Multiple sequence alignment - TraesCS1B01G276000

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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 TraesCS1B01G276000 chr1B 100.000 4326 0 0 1 4326 483590790 483586465 0.000000e+00 7989.0
1 TraesCS1B01G276000 chr1B 84.426 122 17 2 4142 4262 395267902 395267782 7.600000e-23 119.0
2 TraesCS1B01G276000 chr1B 94.444 54 3 0 3827 3880 483586909 483586856 2.770000e-12 84.2
3 TraesCS1B01G276000 chr1B 94.444 54 3 0 3882 3935 483586964 483586911 2.770000e-12 84.2
4 TraesCS1B01G276000 chr1D 91.155 1888 90 28 1735 3591 361152982 361151141 0.000000e+00 2490.0
5 TraesCS1B01G276000 chr1D 93.458 749 41 6 3579 4326 361150855 361150114 0.000000e+00 1105.0
6 TraesCS1B01G276000 chr1D 93.917 674 25 7 1071 1730 361153730 361153059 0.000000e+00 1003.0
7 TraesCS1B01G276000 chr1D 94.141 495 20 5 583 1073 361154261 361153772 0.000000e+00 745.0
8 TraesCS1B01G276000 chr1D 96.188 341 13 0 196 536 361154599 361154259 3.780000e-155 558.0
9 TraesCS1B01G276000 chr1D 96.296 54 2 0 3827 3880 361150556 361150503 5.960000e-14 89.8
10 TraesCS1B01G276000 chr1A 91.176 1734 93 27 1862 3581 460861792 460860105 0.000000e+00 2300.0
11 TraesCS1B01G276000 chr1A 88.549 882 59 24 381 1248 460863717 460862864 0.000000e+00 1031.0
12 TraesCS1B01G276000 chr1A 82.769 325 44 8 1412 1730 460862371 460862053 3.290000e-71 279.0
13 TraesCS1B01G276000 chr1A 97.857 140 3 0 1737 1876 460861959 460861820 4.320000e-60 243.0
14 TraesCS1B01G276000 chr1A 81.699 153 7 5 196 347 460863849 460863717 1.650000e-19 108.0
15 TraesCS1B01G276000 chr1A 79.141 163 28 5 4109 4269 552372841 552372999 1.650000e-19 108.0
16 TraesCS1B01G276000 chr4B 96.471 170 6 0 1 170 460837451 460837282 9.160000e-72 281.0
17 TraesCS1B01G276000 chr7B 94.643 168 8 1 1 167 222068365 222068532 4.290000e-65 259.0
18 TraesCS1B01G276000 chr7B 92.857 168 11 1 1 167 222043900 222044067 4.320000e-60 243.0
19 TraesCS1B01G276000 chr3B 76.128 532 93 23 2167 2686 681176237 681175728 9.290000e-62 248.0
20 TraesCS1B01G276000 chr3D 78.431 306 57 7 2154 2457 517286891 517286593 1.590000e-44 191.0
21 TraesCS1B01G276000 chr3D 88.636 132 13 2 2556 2686 517286486 517286356 4.480000e-35 159.0
22 TraesCS1B01G276000 chr3A 78.840 293 55 6 2167 2457 653304518 653304231 1.590000e-44 191.0
23 TraesCS1B01G276000 chr3A 88.889 135 13 2 2555 2688 653304132 653303999 9.620000e-37 165.0
24 TraesCS1B01G276000 chr3A 80.000 155 25 4 4125 4277 688007724 688007574 4.570000e-20 110.0
25 TraesCS1B01G276000 chr3A 81.295 139 19 6 4128 4262 686856113 686856248 5.920000e-19 106.0
26 TraesCS1B01G276000 chr5B 80.702 171 27 6 4125 4292 609933539 609933706 1.260000e-25 128.0
27 TraesCS1B01G276000 chr2D 84.884 86 13 0 4132 4217 4724909 4724994 2.140000e-13 87.9


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 TraesCS1B01G276000 chr1B 483586465 483590790 4325 True 2719.133333 7989 96.2960 1 4326 3 chr1B.!!$R2 4325
1 TraesCS1B01G276000 chr1D 361150114 361154599 4485 True 998.466667 2490 94.1925 196 4326 6 chr1D.!!$R1 4130
2 TraesCS1B01G276000 chr1A 460860105 460863849 3744 True 792.200000 2300 88.4100 196 3581 5 chr1A.!!$R1 3385
3 TraesCS1B01G276000 chr3B 681175728 681176237 509 True 248.000000 248 76.1280 2167 2686 1 chr3B.!!$R1 519

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
177 178 0.032540 GGTACGGCCCTGGTATTACG 59.967 60.0 0.00 0.00 0.00 3.18 F
192 193 0.035739 TTACGCAGGACTTCCCAACC 59.964 55.0 0.00 0.00 37.41 3.77 F
958 969 0.250597 TGGTTCGTCGAGGAGAGACA 60.251 55.0 7.98 3.89 38.46 3.41 F
2457 3043 0.689623 GCCCCTCTCCATCATGGTAG 59.310 60.0 2.79 2.72 39.03 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 2183 0.400594 AAGTAGGCCTGTGAACACCC 59.599 55.0 17.99 0.0 0.00 4.61 R
1992 2574 0.735978 TACAACGGCATGTCTCTGCG 60.736 55.0 0.00 0.0 43.23 5.18 R
2878 3486 0.541392 AGGAGTATTCATGCACCGCA 59.459 50.0 0.00 0.0 44.86 5.69 R
4277 5188 0.969149 CCATCAGATAGCCGCTACCA 59.031 55.0 1.14 0.0 0.00 3.25 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 5.384063 TCAGCGAAAAATAAAGGCATTGA 57.616 34.783 0.00 0.00 0.00 2.57
24 25 5.777802 TCAGCGAAAAATAAAGGCATTGAA 58.222 33.333 0.00 0.00 0.00 2.69
25 26 6.219473 TCAGCGAAAAATAAAGGCATTGAAA 58.781 32.000 0.00 0.00 0.00 2.69
26 27 6.703607 TCAGCGAAAAATAAAGGCATTGAAAA 59.296 30.769 0.00 0.00 0.00 2.29
27 28 7.387397 TCAGCGAAAAATAAAGGCATTGAAAAT 59.613 29.630 0.00 0.00 0.00 1.82
28 29 8.016801 CAGCGAAAAATAAAGGCATTGAAAATT 58.983 29.630 0.00 0.00 0.00 1.82
29 30 8.567104 AGCGAAAAATAAAGGCATTGAAAATTT 58.433 25.926 0.00 0.00 0.00 1.82
30 31 9.818796 GCGAAAAATAAAGGCATTGAAAATTTA 57.181 25.926 0.00 0.00 0.00 1.40
39 40 9.783081 AAAGGCATTGAAAATTTAAGATTCACT 57.217 25.926 0.00 0.00 33.13 3.41
40 41 9.783081 AAGGCATTGAAAATTTAAGATTCACTT 57.217 25.926 0.00 0.00 42.04 3.16
41 42 9.783081 AGGCATTGAAAATTTAAGATTCACTTT 57.217 25.926 0.00 0.00 39.72 2.66
71 72 7.672983 CAGATATAATTTCTGGGCATAACGT 57.327 36.000 0.00 0.00 37.53 3.99
72 73 8.099364 CAGATATAATTTCTGGGCATAACGTT 57.901 34.615 5.88 5.88 37.53 3.99
73 74 8.017373 CAGATATAATTTCTGGGCATAACGTTG 58.983 37.037 11.99 0.00 37.53 4.10
