Multiple sequence alignment - TraesCS5A01G323100

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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 TraesCS5A01G323100 chr5A 100.000 3119 0 0 1 3119 535234908 535238026 0.000000e+00 5760
1 TraesCS5A01G323100 chr5D 93.750 784 49 0 1305 2088 421651836 421652619 0.000000e+00 1177
2 TraesCS5A01G323100 chr5D 90.244 861 65 12 474 1319 421647757 421648613 0.000000e+00 1107
3 TraesCS5A01G323100 chr5D 83.813 939 134 10 1392 2320 421654792 421655722 0.000000e+00 876
4 TraesCS5A01G323100 chr5D 85.099 604 62 16 2310 2888 421657375 421657975 2.680000e-165 592
5 TraesCS5A01G323100 chr5D 89.474 304 14 2 161 461 421647249 421647537 4.910000e-98 368
6 TraesCS5A01G323100 chr5B 93.691 745 47 0 1305 2049 508015135 508015879 0.000000e+00 1116
7 TraesCS5A01G323100 chr5B 88.966 580 44 6 757 1324 508007212 508007783 0.000000e+00 699
8 TraesCS5A01G323100 chr5B 88.806 536 48 7 2239 2765 508061976 508062508 0.000000e+00 647
9 TraesCS5A01G323100 chr5B 85.876 531 68 6 1715 2240 508061187 508061715 2.720000e-155 558
10 TraesCS5A01G323100 chr5B 95.572 271 12 0 161 431 508004192 508004462 4.780000e-118 435
11 TraesCS5A01G323100 chr5B 91.544 272 14 4 474 736 508006741 508007012 1.770000e-97 366
12 TraesCS5A01G323100 chr5B 83.812 383 49 10 2748 3119 508062548 508062928 4.950000e-93 351
13 TraesCS5A01G323100 chr5B 84.848 165 20 3 1 160 458688974 458689138 8.950000e-36 161
14 TraesCS5A01G323100 chr1B 86.145 166 17 4 1 160 133266617 133266782 1.150000e-39 174
15 TraesCS5A01G323100 chr4B 85.119 168 19 4 1 162 38636153 38635986 1.920000e-37 167
16 TraesCS5A01G323100 chr4B 82.278 158 23 3 1 153 546822166 546822323 7.020000e-27 132
17 TraesCS5A01G323100 chr7B 85.030 167 18 6 1 160 733674285 733674451 2.490000e-36 163
18 TraesCS5A01G323100 chr7B 83.226 155 22 3 2595 2746 716789472 716789319 4.190000e-29 139
19 TraesCS5A01G323100 chr3A 84.940 166 19 4 1 160 673920739 673920904 2.490000e-36 163
20 TraesCS5A01G323100 chr6B 83.537 164 24 2 1 161 288432639 288432476 1.940000e-32 150
21 TraesCS5A01G323100 chr3B 83.537 164 23 4 1 160 31187947 31187784 1.940000e-32 150
22 TraesCS5A01G323100 chr4D 81.503 173 25 6 1 167 505727313 505727484 5.430000e-28 135


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 TraesCS5A01G323100 chr5A 535234908 535238026 3118 False 5760.000000 5760 100.000000 1 3119 1 chr5A.!!$F1 3118
1 TraesCS5A01G323100 chr5D 421647249 421657975 10726 False 824.000000 1177 88.476000 161 2888 5 chr5D.!!$F1 2727
2 TraesCS5A01G323100 chr5B 508015135 508015879 744 False 1116.000000 1116 93.691000 1305 2049 1 chr5B.!!$F2 744
3 TraesCS5A01G323100 chr5B 508061187 508062928 1741 False 518.666667 647 86.164667 1715 3119 3 chr5B.!!$F4 1404
4 TraesCS5A01G323100 chr5B 508004192 508007783 3591 False 500.000000 699 92.027333 161 1324 3 chr5B.!!$F3 1163

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
32 33 0.106819 AGGCATGTGAGAGGGATTGC 60.107 55.0 0.0 0.0 0.0 3.56 F
1200 3644 0.039437 TCTTCACCTGCGAAGACGAC 60.039 55.0 0.0 0.0 45.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 7324 0.031616 GTCCTCATCCTCCTCCCACT 60.032 60.0 0.0 0.0 0.0 4.00 R
2913 13481 0.032615 AACCTGAACCAAGTTGCCCA 60.033 50.0 0.0 0.0 0.0 5.36 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 3.889227 CCCACACGTAGGCATGTG 58.111 61.111 0.00 7.46 45.58 3.21
26 27 0.532573 ACACGTAGGCATGTGAGAGG 59.467 55.000 13.69 0.00 43.26 3.69
27 28 0.179100 CACGTAGGCATGTGAGAGGG 60.179 60.000 0.00 0.00 43.26 4.30
28 29 0.324368 ACGTAGGCATGTGAGAGGGA 60.324 55.000 0.00 0.00 0.00 4.20
29 30 1.043816 CGTAGGCATGTGAGAGGGAT 58.956 55.000 0.00 0.00 0.00 3.85
30 31 1.414181 CGTAGGCATGTGAGAGGGATT 59.586 52.381 0.00 0.00 0.00 3.01
31 32 2.804572 CGTAGGCATGTGAGAGGGATTG 60.805 54.545 0.00 0.00 0.00 2.67
32 33 0.106819 AGGCATGTGAGAGGGATTGC 60.107 55.000 0.00 0.00 0.00 3.56
33 34 1.442526 GGCATGTGAGAGGGATTGCG 61.443 60.000 0.00 0.00 0.00 4.85
34 35 1.442526 GCATGTGAGAGGGATTGCGG 61.443 60.000 0.00 0.00 0.00 5.69
35 36 0.178767 CATGTGAGAGGGATTGCGGA 59.821 55.000 0.00 0.00 0.00 5.54
36 37 0.911769 ATGTGAGAGGGATTGCGGAA 59.088 50.000 0.00 0.00 0.00 4.30
37 38 0.690192 TGTGAGAGGGATTGCGGAAA 59.310 50.000 0.00 0.00 0.00 3.13
38 39 1.073125 TGTGAGAGGGATTGCGGAAAA 59.927 47.619 0.00 0.00 0.00 2.29
39 40 2.159382 GTGAGAGGGATTGCGGAAAAA 58.841 47.619 0.00 0.00 0.00 1.94
55 56 3.371359 AAAAACGCGCGGACATTAC 57.629 47.368 35.22 0.00 0.00 1.89
56 57 0.869730 AAAAACGCGCGGACATTACT 59.130 45.000 35.22 7.19 0.00 2.24
57 58 0.869730 AAAACGCGCGGACATTACTT 59.130 45.000 35.22 13.77 0.00 2.24
58 59 0.165079 AAACGCGCGGACATTACTTG 59.835 50.000 35.22 1.22 0.00 3.16
