Multiple sequence alignment - TraesCS5B01G364500

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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 TraesCS5B01G364500 chr5B 100.000 4819 0 0 1 4819 543247338 543242520 0.000000e+00 8900.0
1 TraesCS5B01G364500 chr5B 84.923 650 89 5 2373 3016 543298640 543297994 0.000000e+00 649.0
2 TraesCS5B01G364500 chr5B 83.771 647 103 2 2373 3018 531193753 531194398 3.190000e-171 612.0
3 TraesCS5B01G364500 chr5B 84.142 618 80 8 1016 1627 543282493 543281888 2.500000e-162 582.0
4 TraesCS5B01G364500 chr5B 82.047 596 88 14 1010 1600 543275902 543275321 1.560000e-134 490.0
5 TraesCS5B01G364500 chr5B 88.346 266 25 5 3254 3514 543297681 543297417 1.010000e-81 315.0
6 TraesCS5B01G364500 chr5B 77.707 471 82 13 3095 3552 531194625 531195085 2.860000e-67 267.0
7 TraesCS5B01G364500 chr5B 84.211 266 38 3 3246 3507 543270125 543269860 6.190000e-64 255.0
8 TraesCS5B01G364500 chr5B 89.000 100 11 0 2186 2285 531205826 531205925 1.820000e-24 124.0
9 TraesCS5B01G364500 chr5B 88.660 97 11 0 2178 2274 543281415 543281319 8.470000e-23 119.0
10 TraesCS5B01G364500 chr5B 79.720 143 24 5 1954 2094 543281663 543281524 1.100000e-16 99.0
11 TraesCS5B01G364500 chr5D 96.448 3998 103 11 838 4817 445405895 445401919 0.000000e+00 6560.0
12 TraesCS5B01G364500 chr5D 89.153 590 34 16 206 776 445406613 445406035 0.000000e+00 708.0
13 TraesCS5B01G364500 chr5D 84.568 648 91 3 2375 3016 445490906 445490262 6.800000e-178 634.0
14 TraesCS5B01G364500 chr5D 84.091 352 42 10 3172 3514 445489986 445489640 1.290000e-85 327.0
15 TraesCS5B01G364500 chr5D 76.829 492 91 13 3074 3552 436983203 436983684 6.190000e-64 255.0
16 TraesCS5B01G364500 chr5D 88.889 207 18 3 1 207 483581576 483581777 2.880000e-62 250.0
17 TraesCS5B01G364500 chr5A 96.135 3312 86 10 838 4126 563256575 563253283 0.000000e+00 5369.0
18 TraesCS5B01G364500 chr5A 89.848 591 30 13 201 776 563257290 563256715 0.000000e+00 732.0
19 TraesCS5B01G364500 chr5A 84.304 618 97 0 2373 2990 552268803 552269420 5.330000e-169 604.0
20 TraesCS5B01G364500 chr5A 78.935 826 152 13 1001 1824 552267413 552268218 4.240000e-150 542.0
21 TraesCS5B01G364500 chr4D 81.731 832 106 35 3061 3877 2975631 2976431 0.000000e+00 652.0
22 TraesCS5B01G364500 chr4D 84.825 514 68 6 2470 2977 2975080 2975589 4.300000e-140 508.0
23 TraesCS5B01G364500 chr4D 80.000 420 78 4 3072 3485 1689482 1689901 6.060000e-79 305.0
24 TraesCS5B01G364500 chr1D 81.546 802 136 11 2358 3150 410458693 410457895 0.000000e+00 651.0
25 TraesCS5B01G364500 chr1D 91.371 197 11 4 1 197 424931772 424931962 1.030000e-66 265.0
26 TraesCS5B01G364500 chr1D 88.995 209 17 4 1 208 463250099 463249896 2.230000e-63 254.0
27 TraesCS5B01G364500 chr7A 83.173 624 90 9 1001 1624 7817259 7817867 1.520000e-154 556.0
28 TraesCS5B01G364500 chr7A 90.411 73 7 0 2189 2261 7818561 7818633 3.970000e-16 97.1
29 TraesCS5B01G364500 chr1B 82.390 636 110 2 2358 2992 553014263 553013629 1.960000e-153 553.0
30 TraesCS5B01G364500 chr2D 91.045 201 13 3 1 201 629577375 629577570 2.860000e-67 267.0
31 TraesCS5B01G364500 chr4A 90.547 201 14 3 1 201 573658487 573658292 1.330000e-65 261.0
32 TraesCS5B01G364500 chr3D 90.196 204 14 4 1 203 612019878 612020076 1.330000e-65 261.0
33 TraesCS5B01G364500 chr3B 90.099 202 15 3 1 202 349938399 349938203 1.720000e-64 257.0
34 TraesCS5B01G364500 chr2A 90.099 202 15 3 1 202 136642528 136642332 1.720000e-64 257.0
35 TraesCS5B01G364500 chr7D 88.942 208 15 6 1 208 46709086 46708887 2.880000e-62 250.0


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 TraesCS5B01G364500 chr5B 543242520 543247338 4818 True 8900.000000 8900 100.0000 1 4819 1 chr5B.!!$R1 4818
1 TraesCS5B01G364500 chr5B 543275321 543275902 581 True 490.000000 490 82.0470 1010 1600 1 chr5B.!!$R3 590
2 TraesCS5B01G364500 chr5B 543297417 543298640 1223 True 482.000000 649 86.6345 2373 3514 2 chr5B.!!$R5 1141
3 TraesCS5B01G364500 chr5B 531193753 531195085 1332 False 439.500000 612 80.7390 2373 3552 2 chr5B.!!$F2 1179
4 TraesCS5B01G364500 chr5B 543281319 543282493 1174 True 266.666667 582 84.1740 1016 2274 3 chr5B.!!$R4 1258
5 TraesCS5B01G364500 chr5D 445401919 445406613 4694 True 3634.000000 6560 92.8005 206 4817 2 chr5D.!!$R1 4611
6 TraesCS5B01G364500 chr5D 445489640 445490906 1266 True 480.500000 634 84.3295 2375 3514 2 chr5D.!!$R2 1139
7 TraesCS5B01G364500 chr5A 563253283 563257290 4007 True 3050.500000 5369 92.9915 201 4126 2 chr5A.!!$R1 3925
8 TraesCS5B01G364500 chr5A 552267413 552269420 2007 False 573.000000 604 81.6195 1001 2990 2 chr5A.!!$F1 1989
9 TraesCS5B01G364500 chr4D 2975080 2976431 1351 False 580.000000 652 83.2780 2470 3877 2 chr4D.!!$F2 1407
10 TraesCS5B01G364500 chr1D 410457895 410458693 798 True 651.000000 651 81.5460 2358 3150 1 chr1D.!!$R1 792
11 TraesCS5B01G364500 chr7A 7817259 7818633 1374 False 326.550000 556 86.7920 1001 2261 2 chr7A.!!$F1 1260
12 TraesCS5B01G364500 chr1B 553013629 553014263 634 True 553.000000 553 82.3900 2358 2992 1 chr1B.!!$R1 634

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
59 60 0.033090 GGACGACCGGATGAATACCC 59.967 60.0 9.46 0.0 0.00 3.69 F
622 639 0.035458 CAAGAGAGGGACGGCAGTTT 59.965 55.0 0.00 0.0 0.00 2.66 F
625 642 0.250513 GAGAGGGACGGCAGTTTGAT 59.749 55.0 0.00 0.0 0.00 2.57 F
