Multiple sequence alignment - TraesCS6B01G272700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G272700 chr6B 100.000 5680 0 0 1 5680 492188655 492194334 0.000000e+00 10490.0
1 TraesCS6B01G272700 chr6D 95.526 3867 92 27 1 3808 328328160 328332004 0.000000e+00 6107.0
2 TraesCS6B01G272700 chr6D 93.219 1165 46 11 3932 5095 328332003 328333135 0.000000e+00 1683.0
3 TraesCS6B01G272700 chr6D 85.632 696 23 14 4795 5424 328332836 328333520 0.000000e+00 660.0
4 TraesCS6B01G272700 chr6D 95.349 129 6 0 3805 3933 160470644 160470772 7.460000e-49 206.0
5 TraesCS6B01G272700 chr6D 95.775 71 3 0 5393 5463 328333520 328333590 1.290000e-21 115.0
6 TraesCS6B01G272700 chr6A 91.669 3037 170 33 1 2990 467042080 467045080 0.000000e+00 4130.0
7 TraesCS6B01G272700 chr6A 94.092 694 34 2 3122 3808 467045269 467045962 0.000000e+00 1048.0
8 TraesCS6B01G272700 chr6A 96.296 405 13 2 4311 4714 467046268 467046671 0.000000e+00 664.0
9 TraesCS6B01G272700 chr6A 85.477 661 49 30 4791 5424 467046695 467047335 0.000000e+00 645.0
10 TraesCS6B01G272700 chr6A 95.608 296 13 0 3932 4227 467045961 467046256 5.150000e-130 475.0
11 TraesCS6B01G272700 chr6A 97.436 39 1 0 4736 4774 467046672 467046710 3.670000e-07 67.6
12 TraesCS6B01G272700 chr4B 84.265 1754 189 45 1196 2928 633936590 633934903 0.000000e+00 1629.0
13 TraesCS6B01G272700 chr4B 84.232 1744 169 42 1208 2928 634079566 634077906 0.000000e+00 1600.0
14 TraesCS6B01G272700 chr4B 86.134 613 58 10 3184 3787 633934108 633933514 2.230000e-178 636.0
15 TraesCS6B01G272700 chr4B 86.348 586 54 7 3203 3779 634077619 634077051 2.910000e-172 616.0
16 TraesCS6B01G272700 chr4B 87.637 364 34 7 4334 4687 634076674 634076312 4.100000e-111 412.0
17 TraesCS6B01G272700 chr4B 91.065 291 26 0 4395 4685 633933112 633932822 1.480000e-105 394.0
18 TraesCS6B01G272700 chr4B 88.435 294 34 0 3934 4227 633933488 633933195 7.000000e-94 355.0
19 TraesCS6B01G272700 chr4B 88.772 285 32 0 3934 4218 634076986 634076702 3.260000e-92 350.0
20 TraesCS6B01G272700 chr4B 75.568 176 28 10 972 1136 633936788 633936617 7.890000e-09 73.1
21 TraesCS6B01G272700 chr5A 84.226 1756 171 42 1196 2928 673836065 673837737 0.000000e+00 1611.0
22 TraesCS6B01G272700 chr5A 83.995 1762 183 41 1196 2930 673932652 673934341 0.000000e+00 1600.0
23 TraesCS6B01G272700 chr5A 83.125 800 91 20 3031 3805 673934524 673935304 0.000000e+00 689.0
24 TraesCS6B01G272700 chr5A 86.159 578 63 12 3203 3773 673838054 673838621 4.870000e-170 608.0
25 TraesCS6B01G272700 chr5A 90.444 293 28 0 4395 4687 673839074 673839366 2.480000e-103 387.0
26 TraesCS6B01G272700 chr5A 89.437 284 30 0 3935 4218 673838693 673838976 5.410000e-95 359.0
27 TraesCS6B01G272700 chr5A 89.139 267 28 1 3940 4206 673935314 673935579 1.180000e-86 331.0
28 TraesCS6B01G272700 chr5A 96.183 131 4 1 3804 3933 687681057 687680927 4.460000e-51 213.0
29 TraesCS6B01G272700 chr4D 84.043 1761 172 52 1196 2931 494514059 494512383 0.000000e+00 1594.0
30 TraesCS6B01G272700 chr4D 83.126 1766 175 51 1196 2933 494476255 494474585 0.000000e+00 1496.0
31 TraesCS6B01G272700 chr4D 83.182 773 85 22 3031 3787 494474408 494473665 0.000000e+00 665.0
32 TraesCS6B01G272700 chr4D 85.785 605 55 11 3203 3796 494512068 494511484 3.760000e-171 612.0
33 TraesCS6B01G272700 chr4D 86.813 364 37 7 4334 4687 494511123 494510761 4.120000e-106 396.0
34 TraesCS6B01G272700 chr4D 80.502 518 62 14 3151 3645 494507699 494507198 1.500000e-95 361.0
35 TraesCS6B01G272700 chr4D 89.046 283 31 0 3936 4218 494511433 494511151 9.050000e-93 351.0
36 TraesCS6B01G272700 chr4D 88.087 277 32 1 3940 4216 494473633 494473358 1.530000e-85 327.0
37 TraesCS6B01G272700 chr4D 88.106 227 24 2 2706 2929 494508121 494507895 3.370000e-67 267.0
38 TraesCS6B01G272700 chr4D 97.436 39 1 0 987 1025 494476437 494476399 3.670000e-07 67.6
39 TraesCS6B01G272700 chr1D 84.416 616 87 7 3170 3779 8921594 8920982 1.050000e-166 597.0
40 TraesCS6B01G272700 chr1D 85.859 297 42 0 4395 4691 8920533 8920237 3.300000e-82 316.0
41 TraesCS6B01G272700 chr1B 82.305 616 99 8 3171 3779 12108949 12108337 5.040000e-145 525.0
42 TraesCS6B01G272700 chr1B 85.668 307 44 0 4377 4683 12107911 12107605 1.970000e-84 324.0
43 TraesCS6B01G272700 chr1B 83.333 78 7 5 1713 1790 12150511 12150440 3.670000e-07 67.6
44 TraesCS6B01G272700 chr1A 81.592 603 87 11 3183 3779 10157072 10156488 1.430000e-130 477.0
45 TraesCS6B01G272700 chr1A 87.458 295 37 0 4395 4689 10156039 10155745 1.960000e-89 340.0
46 TraesCS6B01G272700 chr1A 85.774 239 34 0 3962 4200 10139347 10139109 2.630000e-63 254.0
47 TraesCS6B01G272700 chr1A 96.154 130 5 0 3804 3933 287275140 287275011 4.460000e-51 213.0
48 TraesCS6B01G272700 chr1A 79.310 145 26 3 1689 1830 10159995 10159852 1.300000e-16 99.0
49 TraesCS6B01G272700 chr2A 78.165 632 108 21 1889 2499 662746859 662746237 5.370000e-100 375.0
50 TraesCS6B01G272700 chr3A 95.556 135 6 0 3799 3933 348834438 348834572 3.450000e-52 217.0
51 TraesCS6B01G272700 chr3A 95.455 132 6 0 3802 3933 256533193 256533062 1.600000e-50 211.0
52 TraesCS6B01G272700 chr4A 94.891 137 6 1 3797 3933 680587660 680587795 4.460000e-51 213.0
53 TraesCS6B01G272700 chr2D 95.455 132 6 0 3802 3933 536091158 536091027 1.600000e-50 211.0
54 TraesCS6B01G272700 chr2D 80.800 125 22 2 5460 5583 618702791 618702914 4.680000e-16 97.1
