Multiple sequence alignment - TraesCS1A01G387900

Loading Multiple Alignment...

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 TraesCS1A01G387900 chr1A 100.000 5049 0 0 1 5049 556796685 556791637 0.000000e+00 9324.0
1 TraesCS1A01G387900 chr1A 89.154 461 43 2 2730 3190 556802563 556803016 7.340000e-158 568.0
2 TraesCS1A01G387900 chr1A 84.084 333 41 7 3699 4024 556725921 556725594 1.360000e-80 311.0
3 TraesCS1A01G387900 chr1A 84.615 260 30 6 4792 5049 556785818 556785567 3.020000e-62 250.0
4 TraesCS1A01G387900 chr1D 96.425 3301 97 12 952 4244 464321701 464318414 0.000000e+00 5422.0
5 TraesCS1A01G387900 chr1D 88.038 744 57 14 4076 4810 464303395 464302675 0.000000e+00 852.0
6 TraesCS1A01G387900 chr1D 92.963 540 21 3 3527 4064 464311064 464310540 0.000000e+00 771.0
7 TraesCS1A01G387900 chr1D 91.957 460 28 4 2732 3190 464345298 464345749 1.980000e-178 636.0
8 TraesCS1A01G387900 chr1D 95.238 315 9 1 1 315 464323108 464322800 1.260000e-135 494.0
9 TraesCS1A01G387900 chr1D 90.722 291 25 2 4760 5049 464301457 464301168 2.200000e-103 387.0
10 TraesCS1A01G387900 chr1D 86.813 273 12 16 363 624 464322546 464322287 2.980000e-72 283.0
11 TraesCS1A01G387900 chr1D 91.327 196 16 1 4855 5049 464302675 464302480 3.000000e-67 267.0
12 TraesCS1A01G387900 chr1D 88.614 202 19 4 4850 5049 464316809 464316610 5.050000e-60 243.0
13 TraesCS1A01G387900 chr1D 86.893 206 19 2 3699 3904 464288880 464288683 1.830000e-54 224.0
14 TraesCS1A01G387900 chr1D 83.402 241 26 9 4235 4468 464318661 464318428 1.420000e-50 211.0
15 TraesCS1A01G387900 chr1D 89.552 67 6 1 862 927 464321752 464321686 3.240000e-12 84.2
16 TraesCS1A01G387900 chr1B 95.991 3118 96 13 952 4050 640558156 640555049 0.000000e+00 5038.0
17 TraesCS1A01G387900 chr1B 87.367 1789 144 40 3269 5049 640500883 640499169 0.000000e+00 1977.0
18 TraesCS1A01G387900 chr1B 86.000 1050 134 9 2718 3762 640566705 640567746 0.000000e+00 1112.0
19 TraesCS1A01G387900 chr1B 82.456 1083 141 23 3160 4223 640568543 640569595 0.000000e+00 902.0
20 TraesCS1A01G387900 chr1B 87.056 788 72 18 4097 4880 640555047 640554286 0.000000e+00 863.0
21 TraesCS1A01G387900 chr1B 95.765 307 13 0 4 310 640559971 640559665 3.510000e-136 496.0
22 TraesCS1A01G387900 chr1B 85.319 470 53 9 4589 5049 640483848 640483386 5.920000e-129 472.0
23 TraesCS1A01G387900 chr1B 83.475 472 59 12 4588 5049 640460994 640460532 6.040000e-114 422.0
24 TraesCS1A01G387900 chr1B 86.286 350 34 5 4333 4677 640497193 640496853 7.990000e-98 368.0
25 TraesCS1A01G387900 chr1B 82.171 387 43 15 3748 4115 640459434 640459055 4.910000e-80 309.0
26 TraesCS1A01G387900 chr1B 80.531 452 29 25 363 810 640559420 640559024 4.940000e-75 292.0
27 TraesCS1A01G387900 chr1B 83.178 321 44 7 4232 4546 640569365 640569681 8.270000e-73 285.0
28 TraesCS1A01G387900 chr1B 83.587 329 27 13 3699 4007 640469000 640468679 2.980000e-72 283.0
29 TraesCS1A01G387900 chr1B 82.625 259 33 6 4792 5049 640552276 640552029 8.510000e-53 219.0
30 TraesCS1A01G387900 chr1B 78.474 367 52 13 4548 4900 640572241 640572594 1.100000e-51 215.0
31 TraesCS1A01G387900 chr1B 83.957 187 24 4 4731 4912 640592991 640593176 1.870000e-39 174.0
32 TraesCS1A01G387900 chr1B 78.929 280 39 7 1921 2193 640501346 640501080 6.720000e-39 172.0
33 TraesCS1A01G387900 chr1B 80.676 207 37 3 4844 5049 640597393 640597597 1.880000e-34 158.0
34 TraesCS1A01G387900 chr1B 77.647 170 23 12 4391 4553 640547858 640547697 6.960000e-14 89.8
35 TraesCS1A01G387900 chr1B 91.304 46 2 2 316 361 30543247 30543290 1.520000e-05 62.1
36 TraesCS1A01G387900 chr1B 100.000 29 0 0 2035 2063 640501204 640501176 3.000000e-03 54.7
37 TraesCS1A01G387900 chr5B 100.000 39 0 0 318 356 146825604 146825642 7.010000e-09 73.1
38 TraesCS1A01G387900 chr7A 97.368 38 1 0 319 356 706669778 706669741 1.170000e-06 65.8
39 TraesCS1A01G387900 chr7A 91.489 47 1 3 313 356 286994640 286994594 1.520000e-05 62.1
40 TraesCS1A01G387900 chr4B 93.333 45 2 1 313 356 647306642 647306598 1.170000e-06 65.8
41 TraesCS1A01G387900 chr4B 95.000 40 2 0 317 356 665949498 665949459 4.220000e-06 63.9
42 TraesCS1A01G387900 chr6B 95.122 41 1 1 317 356 438408590 438408550 4.220000e-06 63.9
43 TraesCS1A01G387900 chr2B 95.000 40 2 0 317 356 40498634 40498673 4.220000e-06 63.9
