Multiple sequence alignment - TraesCS7B01G070200

Loading Multiple Alignment...

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 TraesCS7B01G070200 chr7B 100.000 3172 0 0 1 3172 76902925 76906096 0.000000e+00 5858.0
1 TraesCS7B01G070200 chr7B 95.890 146 6 0 1 146 612629351 612629206 1.470000e-58 237.0
2 TraesCS7B01G070200 chr7B 95.302 149 5 2 1 149 747848208 747848354 5.290000e-58 235.0
3 TraesCS7B01G070200 chr7B 93.902 82 5 0 3088 3169 657494331 657494250 1.190000e-24 124.0
4 TraesCS7B01G070200 chr7B 89.247 93 9 1 3078 3170 587901291 587901382 7.190000e-22 115.0
5 TraesCS7B01G070200 chr7B 96.429 56 2 0 142 197 107765295 107765350 3.370000e-15 93.5
6 TraesCS7B01G070200 chr7B 83.333 60 8 2 146 205 528399237 528399180 2.000000e-03 54.7
7 TraesCS7B01G070200 chr7A 90.054 2574 86 61 547 3012 121055762 121058273 0.000000e+00 3179.0
8 TraesCS7B01G070200 chr7A 91.866 209 8 2 347 555 121045029 121045228 1.860000e-72 283.0
9 TraesCS7B01G070200 chr7A 94.048 84 5 0 3087 3170 707996105 707996188 9.240000e-26 128.0
10 TraesCS7B01G070200 chr7A 93.902 82 5 0 3089 3170 509467123 509467204 1.190000e-24 124.0
11 TraesCS7B01G070200 chr7D 91.546 2354 80 54 280 2573 117132039 117134333 0.000000e+00 3134.0
12 TraesCS7B01G070200 chr7D 94.203 483 15 4 2596 3069 117134324 117134802 0.000000e+00 725.0
13 TraesCS7B01G070200 chr7D 88.235 68 5 1 156 220 117131972 117132039 9.430000e-11 78.7
14 TraesCS7B01G070200 chrUn 96.732 153 4 1 1 153 77123311 77123160 1.460000e-63 254.0
15 TraesCS7B01G070200 chr6B 96.732 153 4 1 1 153 98426069 98426220 1.460000e-63 254.0
16 TraesCS7B01G070200 chr6B 91.667 144 12 0 1398 1541 639534393 639534250 1.930000e-47 200.0
17 TraesCS7B01G070200 chr6B 81.026 195 23 10 1013 1199 639534744 639534556 3.300000e-30 143.0
18 TraesCS7B01G070200 chr5B 96.644 149 5 0 1 149 579372014 579371866 6.790000e-62 248.0
19 TraesCS7B01G070200 chr5B 92.857 56 4 0 142 197 691938948 691938893 7.290000e-12 82.4
20 TraesCS7B01G070200 chr4A 95.541 157 4 3 1 156 726513882 726513728 6.790000e-62 248.0
21 TraesCS7B01G070200 chr4A 97.260 146 3 1 1 146 662589070 662589214 2.440000e-61 246.0
22 TraesCS7B01G070200 chr4A 96.599 147 4 1 1 147 608188756 608188611 3.160000e-60 243.0
23 TraesCS7B01G070200 chr4A 96.575 146 5 0 1 146 697964316 697964171 3.160000e-60 243.0
24 TraesCS7B01G070200 chr4A 94.340 53 3 0 142 194 31417403 31417455 7.290000e-12 82.4
25 TraesCS7B01G070200 chr6D 92.361 144 11 0 1398 1541 423816353 423816210 4.150000e-49 206.0
26 TraesCS7B01G070200 chr6D 91.860 86 7 0 3085 3170 445581628 445581543 1.550000e-23 121.0
27 TraesCS7B01G070200 chr6D 96.296 54 2 0 142 195 394210027 394210080 4.360000e-14 89.8
28 TraesCS7B01G070200 chr6A 90.972 144 13 0 1398 1541 568517412 568517269 8.980000e-46 195.0
29 TraesCS7B01G070200 chr6A 81.538 195 22 10 1013 1199 568517761 568517573 7.090000e-32 148.0
30 TraesCS7B01G070200 chr6A 92.857 84 6 0 3087 3170 537876262 537876345 4.300000e-24 122.0
31 TraesCS7B01G070200 chr2D 87.218 133 17 0 1409 1541 546209815 546209947 5.480000e-33 152.0
32 TraesCS7B01G070200 chr2B 87.218 133 17 0 1409 1541 653017848 653017980 5.480000e-33 152.0
33 TraesCS7B01G070200 chr2A 87.218 133 17 0 1409 1541 687050274 687050406 5.480000e-33 152.0
34 TraesCS7B01G070200 chr2A 94.444 54 3 0 142 195 11009268 11009215 2.030000e-12 84.2
35 TraesCS7B01G070200 chr4D 94.048 84 5 0 3087 3170 54289116 54289199 9.240000e-26 128.0
36 TraesCS7B01G070200 chr5A 92.045 88 6 1 3084 3170 29678338 29678251 4.300000e-24 122.0
37 TraesCS7B01G070200 chr3D 91.011 89 8 0 3082 3170 475555029 475555117 1.550000e-23 121.0
38 TraesCS7B01G070200 chr3B 94.643 56 3 0 142 197 11565355 11565300 1.570000e-13 87.9
39 TraesCS7B01G070200 chr3B 94.444 54 3 0 142 195 738194994 738195047 2.030000e-12 84.2
40 TraesCS7B01G070200 chr4B 92.857 56 4 0 142 197 377932598 377932543 7.290000e-12 82.4


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 TraesCS7B01G070200 chr7B 76902925 76906096 3171 False 5858.000000 5858 100.000 1 3172 1 chr7B.!!$F1 3171
1 TraesCS7B01G070200 chr7A 121055762 121058273 2511 False 3179.000000 3179 90.054 547 3012 1 chr7A.!!$F2 2465
2 TraesCS7B01G070200 chr7D 117131972 117134802 2830 False 1312.566667 3134 91.328 156 3069 3 chr7D.!!$F1 2913

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 0.035739 GAAACCGGCACAACCCTCTA 59.964 55.0 0.00 0.0 33.26 2.43 F
