Multiple sequence alignment - TraesCS5B01G556000

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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 TraesCS5B01G556000 chr5B 100.000 5236 0 0 1 5236 704867221 704872456 0.000000e+00 9670.0
1 TraesCS5B01G556000 chr5B 97.143 35 0 1 1 34 70804601 70804635 2.040000e-04 58.4
2 TraesCS5B01G556000 chr5B 100.000 29 0 0 1 29 526558835 526558863 3.000000e-03 54.7
3 TraesCS5B01G556000 chr4A 89.995 2129 111 46 190 2292 610497773 610495721 0.000000e+00 2658.0
4 TraesCS5B01G556000 chr4A 88.426 1391 107 33 3206 4561 610494594 610493223 0.000000e+00 1628.0
5 TraesCS5B01G556000 chr4A 94.891 920 38 7 2291 3208 610495549 610494637 0.000000e+00 1430.0
6 TraesCS5B01G556000 chr4A 95.000 360 12 1 4875 5234 610491957 610491604 1.270000e-155 560.0
7 TraesCS5B01G556000 chr4A 96.753 154 5 0 28 181 610497973 610497820 1.870000e-64 257.0
8 TraesCS5B01G556000 chr4A 100.000 43 0 0 4673 4715 610492241 610492199 4.350000e-11 80.5
9 TraesCS5B01G556000 chr4A 92.308 39 3 0 1 39 603462377 603462339 7.320000e-04 56.5
10 TraesCS5B01G556000 chr5D 88.912 1930 110 44 415 2279 558270462 558268572 0.000000e+00 2283.0
11 TraesCS5B01G556000 chr5D 93.766 1155 43 13 2291 3428 558268425 558267283 0.000000e+00 1707.0
12 TraesCS5B01G556000 chr5D 85.057 1392 126 41 3457 4820 558267282 558265945 0.000000e+00 1343.0
13 TraesCS5B01G556000 chr5D 88.667 450 23 10 4807 5234 558265933 558265490 1.670000e-144 523.0
14 TraesCS5B01G556000 chr5D 89.796 147 9 3 195 341 558270601 558270461 3.220000e-42 183.0
15 TraesCS5B01G556000 chr5D 86.239 109 14 1 233 341 38057198 38057305 3.310000e-22 117.0
16 TraesCS5B01G556000 chr7D 79.808 312 36 14 1840 2127 85619762 85620070 8.890000e-48 202.0
17 TraesCS5B01G556000 chr5A 97.059 34 1 0 1 34 641790147 641790114 2.040000e-04 58.4
18 TraesCS5B01G556000 chr5A 97.143 35 0 1 1 34 676585453 676585487 2.040000e-04 58.4
19 TraesCS5B01G556000 chr2A 94.595 37 2 0 1 37 53624289 53624325 2.040000e-04 58.4
20 TraesCS5B01G556000 chr1A 97.059 34 1 0 1 34 589484313 589484280 2.040000e-04 58.4
21 TraesCS5B01G556000 chr3D 90.909 44 1 3 1 41 311644897 311644854 7.320000e-04 56.5
22 TraesCS5B01G556000 chr3A 90.476 42 3 1 1 41 396299199 396299158 3.000000e-03 54.7


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 TraesCS5B01G556000 chr5B 704867221 704872456 5235 False 9670.00 9670 100.0000 1 5236 1 chr5B.!!$F3 5235
1 TraesCS5B01G556000 chr4A 610491604 610497973 6369 True 1102.25 2658 94.1775 28 5234 6 chr4A.!!$R2 5206
2 TraesCS5B01G556000 chr5D 558265490 558270601 5111 True 1207.80 2283 89.2396 195 5234 5 chr5D.!!$R1 5039

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
819 873 0.249363 GGGACGATCTTAGCCGTTCC 60.249 60.000 8.14 8.14 45.81 3.62 F
822 876 0.460311 ACGATCTTAGCCGTTCCTGG 59.540 55.000 0.00 0.00 35.21 4.45 F
823 877 0.460311 CGATCTTAGCCGTTCCTGGT 59.540 55.000 0.00 0.00 0.00 4.00 F
925 979 1.135333 TCGCGGGCCAAATAAATTTCC 59.865 47.619 6.13 0.00 0.00 3.13 F
1769 1852 1.861542 TTGCTAGCGGCGCATTGTTT 61.862 50.000 35.02 14.87 45.43 2.83 F
2842 3151 0.385390 AACTTTGCTTCTTGGTGGCG 59.615 50.000 0.00 0.00 0.00 5.69 F
3698 4077 0.594602 CCTCCGGTTATCATCGCGTA 59.405 55.000 5.77 0.00 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2780 3089 0.036732 GGACATTGTGGTGCTCCTCA 59.963 55.000 6.34 5.89 35.73 3.86 R
2781 3090 0.036732 TGGACATTGTGGTGCTCCTC 59.963 55.000 6.34 2.98 34.23 3.71 R
2784 3093 1.538047 ATGTGGACATTGTGGTGCTC 58.462 50.000 0.00 0.00 31.37 4.26 R
2842 3151 1.050204 AGAGCTCCTCATCCTGATGC 58.950 55.000 10.93 0.00 38.65 3.91 R
2869 3178 2.046892 CCACTGGGACCGCAGAAG 60.047 66.667 18.93 11.19 35.59 2.85 R
4062 4444 0.112995 TGCTGCTTCCCTTGGTTGAT 59.887 50.000 0.00 0.00 0.00 2.57 R
4841 6235 0.393537 GCTGCTGCAATCTACCACCT 60.394 55.000 11.11 0.00 39.41 4.00 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
26 27 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
