Multiple sequence alignment - TraesCS1B01G055200

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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 TraesCS1B01G055200 chr1B 100.000 2919 0 0 1 2919 37798205 37801123 0.000000e+00 5391.0
1 TraesCS1B01G055200 chr1D 91.796 2121 81 46 193 2281 22438300 22436241 0.000000e+00 2867.0
2 TraesCS1B01G055200 chr1D 93.966 464 21 3 2459 2919 22436012 22435553 0.000000e+00 695.0
3 TraesCS1B01G055200 chr1A 88.350 2103 113 58 197 2255 23338829 23340843 0.000000e+00 2405.0
4 TraesCS1B01G055200 chr1A 88.654 520 30 14 2414 2916 23340908 23341415 8.950000e-170 606.0
5 TraesCS1B01G055200 chr4D 84.058 207 21 11 1249 1449 315597321 315597521 3.840000e-44 189.0
6 TraesCS1B01G055200 chr4B 83.575 207 22 11 1249 1449 393406268 393406468 1.790000e-42 183.0
7 TraesCS1B01G055200 chr4B 89.474 57 2 4 2172 2224 5725458 5725514 5.220000e-08 69.4
8 TraesCS1B01G055200 chr4A 83.575 207 22 11 1249 1449 159294855 159294655 1.790000e-42 183.0
9 TraesCS1B01G055200 chr4A 89.831 59 5 1 2167 2224 596478456 596478514 1.120000e-09 75.0
10 TraesCS1B01G055200 chr3B 82.353 204 36 0 1249 1452 829542126 829541923 8.310000e-41 178.0
11 TraesCS1B01G055200 chr3D 81.863 204 37 0 1249 1452 611919019 611918816 3.870000e-39 172.0
12 TraesCS1B01G055200 chr3D 89.286 112 9 3 2309 2417 349861477 349861588 1.410000e-28 137.0
13 TraesCS1B01G055200 chr2A 82.990 194 27 6 1259 1449 51008487 51008297 1.390000e-38 171.0
14 TraesCS1B01G055200 chr2A 89.583 48 5 0 1413 1460 572486407 572486360 8.730000e-06 62.1
15 TraesCS1B01G055200 chr2D 82.474 194 28 6 1259 1449 48133251 48133441 6.470000e-37 165.0
16 TraesCS1B01G055200 chr2D 79.679 187 32 5 1 185 203454382 203454200 2.360000e-26 130.0
17 TraesCS1B01G055200 chr2D 82.857 70 10 2 1383 1451 417626503 417626571 8.730000e-06 62.1
18 TraesCS1B01G055200 chr6D 90.179 112 10 1 2305 2415 390732677 390732566 8.430000e-31 145.0
19 TraesCS1B01G055200 chr6D 87.611 113 12 2 2305 2415 390481347 390481235 2.360000e-26 130.0
20 TraesCS1B01G055200 chr6D 86.726 113 13 2 2305 2415 390721196 390721084 1.100000e-24 124.0
21 TraesCS1B01G055200 chr6D 86.726 113 12 3 2305 2415 390489514 390489403 3.950000e-24 122.0
22 TraesCS1B01G055200 chr6D 91.228 57 5 0 1404 1460 292737726 292737670 8.670000e-11 78.7
23 TraesCS1B01G055200 chr7A 87.611 113 12 2 2305 2417 518503667 518503557 2.360000e-26 130.0
24 TraesCS1B01G055200 chr6A 87.156 109 12 1 2307 2415 536979783 536979677 3.950000e-24 122.0
25 TraesCS1B01G055200 chr6A 86.087 115 14 2 2303 2415 536996405 536996291 3.950000e-24 122.0
26 TraesCS1B01G055200 chr2B 86.726 113 12 2 2308 2419 231671475 231671585 3.950000e-24 122.0
27 TraesCS1B01G055200 chr2B 86.792 53 6 1 1413 1465 771043860 771043911 1.130000e-04 58.4
28 TraesCS1B01G055200 chr2B 81.429 70 11 2 1383 1451 489850336 489850404 4.060000e-04 56.5
29 TraesCS1B01G055200 chr7B 76.923 208 42 6 1259 1463 241107821 241108025 2.380000e-21 113.0
30 TraesCS1B01G055200 chr7B 88.608 79 8 1 5 82 465298579 465298657 8.610000e-16 95.3
31 TraesCS1B01G055200 chr6B 91.228 57 5 0 1404 1460 457216753 457216697 8.670000e-11 78.7


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 TraesCS1B01G055200 chr1B 37798205 37801123 2918 False 5391.0 5391 100.000 1 2919 1 chr1B.!!$F1 2918
1 TraesCS1B01G055200 chr1D 22435553 22438300 2747 True 1781.0 2867 92.881 193 2919 2 chr1D.!!$R1 2726
2 TraesCS1B01G055200 chr1A 23338829 23341415 2586 False 1505.5 2405 88.502 197 2916 2 chr1A.!!$F1 2719

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
779 801 0.03779 GTGCCACTCACTCTCTCACC 60.038 60.0 0.0 0.0 42.38 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 2870 1.13546 GGTCTGCGCGTATATCTACCC 60.135 57.143 8.43 0.0 0.0 3.69 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
30 31 4.990543 TCAACTGCTGAAACTTGATACG 57.009 40.909 0.00 0.00 0.00 3.06
31 32 4.627058 TCAACTGCTGAAACTTGATACGA 58.373 39.130 0.00 0.00 0.00 3.43
32 33 4.686091 TCAACTGCTGAAACTTGATACGAG 59.314 41.667 0.00 0.00 0.00 4.18
33 34 2.996621 ACTGCTGAAACTTGATACGAGC 59.003 45.455 0.00 0.00 0.00 5.03
34 35 1.992667 TGCTGAAACTTGATACGAGCG 59.007 47.619 0.00 0.00 0.00 5.03
35 36 2.259618 GCTGAAACTTGATACGAGCGA 58.740 47.619 0.00 0.00 0.00 4.93
36 37 2.666508 GCTGAAACTTGATACGAGCGAA 59.333 45.455 0.00 0.00 0.00 4.70
37 38 3.482112 GCTGAAACTTGATACGAGCGAAC 60.482 47.826 0.00 0.00 0.00 3.95
38 39 2.659757 TGAAACTTGATACGAGCGAACG 59.340 45.455 0.00 0.00 39.31 3.95
39 40 2.624316 AACTTGATACGAGCGAACGA 57.376 45.000 8.50 0.00 37.03 3.85
40 41 1.892468 ACTTGATACGAGCGAACGAC 58.108 50.000 8.50 1.60 37.03 4.34
41 42 1.198408 ACTTGATACGAGCGAACGACA 59.802 47.619 8.50 3.73 37.03 4.35
42 43 2.247637 CTTGATACGAGCGAACGACAA 58.752 47.619 8.50 9.65 37.03 3.18
43 44 2.334971 TGATACGAGCGAACGACAAA 57.665 45.000 8.50 0.00 37.03 2.83
44 45 2.663808 TGATACGAGCGAACGACAAAA 58.336 42.857 8.50 0.00 37.03 2.44
45 46 3.247442 TGATACGAGCGAACGACAAAAT 58.753 40.909 8.50 0.00 37.03 1.82
