Multiple sequence alignment - TraesCS5D01G223000

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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 TraesCS5D01G223000 chr5D 100.000 5397 0 0 1 5397 330707925 330713321 0.000000e+00 9967.0
1 TraesCS5D01G223000 chr5D 84.375 192 14 9 335 514 330888566 330888379 2.000000e-39 174.0
2 TraesCS5D01G223000 chr5D 97.297 74 2 0 1261 1334 350371824 350371897 5.670000e-25 126.0
3 TraesCS5D01G223000 chr5D 92.405 79 5 1 1257 1334 361576962 361576884 1.590000e-20 111.0
4 TraesCS5D01G223000 chr5D 97.143 35 0 1 2944 2977 40987605 40987639 2.100000e-04 58.4
5 TraesCS5D01G223000 chr5D 100.000 29 0 0 2944 2972 328513998 328513970 3.000000e-03 54.7
6 TraesCS5D01G223000 chr5B 97.463 2247 47 7 226 2464 383529794 383527550 0.000000e+00 3825.0
7 TraesCS5D01G223000 chr5B 96.525 2302 49 8 2464 4738 383524539 383522242 0.000000e+00 3779.0
8 TraesCS5D01G223000 chr5B 96.667 660 15 2 4738 5397 383522206 383521554 0.000000e+00 1090.0
9 TraesCS5D01G223000 chr5B 83.171 1129 131 32 1669 2766 386566135 386565035 0.000000e+00 977.0
10 TraesCS5D01G223000 chr5B 82.635 835 96 19 3342 4164 386564645 386563848 0.000000e+00 693.0
11 TraesCS5D01G223000 chr5B 87.687 536 46 9 4165 4689 386564003 386563477 1.660000e-169 606.0
12 TraesCS5D01G223000 chr5B 97.391 230 6 0 1 230 383537471 383537242 5.070000e-105 392.0
13 TraesCS5D01G223000 chr5B 83.063 431 72 1 819 1248 386566824 386566394 1.820000e-104 390.0
14 TraesCS5D01G223000 chr5B 86.207 348 34 10 2914 3255 386565032 386564693 1.100000e-96 364.0
15 TraesCS5D01G223000 chr5B 89.744 273 19 6 4737 5000 386563323 386563051 1.860000e-89 340.0
16 TraesCS5D01G223000 chr5B 95.055 182 8 1 5217 5397 386561352 386561171 8.850000e-73 285.0
17 TraesCS5D01G223000 chr5B 83.562 292 26 15 2971 3256 386644568 386644843 2.490000e-63 254.0
18 TraesCS5D01G223000 chr5B 90.909 165 15 0 4000 4164 383522824 383522660 7.040000e-54 222.0
19 TraesCS5D01G223000 chr5B 89.583 144 14 1 5001 5144 386561557 386561415 1.190000e-41 182.0
20 TraesCS5D01G223000 chr5A 84.579 1057 130 22 1669 2700 426287586 426288634 0.000000e+00 1018.0
21 TraesCS5D01G223000 chr5A 85.114 833 95 18 3343 4164 426289082 426289896 0.000000e+00 824.0
22 TraesCS5D01G223000 chr5A 87.805 369 36 8 4166 4529 426289741 426290105 1.800000e-114 424.0
23 TraesCS5D01G223000 chr5A 83.871 434 61 6 819 1245 426286892 426287323 6.510000e-109 405.0
24 TraesCS5D01G223000 chr5A 91.176 238 18 1 4900 5134 426309512 426309749 2.430000e-83 320.0
25 TraesCS5D01G223000 chr5A 82.699 289 33 12 2971 3256 426274129 426274403 1.940000e-59 241.0
26 TraesCS5D01G223000 chr5A 78.521 284 40 15 4612 4875 426291297 426291579 3.340000e-37 167.0
27 TraesCS5D01G223000 chr4D 91.824 159 10 3 2762 2917 74079508 74079350 9.100000e-53 219.0
28 TraesCS5D01G223000 chr4D 91.954 87 2 4 1256 1340 427262318 427262401 3.420000e-22 117.0
29 TraesCS5D01G223000 chr1A 92.208 154 10 2 2765 2916 155857859 155857706 3.270000e-52 217.0
30 TraesCS5D01G223000 chr1A 92.308 39 2 1 2945 2982 430623909 430623871 3.000000e-03 54.7
31 TraesCS5D01G223000 chr1D 91.613 155 11 2 2764 2916 156133338 156133492 4.230000e-51 213.0
32 TraesCS5D01G223000 chr1D 96.053 76 3 0 1259 1334 47323436 47323511 2.040000e-24 124.0
33 TraesCS5D01G223000 chr1D 85.437 103 12 2 1575 1676 105968479 105968379 2.660000e-18 104.0
34 TraesCS5D01G223000 chr7D 91.558 154 12 1 2765 2917 34756866 34757019 1.520000e-50 211.0
35 TraesCS5D01G223000 chr7D 85.484 62 6 2 1289 1350 629406400 629406458 1.620000e-05 62.1
36 TraesCS5D01G223000 chr6B 90.625 160 13 2 2759 2916 617176575 617176734 1.520000e-50 211.0
37 TraesCS5D01G223000 chr3D 91.026 156 13 1 2762 2916 322435447 322435292 5.480000e-50 209.0
38 TraesCS5D01G223000 chr3D 93.671 79 3 1 1261 1337 169888140 169888218 3.420000e-22 117.0
39 TraesCS5D01G223000 chr3D 87.000 100 8 2 1574 1672 457021614 457021519 2.060000e-19 108.0
40 TraesCS5D01G223000 chr3D 83.761 117 13 3 1565 1675 520821281 520821165 7.390000e-19 106.0
41 TraesCS5D01G223000 chr3D 81.731 104 7 2 1257 1349 67481319 67481217 5.800000e-10 76.8
42 TraesCS5D01G223000 chr3B 91.026 156 13 1 2762 2916 396272034 396271879 5.480000e-50 209.0
43 TraesCS5D01G223000 chr3B 90.826 109 9 1 1565 1672 637088495 637088603 1.570000e-30 145.0
