Multiple sequence alignment - TraesCS4A01G442300

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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 TraesCS4A01G442300 chr4A 100.000 3637 0 0 1 3637 710285838 710282202 0.000000e+00 6717.0
1 TraesCS4A01G442300 chr4A 87.747 2024 165 45 1620 3621 710272312 710270350 0.000000e+00 2287.0
2 TraesCS4A01G442300 chr4A 86.153 1726 190 25 971 2685 710695572 710693885 0.000000e+00 1818.0
3 TraesCS4A01G442300 chr4A 94.915 767 34 4 251 1014 710273351 710272587 0.000000e+00 1195.0
4 TraesCS4A01G442300 chr4A 85.741 1080 149 4 1695 2774 710676677 710675603 0.000000e+00 1136.0
5 TraesCS4A01G442300 chr4A 92.814 167 11 1 744 909 517406636 517406470 1.300000e-59 241.0
6 TraesCS4A01G442300 chr7D 89.777 1976 168 19 1692 3637 25898005 25896034 0.000000e+00 2499.0
7 TraesCS4A01G442300 chr7D 87.332 1713 188 9 993 2685 26566523 26564820 0.000000e+00 1934.0
8 TraesCS4A01G442300 chr7D 86.178 1078 144 4 1692 2766 26559457 26558382 0.000000e+00 1160.0
9 TraesCS4A01G442300 chr7D 95.833 624 25 1 971 1594 25898708 25898086 0.000000e+00 1007.0
10 TraesCS4A01G442300 chr7D 88.309 556 61 3 993 1546 27243380 27243933 0.000000e+00 664.0
11 TraesCS4A01G442300 chr7D 90.625 224 14 4 522 745 25899028 25898812 1.280000e-74 291.0
12 TraesCS4A01G442300 chr7D 89.706 68 5 2 258 323 579965583 579965650 6.470000e-13 86.1
13 TraesCS4A01G442300 chr7D 89.655 58 3 2 578 632 26560492 26560435 1.810000e-08 71.3
14 TraesCS4A01G442300 chr7A 93.167 1405 79 3 1692 3095 26823215 26821827 0.000000e+00 2047.0
15 TraesCS4A01G442300 chr7A 87.715 1742 176 15 971 2684 27032989 27031258 0.000000e+00 1997.0
16 TraesCS4A01G442300 chr7A 86.258 1077 145 2 1692 2766 26977626 26976551 0.000000e+00 1166.0
17 TraesCS4A01G442300 chr7A 95.848 578 23 1 1017 1594 26823949 26823373 0.000000e+00 933.0
18 TraesCS4A01G442300 chr7A 89.358 545 57 1 1006 1550 27604635 27605178 0.000000e+00 684.0
19 TraesCS4A01G442300 chr7A 90.498 221 15 5 532 749 26824297 26824080 1.650000e-73 287.0
20 TraesCS4A01G442300 chr7A 88.148 135 16 0 46 180 250864019 250864153 1.050000e-35 161.0
21 TraesCS4A01G442300 chr7A 92.683 41 3 0 258 298 32761248 32761208 3.920000e-05 60.2
22 TraesCS4A01G442300 chr2A 89.434 530 55 1 1010 1538 448294890 448294361 0.000000e+00 667.0
23 TraesCS4A01G442300 chr3B 89.225 529 57 0 1010 1538 224961034 224960506 0.000000e+00 662.0
24 TraesCS4A01G442300 chr3B 100.000 28 0 0 194 221 30960396 30960423 7.000000e-03 52.8
25 TraesCS4A01G442300 chr7B 94.969 159 8 0 745 903 697617446 697617288 2.170000e-62 250.0
26 TraesCS4A01G442300 chr7B 94.410 161 8 1 743 903 679620499 679620658 2.800000e-61 246.0
27 TraesCS4A01G442300 chr5B 94.340 159 9 0 745 903 442783298 442783456 1.010000e-60 244.0
28 TraesCS4A01G442300 chr4B 92.398 171 13 0 740 910 135218217 135218047 1.010000e-60 244.0
29 TraesCS4A01G442300 chr2D 92.353 170 13 0 746 915 87407526 87407357 3.630000e-60 243.0
30 TraesCS4A01G442300 chr1D 92.814 167 12 0 743 909 463382070 463381904 3.630000e-60 243.0
31 TraesCS4A01G442300 chr6B 91.860 172 14 0 739 910 720912048 720912219 1.300000e-59 241.0
32 TraesCS4A01G442300 chr6B 74.346 191 37 9 3269 3451 6614801 6614987 1.810000e-08 71.3
33 TraesCS4A01G442300 chr1B 92.308 169 13 0 747 915 24349213 24349045 1.300000e-59 241.0
34 TraesCS4A01G442300 chr1B 91.503 153 11 2 43 195 503070640 503070790 3.680000e-50 209.0
35 TraesCS4A01G442300 chr1A 90.698 129 12 0 52 180 510534399 510534527 4.830000e-39 172.0
36 TraesCS4A01G442300 chr6D 88.406 138 16 0 43 180 4059409 4059546 2.250000e-37 167.0
37 TraesCS4A01G442300 chr6D 100.000 40 0 0 3202 3241 7865255 7865216 1.400000e-09 75.0
38 TraesCS4A01G442300 chr2B 88.095 84 10 0 820 903 136175098 136175181 2.310000e-17 100.0
39 TraesCS4A01G442300 chr2B 78.030 132 16 6 587 718 800173028 800172910 1.810000e-08 71.3
40 TraesCS4A01G442300 chr5D 73.282 262 47 15 3209 3451 7167677 7167420 1.400000e-09 75.0
41 TraesCS4A01G442300 chr3D 79.412 102 20 1 3271 3371 165856828 165856929 1.810000e-08 71.3
42 TraesCS4A01G442300 chr5A 100.000 33 0 0 3209 3241 4873231 4873263 1.090000e-05 62.1
43 TraesCS4A01G442300 chr6A 88.889 45 5 0 3214 3258 80088913 80088869 5.070000e-04 56.5


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 TraesCS4A01G442300 chr4A 710282202 710285838 3636 True 6717.000000 6717 100.000000 1 3637 1 chr4A.!!$R2 3636
1 TraesCS4A01G442300 chr4A 710693885 710695572 1687 True 1818.000000 1818 86.153000 971 2685 1 chr4A.!!$R4 1714
2 TraesCS4A01G442300 chr4A 710270350 710273351 3001 True 1741.000000 2287 91.331000 251 3621 2 chr4A.!!$R5 3370
3 TraesCS4A01G442300 chr4A 710675603 710676677 1074 True 1136.000000 1136 85.741000 1695 2774 1 chr4A.!!$R3 1079
4 TraesCS4A01G442300 chr7D 26564820 26566523 1703 True 1934.000000 1934 87.332000 993 2685 1 chr7D.!!$R1 1692
5 TraesCS4A01G442300 chr7D 25896034 25899028 2994 True 1265.666667 2499 92.078333 522 3637 3 chr7D.!!$R2 3115