46 47 3.302434 TGATACGAGCGAACGACAAAATC 59.698 43.478 8.50 0.00 37.03 2.17
59 60 5.368552 CGACAAAATCGCAAGTTTCAAAA 57.631 34.783 0.00 0.00 45.52 2.44
60 61 5.780192 CGACAAAATCGCAAGTTTCAAAAA 58.220 33.333 0.00 0.00 45.52 1.94
61 62 5.666454 CGACAAAATCGCAAGTTTCAAAAAC 59.334 36.000 0.00 0.00 45.52 2.43
62 63 6.453659 CGACAAAATCGCAAGTTTCAAAAACT 60.454 34.615 0.00 0.00 45.52 2.66
63 64 6.533185 ACAAAATCGCAAGTTTCAAAAACTG 58.467 32.000 5.88 2.79 39.48 3.16
64 65 6.367422 ACAAAATCGCAAGTTTCAAAAACTGA 59.633 30.769 5.88 0.73 39.48 3.41
65 66 6.959671 AAATCGCAAGTTTCAAAAACTGAA 57.040 29.167 5.88 0.00 42.48 3.02
79 80 9.549078 TTCAAAAACTGAAACTAAAAACTTGGT 57.451 25.926 0.00 0.00 41.21 3.67
80 81 8.983724 TCAAAAACTGAAACTAAAAACTTGGTG 58.016 29.630 0.00 0.00 0.00 4.17
81 82 8.769891 CAAAAACTGAAACTAAAAACTTGGTGT 58.230 29.630 0.00 0.00 0.00 4.16
82 83 7.883229 AAACTGAAACTAAAAACTTGGTGTG 57.117 32.000 0.00 0.00 0.00 3.82
83 84 5.407502 ACTGAAACTAAAAACTTGGTGTGC 58.592 37.500 0.00 0.00 0.00 4.57
84 85 4.749976 TGAAACTAAAAACTTGGTGTGCC 58.250 39.130 0.00 0.00 0.00 5.01
85 86 4.464597 TGAAACTAAAAACTTGGTGTGCCT 59.535 37.500 0.00 0.00 35.27 4.75
86 87 5.046950 TGAAACTAAAAACTTGGTGTGCCTT 60.047 36.000 0.00 0.00 35.27 4.35
87 88 4.649088 ACTAAAAACTTGGTGTGCCTTC 57.351 40.909 0.00 0.00 35.27 3.46
88 89 2.979814 AAAAACTTGGTGTGCCTTCC 57.020 45.000 0.00 0.00 35.27 3.46
89 90 0.744281 AAAACTTGGTGTGCCTTCCG 59.256 50.000 0.00 0.00 35.27 4.30
90 91 1.734388 AAACTTGGTGTGCCTTCCGC 61.734 55.000 0.00 0.00 35.27 5.54
91 92 3.726517 CTTGGTGTGCCTTCCGCG 61.727 66.667 0.00 0.00 42.08 6.46
95 96 2.746277 GTGTGCCTTCCGCGGAAT 60.746 61.111 38.60 0.00 42.08 3.01
96 97 1.448893 GTGTGCCTTCCGCGGAATA 60.449 57.895 38.60 24.96 42.08 1.75
97 98 1.448893 TGTGCCTTCCGCGGAATAC 60.449 57.895 38.60 32.57 42.08 1.89
98 99 1.448893 GTGCCTTCCGCGGAATACA 60.449 57.895 38.60 33.13 42.08 2.29
99 100 1.022451 GTGCCTTCCGCGGAATACAA 61.022 55.000 38.60 22.16 42.08 2.41
100 101 1.022451 TGCCTTCCGCGGAATACAAC 61.022 55.000 38.60 24.93 42.08 3.32
101 102 2.003672 CCTTCCGCGGAATACAACG 58.996 57.895 38.60 25.42 33.28 4.10
102 103 0.458889 CCTTCCGCGGAATACAACGA 60.459 55.000 38.60 16.33 33.28 3.85
103 104 0.643820 CTTCCGCGGAATACAACGAC 59.356 55.000 38.60 0.00 33.28 4.34
104 105 0.244450 TTCCGCGGAATACAACGACT 59.756 50.000 35.81 0.00 0.00 4.18
105 106 0.244450 TCCGCGGAATACAACGACTT 59.756 50.000 28.99 0.00 0.00 3.01
106 107 1.073177 CCGCGGAATACAACGACTTT 58.927 50.000 24.07 0.00 0.00 2.66
107 108 1.201877 CCGCGGAATACAACGACTTTG 60.202 52.381 24.07 0.00 41.49 2.77
119 120 2.914379 GACTTTGTGGGTCGTGAGG 58.086 57.895 0.00 0.00 0.00 3.86
120 121 1.227853 ACTTTGTGGGTCGTGAGGC 60.228 57.895 0.00 0.00 0.00 4.70
121 122 1.227823 CTTTGTGGGTCGTGAGGCA 60.228 57.895 0.00 0.00 37.54 4.75
122 123 0.817634 CTTTGTGGGTCGTGAGGCAA 60.818 55.000 0.00 0.00 37.54 4.52
123 124 0.394488 TTTGTGGGTCGTGAGGCAAA 60.394 50.000 0.00 0.00 37.54 3.68
124 125 0.179004 TTGTGGGTCGTGAGGCAAAT 60.179 50.000 0.00 0.00 37.54 2.32
125 126 0.605319 TGTGGGTCGTGAGGCAAATC 60.605 55.000 0.00 0.00 37.54 2.17
126 127 1.375396 TGGGTCGTGAGGCAAATCG 60.375 57.895 0.00 0.00 37.54 3.34
127 128 2.106683 GGGTCGTGAGGCAAATCGG 61.107 63.158 0.00 0.00 37.54 4.18
128 129 2.106683 GGTCGTGAGGCAAATCGGG 61.107 63.158 0.00 0.00 37.54 5.14
129 130 2.435938 TCGTGAGGCAAATCGGGC 60.436 61.111 0.00 0.00 0.00 6.13
130 131 2.745884 CGTGAGGCAAATCGGGCA 60.746 61.111 0.00 0.00 35.46 5.36
131 132 2.753966 CGTGAGGCAAATCGGGCAG 61.754 63.158 0.00 0.00 35.46 4.85
132 133 1.377202 GTGAGGCAAATCGGGCAGA 60.377 57.895 0.00 0.00 35.46 4.26
133 134 1.377202 TGAGGCAAATCGGGCAGAC 60.377 57.895 0.00 0.00 35.46 3.51
134 135 2.436646 AGGCAAATCGGGCAGACG 60.437 61.111 0.00 0.00 35.46 4.18
135 136 3.508840 GGCAAATCGGGCAGACGG 61.509 66.667 0.00 0.00 0.00 4.79
136 137 2.435938 GCAAATCGGGCAGACGGA 60.436 61.111 0.00 0.00 0.00 4.69
137 138 2.750888 GCAAATCGGGCAGACGGAC 61.751 63.158 0.00 0.00 0.00 4.79
138 139 1.375396 CAAATCGGGCAGACGGACA 60.375 57.895 0.00 0.00 0.00 4.02
139 140 0.953471 CAAATCGGGCAGACGGACAA 60.953 55.000 0.00 0.00 0.00 3.18
140 141 0.673644 AAATCGGGCAGACGGACAAG 60.674 55.000 0.00 0.00 0.00 3.16
141 142 1.827399 AATCGGGCAGACGGACAAGT 61.827 55.000 0.00 0.00 0.00 3.16
142 143 1.827399 ATCGGGCAGACGGACAAGTT 61.827 55.000 0.00 0.00 0.00 2.66
143 144 1.597027 CGGGCAGACGGACAAGTTT 60.597 57.895 0.00 0.00 0.00 2.66
144 145 1.566018 CGGGCAGACGGACAAGTTTC 61.566 60.000 0.00 0.00 0.00 2.78
145 146 0.534203 GGGCAGACGGACAAGTTTCA 60.534 55.000 0.00 0.00 0.00 2.69
146 147 1.305201 GGCAGACGGACAAGTTTCAA 58.695 50.000 0.00 0.00 0.00 2.69
147 148 1.002792 GGCAGACGGACAAGTTTCAAC 60.003 52.381 0.00 0.00 0.00 3.18
148 149 1.940613 GCAGACGGACAAGTTTCAACT 59.059 47.619 0.00 0.00 42.04 3.16
149 150 3.128349 GCAGACGGACAAGTTTCAACTA 58.872 45.455 0.00 0.00 38.57 2.24
150 151 3.059800 GCAGACGGACAAGTTTCAACTAC 60.060 47.826 0.00 0.00 38.57 2.73
151 152 4.116961 CAGACGGACAAGTTTCAACTACA 58.883 43.478 0.00 0.00 38.57 2.74
