Multiple sequence alignment - TraesCS1D01G115400

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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 TraesCS1D01G115400 chr1D 100.000 5446 0 0 1 5446 111088288 111093733 0.000000e+00 10057.0
1 TraesCS1D01G115400 chr1D 80.403 347 43 15 5103 5446 76473917 76474241 1.960000e-59 241.0
2 TraesCS1D01G115400 chr1D 82.474 97 15 2 5198 5292 396741865 396741769 3.500000e-12 84.2
3 TraesCS1D01G115400 chr1D 100.000 32 0 0 1487 1518 5518593 5518624 5.890000e-05 60.2
4 TraesCS1D01G115400 chr1A 95.310 4840 170 26 8 4814 117243568 117248383 0.000000e+00 7627.0
5 TraesCS1D01G115400 chr1A 88.339 283 26 3 4991 5273 117248452 117248727 3.140000e-87 333.0
6 TraesCS1D01G115400 chr1A 86.449 214 23 5 5235 5446 77078756 77078965 4.240000e-56 230.0
7 TraesCS1D01G115400 chr1A 100.000 32 0 0 1487 1518 7185737 7185768 5.890000e-05 60.2
8 TraesCS1D01G115400 chr1B 94.197 4532 163 35 351 4812 169693168 169697669 0.000000e+00 6820.0
9 TraesCS1D01G115400 chr1B 93.948 347 17 4 4 349 169692235 169692578 6.250000e-144 521.0
10 TraesCS1D01G115400 chr1B 81.293 294 33 13 5137 5428 119776399 119776672 9.180000e-53 219.0
11 TraesCS1D01G115400 chr1B 95.238 42 1 1 1748 1789 328937229 328937269 1.270000e-06 65.8
12 TraesCS1D01G115400 chr1B 100.000 32 0 0 1487 1518 8256002 8256033 5.890000e-05 60.2
13 TraesCS1D01G115400 chr3D 82.974 2831 441 33 1042 3844 46580486 46583303 0.000000e+00 2519.0
14 TraesCS1D01G115400 chr3D 89.489 352 37 0 3951 4302 46583411 46583762 3.870000e-121 446.0
15 TraesCS1D01G115400 chr3D 78.531 177 35 3 5216 5390 341677679 341677504 4.460000e-21 113.0
16 TraesCS1D01G115400 chr3A 82.669 2833 450 33 1042 3847 57947705 57944887 0.000000e+00 2473.0
17 TraesCS1D01G115400 chr3A 89.685 349 36 0 3954 4302 57944789 57944441 3.870000e-121 446.0
18 TraesCS1D01G115400 chr3A 77.564 156 18 12 5215 5361 737659654 737659801 1.630000e-10 78.7
19 TraesCS1D01G115400 chr3B 82.558 2838 454 32 1042 3851 72950339 72953163 0.000000e+00 2460.0
20 TraesCS1D01G115400 chr3B 89.049 347 38 0 3956 4302 72953274 72953620 1.080000e-116 431.0
21 TraesCS1D01G115400 chr3B 91.852 135 11 0 4856 4990 704573825 704573959 7.200000e-44 189.0
22 TraesCS1D01G115400 chr6B 95.497 1288 58 0 2304 3591 11954581 11955868 0.000000e+00 2058.0
23 TraesCS1D01G115400 chr6B 92.537 134 10 0 4856 4989 468426546 468426679 5.570000e-45 193.0
24 TraesCS1D01G115400 chr4A 91.912 136 11 0 4855 4990 596216145 596216280 2.000000e-44 191.0
25 TraesCS1D01G115400 chr4A 90.698 43 4 0 3999 4041 737842158 737842200 2.120000e-04 58.4
26 TraesCS1D01G115400 chr4A 90.698 43 4 0 3999 4041 738081464 738081506 2.120000e-04 58.4
27 TraesCS1D01G115400 chrUn 91.852 135 11 0 4856 4990 315368521 315368387 7.200000e-44 189.0
28 TraesCS1D01G115400 chrUn 91.852 135 11 0 4856 4990 357400961 357401095 7.200000e-44 189.0
29 TraesCS1D01G115400 chrUn 91.852 135 11 0 4856 4990 377264479 377264613 7.200000e-44 189.0
30 TraesCS1D01G115400 chrUn 85.714 70 7 3 1342 1410 87691132 87691199 2.720000e-08 71.3
31 TraesCS1D01G115400 chr6A 91.111 135 12 0 4856 4990 485860384 485860518 3.350000e-42 183.0
32 TraesCS1D01G115400 chr5B 90.580 138 13 0 4856 4993 349390634 349390497 3.350000e-42 183.0
33 TraesCS1D01G115400 chr5A 88.742 151 15 2 4846 4995 327927300 327927449 3.350000e-42 183.0
34 TraesCS1D01G115400 chr5D 80.137 146 27 2 5212 5355 278311375 278311230 2.070000e-19 108.0
35 TraesCS1D01G115400 chr5D 92.308 39 3 0 3988 4026 446404460 446404498 7.620000e-04 56.5
36 TraesCS1D01G115400 chr4D 89.062 64 7 0 3980 4043 283882120 283882057 4.520000e-11 80.5
37 TraesCS1D01G115400 chr4D 100.000 31 0 0 5103 5133 324217061 324217031 2.120000e-04 58.4
38 TraesCS1D01G115400 chr7D 85.915 71 10 0 1343 1413 70706992 70707062 5.850000e-10 76.8
39 TraesCS1D01G115400 chr7D 84.722 72 10 1 1342 1413 70062104 70062034 2.720000e-08 71.3
40 TraesCS1D01G115400 chr7B 81.522 92 15 2 1320 1410 698889132 698889222 2.100000e-09 75.0
41 TraesCS1D01G115400 chr7A 90.698 43 4 0 5238 5280 207089117 207089159 2.120000e-04 58.4


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 TraesCS1D01G115400 chr1D 111088288 111093733 5445 False 10057.0 10057 100.0000 1 5446 1 chr1D.!!$F3 5445
1 TraesCS1D01G115400 chr1A 117243568 117248727 5159 False 3980.0 7627 91.8245 8 5273 2 chr1A.!!$F3 5265
2 TraesCS1D01G115400 chr1B 169692235 169697669 5434 False 3670.5 6820 94.0725 4 4812 2 chr1B.!!$F4 4808
3 TraesCS1D01G115400 chr3D 46580486 46583762 3276 False 1482.5 2519 86.2315 1042 4302 2 chr3D.!!$F1 3260
4 TraesCS1D01G115400 chr3A 57944441 57947705 3264 True 1459.5 2473 86.1770 1042 4302 2 chr3A.!!$R1 3260
5 TraesCS1D01G115400 chr3B 72950339 72953620 3281 False 1445.5 2460 85.8035 1042 4302 2 chr3B.!!$F2 3260
6 TraesCS1D01G115400 chr6B 11954581 11955868 1287 False 2058.0 2058 95.4970 2304 3591 1 chr6B.!!$F1 1287

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
623 1219 0.324738 TCAGTGGTAGAGGCCAGAGG 60.325 60.000 5.01 0.0 39.53 3.69 F
2070 2712 1.280421 GGGAACAAGATCTCTGGCACT 59.720 52.381 0.00 0.0 0.00 4.40 F
2566 3208 0.107508 CCTCCACGACAATGCCATCT 60.108 55.000 0.00 0.0 0.00 2.90 F
2619 3261 0.255033 TGCTCTCGCTCCAGTACCTA 59.745 55.000 0.00 0.0 36.97 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2898 0.741221 GAGCATTGGTCGACAGGTCC 60.741 60.000 18.91 0.0 0.00 4.46 R
