Multiple sequence alignment - TraesCS3A01G052600

Loading Multiple Alignment...

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 TraesCS3A01G052600 chr3A 100.000 2471 0 0 1 2471 28392308 28389838 0.000000e+00 4564.0
1 TraesCS3A01G052600 chr3A 85.697 839 77 17 1313 2117 28371217 28370388 0.000000e+00 845.0
2 TraesCS3A01G052600 chr3A 80.494 1215 138 44 746 1890 28231648 28230463 0.000000e+00 839.0
3 TraesCS3A01G052600 chr3A 80.293 751 81 35 750 1462 28323020 28322299 2.840000e-139 505.0
4 TraesCS3A01G052600 chr3A 83.036 224 30 7 1569 1786 28056777 28056556 1.940000e-46 196.0
5 TraesCS3A01G052600 chr3A 83.832 167 20 6 1295 1461 28423677 28423518 4.260000e-33 152.0
6 TraesCS3A01G052600 chr3A 90.000 80 5 1 991 1070 28206767 28206691 1.560000e-17 100.0
7 TraesCS3A01G052600 chr3B 87.831 1890 140 28 648 2467 33299447 33297578 0.000000e+00 2134.0
8 TraesCS3A01G052600 chr3B 87.255 714 70 17 1715 2417 816842709 816843412 0.000000e+00 795.0
9 TraesCS3A01G052600 chr3B 83.462 647 66 21 851 1471 32992152 32991521 4.610000e-157 564.0
10 TraesCS3A01G052600 chr3B 89.461 427 31 5 204 618 33299868 33299444 6.050000e-146 527.0
11 TraesCS3A01G052600 chr3B 77.790 923 139 32 992 1890 33096992 33096112 2.190000e-140 508.0
12 TraesCS3A01G052600 chr3B 80.416 577 73 22 889 1462 33334260 33333721 1.060000e-108 403.0
13 TraesCS3A01G052600 chr3B 79.273 275 30 13 1459 1730 32732898 32732648 1.520000e-37 167.0
14 TraesCS3A01G052600 chr3B 83.333 192 16 10 746 928 33097192 33097008 1.970000e-36 163.0
15 TraesCS3A01G052600 chr3B 73.480 592 92 37 332 897 33336025 33335473 1.970000e-36 163.0
16 TraesCS3A01G052600 chr3B 85.065 154 22 1 28 180 228692417 228692570 3.290000e-34 156.0
17 TraesCS3A01G052600 chr3B 84.071 113 13 3 1325 1436 32712538 32712430 1.210000e-18 104.0
18 TraesCS3A01G052600 chr3B 91.549 71 3 1 1000 1070 32942599 32942532 7.270000e-16 95.3
19 TraesCS3A01G052600 chr3B 81.553 103 19 0 1000 1102 32801696 32801594 4.380000e-13 86.1
20 TraesCS3A01G052600 chr3B 91.837 49 2 2 1566 1614 33261971 33261925 1.590000e-07 67.6
21 TraesCS3A01G052600 chr4A 87.308 780 80 17 1667 2436 723214956 723214186 0.000000e+00 874.0
22 TraesCS3A01G052600 chr4A 83.369 463 54 16 1966 2417 549789976 549790426 8.230000e-110 407.0
23 TraesCS3A01G052600 chr4A 83.153 463 54 17 1966 2417 53710171 53710620 3.830000e-108 401.0
24 TraesCS3A01G052600 chr4A 82.505 463 58 16 1966 2417 598281512 598281962 3.850000e-103 385.0
25 TraesCS3A01G052600 chr7B 87.080 774 81 16 1667 2431 665490128 665490891 0.000000e+00 857.0
26 TraesCS3A01G052600 chr7B 87.360 712 71 14 1716 2417 728924603 728925305 0.000000e+00 798.0
27 TraesCS3A01G052600 chr5B 86.753 770 86 13 1667 2427 169510018 169510780 0.000000e+00 843.0
28 TraesCS3A01G052600 chr5B 87.079 712 75 14 1715 2417 392923957 392923254 0.000000e+00 789.0
29 TraesCS3A01G052600 chr6B 86.247 778 82 19 1672 2436 666654692 666653927 0.000000e+00 821.0
30 TraesCS3A01G052600 chr3D 85.661 809 70 22 1455 2254 20732651 20731880 0.000000e+00 809.0
31 TraesCS3A01G052600 chr3D 79.113 924 113 35 973 1855 20708406 20707522 4.610000e-157 564.0
32 TraesCS3A01G052600 chr3D 85.024 207 10 4 746 941 20708600 20708404 9.020000e-45 191.0
33 TraesCS3A01G052600 chr3D 81.053 190 20 13 1291 1467 20142037 20141851 1.190000e-28 137.0
34 TraesCS3A01G052600 chr3D 84.466 103 16 0 1000 1102 20232904 20232802 4.350000e-18 102.0
35 TraesCS3A01G052600 chr3D 90.141 71 4 1 1000 1070 20555540 20555473 3.380000e-14 89.8
36 TraesCS3A01G052600 chr3D 78.462 130 22 5 1724 1849 20750614 20750487 2.040000e-11 80.5
37 TraesCS3A01G052600 chr6A 92.289 415 30 2 1667 2081 36994 36582 2.740000e-164 588.0
38 TraesCS3A01G052600 chr1A 83.585 463 53 16 1966 2417 38158751 38158301 1.770000e-111 412.0
39 TraesCS3A01G052600 chr2A 83.369 463 54 16 1966 2417 639443857 639444307 8.230000e-110 407.0
40 TraesCS3A01G052600 chr5A 82.900 462 55 17 1966 2417 348824748 348824301 6.410000e-106 394.0
41 TraesCS3A01G052600 chr4B 81.218 197 34 3 2 196 582108675 582108870 3.290000e-34 156.0
42 TraesCS3A01G052600 chr2B 81.461 178 31 2 17 192 18315291 18315114 7.120000e-31 145.0
43 TraesCS3A01G052600 chr1B 80.723 83 16 0 109 191 56308727 56308645 5.700000e-07 65.8


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 TraesCS3A01G052600 chr3A 28389838 28392308 2470 True 4564.0 4564 100.0000 1 2471 1 chr3A.!!$R6 2470
1 TraesCS3A01G052600 chr3A 28370388 28371217 829 True 845.0 845 85.6970 1313 2117 1 chr3A.!!$R5 804
2 TraesCS3A01G052600 chr3A 28230463 28231648 1185 True 839.0 839 80.4940 746 1890 1 chr3A.!!$R3 1144
3 TraesCS3A01G052600 chr3A 28322299 28323020 721 True 505.0 505 80.2930 750 1462 1 chr3A.!!$R4 712
4 TraesCS3A01G052600 chr3B 33297578 33299868 2290 True 1330.5 2134 88.6460 204 2467 2 chr3B.!!$R8 2263
5 TraesCS3A01G052600 chr3B 816842709 816843412 703 False 795.0 795 87.2550 1715 2417 1 chr3B.!!$F2 702