60 61 0.036306 AAACCGGCACAACCCTCTAG 59.964 55.0 0.00 0.0 33.26 2.43 F
73 74 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.0 3.32 0.0 0.00 2.15 F
931 962 0.319900 GACTCGCCTTGCTGAGTGAA 60.320 55.0 14.82 0.0 40.34 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1474 1531 1.541310 CGCAGTACTTGGACTCCCCA 61.541 60.000 0.00 0.0 44.93 4.96 R
1591 1648 2.187946 GACATGGAGAGGGCGGTG 59.812 66.667 0.00 0.0 0.00 4.94 R
2107 2192 5.106515 GCACTGCATGTAGTAGATCGAGATA 60.107 44.000 16.53 0.0 33.69 1.98 R
2589 2720 0.035317 ATCTCTGAGCAACGCAACCA 59.965 50.000 0.00 0.0 0.00 3.67 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
23 24 4.585955 ACCTAGCGTGATACCATGTAAG 57.414 45.455 0.00 0.00 0.00 2.34
24 25 4.212716 ACCTAGCGTGATACCATGTAAGA 58.787 43.478 0.00 0.00 0.00 2.10
25 26 4.037684 ACCTAGCGTGATACCATGTAAGAC 59.962 45.833 0.00 0.00 0.00 3.01
26 27 4.037565 CCTAGCGTGATACCATGTAAGACA 59.962 45.833 0.00 0.00 0.00 3.41
27 28 4.465632 AGCGTGATACCATGTAAGACAA 57.534 40.909 0.00 0.00 0.00 3.18
28 29 5.023533 AGCGTGATACCATGTAAGACAAT 57.976 39.130 0.00 0.00 0.00 2.71
29 30 6.156748 AGCGTGATACCATGTAAGACAATA 57.843 37.500 0.00 0.00 0.00 1.90
30 31 6.216569 AGCGTGATACCATGTAAGACAATAG 58.783 40.000 0.00 0.00 0.00 1.73
31 32 5.405571 GCGTGATACCATGTAAGACAATAGG 59.594 44.000 0.00 0.00 0.00 2.57
32 33 6.513180 CGTGATACCATGTAAGACAATAGGT 58.487 40.000 0.00 0.00 36.36 3.08
33 34 6.984474 CGTGATACCATGTAAGACAATAGGTT 59.016 38.462 6.95 0.00 34.89 3.50
34 35 7.494625 CGTGATACCATGTAAGACAATAGGTTT 59.505 37.037 6.95 1.38 34.89 3.27
35 36 9.174166 GTGATACCATGTAAGACAATAGGTTTT 57.826 33.333 6.95 0.00 34.89 2.43
36 37 9.747898 TGATACCATGTAAGACAATAGGTTTTT 57.252 29.630 6.95 0.00 34.89 1.94
38 39 7.227049 ACCATGTAAGACAATAGGTTTTTGG 57.773 36.000 0.00 0.00 30.92 3.28
39 40 6.210584 ACCATGTAAGACAATAGGTTTTTGGG 59.789 38.462 0.00 0.00 30.92 4.12
40 41 6.350949 CCATGTAAGACAATAGGTTTTTGGGG 60.351 42.308 0.00 0.00 0.00 4.96
41 42 5.954757 TGTAAGACAATAGGTTTTTGGGGA 58.045 37.500 0.00 0.00 0.00 4.81
42 43 6.374588 TGTAAGACAATAGGTTTTTGGGGAA 58.625 36.000 0.00 0.00 0.00 3.97
43 44 6.839657 TGTAAGACAATAGGTTTTTGGGGAAA 59.160 34.615 0.00 0.00 0.00 3.13
44 45 5.801531 AGACAATAGGTTTTTGGGGAAAC 57.198 39.130 0.00 0.00 38.49 2.78
55 56 3.299977 GGGAAACCGGCACAACCC 61.300 66.667 0.00 3.99 43.64 4.11
56 57 2.203437 GGAAACCGGCACAACCCT 60.203 61.111 0.00 0.00 33.26 4.34
57 58 2.265904 GGAAACCGGCACAACCCTC 61.266 63.158 0.00 0.00 33.26 4.30
58 59 1.228154 GAAACCGGCACAACCCTCT 60.228 57.895 0.00 0.00 33.26 3.69
59 60 0.035739 GAAACCGGCACAACCCTCTA 59.964 55.000 0.00 0.00 33.26 2.43
60 61 0.036306 AAACCGGCACAACCCTCTAG 59.964 55.000 0.00 0.00 33.26 2.43
61 62 1.838073 AACCGGCACAACCCTCTAGG 61.838 60.000 0.00 0.00 43.78 3.02
72 73 3.074788 CCTCTAGGGGTGGCCTATC 57.925 63.158 3.32 0.00 0.00 2.08
73 74 0.191064 CCTCTAGGGGTGGCCTATCA 59.809 60.000 3.32 0.00 0.00 2.15
74 75 1.343069 CTCTAGGGGTGGCCTATCAC 58.657 60.000 3.32 0.00 36.95 3.06
75 76 0.639943 TCTAGGGGTGGCCTATCACA 59.360 55.000 3.32 0.00 39.27 3.58
76 77 1.223077 TCTAGGGGTGGCCTATCACAT 59.777 52.381 3.32 0.00 39.27 3.21
77 78 2.453212 TCTAGGGGTGGCCTATCACATA 59.547 50.000 3.32 0.00 39.27 2.29
78 79 2.440494 AGGGGTGGCCTATCACATAT 57.560 50.000 3.32 0.00 39.27 1.78
79 80 3.577968 AGGGGTGGCCTATCACATATA 57.422 47.619 3.32 0.00 39.27 0.86
80 81 4.094216 AGGGGTGGCCTATCACATATAT 57.906 45.455 3.32 0.00 39.27 0.86
81 82 5.235003 AGGGGTGGCCTATCACATATATA 57.765 43.478 3.32 0.00 39.27 0.86
82 83 5.804013 AGGGGTGGCCTATCACATATATAT 58.196 41.667 3.32 0.00 39.27 0.86
83 84 6.945371 AGGGGTGGCCTATCACATATATATA 58.055 40.000 3.32 0.00 39.27 0.86
84 85 7.378326 AGGGGTGGCCTATCACATATATATAA 58.622 38.462 3.32 0.00 39.27 0.98
85 86 8.025089 AGGGGTGGCCTATCACATATATATAAT 58.975 37.037 3.32 0.00 39.27 1.28
86 87 8.103305 GGGGTGGCCTATCACATATATATAATG 58.897 40.741 3.32 0.00 39.27 1.90
87 88 8.880244 GGGTGGCCTATCACATATATATAATGA 58.120 37.037 3.32 10.79 39.27 2.57
88 89 9.935241 GGTGGCCTATCACATATATATAATGAG 57.065 37.037 3.32 5.38 39.27 2.90
89 90 9.935241 GTGGCCTATCACATATATATAATGAGG 57.065 37.037 3.32 11.00 37.57 3.86
90 91 9.674705 TGGCCTATCACATATATATAATGAGGT 57.325 33.333 3.32 4.51 0.00 3.85
91 92 9.935241 GGCCTATCACATATATATAATGAGGTG 57.065 37.037 12.91 8.04 0.00 4.00
92 93 9.935241 GCCTATCACATATATATAATGAGGTGG 57.065 37.037 12.91 13.58 0.00 4.61
107 108 9.778741 ATAATGAGGTGGTATACAATGTTACAG 57.221 33.333 5.01 0.00 0.00 2.74
