Multiple sequence alignment - TraesCS2A01G093700

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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 TraesCS2A01G093700 chr2A 100.000 5075 0 0 1 5075 47834610 47829536 0.000000e+00 9372.0
1 TraesCS2A01G093700 chr2A 91.150 113 10 0 4736 4848 572800189 572800301 2.450000e-33 154.0
2 TraesCS2A01G093700 chr2A 91.509 106 9 0 4743 4848 562606571 562606466 4.090000e-31 147.0
3 TraesCS2A01G093700 chr2B 93.392 3420 172 30 167 3566 69044953 69041568 0.000000e+00 5014.0
4 TraesCS2A01G093700 chr2B 88.426 864 64 24 3746 4585 69041352 69040501 0.000000e+00 1009.0
5 TraesCS2A01G093700 chr2B 91.736 121 9 1 4588 4707 69040412 69040292 3.140000e-37 167.0
6 TraesCS2A01G093700 chr2B 78.648 281 22 21 1872 2150 69055594 69055350 8.800000e-33 152.0
7 TraesCS2A01G093700 chr2D 91.945 2967 166 30 1 2942 43996096 43993178 0.000000e+00 4087.0
8 TraesCS2A01G093700 chr2D 85.181 1876 156 61 2927 4710 43993161 43991316 0.000000e+00 1812.0
9 TraesCS2A01G093700 chr2D 88.957 163 16 2 4914 5075 43988635 43988474 3.100000e-47 200.0
10 TraesCS2A01G093700 chr4A 78.129 791 133 32 1035 1810 143446371 143445606 2.770000e-127 466.0
11 TraesCS2A01G093700 chr4A 92.035 113 8 1 4736 4848 420299981 420300092 1.890000e-34 158.0
12 TraesCS2A01G093700 chr5B 82.735 446 55 13 2652 3088 154053276 154053708 1.330000e-100 377.0
13 TraesCS2A01G093700 chr5B 80.758 343 45 10 2755 3088 154016415 154016085 1.090000e-61 248.0
14 TraesCS2A01G093700 chr7B 82.287 446 55 13 2652 3088 715317650 715318080 1.040000e-96 364.0
15 TraesCS2A01G093700 chr4D 80.625 480 68 17 1036 1509 327428636 327429096 1.050000e-91 348.0
16 TraesCS2A01G093700 chr4D 94.444 54 3 0 4486 4539 73385874 73385821 3.260000e-12 84.2
17 TraesCS2A01G093700 chr4D 93.878 49 3 0 4481 4529 259493156 259493204 1.960000e-09 75.0
18 TraesCS2A01G093700 chr4B 80.417 480 69 17 1036 1509 406803706 406804166 4.870000e-90 342.0
19 TraesCS2A01G093700 chr4B 93.750 48 3 0 4482 4529 255392201 255392154 7.050000e-09 73.1
20 TraesCS2A01G093700 chr7A 91.150 113 10 0 4736 4848 477237128 477237016 2.450000e-33 154.0
21 TraesCS2A01G093700 chr6A 90.265 113 11 0 4736 4848 105870277 105870389 1.140000e-31 148.0
22 TraesCS2A01G093700 chr5D 90.265 113 11 0 4736 4848 341193662 341193774 1.140000e-31 148.0
23 TraesCS2A01G093700 chr5A 90.351 114 10 1 4754 4867 36072170 36072282 1.140000e-31 148.0
24 TraesCS2A01G093700 chr5A 78.519 135 23 5 125 259 9664218 9664090 3.260000e-12 84.2
25 TraesCS2A01G093700 chr6B 87.121 132 14 3 4736 4867 52569414 52569542 4.090000e-31 147.0
26 TraesCS2A01G093700 chr3A 86.719 128 14 3 4734 4860 625556881 625556756 6.850000e-29 139.0
27 TraesCS2A01G093700 chr1D 94.444 54 3 0 4486 4539 20971928 20971875 3.260000e-12 84.2
28 TraesCS2A01G093700 chr1D 100.000 38 0 0 4486 4523 189655479 189655516 2.530000e-08 71.3
29 TraesCS2A01G093700 chr1B 100.000 38 0 0 4486 4523 263552334 263552371 2.530000e-08 71.3
30 TraesCS2A01G093700 chr1A 100.000 38 0 0 4486 4523 221699771 221699808 2.530000e-08 71.3
31 TraesCS2A01G093700 chr3B 93.333 45 3 0 4486 4530 612102844 612102800 3.280000e-07 67.6


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 TraesCS2A01G093700 chr2A 47829536 47834610 5074 True 9372.000000 9372 100.000000 1 5075 1 chr2A.!!$R1 5074
1 TraesCS2A01G093700 chr2B 69040292 69044953 4661 True 2063.333333 5014 91.184667 167 4707 3 chr2B.!!$R2 4540
2 TraesCS2A01G093700 chr2D 43988474 43996096 7622 True 2033.000000 4087 88.694333 1 5075 3 chr2D.!!$R1 5074
3 TraesCS2A01G093700 chr4A 143445606 143446371 765 True 466.000000 466 78.129000 1035 1810 1 chr4A.!!$R1 775

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
212 214 0.095935 CGAAGCGGTCAAATCTGCAG 59.904 55.0 7.63 7.63 41.63 4.41 F
1518 1534 0.034767 AGGGTGAGACGGATCGTGTA 60.035 55.0 0.00 0.00 41.37 2.90 F
2882 2923 0.390124 ACTTTGGTGCCAACATGCTG 59.610 50.0 2.72 0.00 35.46 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1573 0.105964 ACAGCCGGCGATATTTAGCA 59.894 50.0 23.20 0.00 34.54 3.49 R
3371 3480 0.662619 CAAGTTTCAGCCACGCTTGA 59.337 50.0 0.00 0.00 36.40 3.02 R
4775 5284 0.251742 CTCCTTTTGCATGGGTCCCA 60.252 55.0 14.64 14.64 38.19 4.37 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
32 33 5.164100 CGAGTAAAATTGGCCGTTTGATTTG 60.164 40.000 6.69 0.00 0.00 2.32
36 37 2.517650 TTGGCCGTTTGATTTGGTTC 57.482 45.000 0.00 0.00 0.00 3.62
48 49 1.975660 TTTGGTTCTGGTCCCTTTCG 58.024 50.000 0.00 0.00 0.00 3.46
59 60 1.302192 CCCTTTCGCCTTTCGTGGA 60.302 57.895 0.00 0.00 39.67 4.02
73 74 2.772191 TGGACACACACCCAGCCT 60.772 61.111 0.00 0.00 0.00 4.58
80 81 1.541147 CACACACCCAGCCTTTACATG 59.459 52.381 0.00 0.00 0.00 3.21
90 91 1.821216 CCTTTACATGGCCAAGACGT 58.179 50.000 16.33 10.20 0.00 4.34
91 92 1.468520 CCTTTACATGGCCAAGACGTG 59.531 52.381 16.33 8.51 33.07 4.49
