Multiple sequence alignment - TraesCS7D01G342600

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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 TraesCS7D01G342600 chr7D 100.000 6339 0 0 1 6339 438755669 438749331 0.000000e+00 11707.0
1 TraesCS7D01G342600 chr7D 79.381 291 43 10 460 733 87503142 87502852 8.390000e-44 189.0
2 TraesCS7D01G342600 chr7B 94.465 3306 134 15 550 3847 454724138 454727402 0.000000e+00 5046.0
3 TraesCS7D01G342600 chr7B 95.894 2119 80 6 4222 6338 454727406 454729519 0.000000e+00 3424.0
4 TraesCS7D01G342600 chr7B 92.208 462 35 1 1 462 454723011 454723471 0.000000e+00 652.0
5 TraesCS7D01G342600 chr7B 89.385 179 17 2 4039 4216 483862535 483862358 2.300000e-54 224.0
6 TraesCS7D01G342600 chr7B 90.196 51 2 1 462 512 454724094 454724141 5.310000e-06 63.9
7 TraesCS7D01G342600 chr7A 97.494 2953 62 7 901 3847 490171433 490168487 0.000000e+00 5033.0
8 TraesCS7D01G342600 chr7A 96.410 2117 54 3 4222 6338 490168483 490166389 0.000000e+00 3469.0
9 TraesCS7D01G342600 chr7A 90.400 875 53 9 1 875 490175192 490174349 0.000000e+00 1122.0
10 TraesCS7D01G342600 chr7A 92.147 191 12 2 3848 4037 20296286 20296474 3.770000e-67 267.0
11 TraesCS7D01G342600 chr7A 85.000 180 23 4 4039 4217 1908771 1908947 5.050000e-41 180.0
12 TraesCS7D01G342600 chr2D 90.733 464 41 2 1 462 22280644 22281107 9.030000e-173 617.0
13 TraesCS7D01G342600 chr2D 90.364 467 42 3 1 465 67961497 67961032 1.510000e-170 610.0
14 TraesCS7D01G342600 chr2D 88.918 379 39 2 2339 2717 95196556 95196931 1.240000e-126 464.0
15 TraesCS7D01G342600 chrUn 90.108 465 43 3 1 462 175482148 175482612 9.090000e-168 601.0
16 TraesCS7D01G342600 chrUn 90.108 465 41 5 1 462 203459739 203460201 3.270000e-167 599.0
17 TraesCS7D01G342600 chrUn 90.108 465 41 5 1 462 227687356 227686894 3.270000e-167 599.0
18 TraesCS7D01G342600 chrUn 89.892 465 42 5 1 462 12748744 12749206 1.520000e-165 593.0
19 TraesCS7D01G342600 chr5B 90.086 464 42 4 1 462 145039110 145038649 3.270000e-167 599.0
20 TraesCS7D01G342600 chr5B 88.855 332 35 2 2386 2716 589434761 589434431 2.130000e-109 407.0
21 TraesCS7D01G342600 chr5B 88.980 245 25 2 2386 2629 589445720 589445477 1.030000e-77 302.0
22 TraesCS7D01G342600 chr3D 89.871 464 44 3 1 462 306283857 306283395 1.520000e-165 593.0
23 TraesCS7D01G342600 chr3D 91.623 191 14 2 3849 4037 539663734 539663924 4.870000e-66 263.0
24 TraesCS7D01G342600 chr5A 87.402 381 38 4 2337 2717 325195519 325195889 4.540000e-116 429.0
25 TraesCS7D01G342600 chr3B 88.358 335 37 2 2383 2716 355509185 355509518 9.900000e-108 401.0
26 TraesCS7D01G342600 chr1B 87.651 332 38 3 2386 2716 647466219 647465890 3.590000e-102 383.0
27 TraesCS7D01G342600 chr6D 92.147 191 13 2 3849 4037 319289939 319289749 1.050000e-67 268.0
28 TraesCS7D01G342600 chr6D 88.202 178 19 2 4039 4216 4667622 4667797 1.790000e-50 211.0
29 TraesCS7D01G342600 chr2B 92.188 192 12 3 3848 4037 28417261 28417451 1.050000e-67 268.0
30 TraesCS7D01G342600 chr2B 91.534 189 14 2 3851 4037 40447104 40446916 6.300000e-65 259.0
31 TraesCS7D01G342600 chr2B 88.068 176 17 4 4039 4214 28417484 28417655 8.330000e-49 206.0
32 TraesCS7D01G342600 chr2B 86.857 175 22 1 4042 4216 80671985 80671812 1.800000e-45 195.0
33 TraesCS7D01G342600 chr2B 78.545 275 46 10 457 722 764111643 764111373 1.090000e-37 169.0
34 TraesCS7D01G342600 chr2B 96.875 32 0 1 780 811 656940804 656940834 1.100000e-02 52.8
35 TraesCS7D01G342600 chr4A 92.063 189 13 2 3851 4037 618414671 618414483 1.360000e-66 265.0
36 TraesCS7D01G342600 chr6B 92.021 188 13 2 3849 4034 647439323 647439136 4.870000e-66 263.0
37 TraesCS7D01G342600 chr1A 92.021 188 12 2 3851 4037 29095467 29095282 1.750000e-65 261.0
38 TraesCS7D01G342600 chr4D 91.099 191 14 3 3848 4037 3691027 3691215 8.160000e-64 255.0
39 TraesCS7D01G342600 chr5D 78.987 395 49 15 3850 4221 471567496 471567113 8.210000e-59 239.0
40 TraesCS7D01G342600 chr5D 87.778 180 19 3 4039 4217 5005054 5005231 2.320000e-49 207.0
41 TraesCS7D01G342600 chr2A 90.503 179 15 2 4039 4217 40082866 40083042 1.060000e-57 235.0
42 TraesCS7D01G342600 chr2A 76.866 268 48 10 461 717 744411471 744411735 8.570000e-29 139.0
43 TraesCS7D01G342600 chr4B 87.500 184 16 3 4039 4216 101713583 101713401 8.330000e-49 206.0
44 TraesCS7D01G342600 chr3A 79.468 263 39 9 460 720 624427734 624427485 8.450000e-39 172.0
45 TraesCS7D01G342600 chr3A 90.566 53 4 1 679 730 13192575 13192627 1.140000e-07 69.4


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 TraesCS7D01G342600 chr7D 438749331 438755669 6338 True 11707.000 11707 100.00000 1 6339 1 chr7D.!!$R2 6338
1 TraesCS7D01G342600 chr7B 454723011 454729519 6508 False 2296.475 5046 93.19075 1 6338 4 chr7B.!!$F1 6337
2 TraesCS7D01G342600 chr7A 490166389 490175192 8803 True 3208.000 5033 94.76800 1 6338 3 chr7A.!!$R1 6337

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
75 76 0.323957 TGACCGAGACTCCTCTTCGA 59.676 55.000 0.00 0.0 37.28 3.71 F
1203 4719 1.066587 CCGCTCTAAGCCTCTTCGG 59.933 63.158 0.00 0.0 38.18 4.30 F
