Multiple sequence alignment - TraesCS6B01G322900

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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 TraesCS6B01G322900 chr6B 100.000 2480 0 0 1 2480 572089845 572092324 0.000000e+00 4580.0
1 TraesCS6B01G322900 chr6D 88.763 2198 143 49 285 2436 382550142 382552281 0.000000e+00 2595.0
2 TraesCS6B01G322900 chr6D 85.973 221 21 9 67 285 472885983 472886195 6.900000e-56 228.0
3 TraesCS6B01G322900 chr6A 86.695 1398 102 48 373 1741 524331362 524332704 0.000000e+00 1474.0
4 TraesCS6B01G322900 chr6A 90.608 543 32 10 1780 2310 524332697 524333232 0.000000e+00 702.0
5 TraesCS6B01G322900 chr5A 87.146 459 41 12 1985 2432 8059363 8058912 2.850000e-139 505.0
6 TraesCS6B01G322900 chr5D 83.247 579 52 26 1889 2431 10038595 10038026 7.970000e-135 490.0
7 TraesCS6B01G322900 chr5B 80.379 581 60 29 1889 2424 42157838 42158409 2.310000e-105 392.0
8 TraesCS6B01G322900 chr7D 88.095 210 20 4 76 284 107053941 107053736 6.850000e-61 244.0
9 TraesCS6B01G322900 chr2A 86.636 217 23 5 70 284 384888411 384888623 4.120000e-58 235.0
10 TraesCS6B01G322900 chr3D 86.512 215 22 5 73 285 514900970 514900761 1.920000e-56 230.0
11 TraesCS6B01G322900 chr3D 85.586 222 24 6 66 285 143638281 143638496 2.480000e-55 226.0
12 TraesCS6B01G322900 chr4B 85.650 223 21 10 65 284 25280887 25281101 8.930000e-55 224.0
13 TraesCS6B01G322900 chr4B 85.388 219 22 9 70 284 119265133 119264921 4.150000e-53 219.0
14 TraesCS6B01G322900 chr4B 96.970 33 1 0 1154 1186 134047193 134047225 3.450000e-04 56.5
15 TraesCS6B01G322900 chr3B 86.869 198 21 3 89 285 207231483 207231676 1.490000e-52 217.0
16 TraesCS6B01G322900 chr4D 85.185 216 23 7 73 284 64354498 64354708 1.930000e-51 213.0
17 TraesCS6B01G322900 chr4A 96.970 33 1 0 1154 1186 485708820 485708788 3.450000e-04 56.5


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 TraesCS6B01G322900 chr6B 572089845 572092324 2479 False 4580 4580 100.0000 1 2480 1 chr6B.!!$F1 2479
1 TraesCS6B01G322900 chr6D 382550142 382552281 2139 False 2595 2595 88.7630 285 2436 1 chr6D.!!$F1 2151
2 TraesCS6B01G322900 chr6A 524331362 524333232 1870 False 1088 1474 88.6515 373 2310 2 chr6A.!!$F1 1937
3 TraesCS6B01G322900 chr5D 10038026 10038595 569 True 490 490 83.2470 1889 2431 1 chr5D.!!$R1 542
4 TraesCS6B01G322900 chr5B 42157838 42158409 571 False 392 392 80.3790 1889 2424 1 chr5B.!!$F1 535

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
861 902 0.035317 CTCAACACTACTGCCAGCCA 59.965 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2411 0.804364 TCCTGTGTCGAAATGCATGC 59.196 50.0 11.82 11.82 0.0 4.06 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
25 26 3.423344 TCCGTAGAGGAGGCAGATC 57.577 57.895 0.00 0.00 45.98 2.75
26 27 0.178987 TCCGTAGAGGAGGCAGATCC 60.179 60.000 0.00 0.00 45.98 3.36
27 28 1.519751 CCGTAGAGGAGGCAGATCCG 61.520 65.000 0.00 0.00 44.65 4.18
28 29 1.519751 CGTAGAGGAGGCAGATCCGG 61.520 65.000 0.00 0.00 44.65 5.14
29 30 0.468400 GTAGAGGAGGCAGATCCGGT 60.468 60.000 0.00 0.00 44.65 5.28
30 31 0.178987 TAGAGGAGGCAGATCCGGTC 60.179 60.000 0.00 0.00 44.65 4.79
31 32 2.444895 AGGAGGCAGATCCGGTCC 60.445 66.667 0.00 0.00 44.65 4.46
32 33 3.917760 GGAGGCAGATCCGGTCCG 61.918 72.222 3.60 3.60 40.77 4.79
44 45 4.779733 GGTCCGGGCCAGAGAGGA 62.780 72.222 23.50 1.63 41.22 3.71
45 46 3.151022 GTCCGGGCCAGAGAGGAG 61.151 72.222 4.39 0.00 41.22 3.69
46 47 3.347590 TCCGGGCCAGAGAGGAGA 61.348 66.667 4.39 0.00 41.22 3.71
47 48 3.151022 CCGGGCCAGAGAGGAGAC 61.151 72.222 4.39 0.00 41.22 3.36
48 49 3.522731 CGGGCCAGAGAGGAGACG 61.523 72.222 4.39 0.00 41.22 4.18
49 50 2.043852 GGGCCAGAGAGGAGACGA 60.044 66.667 4.39 0.00 41.22 4.20
50 51 2.419739 GGGCCAGAGAGGAGACGAC 61.420 68.421 4.39 0.00 41.22 4.34
51 52 2.419739 GGCCAGAGAGGAGACGACC 61.420 68.421 0.00 0.00 41.22 4.79
52 53 2.766400 GCCAGAGAGGAGACGACCG 61.766 68.421 0.00 0.00 41.22 4.79
53 54 2.115911 CCAGAGAGGAGACGACCGG 61.116 68.421 0.00 0.00 41.22 5.28
54 55 1.377463 CAGAGAGGAGACGACCGGT 60.377 63.158 6.92 6.92 34.73 5.28
55 56 1.377463 AGAGAGGAGACGACCGGTG 60.377 63.158 14.63 7.23 34.73 4.94
56 57 1.376942 GAGAGGAGACGACCGGTGA 60.377 63.158 14.63 0.00 34.73 4.02
57 58 1.646624 GAGAGGAGACGACCGGTGAC 61.647 65.000 14.63 5.01 34.73 3.67
93 94 2.759973 CCGGAGACAGGCAGGCTA 60.760 66.667 0.00 0.00 33.72 3.93
94 95 2.790791 CCGGAGACAGGCAGGCTAG 61.791 68.421 0.00 0.00 33.72 3.42
95 96 2.790791 CGGAGACAGGCAGGCTAGG 61.791 68.421 0.00 0.00 33.72 3.02
96 97 2.439104 GGAGACAGGCAGGCTAGGG 61.439 68.421 0.00 0.00 33.72 3.53
97 98 1.381872 GAGACAGGCAGGCTAGGGA 60.382 63.158 0.00 0.00 33.72 4.20
98 99 1.681486 GAGACAGGCAGGCTAGGGAC 61.681 65.000 0.00 0.00 33.72 4.46