108 109 6.614694 TGAGGTGGTATACAATGTTACAGT 57.385 37.500 5.01 0.00 0.00 3.55
109 110 7.721409 TGAGGTGGTATACAATGTTACAGTA 57.279 36.000 5.01 0.00 0.00 2.74
110 111 8.313944 TGAGGTGGTATACAATGTTACAGTAT 57.686 34.615 5.01 3.40 33.41 2.12
111 112 9.423964 TGAGGTGGTATACAATGTTACAGTATA 57.576 33.333 5.01 0.00 31.46 1.47
112 113 9.688592 GAGGTGGTATACAATGTTACAGTATAC 57.311 37.037 18.61 18.61 44.80 1.47
113 114 9.204337 AGGTGGTATACAATGTTACAGTATACA 57.796 33.333 23.76 14.13 46.18 2.29
114 115 9.252962 GGTGGTATACAATGTTACAGTATACAC 57.747 37.037 23.76 20.07 46.18 2.90
115 116 9.806203 GTGGTATACAATGTTACAGTATACACA 57.194 33.333 23.76 18.84 46.18 3.72
149 150 8.738106 ACAGAAACTATACAGTCTAACACTACC 58.262 37.037 0.00 0.00 32.29 3.18
150 151 8.958506 CAGAAACTATACAGTCTAACACTACCT 58.041 37.037 0.00 0.00 32.29 3.08
160 161 8.991275 ACAGTCTAACACTACCTATCTACTAGT 58.009 37.037 0.00 0.00 32.21 2.57
161 162 9.263538 CAGTCTAACACTACCTATCTACTAGTG 57.736 40.741 5.39 0.00 42.08 2.74
162 163 8.431222 AGTCTAACACTACCTATCTACTAGTGG 58.569 40.741 5.39 1.87 41.11 4.00
166 167 5.671276 ACACTACCTATCTACTAGTGGGAGT 59.329 44.000 8.03 8.03 42.25 3.85
198 199 4.880426 TCTCCTCCCCGCCATCCC 62.880 72.222 0.00 0.00 0.00 3.85
220 224 4.738740 CCAGTCGCGTAATAAACCTTCTAG 59.261 45.833 5.77 0.00 0.00 2.43
221 225 4.738740 CAGTCGCGTAATAAACCTTCTAGG 59.261 45.833 5.77 0.00 42.49 3.02
222 226 4.047142 GTCGCGTAATAAACCTTCTAGGG 58.953 47.826 5.77 0.00 40.58 3.53
223 227 2.798847 CGCGTAATAAACCTTCTAGGGC 59.201 50.000 0.00 0.00 40.58 5.19
224 228 3.738899 CGCGTAATAAACCTTCTAGGGCA 60.739 47.826 0.00 0.00 40.58 5.36
225 229 4.193865 GCGTAATAAACCTTCTAGGGCAA 58.806 43.478 0.00 0.00 40.58 4.52
226 230 4.272748 GCGTAATAAACCTTCTAGGGCAAG 59.727 45.833 0.00 0.00 40.58 4.01
227 231 5.425630 CGTAATAAACCTTCTAGGGCAAGT 58.574 41.667 0.00 0.00 40.58 3.16
228 232 6.576185 CGTAATAAACCTTCTAGGGCAAGTA 58.424 40.000 0.00 0.00 40.58 2.24
229 233 7.043565 CGTAATAAACCTTCTAGGGCAAGTAA 58.956 38.462 0.00 0.00 40.58 2.24
230 234 7.550196 CGTAATAAACCTTCTAGGGCAAGTAAA 59.450 37.037 0.00 0.00 40.58 2.01
231 235 9.234827 GTAATAAACCTTCTAGGGCAAGTAAAA 57.765 33.333 0.00 0.00 40.58 1.52
232 236 8.715190 AATAAACCTTCTAGGGCAAGTAAAAA 57.285 30.769 0.00 0.00 40.58 1.94
278 282 5.731599 AAAATCGCAATTGCAGAAAAACA 57.268 30.435 28.77 6.43 42.21 2.83
279 283 5.731599 AAATCGCAATTGCAGAAAAACAA 57.268 30.435 28.77 5.79 42.21 2.83
284 288 6.644775 TCGCAATTGCAGAAAAACAAATAAC 58.355 32.000 28.77 0.00 42.21 1.89
288 292 7.110079 GCAATTGCAGAAAAACAAATAACGAAC 59.890 33.333 25.36 0.00 41.59 3.95
306 310 4.324991 GGGTTCGTGGCCTCCGTT 62.325 66.667 3.32 0.00 0.00 4.44
307 311 2.741211 GGTTCGTGGCCTCCGTTC 60.741 66.667 3.32 4.45 0.00 3.95
326 330 2.824041 ATGGCTACCGCGGCAAAG 60.824 61.111 28.58 21.21 43.02 2.77
519 523 2.359602 GCAGCAGCAGCAGGAGAA 60.360 61.111 4.63 0.00 45.49 2.87
792 812 1.626356 ATATGTGTCACCGCCCAGCT 61.626 55.000 0.00 0.00 0.00 4.24
877 901 0.545171 ACTCACTCCCATCATGGCTG 59.455 55.000 0.00 0.00 35.79 4.85
906 930 1.755380 TCTACCTCGAGCTTAAAGCCC 59.245 52.381 6.99 0.00 43.77 5.19
909 933 0.462759 CCTCGAGCTTAAAGCCCAGG 60.463 60.000 6.99 0.00 43.77 4.45
916 947 2.007547 GCTTAAAGCCCAGGACGACTC 61.008 57.143 0.00 0.00 34.48 3.36
924 955 2.992114 AGGACGACTCGCCTTGCT 60.992 61.111 8.18 0.00 31.65 3.91
931 962 0.319900 GACTCGCCTTGCTGAGTGAA 60.320 55.000 14.82 0.00 40.34 3.18
971 1006 2.420372 TGTTTAACACTCGCTTTGTGCA 59.580 40.909 0.00 0.00 43.06 4.57
982 1017 0.528249 CTTTGTGCAGTGGTTGGTGC 60.528 55.000 0.00 0.00 40.29 5.01
983 1018 2.276863 TTTGTGCAGTGGTTGGTGCG 62.277 55.000 0.00 0.00 42.96 5.34
1236 1285 4.579340 CAGCCATCCCGTACGTATATATCT 59.421 45.833 15.21 0.16 0.00 1.98
1244 1293 8.122472 TCCCGTACGTATATATCTATCCGATA 57.878 38.462 15.21 0.00 38.88 2.92
1245 1294 8.246871 TCCCGTACGTATATATCTATCCGATAG 58.753 40.741 15.21 8.90 37.98 2.08
1264 1318 5.795939 CGATAGTAGTATCTTGCATCGTTCC 59.204 44.000 14.29 0.00 33.94 3.62
1347 1404 4.485554 TTTTTGCTTGCGTGCGTT 57.514 44.444 0.00 0.00 35.36 4.84
1348 1405 2.283254 TTTTTGCTTGCGTGCGTTC 58.717 47.368 0.00 0.00 35.36 3.95
1349 1406 1.467556 TTTTTGCTTGCGTGCGTTCG 61.468 50.000 0.00 0.00 35.36 3.95
1350 1407 2.585170 TTTTGCTTGCGTGCGTTCGT 62.585 50.000 3.76 0.00 35.36 3.85
1351 1408 3.781926 TTGCTTGCGTGCGTTCGTG 62.782 57.895 3.76 0.00 35.36 4.35
1450 1507 2.356553 CGGACGGACGGCAAGAAA 60.357 61.111 0.00 0.00 0.00 2.52
1474 1531 2.041922 TGCTCCAGGGAGGCGTAT 60.042 61.111 16.70 0.00 42.19 3.06
