 38.49 2.90
3502 5592 8.628280 TCATCAAATGTGACACTTGTGATTTTA 58.372 29.630 19.58 9.41 36.31 1.52
4951 7125 3.726557 TTCAGCATGTCAGGAAGGATT 57.273 42.857 0.00 0.00 37.40 3.01
5898 8271 4.870991 GTCCTGATACCACTTAGAACAAGC 59.129 45.833 0.00 0.00 0.00 4.01
6657 9034 3.006644 TCTCATGCAAGAGCCTAGCTATG 59.993 47.826 14.07 0.00 39.88 2.23
6785 9162 7.497579 ACGAGTGCCTATAGATGATGACTATAG 59.502 40.741 0.00 0.00 44.18 1.31
6790 9167 9.571816 TGCCTATAGATGATGACTATAGATGAG 57.428 37.037 17.89 7.24 45.87 2.90
6805 9182 4.640771 AGATGAGTTGGCAGTTCCTTAA 57.359 40.909 0.00 0.00 35.26 1.85
6806 9183 4.583871 AGATGAGTTGGCAGTTCCTTAAG 58.416 43.478 0.00 0.00 35.26 1.85
6807 9184 2.504367 TGAGTTGGCAGTTCCTTAAGC 58.496 47.619 0.00 0.00 35.26 3.09
7195 9574 6.793482 AGTATCTCCATAGTAGTACTCCCTCA 59.207 42.308 5.96 0.00 0.00 3.86
7253 9647 4.283722 ACAAGTAATATGGATCGGAGGGAC 59.716 45.833 0.00 0.00 0.00 4.46
7520 9940 3.026694 GGCAGATCAGTAATTTTGGCCT 58.973 45.455 3.32 0.00 0.00 5.19
7719 10143 0.958382 TGGTATGCAGCCAAACGACC 60.958 55.000 10.01 0.00 32.29 4.79
8032 10506 3.935203 CAGTTACGGAGATTGCACAAGAT 59.065 43.478 0.00 0.00 0.00 2.40
8078 10552 2.017049 GTAATGGACGCTCATTGCCTT 58.983 47.619 12.33 0.00 37.82 4.35
8167 10647 1.482177 CGAGGATCTCCCCTTCAGGAT 60.482 57.143 0.00 0.00 38.24 3.24
8171 10651 3.407540 AGGATCTCCCCTTCAGGATCATA 59.592 47.826 0.00 0.00 38.24 2.15
8255 10735 2.165641 ACGTTCGAGCAGGATACAATCA 59.834 45.455 0.00 0.00 41.41 2.57
8262 10742 5.536538 TCGAGCAGGATACAATCATCTAACT 59.463 40.000 0.00 0.00 41.41 2.24
8276 10757 3.844577 TCTAACTGTCTCGCTAACCAC 57.155 47.619 0.00 0.00 0.00 4.16
8305 10786 3.015327 GCTGAGGCAGTTCTGATGAAAT 58.985 45.455 3.84 0.00 38.54 2.17
8353 10835 1.378119 GGGTCCTTGGGCGTTTAGG 60.378 63.158 0.00 0.00 0.00 2.69
8381 10863 4.101741 GGTGCTGAGTTCTGGGAGTAATAT 59.898 45.833 0.00 0.00 0.00 1.28
8382 10864 5.304614 GGTGCTGAGTTCTGGGAGTAATATA 59.695 44.000 0.00 0.00 0.00 0.86
8405 10890 8.758633 ATATTTTTGGTATAGCTAGCTACACG 57.241 34.615 26.41 0.00 27.41 4.49
8408 10893 2.292569 TGGTATAGCTAGCTACACGCAC 59.707 50.000 26.41 17.14 42.61 5.34
8416 10901 0.536724 AGCTACACGCACATGATCCA 59.463 50.000 0.00 0.00 42.61 3.41
8432 10917 1.348064 TCCAGGGTTTGACGATCTGT 58.652 50.000 0.00 0.00 0.00 3.41