6 TraesCS4A01G442300 chr7D 27243380 27243933 553 False 664.000000 664 88.309000 993 1546 1 chr7D.!!$F1 553
7 TraesCS4A01G442300 chr7D 26558382 26560492 2110 True 615.650000 1160 87.916500 578 2766 2 chr7D.!!$R3 2188
8 TraesCS4A01G442300 chr7A 27031258 27032989 1731 True 1997.000000 1997 87.715000 971 2684 1 chr7A.!!$R2 1713
9 TraesCS4A01G442300 chr7A 26976551 26977626 1075 True 1166.000000 1166 86.258000 1692 2766 1 chr7A.!!$R1 1074
10 TraesCS4A01G442300 chr7A 26821827 26824297 2470 True 1089.000000 2047 93.171000 532 3095 3 chr7A.!!$R4 2563
11 TraesCS4A01G442300 chr7A 27604635 27605178 543 False 684.000000 684 89.358000 1006 1550 1 chr7A.!!$F1 544
12 TraesCS4A01G442300 chr2A 448294361 448294890 529 True 667.000000 667 89.434000 1010 1538 1 chr2A.!!$R1 528
13 TraesCS4A01G442300 chr3B 224960506 224961034 528 True 662.000000 662 89.225000 1010 1538 1 chr3B.!!$R1 528

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
174 175 0.179051 CCTTGAGGCTGCTCCAGATC 60.179 60.000 0.00 0.0 37.29 2.75 F
210 211 0.314935 TTTGTCCGGACGTGGTCTAC 59.685 55.000 28.70 3.5 32.47 2.59 F
1619 1737 0.395586 TGTTCTTTGGCTGCCTGTGT 60.396 50.000 21.03 0.0 0.00 3.72 F
2082 2376 1.008194 CAACCGTCGAACTCCGTGA 60.008 57.895 0.00 0.0 39.75 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1719 0.031178 CACACAGGCAGCCAAAGAAC 59.969 55.0 15.80 0.0 0.00 3.01 R
1682 1956 0.675083 CTTCTGCACCATTTGTGGCA 59.325 50.0 0.00 0.0 45.55 4.92 R
2462 2756 0.252012 CCACCTCAGTCCTCCTCACT 60.252 60.0 0.00 0.0 0.00 3.41 R
3339 3681 0.608130 AAGTCACTACATGCGCCTCA 59.392 50.0 4.18 0.0 0.00 3.86 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
17 18 3.823330 GCGTCGTCAGGGGTCGAT 61.823 66.667 0.00 0.00 36.97 3.59
18 19 2.408022 CGTCGTCAGGGGTCGATC 59.592 66.667 0.00 0.00 36.97 3.69
19 20 2.806237 GTCGTCAGGGGTCGATCC 59.194 66.667 6.02 6.02 36.97 3.36
32 33 4.301027 GATCCCAGCCCCGCGTAG 62.301 72.222 4.92 0.00 0.00 3.51
33 34 4.853142 ATCCCAGCCCCGCGTAGA 62.853 66.667 4.92 0.00 0.00 2.59
36 37 2.831742 CCAGCCCCGCGTAGACTA 60.832 66.667 4.92 0.00 0.00 2.59
37 38 2.201022 CCAGCCCCGCGTAGACTAT 61.201 63.158 4.92 0.00 0.00 2.12
38 39 0.892358 CCAGCCCCGCGTAGACTATA 60.892 60.000 4.92 0.00 0.00 1.31
39 40 0.956633 CAGCCCCGCGTAGACTATAA 59.043 55.000 4.92 0.00 0.00 0.98
40 41 1.338973 CAGCCCCGCGTAGACTATAAA 59.661 52.381 4.92 0.00 0.00 1.40
41 42 2.034124 AGCCCCGCGTAGACTATAAAA 58.966 47.619 4.92 0.00 0.00 1.52
42 43 2.631545 AGCCCCGCGTAGACTATAAAAT 59.368 45.455 4.92 0.00 0.00 1.82
43 44 3.070590 AGCCCCGCGTAGACTATAAAATT 59.929 43.478 4.92 0.00 0.00 1.82
44 45 3.431233 GCCCCGCGTAGACTATAAAATTC 59.569 47.826 4.92 0.00 0.00 2.17
45 46 3.671928 CCCCGCGTAGACTATAAAATTCG 59.328 47.826 4.92 0.00 0.00 3.34
46 47 3.120782 CCCGCGTAGACTATAAAATTCGC 59.879 47.826 4.92 0.00 39.21 4.70
47 48 3.120782 CCGCGTAGACTATAAAATTCGCC 59.879 47.826 4.92 0.00 39.38 5.54
48 49 3.120782 CGCGTAGACTATAAAATTCGCCC 59.879 47.826 0.00 0.00 39.38 6.13
49 50 3.120782 GCGTAGACTATAAAATTCGCCCG 59.879 47.826 0.00 0.00 37.14 6.13
50 51 4.293415 CGTAGACTATAAAATTCGCCCGT 58.707 43.478 0.00 0.00 0.00 5.28
51 52 4.147653 CGTAGACTATAAAATTCGCCCGTG 59.852 45.833 0.00 0.00 0.00 4.94
52 53 4.395959 AGACTATAAAATTCGCCCGTGA 57.604 40.909 0.00 0.00 0.00 4.35
53 54 4.761975 AGACTATAAAATTCGCCCGTGAA 58.238 39.130 0.00 0.00 0.00 3.18
54 55 4.809426 AGACTATAAAATTCGCCCGTGAAG 59.191 41.667 0.00 0.00 0.00 3.02
55 56 4.761975 ACTATAAAATTCGCCCGTGAAGA 58.238 39.130 0.00 0.00 0.00 2.87
56 57 4.569564 ACTATAAAATTCGCCCGTGAAGAC 59.430 41.667 0.00 0.00 0.00 3.01
57 58 0.515564 AAAATTCGCCCGTGAAGACG 59.484 50.000 0.00 0.00 45.67 4.18
58 59 0.601841 AAATTCGCCCGTGAAGACGT 60.602 50.000 0.00 0.00 44.54 4.34
59 60 1.012486 AATTCGCCCGTGAAGACGTC 61.012 55.000 7.70 7.70 44.54 4.34
60 61 2.830704 ATTCGCCCGTGAAGACGTCC 62.831 60.000 13.01 0.00 44.54 4.79
61 62 4.351938 CGCCCGTGAAGACGTCCA 62.352 66.667 13.01 0.37 44.54 4.02
62 63 2.432628 GCCCGTGAAGACGTCCAG 60.433 66.667 13.01 0.00 44.54 3.86
63 64 2.432628 CCCGTGAAGACGTCCAGC 60.433 66.667 13.01 2.23 44.54 4.85
64 65 2.805353 CCGTGAAGACGTCCAGCG 60.805 66.667 13.01 11.71 44.54 5.18
65 66 2.254350 CGTGAAGACGTCCAGCGA 59.746 61.111 13.01 0.00 44.77 4.93
66 67 2.081212 CGTGAAGACGTCCAGCGAC 61.081 63.158 13.01 1.44 44.77 5.19
67 68 1.286260 GTGAAGACGTCCAGCGACT 59.714 57.895 13.01 0.00 46.45 4.18
68 69 0.729816 GTGAAGACGTCCAGCGACTC 60.730 60.000 13.01 0.00 44.01 3.36
69 70 1.153997 GAAGACGTCCAGCGACTCC 60.154 63.158 13.01 0.00 44.01 3.85
70 71 2.545165 GAAGACGTCCAGCGACTCCC 62.545 65.000 13.01 0.00 44.01 4.30
71 72 4.131088 GACGTCCAGCGACTCCCC 62.131 72.222 3.51 0.00 44.77 4.81
81 82 4.222847 GACTCCCCGCCGTCCATC 62.223 72.222 0.00 0.00 0.00 3.51
99 100 2.578178 CGCAGGAGCTCGAACTCG 60.578 66.667 7.83 3.02 37.57 4.18
100 101 2.883253 GCAGGAGCTCGAACTCGC 60.883 66.667 7.83 5.02 37.57 5.03
101 102 2.881389 CAGGAGCTCGAACTCGCT 59.119 61.111 7.83 3.03 37.57 4.93
102 103 1.515952 CAGGAGCTCGAACTCGCTG 60.516 63.158 15.31 15.31 37.57 5.18