44 TraesCS5D01G223000 chr6D 90.000 160 14 2 2759 2916 410398272 410398431 7.090000e-49 206.0
45 TraesCS5D01G223000 chr6D 97.143 35 0 1 2944 2977 112433546 112433580 2.100000e-04 58.4
46 TraesCS5D01G223000 chr6D 100.000 29 0 0 2944 2972 83109224 83109196 3.000000e-03 54.7
47 TraesCS5D01G223000 chr2A 93.827 81 4 1 1255 1334 704774813 704774893 2.640000e-23 121.0
48 TraesCS5D01G223000 chr2A 92.958 71 4 1 1574 1643 527913909 527913839 9.560000e-18 102.0
49 TraesCS5D01G223000 chr2A 100.000 42 0 0 1632 1673 144653738 144653697 1.610000e-10 78.7
50 TraesCS5D01G223000 chr2B 92.771 83 2 2 1255 1334 762916464 762916545 3.420000e-22 117.0
51 TraesCS5D01G223000 chr2B 93.590 78 2 1 1261 1335 762916545 762916468 4.420000e-21 113.0
52 TraesCS5D01G223000 chr4B 88.000 100 8 2 1574 1672 450911780 450911684 1.230000e-21 115.0
53 TraesCS5D01G223000 chr7A 86.316 95 8 2 1579 1672 712092276 712092186 1.240000e-16 99.0
54 TraesCS5D01G223000 chr6A 86.316 95 8 4 1579 1672 518390790 518390700 1.240000e-16 99.0
55 TraesCS5D01G223000 chr6A 94.872 39 0 2 2940 2977 118284260 118284297 5.840000e-05 60.2
56 TraesCS5D01G223000 chr6A 94.737 38 1 1 2944 2980 99820060 99820023 2.100000e-04 58.4
57 TraesCS5D01G223000 chr2D 94.286 35 1 1 2944 2977 204493587 204493621 1.000000e-02 52.8


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 TraesCS5D01G223000 chr5D 330707925 330713321 5396 False 9967.000 9967 100.000000 1 5397 1 chr5D.!!$F2 5396
1 TraesCS5D01G223000 chr5B 383527550 383529794 2244 True 3825.000 3825 97.463000 226 2464 1 chr5B.!!$R1 2238
2 TraesCS5D01G223000 chr5B 383521554 383524539 2985 True 1697.000 3779 94.700333 2464 5397 3 chr5B.!!$R3 2933
3 TraesCS5D01G223000 chr5B 386561171 386566824 5653 True 479.625 977 87.143125 819 5397 8 chr5B.!!$R4 4578
4 TraesCS5D01G223000 chr5A 426286892 426291579 4687 False 567.600 1018 83.978000 819 4875 5 chr5A.!!$F3 4056

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
93 94 0.105658 TCTCCTCCCCCTATTGGTCG 60.106 60.000 0.00 0.0 0.00 4.79 F
152 153 0.250295 TGGAGAAAGCCAACTGGACG 60.250 55.000 0.00 0.0 37.39 4.79 F
558 562 0.257616 CTCCCCCGCCCAAAAAGATA 59.742 55.000 0.00 0.0 0.00 1.98 F
1359 1377 2.224305 GGTTTATCCTGTAGCGCCTCAT 60.224 50.000 2.29 0.0 0.00 2.90 F
2093 2120 3.063861 TCAATTTCGATGACTGCCATTCG 59.936 43.478 0.00 0.0 35.17 3.34 F
3407 3485 2.342406 TCCTTGTGGAGATCCCTTCA 57.658 50.000 0.00 0.0 37.46 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1019 2.019984 GATGCCTCAAATTCGAGCCTT 58.980 47.619 0.00 0.00 0.00 4.35 R
1056 1064 2.033602 GGGGTGCTGCGGTACTTT 59.966 61.111 13.75 0.00 0.00 2.66 R
2021 2048 2.180131 CTGGCAGCTGCGAAGTTGAC 62.180 60.000 31.19 9.15 43.26 3.18 R
2759 2808 0.971386 TGAACGGAGGGAGTACAACC 59.029 55.000 0.00 0.00 0.00 3.77 R
3670 3752 1.002888 AGCATATCATGAGAAGGGCGG 59.997 52.381 0.09 0.00 0.00 6.13 R
4842 6186 0.933796 GAGTAAGCAGCGATGGAAGC 59.066 55.000 1.46 0.00 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
21 22 3.407967 CGGTGCCCCCATGTACCT 61.408 66.667 0.00 0.00 38.70 3.08
22 23 2.978946 CGGTGCCCCCATGTACCTT 61.979 63.158 0.00 0.00 38.70 3.50
23 24 1.379843 GGTGCCCCCATGTACCTTG 60.380 63.158 0.00 0.00 37.93 3.61
24 25 1.379843 GTGCCCCCATGTACCTTGG 60.380 63.158 5.20 5.20 0.00 3.61
25 26 1.854979 TGCCCCCATGTACCTTGGT 60.855 57.895 10.19 0.00 31.99 3.67
26 27 1.076995 GCCCCCATGTACCTTGGTC 60.077 63.158 10.19 0.00 31.99 4.02
27 28 1.571773 GCCCCCATGTACCTTGGTCT 61.572 60.000 10.19 0.00 31.99 3.85
28 29 0.999712 CCCCCATGTACCTTGGTCTT 59.000 55.000 10.19 0.00 31.99 3.01
29 30 1.064685 CCCCCATGTACCTTGGTCTTC 60.065 57.143 10.19 0.00 31.99 2.87
30 31 1.406887 CCCCATGTACCTTGGTCTTCG 60.407 57.143 10.19 0.00 31.99 3.79
31 32 1.278127 CCCATGTACCTTGGTCTTCGT 59.722 52.381 10.19 0.00 31.99 3.85
32 33 2.618053 CCATGTACCTTGGTCTTCGTC 58.382 52.381 0.00 0.00 0.00 4.20
33 34 2.233922 CCATGTACCTTGGTCTTCGTCT 59.766 50.000 0.00 0.00 0.00 4.18
34 35 3.306780 CCATGTACCTTGGTCTTCGTCTT 60.307 47.826 0.00 0.00 0.00 3.01
35 36 3.380479 TGTACCTTGGTCTTCGTCTTG 57.620 47.619 0.00 0.00 0.00 3.02
36 37 2.960384 TGTACCTTGGTCTTCGTCTTGA 59.040 45.455 0.00 0.00 0.00 3.02
37 38 3.576982 TGTACCTTGGTCTTCGTCTTGAT 59.423 43.478 0.00 0.00 0.00 2.57
38 39 3.045601 ACCTTGGTCTTCGTCTTGATG 57.954 47.619 0.00 0.00 0.00 3.07
