Multiple sequence alignment - TraesCS1D01G304600

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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 TraesCS1D01G304600 chr1D 100.000 8556 0 0 1 8556 402133061 402124506 0.000000e+00 15801.0
1 TraesCS1D01G304600 chr1D 88.498 852 83 7 3713 4551 401710892 401710043 0.000000e+00 1016.0
2 TraesCS1D01G304600 chr1D 92.557 618 36 7 4518 5130 402128338 402127726 0.000000e+00 878.0
3 TraesCS1D01G304600 chr1D 92.557 618 36 7 4724 5336 402128544 402127932 0.000000e+00 878.0
4 TraesCS1D01G304600 chr1D 85.075 603 75 13 5880 6471 401709750 401709152 1.230000e-167 601.0
5 TraesCS1D01G304600 chr1D 91.422 408 29 3 4518 4920 402128132 402127726 9.700000e-154 555.0
6 TraesCS1D01G304600 chr1D 95.000 260 12 1 1915 2173 97740151 97740410 2.880000e-109 407.0
7 TraesCS1D01G304600 chr1D 78.195 665 105 29 7164 7794 401708111 401707453 1.040000e-103 388.0
8 TraesCS1D01G304600 chr1D 85.801 331 39 4 5531 5853 401710034 401709704 2.290000e-90 344.0
9 TraesCS1D01G304600 chr1D 90.854 164 1 1 774 923 402132139 402131976 3.130000e-49 207.0
10 TraesCS1D01G304600 chr1D 90.854 164 1 1 923 1086 402132288 402132139 3.130000e-49 207.0
11 TraesCS1D01G304600 chr1D 96.774 124 4 0 8433 8556 487846091 487846214 3.130000e-49 207.0
12 TraesCS1D01G304600 chr1B 94.010 5793 222 56 2176 7888 539662875 539657128 0.000000e+00 8660.0
13 TraesCS1D01G304600 chr1B 92.094 936 48 18 1 923 539664675 539663753 0.000000e+00 1295.0
14 TraesCS1D01G304600 chr1B 87.224 861 86 12 3713 4551 539577586 539576728 0.000000e+00 959.0
15 TraesCS1D01G304600 chr1B 84.504 1039 85 28 939 1916 539663900 539662877 0.000000e+00 957.0
16 TraesCS1D01G304600 chr1B 92.233 618 38 7 4518 5130 539660297 539659685 0.000000e+00 867.0
17 TraesCS1D01G304600 chr1B 91.912 408 27 3 4518 4920 539660091 539659685 4.480000e-157 566.0
18 TraesCS1D01G304600 chr1B 83.914 603 83 11 5880 6471 539576436 539575837 1.610000e-156 564.0
19 TraesCS1D01G304600 chr1B 86.534 453 31 8 8008 8435 539656901 539656454 1.010000e-128 472.0
20 TraesCS1D01G304600 chr1B 95.785 261 10 1 1914 2173 211479121 211478861 3.690000e-113 420.0
21 TraesCS1D01G304600 chr1B 85.152 330 42 3 5531 5853 539576719 539576390 1.780000e-86 331.0
22 TraesCS1D01G304600 chr1B 92.424 198 13 2 4518 4714 539659881 539659685 1.820000e-71 281.0
23 TraesCS1D01G304600 chr1A 94.472 3274 124 24 4985 8221 497619853 497616600 0.000000e+00 4990.0
24 TraesCS1D01G304600 chr1A 93.080 3295 149 36 2175 5432 497623512 497620260 0.000000e+00 4748.0
25 TraesCS1D01G304600 chr1A 87.356 870 87 13 3699 4551 497541596 497540733 0.000000e+00 976.0
26 TraesCS1D01G304600 chr1A 92.170 613 44 1 4518 5130 497620964 497620356 0.000000e+00 863.0
27 TraesCS1D01G304600 chr1A 84.577 603 79 12 5880 6471 497540441 497539842 3.440000e-163 586.0
28 TraesCS1D01G304600 chr1A 92.308 403 31 0 4518 4920 497620758 497620356 2.680000e-159 573.0
29 TraesCS1D01G304600 chr1A 85.095 577 64 14 924 1483 497625432 497624861 3.470000e-158 569.0
30 TraesCS1D01G304600 chr1A 85.960 349 25 8 598 922 497625618 497625270 1.370000e-92 351.0
31 TraesCS1D01G304600 chr1A 76.958 664 117 26 7161 7794 497539108 497538451 6.360000e-91 346.0
32 TraesCS1D01G304600 chr1A 85.758 330 40 5 5531 5853 497540724 497540395 8.220000e-90 342.0
33 TraesCS1D01G304600 chr1A 92.000 125 10 0 8432 8556 59223025 59222901 8.830000e-40 176.0
34 TraesCS1D01G304600 chr1A 85.567 97 7 6 1815 1910 497623617 497623527 2.540000e-15 95.3
35 TraesCS1D01G304600 chr7B 92.299 1844 87 22 2637 4442 722942692 722940866 0.000000e+00 2567.0
36 TraesCS1D01G304600 chr4B 92.161 1837 105 16 2639 4442 360710732 360708902 0.000000e+00 2558.0
37 TraesCS1D01G304600 chr2A 84.859 1671 221 20 3265 4920 84545457 84547110 0.000000e+00 1655.0
38 TraesCS1D01G304600 chr2A 87.204 930 102 8 4930 5853 84546714 84547632 0.000000e+00 1042.0
39 TraesCS1D01G304600 chr2A 85.012 407 51 3 4724 5130 84546714 84547110 1.030000e-108 405.0
40 TraesCS1D01G304600 chr2A 89.630 135 14 0 8422 8556 79301649 79301515 1.140000e-38 172.0
41 TraesCS1D01G304600 chr2B 83.846 1690 223 24 3265 4920 135682776 135684449 0.000000e+00 1563.0
42 TraesCS1D01G304600 chr2B 87.784 925 100 6 4930 5853 135684053 135684965 0.000000e+00 1070.0
