Multiple sequence alignment - TraesCS2D01G194000

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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 TraesCS2D01G194000 chr2D 100.000 7448 0 0 1 7448 139023291 139030738 0.000000e+00 13754.0
1 TraesCS2D01G194000 chr2D 86.137 981 115 14 6 978 155340902 155339935 0.000000e+00 1038.0
2 TraesCS2D01G194000 chr2D 95.868 121 4 1 2760 2879 45681104 45680984 2.120000e-45 195.0
3 TraesCS2D01G194000 chr2D 95.763 118 5 0 2752 2869 93280578 93280461 2.740000e-44 191.0
4 TraesCS2D01G194000 chr2D 95.000 120 6 0 2760 2879 65564826 65564707 9.870000e-44 189.0
5 TraesCS2D01G194000 chr2B 96.569 4314 83 21 2855 7132 197683315 197687599 0.000000e+00 7086.0
6 TraesCS2D01G194000 chr2B 91.522 1321 55 15 1024 2316 197681575 197682866 0.000000e+00 1766.0
7 TraesCS2D01G194000 chr2B 99.485 388 2 0 2381 2768 197682863 197683250 0.000000e+00 706.0
8 TraesCS2D01G194000 chr2B 84.013 319 30 8 7132 7448 197687559 197687858 3.400000e-73 287.0
9 TraesCS2D01G194000 chr2B 85.590 229 29 2 2207 2434 508959612 508959387 3.470000e-58 237.0
10 TraesCS2D01G194000 chr2B 78.981 157 28 4 7184 7337 2106579 2106733 1.320000e-17 102.0
11 TraesCS2D01G194000 chr2A 89.479 2804 213 33 1 2762 161957026 161954263 0.000000e+00 3469.0
12 TraesCS2D01G194000 chr2A 94.343 1485 71 9 2864 4337 161954266 161952784 0.000000e+00 2265.0
13 TraesCS2D01G194000 chr2A 91.323 1164 63 19 5979 7121 161951042 161949896 0.000000e+00 1555.0
14 TraesCS2D01G194000 chr2A 87.035 995 106 18 6 983 530742818 530741830 0.000000e+00 1101.0
15 TraesCS2D01G194000 chr2A 87.055 842 84 9 5209 6029 161951886 161951049 0.000000e+00 928.0
16 TraesCS2D01G194000 chr2A 77.098 882 127 46 4338 5170 161952750 161951895 2.470000e-119 440.0
17 TraesCS2D01G194000 chr5A 88.708 983 101 9 1 978 10919121 10918144 0.000000e+00 1192.0
18 TraesCS2D01G194000 chr5A 96.667 120 3 1 2748 2867 632877223 632877105 1.640000e-46 198.0
19 TraesCS2D01G194000 chr5A 86.585 82 10 1 4046 4126 667304888 667304807 1.030000e-13 89.8
20 TraesCS2D01G194000 chr5D 89.400 934 87 11 6 932 264882149 264881221 0.000000e+00 1166.0
21 TraesCS2D01G194000 chr5D 78.261 138 26 3 7218 7352 232007252 232007116 1.330000e-12 86.1
22 TraesCS2D01G194000 chr5B 88.110 984 107 9 1 978 249553988 249554967 0.000000e+00 1160.0
23 TraesCS2D01G194000 chr5B 99.091 110 1 0 2757 2866 697185044 697184935 1.640000e-46 198.0
24 TraesCS2D01G194000 chr5B 91.667 132 9 2 2760 2891 110432726 110432597 1.650000e-41 182.0
25 TraesCS2D01G194000 chr6B 88.865 916 89 11 1 911 60582347 60583254 0.000000e+00 1114.0
26 TraesCS2D01G194000 chr6B 91.971 137 7 4 2759 2893 129854504 129854370 9.870000e-44 189.0
27 TraesCS2D01G194000 chr4D 87.553 940 103 12 2 932 486146000 486146934 0.000000e+00 1075.0
28 TraesCS2D01G194000 chr4D 79.878 164 26 6 7193 7352 3355847 3355687 6.110000e-21 113.0
29 TraesCS2D01G194000 chr6D 86.470 983 114 14 6 981 395524117 395523147 0.000000e+00 1061.0
30 TraesCS2D01G194000 chr6D 96.581 117 4 0 2754 2870 112344370 112344486 2.120000e-45 195.0
31 TraesCS2D01G194000 chr3D 86.006 979 118 13 6 978 545715290 545716255 0.000000e+00 1031.0
32 TraesCS2D01G194000 chr3D 78.846 156 30 2 7184 7337 545791399 545791553 1.320000e-17 102.0
33 TraesCS2D01G194000 chr3D 78.481 158 27 6 7184 7337 26308021 26308175 6.150000e-16 97.1
34 TraesCS2D01G194000 chr3D 85.915 71 7 2 4047 4116 107075457 107075525 1.040000e-08 73.1
35 TraesCS2D01G194000 chr3D 96.875 32 1 0 7269 7300 132931634 132931665 4.000000e-03 54.7
36 TraesCS2D01G194000 chr7B 87.137 241 27 4 2207 2446 297400700 297400463 3.420000e-68 270.0
37 TraesCS2D01G194000 chr7B 87.234 235 28 1 2214 2448 156706800 156706568 4.430000e-67 267.0
38 TraesCS2D01G194000 chr7B 78.443 167 33 2 7190 7354 40391422 40391257 1.020000e-18 106.0
39 TraesCS2D01G194000 chr7A 87.444 223 26 1 2220 2442 202747367 202747147 9.590000e-64 255.0
40 TraesCS2D01G194000 chr6A 85.124 242 30 5 2204 2445 63594293 63594058 7.470000e-60 243.0
41 TraesCS2D01G194000 chrUn 85.106 235 33 1 2214 2448 92262836 92262604 9.660000e-59 239.0
42 TraesCS2D01G194000 chr4B 84.120 233 32 3 2185 2414 122218298 122218068 3.500000e-53 220.0