4010 4729 1.002990 CATCTCCAGCAGCACCACA 60.003 57.895 0.00 0.0 0.00 4.17 R
4175 4894 2.753043 CCGAGGGCTTGCAGCATT 60.753 61.111 0.00 0.0 44.75 3.56 R
4519 5268 3.390819 ACATAATTTCTACGGGTCCCCT 58.609 45.455 1.00 0.0 0.00 4.79 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
69 70 8.748380 ATTAAGAATCTTTTTGTTACTGCTGC 57.252 30.769 0.00 0.00 0.00 5.25
92 93 5.360144 GCAGTGGTAGTATCTCCTTGTCTAA 59.640 44.000 0.00 0.00 0.00 2.10
184 187 1.282157 AGAGGAAGAACCCCCAATTCG 59.718 52.381 0.00 0.00 40.05 3.34
220 223 0.764369 TGGACTGTGGGTGCTCTTCT 60.764 55.000 0.00 0.00 37.18 2.85
408 998 4.828296 CTGCCCACCCAGATGCCC 62.828 72.222 0.00 0.00 34.77 5.36
480 1076 2.969821 TAGTTCACCAGTTGGGCATT 57.030 45.000 2.79 0.00 42.05 3.56
515 1111 0.737219 GTTGGTGATCTGATGCCTGC 59.263 55.000 0.00 0.00 0.00 4.85
533 1129 9.533253 GATGCCTGCAGTAACAAATTTAAATAT 57.467 29.630 13.81 0.00 0.00 1.28
534 1130 8.700722 TGCCTGCAGTAACAAATTTAAATATG 57.299 30.769 13.81 0.00 0.00 1.78
608 1204 3.627395 TGAAGGCGGTGATAATTCAGT 57.373 42.857 0.00 0.00 30.85 3.41
609 1205 3.270027 TGAAGGCGGTGATAATTCAGTG 58.730 45.455 0.00 0.00 30.85 3.66
612 1208 2.769663 AGGCGGTGATAATTCAGTGGTA 59.230 45.455 0.00 0.00 30.85 3.25
613 1209 3.131396 GGCGGTGATAATTCAGTGGTAG 58.869 50.000 0.00 0.00 30.85 3.18
614 1210 3.181469 GGCGGTGATAATTCAGTGGTAGA 60.181 47.826 0.00 0.00 30.85 2.59
615 1211 4.051922 GCGGTGATAATTCAGTGGTAGAG 58.948 47.826 0.00 0.00 30.85 2.43
616 1212 4.621991 CGGTGATAATTCAGTGGTAGAGG 58.378 47.826 0.00 0.00 30.85 3.69
617 1213 4.381411 GGTGATAATTCAGTGGTAGAGGC 58.619 47.826 0.00 0.00 30.85 4.70
618 1214 4.381411 GTGATAATTCAGTGGTAGAGGCC 58.619 47.826 0.00 0.00 30.85 5.19
619 1215 4.037222 TGATAATTCAGTGGTAGAGGCCA 58.963 43.478 5.01 0.00 35.93 5.36
620 1216 4.101585 TGATAATTCAGTGGTAGAGGCCAG 59.898 45.833 5.01 0.00 39.53 4.85
621 1217 2.254152 ATTCAGTGGTAGAGGCCAGA 57.746 50.000 5.01 0.00 39.53 3.86
622 1218 1.561643 TTCAGTGGTAGAGGCCAGAG 58.438 55.000 5.01 0.00 39.53 3.35
623 1219 0.324738 TCAGTGGTAGAGGCCAGAGG 60.325 60.000 5.01 0.00 39.53 3.69
771 1388 7.125053 CCTCAAATACTCTCTCTTTAACCTCCT 59.875 40.741 0.00 0.00 0.00 3.69
839 1469 6.046593 TCGCCACTCCATTAATTAGTTACTG 58.953 40.000 0.00 0.00 0.00 2.74
842 1472 6.990349 GCCACTCCATTAATTAGTTACTGCTA 59.010 38.462 0.00 0.00 0.00 3.49
901 1531 4.224370 TCCAATTAACACCTCTAGACCACC 59.776 45.833 0.00 0.00 0.00 4.61
923 1553 4.383552 CCCAATTCTGTAGAGTTAGCTGCT 60.384 45.833 7.57 7.57 0.00 4.24
955 1585 6.886459 ACCTTGTACTCATGTTCTTGCATATT 59.114 34.615 0.00 0.00 0.00 1.28
1554 2196 3.951680 TCATCATCTACGACAACCAGCTA 59.048 43.478 0.00 0.00 0.00 3.32
1665 2307 2.657944 GAGATCGGCAGCTGCTCG 60.658 66.667 35.82 33.16 41.70 5.03
2064 2706 1.480137 CTCAGCGGGAACAAGATCTCT 59.520 52.381 0.00 0.00 0.00 3.10
2070 2712 1.280421 GGGAACAAGATCTCTGGCACT 59.720 52.381 0.00 0.00 0.00 4.40
2566 3208 0.107508 CCTCCACGACAATGCCATCT 60.108 55.000 0.00 0.00 0.00 2.90
2619 3261 0.255033 TGCTCTCGCTCCAGTACCTA 59.745 55.000 0.00 0.00 36.97 3.08
2675 3317 2.125552 CGACATCGGCCTGCTCAA 60.126 61.111 0.00 0.00 35.37 3.02
2841 3483 1.694696 GGACTGGAGATCGCCCTTAAT 59.305 52.381 13.44 0.00 0.00 1.40
2854 3496 2.019984 CCCTTAATCTCAGCTGCAACC 58.980 52.381 9.47 0.00 0.00 3.77
3183 3825 3.311110 GTCGTCCTCCTGGTGGCA 61.311 66.667 9.96 0.00 34.23 4.92
3242 3902 4.020617 TGCCAGCGAGGACAAGGG 62.021 66.667 2.12 0.00 41.22 3.95
3498 4158 2.736995 CACCGCAACATCGTCCGT 60.737 61.111 0.00 0.00 0.00 4.69
3504 4164 1.291877 GCAACATCGTCCGTCTGCTT 61.292 55.000 0.00 0.00 0.00 3.91
3567 4227 2.050350 CCTCCCGAACGGCACTCTA 61.050 63.158 7.80 0.00 0.00 2.43
3570 4230 2.050350 CCCGAACGGCACTCTAGGA 61.050 63.158 7.80 0.00 0.00 2.94
3573 4233 1.313812 CGAACGGCACTCTAGGAGGT 61.314 60.000 0.00 0.00 33.35 3.85
3579 4239 0.744281 GCACTCTAGGAGGTCTGCTC 59.256 60.000 0.00 0.00 33.35 4.26
3618 4278 3.998672 GCCGTCGTGGAGTGGGAA 61.999 66.667 0.51 0.00 42.00 3.97
3965 4684 0.973632 TGGTTGATGCAGAGTACGGT 59.026 50.000 0.00 0.00 0.00 4.83
4007 4726 0.314302 AGAGCGACGTGTACAGCTTT 59.686 50.000 8.56 0.98 40.39 3.51
4010 4729 1.219522 GCGACGTGTACAGCTTTGGT 61.220 55.000 0.00 0.00 0.00 3.67
4175 4894 2.741092 GACACGCAGGTCCAGGAA 59.259 61.111 0.00 0.00 0.00 3.36
4497 5246 1.730121 GCAGTGCGATGTTGACAATGG 60.730 52.381 0.00 0.00 30.51 3.16
4514 5263 7.001674 TGACAATGGAACCTTGTGTACTTTAT 58.998 34.615 11.27 0.00 36.98 1.40
4515 5264 7.504238 TGACAATGGAACCTTGTGTACTTTATT 59.496 33.333 11.27 0.00 36.98 1.40
4516 5265 8.927675 ACAATGGAACCTTGTGTACTTTATTA 57.072 30.769 0.00 0.00 35.57 0.98
4517 5266 9.528489 ACAATGGAACCTTGTGTACTTTATTAT 57.472 29.630 0.00 0.00 35.57 1.28
4630 5391 5.205056 TGGGTACAAATGTTGTTTCCTTCT 58.795 37.500 0.00 0.00 42.22 2.85
4632 5393 4.982295 GGTACAAATGTTGTTTCCTTCTGC 59.018 41.667 0.00 0.00 42.22 4.26
4660 5421 7.989741 GGGATTTAGTGATCATAGGATACCATG 59.010 40.741 0.00 0.00 32.67 3.66
4837 5634 2.099098 GGTCCAACACTGGTTTGTTCTG 59.901 50.000 0.00 0.00 43.97 3.02
4846 5643 5.156355 CACTGGTTTGTTCTGCATTACATC 58.844 41.667 2.31 0.60 0.00 3.06
4847 5644 4.826733 ACTGGTTTGTTCTGCATTACATCA 59.173 37.500 2.31 2.28 0.00 3.07
4848 5645 5.048504 ACTGGTTTGTTCTGCATTACATCAG 60.049 40.000 16.23 16.23 0.00 2.90
4849 5646 4.168760 GGTTTGTTCTGCATTACATCAGC 58.831 43.478 2.31 0.00 0.00 4.26
4850 5647 4.168760 GTTTGTTCTGCATTACATCAGCC 58.831 43.478 2.31 0.00 0.00 4.85