74 75 7.719633 AGATATAATTTCTGGGCATAACGTTGT 59.280 33.333 11.99 0.00 0.00 3.32
75 76 3.848272 ATTTCTGGGCATAACGTTGTG 57.152 42.857 19.49 19.49 0.00 3.33
76 77 0.878416 TTCTGGGCATAACGTTGTGC 59.122 50.000 33.90 33.90 43.50 4.57
77 78 0.250510 TCTGGGCATAACGTTGTGCA 60.251 50.000 38.88 24.89 45.65 4.57
78 79 0.595588 CTGGGCATAACGTTGTGCAA 59.404 50.000 38.88 28.65 45.65 4.08
79 80 1.202114 CTGGGCATAACGTTGTGCAAT 59.798 47.619 38.88 12.88 45.65 3.56
80 81 2.421775 CTGGGCATAACGTTGTGCAATA 59.578 45.455 38.88 26.64 45.65 1.90
81 82 3.020274 TGGGCATAACGTTGTGCAATAT 58.980 40.909 38.88 11.48 45.65 1.28
82 83 3.181492 TGGGCATAACGTTGTGCAATATG 60.181 43.478 38.88 21.97 45.65 1.78
83 84 3.181491 GGGCATAACGTTGTGCAATATGT 60.181 43.478 38.88 2.83 45.65 2.29
84 85 4.035792 GGGCATAACGTTGTGCAATATGTA 59.964 41.667 38.88 6.88 45.65 2.29
85 86 5.449314 GGGCATAACGTTGTGCAATATGTAA 60.449 40.000 38.88 6.68 45.65 2.41
86 87 6.205784 GGCATAACGTTGTGCAATATGTAAT 58.794 36.000 38.88 8.70 45.65 1.89
87 88 6.695278 GGCATAACGTTGTGCAATATGTAATT 59.305 34.615 38.88 1.13 45.65 1.40
88 89 7.305935 GGCATAACGTTGTGCAATATGTAATTG 60.306 37.037 38.88 8.29 45.65 2.32
139 140 8.731275 ATAGGGCCTTATTTTAAATTTTGCAC 57.269 30.769 13.45 0.00 0.00 4.57
140 141 6.538263 AGGGCCTTATTTTAAATTTTGCACA 58.462 32.000 0.00 0.00 0.00 4.57
141 142 6.654582 AGGGCCTTATTTTAAATTTTGCACAG 59.345 34.615 0.00 0.00 0.00 3.66
142 143 6.128035 GGGCCTTATTTTAAATTTTGCACAGG 60.128 38.462 0.84 0.00 0.00 4.00
143 144 6.128035 GGCCTTATTTTAAATTTTGCACAGGG 60.128 38.462 0.00 0.00 0.00 4.45
144 145 6.622679 GCCTTATTTTAAATTTTGCACAGGGC 60.623 38.462 0.00 0.00 45.13 5.19
145 146 6.128035 CCTTATTTTAAATTTTGCACAGGGCC 60.128 38.462 0.00 0.00 43.89 5.80
146 147 4.429854 TTTTAAATTTTGCACAGGGCCT 57.570 36.364 0.00 0.00 43.89 5.19
147 148 3.676291 TTAAATTTTGCACAGGGCCTC 57.324 42.857 0.95 0.00 43.89 4.70
148 149 0.686789 AAATTTTGCACAGGGCCTCC 59.313 50.000 0.95 0.00 43.89 4.30
149 150 0.471591 AATTTTGCACAGGGCCTCCA 60.472 50.000 0.95 0.00 43.89 3.86
150 151 0.471591 ATTTTGCACAGGGCCTCCAA 60.472 50.000 0.95 4.75 43.89 3.53
151 152 0.689080 TTTTGCACAGGGCCTCCAAA 60.689 50.000 0.95 11.16 43.89 3.28
152 153 0.471591 TTTGCACAGGGCCTCCAAAT 60.472 50.000 0.95 0.00 43.89 2.32
153 154 0.471591 TTGCACAGGGCCTCCAAATT 60.472 50.000 0.95 0.00 43.89 1.82
154 155 0.899717 TGCACAGGGCCTCCAAATTC 60.900 55.000 0.95 0.00 43.89 2.17
155 156 0.613012 GCACAGGGCCTCCAAATTCT 60.613 55.000 0.95 0.00 36.11 2.40
156 157 1.928868 CACAGGGCCTCCAAATTCTT 58.071 50.000 0.95 0.00 34.83 2.52
157 158 2.883888 GCACAGGGCCTCCAAATTCTTA 60.884 50.000 0.95 0.00 36.11 2.10
158 159 3.019564 CACAGGGCCTCCAAATTCTTAG 58.980 50.000 0.95 0.00 34.83 2.18
159 160 2.024941 ACAGGGCCTCCAAATTCTTAGG 60.025 50.000 0.95 0.00 34.83 2.69
160 161 2.024941 CAGGGCCTCCAAATTCTTAGGT 60.025 50.000 0.95 0.00 34.83 3.08
161 162 3.202151 CAGGGCCTCCAAATTCTTAGGTA 59.798 47.826 0.95 0.00 34.83 3.08
162 163 3.202373 AGGGCCTCCAAATTCTTAGGTAC 59.798 47.826 0.00 0.00 34.83 3.34
163 164 3.203716 GGCCTCCAAATTCTTAGGTACG 58.796 50.000 0.00 0.00 0.00 3.67
164 165 3.203716 GCCTCCAAATTCTTAGGTACGG 58.796 50.000 0.00 0.00 0.00 4.02
165 166 3.203716 CCTCCAAATTCTTAGGTACGGC 58.796 50.000 0.00 0.00 0.00 5.68
166 167 3.203716 CTCCAAATTCTTAGGTACGGCC 58.796 50.000 0.00 0.00 37.58 6.13
167 168 2.092807 TCCAAATTCTTAGGTACGGCCC 60.093 50.000 0.00 0.00 38.26 5.80
168 169 2.092592 CCAAATTCTTAGGTACGGCCCT 60.093 50.000 0.00 0.56 38.26 5.19
169 170 2.943033 CAAATTCTTAGGTACGGCCCTG 59.057 50.000 0.00 0.00 38.26 4.45
170 171 1.129058 ATTCTTAGGTACGGCCCTGG 58.871 55.000 0.00 0.00 38.26 4.45
171 172 0.252375 TTCTTAGGTACGGCCCTGGT 60.252 55.000 0.00 0.00 38.26 4.00
172 173 0.630673 TCTTAGGTACGGCCCTGGTA 59.369 55.000 0.00 0.00 38.26 3.25
173 174 1.218704 TCTTAGGTACGGCCCTGGTAT 59.781 52.381 0.00 0.00 38.26 2.73
174 175 2.044758 CTTAGGTACGGCCCTGGTATT 58.955 52.381 0.00 0.00 38.26 1.89
175 176 3.117169 TCTTAGGTACGGCCCTGGTATTA 60.117 47.826 0.00 0.00 38.26 0.98
176 177 1.417288 AGGTACGGCCCTGGTATTAC 58.583 55.000 0.00 0.00 38.26 1.89
177 178 0.032540 GGTACGGCCCTGGTATTACG 59.967 60.000 0.00 0.00 0.00 3.18
178 179 0.598419 GTACGGCCCTGGTATTACGC 60.598 60.000 0.00 0.00 0.00 4.42
179 180 1.042003 TACGGCCCTGGTATTACGCA 61.042 55.000 0.00 0.00 0.00 5.24
180 181 1.594293 CGGCCCTGGTATTACGCAG 60.594 63.158 0.00 5.71 0.00 5.18
181 182 1.227853 GGCCCTGGTATTACGCAGG 60.228 63.158 17.71 17.71 36.75 4.85
182 183 1.692173 GGCCCTGGTATTACGCAGGA 61.692 60.000 22.73 0.00 38.20 3.86
183 184 0.532196 GCCCTGGTATTACGCAGGAC 60.532 60.000 22.73 13.71 38.20 3.85
184 185 1.120530 CCCTGGTATTACGCAGGACT 58.879 55.000 22.73 0.00 38.20 3.85
185 186 1.485066 CCCTGGTATTACGCAGGACTT 59.515 52.381 22.73 0.00 38.20 3.01
186 187 2.483188 CCCTGGTATTACGCAGGACTTC 60.483 54.545 22.73 0.00 38.20 3.01
187 188 2.483188 CCTGGTATTACGCAGGACTTCC 60.483 54.545 18.99 0.00 38.20 3.46
188 189 1.483415 TGGTATTACGCAGGACTTCCC 59.517 52.381 0.00 0.00 36.42 3.97
189 190 1.483415 GGTATTACGCAGGACTTCCCA 59.517 52.381 0.00 0.00 37.41 4.37
190 191 2.093341 GGTATTACGCAGGACTTCCCAA 60.093 50.000 0.00 0.00 37.41 4.12