43 TraesCS1D01G304600 chr2B 87.337 766 86 9 5881 6641 135684920 135685679 0.000000e+00 867.0
44 TraesCS1D01G304600 chr2B 95.367 259 10 2 1914 2171 357919820 357919563 2.220000e-110 411.0
45 TraesCS1D01G304600 chr2B 94.615 260 13 1 1915 2173 245947962 245948221 1.340000e-107 401.0
46 TraesCS1D01G304600 chr2B 79.877 487 73 16 7114 7591 135686055 135686525 4.950000e-87 333.0
47 TraesCS1D01G304600 chr2B 91.803 122 10 0 8435 8556 37434778 37434899 4.110000e-38 171.0
48 TraesCS1D01G304600 chr2D 85.601 1382 173 14 3553 4920 83815940 83817309 0.000000e+00 1426.0
49 TraesCS1D01G304600 chr2D 87.284 928 102 8 4930 5853 83816913 83817828 0.000000e+00 1046.0
50 TraesCS1D01G304600 chr2D 83.650 1052 131 23 5881 6919 83817783 83818806 0.000000e+00 952.0
51 TraesCS1D01G304600 chr2D 79.844 640 93 16 7114 7733 83818951 83819574 1.320000e-117 435.0
52 TraesCS1D01G304600 chr2D 82.203 118 16 2 1588 1703 615459480 615459366 7.070000e-16 97.1
53 TraesCS1D01G304600 chr6B 95.753 259 10 1 1916 2173 694428087 694428345 4.780000e-112 416.0
54 TraesCS1D01G304600 chr6B 76.000 175 40 2 1576 1749 290683538 290683365 1.180000e-13 89.8
55 TraesCS1D01G304600 chr6B 76.000 175 40 2 1576 1749 290705219 290705046 1.180000e-13 89.8
56 TraesCS1D01G304600 chr6B 93.750 48 3 0 8509 8556 18184522 18184475 1.190000e-08 73.1
57 TraesCS1D01G304600 chr7A 95.367 259 12 0 1915 2173 44210559 44210817 6.180000e-111 412.0
58 TraesCS1D01G304600 chr3D 95.367 259 10 2 1916 2173 447584884 447585141 2.220000e-110 411.0
59 TraesCS1D01G304600 chr4D 94.656 262 14 0 1915 2176 479154485 479154224 2.880000e-109 407.0
60 TraesCS1D01G304600 chr3B 94.297 263 14 1 1915 2176 507455405 507455143 1.340000e-107 401.0
61 TraesCS1D01G304600 chr3B 76.768 198 43 3 1574 1771 706778560 706778754 3.270000e-19 108.0
62 TraesCS1D01G304600 chr3B 77.500 160 32 4 1567 1724 9580574 9580417 9.140000e-15 93.5
63 TraesCS1D01G304600 chr5D 96.825 126 4 0 8431 8556 274145937 274146062 2.420000e-50 211.0
64 TraesCS1D01G304600 chr5D 79.518 166 28 6 1574 1736 441791866 441791704 7.020000e-21 113.0
65 TraesCS1D01G304600 chr6D 95.082 122 6 0 8435 8556 297842843 297842964 8.760000e-45 193.0
66 TraesCS1D01G304600 chr6D 97.297 37 1 0 8433 8469 8570230 8570194 7.170000e-06 63.9
67 TraesCS1D01G304600 chr5B 89.683 126 13 0 8431 8556 57444050 57444175 2.470000e-35 161.0
68 TraesCS1D01G304600 chrUn 79.870 154 28 3 1575 1727 48697985 48698136 9.080000e-20 110.0
69 TraesCS1D01G304600 chr3A 78.788 132 24 4 1574 1703 638017496 638017625 1.530000e-12 86.1
70 TraesCS1D01G304600 chr5A 100.000 28 0 0 1507 1534 546765372 546765345 1.600000e-02 52.8


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 TraesCS1D01G304600 chr1D 402124506 402133061 8555 True 15801.000000 15801 100.000000 1 8556 1 chr1D.!!$R1 8555
1 TraesCS1D01G304600 chr1D 401707453 401710892 3439 True 587.250000 1016 84.392250 3713 7794 4 chr1D.!!$R2 4081
2 TraesCS1D01G304600 chr1D 402127726 402132288 4562 True 545.000000 878 91.648800 774 5336 5 chr1D.!!$R3 4562
3 TraesCS1D01G304600 chr1B 539656454 539664675 8221 True 1871.142857 8660 90.530143 1 8435 7 chr1B.!!$R3 8434
4 TraesCS1D01G304600 chr1B 539575837 539577586 1749 True 618.000000 959 85.430000 3713 6471 3 chr1B.!!$R2 2758
5 TraesCS1D01G304600 chr1A 497616600 497625618 9018 True 1741.328571 4990 89.807429 598 8221 7 chr1A.!!$R3 7623
6 TraesCS1D01G304600 chr1A 497538451 497541596 3145 True 562.500000 976 83.662250 3699 7794 4 chr1A.!!$R2 4095
7 TraesCS1D01G304600 chr7B 722940866 722942692 1826 True 2567.000000 2567 92.299000 2637 4442 1 chr7B.!!$R1 1805
8 TraesCS1D01G304600 chr4B 360708902 360710732 1830 True 2558.000000 2558 92.161000 2639 4442 1 chr4B.!!$R1 1803
9 TraesCS1D01G304600 chr2A 84545457 84547632 2175 False 1034.000000 1655 85.691667 3265 5853 3 chr2A.!!$F1 2588
10 TraesCS1D01G304600 chr2B 135682776 135686525 3749 False 958.250000 1563 84.711000 3265 7591 4 chr2B.!!$F3 4326
11 TraesCS1D01G304600 chr2D 83815940 83819574 3634 False 964.750000 1426 84.094750 3553 7733 4 chr2D.!!$F1 4180

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
688 701 0.380378 GTCGCGATCTTGCTCTCTCT 59.620 55.0 14.06 0.0 0.0 3.10 F
2871 4172 1.388837 AAACGGGCCTGCGTCTTTTT 61.389 50.0 12.89 0.0 0.0 1.94 F