8454 10939 4.126437 TGGACACGCCATCTTATACATTG 58.874 43.478 0.00 0.00 43.33 2.82
8455 10940 3.498397 GGACACGCCATCTTATACATTGG 59.502 47.826 0.00 0.00 36.34 3.16
8460 10945 3.618594 CGCCATCTTATACATTGGATCCG 59.381 47.826 7.39 0.00 0.00 4.18
8462 10947 5.003804 GCCATCTTATACATTGGATCCGTT 58.996 41.667 7.39 0.00 0.00 4.44
8464 10949 5.997746 CCATCTTATACATTGGATCCGTTGT 59.002 40.000 19.71 19.71 0.00 3.32
8474 10959 7.676004 ACATTGGATCCGTTGTGATGTATATA 58.324 34.615 16.30 0.00 0.00 0.86
8511 10997 1.177401 ACGGAGTTACTTCGGGTACC 58.823 55.000 17.89 2.17 44.33 3.34
8535 11021 8.701895 ACCTGTTTCTTCGATTTAGTCCATATA 58.298 33.333 0.00 0.00 0.00 0.86
8536 11022 8.979574 CCTGTTTCTTCGATTTAGTCCATATAC 58.020 37.037 0.00 0.00 0.00 1.47
8554 11040 7.065324 TCCATATACGTTTCATTTGAAGTCACC 59.935 37.037 0.00 0.00 35.21 4.02
8555 11041 7.065803 CCATATACGTTTCATTTGAAGTCACCT 59.934 37.037 0.00 0.00 35.21 4.00
8576 11062 1.988107 TGACCCTCTTCAGAAGGCATT 59.012 47.619 10.42 0.00 0.00 3.56
8749 11235 4.227538 ACTCTCGTCTTTGTATTGTGTCG 58.772 43.478 0.00 0.00 0.00 4.35
8787 11273 1.991264 CTCATCTCGCTCACACACTTG 59.009 52.381 0.00 0.00 0.00 3.16
8802 11288 4.704540 ACACACTTGACCAAAATTGAGACA 59.295 37.500 0.00 0.00 0.00 3.41
8806 11292 5.745294 CACTTGACCAAAATTGAGACAGTTG 59.255 40.000 0.00 0.00 0.00 3.16
8817 11303 3.797039 TGAGACAGTTGAAGTTGGTGAG 58.203 45.455 0.00 0.00 0.00 3.51
8822 11308 3.134804 ACAGTTGAAGTTGGTGAGCTACT 59.865 43.478 0.00 0.00 0.00 2.57
8840 11326 3.751479 ACTGCCAGGGTTCAAAATTTC 57.249 42.857 0.00 0.00 0.00 2.17
8863 11349 9.703892 TTTCAATGAAATTTCACATATTTCGGT 57.296 25.926 22.71 0.44 42.28 4.69
8869 11355 3.443145 TTCACATATTTCGGTGGGGTT 57.557 42.857 0.00 0.00 35.74 4.11
8892 11378 6.418057 TTGAAATGCTTGTAACCCTGAAAT 57.582 33.333 0.00 0.00 0.00 2.17
8911 11397 4.542662 AATTTTGAGCCAGATTCGATCG 57.457 40.909 9.36 9.36 0.00 3.69
9008 11496 3.829948 ACTTTGAGCTTCAAATCGCATG 58.170 40.909 10.45 0.00 44.37 4.06
9009 11497 3.503363 ACTTTGAGCTTCAAATCGCATGA 59.497 39.130 0.00 0.00 44.37 3.07
9010 11498 3.476295 TTGAGCTTCAAATCGCATGAC 57.524 42.857 0.00 0.00 32.71 3.06
9011 11499 2.425539 TGAGCTTCAAATCGCATGACA 58.574 42.857 0.00 0.00 0.00 3.58