105 106 0.660488 GACGTGCACAACCAACATCA 59.340 50.000 18.64 0.00 0.00 3.07
106 107 1.064803 GACGTGCACAACCAACATCAA 59.935 47.619 18.64 0.00 0.00 2.57
109 110 2.733542 CGTGCACAACCAACATCAACAA 60.734 45.455 18.64 0.00 0.00 2.83
110 111 2.602660 GTGCACAACCAACATCAACAAC 59.397 45.455 13.17 0.00 0.00 3.32
111 112 2.232208 TGCACAACCAACATCAACAACA 59.768 40.909 0.00 0.00 0.00 3.33
112 113 3.118847 TGCACAACCAACATCAACAACAT 60.119 39.130 0.00 0.00 0.00 2.71
113 114 3.245754 GCACAACCAACATCAACAACATG 59.754 43.478 0.00 0.00 0.00 3.21
114 115 3.245754 CACAACCAACATCAACAACATGC 59.754 43.478 0.00 0.00 0.00 4.06
115 116 3.118847 ACAACCAACATCAACAACATGCA 60.119 39.130 0.00 0.00 0.00 3.96
116 117 4.059511 CAACCAACATCAACAACATGCAT 58.940 39.130 0.00 0.00 0.00 3.96
123 124 4.916831 ACATCAACAACATGCATAAACACG 59.083 37.500 0.00 0.00 0.00 4.49
131 132 1.016653 TGCATAAACACGCGCTAGCA 61.017 50.000 16.45 4.28 45.49 3.49
132 133 0.096281 GCATAAACACGCGCTAGCAA 59.904 50.000 16.45 0.00 45.49 3.91
159 160 7.269477 AGCAAAATGATATAAGACCAAGAGC 57.731 36.000 0.00 0.00 0.00 4.09
172 173 5.500234 AGACCAAGAGCTATGCATAAACAA 58.500 37.500 8.00 0.00 0.00 2.83
174 175 7.282585 AGACCAAGAGCTATGCATAAACAATA 58.717 34.615 8.00 0.00 0.00 1.90
200 202 3.691498 AGAAAGAAACAAAACGAAGCGG 58.309 40.909 0.00 0.00 0.00 5.52
212 214 0.095935 CGAAGCGGTCAAATCTGCAG 59.904 55.000 7.63 7.63 41.63 4.41
217 219 0.994995 CGGTCAAATCTGCAGTCGAG 59.005 55.000 14.67 3.19 0.00 4.04
224 226 5.578727 GTCAAATCTGCAGTCGAGAAACTAT 59.421 40.000 14.67 0.00 0.00 2.12
232 234 6.504398 TGCAGTCGAGAAACTATAACTATGG 58.496 40.000 0.00 0.00 0.00 2.74
244 246 4.778213 ATAACTATGGCCATATCCGCAT 57.222 40.909 25.62 11.72 0.00 4.73
255 257 1.399714 TATCCGCATCAACCGTCTCT 58.600 50.000 0.00 0.00 0.00 3.10
259 261 1.428448 CGCATCAACCGTCTCTTGAA 58.572 50.000 0.00 0.00 31.48 2.69
261 263 2.411547 CGCATCAACCGTCTCTTGAAAC 60.412 50.000 0.00 0.00 31.48 2.78
264 266 1.409790 TCAACCGTCTCTTGAAACCGA 59.590 47.619 0.00 0.00 0.00 4.69
274 276 6.569801 CGTCTCTTGAAACCGATATAGGCATA 60.570 42.308 1.12 0.00 33.69 3.14
292 294 7.307131 AGGCATAAATAAATCTCAAATGGGG 57.693 36.000 0.00 0.00 0.00 4.96
294 296 5.934043 GCATAAATAAATCTCAAATGGGGGC 59.066 40.000 0.00 0.00 0.00 5.80
310 312 3.138798 GCGACTAGCCCTCCGTCA 61.139 66.667 0.00 0.00 40.81 4.35
311 313 2.707849 GCGACTAGCCCTCCGTCAA 61.708 63.158 0.00 0.00 40.81 3.18
315 317 0.541863 ACTAGCCCTCCGTCAATTGG 59.458 55.000 5.42 0.00 0.00 3.16
322 324 2.417243 CCCTCCGTCAATTGGAAAATGC 60.417 50.000 5.42 0.00 34.44 3.56
349 352 9.832445 AGTCGGTTTTATTCATACACATCTAAT 57.168 29.630 0.00 0.00 0.00 1.73
365 368 7.011109 ACACATCTAATAAATACTTGCCGTGTC 59.989 37.037 0.00 0.00 0.00 3.67
396 400 9.995003 AAATATTGTTTATCTGGTGCAGAAAAA 57.005 25.926 0.00 0.00 44.04 1.94
487 491 4.612943 GAATCACCGGTAGACTGAGAATC 58.387 47.826 6.87 0.00 0.00 2.52
503 507 1.064654 GAATCAGCAAACCCGATCTGC 59.935 52.381 0.00 0.00 36.29 4.26
659 663 5.635120 AGGCTCTACTTTTGTGAAAGGAAT 58.365 37.500 4.18 0.00 45.24 3.01
660 664 6.071320 AGGCTCTACTTTTGTGAAAGGAATT 58.929 36.000 4.18 0.00 45.24 2.17
661 665 6.551227 AGGCTCTACTTTTGTGAAAGGAATTT 59.449 34.615 4.18 0.00 45.24 1.82
712 723 1.515521 GGGAACACCCTGCACTTTCG 61.516 60.000 0.00 0.00 40.49 3.46
878 890 1.700042 GCCCAGTCCCAGATCCGAAT 61.700 60.000 0.00 0.00 0.00 3.34
884 896 1.837051 CCCAGATCCGAATCCCCGA 60.837 63.158 0.00 0.00 31.78 5.14
885 897 1.367840 CCAGATCCGAATCCCCGAC 59.632 63.158 0.00 0.00 31.78 4.79
891 903 4.189188 CGAATCCCCGACGCGTCT 62.189 66.667 33.94 16.69 0.00 4.18
942 954 2.998279 GCAGGGAATGGTGCACTGC 61.998 63.158 17.98 12.91 46.24 4.40
968 980 1.153745 GGTAGGCAGACACGAGCAG 60.154 63.158 0.00 0.00 0.00 4.24
1040 1052 1.451028 GGAGAAAGATGCCGCTGCT 60.451 57.895 0.70 0.00 38.71 4.24
1518 1534 0.034767 AGGGTGAGACGGATCGTGTA 60.035 55.000 0.00 0.00 41.37 2.90
1523 1539 1.474879 TGAGACGGATCGTGTATGCAA 59.525 47.619 0.00 0.00 41.37 4.08
1557 1573 1.951510 CACGCCTGTTGAGCATGTT 59.048 52.632 0.00 0.00 0.00 2.71
1665 1684 3.834799 GCGTCGGTCGGGGATTCT 61.835 66.667 0.00 0.00 40.26 2.40
1716 1735 1.519455 GCAGCTGCTAACCGTCGAT 60.519 57.895 31.33 0.00 38.21 3.59
1822 1841 5.335976 GGTCAGGAGGTAGCAATTTTCTTTG 60.336 44.000 0.00 0.00 0.00 2.77
2315 2353 2.118313 TGGCTGTGGACATGATTCAG 57.882 50.000 0.00 3.81 0.00 3.02
2631 2669 2.423185 CTGCAATGATCCGGCAAACTTA 59.577 45.455 0.00 0.00 37.06 2.24
2632 2670 2.822561 TGCAATGATCCGGCAAACTTAA 59.177 40.909 0.00 0.00 34.05 1.85
2636 2674 5.649557 CAATGATCCGGCAAACTTAATGAA 58.350 37.500 0.00 0.00 0.00 2.57
2743 2784 4.802039 GCTTGTTGCCTATTTGATCACATG 59.198 41.667 4.56 0.00 35.15 3.21
2798 2839 7.352079 AGGATGTGTTCTTGTCAATTTCTTT 57.648 32.000 0.00 0.00 0.00 2.52
2880 2921 0.600782 CCACTTTGGTGCCAACATGC 60.601 55.000 2.72 0.00 41.75 4.06
2882 2923 0.390124 ACTTTGGTGCCAACATGCTG 59.610 50.000 2.72 0.00 35.46 4.41
