Multiple sequence alignment - TraesCS3B01G255400

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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 TraesCS3B01G255400 chr3B 100.000 3809 0 0 1 3809 411846906 411843098 0.000000e+00 7035
1 TraesCS3B01G255400 chr3B 95.362 733 31 3 3076 3807 354018105 354018835 0.000000e+00 1162
2 TraesCS3B01G255400 chr3B 93.758 737 43 3 3072 3807 129515290 129516024 0.000000e+00 1103
3 TraesCS3B01G255400 chr3B 91.111 90 7 1 2880 2968 223942533 223942622 1.860000e-23 121
4 TraesCS3B01G255400 chr3D 92.185 2879 85 58 77 2888 309652390 309655195 0.000000e+00 3941
5 TraesCS3B01G255400 chr3D 94.059 101 5 1 2972 3071 309655218 309655318 6.590000e-33 152
6 TraesCS3B01G255400 chr3A 90.175 2860 97 73 77 2866 429320307 429323052 0.000000e+00 3555
7 TraesCS3B01G255400 chr3A 87.850 107 9 4 2878 2982 621519373 621519269 5.170000e-24 122
8 TraesCS3B01G255400 chr6B 93.886 736 43 2 3073 3807 595225515 595224781 0.000000e+00 1109
9 TraesCS3B01G255400 chr6B 89.899 99 9 1 2878 2975 123244549 123244647 3.990000e-25 126
10 TraesCS3B01G255400 chr6B 90.217 92 8 1 2885 2975 528204250 528204159 6.680000e-23 119
11 TraesCS3B01G255400 chr4D 93.878 735 43 2 3073 3807 454842338 454841606 0.000000e+00 1107
12 TraesCS3B01G255400 chr4B 93.767 738 45 1 3072 3809 592991147 592991883 0.000000e+00 1107
13 TraesCS3B01G255400 chr4B 90.217 92 8 1 2885 2975 12712768 12712677 6.680000e-23 119
14 TraesCS3B01G255400 chr6D 93.631 738 42 5 3070 3807 467532698 467533430 0.000000e+00 1098
15 TraesCS3B01G255400 chr2B 94.406 715 38 2 3093 3807 728223856 728224568 0.000000e+00 1098
16 TraesCS3B01G255400 chr2B 90.217 92 8 1 2885 2975 399022751 399022660 6.680000e-23 119
17 TraesCS3B01G255400 chr2B 86.408 103 12 2 2884 2985 661614869 661614970 1.120000e-20 111
18 TraesCS3B01G255400 chr1D 93.724 733 43 3 3076 3807 453959099 453958369 0.000000e+00 1096
19 TraesCS3B01G255400 chr1D 93.001 743 48 4 3065 3807 352188947 352188209 0.000000e+00 1081
20 TraesCS3B01G255400 chr1D 86.250 160 22 0 2265 2424 481603405 481603564 1.410000e-39 174
21 TraesCS3B01G255400 chr1B 85.714 161 21 2 2265 2424 670202879 670203038 6.540000e-38 169
22 TraesCS3B01G255400 chr5B 95.349 86 4 0 1 86 309025962 309026047 1.850000e-28 137
23 TraesCS3B01G255400 chr7A 93.976 83 5 0 1 83 188256527 188256445 3.990000e-25 126
24 TraesCS3B01G255400 chr7A 93.976 83 5 0 1 83 342805695 342805777 3.990000e-25 126
25 TraesCS3B01G255400 chr7B 92.941 85 6 0 1 85 328938170 328938254 1.440000e-24 124
26 TraesCS3B01G255400 chr7B 91.011 89 7 1 2885 2972 514167412 514167500 6.680000e-23 119
27 TraesCS3B01G255400 chr7B 88.000 100 9 3 2884 2982 131572569 131572472 8.650000e-22 115
28 TraesCS3B01G255400 chr2A 92.771 83 6 0 1 83 733493428 733493346 1.860000e-23 121
29 TraesCS3B01G255400 chr5D 90.000 80 8 0 6 85 456630992 456630913 1.870000e-18 104


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 TraesCS3B01G255400 chr3B 411843098 411846906 3808 True 7035.0 7035 100.000 1 3809 1 chr3B.!!$R1 3808
1 TraesCS3B01G255400 chr3B 354018105 354018835 730 False 1162.0 1162 95.362 3076 3807 1 chr3B.!!$F3 731
2 TraesCS3B01G255400 chr3B 129515290 129516024 734 False 1103.0 1103 93.758 3072 3807 1 chr3B.!!$F1 735
3 TraesCS3B01G255400 chr3D 309652390 309655318 2928 False 2046.5 3941 93.122 77 3071 2 chr3D.!!$F1 2994
4 TraesCS3B01G255400 chr3A 429320307 429323052 2745 False 3555.0 3555 90.175 77 2866 1 chr3A.!!$F1 2789
5 TraesCS3B01G255400 chr6B 595224781 595225515 734 True 1109.0 1109 93.886 3073 3807 1 chr6B.!!$R2 734
6 TraesCS3B01G255400 chr4D 454841606 454842338 732 True 1107.0 1107 93.878 3073 3807 1 chr4D.!!$R1 734
7 TraesCS3B01G255400 chr4B 592991147 592991883 736 False 1107.0 1107 93.767 3072 3809 1 chr4B.!!$F1 737
8 TraesCS3B01G255400 chr6D 467532698 467533430 732 False 1098.0 1098 93.631 3070 3807 1 chr6D.!!$F1 737
9 TraesCS3B01G255400 chr2B 728223856 728224568 712 False 1098.0 1098 94.406 3093 3807 1 chr2B.!!$F2 714
10 TraesCS3B01G255400 chr1D 453958369 453959099 730 True 1096.0 1096 93.724 3076 3807 1 chr1D.!!$R2 731