6 TraesCS3A01G052600 chr3B 32991521 32992152 631 True 564.0 564 83.4620 851 1471 1 chr3B.!!$R5 620
7 TraesCS3A01G052600 chr3B 33096112 33097192 1080 True 335.5 508 80.5615 746 1890 2 chr3B.!!$R7 1144
8 TraesCS3A01G052600 chr3B 33333721 33336025 2304 True 283.0 403 76.9480 332 1462 2 chr3B.!!$R9 1130
9 TraesCS3A01G052600 chr4A 723214186 723214956 770 True 874.0 874 87.3080 1667 2436 1 chr4A.!!$R1 769
10 TraesCS3A01G052600 chr7B 665490128 665490891 763 False 857.0 857 87.0800 1667 2431 1 chr7B.!!$F1 764
11 TraesCS3A01G052600 chr7B 728924603 728925305 702 False 798.0 798 87.3600 1716 2417 1 chr7B.!!$F2 701
12 TraesCS3A01G052600 chr5B 169510018 169510780 762 False 843.0 843 86.7530 1667 2427 1 chr5B.!!$F1 760
13 TraesCS3A01G052600 chr5B 392923254 392923957 703 True 789.0 789 87.0790 1715 2417 1 chr5B.!!$R1 702
14 TraesCS3A01G052600 chr6B 666653927 666654692 765 True 821.0 821 86.2470 1672 2436 1 chr6B.!!$R1 764
15 TraesCS3A01G052600 chr3D 20731880 20732651 771 True 809.0 809 85.6610 1455 2254 1 chr3D.!!$R4 799
16 TraesCS3A01G052600 chr3D 20707522 20708600 1078 True 377.5 564 82.0685 746 1855 2 chr3D.!!$R6 1109

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
91 92 0.032403 CACCACAACACCAGGCAATG 59.968 55.0 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 3043 0.03563 CCCTGGTTCTTGGCTCTCAG 60.036 60.0 0.0 0.0 0.0 3.35 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
18 19 3.233355 ACGCCATCTTCTGTTGTCC 57.767 52.632 0.00 0.00 0.00 4.02
19 20 0.321653 ACGCCATCTTCTGTTGTCCC 60.322 55.000 0.00 0.00 0.00 4.46
20 21 0.321564 CGCCATCTTCTGTTGTCCCA 60.322 55.000 0.00 0.00 0.00 4.37
21 22 1.679944 CGCCATCTTCTGTTGTCCCAT 60.680 52.381 0.00 0.00 0.00 4.00
22 23 2.450476 GCCATCTTCTGTTGTCCCATT 58.550 47.619 0.00 0.00 0.00 3.16
23 24 2.827921 GCCATCTTCTGTTGTCCCATTT 59.172 45.455 0.00 0.00 0.00 2.32
24 25 3.259123 GCCATCTTCTGTTGTCCCATTTT 59.741 43.478 0.00 0.00 0.00 1.82
25 26 4.813027 CCATCTTCTGTTGTCCCATTTTG 58.187 43.478 0.00 0.00 0.00 2.44
26 27 4.281688 CCATCTTCTGTTGTCCCATTTTGT 59.718 41.667 0.00 0.00 0.00 2.83
27 28 5.476599 CCATCTTCTGTTGTCCCATTTTGTA 59.523 40.000 0.00 0.00 0.00 2.41
28 29 6.015519 CCATCTTCTGTTGTCCCATTTTGTAA 60.016 38.462 0.00 0.00 0.00 2.41
29 30 6.633500 TCTTCTGTTGTCCCATTTTGTAAG 57.367 37.500 0.00 0.00 0.00 2.34
30 31 5.534654 TCTTCTGTTGTCCCATTTTGTAAGG 59.465 40.000 0.00 0.00 0.00 2.69
31 32 5.055265 TCTGTTGTCCCATTTTGTAAGGA 57.945 39.130 0.00 0.00 0.00 3.36
32 33 5.640147 TCTGTTGTCCCATTTTGTAAGGAT 58.360 37.500 0.00 0.00 0.00 3.24
33 34 5.710099 TCTGTTGTCCCATTTTGTAAGGATC 59.290 40.000 0.00 0.00 0.00 3.36
34 35 5.389520 TGTTGTCCCATTTTGTAAGGATCA 58.610 37.500 0.00 0.00 0.00 2.92
35 36 6.015918 TGTTGTCCCATTTTGTAAGGATCAT 58.984 36.000 0.00 0.00 0.00 2.45
36 37 6.496565 TGTTGTCCCATTTTGTAAGGATCATT 59.503 34.615 0.00 0.00 0.00 2.57
37 38 6.528537 TGTCCCATTTTGTAAGGATCATTG 57.471 37.500 2.16 0.00 0.00 2.82
38 39 5.105392 TGTCCCATTTTGTAAGGATCATTGC 60.105 40.000 2.16 1.50 0.00 3.56
39 40 5.022122 TCCCATTTTGTAAGGATCATTGCA 58.978 37.500 6.80 6.80 0.00 4.08
40 41 5.662208 TCCCATTTTGTAAGGATCATTGCAT 59.338 36.000 11.63 0.00 0.00 3.96
41 42 6.838090 TCCCATTTTGTAAGGATCATTGCATA 59.162 34.615 11.63 4.57 0.00 3.14
42 43 7.014518 TCCCATTTTGTAAGGATCATTGCATAG 59.985 37.037 11.63 3.00 0.00 2.23
43 44 7.014518 CCCATTTTGTAAGGATCATTGCATAGA 59.985 37.037 11.63 2.11 0.00 1.98
44 45 7.864379 CCATTTTGTAAGGATCATTGCATAGAC 59.136 37.037 11.63 0.00 0.00 2.59
45 46 6.942532 TTTGTAAGGATCATTGCATAGACC 57.057 37.500 11.63 0.00 0.00 3.85
46 47 5.894298 TGTAAGGATCATTGCATAGACCT 57.106 39.130 6.80 0.00 0.00 3.85
47 48 6.252599 TGTAAGGATCATTGCATAGACCTT 57.747 37.500 6.80 17.92 39.21 3.50
48 49 6.057533 TGTAAGGATCATTGCATAGACCTTG 58.942 40.000 20.35 2.24 36.98 3.61
49 50 3.484407 AGGATCATTGCATAGACCTTGC 58.516 45.455 0.00 0.00 40.55 4.01
50 51 2.555757 GGATCATTGCATAGACCTTGCC 59.444 50.000 0.00 0.00 39.39 4.52
51 52 2.804986 TCATTGCATAGACCTTGCCA 57.195 45.000 0.00 0.00 39.39 4.92
52 53 2.646930 TCATTGCATAGACCTTGCCAG 58.353 47.619 0.00 0.00 39.39 4.85
54 55 0.991146 TTGCATAGACCTTGCCAGGA 59.009 50.000 11.55 0.00 44.19 3.86
55 56 0.991146 TGCATAGACCTTGCCAGGAA 59.009 50.000 11.55 0.00 44.19 3.36
56 57 1.340017 TGCATAGACCTTGCCAGGAAC 60.340 52.381 11.55 4.38 44.19 3.62
57 58 1.340017 GCATAGACCTTGCCAGGAACA 60.340 52.381 11.55 0.00 44.19 3.18
58 59 2.684927 GCATAGACCTTGCCAGGAACAT 60.685 50.000 11.55 0.00 44.19 2.71
59 60 3.209410 CATAGACCTTGCCAGGAACATC 58.791 50.000 11.55 0.00 44.19 3.06
60 61 1.366319 AGACCTTGCCAGGAACATCT 58.634 50.000 11.55 0.00 44.19 2.90
61 62 1.280421 AGACCTTGCCAGGAACATCTC 59.720 52.381 11.55 0.00 44.19 2.75
62 63 0.329596 ACCTTGCCAGGAACATCTCC 59.670 55.000 11.55 0.00 44.19 3.71
63 64 0.394899 CCTTGCCAGGAACATCTCCC 60.395 60.000 0.00 0.00 46.81 4.30