44 TraesCS1A01G387900 chr2B 95.122 41 1 1 317 356 705379629 705379669 4.220000e-06 63.9


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 TraesCS1A01G387900 chr1A 556791637 556796685 5048 True 9324.000000 9324 100.000000 1 5049 1 chr1A.!!$R3 5048
1 TraesCS1A01G387900 chr1D 464316610 464323108 6498 True 1122.866667 5422 90.007333 1 5049 6 chr1D.!!$R4 5048
2 TraesCS1A01G387900 chr1D 464310540 464311064 524 True 771.000000 771 92.963000 3527 4064 1 chr1D.!!$R2 537
3 TraesCS1A01G387900 chr1D 464301168 464303395 2227 True 502.000000 852 90.029000 4076 5049 3 chr1D.!!$R3 973
4 TraesCS1A01G387900 chr1B 640552029 640559971 7942 True 1381.600000 5038 88.393600 4 5049 5 chr1B.!!$R6 5045
5 TraesCS1A01G387900 chr1B 640496853 640501346 4493 True 642.925000 1977 88.145500 1921 5049 4 chr1B.!!$R5 3128
6 TraesCS1A01G387900 chr1B 640566705 640572594 5889 False 628.500000 1112 82.527000 2718 4900 4 chr1B.!!$F4 2182
7 TraesCS1A01G387900 chr1B 640459055 640460994 1939 True 365.500000 422 82.823000 3748 5049 2 chr1B.!!$R4 1301

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
323 330 0.035739 AGCCAAGCCAAGCCAAAATG 59.964 50.0 0.00 0.00 0.00 2.32 F
1058 2115 0.179073 CATCTACACCAAGCGGGGAG 60.179 60.0 3.55 0.00 38.36 4.30 F
2183 3262 0.180171 ATCATCCCGTGCGGAATTGA 59.820 50.0 12.71 11.45 46.47 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 3264 0.320683 CAATCCCGCACTCACTGACA 60.321 55.0 0.00 0.0 0.00 3.58 R
2549 3628 0.536460 GGGCGAGTGGAAAGGTTTGA 60.536 55.0 0.00 0.0 0.00 2.69 R
4316 6836 0.517316 ACGAATTCGCAGGCAGAAAC 59.483 50.0 27.03 0.0 44.43 2.78 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
283 290 3.173965 ACACCACACTGAGGCTATAAGT 58.826 45.455 0.00 0.00 0.00 2.24
315 322 3.130160 GAGCCGAGCCAAGCCAAG 61.130 66.667 0.00 0.00 0.00 3.61
323 330 0.035739 AGCCAAGCCAAGCCAAAATG 59.964 50.000 0.00 0.00 0.00 2.32
326 333 1.622811 CCAAGCCAAGCCAAAATGGTA 59.377 47.619 0.00 0.00 40.46 3.25
327 334 2.612721 CCAAGCCAAGCCAAAATGGTAC 60.613 50.000 0.00 0.00 40.46 3.34
328 335 2.299867 CAAGCCAAGCCAAAATGGTACT 59.700 45.455 0.00 0.00 40.46 2.73
329 336 3.449746 AGCCAAGCCAAAATGGTACTA 57.550 42.857 0.00 0.00 40.46 1.82
330 337 3.089284 AGCCAAGCCAAAATGGTACTAC 58.911 45.455 0.00 0.00 40.46 2.73
331 338 2.165641 GCCAAGCCAAAATGGTACTACC 59.834 50.000 0.00 0.00 40.46 3.18
333 340 3.694566 CCAAGCCAAAATGGTACTACCTC 59.305 47.826 6.79 0.00 40.46 3.85
334 341 3.646736 AGCCAAAATGGTACTACCTCC 57.353 47.619 6.79 0.00 40.46 4.30
335 342 2.093128 AGCCAAAATGGTACTACCTCCG 60.093 50.000 6.79 0.00 40.46 4.63
336 343 2.355412 GCCAAAATGGTACTACCTCCGT 60.355 50.000 6.79 0.00 40.46 4.69
337 344 3.528532 CCAAAATGGTACTACCTCCGTC 58.471 50.000 6.79 0.00 39.58 4.79
338 345 3.528532 CAAAATGGTACTACCTCCGTCC 58.471 50.000 6.79 0.00 39.58 4.79
339 346 1.785647 AATGGTACTACCTCCGTCCC 58.214 55.000 6.79 0.00 39.58 4.46
352 359 1.105457 CCGTCCCGGTGTATAAGTCA 58.895 55.000 0.00 0.00 42.73 3.41
354 361 2.101917 CCGTCCCGGTGTATAAGTCATT 59.898 50.000 0.00 0.00 42.73 2.57
355 362 3.378339 CGTCCCGGTGTATAAGTCATTC 58.622 50.000 0.00 0.00 0.00 2.67
357 364 4.117685 GTCCCGGTGTATAAGTCATTCAC 58.882 47.826 0.00 0.00 34.95 3.18
358 365 4.028131 TCCCGGTGTATAAGTCATTCACT 58.972 43.478 0.00 0.00 35.76 3.41
409 631 9.080097 ACCGTCCTAGGCTTAATATATATCATC 57.920 37.037 2.96 0.00 33.69 2.92
436 658 0.668401 GTTTGTGAGCATGCCCTTGC 60.668 55.000 15.66 1.12 43.09 4.01
482 707 0.878086 GCTCAGGCTATTCTCGGTGC 60.878 60.000 0.00 0.00 35.22 5.01
520 751 3.382227 TGATATTCATTGGCTGGCTGTTG 59.618 43.478 2.00 0.00 0.00 3.33
524 755 1.973281 ATTGGCTGGCTGTTGTCGG 60.973 57.895 2.00 0.00 0.00 4.79
637 868 1.668919 GGCTTTACTGCCGCCTTTTTC 60.669 52.381 0.00 0.00 43.74 2.29
639 870 2.288213 GCTTTACTGCCGCCTTTTTCTT 60.288 45.455 0.00 0.00 0.00 2.52
641 872 1.243902 TACTGCCGCCTTTTTCTTGG 58.756 50.000 0.00 0.00 0.00 3.61
642 873 0.467290 ACTGCCGCCTTTTTCTTGGA 60.467 50.000 0.00 0.00 0.00 3.53
644 875 1.273327 CTGCCGCCTTTTTCTTGGATT 59.727 47.619 0.00 0.00 0.00 3.01
645 876 1.272212 TGCCGCCTTTTTCTTGGATTC 59.728 47.619 0.00 0.00 0.00 2.52
647 878 2.672195 GCCGCCTTTTTCTTGGATTCAG 60.672 50.000 0.00 0.00 0.00 3.02
648 879 2.558359 CCGCCTTTTTCTTGGATTCAGT 59.442 45.455 0.00 0.00 0.00 3.41