191 192 2.109425 ATTACGCAGGACTTCCCAAC 57.891 50.000 0.00 0.00 37.41 3.77
192 193 0.035739 TTACGCAGGACTTCCCAACC 59.964 55.000 0.00 0.00 37.41 3.77
193 194 1.833787 TACGCAGGACTTCCCAACCC 61.834 60.000 0.00 0.00 37.41 4.11
194 195 2.035783 GCAGGACTTCCCAACCCC 59.964 66.667 0.00 0.00 37.41 4.95
204 205 1.305213 CCCAACCCCACCATCCTTG 60.305 63.158 0.00 0.00 0.00 3.61
228 229 4.445385 CACAAGCAGAAAATAAACACAGGC 59.555 41.667 0.00 0.00 0.00 4.85
270 271 1.031571 TTCATCCTGCATTCGGTGGC 61.032 55.000 0.00 0.00 0.00 5.01
324 325 2.362329 GATCTCTGGAGCACCCTCGC 62.362 65.000 0.00 0.00 39.06 5.03
325 326 4.504916 CTCTGGAGCACCCTCGCG 62.505 72.222 0.00 0.00 39.06 5.87
362 363 7.859325 TGTTAGCTAACAATATTTGACTCCC 57.141 36.000 31.99 4.93 42.66 4.30
374 375 3.963476 TTGACTCCCCCTTTCTTTTCA 57.037 42.857 0.00 0.00 0.00 2.69
391 392 5.467035 TTTTCAGAAAAAGGGTATGGCAG 57.533 39.130 5.81 0.00 30.90 4.85
412 414 5.681179 GCAGAAGTCTTAGATCCTTCCAGAC 60.681 48.000 8.41 3.19 36.16 3.51
425 427 5.297547 TCCTTCCAGACGCATGAATATAAC 58.702 41.667 0.00 0.00 0.00 1.89
428 430 4.689071 TCCAGACGCATGAATATAACGTT 58.311 39.130 5.88 5.88 37.05 3.99
543 546 0.909623 AATTAGCTAGTGCACCGGGT 59.090 50.000 14.63 14.35 42.74 5.28
576 585 2.356535 GGTGATGCCAAATCCTGTCTCT 60.357 50.000 0.00 0.00 37.17 3.10
578 587 1.674962 GATGCCAAATCCTGTCTCTGC 59.325 52.381 0.00 0.00 0.00 4.26
580 589 0.674895 GCCAAATCCTGTCTCTGCGT 60.675 55.000 0.00 0.00 0.00 5.24
609 618 2.158325 AGCAAAACAAGATCCTCCCCAA 60.158 45.455 0.00 0.00 0.00 4.12
610 619 2.029020 GCAAAACAAGATCCTCCCCAAC 60.029 50.000 0.00 0.00 0.00 3.77
611 620 3.230134 CAAAACAAGATCCTCCCCAACA 58.770 45.455 0.00 0.00 0.00 3.33
612 621 3.833559 AAACAAGATCCTCCCCAACAT 57.166 42.857 0.00 0.00 0.00 2.71
613 622 3.372440 AACAAGATCCTCCCCAACATC 57.628 47.619 0.00 0.00 0.00 3.06
618 627 0.549950 ATCCTCCCCAACATCTGCTG 59.450 55.000 0.00 0.00 0.00 4.41
651 661 0.616371 TACTGTTTACTGCCCGGCAT 59.384 50.000 13.86 6.08 38.13 4.40
661 671 4.096003 CCCGGCATTCCCACGTCT 62.096 66.667 0.00 0.00 0.00 4.18
663 673 1.445942 CCGGCATTCCCACGTCTAT 59.554 57.895 0.00 0.00 0.00 1.98
671 681 0.757935 TCCCACGTCTATAGGGGCAC 60.758 60.000 7.98 0.00 43.03 5.01
784 795 5.891551 TCTTCCTATATATACGATGCAGCCA 59.108 40.000 0.00 0.00 0.00 4.75
810 821 6.216046 TCCATGTATCCATCATCCACACATAT 59.784 38.462 0.00 0.00 0.00 1.78
822 833 7.108847 TCATCCACACATATGAACACATACAA 58.891 34.615 10.38 0.00 30.73 2.41
927 938 4.676723 CGAGGAGGTCTGTCTTTTCATCTC 60.677 50.000 0.00 0.00 0.00 2.75
930 941 2.003301 GGTCTGTCTTTTCATCTCGGC 58.997 52.381 0.00 0.00 0.00 5.54
955 966 1.166129 TCTTGGTTCGTCGAGGAGAG 58.834 55.000 7.98 5.88 0.00 3.20
956 967 1.166129 CTTGGTTCGTCGAGGAGAGA 58.834 55.000 7.98 0.00 0.00 3.10
957 968 0.879765 TTGGTTCGTCGAGGAGAGAC 59.120 55.000 7.98 4.05 35.41 3.36
958 969 0.250597 TGGTTCGTCGAGGAGAGACA 60.251 55.000 7.98 3.89 38.46 3.41
960 971 1.473278 GGTTCGTCGAGGAGAGACAAT 59.527 52.381 7.98 0.00 38.46 2.71
1035 1049 4.442753 GCCAAGTTCTTGTTTGGGATTTCA 60.443 41.667 10.93 0.00 43.23 2.69
1121 1180 0.953727 TGTGCTGTGGTTTGCTCATC 59.046 50.000 0.00 0.00 0.00 2.92
1237 1298 4.812626 CCCGGTGTAAGTATTTCATGTACC 59.187 45.833 0.00 0.00 0.00 3.34
1329 1770 3.169099 AGACAGCAGAGTGTTACTGGAT 58.831 45.455 0.00 0.00 36.09 3.41
1360 1801 8.588472 CACTTTTCTCCCTTTTATTGGAAGAAT 58.412 33.333 0.00 0.00 0.00 2.40
1562 2011 2.091885 GCTTGAATTCCTGGGGTCCATA 60.092 50.000 2.27 0.00 30.82 2.74
1575 2024 6.294361 TGGGGTCCATACATCTATTAATCG 57.706 41.667 0.00 0.00 0.00 3.34
1598 2047 8.467402 TCGCTCTTAATTTAATCTAGCTATGC 57.533 34.615 0.00 0.00 0.00 3.14
1730 2183 6.892310 TCTATTCATGATGTTGAGAACGTG 57.108 37.500 0.00 0.00 0.00 4.49
1731 2184 4.952262 ATTCATGATGTTGAGAACGTGG 57.048 40.909 0.00 0.00 0.00 4.94
1732 2185 2.698803 TCATGATGTTGAGAACGTGGG 58.301 47.619 0.00 0.00 0.00 4.61
1733 2186 2.038426 TCATGATGTTGAGAACGTGGGT 59.962 45.455 0.00 0.00 0.00 4.51
1868 2408 6.607198 ACCTCTCAATTTTCTCCAAGAACAAA 59.393 34.615 0.00 0.00 33.26 2.83
1878 2460 9.712305 TTTTCTCCAAGAACAAATTAACAACAA 57.288 25.926 0.00 0.00 33.26 2.83
1879 2461 8.696410 TTCTCCAAGAACAAATTAACAACAAC 57.304 30.769 0.00 0.00 0.00 3.32
1884 2466 8.663911 CCAAGAACAAATTAACAACAACACAAT 58.336 29.630 0.00 0.00 0.00 2.71
1992 2574 1.721926 GCTTCTGCAACGTGTCTCTAC 59.278 52.381 0.00 0.00 39.41 2.59
2057 2639 6.490040 ACACAAGTGCATAAACTATCCTTGTT 59.510 34.615 9.94 2.18 39.04 2.83
2058 2640 7.023575 CACAAGTGCATAAACTATCCTTGTTC 58.976 38.462 9.94 0.00 39.04 3.18
2059 2641 6.151144 ACAAGTGCATAAACTATCCTTGTTCC 59.849 38.462 7.51 0.00 38.19 3.62
2060 2642 5.815581 AGTGCATAAACTATCCTTGTTCCA 58.184 37.500 0.00 0.00 0.00 3.53
2061 2643 5.882557 AGTGCATAAACTATCCTTGTTCCAG 59.117 40.000 0.00 0.00 0.00 3.86
2062 2644 5.648092 GTGCATAAACTATCCTTGTTCCAGT 59.352 40.000 0.00 0.00 0.00 4.00
2063 2645 5.647658 TGCATAAACTATCCTTGTTCCAGTG 59.352 40.000 0.00 0.00 0.00 3.66
2064 2646 5.648092 GCATAAACTATCCTTGTTCCAGTGT 59.352 40.000 0.00 0.00 0.00 3.55
2065 2647 6.183360 GCATAAACTATCCTTGTTCCAGTGTC 60.183 42.308 0.00 0.00 0.00 3.67
2066 2648 5.568620 AAACTATCCTTGTTCCAGTGTCT 57.431 39.130 0.00 0.00 0.00 3.41