11 TraesCS3B01G255400 chr1D 352188209 352188947 738 True 1081.0 1081 93.001 3065 3807 1 chr1D.!!$R1 742

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
789 819 0.035056 CCCCGAACAATGGAGAGCTT 60.035 55.000 0.0 0.0 0.00 3.74 F
858 888 1.062581 TCTCTCTTATCCCCTGCTGCT 60.063 52.381 0.0 0.0 0.00 4.24 F
2297 2369 0.393537 AGTGTAGCAGCATGAAGGGC 60.394 55.000 0.0 0.0 39.69 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 1907 0.318441 GCTATCTGGCTATGCACGGA 59.682 55.000 0.0 0.0 0.00 4.69 R
2615 2702 0.394192 GATCCAGATCGCCATCCACA 59.606 55.000 0.0 0.0 0.00 4.17 R
3227 3321 1.153647 CCGCAGAAGCCGACACATA 60.154 57.895 0.0 0.0 37.52 2.29 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
25 26 7.225784 TCATGTGCTTTATAACCAAACATGT 57.774 32.000 19.24 0.00 42.41 3.21
26 27 7.665690 TCATGTGCTTTATAACCAAACATGTT 58.334 30.769 19.24 4.92 42.41 2.71
27 28 8.147058 TCATGTGCTTTATAACCAAACATGTTT 58.853 29.630 18.13 18.13 42.41 2.83
28 29 9.416794 CATGTGCTTTATAACCAAACATGTTTA 57.583 29.630 22.87 8.67 38.90 2.01
30 31 9.988815 TGTGCTTTATAACCAAACATGTTTATT 57.011 25.926 22.87 20.40 0.00 1.40
51 52 4.946478 TTTTTGAACGATTCCAACCCAT 57.054 36.364 0.00 0.00 0.00 4.00
52 53 4.946478 TTTTGAACGATTCCAACCCATT 57.054 36.364 0.00 0.00 0.00 3.16
53 54 4.513198 TTTGAACGATTCCAACCCATTC 57.487 40.909 0.00 0.00 0.00 2.67
54 55 3.147553 TGAACGATTCCAACCCATTCA 57.852 42.857 0.00 0.00 0.00 2.57
55 56 3.696045 TGAACGATTCCAACCCATTCAT 58.304 40.909 0.00 0.00 0.00 2.57
56 57 4.849518 TGAACGATTCCAACCCATTCATA 58.150 39.130 0.00 0.00 0.00 2.15
57 58 5.257262 TGAACGATTCCAACCCATTCATAA 58.743 37.500 0.00 0.00 0.00 1.90
58 59 5.124776 TGAACGATTCCAACCCATTCATAAC 59.875 40.000 0.00 0.00 0.00 1.89
59 60 3.951680 ACGATTCCAACCCATTCATAACC 59.048 43.478 0.00 0.00 0.00 2.85
60 61 3.951037 CGATTCCAACCCATTCATAACCA 59.049 43.478 0.00 0.00 0.00 3.67
61 62 4.202010 CGATTCCAACCCATTCATAACCAC 60.202 45.833 0.00 0.00 0.00 4.16
62 63 3.094484 TCCAACCCATTCATAACCACC 57.906 47.619 0.00 0.00 0.00 4.61
63 64 2.107366 CCAACCCATTCATAACCACCC 58.893 52.381 0.00 0.00 0.00 4.61
64 65 2.292192 CCAACCCATTCATAACCACCCT 60.292 50.000 0.00 0.00 0.00 4.34
65 66 3.440127 CAACCCATTCATAACCACCCTT 58.560 45.455 0.00 0.00 0.00 3.95
66 67 4.570933 CCAACCCATTCATAACCACCCTTA 60.571 45.833 0.00 0.00 0.00 2.69
67 68 5.208121 CAACCCATTCATAACCACCCTTAT 58.792 41.667 0.00 0.00 0.00 1.73
68 69 6.369629 CAACCCATTCATAACCACCCTTATA 58.630 40.000 0.00 0.00 0.00 0.98
69 70 6.599986 ACCCATTCATAACCACCCTTATAA 57.400 37.500 0.00 0.00 0.00 0.98
70 71 6.370453 ACCCATTCATAACCACCCTTATAAC 58.630 40.000 0.00 0.00 0.00 1.89
71 72 5.773176 CCCATTCATAACCACCCTTATAACC 59.227 44.000 0.00 0.00 0.00 2.85
72 73 6.369629 CCATTCATAACCACCCTTATAACCA 58.630 40.000 0.00 0.00 0.00 3.67
73 74 6.836527 CCATTCATAACCACCCTTATAACCAA 59.163 38.462 0.00 0.00 0.00 3.67
74 75 7.343316 CCATTCATAACCACCCTTATAACCAAA 59.657 37.037 0.00 0.00 0.00 3.28
75 76 7.706100 TTCATAACCACCCTTATAACCAAAC 57.294 36.000 0.00 0.00 0.00 2.93
80 81 2.162809 CACCCTTATAACCAAACGCACC 59.837 50.000 0.00 0.00 0.00 5.01
226 233 1.736032 CGCACTAGGCAAGACCAGTAC 60.736 57.143 0.00 0.00 45.17 2.73
227 234 1.550976 GCACTAGGCAAGACCAGTACT 59.449 52.381 0.00 0.00 43.14 2.73
228 235 2.417515 GCACTAGGCAAGACCAGTACTC 60.418 54.545 0.00 0.00 43.14 2.59
229 236 2.166664 CACTAGGCAAGACCAGTACTCC 59.833 54.545 0.00 0.00 43.14 3.85
230 237 2.043252 ACTAGGCAAGACCAGTACTCCT 59.957 50.000 0.00 0.00 43.14 3.69
231 238 2.921834 AGGCAAGACCAGTACTCCTA 57.078 50.000 0.00 0.00 43.14 2.94
232 239 2.741145 AGGCAAGACCAGTACTCCTAG 58.259 52.381 0.00 0.00 43.14 3.02
233 240 2.043252 AGGCAAGACCAGTACTCCTAGT 59.957 50.000 0.00 0.00 43.14 2.57
235 242 3.633065 GGCAAGACCAGTACTCCTAGTAG 59.367 52.174 0.00 0.00 38.86 2.57
236 243 3.633065 GCAAGACCAGTACTCCTAGTAGG 59.367 52.174 10.24 10.24 36.46 3.18
237 244 3.581265 AGACCAGTACTCCTAGTAGGC 57.419 52.381 11.75 0.00 34.61 3.93
238 245 2.851194 AGACCAGTACTCCTAGTAGGCA 59.149 50.000 11.75 0.01 34.61 4.75
254 265 0.723981 GGCAACTAGAAAGAGCAGCG 59.276 55.000 0.00 0.00 0.00 5.18
255 266 0.096108 GCAACTAGAAAGAGCAGCGC 59.904 55.000 0.00 0.00 0.00 5.92