47 48 2.939103 AGTGTTTCACAAGCAGAGACAC 59.061 45.455 8.42 8.42 45.93 3.67
48 49 2.677836 GTGTTTCACAAGCAGAGACACA 59.322 45.455 10.81 5.06 45.30 3.72
72 73 0.889994 TTGCAGCCCAAGTAGCAATG 59.110 50.000 0.00 0.00 41.55 2.82
152 153 3.696051 AGACTAAATGGACTAACGCCGTA 59.304 43.478 0.00 0.00 0.00 4.02
167 168 1.144969 CCGTAGCAACACGACACAAT 58.855 50.000 7.04 0.00 44.69 2.71
181 182 1.545582 ACACAATGCGCATTTAAGGCT 59.454 42.857 32.13 7.88 0.00 4.58
183 184 3.192422 ACACAATGCGCATTTAAGGCTAA 59.808 39.130 32.13 0.00 0.00 3.09
184 185 3.547468 CACAATGCGCATTTAAGGCTAAC 59.453 43.478 32.13 0.00 0.00 2.34
185 186 3.192422 ACAATGCGCATTTAAGGCTAACA 59.808 39.130 32.13 0.00 0.00 2.41
186 187 2.911819 TGCGCATTTAAGGCTAACAC 57.088 45.000 5.66 0.00 0.00 3.32
187 188 2.155279 TGCGCATTTAAGGCTAACACA 58.845 42.857 5.66 0.00 0.00 3.72
188 189 2.554462 TGCGCATTTAAGGCTAACACAA 59.446 40.909 5.66 0.00 0.00 3.33
189 190 3.192422 TGCGCATTTAAGGCTAACACAAT 59.808 39.130 5.66 0.00 0.00 2.71
190 191 4.396478 TGCGCATTTAAGGCTAACACAATA 59.604 37.500 5.66 0.00 0.00 1.90
191 192 4.733405 GCGCATTTAAGGCTAACACAATAC 59.267 41.667 0.30 0.00 0.00 1.89
192 193 5.448632 GCGCATTTAAGGCTAACACAATACT 60.449 40.000 0.30 0.00 0.00 2.12
194 195 7.677747 GCGCATTTAAGGCTAACACAATACTAA 60.678 37.037 0.30 0.00 0.00 2.24
195 196 7.850982 CGCATTTAAGGCTAACACAATACTAAG 59.149 37.037 0.00 0.00 0.00 2.18
196 197 7.644157 GCATTTAAGGCTAACACAATACTAAGC 59.356 37.037 0.00 0.00 0.00 3.09
197 198 8.673711 CATTTAAGGCTAACACAATACTAAGCA 58.326 33.333 0.00 0.00 0.00 3.91
198 199 8.624367 TTTAAGGCTAACACAATACTAAGCAA 57.376 30.769 0.00 0.00 0.00 3.91
199 200 8.624367 TTAAGGCTAACACAATACTAAGCAAA 57.376 30.769 0.00 0.00 0.00 3.68
223 261 1.141657 ACAGAGCAAGTGGAAGCAGAA 59.858 47.619 0.00 0.00 0.00 3.02
225 263 1.163554 GAGCAAGTGGAAGCAGAAGG 58.836 55.000 0.00 0.00 0.00 3.46
227 265 1.143684 AGCAAGTGGAAGCAGAAGGAA 59.856 47.619 0.00 0.00 0.00 3.36
228 266 1.538950 GCAAGTGGAAGCAGAAGGAAG 59.461 52.381 0.00 0.00 0.00 3.46
229 267 2.157738 CAAGTGGAAGCAGAAGGAAGG 58.842 52.381 0.00 0.00 0.00 3.46
230 268 1.439543 AGTGGAAGCAGAAGGAAGGT 58.560 50.000 0.00 0.00 0.00 3.50
231 269 1.072965 AGTGGAAGCAGAAGGAAGGTG 59.927 52.381 0.00 0.00 0.00 4.00
440 480 2.359975 CCGGTCTTGGGCTTCCAC 60.360 66.667 0.00 0.00 40.91 4.02
681 724 2.125350 GCGCTTCCTCCCTCACTG 60.125 66.667 0.00 0.00 0.00 3.66
810 864 2.041265 AGGGCCAGGGACGATCTT 59.959 61.111 6.18 0.00 0.00 2.40
811 865 1.048724 CAGGGCCAGGGACGATCTTA 61.049 60.000 6.18 0.00 0.00 2.10
819 873 0.249363 GGGACGATCTTAGCCGTTCC 60.249 60.000 8.14 8.14 45.81 3.62
822 876 0.460311 ACGATCTTAGCCGTTCCTGG 59.540 55.000 0.00 0.00 35.21 4.45
823 877 0.460311 CGATCTTAGCCGTTCCTGGT 59.540 55.000 0.00 0.00 0.00 4.00
882 936 1.935933 CACGTCTATTTTCGGAGGGG 58.064 55.000 0.00 0.00 0.00 4.79
925 979 1.135333 TCGCGGGCCAAATAAATTTCC 59.865 47.619 6.13 0.00 0.00 3.13
1287 1368 4.131088 GACGAGGTGGAGTCCGGC 62.131 72.222 4.30 0.00 0.00 6.13
1545 1626 2.275748 TCCGTCAGGATCCGCTCT 59.724 61.111 5.98 0.00 42.75 4.09
1575 1656 4.855596 GACGTCAGTACCGTCCAC 57.144 61.111 11.55 0.00 46.73 4.02
1615 1696 7.331440 TGCTTATGCATTTGTGGATAGTTTTTG 59.669 33.333 3.54 0.00 45.31 2.44
1639 1720 4.580167 GCCTTGGTGTGCTAATCAATCATA 59.420 41.667 0.00 0.00 0.00 2.15
1643 1724 7.201848 CCTTGGTGTGCTAATCAATCATATGTT 60.202 37.037 1.90 0.00 0.00 2.71
1734 1815 4.152402 GTCGACAAGTGAGTGCATTGTTAT 59.848 41.667 11.55 0.00 37.29 1.89
1735 1816 5.347635 GTCGACAAGTGAGTGCATTGTTATA 59.652 40.000 11.55 0.00 37.29 0.98
1736 1817 5.347635 TCGACAAGTGAGTGCATTGTTATAC 59.652 40.000 4.25 0.00 37.29 1.47
1737 1818 5.348724 CGACAAGTGAGTGCATTGTTATACT 59.651 40.000 4.25 0.00 37.29 2.12
1738 1819 6.530181 CGACAAGTGAGTGCATTGTTATACTA 59.470 38.462 4.25 0.00 37.29 1.82
1760 1843 3.941483 ACATAATATGGATTGCTAGCGGC 59.059 43.478 10.77 1.28 36.57 6.53
1769 1852 1.861542 TTGCTAGCGGCGCATTGTTT 61.862 50.000 35.02 14.87 45.43 2.83
1779 1862 3.490078 CGGCGCATTGTTTGGGTTATTAT 60.490 43.478 10.83 0.00 40.30 1.28
