Multiple sequence alignment - TraesCS4A01G393900

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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 TraesCS4A01G393900 chr4A 100.000 2450 0 0 1 2450 669430042 669432491 0.000000e+00 4525
1 TraesCS4A01G393900 chr7D 90.123 2106 162 20 270 2352 538053449 538055531 0.000000e+00 2695
2 TraesCS4A01G393900 chr7D 87.272 2192 220 31 199 2356 563060862 563058696 0.000000e+00 2447
3 TraesCS4A01G393900 chr7D 93.043 115 5 3 2338 2450 137687761 137687874 5.420000e-37 165
4 TraesCS4A01G393900 chr2D 89.336 2185 173 30 198 2356 257410234 257412384 0.000000e+00 2689
5 TraesCS4A01G393900 chr2D 97.170 106 1 2 2347 2450 337391415 337391310 6.960000e-41 178
6 TraesCS4A01G393900 chr2D 96.226 106 1 3 2346 2450 115283235 115283338 1.160000e-38 171
7 TraesCS4A01G393900 chr6D 88.774 2129 194 24 249 2356 46611280 46609176 0.000000e+00 2566
8 TraesCS4A01G393900 chr6D 88.004 2184 192 25 198 2356 84484185 84482047 0.000000e+00 2518
9 TraesCS4A01G393900 chr6D 87.420 2178 217 37 199 2356 106706136 106708276 0.000000e+00 2451
10 TraesCS4A01G393900 chr6D 86.831 2187 237 26 190 2356 351473934 351476089 0.000000e+00 2396
11 TraesCS4A01G393900 chr6D 94.495 109 4 2 2343 2450 360583180 360583073 1.510000e-37 167
12 TraesCS4A01G393900 chr6B 88.774 2129 191 26 253 2356 486520944 486523049 0.000000e+00 2564
13 TraesCS4A01G393900 chr4D 88.316 2174 184 31 199 2356 121444482 121446601 0.000000e+00 2543
14 TraesCS4A01G393900 chr1B 88.163 2129 204 33 249 2356 592957406 592955305 0.000000e+00 2492
15 TraesCS4A01G393900 chr5D 88.765 1976 175 27 398 2356 536380364 536378419 0.000000e+00 2375
16 TraesCS4A01G393900 chr5D 95.370 108 4 1 2344 2450 542050757 542050864 1.160000e-38 171
17 TraesCS4A01G393900 chr3B 85.257 1282 125 32 199 1455 809385043 809386285 0.000000e+00 1262
18 TraesCS4A01G393900 chr3D 84.427 777 80 27 194 949 464198846 464199602 0.000000e+00 726
19 TraesCS4A01G393900 chr2A 89.062 192 18 3 199 389 773077664 773077853 4.070000e-58 235
20 TraesCS4A01G393900 chr2A 95.370 108 3 2 2344 2450 158152993 158153099 1.160000e-38 171
21 TraesCS4A01G393900 chr2A 92.920 113 6 2 2340 2450 382640961 382640849 1.950000e-36 163
22 TraesCS4A01G393900 chr7A 81.250 240 40 5 199 434 611315509 611315271 3.220000e-44 189
23 TraesCS4A01G393900 chr7A 95.413 109 3 2 2343 2450 710042790 710042897 3.240000e-39 172
24 TraesCS4A01G393900 chr1D 94.545 110 4 2 2342 2450 438744703 438744595 4.190000e-38 169


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 TraesCS4A01G393900 chr4A 669430042 669432491 2449 False 4525 4525 100.000 1 2450 1 chr4A.!!$F1 2449
1 TraesCS4A01G393900 chr7D 538053449 538055531 2082 False 2695 2695 90.123 270 2352 1 chr7D.!!$F2 2082
2 TraesCS4A01G393900 chr7D 563058696 563060862 2166 True 2447 2447 87.272 199 2356 1 chr7D.!!$R1 2157
3 TraesCS4A01G393900 chr2D 257410234 257412384 2150 False 2689 2689 89.336 198 2356 1 chr2D.!!$F2 2158
4 TraesCS4A01G393900 chr6D 46609176 46611280 2104 True 2566 2566 88.774 249 2356 1 chr6D.!!$R1 2107
5 TraesCS4A01G393900 chr6D 84482047 84484185 2138 True 2518 2518 88.004 198 2356 1 chr6D.!!$R2 2158
6 TraesCS4A01G393900 chr6D 106706136 106708276 2140 False 2451 2451 87.420 199 2356 1 chr6D.!!$F1 2157
7 TraesCS4A01G393900 chr6D 351473934 351476089 2155 False 2396 2396 86.831 190 2356 1 chr6D.!!$F2 2166
8 TraesCS4A01G393900 chr6B 486520944 486523049 2105 False 2564 2564 88.774 253 2356 1 chr6B.!!$F1 2103
9 TraesCS4A01G393900 chr4D 121444482 121446601 2119 False 2543 2543 88.316 199 2356 1 chr4D.!!$F1 2157
10 TraesCS4A01G393900 chr1B 592955305 592957406 2101 True 2492 2492 88.163 249 2356 1 chr1B.!!$R1 2107
11 TraesCS4A01G393900 chr5D 536378419 536380364 1945 True 2375 2375 88.765 398 2356 1 chr5D.!!$R1 1958
12 TraesCS4A01G393900 chr3B 809385043 809386285 1242 False 1262 1262 85.257 199 1455 1 chr3B.!!$F1 1256
13 TraesCS4A01G393900 chr3D 464198846 464199602 756 False 726 726 84.427 194 949 1 chr3D.!!$F1 755