256 267 0.368227 CAACTAGAAAGAGCAGCGCG 59.632 55.000 0.00 0.00 0.00 6.86
257 268 1.355066 AACTAGAAAGAGCAGCGCGC 61.355 55.000 26.66 26.66 42.91 6.86
355 367 1.308998 CTTGTCGTGGCCAAAAGACT 58.691 50.000 27.02 0.00 34.92 3.24
380 392 1.594293 CACTCCACCGTCGCTTTGT 60.594 57.895 0.00 0.00 0.00 2.83
639 669 1.384222 GGCCCCTTTAATGACGCCAG 61.384 60.000 0.00 0.00 36.38 4.85
669 699 4.081476 CCATCCAAAGATTCCACCCTTTTC 60.081 45.833 0.00 0.00 30.89 2.29
670 700 4.469469 TCCAAAGATTCCACCCTTTTCT 57.531 40.909 0.00 0.00 30.89 2.52
672 702 4.832823 TCCAAAGATTCCACCCTTTTCTTC 59.167 41.667 0.00 0.00 30.89 2.87
673 703 4.835056 CCAAAGATTCCACCCTTTTCTTCT 59.165 41.667 0.00 0.00 30.89 2.85
674 704 6.010219 CCAAAGATTCCACCCTTTTCTTCTA 58.990 40.000 0.00 0.00 30.89 2.10
675 705 6.151817 CCAAAGATTCCACCCTTTTCTTCTAG 59.848 42.308 0.00 0.00 30.89 2.43
768 798 2.819608 GCCCTTTTGACAAGTGCATAGA 59.180 45.455 0.00 0.00 0.00 1.98
769 799 3.119708 GCCCTTTTGACAAGTGCATAGAG 60.120 47.826 0.00 0.00 0.00 2.43
770 800 3.119708 CCCTTTTGACAAGTGCATAGAGC 60.120 47.826 0.00 0.00 45.96 4.09
771 801 3.119708 CCTTTTGACAAGTGCATAGAGCC 60.120 47.826 0.00 0.00 44.83 4.70
772 802 2.113860 TTGACAAGTGCATAGAGCCC 57.886 50.000 0.00 0.00 44.83 5.19
773 803 0.253044 TGACAAGTGCATAGAGCCCC 59.747 55.000 0.00 0.00 44.83 5.80
775 805 1.264749 ACAAGTGCATAGAGCCCCGA 61.265 55.000 0.00 0.00 44.83 5.14
776 806 0.107703 CAAGTGCATAGAGCCCCGAA 60.108 55.000 0.00 0.00 44.83 4.30
778 808 1.220749 GTGCATAGAGCCCCGAACA 59.779 57.895 0.00 0.00 44.83 3.18
779 809 0.392461 GTGCATAGAGCCCCGAACAA 60.392 55.000 0.00 0.00 44.83 2.83
780 810 0.546122 TGCATAGAGCCCCGAACAAT 59.454 50.000 0.00 0.00 44.83 2.71
781 811 0.947244 GCATAGAGCCCCGAACAATG 59.053 55.000 0.00 0.00 37.23 2.82
782 812 1.597742 CATAGAGCCCCGAACAATGG 58.402 55.000 0.00 0.00 0.00 3.16
783 813 1.140852 CATAGAGCCCCGAACAATGGA 59.859 52.381 0.00 0.00 0.00 3.41
784 814 0.830648 TAGAGCCCCGAACAATGGAG 59.169 55.000 0.00 0.00 0.00 3.86
785 815 0.909610 AGAGCCCCGAACAATGGAGA 60.910 55.000 0.00 0.00 0.00 3.71
786 816 0.462759 GAGCCCCGAACAATGGAGAG 60.463 60.000 0.00 0.00 0.00 3.20
787 817 2.115291 GCCCCGAACAATGGAGAGC 61.115 63.158 0.00 0.00 0.00 4.09
789 819 0.035056 CCCCGAACAATGGAGAGCTT 60.035 55.000 0.00 0.00 0.00 3.74
791 821 1.373570 CCGAACAATGGAGAGCTTCC 58.626 55.000 7.71 7.71 46.98 3.46
808 838 5.162637 AGCTTCCATATACAATGGGGAGTA 58.837 41.667 4.27 0.00 39.60 2.59
855 885 3.697190 TCTTCTCTCTTATCCCCTGCT 57.303 47.619 0.00 0.00 0.00 4.24
856 886 3.303938 TCTTCTCTCTTATCCCCTGCTG 58.696 50.000 0.00 0.00 0.00 4.41
857 887 1.418334 TCTCTCTTATCCCCTGCTGC 58.582 55.000 0.00 0.00 0.00 5.25
858 888 1.062581 TCTCTCTTATCCCCTGCTGCT 60.063 52.381 0.00 0.00 0.00 4.24
948 980 1.136984 CCACTCCAGTACGCGTCTC 59.863 63.158 18.63 11.00 0.00 3.36
1026 1061 1.482177 CCAAAAGTCAACCCCATCCCA 60.482 52.381 0.00 0.00 0.00 4.37
1050 1085 3.687102 CCACCACCACGCGTCCTA 61.687 66.667 9.86 0.00 0.00 2.94
1055 1090 1.432251 CACCACGCGTCCTACCTAG 59.568 63.158 9.86 0.00 0.00 3.02
1058 1093 1.355916 CACGCGTCCTACCTAGCTC 59.644 63.158 9.86 0.00 0.00 4.09
1195 1234 1.081092 CCACCTTCTCCTCCTCCCA 59.919 63.158 0.00 0.00 0.00 4.37
1204 1243 4.675303 CTCCTCCCACCACCCCCA 62.675 72.222 0.00 0.00 0.00 4.96
1205 1244 4.675303 TCCTCCCACCACCCCCAG 62.675 72.222 0.00 0.00 0.00 4.45
1207 1246 4.675303 CTCCCACCACCCCCAGGA 62.675 72.222 0.00 0.00 36.73 3.86
1208 1247 4.209620 TCCCACCACCCCCAGGAA 62.210 66.667 0.00 0.00 36.73 3.36
1209 1248 3.661648 CCCACCACCCCCAGGAAG 61.662 72.222 0.00 0.00 36.73 3.46
1514 1553 2.173669 CATACGAAGCAGCACCCCG 61.174 63.158 0.00 0.00 0.00 5.73
1536 1575 2.265683 GCCCGAAAAGAAGGTACGTAG 58.734 52.381 0.00 0.00 0.00 3.51
1641 1685 2.169352 TGATTTTGTTTGGTGGTGGTGG 59.831 45.455 0.00 0.00 0.00 4.61
1739 1783 3.665675 CTCCTCCGACCTTTGGGCG 62.666 68.421 4.65 4.65 35.63 6.13
1805 1852 5.071653 TCCCCGGTAATTAACTATAACCACC 59.928 44.000 0.00 0.00 0.00 4.61
1858 1907 1.600013 CTCGTCGATGCACTAGCTACT 59.400 52.381 0.00 0.00 42.74 2.57
1868 1917 3.275400 CACTAGCTACTCCGTGCATAG 57.725 52.381 0.00 0.00 0.00 2.23