1543 1600 1.214175 TCAAGAAAGCCTGTGGAACCA 59.786 47.619 0.00 0.00 34.36 3.67
1549 1606 0.610232 AGCCTGTGGAACCAATGAGC 60.610 55.000 0.00 0.00 34.36 4.26
1553 1610 0.321564 TGTGGAACCAATGAGCTCCG 60.322 55.000 12.15 0.00 34.36 4.63
1964 2045 3.443045 GGAACGCCGTCGAGGGTA 61.443 66.667 24.11 0.00 41.48 3.69
2107 2192 1.909376 CGTGAAAGATCGGTCGATGT 58.091 50.000 10.77 3.79 34.60 3.06
2129 2231 5.998363 TGTATCTCGATCTACTACATGCAGT 59.002 40.000 3.59 3.59 0.00 4.40
2201 2303 3.536917 CGGATCCCGGTGCTGCTA 61.537 66.667 6.06 0.00 44.15 3.49
2202 2304 2.423446 GGATCCCGGTGCTGCTAG 59.577 66.667 0.00 0.00 0.00 3.42
2208 2310 0.460987 CCCGGTGCTGCTAGAAGAAG 60.461 60.000 0.27 0.00 0.00 2.85
2235 2337 0.252012 CTCCAGTCCAGTCCAGTCCT 60.252 60.000 0.00 0.00 0.00 3.85
2236 2338 0.191064 TCCAGTCCAGTCCAGTCCTT 59.809 55.000 0.00 0.00 0.00 3.36
2238 2340 1.638529 CAGTCCAGTCCAGTCCTTCT 58.361 55.000 0.00 0.00 0.00 2.85
2239 2341 1.274728 CAGTCCAGTCCAGTCCTTCTG 59.725 57.143 0.00 0.00 43.27 3.02
2240 2342 0.036858 GTCCAGTCCAGTCCTTCTGC 60.037 60.000 0.00 0.00 42.38 4.26
2243 2345 2.811317 GTCCAGTCCTTCTGCGCG 60.811 66.667 0.00 0.00 42.38 6.86
2248 2350 4.789075 GTCCTTCTGCGCGCCGTA 62.789 66.667 30.77 15.69 0.00 4.02
2254 2363 4.778415 CTGCGCGCCGTAGTCAGT 62.778 66.667 30.77 0.00 35.06 3.41
2270 2379 5.543507 AGTCAGTGGATATGAAGTGATCC 57.456 43.478 0.00 0.00 41.85 3.36
2373 2487 1.827399 AACGTCCAGAGCAACCCGAT 61.827 55.000 0.00 0.00 0.00 4.18
2589 2720 2.587194 GCGCGGCATGACTCATCT 60.587 61.111 8.83 0.00 0.00 2.90
2590 2721 2.879070 GCGCGGCATGACTCATCTG 61.879 63.158 8.83 0.00 0.00 2.90
2591 2722 2.242572 CGCGGCATGACTCATCTGG 61.243 63.158 0.00 0.00 0.00 3.86
2592 2723 1.153289 GCGGCATGACTCATCTGGT 60.153 57.895 0.00 0.00 0.00 4.00
2593 2724 0.745845 GCGGCATGACTCATCTGGTT 60.746 55.000 0.00 0.00 0.00 3.67
2594 2725 1.012086 CGGCATGACTCATCTGGTTG 58.988 55.000 0.00 0.00 0.00 3.77
2595 2726 0.737219 GGCATGACTCATCTGGTTGC 59.263 55.000 0.00 0.00 0.00 4.17
2596 2727 0.376152 GCATGACTCATCTGGTTGCG 59.624 55.000 0.00 0.00 0.00 4.85
2597 2728 1.730501 CATGACTCATCTGGTTGCGT 58.269 50.000 0.00 0.00 0.00 5.24
2598 2729 2.079158 CATGACTCATCTGGTTGCGTT 58.921 47.619 0.00 0.00 0.00 4.84
2938 3080 2.345760 TACTTGTCCGGACGCCTCC 61.346 63.158 28.70 5.25 0.00 4.30
2950 3092 3.827898 GCCTCCCTCGTGTCTCGG 61.828 72.222 0.00 0.00 40.32 4.63
2976 3118 3.181475 CGTGCCAACTGTAGAGGATACAT 60.181 47.826 0.00 0.00 41.41 2.29
2983 3125 6.239714 CCAACTGTAGAGGATACATAAGGCAT 60.240 42.308 0.00 0.00 41.41 4.40
2990 3132 9.289782 GTAGAGGATACATAAGGCATTTTGATT 57.710 33.333 8.54 0.00 41.41 2.57
2991 3133 8.174733 AGAGGATACATAAGGCATTTTGATTG 57.825 34.615 8.54 0.00 41.41 2.67
2992 3134 7.781693 AGAGGATACATAAGGCATTTTGATTGT 59.218 33.333 8.54 0.00 41.41 2.71
3029 3171 0.928505 TACGAGGGAGGGGATGTGTA 59.071 55.000 0.00 0.00 0.00 2.90
3035 3177 1.327690 GGAGGGGATGTGTAGCACGA 61.328 60.000 0.00 0.00 37.14 4.35
3042 3184 2.813908 GTGTAGCACGAAGGGCCG 60.814 66.667 0.00 0.00 0.00 6.13
3069 3211 1.434696 CAGATTGTGGCCGCCAATC 59.565 57.895 28.05 28.05 45.46 2.67
3070 3212 1.754234 AGATTGTGGCCGCCAATCC 60.754 57.895 30.00 18.96 45.99 3.01
3071 3213 2.037049 ATTGTGGCCGCCAATCCA 59.963 55.556 15.39 5.25 34.18 3.41
3077 3219 3.053291 GCCGCCAATCCACGTGAA 61.053 61.111 19.30 0.00 0.00 3.18
3078 3220 2.406616 GCCGCCAATCCACGTGAAT 61.407 57.895 19.30 0.00 0.00 2.57
3079 3221 1.092921 GCCGCCAATCCACGTGAATA 61.093 55.000 19.30 1.97 0.00 1.75
3080 3222 0.655733 CCGCCAATCCACGTGAATAC 59.344 55.000 19.30 0.00 0.00 1.89
3081 3223 1.651987 CGCCAATCCACGTGAATACT 58.348 50.000 19.30 0.00 0.00 2.12
3082 3224 2.006888 CGCCAATCCACGTGAATACTT 58.993 47.619 19.30 0.00 0.00 2.24
3083 3225 2.223021 CGCCAATCCACGTGAATACTTG 60.223 50.000 19.30 11.92 0.00 3.16
3084 3226 3.006940 GCCAATCCACGTGAATACTTGA 58.993 45.455 19.30 3.75 0.00 3.02
3085 3227 3.438781 GCCAATCCACGTGAATACTTGAA 59.561 43.478 19.30 0.00 0.00 2.69
3086 3228 4.083003 GCCAATCCACGTGAATACTTGAAA 60.083 41.667 19.30 0.00 0.00 2.69
3087 3229 5.393027 GCCAATCCACGTGAATACTTGAAAT 60.393 40.000 19.30 0.00 0.00 2.17
3088 3230 6.029607 CCAATCCACGTGAATACTTGAAATG 58.970 40.000 19.30 7.37 0.00 2.32
3089 3231 5.818136 ATCCACGTGAATACTTGAAATGG 57.182 39.130 19.30 0.00 0.00 3.16
3090 3232 4.006989 TCCACGTGAATACTTGAAATGGG 58.993 43.478 19.30 0.00 0.00 4.00
3091 3233 3.756434 CCACGTGAATACTTGAAATGGGT 59.244 43.478 19.30 0.00 0.00 4.51