4851 5648 3.070476 TGTTCTGCATTACATCAGCCA 57.930 42.857 0.00 0.00 0.00 4.75
4852 5649 3.011818 TGTTCTGCATTACATCAGCCAG 58.988 45.455 0.00 0.00 0.00 4.85
4853 5650 3.273434 GTTCTGCATTACATCAGCCAGA 58.727 45.455 0.00 0.00 0.00 3.86
4854 5651 3.851458 TCTGCATTACATCAGCCAGAT 57.149 42.857 0.00 0.00 37.48 2.90
4862 5659 2.131405 ATCAGCCAGATGGACGAGG 58.869 57.895 2.18 0.00 35.06 4.63
4863 5660 0.397675 ATCAGCCAGATGGACGAGGA 60.398 55.000 2.18 0.00 35.06 3.71
4864 5661 0.397675 TCAGCCAGATGGACGAGGAT 60.398 55.000 2.18 0.00 37.39 3.24
4865 5662 0.033228 CAGCCAGATGGACGAGGATC 59.967 60.000 2.18 0.00 37.39 3.36
4866 5663 1.118356 AGCCAGATGGACGAGGATCC 61.118 60.000 2.48 2.48 39.45 3.36
4867 5664 2.053618 CCAGATGGACGAGGATCCC 58.946 63.158 8.55 0.00 38.06 3.85
4868 5665 1.476007 CCAGATGGACGAGGATCCCC 61.476 65.000 8.55 2.57 38.06 4.81
4869 5666 3.856539 CCAGATGGACGAGGATCCCCT 62.857 61.905 8.55 0.00 41.28 4.79
4870 5667 0.470833 AGATGGACGAGGATCCCCTG 60.471 60.000 8.55 0.45 44.53 4.45
4871 5668 2.105806 GATGGACGAGGATCCCCTGC 62.106 65.000 8.55 0.00 44.53 4.85
4872 5669 2.444895 GGACGAGGATCCCCTGCT 60.445 66.667 8.55 0.00 44.53 4.24
4873 5670 2.801631 GGACGAGGATCCCCTGCTG 61.802 68.421 8.55 0.00 44.53 4.41
4874 5671 2.039624 ACGAGGATCCCCTGCTGT 59.960 61.111 8.55 0.00 44.53 4.40
4875 5672 2.303549 GACGAGGATCCCCTGCTGTG 62.304 65.000 8.55 0.00 44.53 3.66
4876 5673 2.191641 GAGGATCCCCTGCTGTGC 59.808 66.667 8.55 0.00 44.53 4.57
4877 5674 3.412624 GAGGATCCCCTGCTGTGCC 62.413 68.421 8.55 0.00 44.53 5.01
4878 5675 4.512914 GGATCCCCTGCTGTGCCC 62.513 72.222 0.00 0.00 0.00 5.36
4879 5676 4.512914 GATCCCCTGCTGTGCCCC 62.513 72.222 0.00 0.00 0.00 5.80
4888 5685 3.011517 CTGTGCCCCAGCCTACCT 61.012 66.667 0.00 0.00 38.69 3.08
4889 5686 2.531685 TGTGCCCCAGCCTACCTT 60.532 61.111 0.00 0.00 38.69 3.50
4890 5687 2.142292 CTGTGCCCCAGCCTACCTTT 62.142 60.000 0.00 0.00 38.69 3.11
4891 5688 1.678970 GTGCCCCAGCCTACCTTTG 60.679 63.158 0.00 0.00 38.69 2.77
4892 5689 1.850289 TGCCCCAGCCTACCTTTGA 60.850 57.895 0.00 0.00 38.69 2.69
4893 5690 1.077429 GCCCCAGCCTACCTTTGAG 60.077 63.158 0.00 0.00 0.00 3.02
4894 5691 1.853250 GCCCCAGCCTACCTTTGAGT 61.853 60.000 0.00 0.00 0.00 3.41
4895 5692 0.253327 CCCCAGCCTACCTTTGAGTC 59.747 60.000 0.00 0.00 0.00 3.36
4896 5693 0.984230 CCCAGCCTACCTTTGAGTCA 59.016 55.000 0.00 0.00 0.00 3.41
4897 5694 1.339151 CCCAGCCTACCTTTGAGTCAC 60.339 57.143 0.00 0.00 0.00 3.67
4898 5695 1.625818 CCAGCCTACCTTTGAGTCACT 59.374 52.381 0.00 0.00 0.00 3.41
4899 5696 2.613977 CCAGCCTACCTTTGAGTCACTG 60.614 54.545 0.00 0.00 0.00 3.66
4900 5697 2.300152 CAGCCTACCTTTGAGTCACTGA 59.700 50.000 0.00 0.00 0.00 3.41
4901 5698 2.300437 AGCCTACCTTTGAGTCACTGAC 59.700 50.000 0.38 0.38 0.00 3.51
4902 5699 2.037251 GCCTACCTTTGAGTCACTGACA 59.963 50.000 11.80 0.00 34.60 3.58
4903 5700 3.654414 CCTACCTTTGAGTCACTGACAC 58.346 50.000 11.80 5.84 34.60 3.67
4904 5701 3.069586 CCTACCTTTGAGTCACTGACACA 59.930 47.826 11.80 8.49 34.60 3.72
4905 5702 3.845781 ACCTTTGAGTCACTGACACAT 57.154 42.857 11.80 0.00 33.67 3.21
4906 5703 3.470709 ACCTTTGAGTCACTGACACATG 58.529 45.455 11.80 7.34 33.67 3.21
4907 5704 2.810274 CCTTTGAGTCACTGACACATGG 59.190 50.000 11.80 11.74 33.67 3.66
4908 5705 2.549064 TTGAGTCACTGACACATGGG 57.451 50.000 11.80 0.00 33.67 4.00
4909 5706 1.423584 TGAGTCACTGACACATGGGT 58.576 50.000 0.00 0.00 34.60 4.51
4910 5707 1.344438 TGAGTCACTGACACATGGGTC 59.656 52.381 21.62 21.62 38.29 4.46
4911 5708 0.687354 AGTCACTGACACATGGGTCC 59.313 55.000 25.06 9.33 36.97 4.46
4912 5709 0.321653 GTCACTGACACATGGGTCCC 60.322 60.000 25.06 0.00 36.97 4.46
4913 5710 0.766288 TCACTGACACATGGGTCCCA 60.766 55.000 25.06 14.64 36.97 4.37
4914 5711 0.606401 CACTGACACATGGGTCCCAC 60.606 60.000 25.06 1.17 35.80 4.61
4915 5712 1.059584 ACTGACACATGGGTCCCACA 61.060 55.000 25.06 6.33 35.80 4.17
4916 5713 0.321919 CTGACACATGGGTCCCACAG 60.322 60.000 25.06 12.57 35.80 3.66
4917 5714 0.766288 TGACACATGGGTCCCACAGA 60.766 55.000 25.06 2.26 35.80 3.41
4918 5715 0.036010 GACACATGGGTCCCACAGAG 60.036 60.000 17.79 10.30 35.80 3.35
4919 5716 1.377725 CACATGGGTCCCACAGAGC 60.378 63.158 14.57 0.00 42.55 4.09
4920 5717 1.847506 ACATGGGTCCCACAGAGCA 60.848 57.895 14.57 0.00 45.21 4.26
4921 5718 1.210204 ACATGGGTCCCACAGAGCAT 61.210 55.000 14.57 0.00 45.21 3.79
4922 5719 0.750546 CATGGGTCCCACAGAGCATG 60.751 60.000 14.57 1.23 45.21 4.06
4923 5720 1.929860 ATGGGTCCCACAGAGCATGG 61.930 60.000 14.57 0.00 45.21 3.66
4929 5726 4.051167 CACAGAGCATGGGGCCCA 62.051 66.667 30.97 30.97 46.50 5.36
4930 5727 4.052518 ACAGAGCATGGGGCCCAC 62.053 66.667 31.54 17.27 46.50 4.61
4931 5728 4.828296 CAGAGCATGGGGCCCACC 62.828 72.222 31.54 22.16 46.50 4.61
4933 5730 4.828296 GAGCATGGGGCCCACCTG 62.828 72.222 31.54 24.79 46.50 4.00
4936 5733 3.660571 CATGGGGCCCACCTGTCA 61.661 66.667 31.54 11.89 35.80 3.58
4937 5734 3.341629 ATGGGGCCCACCTGTCAG 61.342 66.667 31.54 0.00 35.80 3.51
4938 5735 4.918360 TGGGGCCCACCTGTCAGT 62.918 66.667 24.76 0.00 40.03 3.41
4939 5736 4.351054 GGGGCCCACCTGTCAGTG 62.351 72.222 26.86 0.00 40.03 3.66
4946 5743 3.402186 CACCTGTCAGTGGCTCAAA 57.598 52.632 0.00 0.00 33.95 2.69
4947 5744 1.233019 CACCTGTCAGTGGCTCAAAG 58.767 55.000 0.00 0.00 33.95 2.77
4948 5745 0.109342 ACCTGTCAGTGGCTCAAAGG 59.891 55.000 0.00 0.00 0.00 3.11