55 TraesCS6B01G272700 chr2B 94.776 134 7 0 3802 3935 4632111 4632244 5.770000e-50 209.0
56 TraesCS6B01G272700 chr2B 88.824 170 12 6 3798 3965 753999072 753998908 9.650000e-48 202.0
57 TraesCS6B01G272700 chr7D 84.091 88 13 1 5498 5584 251355682 251355595 3.650000e-12 84.2


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 TraesCS6B01G272700 chr6B 492188655 492194334 5679 False 10490.000000 10490 100.000000 1 5680 1 chr6B.!!$F1 5679
1 TraesCS6B01G272700 chr6D 328328160 328333590 5430 False 2141.250000 6107 92.538000 1 5463 4 chr6D.!!$F2 5462
2 TraesCS6B01G272700 chr6A 467042080 467047335 5255 False 1171.600000 4130 93.429667 1 5424 6 chr6A.!!$F1 5423
3 TraesCS6B01G272700 chr4B 634076312 634079566 3254 True 744.500000 1600 86.747250 1208 4687 4 chr4B.!!$R2 3479
4 TraesCS6B01G272700 chr4B 633932822 633936788 3966 True 617.420000 1629 85.093400 972 4685 5 chr4B.!!$R1 3713
5 TraesCS6B01G272700 chr5A 673932652 673935579 2927 False 873.333333 1600 85.419667 1196 4206 3 chr5A.!!$F2 3010
6 TraesCS6B01G272700 chr5A 673836065 673839366 3301 False 741.250000 1611 87.566500 1196 4687 4 chr5A.!!$F1 3491
7 TraesCS6B01G272700 chr4D 494473358 494476437 3079 True 638.900000 1496 87.957750 987 4216 4 chr4D.!!$R1 3229
8 TraesCS6B01G272700 chr4D 494507198 494514059 6861 True 596.833333 1594 85.715833 1196 4687 6 chr4D.!!$R2 3491
9 TraesCS6B01G272700 chr1D 8920237 8921594 1357 True 456.500000 597 85.137500 3170 4691 2 chr1D.!!$R1 1521
10 TraesCS6B01G272700 chr1B 12107605 12108949 1344 True 424.500000 525 83.986500 3171 4683 2 chr1B.!!$R2 1512
11 TraesCS6B01G272700 chr1A 10155745 10159995 4250 True 305.333333 477 82.786667 1689 4689 3 chr1A.!!$R3 3000
12 TraesCS6B01G272700 chr2A 662746237 662746859 622 True 375.000000 375 78.165000 1889 2499 1 chr2A.!!$R1 610

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
308 331 0.033601 TCCTTAAACATGGCCGGCAT 60.034 50.000 30.85 17.04 0.00 4.40 F
388 415 0.108520 ATTGGGCGTGTACGGTGTAG 60.109 55.000 6.55 0.00 40.23 2.74 F
391 418 0.179163 GGGCGTGTACGGTGTAGTAC 60.179 60.000 6.55 0.00 45.22 2.73 F
864 910 0.473117 TTGTTCCCGAACCCTCTCCT 60.473 55.000 5.17 0.00 40.46 3.69 F
865 911 0.903454 TGTTCCCGAACCCTCTCCTC 60.903 60.000 5.17 0.00 40.46 3.71 F
1548 1686 1.663702 GTCGTCACACCCGTCCTTG 60.664 63.158 0.00 0.00 0.00 3.61 F
4271 6785 1.138069 GGGAGCTTTCCTCTGCTACTC 59.862 57.143 0.00 0.00 39.90 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2454 1.148310 CGTCGAACAAGAAGTGCCAT 58.852 50.000 0.00 0.00 0.0 4.40 R
3081 5414 1.004610 CGAACACAACAGTGCACTCTG 60.005 52.381 18.64 19.14 40.8 3.35 R
3154 5543 5.902613 TTGAAATATTGAAGTGAGGGCAG 57.097 39.130 0.00 0.00 0.0 4.85 R
3407 5848 4.816385 TCGGCAGAAATCAATGATAACTCC 59.184 41.667 0.00 3.10 0.0 3.85 R
3452 5893 7.252612 TCACCTACAGAAGAAACCATATGAA 57.747 36.000 3.65 0.00 0.0 2.57 R
4284 6798 0.107066 CTGACCATACATGCCTGCCA 60.107 55.000 0.00 0.00 0.0 4.92 R
5496 9920 0.179020 CCCAGGGCAGCGATATTTCA 60.179 55.000 0.00 0.00 0.0 2.69 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
29 30 0.825840 GGATGGGTCCTCTCCTCTCG 60.826 65.000 3.70 0.00 41.60 4.04
64 65 1.592400 CGTCAAGCCGACCTCCTGTA 61.592 60.000 0.00 0.00 42.07 2.74
81 88 2.922950 TACCGTCCGCCACTGTGTC 61.923 63.158 7.08 0.00 0.00 3.67
90 97 1.825090 GCCACTGTGTCATTCCATCA 58.175 50.000 7.08 0.00 0.00 3.07
107 115 6.388619 TCCATCATCTCCATGATCATCATT 57.611 37.500 4.86 0.00 45.26 2.57
216 239 3.882025 GCCGAAAGCAGAGGTCAG 58.118 61.111 0.00 0.00 42.97 3.51
236 259 3.064079 TGCTAAGCATGCCTGTACG 57.936 52.632 15.66 0.00 31.71 3.67
240 263 1.528586 CTAAGCATGCCTGTACGATGC 59.471 52.381 15.66 9.69 42.37 3.91
241 264 1.524002 AGCATGCCTGTACGATGCT 59.476 52.632 15.66 12.99 46.30 3.79
242 265 2.397751 GCATGCCTGTACGATGCTT 58.602 52.632 6.36 0.00 39.54 3.91
243 266 0.734889 GCATGCCTGTACGATGCTTT 59.265 50.000 6.36 0.00 39.54 3.51
269 292 3.627123 TGTATCGATGGTGCCAATCTTTG 59.373 43.478 8.54 0.00 0.00 2.77
278 301 0.608035 GCCAATCTTTGTCCACGGGA 60.608 55.000 0.00 0.00 0.00 5.14
279 302 1.904287 CCAATCTTTGTCCACGGGAA 58.096 50.000 0.00 0.00 31.38 3.97
308 331 0.033601 TCCTTAAACATGGCCGGCAT 60.034 50.000 30.85 17.04 0.00 4.40
388 415 0.108520 ATTGGGCGTGTACGGTGTAG 60.109 55.000 6.55 0.00 40.23 2.74
389 416 1.462731 TTGGGCGTGTACGGTGTAGT 61.463 55.000 6.55 0.00 40.23 2.73
390 417 0.607762 TGGGCGTGTACGGTGTAGTA 60.608 55.000 6.55 0.00 40.23 1.82
391 418 0.179163 GGGCGTGTACGGTGTAGTAC 60.179 60.000 6.55 0.00 45.22 2.73
392 419 0.179163 GGCGTGTACGGTGTAGTACC 60.179 60.000 6.55 0.00 44.59 3.34
479 506 4.527816 ACACCTAAAATACCGTACTGTGGA 59.472 41.667 0.00 0.00 0.00 4.02
488 515 1.201647 CCGTACTGTGGACTGTGGTAG 59.798 57.143 0.00 0.00 0.00 3.18
489 516 2.156917 CGTACTGTGGACTGTGGTAGA 58.843 52.381 0.00 0.00 0.00 2.59
532 560 4.665833 TTTCTTCTCGTCTCTTTCACCA 57.334 40.909 0.00 0.00 0.00 4.17
569 597 8.842280 TCGACAAGTTAATTCACTACCAAAAAT 58.158 29.630 0.00 0.00 0.00 1.82
684 712 8.477419 AAATCAGTTTGTTTAATCTCTTCCCA 57.523 30.769 0.00 0.00 0.00 4.37
833 879 1.134946 GCCAAGTGTTGTCAGCTTTGT 59.865 47.619 0.00 0.00 0.00 2.83
864 910 0.473117 TTGTTCCCGAACCCTCTCCT 60.473 55.000 5.17 0.00 40.46 3.69
865 911 0.903454 TGTTCCCGAACCCTCTCCTC 60.903 60.000 5.17 0.00 40.46 3.71
866 912 0.903454 GTTCCCGAACCCTCTCCTCA 60.903 60.000 0.00 0.00 35.36 3.86