3092 3234 4.142687 CCACGTGAATACTTGAAATGGGTC 60.143 45.833 19.30 0.00 0.00 4.46
3093 3235 4.695455 CACGTGAATACTTGAAATGGGTCT 59.305 41.667 10.90 0.00 0.00 3.85
3094 3236 4.695455 ACGTGAATACTTGAAATGGGTCTG 59.305 41.667 0.00 0.00 0.00 3.51
3095 3237 4.695455 CGTGAATACTTGAAATGGGTCTGT 59.305 41.667 0.00 0.00 0.00 3.41
3096 3238 5.181245 CGTGAATACTTGAAATGGGTCTGTT 59.819 40.000 0.00 0.00 0.00 3.16
3097 3239 6.293955 CGTGAATACTTGAAATGGGTCTGTTT 60.294 38.462 0.00 0.00 0.00 2.83
3098 3240 7.094975 CGTGAATACTTGAAATGGGTCTGTTTA 60.095 37.037 0.00 0.00 0.00 2.01
3099 3241 8.739972 GTGAATACTTGAAATGGGTCTGTTTAT 58.260 33.333 0.00 0.00 0.00 1.40
3100 3242 8.739039 TGAATACTTGAAATGGGTCTGTTTATG 58.261 33.333 0.00 0.00 0.00 1.90
3101 3243 8.877864 AATACTTGAAATGGGTCTGTTTATGA 57.122 30.769 0.00 0.00 0.00 2.15
3102 3244 6.575162 ACTTGAAATGGGTCTGTTTATGAC 57.425 37.500 0.00 0.00 0.00 3.06
3103 3245 6.068010 ACTTGAAATGGGTCTGTTTATGACA 58.932 36.000 0.00 0.00 36.26 3.58
3104 3246 5.957842 TGAAATGGGTCTGTTTATGACAC 57.042 39.130 0.00 0.00 38.26 3.67
3108 3250 4.908601 TGGGTCTGTTTATGACACATCT 57.091 40.909 0.00 0.00 42.18 2.90
3110 3252 5.977635 TGGGTCTGTTTATGACACATCTAG 58.022 41.667 0.00 0.00 42.18 2.43
3111 3253 5.719563 TGGGTCTGTTTATGACACATCTAGA 59.280 40.000 0.00 0.00 42.18 2.43
3112 3254 6.384015 TGGGTCTGTTTATGACACATCTAGAT 59.616 38.462 0.00 0.00 42.18 1.98
3113 3255 6.703607 GGGTCTGTTTATGACACATCTAGATG 59.296 42.308 27.63 27.63 44.15 2.90
3159 3301 9.357652 CTAACCTGATTTTCATTATGTTTGTGG 57.642 33.333 0.00 0.00 0.00 4.17
3160 3302 7.301868 ACCTGATTTTCATTATGTTTGTGGT 57.698 32.000 0.00 0.00 0.00 4.16
3161 3303 7.378181 ACCTGATTTTCATTATGTTTGTGGTC 58.622 34.615 0.00 0.00 0.00 4.02
3162 3304 7.233348 ACCTGATTTTCATTATGTTTGTGGTCT 59.767 33.333 0.00 0.00 0.00 3.85
3163 3305 8.739039 CCTGATTTTCATTATGTTTGTGGTCTA 58.261 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.829391 TCTTACATGGTATCACGCTAGGTTA 59.171 40.000 0.00 0.00 0.00 2.85
1 2 4.647853 TCTTACATGGTATCACGCTAGGTT 59.352 41.667 0.00 0.00 0.00 3.50
2 3 4.037684 GTCTTACATGGTATCACGCTAGGT 59.962 45.833 0.00 0.00 0.00 3.08
3 4 4.037565 TGTCTTACATGGTATCACGCTAGG 59.962 45.833 0.00 0.00 0.00 3.02
4 5 5.183014 TGTCTTACATGGTATCACGCTAG 57.817 43.478 0.00 0.00 0.00 3.42
5 6 5.585820 TTGTCTTACATGGTATCACGCTA 57.414 39.130 0.00 0.00 0.00 4.26
6 7 4.465632 TTGTCTTACATGGTATCACGCT 57.534 40.909 0.00 0.00 0.00 5.07
7 8 5.405571 CCTATTGTCTTACATGGTATCACGC 59.594 44.000 0.00 0.00 0.00 5.34
8 9 6.513180 ACCTATTGTCTTACATGGTATCACG 58.487 40.000 0.00 0.00 29.37 4.35
9 10 8.732746 AAACCTATTGTCTTACATGGTATCAC 57.267 34.615 0.00 0.00 30.40 3.06
10 11 9.747898 AAAAACCTATTGTCTTACATGGTATCA 57.252 29.630 0.00 0.00 30.40 2.15
12 13 8.966868 CCAAAAACCTATTGTCTTACATGGTAT 58.033 33.333 0.00 0.00 30.40 2.73
13 14 7.394923 CCCAAAAACCTATTGTCTTACATGGTA 59.605 37.037 0.00 0.00 30.40 3.25
14 15 6.210584 CCCAAAAACCTATTGTCTTACATGGT 59.789 38.462 0.00 0.00 31.33 3.55
15 16 6.350949 CCCCAAAAACCTATTGTCTTACATGG 60.351 42.308 0.00 0.00 0.00 3.66
16 17 6.435904 TCCCCAAAAACCTATTGTCTTACATG 59.564 38.462 0.00 0.00 0.00 3.21
17 18 6.557568 TCCCCAAAAACCTATTGTCTTACAT 58.442 36.000 0.00 0.00 0.00 2.29
18 19 5.954757 TCCCCAAAAACCTATTGTCTTACA 58.045 37.500 0.00 0.00 0.00 2.41
19 20 6.904463 TTCCCCAAAAACCTATTGTCTTAC 57.096 37.500 0.00 0.00 0.00 2.34
20 21 7.292713 GTTTCCCCAAAAACCTATTGTCTTA 57.707 36.000 0.00 0.00 33.86 2.10
21 22 6.169557 GTTTCCCCAAAAACCTATTGTCTT 57.830 37.500 0.00 0.00 33.86 3.01
22 23 5.801531 GTTTCCCCAAAAACCTATTGTCT 57.198 39.130 0.00 0.00 33.86 3.41
31 32 0.531090 GTGCCGGTTTCCCCAAAAAC 60.531 55.000 1.90 0.00 38.21 2.43
32 33 0.976073 TGTGCCGGTTTCCCCAAAAA 60.976 50.000 1.90 0.00 0.00 1.94
33 34 0.976073 TTGTGCCGGTTTCCCCAAAA 60.976 50.000 1.90 0.00 0.00 2.44
34 35 1.381327 TTGTGCCGGTTTCCCCAAA 60.381 52.632 1.90 0.00 0.00 3.28
35 36 2.128507 GTTGTGCCGGTTTCCCCAA 61.129 57.895 1.90 0.00 0.00 4.12
36 37 2.519780 GTTGTGCCGGTTTCCCCA 60.520 61.111 1.90 0.00 0.00 4.96
37 38 3.299977 GGTTGTGCCGGTTTCCCC 61.300 66.667 1.90 0.00 0.00 4.81
38 39 3.299977 GGGTTGTGCCGGTTTCCC 61.300 66.667 1.90 4.94 38.44 3.97
39 40 2.203437 AGGGTTGTGCCGGTTTCC 60.203 61.111 1.90 0.00 38.44 3.13
40 41 0.035739 TAGAGGGTTGTGCCGGTTTC 59.964 55.000 1.90 0.00 38.44 2.78
41 42 0.036306 CTAGAGGGTTGTGCCGGTTT 59.964 55.000 1.90 0.00 38.44 3.27
42 43 1.677552 CTAGAGGGTTGTGCCGGTT 59.322 57.895 1.90 0.00 38.44 4.44