1780 1863 4.438148 GGCGCATTGTTTGGGTTATTATT 58.562 39.130 10.83 0.00 40.30 1.40
1781 1864 5.593010 GGCGCATTGTTTGGGTTATTATTA 58.407 37.500 10.83 0.00 40.30 0.98
1786 1869 7.307101 CGCATTGTTTGGGTTATTATTATTGCC 60.307 37.037 0.00 0.00 33.74 4.52
1794 1877 9.482175 TTGGGTTATTATTATTGCCTAACAAGT 57.518 29.630 0.00 0.00 42.87 3.16
1828 1911 9.696572 ATGCTATGCTTGGATAAATAGATGATT 57.303 29.630 0.00 0.00 0.00 2.57
1883 1971 8.445493 GCCATAAATTTCAGTTGGAATTTCTTG 58.555 33.333 13.05 11.93 34.91 3.02
1888 1976 8.597662 AATTTCAGTTGGAATTTCTTGATGTG 57.402 30.769 0.00 0.00 34.91 3.21
1914 2002 4.338879 AGCACCTGACTGCAATTAGAAAT 58.661 39.130 0.00 0.00 39.86 2.17
1967 2056 5.706916 CATTTCTGTGCTACTTCTGCAATT 58.293 37.500 0.00 0.00 42.41 2.32
2039 2147 9.019656 TCCTTTGCTTTTATGAGCTGTTAATAA 57.980 29.630 0.00 0.00 43.11 1.40
2040 2148 9.076596 CCTTTGCTTTTATGAGCTGTTAATAAC 57.923 33.333 0.00 0.00 43.11 1.89
2118 2226 5.109662 TCTCTAAGGAATATTCAGCGTCG 57.890 43.478 17.07 1.96 0.00 5.12
2140 2248 7.906010 CGTCGCATAATTTTGGTGAAACTATTA 59.094 33.333 0.00 0.00 36.74 0.98
2234 2366 8.196771 TGAAGCAAAGTAACTCATTGTTTTCAT 58.803 29.630 0.00 0.00 39.89 2.57
2235 2367 8.579682 AAGCAAAGTAACTCATTGTTTTCATC 57.420 30.769 0.00 0.00 39.89 2.92
2238 2370 9.677567 GCAAAGTAACTCATTGTTTTCATCTTA 57.322 29.630 0.00 0.00 39.89 2.10
2250 2382 6.243148 TGTTTTCATCTTAGTTTAGTCCCCC 58.757 40.000 0.00 0.00 0.00 5.40
2281 2413 8.350722 GCTGTTATGACGCTTAGGCTATATATA 58.649 37.037 0.00 0.00 36.09 0.86
2284 2416 9.627395 GTTATGACGCTTAGGCTATATATATGG 57.373 37.037 5.44 3.57 36.09 2.74
2285 2417 7.841282 ATGACGCTTAGGCTATATATATGGT 57.159 36.000 5.44 0.00 36.09 3.55
2286 2418 8.935614 ATGACGCTTAGGCTATATATATGGTA 57.064 34.615 5.44 0.00 36.09 3.25
2288 2420 7.997223 TGACGCTTAGGCTATATATATGGTAGT 59.003 37.037 5.44 0.00 36.09 2.73
2328 2631 7.102993 ACACAAGGAATTGTTTAGCTGTTTTT 58.897 30.769 0.00 0.00 31.86 1.94
2340 2643 2.072298 GCTGTTTTTGTGCCACAAACA 58.928 42.857 21.90 16.94 46.53 2.83
2363 2666 2.226437 ACTGTATGCCTGTTGCTTTTCG 59.774 45.455 0.00 0.00 42.00 3.46
2373 2676 5.121768 GCCTGTTGCTTTTCGAACTCTTATA 59.878 40.000 0.00 0.00 36.87 0.98
2549 2854 8.953313 TCTTAAGAACGTTCTGTGTCATATCTA 58.047 33.333 30.33 12.52 37.65 1.98
2749 3058 2.945668 GTGTCCATTCTTGTATGGCTCC 59.054 50.000 0.00 0.00 43.94 4.70
2842 3151 0.385390 AACTTTGCTTCTTGGTGGCG 59.615 50.000 0.00 0.00 0.00 5.69
3111 3428 3.648339 AATCCTTGTGTGATTGTGCAC 57.352 42.857 10.75 10.75 39.22 4.57
3138 3455 9.751542 AACATTCCTTGAAGATAGTATCGTTAG 57.248 33.333 4.48 3.99 0.00 2.34
3251 3613 9.627123 ATCAGTTTATATAAGCAGGCTGTAAAA 57.373 29.630 17.16 0.00 0.00 1.52
3253 3615 9.503427 CAGTTTATATAAGCAGGCTGTAAAAAC 57.497 33.333 17.16 15.20 0.00 2.43
3258 3620 4.505313 AAGCAGGCTGTAAAAACTAAGC 57.495 40.909 17.16 0.00 34.86 3.09
3323 3688 6.985188 TCTAACAGAGTTCATTTATGGTGC 57.015 37.500 0.00 0.00 0.00 5.01
3345 3710 5.048782 TGCCTTACATTGTTGAGTGTTGATC 60.049 40.000 0.00 0.00 0.00 2.92
3356 3721 6.770303 TGTTGAGTGTTGATCATCTTTAACCA 59.230 34.615 0.00 0.00 0.00 3.67
3433 3798 7.831193 AGTTTATGCTGGATCAGTTCAGTTATT 59.169 33.333 0.00 0.00 33.43 1.40
3434 3799 7.792374 TTATGCTGGATCAGTTCAGTTATTC 57.208 36.000 0.00 0.00 33.43 1.75
3435 3800 5.426689 TGCTGGATCAGTTCAGTTATTCT 57.573 39.130 0.00 0.00 33.43 2.40
3436 3801 5.809001 TGCTGGATCAGTTCAGTTATTCTT 58.191 37.500 0.00 0.00 33.43 2.52
3438 3803 6.716628 TGCTGGATCAGTTCAGTTATTCTTTT 59.283 34.615 0.00 0.00 33.43 2.27
3439 3804 7.231317 TGCTGGATCAGTTCAGTTATTCTTTTT 59.769 33.333 0.00 0.00 33.43 1.94
3503 3875 3.564455 CTCGATGCCGGGTAACTAC 57.436 57.895 2.18 0.00 36.24 2.73
3516 3888 6.040878 CCGGGTAACTACATCTACTTTGAAG 58.959 44.000 0.00 0.00 0.00 3.02
3517 3889 6.040878 CGGGTAACTACATCTACTTTGAAGG 58.959 44.000 0.00 0.00 0.00 3.46
3518 3890 5.816258 GGGTAACTACATCTACTTTGAAGGC 59.184 44.000 0.00 0.00 0.00 4.35
3519 3891 6.351966 GGGTAACTACATCTACTTTGAAGGCT 60.352 42.308 0.00 0.00 0.00 4.58
3540 3912 4.323792 GCTGGCTTATTATGATCCTGGCTA 60.324 45.833 0.00 0.00 0.00 3.93