152 153 4.569162 CAGACGGACAAGTTTCAACTACAA 59.431 41.667 0.00 0.00 38.57 2.41
153 154 5.064198 CAGACGGACAAGTTTCAACTACAAA 59.936 40.000 0.00 0.00 38.57 2.83
154 155 5.644636 AGACGGACAAGTTTCAACTACAAAA 59.355 36.000 0.00 0.00 38.57 2.44
155 156 6.149807 AGACGGACAAGTTTCAACTACAAAAA 59.850 34.615 0.00 0.00 38.57 1.94
156 157 6.088173 ACGGACAAGTTTCAACTACAAAAAC 58.912 36.000 0.00 0.00 38.57 2.43
157 158 6.072342 ACGGACAAGTTTCAACTACAAAAACT 60.072 34.615 0.00 0.00 43.22 2.66
159 160 7.327518 CGGACAAGTTTCAACTACAAAAACTTT 59.672 33.333 9.14 3.30 45.92 2.66
160 161 8.984764 GGACAAGTTTCAACTACAAAAACTTTT 58.015 29.630 9.14 4.50 45.92 2.27
172 173 9.896263 ACTACAAAAACTTTTTAGAAACAACGA 57.104 25.926 0.00 0.00 0.00 3.85
188 189 9.128107 AGAAACAACGATAAATTTAGCAACATG 57.872 29.630 13.48 8.26 0.00 3.21
189 190 6.869421 ACAACGATAAATTTAGCAACATGC 57.131 33.333 13.48 0.00 45.46 4.06
271 272 4.019174 TGGATGGCAAGAATCTCTTTTCC 58.981 43.478 0.00 0.00 33.78 3.13
420 421 2.009774 GCGGTTGTATCAGCTTGACAT 58.990 47.619 0.00 0.00 0.00 3.06
422 423 2.352651 CGGTTGTATCAGCTTGACATGG 59.647 50.000 0.00 0.00 0.00 3.66
425 426 3.979101 TGTATCAGCTTGACATGGTGA 57.021 42.857 21.17 21.17 44.37 4.02
450 451 3.971032 CCTGAAATTAGGTTCCATCGC 57.029 47.619 0.00 0.00 32.99 4.58
451 452 2.618709 CCTGAAATTAGGTTCCATCGCC 59.381 50.000 0.00 0.00 32.99 5.54
561 565 2.948386 GGTTTGAGACCTTGAGGCC 58.052 57.895 0.00 0.00 45.55 5.19
711 726 4.344865 ATCCACCACCACCGTGCC 62.345 66.667 0.00 0.00 38.79 5.01
777 799 0.178950 AGGTGCCACTCACTCTCTCA 60.179 55.000 0.00 0.00 44.98 3.27
779 801 0.037790 GTGCCACTCACTCTCTCACC 60.038 60.000 0.00 0.00 42.38 4.02
780 802 0.178950 TGCCACTCACTCTCTCACCT 60.179 55.000 0.00 0.00 0.00 4.00
781 803 0.972883 GCCACTCACTCTCTCACCTT 59.027 55.000 0.00 0.00 0.00 3.50
782 804 1.337635 GCCACTCACTCTCTCACCTTG 60.338 57.143 0.00 0.00 0.00 3.61
783 805 1.274728 CCACTCACTCTCTCACCTTGG 59.725 57.143 0.00 0.00 0.00 3.61
784 806 0.972883 ACTCACTCTCTCACCTTGGC 59.027 55.000 0.00 0.00 0.00 4.52
786 808 2.225142 ACTCACTCTCTCACCTTGGCTA 60.225 50.000 0.00 0.00 0.00 3.93
788 810 2.175202 CACTCTCTCACCTTGGCTAGT 58.825 52.381 0.00 0.00 0.00 2.57
789 811 3.010250 TCACTCTCTCACCTTGGCTAGTA 59.990 47.826 0.00 0.00 0.00 1.82
791 813 3.010808 ACTCTCTCACCTTGGCTAGTACT 59.989 47.826 0.00 0.00 0.00 2.73
793 815 5.103855 ACTCTCTCACCTTGGCTAGTACTAT 60.104 44.000 2.33 0.00 0.00 2.12
794 816 6.101442 ACTCTCTCACCTTGGCTAGTACTATA 59.899 42.308 2.33 0.00 0.00 1.31
911 958 6.502158 TCTTTCTCCTCTTTCTTCAGGGTAAT 59.498 38.462 0.00 0.00 0.00 1.89
912 959 6.704056 TTCTCCTCTTTCTTCAGGGTAATT 57.296 37.500 0.00 0.00 0.00 1.40
913 960 7.808279 TTCTCCTCTTTCTTCAGGGTAATTA 57.192 36.000 0.00 0.00 0.00 1.40
914 961 7.996758 TCTCCTCTTTCTTCAGGGTAATTAT 57.003 36.000 0.00 0.00 0.00 1.28
927 974 3.434596 GGGTAATTATTTGGCCGGAGTCT 60.435 47.826 5.05 0.00 0.00 3.24
940 987 2.282958 AGTCTGGGACGAAGCCGA 60.283 61.111 0.00 0.00 37.67 5.54
943 990 3.744719 CTGGGACGAAGCCGACGA 61.745 66.667 0.00 0.00 39.50 4.20
959 1006 3.751470 GACGAAGACGAAGACGCC 58.249 61.111 0.00 0.00 43.96 5.68
960 1007 1.081641 GACGAAGACGAAGACGCCA 60.082 57.895 0.00 0.00 43.96 5.69
961 1008 1.066114 GACGAAGACGAAGACGCCAG 61.066 60.000 0.00 0.00 43.96 4.85
986 1033 3.244353 GGAGGATCATCGGTTCATCACAT 60.244 47.826 0.56 0.00 36.25 3.21
1202 1249 3.879892 GGCCAGTCACCATTAATCTTCTC 59.120 47.826 0.00 0.00 0.00 2.87
1214 1261 6.554605 CCATTAATCTTCTCTCTTCTCCCTCT 59.445 42.308 0.00 0.00 0.00 3.69
1218 1265 3.053693 TCTTCTCTCTTCTCCCTCTCCTG 60.054 52.174 0.00 0.00 0.00 3.86
1483 1530 0.758123 CCCAGGAGGAGAAGATGCTC 59.242 60.000 0.00 0.00 45.25 4.26
1492 1539 1.663135 GAGAAGATGCTCGCCAAGAAC 59.337 52.381 0.00 0.00 0.00 3.01
1527 1586 4.816984 GTCCTCCTCCTCCGCCGA 62.817 72.222 0.00 0.00 0.00 5.54
1528 1587 4.816984 TCCTCCTCCTCCGCCGAC 62.817 72.222 0.00 0.00 0.00 4.79
1529 1588 4.824515 CCTCCTCCTCCGCCGACT 62.825 72.222 0.00 0.00 0.00 4.18
1782 1844 1.703014 ATGATGATGAGCTGGGGCGT 61.703 55.000 0.00 0.00 44.37 5.68
1834 1896 3.818787 GAGCCTTCGTCGCCGGTA 61.819 66.667 1.90 0.00 33.95 4.02
1986 2052 6.258947 GCTAGCTAGCTTAATTGCACTACTTT 59.741 38.462 33.71 0.00 45.62 2.66
1988 2054 6.846350 AGCTAGCTTAATTGCACTACTTTTG 58.154 36.000 12.68 0.00 34.99 2.44
1990 2056 7.606456 AGCTAGCTTAATTGCACTACTTTTGTA 59.394 33.333 12.68 0.00 34.99 2.41
1991 2057 8.398665 GCTAGCTTAATTGCACTACTTTTGTAT 58.601 33.333 7.70 0.00 32.97 2.29
2070 2136 8.331022 GTTGTGACATTATATTAGTGACAGCTG 58.669 37.037 13.48 13.48 31.42 4.24
2079 2149 1.683943 AGTGACAGCTGTTTGTGCAT 58.316 45.000 22.65 0.00 0.00 3.96
2081 2151 3.415212 AGTGACAGCTGTTTGTGCATAT 58.585 40.909 22.65 4.26 0.00 1.78
2082 2152 3.189910 AGTGACAGCTGTTTGTGCATATG 59.810 43.478 22.65 0.00 0.00 1.78
2092 2162 5.756849 TGTTTGTGCATATGTGTGTAAGTG 58.243 37.500 4.29 0.00 0.00 3.16
2095 2165 3.677596 TGTGCATATGTGTGTAAGTGACG 59.322 43.478 4.29 0.00 0.00 4.35
2097 2167 3.924073 TGCATATGTGTGTAAGTGACGAC 59.076 43.478 4.29 0.00 0.00 4.34