4949 5746 1.239968 CCTGTCAGTGGCTCAAAGGC 61.240 60.000 0.00 0.00 41.77 4.35
4955 5752 3.914645 TGGCTCAAAGGCAGGGTA 58.085 55.556 0.00 0.00 46.47 3.69
4956 5753 2.397815 TGGCTCAAAGGCAGGGTAT 58.602 52.632 0.00 0.00 46.47 2.73
4957 5754 1.590591 TGGCTCAAAGGCAGGGTATA 58.409 50.000 0.00 0.00 46.47 1.47
4958 5755 1.490490 TGGCTCAAAGGCAGGGTATAG 59.510 52.381 0.00 0.00 46.47 1.31
4959 5756 1.598882 GCTCAAAGGCAGGGTATAGC 58.401 55.000 0.00 0.00 0.00 2.97
4960 5757 1.134098 GCTCAAAGGCAGGGTATAGCA 60.134 52.381 4.02 0.00 0.00 3.49
4961 5758 2.843701 CTCAAAGGCAGGGTATAGCAG 58.156 52.381 4.02 0.00 0.00 4.24
4962 5759 1.490490 TCAAAGGCAGGGTATAGCAGG 59.510 52.381 4.02 0.00 0.00 4.85
4963 5760 0.846693 AAAGGCAGGGTATAGCAGGG 59.153 55.000 4.02 0.00 0.00 4.45
4964 5761 0.030092 AAGGCAGGGTATAGCAGGGA 60.030 55.000 4.02 0.00 0.00 4.20
4965 5762 0.194587 AGGCAGGGTATAGCAGGGAT 59.805 55.000 4.02 0.00 0.00 3.85
4966 5763 1.068121 GGCAGGGTATAGCAGGGATT 58.932 55.000 4.02 0.00 0.00 3.01
4967 5764 1.271597 GGCAGGGTATAGCAGGGATTG 60.272 57.143 4.02 0.00 0.00 2.67
4975 5772 4.301505 GCAGGGATTGCGAAGTCA 57.698 55.556 0.00 0.00 44.09 3.41
4976 5773 2.093216 GCAGGGATTGCGAAGTCAG 58.907 57.895 0.00 0.00 44.09 3.51
4977 5774 0.391661 GCAGGGATTGCGAAGTCAGA 60.392 55.000 0.00 0.00 44.09 3.27
4978 5775 1.649664 CAGGGATTGCGAAGTCAGAG 58.350 55.000 0.00 0.00 0.00 3.35
4979 5776 0.539051 AGGGATTGCGAAGTCAGAGG 59.461 55.000 0.00 0.00 0.00 3.69
4980 5777 0.537188 GGGATTGCGAAGTCAGAGGA 59.463 55.000 0.00 0.00 0.00 3.71
4981 5778 1.139853 GGGATTGCGAAGTCAGAGGAT 59.860 52.381 0.00 0.00 0.00 3.24
4982 5779 2.478831 GGATTGCGAAGTCAGAGGATC 58.521 52.381 0.00 0.00 0.00 3.36
4983 5780 2.478831 GATTGCGAAGTCAGAGGATCC 58.521 52.381 2.48 2.48 33.66 3.36
4984 5781 1.266178 TTGCGAAGTCAGAGGATCCA 58.734 50.000 15.82 0.00 33.66 3.41
4985 5782 1.489481 TGCGAAGTCAGAGGATCCAT 58.511 50.000 15.82 0.00 33.66 3.41
4986 5783 1.137675 TGCGAAGTCAGAGGATCCATG 59.862 52.381 15.82 12.51 33.66 3.66
4987 5784 1.137872 GCGAAGTCAGAGGATCCATGT 59.862 52.381 15.82 0.00 33.66 3.21
4988 5785 2.801342 GCGAAGTCAGAGGATCCATGTC 60.801 54.545 15.82 10.03 33.66 3.06
4989 5786 2.223923 CGAAGTCAGAGGATCCATGTCC 60.224 54.545 15.82 7.71 38.62 4.02
5017 5814 5.505654 CCAGATGCGTTTTTAGAAGTTGTGT 60.506 40.000 0.00 0.00 0.00 3.72
5038 5835 6.945435 TGTGTATCAGTTTGTACAAATGGGAT 59.055 34.615 23.11 23.44 33.05 3.85
5047 5844 5.999205 TGTACAAATGGGATCTGCATTTT 57.001 34.783 0.00 0.00 0.00 1.82
5065 5862 7.669427 TGCATTTTTGGATTGAACTGTCTAAT 58.331 30.769 0.00 0.00 0.00 1.73
5067 5864 9.638239 GCATTTTTGGATTGAACTGTCTAATTA 57.362 29.630 0.00 0.00 0.00 1.40
5076 5873 7.391148 TTGAACTGTCTAATTAATCAAGCCC 57.609 36.000 0.00 0.00 0.00 5.19
5101 5898 8.494433 CCTTATAGGCTAGCAATATGGGATAAA 58.506 37.037 18.24 3.88 0.00 1.40
5114 5911 4.634012 TGGGATAAAAGATGATACCCCG 57.366 45.455 0.00 0.00 35.42 5.73
5142 5939 5.365403 TGTTGCGGTAATCCTGTTAAAAG 57.635 39.130 0.00 0.00 0.00 2.27
5225 6022 8.421784 AGTATTCTCAGTCGGATTTGCTAATTA 58.578 33.333 0.00 0.00 0.00 1.40
5228 6025 6.816136 TCTCAGTCGGATTTGCTAATTATCA 58.184 36.000 0.00 0.00 0.00 2.15
5229 6026 7.445121 TCTCAGTCGGATTTGCTAATTATCAT 58.555 34.615 0.00 0.00 0.00 2.45
5230 6027 7.600375 TCTCAGTCGGATTTGCTAATTATCATC 59.400 37.037 0.00 0.00 0.00 2.92
5231 6028 7.445121 TCAGTCGGATTTGCTAATTATCATCT 58.555 34.615 0.00 0.00 0.00 2.90
5232 6029 7.386025 TCAGTCGGATTTGCTAATTATCATCTG 59.614 37.037 0.00 1.48 0.00 2.90
5233 6030 6.652481 AGTCGGATTTGCTAATTATCATCTGG 59.348 38.462 0.00 0.00 0.00 3.86
5234 6031 6.650807 GTCGGATTTGCTAATTATCATCTGGA 59.349 38.462 0.00 0.00 0.00 3.86
5235 6032 7.335422 GTCGGATTTGCTAATTATCATCTGGAT 59.665 37.037 0.00 0.00 40.14 3.41
5236 6033 8.539544 TCGGATTTGCTAATTATCATCTGGATA 58.460 33.333 0.00 0.00 37.44 2.59
5263 6060 8.261522 AGGATTAACAAAGTCTCATCTAACTCC 58.738 37.037 0.00 0.00 0.00 3.85
5273 6070 6.670027 AGTCTCATCTAACTCCTACACCAATT 59.330 38.462 0.00 0.00 0.00 2.32
5274 6071 6.758886 GTCTCATCTAACTCCTACACCAATTG 59.241 42.308 0.00 0.00 0.00 2.32
5275 6072 6.667848 TCTCATCTAACTCCTACACCAATTGA 59.332 38.462 7.12 0.00 0.00 2.57
5276 6073 7.345653 TCTCATCTAACTCCTACACCAATTGAT 59.654 37.037 7.12 0.00 0.00 2.57
5277 6074 7.861629 TCATCTAACTCCTACACCAATTGATT 58.138 34.615 7.12 0.00 0.00 2.57
5278 6075 8.988060 TCATCTAACTCCTACACCAATTGATTA 58.012 33.333 7.12 0.00 0.00 1.75
5279 6076 9.613428 CATCTAACTCCTACACCAATTGATTAA 57.387 33.333 7.12 0.00 0.00 1.40
5285 6082 9.614792 ACTCCTACACCAATTGATTAATAGAAC 57.385 33.333 7.12 0.00 0.00 3.01
5286 6083 9.613428 CTCCTACACCAATTGATTAATAGAACA 57.387 33.333 7.12 0.00 0.00 3.18
5287 6084 9.967451 TCCTACACCAATTGATTAATAGAACAA 57.033 29.630 7.12 0.00 0.00 2.83
5322 6119 3.508744 AAAATCCACATGAATCACCGC 57.491 42.857 0.00 0.00 0.00 5.68
5323 6120 1.016627 AATCCACATGAATCACCGCG 58.983 50.000 0.00 0.00 0.00 6.46
5324 6121 0.107703 ATCCACATGAATCACCGCGT 60.108 50.000 4.92 0.00 0.00 6.01
5325 6122 0.533032 TCCACATGAATCACCGCGTA 59.467 50.000 4.92 0.00 0.00 4.42
5326 6123 1.066787 TCCACATGAATCACCGCGTAA 60.067 47.619 4.92 0.00 0.00 3.18
5327 6124 1.735018 CCACATGAATCACCGCGTAAA 59.265 47.619 4.92 0.00 0.00 2.01
5328 6125 2.160615 CCACATGAATCACCGCGTAAAA 59.839 45.455 4.92 0.00 0.00 1.52
5329 6126 3.181501 CCACATGAATCACCGCGTAAAAT 60.182 43.478 4.92 0.00 0.00 1.82
5330 6127 4.028383 CACATGAATCACCGCGTAAAATC 58.972 43.478 4.92 0.00 0.00 2.17