2067 2649 6.681729 AAACTATCCTTGTTCCAGTGTCTA 57.318 37.500 0.00 0.00 0.00 2.59
2068 2650 6.681729 AACTATCCTTGTTCCAGTGTCTAA 57.318 37.500 0.00 0.00 0.00 2.10
2069 2651 6.681729 ACTATCCTTGTTCCAGTGTCTAAA 57.318 37.500 0.00 0.00 0.00 1.85
2070 2652 7.074653 ACTATCCTTGTTCCAGTGTCTAAAA 57.925 36.000 0.00 0.00 0.00 1.52
2071 2653 7.514721 ACTATCCTTGTTCCAGTGTCTAAAAA 58.485 34.615 0.00 0.00 0.00 1.94
2101 2683 2.762535 TGTTCCCTTCCGATCTTGTC 57.237 50.000 0.00 0.00 0.00 3.18
2115 2701 3.896648 TCTTGTCGATGGTTCAAAAGC 57.103 42.857 0.00 0.00 0.00 3.51
2134 2720 1.450905 GCTCGACGTGTTACAAGTGAC 59.549 52.381 8.88 0.00 0.00 3.67
2137 2723 1.189446 CGACGTGTTACAAGTGACAGC 59.811 52.381 8.88 0.00 29.42 4.40
2457 3043 0.689623 GCCCCTCTCCATCATGGTAG 59.310 60.000 2.79 2.72 39.03 3.18
2686 3280 1.135460 CCTCTTCGTCACGGTAAGTCC 60.135 57.143 0.00 0.00 0.00 3.85
2695 3289 4.574013 CGTCACGGTAAGTCCTATTAGTCT 59.426 45.833 0.00 0.00 0.00 3.24
2696 3290 5.755375 CGTCACGGTAAGTCCTATTAGTCTA 59.245 44.000 0.00 0.00 0.00 2.59
2700 3294 6.317140 CACGGTAAGTCCTATTAGTCTACACA 59.683 42.308 0.00 0.00 0.00 3.72
2712 3306 2.202756 TACACACACGCACGCACA 60.203 55.556 0.00 0.00 0.00 4.57
2743 3337 1.008538 CCAACTTTGCTGTGCCGTC 60.009 57.895 0.00 0.00 0.00 4.79
2774 3369 2.662006 TCTCTTTCTGATGCCGACAG 57.338 50.000 0.00 0.00 36.80 3.51
2816 3411 2.638480 TGAAGGAAACTGTGAGTGGG 57.362 50.000 0.00 0.00 42.68 4.61
2819 3414 0.773644 AGGAAACTGTGAGTGGGCAT 59.226 50.000 0.00 0.00 41.13 4.40
2850 3453 4.698276 CACTAACTGCGTTGTCATTGTAC 58.302 43.478 4.52 0.00 0.00 2.90
2896 3504 0.940126 CTGCGGTGCATGAATACTCC 59.060 55.000 0.00 0.00 38.13 3.85
2908 3516 6.088824 GCATGAATACTCCTTTTGACTTGTG 58.911 40.000 0.00 0.00 0.00 3.33
3109 3718 4.494350 TTGATGCTCTGTTCTTCTTTGC 57.506 40.909 0.00 0.00 0.00 3.68
3218 3830 4.408821 CCGGCAAGCTACAGGGCA 62.409 66.667 0.00 0.00 34.17 5.36
3346 3958 2.550606 GCTAGATCGGTCGAAGATCAGT 59.449 50.000 24.88 13.53 45.05 3.41
3398 4010 0.036765 TACTGCAAGAATCCCGCGTT 60.037 50.000 4.92 0.00 37.43 4.84
3430 4042 6.582636 TGTGTAATTAGCCAATAGAGGACTG 58.417 40.000 0.00 0.00 0.00 3.51
3464 4076 3.566742 CCACCCTTGTACCTGTTTGTAAC 59.433 47.826 0.00 0.00 0.00 2.50
3468 4080 5.132480 ACCCTTGTACCTGTTTGTAACCTAA 59.868 40.000 0.00 0.00 0.00 2.69
3469 4081 5.704053 CCCTTGTACCTGTTTGTAACCTAAG 59.296 44.000 0.00 0.00 0.00 2.18
3470 4082 6.464749 CCCTTGTACCTGTTTGTAACCTAAGA 60.465 42.308 0.00 0.00 0.00 2.10
3471 4083 7.166167 CCTTGTACCTGTTTGTAACCTAAGAT 58.834 38.462 0.00 0.00 0.00 2.40
3472 4084 7.119262 CCTTGTACCTGTTTGTAACCTAAGATG 59.881 40.741 0.00 0.00 0.00 2.90
3473 4085 7.069877 TGTACCTGTTTGTAACCTAAGATGT 57.930 36.000 0.00 0.00 0.00 3.06
3474 4086 8.192743 TGTACCTGTTTGTAACCTAAGATGTA 57.807 34.615 0.00 0.00 0.00 2.29
3475 4087 8.308931 TGTACCTGTTTGTAACCTAAGATGTAG 58.691 37.037 0.00 0.00 0.00 2.74
3476 4088 6.171213 ACCTGTTTGTAACCTAAGATGTAGC 58.829 40.000 0.00 0.00 0.00 3.58
3477 4089 6.170506 CCTGTTTGTAACCTAAGATGTAGCA 58.829 40.000 0.00 0.00 0.00 3.49
3499 4111 6.641176 CAGTATTGCATACGTGTACTGAAA 57.359 37.500 6.36 0.00 42.90 2.69
3510 4122 3.181526 CGTGTACTGAAATCTGAAGCTGC 60.182 47.826 0.00 0.00 0.00 5.25
3511 4123 3.126000 GTGTACTGAAATCTGAAGCTGCC 59.874 47.826 0.00 0.00 0.00 4.85
3521 4133 4.357918 TCTGAAGCTGCCTTTTCTACTT 57.642 40.909 0.00 0.00 0.00 2.24
3608 4518 7.322938 GTGATCACGAATGATGCATTTGATAAG 59.677 37.037 10.69 0.00 46.01 1.73
3609 4519 5.513376 TCACGAATGATGCATTTGATAAGC 58.487 37.500 12.92 0.00 37.41 3.09
3628 4538 8.721478 TGATAAGCAAACTATGAAGAACTTGAC 58.279 33.333 0.00 0.00 0.00 3.18
3629 4539 8.854614 ATAAGCAAACTATGAAGAACTTGACT 57.145 30.769 0.00 0.00 0.00 3.41
3654 4564 7.345422 TCTGATGTTGGAGATTTGAACAAAA 57.655 32.000 4.12 0.00 33.50 2.44
3655 4565 7.780064 TCTGATGTTGGAGATTTGAACAAAAA 58.220 30.769 4.12 0.00 33.50 1.94
3656 4566 8.423349 TCTGATGTTGGAGATTTGAACAAAAAT 58.577 29.630 4.12 0.00 33.50 1.82
3657 4567 8.592105 TGATGTTGGAGATTTGAACAAAAATC 57.408 30.769 4.12 5.58 43.79 2.17
3715 4625 3.798202 AGAGGTTGACGATATTTCTGCC 58.202 45.455 0.00 0.00 0.00 4.85
3716 4626 2.540101 GAGGTTGACGATATTTCTGCCG 59.460 50.000 0.00 0.00 0.00 5.69
3721 4631 2.201732 GACGATATTTCTGCCGCTCAA 58.798 47.619 0.00 0.00 0.00 3.02
3764 4674 5.793817 TGCTAGAGTGCAAAAACTGATAGA 58.206 37.500 0.00 0.00 40.29 1.98
3766 4676 6.710295 TGCTAGAGTGCAAAAACTGATAGAAA 59.290 34.615 0.00 0.00 40.29 2.52
3767 4677 7.391554 TGCTAGAGTGCAAAAACTGATAGAAAT 59.608 33.333 0.00 0.00 40.29 2.17
3804 4714 3.876320 GCCTAGCTCCAAAGATTCAAGAG 59.124 47.826 0.00 0.00 0.00 2.85
3819 4729 2.028294 TCAAGAGCTTGAGAAGAGGCAG 60.028 50.000 8.76 0.00 43.90 4.85
3839 4749 2.093106 GTCTCGTGTGGACTGGTATCT 58.907 52.381 0.00 0.00 0.00 1.98
3852 4762 4.480115 ACTGGTATCTTATCGTGATCCCA 58.520 43.478 0.00 0.00 30.84 4.37
3880 4790 2.653726 ACATGAAGGTGTGCTCAACAA 58.346 42.857 6.58 0.00 41.57 2.83
3931 4841 0.888736 TGAACATGAAGGTGTGCCCG 60.889 55.000 0.00 0.00 38.74 6.13
3949 4859 2.700897 CCCGACAGGAAGGATGACTAAT 59.299 50.000 0.00 0.00 41.02 1.73
4048 4958 3.730662 CGGAAACACAAACTGAACACAGG 60.731 47.826 0.00 0.00 36.12 4.00
4054 4964 4.142403 ACACAAACTGAACACAGGAATGTG 60.142 41.667 19.73 19.73 42.30 3.21