649 880 3.568538 CGCCTTTTTCTTGGATTCAGTG 58.431 45.455 0.00 0.00 0.00 3.66
650 881 3.320626 GCCTTTTTCTTGGATTCAGTGC 58.679 45.455 0.00 0.00 0.00 4.40
652 883 4.553323 CCTTTTTCTTGGATTCAGTGCTG 58.447 43.478 0.00 0.00 0.00 4.41
653 884 3.648339 TTTTCTTGGATTCAGTGCTGC 57.352 42.857 0.00 0.00 0.00 5.25
654 885 1.538047 TTCTTGGATTCAGTGCTGCC 58.462 50.000 0.00 0.00 0.00 4.85
655 886 0.694771 TCTTGGATTCAGTGCTGCCT 59.305 50.000 0.00 0.00 0.00 4.75
656 887 0.809385 CTTGGATTCAGTGCTGCCTG 59.191 55.000 10.65 10.65 0.00 4.85
657 888 0.609957 TTGGATTCAGTGCTGCCTGG 60.610 55.000 15.08 0.00 33.14 4.45
658 889 2.413142 GGATTCAGTGCTGCCTGGC 61.413 63.158 12.87 12.87 33.14 4.85
659 890 1.676635 GATTCAGTGCTGCCTGGCA 60.677 57.895 21.96 21.96 40.15 4.92
660 891 1.000019 ATTCAGTGCTGCCTGGCAT 60.000 52.632 23.64 3.86 44.34 4.40
661 892 1.035932 ATTCAGTGCTGCCTGGCATC 61.036 55.000 23.64 19.19 44.34 3.91
692 923 3.370315 GGCTCATCACTTCTCAACCAGAT 60.370 47.826 0.00 0.00 0.00 2.90
693 924 4.260170 GCTCATCACTTCTCAACCAGATT 58.740 43.478 0.00 0.00 0.00 2.40
694 925 4.699257 GCTCATCACTTCTCAACCAGATTT 59.301 41.667 0.00 0.00 0.00 2.17
695 926 5.182760 GCTCATCACTTCTCAACCAGATTTT 59.817 40.000 0.00 0.00 0.00 1.82
697 928 7.206981 TCATCACTTCTCAACCAGATTTTTC 57.793 36.000 0.00 0.00 0.00 2.29
698 929 7.000472 TCATCACTTCTCAACCAGATTTTTCT 59.000 34.615 0.00 0.00 0.00 2.52
700 931 6.356556 TCACTTCTCAACCAGATTTTTCTCA 58.643 36.000 0.00 0.00 0.00 3.27
701 932 6.828273 TCACTTCTCAACCAGATTTTTCTCAA 59.172 34.615 0.00 0.00 0.00 3.02
702 933 6.914757 CACTTCTCAACCAGATTTTTCTCAAC 59.085 38.462 0.00 0.00 0.00 3.18
703 934 6.603201 ACTTCTCAACCAGATTTTTCTCAACA 59.397 34.615 0.00 0.00 0.00 3.33
704 935 7.122650 ACTTCTCAACCAGATTTTTCTCAACAA 59.877 33.333 0.00 0.00 0.00 2.83
705 936 7.587037 TCTCAACCAGATTTTTCTCAACAAT 57.413 32.000 0.00 0.00 0.00 2.71
751 982 7.496591 AGTTATTATTATTTCTTCCCACGCGAA 59.503 33.333 15.93 0.00 0.00 4.70
754 985 1.439679 ATTTCTTCCCACGCGAAGAC 58.560 50.000 15.93 0.00 46.10 3.01
774 1005 5.848406 AGACAACTGAAGAGAAGAAATCGT 58.152 37.500 0.00 0.00 0.00 3.73
775 1006 5.694006 AGACAACTGAAGAGAAGAAATCGTG 59.306 40.000 0.00 0.00 0.00 4.35
777 1008 5.463724 ACAACTGAAGAGAAGAAATCGTGAC 59.536 40.000 0.00 0.00 0.00 3.67
778 1009 4.230657 ACTGAAGAGAAGAAATCGTGACG 58.769 43.478 0.00 0.00 0.00 4.35
810 1041 1.264749 ACGGCAGCTGAATACCTGGA 61.265 55.000 20.43 0.00 0.00 3.86
844 1120 4.221703 CAGGATAGGAGCCTCGTTATCATT 59.778 45.833 13.54 3.06 32.12 2.57
845 1121 4.841246 AGGATAGGAGCCTCGTTATCATTT 59.159 41.667 13.54 1.32 0.00 2.32
846 1122 5.308237 AGGATAGGAGCCTCGTTATCATTTT 59.692 40.000 13.54 0.00 0.00 1.82
847 1123 5.998363 GGATAGGAGCCTCGTTATCATTTTT 59.002 40.000 13.54 0.00 0.00 1.94
914 1966 8.893563 ACATAAAAGTGAGATAAAATTCCCCA 57.106 30.769 0.00 0.00 0.00 4.96
915 1967 9.492730 ACATAAAAGTGAGATAAAATTCCCCAT 57.507 29.630 0.00 0.00 0.00 4.00
916 1968 9.971922 CATAAAAGTGAGATAAAATTCCCCATC 57.028 33.333 0.00 0.00 0.00 3.51
917 1969 9.942526 ATAAAAGTGAGATAAAATTCCCCATCT 57.057 29.630 0.00 0.00 0.00 2.90
919 1971 8.753497 AAAGTGAGATAAAATTCCCCATCTAC 57.247 34.615 0.00 0.00 0.00 2.59
920 1972 6.842676 AGTGAGATAAAATTCCCCATCTACC 58.157 40.000 0.00 0.00 0.00 3.18
921 1973 6.389869 AGTGAGATAAAATTCCCCATCTACCA 59.610 38.462 0.00 0.00 0.00 3.25
922 1974 6.486993 GTGAGATAAAATTCCCCATCTACCAC 59.513 42.308 0.00 0.00 0.00 4.16
923 1975 5.953571 AGATAAAATTCCCCATCTACCACC 58.046 41.667 0.00 0.00 0.00 4.61
924 1976 5.435041 AGATAAAATTCCCCATCTACCACCA 59.565 40.000 0.00 0.00 0.00 4.17
925 1977 3.382083 AAATTCCCCATCTACCACCAC 57.618 47.619 0.00 0.00 0.00 4.16
926 1978 2.286935 ATTCCCCATCTACCACCACT 57.713 50.000 0.00 0.00 0.00 4.00
927 1979 2.053747 TTCCCCATCTACCACCACTT 57.946 50.000 0.00 0.00 0.00 3.16
928 1980 2.053747 TCCCCATCTACCACCACTTT 57.946 50.000 0.00 0.00 0.00 2.66
929 1981 2.354328 TCCCCATCTACCACCACTTTT 58.646 47.619 0.00 0.00 0.00 2.27
930 1982 2.719705 TCCCCATCTACCACCACTTTTT 59.280 45.455 0.00 0.00 0.00 1.94
1054 2111 1.066143 ACTTCCATCTACACCAAGCGG 60.066 52.381 0.00 0.00 38.77 5.52
1055 2112 0.251916 TTCCATCTACACCAAGCGGG 59.748 55.000 0.00 0.00 44.81 6.13
1056 2113 1.153168 CCATCTACACCAAGCGGGG 60.153 63.158 2.46 0.00 43.84 5.73