2872 4173 1.792118 AACGGGCCTGCGTCTTTTTC 61.792 55.0 12.89 0.0 0.0 2.29 F
5349 7596 2.425143 AATCCACTCGCCACATCAAT 57.575 45.0 0.00 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2871 4172 0.323542 GGAGGAACTGACGGAGAGGA 60.324 60.000 0.00 0.0 41.55 3.71 R
5180 7427 3.578282 TCACATACTTCTGAAGGACAGCA 59.422 43.478 20.61 0.0 45.38 4.41 R
5349 7596 3.381272 CACTTGTCCAGGCAAAGAAGAAA 59.619 43.478 7.72 0.0 0.00 2.52 R
7800 10655 0.744281 CAGTCACCGCCAAAAAGGTT 59.256 50.000 0.00 0.0 39.00 3.50 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 8.957466 GTTCTACACCTTTTTATGCTAATTCCT 58.043 33.333 0.00 0.00 0.00 3.36
172 174 6.777213 AAGAACTAGTGGTGGTCATACTAG 57.223 41.667 16.58 16.58 45.81 2.57
226 228 9.672673 TTTTTAAAGAAACAAATCCATCACCAA 57.327 25.926 0.00 0.00 0.00 3.67
227 229 9.672673 TTTTAAAGAAACAAATCCATCACCAAA 57.327 25.926 0.00 0.00 0.00 3.28
228 230 9.844257 TTTAAAGAAACAAATCCATCACCAAAT 57.156 25.926 0.00 0.00 0.00 2.32
229 231 9.844257 TTAAAGAAACAAATCCATCACCAAATT 57.156 25.926 0.00 0.00 0.00 1.82
303 305 9.853555 ATTTTATTGCTTGTAAACGATGATTGA 57.146 25.926 0.00 0.00 0.00 2.57
355 357 2.359975 CCCACCCCTCTTCAACGC 60.360 66.667 0.00 0.00 0.00 4.84
375 377 7.752686 TCAACGCGAATCAAAATCATTGAAATA 59.247 29.630 15.93 0.00 31.55 1.40
376 378 8.533965 CAACGCGAATCAAAATCATTGAAATAT 58.466 29.630 15.93 0.00 31.55 1.28
496 499 5.115472 CGTCACATGTTTATTGTTTGCACTC 59.885 40.000 0.00 0.00 0.00 3.51
508 511 2.568696 TTGCACTCTAGTCGATGCTC 57.431 50.000 7.83 0.00 38.90 4.26
572 575 0.608640 CGGCCTTTATATCTCCCGCT 59.391 55.000 0.00 0.00 0.00 5.52
574 577 1.903183 GGCCTTTATATCTCCCGCTCT 59.097 52.381 0.00 0.00 0.00 4.09
581 584 5.470047 TTATATCTCCCGCTCTCTTTTCC 57.530 43.478 0.00 0.00 0.00 3.13
608 612 1.902508 CACATATCCCATCGCCCTAGT 59.097 52.381 0.00 0.00 0.00 2.57
636 643 2.596851 GCCAGGCTCCCAGACTTCA 61.597 63.158 3.29 0.00 24.26 3.02
669 682 1.546476 AGACAACTAGCCAACTCTCCG 59.454 52.381 0.00 0.00 0.00 4.63
682 695 2.103143 CTCCGTCGCGATCTTGCT 59.897 61.111 14.06 0.00 0.00 3.91
688 701 0.380378 GTCGCGATCTTGCTCTCTCT 59.620 55.000 14.06 0.00 0.00 3.10
2871 4172 1.388837 AAACGGGCCTGCGTCTTTTT 61.389 50.000 12.89 0.00 0.00 1.94
2872 4173 1.792118 AACGGGCCTGCGTCTTTTTC 61.792 55.000 12.89 0.00 0.00 2.29
5349 7596 2.425143 AATCCACTCGCCACATCAAT 57.575 45.000 0.00 0.00 0.00 2.57
5669 7923 8.530311 TGTATTTCATCATTACAGCCAATGTTT 58.470 29.630 3.93 0.00 39.96 2.83
5938 8199 7.526608 TCTAAACAATACTAGCAAACATGTGC 58.473 34.615 0.00 0.00 45.28 4.57
6115 8385 1.075601 AACCTTGGCTGAGGAATGGA 58.924 50.000 13.31 0.00 39.25 3.41
6272 8542 6.385649 TCTCCCTTGTTTTGTATTGTTGAC 57.614 37.500 0.00 0.00 0.00 3.18
6302 8572 3.340814 ACTACCTCCAAACTCATGCTG 57.659 47.619 0.00 0.00 0.00 4.41
6353 8627 7.118723 TGGTCTATTTGCACTTCCATTTATCT 58.881 34.615 0.00 0.00 0.00 1.98
6412 8687 7.613022 AGAATATCATTTCTCCTTGCACTGAAA 59.387 33.333 0.00 0.00 29.99 2.69
6413 8688 5.640189 ATCATTTCTCCTTGCACTGAAAG 57.360 39.130 0.00 0.00 42.29 2.62
6583 8858 2.994578 GACCAACGAAAGGAAGAGCTAC 59.005 50.000 0.00 0.00 0.00 3.58
6621 8896 7.613801 AGGTATGTAAACATGTCTGGCAATAAA 59.386 33.333 0.00 0.00 37.15 1.40
6622 8897 8.413229 GGTATGTAAACATGTCTGGCAATAAAT 58.587 33.333 0.00 0.00 37.15 1.40
6742 9024 6.821160 TCTTTTTGTCAAAAGGTTTGGGAATC 59.179 34.615 16.96 0.00 46.30 2.52
6859 9528 5.476945 AGAAATTTAGGTGTTCCATGGTCAC 59.523 40.000 24.07 24.07 35.89 3.67
6863 9532 3.634397 AGGTGTTCCATGGTCACTATG 57.366 47.619 27.74 0.00 35.89 2.23
7024 9698 1.066143 TCGAGGAAGCTGGAAACATCC 60.066 52.381 0.00 0.00 41.51 3.51
7094 9768 2.608268 TGCGATGTTTTGGAATGCATG 58.392 42.857 0.00 0.00 0.00 4.06
7425 10245 4.307432 TCGGATTTCGATCTTATCCTTGC 58.693 43.478 12.80 0.00 43.74 4.01
7514 10334 0.459899 CCACGCTATCCTGTGCTACA 59.540 55.000 0.00 0.00 34.77 2.74
7531 10351 2.203070 AATGCGCGGATCCTGGAC 60.203 61.111 15.23 0.00 0.00 4.02
7711 10561 2.997303 GGGTGGTGTTTGTTGTTGTTTC 59.003 45.455 0.00 0.00 0.00 2.78
7799 10654 2.200899 GCGCTTGTTGTGAAATGGTTT 58.799 42.857 0.00 0.00 0.00 3.27
7800 10655 3.376540 GCGCTTGTTGTGAAATGGTTTA 58.623 40.909 0.00 0.00 0.00 2.01
7803 10658 4.208253 CGCTTGTTGTGAAATGGTTTAACC 59.792 41.667 7.27 7.27 39.22 2.85
7834 10689 1.843851 TGACTGAAACCTCTGTTGGGT 59.156 47.619 0.00 0.00 38.94 4.51
7877 10732 5.684704 TGGATTGTCAACTCTGAAGAAGTT 58.315 37.500 0.00 0.00 31.88 2.66