2106 2176 7.025365 TGTGTGTAAGTGACGACTTATCATAC 58.975 38.462 0.61 8.65 44.65 2.39
2119 2189 7.504238 ACGACTTATCATACTTCTGGAGAATCT 59.496 37.037 0.00 0.00 33.01 2.40
2120 2190 7.807433 CGACTTATCATACTTCTGGAGAATCTG 59.193 40.741 0.00 0.00 33.01 2.90
2157 2227 8.352201 TGAACTTGTCAAAATCAAAGATAGTGG 58.648 33.333 0.00 0.00 31.51 4.00
2160 2230 7.502226 ACTTGTCAAAATCAAAGATAGTGGACA 59.498 33.333 0.00 0.00 0.00 4.02
2161 2231 7.202016 TGTCAAAATCAAAGATAGTGGACAC 57.798 36.000 0.00 0.00 0.00 3.67
2167 2237 9.793259 AAAATCAAAGATAGTGGACACTAGAAA 57.207 29.630 16.33 0.00 45.94 2.52
2173 2243 7.354751 AGATAGTGGACACTAGAAATTCTCC 57.645 40.000 16.33 0.00 45.94 3.71
2242 2314 1.629043 AGTCAACTAGTTCTCCGGCA 58.371 50.000 4.77 0.00 0.00 5.69
2274 2346 3.608316 AGGAGAGAGATGCACAAAGTC 57.392 47.619 0.00 0.00 0.00 3.01
2277 2349 2.672381 GAGAGAGATGCACAAAGTCTGC 59.328 50.000 0.00 0.00 35.03 4.26
2281 2353 2.736721 GAGATGCACAAAGTCTGCGTTA 59.263 45.455 0.00 0.00 37.46 3.18
2283 2355 2.967459 TGCACAAAGTCTGCGTTATG 57.033 45.000 0.00 0.00 37.46 1.90
2342 2600 5.376854 AAAATGCTTGCACGAATCTTAGT 57.623 34.783 0.00 0.00 0.00 2.24
2343 2601 4.346734 AATGCTTGCACGAATCTTAGTG 57.653 40.909 0.00 0.00 41.01 2.74
2344 2602 2.766313 TGCTTGCACGAATCTTAGTGT 58.234 42.857 0.00 0.00 40.26 3.55
2345 2603 3.920446 TGCTTGCACGAATCTTAGTGTA 58.080 40.909 0.00 0.00 40.26 2.90
2346 2604 4.311606 TGCTTGCACGAATCTTAGTGTAA 58.688 39.130 0.00 6.55 39.83 2.41
2347 2605 4.752604 TGCTTGCACGAATCTTAGTGTAAA 59.247 37.500 7.75 2.50 41.10 2.01
2348 2606 5.237561 TGCTTGCACGAATCTTAGTGTAAAA 59.762 36.000 7.75 0.00 41.10 1.52
2349 2607 6.072728 TGCTTGCACGAATCTTAGTGTAAAAT 60.073 34.615 7.75 0.00 41.10 1.82
2350 2608 6.801862 GCTTGCACGAATCTTAGTGTAAAATT 59.198 34.615 7.75 0.00 41.10 1.82
2351 2609 7.960738 GCTTGCACGAATCTTAGTGTAAAATTA 59.039 33.333 7.75 0.00 41.10 1.40
2352 2610 9.820229 CTTGCACGAATCTTAGTGTAAAATTAA 57.180 29.630 7.75 0.00 41.10 1.40
2354 2612 9.767684 TGCACGAATCTTAGTGTAAAATTAATG 57.232 29.630 5.31 0.00 40.26 1.90
2355 2613 9.221775 GCACGAATCTTAGTGTAAAATTAATGG 57.778 33.333 5.31 0.00 40.26 3.16
2356 2614 9.221775 CACGAATCTTAGTGTAAAATTAATGGC 57.778 33.333 0.00 0.00 33.97 4.40
2357 2615 8.952278 ACGAATCTTAGTGTAAAATTAATGGCA 58.048 29.630 0.00 0.00 0.00 4.92
2358 2616 9.950680 CGAATCTTAGTGTAAAATTAATGGCAT 57.049 29.630 0.00 0.00 0.00 4.40
2364 2622 9.914834 TTAGTGTAAAATTAATGGCATAGGACT 57.085 29.630 0.00 0.00 0.00 3.85
2365 2623 8.823220 AGTGTAAAATTAATGGCATAGGACTT 57.177 30.769 0.00 0.00 0.00 3.01
2366 2624 9.914834 AGTGTAAAATTAATGGCATAGGACTTA 57.085 29.630 0.00 0.00 0.00 2.24
2371 2629 9.646522 AAAATTAATGGCATAGGACTTAGATGT 57.353 29.630 0.00 0.00 0.00 3.06
2372 2630 8.627208 AATTAATGGCATAGGACTTAGATGTG 57.373 34.615 0.00 0.00 0.00 3.21
2373 2631 3.475566 TGGCATAGGACTTAGATGTGC 57.524 47.619 0.00 0.00 0.00 4.57
2374 2632 2.771372 TGGCATAGGACTTAGATGTGCA 59.229 45.455 0.00 0.00 33.05 4.57
2375 2633 3.199727 TGGCATAGGACTTAGATGTGCAA 59.800 43.478 0.00 0.00 33.05 4.08
2376 2634 4.141413 TGGCATAGGACTTAGATGTGCAAT 60.141 41.667 0.00 0.00 33.05 3.56
2377 2635 5.071653 TGGCATAGGACTTAGATGTGCAATA 59.928 40.000 0.00 0.00 33.05 1.90
2378 2636 6.176183 GGCATAGGACTTAGATGTGCAATAT 58.824 40.000 0.00 0.00 33.05 1.28
2379 2637 6.656693 GGCATAGGACTTAGATGTGCAATATT 59.343 38.462 0.00 0.00 33.05 1.28
2380 2638 7.175641 GGCATAGGACTTAGATGTGCAATATTT 59.824 37.037 0.00 0.00 33.05 1.40
2381 2639 8.019669 GCATAGGACTTAGATGTGCAATATTTG 58.980 37.037 0.00 0.00 0.00 2.32
2382 2640 6.949352 AGGACTTAGATGTGCAATATTTGG 57.051 37.500 0.00 0.00 0.00 3.28
2383 2641 6.662755 AGGACTTAGATGTGCAATATTTGGA 58.337 36.000 0.00 0.00 0.00 3.53
2384 2642 7.118723 AGGACTTAGATGTGCAATATTTGGAA 58.881 34.615 0.00 0.00 30.97 3.53
2385 2643 7.067494 AGGACTTAGATGTGCAATATTTGGAAC 59.933 37.037 0.00 0.00 30.97 3.62
2386 2644 7.148086 GGACTTAGATGTGCAATATTTGGAACA 60.148 37.037 0.00 0.00 30.97 3.18
2387 2645 7.538575 ACTTAGATGTGCAATATTTGGAACAC 58.461 34.615 0.00 0.00 39.29 3.32
2388 2646 5.981088 AGATGTGCAATATTTGGAACACA 57.019 34.783 0.00 0.00 39.29 3.72
2391 2649 5.981088 TGTGCAATATTTGGAACACATCT 57.019 34.783 0.00 0.00 39.29 2.90
2392 2650 7.643569 ATGTGCAATATTTGGAACACATCTA 57.356 32.000 0.00 0.00 43.27 1.98
2393 2651 7.087409 TGTGCAATATTTGGAACACATCTAG 57.913 36.000 0.00 0.00 39.29 2.43
2394 2652 6.883756 TGTGCAATATTTGGAACACATCTAGA 59.116 34.615 0.00 0.00 39.29 2.43
2395 2653 7.557358 TGTGCAATATTTGGAACACATCTAGAT 59.443 33.333 0.00 0.00 39.29 1.98
2396 2654 9.056005 GTGCAATATTTGGAACACATCTAGATA 57.944 33.333 4.54 0.00 39.29 1.98
2397 2655 9.797642 TGCAATATTTGGAACACATCTAGATAT 57.202 29.630 4.54 0.00 39.29 1.63
2402 2660 8.757982 ATTTGGAACACATCTAGATATGCTTT 57.242 30.769 10.98 0.00 39.29 3.51
2403 2661 9.851686 ATTTGGAACACATCTAGATATGCTTTA 57.148 29.630 10.98 0.00 39.29 1.85
2404 2662 8.893219 TTGGAACACATCTAGATATGCTTTAG 57.107 34.615 10.98 0.00 39.29 1.85
2405 2663 6.931281 TGGAACACATCTAGATATGCTTTAGC 59.069 38.462 10.98 0.00 42.50 3.09