99 100 1.990060 GACAGGCAGGCTAGGGACA 60.990 63.158 0.00 0.00 0.00 4.02
100 101 1.965754 GACAGGCAGGCTAGGGACAG 61.966 65.000 0.00 0.00 0.00 3.51
101 102 2.366167 AGGCAGGCTAGGGACAGG 60.366 66.667 0.00 0.00 0.00 4.00
102 103 3.483869 GGCAGGCTAGGGACAGGG 61.484 72.222 0.00 0.00 0.00 4.45
103 104 4.182433 GCAGGCTAGGGACAGGGC 62.182 72.222 0.00 0.00 0.00 5.19
104 105 3.854669 CAGGCTAGGGACAGGGCG 61.855 72.222 0.00 0.00 33.67 6.13
107 108 4.840005 GCTAGGGACAGGGCGCAC 62.840 72.222 10.83 5.15 0.00 5.34
108 109 3.390521 CTAGGGACAGGGCGCACA 61.391 66.667 14.57 0.00 0.00 4.57
109 110 3.376935 CTAGGGACAGGGCGCACAG 62.377 68.421 14.57 6.41 0.00 3.66
110 111 3.897681 TAGGGACAGGGCGCACAGA 62.898 63.158 14.57 0.00 0.00 3.41
111 112 4.767255 GGGACAGGGCGCACAGAG 62.767 72.222 14.57 3.30 0.00 3.35
112 113 4.008933 GGACAGGGCGCACAGAGT 62.009 66.667 14.57 7.39 0.00 3.24
113 114 2.031163 GACAGGGCGCACAGAGTT 59.969 61.111 14.57 0.00 0.00 3.01
114 115 2.281070 ACAGGGCGCACAGAGTTG 60.281 61.111 14.57 2.59 0.00 3.16
115 116 3.730761 CAGGGCGCACAGAGTTGC 61.731 66.667 14.57 0.00 39.28 4.17
116 117 4.254709 AGGGCGCACAGAGTTGCA 62.255 61.111 14.57 0.00 43.15 4.08
117 118 3.058160 GGGCGCACAGAGTTGCAT 61.058 61.111 10.83 0.00 43.15 3.96
118 119 2.482374 GGCGCACAGAGTTGCATC 59.518 61.111 10.83 0.00 43.15 3.91
119 120 2.097160 GCGCACAGAGTTGCATCG 59.903 61.111 0.30 0.00 43.15 3.84
120 121 2.671177 GCGCACAGAGTTGCATCGT 61.671 57.895 0.30 0.00 43.15 3.73
121 122 1.131218 CGCACAGAGTTGCATCGTG 59.869 57.895 0.00 0.00 43.15 4.35
122 123 1.154338 GCACAGAGTTGCATCGTGC 60.154 57.895 15.96 15.96 45.29 5.34
141 142 2.286962 GGGGGAAGGGGCTAACCT 60.287 66.667 0.00 0.00 44.56 3.50
142 143 1.005156 GGGGGAAGGGGCTAACCTA 59.995 63.158 0.00 0.00 40.87 3.08
143 144 1.060743 GGGGGAAGGGGCTAACCTAG 61.061 65.000 0.00 0.00 40.87 3.02
160 161 8.484641 CTAACCTAGCATATGATACCATGTTG 57.515 38.462 6.97 0.00 34.31 3.33
161 162 5.809001 ACCTAGCATATGATACCATGTTGG 58.191 41.667 6.97 2.83 45.02 3.77
162 163 5.547666 ACCTAGCATATGATACCATGTTGGA 59.452 40.000 6.97 0.00 40.96 3.53
163 164 6.216251 ACCTAGCATATGATACCATGTTGGAT 59.784 38.462 6.97 0.00 40.96 3.41
164 165 7.402941 ACCTAGCATATGATACCATGTTGGATA 59.597 37.037 6.97 0.00 40.96 2.59
165 166 8.267183 CCTAGCATATGATACCATGTTGGATAA 58.733 37.037 6.97 0.00 40.96 1.75
166 167 9.842775 CTAGCATATGATACCATGTTGGATAAT 57.157 33.333 6.97 0.00 40.96 1.28
172 173 8.938801 ATGATACCATGTTGGATAATTAGCAA 57.061 30.769 2.72 0.00 40.96 3.91
173 174 8.165239 TGATACCATGTTGGATAATTAGCAAC 57.835 34.615 2.72 6.17 40.96 4.17
174 175 7.998383 TGATACCATGTTGGATAATTAGCAACT 59.002 33.333 2.72 0.00 40.96 3.16
175 176 9.502091 GATACCATGTTGGATAATTAGCAACTA 57.498 33.333 2.72 0.00 40.96 2.24
176 177 7.568199 ACCATGTTGGATAATTAGCAACTAC 57.432 36.000 2.72 0.00 40.96 2.73
177 178 7.346471 ACCATGTTGGATAATTAGCAACTACT 58.654 34.615 2.72 0.00 40.96 2.57
178 179 8.491134 ACCATGTTGGATAATTAGCAACTACTA 58.509 33.333 2.72 0.00 40.96 1.82
179 180 8.993121 CCATGTTGGATAATTAGCAACTACTAG 58.007 37.037 2.72 0.00 40.96 2.57
180 181 9.547753 CATGTTGGATAATTAGCAACTACTAGT 57.452 33.333 0.00 0.00 0.00 2.57
191 192 6.458232 AGCAACTACTAGTATTGACTGAGG 57.542 41.667 20.19 4.57 36.28 3.86
192 193 5.361285 AGCAACTACTAGTATTGACTGAGGG 59.639 44.000 20.19 4.01 36.28 4.30
193 194 5.593010 CAACTACTAGTATTGACTGAGGGC 58.407 45.833 2.33 0.00 36.28 5.19
194 195 4.216708 ACTACTAGTATTGACTGAGGGCC 58.783 47.826 2.33 0.00 36.28 5.80
195 196 3.116096 ACTAGTATTGACTGAGGGCCA 57.884 47.619 6.18 0.00 36.28 5.36
196 197 3.450904 ACTAGTATTGACTGAGGGCCAA 58.549 45.455 6.18 0.00 36.28 4.52
197 198 3.844211 ACTAGTATTGACTGAGGGCCAAA 59.156 43.478 6.18 0.00 36.28 3.28
198 199 3.356529 AGTATTGACTGAGGGCCAAAG 57.643 47.619 6.18 4.93 33.41 2.77
199 200 2.025887 AGTATTGACTGAGGGCCAAAGG 60.026 50.000 6.18 0.00 33.41 3.11
200 201 5.772274 AGTATTGACTGAGGGCCAAAGGC 62.772 52.174 6.18 5.15 40.69 4.35
214 215 5.982890 GCCAAAGGCCAATACATATACAT 57.017 39.130 5.01 0.00 44.06 2.29
215 216 5.713025 GCCAAAGGCCAATACATATACATG 58.287 41.667 5.01 0.00 44.06 3.21
216 217 5.243730 GCCAAAGGCCAATACATATACATGT 59.756 40.000 5.01 2.69 44.58 3.21
217 218 6.432783 GCCAAAGGCCAATACATATACATGTA 59.567 38.462 8.27 8.27 45.51 2.29
236 237 8.915871 ACATGTATGATAAAGTGCATGAAAAC 57.084 30.769 0.00 0.00 39.74 2.43
237 238 7.975616 ACATGTATGATAAAGTGCATGAAAACC 59.024 33.333 0.00 0.00 39.74 3.27
238 239 6.862209 TGTATGATAAAGTGCATGAAAACCC 58.138 36.000 0.00 0.00 0.00 4.11
239 240 4.799564 TGATAAAGTGCATGAAAACCCC 57.200 40.909 0.00 0.00 0.00 4.95
240 241 4.415596 TGATAAAGTGCATGAAAACCCCT 58.584 39.130 0.00 0.00 0.00 4.79
241 242 4.837860 TGATAAAGTGCATGAAAACCCCTT 59.162 37.500 0.00 0.00 0.00 3.95
242 243 6.013379 TGATAAAGTGCATGAAAACCCCTTA 58.987 36.000 0.00 0.00 0.00 2.69