1869 1918 1.609555 ACTAGCTACTCCGTGCATAGC 59.390 52.381 7.98 7.98 41.39 2.97
1870 1919 0.959553 TAGCTACTCCGTGCATAGCC 59.040 55.000 11.68 0.00 41.91 3.93
1871 1920 1.043116 AGCTACTCCGTGCATAGCCA 61.043 55.000 11.68 0.00 41.91 4.75
1872 1921 0.598680 GCTACTCCGTGCATAGCCAG 60.599 60.000 5.16 0.03 36.18 4.85
1873 1922 1.032794 CTACTCCGTGCATAGCCAGA 58.967 55.000 0.00 0.00 0.00 3.86
1874 1923 1.615883 CTACTCCGTGCATAGCCAGAT 59.384 52.381 0.00 0.00 0.00 2.90
1900 1949 0.889306 GAGTCCAGTCACTACCGCTT 59.111 55.000 0.00 0.00 0.00 4.68
1901 1950 2.089980 GAGTCCAGTCACTACCGCTTA 58.910 52.381 0.00 0.00 0.00 3.09
1902 1951 2.093106 AGTCCAGTCACTACCGCTTAG 58.907 52.381 0.00 0.00 0.00 2.18
1903 1952 1.817447 GTCCAGTCACTACCGCTTAGT 59.183 52.381 0.00 0.00 42.23 2.24
1904 1953 2.089980 TCCAGTCACTACCGCTTAGTC 58.910 52.381 0.00 0.00 39.18 2.59
1905 1954 1.134560 CCAGTCACTACCGCTTAGTCC 59.865 57.143 0.00 0.00 39.18 3.85
1906 1955 1.816835 CAGTCACTACCGCTTAGTCCA 59.183 52.381 0.00 0.00 39.18 4.02
1907 1956 2.093106 AGTCACTACCGCTTAGTCCAG 58.907 52.381 0.00 0.00 39.18 3.86
1908 1957 1.817447 GTCACTACCGCTTAGTCCAGT 59.183 52.381 0.00 0.00 39.18 4.00
1909 1958 2.089980 TCACTACCGCTTAGTCCAGTC 58.910 52.381 0.00 0.00 39.18 3.51
1910 1959 1.816835 CACTACCGCTTAGTCCAGTCA 59.183 52.381 0.00 0.00 39.18 3.41
1911 1960 1.817447 ACTACCGCTTAGTCCAGTCAC 59.183 52.381 0.00 0.00 36.09 3.67
1912 1961 2.093106 CTACCGCTTAGTCCAGTCACT 58.907 52.381 0.00 0.00 0.00 3.41
1913 1962 2.211250 ACCGCTTAGTCCAGTCACTA 57.789 50.000 0.00 0.00 0.00 2.74
1914 1963 1.817447 ACCGCTTAGTCCAGTCACTAC 59.183 52.381 0.00 0.00 0.00 2.73
1915 1964 1.202154 CCGCTTAGTCCAGTCACTACG 60.202 57.143 0.00 0.00 0.00 3.51
1916 1965 1.202154 CGCTTAGTCCAGTCACTACGG 60.202 57.143 0.00 0.00 0.00 4.02
1917 1966 1.469423 GCTTAGTCCAGTCACTACGGC 60.469 57.143 0.00 0.00 0.00 5.68
1918 1967 2.093106 CTTAGTCCAGTCACTACGGCT 58.907 52.381 0.00 0.00 0.00 5.52
1919 1968 2.211250 TAGTCCAGTCACTACGGCTT 57.789 50.000 0.00 0.00 0.00 4.35
1930 1979 4.878397 GTCACTACGGCTTAGTACCTTCTA 59.122 45.833 3.09 0.00 39.18 2.10
1961 2010 7.637229 AGATTCGCAATAACTGATTTCTCATG 58.363 34.615 0.00 0.00 0.00 3.07
1992 2041 6.976088 ACATTTACACGGATTTCATCAAACA 58.024 32.000 0.00 0.00 0.00 2.83
2070 2133 4.223923 ACCTGATGCTTAGAACTTGCTAGT 59.776 41.667 0.00 0.00 35.68 2.57
2072 2135 5.751028 CCTGATGCTTAGAACTTGCTAGTAC 59.249 44.000 0.00 0.00 33.17 2.73
2121 2184 2.477845 GGCATCAAGTTTTGGCCAAT 57.522 45.000 21.26 0.42 44.01 3.16
2132 2195 1.112315 TTGGCCAATCACACACCACC 61.112 55.000 16.05 0.00 0.00 4.61
2134 2197 1.244019 GGCCAATCACACACCACCTC 61.244 60.000 0.00 0.00 0.00 3.85
2297 2369 0.393537 AGTGTAGCAGCATGAAGGGC 60.394 55.000 0.00 0.00 39.69 5.19
2402 2474 2.809174 CCGACGCAGATCAACGCA 60.809 61.111 7.24 0.00 0.00 5.24
2438 2510 2.669569 CACAAGACCACCCCTGCG 60.670 66.667 0.00 0.00 0.00 5.18
2498 2585 4.803426 GAGGCGGTGAGGTGCGAG 62.803 72.222 0.00 0.00 0.00 5.03
2515 2602 1.732732 CGAGGACGAAAGCAACGAGAT 60.733 52.381 0.00 0.00 42.66 2.75
2538 2625 3.829044 CGATGGCGGTGGACGGTA 61.829 66.667 0.00 0.00 44.51 4.02
2549 2636 0.611062 TGGACGGTACCACTGAGGAG 60.611 60.000 13.54 0.00 41.22 3.69
2615 2702 2.665185 GACGAGTTGTTGGCGCCT 60.665 61.111 29.70 5.42 0.00 5.52
2651 2738 2.294791 GGATCATGTCTTCGACGAGGAT 59.705 50.000 13.12 3.87 34.95 3.24
2653 2740 1.405463 TCATGTCTTCGACGAGGATGG 59.595 52.381 13.12 6.12 34.95 3.51
2810 2901 3.428163 CCATATGCGTTTGATGTGTGTG 58.572 45.455 0.00 0.00 0.00 3.82
2822 2913 2.627863 TGTGTGTGTTTGTGCTTGAC 57.372 45.000 0.00 0.00 0.00 3.18
2866 2958 7.624549 TGAAGATTTCTTATGTAGCTCCAGTT 58.375 34.615 0.00 0.00 36.11 3.16
2880 2972 0.036765 CCAGTTAACGGCTGCCTACA 60.037 55.000 17.92 0.00 32.93 2.74
2883 2975 2.550606 CAGTTAACGGCTGCCTACAAAA 59.449 45.455 17.92 1.08 0.00 2.44
2888 2980 2.629051 ACGGCTGCCTACAAAATACTC 58.371 47.619 17.92 0.00 0.00 2.59
2889 2981 1.940613 CGGCTGCCTACAAAATACTCC 59.059 52.381 17.92 0.00 0.00 3.85
2890 2982 2.298610 GGCTGCCTACAAAATACTCCC 58.701 52.381 12.43 0.00 0.00 4.30
2891 2983 2.092375 GGCTGCCTACAAAATACTCCCT 60.092 50.000 12.43 0.00 0.00 4.20
