Multiple sequence alignment - TraesCS5D01G477800

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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 TraesCS5D01G477800 chr5D 100.000 5726 0 0 1 5726 516823021 516817296 0.000000e+00 10575.0
1 TraesCS5D01G477800 chr5A 91.286 3156 164 54 65 3189 644140135 644137060 0.000000e+00 4202.0
2 TraesCS5D01G477800 chr5A 93.298 1507 87 8 3306 4807 644136987 644135490 0.000000e+00 2211.0
3 TraesCS5D01G477800 chr5A 92.698 986 60 8 4747 5726 644135495 644134516 0.000000e+00 1411.0
4 TraesCS5D01G477800 chr5B 93.444 1571 68 18 140 1689 649408545 649406989 0.000000e+00 2298.0
5 TraesCS5D01G477800 chr5B 94.170 1458 71 7 3352 4809 649405043 649403600 0.000000e+00 2209.0
6 TraesCS5D01G477800 chr5B 90.993 1632 103 18 1576 3201 649406779 649405186 0.000000e+00 2159.0
7 TraesCS5D01G477800 chr5B 93.480 997 49 10 4744 5726 649403607 649402613 0.000000e+00 1467.0
8 TraesCS5D01G477800 chr5B 88.060 469 27 7 77 538 649416013 649415567 3.930000e-146 529.0
9 TraesCS5D01G477800 chr5B 84.483 174 18 7 1779 1949 649406437 649406270 4.590000e-36 163.0
10 TraesCS5D01G477800 chr1B 90.732 1025 73 13 4701 5716 34729620 34730631 0.000000e+00 1347.0
11 TraesCS5D01G477800 chr1B 92.199 846 62 3 3394 4239 34727008 34727849 0.000000e+00 1194.0
12 TraesCS5D01G477800 chr1B 92.510 494 27 4 2331 2823 34699807 34700291 0.000000e+00 699.0
13 TraesCS5D01G477800 chr1B 90.517 348 30 3 1992 2338 34699276 34699621 1.880000e-124 457.0
14 TraesCS5D01G477800 chr1B 88.350 309 32 4 2816 3121 34726571 34726878 9.060000e-98 368.0
15 TraesCS5D01G477800 chr1B 83.835 266 34 7 4493 4757 34729317 34729574 1.590000e-60 244.0
16 TraesCS5D01G477800 chr1B 89.394 132 9 3 4368 4498 34727857 34727984 1.650000e-35 161.0
17 TraesCS5D01G477800 chr1B 89.474 57 6 0 4701 4757 34729569 34729625 7.960000e-09 73.1
18 TraesCS5D01G477800 chr3A 86.730 211 22 4 3374 3584 611186965 611186761 4.460000e-56 230.0
19 TraesCS5D01G477800 chr1A 86.256 211 23 5 3374 3584 481643556 481643760 2.080000e-54 224.0
20 TraesCS5D01G477800 chr1A 85.782 211 24 5 3374 3584 34349133 34349337 9.660000e-53 219.0
21 TraesCS5D01G477800 chr7A 85.782 211 24 4 3374 3584 158275506 158275302 9.660000e-53 219.0


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 TraesCS5D01G477800 chr5D 516817296 516823021 5725 True 10575.000000 10575 100.000000 1 5726 1 chr5D.!!$R1 5725
1 TraesCS5D01G477800 chr5A 644134516 644140135 5619 True 2608.000000 4202 92.427333 65 5726 3 chr5A.!!$R1 5661
2 TraesCS5D01G477800 chr5B 649402613 649408545 5932 True 1659.200000 2298 91.314000 140 5726 5 chr5B.!!$R2 5586
3 TraesCS5D01G477800 chr1B 34699276 34700291 1015 False 578.000000 699 91.513500 1992 2823 2 chr1B.!!$F1 831
4 TraesCS5D01G477800 chr1B 34726571 34730631 4060 False 564.516667 1347 88.997333 2816 5716 6 chr1B.!!$F2 2900

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
163 167 0.107410 TTCAGGTGCAACTGTCGGTT 60.107 50.000 30.13 0.00 39.48 4.44 F
550 567 0.250467 AGGCGATCGGATTTCCCATG 60.250 55.000 18.30 0.00 34.14 3.66 F
790 837 1.003118 TCATTGGCTTGTCCGCTTACT 59.997 47.619 0.00 0.00 37.80 2.24 F
1414 1463 1.196354 CGGACTTCTACGACGTTGAGT 59.804 52.381 10.51 9.71 0.00 3.41 F
2386 2981 0.817654 TAGTGGCAGGATCGAGTGTG 59.182 55.000 0.00 0.00 0.00 3.82 F
3427 4102 0.813184 AGACATTGCAATGCCTTCCG 59.187 50.000 33.94 13.40 40.04 4.30 F
4350 5028 0.100861 GAGCTACTACACCAGACGGC 59.899 60.000 0.00 0.00 34.57 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1332 1381 2.490217 CGCACCCACTCCTCGTAG 59.510 66.667 0.00 0.0 0.00 3.51 R
2359 2954 0.188587 ATCCTGCCACTATCCGAGGA 59.811 55.000 0.00 0.0 37.24 3.71 R
2371 2966 2.185310 AACCCACACTCGATCCTGCC 62.185 60.000 0.00 0.0 0.00 4.85 R
2800 3396 0.329261 CTGGATCTGTGGCAAAGGGA 59.671 55.000 4.51 0.0 0.00 4.20 R
3486 4161 0.108472 CCATCTCAGCAAGACGAGCA 60.108 55.000 0.00 0.0 36.65 4.26 R
4626 6641 1.153349 GGGATTGTCCGAGTCAGCC 60.153 63.158 0.00 0.0 37.43 4.85 R
5510 7656 2.507484 CAAAAGGGTGATGCAGTGAGA 58.493 47.619 0.00 0.0 0.00 3.27 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
22 23 4.892655 TGCTATCTAAACGTTCGCAAATG 58.107 39.130 0.00 0.00 0.00 2.32
23 24 4.390603 TGCTATCTAAACGTTCGCAAATGT 59.609 37.500 0.00 0.00 36.14 2.71
24 25 4.956184 GCTATCTAAACGTTCGCAAATGTC 59.044 41.667 0.00 0.00 33.42 3.06
25 26 3.427516 TCTAAACGTTCGCAAATGTCG 57.572 42.857 0.00 0.00 33.42 4.35
26 27 3.051327 TCTAAACGTTCGCAAATGTCGA 58.949 40.909 0.00 0.00 33.42 4.20
27 28 2.013286 AAACGTTCGCAAATGTCGAC 57.987 45.000 9.11 9.11 33.42 4.20