3559 3931 5.887598 TGGCTAGTCAATTGCATCTGTTTAT 59.112 36.000 0.00 0.00 0.00 1.40
3639 4014 8.740123 TTTGAACATTGTGACTTACTAAGGAA 57.260 30.769 0.88 0.00 0.00 3.36
3640 4015 8.740123 TTGAACATTGTGACTTACTAAGGAAA 57.260 30.769 0.88 0.00 0.00 3.13
3641 4016 8.740123 TGAACATTGTGACTTACTAAGGAAAA 57.260 30.769 0.88 0.00 0.00 2.29
3642 4017 9.179909 TGAACATTGTGACTTACTAAGGAAAAA 57.820 29.630 0.88 0.00 0.00 1.94
3669 4044 7.281774 ACTCTATTTTCTGAGGCACATAACATG 59.718 37.037 0.00 0.00 34.84 3.21
3676 4051 7.786178 TCTGAGGCACATAACATGTTATAAC 57.214 36.000 26.59 18.84 42.70 1.89
3682 4061 6.292703 GGCACATAACATGTTATAACGACCTC 60.293 42.308 26.59 12.10 42.70 3.85
3683 4062 6.292703 GCACATAACATGTTATAACGACCTCC 60.293 42.308 26.59 7.87 42.70 4.30
3686 4065 2.762327 ACATGTTATAACGACCTCCGGT 59.238 45.455 10.92 0.00 43.93 5.28
3694 4073 0.666913 ACGACCTCCGGTTATCATCG 59.333 55.000 0.00 6.55 43.93 3.84
3695 4074 0.663568 CGACCTCCGGTTATCATCGC 60.664 60.000 0.00 0.00 35.25 4.58
3698 4077 0.594602 CCTCCGGTTATCATCGCGTA 59.405 55.000 5.77 0.00 0.00 4.42
3700 4079 2.352421 CCTCCGGTTATCATCGCGTAAT 60.352 50.000 5.77 0.62 0.00 1.89
3736 4115 5.627499 TTTTCCACATTCTCTGCATACAC 57.373 39.130 0.00 0.00 0.00 2.90
3757 4136 4.578516 CACTGTTATCTCGTCAGGATCTCT 59.421 45.833 0.00 0.00 34.02 3.10
3758 4137 4.819630 ACTGTTATCTCGTCAGGATCTCTC 59.180 45.833 0.00 0.00 34.02 3.20
3759 4138 5.042463 TGTTATCTCGTCAGGATCTCTCT 57.958 43.478 0.00 0.00 0.00 3.10
3760 4139 5.060506 TGTTATCTCGTCAGGATCTCTCTC 58.939 45.833 0.00 0.00 0.00 3.20
3771 4150 7.168972 CGTCAGGATCTCTCTCATAATTGTTTC 59.831 40.741 0.00 0.00 0.00 2.78
3773 4152 8.712103 TCAGGATCTCTCTCATAATTGTTTCAT 58.288 33.333 0.00 0.00 0.00 2.57
3779 4158 9.288576 TCTCTCTCATAATTGTTTCATTGTGTT 57.711 29.630 0.00 0.00 0.00 3.32
3809 4188 2.481952 GGAAGCTGCTAACTCTGTTGTG 59.518 50.000 0.90 0.00 0.00 3.33
3836 4215 2.166664 ACGTGGCCTTAAGATCAGAGAC 59.833 50.000 3.32 0.00 0.00 3.36
3950 4332 3.946201 ACGCCAGGCAGCAAGTCT 61.946 61.111 13.30 0.00 0.00 3.24
4025 4407 1.087501 GCCTGAAGTCGACCAAATCC 58.912 55.000 13.01 0.00 0.00 3.01
4175 4557 2.591066 CGAAGCAGCTGAACAAGAAG 57.409 50.000 20.43 0.00 0.00 2.85
4246 4633 0.910088 AGGAAGTAGCCACCCCTGTC 60.910 60.000 0.00 0.00 29.77 3.51
4253 4640 1.217057 AGCCACCCCTGTCATGGATT 61.217 55.000 0.00 0.00 35.33 3.01
4263 4650 2.743664 CTGTCATGGATTGTTCGCTTCA 59.256 45.455 0.00 0.00 0.00 3.02
4264 4651 2.483877 TGTCATGGATTGTTCGCTTCAC 59.516 45.455 0.00 0.00 0.00 3.18
4274 4661 7.120579 TGGATTGTTCGCTTCACTTTGTAATAT 59.879 33.333 0.00 0.00 0.00 1.28
4285 4672 7.905604 TCACTTTGTAATATGAGTGTTGAGG 57.094 36.000 0.00 0.00 40.21 3.86
4294 4681 3.593442 TGAGTGTTGAGGGTTTTGGAT 57.407 42.857 0.00 0.00 0.00 3.41
4295 4682 3.221771 TGAGTGTTGAGGGTTTTGGATG 58.778 45.455 0.00 0.00 0.00 3.51
4299 4686 3.253432 GTGTTGAGGGTTTTGGATGAGAC 59.747 47.826 0.00 0.00 0.00 3.36
4356 4749 6.811253 AAAAATACGAGGTTGACATTGCTA 57.189 33.333 0.00 0.00 0.00 3.49
4383 4776 3.179443 TGCTGAAAAGAGTCGAGTGTT 57.821 42.857 0.00 0.00 0.00 3.32
4387 4780 4.112634 CTGAAAAGAGTCGAGTGTTGTCA 58.887 43.478 18.98 18.98 0.00 3.58
4405 4798 3.320541 TGTCATTTGGTACTTGCCTTTGG 59.679 43.478 0.00 0.00 0.00 3.28
4416 4809 2.335712 GCCTTTGGAGTCTTGGCCG 61.336 63.158 0.00 0.00 37.81 6.13
4432 4825 1.933853 GGCCGCTGTACTAATGTCAAG 59.066 52.381 0.00 0.00 0.00 3.02
4469 4862 4.490743 TGTAACATCATGTACTGACACCG 58.509 43.478 0.00 0.00 38.76 4.94
4519 4924 8.321353 TCAATCAAGTGATGGAACTACAAGTAT 58.679 33.333 0.00 0.00 31.82 2.12
4530 4935 7.001674 TGGAACTACAAGTATCATGTTTGGTT 58.998 34.615 0.00 0.00 32.27 3.67
4570 4977 4.791334 TCTTGGTAAAGACCCCATTCCATA 59.209 41.667 0.00 0.00 46.32 2.74
4571 4978 5.254267 TCTTGGTAAAGACCCCATTCCATAA 59.746 40.000 0.00 0.00 46.32 1.90
4577 4984 8.983789 GGTAAAGACCCCATTCCATAATTTTTA 58.016 33.333 0.00 0.00 40.23 1.52
4580 4987 9.904198 AAAGACCCCATTCCATAATTTTTATTG 57.096 29.630 0.00 0.00 0.00 1.90
4616 5039 2.619931 TGGAACAGAGGGATTGACTGA 58.380 47.619 0.00 0.00 35.85 3.41