2893 2985 3.118223 GCTGCCTACAAAATACTCCCTCT 60.118 47.826 0.00 0.00 0.00 3.69
2894 2986 4.446371 CTGCCTACAAAATACTCCCTCTG 58.554 47.826 0.00 0.00 0.00 3.35
2896 2988 4.081087 TGCCTACAAAATACTCCCTCTGTC 60.081 45.833 0.00 0.00 0.00 3.51
2897 2989 4.162509 GCCTACAAAATACTCCCTCTGTCT 59.837 45.833 0.00 0.00 0.00 3.41
2898 2990 5.682730 GCCTACAAAATACTCCCTCTGTCTC 60.683 48.000 0.00 0.00 0.00 3.36
2901 2993 7.287927 CCTACAAAATACTCCCTCTGTCTCATA 59.712 40.741 0.00 0.00 0.00 2.15
2902 2994 7.682787 ACAAAATACTCCCTCTGTCTCATAT 57.317 36.000 0.00 0.00 0.00 1.78
2904 2996 9.386122 ACAAAATACTCCCTCTGTCTCATATAT 57.614 33.333 0.00 0.00 0.00 0.86
2910 3002 8.588290 ACTCCCTCTGTCTCATATATATGAAC 57.412 38.462 22.62 21.11 41.72 3.18
2911 3003 7.338196 ACTCCCTCTGTCTCATATATATGAACG 59.662 40.741 22.62 14.06 41.72 3.95
2912 3004 7.175797 TCCCTCTGTCTCATATATATGAACGT 58.824 38.462 22.62 0.00 41.72 3.99
2913 3005 7.670140 TCCCTCTGTCTCATATATATGAACGTT 59.330 37.037 22.62 0.00 41.72 3.99
2914 3006 8.307483 CCCTCTGTCTCATATATATGAACGTTT 58.693 37.037 22.62 0.00 41.72 3.60
2915 3007 9.698309 CCTCTGTCTCATATATATGAACGTTTT 57.302 33.333 22.62 0.00 41.72 2.43
2920 3012 9.779237 GTCTCATATATATGAACGTTTTTGACG 57.221 33.333 22.62 9.46 45.75 4.35
2921 3013 9.524106 TCTCATATATATGAACGTTTTTGACGT 57.476 29.630 22.62 0.00 46.89 4.34
2933 3025 6.867931 CGTTTTTGACGTTAATGTAGTGTC 57.132 37.500 0.00 0.00 46.49 3.67
2934 3026 6.412460 CGTTTTTGACGTTAATGTAGTGTCA 58.588 36.000 0.00 0.00 46.49 3.58
2935 3027 6.900828 CGTTTTTGACGTTAATGTAGTGTCAA 59.099 34.615 0.00 2.26 46.49 3.18
2940 3032 7.304919 TGACGTTAATGTAGTGTCAAAAACA 57.695 32.000 0.00 0.00 36.69 2.83
2941 3033 7.921787 TGACGTTAATGTAGTGTCAAAAACAT 58.078 30.769 0.00 0.00 40.80 2.71
2942 3034 8.399425 TGACGTTAATGTAGTGTCAAAAACATT 58.601 29.630 0.00 11.36 43.17 2.71
2943 3035 8.776680 ACGTTAATGTAGTGTCAAAAACATTC 57.223 30.769 0.00 1.07 40.67 2.67
2944 3036 8.617809 ACGTTAATGTAGTGTCAAAAACATTCT 58.382 29.630 0.00 0.00 40.67 2.40
2945 3037 9.445786 CGTTAATGTAGTGTCAAAAACATTCTT 57.554 29.630 10.40 0.00 40.67 2.52
3022 3114 1.227823 CCACACCGAGCCAACAAGA 60.228 57.895 0.00 0.00 0.00 3.02
3040 3133 3.605664 GCTTGGCACCTGGCGTTT 61.606 61.111 0.00 0.00 46.16 3.60
3053 3146 0.521242 GGCGTTTGATGTGCGTGATC 60.521 55.000 0.00 0.00 0.00 2.92
3094 3187 2.230130 AGAGCAACTCTAGCAGACCT 57.770 50.000 0.00 0.00 39.28 3.85
3101 3194 1.317613 CTCTAGCAGACCTCGCATCT 58.682 55.000 0.00 0.00 0.00 2.90
3142 3235 0.240678 TGCAGTTCGCGCAAAATCAT 59.759 45.000 8.75 0.00 46.97 2.45
3313 3407 8.321353 ACTACAAATCTCACATTTGACATAGGA 58.679 33.333 12.82 0.00 40.42 2.94
3371 3466 1.707632 TTGCGCGCAAATAAAAGCAT 58.292 40.000 41.45 0.00 34.44 3.79
3519 3616 2.966309 GCTTGTTCCAACTCCCGCG 61.966 63.158 0.00 0.00 0.00 6.46
3564 3661 4.212847 CCATATGGAGCAGAGAAAACATCG 59.787 45.833 17.49 0.00 37.39 3.84
3658 3755 0.531090 TGTTTTGGTGAGGTCGTCCG 60.531 55.000 0.00 0.00 39.05 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.665690 ACATGTTTGGTTATAAAGCACATGAA 58.334 30.769 22.73 1.35 41.79 2.57
2 3 7.887996 AACATGTTTGGTTATAAAGCACATG 57.112 32.000 4.92 18.14 43.36 3.21
4 5 9.988815 AATAAACATGTTTGGTTATAAAGCACA 57.011 25.926 29.72 8.37 43.42 4.57
30 31 4.946478 ATGGGTTGGAATCGTTCAAAAA 57.054 36.364 1.25 0.00 0.00 1.94
31 32 4.342378 TGAATGGGTTGGAATCGTTCAAAA 59.658 37.500 0.00 0.00 34.64 2.44
32 33 3.891977 TGAATGGGTTGGAATCGTTCAAA 59.108 39.130 0.00 0.00 34.64 2.69
33 34 3.491342 TGAATGGGTTGGAATCGTTCAA 58.509 40.909 0.00 0.00 34.64 2.69
34 35 3.147553 TGAATGGGTTGGAATCGTTCA 57.852 42.857 0.00 0.00 35.03 3.18
35 36 5.449999 GGTTATGAATGGGTTGGAATCGTTC 60.450 44.000 0.00 0.00 0.00 3.95
36 37 4.401202 GGTTATGAATGGGTTGGAATCGTT 59.599 41.667 0.00 0.00 0.00 3.85
37 38 3.951680 GGTTATGAATGGGTTGGAATCGT 59.048 43.478 0.00 0.00 0.00 3.73
38 39 3.951037 TGGTTATGAATGGGTTGGAATCG 59.049 43.478 0.00 0.00 0.00 3.34
39 40 4.099419 GGTGGTTATGAATGGGTTGGAATC 59.901 45.833 0.00 0.00 0.00 2.52
40 41 4.030216 GGTGGTTATGAATGGGTTGGAAT 58.970 43.478 0.00 0.00 0.00 3.01
41 42 3.436243 GGTGGTTATGAATGGGTTGGAA 58.564 45.455 0.00 0.00 0.00 3.53
42 43 2.291930 GGGTGGTTATGAATGGGTTGGA 60.292 50.000 0.00 0.00 0.00 3.53