2915 2957 4.695606 TCAAGTACCTACTCCCATTCCTT 58.304 43.478 0.00 0.00 34.99 3.36
3097 3175 5.536538 TCGGAATAGAGTAATCAGTGCAGAT 59.463 40.000 0.00 0.00 0.00 2.90
3107 3191 8.067751 AGTAATCAGTGCAGATAAACTCAGTA 57.932 34.615 0.00 0.00 0.00 2.74
3113 3197 6.035435 CAGTGCAGATAAACTCAGTATGACAC 59.965 42.308 0.00 0.00 42.56 3.67
3141 3236 5.045651 TCAGTCATCCATCTGTAATTGGTGT 60.046 40.000 0.00 0.00 34.48 4.16
3142 3237 5.295292 CAGTCATCCATCTGTAATTGGTGTC 59.705 44.000 0.00 0.00 34.48 3.67
3143 3238 5.045651 AGTCATCCATCTGTAATTGGTGTCA 60.046 40.000 0.00 0.00 34.48 3.58
3144 3239 5.824624 GTCATCCATCTGTAATTGGTGTCAT 59.175 40.000 0.00 0.00 34.48 3.06
3145 3240 5.824097 TCATCCATCTGTAATTGGTGTCATG 59.176 40.000 0.00 0.00 34.48 3.07
3146 3241 5.178096 TCCATCTGTAATTGGTGTCATGT 57.822 39.130 0.00 0.00 34.48 3.21
3147 3242 4.943093 TCCATCTGTAATTGGTGTCATGTG 59.057 41.667 0.00 0.00 34.48 3.21
3148 3243 4.943093 CCATCTGTAATTGGTGTCATGTGA 59.057 41.667 0.00 0.00 0.00 3.58
3149 3244 5.591472 CCATCTGTAATTGGTGTCATGTGAT 59.409 40.000 0.00 0.00 0.00 3.06
3150 3245 6.095860 CCATCTGTAATTGGTGTCATGTGATT 59.904 38.462 0.00 0.00 0.00 2.57
3151 3246 6.499234 TCTGTAATTGGTGTCATGTGATTG 57.501 37.500 0.00 0.00 0.00 2.67
3152 3247 6.003326 TCTGTAATTGGTGTCATGTGATTGT 58.997 36.000 0.00 0.00 0.00 2.71
3153 3248 6.011476 TGTAATTGGTGTCATGTGATTGTG 57.989 37.500 0.00 0.00 0.00 3.33
3244 3353 3.193263 CAGGATGATTCTCTTGACACGG 58.807 50.000 0.00 0.00 39.69 4.94
3271 3380 7.920160 ATTTGTTGAAACCTTTTGTTGACAT 57.080 28.000 0.00 0.00 37.23 3.06
3289 3398 6.839124 TGACATCTTGCATCACCTTTATTT 57.161 33.333 0.00 0.00 0.00 1.40
3290 3399 6.855836 TGACATCTTGCATCACCTTTATTTC 58.144 36.000 0.00 0.00 0.00 2.17
3383 3492 5.459762 CCATTTAATTAATCAAGCGTGGCTG 59.540 40.000 0.00 0.00 39.62 4.85
3550 3671 3.054728 TCGGTCTTTCCATTTGGCATCTA 60.055 43.478 0.00 0.00 35.57 1.98
3556 3677 7.099120 GTCTTTCCATTTGGCATCTACATTTT 58.901 34.615 0.00 0.00 34.44 1.82
3576 3697 2.740506 AGAGTAGGTCTGGAGGTAGC 57.259 55.000 0.00 0.00 32.57 3.58
3577 3698 1.923850 AGAGTAGGTCTGGAGGTAGCA 59.076 52.381 0.00 0.00 32.57 3.49
3624 3745 7.661437 ACTTCTTTCTGTAGATTGCACATGTAA 59.339 33.333 0.00 0.00 0.00 2.41
3626 3747 9.665719 TTCTTTCTGTAGATTGCACATGTAATA 57.334 29.630 0.00 0.00 30.53 0.98
3692 3977 7.978975 AGAGTGATTAGAACATAAGTCTGCTTC 59.021 37.037 0.00 0.00 36.22 3.86
3711 3996 4.203160 GCTTCGAAGCGCTTTTGAAATATC 59.797 41.667 32.36 17.90 42.88 1.63
3837 4122 0.532115 CCAGGCCATTAAGCACCAAC 59.468 55.000 5.01 0.00 0.00 3.77
3843 4128 2.687370 CCATTAAGCACCAACCTTTGC 58.313 47.619 0.00 0.00 39.16 3.68
3981 4266 1.134995 CACTGCTCTTCTCCATACGCA 60.135 52.381 0.00 0.00 0.00 5.24
4186 4471 6.803154 ATTGTTTGCTGAACCTAACTAGAC 57.197 37.500 0.00 0.00 37.45 2.59
4256 4541 8.224025 TGCCTATGAACAATCCTAATATTGGAA 58.776 33.333 0.00 0.00 40.48 3.53
4257 4542 8.734386 GCCTATGAACAATCCTAATATTGGAAG 58.266 37.037 0.00 4.82 40.48 3.46
4260 4545 7.880160 TGAACAATCCTAATATTGGAAGTGG 57.120 36.000 0.00 0.17 40.48 4.00
4263 4548 8.664669 AACAATCCTAATATTGGAAGTGGTTT 57.335 30.769 0.00 0.00 40.48 3.27
4264 4549 8.664669 ACAATCCTAATATTGGAAGTGGTTTT 57.335 30.769 0.00 0.00 40.48 2.43
4265 4550 9.100197 ACAATCCTAATATTGGAAGTGGTTTTT 57.900 29.630 0.00 0.00 40.48 1.94
4293 4578 1.504359 TTTGAGGAAACTACGGTGCG 58.496 50.000 0.00 0.00 44.43 5.34
4300 4585 0.599204 AAACTACGGTGCGGACTGTG 60.599 55.000 29.31 20.64 42.04 3.66
4351 4639 9.906660 CCTATATTTTGTGTGTTTGTGTGTTAT 57.093 29.630 0.00 0.00 0.00 1.89
4370 4658 9.256477 TGTGTTATGGTCGATCATTTCTATTAC 57.744 33.333 17.88 7.53 0.00 1.89
4371 4659 8.709646 GTGTTATGGTCGATCATTTCTATTACC 58.290 37.037 17.88 0.00 0.00 2.85
4413 4709 3.548770 CTGGAAGCAAATGATCTGCCTA 58.451 45.455 2.04 0.00 40.86 3.93
4415 4711 4.539726 TGGAAGCAAATGATCTGCCTATT 58.460 39.130 2.04 0.00 40.86 1.73
4417 4713 5.163488 TGGAAGCAAATGATCTGCCTATTTG 60.163 40.000 9.85 9.85 42.03 2.32
4419 4715 5.511234 AGCAAATGATCTGCCTATTTGAC 57.489 39.130 15.82 9.26 41.81 3.18
4426 4722 0.748005 CTGCCTATTTGACCACCGGG 60.748 60.000 6.32 0.00 41.29 5.73
4442 4738 1.414550 CCGGGTTTTGGTTGTTTCCAT 59.585 47.619 0.00 0.00 37.33 3.41
4445 4741 3.068307 CGGGTTTTGGTTGTTTCCATGTA 59.932 43.478 0.00 0.00 37.33 2.29
4448 4744 4.450757 GGTTTTGGTTGTTTCCATGTATGC 59.549 41.667 0.00 0.00 37.33 3.14
4449 4745 4.944619 TTTGGTTGTTTCCATGTATGCA 57.055 36.364 0.00 0.00 37.33 3.96
4450 4746 3.932545 TGGTTGTTTCCATGTATGCAC 57.067 42.857 0.00 0.00 31.96 4.57
4577 4930 6.096705 TCCTTTGTTATATGTGCAAGGAATGG 59.903 38.462 0.00 0.00 0.00 3.16
4606 5045 7.559590 ACTTTAGAAGTTGGCTATATTGCAG 57.440 36.000 11.27 0.00 39.04 4.41
4659 5098 2.801631 CCATCTCCACTCGGGCCTC 61.802 68.421 0.84 0.00 36.21 4.70
4666 5105 1.617018 CCACTCGGGCCTCTTGATCA 61.617 60.000 0.84 0.00 0.00 2.92
4674 5114 4.103153 TCGGGCCTCTTGATCAATAAAGAT 59.897 41.667 8.96 0.00 32.20 2.40
4710 5219 3.455619 AAAACATCGCATCAAGACGAC 57.544 42.857 0.00 0.00 41.76 4.34