59 60 0.947180 AACGCGCGGACATTACTTGT 60.947 50.000 35.22 4.80 42.79 3.16
60 61 0.947180 ACGCGCGGACATTACTTGTT 60.947 50.000 35.22 4.55 39.18 2.83
61 62 0.165079 CGCGCGGACATTACTTGTTT 59.835 50.000 24.84 0.00 39.18 2.83
62 63 1.785518 CGCGCGGACATTACTTGTTTC 60.786 52.381 24.84 0.00 39.18 2.78
63 64 1.785518 GCGCGGACATTACTTGTTTCG 60.786 52.381 8.83 0.00 39.18 3.46
64 65 1.878373 GCGGACATTACTTGTTTCGC 58.122 50.000 10.06 10.06 46.11 4.70
65 66 1.465187 GCGGACATTACTTGTTTCGCC 60.465 52.381 12.86 0.00 46.26 5.54
66 67 1.129811 CGGACATTACTTGTTTCGCCC 59.870 52.381 0.00 0.00 39.18 6.13
67 68 2.156098 GGACATTACTTGTTTCGCCCA 58.844 47.619 0.00 0.00 39.18 5.36
68 69 2.095415 GGACATTACTTGTTTCGCCCAC 60.095 50.000 0.00 0.00 39.18 4.61
69 70 2.550606 GACATTACTTGTTTCGCCCACA 59.449 45.455 0.00 0.00 39.18 4.17
70 71 2.292292 ACATTACTTGTTTCGCCCACAC 59.708 45.455 0.00 0.00 33.74 3.82
71 72 0.938713 TTACTTGTTTCGCCCACACG 59.061 50.000 0.00 0.00 0.00 4.49
72 73 0.179078 TACTTGTTTCGCCCACACGT 60.179 50.000 0.00 0.00 31.97 4.49
73 74 0.179078 ACTTGTTTCGCCCACACGTA 60.179 50.000 0.00 0.00 0.00 3.57
74 75 1.153353 CTTGTTTCGCCCACACGTAT 58.847 50.000 0.00 0.00 0.00 3.06
75 76 0.869068 TTGTTTCGCCCACACGTATG 59.131 50.000 0.00 0.00 0.00 2.39
76 77 1.133869 GTTTCGCCCACACGTATGC 59.866 57.895 0.00 0.00 0.00 3.14
87 88 2.125713 CGTATGCGTGTGGGCTGA 60.126 61.111 0.00 0.00 0.00 4.26
88 89 1.521457 CGTATGCGTGTGGGCTGAT 60.521 57.895 0.00 0.00 0.00 2.90
89 90 0.249280 CGTATGCGTGTGGGCTGATA 60.249 55.000 0.00 0.00 0.00 2.15
90 91 1.217882 GTATGCGTGTGGGCTGATAC 58.782 55.000 0.00 0.00 0.00 2.24
91 92 1.119684 TATGCGTGTGGGCTGATACT 58.880 50.000 0.00 0.00 0.00 2.12
92 93 0.179073 ATGCGTGTGGGCTGATACTC 60.179 55.000 0.00 0.00 0.00 2.59
93 94 1.257750 TGCGTGTGGGCTGATACTCT 61.258 55.000 0.00 0.00 0.00 3.24
94 95 0.108138 GCGTGTGGGCTGATACTCTT 60.108 55.000 0.00 0.00 0.00 2.85
95 96 1.136305 GCGTGTGGGCTGATACTCTTA 59.864 52.381 0.00 0.00 0.00 2.10
96 97 2.799917 GCGTGTGGGCTGATACTCTTAG 60.800 54.545 0.00 0.00 0.00 2.18
97 98 2.688446 CGTGTGGGCTGATACTCTTAGA 59.312 50.000 0.00 0.00 0.00 2.10
98 99 3.489398 CGTGTGGGCTGATACTCTTAGAC 60.489 52.174 0.00 0.00 0.00 2.59
99 100 3.447586 GTGTGGGCTGATACTCTTAGACA 59.552 47.826 0.00 0.00 0.00 3.41
100 101 3.447586 TGTGGGCTGATACTCTTAGACAC 59.552 47.826 0.00 0.00 0.00 3.67
101 102 3.031736 TGGGCTGATACTCTTAGACACC 58.968 50.000 0.00 0.00 0.00 4.16
102 103 3.031736 GGGCTGATACTCTTAGACACCA 58.968 50.000 0.00 0.00 0.00 4.17
103 104 3.181474 GGGCTGATACTCTTAGACACCAC 60.181 52.174 0.00 0.00 0.00 4.16
104 105 3.447586 GGCTGATACTCTTAGACACCACA 59.552 47.826 0.00 0.00 0.00 4.17
105 106 4.425520 GCTGATACTCTTAGACACCACAC 58.574 47.826 0.00 0.00 0.00 3.82
106 107 4.082190 GCTGATACTCTTAGACACCACACA 60.082 45.833 0.00 0.00 0.00 3.72
107 108 5.566826 GCTGATACTCTTAGACACCACACAA 60.567 44.000 0.00 0.00 0.00 3.33
108 109 5.779922 TGATACTCTTAGACACCACACAAC 58.220 41.667 0.00 0.00 0.00 3.32
109 110 5.303333 TGATACTCTTAGACACCACACAACA 59.697 40.000 0.00 0.00 0.00 3.33
110 111 4.689612 ACTCTTAGACACCACACAACAT 57.310 40.909 0.00 0.00 0.00 2.71
111 112 5.801531 ACTCTTAGACACCACACAACATA 57.198 39.130 0.00 0.00 0.00 2.29
112 113 6.360370 ACTCTTAGACACCACACAACATAT 57.640 37.500 0.00 0.00 0.00 1.78
113 114 6.166279 ACTCTTAGACACCACACAACATATG 58.834 40.000 0.00 0.00 0.00 1.78
114 115 6.109156 TCTTAGACACCACACAACATATGT 57.891 37.500 1.41 1.41 45.34 2.29
124 125 2.936202 ACAACATATGTGGGCAGATCC 58.064 47.619 14.82 0.00 41.93 3.36
125 126 2.241941 ACAACATATGTGGGCAGATCCA 59.758 45.455 14.82 0.00 41.93 3.41
126 127 3.117398 ACAACATATGTGGGCAGATCCAT 60.117 43.478 14.82 0.00 41.93 3.41
127 128 3.889859 ACATATGTGGGCAGATCCATT 57.110 42.857 7.78 0.00 39.26 3.16
128 129 4.999469 ACATATGTGGGCAGATCCATTA 57.001 40.909 7.78 0.00 39.26 1.90
129 130 5.323382 ACATATGTGGGCAGATCCATTAA 57.677 39.130 7.78 0.00 39.26 1.40
130 131 5.072741 ACATATGTGGGCAGATCCATTAAC 58.927 41.667 7.78 0.00 39.26 2.01
131 132 3.668141 ATGTGGGCAGATCCATTAACA 57.332 42.857 0.00 0.00 39.26 2.41
132 133 2.722094 TGTGGGCAGATCCATTAACAC 58.278 47.619 0.00 0.00 39.26 3.32
133 134 2.024414 GTGGGCAGATCCATTAACACC 58.976 52.381 0.00 0.00 39.26 4.16
134 135 1.064017 TGGGCAGATCCATTAACACCC 60.064 52.381 0.00 0.00 36.21 4.61
135 136 1.064017 GGGCAGATCCATTAACACCCA 60.064 52.381 0.00 0.00 36.07 4.51
136 137 2.024414 GGCAGATCCATTAACACCCAC 58.976 52.381 0.00 0.00 34.01 4.61
137 138 2.620367 GGCAGATCCATTAACACCCACA 60.620 50.000 0.00 0.00 34.01 4.17
138 139 3.088532 GCAGATCCATTAACACCCACAA 58.911 45.455 0.00 0.00 0.00 3.33
139 140 3.129287 GCAGATCCATTAACACCCACAAG 59.871 47.826 0.00 0.00 0.00 3.16