43 44 2.107366 GGGTGGTTATGAATGGGTTGG 58.893 52.381 0.00 0.00 0.00 3.77
44 45 3.100207 AGGGTGGTTATGAATGGGTTG 57.900 47.619 0.00 0.00 0.00 3.77
45 46 3.845109 AAGGGTGGTTATGAATGGGTT 57.155 42.857 0.00 0.00 0.00 4.11
46 47 6.370453 GTTATAAGGGTGGTTATGAATGGGT 58.630 40.000 0.00 0.00 0.00 4.51
47 48 5.773176 GGTTATAAGGGTGGTTATGAATGGG 59.227 44.000 0.00 0.00 0.00 4.00
48 49 6.369629 TGGTTATAAGGGTGGTTATGAATGG 58.630 40.000 0.00 0.00 0.00 3.16
49 50 7.889873 TTGGTTATAAGGGTGGTTATGAATG 57.110 36.000 0.00 0.00 0.00 2.67
50 51 7.067737 CGTTTGGTTATAAGGGTGGTTATGAAT 59.932 37.037 0.00 0.00 0.00 2.57
51 52 6.374894 CGTTTGGTTATAAGGGTGGTTATGAA 59.625 38.462 0.00 0.00 0.00 2.57
52 53 5.881443 CGTTTGGTTATAAGGGTGGTTATGA 59.119 40.000 0.00 0.00 0.00 2.15
53 54 5.449451 GCGTTTGGTTATAAGGGTGGTTATG 60.449 44.000 0.00 0.00 0.00 1.90
54 55 4.641541 GCGTTTGGTTATAAGGGTGGTTAT 59.358 41.667 0.00 0.00 0.00 1.89
55 56 4.009002 GCGTTTGGTTATAAGGGTGGTTA 58.991 43.478 0.00 0.00 0.00 2.85
56 57 2.821378 GCGTTTGGTTATAAGGGTGGTT 59.179 45.455 0.00 0.00 0.00 3.67
57 58 2.224818 TGCGTTTGGTTATAAGGGTGGT 60.225 45.455 0.00 0.00 0.00 4.16
58 59 2.162809 GTGCGTTTGGTTATAAGGGTGG 59.837 50.000 0.00 0.00 0.00 4.61
59 60 2.162809 GGTGCGTTTGGTTATAAGGGTG 59.837 50.000 0.00 0.00 0.00 4.61
60 61 2.439409 GGTGCGTTTGGTTATAAGGGT 58.561 47.619 0.00 0.00 0.00 4.34
61 62 1.746787 GGGTGCGTTTGGTTATAAGGG 59.253 52.381 0.00 0.00 0.00 3.95
62 63 2.718563 AGGGTGCGTTTGGTTATAAGG 58.281 47.619 0.00 0.00 0.00 2.69
63 64 4.939439 ACTAAGGGTGCGTTTGGTTATAAG 59.061 41.667 0.00 0.00 0.00 1.73
64 65 4.909001 ACTAAGGGTGCGTTTGGTTATAA 58.091 39.130 0.00 0.00 0.00 0.98
65 66 4.556592 ACTAAGGGTGCGTTTGGTTATA 57.443 40.909 0.00 0.00 0.00 0.98
66 67 3.428413 ACTAAGGGTGCGTTTGGTTAT 57.572 42.857 0.00 0.00 0.00 1.89
67 68 2.934886 ACTAAGGGTGCGTTTGGTTA 57.065 45.000 0.00 0.00 0.00 2.85
68 69 2.061509 AACTAAGGGTGCGTTTGGTT 57.938 45.000 0.00 0.00 0.00 3.67
69 70 2.934886 TAACTAAGGGTGCGTTTGGT 57.065 45.000 0.00 0.00 0.00 3.67
70 71 2.681344 GGATAACTAAGGGTGCGTTTGG 59.319 50.000 0.00 0.00 0.00 3.28
71 72 3.340034 TGGATAACTAAGGGTGCGTTTG 58.660 45.455 0.00 0.00 0.00 2.93
72 73 3.706600 TGGATAACTAAGGGTGCGTTT 57.293 42.857 0.00 0.00 0.00 3.60
73 74 3.926058 ATGGATAACTAAGGGTGCGTT 57.074 42.857 0.00 0.00 0.00 4.84
74 75 4.838986 AGATATGGATAACTAAGGGTGCGT 59.161 41.667 0.00 0.00 0.00 5.24
75 76 5.407407 AGATATGGATAACTAAGGGTGCG 57.593 43.478 0.00 0.00 0.00 5.34
80 81 9.799106 ACAATTGGAAGATATGGATAACTAAGG 57.201 33.333 10.83 0.00 0.00 2.69
216 223 3.268856 TGCCTACTAGGAGTACTGGTCTT 59.731 47.826 0.00 0.00 40.42 3.01
230 237 4.142138 GCTGCTCTTTCTAGTTGCCTACTA 60.142 45.833 0.00 0.00 38.33 1.82
231 238 3.368948 GCTGCTCTTTCTAGTTGCCTACT 60.369 47.826 0.00 0.00 41.04 2.57
232 239 2.933260 GCTGCTCTTTCTAGTTGCCTAC 59.067 50.000 0.00 0.00 0.00 3.18
233 240 2.417379 CGCTGCTCTTTCTAGTTGCCTA 60.417 50.000 0.00 0.00 0.00 3.93
235 242 0.723981 CGCTGCTCTTTCTAGTTGCC 59.276 55.000 0.00 0.00 0.00 4.52
236 243 0.096108 GCGCTGCTCTTTCTAGTTGC 59.904 55.000 0.00 0.00 0.00 4.17
237 244 0.368227 CGCGCTGCTCTTTCTAGTTG 59.632 55.000 5.56 0.00 0.00 3.16
238 245 1.355066 GCGCGCTGCTCTTTCTAGTT 61.355 55.000 26.67 0.00 41.73 2.24
355 367 1.304217 GACGGTGGAGTGGAGGAGA 60.304 63.158 0.00 0.00 0.00 3.71
380 392 4.215742 CGGCGCGGGGATAAGTGA 62.216 66.667 8.83 0.00 0.00 3.41
537 561 1.755179 ATTATTGGCTGCGCTTGACT 58.245 45.000 9.73 0.00 0.00 3.41
639 669 4.637977 GTGGAATCTTTGGATGGAACTCTC 59.362 45.833 0.00 0.00 31.75 3.20
669 699 3.295973 AGAGGGCAAGCTAGACTAGAAG 58.704 50.000 13.91 3.15 0.00 2.85
670 700 3.053245 AGAGAGGGCAAGCTAGACTAGAA 60.053 47.826 13.91 0.00 0.00 2.10
672 702 2.884639 GAGAGAGGGCAAGCTAGACTAG 59.115 54.545 5.03 5.03 0.00 2.57
673 703 2.423660 GGAGAGAGGGCAAGCTAGACTA 60.424 54.545 0.00 0.00 0.00 2.59
674 704 1.687996 GGAGAGAGGGCAAGCTAGACT 60.688 57.143 0.00 0.00 0.00 3.24
675 705 0.750249 GGAGAGAGGGCAAGCTAGAC 59.250 60.000 0.00 0.00 0.00 2.59
768 798 1.604378 CTCTCCATTGTTCGGGGCT 59.396 57.895 0.00 0.00 0.00 5.19
769 799 2.115291 GCTCTCCATTGTTCGGGGC 61.115 63.158 0.00 0.00 0.00 5.80