1386 1488 2.190578 CAGGCATCGTCCCCTTCC 59.809 66.667 0.00 0.00 0.00 3.46
1548 1686 1.663702 GTCGTCACACCCGTCCTTG 60.664 63.158 0.00 0.00 0.00 3.61
1611 1749 4.813526 CGCCAGTCGTCCTCGTCG 62.814 72.222 0.00 0.00 38.33 5.12
2268 2454 4.373116 GGCCTGGTTCTCGCGTCA 62.373 66.667 5.77 0.00 0.00 4.35
2373 2565 4.498520 ACGCTCATCCGCCTCGTG 62.499 66.667 0.00 0.00 31.74 4.35
3081 5414 3.441572 ACAGCATGCTAATTGTTGGACTC 59.558 43.478 22.19 0.00 42.53 3.36
3224 5631 8.469200 TGGCAATTTACTTATTCAGATTCTTGG 58.531 33.333 0.00 0.00 0.00 3.61
3430 5871 4.816385 GGAGTTATCATTGATTTCTGCCGA 59.184 41.667 4.14 0.00 0.00 5.54
3438 5879 5.879777 TCATTGATTTCTGCCGACAAGATAA 59.120 36.000 0.00 0.00 0.00 1.75
3451 5892 7.820386 TGCCGACAAGATAACTTTTCTAACATA 59.180 33.333 0.00 0.00 32.56 2.29
3452 5893 8.827677 GCCGACAAGATAACTTTTCTAACATAT 58.172 33.333 0.00 0.00 32.56 1.78
3773 6217 6.881065 TGAGATTGAAGAAGTTCAGGTAATGG 59.119 38.462 5.50 0.00 43.66 3.16
3808 6288 5.049267 TCGGTGCTCCTTGTTTGTTTAATAC 60.049 40.000 2.85 0.00 0.00 1.89
3809 6289 5.048991 CGGTGCTCCTTGTTTGTTTAATACT 60.049 40.000 2.85 0.00 0.00 2.12
3810 6290 6.379386 GGTGCTCCTTGTTTGTTTAATACTC 58.621 40.000 0.00 0.00 0.00 2.59
3811 6291 6.379386 GTGCTCCTTGTTTGTTTAATACTCC 58.621 40.000 0.00 0.00 0.00 3.85
3812 6292 6.016610 GTGCTCCTTGTTTGTTTAATACTCCA 60.017 38.462 0.00 0.00 0.00 3.86
3813 6293 6.719370 TGCTCCTTGTTTGTTTAATACTCCAT 59.281 34.615 0.00 0.00 0.00 3.41
3814 6294 7.094377 TGCTCCTTGTTTGTTTAATACTCCATC 60.094 37.037 0.00 0.00 0.00 3.51
3815 6295 7.628580 GCTCCTTGTTTGTTTAATACTCCATCC 60.629 40.741 0.00 0.00 0.00 3.51
3816 6296 6.373216 TCCTTGTTTGTTTAATACTCCATCCG 59.627 38.462 0.00 0.00 0.00 4.18
3817 6297 6.150474 CCTTGTTTGTTTAATACTCCATCCGT 59.850 38.462 0.00 0.00 0.00 4.69
3818 6298 6.730960 TGTTTGTTTAATACTCCATCCGTC 57.269 37.500 0.00 0.00 0.00 4.79
3819 6299 5.644636 TGTTTGTTTAATACTCCATCCGTCC 59.355 40.000 0.00 0.00 0.00 4.79
3820 6300 4.411256 TGTTTAATACTCCATCCGTCCC 57.589 45.455 0.00 0.00 0.00 4.46
3821 6301 3.775866 TGTTTAATACTCCATCCGTCCCA 59.224 43.478 0.00 0.00 0.00 4.37
3822 6302 4.225492 TGTTTAATACTCCATCCGTCCCAA 59.775 41.667 0.00 0.00 0.00 4.12
3823 6303 5.187687 GTTTAATACTCCATCCGTCCCAAA 58.812 41.667 0.00 0.00 0.00 3.28
3824 6304 5.438698 TTAATACTCCATCCGTCCCAAAA 57.561 39.130 0.00 0.00 0.00 2.44
3825 6305 4.519906 AATACTCCATCCGTCCCAAAAT 57.480 40.909 0.00 0.00 0.00 1.82
3826 6306 2.899303 ACTCCATCCGTCCCAAAATT 57.101 45.000 0.00 0.00 0.00 1.82
3827 6307 2.723273 ACTCCATCCGTCCCAAAATTC 58.277 47.619 0.00 0.00 0.00 2.17
3828 6308 2.308866 ACTCCATCCGTCCCAAAATTCT 59.691 45.455 0.00 0.00 0.00 2.40
3829 6309 3.245264 ACTCCATCCGTCCCAAAATTCTT 60.245 43.478 0.00 0.00 0.00 2.52
3830 6310 3.088532 TCCATCCGTCCCAAAATTCTTG 58.911 45.455 0.00 0.00 0.00 3.02
3831 6311 2.825532 CCATCCGTCCCAAAATTCTTGT 59.174 45.455 0.00 0.00 0.00 3.16
3832 6312 3.119495 CCATCCGTCCCAAAATTCTTGTC 60.119 47.826 0.00 0.00 0.00 3.18
3833 6313 3.502123 TCCGTCCCAAAATTCTTGTCT 57.498 42.857 0.00 0.00 0.00 3.41
3834 6314 3.827722 TCCGTCCCAAAATTCTTGTCTT 58.172 40.909 0.00 0.00 0.00 3.01
3835 6315 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3836 6316 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3837 6317 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3838 6318 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3839 6319 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3840 6320 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3841 6321 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3842 6322 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3843 6323 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3844 6324 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3852 6332 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3853 6333 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3854 6334 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
3855 6335 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3856 6336 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3857 6337 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3875 6355 9.970395 ACGGATGTATCTAATATTAAAACGTGA 57.030 29.630 0.00 0.00 0.00 4.35
3888 6368 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
3889 6369 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
3890 6370 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
3891 6371 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
3892 6372 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
3893 6373 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
3894 6374 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
3895 6375 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
3896 6376 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
3897 6377 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
3898 6378 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
3899 6379 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
3900 6380 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
3901 6381 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
3920 6400 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
3921 6401 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