4726 5235 1.387756 ACGACGAAAAGAATAACGCCG 59.612 47.619 0.00 0.00 37.59 6.46
4733 5242 4.325472 CGAAAAGAATAACGCCGTCTAAGT 59.675 41.667 0.00 0.00 0.00 2.24
4735 5244 6.549912 AAAAGAATAACGCCGTCTAAGTTT 57.450 33.333 0.00 0.00 0.00 2.66
4736 5245 5.526010 AAGAATAACGCCGTCTAAGTTTG 57.474 39.130 0.00 0.00 0.00 2.93
4737 5246 4.813027 AGAATAACGCCGTCTAAGTTTGA 58.187 39.130 0.00 0.00 0.00 2.69
4738 5247 4.624452 AGAATAACGCCGTCTAAGTTTGAC 59.376 41.667 7.32 7.32 0.00 3.18
4739 5248 1.505425 AACGCCGTCTAAGTTTGACC 58.495 50.000 11.15 0.00 0.00 4.02
4741 5250 0.788391 CGCCGTCTAAGTTTGACCAC 59.212 55.000 11.15 3.75 0.00 4.16
4742 5251 1.870580 CGCCGTCTAAGTTTGACCACA 60.871 52.381 11.15 0.00 0.00 4.17
4743 5252 1.529865 GCCGTCTAAGTTTGACCACAC 59.470 52.381 11.15 0.00 0.00 3.82
4744 5253 2.805657 GCCGTCTAAGTTTGACCACACT 60.806 50.000 11.15 0.00 0.00 3.55
4745 5254 3.463944 CCGTCTAAGTTTGACCACACTT 58.536 45.455 11.15 6.75 37.08 3.16
4746 5255 3.875134 CCGTCTAAGTTTGACCACACTTT 59.125 43.478 11.15 0.00 34.92 2.66
4747 5256 4.334481 CCGTCTAAGTTTGACCACACTTTT 59.666 41.667 11.15 0.00 34.92 2.27
4749 5258 5.963586 CGTCTAAGTTTGACCACACTTTTTC 59.036 40.000 11.15 0.00 34.92 2.29
4750 5259 6.402766 CGTCTAAGTTTGACCACACTTTTTCA 60.403 38.462 11.15 0.00 34.92 2.69
4752 5261 5.722021 AAGTTTGACCACACTTTTTCAGT 57.278 34.783 0.00 0.00 35.35 3.41
4753 5262 5.722021 AGTTTGACCACACTTTTTCAGTT 57.278 34.783 0.00 0.00 30.92 3.16
4754 5263 6.096673 AGTTTGACCACACTTTTTCAGTTT 57.903 33.333 0.00 0.00 30.92 2.66
4755 5264 5.925969 AGTTTGACCACACTTTTTCAGTTTG 59.074 36.000 0.00 0.00 33.49 2.93
4757 5266 5.461032 TGACCACACTTTTTCAGTTTGTT 57.539 34.783 0.00 0.00 31.98 2.83
4758 5267 5.848406 TGACCACACTTTTTCAGTTTGTTT 58.152 33.333 0.00 0.00 31.98 2.83
4759 5268 6.284459 TGACCACACTTTTTCAGTTTGTTTT 58.716 32.000 0.00 0.00 31.98 2.43
4782 5291 6.783708 TTTTATGTAAATGTGATGGGACCC 57.216 37.500 2.45 2.45 0.00 4.46
4785 5294 3.630168 TGTAAATGTGATGGGACCCATG 58.370 45.455 31.39 0.00 45.26 3.66
4786 5295 1.488390 AAATGTGATGGGACCCATGC 58.512 50.000 31.39 21.67 45.26 4.06
4787 5296 0.335705 AATGTGATGGGACCCATGCA 59.664 50.000 31.39 26.12 45.26 3.96
4801 7271 2.242043 CCATGCAAAAGGAGGTGACTT 58.758 47.619 0.00 0.00 44.43 3.01
4803 7273 4.019174 CCATGCAAAAGGAGGTGACTTAT 58.981 43.478 0.00 0.00 44.43 1.73
4804 7274 5.192927 CCATGCAAAAGGAGGTGACTTATA 58.807 41.667 0.00 0.00 44.43 0.98
4805 7275 5.652014 CCATGCAAAAGGAGGTGACTTATAA 59.348 40.000 0.00 0.00 44.43 0.98
4807 7277 5.876357 TGCAAAAGGAGGTGACTTATAAGT 58.124 37.500 18.05 18.05 44.43 2.24
4810 7280 7.286775 TGCAAAAGGAGGTGACTTATAAGTTTT 59.713 33.333 18.96 10.67 44.43 2.43
4816 7286 9.503399 AGGAGGTGACTTATAAGTTTTAAGTTG 57.497 33.333 18.96 0.00 44.43 3.16
4817 7287 9.498176 GGAGGTGACTTATAAGTTTTAAGTTGA 57.502 33.333 18.96 7.23 44.43 3.18
4820 7290 9.281371 GGTGACTTATAAGTTTTAAGTTGAGGT 57.719 33.333 18.96 0.00 39.40 3.85
4822 7292 9.280174 TGACTTATAAGTTTTAAGTTGAGGTGG 57.720 33.333 18.96 0.00 39.40 4.61
4823 7293 9.498176 GACTTATAAGTTTTAAGTTGAGGTGGA 57.502 33.333 18.96 0.00 39.40 4.02
4825 7295 6.819397 ATAAGTTTTAAGTTGAGGTGGAGC 57.181 37.500 0.00 0.00 0.00 4.70
4826 7296 4.164843 AGTTTTAAGTTGAGGTGGAGCA 57.835 40.909 0.00 0.00 0.00 4.26
4827 7297 4.532834 AGTTTTAAGTTGAGGTGGAGCAA 58.467 39.130 0.00 0.00 0.00 3.91
4829 7299 5.598417 AGTTTTAAGTTGAGGTGGAGCAATT 59.402 36.000 0.00 0.00 0.00 2.32
4830 7300 6.098266 AGTTTTAAGTTGAGGTGGAGCAATTT 59.902 34.615 0.00 0.00 0.00 1.82
4831 7301 7.286775 AGTTTTAAGTTGAGGTGGAGCAATTTA 59.713 33.333 0.00 0.00 0.00 1.40
4836 7306 5.954150 AGTTGAGGTGGAGCAATTTATGATT 59.046 36.000 0.00 0.00 0.00 2.57
4837 7307 6.438425 AGTTGAGGTGGAGCAATTTATGATTT 59.562 34.615 0.00 0.00 0.00 2.17
4839 7309 8.416329 GTTGAGGTGGAGCAATTTATGATTTAT 58.584 33.333 0.00 0.00 0.00 1.40
4840 7310 9.639563 TTGAGGTGGAGCAATTTATGATTTATA 57.360 29.630 0.00 0.00 0.00 0.98
4841 7311 9.639563 TGAGGTGGAGCAATTTATGATTTATAA 57.360 29.630 0.00 0.00 0.00 0.98
4843 7313 9.646522 AGGTGGAGCAATTTATGATTTATAAGT 57.353 29.630 0.00 0.00 33.03 2.24
4847 7317 9.696917 GGAGCAATTTATGATTTATAAGTTGGG 57.303 33.333 14.23 0.00 43.59 4.12
4888 7358 4.946478 TGGTAATTGAAACCAAACAGGG 57.054 40.909 0.00 0.00 43.99 4.45
4889 7359 3.070302 TGGTAATTGAAACCAAACAGGGC 59.930 43.478 0.00 0.00 43.99 5.19
4890 7360 2.928801 AATTGAAACCAAACAGGGCC 57.071 45.000 0.00 0.00 43.89 5.80
4891 7361 2.101640 ATTGAAACCAAACAGGGCCT 57.898 45.000 0.00 0.00 43.89 5.19
4892 7362 1.872773 TTGAAACCAAACAGGGCCTT 58.127 45.000 1.32 0.00 43.89 4.35
4893 7363 2.757894 TGAAACCAAACAGGGCCTTA 57.242 45.000 1.32 0.00 43.89 2.69
4894 7364 3.033659 TGAAACCAAACAGGGCCTTAA 57.966 42.857 1.32 0.00 43.89 1.85
4895 7365 3.582164 TGAAACCAAACAGGGCCTTAAT 58.418 40.909 1.32 0.00 43.89 1.40
4896 7366 3.323403 TGAAACCAAACAGGGCCTTAATG 59.677 43.478 1.32 2.35 43.89 1.90
