Multiple sequence alignment - TraesCS3D01G449800

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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 TraesCS3D01G449800 chr3D 100.000 4339 0 0 1 4339 557913603 557917941 0.000000e+00 8013.0
1 TraesCS3D01G449800 chr3D 83.966 2582 273 64 592 3097 557794859 557797375 0.000000e+00 2344.0
2 TraesCS3D01G449800 chr3D 84.848 2079 224 49 639 2684 557879051 557881071 0.000000e+00 2010.0
3 TraesCS3D01G449800 chr3D 87.987 308 34 3 658 964 557721142 557721447 1.150000e-95 361.0
4 TraesCS3D01G449800 chr3D 85.042 361 45 5 2131 2489 557922384 557922737 4.130000e-95 359.0
5 TraesCS3D01G449800 chr3D 83.957 374 56 4 2681 3054 557763119 557762750 5.340000e-94 355.0
6 TraesCS3D01G449800 chr3D 83.976 337 32 10 3163 3494 557923304 557923623 1.960000e-78 303.0
7 TraesCS3D01G449800 chr3A 94.274 2375 94 10 531 2901 693646936 693649272 0.000000e+00 3594.0
8 TraesCS3D01G449800 chr3A 95.513 936 26 2 2898 3825 693649570 693650497 0.000000e+00 1482.0
9 TraesCS3D01G449800 chr3A 85.506 1373 144 29 1250 2607 693581528 693582860 0.000000e+00 1382.0
10 TraesCS3D01G449800 chr3A 81.170 940 139 25 1213 2120 693484645 693485578 0.000000e+00 721.0
11 TraesCS3D01G449800 chr3A 83.442 616 62 16 638 1238 693571889 693572479 1.780000e-148 536.0
12 TraesCS3D01G449800 chr3A 82.243 535 64 19 2589 3097 693583247 693583776 2.400000e-117 433.0
13 TraesCS3D01G449800 chr3A 86.313 358 35 9 620 964 671759945 671760301 1.140000e-100 377.0
14 TraesCS3D01G449800 chr3A 83.929 392 47 9 2299 2684 693614789 693615170 1.150000e-95 361.0
15 TraesCS3D01G449800 chr3A 87.662 308 35 3 658 964 693484069 693484374 5.340000e-94 355.0
16 TraesCS3D01G449800 chr3A 95.545 202 7 2 3821 4020 30752870 30752669 5.410000e-84 322.0
17 TraesCS3D01G449800 chr3A 85.887 248 32 3 2681 2928 693548182 693547938 1.200000e-65 261.0
18 TraesCS3D01G449800 chr3A 94.000 150 7 2 206 354 693646410 693646558 4.370000e-55 226.0
19 TraesCS3D01G449800 chr3A 92.857 154 8 2 4017 4168 693650493 693650645 2.030000e-53 220.0
20 TraesCS3D01G449800 chr3A 98.701 77 0 1 135 211 693631043 693631118 7.570000e-28 135.0
21 TraesCS3D01G449800 chr3A 87.719 114 12 2 4150 4263 693586680 693586791 9.790000e-27 132.0
22 TraesCS3D01G449800 chr3A 100.000 66 0 0 430 495 693646875 693646940 5.890000e-24 122.0
23 TraesCS3D01G449800 chr3B 96.069 1501 46 5 366 1857 740514258 740515754 0.000000e+00 2433.0
24 TraesCS3D01G449800 chr3B 85.255 2082 224 45 638 2684 740503033 740505066 0.000000e+00 2067.0
25 TraesCS3D01G449800 chr3B 93.615 1159 44 12 2673 3824 740517650 740518785 0.000000e+00 1703.0
26 TraesCS3D01G449800 chr3B 86.755 1359 147 16 592 1932 740051376 740052719 0.000000e+00 1482.0
27 TraesCS3D01G449800 chr3B 88.337 926 95 8 1245 2160 740101309 740102231 0.000000e+00 1099.0
28 TraesCS3D01G449800 chr3B 83.543 1191 134 36 1949 3097 740052861 740054031 0.000000e+00 1057.0
29 TraesCS3D01G449800 chr3B 96.726 336 10 1 2346 2681 740517170 740517504 3.790000e-155 558.0
30 TraesCS3D01G449800 chr3B 97.378 267 6 1 2084 2349 740516729 740516995 1.840000e-123 453.0
31 TraesCS3D01G449800 chr3B 82.772 534 61 11 678 1199 740100122 740100636 8.560000e-122 448.0
32 TraesCS3D01G449800 chr3B 91.950 323 20 3 4017 4339 740518782 740519098 8.560000e-122 448.0
33 TraesCS3D01G449800 chr3B 86.761 355 34 9 621 964 708796700 708797052 2.450000e-102 383.0
34 TraesCS3D01G449800 chr3B 85.319 361 44 5 2131 2489 740542108 740542461 8.870000e-97 364.0
35 TraesCS3D01G449800 chr3B 82.058 379 61 6 2724 3097 740495650 740496026 2.520000e-82 316.0
36 TraesCS3D01G449800 chr3B 86.508 252 26 8 3163 3412 740543033 740543278 1.990000e-68 270.0
37 TraesCS3D01G449800 chr3B 83.803 284 26 11 1 279 740513735 740514003 7.200000e-63 252.0
38 TraesCS3D01G449800 chr3B 81.620 321 41 13 3095 3412 740054145 740054450 2.590000e-62 250.0
39 TraesCS3D01G449800 chr3B 84.729 203 28 3 4028 4228 740508791 740508992 2.650000e-47 200.0
40 TraesCS3D01G449800 chr3B 76.102 431 69 23 3095 3518 708798578 708798981 1.230000e-45 195.0
41 TraesCS3D01G449800 chr3B 91.753 97 7 1 429 525 740540467 740540562 2.720000e-27 134.0
42 TraesCS3D01G449800 chr3B 91.111 90 2 4 271 354 740514186 740514275 2.740000e-22 117.0
43 TraesCS3D01G449800 chr3B 100.000 33 0 0 73 105 740513868 740513836 1.300000e-05 62.1
44 TraesCS3D01G449800 chrUn 84.553 369 40 9 2131 2489 295852379 295852740 2.480000e-92 350.0
45 TraesCS3D01G449800 chr7B 95.522 201 7 2 3822 4020 521121072 521120872 1.950000e-83 320.0
46 TraesCS3D01G449800 chr2B 95.074 203 8 2 3822 4022 65096470 65096268 7.000000e-83 318.0
47 TraesCS3D01G449800 chr7D 94.175 206 10 2 3816 4019 28071204 28070999 3.260000e-81 313.0
48 TraesCS3D01G449800 chr7D 93.689 206 11 2 3818 4021 32059753 32059958 1.520000e-79 307.0
49 TraesCS3D01G449800 chr6B 93.780 209 11 2 3815 4021 88720430 88720222 3.260000e-81 313.0