4075 4985 7.447374 TGTGGTCGTTCATAATCTTTCATTT 57.553 32.000 0.00 0.00 0.00 2.32
4076 4986 7.304735 TGTGGTCGTTCATAATCTTTCATTTG 58.695 34.615 0.00 0.00 0.00 2.32
4077 4987 7.040755 TGTGGTCGTTCATAATCTTTCATTTGT 60.041 33.333 0.00 0.00 0.00 2.83
4091 5001 1.019278 ATTTGTCGTGCGAGGCGAAT 61.019 50.000 0.00 0.00 40.19 3.34
4119 5029 2.864968 CGACTCTTGTCTAGGGTTTCG 58.135 52.381 0.00 0.00 37.84 3.46
4159 5069 4.162690 GCCGGTCCGCCTCATCTT 62.163 66.667 5.50 0.00 0.00 2.40
4228 5139 4.501743 GGCGAGAGGACTCTATTTTTAGGG 60.502 50.000 1.10 0.00 40.61 3.53
4234 5145 7.807198 AGAGGACTCTATTTTTAGGGGATTTC 58.193 38.462 0.00 0.00 38.35 2.17
4245 5156 5.722021 TTAGGGGATTTCTTCAGTTTTGC 57.278 39.130 0.00 0.00 0.00 3.68
4248 5159 5.393866 AGGGGATTTCTTCAGTTTTGCTAA 58.606 37.500 0.00 0.00 0.00 3.09
4277 5188 1.115467 CATGCCTAGAAGGACGAGGT 58.885 55.000 0.00 0.00 42.23 3.85
4288 5199 2.044650 ACGAGGTGGTAGCGGCTA 60.045 61.111 5.42 5.42 0.00 3.93
4289 5200 1.453762 GACGAGGTGGTAGCGGCTAT 61.454 60.000 13.60 0.00 0.00 2.97
4291 5202 1.173444 CGAGGTGGTAGCGGCTATCT 61.173 60.000 20.15 11.97 0.00 1.98
4292 5203 0.315568 GAGGTGGTAGCGGCTATCTG 59.684 60.000 20.15 0.00 0.00 2.90
4318 5229 0.749649 CTTCTAGCATCGCCAGAGGT 59.250 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.777802 TCAATGCCTTTATTTTTCGCTGAA 58.222 33.333 0.00 0.00 0.00 3.02
1 2 5.384063 TCAATGCCTTTATTTTTCGCTGA 57.616 34.783 0.00 0.00 0.00 4.26
2 3 6.464895 TTTCAATGCCTTTATTTTTCGCTG 57.535 33.333 0.00 0.00 0.00 5.18
3 4 7.671495 ATTTTCAATGCCTTTATTTTTCGCT 57.329 28.000 0.00 0.00 0.00 4.93
4 5 8.726650 AAATTTTCAATGCCTTTATTTTTCGC 57.273 26.923 0.00 0.00 0.00 4.70
13 14 9.783081 AGTGAATCTTAAATTTTCAATGCCTTT 57.217 25.926 0.00 0.00 31.66 3.11
14 15 9.783081 AAGTGAATCTTAAATTTTCAATGCCTT 57.217 25.926 0.00 0.00 34.23 4.35
15 16 9.783081 AAAGTGAATCTTAAATTTTCAATGCCT 57.217 25.926 0.00 0.00 35.02 4.75
47 48 7.672983 ACGTTATGCCCAGAAATTATATCTG 57.327 36.000 0.00 0.00 43.15 2.90
48 49 7.719633 ACAACGTTATGCCCAGAAATTATATCT 59.280 33.333 0.00 0.00 0.00 1.98
49 50 7.803189 CACAACGTTATGCCCAGAAATTATATC 59.197 37.037 0.00 0.00 0.00 1.63
50 51 7.648142 CACAACGTTATGCCCAGAAATTATAT 58.352 34.615 0.00 0.00 0.00 0.86
51 52 6.459024 GCACAACGTTATGCCCAGAAATTATA 60.459 38.462 20.68 0.00 35.73 0.98
52 53 5.678616 GCACAACGTTATGCCCAGAAATTAT 60.679 40.000 20.68 0.00 35.73 1.28
53 54 4.380023 GCACAACGTTATGCCCAGAAATTA 60.380 41.667 20.68 0.00 35.73 1.40
54 55 3.613910 GCACAACGTTATGCCCAGAAATT 60.614 43.478 20.68 0.00 35.73 1.82
55 56 2.094752 GCACAACGTTATGCCCAGAAAT 60.095 45.455 20.68 0.00 35.73 2.17
56 57 1.268352 GCACAACGTTATGCCCAGAAA 59.732 47.619 20.68 0.00 35.73 2.52
57 58 0.878416 GCACAACGTTATGCCCAGAA 59.122 50.000 20.68 0.00 35.73 3.02
58 59 0.250510 TGCACAACGTTATGCCCAGA 60.251 50.000 27.26 7.16 41.33 3.86
59 60 0.595588 TTGCACAACGTTATGCCCAG 59.404 50.000 27.26 3.49 41.33 4.45
60 61 1.252175 ATTGCACAACGTTATGCCCA 58.748 45.000 27.26 15.25 41.33 5.36
61 62 3.181491 ACATATTGCACAACGTTATGCCC 60.181 43.478 27.26 3.14 41.33 5.36
62 63 4.027572 ACATATTGCACAACGTTATGCC 57.972 40.909 27.26 11.07 41.33 4.40
63 64 7.546277 CAATTACATATTGCACAACGTTATGC 58.454 34.615 24.14 24.14 42.40 3.14
113 114 9.825109 GTGCAAAATTTAAAATAAGGCCCTATA 57.175 29.630 0.00 0.00 0.00 1.31
114 115 8.325046 TGTGCAAAATTTAAAATAAGGCCCTAT 58.675 29.630 0.00 0.00 0.00 2.57
115 116 7.680730 TGTGCAAAATTTAAAATAAGGCCCTA 58.319 30.769 0.00 0.00 0.00 3.53
116 117 6.538263 TGTGCAAAATTTAAAATAAGGCCCT 58.462 32.000 0.00 0.00 0.00 5.19
117 118 6.128035 CCTGTGCAAAATTTAAAATAAGGCCC 60.128 38.462 0.00 0.00 0.00 5.80
118 119 6.128035 CCCTGTGCAAAATTTAAAATAAGGCC 60.128 38.462 0.00 0.00 0.00 5.19
119 120 6.622679 GCCCTGTGCAAAATTTAAAATAAGGC 60.623 38.462 0.00 0.00 40.77 4.35
120 121 6.128035 GGCCCTGTGCAAAATTTAAAATAAGG 60.128 38.462 0.00 0.00 43.89 2.69
121 122 6.654582 AGGCCCTGTGCAAAATTTAAAATAAG 59.345 34.615 0.00 0.00 43.89 1.73
122 123 6.538263 AGGCCCTGTGCAAAATTTAAAATAA 58.462 32.000 0.00 0.00 43.89 1.40
123 124 6.120507 AGGCCCTGTGCAAAATTTAAAATA 57.879 33.333 0.00 0.00 43.89 1.40
124 125 4.984295 AGGCCCTGTGCAAAATTTAAAAT 58.016 34.783 0.00 0.00 43.89 1.82
125 126 4.384940 GAGGCCCTGTGCAAAATTTAAAA 58.615 39.130 0.00 0.00 43.89 1.52
126 127 3.244387 GGAGGCCCTGTGCAAAATTTAAA 60.244 43.478 0.00 0.00 43.89 1.52
127 128 2.301583 GGAGGCCCTGTGCAAAATTTAA 59.698 45.455 0.00 0.00 43.89 1.52
128 129 1.899142 GGAGGCCCTGTGCAAAATTTA 59.101 47.619 0.00 0.00 43.89 1.40
129 130 0.686789 GGAGGCCCTGTGCAAAATTT 59.313 50.000 0.00 0.00 43.89 1.82
130 131 0.471591 TGGAGGCCCTGTGCAAAATT 60.472 50.000 0.00 0.00 43.89 1.82
131 132 0.471591 TTGGAGGCCCTGTGCAAAAT 60.472 50.000 0.00 0.00 43.89 1.82
132 133 0.689080 TTTGGAGGCCCTGTGCAAAA 60.689 50.000 7.56 0.00 43.89 2.44
133 134 0.471591 ATTTGGAGGCCCTGTGCAAA 60.472 50.000 11.65 11.65 43.89 3.68
134 135 0.471591 AATTTGGAGGCCCTGTGCAA 60.472 50.000 0.00 0.00 43.89 4.08
135 136 0.899717 GAATTTGGAGGCCCTGTGCA 60.900 55.000 0.00 0.00 43.89 4.57
136 137 0.613012 AGAATTTGGAGGCCCTGTGC 60.613 55.000 0.00 0.00 40.16 4.57
137 138 1.928868 AAGAATTTGGAGGCCCTGTG 58.071 50.000 0.00 0.00 0.00 3.66