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
25 26 0.103755 TTGGAATTTTGTGCTGCGCA 59.896 45.0 12.53 12.53 35.6 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1918 0.316278 CAGGATAGCTGTCGTCGTCG 60.316 60.0 2.36 0.0 38.55 5.12 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
20 21 3.518634 AACACGTTGGAATTTTGTGCT 57.481 38.095 0.00 0.00 33.96 4.40
21 22 2.808244 ACACGTTGGAATTTTGTGCTG 58.192 42.857 0.00 0.00 33.96 4.41
22 23 1.522258 CACGTTGGAATTTTGTGCTGC 59.478 47.619 0.00 0.00 0.00 5.25
23 24 0.777631 CGTTGGAATTTTGTGCTGCG 59.222 50.000 0.00 0.00 0.00 5.18
24 25 0.508213 GTTGGAATTTTGTGCTGCGC 59.492 50.000 6.19 6.19 0.00 6.09
25 26 0.103755 TTGGAATTTTGTGCTGCGCA 59.896 45.000 12.53 12.53 35.60 6.09
26 27 0.103755 TGGAATTTTGTGCTGCGCAA 59.896 45.000 23.38 23.38 41.47 4.85
27 28 0.508213 GGAATTTTGTGCTGCGCAAC 59.492 50.000 26.47 15.43 41.47 4.17
28 29 1.490621 GAATTTTGTGCTGCGCAACT 58.509 45.000 26.47 14.92 41.47 3.16
29 30 1.190763 GAATTTTGTGCTGCGCAACTG 59.809 47.619 26.47 0.00 41.47 3.16
30 31 0.385029 ATTTTGTGCTGCGCAACTGA 59.615 45.000 26.47 16.14 41.47 3.41
31 32 0.385029 TTTTGTGCTGCGCAACTGAT 59.615 45.000 26.47 0.00 41.47 2.90
32 33 0.385029 TTTGTGCTGCGCAACTGATT 59.615 45.000 26.47 0.00 41.47 2.57
33 34 0.385029 TTGTGCTGCGCAACTGATTT 59.615 45.000 23.38 0.00 41.47 2.17
34 35 0.318022 TGTGCTGCGCAACTGATTTG 60.318 50.000 14.31 0.00 41.47 2.32
46 47 4.601019 CAACTGATTTGCGTCTTTTCTGT 58.399 39.130 0.00 0.00 0.00 3.41
47 48 4.900635 ACTGATTTGCGTCTTTTCTGTT 57.099 36.364 0.00 0.00 0.00 3.16
48 49 4.848757 ACTGATTTGCGTCTTTTCTGTTC 58.151 39.130 0.00 0.00 0.00 3.18
49 50 4.576463 ACTGATTTGCGTCTTTTCTGTTCT 59.424 37.500 0.00 0.00 0.00 3.01
50 51 5.066505 ACTGATTTGCGTCTTTTCTGTTCTT 59.933 36.000 0.00 0.00 0.00 2.52
51 52 5.273170 TGATTTGCGTCTTTTCTGTTCTTG 58.727 37.500 0.00 0.00 0.00 3.02
52 53 4.695217 TTTGCGTCTTTTCTGTTCTTGT 57.305 36.364 0.00 0.00 0.00 3.16
53 54 4.695217 TTGCGTCTTTTCTGTTCTTGTT 57.305 36.364 0.00 0.00 0.00 2.83
54 55 4.014847 TGCGTCTTTTCTGTTCTTGTTG 57.985 40.909 0.00 0.00 0.00 3.33
55 56 3.438781 TGCGTCTTTTCTGTTCTTGTTGT 59.561 39.130 0.00 0.00 0.00 3.32
56 57 4.083003 TGCGTCTTTTCTGTTCTTGTTGTT 60.083 37.500 0.00 0.00 0.00 2.83
57 58 4.857037 GCGTCTTTTCTGTTCTTGTTGTTT 59.143 37.500 0.00 0.00 0.00 2.83
58 59 5.344933 GCGTCTTTTCTGTTCTTGTTGTTTT 59.655 36.000 0.00 0.00 0.00 2.43
59 60 6.128929 GCGTCTTTTCTGTTCTTGTTGTTTTT 60.129 34.615 0.00 0.00 0.00 1.94
60 61 7.061326 GCGTCTTTTCTGTTCTTGTTGTTTTTA 59.939 33.333 0.00 0.00 0.00 1.52
61 62 9.072294 CGTCTTTTCTGTTCTTGTTGTTTTTAT 57.928 29.630 0.00 0.00 0.00 1.40
65 66 9.936759 TTTTCTGTTCTTGTTGTTTTTATTCCT 57.063 25.926 0.00 0.00 0.00 3.36
66 67 9.936759 TTTCTGTTCTTGTTGTTTTTATTCCTT 57.063 25.926 0.00 0.00 0.00 3.36
67 68 8.925161 TCTGTTCTTGTTGTTTTTATTCCTTG 57.075 30.769 0.00 0.00 0.00 3.61
68 69 8.527810 TCTGTTCTTGTTGTTTTTATTCCTTGT 58.472 29.630 0.00 0.00 0.00 3.16
69 70 8.472683 TGTTCTTGTTGTTTTTATTCCTTGTG 57.527 30.769 0.00 0.00 0.00 3.33
70 71 8.091449 TGTTCTTGTTGTTTTTATTCCTTGTGT 58.909 29.630 0.00 0.00 0.00 3.72
71 72 9.575783 GTTCTTGTTGTTTTTATTCCTTGTGTA 57.424 29.630 0.00 0.00 0.00 2.90
73 74 9.575783 TCTTGTTGTTTTTATTCCTTGTGTAAC 57.424 29.630 0.00 0.00 37.35 2.50
83 84 4.413928 TGTGTAACAGCCATGCCC 57.586 55.556 0.00 0.00 45.67 5.36
84 85 1.673993 TGTGTAACAGCCATGCCCG 60.674 57.895 0.00 0.00 45.67 6.13
85 86 1.376683 GTGTAACAGCCATGCCCGA 60.377 57.895 0.00 0.00 36.32 5.14
86 87 0.748005 GTGTAACAGCCATGCCCGAT 60.748 55.000 0.00 0.00 36.32 4.18
87 88 0.463654 TGTAACAGCCATGCCCGATC 60.464 55.000 0.00 0.00 0.00 3.69
88 89 0.463654 GTAACAGCCATGCCCGATCA 60.464 55.000 0.00 0.00 0.00 2.92
89 90 0.254462 TAACAGCCATGCCCGATCAA 59.746 50.000 0.00 0.00 0.00 2.57
90 91 1.033746 AACAGCCATGCCCGATCAAG 61.034 55.000 0.00 0.00 0.00 3.02
91 92 1.153107 CAGCCATGCCCGATCAAGA 60.153 57.895 0.00 0.00 0.00 3.02
92 93 1.153086 AGCCATGCCCGATCAAGAC 60.153 57.895 0.00 0.00 0.00 3.01