50 TraesCS3D01G449800 chr6B 94.203 207 9 3 3818 4021 718624389 718624595 3.260000e-81 313.0
51 TraesCS3D01G449800 chr4D 94.554 202 9 2 3822 4021 508284679 508284478 1.170000e-80 311.0
52 TraesCS3D01G449800 chr4B 94.118 204 10 2 3822 4023 172375484 172375281 4.210000e-80 309.0
53 TraesCS3D01G449800 chr4B 73.571 420 74 23 2681 3085 667679449 667679846 4.560000e-25 126.0
54 TraesCS3D01G449800 chr5A 73.952 334 64 14 2676 3003 706442601 706442285 3.550000e-21 113.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G449800 chr3D 557913603 557917941 4338 False 8013.000000 8013 100.000000 1 4339 1 chr3D.!!$F4 4338
1 TraesCS3D01G449800 chr3D 557794859 557797375 2516 False 2344.000000 2344 83.966000 592 3097 1 chr3D.!!$F2 2505
2 TraesCS3D01G449800 chr3D 557879051 557881071 2020 False 2010.000000 2010 84.848000 639 2684 1 chr3D.!!$F3 2045
3 TraesCS3D01G449800 chr3D 557922384 557923623 1239 False 331.000000 359 84.509000 2131 3494 2 chr3D.!!$F5 1363
4 TraesCS3D01G449800 chr3A 693646410 693650645 4235 False 1128.800000 3594 95.328800 206 4168 5 chr3A.!!$F7 3962
5 TraesCS3D01G449800 chr3A 693581528 693586791 5263 False 649.000000 1382 85.156000 1250 4263 3 chr3A.!!$F6 3013
6 TraesCS3D01G449800 chr3A 693484069 693485578 1509 False 538.000000 721 84.416000 658 2120 2 chr3A.!!$F5 1462
7 TraesCS3D01G449800 chr3A 693571889 693572479 590 False 536.000000 536 83.442000 638 1238 1 chr3A.!!$F2 600
8 TraesCS3D01G449800 chr3B 740503033 740508992 5959 False 1133.500000 2067 84.992000 638 4228 2 chr3B.!!$F5 3590
9 TraesCS3D01G449800 chr3B 740051376 740054450 3074 False 929.666667 1482 83.972667 592 3412 3 chr3B.!!$F3 2820
10 TraesCS3D01G449800 chr3B 740513735 740519098 5363 False 852.000000 2433 92.950286 1 4339 7 chr3B.!!$F6 4338
11 TraesCS3D01G449800 chr3B 740100122 740102231 2109 False 773.500000 1099 85.554500 678 2160 2 chr3B.!!$F4 1482
12 TraesCS3D01G449800 chr3B 708796700 708798981 2281 False 289.000000 383 81.431500 621 3518 2 chr3B.!!$F2 2897
13 TraesCS3D01G449800 chr3B 740540467 740543278 2811 False 256.000000 364 87.860000 429 3412 3 chr3B.!!$F7 2983

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
348 547 0.386838 GCACCATAATTGCCTCCTGC 59.613 55.000 0.0 0.0 41.77 4.85 F
569 1039 1.220206 CTGCTTCACTCCATCGGCT 59.780 57.895 0.0 0.0 0.00 5.52 F
1363 2679 1.476845 TAGTCCCAAAGGCGTGCTCA 61.477 55.000 0.0 0.0 0.00 4.26 F
1754 3079 1.927174 GCGTAAAGTGTGCGAGATGAT 59.073 47.619 0.0 0.0 37.56 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 2601 1.547372 GAGATGTTTGTGCCAGGCATT 59.453 47.619 19.75 0.0 41.91 3.56 R
2317 4645 2.224378 ACCTGCATCCATCCATAACTCG 60.224 50.000 0.00 0.0 0.00 4.18 R
3105 8821 1.333619 CAAAAGTTACAGCAGCACGGT 59.666 47.619 0.00 0.0 0.00 4.83 R
3378 9113 1.002274 TTGGTTGGTGGCACCCTTT 59.998 52.632 32.61 0.0 37.50 3.11 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
78 79 4.790937 TGGTTGCTAGCCATCATTCAATA 58.209 39.130 13.29 0.00 0.00 1.90
80 81 5.655974 TGGTTGCTAGCCATCATTCAATAAA 59.344 36.000 13.29 0.00 0.00 1.40
82 83 5.443185 TGCTAGCCATCATTCAATAAAGC 57.557 39.130 13.29 0.00 0.00 3.51
84 85 4.522022 GCTAGCCATCATTCAATAAAGCCT 59.478 41.667 2.29 0.00 0.00 4.58
85 86 5.707298 GCTAGCCATCATTCAATAAAGCCTA 59.293 40.000 2.29 0.00 0.00 3.93
86 87 6.128063 GCTAGCCATCATTCAATAAAGCCTAG 60.128 42.308 2.29 0.00 0.00 3.02
87 88 4.522022 AGCCATCATTCAATAAAGCCTAGC 59.478 41.667 0.00 0.00 0.00 3.42
88 89 4.522022 GCCATCATTCAATAAAGCCTAGCT 59.478 41.667 0.00 0.00 42.56 3.32
89 90 5.564259 GCCATCATTCAATAAAGCCTAGCTG 60.564 44.000 0.00 0.00 39.62 4.24
90 91 5.458891 CATCATTCAATAAAGCCTAGCTGC 58.541 41.667 0.00 0.00 39.62 5.25
91 92 4.785301 TCATTCAATAAAGCCTAGCTGCT 58.215 39.130 7.57 7.57 45.43 4.24
98 99 3.353342 AGCCTAGCTGCTTTTTGCT 57.647 47.368 7.79 8.23 38.85 3.91
99 100 1.172175 AGCCTAGCTGCTTTTTGCTC 58.828 50.000 7.79 0.00 38.85 4.26
101 102 1.270550 GCCTAGCTGCTTTTTGCTCAA 59.729 47.619 7.79 0.00 43.37 3.02
102 103 2.288395 GCCTAGCTGCTTTTTGCTCAAA 60.288 45.455 7.79 0.00 43.37 2.69
103 104 3.799917 GCCTAGCTGCTTTTTGCTCAAAA 60.800 43.478 7.79 3.86 43.37 2.44
104 105 4.370917 CCTAGCTGCTTTTTGCTCAAAAA 58.629 39.130 7.79 16.65 44.98 1.94
198 199 3.341270 AGGCACTCCCAACCACAA 58.659 55.556 0.00 0.00 35.39 3.33
284 483 5.163612 GCTCTAGGCTCAAAATTAAACCCAG 60.164 44.000 0.00 0.00 38.06 4.45
285 484 3.961480 AGGCTCAAAATTAAACCCAGC 57.039 42.857 0.00 0.00 0.00 4.85
324 523 6.425577 ACTGTACTCGTTGATCTCTCTAAC 57.574 41.667 0.00 0.00 0.00 2.34
340 539 4.634004 TCTCTAACAACGGCACCATAATTG 59.366 41.667 0.00 0.00 0.00 2.32
341 540 2.362169 AACAACGGCACCATAATTGC 57.638 45.000 0.00 0.00 39.41 3.56
348 547 0.386838 GCACCATAATTGCCTCCTGC 59.613 55.000 0.00 0.00 41.77 4.85
544 1014 1.598962 GCTCTGCTTCACTGCACCA 60.599 57.895 0.00 0.00 38.12 4.17
569 1039 1.220206 CTGCTTCACTCCATCGGCT 59.780 57.895 0.00 0.00 0.00 5.52
