Multiple sequence alignment - TraesCS2D01G355000

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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 TraesCS2D01G355000 chr2D 100.000 5187 0 0 1 5187 455935812 455940998 0.000000e+00 9579.0
1 TraesCS2D01G355000 chr2D 89.619 289 29 1 4891 5179 423119761 423120048 2.950000e-97 366.0
2 TraesCS2D01G355000 chr2D 85.417 144 9 4 4392 4531 349588032 349588167 7.000000e-29 139.0
3 TraesCS2D01G355000 chr2D 81.429 140 24 2 1 138 547700012 547699873 4.250000e-21 113.0
4 TraesCS2D01G355000 chr2D 95.455 44 0 2 4532 4575 455940309 455940350 9.320000e-08 69.4
5 TraesCS2D01G355000 chr2D 94.595 37 1 1 4629 4664 455940469 455940505 7.260000e-04 56.5
6 TraesCS2D01G355000 chr2B 90.853 2733 159 35 1816 4475 536816798 536819512 0.000000e+00 3578.0
7 TraesCS2D01G355000 chr2B 92.681 1708 62 11 132 1778 536814659 536816364 0.000000e+00 2403.0
8 TraesCS2D01G355000 chr2B 85.608 674 38 13 4541 5187 536819526 536820167 0.000000e+00 652.0
9 TraesCS2D01G355000 chr2B 88.889 297 29 3 4892 5187 495838285 495838578 3.820000e-96 363.0
10 TraesCS2D01G355000 chr2B 88.889 297 30 3 4891 5187 719433517 719433810 3.820000e-96 363.0
11 TraesCS2D01G355000 chr2B 86.036 222 31 0 4665 4886 235061247 235061026 6.710000e-59 239.0
12 TraesCS2D01G355000 chr2B 85.806 155 7 7 4392 4539 416184672 416184526 3.240000e-32 150.0
13 TraesCS2D01G355000 chr2B 90.265 113 8 2 4533 4642 104953013 104952901 1.510000e-30 145.0
14 TraesCS2D01G355000 chr2B 98.387 62 1 0 1762 1823 536816469 536816530 5.490000e-20 110.0
15 TraesCS2D01G355000 chr2A 93.445 2090 92 15 2466 4533 594996748 594994682 0.000000e+00 3059.0
16 TraesCS2D01G355000 chr2A 92.373 2124 90 20 421 2478 594998998 594996881 0.000000e+00 2959.0
17 TraesCS2D01G355000 chr2A 92.000 350 12 3 4691 5036 594994376 594994039 1.310000e-130 477.0
18 TraesCS2D01G355000 chr2A 90.830 229 5 5 251 469 594999250 594999028 5.080000e-75 292.0
19 TraesCS2D01G355000 chr2A 86.607 224 29 1 4662 4885 727919285 727919507 4.010000e-61 246.0
20 TraesCS2D01G355000 chr2A 86.161 224 17 3 4541 4763 594994708 594994498 4.040000e-56 230.0
21 TraesCS2D01G355000 chr2A 93.600 125 4 2 135 255 595000208 595000084 3.190000e-42 183.0
22 TraesCS2D01G355000 chr2A 82.270 141 23 2 1 139 79539484 79539624 2.540000e-23 121.0
23 TraesCS2D01G355000 chr2A 78.723 141 28 2 1 139 638588904 638588764 5.530000e-15 93.5
24 TraesCS2D01G355000 chr2A 78.986 138 27 2 3 138 653029869 653030006 5.530000e-15 93.5
25 TraesCS2D01G355000 chr3D 91.468 293 21 2 4895 5187 151436220 151435932 2.910000e-107 399.0
26 TraesCS2D01G355000 chr3D 90.816 294 26 1 4894 5187 182049920 182049628 4.870000e-105 392.0
27 TraesCS2D01G355000 chr3D 85.417 144 9 6 4392 4531 613620741 613620876 7.000000e-29 139.0
28 TraesCS2D01G355000 chr1B 89.761 293 29 1 4895 5187 305266560 305266269 1.760000e-99 374.0
29 TraesCS2D01G355000 chr1B 87.330 221 28 0 4665 4885 286952398 286952618 2.400000e-63 254.0
30 TraesCS2D01G355000 chr7B 88.889 297 31 2 4891 5187 638734924 638735218 1.060000e-96 364.0
31 TraesCS2D01G355000 chr7B 83.824 136 20 2 1 134 516898129 516898264 1.520000e-25 128.0
32 TraesCS2D01G355000 chr7B 83.448 145 11 9 4389 4531 58641511 58641644 7.050000e-24 122.0
33 TraesCS2D01G355000 chr4A 88.475 295 31 3 4894 5187 30189237 30188945 2.300000e-93 353.0
34 TraesCS2D01G355000 chr4A 80.925 346 46 7 4541 4885 433848128 433847802 6.670000e-64 255.0
35 TraesCS2D01G355000 chr4A 86.878 221 28 1 4665 4885 30166170 30165951 4.010000e-61 246.0
36 TraesCS2D01G355000 chr3A 88.294 299 29 5 4891 5187 617541874 617542168 2.300000e-93 353.0
37 TraesCS2D01G355000 chr3A 83.448 145 10 7 4391 4531 745372894 745373028 7.050000e-24 122.0
38 TraesCS2D01G355000 chr1A 87.111 225 28 1 4662 4885 266878818 266879042 2.400000e-63 254.0
39 TraesCS2D01G355000 chr1A 82.734 139 22 2 1 138 523005895 523006032 7.050000e-24 122.0
40 TraesCS2D01G355000 chr1A 82.014 139 23 2 1 138 525102821 525102684 3.280000e-22 117.0
41 TraesCS2D01G355000 chr5D 86.607 224 28 2 4662 4885 216159443 216159664 4.010000e-61 246.0
42 TraesCS2D01G355000 chr5D 84.967 153 10 6 4392 4539 242571910 242572054 5.410000e-30 143.0
43 TraesCS2D01G355000 chr5D 85.517 145 7 7 4402 4540 335661755 335661619 7.000000e-29 139.0