4622 5045 2.301296 CAGAGGGATTGACTGACAGTGT 59.699 50.000 14.14 0.00 34.07 3.55
4670 5093 6.553100 TCAAGATCAAACATGGGTTTAGGTTT 59.447 34.615 0.00 0.00 45.18 3.27
4671 5094 6.994421 AGATCAAACATGGGTTTAGGTTTT 57.006 33.333 0.00 0.00 45.18 2.43
4715 6019 6.247676 TCTTGTTCCATGATCCATCTCAAAA 58.752 36.000 0.00 0.00 0.00 2.44
4717 6021 4.395854 TGTTCCATGATCCATCTCAAAACG 59.604 41.667 0.00 0.00 0.00 3.60
4719 6023 3.199727 TCCATGATCCATCTCAAAACGGA 59.800 43.478 0.00 0.00 0.00 4.69
4728 6032 5.064707 TCCATCTCAAAACGGAAATTCGATC 59.935 40.000 0.00 0.00 0.00 3.69
4734 6038 1.151777 ACGGAAATTCGATCGCGCAT 61.152 50.000 11.09 0.00 37.46 4.73
4753 6057 3.265221 GCATTCCTGGATCTGGATGGATA 59.735 47.826 0.00 0.00 31.78 2.59
4759 6063 4.323333 CCTGGATCTGGATGGATATCACAC 60.323 50.000 4.83 0.00 34.90 3.82
4760 6064 3.584406 TGGATCTGGATGGATATCACACC 59.416 47.826 4.83 4.88 34.90 4.16
4781 6085 3.498397 CCAAACATAGCACAACTCGAAGT 59.502 43.478 0.00 0.00 0.00 3.01
4802 6106 6.140303 AGTGGCAGTTCATAATTTGCATAG 57.860 37.500 0.00 0.00 38.27 2.23
4820 6188 6.680810 TGCATAGAAAATCAAAGTGGAAGTG 58.319 36.000 0.00 0.00 0.00 3.16
4821 6189 6.489700 TGCATAGAAAATCAAAGTGGAAGTGA 59.510 34.615 0.00 0.00 0.00 3.41
4822 6190 7.025963 GCATAGAAAATCAAAGTGGAAGTGAG 58.974 38.462 0.00 0.00 0.00 3.51
4883 6315 0.609957 AGCAGCAGCAGCAAACCATA 60.610 50.000 12.92 0.00 45.49 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
1 2 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
2 3 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4 5 9.710818 ACACTCCCTCTGTAAACTAATATAAGA 57.289 33.333 0.00 0.00 0.00 2.10
8 9 8.822805 TGAAACACTCCCTCTGTAAACTAATAT 58.177 33.333 0.00 0.00 0.00 1.28
9 10 8.092687 GTGAAACACTCCCTCTGTAAACTAATA 58.907 37.037 0.00 0.00 36.32 0.98
10 11 6.935208 GTGAAACACTCCCTCTGTAAACTAAT 59.065 38.462 0.00 0.00 36.32 1.73
11 12 6.126997 TGTGAAACACTCCCTCTGTAAACTAA 60.127 38.462 0.00 0.00 45.67 2.24
12 13 5.364446 TGTGAAACACTCCCTCTGTAAACTA 59.636 40.000 0.00 0.00 45.67 2.24
13 14 4.163458 TGTGAAACACTCCCTCTGTAAACT 59.837 41.667 0.00 0.00 45.67 2.66
14 15 4.448210 TGTGAAACACTCCCTCTGTAAAC 58.552 43.478 0.00 0.00 45.67 2.01
15 16 4.764050 TGTGAAACACTCCCTCTGTAAA 57.236 40.909 0.00 0.00 45.67 2.01
47 48 1.747355 CTACTTGGGCTGCAAATCCTG 59.253 52.381 0.50 0.00 0.00 3.86
48 49 1.957113 GCTACTTGGGCTGCAAATCCT 60.957 52.381 0.50 0.00 0.00 3.24
72 73 3.951655 CTTGTGGGCGCGCAATGTC 62.952 63.158 34.42 16.87 0.00 3.06
152 153 1.279539 CGCATTGTGTCGTGTTGCT 59.720 52.632 0.00 0.00 0.00 3.91
167 168 2.155279 TGTGTTAGCCTTAAATGCGCA 58.845 42.857 14.96 14.96 0.00 6.09
199 200 2.760092 TGCTTCCACTTGCTCTGTTTTT 59.240 40.909 0.00 0.00 0.00 1.94
213 251 0.401738 CCACCTTCCTTCTGCTTCCA 59.598 55.000 0.00 0.00 0.00 3.53
215 253 0.962855 GCCCACCTTCCTTCTGCTTC 60.963 60.000 0.00 0.00 0.00 3.86
223 261 2.208349 AGGTCAGCCCACCTTCCT 59.792 61.111 0.00 0.00 45.24 3.36
225 263 0.322008 CTTCAGGTCAGCCCACCTTC 60.322 60.000 1.21 0.00 45.24 3.46
228 266 0.606673 GTTCTTCAGGTCAGCCCACC 60.607 60.000 0.00 0.00 36.58 4.61
229 267 0.951040 CGTTCTTCAGGTCAGCCCAC 60.951 60.000 0.00 0.00 34.66 4.61
230 268 1.118965 TCGTTCTTCAGGTCAGCCCA 61.119 55.000 0.00 0.00 34.66 5.36
231 269 0.390472 CTCGTTCTTCAGGTCAGCCC 60.390 60.000 0.00 0.00 34.57 5.19
440 480 2.509336 GCGTCCATCGAGGTGGTG 60.509 66.667 5.00 1.23 42.86 4.17
637 677 2.774351 GGTGAGGGATGGAGGGGG 60.774 72.222 0.00 0.00 0.00 5.40
638 678 1.768077 GAGGTGAGGGATGGAGGGG 60.768 68.421 0.00 0.00 0.00 4.79
810 864 1.315690 CGATCTACCAGGAACGGCTA 58.684 55.000 0.00 0.00 0.00 3.93
811 865 1.392710 CCGATCTACCAGGAACGGCT 61.393 60.000 0.00 0.00 42.73 5.52
819 873 1.360551 CAGCCGTCCGATCTACCAG 59.639 63.158 0.00 0.00 0.00 4.00
822 876 2.353607 CGCAGCCGTCCGATCTAC 60.354 66.667 0.00 0.00 0.00 2.59
823 877 3.592814 CCGCAGCCGTCCGATCTA 61.593 66.667 0.00 0.00 0.00 1.98
925 979 1.443802 GCGAGGAGAAGAAAAGGTGG 58.556 55.000 0.00 0.00 0.00 4.61
985 1042 2.196925 CCATCTCCCTCGTCCTCGG 61.197 68.421 0.00 0.00 37.69 4.63