9012 11500 3.011818 TGAGCTTCAAATCGCATGACAT 58.988 40.909 0.00 0.00 0.00 3.06
9013 11501 3.181504 TGAGCTTCAAATCGCATGACATG 60.182 43.478 11.27 11.27 0.00 3.21
9014 11502 2.098607 AGCTTCAAATCGCATGACATGG 59.901 45.455 17.03 7.46 0.00 3.66
9015 11503 2.159338 GCTTCAAATCGCATGACATGGT 60.159 45.455 17.03 0.00 0.00 3.55
9016 11504 3.065233 GCTTCAAATCGCATGACATGGTA 59.935 43.478 17.03 0.00 0.00 3.25
9017 11505 4.591202 CTTCAAATCGCATGACATGGTAC 58.409 43.478 17.03 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.153349 GGAGACAAGGCGGGTCATC 60.153 63.158 12.83 7.89 37.74 2.92
107 109 0.814457 CTTCTCTCTGACCGTCCCAG 59.186 60.000 0.00 0.00 0.00 4.45
117 119 0.891373 TGGCGTCTTCCTTCTCTCTG 59.109 55.000 0.00 0.00 0.00 3.35
120 122 0.605589 CTGTGGCGTCTTCCTTCTCT 59.394 55.000 0.00 0.00 0.00 3.10
122 124 0.318762 GTCTGTGGCGTCTTCCTTCT 59.681 55.000 0.00 0.00 0.00 2.85
124 126 0.687354 ATGTCTGTGGCGTCTTCCTT 59.313 50.000 0.00 0.00 0.00 3.36
135 137 1.081242 GTTTGCCGCCATGTCTGTG 60.081 57.895 0.00 0.00 0.00 3.66
136 138 2.616330 CGTTTGCCGCCATGTCTGT 61.616 57.895 0.00 0.00 0.00 3.41
138 140 1.599518 TTCGTTTGCCGCCATGTCT 60.600 52.632 0.00 0.00 36.19 3.41
150 152 0.179001 CCCTCCCACCTTGTTCGTTT 60.179 55.000 0.00 0.00 0.00 3.60
152 154 1.460689 TCCCTCCCACCTTGTTCGT 60.461 57.895 0.00 0.00 0.00 3.85
153 155 1.296715 CTCCCTCCCACCTTGTTCG 59.703 63.158 0.00 0.00 0.00 3.95
192 194 1.203038 TCACAATCAACACAGCCCCAT 60.203 47.619 0.00 0.00 0.00 4.00
196 198 0.883833 CCCTCACAATCAACACAGCC 59.116 55.000 0.00 0.00 0.00 4.85
276 279 2.740055 CTGAGCCGTGCCTGTGAC 60.740 66.667 0.00 0.00 0.00 3.67
300 303 2.418083 GGCTCGGGCATTTTCCTGG 61.418 63.158 10.74 0.00 40.87 4.45
336 340 0.955428 AGCCGGCATTATATGTGCGG 60.955 55.000 31.54 12.53 43.40 5.69
365 369 1.452651 CAGCCCTGTCCGCATTGAT 60.453 57.895 0.00 0.00 0.00 2.57
375 379 2.378547 TCTAAAAATGACCCAGCCCTGT 59.621 45.455 0.00 0.00 0.00 4.00
376 380 3.085952 TCTAAAAATGACCCAGCCCTG 57.914 47.619 0.00 0.00 0.00 4.45
377 381 3.685550 CGATCTAAAAATGACCCAGCCCT 60.686 47.826 0.00 0.00 0.00 5.19
378 382 2.618709 CGATCTAAAAATGACCCAGCCC 59.381 50.000 0.00 0.00 0.00 5.19
379 383 3.541632 TCGATCTAAAAATGACCCAGCC 58.458 45.455 0.00 0.00 0.00 4.85
419 425 6.041637 TGGATCTATGCTCGTACTGGTATTTT 59.958 38.462 0.00 0.00 0.00 1.82