1057 2114 1.622607 CCATCTACACCAAGCGGGGA 61.623 60.000 3.55 0.00 38.36 4.81
1058 2115 0.179073 CATCTACACCAAGCGGGGAG 60.179 60.000 3.55 0.00 38.36 4.30
1059 2116 1.338136 ATCTACACCAAGCGGGGAGG 61.338 60.000 3.55 0.00 38.36 4.30
1060 2117 3.006728 TACACCAAGCGGGGAGGG 61.007 66.667 3.55 0.00 38.36 4.30
1063 2120 4.760220 ACCAAGCGGGGAGGGGAT 62.760 66.667 3.55 0.00 42.91 3.85
1090 2147 1.346068 GGAAGGAGATCTCAATCCCCG 59.654 57.143 25.14 0.00 35.02 5.73
1325 2392 4.689549 TCCTCTTCGGCCCGGACA 62.690 66.667 0.73 0.00 0.00 4.02
1326 2393 3.702048 CCTCTTCGGCCCGGACAA 61.702 66.667 0.73 0.00 0.00 3.18
1431 2498 4.882396 GCTCTCCTTCTCCGGCGC 62.882 72.222 0.00 0.00 0.00 6.53
1486 2559 4.736896 AACCGCCGCCTCTTCGAC 62.737 66.667 0.00 0.00 0.00 4.20
2183 3262 0.180171 ATCATCCCGTGCGGAATTGA 59.820 50.000 12.71 11.45 46.47 2.57
2185 3264 0.744414 CATCCCGTGCGGAATTGACT 60.744 55.000 12.71 0.00 46.47 3.41
2189 3268 0.948623 CCGTGCGGAATTGACTGTCA 60.949 55.000 6.36 6.36 37.50 3.58
2359 3438 3.817084 GGGGTTTGAAGTACAACTACACC 59.183 47.826 0.00 0.00 36.19 4.16
2477 3556 1.673920 TCCGGTTCAACTTGCAGAAAC 59.326 47.619 0.00 0.00 0.00 2.78
2512 3591 1.089481 ACGCATCGCCGATCACAATT 61.089 50.000 0.00 0.00 0.00 2.32
2515 3594 0.308684 CATCGCCGATCACAATTGGG 59.691 55.000 10.83 5.72 36.97 4.12
2516 3595 0.180171 ATCGCCGATCACAATTGGGA 59.820 50.000 13.90 13.90 36.97 4.37
2593 3672 0.895559 TGCTGGAGACGAAGCAGAGA 60.896 55.000 0.00 0.00 44.26 3.10
2594 3673 0.457681 GCTGGAGACGAAGCAGAGAC 60.458 60.000 0.00 0.00 39.31 3.36
2620 3699 7.050970 ACTTAATGTCAGCTACAATATCCGA 57.949 36.000 0.00 0.00 42.70 4.55
2631 3710 4.365514 ACAATATCCGATATGTTGGGCA 57.634 40.909 1.50 0.00 0.00 5.36
2653 3732 5.771469 CATTGGTCACTAGCAACATTTCAA 58.229 37.500 0.00 0.00 45.27 2.69
2655 3734 3.568007 TGGTCACTAGCAACATTTCAACC 59.432 43.478 0.00 0.00 0.00 3.77
2872 3951 3.003275 TCTTTGAAACGCTGGACATTGAC 59.997 43.478 0.00 0.00 0.00 3.18
2924 4003 6.432472 GGAAGAATCAATATGGAGAATGGACC 59.568 42.308 0.00 0.00 0.00 4.46
3043 4123 5.882000 TGCTATGTCAATCACTATGCTTGTT 59.118 36.000 0.00 0.00 0.00 2.83
3731 6206 4.715523 TTGGGGGCGCCTTCTTCG 62.716 66.667 28.56 0.00 0.00 3.79
3735 6210 2.718073 GGGGCGCCTTCTTCGTCTA 61.718 63.158 28.56 0.00 0.00 2.59
3820 6295 2.076100 CCTACAGCTTTGTTCATCGCA 58.924 47.619 0.00 0.00 0.00 5.10
3893 6381 5.964958 TTTCTGTTTCCTGATGGATGAAC 57.035 39.130 0.00 0.00 42.81 3.18
3904 6392 4.940483 TGATGGATGAACATTTACCCCAA 58.060 39.130 0.00 0.00 0.00 4.12
4013 6525 5.529060 CACAGTTCCTTTTCCTATGCTATCC 59.471 44.000 0.00 0.00 0.00 2.59
4028 6540 5.913137 TGCTATCCTTTGGTTTATGGTTG 57.087 39.130 0.00 0.00 0.00 3.77
4041 6553 1.604604 ATGGTTGACGTTCCCTGTTG 58.395 50.000 0.00 0.00 0.00 3.33
4064 6576 3.300388 TCTGGTATTCAGTCAGGGCTAG 58.700 50.000 0.00 0.00 43.76 3.42
4065 6577 1.762957 TGGTATTCAGTCAGGGCTAGC 59.237 52.381 6.04 6.04 0.00 3.42
4066 6578 2.043227 GGTATTCAGTCAGGGCTAGCT 58.957 52.381 15.72 0.00 0.00 3.32
4067 6579 3.231818 GGTATTCAGTCAGGGCTAGCTA 58.768 50.000 15.72 0.00 0.00 3.32
4068 6580 3.835395 GGTATTCAGTCAGGGCTAGCTAT 59.165 47.826 15.72 0.00 0.00 2.97
4069 6581 4.284746 GGTATTCAGTCAGGGCTAGCTATT 59.715 45.833 15.72 0.00 0.00 1.73
4070 6582 5.480772 GGTATTCAGTCAGGGCTAGCTATTA 59.519 44.000 15.72 0.00 0.00 0.98
4071 6583 5.736951 ATTCAGTCAGGGCTAGCTATTAG 57.263 43.478 15.72 0.90 0.00 1.73
4085 6597 7.719871 CTAGCTATTAGCCCAGGTAGATTTA 57.280 40.000 12.05 0.00 43.77 1.40
4141 6657 3.433274 TCTTTATGTGAGCTCTGCGTTTG 59.567 43.478 16.19 1.12 0.00 2.93
4142 6658 2.455674 TATGTGAGCTCTGCGTTTGT 57.544 45.000 16.19 0.00 0.00 2.83
4152 6668 1.807142 TCTGCGTTTGTGTGTGTTTGA 59.193 42.857 0.00 0.00 0.00 2.69
4160 6676 5.636837 GTTTGTGTGTGTTTGATGTGTAGT 58.363 37.500 0.00 0.00 0.00 2.73
4174 6690 2.758423 TGTGTAGTGTATGCATCCGAGT 59.242 45.455 0.19 0.00 0.00 4.18
4180 6697 1.831106 TGTATGCATCCGAGTCCTGTT 59.169 47.619 0.19 0.00 0.00 3.16
4183 6700 0.036388 TGCATCCGAGTCCTGTTTCC 60.036 55.000 0.00 0.00 0.00 3.13
4204 6721 4.077108 CCCTGTTTACTGTTTTCCTACCC 58.923 47.826 0.00 0.00 0.00 3.69
4205 6722 4.077108 CCTGTTTACTGTTTTCCTACCCC 58.923 47.826 0.00 0.00 0.00 4.95
4208 6725 3.793819 TTACTGTTTTCCTACCCCCAC 57.206 47.619 0.00 0.00 0.00 4.61