770 800 0.035056 AAGCTCTCCATTGTTCGGGG 60.035 55.000 0.00 0.00 0.00 5.73
771 801 1.373570 GAAGCTCTCCATTGTTCGGG 58.626 55.000 0.00 0.00 0.00 5.14
772 802 1.373570 GGAAGCTCTCCATTGTTCGG 58.626 55.000 9.31 0.00 44.67 4.30
781 811 4.566488 CCCCATTGTATATGGAAGCTCTCC 60.566 50.000 5.38 7.71 45.64 3.71
782 812 4.287067 TCCCCATTGTATATGGAAGCTCTC 59.713 45.833 5.38 0.00 41.64 3.20
783 813 4.242811 TCCCCATTGTATATGGAAGCTCT 58.757 43.478 5.38 0.00 41.64 4.09
784 814 4.042187 ACTCCCCATTGTATATGGAAGCTC 59.958 45.833 5.38 0.00 41.64 4.09
785 815 3.983410 ACTCCCCATTGTATATGGAAGCT 59.017 43.478 5.38 0.00 41.64 3.74
786 816 4.373156 ACTCCCCATTGTATATGGAAGC 57.627 45.455 5.38 0.00 41.64 3.86
787 817 5.249393 AGCTACTCCCCATTGTATATGGAAG 59.751 44.000 5.38 5.31 41.64 3.46
789 819 4.532126 CAGCTACTCCCCATTGTATATGGA 59.468 45.833 5.38 0.00 41.64 3.41
791 821 5.745312 TCAGCTACTCCCCATTGTATATG 57.255 43.478 0.00 0.00 0.00 1.78
792 822 6.025539 TGATCAGCTACTCCCCATTGTATAT 58.974 40.000 0.00 0.00 0.00 0.86
793 823 5.402630 TGATCAGCTACTCCCCATTGTATA 58.597 41.667 0.00 0.00 0.00 1.47
802 832 5.240403 GGATTTGAAATGATCAGCTACTCCC 59.760 44.000 0.09 0.00 39.77 4.30
808 838 3.629398 GTCCGGATTTGAAATGATCAGCT 59.371 43.478 7.81 0.00 39.77 4.24
1003 1038 1.273327 GATGGGGTTGACTTTTGGCAG 59.727 52.381 0.00 0.00 39.52 4.85
1049 1084 2.017782 CGAAGTGAGCTGAGCTAGGTA 58.982 52.381 7.08 0.00 39.88 3.08
1050 1085 0.814457 CGAAGTGAGCTGAGCTAGGT 59.186 55.000 7.08 0.00 39.88 3.08
1195 1234 2.204151 CCTCTTCCTGGGGGTGGT 60.204 66.667 0.00 0.00 0.00 4.16
1256 1295 3.834373 CGCTTTACCGGCGTGTCG 61.834 66.667 6.01 0.00 46.37 4.35
1514 1553 1.792301 GTACCTTCTTTTCGGGCGC 59.208 57.895 0.00 0.00 0.00 6.53
1536 1575 7.193595 GGTGCACAAATCAACTTGGTATATAC 58.806 38.462 20.43 4.14 0.00 1.47
1539 1578 4.461081 GGGTGCACAAATCAACTTGGTATA 59.539 41.667 20.43 0.00 0.00 1.47
1540 1579 3.258123 GGGTGCACAAATCAACTTGGTAT 59.742 43.478 20.43 0.00 0.00 2.73
1641 1685 0.606401 CTCACCATCACCACCACCAC 60.606 60.000 0.00 0.00 0.00 4.16
1739 1783 1.500512 TTTGACCGTACTTGCGCCAC 61.501 55.000 4.18 0.00 0.00 5.01
1858 1907 0.318441 GCTATCTGGCTATGCACGGA 59.682 55.000 0.00 0.00 0.00 4.69
1868 1917 0.833287 TGGACTCAAGGCTATCTGGC 59.167 55.000 0.00 0.00 42.15 4.85
1869 1918 2.102252 GACTGGACTCAAGGCTATCTGG 59.898 54.545 0.00 0.00 0.00 3.86
1870 1919 2.762887 TGACTGGACTCAAGGCTATCTG 59.237 50.000 0.00 0.00 0.00 2.90
1871 1920 2.763448 GTGACTGGACTCAAGGCTATCT 59.237 50.000 0.00 0.00 0.00 1.98
1872 1921 2.763448 AGTGACTGGACTCAAGGCTATC 59.237 50.000 0.00 0.00 0.00 2.08
1873 1922 2.826488 AGTGACTGGACTCAAGGCTAT 58.174 47.619 0.00 0.00 0.00 2.97
1874 1923 2.310779 AGTGACTGGACTCAAGGCTA 57.689 50.000 0.00 0.00 0.00 3.93
1900 1949 2.211250 AAGCCGTAGTGACTGGACTA 57.789 50.000 0.00 0.00 0.00 2.59
1901 1950 2.093106 CTAAGCCGTAGTGACTGGACT 58.907 52.381 0.00 0.00 0.00 3.85
1902 1951 1.817447 ACTAAGCCGTAGTGACTGGAC 59.183 52.381 0.00 0.00 41.75 4.02
1903 1952 2.211250 ACTAAGCCGTAGTGACTGGA 57.789 50.000 0.00 0.00 41.75 3.86
1904 1953 2.098770 GGTACTAAGCCGTAGTGACTGG 59.901 54.545 7.73 0.00 43.24 4.00
1905 1954 3.015327 AGGTACTAAGCCGTAGTGACTG 58.985 50.000 7.73 0.00 43.24 3.51
1906 1955 3.362870 AGGTACTAAGCCGTAGTGACT 57.637 47.619 7.73 0.00 43.24 3.41
1907 1956 3.693578 AGAAGGTACTAAGCCGTAGTGAC 59.306 47.826 7.73 1.80 43.24 3.67
1908 1957 3.960571 AGAAGGTACTAAGCCGTAGTGA 58.039 45.455 7.73 0.00 43.24 3.41
1909 1958 6.388435 AATAGAAGGTACTAAGCCGTAGTG 57.612 41.667 7.73 0.00 43.24 2.74
1910 1959 8.703378 ATTAATAGAAGGTACTAAGCCGTAGT 57.297 34.615 3.39 3.39 45.42 2.73
1913 1962 8.930846 TCTATTAATAGAAGGTACTAAGCCGT 57.069 34.615 20.53 0.00 38.49 5.68
1961 2010 3.944422 ATCCGTGTAAATGTTCATCGC 57.056 42.857 0.00 0.00 0.00 4.58
2052 2115 7.883391 TCTAGTACTAGCAAGTTCTAAGCAT 57.117 36.000 22.87 0.00 35.81 3.79
2070 2133 2.466846 GTGCGCGGCTAAAATCTAGTA 58.533 47.619 8.83 0.00 0.00 1.82
2072 2135 0.582005 GGTGCGCGGCTAAAATCTAG 59.418 55.000 8.83 0.00 0.00 2.43
2121 2184 3.804036 CAAAAGTAGAGGTGGTGTGTGA 58.196 45.455 0.00 0.00 0.00 3.58
2132 2195 4.608445 GCGTGTTGTACTGCAAAAGTAGAG 60.608 45.833 0.00 0.00 42.15 2.43