243 244 6.667414 TGATAAAGTGCATGAAAACCCCTTAT 59.333 34.615 0.00 0.00 0.00 1.73
244 245 7.836685 TGATAAAGTGCATGAAAACCCCTTATA 59.163 33.333 0.00 0.00 0.00 0.98
245 246 5.914898 AAGTGCATGAAAACCCCTTATAC 57.085 39.130 0.00 0.00 0.00 1.47
246 247 4.929479 AGTGCATGAAAACCCCTTATACA 58.071 39.130 0.00 0.00 0.00 2.29
247 248 5.329399 AGTGCATGAAAACCCCTTATACAA 58.671 37.500 0.00 0.00 0.00 2.41
248 249 5.957774 AGTGCATGAAAACCCCTTATACAAT 59.042 36.000 0.00 0.00 0.00 2.71
249 250 7.122715 AGTGCATGAAAACCCCTTATACAATA 58.877 34.615 0.00 0.00 0.00 1.90
250 251 7.285401 AGTGCATGAAAACCCCTTATACAATAG 59.715 37.037 0.00 0.00 0.00 1.73
251 252 6.549364 TGCATGAAAACCCCTTATACAATAGG 59.451 38.462 0.00 0.00 0.00 2.57
252 253 6.775629 GCATGAAAACCCCTTATACAATAGGA 59.224 38.462 0.00 0.00 33.13 2.94
253 254 7.451566 GCATGAAAACCCCTTATACAATAGGAT 59.548 37.037 0.00 0.00 33.13 3.24
297 298 7.310664 ACACATTTAACAAGATGCAAGAGATG 58.689 34.615 0.00 0.00 0.00 2.90
312 313 8.250143 TGCAAGAGATGGATCTATAGTAAACA 57.750 34.615 0.00 0.00 37.25 2.83
364 365 8.706322 ATGTTTAACCTTTGACCTTCTATTGT 57.294 30.769 0.00 0.00 0.00 2.71
399 437 3.150767 CGGATTGTTTACCCAGAAACCA 58.849 45.455 0.00 0.00 38.33 3.67
457 497 6.872020 ACTGTGTAGCAATAATAACACTTCGT 59.128 34.615 6.08 0.00 42.12 3.85
479 519 0.732880 CCACGACAAGTCTACTGGCG 60.733 60.000 0.00 0.00 0.00 5.69
528 568 1.549950 GCAATGAAACTCCCCCTTCCA 60.550 52.381 0.00 0.00 0.00 3.53
535 575 1.772156 CTCCCCCTTCCATCCCCTC 60.772 68.421 0.00 0.00 0.00 4.30
605 645 1.665442 GCACCGCCACCTTTGATTT 59.335 52.632 0.00 0.00 0.00 2.17
689 730 2.643551 TGGCTGCTATTTTACTCCTGC 58.356 47.619 0.00 0.00 0.00 4.85
690 731 2.026356 TGGCTGCTATTTTACTCCTGCA 60.026 45.455 0.00 0.00 0.00 4.41
737 778 3.528370 CTCCCCGCCACCGACTAG 61.528 72.222 0.00 0.00 36.29 2.57
740 781 4.208686 CCCGCCACCGACTAGCTC 62.209 72.222 0.00 0.00 36.29 4.09
741 782 3.141488 CCGCCACCGACTAGCTCT 61.141 66.667 0.00 0.00 36.29 4.09
742 783 2.103143 CGCCACCGACTAGCTCTG 59.897 66.667 0.00 0.00 36.29 3.35
858 899 1.895798 TCTCCTCAACACTACTGCCAG 59.104 52.381 0.00 0.00 0.00 4.85
859 900 0.321671 TCCTCAACACTACTGCCAGC 59.678 55.000 0.00 0.00 0.00 4.85
860 901 0.674895 CCTCAACACTACTGCCAGCC 60.675 60.000 0.00 0.00 0.00 4.85
861 902 0.035317 CTCAACACTACTGCCAGCCA 59.965 55.000 0.00 0.00 0.00 4.75
872 913 2.205074 CTGCCAGCCACTAAATACTCG 58.795 52.381 0.00 0.00 0.00 4.18
873 914 1.134521 TGCCAGCCACTAAATACTCGG 60.135 52.381 0.00 0.00 0.00 4.63
889 930 2.187493 CGGTGCCTAGCTAGCTCGA 61.187 63.158 23.26 3.28 32.35 4.04
965 1006 2.084610 TCGATCTTGTCAGCCAGTTG 57.915 50.000 0.00 0.00 0.00 3.16
995 1036 3.253677 AGTGTCACTGTCACTAGTAGTGC 59.746 47.826 23.14 18.14 45.54 4.40
996 1037 2.225727 TGTCACTGTCACTAGTAGTGCG 59.774 50.000 23.14 16.01 45.54 5.34
997 1038 1.199327 TCACTGTCACTAGTAGTGCGC 59.801 52.381 23.14 18.00 45.54 6.09
1074 1120 2.124819 CTGATGCTCGGCCTGCTT 60.125 61.111 16.66 11.38 0.00 3.91
1116 1162 0.745845 AGTACACGGTCGGCGACTAT 60.746 55.000 35.42 22.69 32.47 2.12
1143 1189 1.952635 GAAGTTCAACGTCGCCGGT 60.953 57.895 1.90 0.00 38.78 5.28
1231 1277 0.524816 CGCCGCTCGCTAGTTTCTAA 60.525 55.000 0.00 0.00 34.21 2.10
1232 1278 0.922032 GCCGCTCGCTAGTTTCTAAC 59.078 55.000 0.00 0.00 0.00 2.34
1235 1281 1.584308 CGCTCGCTAGTTTCTAACAGC 59.416 52.381 0.00 0.00 34.43 4.40
1238 1289 4.360563 GCTCGCTAGTTTCTAACAGCATA 58.639 43.478 11.58 2.82 36.20 3.14
1290 1369 3.809832 GTGTGTGTGCAGAGTTCAAGTAT 59.190 43.478 0.00 0.00 0.00 2.12
1420 1499 2.027192 GTCAAGGGGATGCACTACTTCA 60.027 50.000 0.00 0.00 0.00 3.02
1469 1548 1.731709 CAACATGAAGATCGCCGTCAA 59.268 47.619 0.00 0.00 36.87 3.18
1480 1559 0.456221 CGCCGTCAAGGTCATCTAGT 59.544 55.000 0.00 0.00 43.70 2.57
1481 1560 1.534175 CGCCGTCAAGGTCATCTAGTC 60.534 57.143 0.00 0.00 43.70 2.59
1483 1562 2.950309 GCCGTCAAGGTCATCTAGTCTA 59.050 50.000 0.00 0.00 43.70 2.59
1484 1563 3.003897 GCCGTCAAGGTCATCTAGTCTAG 59.996 52.174 0.00 0.00 43.70 2.43
1488 1567 5.235616 CGTCAAGGTCATCTAGTCTAGAGAC 59.764 48.000 20.33 20.33 45.08 3.36
1489 1568 9.730489 CCGTCAAGGTCATCTAGTCTAGAGACT 62.730 48.148 23.89 16.13 45.53 3.24
1514 1593 4.714632 AGTGGCTAGCTACTTGTTTTCAA 58.285 39.130 26.43 0.00 33.97 2.69
1515 1594 4.515567 AGTGGCTAGCTACTTGTTTTCAAC 59.484 41.667 26.43 0.00 33.97 3.18
1516 1595 4.515567 GTGGCTAGCTACTTGTTTTCAACT 59.484 41.667 22.73 0.00 35.77 3.16
1517 1596 5.699458 GTGGCTAGCTACTTGTTTTCAACTA 59.301 40.000 22.73 0.00 35.77 2.24
1524 1614 6.651225 AGCTACTTGTTTTCAACTACAGATCC 59.349 38.462 0.00 0.00 35.77 3.36
1526 1616 6.867662 ACTTGTTTTCAACTACAGATCCAG 57.132 37.500 0.00 0.00 35.77 3.86
1580 1670 5.982516 TGCTTAATGCTTAAACCAACTGTTG 59.017 36.000 13.50 13.50 43.37 3.33