1465 4981 0.396974 TTCCAGCTTGGCTTTGGTGT 60.397 50.000 0.00 0.0 36.40 4.16 F
2212 5735 0.320683 TGCACGCTGTATGCTGACTT 60.321 50.000 6.79 0.0 43.77 3.01 F
3554 7077 0.179134 GTCGAGGAATCGGGTCACAG 60.179 60.000 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 4939 0.321671 TTCTTCTCCTTCACGGCTGG 59.678 55.000 0.00 0.00 0.00 4.85 R
2085 5602 2.031258 TTGTGTCCGCTTCACAAGAA 57.969 45.000 11.96 0.00 46.35 2.52 R
3222 6745 2.025981 TGCCAACAGTATCCTGCAGAAT 60.026 45.455 17.39 1.69 42.81 2.40 R
3851 7380 0.034089 CCCGGGCTCAGAAAAGGATT 60.034 55.000 8.08 0.00 0.00 3.01 R
5433 8963 1.750778 CAACCACTTGTGCCAACTTCT 59.249 47.619 0.00 0.00 0.00 2.85 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
17 18 3.978373 CTAGCGCTACCGAACGTG 58.022 61.111 14.45 0.00 36.29 4.49
72 73 2.096248 GACATGACCGAGACTCCTCTT 58.904 52.381 0.00 0.00 37.28 2.85
75 76 0.323957 TGACCGAGACTCCTCTTCGA 59.676 55.000 0.00 0.00 37.28 3.71
130 131 7.824289 CCATATTGGTTCCTACATATTCACGAT 59.176 37.037 0.00 0.00 31.35 3.73
132 133 4.956085 TGGTTCCTACATATTCACGATGG 58.044 43.478 0.00 0.00 0.00 3.51
154 155 4.628766 GGTCTTTATAGGTTGAACCACGAC 59.371 45.833 17.83 8.59 41.95 4.34
214 215 1.540363 CCCGCGATATGTTACTTGCCT 60.540 52.381 8.23 0.00 0.00 4.75
413 414 5.889853 ACAAATCACAGTATTGATCCATGCT 59.110 36.000 0.00 0.00 35.02 3.79
430 431 4.097892 CCATGCTACCCAACAAATACCTTC 59.902 45.833 0.00 0.00 0.00 3.46
439 440 4.814771 CCAACAAATACCTTCGGAGATACC 59.185 45.833 0.00 0.00 35.04 2.73
468 1092 6.326064 AGAGCACATTTATGATCACTAGGACT 59.674 38.462 0.00 0.00 37.47 3.85
515 1139 4.673298 ACGCCATCGCCGTCACAA 62.673 61.111 0.00 0.00 39.84 3.33
516 1140 4.147322 CGCCATCGCCGTCACAAC 62.147 66.667 0.00 0.00 0.00 3.32
517 1141 3.047280 GCCATCGCCGTCACAACA 61.047 61.111 0.00 0.00 0.00 3.33
518 1142 3.027170 GCCATCGCCGTCACAACAG 62.027 63.158 0.00 0.00 0.00 3.16
574 1198 2.125512 GCTGAAGACGGACGCCAT 60.126 61.111 0.00 0.00 0.00 4.40
600 1224 3.146182 GGATCCTGATCCGCTGCT 58.854 61.111 10.29 0.00 46.84 4.24
1002 4518 6.270815 AGCAAATCAAATGGAGATCGAAATG 58.729 36.000 0.00 0.00 0.00 2.32
1134 4650 3.008408 TCCCTCTCTCCTCGGGAC 58.992 66.667 0.00 0.00 41.95 4.46
1203 4719 1.066587 CCGCTCTAAGCCTCTTCGG 59.933 63.158 0.00 0.00 38.18 4.30
1465 4981 0.396974 TTCCAGCTTGGCTTTGGTGT 60.397 50.000 0.00 0.00 36.40 4.16
1525 5041 2.018542 TGCTAATTGCCTCGTACACC 57.981 50.000 0.00 0.00 42.00 4.16
1557 5073 4.437682 TTAGGGTTCATAGAATGCAGGG 57.562 45.455 0.00 0.00 0.00 4.45
1795 5311 3.616219 TGTGGTTGTAGAAAGTGCTGTT 58.384 40.909 0.00 0.00 0.00 3.16
1929 5446 4.100189 TCCAAGTCCTAGCTAAGAATGAGC 59.900 45.833 7.61 0.00 45.65 4.26
2085 5602 3.377798 GCGCTGTTAGAGTAGGTAGAAGT 59.622 47.826 0.00 0.00 0.00 3.01
2212 5735 0.320683 TGCACGCTGTATGCTGACTT 60.321 50.000 6.79 0.00 43.77 3.01
2444 5967 6.032956 TGGTGTGTATTTATATCGGCCTAG 57.967 41.667 0.00 0.00 0.00 3.02
2579 6102 6.785466 ACTAACCTGGATTGGGTTATTTGTTT 59.215 34.615 0.00 0.00 44.91 2.83
2672 6195 2.017049 CATCCATTTCTCCCGACCAAC 58.983 52.381 0.00 0.00 0.00 3.77
3128 6651 6.816134 ACATTGTTCAGCATGTTACACATA 57.184 33.333 0.00 0.00 36.53 2.29
3222 6745 7.066163 GTCCAGTGTCATGTCAATCATCATAAA 59.934 37.037 0.00 0.00 34.09 1.40
3526 7049 2.124011 AGCACAGTCGCAAAAACATG 57.876 45.000 0.00 0.00 0.00 3.21
3554 7077 0.179134 GTCGAGGAATCGGGTCACAG 60.179 60.000 0.00 0.00 0.00 3.66
3819 7348 4.690280 GCAAAGTGAGAAAGAGAGGAGAAG 59.310 45.833 0.00 0.00 0.00 2.85
3847 7376 5.360649 AAGTAGGAAGGCAAGGATAAGTC 57.639 43.478 0.00 0.00 0.00 3.01
3848 7377 2.990066 AGGAAGGCAAGGATAAGTCG 57.010 50.000 0.00 0.00 0.00 4.18
3849 7378 1.486726 AGGAAGGCAAGGATAAGTCGG 59.513 52.381 0.00 0.00 0.00 4.79
3850 7379 1.485066 GGAAGGCAAGGATAAGTCGGA 59.515 52.381 0.00 0.00 0.00 4.55
3851 7380 2.093128 GGAAGGCAAGGATAAGTCGGAA 60.093 50.000 0.00 0.00 0.00 4.30
3852 7381 3.606687 GAAGGCAAGGATAAGTCGGAAA 58.393 45.455 0.00 0.00 0.00 3.13
3853 7382 3.933861 AGGCAAGGATAAGTCGGAAAT 57.066 42.857 0.00 0.00 0.00 2.17
3854 7383 3.809905 AGGCAAGGATAAGTCGGAAATC 58.190 45.455 0.00 0.00 0.00 2.17
3855 7384 2.879026 GGCAAGGATAAGTCGGAAATCC 59.121 50.000 7.03 7.03 39.64 3.01
3861 7390 6.314899 AGGATAAGTCGGAAATCCTTTTCT 57.685 37.500 10.48 0.00 45.82 2.52
3862 7391 6.116126 AGGATAAGTCGGAAATCCTTTTCTG 58.884 40.000 10.48 1.67 45.82 3.02
3867 7396 1.745653 CGGAAATCCTTTTCTGAGCCC 59.254 52.381 1.85 0.00 46.80 5.19
3868 7397 1.745653 GGAAATCCTTTTCTGAGCCCG 59.254 52.381 0.00 0.00 40.91 6.13
3869 7398 1.745653 GAAATCCTTTTCTGAGCCCGG 59.254 52.381 0.00 0.00 38.56 5.73
3870 7399 0.034089 AATCCTTTTCTGAGCCCGGG 60.034 55.000 19.09 19.09 0.00 5.73
3871 7400 2.558380 ATCCTTTTCTGAGCCCGGGC 62.558 60.000 39.29 39.29 42.33 6.13
3882 7411 4.864334 CCCGGGCTCATCTGCACC 62.864 72.222 8.08 0.00 31.60 5.01
3883 7412 3.790437 CCGGGCTCATCTGCACCT 61.790 66.667 0.00 0.00 31.60 4.00
3884 7413 2.513204 CGGGCTCATCTGCACCTG 60.513 66.667 0.00 0.00 31.60 4.00
3885 7414 2.673523 GGGCTCATCTGCACCTGT 59.326 61.111 0.00 0.00 34.04 4.00
3886 7415 1.748122 GGGCTCATCTGCACCTGTG 60.748 63.158 0.00 0.00 34.04 3.66