39 40 1.734465 CCTTGGTCTTCGTCTTGATGC 59.266 52.381 0.00 0.00 0.00 3.91
40 41 2.613977 CCTTGGTCTTCGTCTTGATGCT 60.614 50.000 0.00 0.00 0.00 3.79
41 42 2.370281 TGGTCTTCGTCTTGATGCTC 57.630 50.000 0.00 0.00 0.00 4.26
42 43 1.066858 TGGTCTTCGTCTTGATGCTCC 60.067 52.381 0.00 0.00 0.00 4.70
43 44 1.205893 GGTCTTCGTCTTGATGCTCCT 59.794 52.381 0.00 0.00 0.00 3.69
44 45 2.535331 GTCTTCGTCTTGATGCTCCTC 58.465 52.381 0.00 0.00 0.00 3.71
45 46 2.165437 GTCTTCGTCTTGATGCTCCTCT 59.835 50.000 0.00 0.00 0.00 3.69
46 47 2.828520 TCTTCGTCTTGATGCTCCTCTT 59.171 45.455 0.00 0.00 0.00 2.85
47 48 2.949451 TCGTCTTGATGCTCCTCTTC 57.051 50.000 0.00 0.00 0.00 2.87
48 49 2.451490 TCGTCTTGATGCTCCTCTTCT 58.549 47.619 0.00 0.00 0.00 2.85
49 50 3.621558 TCGTCTTGATGCTCCTCTTCTA 58.378 45.455 0.00 0.00 0.00 2.10
50 51 3.378742 TCGTCTTGATGCTCCTCTTCTAC 59.621 47.826 0.00 0.00 0.00 2.59
51 52 3.380004 CGTCTTGATGCTCCTCTTCTACT 59.620 47.826 0.00 0.00 0.00 2.57
52 53 4.497340 CGTCTTGATGCTCCTCTTCTACTC 60.497 50.000 0.00 0.00 0.00 2.59
53 54 3.629855 TCTTGATGCTCCTCTTCTACTCG 59.370 47.826 0.00 0.00 0.00 4.18
54 55 3.283259 TGATGCTCCTCTTCTACTCGA 57.717 47.619 0.00 0.00 0.00 4.04
55 56 2.946329 TGATGCTCCTCTTCTACTCGAC 59.054 50.000 0.00 0.00 0.00 4.20
56 57 2.791347 TGCTCCTCTTCTACTCGACT 57.209 50.000 0.00 0.00 0.00 4.18
57 58 3.074675 TGCTCCTCTTCTACTCGACTT 57.925 47.619 0.00 0.00 0.00 3.01
58 59 2.750166 TGCTCCTCTTCTACTCGACTTG 59.250 50.000 0.00 0.00 0.00 3.16
59 60 2.750712 GCTCCTCTTCTACTCGACTTGT 59.249 50.000 0.00 0.00 0.00 3.16
60 61 3.181504 GCTCCTCTTCTACTCGACTTGTC 60.182 52.174 0.00 0.00 0.00 3.18
61 62 4.258543 CTCCTCTTCTACTCGACTTGTCT 58.741 47.826 0.00 0.00 0.00 3.41
62 63 4.653868 TCCTCTTCTACTCGACTTGTCTT 58.346 43.478 0.00 0.00 0.00 3.01
63 64 4.456222 TCCTCTTCTACTCGACTTGTCTTG 59.544 45.833 0.00 0.00 0.00 3.02
64 65 4.380023 CCTCTTCTACTCGACTTGTCTTGG 60.380 50.000 0.00 0.00 0.00 3.61
65 66 4.142790 TCTTCTACTCGACTTGTCTTGGT 58.857 43.478 0.00 0.00 0.00 3.67
66 67 4.215827 TCTTCTACTCGACTTGTCTTGGTC 59.784 45.833 0.00 0.00 0.00 4.02
70 71 4.695560 GACTTGTCTTGGTCGGGG 57.304 61.111 0.00 0.00 0.00 5.73
71 72 1.003718 GACTTGTCTTGGTCGGGGG 60.004 63.158 0.00 0.00 0.00 5.40
72 73 2.359975 CTTGTCTTGGTCGGGGGC 60.360 66.667 0.00 0.00 0.00 5.80
73 74 3.172106 TTGTCTTGGTCGGGGGCA 61.172 61.111 0.00 0.00 0.00 5.36
74 75 2.484287 CTTGTCTTGGTCGGGGGCAT 62.484 60.000 0.00 0.00 0.00 4.40
75 76 2.124695 GTCTTGGTCGGGGGCATC 60.125 66.667 0.00 0.00 0.00 3.91
76 77 2.285368 TCTTGGTCGGGGGCATCT 60.285 61.111 0.00 0.00 0.00 2.90
77 78 2.190578 CTTGGTCGGGGGCATCTC 59.809 66.667 0.00 0.00 0.00 2.75
78 79 3.406595 CTTGGTCGGGGGCATCTCC 62.407 68.421 0.00 0.00 0.00 3.71
79 80 3.943137 TTGGTCGGGGGCATCTCCT 62.943 63.158 0.00 0.00 34.39 3.69
80 81 3.551407 GGTCGGGGGCATCTCCTC 61.551 72.222 0.00 0.00 34.39 3.71
86 87 2.621115 GGGCATCTCCTCCCCCTA 59.379 66.667 0.00 0.00 36.50 3.53
87 88 1.162085 GGGCATCTCCTCCCCCTAT 59.838 63.158 0.00 0.00 36.50 2.57
88 89 0.476611 GGGCATCTCCTCCCCCTATT 60.477 60.000 0.00 0.00 36.50 1.73
89 90 0.695347 GGCATCTCCTCCCCCTATTG 59.305 60.000 0.00 0.00 0.00 1.90
90 91 0.695347 GCATCTCCTCCCCCTATTGG 59.305 60.000 0.00 0.00 0.00 3.16
91 92 2.047742 GCATCTCCTCCCCCTATTGGT 61.048 57.143 0.00 0.00 0.00 3.67
92 93 1.981495 CATCTCCTCCCCCTATTGGTC 59.019 57.143 0.00 0.00 0.00 4.02
93 94 0.105658 TCTCCTCCCCCTATTGGTCG 60.106 60.000 0.00 0.00 0.00 4.79
94 95 1.074775 TCCTCCCCCTATTGGTCGG 60.075 63.158 0.00 0.00 0.00 4.79
95 96 2.819284 CCTCCCCCTATTGGTCGGC 61.819 68.421 0.00 0.00 0.00 5.54
96 97 3.158648 TCCCCCTATTGGTCGGCG 61.159 66.667 0.00 0.00 0.00 6.46
97 98 4.250305 CCCCCTATTGGTCGGCGG 62.250 72.222 7.21 0.00 0.00 6.13
98 99 4.929707 CCCCTATTGGTCGGCGGC 62.930 72.222 7.21 4.32 0.00 6.53
99 100 4.929707 CCCTATTGGTCGGCGGCC 62.930 72.222 26.28 26.28 0.00 6.13
122 123 2.441164 AGCGGGAGAGCTCATCGT 60.441 61.111 17.77 0.00 45.67 3.73
123 124 2.279120 GCGGGAGAGCTCATCGTG 60.279 66.667 17.77 7.52 32.95 4.35
124 125 2.415010 CGGGAGAGCTCATCGTGG 59.585 66.667 17.77 0.00 0.00 4.94
125 126 2.418910 CGGGAGAGCTCATCGTGGT 61.419 63.158 17.77 0.00 0.00 4.16
126 127 1.439644 GGGAGAGCTCATCGTGGTC 59.560 63.158 17.77 2.15 0.00 4.02
127 128 1.064946 GGAGAGCTCATCGTGGTCG 59.935 63.158 17.77 0.00 37.07 4.79
128 129 1.064946 GAGAGCTCATCGTGGTCGG 59.935 63.158 17.77 0.00 37.07 4.79