1592 1682 1.119684 AACTGTTGGTTTGCTTCCCC 58.880 50.000 0.00 0.00 33.90 4.81
1596 1686 0.249280 GTTGGTTTGCTTCCCCGTTG 60.249 55.000 0.00 0.00 0.00 4.10
1597 1687 0.395862 TTGGTTTGCTTCCCCGTTGA 60.396 50.000 0.00 0.00 0.00 3.18
1599 1689 0.966179 GGTTTGCTTCCCCGTTGATT 59.034 50.000 0.00 0.00 0.00 2.57
1601 1691 2.403259 GTTTGCTTCCCCGTTGATTTG 58.597 47.619 0.00 0.00 0.00 2.32
1603 1693 1.215382 GCTTCCCCGTTGATTTGCC 59.785 57.895 0.00 0.00 0.00 4.52
1605 1695 1.256812 CTTCCCCGTTGATTTGCCTT 58.743 50.000 0.00 0.00 0.00 4.35
1606 1696 0.965439 TTCCCCGTTGATTTGCCTTG 59.035 50.000 0.00 0.00 0.00 3.61
1674 1765 6.588719 TTTGAATATGGGTCTGAAGGTTTG 57.411 37.500 0.00 0.00 0.00 2.93
1702 1793 1.134670 ACTGGATGGACTAGCGCTTTC 60.135 52.381 18.68 13.08 0.00 2.62
1805 1901 1.299976 GGGCACTCACGGGAAGATT 59.700 57.895 0.00 0.00 0.00 2.40
1931 2034 6.947733 TCATCATAAAGATCCACAAACCTTGT 59.052 34.615 0.00 0.00 38.69 3.16
1946 2049 9.426837 CACAAACCTTGTCATGATAAATTTCAT 57.573 29.630 6.35 0.00 43.23 2.57
2166 2321 3.378742 AGTTCTGAGCTACATAGACACCG 59.621 47.826 0.00 0.00 0.00 4.94
2169 2324 1.134367 TGAGCTACATAGACACCGCAC 59.866 52.381 0.00 0.00 0.00 5.34
2183 2338 4.351054 GCACCCCACTCCCACCAG 62.351 72.222 0.00 0.00 0.00 4.00
2245 2404 4.090090 ACCTGGAGACGATGATATAAGGG 58.910 47.826 0.00 0.00 0.00 3.95
2252 2411 7.036220 GGAGACGATGATATAAGGGTTATGTG 58.964 42.308 0.00 0.00 0.00 3.21
2311 2486 9.349713 TGGTAAATAAGAAGATGACACAAAAGT 57.650 29.630 0.00 0.00 0.00 2.66
2326 2501 3.195396 ACAAAAGTTTGCTGTCATGTGGT 59.805 39.130 3.68 0.00 41.79 4.16
2408 2596 5.675538 ACTTGCAGAAGAAAGTACAGAAGT 58.324 37.500 0.00 0.00 41.99 3.01
2412 2600 6.578944 TGCAGAAGAAAGTACAGAAGTTACA 58.421 36.000 0.00 0.00 0.00 2.41
2436 2624 5.804692 TTACTGGCATTGTGTAATAACGG 57.195 39.130 0.00 0.00 0.00 4.44
2437 2625 3.945346 ACTGGCATTGTGTAATAACGGA 58.055 40.909 0.00 0.00 0.00 4.69
2438 2626 3.687698 ACTGGCATTGTGTAATAACGGAC 59.312 43.478 0.00 0.00 0.00 4.79
2439 2627 2.673862 TGGCATTGTGTAATAACGGACG 59.326 45.455 0.00 0.00 0.00 4.79
2440 2628 2.674357 GGCATTGTGTAATAACGGACGT 59.326 45.455 0.00 0.00 0.00 4.34
2441 2629 3.125658 GGCATTGTGTAATAACGGACGTT 59.874 43.478 14.82 14.82 41.65 3.99
2442 2630 4.378666 GGCATTGTGTAATAACGGACGTTT 60.379 41.667 15.64 1.23 39.31 3.60
2443 2631 4.551892 GCATTGTGTAATAACGGACGTTTG 59.448 41.667 15.64 5.70 39.31 2.93
2444 2632 5.615106 GCATTGTGTAATAACGGACGTTTGA 60.615 40.000 15.64 0.00 39.31 2.69
2445 2633 6.539324 CATTGTGTAATAACGGACGTTTGAT 58.461 36.000 15.64 1.26 39.31 2.57
2446 2634 5.766702 TGTGTAATAACGGACGTTTGATC 57.233 39.130 15.64 5.69 39.31 2.92
2447 2635 5.228665 TGTGTAATAACGGACGTTTGATCA 58.771 37.500 15.64 7.96 39.31 2.92
2448 2636 5.870433 TGTGTAATAACGGACGTTTGATCAT 59.130 36.000 15.64 0.00 39.31 2.45
2449 2637 6.369340 TGTGTAATAACGGACGTTTGATCATT 59.631 34.615 15.64 10.78 39.31 2.57
2450 2638 7.544915 TGTGTAATAACGGACGTTTGATCATTA 59.455 33.333 15.64 9.87 39.31 1.90
2451 2639 7.842721 GTGTAATAACGGACGTTTGATCATTAC 59.157 37.037 21.40 21.40 39.31 1.89
2452 2640 6.971527 AATAACGGACGTTTGATCATTACA 57.028 33.333 15.64 0.00 39.31 2.41
2453 2641 4.921470 AACGGACGTTTGATCATTACAG 57.079 40.909 3.99 0.00 34.22 2.74
2454 2642 4.182693 ACGGACGTTTGATCATTACAGA 57.817 40.909 0.00 0.00 0.00 3.41
2455 2643 3.924686 ACGGACGTTTGATCATTACAGAC 59.075 43.478 0.00 0.00 0.00 3.51
2456 2644 3.924073 CGGACGTTTGATCATTACAGACA 59.076 43.478 0.00 0.00 0.00 3.41
2457 2645 4.031765 CGGACGTTTGATCATTACAGACAG 59.968 45.833 0.00 0.00 0.00 3.51
2458 2646 5.168569 GGACGTTTGATCATTACAGACAGA 58.831 41.667 0.00 0.00 0.00 3.41
2459 2647 5.637810 GGACGTTTGATCATTACAGACAGAA 59.362 40.000 0.00 0.00 0.00 3.02
2460 2648 6.313905 GGACGTTTGATCATTACAGACAGAAT 59.686 38.462 0.00 0.00 0.00 2.40
2461 2649 7.148407 GGACGTTTGATCATTACAGACAGAATT 60.148 37.037 0.00 0.00 0.00 2.17
2462 2650 7.743104 ACGTTTGATCATTACAGACAGAATTC 58.257 34.615 0.00 0.00 0.00 2.17
2463 2651 7.148407 ACGTTTGATCATTACAGACAGAATTCC 60.148 37.037 0.65 0.00 0.00 3.01
2464 2652 7.475840 GTTTGATCATTACAGACAGAATTCCC 58.524 38.462 0.65 0.00 0.00 3.97
2465 2653 6.312141 TGATCATTACAGACAGAATTCCCA 57.688 37.500 0.65 0.00 0.00 4.37
2466 2654 6.720309 TGATCATTACAGACAGAATTCCCAA 58.280 36.000 0.65 0.00 0.00 4.12
2467 2655 6.599244 TGATCATTACAGACAGAATTCCCAAC 59.401 38.462 0.65 0.00 0.00 3.77
2468 2656 4.935205 TCATTACAGACAGAATTCCCAACG 59.065 41.667 0.65 0.00 0.00 4.10
2469 2657 2.930826 ACAGACAGAATTCCCAACGT 57.069 45.000 0.65 0.00 0.00 3.99
2470 2658 2.767505 ACAGACAGAATTCCCAACGTC 58.232 47.619 0.65 2.07 0.00 4.34
2471 2659 2.104111 ACAGACAGAATTCCCAACGTCA 59.896 45.455 0.65 0.00 0.00 4.35
2472 2660 2.738846 CAGACAGAATTCCCAACGTCAG 59.261 50.000 0.65 0.00 0.00 3.51