5331 6128 3.687212 ACATGAATCACCGCGTAAAATCA 59.313 39.130 4.92 4.40 0.00 2.57
5332 6129 4.155099 ACATGAATCACCGCGTAAAATCAA 59.845 37.500 4.92 0.00 0.00 2.57
5333 6130 4.750952 TGAATCACCGCGTAAAATCAAA 57.249 36.364 4.92 0.00 0.00 2.69
5334 6131 5.303747 TGAATCACCGCGTAAAATCAAAT 57.696 34.783 4.92 0.00 0.00 2.32
5335 6132 5.092105 TGAATCACCGCGTAAAATCAAATG 58.908 37.500 4.92 0.00 0.00 2.32
5336 6133 3.479505 TCACCGCGTAAAATCAAATGG 57.520 42.857 4.92 0.00 0.00 3.16
5337 6134 2.814919 TCACCGCGTAAAATCAAATGGT 59.185 40.909 4.92 0.00 0.00 3.55
5338 6135 4.001652 TCACCGCGTAAAATCAAATGGTA 58.998 39.130 4.92 0.00 0.00 3.25
5339 6136 4.636648 TCACCGCGTAAAATCAAATGGTAT 59.363 37.500 4.92 0.00 0.00 2.73
5340 6137 5.816258 TCACCGCGTAAAATCAAATGGTATA 59.184 36.000 4.92 0.00 0.00 1.47
5341 6138 6.018588 TCACCGCGTAAAATCAAATGGTATAG 60.019 38.462 4.92 0.00 0.00 1.31
5342 6139 5.237779 ACCGCGTAAAATCAAATGGTATAGG 59.762 40.000 4.92 0.00 0.00 2.57
5343 6140 5.237779 CCGCGTAAAATCAAATGGTATAGGT 59.762 40.000 4.92 0.00 0.00 3.08
5344 6141 6.133392 CGCGTAAAATCAAATGGTATAGGTG 58.867 40.000 0.00 0.00 0.00 4.00
5345 6142 6.238266 CGCGTAAAATCAAATGGTATAGGTGT 60.238 38.462 0.00 0.00 0.00 4.16
5346 6143 7.477494 GCGTAAAATCAAATGGTATAGGTGTT 58.523 34.615 0.00 0.00 0.00 3.32
5347 6144 8.614346 GCGTAAAATCAAATGGTATAGGTGTTA 58.386 33.333 0.00 0.00 0.00 2.41
5389 6186 5.207110 TCATCTAAATGAGAGCTAGCCAC 57.793 43.478 12.13 6.24 36.98 5.01
5390 6187 4.651045 TCATCTAAATGAGAGCTAGCCACA 59.349 41.667 12.13 9.75 36.98 4.17
5391 6188 4.392921 TCTAAATGAGAGCTAGCCACAC 57.607 45.455 12.13 5.59 0.00 3.82
5392 6189 4.026744 TCTAAATGAGAGCTAGCCACACT 58.973 43.478 12.13 6.07 0.00 3.55
5393 6190 2.977772 AATGAGAGCTAGCCACACTC 57.022 50.000 12.13 15.00 0.00 3.51
5394 6191 1.857965 ATGAGAGCTAGCCACACTCA 58.142 50.000 23.42 23.42 40.88 3.41
5395 6192 1.857965 TGAGAGCTAGCCACACTCAT 58.142 50.000 19.92 0.00 33.57 2.90
5396 6193 2.182827 TGAGAGCTAGCCACACTCATT 58.817 47.619 19.92 0.00 33.57 2.57
5397 6194 2.167281 TGAGAGCTAGCCACACTCATTC 59.833 50.000 19.92 6.97 33.57 2.67
5398 6195 2.430332 GAGAGCTAGCCACACTCATTCT 59.570 50.000 12.13 3.90 32.71 2.40
5399 6196 3.634448 GAGAGCTAGCCACACTCATTCTA 59.366 47.826 12.13 0.00 32.71 2.10
5400 6197 4.222336 AGAGCTAGCCACACTCATTCTAT 58.778 43.478 12.13 0.00 32.71 1.98
5401 6198 5.389520 AGAGCTAGCCACACTCATTCTATA 58.610 41.667 12.13 0.00 32.71 1.31
5402 6199 5.242838 AGAGCTAGCCACACTCATTCTATAC 59.757 44.000 12.13 0.00 32.71 1.47
5403 6200 5.144100 AGCTAGCCACACTCATTCTATACT 58.856 41.667 12.13 0.00 0.00 2.12
5404 6201 5.600484 AGCTAGCCACACTCATTCTATACTT 59.400 40.000 12.13 0.00 0.00 2.24
5405 6202 6.778069 AGCTAGCCACACTCATTCTATACTTA 59.222 38.462 12.13 0.00 0.00 2.24
5406 6203 6.864165 GCTAGCCACACTCATTCTATACTTAC 59.136 42.308 2.29 0.00 0.00 2.34
5407 6204 6.791867 AGCCACACTCATTCTATACTTACA 57.208 37.500 0.00 0.00 0.00 2.41
5408 6205 6.574350 AGCCACACTCATTCTATACTTACAC 58.426 40.000 0.00 0.00 0.00 2.90
5409 6206 6.381420 AGCCACACTCATTCTATACTTACACT 59.619 38.462 0.00 0.00 0.00 3.55
5410 6207 7.042335 GCCACACTCATTCTATACTTACACTT 58.958 38.462 0.00 0.00 0.00 3.16
5411 6208 7.549488 GCCACACTCATTCTATACTTACACTTT 59.451 37.037 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 6.147864 TGCAGCAGTAACAAAAAGATTCTT 57.852 33.333 0.00 0.00 0.00 2.52
69 70 7.589958 ATTAGACAAGGAGATACTACCACTG 57.410 40.000 0.00 0.00 0.00 3.66
92 93 9.927081 ATTCCTACACAAAGATTGGAGATTAAT 57.073 29.630 0.00 0.00 34.12 1.40
116 117 8.836735 TCTCCCTATTTAAGTCTCCAAGAAATT 58.163 33.333 0.00 0.00 0.00 1.82
184 187 7.382218 CCACAGTCCAACAGTTTGAAATAAATC 59.618 37.037 0.00 0.00 34.24 2.17
220 223 3.348119 CAGTGCTAGTAGTGAGACCTGA 58.652 50.000 9.89 0.00 0.00 3.86
298 301 7.771826 GCCTGTAACTTGGATTGGTTACTATTA 59.228 37.037 14.25 0.00 44.46 0.98
300 303 6.069615 AGCCTGTAACTTGGATTGGTTACTAT 60.070 38.462 14.25 0.15 44.46 2.12
408 998 2.487372 GCAGCCAGGAGAAAGAAAAGAG 59.513 50.000 0.00 0.00 0.00 2.85
480 1076 2.621055 ACCAACGTCTAATTGCTTTGCA 59.379 40.909 0.00 0.00 36.47 4.08
533 1129 1.541169 ACCCATTGGTGGTTGAGCA 59.459 52.632 1.20 0.00 45.58 4.26
534 1130 4.519610 ACCCATTGGTGGTTGAGC 57.480 55.556 1.20 0.00 45.58 4.26
608 1204 0.260230 CTCTCCTCTGGCCTCTACCA 59.740 60.000 3.32 0.00 38.29 3.25
609 1205 0.260523 ACTCTCCTCTGGCCTCTACC 59.739 60.000 3.32 0.00 0.00 3.18
612 1208 1.003646 TGTACTCTCCTCTGGCCTCT 58.996 55.000 3.32 0.00 0.00 3.69
613 1209 1.960689 GATGTACTCTCCTCTGGCCTC 59.039 57.143 3.32 0.00 0.00 4.70
614 1210 1.573376 AGATGTACTCTCCTCTGGCCT 59.427 52.381 3.32 0.00 0.00 5.19
615 1211 1.686052 CAGATGTACTCTCCTCTGGCC 59.314 57.143 0.00 0.00 33.15 5.36
616 1212 2.660572 TCAGATGTACTCTCCTCTGGC 58.339 52.381 0.00 0.00 36.59 4.85
617 1213 4.019858 TGTTCAGATGTACTCTCCTCTGG 58.980 47.826 0.00 0.00 36.59 3.86
618 1214 5.651387 TTGTTCAGATGTACTCTCCTCTG 57.349 43.478 0.00 0.00 37.14 3.35
619 1215 6.865834 AATTGTTCAGATGTACTCTCCTCT 57.134 37.500 0.00 0.00 29.16 3.69
620 1216 6.536941 GGAAATTGTTCAGATGTACTCTCCTC 59.463 42.308 0.00 0.00 35.25 3.71
621 1217 6.214412 AGGAAATTGTTCAGATGTACTCTCCT 59.786 38.462 0.00 0.00 35.25 3.69
622 1218 6.410540 AGGAAATTGTTCAGATGTACTCTCC 58.589 40.000 0.00 0.00 35.25 3.71
623 1219 7.708752 CCTAGGAAATTGTTCAGATGTACTCTC 59.291 40.741 1.05 0.00 35.25 3.20
771 1388 0.923358 GAGTGAGAGAGAGGGGAGGA 59.077 60.000 0.00 0.00 0.00 3.71
