Multiple sequence alignment - TraesCS2D01G256000

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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 TraesCS2D01G256000 chr2D 100.000 3947 0 0 1 3947 309067464 309063518 0.000000e+00 7289.0
1 TraesCS2D01G256000 chr2D 100.000 3421 0 0 4301 7721 309063164 309059744 0.000000e+00 6318.0
2 TraesCS2D01G256000 chr2D 94.748 457 21 3 1 454 517193777 517193321 0.000000e+00 708.0
3 TraesCS2D01G256000 chr2D 80.205 293 46 11 6059 6345 574656799 574657085 7.850000e-50 209.0
4 TraesCS2D01G256000 chr2D 80.000 80 8 4 1815 1894 516650315 516650386 1.400000e-02 52.8
5 TraesCS2D01G256000 chr2A 94.039 2634 90 29 5138 7721 430707147 430709763 0.000000e+00 3932.0
6 TraesCS2D01G256000 chr2A 92.442 2117 92 24 744 2834 430704366 430706440 0.000000e+00 2961.0
7 TraesCS2D01G256000 chr2A 97.076 342 9 1 4644 4984 430706430 430706771 6.720000e-160 575.0
8 TraesCS2D01G256000 chr2A 94.907 216 7 3 4968 5180 430706941 430707155 1.240000e-87 335.0
9 TraesCS2D01G256000 chr2A 94.554 202 11 0 550 751 430689669 430689870 5.820000e-81 313.0
10 TraesCS2D01G256000 chr2A 75.000 516 97 26 6059 6567 713016598 713017088 7.850000e-50 209.0
11 TraesCS2D01G256000 chr2A 73.230 452 96 21 6141 6584 587405897 587406331 2.900000e-29 141.0
12 TraesCS2D01G256000 chr2A 79.695 197 34 3 7524 7719 755249797 755249606 3.760000e-28 137.0
13 TraesCS2D01G256000 chr2A 75.966 233 47 5 1237 1463 564098441 564098670 2.280000e-20 111.0
14 TraesCS2D01G256000 chr2A 100.000 28 0 0 1867 1894 660503072 660503099 1.400000e-02 52.8
15 TraesCS2D01G256000 chr2B 95.036 1793 57 17 5148 6915 359132984 359134769 0.000000e+00 2789.0
16 TraesCS2D01G256000 chr2B 92.920 1921 85 19 559 2449 359130086 359131985 0.000000e+00 2747.0
17 TraesCS2D01G256000 chr2B 96.950 787 23 1 6936 7721 359176677 359177463 0.000000e+00 1319.0
18 TraesCS2D01G256000 chr2B 91.354 960 78 4 2831 3787 31605932 31604975 0.000000e+00 1308.0
19 TraesCS2D01G256000 chr2B 92.871 505 20 11 4644 5138 359132270 359132768 0.000000e+00 719.0
20 TraesCS2D01G256000 chr2B 92.488 426 31 1 3476 3901 122441895 122441471 6.630000e-170 608.0
21 TraesCS2D01G256000 chr2B 93.023 301 15 3 2539 2834 359131981 359132280 1.190000e-117 435.0
22 TraesCS2D01G256000 chr2B 75.629 517 95 26 6059 6567 690931108 690931601 2.170000e-55 228.0
23 TraesCS2D01G256000 chr2B 78.086 324 59 11 1933 2246 589087491 589087812 2.200000e-45 195.0
24 TraesCS2D01G256000 chr2B 92.727 110 5 2 4514 4623 122440861 122440755 1.040000e-33 156.0
25 TraesCS2D01G256000 chr2B 73.128 454 93 23 6141 6584 523234236 523234670 1.350000e-27 135.0
26 TraesCS2D01G256000 chr2B 77.209 215 40 5 1255 1463 498427109 498426898 4.900000e-22 117.0
27 TraesCS2D01G256000 chr2B 92.500 40 3 0 1867 1906 608364753 608364792 3.010000e-04 58.4
28 TraesCS2D01G256000 chr5D 90.451 1152 70 17 2834 3947 370715424 370716573 0.000000e+00 1482.0
29 TraesCS2D01G256000 chr1B 89.199 1148 86 17 2830 3947 334687363 334688502 0.000000e+00 1399.0
30 TraesCS2D01G256000 chr1B 93.883 703 40 2 2831 3531 502945933 502946634 0.000000e+00 1057.0
31 TraesCS2D01G256000 chr1B 93.192 426 29 0 3476 3901 502946695 502947120 1.830000e-175 627.0
32 TraesCS2D01G256000 chr1B 74.561 456 94 16 6117 6567 482697876 482698314 6.160000e-41 180.0
33 TraesCS2D01G256000 chr1B 94.737 114 6 0 4301 4414 334689039 334689152 2.210000e-40 178.0
34 TraesCS2D01G256000 chr1B 80.342 234 39 7 1237 1466 482696936 482697166 3.700000e-38 171.0
35 TraesCS2D01G256000 chr1B 93.519 108 6 1 4515 4622 502947671 502947777 8.020000e-35 159.0
36 TraesCS2D01G256000 chr6B 95.007 701 32 2 2830 3528 173799723 173799024 0.000000e+00 1098.0
37 TraesCS2D01G256000 chr6B 93.662 426 27 0 3476 3901 173798989 173798564 8.450000e-179 638.0
38 TraesCS2D01G256000 chr6B 83.750 400 51 10 7322 7719 129603616 129604003 4.400000e-97 366.0
39 TraesCS2D01G256000 chr6B 88.889 198 20 2 7524 7719 129553111 129553308 7.740000e-60 243.0
40 TraesCS2D01G256000 chr6B 95.370 108 4 1 4515 4622 173798121 173798015 3.700000e-38 171.0
41 TraesCS2D01G256000 chr6B 79.237 236 43 4 1940 2174 276744202 276743972 8.020000e-35 159.0
42 TraesCS2D01G256000 chr7B 94.729 702 34 2 2832 3531 231724371 231723671 0.000000e+00 1088.0
43 TraesCS2D01G256000 chr7B 93.447 702 43 2 2832 3531 517318215 517318915 0.000000e+00 1038.0
44 TraesCS2D01G256000 chr7B 93.976 415 25 0 3476 3890 231723610 231723196 5.090000e-176 628.0
45 TraesCS2D01G256000 chr7B 90.254 472 44 2 3476 3947 733261087 733260618 3.960000e-172 616.0
46 TraesCS2D01G256000 chr7B 84.464 560 62 19 1 543 750214961 750215512 5.310000e-146 529.0
47 TraesCS2D01G256000 chr7B 95.413 109 4 1 4515 4623 231722999 231722892 1.030000e-38 172.0
48 TraesCS2D01G256000 chr5B 94.269 698 37 2 2831 3526 358621568 358620872 0.000000e+00 1064.0
49 TraesCS2D01G256000 chr5B 91.547 556 36 9 1 546 185537550 185538104 0.000000e+00 756.0
50 TraesCS2D01G256000 chr5B 92.258 155 11 1 7353 7507 194135934 194136087 1.300000e-52 219.0
51 TraesCS2D01G256000 chr5B 94.643 112 6 0 4312 4423 358619888 358619777 2.860000e-39 174.0
52 TraesCS2D01G256000 chr5B 94.340 106 5 1 4515 4620 527148692 527148796 2.230000e-35 161.0
53 TraesCS2D01G256000 chr5B 97.143 35 0 1 1867 1901 668192214 668192247 3.010000e-04 58.4
54 TraesCS2D01G256000 chr3D 94.017 702 39 2 2832 3531 170543174 170543874 0.000000e+00 1061.0
55 TraesCS2D01G256000 chr3D 91.176 272 20 4 206 475 560700693 560700962 4.400000e-97 366.0
56 TraesCS2D01G256000 chr3D 86.432 199 26 1 7524 7721 354612845 354613043 4.690000e-52 217.0