64 65 0.745845 CTTGCCAGGAACATCTCCCG 60.746 60.000 0.00 0.00 46.81 5.14
65 66 1.488705 TTGCCAGGAACATCTCCCGT 61.489 55.000 0.00 0.00 46.81 5.28
66 67 1.153349 GCCAGGAACATCTCCCGTC 60.153 63.158 0.00 0.00 46.81 4.79
67 68 1.141881 CCAGGAACATCTCCCGTCG 59.858 63.158 0.00 0.00 46.81 5.12
68 69 1.320344 CCAGGAACATCTCCCGTCGA 61.320 60.000 0.00 0.00 46.81 4.20
69 70 0.179134 CAGGAACATCTCCCGTCGAC 60.179 60.000 5.18 5.18 46.81 4.20
70 71 0.611062 AGGAACATCTCCCGTCGACA 60.611 55.000 17.16 0.00 46.81 4.35
71 72 0.460311 GGAACATCTCCCGTCGACAT 59.540 55.000 17.16 0.00 38.44 3.06
72 73 1.536284 GGAACATCTCCCGTCGACATC 60.536 57.143 17.16 0.00 38.44 3.06
73 74 1.134367 GAACATCTCCCGTCGACATCA 59.866 52.381 17.16 0.00 0.00 3.07
74 75 0.456221 ACATCTCCCGTCGACATCAC 59.544 55.000 17.16 0.00 0.00 3.06
75 76 0.249073 CATCTCCCGTCGACATCACC 60.249 60.000 17.16 0.00 0.00 4.02
76 77 0.683179 ATCTCCCGTCGACATCACCA 60.683 55.000 17.16 0.00 0.00 4.17
77 78 1.153823 CTCCCGTCGACATCACCAC 60.154 63.158 17.16 0.00 0.00 4.16
78 79 1.873270 CTCCCGTCGACATCACCACA 61.873 60.000 17.16 0.00 0.00 4.17
79 80 1.005512 CCCGTCGACATCACCACAA 60.006 57.895 17.16 0.00 0.00 3.33
80 81 1.289109 CCCGTCGACATCACCACAAC 61.289 60.000 17.16 0.00 0.00 3.32
81 82 0.598942 CCGTCGACATCACCACAACA 60.599 55.000 17.16 0.00 0.00 3.33
82 83 0.506932 CGTCGACATCACCACAACAC 59.493 55.000 17.16 0.00 0.00 3.32
83 84 0.865769 GTCGACATCACCACAACACC 59.134 55.000 11.55 0.00 0.00 4.16
84 85 0.466124 TCGACATCACCACAACACCA 59.534 50.000 0.00 0.00 0.00 4.17
85 86 0.867746 CGACATCACCACAACACCAG 59.132 55.000 0.00 0.00 0.00 4.00
86 87 1.238439 GACATCACCACAACACCAGG 58.762 55.000 0.00 0.00 0.00 4.45
87 88 0.823356 ACATCACCACAACACCAGGC 60.823 55.000 0.00 0.00 0.00 4.85
88 89 0.822944 CATCACCACAACACCAGGCA 60.823 55.000 0.00 0.00 0.00 4.75
89 90 0.106268 ATCACCACAACACCAGGCAA 60.106 50.000 0.00 0.00 0.00 4.52
90 91 0.106268 TCACCACAACACCAGGCAAT 60.106 50.000 0.00 0.00 0.00 3.56
91 92 0.032403 CACCACAACACCAGGCAATG 59.968 55.000 0.00 0.00 0.00 2.82
92 93 1.005867 CCACAACACCAGGCAATGC 60.006 57.895 0.00 0.00 0.00 3.56
103 104 4.446413 GCAATGCCACCAGCCTGC 62.446 66.667 0.00 0.00 42.71 4.85
104 105 2.992689 CAATGCCACCAGCCTGCA 60.993 61.111 0.00 0.00 42.71 4.41
105 106 2.993264 AATGCCACCAGCCTGCAC 60.993 61.111 0.00 0.00 42.71 4.57
112 113 4.435436 CCAGCCTGCACGCGTCTA 62.435 66.667 9.86 0.00 0.00 2.59
113 114 2.202797 CAGCCTGCACGCGTCTAT 60.203 61.111 9.86 0.00 0.00 1.98
114 115 2.105128 AGCCTGCACGCGTCTATC 59.895 61.111 9.86 0.00 0.00 2.08
115 116 2.202743 GCCTGCACGCGTCTATCA 60.203 61.111 9.86 4.19 0.00 2.15
116 117 1.809619 GCCTGCACGCGTCTATCAA 60.810 57.895 9.86 0.00 0.00 2.57
117 118 1.358725 GCCTGCACGCGTCTATCAAA 61.359 55.000 9.86 0.00 0.00 2.69
118 119 0.370273 CCTGCACGCGTCTATCAAAC 59.630 55.000 9.86 0.00 0.00 2.93
119 120 0.370273 CTGCACGCGTCTATCAAACC 59.630 55.000 9.86 0.00 0.00 3.27
120 121 1.343821 GCACGCGTCTATCAAACCG 59.656 57.895 9.86 0.00 0.00 4.44
121 122 1.349259 GCACGCGTCTATCAAACCGT 61.349 55.000 9.86 0.00 0.00 4.83
122 123 0.365523 CACGCGTCTATCAAACCGTG 59.634 55.000 9.86 0.00 39.75 4.94
123 124 1.343821 CGCGTCTATCAAACCGTGC 59.656 57.895 0.00 0.00 0.00 5.34
124 125 1.713830 GCGTCTATCAAACCGTGCC 59.286 57.895 0.00 0.00 0.00 5.01
125 126 1.702491 GCGTCTATCAAACCGTGCCC 61.702 60.000 0.00 0.00 0.00 5.36
126 127 0.390603 CGTCTATCAAACCGTGCCCA 60.391 55.000 0.00 0.00 0.00 5.36
127 128 1.816074 GTCTATCAAACCGTGCCCAA 58.184 50.000 0.00 0.00 0.00 4.12
128 129 2.365582 GTCTATCAAACCGTGCCCAAT 58.634 47.619 0.00 0.00 0.00 3.16
129 130 2.752903 GTCTATCAAACCGTGCCCAATT 59.247 45.455 0.00 0.00 0.00 2.32
130 131 3.013921 TCTATCAAACCGTGCCCAATTC 58.986 45.455 0.00 0.00 0.00 2.17
131 132 0.894835 ATCAAACCGTGCCCAATTCC 59.105 50.000 0.00 0.00 0.00 3.01
132 133 1.080839 CAAACCGTGCCCAATTCCG 60.081 57.895 0.00 0.00 0.00 4.30
133 134 1.228306 AAACCGTGCCCAATTCCGA 60.228 52.632 0.00 0.00 0.00 4.55
134 135 1.241315 AAACCGTGCCCAATTCCGAG 61.241 55.000 0.00 0.00 0.00 4.63
135 136 2.119484 AACCGTGCCCAATTCCGAGA 62.119 55.000 0.00 0.00 0.00 4.04
136 137 2.106683 CCGTGCCCAATTCCGAGAC 61.107 63.158 0.00 0.00 0.00 3.36
137 138 1.079127 CGTGCCCAATTCCGAGACT 60.079 57.895 0.00 0.00 0.00 3.24
138 139 1.084370 CGTGCCCAATTCCGAGACTC 61.084 60.000 0.00 0.00 0.00 3.36
139 140 0.744771 GTGCCCAATTCCGAGACTCC 60.745 60.000 0.00 0.00 0.00 3.85
140 141 1.198094 TGCCCAATTCCGAGACTCCA 61.198 55.000 0.00 0.00 0.00 3.86
141 142 0.744771 GCCCAATTCCGAGACTCCAC 60.745 60.000 0.00 0.00 0.00 4.02
142 143 0.905357 CCCAATTCCGAGACTCCACT 59.095 55.000 0.00 0.00 0.00 4.00
143 144 1.406069 CCCAATTCCGAGACTCCACTG 60.406 57.143 0.00 0.00 0.00 3.66
144 145 1.363744 CAATTCCGAGACTCCACTGC 58.636 55.000 0.00 0.00 0.00 4.40
145 146 1.066573 CAATTCCGAGACTCCACTGCT 60.067 52.381 0.00 0.00 0.00 4.24
146 147 0.820871 ATTCCGAGACTCCACTGCTC 59.179 55.000 0.00 0.00 0.00 4.26