839 1469 3.002759 GCTTATGTTGCAAGCCTAGTAGC 59.997 47.826 0.00 0.00 42.08 3.58
842 1472 3.071874 TGCTTATGTTGCAAGCCTAGT 57.928 42.857 0.00 0.00 46.32 2.57
901 1531 4.569966 CAGCAGCTAACTCTACAGAATTGG 59.430 45.833 0.00 0.00 0.00 3.16
923 1553 2.567169 ACATGAGTACAAGGTAGCAGCA 59.433 45.455 0.00 0.00 0.00 4.41
927 1557 4.093556 GCAAGAACATGAGTACAAGGTAGC 59.906 45.833 0.00 0.00 0.00 3.58
955 1585 4.242475 CATGCAACTACCGAAGTACAAGA 58.758 43.478 0.00 0.00 37.50 3.02
1537 2179 1.409427 GCCTAGCTGGTTGTCGTAGAT 59.591 52.381 0.00 0.00 37.14 1.98
1665 2307 2.187946 CCGACCATGGTGAGCCTC 59.812 66.667 25.52 5.40 35.27 4.70
2256 2898 0.741221 GAGCATTGGTCGACAGGTCC 60.741 60.000 18.91 0.00 0.00 4.46
2619 3261 2.254152 TGGCATTGTAGGAGAGGTCT 57.746 50.000 0.00 0.00 0.00 3.85
2675 3317 4.756642 TGAGAATGAGCTTTGTCAACGAAT 59.243 37.500 0.00 0.00 0.00 3.34
2730 3372 2.485795 GGAGCACGAGCCGATCTCT 61.486 63.158 0.00 0.00 43.56 3.10
2751 3393 1.745864 GACGTCGAGGAGCTGGAGA 60.746 63.158 12.85 0.00 0.00 3.71
2841 3483 1.669115 GAAGCGGTTGCAGCTGAGA 60.669 57.895 20.43 0.77 45.31 3.27
2854 3496 2.656651 CATCGAGCCGGAGAAGCG 60.657 66.667 5.05 0.00 34.64 4.68
3042 3684 4.052229 CCCTCGACGTCGCTGGTT 62.052 66.667 32.02 0.00 39.60 3.67
3183 3825 3.575351 GAACAGGACGAGCACCGCT 62.575 63.158 0.00 0.00 43.88 5.52
3498 4158 2.268920 GACGCCCATCCAAGCAGA 59.731 61.111 0.00 0.00 0.00 4.26
3531 4191 3.469739 GAGGTAGTCGTAGAAGAGGAGG 58.530 54.545 0.00 0.00 39.69 4.30
3910 4574 8.483307 TGTTAATCCGGTAGTTCATCTTTTAC 57.517 34.615 0.00 0.00 0.00 2.01
3965 4684 2.557924 GGTTGTGATCTTGGTCATGCAA 59.442 45.455 0.00 0.00 0.00 4.08
4007 4726 3.480679 CTCCAGCAGCACCACACCA 62.481 63.158 0.00 0.00 0.00 4.17
4010 4729 1.002990 CATCTCCAGCAGCACCACA 60.003 57.895 0.00 0.00 0.00 4.17
4175 4894 2.753043 CCGAGGGCTTGCAGCATT 60.753 61.111 0.00 0.00 44.75 3.56
4497 5246 9.117183 CCCCTAATAATAAAGTACACAAGGTTC 57.883 37.037 0.00 0.00 0.00 3.62
4514 5263 7.293062 ACATAATTTCTACGGGTCCCCTAATAA 59.707 37.037 1.00 0.00 0.00 1.40
4515 5264 6.788957 ACATAATTTCTACGGGTCCCCTAATA 59.211 38.462 1.00 0.00 0.00 0.98
4516 5265 5.609708 ACATAATTTCTACGGGTCCCCTAAT 59.390 40.000 1.00 0.00 0.00 1.73
4517 5266 4.970640 ACATAATTTCTACGGGTCCCCTAA 59.029 41.667 1.00 0.00 0.00 2.69
4518 5267 4.559726 ACATAATTTCTACGGGTCCCCTA 58.440 43.478 1.00 0.00 0.00 3.53
4519 5268 3.390819 ACATAATTTCTACGGGTCCCCT 58.609 45.455 1.00 0.00 0.00 4.79
4630 5391 4.907269 TCCTATGATCACTAAATCCCTGCA 59.093 41.667 0.00 0.00 0.00 4.41
4632 5393 7.180946 TGGTATCCTATGATCACTAAATCCCTG 59.819 40.741 0.00 0.00 32.18 4.45
4660 5421 0.755686 CCCTGCTGGACCATCTAGAC 59.244 60.000 11.88 0.00 35.39 2.59
4781 5542 3.057946 GTGCTCCCTTTGACAAACATCTC 60.058 47.826 0.00 0.00 0.00 2.75
4846 5643 0.033228 GATCCTCGTCCATCTGGCTG 59.967 60.000 0.00 0.00 34.44 4.85
4847 5644 1.118356 GGATCCTCGTCCATCTGGCT 61.118 60.000 3.84 0.00 38.20 4.75
4848 5645 1.369321 GGATCCTCGTCCATCTGGC 59.631 63.158 3.84 0.00 38.20 4.85
4849 5646 1.476007 GGGGATCCTCGTCCATCTGG 61.476 65.000 12.58 0.00 40.17 3.86
4850 5647 0.470833 AGGGGATCCTCGTCCATCTG 60.471 60.000 12.58 0.00 39.80 2.90
4851 5648 0.470833 CAGGGGATCCTCGTCCATCT 60.471 60.000 12.58 0.00 42.67 2.90
4852 5649 2.053618 CAGGGGATCCTCGTCCATC 58.946 63.158 12.58 0.00 42.67 3.51
4853 5650 2.143419 GCAGGGGATCCTCGTCCAT 61.143 63.158 12.58 0.00 42.67 3.41
4854 5651 2.764128 GCAGGGGATCCTCGTCCA 60.764 66.667 12.58 0.00 42.67 4.02
4855 5652 2.444895 AGCAGGGGATCCTCGTCC 60.445 66.667 12.58 3.97 42.67 4.79
4856 5653 2.060980 ACAGCAGGGGATCCTCGTC 61.061 63.158 12.58 4.80 42.67 4.20
4857 5654 2.039624 ACAGCAGGGGATCCTCGT 59.960 61.111 12.58 0.00 42.67 4.18
4858 5655 2.503061 CACAGCAGGGGATCCTCG 59.497 66.667 12.58 5.37 42.67 4.63
4859 5656 2.191641 GCACAGCAGGGGATCCTC 59.808 66.667 12.58 7.90 42.67 3.71
4860 5657 3.415087 GGCACAGCAGGGGATCCT 61.415 66.667 12.58 0.00 46.26 3.24
4861 5658 4.512914 GGGCACAGCAGGGGATCC 62.513 72.222 1.92 1.92 0.00 3.36
4862 5659 4.512914 GGGGCACAGCAGGGGATC 62.513 72.222 0.00 0.00 0.00 3.36
4872 5669 2.160171 AAAGGTAGGCTGGGGCACA 61.160 57.895 0.00 0.00 40.87 4.57
4873 5670 1.678970 CAAAGGTAGGCTGGGGCAC 60.679 63.158 0.00 0.00 40.87 5.01
4874 5671 1.850289 TCAAAGGTAGGCTGGGGCA 60.850 57.895 0.00 0.00 40.87 5.36
4875 5672 1.077429 CTCAAAGGTAGGCTGGGGC 60.077 63.158 0.00 0.00 37.82 5.80
4876 5673 0.253327 GACTCAAAGGTAGGCTGGGG 59.747 60.000 0.00 0.00 0.00 4.96
4877 5674 0.984230 TGACTCAAAGGTAGGCTGGG 59.016 55.000 0.00 0.00 0.00 4.45
4878 5675 1.625818 AGTGACTCAAAGGTAGGCTGG 59.374 52.381 0.00 0.00 0.00 4.85
4879 5676 2.300152 TCAGTGACTCAAAGGTAGGCTG 59.700 50.000 0.00 0.00 0.00 4.85
4880 5677 2.300437 GTCAGTGACTCAAAGGTAGGCT 59.700 50.000 16.26 0.00 0.00 4.58
4881 5678 2.037251 TGTCAGTGACTCAAAGGTAGGC 59.963 50.000 23.29 0.00 33.15 3.93
4882 5679 3.069586 TGTGTCAGTGACTCAAAGGTAGG 59.930 47.826 22.30 0.00 33.95 3.18
4883 5680 4.322080 TGTGTCAGTGACTCAAAGGTAG 57.678 45.455 22.30 0.00 33.95 3.18
4884 5681 4.503123 CCATGTGTCAGTGACTCAAAGGTA 60.503 45.833 26.67 7.51 39.05 3.08
4885 5682 3.470709 CATGTGTCAGTGACTCAAAGGT 58.529 45.455 26.67 11.61 39.05 3.50
4886 5683 2.810274 CCATGTGTCAGTGACTCAAAGG 59.190 50.000 26.67 25.08 39.05 3.11
4887 5684 2.810274 CCCATGTGTCAGTGACTCAAAG 59.190 50.000 26.67 21.50 39.05 2.77
4888 5685 2.172505 ACCCATGTGTCAGTGACTCAAA 59.827 45.455 26.67 9.46 39.05 2.69