1347 1428 3.665675 CTTCCTCTTGGCCCCGACG 62.666 68.421 0.00 0.00 0.00 5.12
1575 1656 3.686726 GCATAAGCAGGAATCTAATCCGG 59.313 47.826 0.00 0.00 44.60 5.14
1615 1696 1.544724 TTGATTAGCACACCAAGGCC 58.455 50.000 0.00 0.00 0.00 5.19
1639 1720 3.277652 GCAGCAAGCACACAAACAT 57.722 47.368 0.00 0.00 44.79 2.71
1734 1815 7.489160 CCGCTAGCAATCCATATTATGTAGTA 58.511 38.462 16.45 0.00 0.00 1.82
1735 1816 6.341316 CCGCTAGCAATCCATATTATGTAGT 58.659 40.000 16.45 0.00 0.00 2.73
1736 1817 5.235186 GCCGCTAGCAATCCATATTATGTAG 59.765 44.000 16.45 0.00 42.97 2.74
1737 1818 5.116180 GCCGCTAGCAATCCATATTATGTA 58.884 41.667 16.45 0.00 42.97 2.29
1738 1819 3.941483 GCCGCTAGCAATCCATATTATGT 59.059 43.478 16.45 0.00 42.97 2.29
1758 1841 2.378445 AATAACCCAAACAATGCGCC 57.622 45.000 4.18 0.00 0.00 6.53
1760 1843 7.307101 GGCAATAATAATAACCCAAACAATGCG 60.307 37.037 0.00 0.00 0.00 4.73
1769 1852 8.908903 CACTTGTTAGGCAATAATAATAACCCA 58.091 33.333 0.00 0.00 36.36 4.51
1779 1862 7.978975 GCATAAATTCCACTTGTTAGGCAATAA 59.021 33.333 0.00 0.00 36.36 1.40
1780 1863 7.341769 AGCATAAATTCCACTTGTTAGGCAATA 59.658 33.333 0.00 0.00 36.10 1.90
1781 1864 6.155049 AGCATAAATTCCACTTGTTAGGCAAT 59.845 34.615 0.00 0.00 36.10 3.56
1786 1869 7.934457 AGCATAGCATAAATTCCACTTGTTAG 58.066 34.615 0.00 0.00 0.00 2.34
1794 1877 8.476064 TTTATCCAAGCATAGCATAAATTCCA 57.524 30.769 0.00 0.00 0.00 3.53
1824 1907 6.167685 CAAAGCAGATGGGAAAAATCAATCA 58.832 36.000 0.00 0.00 0.00 2.57
1825 1908 6.091713 CACAAAGCAGATGGGAAAAATCAATC 59.908 38.462 0.00 0.00 0.00 2.67
1826 1909 5.935789 CACAAAGCAGATGGGAAAAATCAAT 59.064 36.000 0.00 0.00 0.00 2.57
1827 1910 5.299148 CACAAAGCAGATGGGAAAAATCAA 58.701 37.500 0.00 0.00 0.00 2.57
1828 1911 4.800249 GCACAAAGCAGATGGGAAAAATCA 60.800 41.667 0.00 0.00 44.79 2.57
1888 1976 1.818642 ATTGCAGTCAGGTGCTTCTC 58.181 50.000 0.00 0.00 44.32 2.87
1914 2002 3.662759 AACAACAGGGGAAGTTCTGAA 57.337 42.857 2.25 0.00 35.20 3.02
2020 2125 9.559958 CTTGTGGTTATTAACAGCTCATAAAAG 57.440 33.333 8.73 1.29 0.00 2.27
2095 2203 5.520632 CGACGCTGAATATTCCTTAGAGAA 58.479 41.667 12.90 0.00 0.00 2.87
2104 2212 6.086765 CCAAAATTATGCGACGCTGAATATTC 59.913 38.462 22.08 8.60 0.00 1.75
2105 2213 5.914635 CCAAAATTATGCGACGCTGAATATT 59.085 36.000 22.08 10.26 0.00 1.28
2106 2214 5.008613 ACCAAAATTATGCGACGCTGAATAT 59.991 36.000 22.08 8.12 0.00 1.28
2140 2248 4.202461 ACATGTGTGAACAAGGGACTATGT 60.202 41.667 0.00 0.00 38.49 2.29
2209 2341 7.985634 TGAAAACAATGAGTTACTTTGCTTC 57.014 32.000 0.00 2.46 40.26 3.86
2281 2413 3.566351 TCCATCATCGTCTCACTACCAT 58.434 45.455 0.00 0.00 0.00 3.55
2282 2414 3.012934 TCCATCATCGTCTCACTACCA 57.987 47.619 0.00 0.00 0.00 3.25
2283 2415 3.130516 TGTTCCATCATCGTCTCACTACC 59.869 47.826 0.00 0.00 0.00 3.18
2284 2416 4.106197 GTGTTCCATCATCGTCTCACTAC 58.894 47.826 0.00 0.00 0.00 2.73
2285 2417 3.761752 TGTGTTCCATCATCGTCTCACTA 59.238 43.478 0.00 0.00 0.00 2.74
2286 2418 2.562738 TGTGTTCCATCATCGTCTCACT 59.437 45.455 0.00 0.00 0.00 3.41
2288 2420 3.588955 CTTGTGTTCCATCATCGTCTCA 58.411 45.455 0.00 0.00 0.00 3.27
2373 2676 9.060347 CATGTACACTGCAAAGGATATAAGAAT 57.940 33.333 0.00 0.00 0.00 2.40
2764 3073 7.220030 GTGCTCCTCATCCTATCATTTCTTAA 58.780 38.462 0.00 0.00 0.00 1.85
2765 3074 6.239714 GGTGCTCCTCATCCTATCATTTCTTA 60.240 42.308 0.00 0.00 0.00 2.10
2778 3087 2.012673 GACATTGTGGTGCTCCTCATC 58.987 52.381 10.14 2.46 37.13 2.92
2779 3088 1.340405 GGACATTGTGGTGCTCCTCAT 60.340 52.381 10.14 0.00 37.13 2.90
2780 3089 0.036732 GGACATTGTGGTGCTCCTCA 59.963 55.000 6.34 5.89 35.73 3.86
2781 3090 0.036732 TGGACATTGTGGTGCTCCTC 59.963 55.000 6.34 2.98 34.23 3.71
2784 3093 1.538047 ATGTGGACATTGTGGTGCTC 58.462 50.000 0.00 0.00 31.37 4.26
2842 3151 1.050204 AGAGCTCCTCATCCTGATGC 58.950 55.000 10.93 0.00 38.65 3.91
2869 3178 2.046892 CCACTGGGACCGCAGAAG 60.047 66.667 18.93 11.19 35.59 2.85
3048 3365 3.686016 ACTTCTTATGCACCCGACAATT 58.314 40.909 0.00 0.00 0.00 2.32
3049 3366 3.350219 ACTTCTTATGCACCCGACAAT 57.650 42.857 0.00 0.00 0.00 2.71