4897 7367 2.990740 ACCAAACAGGGCCTTAATGA 57.009 45.000 1.32 0.00 43.89 2.57
4898 7368 3.252554 ACCAAACAGGGCCTTAATGAA 57.747 42.857 1.32 0.00 43.89 2.57
4899 7369 2.897326 ACCAAACAGGGCCTTAATGAAC 59.103 45.455 1.32 0.00 43.89 3.18
4900 7370 2.896685 CCAAACAGGGCCTTAATGAACA 59.103 45.455 1.32 0.00 0.00 3.18
4901 7371 3.056607 CCAAACAGGGCCTTAATGAACAG 60.057 47.826 1.32 0.00 0.00 3.16
4902 7372 1.839424 ACAGGGCCTTAATGAACAGC 58.161 50.000 1.32 0.00 0.00 4.40
4903 7373 0.734889 CAGGGCCTTAATGAACAGCG 59.265 55.000 1.32 0.00 0.00 5.18
4904 7374 1.032114 AGGGCCTTAATGAACAGCGC 61.032 55.000 0.00 0.00 36.72 5.92
4905 7375 1.312371 GGGCCTTAATGAACAGCGCA 61.312 55.000 11.47 0.00 36.51 6.09
4924 7394 5.411361 AGCGCATATACTTTCACTGTGAAAA 59.589 36.000 29.44 19.75 44.69 2.29
4925 7395 5.734498 GCGCATATACTTTCACTGTGAAAAG 59.266 40.000 29.44 24.61 44.69 2.27
4926 7396 6.250819 CGCATATACTTTCACTGTGAAAAGG 58.749 40.000 29.44 22.69 44.69 3.11
4927 7397 6.555315 GCATATACTTTCACTGTGAAAAGGG 58.445 40.000 29.44 22.12 44.69 3.95
4928 7398 6.555315 CATATACTTTCACTGTGAAAAGGGC 58.445 40.000 29.44 0.00 44.69 5.19
4930 7400 1.946768 CTTTCACTGTGAAAAGGGCGA 59.053 47.619 29.44 11.78 44.69 5.54
4931 7401 1.593196 TTCACTGTGAAAAGGGCGAG 58.407 50.000 20.14 0.00 32.71 5.03
4932 7402 0.756294 TCACTGTGAAAAGGGCGAGA 59.244 50.000 8.27 0.00 0.00 4.04
4933 7403 1.151668 CACTGTGAAAAGGGCGAGAG 58.848 55.000 0.32 0.00 0.00 3.20
4934 7404 0.035458 ACTGTGAAAAGGGCGAGAGG 59.965 55.000 0.00 0.00 0.00 3.69
4935 7405 0.674895 CTGTGAAAAGGGCGAGAGGG 60.675 60.000 0.00 0.00 0.00 4.30
4936 7406 1.377333 GTGAAAAGGGCGAGAGGGG 60.377 63.158 0.00 0.00 0.00 4.79
4948 7896 2.125225 GAGGGGGAACAGGGGAGT 59.875 66.667 0.00 0.00 0.00 3.85
4962 7910 1.569030 GGGAGTCCCAAACCCTACCC 61.569 65.000 24.35 0.00 44.65 3.69
4986 7934 1.604147 CGCCCCCTCAAATTCCCAAC 61.604 60.000 0.00 0.00 0.00 3.77
4994 7942 3.214328 CTCAAATTCCCAACCTATCCCG 58.786 50.000 0.00 0.00 0.00 5.14
4995 7943 1.681264 CAAATTCCCAACCTATCCCGC 59.319 52.381 0.00 0.00 0.00 6.13
4997 7945 2.052047 ATTCCCAACCTATCCCGCCG 62.052 60.000 0.00 0.00 0.00 6.46
4998 7946 4.250305 CCCAACCTATCCCGCCGG 62.250 72.222 0.00 0.00 0.00 6.13
5004 7953 2.108362 CTATCCCGCCGGAACACC 59.892 66.667 5.05 0.00 43.10 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.752604 ACCAAATCAAACGGCCAATTTTAC 59.247 37.500 2.24 0.00 0.00 2.01
17 18 2.035632 AGAACCAAATCAAACGGCCAA 58.964 42.857 2.24 0.00 0.00 4.52
22 23 2.030274 GGGACCAGAACCAAATCAAACG 60.030 50.000 0.00 0.00 0.00 3.60
32 33 1.674651 GGCGAAAGGGACCAGAACC 60.675 63.158 0.00 0.00 0.00 3.62
36 37 1.298859 CGAAAGGCGAAAGGGACCAG 61.299 60.000 0.00 0.00 44.57 4.00
48 49 1.647084 GTGTGTGTCCACGAAAGGC 59.353 57.895 0.00 0.00 44.92 4.35
59 60 0.548989 TGTAAAGGCTGGGTGTGTGT 59.451 50.000 0.00 0.00 0.00 3.72
73 74 0.878416 GCACGTCTTGGCCATGTAAA 59.122 50.000 17.54 0.00 0.00 2.01
80 81 2.331451 GTTGTGCACGTCTTGGCC 59.669 61.111 13.13 0.00 0.00 5.36
82 83 0.248458 GTTGGTTGTGCACGTCTTGG 60.248 55.000 13.13 0.00 0.00 3.61
83 84 0.449786 TGTTGGTTGTGCACGTCTTG 59.550 50.000 13.13 0.00 0.00 3.02
88 89 1.202234 TGTTGATGTTGGTTGTGCACG 60.202 47.619 13.13 0.00 0.00 5.34
90 91 2.232208 TGTTGTTGATGTTGGTTGTGCA 59.768 40.909 0.00 0.00 0.00 4.57
91 92 2.886081 TGTTGTTGATGTTGGTTGTGC 58.114 42.857 0.00 0.00 0.00 4.57
105 106 2.315011 CGCGTGTTTATGCATGTTGTT 58.685 42.857 10.16 0.00 38.79 2.83
106 107 1.962412 CGCGTGTTTATGCATGTTGT 58.038 45.000 10.16 0.00 38.79 3.32
109 110 1.327460 CTAGCGCGTGTTTATGCATGT 59.673 47.619 10.16 0.00 38.79 3.21
110 111 1.917252 GCTAGCGCGTGTTTATGCATG 60.917 52.381 10.16 0.00 38.79 4.06
111 112 0.304705 GCTAGCGCGTGTTTATGCAT 59.695 50.000 8.43 3.79 38.79 3.96
112 113 1.016653 TGCTAGCGCGTGTTTATGCA 61.017 50.000 10.77 6.47 38.79 3.96
113 114 0.096281 TTGCTAGCGCGTGTTTATGC 59.904 50.000 10.77 3.77 39.65 3.14
114 115 2.519002 TTTGCTAGCGCGTGTTTATG 57.481 45.000 10.77 0.00 39.65 1.90
115 116 3.303132 GCTATTTGCTAGCGCGTGTTTAT 60.303 43.478 10.77 0.00 43.30 1.40
116 117 2.029970 GCTATTTGCTAGCGCGTGTTTA 59.970 45.455 10.77 0.00 43.30 2.01
152 153 9.585099 TTTTTATTGTTTATGCATAGCTCTTGG 57.415 29.630 6.50 0.00 0.00 3.61
188 189 2.973224 CAGATTTGACCGCTTCGTTTTG 59.027 45.455 0.00 0.00 0.00 2.44
200 202 3.743396 AGTTTCTCGACTGCAGATTTGAC 59.257 43.478 23.35 9.66 0.00 3.18
212 214 5.839621 TGGCCATAGTTATAGTTTCTCGAC 58.160 41.667 0.00 0.00 0.00 4.20
217 219 6.258068 GCGGATATGGCCATAGTTATAGTTTC 59.742 42.308 28.58 17.67 0.00 2.78
224 226 3.517500 TGATGCGGATATGGCCATAGTTA 59.482 43.478 28.58 10.07 0.00 2.24
232 234 0.884704 ACGGTTGATGCGGATATGGC 60.885 55.000 0.00 0.00 0.00 4.40
244 246 1.409790 TCGGTTTCAAGAGACGGTTGA 59.590 47.619 0.00 0.00 31.98 3.18
274 276 4.099419 GTCGCCCCCATTTGAGATTTATTT 59.901 41.667 0.00 0.00 0.00 1.40
279 281 0.625849 AGTCGCCCCCATTTGAGATT 59.374 50.000 0.00 0.00 0.00 2.40
294 296 0.460311 AATTGACGGAGGGCTAGTCG 59.540 55.000 0.00 0.00 37.69 4.18