1232 1356 0.254178 AGTCAGGATCATGGTGGTGC 59.746 55.0 7.64 0.0 0.00 5.01 F
1538 1668 0.747852 AGCCTAGTAAGCTCTTCCGC 59.252 55.0 0.00 0.0 34.91 5.54 F
3244 3971 0.036765 CAATGGGCTGCTGCAAATGT 60.037 50.0 17.89 0.0 41.91 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1913 0.755079 TGATCGGGCTCAAGATCCAG 59.245 55.000 0.00 0.0 41.76 3.86 R
1846 2000 4.079970 TCCATTATTTGGTTTACGTGGCA 58.920 39.130 0.00 0.0 46.52 4.92 R
2632 3084 4.332268 CCTTAAGCTGCAACTGAGATCTTC 59.668 45.833 1.02 0.0 0.00 2.87 R
2895 3347 0.107654 GATTTCGCCTAGTGCCTGGT 60.108 55.000 0.00 0.0 36.24 4.00 R
3315 4045 0.032912 TGGCATGTAGGTACCCTCGA 60.033 55.000 8.74 0.0 34.61 4.04 R
4688 5449 0.038343 GTGTTCAATGCCACGCCAAT 60.038 50.000 0.00 0.0 0.00 3.16 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 4.426313 GCCCACACACTAGCCCCC 62.426 72.222 0.00 0.00 0.00 5.40
18 19 4.096003 CCCACACACTAGCCCCCG 62.096 72.222 0.00 0.00 0.00 5.73
19 20 4.096003 CCACACACTAGCCCCCGG 62.096 72.222 0.00 0.00 0.00 5.73
20 21 3.319198 CACACACTAGCCCCCGGT 61.319 66.667 0.00 0.00 0.00 5.28
21 22 3.319198 ACACACTAGCCCCCGGTG 61.319 66.667 0.00 0.00 37.05 4.94
22 23 3.319198 CACACTAGCCCCCGGTGT 61.319 66.667 0.00 0.00 43.74 4.16
23 24 3.319198 ACACTAGCCCCCGGTGTG 61.319 66.667 0.00 2.22 41.75 3.82
24 25 4.096003 CACTAGCCCCCGGTGTGG 62.096 72.222 0.00 0.00 37.55 4.17
25 26 4.651516 ACTAGCCCCCGGTGTGGT 62.652 66.667 0.00 0.00 35.15 4.16
26 27 2.364579 CTAGCCCCCGGTGTGGTA 60.365 66.667 0.00 0.00 35.15 3.25
27 28 1.991167 CTAGCCCCCGGTGTGGTAA 60.991 63.158 0.00 0.00 35.15 2.85
28 29 1.538382 TAGCCCCCGGTGTGGTAAA 60.538 57.895 0.00 0.00 35.15 2.01
29 30 1.132554 TAGCCCCCGGTGTGGTAAAA 61.133 55.000 0.00 0.00 35.15 1.52
30 31 1.531128 GCCCCCGGTGTGGTAAAAA 60.531 57.895 0.00 0.00 35.15 1.94
48 49 1.508632 AAAAGACATGTGGACGACCG 58.491 50.000 1.15 0.00 39.42 4.79
49 50 0.320421 AAAGACATGTGGACGACCGG 60.320 55.000 1.15 0.00 39.42 5.28
50 51 1.183030 AAGACATGTGGACGACCGGA 61.183 55.000 9.46 0.00 39.42 5.14
51 52 0.970937 AGACATGTGGACGACCGGAT 60.971 55.000 9.46 0.00 39.42 4.18
52 53 0.806102 GACATGTGGACGACCGGATG 60.806 60.000 9.46 11.60 39.42 3.51
53 54 1.254975 ACATGTGGACGACCGGATGA 61.255 55.000 9.46 0.00 39.42 2.92
54 55 0.108377 CATGTGGACGACCGGATGAA 60.108 55.000 9.46 0.00 39.42 2.57
55 56 0.830648 ATGTGGACGACCGGATGAAT 59.169 50.000 9.46 0.00 39.42 2.57
56 57 1.476477 TGTGGACGACCGGATGAATA 58.524 50.000 9.46 0.00 39.42 1.75
57 58 1.135527 TGTGGACGACCGGATGAATAC 59.864 52.381 9.46 0.63 39.42 1.89
58 59 0.748450 TGGACGACCGGATGAATACC 59.252 55.000 9.46 2.55 39.42 2.73
59 60 0.033090 GGACGACCGGATGAATACCC 59.967 60.000 9.46 0.00 0.00 3.69
60 61 0.748450 GACGACCGGATGAATACCCA 59.252 55.000 9.46 0.00 0.00 4.51
61 62 0.462789 ACGACCGGATGAATACCCAC 59.537 55.000 9.46 0.00 0.00 4.61
62 63 0.462375 CGACCGGATGAATACCCACA 59.538 55.000 9.46 0.00 0.00 4.17
63 64 1.805120 CGACCGGATGAATACCCACAC 60.805 57.143 9.46 0.00 0.00 3.82
64 65 1.208535 GACCGGATGAATACCCACACA 59.791 52.381 9.46 0.00 0.00 3.72
65 66 1.065709 ACCGGATGAATACCCACACAC 60.066 52.381 9.46 0.00 0.00 3.82
66 67 1.663695 CGGATGAATACCCACACACC 58.336 55.000 0.00 0.00 0.00 4.16
67 68 1.065782 CGGATGAATACCCACACACCA 60.066 52.381 0.00 0.00 0.00 4.17
68 69 2.643551 GGATGAATACCCACACACCAG 58.356 52.381 0.00 0.00 0.00 4.00
69 70 2.017049 GATGAATACCCACACACCAGC 58.983 52.381 0.00 0.00 0.00 4.85
70 71 1.064003 TGAATACCCACACACCAGCT 58.936 50.000 0.00 0.00 0.00 4.24
71 72 1.423541 TGAATACCCACACACCAGCTT 59.576 47.619 0.00 0.00 0.00 3.74
72 73 2.640332 TGAATACCCACACACCAGCTTA 59.360 45.455 0.00 0.00 0.00 3.09
73 74 3.270877 GAATACCCACACACCAGCTTAG 58.729 50.000 0.00 0.00 0.00 2.18
74 75 1.724545 TACCCACACACCAGCTTAGT 58.275 50.000 0.00 0.00 0.00 2.24
75 76 0.396811 ACCCACACACCAGCTTAGTC 59.603 55.000 0.00 0.00 0.00 2.59
76 77 0.687354 CCCACACACCAGCTTAGTCT 59.313 55.000 0.00 0.00 0.00 3.24
77 78 1.072331 CCCACACACCAGCTTAGTCTT 59.928 52.381 0.00 0.00 0.00 3.01
78 79 2.301870 CCCACACACCAGCTTAGTCTTA 59.698 50.000 0.00 0.00 0.00 2.10
79 80 3.326747 CCACACACCAGCTTAGTCTTAC 58.673 50.000 0.00 0.00 0.00 2.34
80 81 2.987149 CACACACCAGCTTAGTCTTACG 59.013 50.000 0.00 0.00 0.00 3.18
81 82 2.626743 ACACACCAGCTTAGTCTTACGT 59.373 45.455 0.00 0.00 0.00 3.57
82 83 3.822735 ACACACCAGCTTAGTCTTACGTA 59.177 43.478 0.00 0.00 0.00 3.57
83 84 4.279169 ACACACCAGCTTAGTCTTACGTAA 59.721 41.667 7.94 7.94 0.00 3.18
84 85 4.620184 CACACCAGCTTAGTCTTACGTAAC 59.380 45.833 3.29 0.00 0.00 2.50
85 86 3.850273 CACCAGCTTAGTCTTACGTAACG 59.150 47.826 3.29 1.35 0.00 3.18
86 87 3.503748 ACCAGCTTAGTCTTACGTAACGT 59.496 43.478 3.29 0.00 44.35 3.99
87 88 3.850273 CCAGCTTAGTCTTACGTAACGTG 59.150 47.826 3.29 0.00 41.39 4.49
88 89 3.850273 CAGCTTAGTCTTACGTAACGTGG 59.150 47.826 3.29 0.00 41.39 4.94
89 90 2.595977 GCTTAGTCTTACGTAACGTGGC 59.404 50.000 3.29 0.00 41.39 5.01
90 91 3.825308 CTTAGTCTTACGTAACGTGGCA 58.175 45.455 3.29 0.00 41.39 4.92
91 92 2.056094 AGTCTTACGTAACGTGGCAC 57.944 50.000 7.79 7.79 41.39 5.01
92 93 1.337703 AGTCTTACGTAACGTGGCACA 59.662 47.619 19.09 0.00 41.39 4.57
106 107 3.876274 TGGCACACAAAAACTGCTAAA 57.124 38.095 0.00 0.00 0.00 1.85
107 108 4.193826 TGGCACACAAAAACTGCTAAAA 57.806 36.364 0.00 0.00 0.00 1.52
108 109 3.929610 TGGCACACAAAAACTGCTAAAAC 59.070 39.130 0.00 0.00 0.00 2.43