3887 7416 1.002868 GGCTCATCTGCACCTGTGT 60.003 57.895 0.00 0.00 34.04 3.72
3888 7417 0.607489 GGCTCATCTGCACCTGTGTT 60.607 55.000 0.00 0.00 34.04 3.32
3889 7418 0.520404 GCTCATCTGCACCTGTGTTG 59.480 55.000 0.00 0.00 0.00 3.33
3890 7419 1.879372 GCTCATCTGCACCTGTGTTGA 60.879 52.381 0.00 0.00 0.00 3.18
3891 7420 2.497138 CTCATCTGCACCTGTGTTGAA 58.503 47.619 0.00 0.00 0.00 2.69
3892 7421 3.079578 CTCATCTGCACCTGTGTTGAAT 58.920 45.455 0.00 0.00 0.00 2.57
3893 7422 4.256110 CTCATCTGCACCTGTGTTGAATA 58.744 43.478 0.00 0.00 0.00 1.75
3894 7423 4.650734 TCATCTGCACCTGTGTTGAATAA 58.349 39.130 0.00 0.00 0.00 1.40
3895 7424 5.069318 TCATCTGCACCTGTGTTGAATAAA 58.931 37.500 0.00 0.00 0.00 1.40
3896 7425 5.534278 TCATCTGCACCTGTGTTGAATAAAA 59.466 36.000 0.00 0.00 0.00 1.52
3897 7426 5.843673 TCTGCACCTGTGTTGAATAAAAA 57.156 34.783 0.00 0.00 0.00 1.94
3962 7491 8.845413 TTTTTCCCATGGTAGAAAATTTGATG 57.155 30.769 22.08 0.27 40.58 3.07
3963 7492 5.596836 TCCCATGGTAGAAAATTTGATGC 57.403 39.130 11.73 0.00 0.00 3.91
3964 7493 4.097741 TCCCATGGTAGAAAATTTGATGCG 59.902 41.667 11.73 0.00 0.00 4.73
3965 7494 4.142182 CCCATGGTAGAAAATTTGATGCGT 60.142 41.667 11.73 0.00 0.00 5.24
3966 7495 4.799949 CCATGGTAGAAAATTTGATGCGTG 59.200 41.667 2.57 0.00 0.00 5.34
3967 7496 5.392919 CCATGGTAGAAAATTTGATGCGTGA 60.393 40.000 2.57 0.00 0.00 4.35
3968 7497 5.295431 TGGTAGAAAATTTGATGCGTGAG 57.705 39.130 0.00 0.00 0.00 3.51
3969 7498 4.155826 TGGTAGAAAATTTGATGCGTGAGG 59.844 41.667 0.00 0.00 0.00 3.86
3970 7499 4.156008 GGTAGAAAATTTGATGCGTGAGGT 59.844 41.667 0.00 0.00 0.00 3.85
3971 7500 4.425577 AGAAAATTTGATGCGTGAGGTC 57.574 40.909 0.00 0.00 0.00 3.85
3972 7501 3.191371 AGAAAATTTGATGCGTGAGGTCC 59.809 43.478 0.00 0.00 0.00 4.46
3973 7502 1.086696 AATTTGATGCGTGAGGTCCG 58.913 50.000 0.00 0.00 0.00 4.79
3980 7509 4.096003 CGTGAGGTCCGCCCCATT 62.096 66.667 0.00 0.00 34.57 3.16
3981 7510 2.355115 GTGAGGTCCGCCCCATTT 59.645 61.111 0.00 0.00 34.57 2.32
3982 7511 1.304134 GTGAGGTCCGCCCCATTTT 60.304 57.895 0.00 0.00 34.57 1.82
3983 7512 0.898326 GTGAGGTCCGCCCCATTTTT 60.898 55.000 0.00 0.00 34.57 1.94
3984 7513 0.610785 TGAGGTCCGCCCCATTTTTC 60.611 55.000 0.00 0.00 34.57 2.29
3985 7514 0.610785 GAGGTCCGCCCCATTTTTCA 60.611 55.000 0.00 0.00 34.57 2.69
3986 7515 0.178947 AGGTCCGCCCCATTTTTCAA 60.179 50.000 0.00 0.00 34.57 2.69
3987 7516 0.682292 GGTCCGCCCCATTTTTCAAA 59.318 50.000 0.00 0.00 0.00 2.69
3988 7517 1.277842 GGTCCGCCCCATTTTTCAAAT 59.722 47.619 0.00 0.00 0.00 2.32
3989 7518 2.616960 GTCCGCCCCATTTTTCAAATC 58.383 47.619 0.00 0.00 0.00 2.17
3990 7519 2.028567 GTCCGCCCCATTTTTCAAATCA 60.029 45.455 0.00 0.00 0.00 2.57
3991 7520 2.836981 TCCGCCCCATTTTTCAAATCAT 59.163 40.909 0.00 0.00 0.00 2.45
3992 7521 3.262915 TCCGCCCCATTTTTCAAATCATT 59.737 39.130 0.00 0.00 0.00 2.57
3993 7522 4.009002 CCGCCCCATTTTTCAAATCATTT 58.991 39.130 0.00 0.00 0.00 2.32
3994 7523 4.142643 CCGCCCCATTTTTCAAATCATTTG 60.143 41.667 3.46 3.46 41.96 2.32
4005 7534 4.801891 TCAAATCATTTGAGCAACTGAGC 58.198 39.130 8.85 0.00 44.21 4.26
4006 7535 4.278919 TCAAATCATTTGAGCAACTGAGCA 59.721 37.500 8.85 0.00 44.21 4.26
4007 7536 4.859304 AATCATTTGAGCAACTGAGCAA 57.141 36.364 8.80 0.00 34.26 3.91
4008 7537 3.631145 TCATTTGAGCAACTGAGCAAC 57.369 42.857 0.00 0.00 36.85 4.17
4009 7538 3.216800 TCATTTGAGCAACTGAGCAACT 58.783 40.909 0.00 0.00 36.85 3.16
4010 7539 3.251729 TCATTTGAGCAACTGAGCAACTC 59.748 43.478 0.00 0.00 36.85 3.01
4011 7540 2.627515 TTGAGCAACTGAGCAACTCT 57.372 45.000 0.00 0.00 36.85 3.24
4012 7541 2.160822 TGAGCAACTGAGCAACTCTC 57.839 50.000 0.00 0.00 42.23 3.20
4013 7542 1.066914 GAGCAACTGAGCAACTCTCG 58.933 55.000 0.00 0.00 44.86 4.04
4017 7546 4.182132 CTGAGCAACTCTCGGCAG 57.818 61.111 0.00 0.00 44.86 4.85
4018 7547 1.588597 CTGAGCAACTCTCGGCAGA 59.411 57.895 0.00 0.00 44.86 4.26
4019 7548 0.037882 CTGAGCAACTCTCGGCAGAA 60.038 55.000 0.00 0.00 44.86 3.02
4020 7549 0.392706 TGAGCAACTCTCGGCAGAAA 59.607 50.000 0.00 0.00 44.86 2.52
4021 7550 1.202639 TGAGCAACTCTCGGCAGAAAA 60.203 47.619 0.00 0.00 44.86 2.29
4022 7551 1.462670 GAGCAACTCTCGGCAGAAAAG 59.537 52.381 0.00 0.00 31.20 2.27
4023 7552 1.070758 AGCAACTCTCGGCAGAAAAGA 59.929 47.619 3.45 0.00 0.00 2.52
4024 7553 1.195674 GCAACTCTCGGCAGAAAAGAC 59.804 52.381 3.45 0.00 0.00 3.01
4025 7554 2.483876 CAACTCTCGGCAGAAAAGACA 58.516 47.619 3.45 0.00 0.00 3.41
4026 7555 2.872245 CAACTCTCGGCAGAAAAGACAA 59.128 45.455 3.45 0.00 0.00 3.18
4027 7556 3.194005 ACTCTCGGCAGAAAAGACAAA 57.806 42.857 3.45 0.00 0.00 2.83
4028 7557 3.744660 ACTCTCGGCAGAAAAGACAAAT 58.255 40.909 3.45 0.00 0.00 2.32
4029 7558 4.137543 ACTCTCGGCAGAAAAGACAAATT 58.862 39.130 3.45 0.00 0.00 1.82
4030 7559 4.214332 ACTCTCGGCAGAAAAGACAAATTC 59.786 41.667 3.45 0.00 0.00 2.17
4031 7560 3.186409 TCTCGGCAGAAAAGACAAATTCG 59.814 43.478 0.00 0.00 0.00 3.34
4032 7561 2.225491 TCGGCAGAAAAGACAAATTCGG 59.775 45.455 0.00 0.00 0.00 4.30
4033 7562 2.668279 CGGCAGAAAAGACAAATTCGGG 60.668 50.000 0.00 0.00 0.00 5.14