138 139 2.024941 CCTAAGAATTTGGAGGCCCTGT 60.025 50.000 0.00 0.00 44.03 4.00
139 140 2.024941 ACCTAAGAATTTGGAGGCCCTG 60.025 50.000 0.00 0.00 44.03 4.45
140 141 2.288525 ACCTAAGAATTTGGAGGCCCT 58.711 47.619 0.00 0.00 44.03 5.19
141 142 2.828661 ACCTAAGAATTTGGAGGCCC 57.171 50.000 0.00 0.00 44.03 5.80
142 143 3.203716 CGTACCTAAGAATTTGGAGGCC 58.796 50.000 0.00 0.00 44.03 5.19
143 144 3.203716 CCGTACCTAAGAATTTGGAGGC 58.796 50.000 0.00 0.00 44.03 4.70
144 145 3.203716 GCCGTACCTAAGAATTTGGAGG 58.796 50.000 0.00 0.00 44.03 4.30
145 146 3.203716 GGCCGTACCTAAGAATTTGGAG 58.796 50.000 0.00 0.00 44.03 3.86
146 147 2.092807 GGGCCGTACCTAAGAATTTGGA 60.093 50.000 0.00 0.00 44.03 3.53
147 148 2.092592 AGGGCCGTACCTAAGAATTTGG 60.093 50.000 0.00 0.00 46.76 3.28
148 149 2.943033 CAGGGCCGTACCTAAGAATTTG 59.057 50.000 0.00 0.00 39.34 2.32
149 150 2.092592 CCAGGGCCGTACCTAAGAATTT 60.093 50.000 0.00 0.00 39.34 1.82
150 151 1.489230 CCAGGGCCGTACCTAAGAATT 59.511 52.381 0.00 0.00 39.34 2.17
151 152 1.129058 CCAGGGCCGTACCTAAGAAT 58.871 55.000 0.00 0.00 39.34 2.40
152 153 0.252375 ACCAGGGCCGTACCTAAGAA 60.252 55.000 0.00 0.00 39.34 2.52
153 154 0.630673 TACCAGGGCCGTACCTAAGA 59.369 55.000 0.00 0.00 39.34 2.10
154 155 1.713297 ATACCAGGGCCGTACCTAAG 58.287 55.000 0.00 0.00 39.34 2.18
155 156 2.179377 AATACCAGGGCCGTACCTAA 57.821 50.000 0.00 0.00 39.34 2.69
156 157 2.597455 GTAATACCAGGGCCGTACCTA 58.403 52.381 0.00 0.00 39.34 3.08
157 158 1.417288 GTAATACCAGGGCCGTACCT 58.583 55.000 0.00 0.00 43.08 3.08
158 159 0.032540 CGTAATACCAGGGCCGTACC 59.967 60.000 0.00 0.00 37.93 3.34
159 160 0.598419 GCGTAATACCAGGGCCGTAC 60.598 60.000 0.00 0.00 0.00 3.67
160 161 1.042003 TGCGTAATACCAGGGCCGTA 61.042 55.000 0.00 0.00 0.00 4.02
161 162 2.306255 CTGCGTAATACCAGGGCCGT 62.306 60.000 0.00 0.00 0.00 5.68
162 163 1.594293 CTGCGTAATACCAGGGCCG 60.594 63.158 0.00 0.00 0.00 6.13
163 164 1.227853 CCTGCGTAATACCAGGGCC 60.228 63.158 15.67 0.00 43.87 5.80
164 165 0.532196 GTCCTGCGTAATACCAGGGC 60.532 60.000 20.26 17.22 46.79 5.19
165 166 1.120530 AGTCCTGCGTAATACCAGGG 58.879 55.000 20.26 6.14 46.79 4.45
167 168 2.483188 GGGAAGTCCTGCGTAATACCAG 60.483 54.545 0.00 3.05 35.95 4.00
168 169 1.483415 GGGAAGTCCTGCGTAATACCA 59.517 52.381 0.00 0.00 35.95 3.25
169 170 1.483415 TGGGAAGTCCTGCGTAATACC 59.517 52.381 0.00 0.00 36.20 2.73
170 171 2.934553 GTTGGGAAGTCCTGCGTAATAC 59.065 50.000 0.00 0.00 36.20 1.89
171 172 2.093341 GGTTGGGAAGTCCTGCGTAATA 60.093 50.000 0.00 0.00 36.20 0.98
172 173 1.339727 GGTTGGGAAGTCCTGCGTAAT 60.340 52.381 0.00 0.00 36.20 1.89
173 174 0.035739 GGTTGGGAAGTCCTGCGTAA 59.964 55.000 0.00 0.00 36.20 3.18
174 175 1.675219 GGTTGGGAAGTCCTGCGTA 59.325 57.895 0.00 0.00 36.20 4.42
175 176 2.430367 GGTTGGGAAGTCCTGCGT 59.570 61.111 0.00 0.00 36.20 5.24
176 177 2.359975 GGGTTGGGAAGTCCTGCG 60.360 66.667 0.00 0.00 36.20 5.18
177 178 2.035783 GGGGTTGGGAAGTCCTGC 59.964 66.667 0.00 0.00 36.20 4.85
178 179 1.074951 GTGGGGTTGGGAAGTCCTG 59.925 63.158 0.00 0.00 36.20 3.86
179 180 2.160853 GGTGGGGTTGGGAAGTCCT 61.161 63.158 0.00 0.00 36.20 3.85
180 181 1.800229 ATGGTGGGGTTGGGAAGTCC 61.800 60.000 0.00 0.00 0.00 3.85
181 182 0.323451 GATGGTGGGGTTGGGAAGTC 60.323 60.000 0.00 0.00 0.00 3.01
182 183 1.774300 GATGGTGGGGTTGGGAAGT 59.226 57.895 0.00 0.00 0.00 3.01
183 184 1.000359 GGATGGTGGGGTTGGGAAG 60.000 63.158 0.00 0.00 0.00 3.46
184 185 1.077298 AAGGATGGTGGGGTTGGGAA 61.077 55.000 0.00 0.00 0.00 3.97
185 186 1.467190 AAGGATGGTGGGGTTGGGA 60.467 57.895 0.00 0.00 0.00 4.37
186 187 1.305213 CAAGGATGGTGGGGTTGGG 60.305 63.158 0.00 0.00 0.00 4.12
187 188 1.984026 GCAAGGATGGTGGGGTTGG 60.984 63.158 0.00 0.00 0.00 3.77
188 189 1.228831 TGCAAGGATGGTGGGGTTG 60.229 57.895 0.00 0.00 0.00 3.77
189 190 1.228862 GTGCAAGGATGGTGGGGTT 60.229 57.895 0.00 0.00 0.00 4.11
190 191 2.017668 TTGTGCAAGGATGGTGGGGT 62.018 55.000 0.00 0.00 0.00 4.95
191 192 1.228831 TTGTGCAAGGATGGTGGGG 60.229 57.895 0.00 0.00 0.00 4.96
192 193 1.880819 GCTTGTGCAAGGATGGTGGG 61.881 60.000 13.07 0.00 38.80 4.61
193 194 1.588082 GCTTGTGCAAGGATGGTGG 59.412 57.895 13.07 0.00 38.80 4.61
204 205 4.445385 CCTGTGTTTATTTTCTGCTTGTGC 59.555 41.667 0.00 0.00 40.20 4.57
228 229 2.051423 CGTCGTCGATACATCCAATGG 58.949 52.381 0.00 0.00 39.71 3.16
324 325 1.353609 CTAACAACGTTACCCGGGCG 61.354 60.000 24.08 19.54 42.24 6.13
325 326 1.638388 GCTAACAACGTTACCCGGGC 61.638 60.000 24.08 2.74 42.24 6.13
374 375 4.043435 AGACTTCTGCCATACCCTTTTTCT 59.957 41.667 0.00 0.00 0.00 2.52
391 392 4.735283 GCGTCTGGAAGGATCTAAGACTTC 60.735 50.000 0.00 0.00 37.22 3.01
412 414 4.685824 TCGTCAACGTTATATTCATGCG 57.314 40.909 0.00 0.00 40.80 4.73
425 427 4.201881 TGTGGTCTGTATAGATCGTCAACG 60.202 45.833 0.00 0.00 36.82 4.10
428 430 4.095932 GTGTGTGGTCTGTATAGATCGTCA 59.904 45.833 0.00 0.00 36.82 4.35
563 566 1.081892 CCACGCAGAGACAGGATTTG 58.918 55.000 0.00 0.00 0.00 2.32
564 567 0.687354 ACCACGCAGAGACAGGATTT 59.313 50.000 0.00 0.00 0.00 2.17
566 569 0.900182 TCACCACGCAGAGACAGGAT 60.900 55.000 0.00 0.00 0.00 3.24
567 570 1.530655 TCACCACGCAGAGACAGGA 60.531 57.895 0.00 0.00 0.00 3.86