140 141 4.335416 CAGATCCATTAACACCCACAAGT 58.665 43.478 0.00 0.00 0.00 3.16
141 142 4.156556 CAGATCCATTAACACCCACAAGTG 59.843 45.833 0.00 0.00 43.65 3.16
153 154 0.442310 CACAAGTGTGGGCGTTATCG 59.558 55.000 3.39 0.00 42.10 2.92
154 155 0.672401 ACAAGTGTGGGCGTTATCGG 60.672 55.000 0.00 0.00 37.56 4.18
180 181 4.766891 TCCTATCTTTTTGTTGCAGGGAAG 59.233 41.667 0.00 0.00 0.00 3.46
201 202 3.527665 AGTAAACCCCATATCTGGTTGCT 59.472 43.478 6.25 5.68 43.94 3.91
208 209 3.494924 CCCATATCTGGTTGCTCAATCGA 60.495 47.826 0.00 0.00 41.37 3.59
262 263 1.349688 TCGCCAACCATGAGTAAAGGT 59.650 47.619 0.00 0.00 37.20 3.50
377 378 7.553881 AATGAATATCGTTCCAAGATTCGTT 57.446 32.000 0.00 0.00 33.16 3.85
406 407 9.799106 CCTCTCTTATCTCTCTCTATCTTTCTT 57.201 37.037 0.00 0.00 0.00 2.52
520 2760 8.730680 GCGATATATAATGGAATGGTTTCAGTT 58.269 33.333 0.00 0.00 33.23 3.16
528 2768 2.957402 ATGGTTTCAGTTCTCCAGCA 57.043 45.000 0.00 0.00 33.33 4.41
544 2784 3.640498 TCCAGCATGAACCAACATTTTGA 59.360 39.130 0.00 0.00 39.69 2.69
573 2813 1.271926 ACAAATCAACCCTTCCCTCGG 60.272 52.381 0.00 0.00 0.00 4.63
646 2895 4.730949 ATTTGCCTTGATCATGTGAAGG 57.269 40.909 6.08 6.08 39.51 3.46
689 2938 9.166126 GTCGGCAGCTATTTTTACATTATAAAC 57.834 33.333 0.00 0.00 0.00 2.01
696 2945 9.498307 GCTATTTTTACATTATAAACTGCACGT 57.502 29.630 0.00 0.00 0.00 4.49
736 2985 1.130777 TGCATACATCTAGCTGGCCA 58.869 50.000 4.71 4.71 0.00 5.36
737 2986 1.701292 TGCATACATCTAGCTGGCCAT 59.299 47.619 5.51 0.00 0.00 4.40
908 3342 7.209340 TCTCCTATAAGATATCCCTCGCTAA 57.791 40.000 0.00 0.00 0.00 3.09
943 3377 4.379918 CCACACAACAACAACACACACATA 60.380 41.667 0.00 0.00 0.00 2.29
944 3378 4.556912 CACACAACAACAACACACACATAC 59.443 41.667 0.00 0.00 0.00 2.39
945 3379 4.216472 ACACAACAACAACACACACATACA 59.784 37.500 0.00 0.00 0.00 2.29
947 3381 4.457603 ACAACAACAACACACACATACACT 59.542 37.500 0.00 0.00 0.00 3.55
948 3382 4.614555 ACAACAACACACACATACACTG 57.385 40.909 0.00 0.00 0.00 3.66
949 3383 4.257731 ACAACAACACACACATACACTGA 58.742 39.130 0.00 0.00 0.00 3.41
950 3384 4.881273 ACAACAACACACACATACACTGAT 59.119 37.500 0.00 0.00 0.00 2.90
988 3425 2.174854 TCATCTAGATCGACCACCCTCA 59.825 50.000 1.03 0.00 0.00 3.86
1028 3465 1.376466 CACTGGTAGGCTGGTGCTT 59.624 57.895 0.00 0.00 39.59 3.91
1032 3469 0.771127 TGGTAGGCTGGTGCTTCTTT 59.229 50.000 0.00 0.00 39.59 2.52
1045 3482 0.962356 CTTCTTTCTGGTGGCGGCAT 60.962 55.000 17.19 0.00 0.00 4.40
1097 3534 1.457380 TACACCCCTCCTCCTTCCCA 61.457 60.000 0.00 0.00 0.00 4.37
1153 3597 2.360726 CCAACGGCCAACCCTACC 60.361 66.667 2.24 0.00 0.00 3.18
1159 3603 2.745037 GCCAACCCTACCGTGTCA 59.255 61.111 0.00 0.00 0.00 3.58
1170 3614 4.121317 CCTACCGTGTCAACTACAACAAA 58.879 43.478 0.00 0.00 40.63 2.83
1200 3644 0.039437 TCTTCACCTGCGAAGACGAC 60.039 55.000 0.00 0.00 45.00 4.34
1209 3653 2.893398 GAAGACGACTGGGGCGAT 59.107 61.111 0.00 0.00 0.00 4.58
1212 3656 0.968901 AAGACGACTGGGGCGATACA 60.969 55.000 0.00 0.00 0.00 2.29
1216 3660 1.146041 GACTGGGGCGATACATGCA 59.854 57.895 0.00 0.00 0.00 3.96
1239 3683 2.671070 CAATGCCCGGACCTCTGT 59.329 61.111 0.73 0.00 0.00 3.41
1252 3696 1.197430 CCTCTGTCCCAAGTCCTGCT 61.197 60.000 0.00 0.00 0.00 4.24
1255 3699 1.461268 TGTCCCAAGTCCTGCTCCA 60.461 57.895 0.00 0.00 0.00 3.86
1256 3700 0.842030 TGTCCCAAGTCCTGCTCCAT 60.842 55.000 0.00 0.00 0.00 3.41
1281 3725 1.586541 CAGCTACTGCGAGACCACA 59.413 57.895 0.00 0.00 45.42 4.17
1290 3734 0.389817 GCGAGACCACATGCAGTACA 60.390 55.000 0.00 0.00 0.00 2.90
1293 3737 2.196749 GAGACCACATGCAGTACATCG 58.803 52.381 0.00 0.00 36.64 3.84
1329 7010 8.872845 TCATATGTCGATCAATATGTTGCATAC 58.127 33.333 17.90 0.00 35.26 2.39
1387 7068 6.978343 TTATACACCTTTGAGTTTGATCCG 57.022 37.500 0.00 0.00 0.00 4.18
1443 7124 2.187163 GGCGACCCTAGCTTCACC 59.813 66.667 0.00 0.00 34.52 4.02
1446 7127 2.348888 CGACCCTAGCTTCACCGGT 61.349 63.158 0.00 0.00 0.00 5.28
1473 7154 2.758979 CGGTGTCACCTACTACTTCCAT 59.241 50.000 19.82 0.00 35.66 3.41
1530 7211 0.530288 TCGATCTCCACATCAACGCA 59.470 50.000 0.00 0.00 0.00 5.24
1557 7238 3.292159 GGCAACCACAACCCCGTC 61.292 66.667 0.00 0.00 0.00 4.79
1561 7242 0.313672 CAACCACAACCCCGTCAATG 59.686 55.000 0.00 0.00 0.00 2.82
1632 7313 2.167861 CCTCTTTGTAGGCGCTCGC 61.168 63.158 7.64 5.60 41.06 5.03
1638 7319 4.821589 GTAGGCGCTCGCAAGGCT 62.822 66.667 16.36 6.32 45.47 4.58
1656 7337 0.396417 CTGTCGAGTGGGAGGAGGAT 60.396 60.000 0.00 0.00 0.00 3.24
1668 7349 2.122768 GAGGAGGATGAGGACCACATT 58.877 52.381 5.83 0.00 0.00 2.71
1683 7364 5.888161 GGACCACATTGAGATAACCTTCAAT 59.112 40.000 0.00 0.00 33.62 2.57
1792 7473 3.074390 TGTCAACTCCATCAAGGTGGATT 59.926 43.478 1.90 0.00 46.67 3.01