129 130 2.105128 GAGCTCATCGTGGTCGGG 59.895 66.667 9.40 0.00 37.69 5.14
130 131 3.432051 GAGCTCATCGTGGTCGGGG 62.432 68.421 9.40 0.00 37.69 5.73
132 133 3.461773 CTCATCGTGGTCGGGGCT 61.462 66.667 0.00 0.00 37.69 5.19
133 134 3.000819 TCATCGTGGTCGGGGCTT 61.001 61.111 0.00 0.00 37.69 4.35
134 135 2.819595 CATCGTGGTCGGGGCTTG 60.820 66.667 0.00 0.00 37.69 4.01
135 136 4.096003 ATCGTGGTCGGGGCTTGG 62.096 66.667 0.00 0.00 37.69 3.61
137 138 4.760047 CGTGGTCGGGGCTTGGAG 62.760 72.222 0.00 0.00 0.00 3.86
138 139 3.319198 GTGGTCGGGGCTTGGAGA 61.319 66.667 0.00 0.00 0.00 3.71
139 140 2.528127 TGGTCGGGGCTTGGAGAA 60.528 61.111 0.00 0.00 0.00 2.87
140 141 2.150719 TGGTCGGGGCTTGGAGAAA 61.151 57.895 0.00 0.00 0.00 2.52
141 142 1.377333 GGTCGGGGCTTGGAGAAAG 60.377 63.158 0.00 0.00 39.07 2.62
150 151 2.276732 CTTGGAGAAAGCCAACTGGA 57.723 50.000 0.00 0.00 42.75 3.86
151 152 1.882623 CTTGGAGAAAGCCAACTGGAC 59.117 52.381 0.00 0.00 42.75 4.02
152 153 0.250295 TGGAGAAAGCCAACTGGACG 60.250 55.000 0.00 0.00 37.39 4.79
153 154 1.578206 GGAGAAAGCCAACTGGACGC 61.578 60.000 0.00 0.00 37.39 5.19
154 155 1.901650 GAGAAAGCCAACTGGACGCG 61.902 60.000 3.53 3.53 37.39 6.01
155 156 1.959226 GAAAGCCAACTGGACGCGA 60.959 57.895 15.93 0.00 37.39 5.87
156 157 1.901650 GAAAGCCAACTGGACGCGAG 61.902 60.000 15.93 1.31 37.39 5.03
159 160 2.664851 CCAACTGGACGCGAGCAA 60.665 61.111 15.93 0.00 37.39 3.91
160 161 2.250939 CCAACTGGACGCGAGCAAA 61.251 57.895 15.93 0.00 37.39 3.68
161 162 1.646540 CAACTGGACGCGAGCAAAA 59.353 52.632 15.93 0.00 0.00 2.44
162 163 0.384725 CAACTGGACGCGAGCAAAAG 60.385 55.000 15.93 3.71 0.00 2.27
163 164 1.507141 AACTGGACGCGAGCAAAAGG 61.507 55.000 15.93 0.00 0.00 3.11
164 165 1.961277 CTGGACGCGAGCAAAAGGT 60.961 57.895 15.93 0.00 0.00 3.50
165 166 0.669318 CTGGACGCGAGCAAAAGGTA 60.669 55.000 15.93 0.00 0.00 3.08
166 167 0.947180 TGGACGCGAGCAAAAGGTAC 60.947 55.000 15.93 0.00 0.00 3.34
182 183 4.245251 AGGTACTTGTTTGTTTCTGGGT 57.755 40.909 0.00 0.00 27.25 4.51
183 184 3.951680 AGGTACTTGTTTGTTTCTGGGTG 59.048 43.478 0.00 0.00 27.25 4.61
184 185 2.959507 ACTTGTTTGTTTCTGGGTGC 57.040 45.000 0.00 0.00 0.00 5.01
185 186 1.134175 ACTTGTTTGTTTCTGGGTGCG 59.866 47.619 0.00 0.00 0.00 5.34
186 187 1.134175 CTTGTTTGTTTCTGGGTGCGT 59.866 47.619 0.00 0.00 0.00 5.24
187 188 0.736053 TGTTTGTTTCTGGGTGCGTC 59.264 50.000 0.00 0.00 0.00 5.19
188 189 1.021968 GTTTGTTTCTGGGTGCGTCT 58.978 50.000 0.00 0.00 0.00 4.18
189 190 1.002792 GTTTGTTTCTGGGTGCGTCTC 60.003 52.381 0.00 0.00 0.00 3.36
190 191 0.878523 TTGTTTCTGGGTGCGTCTCG 60.879 55.000 0.00 0.00 0.00 4.04
191 192 1.300697 GTTTCTGGGTGCGTCTCGT 60.301 57.895 0.00 0.00 0.00 4.18
192 193 1.006571 TTTCTGGGTGCGTCTCGTC 60.007 57.895 0.00 0.00 0.00 4.20
193 194 1.461091 TTTCTGGGTGCGTCTCGTCT 61.461 55.000 0.00 0.00 0.00 4.18
194 195 1.863662 TTCTGGGTGCGTCTCGTCTC 61.864 60.000 0.00 0.00 0.00 3.36
195 196 2.596338 TGGGTGCGTCTCGTCTCA 60.596 61.111 0.00 0.00 0.00 3.27
196 197 2.126424 GGGTGCGTCTCGTCTCAC 60.126 66.667 0.00 0.00 0.00 3.51
197 198 2.126424 GGTGCGTCTCGTCTCACC 60.126 66.667 0.00 0.00 41.66 4.02
198 199 2.126424 GTGCGTCTCGTCTCACCC 60.126 66.667 0.00 0.00 0.00 4.61
199 200 3.733960 TGCGTCTCGTCTCACCCG 61.734 66.667 0.00 0.00 0.00 5.28
200 201 4.477975 GCGTCTCGTCTCACCCGG 62.478 72.222 0.00 0.00 0.00 5.73
201 202 4.477975 CGTCTCGTCTCACCCGGC 62.478 72.222 0.00 0.00 0.00 6.13
202 203 4.131088 GTCTCGTCTCACCCGGCC 62.131 72.222 0.00 0.00 0.00 6.13
274 275 5.869649 TCTGAACCATCGAAATCCATCTA 57.130 39.130 0.00 0.00 0.00 1.98
288 289 1.007271 ATCTATCCGCCGCGACTTG 60.007 57.895 15.93 2.08 0.00 3.16
302 303 1.743996 GACTTGTCCTGATCCTTGCC 58.256 55.000 0.00 0.00 0.00 4.52
412 416 1.066858 CGGCTCTTTGCTAGACTCCAA 60.067 52.381 0.00 0.00 42.39 3.53
558 562 0.257616 CTCCCCCGCCCAAAAAGATA 59.742 55.000 0.00 0.00 0.00 1.98
565 569 4.384427 CCCCGCCCAAAAAGATAAGTAGTA 60.384 45.833 0.00 0.00 0.00 1.82
712 719 7.787904 TGCCTCTTATCTTACCCTAACTGATTA 59.212 37.037 0.00 0.00 0.00 1.75
741 748 5.014123 TCAAAGAGGACTTGTGTAATCCCAT 59.986 40.000 0.00 0.00 36.39 4.00
743 750 6.831664 AAGAGGACTTGTGTAATCCCATAT 57.168 37.500 0.00 0.00 34.80 1.78
847 854 2.536365 GATCTACGCGGTGTTGATGAA 58.464 47.619 20.29 0.00 42.05 2.57
1056 1064 2.606587 GGGCAAGGAGGAGCAGGAA 61.607 63.158 0.00 0.00 0.00 3.36