44 TraesCS2D01G355000 chr3B 86.161 224 31 0 4662 4885 566473582 566473805 5.190000e-60 243.0
45 TraesCS2D01G355000 chr3B 89.474 95 10 0 4541 4635 409960798 409960704 2.540000e-23 121.0
46 TraesCS2D01G355000 chr1D 85.714 224 32 0 4662 4885 211620013 211620236 2.410000e-58 237.0
47 TraesCS2D01G355000 chr7D 86.957 138 16 2 1 136 70816716 70816579 2.500000e-33 154.0
48 TraesCS2D01G355000 chr7D 85.915 142 7 7 4393 4529 257512119 257511986 7.000000e-29 139.0
49 TraesCS2D01G355000 chr5B 85.333 150 9 7 4395 4539 256050475 256050334 5.410000e-30 143.0
50 TraesCS2D01G355000 chr6B 85.315 143 9 5 4393 4531 72885268 72885402 2.520000e-28 137.0
51 TraesCS2D01G355000 chr6D 82.394 142 22 3 1 140 413041716 413041856 2.540000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G355000 chr2D 455935812 455940998 5186 False 3234.966667 9579 96.683333 1 5187 3 chr2D.!!$F3 5186
1 TraesCS2D01G355000 chr2B 536814659 536820167 5508 False 1685.750000 3578 91.882250 132 5187 4 chr2B.!!$F3 5055
2 TraesCS2D01G355000 chr2A 594994039 595000208 6169 True 1200.000000 3059 91.401500 135 5036 6 chr2A.!!$R2 4901

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
98 99 0.110238 CGTGCCAACTCAAACGGATG 60.110 55.0 0.0 0.00 32.55 3.51 F
1014 1980 0.175760 TCGCAATGTCTGGGTCTAGC 59.824 55.0 0.0 0.00 39.04 3.42 F
1407 2373 0.986527 TCTCTGCCATGCTGGAAAGA 59.013 50.0 6.4 6.98 40.96 2.52 F
2593 4177 0.550914 TCCCTGTTTTGCTCCAGTGT 59.449 50.0 0.0 0.00 0.00 3.55 F
3678 5286 0.593128 ACTGACATTTTGGACGCAGC 59.407 50.0 0.0 0.00 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 2373 1.122227 GAGAAGCAGATCCAGCCTCT 58.878 55.000 8.23 8.23 35.59 3.69 R
1871 3265 1.140312 ACACAACCACACTGGATCCT 58.860 50.000 14.23 0.00 40.96 3.24 R
3318 4907 1.277579 TGCCAAATGCCAACATCCAT 58.722 45.000 0.00 0.00 40.16 3.41 R
3998 5607 0.107654 GCAAACCGGTAGCAGGAGAT 60.108 55.000 22.82 0.00 0.00 2.75 R
4686 6379 1.404391 GGTCGCTCTTTCGGTCTATCA 59.596 52.381 0.00 0.00 0.00 2.15 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
30 31 3.978764 CGTCGACACGCACGCAAA 61.979 61.111 17.16 0.00 39.69 3.68
31 32 2.321740 GTCGACACGCACGCAAAA 59.678 55.556 11.55 0.00 0.00 2.44
32 33 1.996713 GTCGACACGCACGCAAAAC 60.997 57.895 11.55 0.00 0.00 2.43
42 43 2.867472 CGCAAAACGGGCTCGATT 59.133 55.556 15.95 3.34 40.11 3.34
43 44 1.209127 CGCAAAACGGGCTCGATTT 59.791 52.632 15.95 11.75 41.01 2.17
46 47 2.263153 AAAACGGGCTCGATTTGGG 58.737 52.632 15.95 0.00 39.34 4.12
47 48 0.538746 AAAACGGGCTCGATTTGGGT 60.539 50.000 15.95 0.00 39.34 4.51
48 49 0.538746 AAACGGGCTCGATTTGGGTT 60.539 50.000 15.95 0.00 40.11 4.11
49 50 0.538746 AACGGGCTCGATTTGGGTTT 60.539 50.000 15.95 0.00 40.11 3.27
50 51 1.241315 ACGGGCTCGATTTGGGTTTG 61.241 55.000 15.95 0.00 40.11 2.93
51 52 1.890174 GGGCTCGATTTGGGTTTGG 59.110 57.895 0.00 0.00 0.00 3.28
52 53 1.604147 GGGCTCGATTTGGGTTTGGG 61.604 60.000 0.00 0.00 0.00 4.12
53 54 0.898326 GGCTCGATTTGGGTTTGGGT 60.898 55.000 0.00 0.00 0.00 4.51
54 55 0.526211 GCTCGATTTGGGTTTGGGTC 59.474 55.000 0.00 0.00 0.00 4.46
55 56 0.802494 CTCGATTTGGGTTTGGGTCG 59.198 55.000 0.00 0.00 0.00 4.79
56 57 0.606944 TCGATTTGGGTTTGGGTCGG 60.607 55.000 0.00 0.00 0.00 4.79
57 58 1.589630 GATTTGGGTTTGGGTCGGC 59.410 57.895 0.00 0.00 0.00 5.54
58 59 2.207788 GATTTGGGTTTGGGTCGGCG 62.208 60.000 0.00 0.00 0.00 6.46
62 63 3.370231 GGTTTGGGTCGGCGCATT 61.370 61.111 7.88 0.00 37.40 3.56
63 64 2.126502 GTTTGGGTCGGCGCATTG 60.127 61.111 7.88 0.00 37.40 2.82
64 65 3.369400 TTTGGGTCGGCGCATTGG 61.369 61.111 7.88 0.00 37.40 3.16
73 74 2.973082 GCGCATTGGGCCTCTTTT 59.027 55.556 14.33 0.00 40.31 2.27
74 75 1.293179 GCGCATTGGGCCTCTTTTT 59.707 52.632 14.33 0.00 40.31 1.94
90 91 1.464734 TTTTTGTCCGTGCCAACTCA 58.535 45.000 0.00 0.00 0.00 3.41
91 92 1.464734 TTTTGTCCGTGCCAACTCAA 58.535 45.000 0.00 0.00 0.00 3.02
92 93 1.464734 TTTGTCCGTGCCAACTCAAA 58.535 45.000 0.00 0.00 0.00 2.69
93 94 0.736053 TTGTCCGTGCCAACTCAAAC 59.264 50.000 0.00 0.00 0.00 2.93
94 95 1.278637 GTCCGTGCCAACTCAAACG 59.721 57.895 0.00 0.00 35.85 3.60
96 97 3.725819 CGTGCCAACTCAAACGGA 58.274 55.556 0.00 0.00 32.55 4.69
97 98 2.244000 CGTGCCAACTCAAACGGAT 58.756 52.632 0.00 0.00 32.55 4.18