437 444 1.681486 TTCGCCCGCATGTGGATCTA 61.681 55.000 27.12 7.21 0.00 1.98
507 514 5.751586 TGAATTATACAAGGGGGAAGACAC 58.248 41.667 0.00 0.00 0.00 3.67
508 515 6.590656 ATGAATTATACAAGGGGGAAGACA 57.409 37.500 0.00 0.00 0.00 3.41
509 516 8.990163 TTAATGAATTATACAAGGGGGAAGAC 57.010 34.615 0.00 0.00 0.00 3.01
510 517 9.807921 GATTAATGAATTATACAAGGGGGAAGA 57.192 33.333 0.00 0.00 0.00 2.87
511 518 8.730680 CGATTAATGAATTATACAAGGGGGAAG 58.269 37.037 0.00 0.00 0.00 3.46
512 519 8.441572 TCGATTAATGAATTATACAAGGGGGAA 58.558 33.333 0.00 0.00 0.00 3.97
513 520 7.980032 TCGATTAATGAATTATACAAGGGGGA 58.020 34.615 0.00 0.00 0.00 4.81
514 521 8.807948 ATCGATTAATGAATTATACAAGGGGG 57.192 34.615 0.00 0.00 0.00 5.40
515 522 8.604035 CGATCGATTAATGAATTATACAAGGGG 58.396 37.037 10.26 0.00 0.00 4.79
516 523 9.151471 ACGATCGATTAATGAATTATACAAGGG 57.849 33.333 24.34 0.00 0.00 3.95
525 532 9.221775 GCAAACTTAACGATCGATTAATGAATT 57.778 29.630 24.34 4.52 0.00 2.17
526 533 8.394877 TGCAAACTTAACGATCGATTAATGAAT 58.605 29.630 24.34 6.99 0.00 2.57
527 534 7.744059 TGCAAACTTAACGATCGATTAATGAA 58.256 30.769 24.34 9.69 0.00 2.57
528 535 7.297229 TGCAAACTTAACGATCGATTAATGA 57.703 32.000 24.34 1.81 0.00 2.57
529 536 7.946918 TTGCAAACTTAACGATCGATTAATG 57.053 32.000 24.34 16.40 0.00 1.90
530 537 8.394877 TCATTGCAAACTTAACGATCGATTAAT 58.605 29.630 24.34 6.35 0.00 1.40
531 538 7.690637 GTCATTGCAAACTTAACGATCGATTAA 59.309 33.333 24.34 19.25 0.00 1.40
532 539 7.177407 GTCATTGCAAACTTAACGATCGATTA 58.823 34.615 24.34 13.42 0.00 1.75
533 540 6.021596 GTCATTGCAAACTTAACGATCGATT 58.978 36.000 24.34 14.44 0.00 3.34
534 541 5.560148 GTCATTGCAAACTTAACGATCGAT 58.440 37.500 24.34 13.45 0.00 3.59
535 542 4.433674 CGTCATTGCAAACTTAACGATCGA 60.434 41.667 24.34 0.00 0.00 3.59
536 543 3.773549 CGTCATTGCAAACTTAACGATCG 59.226 43.478 14.88 14.88 0.00 3.69
537 544 4.708601 ACGTCATTGCAAACTTAACGATC 58.291 39.130 21.18 0.00 33.25 3.69
538 545 4.742438 ACGTCATTGCAAACTTAACGAT 57.258 36.364 21.18 9.08 33.25 3.73
539 546 4.507021 TGTACGTCATTGCAAACTTAACGA 59.493 37.500 21.18 8.70 33.25 3.85
540 547 4.763874 TGTACGTCATTGCAAACTTAACG 58.236 39.130 1.71 11.51 35.00 3.18