1270 1288 6.730001 TGTACCTATATGATACTCCCTCCA 57.270 41.667 0.00 0.00 0.00 3.86
1359 1377 2.224305 GGTTTATCCTGTAGCGCCTCAT 60.224 50.000 2.29 0.00 0.00 2.90
1426 1445 4.698304 GGGTTCCATCTTTTGACGTTGATA 59.302 41.667 0.00 0.00 0.00 2.15
1567 1588 7.086376 CAGCGGGTTATATACGTTAGTGTTAT 58.914 38.462 0.00 0.00 0.00 1.89
1587 1608 4.898014 ATCCCCATCCCAAATTACTTGA 57.102 40.909 0.00 0.00 37.17 3.02
1661 1682 8.047310 ACAAATCTAAGACAAGTAATTCGGGAT 58.953 33.333 0.00 0.00 0.00 3.85
1774 1797 4.862371 TGAGTTTCTAAAGGGTGTTGGTT 58.138 39.130 0.00 0.00 0.00 3.67
2079 2106 5.059221 GCGGACACTACATTTTTCAATTTCG 59.941 40.000 0.00 0.00 0.00 3.46
2093 2120 3.063861 TCAATTTCGATGACTGCCATTCG 59.936 43.478 0.00 0.00 35.17 3.34
2382 2418 6.493802 AGGTTTAAGGATCTCGCTGTATATCA 59.506 38.462 0.00 0.00 0.00 2.15
2822 2871 7.710044 GCATATCTCAAGATGGACTACATATGG 59.290 40.741 7.80 0.00 40.72 2.74
2840 2889 8.048534 ACATATGGACTGAAATGAGTGAAAAG 57.951 34.615 7.80 0.00 0.00 2.27
2841 2890 4.836125 TGGACTGAAATGAGTGAAAAGC 57.164 40.909 0.00 0.00 0.00 3.51
2935 2984 9.327628 GGGAGTAGGAACTAAATTTATGACTTC 57.672 37.037 0.00 0.00 45.48 3.01
3025 3075 5.690409 CACGGATATAAATCTGCTGTAACGT 59.310 40.000 0.00 0.00 41.54 3.99
3407 3485 2.342406 TCCTTGTGGAGATCCCTTCA 57.658 50.000 0.00 0.00 37.46 3.02
3489 3570 2.814805 AGCCACCAACTGAGCATAAT 57.185 45.000 0.00 0.00 0.00 1.28
3670 3752 7.495934 TCTGAAAAGCTTTATCTGCAGTATACC 59.504 37.037 13.10 0.00 0.00 2.73
3671 3753 6.542370 TGAAAAGCTTTATCTGCAGTATACCC 59.458 38.462 13.10 0.00 0.00 3.69
3742 3825 5.886960 ATCTTTGATACGCTTCTTGCTTT 57.113 34.783 0.00 0.00 40.11 3.51
3744 3827 6.795098 TCTTTGATACGCTTCTTGCTTTAA 57.205 33.333 0.00 0.00 40.11 1.52
3745 3828 6.599437 TCTTTGATACGCTTCTTGCTTTAAC 58.401 36.000 0.00 0.00 40.11 2.01
3746 3829 6.426937 TCTTTGATACGCTTCTTGCTTTAACT 59.573 34.615 0.00 0.00 40.11 2.24
3747 3830 5.530519 TGATACGCTTCTTGCTTTAACTG 57.469 39.130 0.00 0.00 40.11 3.16
3749 3832 5.468746 TGATACGCTTCTTGCTTTAACTGTT 59.531 36.000 0.00 0.00 40.11 3.16
3750 3833 3.952535 ACGCTTCTTGCTTTAACTGTTG 58.047 40.909 2.69 0.00 40.11 3.33
4121 4209 2.150397 ACGAGTTGTGCTTCAGGTAC 57.850 50.000 0.00 0.00 0.00 3.34
4203 4291 5.123344 ACAAGGTATACATTTTCTCGGTTGC 59.877 40.000 5.01 0.00 0.00 4.17
4224 4312 4.935205 TGCGCTTCTTACTTACATTGATGT 59.065 37.500 9.73 1.84 44.48 3.06
4562 4753 9.643735 AGTTAGAACATACTAGCTAATACAGGT 57.356 33.333 0.00 0.00 38.84 4.00
4601 4792 4.911390 ACATTCACTCCCTTCTTTGGTAG 58.089 43.478 0.00 0.00 0.00 3.18
4640 5844 2.242043 CAGGATTGGAACTGGTTTGCT 58.758 47.619 0.00 0.00 0.00 3.91
4696 5900 6.404403 CCTTCATCTTTCTCACCACATGAATG 60.404 42.308 0.00 0.00 36.69 2.67
4835 6179 0.676736 TTTTTGGACGGCATCAACCC 59.323 50.000 0.00 0.00 0.00 4.11
4842 6186 0.107508 ACGGCATCAACCCATCTCAG 60.108 55.000 0.00 0.00 0.00 3.35
4904 6249 0.305922 GCCAAGCTCATCACGTATGC 59.694 55.000 0.00 0.00 35.38 3.14
4971 6318 2.300152 TCGATCTGCCCCTCATGTTATC 59.700 50.000 0.00 0.00 0.00 1.75
5033 7873 3.581265 TGCCAAGATCATGGAATGCTA 57.419 42.857 21.00 0.00 46.21 3.49
5056 7896 2.302733 TGCTCTAGGTGCATGAAGAACA 59.697 45.455 0.00 0.00 35.31 3.18
5204 8044 8.029642 ACTTCTCCAACTCAAATACAAATACG 57.970 34.615 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.379843 CCAAGGTACATGGGGGCAC 60.380 63.158 8.66 0.00 44.48 5.01
7 8 3.095421 CCAAGGTACATGGGGGCA 58.905 61.111 8.66 0.00 44.48 5.36
13 14 3.594603 AGACGAAGACCAAGGTACATG 57.405 47.619 0.00 0.00 0.00 3.21
14 15 3.576982 TCAAGACGAAGACCAAGGTACAT 59.423 43.478 0.00 0.00 0.00 2.29
15 16 2.960384 TCAAGACGAAGACCAAGGTACA 59.040 45.455 0.00 0.00 0.00 2.90
16 17 3.655276 TCAAGACGAAGACCAAGGTAC 57.345 47.619 0.00 0.00 0.00 3.34
17 18 3.616560 GCATCAAGACGAAGACCAAGGTA 60.617 47.826 0.00 0.00 0.00 3.08
18 19 2.872038 GCATCAAGACGAAGACCAAGGT 60.872 50.000 0.00 0.00 0.00 3.50
19 20 1.734465 GCATCAAGACGAAGACCAAGG 59.266 52.381 0.00 0.00 0.00 3.61
20 21 2.670414 GAGCATCAAGACGAAGACCAAG 59.330 50.000 0.00 0.00 33.17 3.61
21 22 2.612972 GGAGCATCAAGACGAAGACCAA 60.613 50.000 0.00 0.00 36.25 3.67
22 23 1.066858 GGAGCATCAAGACGAAGACCA 60.067 52.381 0.00 0.00 36.25 4.02
23 24 1.205893 AGGAGCATCAAGACGAAGACC 59.794 52.381 0.00 0.00 36.25 3.85
24 25 2.165437 AGAGGAGCATCAAGACGAAGAC 59.835 50.000 0.00 0.00 36.25 3.01
25 26 2.451490 AGAGGAGCATCAAGACGAAGA 58.549 47.619 0.00 0.00 36.25 2.87