109 110 3.000177 GGCACACAAAAACTGCTAAAACG 60.000 43.478 0.00 0.00 0.00 3.60
110 111 3.541322 GCACACAAAAACTGCTAAAACGC 60.541 43.478 0.00 0.00 0.00 4.84
111 112 2.849473 ACACAAAAACTGCTAAAACGCG 59.151 40.909 3.53 3.53 0.00 6.01
112 113 2.849473 CACAAAAACTGCTAAAACGCGT 59.151 40.909 5.58 5.58 0.00 6.01
113 114 3.062124 CACAAAAACTGCTAAAACGCGTC 60.062 43.478 14.44 0.00 0.00 5.19
114 115 3.102276 CAAAAACTGCTAAAACGCGTCA 58.898 40.909 14.44 4.52 0.00 4.35
115 116 3.408288 AAAACTGCTAAAACGCGTCAA 57.592 38.095 14.44 0.00 0.00 3.18
116 117 2.663279 AACTGCTAAAACGCGTCAAG 57.337 45.000 14.44 11.73 0.00 3.02
117 118 1.860676 ACTGCTAAAACGCGTCAAGA 58.139 45.000 14.44 0.00 0.00 3.02
118 119 2.413837 ACTGCTAAAACGCGTCAAGAT 58.586 42.857 14.44 0.00 0.00 2.40
119 120 2.806244 ACTGCTAAAACGCGTCAAGATT 59.194 40.909 14.44 0.00 0.00 2.40
120 121 3.120649 ACTGCTAAAACGCGTCAAGATTC 60.121 43.478 14.44 0.00 0.00 2.52
121 122 2.159894 TGCTAAAACGCGTCAAGATTCG 60.160 45.455 14.44 0.76 0.00 3.34
122 123 2.159881 GCTAAAACGCGTCAAGATTCGT 60.160 45.455 14.44 0.00 36.67 3.85
123 124 2.294479 AAAACGCGTCAAGATTCGTG 57.706 45.000 14.44 0.00 42.16 4.35
124 125 4.647654 ACGCGTCAAGATTCGTGT 57.352 50.000 5.58 0.00 44.04 4.49
125 126 3.778969 ACGCGTCAAGATTCGTGTA 57.221 47.368 5.58 0.00 46.29 2.90
126 127 1.614385 ACGCGTCAAGATTCGTGTAG 58.386 50.000 5.58 0.00 46.29 2.74
127 128 1.198408 ACGCGTCAAGATTCGTGTAGA 59.802 47.619 5.58 0.00 46.29 2.59
128 129 2.247637 CGCGTCAAGATTCGTGTAGAA 58.752 47.619 0.00 0.00 43.93 2.10
139 140 5.818136 ATTCGTGTAGAATTGGTTGGATG 57.182 39.130 0.00 0.00 46.80 3.51
140 141 4.545208 TCGTGTAGAATTGGTTGGATGA 57.455 40.909 0.00 0.00 0.00 2.92
141 142 4.503910 TCGTGTAGAATTGGTTGGATGAG 58.496 43.478 0.00 0.00 0.00 2.90
142 143 3.623060 CGTGTAGAATTGGTTGGATGAGG 59.377 47.826 0.00 0.00 0.00 3.86
143 144 4.622933 CGTGTAGAATTGGTTGGATGAGGA 60.623 45.833 0.00 0.00 0.00 3.71
144 145 5.440610 GTGTAGAATTGGTTGGATGAGGAT 58.559 41.667 0.00 0.00 0.00 3.24
145 146 5.529060 GTGTAGAATTGGTTGGATGAGGATC 59.471 44.000 0.00 0.00 0.00 3.36
153 154 2.924185 GGATGAGGATCCATGCGTG 58.076 57.895 15.82 0.00 46.93 5.34
154 155 0.107456 GGATGAGGATCCATGCGTGT 59.893 55.000 15.82 0.00 46.93 4.49
155 156 1.224075 GATGAGGATCCATGCGTGTG 58.776 55.000 15.82 0.00 0.00 3.82
156 157 0.179037 ATGAGGATCCATGCGTGTGG 60.179 55.000 15.82 0.40 40.76 4.17
157 158 1.524621 GAGGATCCATGCGTGTGGG 60.525 63.158 15.82 0.00 39.80 4.61
158 159 3.211963 GGATCCATGCGTGTGGGC 61.212 66.667 6.95 0.00 39.80 5.36
159 160 3.576356 GATCCATGCGTGTGGGCG 61.576 66.667 4.96 0.00 39.80 6.13
160 161 4.094646 ATCCATGCGTGTGGGCGA 62.095 61.111 4.96 0.00 39.80 5.54
161 162 4.758251 TCCATGCGTGTGGGCGAG 62.758 66.667 4.96 0.00 39.80 5.03
163 164 3.049674 CATGCGTGTGGGCGAGTT 61.050 61.111 0.00 0.00 35.06 3.01
164 165 3.049674 ATGCGTGTGGGCGAGTTG 61.050 61.111 0.00 0.00 35.06 3.16
175 176 4.680237 CGAGTTGCCAGACGCCCA 62.680 66.667 0.00 0.00 36.24 5.36
176 177 3.050275 GAGTTGCCAGACGCCCAC 61.050 66.667 0.00 0.00 36.24 4.61
177 178 3.825160 GAGTTGCCAGACGCCCACA 62.825 63.158 0.00 0.00 36.24 4.17
178 179 3.660111 GTTGCCAGACGCCCACAC 61.660 66.667 0.00 0.00 36.24 3.82
194 195 2.293765 CACGTGTGTGCGTTAGTGT 58.706 52.632 7.58 0.00 43.83 3.55
195 196 0.648441 CACGTGTGTGCGTTAGTGTT 59.352 50.000 7.58 0.00 43.83 3.32
196 197 1.061421 CACGTGTGTGCGTTAGTGTTT 59.939 47.619 7.58 0.00 43.83 2.83
197 198 1.325338 ACGTGTGTGCGTTAGTGTTTC 59.675 47.619 0.00 0.00 43.04 2.78
198 199 1.332552 CGTGTGTGCGTTAGTGTTTCC 60.333 52.381 0.00 0.00 0.00 3.13
199 200 0.931702 TGTGTGCGTTAGTGTTTCCG 59.068 50.000 0.00 0.00 0.00 4.30
214 215 4.799949 GTGTTTCCGTTTGTTTTTCCTACC 59.200 41.667 0.00 0.00 0.00 3.18
220 221 3.484285 CGTTTGTTTTTCCTACCGCAAAG 59.516 43.478 0.00 0.00 0.00 2.77
222 223 2.933573 TGTTTTTCCTACCGCAAAGGA 58.066 42.857 0.00 0.00 45.00 3.36
437 441 3.474570 GATGGGAGGAGCGGCAGT 61.475 66.667 1.45 0.00 0.00 4.40
452 456 1.587054 CAGTCACAGAGTCGGGACC 59.413 63.158 11.96 0.00 0.00 4.46
589 606 2.675423 GGGACGGGCCAAGGAAAC 60.675 66.667 4.39 0.00 38.95 2.78
622 639 0.035458 CAAGAGAGGGACGGCAGTTT 59.965 55.000 0.00 0.00 0.00 2.66
623 640 0.035458 AAGAGAGGGACGGCAGTTTG 59.965 55.000 0.00 0.00 0.00 2.93
624 641 0.832135 AGAGAGGGACGGCAGTTTGA 60.832 55.000 0.00 0.00 0.00 2.69
625 642 0.250513 GAGAGGGACGGCAGTTTGAT 59.749 55.000 0.00 0.00 0.00 2.57
640 657 5.372373 CAGTTTGATTAGGGGATCTTCCTC 58.628 45.833 10.64 0.00 37.26 3.71
689 706 4.448720 TCCACCTGCTACTGCTAGTATA 57.551 45.455 0.00 0.00 40.48 1.47
760 779 6.630444 AATATGCATCTTTTTCAGCTCGAT 57.370 33.333 0.19 0.00 0.00 3.59
764 783 5.872635 TGCATCTTTTTCAGCTCGATTAAG 58.127 37.500 0.00 0.00 0.00 1.85
776 795 3.002759 GCTCGATTAAGCTGGTTTGATCC 59.997 47.826 0.00 0.00 39.27 3.36
777 796 4.191544 CTCGATTAAGCTGGTTTGATCCA 58.808 43.478 0.00 0.00 36.00 3.41
785 804 3.030668 CTGGTTTGATCCAGCCAAAAC 57.969 47.619 3.92 0.35 46.53 2.43
786 805 1.339610 TGGTTTGATCCAGCCAAAACG 59.660 47.619 0.00 0.00 42.43 3.60
787 806 1.611491 GGTTTGATCCAGCCAAAACGA 59.389 47.619 0.00 0.00 35.57 3.85
788 807 2.231235 GGTTTGATCCAGCCAAAACGAT 59.769 45.455 0.00 0.00 35.57 3.73
789 808 3.244976 GTTTGATCCAGCCAAAACGATG 58.755 45.455 0.00 0.00 35.57 3.84
790 809 2.198827 TGATCCAGCCAAAACGATGT 57.801 45.000 0.00 0.00 0.00 3.06
791 810 2.513753 TGATCCAGCCAAAACGATGTT 58.486 42.857 0.00 0.00 0.00 2.71