93 94 2.537560 GCCATGCCCGATCAAGACG 61.538 63.158 0.00 0.00 0.00 4.18
94 95 2.537560 CCATGCCCGATCAAGACGC 61.538 63.158 0.00 0.00 0.00 5.19
95 96 2.203070 ATGCCCGATCAAGACGCC 60.203 61.111 0.00 0.00 0.00 5.68
96 97 3.030168 ATGCCCGATCAAGACGCCA 62.030 57.895 0.00 0.00 0.00 5.69
97 98 2.203070 GCCCGATCAAGACGCCAT 60.203 61.111 0.00 0.00 0.00 4.40
98 99 2.537560 GCCCGATCAAGACGCCATG 61.538 63.158 0.00 0.00 0.00 3.66
99 100 2.537560 CCCGATCAAGACGCCATGC 61.538 63.158 0.00 0.00 0.00 4.06
100 101 2.537560 CCGATCAAGACGCCATGCC 61.538 63.158 0.00 0.00 0.00 4.40
101 102 2.537560 CGATCAAGACGCCATGCCC 61.538 63.158 0.00 0.00 0.00 5.36
102 103 2.514592 ATCAAGACGCCATGCCCG 60.515 61.111 2.92 2.92 0.00 6.13
103 104 3.329542 ATCAAGACGCCATGCCCGT 62.330 57.895 9.03 9.03 42.31 5.28
104 105 3.803082 CAAGACGCCATGCCCGTG 61.803 66.667 13.29 0.00 39.30 4.94
128 129 4.922026 GTGCCACCCCACGTCGTT 62.922 66.667 0.00 0.00 0.00 3.85
129 130 3.232483 TGCCACCCCACGTCGTTA 61.232 61.111 0.00 0.00 0.00 3.18
130 131 2.433664 GCCACCCCACGTCGTTAG 60.434 66.667 0.00 0.00 0.00 2.34
131 132 2.263540 CCACCCCACGTCGTTAGG 59.736 66.667 8.57 8.57 0.00 2.69
132 133 2.277591 CCACCCCACGTCGTTAGGA 61.278 63.158 15.64 0.00 0.00 2.94
133 134 1.610554 CCACCCCACGTCGTTAGGAT 61.611 60.000 15.64 0.00 0.00 3.24
134 135 0.179119 CACCCCACGTCGTTAGGATC 60.179 60.000 15.64 0.00 0.00 3.36
135 136 0.612732 ACCCCACGTCGTTAGGATCA 60.613 55.000 15.64 0.00 0.00 2.92
136 137 0.750850 CCCCACGTCGTTAGGATCAT 59.249 55.000 11.93 0.00 0.00 2.45
137 138 1.538204 CCCCACGTCGTTAGGATCATG 60.538 57.143 11.93 0.00 0.00 3.07
138 139 1.538204 CCCACGTCGTTAGGATCATGG 60.538 57.143 5.42 0.00 0.00 3.66
139 140 1.209128 CACGTCGTTAGGATCATGGC 58.791 55.000 0.00 0.00 0.00 4.40
140 141 0.104304 ACGTCGTTAGGATCATGGCC 59.896 55.000 0.00 0.00 0.00 5.36
141 142 0.104120 CGTCGTTAGGATCATGGCCA 59.896 55.000 8.56 8.56 0.00 5.36
142 143 1.583054 GTCGTTAGGATCATGGCCAC 58.417 55.000 8.16 0.00 0.00 5.01
143 144 0.104120 TCGTTAGGATCATGGCCACG 59.896 55.000 8.16 0.00 0.00 4.94
144 145 1.498865 CGTTAGGATCATGGCCACGC 61.499 60.000 8.16 0.00 0.00 5.34
145 146 0.463654 GTTAGGATCATGGCCACGCA 60.464 55.000 8.16 0.00 0.00 5.24
146 147 0.473755 TTAGGATCATGGCCACGCAT 59.526 50.000 8.16 0.00 0.00 4.73
147 148 1.347062 TAGGATCATGGCCACGCATA 58.653 50.000 8.16 0.00 0.00 3.14
148 149 0.250467 AGGATCATGGCCACGCATAC 60.250 55.000 8.16 0.02 0.00 2.39
150 151 2.175184 GATCATGGCCACGCATACGC 62.175 60.000 8.16 0.00 45.53 4.42
151 152 2.665008 ATCATGGCCACGCATACGCT 62.665 55.000 8.16 0.00 45.53 5.07
152 153 2.896854 ATGGCCACGCATACGCTG 60.897 61.111 8.16 0.00 45.53 5.18
161 162 2.661866 CATACGCTGCTACCGGCC 60.662 66.667 0.00 0.00 40.34 6.13
162 163 3.925090 ATACGCTGCTACCGGCCC 61.925 66.667 0.00 0.00 40.34 5.80
179 180 4.289379 CGCCGTGCTCGCATCATG 62.289 66.667 1.89 0.00 35.54 3.07
180 181 2.891936 GCCGTGCTCGCATCATGA 60.892 61.111 0.00 0.00 35.54 3.07
181 182 3.009140 CCGTGCTCGCATCATGAC 58.991 61.111 0.00 0.00 35.54 3.06
182 183 2.528743 CCGTGCTCGCATCATGACC 61.529 63.158 0.00 0.00 35.54 4.02
183 184 1.520120 CGTGCTCGCATCATGACCT 60.520 57.895 0.00 0.00 0.00 3.85
184 185 1.759293 CGTGCTCGCATCATGACCTG 61.759 60.000 0.00 0.00 0.00 4.00
185 186 1.153309 TGCTCGCATCATGACCTGG 60.153 57.895 0.00 0.00 0.00 4.45
186 187 2.541120 GCTCGCATCATGACCTGGC 61.541 63.158 0.00 0.00 0.00 4.85
187 188 1.890979 CTCGCATCATGACCTGGCC 60.891 63.158 0.00 0.00 0.00 5.36
188 189 2.903855 CGCATCATGACCTGGCCC 60.904 66.667 0.00 0.00 0.00 5.80
189 190 2.599597 GCATCATGACCTGGCCCT 59.400 61.111 0.00 0.00 0.00 5.19
190 191 1.076485 GCATCATGACCTGGCCCTT 60.076 57.895 0.00 0.00 0.00 3.95
191 192 1.105759 GCATCATGACCTGGCCCTTC 61.106 60.000 0.00 0.00 0.00 3.46
192 193 0.549950 CATCATGACCTGGCCCTTCT 59.450 55.000 0.00 0.00 0.00 2.85
193 194 1.770658 CATCATGACCTGGCCCTTCTA 59.229 52.381 0.00 0.00 0.00 2.10
194 195 1.204146 TCATGACCTGGCCCTTCTAC 58.796 55.000 0.00 0.00 0.00 2.59
195 196 1.207791 CATGACCTGGCCCTTCTACT 58.792 55.000 0.00 0.00 0.00 2.57