57 TraesCS2D01G256000 chr3D 81.910 199 34 2 1237 1434 497722681 497722484 4.790000e-37 167.0
58 TraesCS2D01G256000 chr3D 96.739 92 3 0 4425 4516 581041406 581041497 3.730000e-33 154.0
59 TraesCS2D01G256000 chr7A 93.466 704 43 3 2830 3531 464568553 464567851 0.000000e+00 1042.0
60 TraesCS2D01G256000 chr7A 84.358 537 59 19 1 520 42733170 42733698 3.220000e-138 503.0
61 TraesCS2D01G256000 chr1D 91.950 559 34 9 1 549 19525483 19524926 0.000000e+00 773.0
62 TraesCS2D01G256000 chr1D 94.928 414 20 1 3477 3890 408966009 408965597 0.000000e+00 647.0
63 TraesCS2D01G256000 chr1D 85.053 562 54 15 4 543 467388349 467388902 5.270000e-151 545.0
64 TraesCS2D01G256000 chr1D 85.930 398 45 9 7327 7717 488581482 488581875 1.550000e-111 414.0
65 TraesCS2D01G256000 chr1D 97.541 122 3 0 4301 4422 408965207 408965086 7.850000e-50 209.0
66 TraesCS2D01G256000 chr1D 80.804 224 37 6 1237 1457 360467202 360467422 3.700000e-38 171.0
67 TraesCS2D01G256000 chr1D 94.545 110 5 1 4515 4624 408965073 408964965 1.330000e-37 169.0
68 TraesCS2D01G256000 chr1D 96.703 91 3 0 4426 4516 414917483 414917393 1.340000e-32 152.0
69 TraesCS2D01G256000 chr4A 90.586 563 34 12 1 546 655655326 655655886 0.000000e+00 728.0
70 TraesCS2D01G256000 chr4A 84.353 556 59 20 1 538 731088442 731088987 3.190000e-143 520.0
71 TraesCS2D01G256000 chr5A 89.910 555 47 7 3 548 73824260 73823706 0.000000e+00 706.0
72 TraesCS2D01G256000 chr5A 88.172 186 22 0 7322 7507 200328035 200327850 1.010000e-53 222.0
73 TraesCS2D01G256000 chr3A 91.755 473 38 1 3476 3947 691398364 691398836 0.000000e+00 656.0
74 TraesCS2D01G256000 chr3A 84.615 182 27 1 7541 7721 473206259 473206440 6.160000e-41 180.0
75 TraesCS2D01G256000 chr3A 94.737 114 6 0 4303 4416 691398886 691398999 2.210000e-40 178.0
76 TraesCS2D01G256000 chr3A 81.407 199 35 2 1237 1434 636859663 636859860 2.230000e-35 161.0
77 TraesCS2D01G256000 chr3A 96.842 95 3 0 4321 4415 495016569 495016475 8.020000e-35 159.0
78 TraesCS2D01G256000 chr3A 94.737 38 2 0 1867 1904 202594294 202594257 8.370000e-05 60.2
79 TraesCS2D01G256000 chrUn 85.194 412 47 7 7322 7721 2217085 2216676 2.010000e-110 411.0
80 TraesCS2D01G256000 chrUn 83.498 303 40 7 7424 7718 2215540 2215240 2.750000e-69 274.0
81 TraesCS2D01G256000 chrUn 97.727 88 2 0 4429 4516 216513687 216513600 1.340000e-32 152.0
82 TraesCS2D01G256000 chrUn 96.703 91 3 0 4426 4516 286269693 286269783 1.340000e-32 152.0
83 TraesCS2D01G256000 chrUn 97.727 88 2 0 4429 4516 379971460 379971373 1.340000e-32 152.0
84 TraesCS2D01G256000 chrUn 96.703 91 3 0 4426 4516 410662104 410662194 1.340000e-32 152.0
85 TraesCS2D01G256000 chrUn 96.703 91 3 0 4426 4516 420150337 420150427 1.340000e-32 152.0
86 TraesCS2D01G256000 chr3B 87.273 165 21 0 7557 7721 455056402 455056566 1.020000e-43 189.0
87 TraesCS2D01G256000 chr3B 79.899 199 38 2 1237 1434 657782393 657782196 2.250000e-30 145.0
88 TraesCS2D01G256000 chr1A 74.672 458 90 20 6117 6567 460281896 460282334 6.160000e-41 180.0
89 TraesCS2D01G256000 chr7D 81.081 222 40 2 1237 1457 502231650 502231870 7.960000e-40 176.0
90 TraesCS2D01G256000 chr7D 97.143 35 1 0 1867 1901 167525864 167525830 8.370000e-05 60.2
91 TraesCS2D01G256000 chr6D 96.703 91 3 0 4426 4516 168262585 168262675 1.340000e-32 152.0
92 TraesCS2D01G256000 chr6A 96.703 91 3 0 4426 4516 84401418 84401508 1.340000e-32 152.0
93 TraesCS2D01G256000 chr4D 96.970 33 1 0 1867 1899 504324951 504324983 1.000000e-03 56.5


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 TraesCS2D01G256000 chr2D 309059744 309067464 7720 True 6803.500000 7289 100.000000 1 7721 2 chr2D.!!$R2 7720
1 TraesCS2D01G256000 chr2A 430704366 430709763 5397 False 1950.750000 3932 94.616000 744 7721 4 chr2A.!!$F6 6977
2 TraesCS2D01G256000 chr2B 359130086 359134769 4683 False 1672.500000 2789 93.462500 559 6915 4 chr2B.!!$F6 6356
3 TraesCS2D01G256000 chr2B 359176677 359177463 786 False 1319.000000 1319 96.950000 6936 7721 1 chr2B.!!$F1 785
4 TraesCS2D01G256000 chr2B 31604975 31605932 957 True 1308.000000 1308 91.354000 2831 3787 1 chr2B.!!$R1 956
5 TraesCS2D01G256000 chr2B 122440755 122441895 1140 True 382.000000 608 92.607500 3476 4623 2 chr2B.!!$R3 1147
6 TraesCS2D01G256000 chr5D 370715424 370716573 1149 False 1482.000000 1482 90.451000 2834 3947 1 chr5D.!!$F1 1113
7 TraesCS2D01G256000 chr1B 334687363 334689152 1789 False 788.500000 1399 91.968000 2830 4414 2 chr1B.!!$F1 1584
8 TraesCS2D01G256000 chr1B 502945933 502947777 1844 False 614.333333 1057 93.531333 2831 4622 3 chr1B.!!$F3 1791
9 TraesCS2D01G256000 chr6B 173798015 173799723 1708 True 635.666667 1098 94.679667 2830 4622 3 chr6B.!!$R2 1792
10 TraesCS2D01G256000 chr7B 517318215 517318915 700 False 1038.000000 1038 93.447000 2832 3531 1 chr7B.!!$F1 699
11 TraesCS2D01G256000 chr7B 231722892 231724371 1479 True 629.333333 1088 94.706000 2832 4623 3 chr7B.!!$R2 1791
12 TraesCS2D01G256000 chr7B 750214961 750215512 551 False 529.000000 529 84.464000 1 543 1 chr7B.!!$F2 542
13 TraesCS2D01G256000 chr5B 185537550 185538104 554 False 756.000000 756 91.547000 1 546 1 chr5B.!!$F1 545
14 TraesCS2D01G256000 chr5B 358619777 358621568 1791 True 619.000000 1064 94.456000 2831 4423 2 chr5B.!!$R1 1592
15 TraesCS2D01G256000 chr3D 170543174 170543874 700 False 1061.000000 1061 94.017000 2832 3531 1 chr3D.!!$F1 699
16 TraesCS2D01G256000 chr7A 464567851 464568553 702 True 1042.000000 1042 93.466000 2830 3531 1 chr7A.!!$R1 701
17 TraesCS2D01G256000 chr7A 42733170 42733698 528 False 503.000000 503 84.358000 1 520 1 chr7A.!!$F1 519