7888 10743 6.045955 ACTCTGAAGAAGTTCTCAACTGTTC 58.954 40.000 5.70 0.00 41.91 3.18
7919 10811 4.749245 TCCTTGCATCTTTCTTTCGTTC 57.251 40.909 0.00 0.00 0.00 3.95
7928 10820 6.142320 GCATCTTTCTTTCGTTCGTCAAATTT 59.858 34.615 0.00 0.00 0.00 1.82
7977 10871 7.573843 GCTTTGCTGTCACACTTCATAGTATTT 60.574 37.037 0.00 0.00 31.96 1.40
7978 10872 6.726258 TGCTGTCACACTTCATAGTATTTG 57.274 37.500 0.00 0.00 31.96 2.32
7979 10873 5.122239 TGCTGTCACACTTCATAGTATTTGC 59.878 40.000 0.00 0.00 31.96 3.68
7980 10874 5.122239 GCTGTCACACTTCATAGTATTTGCA 59.878 40.000 0.00 0.00 31.96 4.08
7981 10875 6.183360 GCTGTCACACTTCATAGTATTTGCAT 60.183 38.462 0.00 0.00 31.96 3.96
7982 10876 7.011389 GCTGTCACACTTCATAGTATTTGCATA 59.989 37.037 0.00 0.00 31.96 3.14
7984 10878 9.394767 TGTCACACTTCATAGTATTTGCATATT 57.605 29.630 0.00 0.00 31.96 1.28
7987 10881 9.817365 CACACTTCATAGTATTTGCATATTAGC 57.183 33.333 0.00 0.00 31.96 3.09
7988 10882 9.784531 ACACTTCATAGTATTTGCATATTAGCT 57.215 29.630 0.00 0.00 31.96 3.32
8010 10904 3.705051 AGACATCAAAATGCCCTCACAT 58.295 40.909 0.00 0.00 36.26 3.21
8011 10905 4.858850 AGACATCAAAATGCCCTCACATA 58.141 39.130 0.00 0.00 36.26 2.29
8232 11195 3.173599 CACGCATGTGCTTTTGATTAGG 58.826 45.455 6.08 0.00 39.67 2.69
8233 11196 2.187707 CGCATGTGCTTTTGATTAGGC 58.812 47.619 3.25 0.00 39.32 3.93
8234 11197 2.415759 CGCATGTGCTTTTGATTAGGCA 60.416 45.455 3.25 0.00 39.32 4.75
8235 11198 3.735820 CGCATGTGCTTTTGATTAGGCAT 60.736 43.478 3.25 0.00 39.32 4.40
8241 11204 8.737175 CATGTGCTTTTGATTAGGCATATATCT 58.263 33.333 0.00 0.00 35.42 1.98
8247 11210 8.696043 TTTTGATTAGGCATATATCTTGCTGT 57.304 30.769 9.64 2.42 40.03 4.40
8259 11222 0.590195 CTTGCTGTCTTGTGACCTGC 59.410 55.000 0.00 0.00 42.28 4.85
8276 11239 4.469883 CCAGCAGGCATAAGCGAT 57.530 55.556 0.00 0.00 43.41 4.58
8305 11268 1.148310 ACATTCCACGACTTTGCTCG 58.852 50.000 0.00 0.00 39.68 5.03
8306 11269 1.270094 ACATTCCACGACTTTGCTCGA 60.270 47.619 0.00 0.00 37.11 4.04
8307 11270 1.391485 CATTCCACGACTTTGCTCGAG 59.609 52.381 8.45 8.45 37.11 4.04
8308 11271 0.944311 TTCCACGACTTTGCTCGAGC 60.944 55.000 30.42 30.42 42.50 5.03
8309 11272 1.373497 CCACGACTTTGCTCGAGCT 60.373 57.895 35.27 17.76 42.66 4.09
8310 11273 1.347817 CCACGACTTTGCTCGAGCTC 61.348 60.000 35.27 23.71 42.66 4.09
8311 11274 0.664466 CACGACTTTGCTCGAGCTCA 60.664 55.000 35.27 20.87 42.66 4.26
8332 11316 0.528924 CCCCAACTGACATGCACATG 59.471 55.000 9.06 9.06 44.15 3.21
8367 11354 3.502920 CAAACCGCACTACTACTCAGAG 58.497 50.000 0.00 0.00 0.00 3.35
8368 11355 2.783609 ACCGCACTACTACTCAGAGA 57.216 50.000 3.79 0.00 0.00 3.10
8428 11415 8.258007 ACTAACTCGATGATCCAAGAAAACATA 58.742 33.333 0.00 0.00 0.00 2.29
8435 11422 8.664798 CGATGATCCAAGAAAACATACACTTAA 58.335 33.333 0.00 0.00 0.00 1.85
8436 11423 9.994432 GATGATCCAAGAAAACATACACTTAAG 57.006 33.333 0.00 0.00 0.00 1.85
8437 11424 7.816640 TGATCCAAGAAAACATACACTTAAGC 58.183 34.615 1.29 0.00 0.00 3.09
8438 11425 6.569179 TCCAAGAAAACATACACTTAAGCC 57.431 37.500 1.29 0.00 0.00 4.35
8439 11426 5.475564 TCCAAGAAAACATACACTTAAGCCC 59.524 40.000 1.29 0.00 0.00 5.19
8440 11427 5.476945 CCAAGAAAACATACACTTAAGCCCT 59.523 40.000 1.29 0.00 0.00 5.19
8441 11428 6.381801 CAAGAAAACATACACTTAAGCCCTG 58.618 40.000 1.29 0.00 0.00 4.45
8442 11429 5.631119 AGAAAACATACACTTAAGCCCTGT 58.369 37.500 1.29 2.37 0.00 4.00
8443 11430 6.068670 AGAAAACATACACTTAAGCCCTGTT 58.931 36.000 1.29 5.10 0.00 3.16
8444 11431 5.959618 AAACATACACTTAAGCCCTGTTC 57.040 39.130 1.29 0.00 0.00 3.18
8445 11432 3.596214 ACATACACTTAAGCCCTGTTCG 58.404 45.455 1.29 0.00 0.00 3.95
8446 11433 2.754946 TACACTTAAGCCCTGTTCGG 57.245 50.000 1.29 0.00 0.00 4.30
8447 11434 1.053424 ACACTTAAGCCCTGTTCGGA 58.947 50.000 1.29 0.00 33.16 4.55
8448 11435 1.002087 ACACTTAAGCCCTGTTCGGAG 59.998 52.381 1.29 0.00 33.16 4.63
8449 11436 1.002087 CACTTAAGCCCTGTTCGGAGT 59.998 52.381 1.29 0.00 33.16 3.85
8450 11437 1.275573 ACTTAAGCCCTGTTCGGAGTC 59.724 52.381 1.29 0.00 33.16 3.36
8451 11438 0.611714 TTAAGCCCTGTTCGGAGTCC 59.388 55.000 0.00 0.00 33.16 3.85
8452 11439 1.262640 TAAGCCCTGTTCGGAGTCCC 61.263 60.000 2.80 0.00 33.16 4.46
8453 11440 3.003763 GCCCTGTTCGGAGTCCCT 61.004 66.667 2.80 0.00 33.16 4.20
8454 11441 3.020237 GCCCTGTTCGGAGTCCCTC 62.020 68.421 2.80 0.00 33.16 4.30