103 104 1.974343 AGGAGCTCGAACTCGCTGT 60.974 57.895 7.83 0.00 37.57 4.40
104 105 1.803519 GGAGCTCGAACTCGCTGTG 60.804 63.158 7.83 0.00 37.57 3.66
105 106 2.431601 AGCTCGAACTCGCTGTGC 60.432 61.111 0.00 0.00 39.60 4.57
106 107 2.734723 GCTCGAACTCGCTGTGCA 60.735 61.111 0.00 0.00 39.60 4.57
107 108 2.310233 GCTCGAACTCGCTGTGCAA 61.310 57.895 0.00 0.00 39.60 4.08
108 109 1.488957 CTCGAACTCGCTGTGCAAC 59.511 57.895 0.00 0.00 39.60 4.17
109 110 2.168621 CGAACTCGCTGTGCAACG 59.831 61.111 0.00 0.00 42.39 4.10
110 111 2.585869 CGAACTCGCTGTGCAACGT 61.586 57.895 0.00 0.00 42.39 3.99
111 112 1.083401 GAACTCGCTGTGCAACGTG 60.083 57.895 0.00 0.00 42.39 4.49
112 113 2.430080 GAACTCGCTGTGCAACGTGG 62.430 60.000 10.54 0.00 42.39 4.94
113 114 4.374702 CTCGCTGTGCAACGTGGC 62.375 66.667 8.35 8.35 42.39 5.01
116 117 4.332637 GCTGTGCAACGTGGCCAG 62.333 66.667 22.09 22.09 42.39 4.85
117 118 4.332637 CTGTGCAACGTGGCCAGC 62.333 66.667 13.54 6.74 42.39 4.85
172 173 3.396767 CCTTGAGGCTGCTCCAGA 58.603 61.111 0.00 0.00 37.29 3.86
173 174 1.913722 CCTTGAGGCTGCTCCAGAT 59.086 57.895 0.00 0.00 37.29 2.90
174 175 0.179051 CCTTGAGGCTGCTCCAGATC 60.179 60.000 0.00 0.00 37.29 2.75
175 176 0.831966 CTTGAGGCTGCTCCAGATCT 59.168 55.000 0.00 0.00 37.29 2.75
176 177 0.829333 TTGAGGCTGCTCCAGATCTC 59.171 55.000 0.00 3.39 37.29 2.75
177 178 1.047596 TGAGGCTGCTCCAGATCTCC 61.048 60.000 0.00 0.00 34.73 3.71
178 179 2.086251 GAGGCTGCTCCAGATCTCCG 62.086 65.000 0.00 0.00 37.29 4.63
179 180 2.280052 GCTGCTCCAGATCTCCGC 60.280 66.667 0.00 0.00 32.44 5.54
180 181 2.027314 CTGCTCCAGATCTCCGCG 59.973 66.667 0.00 0.00 32.44 6.46
181 182 3.496875 CTGCTCCAGATCTCCGCGG 62.497 68.421 22.12 22.12 32.44 6.46
182 183 4.959596 GCTCCAGATCTCCGCGGC 62.960 72.222 23.51 6.27 0.00 6.53
183 184 4.292178 CTCCAGATCTCCGCGGCC 62.292 72.222 23.51 9.48 0.00 6.13
194 195 4.383602 CGCGGCCGGTCAACTTTG 62.384 66.667 29.38 0.00 0.00 2.77
195 196 3.284449 GCGGCCGGTCAACTTTGT 61.284 61.111 29.38 0.00 0.00 2.83
196 197 2.943653 CGGCCGGTCAACTTTGTC 59.056 61.111 20.10 0.00 0.00 3.18
197 198 2.613506 CGGCCGGTCAACTTTGTCC 61.614 63.158 20.10 0.00 33.80 4.02
202 203 2.231820 GGTCAACTTTGTCCGGACG 58.768 57.895 28.70 17.41 0.00 4.79
203 204 0.531311 GGTCAACTTTGTCCGGACGT 60.531 55.000 28.70 18.09 0.00 4.34
204 205 0.580104 GTCAACTTTGTCCGGACGTG 59.420 55.000 28.70 21.81 0.00 4.49
205 206 0.531090 TCAACTTTGTCCGGACGTGG 60.531 55.000 28.70 21.37 0.00 4.94
206 207 0.812412 CAACTTTGTCCGGACGTGGT 60.812 55.000 28.70 21.98 0.00 4.16
207 208 0.531311 AACTTTGTCCGGACGTGGTC 60.531 55.000 28.70 5.25 0.00 4.02
208 209 1.366366 CTTTGTCCGGACGTGGTCT 59.634 57.895 28.70 0.00 32.47 3.85
209 210 0.599558 CTTTGTCCGGACGTGGTCTA 59.400 55.000 28.70 7.30 32.47 2.59
210 211 0.314935 TTTGTCCGGACGTGGTCTAC 59.685 55.000 28.70 3.50 32.47 2.59
226 227 7.334844 GTGGTCTACGGATATGATGATATGA 57.665 40.000 0.00 0.00 0.00 2.15
227 228 7.946207 GTGGTCTACGGATATGATGATATGAT 58.054 38.462 0.00 0.00 0.00 2.45
228 229 7.864882 GTGGTCTACGGATATGATGATATGATG 59.135 40.741 0.00 0.00 0.00 3.07
229 230 6.865726 GGTCTACGGATATGATGATATGATGC 59.134 42.308 0.00 0.00 0.00 3.91
230 231 6.580416 GTCTACGGATATGATGATATGATGCG 59.420 42.308 0.00 0.00 37.37 4.73
231 232 4.625028 ACGGATATGATGATATGATGCGG 58.375 43.478 0.00 0.00 35.91 5.69
232 233 3.992427 CGGATATGATGATATGATGCGGG 59.008 47.826 0.00 0.00 0.00 6.13
233 234 4.262164 CGGATATGATGATATGATGCGGGA 60.262 45.833 0.00 0.00 0.00 5.14
234 235 5.236282 GGATATGATGATATGATGCGGGAG 58.764 45.833 0.00 0.00 0.00 4.30
247 248 3.483954 CGGGAGCTGGTCATCAATT 57.516 52.632 9.30 0.00 0.00 2.32
248 249 2.620251 CGGGAGCTGGTCATCAATTA 57.380 50.000 9.30 0.00 0.00 1.40
249 250 3.131709 CGGGAGCTGGTCATCAATTAT 57.868 47.619 9.30 0.00 0.00 1.28
255 256 6.716628 GGGAGCTGGTCATCAATTATTCAATA 59.283 38.462 9.30 0.00 0.00 1.90
289 290 3.522483 TCCGATTGGGAGGAGAGAG 57.478 57.895 0.00 0.00 40.94 3.20
297 300 1.498576 TGGGAGGAGAGAGATGAGAGG 59.501 57.143 0.00 0.00 0.00 3.69
306 309 1.775459 AGAGATGAGAGGCCATGCATT 59.225 47.619 5.01 0.00 0.00 3.56
313 316 2.358267 GAGAGGCCATGCATTTGAAGAG 59.642 50.000 5.01 0.00 0.00 2.85
322 325 6.684686 CCATGCATTTGAAGAGAGAGAAAAA 58.315 36.000 0.00 0.00 0.00 1.94
353 356 3.988819 CCATGTGGTTACTTTTGGTTGG 58.011 45.455 0.00 0.00 0.00 3.77
355 358 4.141824 CCATGTGGTTACTTTTGGTTGGTT 60.142 41.667 0.00 0.00 0.00 3.67
360 363 6.127675 TGTGGTTACTTTTGGTTGGTTAAGTC 60.128 38.462 0.00 0.00 33.28 3.01
361 364 5.066246 TGGTTACTTTTGGTTGGTTAAGTCG 59.934 40.000 0.00 0.00 33.28 4.18
374 377 1.386533 TAAGTCGATGTCCGGACTCC 58.613 55.000 33.39 22.95 39.14 3.85
424 428 4.795970 CTGCTAAGCAAACGTATAAGGG 57.204 45.455 0.00 0.00 38.41 3.95
426 430 3.198200 TGCTAAGCAAACGTATAAGGGGA 59.802 43.478 0.00 0.00 34.76 4.81
446 450 4.182339 GGACCCTCTTAGATGACGAAAAC 58.818 47.826 0.00 0.00 0.00 2.43
460 464 1.805120 CGAAAACGGTCCAGACACTGT 60.805 52.381 0.00 0.00 37.49 3.55
463 467 2.357517 CGGTCCAGACACTGTGGC 60.358 66.667 13.09 9.54 34.77 5.01