28 29 0.233848 AACGTTCGCAAATGTCGACC 59.766 50.000 14.12 0.00 33.42 4.79
29 30 1.131826 CGTTCGCAAATGTCGACCC 59.868 57.895 14.12 0.00 35.51 4.46
30 31 1.289109 CGTTCGCAAATGTCGACCCT 61.289 55.000 14.12 0.00 35.51 4.34
31 32 0.872388 GTTCGCAAATGTCGACCCTT 59.128 50.000 14.12 3.74 35.51 3.95
32 33 1.136057 GTTCGCAAATGTCGACCCTTC 60.136 52.381 14.12 0.00 35.51 3.46
33 34 0.672401 TCGCAAATGTCGACCCTTCC 60.672 55.000 14.12 0.00 0.00 3.46
34 35 1.794222 GCAAATGTCGACCCTTCCG 59.206 57.895 14.12 3.50 0.00 4.30
35 36 0.672401 GCAAATGTCGACCCTTCCGA 60.672 55.000 14.12 0.00 0.00 4.55
36 37 1.359848 CAAATGTCGACCCTTCCGAG 58.640 55.000 14.12 0.00 36.66 4.63
37 38 0.391263 AAATGTCGACCCTTCCGAGC 60.391 55.000 14.12 0.00 36.66 5.03
38 39 1.541310 AATGTCGACCCTTCCGAGCA 61.541 55.000 14.12 0.00 36.66 4.26
39 40 1.541310 ATGTCGACCCTTCCGAGCAA 61.541 55.000 14.12 0.00 36.66 3.91
40 41 1.005394 GTCGACCCTTCCGAGCAAA 60.005 57.895 3.51 0.00 36.66 3.68
41 42 1.005394 TCGACCCTTCCGAGCAAAC 60.005 57.895 0.00 0.00 0.00 2.93
42 43 1.301401 CGACCCTTCCGAGCAAACA 60.301 57.895 0.00 0.00 0.00 2.83
43 44 0.673644 CGACCCTTCCGAGCAAACAT 60.674 55.000 0.00 0.00 0.00 2.71
44 45 1.087501 GACCCTTCCGAGCAAACATC 58.912 55.000 0.00 0.00 0.00 3.06
45 46 0.322546 ACCCTTCCGAGCAAACATCC 60.323 55.000 0.00 0.00 0.00 3.51
46 47 1.369091 CCCTTCCGAGCAAACATCCG 61.369 60.000 0.00 0.00 0.00 4.18
47 48 1.425428 CTTCCGAGCAAACATCCGC 59.575 57.895 0.00 0.00 0.00 5.54
48 49 1.982073 CTTCCGAGCAAACATCCGCC 61.982 60.000 0.00 0.00 0.00 6.13
49 50 3.864686 CCGAGCAAACATCCGCCG 61.865 66.667 0.00 0.00 0.00 6.46
50 51 3.864686 CGAGCAAACATCCGCCGG 61.865 66.667 0.00 0.00 0.00 6.13
51 52 2.746277 GAGCAAACATCCGCCGGT 60.746 61.111 1.63 0.00 0.00 5.28
52 53 2.282180 AGCAAACATCCGCCGGTT 60.282 55.556 1.63 0.00 0.00 4.44
53 54 1.003112 AGCAAACATCCGCCGGTTA 60.003 52.632 1.63 0.00 0.00 2.85
54 55 0.606944 AGCAAACATCCGCCGGTTAA 60.607 50.000 1.63 0.00 0.00 2.01
55 56 0.179174 GCAAACATCCGCCGGTTAAG 60.179 55.000 1.63 0.00 0.00 1.85
56 57 1.444836 CAAACATCCGCCGGTTAAGA 58.555 50.000 1.63 0.00 0.00 2.10
57 58 1.396996 CAAACATCCGCCGGTTAAGAG 59.603 52.381 1.63 0.00 0.00 2.85
58 59 0.107848 AACATCCGCCGGTTAAGAGG 60.108 55.000 1.63 0.00 0.00 3.69
59 60 1.227556 CATCCGCCGGTTAAGAGGG 60.228 63.158 1.63 0.00 0.00 4.30
60 61 1.688187 ATCCGCCGGTTAAGAGGGT 60.688 57.895 1.63 0.00 0.00 4.34
61 62 1.683418 ATCCGCCGGTTAAGAGGGTC 61.683 60.000 1.63 0.00 0.00 4.46
62 63 2.186125 CGCCGGTTAAGAGGGTCC 59.814 66.667 1.90 0.00 0.00 4.46
63 64 2.356780 CGCCGGTTAAGAGGGTCCT 61.357 63.158 1.90 0.00 0.00 3.85
67 68 2.026915 GCCGGTTAAGAGGGTCCTTAAA 60.027 50.000 1.90 0.00 39.48 1.52
75 76 7.396339 GGTTAAGAGGGTCCTTAAAAATCACAT 59.604 37.037 0.00 0.00 39.48 3.21
76 77 8.803235 GTTAAGAGGGTCCTTAAAAATCACATT 58.197 33.333 0.00 0.00 39.48 2.71
90 91 2.989909 TCACATTTGCTCGACCATGAT 58.010 42.857 0.00 0.00 0.00 2.45
94 95 5.414144 TCACATTTGCTCGACCATGATTTTA 59.586 36.000 0.00 0.00 0.00 1.52
95 96 6.095300 TCACATTTGCTCGACCATGATTTTAT 59.905 34.615 0.00 0.00 0.00 1.40
97 98 7.914871 CACATTTGCTCGACCATGATTTTATAA 59.085 33.333 0.00 0.00 0.00 0.98
98 99 8.632679 ACATTTGCTCGACCATGATTTTATAAT 58.367 29.630 0.00 0.00 0.00 1.28
99 100 9.467258 CATTTGCTCGACCATGATTTTATAATT 57.533 29.630 0.00 0.00 0.00 1.40
125 126 4.100963 GGAAAGAAAACATCCACAAACCCT 59.899 41.667 0.00 0.00 33.30 4.34
154 158 7.395772 TCAGGTTATGATATTTTTCAGGTGCAA 59.604 33.333 0.00 0.00 31.12 4.08
155 159 7.489113 CAGGTTATGATATTTTTCAGGTGCAAC 59.511 37.037 0.00 0.00 0.00 4.17
163 167 0.107410 TTCAGGTGCAACTGTCGGTT 60.107 50.000 30.13 0.00 39.48 4.44
222 226 1.801395 CGATACGGGCACGACTCATTT 60.801 52.381 19.19 0.00 44.60 2.32
539 556 0.391661 CATAATCCCCCAGGCGATCG 60.392 60.000 11.69 11.69 0.00 3.69
548 565 1.146041 CAGGCGATCGGATTTCCCA 59.854 57.895 18.30 0.00 34.14 4.37
550 567 0.250467 AGGCGATCGGATTTCCCATG 60.250 55.000 18.30 0.00 34.14 3.66
675 707 4.961511 TCGTGCGACCACTGTGCC 62.962 66.667 1.29 0.00 39.86 5.01
696 728 2.710724 ATTTAGGTCGCCGGGATCGC 62.711 60.000 2.18 0.00 34.56 4.58
737 782 4.495844 CCGCTCGAAATTGGATCCTTTTAC 60.496 45.833 14.23 6.69 0.00 2.01
788 835 1.810151 GTTCATTGGCTTGTCCGCTTA 59.190 47.619 0.00 0.00 37.80 3.09
789 836 1.448985 TCATTGGCTTGTCCGCTTAC 58.551 50.000 0.00 0.00 37.80 2.34
790 837 1.003118 TCATTGGCTTGTCCGCTTACT 59.997 47.619 0.00 0.00 37.80 2.24
791 838 2.235155 TCATTGGCTTGTCCGCTTACTA 59.765 45.455 0.00 0.00 37.80 1.82
792 839 3.118408 TCATTGGCTTGTCCGCTTACTAT 60.118 43.478 0.00 0.00 37.80 2.12