43 TraesCS2D01G194000 chr3A 90.580 138 12 1 2759 2896 296504283 296504147 1.650000e-41 182.0
44 TraesCS2D01G194000 chr3A 77.848 158 28 6 7184 7337 86382843 86382997 2.860000e-14 91.6
45 TraesCS2D01G194000 chr3A 85.000 80 9 2 4047 4125 549616726 549616649 2.230000e-10 78.7
46 TraesCS2D01G194000 chr1D 83.562 146 22 2 7194 7337 468038650 468038505 1.300000e-27 135.0
47 TraesCS2D01G194000 chr7D 81.132 159 27 2 7181 7337 616168258 616168415 2.820000e-24 124.0
48 TraesCS2D01G194000 chr7D 81.416 113 18 3 7190 7300 31046731 31046620 1.030000e-13 89.8
49 TraesCS2D01G194000 chr1A 80.625 160 29 2 7191 7348 561138740 561138899 1.010000e-23 122.0
50 TraesCS2D01G194000 chr3B 85.915 71 7 2 4047 4116 157925023 157925091 1.040000e-08 73.1


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 TraesCS2D01G194000 chr2D 139023291 139030738 7447 False 13754.00 13754 100.00000 1 7448 1 chr2D.!!$F1 7447
1 TraesCS2D01G194000 chr2D 155339935 155340902 967 True 1038.00 1038 86.13700 6 978 1 chr2D.!!$R4 972
2 TraesCS2D01G194000 chr2B 197681575 197687858 6283 False 2461.25 7086 92.89725 1024 7448 4 chr2B.!!$F2 6424
3 TraesCS2D01G194000 chr2A 161949896 161957026 7130 True 1731.40 3469 87.85960 1 7121 5 chr2A.!!$R2 7120
4 TraesCS2D01G194000 chr2A 530741830 530742818 988 True 1101.00 1101 87.03500 6 983 1 chr2A.!!$R1 977
5 TraesCS2D01G194000 chr5A 10918144 10919121 977 True 1192.00 1192 88.70800 1 978 1 chr5A.!!$R1 977
6 TraesCS2D01G194000 chr5D 264881221 264882149 928 True 1166.00 1166 89.40000 6 932 1 chr5D.!!$R2 926
7 TraesCS2D01G194000 chr5B 249553988 249554967 979 False 1160.00 1160 88.11000 1 978 1 chr5B.!!$F1 977
8 TraesCS2D01G194000 chr6B 60582347 60583254 907 False 1114.00 1114 88.86500 1 911 1 chr6B.!!$F1 910
9 TraesCS2D01G194000 chr4D 486146000 486146934 934 False 1075.00 1075 87.55300 2 932 1 chr4D.!!$F1 930
10 TraesCS2D01G194000 chr6D 395523147 395524117 970 True 1061.00 1061 86.47000 6 981 1 chr6D.!!$R1 975
11 TraesCS2D01G194000 chr3D 545715290 545716255 965 False 1031.00 1031 86.00600 6 978 1 chr3D.!!$F4 972

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
37 39 0.232303 GTCGCCGACACTTGTTCTTG 59.768 55.000 13.23 0.00 32.09 3.02 F
189 191 0.320697 GGCCAAGGAGACGTACAAGT 59.679 55.000 0.00 0.00 0.00 3.16 F
1299 1328 0.097325 CGACTCCACACTCTCTACGC 59.903 60.000 0.00 0.00 0.00 4.42 F
1613 1663 0.252103 TAGACGGCTCCCCTGTTCTT 60.252 55.000 0.00 0.00 0.00 2.52 F
2088 2159 0.394352 AGGGGCCATGTGATTCGTTC 60.394 55.000 4.39 0.00 0.00 3.95 F
2777 2852 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01 F
4566 4690 0.040514 TTCCAATGCTGCGAACAACG 60.041 50.000 0.00 0.00 45.66 4.10 F
6134 6400 1.134220 GTCCCGCACCATATTTCTCCA 60.134 52.381 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1192 1220 0.110056 GGTTGTGATGAACGCAGCAG 60.110 55.000 0.00 0.00 41.74 4.24 R
2088 2159 0.250553 TCCGTGCCCAAGGTTTACAG 60.251 55.000 0.34 0.00 0.00 2.74 R
2851 2926 0.108945 GTTGGTACTCCCTCCGTTCG 60.109 60.000 0.00 0.00 0.00 3.95 R
2852 2927 1.264295 AGTTGGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95 R
3829 3908 2.287788 GCCACATCAACCTGACAAGTTG 60.288 50.000 10.19 10.19 44.80 3.16 R
4695 4829 1.611673 CCCGTGCTTGGTTGAGAGAAT 60.612 52.381 0.00 0.00 0.00 2.40 R
6294 6563 1.000521 CCAATTCCAGCTGGCCTCA 60.001 57.895 28.91 7.98 34.44 3.86 R
7350 7649 0.040058 TAGGGGTACGAGGAGCAACA 59.960 55.000 0.00 0.00 0.00 3.33 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
37 39 0.232303 GTCGCCGACACTTGTTCTTG 59.768 55.000 13.23 0.00 32.09 3.02
60 62 1.737838 GCAGATGGTTCGGATGTTCA 58.262 50.000 0.00 0.00 0.00 3.18
113 115 3.759581 AGAGTTCAAGTACCTCCACGTA 58.240 45.455 0.00 0.00 0.00 3.57
189 191 0.320697 GGCCAAGGAGACGTACAAGT 59.679 55.000 0.00 0.00 0.00 3.16
270 272 2.126071 CGAAGGACGACGTGCCAT 60.126 61.111 16.35 5.45 45.77 4.40
277 279 0.660595 GACGACGTGCCATCTATCGG 60.661 60.000 4.58 0.00 37.11 4.18
278 280 1.359117 CGACGTGCCATCTATCGGT 59.641 57.895 0.00 0.00 0.00 4.69
311 313 1.520120 CCATCGAGCAGTGCATCGT 60.520 57.895 25.55 15.84 39.86 3.73
531 537 0.745845 CGGCCTCATCTTGAACCAGG 60.746 60.000 0.00 0.00 0.00 4.45
709 726 1.467883 GCTTGATGCATTGCTTACGCA 60.468 47.619 10.49 0.00 42.60 5.24