541 548 7.617533 AATTGTACGTCATTGCAAACTTAAC 57.382 32.000 1.71 0.00 0.00 2.01
542 549 7.915923 TGAAATTGTACGTCATTGCAAACTTAA 59.084 29.630 1.71 0.00 0.00 1.85
543 550 7.418408 TGAAATTGTACGTCATTGCAAACTTA 58.582 30.769 1.71 0.00 0.00 2.24
553 560 5.047306 TCCTGTCTCTGAAATTGTACGTCAT 60.047 40.000 0.00 0.00 0.00 3.06
560 567 4.090761 TGCTTCCTGTCTCTGAAATTGT 57.909 40.909 0.00 0.00 0.00 2.71
594 601 3.183754 CGACGGAACTTTTTGGCTTTTT 58.816 40.909 0.00 0.00 0.00 1.94
596 603 1.535226 GCGACGGAACTTTTTGGCTTT 60.535 47.619 0.00 0.00 0.00 3.51
682 693 2.104111 TGTTGTAGAGGGAACACCACAG 59.896 50.000 0.00 0.00 43.89 3.66
684 695 2.922740 TGTTGTAGAGGGAACACCAC 57.077 50.000 0.00 0.00 43.89 4.16
698 709 8.840833 AATAACCAACTTGAAACTTTTGTTGT 57.159 26.923 0.00 0.00 42.67 3.32
699 710 9.150348 AGAATAACCAACTTGAAACTTTTGTTG 57.850 29.630 0.00 0.00 42.67 3.33
707 718 4.473199 GCCGAGAATAACCAACTTGAAAC 58.527 43.478 0.00 0.00 0.00 2.78
710 721 2.304761 AGGCCGAGAATAACCAACTTGA 59.695 45.455 0.00 0.00 0.00 3.02
711 722 2.711542 AGGCCGAGAATAACCAACTTG 58.288 47.619 0.00 0.00 0.00 3.16
722 733 2.186903 GGCGATCAAGGCCGAGAA 59.813 61.111 0.00 0.00 41.39 2.87
908 932 1.381165 CGGGGGTTTTGGCGATAAGG 61.381 60.000 0.00 0.00 0.00 2.69
962 992 4.026357 GAGGGAGTGGGGAGGGGT 62.026 72.222 0.00 0.00 0.00 4.95
1258 1288 3.344137 ATGTGATGCACCCGGACCC 62.344 63.158 0.73 0.00 32.73 4.46
1259 1289 2.114670 CATGTGATGCACCCGGACC 61.115 63.158 0.73 0.00 32.73 4.46
1260 1290 1.078497 TCATGTGATGCACCCGGAC 60.078 57.895 0.73 0.00 32.73 4.79
1261 1291 1.221566 CTCATGTGATGCACCCGGA 59.778 57.895 0.73 0.00 32.73 5.14
1264 1294 0.543277 TCTCCTCATGTGATGCACCC 59.457 55.000 0.00 0.00 32.73 4.61
1265 1295 2.634815 ATCTCCTCATGTGATGCACC 57.365 50.000 0.00 0.00 32.73 5.01
1268 3337 4.447054 CGACTAAATCTCCTCATGTGATGC 59.553 45.833 0.00 0.00 0.00 3.91
1272 3341 4.115516 CCACGACTAAATCTCCTCATGTG 58.884 47.826 0.00 0.00 0.00 3.21
1277 3346 5.420409 ACAATTCCACGACTAAATCTCCTC 58.580 41.667 0.00 0.00 0.00 3.71
1374 3443 7.202016 TGTGAATTTAGCTAAAGTCCTTGTG 57.798 36.000 32.38 0.00 38.93 3.33
1459 3529 2.163010 GCTCTTGTCAATGGTGATGGTG 59.837 50.000 0.00 0.00 35.80 4.17
1463 3533 5.255687 TGTAATGCTCTTGTCAATGGTGAT 58.744 37.500 0.00 0.00 35.80 3.06