793 840 4.100344 TCATTGGCTTGTCCGCTTACTATA 59.900 41.667 0.00 0.00 37.80 1.31
794 841 4.682778 TTGGCTTGTCCGCTTACTATAT 57.317 40.909 0.00 0.00 37.80 0.86
795 842 4.252971 TGGCTTGTCCGCTTACTATATC 57.747 45.455 0.00 0.00 37.80 1.63
796 843 3.895656 TGGCTTGTCCGCTTACTATATCT 59.104 43.478 0.00 0.00 37.80 1.98
797 844 4.022242 TGGCTTGTCCGCTTACTATATCTC 60.022 45.833 0.00 0.00 37.80 2.75
798 845 4.159857 GCTTGTCCGCTTACTATATCTCG 58.840 47.826 0.00 0.00 0.00 4.04
815 862 4.903638 TCTCGCGTAAAGATCAGTTTTG 57.096 40.909 5.77 0.00 0.00 2.44
896 945 2.289002 GGTTGCTTCTGCTGATAATCCG 59.711 50.000 0.00 0.00 40.48 4.18
922 971 2.689646 GCTTTTTCTACCGAGCTCAGT 58.310 47.619 15.40 11.55 32.54 3.41
994 1043 2.417719 GCCGAGTGACTTCATTTCAGT 58.582 47.619 0.00 0.00 0.00 3.41
1375 1424 1.338105 CCAAGGTGCTCGACAGAATGA 60.338 52.381 0.00 0.00 39.69 2.57
1414 1463 1.196354 CGGACTTCTACGACGTTGAGT 59.804 52.381 10.51 9.71 0.00 3.41
1416 1465 2.978489 GGACTTCTACGACGTTGAGTTG 59.022 50.000 10.51 6.71 40.15 3.16
1645 1694 4.023291 CCAAGGTTGTGGTAAATGGCTAT 58.977 43.478 0.00 0.00 33.63 2.97
1684 2052 7.609056 AGGAATCAATTGTCTCATTCTTTTGG 58.391 34.615 14.01 0.00 0.00 3.28
1685 2053 7.234166 AGGAATCAATTGTCTCATTCTTTTGGT 59.766 33.333 14.01 0.00 0.00 3.67
1686 2054 7.874528 GGAATCAATTGTCTCATTCTTTTGGTT 59.125 33.333 14.01 0.00 0.00 3.67
1687 2055 8.822652 AATCAATTGTCTCATTCTTTTGGTTC 57.177 30.769 5.13 0.00 0.00 3.62
1731 2099 4.549458 GCATATATGTTGGGTCATTGCAC 58.451 43.478 14.14 0.00 32.61 4.57
1749 2128 7.712639 TCATTGCACTTCTTATTCTCCAGTATC 59.287 37.037 0.00 0.00 0.00 2.24
1756 2135 5.784177 TCTTATTCTCCAGTATCCATTCGC 58.216 41.667 0.00 0.00 0.00 4.70
1779 2158 7.067129 TCGCTTATTCTTAGTATCTATGCCGAT 59.933 37.037 0.00 0.00 0.00 4.18
1780 2159 7.702772 CGCTTATTCTTAGTATCTATGCCGATT 59.297 37.037 0.00 0.00 0.00 3.34
1781 2160 9.372369 GCTTATTCTTAGTATCTATGCCGATTT 57.628 33.333 0.00 0.00 0.00 2.17
1799 2178 9.542462 TGCCGATTTATTCTTAGTATATATGCC 57.458 33.333 0.00 0.00 0.00 4.40
1800 2179 9.542462 GCCGATTTATTCTTAGTATATATGCCA 57.458 33.333 0.00 0.00 0.00 4.92
1833 2222 8.556213 TGTCAATTGTTATAGTTGGTTCCTAC 57.444 34.615 5.13 0.00 0.00 3.18
1847 2236 3.243737 GGTTCCTACAAAAAGGTTGGCTG 60.244 47.826 0.00 0.00 37.91 4.85
1861 2250 3.821033 GGTTGGCTGAGTGTTTCTATGTT 59.179 43.478 0.00 0.00 0.00 2.71
1862 2251 5.001232 GGTTGGCTGAGTGTTTCTATGTTA 58.999 41.667 0.00 0.00 0.00 2.41
1863 2252 5.106673 GGTTGGCTGAGTGTTTCTATGTTAC 60.107 44.000 0.00 0.00 0.00 2.50
1920 2309 7.487484 TCAACTGAAAATTATGCACTGTCAAA 58.513 30.769 0.00 0.00 0.00 2.69
1928 2317 5.648178 TTATGCACTGTCAAATGCTGAAT 57.352 34.783 9.51 0.00 42.55 2.57
1930 2319 3.644823 TGCACTGTCAAATGCTGAATTG 58.355 40.909 9.51 0.00 42.55 2.32
1969 2359 7.445402 TCCATTTCTTAGTATTTATGCTGAGGC 59.555 37.037 1.04 0.00 39.26 4.70
1982 2372 4.354893 TGCTGAGGCCATTTTCAAATTT 57.645 36.364 5.01 0.00 37.74 1.82
1983 2373 4.716794 TGCTGAGGCCATTTTCAAATTTT 58.283 34.783 5.01 0.00 37.74 1.82
1984 2374 5.862845 TGCTGAGGCCATTTTCAAATTTTA 58.137 33.333 5.01 0.00 37.74 1.52
1985 2375 6.474630 TGCTGAGGCCATTTTCAAATTTTAT 58.525 32.000 5.01 0.00 37.74 1.40
1986 2376 7.619050 TGCTGAGGCCATTTTCAAATTTTATA 58.381 30.769 5.01 0.00 37.74 0.98
1987 2377 7.765360 TGCTGAGGCCATTTTCAAATTTTATAG 59.235 33.333 5.01 0.00 37.74 1.31
1988 2378 7.225341 GCTGAGGCCATTTTCAAATTTTATAGG 59.775 37.037 5.01 0.00 0.00 2.57
1989 2379 8.144862 TGAGGCCATTTTCAAATTTTATAGGT 57.855 30.769 5.01 0.00 0.00 3.08
1990 2380 8.040132 TGAGGCCATTTTCAAATTTTATAGGTG 58.960 33.333 5.01 0.00 0.00 4.00
2030 2430 4.759693 TGGCCAAGTGTTTCTATGTTACAG 59.240 41.667 0.61 0.00 0.00 2.74
2095 2497 8.074474 TGCATTGTCAAATGTTCAATTAACTG 57.926 30.769 0.00 0.00 44.34 3.16
2120 2522 6.620877 ACTATCTTCCATTCTGGTTACACA 57.379 37.500 0.00 0.00 39.03 3.72
2149 2551 2.418368 TTGTAATGCAGGTGCCTAGG 57.582 50.000 3.67 3.67 41.18 3.02
2152 2554 1.416401 GTAATGCAGGTGCCTAGGCTA 59.584 52.381 33.07 17.60 42.51 3.93
2311 2713 4.366684 GGGGGTGCTTCACTGGGG 62.367 72.222 0.00 0.00 34.40 4.96
2359 2954 6.183360 AAACTTTGGTTGAGCATAAGCTTCTT 60.183 34.615 0.00 0.00 42.63 2.52
2371 2966 3.810310 AAGCTTCTTCCTCGGATAGTG 57.190 47.619 0.00 0.00 0.00 2.74
2386 2981 0.817654 TAGTGGCAGGATCGAGTGTG 59.182 55.000 0.00 0.00 0.00 3.82
2506 3101 3.626930 AGGTGGAGTTTTTGCTGTTACA 58.373 40.909 0.00 0.00 0.00 2.41
2800 3396 2.092212 CCACATAGTTCCCTTCCATGCT 60.092 50.000 0.00 0.00 0.00 3.79
3085 3696 2.097142 GCATGCAGGACTTTAGCTCTTG 59.903 50.000 14.21 0.00 0.00 3.02