4034 7563 2.352715 GGCAGAAAAGACAAATTCGGGG 60.353 50.000 0.00 0.00 0.00 5.73
4035 7564 2.296190 GCAGAAAAGACAAATTCGGGGT 59.704 45.455 0.00 0.00 0.00 4.95
4036 7565 3.611766 GCAGAAAAGACAAATTCGGGGTC 60.612 47.826 0.00 0.00 0.00 4.46
4037 7566 2.812011 AGAAAAGACAAATTCGGGGTCG 59.188 45.455 0.00 0.00 36.68 4.79
4038 7567 1.530323 AAAGACAAATTCGGGGTCGG 58.470 50.000 0.00 0.00 36.68 4.79
4039 7568 0.688487 AAGACAAATTCGGGGTCGGA 59.312 50.000 0.00 0.00 36.68 4.55
4040 7569 0.036671 AGACAAATTCGGGGTCGGAC 60.037 55.000 0.00 0.00 36.68 4.79
4041 7570 1.002990 ACAAATTCGGGGTCGGACC 60.003 57.895 19.06 19.06 37.60 4.46
4054 7583 2.554370 TCGGACCCGATTTGTCTTTT 57.446 45.000 7.11 0.00 44.01 2.27
4055 7584 2.853705 TCGGACCCGATTTGTCTTTTT 58.146 42.857 7.11 0.00 44.01 1.94
4081 7610 4.727507 GAGAGCTACTCAGATGTCCAAA 57.272 45.455 7.93 0.00 44.36 3.28
4082 7611 5.275067 GAGAGCTACTCAGATGTCCAAAT 57.725 43.478 7.93 0.00 44.36 2.32
4083 7612 5.021033 AGAGCTACTCAGATGTCCAAATG 57.979 43.478 0.00 0.00 32.06 2.32
4084 7613 4.713814 AGAGCTACTCAGATGTCCAAATGA 59.286 41.667 0.00 0.00 32.06 2.57
4085 7614 5.021033 AGCTACTCAGATGTCCAAATGAG 57.979 43.478 9.37 9.37 43.81 2.90
4086 7615 3.559242 GCTACTCAGATGTCCAAATGAGC 59.441 47.826 10.38 0.00 42.33 4.26
4087 7616 3.996921 ACTCAGATGTCCAAATGAGCT 57.003 42.857 10.38 0.00 42.33 4.09
4088 7617 5.452496 GCTACTCAGATGTCCAAATGAGCTA 60.452 44.000 10.38 4.48 42.33 3.32
4089 7618 5.426689 ACTCAGATGTCCAAATGAGCTAA 57.573 39.130 10.38 0.00 42.33 3.09
4090 7619 5.809001 ACTCAGATGTCCAAATGAGCTAAA 58.191 37.500 10.38 0.00 42.33 1.85
4091 7620 6.240894 ACTCAGATGTCCAAATGAGCTAAAA 58.759 36.000 10.38 0.00 42.33 1.52
4092 7621 6.888632 ACTCAGATGTCCAAATGAGCTAAAAT 59.111 34.615 10.38 0.00 42.33 1.82
4093 7622 7.395489 ACTCAGATGTCCAAATGAGCTAAAATT 59.605 33.333 10.38 0.00 42.33 1.82
4094 7623 8.125978 TCAGATGTCCAAATGAGCTAAAATTT 57.874 30.769 0.00 0.00 0.00 1.82
4095 7624 8.030692 TCAGATGTCCAAATGAGCTAAAATTTG 58.969 33.333 16.57 16.57 41.41 2.32
4100 7629 5.691508 CAAATGAGCTAAAATTTGGAGCG 57.308 39.130 15.87 2.16 41.23 5.03
4101 7630 5.401550 CAAATGAGCTAAAATTTGGAGCGA 58.598 37.500 15.87 9.71 41.23 4.93
4102 7631 5.643379 AATGAGCTAAAATTTGGAGCGAA 57.357 34.783 15.87 10.67 41.23 4.70
4103 7632 4.419522 TGAGCTAAAATTTGGAGCGAAC 57.580 40.909 15.87 12.76 41.23 3.95
4104 7633 3.190535 TGAGCTAAAATTTGGAGCGAACC 59.809 43.478 15.87 9.65 41.23 3.62
4105 7634 3.421844 AGCTAAAATTTGGAGCGAACCT 58.578 40.909 15.87 0.80 41.23 3.50
4106 7635 3.440522 AGCTAAAATTTGGAGCGAACCTC 59.559 43.478 15.87 0.00 41.23 3.85
4107 7636 3.190535 GCTAAAATTTGGAGCGAACCTCA 59.809 43.478 9.01 0.00 42.62 3.86
4108 7637 3.643159 AAAATTTGGAGCGAACCTCAC 57.357 42.857 0.00 0.00 42.62 3.51
4109 7638 1.156736 AATTTGGAGCGAACCTCACG 58.843 50.000 0.00 0.00 42.62 4.35
4120 7649 4.078363 CGAACCTCACGCAATAAATTGT 57.922 40.909 4.71 0.00 39.88 2.71
4121 7650 4.088648 CGAACCTCACGCAATAAATTGTC 58.911 43.478 4.71 0.00 39.88 3.18
4122 7651 4.142902 CGAACCTCACGCAATAAATTGTCT 60.143 41.667 4.71 0.00 39.88 3.41
4123 7652 5.062934 CGAACCTCACGCAATAAATTGTCTA 59.937 40.000 4.71 0.00 39.88 2.59
4124 7653 5.796350 ACCTCACGCAATAAATTGTCTAC 57.204 39.130 4.71 0.00 39.88 2.59
4125 7654 5.242434 ACCTCACGCAATAAATTGTCTACA 58.758 37.500 4.71 0.00 39.88 2.74
4126 7655 5.703592 ACCTCACGCAATAAATTGTCTACAA 59.296 36.000 4.71 0.00 39.88 2.41
4128 7657 6.688385 CCTCACGCAATAAATTGTCTACAATG 59.312 38.462 9.01 0.00 45.06 2.82
4129 7658 6.550843 TCACGCAATAAATTGTCTACAATGG 58.449 36.000 9.01 0.00 45.06 3.16
4130 7659 5.743398 CACGCAATAAATTGTCTACAATGGG 59.257 40.000 9.01 8.52 45.06 4.00
4131 7660 5.650266 ACGCAATAAATTGTCTACAATGGGA 59.350 36.000 9.01 0.00 45.06 4.37
4132 7661 6.151985 ACGCAATAAATTGTCTACAATGGGAA 59.848 34.615 9.01 0.00 45.06 3.97
4133 7662 7.032580 CGCAATAAATTGTCTACAATGGGAAA 58.967 34.615 9.01 0.00 45.06 3.13
4134 7663 7.543868 CGCAATAAATTGTCTACAATGGGAAAA 59.456 33.333 9.01 0.00 45.06 2.29
4135 7664 9.213799 GCAATAAATTGTCTACAATGGGAAAAA 57.786 29.630 9.01 0.00 45.06 1.94
4185 7714 4.988744 TTTTTCTGGACGGGTGCA 57.011 50.000 0.00 0.00 0.00 4.57
4192 7721 1.220749 TGGACGGGTGCAGATAAGC 59.779 57.895 0.00 0.00 0.00 3.09
4193 7722 1.523938 GGACGGGTGCAGATAAGCC 60.524 63.158 0.00 0.00 0.00 4.35
4194 7723 1.523938 GACGGGTGCAGATAAGCCC 60.524 63.158 0.00 0.00 37.79 5.19
4196 7725 2.203209 GGGTGCAGATAAGCCCGG 60.203 66.667 0.00 0.00 0.00 5.73
4197 7726 2.203209 GGTGCAGATAAGCCCGGG 60.203 66.667 19.09 19.09 0.00 5.73
4198 7727 2.902343 GTGCAGATAAGCCCGGGC 60.902 66.667 39.29 39.29 42.33 6.13
4199 7728 3.407083 TGCAGATAAGCCCGGGCA 61.407 61.111 45.13 28.44 44.88 5.36
4200 7729 2.902343 GCAGATAAGCCCGGGCAC 60.902 66.667 45.13 30.72 44.88 5.01
4213 7742 4.166011 GGCACCGAATCGCTGCAC 62.166 66.667 22.09 9.74 39.78 4.57
4214 7743 3.121030 GCACCGAATCGCTGCACT 61.121 61.111 16.90 0.00 38.19 4.40
4215 7744 3.084579 CACCGAATCGCTGCACTC 58.915 61.111 0.00 0.00 0.00 3.51
4216 7745 1.737735 CACCGAATCGCTGCACTCA 60.738 57.895 0.00 0.00 0.00 3.41
4217 7746 1.086067 CACCGAATCGCTGCACTCAT 61.086 55.000 0.00 0.00 0.00 2.90