98 99 0.110238 CGTGCCAACTCAAACGGATG 60.110 55.000 0.00 0.00 32.55 3.51
99 100 0.240945 GTGCCAACTCAAACGGATGG 59.759 55.000 0.00 0.00 0.00 3.51
101 102 1.501741 CCAACTCAAACGGATGGCG 59.498 57.895 0.00 0.00 0.00 5.69
102 103 1.501741 CAACTCAAACGGATGGCGG 59.498 57.895 0.00 0.00 0.00 6.13
103 104 2.332654 AACTCAAACGGATGGCGGC 61.333 57.895 0.00 0.00 0.00 6.53
104 105 2.745884 CTCAAACGGATGGCGGCA 60.746 61.111 16.34 16.34 0.00 5.69
105 106 2.745884 TCAAACGGATGGCGGCAG 60.746 61.111 19.29 6.47 0.00 4.85
106 107 2.745884 CAAACGGATGGCGGCAGA 60.746 61.111 19.29 0.00 0.00 4.26
107 108 2.746277 AAACGGATGGCGGCAGAC 60.746 61.111 19.29 13.80 0.00 3.51
119 120 1.710339 GGCAGACGAAATGAGTCGC 59.290 57.895 0.00 5.22 45.00 5.19
120 121 1.696832 GGCAGACGAAATGAGTCGCC 61.697 60.000 13.15 13.15 45.00 5.54
121 122 1.696832 GCAGACGAAATGAGTCGCCC 61.697 60.000 0.00 0.00 45.00 6.13
122 123 0.389817 CAGACGAAATGAGTCGCCCA 60.390 55.000 0.00 0.00 45.00 5.36
123 124 0.537188 AGACGAAATGAGTCGCCCAT 59.463 50.000 0.00 0.00 45.00 4.00
124 125 1.066143 AGACGAAATGAGTCGCCCATT 60.066 47.619 0.00 0.00 45.00 3.16
125 126 1.062587 GACGAAATGAGTCGCCCATTG 59.937 52.381 0.00 0.00 45.00 2.82
126 127 1.338674 ACGAAATGAGTCGCCCATTGA 60.339 47.619 0.00 0.00 45.00 2.57
127 128 1.737236 CGAAATGAGTCGCCCATTGAA 59.263 47.619 0.00 0.00 34.75 2.69
128 129 2.223112 CGAAATGAGTCGCCCATTGAAG 60.223 50.000 0.00 0.00 34.75 3.02
129 130 2.496899 AATGAGTCGCCCATTGAAGT 57.503 45.000 0.00 0.00 33.41 3.01
130 131 2.496899 ATGAGTCGCCCATTGAAGTT 57.503 45.000 0.00 0.00 0.00 2.66
133 134 0.250901 AGTCGCCCATTGAAGTTGCT 60.251 50.000 0.00 0.00 0.00 3.91
145 146 7.318141 CCATTGAAGTTGCTCTAACAATGATT 58.682 34.615 23.99 2.39 44.10 2.57
152 153 3.374988 TGCTCTAACAATGATTGAAGGCG 59.625 43.478 12.80 5.49 0.00 5.52
270 1116 1.276138 TGAGGCATCTCTCGAAGCAAA 59.724 47.619 0.00 0.00 40.58 3.68
278 1124 0.321671 TCTCGAAGCAAAGGGACAGG 59.678 55.000 0.00 0.00 0.00 4.00
378 1225 4.499037 AAACACCTCGCTAAACCAAATC 57.501 40.909 0.00 0.00 0.00 2.17
379 1226 3.418684 ACACCTCGCTAAACCAAATCT 57.581 42.857 0.00 0.00 0.00 2.40
380 1227 4.546829 ACACCTCGCTAAACCAAATCTA 57.453 40.909 0.00 0.00 0.00 1.98
469 1411 1.376942 CTGCTACTGCTGCCTGCTT 60.377 57.895 0.00 0.00 43.37 3.91
544 1510 1.110518 CGCTCCTAGGGTTCCCTCTC 61.111 65.000 14.24 0.13 37.64 3.20
546 1512 0.259356 CTCCTAGGGTTCCCTCTCGT 59.741 60.000 14.24 0.00 37.64 4.18
549 1515 1.342175 CCTAGGGTTCCCTCTCGTCTT 60.342 57.143 14.24 0.00 37.64 3.01
557 1523 2.277628 CTCTCGTCTTCTCGCGCC 60.278 66.667 0.00 0.00 0.00 6.53
694 1660 2.291741 CTGAGCTTTCGTTTTTGCCTCT 59.708 45.455 0.00 0.00 0.00 3.69
698 1664 2.605580 GCTTTCGTTTTTGCCTCTGAGG 60.606 50.000 19.55 19.55 38.80 3.86
779 1745 4.424711 GCAATGCCGGGGAGGTCA 62.425 66.667 2.18 0.00 43.70 4.02
845 1811 1.153249 GGGGATCGTTCGGAATGCA 60.153 57.895 5.06 0.00 0.00 3.96
871 1837 2.997315 CCCGAGGTCTGGTGCTCA 60.997 66.667 0.00 0.00 0.00 4.26
945 1911 0.840288 TGCTAAGCCTGTGAAGGGGA 60.840 55.000 0.00 0.00 0.00 4.81
1005 1971 1.470098 GCTGATTTGGTCGCAATGTCT 59.530 47.619 0.00 0.00 0.00 3.41
1014 1980 0.175760 TCGCAATGTCTGGGTCTAGC 59.824 55.000 0.00 0.00 39.04 3.42
1203 2169 1.065126 GTGCCTACATTGCTCCCTTCT 60.065 52.381 0.00 0.00 0.00 2.85
1263 2229 1.140804 GCGCTCAGGGTTCTCTCTC 59.859 63.158 0.00 0.00 0.00 3.20
1407 2373 0.986527 TCTCTGCCATGCTGGAAAGA 59.013 50.000 6.40 6.98 40.96 2.52
1512 2479 5.927954 TTTCCATTGCTTTGCATTTTCTC 57.072 34.783 0.00 0.00 38.76 2.87
1569 2536 3.674997 TGGTCTAGTGCAATGGTTTCTC 58.325 45.455 0.00 0.00 0.00 2.87
1604 2571 2.093394 GCCTTTGTTCTAGGGAGAGGAC 60.093 54.545 0.00 0.00 33.19 3.85
1618 2585 1.140452 AGAGGACGCAATCTGCATCAT 59.860 47.619 0.00 0.00 45.36 2.45
1619 2586 1.945394 GAGGACGCAATCTGCATCATT 59.055 47.619 0.00 0.00 45.36 2.57
1655 2622 7.490402 CAGATGAAAAGGTCCATTTTATTGAGC 59.510 37.037 0.00 0.00 32.62 4.26
1736 2726 8.037758 TCTCTGATCTTTAAGATTCCAACTGTC 58.962 37.037 8.99 0.00 34.53 3.51
1854 3248 9.856488 TTACTCACTGTATCAGTATTCTTGTTC 57.144 33.333 2.03 0.00 43.43 3.18
1877 3271 4.442706 ACATTAATGTGTCGTGAGGATCC 58.557 43.478 20.19 2.48 40.03 3.36
1878 3272 4.081142 ACATTAATGTGTCGTGAGGATCCA 60.081 41.667 20.19 0.00 40.03 3.41
1898 3292 2.618241 CAGTGTGGTTGTGTGTAAGCAT 59.382 45.455 0.00 0.00 39.84 3.79