2134 2197 3.001838 TGCGTGTTGTACTGCAAAAGTAG 59.998 43.478 0.00 0.00 42.15 2.57
2216 2280 2.036475 AGTATGCAGACCAGGATTAGCG 59.964 50.000 8.08 0.00 0.00 4.26
2218 2282 3.900601 AGGAGTATGCAGACCAGGATTAG 59.099 47.826 8.08 0.00 0.00 1.73
2219 2283 3.928754 AGGAGTATGCAGACCAGGATTA 58.071 45.455 8.08 0.00 0.00 1.75
2220 2284 2.769209 AGGAGTATGCAGACCAGGATT 58.231 47.619 8.08 0.00 0.00 3.01
2221 2285 2.485966 AGGAGTATGCAGACCAGGAT 57.514 50.000 8.08 0.00 0.00 3.24
2297 2369 2.361610 AGTTTCCGGGCCATGCAG 60.362 61.111 4.39 0.00 0.00 4.41
2451 2523 3.284449 GTGGCTTTTGGGCGTCGT 61.284 61.111 0.00 0.00 44.11 4.34
2498 2585 1.390463 GACATCTCGTTGCTTTCGTCC 59.610 52.381 0.00 0.00 0.00 4.79
2515 2602 4.429212 CCACCGCCATCGACGACA 62.429 66.667 0.00 0.00 38.10 4.35
2522 2609 2.202837 GTACCGTCCACCGCCATC 60.203 66.667 0.00 0.00 34.38 3.51
2582 2669 2.203788 TCCAGGTCCAGCTCCGTT 60.204 61.111 0.00 0.00 0.00 4.44
2615 2702 0.394192 GATCCAGATCGCCATCCACA 59.606 55.000 0.00 0.00 0.00 4.17
2714 2801 1.604604 AAGTTGTCAATCGGTGGTGG 58.395 50.000 0.00 0.00 0.00 4.61
2810 2901 1.239347 GAGAGGGGTCAAGCACAAAC 58.761 55.000 0.00 0.00 0.00 2.93
2822 2913 5.477984 TCTTCATCAATTTTGTTGAGAGGGG 59.522 40.000 4.71 0.00 37.94 4.79
2866 2958 4.186159 GAGTATTTTGTAGGCAGCCGTTA 58.814 43.478 5.55 0.00 0.00 3.18
2888 2980 7.397892 ACGTTCATATATATGAGACAGAGGG 57.602 40.000 21.60 13.05 42.99 4.30
2889 2981 9.698309 AAAACGTTCATATATATGAGACAGAGG 57.302 33.333 21.60 15.45 42.99 3.69
2894 2986 9.779237 CGTCAAAAACGTTCATATATATGAGAC 57.221 33.333 21.60 19.80 46.42 3.36
2915 3007 7.749808 TGTTTTTGACACTACATTAACGTCAA 58.250 30.769 0.00 0.00 42.98 3.18
2916 3008 7.304919 TGTTTTTGACACTACATTAACGTCA 57.695 32.000 0.00 0.00 34.92 4.35
2917 3009 8.776680 AATGTTTTTGACACTACATTAACGTC 57.223 30.769 0.00 0.00 42.04 4.34
2918 3010 8.617809 AGAATGTTTTTGACACTACATTAACGT 58.382 29.630 0.00 0.00 42.04 3.99
2919 3011 9.445786 AAGAATGTTTTTGACACTACATTAACG 57.554 29.630 0.00 0.00 42.04 3.18
2936 3028 9.799106 CCTCTGTCCCATAATATAAGAATGTTT 57.201 33.333 0.00 0.00 0.00 2.83
2937 3029 9.170890 TCCTCTGTCCCATAATATAAGAATGTT 57.829 33.333 0.00 0.00 0.00 2.71
2938 3030 8.742125 TCCTCTGTCCCATAATATAAGAATGT 57.258 34.615 0.00 0.00 0.00 2.71
2939 3031 9.664332 CTTCCTCTGTCCCATAATATAAGAATG 57.336 37.037 0.00 0.00 0.00 2.67
2940 3032 9.398921 ACTTCCTCTGTCCCATAATATAAGAAT 57.601 33.333 0.00 0.00 0.00 2.40
2941 3033 8.798975 ACTTCCTCTGTCCCATAATATAAGAA 57.201 34.615 0.00 0.00 0.00 2.52
2942 3034 9.535170 CTACTTCCTCTGTCCCATAATATAAGA 57.465 37.037 0.00 0.00 0.00 2.10
2943 3035 9.315363 ACTACTTCCTCTGTCCCATAATATAAG 57.685 37.037 0.00 0.00 0.00 1.73
2949 3041 9.750783 GTATATACTACTTCCTCTGTCCCATAA 57.249 37.037 5.58 0.00 0.00 1.90
2950 3042 8.897692 TGTATATACTACTTCCTCTGTCCCATA 58.102 37.037 13.89 0.00 0.00 2.74
2951 3043 7.766628 TGTATATACTACTTCCTCTGTCCCAT 58.233 38.462 13.89 0.00 0.00 4.00
2952 3044 7.157947 TGTATATACTACTTCCTCTGTCCCA 57.842 40.000 13.89 0.00 0.00 4.37
2953 3045 7.670559 ACATGTATATACTACTTCCTCTGTCCC 59.329 40.741 13.89 0.00 0.00 4.46
2954 3046 8.638629 ACATGTATATACTACTTCCTCTGTCC 57.361 38.462 13.89 0.00 0.00 4.02
2984 3076 3.068024 TGGTCAAGGCTTTGATGAACAAC 59.932 43.478 14.90 0.25 44.62 3.32
2986 3078 2.622942 GTGGTCAAGGCTTTGATGAACA 59.377 45.455 14.90 8.93 44.62 3.18
3022 3114 4.586235 AACGCCAGGTGCCAAGCT 62.586 61.111 0.00 0.00 36.24 3.74
3040 3133 0.461548 GAGAGGGATCACGCACATCA 59.538 55.000 0.26 0.00 0.00 3.07
3197 3291 7.061752 AGCATATTCCGCGAATATACTTTTC 57.938 36.000 8.23 2.52 41.52 2.29
3227 3321 1.153647 CCGCAGAAGCCGACACATA 60.154 57.895 0.00 0.00 37.52 2.29
3313 3407 6.998968 TGAATTTGAACTTGTTTGCCAAAT 57.001 29.167 0.00 0.00 38.59 2.32
3371 3466 3.687698 GCCCTCTTTTGCGTAATGAACTA 59.312 43.478 0.00 0.00 0.00 2.24
3519 3616 1.536709 GGCAATGTGGATGATTTCGGC 60.537 52.381 0.00 0.00 0.00 5.54
3564 3661 3.047877 CCGTGTTCCAGTTCCGGC 61.048 66.667 0.00 0.00 0.00 6.13
3658 3755 2.987413 TCAATGAACCGCAATGACAC 57.013 45.000 0.00 0.00 31.61 3.67


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

AutoCloner maintained by Alex Coulton.