3128 3740 4.927978 TCTCCTGCTCTTGAATACTAGC 57.072 45.455 0.00 0.00 35.51 3.42
3141 3753 5.869579 TGAATACTAGCTCATCATTTCCCC 58.130 41.667 0.00 0.00 0.00 4.81
3142 3754 5.369404 TGAATACTAGCTCATCATTTCCCCA 59.631 40.000 0.00 0.00 0.00 4.96
3147 3759 1.474077 GCTCATCATTTCCCCACACAC 59.526 52.381 0.00 0.00 0.00 3.82
3154 3766 3.772025 TCATTTCCCCACACACAAAAAGT 59.228 39.130 0.00 0.00 0.00 2.66
3156 3768 3.878160 TTCCCCACACACAAAAAGTTC 57.122 42.857 0.00 0.00 0.00 3.01
3157 3769 3.094484 TCCCCACACACAAAAAGTTCT 57.906 42.857 0.00 0.00 0.00 3.01
3158 3770 3.020984 TCCCCACACACAAAAAGTTCTC 58.979 45.455 0.00 0.00 0.00 2.87
3159 3771 2.757868 CCCCACACACAAAAAGTTCTCA 59.242 45.455 0.00 0.00 0.00 3.27
3189 3802 2.017783 CGTGTTGCTGCACAATGCC 61.018 57.895 0.00 0.00 44.23 4.40
3201 3814 3.007940 TGCACAATGCCTAACTGTCTACT 59.992 43.478 0.00 0.00 44.23 2.57
3203 3816 5.104941 TGCACAATGCCTAACTGTCTACTAT 60.105 40.000 0.00 0.00 44.23 2.12
3205 3818 6.642950 GCACAATGCCTAACTGTCTACTATAG 59.357 42.308 0.00 0.00 37.42 1.31
3208 3821 9.148879 ACAATGCCTAACTGTCTACTATAGATT 57.851 33.333 6.78 0.00 37.13 2.40
3209 3822 9.988815 CAATGCCTAACTGTCTACTATAGATTT 57.011 33.333 6.78 0.00 37.13 2.17
3211 3824 8.998277 TGCCTAACTGTCTACTATAGATTTCT 57.002 34.615 6.78 0.00 37.13 2.52
3212 3825 9.422681 TGCCTAACTGTCTACTATAGATTTCTT 57.577 33.333 6.78 0.00 37.13 2.52
3229 3842 8.586879 AGATTTCTTTTCTTCTAAATGGAGGG 57.413 34.615 0.00 0.00 0.00 4.30
3230 3843 8.173412 AGATTTCTTTTCTTCTAAATGGAGGGT 58.827 33.333 0.00 0.00 0.00 4.34
3231 3844 8.727100 ATTTCTTTTCTTCTAAATGGAGGGTT 57.273 30.769 0.00 0.00 0.00 4.11
3232 3845 8.547481 TTTCTTTTCTTCTAAATGGAGGGTTT 57.453 30.769 0.00 0.00 0.00 3.27
3233 3846 7.761038 TCTTTTCTTCTAAATGGAGGGTTTC 57.239 36.000 0.00 0.00 0.00 2.78
3234 3847 6.719829 TCTTTTCTTCTAAATGGAGGGTTTCC 59.280 38.462 0.00 0.00 46.98 3.13
3235 3848 4.586306 TCTTCTAAATGGAGGGTTTCCC 57.414 45.455 0.00 0.00 46.19 3.97
3262 3875 3.560896 GTCTCCGCCTAACTGTCTACTAG 59.439 52.174 0.00 0.00 0.00 2.57
3292 3932 5.163099 TGCAATAACTGGCTAATGGTAGGAT 60.163 40.000 0.00 0.00 0.00 3.24
3350 3991 7.161773 AGCAATGTTCTGTAGCAAATACATT 57.838 32.000 0.00 0.00 43.44 2.71
3420 4095 5.179929 TCACTGAACACTAGACATTGCAATG 59.820 40.000 32.74 32.74 42.10 2.82
3427 4102 0.813184 AGACATTGCAATGCCTTCCG 59.187 50.000 33.94 13.40 40.04 4.30
3431 4106 2.198406 CATTGCAATGCCTTCCGAATG 58.802 47.619 25.50 0.88 0.00 2.67
3450 4125 4.621068 ATGTCAATTCATACCTGTTGCG 57.379 40.909 0.00 0.00 0.00 4.85
3458 4133 1.396996 CATACCTGTTGCGTTACCAGC 59.603 52.381 0.00 0.00 0.00 4.85
3475 4150 7.921214 CGTTACCAGCTCTAATTCTGATCTAAA 59.079 37.037 0.00 0.00 32.26 1.85
3525 4200 6.495181 AGATGGAGGTGAAGTATCGATGTAAT 59.505 38.462 8.54 0.00 0.00 1.89
3588 4263 2.627699 GTTGTTTGCTCAGGATTGGGAA 59.372 45.455 0.00 0.00 0.00 3.97
3981 4659 2.038952 GGTACCATCATGGAGCTGCATA 59.961 50.000 21.21 9.80 40.96 3.14
4011 4689 6.375418 AGAGAATTCATCAGGATCTCTCTCA 58.625 40.000 8.44 0.00 42.28 3.27
4101 4779 3.182182 CACGTCTCATCATGTTCGTCAT 58.818 45.455 0.00 0.00 37.22 3.06
4113 4791 3.845178 TGTTCGTCATAGGTCACATGAC 58.155 45.455 0.00 3.27 45.76 3.06
4144 4822 1.866063 GCGAATCAGAGACCATCGACC 60.866 57.143 0.00 0.00 35.65 4.79
4149 4827 5.508153 CGAATCAGAGACCATCGACCTAAAT 60.508 44.000 0.00 0.00 35.65 1.40
4242 4920 3.082548 TCTCGAGATTGAGTCCGAGTTT 58.917 45.455 12.08 0.00 42.81 2.66
4350 5028 0.100861 GAGCTACTACACCAGACGGC 59.899 60.000 0.00 0.00 34.57 5.68
4394 5072 3.811497 TCTGAAACAGAGTCATGCAACAG 59.189 43.478 0.00 0.00 35.39 3.16
4395 5073 3.544684 TGAAACAGAGTCATGCAACAGT 58.455 40.909 0.00 0.00 0.00 3.55
4396 5074 4.702831 TGAAACAGAGTCATGCAACAGTA 58.297 39.130 0.00 0.00 0.00 2.74
4406 5084 2.519377 TGCAACAGTACTAGCAACGT 57.481 45.000 12.70 0.00 33.48 3.99
4413 5091 4.421948 ACAGTACTAGCAACGTAAGCATC 58.578 43.478 14.34 1.74 45.62 3.91
4543 6558 1.737201 GCCGAGAGCTCCTTACCTC 59.263 63.158 10.93 0.00 38.99 3.85
4626 6641 6.370994 ACAGCTCTGAAGATAACAAAGATGTG 59.629 38.462 3.60 0.00 40.46 3.21
4748 6814 2.961741 TCTTAATGGTTTGGTGCAGCAA 59.038 40.909 26.54 26.54 0.00 3.91
4765 6885 5.757808 TGCAGCAACAATGATGTACGTATAT 59.242 36.000 4.30 4.30 44.75 0.86
4822 6942 3.004862 CAGCAGCATATCTGTTGTGTGA 58.995 45.455 0.00 0.00 45.45 3.58
4823 6943 3.437741 CAGCAGCATATCTGTTGTGTGAA 59.562 43.478 0.00 0.00 45.45 3.18
4826 6946 4.631377 GCAGCATATCTGTTGTGTGAAGTA 59.369 41.667 0.00 0.00 44.66 2.24
4827 6947 5.220548 GCAGCATATCTGTTGTGTGAAGTAG 60.221 44.000 0.00 0.00 44.66 2.57
4828 6948 6.101997 CAGCATATCTGTTGTGTGAAGTAGA 58.898 40.000 0.00 0.00 38.02 2.59