576 585 0.179150 GTTTTGCTTGTCACCACGCA 60.179 50.000 0.00 0.00 43.30 5.24
578 587 2.159448 TCTTGTTTTGCTTGTCACCACG 60.159 45.455 0.00 0.00 0.00 4.94
580 589 3.068024 GGATCTTGTTTTGCTTGTCACCA 59.932 43.478 0.00 0.00 0.00 4.17
609 618 0.111061 TTTCCAGCACCAGCAGATGT 59.889 50.000 0.00 0.00 45.49 3.06
610 619 0.524862 GTTTCCAGCACCAGCAGATG 59.475 55.000 0.00 0.00 45.49 2.90
611 620 0.957395 CGTTTCCAGCACCAGCAGAT 60.957 55.000 0.00 0.00 45.49 2.90
612 621 1.597854 CGTTTCCAGCACCAGCAGA 60.598 57.895 0.00 0.00 45.49 4.26
613 622 1.447317 AACGTTTCCAGCACCAGCAG 61.447 55.000 0.00 0.00 45.49 4.24
618 627 1.589803 ACAGTAACGTTTCCAGCACC 58.410 50.000 5.91 0.00 0.00 5.01
651 661 0.031917 TGCCCCTATAGACGTGGGAA 60.032 55.000 14.23 2.58 43.47 3.97
661 671 2.422235 CCATGAAAACGGTGCCCCTATA 60.422 50.000 0.00 0.00 0.00 1.31
663 673 0.322997 CCATGAAAACGGTGCCCCTA 60.323 55.000 0.00 0.00 0.00 3.53
671 681 0.893270 TGGCCACTCCATGAAAACGG 60.893 55.000 0.00 0.00 40.72 4.44
810 821 7.807433 GCTAAATGACAATGTTGTATGTGTTCA 59.193 33.333 0.00 0.00 42.43 3.18
822 833 5.242393 AGCAAGAACAGCTAAATGACAATGT 59.758 36.000 0.00 0.00 41.32 2.71
927 938 0.661020 ACGAACCAAGAACAAAGCCG 59.339 50.000 0.00 0.00 0.00 5.52
930 941 2.221055 CCTCGACGAACCAAGAACAAAG 59.779 50.000 0.00 0.00 0.00 2.77
1035 1049 4.437682 TGAAAATCAGGAACACTCACCT 57.562 40.909 0.00 0.00 36.92 4.00
1121 1180 0.881118 CCCAACAAGAACATCCACCG 59.119 55.000 0.00 0.00 0.00 4.94
1199 1260 2.117051 ACCGGGGATAGGAAGAGAAAC 58.883 52.381 6.32 0.00 0.00 2.78
1273 1644 5.355350 ACTGTAACCATCTCTTGCAAATAGC 59.645 40.000 0.00 0.00 45.96 2.97
1280 1651 3.686726 CCTTCACTGTAACCATCTCTTGC 59.313 47.826 0.00 0.00 0.00 4.01
1294 1671 1.869767 GCTGTCTTGACACCTTCACTG 59.130 52.381 0.00 0.00 32.26 3.66
1329 1770 6.946009 CCAATAAAAGGGAGAAAAGTGTAGGA 59.054 38.462 0.00 0.00 0.00 2.94
1360 1801 9.331282 GAAAGAGAGAGCAAAATAGCCTAATTA 57.669 33.333 0.00 0.00 34.23 1.40
1363 1804 6.951971 AGAAAGAGAGAGCAAAATAGCCTAA 58.048 36.000 0.00 0.00 34.23 2.69
1364 1805 6.552445 AGAAAGAGAGAGCAAAATAGCCTA 57.448 37.500 0.00 0.00 34.23 3.93
1366 1807 5.645497 TGAAGAAAGAGAGAGCAAAATAGCC 59.355 40.000 0.00 0.00 34.23 3.93
1469 1913 1.109323 AGTTGAGTGCACCAAAGGGC 61.109 55.000 14.63 5.87 37.90 5.19
1533 1982 3.056322 CCCAGGAATTCAAGCTCCTTTTG 60.056 47.826 7.93 0.00 40.22 2.44
1575 2024 8.993121 TGTGCATAGCTAGATTAAATTAAGAGC 58.007 33.333 0.00 8.26 0.00 4.09
1596 2045 4.693566 CCGGAAGTTTCTAGTTTATGTGCA 59.306 41.667 0.00 0.00 0.00 4.57
1598 2047 4.693566 TGCCGGAAGTTTCTAGTTTATGTG 59.306 41.667 5.05 0.00 0.00 3.21
1678 2128 9.553064 GATACTATCAGAAATTGGACACTGAAT 57.447 33.333 0.00 0.00 41.57 2.57
1717 2170 2.218603 GAACACCCACGTTCTCAACAT 58.781 47.619 0.00 0.00 41.70 2.71
1730 2183 0.400594 AAGTAGGCCTGTGAACACCC 59.599 55.000 17.99 0.00 0.00 4.61
1731 2184 2.152016 GAAAGTAGGCCTGTGAACACC 58.848 52.381 17.99 0.00 0.00 4.16
1732 2185 2.808543 CAGAAAGTAGGCCTGTGAACAC 59.191 50.000 17.99 3.82 0.00 3.32
1733 2186 2.224523 CCAGAAAGTAGGCCTGTGAACA 60.225 50.000 17.99 0.00 0.00 3.18
1884 2466 3.861113 GCCTCGTAAATCACAATCACGTA 59.139 43.478 0.00 0.00 34.39 3.57
1939 2521 2.269940 AGTGAGGGTGGCAGTTTCTAT 58.730 47.619 0.00 0.00 0.00 1.98
1992 2574 0.735978 TACAACGGCATGTCTCTGCG 60.736 55.000 0.00 0.00 43.23 5.18
2070 2652 6.066032 TCGGAAGGGAACAAGAATAGTTTTT 58.934 36.000 0.00 0.00 0.00 1.94
2071 2653 5.627135 TCGGAAGGGAACAAGAATAGTTTT 58.373 37.500 0.00 0.00 0.00 2.43
2072 2654 5.237236 TCGGAAGGGAACAAGAATAGTTT 57.763 39.130 0.00 0.00 0.00 2.66
2073 2655 4.903045 TCGGAAGGGAACAAGAATAGTT 57.097 40.909 0.00 0.00 0.00 2.24
2074 2656 4.717280 AGATCGGAAGGGAACAAGAATAGT 59.283 41.667 0.00 0.00 0.00 2.12
2075 2657 5.283457 AGATCGGAAGGGAACAAGAATAG 57.717 43.478 0.00 0.00 0.00 1.73
2076 2658 5.045869 ACAAGATCGGAAGGGAACAAGAATA 60.046 40.000 0.00 0.00 0.00 1.75
2077 2659 4.263506 ACAAGATCGGAAGGGAACAAGAAT 60.264 41.667 0.00 0.00 0.00 2.40
2078 2660 3.072476 ACAAGATCGGAAGGGAACAAGAA 59.928 43.478 0.00 0.00 0.00 2.52
2079 2661 2.637872 ACAAGATCGGAAGGGAACAAGA 59.362 45.455 0.00 0.00 0.00 3.02
2080 2662 3.003480 GACAAGATCGGAAGGGAACAAG 58.997 50.000 0.00 0.00 0.00 3.16
2081 2663 3.053831 GACAAGATCGGAAGGGAACAA 57.946 47.619 0.00 0.00 0.00 2.83
2082 2664 2.762535 GACAAGATCGGAAGGGAACA 57.237 50.000 0.00 0.00 0.00 3.18
2101 2683 1.201812 CGTCGAGCTTTTGAACCATCG 60.202 52.381 0.00 0.00 0.00 3.84
2108 2694 2.811855 TGTAACACGTCGAGCTTTTGA 58.188 42.857 0.00 0.00 0.00 2.69
2115 2701 2.719556 CTGTCACTTGTAACACGTCGAG 59.280 50.000 0.00 0.00 0.00 4.04
2134 2720 1.512734 GCGGCAAGATCAAACGCTG 60.513 57.895 14.12 8.05 46.02 5.18
2137 2723 1.059657 CAACGCGGCAAGATCAAACG 61.060 55.000 12.47 0.00 0.00 3.60
2402 2988 1.153349 GGAGAAGACGGTCATGGCC 60.153 63.158 6.17 6.17 0.00 5.36
2457 3043 2.327568 CATGCATGGACGAACAAAACC 58.672 47.619 19.40 0.00 0.00 3.27
2534 3124 2.622436 GAGAAATCGACAAGTCCCAGG 58.378 52.381 0.00 0.00 0.00 4.45
2686 3280 3.784468 CGTGCGTGTGTGTAGACTAATAG 59.216 47.826 0.00 0.00 0.00 1.73
2695 3289 2.202756 TGTGCGTGCGTGTGTGTA 60.203 55.556 0.00 0.00 0.00 2.90
2696 3290 3.860125 GTGTGCGTGCGTGTGTGT 61.860 61.111 0.00 0.00 0.00 3.72