4218 7747 0.459899 ACCGAATCGCTGCACTCATA 59.540 50.000 0.00 0.00 0.00 2.15
4219 7748 1.135046 CCGAATCGCTGCACTCATAG 58.865 55.000 0.00 0.00 0.00 2.23
4220 7749 1.536922 CCGAATCGCTGCACTCATAGT 60.537 52.381 0.00 0.00 0.00 2.12
4262 7791 2.496871 TCATGCTAATGCCCAAAACCAG 59.503 45.455 0.00 0.00 38.71 4.00
5264 8793 3.441163 GCTGGTACGTCGTTGATAATCA 58.559 45.455 1.78 0.00 0.00 2.57
5561 9091 5.675323 GCATAGCGGGTTTTCGTATTTTTCT 60.675 40.000 0.00 0.00 0.00 2.52
5629 9159 5.705609 TTCTTAAATGACCTGTTCTTGGC 57.294 39.130 0.00 0.00 0.00 4.52
5661 9191 5.825151 AGAAGCTGGCTAAATTAGTTGGATC 59.175 40.000 1.68 0.00 0.00 3.36
5832 9362 7.884816 ATAAAGGTCGTAACATGGATATTCG 57.115 36.000 0.00 0.00 0.00 3.34
5864 9394 5.870433 TGTTGGCTCATTTAAAGATGCATTG 59.130 36.000 0.00 0.00 0.00 2.82
5964 9494 7.095816 GGGCTGTATCACAATTTGTTGTTTTAC 60.096 37.037 0.00 0.00 31.86 2.01
6027 9557 1.808390 CCTTCGTTTCCGCGGTAGG 60.808 63.158 27.15 19.11 0.00 3.18
6084 9614 4.412199 CAGGAATTCAGAGGGGGTAATACA 59.588 45.833 7.93 0.00 0.00 2.29
6143 9673 2.001159 GACAAGCTGTCTCATGAGCAG 58.999 52.381 28.36 28.36 43.73 4.24
6166 9696 2.715046 CAGGTGCCAACATATGTGAGT 58.285 47.619 9.63 0.00 0.00 3.41
6180 9710 9.733556 AACATATGTGAGTATTTCTGTGGTTTA 57.266 29.630 9.63 0.00 0.00 2.01
6196 9726 6.374578 TGTGGTTTAAAAGCAAAAGCAAAAC 58.625 32.000 2.40 0.00 43.57 2.43
6198 9728 6.858478 GTGGTTTAAAAGCAAAAGCAAAACAA 59.142 30.769 2.40 0.00 43.57 2.83
6224 9755 2.799017 TGCTGTGAAATTGCATCCTCT 58.201 42.857 0.00 0.00 0.00 3.69
6225 9756 2.751259 TGCTGTGAAATTGCATCCTCTC 59.249 45.455 0.00 0.00 0.00 3.20
6230 9761 5.258841 TGTGAAATTGCATCCTCTCATCTT 58.741 37.500 0.00 0.00 0.00 2.40
6231 9762 5.713389 TGTGAAATTGCATCCTCTCATCTTT 59.287 36.000 0.00 0.00 0.00 2.52
6248 9779 4.657408 TGTGGCAGGCGCAATGGA 62.657 61.111 10.83 0.00 41.24 3.41
6277 9808 4.938832 TGTACTGGTATTGGTACATGTTGC 59.061 41.667 2.30 0.00 41.90 4.17
6281 9812 2.752354 GGTATTGGTACATGTTGCTGCA 59.248 45.455 2.30 0.00 39.30 4.41
6302 9833 4.097892 GCAAATATGGTACTGTTGGGGAAG 59.902 45.833 0.00 0.00 0.00 3.46
6303 9834 3.577805 ATATGGTACTGTTGGGGAAGC 57.422 47.619 0.00 0.00 0.00 3.86
6307 9838 1.886542 GGTACTGTTGGGGAAGCTTTG 59.113 52.381 0.00 0.00 0.00 2.77
6316 9847 1.066645 GGGGAAGCTTTGCAATCAAGG 60.067 52.381 0.00 0.00 33.12 3.61
6319 9850 3.429960 GGGAAGCTTTGCAATCAAGGATC 60.430 47.826 0.00 0.00 31.65 3.36
6338 9869 2.434185 GGCGATCTGGTTGCACGA 60.434 61.111 2.00 0.00 39.13 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.164252 CGTAGGGTCGCACACTTC 57.836 61.111 0.00 0.00 31.80 3.01
72 73 5.221481 TGTCCCGCTATTGGTTATTTATCGA 60.221 40.000 0.00 0.00 0.00 3.59
75 76 5.710099 CCATGTCCCGCTATTGGTTATTTAT 59.290 40.000 0.00 0.00 0.00 1.40
130 131 4.283978 TCGTGGTTCAACCTATAAAGACCA 59.716 41.667 8.40 0.00 39.58 4.02
132 133 4.325472 CGTCGTGGTTCAACCTATAAAGAC 59.675 45.833 8.40 4.50 39.58 3.01
214 215 3.400255 AGATACCGACGATCGAATCTCA 58.600 45.455 24.34 2.26 43.74 3.27
338 339 2.035576 GCCCTCTCGGTAATACGACATT 59.964 50.000 0.00 0.00 38.06 2.71
396 397 3.716353 TGGGTAGCATGGATCAATACTGT 59.284 43.478 0.00 0.00 0.00 3.55
403 404 3.448093 TTTGTTGGGTAGCATGGATCA 57.552 42.857 0.00 0.00 0.00 2.92
430 431 2.298610 TGTGCTCTACAGGTATCTCCG 58.701 52.381 0.00 0.00 41.99 4.63
439 440 7.598118 CCTAGTGATCATAAATGTGCTCTACAG 59.402 40.741 0.00 0.00 43.80 2.74
468 1092 4.966787 GGGAGCGGTTTGGTGGCA 62.967 66.667 0.00 0.00 0.00 4.92
512 1136 2.426023 GCCGGTGTCCTCTGTTGT 59.574 61.111 1.90 0.00 0.00 3.32
513 1137 2.358737 GGCCGGTGTCCTCTGTTG 60.359 66.667 1.90 0.00 0.00 3.33
514 1138 3.637273 GGGCCGGTGTCCTCTGTT 61.637 66.667 1.90 0.00 31.67 3.16
574 1198 0.970937 GATCAGGATCCGCCCCGATA 60.971 60.000 5.98 0.00 37.37 2.92
610 1234 1.815421 GATGGCGGATCGTGCAAGT 60.815 57.895 10.30 0.00 0.00 3.16
618 1242 1.528129 GGGATTTGAGATGGCGGATC 58.472 55.000 0.00 0.00 0.00 3.36
661 1285 2.186903 GTGTCGGCGGATCCACAT 59.813 61.111 13.41 0.00 31.72 3.21
970 4486 2.757868 CCATTTGATTTGCTTCCCGGTA 59.242 45.455 0.00 0.00 0.00 4.02
971 4487 1.550072 CCATTTGATTTGCTTCCCGGT 59.450 47.619 0.00 0.00 0.00 5.28
1134 4650 3.827898 GAGAGGGGGAGCACGTCG 61.828 72.222 0.00 0.00 0.00 5.12
1211 4727 3.197790 CTGCGCCTTGGTCGATGG 61.198 66.667 4.18 0.00 0.00 3.51
1423 4939 0.321671 TTCTTCTCCTTCACGGCTGG 59.678 55.000 0.00 0.00 0.00 4.85
1465 4981 3.144068 TGGATTGATGGGAGGGTAAGA 57.856 47.619 0.00 0.00 0.00 2.10
1525 5041 7.111247 TCTATGAACCCTAAAATGGCAATTG 57.889 36.000 0.00 0.00 0.00 2.32
1557 5073 5.125417 TCAACCAAAAGCTATAGGATTGTGC 59.875 40.000 1.04 0.00 27.89 4.57
1661 5177 4.439305 TGCAATTTCCATGCTGTTACTC 57.561 40.909 0.00 0.00 44.14 2.59
1795 5311 4.094476 CCAAGACCTACAGAAAGGAGGTA 58.906 47.826 0.00 0.00 43.78 3.08
1929 5446 7.220599 ACATCACAATCAAAAACTGAAAACG 57.779 32.000 0.00 0.00 37.67 3.60
2085 5602 2.031258 TTGTGTCCGCTTCACAAGAA 57.969 45.000 11.96 0.00 46.35 2.52
2422 5945 4.868734 GCTAGGCCGATATAAATACACACC 59.131 45.833 0.00 0.00 0.00 4.16
2444 5967 5.470368 TCGTGATGTGCTAAATCTATAGGC 58.530 41.667 0.00 0.00 0.00 3.93