4835 6959 5.934043 TCTGTTGTGTGAAGTAGATGATTGG 59.066 40.000 0.00 0.00 0.00 3.16
4910 7035 2.021457 GTGTTTGTTGTACCACAGGCT 58.979 47.619 0.00 0.00 0.00 4.58
5057 7191 4.202253 ACAGGGCTTCCAACTCAAATTTTC 60.202 41.667 0.00 0.00 0.00 2.29
5058 7192 3.005791 AGGGCTTCCAACTCAAATTTTCG 59.994 43.478 0.00 0.00 0.00 3.46
5060 7194 4.500716 GGGCTTCCAACTCAAATTTTCGAA 60.501 41.667 0.00 0.00 0.00 3.71
5061 7195 4.681483 GGCTTCCAACTCAAATTTTCGAAG 59.319 41.667 0.00 0.00 0.00 3.79
5063 7197 5.748630 GCTTCCAACTCAAATTTTCGAAGTT 59.251 36.000 0.00 0.00 0.00 2.66
5064 7198 6.915843 GCTTCCAACTCAAATTTTCGAAGTTA 59.084 34.615 0.00 0.00 0.00 2.24
5210 7347 9.250624 CACTGTCCTTAAGCACTAATATAGAAC 57.749 37.037 0.00 0.00 0.00 3.01
5510 7656 1.479389 CCAACAAAGGCCAGGAAGTCT 60.479 52.381 5.01 0.00 0.00 3.24
5528 7674 1.980765 TCTCTCACTGCATCACCCTTT 59.019 47.619 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.893795 ACATTTGCGAACGTTTAGATAGC 58.106 39.130 0.46 2.77 0.00 2.97
3 4 4.858140 TCGACATTTGCGAACGTTTAGATA 59.142 37.500 0.46 0.00 34.45 1.98
4 5 3.676172 TCGACATTTGCGAACGTTTAGAT 59.324 39.130 0.46 0.00 34.45 1.98
5 6 3.051327 TCGACATTTGCGAACGTTTAGA 58.949 40.909 0.46 0.00 34.45 2.10
6 7 3.143279 GTCGACATTTGCGAACGTTTAG 58.857 45.455 11.55 0.80 39.73 1.85
7 8 2.096811 GGTCGACATTTGCGAACGTTTA 60.097 45.455 18.91 0.00 39.73 2.01
8 9 1.333435 GGTCGACATTTGCGAACGTTT 60.333 47.619 18.91 0.00 39.73 3.60
9 10 0.233848 GGTCGACATTTGCGAACGTT 59.766 50.000 18.91 0.00 39.73 3.99
10 11 1.562575 GGGTCGACATTTGCGAACGT 61.563 55.000 18.91 0.00 45.86 3.99
11 12 1.131826 GGGTCGACATTTGCGAACG 59.868 57.895 18.91 0.00 45.86 3.95
12 13 0.872388 AAGGGTCGACATTTGCGAAC 59.128 50.000 18.91 0.00 44.29 3.95
13 14 1.153353 GAAGGGTCGACATTTGCGAA 58.847 50.000 18.91 0.00 39.73 4.70
14 15 0.672401 GGAAGGGTCGACATTTGCGA 60.672 55.000 18.91 0.00 35.08 5.10
15 16 1.794222 GGAAGGGTCGACATTTGCG 59.206 57.895 18.91 0.00 0.00 4.85
16 17 0.672401 TCGGAAGGGTCGACATTTGC 60.672 55.000 18.91 14.29 0.00 3.68
17 18 1.359848 CTCGGAAGGGTCGACATTTG 58.640 55.000 18.91 8.40 32.86 2.32
18 19 0.391263 GCTCGGAAGGGTCGACATTT 60.391 55.000 18.91 10.67 32.86 2.32
19 20 1.218316 GCTCGGAAGGGTCGACATT 59.782 57.895 18.91 11.47 32.86 2.71
20 21 1.541310 TTGCTCGGAAGGGTCGACAT 61.541 55.000 18.91 1.75 32.86 3.06
21 22 1.750341 TTTGCTCGGAAGGGTCGACA 61.750 55.000 18.91 0.00 32.86 4.35
22 23 1.005394 TTTGCTCGGAAGGGTCGAC 60.005 57.895 7.13 7.13 32.86 4.20
23 24 1.005394 GTTTGCTCGGAAGGGTCGA 60.005 57.895 0.00 0.00 35.24 4.20
24 25 0.673644 ATGTTTGCTCGGAAGGGTCG 60.674 55.000 0.00 0.00 0.00 4.79
25 26 1.087501 GATGTTTGCTCGGAAGGGTC 58.912 55.000 0.00 0.00 0.00 4.46
26 27 0.322546 GGATGTTTGCTCGGAAGGGT 60.323 55.000 0.00 0.00 0.00 4.34
27 28 1.369091 CGGATGTTTGCTCGGAAGGG 61.369 60.000 0.00 0.00 0.00 3.95
28 29 1.982073 GCGGATGTTTGCTCGGAAGG 61.982 60.000 0.00 0.00 0.00 3.46
29 30 1.425428 GCGGATGTTTGCTCGGAAG 59.575 57.895 0.00 0.00 0.00 3.46
30 31 2.038269 GGCGGATGTTTGCTCGGAA 61.038 57.895 0.00 0.00 0.00 4.30
31 32 2.435938 GGCGGATGTTTGCTCGGA 60.436 61.111 0.00 0.00 0.00 4.55
32 33 3.864686 CGGCGGATGTTTGCTCGG 61.865 66.667 0.00 0.00 0.00 4.63
33 34 3.864686 CCGGCGGATGTTTGCTCG 61.865 66.667 24.41 0.00 0.00 5.03
34 35 1.022451 TAACCGGCGGATGTTTGCTC 61.022 55.000 35.78 0.00 0.00 4.26
35 36 0.606944 TTAACCGGCGGATGTTTGCT 60.607 50.000 35.78 3.72 0.00 3.91
36 37 0.179174 CTTAACCGGCGGATGTTTGC 60.179 55.000 35.78 0.00 0.00 3.68
37 38 1.396996 CTCTTAACCGGCGGATGTTTG 59.603 52.381 35.78 16.48 0.00 2.93
38 39 1.677820 CCTCTTAACCGGCGGATGTTT 60.678 52.381 35.78 19.05 0.00 2.83
39 40 0.107848 CCTCTTAACCGGCGGATGTT 60.108 55.000 35.78 19.45 0.00 2.71
40 41 1.520666 CCTCTTAACCGGCGGATGT 59.479 57.895 35.78 19.31 0.00 3.06
41 42 1.227556 CCCTCTTAACCGGCGGATG 60.228 63.158 35.78 18.28 0.00 3.51
42 43 1.683418 GACCCTCTTAACCGGCGGAT 61.683 60.000 35.78 25.18 0.00 4.18
43 44 2.284112 ACCCTCTTAACCGGCGGA 60.284 61.111 35.78 8.46 0.00 5.54
44 45 2.186125 GACCCTCTTAACCGGCGG 59.814 66.667 27.06 27.06 0.00 6.13
45 46 1.896122 AAGGACCCTCTTAACCGGCG 61.896 60.000 0.00 0.00 0.00 6.46
46 47 1.197812 TAAGGACCCTCTTAACCGGC 58.802 55.000 0.00 0.00 0.00 6.13
47 48 3.986996 TTTAAGGACCCTCTTAACCGG 57.013 47.619 0.00 0.00 38.49 5.28
48 49 5.941647 TGATTTTTAAGGACCCTCTTAACCG 59.058 40.000 0.00 0.00 38.49 4.44
49 50 6.717997 TGTGATTTTTAAGGACCCTCTTAACC 59.282 38.462 0.00 0.00 38.49 2.85
50 51 7.754851 TGTGATTTTTAAGGACCCTCTTAAC 57.245 36.000 0.00 0.00 38.49 2.01