18 TraesCS2D01G256000 chr1D 19524926 19525483 557 True 773.000000 773 91.950000 1 549 1 chr1D.!!$R1 548
19 TraesCS2D01G256000 chr1D 467388349 467388902 553 False 545.000000 545 85.053000 4 543 1 chr1D.!!$F2 539
20 TraesCS2D01G256000 chr1D 408964965 408966009 1044 True 341.666667 647 95.671333 3477 4624 3 chr1D.!!$R3 1147
21 TraesCS2D01G256000 chr4A 655655326 655655886 560 False 728.000000 728 90.586000 1 546 1 chr4A.!!$F1 545
22 TraesCS2D01G256000 chr4A 731088442 731088987 545 False 520.000000 520 84.353000 1 538 1 chr4A.!!$F2 537
23 TraesCS2D01G256000 chr5A 73823706 73824260 554 True 706.000000 706 89.910000 3 548 1 chr5A.!!$R1 545
24 TraesCS2D01G256000 chr3A 691398364 691398999 635 False 417.000000 656 93.246000 3476 4416 2 chr3A.!!$F3 940
25 TraesCS2D01G256000 chrUn 2215240 2217085 1845 True 342.500000 411 84.346000 7322 7721 2 chrUn.!!$R3 399

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
84 86 0.179037 ATGATCTGACCGCCACCATG 60.179 55.000 0.0 0.0 0.00 3.66 F
314 317 0.748005 GCGCTGGGGTATGATTGTGT 60.748 55.000 0.0 0.0 0.00 3.72 F
1187 1210 0.868602 GTGCCATGCGTGCAATCATC 60.869 55.000 0.0 0.0 41.06 2.92 F
2119 2160 1.077169 AGGGGATTTGACTGGGTTTCC 59.923 52.381 0.0 0.0 0.00 3.13 F
2886 2940 0.665835 GCATCGACCAACAACAACCA 59.334 50.000 0.0 0.0 0.00 3.67 F
4486 5880 0.178944 TGGGGGAGTCAGAGTCGAAA 60.179 55.000 0.0 0.0 0.00 3.46 F
4625 6020 0.466922 GACTCGGGAGGGGAACGATA 60.467 60.000 0.0 0.0 35.93 2.92 F
4627 6022 0.467659 CTCGGGAGGGGAACGATACT 60.468 60.000 0.0 0.0 35.93 2.12 F
4628 6023 0.466922 TCGGGAGGGGAACGATACTC 60.467 60.000 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2029 1.506028 GGGATCAACCAACCCCCTCA 61.506 60.000 0.0 0.0 41.20 3.86 R
2086 2127 0.552367 ATCCCCTGACAACCCCATGA 60.552 55.000 0.0 0.0 0.00 3.07 R
2720 2771 0.179094 CTAACCCGCGCCAATACAGA 60.179 55.000 0.0 0.0 0.00 3.41 R
3103 3157 1.945580 AGGGGAAACTCTGACTCTCC 58.054 55.000 0.0 0.0 42.28 3.71 R
4498 5892 0.026027 GCGCATGAGAGAAAGAAGCG 59.974 55.000 0.3 0.0 45.68 4.68 R
5919 7740 0.823356 GCACTGGTCTGCCAAAGGAA 60.823 55.000 0.0 0.0 45.51 3.36 R
6540 8372 2.297698 TCTCAACGGGGAAGTAGACA 57.702 50.000 0.0 0.0 0.00 3.41 R
6705 8537 6.697892 CGAATAGATGTTAGGAGACCTTGAAC 59.302 42.308 0.0 0.0 34.61 3.18 R
6789 8631 7.344095 AGATTAAAGCATGAAAGAGGGATTG 57.656 36.000 0.0 0.0 0.00 2.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 0.179037 ATGATCTGACCGCCACCATG 60.179 55.000 0.00 0.00 0.00 3.66
100 102 1.667830 ATGTTGTGTCGTCGGCCTG 60.668 57.895 0.00 0.00 0.00 4.85
179 181 1.693083 CGTCGTGGCCTTCCGATTTC 61.693 60.000 14.20 3.47 35.30 2.17
294 297 2.305928 GCCCCATGTACATGCATACAA 58.694 47.619 27.27 0.00 38.53 2.41
314 317 0.748005 GCGCTGGGGTATGATTGTGT 60.748 55.000 0.00 0.00 0.00 3.72
323 326 0.998669 TATGATTGTGTGCGCAGACG 59.001 50.000 29.49 0.00 44.07 4.18
489 506 2.367107 GGGGGAGGGAGGAAGGTC 60.367 72.222 0.00 0.00 0.00 3.85
490 507 2.454941 GGGGAGGGAGGAAGGTCA 59.545 66.667 0.00 0.00 0.00 4.02
491 508 1.690985 GGGGAGGGAGGAAGGTCAG 60.691 68.421 0.00 0.00 0.00 3.51
492 509 2.371259 GGGAGGGAGGAAGGTCAGC 61.371 68.421 0.00 0.00 0.00 4.26
493 510 2.726351 GGAGGGAGGAAGGTCAGCG 61.726 68.421 0.00 0.00 0.00 5.18
494 511 2.685380 AGGGAGGAAGGTCAGCGG 60.685 66.667 0.00 0.00 0.00 5.52
495 512 4.475135 GGGAGGAAGGTCAGCGGC 62.475 72.222 0.00 0.00 0.00 6.53
496 513 3.394836 GGAGGAAGGTCAGCGGCT 61.395 66.667 0.00 0.00 0.00 5.52
497 514 2.125350 GAGGAAGGTCAGCGGCTG 60.125 66.667 23.72 23.72 0.00 4.85
498 515 3.672295 GAGGAAGGTCAGCGGCTGG 62.672 68.421 28.18 11.17 31.51 4.85
499 516 4.785453 GGAAGGTCAGCGGCTGGG 62.785 72.222 28.18 5.52 31.51 4.45
500 517 3.706373 GAAGGTCAGCGGCTGGGA 61.706 66.667 28.18 8.76 31.51 4.37
501 518 3.959991 GAAGGTCAGCGGCTGGGAC 62.960 68.421 28.18 19.69 31.51 4.46
506 523 4.077184 CAGCGGCTGGGACGGTAA 62.077 66.667 22.11 0.00 45.34 2.85
507 524 3.771160 AGCGGCTGGGACGGTAAG 61.771 66.667 0.00 0.00 45.24 2.34
508 525 4.832608 GCGGCTGGGACGGTAAGG 62.833 72.222 0.00 0.00 36.83 2.69
509 526 3.387947 CGGCTGGGACGGTAAGGT 61.388 66.667 0.00 0.00 36.83 3.50
510 527 2.582978 GGCTGGGACGGTAAGGTC 59.417 66.667 0.00 0.00 36.83 3.85
516 533 2.362889 GACGGTAAGGTCCCCCGA 60.363 66.667 16.70 0.00 44.41 5.14
517 534 2.363406 ACGGTAAGGTCCCCCGAG 60.363 66.667 16.70 0.00 44.41 4.63
518 535 2.363406 CGGTAAGGTCCCCCGAGT 60.363 66.667 6.41 0.00 44.41 4.18
519 536 2.421399 CGGTAAGGTCCCCCGAGTC 61.421 68.421 6.41 0.00 44.41 3.36
520 537 2.421399 GGTAAGGTCCCCCGAGTCG 61.421 68.421 5.29 5.29 35.12 4.18
521 538 2.757099 TAAGGTCCCCCGAGTCGC 60.757 66.667 7.12 0.00 35.12 5.19
552 569 4.241555 CGCGAGGGCTGGGCTAAT 62.242 66.667 0.00 0.00 36.88 1.73
553 570 2.592861 GCGAGGGCTGGGCTAATG 60.593 66.667 0.00 0.00 35.83 1.90
554 571 2.111878 CGAGGGCTGGGCTAATGG 59.888 66.667 0.00 0.00 0.00 3.16
555 572 2.746375 CGAGGGCTGGGCTAATGGT 61.746 63.158 0.00 0.00 0.00 3.55
556 573 1.149401 GAGGGCTGGGCTAATGGTC 59.851 63.158 0.00 0.00 0.00 4.02
557 574 2.195956 GGGCTGGGCTAATGGTCC 59.804 66.667 0.00 0.00 40.85 4.46
572 589 3.323622 TCCGCATTGGAGATGCCT 58.676 55.556 5.51 0.00 43.74 4.75
575 592 1.211703 TCCGCATTGGAGATGCCTTTA 59.788 47.619 5.51 0.00 43.74 1.85
581 598 4.521146 CATTGGAGATGCCTTTACTGAGT 58.479 43.478 0.00 0.00 37.63 3.41
584 601 3.133003 TGGAGATGCCTTTACTGAGTAGC 59.867 47.826 0.00 0.00 37.63 3.58
618 638 3.879892 GACGGTAGGAGTAGTACGGAAAT 59.120 47.826 0.00 0.00 0.00 2.17
684 704 7.278646 GGCAAGTTTCAATCTTTCAAACTTTCT 59.721 33.333 6.34 0.00 44.30 2.52
688 708 9.183368 AGTTTCAATCTTTCAAACTTTCTCTCT 57.817 29.630 0.00 0.00 37.09 3.10