8455 11442 2.359967 CCCTGTTCGGAGTCCCTCC 61.360 68.421 2.80 0.00 46.44 4.30
8463 11450 2.363147 GAGTCCCTCCACTCCGCT 60.363 66.667 0.00 0.00 37.43 5.52
8464 11451 2.681778 AGTCCCTCCACTCCGCTG 60.682 66.667 0.00 0.00 0.00 5.18
8465 11452 4.459089 GTCCCTCCACTCCGCTGC 62.459 72.222 0.00 0.00 0.00 5.25
8466 11453 4.704103 TCCCTCCACTCCGCTGCT 62.704 66.667 0.00 0.00 0.00 4.24
8467 11454 4.154347 CCCTCCACTCCGCTGCTC 62.154 72.222 0.00 0.00 0.00 4.26
8468 11455 4.154347 CCTCCACTCCGCTGCTCC 62.154 72.222 0.00 0.00 0.00 4.70
8469 11456 3.385384 CTCCACTCCGCTGCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
8470 11457 3.655810 CTCCACTCCGCTGCTCCAC 62.656 68.421 0.00 0.00 0.00 4.02
8471 11458 3.699894 CCACTCCGCTGCTCCACT 61.700 66.667 0.00 0.00 0.00 4.00
8472 11459 2.125753 CACTCCGCTGCTCCACTC 60.126 66.667 0.00 0.00 0.00 3.51
8473 11460 3.386237 ACTCCGCTGCTCCACTCC 61.386 66.667 0.00 0.00 0.00 3.85
8474 11461 4.504916 CTCCGCTGCTCCACTCCG 62.505 72.222 0.00 0.00 0.00 4.63
8498 11485 3.966215 GCGTGGAGCTGCAGTTAA 58.034 55.556 16.64 0.00 44.04 2.01
8499 11486 2.244000 GCGTGGAGCTGCAGTTAAA 58.756 52.632 16.64 0.00 44.04 1.52
8500 11487 0.110192 GCGTGGAGCTGCAGTTAAAC 60.110 55.000 16.64 10.05 44.04 2.01
8501 11488 1.225855 CGTGGAGCTGCAGTTAAACA 58.774 50.000 16.64 6.78 0.00 2.83
8502 11489 1.195448 CGTGGAGCTGCAGTTAAACAG 59.805 52.381 16.64 4.49 36.96 3.16
8503 11490 2.222027 GTGGAGCTGCAGTTAAACAGT 58.778 47.619 16.64 0.00 36.26 3.55
8504 11491 3.399330 GTGGAGCTGCAGTTAAACAGTA 58.601 45.455 16.64 0.00 36.26 2.74
8505 11492 3.186613 GTGGAGCTGCAGTTAAACAGTAC 59.813 47.826 16.64 0.00 36.26 2.73
8506 11493 2.412089 GGAGCTGCAGTTAAACAGTACG 59.588 50.000 16.64 0.00 36.26 3.67
8507 11494 3.314553 GAGCTGCAGTTAAACAGTACGA 58.685 45.455 16.64 0.00 36.26 3.43
8508 11495 3.724374 AGCTGCAGTTAAACAGTACGAA 58.276 40.909 16.64 0.00 36.26 3.85
8509 11496 3.741344 AGCTGCAGTTAAACAGTACGAAG 59.259 43.478 16.64 0.00 36.26 3.79
8510 11497 3.664537 GCTGCAGTTAAACAGTACGAAGC 60.665 47.826 16.64 0.00 36.26 3.86
8511 11498 3.724374 TGCAGTTAAACAGTACGAAGCT 58.276 40.909 0.00 0.00 0.00 3.74
8512 11499 3.493129 TGCAGTTAAACAGTACGAAGCTG 59.507 43.478 0.00 0.00 39.67 4.24
8513 11500 3.664537 GCAGTTAAACAGTACGAAGCTGC 60.665 47.826 0.00 0.00 39.65 5.25
8514 11501 3.493129 CAGTTAAACAGTACGAAGCTGCA 59.507 43.478 1.02 0.00 37.47 4.41
8515 11502 3.741344 AGTTAAACAGTACGAAGCTGCAG 59.259 43.478 10.11 10.11 37.47 4.41
8516 11503 2.240493 AAACAGTACGAAGCTGCAGT 57.760 45.000 16.64 0.00 37.47 4.40
8517 11504 1.784525 AACAGTACGAAGCTGCAGTC 58.215 50.000 16.64 7.83 37.47 3.51
8518 11505 0.038159 ACAGTACGAAGCTGCAGTCC 60.038 55.000 16.64 0.00 37.47 3.85
8519 11506 0.038251 CAGTACGAAGCTGCAGTCCA 60.038 55.000 16.64 0.00 0.00 4.02
8520 11507 0.898320 AGTACGAAGCTGCAGTCCAT 59.102 50.000 16.64 0.00 0.00 3.41
8521 11508 1.134965 AGTACGAAGCTGCAGTCCATC 60.135 52.381 16.64 7.74 0.00 3.51
8522 11509 0.175760 TACGAAGCTGCAGTCCATCC 59.824 55.000 16.64 0.00 0.00 3.51
8523 11510 1.078918 CGAAGCTGCAGTCCATCCA 60.079 57.895 16.64 0.00 0.00 3.41
8524 11511 1.364626 CGAAGCTGCAGTCCATCCAC 61.365 60.000 16.64 0.00 0.00 4.02
8525 11512 0.035630 GAAGCTGCAGTCCATCCACT 60.036 55.000 16.64 0.00 0.00 4.00
8526 11513 0.035630 AAGCTGCAGTCCATCCACTC 60.036 55.000 16.64 0.00 0.00 3.51
8527 11514 0.908656 AGCTGCAGTCCATCCACTCT 60.909 55.000 16.64 0.00 0.00 3.24
8528 11515 0.743701 GCTGCAGTCCATCCACTCTG 60.744 60.000 16.64 0.00 0.00 3.35
8529 11516 4.215349 GCAGTCCATCCACTCTGC 57.785 61.111 0.00 0.00 44.50 4.26
8531 11518 3.455328 CAGTCCATCCACTCTGCAG 57.545 57.895 7.63 7.63 0.00 4.41
8532 11519 0.743701 CAGTCCATCCACTCTGCAGC 60.744 60.000 9.47 0.00 0.00 5.25
8533 11520 0.908656 AGTCCATCCACTCTGCAGCT 60.909 55.000 9.47 0.00 0.00 4.24
8534 11521 0.461693 GTCCATCCACTCTGCAGCTC 60.462 60.000 9.47 0.00 0.00 4.09
8535 11522 1.153208 CCATCCACTCTGCAGCTCC 60.153 63.158 9.47 0.00 0.00 4.70
8536 11523 1.624479 CCATCCACTCTGCAGCTCCT 61.624 60.000 9.47 0.00 0.00 3.69
8537 11524 0.179078 CATCCACTCTGCAGCTCCTC 60.179 60.000 9.47 0.00 0.00 3.71
8538 11525 1.674764 ATCCACTCTGCAGCTCCTCG 61.675 60.000 9.47 0.00 0.00 4.63
8539 11526 2.644212 CCACTCTGCAGCTCCTCGT 61.644 63.158 9.47 0.00 0.00 4.18
8540 11527 1.315981 CCACTCTGCAGCTCCTCGTA 61.316 60.000 9.47 0.00 0.00 3.43