469 473 0.548031 CCAGACACTGTGGCCCATAT 59.452 55.000 10.66 0.00 0.00 1.78
470 474 1.671979 CAGACACTGTGGCCCATATG 58.328 55.000 10.66 0.00 0.00 1.78
498 502 2.346847 CGAGATTTGAGAGTCGGCTTTG 59.653 50.000 0.00 0.00 0.00 2.77
501 505 2.169832 TTTGAGAGTCGGCTTTGGAG 57.830 50.000 0.00 0.00 0.00 3.86
506 510 1.078143 AGTCGGCTTTGGAGATGCC 60.078 57.895 0.00 0.00 43.38 4.40
818 834 9.956720 AAACTACATACGGTTGTATATAGACAC 57.043 33.333 0.00 0.00 39.42 3.67
1320 1405 1.001641 CCCCAGGTTCAAGGAGCTG 60.002 63.158 0.00 0.53 43.07 4.24
1340 1425 1.372997 TCGTCAAGCTCAACGAGGC 60.373 57.895 16.82 0.00 42.49 4.70
1344 1429 4.314440 AAGCTCAACGAGGCGGCA 62.314 61.111 13.08 0.00 0.00 5.69
1565 1657 6.317391 TCATGTCTCTCTCTGTACATACACAG 59.683 42.308 0.00 0.00 46.04 3.66
1588 1706 5.532779 AGGAAAACCAGCTTTCTTCAACTAG 59.467 40.000 0.00 0.00 35.91 2.57
1593 1711 3.817647 CCAGCTTTCTTCAACTAGCAAGT 59.182 43.478 0.00 0.00 37.65 3.16
1594 1712 4.997395 CCAGCTTTCTTCAACTAGCAAGTA 59.003 41.667 0.00 0.00 33.75 2.24
1595 1713 5.470098 CCAGCTTTCTTCAACTAGCAAGTAA 59.530 40.000 0.00 0.00 33.75 2.24
1596 1714 6.366630 CAGCTTTCTTCAACTAGCAAGTAAC 58.633 40.000 0.00 0.00 33.75 2.50
1597 1715 6.017934 CAGCTTTCTTCAACTAGCAAGTAACA 60.018 38.462 0.00 0.00 33.75 2.41
1598 1716 6.017852 AGCTTTCTTCAACTAGCAAGTAACAC 60.018 38.462 0.00 0.00 33.75 3.32
1599 1717 6.238374 GCTTTCTTCAACTAGCAAGTAACACA 60.238 38.462 0.00 0.00 33.75 3.72
1600 1718 7.520614 GCTTTCTTCAACTAGCAAGTAACACAT 60.521 37.037 0.00 0.00 33.75 3.21
1601 1719 6.785488 TCTTCAACTAGCAAGTAACACATG 57.215 37.500 0.00 0.00 33.75 3.21
1603 1721 6.765989 TCTTCAACTAGCAAGTAACACATGTT 59.234 34.615 0.00 2.32 41.73 2.71
1604 1722 6.539649 TCAACTAGCAAGTAACACATGTTC 57.460 37.500 0.00 0.00 39.31 3.18
1608 1726 6.959361 ACTAGCAAGTAACACATGTTCTTTG 58.041 36.000 0.00 8.30 39.31 2.77
1610 1728 3.735746 GCAAGTAACACATGTTCTTTGGC 59.264 43.478 16.50 10.54 39.31 4.52
1613 1731 2.514205 AACACATGTTCTTTGGCTGC 57.486 45.000 0.00 0.00 31.64 5.25
1614 1732 0.675633 ACACATGTTCTTTGGCTGCC 59.324 50.000 12.87 12.87 0.00 4.85
1615 1733 0.963962 CACATGTTCTTTGGCTGCCT 59.036 50.000 21.03 0.00 0.00 4.75
1616 1734 0.963962 ACATGTTCTTTGGCTGCCTG 59.036 50.000 21.03 9.43 0.00 4.85
1617 1735 0.963962 CATGTTCTTTGGCTGCCTGT 59.036 50.000 21.03 0.00 0.00 4.00
1618 1736 0.963962 ATGTTCTTTGGCTGCCTGTG 59.036 50.000 21.03 9.43 0.00 3.66
1619 1737 0.395586 TGTTCTTTGGCTGCCTGTGT 60.396 50.000 21.03 0.00 0.00 3.72
1682 1956 7.099120 GCAAAGGGTGAATTTTATTGACTCAT 58.901 34.615 0.00 0.00 0.00 2.90
1689 1965 6.867816 GTGAATTTTATTGACTCATGCCACAA 59.132 34.615 0.00 0.00 0.00 3.33
1832 2126 4.156556 CCCGATGACATCATGTTCAACTTT 59.843 41.667 15.58 0.00 36.57 2.66
1899 2193 1.837051 AACACCTGGGACGAGCTCA 60.837 57.895 15.40 0.00 0.00 4.26
1902 2196 1.837051 ACCTGGGACGAGCTCAACA 60.837 57.895 15.40 5.55 0.00 3.33
1905 2199 2.432628 GGGACGAGCTCAACACGG 60.433 66.667 15.40 0.00 36.60 4.94
1906 2200 2.649034 GGACGAGCTCAACACGGA 59.351 61.111 15.40 0.00 36.60 4.69
2082 2376 1.008194 CAACCGTCGAACTCCGTGA 60.008 57.895 0.00 0.00 39.75 4.35
2129 2423 3.620488 GGTGATGTCCAAGGAGCATTTA 58.380 45.455 0.00 0.00 0.00 1.40
2140 2434 4.222124 AGGAGCATTTATTGGAGTTCGT 57.778 40.909 0.00 0.00 0.00 3.85
2372 2666 4.539083 ATATGCGGCGGCGTTCCA 62.539 61.111 32.35 21.91 44.10 3.53
2451 2745 3.958860 GGGGCATCGGGATGGAGG 61.959 72.222 10.44 0.00 39.16 4.30
2453 2747 2.427753 GGCATCGGGATGGAGGTC 59.572 66.667 10.44 0.00 39.16 3.85
2454 2748 2.443394 GGCATCGGGATGGAGGTCA 61.443 63.158 10.44 0.00 39.16 4.02
2462 2756 1.584724 GGATGGAGGTCAGGGAAGAA 58.415 55.000 0.00 0.00 0.00 2.52
2474 2768 1.435168 AGGGAAGAAGTGAGGAGGACT 59.565 52.381 0.00 0.00 0.00 3.85
2507 2801 2.398754 TGATACGGGAGGTCATGGAT 57.601 50.000 0.00 0.00 0.00 3.41
2516 2810 1.846439 GAGGTCATGGATGGGGAGAAA 59.154 52.381 0.00 0.00 0.00 2.52
2730 3028 8.167392 TCCCTTATCAATTTCAAAGTTCCAGTA 58.833 33.333 0.00 0.00 0.00 2.74
2761 3059 3.869246 AGCGGTTAGTTGAATGGATTACG 59.131 43.478 0.00 0.00 0.00 3.18
2796 3094 8.442384 GTTACCAACATGATGGCAAAATAAAAG 58.558 33.333 21.09 0.00 44.75 2.27
2835 3133 0.687757 AGGAGCTCCTTCCACGCATA 60.688 55.000 30.40 0.00 46.09 3.14
2838 3136 2.037251 GGAGCTCCTTCCACGCATAATA 59.963 50.000 26.25 0.00 37.20 0.98
2889 3188 2.740055 CGCTCTGTGCACCTGGAC 60.740 66.667 15.69 0.00 43.06 4.02
2904 3203 1.067821 CTGGACGGAGGAAGTAGCATC 59.932 57.143 0.00 0.00 0.00 3.91
2921 3220 4.145052 AGCATCATTCACATCTGCATCAT 58.855 39.130 0.00 0.00 35.32 2.45
2925 3227 6.294010 GCATCATTCACATCTGCATCATACTT 60.294 38.462 0.00 0.00 33.13 2.24
2926 3228 6.613755 TCATTCACATCTGCATCATACTTG 57.386 37.500 0.00 0.00 0.00 3.16
3077 3379 2.044946 GGACCTGCACCCCATGAC 60.045 66.667 0.00 0.00 0.00 3.06
3127 3461 7.513371 TTCGGTTAAAGATGTTGGTTAATGT 57.487 32.000 0.00 0.00 0.00 2.71
3129 3463 8.031848 TCGGTTAAAGATGTTGGTTAATGTAC 57.968 34.615 0.00 0.00 0.00 2.90
3153 3489 8.821147 ACGATTGTACACACTTGTATTTCTTA 57.179 30.769 0.00 0.00 40.40 2.10
3163 3499 6.757010 ACACTTGTATTTCTTATAGACCGCTG 59.243 38.462 0.00 0.00 0.00 5.18