1289 2599 9.868277 AAATGTGTATATGTTACAAAATGGTGG 57.132 29.630 0.00 0.00 0.00 4.61
1291 2601 9.688091 ATGTGTATATGTTACAAAATGGTGGTA 57.312 29.630 0.00 0.00 0.00 3.25
1319 2629 1.956477 GCACAAACATCTCACCTTGGT 59.044 47.619 0.00 0.00 0.00 3.67
1363 2679 1.476845 TAGTCCCAAAGGCGTGCTCA 61.477 55.000 0.00 0.00 0.00 4.26
1754 3079 1.927174 GCGTAAAGTGTGCGAGATGAT 59.073 47.619 0.00 0.00 37.56 2.45
1939 4124 9.587772 CTCATTGTTTAGTATAGCTGTGTACTT 57.412 33.333 11.80 0.82 33.08 2.24
1947 4132 6.628185 AGTATAGCTGTGTACTTGTGTTACC 58.372 40.000 0.00 0.00 26.40 2.85
2651 5592 2.908940 GCTTGTGCTGCCACCAGT 60.909 61.111 0.00 0.00 41.35 4.00
2720 5815 4.414852 CAGAATTGCAAATTGGACCTACG 58.585 43.478 1.71 0.00 0.00 3.51
3105 8821 6.945435 TGACATTCTAGTCCAAGGCATTTAAA 59.055 34.615 0.00 0.00 37.73 1.52
3107 8823 6.152831 ACATTCTAGTCCAAGGCATTTAAACC 59.847 38.462 0.00 0.00 0.00 3.27
3246 8965 6.647895 GGCCCATCTTATAATTTTGATGCTTG 59.352 38.462 0.00 1.34 36.08 4.01
3377 9112 4.301628 GAAAGCTTTTGGATGAGTTGTGG 58.698 43.478 14.05 0.00 0.00 4.17
3378 9113 3.228188 AGCTTTTGGATGAGTTGTGGA 57.772 42.857 0.00 0.00 0.00 4.02
3405 9141 0.179020 CCACCAACCAAGAGCACAGA 60.179 55.000 0.00 0.00 0.00 3.41
3512 9256 3.079578 CTCTTGTCATGTGGCATCAGTT 58.920 45.455 0.00 0.00 0.00 3.16
3521 9265 4.359434 TGTGGCATCAGTTGGTTAGTAA 57.641 40.909 0.00 0.00 0.00 2.24
3522 9266 4.069304 TGTGGCATCAGTTGGTTAGTAAC 58.931 43.478 4.32 4.32 0.00 2.50
3523 9267 4.202419 TGTGGCATCAGTTGGTTAGTAACT 60.202 41.667 12.65 0.00 38.84 2.24
3710 9510 0.525761 TTGGACAAGCGCCTTATTGC 59.474 50.000 2.29 0.00 0.00 3.56
3825 9921 2.485426 CACATGTGCTGGTTCACTAAGG 59.515 50.000 13.94 0.00 37.81 2.69
3826 9922 1.470098 CATGTGCTGGTTCACTAAGGC 59.530 52.381 0.00 0.00 37.81 4.35
3827 9923 0.764890 TGTGCTGGTTCACTAAGGCT 59.235 50.000 0.00 0.00 37.81 4.58
3828 9924 1.142870 TGTGCTGGTTCACTAAGGCTT 59.857 47.619 4.58 4.58 37.81 4.35
3829 9925 1.537202 GTGCTGGTTCACTAAGGCTTG 59.463 52.381 10.69 2.52 34.29 4.01
3830 9926 1.142870 TGCTGGTTCACTAAGGCTTGT 59.857 47.619 10.69 3.20 0.00 3.16
3831 9927 2.370519 TGCTGGTTCACTAAGGCTTGTA 59.629 45.455 10.69 0.00 0.00 2.41
3832 9928 2.742589 GCTGGTTCACTAAGGCTTGTAC 59.257 50.000 10.69 0.00 0.00 2.90
3833 9929 3.805807 GCTGGTTCACTAAGGCTTGTACA 60.806 47.826 10.69 0.00 0.00 2.90
3834 9930 4.385825 CTGGTTCACTAAGGCTTGTACAA 58.614 43.478 10.69 8.28 0.00 2.41
3835 9931 4.980573 TGGTTCACTAAGGCTTGTACAAT 58.019 39.130 10.69 0.00 0.00 2.71
3836 9932 4.759693 TGGTTCACTAAGGCTTGTACAATG 59.240 41.667 10.69 2.74 0.00 2.82
3837 9933 4.156008 GGTTCACTAAGGCTTGTACAATGG 59.844 45.833 10.69 0.00 0.00 3.16
3838 9934 3.950397 TCACTAAGGCTTGTACAATGGG 58.050 45.455 10.69 0.00 0.00 4.00
3839 9935 3.585289 TCACTAAGGCTTGTACAATGGGA 59.415 43.478 10.69 0.00 0.00 4.37
3840 9936 3.941483 CACTAAGGCTTGTACAATGGGAG 59.059 47.826 10.69 6.02 0.00 4.30
3841 9937 3.844211 ACTAAGGCTTGTACAATGGGAGA 59.156 43.478 10.69 0.00 0.00 3.71
3842 9938 4.475016 ACTAAGGCTTGTACAATGGGAGAT 59.525 41.667 10.69 0.00 0.00 2.75
3843 9939 3.287867 AGGCTTGTACAATGGGAGATG 57.712 47.619 9.13 0.00 0.00 2.90
3844 9940 1.678101 GGCTTGTACAATGGGAGATGC 59.322 52.381 9.13 6.22 0.00 3.91
3845 9941 2.648059 GCTTGTACAATGGGAGATGCT 58.352 47.619 9.13 0.00 0.00 3.79
3846 9942 3.019564 GCTTGTACAATGGGAGATGCTT 58.980 45.455 9.13 0.00 0.00 3.91
3847 9943 4.199310 GCTTGTACAATGGGAGATGCTTA 58.801 43.478 9.13 0.00 0.00 3.09
3848 9944 4.274459 GCTTGTACAATGGGAGATGCTTAG 59.726 45.833 9.13 0.00 0.00 2.18
3849 9945 5.674525 CTTGTACAATGGGAGATGCTTAGA 58.325 41.667 9.13 0.00 0.00 2.10
3850 9946 5.282055 TGTACAATGGGAGATGCTTAGAG 57.718 43.478 0.00 0.00 0.00 2.43
3851 9947 4.962362 TGTACAATGGGAGATGCTTAGAGA 59.038 41.667 0.00 0.00 0.00 3.10
3852 9948 4.686191 ACAATGGGAGATGCTTAGAGAG 57.314 45.455 0.00 0.00 0.00 3.20
3853 9949 4.293494 ACAATGGGAGATGCTTAGAGAGA 58.707 43.478 0.00 0.00 0.00 3.10
3854 9950 4.906664 ACAATGGGAGATGCTTAGAGAGAT 59.093 41.667 0.00 0.00 0.00 2.75
3855 9951 5.221682 ACAATGGGAGATGCTTAGAGAGATG 60.222 44.000 0.00 0.00 0.00 2.90
3856 9952 2.632028 TGGGAGATGCTTAGAGAGATGC 59.368 50.000 0.00 0.00 0.00 3.91
3857 9953 2.899256 GGGAGATGCTTAGAGAGATGCT 59.101 50.000 0.00 0.00 0.00 3.79
3858 9954 3.324556 GGGAGATGCTTAGAGAGATGCTT 59.675 47.826 0.00 0.00 0.00 3.91
3859 9955 4.526262 GGGAGATGCTTAGAGAGATGCTTA 59.474 45.833 0.00 0.00 0.00 3.09
3860 9956 5.336690 GGGAGATGCTTAGAGAGATGCTTAG 60.337 48.000 0.00 0.00 0.00 2.18
3861 9957 5.476599 GGAGATGCTTAGAGAGATGCTTAGA 59.523 44.000 0.00 0.00 0.00 2.10
3862 9958 6.015519 GGAGATGCTTAGAGAGATGCTTAGAA 60.016 42.308 0.00 0.00 0.00 2.10
3863 9959 7.358770 AGATGCTTAGAGAGATGCTTAGAAA 57.641 36.000 0.00 0.00 0.00 2.52
3864 9960 7.790027 AGATGCTTAGAGAGATGCTTAGAAAA 58.210 34.615 0.00 0.00 0.00 2.29
3865 9961 8.263640 AGATGCTTAGAGAGATGCTTAGAAAAA 58.736 33.333 0.00 0.00 0.00 1.94