8541 11528 0.743688 CACTCTGCAGCTCCTCGTAT 59.256 55.000 9.47 0.00 0.00 3.06
8542 11529 1.135915 CACTCTGCAGCTCCTCGTATT 59.864 52.381 9.47 0.00 0.00 1.89
8543 11530 1.827969 ACTCTGCAGCTCCTCGTATTT 59.172 47.619 9.47 0.00 0.00 1.40
8544 11531 2.234908 ACTCTGCAGCTCCTCGTATTTT 59.765 45.455 9.47 0.00 0.00 1.82
8545 11532 2.606725 CTCTGCAGCTCCTCGTATTTTG 59.393 50.000 9.47 0.00 0.00 2.44
8546 11533 2.233676 TCTGCAGCTCCTCGTATTTTGA 59.766 45.455 9.47 0.00 0.00 2.69
8547 11534 2.606725 CTGCAGCTCCTCGTATTTTGAG 59.393 50.000 0.00 0.00 0.00 3.02
8555 11542 3.252974 CTCGTATTTTGAGGAGCTGGT 57.747 47.619 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 118 7.093771 CCCTTAGACTTGCATGGTTTCTAAAAT 60.094 37.037 4.44 0.00 30.37 1.82
123 125 2.557452 CCCCCTTAGACTTGCATGGTTT 60.557 50.000 4.44 0.00 0.00 3.27
172 174 2.294512 GGCATTAAGACATAGGCAAGCC 59.705 50.000 2.02 2.02 0.00 4.35
269 271 9.051027 CGTTTACAAGCAATAAAATGAGTGTAG 57.949 33.333 0.00 0.00 0.00 2.74
303 305 4.080526 GTGGTGAATGTACTTGGGTCCTAT 60.081 45.833 0.00 0.00 0.00 2.57
413 415 9.896645 ATTGATTGCCGAGATATAAGATTATGT 57.103 29.630 0.00 0.00 0.00 2.29
470 473 5.910166 GTGCAAACAATAAACATGTGACGTA 59.090 36.000 0.00 0.00 0.00 3.57
508 511 4.150980 TCTTGTAGCAAATTGTACCGTTCG 59.849 41.667 0.00 0.00 0.00 3.95
572 575 0.765135 TGTGGTCGGGGGAAAAGAGA 60.765 55.000 0.00 0.00 0.00 3.10
574 577 1.659022 TATGTGGTCGGGGGAAAAGA 58.341 50.000 0.00 0.00 0.00 2.52
581 584 0.324943 GATGGGATATGTGGTCGGGG 59.675 60.000 0.00 0.00 0.00 5.73
630 637 3.243177 GTCTATTCGATGCGGTTGAAGTC 59.757 47.826 0.00 0.00 33.75 3.01
632 639 3.186909 TGTCTATTCGATGCGGTTGAAG 58.813 45.455 0.00 0.00 33.75 3.02
636 643 3.247006 AGTTGTCTATTCGATGCGGTT 57.753 42.857 0.00 0.00 0.00 4.44
669 682 0.380378 AGAGAGAGCAAGATCGCGAC 59.620 55.000 12.93 5.67 36.85 5.19
682 695 2.370281 CTTAACCAAGCGCAGAGAGA 57.630 50.000 11.47 0.00 0.00 3.10
1096 1110 0.456653 GCTGATGCGCGGAACAAAAT 60.457 50.000 12.25 0.00 0.00 1.82
2871 4172 0.323542 GGAGGAACTGACGGAGAGGA 60.324 60.000 0.00 0.00 41.55 3.71
2872 4173 0.612174 TGGAGGAACTGACGGAGAGG 60.612 60.000 0.00 0.00 41.55 3.69
5180 7427 3.578282 TCACATACTTCTGAAGGACAGCA 59.422 43.478 20.61 0.00 45.38 4.41
5349 7596 3.381272 CACTTGTCCAGGCAAAGAAGAAA 59.619 43.478 7.72 0.00 0.00 2.52
5468 7721 9.921637 CTTTAACTAAATATTGGCTGGAACAAA 57.078 29.630 0.00 0.00 38.70 2.83
5669 7923 3.328931 AGCAGAAATTCTTCCTCTGTCCA 59.671 43.478 0.00 0.00 39.05 4.02
5938 8199 1.155889 TGCTGCATTACTTGTCCACG 58.844 50.000 0.00 0.00 0.00 4.94
6115 8385 7.226325 CACAATTACATGGGTCACATTTTTGTT 59.774 33.333 0.00 0.00 37.84 2.83
6272 8542 7.262772 TGAGTTTGGAGGTAGTACAATAATCG 58.737 38.462 2.06 0.00 0.00 3.34
6353 8627 5.353394 AGGATAAGTTTTAGATCGCCACA 57.647 39.130 0.00 0.00 0.00 4.17
6412 8687 6.214191 AGACATGAATATGACGTGAACTCT 57.786 37.500 0.00 1.12 37.73 3.24
6413 8688 6.893958 AAGACATGAATATGACGTGAACTC 57.106 37.500 0.00 0.00 37.73 3.01
6583 8858 2.105006 ACATACCTGTTCAGCAGCTG 57.895 50.000 17.10 17.10 43.71 4.24
6595 8870 4.568072 TGCCAGACATGTTTACATACCT 57.432 40.909 0.00 0.00 34.26 3.08
6672 8954 2.566952 GCATAAGGCAAACTGCGATT 57.433 45.000 0.00 0.00 46.21 3.34
6863 9532 8.577296 ACCTTATAAAAGAAAAGCTCTTGGAAC 58.423 33.333 0.00 0.00 44.00 3.62
7024 9698 7.962917 AGAATTTGTAAAACAACACTGCAAAG 58.037 30.769 0.00 0.00 37.90 2.77
7094 9768 8.449397 GCATTCATAAGATCCATGACTATTGAC 58.551 37.037 7.03 0.00 32.23 3.18
7238 10058 4.017407 TCTGTCTTCAGGGTCTATGTAGGT 60.017 45.833 0.00 0.00 41.59 3.08
7425 10245 1.836166 TGCTCTCCTGAATCTCCTTGG 59.164 52.381 0.00 0.00 0.00 3.61
7496 10316 2.293677 TTGTAGCACAGGATAGCGTG 57.706 50.000 0.00 0.00 36.18 5.34
7514 10334 2.203070 GTCCAGGATCCGCGCATT 60.203 61.111 8.75 0.00 0.00 3.56
7531 10351 1.048724 TATCTTGGTGAGGCCTCCGG 61.049 60.000 29.95 14.47 38.35 5.14
7711 10561 1.577328 AAACGAGCAATCCAGCACCG 61.577 55.000 0.00 0.00 38.29 4.94
7799 10654 1.950909 CAGTCACCGCCAAAAAGGTTA 59.049 47.619 0.00 0.00 39.00 2.85
7800 10655 0.744281 CAGTCACCGCCAAAAAGGTT 59.256 50.000 0.00 0.00 39.00 3.50
7803 10658 2.459934 GTTTCAGTCACCGCCAAAAAG 58.540 47.619 0.00 0.00 0.00 2.27
7834 10689 8.361889 CAATCCAATTCCAAACATATGATGCTA 58.638 33.333 10.38 0.00 0.00 3.49
7877 10732 3.662759 ACAAAAGGGGAACAGTTGAGA 57.337 42.857 0.00 0.00 0.00 3.27