728 746 2.029918 GCATCCTTCCTTTTTGAACGCT 60.030 45.455 0.00 0.00 0.00 5.07
941 966 2.613691 GAAGGGTCAAAATAGCGTCGA 58.386 47.619 0.00 0.00 0.00 4.20
972 998 1.212229 GGGACGAACGAGTGGAGAC 59.788 63.158 0.14 0.00 0.00 3.36
1010 1036 4.161377 TGATTGATGGTCTATGTTCACGGA 59.839 41.667 0.00 0.00 0.00 4.69
1072 1100 6.657541 GTGTTCCTATATCCCTTTTTGTGACA 59.342 38.462 0.00 0.00 0.00 3.58
1146 1174 4.849310 TTATCGCGCCCCAGCCAC 62.849 66.667 0.00 0.00 34.57 5.01
1269 1298 2.575993 CACACTCCTCTCGCCAGG 59.424 66.667 0.00 0.00 34.40 4.45
1270 1299 3.386237 ACACTCCTCTCGCCAGGC 61.386 66.667 0.00 0.00 32.91 4.85
1295 1324 2.336478 CGCCGACTCCACACTCTCT 61.336 63.158 0.00 0.00 0.00 3.10
1296 1325 1.025113 CGCCGACTCCACACTCTCTA 61.025 60.000 0.00 0.00 0.00 2.43
1299 1328 0.097325 CGACTCCACACTCTCTACGC 59.903 60.000 0.00 0.00 0.00 4.42
1302 1331 0.375454 CTCCACACTCTCTACGCTCG 59.625 60.000 0.00 0.00 0.00 5.03
1532 1580 0.965866 CGGGAGCTCTGTCAGGTACA 60.966 60.000 14.64 0.00 34.72 2.90
1613 1663 0.252103 TAGACGGCTCCCCTGTTCTT 60.252 55.000 0.00 0.00 0.00 2.52
1615 1665 2.747855 CGGCTCCCCTGTTCTTGC 60.748 66.667 0.00 0.00 0.00 4.01
1616 1666 2.759795 GGCTCCCCTGTTCTTGCT 59.240 61.111 0.00 0.00 0.00 3.91
1618 1668 1.676967 GCTCCCCTGTTCTTGCTGG 60.677 63.158 0.00 0.00 0.00 4.85
1624 1674 1.340405 CCCTGTTCTTGCTGGCATAGT 60.340 52.381 0.00 0.00 0.00 2.12
1660 1710 4.137543 GCCTGGAATATAACTGTTCAGGG 58.862 47.826 19.29 7.07 29.62 4.45
1743 1793 0.465460 GCATGGCGGGAATACAAGGA 60.465 55.000 0.00 0.00 0.00 3.36
1816 1868 2.286365 TTGGTAGAAAGGCTTGTGGG 57.714 50.000 0.00 0.00 0.00 4.61
1837 1889 1.118965 TTGGACTCTGGCGGTTGAGA 61.119 55.000 0.00 0.00 34.65 3.27
1872 1924 2.298158 CTGGCGACCGTAGAGGCAAT 62.298 60.000 0.00 0.00 46.52 3.56
2020 2072 2.182732 GAGAAGGAGGCAGTGCAGCT 62.183 60.000 18.61 5.40 34.17 4.24
2074 2145 1.751351 GCACAAGGAAGAATAAGGGGC 59.249 52.381 0.00 0.00 0.00 5.80
2076 2147 2.000048 ACAAGGAAGAATAAGGGGCCA 59.000 47.619 4.39 0.00 0.00 5.36
2088 2159 0.394352 AGGGGCCATGTGATTCGTTC 60.394 55.000 4.39 0.00 0.00 3.95
2094 2165 3.438781 GGCCATGTGATTCGTTCTGTAAA 59.561 43.478 0.00 0.00 0.00 2.01
2198 2269 3.834813 GCTCATCACATATACTCCCTCCA 59.165 47.826 0.00 0.00 0.00 3.86
2773 2848 4.333417 AGGTACTCCCTCCGTTCG 57.667 61.111 0.00 0.00 40.71 3.95
2774 2849 1.379576 AGGTACTCCCTCCGTTCGG 60.380 63.158 4.74 4.74 40.71 4.30
2775 2850 1.379044 GGTACTCCCTCCGTTCGGA 60.379 63.158 13.34 13.34 0.00 4.55
2777 2852 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2780 2855 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2781 2856 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2782 2857 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2784 2859 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2785 2860 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2786 2861 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2787 2862 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2788 2863 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2789 2864 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2790 2865 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2792 2867 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2793 2868 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
2794 2869 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
2795 2870 4.868171 CGGAATTACTTGTCTCGGAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2797 2872 6.037172 CGGAATTACTTGTCTCGGAAATGAAT 59.963 38.462 0.00 0.00 0.00 2.57
2798 2873 7.189512 GGAATTACTTGTCTCGGAAATGAATG 58.810 38.462 0.00 0.00 0.00 2.67
2799 2874 7.148239 GGAATTACTTGTCTCGGAAATGAATGT 60.148 37.037 0.00 0.00 0.00 2.71
2801 2876 8.964476 ATTACTTGTCTCGGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2802 2877 6.910536 ACTTGTCTCGGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2806 2881 7.582667 TGTCTCGGAAATGAATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
2807 2882 8.007405 TGTCTCGGAAATGAATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
2808 2883 7.921214 TGTCTCGGAAATGAATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
2810 2885 9.350951 TCTCGGAAATGAATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