2454 2712 5.891810 TTTTTCTTTGTTTTATTCGCGGG 57.108 34.783 6.13 0.00 0.00 6.13
2455 2713 4.571372 TTTCTTTGTTTTATTCGCGGGT 57.429 36.364 6.13 0.00 0.00 5.28
2456 2714 3.546002 TCTTTGTTTTATTCGCGGGTG 57.454 42.857 6.13 0.00 0.00 4.61
2457 2715 2.879646 TCTTTGTTTTATTCGCGGGTGT 59.120 40.909 6.13 0.00 0.00 4.16
2596 2890 1.135460 GGGTAGATATACGCGCAGACC 60.135 57.143 5.73 4.09 0.00 3.85
2613 2907 6.039270 GCGCAGACCTATAGATATCATCTTCT 59.961 42.308 0.30 0.00 40.76 2.85
2687 2981 7.120138 GGAATCCATTTCTGAAAAATTGCATGT 59.880 33.333 6.95 0.00 34.56 3.21
2688 2982 6.788684 TCCATTTCTGAAAAATTGCATGTG 57.211 33.333 6.95 0.00 0.00 3.21
2689 2983 6.522946 TCCATTTCTGAAAAATTGCATGTGA 58.477 32.000 6.95 0.00 0.00 3.58
2690 2984 7.162761 TCCATTTCTGAAAAATTGCATGTGAT 58.837 30.769 6.95 0.00 0.00 3.06
2691 2985 7.332430 TCCATTTCTGAAAAATTGCATGTGATC 59.668 33.333 6.95 0.00 0.00 2.92
2756 3050 5.353678 ACTTGCTAGATCAAAAGATGCTCAC 59.646 40.000 1.04 0.00 0.00 3.51
2778 3072 2.689034 GGAGGCCAGCTGGTACCT 60.689 66.667 32.81 29.60 37.57 3.08
2802 3096 4.406456 TGGAATAGCAAGGAAGAAGCAAA 58.594 39.130 0.00 0.00 0.00 3.68
2908 3215 6.591935 TCAAATCCCATCTGATAACAGTACC 58.408 40.000 0.00 0.00 43.81 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.053811 TCGTATCAAGTTTCAGCAGTTGAA 58.946 37.500 0.00 0.00 43.92 2.69
9 10 4.627058 TCGTATCAAGTTTCAGCAGTTGA 58.373 39.130 0.00 0.00 39.81 3.18
10 11 4.667668 GCTCGTATCAAGTTTCAGCAGTTG 60.668 45.833 0.00 0.00 0.00 3.16
11 12 3.433615 GCTCGTATCAAGTTTCAGCAGTT 59.566 43.478 0.00 0.00 0.00 3.16
12 13 2.996621 GCTCGTATCAAGTTTCAGCAGT 59.003 45.455 0.00 0.00 0.00 4.40
13 14 2.028523 CGCTCGTATCAAGTTTCAGCAG 59.971 50.000 0.00 0.00 0.00 4.24
14 15 1.992667 CGCTCGTATCAAGTTTCAGCA 59.007 47.619 0.00 0.00 0.00 4.41
15 16 2.259618 TCGCTCGTATCAAGTTTCAGC 58.740 47.619 0.00 0.00 0.00 4.26
16 17 3.241364 CGTTCGCTCGTATCAAGTTTCAG 60.241 47.826 0.00 0.00 0.00 3.02
17 18 2.659757 CGTTCGCTCGTATCAAGTTTCA 59.340 45.455 0.00 0.00 0.00 2.69
18 19 2.912967 TCGTTCGCTCGTATCAAGTTTC 59.087 45.455 0.00 0.00 0.00 2.78
19 20 2.660236 GTCGTTCGCTCGTATCAAGTTT 59.340 45.455 0.00 0.00 0.00 2.66
20 21 2.248487 GTCGTTCGCTCGTATCAAGTT 58.752 47.619 0.00 0.00 0.00 2.66
21 22 1.198408 TGTCGTTCGCTCGTATCAAGT 59.802 47.619 0.00 0.00 0.00 3.16
22 23 1.891178 TGTCGTTCGCTCGTATCAAG 58.109 50.000 0.00 0.00 0.00 3.02
23 24 2.334971 TTGTCGTTCGCTCGTATCAA 57.665 45.000 0.00 0.00 0.00 2.57
24 25 2.334971 TTTGTCGTTCGCTCGTATCA 57.665 45.000 0.00 0.00 0.00 2.15
25 26 3.596454 CGATTTTGTCGTTCGCTCGTATC 60.596 47.826 0.00 0.00 45.19 2.24
26 27 2.278094 CGATTTTGTCGTTCGCTCGTAT 59.722 45.455 0.00 0.00 45.19 3.06
27 28 1.645265 CGATTTTGTCGTTCGCTCGTA 59.355 47.619 0.00 0.00 45.19 3.43
28 29 0.433492 CGATTTTGTCGTTCGCTCGT 59.567 50.000 0.00 0.00 45.19 4.18
29 30 3.168492 CGATTTTGTCGTTCGCTCG 57.832 52.632 0.00 0.00 45.19 5.03
38 39 6.678245 CAGTTTTTGAAACTTGCGATTTTGTC 59.322 34.615 3.46 0.00 0.00 3.18
39 40 6.367422 TCAGTTTTTGAAACTTGCGATTTTGT 59.633 30.769 3.46 0.00 31.34 2.83
40 41 6.760127 TCAGTTTTTGAAACTTGCGATTTTG 58.240 32.000 3.46 0.00 31.34 2.44
41 42 6.959671 TCAGTTTTTGAAACTTGCGATTTT 57.040 29.167 3.46 0.00 31.34 1.82
42 43 6.959671 TTCAGTTTTTGAAACTTGCGATTT 57.040 29.167 3.46 0.00 42.69 2.17
53 54 9.549078 ACCAAGTTTTTAGTTTCAGTTTTTGAA 57.451 25.926 0.00 0.00 43.92 2.69
54 55 8.983724 CACCAAGTTTTTAGTTTCAGTTTTTGA 58.016 29.630 0.00 0.00 0.00 2.69
55 56 8.769891 ACACCAAGTTTTTAGTTTCAGTTTTTG 58.230 29.630 0.00 0.00 0.00 2.44
56 57 8.769891 CACACCAAGTTTTTAGTTTCAGTTTTT 58.230 29.630 0.00 0.00 0.00 1.94
57 58 7.095397 GCACACCAAGTTTTTAGTTTCAGTTTT 60.095 33.333 0.00 0.00 0.00 2.43
58 59 6.367695 GCACACCAAGTTTTTAGTTTCAGTTT 59.632 34.615 0.00 0.00 0.00 2.66
59 60 5.867174 GCACACCAAGTTTTTAGTTTCAGTT 59.133 36.000 0.00 0.00 0.00 3.16
60 61 5.407502 GCACACCAAGTTTTTAGTTTCAGT 58.592 37.500 0.00 0.00 0.00 3.41
61 62 4.803613 GGCACACCAAGTTTTTAGTTTCAG 59.196 41.667 0.00 0.00 35.26 3.02
62 63 4.464597 AGGCACACCAAGTTTTTAGTTTCA 59.535 37.500 0.00 0.00 39.06 2.69
63 64 5.006153 AGGCACACCAAGTTTTTAGTTTC 57.994 39.130 0.00 0.00 39.06 2.78
64 65 5.414789 AAGGCACACCAAGTTTTTAGTTT 57.585 34.783 0.00 0.00 39.06 2.66
65 66 4.142026 GGAAGGCACACCAAGTTTTTAGTT 60.142 41.667 0.00 0.00 39.06 2.24
66 67 3.383505 GGAAGGCACACCAAGTTTTTAGT 59.616 43.478 0.00 0.00 39.06 2.24
67 68 3.550030 CGGAAGGCACACCAAGTTTTTAG 60.550 47.826 0.00 0.00 39.06 1.85
68 69 2.359531 CGGAAGGCACACCAAGTTTTTA 59.640 45.455 0.00 0.00 39.06 1.52
69 70 1.136110 CGGAAGGCACACCAAGTTTTT 59.864 47.619 0.00 0.00 39.06 1.94
70 71 0.744281 CGGAAGGCACACCAAGTTTT 59.256 50.000 0.00 0.00 39.06 2.43
71 72 1.734388 GCGGAAGGCACACCAAGTTT 61.734 55.000 0.00 0.00 42.87 2.66
72 73 2.193536 GCGGAAGGCACACCAAGTT 61.194 57.895 0.00 0.00 42.87 2.66
73 74 2.594592 GCGGAAGGCACACCAAGT 60.595 61.111 0.00 0.00 42.87 3.16
74 75 3.726517 CGCGGAAGGCACACCAAG 61.727 66.667 0.00 0.00 43.84 3.61
77 78 2.862674 TATTCCGCGGAAGGCACACC 62.863 60.000 40.09 0.00 43.84 4.16
78 79 1.448893 TATTCCGCGGAAGGCACAC 60.449 57.895 40.09 0.00 43.84 3.82