147 148 1.251527 TTCCGAGACTCCACTGCTCC 61.252 60.000 0.00 0.00 0.00 4.70
148 149 1.979155 CCGAGACTCCACTGCTCCA 60.979 63.158 0.00 0.00 0.00 3.86
149 150 1.326213 CCGAGACTCCACTGCTCCAT 61.326 60.000 0.00 0.00 0.00 3.41
150 151 0.179116 CGAGACTCCACTGCTCCATG 60.179 60.000 0.00 0.00 0.00 3.66
151 152 0.461693 GAGACTCCACTGCTCCATGC 60.462 60.000 0.00 0.00 43.25 4.06
152 153 1.451028 GACTCCACTGCTCCATGCC 60.451 63.158 0.00 0.00 42.00 4.40
153 154 2.513204 CTCCACTGCTCCATGCCG 60.513 66.667 0.00 0.00 42.00 5.69
154 155 4.783621 TCCACTGCTCCATGCCGC 62.784 66.667 0.00 0.00 42.00 6.53
161 162 4.899239 CTCCATGCCGCCGAGACC 62.899 72.222 0.00 0.00 0.00 3.85
175 176 4.094684 GACCTGCCGTCTTCGATG 57.905 61.111 0.00 0.00 38.57 3.84
176 177 2.125512 ACCTGCCGTCTTCGATGC 60.126 61.111 0.00 0.00 39.71 3.91
177 178 3.257561 CCTGCCGTCTTCGATGCG 61.258 66.667 7.73 7.73 39.71 4.73
179 180 3.989698 CTGCCGTCTTCGATGCGGT 62.990 63.158 24.11 0.00 46.41 5.68
180 181 2.103538 GCCGTCTTCGATGCGGTA 59.896 61.111 24.11 0.00 46.41 4.02
181 182 1.517694 GCCGTCTTCGATGCGGTAA 60.518 57.895 24.11 0.00 46.41 2.85
182 183 1.079875 GCCGTCTTCGATGCGGTAAA 61.080 55.000 24.11 0.00 46.41 2.01
183 184 1.567504 CCGTCTTCGATGCGGTAAAT 58.432 50.000 19.02 0.00 40.53 1.40
184 185 1.257936 CCGTCTTCGATGCGGTAAATG 59.742 52.381 19.02 0.00 40.53 2.32
185 186 1.332028 CGTCTTCGATGCGGTAAATGC 60.332 52.381 0.00 0.00 39.71 3.56
187 188 2.095213 GTCTTCGATGCGGTAAATGCAA 59.905 45.455 0.00 0.00 46.87 4.08
188 189 2.095213 TCTTCGATGCGGTAAATGCAAC 59.905 45.455 0.00 0.00 46.87 4.17
189 190 1.443802 TCGATGCGGTAAATGCAACA 58.556 45.000 0.00 0.00 46.87 3.33
190 191 1.129624 TCGATGCGGTAAATGCAACAC 59.870 47.619 0.00 0.00 46.87 3.32
191 192 1.793714 CGATGCGGTAAATGCAACACC 60.794 52.381 0.00 0.00 46.87 4.16
192 193 1.472480 GATGCGGTAAATGCAACACCT 59.528 47.619 11.58 0.00 46.87 4.00
193 194 0.595588 TGCGGTAAATGCAACACCTG 59.404 50.000 11.58 7.36 39.87 4.00
223 224 6.308766 GCAAGTATTTGGCAGAACTACAAATG 59.691 38.462 18.17 10.00 42.74 2.32
224 225 7.370383 CAAGTATTTGGCAGAACTACAAATGT 58.630 34.615 18.17 0.00 42.74 2.71
228 229 5.375417 TTGGCAGAACTACAAATGTCATG 57.625 39.130 0.00 0.00 0.00 3.07
239 240 8.181904 ACTACAAATGTCATGACCAAATTCTT 57.818 30.769 22.85 8.98 0.00 2.52
268 271 0.660300 GAAAACCTGCGTTCGCAAGG 60.660 55.000 19.80 21.79 40.86 3.61
290 293 3.685265 GCAGTGGGTATCATGAACATGGA 60.685 47.826 13.67 3.04 39.24 3.41
294 297 2.224867 GGGTATCATGAACATGGAGGGG 60.225 54.545 13.67 0.00 39.24 4.79
305 308 4.209866 GGAGGGGGCATCGGCAAT 62.210 66.667 0.00 0.00 43.71 3.56
309 312 3.219198 GGGGCATCGGCAATGGTC 61.219 66.667 1.09 0.00 43.71 4.02
319 322 1.639298 GGCAATGGTCAGTCTGTCGC 61.639 60.000 0.00 0.00 0.00 5.19
371 383 4.813296 AAAGTCGTGTTCCAAGATGAAC 57.187 40.909 0.00 0.00 43.90 3.18
384 398 0.739813 GATGAACGAACACGGAGGGG 60.740 60.000 0.00 0.00 0.00 4.79
430 445 4.643795 CCGTCCATGAGGCAACAT 57.356 55.556 0.00 0.00 41.41 2.71
484 500 4.202212 GCATTTCCAAACCCAAACAGTACT 60.202 41.667 0.00 0.00 0.00 2.73
488 504 1.339929 CAAACCCAAACAGTACTGCCC 59.660 52.381 22.90 0.00 0.00 5.36
492 508 2.358247 AAACAGTACTGCCCGCGG 60.358 61.111 22.90 21.04 0.00 6.46
591 607 3.036084 CACCTCGCAAGCGTTCGT 61.036 61.111 14.57 6.22 40.74 3.85
626 654 1.026718 CGATTTGACTGGGGGAGCAC 61.027 60.000 0.00 0.00 0.00 4.40
630 658 2.997897 GACTGGGGGAGCACGACT 60.998 66.667 0.00 0.00 0.00 4.18
643 671 0.924363 CACGACTCCGACGCGATAAG 60.924 60.000 15.93 7.08 39.50 1.73
644 672 1.368969 CGACTCCGACGCGATAAGG 60.369 63.158 15.93 10.45 38.22 2.69
645 673 1.726265 GACTCCGACGCGATAAGGT 59.274 57.895 15.93 5.74 0.00 3.50
648 682 0.591741 CTCCGACGCGATAAGGTCAC 60.592 60.000 15.93 0.00 32.74 3.67
652 686 1.731424 CGACGCGATAAGGTCACTGTT 60.731 52.381 15.93 0.00 32.74 3.16
673 707 1.203287 CTCAAGCCGAGACTGATGACA 59.797 52.381 0.00 0.00 45.45 3.58
680 714 1.468914 CGAGACTGATGACACGAAGGA 59.531 52.381 0.00 0.00 0.00 3.36
688 722 1.153745 GACACGAAGGAGCGATGCT 60.154 57.895 0.00 0.00 43.88 3.79
858 919 4.669700 AGCATATATACCCGTACCACTGA 58.330 43.478 0.00 0.00 0.00 3.41
876 937 1.383943 ACACCACCACCAGTCCAGA 60.384 57.895 0.00 0.00 0.00 3.86
900 2183 1.363744 CAGCCAGTTAAGCTTCCTCG 58.636 55.000 0.00 0.00 38.95 4.63
901 2184 0.250513 AGCCAGTTAAGCTTCCTCGG 59.749 55.000 0.00 0.93 37.24 4.63
902 2185 0.036294 GCCAGTTAAGCTTCCTCGGT 60.036 55.000 0.00 0.00 0.00 4.69
903 2186 1.726853 CCAGTTAAGCTTCCTCGGTG 58.273 55.000 0.00 0.00 0.00 4.94
904 2187 1.079503 CAGTTAAGCTTCCTCGGTGC 58.920 55.000 0.00 0.00 0.00 5.01
905 2188 0.685097 AGTTAAGCTTCCTCGGTGCA 59.315 50.000 0.00 0.00 0.00 4.57
907 2190 0.321298 TTAAGCTTCCTCGGTGCACC 60.321 55.000 26.78 26.78 0.00 5.01
908 2191 1.192146 TAAGCTTCCTCGGTGCACCT 61.192 55.000 32.28 13.66 0.00 4.00
909 2192 2.435059 GCTTCCTCGGTGCACCTC 60.435 66.667 32.28 8.73 0.00 3.85
914 2200 2.997315 CTCGGTGCACCTCCCTCA 60.997 66.667 32.28 9.02 0.00 3.86