196 197 1.561542 CATGACCTGGCCCTTCTACTT 59.438 52.381 0.00 0.00 0.00 2.24
217 218 5.987953 ACTTTCACTAGTAGAAAAACGACCC 59.012 40.000 16.20 0.00 34.84 4.46
283 284 3.222173 TGTGACCATTAGTGCTGGTTT 57.778 42.857 0.00 0.00 46.95 3.27
332 333 3.380479 TCTCGGTTCGTGTTGAATCTT 57.620 42.857 0.00 0.00 39.21 2.40
371 372 2.094675 CGAACCGGGACTAAAGAGGTA 58.905 52.381 6.32 0.00 34.35 3.08
419 468 1.756408 TTAGTCCCGGTTCGTGGCAA 61.756 55.000 0.00 0.00 0.00 4.52
502 568 6.429078 GGTTTTCCTATATAAACCCATCGTCC 59.571 42.308 6.60 0.00 44.78 4.79
503 569 6.750660 TTTCCTATATAAACCCATCGTCCA 57.249 37.500 0.00 0.00 0.00 4.02
504 570 5.995565 TCCTATATAAACCCATCGTCCAG 57.004 43.478 0.00 0.00 0.00 3.86
505 571 4.222145 TCCTATATAAACCCATCGTCCAGC 59.778 45.833 0.00 0.00 0.00 4.85
506 572 4.020573 CCTATATAAACCCATCGTCCAGCA 60.021 45.833 0.00 0.00 0.00 4.41
507 573 2.038387 ATAAACCCATCGTCCAGCAC 57.962 50.000 0.00 0.00 0.00 4.40
522 590 2.352915 CACGCGATCGAGCTCTCC 60.353 66.667 21.57 0.00 39.41 3.71
587 669 3.128242 CGAGCTCATCTTTCATTTTGGCT 59.872 43.478 15.40 0.00 0.00 4.75
664 748 6.299141 AGCAACTTTGTCCTTTTATCTCTCA 58.701 36.000 0.00 0.00 0.00 3.27
665 749 6.772716 AGCAACTTTGTCCTTTTATCTCTCAA 59.227 34.615 0.00 0.00 0.00 3.02
726 810 5.659079 AGTGATTTGTGGGTTTTAGTTTGGA 59.341 36.000 0.00 0.00 0.00 3.53
832 918 0.474854 TTAGTGCCTTCCTGTCCCCA 60.475 55.000 0.00 0.00 0.00 4.96
861 947 4.832608 GTCGATCACCCGCACCCC 62.833 72.222 0.00 0.00 0.00 4.95
883 973 4.155733 CATCGCCGGCACCACCTA 62.156 66.667 28.98 2.01 35.61 3.08
884 974 3.849951 ATCGCCGGCACCACCTAG 61.850 66.667 28.98 7.38 35.61 3.02
903 995 1.322442 GCTTGGTGAGCCTCTTGTTT 58.678 50.000 0.00 0.00 46.01 2.83
1005 1108 4.071961 TGTCATACATAGTGCCATGGTC 57.928 45.455 14.67 6.41 0.00 4.02
1012 1115 4.965814 ACATAGTGCCATGGTCTTGATAG 58.034 43.478 14.67 0.00 0.00 2.08
1013 1116 4.655649 ACATAGTGCCATGGTCTTGATAGA 59.344 41.667 14.67 0.00 0.00 1.98
1043 1146 1.219935 GCCCTCGTCCGGTTTATGT 59.780 57.895 0.00 0.00 0.00 2.29
1055 1158 2.745281 CGGTTTATGTTTCGGATGTGGT 59.255 45.455 0.00 0.00 0.00 4.16
1056 1159 3.933955 CGGTTTATGTTTCGGATGTGGTA 59.066 43.478 0.00 0.00 0.00 3.25
1057 1160 4.573201 CGGTTTATGTTTCGGATGTGGTAT 59.427 41.667 0.00 0.00 0.00 2.73
1058 1161 5.754406 CGGTTTATGTTTCGGATGTGGTATA 59.246 40.000 0.00 0.00 0.00 1.47
1059 1162 6.425721 CGGTTTATGTTTCGGATGTGGTATAT 59.574 38.462 0.00 0.00 0.00 0.86
1060 1163 7.599621 CGGTTTATGTTTCGGATGTGGTATATA 59.400 37.037 0.00 0.00 0.00 0.86
1103 1208 1.982223 TGTTGCATTTCGCGTTTATGC 59.018 42.857 24.87 24.87 46.97 3.14
1120 1226 5.883685 TTATGCCAATTATGCCCATCAAA 57.116 34.783 0.00 0.00 0.00 2.69
1176 1284 1.546773 CCAGAAATTCCAACCGACCCA 60.547 52.381 0.00 0.00 0.00 4.51
1284 1392 2.747446 GGAGTTGTATGTTGCCGATGTT 59.253 45.455 0.00 0.00 0.00 2.71
1404 1512 9.941664 GATGTTGGATCAATTGTTATCTTAGTG 57.058 33.333 5.13 0.00 0.00 2.74
1476 1584 7.011482 AGAGTGTGTGAGTTGTTTTATGAGAAC 59.989 37.037 0.00 0.00 0.00 3.01
1531 1640 9.843334 TGTATTAATTTGGTATTTTCGGTGTTC 57.157 29.630 0.00 0.00 0.00 3.18
1555 1664 7.168219 TCTATAATGAAGATTAGCCGGCAATT 58.832 34.615 31.54 15.12 0.00 2.32
1665 1774 5.048364 GGTTTTATGTGTTGTCCATGTGCTA 60.048 40.000 0.00 0.00 0.00 3.49
1757 1867 3.010696 TGCCCCACTATAATGTTTGGACA 59.989 43.478 0.00 0.00 40.71 4.02
1759 1869 4.097892 GCCCCACTATAATGTTTGGACAAG 59.902 45.833 0.00 0.00 39.66 3.16
1793 1904 5.102609 AGAGGGGTCCTAATGGAAGAGAATA 60.103 44.000 0.00 0.00 45.18 1.75
1794 1905 5.548573 AGGGGTCCTAATGGAAGAGAATAA 58.451 41.667 0.00 0.00 45.18 1.40
1795 1906 5.976870 AGGGGTCCTAATGGAAGAGAATAAA 59.023 40.000 0.00 0.00 45.18 1.40
1994 2108 8.990163 TGAAAAGGAGAGGTTAAAGTTACAAT 57.010 30.769 0.00 0.00 0.00 2.71
2020 2134 7.148188 TGCATGTTAGAGGATCACAAGAAATTC 60.148 37.037 0.00 0.00 37.82 2.17
2044 2158 3.689161 TGTACCCAAATTGCGAAGATGAG 59.311 43.478 0.00 0.00 0.00 2.90
2057 2171 4.083590 GCGAAGATGAGAAGAAAAAGCTGT 60.084 41.667 0.00 0.00 0.00 4.40
2059 2173 4.762956 AGATGAGAAGAAAAAGCTGTGC 57.237 40.909 0.00 0.00 0.00 4.57