792 811 2.890311 TGATCCAGCCAAAACGATGTTT 59.110 40.909 0.00 0.00 0.00 2.83
793 812 2.791383 TCCAGCCAAAACGATGTTTG 57.209 45.000 0.00 0.00 38.07 2.93
794 813 1.139163 CCAGCCAAAACGATGTTTGC 58.861 50.000 0.00 0.00 37.20 3.68
795 814 1.269726 CCAGCCAAAACGATGTTTGCT 60.270 47.619 0.00 0.00 37.20 3.91
796 815 2.472816 CAGCCAAAACGATGTTTGCTT 58.527 42.857 4.96 0.00 37.20 3.91
797 816 2.865551 CAGCCAAAACGATGTTTGCTTT 59.134 40.909 4.96 0.00 37.20 3.51
798 817 2.865551 AGCCAAAACGATGTTTGCTTTG 59.134 40.909 0.00 0.00 37.20 2.77
799 818 2.863137 GCCAAAACGATGTTTGCTTTGA 59.137 40.909 0.00 0.00 37.20 2.69
800 819 3.308323 GCCAAAACGATGTTTGCTTTGAA 59.692 39.130 0.00 0.00 37.20 2.69
801 820 4.781883 GCCAAAACGATGTTTGCTTTGAAC 60.782 41.667 0.00 0.00 37.20 3.18
802 821 4.260172 CCAAAACGATGTTTGCTTTGAACC 60.260 41.667 0.00 0.00 37.20 3.62
803 822 2.399396 ACGATGTTTGCTTTGAACCG 57.601 45.000 0.00 0.00 0.00 4.44
824 843 4.539870 CGGCTTGATTATAACAATGCAGG 58.460 43.478 0.00 0.00 0.00 4.85
832 851 8.607441 TGATTATAACAATGCAGGTCATCTAC 57.393 34.615 0.00 0.00 33.40 2.59
833 852 8.210265 TGATTATAACAATGCAGGTCATCTACA 58.790 33.333 0.00 0.00 33.40 2.74
834 853 7.786178 TTATAACAATGCAGGTCATCTACAC 57.214 36.000 0.00 0.00 33.40 2.90
836 855 1.935873 CAATGCAGGTCATCTACACCG 59.064 52.381 0.00 0.00 39.13 4.94
842 966 3.181469 GCAGGTCATCTACACCGGATTAA 60.181 47.826 9.46 0.00 39.13 1.40
865 989 7.944729 AACATATGAAAAGTCAGTAGGCAAT 57.055 32.000 10.38 0.00 37.14 3.56
939 1063 3.181511 TGGATCAACGTGCGAAATGAATC 60.182 43.478 0.00 0.00 0.00 2.52
940 1064 2.502280 TCAACGTGCGAAATGAATCG 57.498 45.000 0.00 0.00 45.41 3.34
941 1065 1.127766 TCAACGTGCGAAATGAATCGG 59.872 47.619 0.00 0.00 42.93 4.18
988 1112 2.888863 CGAGGGAGAGCCAGACAC 59.111 66.667 0.00 0.00 35.15 3.67
989 1113 1.979155 CGAGGGAGAGCCAGACACA 60.979 63.158 0.00 0.00 35.15 3.72
990 1114 1.896694 GAGGGAGAGCCAGACACAG 59.103 63.158 0.00 0.00 35.15 3.66
991 1115 0.902516 GAGGGAGAGCCAGACACAGT 60.903 60.000 0.00 0.00 35.15 3.55
992 1116 0.902516 AGGGAGAGCCAGACACAGTC 60.903 60.000 0.00 0.00 35.15 3.51
993 1117 1.214062 GGAGAGCCAGACACAGTCG 59.786 63.158 0.00 0.00 37.67 4.18
994 1118 1.528292 GGAGAGCCAGACACAGTCGT 61.528 60.000 0.00 0.00 37.67 4.34
1004 1128 1.000163 GACACAGTCGTCAGTCATGGT 60.000 52.381 0.00 0.00 35.88 3.55
1033 1157 2.048603 GCTGTGGAATGGTGGGAGC 61.049 63.158 0.00 0.00 0.00 4.70
1072 1196 1.603236 CGTCCTCAGCAGCCTCTTCT 61.603 60.000 0.00 0.00 0.00 2.85
1096 1220 1.190643 GTACCTCCTGCTCTGCTCTT 58.809 55.000 0.00 0.00 0.00 2.85
1228 1352 2.102757 CAGAGGAGTCAGGATCATGGTG 59.897 54.545 7.64 0.00 0.00 4.17
1232 1356 0.254178 AGTCAGGATCATGGTGGTGC 59.746 55.000 7.64 0.00 0.00 5.01
1538 1668 0.747852 AGCCTAGTAAGCTCTTCCGC 59.252 55.000 0.00 0.00 34.91 5.54
2312 2679 1.682854 CTGTGCTTCCTTTGCCTTTGA 59.317 47.619 0.00 0.00 0.00 2.69
2632 3084 0.874175 TCAGTCCAACAACTGCGACG 60.874 55.000 0.00 0.00 45.12 5.12
2895 3347 3.562182 TGTCAATCCCGAGATGCTACTA 58.438 45.455 0.00 0.00 31.29 1.82
3244 3971 0.036765 CAATGGGCTGCTGCAAATGT 60.037 50.000 17.89 0.00 41.91 2.71
3315 4045 1.104630 GCTTCTCGGCTAGTAGGTGT 58.895 55.000 0.00 0.00 0.00 4.16
3498 4233 1.847798 TTAGCACCGCCACTGGGAAT 61.848 55.000 0.00 0.00 35.59 3.01
3591 4333 8.816640 TTTCTTATTGATGGAAGTTCTTTTGC 57.183 30.769 2.25 0.00 0.00 3.68
3623 4369 6.379386 TCATTGTGATATTCCGTCTATCGTC 58.621 40.000 0.00 0.00 37.94 4.20
3624 4370 6.206829 TCATTGTGATATTCCGTCTATCGTCT 59.793 38.462 0.00 0.00 37.94 4.18
3625 4371 5.608676 TGTGATATTCCGTCTATCGTCTC 57.391 43.478 0.00 0.00 37.94 3.36
3629 4383 0.926155 TTCCGTCTATCGTCTCGTCG 59.074 55.000 0.00 0.00 37.94 5.12
3718 4472 2.108168 TGTGATCTACCAGGTACCTGC 58.892 52.381 32.98 19.77 42.35 4.85
3723 4477 1.304630 TACCAGGTACCTGCGAGCA 60.305 57.895 32.98 14.24 42.35 4.26
3801 4555 3.611970 TCTACCTCTCGACCTCAAGAAG 58.388 50.000 0.00 0.00 0.00 2.85
3817 4571 4.756642 TCAAGAAGTACAACCAGCTGAATG 59.243 41.667 17.39 15.77 0.00 2.67
3984 4740 8.691661 TCTGCTATACATGTAGATAGTGTCAA 57.308 34.615 11.91 0.00 0.00 3.18
4147 4908 8.968242 GTTTGTCCTATTTTCTGACAATTGTTC 58.032 33.333 13.36 6.80 45.41 3.18
4174 4935 1.190643 GTCTCCCAGGAGGTGAAGAG 58.809 60.000 13.73 0.00 39.82 2.85
4189 4950 5.239525 AGGTGAAGAGTATTTTGCAAGTCAC 59.760 40.000 0.00 4.97 33.70 3.67
4212 4973 1.177401 GGAGGTGTTTGATCCCAAGC 58.823 55.000 0.00 0.00 33.23 4.01
4216 4977 2.042162 AGGTGTTTGATCCCAAGCATCT 59.958 45.455 2.63 2.63 45.92 2.90
4259 5020 5.299531 GGGTAGAATGCATAAAGGGAAGTTC 59.700 44.000 0.00 0.00 0.00 3.01
4327 5088 4.158579 TGAACGCTATATGGCCTCATCTAG 59.841 45.833 3.32 0.00 34.84 2.43
4354 5115 6.681777 AGGAAATATTGATTAAATCTGCGGC 58.318 36.000 0.00 0.00 0.00 6.53
4356 5117 5.391312 AATATTGATTAAATCTGCGGCCC 57.609 39.130 0.00 0.00 0.00 5.80
4371 5132 1.615262 GCCCAGGCTATTCCCACTT 59.385 57.895 0.08 0.00 38.26 3.16
4372 5133 0.843984 GCCCAGGCTATTCCCACTTA 59.156 55.000 0.08 0.00 38.26 2.24
4373 5134 1.477014 GCCCAGGCTATTCCCACTTAC 60.477 57.143 0.08 0.00 38.26 2.34
4374 5135 1.202651 CCCAGGCTATTCCCACTTACG 60.203 57.143 0.00 0.00 34.51 3.18
4393 5154 7.891220 CACTTACGTATGTTATGAGTGTTTTCG 59.109 37.037 11.13 0.00 0.00 3.46
4399 5160 7.682865 CGTATGTTATGAGTGTTTTCGAACTTC 59.317 37.037 0.00 0.00 0.00 3.01
4400 5161 7.730364 ATGTTATGAGTGTTTTCGAACTTCT 57.270 32.000 0.00 0.00 0.00 2.85