26 27 2.957491 AGAGGAGCATCAAGACGAAG 57.043 50.000 0.00 0.00 36.25 3.79
27 28 2.828520 AGAAGAGGAGCATCAAGACGAA 59.171 45.455 0.00 0.00 36.25 3.85
28 29 2.451490 AGAAGAGGAGCATCAAGACGA 58.549 47.619 0.00 0.00 36.25 4.20
29 30 2.957491 AGAAGAGGAGCATCAAGACG 57.043 50.000 0.00 0.00 36.25 4.18
30 31 4.497340 CGAGTAGAAGAGGAGCATCAAGAC 60.497 50.000 0.00 0.00 36.25 3.01
31 32 3.629855 CGAGTAGAAGAGGAGCATCAAGA 59.370 47.826 0.00 0.00 36.25 3.02
32 33 3.629855 TCGAGTAGAAGAGGAGCATCAAG 59.370 47.826 0.00 0.00 36.25 3.02
33 34 3.378742 GTCGAGTAGAAGAGGAGCATCAA 59.621 47.826 0.00 0.00 36.25 2.57
34 35 2.946329 GTCGAGTAGAAGAGGAGCATCA 59.054 50.000 0.00 0.00 36.25 3.07
35 36 3.211045 AGTCGAGTAGAAGAGGAGCATC 58.789 50.000 0.00 0.00 0.00 3.91
36 37 3.290948 AGTCGAGTAGAAGAGGAGCAT 57.709 47.619 0.00 0.00 0.00 3.79
37 38 2.750166 CAAGTCGAGTAGAAGAGGAGCA 59.250 50.000 0.00 0.00 0.00 4.26
38 39 2.750712 ACAAGTCGAGTAGAAGAGGAGC 59.249 50.000 0.00 0.00 0.00 4.70
39 40 4.258543 AGACAAGTCGAGTAGAAGAGGAG 58.741 47.826 0.00 0.00 34.09 3.69
40 41 4.289238 AGACAAGTCGAGTAGAAGAGGA 57.711 45.455 0.00 0.00 34.09 3.71
41 42 4.380023 CCAAGACAAGTCGAGTAGAAGAGG 60.380 50.000 0.00 0.00 34.09 3.69
42 43 4.216687 ACCAAGACAAGTCGAGTAGAAGAG 59.783 45.833 0.00 0.00 34.09 2.85
43 44 4.142790 ACCAAGACAAGTCGAGTAGAAGA 58.857 43.478 0.00 0.00 34.09 2.87
44 45 4.477780 GACCAAGACAAGTCGAGTAGAAG 58.522 47.826 0.00 0.00 34.09 2.85
45 46 4.500603 GACCAAGACAAGTCGAGTAGAA 57.499 45.455 0.00 0.00 34.09 2.10
53 54 1.003718 CCCCCGACCAAGACAAGTC 60.004 63.158 0.00 0.00 0.00 3.01
54 55 3.157680 CCCCCGACCAAGACAAGT 58.842 61.111 0.00 0.00 0.00 3.16
55 56 2.359975 GCCCCCGACCAAGACAAG 60.360 66.667 0.00 0.00 0.00 3.16
56 57 2.478335 GATGCCCCCGACCAAGACAA 62.478 60.000 0.00 0.00 0.00 3.18
57 58 2.933287 ATGCCCCCGACCAAGACA 60.933 61.111 0.00 0.00 0.00 3.41
58 59 2.124695 GATGCCCCCGACCAAGAC 60.125 66.667 0.00 0.00 0.00 3.01
59 60 2.285368 AGATGCCCCCGACCAAGA 60.285 61.111 0.00 0.00 0.00 3.02
60 61 2.190578 GAGATGCCCCCGACCAAG 59.809 66.667 0.00 0.00 0.00 3.61
61 62 3.407967 GGAGATGCCCCCGACCAA 61.408 66.667 0.00 0.00 0.00 3.67
62 63 4.414956 AGGAGATGCCCCCGACCA 62.415 66.667 0.00 0.00 37.37 4.02
63 64 3.551407 GAGGAGATGCCCCCGACC 61.551 72.222 0.00 0.00 37.37 4.79
64 65 3.551407 GGAGGAGATGCCCCCGAC 61.551 72.222 0.00 0.00 37.37 4.79
65 66 4.880426 GGGAGGAGATGCCCCCGA 62.880 72.222 0.00 0.00 37.39 5.14
70 71 0.695347 CAATAGGGGGAGGAGATGCC 59.305 60.000 0.00 0.00 39.11 4.40
71 72 0.695347 CCAATAGGGGGAGGAGATGC 59.305 60.000 0.00 0.00 0.00 3.91
72 73 1.981495 GACCAATAGGGGGAGGAGATG 59.019 57.143 0.00 0.00 42.91 2.90
73 74 1.483307 CGACCAATAGGGGGAGGAGAT 60.483 57.143 0.00 0.00 42.91 2.75
74 75 0.105658 CGACCAATAGGGGGAGGAGA 60.106 60.000 0.00 0.00 42.91 3.71
75 76 1.122019 CCGACCAATAGGGGGAGGAG 61.122 65.000 0.00 0.00 42.91 3.69
76 77 1.074775 CCGACCAATAGGGGGAGGA 60.075 63.158 0.00 0.00 42.91 3.71
77 78 2.819284 GCCGACCAATAGGGGGAGG 61.819 68.421 0.00 0.00 42.91 4.30
78 79 2.829592 GCCGACCAATAGGGGGAG 59.170 66.667 0.00 0.00 42.91 4.30
79 80 3.158648 CGCCGACCAATAGGGGGA 61.159 66.667 0.00 0.00 42.91 4.81
81 82 4.929707 GCCGCCGACCAATAGGGG 62.930 72.222 0.00 0.00 42.91 4.79
82 83 4.929707 GGCCGCCGACCAATAGGG 62.930 72.222 0.00 0.00 44.81 3.53
100 101 4.828925 GAGCTCTCCCGCTGCCAC 62.829 72.222 6.43 0.00 41.08 5.01
102 103 3.805891 GATGAGCTCTCCCGCTGCC 62.806 68.421 16.19 0.00 41.08 4.85
103 104 2.280052 GATGAGCTCTCCCGCTGC 60.280 66.667 16.19 0.00 41.08 5.25
104 105 2.027314 CGATGAGCTCTCCCGCTG 59.973 66.667 16.19 0.00 41.08 5.18
105 106 2.441164 ACGATGAGCTCTCCCGCT 60.441 61.111 16.19 4.27 44.33 5.52
106 107 2.279120 CACGATGAGCTCTCCCGC 60.279 66.667 16.19 0.00 0.00 6.13
107 108 2.343163 GACCACGATGAGCTCTCCCG 62.343 65.000 16.19 16.69 0.00 5.14
108 109 1.439644 GACCACGATGAGCTCTCCC 59.560 63.158 16.19 2.98 0.00 4.30
109 110 1.064946 CGACCACGATGAGCTCTCC 59.935 63.158 16.19 5.58 42.66 3.71
110 111 1.064946 CCGACCACGATGAGCTCTC 59.935 63.158 16.19 9.01 42.66 3.20
111 112 2.418910 CCCGACCACGATGAGCTCT 61.419 63.158 16.19 0.00 42.66 4.09
112 113 2.105128 CCCGACCACGATGAGCTC 59.895 66.667 6.82 6.82 42.66 4.09
113 114 3.461773 CCCCGACCACGATGAGCT 61.462 66.667 0.00 0.00 42.66 4.09
115 116 3.019003 AAGCCCCGACCACGATGAG 62.019 63.158 0.00 0.00 42.66 2.90