717 737 3.085533 TGTCGGAGAGGAGAGAGAAAAG 58.914 50.000 0.00 0.00 36.95 2.27
728 748 5.185056 AGGAGAGAGAAAAGACAAGCTAGTC 59.815 44.000 0.00 0.00 38.81 2.59
735 755 3.686916 AAGACAAGCTAGTCCTGGAAC 57.313 47.619 0.00 0.00 39.34 3.62
835 856 3.728772 GGTCCCAGACCCCTCTTC 58.271 66.667 2.14 0.00 46.19 2.87
857 878 1.383248 CTCCATTCCGGTCCTCCCT 60.383 63.158 0.00 0.00 35.57 4.20
954 977 1.598130 AGCGGTGCAAAGGAGACAC 60.598 57.895 0.00 0.00 0.00 3.67
976 999 1.860676 GTACGTCCTTGTGCTTGTGA 58.139 50.000 0.00 0.00 0.00 3.58
977 1000 2.206750 GTACGTCCTTGTGCTTGTGAA 58.793 47.619 0.00 0.00 0.00 3.18
980 1003 2.687935 ACGTCCTTGTGCTTGTGAAAAT 59.312 40.909 0.00 0.00 0.00 1.82
1187 1210 0.868602 GTGCCATGCGTGCAATCATC 60.869 55.000 0.00 0.00 41.06 2.92
1235 1258 1.202382 GGTGATACAGGTACGCTGGTC 60.202 57.143 13.68 11.51 0.00 4.02
1894 1935 5.957842 TCCATTTGAGCGACAACTAATTT 57.042 34.783 0.00 0.00 38.29 1.82
1908 1949 6.884832 ACAACTAATTTCGGATGTAGGATGA 58.115 36.000 0.00 0.00 0.00 2.92
1934 1975 1.754226 GGTTGCACCAGAAGAAAACCA 59.246 47.619 0.00 0.00 38.42 3.67
2031 2072 1.477558 CCATCACCCATTCCCTGTAGC 60.478 57.143 0.00 0.00 0.00 3.58
2086 2127 3.575256 GAGGTTGTTTCCCCGGTTAAAAT 59.425 43.478 0.00 0.00 0.00 1.82
2088 2129 3.321396 GGTTGTTTCCCCGGTTAAAATCA 59.679 43.478 0.00 0.00 0.00 2.57
2098 2139 3.119280 CCGGTTAAAATCATGGGGTTGTC 60.119 47.826 0.00 0.00 0.00 3.18
2119 2160 1.077169 AGGGGATTTGACTGGGTTTCC 59.923 52.381 0.00 0.00 0.00 3.13
2138 2179 2.835156 TCCATCACAGTCGGGAATTACA 59.165 45.455 0.00 0.00 0.00 2.41
2139 2180 3.454447 TCCATCACAGTCGGGAATTACAT 59.546 43.478 0.00 0.00 0.00 2.29
2218 2264 3.227614 GTGTTTTGACCCCAATACTGGT 58.772 45.455 0.00 0.00 41.72 4.00
2219 2265 3.005367 GTGTTTTGACCCCAATACTGGTG 59.995 47.826 0.00 0.00 41.72 4.17
2225 2271 2.124320 CCAATACTGGTGGGGGCG 60.124 66.667 0.00 0.00 38.00 6.13
2228 2275 4.752594 ATACTGGTGGGGGCGGGT 62.753 66.667 0.00 0.00 0.00 5.28
2276 2323 7.444183 GCTTTCAAGTAATATAGGTGTATGCCA 59.556 37.037 0.00 0.00 0.00 4.92
2290 2337 4.397730 GTGTATGCCATGGTTGTCAATGTA 59.602 41.667 14.67 0.00 0.00 2.29
2291 2338 4.397730 TGTATGCCATGGTTGTCAATGTAC 59.602 41.667 14.67 3.43 0.00 2.90
2472 2522 8.934023 TTGAACTAAAACAACCATAATCCTCT 57.066 30.769 0.00 0.00 0.00 3.69
2473 2523 8.335532 TGAACTAAAACAACCATAATCCTCTG 57.664 34.615 0.00 0.00 0.00 3.35
2539 2589 9.520515 TCCTACAAAATTCTAAAAAGAGAGCAT 57.479 29.630 0.00 0.00 0.00 3.79
2609 2659 4.024725 CGTTAGGTTCGATCCAACAAACAA 60.025 41.667 14.83 0.31 0.00 2.83
2720 2771 5.449553 ACAGAATCTTCAAAAAGGAGTGGT 58.550 37.500 0.00 0.00 33.03 4.16
2754 2805 5.106830 CGCGGGTTAGAACTTAGAACAAAAT 60.107 40.000 0.00 0.00 0.00 1.82
2798 2852 4.430007 CTGGCAAATGATTGATTGGTCAG 58.570 43.478 0.00 0.00 40.58 3.51
2799 2853 4.087907 TGGCAAATGATTGATTGGTCAGA 58.912 39.130 0.00 0.00 38.94 3.27
2886 2940 0.665835 GCATCGACCAACAACAACCA 59.334 50.000 0.00 0.00 0.00 3.67
2891 2945 2.105134 TCGACCAACAACAACCAGGTAT 59.895 45.455 0.00 0.00 31.57 2.73
2896 2950 5.202004 ACCAACAACAACCAGGTATAAACA 58.798 37.500 0.00 0.00 0.00 2.83
2920 2974 0.675083 CCACCACAACACATGCACAT 59.325 50.000 0.00 0.00 0.00 3.21
3134 3188 0.323629 TTTCCCCTAGAGCAACACGG 59.676 55.000 0.00 0.00 0.00 4.94
3275 3331 2.111043 CGACCATGCCGCCCTTAT 59.889 61.111 0.00 0.00 0.00 1.73
3345 3401 3.570212 GACACCACCACCAGGGCT 61.570 66.667 0.00 0.00 42.05 5.19
3647 3935 2.390288 CGACGCCGAAACATGTCG 59.610 61.111 0.00 0.00 46.57 4.35
3840 4128 2.124320 ACACCACCACACCTGTGC 60.124 61.111 0.00 0.00 44.34 4.57
3849 4140 4.015406 CACCTGTGCCGCCACCTA 62.015 66.667 0.00 0.00 41.35 3.08
4430 5824 3.332493 GACGGCGAGGCGACAACTA 62.332 63.158 25.16 0.00 32.52 2.24
4431 5825 2.879462 CGGCGAGGCGACAACTAC 60.879 66.667 13.92 0.00 32.52 2.73
4432 5826 2.572284 GGCGAGGCGACAACTACT 59.428 61.111 0.00 0.00 33.63 2.57
4433 5827 1.080025 GGCGAGGCGACAACTACTT 60.080 57.895 0.00 0.00 33.63 2.24
4434 5828 0.669625 GGCGAGGCGACAACTACTTT 60.670 55.000 0.00 0.00 33.63 2.66
4435 5829 1.145803 GCGAGGCGACAACTACTTTT 58.854 50.000 0.00 0.00 0.00 2.27
4436 5830 1.136336 GCGAGGCGACAACTACTTTTG 60.136 52.381 0.00 0.00 0.00 2.44
4437 5831 2.400399 CGAGGCGACAACTACTTTTGA 58.600 47.619 0.00 0.00 0.00 2.69
4438 5832 2.798283 CGAGGCGACAACTACTTTTGAA 59.202 45.455 0.00 0.00 0.00 2.69
4439 5833 3.120991 CGAGGCGACAACTACTTTTGAAG 60.121 47.826 0.00 0.00 0.00 3.02
4440 5834 3.805207 AGGCGACAACTACTTTTGAAGT 58.195 40.909 0.00 0.00 45.40 3.01
4441 5835 4.952460 AGGCGACAACTACTTTTGAAGTA 58.048 39.130 0.00 1.11 42.81 2.24
4442 5836 5.362263 AGGCGACAACTACTTTTGAAGTAA 58.638 37.500 0.00 0.00 42.99 2.24
4443 5837 5.235831 AGGCGACAACTACTTTTGAAGTAAC 59.764 40.000 0.00 0.00 42.99 2.50
4444 5838 5.006941 GGCGACAACTACTTTTGAAGTAACA 59.993 40.000 2.58 0.00 42.99 2.41
4445 5839 6.127403 GCGACAACTACTTTTGAAGTAACAG 58.873 40.000 2.58 0.00 42.99 3.16
4446 5840 6.019318 GCGACAACTACTTTTGAAGTAACAGA 60.019 38.462 2.58 0.00 42.99 3.41
4447 5841 7.464977 GCGACAACTACTTTTGAAGTAACAGAA 60.465 37.037 2.58 0.00 42.99 3.02
4448 5842 8.385111 CGACAACTACTTTTGAAGTAACAGAAA 58.615 33.333 2.58 0.00 42.99 2.52
4449 5843 9.704098 GACAACTACTTTTGAAGTAACAGAAAG 57.296 33.333 2.58 0.00 42.99 2.62
4450 5844 9.444600 ACAACTACTTTTGAAGTAACAGAAAGA 57.555 29.630 2.58 0.00 42.99 2.52
4455 5849 8.689251 ACTTTTGAAGTAACAGAAAGAAAAGC 57.311 30.769 0.00 0.00 40.69 3.51
4456 5850 8.303876 ACTTTTGAAGTAACAGAAAGAAAAGCA 58.696 29.630 0.00 0.00 40.69 3.91
4457 5851 9.139174 CTTTTGAAGTAACAGAAAGAAAAGCAA 57.861 29.630 0.00 0.00 30.83 3.91