3128 6651 7.902920 ATGATACCACCAGCATAATTTTTCT 57.097 32.000 0.00 0.00 0.00 2.52
3222 6745 2.025981 TGCCAACAGTATCCTGCAGAAT 60.026 45.455 17.39 1.69 42.81 2.40
3526 7049 3.665675 ATTCCTCGACCACGCAGCC 62.666 63.158 0.00 0.00 39.58 4.85
3567 7096 5.163642 TGCTTTACAACCGTAAAAGCTTCAA 60.164 36.000 17.03 0.00 44.82 2.69
3575 7104 6.870971 ATTTCTCTGCTTTACAACCGTAAA 57.129 33.333 0.00 0.00 43.66 2.01
3593 7122 4.215613 GGTGCCACTCGTTTTTCTATTTCT 59.784 41.667 0.00 0.00 0.00 2.52
3819 7348 3.454812 TCCTTGCCTTCCTACTTCCATAC 59.545 47.826 0.00 0.00 0.00 2.39
3847 7376 1.745653 GGGCTCAGAAAAGGATTTCCG 59.254 52.381 0.00 0.00 44.96 4.30
3848 7377 1.745653 CGGGCTCAGAAAAGGATTTCC 59.254 52.381 0.00 0.00 44.96 3.13
3849 7378 1.745653 CCGGGCTCAGAAAAGGATTTC 59.254 52.381 0.00 0.00 44.34 2.17
3850 7379 1.616994 CCCGGGCTCAGAAAAGGATTT 60.617 52.381 8.08 0.00 42.41 2.17
3851 7380 0.034089 CCCGGGCTCAGAAAAGGATT 60.034 55.000 8.08 0.00 0.00 3.01
3852 7381 1.609783 CCCGGGCTCAGAAAAGGAT 59.390 57.895 8.08 0.00 0.00 3.24
3853 7382 3.077907 CCCGGGCTCAGAAAAGGA 58.922 61.111 8.08 0.00 0.00 3.36
3854 7383 2.751837 GCCCGGGCTCAGAAAAGG 60.752 66.667 38.76 0.00 38.26 3.11
3865 7394 4.864334 GGTGCAGATGAGCCCGGG 62.864 72.222 19.09 19.09 0.00 5.73
3866 7395 3.790437 AGGTGCAGATGAGCCCGG 61.790 66.667 0.00 0.00 32.32 5.73
3867 7396 2.513204 CAGGTGCAGATGAGCCCG 60.513 66.667 0.00 0.00 32.32 6.13
3868 7397 1.748122 CACAGGTGCAGATGAGCCC 60.748 63.158 5.13 0.00 0.00 5.19
3869 7398 0.607489 AACACAGGTGCAGATGAGCC 60.607 55.000 5.13 0.00 0.00 4.70
3870 7399 0.520404 CAACACAGGTGCAGATGAGC 59.480 55.000 5.13 0.00 0.00 4.26
3871 7400 2.174363 TCAACACAGGTGCAGATGAG 57.826 50.000 5.13 0.02 0.00 2.90
3872 7401 2.636647 TTCAACACAGGTGCAGATGA 57.363 45.000 5.13 0.00 0.00 2.92
3873 7402 5.375417 TTTATTCAACACAGGTGCAGATG 57.625 39.130 0.00 0.00 0.00 2.90
3874 7403 6.403866 TTTTTATTCAACACAGGTGCAGAT 57.596 33.333 0.00 0.00 0.00 2.90
3875 7404 5.843673 TTTTTATTCAACACAGGTGCAGA 57.156 34.783 0.00 0.00 0.00 4.26
3937 7466 7.390162 GCATCAAATTTTCTACCATGGGAAAAA 59.610 33.333 24.04 20.99 42.25 1.94
3938 7467 6.878389 GCATCAAATTTTCTACCATGGGAAAA 59.122 34.615 23.07 23.07 42.83 2.29
3939 7468 6.405538 GCATCAAATTTTCTACCATGGGAAA 58.594 36.000 18.09 13.93 0.00 3.13
3940 7469 5.394005 CGCATCAAATTTTCTACCATGGGAA 60.394 40.000 18.09 8.07 0.00 3.97
3941 7470 4.097741 CGCATCAAATTTTCTACCATGGGA 59.902 41.667 18.09 6.59 0.00 4.37
3942 7471 4.142182 ACGCATCAAATTTTCTACCATGGG 60.142 41.667 18.09 0.00 0.00 4.00
3943 7472 4.799949 CACGCATCAAATTTTCTACCATGG 59.200 41.667 11.19 11.19 0.00 3.66
3944 7473 5.639757 TCACGCATCAAATTTTCTACCATG 58.360 37.500 0.00 0.00 0.00 3.66
3945 7474 5.163622 CCTCACGCATCAAATTTTCTACCAT 60.164 40.000 0.00 0.00 0.00 3.55
3946 7475 4.155826 CCTCACGCATCAAATTTTCTACCA 59.844 41.667 0.00 0.00 0.00 3.25
3947 7476 4.156008 ACCTCACGCATCAAATTTTCTACC 59.844 41.667 0.00 0.00 0.00 3.18
3948 7477 5.296813 ACCTCACGCATCAAATTTTCTAC 57.703 39.130 0.00 0.00 0.00 2.59
3949 7478 4.394920 GGACCTCACGCATCAAATTTTCTA 59.605 41.667 0.00 0.00 0.00 2.10
3950 7479 3.191371 GGACCTCACGCATCAAATTTTCT 59.809 43.478 0.00 0.00 0.00 2.52
3951 7480 3.501950 GGACCTCACGCATCAAATTTTC 58.498 45.455 0.00 0.00 0.00 2.29
3952 7481 2.095263 CGGACCTCACGCATCAAATTTT 60.095 45.455 0.00 0.00 0.00 1.82
3953 7482 1.468520 CGGACCTCACGCATCAAATTT 59.531 47.619 0.00 0.00 0.00 1.82
3954 7483 1.086696 CGGACCTCACGCATCAAATT 58.913 50.000 0.00 0.00 0.00 1.82
3955 7484 2.767536 CGGACCTCACGCATCAAAT 58.232 52.632 0.00 0.00 0.00 2.32
3956 7485 4.277239 CGGACCTCACGCATCAAA 57.723 55.556 0.00 0.00 0.00 2.69
3966 7495 0.610785 TGAAAAATGGGGCGGACCTC 60.611 55.000 0.00 0.00 40.03 3.85
3967 7496 0.178947 TTGAAAAATGGGGCGGACCT 60.179 50.000 0.00 0.00 40.03 3.85
3968 7497 0.682292 TTTGAAAAATGGGGCGGACC 59.318 50.000 0.00 0.00 39.11 4.46
3969 7498 2.028567 TGATTTGAAAAATGGGGCGGAC 60.029 45.455 0.00 0.00 0.00 4.79
3970 7499 2.251818 TGATTTGAAAAATGGGGCGGA 58.748 42.857 0.00 0.00 0.00 5.54
3971 7500 2.758736 TGATTTGAAAAATGGGGCGG 57.241 45.000 0.00 0.00 0.00 6.13
3972 7501 4.694509 TCAAATGATTTGAAAAATGGGGCG 59.305 37.500 17.50 0.00 45.94 6.13
3983 7512 4.278919 TGCTCAGTTGCTCAAATGATTTGA 59.721 37.500 18.53 18.53 43.23 2.69
3984 7513 4.552355 TGCTCAGTTGCTCAAATGATTTG 58.448 39.130 11.54 11.54 43.23 2.32
3985 7514 4.859304 TGCTCAGTTGCTCAAATGATTT 57.141 36.364 12.27 0.00 43.23 2.17
3986 7515 4.280174 AGTTGCTCAGTTGCTCAAATGATT 59.720 37.500 12.27 0.00 43.23 2.57
3987 7516 3.825014 AGTTGCTCAGTTGCTCAAATGAT 59.175 39.130 12.27 0.00 43.23 2.45
3988 7517 3.216800 AGTTGCTCAGTTGCTCAAATGA 58.783 40.909 11.49 11.49 42.21 2.57
3989 7518 3.252701 AGAGTTGCTCAGTTGCTCAAATG 59.747 43.478 3.91 3.91 37.70 2.32
3990 7519 3.484407 AGAGTTGCTCAGTTGCTCAAAT 58.516 40.909 0.00 0.00 32.06 2.32
3991 7520 2.874701 GAGAGTTGCTCAGTTGCTCAAA 59.125 45.455 0.00 0.00 43.38 2.69
3992 7521 2.487934 GAGAGTTGCTCAGTTGCTCAA 58.512 47.619 0.00 0.00 43.38 3.02
3993 7522 1.603931 CGAGAGTTGCTCAGTTGCTCA 60.604 52.381 0.00 0.00 44.15 4.26