7888 10743 2.250924 AGATGCAAGGAACAAAAGGGG 58.749 47.619 0.00 0.00 0.00 4.79
7977 10871 7.308770 GGCATTTTGATGTCTAGCTAATATGCA 60.309 37.037 15.64 0.00 36.22 3.96
7978 10872 7.025963 GGCATTTTGATGTCTAGCTAATATGC 58.974 38.462 8.96 8.96 34.36 3.14
7979 10873 7.392673 AGGGCATTTTGATGTCTAGCTAATATG 59.607 37.037 0.00 0.00 0.00 1.78
7980 10874 7.465116 AGGGCATTTTGATGTCTAGCTAATAT 58.535 34.615 0.00 0.00 0.00 1.28
7981 10875 6.841601 AGGGCATTTTGATGTCTAGCTAATA 58.158 36.000 0.00 0.00 0.00 0.98
7982 10876 5.699143 AGGGCATTTTGATGTCTAGCTAAT 58.301 37.500 0.00 0.00 0.00 1.73
7984 10878 4.164030 TGAGGGCATTTTGATGTCTAGCTA 59.836 41.667 0.00 0.00 0.00 3.32
7985 10879 3.054139 TGAGGGCATTTTGATGTCTAGCT 60.054 43.478 0.00 0.00 0.00 3.32
7986 10880 3.065925 GTGAGGGCATTTTGATGTCTAGC 59.934 47.826 0.00 0.00 0.00 3.42
7987 10881 4.264253 TGTGAGGGCATTTTGATGTCTAG 58.736 43.478 0.00 0.00 0.00 2.43
7988 10882 4.299586 TGTGAGGGCATTTTGATGTCTA 57.700 40.909 0.00 0.00 0.00 2.59
7989 10883 3.159213 TGTGAGGGCATTTTGATGTCT 57.841 42.857 0.00 0.00 0.00 3.41
7990 10884 4.641989 ACTATGTGAGGGCATTTTGATGTC 59.358 41.667 0.00 0.00 0.00 3.06
7998 10892 2.500098 ACACGTACTATGTGAGGGCATT 59.500 45.455 14.27 0.00 37.29 3.56
8010 10904 1.167851 CCGGTCCTTGACACGTACTA 58.832 55.000 0.00 0.00 33.68 1.82
8011 10905 1.962144 CCGGTCCTTGACACGTACT 59.038 57.895 0.00 0.00 33.68 2.73
8081 11043 1.683385 GCTTGGCCTCTGACTTTTGTT 59.317 47.619 3.32 0.00 0.00 2.83
8221 11184 8.790718 ACAGCAAGATATATGCCTAATCAAAAG 58.209 33.333 8.87 0.00 44.91 2.27
8222 11185 8.696043 ACAGCAAGATATATGCCTAATCAAAA 57.304 30.769 8.87 0.00 44.91 2.44
8223 11186 8.159447 AGACAGCAAGATATATGCCTAATCAAA 58.841 33.333 8.87 0.00 44.91 2.69
8224 11187 7.683578 AGACAGCAAGATATATGCCTAATCAA 58.316 34.615 8.87 0.00 44.91 2.57
8225 11188 7.250032 AGACAGCAAGATATATGCCTAATCA 57.750 36.000 8.87 0.00 44.91 2.57
8226 11189 7.605691 ACAAGACAGCAAGATATATGCCTAATC 59.394 37.037 8.87 3.52 44.91 1.75
8228 11191 6.707608 CACAAGACAGCAAGATATATGCCTAA 59.292 38.462 8.87 0.00 44.91 2.69
8229 11192 6.041979 TCACAAGACAGCAAGATATATGCCTA 59.958 38.462 8.87 0.00 44.91 3.93
8230 11193 5.061853 CACAAGACAGCAAGATATATGCCT 58.938 41.667 8.87 0.00 44.91 4.75
8231 11194 5.049818 GTCACAAGACAGCAAGATATATGCC 60.050 44.000 8.87 0.00 44.34 4.40
8232 11195 5.049818 GGTCACAAGACAGCAAGATATATGC 60.050 44.000 5.09 5.09 46.80 3.14
8233 11196 6.202379 CAGGTCACAAGACAGCAAGATATATG 59.798 42.308 0.00 0.00 46.80 1.78
8234 11197 6.286758 CAGGTCACAAGACAGCAAGATATAT 58.713 40.000 0.00 0.00 46.80 0.86
8235 11198 5.664457 CAGGTCACAAGACAGCAAGATATA 58.336 41.667 0.00 0.00 46.80 0.86
8241 11204 0.819259 GGCAGGTCACAAGACAGCAA 60.819 55.000 12.16 0.00 46.80 3.91
8247 11210 1.071987 CTGCTGGCAGGTCACAAGA 59.928 57.895 17.64 0.00 40.17 3.02
8259 11222 0.533531 TCATCGCTTATGCCTGCTGG 60.534 55.000 5.03 5.03 35.38 4.85
8276 11239 3.006859 AGTCGTGGAATGTTCATCTGTCA 59.993 43.478 0.00 0.00 0.00 3.58
8281 11244 3.189287 AGCAAAGTCGTGGAATGTTCATC 59.811 43.478 0.00 0.00 0.00 2.92
8283 11246 2.548057 GAGCAAAGTCGTGGAATGTTCA 59.452 45.455 0.00 0.00 0.00 3.18
8305 11268 0.108585 TGTCAGTTGGGGTTGAGCTC 59.891 55.000 6.82 6.82 0.00 4.09
8306 11269 0.773644 ATGTCAGTTGGGGTTGAGCT 59.226 50.000 0.00 0.00 0.00 4.09
8307 11270 0.883833 CATGTCAGTTGGGGTTGAGC 59.116 55.000 0.00 0.00 0.00 4.26
8308 11271 0.883833 GCATGTCAGTTGGGGTTGAG 59.116 55.000 0.00 0.00 0.00 3.02
8309 11272 0.184692 TGCATGTCAGTTGGGGTTGA 59.815 50.000 0.00 0.00 0.00 3.18
8310 11273 0.314935 GTGCATGTCAGTTGGGGTTG 59.685 55.000 0.00 0.00 0.00 3.77
8311 11274 0.106268 TGTGCATGTCAGTTGGGGTT 60.106 50.000 0.00 0.00 0.00 4.11
8332 11316 1.326548 CGGTTTGCTAGTCGGCATTAC 59.673 52.381 0.00 0.00 42.09 1.89
8403 11390 6.968131 TGTTTTCTTGGATCATCGAGTTAG 57.032 37.500 0.00 0.00 0.00 2.34
8428 11415 1.002087 CTCCGAACAGGGCTTAAGTGT 59.998 52.381 4.02 0.00 41.52 3.55
8435 11422 3.003763 GGGACTCCGAACAGGGCT 61.004 66.667 0.00 0.00 41.52 5.19
8436 11423 3.003763 AGGGACTCCGAACAGGGC 61.004 66.667 0.00 0.00 41.52 5.19
8448 11435 4.459089 GCAGCGGAGTGGAGGGAC 62.459 72.222 0.00 0.00 0.00 4.46
8449 11436 4.704103 AGCAGCGGAGTGGAGGGA 62.704 66.667 0.00 0.00 0.00 4.20
8450 11437 4.154347 GAGCAGCGGAGTGGAGGG 62.154 72.222 0.00 0.00 0.00 4.30
8451 11438 4.154347 GGAGCAGCGGAGTGGAGG 62.154 72.222 0.00 0.00 0.00 4.30