3866 9962 8.977267 ATGCTTAGAGAGATGCTTAGAAAAAT 57.023 30.769 0.00 0.00 0.00 1.82
3868 9964 9.890629 TGCTTAGAGAGATGCTTAGAAAAATAA 57.109 29.630 0.00 0.00 0.00 1.40
3872 9968 8.202745 AGAGAGATGCTTAGAAAAATAAACCG 57.797 34.615 0.00 0.00 0.00 4.44
3873 9969 7.281100 AGAGAGATGCTTAGAAAAATAAACCGG 59.719 37.037 0.00 0.00 0.00 5.28
3874 9970 6.318900 AGAGATGCTTAGAAAAATAAACCGGG 59.681 38.462 6.32 0.00 0.00 5.73
3875 9971 5.949952 AGATGCTTAGAAAAATAAACCGGGT 59.050 36.000 6.32 0.00 0.00 5.28
3876 9972 6.436218 AGATGCTTAGAAAAATAAACCGGGTT 59.564 34.615 10.96 10.96 0.00 4.11
3877 9973 6.408107 TGCTTAGAAAAATAAACCGGGTTT 57.592 33.333 26.79 26.79 39.24 3.27
3878 9974 6.818233 TGCTTAGAAAAATAAACCGGGTTTT 58.182 32.000 28.50 11.74 37.01 2.43
3879 9975 6.924612 TGCTTAGAAAAATAAACCGGGTTTTC 59.075 34.615 28.50 19.21 39.28 2.29
3880 9976 7.149973 GCTTAGAAAAATAAACCGGGTTTTCT 58.850 34.615 28.50 24.24 46.62 2.52
3881 9977 7.115805 GCTTAGAAAAATAAACCGGGTTTTCTG 59.884 37.037 28.50 14.70 45.33 3.02
3882 9978 6.718522 AGAAAAATAAACCGGGTTTTCTGA 57.281 33.333 28.50 12.48 44.54 3.27
3883 9979 7.114866 AGAAAAATAAACCGGGTTTTCTGAA 57.885 32.000 28.50 12.10 44.54 3.02
3884 9980 7.207383 AGAAAAATAAACCGGGTTTTCTGAAG 58.793 34.615 28.50 0.00 44.54 3.02
3885 9981 4.514781 AATAAACCGGGTTTTCTGAAGC 57.485 40.909 28.50 0.00 37.01 3.86
3886 9982 1.770294 AAACCGGGTTTTCTGAAGCA 58.230 45.000 19.22 0.00 31.10 3.91
3887 9983 1.029681 AACCGGGTTTTCTGAAGCAC 58.970 50.000 6.59 0.00 0.00 4.40
3888 9984 0.822121 ACCGGGTTTTCTGAAGCACC 60.822 55.000 6.32 10.82 0.00 5.01
3889 9985 1.574428 CGGGTTTTCTGAAGCACCG 59.426 57.895 12.10 12.10 0.00 4.94
3890 9986 1.852067 CGGGTTTTCTGAAGCACCGG 61.852 60.000 16.07 0.00 36.45 5.28
3891 9987 0.822121 GGGTTTTCTGAAGCACCGGT 60.822 55.000 0.00 0.00 0.00 5.28
3892 9988 0.310854 GGTTTTCTGAAGCACCGGTG 59.689 55.000 30.66 30.66 0.00 4.94
3904 10000 2.684001 CACCGGTGCCTATTTCTACA 57.316 50.000 24.02 0.00 0.00 2.74
3905 10001 2.550978 CACCGGTGCCTATTTCTACAG 58.449 52.381 24.02 0.00 0.00 2.74
3906 10002 1.485066 ACCGGTGCCTATTTCTACAGG 59.515 52.381 6.12 0.00 35.04 4.00
3907 10003 1.760613 CCGGTGCCTATTTCTACAGGA 59.239 52.381 0.00 0.00 33.42 3.86
3908 10004 2.224066 CCGGTGCCTATTTCTACAGGAG 60.224 54.545 0.00 0.00 33.42 3.69
3909 10005 2.693591 CGGTGCCTATTTCTACAGGAGA 59.306 50.000 0.00 0.00 33.42 3.71
3910 10006 3.243569 CGGTGCCTATTTCTACAGGAGAG 60.244 52.174 0.00 0.00 34.93 3.20
3911 10007 3.961408 GGTGCCTATTTCTACAGGAGAGA 59.039 47.826 0.00 0.00 34.93 3.10
3912 10008 4.202172 GGTGCCTATTTCTACAGGAGAGAC 60.202 50.000 0.00 0.00 34.93 3.36
3913 10009 3.632604 TGCCTATTTCTACAGGAGAGACG 59.367 47.826 0.00 0.00 34.93 4.18
3914 10010 3.551250 GCCTATTTCTACAGGAGAGACGC 60.551 52.174 0.00 0.00 34.93 5.19
3915 10011 3.886505 CCTATTTCTACAGGAGAGACGCT 59.113 47.826 0.00 0.00 34.93 5.07
3916 10012 4.339814 CCTATTTCTACAGGAGAGACGCTT 59.660 45.833 0.00 0.00 34.93 4.68
3917 10013 5.531659 CCTATTTCTACAGGAGAGACGCTTA 59.468 44.000 0.00 0.00 34.93 3.09
3918 10014 4.966965 TTTCTACAGGAGAGACGCTTAG 57.033 45.455 0.00 0.00 34.93 2.18
3919 10015 3.630892 TCTACAGGAGAGACGCTTAGT 57.369 47.619 0.00 0.00 0.00 2.24
3920 10016 3.952931 TCTACAGGAGAGACGCTTAGTT 58.047 45.455 0.00 0.00 0.00 2.24
3921 10017 5.095145 TCTACAGGAGAGACGCTTAGTTA 57.905 43.478 0.00 0.00 0.00 2.24
3922 10018 5.494724 TCTACAGGAGAGACGCTTAGTTAA 58.505 41.667 0.00 0.00 0.00 2.01
3923 10019 4.705337 ACAGGAGAGACGCTTAGTTAAG 57.295 45.455 0.00 0.00 36.40 1.85
3924 10020 9.223557 TTCTACAGGAGAGACGCTTAGTTAAGC 62.224 44.444 12.72 12.72 44.08 3.09
3939 10035 8.906636 CTTAGTTAAGCGTCTATTCTGTACAA 57.093 34.615 0.00 0.00 0.00 2.41
3940 10036 9.350357 CTTAGTTAAGCGTCTATTCTGTACAAA 57.650 33.333 0.00 0.00 0.00 2.83
3941 10037 9.865321 TTAGTTAAGCGTCTATTCTGTACAAAT 57.135 29.630 0.00 3.07 0.00 2.32
3943 10039 9.865321 AGTTAAGCGTCTATTCTGTACAAATAA 57.135 29.630 0.00 0.00 0.00 1.40
3945 10041 9.865321 TTAAGCGTCTATTCTGTACAAATAAGT 57.135 29.630 0.00 0.00 0.00 2.24
3947 10043 8.853469 AGCGTCTATTCTGTACAAATAAGTAC 57.147 34.615 0.00 0.00 43.58 2.73
3948 10044 8.684520 AGCGTCTATTCTGTACAAATAAGTACT 58.315 33.333 0.00 0.00 43.65 2.73
3949 10045 8.744011 GCGTCTATTCTGTACAAATAAGTACTG 58.256 37.037 0.00 5.54 43.65 2.74
3950 10046 9.234384 CGTCTATTCTGTACAAATAAGTACTGG 57.766 37.037 0.00 2.87 43.65 4.00
3953 10049 7.611213 ATTCTGTACAAATAAGTACTGGTGC 57.389 36.000 0.00 0.00 43.65 5.01
3954 10050 6.354794 TCTGTACAAATAAGTACTGGTGCT 57.645 37.500 0.00 0.00 43.65 4.40
3955 10051 6.765403 TCTGTACAAATAAGTACTGGTGCTT 58.235 36.000 0.00 8.87 43.65 3.91
3956 10052 7.898918 TCTGTACAAATAAGTACTGGTGCTTA 58.101 34.615 12.20 12.20 43.65 3.09
3957 10053 8.369424 TCTGTACAAATAAGTACTGGTGCTTAA 58.631 33.333 13.43 0.00 43.65 1.85
3958 10054 8.542497 TGTACAAATAAGTACTGGTGCTTAAG 57.458 34.615 13.43 0.00 43.65 1.85
3959 10055 7.604927 TGTACAAATAAGTACTGGTGCTTAAGG 59.395 37.037 13.43 9.34 43.65 2.69