3167 3503 7.062749 TGTATTTCTTATAGACCGCTGGAAT 57.937 36.000 1.50 0.00 0.00 3.01
3168 3504 8.185506 TGTATTTCTTATAGACCGCTGGAATA 57.814 34.615 1.50 0.00 0.00 1.75
3182 3518 8.911918 ACCGCTGGAATAAATACATTATACAA 57.088 30.769 1.50 0.00 32.96 2.41
3183 3519 9.344772 ACCGCTGGAATAAATACATTATACAAA 57.655 29.630 1.50 0.00 32.96 2.83
3214 3556 1.858458 CAAACGACGAACTGAGCTCAA 59.142 47.619 18.85 1.63 0.00 3.02
3260 3602 2.890945 CCTTTCCACGAGGGTTCAAATT 59.109 45.455 0.00 0.00 38.11 1.82
3262 3604 2.940994 TCCACGAGGGTTCAAATTCA 57.059 45.000 0.00 0.00 38.11 2.57
3263 3605 2.500229 TCCACGAGGGTTCAAATTCAC 58.500 47.619 0.00 0.00 38.11 3.18
3278 3620 1.514003 TTCACGTGCGCATTTTCCTA 58.486 45.000 15.91 0.00 0.00 2.94
3290 3632 6.183360 TGCGCATTTTCCTAGATTTACTTCAG 60.183 38.462 5.66 0.00 0.00 3.02
3298 3640 7.914427 TCCTAGATTTACTTCAGGCTATTCA 57.086 36.000 0.00 0.00 0.00 2.57
3325 3667 3.924114 TTTGTTCACTGGGAGAAGACA 57.076 42.857 0.00 0.00 0.00 3.41
3339 3681 4.202030 GGAGAAGACATTTCCGTCGACTAT 60.202 45.833 14.70 0.00 40.98 2.12
3344 3686 2.128035 CATTTCCGTCGACTATGAGGC 58.872 52.381 14.70 0.00 0.00 4.70
3351 3693 3.865700 CGACTATGAGGCGCATGTA 57.134 52.632 14.31 0.00 41.27 2.29
3352 3694 1.691127 CGACTATGAGGCGCATGTAG 58.309 55.000 14.31 9.62 41.27 2.74
3362 3704 0.640768 GCGCATGTAGTGACTTCGTC 59.359 55.000 0.30 0.00 0.00 4.20
3365 3707 2.090658 CGCATGTAGTGACTTCGTCAAC 59.909 50.000 0.00 0.00 44.49 3.18
3371 3713 3.536956 AGTGACTTCGTCAACCTCAAA 57.463 42.857 0.00 0.00 44.49 2.69
3373 3715 4.258543 AGTGACTTCGTCAACCTCAAAAA 58.741 39.130 0.00 0.00 44.49 1.94
3379 3721 5.644636 ACTTCGTCAACCTCAAAAAGTTGTA 59.355 36.000 3.11 0.00 43.10 2.41
3382 3724 6.053005 TCGTCAACCTCAAAAAGTTGTATCT 58.947 36.000 3.11 0.00 43.10 1.98
3386 3728 5.948992 ACCTCAAAAAGTTGTATCTGCTC 57.051 39.130 0.00 0.00 36.07 4.26
3389 3731 6.321181 ACCTCAAAAAGTTGTATCTGCTCAAA 59.679 34.615 0.00 0.00 36.07 2.69
3397 3739 8.807667 AAGTTGTATCTGCTCAAAATTTTCAG 57.192 30.769 0.00 6.15 0.00 3.02
3400 3742 7.984422 TGTATCTGCTCAAAATTTTCAGAGA 57.016 32.000 19.55 15.00 37.24 3.10
3412 3754 9.850628 CAAAATTTTCAGAGATGCTCATAAAGA 57.149 29.630 0.00 0.00 32.06 2.52
3438 3780 6.887626 AGATATGCATGCATGTGTTCATAA 57.112 33.333 37.43 18.44 37.82 1.90
3454 3796 7.877612 TGTGTTCATAAGAATGAGTGTATGTGT 59.122 33.333 0.00 0.00 42.97 3.72
3466 3808 3.370978 AGTGTATGTGTATTTGTGAGCGC 59.629 43.478 0.00 0.00 0.00 5.92
3478 3820 3.603158 TGTGAGCGCCTCTAATTGTAA 57.397 42.857 2.29 0.00 0.00 2.41
3479 3821 3.521560 TGTGAGCGCCTCTAATTGTAAG 58.478 45.455 2.29 0.00 0.00 2.34
3501 3849 1.047596 AAGCAAATGTGTGTGCCCCA 61.048 50.000 0.00 0.00 41.88 4.96
3559 3907 0.104487 CAACCTTGTGGCACATGCAA 59.896 50.000 22.73 5.25 44.52 4.08
3564 3912 1.610038 CTTGTGGCACATGCAAGAAGA 59.390 47.619 22.73 1.57 45.27 2.87
3624 3976 8.519526 TCTTTTAATAAAACATGCACGAGGATT 58.480 29.630 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.753070 GATCGACCCCTGACGACGC 62.753 68.421 0.00 0.00 41.15 5.19
1 2 2.408022 GATCGACCCCTGACGACG 59.592 66.667 0.00 0.00 41.15 5.12
2 3 2.806237 GGATCGACCCCTGACGAC 59.194 66.667 0.00 0.00 41.15 4.34
15 16 4.301027 CTACGCGGGGCTGGGATC 62.301 72.222 12.47 0.00 0.00 3.36
16 17 4.853142 TCTACGCGGGGCTGGGAT 62.853 66.667 12.47 0.00 0.00 3.85
19 20 0.892358 TATAGTCTACGCGGGGCTGG 60.892 60.000 12.47 0.00 0.00 4.85
20 21 0.956633 TTATAGTCTACGCGGGGCTG 59.043 55.000 12.47 0.00 0.00 4.85
21 22 1.696063 TTTATAGTCTACGCGGGGCT 58.304 50.000 12.47 12.52 0.00 5.19
22 23 2.514205 TTTTATAGTCTACGCGGGGC 57.486 50.000 12.47 4.13 0.00 5.80
23 24 3.671928 CGAATTTTATAGTCTACGCGGGG 59.328 47.826 12.47 2.04 0.00 5.73
24 25 3.120782 GCGAATTTTATAGTCTACGCGGG 59.879 47.826 12.47 2.47 35.98 6.13
25 26 3.120782 GGCGAATTTTATAGTCTACGCGG 59.879 47.826 12.47 0.00 44.49 6.46
26 27 3.120782 GGGCGAATTTTATAGTCTACGCG 59.879 47.826 3.53 3.53 44.49 6.01
27 28 3.120782 CGGGCGAATTTTATAGTCTACGC 59.879 47.826 0.00 0.00 43.19 4.42
28 29 4.147653 CACGGGCGAATTTTATAGTCTACG 59.852 45.833 0.00 0.00 0.00 3.51
29 30 5.284079 TCACGGGCGAATTTTATAGTCTAC 58.716 41.667 0.00 0.00 0.00 2.59
30 31 5.518848 TCACGGGCGAATTTTATAGTCTA 57.481 39.130 0.00 0.00 0.00 2.59
31 32 4.395959 TCACGGGCGAATTTTATAGTCT 57.604 40.909 0.00 0.00 0.00 3.24
32 33 4.807304 TCTTCACGGGCGAATTTTATAGTC 59.193 41.667 0.00 0.00 0.00 2.59
33 34 4.569564 GTCTTCACGGGCGAATTTTATAGT 59.430 41.667 0.00 0.00 0.00 2.12
34 35 4.317839 CGTCTTCACGGGCGAATTTTATAG 60.318 45.833 0.00 0.00 42.73 1.31
35 36 3.552699 CGTCTTCACGGGCGAATTTTATA 59.447 43.478 0.00 0.00 42.73 0.98
36 37 2.350498 CGTCTTCACGGGCGAATTTTAT 59.650 45.455 0.00 0.00 42.73 1.40
37 38 1.727880 CGTCTTCACGGGCGAATTTTA 59.272 47.619 0.00 0.00 42.73 1.52
38 39 0.515564 CGTCTTCACGGGCGAATTTT 59.484 50.000 0.00 0.00 42.73 1.82
39 40 2.159181 CGTCTTCACGGGCGAATTT 58.841 52.632 0.00 0.00 42.73 1.82
40 41 3.870606 CGTCTTCACGGGCGAATT 58.129 55.556 0.00 0.00 42.73 2.17
49 50 3.843985 GTCGCTGGACGTCTTCAC 58.156 61.111 16.46 0.00 44.19 3.18