1820 7501 0.955428 GTGTTCAGCATCTCGGCCAA 60.955 55.000 2.24 0.00 0.00 4.52
1823 7504 2.434884 CAGCATCTCGGCCAACGT 60.435 61.111 2.24 0.00 44.69 3.99
1859 7540 3.695060 GACGAGGACTCTAAGATCCACAA 59.305 47.826 0.00 0.00 37.47 3.33
1863 7544 5.220892 CGAGGACTCTAAGATCCACAACTAC 60.221 48.000 0.00 0.00 37.47 2.73
1883 7564 1.959226 GCAAGACCGCGAAGGACAA 60.959 57.895 8.23 0.00 45.00 3.18
1926 7607 3.057245 GCTTCAAGTTTCATTCCCTCACC 60.057 47.826 0.00 0.00 0.00 4.02
1947 7628 2.778679 GTTGTCGATGGCGTGCTC 59.221 61.111 0.00 0.00 38.98 4.26
1992 7673 7.320399 ACTACGTCAATAAGATGAATGTCACA 58.680 34.615 0.00 0.00 36.71 3.58
2034 7715 1.508632 GCACGCCAAAGTACTTCTCA 58.491 50.000 8.95 0.00 0.00 3.27
2061 7742 0.456142 TCTTCTCGACGGATTGTGCG 60.456 55.000 0.00 0.00 37.19 5.34
2081 7762 2.297701 GGTCTCCAAGTTTCAGCACAA 58.702 47.619 0.00 0.00 0.00 3.33
2091 10644 3.672447 CAGCACAATGGTGGCGCA 61.672 61.111 10.83 0.00 45.38 6.09
2093 10646 2.431260 GCACAATGGTGGCGCAAG 60.431 61.111 10.83 0.00 45.38 4.01
2107 10660 2.918345 GCAAGCCATGTTCGTGCCA 61.918 57.895 10.48 0.00 33.81 4.92
2121 10674 1.608109 CGTGCCATGGCTGCATAAATA 59.392 47.619 35.53 11.01 41.46 1.40
2186 10739 3.273434 GAATAAGGCAGTGAGTGATGCA 58.727 45.455 0.00 0.00 44.37 3.96
2235 10797 8.748380 TCACGATGATAAATAAGCTCTATGTG 57.252 34.615 0.00 0.00 0.00 3.21
2259 11083 6.979817 TGGCTATCATTGTAAAATGAATGTGC 59.020 34.615 12.34 12.67 41.90 4.57
2270 11095 6.704512 AAAATGAATGTGCACCGTTAATTC 57.295 33.333 15.69 15.96 0.00 2.17
2284 11109 1.948104 TAATTCGGCCGTGGATCTTG 58.052 50.000 27.15 0.00 0.00 3.02
2332 12821 6.747414 TGGAGTGCATTAACCAGTATAGAT 57.253 37.500 0.00 0.00 0.00 1.98
2344 12833 9.674068 TTAACCAGTATAGATGCAAATACAACA 57.326 29.630 15.50 0.00 32.14 3.33
2390 12879 5.568620 AGGTCCCTAACTGCTAATTATGG 57.431 43.478 0.00 0.00 0.00 2.74
2409 12898 4.870123 TGGCAACACATCAAGCTTAATT 57.130 36.364 0.00 0.00 46.17 1.40
2410 12899 4.558178 TGGCAACACATCAAGCTTAATTG 58.442 39.130 0.00 0.00 46.17 2.32
2432 12921 3.369892 GGGATAGACTGTGTGCATCACTT 60.370 47.826 16.70 7.17 46.27 3.16
2437 12926 1.311859 CTGTGTGCATCACTTGGTGT 58.688 50.000 16.70 0.00 46.27 4.16
2445 12934 2.616510 GCATCACTTGGTGTAGAGGCTT 60.617 50.000 0.00 0.00 33.83 4.35
2469 12958 8.937634 TTATTGTCTTCCCTATTTTCGTAGAC 57.062 34.615 0.00 0.00 34.32 2.59
2505 12994 4.879545 GGTTAATCGGTAATTGAGAAGCCA 59.120 41.667 0.00 0.00 0.00 4.75
2508 12997 1.006832 CGGTAATTGAGAAGCCACCG 58.993 55.000 0.00 0.00 42.41 4.94
2512 13001 3.118884 GGTAATTGAGAAGCCACCGTAGA 60.119 47.826 0.00 0.00 0.00 2.59
2563 13052 3.724508 TGTTGGCATATTTTATGCGGG 57.275 42.857 12.05 0.00 45.41 6.13
2566 13055 4.036971 TGTTGGCATATTTTATGCGGGTAC 59.963 41.667 12.05 8.37 45.41 3.34
2578 13067 8.734218 TTTTATGCGGGTACATAAATACTTCA 57.266 30.769 9.73 0.00 46.47 3.02
2699 13189 5.509716 TTACTTCTCGTTGTGACTGAAGA 57.490 39.130 7.85 0.00 37.41 2.87
2712 13202 7.156876 TGTGACTGAAGAAAGACATTTTGTT 57.843 32.000 0.00 0.00 0.00 2.83
2716 13206 7.970061 TGACTGAAGAAAGACATTTTGTTCAAG 59.030 33.333 11.62 9.07 34.14 3.02
2756 13311 1.363744 CATGAGACCTTTCGACCTGC 58.636 55.000 0.00 0.00 0.00 4.85
2764 13319 2.572104 ACCTTTCGACCTGCCTTATCTT 59.428 45.455 0.00 0.00 0.00 2.40
2818 13373 8.148807 TCTATCTTGATCTCTTGTCTTCTACG 57.851 38.462 0.00 0.00 0.00 3.51
2819 13374 6.767524 ATCTTGATCTCTTGTCTTCTACGT 57.232 37.500 0.00 0.00 0.00 3.57
2833 13401 6.183360 TGTCTTCTACGTCATCTCCAGTAATG 60.183 42.308 0.00 0.00 0.00 1.90
2838 13406 3.386078 ACGTCATCTCCAGTAATGAGCAT 59.614 43.478 0.00 0.00 32.76 3.79
2858 13426 4.335416 CATACCCACTCAACCAAGTCATT 58.665 43.478 0.00 0.00 0.00 2.57
2860 13428 1.270550 CCCACTCAACCAAGTCATTGC 59.729 52.381 0.00 0.00 34.91 3.56
2867 13435 5.083533 TCAACCAAGTCATTGCTGTTTTT 57.916 34.783 0.00 0.00 34.91 1.94
2871 13439 6.655078 ACCAAGTCATTGCTGTTTTTATCT 57.345 33.333 0.00 0.00 34.91 1.98
2872 13440 6.449698 ACCAAGTCATTGCTGTTTTTATCTG 58.550 36.000 0.00 0.00 34.91 2.90
2895 13463 9.412460 TCTGGAATTTTGAATGATAGCATAACT 57.588 29.630 0.00 0.00 33.44 2.24
2913 13481 3.241067 ACTGTAATATGTCAACCGCGT 57.759 42.857 4.92 0.00 0.00 6.01
2915 13483 2.272678 TGTAATATGTCAACCGCGTGG 58.727 47.619 14.93 14.93 42.84 4.94
2956 13524 4.529897 TCTTTAGGGTGTCTATGCGACTA 58.470 43.478 0.00 0.00 43.25 2.59
2957 13525 4.579340 TCTTTAGGGTGTCTATGCGACTAG 59.421 45.833 0.00 0.00 43.25 2.57
2958 13526 2.730934 AGGGTGTCTATGCGACTAGA 57.269 50.000 0.00 0.00 43.25 2.43
2964 13532 4.045104 GTGTCTATGCGACTAGATTGTGG 58.955 47.826 0.00 0.00 43.25 4.17
2965 13533 3.053455 GTCTATGCGACTAGATTGTGGC 58.947 50.000 0.00 0.00 41.10 5.01
2973 13541 2.298158 CTAGATTGTGGCGGCGAGGT 62.298 60.000 12.98 0.00 0.00 3.85