116 117 3.000819 AAGCCCCGACCACGATGA 61.001 61.111 0.00 0.00 42.66 2.92
117 118 2.819595 CAAGCCCCGACCACGATG 60.820 66.667 0.00 0.00 42.66 3.84
118 119 4.096003 CCAAGCCCCGACCACGAT 62.096 66.667 0.00 0.00 42.66 3.73
120 121 4.760047 CTCCAAGCCCCGACCACG 62.760 72.222 0.00 0.00 39.43 4.94
121 122 2.406002 TTTCTCCAAGCCCCGACCAC 62.406 60.000 0.00 0.00 0.00 4.16
122 123 2.124507 CTTTCTCCAAGCCCCGACCA 62.125 60.000 0.00 0.00 0.00 4.02
123 124 1.377333 CTTTCTCCAAGCCCCGACC 60.377 63.158 0.00 0.00 0.00 4.79
124 125 4.303257 CTTTCTCCAAGCCCCGAC 57.697 61.111 0.00 0.00 0.00 4.79
131 132 1.882623 GTCCAGTTGGCTTTCTCCAAG 59.117 52.381 0.00 0.00 45.90 3.61
132 133 1.813862 CGTCCAGTTGGCTTTCTCCAA 60.814 52.381 0.00 0.00 43.36 3.53
133 134 0.250295 CGTCCAGTTGGCTTTCTCCA 60.250 55.000 0.00 0.00 34.44 3.86
134 135 1.578206 GCGTCCAGTTGGCTTTCTCC 61.578 60.000 0.00 0.00 34.44 3.71
135 136 1.869690 GCGTCCAGTTGGCTTTCTC 59.130 57.895 0.00 0.00 34.44 2.87
136 137 1.961277 CGCGTCCAGTTGGCTTTCT 60.961 57.895 0.00 0.00 34.44 2.52
137 138 1.901650 CTCGCGTCCAGTTGGCTTTC 61.902 60.000 5.77 0.00 34.44 2.62
138 139 1.961277 CTCGCGTCCAGTTGGCTTT 60.961 57.895 5.77 0.00 34.44 3.51
139 140 2.357517 CTCGCGTCCAGTTGGCTT 60.358 61.111 5.77 0.00 34.44 4.35
142 143 1.781025 TTTTGCTCGCGTCCAGTTGG 61.781 55.000 5.77 0.00 0.00 3.77
143 144 0.384725 CTTTTGCTCGCGTCCAGTTG 60.385 55.000 5.77 0.00 0.00 3.16
144 145 1.507141 CCTTTTGCTCGCGTCCAGTT 61.507 55.000 5.77 0.00 0.00 3.16
145 146 1.961277 CCTTTTGCTCGCGTCCAGT 60.961 57.895 5.77 0.00 0.00 4.00
146 147 0.669318 TACCTTTTGCTCGCGTCCAG 60.669 55.000 5.77 0.00 0.00 3.86
147 148 0.947180 GTACCTTTTGCTCGCGTCCA 60.947 55.000 5.77 0.99 0.00 4.02
148 149 0.669625 AGTACCTTTTGCTCGCGTCC 60.670 55.000 5.77 0.00 0.00 4.79
149 150 1.136336 CAAGTACCTTTTGCTCGCGTC 60.136 52.381 5.77 0.00 0.00 5.19
150 151 0.865769 CAAGTACCTTTTGCTCGCGT 59.134 50.000 5.77 0.00 0.00 6.01
151 152 0.865769 ACAAGTACCTTTTGCTCGCG 59.134 50.000 0.00 0.00 0.00 5.87
152 153 3.042887 CAAACAAGTACCTTTTGCTCGC 58.957 45.455 0.00 0.00 0.00 5.03
153 154 4.287238 ACAAACAAGTACCTTTTGCTCG 57.713 40.909 10.03 0.00 34.22 5.03
154 155 6.253512 CAGAAACAAACAAGTACCTTTTGCTC 59.746 38.462 10.03 7.95 34.22 4.26
155 156 6.099341 CAGAAACAAACAAGTACCTTTTGCT 58.901 36.000 10.03 0.00 34.22 3.91
156 157 5.290885 CCAGAAACAAACAAGTACCTTTTGC 59.709 40.000 10.03 0.00 34.22 3.68
157 158 5.810074 CCCAGAAACAAACAAGTACCTTTTG 59.190 40.000 8.98 8.98 36.49 2.44
158 159 5.482526 ACCCAGAAACAAACAAGTACCTTTT 59.517 36.000 0.00 0.00 0.00 2.27
159 160 5.020795 ACCCAGAAACAAACAAGTACCTTT 58.979 37.500 0.00 0.00 0.00 3.11
160 161 4.401202 CACCCAGAAACAAACAAGTACCTT 59.599 41.667 0.00 0.00 0.00 3.50
161 162 3.951680 CACCCAGAAACAAACAAGTACCT 59.048 43.478 0.00 0.00 0.00 3.08
162 163 3.490249 GCACCCAGAAACAAACAAGTACC 60.490 47.826 0.00 0.00 0.00 3.34
163 164 3.702330 GCACCCAGAAACAAACAAGTAC 58.298 45.455 0.00 0.00 0.00 2.73
164 165 2.356382 CGCACCCAGAAACAAACAAGTA 59.644 45.455 0.00 0.00 0.00 2.24
165 166 1.134175 CGCACCCAGAAACAAACAAGT 59.866 47.619 0.00 0.00 0.00 3.16
166 167 1.134175 ACGCACCCAGAAACAAACAAG 59.866 47.619 0.00 0.00 0.00 3.16
167 168 1.133407 GACGCACCCAGAAACAAACAA 59.867 47.619 0.00 0.00 0.00 2.83
168 169 0.736053 GACGCACCCAGAAACAAACA 59.264 50.000 0.00 0.00 0.00 2.83
169 170 1.002792 GAGACGCACCCAGAAACAAAC 60.003 52.381 0.00 0.00 0.00 2.93
170 171 1.305201 GAGACGCACCCAGAAACAAA 58.695 50.000 0.00 0.00 0.00 2.83
171 172 0.878523 CGAGACGCACCCAGAAACAA 60.879 55.000 0.00 0.00 0.00 2.83
172 173 1.300620 CGAGACGCACCCAGAAACA 60.301 57.895 0.00 0.00 0.00 2.83
173 174 1.282930 GACGAGACGCACCCAGAAAC 61.283 60.000 0.00 0.00 0.00 2.78
174 175 1.006571 GACGAGACGCACCCAGAAA 60.007 57.895 0.00 0.00 0.00 2.52
175 176 1.863662 GAGACGAGACGCACCCAGAA 61.864 60.000 0.00 0.00 0.00 3.02
176 177 2.282251 AGACGAGACGCACCCAGA 60.282 61.111 0.00 0.00 0.00 3.86
177 178 2.179517 GAGACGAGACGCACCCAG 59.820 66.667 0.00 0.00 0.00 4.45
178 179 2.596338 TGAGACGAGACGCACCCA 60.596 61.111 0.00 0.00 0.00 4.51
179 180 2.126424 GTGAGACGAGACGCACCC 60.126 66.667 0.00 0.00 35.25 4.61
181 182 2.126424 GGGTGAGACGAGACGCAC 60.126 66.667 0.00 0.00 39.23 5.34
182 183 3.733960 CGGGTGAGACGAGACGCA 61.734 66.667 0.00 0.00 0.00 5.24
183 184 4.477975 CCGGGTGAGACGAGACGC 62.478 72.222 0.00 0.00 0.00 5.19