2700 3294 3.860125 GTGTGTGTGCGTGCGTGT 61.860 61.111 0.00 0.00 0.00 4.49
2712 3306 3.181476 GCAAAGTTGGATTTGAGGTGTGT 60.181 43.478 3.49 0.00 41.71 3.72
2743 3337 4.424626 TCAGAAAGAGAAACATCGATCCG 58.575 43.478 0.00 0.00 0.00 4.18
2781 3376 6.576662 TTCCTTCAATTTTGTGCGGTTATA 57.423 33.333 0.00 0.00 0.00 0.98
2787 3382 4.026640 CACAGTTTCCTTCAATTTTGTGCG 60.027 41.667 0.00 0.00 0.00 5.34
2878 3486 0.541392 AGGAGTATTCATGCACCGCA 59.459 50.000 0.00 0.00 44.86 5.69
2879 3487 1.668419 AAGGAGTATTCATGCACCGC 58.332 50.000 0.00 0.00 0.00 5.68
2880 3488 3.689161 TCAAAAGGAGTATTCATGCACCG 59.311 43.478 0.00 0.00 0.00 4.94
2881 3489 4.702131 AGTCAAAAGGAGTATTCATGCACC 59.298 41.667 0.00 0.00 0.00 5.01
2882 3490 5.886960 AGTCAAAAGGAGTATTCATGCAC 57.113 39.130 0.00 0.00 0.00 4.57
2883 3491 5.769662 ACAAGTCAAAAGGAGTATTCATGCA 59.230 36.000 0.00 0.00 0.00 3.96
2884 3492 6.088824 CACAAGTCAAAAGGAGTATTCATGC 58.911 40.000 0.00 0.00 0.00 4.06
2885 3493 7.206981 ACACAAGTCAAAAGGAGTATTCATG 57.793 36.000 0.00 0.00 0.00 3.07
2896 3504 4.466567 TCGCACATACACAAGTCAAAAG 57.533 40.909 0.00 0.00 0.00 2.27
2908 3516 1.400629 GCATGCATGGATCGCACATAC 60.401 52.381 27.34 2.90 43.35 2.39
2961 3569 1.106285 GCAAGGCCCATTTACTCAGG 58.894 55.000 0.00 0.00 0.00 3.86
2963 3571 3.281332 GGCAAGGCCCATTTACTCA 57.719 52.632 0.00 0.00 44.06 3.41
3157 3766 0.107066 TCCGGTAGATGGCGTACAGA 60.107 55.000 0.00 0.00 0.00 3.41
3218 3830 1.211969 CGGACATCTCCACGTCGTT 59.788 57.895 0.00 0.00 36.12 3.85
3237 3849 4.680237 TGCTGTTCCTGCCGTCGG 62.680 66.667 6.99 6.99 0.00 4.79
3291 3903 2.954684 ATCTTGCCGGCCTTCGTCA 61.955 57.895 26.77 0.00 37.11 4.35
3312 3924 2.546795 CGATCTAGCTAAACCTGGCTGG 60.547 54.545 9.11 9.11 40.10 4.85
3398 4010 6.909550 ATTGGCTAATTACACAAGGTCAAA 57.090 33.333 0.00 0.00 0.00 2.69
3430 4042 3.437213 ACAAGGGTGGTAATTAAAGGCC 58.563 45.455 0.00 0.00 0.00 5.19
3441 4053 1.567175 ACAAACAGGTACAAGGGTGGT 59.433 47.619 0.00 0.00 0.00 4.16
3445 4057 4.094830 AGGTTACAAACAGGTACAAGGG 57.905 45.455 0.00 0.00 0.00 3.95
3498 4110 4.916183 AGTAGAAAAGGCAGCTTCAGATT 58.084 39.130 0.00 0.00 0.00 2.40
3499 4111 4.566426 AGTAGAAAAGGCAGCTTCAGAT 57.434 40.909 0.00 0.00 0.00 2.90
3554 4166 2.221055 GGGCGATACAAGTTAATGCTCG 59.779 50.000 0.00 0.00 34.05 5.03
3608 4518 7.041780 TCAGAAGTCAAGTTCTTCATAGTTTGC 60.042 37.037 6.98 0.00 42.35 3.68
3609 4519 8.370493 TCAGAAGTCAAGTTCTTCATAGTTTG 57.630 34.615 6.98 0.00 42.35 2.93
3612 4522 7.675062 ACATCAGAAGTCAAGTTCTTCATAGT 58.325 34.615 6.98 0.00 42.35 2.12
3613 4523 8.441608 CAACATCAGAAGTCAAGTTCTTCATAG 58.558 37.037 6.98 0.00 42.35 2.23
3614 4524 7.388776 CCAACATCAGAAGTCAAGTTCTTCATA 59.611 37.037 6.98 0.00 42.35 2.15
3615 4525 6.206243 CCAACATCAGAAGTCAAGTTCTTCAT 59.794 38.462 6.98 0.00 42.35 2.57
3618 4528 5.684704 TCCAACATCAGAAGTCAAGTTCTT 58.315 37.500 0.00 0.00 34.38 2.52
3628 4538 6.564709 TGTTCAAATCTCCAACATCAGAAG 57.435 37.500 0.00 0.00 0.00 2.85
3629 4539 6.957920 TTGTTCAAATCTCCAACATCAGAA 57.042 33.333 0.00 0.00 30.28 3.02
3654 4564 7.012421 CGATATTCCTTCCCTTTTCTTTCGATT 59.988 37.037 0.00 0.00 0.00 3.34
3655 4565 6.483640 CGATATTCCTTCCCTTTTCTTTCGAT 59.516 38.462 0.00 0.00 0.00 3.59
3656 4566 5.815740 CGATATTCCTTCCCTTTTCTTTCGA 59.184 40.000 0.00 0.00 0.00 3.71
3657 4567 5.815740 TCGATATTCCTTCCCTTTTCTTTCG 59.184 40.000 0.00 0.00 0.00 3.46
3672 4582 3.422796 TCCCTAGCAGAGTCGATATTCC 58.577 50.000 0.00 0.00 0.00 3.01
3678 4588 1.408961 CCTCTTCCCTAGCAGAGTCGA 60.409 57.143 9.69 0.00 35.64 4.20
3804 4714 1.735369 CGAGACTGCCTCTTCTCAAGC 60.735 57.143 0.00 0.00 38.59 4.01
3819 4729 2.093106 AGATACCAGTCCACACGAGAC 58.907 52.381 0.00 0.00 34.31 3.36
3839 4749 6.228616 TGTTCAACTATGGGATCACGATAA 57.771 37.500 0.00 0.00 0.00 1.75
3852 4762 4.655963 AGCACACCTTCATGTTCAACTAT 58.344 39.130 0.00 0.00 0.00 2.12
3880 4790 6.655848 GGATCACGATAAGATACTAGTCCACT 59.344 42.308 0.00 0.00 0.00 4.00
3931 4841 5.344743 TGTCATTAGTCATCCTTCCTGTC 57.655 43.478 0.00 0.00 0.00 3.51
3949 4859 4.971282 AGGTTATGAGAATCCTCCATGTCA 59.029 41.667 0.00 0.00 38.66 3.58
4048 4958 7.072177 TGAAAGATTATGAACGACCACATTC 57.928 36.000 0.00 0.00 0.00 2.67
4054 4964 6.682863 CGACAAATGAAAGATTATGAACGACC 59.317 38.462 0.00 0.00 0.00 4.79
4075 4985 1.515519 GTATTCGCCTCGCACGACA 60.516 57.895 0.00 0.00 39.67 4.35
4076 4986 2.228914 GGTATTCGCCTCGCACGAC 61.229 63.158 0.00 0.00 39.67 4.34
4077 4987 2.103538 GGTATTCGCCTCGCACGA 59.896 61.111 0.00 0.00 37.86 4.35
4091 5001 2.273908 GACAAGAGTCGCCTGGGTA 58.726 57.895 0.00 0.00 34.60 3.69
4119 5029 2.358247 TGCCGGCGAGAGGTTTTC 60.358 61.111 23.90 0.00 0.00 2.29
4199 5109 3.991536 GAGTCCTCTCGCCGGCAAC 62.992 68.421 28.98 13.53 0.00 4.17
4213 5124 9.114952 CTGAAGAAATCCCCTAAAAATAGAGTC 57.885 37.037 0.00 0.00 0.00 3.36
4214 5125 8.615705 ACTGAAGAAATCCCCTAAAAATAGAGT 58.384 33.333 0.00 0.00 0.00 3.24
4228 5139 6.018589 AGCTTAGCAAAACTGAAGAAATCC 57.981 37.500 7.07 0.00 0.00 3.01
4234 5145 4.207841 GCACAAAGCTTAGCAAAACTGAAG 59.792 41.667 7.07 0.00 41.15 3.02
4277 5188 0.969149 CCATCAGATAGCCGCTACCA 59.031 55.000 1.14 0.00 0.00 3.25
4307 5218 2.573869 CACACGACCTCTGGCGAT 59.426 61.111 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.