3960 10056 6.775708 ACAAATAAGTACTGGTGCTTAAGGA 58.224 36.000 13.43 0.00 40.26 3.36
3961 10057 7.228590 ACAAATAAGTACTGGTGCTTAAGGAA 58.771 34.615 13.43 0.00 40.26 3.36
3962 10058 7.722285 ACAAATAAGTACTGGTGCTTAAGGAAA 59.278 33.333 13.43 0.00 40.26 3.13
3963 10059 7.923414 AATAAGTACTGGTGCTTAAGGAAAG 57.077 36.000 13.43 5.57 40.26 2.62
3977 10073 7.468141 CTTAAGGAAAGCCTGGTTTATTTCT 57.532 36.000 0.00 0.00 46.28 2.52
3978 10074 5.984695 AAGGAAAGCCTGGTTTATTTCTC 57.015 39.130 0.00 0.00 46.28 2.87
3979 10075 5.262455 AGGAAAGCCTGGTTTATTTCTCT 57.738 39.130 0.00 0.41 44.90 3.10
3980 10076 6.388619 AGGAAAGCCTGGTTTATTTCTCTA 57.611 37.500 0.00 0.00 44.90 2.43
3981 10077 6.790319 AGGAAAGCCTGGTTTATTTCTCTAA 58.210 36.000 0.00 0.00 44.90 2.10
3982 10078 6.887002 AGGAAAGCCTGGTTTATTTCTCTAAG 59.113 38.462 0.00 0.00 44.90 2.18
3983 10079 6.404844 GGAAAGCCTGGTTTATTTCTCTAAGC 60.405 42.308 0.00 0.00 33.25 3.09
3984 10080 5.179452 AGCCTGGTTTATTTCTCTAAGCA 57.821 39.130 0.00 0.00 0.00 3.91
3985 10081 4.944317 AGCCTGGTTTATTTCTCTAAGCAC 59.056 41.667 0.00 0.00 0.00 4.40
3986 10082 4.096532 GCCTGGTTTATTTCTCTAAGCACC 59.903 45.833 0.00 0.00 0.00 5.01
3987 10083 5.501156 CCTGGTTTATTTCTCTAAGCACCT 58.499 41.667 0.00 0.00 0.00 4.00
3988 10084 5.946377 CCTGGTTTATTTCTCTAAGCACCTT 59.054 40.000 0.00 0.00 0.00 3.50
3989 10085 6.094186 CCTGGTTTATTTCTCTAAGCACCTTC 59.906 42.308 0.00 0.00 0.00 3.46
3990 10086 5.944007 TGGTTTATTTCTCTAAGCACCTTCC 59.056 40.000 0.00 0.00 0.00 3.46
3991 10087 5.357314 GGTTTATTTCTCTAAGCACCTTCCC 59.643 44.000 0.00 0.00 0.00 3.97
3992 10088 6.181190 GTTTATTTCTCTAAGCACCTTCCCT 58.819 40.000 0.00 0.00 0.00 4.20
3993 10089 7.336396 GTTTATTTCTCTAAGCACCTTCCCTA 58.664 38.462 0.00 0.00 0.00 3.53
3994 10090 7.504926 TTATTTCTCTAAGCACCTTCCCTAA 57.495 36.000 0.00 0.00 0.00 2.69
3995 10091 5.422214 TTTCTCTAAGCACCTTCCCTAAG 57.578 43.478 0.00 0.00 0.00 2.18
3996 10092 2.766828 TCTCTAAGCACCTTCCCTAAGC 59.233 50.000 0.00 0.00 0.00 3.09
3997 10093 2.501723 CTCTAAGCACCTTCCCTAAGCA 59.498 50.000 0.00 0.00 0.00 3.91
3998 10094 2.236395 TCTAAGCACCTTCCCTAAGCAC 59.764 50.000 0.00 0.00 0.00 4.40
3999 10095 0.038310 AAGCACCTTCCCTAAGCACC 59.962 55.000 0.00 0.00 0.00 5.01
4000 10096 0.842467 AGCACCTTCCCTAAGCACCT 60.842 55.000 0.00 0.00 0.00 4.00
4001 10097 0.393132 GCACCTTCCCTAAGCACCTC 60.393 60.000 0.00 0.00 0.00 3.85
4002 10098 0.253327 CACCTTCCCTAAGCACCTCC 59.747 60.000 0.00 0.00 0.00 4.30
4003 10099 0.914902 ACCTTCCCTAAGCACCTCCC 60.915 60.000 0.00 0.00 0.00 4.30
4004 10100 0.914417 CCTTCCCTAAGCACCTCCCA 60.914 60.000 0.00 0.00 0.00 4.37
4005 10101 1.216990 CTTCCCTAAGCACCTCCCAT 58.783 55.000 0.00 0.00 0.00 4.00
4006 10102 1.566231 CTTCCCTAAGCACCTCCCATT 59.434 52.381 0.00 0.00 0.00 3.16
4007 10103 0.918983 TCCCTAAGCACCTCCCATTG 59.081 55.000 0.00 0.00 0.00 2.82
4008 10104 0.625849 CCCTAAGCACCTCCCATTGT 59.374 55.000 0.00 0.00 0.00 2.71
4009 10105 1.843851 CCCTAAGCACCTCCCATTGTA 59.156 52.381 0.00 0.00 0.00 2.41
4010 10106 2.421529 CCCTAAGCACCTCCCATTGTAC 60.422 54.545 0.00 0.00 0.00 2.90
4011 10107 2.238646 CCTAAGCACCTCCCATTGTACA 59.761 50.000 0.00 0.00 0.00 2.90
4012 10108 2.969821 AAGCACCTCCCATTGTACAA 57.030 45.000 11.41 11.41 0.00 2.41
4013 10109 2.496899 AGCACCTCCCATTGTACAAG 57.503 50.000 14.65 6.30 0.00 3.16
4014 10110 1.004745 AGCACCTCCCATTGTACAAGG 59.995 52.381 14.65 13.92 0.00 3.61
4015 10111 1.463674 CACCTCCCATTGTACAAGGC 58.536 55.000 14.66 0.00 0.00 4.35
4016 10112 0.331616 ACCTCCCATTGTACAAGGCC 59.668 55.000 14.66 0.00 0.00 5.19
4017 10113 0.625849 CCTCCCATTGTACAAGGCCT 59.374 55.000 14.66 0.00 0.00 5.19
4018 10114 1.843851 CCTCCCATTGTACAAGGCCTA 59.156 52.381 14.66 1.57 0.00 3.93
4019 10115 2.241176 CCTCCCATTGTACAAGGCCTAA 59.759 50.000 14.66 0.00 0.00 2.69
4020 10116 3.545703 CTCCCATTGTACAAGGCCTAAG 58.454 50.000 14.66 4.24 0.00 2.18
4081 10178 0.902531 GCACTAGCCAGTAGGGTCAA 59.097 55.000 0.00 0.00 43.69 3.18
4093 10190 5.256474 CAGTAGGGTCAAGGTGAATTCATT 58.744 41.667 12.12 0.00 0.00 2.57
4101 10198 6.884836 GGTCAAGGTGAATTCATTAGGTAAGT 59.115 38.462 12.12 0.00 0.00 2.24
4136 12254 4.024893 GCAGAAGTCTCGAAACACAAATCA 60.025 41.667 0.00 0.00 0.00 2.57
4227 12347 4.443621 TGACACTATTCACACGACCAAAA 58.556 39.130 0.00 0.00 0.00 2.44
4230 12350 4.879545 ACACTATTCACACGACCAAAAAGT 59.120 37.500 0.00 0.00 0.00 2.66
4289 12409 4.147449 CTCGCCGGTGCTCATCCA 62.147 66.667 11.05 0.00 34.43 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 8.877864 AACTCCATTCCTGTAAACATTATCAA 57.122 30.769 0.00 0.00 0.00 2.57
198 199 1.548582 CCCTTTCTCCTGGTGCACATT 60.549 52.381 20.43 0.00 0.00 2.71
279 281 0.396811 AGCTTTTAGTCACGCTGGGT 59.603 50.000 0.00 0.00 0.00 4.51
281 480 3.746492 AGTAAAGCTTTTAGTCACGCTGG 59.254 43.478 18.47 0.00 32.22 4.85
284 483 4.727235 ACAGTAAAGCTTTTAGTCACGC 57.273 40.909 18.47 0.00 0.00 5.34