64 65 4.222847 GATGGACGGCGGGGAGTC 62.223 72.222 13.24 0.00 36.70 3.36
72 73 4.899239 CTCCTGCGGATGGACGGC 62.899 72.222 0.00 0.00 43.60 5.68
73 74 4.899239 GCTCCTGCGGATGGACGG 62.899 72.222 0.00 0.00 0.00 4.79
74 75 3.781770 GAGCTCCTGCGGATGGACG 62.782 68.421 0.87 0.00 45.42 4.79
75 76 2.107953 GAGCTCCTGCGGATGGAC 59.892 66.667 0.87 0.00 45.42 4.02
76 77 3.531207 CGAGCTCCTGCGGATGGA 61.531 66.667 8.47 0.00 45.42 3.41
77 78 3.081311 TTCGAGCTCCTGCGGATGG 62.081 63.158 8.47 0.00 45.42 3.51
78 79 1.880340 GTTCGAGCTCCTGCGGATG 60.880 63.158 8.47 0.00 45.42 3.51
79 80 2.010582 GAGTTCGAGCTCCTGCGGAT 62.011 60.000 17.67 0.00 45.42 4.18
80 81 2.676822 AGTTCGAGCTCCTGCGGA 60.677 61.111 8.47 0.00 45.42 5.54
81 82 2.202676 GAGTTCGAGCTCCTGCGG 60.203 66.667 17.67 0.00 45.42 5.69
82 83 2.578178 CGAGTTCGAGCTCCTGCG 60.578 66.667 21.70 8.53 45.42 5.18
83 84 2.883253 GCGAGTTCGAGCTCCTGC 60.883 66.667 21.70 16.57 43.02 4.85
84 85 1.515952 CAGCGAGTTCGAGCTCCTG 60.516 63.158 21.70 22.46 42.52 3.86
85 86 1.974343 ACAGCGAGTTCGAGCTCCT 60.974 57.895 21.70 16.54 42.52 3.69
86 87 1.803519 CACAGCGAGTTCGAGCTCC 60.804 63.158 21.70 14.76 42.52 4.70
87 88 2.440569 GCACAGCGAGTTCGAGCTC 61.441 63.158 18.39 18.39 42.52 4.09
88 89 2.431601 GCACAGCGAGTTCGAGCT 60.432 61.111 0.00 0.00 45.74 4.09
89 90 2.310233 TTGCACAGCGAGTTCGAGC 61.310 57.895 5.60 4.07 43.02 5.03
90 91 1.488957 GTTGCACAGCGAGTTCGAG 59.511 57.895 5.60 0.00 43.02 4.04
91 92 2.300066 CGTTGCACAGCGAGTTCGA 61.300 57.895 5.60 0.00 43.02 3.71
92 93 2.168621 CGTTGCACAGCGAGTTCG 59.831 61.111 0.13 0.00 43.27 3.95
93 94 1.083401 CACGTTGCACAGCGAGTTC 60.083 57.895 13.86 0.00 38.42 3.01
94 95 2.534019 CCACGTTGCACAGCGAGTT 61.534 57.895 13.86 0.00 38.42 3.01
95 96 2.967076 CCACGTTGCACAGCGAGT 60.967 61.111 13.86 0.00 38.42 4.18
96 97 4.374702 GCCACGTTGCACAGCGAG 62.375 66.667 13.86 5.65 38.42 5.03
99 100 4.332637 CTGGCCACGTTGCACAGC 62.333 66.667 14.15 0.00 0.00 4.40
100 101 4.332637 GCTGGCCACGTTGCACAG 62.333 66.667 19.16 19.16 34.59 3.66
155 156 0.179051 GATCTGGAGCAGCCTCAAGG 60.179 60.000 0.00 0.00 39.28 3.61
156 157 0.831966 AGATCTGGAGCAGCCTCAAG 59.168 55.000 0.00 0.00 40.03 3.02
157 158 0.829333 GAGATCTGGAGCAGCCTCAA 59.171 55.000 0.00 0.00 39.96 3.02
158 159 1.047596 GGAGATCTGGAGCAGCCTCA 61.048 60.000 0.00 0.00 39.96 3.86
159 160 1.747774 GGAGATCTGGAGCAGCCTC 59.252 63.158 0.00 0.00 37.63 4.70
160 161 2.132996 CGGAGATCTGGAGCAGCCT 61.133 63.158 0.00 0.00 37.63 4.58
161 162 2.420890 CGGAGATCTGGAGCAGCC 59.579 66.667 0.00 0.00 37.10 4.85
162 163 2.280052 GCGGAGATCTGGAGCAGC 60.280 66.667 0.00 0.00 0.00 5.25
163 164 2.027314 CGCGGAGATCTGGAGCAG 59.973 66.667 0.00 0.00 0.00 4.24
164 165 3.531207 CCGCGGAGATCTGGAGCA 61.531 66.667 24.07 0.00 0.00 4.26
165 166 4.959596 GCCGCGGAGATCTGGAGC 62.960 72.222 33.48 4.85 0.00 4.70
166 167 4.292178 GGCCGCGGAGATCTGGAG 62.292 72.222 33.48 0.00 0.00 3.86
177 178 4.383602 CAAAGTTGACCGGCCGCG 62.384 66.667 22.85 16.22 0.00 6.46
178 179 3.249973 GACAAAGTTGACCGGCCGC 62.250 63.158 22.85 7.92 0.00 6.53
179 180 2.613506 GGACAAAGTTGACCGGCCG 61.614 63.158 21.04 21.04 33.67 6.13
180 181 3.351450 GGACAAAGTTGACCGGCC 58.649 61.111 0.00 0.00 33.67 6.13
184 185 0.531311 ACGTCCGGACAAAGTTGACC 60.531 55.000 32.80 3.23 39.19 4.02
185 186 0.580104 CACGTCCGGACAAAGTTGAC 59.420 55.000 32.80 4.66 0.00 3.18
186 187 0.531090 CCACGTCCGGACAAAGTTGA 60.531 55.000 32.80 0.00 0.00 3.18
187 188 0.812412 ACCACGTCCGGACAAAGTTG 60.812 55.000 32.80 20.14 0.00 3.16
188 189 0.531311 GACCACGTCCGGACAAAGTT 60.531 55.000 32.80 13.48 0.00 2.66
189 190 1.068585 GACCACGTCCGGACAAAGT 59.931 57.895 32.80 24.71 0.00 2.66
190 191 0.599558 TAGACCACGTCCGGACAAAG 59.400 55.000 32.80 21.79 32.18 2.77
191 192 0.314935 GTAGACCACGTCCGGACAAA 59.685 55.000 32.80 7.78 32.18 2.83
192 193 1.855213 CGTAGACCACGTCCGGACAA 61.855 60.000 32.80 7.08 45.82 3.18
193 194 2.327343 CGTAGACCACGTCCGGACA 61.327 63.158 32.80 10.01 45.82 4.02
194 195 2.482374 CGTAGACCACGTCCGGAC 59.518 66.667 25.28 25.28 45.82 4.79
202 203 7.334844 TCATATCATCATATCCGTAGACCAC 57.665 40.000 0.00 0.00 0.00 4.16
203 204 7.470563 GCATCATATCATCATATCCGTAGACCA 60.471 40.741 0.00 0.00 0.00 4.02
204 205 6.865726 GCATCATATCATCATATCCGTAGACC 59.134 42.308 0.00 0.00 0.00 3.85
205 206 6.580416 CGCATCATATCATCATATCCGTAGAC 59.420 42.308 0.00 0.00 0.00 2.59
206 207 6.294176 CCGCATCATATCATCATATCCGTAGA 60.294 42.308 0.00 0.00 0.00 2.59
207 208 5.860716 CCGCATCATATCATCATATCCGTAG 59.139 44.000 0.00 0.00 0.00 3.51
208 209 5.278957 CCCGCATCATATCATCATATCCGTA 60.279 44.000 0.00 0.00 0.00 4.02
209 210 4.502087 CCCGCATCATATCATCATATCCGT 60.502 45.833 0.00 0.00 0.00 4.69
210 211 3.992427 CCCGCATCATATCATCATATCCG 59.008 47.826 0.00 0.00 0.00 4.18
211 212 5.219343 TCCCGCATCATATCATCATATCC 57.781 43.478 0.00 0.00 0.00 2.59
212 213 4.689812 GCTCCCGCATCATATCATCATATC 59.310 45.833 0.00 0.00 35.78 1.63
213 214 4.347292 AGCTCCCGCATCATATCATCATAT 59.653 41.667 0.00 0.00 39.10 1.78