928 2214 3.326297 CCTCCCTCAAATCCAGATAGTCC 59.674 52.174 0.00 0.00 0.00 3.85
1073 2377 3.499737 CGAGCGGTCCAACCATGC 61.500 66.667 9.39 0.00 38.47 4.06
1128 2438 3.396570 GGGGACCGTGGGAACGAT 61.397 66.667 0.00 0.00 40.86 3.73
1138 2448 0.325296 TGGGAACGATGCCTCCTACT 60.325 55.000 4.57 0.00 38.04 2.57
1275 2603 1.070786 CGGTGGCCACGGCTATTAT 59.929 57.895 29.08 0.00 41.60 1.28
1278 2606 0.535102 GTGGCCACGGCTATTATGCT 60.535 55.000 22.49 0.00 41.60 3.79
1289 2617 1.006825 TATTATGCTGCCTACGCGCG 61.007 55.000 30.96 30.96 37.34 6.86
1491 2870 1.684983 CATGGCAGTTCATCAATCCCC 59.315 52.381 0.00 0.00 0.00 4.81
1538 2919 6.054941 TGCTTCTGTTAATCTGTTCTGTTCA 58.945 36.000 0.00 0.00 0.00 3.18
1548 2929 3.256879 TCTGTTCTGTTCAGTAGCTCTGG 59.743 47.826 11.63 0.00 43.76 3.86
1571 2984 7.768240 TGGTTTTCTACTCTGTTTTTCCTTTC 58.232 34.615 0.00 0.00 0.00 2.62
1608 3043 2.789409 AAGGCACCTGGAATAGTGTC 57.211 50.000 0.00 0.00 38.91 3.67
1618 3053 3.173151 TGGAATAGTGTCTGAGAGCCAA 58.827 45.455 0.00 0.00 0.00 4.52
1634 3069 1.004277 GCCAAGAACCAGGGTGATGTA 59.996 52.381 0.00 0.00 0.00 2.29
1636 3071 2.356125 CCAAGAACCAGGGTGATGTAGG 60.356 54.545 0.00 0.00 0.00 3.18
1707 3149 4.862641 ACAGCACCAGGGATATTTTACT 57.137 40.909 0.00 0.00 0.00 2.24
1721 3163 7.201705 GGGATATTTTACTACTCCTGTTTGTGC 60.202 40.741 0.00 0.00 0.00 4.57
1760 3208 5.105351 ACTTTTAGTTGTGGCTGCTTTCTTT 60.105 36.000 0.00 0.00 0.00 2.52
1944 3409 6.677920 GCCAATTCGCATGTCAACTACTAAAT 60.678 38.462 0.00 0.00 0.00 1.40
1950 3415 5.233050 CGCATGTCAACTACTAAATCCTCAG 59.767 44.000 0.00 0.00 0.00 3.35
1972 3437 8.044574 TCAGGAATATTCATCCATTCTGGTAA 57.955 34.615 17.07 0.00 39.55 2.85
2008 3473 2.416747 CATTCTGAAGCACTCGAACCA 58.583 47.619 0.00 0.00 0.00 3.67
2041 3506 3.799432 ATAGCCCACCACAGTTTGTTA 57.201 42.857 0.00 0.00 0.00 2.41
2088 3555 2.573462 TCTACTGCTTGAAAGAGCCCAT 59.427 45.455 0.00 0.00 42.01 4.00
2093 3561 1.615384 GCTTGAAAGAGCCCATCCACT 60.615 52.381 0.00 0.00 36.66 4.00
2133 3611 4.662179 ACCATCAACATATGATCAGGTCCT 59.338 41.667 10.38 0.00 45.91 3.85
2175 3668 5.371115 TTTTTCAATAGAAGCTTCACCCG 57.629 39.130 27.57 13.40 34.71 5.28
2200 3694 6.894339 TTTCCATTAAGAGAAACCAGAACC 57.106 37.500 0.00 0.00 0.00 3.62
2201 3695 5.576563 TCCATTAAGAGAAACCAGAACCA 57.423 39.130 0.00 0.00 0.00 3.67
2224 3718 7.033791 CCAGCTACAAAGTCTCGAATACTAAA 58.966 38.462 0.81 0.00 0.00 1.85
2258 3752 9.088512 ACTATGTGCTTTCTTTTCTATAACTCG 57.911 33.333 0.00 0.00 0.00 4.18
2261 3755 6.147164 TGTGCTTTCTTTTCTATAACTCGTGG 59.853 38.462 0.00 0.00 0.00 4.94
2282 3776 2.493278 GCAGGTGGCACATATGTTTCTT 59.507 45.455 20.82 0.00 44.52 2.52
2375 3870 7.888250 AGTTTCAAAAAGATGAGAGGAGTTT 57.112 32.000 0.00 0.00 0.00 2.66
2380 3875 9.627123 TTCAAAAAGATGAGAGGAGTTTTCTTA 57.373 29.630 0.00 0.00 0.00 2.10
2437 3932 1.078426 GTGTCATGGTCTTCCCGGG 60.078 63.158 16.85 16.85 35.15 5.73
2447 3942 1.004394 GTCTTCCCGGGAAAGAATGGT 59.996 52.381 34.78 0.00 33.34 3.55
2455 3950 4.013728 CCGGGAAAGAATGGTCACATAAA 58.986 43.478 0.00 0.00 35.94 1.40
2470 3965 4.819630 TCACATAAAGGAAGTGTGAACACC 59.180 41.667 9.91 0.00 46.45 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.321653 GGGACAACAGAAGATGGCGT 60.322 55.000 0.00 0.00 0.00 5.68
1 2 0.321564 TGGGACAACAGAAGATGGCG 60.322 55.000 0.00 0.00 31.92 5.69
2 3 3.650647 TGGGACAACAGAAGATGGC 57.349 52.632 0.00 0.00 31.92 4.40
15 16 5.105392 TGCAATGATCCTTACAAAATGGGAC 60.105 40.000 0.00 0.00 0.00 4.46
16 17 5.022122 TGCAATGATCCTTACAAAATGGGA 58.978 37.500 0.00 0.00 0.00 4.37
17 18 5.341872 TGCAATGATCCTTACAAAATGGG 57.658 39.130 0.00 0.00 0.00 4.00
18 19 7.864379 GTCTATGCAATGATCCTTACAAAATGG 59.136 37.037 0.00 0.00 0.00 3.16
19 20 7.864379 GGTCTATGCAATGATCCTTACAAAATG 59.136 37.037 0.00 0.00 0.00 2.32
20 21 7.781693 AGGTCTATGCAATGATCCTTACAAAAT 59.218 33.333 0.00 0.00 0.00 1.82
21 22 7.118723 AGGTCTATGCAATGATCCTTACAAAA 58.881 34.615 0.00 0.00 0.00 2.44
22 23 6.662755 AGGTCTATGCAATGATCCTTACAAA 58.337 36.000 0.00 0.00 0.00 2.83
23 24 6.252599 AGGTCTATGCAATGATCCTTACAA 57.747 37.500 0.00 0.00 0.00 2.41
24 25 5.894298 AGGTCTATGCAATGATCCTTACA 57.106 39.130 0.00 0.00 0.00 2.41
25 26 5.049129 GCAAGGTCTATGCAATGATCCTTAC 60.049 44.000 17.09 12.30 43.29 2.34
26 27 5.065914 GCAAGGTCTATGCAATGATCCTTA 58.934 41.667 17.09 0.00 43.29 2.69
27 28 3.887716 GCAAGGTCTATGCAATGATCCTT 59.112 43.478 14.31 14.31 43.29 3.36
28 29 3.484407 GCAAGGTCTATGCAATGATCCT 58.516 45.455 0.00 0.00 43.29 3.24
29 30 2.555757 GGCAAGGTCTATGCAATGATCC 59.444 50.000 0.00 0.00 45.60 3.36
30 31 3.216800 TGGCAAGGTCTATGCAATGATC 58.783 45.455 0.00 0.00 45.60 2.92
31 32 3.220110 CTGGCAAGGTCTATGCAATGAT 58.780 45.455 0.00 0.00 45.60 2.45
32 33 2.646930 CTGGCAAGGTCTATGCAATGA 58.353 47.619 0.00 0.00 45.60 2.57
33 34 1.679680 CCTGGCAAGGTCTATGCAATG 59.320 52.381 0.00 0.00 45.60 2.82
34 35 1.565759 TCCTGGCAAGGTCTATGCAAT 59.434 47.619 7.13 0.00 45.60 3.56