2996 13564 4.192317 GGCTTCATTGTCCTAGTGTAAGG 58.808 47.826 0.00 0.00 38.06 2.69
3014 13582 1.375326 GATAATGTCCTCCCCGCCC 59.625 63.158 0.00 0.00 0.00 6.13
3020 13588 3.117648 TCCTCCCCGCCCTATCCT 61.118 66.667 0.00 0.00 0.00 3.24
3030 13598 2.358898 CCGCCCTATCCTCATTTTGTTG 59.641 50.000 0.00 0.00 0.00 3.33
3031 13599 2.358898 CGCCCTATCCTCATTTTGTTGG 59.641 50.000 0.00 0.00 0.00 3.77
3043 13611 4.277174 TCATTTTGTTGGTGTGCTTATCGT 59.723 37.500 0.00 0.00 0.00 3.73
3047 13615 1.017177 TTGGTGTGCTTATCGTCGGC 61.017 55.000 0.00 0.00 0.00 5.54
3052 13620 0.179134 GTGCTTATCGTCGGCAGAGT 60.179 55.000 0.00 0.00 36.62 3.24
3071 13639 1.881973 GTGCATGTGGATGTGTGTCTT 59.118 47.619 0.00 0.00 31.50 3.01
3074 13642 2.687370 CATGTGGATGTGTGTCTTCGA 58.313 47.619 0.00 0.00 0.00 3.71
3084 13652 4.079970 TGTGTGTCTTCGATAGGTCTTCT 58.920 43.478 0.00 0.00 0.00 2.85
3089 13657 5.766174 GTGTCTTCGATAGGTCTTCTAGGAT 59.234 44.000 0.00 0.00 0.00 3.24
3092 13660 4.995624 TCGATAGGTCTTCTAGGATCCA 57.004 45.455 15.82 0.00 0.00 3.41
3096 13664 5.514136 CGATAGGTCTTCTAGGATCCAGTCT 60.514 48.000 15.82 7.43 0.00 3.24
3098 13666 3.529734 AGGTCTTCTAGGATCCAGTCTGA 59.470 47.826 15.82 3.60 0.00 3.27
3099 13667 4.017037 AGGTCTTCTAGGATCCAGTCTGAA 60.017 45.833 15.82 9.21 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.179100 CCCTCTCACATGCCTACGTG 60.179 60.000 0.00 0.00 38.85 4.49
9 10 0.324368 TCCCTCTCACATGCCTACGT 60.324 55.000 0.00 0.00 0.00 3.57
10 11 1.043816 ATCCCTCTCACATGCCTACG 58.956 55.000 0.00 0.00 0.00 3.51
11 12 2.843701 CAATCCCTCTCACATGCCTAC 58.156 52.381 0.00 0.00 0.00 3.18
12 13 1.141657 GCAATCCCTCTCACATGCCTA 59.858 52.381 0.00 0.00 0.00 3.93
13 14 0.106819 GCAATCCCTCTCACATGCCT 60.107 55.000 0.00 0.00 0.00 4.75
14 15 1.442526 CGCAATCCCTCTCACATGCC 61.443 60.000 0.00 0.00 0.00 4.40
15 16 1.442526 CCGCAATCCCTCTCACATGC 61.443 60.000 0.00 0.00 0.00 4.06
16 17 0.178767 TCCGCAATCCCTCTCACATG 59.821 55.000 0.00 0.00 0.00 3.21
17 18 0.911769 TTCCGCAATCCCTCTCACAT 59.088 50.000 0.00 0.00 0.00 3.21
18 19 0.690192 TTTCCGCAATCCCTCTCACA 59.310 50.000 0.00 0.00 0.00 3.58
19 20 1.821216 TTTTCCGCAATCCCTCTCAC 58.179 50.000 0.00 0.00 0.00 3.51
20 21 2.577606 TTTTTCCGCAATCCCTCTCA 57.422 45.000 0.00 0.00 0.00 3.27
37 38 0.869730 AGTAATGTCCGCGCGTTTTT 59.130 45.000 29.95 17.87 0.00 1.94
38 39 0.869730 AAGTAATGTCCGCGCGTTTT 59.130 45.000 29.95 17.53 0.00 2.43
39 40 0.165079 CAAGTAATGTCCGCGCGTTT 59.835 50.000 29.95 17.88 0.00 3.60
40 41 0.947180 ACAAGTAATGTCCGCGCGTT 60.947 50.000 29.95 18.56 37.96 4.84
41 42 0.947180 AACAAGTAATGTCCGCGCGT 60.947 50.000 29.95 12.50 42.99 6.01
42 43 0.165079 AAACAAGTAATGTCCGCGCG 59.835 50.000 25.67 25.67 42.99 6.86
43 44 1.785518 CGAAACAAGTAATGTCCGCGC 60.786 52.381 0.00 0.00 42.99 6.86
44 45 1.785518 GCGAAACAAGTAATGTCCGCG 60.786 52.381 0.00 0.00 46.35 6.46
46 47 1.129811 GGGCGAAACAAGTAATGTCCG 59.870 52.381 0.00 0.00 42.99 4.79
47 48 2.095415 GTGGGCGAAACAAGTAATGTCC 60.095 50.000 0.00 0.00 42.99 4.02
48 49 2.550606 TGTGGGCGAAACAAGTAATGTC 59.449 45.455 0.00 0.00 42.99 3.06
49 50 2.292292 GTGTGGGCGAAACAAGTAATGT 59.708 45.455 0.00 0.00 46.82 2.71
50 51 2.664424 CGTGTGGGCGAAACAAGTAATG 60.664 50.000 0.00 0.00 0.00 1.90
51 52 1.533731 CGTGTGGGCGAAACAAGTAAT 59.466 47.619 0.00 0.00 0.00 1.89
52 53 0.938713 CGTGTGGGCGAAACAAGTAA 59.061 50.000 0.00 0.00 0.00 2.24
53 54 0.179078 ACGTGTGGGCGAAACAAGTA 60.179 50.000 0.00 0.00 38.27 2.24
54 55 0.179078 TACGTGTGGGCGAAACAAGT 60.179 50.000 0.00 9.32 41.91 3.16
55 56 1.136085 CATACGTGTGGGCGAAACAAG 60.136 52.381 4.09 0.00 35.59 3.16
56 57 0.869068 CATACGTGTGGGCGAAACAA 59.131 50.000 4.09 0.00 35.59 2.83
57 58 1.570347 GCATACGTGTGGGCGAAACA 61.570 55.000 14.49 0.00 35.59 2.83
58 59 1.133869 GCATACGTGTGGGCGAAAC 59.866 57.895 14.49 0.00 35.59 2.78
59 60 3.568686 GCATACGTGTGGGCGAAA 58.431 55.556 14.49 0.00 35.59 3.46
71 72 1.202533 AGTATCAGCCCACACGCATAC 60.203 52.381 0.00 0.00 0.00 2.39
72 73 1.068588 GAGTATCAGCCCACACGCATA 59.931 52.381 0.00 0.00 33.17 3.14
73 74 0.179073 GAGTATCAGCCCACACGCAT 60.179 55.000 0.00 0.00 33.17 4.73
74 75 1.218047 GAGTATCAGCCCACACGCA 59.782 57.895 0.00 0.00 33.17 5.24
75 76 0.108138 AAGAGTATCAGCCCACACGC 60.108 55.000 0.00 0.00 37.82 5.34
76 77 2.688446 TCTAAGAGTATCAGCCCACACG 59.312 50.000 0.00 0.00 37.82 4.49
77 78 3.447586 TGTCTAAGAGTATCAGCCCACAC 59.552 47.826 0.00 0.00 37.82 3.82
78 79 3.447586 GTGTCTAAGAGTATCAGCCCACA 59.552 47.826 0.00 0.00 37.82 4.17
79 80 3.181474 GGTGTCTAAGAGTATCAGCCCAC 60.181 52.174 0.00 0.00 37.82 4.61
80 81 3.031736 GGTGTCTAAGAGTATCAGCCCA 58.968 50.000 0.00 0.00 37.82 5.36
81 82 3.031736 TGGTGTCTAAGAGTATCAGCCC 58.968 50.000 0.00 0.00 37.82 5.19