43 44 2.291043 CCTAGAGGGTTGTGCCGGT 61.291 63.158 1.90 0.00 38.44 5.28
44 45 2.584608 CCTAGAGGGTTGTGCCGG 59.415 66.667 0.00 0.00 38.44 6.13
60 61 7.626999 TTATATATATGTGATAGGCCACCCC 57.373 40.000 5.01 0.00 36.26 4.95
61 62 8.880244 TCATTATATATATGTGATAGGCCACCC 58.120 37.037 5.01 0.00 36.26 4.61
62 63 9.935241 CTCATTATATATATGTGATAGGCCACC 57.065 37.037 5.01 0.00 36.26 4.61
63 64 9.935241 CCTCATTATATATATGTGATAGGCCAC 57.065 37.037 5.01 0.00 37.55 5.01
64 65 9.674705 ACCTCATTATATATATGTGATAGGCCA 57.325 33.333 5.01 0.00 0.00 5.36
65 66 9.935241 CACCTCATTATATATATGTGATAGGCC 57.065 37.037 5.44 0.00 0.00 5.19
66 67 9.935241 CCACCTCATTATATATATGTGATAGGC 57.065 37.037 5.44 0.00 0.00 3.93
81 82 9.778741 CTGTAACATTGTATACCACCTCATTAT 57.221 33.333 0.00 0.00 0.00 1.28
82 83 8.764558 ACTGTAACATTGTATACCACCTCATTA 58.235 33.333 0.00 0.00 0.00 1.90
83 84 7.630082 ACTGTAACATTGTATACCACCTCATT 58.370 34.615 0.00 0.00 0.00 2.57
84 85 7.195374 ACTGTAACATTGTATACCACCTCAT 57.805 36.000 0.00 0.00 0.00 2.90
85 86 6.614694 ACTGTAACATTGTATACCACCTCA 57.385 37.500 0.00 0.00 0.00 3.86
86 87 9.688592 GTATACTGTAACATTGTATACCACCTC 57.311 37.037 0.00 0.00 41.00 3.85
87 88 9.204337 TGTATACTGTAACATTGTATACCACCT 57.796 33.333 15.44 0.00 43.73 4.00
88 89 9.252962 GTGTATACTGTAACATTGTATACCACC 57.747 37.037 15.44 5.02 43.73 4.61
89 90 9.806203 TGTGTATACTGTAACATTGTATACCAC 57.194 33.333 15.44 13.78 43.73 4.16
123 124 8.738106 GGTAGTGTTAGACTGTATAGTTTCTGT 58.262 37.037 0.00 0.00 37.25 3.41
124 125 8.958506 AGGTAGTGTTAGACTGTATAGTTTCTG 58.041 37.037 0.00 0.00 37.25 3.02
134 135 8.991275 ACTAGTAGATAGGTAGTGTTAGACTGT 58.009 37.037 3.59 0.00 34.36 3.55
135 136 9.263538 CACTAGTAGATAGGTAGTGTTAGACTG 57.736 40.741 3.59 0.00 39.13 3.51
136 137 8.431222 CCACTAGTAGATAGGTAGTGTTAGACT 58.569 40.741 3.59 0.00 41.36 3.24
137 138 7.661027 CCCACTAGTAGATAGGTAGTGTTAGAC 59.339 44.444 3.59 0.00 41.36 2.59
138 139 7.570232 TCCCACTAGTAGATAGGTAGTGTTAGA 59.430 40.741 3.59 0.63 41.36 2.10
139 140 7.743749 TCCCACTAGTAGATAGGTAGTGTTAG 58.256 42.308 3.59 0.00 41.36 2.34
140 141 7.349330 ACTCCCACTAGTAGATAGGTAGTGTTA 59.651 40.741 3.59 0.00 41.36 2.41
141 142 6.160105 ACTCCCACTAGTAGATAGGTAGTGTT 59.840 42.308 3.59 0.00 41.36 3.32
142 143 5.671276 ACTCCCACTAGTAGATAGGTAGTGT 59.329 44.000 3.59 0.00 41.36 3.55
143 144 6.190346 ACTCCCACTAGTAGATAGGTAGTG 57.810 45.833 3.59 0.00 42.20 2.74
144 145 5.011943 CGACTCCCACTAGTAGATAGGTAGT 59.988 48.000 3.59 5.25 35.63 2.73
145 146 5.245751 TCGACTCCCACTAGTAGATAGGTAG 59.754 48.000 3.59 2.15 35.63 3.18
146 147 5.150715 TCGACTCCCACTAGTAGATAGGTA 58.849 45.833 3.59 0.00 35.63 3.08
147 148 3.972638 TCGACTCCCACTAGTAGATAGGT 59.027 47.826 3.59 0.00 35.63 3.08
148 149 4.283978 TCTCGACTCCCACTAGTAGATAGG 59.716 50.000 3.59 2.86 35.63 2.57
149 150 5.221481 TGTCTCGACTCCCACTAGTAGATAG 60.221 48.000 3.59 0.00 37.53 2.08
150 151 4.652881 TGTCTCGACTCCCACTAGTAGATA 59.347 45.833 3.59 0.00 31.82 1.98
151 152 3.455177 TGTCTCGACTCCCACTAGTAGAT 59.545 47.826 3.59 0.00 31.82 1.98
152 153 2.836372 TGTCTCGACTCCCACTAGTAGA 59.164 50.000 3.59 0.00 31.44 2.59
153 154 2.937799 GTGTCTCGACTCCCACTAGTAG 59.062 54.545 0.00 0.00 0.00 2.57
154 155 2.355513 GGTGTCTCGACTCCCACTAGTA 60.356 54.545 0.00 0.00 38.63 1.82
155 156 1.613785 GGTGTCTCGACTCCCACTAGT 60.614 57.143 6.85 0.00 38.63 2.57
156 157 1.096416 GGTGTCTCGACTCCCACTAG 58.904 60.000 6.85 0.00 38.63 2.57
157 158 0.402887 TGGTGTCTCGACTCCCACTA 59.597 55.000 13.75 0.00 42.61 2.74
158 159 0.896019 CTGGTGTCTCGACTCCCACT 60.896 60.000 13.75 0.00 42.61 4.00
159 160 1.587054 CTGGTGTCTCGACTCCCAC 59.413 63.158 13.75 0.00 42.61 4.61
160 161 1.606601 CCTGGTGTCTCGACTCCCA 60.607 63.158 13.75 10.78 42.61 4.37
161 162 0.684805 ATCCTGGTGTCTCGACTCCC 60.685 60.000 13.75 7.33 42.61 4.30
162 163 1.135333 GAATCCTGGTGTCTCGACTCC 59.865 57.143 10.41 10.41 43.33 3.85
198 199 4.738740 CCTAGAAGGTTTATTACGCGACTG 59.261 45.833 15.93 0.00 0.00 3.51
203 204 3.800531 TGCCCTAGAAGGTTTATTACGC 58.199 45.455 0.00 0.00 31.93 4.42
255 259 6.116680 TGTTTTTCTGCAATTGCGATTTTT 57.883 29.167 24.58 0.00 45.83 1.94
256 260 5.731599 TGTTTTTCTGCAATTGCGATTTT 57.268 30.435 24.58 0.00 45.83 1.82
257 261 5.731599 TTGTTTTTCTGCAATTGCGATTT 57.268 30.435 24.58 0.00 45.83 2.17
258 262 5.731599 TTTGTTTTTCTGCAATTGCGATT 57.268 30.435 24.58 0.00 45.83 3.34
259 263 5.927954 ATTTGTTTTTCTGCAATTGCGAT 57.072 30.435 24.58 5.64 45.83 4.58
260 264 6.561166 CGTTATTTGTTTTTCTGCAATTGCGA 60.561 34.615 24.58 20.45 45.83 5.10