79 80 1.448893 GTATTCCGCGGAAGGCACA 60.449 57.895 40.09 21.50 43.84 4.57
80 81 1.022451 TTGTATTCCGCGGAAGGCAC 61.022 55.000 40.09 33.85 43.84 5.01
81 82 1.022451 GTTGTATTCCGCGGAAGGCA 61.022 55.000 40.09 34.87 43.84 4.75
82 83 1.719709 GTTGTATTCCGCGGAAGGC 59.280 57.895 40.09 33.04 37.56 4.35
83 84 0.458889 TCGTTGTATTCCGCGGAAGG 60.459 55.000 40.09 25.00 37.56 3.46
84 85 0.643820 GTCGTTGTATTCCGCGGAAG 59.356 55.000 40.09 27.20 37.56 3.46
85 86 0.244450 AGTCGTTGTATTCCGCGGAA 59.756 50.000 40.11 40.11 38.59 4.30
86 87 0.244450 AAGTCGTTGTATTCCGCGGA 59.756 50.000 27.28 27.28 0.00 5.54
87 88 1.073177 AAAGTCGTTGTATTCCGCGG 58.927 50.000 22.12 22.12 0.00 6.46
88 89 2.139336 CAAAGTCGTTGTATTCCGCG 57.861 50.000 0.00 0.00 32.08 6.46
101 102 1.228657 GCCTCACGACCCACAAAGTC 61.229 60.000 0.00 0.00 0.00 3.01
102 103 1.227853 GCCTCACGACCCACAAAGT 60.228 57.895 0.00 0.00 0.00 2.66
103 104 0.817634 TTGCCTCACGACCCACAAAG 60.818 55.000 0.00 0.00 0.00 2.77
104 105 0.394488 TTTGCCTCACGACCCACAAA 60.394 50.000 0.00 0.00 0.00 2.83
105 106 0.179004 ATTTGCCTCACGACCCACAA 60.179 50.000 0.00 0.00 0.00 3.33
106 107 0.605319 GATTTGCCTCACGACCCACA 60.605 55.000 0.00 0.00 0.00 4.17
107 108 1.635663 CGATTTGCCTCACGACCCAC 61.636 60.000 0.00 0.00 0.00 4.61
108 109 1.375396 CGATTTGCCTCACGACCCA 60.375 57.895 0.00 0.00 0.00 4.51
109 110 2.106683 CCGATTTGCCTCACGACCC 61.107 63.158 0.00 0.00 0.00 4.46
110 111 2.106683 CCCGATTTGCCTCACGACC 61.107 63.158 0.00 0.00 0.00 4.79
111 112 2.750888 GCCCGATTTGCCTCACGAC 61.751 63.158 0.00 0.00 0.00 4.34
112 113 2.435938 GCCCGATTTGCCTCACGA 60.436 61.111 0.00 0.00 0.00 4.35
113 114 2.745884 TGCCCGATTTGCCTCACG 60.746 61.111 0.00 0.00 0.00 4.35
114 115 1.377202 TCTGCCCGATTTGCCTCAC 60.377 57.895 0.00 0.00 0.00 3.51
115 116 1.377202 GTCTGCCCGATTTGCCTCA 60.377 57.895 0.00 0.00 0.00 3.86
116 117 2.464459 CGTCTGCCCGATTTGCCTC 61.464 63.158 0.00 0.00 0.00 4.70
117 118 2.436646 CGTCTGCCCGATTTGCCT 60.437 61.111 0.00 0.00 0.00 4.75
118 119 3.508840 CCGTCTGCCCGATTTGCC 61.509 66.667 0.00 0.00 0.00 4.52
119 120 2.435938 TCCGTCTGCCCGATTTGC 60.436 61.111 0.00 0.00 0.00 3.68
120 121 0.953471 TTGTCCGTCTGCCCGATTTG 60.953 55.000 0.00 0.00 0.00 2.32
121 122 0.673644 CTTGTCCGTCTGCCCGATTT 60.674 55.000 0.00 0.00 0.00 2.17
122 123 1.079127 CTTGTCCGTCTGCCCGATT 60.079 57.895 0.00 0.00 0.00 3.34
123 124 1.827399 AACTTGTCCGTCTGCCCGAT 61.827 55.000 0.00 0.00 0.00 4.18
124 125 2.035237 AAACTTGTCCGTCTGCCCGA 62.035 55.000 0.00 0.00 0.00 5.14
125 126 1.566018 GAAACTTGTCCGTCTGCCCG 61.566 60.000 0.00 0.00 0.00 6.13
126 127 0.534203 TGAAACTTGTCCGTCTGCCC 60.534 55.000 0.00 0.00 0.00 5.36
127 128 1.002792 GTTGAAACTTGTCCGTCTGCC 60.003 52.381 0.00 0.00 0.00 4.85
128 129 1.940613 AGTTGAAACTTGTCCGTCTGC 59.059 47.619 0.00 0.00 35.21 4.26
129 130 4.116961 TGTAGTTGAAACTTGTCCGTCTG 58.883 43.478 0.21 0.00 40.37 3.51
130 131 4.395959 TGTAGTTGAAACTTGTCCGTCT 57.604 40.909 0.21 0.00 40.37 4.18
131 132 5.473796 TTTGTAGTTGAAACTTGTCCGTC 57.526 39.130 0.21 0.00 40.37 4.79
132 133 5.883503 TTTTGTAGTTGAAACTTGTCCGT 57.116 34.783 0.21 0.00 40.37 4.69
133 134 6.319399 AGTTTTTGTAGTTGAAACTTGTCCG 58.681 36.000 0.21 0.00 39.79 4.79
134 135 8.528917 AAAGTTTTTGTAGTTGAAACTTGTCC 57.471 30.769 12.49 0.00 46.87 4.02
146 147 9.896263 TCGTTGTTTCTAAAAAGTTTTTGTAGT 57.104 25.926 21.25 0.00 0.00 2.73
162 163 9.128107 CATGTTGCTAAATTTATCGTTGTTTCT 57.872 29.630 0.00 0.00 0.00 2.52
163 164 7.892731 GCATGTTGCTAAATTTATCGTTGTTTC 59.107 33.333 0.00 0.00 40.96 2.78
164 165 7.728895 GCATGTTGCTAAATTTATCGTTGTTT 58.271 30.769 0.00 0.00 40.96 2.83
165 166 7.276953 GCATGTTGCTAAATTTATCGTTGTT 57.723 32.000 0.00 0.00 40.96 2.83
166 167 6.869421 GCATGTTGCTAAATTTATCGTTGT 57.131 33.333 0.00 0.00 40.96 3.32
271 272 6.844696 TTTGCTGAGCTAATAAATAGTCGG 57.155 37.500 5.83 0.00 33.87 4.79
450 451 4.034510 CCTCCTGATTCGATTTTTCTTCGG 59.965 45.833 0.00 0.00 37.22 4.30
451 452 4.494855 GCCTCCTGATTCGATTTTTCTTCG 60.495 45.833 0.00 0.00 37.94 3.79
601 609 2.758089 CCAGCTGCCTGTCAATCGC 61.758 63.158 8.66 0.00 37.38 4.58
657 672 1.879380 CCACTGATTGCAAGGACGAAA 59.121 47.619 4.94 0.00 0.00 3.46
711 726 2.436646 GCGGTGATGTCAGTGGGG 60.437 66.667 0.00 0.00 0.00 4.96
777 799 6.716173 GCTAAGAGTATAGTACTAGCCAAGGT 59.284 42.308 8.85 0.00 39.59 3.50
779 801 7.881232 AGAGCTAAGAGTATAGTACTAGCCAAG 59.119 40.741 8.85 1.32 38.20 3.61
780 802 7.747690 AGAGCTAAGAGTATAGTACTAGCCAA 58.252 38.462 8.85 0.00 38.20 4.52
781 803 7.319052 AGAGCTAAGAGTATAGTACTAGCCA 57.681 40.000 8.85 0.00 38.20 4.75
793 815 8.776119 ACCGGGTTATATATAGAGCTAAGAGTA 58.224 37.037 6.32 0.00 0.00 2.59
794 816 7.556996 CACCGGGTTATATATAGAGCTAAGAGT 59.443 40.741 6.32 0.00 0.00 3.24
911 958 0.254747 CCCAGACTCCGGCCAAATAA 59.745 55.000 2.24 0.00 0.00 1.40
912 959 0.619255 TCCCAGACTCCGGCCAAATA 60.619 55.000 2.24 0.00 0.00 1.40
913 960 1.923395 TCCCAGACTCCGGCCAAAT 60.923 57.895 2.24 0.00 0.00 2.32
914 961 2.528127 TCCCAGACTCCGGCCAAA 60.528 61.111 2.24 0.00 0.00 3.28