4408 5169 7.042725 TGAGTGTTTTCGAACTTCTGTATTCTG 60.043 37.037 0.00 0.00 0.00 3.02
4417 5178 5.276461 ACTTCTGTATTCTGTGTGTGACA 57.724 39.130 0.00 0.00 0.00 3.58
4463 5224 1.741028 TGGTGGGGAGTTGAGAATGA 58.259 50.000 0.00 0.00 0.00 2.57
4491 5252 2.549064 AAATGGCTTGGGTTTCTTGC 57.451 45.000 0.00 0.00 0.00 4.01
4578 5339 1.379044 ATTGCTGGCTACACAGGCC 60.379 57.895 0.00 0.00 46.65 5.19
4638 5399 2.795470 GCTGTTGCGAGCTAGGTATTAC 59.205 50.000 0.00 0.00 35.95 1.89
4688 5449 1.815003 CAGTCAATGCATCCGCGGA 60.815 57.895 33.12 33.12 42.97 5.54
4707 5468 0.038343 ATTGGCGTGGCATTGAACAC 60.038 50.000 0.00 0.00 0.00 3.32
4760 5521 3.322254 TGGCGTGTTGGTAATGGAATTTT 59.678 39.130 0.00 0.00 37.87 1.82
4768 5529 6.015010 TGTTGGTAATGGAATTTTGATTCGGT 60.015 34.615 0.00 0.00 37.87 4.69
4774 5535 4.148838 TGGAATTTTGATTCGGTCTTGGT 58.851 39.130 0.00 0.00 0.00 3.67
4813 5574 1.668419 GGGTCCATCATTTCGTCCAG 58.332 55.000 0.00 0.00 0.00 3.86
4817 5578 4.451900 GGTCCATCATTTCGTCCAGTTAT 58.548 43.478 0.00 0.00 0.00 1.89
4818 5579 4.273480 GGTCCATCATTTCGTCCAGTTATG 59.727 45.833 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.426313 GGGGGCTAGTGTGTGGGC 62.426 72.222 0.00 0.00 0.00 5.36
1 2 4.096003 CGGGGGCTAGTGTGTGGG 62.096 72.222 0.00 0.00 0.00 4.61
2 3 4.096003 CCGGGGGCTAGTGTGTGG 62.096 72.222 0.00 0.00 0.00 4.17
3 4 3.319198 ACCGGGGGCTAGTGTGTG 61.319 66.667 6.32 0.00 0.00 3.82
4 5 3.319198 CACCGGGGGCTAGTGTGT 61.319 66.667 6.32 0.00 0.00 3.72
5 6 3.319198 ACACCGGGGGCTAGTGTG 61.319 66.667 9.50 0.00 42.89 3.82
6 7 3.319198 CACACCGGGGGCTAGTGT 61.319 66.667 9.50 0.00 45.31 3.55
7 8 4.096003 CCACACCGGGGGCTAGTG 62.096 72.222 9.50 5.57 37.53 2.74
8 9 2.752036 TTACCACACCGGGGGCTAGT 62.752 60.000 9.50 1.44 40.22 2.57
9 10 1.555477 TTTACCACACCGGGGGCTAG 61.555 60.000 9.50 0.00 40.22 3.42
10 11 1.132554 TTTTACCACACCGGGGGCTA 61.133 55.000 9.50 0.00 40.22 3.93
11 12 2.009208 TTTTTACCACACCGGGGGCT 62.009 55.000 9.50 0.00 40.22 5.19
12 13 1.531128 TTTTTACCACACCGGGGGC 60.531 57.895 9.50 0.00 40.22 5.80
13 14 4.925311 TTTTTACCACACCGGGGG 57.075 55.556 9.50 8.26 40.22 5.40
28 29 1.871039 CGGTCGTCCACATGTCTTTTT 59.129 47.619 0.00 0.00 0.00 1.94
29 30 1.508632 CGGTCGTCCACATGTCTTTT 58.491 50.000 0.00 0.00 0.00 2.27
30 31 0.320421 CCGGTCGTCCACATGTCTTT 60.320 55.000 0.00 0.00 0.00 2.52
31 32 1.183030 TCCGGTCGTCCACATGTCTT 61.183 55.000 0.00 0.00 0.00 3.01
32 33 0.970937 ATCCGGTCGTCCACATGTCT 60.971 55.000 0.00 0.00 0.00 3.41
33 34 0.806102 CATCCGGTCGTCCACATGTC 60.806 60.000 0.00 0.00 0.00 3.06
34 35 1.218047 CATCCGGTCGTCCACATGT 59.782 57.895 0.00 0.00 0.00 3.21
35 36 0.108377 TTCATCCGGTCGTCCACATG 60.108 55.000 0.00 0.00 0.00 3.21
36 37 0.830648 ATTCATCCGGTCGTCCACAT 59.169 50.000 0.00 0.00 0.00 3.21
37 38 1.135527 GTATTCATCCGGTCGTCCACA 59.864 52.381 0.00 0.00 0.00 4.17
38 39 1.537562 GGTATTCATCCGGTCGTCCAC 60.538 57.143 0.00 0.00 0.00 4.02
39 40 0.748450 GGTATTCATCCGGTCGTCCA 59.252 55.000 0.00 0.00 0.00 4.02
40 41 0.033090 GGGTATTCATCCGGTCGTCC 59.967 60.000 0.00 0.00 0.00 4.79
41 42 0.748450 TGGGTATTCATCCGGTCGTC 59.252 55.000 0.00 0.00 0.00 4.20
42 43 0.462789 GTGGGTATTCATCCGGTCGT 59.537 55.000 0.00 0.00 0.00 4.34
43 44 0.462375 TGTGGGTATTCATCCGGTCG 59.538 55.000 0.00 0.00 0.00 4.79
44 45 1.208535 TGTGTGGGTATTCATCCGGTC 59.791 52.381 0.00 0.00 0.00 4.79
45 46 1.065709 GTGTGTGGGTATTCATCCGGT 60.066 52.381 0.00 0.00 0.00 5.28
46 47 1.663695 GTGTGTGGGTATTCATCCGG 58.336 55.000 0.00 0.00 0.00 5.14
47 48 1.065782 TGGTGTGTGGGTATTCATCCG 60.066 52.381 0.00 0.00 0.00 4.18
48 49 2.643551 CTGGTGTGTGGGTATTCATCC 58.356 52.381 0.00 0.00 0.00 3.51
49 50 2.017049 GCTGGTGTGTGGGTATTCATC 58.983 52.381 0.00 0.00 0.00 2.92
50 51 1.635487 AGCTGGTGTGTGGGTATTCAT 59.365 47.619 0.00 0.00 0.00 2.57
51 52 1.064003 AGCTGGTGTGTGGGTATTCA 58.936 50.000 0.00 0.00 0.00 2.57
52 53 2.200373 AAGCTGGTGTGTGGGTATTC 57.800 50.000 0.00 0.00 0.00 1.75
53 54 2.642807 ACTAAGCTGGTGTGTGGGTATT 59.357 45.455 0.00 0.00 0.00 1.89
54 55 2.236395 GACTAAGCTGGTGTGTGGGTAT 59.764 50.000 0.00 0.00 0.00 2.73
55 56 1.621814 GACTAAGCTGGTGTGTGGGTA 59.378 52.381 0.00 0.00 0.00 3.69
56 57 0.396811 GACTAAGCTGGTGTGTGGGT 59.603 55.000 0.00 0.00 0.00 4.51
57 58 0.687354 AGACTAAGCTGGTGTGTGGG 59.313 55.000 0.00 0.00 0.00 4.61
58 59 2.550830 AAGACTAAGCTGGTGTGTGG 57.449 50.000 0.00 0.00 0.00 4.17
59 60 2.987149 CGTAAGACTAAGCTGGTGTGTG 59.013 50.000 0.00 0.00 43.02 3.82
60 61 2.626743 ACGTAAGACTAAGCTGGTGTGT 59.373 45.455 0.00 0.00 43.62 3.72
61 62 3.299340 ACGTAAGACTAAGCTGGTGTG 57.701 47.619 0.00 0.00 43.62 3.82
62 63 4.614535 CGTTACGTAAGACTAAGCTGGTGT 60.615 45.833 8.60 0.00 43.62 4.16
63 64 3.850273 CGTTACGTAAGACTAAGCTGGTG 59.150 47.826 8.60 0.00 43.62 4.17
64 65 3.503748 ACGTTACGTAAGACTAAGCTGGT 59.496 43.478 9.22 0.00 38.73 4.00
65 66 3.850273 CACGTTACGTAAGACTAAGCTGG 59.150 47.826 10.89 0.00 38.32 4.85
66 67 3.850273 CCACGTTACGTAAGACTAAGCTG 59.150 47.826 10.89 0.00 38.32 4.24
67 68 3.671702 GCCACGTTACGTAAGACTAAGCT 60.672 47.826 10.89 0.00 38.32 3.74
68 69 2.595977 GCCACGTTACGTAAGACTAAGC 59.404 50.000 10.89 3.93 38.32 3.09
69 70 3.605486 GTGCCACGTTACGTAAGACTAAG 59.395 47.826 10.89 0.00 38.32 2.18
70 71 3.004210 TGTGCCACGTTACGTAAGACTAA 59.996 43.478 10.89 0.00 38.32 2.24
71 72 2.551887 TGTGCCACGTTACGTAAGACTA 59.448 45.455 10.89 0.00 38.32 2.59