35 36 0.991146 TCCTGGCAAGGTCTATGCAA 59.009 50.000 7.13 0.00 45.60 4.08
36 37 0.991146 TTCCTGGCAAGGTCTATGCA 59.009 50.000 7.13 0.00 45.60 3.96
37 38 1.340017 TGTTCCTGGCAAGGTCTATGC 60.340 52.381 7.13 0.00 44.82 3.14
38 39 2.787473 TGTTCCTGGCAAGGTCTATG 57.213 50.000 7.13 0.00 44.82 2.23
39 40 3.118531 AGATGTTCCTGGCAAGGTCTAT 58.881 45.455 7.13 0.00 44.82 1.98
40 41 2.501723 GAGATGTTCCTGGCAAGGTCTA 59.498 50.000 7.13 0.00 44.82 2.59
41 42 1.280421 GAGATGTTCCTGGCAAGGTCT 59.720 52.381 7.13 1.84 44.82 3.85
42 43 1.680249 GGAGATGTTCCTGGCAAGGTC 60.680 57.143 7.13 2.56 44.82 3.85
43 44 0.329596 GGAGATGTTCCTGGCAAGGT 59.670 55.000 7.13 0.00 44.82 3.50
44 45 0.394899 GGGAGATGTTCCTGGCAAGG 60.395 60.000 0.00 0.00 45.98 3.61
45 46 0.745845 CGGGAGATGTTCCTGGCAAG 60.746 60.000 0.00 0.00 46.98 4.01
46 47 1.299648 CGGGAGATGTTCCTGGCAA 59.700 57.895 0.00 0.00 46.98 4.52
47 48 2.989639 CGGGAGATGTTCCTGGCA 59.010 61.111 0.00 0.00 46.98 4.92
51 52 0.611062 TGTCGACGGGAGATGTTCCT 60.611 55.000 11.62 0.00 45.98 3.36
52 53 0.460311 ATGTCGACGGGAGATGTTCC 59.540 55.000 11.62 0.00 46.00 3.62
53 54 1.134367 TGATGTCGACGGGAGATGTTC 59.866 52.381 11.62 0.00 0.00 3.18
54 55 1.135083 GTGATGTCGACGGGAGATGTT 60.135 52.381 11.62 0.00 0.00 2.71
55 56 0.456221 GTGATGTCGACGGGAGATGT 59.544 55.000 11.62 0.00 0.00 3.06
56 57 0.249073 GGTGATGTCGACGGGAGATG 60.249 60.000 11.62 0.00 0.00 2.90
57 58 0.683179 TGGTGATGTCGACGGGAGAT 60.683 55.000 11.62 0.00 0.00 2.75
58 59 1.303806 TGGTGATGTCGACGGGAGA 60.304 57.895 11.62 0.00 0.00 3.71
59 60 1.153823 GTGGTGATGTCGACGGGAG 60.154 63.158 11.62 0.00 0.00 4.30
60 61 1.465200 TTGTGGTGATGTCGACGGGA 61.465 55.000 11.62 0.00 0.00 5.14
61 62 1.005512 TTGTGGTGATGTCGACGGG 60.006 57.895 11.62 0.00 0.00 5.28
62 63 0.598942 TGTTGTGGTGATGTCGACGG 60.599 55.000 11.62 0.00 0.00 4.79
63 64 0.506932 GTGTTGTGGTGATGTCGACG 59.493 55.000 11.62 0.00 0.00 5.12
64 65 0.865769 GGTGTTGTGGTGATGTCGAC 59.134 55.000 9.11 9.11 0.00 4.20
65 66 0.466124 TGGTGTTGTGGTGATGTCGA 59.534 50.000 0.00 0.00 0.00 4.20
66 67 0.867746 CTGGTGTTGTGGTGATGTCG 59.132 55.000 0.00 0.00 0.00 4.35
67 68 1.238439 CCTGGTGTTGTGGTGATGTC 58.762 55.000 0.00 0.00 0.00 3.06
68 69 0.823356 GCCTGGTGTTGTGGTGATGT 60.823 55.000 0.00 0.00 0.00 3.06
69 70 0.822944 TGCCTGGTGTTGTGGTGATG 60.823 55.000 0.00 0.00 0.00 3.07
70 71 0.106268 TTGCCTGGTGTTGTGGTGAT 60.106 50.000 0.00 0.00 0.00 3.06
71 72 0.106268 ATTGCCTGGTGTTGTGGTGA 60.106 50.000 0.00 0.00 0.00 4.02
72 73 0.032403 CATTGCCTGGTGTTGTGGTG 59.968 55.000 0.00 0.00 0.00 4.17
73 74 1.747325 GCATTGCCTGGTGTTGTGGT 61.747 55.000 0.00 0.00 0.00 4.16
74 75 1.005867 GCATTGCCTGGTGTTGTGG 60.006 57.895 0.00 0.00 0.00 4.17
75 76 1.005867 GGCATTGCCTGGTGTTGTG 60.006 57.895 20.66 0.00 46.69 3.33
76 77 3.458653 GGCATTGCCTGGTGTTGT 58.541 55.556 20.66 0.00 46.69 3.32
86 87 4.446413 GCAGGCTGGTGGCATTGC 62.446 66.667 17.64 0.00 42.53 3.56
87 88 2.992689 TGCAGGCTGGTGGCATTG 60.993 61.111 17.64 0.00 44.01 2.82
88 89 2.993264 GTGCAGGCTGGTGGCATT 60.993 61.111 17.64 0.00 44.01 3.56
95 96 3.723235 ATAGACGCGTGCAGGCTGG 62.723 63.158 27.01 15.98 0.00 4.85
96 97 2.202797 ATAGACGCGTGCAGGCTG 60.203 61.111 27.01 21.70 0.00 4.85
97 98 2.105128 GATAGACGCGTGCAGGCT 59.895 61.111 27.01 9.99 0.00 4.58
98 99 1.358725 TTTGATAGACGCGTGCAGGC 61.359 55.000 20.70 21.16 0.00 4.85
99 100 0.370273 GTTTGATAGACGCGTGCAGG 59.630 55.000 20.70 1.01 0.00 4.85
100 101 0.370273 GGTTTGATAGACGCGTGCAG 59.630 55.000 20.70 0.00 0.00 4.41
101 102 1.348538 CGGTTTGATAGACGCGTGCA 61.349 55.000 20.70 6.53 0.00 4.57
102 103 1.343821 CGGTTTGATAGACGCGTGC 59.656 57.895 20.70 8.74 0.00 5.34
103 104 0.365523 CACGGTTTGATAGACGCGTG 59.634 55.000 20.70 0.00 36.31 5.34
104 105 1.349259 GCACGGTTTGATAGACGCGT 61.349 55.000 13.85 13.85 0.00 6.01
105 106 1.343821 GCACGGTTTGATAGACGCG 59.656 57.895 3.53 3.53 0.00 6.01
106 107 1.702491 GGGCACGGTTTGATAGACGC 61.702 60.000 0.00 0.00 0.00 5.19
107 108 0.390603 TGGGCACGGTTTGATAGACG 60.391 55.000 0.00 0.00 0.00 4.18
108 109 1.816074 TTGGGCACGGTTTGATAGAC 58.184 50.000 0.00 0.00 0.00 2.59
109 110 2.799126 ATTGGGCACGGTTTGATAGA 57.201 45.000 0.00 0.00 0.00 1.98
110 111 2.099098 GGAATTGGGCACGGTTTGATAG 59.901 50.000 0.00 0.00 0.00 2.08
111 112 2.096248 GGAATTGGGCACGGTTTGATA 58.904 47.619 0.00 0.00 0.00 2.15
112 113 0.894835 GGAATTGGGCACGGTTTGAT 59.105 50.000 0.00 0.00 0.00 2.57
113 114 1.519751 CGGAATTGGGCACGGTTTGA 61.520 55.000 0.00 0.00 0.00 2.69
114 115 1.080839 CGGAATTGGGCACGGTTTG 60.081 57.895 0.00 0.00 0.00 2.93
115 116 1.228306 TCGGAATTGGGCACGGTTT 60.228 52.632 0.00 0.00 0.00 3.27
116 117 1.674322 CTCGGAATTGGGCACGGTT 60.674 57.895 0.00 0.00 0.00 4.44
117 118 2.046314 CTCGGAATTGGGCACGGT 60.046 61.111 0.00 0.00 0.00 4.83
118 119 2.106683 GTCTCGGAATTGGGCACGG 61.107 63.158 0.00 0.00 0.00 4.94
119 120 1.079127 AGTCTCGGAATTGGGCACG 60.079 57.895 0.00 0.00 0.00 5.34