214 215 3.708121 AGCTCCCGCATCATATCATCATA 59.292 43.478 0.00 0.00 39.10 2.15
215 216 2.504585 AGCTCCCGCATCATATCATCAT 59.495 45.455 0.00 0.00 39.10 2.45
216 217 1.904537 AGCTCCCGCATCATATCATCA 59.095 47.619 0.00 0.00 39.10 3.07
217 218 2.277969 CAGCTCCCGCATCATATCATC 58.722 52.381 0.00 0.00 39.10 2.92
218 219 1.065636 CCAGCTCCCGCATCATATCAT 60.066 52.381 0.00 0.00 39.10 2.45
219 220 0.322648 CCAGCTCCCGCATCATATCA 59.677 55.000 0.00 0.00 39.10 2.15
220 221 0.322975 ACCAGCTCCCGCATCATATC 59.677 55.000 0.00 0.00 39.10 1.63
221 222 0.322975 GACCAGCTCCCGCATCATAT 59.677 55.000 0.00 0.00 39.10 1.78
222 223 1.048160 TGACCAGCTCCCGCATCATA 61.048 55.000 0.00 0.00 39.10 2.15
223 224 1.703014 ATGACCAGCTCCCGCATCAT 61.703 55.000 0.00 0.00 39.10 2.45
224 225 2.315781 GATGACCAGCTCCCGCATCA 62.316 60.000 9.35 0.00 39.10 3.07
225 226 1.596477 GATGACCAGCTCCCGCATC 60.596 63.158 0.00 0.00 39.10 3.91
226 227 1.913951 TTGATGACCAGCTCCCGCAT 61.914 55.000 0.00 0.00 39.10 4.73
227 228 1.913951 ATTGATGACCAGCTCCCGCA 61.914 55.000 0.00 0.00 39.10 5.69
228 229 0.749454 AATTGATGACCAGCTCCCGC 60.749 55.000 0.00 0.00 0.00 6.13
229 230 2.620251 TAATTGATGACCAGCTCCCG 57.380 50.000 0.00 0.00 0.00 5.14
230 231 4.464008 TGAATAATTGATGACCAGCTCCC 58.536 43.478 0.00 0.00 0.00 4.30
231 232 6.645790 ATTGAATAATTGATGACCAGCTCC 57.354 37.500 0.00 0.00 0.00 4.70
266 267 4.493618 TCTCTCCTCCCAATCGGATTAAT 58.506 43.478 2.35 0.00 41.00 1.40
287 288 2.273538 AATGCATGGCCTCTCATCTC 57.726 50.000 3.32 0.00 0.00 2.75
289 290 2.304092 TCAAATGCATGGCCTCTCATC 58.696 47.619 3.32 0.00 0.00 2.92
297 300 3.276857 TCTCTCTCTTCAAATGCATGGC 58.723 45.455 0.00 0.00 0.00 4.40
353 356 2.479219 GGAGTCCGGACATCGACTTAAC 60.479 54.545 35.00 11.58 42.43 2.01
355 358 1.340308 TGGAGTCCGGACATCGACTTA 60.340 52.381 35.00 10.32 42.43 2.24
360 363 1.000163 CCTATTGGAGTCCGGACATCG 60.000 57.143 35.00 15.83 35.25 3.84
361 364 2.317040 TCCTATTGGAGTCCGGACATC 58.683 52.381 35.00 26.30 37.46 3.06
374 377 6.444633 ACGTACGGATTTCAGTATCCTATTG 58.555 40.000 21.06 0.00 41.65 1.90
393 396 1.877165 GCTTAGCAGCCGGACGTAC 60.877 63.158 5.05 0.00 40.61 3.67
397 400 1.502190 GTTTGCTTAGCAGCCGGAC 59.498 57.895 5.05 0.00 46.74 4.79
424 428 4.182339 GTTTTCGTCATCTAAGAGGGTCC 58.818 47.826 0.00 0.00 0.00 4.46
426 430 3.368116 CCGTTTTCGTCATCTAAGAGGGT 60.368 47.826 0.00 0.00 42.35 4.34
434 438 1.616865 TCTGGACCGTTTTCGTCATCT 59.383 47.619 0.00 0.00 42.35 2.90
439 443 0.462789 AGTGTCTGGACCGTTTTCGT 59.537 50.000 0.00 0.00 42.35 3.85
441 445 1.597663 CACAGTGTCTGGACCGTTTTC 59.402 52.381 0.00 0.00 35.51 2.29
446 450 2.357517 GCCACAGTGTCTGGACCG 60.358 66.667 3.98 0.00 35.51 4.79
469 473 4.201920 CGACTCTCAAATCTCGTCCATACA 60.202 45.833 0.00 0.00 0.00 2.29
470 474 4.283678 CGACTCTCAAATCTCGTCCATAC 58.716 47.826 0.00 0.00 0.00 2.39
488 492 1.078143 GGCATCTCCAAAGCCGACT 60.078 57.895 0.00 0.00 38.86 4.18
498 502 7.386573 GCTATTCTAAACTCTAAAGGCATCTCC 59.613 40.741 0.00 0.00 0.00 3.71
501 505 6.146347 CGGCTATTCTAAACTCTAAAGGCATC 59.854 42.308 0.00 0.00 0.00 3.91
506 510 8.552034 CATTTCCGGCTATTCTAAACTCTAAAG 58.448 37.037 0.00 0.00 0.00 1.85
1062 1135 2.359850 GGCGTGATGTGGCCTTGA 60.360 61.111 3.32 0.00 45.93 3.02
1320 1405 1.009389 CCTCGTTGAGCTTGACGACC 61.009 60.000 17.96 0.00 42.67 4.79
1565 1657 4.655762 AGTTGAAGAAAGCTGGTTTTCC 57.344 40.909 6.27 0.00 37.70 3.13
1588 1706 3.735746 GCCAAAGAACATGTGTTACTTGC 59.264 43.478 0.00 1.32 38.56 4.01
1593 1711 2.295909 GGCAGCCAAAGAACATGTGTTA 59.704 45.455 6.55 0.00 38.56 2.41
1594 1712 1.069049 GGCAGCCAAAGAACATGTGTT 59.931 47.619 6.55 0.00 41.64 3.32
1595 1713 0.675633 GGCAGCCAAAGAACATGTGT 59.324 50.000 6.55 0.00 0.00 3.72
1596 1714 0.963962 AGGCAGCCAAAGAACATGTG 59.036 50.000 15.80 0.00 0.00 3.21
1597 1715 0.963962 CAGGCAGCCAAAGAACATGT 59.036 50.000 15.80 0.00 0.00 3.21
1598 1716 0.963962 ACAGGCAGCCAAAGAACATG 59.036 50.000 15.80 2.50 0.00 3.21
1599 1717 0.963962 CACAGGCAGCCAAAGAACAT 59.036 50.000 15.80 0.00 0.00 2.71
1600 1718 0.395586 ACACAGGCAGCCAAAGAACA 60.396 50.000 15.80 0.00 0.00 3.18
1601 1719 0.031178 CACACAGGCAGCCAAAGAAC 59.969 55.000 15.80 0.00 0.00 3.01
1603 1721 2.195567 GCACACAGGCAGCCAAAGA 61.196 57.895 15.80 0.00 0.00 2.52
1604 1722 2.337532 GCACACAGGCAGCCAAAG 59.662 61.111 15.80 5.54 0.00 2.77
1610 1728 1.713937 TTTGACGTGCACACAGGCAG 61.714 55.000 18.64 0.40 45.96 4.85
1613 1731 2.490328 AATTTTGACGTGCACACAGG 57.510 45.000 18.64 2.44 37.69 4.00
1614 1732 5.940603 TTTTAATTTTGACGTGCACACAG 57.059 34.783 18.64 2.84 0.00 3.66
1615 1733 5.233050 CCATTTTAATTTTGACGTGCACACA 59.767 36.000 18.64 13.38 0.00 3.72
1616 1734 5.460419 TCCATTTTAATTTTGACGTGCACAC 59.540 36.000 18.64 10.76 0.00 3.82
1617 1735 5.592054 TCCATTTTAATTTTGACGTGCACA 58.408 33.333 18.64 0.00 0.00 4.57
1618 1736 5.118510 CCTCCATTTTAATTTTGACGTGCAC 59.881 40.000 6.82 6.82 0.00 4.57
1619 1737 5.221342 ACCTCCATTTTAATTTTGACGTGCA 60.221 36.000 0.00 0.00 0.00 4.57
1654 1926 4.282195 TCAATAAAATTCACCCTTTGCCGT 59.718 37.500 0.00 0.00 0.00 5.68