2473 2661 2.076863 GACAGAATTCCCAACGTCAGG 58.923 52.381 0.65 0.00 0.00 3.86
2474 2662 1.697432 ACAGAATTCCCAACGTCAGGA 59.303 47.619 8.47 5.53 0.00 3.86
2475 2663 2.305927 ACAGAATTCCCAACGTCAGGAT 59.694 45.455 7.30 0.00 30.55 3.24
2476 2664 2.679837 CAGAATTCCCAACGTCAGGATG 59.320 50.000 7.30 0.08 37.54 3.51
2477 2665 2.305927 AGAATTCCCAACGTCAGGATGT 59.694 45.455 7.30 0.00 37.40 3.06
2478 2666 2.879103 ATTCCCAACGTCAGGATGTT 57.121 45.000 7.30 1.12 40.89 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.127352 CTCCTCTACGGACGGCTGC 62.127 68.421 0.00 0.00 36.69 5.25
1 2 2.482333 CCTCCTCTACGGACGGCTG 61.482 68.421 0.00 0.00 36.69 4.85
2 3 2.124236 CCTCCTCTACGGACGGCT 60.124 66.667 0.00 0.00 36.69 5.52
3 4 3.902086 GCCTCCTCTACGGACGGC 61.902 72.222 0.00 0.00 43.79 5.68
4 5 2.439701 TGCCTCCTCTACGGACGG 60.440 66.667 0.00 0.00 36.69 4.79
5 6 0.820074 ATCTGCCTCCTCTACGGACG 60.820 60.000 0.00 0.00 36.69 4.79
6 7 0.955905 GATCTGCCTCCTCTACGGAC 59.044 60.000 0.00 0.00 36.69 4.79
7 8 0.178987 GGATCTGCCTCCTCTACGGA 60.179 60.000 0.00 0.00 40.30 4.69
8 9 1.519751 CGGATCTGCCTCCTCTACGG 61.520 65.000 0.00 0.00 32.77 4.02
9 10 1.519751 CCGGATCTGCCTCCTCTACG 61.520 65.000 0.00 0.00 32.77 3.51
10 11 0.468400 ACCGGATCTGCCTCCTCTAC 60.468 60.000 9.46 0.00 32.77 2.59
11 12 0.178987 GACCGGATCTGCCTCCTCTA 60.179 60.000 9.46 0.00 32.77 2.43
12 13 1.456705 GACCGGATCTGCCTCCTCT 60.457 63.158 9.46 0.00 32.77 3.69
13 14 2.503382 GGACCGGATCTGCCTCCTC 61.503 68.421 9.46 0.00 32.77 3.71
14 15 2.444895 GGACCGGATCTGCCTCCT 60.445 66.667 9.46 0.00 32.77 3.69
15 16 3.917760 CGGACCGGATCTGCCTCC 61.918 72.222 9.46 0.60 0.00 4.30
27 28 4.779733 TCCTCTCTGGCCCGGACC 62.780 72.222 0.73 0.00 35.26 4.46
28 29 3.151022 CTCCTCTCTGGCCCGGAC 61.151 72.222 0.73 0.00 35.26 4.79
29 30 3.347590 TCTCCTCTCTGGCCCGGA 61.348 66.667 0.73 0.00 35.26 5.14
30 31 3.151022 GTCTCCTCTCTGGCCCGG 61.151 72.222 0.00 0.00 35.26 5.73
31 32 3.522731 CGTCTCCTCTCTGGCCCG 61.523 72.222 0.00 0.00 35.26 6.13
32 33 2.043852 TCGTCTCCTCTCTGGCCC 60.044 66.667 0.00 0.00 35.26 5.80
33 34 2.419739 GGTCGTCTCCTCTCTGGCC 61.420 68.421 0.00 0.00 35.26 5.36
34 35 2.766400 CGGTCGTCTCCTCTCTGGC 61.766 68.421 0.00 0.00 35.26 4.85
35 36 2.115911 CCGGTCGTCTCCTCTCTGG 61.116 68.421 0.00 0.00 37.10 3.86
36 37 1.377463 ACCGGTCGTCTCCTCTCTG 60.377 63.158 0.00 0.00 0.00 3.35
37 38 1.377463 CACCGGTCGTCTCCTCTCT 60.377 63.158 2.59 0.00 0.00 3.10
38 39 1.376942 TCACCGGTCGTCTCCTCTC 60.377 63.158 2.59 0.00 0.00 3.20
39 40 1.674980 GTCACCGGTCGTCTCCTCT 60.675 63.158 2.59 0.00 0.00 3.69
40 41 2.876219 GTCACCGGTCGTCTCCTC 59.124 66.667 2.59 0.00 0.00 3.71
41 42 3.054503 CGTCACCGGTCGTCTCCT 61.055 66.667 2.59 0.00 0.00 3.69
76 77 2.759973 TAGCCTGCCTGTCTCCGG 60.760 66.667 0.00 0.00 0.00 5.14
77 78 2.790791 CCTAGCCTGCCTGTCTCCG 61.791 68.421 0.00 0.00 0.00 4.63
78 79 2.439104 CCCTAGCCTGCCTGTCTCC 61.439 68.421 0.00 0.00 0.00 3.71
79 80 1.381872 TCCCTAGCCTGCCTGTCTC 60.382 63.158 0.00 0.00 0.00 3.36
80 81 1.687493 GTCCCTAGCCTGCCTGTCT 60.687 63.158 0.00 0.00 0.00 3.41
81 82 1.965754 CTGTCCCTAGCCTGCCTGTC 61.966 65.000 0.00 0.00 0.00 3.51
82 83 1.992277 CTGTCCCTAGCCTGCCTGT 60.992 63.158 0.00 0.00 0.00 4.00
83 84 2.739996 CCTGTCCCTAGCCTGCCTG 61.740 68.421 0.00 0.00 0.00 4.85
84 85 2.366167 CCTGTCCCTAGCCTGCCT 60.366 66.667 0.00 0.00 0.00 4.75
85 86 3.483869 CCCTGTCCCTAGCCTGCC 61.484 72.222 0.00 0.00 0.00 4.85
86 87 4.182433 GCCCTGTCCCTAGCCTGC 62.182 72.222 0.00 0.00 0.00 4.85
87 88 3.854669 CGCCCTGTCCCTAGCCTG 61.855 72.222 0.00 0.00 0.00 4.85
90 91 4.840005 GTGCGCCCTGTCCCTAGC 62.840 72.222 4.18 0.00 0.00 3.42
91 92 3.376935 CTGTGCGCCCTGTCCCTAG 62.377 68.421 4.18 0.00 0.00 3.02
92 93 3.390521 CTGTGCGCCCTGTCCCTA 61.391 66.667 4.18 0.00 0.00 3.53
94 95 4.767255 CTCTGTGCGCCCTGTCCC 62.767 72.222 4.18 0.00 0.00 4.46
95 96 3.537206 AACTCTGTGCGCCCTGTCC 62.537 63.158 4.18 0.00 0.00 4.02
96 97 2.031163 AACTCTGTGCGCCCTGTC 59.969 61.111 4.18 0.00 0.00 3.51
97 98 2.281070 CAACTCTGTGCGCCCTGT 60.281 61.111 4.18 0.00 0.00 4.00
98 99 3.730761 GCAACTCTGTGCGCCCTG 61.731 66.667 4.18 0.00 34.21 4.45
105 106 1.131218 CGCACGATGCAACTCTGTG 59.869 57.895 9.95 0.00 45.36 3.66
106 107 2.029288 CCGCACGATGCAACTCTGT 61.029 57.895 9.95 0.00 45.36 3.41
107 108 2.743752 CCCGCACGATGCAACTCTG 61.744 63.158 9.95 0.00 45.36 3.35
108 109 2.434884 CCCGCACGATGCAACTCT 60.435 61.111 9.95 0.00 45.36 3.24
109 110 3.499737 CCCCGCACGATGCAACTC 61.500 66.667 9.95 0.00 45.36 3.01
124 125 1.005156 TAGGTTAGCCCCTTCCCCC 59.995 63.158 0.00 0.00 35.97 5.40
125 126 1.706995 GCTAGGTTAGCCCCTTCCCC 61.707 65.000 0.00 0.00 45.95 4.81
126 127 1.837789 GCTAGGTTAGCCCCTTCCC 59.162 63.158 0.00 0.00 45.95 3.97