3922 6402 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
3923 6403 9.323985 CAAATTTAAGACAAGAATTTTGGGACA 57.676 29.630 0.00 0.00 32.35 4.02
3924 6404 8.887036 AATTTAAGACAAGAATTTTGGGACAC 57.113 30.769 5.68 0.00 39.29 3.67
3925 6405 7.411486 TTTAAGACAAGAATTTTGGGACACA 57.589 32.000 5.68 0.00 39.29 3.72
3926 6406 5.520376 AAGACAAGAATTTTGGGACACAG 57.480 39.130 5.68 0.00 39.29 3.66
3927 6407 3.891366 AGACAAGAATTTTGGGACACAGG 59.109 43.478 5.68 0.00 39.29 4.00
3928 6408 2.965147 ACAAGAATTTTGGGACACAGGG 59.035 45.455 5.68 0.00 39.29 4.45
3929 6409 3.230134 CAAGAATTTTGGGACACAGGGA 58.770 45.455 0.00 0.00 39.29 4.20
3930 6410 3.160679 AGAATTTTGGGACACAGGGAG 57.839 47.619 0.00 0.00 39.29 4.30
3931 6411 2.447047 AGAATTTTGGGACACAGGGAGT 59.553 45.455 0.00 0.00 39.29 3.85
3932 6412 3.655777 AGAATTTTGGGACACAGGGAGTA 59.344 43.478 0.00 0.00 39.29 2.59
3952 6432 5.238583 AGTAGGATAATACCTTGCATTCGC 58.761 41.667 0.00 0.00 41.00 4.70
3970 6450 1.460267 CGCTGACTGACGTTTTAAGCG 60.460 52.381 15.59 15.59 44.83 4.68
4096 6576 7.175990 ACCAAGCCGATTTTTAATTTCTACAGA 59.824 33.333 0.00 0.00 0.00 3.41
4218 6732 4.393371 GGTGCTTCTGTTATCTCAGTTTCC 59.607 45.833 0.00 0.00 36.85 3.13
4227 6741 5.991606 TGTTATCTCAGTTTCCTGTTGACAG 59.008 40.000 4.15 4.15 43.40 3.51
4230 6744 5.201713 TCTCAGTTTCCTGTTGACAGTAG 57.798 43.478 10.03 0.00 42.27 2.57
4231 6745 4.039245 TCTCAGTTTCCTGTTGACAGTAGG 59.961 45.833 10.03 1.62 42.27 3.18
4232 6746 3.709653 TCAGTTTCCTGTTGACAGTAGGT 59.290 43.478 10.03 0.00 42.27 3.08
4235 6749 4.652421 AGTTTCCTGTTGACAGTAGGTGTA 59.348 41.667 10.03 0.00 40.56 2.90
4266 6780 1.301677 CGTTGGGAGCTTTCCTCTGC 61.302 60.000 8.27 0.00 40.57 4.26
4271 6785 1.138069 GGGAGCTTTCCTCTGCTACTC 59.862 57.143 0.00 0.00 39.90 2.59
4275 6789 1.202582 GCTTTCCTCTGCTACTCGTCA 59.797 52.381 0.00 0.00 0.00 4.35
4284 6798 4.883083 TCTGCTACTCGTCAAATTCAGTT 58.117 39.130 0.00 0.00 0.00 3.16
4332 6846 5.965334 GGAACATACGCATATGAAGTTTGTG 59.035 40.000 19.84 13.95 40.75 3.33
4713 7238 2.962421 GAGGGCTAGAAGATACAGCAGT 59.038 50.000 0.00 0.00 37.02 4.40
4772 7315 3.150848 GCCATTAGCTGTTAGTTTGCC 57.849 47.619 0.00 0.00 38.99 4.52
4773 7316 2.755103 GCCATTAGCTGTTAGTTTGCCT 59.245 45.455 0.00 0.00 38.99 4.75
4774 7317 3.181496 GCCATTAGCTGTTAGTTTGCCTC 60.181 47.826 0.00 0.00 38.99 4.70
4775 7318 3.378427 CCATTAGCTGTTAGTTTGCCTCC 59.622 47.826 0.00 0.00 0.00 4.30
4776 7319 2.781681 TAGCTGTTAGTTTGCCTCCC 57.218 50.000 0.00 0.00 0.00 4.30
4777 7320 0.038310 AGCTGTTAGTTTGCCTCCCC 59.962 55.000 0.00 0.00 0.00 4.81
4778 7321 0.965866 GCTGTTAGTTTGCCTCCCCC 60.966 60.000 0.00 0.00 0.00 5.40
4779 7322 0.698818 CTGTTAGTTTGCCTCCCCCT 59.301 55.000 0.00 0.00 0.00 4.79
4780 7323 0.696501 TGTTAGTTTGCCTCCCCCTC 59.303 55.000 0.00 0.00 0.00 4.30
4781 7324 0.696501 GTTAGTTTGCCTCCCCCTCA 59.303 55.000 0.00 0.00 0.00 3.86
4782 7325 1.074889 GTTAGTTTGCCTCCCCCTCAA 59.925 52.381 0.00 0.00 0.00 3.02
4783 7326 1.451449 TAGTTTGCCTCCCCCTCAAA 58.549 50.000 0.00 0.00 0.00 2.69
4784 7327 0.560688 AGTTTGCCTCCCCCTCAAAA 59.439 50.000 0.00 0.00 32.36 2.44
4785 7328 1.062505 AGTTTGCCTCCCCCTCAAAAA 60.063 47.619 0.00 0.00 32.36 1.94
4823 7380 4.151335 GTGTCTGATGTGATGAGTGTGTTC 59.849 45.833 0.00 0.00 0.00 3.18
4978 8409 0.526211 CTGGTGATGGAACGAGACGA 59.474 55.000 0.00 0.00 0.00 4.20
5141 8616 4.636435 CGTGGGCGTTGAGGGGTT 62.636 66.667 0.00 0.00 0.00 4.11
5160 8635 5.189180 GGGTTGTCTTCTGAAGCATCTTAT 58.811 41.667 12.54 0.00 0.00 1.73
5310 8836 3.025322 TGTGGATGTGGGTTTCAAACT 57.975 42.857 0.00 0.00 0.00 2.66
5336 8863 3.456280 CTTGAGAGCATTGAGAGGCTAC 58.544 50.000 0.00 0.00 44.07 3.58
5351 8878 2.022240 GCTACAAGAGGAGGGGCTCG 62.022 65.000 0.00 0.00 0.00 5.03
5368 8895 1.802960 CTCGTTGATGCTGAGCTTTGT 59.197 47.619 5.83 0.00 0.00 2.83
5424 8951 5.797042 ATGAAATCCTCACGAACGAAGAGTT 60.797 40.000 15.23 6.74 40.80 3.01
5463 9887 1.512926 AGTGAACGCTGGTTGCTTAG 58.487 50.000 0.00 0.00 40.11 2.18
5464 9888 1.070134 AGTGAACGCTGGTTGCTTAGA 59.930 47.619 0.00 0.00 40.11 2.10
5465 9889 1.461127 GTGAACGCTGGTTGCTTAGAG 59.539 52.381 0.00 0.00 40.11 2.43
5466 9890 0.444260 GAACGCTGGTTGCTTAGAGC 59.556 55.000 0.00 0.00 42.82 4.09
5480 9904 4.625800 GAGCATCTCCAGCCGTTT 57.374 55.556 0.00 0.00 0.00 3.60
5481 9905 3.760693 GAGCATCTCCAGCCGTTTA 57.239 52.632 0.00 0.00 0.00 2.01
5482 9906 1.291132 GAGCATCTCCAGCCGTTTAC 58.709 55.000 0.00 0.00 0.00 2.01
5483 9907 0.905357 AGCATCTCCAGCCGTTTACT 59.095 50.000 0.00 0.00 0.00 2.24
5484 9908 1.279271 AGCATCTCCAGCCGTTTACTT 59.721 47.619 0.00 0.00 0.00 2.24
5485 9909 1.666189 GCATCTCCAGCCGTTTACTTC 59.334 52.381 0.00 0.00 0.00 3.01
5486 9910 2.280628 CATCTCCAGCCGTTTACTTCC 58.719 52.381 0.00 0.00 0.00 3.46
5488 9912 0.392595 CTCCAGCCGTTTACTTCCCC 60.393 60.000 0.00 0.00 0.00 4.81
5489 9913 1.128809 TCCAGCCGTTTACTTCCCCA 61.129 55.000 0.00 0.00 0.00 4.96
5490 9914 0.676782 CCAGCCGTTTACTTCCCCAG 60.677 60.000 0.00 0.00 0.00 4.45
5491 9915 0.676782 CAGCCGTTTACTTCCCCAGG 60.677 60.000 0.00 0.00 0.00 4.45
5492 9916 1.378119 GCCGTTTACTTCCCCAGGG 60.378 63.158 0.00 0.00 0.00 4.45
5493 9917 1.301954 CCGTTTACTTCCCCAGGGG 59.698 63.158 20.55 20.55 46.11 4.79
5507 9931 2.224867 CCCAGGGGATTGAAATATCGCT 60.225 50.000 0.00 0.00 37.56 4.93
5508 9932 2.816087 CCAGGGGATTGAAATATCGCTG 59.184 50.000 12.15 12.15 37.56 5.18