1928 3322 3.012518 ACTGATTGTGTATGCAGAAGGC 58.987 45.455 0.00 0.00 45.13 4.35
2004 3403 9.485206 TTTTGTCATACAGGAACTTTACTCTAC 57.515 33.333 0.00 0.00 34.60 2.59
2112 3526 8.504005 TGAAAGCACAGCTATAAACTTAGAAAC 58.496 33.333 0.00 0.00 38.25 2.78
2114 3528 5.063564 AGCACAGCTATAAACTTAGAAACGC 59.936 40.000 0.00 0.00 36.99 4.84
2115 3529 5.163893 GCACAGCTATAAACTTAGAAACGCA 60.164 40.000 0.00 0.00 0.00 5.24
2130 3544 5.853081 AGAAACGCAAAACAATGTTTTGTC 58.147 33.333 36.48 28.99 45.30 3.18
2144 3558 7.551262 ACAATGTTTTGTCGGACTAGCAATATA 59.449 33.333 9.88 0.00 42.43 0.86
2146 3560 9.772973 AATGTTTTGTCGGACTAGCAATATATA 57.227 29.630 9.88 0.00 0.00 0.86
2214 3632 9.138596 GACCTTATAGAAGAGAGTAGGTGAAAT 57.861 37.037 0.00 0.00 34.82 2.17
2266 3684 4.394920 AGTTAAGGACTTTGTGTGTGTGTG 59.605 41.667 0.00 0.00 33.92 3.82
2357 3775 4.613167 GCATTCTATTACAGAGCTGCATGC 60.613 45.833 11.82 11.82 40.69 4.06
2366 3784 2.825836 GCTGCATGCGGGCTACTT 60.826 61.111 27.34 0.00 34.04 2.24
2401 3837 5.413833 CCAGTAGAGCAACAAATTCACTGAT 59.586 40.000 0.00 0.00 35.32 2.90
2498 4079 4.283212 TGGATTTCCAAGTTGGGATGTTTC 59.717 41.667 21.85 8.00 44.35 2.78
2592 4176 1.610522 CTTCCCTGTTTTGCTCCAGTG 59.389 52.381 0.00 0.00 0.00 3.66
2593 4177 0.550914 TCCCTGTTTTGCTCCAGTGT 59.449 50.000 0.00 0.00 0.00 3.55
2610 4194 6.908825 TCCAGTGTTGCTATTTTCATTACAC 58.091 36.000 0.00 0.00 35.78 2.90
2636 4220 7.067496 AGGACCTGGTAATATGTAATCACAG 57.933 40.000 0.00 0.00 38.30 3.66
2715 4300 7.031226 CCAGTGTGGGACTATCATAAATTTG 57.969 40.000 0.00 0.00 32.67 2.32
2735 4321 5.367945 TTGGGGACATGAACTTATACTCC 57.632 43.478 0.00 0.00 42.32 3.85
2758 4344 5.142061 TGAGCGAAGTGTAGGATTGTTAA 57.858 39.130 0.00 0.00 0.00 2.01
2791 4378 9.378551 TGCATTTCACTACGTAGATATTCTTTT 57.621 29.630 28.74 0.00 0.00 2.27
2835 4422 6.460537 CCAATTGCTGCAATAAGATCAAGCTA 60.461 38.462 26.48 0.00 32.43 3.32
2875 4462 8.411683 TCTAGTGTTTATTTAGAGAATCCGTCC 58.588 37.037 0.00 0.00 33.66 4.79
2882 4469 4.931661 TTAGAGAATCCGTCCCATGTAC 57.068 45.455 0.00 0.00 33.66 2.90
3060 4648 4.408993 TGTTGCATTTCATGACGAAGAG 57.591 40.909 0.00 0.00 34.32 2.85
3096 4684 2.666022 TCATGACGACAAGTATGCAACG 59.334 45.455 0.00 0.00 0.00 4.10
3109 4698 3.770263 ATGCAACGATGAACCTTGATG 57.230 42.857 0.00 0.00 0.00 3.07
3199 4788 9.453572 AAAGAATGTCTTATGAAGTGCTTATGA 57.546 29.630 0.00 0.00 35.27 2.15
3318 4907 7.386848 GGTAGCTCTTTACACTTTTGATGTACA 59.613 37.037 0.00 0.00 32.30 2.90
3478 5067 5.295431 TGTTATCTGAACAGAAATTGCGG 57.705 39.130 8.59 0.00 41.36 5.69
3496 5085 1.676006 CGGGGTGTTATTGAGAATGCC 59.324 52.381 0.00 0.00 0.00 4.40
3535 5127 6.828785 AGGTTAGCCCTTTACTCATAATTGTG 59.171 38.462 0.00 0.00 42.73 3.33
3575 5183 2.821969 ACTAAGTGCTGCTTTGGGATTG 59.178 45.455 0.00 0.00 38.57 2.67
3621 5229 7.604545 AGCTGTATTTCACTCTCCTTAAGTTTC 59.395 37.037 0.97 0.00 0.00 2.78
3636 5244 4.755266 AAGTTTCGGTAGCTCCATATGT 57.245 40.909 1.24 0.00 35.57 2.29
3678 5286 0.593128 ACTGACATTTTGGACGCAGC 59.407 50.000 0.00 0.00 0.00 5.25
3704 5313 6.530120 TCTTGCACCACTTCTACTGATAAAA 58.470 36.000 0.00 0.00 0.00 1.52
3758 5367 4.062293 TCTTGAACCATGTTGTCTTACCG 58.938 43.478 0.00 0.00 0.00 4.02
3772 5381 3.059188 GTCTTACCGTCACCATGTGTTTG 60.059 47.826 0.00 0.00 34.79 2.93
3976 5585 3.324846 TGTACACCTTCATGCAAGTCTCT 59.675 43.478 0.00 0.00 0.00 3.10
3985 5594 0.671472 TGCAAGTCTCTGGCATGACG 60.671 55.000 12.82 0.00 35.23 4.35
3988 5597 2.625737 CAAGTCTCTGGCATGACGAAT 58.374 47.619 12.82 4.09 38.16 3.34
3998 5607 1.675714 GCATGACGAATGACCACCTCA 60.676 52.381 0.00 0.00 38.72 3.86
4188 5797 0.383590 GAGCTCAGCATCTCGTAGCA 59.616 55.000 9.40 0.00 35.63 3.49
4476 6088 9.569167 TTTACAAGAGTATCAACAATCTCTACG 57.431 33.333 0.00 0.00 37.82 3.51
4478 6090 6.377429 ACAAGAGTATCAACAATCTCTACGGA 59.623 38.462 0.00 0.00 37.82 4.69
4490 6102 6.042552 ACAATCTCTACGGATGGATCTTTCAT 59.957 38.462 0.00 0.00 0.00 2.57
4501 6113 2.019984 GATCTTTCATCCACCCTGCAC 58.980 52.381 0.00 0.00 0.00 4.57
4508 6120 1.719063 ATCCACCCTGCACACACCTT 61.719 55.000 0.00 0.00 0.00 3.50
4509 6121 1.898574 CCACCCTGCACACACCTTC 60.899 63.158 0.00 0.00 0.00 3.46
4525 6137 6.183361 ACACACCTTCTAACTAGTTTGGCTAA 60.183 38.462 14.49 1.80 0.00 3.09
4526 6138 6.708949 CACACCTTCTAACTAGTTTGGCTAAA 59.291 38.462 14.49 1.45 0.00 1.85