131 132 9.740394 CATGGTATCATATGCTAGGTTAGCCCC 62.740 48.148 0.00 0.00 40.41 5.80
132 133 6.909698 CATGGTATCATATGCTAGGTTAGCCC 60.910 46.154 0.00 0.00 40.41 5.19
133 134 6.051717 CATGGTATCATATGCTAGGTTAGCC 58.948 44.000 0.00 0.00 40.41 3.93
134 135 6.644347 ACATGGTATCATATGCTAGGTTAGC 58.356 40.000 0.00 1.21 40.99 3.09
135 136 7.550551 CCAACATGGTATCATATGCTAGGTTAG 59.449 40.741 0.00 0.00 29.92 2.34
136 137 7.236640 TCCAACATGGTATCATATGCTAGGTTA 59.763 37.037 0.00 0.00 39.03 2.85
137 138 6.044287 TCCAACATGGTATCATATGCTAGGTT 59.956 38.462 0.00 0.00 39.03 3.50
138 139 5.547666 TCCAACATGGTATCATATGCTAGGT 59.452 40.000 0.00 0.00 39.03 3.08
139 140 6.053632 TCCAACATGGTATCATATGCTAGG 57.946 41.667 0.00 0.00 39.03 3.02
140 141 9.842775 ATTATCCAACATGGTATCATATGCTAG 57.157 33.333 0.00 0.00 39.03 3.42
147 148 8.796475 GTTGCTAATTATCCAACATGGTATCAT 58.204 33.333 17.52 0.00 39.03 2.45
148 149 7.998383 AGTTGCTAATTATCCAACATGGTATCA 59.002 33.333 21.47 0.00 40.85 2.15
149 150 8.396272 AGTTGCTAATTATCCAACATGGTATC 57.604 34.615 21.47 3.27 40.85 2.24
150 151 9.284968 GTAGTTGCTAATTATCCAACATGGTAT 57.715 33.333 21.47 9.68 40.85 2.73
151 152 8.491134 AGTAGTTGCTAATTATCCAACATGGTA 58.509 33.333 21.47 9.73 40.85 3.25
152 153 7.346471 AGTAGTTGCTAATTATCCAACATGGT 58.654 34.615 21.47 10.38 40.85 3.55
153 154 7.807977 AGTAGTTGCTAATTATCCAACATGG 57.192 36.000 21.47 0.00 40.85 3.66
154 155 9.547753 ACTAGTAGTTGCTAATTATCCAACATG 57.452 33.333 21.47 0.00 40.85 3.21
165 166 8.634444 CCTCAGTCAATACTAGTAGTTGCTAAT 58.366 37.037 8.40 0.00 33.48 1.73
166 167 7.068348 CCCTCAGTCAATACTAGTAGTTGCTAA 59.932 40.741 8.40 0.00 33.48 3.09
167 168 6.546403 CCCTCAGTCAATACTAGTAGTTGCTA 59.454 42.308 8.40 0.00 33.48 3.49
168 169 5.361285 CCCTCAGTCAATACTAGTAGTTGCT 59.639 44.000 8.40 10.63 33.48 3.91
169 170 5.593010 CCCTCAGTCAATACTAGTAGTTGC 58.407 45.833 8.40 9.01 33.48 4.17
170 171 5.452077 GGCCCTCAGTCAATACTAGTAGTTG 60.452 48.000 8.40 12.18 33.48 3.16
171 172 4.650131 GGCCCTCAGTCAATACTAGTAGTT 59.350 45.833 8.40 0.86 33.48 2.24
172 173 4.216708 GGCCCTCAGTCAATACTAGTAGT 58.783 47.826 8.85 8.14 33.48 2.73
173 174 4.215908 TGGCCCTCAGTCAATACTAGTAG 58.784 47.826 8.85 0.00 33.48 2.57
174 175 4.259933 TGGCCCTCAGTCAATACTAGTA 57.740 45.455 4.77 4.77 33.48 1.82
175 176 3.116096 TGGCCCTCAGTCAATACTAGT 57.884 47.619 0.00 0.00 33.48 2.57
176 177 4.446371 CTTTGGCCCTCAGTCAATACTAG 58.554 47.826 0.00 0.00 33.48 2.57
177 178 3.199946 CCTTTGGCCCTCAGTCAATACTA 59.800 47.826 0.00 0.00 33.48 1.82
178 179 2.025887 CCTTTGGCCCTCAGTCAATACT 60.026 50.000 0.00 0.00 35.91 2.12
179 180 2.369394 CCTTTGGCCCTCAGTCAATAC 58.631 52.381 0.00 0.00 0.00 1.89
180 181 1.340991 GCCTTTGGCCCTCAGTCAATA 60.341 52.381 0.00 0.00 44.06 1.90
181 182 0.613012 GCCTTTGGCCCTCAGTCAAT 60.613 55.000 0.00 0.00 44.06 2.57
182 183 1.228552 GCCTTTGGCCCTCAGTCAA 60.229 57.895 0.00 0.00 44.06 3.18
183 184 2.436109 GCCTTTGGCCCTCAGTCA 59.564 61.111 0.00 0.00 44.06 3.41
192 193 5.243730 ACATGTATATGTATTGGCCTTTGGC 59.756 40.000 3.32 0.00 45.45 4.52
193 194 6.899393 ACATGTATATGTATTGGCCTTTGG 57.101 37.500 3.32 0.00 45.45 3.28
211 212 7.975616 GGTTTTCATGCACTTTATCATACATGT 59.024 33.333 2.69 2.69 36.96 3.21
212 213 7.436080 GGGTTTTCATGCACTTTATCATACATG 59.564 37.037 0.00 0.00 36.97 3.21
213 214 7.417797 GGGGTTTTCATGCACTTTATCATACAT 60.418 37.037 0.00 0.00 0.00 2.29
214 215 6.127479 GGGGTTTTCATGCACTTTATCATACA 60.127 38.462 0.00 0.00 0.00 2.29
215 216 6.096846 AGGGGTTTTCATGCACTTTATCATAC 59.903 38.462 0.00 0.00 0.00 2.39
216 217 6.194235 AGGGGTTTTCATGCACTTTATCATA 58.806 36.000 0.00 0.00 0.00 2.15
217 218 5.025453 AGGGGTTTTCATGCACTTTATCAT 58.975 37.500 0.00 0.00 0.00 2.45
218 219 4.415596 AGGGGTTTTCATGCACTTTATCA 58.584 39.130 0.00 0.00 0.00 2.15
219 220 5.405935 AAGGGGTTTTCATGCACTTTATC 57.594 39.130 0.00 0.00 0.00 1.75
220 221 7.617723 TGTATAAGGGGTTTTCATGCACTTTAT 59.382 33.333 0.00 0.00 0.00 1.40
221 222 6.948886 TGTATAAGGGGTTTTCATGCACTTTA 59.051 34.615 0.00 0.00 0.00 1.85
222 223 5.777732 TGTATAAGGGGTTTTCATGCACTTT 59.222 36.000 0.00 0.00 0.00 2.66
223 224 5.329399 TGTATAAGGGGTTTTCATGCACTT 58.671 37.500 0.00 0.00 0.00 3.16
224 225 4.929479 TGTATAAGGGGTTTTCATGCACT 58.071 39.130 0.00 0.00 0.00 4.40
225 226 5.652994 TTGTATAAGGGGTTTTCATGCAC 57.347 39.130 0.00 0.00 0.00 4.57
226 227 6.549364 CCTATTGTATAAGGGGTTTTCATGCA 59.451 38.462 0.00 0.00 0.00 3.96
227 228 6.775629 TCCTATTGTATAAGGGGTTTTCATGC 59.224 38.462 0.00 0.00 33.40 4.06
228 229 8.940397 ATCCTATTGTATAAGGGGTTTTCATG 57.060 34.615 0.00 0.00 33.40 3.07
260 261 9.802039 TCTTGTTAAATGTGTATAGTCCCTTTT 57.198 29.630 0.00 0.00 0.00 2.27
261 262 9.975218 ATCTTGTTAAATGTGTATAGTCCCTTT 57.025 29.630 0.00 0.00 0.00 3.11
262 263 9.396022 CATCTTGTTAAATGTGTATAGTCCCTT 57.604 33.333 0.00 0.00 0.00 3.95