2811 2886 9.967346 CTCGGAAATGAATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
2838 2913 6.604735 ACGTCTAGATACATCCATTTTTGC 57.395 37.500 0.00 0.00 0.00 3.68
2839 2914 5.234329 ACGTCTAGATACATCCATTTTTGCG 59.766 40.000 0.00 0.00 0.00 4.85
2840 2915 5.462068 CGTCTAGATACATCCATTTTTGCGA 59.538 40.000 0.00 0.00 0.00 5.10
2841 2916 6.562270 CGTCTAGATACATCCATTTTTGCGAC 60.562 42.308 0.00 0.00 0.00 5.19
2842 2917 6.257849 GTCTAGATACATCCATTTTTGCGACA 59.742 38.462 0.00 0.00 0.00 4.35
2843 2918 5.895636 AGATACATCCATTTTTGCGACAA 57.104 34.783 0.00 0.00 0.00 3.18
2844 2919 5.883661 AGATACATCCATTTTTGCGACAAG 58.116 37.500 0.00 0.00 0.00 3.16
2845 2920 5.415701 AGATACATCCATTTTTGCGACAAGT 59.584 36.000 0.00 0.00 0.00 3.16
2846 2921 6.597672 AGATACATCCATTTTTGCGACAAGTA 59.402 34.615 0.00 0.00 0.00 2.24
2847 2922 5.446143 ACATCCATTTTTGCGACAAGTAA 57.554 34.783 0.00 0.00 0.00 2.24
2848 2923 6.024552 ACATCCATTTTTGCGACAAGTAAT 57.975 33.333 0.00 0.00 0.00 1.89
2849 2924 6.454795 ACATCCATTTTTGCGACAAGTAATT 58.545 32.000 0.00 0.00 0.00 1.40
2850 2925 6.586082 ACATCCATTTTTGCGACAAGTAATTC 59.414 34.615 0.00 0.00 0.00 2.17
2851 2926 5.465935 TCCATTTTTGCGACAAGTAATTCC 58.534 37.500 0.00 0.00 0.00 3.01
2852 2927 4.323336 CCATTTTTGCGACAAGTAATTCCG 59.677 41.667 0.00 0.00 0.00 4.30
2853 2928 4.815040 TTTTTGCGACAAGTAATTCCGA 57.185 36.364 0.00 0.00 0.00 4.55
3320 3399 4.855298 TTACCCTTATGAACCTTGGAGG 57.145 45.455 0.00 0.00 42.49 4.30
4260 4346 7.150783 ACAAGCTAGAACTCCAAATGATTTC 57.849 36.000 0.00 0.00 33.91 2.17
4441 4561 0.391597 GGAATTATCCCGTCGGAGCA 59.608 55.000 14.39 0.00 43.12 4.26
4566 4690 0.040514 TTCCAATGCTGCGAACAACG 60.041 50.000 0.00 0.00 45.66 4.10
4694 4828 2.632996 GGACATATAGCAGCACCCACTA 59.367 50.000 0.00 0.00 0.00 2.74
4695 4829 3.071023 GGACATATAGCAGCACCCACTAA 59.929 47.826 0.00 0.00 0.00 2.24
4855 5013 2.359011 CAGGTTTAGGGGTGGGGC 59.641 66.667 0.00 0.00 0.00 5.80
4909 5067 1.343069 CGGGCTTAGAGGGATAGCTT 58.657 55.000 0.00 0.00 35.30 3.74
5031 5206 2.660064 ATCGGAGAGGCGGCAGTTT 61.660 57.895 13.08 0.00 43.63 2.66
5033 5208 2.665603 GGAGAGGCGGCAGTTTCT 59.334 61.111 13.08 4.70 0.00 2.52
5035 5210 1.743252 GAGAGGCGGCAGTTTCTGG 60.743 63.158 13.08 0.00 31.21 3.86
5572 5759 6.039605 TCCATGTTGATTTTCATCGCATATGT 59.960 34.615 4.29 0.00 30.75 2.29
5662 5849 6.991485 TGCTTCGTCTTTCAATTGAAAATC 57.009 33.333 28.49 22.42 42.72 2.17
5760 5947 1.947456 GATGTTATGGGGCCTTCGAAC 59.053 52.381 0.84 3.41 0.00 3.95
5839 6026 3.660865 AGTTTAGGACTAACCGTGCAAG 58.339 45.455 0.00 0.00 44.74 4.01
6113 6379 6.035843 CCTTTGCCATGACATAAATGTACAC 58.964 40.000 0.00 0.00 41.95 2.90
6134 6400 1.134220 GTCCCGCACCATATTTCTCCA 60.134 52.381 0.00 0.00 0.00 3.86
6294 6563 7.117285 TGTCTTCTGTCTGCAGTATATCAAT 57.883 36.000 14.67 0.00 43.05 2.57
6331 6600 3.884895 TGGCGGTTGATGAAGACAATAT 58.115 40.909 0.00 0.00 0.00 1.28
6339 6608 7.277760 CGGTTGATGAAGACAATATTGACTACA 59.722 37.037 22.16 15.08 33.07 2.74
6560 6832 2.167075 AGGCATGGCTTTTATTGTGAGC 59.833 45.455 17.44 0.00 35.71 4.26
6578 6850 1.447643 CCGGCAGGGATACTCCTTG 59.552 63.158 0.00 1.16 45.46 3.61
6628 6900 5.048643 GCCTGGAGTTTTACCTTTTCTCTTC 60.049 44.000 0.00 0.00 0.00 2.87
6632 6904 5.241064 GGAGTTTTACCTTTTCTCTTCACCC 59.759 44.000 0.00 0.00 0.00 4.61
6633 6905 4.820173 AGTTTTACCTTTTCTCTTCACCCG 59.180 41.667 0.00 0.00 0.00 5.28
6634 6906 2.467566 TACCTTTTCTCTTCACCCGC 57.532 50.000 0.00 0.00 0.00 6.13
6636 6908 1.133915 ACCTTTTCTCTTCACCCGCAA 60.134 47.619 0.00 0.00 0.00 4.85
6637 6909 1.953686 CCTTTTCTCTTCACCCGCAAA 59.046 47.619 0.00 0.00 0.00 3.68
6639 6911 3.181480 CCTTTTCTCTTCACCCGCAAAAA 60.181 43.478 0.00 0.00 0.00 1.94
6752 7030 8.578308 TTTCACATTCATTCTCATTCAAACAC 57.422 30.769 0.00 0.00 0.00 3.32
6800 7078 5.258456 AGATTGCATCAGTAAAATGGCAG 57.742 39.130 0.00 0.00 0.00 4.85
6802 7080 2.169330 TGCATCAGTAAAATGGCAGCA 58.831 42.857 0.00 0.00 0.00 4.41
6844 7122 3.266772 TGAAGTTCCAGGCCATTATCTGT 59.733 43.478 5.01 0.00 0.00 3.41
6946 7224 2.744352 ATTTCCATCTGAGGGCTTCC 57.256 50.000 2.89 0.00 0.00 3.46
7013 7291 8.504815 GGTTAGTCAATCTACCTGAAAAGTTTC 58.495 37.037 0.00 0.00 37.69 2.78
7048 7326 2.309764 GAAATGGTGTGGCTAGCGCG 62.310 60.000 9.00 0.00 36.88 6.86