4889 5686 1.768275 ACCCATGTGTCAGTGACTCAA 59.232 47.619 26.67 12.54 39.05 3.02
4890 5687 1.344438 GACCCATGTGTCAGTGACTCA 59.656 52.381 25.52 25.52 39.71 3.41
4891 5688 1.338200 GGACCCATGTGTCAGTGACTC 60.338 57.143 23.29 19.84 36.97 3.36
4892 5689 0.687354 GGACCCATGTGTCAGTGACT 59.313 55.000 23.29 1.59 36.97 3.41
4893 5690 0.321653 GGGACCCATGTGTCAGTGAC 60.322 60.000 16.68 16.68 36.97 3.67
4894 5691 0.766288 TGGGACCCATGTGTCAGTGA 60.766 55.000 9.95 0.00 36.97 3.41
4895 5692 0.606401 GTGGGACCCATGTGTCAGTG 60.606 60.000 18.51 0.00 35.28 3.66
4896 5693 1.059584 TGTGGGACCCATGTGTCAGT 61.060 55.000 18.51 0.00 35.28 3.41
4897 5694 0.321919 CTGTGGGACCCATGTGTCAG 60.322 60.000 18.51 14.85 35.28 3.51
4898 5695 0.766288 TCTGTGGGACCCATGTGTCA 60.766 55.000 18.51 8.62 35.28 3.58
4899 5696 0.036010 CTCTGTGGGACCCATGTGTC 60.036 60.000 18.51 3.49 35.28 3.67
4900 5697 2.069776 CTCTGTGGGACCCATGTGT 58.930 57.895 18.51 0.00 35.28 3.72
4901 5698 1.377725 GCTCTGTGGGACCCATGTG 60.378 63.158 18.51 14.22 35.28 3.21
4902 5699 1.210204 ATGCTCTGTGGGACCCATGT 61.210 55.000 18.51 0.00 35.28 3.21
4903 5700 0.750546 CATGCTCTGTGGGACCCATG 60.751 60.000 18.51 13.14 35.28 3.66
4904 5701 1.611419 CATGCTCTGTGGGACCCAT 59.389 57.895 18.51 0.00 35.28 4.00
4905 5702 2.605607 CCATGCTCTGTGGGACCCA 61.606 63.158 9.95 9.95 32.98 4.51
4906 5703 2.273449 CCATGCTCTGTGGGACCC 59.727 66.667 2.45 2.45 32.98 4.46
4911 5708 4.828296 GGGCCCCATGCTCTGTGG 62.828 72.222 12.23 0.00 37.53 4.17
4912 5709 4.051167 TGGGCCCCATGCTCTGTG 62.051 66.667 22.27 0.00 42.79 3.66
4913 5710 4.052518 GTGGGCCCCATGCTCTGT 62.053 66.667 22.27 0.00 42.79 3.41
4914 5711 4.828296 GGTGGGCCCCATGCTCTG 62.828 72.222 22.27 0.00 42.79 3.35
4916 5713 4.828296 CAGGTGGGCCCCATGCTC 62.828 72.222 22.27 1.93 42.61 4.26
4919 5716 3.650298 CTGACAGGTGGGCCCCATG 62.650 68.421 22.27 20.55 35.28 3.66
4920 5717 3.341629 CTGACAGGTGGGCCCCAT 61.342 66.667 22.27 5.27 35.28 4.00
4921 5718 4.918360 ACTGACAGGTGGGCCCCA 62.918 66.667 22.27 7.77 34.57 4.96
4922 5719 4.351054 CACTGACAGGTGGGCCCC 62.351 72.222 22.27 10.91 33.95 5.80
4928 5725 1.233019 CTTTGAGCCACTGACAGGTG 58.767 55.000 7.51 2.99 37.00 4.00
4929 5726 0.109342 CCTTTGAGCCACTGACAGGT 59.891 55.000 7.51 0.00 0.00 4.00
4930 5727 1.239968 GCCTTTGAGCCACTGACAGG 61.240 60.000 7.51 0.00 0.00 4.00
4931 5728 0.535780 TGCCTTTGAGCCACTGACAG 60.536 55.000 0.00 0.00 0.00 3.51
4932 5729 0.535780 CTGCCTTTGAGCCACTGACA 60.536 55.000 0.00 0.00 0.00 3.58
4933 5730 1.239968 CCTGCCTTTGAGCCACTGAC 61.240 60.000 0.00 0.00 0.00 3.51
4934 5731 1.073722 CCTGCCTTTGAGCCACTGA 59.926 57.895 0.00 0.00 0.00 3.41
4935 5732 1.975407 CCCTGCCTTTGAGCCACTG 60.975 63.158 0.00 0.00 0.00 3.66
4936 5733 1.133809 TACCCTGCCTTTGAGCCACT 61.134 55.000 0.00 0.00 0.00 4.00
4937 5734 0.034089 ATACCCTGCCTTTGAGCCAC 60.034 55.000 0.00 0.00 0.00 5.01
4938 5735 1.490490 CTATACCCTGCCTTTGAGCCA 59.510 52.381 0.00 0.00 0.00 4.75
4939 5736 1.815795 GCTATACCCTGCCTTTGAGCC 60.816 57.143 0.00 0.00 0.00 4.70
4940 5737 1.134098 TGCTATACCCTGCCTTTGAGC 60.134 52.381 0.00 0.00 0.00 4.26
4941 5738 2.486191 CCTGCTATACCCTGCCTTTGAG 60.486 54.545 0.00 0.00 0.00 3.02
4942 5739 1.490490 CCTGCTATACCCTGCCTTTGA 59.510 52.381 0.00 0.00 0.00 2.69
4943 5740 1.477558 CCCTGCTATACCCTGCCTTTG 60.478 57.143 0.00 0.00 0.00 2.77
4944 5741 0.846693 CCCTGCTATACCCTGCCTTT 59.153 55.000 0.00 0.00 0.00 3.11
4945 5742 0.030092 TCCCTGCTATACCCTGCCTT 60.030 55.000 0.00 0.00 0.00 4.35
4946 5743 0.194587 ATCCCTGCTATACCCTGCCT 59.805 55.000 0.00 0.00 0.00 4.75
4947 5744 1.068121 AATCCCTGCTATACCCTGCC 58.932 55.000 0.00 0.00 0.00 4.85
4948 5745 2.191128 CAATCCCTGCTATACCCTGC 57.809 55.000 0.00 0.00 0.00 4.85
4959 5756 1.649664 CTCTGACTTCGCAATCCCTG 58.350 55.000 0.00 0.00 0.00 4.45
4960 5757 0.539051 CCTCTGACTTCGCAATCCCT 59.461 55.000 0.00 0.00 0.00 4.20
4961 5758 0.537188 TCCTCTGACTTCGCAATCCC 59.463 55.000 0.00 0.00 0.00 3.85
4962 5759 2.478831 GATCCTCTGACTTCGCAATCC 58.521 52.381 0.00 0.00 0.00 3.01
4963 5760 2.159043 TGGATCCTCTGACTTCGCAATC 60.159 50.000 14.23 0.00 0.00 2.67
4964 5761 1.833630 TGGATCCTCTGACTTCGCAAT 59.166 47.619 14.23 0.00 0.00 3.56
4965 5762 1.266178 TGGATCCTCTGACTTCGCAA 58.734 50.000 14.23 0.00 0.00 4.85
4966 5763 1.137675 CATGGATCCTCTGACTTCGCA 59.862 52.381 14.23 0.00 0.00 5.10
4967 5764 1.137872 ACATGGATCCTCTGACTTCGC 59.862 52.381 14.23 0.00 0.00 4.70
4968 5765 2.223923 GGACATGGATCCTCTGACTTCG 60.224 54.545 14.23 0.00 35.68 3.79
4969 5766 3.037549 AGGACATGGATCCTCTGACTTC 58.962 50.000 14.23 4.69 46.92 3.01
4970 5767 3.127791 AGGACATGGATCCTCTGACTT 57.872 47.619 14.23 4.90 46.92 3.01
4971 5768 2.864885 AGGACATGGATCCTCTGACT 57.135 50.000 14.23 11.02 46.92 3.41
4972 5769 2.298729 GCTAGGACATGGATCCTCTGAC 59.701 54.545 14.23 10.53 46.92 3.51
4973 5770 2.603021 GCTAGGACATGGATCCTCTGA 58.397 52.381 14.23 0.00 46.92 3.27
4974 5771 1.622811 GGCTAGGACATGGATCCTCTG 59.377 57.143 14.23 12.85 46.92 3.35
4975 5772 1.221523 TGGCTAGGACATGGATCCTCT 59.778 52.381 14.23 5.48 46.92 3.69
4976 5773 1.622811 CTGGCTAGGACATGGATCCTC 59.377 57.143 14.23 1.71 46.92 3.71
4978 5775 1.722034 TCTGGCTAGGACATGGATCC 58.278 55.000 4.20 4.20 39.28 3.36
4979 5776 2.614987 GCATCTGGCTAGGACATGGATC 60.615 54.545 0.00 0.00 40.25 3.36
4980 5777 1.350351 GCATCTGGCTAGGACATGGAT 59.650 52.381 0.00 0.00 40.25 3.41