2060 2174 4.139786 AGATGAGAAGAAAAAGCTGTGCA 58.860 39.130 0.00 0.00 0.00 4.57
2091 2205 2.223572 GGAATTGCTGTAATGGAAGGCG 60.224 50.000 0.00 0.00 0.00 5.52
2100 2214 0.918983 AATGGAAGGCGGAGAATGGA 59.081 50.000 0.00 0.00 0.00 3.41
2101 2215 0.918983 ATGGAAGGCGGAGAATGGAA 59.081 50.000 0.00 0.00 0.00 3.53
2119 2233 8.727149 AGAATGGAATATCTGACAAGGGATTTA 58.273 33.333 0.00 0.00 0.00 1.40
2135 2249 9.487790 CAAGGGATTTAAAAAGTTGCTGATAAA 57.512 29.630 0.00 0.00 0.00 1.40
2152 2266 8.796475 TGCTGATAAAGTTAAAGAAGATGCTTT 58.204 29.630 0.00 0.00 40.85 3.51
2190 2309 9.250624 GAATTAGAGTACATACGAAGCAAAGAT 57.749 33.333 0.00 0.00 0.00 2.40
2207 2326 1.834263 AGATGGTTGTCTGCCCTCTAC 59.166 52.381 0.00 0.00 30.84 2.59
2211 2330 1.471676 GGTTGTCTGCCCTCTACGATG 60.472 57.143 0.00 0.00 0.00 3.84
2212 2331 0.824109 TTGTCTGCCCTCTACGATGG 59.176 55.000 0.00 0.00 0.00 3.51
2308 2427 0.936600 CGATATGCGGTGCAATGTGA 59.063 50.000 0.00 0.00 43.62 3.58
2310 2429 2.031769 CGATATGCGGTGCAATGTGATT 60.032 45.455 0.00 0.00 43.62 2.57
2323 2442 4.201950 GCAATGTGATTTAAGATCAGCCGT 60.202 41.667 0.00 0.00 0.00 5.68
2362 2481 2.279517 GGCGAGCACCCTGATACG 60.280 66.667 0.00 0.00 0.00 3.06
2363 2482 2.494918 GCGAGCACCCTGATACGT 59.505 61.111 0.00 0.00 0.00 3.57
2364 2483 1.589196 GCGAGCACCCTGATACGTC 60.589 63.158 0.00 0.00 0.00 4.34
2365 2484 2.005960 GCGAGCACCCTGATACGTCT 62.006 60.000 0.00 0.00 0.00 4.18
2366 2485 0.029567 CGAGCACCCTGATACGTCTC 59.970 60.000 0.00 0.00 0.00 3.36
2367 2486 0.386113 GAGCACCCTGATACGTCTCC 59.614 60.000 0.00 0.00 0.00 3.71
2368 2487 0.324368 AGCACCCTGATACGTCTCCA 60.324 55.000 0.00 0.00 0.00 3.86
2369 2488 0.535335 GCACCCTGATACGTCTCCAA 59.465 55.000 0.00 0.00 0.00 3.53
2370 2489 1.739371 GCACCCTGATACGTCTCCAAC 60.739 57.143 0.00 0.00 0.00 3.77
2387 2506 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
2430 2549 8.947055 ATATTCTGTTTTGAACATTATTGGGC 57.053 30.769 0.00 0.00 41.26 5.36
2431 2550 6.418057 TTCTGTTTTGAACATTATTGGGCT 57.582 33.333 0.00 0.00 41.26 5.19
2432 2551 6.418057 TCTGTTTTGAACATTATTGGGCTT 57.582 33.333 0.00 0.00 41.26 4.35
2433 2552 6.825610 TCTGTTTTGAACATTATTGGGCTTT 58.174 32.000 0.00 0.00 41.26 3.51
2434 2553 7.957002 TCTGTTTTGAACATTATTGGGCTTTA 58.043 30.769 0.00 0.00 41.26 1.85
2435 2554 8.592809 TCTGTTTTGAACATTATTGGGCTTTAT 58.407 29.630 0.00 0.00 41.26 1.40
2436 2555 9.218440 CTGTTTTGAACATTATTGGGCTTTATT 57.782 29.630 0.00 0.00 41.26 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.808244 CAGCACAAAATTCCAACGTGT 58.192 42.857 0.00 0.00 0.00 4.49
4 5 0.777631 CGCAGCACAAAATTCCAACG 59.222 50.000 0.00 0.00 0.00 4.10
24 25 4.601019 ACAGAAAAGACGCAAATCAGTTG 58.399 39.130 0.00 0.00 40.50 3.16
25 26 4.900635 ACAGAAAAGACGCAAATCAGTT 57.099 36.364 0.00 0.00 0.00 3.16
26 27 4.576463 AGAACAGAAAAGACGCAAATCAGT 59.424 37.500 0.00 0.00 0.00 3.41
27 28 5.100751 AGAACAGAAAAGACGCAAATCAG 57.899 39.130 0.00 0.00 0.00 2.90
28 29 5.163663 ACAAGAACAGAAAAGACGCAAATCA 60.164 36.000 0.00 0.00 0.00 2.57
29 30 5.273944 ACAAGAACAGAAAAGACGCAAATC 58.726 37.500 0.00 0.00 0.00 2.17
30 31 5.248870 ACAAGAACAGAAAAGACGCAAAT 57.751 34.783 0.00 0.00 0.00 2.32
31 32 4.695217 ACAAGAACAGAAAAGACGCAAA 57.305 36.364 0.00 0.00 0.00 3.68
32 33 4.083003 ACAACAAGAACAGAAAAGACGCAA 60.083 37.500 0.00 0.00 0.00 4.85
33 34 3.438781 ACAACAAGAACAGAAAAGACGCA 59.561 39.130 0.00 0.00 0.00 5.24
34 35 4.016113 ACAACAAGAACAGAAAAGACGC 57.984 40.909 0.00 0.00 0.00 5.19
35 36 6.927933 AAAACAACAAGAACAGAAAAGACG 57.072 33.333 0.00 0.00 0.00 4.18
39 40 9.936759 AGGAATAAAAACAACAAGAACAGAAAA 57.063 25.926 0.00 0.00 0.00 2.29
40 41 9.936759 AAGGAATAAAAACAACAAGAACAGAAA 57.063 25.926 0.00 0.00 0.00 2.52
41 42 9.364989 CAAGGAATAAAAACAACAAGAACAGAA 57.635 29.630 0.00 0.00 0.00 3.02
42 43 8.527810 ACAAGGAATAAAAACAACAAGAACAGA 58.472 29.630 0.00 0.00 0.00 3.41
43 44 8.594687 CACAAGGAATAAAAACAACAAGAACAG 58.405 33.333 0.00 0.00 0.00 3.16
44 45 8.091449 ACACAAGGAATAAAAACAACAAGAACA 58.909 29.630 0.00 0.00 0.00 3.18