263 264 7.499232 GCATCTTGTTAAATGTGTATAGTCCCT 59.501 37.037 0.00 0.00 0.00 4.20
264 265 7.282224 TGCATCTTGTTAAATGTGTATAGTCCC 59.718 37.037 0.00 0.00 0.00 4.46
265 266 8.208718 TGCATCTTGTTAAATGTGTATAGTCC 57.791 34.615 0.00 0.00 0.00 3.85
266 267 9.708222 CTTGCATCTTGTTAAATGTGTATAGTC 57.292 33.333 0.00 0.00 0.00 2.59
267 268 9.448438 TCTTGCATCTTGTTAAATGTGTATAGT 57.552 29.630 0.00 0.00 0.00 2.12
268 269 9.926751 CTCTTGCATCTTGTTAAATGTGTATAG 57.073 33.333 0.00 0.00 0.00 1.31
269 270 9.665719 TCTCTTGCATCTTGTTAAATGTGTATA 57.334 29.630 0.00 0.00 0.00 1.47
270 271 8.565896 TCTCTTGCATCTTGTTAAATGTGTAT 57.434 30.769 0.00 0.00 0.00 2.29
271 272 7.977789 TCTCTTGCATCTTGTTAAATGTGTA 57.022 32.000 0.00 0.00 0.00 2.90
272 273 6.882610 TCTCTTGCATCTTGTTAAATGTGT 57.117 33.333 0.00 0.00 0.00 3.72
273 274 6.750501 CCATCTCTTGCATCTTGTTAAATGTG 59.249 38.462 0.00 0.00 0.00 3.21
274 275 6.660521 TCCATCTCTTGCATCTTGTTAAATGT 59.339 34.615 0.00 0.00 0.00 2.71
275 276 7.092137 TCCATCTCTTGCATCTTGTTAAATG 57.908 36.000 0.00 0.00 0.00 2.32
276 277 7.778853 AGATCCATCTCTTGCATCTTGTTAAAT 59.221 33.333 0.00 0.00 29.30 1.40
277 278 7.114754 AGATCCATCTCTTGCATCTTGTTAAA 58.885 34.615 0.00 0.00 29.30 1.52
278 279 6.656902 AGATCCATCTCTTGCATCTTGTTAA 58.343 36.000 0.00 0.00 29.30 2.01
279 280 6.244552 AGATCCATCTCTTGCATCTTGTTA 57.755 37.500 0.00 0.00 29.30 2.41
280 281 5.113446 AGATCCATCTCTTGCATCTTGTT 57.887 39.130 0.00 0.00 29.30 2.83
281 282 4.774660 AGATCCATCTCTTGCATCTTGT 57.225 40.909 0.00 0.00 29.30 3.16
282 283 7.613585 ACTATAGATCCATCTCTTGCATCTTG 58.386 38.462 6.78 0.00 38.32 3.02
283 284 7.795534 ACTATAGATCCATCTCTTGCATCTT 57.204 36.000 6.78 0.00 38.32 2.40
347 348 5.941948 ACGAAACAATAGAAGGTCAAAGG 57.058 39.130 0.00 0.00 0.00 3.11
364 365 7.643371 GGTAAACAATCCGACTTTAAAACGAAA 59.357 33.333 13.54 4.78 0.00 3.46
457 497 1.611977 CCAGTAGACTTGTCGTGGACA 59.388 52.381 11.76 0.00 41.09 4.02
479 519 1.410517 TCGATCTGGGAAGTGCATCTC 59.589 52.381 0.00 0.00 0.00 2.75
492 532 3.562557 TCATTGCATGTTGGATCGATCTG 59.437 43.478 23.96 15.05 0.00 2.90
519 559 1.221213 TTTGAGGGGATGGAAGGGGG 61.221 60.000 0.00 0.00 0.00 5.40
543 583 9.992910 AAGAAGTTTCATTGCATTTTTCTTTTC 57.007 25.926 0.00 0.00 31.63 2.29
545 585 9.992910 GAAAGAAGTTTCATTGCATTTTTCTTT 57.007 25.926 14.09 14.09 42.79 2.52
546 586 8.615211 GGAAAGAAGTTTCATTGCATTTTTCTT 58.385 29.630 0.00 0.00 43.52 2.52
547 587 7.769970 TGGAAAGAAGTTTCATTGCATTTTTCT 59.230 29.630 0.86 0.00 43.52 2.52
548 588 7.918643 TGGAAAGAAGTTTCATTGCATTTTTC 58.081 30.769 0.86 0.00 43.52 2.29
605 645 4.996793 TCCCATCCAAATCTGAAACTGAA 58.003 39.130 0.00 0.00 0.00 3.02
653 694 2.941064 CAGCCATGTCTGATGATTTCGT 59.059 45.455 0.00 0.00 36.19 3.85
689 730 3.038710 GCAACAAAAAGACGAGCTCTTG 58.961 45.455 12.85 10.61 39.36 3.02
690 731 2.286418 CGCAACAAAAAGACGAGCTCTT 60.286 45.455 12.85 1.07 41.39 2.85
737 778 0.948678 CTACCGAGCTAGTCCAGAGC 59.051 60.000 0.00 0.00 40.42 4.09
738 779 0.948678 GCTACCGAGCTAGTCCAGAG 59.051 60.000 0.00 0.00 45.98 3.35
739 780 3.097461 GCTACCGAGCTAGTCCAGA 57.903 57.895 0.00 0.00 45.98 3.86
858 899 1.296727 GGCACCGAGTATTTAGTGGC 58.703 55.000 0.00 0.00 46.49 5.01
859 900 2.981859 AGGCACCGAGTATTTAGTGG 57.018 50.000 0.00 0.00 0.00 4.00
860 901 3.068307 AGCTAGGCACCGAGTATTTAGTG 59.932 47.826 0.00 0.00 0.00 2.74
861 902 3.297736 AGCTAGGCACCGAGTATTTAGT 58.702 45.455 0.00 0.00 0.00 2.24
872 913 1.360911 GTCGAGCTAGCTAGGCACC 59.639 63.158 22.60 6.68 0.00 5.01
873 914 1.360911 GGTCGAGCTAGCTAGGCAC 59.639 63.158 27.32 17.33 0.00 5.01
965 1006 2.866762 GTGACAGTGACACTCAAGTTCC 59.133 50.000 16.93 0.00 35.66 3.62
997 1038 1.445095 CTCTTCCCAGAGCCATCGG 59.555 63.158 0.00 0.00 40.39 4.18
1060 1106 2.547640 ATCACAAGCAGGCCGAGCAT 62.548 55.000 22.53 10.24 0.00 3.79
1074 1120 4.819761 GCCTCGGCGCTCATCACA 62.820 66.667 7.64 0.00 0.00 3.58
1116 1162 1.152830 GTTGAACTTCCAGCCCCCA 59.847 57.895 0.00 0.00 0.00 4.96
1231 1277 2.220133 GTCACGAACAAACGTATGCTGT 59.780 45.455 0.00 0.00 44.76 4.40
1232 1278 2.219903 TGTCACGAACAAACGTATGCTG 59.780 45.455 0.00 0.00 44.76 4.41
1235 1281 2.806453 CGTGTCACGAACAAACGTATG 58.194 47.619 20.75 0.00 46.05 2.39
1437 1516 0.467844 TCATGTTGGCCTTGCAGTGT 60.468 50.000 3.32 0.00 0.00 3.55
1480 1559 3.971305 AGCTAGCCACTCTAGTCTCTAGA 59.029 47.826 12.13 6.37 45.22 2.43
1481 1560 4.351874 AGCTAGCCACTCTAGTCTCTAG 57.648 50.000 12.13 9.30 45.22 2.43
1483 1562 3.714798 AGTAGCTAGCCACTCTAGTCTCT 59.285 47.826 10.24 0.00 45.22 3.10
1484 1563 4.081322 AGTAGCTAGCCACTCTAGTCTC 57.919 50.000 10.24 0.00 45.22 3.36
1488 1567 4.993029 AACAAGTAGCTAGCCACTCTAG 57.007 45.455 16.38 11.57 46.01 2.43
1489 1568 5.245301 TGAAAACAAGTAGCTAGCCACTCTA 59.755 40.000 16.38 0.00 0.00 2.43