82 83 3.447586 TGTGGTGTCTAAGAGTATCAGCC 59.552 47.826 0.00 0.00 37.82 4.85
83 84 4.082190 TGTGTGGTGTCTAAGAGTATCAGC 60.082 45.833 0.00 0.00 37.82 4.26
84 85 5.644977 TGTGTGGTGTCTAAGAGTATCAG 57.355 43.478 0.00 0.00 37.82 2.90
85 86 5.303333 TGTTGTGTGGTGTCTAAGAGTATCA 59.697 40.000 0.00 0.00 37.82 2.15
86 87 5.779922 TGTTGTGTGGTGTCTAAGAGTATC 58.220 41.667 0.00 0.00 0.00 2.24
87 88 5.801531 TGTTGTGTGGTGTCTAAGAGTAT 57.198 39.130 0.00 0.00 0.00 2.12
88 89 5.801531 ATGTTGTGTGGTGTCTAAGAGTA 57.198 39.130 0.00 0.00 0.00 2.59
89 90 4.689612 ATGTTGTGTGGTGTCTAAGAGT 57.310 40.909 0.00 0.00 0.00 3.24
90 91 6.166279 ACATATGTTGTGTGGTGTCTAAGAG 58.834 40.000 1.41 0.00 37.11 2.85
91 92 6.109156 ACATATGTTGTGTGGTGTCTAAGA 57.891 37.500 1.41 0.00 37.11 2.10
104 105 2.241941 TGGATCTGCCCACATATGTTGT 59.758 45.455 5.37 0.00 34.68 3.32
105 106 2.934887 TGGATCTGCCCACATATGTTG 58.065 47.619 5.37 2.32 34.97 3.33
106 107 3.889859 ATGGATCTGCCCACATATGTT 57.110 42.857 5.37 0.00 39.34 2.71
107 108 3.889859 AATGGATCTGCCCACATATGT 57.110 42.857 1.41 1.41 39.34 2.29
108 109 5.048504 GTGTTAATGGATCTGCCCACATATG 60.049 44.000 0.00 0.00 39.34 1.78
109 110 5.072741 GTGTTAATGGATCTGCCCACATAT 58.927 41.667 0.00 0.00 39.34 1.78
110 111 4.460263 GTGTTAATGGATCTGCCCACATA 58.540 43.478 0.00 0.00 39.34 2.29
111 112 3.290710 GTGTTAATGGATCTGCCCACAT 58.709 45.455 0.00 0.00 39.34 3.21
112 113 2.620367 GGTGTTAATGGATCTGCCCACA 60.620 50.000 0.00 0.00 39.34 4.17
113 114 2.024414 GGTGTTAATGGATCTGCCCAC 58.976 52.381 0.00 0.00 39.34 4.61
114 115 1.064017 GGGTGTTAATGGATCTGCCCA 60.064 52.381 0.00 0.00 41.05 5.36
115 116 1.064017 TGGGTGTTAATGGATCTGCCC 60.064 52.381 0.00 0.00 34.97 5.36
116 117 2.024414 GTGGGTGTTAATGGATCTGCC 58.976 52.381 0.00 0.00 37.10 4.85
117 118 2.722094 TGTGGGTGTTAATGGATCTGC 58.278 47.619 0.00 0.00 0.00 4.26
118 119 4.156556 CACTTGTGGGTGTTAATGGATCTG 59.843 45.833 0.00 0.00 33.04 2.90
119 120 4.202567 ACACTTGTGGGTGTTAATGGATCT 60.203 41.667 5.72 0.00 46.71 2.75
120 121 4.079253 ACACTTGTGGGTGTTAATGGATC 58.921 43.478 5.72 0.00 46.71 3.36
121 122 3.826157 CACACTTGTGGGTGTTAATGGAT 59.174 43.478 5.72 0.00 46.71 3.41
122 123 3.218453 CACACTTGTGGGTGTTAATGGA 58.782 45.455 5.72 0.00 46.71 3.41
123 124 3.641437 CACACTTGTGGGTGTTAATGG 57.359 47.619 5.72 0.00 46.71 3.16
134 135 0.442310 CGATAACGCCCACACTTGTG 59.558 55.000 2.13 2.13 45.23 3.33
135 136 0.672401 CCGATAACGCCCACACTTGT 60.672 55.000 0.00 0.00 38.29 3.16
136 137 1.977594 GCCGATAACGCCCACACTTG 61.978 60.000 0.00 0.00 38.29 3.16
137 138 1.743995 GCCGATAACGCCCACACTT 60.744 57.895 0.00 0.00 38.29 3.16
138 139 2.125269 GCCGATAACGCCCACACT 60.125 61.111 0.00 0.00 38.29 3.55
139 140 3.560278 CGCCGATAACGCCCACAC 61.560 66.667 0.00 0.00 38.29 3.82
140 141 3.993376 GACGCCGATAACGCCCACA 62.993 63.158 0.00 0.00 38.29 4.17
141 142 3.259751 GACGCCGATAACGCCCAC 61.260 66.667 0.00 0.00 38.29 4.61
142 143 4.517815 GGACGCCGATAACGCCCA 62.518 66.667 0.00 0.00 38.29 5.36
143 144 2.151049 ATAGGACGCCGATAACGCCC 62.151 60.000 0.00 0.00 38.29 6.13
144 145 0.731855 GATAGGACGCCGATAACGCC 60.732 60.000 0.00 0.00 38.29 5.68
145 146 0.240411 AGATAGGACGCCGATAACGC 59.760 55.000 0.00 0.00 38.29 4.84
146 147 2.701073 AAGATAGGACGCCGATAACG 57.299 50.000 0.00 0.00 39.43 3.18
147 148 4.569564 ACAAAAAGATAGGACGCCGATAAC 59.430 41.667 0.00 0.00 0.00 1.89
148 149 4.761975 ACAAAAAGATAGGACGCCGATAA 58.238 39.130 0.00 0.00 0.00 1.75
149 150 4.395959 ACAAAAAGATAGGACGCCGATA 57.604 40.909 0.00 0.00 0.00 2.92
150 151 3.261981 ACAAAAAGATAGGACGCCGAT 57.738 42.857 0.00 0.00 0.00 4.18
151 152 2.739913 CAACAAAAAGATAGGACGCCGA 59.260 45.455 0.00 0.00 0.00 5.54
152 153 2.727916 GCAACAAAAAGATAGGACGCCG 60.728 50.000 0.00 0.00 0.00 6.46
153 154 2.227865 TGCAACAAAAAGATAGGACGCC 59.772 45.455 0.00 0.00 0.00 5.68
154 155 3.492313 CTGCAACAAAAAGATAGGACGC 58.508 45.455 0.00 0.00 0.00 5.19
155 156 3.119849 CCCTGCAACAAAAAGATAGGACG 60.120 47.826 0.00 0.00 0.00 4.79
156 157 4.079253 TCCCTGCAACAAAAAGATAGGAC 58.921 43.478 0.00 0.00 0.00 3.85
157 158 4.380843 TCCCTGCAACAAAAAGATAGGA 57.619 40.909 0.00 0.00 0.00 2.94
158 159 4.524328 ACTTCCCTGCAACAAAAAGATAGG 59.476 41.667 0.00 0.00 0.00 2.57
159 160 5.712152 ACTTCCCTGCAACAAAAAGATAG 57.288 39.130 0.00 0.00 0.00 2.08
180 181 3.883489 GAGCAACCAGATATGGGGTTTAC 59.117 47.826 11.86 0.00 44.78 2.01
201 202 5.147330 TCTAGGAAAGCAAACTCGATTGA 57.853 39.130 2.94 0.00 31.84 2.57
208 209 3.010420 GCCGATTCTAGGAAAGCAAACT 58.990 45.455 0.00 0.00 0.00 2.66
262 263 3.222855 CGCCCAACCTTGTTGCCA 61.223 61.111 1.46 0.00 0.00 4.92
314 315 7.437862 ACGTGTGAATAAATTTCAAGCAATTGT 59.562 29.630 7.40 0.00 0.00 2.71