4981 5778 0.761187 GCATCTGGCTAGGACATGGA 59.239 55.000 0.00 0.00 40.25 3.41
4982 5779 0.602106 CGCATCTGGCTAGGACATGG 60.602 60.000 0.00 0.00 41.67 3.66
4983 5780 0.105593 ACGCATCTGGCTAGGACATG 59.894 55.000 0.00 0.00 41.67 3.21
4984 5781 0.833287 AACGCATCTGGCTAGGACAT 59.167 50.000 0.00 0.00 41.67 3.06
4985 5782 0.613260 AAACGCATCTGGCTAGGACA 59.387 50.000 0.00 0.00 41.67 4.02
4986 5783 1.739067 AAAACGCATCTGGCTAGGAC 58.261 50.000 0.00 0.00 41.67 3.85
4987 5784 2.489938 AAAAACGCATCTGGCTAGGA 57.510 45.000 0.00 0.00 41.67 2.94
4988 5785 3.531538 TCTAAAAACGCATCTGGCTAGG 58.468 45.455 0.00 0.00 41.67 3.02
4989 5786 4.631813 ACTTCTAAAAACGCATCTGGCTAG 59.368 41.667 0.00 0.00 41.67 3.42
4992 5789 3.831715 ACTTCTAAAAACGCATCTGGC 57.168 42.857 0.00 0.00 39.90 4.85
5006 5803 9.602568 TTTGTACAAACTGATACACAACTTCTA 57.397 29.630 17.01 0.00 31.09 2.10
5017 5814 6.318648 GCAGATCCCATTTGTACAAACTGATA 59.681 38.462 26.25 16.14 32.51 2.15
5038 5835 5.302568 AGACAGTTCAATCCAAAAATGCAGA 59.697 36.000 0.00 0.00 0.00 4.26
5076 5873 9.905713 TTTTATCCCATATTGCTAGCCTATAAG 57.094 33.333 13.29 7.16 0.00 1.73
5091 5888 5.788533 ACGGGGTATCATCTTTTATCCCATA 59.211 40.000 0.00 0.00 38.49 2.74
5101 5898 2.092429 ACAATGCACGGGGTATCATCTT 60.092 45.455 0.00 0.00 0.00 2.40
5125 5922 5.737290 CGCATTTCTTTTAACAGGATTACCG 59.263 40.000 0.00 0.00 41.83 4.02
5133 5930 6.586082 ACCTAATTGCGCATTTCTTTTAACAG 59.414 34.615 19.84 9.79 0.00 3.16
5205 6002 7.601886 AGATGATAATTAGCAAATCCGACTGAG 59.398 37.037 7.61 0.00 0.00 3.35
5207 6004 7.360691 CCAGATGATAATTAGCAAATCCGACTG 60.361 40.741 7.61 8.42 0.00 3.51
5208 6005 6.652481 CCAGATGATAATTAGCAAATCCGACT 59.348 38.462 7.61 0.00 0.00 4.18
5225 6022 9.566432 GACTTTGTTAATCCTTATCCAGATGAT 57.434 33.333 0.00 0.00 37.49 2.45
5228 6025 8.772250 TGAGACTTTGTTAATCCTTATCCAGAT 58.228 33.333 0.00 0.00 0.00 2.90
5229 6026 8.146053 TGAGACTTTGTTAATCCTTATCCAGA 57.854 34.615 0.00 0.00 0.00 3.86
5230 6027 8.970859 ATGAGACTTTGTTAATCCTTATCCAG 57.029 34.615 0.00 0.00 0.00 3.86
5231 6028 8.772250 AGATGAGACTTTGTTAATCCTTATCCA 58.228 33.333 0.00 0.00 0.00 3.41
5236 6033 9.660180 GAGTTAGATGAGACTTTGTTAATCCTT 57.340 33.333 0.00 0.00 0.00 3.36
5301 6098 3.673052 CGCGGTGATTCATGTGGATTTTT 60.673 43.478 0.00 0.00 0.00 1.94
5302 6099 2.159393 CGCGGTGATTCATGTGGATTTT 60.159 45.455 0.00 0.00 0.00 1.82
5303 6100 1.401552 CGCGGTGATTCATGTGGATTT 59.598 47.619 0.00 0.00 0.00 2.17
5304 6101 1.016627 CGCGGTGATTCATGTGGATT 58.983 50.000 0.00 0.00 0.00 3.01
5305 6102 0.107703 ACGCGGTGATTCATGTGGAT 60.108 50.000 12.47 0.00 0.00 3.41
5306 6103 0.533032 TACGCGGTGATTCATGTGGA 59.467 50.000 12.47 0.00 0.00 4.02
5307 6104 1.364721 TTACGCGGTGATTCATGTGG 58.635 50.000 12.47 0.00 0.00 4.17
5308 6105 3.463533 TTTTACGCGGTGATTCATGTG 57.536 42.857 12.47 0.00 0.00 3.21
5309 6106 3.687212 TGATTTTACGCGGTGATTCATGT 59.313 39.130 12.47 0.00 0.00 3.21
5310 6107 4.271590 TGATTTTACGCGGTGATTCATG 57.728 40.909 12.47 0.00 0.00 3.07
5311 6108 4.955925 TTGATTTTACGCGGTGATTCAT 57.044 36.364 12.47 0.00 0.00 2.57
5312 6109 4.750952 TTTGATTTTACGCGGTGATTCA 57.249 36.364 12.47 5.07 0.00 2.57
5313 6110 4.499040 CCATTTGATTTTACGCGGTGATTC 59.501 41.667 12.47 2.10 0.00 2.52
5314 6111 4.082463 ACCATTTGATTTTACGCGGTGATT 60.082 37.500 12.47 0.00 0.00 2.57
5315 6112 3.442273 ACCATTTGATTTTACGCGGTGAT 59.558 39.130 12.47 0.00 0.00 3.06
5316 6113 2.814919 ACCATTTGATTTTACGCGGTGA 59.185 40.909 12.47 0.00 0.00 4.02
5317 6114 3.210358 ACCATTTGATTTTACGCGGTG 57.790 42.857 12.47 0.00 0.00 4.94
5318 6115 5.237779 CCTATACCATTTGATTTTACGCGGT 59.762 40.000 12.47 0.00 0.00 5.68
5319 6116 5.237779 ACCTATACCATTTGATTTTACGCGG 59.762 40.000 12.47 0.00 0.00 6.46
5320 6117 6.133392 CACCTATACCATTTGATTTTACGCG 58.867 40.000 3.53 3.53 0.00 6.01
5321 6118 7.023197 ACACCTATACCATTTGATTTTACGC 57.977 36.000 0.00 0.00 0.00 4.42
5367 6164 4.651045 TGTGGCTAGCTCTCATTTAGATGA 59.349 41.667 15.72 0.00 39.92 2.92
5368 6165 4.749099 GTGTGGCTAGCTCTCATTTAGATG 59.251 45.833 15.72 0.00 32.41 2.90
5369 6166 4.653341 AGTGTGGCTAGCTCTCATTTAGAT 59.347 41.667 15.72 0.00 32.41 1.98
5370 6167 4.026744 AGTGTGGCTAGCTCTCATTTAGA 58.973 43.478 15.72 0.00 0.00 2.10
5371 6168 4.142071 TGAGTGTGGCTAGCTCTCATTTAG 60.142 45.833 15.72 0.00 31.51 1.85
5372 6169 3.769300 TGAGTGTGGCTAGCTCTCATTTA 59.231 43.478 15.72 3.42 31.51 1.40
5373 6170 2.568956 TGAGTGTGGCTAGCTCTCATTT 59.431 45.455 15.72 5.15 31.51 2.32
5374 6171 2.182827 TGAGTGTGGCTAGCTCTCATT 58.817 47.619 15.72 8.57 31.51 2.57
5375 6172 1.857965 TGAGTGTGGCTAGCTCTCAT 58.142 50.000 15.72 0.00 31.51 2.90
5376 6173 1.857965 ATGAGTGTGGCTAGCTCTCA 58.142 50.000 23.02 23.02 39.05 3.27
5377 6174 2.430332 AGAATGAGTGTGGCTAGCTCTC 59.570 50.000 15.72 16.23 0.00 3.20
5378 6175 2.465813 AGAATGAGTGTGGCTAGCTCT 58.534 47.619 15.72 8.19 0.00 4.09
5379 6176 2.977772 AGAATGAGTGTGGCTAGCTC 57.022 50.000 15.72 8.97 0.00 4.09
5380 6177 5.144100 AGTATAGAATGAGTGTGGCTAGCT 58.856 41.667 15.72 0.00 0.00 3.32
5381 6178 5.461032 AGTATAGAATGAGTGTGGCTAGC 57.539 43.478 6.04 6.04 0.00 3.42
5382 6179 7.863375 GTGTAAGTATAGAATGAGTGTGGCTAG 59.137 40.741 0.00 0.00 0.00 3.42
5383 6180 7.560262 AGTGTAAGTATAGAATGAGTGTGGCTA 59.440 37.037 0.00 0.00 0.00 3.93
5384 6181 6.381420 AGTGTAAGTATAGAATGAGTGTGGCT 59.619 38.462 0.00 0.00 0.00 4.75
5385 6182 6.574350 AGTGTAAGTATAGAATGAGTGTGGC 58.426 40.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.