4458 5852 8.460831 TTTGAAGTAACAGAAAGAAAAGCAAC 57.539 30.769 0.00 0.00 0.00 4.17
4459 5853 6.255215 TGAAGTAACAGAAAGAAAAGCAACG 58.745 36.000 0.00 0.00 0.00 4.10
4460 5854 6.092944 TGAAGTAACAGAAAGAAAAGCAACGA 59.907 34.615 0.00 0.00 0.00 3.85
4461 5855 5.807344 AGTAACAGAAAGAAAAGCAACGAC 58.193 37.500 0.00 0.00 0.00 4.34
4462 5856 4.965119 AACAGAAAGAAAAGCAACGACT 57.035 36.364 0.00 0.00 0.00 4.18
4463 5857 4.278678 ACAGAAAGAAAAGCAACGACTG 57.721 40.909 0.00 0.00 0.00 3.51
4464 5858 3.065371 ACAGAAAGAAAAGCAACGACTGG 59.935 43.478 0.00 0.00 0.00 4.00
4465 5859 3.312421 CAGAAAGAAAAGCAACGACTGGA 59.688 43.478 0.00 0.00 0.00 3.86
4466 5860 3.561725 AGAAAGAAAAGCAACGACTGGAG 59.438 43.478 0.00 0.00 0.00 3.86
4467 5861 2.622064 AGAAAAGCAACGACTGGAGT 57.378 45.000 0.00 0.00 0.00 3.85
4468 5862 2.213499 AGAAAAGCAACGACTGGAGTG 58.787 47.619 0.00 0.00 0.00 3.51
4469 5863 1.264288 GAAAAGCAACGACTGGAGTGG 59.736 52.381 0.00 0.00 0.00 4.00
4470 5864 0.535102 AAAGCAACGACTGGAGTGGG 60.535 55.000 0.00 0.00 0.00 4.61
4471 5865 2.358737 GCAACGACTGGAGTGGGG 60.359 66.667 0.00 0.00 0.00 4.96
4472 5866 2.347490 CAACGACTGGAGTGGGGG 59.653 66.667 0.00 0.00 0.00 5.40
4473 5867 2.203182 AACGACTGGAGTGGGGGA 59.797 61.111 0.00 0.00 0.00 4.81
4474 5868 1.913762 AACGACTGGAGTGGGGGAG 60.914 63.158 0.00 0.00 0.00 4.30
4475 5869 2.283966 CGACTGGAGTGGGGGAGT 60.284 66.667 0.00 0.00 0.00 3.85
4476 5870 2.352032 CGACTGGAGTGGGGGAGTC 61.352 68.421 0.00 0.00 32.99 3.36
4477 5871 1.229209 GACTGGAGTGGGGGAGTCA 60.229 63.158 0.00 0.00 35.82 3.41
4478 5872 1.229336 ACTGGAGTGGGGGAGTCAG 60.229 63.158 0.00 0.00 0.00 3.51
4479 5873 1.079256 CTGGAGTGGGGGAGTCAGA 59.921 63.158 0.00 0.00 0.00 3.27
4480 5874 0.975040 CTGGAGTGGGGGAGTCAGAG 60.975 65.000 0.00 0.00 0.00 3.35
4481 5875 1.079438 GGAGTGGGGGAGTCAGAGT 59.921 63.158 0.00 0.00 0.00 3.24
4482 5876 0.973496 GGAGTGGGGGAGTCAGAGTC 60.973 65.000 0.00 0.00 0.00 3.36
4483 5877 1.304547 AGTGGGGGAGTCAGAGTCG 60.305 63.158 0.00 0.00 0.00 4.18
4484 5878 1.304217 GTGGGGGAGTCAGAGTCGA 60.304 63.158 0.00 0.00 0.00 4.20
4485 5879 0.898789 GTGGGGGAGTCAGAGTCGAA 60.899 60.000 0.00 0.00 0.00 3.71
4486 5880 0.178944 TGGGGGAGTCAGAGTCGAAA 60.179 55.000 0.00 0.00 0.00 3.46
4487 5881 0.974383 GGGGGAGTCAGAGTCGAAAA 59.026 55.000 0.00 0.00 0.00 2.29
4488 5882 1.346722 GGGGGAGTCAGAGTCGAAAAA 59.653 52.381 0.00 0.00 0.00 1.94
4507 5901 5.378292 AAAAAGGATTCCTCGCTTCTTTC 57.622 39.130 5.48 0.00 30.89 2.62
4508 5902 3.990959 AAGGATTCCTCGCTTCTTTCT 57.009 42.857 5.48 0.00 30.89 2.52
4509 5903 3.535280 AGGATTCCTCGCTTCTTTCTC 57.465 47.619 0.00 0.00 0.00 2.87
4510 5904 3.103742 AGGATTCCTCGCTTCTTTCTCT 58.896 45.455 0.00 0.00 0.00 3.10
4511 5905 3.132111 AGGATTCCTCGCTTCTTTCTCTC 59.868 47.826 0.00 0.00 0.00 3.20
4512 5906 3.118956 GGATTCCTCGCTTCTTTCTCTCA 60.119 47.826 0.00 0.00 0.00 3.27
4554 5949 0.692756 GGGAGAGGGGAAGAAGGAGG 60.693 65.000 0.00 0.00 0.00 4.30
4624 6019 1.757340 GACTCGGGAGGGGAACGAT 60.757 63.158 0.00 0.00 35.93 3.73
4625 6020 0.466922 GACTCGGGAGGGGAACGATA 60.467 60.000 0.00 0.00 35.93 2.92
4626 6021 0.754587 ACTCGGGAGGGGAACGATAC 60.755 60.000 0.00 0.00 35.93 2.24
4627 6022 0.467659 CTCGGGAGGGGAACGATACT 60.468 60.000 0.00 0.00 35.93 2.12
4628 6023 0.466922 TCGGGAGGGGAACGATACTC 60.467 60.000 0.00 0.00 0.00 2.59
4629 6024 1.461911 CGGGAGGGGAACGATACTCC 61.462 65.000 0.00 0.00 46.85 3.85
4637 6032 2.933573 GGAACGATACTCCCTCTGAGA 58.066 52.381 6.17 0.00 44.42 3.27
4638 6033 3.492337 GGAACGATACTCCCTCTGAGAT 58.508 50.000 6.17 0.00 44.42 2.75
4639 6034 3.892588 GGAACGATACTCCCTCTGAGATT 59.107 47.826 6.17 0.00 44.42 2.40
4640 6035 4.022676 GGAACGATACTCCCTCTGAGATTC 60.023 50.000 6.17 0.00 44.42 2.52
4641 6036 3.492337 ACGATACTCCCTCTGAGATTCC 58.508 50.000 6.17 0.00 44.42 3.01
4642 6037 3.117474 ACGATACTCCCTCTGAGATTCCA 60.117 47.826 6.17 0.00 44.42 3.53
4804 6200 1.875963 GAAGCATCCAACACCACCG 59.124 57.895 0.00 0.00 0.00 4.94
4911 6307 1.101635 TCATGTCCCTCGCCTACTCG 61.102 60.000 0.00 0.00 0.00 4.18
5131 6720 9.221933 TGATAATGTACAAACAATAACTTCCGT 57.778 29.630 0.00 0.00 39.58 4.69
5342 7136 0.480690 TGTTGTAGGTGGGGTGCATT 59.519 50.000 0.00 0.00 0.00 3.56
5551 7347 6.256975 TCGAAATAGATGATTGTTTGTACCCG 59.743 38.462 0.00 0.00 0.00 5.28
5573 7369 7.615757 ACCCGACATTCATATGACTAGATATCA 59.384 37.037 4.48 0.00 35.65 2.15
5836 7657 4.008933 AGACTCCACGGTGCAGGC 62.009 66.667 3.79 0.00 0.00 4.85
5946 7767 0.671781 GCAGACCAGTGCGAATGTCT 60.672 55.000 0.00 0.00 38.56 3.41
6014 7837 3.612423 CAGACAATGTCGAATTCGCAGTA 59.388 43.478 22.90 9.01 37.67 2.74
6243 8069 3.211288 CCCTTCTGGCTCGTCGAT 58.789 61.111 0.00 0.00 0.00 3.59
6285 8111 2.186903 CACCTCGTTGGCGCCTAT 59.813 61.111 29.70 0.59 40.22 2.57
6327 8153 2.811317 CAGTTCGTCGAGGGCTGC 60.811 66.667 14.19 0.00 0.00 5.25
6486 8318 2.036256 GTGGCCATGCTGTTCCCT 59.964 61.111 9.72 0.00 0.00 4.20
6540 8372 1.961277 CTCGTTTTGGCCGCTCACT 60.961 57.895 0.00 0.00 0.00 3.41
6705 8537 2.813908 GTCGCAGGGTACAAGCCG 60.814 66.667 0.00 0.00 41.56 5.52
6739 8578 2.225068 ACATCTATTCGGACAAGGCG 57.775 50.000 0.00 0.00 0.00 5.52
6742 8581 0.892755 TCTATTCGGACAAGGCGTGT 59.107 50.000 5.57 5.57 45.74 4.49
6752 8591 3.181479 GGACAAGGCGTGTATAGTGATGA 60.181 47.826 5.94 0.00 41.96 2.92
6789 8631 1.777941 ATAGGTGAAGGGTCGAGGTC 58.222 55.000 0.00 0.00 0.00 3.85
6797 8639 0.688087 AGGGTCGAGGTCAATCCCTC 60.688 60.000 1.76 0.00 44.32 4.30
6910 8752 5.991328 AGTTGACAGTTGACTACATGTTG 57.009 39.130 2.30 4.29 0.00 3.33
6915 8757 7.851387 TGACAGTTGACTACATGTTGTTTTA 57.149 32.000 14.14 2.23 0.00 1.52