5509 9933 2.227388 CAGGGGATTGAAATATCGCTGC 59.773 50.000 0.00 0.00 37.56 5.25
5510 9934 1.541588 GGGGATTGAAATATCGCTGCC 59.458 52.381 0.00 0.00 37.56 4.85
5511 9935 1.541588 GGGATTGAAATATCGCTGCCC 59.458 52.381 0.00 0.00 35.33 5.36
5513 9937 2.227388 GGATTGAAATATCGCTGCCCTG 59.773 50.000 0.00 0.00 0.00 4.45
5515 9939 0.179020 TGAAATATCGCTGCCCTGGG 60.179 55.000 8.86 8.86 0.00 4.45
5516 9940 0.890996 GAAATATCGCTGCCCTGGGG 60.891 60.000 16.03 4.75 38.57 4.96
5534 9958 3.649986 GCGCGCCGGCTGAAATAT 61.650 61.111 26.68 0.00 36.88 1.28
5535 9959 2.551270 CGCGCCGGCTGAAATATC 59.449 61.111 26.68 3.29 36.88 1.63
5545 9969 0.947244 CTGAAATATCAGCGTGGGCC 59.053 55.000 0.00 0.00 46.11 5.80
5546 9970 0.813610 TGAAATATCAGCGTGGGCCG 60.814 55.000 0.00 0.00 41.24 6.13
5548 9972 0.108585 AAATATCAGCGTGGGCCGAT 59.891 50.000 0.00 0.00 39.55 4.18
5549 9973 0.320771 AATATCAGCGTGGGCCGATC 60.321 55.000 0.00 0.00 37.48 3.69
5550 9974 2.492449 ATATCAGCGTGGGCCGATCG 62.492 60.000 8.51 8.51 37.48 3.69
5556 9980 4.851179 GTGGGCCGATCGGGTTCC 62.851 72.222 33.98 25.56 38.44 3.62
5559 9983 4.104183 GGCCGATCGGGTTCCCAA 62.104 66.667 33.98 0.00 38.44 4.12
5560 9984 2.822701 GCCGATCGGGTTCCCAAC 60.823 66.667 33.98 12.15 38.44 3.77
5568 9992 2.754254 GGTTCCCAACCGCCATCC 60.754 66.667 0.00 0.00 42.62 3.51
5569 9993 2.754254 GTTCCCAACCGCCATCCC 60.754 66.667 0.00 0.00 0.00 3.85
5570 9994 2.938798 TTCCCAACCGCCATCCCT 60.939 61.111 0.00 0.00 0.00 4.20
5571 9995 1.616930 TTCCCAACCGCCATCCCTA 60.617 57.895 0.00 0.00 0.00 3.53
5573 9997 2.510906 CCAACCGCCATCCCTAGG 59.489 66.667 0.06 0.06 0.00 3.02
5580 10004 3.314331 CCATCCCTAGGCGCCGAT 61.314 66.667 23.20 15.00 0.00 4.18
5581 10005 2.743718 CATCCCTAGGCGCCGATT 59.256 61.111 23.20 6.30 0.00 3.34
5582 10006 1.071471 CATCCCTAGGCGCCGATTT 59.929 57.895 23.20 5.85 0.00 2.17
5583 10007 0.951040 CATCCCTAGGCGCCGATTTC 60.951 60.000 23.20 0.00 0.00 2.17
5585 10009 0.468585 TCCCTAGGCGCCGATTTCTA 60.469 55.000 23.20 5.64 0.00 2.10
5587 10011 1.202604 CCCTAGGCGCCGATTTCTAAA 60.203 52.381 23.20 0.00 0.00 1.85
5591 10015 1.092348 GGCGCCGATTTCTAAAGGTT 58.908 50.000 12.58 0.00 0.00 3.50
5592 10016 1.471287 GGCGCCGATTTCTAAAGGTTT 59.529 47.619 12.58 0.00 0.00 3.27
5593 10017 2.094906 GGCGCCGATTTCTAAAGGTTTT 60.095 45.455 12.58 0.00 0.00 2.43
5594 10018 3.571571 GCGCCGATTTCTAAAGGTTTTT 58.428 40.909 0.00 0.00 0.00 1.94
5631 10055 4.026293 CCAAATTTTGGCCAAACACAAC 57.974 40.909 30.43 0.00 45.17 3.32
5632 10056 3.441572 CCAAATTTTGGCCAAACACAACA 59.558 39.130 30.43 15.31 45.17 3.33
5633 10057 4.097589 CCAAATTTTGGCCAAACACAACAT 59.902 37.500 30.43 16.95 45.17 2.71
5634 10058 5.297776 CCAAATTTTGGCCAAACACAACATA 59.702 36.000 30.43 13.76 45.17 2.29
5635 10059 6.428799 CAAATTTTGGCCAAACACAACATAG 58.571 36.000 30.43 12.11 0.00 2.23
5638 10062 5.543507 TTTGGCCAAACACAACATAGATT 57.456 34.783 27.13 0.00 0.00 2.40
5639 10063 6.656632 TTTGGCCAAACACAACATAGATTA 57.343 33.333 27.13 0.00 0.00 1.75
5640 10064 5.895636 TGGCCAAACACAACATAGATTAG 57.104 39.130 0.61 0.00 0.00 1.73
5641 10065 4.704540 TGGCCAAACACAACATAGATTAGG 59.295 41.667 0.61 0.00 0.00 2.69
5643 10067 4.730613 GCCAAACACAACATAGATTAGGCG 60.731 45.833 0.00 0.00 0.00 5.52
5644 10068 4.634004 CCAAACACAACATAGATTAGGCGA 59.366 41.667 0.00 0.00 0.00 5.54
5645 10069 5.123186 CCAAACACAACATAGATTAGGCGAA 59.877 40.000 0.00 0.00 0.00 4.70
5647 10071 5.796350 ACACAACATAGATTAGGCGAAAC 57.204 39.130 0.00 0.00 0.00 2.78
5648 10072 5.242434 ACACAACATAGATTAGGCGAAACA 58.758 37.500 0.00 0.00 0.00 2.83
5649 10073 5.880332 ACACAACATAGATTAGGCGAAACAT 59.120 36.000 0.00 0.00 0.00 2.71
5650 10074 7.045416 ACACAACATAGATTAGGCGAAACATA 58.955 34.615 0.00 0.00 0.00 2.29
5651 10075 7.011109 ACACAACATAGATTAGGCGAAACATAC 59.989 37.037 0.00 0.00 0.00 2.39
5652 10076 7.224753 CACAACATAGATTAGGCGAAACATACT 59.775 37.037 0.00 0.00 0.00 2.12
5653 10077 7.438459 ACAACATAGATTAGGCGAAACATACTC 59.562 37.037 0.00 0.00 0.00 2.59
5655 10079 4.650754 AGATTAGGCGAAACATACTCGT 57.349 40.909 0.00 0.00 38.57 4.18
5657 10081 5.416947 AGATTAGGCGAAACATACTCGTTT 58.583 37.500 0.00 0.00 41.72 3.60
5658 10082 5.873164 AGATTAGGCGAAACATACTCGTTTT 59.127 36.000 0.00 0.00 39.17 2.43
5659 10083 5.927954 TTAGGCGAAACATACTCGTTTTT 57.072 34.783 0.00 0.00 39.17 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.295119 GACACAGTGGCGGACGGT 62.295 66.667 5.31 0.00 32.54 4.83
90 97 4.285260 TGGACGAATGATGATCATGGAGAT 59.715 41.667 14.30 0.00 37.15 2.75
177 199 1.094073 CGTCACCGGTCGTATCTCCT 61.094 60.000 2.59 0.00 0.00 3.69
230 253 5.515270 TCGATACAAAGAAAGCATCGTACAG 59.485 40.000 0.00 0.00 39.50 2.74
236 259 5.505286 CACCATCGATACAAAGAAAGCATC 58.495 41.667 0.00 0.00 0.00 3.91
240 263 3.689161 TGGCACCATCGATACAAAGAAAG 59.311 43.478 0.00 0.00 0.00 2.62
241 264 3.680490 TGGCACCATCGATACAAAGAAA 58.320 40.909 0.00 0.00 0.00 2.52
242 265 3.342377 TGGCACCATCGATACAAAGAA 57.658 42.857 0.00 0.00 0.00 2.52
243 266 3.342377 TTGGCACCATCGATACAAAGA 57.658 42.857 0.00 0.00 0.00 2.52
269 292 1.226603 CGATCTCGTTCCCGTGGAC 60.227 63.158 0.00 0.00 35.01 4.02
278 301 5.050490 CCATGTTTAAGGATCGATCTCGTT 58.950 41.667 23.96 16.67 40.80 3.85
279 302 4.621991 CCATGTTTAAGGATCGATCTCGT 58.378 43.478 23.96 14.58 40.80 4.18
283 306 2.480419 CGGCCATGTTTAAGGATCGATC 59.520 50.000 17.36 17.36 0.00 3.69
284 307 2.494059 CGGCCATGTTTAAGGATCGAT 58.506 47.619 2.24 0.00 0.00 3.59