72 73 1.337703 TGTGCCACGTTACGTAAGACT 59.662 47.619 10.89 0.00 38.32 3.24
73 74 1.453148 GTGTGCCACGTTACGTAAGAC 59.547 52.381 10.89 7.67 38.32 3.01
74 75 1.066757 TGTGTGCCACGTTACGTAAGA 59.933 47.619 10.89 0.00 38.32 2.10
75 76 1.489574 TGTGTGCCACGTTACGTAAG 58.510 50.000 10.89 6.41 38.32 2.34
76 77 1.931906 TTGTGTGCCACGTTACGTAA 58.068 45.000 10.89 3.29 38.32 3.18
77 78 1.931906 TTTGTGTGCCACGTTACGTA 58.068 45.000 10.89 0.00 38.32 3.57
78 79 1.085091 TTTTGTGTGCCACGTTACGT 58.915 45.000 3.95 3.95 42.36 3.57
79 80 1.841342 GTTTTTGTGTGCCACGTTACG 59.159 47.619 2.19 2.19 37.14 3.18
80 81 2.849473 CAGTTTTTGTGTGCCACGTTAC 59.151 45.455 0.00 0.00 37.14 2.50
81 82 2.732597 GCAGTTTTTGTGTGCCACGTTA 60.733 45.455 0.00 0.00 37.14 3.18
82 83 1.989430 CAGTTTTTGTGTGCCACGTT 58.011 45.000 0.00 0.00 37.14 3.99
83 84 0.457681 GCAGTTTTTGTGTGCCACGT 60.458 50.000 0.00 0.00 37.14 4.49
84 85 0.179140 AGCAGTTTTTGTGTGCCACG 60.179 50.000 0.00 0.00 37.98 4.94
85 86 2.861462 TAGCAGTTTTTGTGTGCCAC 57.139 45.000 0.00 0.00 37.98 5.01
86 87 3.876274 TTTAGCAGTTTTTGTGTGCCA 57.124 38.095 0.00 0.00 37.98 4.92
87 88 3.000177 CGTTTTAGCAGTTTTTGTGTGCC 60.000 43.478 0.00 0.00 37.98 5.01
88 89 3.541322 GCGTTTTAGCAGTTTTTGTGTGC 60.541 43.478 0.00 0.00 37.48 4.57
89 90 3.300880 CGCGTTTTAGCAGTTTTTGTGTG 60.301 43.478 0.00 0.00 36.85 3.82
90 91 2.849473 CGCGTTTTAGCAGTTTTTGTGT 59.151 40.909 0.00 0.00 36.85 3.72
91 92 2.849473 ACGCGTTTTAGCAGTTTTTGTG 59.151 40.909 5.58 0.00 36.85 3.33
92 93 3.103007 GACGCGTTTTAGCAGTTTTTGT 58.897 40.909 15.53 0.00 36.85 2.83
93 94 3.102276 TGACGCGTTTTAGCAGTTTTTG 58.898 40.909 15.53 0.00 36.85 2.44
94 95 3.408288 TGACGCGTTTTAGCAGTTTTT 57.592 38.095 15.53 0.00 36.85 1.94
95 96 3.064271 TCTTGACGCGTTTTAGCAGTTTT 59.936 39.130 15.53 0.00 36.85 2.43
96 97 2.610374 TCTTGACGCGTTTTAGCAGTTT 59.390 40.909 15.53 0.00 36.85 2.66
97 98 2.206750 TCTTGACGCGTTTTAGCAGTT 58.793 42.857 15.53 0.00 36.85 3.16
98 99 1.860676 TCTTGACGCGTTTTAGCAGT 58.139 45.000 15.53 0.00 36.85 4.40
99 100 3.408150 GAATCTTGACGCGTTTTAGCAG 58.592 45.455 15.53 3.56 36.85 4.24
100 101 2.159894 CGAATCTTGACGCGTTTTAGCA 60.160 45.455 15.53 2.61 36.85 3.49
101 102 2.159881 ACGAATCTTGACGCGTTTTAGC 60.160 45.455 15.53 0.00 32.42 3.09
102 103 3.121126 ACACGAATCTTGACGCGTTTTAG 60.121 43.478 15.53 11.51 34.37 1.85
103 104 2.796031 ACACGAATCTTGACGCGTTTTA 59.204 40.909 15.53 0.00 34.37 1.52
104 105 1.595794 ACACGAATCTTGACGCGTTTT 59.404 42.857 15.53 2.41 34.37 2.43
105 106 1.214367 ACACGAATCTTGACGCGTTT 58.786 45.000 15.53 2.07 34.37 3.60
106 107 1.983605 CTACACGAATCTTGACGCGTT 59.016 47.619 15.53 0.00 34.37 4.84
107 108 1.198408 TCTACACGAATCTTGACGCGT 59.802 47.619 13.85 13.85 37.48 6.01
108 109 1.891178 TCTACACGAATCTTGACGCG 58.109 50.000 3.53 3.53 0.00 6.01
109 110 4.492570 CCAATTCTACACGAATCTTGACGC 60.493 45.833 0.00 0.00 41.42 5.19
110 111 4.625742 ACCAATTCTACACGAATCTTGACG 59.374 41.667 0.00 0.00 41.42 4.35
111 112 6.307155 CAACCAATTCTACACGAATCTTGAC 58.693 40.000 0.00 0.00 41.42 3.18
112 113 5.411361 CCAACCAATTCTACACGAATCTTGA 59.589 40.000 0.00 0.00 41.42 3.02
113 114 5.411361 TCCAACCAATTCTACACGAATCTTG 59.589 40.000 0.00 0.00 41.42 3.02
114 115 5.556915 TCCAACCAATTCTACACGAATCTT 58.443 37.500 0.00 0.00 41.42 2.40
115 116 5.160607 TCCAACCAATTCTACACGAATCT 57.839 39.130 0.00 0.00 41.42 2.40
116 117 5.584649 TCATCCAACCAATTCTACACGAATC 59.415 40.000 0.00 0.00 41.42 2.52
117 118 5.496556 TCATCCAACCAATTCTACACGAAT 58.503 37.500 0.00 0.00 44.10 3.34
118 119 4.900684 TCATCCAACCAATTCTACACGAA 58.099 39.130 0.00 0.00 35.78 3.85
119 120 4.503910 CTCATCCAACCAATTCTACACGA 58.496 43.478 0.00 0.00 0.00 4.35
120 121 3.623060 CCTCATCCAACCAATTCTACACG 59.377 47.826 0.00 0.00 0.00 4.49
121 122 4.843728 TCCTCATCCAACCAATTCTACAC 58.156 43.478 0.00 0.00 0.00 2.90
122 123 5.684704 GATCCTCATCCAACCAATTCTACA 58.315 41.667 0.00 0.00 0.00 2.74
136 137 1.224075 CACACGCATGGATCCTCATC 58.776 55.000 14.23 0.00 0.00 2.92
137 138 0.179037 CCACACGCATGGATCCTCAT 60.179 55.000 14.23 0.00 43.02 2.90
138 139 1.221566 CCACACGCATGGATCCTCA 59.778 57.895 14.23 0.00 43.02 3.86
139 140 1.524621 CCCACACGCATGGATCCTC 60.525 63.158 14.23 1.21 43.02 3.71
140 141 2.591753 CCCACACGCATGGATCCT 59.408 61.111 14.23 0.00 43.02 3.24
141 142 3.211963 GCCCACACGCATGGATCC 61.212 66.667 4.20 4.20 43.02 3.36
142 143 3.576356 CGCCCACACGCATGGATC 61.576 66.667 7.11 0.00 43.02 3.36
143 144 4.094646 TCGCCCACACGCATGGAT 62.095 61.111 7.11 0.00 43.02 3.41
144 145 4.758251 CTCGCCCACACGCATGGA 62.758 66.667 7.11 0.00 43.02 3.41
146 147 3.049674 AACTCGCCCACACGCATG 61.050 61.111 0.00 0.00 0.00 4.06
147 148 3.049674 CAACTCGCCCACACGCAT 61.050 61.111 0.00 0.00 0.00 4.73
158 159 4.680237 TGGGCGTCTGGCAACTCG 62.680 66.667 0.00 0.00 46.16 4.18
159 160 3.050275 GTGGGCGTCTGGCAACTC 61.050 66.667 0.00 0.00 46.16 3.01
160 161 3.872603 TGTGGGCGTCTGGCAACT 61.873 61.111 0.00 0.00 44.75 3.16
161 162 3.660111 GTGTGGGCGTCTGGCAAC 61.660 66.667 0.00 0.00 46.16 4.17
165 166 4.602259 ACACGTGTGGGCGTCTGG 62.602 66.667 22.71 0.00 43.83 3.86
166 167 3.337889 CACACGTGTGGGCGTCTG 61.338 66.667 35.65 12.14 43.83 3.51
178 179 1.332552 GGAAACACTAACGCACACACG 60.333 52.381 0.00 0.00 39.50 4.49
179 180 1.332552 CGGAAACACTAACGCACACAC 60.333 52.381 0.00 0.00 0.00 3.82
180 181 0.931702 CGGAAACACTAACGCACACA 59.068 50.000 0.00 0.00 0.00 3.72