7049 7327 2.796483 AAATGGTGTGGCTAGCGCGA 62.796 55.000 12.10 0.00 36.88 5.87
7050 7328 2.796483 AATGGTGTGGCTAGCGCGAA 62.796 55.000 12.10 0.00 36.88 4.70
7054 7332 2.182030 GTGGCTAGCGCGAAGTCT 59.818 61.111 12.10 0.00 36.88 3.24
7056 7334 2.340328 TGGCTAGCGCGAAGTCTCA 61.340 57.895 12.10 4.15 36.88 3.27
7058 7336 1.137825 GCTAGCGCGAAGTCTCAGT 59.862 57.895 12.10 0.00 0.00 3.41
7121 7419 4.024387 TCGTATCTGTGTGTTGCTTTTTCC 60.024 41.667 0.00 0.00 0.00 3.13
7122 7420 2.842208 TCTGTGTGTTGCTTTTTCCG 57.158 45.000 0.00 0.00 0.00 4.30
7123 7421 1.403679 TCTGTGTGTTGCTTTTTCCGG 59.596 47.619 0.00 0.00 0.00 5.14
7124 7422 0.179124 TGTGTGTTGCTTTTTCCGGC 60.179 50.000 0.00 0.00 0.00 6.13
7125 7423 0.102300 GTGTGTTGCTTTTTCCGGCT 59.898 50.000 0.00 0.00 0.00 5.52
7126 7424 0.820871 TGTGTTGCTTTTTCCGGCTT 59.179 45.000 0.00 0.00 0.00 4.35
7127 7425 1.208259 GTGTTGCTTTTTCCGGCTTG 58.792 50.000 0.00 0.00 0.00 4.01
7128 7426 0.529555 TGTTGCTTTTTCCGGCTTGC 60.530 50.000 0.00 0.00 0.00 4.01
7129 7427 1.068921 TTGCTTTTTCCGGCTTGCC 59.931 52.632 0.00 0.75 0.00 4.52
7130 7428 2.430751 GCTTTTTCCGGCTTGCCG 60.431 61.111 25.17 25.17 0.00 5.69
7180 7478 4.030452 GCTTGCCGGTGCTGTCAC 62.030 66.667 1.90 0.00 42.40 3.67
7181 7479 3.716006 CTTGCCGGTGCTGTCACG 61.716 66.667 1.90 0.00 44.03 4.35
7186 7484 4.969196 CGGTGCTGTCACGGTGCT 62.969 66.667 2.51 0.00 44.03 4.40
7187 7485 3.044305 GGTGCTGTCACGGTGCTC 61.044 66.667 2.51 0.00 44.03 4.26
7188 7486 2.029666 GTGCTGTCACGGTGCTCT 59.970 61.111 2.51 0.00 32.98 4.09
7189 7487 2.024319 GTGCTGTCACGGTGCTCTC 61.024 63.158 2.51 0.00 32.98 3.20
7220 7518 1.153127 TGCGGGTGTCGTTTTCCTT 60.153 52.632 0.00 0.00 41.72 3.36
7228 7526 3.875134 GGTGTCGTTTTCCTTCTTGAAGA 59.125 43.478 11.53 0.00 0.00 2.87
7234 7532 4.233005 GTTTTCCTTCTTGAAGATGCTGC 58.767 43.478 11.53 0.00 0.00 5.25
7235 7533 2.119801 TCCTTCTTGAAGATGCTGCC 57.880 50.000 11.53 0.00 0.00 4.85
7236 7534 1.352017 TCCTTCTTGAAGATGCTGCCA 59.648 47.619 11.53 0.00 0.00 4.92
7246 7544 1.001248 ATGCTGCCATGGCCTTCTT 59.999 52.632 33.44 16.61 41.09 2.52
7250 7548 0.323178 CTGCCATGGCCTTCTTCTGT 60.323 55.000 33.44 0.00 41.09 3.41
7256 7554 2.759795 GCCTTCTTCTGTGCCCCT 59.240 61.111 0.00 0.00 0.00 4.79
7288 7587 1.571955 GGAAACCCTAGGTCCGGTTA 58.428 55.000 8.29 0.00 41.58 2.85
7290 7589 2.103771 GGAAACCCTAGGTCCGGTTATC 59.896 54.545 8.29 5.46 41.58 1.75
7309 7608 2.237751 CGGATCGGATGACAACGGC 61.238 63.158 0.00 0.00 0.00 5.68
7314 7613 3.799755 GGATGACAACGGCGCCAC 61.800 66.667 28.98 12.10 0.00 5.01
7315 7614 4.147322 GATGACAACGGCGCCACG 62.147 66.667 28.98 16.39 40.31 4.94
7331 7630 1.202177 CCACGGCATCATTTTCCTTCG 60.202 52.381 0.00 0.00 0.00 3.79
7337 7636 3.440173 GGCATCATTTTCCTTCGTGAAGA 59.560 43.478 11.11 0.00 40.79 2.87
7356 7655 3.960571 AGATGCTATCTTGGTTGTTGCT 58.039 40.909 0.00 0.00 35.76 3.91
7357 7656 3.944015 AGATGCTATCTTGGTTGTTGCTC 59.056 43.478 0.00 0.00 35.76 4.26
7358 7657 2.436417 TGCTATCTTGGTTGTTGCTCC 58.564 47.619 0.00 0.00 0.00 4.70
7359 7658 2.040278 TGCTATCTTGGTTGTTGCTCCT 59.960 45.455 0.00 0.00 0.00 3.69
7360 7659 2.680339 GCTATCTTGGTTGTTGCTCCTC 59.320 50.000 0.00 0.00 0.00 3.71
7364 7663 1.798813 CTTGGTTGTTGCTCCTCGTAC 59.201 52.381 0.00 0.00 0.00 3.67
7378 7677 1.680207 CTCGTACCCCTAGTGTTAGCC 59.320 57.143 0.00 0.00 0.00 3.93
7379 7678 1.005805 TCGTACCCCTAGTGTTAGCCA 59.994 52.381 0.00 0.00 0.00 4.75
7380 7679 1.135721 CGTACCCCTAGTGTTAGCCAC 59.864 57.143 0.00 0.00 44.89 5.01
7396 7695 1.821216 CCACTTTTGGCGATGGTAGT 58.179 50.000 0.00 0.00 35.56 2.73
7402 7701 2.672961 TTGGCGATGGTAGTCTTCAG 57.327 50.000 0.00 0.00 0.00 3.02
7404 7703 0.530870 GGCGATGGTAGTCTTCAGGC 60.531 60.000 0.00 0.00 0.00 4.85
7418 7717 0.823356 TCAGGCTGGTTTGTCTTGCC 60.823 55.000 15.73 0.00 43.52 4.52
7428 7727 2.557056 GTTTGTCTTGCCCCTCTAAACC 59.443 50.000 0.00 0.00 0.00 3.27
7429 7728 1.742308 TGTCTTGCCCCTCTAAACCT 58.258 50.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 3.757248 ATCCGAACCATCTGCGCCC 62.757 63.158 4.18 0.00 0.00 6.13
60 62 1.899437 CTGTCCTGGCGGTACATGGT 61.899 60.000 0.00 0.00 0.00 3.55
113 115 1.683917 CACTTCTCGATCCGGGAGAAT 59.316 52.381 18.35 9.02 46.27 2.40