3082 3399 9.689976 CACAATCACACAAGGATTAACAAATTA 57.310 29.630 0.00 0.00 33.40 1.40
3111 3428 8.425577 AACGATACTATCTTCAAGGAATGTTG 57.574 34.615 0.00 0.00 0.00 3.33
3138 3455 8.383318 ACTAGCATTTAACCATATGACATGAC 57.617 34.615 3.65 0.00 0.00 3.06
3218 3580 7.013274 GCCTGCTTATATAAACTGATGTTTCCA 59.987 37.037 4.78 0.00 44.35 3.53
3232 3594 9.052759 GCTTAGTTTTTACAGCCTGCTTATATA 57.947 33.333 0.00 0.00 0.00 0.86
3233 3595 7.931275 GCTTAGTTTTTACAGCCTGCTTATAT 58.069 34.615 0.00 0.00 0.00 0.86
3251 3613 6.296026 TGTGAGTCTACAAATTGGCTTAGTT 58.704 36.000 0.00 0.00 0.00 2.24
3253 3615 5.163814 GCTGTGAGTCTACAAATTGGCTTAG 60.164 44.000 0.00 0.00 0.00 2.18
3255 3617 3.503748 GCTGTGAGTCTACAAATTGGCTT 59.496 43.478 0.00 0.00 0.00 4.35
3257 3619 2.162408 GGCTGTGAGTCTACAAATTGGC 59.838 50.000 0.00 0.00 0.00 4.52
3258 3620 2.749621 GGGCTGTGAGTCTACAAATTGG 59.250 50.000 0.00 0.00 0.00 3.16
3323 3688 6.558771 TGATCAACACTCAACAATGTAAGG 57.441 37.500 0.00 0.00 0.00 2.69
3345 3710 4.326826 TCCTGCTCAGTTGGTTAAAGATG 58.673 43.478 0.00 0.00 0.00 2.90
3356 3721 2.554032 CGTTTTTCCATCCTGCTCAGTT 59.446 45.455 0.00 0.00 0.00 3.16
3442 3807 9.059260 GTTTATAACTGAACTGGTTCACCTAAA 57.941 33.333 11.53 9.87 43.90 1.85
3443 3808 8.434392 AGTTTATAACTGAACTGGTTCACCTAA 58.566 33.333 11.53 5.55 43.90 2.69
3444 3809 7.970102 AGTTTATAACTGAACTGGTTCACCTA 58.030 34.615 11.53 7.02 43.90 3.08
3445 3810 6.838382 AGTTTATAACTGAACTGGTTCACCT 58.162 36.000 11.53 5.28 43.90 4.00
3446 3811 7.876582 AGTAGTTTATAACTGAACTGGTTCACC 59.123 37.037 11.53 0.00 43.90 4.02
3447 3812 8.828688 AGTAGTTTATAACTGAACTGGTTCAC 57.171 34.615 11.53 1.31 43.90 3.18
3488 3860 3.573110 AGTAGATGTAGTTACCCGGCATC 59.427 47.826 0.00 1.40 36.97 3.91
3503 3875 2.996631 AGCCAGCCTTCAAAGTAGATG 58.003 47.619 0.00 0.00 0.00 2.90
3516 3888 3.350833 CCAGGATCATAATAAGCCAGCC 58.649 50.000 0.00 0.00 0.00 4.85
3517 3889 2.751806 GCCAGGATCATAATAAGCCAGC 59.248 50.000 0.00 0.00 0.00 4.85
3518 3890 4.298103 AGCCAGGATCATAATAAGCCAG 57.702 45.455 0.00 0.00 0.00 4.85
3519 3891 4.846367 ACTAGCCAGGATCATAATAAGCCA 59.154 41.667 0.00 0.00 0.00 4.75
3559 3931 8.375506 AGTAATGAACTGACTGGACAATTCTAA 58.624 33.333 0.00 0.00 36.93 2.10
3616 3991 8.740123 TTTTCCTTAGTAAGTCACAATGTTCA 57.260 30.769 9.05 0.00 0.00 3.18
3639 4014 6.959639 TGTGCCTCAGAAAATAGAGTTTTT 57.040 33.333 0.00 0.00 0.00 1.94
3640 4015 8.515414 GTTATGTGCCTCAGAAAATAGAGTTTT 58.485 33.333 0.00 0.00 0.00 2.43
3641 4016 7.665559 TGTTATGTGCCTCAGAAAATAGAGTTT 59.334 33.333 0.00 0.00 0.00 2.66
3642 4017 7.168219 TGTTATGTGCCTCAGAAAATAGAGTT 58.832 34.615 0.00 0.00 0.00 3.01
3648 4023 6.594788 AACATGTTATGTGCCTCAGAAAAT 57.405 33.333 9.97 0.00 44.07 1.82
3659 4034 6.074516 CGGAGGTCGTTATAACATGTTATGTG 60.075 42.308 32.16 22.95 44.07 3.21
3682 4061 3.000078 GCATATTACGCGATGATAACCGG 60.000 47.826 15.93 0.00 0.00 5.28
3683 4062 3.857665 AGCATATTACGCGATGATAACCG 59.142 43.478 15.93 2.80 0.00 4.44
3686 4065 7.042389 TGTTCAAAGCATATTACGCGATGATAA 60.042 33.333 15.93 0.05 31.85 1.75
3694 4073 7.062839 TGGAAAATTGTTCAAAGCATATTACGC 59.937 33.333 0.00 0.00 0.00 4.42
3695 4074 8.372521 GTGGAAAATTGTTCAAAGCATATTACG 58.627 33.333 0.00 0.00 0.00 3.18
3698 4077 8.851541 ATGTGGAAAATTGTTCAAAGCATATT 57.148 26.923 0.00 0.00 0.00 1.28
3700 4079 8.149647 AGAATGTGGAAAATTGTTCAAAGCATA 58.850 29.630 0.00 0.00 0.00 3.14
3736 4115 5.063204 AGAGAGATCCTGACGAGATAACAG 58.937 45.833 0.00 0.00 0.00 3.16
3771 4150 5.975344 CAGCTTCCTGCATAATAACACAATG 59.025 40.000 0.00 0.00 45.94 2.82
3773 4152 5.565592 CAGCTTCCTGCATAATAACACAA 57.434 39.130 0.00 0.00 45.94 3.33
3836 4215 1.581447 GGTGAGCCTCAAAAAGCGG 59.419 57.895 0.00 0.00 0.00 5.52
4025 4407 2.049433 ACCTTCTTCACGACGCCG 60.049 61.111 0.00 0.00 42.50 6.46
4062 4444 0.112995 TGCTGCTTCCCTTGGTTGAT 59.887 50.000 0.00 0.00 0.00 2.57
4148 4530 1.673665 CAGCTGCTTCGCCTTCCTT 60.674 57.895 0.00 0.00 0.00 3.36
4238 4620 1.340017 CGAACAATCCATGACAGGGGT 60.340 52.381 6.25 0.00 0.00 4.95