285 484 6.183359 CGAGTACAGTAAAGCTTTTAGTCACG 60.183 42.308 18.47 14.11 0.00 4.35
355 554 4.881920 GCAGGAGGCAATTGTTCTAAAAA 58.118 39.130 7.40 0.00 43.97 1.94
356 555 4.519540 GCAGGAGGCAATTGTTCTAAAA 57.480 40.909 7.40 0.00 43.97 1.52
544 1014 1.260538 TGGAGTGAAGCAGAGCCGAT 61.261 55.000 0.00 0.00 0.00 4.18
569 1039 3.255642 GCTATCAAAGACTGGCAACCAAA 59.744 43.478 0.00 0.00 30.80 3.28
1278 2588 2.566724 CCAGGCATTACCACCATTTTGT 59.433 45.455 0.00 0.00 43.14 2.83
1289 2599 2.493278 AGATGTTTGTGCCAGGCATTAC 59.507 45.455 19.75 16.00 41.91 1.89
1291 2601 1.547372 GAGATGTTTGTGCCAGGCATT 59.453 47.619 19.75 0.00 41.91 3.56
1319 2629 2.680352 GCCAGAGGAGGTCCGACA 60.680 66.667 0.00 0.00 42.08 4.35
1363 2679 5.121611 TCGCGACATAGATTTTGTTGTCAAT 59.878 36.000 3.71 0.00 38.68 2.57
1754 3079 5.366477 TCACCCAAATGATACTCATCTGCTA 59.634 40.000 0.00 0.00 35.76 3.49
1875 4052 9.284968 ACATTGCAAAACTATGTAAACTCTACT 57.715 29.630 1.71 0.00 41.98 2.57
1939 4124 8.862325 AAAGAATCAATCACATAGGTAACACA 57.138 30.769 0.00 0.00 41.41 3.72
2317 4645 2.224378 ACCTGCATCCATCCATAACTCG 60.224 50.000 0.00 0.00 0.00 4.18
2634 5575 1.580845 CTACTGGTGGCAGCACAAGC 61.581 60.000 16.56 0.00 42.56 4.01
2651 5592 2.618816 CCAAGTTCAGGAAGCATGGCTA 60.619 50.000 0.00 0.00 38.25 3.93
3105 8821 1.333619 CAAAAGTTACAGCAGCACGGT 59.666 47.619 0.00 0.00 0.00 4.83
3107 8823 1.601903 TCCAAAAGTTACAGCAGCACG 59.398 47.619 0.00 0.00 0.00 5.34
3246 8965 3.974871 TCGGTTTGCCACTTTAACTTC 57.025 42.857 0.00 0.00 34.09 3.01
3377 9112 1.045911 TTGGTTGGTGGCACCCTTTC 61.046 55.000 32.61 19.28 37.50 2.62
3378 9113 1.002274 TTGGTTGGTGGCACCCTTT 59.998 52.632 32.61 0.00 37.50 3.11
3405 9141 1.372087 GCTACCGCAGAAATGCAGCT 61.372 55.000 0.00 0.00 35.78 4.24
3512 9256 8.074613 ACTGATGCATACTAAGTTACTAACCA 57.925 34.615 0.00 0.00 0.00 3.67
3521 9265 8.191446 CACTAACACTACTGATGCATACTAAGT 58.809 37.037 0.00 4.14 0.00 2.24
3522 9266 8.191446 ACACTAACACTACTGATGCATACTAAG 58.809 37.037 0.00 0.00 0.00 2.18
3523 9267 7.973944 CACACTAACACTACTGATGCATACTAA 59.026 37.037 0.00 0.00 0.00 2.24
3710 9510 1.091771 ACCGATTCTGCAATGGCGAG 61.092 55.000 0.00 0.00 45.35 5.03
3825 9921 2.648059 AGCATCTCCCATTGTACAAGC 58.352 47.619 14.65 9.05 0.00 4.01
3826 9922 5.674525 TCTAAGCATCTCCCATTGTACAAG 58.325 41.667 14.65 6.30 0.00 3.16
3827 9923 5.425217 TCTCTAAGCATCTCCCATTGTACAA 59.575 40.000 11.41 11.41 0.00 2.41
3828 9924 4.962362 TCTCTAAGCATCTCCCATTGTACA 59.038 41.667 0.00 0.00 0.00 2.90
3829 9925 5.303078 TCTCTCTAAGCATCTCCCATTGTAC 59.697 44.000 0.00 0.00 0.00 2.90
3830 9926 5.458595 TCTCTCTAAGCATCTCCCATTGTA 58.541 41.667 0.00 0.00 0.00 2.41
3831 9927 4.293494 TCTCTCTAAGCATCTCCCATTGT 58.707 43.478 0.00 0.00 0.00 2.71
3832 9928 4.952071 TCTCTCTAAGCATCTCCCATTG 57.048 45.455 0.00 0.00 0.00 2.82
3833 9929 4.262981 GCATCTCTCTAAGCATCTCCCATT 60.263 45.833 0.00 0.00 0.00 3.16
3834 9930 3.261390 GCATCTCTCTAAGCATCTCCCAT 59.739 47.826 0.00 0.00 0.00 4.00
3835 9931 2.632028 GCATCTCTCTAAGCATCTCCCA 59.368 50.000 0.00 0.00 0.00 4.37
3836 9932 2.899256 AGCATCTCTCTAAGCATCTCCC 59.101 50.000 0.00 0.00 0.00 4.30
3837 9933 4.605640 AAGCATCTCTCTAAGCATCTCC 57.394 45.455 0.00 0.00 0.00 3.71
3838 9934 6.573664 TCTAAGCATCTCTCTAAGCATCTC 57.426 41.667 0.00 0.00 0.00 2.75
3839 9935 6.975196 TTCTAAGCATCTCTCTAAGCATCT 57.025 37.500 0.00 0.00 0.00 2.90
3840 9936 8.430801 TTTTTCTAAGCATCTCTCTAAGCATC 57.569 34.615 0.00 0.00 0.00 3.91
3841 9937 8.977267 ATTTTTCTAAGCATCTCTCTAAGCAT 57.023 30.769 0.00 0.00 0.00 3.79
3842 9938 9.890629 TTATTTTTCTAAGCATCTCTCTAAGCA 57.109 29.630 0.00 0.00 0.00 3.91
3846 9942 9.314321 CGGTTTATTTTTCTAAGCATCTCTCTA 57.686 33.333 0.00 0.00 0.00 2.43
3847 9943 7.281100 CCGGTTTATTTTTCTAAGCATCTCTCT 59.719 37.037 0.00 0.00 0.00 3.10
3848 9944 7.410485 CCGGTTTATTTTTCTAAGCATCTCTC 58.590 38.462 0.00 0.00 0.00 3.20
3849 9945 6.318900 CCCGGTTTATTTTTCTAAGCATCTCT 59.681 38.462 0.00 0.00 0.00 3.10
3850 9946 6.095021 ACCCGGTTTATTTTTCTAAGCATCTC 59.905 38.462 0.00 0.00 0.00 2.75
3851 9947 5.949952 ACCCGGTTTATTTTTCTAAGCATCT 59.050 36.000 0.00 0.00 0.00 2.90
3852 9948 6.203808 ACCCGGTTTATTTTTCTAAGCATC 57.796 37.500 0.00 0.00 0.00 3.91
3853 9949 6.599356 AACCCGGTTTATTTTTCTAAGCAT 57.401 33.333 0.00 0.00 0.00 3.79
3854 9950 6.408107 AAACCCGGTTTATTTTTCTAAGCA 57.592 33.333 14.16 0.00 33.70 3.91
3855 9951 7.115805 CAGAAAACCCGGTTTATTTTTCTAAGC 59.884 37.037 16.03 2.68 43.28 3.09
3856 9952 8.354426 TCAGAAAACCCGGTTTATTTTTCTAAG 58.646 33.333 16.03 4.76 43.28 2.18
3857 9953 8.235359 TCAGAAAACCCGGTTTATTTTTCTAA 57.765 30.769 16.03 0.00 43.28 2.10
3858 9954 7.820578 TCAGAAAACCCGGTTTATTTTTCTA 57.179 32.000 16.03 2.55 43.28 2.10
3859 9955 6.718522 TCAGAAAACCCGGTTTATTTTTCT 57.281 33.333 16.03 11.46 45.05 2.52
3860 9956 6.073980 GCTTCAGAAAACCCGGTTTATTTTTC 60.074 38.462 16.03 9.42 34.43 2.29
3861 9957 5.756347 GCTTCAGAAAACCCGGTTTATTTTT 59.244 36.000 16.03 0.00 34.43 1.94