51 52 8.950007 AATGTGATTTTTAAGGACCCTCTTAA 57.050 30.769 0.00 0.00 37.42 1.85
52 53 8.802267 CAAATGTGATTTTTAAGGACCCTCTTA 58.198 33.333 0.00 0.00 0.00 2.10
53 54 7.670364 CAAATGTGATTTTTAAGGACCCTCTT 58.330 34.615 0.00 0.00 0.00 2.85
54 55 6.295292 GCAAATGTGATTTTTAAGGACCCTCT 60.295 38.462 0.00 0.00 0.00 3.69
55 56 5.869344 GCAAATGTGATTTTTAAGGACCCTC 59.131 40.000 0.00 0.00 0.00 4.30
56 57 5.543790 AGCAAATGTGATTTTTAAGGACCCT 59.456 36.000 0.00 0.00 0.00 4.34
57 58 5.793817 AGCAAATGTGATTTTTAAGGACCC 58.206 37.500 0.00 0.00 0.00 4.46
58 59 5.572896 CGAGCAAATGTGATTTTTAAGGACC 59.427 40.000 0.00 0.00 0.00 4.46
59 60 6.305638 GTCGAGCAAATGTGATTTTTAAGGAC 59.694 38.462 0.00 0.00 0.00 3.85
60 61 6.378582 GTCGAGCAAATGTGATTTTTAAGGA 58.621 36.000 0.00 0.00 0.00 3.36
61 62 5.572896 GGTCGAGCAAATGTGATTTTTAAGG 59.427 40.000 10.30 0.00 0.00 2.69
62 63 6.148948 TGGTCGAGCAAATGTGATTTTTAAG 58.851 36.000 16.20 0.00 0.00 1.85
63 64 6.078202 TGGTCGAGCAAATGTGATTTTTAA 57.922 33.333 16.20 0.00 0.00 1.52
67 68 3.758023 TCATGGTCGAGCAAATGTGATTT 59.242 39.130 22.64 0.00 0.00 2.17
76 77 8.783093 CCTAATTATAAAATCATGGTCGAGCAA 58.217 33.333 22.64 6.41 0.00 3.91
94 95 8.893563 TGTGGATGTTTTCTTTCCCTAATTAT 57.106 30.769 0.00 0.00 0.00 1.28
95 96 8.713708 TTGTGGATGTTTTCTTTCCCTAATTA 57.286 30.769 0.00 0.00 0.00 1.40
97 98 7.441836 GTTTGTGGATGTTTTCTTTCCCTAAT 58.558 34.615 0.00 0.00 0.00 1.73
98 99 6.183360 GGTTTGTGGATGTTTTCTTTCCCTAA 60.183 38.462 0.00 0.00 0.00 2.69
99 100 5.303333 GGTTTGTGGATGTTTTCTTTCCCTA 59.697 40.000 0.00 0.00 0.00 3.53
100 101 4.100963 GGTTTGTGGATGTTTTCTTTCCCT 59.899 41.667 0.00 0.00 0.00 4.20
101 102 4.377021 GGTTTGTGGATGTTTTCTTTCCC 58.623 43.478 0.00 0.00 0.00 3.97
163 167 3.614092 CTGTGGACTACGGTAGGAGTAA 58.386 50.000 18.73 1.82 0.00 2.24
222 226 2.112297 GGAAAGTGGCCGTGACCA 59.888 61.111 0.00 0.00 37.38 4.02
244 248 4.394712 AGGCCGCAACGAGAAGGG 62.395 66.667 0.00 0.00 0.00 3.95
313 321 2.096069 GTCGCCGGATTTGATGATGATG 60.096 50.000 5.05 0.00 0.00 3.07
314 322 2.146342 GTCGCCGGATTTGATGATGAT 58.854 47.619 5.05 0.00 0.00 2.45
315 323 1.581934 GTCGCCGGATTTGATGATGA 58.418 50.000 5.05 0.00 0.00 2.92
364 375 2.031870 GGGAGGAATTTTAATGGCGCT 58.968 47.619 7.64 0.00 0.00 5.92
527 544 1.598130 GAAATCCGATCGCCTGGGG 60.598 63.158 10.32 4.03 0.00 4.96
539 556 2.460669 AGCTTCCAACATGGGAAATCC 58.539 47.619 5.15 0.00 45.87 3.01
647 679 3.024609 CGCACGATCCCGATCACG 61.025 66.667 5.59 2.27 37.69 4.35
648 680 1.944676 GTCGCACGATCCCGATCAC 60.945 63.158 5.59 0.00 37.69 3.06
649 681 2.411701 GTCGCACGATCCCGATCA 59.588 61.111 5.59 0.00 37.69 2.92
650 682 2.354773 GGTCGCACGATCCCGATC 60.355 66.667 0.00 0.00 39.50 3.69
651 683 3.144871 TGGTCGCACGATCCCGAT 61.145 61.111 0.11 0.00 39.50 4.18
652 684 4.124351 GTGGTCGCACGATCCCGA 62.124 66.667 0.11 0.00 39.50 5.14
653 685 4.129737 AGTGGTCGCACGATCCCG 62.130 66.667 0.11 0.00 42.50 5.14
654 686 2.509336 CAGTGGTCGCACGATCCC 60.509 66.667 0.11 0.00 0.00 3.85
655 687 2.094659 CACAGTGGTCGCACGATCC 61.095 63.158 0.11 3.13 0.00 3.36
675 707 1.402456 CGATCCCGGCGACCTAAATAG 60.402 57.143 9.30 0.00 0.00 1.73
737 782 3.110178 GGCGACACGAAACCGAGG 61.110 66.667 0.00 0.00 0.00 4.63
770 817 1.003118 AGTAAGCGGACAAGCCAATGA 59.997 47.619 0.00 0.00 38.01 2.57
771 818 1.453155 AGTAAGCGGACAAGCCAATG 58.547 50.000 0.00 0.00 38.01 2.82
788 835 6.804770 ACTGATCTTTACGCGAGATATAGT 57.195 37.500 15.93 14.99 34.13 2.12
789 836 8.420945 CAAAACTGATCTTTACGCGAGATATAG 58.579 37.037 15.93 14.39 34.13 1.31
790 837 7.381408 CCAAAACTGATCTTTACGCGAGATATA 59.619 37.037 15.93 2.99 34.13 0.86
791 838 6.201044 CCAAAACTGATCTTTACGCGAGATAT 59.799 38.462 15.93 0.00 34.13 1.63
792 839 5.518847 CCAAAACTGATCTTTACGCGAGATA 59.481 40.000 15.93 0.00 34.13 1.98
793 840 4.330074 CCAAAACTGATCTTTACGCGAGAT 59.670 41.667 15.93 11.38 36.60 2.75
794 841 3.678072 CCAAAACTGATCTTTACGCGAGA 59.322 43.478 15.93 5.60 0.00 4.04
795 842 3.725010 GCCAAAACTGATCTTTACGCGAG 60.725 47.826 15.93 0.00 0.00 5.03
796 843 2.158841 GCCAAAACTGATCTTTACGCGA 59.841 45.455 15.93 0.00 0.00 5.87
797 844 2.159627 AGCCAAAACTGATCTTTACGCG 59.840 45.455 3.53 3.53 0.00 6.01
798 845 3.831715 AGCCAAAACTGATCTTTACGC 57.168 42.857 0.00 0.00 0.00 4.42
896 945 1.992170 TCGGTAGAAAAAGCGAGCTC 58.008 50.000 2.73 2.73 43.75 4.09
922 971 3.119137 TCCAGCTCGATTTCAATCTCGAA 60.119 43.478 0.00 0.00 42.73 3.71
953 1002 1.292223 CTCCGGCGAGGTCAGAAAA 59.708 57.895 9.30 0.00 41.99 2.29
994 1043 1.320344 CCGGACTCCTCCATTGACGA 61.320 60.000 0.00 0.00 36.12 4.20
1332 1381 2.490217 CGCACCCACTCCTCGTAG 59.510 66.667 0.00 0.00 0.00 3.51