4211 6728 1.001764 GTTTTCCTACCCCCACCCG 60.002 63.158 0.00 0.00 0.00 5.28
4225 6742 3.418047 CCCACCCGTAGTTTCTTGAATT 58.582 45.455 0.00 0.00 0.00 2.17
4256 6773 6.126409 TCCTTTTCCTATTGCCATAATTCGT 58.874 36.000 0.00 0.00 0.00 3.85
4290 6807 6.402981 ACCCTCCTTGTTATTCTGGTATTT 57.597 37.500 0.00 0.00 0.00 1.40
4373 6913 3.369261 CCTGTTCTTGCTATGAGCTCTGT 60.369 47.826 16.19 6.35 42.97 3.41
4389 6937 2.415168 CTCTGTGTCGTGTGTTTGTGTT 59.585 45.455 0.00 0.00 0.00 3.32
4390 6938 2.158645 TCTGTGTCGTGTGTTTGTGTTG 59.841 45.455 0.00 0.00 0.00 3.33
4391 6939 1.874231 TGTGTCGTGTGTTTGTGTTGT 59.126 42.857 0.00 0.00 0.00 3.32
4392 6940 2.238363 GTGTCGTGTGTTTGTGTTGTG 58.762 47.619 0.00 0.00 0.00 3.33
4393 6941 1.874231 TGTCGTGTGTTTGTGTTGTGT 59.126 42.857 0.00 0.00 0.00 3.72
4394 6942 2.238363 GTCGTGTGTTTGTGTTGTGTG 58.762 47.619 0.00 0.00 0.00 3.82
4417 6973 3.868077 GTGTATGCATCTGAGAACTGTCC 59.132 47.826 0.19 0.00 0.00 4.02
4418 6974 2.306341 ATGCATCTGAGAACTGTCCG 57.694 50.000 0.00 0.00 0.00 4.79
4419 6975 0.969149 TGCATCTGAGAACTGTCCGT 59.031 50.000 0.00 0.00 0.00 4.69
4420 6976 1.067565 TGCATCTGAGAACTGTCCGTC 60.068 52.381 0.00 0.00 0.00 4.79
4421 6977 1.737363 GCATCTGAGAACTGTCCGTCC 60.737 57.143 0.00 0.00 0.00 4.79
4465 7022 4.122776 CCATCCATAGTTTCTTGACTCGG 58.877 47.826 0.00 0.00 0.00 4.63
4526 7084 2.687425 TGGTTTGGATAATGTCATGCGG 59.313 45.455 0.00 0.00 0.00 5.69
4529 7087 0.105778 TGGATAATGTCATGCGGCGA 59.894 50.000 12.98 0.00 0.00 5.54
4535 7093 2.755836 ATGTCATGCGGCGATTTTAC 57.244 45.000 12.98 1.63 0.00 2.01
4549 9666 5.051240 GGCGATTTTACATAGTCCAACGTAG 60.051 44.000 0.00 0.00 0.00 3.51
4553 9670 7.487189 CGATTTTACATAGTCCAACGTAGAAGT 59.513 37.037 0.00 0.00 0.00 3.01
4557 9674 4.521639 ACATAGTCCAACGTAGAAGTGTGA 59.478 41.667 0.00 0.00 0.00 3.58
4562 9679 5.820947 AGTCCAACGTAGAAGTGTGAAAATT 59.179 36.000 0.00 0.00 0.00 1.82
4657 9775 9.620259 AATTTTTGCCTGTCCTATTTGTTAAAA 57.380 25.926 0.00 0.00 0.00 1.52
4693 9819 9.845305 GACGTAGATACCGAATAAAGATTTTTG 57.155 33.333 0.00 0.00 0.00 2.44
4751 9877 8.952278 TGCGGAAGTTATATTTAACATTCACTT 58.048 29.630 8.50 0.00 40.20 3.16
4811 9943 5.634118 ACCAGAAGAATGAAGATTCAACCA 58.366 37.500 0.00 0.00 40.59 3.67
4831 9963 4.534103 ACCAAGACTTGCTTAGAAGATCCT 59.466 41.667 9.85 0.00 34.31 3.24
4836 9968 4.837972 ACTTGCTTAGAAGATCCTTGGTC 58.162 43.478 0.00 0.00 0.00 4.02
4837 9969 4.287067 ACTTGCTTAGAAGATCCTTGGTCA 59.713 41.667 0.00 0.00 0.00 4.02
4838 9970 4.908601 TGCTTAGAAGATCCTTGGTCAA 57.091 40.909 0.00 0.00 0.00 3.18
4840 9972 5.003804 TGCTTAGAAGATCCTTGGTCAAAC 58.996 41.667 0.00 0.00 0.00 2.93
4842 9974 5.649831 GCTTAGAAGATCCTTGGTCAAACAT 59.350 40.000 0.00 0.00 0.00 2.71
4874 10006 0.252696 TGCACTAGGTGGATCCAGGT 60.253 55.000 16.81 7.93 39.02 4.00
4893 10025 5.403246 CAGGTAGTACACTTGTCATCAGTC 58.597 45.833 2.06 0.00 29.82 3.51
4903 10035 0.737715 GTCATCAGTCAGTGACCGGC 60.738 60.000 19.71 4.18 38.28 6.13
4912 10045 1.002134 AGTGACCGGCTGGGAAATG 60.002 57.895 18.00 0.00 40.75 2.32
4913 10046 1.002624 GTGACCGGCTGGGAAATGA 60.003 57.895 18.00 0.00 40.75 2.57
4970 10103 3.181397 CTGTGTTGAGTTGCTGTTTTGG 58.819 45.455 0.00 0.00 0.00 3.28
4975 10108 5.810074 GTGTTGAGTTGCTGTTTTGGTTATT 59.190 36.000 0.00 0.00 0.00 1.40
4987 10120 5.647658 TGTTTTGGTTATTCGCTGATCATCT 59.352 36.000 0.00 0.00 0.00 2.90
5040 10173 2.224305 ACAATATTCCAGTCCCTAGCGC 60.224 50.000 0.00 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 239 2.427245 CCTCTAGAGGTGGTGCCGG 61.427 68.421 28.12 0.00 43.61 6.13
308 315 2.608623 AGTACCATTTTGGCTTGGCTT 58.391 42.857 0.00 0.00 42.67 4.35
315 322 2.285977 CGGAGGTAGTACCATTTTGGC 58.714 52.381 21.49 1.81 42.67 4.52
316 323 3.528532 GACGGAGGTAGTACCATTTTGG 58.471 50.000 21.49 6.68 41.95 3.28
317 324 3.528532 GGACGGAGGTAGTACCATTTTG 58.471 50.000 21.49 8.51 41.95 2.44
335 342 4.117685 GTGAATGACTTATACACCGGGAC 58.882 47.826 6.32 0.00 0.00 4.46
336 343 4.028131 AGTGAATGACTTATACACCGGGA 58.972 43.478 6.32 0.00 32.76 5.14
337 344 4.402056 AGTGAATGACTTATACACCGGG 57.598 45.455 6.32 0.00 32.76 5.73
338 345 5.063438 CACAAGTGAATGACTTATACACCGG 59.937 44.000 0.00 0.00 43.52 5.28
339 346 5.867174 TCACAAGTGAATGACTTATACACCG 59.133 40.000 0.00 0.00 43.52 4.94
342 349 7.896811 AGTCTCACAAGTGAATGACTTATACA 58.103 34.615 15.37 0.00 43.52 2.29