225 227 1.495584 GCTCGTTTGTTGCCGTCTGA 61.496 55.000 0.00 0.00 0.00 3.27
262 264 0.309922 CGTACCGATAGATGGCACGT 59.690 55.000 0.00 0.00 39.76 4.49
270 272 0.313987 CATGCAGCCGTACCGATAGA 59.686 55.000 0.00 0.00 39.76 1.98
277 279 3.564027 GGACGCATGCAGCCGTAC 61.564 66.667 19.57 10.84 41.38 3.67
278 280 3.384275 ATGGACGCATGCAGCCGTA 62.384 57.895 19.57 3.48 41.38 4.02
311 313 2.355363 CGTGGTTCTTGGCGTCGA 60.355 61.111 0.00 0.00 0.00 4.20
709 726 3.486383 TCAGCGTTCAAAAAGGAAGGAT 58.514 40.909 0.00 0.00 35.29 3.24
728 746 4.328983 GGCGATCAATAACTCGAAAGTTCA 59.671 41.667 0.00 0.00 44.64 3.18
957 983 2.185103 GAGCGTCTCCACTCGTTCGT 62.185 60.000 0.00 0.00 0.00 3.85
985 1011 5.528690 CCGTGAACATAGACCATCAATCAAT 59.471 40.000 0.00 0.00 0.00 2.57
1010 1036 1.228245 ACATGAAACCTGCGTGGCT 60.228 52.632 0.00 0.00 40.22 4.75
1072 1100 9.956640 TGCCAAAGGATTTATATCAATTTTTGT 57.043 25.926 13.64 0.00 35.03 2.83
1079 1107 4.642437 TGCGTGCCAAAGGATTTATATCAA 59.358 37.500 0.00 0.00 35.03 2.57
1081 1109 4.829064 TGCGTGCCAAAGGATTTATATC 57.171 40.909 0.00 0.00 35.03 1.63
1119 1147 3.330853 CGCGATAACGGCCAGAGC 61.331 66.667 0.00 0.00 40.15 4.09
1128 1156 4.849310 TGGCTGGGGCGCGATAAC 62.849 66.667 12.10 0.00 39.81 1.89
1191 1219 0.727122 GTTGTGATGAACGCAGCAGC 60.727 55.000 0.00 0.00 41.74 5.25
1192 1220 0.110056 GGTTGTGATGAACGCAGCAG 60.110 55.000 0.00 0.00 41.74 4.24
1193 1221 0.817229 TGGTTGTGATGAACGCAGCA 60.817 50.000 0.00 0.00 40.94 4.41
1282 1311 1.455248 GAGCGTAGAGAGTGTGGAGT 58.545 55.000 0.00 0.00 0.00 3.85
1532 1580 4.753662 TGCTAGGACGGCGGGACT 62.754 66.667 13.24 8.72 0.00 3.85
1624 1674 2.441410 TCCAGGCAATTCAACGCATTA 58.559 42.857 0.00 0.00 0.00 1.90
1660 1710 2.159057 GCATGGTGATTTCCCATCCAAC 60.159 50.000 0.00 0.00 40.76 3.77
1743 1793 6.649155 TGTAATGCTACATACAAGGACACAT 58.351 36.000 0.00 0.00 32.93 3.21
1816 1868 2.032681 AACCGCCAGAGTCCAAGC 59.967 61.111 0.00 0.00 0.00 4.01
1854 1906 1.038681 TATTGCCTCTACGGTCGCCA 61.039 55.000 0.00 0.00 34.25 5.69
1872 1924 3.698250 GTGTGCCACCTTGTCACTA 57.302 52.632 0.00 0.00 0.00 2.74
2020 2072 0.994247 TCCTCCTACTCCACACGGTA 59.006 55.000 0.00 0.00 0.00 4.02
2074 2145 4.695455 AGGTTTACAGAACGAATCACATGG 59.305 41.667 0.00 0.00 0.00 3.66
2076 2147 5.181245 CCAAGGTTTACAGAACGAATCACAT 59.819 40.000 0.00 0.00 0.00 3.21
2088 2159 0.250553 TCCGTGCCCAAGGTTTACAG 60.251 55.000 0.34 0.00 0.00 2.74
2094 2165 2.308722 ATGGATCCGTGCCCAAGGT 61.309 57.895 5.41 0.00 35.85 3.50
2768 2843 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
2771 2846 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2772 2847 4.868171 TCATTTCCGAGACAAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
2773 2848 6.737254 TTCATTTCCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2774 2849 7.752695 ACATTCATTTCCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2775 2850 7.687941 ACATTCATTTCCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2777 2852 8.258007 AGATACATTCATTTCCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2780 2855 8.138074 TCTAGATACATTCATTTCCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
2781 2856 8.007405 TCTAGATACATTCATTTCCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
2782 2857 7.582667 TCTAGATACATTCATTTCCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
2784 2859 8.239038 AGTTCTAGATACATTCATTTCCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
2785 2860 9.967346 TTAGTTCTAGATACATTCATTTCCGAG 57.033 33.333 0.00 0.00 0.00 4.63
2814 2889 6.419710 CGCAAAAATGGATGTATCTAGACGTA 59.580 38.462 0.00 0.00 0.00 3.57
2815 2890 5.234329 CGCAAAAATGGATGTATCTAGACGT 59.766 40.000 0.00 0.00 0.00 4.34
2816 2891 5.462068 TCGCAAAAATGGATGTATCTAGACG 59.538 40.000 0.00 0.00 0.00 4.18
2817 2892 6.257849 TGTCGCAAAAATGGATGTATCTAGAC 59.742 38.462 0.00 0.00 0.00 2.59
2821 2896 5.415701 ACTTGTCGCAAAAATGGATGTATCT 59.584 36.000 0.00 0.00 0.00 1.98
2822 2897 5.640732 ACTTGTCGCAAAAATGGATGTATC 58.359 37.500 0.00 0.00 0.00 2.24
2823 2898 5.643379 ACTTGTCGCAAAAATGGATGTAT 57.357 34.783 0.00 0.00 0.00 2.29
2824 2899 6.561737 TTACTTGTCGCAAAAATGGATGTA 57.438 33.333 0.00 0.00 0.00 2.29
2825 2900 5.446143 TTACTTGTCGCAAAAATGGATGT 57.554 34.783 0.00 0.00 0.00 3.06