927 974 4.047059 GTCGTCGGCTTCGTCCCA 62.047 66.667 0.00 0.00 35.06 4.37
940 987 1.440023 GCGTCTTCGTCTTCGTCGT 60.440 57.895 0.00 0.00 39.49 4.34
943 990 1.081376 CTGGCGTCTTCGTCTTCGT 60.081 57.895 0.00 0.00 42.59 3.85
951 998 1.045911 ATCCTCCTCCTGGCGTCTTC 61.046 60.000 0.00 0.00 0.00 2.87
952 999 1.002274 ATCCTCCTCCTGGCGTCTT 59.998 57.895 0.00 0.00 0.00 3.01
953 1000 1.456705 GATCCTCCTCCTGGCGTCT 60.457 63.158 0.00 0.00 0.00 4.18
954 1001 1.118356 ATGATCCTCCTCCTGGCGTC 61.118 60.000 0.00 0.00 0.00 5.19
956 1003 1.670590 GATGATCCTCCTCCTGGCG 59.329 63.158 0.00 0.00 0.00 5.69
957 1004 1.670590 CGATGATCCTCCTCCTGGC 59.329 63.158 0.00 0.00 0.00 4.85
958 1005 0.470833 ACCGATGATCCTCCTCCTGG 60.471 60.000 0.00 0.00 0.00 4.45
959 1006 1.342819 GAACCGATGATCCTCCTCCTG 59.657 57.143 0.00 0.00 0.00 3.86
960 1007 1.062886 TGAACCGATGATCCTCCTCCT 60.063 52.381 0.00 0.00 0.00 3.69
961 1008 1.414158 TGAACCGATGATCCTCCTCC 58.586 55.000 0.00 0.00 0.00 4.30
975 1022 4.302455 CTGGTCGATCTATGTGATGAACC 58.698 47.826 0.00 0.00 37.10 3.62
986 1033 1.485124 ACACATGGCTGGTCGATCTA 58.515 50.000 0.00 0.00 0.00 1.98
1202 1249 1.402787 GAGCAGGAGAGGGAGAAGAG 58.597 60.000 0.00 0.00 0.00 2.85
1214 1261 4.373116 GAACACGCCGGAGCAGGA 62.373 66.667 5.05 0.00 39.83 3.86
1345 1392 1.828768 GTGGAGGCTGAGGATGAGG 59.171 63.158 0.00 0.00 0.00 3.86
1381 1428 2.503061 CTGGCGATCCTGGACCAG 59.497 66.667 15.15 15.15 43.45 4.00
1492 1539 4.168291 GGCGAGGAGGAGGCCTTG 62.168 72.222 6.77 0.00 43.52 3.61
1510 1569 4.816984 TCGGCGGAGGAGGAGGAC 62.817 72.222 7.21 0.00 0.00 3.85
1526 1585 4.053067 CGTAAGCGACGTGGAGTC 57.947 61.111 0.11 0.00 46.86 3.36
1540 1599 2.733671 CGAGCAGGTCGTCGTCGTA 61.734 63.158 14.02 0.00 44.20 3.43
1624 1683 2.887568 GCCTCGTCGTCCATGCTG 60.888 66.667 0.00 0.00 0.00 4.41
1706 1768 2.268920 CTGGTCCATGTCCACGGG 59.731 66.667 0.00 0.00 0.00 5.28
1753 1815 2.353208 GCTCATCATCATCTCCGGGTAC 60.353 54.545 0.00 0.00 0.00 3.34
1834 1896 1.207791 AATCCTCGCAGAACTCCCAT 58.792 50.000 0.00 0.00 34.09 4.00
1998 2064 9.816354 ACATGCATGCACGAATTAGTATATATA 57.184 29.630 25.37 0.00 0.00 0.86
1999 2065 8.722480 ACATGCATGCACGAATTAGTATATAT 57.278 30.769 25.37 0.00 0.00 0.86
2012 2078 8.947304 TTTACATATAATTACATGCATGCACG 57.053 30.769 25.37 19.13 0.00 5.34
2051 2117 7.641411 GCACAAACAGCTGTCACTAATATAATG 59.359 37.037 21.95 5.06 0.00 1.90
2070 2136 5.851177 GTCACTTACACACATATGCACAAAC 59.149 40.000 1.58 0.00 0.00 2.93
2079 2149 7.148355 TGATAAGTCGTCACTTACACACATA 57.852 36.000 0.00 0.00 45.90 2.29
2081 2151 5.441709 TGATAAGTCGTCACTTACACACA 57.558 39.130 0.00 0.00 45.90 3.72
2082 2152 7.249147 AGTATGATAAGTCGTCACTTACACAC 58.751 38.462 0.00 1.32 45.90 3.82
2092 2162 6.621316 TCTCCAGAAGTATGATAAGTCGTC 57.379 41.667 0.00 0.00 0.00 4.20
2095 2165 8.637986 ACAGATTCTCCAGAAGTATGATAAGTC 58.362 37.037 0.00 0.00 37.48 3.01
2097 2167 8.420222 ACACAGATTCTCCAGAAGTATGATAAG 58.580 37.037 0.00 0.00 37.48 1.73
2106 2176 3.405831 TGCAACACAGATTCTCCAGAAG 58.594 45.455 0.00 0.00 37.48 2.85
2119 2189 4.814147 TGACAAGTTCATTTTGCAACACA 58.186 34.783 0.00 0.00 0.00 3.72
2120 2190 5.776519 TTGACAAGTTCATTTTGCAACAC 57.223 34.783 0.00 0.00 32.84 3.32
2157 2227 5.337578 AGCAGAGGAGAATTTCTAGTGTC 57.662 43.478 0.00 0.00 0.00 3.67
2167 2237 8.370940 TCATCGATTAATTAAGCAGAGGAGAAT 58.629 33.333 13.48 0.00 0.00 2.40
2173 2243 7.936950 TGTCTCATCGATTAATTAAGCAGAG 57.063 36.000 13.48 14.80 0.00 3.35
2242 2314 7.014518 GTGCATCTCTCTCCTATATATGCAGAT 59.985 40.741 7.28 0.00 46.16 2.90
2274 2346 6.616947 TCTTTGGATTTAAACCATAACGCAG 58.383 36.000 9.41 2.66 37.26 5.18
2277 2349 7.985634 CCATCTTTGGATTTAAACCATAACG 57.014 36.000 9.41 0.00 46.92 3.18
2319 2577 5.630680 CACTAAGATTCGTGCAAGCATTTTT 59.369 36.000 0.00 0.00 0.00 1.94
2320 2578 5.156355 CACTAAGATTCGTGCAAGCATTTT 58.844 37.500 0.00 0.00 0.00 1.82
2321 2579 4.216257 ACACTAAGATTCGTGCAAGCATTT 59.784 37.500 0.00 0.00 34.58 2.32
2322 2580 3.753272 ACACTAAGATTCGTGCAAGCATT 59.247 39.130 0.00 0.00 34.58 3.56
2323 2581 3.338249 ACACTAAGATTCGTGCAAGCAT 58.662 40.909 0.00 0.00 34.58 3.79
2324 2582 2.766313 ACACTAAGATTCGTGCAAGCA 58.234 42.857 0.00 0.00 34.58 3.91
2325 2583 4.921470 TTACACTAAGATTCGTGCAAGC 57.079 40.909 0.00 0.00 34.58 4.01
2326 2584 9.820229 TTAATTTTACACTAAGATTCGTGCAAG 57.180 29.630 0.00 0.00 34.58 4.01
2328 2586 9.767684 CATTAATTTTACACTAAGATTCGTGCA 57.232 29.630 0.00 0.00 34.58 4.57
2329 2587 9.221775 CCATTAATTTTACACTAAGATTCGTGC 57.778 33.333 0.00 0.00 34.58 5.34
2330 2588 9.221775 GCCATTAATTTTACACTAAGATTCGTG 57.778 33.333 0.00 0.00 37.18 4.35
2331 2589 8.952278 TGCCATTAATTTTACACTAAGATTCGT 58.048 29.630 0.00 0.00 0.00 3.85
2332 2590 9.950680 ATGCCATTAATTTTACACTAAGATTCG 57.049 29.630 0.00 0.00 0.00 3.34
2338 2596 9.914834 AGTCCTATGCCATTAATTTTACACTAA 57.085 29.630 0.00 0.00 0.00 2.24
2339 2597 9.914834 AAGTCCTATGCCATTAATTTTACACTA 57.085 29.630 0.00 0.00 0.00 2.74
2340 2598 8.823220 AAGTCCTATGCCATTAATTTTACACT 57.177 30.769 0.00 0.00 0.00 3.55
2345 2603 9.646522 ACATCTAAGTCCTATGCCATTAATTTT 57.353 29.630 0.00 0.00 0.00 1.82