344 351 8.354711 AGAGTCTCACAAGTGAATGACTTATA 57.645 34.615 19.64 0.00 43.52 0.98
347 354 5.543507 AGAGTCTCACAAGTGAATGACTT 57.456 39.130 19.64 11.12 46.52 3.01
348 355 5.543507 AAGAGTCTCACAAGTGAATGACT 57.456 39.130 19.07 19.07 43.42 3.41
349 356 7.093354 TCATAAGAGTCTCACAAGTGAATGAC 58.907 38.462 12.21 12.21 39.39 3.06
350 357 7.232118 TCATAAGAGTCTCACAAGTGAATGA 57.768 36.000 1.94 5.99 39.39 2.57
354 361 9.591792 CATTAATCATAAGAGTCTCACAAGTGA 57.408 33.333 1.94 2.56 38.06 3.41
355 362 9.376075 ACATTAATCATAAGAGTCTCACAAGTG 57.624 33.333 1.94 0.00 0.00 3.16
357 364 9.591792 TGACATTAATCATAAGAGTCTCACAAG 57.408 33.333 1.94 0.00 34.03 3.16
358 365 9.371136 GTGACATTAATCATAAGAGTCTCACAA 57.629 33.333 1.94 0.00 34.03 3.33
409 631 2.159421 GCATGCTCACAAACTCCATCAG 60.159 50.000 11.37 0.00 0.00 2.90
436 658 1.078143 CAAAGAAGGAGCGAGGGGG 60.078 63.158 0.00 0.00 0.00 5.40
471 693 4.631377 CAGATTCAACAAGCACCGAGAATA 59.369 41.667 0.00 0.00 0.00 1.75
472 694 3.438087 CAGATTCAACAAGCACCGAGAAT 59.562 43.478 0.00 0.00 0.00 2.40
524 755 2.109425 ATACAAGGCCTCGGAAACAC 57.891 50.000 5.23 0.00 0.00 3.32
628 859 3.568538 CACTGAATCCAAGAAAAAGGCG 58.431 45.455 0.00 0.00 0.00 5.52
631 862 3.985925 GCAGCACTGAATCCAAGAAAAAG 59.014 43.478 0.81 0.00 0.00 2.27
632 863 3.243839 GGCAGCACTGAATCCAAGAAAAA 60.244 43.478 0.81 0.00 0.00 1.94
637 868 0.809385 CAGGCAGCACTGAATCCAAG 59.191 55.000 0.81 0.00 40.97 3.61
639 870 1.001764 CCAGGCAGCACTGAATCCA 60.002 57.895 11.35 0.00 40.97 3.41
641 872 1.676635 TGCCAGGCAGCACTGAATC 60.677 57.895 11.22 3.05 40.97 2.52
642 873 2.437449 TGCCAGGCAGCACTGAAT 59.563 55.556 11.22 0.00 40.97 2.57
644 875 3.963687 CGATGCCAGGCAGCACTGA 62.964 63.158 28.84 0.00 45.92 3.41
645 876 3.506096 CGATGCCAGGCAGCACTG 61.506 66.667 28.84 9.59 45.92 3.66
647 878 3.503363 GACGATGCCAGGCAGCAC 61.503 66.667 28.84 17.89 45.92 4.40
648 879 4.783621 GGACGATGCCAGGCAGCA 62.784 66.667 28.84 0.60 45.92 4.41
649 880 4.783621 TGGACGATGCCAGGCAGC 62.784 66.667 20.52 20.52 43.65 5.25
672 903 6.814506 AAAATCTGGTTGAGAAGTGATGAG 57.185 37.500 0.00 0.00 33.12 2.90
673 904 7.000472 AGAAAAATCTGGTTGAGAAGTGATGA 59.000 34.615 0.00 0.00 33.12 2.92
692 923 3.253188 CGAGGCTGGATTGTTGAGAAAAA 59.747 43.478 0.00 0.00 0.00 1.94
693 924 2.813754 CGAGGCTGGATTGTTGAGAAAA 59.186 45.455 0.00 0.00 0.00 2.29
694 925 2.224523 ACGAGGCTGGATTGTTGAGAAA 60.225 45.455 2.65 0.00 0.00 2.52
695 926 1.347707 ACGAGGCTGGATTGTTGAGAA 59.652 47.619 2.65 0.00 0.00 2.87
697 928 1.734465 GAACGAGGCTGGATTGTTGAG 59.266 52.381 2.65 0.00 0.00 3.02
698 929 1.071542 TGAACGAGGCTGGATTGTTGA 59.928 47.619 2.65 0.00 0.00 3.18
700 931 2.496899 ATGAACGAGGCTGGATTGTT 57.503 45.000 2.65 0.00 0.00 2.83
701 932 2.236146 TGTATGAACGAGGCTGGATTGT 59.764 45.455 2.65 0.00 0.00 2.71
702 933 2.609459 GTGTATGAACGAGGCTGGATTG 59.391 50.000 2.65 0.00 0.00 2.67
703 934 2.738643 CGTGTATGAACGAGGCTGGATT 60.739 50.000 2.65 0.00 46.49 3.01
704 935 1.202417 CGTGTATGAACGAGGCTGGAT 60.202 52.381 2.65 0.00 46.49 3.41
705 936 0.172578 CGTGTATGAACGAGGCTGGA 59.827 55.000 2.65 0.00 46.49 3.86
739 970 0.600255 AGTTGTCTTCGCGTGGGAAG 60.600 55.000 17.69 17.69 43.78 3.46
751 982 5.694006 CACGATTTCTTCTCTTCAGTTGTCT 59.306 40.000 0.00 0.00 0.00 3.41
754 985 5.387855 CGTCACGATTTCTTCTCTTCAGTTG 60.388 44.000 0.00 0.00 0.00 3.16
774 1005 2.758009 CCGTAAAAAGAGGGTTCGTCA 58.242 47.619 0.00 0.00 0.00 4.35
775 1006 1.462283 GCCGTAAAAAGAGGGTTCGTC 59.538 52.381 0.00 0.00 0.00 4.20
777 1008 1.463444 CTGCCGTAAAAAGAGGGTTCG 59.537 52.381 0.00 0.00 0.00 3.95
778 1009 1.199327 GCTGCCGTAAAAAGAGGGTTC 59.801 52.381 0.00 0.00 0.00 3.62
810 1041 0.697079 CCTATCCTGCCATGGCTCAT 59.303 55.000 35.53 24.88 42.51 2.90
940 1992 4.830600 GGTGGTAGATGGGACTTTCAAAAA 59.169 41.667 0.00 0.00 0.00 1.94
941 1993 4.141135 TGGTGGTAGATGGGACTTTCAAAA 60.141 41.667 0.00 0.00 0.00 2.44
942 1994 3.396276 TGGTGGTAGATGGGACTTTCAAA 59.604 43.478 0.00 0.00 0.00 2.69
943 1995 2.983192 TGGTGGTAGATGGGACTTTCAA 59.017 45.455 0.00 0.00 0.00 2.69
944 1996 2.304761 GTGGTGGTAGATGGGACTTTCA 59.695 50.000 0.00 0.00 0.00 2.69
945 1997 2.572104 AGTGGTGGTAGATGGGACTTTC 59.428 50.000 0.00 0.00 0.00 2.62
946 1998 2.305927 CAGTGGTGGTAGATGGGACTTT 59.694 50.000 0.00 0.00 0.00 2.66