1473 3543 4.821260 TGTGTTGTCATGTAATGCTCTTGT 59.179 37.500 0.00 0.00 46.21 3.16
1519 3589 3.936203 GTGTGCGTCTGGTGGGGA 61.936 66.667 0.00 0.00 0.00 4.81
1527 3597 1.202582 GTGATCCTGTAGTGTGCGTCT 59.797 52.381 0.00 0.00 0.00 4.18
1718 3788 1.069159 ACGCTGTCTCAACTACACTCG 60.069 52.381 0.00 0.00 0.00 4.18
1802 3872 0.609957 CTGTCCCTGCAATGGCTTGA 60.610 55.000 0.00 0.00 41.91 3.02
1804 3874 1.304713 CCTGTCCCTGCAATGGCTT 60.305 57.895 0.00 0.00 41.91 4.35
1850 3920 0.761187 TTGTGCTCTCAAGACTGGCT 59.239 50.000 0.00 0.00 0.00 4.75
1889 3959 2.018679 TAGCTAGGAGGGGGCTCCA 61.019 63.158 5.99 0.00 45.66 3.86
1990 4060 1.546476 CAGTCCACTGACCTCTGGTAC 59.454 57.143 0.00 0.00 46.59 3.34
2186 4264 2.168313 CCTTTTGTCCCAAGCAAGTTGT 59.832 45.455 4.48 0.00 33.87 3.32
2430 4509 4.594920 TCCTGAAGAACAAGACAGAATCCT 59.405 41.667 0.00 0.00 32.90 3.24
2467 4549 6.660521 TCTTACTATCCGACAGTTCCTTTGTA 59.339 38.462 0.00 0.00 0.00 2.41
2855 4938 5.955488 TCGAATGTCCAAACTTCACAAAAA 58.045 33.333 0.00 0.00 0.00 1.94
3308 5395 6.048509 TCAGTCACGATGCACATTATATGTT 58.951 36.000 0.00 0.00 42.70 2.71
3467 5557 7.143340 AGTGTCACATTTGATGATTTGAACAG 58.857 34.615 5.62 0.00 33.11 3.16
3502 5592 5.068636 CCTTGCTGCCATAAACTATCTGAT 58.931 41.667 0.00 0.00 0.00 2.90
4037 6208 2.311841 AGTTTATAGGTTTGGCTGGCCT 59.688 45.455 13.05 0.00 36.94 5.19
4041 6212 7.441458 GTGTAGGATAGTTTATAGGTTTGGCTG 59.559 40.741 0.00 0.00 0.00 4.85
4951 7125 7.048629 TGGCATACACTCTCAAATTTGAAAA 57.951 32.000 20.82 11.56 36.64 2.29
5096 7274 4.371855 AATGCATCATCAAGCTGAGTTG 57.628 40.909 0.00 0.00 0.00 3.16
5220 7398 6.039605 TGAGCATGTCATTTTTGTTGAGAAGA 59.960 34.615 0.00 0.00 0.00 2.87
5227 7405 3.311106 CGCTGAGCATGTCATTTTTGTT 58.689 40.909 4.88 0.00 33.51 2.83
5228 7406 2.352030 CCGCTGAGCATGTCATTTTTGT 60.352 45.455 4.88 0.00 33.51 2.83
5229 7407 2.256174 CCGCTGAGCATGTCATTTTTG 58.744 47.619 4.88 0.00 33.51 2.44
5230 7408 1.203052 CCCGCTGAGCATGTCATTTTT 59.797 47.619 4.88 0.00 33.51 1.94
5231 7409 0.813184 CCCGCTGAGCATGTCATTTT 59.187 50.000 4.88 0.00 33.51 1.82
5232 7410 0.322816 ACCCGCTGAGCATGTCATTT 60.323 50.000 4.88 0.00 33.51 2.32
5233 7411 0.745845 GACCCGCTGAGCATGTCATT 60.746 55.000 15.75 0.00 33.51 2.57
5234 7412 1.153289 GACCCGCTGAGCATGTCAT 60.153 57.895 15.75 0.00 33.51 3.06