6916 8758 8.270080 TGACAGTTGACTACATGTTGTTTTAA 57.730 30.769 14.14 7.74 0.00 1.52
6917 8759 8.898761 TGACAGTTGACTACATGTTGTTTTAAT 58.101 29.630 14.14 0.40 0.00 1.40
6918 8760 9.382244 GACAGTTGACTACATGTTGTTTTAATC 57.618 33.333 14.14 5.39 0.00 1.75
6919 8761 9.120538 ACAGTTGACTACATGTTGTTTTAATCT 57.879 29.630 14.14 5.39 0.00 2.40
7080 8936 3.378112 TCCATCCGAATGAACTGCAAATC 59.622 43.478 0.00 0.00 34.61 2.17
7257 9113 4.277174 TGATGCCACACGTTAAAAGAACAT 59.723 37.500 0.00 0.00 0.00 2.71
7387 9243 7.042321 TGCCGCAACATATATAAAGTACAAGAC 60.042 37.037 0.00 0.00 0.00 3.01
7583 9452 0.679505 CTCCTCAAAGGTGGACGTCA 59.320 55.000 18.91 0.27 36.53 4.35
7706 9575 3.049674 CGATGTGCTTGGTGCGGT 61.050 61.111 0.00 0.00 46.63 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 86 2.028484 TCAGGCCGACGACACAAC 59.972 61.111 0.00 0.00 0.00 3.32
294 297 0.464373 CACAATCATACCCCAGCGCT 60.464 55.000 2.64 2.64 0.00 5.92
314 317 4.794439 CCGGATCACGTCTGCGCA 62.794 66.667 10.98 10.98 42.83 6.09
346 355 3.153130 CTCGGATCTGATCTAGGCTTGA 58.847 50.000 16.61 0.14 0.00 3.02
378 387 0.833287 TAGCCTGGGCACTCTTCATC 59.167 55.000 14.39 0.00 44.88 2.92
472 489 2.367107 GACCTTCCTCCCTCCCCC 60.367 72.222 0.00 0.00 0.00 5.40
473 490 1.690985 CTGACCTTCCTCCCTCCCC 60.691 68.421 0.00 0.00 0.00 4.81
474 491 2.371259 GCTGACCTTCCTCCCTCCC 61.371 68.421 0.00 0.00 0.00 4.30
475 492 2.726351 CGCTGACCTTCCTCCCTCC 61.726 68.421 0.00 0.00 0.00 4.30
476 493 2.726351 CCGCTGACCTTCCTCCCTC 61.726 68.421 0.00 0.00 0.00 4.30
477 494 2.685380 CCGCTGACCTTCCTCCCT 60.685 66.667 0.00 0.00 0.00 4.20
478 495 4.475135 GCCGCTGACCTTCCTCCC 62.475 72.222 0.00 0.00 0.00 4.30
479 496 3.394836 AGCCGCTGACCTTCCTCC 61.395 66.667 0.00 0.00 0.00 4.30
480 497 2.125350 CAGCCGCTGACCTTCCTC 60.125 66.667 15.74 0.00 32.44 3.71
481 498 3.710722 CCAGCCGCTGACCTTCCT 61.711 66.667 22.35 0.00 32.44 3.36
482 499 4.785453 CCCAGCCGCTGACCTTCC 62.785 72.222 22.35 0.00 32.44 3.46
483 500 3.706373 TCCCAGCCGCTGACCTTC 61.706 66.667 22.35 0.00 32.44 3.46
484 501 4.021925 GTCCCAGCCGCTGACCTT 62.022 66.667 22.35 0.00 32.44 3.50
489 506 4.077184 TTACCGTCCCAGCCGCTG 62.077 66.667 13.82 13.82 0.00 5.18
490 507 3.771160 CTTACCGTCCCAGCCGCT 61.771 66.667 0.00 0.00 0.00 5.52
491 508 4.832608 CCTTACCGTCCCAGCCGC 62.833 72.222 0.00 0.00 0.00 6.53
492 509 3.366739 GACCTTACCGTCCCAGCCG 62.367 68.421 0.00 0.00 0.00 5.52
493 510 2.582978 GACCTTACCGTCCCAGCC 59.417 66.667 0.00 0.00 0.00 4.85
494 511 2.582978 GGACCTTACCGTCCCAGC 59.417 66.667 0.00 0.00 45.72 4.85
535 552 4.241555 ATTAGCCCAGCCCTCGCG 62.242 66.667 0.00 0.00 41.18 5.87
536 553 2.592861 CATTAGCCCAGCCCTCGC 60.593 66.667 0.00 0.00 0.00 5.03
537 554 2.111878 CCATTAGCCCAGCCCTCG 59.888 66.667 0.00 0.00 0.00 4.63
538 555 1.149401 GACCATTAGCCCAGCCCTC 59.851 63.158 0.00 0.00 0.00 4.30
539 556 2.386935 GGACCATTAGCCCAGCCCT 61.387 63.158 0.00 0.00 0.00 5.19
540 557 2.195956 GGACCATTAGCCCAGCCC 59.804 66.667 0.00 0.00 0.00 5.19
541 558 2.203209 CGGACCATTAGCCCAGCC 60.203 66.667 0.00 0.00 0.00 4.85
542 559 2.902343 GCGGACCATTAGCCCAGC 60.902 66.667 0.00 0.00 0.00 4.85
543 560 0.466189 AATGCGGACCATTAGCCCAG 60.466 55.000 0.00 0.00 42.24 4.45
544 561 0.751277 CAATGCGGACCATTAGCCCA 60.751 55.000 0.00 0.00 42.15 5.36
545 562 1.455383 CCAATGCGGACCATTAGCCC 61.455 60.000 0.00 0.00 42.15 5.19
546 563 0.465460 TCCAATGCGGACCATTAGCC 60.465 55.000 0.00 0.00 42.15 3.93
547 564 0.947244 CTCCAATGCGGACCATTAGC 59.053 55.000 0.00 0.00 42.15 3.09
548 565 2.620251 TCTCCAATGCGGACCATTAG 57.380 50.000 0.00 0.00 42.15 1.73
549 566 2.849942 CATCTCCAATGCGGACCATTA 58.150 47.619 0.00 0.00 42.15 1.90
550 567 1.683943 CATCTCCAATGCGGACCATT 58.316 50.000 0.00 0.00 44.86 3.16
551 568 0.820891 GCATCTCCAATGCGGACCAT 60.821 55.000 0.00 0.00 39.64 3.55
552 569 1.451927 GCATCTCCAATGCGGACCA 60.452 57.895 0.00 0.00 39.64 4.02
553 570 2.189499 GGCATCTCCAATGCGGACC 61.189 63.158 4.11 0.00 45.41 4.46
554 571 0.749454 AAGGCATCTCCAATGCGGAC 60.749 55.000 4.11 0.00 45.41 4.79
555 572 0.034186 AAAGGCATCTCCAATGCGGA 60.034 50.000 4.11 0.00 45.41 5.54
556 573 1.334869 GTAAAGGCATCTCCAATGCGG 59.665 52.381 4.11 0.00 45.41 5.69
557 574 2.032550 CAGTAAAGGCATCTCCAATGCG 59.967 50.000 4.11 0.00 45.41 4.73
572 589 2.562738 TCTGCTGCTGCTACTCAGTAAA 59.437 45.455 17.00 0.00 44.66 2.01
575 592 0.531657 CTCTGCTGCTGCTACTCAGT 59.468 55.000 17.00 0.00 44.66 3.41
581 598 1.661498 CCGTCTCTCTGCTGCTGCTA 61.661 60.000 17.00 4.24 40.48 3.49
584 601 0.100325 CTACCGTCTCTCTGCTGCTG 59.900 60.000 0.00 0.00 0.00 4.41
618 638 6.907853 TGATCAAATTTACCACCAACATGA 57.092 33.333 0.00 0.00 0.00 3.07
684 704 3.073274 TCTCCGACAATGTGAGAGAGA 57.927 47.619 7.61 3.38 31.75 3.10
688 708 2.095461 CTCCTCTCCGACAATGTGAGA 58.905 52.381 0.00 0.00 34.20 3.27
717 737 1.404315 CCGTTCCAGGACTAGCTTGTC 60.404 57.143 18.55 18.55 36.31 3.18
742 762 2.446435 GGGAAGAAAATGCTGCCTGTA 58.554 47.619 0.00 0.00 33.72 2.74
800 820 0.165944 CCGTCGGAAGCATGTGTTTC 59.834 55.000 4.91 1.50 34.99 2.78
835 856 1.383248 AGGACCGGAATGGAGGAGG 60.383 63.158 9.46 0.00 42.00 4.30
857 878 1.149361 CTTATGTAAGCGCGCCGGAA 61.149 55.000 30.33 12.46 0.00 4.30
945 968 0.595095 GGACGTACGTGTGTCTCCTT 59.405 55.000 28.16 0.00 35.45 3.36
954 977 0.506932 CAAGCACAAGGACGTACGTG 59.493 55.000 28.16 12.50 0.00 4.49
1187 1210 4.260985 TCAACATGCATGTAGGTTACCAG 58.739 43.478 31.55 13.04 40.80 4.00
1864 1900 5.503819 TTGTCGCTCAAATGGATGTATCCG 61.504 45.833 6.43 0.00 40.33 4.18
1894 1935 6.230472 CAACCAAATATCATCCTACATCCGA 58.770 40.000 0.00 0.00 0.00 4.55
1934 1975 7.208080 CCTAGTAACCGAACATAGCTTTATGT 58.792 38.462 0.00 0.00 42.00 2.29