947 1999 1.909302 CAGTGGTGGTAGATGGGACTT 59.091 52.381 0.00 0.00 0.00 3.01
948 2000 1.573108 CAGTGGTGGTAGATGGGACT 58.427 55.000 0.00 0.00 0.00 3.85
949 2001 0.541863 CCAGTGGTGGTAGATGGGAC 59.458 60.000 0.00 0.00 39.30 4.46
950 2002 3.006061 CCAGTGGTGGTAGATGGGA 57.994 57.895 0.00 0.00 39.30 4.37
974 2027 3.261897 ACTCTCTGTGATGTGGGGTTTAG 59.738 47.826 0.00 0.00 0.00 1.85
1054 2111 2.122189 CCCCTCTCATCCCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
1055 2112 0.766288 CTTCCCCTCTCATCCCCTCC 60.766 65.000 0.00 0.00 0.00 4.30
1056 2113 0.766288 CCTTCCCCTCTCATCCCCTC 60.766 65.000 0.00 0.00 0.00 4.30
1057 2114 1.238896 TCCTTCCCCTCTCATCCCCT 61.239 60.000 0.00 0.00 0.00 4.79
1058 2115 0.766288 CTCCTTCCCCTCTCATCCCC 60.766 65.000 0.00 0.00 0.00 4.81
1059 2116 0.266152 TCTCCTTCCCCTCTCATCCC 59.734 60.000 0.00 0.00 0.00 3.85
1060 2117 2.158173 AGATCTCCTTCCCCTCTCATCC 60.158 54.545 0.00 0.00 0.00 3.51
1061 2118 3.165071 GAGATCTCCTTCCCCTCTCATC 58.835 54.545 12.00 0.00 34.00 2.92
1062 2119 2.521841 TGAGATCTCCTTCCCCTCTCAT 59.478 50.000 20.03 0.00 37.89 2.90
1063 2120 1.933051 TGAGATCTCCTTCCCCTCTCA 59.067 52.381 20.03 0.00 39.87 3.27
1486 2559 4.435436 TGCTGCTGGCCGTCGTAG 62.435 66.667 0.00 0.00 40.92 3.51
2137 3216 3.511146 AGTTTACCACATGGCATCCTTTG 59.489 43.478 0.00 0.00 39.32 2.77
2183 3262 1.188219 ATCCCGCACTCACTGACAGT 61.188 55.000 1.07 1.07 0.00 3.55
2185 3264 0.320683 CAATCCCGCACTCACTGACA 60.321 55.000 0.00 0.00 0.00 3.58
2189 3268 1.274703 ATCCCAATCCCGCACTCACT 61.275 55.000 0.00 0.00 0.00 3.41
2477 3556 2.666812 GTACCCAGAACCACCCCG 59.333 66.667 0.00 0.00 0.00 5.73
2512 3591 1.004628 CCATCAGACAACATGGTCCCA 59.995 52.381 0.00 0.00 38.59 4.37
2515 3594 2.636830 CTCCCATCAGACAACATGGTC 58.363 52.381 0.00 0.00 38.37 4.02
2516 3595 1.340405 GCTCCCATCAGACAACATGGT 60.340 52.381 0.00 0.00 38.37 3.55
2549 3628 0.536460 GGGCGAGTGGAAAGGTTTGA 60.536 55.000 0.00 0.00 0.00 2.69
2552 3631 1.073199 CAGGGCGAGTGGAAAGGTT 59.927 57.895 0.00 0.00 0.00 3.50
2593 3672 8.082852 CGGATATTGTAGCTGACATTAAGTAGT 58.917 37.037 0.00 0.00 38.07 2.73
2594 3673 8.297426 TCGGATATTGTAGCTGACATTAAGTAG 58.703 37.037 0.00 0.00 38.07 2.57
2620 3699 3.386932 AGTGACCAATGCCCAACATAT 57.613 42.857 0.00 0.00 38.34 1.78
2631 3710 5.278957 GGTTGAAATGTTGCTAGTGACCAAT 60.279 40.000 0.00 0.00 0.00 3.16
2653 3732 2.125512 GCCGAGATCTGTTGCGGT 60.126 61.111 18.62 0.00 45.22 5.68
2655 3734 3.257561 CCGCCGAGATCTGTTGCG 61.258 66.667 18.31 18.31 44.47 4.85
2872 3951 4.471025 TGGCCTATGTACATCCCATATGAG 59.529 45.833 12.68 1.20 0.00 2.90
2924 4003 2.353610 GGGCCATGGTGCTTTCCAG 61.354 63.158 14.67 0.00 41.05 3.86
3043 4123 1.292223 GTAACCCAGAGCGAGCACA 59.708 57.895 0.00 0.00 0.00 4.57
3731 6206 2.159352 GCTTCCGTCTCTTGGAGTAGAC 60.159 54.545 0.00 0.00 39.00 2.59
3735 6210 0.832135 TGGCTTCCGTCTCTTGGAGT 60.832 55.000 0.00 0.00 36.72 3.85
3820 6295 5.212745 CCCTCCTCTACTTCCACTTATCTT 58.787 45.833 0.00 0.00 0.00 2.40
4013 6525 4.542735 GGAACGTCAACCATAAACCAAAG 58.457 43.478 0.00 0.00 0.00 2.77
4028 6540 1.226746 CCAGAACAACAGGGAACGTC 58.773 55.000 0.00 0.00 0.00 4.34
4041 6553 2.237392 AGCCCTGACTGAATACCAGAAC 59.763 50.000 0.00 0.00 45.78 3.01
4064 6576 6.712276 ACATAAATCTACCTGGGCTAATAGC 58.288 40.000 3.17 3.17 41.46 2.97
4065 6577 8.037758 CAGACATAAATCTACCTGGGCTAATAG 58.962 40.741 0.00 0.00 0.00 1.73
4066 6578 7.733047 TCAGACATAAATCTACCTGGGCTAATA 59.267 37.037 0.00 0.00 0.00 0.98
4067 6579 6.558775 TCAGACATAAATCTACCTGGGCTAAT 59.441 38.462 0.00 0.00 0.00 1.73
4068 6580 5.903010 TCAGACATAAATCTACCTGGGCTAA 59.097 40.000 0.00 0.00 0.00 3.09
4069 6581 5.464069 TCAGACATAAATCTACCTGGGCTA 58.536 41.667 0.00 0.00 0.00 3.93
4070 6582 4.298626 TCAGACATAAATCTACCTGGGCT 58.701 43.478 0.00 0.00 0.00 5.19
4071 6583 4.689612 TCAGACATAAATCTACCTGGGC 57.310 45.455 0.00 0.00 0.00 5.36
4072 6584 6.425114 CGAATTCAGACATAAATCTACCTGGG 59.575 42.308 6.22 0.00 0.00 4.45
4073 6585 6.986817 ACGAATTCAGACATAAATCTACCTGG 59.013 38.462 6.22 0.00 0.00 4.45
4074 6586 8.331022 CAACGAATTCAGACATAAATCTACCTG 58.669 37.037 6.22 0.00 0.00 4.00
4079 6591 7.921786 TTCCAACGAATTCAGACATAAATCT 57.078 32.000 6.22 0.00 0.00 2.40
4085 6597 8.400947 CAGATTAATTCCAACGAATTCAGACAT 58.599 33.333 6.22 0.00 43.79 3.06