1490 1569 4.040461 TGAAAACAAGTAGCTAGCCACTCT 59.960 41.667 16.38 4.46 0.00 3.24
1491 1570 4.315803 TGAAAACAAGTAGCTAGCCACTC 58.684 43.478 16.38 3.85 0.00 3.51
1514 1593 2.409948 GCTTTGGCTGGATCTGTAGT 57.590 50.000 0.00 0.00 35.22 2.73
1580 1670 0.966179 AATCAACGGGGAAGCAAACC 59.034 50.000 0.00 0.00 0.00 3.27
1592 1682 2.287788 ACAAGAGCAAGGCAAATCAACG 60.288 45.455 0.00 0.00 0.00 4.10
1596 1686 3.930634 AGAACAAGAGCAAGGCAAATC 57.069 42.857 0.00 0.00 0.00 2.17
1597 1687 4.655963 TCTAGAACAAGAGCAAGGCAAAT 58.344 39.130 0.00 0.00 0.00 2.32
1599 1689 3.769739 TCTAGAACAAGAGCAAGGCAA 57.230 42.857 0.00 0.00 0.00 4.52
1601 1691 2.354199 GCATCTAGAACAAGAGCAAGGC 59.646 50.000 0.00 0.00 0.00 4.35
1603 1693 2.606725 CCGCATCTAGAACAAGAGCAAG 59.393 50.000 0.00 0.00 0.00 4.01
1605 1695 1.740380 GCCGCATCTAGAACAAGAGCA 60.740 52.381 0.00 0.00 0.00 4.26
1606 1696 0.933796 GCCGCATCTAGAACAAGAGC 59.066 55.000 0.00 0.00 0.00 4.09
1749 1842 3.332783 CCTTACTGGTTAGGTTTTCCCCT 59.667 47.826 0.00 0.00 41.86 4.79
1750 1843 3.331591 TCCTTACTGGTTAGGTTTTCCCC 59.668 47.826 5.82 0.00 37.66 4.81
1751 1844 4.645863 TCCTTACTGGTTAGGTTTTCCC 57.354 45.455 5.82 0.00 37.66 3.97
1752 1845 5.872963 TCTTCCTTACTGGTTAGGTTTTCC 58.127 41.667 5.82 0.00 37.39 3.13
1805 1901 8.479689 TCATAATAAATGGAACCTCTTGTCGTA 58.520 33.333 0.00 0.00 0.00 3.43
1857 1955 2.851195 AGGTATGCAAACATCCGATCC 58.149 47.619 0.00 0.00 37.74 3.36
2166 2321 4.351054 CTGGTGGGAGTGGGGTGC 62.351 72.222 0.00 0.00 0.00 5.01
2169 2324 1.074951 GTTTCTGGTGGGAGTGGGG 59.925 63.158 0.00 0.00 0.00 4.96
2183 2338 2.762745 TCGGTGGTAGCTTCAAGTTTC 58.237 47.619 0.00 0.00 0.00 2.78
2245 2404 3.543494 GTGTCGAAATGCATGCACATAAC 59.457 43.478 25.37 17.34 0.00 1.89
2252 2411 0.804364 TCCTGTGTCGAAATGCATGC 59.196 50.000 11.82 11.82 0.00 4.06
2282 2447 8.862325 TTGTGTCATCTTCTTATTTACCATGT 57.138 30.769 0.00 0.00 0.00 3.21
2292 2458 7.148086 ACAGCAAACTTTTGTGTCATCTTCTTA 60.148 33.333 3.74 0.00 40.24 2.10
2295 2461 5.343249 ACAGCAAACTTTTGTGTCATCTTC 58.657 37.500 3.74 0.00 40.24 2.87
2298 2464 4.671377 TGACAGCAAACTTTTGTGTCATC 58.329 39.130 22.42 9.45 44.39 2.92
2303 2469 3.552699 CCACATGACAGCAAACTTTTGTG 59.447 43.478 0.00 0.00 40.24 3.33
2309 2484 3.769739 TCTACCACATGACAGCAAACT 57.230 42.857 0.00 0.00 0.00 2.66
2311 2486 4.036262 GTGTTTCTACCACATGACAGCAAA 59.964 41.667 0.00 0.00 33.00 3.68
2326 2501 8.185506 TGTTTGGATAGAGTAGTGTGTTTCTA 57.814 34.615 0.00 0.00 0.00 2.10
2412 2600 6.600032 TCCGTTATTACACAATGCCAGTAAAT 59.400 34.615 0.00 0.00 32.18 1.40
2436 2624 6.706055 TTCTGTCTGTAATGATCAAACGTC 57.294 37.500 0.00 0.00 0.00 4.34
2437 2625 7.148407 GGAATTCTGTCTGTAATGATCAAACGT 60.148 37.037 0.00 0.00 0.00 3.99
2438 2626 7.182761 GGAATTCTGTCTGTAATGATCAAACG 58.817 38.462 0.00 0.00 0.00 3.60
2439 2627 7.121168 TGGGAATTCTGTCTGTAATGATCAAAC 59.879 37.037 0.00 1.73 0.00 2.93
2440 2628 7.174413 TGGGAATTCTGTCTGTAATGATCAAA 58.826 34.615 0.00 0.00 0.00 2.69
2441 2629 6.720309 TGGGAATTCTGTCTGTAATGATCAA 58.280 36.000 0.00 0.00 0.00 2.57
2442 2630 6.312141 TGGGAATTCTGTCTGTAATGATCA 57.688 37.500 5.23 0.00 0.00 2.92
2443 2631 6.238211 CGTTGGGAATTCTGTCTGTAATGATC 60.238 42.308 5.23 0.00 0.00 2.92
2444 2632 5.586243 CGTTGGGAATTCTGTCTGTAATGAT 59.414 40.000 5.23 0.00 0.00 2.45
2445 2633 4.935205 CGTTGGGAATTCTGTCTGTAATGA 59.065 41.667 5.23 0.00 0.00 2.57
2446 2634 4.695455 ACGTTGGGAATTCTGTCTGTAATG 59.305 41.667 5.23 0.00 0.00 1.90
2447 2635 4.906618 ACGTTGGGAATTCTGTCTGTAAT 58.093 39.130 5.23 0.00 0.00 1.89
2448 2636 4.202274 TGACGTTGGGAATTCTGTCTGTAA 60.202 41.667 5.23 0.00 0.00 2.41
2449 2637 3.322541 TGACGTTGGGAATTCTGTCTGTA 59.677 43.478 5.23 0.00 0.00 2.74
2450 2638 2.104111 TGACGTTGGGAATTCTGTCTGT 59.896 45.455 5.23 0.00 0.00 3.41
2451 2639 2.738846 CTGACGTTGGGAATTCTGTCTG 59.261 50.000 5.23 6.61 0.00 3.51
2452 2640 2.289694 CCTGACGTTGGGAATTCTGTCT 60.290 50.000 5.23 0.00 0.00 3.41
2453 2641 2.076863 CCTGACGTTGGGAATTCTGTC 58.923 52.381 5.23 6.84 0.00 3.51
2454 2642 1.697432 TCCTGACGTTGGGAATTCTGT 59.303 47.619 5.23 0.00 0.00 3.41
2455 2643 2.472695 TCCTGACGTTGGGAATTCTG 57.527 50.000 5.23 0.00 0.00 3.02
2456 2644 2.305927 ACATCCTGACGTTGGGAATTCT 59.694 45.455 13.11 0.00 35.08 2.40
2457 2645 2.711542 ACATCCTGACGTTGGGAATTC 58.288 47.619 13.11 0.00 35.08 2.17
2458 2646 2.819608 CAACATCCTGACGTTGGGAATT 59.180 45.455 13.11 8.82 39.05 2.17
2459 2647 2.436417 CAACATCCTGACGTTGGGAAT 58.564 47.619 13.11 4.03 39.05 3.01
2460 2648 1.890876 CAACATCCTGACGTTGGGAA 58.109 50.000 13.11 0.18 39.05 3.97
2461 2649 3.623848 CAACATCCTGACGTTGGGA 57.376 52.632 11.81 11.81 39.05 4.37


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

AutoCloner maintained by Alex Coulton.