377 378 7.872061 AGATAGAGAGAGATAAGAGAGGTGA 57.128 40.000 0.00 0.00 0.00 4.02
406 407 3.578282 TCAGGATATAATGAAGCCGCTCA 59.422 43.478 0.00 0.00 0.00 4.26
462 2429 9.768215 TCATGGATTCTCAGGTGTGTATATATA 57.232 33.333 0.00 0.00 0.00 0.86
465 2432 6.784473 TCTCATGGATTCTCAGGTGTGTATAT 59.216 38.462 0.00 0.00 0.00 0.86
466 2433 6.136155 TCTCATGGATTCTCAGGTGTGTATA 58.864 40.000 0.00 0.00 0.00 1.47
469 2436 3.176411 TCTCATGGATTCTCAGGTGTGT 58.824 45.455 0.00 0.00 0.00 3.72
470 2437 3.900966 TCTCATGGATTCTCAGGTGTG 57.099 47.619 0.00 0.00 0.00 3.82
471 2438 4.778579 CATTCTCATGGATTCTCAGGTGT 58.221 43.478 0.00 0.00 0.00 4.16
520 2760 2.885135 ATGTTGGTTCATGCTGGAGA 57.115 45.000 0.00 0.00 0.00 3.71
528 2768 5.598005 TCAAGAGGTCAAAATGTTGGTTCAT 59.402 36.000 0.00 0.00 35.29 2.57
544 2784 4.184649 AGGGTTGATTTGTTCAAGAGGT 57.815 40.909 0.00 0.00 44.89 3.85
573 2813 5.446473 CGGATCAGCATCTGTTTGTAGTTTC 60.446 44.000 0.00 0.00 31.37 2.78
646 2895 1.461127 CGACAGGTACTTTTGCTGCTC 59.539 52.381 0.00 0.00 34.60 4.26
696 2945 1.391577 AGCCGTGATATTTGCATGCA 58.608 45.000 18.46 18.46 0.00 3.96
761 3189 4.985538 ATTGACTAAGTCAGGGTCTACG 57.014 45.455 0.00 0.00 43.69 3.51
908 3342 2.038426 TGTTGTGTGGCAGCTATAGTGT 59.962 45.455 0.84 0.00 0.00 3.55
943 3377 2.908688 TGCAGTGTGTGTATCAGTGT 57.091 45.000 0.00 0.00 38.19 3.55
944 3378 6.092533 TGAATATTGCAGTGTGTGTATCAGTG 59.907 38.462 0.00 0.00 38.72 3.66
945 3379 6.172630 TGAATATTGCAGTGTGTGTATCAGT 58.827 36.000 0.00 0.00 0.00 3.41
947 3381 7.049754 AGATGAATATTGCAGTGTGTGTATCA 58.950 34.615 0.00 0.00 0.00 2.15
948 3382 7.488187 AGATGAATATTGCAGTGTGTGTATC 57.512 36.000 0.00 0.00 0.00 2.24
949 3383 8.424133 TCTAGATGAATATTGCAGTGTGTGTAT 58.576 33.333 0.00 0.00 0.00 2.29
950 3384 7.781056 TCTAGATGAATATTGCAGTGTGTGTA 58.219 34.615 0.00 0.00 0.00 2.90
988 3425 1.647545 CGAGCCATTGTTGCCACGAT 61.648 55.000 0.00 0.00 33.21 3.73
1028 3465 0.539438 AAATGCCGCCACCAGAAAGA 60.539 50.000 0.00 0.00 0.00 2.52
1032 3469 3.372730 GCAAATGCCGCCACCAGA 61.373 61.111 0.00 0.00 34.31 3.86
1045 3482 2.735478 CACGACGCCTACCGCAAA 60.735 61.111 0.00 0.00 41.76 3.68
1060 3497 4.512914 GGGAGGATGCTGGCCCAC 62.513 72.222 0.00 0.00 40.39 4.61
1061 3498 3.346035 TAGGGAGGATGCTGGCCCA 62.346 63.158 12.79 0.00 43.20 5.36
1070 3507 0.936863 AGGAGGGGTGTAGGGAGGAT 60.937 60.000 0.00 0.00 0.00 3.24
1146 3590 1.999648 TGTAGTTGACACGGTAGGGT 58.000 50.000 0.00 0.00 36.16 4.34
1151 3595 2.679336 GGTTTGTTGTAGTTGACACGGT 59.321 45.455 0.00 0.00 37.96 4.83
1153 3597 2.678836 TGGGTTTGTTGTAGTTGACACG 59.321 45.455 0.00 0.00 37.96 4.49
1155 3599 3.444388 GGTTGGGTTTGTTGTAGTTGACA 59.556 43.478 0.00 0.00 35.78 3.58
1159 3603 1.406180 GCGGTTGGGTTTGTTGTAGTT 59.594 47.619 0.00 0.00 0.00 2.24
1170 3614 1.303317 GGTGAAGATGCGGTTGGGT 60.303 57.895 0.00 0.00 0.00 4.51
1200 3644 1.293963 CGATGCATGTATCGCCCCAG 61.294 60.000 28.85 6.50 42.74 4.45
1235 3679 1.194781 GGAGCAGGACTTGGGACAGA 61.195 60.000 0.00 0.00 42.39 3.41
1239 3683 0.842030 ACATGGAGCAGGACTTGGGA 60.842 55.000 0.00 0.00 0.00 4.37
1252 3696 2.320745 CAGTAGCTGCATGACATGGA 57.679 50.000 17.03 13.35 0.00 3.41
1279 3723 8.739972 TGAATATATACTCGATGTACTGCATGT 58.260 33.333 0.00 0.00 38.06 3.21
1387 7068 2.565834 ACTCCACACACCCTACATACAC 59.434 50.000 0.00 0.00 0.00 2.90
1473 7154 1.600058 AATCCTGATCCTTCCTGCCA 58.400 50.000 0.00 0.00 0.00 4.92
1485 7166 2.159043 GGAGACGATGCAGAAATCCTGA 60.159 50.000 0.00 0.00 45.78 3.86
1530 7211 2.264005 TGTGGTTGCCGATAAAGTGT 57.736 45.000 0.00 0.00 0.00 3.55
1557 7238 4.582869 TCCATGTGAAGTTCCTCTCATTG 58.417 43.478 0.00 0.00 29.32 2.82
1561 7242 5.344743 TGTATCCATGTGAAGTTCCTCTC 57.655 43.478 0.00 0.00 0.00 3.20
1584 7265 1.021390 CGAAGGTGACACTGATGGCC 61.021 60.000 5.39 0.00 29.67 5.36
1619 7300 2.434185 CCTTGCGAGCGCCTACAA 60.434 61.111 12.70 4.96 41.09 2.41
1632 7313 1.079543 CTCCCACTCGACAGCCTTG 60.080 63.158 0.00 0.00 0.00 3.61
1638 7319 0.684479 CATCCTCCTCCCACTCGACA 60.684 60.000 0.00 0.00 0.00 4.35
1643 7324 0.031616 GTCCTCATCCTCCTCCCACT 60.032 60.000 0.00 0.00 0.00 4.00
1656 7337 4.104086 AGGTTATCTCAATGTGGTCCTCA 58.896 43.478 0.00 0.00 0.00 3.86
1668 7349 3.117888 GCTCCCCATTGAAGGTTATCTCA 60.118 47.826 0.00 0.00 0.00 3.27
1770 7451 2.054021 TCCACCTTGATGGAGTTGACA 58.946 47.619 0.00 0.00 44.14 3.58
1792 7473 1.199789 GATGCTGAACACATTGGCGAA 59.800 47.619 0.00 0.00 0.00 4.70
1883 7564 0.687354 AAGGTCAAGGTGCACGAGAT 59.313 50.000 11.45 0.00 0.00 2.75
1992 7673 3.127099 CATGATGGGCATCTTGGCT 57.873 52.632 0.00 0.00 43.20 4.75
2017 7698 2.607187 CGATGAGAAGTACTTTGGCGT 58.393 47.619 10.02 3.85 0.00 5.68
2034 7715 2.482333 CGTCGAGAAGAGGCCCGAT 61.482 63.158 0.00 0.00 33.47 4.18