4527 6139 7.390718 CACACCTTCTAACTAGTTTGGCTAAAT 59.609 37.037 14.49 0.00 0.00 1.40
4528 6140 7.606839 ACACCTTCTAACTAGTTTGGCTAAATC 59.393 37.037 14.49 0.00 0.00 2.17
4529 6141 7.606456 CACCTTCTAACTAGTTTGGCTAAATCA 59.394 37.037 14.49 0.00 0.00 2.57
4530 6142 8.329502 ACCTTCTAACTAGTTTGGCTAAATCAT 58.670 33.333 14.49 0.00 0.00 2.45
4531 6143 9.178758 CCTTCTAACTAGTTTGGCTAAATCATT 57.821 33.333 14.49 0.00 0.00 2.57
4532 6144 9.994432 CTTCTAACTAGTTTGGCTAAATCATTG 57.006 33.333 14.49 0.00 0.00 2.82
4533 6145 7.985476 TCTAACTAGTTTGGCTAAATCATTGC 58.015 34.615 14.49 0.00 0.00 3.56
4534 6146 6.588719 AACTAGTTTGGCTAAATCATTGCA 57.411 33.333 1.12 0.00 0.00 4.08
4535 6147 5.954335 ACTAGTTTGGCTAAATCATTGCAC 58.046 37.500 0.00 0.00 0.00 4.57
4536 6148 4.870123 AGTTTGGCTAAATCATTGCACA 57.130 36.364 0.00 0.00 0.00 4.57
4537 6149 4.559153 AGTTTGGCTAAATCATTGCACAC 58.441 39.130 0.00 0.00 0.00 3.82
4538 6150 4.039004 AGTTTGGCTAAATCATTGCACACA 59.961 37.500 0.00 0.00 0.00 3.72
4539 6151 3.574284 TGGCTAAATCATTGCACACAC 57.426 42.857 0.00 0.00 0.00 3.82
4588 6200 4.222810 TGGCAGCACAATTAGTCTCTCTAA 59.777 41.667 0.00 0.00 41.98 2.10
4613 6225 9.590451 AAGAGCATGTTCAAAAATAATATGTGG 57.410 29.630 12.41 0.00 30.62 4.17
4663 6275 6.902341 TCATCAAAAACTGTTGCTGATAGAC 58.098 36.000 13.97 0.00 30.73 2.59
4665 6277 6.882610 TCAAAAACTGTTGCTGATAGACAT 57.117 33.333 0.00 0.00 0.00 3.06
4666 6278 7.977789 TCAAAAACTGTTGCTGATAGACATA 57.022 32.000 0.00 0.00 0.00 2.29
4668 6280 9.665719 TCAAAAACTGTTGCTGATAGACATATA 57.334 29.630 0.00 0.00 0.00 0.86
4686 6379 9.182214 AGACATATATCATCAAAAACTGTTGCT 57.818 29.630 0.00 0.00 0.00 3.91
4751 6444 3.624305 CGATGTCGTCGGAGTTCAT 57.376 52.632 6.56 0.00 46.47 2.57
4756 6550 4.669318 GATGTCGTCGGAGTTCATCTTTA 58.331 43.478 0.00 0.00 34.12 1.85
4887 6681 4.835615 AGGAATATGCCATTCGAGTCTAGT 59.164 41.667 1.47 0.00 0.00 2.57
4893 6687 3.067320 TGCCATTCGAGTCTAGTCTCATG 59.933 47.826 15.79 12.12 34.46 3.07
5059 6880 4.142271 CGCACTAACTTTCTCCTCTCTCAT 60.142 45.833 0.00 0.00 0.00 2.90
5109 6930 3.120165 GCTTCCGTTGAATTTCTCAGACC 60.120 47.826 0.00 0.00 34.81 3.85
5119 6940 2.215942 TTCTCAGACCGAGGATCACA 57.784 50.000 0.00 0.00 42.55 3.58
5137 6958 2.880268 CACACATTCTTCAGCTGGTTGA 59.120 45.455 15.13 6.99 0.00 3.18
5157 6978 8.451908 GGTTGAACCAATAAATACTCTAGCAT 57.548 34.615 9.98 0.00 38.42 3.79
5182 7003 0.873312 CTCCTGCATGATCCACGACG 60.873 60.000 0.00 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.996713 GTTTTGCGTGCGTGTCGAC 60.997 57.895 9.11 9.11 0.00 4.20
15 16 2.321740 GTTTTGCGTGCGTGTCGA 59.678 55.556 0.00 0.00 0.00 4.20
16 17 3.076727 CGTTTTGCGTGCGTGTCG 61.077 61.111 0.00 0.00 35.54 4.35
17 18 2.720750 CCGTTTTGCGTGCGTGTC 60.721 61.111 0.00 0.00 39.32 3.67
18 19 4.244802 CCCGTTTTGCGTGCGTGT 62.245 61.111 0.00 0.00 39.32 4.49
23 24 2.182614 AATCGAGCCCGTTTTGCGTG 62.183 55.000 0.00 0.00 39.32 5.34
24 25 1.512156 AAATCGAGCCCGTTTTGCGT 61.512 50.000 0.00 0.00 36.63 5.24
25 26 1.065031 CAAATCGAGCCCGTTTTGCG 61.065 55.000 10.57 0.00 43.73 4.85
26 27 0.732538 CCAAATCGAGCCCGTTTTGC 60.733 55.000 16.07 0.00 46.18 3.68
27 28 0.109319 CCCAAATCGAGCCCGTTTTG 60.109 55.000 14.93 14.93 46.66 2.44
28 29 0.538746 ACCCAAATCGAGCCCGTTTT 60.539 50.000 0.00 0.00 37.97 2.43
29 30 0.538746 AACCCAAATCGAGCCCGTTT 60.539 50.000 0.00 0.00 37.05 3.60
30 31 0.538746 AAACCCAAATCGAGCCCGTT 60.539 50.000 0.00 0.00 37.05 4.44
31 32 1.074248 AAACCCAAATCGAGCCCGT 59.926 52.632 0.00 0.00 37.05 5.28
32 33 1.506262 CAAACCCAAATCGAGCCCG 59.494 57.895 0.00 0.00 37.07 6.13
33 34 1.604147 CCCAAACCCAAATCGAGCCC 61.604 60.000 0.00 0.00 0.00 5.19
34 35 0.898326 ACCCAAACCCAAATCGAGCC 60.898 55.000 0.00 0.00 0.00 4.70
35 36 0.526211 GACCCAAACCCAAATCGAGC 59.474 55.000 0.00 0.00 0.00 5.03
36 37 0.802494 CGACCCAAACCCAAATCGAG 59.198 55.000 0.00 0.00 0.00 4.04
37 38 0.606944 CCGACCCAAACCCAAATCGA 60.607 55.000 0.00 0.00 0.00 3.59
38 39 1.880186 CCGACCCAAACCCAAATCG 59.120 57.895 0.00 0.00 0.00 3.34
39 40 1.589630 GCCGACCCAAACCCAAATC 59.410 57.895 0.00 0.00 0.00 2.17
40 41 2.272447 CGCCGACCCAAACCCAAAT 61.272 57.895 0.00 0.00 0.00 2.32
41 42 2.907917 CGCCGACCCAAACCCAAA 60.908 61.111 0.00 0.00 0.00 3.28
45 46 3.370231 AATGCGCCGACCCAAACC 61.370 61.111 4.18 0.00 0.00 3.27