3862 9958 5.163395 TGCTTCAGAAAACCCGGTTTATTTT 60.163 36.000 16.03 0.06 34.43 1.82
3863 9959 4.342665 TGCTTCAGAAAACCCGGTTTATTT 59.657 37.500 16.03 0.45 34.43 1.40
3864 9960 3.892588 TGCTTCAGAAAACCCGGTTTATT 59.107 39.130 16.03 1.22 34.43 1.40
3865 9961 3.254903 GTGCTTCAGAAAACCCGGTTTAT 59.745 43.478 16.03 5.49 34.43 1.40
3866 9962 2.619646 GTGCTTCAGAAAACCCGGTTTA 59.380 45.455 16.03 0.00 34.43 2.01
3867 9963 1.407618 GTGCTTCAGAAAACCCGGTTT 59.592 47.619 9.92 9.92 37.34 3.27
3868 9964 1.029681 GTGCTTCAGAAAACCCGGTT 58.970 50.000 0.00 0.00 0.00 4.44
3869 9965 0.822121 GGTGCTTCAGAAAACCCGGT 60.822 55.000 0.00 0.00 0.00 5.28
3870 9966 1.852067 CGGTGCTTCAGAAAACCCGG 61.852 60.000 0.00 0.00 0.00 5.73
3871 9967 1.574428 CGGTGCTTCAGAAAACCCG 59.426 57.895 8.50 4.87 0.00 5.28
3872 9968 0.822121 ACCGGTGCTTCAGAAAACCC 60.822 55.000 6.12 0.00 0.00 4.11
3873 9969 0.310854 CACCGGTGCTTCAGAAAACC 59.689 55.000 24.02 5.02 0.00 3.27
3874 9970 3.845625 CACCGGTGCTTCAGAAAAC 57.154 52.632 24.02 0.00 0.00 2.43
3885 9981 2.550978 CTGTAGAAATAGGCACCGGTG 58.449 52.381 30.66 30.66 0.00 4.94
3886 9982 1.485066 CCTGTAGAAATAGGCACCGGT 59.515 52.381 0.00 0.00 0.00 5.28
3887 9983 1.760613 TCCTGTAGAAATAGGCACCGG 59.239 52.381 0.00 0.00 34.08 5.28
3888 9984 2.693591 TCTCCTGTAGAAATAGGCACCG 59.306 50.000 0.00 0.00 34.08 4.94
3889 9985 3.961408 TCTCTCCTGTAGAAATAGGCACC 59.039 47.826 0.00 0.00 34.08 5.01
3890 9986 4.498345 CGTCTCTCCTGTAGAAATAGGCAC 60.498 50.000 0.00 0.00 34.08 5.01
3891 9987 3.632604 CGTCTCTCCTGTAGAAATAGGCA 59.367 47.826 0.00 0.00 34.08 4.75
3892 9988 3.551250 GCGTCTCTCCTGTAGAAATAGGC 60.551 52.174 0.00 0.00 34.08 3.93
3893 9989 3.886505 AGCGTCTCTCCTGTAGAAATAGG 59.113 47.826 0.00 0.00 35.36 2.57
3894 9990 5.508200 AAGCGTCTCTCCTGTAGAAATAG 57.492 43.478 0.00 0.00 32.46 1.73
3895 9991 6.120905 ACTAAGCGTCTCTCCTGTAGAAATA 58.879 40.000 0.00 0.00 32.46 1.40
3896 9992 4.951094 ACTAAGCGTCTCTCCTGTAGAAAT 59.049 41.667 0.00 0.00 32.46 2.17
3897 9993 4.333690 ACTAAGCGTCTCTCCTGTAGAAA 58.666 43.478 0.00 0.00 32.46 2.52
3898 9994 3.952931 ACTAAGCGTCTCTCCTGTAGAA 58.047 45.455 0.00 0.00 32.46 2.10
3899 9995 3.630892 ACTAAGCGTCTCTCCTGTAGA 57.369 47.619 0.00 0.00 0.00 2.59
3900 9996 5.812652 CTTAACTAAGCGTCTCTCCTGTAG 58.187 45.833 0.00 0.00 0.00 2.74
3901 9997 5.814764 CTTAACTAAGCGTCTCTCCTGTA 57.185 43.478 0.00 0.00 0.00 2.74
3902 9998 4.705337 CTTAACTAAGCGTCTCTCCTGT 57.295 45.455 0.00 0.00 0.00 4.00
3914 10010 8.906636 TTGTACAGAATAGACGCTTAACTAAG 57.093 34.615 0.00 0.00 36.40 2.18
3915 10011 9.865321 ATTTGTACAGAATAGACGCTTAACTAA 57.135 29.630 0.00 0.00 0.00 2.24
3917 10013 9.865321 TTATTTGTACAGAATAGACGCTTAACT 57.135 29.630 0.00 0.00 0.00 2.24
3919 10015 9.865321 ACTTATTTGTACAGAATAGACGCTTAA 57.135 29.630 0.00 0.00 0.00 1.85
3921 10017 9.298774 GTACTTATTTGTACAGAATAGACGCTT 57.701 33.333 0.00 0.00 41.57 4.68
3922 10018 8.684520 AGTACTTATTTGTACAGAATAGACGCT 58.315 33.333 0.00 0.59 43.65 5.07
3923 10019 8.744011 CAGTACTTATTTGTACAGAATAGACGC 58.256 37.037 0.00 0.00 43.65 5.19
3924 10020 9.234384 CCAGTACTTATTTGTACAGAATAGACG 57.766 37.037 0.00 0.00 43.65 4.18
3927 10023 8.818057 GCACCAGTACTTATTTGTACAGAATAG 58.182 37.037 0.00 0.00 43.65 1.73
3928 10024 8.537016 AGCACCAGTACTTATTTGTACAGAATA 58.463 33.333 0.00 1.50 43.65 1.75
3929 10025 7.394816 AGCACCAGTACTTATTTGTACAGAAT 58.605 34.615 0.00 2.44 43.65 2.40
3930 10026 6.765403 AGCACCAGTACTTATTTGTACAGAA 58.235 36.000 0.00 0.00 43.65 3.02
3931 10027 6.354794 AGCACCAGTACTTATTTGTACAGA 57.645 37.500 0.00 0.00 43.65 3.41
3932 10028 8.542497 TTAAGCACCAGTACTTATTTGTACAG 57.458 34.615 0.00 0.05 43.65 2.74
3933 10029 7.604927 CCTTAAGCACCAGTACTTATTTGTACA 59.395 37.037 0.00 0.00 43.65 2.90
3934 10030 7.820872 TCCTTAAGCACCAGTACTTATTTGTAC 59.179 37.037 0.00 0.00 42.09 2.90
3935 10031 7.909518 TCCTTAAGCACCAGTACTTATTTGTA 58.090 34.615 0.00 0.00 0.00 2.41
3936 10032 6.775708 TCCTTAAGCACCAGTACTTATTTGT 58.224 36.000 0.00 0.00 0.00 2.83
3937 10033 7.681939 TTCCTTAAGCACCAGTACTTATTTG 57.318 36.000 0.00 0.00 0.00 2.32
3938 10034 8.336801 CTTTCCTTAAGCACCAGTACTTATTT 57.663 34.615 0.00 0.00 0.00 1.40
3939 10035 7.923414 CTTTCCTTAAGCACCAGTACTTATT 57.077 36.000 0.00 0.00 0.00 1.40
3953 10049 7.394641 AGAGAAATAAACCAGGCTTTCCTTAAG 59.605 37.037 0.00 0.00 41.93 1.85
3954 10050 7.238710 AGAGAAATAAACCAGGCTTTCCTTAA 58.761 34.615 0.00 0.00 41.93 1.85
3955 10051 6.790319 AGAGAAATAAACCAGGCTTTCCTTA 58.210 36.000 0.00 0.00 41.93 2.69
3956 10052 5.645201 AGAGAAATAAACCAGGCTTTCCTT 58.355 37.500 0.00 0.00 41.93 3.36
3957 10053 5.262455 AGAGAAATAAACCAGGCTTTCCT 57.738 39.130 0.00 0.00 45.66 3.36
3958 10054 6.404844 GCTTAGAGAAATAAACCAGGCTTTCC 60.405 42.308 0.00 0.00 0.00 3.13
3959 10055 6.151144 TGCTTAGAGAAATAAACCAGGCTTTC 59.849 38.462 0.00 0.00 0.00 2.62
3960 10056 6.010219 TGCTTAGAGAAATAAACCAGGCTTT 58.990 36.000 0.00 0.00 0.00 3.51