8452 11439 3.385384 TGGAGCAGCGGAGTGGAG 61.385 66.667 0.00 0.00 0.00 3.86
8453 11440 3.695606 GTGGAGCAGCGGAGTGGA 61.696 66.667 0.00 0.00 0.00 4.02
8454 11441 3.655810 GAGTGGAGCAGCGGAGTGG 62.656 68.421 0.00 0.00 0.00 4.00
8455 11442 2.125753 GAGTGGAGCAGCGGAGTG 60.126 66.667 0.00 0.00 0.00 3.51
8456 11443 3.386237 GGAGTGGAGCAGCGGAGT 61.386 66.667 0.00 0.00 0.00 3.85
8457 11444 4.504916 CGGAGTGGAGCAGCGGAG 62.505 72.222 0.00 0.00 0.00 4.63
8461 11448 4.154347 CTCCCGGAGTGGAGCAGC 62.154 72.222 0.73 0.00 45.13 5.25
8481 11468 0.110192 GTTTAACTGCAGCTCCACGC 60.110 55.000 15.27 0.00 39.57 5.34
8482 11469 1.195448 CTGTTTAACTGCAGCTCCACG 59.805 52.381 15.27 0.00 0.00 4.94
8483 11470 2.222027 ACTGTTTAACTGCAGCTCCAC 58.778 47.619 15.27 6.69 36.26 4.02
8484 11471 2.638480 ACTGTTTAACTGCAGCTCCA 57.362 45.000 15.27 2.81 36.26 3.86
8485 11472 2.412089 CGTACTGTTTAACTGCAGCTCC 59.588 50.000 15.27 0.00 36.26 4.70
8486 11473 3.314553 TCGTACTGTTTAACTGCAGCTC 58.685 45.455 15.27 0.40 36.26 4.09
8487 11474 3.380479 TCGTACTGTTTAACTGCAGCT 57.620 42.857 15.27 3.62 36.26 4.24
8488 11475 3.664537 GCTTCGTACTGTTTAACTGCAGC 60.665 47.826 15.27 0.00 36.26 5.25
8489 11476 3.741344 AGCTTCGTACTGTTTAACTGCAG 59.259 43.478 13.48 13.48 38.58 4.41
8490 11477 3.493129 CAGCTTCGTACTGTTTAACTGCA 59.507 43.478 1.90 0.00 0.00 4.41
8491 11478 3.664537 GCAGCTTCGTACTGTTTAACTGC 60.665 47.826 1.90 0.00 40.89 4.40
8492 11479 3.493129 TGCAGCTTCGTACTGTTTAACTG 59.507 43.478 0.44 0.44 37.47 3.16
8493 11480 3.724374 TGCAGCTTCGTACTGTTTAACT 58.276 40.909 0.00 0.00 37.47 2.24
8494 11481 3.493503 ACTGCAGCTTCGTACTGTTTAAC 59.506 43.478 15.27 0.00 37.47 2.01
8495 11482 3.724374 ACTGCAGCTTCGTACTGTTTAA 58.276 40.909 15.27 0.00 37.47 1.52
8496 11483 3.314553 GACTGCAGCTTCGTACTGTTTA 58.685 45.455 15.27 0.00 37.47 2.01
8497 11484 2.135933 GACTGCAGCTTCGTACTGTTT 58.864 47.619 15.27 0.00 37.47 2.83
8498 11485 1.605712 GGACTGCAGCTTCGTACTGTT 60.606 52.381 15.27 0.00 37.47 3.16
8499 11486 0.038159 GGACTGCAGCTTCGTACTGT 60.038 55.000 15.27 0.00 37.47 3.55
8500 11487 0.038251 TGGACTGCAGCTTCGTACTG 60.038 55.000 15.27 0.00 38.22 2.74
8501 11488 0.898320 ATGGACTGCAGCTTCGTACT 59.102 50.000 15.27 0.00 0.00 2.73
8502 11489 1.281899 GATGGACTGCAGCTTCGTAC 58.718 55.000 15.27 0.00 0.00 3.67
8503 11490 0.175760 GGATGGACTGCAGCTTCGTA 59.824 55.000 15.27 0.00 0.00 3.43
8504 11491 1.078848 GGATGGACTGCAGCTTCGT 60.079 57.895 15.27 4.73 0.00 3.85
8505 11492 1.078918 TGGATGGACTGCAGCTTCG 60.079 57.895 15.27 0.00 0.00 3.79
8506 11493 0.035630 AGTGGATGGACTGCAGCTTC 60.036 55.000 15.27 4.48 0.00 3.86
8507 11494 0.035630 GAGTGGATGGACTGCAGCTT 60.036 55.000 15.27 0.00 0.00 3.74
8508 11495 0.908656 AGAGTGGATGGACTGCAGCT 60.909 55.000 15.27 0.23 0.00 4.24
8509 11496 0.743701 CAGAGTGGATGGACTGCAGC 60.744 60.000 15.27 6.61 0.00 5.25
8510 11497 3.455328 CAGAGTGGATGGACTGCAG 57.545 57.895 13.48 13.48 0.00 4.41
8512 11499 4.215349 GCAGAGTGGATGGACTGC 57.785 61.111 0.00 0.00 46.25 4.40
8513 11500 0.743701 GCTGCAGAGTGGATGGACTG 60.744 60.000 20.43 0.00 0.00 3.51
8514 11501 0.908656 AGCTGCAGAGTGGATGGACT 60.909 55.000 20.43 0.00 0.00 3.85
8515 11502 0.461693 GAGCTGCAGAGTGGATGGAC 60.462 60.000 20.43 0.00 0.00 4.02
8516 11503 1.620739 GGAGCTGCAGAGTGGATGGA 61.621 60.000 20.43 0.00 0.00 3.41
8517 11504 1.153208 GGAGCTGCAGAGTGGATGG 60.153 63.158 20.43 0.00 0.00 3.51
8518 11505 0.179078 GAGGAGCTGCAGAGTGGATG 60.179 60.000 20.43 0.00 0.00 3.51
8519 11506 1.674764 CGAGGAGCTGCAGAGTGGAT 61.675 60.000 20.43 0.00 0.00 3.41
8520 11507 2.346541 CGAGGAGCTGCAGAGTGGA 61.347 63.158 20.43 0.00 0.00 4.02
8521 11508 1.315981 TACGAGGAGCTGCAGAGTGG 61.316 60.000 20.43 3.06 0.00 4.00
8522 11509 0.743688 ATACGAGGAGCTGCAGAGTG 59.256 55.000 20.43 2.51 0.00 3.51
8523 11510 1.479709 AATACGAGGAGCTGCAGAGT 58.520 50.000 20.43 2.61 0.00 3.24
8524 11511 2.593346 AAATACGAGGAGCTGCAGAG 57.407 50.000 20.43 3.09 0.00 3.35
8525 11512 2.233676 TCAAAATACGAGGAGCTGCAGA 59.766 45.455 20.43 0.00 0.00 4.26
8526 11513 2.606725 CTCAAAATACGAGGAGCTGCAG 59.393 50.000 10.11 10.11 0.00 4.41
8527 11514 2.621338 CTCAAAATACGAGGAGCTGCA 58.379 47.619 8.35 0.00 0.00 4.41
8535 11522 3.252974 ACCAGCTCCTCAAAATACGAG 57.747 47.619 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.