285 308 1.474320 CCGGCCATGTTTAAGGATCGA 60.474 52.381 2.24 0.00 0.00 3.59
308 331 2.225791 CTCGTGCCAATCTCCGGTCA 62.226 60.000 0.00 0.00 0.00 4.02
313 340 0.532573 TCTCACTCGTGCCAATCTCC 59.467 55.000 0.00 0.00 0.00 3.71
388 415 3.061697 CGCAGGAGAAAAATGTACGGTAC 59.938 47.826 11.33 11.33 0.00 3.34
389 416 3.255725 CGCAGGAGAAAAATGTACGGTA 58.744 45.455 0.00 0.00 0.00 4.02
390 417 2.073816 CGCAGGAGAAAAATGTACGGT 58.926 47.619 0.00 0.00 0.00 4.83
391 418 2.073816 ACGCAGGAGAAAAATGTACGG 58.926 47.619 0.00 0.00 0.00 4.02
392 419 2.159707 CCACGCAGGAGAAAAATGTACG 60.160 50.000 0.00 0.00 41.22 3.67
393 420 3.071479 TCCACGCAGGAGAAAAATGTAC 58.929 45.455 0.00 0.00 43.07 2.90
394 421 3.410631 TCCACGCAGGAGAAAAATGTA 57.589 42.857 0.00 0.00 43.07 2.29
395 422 2.270352 TCCACGCAGGAGAAAAATGT 57.730 45.000 0.00 0.00 43.07 2.71
451 478 6.591448 ACAGTACGGTATTTTAGGTGTAAAGC 59.409 38.462 0.00 0.00 29.71 3.51
479 506 5.453866 ACTCCTGTATACTCTACCACAGT 57.546 43.478 4.17 0.00 37.32 3.55
488 515 6.864360 AAGATCGTGTACTCCTGTATACTC 57.136 41.667 4.17 0.00 38.23 2.59
489 516 7.556996 AGAAAAGATCGTGTACTCCTGTATACT 59.443 37.037 4.17 0.00 38.23 2.12
684 712 3.894947 GTGGCGCGGTGTTGGTTT 61.895 61.111 8.83 0.00 0.00 3.27
833 879 2.970324 GAACAACGTGGAGCGGCA 60.970 61.111 1.45 0.00 46.52 5.69
864 910 3.444417 TCTAGGGCCCCGGGATGA 61.444 66.667 26.32 7.51 0.00 2.92
865 911 3.242291 GTCTAGGGCCCCGGGATG 61.242 72.222 26.32 7.36 0.00 3.51
866 912 3.036045 AAGTCTAGGGCCCCGGGAT 62.036 63.158 26.32 7.45 0.00 3.85
1179 1275 1.301401 CTTGGCGTCGGAGTTGGAA 60.301 57.895 0.00 0.00 0.00 3.53
1548 1686 4.573162 CGTTCTCGGGAGTTGGAC 57.427 61.111 0.00 0.00 0.00 4.02
1611 1749 2.030981 GGTATCGGAGTCGGATGAAGAC 60.031 54.545 20.27 11.63 38.81 3.01
2268 2454 1.148310 CGTCGAACAAGAAGTGCCAT 58.852 50.000 0.00 0.00 0.00 4.40
3081 5414 1.004610 CGAACACAACAGTGCACTCTG 60.005 52.381 18.64 19.14 40.80 3.35
3154 5543 5.902613 TTGAAATATTGAAGTGAGGGCAG 57.097 39.130 0.00 0.00 0.00 4.85
3224 5631 7.605449 ACCTGCATTATTCATACATTTATGGC 58.395 34.615 0.00 0.00 36.47 4.40
3407 5848 4.816385 TCGGCAGAAATCAATGATAACTCC 59.184 41.667 0.00 3.10 0.00 3.85
3451 5892 7.861629 TCACCTACAGAAGAAACCATATGAAT 58.138 34.615 3.65 0.00 0.00 2.57
3452 5893 7.252612 TCACCTACAGAAGAAACCATATGAA 57.747 36.000 3.65 0.00 0.00 2.57
3773 6217 2.159028 AGGAGCACCGAGAAGCTATTTC 60.159 50.000 0.00 0.00 42.04 2.17
3808 6288 3.004752 AGAATTTTGGGACGGATGGAG 57.995 47.619 0.00 0.00 0.00 3.86
3809 6289 3.088532 CAAGAATTTTGGGACGGATGGA 58.911 45.455 0.00 0.00 0.00 3.41
3810 6290 2.825532 ACAAGAATTTTGGGACGGATGG 59.174 45.455 0.00 0.00 0.00 3.51
3811 6291 3.758554 AGACAAGAATTTTGGGACGGATG 59.241 43.478 0.00 0.00 0.00 3.51
3812 6292 4.034285 AGACAAGAATTTTGGGACGGAT 57.966 40.909 0.00 0.00 0.00 4.18
3813 6293 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3814 6294 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3815 6295 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3816 6296 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3817 6297 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3818 6298 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3826 6306 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3827 6307 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3828 6308 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3829 6309 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
3830 6310 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3831 6311 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3849 6329 9.970395 TCACGTTTTAATATTAGATACATCCGT 57.030 29.630 0.00 0.00 0.00 4.69
3862 6342 8.761497 CGGATGTATCAAGTCACGTTTTAATAT 58.239 33.333 0.00 0.00 0.00 1.28
3863 6343 7.760794 ACGGATGTATCAAGTCACGTTTTAATA 59.239 33.333 0.00 0.00 0.00 0.98
3864 6344 6.592607 ACGGATGTATCAAGTCACGTTTTAAT 59.407 34.615 0.00 0.00 0.00 1.40
3865 6345 5.927689 ACGGATGTATCAAGTCACGTTTTAA 59.072 36.000 0.00 0.00 0.00 1.52
3866 6346 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
3867 6347 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
3868 6348 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
3869 6349 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
3870 6350 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
3871 6351 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
3872 6352 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
3873 6353 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
3874 6354 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
3875 6355 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
3894 6374 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
3895 6375 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
3896 6376 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
3897 6377 9.323985 TGTCCCAAAATTCTTGTCTTAAATTTG 57.676 29.630 0.00 0.00 33.95 2.32
3898 6378 9.325198 GTGTCCCAAAATTCTTGTCTTAAATTT 57.675 29.630 0.00 0.00 34.86 1.82
3899 6379 8.482128 TGTGTCCCAAAATTCTTGTCTTAAATT 58.518 29.630 0.00 0.00 0.00 1.82
3900 6380 8.017418 TGTGTCCCAAAATTCTTGTCTTAAAT 57.983 30.769 0.00 0.00 0.00 1.40
3901 6381 7.411486 TGTGTCCCAAAATTCTTGTCTTAAA 57.589 32.000 0.00 0.00 0.00 1.52
3902 6382 6.040391 CCTGTGTCCCAAAATTCTTGTCTTAA 59.960 38.462 0.00 0.00 0.00 1.85