3994 7523 1.066914 CGAGAGTTGCTCAGTTGCTC 58.933 55.000 0.00 0.00 44.15 4.26
3995 7524 0.320247 CCGAGAGTTGCTCAGTTGCT 60.320 55.000 0.00 0.00 44.15 3.91
3996 7525 1.905922 GCCGAGAGTTGCTCAGTTGC 61.906 60.000 0.00 0.00 44.15 4.17
3997 7526 0.601046 TGCCGAGAGTTGCTCAGTTG 60.601 55.000 0.00 0.00 44.15 3.16
3998 7527 0.320247 CTGCCGAGAGTTGCTCAGTT 60.320 55.000 0.00 0.00 44.15 3.16
3999 7528 1.181741 TCTGCCGAGAGTTGCTCAGT 61.182 55.000 0.00 0.00 44.15 3.41
4000 7529 0.037882 TTCTGCCGAGAGTTGCTCAG 60.038 55.000 0.00 0.00 44.15 3.35
4001 7530 0.392706 TTTCTGCCGAGAGTTGCTCA 59.607 50.000 0.00 0.00 44.15 4.26
4002 7531 1.462670 CTTTTCTGCCGAGAGTTGCTC 59.537 52.381 0.00 0.00 40.38 4.26
4003 7532 1.070758 TCTTTTCTGCCGAGAGTTGCT 59.929 47.619 0.00 0.00 0.00 3.91
4004 7533 1.195674 GTCTTTTCTGCCGAGAGTTGC 59.804 52.381 0.00 0.00 0.00 4.17
4005 7534 2.483876 TGTCTTTTCTGCCGAGAGTTG 58.516 47.619 0.00 0.00 0.00 3.16
4006 7535 2.910688 TGTCTTTTCTGCCGAGAGTT 57.089 45.000 0.00 0.00 0.00 3.01
4007 7536 2.910688 TTGTCTTTTCTGCCGAGAGT 57.089 45.000 0.00 0.00 0.00 3.24
4008 7537 4.667668 CGAATTTGTCTTTTCTGCCGAGAG 60.668 45.833 0.00 0.00 0.00 3.20
4009 7538 3.186409 CGAATTTGTCTTTTCTGCCGAGA 59.814 43.478 0.00 0.00 0.00 4.04
4010 7539 3.482786 CGAATTTGTCTTTTCTGCCGAG 58.517 45.455 0.00 0.00 0.00 4.63
4011 7540 2.225491 CCGAATTTGTCTTTTCTGCCGA 59.775 45.455 0.00 0.00 0.00 5.54
4012 7541 2.584791 CCGAATTTGTCTTTTCTGCCG 58.415 47.619 0.00 0.00 0.00 5.69
4013 7542 2.352715 CCCCGAATTTGTCTTTTCTGCC 60.353 50.000 0.00 0.00 0.00 4.85
4014 7543 2.296190 ACCCCGAATTTGTCTTTTCTGC 59.704 45.455 0.00 0.00 0.00 4.26
4015 7544 3.364964 CGACCCCGAATTTGTCTTTTCTG 60.365 47.826 0.00 0.00 38.22 3.02
4016 7545 2.812011 CGACCCCGAATTTGTCTTTTCT 59.188 45.455 0.00 0.00 38.22 2.52
4017 7546 2.095415 CCGACCCCGAATTTGTCTTTTC 60.095 50.000 0.00 0.00 38.22 2.29
4018 7547 1.883926 CCGACCCCGAATTTGTCTTTT 59.116 47.619 0.00 0.00 38.22 2.27
4019 7548 1.072648 TCCGACCCCGAATTTGTCTTT 59.927 47.619 0.00 0.00 38.22 2.52
4020 7549 0.688487 TCCGACCCCGAATTTGTCTT 59.312 50.000 0.00 0.00 38.22 3.01
4021 7550 0.036671 GTCCGACCCCGAATTTGTCT 60.037 55.000 0.00 0.00 38.22 3.41
4022 7551 1.022982 GGTCCGACCCCGAATTTGTC 61.023 60.000 6.25 0.00 38.22 3.18
4023 7552 1.002990 GGTCCGACCCCGAATTTGT 60.003 57.895 6.25 0.00 38.22 2.83
4024 7553 3.899395 GGTCCGACCCCGAATTTG 58.101 61.111 6.25 0.00 38.22 2.32
4060 7589 4.727507 TTTGGACATCTGAGTAGCTCTC 57.272 45.455 0.00 0.00 43.03 3.20
4061 7590 4.713814 TCATTTGGACATCTGAGTAGCTCT 59.286 41.667 0.00 0.00 0.00 4.09
4062 7591 5.016051 TCATTTGGACATCTGAGTAGCTC 57.984 43.478 0.00 0.00 0.00 4.09
4063 7592 4.682859 GCTCATTTGGACATCTGAGTAGCT 60.683 45.833 0.00 0.00 37.90 3.32
4064 7593 3.559242 GCTCATTTGGACATCTGAGTAGC 59.441 47.826 11.08 0.00 37.90 3.58
4065 7594 5.021033 AGCTCATTTGGACATCTGAGTAG 57.979 43.478 11.08 0.00 37.90 2.57
4066 7595 6.544928 TTAGCTCATTTGGACATCTGAGTA 57.455 37.500 0.00 3.61 37.90 2.59
4067 7596 3.996921 AGCTCATTTGGACATCTGAGT 57.003 42.857 11.08 0.00 37.90 3.41
4068 7597 6.748333 TTTTAGCTCATTTGGACATCTGAG 57.252 37.500 0.00 7.08 38.49 3.35
4069 7598 7.707624 AATTTTAGCTCATTTGGACATCTGA 57.292 32.000 0.00 0.00 0.00 3.27
4070 7599 8.181487 CAAATTTTAGCTCATTTGGACATCTG 57.819 34.615 14.18 0.00 36.93 2.90
4078 7607 5.401550 TCGCTCCAAATTTTAGCTCATTTG 58.598 37.500 16.39 14.72 39.25 2.32
4079 7608 5.643379 TCGCTCCAAATTTTAGCTCATTT 57.357 34.783 16.39 0.00 34.03 2.32
4080 7609 5.402398 GTTCGCTCCAAATTTTAGCTCATT 58.598 37.500 16.39 0.00 34.03 2.57
4081 7610 4.142381 GGTTCGCTCCAAATTTTAGCTCAT 60.142 41.667 16.39 0.00 34.03 2.90
4082 7611 3.190535 GGTTCGCTCCAAATTTTAGCTCA 59.809 43.478 16.39 4.54 34.03 4.26
4083 7612 3.440522 AGGTTCGCTCCAAATTTTAGCTC 59.559 43.478 16.39 9.14 34.03 4.09
4084 7613 3.421844 AGGTTCGCTCCAAATTTTAGCT 58.578 40.909 16.39 0.00 34.03 3.32
4085 7614 3.190535 TGAGGTTCGCTCCAAATTTTAGC 59.809 43.478 10.87 10.87 0.00 3.09
4086 7615 4.669197 CGTGAGGTTCGCTCCAAATTTTAG 60.669 45.833 0.00 0.00 0.00 1.85
4087 7616 3.187637 CGTGAGGTTCGCTCCAAATTTTA 59.812 43.478 0.00 0.00 0.00 1.52
4088 7617 2.031157 CGTGAGGTTCGCTCCAAATTTT 60.031 45.455 0.00 0.00 0.00 1.82
4089 7618 1.535462 CGTGAGGTTCGCTCCAAATTT 59.465 47.619 0.00 0.00 0.00 1.82
4090 7619 1.156736 CGTGAGGTTCGCTCCAAATT 58.843 50.000 0.00 0.00 0.00 1.82
4091 7620 2.840974 CGTGAGGTTCGCTCCAAAT 58.159 52.632 0.00 0.00 0.00 2.32
4092 7621 4.354155 CGTGAGGTTCGCTCCAAA 57.646 55.556 0.00 0.00 0.00 3.28
4099 7628 4.078363 ACAATTTATTGCGTGAGGTTCG 57.922 40.909 2.46 0.00 41.38 3.95
4100 7629 5.296813 AGACAATTTATTGCGTGAGGTTC 57.703 39.130 2.46 0.00 41.38 3.62
4101 7630 5.703592 TGTAGACAATTTATTGCGTGAGGTT 59.296 36.000 2.46 0.00 41.38 3.50
4102 7631 5.242434 TGTAGACAATTTATTGCGTGAGGT 58.758 37.500 2.46 0.00 41.38 3.85
4103 7632 5.794687 TGTAGACAATTTATTGCGTGAGG 57.205 39.130 2.46 0.00 41.38 3.86
4104 7633 6.688385 CCATTGTAGACAATTTATTGCGTGAG 59.312 38.462 5.14 0.00 43.48 3.51
4105 7634 6.404184 CCCATTGTAGACAATTTATTGCGTGA 60.404 38.462 5.14 0.00 43.48 4.35