181 182 0.932399 ACGGAAACACTAACGCACAC 59.068 50.000 0.00 0.00 0.00 3.82
182 183 1.654317 AACGGAAACACTAACGCACA 58.346 45.000 0.00 0.00 0.00 4.57
183 184 2.223089 ACAAACGGAAACACTAACGCAC 60.223 45.455 0.00 0.00 0.00 5.34
184 185 2.008329 ACAAACGGAAACACTAACGCA 58.992 42.857 0.00 0.00 0.00 5.24
185 186 2.742954 ACAAACGGAAACACTAACGC 57.257 45.000 0.00 0.00 0.00 4.84
186 187 5.003684 GGAAAAACAAACGGAAACACTAACG 59.996 40.000 0.00 0.00 0.00 3.18
187 188 6.094719 AGGAAAAACAAACGGAAACACTAAC 58.905 36.000 0.00 0.00 0.00 2.34
188 189 6.270156 AGGAAAAACAAACGGAAACACTAA 57.730 33.333 0.00 0.00 0.00 2.24
189 190 5.900865 AGGAAAAACAAACGGAAACACTA 57.099 34.783 0.00 0.00 0.00 2.74
190 191 4.794278 AGGAAAAACAAACGGAAACACT 57.206 36.364 0.00 0.00 0.00 3.55
191 192 4.799949 GGTAGGAAAAACAAACGGAAACAC 59.200 41.667 0.00 0.00 0.00 3.32
192 193 4.438472 CGGTAGGAAAAACAAACGGAAACA 60.438 41.667 0.00 0.00 0.00 2.83
193 194 4.037021 CGGTAGGAAAAACAAACGGAAAC 58.963 43.478 0.00 0.00 0.00 2.78
194 195 3.488890 GCGGTAGGAAAAACAAACGGAAA 60.489 43.478 0.00 0.00 0.00 3.13
195 196 2.033174 GCGGTAGGAAAAACAAACGGAA 59.967 45.455 0.00 0.00 0.00 4.30
196 197 1.603326 GCGGTAGGAAAAACAAACGGA 59.397 47.619 0.00 0.00 0.00 4.69
197 198 1.334243 TGCGGTAGGAAAAACAAACGG 59.666 47.619 0.00 0.00 0.00 4.44
198 199 2.759538 TGCGGTAGGAAAAACAAACG 57.240 45.000 0.00 0.00 0.00 3.60
199 200 3.799963 CCTTTGCGGTAGGAAAAACAAAC 59.200 43.478 0.00 0.00 37.24 2.93
329 332 4.400567 GCAGTGATTTAGGGCATCTTTCTT 59.599 41.667 0.00 0.00 0.00 2.52
411 414 1.382557 TCCTCCCATCCGCTTGCTA 60.383 57.895 0.00 0.00 0.00 3.49
437 441 2.283676 GGGGTCCCGACTCTGTGA 60.284 66.667 0.48 0.00 30.95 3.58
452 456 1.178534 GCCGATCTGGAGAGAGAGGG 61.179 65.000 7.64 0.00 42.00 4.30
516 520 0.179084 TCTTATTGCTCCGCCCTTCG 60.179 55.000 0.00 0.00 38.08 3.79
580 584 4.383602 CGCACGCCGTTTCCTTGG 62.384 66.667 0.00 0.00 0.00 3.61
602 619 1.831652 AACTGCCGTCCCTCTCTTGG 61.832 60.000 0.00 0.00 0.00 3.61
603 620 0.035458 AAACTGCCGTCCCTCTCTTG 59.965 55.000 0.00 0.00 0.00 3.02
640 657 0.822164 AATCGACGAACCTGGTAGGG 59.178 55.000 0.00 0.00 40.58 3.53
645 662 0.170561 ACTCGAATCGACGAACCTGG 59.829 55.000 0.00 0.00 41.67 4.45
700 717 5.525378 CAGAAAGGTGGAGCAATACTATGAC 59.475 44.000 0.00 0.00 0.00 3.06
776 795 2.138596 AGCAAACATCGTTTTGGCTG 57.861 45.000 4.26 0.00 37.02 4.85
777 796 2.865551 CAAAGCAAACATCGTTTTGGCT 59.134 40.909 8.33 0.14 37.02 4.75
778 797 2.863137 TCAAAGCAAACATCGTTTTGGC 59.137 40.909 8.33 0.00 37.02 4.52
779 798 4.260172 GGTTCAAAGCAAACATCGTTTTGG 60.260 41.667 8.33 0.00 37.02 3.28
780 799 4.547966 CGGTTCAAAGCAAACATCGTTTTG 60.548 41.667 0.00 0.00 39.15 2.44
781 800 3.549873 CGGTTCAAAGCAAACATCGTTTT 59.450 39.130 0.00 0.00 0.00 2.43
782 801 3.112580 CGGTTCAAAGCAAACATCGTTT 58.887 40.909 0.00 0.00 0.00 3.60
783 802 2.542824 CCGGTTCAAAGCAAACATCGTT 60.543 45.455 0.00 0.00 0.00 3.85
784 803 1.001815 CCGGTTCAAAGCAAACATCGT 60.002 47.619 0.00 0.00 0.00 3.73
785 804 1.685302 CCGGTTCAAAGCAAACATCG 58.315 50.000 0.00 0.00 0.00 3.84
786 805 1.000274 AGCCGGTTCAAAGCAAACATC 60.000 47.619 1.90 0.00 0.00 3.06
787 806 1.039856 AGCCGGTTCAAAGCAAACAT 58.960 45.000 1.90 0.00 0.00 2.71
788 807 0.820871 AAGCCGGTTCAAAGCAAACA 59.179 45.000 1.90 0.00 0.00 2.83
789 808 1.202359 TCAAGCCGGTTCAAAGCAAAC 60.202 47.619 1.90 0.00 0.00 2.93
790 809 1.107114 TCAAGCCGGTTCAAAGCAAA 58.893 45.000 1.90 0.00 0.00 3.68
791 810 1.327303 ATCAAGCCGGTTCAAAGCAA 58.673 45.000 1.90 0.00 0.00 3.91
792 811 1.327303 AATCAAGCCGGTTCAAAGCA 58.673 45.000 1.90 0.00 0.00 3.91
793 812 3.782889 ATAATCAAGCCGGTTCAAAGC 57.217 42.857 1.90 0.00 0.00 3.51
794 813 6.189677 TGTTATAATCAAGCCGGTTCAAAG 57.810 37.500 1.90 0.00 0.00 2.77
795 814 6.576662 TTGTTATAATCAAGCCGGTTCAAA 57.423 33.333 1.90 0.00 0.00 2.69
796 815 6.559810 CATTGTTATAATCAAGCCGGTTCAA 58.440 36.000 1.90 0.00 0.00 2.69
797 816 5.449862 GCATTGTTATAATCAAGCCGGTTCA 60.450 40.000 1.90 0.00 0.00 3.18
798 817 4.976116 GCATTGTTATAATCAAGCCGGTTC 59.024 41.667 1.90 0.00 0.00 3.62
799 818 4.400884 TGCATTGTTATAATCAAGCCGGTT 59.599 37.500 1.90 0.00 0.00 4.44
800 819 3.951037 TGCATTGTTATAATCAAGCCGGT 59.049 39.130 1.90 0.00 0.00 5.28
801 820 4.539870 CTGCATTGTTATAATCAAGCCGG 58.460 43.478 0.00 0.00 0.00 6.13
802 821 4.036734 ACCTGCATTGTTATAATCAAGCCG 59.963 41.667 0.00 0.00 0.00 5.52
803 822 5.067674 TGACCTGCATTGTTATAATCAAGCC 59.932 40.000 0.00 0.00 0.00 4.35
824 843 7.375834 TCATATGTTAATCCGGTGTAGATGAC 58.624 38.462 0.00 0.00 0.00 3.06
832 851 7.065803 ACTGACTTTTCATATGTTAATCCGGTG 59.934 37.037 0.00 0.00 0.00 4.94
833 852 7.110155 ACTGACTTTTCATATGTTAATCCGGT 58.890 34.615 0.00 0.00 0.00 5.28
834 853 7.553881 ACTGACTTTTCATATGTTAATCCGG 57.446 36.000 1.90 0.00 0.00 5.14
836 855 8.560374 GCCTACTGACTTTTCATATGTTAATCC 58.440 37.037 1.90 0.00 0.00 3.01
842 966 9.113838 CTTATTGCCTACTGACTTTTCATATGT 57.886 33.333 1.90 0.00 0.00 2.29
865 989 2.237143 CCACTCCAGCATTGTCTCCTTA 59.763 50.000 0.00 0.00 0.00 2.69
939 1063 3.121030 CAAAGTGAGAGGCCGCCG 61.121 66.667 1.49 0.00 0.00 6.46
940 1064 2.032681 ACAAAGTGAGAGGCCGCC 59.967 61.111 1.49 0.00 0.00 6.13
941 1065 2.970974 GCACAAAGTGAGAGGCCGC 61.971 63.158 0.00 0.00 35.23 6.53
982 1106 2.323059 CATGACTGACGACTGTGTCTG 58.677 52.381 1.77 12.22 41.81 3.51
988 1112 5.831997 TGATATAACCATGACTGACGACTG 58.168 41.667 0.00 0.00 0.00 3.51