4141 6657 4.875544 ACACTACACATCAAACACACAC 57.124 40.909 0.00 0.00 0.00 3.82
4142 6658 5.049749 GCATACACTACACATCAAACACACA 60.050 40.000 0.00 0.00 0.00 3.72
4152 6668 3.384789 ACTCGGATGCATACACTACACAT 59.615 43.478 10.18 0.00 0.00 3.21
4160 6676 1.485124 ACAGGACTCGGATGCATACA 58.515 50.000 10.18 0.00 0.00 2.29
4174 6690 4.513406 AACAGTAAACAGGGAAACAGGA 57.487 40.909 0.00 0.00 0.00 3.86
4180 6697 5.379187 GGTAGGAAAACAGTAAACAGGGAA 58.621 41.667 0.00 0.00 0.00 3.97
4183 6700 4.077108 GGGGTAGGAAAACAGTAAACAGG 58.923 47.826 0.00 0.00 0.00 4.00
4204 6721 2.554370 TTCAAGAAACTACGGGTGGG 57.446 50.000 0.00 0.00 0.00 4.61
4205 6722 3.818773 ACAATTCAAGAAACTACGGGTGG 59.181 43.478 0.00 0.00 0.00 4.61
4208 6725 5.682943 TCAACAATTCAAGAAACTACGGG 57.317 39.130 0.00 0.00 0.00 5.28
4211 6728 9.750125 AAAGGAATCAACAATTCAAGAAACTAC 57.250 29.630 0.72 0.00 44.81 2.73
4225 6742 5.083122 TGGCAATAGGAAAAGGAATCAACA 58.917 37.500 0.00 0.00 0.00 3.33
4256 6773 8.959676 AATAACAAGGAGGGTAAACCATAAAA 57.040 30.769 0.81 0.00 43.89 1.52
4316 6836 0.517316 ACGAATTCGCAGGCAGAAAC 59.483 50.000 27.03 0.00 44.43 2.78
4349 6889 3.118811 AGAGCTCATAGCAAGAACAGGTC 60.119 47.826 17.77 0.00 45.56 3.85
4373 6913 1.874231 ACACAACACAAACACACGACA 59.126 42.857 0.00 0.00 0.00 4.35
4389 6937 2.566724 TCTCAGATGCATACACCACACA 59.433 45.455 0.00 0.00 0.00 3.72
4390 6938 3.251479 TCTCAGATGCATACACCACAC 57.749 47.619 0.00 0.00 0.00 3.82
4391 6939 3.261643 AGTTCTCAGATGCATACACCACA 59.738 43.478 0.00 0.00 0.00 4.17
4392 6940 3.620374 CAGTTCTCAGATGCATACACCAC 59.380 47.826 0.00 0.00 0.00 4.16
4393 6941 3.261643 ACAGTTCTCAGATGCATACACCA 59.738 43.478 0.00 0.00 0.00 4.17
4394 6942 3.866651 ACAGTTCTCAGATGCATACACC 58.133 45.455 0.00 0.00 0.00 4.16
4417 6973 2.701073 AAACAGTAGACAGACGGACG 57.299 50.000 0.00 0.00 0.00 4.79
4418 6974 3.005578 AGGAAAACAGTAGACAGACGGAC 59.994 47.826 0.00 0.00 0.00 4.79
4419 6975 3.228453 AGGAAAACAGTAGACAGACGGA 58.772 45.455 0.00 0.00 0.00 4.69
4420 6976 3.662247 AGGAAAACAGTAGACAGACGG 57.338 47.619 0.00 0.00 0.00 4.79
4421 6977 4.483311 GGTAGGAAAACAGTAGACAGACG 58.517 47.826 0.00 0.00 0.00 4.18
4465 7022 0.835941 AGGCATCTCAGATGGACCAC 59.164 55.000 16.70 0.00 0.00 4.16
4526 7084 4.852609 ACGTTGGACTATGTAAAATCGC 57.147 40.909 0.00 0.00 0.00 4.58
4529 7087 8.092687 ACACTTCTACGTTGGACTATGTAAAAT 58.907 33.333 0.00 0.00 0.00 1.82
4535 7093 5.055642 TCACACTTCTACGTTGGACTATG 57.944 43.478 0.00 0.00 0.00 2.23
4637 9755 5.010213 GTGGTTTTAACAAATAGGACAGGCA 59.990 40.000 0.00 0.00 0.00 4.75
4640 9758 6.715264 AGGAGTGGTTTTAACAAATAGGACAG 59.285 38.462 0.00 0.00 0.00 3.51
4657 9775 2.559440 GTATCTACGTCGAGGAGTGGT 58.441 52.381 12.85 0.39 30.93 4.16
4693 9819 2.863809 TGAAAGCTCAACCTTCCCTTC 58.136 47.619 0.00 0.00 0.00 3.46
4787 9918 6.778821 TGGTTGAATCTTCATTCTTCTGGTA 58.221 36.000 0.00 0.00 39.49 3.25
4811 9943 5.013599 ACCAAGGATCTTCTAAGCAAGTCTT 59.986 40.000 0.00 0.00 38.79 3.01
4831 9963 7.372714 CAGATTCTTGATGAATGTTTGACCAA 58.627 34.615 0.00 0.00 44.70 3.67
4836 9968 6.387465 AGTGCAGATTCTTGATGAATGTTTG 58.613 36.000 0.00 0.00 44.70 2.93
4837 9969 6.585695 AGTGCAGATTCTTGATGAATGTTT 57.414 33.333 0.00 0.00 44.70 2.83
4838 9970 6.318144 CCTAGTGCAGATTCTTGATGAATGTT 59.682 38.462 0.00 0.00 44.70 2.71
4840 9972 5.821470 ACCTAGTGCAGATTCTTGATGAATG 59.179 40.000 0.00 0.00 44.70 2.67
4842 9974 5.181009 CACCTAGTGCAGATTCTTGATGAA 58.819 41.667 0.00 0.00 39.24 2.57
4874 10006 5.768164 TCACTGACTGATGACAAGTGTACTA 59.232 40.000 0.00 0.00 0.00 1.82
4893 10025 1.002134 ATTTCCCAGCCGGTCACTG 60.002 57.895 1.90 1.28 34.82 3.66
4903 10035 3.652057 ACCATACCAGTCATTTCCCAG 57.348 47.619 0.00 0.00 0.00 4.45
4912 10045 4.104420 TCCTCCTACTCTACCATACCAGTC 59.896 50.000 0.00 0.00 0.00 3.51
4913 10046 4.052922 TCCTCCTACTCTACCATACCAGT 58.947 47.826 0.00 0.00 0.00 4.00
4955 10088 4.791411 GCGAATAACCAAAACAGCAACTCA 60.791 41.667 0.00 0.00 0.00 3.41
4970 10103 8.247562 AGGAACTATAGATGATCAGCGAATAAC 58.752 37.037 6.78 3.37 36.02 1.89
4975 10108 4.460731 CCAGGAACTATAGATGATCAGCGA 59.539 45.833 6.78 0.00 36.02 4.93
4987 10120 2.868964 AGGAGGCACCAGGAACTATA 57.131 50.000 3.18 0.00 42.04 1.31


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

AutoCloner maintained by Alex Coulton.