4106 7635 5.743398 CCCATTGTAGACAATTTATTGCGTG 59.257 40.000 5.14 0.00 43.48 5.34
4107 7636 5.650266 TCCCATTGTAGACAATTTATTGCGT 59.350 36.000 5.14 0.00 43.48 5.24
4108 7637 6.130298 TCCCATTGTAGACAATTTATTGCG 57.870 37.500 5.14 0.00 43.48 4.85
4109 7638 8.770438 TTTTCCCATTGTAGACAATTTATTGC 57.230 30.769 5.14 0.00 43.48 3.56
4168 7697 0.181587 TCTGCACCCGTCCAGAAAAA 59.818 50.000 0.00 0.00 35.32 1.94
4169 7698 0.400213 ATCTGCACCCGTCCAGAAAA 59.600 50.000 0.00 0.00 41.04 2.29
4170 7699 1.271856 TATCTGCACCCGTCCAGAAA 58.728 50.000 0.00 0.00 41.04 2.52
4171 7700 1.207089 CTTATCTGCACCCGTCCAGAA 59.793 52.381 0.00 0.00 41.04 3.02
4172 7701 0.824109 CTTATCTGCACCCGTCCAGA 59.176 55.000 0.00 0.00 41.81 3.86
4173 7702 0.811616 GCTTATCTGCACCCGTCCAG 60.812 60.000 0.00 0.00 0.00 3.86
4174 7703 1.220749 GCTTATCTGCACCCGTCCA 59.779 57.895 0.00 0.00 0.00 4.02
4175 7704 1.523938 GGCTTATCTGCACCCGTCC 60.524 63.158 0.00 0.00 34.04 4.79
4176 7705 1.523938 GGGCTTATCTGCACCCGTC 60.524 63.158 0.00 0.00 31.32 4.79
4177 7706 2.590092 GGGCTTATCTGCACCCGT 59.410 61.111 0.00 0.00 31.32 5.28
4179 7708 2.203209 CCGGGCTTATCTGCACCC 60.203 66.667 0.00 0.00 39.12 4.61
4180 7709 2.203209 CCCGGGCTTATCTGCACC 60.203 66.667 8.08 0.00 31.60 5.01
4181 7710 2.902343 GCCCGGGCTTATCTGCAC 60.902 66.667 38.76 4.71 38.26 4.57
4182 7711 3.407083 TGCCCGGGCTTATCTGCA 61.407 61.111 43.34 20.74 42.51 4.41
4183 7712 2.902343 GTGCCCGGGCTTATCTGC 60.902 66.667 43.34 21.05 42.51 4.26
4184 7713 2.203209 GGTGCCCGGGCTTATCTG 60.203 66.667 43.34 6.35 42.51 2.90
4185 7714 3.861797 CGGTGCCCGGGCTTATCT 61.862 66.667 43.34 0.00 44.15 1.98
4199 7728 0.459899 TATGAGTGCAGCGATTCGGT 59.540 50.000 4.68 4.68 38.40 4.69
4200 7729 1.135046 CTATGAGTGCAGCGATTCGG 58.865 55.000 8.34 0.00 0.00 4.30
4201 7730 1.783711 GACTATGAGTGCAGCGATTCG 59.216 52.381 0.62 0.62 0.00 3.34
4202 7731 3.090952 AGACTATGAGTGCAGCGATTC 57.909 47.619 0.00 0.00 0.00 2.52
4203 7732 4.862902 ATAGACTATGAGTGCAGCGATT 57.137 40.909 0.00 0.00 0.00 3.34
4204 7733 4.862902 AATAGACTATGAGTGCAGCGAT 57.137 40.909 0.00 0.00 0.00 4.58
4205 7734 5.473504 TGATAATAGACTATGAGTGCAGCGA 59.526 40.000 0.00 0.00 0.00 4.93
4206 7735 5.703876 TGATAATAGACTATGAGTGCAGCG 58.296 41.667 0.00 0.00 0.00 5.18
4207 7736 7.374272 TCTTGATAATAGACTATGAGTGCAGC 58.626 38.462 0.00 0.00 0.00 5.25
4208 7737 9.755804 TTTCTTGATAATAGACTATGAGTGCAG 57.244 33.333 0.00 0.00 0.00 4.41
4262 7791 5.156804 AGTGAAAAGTGACATTGTCGTTC 57.843 39.130 11.97 12.01 34.95 3.95
5264 8793 6.540914 TGTTTCGAACTACTTTCAGTCCAATT 59.459 34.615 0.00 0.00 33.24 2.32
5433 8963 1.750778 CAACCACTTGTGCCAACTTCT 59.249 47.619 0.00 0.00 0.00 2.85
5434 8964 1.802508 GCAACCACTTGTGCCAACTTC 60.803 52.381 0.00 0.00 0.00 3.01
5561 9091 4.203226 TGCTTTGTGAATTGTCTACACCA 58.797 39.130 0.00 0.00 34.18 4.17
5656 9186 7.517254 TCCTCCTTATGATGAAATTAGGATCCA 59.483 37.037 15.82 0.00 31.82 3.41
5661 9191 9.578576 TGAATTCCTCCTTATGATGAAATTAGG 57.421 33.333 2.27 0.00 32.37 2.69
5726 9256 3.515502 TGAGATTCTAGTTGGGACACAGG 59.484 47.826 0.00 0.00 39.29 4.00
5864 9394 4.518970 TGCTCAGTTTTAAGGACCAACATC 59.481 41.667 0.00 0.00 0.00 3.06
5964 9494 9.450807 CAGAGTTAAAACTTTACCATGTTTGAG 57.549 33.333 0.00 0.00 39.88 3.02
6084 9614 2.358003 GTTGCTGCTCCTGTCGCT 60.358 61.111 0.00 0.00 0.00 4.93
6154 9684 8.635765 AAACCACAGAAATACTCACATATGTT 57.364 30.769 5.37 0.00 0.00 2.71
6166 9696 8.137210 GCTTTTGCTTTTAAACCACAGAAATA 57.863 30.769 0.00 0.00 43.35 1.40
6196 9726 6.361214 GGATGCAATTTCACAGCAAATTTTTG 59.639 34.615 0.00 0.00 42.15 2.44
6198 9728 5.766174 AGGATGCAATTTCACAGCAAATTTT 59.234 32.000 0.00 0.00 42.15 1.82
6202 9733 3.575256 AGAGGATGCAATTTCACAGCAAA 59.425 39.130 0.00 0.00 42.15 3.68
6203 9734 3.159472 AGAGGATGCAATTTCACAGCAA 58.841 40.909 0.00 0.00 42.15 3.91
6209 9740 5.713389 ACAAAGATGAGAGGATGCAATTTCA 59.287 36.000 0.00 0.00 0.00 2.69
6210 9741 6.034591 CACAAAGATGAGAGGATGCAATTTC 58.965 40.000 0.00 0.00 0.00 2.17
6224 9755 2.334946 GCGCCTGCCACAAAGATGA 61.335 57.895 0.00 0.00 33.98 2.92
6225 9756 2.144833 TTGCGCCTGCCACAAAGATG 62.145 55.000 4.18 0.00 41.78 2.90
6230 9761 3.682885 CCATTGCGCCTGCCACAA 61.683 61.111 4.18 0.00 41.78 3.33
6231 9762 3.942377 ATCCATTGCGCCTGCCACA 62.942 57.895 4.18 0.00 41.78 4.17
6248 9779 6.740944 TGTACCAATACCAGTACATAGCAT 57.259 37.500 0.00 0.00 42.87 3.79
6258 9789 3.181497 GCAGCAACATGTACCAATACCAG 60.181 47.826 0.00 0.00 0.00 4.00
6273 9804 4.701956 ACAGTACCATATTTGCAGCAAC 57.298 40.909 7.54 0.00 0.00 4.17
6277 9808 3.381272 CCCCAACAGTACCATATTTGCAG 59.619 47.826 0.00 0.00 0.00 4.41
6281 9812 4.017499 AGCTTCCCCAACAGTACCATATTT 60.017 41.667 0.00 0.00 0.00 1.40
6302 9833 2.737679 GCCTGATCCTTGATTGCAAAGC 60.738 50.000 1.71 0.00 32.73 3.51
6303 9834 2.479049 CGCCTGATCCTTGATTGCAAAG 60.479 50.000 1.71 0.00 32.73 2.77
6307 9838 1.534595 GATCGCCTGATCCTTGATTGC 59.465 52.381 0.00 0.00 44.39 3.56
6319 9850 2.743752 CGTGCAACCAGATCGCCTG 61.744 63.158 0.00 0.00 42.55 4.85


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

AutoCloner maintained by Alex Coulton.