261 265 5.555927 CGTTATTTGTTTTTCTGCAATTGCG 59.444 36.000 24.58 18.63 45.83 4.85
262 266 6.644775 TCGTTATTTGTTTTTCTGCAATTGC 58.355 32.000 23.69 23.69 42.50 3.56
263 267 7.315407 CGTTCGTTATTTGTTTTTCTGCAATTG 59.685 33.333 0.00 0.00 0.00 2.32
264 268 7.334009 CGTTCGTTATTTGTTTTTCTGCAATT 58.666 30.769 0.00 0.00 0.00 2.32
265 269 6.074569 CCGTTCGTTATTTGTTTTTCTGCAAT 60.075 34.615 0.00 0.00 0.00 3.56
266 270 5.230306 CCGTTCGTTATTTGTTTTTCTGCAA 59.770 36.000 0.00 0.00 0.00 4.08
267 271 4.735822 CCGTTCGTTATTTGTTTTTCTGCA 59.264 37.500 0.00 0.00 0.00 4.41
268 272 4.147479 CCCGTTCGTTATTTGTTTTTCTGC 59.853 41.667 0.00 0.00 0.00 4.26
269 273 5.275494 ACCCGTTCGTTATTTGTTTTTCTG 58.725 37.500 0.00 0.00 0.00 3.02
270 274 5.503662 ACCCGTTCGTTATTTGTTTTTCT 57.496 34.783 0.00 0.00 0.00 2.52
271 275 6.189041 GAACCCGTTCGTTATTTGTTTTTC 57.811 37.500 0.00 0.00 0.00 2.29
304 308 2.895372 CCGCGGTAGCCATGGAAC 60.895 66.667 19.50 12.63 41.18 3.62
305 309 4.849310 GCCGCGGTAGCCATGGAA 62.849 66.667 28.70 0.00 41.18 3.53
326 330 3.187432 GCTCTTTGCTCTTCCTGTTACAC 59.813 47.826 0.00 0.00 38.95 2.90
390 394 2.046285 CGGTGGGAAATGGGACTGC 61.046 63.158 0.00 0.00 0.00 4.40
426 430 4.737649 GCAGGTTTTCAACTTTGAAGGAGG 60.738 45.833 4.66 0.00 46.68 4.30
432 436 2.167487 GGTGGCAGGTTTTCAACTTTGA 59.833 45.455 0.00 0.00 34.92 2.69
505 509 2.039405 CCTGTTCTCCTGCTGCTGC 61.039 63.158 8.89 8.89 40.20 5.25
513 517 2.685380 CGGGGCTCCTGTTCTCCT 60.685 66.667 0.00 0.00 0.00 3.69
515 519 4.475135 GGCGGGGCTCCTGTTCTC 62.475 72.222 0.00 0.00 31.34 2.87
536 540 1.531578 GTGAGGAAAGAAACCACTCGC 59.468 52.381 0.00 0.00 0.00 5.03
662 682 1.968540 GCCAGTGTTGAGGTCAGGC 60.969 63.158 0.00 0.00 0.00 4.85
663 683 1.302832 GGCCAGTGTTGAGGTCAGG 60.303 63.158 0.00 0.00 0.00 3.86
664 684 1.669115 CGGCCAGTGTTGAGGTCAG 60.669 63.158 2.24 0.00 0.00 3.51
665 685 1.691195 TTCGGCCAGTGTTGAGGTCA 61.691 55.000 2.24 0.00 0.00 4.02
746 766 2.367648 TCAGGTGGGTGTGGGTGT 60.368 61.111 0.00 0.00 0.00 4.16
877 901 1.538075 GCTCGAGGTAGATAGAGGCAC 59.462 57.143 15.58 0.00 0.00 5.01
906 930 2.811317 GCAAGGCGAGTCGTCCTG 60.811 66.667 23.27 18.23 34.72 3.86
909 933 1.803519 CTCAGCAAGGCGAGTCGTC 60.804 63.158 9.65 9.65 0.00 4.20
916 947 0.167470 CACATTCACTCAGCAAGGCG 59.833 55.000 0.00 0.00 0.00 5.52
924 955 2.896044 AGAGCTCACTCACATTCACTCA 59.104 45.455 17.77 0.00 46.09 3.41
950 981 3.059634 GCACAAAGCGAGTGTTAAACA 57.940 42.857 7.79 0.00 39.17 2.83
987 1022 1.670590 CATCATCTCTCCGGGCTCC 59.329 63.158 0.00 0.00 0.00 4.70
989 1024 1.459158 AGCATCATCTCTCCGGGCT 60.459 57.895 0.00 0.00 0.00 5.19
991 1026 1.370437 CCAGCATCATCTCTCCGGG 59.630 63.158 0.00 0.00 0.00 5.73
992 1027 1.117749 TCCCAGCATCATCTCTCCGG 61.118 60.000 0.00 0.00 0.00 5.14
993 1028 0.317799 CTCCCAGCATCATCTCTCCG 59.682 60.000 0.00 0.00 0.00 4.63
1035 1081 2.358737 GTGAACAGGCACCTCCCG 60.359 66.667 0.00 0.00 34.51 5.14
1036 1082 2.358737 CGTGAACAGGCACCTCCC 60.359 66.667 0.00 0.00 35.37 4.30
1037 1083 2.358737 CCGTGAACAGGCACCTCC 60.359 66.667 0.00 0.00 35.37 4.30
1236 1285 6.822170 ACGATGCAAGATACTACTATCGGATA 59.178 38.462 0.00 0.00 39.93 2.59
1244 1293 5.599999 AAGGAACGATGCAAGATACTACT 57.400 39.130 0.00 0.00 0.00 2.57
1245 1294 5.810587 TCAAAGGAACGATGCAAGATACTAC 59.189 40.000 0.00 0.00 0.00 2.73
1288 1342 6.475076 GCATCACAGTCAGTTACTAGATCAAG 59.525 42.308 0.00 0.00 35.76 3.02
1334 1391 4.292208 CACGAACGCACGCAAGCA 62.292 61.111 0.00 0.00 45.62 3.91
1341 1398 4.993945 CTGCACGCACGAACGCAC 62.994 66.667 0.00 0.00 36.19 5.34
1343 1400 4.993945 CACTGCACGCACGAACGC 62.994 66.667 0.00 0.00 36.19 4.84
1344 1401 4.354212 CCACTGCACGCACGAACG 62.354 66.667 0.00 0.00 39.50 3.95
1345 1402 4.012895 CCCACTGCACGCACGAAC 62.013 66.667 0.00 0.00 0.00 3.95
1456 1513 2.435693 ATACGCCTCCCTGGAGCAC 61.436 63.158 7.73 1.44 40.69 4.40
1474 1531 1.541310 CGCAGTACTTGGACTCCCCA 61.541 60.000 0.00 0.00 44.93 4.96
1549 1606 3.213402 GAGACGGAGGAGGCGGAG 61.213 72.222 0.00 0.00 0.00 4.63
1553 1610 2.835895 GGAGGAGACGGAGGAGGC 60.836 72.222 0.00 0.00 0.00 4.70
1591 1648 2.187946 GACATGGAGAGGGCGGTG 59.812 66.667 0.00 0.00 0.00 4.94
2107 2192 5.106515 GCACTGCATGTAGTAGATCGAGATA 60.107 44.000 16.53 0.00 33.69 1.98
2158 2260 5.504665 CGGTTGGTTGATTATTCATCTGCTC 60.505 44.000 0.00 0.00 32.34 4.26
2193 2295 1.367659 CAGCCTTCTTCTAGCAGCAC 58.632 55.000 0.00 0.00 0.00 4.40
2208 2310 1.078567 CTGGACTGGAGAAGCAGCC 60.079 63.158 0.00 0.00 0.00 4.85