184 185 4.477975 GCCGGGTGAGACGAGACG 62.478 72.222 2.18 0.00 0.00 4.18
185 186 4.131088 GGCCGGGTGAGACGAGAC 62.131 72.222 2.18 0.00 0.00 3.36
224 225 3.756727 GTCAGACCCGACCCGACC 61.757 72.222 0.00 0.00 0.00 4.79
274 275 4.814294 GGACAAGTCGCGGCGGAT 62.814 66.667 23.46 8.55 0.00 4.18
288 289 1.283321 AGGAAAGGCAAGGATCAGGAC 59.717 52.381 0.00 0.00 0.00 3.85
302 303 4.566697 GGAAAGAGGAAGGAGGAAGGAAAG 60.567 50.000 0.00 0.00 0.00 2.62
412 416 0.179073 GATCTATGGCGCAGTGTGGT 60.179 55.000 10.83 0.00 0.00 4.16
499 503 7.206789 TGATACCTCCAAAATCAATGTCCTA 57.793 36.000 0.00 0.00 0.00 2.94
649 656 7.038302 TGTCCTTCTAATAAGAGGCAGAGAAAA 60.038 37.037 0.00 0.00 31.96 2.29
712 719 3.825328 ACACAAGTCCTCTTTGAGCAAT 58.175 40.909 0.00 0.00 0.00 3.56
714 721 4.415881 TTACACAAGTCCTCTTTGAGCA 57.584 40.909 0.00 0.00 0.00 4.26
717 724 4.349636 TGGGATTACACAAGTCCTCTTTGA 59.650 41.667 0.00 0.00 32.55 2.69
741 748 5.729229 TGGGAGGAGATGGTTAAAGTTGATA 59.271 40.000 0.00 0.00 0.00 2.15
743 750 3.913799 TGGGAGGAGATGGTTAAAGTTGA 59.086 43.478 0.00 0.00 0.00 3.18
1011 1019 2.019984 GATGCCTCAAATTCGAGCCTT 58.980 47.619 0.00 0.00 0.00 4.35
1056 1064 2.033602 GGGGTGCTGCGGTACTTT 59.966 61.111 13.75 0.00 0.00 2.66
1160 1168 6.911250 TGTGTGAGGACTATGTTAGAAAGA 57.089 37.500 0.00 0.00 0.00 2.52
1306 1324 6.756221 TCCCTCGGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
1309 1327 9.640963 CATACTCCCTCGGTAAAGAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
1324 1342 3.305199 GGATAAACCGACATACTCCCTCG 60.305 52.174 0.00 0.00 0.00 4.63
1359 1377 8.239038 TCAAAAGTAACACCCATCAATAAACA 57.761 30.769 0.00 0.00 0.00 2.83
1426 1445 7.496346 TCAGTACAGATATTCTCCCAAACTT 57.504 36.000 0.00 0.00 0.00 2.66
1567 1588 3.596046 AGTCAAGTAATTTGGGATGGGGA 59.404 43.478 0.00 0.00 37.39 4.81
1587 1608 7.304497 ACATCTGTTCTAGACAAACCTAAGT 57.696 36.000 0.00 0.00 38.49 2.24
1661 1682 3.460825 AGCCAAGTTAATACTCCCTCCA 58.539 45.455 0.00 0.00 31.99 3.86
1774 1797 4.617253 AACTAGCAGATGTTACCACACA 57.383 40.909 0.00 0.00 35.03 3.72
1960 1987 3.616956 TTGATACTGAGCCCTCAAGTG 57.383 47.619 0.00 0.00 39.39 3.16
2021 2048 2.180131 CTGGCAGCTGCGAAGTTGAC 62.180 60.000 31.19 9.15 43.26 3.18
2079 2106 3.624861 ACATCTTTCGAATGGCAGTCATC 59.375 43.478 15.84 0.00 34.44 2.92
2093 2120 4.201822 CGGCCTAAAGCTACAACATCTTTC 60.202 45.833 0.00 0.00 43.05 2.62
2287 2314 7.800847 GCACAAAAAGAAGCAAAACACTAAAAA 59.199 29.630 0.00 0.00 0.00 1.94
2759 2808 0.971386 TGAACGGAGGGAGTACAACC 59.029 55.000 0.00 0.00 0.00 3.77
2822 2871 4.972440 GTGTGCTTTTCACTCATTTCAGTC 59.028 41.667 0.00 0.00 45.81 3.51
2935 2984 2.002586 CACCCATTTCAGTACAGAGCG 58.997 52.381 0.00 0.00 0.00 5.03
3025 3075 9.679661 TGAAGAAATTTCCTAACATATAGCACA 57.320 29.630 14.61 0.00 0.00 4.57
3402 3480 4.036262 TGACCGTGTCTGAAAAATTGAAGG 59.964 41.667 5.77 0.00 33.15 3.46
3407 3485 4.202010 CCTGTTGACCGTGTCTGAAAAATT 60.202 41.667 5.77 0.00 33.15 1.82
3489 3570 9.677567 GTGAAGAAACAAAGTTCTATTTATGCA 57.322 29.630 0.00 0.00 36.84 3.96
3523 3604 7.907045 CAGTCATGCTATGTCTAAAACATTGTC 59.093 37.037 0.00 0.00 46.73 3.18
3670 3752 1.002888 AGCATATCATGAGAAGGGCGG 59.997 52.381 0.09 0.00 0.00 6.13
3671 3753 2.469274 AGCATATCATGAGAAGGGCG 57.531 50.000 0.09 0.00 0.00 6.13
3859 3944 9.507329 ACTCATTAATGCTAGAAAGAGAAACAA 57.493 29.630 10.76 0.00 0.00 2.83
4203 4291 6.408858 ACACATCAATGTAAGTAAGAAGCG 57.591 37.500 0.00 0.00 39.39 4.68
4284 4373 7.555554 CCTTTATCTCAGAATGTTCAGGTGAAT 59.444 37.037 0.00 0.00 36.33 2.57
4562 4753 7.844009 AGTGAATGTTTTTCGTAGTAGGGATA 58.156 34.615 0.00 0.00 0.00 2.59
4601 4792 5.308825 TCCTGGTTCTTTTCAGATCTTGTC 58.691 41.667 0.00 0.00 33.11 3.18
4640 5844 2.220837 TCCATATCCCATTCCCACCA 57.779 50.000 0.00 0.00 0.00 4.17
4696 5900 1.825474 TCATGTCGAGGAAGAAGGGTC 59.175 52.381 0.00 0.00 0.00 4.46
4835 6179 3.682766 AGCGATGGAAGCTGAGATG 57.317 52.632 0.00 0.00 44.22 2.90
4842 6186 0.933796 GAGTAAGCAGCGATGGAAGC 59.066 55.000 1.46 0.00 0.00 3.86
4904 6249 2.045131 GGCAAGGGAGCAGCTCAAG 61.045 63.158 24.09 10.91 35.83 3.02
5033 7873 2.182827 TCTTCATGCACCTAGAGCAGT 58.817 47.619 13.87 2.53 46.36 4.40
5056 7896 1.840650 CTCCGGAGCCATGGAGGAT 60.841 63.158 20.67 0.00 46.55 3.24


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

AutoCloner maintained by Alex Coulton.