5235 7413 0.970427 TAGACCCGCTGAGCATGTCA 60.970 55.000 20.73 8.14 33.21 3.58
5236 7414 0.249238 CTAGACCCGCTGAGCATGTC 60.249 60.000 13.55 13.55 0.00 3.06
5237 7415 1.819229 CTAGACCCGCTGAGCATGT 59.181 57.895 4.88 0.00 0.00 3.21
5238 7416 1.593750 GCTAGACCCGCTGAGCATG 60.594 63.158 4.88 0.00 34.96 4.06
5239 7417 1.333636 AAGCTAGACCCGCTGAGCAT 61.334 55.000 4.88 0.00 37.87 3.79
5298 7476 1.134995 GCTTCCCTGTAGGCAAAATGC 60.135 52.381 0.00 0.00 44.08 3.56
5898 8271 6.477053 TCAGAAAATCTCCAGAGATACAGG 57.523 41.667 10.49 1.38 46.75 4.00
6599 8974 4.815269 ACTTTTTCACATCTCTCTCCTCG 58.185 43.478 0.00 0.00 0.00 4.63
6785 9162 3.127721 GCTTAAGGAACTGCCAACTCATC 59.872 47.826 4.29 0.00 40.86 2.92
6809 9186 6.375455 GCATGGTTAATAATATAGCCAGCTGT 59.625 38.462 13.81 0.00 39.18 4.40
6885 9264 5.056480 AGCCTTTACCTGCAATTTTTCAAC 58.944 37.500 0.00 0.00 0.00 3.18
7195 9574 9.080097 ACTAAAGCTACGAAGTAATATGGATCT 57.920 33.333 0.00 0.00 45.13 2.75
7520 9940 4.469469 AAAGGGAAGAAAGATGGAACCA 57.531 40.909 0.00 0.00 0.00 3.67
7719 10143 5.846203 ACATGATTTTGTCAGTTTGGAAGG 58.154 37.500 0.00 0.00 40.92 3.46
8032 10506 1.066605 GCGAGCATTTACTCCTCCGTA 59.933 52.381 0.00 0.00 32.79 4.02
8078 10552 2.123018 ATATCCATGTCCAGGGAGCA 57.877 50.000 6.82 0.00 45.19 4.26
8167 10647 4.700700 TGATACCGAACTCGAGAGTATGA 58.299 43.478 21.68 11.27 41.58 2.15
8171 10651 2.033550 GCATGATACCGAACTCGAGAGT 59.966 50.000 21.68 12.77 44.94 3.24
8255 10735 4.017808 AGTGGTTAGCGAGACAGTTAGAT 58.982 43.478 0.00 0.00 0.00 1.98
8262 10742 3.390135 CTCAAAAGTGGTTAGCGAGACA 58.610 45.455 0.00 0.00 0.00 3.41
8276 10757 1.538950 GAACTGCCTCAGCCTCAAAAG 59.461 52.381 0.00 0.00 38.69 2.27
8305 10786 2.808919 TCAACCAAACCAAACCTGTGA 58.191 42.857 0.00 0.00 0.00 3.58
8313 10794 4.384647 CCCAAGGAAATTCAACCAAACCAA 60.385 41.667 0.00 0.00 0.00 3.67
8353 10835 0.951040 CCAGAACTCAGCACCCGAAC 60.951 60.000 0.00 0.00 0.00 3.95
8381 10863 6.643770 GCGTGTAGCTAGCTATACCAAAAATA 59.356 38.462 33.17 8.43 44.04 1.40
8382 10864 5.465724 GCGTGTAGCTAGCTATACCAAAAAT 59.534 40.000 33.17 7.80 44.04 1.82
8405 10890 1.474077 GTCAAACCCTGGATCATGTGC 59.526 52.381 0.00 0.00 0.00 4.57
8408 10893 2.401583 TCGTCAAACCCTGGATCATG 57.598 50.000 0.00 0.00 0.00 3.07