1682 1956 0.675083 CTTCTGCACCATTTGTGGCA 59.325 50.000 0.00 0.00 45.55 4.92
1689 1965 2.042831 GCGCCTCTTCTGCACCATT 61.043 57.895 0.00 0.00 0.00 3.16
1899 2193 1.079819 CATCGAGCAGGTCCGTGTT 60.080 57.895 0.00 0.00 0.00 3.32
2070 2364 4.968812 TTACATACATCACGGAGTTCGA 57.031 40.909 0.00 0.00 41.61 3.71
2082 2376 7.491682 GTGATGCTCCCAAAATTTACATACAT 58.508 34.615 0.00 0.00 0.00 2.29
2129 2423 1.378762 CCCCCACACGAACTCCAAT 59.621 57.895 0.00 0.00 0.00 3.16
2140 2434 3.755626 TGTTGGCCAACCCCCACA 61.756 61.111 38.90 22.31 40.46 4.17
2217 2511 2.632987 AAAAACTCTGGCGGTAGTGT 57.367 45.000 0.00 0.00 0.00 3.55
2372 2666 0.188342 AGAAGGGCCAACACACCATT 59.812 50.000 6.18 0.00 31.44 3.16
2451 2745 1.552792 CCTCCTCACTTCTTCCCTGAC 59.447 57.143 0.00 0.00 0.00 3.51
2453 2747 1.552792 GTCCTCCTCACTTCTTCCCTG 59.447 57.143 0.00 0.00 0.00 4.45
2454 2748 1.435168 AGTCCTCCTCACTTCTTCCCT 59.565 52.381 0.00 0.00 0.00 4.20
2462 2756 0.252012 CCACCTCAGTCCTCCTCACT 60.252 60.000 0.00 0.00 0.00 3.41
2474 2768 1.131638 GTATCATGGCCTCCACCTCA 58.868 55.000 3.32 0.00 35.80 3.86
2507 2801 1.990060 CTCTCGCCCTTTCTCCCCA 60.990 63.158 0.00 0.00 0.00 4.96
2516 2810 3.893763 CGTCGCATCTCTCGCCCT 61.894 66.667 0.00 0.00 0.00 5.19
2730 3028 5.570234 TTCAACTAACCGCTCAAAAAGTT 57.430 34.783 0.00 0.00 0.00 2.66
2733 3031 4.580995 TCCATTCAACTAACCGCTCAAAAA 59.419 37.500 0.00 0.00 0.00 1.94
2796 3094 8.411683 AGCTCCTCATTTTTCATGATCATTAAC 58.588 33.333 5.16 0.00 0.00 2.01
2875 3174 2.523168 TCCGTCCAGGTGCACAGA 60.523 61.111 20.43 9.31 41.99 3.41
2878 3177 2.788191 CTTCCTCCGTCCAGGTGCAC 62.788 65.000 8.80 8.80 41.99 4.57
2889 3188 3.126831 GTGAATGATGCTACTTCCTCCG 58.873 50.000 0.00 0.00 0.00 4.63
2904 3203 6.260271 AGACAAGTATGATGCAGATGTGAATG 59.740 38.462 0.00 0.00 0.00 2.67
2921 3220 2.038557 GGGCCAACTTCTGAGACAAGTA 59.961 50.000 4.39 0.00 32.71 2.24
2925 3227 0.768221 AGGGGCCAACTTCTGAGACA 60.768 55.000 4.39 0.00 0.00 3.41
2926 3228 1.276622 TAGGGGCCAACTTCTGAGAC 58.723 55.000 4.39 0.00 0.00 3.36
3127 3461 8.821147 AAGAAATACAAGTGTGTACAATCGTA 57.179 30.769 0.00 0.00 42.99 3.43
3140 3476 6.097839 TCCAGCGGTCTATAAGAAATACAAGT 59.902 38.462 0.00 0.00 0.00 3.16
3182 3518 4.086199 TCGTCGTTTGCTTTCAACTTTT 57.914 36.364 0.00 0.00 30.75 2.27
3183 3519 3.750639 TCGTCGTTTGCTTTCAACTTT 57.249 38.095 0.00 0.00 30.75 2.66
3184 3520 3.126343 AGTTCGTCGTTTGCTTTCAACTT 59.874 39.130 0.00 0.00 30.75 2.66
3190 3526 1.003866 GCTCAGTTCGTCGTTTGCTTT 60.004 47.619 0.00 0.00 0.00 3.51
3198 3535 1.391485 CCATTTGAGCTCAGTTCGTCG 59.609 52.381 17.43 2.78 0.00 5.12
3214 3556 3.895041 CCACCACAAAGAACCTAACCATT 59.105 43.478 0.00 0.00 0.00 3.16
3241 3583 3.316868 GTGAATTTGAACCCTCGTGGAAA 59.683 43.478 4.76 0.00 38.00 3.13
3242 3584 2.882137 GTGAATTTGAACCCTCGTGGAA 59.118 45.455 4.76 0.00 38.00 3.53
3248 3590 1.399727 CGCACGTGAATTTGAACCCTC 60.400 52.381 22.23 0.00 0.00 4.30
3260 3602 1.075542 CTAGGAAAATGCGCACGTGA 58.924 50.000 22.23 0.00 0.00 4.35
3262 3604 2.024176 ATCTAGGAAAATGCGCACGT 57.976 45.000 14.90 3.86 0.00 4.49
3263 3605 3.405170 AAATCTAGGAAAATGCGCACG 57.595 42.857 14.90 0.00 0.00 5.34
3298 3640 3.197766 TCTCCCAGTGAACAAATATCGCT 59.802 43.478 0.00 0.00 38.13 4.93
3308 3650 3.753797 GGAAATGTCTTCTCCCAGTGAAC 59.246 47.826 0.00 0.00 0.00 3.18
3325 3667 1.269102 CGCCTCATAGTCGACGGAAAT 60.269 52.381 10.46 0.00 0.00 2.17
3339 3681 0.608130 AAGTCACTACATGCGCCTCA 59.392 50.000 4.18 0.00 0.00 3.86
3362 3704 6.076981 AGCAGATACAACTTTTTGAGGTTG 57.923 37.500 0.00 0.00 45.55 3.77
3365 3707 5.947228 TGAGCAGATACAACTTTTTGAGG 57.053 39.130 0.00 0.00 36.48 3.86
3371 3713 9.252962 CTGAAAATTTTGAGCAGATACAACTTT 57.747 29.630 8.47 0.00 0.00 2.66
3373 3715 8.169977 TCTGAAAATTTTGAGCAGATACAACT 57.830 30.769 12.03 0.00 31.24 3.16
3379 3721 6.153000 AGCATCTCTGAAAATTTTGAGCAGAT 59.847 34.615 16.72 17.32 35.32 2.90
3382 3724 5.242171 TGAGCATCTCTGAAAATTTTGAGCA 59.758 36.000 12.03 2.53 34.92 4.26
3386 3728 9.850628 TCTTTATGAGCATCTCTGAAAATTTTG 57.149 29.630 8.47 0.00 34.92 2.44
3397 3739 9.597170 TGCATATCTTATCTTTATGAGCATCTC 57.403 33.333 0.00 0.00 34.92 2.75
3400 3742 8.622157 GCATGCATATCTTATCTTTATGAGCAT 58.378 33.333 14.21 0.00 38.23 3.79
3412 3754 6.887626 TGAACACATGCATGCATATCTTAT 57.112 33.333 31.73 16.16 34.91 1.73
3415 3757 6.713450 TCTTATGAACACATGCATGCATATCT 59.287 34.615 31.73 16.75 34.91 1.98
3417 3759 6.887626 TCTTATGAACACATGCATGCATAT 57.112 33.333 31.73 20.24 34.91 1.78
3438 3780 7.065085 GCTCACAAATACACATACACTCATTCT 59.935 37.037 0.00 0.00 0.00 2.40
3454 3796 4.513442 ACAATTAGAGGCGCTCACAAATA 58.487 39.130 7.64 0.00 32.06 1.40
3466 3808 9.132521 CACATTTGCTTTTCTTACAATTAGAGG 57.867 33.333 0.00 0.00 0.00 3.69
3478 3820 2.483538 GGGCACACACATTTGCTTTTCT 60.484 45.455 0.00 0.00 38.85 2.52
3479 3821 1.866601 GGGCACACACATTTGCTTTTC 59.133 47.619 0.00 0.00 38.85 2.29
3501 3849 2.445525 TCCACCCCTGCTTAAACTTCTT 59.554 45.455 0.00 0.00 0.00 2.52
3606 3954 3.190327 CACCAATCCTCGTGCATGTTTTA 59.810 43.478 5.68 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.