306 308 2.910482 CGACTGCATTTTCCAATTGACG 59.090 45.455 7.12 0.00 0.00 4.35
310 312 4.335400 AAACCGACTGCATTTTCCAATT 57.665 36.364 0.00 0.00 0.00 2.32
311 313 4.335400 AAAACCGACTGCATTTTCCAAT 57.665 36.364 0.00 0.00 0.00 3.16
315 317 7.753132 TGTATGAATAAAACCGACTGCATTTTC 59.247 33.333 0.00 0.00 0.00 2.29
322 324 7.539712 AGATGTGTATGAATAAAACCGACTG 57.460 36.000 0.00 0.00 0.00 3.51
358 361 9.730420 AGATAAACAATATTTTAATGACACGGC 57.270 29.630 0.00 0.00 0.00 5.68
396 400 6.127758 TGAGTTGTGAAAACAAGCACTACATT 60.128 34.615 0.00 0.00 41.17 2.71
450 454 6.358118 CGGTGATTCGGAAAATCTCATTTA 57.642 37.500 0.00 0.00 0.00 1.40
451 455 5.235305 CGGTGATTCGGAAAATCTCATTT 57.765 39.130 0.00 0.00 0.00 2.32
487 491 0.813184 ATTGCAGATCGGGTTTGCTG 59.187 50.000 5.32 0.00 38.60 4.41
706 717 2.224450 ACGAGTGGGATTTTCCGAAAGT 60.224 45.455 0.00 0.00 37.43 2.66
712 723 1.407025 GGAGGACGAGTGGGATTTTCC 60.407 57.143 0.00 0.00 35.23 3.13
1518 1534 2.480759 GCTCTGAAATCGCCATTTGCAT 60.481 45.455 0.00 0.00 41.33 3.96
1523 1539 0.729116 CGTGCTCTGAAATCGCCATT 59.271 50.000 0.00 0.00 0.00 3.16
1530 1546 0.877071 CAACAGGCGTGCTCTGAAAT 59.123 50.000 6.26 1.84 36.22 2.17
1533 1549 1.005748 CTCAACAGGCGTGCTCTGA 60.006 57.895 6.26 6.32 36.22 3.27
1535 1551 2.358003 GCTCAACAGGCGTGCTCT 60.358 61.111 6.26 0.00 0.00 4.09
1557 1573 0.105964 ACAGCCGGCGATATTTAGCA 59.894 50.000 23.20 0.00 34.54 3.49
1665 1684 2.662596 GTGTCCAGGATGCACCGA 59.337 61.111 0.00 0.00 44.74 4.69
1716 1735 0.907486 CATTCTCCTCCAGCCTGTGA 59.093 55.000 0.00 0.00 0.00 3.58
1822 1841 0.108019 AGGGACAGTTTGTTCGGTCC 59.892 55.000 7.31 7.31 46.57 4.46
2070 2089 4.058817 AGAACTCCACAAAAGAAGCTACG 58.941 43.478 0.00 0.00 0.00 3.51
2262 2300 3.304525 GGTACTACATGCTACTGGCTACG 60.305 52.174 0.00 0.00 42.39 3.51
2308 2346 5.477637 TCAGAATTGGCAATTGACTGAATCA 59.522 36.000 28.24 14.80 32.21 2.57
2343 2381 3.770263 TCAAAGCTTGCTGCATACATC 57.230 42.857 1.84 0.00 45.94 3.06
2722 2763 4.381825 GGCATGTGATCAAATAGGCAACAA 60.382 41.667 9.69 0.00 41.41 2.83
2767 2808 9.911788 AATTGACAAGAACACATCCTAATCTAT 57.088 29.630 0.00 0.00 0.00 1.98
2798 2839 4.527816 ACAAAAAGGCTATCCAAATGCTCA 59.472 37.500 0.00 0.00 33.74 4.26
2889 2931 6.906901 AGGAATGGGAGTAGGTACTTGATAAA 59.093 38.462 0.00 0.00 41.75 1.40
2915 2957 6.238897 GGTTCTTGTCACACATAACAATGGAA 60.239 38.462 0.00 0.00 35.03 3.53
2970 3043 6.144886 AGCATATGCACAAAAATAATCATGCG 59.855 34.615 28.62 0.00 45.16 4.73
3097 3175 6.010850 ACTGAGGAGTGTCATACTGAGTTTA 58.989 40.000 0.00 0.00 40.53 2.01
3113 3197 5.804944 ATTACAGATGGATGACTGAGGAG 57.195 43.478 0.00 0.00 37.54 3.69
3143 3238 8.415399 CGCAATAAGCATGATTCACAATCACAT 61.415 37.037 0.00 0.00 43.19 3.21
3144 3239 7.166161 CGCAATAAGCATGATTCACAATCACA 61.166 38.462 0.00 0.00 43.19 3.58
3145 3240 5.172591 CGCAATAAGCATGATTCACAATCAC 59.827 40.000 0.00 0.00 43.19 3.06
3146 3241 5.066246 TCGCAATAAGCATGATTCACAATCA 59.934 36.000 0.00 1.50 44.00 2.57
3147 3242 5.397534 GTCGCAATAAGCATGATTCACAATC 59.602 40.000 0.00 0.00 46.13 2.67
3148 3243 5.066893 AGTCGCAATAAGCATGATTCACAAT 59.933 36.000 0.00 0.00 46.13 2.71
3149 3244 4.395854 AGTCGCAATAAGCATGATTCACAA 59.604 37.500 0.00 0.00 46.13 3.33
3150 3245 3.940852 AGTCGCAATAAGCATGATTCACA 59.059 39.130 0.00 0.00 46.13 3.58
3151 3246 4.521943 GAGTCGCAATAAGCATGATTCAC 58.478 43.478 0.00 0.00 46.13 3.18
3152 3247 3.561310 GGAGTCGCAATAAGCATGATTCA 59.439 43.478 0.00 0.00 46.13 2.57
3153 3248 3.812053 AGGAGTCGCAATAAGCATGATTC 59.188 43.478 0.00 0.00 46.13 2.52
3194 3289 7.878127 GCCAGTAGCTATCCATAGAATTTGTTA 59.122 37.037 0.00 0.00 38.99 2.41
3196 3291 6.183361 TGCCAGTAGCTATCCATAGAATTTGT 60.183 38.462 0.00 0.00 44.23 2.83
3197 3292 6.233434 TGCCAGTAGCTATCCATAGAATTTG 58.767 40.000 0.00 0.00 44.23 2.32
3244 3353 8.713271 TGTCAACAAAAGGTTTCAACAAATAAC 58.287 29.630 0.00 0.00 37.72 1.89
3368 3477 2.778299 AGTTTCAGCCACGCTTGATTA 58.222 42.857 0.00 0.00 36.40 1.75
3369 3478 1.609208 AGTTTCAGCCACGCTTGATT 58.391 45.000 0.00 0.00 36.40 2.57
3370 3479 1.267806 CAAGTTTCAGCCACGCTTGAT 59.732 47.619 0.00 0.00 36.40 2.57
3371 3480 0.662619 CAAGTTTCAGCCACGCTTGA 59.337 50.000 0.00 0.00 36.40 3.02
3376 3485 1.526575 ATGCCCAAGTTTCAGCCACG 61.527 55.000 0.00 0.00 0.00 4.94
3383 3492 3.366374 GCACAGAACTATGCCCAAGTTTC 60.366 47.826 0.00 0.00 37.31 2.78
3478 3588 5.627182 AAGCATACCATGAGAGAAGACAT 57.373 39.130 0.00 0.00 0.00 3.06
3537 3658 7.338800 ACTCTAAAATGTAGATGCCAAATGG 57.661 36.000 0.00 0.00 38.53 3.16
3550 3671 5.342866 ACCTCCAGACCTACTCTAAAATGT 58.657 41.667 0.00 0.00 0.00 2.71
3556 3677 3.120898 TGCTACCTCCAGACCTACTCTA 58.879 50.000 0.00 0.00 0.00 2.43
3576 3697 8.498054 AAGTACTGAAATGTAGGAATGACATG 57.502 34.615 0.00 0.00 37.59 3.21
3577 3698 8.543774 AGAAGTACTGAAATGTAGGAATGACAT 58.456 33.333 0.00 0.00 39.22 3.06
3655 3776 5.914898 TCTAATCACTCTTCATCACGGAA 57.085 39.130 0.00 0.00 0.00 4.30