3903 6383 5.534654 CCTGTGTCCCAAAATTCTTGTCTTA 59.465 40.000 0.00 0.00 0.00 2.10
3904 6384 4.342092 CCTGTGTCCCAAAATTCTTGTCTT 59.658 41.667 0.00 0.00 0.00 3.01
3905 6385 3.891366 CCTGTGTCCCAAAATTCTTGTCT 59.109 43.478 0.00 0.00 0.00 3.41
3906 6386 3.005791 CCCTGTGTCCCAAAATTCTTGTC 59.994 47.826 0.00 0.00 0.00 3.18
3907 6387 2.965147 CCCTGTGTCCCAAAATTCTTGT 59.035 45.455 0.00 0.00 0.00 3.16
3908 6388 3.230134 TCCCTGTGTCCCAAAATTCTTG 58.770 45.455 0.00 0.00 0.00 3.02
3909 6389 3.117131 ACTCCCTGTGTCCCAAAATTCTT 60.117 43.478 0.00 0.00 0.00 2.52
3910 6390 2.447047 ACTCCCTGTGTCCCAAAATTCT 59.553 45.455 0.00 0.00 0.00 2.40
3911 6391 2.876581 ACTCCCTGTGTCCCAAAATTC 58.123 47.619 0.00 0.00 0.00 2.17
3912 6392 3.245264 CCTACTCCCTGTGTCCCAAAATT 60.245 47.826 0.00 0.00 0.00 1.82
3913 6393 2.308866 CCTACTCCCTGTGTCCCAAAAT 59.691 50.000 0.00 0.00 0.00 1.82
3914 6394 1.702957 CCTACTCCCTGTGTCCCAAAA 59.297 52.381 0.00 0.00 0.00 2.44
3915 6395 1.132657 TCCTACTCCCTGTGTCCCAAA 60.133 52.381 0.00 0.00 0.00 3.28
3916 6396 0.490017 TCCTACTCCCTGTGTCCCAA 59.510 55.000 0.00 0.00 0.00 4.12
3917 6397 0.716591 ATCCTACTCCCTGTGTCCCA 59.283 55.000 0.00 0.00 0.00 4.37
3918 6398 2.769602 TATCCTACTCCCTGTGTCCC 57.230 55.000 0.00 0.00 0.00 4.46
3919 6399 4.527427 GGTATTATCCTACTCCCTGTGTCC 59.473 50.000 0.00 0.00 0.00 4.02
3920 6400 5.395611 AGGTATTATCCTACTCCCTGTGTC 58.604 45.833 0.00 0.00 35.87 3.67
3921 6401 5.420215 AGGTATTATCCTACTCCCTGTGT 57.580 43.478 0.00 0.00 35.87 3.72
3922 6402 5.511545 GCAAGGTATTATCCTACTCCCTGTG 60.512 48.000 0.00 0.00 36.74 3.66
3923 6403 4.593634 GCAAGGTATTATCCTACTCCCTGT 59.406 45.833 0.00 0.00 36.74 4.00
3924 6404 4.593206 TGCAAGGTATTATCCTACTCCCTG 59.407 45.833 0.00 0.00 36.74 4.45
3925 6405 4.827789 TGCAAGGTATTATCCTACTCCCT 58.172 43.478 0.00 0.00 36.74 4.20
3926 6406 5.763876 ATGCAAGGTATTATCCTACTCCC 57.236 43.478 0.00 0.00 36.74 4.30
3927 6407 5.869888 CGAATGCAAGGTATTATCCTACTCC 59.130 44.000 0.00 0.00 36.74 3.85
3928 6408 5.348997 GCGAATGCAAGGTATTATCCTACTC 59.651 44.000 0.00 0.00 42.15 2.59
3929 6409 5.012148 AGCGAATGCAAGGTATTATCCTACT 59.988 40.000 0.00 0.00 46.23 2.57
3930 6410 5.120830 CAGCGAATGCAAGGTATTATCCTAC 59.879 44.000 0.00 0.00 46.23 3.18
3931 6411 5.011635 TCAGCGAATGCAAGGTATTATCCTA 59.988 40.000 0.00 0.00 46.23 2.94
3932 6412 4.067896 CAGCGAATGCAAGGTATTATCCT 58.932 43.478 0.00 0.00 46.23 3.24
3952 6432 1.792949 AGCGCTTAAAACGTCAGTCAG 59.207 47.619 2.64 0.00 0.00 3.51
3970 6450 3.803778 CCACAACAACCTGAAATTCAAGC 59.196 43.478 0.00 0.00 0.00 4.01
4096 6576 4.286813 TCCTTCTCCCATATCAGGACTT 57.713 45.455 0.00 0.00 0.00 3.01
4227 6741 8.177013 CCCAACGTTATGTTTATTTACACCTAC 58.823 37.037 0.00 0.00 39.29 3.18
4230 6744 7.143514 TCCCAACGTTATGTTTATTTACACC 57.856 36.000 0.00 0.00 39.29 4.16
4231 6745 6.744082 GCTCCCAACGTTATGTTTATTTACAC 59.256 38.462 0.00 0.00 39.29 2.90
4232 6746 6.655848 AGCTCCCAACGTTATGTTTATTTACA 59.344 34.615 0.00 0.00 39.29 2.41
4235 6749 6.584185 AAGCTCCCAACGTTATGTTTATTT 57.416 33.333 0.00 0.00 39.29 1.40
4266 6780 3.745975 TGCCAACTGAATTTGACGAGTAG 59.254 43.478 0.00 0.00 0.00 2.57
4271 6785 1.666888 GCCTGCCAACTGAATTTGACG 60.667 52.381 0.00 0.00 0.00 4.35
4275 6789 1.972795 ACATGCCTGCCAACTGAATTT 59.027 42.857 0.00 0.00 0.00 1.82
4284 6798 0.107066 CTGACCATACATGCCTGCCA 60.107 55.000 0.00 0.00 0.00 4.92
4393 6918 5.011329 TCCTTCTTACCGTCAATGTAACTGT 59.989 40.000 0.00 0.00 0.00 3.55
4713 7238 2.971598 GCCAGGCTCCTGCAGGTAA 61.972 63.158 31.58 13.44 42.35 2.85
4786 7329 5.590259 ACATCAGACACACTAACAGCTTTTT 59.410 36.000 0.00 0.00 0.00 1.94
4787 7330 5.008019 CACATCAGACACACTAACAGCTTTT 59.992 40.000 0.00 0.00 0.00 2.27
4788 7331 4.512944 CACATCAGACACACTAACAGCTTT 59.487 41.667 0.00 0.00 0.00 3.51
4789 7332 4.060900 CACATCAGACACACTAACAGCTT 58.939 43.478 0.00 0.00 0.00 3.74
4790 7333 3.321968 TCACATCAGACACACTAACAGCT 59.678 43.478 0.00 0.00 0.00 4.24
4791 7334 3.653344 TCACATCAGACACACTAACAGC 58.347 45.455 0.00 0.00 0.00 4.40
4792 7335 5.473039 TCATCACATCAGACACACTAACAG 58.527 41.667 0.00 0.00 0.00 3.16
4793 7336 5.011023 ACTCATCACATCAGACACACTAACA 59.989 40.000 0.00 0.00 0.00 2.41
4794 7337 5.347093 CACTCATCACATCAGACACACTAAC 59.653 44.000 0.00 0.00 0.00 2.34
4795 7338 5.011023 ACACTCATCACATCAGACACACTAA 59.989 40.000 0.00 0.00 0.00 2.24
4796 7339 4.524328 ACACTCATCACATCAGACACACTA 59.476 41.667 0.00 0.00 0.00 2.74
4803 7346 4.039609 ACAGAACACACTCATCACATCAGA 59.960 41.667 0.00 0.00 0.00 3.27
4807 7350 5.474578 ACTACAGAACACACTCATCACAT 57.525 39.130 0.00 0.00 0.00 3.21
4823 7380 5.347635 TGCACGAAAGCTTGTTATACTACAG 59.652 40.000 0.00 0.00 34.99 2.74
4905 8333 0.845768 CAACAAAAGTTTCAGCGGCG 59.154 50.000 0.51 0.51 0.00 6.46
5135 8608 1.140312 TGCTTCAGAAGACAACCCCT 58.860 50.000 14.86 0.00 0.00 4.79
5336 8863 1.078848 CAACGAGCCCCTCCTCTTG 60.079 63.158 0.00 0.00 0.00 3.02
5351 8878 3.303406 GACAACAAAGCTCAGCATCAAC 58.697 45.455 0.00 0.00 0.00 3.18
5368 8895 1.605058 GCAGAGAGGCCCTACGACAA 61.605 60.000 0.00 0.00 0.00 3.18
5424 8951 4.761739 CACTAGATTGTTGGAGCCAAAAGA 59.238 41.667 3.05 0.00 37.70 2.52
5463 9887 1.134670 AGTAAACGGCTGGAGATGCTC 60.135 52.381 0.00 0.00 0.00 4.26
5464 9888 0.905357 AGTAAACGGCTGGAGATGCT 59.095 50.000 0.00 0.00 0.00 3.79
5465 9889 1.666189 GAAGTAAACGGCTGGAGATGC 59.334 52.381 0.00 0.00 0.00 3.91