3961 10057 5.416013 GTGCTTAGAGAAATAAACCAGGCTT 59.584 40.000 0.00 0.00 0.00 4.35
3962 10058 4.944317 GTGCTTAGAGAAATAAACCAGGCT 59.056 41.667 0.00 0.00 0.00 4.58
3963 10059 4.096532 GGTGCTTAGAGAAATAAACCAGGC 59.903 45.833 0.00 0.00 0.00 4.85
3964 10060 5.501156 AGGTGCTTAGAGAAATAAACCAGG 58.499 41.667 0.00 0.00 0.00 4.45
3965 10061 6.094186 GGAAGGTGCTTAGAGAAATAAACCAG 59.906 42.308 0.00 0.00 0.00 4.00
3966 10062 5.944007 GGAAGGTGCTTAGAGAAATAAACCA 59.056 40.000 0.00 0.00 0.00 3.67
3967 10063 5.357314 GGGAAGGTGCTTAGAGAAATAAACC 59.643 44.000 0.00 0.00 0.00 3.27
3968 10064 6.181190 AGGGAAGGTGCTTAGAGAAATAAAC 58.819 40.000 0.00 0.00 0.00 2.01
3969 10065 6.388619 AGGGAAGGTGCTTAGAGAAATAAA 57.611 37.500 0.00 0.00 0.00 1.40
3970 10066 7.504926 TTAGGGAAGGTGCTTAGAGAAATAA 57.495 36.000 0.00 0.00 0.00 1.40
3971 10067 6.408206 GCTTAGGGAAGGTGCTTAGAGAAATA 60.408 42.308 0.00 0.00 32.84 1.40
3972 10068 5.630304 GCTTAGGGAAGGTGCTTAGAGAAAT 60.630 44.000 0.00 0.00 32.84 2.17
3973 10069 4.323562 GCTTAGGGAAGGTGCTTAGAGAAA 60.324 45.833 0.00 0.00 32.84 2.52
3974 10070 3.197983 GCTTAGGGAAGGTGCTTAGAGAA 59.802 47.826 0.00 0.00 32.84 2.87
3975 10071 2.766828 GCTTAGGGAAGGTGCTTAGAGA 59.233 50.000 0.00 0.00 32.84 3.10
3976 10072 2.501723 TGCTTAGGGAAGGTGCTTAGAG 59.498 50.000 0.00 0.00 32.84 2.43
3977 10073 2.236395 GTGCTTAGGGAAGGTGCTTAGA 59.764 50.000 0.00 0.00 32.84 2.10
3978 10074 2.633488 GTGCTTAGGGAAGGTGCTTAG 58.367 52.381 0.00 0.00 32.84 2.18
3979 10075 1.280998 GGTGCTTAGGGAAGGTGCTTA 59.719 52.381 0.00 0.00 32.84 3.09
3980 10076 0.038310 GGTGCTTAGGGAAGGTGCTT 59.962 55.000 0.00 0.00 32.84 3.91
3981 10077 0.842467 AGGTGCTTAGGGAAGGTGCT 60.842 55.000 0.00 0.00 32.84 4.40
3982 10078 0.393132 GAGGTGCTTAGGGAAGGTGC 60.393 60.000 0.00 0.00 32.84 5.01
3983 10079 0.253327 GGAGGTGCTTAGGGAAGGTG 59.747 60.000 0.00 0.00 32.84 4.00
3984 10080 0.914902 GGGAGGTGCTTAGGGAAGGT 60.915 60.000 0.00 0.00 32.84 3.50
3985 10081 0.914417 TGGGAGGTGCTTAGGGAAGG 60.914 60.000 0.00 0.00 32.84 3.46
3986 10082 1.216990 ATGGGAGGTGCTTAGGGAAG 58.783 55.000 0.00 0.00 35.60 3.46
3987 10083 1.284785 CAATGGGAGGTGCTTAGGGAA 59.715 52.381 0.00 0.00 0.00 3.97
3988 10084 0.918983 CAATGGGAGGTGCTTAGGGA 59.081 55.000 0.00 0.00 0.00 4.20
3989 10085 0.625849 ACAATGGGAGGTGCTTAGGG 59.374 55.000 0.00 0.00 0.00 3.53
3990 10086 2.238646 TGTACAATGGGAGGTGCTTAGG 59.761 50.000 0.00 0.00 0.00 2.69
3991 10087 3.627395 TGTACAATGGGAGGTGCTTAG 57.373 47.619 0.00 0.00 0.00 2.18
3992 10088 3.308117 CCTTGTACAATGGGAGGTGCTTA 60.308 47.826 9.13 0.00 0.00 3.09
3993 10089 2.555227 CCTTGTACAATGGGAGGTGCTT 60.555 50.000 9.13 0.00 0.00 3.91
3994 10090 1.004745 CCTTGTACAATGGGAGGTGCT 59.995 52.381 9.13 0.00 0.00 4.40
3995 10091 1.463674 CCTTGTACAATGGGAGGTGC 58.536 55.000 9.13 0.00 0.00 5.01
3996 10092 1.463674 GCCTTGTACAATGGGAGGTG 58.536 55.000 16.08 0.00 0.00 4.00
3997 10093 0.331616 GGCCTTGTACAATGGGAGGT 59.668 55.000 16.08 0.00 0.00 3.85
3998 10094 0.625849 AGGCCTTGTACAATGGGAGG 59.374 55.000 16.08 11.34 0.00 4.30
3999 10095 3.199946 TCTTAGGCCTTGTACAATGGGAG 59.800 47.826 12.58 6.16 0.00 4.30
4000 10096 3.186283 TCTTAGGCCTTGTACAATGGGA 58.814 45.455 12.58 6.88 0.00 4.37
4001 10097 3.644966 TCTTAGGCCTTGTACAATGGG 57.355 47.619 12.58 14.91 0.00 4.00
4002 10098 7.339466 AGTTATTTCTTAGGCCTTGTACAATGG 59.661 37.037 12.58 13.26 0.00 3.16
4003 10099 8.281212 AGTTATTTCTTAGGCCTTGTACAATG 57.719 34.615 12.58 7.68 0.00 2.82
4004 10100 9.392259 GTAGTTATTTCTTAGGCCTTGTACAAT 57.608 33.333 12.58 6.35 0.00 2.71
4005 10101 8.599792 AGTAGTTATTTCTTAGGCCTTGTACAA 58.400 33.333 12.58 8.28 0.00 2.41
4006 10102 8.142485 AGTAGTTATTTCTTAGGCCTTGTACA 57.858 34.615 12.58 0.00 0.00 2.90
4007 10103 9.445878 AAAGTAGTTATTTCTTAGGCCTTGTAC 57.554 33.333 12.58 1.65 0.00 2.90
4008 10104 9.444600 CAAAGTAGTTATTTCTTAGGCCTTGTA 57.555 33.333 12.58 0.00 0.00 2.41
4009 10105 7.942894 ACAAAGTAGTTATTTCTTAGGCCTTGT 59.057 33.333 12.58 0.00 0.00 3.16
4010 10106 8.336801 ACAAAGTAGTTATTTCTTAGGCCTTG 57.663 34.615 12.58 4.55 0.00 3.61
4011 10107 8.793592 CAACAAAGTAGTTATTTCTTAGGCCTT 58.206 33.333 12.58 0.00 0.00 4.35
4012 10108 7.942894 ACAACAAAGTAGTTATTTCTTAGGCCT 59.057 33.333 11.78 11.78 0.00 5.19
4013 10109 8.107399 ACAACAAAGTAGTTATTTCTTAGGCC 57.893 34.615 0.00 0.00 0.00 5.19
4081 10178 6.180472 CCACACTTACCTAATGAATTCACCT 58.820 40.000 11.07 3.64 0.00 4.00
4136 12254 6.373216 GCTCAGATTATAGGTCACGTCTCTAT 59.627 42.308 0.00 0.00 0.00 1.98
4185 12305 0.729116 GCCTGTTCACGGATCACATG 59.271 55.000 0.00 0.00 0.00 3.21
4186 12306 0.615331 AGCCTGTTCACGGATCACAT 59.385 50.000 0.00 0.00 0.00 3.21
4304 12424 1.941812 CACAACAGCAAGGACCGTC 59.058 57.895 0.00 0.00 0.00 4.79
4316 12436 1.098869 ACAACAATGTCGGCACAACA 58.901 45.000 0.00 0.00 33.41 3.33


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

AutoCloner maintained by Alex Coulton.