3657 3778 5.410924 TGTTCTAATCACTCTTCATCACGG 58.589 41.667 0.00 0.00 0.00 4.94
3659 3780 9.593134 ACTTATGTTCTAATCACTCTTCATCAC 57.407 33.333 0.00 0.00 0.00 3.06
3692 3977 3.474961 CACGATATTTCAAAAGCGCTTCG 59.525 43.478 25.24 20.87 0.00 3.79
3731 4016 1.970640 TCAGAAGTTAGGCAGCTGACA 59.029 47.619 24.55 4.76 31.24 3.58
3743 4028 6.515272 AAAACACAACACTGATCAGAAGTT 57.485 33.333 29.27 25.64 33.22 2.66
3843 4128 1.222936 CCTACCCAGCCTGCAAGAG 59.777 63.158 0.00 0.00 34.07 2.85
4186 4471 4.073293 ACAATTTATACCGGGCTGAGAG 57.927 45.455 6.32 0.00 0.00 3.20
4265 4550 9.590451 CACCGTAGTTTCCTCAAAAGTATATTA 57.410 33.333 0.00 0.00 35.68 0.98
4272 4557 2.096417 CGCACCGTAGTTTCCTCAAAAG 60.096 50.000 0.00 0.00 0.00 2.27
4274 4559 1.504359 CGCACCGTAGTTTCCTCAAA 58.496 50.000 0.00 0.00 0.00 2.69
4276 4561 1.180456 TCCGCACCGTAGTTTCCTCA 61.180 55.000 0.00 0.00 0.00 3.86
4300 4585 7.399523 CAGATCATTTCTCCCACACAATGGC 62.400 48.000 0.00 0.00 38.97 4.40
4330 4616 6.402222 ACCATAACACACAAACACACAAAAT 58.598 32.000 0.00 0.00 0.00 1.82
4332 4618 5.392767 ACCATAACACACAAACACACAAA 57.607 34.783 0.00 0.00 0.00 2.83
4351 4639 7.735917 AGATTGGTAATAGAAATGATCGACCA 58.264 34.615 0.00 0.00 32.88 4.02
4371 4659 5.865552 CCAGCAAAACTACATTCCAAGATTG 59.134 40.000 0.00 0.00 0.00 2.67
4403 4691 2.419990 CGGTGGTCAAATAGGCAGATCA 60.420 50.000 0.00 0.00 0.00 2.92
4404 4692 2.213499 CGGTGGTCAAATAGGCAGATC 58.787 52.381 0.00 0.00 0.00 2.75
4407 4695 0.748005 CCCGGTGGTCAAATAGGCAG 60.748 60.000 0.00 0.00 0.00 4.85
4408 4696 1.301623 CCCGGTGGTCAAATAGGCA 59.698 57.895 0.00 0.00 0.00 4.75
4413 4709 1.689892 ACCAAAACCCGGTGGTCAAAT 60.690 47.619 8.62 0.00 45.18 2.32
4415 4711 1.306970 ACCAAAACCCGGTGGTCAA 59.693 52.632 8.62 0.00 45.18 3.18
4419 4715 0.537653 AAACAACCAAAACCCGGTGG 59.462 50.000 7.26 7.26 41.00 4.61
4442 4738 3.253188 GTGCAGAAGAAAAGGTGCATACA 59.747 43.478 0.00 0.00 46.93 2.29
4445 4741 2.309613 TGTGCAGAAGAAAAGGTGCAT 58.690 42.857 0.00 0.00 46.93 3.96
4448 4744 4.108699 TGTTTGTGCAGAAGAAAAGGTG 57.891 40.909 0.00 0.00 0.00 4.00
4449 4745 4.402155 TCATGTTTGTGCAGAAGAAAAGGT 59.598 37.500 0.00 0.00 0.00 3.50
4450 4746 4.935702 TCATGTTTGTGCAGAAGAAAAGG 58.064 39.130 0.00 0.00 0.00 3.11
4507 4839 5.606749 TGCTACTCCCTCATATATTGGTTGT 59.393 40.000 0.00 3.04 0.00 3.32
4509 4841 6.959606 ATGCTACTCCCTCATATATTGGTT 57.040 37.500 0.00 0.00 0.00 3.67
4510 4842 6.959606 AATGCTACTCCCTCATATATTGGT 57.040 37.500 0.00 0.00 0.00 3.67
4541 4873 8.712363 CACATATAACAAAGGAATCCAGATACG 58.288 37.037 0.61 0.00 0.00 3.06
4579 4932 9.109393 TGCAATATAGCCAACTTCTAAAGTAAG 57.891 33.333 0.00 0.00 41.91 2.34
4606 5045 3.729163 GCGATTAGCCAACAAAAGCTCTC 60.729 47.826 0.00 0.00 40.56 3.20
4695 5135 1.990799 TTTCGTCGTCTTGATGCGAT 58.009 45.000 9.02 0.00 39.38 4.58
4710 5219 4.325472 ACTTAGACGGCGTTATTCTTTTCG 59.675 41.667 16.19 0.00 0.00 3.46
4726 5235 6.848451 TGAAAAAGTGTGGTCAAACTTAGAC 58.152 36.000 6.93 3.26 35.60 2.59
4733 5242 6.284459 AACAAACTGAAAAAGTGTGGTCAAA 58.716 32.000 1.04 0.00 40.27 2.69
4735 5244 5.461032 AACAAACTGAAAAAGTGTGGTCA 57.539 34.783 1.04 0.00 40.27 4.02
4736 5245 6.779115 AAAACAAACTGAAAAAGTGTGGTC 57.221 33.333 1.04 0.00 43.82 4.02
4758 5267 6.726299 TGGGTCCCATCACATTTACATAAAAA 59.274 34.615 6.47 0.00 0.00 1.94
4759 5268 6.256819 TGGGTCCCATCACATTTACATAAAA 58.743 36.000 6.47 0.00 0.00 1.52
4761 5270 5.458451 TGGGTCCCATCACATTTACATAA 57.542 39.130 6.47 0.00 0.00 1.90
4762 5271 5.384336 CATGGGTCCCATCACATTTACATA 58.616 41.667 21.49 0.00 43.15 2.29
4763 5272 4.217510 CATGGGTCCCATCACATTTACAT 58.782 43.478 21.49 0.00 43.15 2.29
4764 5273 3.630168 CATGGGTCCCATCACATTTACA 58.370 45.455 21.49 0.00 43.15 2.41
4765 5274 2.362077 GCATGGGTCCCATCACATTTAC 59.638 50.000 21.49 0.00 43.15 2.01
4767 5276 1.273154 TGCATGGGTCCCATCACATTT 60.273 47.619 21.49 0.00 43.15 2.32
4768 5277 0.335705 TGCATGGGTCCCATCACATT 59.664 50.000 21.49 0.00 43.15 2.71
4771 5280 1.205417 CTTTTGCATGGGTCCCATCAC 59.795 52.381 21.49 16.04 43.15 3.06
4773 5282 0.826062 CCTTTTGCATGGGTCCCATC 59.174 55.000 21.49 15.47 43.15 3.51
4774 5283 0.413037 TCCTTTTGCATGGGTCCCAT 59.587 50.000 18.56 18.56 46.37 4.00
4775 5284 0.251742 CTCCTTTTGCATGGGTCCCA 60.252 55.000 14.64 14.64 38.19 4.37
4777 5286 0.251787 ACCTCCTTTTGCATGGGTCC 60.252 55.000 0.00 0.00 0.00 4.46
4778 5287 0.890683 CACCTCCTTTTGCATGGGTC 59.109 55.000 0.00 0.00 0.00 4.46
4780 5289 0.890683 GTCACCTCCTTTTGCATGGG 59.109 55.000 0.00 0.00 0.00 4.00
4781 5290 1.915141 AGTCACCTCCTTTTGCATGG 58.085 50.000 0.00 0.00 0.00 3.66
4782 5291 6.375455 ACTTATAAGTCACCTCCTTTTGCATG 59.625 38.462 12.50 0.00 32.86 4.06
4785 5294 6.819397 AACTTATAAGTCACCTCCTTTTGC 57.181 37.500 18.28 0.00 38.57 3.68
4800 7270 7.940137 TGCTCCACCTCAACTTAAAACTTATAA 59.060 33.333 0.00 0.00 0.00 0.98
4801 7271 7.455058 TGCTCCACCTCAACTTAAAACTTATA 58.545 34.615 0.00 0.00 0.00 0.98