2826 2901 6.034898 GGAATTACTTGTCGCAAAAATGGATG 59.965 38.462 0.00 0.00 0.00 3.51
2828 2903 5.465935 GGAATTACTTGTCGCAAAAATGGA 58.534 37.500 0.00 0.00 0.00 3.41
2829 2904 4.323336 CGGAATTACTTGTCGCAAAAATGG 59.677 41.667 0.00 0.00 0.00 3.16
2830 2905 5.150683 TCGGAATTACTTGTCGCAAAAATG 58.849 37.500 0.00 0.00 0.00 2.32
2831 2906 5.365403 TCGGAATTACTTGTCGCAAAAAT 57.635 34.783 0.00 0.00 0.00 1.82
2832 2907 4.815040 TCGGAATTACTTGTCGCAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
2833 2908 4.529446 GTTCGGAATTACTTGTCGCAAAA 58.471 39.130 0.00 0.00 0.00 2.44
2834 2909 3.363182 CGTTCGGAATTACTTGTCGCAAA 60.363 43.478 0.00 0.00 0.00 3.68
2835 2910 2.156117 CGTTCGGAATTACTTGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
2836 2911 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2837 2912 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2838 2913 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2839 2914 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2840 2915 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2841 2916 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2842 2917 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2843 2918 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2844 2919 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2845 2920 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2846 2921 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2847 2922 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2848 2923 0.967380 GGTACTCCCTCCGTTCGGAA 60.967 60.000 14.79 0.04 33.41 4.30
2849 2924 1.379044 GGTACTCCCTCCGTTCGGA 60.379 63.158 13.34 13.34 0.00 4.55
2850 2925 1.252904 TTGGTACTCCCTCCGTTCGG 61.253 60.000 4.74 4.74 0.00 4.30
2851 2926 0.108945 GTTGGTACTCCCTCCGTTCG 60.109 60.000 0.00 0.00 0.00 3.95
2852 2927 1.264295 AGTTGGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
2853 2928 2.042162 TCTAGTTGGTACTCCCTCCGTT 59.958 50.000 0.00 0.00 35.78 4.44
3320 3399 4.641954 CGTGATGTCTGTCATGCTTAAAC 58.358 43.478 0.00 0.00 36.83 2.01
3829 3908 2.287788 GCCACATCAACCTGACAAGTTG 60.288 50.000 10.19 10.19 44.80 3.16
4138 4218 7.014711 TCCTGCTCCTATACAACTTCTCTAATG 59.985 40.741 0.00 0.00 0.00 1.90
4140 4220 6.432581 TCCTGCTCCTATACAACTTCTCTAA 58.567 40.000 0.00 0.00 0.00 2.10
4223 4308 4.553323 TCTAGCTTGTCGTAAGTCAAACC 58.447 43.478 0.00 0.00 44.29 3.27
4260 4346 2.125912 CAGTGCTCCCTCCGTTCG 60.126 66.667 0.00 0.00 0.00 3.95
4566 4690 7.764901 GCTCCACCTATATTTTATAGTGTAGCC 59.235 40.741 0.00 0.00 0.00 3.93
4694 4828 2.154462 CCGTGCTTGGTTGAGAGAATT 58.846 47.619 0.00 0.00 0.00 2.17
4695 4829 1.611673 CCCGTGCTTGGTTGAGAGAAT 60.612 52.381 0.00 0.00 0.00 2.40
4855 5013 1.892862 GCTAGAGCCAGCATGCCAG 60.893 63.158 15.66 7.19 41.40 4.85
4868 5026 0.328258 GGGCCAGGTTCTTTGCTAGA 59.672 55.000 4.39 0.00 0.00 2.43
5031 5206 3.006940 GTGTTCGGAACATAATGCCAGA 58.993 45.455 24.81 0.00 44.35 3.86
5033 5208 2.784347 TGTGTTCGGAACATAATGCCA 58.216 42.857 24.81 14.63 44.35 4.92
5035 5210 5.861251 TCATTTTGTGTTCGGAACATAATGC 59.139 36.000 28.47 18.66 44.35 3.56
5036 5211 6.860539 TGTCATTTTGTGTTCGGAACATAATG 59.139 34.615 26.50 27.39 44.35 1.90
5037 5212 6.976088 TGTCATTTTGTGTTCGGAACATAAT 58.024 32.000 26.50 20.92 44.35 1.28
5039 5214 5.529430 ACTGTCATTTTGTGTTCGGAACATA 59.471 36.000 24.81 19.97 44.35 2.29
5041 5216 3.692101 ACTGTCATTTTGTGTTCGGAACA 59.308 39.130 19.07 19.07 39.52 3.18
5522 5709 9.185192 GACATCATTTCCTGAAAGTTTGTTTAG 57.815 33.333 0.00 0.00 37.44 1.85
5662 5849 3.921677 AGCATGCTGGTGAATTTTCTTG 58.078 40.909 21.98 0.00 0.00 3.02
5697 5884 9.069082 TCCAAAATGAAAAATGAATTGCAATCT 57.931 25.926 13.38 3.05 0.00 2.40
6134 6400 7.361799 GCACGAAGGTTATAACTTGGAATTCTT 60.362 37.037 15.05 7.27 0.00 2.52
6294 6563 1.000521 CCAATTCCAGCTGGCCTCA 60.001 57.895 28.91 7.98 34.44 3.86
6331 6600 4.875536 GTCATACACATGGCATGTAGTCAA 59.124 41.667 30.96 17.12 42.70 3.18
6339 6608 4.847198 TCTCTTTGTCATACACATGGCAT 58.153 39.130 0.00 0.00 45.87 4.40
6453 6722 4.642437 TCTCTGACTAGTCAATGGTAGCAG 59.358 45.833 25.14 11.16 39.39 4.24
6578 6850 6.399204 CTTTCAATAAAAGCCATCTGCAAC 57.601 37.500 0.00 0.00 44.83 4.17
6642 6914 7.771183 TGTTTCTACTTGTTTGAGCATCTTTT 58.229 30.769 0.00 0.00 34.92 2.27