2346 2604 9.071276 CACATCTAAGTCCTATGCCATTAATTT 57.929 33.333 0.00 0.00 0.00 1.82
2347 2605 7.175641 GCACATCTAAGTCCTATGCCATTAATT 59.824 37.037 0.00 0.00 0.00 1.40
2348 2606 6.656693 GCACATCTAAGTCCTATGCCATTAAT 59.343 38.462 0.00 0.00 0.00 1.40
2349 2607 5.997746 GCACATCTAAGTCCTATGCCATTAA 59.002 40.000 0.00 0.00 0.00 1.40
2350 2608 5.071653 TGCACATCTAAGTCCTATGCCATTA 59.928 40.000 0.00 0.00 0.00 1.90
2351 2609 4.141413 TGCACATCTAAGTCCTATGCCATT 60.141 41.667 0.00 0.00 0.00 3.16
2352 2610 3.392285 TGCACATCTAAGTCCTATGCCAT 59.608 43.478 0.00 0.00 0.00 4.40
2353 2611 2.771372 TGCACATCTAAGTCCTATGCCA 59.229 45.455 0.00 0.00 0.00 4.92
2354 2612 3.475566 TGCACATCTAAGTCCTATGCC 57.524 47.619 0.00 0.00 0.00 4.40
2355 2613 7.678947 AATATTGCACATCTAAGTCCTATGC 57.321 36.000 0.00 0.00 0.00 3.14
2356 2614 8.509690 CCAAATATTGCACATCTAAGTCCTATG 58.490 37.037 0.00 0.00 0.00 2.23
2357 2615 8.439971 TCCAAATATTGCACATCTAAGTCCTAT 58.560 33.333 0.00 0.00 0.00 2.57
2358 2616 7.801104 TCCAAATATTGCACATCTAAGTCCTA 58.199 34.615 0.00 0.00 0.00 2.94
2359 2617 6.662755 TCCAAATATTGCACATCTAAGTCCT 58.337 36.000 0.00 0.00 0.00 3.85
2360 2618 6.942532 TCCAAATATTGCACATCTAAGTCC 57.057 37.500 0.00 0.00 0.00 3.85
2361 2619 7.698130 GTGTTCCAAATATTGCACATCTAAGTC 59.302 37.037 0.00 0.00 0.00 3.01
2362 2620 7.176515 TGTGTTCCAAATATTGCACATCTAAGT 59.823 33.333 0.00 0.00 32.79 2.24
2363 2621 7.537715 TGTGTTCCAAATATTGCACATCTAAG 58.462 34.615 0.00 0.00 32.79 2.18
2364 2622 7.459795 TGTGTTCCAAATATTGCACATCTAA 57.540 32.000 0.00 0.00 32.79 2.10
2365 2623 7.643569 ATGTGTTCCAAATATTGCACATCTA 57.356 32.000 12.75 0.00 41.81 1.98
2366 2624 5.981088 TGTGTTCCAAATATTGCACATCT 57.019 34.783 0.00 0.00 32.79 2.90
2368 2626 6.534475 AGATGTGTTCCAAATATTGCACAT 57.466 33.333 15.93 15.93 46.19 3.21
2369 2627 5.981088 AGATGTGTTCCAAATATTGCACA 57.019 34.783 0.00 0.00 40.42 4.57
2370 2628 7.320443 TCTAGATGTGTTCCAAATATTGCAC 57.680 36.000 0.00 0.00 0.00 4.57
2371 2629 9.797642 ATATCTAGATGTGTTCCAAATATTGCA 57.202 29.630 15.79 0.00 0.00 4.08
2376 2634 9.851686 AAAGCATATCTAGATGTGTTCCAAATA 57.148 29.630 25.01 0.00 33.21 1.40
2377 2635 8.757982 AAAGCATATCTAGATGTGTTCCAAAT 57.242 30.769 25.01 6.51 33.21 2.32
2378 2636 9.330063 CTAAAGCATATCTAGATGTGTTCCAAA 57.670 33.333 25.01 9.87 33.21 3.28
2379 2637 7.442364 GCTAAAGCATATCTAGATGTGTTCCAA 59.558 37.037 25.01 11.23 41.59 3.53
2380 2638 6.931281 GCTAAAGCATATCTAGATGTGTTCCA 59.069 38.462 25.01 12.89 41.59 3.53
2381 2639 7.357951 GCTAAAGCATATCTAGATGTGTTCC 57.642 40.000 25.01 12.53 41.59 3.62
2428 2686 8.652463 CCCGCGAATAAAACAAAGAAAAATATT 58.348 29.630 8.23 0.00 0.00 1.28
2429 2687 7.815549 ACCCGCGAATAAAACAAAGAAAAATAT 59.184 29.630 8.23 0.00 0.00 1.28
2430 2688 7.115095 CACCCGCGAATAAAACAAAGAAAAATA 59.885 33.333 8.23 0.00 0.00 1.40
2431 2689 5.986741 ACCCGCGAATAAAACAAAGAAAAAT 59.013 32.000 8.23 0.00 0.00 1.82
2432 2690 5.232414 CACCCGCGAATAAAACAAAGAAAAA 59.768 36.000 8.23 0.00 0.00 1.94
2433 2691 4.740695 CACCCGCGAATAAAACAAAGAAAA 59.259 37.500 8.23 0.00 0.00 2.29
2434 2692 4.202030 ACACCCGCGAATAAAACAAAGAAA 60.202 37.500 8.23 0.00 0.00 2.52
2435 2693 3.315749 ACACCCGCGAATAAAACAAAGAA 59.684 39.130 8.23 0.00 0.00 2.52
2436 2694 2.879646 ACACCCGCGAATAAAACAAAGA 59.120 40.909 8.23 0.00 0.00 2.52
2437 2695 3.276882 ACACCCGCGAATAAAACAAAG 57.723 42.857 8.23 0.00 0.00 2.77
2438 2696 3.712091 AACACCCGCGAATAAAACAAA 57.288 38.095 8.23 0.00 0.00 2.83
2439 2697 3.562973 TGTAACACCCGCGAATAAAACAA 59.437 39.130 8.23 0.00 0.00 2.83
2440 2698 3.059051 GTGTAACACCCGCGAATAAAACA 60.059 43.478 8.23 2.04 36.32 2.83
2441 2699 3.059051 TGTGTAACACCCGCGAATAAAAC 60.059 43.478 8.23 0.00 45.67 2.43
2442 2700 3.136763 TGTGTAACACCCGCGAATAAAA 58.863 40.909 8.23 0.00 45.67 1.52
2443 2701 2.763933 TGTGTAACACCCGCGAATAAA 58.236 42.857 8.23 0.00 45.67 1.40
2444 2702 2.452295 TGTGTAACACCCGCGAATAA 57.548 45.000 8.23 0.00 45.67 1.40
2456 2714 9.872757 TTCTCTCGAAAATTATTTGTGTGTAAC 57.127 29.630 0.00 0.00 37.35 2.50
2457 2715 9.872757 GTTCTCTCGAAAATTATTTGTGTGTAA 57.127 29.630 0.00 0.00 0.00 2.41
2477 2735 9.965902 ACAGGTTGAATAAATATCAAGTTCTCT 57.034 29.630 0.00 0.00 37.46 3.10
2502 2793 6.790336 AAAATGCGCGAATATTTCTTGTAC 57.210 33.333 12.10 0.00 0.00 2.90
2576 2870 1.135460 GGTCTGCGCGTATATCTACCC 60.135 57.143 8.43 0.00 0.00 3.69
2634 2928 2.631062 ACTCGTGTGTTGGTATCTTGGA 59.369 45.455 0.00 0.00 0.00 3.53
2687 2981 4.323028 GGGCTCTATCATTGGATTCGATCA 60.323 45.833 0.00 0.00 34.89 2.92
2688 2982 4.081198 AGGGCTCTATCATTGGATTCGATC 60.081 45.833 0.00 0.00 34.89 3.69
2689 2983 3.843027 AGGGCTCTATCATTGGATTCGAT 59.157 43.478 0.00 0.00 34.89 3.59
2690 2984 3.242867 AGGGCTCTATCATTGGATTCGA 58.757 45.455 0.00 0.00 34.89 3.71
2691 2985 3.692257 AGGGCTCTATCATTGGATTCG 57.308 47.619 0.00 0.00 34.89 3.34
2756 3050 1.340399 TACCAGCTGGCCTCCTGATG 61.340 60.000 33.06 5.14 38.33 3.07
2778 3072 5.372343 TGCTTCTTCCTTGCTATTCCATA 57.628 39.130 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.