46 47 2.126502 CAATGCGCCGACCCAAAC 60.127 61.111 4.18 0.00 0.00 2.93
47 48 3.369400 CCAATGCGCCGACCCAAA 61.369 61.111 4.18 0.00 0.00 3.28
56 57 1.293179 AAAAAGAGGCCCAATGCGC 59.707 52.632 0.00 0.00 42.61 6.09
71 72 1.464734 TGAGTTGGCACGGACAAAAA 58.535 45.000 0.00 0.00 29.78 1.94
72 73 1.464734 TTGAGTTGGCACGGACAAAA 58.535 45.000 0.00 0.00 29.78 2.44
73 74 1.133407 GTTTGAGTTGGCACGGACAAA 59.867 47.619 0.00 0.00 29.78 2.83
74 75 0.736053 GTTTGAGTTGGCACGGACAA 59.264 50.000 0.00 0.00 0.00 3.18
75 76 1.433053 CGTTTGAGTTGGCACGGACA 61.433 55.000 0.00 0.00 0.00 4.02
76 77 1.278637 CGTTTGAGTTGGCACGGAC 59.721 57.895 0.00 0.00 0.00 4.79
77 78 3.725819 CGTTTGAGTTGGCACGGA 58.274 55.556 0.00 0.00 0.00 4.69
78 79 2.637025 CCGTTTGAGTTGGCACGG 59.363 61.111 0.00 0.00 45.75 4.94
79 80 0.110238 CATCCGTTTGAGTTGGCACG 60.110 55.000 0.00 0.00 0.00 5.34
80 81 0.240945 CCATCCGTTTGAGTTGGCAC 59.759 55.000 0.00 0.00 0.00 5.01
81 82 2.639970 CCATCCGTTTGAGTTGGCA 58.360 52.632 0.00 0.00 0.00 4.92
82 83 1.212751 GCCATCCGTTTGAGTTGGC 59.787 57.895 0.00 0.00 45.31 4.52
83 84 1.501741 CGCCATCCGTTTGAGTTGG 59.498 57.895 0.00 0.00 0.00 3.77
84 85 1.501741 CCGCCATCCGTTTGAGTTG 59.498 57.895 0.00 0.00 34.38 3.16
85 86 2.332654 GCCGCCATCCGTTTGAGTT 61.333 57.895 0.00 0.00 34.38 3.01
86 87 2.746277 GCCGCCATCCGTTTGAGT 60.746 61.111 0.00 0.00 34.38 3.41
87 88 2.745884 TGCCGCCATCCGTTTGAG 60.746 61.111 0.00 0.00 34.38 3.02
88 89 2.745884 CTGCCGCCATCCGTTTGA 60.746 61.111 0.00 0.00 34.38 2.69
89 90 2.745884 TCTGCCGCCATCCGTTTG 60.746 61.111 0.00 0.00 34.38 2.93
90 91 2.746277 GTCTGCCGCCATCCGTTT 60.746 61.111 0.00 0.00 34.38 3.60
93 94 4.812476 TTCGTCTGCCGCCATCCG 62.812 66.667 0.00 0.00 36.19 4.18
94 95 1.819632 ATTTCGTCTGCCGCCATCC 60.820 57.895 0.00 0.00 36.19 3.51
95 96 1.089481 TCATTTCGTCTGCCGCCATC 61.089 55.000 0.00 0.00 36.19 3.51
96 97 1.078497 TCATTTCGTCTGCCGCCAT 60.078 52.632 0.00 0.00 36.19 4.40
97 98 1.741401 CTCATTTCGTCTGCCGCCA 60.741 57.895 0.00 0.00 36.19 5.69
98 99 1.696832 GACTCATTTCGTCTGCCGCC 61.697 60.000 0.00 0.00 36.19 6.13
99 100 1.710339 GACTCATTTCGTCTGCCGC 59.290 57.895 0.00 0.00 36.19 6.53
100 101 1.991430 CGACTCATTTCGTCTGCCG 59.009 57.895 0.00 0.00 34.16 5.69
101 102 1.696832 GGCGACTCATTTCGTCTGCC 61.697 60.000 0.00 0.00 40.53 4.85
102 103 1.696832 GGGCGACTCATTTCGTCTGC 61.697 60.000 0.00 0.00 43.29 4.26
103 104 0.389817 TGGGCGACTCATTTCGTCTG 60.390 55.000 0.00 0.00 43.29 3.51
104 105 0.537188 ATGGGCGACTCATTTCGTCT 59.463 50.000 0.00 0.00 43.29 4.18
105 106 1.062587 CAATGGGCGACTCATTTCGTC 59.937 52.381 2.59 0.00 43.02 4.20
106 107 1.086696 CAATGGGCGACTCATTTCGT 58.913 50.000 2.59 0.00 41.26 3.85
107 108 1.368641 TCAATGGGCGACTCATTTCG 58.631 50.000 2.59 0.00 42.15 3.46
108 109 2.749621 ACTTCAATGGGCGACTCATTTC 59.250 45.455 2.59 0.00 33.08 2.17
109 110 2.795329 ACTTCAATGGGCGACTCATTT 58.205 42.857 2.59 0.00 33.08 2.32
110 111 2.489329 CAACTTCAATGGGCGACTCATT 59.511 45.455 0.00 0.00 35.45 2.57
111 112 2.086869 CAACTTCAATGGGCGACTCAT 58.913 47.619 0.00 0.00 0.00 2.90
112 113 1.522668 CAACTTCAATGGGCGACTCA 58.477 50.000 0.00 0.00 0.00 3.41
113 114 0.169009 GCAACTTCAATGGGCGACTC 59.831 55.000 0.00 0.00 0.00 3.36
114 115 0.250901 AGCAACTTCAATGGGCGACT 60.251 50.000 0.00 0.00 0.00 4.18
115 116 0.169009 GAGCAACTTCAATGGGCGAC 59.831 55.000 0.00 0.00 0.00 5.19
116 117 0.036732 AGAGCAACTTCAATGGGCGA 59.963 50.000 0.00 0.00 0.00 5.54
117 118 1.737838 TAGAGCAACTTCAATGGGCG 58.262 50.000 0.00 0.00 0.00 6.13
118 119 2.819608 TGTTAGAGCAACTTCAATGGGC 59.180 45.455 0.00 0.00 38.05 5.36
119 120 5.183713 TCATTGTTAGAGCAACTTCAATGGG 59.816 40.000 22.84 11.78 42.47 4.00
120 121 6.258230 TCATTGTTAGAGCAACTTCAATGG 57.742 37.500 22.84 14.24 42.47 3.16
121 122 8.024865 TCAATCATTGTTAGAGCAACTTCAATG 58.975 33.333 20.44 20.44 42.91 2.82
122 123 8.114331 TCAATCATTGTTAGAGCAACTTCAAT 57.886 30.769 0.00 0.00 38.05 2.57
123 124 7.509141 TCAATCATTGTTAGAGCAACTTCAA 57.491 32.000 0.00 0.00 38.05 2.69
124 125 7.308770 CCTTCAATCATTGTTAGAGCAACTTCA 60.309 37.037 0.00 0.00 38.05 3.02
125 126 7.025963 CCTTCAATCATTGTTAGAGCAACTTC 58.974 38.462 0.00 0.00 38.05 3.01
126 127 6.571150 GCCTTCAATCATTGTTAGAGCAACTT 60.571 38.462 0.00 0.00 38.05 2.66