8416 10901 1.002087 GTCCACAGATCGTCAAACCCT 59.998 52.381 0.00 0.00 0.00 4.34
8454 10939 5.946298 TCGTATATACATCACAACGGATCC 58.054 41.667 13.22 0.00 0.00 3.36
8455 10940 7.473366 AGATCGTATATACATCACAACGGATC 58.527 38.462 13.22 11.84 0.00 3.36
8460 10945 7.963465 ACATCGAGATCGTATATACATCACAAC 59.037 37.037 13.22 7.32 40.80 3.32
8462 10947 7.611213 ACATCGAGATCGTATATACATCACA 57.389 36.000 13.22 4.40 40.80 3.58
8474 10959 5.873712 ACTCCGTTATATACATCGAGATCGT 59.126 40.000 1.70 0.00 40.80 3.73
8508 10994 6.349243 TGGACTAAATCGAAGAAACAGGTA 57.651 37.500 0.00 0.00 43.58 3.08
8511 10997 8.691727 CGTATATGGACTAAATCGAAGAAACAG 58.308 37.037 0.00 0.00 43.58 3.16
8554 11040 1.349026 TGCCTTCTGAAGAGGGTCAAG 59.651 52.381 18.68 0.74 42.66 3.02
8555 11041 1.434188 TGCCTTCTGAAGAGGGTCAA 58.566 50.000 18.68 0.00 42.66 3.18
8566 11052 1.065418 ACCCTTCGGTAATGCCTTCTG 60.065 52.381 0.00 0.00 42.18 3.02
8576 11062 6.183360 CCATAATCTCAAGTTACCCTTCGGTA 60.183 42.308 0.00 0.00 42.18 4.02
8585 11071 6.701841 TCTGCGATTCCATAATCTCAAGTTAC 59.298 38.462 0.00 0.00 36.62 2.50
8592 11078 4.021544 AGTCCTCTGCGATTCCATAATCTC 60.022 45.833 0.00 0.00 39.56 2.75
8640 11126 6.099557 TGTGGGAAAACAGAAATTCCATCTTT 59.900 34.615 6.85 0.00 45.64 2.52
8787 11273 6.136541 ACTTCAACTGTCTCAATTTTGGTC 57.863 37.500 0.00 0.00 0.00 4.02
8802 11288 3.733337 CAGTAGCTCACCAACTTCAACT 58.267 45.455 0.00 0.00 0.00 3.16
8806 11292 1.270839 TGGCAGTAGCTCACCAACTTC 60.271 52.381 0.00 0.00 41.70 3.01
8817 11303 1.616159 TTTTGAACCCTGGCAGTAGC 58.384 50.000 14.43 0.43 41.10 3.58
8822 11308 4.102210 TCATTGAAATTTTGAACCCTGGCA 59.898 37.500 0.00 0.00 0.00 4.92
8840 11326 7.010367 CCCACCGAAATATGTGAAATTTCATTG 59.990 37.037 23.05 10.18 41.40 2.82
8863 11349 3.070302 GGTTACAAGCATTTCAAACCCCA 59.930 43.478 0.00 0.00 32.09 4.96
8869 11355 5.860941 TTTCAGGGTTACAAGCATTTCAA 57.139 34.783 0.00 0.00 0.00 2.69
8892 11378 3.245518 TCGATCGAATCTGGCTCAAAA 57.754 42.857 16.99 0.00 0.00 2.44
8973 11461 3.563808 GCTCAAAGTCAATACACACACCA 59.436 43.478 0.00 0.00 0.00 4.17
9013 11501 5.560966 CCATTAAGATGGTGTTGTGTACC 57.439 43.478 0.00 0.00 46.48 3.34


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

AutoCloner maintained by Alex Coulton.