45 46 8.474006 ACACAAGGAATAAAAACAACAAGAAC 57.526 30.769 0.00 0.00 0.00 3.01
47 48 9.575783 GTTACACAAGGAATAAAAACAACAAGA 57.424 29.630 0.00 0.00 0.00 3.02
48 49 9.360093 TGTTACACAAGGAATAAAAACAACAAG 57.640 29.630 0.00 0.00 0.00 3.16
49 50 9.360093 CTGTTACACAAGGAATAAAAACAACAA 57.640 29.630 0.00 0.00 0.00 2.83
50 51 7.489757 GCTGTTACACAAGGAATAAAAACAACA 59.510 33.333 0.00 0.00 0.00 3.33
51 52 7.042992 GGCTGTTACACAAGGAATAAAAACAAC 60.043 37.037 0.00 0.00 0.00 3.32
52 53 6.981559 GGCTGTTACACAAGGAATAAAAACAA 59.018 34.615 0.00 0.00 0.00 2.83
53 54 6.096987 TGGCTGTTACACAAGGAATAAAAACA 59.903 34.615 0.00 0.00 0.00 2.83
54 55 6.508777 TGGCTGTTACACAAGGAATAAAAAC 58.491 36.000 0.00 0.00 0.00 2.43
55 56 6.716934 TGGCTGTTACACAAGGAATAAAAA 57.283 33.333 0.00 0.00 0.00 1.94
56 57 6.686630 CATGGCTGTTACACAAGGAATAAAA 58.313 36.000 0.00 0.00 0.00 1.52
57 58 5.336372 GCATGGCTGTTACACAAGGAATAAA 60.336 40.000 0.00 0.00 0.00 1.40
58 59 4.157656 GCATGGCTGTTACACAAGGAATAA 59.842 41.667 0.00 0.00 0.00 1.40
59 60 3.694072 GCATGGCTGTTACACAAGGAATA 59.306 43.478 0.00 0.00 0.00 1.75
60 61 2.493278 GCATGGCTGTTACACAAGGAAT 59.507 45.455 0.00 0.00 0.00 3.01
61 62 1.885887 GCATGGCTGTTACACAAGGAA 59.114 47.619 0.00 0.00 0.00 3.36
62 63 1.533625 GCATGGCTGTTACACAAGGA 58.466 50.000 0.00 0.00 0.00 3.36
63 64 0.527565 GGCATGGCTGTTACACAAGG 59.472 55.000 12.86 0.00 0.00 3.61
64 65 0.527565 GGGCATGGCTGTTACACAAG 59.472 55.000 19.78 0.00 0.00 3.16
65 66 1.240641 CGGGCATGGCTGTTACACAA 61.241 55.000 19.65 0.00 0.00 3.33
66 67 1.673993 CGGGCATGGCTGTTACACA 60.674 57.895 19.65 0.00 0.00 3.72
67 68 0.748005 ATCGGGCATGGCTGTTACAC 60.748 55.000 25.80 3.76 0.00 2.90
68 69 0.463654 GATCGGGCATGGCTGTTACA 60.464 55.000 25.80 8.76 0.00 2.41
69 70 0.463654 TGATCGGGCATGGCTGTTAC 60.464 55.000 25.80 17.90 0.00 2.50
70 71 0.254462 TTGATCGGGCATGGCTGTTA 59.746 50.000 25.80 9.87 0.00 2.41
71 72 1.001020 TTGATCGGGCATGGCTGTT 60.001 52.632 25.80 18.78 0.00 3.16
72 73 1.452651 CTTGATCGGGCATGGCTGT 60.453 57.895 25.80 14.34 0.00 4.40
73 74 1.153107 TCTTGATCGGGCATGGCTG 60.153 57.895 21.71 21.71 0.00 4.85
74 75 1.153086 GTCTTGATCGGGCATGGCT 60.153 57.895 19.78 0.00 0.00 4.75
75 76 2.537560 CGTCTTGATCGGGCATGGC 61.538 63.158 11.56 11.56 0.00 4.40
76 77 2.537560 GCGTCTTGATCGGGCATGG 61.538 63.158 0.00 0.00 0.00 3.66
77 78 2.537560 GGCGTCTTGATCGGGCATG 61.538 63.158 0.00 0.00 0.00 4.06
78 79 2.203070 GGCGTCTTGATCGGGCAT 60.203 61.111 0.00 0.00 0.00 4.40
79 80 3.030168 ATGGCGTCTTGATCGGGCA 62.030 57.895 0.00 0.00 39.37 5.36
80 81 2.203070 ATGGCGTCTTGATCGGGC 60.203 61.111 0.00 0.00 0.00 6.13
81 82 2.537560 GCATGGCGTCTTGATCGGG 61.538 63.158 7.14 0.00 0.00 5.14
82 83 2.537560 GGCATGGCGTCTTGATCGG 61.538 63.158 7.14 0.00 0.00 4.18
83 84 2.537560 GGGCATGGCGTCTTGATCG 61.538 63.158 13.76 0.00 0.00 3.69
84 85 2.537560 CGGGCATGGCGTCTTGATC 61.538 63.158 13.76 0.00 0.00 2.92
85 86 2.514592 CGGGCATGGCGTCTTGAT 60.515 61.111 13.76 0.00 0.00 2.57
86 87 4.015406 ACGGGCATGGCGTCTTGA 62.015 61.111 13.76 0.00 0.00 3.02
87 88 3.803082 CACGGGCATGGCGTCTTG 61.803 66.667 13.76 0.00 0.00 3.02
111 112 3.518419 TAACGACGTGGGGTGGCAC 62.518 63.158 9.70 9.70 0.00 5.01
112 113 3.229156 CTAACGACGTGGGGTGGCA 62.229 63.158 0.00 0.00 0.00 4.92
113 114 2.433664 CTAACGACGTGGGGTGGC 60.434 66.667 0.00 0.00 0.00 5.01
114 115 1.610554 ATCCTAACGACGTGGGGTGG 61.611 60.000 16.73 8.80 0.00 4.61
115 116 0.179119 GATCCTAACGACGTGGGGTG 60.179 60.000 16.73 0.05 0.00 4.61
116 117 0.612732 TGATCCTAACGACGTGGGGT 60.613 55.000 16.73 11.81 0.00 4.95
117 118 0.750850 ATGATCCTAACGACGTGGGG 59.249 55.000 16.73 14.33 0.00 4.96
118 119 1.538204 CCATGATCCTAACGACGTGGG 60.538 57.143 0.00 7.61 36.24 4.61
119 120 1.852942 CCATGATCCTAACGACGTGG 58.147 55.000 0.00 0.00 33.98 4.94
120 121 1.209128 GCCATGATCCTAACGACGTG 58.791 55.000 0.00 0.00 0.00 4.49
121 122 0.104304 GGCCATGATCCTAACGACGT 59.896 55.000 0.00 0.00 0.00 4.34
122 123 0.104120 TGGCCATGATCCTAACGACG 59.896 55.000 0.00 0.00 0.00 5.12
123 124 1.583054 GTGGCCATGATCCTAACGAC 58.417 55.000 9.72 0.00 0.00 4.34