1414 1463 2.903357 GAGCCTGCTCCCGATCAA 59.097 61.111 7.95 0.00 37.11 2.57
1416 1465 3.219928 TCGAGCCTGCTCCCGATC 61.220 66.667 13.23 0.00 39.77 3.69
1446 1495 3.752167 GACCCCTCCTCCCTCCGA 61.752 72.222 0.00 0.00 0.00 4.55
1684 2052 9.865484 GCGTAAATTTAGATAATGGAGAAGAAC 57.135 33.333 0.00 0.00 0.00 3.01
1685 2053 9.607988 TGCGTAAATTTAGATAATGGAGAAGAA 57.392 29.630 0.00 0.00 0.00 2.52
1686 2054 9.778741 ATGCGTAAATTTAGATAATGGAGAAGA 57.221 29.630 0.00 0.00 0.00 2.87
1705 2073 5.049060 GCAATGACCCAACATATATGCGTAA 60.049 40.000 12.79 0.00 0.00 3.18
1707 2075 3.253188 GCAATGACCCAACATATATGCGT 59.747 43.478 12.79 4.09 0.00 5.24
1708 2076 3.252944 TGCAATGACCCAACATATATGCG 59.747 43.478 12.79 4.33 35.56 4.73
1731 2099 6.367422 GCGAATGGATACTGGAGAATAAGAAG 59.633 42.308 0.00 0.00 37.61 2.85
1749 2128 8.812329 GCATAGATACTAAGAATAAGCGAATGG 58.188 37.037 0.00 0.00 0.00 3.16
1798 2177 7.322664 ACTATAACAATTGACAATGCCTTTGG 58.677 34.615 13.59 0.00 39.80 3.28
1799 2178 8.649841 CAACTATAACAATTGACAATGCCTTTG 58.350 33.333 13.59 0.00 41.36 2.77
1800 2179 7.818930 CCAACTATAACAATTGACAATGCCTTT 59.181 33.333 13.59 0.00 0.00 3.11
1801 2180 7.039082 ACCAACTATAACAATTGACAATGCCTT 60.039 33.333 13.59 0.00 0.00 4.35
1809 2188 8.556213 TGTAGGAACCAACTATAACAATTGAC 57.444 34.615 13.59 0.00 0.00 3.18
1814 2193 8.852135 CCTTTTTGTAGGAACCAACTATAACAA 58.148 33.333 0.00 0.00 37.50 2.83
1833 2222 3.525268 AACACTCAGCCAACCTTTTTG 57.475 42.857 0.00 0.00 0.00 2.44
1839 2228 3.412386 ACATAGAAACACTCAGCCAACC 58.588 45.455 0.00 0.00 0.00 3.77
1847 2236 8.828688 AGGTTTGTAGTAACATAGAAACACTC 57.171 34.615 8.25 0.00 39.45 3.51
1920 2309 6.989169 GGAAGACAGTATAGTCAATTCAGCAT 59.011 38.462 0.00 0.00 40.98 3.79
1958 2348 5.680594 ATTTGAAAATGGCCTCAGCATAA 57.319 34.783 3.32 0.00 42.56 1.90
1967 2357 8.560355 AACACCTATAAAATTTGAAAATGGCC 57.440 30.769 0.00 0.00 0.00 5.36
1969 2359 9.942850 AGGAACACCTATAAAATTTGAAAATGG 57.057 29.630 0.00 0.00 31.52 3.16
2005 2405 5.772672 TGTAACATAGAAACACTTGGCCAAT 59.227 36.000 20.85 2.71 0.00 3.16
2120 2522 5.297776 GCACCTGCATTACAATAGATCAACT 59.702 40.000 0.00 0.00 41.59 3.16
2149 2551 8.398665 ACCTCGTCAATGAAATCTTTTATTAGC 58.601 33.333 0.00 0.00 0.00 3.09
2152 2554 9.626045 GAAACCTCGTCAATGAAATCTTTTATT 57.374 29.630 0.00 0.00 0.00 1.40
2170 2572 2.417339 TCAGTTGAGTCGAAACCTCG 57.583 50.000 0.00 0.00 46.87 4.63
2218 2620 5.047731 GGCAAGCTTCTCTTCCAAAAGTAAT 60.048 40.000 0.00 0.00 33.95 1.89
2359 2954 0.188587 ATCCTGCCACTATCCGAGGA 59.811 55.000 0.00 0.00 37.24 3.71
2371 2966 2.185310 AACCCACACTCGATCCTGCC 62.185 60.000 0.00 0.00 0.00 4.85
2386 2981 6.568462 CGACAATTGAGCATATAATGGAACCC 60.568 42.308 13.59 0.00 0.00 4.11
2506 3101 4.157105 GCACCATAAGTCATAACCCGTTTT 59.843 41.667 0.00 0.00 0.00 2.43
2800 3396 0.329261 CTGGATCTGTGGCAAAGGGA 59.671 55.000 4.51 0.00 0.00 4.20
3035 3643 4.394439 AACCACACACAAACCATTAACC 57.606 40.909 0.00 0.00 0.00 2.85
3042 3650 5.009210 TGCTAAGATAAACCACACACAAACC 59.991 40.000 0.00 0.00 0.00 3.27
3085 3696 7.486232 GGAGAACAATTCTAAATTACTTGCAGC 59.514 37.037 0.00 0.00 40.87 5.25
3128 3740 2.794103 TGTGTGTGGGGAAATGATGAG 58.206 47.619 0.00 0.00 0.00 2.90
3141 3753 7.760131 AAATGATGAGAACTTTTTGTGTGTG 57.240 32.000 0.00 0.00 0.00 3.82
3142 3754 7.492344 GGAAAATGATGAGAACTTTTTGTGTGT 59.508 33.333 0.00 0.00 0.00 3.72
3147 3759 6.144402 CGTGGGAAAATGATGAGAACTTTTTG 59.856 38.462 0.00 0.00 0.00 2.44
3154 3766 3.750371 ACACGTGGGAAAATGATGAGAA 58.250 40.909 21.57 0.00 0.00 2.87
3156 3768 3.825308 CAACACGTGGGAAAATGATGAG 58.175 45.455 21.57 0.00 0.00 2.90
3157 3769 2.030363 GCAACACGTGGGAAAATGATGA 60.030 45.455 21.57 0.00 0.00 2.92
3158 3770 2.030007 AGCAACACGTGGGAAAATGATG 60.030 45.455 21.57 5.52 0.00 3.07
3159 3771 2.030007 CAGCAACACGTGGGAAAATGAT 60.030 45.455 21.57 4.70 0.00 2.45
3203 3816 9.686683 CCCTCCATTTAGAAGAAAAGAAATCTA 57.313 33.333 0.00 0.00 0.00 1.98
3205 3818 8.354711 ACCCTCCATTTAGAAGAAAAGAAATC 57.645 34.615 0.00 0.00 0.00 2.17
3208 3821 7.232737 GGAAACCCTCCATTTAGAAGAAAAGAA 59.767 37.037 0.00 0.00 44.67 2.52
3209 3822 6.719829 GGAAACCCTCCATTTAGAAGAAAAGA 59.280 38.462 0.00 0.00 44.67 2.52
3210 3823 6.925211 GGAAACCCTCCATTTAGAAGAAAAG 58.075 40.000 0.00 0.00 44.67 2.27
3211 3824 6.911250 GGAAACCCTCCATTTAGAAGAAAA 57.089 37.500 0.00 0.00 44.67 2.29
3239 3852 1.404748 GTAGACAGTTAGGCGGAGACC 59.595 57.143 0.00 0.00 31.70 3.85
3240 3853 2.367486 AGTAGACAGTTAGGCGGAGAC 58.633 52.381 0.00 0.00 0.00 3.36
3241 3854 2.803030 AGTAGACAGTTAGGCGGAGA 57.197 50.000 0.00 0.00 0.00 3.71