1988 2029 1.506028 GGGATCAACCAACCCCCTCA 61.506 60.000 0.00 0.00 41.20 3.86
2086 2127 0.552367 ATCCCCTGACAACCCCATGA 60.552 55.000 0.00 0.00 0.00 3.07
2088 2129 1.092549 AAATCCCCTGACAACCCCAT 58.907 50.000 0.00 0.00 0.00 4.00
2098 2139 2.171003 GAAACCCAGTCAAATCCCCTG 58.829 52.381 0.00 0.00 0.00 4.45
2119 2160 6.566564 GCATTATGTAATTCCCGACTGTGATG 60.567 42.308 0.00 0.00 0.00 3.07
2139 2180 9.267084 TCGCTATTTGTTTCATATAGTGCATTA 57.733 29.630 12.42 0.00 36.54 1.90
2218 2264 1.849975 TTCGATTAAACCCGCCCCCA 61.850 55.000 0.00 0.00 0.00 4.96
2219 2265 1.077572 TTCGATTAAACCCGCCCCC 60.078 57.895 0.00 0.00 0.00 5.40
2225 2271 2.285977 AGGCATCGTTCGATTAAACCC 58.714 47.619 4.92 2.31 0.00 4.11
2228 2275 5.295787 AGCAATTAGGCATCGTTCGATTAAA 59.704 36.000 4.92 0.00 35.83 1.52
2276 2323 8.650143 AATTTCCTTAGTACATTGACAACCAT 57.350 30.769 0.00 0.00 0.00 3.55
2290 2337 7.068716 GCCAACCTCATGAATAATTTCCTTAGT 59.931 37.037 0.00 0.00 0.00 2.24
2291 2338 7.286316 AGCCAACCTCATGAATAATTTCCTTAG 59.714 37.037 0.00 0.00 0.00 2.18
2472 2522 7.122650 GGATCCTTTGACAAGAATTATGGAACA 59.877 37.037 3.84 0.00 35.40 3.18
2473 2523 7.340487 AGGATCCTTTGACAAGAATTATGGAAC 59.660 37.037 9.02 0.00 30.57 3.62
2526 2576 7.765695 AATGACCAGAAATGCTCTCTTTTTA 57.234 32.000 0.00 0.00 29.07 1.52
2539 2589 7.715249 GGCATAGTGTAGATAAATGACCAGAAA 59.285 37.037 0.00 0.00 0.00 2.52
2668 2718 4.451435 GGCAAAAGTAGTACTGTGGTCTTC 59.549 45.833 5.39 0.00 0.00 2.87
2670 2720 3.646637 AGGCAAAAGTAGTACTGTGGTCT 59.353 43.478 5.39 0.00 0.00 3.85
2671 2721 4.004196 AGGCAAAAGTAGTACTGTGGTC 57.996 45.455 5.39 0.00 0.00 4.02
2672 2722 4.432980 AAGGCAAAAGTAGTACTGTGGT 57.567 40.909 5.39 0.00 0.00 4.16
2674 2724 7.699566 TGTTTTAAGGCAAAAGTAGTACTGTG 58.300 34.615 5.39 6.72 36.79 3.66
2720 2771 0.179094 CTAACCCGCGCCAATACAGA 60.179 55.000 0.00 0.00 0.00 3.41
2754 2805 8.148351 GCCAGTAGTCACCAATAAGTATGATTA 58.852 37.037 0.00 0.00 0.00 1.75
2819 2873 7.892609 AGCCTTTTTCGGTAATTTGTAATCTT 58.107 30.769 0.00 0.00 0.00 2.40
2822 2876 7.327518 CGAAAGCCTTTTTCGGTAATTTGTAAT 59.672 33.333 12.72 0.00 45.17 1.89
2823 2877 6.637658 CGAAAGCCTTTTTCGGTAATTTGTAA 59.362 34.615 12.72 0.00 45.17 2.41
2824 2878 6.144175 CGAAAGCCTTTTTCGGTAATTTGTA 58.856 36.000 12.72 0.00 45.17 2.41
2825 2879 4.979815 CGAAAGCCTTTTTCGGTAATTTGT 59.020 37.500 12.72 0.00 45.17 2.83
2826 2880 5.494863 CGAAAGCCTTTTTCGGTAATTTG 57.505 39.130 12.72 0.00 45.17 2.32
2886 2940 1.348366 TGGTGGCGTGTGTTTATACCT 59.652 47.619 0.00 0.00 0.00 3.08
2891 2945 0.733729 GTTGTGGTGGCGTGTGTTTA 59.266 50.000 0.00 0.00 0.00 2.01
2896 2950 1.453015 ATGTGTTGTGGTGGCGTGT 60.453 52.632 0.00 0.00 0.00 4.49
2920 2974 5.779922 CGCTTATGTATCTTGCCTTAGGTA 58.220 41.667 0.00 0.00 0.00 3.08
3103 3157 1.945580 AGGGGAAACTCTGACTCTCC 58.054 55.000 0.00 0.00 42.28 3.71
3535 3823 4.056125 GCTTTTCCCAGCCGTGGC 62.056 66.667 1.67 1.67 43.44 5.01
4430 5824 8.303876 TGCTTTTCTTTCTGTTACTTCAAAAGT 58.696 29.630 0.00 0.00 45.40 2.66
4431 5825 8.687824 TGCTTTTCTTTCTGTTACTTCAAAAG 57.312 30.769 0.00 0.00 34.26 2.27
4432 5826 8.921670 GTTGCTTTTCTTTCTGTTACTTCAAAA 58.078 29.630 0.00 0.00 0.00 2.44
4433 5827 7.272515 CGTTGCTTTTCTTTCTGTTACTTCAAA 59.727 33.333 0.00 0.00 0.00 2.69
4434 5828 6.745450 CGTTGCTTTTCTTTCTGTTACTTCAA 59.255 34.615 0.00 0.00 0.00 2.69
4435 5829 6.092944 TCGTTGCTTTTCTTTCTGTTACTTCA 59.907 34.615 0.00 0.00 0.00 3.02
4436 5830 6.411203 GTCGTTGCTTTTCTTTCTGTTACTTC 59.589 38.462 0.00 0.00 0.00 3.01
4437 5831 6.093633 AGTCGTTGCTTTTCTTTCTGTTACTT 59.906 34.615 0.00 0.00 0.00 2.24
4438 5832 5.585047 AGTCGTTGCTTTTCTTTCTGTTACT 59.415 36.000 0.00 0.00 0.00 2.24
4439 5833 5.677178 CAGTCGTTGCTTTTCTTTCTGTTAC 59.323 40.000 0.00 0.00 0.00 2.50
4440 5834 5.220777 CCAGTCGTTGCTTTTCTTTCTGTTA 60.221 40.000 0.00 0.00 0.00 2.41
4441 5835 4.438744 CCAGTCGTTGCTTTTCTTTCTGTT 60.439 41.667 0.00 0.00 0.00 3.16
4442 5836 3.065371 CCAGTCGTTGCTTTTCTTTCTGT 59.935 43.478 0.00 0.00 0.00 3.41
4443 5837 3.312421 TCCAGTCGTTGCTTTTCTTTCTG 59.688 43.478 0.00 0.00 0.00 3.02
4444 5838 3.541632 TCCAGTCGTTGCTTTTCTTTCT 58.458 40.909 0.00 0.00 0.00 2.52
4445 5839 3.312697 ACTCCAGTCGTTGCTTTTCTTTC 59.687 43.478 0.00 0.00 0.00 2.62
4446 5840 3.065371 CACTCCAGTCGTTGCTTTTCTTT 59.935 43.478 0.00 0.00 0.00 2.52
4447 5841 2.614057 CACTCCAGTCGTTGCTTTTCTT 59.386 45.455 0.00 0.00 0.00 2.52
4448 5842 2.213499 CACTCCAGTCGTTGCTTTTCT 58.787 47.619 0.00 0.00 0.00 2.52
4449 5843 1.264288 CCACTCCAGTCGTTGCTTTTC 59.736 52.381 0.00 0.00 0.00 2.29
4450 5844 1.308998 CCACTCCAGTCGTTGCTTTT 58.691 50.000 0.00 0.00 0.00 2.27
4451 5845 0.535102 CCCACTCCAGTCGTTGCTTT 60.535 55.000 0.00 0.00 0.00 3.51
4452 5846 1.071471 CCCACTCCAGTCGTTGCTT 59.929 57.895 0.00 0.00 0.00 3.91
4453 5847 2.743718 CCCACTCCAGTCGTTGCT 59.256 61.111 0.00 0.00 0.00 3.91
4454 5848 2.358737 CCCCACTCCAGTCGTTGC 60.359 66.667 0.00 0.00 0.00 4.17
4455 5849 2.172483 CTCCCCCACTCCAGTCGTTG 62.172 65.000 0.00 0.00 0.00 4.10
4456 5850 1.913762 CTCCCCCACTCCAGTCGTT 60.914 63.158 0.00 0.00 0.00 3.85
4457 5851 2.283966 CTCCCCCACTCCAGTCGT 60.284 66.667 0.00 0.00 0.00 4.34
4458 5852 2.283966 ACTCCCCCACTCCAGTCG 60.284 66.667 0.00 0.00 0.00 4.18
4459 5853 1.229209 TGACTCCCCCACTCCAGTC 60.229 63.158 0.00 0.00 36.57 3.51
4460 5854 1.229336 CTGACTCCCCCACTCCAGT 60.229 63.158 0.00 0.00 0.00 4.00
4461 5855 0.975040 CTCTGACTCCCCCACTCCAG 60.975 65.000 0.00 0.00 0.00 3.86
4462 5856 1.079256 CTCTGACTCCCCCACTCCA 59.921 63.158 0.00 0.00 0.00 3.86
4463 5857 0.973496 GACTCTGACTCCCCCACTCC 60.973 65.000 0.00 0.00 0.00 3.85