124 125 0.104120 CGTGGCCATGATCCTAACGA 59.896 55.000 21.08 0.00 0.00 3.85
125 126 1.498865 GCGTGGCCATGATCCTAACG 61.499 60.000 29.54 15.46 0.00 3.18
126 127 0.463654 TGCGTGGCCATGATCCTAAC 60.464 55.000 29.54 9.29 0.00 2.34
127 128 0.473755 ATGCGTGGCCATGATCCTAA 59.526 50.000 29.54 6.27 0.00 2.69
128 129 1.001974 GTATGCGTGGCCATGATCCTA 59.998 52.381 29.54 10.21 0.00 2.94
129 130 0.250467 GTATGCGTGGCCATGATCCT 60.250 55.000 29.54 11.20 0.00 3.24
130 131 1.568612 CGTATGCGTGGCCATGATCC 61.569 60.000 29.54 11.57 0.00 3.36
131 132 1.862123 CGTATGCGTGGCCATGATC 59.138 57.895 29.54 12.34 0.00 2.92
132 133 2.253758 GCGTATGCGTGGCCATGAT 61.254 57.895 29.54 19.51 40.81 2.45
133 134 2.894879 GCGTATGCGTGGCCATGA 60.895 61.111 29.54 13.90 40.81 3.07
144 145 2.661866 GGCCGGTAGCAGCGTATG 60.662 66.667 1.90 0.00 46.50 2.39
145 146 3.925090 GGGCCGGTAGCAGCGTAT 61.925 66.667 1.90 0.00 46.50 3.06
162 163 4.289379 CATGATGCGAGCACGGCG 62.289 66.667 4.80 4.80 40.15 6.46
163 164 2.891936 TCATGATGCGAGCACGGC 60.892 61.111 5.52 0.00 40.15 5.68
164 165 2.528743 GGTCATGATGCGAGCACGG 61.529 63.158 5.52 0.00 40.15 4.94
165 166 1.520120 AGGTCATGATGCGAGCACG 60.520 57.895 0.00 0.00 42.93 5.34
166 167 1.434622 CCAGGTCATGATGCGAGCAC 61.435 60.000 0.00 0.00 33.29 4.40
167 168 1.153309 CCAGGTCATGATGCGAGCA 60.153 57.895 0.00 0.00 33.29 4.26
168 169 2.541120 GCCAGGTCATGATGCGAGC 61.541 63.158 0.00 0.00 0.00 5.03
169 170 1.890979 GGCCAGGTCATGATGCGAG 60.891 63.158 0.00 0.00 0.00 5.03
170 171 2.190313 GGCCAGGTCATGATGCGA 59.810 61.111 0.00 0.00 0.00 5.10
171 172 2.898920 AAGGGCCAGGTCATGATGCG 62.899 60.000 6.18 0.00 0.00 4.73
172 173 1.076485 AAGGGCCAGGTCATGATGC 60.076 57.895 6.18 0.00 0.00 3.91
173 174 0.549950 AGAAGGGCCAGGTCATGATG 59.450 55.000 6.18 0.00 0.00 3.07
174 175 1.771255 GTAGAAGGGCCAGGTCATGAT 59.229 52.381 6.18 0.00 0.00 2.45
175 176 1.204146 GTAGAAGGGCCAGGTCATGA 58.796 55.000 6.18 0.00 0.00 3.07
176 177 1.207791 AGTAGAAGGGCCAGGTCATG 58.792 55.000 6.18 0.00 0.00 3.07
177 178 1.972588 AAGTAGAAGGGCCAGGTCAT 58.027 50.000 6.18 0.00 0.00 3.06
178 179 1.628846 GAAAGTAGAAGGGCCAGGTCA 59.371 52.381 6.18 0.00 0.00 4.02
179 180 1.628846 TGAAAGTAGAAGGGCCAGGTC 59.371 52.381 6.18 0.00 0.00 3.85
180 181 1.351350 GTGAAAGTAGAAGGGCCAGGT 59.649 52.381 6.18 0.00 0.00 4.00
181 182 1.630878 AGTGAAAGTAGAAGGGCCAGG 59.369 52.381 6.18 0.00 0.00 4.45
182 183 3.515901 ACTAGTGAAAGTAGAAGGGCCAG 59.484 47.826 6.18 0.00 42.59 4.85
183 184 3.517612 ACTAGTGAAAGTAGAAGGGCCA 58.482 45.455 6.18 0.00 42.59 5.36
191 192 7.328005 GGGTCGTTTTTCTACTAGTGAAAGTAG 59.672 40.741 5.39 4.94 46.92 2.57
192 193 7.014615 AGGGTCGTTTTTCTACTAGTGAAAGTA 59.985 37.037 5.39 3.84 35.27 2.24
193 194 5.987953 GGGTCGTTTTTCTACTAGTGAAAGT 59.012 40.000 5.39 0.00 35.27 2.66
194 195 6.221659 AGGGTCGTTTTTCTACTAGTGAAAG 58.778 40.000 5.39 0.00 35.27 2.62
195 196 6.165700 AGGGTCGTTTTTCTACTAGTGAAA 57.834 37.500 5.39 10.49 0.00 2.69
196 197 5.796424 AGGGTCGTTTTTCTACTAGTGAA 57.204 39.130 5.39 4.72 0.00 3.18
217 218 8.425577 AATCGAAACTAATGAGGTGAACATAG 57.574 34.615 0.00 0.00 0.00 2.23
332 333 0.108520 GTGCCACGAATCGGGACTAA 60.109 55.000 6.42 0.00 41.35 2.24
419 468 2.754002 GTGAGCTTCTAGTACCGGTTCT 59.246 50.000 15.04 17.06 0.00 3.01
505 571 2.352915 GGAGAGCTCGATCGCGTG 60.353 66.667 11.09 4.24 38.98 5.34
506 572 3.943034 CGGAGAGCTCGATCGCGT 61.943 66.667 11.09 0.00 38.98 6.01
507 573 3.456431 AACGGAGAGCTCGATCGCG 62.456 63.158 20.37 5.24 39.35 5.87
508 574 1.655959 GAACGGAGAGCTCGATCGC 60.656 63.158 20.37 0.00 0.00 4.58
509 575 0.378962 AAGAACGGAGAGCTCGATCG 59.621 55.000 19.36 19.36 35.17 3.69
510 576 1.268845 GGAAGAACGGAGAGCTCGATC 60.269 57.143 8.37 0.68 0.00 3.69
511 577 0.741915 GGAAGAACGGAGAGCTCGAT 59.258 55.000 8.37 0.00 0.00 3.59
512 578 1.313812 GGGAAGAACGGAGAGCTCGA 61.314 60.000 8.37 0.00 0.00 4.04
513 579 1.139947 GGGAAGAACGGAGAGCTCG 59.860 63.158 8.37 0.00 0.00 5.03
522 590 2.615747 GGAGAAGGAAAGGGGAAGAACG 60.616 54.545 0.00 0.00 0.00 3.95