127 128 5.105997 GCCTTCAATCATTGTTAGAGCAACT 60.106 40.000 0.00 0.00 38.05 3.16
128 129 5.098211 GCCTTCAATCATTGTTAGAGCAAC 58.902 41.667 0.00 0.00 37.67 4.17
129 130 4.142622 CGCCTTCAATCATTGTTAGAGCAA 60.143 41.667 0.00 0.00 0.00 3.91
130 131 3.374988 CGCCTTCAATCATTGTTAGAGCA 59.625 43.478 0.00 0.00 0.00 4.26
133 134 6.567687 TTTTCGCCTTCAATCATTGTTAGA 57.432 33.333 0.00 0.00 0.00 2.10
162 164 5.242393 TCCTTCTTTGCCTTCAATCTTTCTG 59.758 40.000 0.00 0.00 31.33 3.02
270 1116 0.759346 GTTCACTGTGACCTGTCCCT 59.241 55.000 10.56 0.00 0.00 4.20
278 1124 1.789464 CAGCTCGAAGTTCACTGTGAC 59.211 52.381 10.56 6.16 0.00 3.67
409 1256 0.679960 GGTATTGGTGGGTGGCACTC 60.680 60.000 18.45 15.20 0.00 3.51
413 1337 2.052104 GCTGGTATTGGTGGGTGGC 61.052 63.158 0.00 0.00 0.00 5.01
469 1411 0.117140 AGATGGAGTGAGGTGTCCCA 59.883 55.000 0.00 0.00 31.04 4.37
570 1536 4.148825 CTCCTCCGAACCCCAGCG 62.149 72.222 0.00 0.00 0.00 5.18
573 1539 4.733725 CCCCTCCTCCGAACCCCA 62.734 72.222 0.00 0.00 0.00 4.96
779 1745 1.614241 AACCCTAGCAATCGACGCCT 61.614 55.000 5.09 0.00 0.00 5.52
845 1811 4.070552 GACCTCGGGCAACTCGCT 62.071 66.667 0.00 0.00 41.91 4.93
871 1837 2.704725 ACATCAAATTGCGCGAAAGT 57.295 40.000 12.10 0.00 0.00 2.66
912 1878 2.159379 GCTTAGCAGGAAACCAAATCGG 60.159 50.000 0.00 0.00 42.50 4.18
945 1911 2.108208 AAACCCCTCCTCCTCCTCGT 62.108 60.000 0.00 0.00 0.00 4.18
1005 1971 2.279073 CCCCTCGAGCTAGACCCA 59.721 66.667 6.99 0.00 0.00 4.51
1407 2373 1.122227 GAGAAGCAGATCCAGCCTCT 58.878 55.000 8.23 8.23 35.59 3.69
1569 2536 1.726791 CAAAGGCACTACTGCAGTACG 59.273 52.381 22.67 19.16 46.28 3.67
1584 2551 2.166664 CGTCCTCTCCCTAGAACAAAGG 59.833 54.545 0.00 0.00 0.00 3.11
1592 2559 1.339610 CAGATTGCGTCCTCTCCCTAG 59.660 57.143 0.00 0.00 0.00 3.02
1618 2585 7.777910 TGGACCTTTTCATCTGAACTTTAGAAA 59.222 33.333 0.00 0.00 33.13 2.52
1619 2586 7.287061 TGGACCTTTTCATCTGAACTTTAGAA 58.713 34.615 0.00 0.00 33.13 2.10
1655 2622 7.174426 TGCATCATTGGAATCTAGCATTCTAAG 59.826 37.037 14.30 9.51 33.22 2.18
1871 3265 1.140312 ACACAACCACACTGGATCCT 58.860 50.000 14.23 0.00 40.96 3.24
1877 3271 2.013400 TGCTTACACACAACCACACTG 58.987 47.619 0.00 0.00 0.00 3.66
1878 3272 2.411628 TGCTTACACACAACCACACT 57.588 45.000 0.00 0.00 0.00 3.55
1928 3322 6.320494 ACTAGTCGCATCTAGAAATACCTG 57.680 41.667 15.93 0.00 39.57 4.00
2004 3403 2.099405 ACCCACTGTGTGAAGGTTTTG 58.901 47.619 7.08 0.00 35.23 2.44
2112 3526 2.854777 TCCGACAAAACATTGTTTTGCG 59.145 40.909 36.99 35.41 41.66 4.85
2114 3528 5.173131 GCTAGTCCGACAAAACATTGTTTTG 59.827 40.000 36.09 36.09 43.09 2.44
2115 3529 5.163602 TGCTAGTCCGACAAAACATTGTTTT 60.164 36.000 19.31 19.31 34.90 2.43
2144 3558 6.767902 ACATCGCTGGTCATGTTCTAAAATAT 59.232 34.615 0.00 0.00 28.27 1.28
2146 3560 4.943705 ACATCGCTGGTCATGTTCTAAAAT 59.056 37.500 0.00 0.00 28.27 1.82
2150 3564 3.610040 AACATCGCTGGTCATGTTCTA 57.390 42.857 0.00 0.00 38.59 2.10
2196 3614 7.546250 TTCTCAATTTCACCTACTCTCTTCT 57.454 36.000 0.00 0.00 0.00 2.85
2214 3632 7.039784 CCAAGAAGATACCAACCAAATTCTCAA 60.040 37.037 0.00 0.00 0.00 3.02
2384 3802 5.518848 TTGTGATCAGTGAATTTGTTGCT 57.481 34.783 0.00 0.00 0.00 3.91
2401 3837 9.996554 ACTCAACGATTATATCCATATTTGTGA 57.003 29.630 0.00 0.00 0.00 3.58
2498 4079 5.292589 GGCAAGCATGTGAAAATTATTCCAG 59.707 40.000 0.00 0.00 0.00 3.86
2592 4176 6.806739 GGTCCTTGTGTAATGAAAATAGCAAC 59.193 38.462 0.00 0.00 0.00 4.17
2593 4177 6.719370 AGGTCCTTGTGTAATGAAAATAGCAA 59.281 34.615 0.00 0.00 0.00 3.91
2610 4194 7.279615 TGTGATTACATATTACCAGGTCCTTG 58.720 38.462 0.00 0.00 0.00 3.61
2650 4234 5.299949 TGCATATCGCTGTTATGATTCACT 58.700 37.500 9.39 0.00 43.06 3.41
2715 4300 4.654262 TCAGGAGTATAAGTTCATGTCCCC 59.346 45.833 0.00 0.00 0.00 4.81
2735 4321 3.238108 ACAATCCTACACTTCGCTCAG 57.762 47.619 0.00 0.00 0.00 3.35
2806 4393 7.167924 TGATCTTATTGCAGCAATTGGTAAA 57.832 32.000 25.54 12.32 35.54 2.01
2872 4459 2.618709 GGCAATAGCTTGTACATGGGAC 59.381 50.000 10.47 0.00 41.70 4.46
2875 4462 2.936202 AGGGCAATAGCTTGTACATGG 58.064 47.619 10.47 1.92 41.70 3.66
2882 4469 5.105997 GGCAATAAGATAGGGCAATAGCTTG 60.106 44.000 9.04 0.00 41.70 4.01
3060 4648 1.351017 TCATGAACTGGAACTCCCCAC 59.649 52.381 0.00 0.00 34.29 4.61
3318 4907 1.277579 TGCCAAATGCCAACATCCAT 58.722 45.000 0.00 0.00 40.16 3.41