3242 3855 3.806380 TCTAGTAGACAGTTAGGCGGAG 58.194 50.000 0.00 0.00 0.00 4.63
3243 3856 3.920231 TCTAGTAGACAGTTAGGCGGA 57.080 47.619 0.00 0.00 0.00 5.54
3244 3857 7.467539 GCATATATCTAGTAGACAGTTAGGCGG 60.468 44.444 0.85 0.00 0.00 6.13
3245 3858 7.065923 TGCATATATCTAGTAGACAGTTAGGCG 59.934 40.741 0.85 0.00 0.00 5.52
3262 3875 8.511604 ACCATTAGCCAGTTATTGCATATATC 57.488 34.615 0.00 0.00 0.00 1.63
3275 3888 2.057922 CCCATCCTACCATTAGCCAGT 58.942 52.381 0.00 0.00 0.00 4.00
3292 3932 7.451255 CCTCCATCAAATAATAATAGCAACCCA 59.549 37.037 0.00 0.00 0.00 4.51
3327 3968 7.669098 CAAATGTATTTGCTACAGAACATTGC 58.331 34.615 4.57 0.00 43.44 3.56
3350 3991 9.906660 CAAAGTTGTAAGATAAATTAGGTGCAA 57.093 29.630 0.00 0.00 0.00 4.08
3392 4067 5.641209 GCAATGTCTAGTGTTCAGTGAAGAT 59.359 40.000 5.62 0.00 30.35 2.40
3420 4095 4.261197 GGTATGAATTGACATTCGGAAGGC 60.261 45.833 1.76 0.00 41.77 4.35
3427 4102 5.030295 CGCAACAGGTATGAATTGACATTC 58.970 41.667 0.00 0.00 39.58 2.67
3431 4106 4.419522 AACGCAACAGGTATGAATTGAC 57.580 40.909 0.00 0.00 0.00 3.18
3450 4125 9.771534 ATTTAGATCAGAATTAGAGCTGGTAAC 57.228 33.333 8.05 0.00 33.24 2.50
3475 4150 3.557595 GCAAGACGAGCAAGCTATACAAT 59.442 43.478 0.00 0.00 0.00 2.71
3486 4161 0.108472 CCATCTCAGCAAGACGAGCA 60.108 55.000 0.00 0.00 36.65 4.26
3525 4200 3.157087 GAGGCCAATTTCCAGAACTTGA 58.843 45.455 5.01 0.00 34.20 3.02
3659 4334 3.885297 CCAAAGGACCAGCATTACCTATG 59.115 47.826 0.00 0.00 37.31 2.23
3981 4659 5.598005 AGATCCTGATGAATTCTCTCGACTT 59.402 40.000 7.05 0.00 0.00 3.01
4011 4689 1.153549 GGCCGCGAAGTGATCTTCT 60.154 57.895 8.23 0.00 45.47 2.85
4101 4779 2.492088 CTCACTTCCGTCATGTGACCTA 59.508 50.000 7.51 0.00 41.86 3.08
4113 4791 1.133216 TCTGATTCGCTCTCACTTCCG 59.867 52.381 0.00 0.00 0.00 4.30
4144 4822 4.202441 CCACTCCTGGTCCATGAATTTAG 58.798 47.826 0.00 0.00 32.03 1.85
4149 4827 1.685224 GCCACTCCTGGTCCATGAA 59.315 57.895 0.00 0.00 40.17 2.57
4167 4845 3.866582 GTCCTCATCAGGGGCCCG 61.867 72.222 18.95 12.69 40.80 6.13
4242 4920 4.350816 CCCTCTATTGTATGAACCCCATCA 59.649 45.833 0.00 0.00 36.71 3.07
4350 5028 2.045524 ACCTCTGTGCATCTATCTGGG 58.954 52.381 0.00 0.00 0.00 4.45
4394 5072 2.215812 GCGATGCTTACGTTGCTAGTAC 59.784 50.000 13.06 0.00 38.91 2.73
4395 5073 2.456989 GCGATGCTTACGTTGCTAGTA 58.543 47.619 13.06 0.00 38.91 1.82
4396 5074 1.278238 GCGATGCTTACGTTGCTAGT 58.722 50.000 13.06 1.83 38.91 2.57
4406 5084 2.610433 CTTCAGACACAGCGATGCTTA 58.390 47.619 0.00 0.00 36.40 3.09
4413 5091 1.476085 AGATCTCCTTCAGACACAGCG 59.524 52.381 0.00 0.00 32.26 5.18
4543 6558 3.752747 TGTGTTCTGTCCACATATGCTTG 59.247 43.478 1.58 0.00 37.88 4.01
4626 6641 1.153349 GGGATTGTCCGAGTCAGCC 60.153 63.158 0.00 0.00 37.43 4.85
4739 6805 2.728846 CGTACATCATTGTTGCTGCACC 60.729 50.000 0.00 0.00 37.28 5.01
4740 6806 2.095768 ACGTACATCATTGTTGCTGCAC 60.096 45.455 0.00 0.00 37.28 4.57
4765 6885 9.755804 CTCTCTAAATAGACACTGCAATTATCA 57.244 33.333 0.00 0.00 0.00 2.15
4822 6942 9.147732 TGTATCATCAGTACCAATCATCTACTT 57.852 33.333 0.00 0.00 0.00 2.24
4823 6943 8.712228 TGTATCATCAGTACCAATCATCTACT 57.288 34.615 0.00 0.00 0.00 2.57
4826 6946 8.654094 TCAATGTATCATCAGTACCAATCATCT 58.346 33.333 0.00 0.00 0.00 2.90
4827 6947 8.837788 TCAATGTATCATCAGTACCAATCATC 57.162 34.615 0.00 0.00 0.00 2.92
4835 6959 8.310382 AGGCTTCTATCAATGTATCATCAGTAC 58.690 37.037 0.00 0.00 0.00 2.73
4910 7035 5.333581 TCAGAAGAATCTTGACCAGGTAGA 58.666 41.667 0.00 0.00 32.03 2.59
4916 7041 7.226720 GTGTTTAGTTCAGAAGAATCTTGACCA 59.773 37.037 0.00 0.00 35.92 4.02
4917 7042 7.226720 TGTGTTTAGTTCAGAAGAATCTTGACC 59.773 37.037 0.00 0.00 35.92 4.02
4918 7043 8.064814 GTGTGTTTAGTTCAGAAGAATCTTGAC 58.935 37.037 0.00 0.00 35.92 3.18
4999 7126 9.932207 ATATGATTTTCTCAGAATTTTTGTGCA 57.068 25.926 0.00 0.00 37.28 4.57
5035 7169 4.309933 GAAAATTTGAGTTGGAAGCCCTG 58.690 43.478 0.00 0.00 0.00 4.45
5057 7191 6.013689 GCGAAATAGAAACCAGTTAACTTCG 58.986 40.000 5.07 9.72 0.00 3.79
5058 7192 6.894828 TGCGAAATAGAAACCAGTTAACTTC 58.105 36.000 5.07 0.84 0.00 3.01
5060 7194 6.228258 TCTGCGAAATAGAAACCAGTTAACT 58.772 36.000 1.12 1.12 0.00 2.24
5061 7195 6.476243 TCTGCGAAATAGAAACCAGTTAAC 57.524 37.500 0.00 0.00 0.00 2.01
5063 7197 9.472361 GTATATCTGCGAAATAGAAACCAGTTA 57.528 33.333 0.00 0.00 0.00 2.24
5064 7198 8.204836 AGTATATCTGCGAAATAGAAACCAGTT 58.795 33.333 0.00 0.00 0.00 3.16
5183 7320 7.434492 TCTATATTAGTGCTTAAGGACAGTGC 58.566 38.462 26.40 1.80 38.96 4.40
5510 7656 2.507484 CAAAAGGGTGATGCAGTGAGA 58.493 47.619 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.