120 121 0.744771 GGAGTCTCGGAATTGGGCAC 60.745 60.000 0.00 0.00 0.00 5.01
121 122 1.198094 TGGAGTCTCGGAATTGGGCA 61.198 55.000 0.00 0.00 0.00 5.36
122 123 0.744771 GTGGAGTCTCGGAATTGGGC 60.745 60.000 0.00 0.00 0.00 5.36
123 124 0.905357 AGTGGAGTCTCGGAATTGGG 59.095 55.000 0.00 0.00 0.00 4.12
124 125 2.009042 GCAGTGGAGTCTCGGAATTGG 61.009 57.143 0.00 0.00 0.00 3.16
125 126 1.066573 AGCAGTGGAGTCTCGGAATTG 60.067 52.381 0.00 0.00 0.00 2.32
126 127 1.205893 GAGCAGTGGAGTCTCGGAATT 59.794 52.381 0.00 0.00 0.00 2.17
127 128 0.820871 GAGCAGTGGAGTCTCGGAAT 59.179 55.000 0.00 0.00 0.00 3.01
128 129 1.251527 GGAGCAGTGGAGTCTCGGAA 61.252 60.000 0.00 0.00 0.00 4.30
129 130 1.679305 GGAGCAGTGGAGTCTCGGA 60.679 63.158 0.00 0.00 0.00 4.55
130 131 1.326213 ATGGAGCAGTGGAGTCTCGG 61.326 60.000 0.00 0.00 0.00 4.63
131 132 0.179116 CATGGAGCAGTGGAGTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
132 133 0.461693 GCATGGAGCAGTGGAGTCTC 60.462 60.000 0.00 0.00 44.79 3.36
133 134 1.601171 GCATGGAGCAGTGGAGTCT 59.399 57.895 0.00 0.00 44.79 3.24
134 135 4.215349 GCATGGAGCAGTGGAGTC 57.785 61.111 0.00 0.00 44.79 3.36
144 145 4.899239 GGTCTCGGCGGCATGGAG 62.899 72.222 10.53 7.95 0.00 3.86
158 159 2.167861 GCATCGAAGACGGCAGGTC 61.168 63.158 0.00 0.00 42.51 3.85
159 160 2.125512 GCATCGAAGACGGCAGGT 60.126 61.111 0.00 0.00 42.51 4.00
160 161 3.257561 CGCATCGAAGACGGCAGG 61.258 66.667 0.00 0.00 42.51 4.85
161 162 3.257561 CCGCATCGAAGACGGCAG 61.258 66.667 10.60 0.00 42.51 4.85
165 166 1.332028 GCATTTACCGCATCGAAGACG 60.332 52.381 0.00 0.00 42.51 4.18
166 167 1.663643 TGCATTTACCGCATCGAAGAC 59.336 47.619 0.00 0.00 42.51 3.01
167 168 2.017138 TGCATTTACCGCATCGAAGA 57.983 45.000 0.00 0.00 45.75 2.87
168 169 2.159585 TGTTGCATTTACCGCATCGAAG 60.160 45.455 0.00 0.00 39.58 3.79
169 170 1.807142 TGTTGCATTTACCGCATCGAA 59.193 42.857 0.00 0.00 39.58 3.71
170 171 1.129624 GTGTTGCATTTACCGCATCGA 59.870 47.619 0.00 0.00 39.58 3.59
171 172 1.534028 GTGTTGCATTTACCGCATCG 58.466 50.000 0.00 0.00 39.58 3.84
172 173 1.472480 AGGTGTTGCATTTACCGCATC 59.528 47.619 8.38 0.00 39.58 3.91
173 174 1.202114 CAGGTGTTGCATTTACCGCAT 59.798 47.619 8.38 0.00 39.58 4.73
174 175 0.595588 CAGGTGTTGCATTTACCGCA 59.404 50.000 8.38 0.00 39.46 5.69
175 176 3.399879 CAGGTGTTGCATTTACCGC 57.600 52.632 8.38 0.00 39.46 5.68
184 185 2.019897 ACTTGCCAAGCAGGTGTTGC 62.020 55.000 3.88 0.00 46.65 4.17
185 186 2.118132 ACTTGCCAAGCAGGTGTTG 58.882 52.632 3.88 0.00 46.65 3.33
186 187 4.684623 ACTTGCCAAGCAGGTGTT 57.315 50.000 3.88 0.00 46.65 3.32
190 191 1.404583 GCCAAATACTTGCCAAGCAGG 60.405 52.381 3.88 0.91 40.61 4.85
191 192 1.273048 TGCCAAATACTTGCCAAGCAG 59.727 47.619 3.88 0.00 40.61 4.24
192 193 1.273048 CTGCCAAATACTTGCCAAGCA 59.727 47.619 3.88 0.00 36.47 3.91
193 194 1.545582 TCTGCCAAATACTTGCCAAGC 59.454 47.619 3.88 0.00 0.00 4.01
194 195 3.256631 AGTTCTGCCAAATACTTGCCAAG 59.743 43.478 2.11 2.11 0.00 3.61
195 196 3.230134 AGTTCTGCCAAATACTTGCCAA 58.770 40.909 0.00 0.00 0.00 4.52
196 197 2.875296 AGTTCTGCCAAATACTTGCCA 58.125 42.857 0.00 0.00 0.00 4.92
197 198 3.756434 TGTAGTTCTGCCAAATACTTGCC 59.244 43.478 5.14 0.00 0.00 4.52
198 199 5.371115 TTGTAGTTCTGCCAAATACTTGC 57.629 39.130 5.14 0.00 0.00 4.01
199 200 7.370383 ACATTTGTAGTTCTGCCAAATACTTG 58.630 34.615 9.95 3.74 36.84 3.16
200 201 7.230510 TGACATTTGTAGTTCTGCCAAATACTT 59.769 33.333 9.95 2.49 36.84 2.24
201 202 6.714810 TGACATTTGTAGTTCTGCCAAATACT 59.285 34.615 9.95 0.00 36.84 2.12
202 203 6.908825 TGACATTTGTAGTTCTGCCAAATAC 58.091 36.000 9.95 0.00 36.84 1.89
216 217 8.408043 AGAAGAATTTGGTCATGACATTTGTA 57.592 30.769 26.47 6.50 0.00 2.41
218 219 8.492748 CAAAGAAGAATTTGGTCATGACATTTG 58.507 33.333 26.47 14.92 36.68 2.32
223 224 6.974965 AGACAAAGAAGAATTTGGTCATGAC 58.025 36.000 17.91 17.91 43.10 3.06
224 225 7.285172 TCAAGACAAAGAAGAATTTGGTCATGA 59.715 33.333 0.00 0.00 43.10 3.07
228 229 8.595533 GTTTTCAAGACAAAGAAGAATTTGGTC 58.404 33.333 4.42 0.00 43.10 4.02
239 240 3.013921 ACGCAGGTTTTCAAGACAAAGA 58.986 40.909 0.00 0.00 0.00 2.52
268 271 2.620115 CCATGTTCATGATACCCACTGC 59.380 50.000 13.51 0.00 0.00 4.40
290 293 4.528039 CCATTGCCGATGCCCCCT 62.528 66.667 0.00 0.00 36.33 4.79
294 297 1.718757 GACTGACCATTGCCGATGCC 61.719 60.000 0.00 0.00 36.33 4.40
305 308 2.023414 AAACGGCGACAGACTGACCA 62.023 55.000 16.62 0.00 0.00 4.02
309 312 0.878523 TCCAAAACGGCGACAGACTG 60.879 55.000 16.62 0.00 33.14 3.51
319 322 5.219633 CAGGTAGAATTTTGTCCAAAACGG 58.780 41.667 7.31 0.00 42.32 4.44
371 383 2.678934 TCTCCCCCTCCGTGTTCG 60.679 66.667 0.00 0.00 0.00 3.95
384 398 3.551863 CGACTGTTATCCATGCTCTCTCC 60.552 52.174 0.00 0.00 0.00 3.71
430 445 1.073284 GTTGGGGTTCTGTCTTAGGCA 59.927 52.381 0.00 0.00 0.00 4.75
492 508 2.194326 GGAGGGAGGCCAAGATGC 59.806 66.667 5.01 0.00 0.00 3.91
578 594 2.430244 GGAGACGAACGCTTGCGA 60.430 61.111 22.03 0.00 0.00 5.10
579 595 3.479269 GGGAGACGAACGCTTGCG 61.479 66.667 13.70 13.70 0.00 4.85