4464 5858 1.316706 CGACTCTGACTCCCCCACTC 61.317 65.000 0.00 0.00 0.00 3.51
4465 5859 1.304547 CGACTCTGACTCCCCCACT 60.305 63.158 0.00 0.00 0.00 4.00
4466 5860 0.898789 TTCGACTCTGACTCCCCCAC 60.899 60.000 0.00 0.00 0.00 4.61
4467 5861 0.178944 TTTCGACTCTGACTCCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
4468 5862 0.974383 TTTTCGACTCTGACTCCCCC 59.026 55.000 0.00 0.00 0.00 5.40
4469 5863 2.833631 TTTTTCGACTCTGACTCCCC 57.166 50.000 0.00 0.00 0.00 4.81
4485 5879 5.073428 AGAAAGAAGCGAGGAATCCTTTTT 58.927 37.500 2.09 0.00 31.76 1.94
4486 5880 4.657013 AGAAAGAAGCGAGGAATCCTTTT 58.343 39.130 2.09 0.00 31.76 2.27
4487 5881 4.019771 AGAGAAAGAAGCGAGGAATCCTTT 60.020 41.667 2.09 0.00 31.76 3.11
4488 5882 3.517500 AGAGAAAGAAGCGAGGAATCCTT 59.482 43.478 2.09 0.00 31.76 3.36
4489 5883 3.103742 AGAGAAAGAAGCGAGGAATCCT 58.896 45.455 0.00 0.00 36.03 3.24
4490 5884 3.118956 TGAGAGAAAGAAGCGAGGAATCC 60.119 47.826 0.00 0.00 0.00 3.01
4491 5885 4.116747 TGAGAGAAAGAAGCGAGGAATC 57.883 45.455 0.00 0.00 0.00 2.52
4492 5886 4.440880 CATGAGAGAAAGAAGCGAGGAAT 58.559 43.478 0.00 0.00 0.00 3.01
4493 5887 3.854666 CATGAGAGAAAGAAGCGAGGAA 58.145 45.455 0.00 0.00 0.00 3.36
4494 5888 2.417924 GCATGAGAGAAAGAAGCGAGGA 60.418 50.000 0.00 0.00 0.00 3.71
4495 5889 1.932511 GCATGAGAGAAAGAAGCGAGG 59.067 52.381 0.00 0.00 0.00 4.63
4496 5890 1.587490 CGCATGAGAGAAAGAAGCGAG 59.413 52.381 0.00 0.00 45.78 5.03
4497 5891 1.633561 CGCATGAGAGAAAGAAGCGA 58.366 50.000 0.00 0.00 45.78 4.93
4498 5892 0.026027 GCGCATGAGAGAAAGAAGCG 59.974 55.000 0.30 0.00 45.68 4.68
4499 5893 0.376502 GGCGCATGAGAGAAAGAAGC 59.623 55.000 10.83 0.00 0.00 3.86
4500 5894 1.012841 GGGCGCATGAGAGAAAGAAG 58.987 55.000 10.83 0.00 0.00 2.85
4501 5895 0.615331 AGGGCGCATGAGAGAAAGAA 59.385 50.000 10.83 0.00 0.00 2.52
4502 5896 0.176680 GAGGGCGCATGAGAGAAAGA 59.823 55.000 10.83 0.00 0.00 2.52
4503 5897 0.177604 AGAGGGCGCATGAGAGAAAG 59.822 55.000 10.83 0.00 0.00 2.62
4504 5898 0.107993 CAGAGGGCGCATGAGAGAAA 60.108 55.000 10.83 0.00 0.00 2.52
4505 5899 1.519246 CAGAGGGCGCATGAGAGAA 59.481 57.895 10.83 0.00 0.00 2.87
4506 5900 2.429767 CCAGAGGGCGCATGAGAGA 61.430 63.158 10.83 0.00 0.00 3.10
4507 5901 2.108566 CCAGAGGGCGCATGAGAG 59.891 66.667 10.83 0.00 0.00 3.20
4624 6019 4.229812 TGTAGTGGAATCTCAGAGGGAGTA 59.770 45.833 0.00 0.00 44.40 2.59
4625 6020 2.938428 AGTGGAATCTCAGAGGGAGT 57.062 50.000 0.00 0.00 44.40 3.85
4626 6021 3.636679 TGTAGTGGAATCTCAGAGGGAG 58.363 50.000 0.00 0.00 45.49 4.30
4627 6022 3.757947 TGTAGTGGAATCTCAGAGGGA 57.242 47.619 0.00 0.00 0.00 4.20
4628 6023 4.826274 TTTGTAGTGGAATCTCAGAGGG 57.174 45.455 0.00 0.00 0.00 4.30
4629 6024 7.560368 AGTAATTTGTAGTGGAATCTCAGAGG 58.440 38.462 0.00 0.00 0.00 3.69
4632 6027 9.877178 ACTTAGTAATTTGTAGTGGAATCTCAG 57.123 33.333 0.00 0.00 0.00 3.35
4686 6082 8.786826 TTAGATGTTCCGACAAGTAATTGAAT 57.213 30.769 10.35 0.00 39.66 2.57
4701 6097 3.058639 GCATCGCCTTGATTAGATGTTCC 60.059 47.826 6.23 0.00 41.64 3.62
4788 6184 1.302511 GTCGGTGGTGTTGGATGCT 60.303 57.895 0.00 0.00 0.00 3.79
4804 6200 6.071784 TGGATGGCAGCAAATATAATCATGTC 60.072 38.462 4.64 0.00 0.00 3.06
4911 6307 1.153349 GAGGCCGAGACCAATGGAC 60.153 63.158 6.16 0.00 0.00 4.02
4965 6361 6.202937 TGAATTAAAAGCCAAAGTACGTGTG 58.797 36.000 0.00 0.00 0.00 3.82
5129 6718 5.018539 TCTCTCTCTCTCTCTTCCTTACG 57.981 47.826 0.00 0.00 0.00 3.18
5130 6719 6.098409 TCTCTCTCTCTCTCTCTCTTCCTTAC 59.902 46.154 0.00 0.00 0.00 2.34
5131 6720 6.202331 TCTCTCTCTCTCTCTCTCTTCCTTA 58.798 44.000 0.00 0.00 0.00 2.69
5133 6722 4.624913 TCTCTCTCTCTCTCTCTCTTCCT 58.375 47.826 0.00 0.00 0.00 3.36
5135 6724 5.596361 TCTCTCTCTCTCTCTCTCTCTCTTC 59.404 48.000 0.00 0.00 0.00 2.87
5342 7136 1.270625 CCCTGTTAGCGTTGTCTTGGA 60.271 52.381 0.00 0.00 0.00 3.53
5836 7657 4.201657 TGATTGTTCATACCCATGCAGAG 58.798 43.478 0.00 0.00 31.73 3.35
5919 7740 0.823356 GCACTGGTCTGCCAAAGGAA 60.823 55.000 0.00 0.00 45.51 3.36
5946 7767 6.465948 AGCCTGCATATTTTCATCAACAAAA 58.534 32.000 0.00 0.00 0.00 2.44
6285 8111 2.596851 GGGCTGGCAGAAGACCTGA 61.597 63.158 20.86 0.00 45.78 3.86
6486 8318 2.616842 GCCAAGGAAGTCGTTGAAGAAA 59.383 45.455 13.81 0.00 42.45 2.52
6540 8372 2.297698 TCTCAACGGGGAAGTAGACA 57.702 50.000 0.00 0.00 0.00 3.41
6705 8537 6.697892 CGAATAGATGTTAGGAGACCTTGAAC 59.302 42.308 0.00 0.00 34.61 3.18
6789 8631 7.344095 AGATTAAAGCATGAAAGAGGGATTG 57.656 36.000 0.00 0.00 0.00 2.67
6797 8639 9.696917 ACCACTTTTTAGATTAAAGCATGAAAG 57.303 29.630 0.00 0.00 36.33 2.62
6915 8757 8.966868 CAGTAACCCACCAATGTTTTATAGATT 58.033 33.333 0.00 0.00 0.00 2.40
6916 8758 8.113462 ACAGTAACCCACCAATGTTTTATAGAT 58.887 33.333 0.00 0.00 0.00 1.98
6917 8759 7.463431 ACAGTAACCCACCAATGTTTTATAGA 58.537 34.615 0.00 0.00 0.00 1.98
6918 8760 7.610305 AGACAGTAACCCACCAATGTTTTATAG 59.390 37.037 0.00 0.00 0.00 1.31
6919 8761 7.463431 AGACAGTAACCCACCAATGTTTTATA 58.537 34.615 0.00 0.00 0.00 0.98
6920 8762 6.311735 AGACAGTAACCCACCAATGTTTTAT 58.688 36.000 0.00 0.00 0.00 1.40
6922 8764 4.542697 AGACAGTAACCCACCAATGTTTT 58.457 39.130 0.00 0.00 0.00 2.43
6923 8765 4.178956 AGACAGTAACCCACCAATGTTT 57.821 40.909 0.00 0.00 0.00 2.83
6924 8766 3.876309 AGACAGTAACCCACCAATGTT 57.124 42.857 0.00 0.00 0.00 2.71
7080 8936 2.384391 GATCGCATGAGCTTTGGCCG 62.384 60.000 0.00 0.00 39.73 6.13
7257 9113 9.134055 TCTCCATGAATATAATGCAAATGAACA 57.866 29.630 0.00 0.00 0.00 3.18
7387 9243 1.060713 CCGTTGAGATATTAGCCGCG 58.939 55.000 0.00 0.00 0.00 6.46
7583 9452 4.340381 GGATATCATGACAAAAGGCTTGCT 59.660 41.667 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.