989 1113 5.010112 CCTGATATAACCATGACTGACGACT 59.990 44.000 0.00 0.00 0.00 4.18
990 1114 5.221263 ACCTGATATAACCATGACTGACGAC 60.221 44.000 0.00 0.00 0.00 4.34
991 1115 4.893524 ACCTGATATAACCATGACTGACGA 59.106 41.667 0.00 0.00 0.00 4.20
992 1116 4.984785 CACCTGATATAACCATGACTGACG 59.015 45.833 0.00 0.00 0.00 4.35
993 1117 4.752101 GCACCTGATATAACCATGACTGAC 59.248 45.833 0.00 0.00 0.00 3.51
994 1118 4.655649 AGCACCTGATATAACCATGACTGA 59.344 41.667 0.00 0.00 0.00 3.41
1004 1128 4.165950 ACCATTCCACAGCACCTGATATAA 59.834 41.667 0.00 0.00 35.18 0.98
1033 1157 2.713770 GATGCGCAGATGCCACTG 59.286 61.111 18.32 3.35 40.43 3.66
1072 1196 1.561643 CAGAGCAGGAGGTACTGGAA 58.438 55.000 0.00 0.00 41.55 3.53
1096 1220 1.071699 AGCAAACTTACGCAAGGGAGA 59.928 47.619 0.00 0.00 46.39 3.71
1228 1352 2.357637 TGTTGTTTGCAGAAGTAGCACC 59.642 45.455 0.00 0.00 42.54 5.01
1232 1356 4.511454 TGCTACTGTTGTTTGCAGAAGTAG 59.489 41.667 8.70 8.70 41.01 2.57
1278 1402 0.803768 CGAGGTGCATCAGGAGAACG 60.804 60.000 0.00 0.00 0.00 3.95
1551 1681 1.610102 CCTTCTCTGGTGGCAGTTCTG 60.610 57.143 0.00 0.00 0.00 3.02
1765 1913 0.755079 TGATCGGGCTCAAGATCCAG 59.245 55.000 0.00 0.00 41.76 3.86
1846 2000 4.079970 TCCATTATTTGGTTTACGTGGCA 58.920 39.130 0.00 0.00 46.52 4.92
2632 3084 4.332268 CCTTAAGCTGCAACTGAGATCTTC 59.668 45.833 1.02 0.00 0.00 2.87
2780 3232 1.167851 CCAAACAGCACACCGATGAT 58.832 50.000 0.00 0.00 0.00 2.45
2785 3237 1.063972 CACACCAAACAGCACACCG 59.936 57.895 0.00 0.00 0.00 4.94
2895 3347 0.107654 GATTTCGCCTAGTGCCTGGT 60.108 55.000 0.00 0.00 36.24 4.00
3244 3971 2.026915 CCTCCCACATCTTGTCATCACA 60.027 50.000 0.00 0.00 0.00 3.58
3315 4045 0.032912 TGGCATGTAGGTACCCTCGA 60.033 55.000 8.74 0.00 34.61 4.04
3498 4233 5.244402 ACAGCATCATTTCTCAAACAATGGA 59.756 36.000 0.00 0.00 32.17 3.41
3575 4317 6.183309 ACGAATAGCAAAAGAACTTCCATC 57.817 37.500 0.00 0.00 0.00 3.51
3591 4333 7.382488 AGACGGAATATCACAATGAACGAATAG 59.618 37.037 0.00 0.00 0.00 1.73
3623 4369 4.352600 AACACTAGAATACCACGACGAG 57.647 45.455 0.00 0.00 0.00 4.18
3624 4370 6.127925 ACAATAACACTAGAATACCACGACGA 60.128 38.462 0.00 0.00 0.00 4.20
3625 4371 6.032094 ACAATAACACTAGAATACCACGACG 58.968 40.000 0.00 0.00 0.00 5.12
3629 4383 9.431887 TGAAGAACAATAACACTAGAATACCAC 57.568 33.333 0.00 0.00 0.00 4.16
3660 4414 7.228706 AGTTAAAATATATCTCCAAACCTGGCG 59.771 37.037 0.00 0.00 43.17 5.69
3686 4440 9.547279 ACCTGGTAGATCACATATTCACATATA 57.453 33.333 0.00 0.00 0.00 0.86
3687 4441 8.441311 ACCTGGTAGATCACATATTCACATAT 57.559 34.615 0.00 0.00 0.00 1.78
3718 4472 2.358737 GTGGTGGGTCCTTGCTCG 60.359 66.667 0.00 0.00 37.07 5.03
3723 4477 1.386772 TCAAGGGTGGTGGGTCCTT 60.387 57.895 0.00 0.00 41.15 3.36
3801 4555 2.744202 CAGGTCATTCAGCTGGTTGTAC 59.256 50.000 15.13 11.03 45.53 2.90
3817 4571 6.183360 ACACGGAGATAATAACTTCTCAGGTC 60.183 42.308 5.35 0.00 40.13 3.85
3984 4740 9.886132 CAGACTGGTAGGTAATAAAACAATACT 57.114 33.333 0.00 0.00 0.00 2.12
4147 4908 1.305633 TCCTGGGAGACTGGCAGAG 60.306 63.158 23.66 6.58 38.04 3.35
4174 4935 4.154918 CCTCCTGAGTGACTTGCAAAATAC 59.845 45.833 0.00 0.00 0.00 1.89
4189 4950 1.630369 TGGGATCAAACACCTCCTGAG 59.370 52.381 0.00 0.00 0.00 3.35
4242 5003 4.018050 AGTCTGGAACTTCCCTTTATGCAT 60.018 41.667 3.79 3.79 35.03 3.96
4244 5005 3.956744 AGTCTGGAACTTCCCTTTATGC 58.043 45.455 5.30 0.00 35.03 3.14
4290 5051 2.301870 AGCGTTCACTCCAATCCACTAA 59.698 45.455 0.00 0.00 0.00 2.24
4327 5088 9.612620 CCGCAGATTTAATCAATATTTCCTTAC 57.387 33.333 7.74 0.00 0.00 2.34
4351 5112 3.488569 TGGGAATAGCCTGGGCCG 61.489 66.667 8.11 0.00 43.17 6.13
4354 5115 1.202651 CGTAAGTGGGAATAGCCTGGG 60.203 57.143 0.00 0.00 36.66 4.45
4371 5132 7.809331 AGTTCGAAAACACTCATAACATACGTA 59.191 33.333 0.00 0.00 37.88 3.57
4372 5133 6.643770 AGTTCGAAAACACTCATAACATACGT 59.356 34.615 0.00 0.00 37.88 3.57
4373 5134 7.045725 AGTTCGAAAACACTCATAACATACG 57.954 36.000 0.00 0.00 37.88 3.06
4374 5135 8.709646 AGAAGTTCGAAAACACTCATAACATAC 58.290 33.333 0.00 0.00 37.88 2.39
4393 5154 5.753438 TGTCACACACAGAATACAGAAGTTC 59.247 40.000 0.00 0.00 0.00 3.01
4399 5160 4.380531 AGGTTGTCACACACAGAATACAG 58.619 43.478 0.00 0.00 35.97 2.74
4400 5161 4.141824 TGAGGTTGTCACACACAGAATACA 60.142 41.667 0.00 0.00 35.97 2.29
4417 5178 2.086869 CCGCATCATTCTTGTGAGGTT 58.913 47.619 0.00 0.00 32.79 3.50
4463 5224 3.317406 ACCCAAGCCATTTTCCTTCTTT 58.683 40.909 0.00 0.00 0.00 2.52
4571 5332 2.237143 TCAATAAGTCTCCAGGCCTGTG 59.763 50.000 30.63 22.02 0.00 3.66
4578 5339 4.122776 CCGGTTGATCAATAAGTCTCCAG 58.877 47.826 12.12 3.31 0.00 3.86
4638 5399 3.290948 TCCCCAAGATTTCCATTACGG 57.709 47.619 0.00 0.00 0.00 4.02
4673 5434 1.446516 CCAATCCGCGGATGCATTGA 61.447 55.000 39.53 11.89 42.97 2.57
4688 5449 0.038343 GTGTTCAATGCCACGCCAAT 60.038 50.000 0.00 0.00 0.00 3.16
4698 5459 0.606401 ACTCCAGCCCGTGTTCAATG 60.606 55.000 0.00 0.00 0.00 2.82
4736 5497 1.529226 TCCATTACCAACACGCCAAG 58.471 50.000 0.00 0.00 0.00 3.61
4740 5501 4.551388 TCAAAATTCCATTACCAACACGC 58.449 39.130 0.00 0.00 0.00 5.34
4760 5521 0.323629 GTCCCACCAAGACCGAATCA 59.676 55.000 0.00 0.00 0.00 2.57
4768 5529 0.552367 ATCCATGGGTCCCACCAAGA 60.552 55.000 14.57 8.11 45.13 3.02
4774 5535 0.630673 CTTGGAATCCATGGGTCCCA 59.369 55.000 24.64 14.64 38.19 4.37


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

AutoCloner maintained by Alex Coulton.