626 654 1.368969 CCTTATCGCGTCGGAGTCG 60.369 63.158 5.77 0.00 42.81 4.18
630 658 1.028330 AGTGACCTTATCGCGTCGGA 61.028 55.000 5.77 0.00 43.10 4.55
636 664 3.232213 TGAGAACAGTGACCTTATCGC 57.768 47.619 0.00 0.00 38.19 4.58
638 666 3.935828 GGCTTGAGAACAGTGACCTTATC 59.064 47.826 0.00 0.00 0.00 1.75
643 671 0.033504 TCGGCTTGAGAACAGTGACC 59.966 55.000 0.00 0.00 0.00 4.02
644 672 3.588277 TCGGCTTGAGAACAGTGAC 57.412 52.632 0.00 0.00 0.00 3.67
673 707 2.172483 AACCAGCATCGCTCCTTCGT 62.172 55.000 0.00 0.00 36.40 3.85
688 722 3.235481 TCTTCACCGGGCGAACCA 61.235 61.111 6.32 0.00 40.22 3.67
858 919 0.986019 TTCTGGACTGGTGGTGGTGT 60.986 55.000 0.00 0.00 0.00 4.16
876 937 3.092301 GGAAGCTTAACTGGCTGGATTT 58.908 45.455 0.00 0.00 40.19 2.17
900 2183 0.681243 GGATTTGAGGGAGGTGCACC 60.681 60.000 29.22 29.22 0.00 5.01
901 2184 0.038166 TGGATTTGAGGGAGGTGCAC 59.962 55.000 8.80 8.80 0.00 4.57
902 2185 0.329261 CTGGATTTGAGGGAGGTGCA 59.671 55.000 0.00 0.00 0.00 4.57
903 2186 0.620556 TCTGGATTTGAGGGAGGTGC 59.379 55.000 0.00 0.00 0.00 5.01
904 2187 3.713764 ACTATCTGGATTTGAGGGAGGTG 59.286 47.826 0.00 0.00 0.00 4.00
905 2188 3.970640 GACTATCTGGATTTGAGGGAGGT 59.029 47.826 0.00 0.00 0.00 3.85
907 2190 4.040217 CAGGACTATCTGGATTTGAGGGAG 59.960 50.000 0.00 0.00 0.00 4.30
908 2191 3.969976 CAGGACTATCTGGATTTGAGGGA 59.030 47.826 0.00 0.00 0.00 4.20
909 2192 3.713764 ACAGGACTATCTGGATTTGAGGG 59.286 47.826 0.00 0.00 38.98 4.30
914 2200 6.678547 AGACTAGACAGGACTATCTGGATTT 58.321 40.000 0.00 0.00 38.98 2.17
928 2214 2.159310 GCACTGGCACTAGACTAGACAG 60.159 54.545 16.55 19.48 40.72 3.51
952 2241 5.065346 GGCTACCTCTATCTGTTTTCTTTGC 59.935 44.000 0.00 0.00 0.00 3.68
1118 2428 0.179081 GTAGGAGGCATCGTTCCCAC 60.179 60.000 0.00 0.00 33.83 4.61
1119 2429 0.325296 AGTAGGAGGCATCGTTCCCA 60.325 55.000 0.00 0.00 33.83 4.37
1120 2430 1.340568 GTAGTAGGAGGCATCGTTCCC 59.659 57.143 0.00 0.00 33.83 3.97
1171 2487 4.660938 GGCCGGCTGGTGGTCTTT 62.661 66.667 28.56 0.00 37.67 2.52
1278 2606 3.964221 CTTGTCTCGCGCGTAGGCA 62.964 63.158 30.98 27.53 39.92 4.75
1289 2617 1.079750 GTCTCGTGGGCCTTGTCTC 60.080 63.158 4.53 0.00 0.00 3.36
1311 2639 1.214589 GTGCCATGCAGGAAGCTTG 59.785 57.895 2.10 0.00 45.94 4.01
1491 2870 0.253327 GCAGTGTTTAGGAGGAGGGG 59.747 60.000 0.00 0.00 0.00 4.79
1538 2919 5.081032 ACAGAGTAGAAAACCAGAGCTACT 58.919 41.667 0.00 0.00 44.41 2.57
1548 2929 7.851472 CGAGAAAGGAAAAACAGAGTAGAAAAC 59.149 37.037 0.00 0.00 0.00 2.43
1571 2984 2.478134 CCTTTCAGTTTCAGCAGACGAG 59.522 50.000 0.00 0.00 0.00 4.18
1608 3043 0.035630 CCCTGGTTCTTGGCTCTCAG 60.036 60.000 0.00 0.00 0.00 3.35
1618 3053 2.344093 ACCTACATCACCCTGGTTCT 57.656 50.000 0.00 0.00 0.00 3.01
1634 3069 1.988107 TGGAGGCTCTGATCAAAACCT 59.012 47.619 15.23 9.27 0.00 3.50
1636 3071 1.734465 CGTGGAGGCTCTGATCAAAAC 59.266 52.381 15.23 0.00 0.00 2.43
1707 3149 1.946768 GCAACTGCACAAACAGGAGTA 59.053 47.619 0.00 0.00 42.21 2.59
1721 3163 8.921670 ACAACTAAAAGTAAAAACAAGCAACTG 58.078 29.630 0.00 0.00 0.00 3.16
1944 3409 6.776744 CAGAATGGATGAATATTCCTGAGGA 58.223 40.000 12.90 0.00 34.60 3.71
1972 3437 4.163649 TCAGAATGGCTGTGAGATGAGAAT 59.836 41.667 0.00 0.00 45.14 2.40
2008 3473 3.763897 GGTGGGCTATTTCAAGACATTGT 59.236 43.478 0.00 0.00 37.68 2.71
2088 3555 5.475564 GGTTCAGGCTTAATACAAAAGTGGA 59.524 40.000 0.00 0.00 0.00 4.02
2093 3561 7.014711 TGTTGATGGTTCAGGCTTAATACAAAA 59.985 33.333 0.00 0.00 32.27 2.44
2158 3638 4.035675 GGAAATCGGGTGAAGCTTCTATTG 59.964 45.833 26.09 14.02 0.00 1.90
2159 3639 4.200092 GGAAATCGGGTGAAGCTTCTATT 58.800 43.478 26.09 14.44 0.00 1.73
2160 3640 3.199946 TGGAAATCGGGTGAAGCTTCTAT 59.800 43.478 26.09 9.82 0.00 1.98
2162 3642 1.351017 TGGAAATCGGGTGAAGCTTCT 59.649 47.619 26.09 4.10 0.00 2.85
2163 3643 1.821216 TGGAAATCGGGTGAAGCTTC 58.179 50.000 19.89 19.89 0.00 3.86
2167 3660 5.428253 TCTCTTAATGGAAATCGGGTGAAG 58.572 41.667 0.00 0.00 0.00 3.02
2175 3668 7.176690 TGGTTCTGGTTTCTCTTAATGGAAATC 59.823 37.037 6.36 6.49 34.60 2.17
2200 3694 7.755822 AGTTTAGTATTCGAGACTTTGTAGCTG 59.244 37.037 7.30 0.00 0.00 4.24
2201 3695 7.828712 AGTTTAGTATTCGAGACTTTGTAGCT 58.171 34.615 7.30 0.00 0.00 3.32
2254 3748 4.626081 GTGCCACCTGCCACGAGT 62.626 66.667 0.00 0.00 40.16 4.18
2255 3749 2.520465 TATGTGCCACCTGCCACGAG 62.520 60.000 0.00 0.00 40.16 4.18
2258 3752 0.680921 ACATATGTGCCACCTGCCAC 60.681 55.000 7.78 0.00 40.16 5.01
2261 3755 2.094675 AGAAACATATGTGCCACCTGC 58.905 47.619 9.63 0.00 41.77 4.85
2356 3851 9.670719 GTTAAGAAAACTCCTCTCATCTTTTTG 57.329 33.333 0.00 0.00 0.00 2.44
2402 3897 9.561069 ACCATGACACATCCTACTATTATTTTC 57.439 33.333 0.00 0.00 0.00 2.29
2407 3902 7.015292 GGAAGACCATGACACATCCTACTATTA 59.985 40.741 0.00 0.00 35.97 0.98
2437 3932 7.040409 ACACTTCCTTTATGTGACCATTCTTTC 60.040 37.037 0.00 0.00 36.86 2.62


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

AutoCloner maintained by Alex Coulton.