5466 9890 2.280628 GGAAGTAAACGGCTGGAGATG 58.719 52.381 0.00 0.00 0.00 2.90
5468 9892 0.611714 GGGAAGTAAACGGCTGGAGA 59.388 55.000 0.00 0.00 0.00 3.71
5469 9893 0.392595 GGGGAAGTAAACGGCTGGAG 60.393 60.000 0.00 0.00 0.00 3.86
5470 9894 1.128809 TGGGGAAGTAAACGGCTGGA 61.129 55.000 0.00 0.00 0.00 3.86
5471 9895 0.676782 CTGGGGAAGTAAACGGCTGG 60.677 60.000 0.00 0.00 0.00 4.85
5472 9896 0.676782 CCTGGGGAAGTAAACGGCTG 60.677 60.000 0.00 0.00 0.00 4.85
5473 9897 1.683441 CCTGGGGAAGTAAACGGCT 59.317 57.895 0.00 0.00 0.00 5.52
5474 9898 1.378119 CCCTGGGGAAGTAAACGGC 60.378 63.158 4.27 0.00 37.50 5.68
5485 9909 2.795329 CGATATTTCAATCCCCTGGGG 58.205 52.381 26.87 26.87 46.11 4.96
5486 9910 2.162681 GCGATATTTCAATCCCCTGGG 58.837 52.381 5.50 5.50 0.00 4.45
5488 9912 2.227388 GCAGCGATATTTCAATCCCCTG 59.773 50.000 0.00 0.00 0.00 4.45
5489 9913 2.508526 GCAGCGATATTTCAATCCCCT 58.491 47.619 0.00 0.00 0.00 4.79
5490 9914 1.541588 GGCAGCGATATTTCAATCCCC 59.458 52.381 0.00 0.00 0.00 4.81
5491 9915 1.541588 GGGCAGCGATATTTCAATCCC 59.458 52.381 0.00 0.00 0.00 3.85
5492 9916 2.227388 CAGGGCAGCGATATTTCAATCC 59.773 50.000 0.00 0.00 0.00 3.01
5493 9917 2.227388 CCAGGGCAGCGATATTTCAATC 59.773 50.000 0.00 0.00 0.00 2.67
5494 9918 2.233271 CCAGGGCAGCGATATTTCAAT 58.767 47.619 0.00 0.00 0.00 2.57
5496 9920 0.179020 CCCAGGGCAGCGATATTTCA 60.179 55.000 0.00 0.00 0.00 2.69
5497 9921 0.890996 CCCCAGGGCAGCGATATTTC 60.891 60.000 0.00 0.00 0.00 2.17
5498 9922 1.151450 CCCCAGGGCAGCGATATTT 59.849 57.895 0.00 0.00 0.00 1.40
5499 9923 2.833913 CCCCCAGGGCAGCGATATT 61.834 63.158 0.00 0.00 35.35 1.28
5517 9941 3.579626 GATATTTCAGCCGGCGCGC 62.580 63.158 25.94 25.94 41.18 6.86
5518 9942 2.162921 CTGATATTTCAGCCGGCGCG 62.163 60.000 23.20 17.14 42.79 6.86
5519 9943 1.571460 CTGATATTTCAGCCGGCGC 59.429 57.895 23.20 0.00 42.79 6.53
5527 9951 0.813610 CGGCCCACGCTGATATTTCA 60.814 55.000 0.00 0.00 44.91 2.69
5528 9952 0.531974 TCGGCCCACGCTGATATTTC 60.532 55.000 0.00 0.00 45.71 2.17
5539 9963 4.851179 GGAACCCGATCGGCCCAC 62.851 72.222 29.12 17.50 33.26 4.61
5552 9976 1.917336 TAGGGATGGCGGTTGGGAAC 61.917 60.000 0.00 0.00 0.00 3.62
5554 9978 2.041430 TAGGGATGGCGGTTGGGA 59.959 61.111 0.00 0.00 0.00 4.37
5555 9979 2.510906 CTAGGGATGGCGGTTGGG 59.489 66.667 0.00 0.00 0.00 4.12
5556 9980 2.510906 CCTAGGGATGGCGGTTGG 59.489 66.667 0.00 0.00 0.00 3.77
5557 9981 2.203209 GCCTAGGGATGGCGGTTG 60.203 66.667 11.72 0.00 41.03 3.77
5563 9987 2.397413 AAATCGGCGCCTAGGGATGG 62.397 60.000 26.68 6.06 0.00 3.51
5564 9988 0.951040 GAAATCGGCGCCTAGGGATG 60.951 60.000 26.68 6.92 0.00 3.51
5565 9989 1.122019 AGAAATCGGCGCCTAGGGAT 61.122 55.000 26.68 16.81 0.00 3.85
5566 9990 0.468585 TAGAAATCGGCGCCTAGGGA 60.469 55.000 26.68 15.03 0.00 4.20
5568 9992 2.135933 CTTTAGAAATCGGCGCCTAGG 58.864 52.381 26.68 9.50 0.00 3.02
5569 9993 2.135933 CCTTTAGAAATCGGCGCCTAG 58.864 52.381 26.68 10.37 0.00 3.02
5570 9994 1.483415 ACCTTTAGAAATCGGCGCCTA 59.517 47.619 26.68 15.56 0.00 3.93
5571 9995 0.252197 ACCTTTAGAAATCGGCGCCT 59.748 50.000 26.68 4.89 0.00 5.52
5573 9997 2.913777 AAACCTTTAGAAATCGGCGC 57.086 45.000 0.00 0.00 0.00 6.53
5594 10018 9.372369 CCAAAATTTGGCCGAGTATATTTTTAA 57.628 29.630 12.23 0.00 45.17 1.52
5595 10019 8.934507 CCAAAATTTGGCCGAGTATATTTTTA 57.065 30.769 12.23 0.00 45.17 1.52
5611 10035 4.691860 TGTTGTGTTTGGCCAAAATTTG 57.308 36.364 31.92 0.00 31.33 2.32
5612 10036 6.352516 TCTATGTTGTGTTTGGCCAAAATTT 58.647 32.000 31.92 14.62 31.33 1.82
5613 10037 5.923204 TCTATGTTGTGTTTGGCCAAAATT 58.077 33.333 31.92 13.66 31.33 1.82
5614 10038 5.543507 TCTATGTTGTGTTTGGCCAAAAT 57.456 34.783 31.92 21.71 31.33 1.82
5615 10039 5.543507 ATCTATGTTGTGTTTGGCCAAAA 57.456 34.783 31.92 18.84 31.33 2.44
5616 10040 5.543507 AATCTATGTTGTGTTTGGCCAAA 57.456 34.783 27.13 27.13 0.00 3.28
5617 10041 5.184864 CCTAATCTATGTTGTGTTTGGCCAA 59.815 40.000 16.05 16.05 0.00 4.52
5618 10042 4.704540 CCTAATCTATGTTGTGTTTGGCCA 59.295 41.667 0.00 0.00 0.00 5.36
5619 10043 4.440112 GCCTAATCTATGTTGTGTTTGGCC 60.440 45.833 0.00 0.00 35.57 5.36
5620 10044 4.672409 GCCTAATCTATGTTGTGTTTGGC 58.328 43.478 0.00 0.00 34.58 4.52
5621 10045 4.634004 TCGCCTAATCTATGTTGTGTTTGG 59.366 41.667 0.00 0.00 0.00 3.28
5622 10046 5.794687 TCGCCTAATCTATGTTGTGTTTG 57.205 39.130 0.00 0.00 0.00 2.93
5623 10047 6.205853 TGTTTCGCCTAATCTATGTTGTGTTT 59.794 34.615 0.00 0.00 0.00 2.83
5626 10050 5.794687 TGTTTCGCCTAATCTATGTTGTG 57.205 39.130 0.00 0.00 0.00 3.33
5627 10051 7.272978 AGTATGTTTCGCCTAATCTATGTTGT 58.727 34.615 0.00 0.00 0.00 3.32
5628 10052 7.358435 CGAGTATGTTTCGCCTAATCTATGTTG 60.358 40.741 0.00 0.00 0.00 3.33
5629 10053 6.641314 CGAGTATGTTTCGCCTAATCTATGTT 59.359 38.462 0.00 0.00 0.00 2.71
5630 10054 6.150318 CGAGTATGTTTCGCCTAATCTATGT 58.850 40.000 0.00 0.00 0.00 2.29
5631 10055 6.150318 ACGAGTATGTTTCGCCTAATCTATG 58.850 40.000 0.00 0.00 41.57 2.23
5632 10056 6.328641 ACGAGTATGTTTCGCCTAATCTAT 57.671 37.500 0.00 0.00 41.57 1.98
5633 10057 5.762825 ACGAGTATGTTTCGCCTAATCTA 57.237 39.130 0.00 0.00 41.57 1.98
5634 10058 4.650754 ACGAGTATGTTTCGCCTAATCT 57.349 40.909 0.00 0.00 41.57 2.40
5635 10059 5.713822 AAACGAGTATGTTTCGCCTAATC 57.286 39.130 0.00 0.00 41.57 1.75


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

AutoCloner maintained by Alex Coulton.