4239 4621 1.382522 CGAACAATCCATGACAGGGG 58.617 55.000 6.25 0.00 0.00 4.79
4246 4633 3.837213 AAGTGAAGCGAACAATCCATG 57.163 42.857 0.00 0.00 0.00 3.66
4253 4640 6.649141 ACTCATATTACAAAGTGAAGCGAACA 59.351 34.615 0.00 0.00 0.00 3.18
4263 4650 6.779860 ACCCTCAACACTCATATTACAAAGT 58.220 36.000 0.00 0.00 0.00 2.66
4264 4651 7.687941 AACCCTCAACACTCATATTACAAAG 57.312 36.000 0.00 0.00 0.00 2.77
4274 4661 3.117701 TCATCCAAAACCCTCAACACTCA 60.118 43.478 0.00 0.00 0.00 3.41
4285 4672 2.347731 GGACTCGTCTCATCCAAAACC 58.652 52.381 0.00 0.00 32.35 3.27
4294 4681 1.323271 GCCATCAGGGACTCGTCTCA 61.323 60.000 0.00 0.00 40.01 3.27
4295 4682 1.439644 GCCATCAGGGACTCGTCTC 59.560 63.158 0.00 0.00 40.01 3.36
4349 4742 7.972277 ACTCTTTTCAGCATTACATTAGCAATG 59.028 33.333 7.16 7.16 44.48 2.82
4350 4743 8.059798 ACTCTTTTCAGCATTACATTAGCAAT 57.940 30.769 0.00 0.00 0.00 3.56
4356 4749 5.934625 ACTCGACTCTTTTCAGCATTACATT 59.065 36.000 0.00 0.00 0.00 2.71
4383 4776 3.320541 CCAAAGGCAAGTACCAAATGACA 59.679 43.478 0.00 0.00 0.00 3.58
4387 4780 3.826729 GACTCCAAAGGCAAGTACCAAAT 59.173 43.478 0.00 0.00 0.00 2.32
4405 4798 0.815734 TAGTACAGCGGCCAAGACTC 59.184 55.000 2.24 0.00 0.00 3.36
4416 4809 5.757320 AGCATCATCTTGACATTAGTACAGC 59.243 40.000 0.00 0.00 0.00 4.40
4469 4862 1.939934 GGGAACAAGCAAGGCAAAAAC 59.060 47.619 0.00 0.00 0.00 2.43
4557 4964 7.714813 CCACAATAAAAATTATGGAATGGGGTC 59.285 37.037 0.00 0.00 0.00 4.46
4577 4984 8.970859 TGTTCCATTTGAATTTAAACCACAAT 57.029 26.923 0.00 0.00 34.90 2.71
4580 4987 7.384932 CCTCTGTTCCATTTGAATTTAAACCAC 59.615 37.037 0.00 0.00 34.90 4.16
4587 5010 6.497954 TCAATCCCTCTGTTCCATTTGAATTT 59.502 34.615 0.00 0.00 34.90 1.82
4589 5012 5.420104 GTCAATCCCTCTGTTCCATTTGAAT 59.580 40.000 0.00 0.00 34.90 2.57
4610 5033 2.874086 CTGCATTTGACACTGTCAGTCA 59.126 45.455 11.67 7.86 43.69 3.41
4611 5034 3.133691 TCTGCATTTGACACTGTCAGTC 58.866 45.455 11.67 4.16 43.69 3.51
4616 5039 2.300433 TGCTTCTGCATTTGACACTGT 58.700 42.857 0.00 0.00 45.31 3.55
4670 5093 6.097915 AGAGTTCCTTGTCGAATTCAGTAA 57.902 37.500 6.22 0.00 32.49 2.24
4671 5094 5.723672 AGAGTTCCTTGTCGAATTCAGTA 57.276 39.130 6.22 0.00 32.49 2.74
4715 6019 1.151777 ATGCGCGATCGAATTTCCGT 61.152 50.000 21.57 0.00 38.10 4.69
4717 6021 1.660333 GGAATGCGCGATCGAATTTCC 60.660 52.381 21.57 19.08 43.65 3.13
4719 6023 1.003545 CAGGAATGCGCGATCGAATTT 60.004 47.619 21.57 6.01 43.65 1.82
4728 6032 2.249535 CCAGATCCAGGAATGCGCG 61.250 63.158 0.00 0.00 0.00 6.86
4734 6038 4.533707 GTGATATCCATCCAGATCCAGGAA 59.466 45.833 8.43 0.00 38.93 3.36
4753 6057 4.144297 AGTTGTGCTATGTTTGGTGTGAT 58.856 39.130 0.00 0.00 0.00 3.06
4759 6063 3.498397 ACTTCGAGTTGTGCTATGTTTGG 59.502 43.478 0.00 0.00 0.00 3.28
4760 6064 4.457810 CACTTCGAGTTGTGCTATGTTTG 58.542 43.478 3.12 0.00 0.00 2.93
4781 6085 6.772360 TTCTATGCAAATTATGAACTGCCA 57.228 33.333 0.00 0.00 33.78 4.92
4802 6106 6.625873 ACTCTCACTTCCACTTTGATTTTC 57.374 37.500 0.00 0.00 0.00 2.29
4820 6188 9.482627 CCACCTCTATGTAAATTATGAACTCTC 57.517 37.037 0.00 0.00 0.00 3.20
4821 6189 8.993424 ACCACCTCTATGTAAATTATGAACTCT 58.007 33.333 0.00 0.00 0.00 3.24
4840 6234 1.661341 CTGCTGCAATCTACCACCTC 58.339 55.000 3.02 0.00 0.00 3.85
4841 6235 0.393537 GCTGCTGCAATCTACCACCT 60.394 55.000 11.11 0.00 39.41 4.00
4842 6236 2.101700 GCTGCTGCAATCTACCACC 58.898 57.895 11.11 0.00 39.41 4.61
4864 6258 0.609957 TATGGTTTGCTGCTGCTGCT 60.610 50.000 27.67 12.30 40.48 4.24
4865 6259 0.458669 ATATGGTTTGCTGCTGCTGC 59.541 50.000 22.51 22.51 40.48 5.25
4868 6262 1.477700 TCCAATATGGTTTGCTGCTGC 59.522 47.619 8.89 8.89 39.03 5.25
4869 6263 3.382227 TCATCCAATATGGTTTGCTGCTG 59.618 43.478 0.00 0.00 39.03 4.41
4870 6264 3.634504 TCATCCAATATGGTTTGCTGCT 58.365 40.909 0.00 0.00 39.03 4.24
4871 6265 4.595762 ATCATCCAATATGGTTTGCTGC 57.404 40.909 0.00 0.00 39.03 5.25
4883 6315 6.292865 CGTGCACGAGTAATAAATCATCCAAT 60.293 38.462 34.93 0.00 43.02 3.16


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

AutoCloner maintained by Alex Coulton.