4803 7273 5.686753 TGCTCCACCTCAACTTAAAACTTA 58.313 37.500 0.00 0.00 0.00 2.24
4804 7274 4.532834 TGCTCCACCTCAACTTAAAACTT 58.467 39.130 0.00 0.00 0.00 2.66
4805 7275 4.164843 TGCTCCACCTCAACTTAAAACT 57.835 40.909 0.00 0.00 0.00 2.66
4807 7277 6.478512 AAATTGCTCCACCTCAACTTAAAA 57.521 33.333 0.00 0.00 0.00 1.52
4810 7280 6.480763 TCATAAATTGCTCCACCTCAACTTA 58.519 36.000 0.00 0.00 0.00 2.24
4812 7282 4.922206 TCATAAATTGCTCCACCTCAACT 58.078 39.130 0.00 0.00 0.00 3.16
4813 7283 5.841957 ATCATAAATTGCTCCACCTCAAC 57.158 39.130 0.00 0.00 0.00 3.18
4814 7284 6.855763 AAATCATAAATTGCTCCACCTCAA 57.144 33.333 0.00 0.00 0.00 3.02
4815 7285 9.639563 TTATAAATCATAAATTGCTCCACCTCA 57.360 29.630 0.00 0.00 0.00 3.86
4817 7287 9.646522 ACTTATAAATCATAAATTGCTCCACCT 57.353 29.630 0.00 0.00 0.00 4.00
4821 7291 9.696917 CCCAACTTATAAATCATAAATTGCTCC 57.303 33.333 0.00 0.00 35.79 4.70
4867 7337 3.070302 GCCCTGTTTGGTTTCAATTACCA 59.930 43.478 0.00 0.00 43.71 3.25
4868 7338 3.556213 GGCCCTGTTTGGTTTCAATTACC 60.556 47.826 0.00 0.00 36.17 2.85
4869 7339 3.323691 AGGCCCTGTTTGGTTTCAATTAC 59.676 43.478 0.00 0.00 32.28 1.89
4870 7340 3.582164 AGGCCCTGTTTGGTTTCAATTA 58.418 40.909 0.00 0.00 32.28 1.40
4872 7342 2.101640 AGGCCCTGTTTGGTTTCAAT 57.898 45.000 0.00 0.00 32.28 2.57
4873 7343 1.872773 AAGGCCCTGTTTGGTTTCAA 58.127 45.000 0.00 0.00 0.00 2.69
4874 7344 2.757894 TAAGGCCCTGTTTGGTTTCA 57.242 45.000 0.00 0.00 0.00 2.69
4875 7345 3.576550 TCATTAAGGCCCTGTTTGGTTTC 59.423 43.478 0.00 0.00 0.00 2.78
4876 7346 3.582164 TCATTAAGGCCCTGTTTGGTTT 58.418 40.909 0.00 0.00 0.00 3.27
4877 7347 3.252554 TCATTAAGGCCCTGTTTGGTT 57.747 42.857 0.00 0.00 0.00 3.67
4878 7348 2.897326 GTTCATTAAGGCCCTGTTTGGT 59.103 45.455 0.00 0.00 0.00 3.67
4879 7349 2.896685 TGTTCATTAAGGCCCTGTTTGG 59.103 45.455 0.00 0.00 0.00 3.28
4880 7350 3.614870 GCTGTTCATTAAGGCCCTGTTTG 60.615 47.826 0.00 0.00 0.00 2.93
4881 7351 2.562738 GCTGTTCATTAAGGCCCTGTTT 59.437 45.455 0.00 0.00 0.00 2.83
4882 7352 2.171003 GCTGTTCATTAAGGCCCTGTT 58.829 47.619 0.00 0.00 0.00 3.16
4883 7353 1.839424 GCTGTTCATTAAGGCCCTGT 58.161 50.000 0.00 0.00 0.00 4.00
4884 7354 0.734889 CGCTGTTCATTAAGGCCCTG 59.265 55.000 0.00 0.00 0.00 4.45
4885 7355 1.032114 GCGCTGTTCATTAAGGCCCT 61.032 55.000 0.00 0.00 0.00 5.19
4886 7356 1.312371 TGCGCTGTTCATTAAGGCCC 61.312 55.000 9.73 0.00 0.00 5.80
4887 7357 0.740737 ATGCGCTGTTCATTAAGGCC 59.259 50.000 9.73 0.00 0.00 5.19
4888 7358 3.904136 ATATGCGCTGTTCATTAAGGC 57.096 42.857 9.73 0.00 0.00 4.35
4889 7359 6.545504 AAGTATATGCGCTGTTCATTAAGG 57.454 37.500 9.73 0.00 0.00 2.69
4890 7360 7.584123 GTGAAAGTATATGCGCTGTTCATTAAG 59.416 37.037 9.73 0.00 0.00 1.85
4891 7361 7.279981 AGTGAAAGTATATGCGCTGTTCATTAA 59.720 33.333 9.73 0.00 0.00 1.40
4892 7362 6.761242 AGTGAAAGTATATGCGCTGTTCATTA 59.239 34.615 9.73 0.00 0.00 1.90
4893 7363 5.586243 AGTGAAAGTATATGCGCTGTTCATT 59.414 36.000 9.73 2.17 0.00 2.57
4894 7364 5.007039 CAGTGAAAGTATATGCGCTGTTCAT 59.993 40.000 9.73 0.00 34.96 2.57
4895 7365 4.329801 CAGTGAAAGTATATGCGCTGTTCA 59.670 41.667 9.73 5.01 34.96 3.18
4896 7366 4.330074 ACAGTGAAAGTATATGCGCTGTTC 59.670 41.667 9.73 2.39 46.40 3.18
4897 7367 4.093408 CACAGTGAAAGTATATGCGCTGTT 59.907 41.667 9.73 0.00 46.40 3.16
4898 7368 3.861840 ACAGTGAAAGTATATGCGCTGT 58.138 40.909 9.73 0.00 44.50 4.40
4899 7369 3.865164 TCACAGTGAAAGTATATGCGCTG 59.135 43.478 9.73 0.00 42.75 5.18
4900 7370 4.123497 TCACAGTGAAAGTATATGCGCT 57.877 40.909 9.73 0.00 0.00 5.92
4901 7371 4.857871 TTCACAGTGAAAGTATATGCGC 57.142 40.909 13.90 0.00 32.71 6.09
4902 7372 6.250819 CCTTTTCACAGTGAAAGTATATGCG 58.749 40.000 24.42 9.80 45.77 4.73
4903 7373 6.555315 CCCTTTTCACAGTGAAAGTATATGC 58.445 40.000 24.42 0.00 45.77 3.14
4904 7374 6.555315 GCCCTTTTCACAGTGAAAGTATATG 58.445 40.000 24.42 14.05 45.77 1.78
4905 7375 5.354234 CGCCCTTTTCACAGTGAAAGTATAT 59.646 40.000 24.42 0.00 45.77 0.86
4924 7394 4.332543 TGTTCCCCCTCTCGCCCT 62.333 66.667 0.00 0.00 0.00 5.19
4925 7395 3.787001 CTGTTCCCCCTCTCGCCC 61.787 72.222 0.00 0.00 0.00 6.13
4926 7396 3.787001 CCTGTTCCCCCTCTCGCC 61.787 72.222 0.00 0.00 0.00 5.54
4927 7397 3.787001 CCCTGTTCCCCCTCTCGC 61.787 72.222 0.00 0.00 0.00 5.03
4928 7398 3.083997 CCCCTGTTCCCCCTCTCG 61.084 72.222 0.00 0.00 0.00 4.04
4930 7400 2.456840 CTCCCCTGTTCCCCCTCT 59.543 66.667 0.00 0.00 0.00 3.69
4931 7401 1.996187 GACTCCCCTGTTCCCCCTC 60.996 68.421 0.00 0.00 0.00 4.30
4932 7402 2.125225 GACTCCCCTGTTCCCCCT 59.875 66.667 0.00 0.00 0.00 4.79
4933 7403 3.015753 GGACTCCCCTGTTCCCCC 61.016 72.222 0.00 0.00 0.00 5.40
4948 7896 2.611486 CGGGGGTAGGGTTTGGGA 60.611 66.667 0.00 0.00 0.00 4.37
4977 7925 0.185175 GGCGGGATAGGTTGGGAATT 59.815 55.000 0.00 0.00 0.00 2.17
4986 7934 2.108362 GTGTTCCGGCGGGATAGG 59.892 66.667 27.98 0.00 43.41 2.57


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

AutoCloner maintained by Alex Coulton.