2235 2337 3.964221 CTGACTACGGCGCGCAGAA 62.964 63.158 36.82 17.77 0.00 3.02
2236 2338 4.476410 CTGACTACGGCGCGCAGA 62.476 66.667 36.82 19.04 0.00 4.26
2240 2342 2.055310 TATCCACTGACTACGGCGCG 62.055 60.000 6.90 0.00 0.00 6.86
2243 2345 3.068307 ACTTCATATCCACTGACTACGGC 59.932 47.826 0.00 0.00 0.00 5.68
2245 2347 5.500645 TCACTTCATATCCACTGACTACG 57.499 43.478 0.00 0.00 0.00 3.51
2246 2348 6.040955 TGGATCACTTCATATCCACTGACTAC 59.959 42.308 0.00 0.00 45.28 2.73
2247 2349 6.136155 TGGATCACTTCATATCCACTGACTA 58.864 40.000 0.00 0.00 45.28 2.59
2248 2350 4.964897 TGGATCACTTCATATCCACTGACT 59.035 41.667 0.00 0.00 45.28 3.41
2270 2379 5.352284 CAGGTACTAGCACTAGGTTTCATG 58.648 45.833 9.41 0.00 36.02 3.07
2272 2381 3.767673 CCAGGTACTAGCACTAGGTTTCA 59.232 47.826 9.41 0.00 36.02 2.69
2373 2487 3.340928 CTCACATGGAGCACAGATGAAA 58.659 45.455 0.00 0.00 36.69 2.69
2401 2519 9.388672 ACTCCTATTACACTCTAGAGTCTAGAT 57.611 37.037 26.44 16.33 40.20 1.98
2589 2720 0.035317 ATCTCTGAGCAACGCAACCA 59.965 50.000 0.00 0.00 0.00 3.67
2590 2721 0.445436 CATCTCTGAGCAACGCAACC 59.555 55.000 0.00 0.00 0.00 3.77
2591 2722 0.179205 GCATCTCTGAGCAACGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
2592 2723 1.629345 CGCATCTCTGAGCAACGCAA 61.629 55.000 0.00 0.00 0.00 4.85
2593 2724 2.096442 CGCATCTCTGAGCAACGCA 61.096 57.895 0.00 0.00 0.00 5.24
2594 2725 2.699809 CGCATCTCTGAGCAACGC 59.300 61.111 0.00 0.00 0.00 4.84
2595 2726 2.699809 GCGCATCTCTGAGCAACG 59.300 61.111 0.30 4.41 46.23 4.10
2671 2802 6.238759 CCTTGTTTCTTTCTCCAAAGACGATT 60.239 38.462 0.00 0.00 46.38 3.34
2802 2935 3.322466 CGGGCCTCTTGACCCTGT 61.322 66.667 0.84 0.00 44.63 4.00
2841 2976 6.840527 TCATTCATAGGCAGTGGAATAATGA 58.159 36.000 0.00 0.00 0.00 2.57
2891 3033 4.642542 GGCGATCGAGGTACCCGC 62.643 72.222 21.57 20.18 44.45 6.13
2938 3080 2.033755 ACGAGACCGAGACACGAGG 61.034 63.158 0.00 0.00 45.77 4.63
2950 3092 1.402984 CCTCTACAGTTGGCACGAGAC 60.403 57.143 0.00 0.00 0.00 3.36
2976 3118 8.040132 CCCAAGAAATACAATCAAAATGCCTTA 58.960 33.333 0.00 0.00 0.00 2.69
2983 3125 6.662865 TCTGCCCAAGAAATACAATCAAAA 57.337 33.333 0.00 0.00 29.54 2.44
3042 3184 3.443045 CACAATCTGCGTGCCCCC 61.443 66.667 0.00 0.00 0.00 5.40
3069 3211 3.756434 ACCCATTTCAAGTATTCACGTGG 59.244 43.478 17.00 0.00 35.18 4.94
3070 3212 4.695455 AGACCCATTTCAAGTATTCACGTG 59.305 41.667 9.94 9.94 35.70 4.49
3071 3213 4.695455 CAGACCCATTTCAAGTATTCACGT 59.305 41.667 0.00 0.00 0.00 4.49
3072 3214 4.695455 ACAGACCCATTTCAAGTATTCACG 59.305 41.667 0.00 0.00 0.00 4.35
3073 3215 6.575162 AACAGACCCATTTCAAGTATTCAC 57.425 37.500 0.00 0.00 0.00 3.18
3074 3216 8.739039 CATAAACAGACCCATTTCAAGTATTCA 58.261 33.333 0.00 0.00 0.00 2.57
3075 3217 8.956426 TCATAAACAGACCCATTTCAAGTATTC 58.044 33.333 0.00 0.00 0.00 1.75
3076 3218 8.739972 GTCATAAACAGACCCATTTCAAGTATT 58.260 33.333 0.00 0.00 0.00 1.89
3077 3219 7.888021 TGTCATAAACAGACCCATTTCAAGTAT 59.112 33.333 0.00 0.00 35.15 2.12
3078 3220 7.174253 GTGTCATAAACAGACCCATTTCAAGTA 59.826 37.037 0.00 0.00 38.97 2.24
3079 3221 6.016276 GTGTCATAAACAGACCCATTTCAAGT 60.016 38.462 0.00 0.00 38.97 3.16
3080 3222 6.016360 TGTGTCATAAACAGACCCATTTCAAG 60.016 38.462 0.00 0.00 38.97 3.02
3081 3223 5.830457 TGTGTCATAAACAGACCCATTTCAA 59.170 36.000 0.00 0.00 38.97 2.69
3082 3224 5.380900 TGTGTCATAAACAGACCCATTTCA 58.619 37.500 0.00 0.00 38.97 2.69
3083 3225 5.957842 TGTGTCATAAACAGACCCATTTC 57.042 39.130 0.00 0.00 38.97 2.17
3084 3226 6.248433 AGATGTGTCATAAACAGACCCATTT 58.752 36.000 0.00 0.00 38.97 2.32
3085 3227 5.819991 AGATGTGTCATAAACAGACCCATT 58.180 37.500 0.00 0.00 38.97 3.16
3086 3228 5.441718 AGATGTGTCATAAACAGACCCAT 57.558 39.130 0.00 0.00 38.97 4.00
3087 3229 4.908601 AGATGTGTCATAAACAGACCCA 57.091 40.909 0.00 0.00 38.97 4.51
3088 3230 6.222038 TCTAGATGTGTCATAAACAGACCC 57.778 41.667 0.00 0.00 38.97 4.46
3089 3231 7.706281 CATCTAGATGTGTCATAAACAGACC 57.294 40.000 22.42 0.00 38.97 3.85
3112 3254 9.811995 GGTTAGATGTAACATAACTATGTCACA 57.188 33.333 14.11 8.03 45.86 3.58
3133 3275 9.357652 CCACAAACATAATGAAAATCAGGTTAG 57.642 33.333 0.00 0.00 0.00 2.34
3134 3276 8.865090 ACCACAAACATAATGAAAATCAGGTTA 58.135 29.630 0.00 0.00 0.00 2.85
3135 3277 7.734942 ACCACAAACATAATGAAAATCAGGTT 58.265 30.769 0.00 0.00 0.00 3.50
3136 3278 7.233348 AGACCACAAACATAATGAAAATCAGGT 59.767 33.333 0.00 0.00 0.00 4.00
3137 3279 7.605449 AGACCACAAACATAATGAAAATCAGG 58.395 34.615 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.