587 669 6.463360 GGGCCTTCAAATCTTGACAATTTTA 58.537 36.000 0.84 0.00 39.87 1.52
624 707 3.758554 AGTTGCTAACCATTGTGATCACC 59.241 43.478 22.85 5.91 0.00 4.02
783 867 4.808895 CGCACCTACATATGCAAACTAAGA 59.191 41.667 1.58 0.00 42.17 2.10
832 918 2.159142 GGTGATCGACGGTGGTTAGAAT 60.159 50.000 0.00 0.00 0.00 2.40
976 1079 5.532779 TGGCACTATGTATGACAAACAAACA 59.467 36.000 0.00 0.00 30.00 2.83
978 1081 6.350027 CCATGGCACTATGTATGACAAACAAA 60.350 38.462 0.00 0.00 38.97 2.83
987 1090 4.707105 TCAAGACCATGGCACTATGTATG 58.293 43.478 13.04 6.73 0.00 2.39
1005 1108 1.000163 CCGACGGGGACATCTATCAAG 60.000 57.143 5.81 0.00 38.47 3.02
1103 1208 5.672503 TGTCAATTTGATGGGCATAATTGG 58.327 37.500 1.78 0.00 36.60 3.16
1147 1255 5.391950 CGGTTGGAATTTCTGGTTCACATAG 60.392 44.000 0.00 0.00 0.00 2.23
1340 1448 8.716674 ATCCTCACTATCAATGGCATATTTTT 57.283 30.769 0.00 0.00 0.00 1.94
1364 1472 9.590828 TTGATCCAACATCATAATGATACCAAT 57.409 29.630 0.00 0.00 34.28 3.16
1442 1550 4.457603 ACAACTCACACACTCTCTAGCTAG 59.542 45.833 15.01 15.01 0.00 3.42
1455 1563 7.429340 CACTTGTTCTCATAAAACAACTCACAC 59.571 37.037 0.00 0.00 40.64 3.82
1459 1567 7.472543 ACACACTTGTTCTCATAAAACAACTC 58.527 34.615 0.00 0.00 40.64 3.01
1460 1568 7.391148 ACACACTTGTTCTCATAAAACAACT 57.609 32.000 0.00 0.00 40.64 3.16
1531 1640 6.992063 ATTGCCGGCTAATCTTCATTATAG 57.008 37.500 29.70 0.00 0.00 1.31
1533 1642 5.769662 TCAATTGCCGGCTAATCTTCATTAT 59.230 36.000 29.70 5.31 0.00 1.28
1544 1653 1.137282 TCGTACATCAATTGCCGGCTA 59.863 47.619 29.70 22.36 0.00 3.93
1555 1664 1.681264 AGCATCGGTCATCGTACATCA 59.319 47.619 0.00 0.00 40.32 3.07
1757 1867 0.551131 ACCCCTCTTCTCCATGCCTT 60.551 55.000 0.00 0.00 0.00 4.35
1759 1869 1.529309 GACCCCTCTTCTCCATGCC 59.471 63.158 0.00 0.00 0.00 4.40
1793 1904 2.032550 TGTCGTCGTCGTCTTCTTCTTT 59.967 45.455 1.33 0.00 38.33 2.52
1794 1905 1.600957 TGTCGTCGTCGTCTTCTTCTT 59.399 47.619 1.33 0.00 38.33 2.52
1795 1906 1.194997 CTGTCGTCGTCGTCTTCTTCT 59.805 52.381 1.33 0.00 38.33 2.85
1804 1918 0.316278 CAGGATAGCTGTCGTCGTCG 60.316 60.000 2.36 0.00 38.55 5.12
1855 1969 1.774856 GGCTTAGCTTCTTCCCCCATA 59.225 52.381 3.59 0.00 0.00 2.74
1994 2108 4.824479 TCTTGTGATCCTCTAACATGCA 57.176 40.909 0.00 0.00 0.00 3.96
2020 2134 4.155826 TCATCTTCGCAATTTGGGTACAAG 59.844 41.667 12.54 9.40 37.97 3.16
2044 2158 2.159254 TGGTGTGCACAGCTTTTTCTTC 60.159 45.455 39.46 17.40 44.12 2.87
2057 2171 1.031235 CAATTCCAGTGTGGTGTGCA 58.969 50.000 0.00 0.00 39.03 4.57
2059 2173 1.001048 CAGCAATTCCAGTGTGGTGTG 60.001 52.381 3.23 0.00 39.03 3.82
2060 2174 1.321474 CAGCAATTCCAGTGTGGTGT 58.679 50.000 3.23 0.00 39.03 4.16
2091 2205 5.072329 TCCCTTGTCAGATATTCCATTCTCC 59.928 44.000 0.00 0.00 0.00 3.71
2135 2249 7.285401 TGTCCTTTGAAAGCATCTTCTTTAACT 59.715 33.333 0.00 0.00 36.50 2.24
2152 2266 6.751157 TGTACTCTAATTCGTTGTCCTTTGA 58.249 36.000 0.00 0.00 0.00 2.69
2190 2309 0.541063 TCGTAGAGGGCAGACAACCA 60.541 55.000 0.00 0.00 0.00 3.67
2207 2326 0.467384 ATCTTCTGCACCTCCCATCG 59.533 55.000 0.00 0.00 0.00 3.84
2211 2330 2.843701 CATGTATCTTCTGCACCTCCC 58.156 52.381 0.00 0.00 0.00 4.30
2212 2331 2.216898 GCATGTATCTTCTGCACCTCC 58.783 52.381 0.00 0.00 35.96 4.30
2308 2427 4.130118 GGTCATCACGGCTGATCTTAAAT 58.870 43.478 0.00 0.00 34.65 1.40
2310 2429 2.158957 GGGTCATCACGGCTGATCTTAA 60.159 50.000 0.00 0.00 34.65 1.85
2323 2442 0.625316 CAACATCCCCAGGGTCATCA 59.375 55.000 4.22 0.00 36.47 3.07
2405 2524 8.761689 AGCCCAATAATGTTCAAAACAGAATAT 58.238 29.630 0.00 0.00 45.95 1.28
2406 2525 8.133024 AGCCCAATAATGTTCAAAACAGAATA 57.867 30.769 0.00 0.00 45.95 1.75
2407 2526 7.008021 AGCCCAATAATGTTCAAAACAGAAT 57.992 32.000 0.00 0.00 45.95 2.40
2408 2527 6.418057 AGCCCAATAATGTTCAAAACAGAA 57.582 33.333 0.00 0.00 45.95 3.02
2409 2528 6.418057 AAGCCCAATAATGTTCAAAACAGA 57.582 33.333 0.00 0.00 45.95 3.41
2410 2529 8.776376 ATAAAGCCCAATAATGTTCAAAACAG 57.224 30.769 0.00 0.00 45.95 3.16


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

AutoCloner maintained by Alex Coulton.