2061 7742 1.967319 TGTGCTGAAACTTGGAGACC 58.033 50.000 0.00 0.00 0.00 3.85
2091 10644 1.885157 CATGGCACGAACATGGCTT 59.115 52.632 0.00 0.00 45.16 4.35
2121 10674 1.134371 GCGTATCTCCTTGGAGGCTTT 60.134 52.381 15.81 3.05 34.61 3.51
2127 10680 1.476891 GTGACTGCGTATCTCCTTGGA 59.523 52.381 0.00 0.00 0.00 3.53
2186 10739 2.299013 TCGTTACACTCACTCAATGCCT 59.701 45.455 0.00 0.00 0.00 4.75
2235 10797 6.979817 TGCACATTCATTTTACAATGATAGCC 59.020 34.615 5.17 0.00 46.68 3.93
2270 11095 1.217882 GTTATCAAGATCCACGGCCG 58.782 55.000 26.86 26.86 0.00 6.13
2332 12821 6.862209 AGTTCTTCAAACTGTTGTATTTGCA 58.138 32.000 0.00 0.00 36.06 4.08
2344 12833 4.457949 ACGTTCAACCAAGTTCTTCAAACT 59.542 37.500 0.00 0.00 0.00 2.66
2390 12879 3.928375 CCCAATTAAGCTTGATGTGTTGC 59.072 43.478 9.86 0.00 0.00 4.17
2409 12898 2.187100 TGATGCACACAGTCTATCCCA 58.813 47.619 0.00 0.00 0.00 4.37
2410 12899 2.988010 TGATGCACACAGTCTATCCC 57.012 50.000 0.00 0.00 0.00 3.85
2432 12921 4.081087 GGAAGACAATAAGCCTCTACACCA 60.081 45.833 0.00 0.00 0.00 4.17
2437 12926 7.691993 AAATAGGGAAGACAATAAGCCTCTA 57.308 36.000 0.00 0.00 0.00 2.43
2445 12934 7.067372 TCGTCTACGAAAATAGGGAAGACAATA 59.933 37.037 2.10 0.00 46.30 1.90
2478 12967 6.967199 GCTTCTCAATTACCGATTAACCTTTG 59.033 38.462 0.00 0.00 0.00 2.77
2479 12968 6.095021 GGCTTCTCAATTACCGATTAACCTTT 59.905 38.462 0.00 0.00 0.00 3.11
2492 12981 3.132289 CCTCTACGGTGGCTTCTCAATTA 59.868 47.826 0.00 0.00 0.00 1.40
2607 13096 8.842280 TCAAAGTCAACCAACGTTTTTATCTAT 58.158 29.630 0.00 0.00 0.00 1.98
2619 13109 9.180678 CAACACTTTATATCAAAGTCAACCAAC 57.819 33.333 0.00 0.00 38.32 3.77
2671 13161 7.375834 TCAGTCACAACGAGAAGTAATATTGT 58.624 34.615 0.00 0.00 0.00 2.71
2673 13163 8.304596 TCTTCAGTCACAACGAGAAGTAATATT 58.695 33.333 0.00 0.00 40.38 1.28
2679 13169 4.386867 TTCTTCAGTCACAACGAGAAGT 57.613 40.909 0.00 0.00 40.38 3.01
2756 13311 7.366847 TCCAGAAAGATGGAGTAAGATAAGG 57.633 40.000 0.00 0.00 44.56 2.69
2818 13373 5.233988 GGTATGCTCATTACTGGAGATGAC 58.766 45.833 0.00 0.00 34.24 3.06
2819 13374 4.284490 GGGTATGCTCATTACTGGAGATGA 59.716 45.833 0.00 0.00 34.24 2.92
2833 13401 2.290323 ACTTGGTTGAGTGGGTATGCTC 60.290 50.000 0.00 0.00 0.00 4.26
2838 13406 3.750371 CAATGACTTGGTTGAGTGGGTA 58.250 45.455 0.00 0.00 0.00 3.69
2858 13426 8.991026 CATTCAAAATTCCAGATAAAAACAGCA 58.009 29.630 0.00 0.00 0.00 4.41
2871 13439 8.970020 ACAGTTATGCTATCATTCAAAATTCCA 58.030 29.630 0.00 0.00 34.22 3.53
2888 13456 5.440685 GCGGTTGACATATTACAGTTATGC 58.559 41.667 0.00 0.00 31.54 3.14
2889 13457 5.233476 ACGCGGTTGACATATTACAGTTATG 59.767 40.000 12.47 0.00 34.03 1.90
2890 13458 5.233476 CACGCGGTTGACATATTACAGTTAT 59.767 40.000 12.47 0.00 0.00 1.89
2892 13460 3.369756 CACGCGGTTGACATATTACAGTT 59.630 43.478 12.47 0.00 0.00 3.16
2895 13463 2.272678 CCACGCGGTTGACATATTACA 58.727 47.619 12.47 0.00 0.00 2.41
2913 13481 0.032615 AACCTGAACCAAGTTGCCCA 60.033 50.000 0.00 0.00 0.00 5.36
2915 13483 2.430694 AGAAAACCTGAACCAAGTTGCC 59.569 45.455 0.00 0.00 0.00 4.52
2956 13524 3.706373 ACCTCGCCGCCACAATCT 61.706 61.111 0.00 0.00 0.00 2.40
2957 13525 3.499737 CACCTCGCCGCCACAATC 61.500 66.667 0.00 0.00 0.00 2.67
2965 13533 2.436646 AATGAAGCCACCTCGCCG 60.437 61.111 0.00 0.00 0.00 6.46
2973 13541 4.323485 CCTTACACTAGGACAATGAAGCCA 60.323 45.833 0.00 0.00 37.50 4.75
2996 13564 1.128188 AGGGCGGGGAGGACATTATC 61.128 60.000 0.00 0.00 0.00 1.75
3014 13582 4.460382 AGCACACCAACAAAATGAGGATAG 59.540 41.667 0.00 0.00 0.00 2.08
3020 13588 4.277174 ACGATAAGCACACCAACAAAATGA 59.723 37.500 0.00 0.00 0.00 2.57
3030 13598 1.421410 CTGCCGACGATAAGCACACC 61.421 60.000 0.00 0.00 32.06 4.16
3031 13599 0.457853 TCTGCCGACGATAAGCACAC 60.458 55.000 0.00 0.00 32.06 3.82
3043 13611 1.902765 ATCCACATGCACTCTGCCGA 61.903 55.000 0.00 0.00 44.23 5.54
3047 13615 1.467342 CACACATCCACATGCACTCTG 59.533 52.381 0.00 0.00 32.57 3.35
3052 13620 2.153645 GAAGACACACATCCACATGCA 58.846 47.619 0.00 0.00 32.57 3.96
3062 13630 4.079970 AGAAGACCTATCGAAGACACACA 58.920 43.478 0.00 0.00 42.51 3.72
3071 13639 4.351407 ACTGGATCCTAGAAGACCTATCGA 59.649 45.833 14.23 0.00 0.00 3.59
3074 13642 5.374154 TCAGACTGGATCCTAGAAGACCTAT 59.626 44.000 14.23 0.00 0.00 2.57
3084 13652 5.221521 CGGAATCAATTCAGACTGGATCCTA 60.222 44.000 14.23 0.00 38.53 2.94
3089 13657 2.571653 ACCGGAATCAATTCAGACTGGA 59.428 45.455 9.46 0.00 38.53 3.86
3092 13660 2.571653 TCCACCGGAATCAATTCAGACT 59.428 45.455 9.46 0.00 38.53 3.24
3096 13664 3.054434 ACAGATCCACCGGAATCAATTCA 60.054 43.478 9.46 0.00 38.53 2.57
3098 13666 3.652057 ACAGATCCACCGGAATCAATT 57.348 42.857 9.46 0.00 34.34 2.32


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

AutoCloner maintained by Alex Coulton.