3478 5067 1.676006 CGGGCATTCTCAATAACACCC 59.324 52.381 0.00 0.00 0.00 4.61
3496 5085 3.621715 GGCTAACCTTCAGTATTTGTCGG 59.378 47.826 0.00 0.00 0.00 4.79
3605 5213 4.082136 AGCTACCGAAACTTAAGGAGAGTG 60.082 45.833 7.53 0.00 0.00 3.51
3621 5229 6.481976 TGTTTCATTTACATATGGAGCTACCG 59.518 38.462 7.80 0.00 42.61 4.02
3678 5286 3.995199 TCAGTAGAAGTGGTGCAAGAAG 58.005 45.455 0.00 0.00 0.00 2.85
3704 5313 2.927871 GCAAAGATCATGTGCGGCTTTT 60.928 45.455 0.00 0.00 0.00 2.27
3745 5354 3.695830 ATGGTGACGGTAAGACAACAT 57.304 42.857 0.00 0.00 45.11 2.71
3758 5367 3.052036 GCAATGACAAACACATGGTGAC 58.948 45.455 2.98 0.00 36.96 3.67
3772 5381 5.283457 ACTCCTCTATAACCTGCAATGAC 57.717 43.478 0.00 0.00 0.00 3.06
3976 5585 0.676466 GGTGGTCATTCGTCATGCCA 60.676 55.000 0.00 8.36 36.97 4.92
3985 5594 2.744494 GCAGGAGATGAGGTGGTCATTC 60.744 54.545 0.00 0.00 46.64 2.67
3988 5597 0.252421 AGCAGGAGATGAGGTGGTCA 60.252 55.000 0.00 0.00 40.38 4.02
3998 5607 0.107654 GCAAACCGGTAGCAGGAGAT 60.108 55.000 22.82 0.00 0.00 2.75
4100 5709 2.604174 CGTTCGCCTTTTGCTCCGT 61.604 57.895 0.00 0.00 38.05 4.69
4322 5931 5.987347 CACTGATTCAGGAAAAACAAATGCT 59.013 36.000 17.66 0.00 35.51 3.79
4490 6102 2.337879 GAAGGTGTGTGCAGGGTGGA 62.338 60.000 0.00 0.00 0.00 4.02
4497 6109 4.682778 AACTAGTTAGAAGGTGTGTGCA 57.317 40.909 6.26 0.00 0.00 4.57
4501 6113 4.642429 AGCCAAACTAGTTAGAAGGTGTG 58.358 43.478 8.92 0.56 0.00 3.82
4508 6120 7.609918 TGCAATGATTTAGCCAAACTAGTTAGA 59.390 33.333 8.92 0.00 30.79 2.10
4509 6121 7.698130 GTGCAATGATTTAGCCAAACTAGTTAG 59.302 37.037 8.92 4.88 30.79 2.34
4525 6137 5.072741 AGTTAGAAGGTGTGTGCAATGATT 58.927 37.500 0.00 0.00 0.00 2.57
4526 6138 4.655963 AGTTAGAAGGTGTGTGCAATGAT 58.344 39.130 0.00 0.00 0.00 2.45
4527 6139 4.085357 AGTTAGAAGGTGTGTGCAATGA 57.915 40.909 0.00 0.00 0.00 2.57
4528 6140 4.997395 ACTAGTTAGAAGGTGTGTGCAATG 59.003 41.667 0.00 0.00 0.00 2.82
4529 6141 5.228945 ACTAGTTAGAAGGTGTGTGCAAT 57.771 39.130 0.00 0.00 0.00 3.56
4530 6142 4.682778 ACTAGTTAGAAGGTGTGTGCAA 57.317 40.909 0.00 0.00 0.00 4.08
4531 6143 4.682778 AACTAGTTAGAAGGTGTGTGCA 57.317 40.909 6.26 0.00 0.00 4.57
4532 6144 4.213482 CCAAACTAGTTAGAAGGTGTGTGC 59.787 45.833 8.92 0.00 0.00 4.57
4533 6145 4.213482 GCCAAACTAGTTAGAAGGTGTGTG 59.787 45.833 8.92 0.00 0.00 3.82
4534 6146 4.102681 AGCCAAACTAGTTAGAAGGTGTGT 59.897 41.667 8.92 0.00 0.00 3.72
4535 6147 4.642429 AGCCAAACTAGTTAGAAGGTGTG 58.358 43.478 8.92 0.56 0.00 3.82
4536 6148 4.976540 AGCCAAACTAGTTAGAAGGTGT 57.023 40.909 8.92 0.00 0.00 4.16
4537 6149 7.606456 TGATTTAGCCAAACTAGTTAGAAGGTG 59.394 37.037 8.92 2.08 30.79 4.00
4538 6150 7.686434 TGATTTAGCCAAACTAGTTAGAAGGT 58.314 34.615 8.92 6.33 30.79 3.50
4539 6151 8.738645 ATGATTTAGCCAAACTAGTTAGAAGG 57.261 34.615 8.92 9.84 30.79 3.46
4588 6200 8.199449 CCCACATATTATTTTTGAACATGCTCT 58.801 33.333 0.00 0.00 0.00 4.09
4660 6272 9.182214 AGCAACAGTTTTTGATGATATATGTCT 57.818 29.630 0.89 0.00 31.66 3.41
4661 6273 9.229784 CAGCAACAGTTTTTGATGATATATGTC 57.770 33.333 0.00 0.00 44.06 3.06
4670 6282 6.088824 GGTCTATCAGCAACAGTTTTTGATG 58.911 40.000 15.21 2.03 42.95 3.07
4686 6379 1.404391 GGTCGCTCTTTCGGTCTATCA 59.596 52.381 0.00 0.00 0.00 2.15
4751 6444 5.034797 CAGTCGAGTGTAATCGCATAAAGA 58.965 41.667 12.29 0.00 42.43 2.52
4756 6550 2.941453 ACAGTCGAGTGTAATCGCAT 57.059 45.000 24.15 0.00 42.43 4.73
4786 6580 1.439679 GCCTTACGGTTTGGTCTCAG 58.560 55.000 0.00 0.00 0.00 3.35
4870 6664 3.291584 TGAGACTAGACTCGAATGGCAT 58.708 45.455 15.82 0.00 39.49 4.40
4887 6681 6.092670 GCAACTATGTGAAGCTAAACATGAGA 59.907 38.462 19.47 4.24 37.57 3.27
4893 6687 4.938226 AGGAGCAACTATGTGAAGCTAAAC 59.062 41.667 0.00 0.00 35.36 2.01
5030 6851 3.933332 AGGAGAAAGTTAGTGCGTAATGC 59.067 43.478 0.00 0.00 46.70 3.56
5036 6857 3.191581 TGAGAGAGGAGAAAGTTAGTGCG 59.808 47.826 0.00 0.00 0.00 5.34
5059 6880 6.905736 TGCTATTGGTTCCTGGTATTTATGA 58.094 36.000 0.00 0.00 0.00 2.15
5109 6930 2.606725 GCTGAAGAATGTGTGATCCTCG 59.393 50.000 0.00 0.00 0.00 4.63
5119 6940 2.887152 GGTTCAACCAGCTGAAGAATGT 59.113 45.455 17.39 0.00 38.42 2.71
5149 6970 4.662468 TGCAGGAGAAACTATGCTAGAG 57.338 45.455 0.00 0.00 39.42 2.43
5157 6978 3.430790 CGTGGATCATGCAGGAGAAACTA 60.431 47.826 7.33 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.