6643 6915 7.333528 TGTTTCTACTTGTTTGAGCATCTTT 57.666 32.000 0.00 0.00 34.92 2.52
6752 7030 1.013596 TGTTCGTGTCACTTTGCTGG 58.986 50.000 0.65 0.00 0.00 4.85
6800 7078 6.029607 TCATTTCTTGAACTTGCGATATTGC 58.970 36.000 8.10 8.10 0.00 3.56
6802 7080 7.820648 ACTTCATTTCTTGAACTTGCGATATT 58.179 30.769 0.00 0.00 39.44 1.28
6844 7122 2.203056 CGGCGCAATGGAGATGGA 60.203 61.111 10.83 0.00 0.00 3.41
7013 7291 5.195940 ACCATTTCTACAAGGTGATGATGG 58.804 41.667 0.00 0.00 32.04 3.51
7124 7422 2.901051 ATACGAACGGAGCCGGCAAG 62.901 60.000 31.54 21.17 44.69 4.01
7125 7423 2.894240 GATACGAACGGAGCCGGCAA 62.894 60.000 31.54 1.93 44.69 4.52
7126 7424 3.420214 GATACGAACGGAGCCGGCA 62.420 63.158 31.54 4.05 44.69 5.69
7127 7425 2.657620 GATACGAACGGAGCCGGC 60.658 66.667 21.89 21.89 44.69 6.13
7128 7426 1.299165 CAGATACGAACGGAGCCGG 60.299 63.158 14.07 0.00 44.69 6.13
7129 7427 1.944676 GCAGATACGAACGGAGCCG 60.945 63.158 7.48 7.48 46.03 5.52
7130 7428 1.944676 CGCAGATACGAACGGAGCC 60.945 63.158 0.00 0.00 34.06 4.70
7131 7429 1.226603 ACGCAGATACGAACGGAGC 60.227 57.895 0.00 0.00 36.70 4.70
7132 7430 0.179171 ACACGCAGATACGAACGGAG 60.179 55.000 0.00 0.00 36.70 4.63
7133 7431 0.241749 AACACGCAGATACGAACGGA 59.758 50.000 0.00 0.00 36.70 4.69
7134 7432 0.365523 CAACACGCAGATACGAACGG 59.634 55.000 0.00 0.00 36.70 4.44
7135 7433 0.246757 GCAACACGCAGATACGAACG 60.247 55.000 0.00 0.00 41.79 3.95
7136 7434 1.068474 AGCAACACGCAGATACGAAC 58.932 50.000 0.00 0.00 46.13 3.95
7137 7435 1.790755 AAGCAACACGCAGATACGAA 58.209 45.000 0.00 0.00 46.13 3.85
7185 7483 3.805307 AGACGTCGCCGCTGAGAG 61.805 66.667 10.46 0.00 37.70 3.20
7186 7484 4.103103 CAGACGTCGCCGCTGAGA 62.103 66.667 10.46 0.00 39.18 3.27
7200 7498 1.595929 GGAAAACGACACCCGCAGA 60.596 57.895 0.00 0.00 43.32 4.26
7212 7510 4.233005 GCAGCATCTTCAAGAAGGAAAAC 58.767 43.478 9.73 0.00 38.88 2.43
7220 7518 1.758936 CCATGGCAGCATCTTCAAGA 58.241 50.000 0.00 0.00 0.00 3.02
7228 7526 1.001248 AAGAAGGCCATGGCAGCAT 59.999 52.632 36.56 19.62 44.11 3.79
7234 7532 1.318158 GGCACAGAAGAAGGCCATGG 61.318 60.000 7.63 7.63 45.70 3.66
7235 7533 2.187073 GGCACAGAAGAAGGCCATG 58.813 57.895 5.01 0.00 45.70 3.66
7236 7534 4.751431 GGCACAGAAGAAGGCCAT 57.249 55.556 5.01 0.00 45.70 4.40
7246 7544 0.984230 AAATCGAAGAGGGGCACAGA 59.016 50.000 0.00 0.00 43.63 3.41
7250 7548 0.837272 CCCTAAATCGAAGAGGGGCA 59.163 55.000 17.87 0.00 45.53 5.36
7309 7608 1.226660 GGAAAATGATGCCGTGGCG 60.227 57.895 6.37 0.00 45.51 5.69
7314 7613 1.737236 TCACGAAGGAAAATGATGCCG 59.263 47.619 0.00 0.00 0.00 5.69
7315 7614 3.440173 TCTTCACGAAGGAAAATGATGCC 59.560 43.478 6.94 0.00 38.88 4.40
7318 7617 4.946157 AGCATCTTCACGAAGGAAAATGAT 59.054 37.500 6.94 0.00 38.88 2.45
7331 7630 5.634896 CAACAACCAAGATAGCATCTTCAC 58.365 41.667 8.01 0.00 46.17 3.18
7337 7636 3.019564 GGAGCAACAACCAAGATAGCAT 58.980 45.455 0.00 0.00 0.00 3.79
7350 7649 0.040058 TAGGGGTACGAGGAGCAACA 59.960 55.000 0.00 0.00 0.00 3.33
7352 7651 0.333993 ACTAGGGGTACGAGGAGCAA 59.666 55.000 0.00 0.00 0.00 3.91
7354 7653 0.395448 ACACTAGGGGTACGAGGAGC 60.395 60.000 0.00 0.00 0.00 4.70
7355 7654 2.140839 AACACTAGGGGTACGAGGAG 57.859 55.000 0.00 0.00 0.00 3.69
7356 7655 2.684927 GCTAACACTAGGGGTACGAGGA 60.685 54.545 0.00 0.00 0.00 3.71
7357 7656 1.680207 GCTAACACTAGGGGTACGAGG 59.320 57.143 0.00 0.00 0.00 4.63
7358 7657 1.680207 GGCTAACACTAGGGGTACGAG 59.320 57.143 0.00 0.00 0.00 4.18
7359 7658 1.005805 TGGCTAACACTAGGGGTACGA 59.994 52.381 0.00 0.00 0.00 3.43
7360 7659 1.135721 GTGGCTAACACTAGGGGTACG 59.864 57.143 0.00 0.00 46.72 3.67
7378 7677 2.699954 AGACTACCATCGCCAAAAGTG 58.300 47.619 0.00 0.00 0.00 3.16
7379 7678 3.244422 TGAAGACTACCATCGCCAAAAGT 60.244 43.478 0.00 0.00 0.00 2.66
7380 7679 3.334691 TGAAGACTACCATCGCCAAAAG 58.665 45.455 0.00 0.00 0.00 2.27
7396 7695 2.575532 CAAGACAAACCAGCCTGAAGA 58.424 47.619 0.00 0.00 0.00 2.87
7402 7701 2.574018 GGGGCAAGACAAACCAGCC 61.574 63.158 0.00 0.00 44.48 4.85
7404 7703 0.111253 AGAGGGGCAAGACAAACCAG 59.889 55.000 0.00 0.00 0.00 4.00
7428 7727 0.966179 GCTAAACCCACAAACCCCAG 59.034 55.000 0.00 0.00 0.00 4.45
7429 7728 3.135027 GCTAAACCCACAAACCCCA 57.865 52.632 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.