Multiple sequence alignment - TraesCS1D01G279500

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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 TraesCS1D01G279500 chr1D 100.000 5343 0 0 1 5343 377196426 377191084 0.000000e+00 9867.0
1 TraesCS1D01G279500 chr1A 93.556 3507 157 27 271 3727 477739907 477736420 0.000000e+00 5160.0
2 TraesCS1D01G279500 chr1A 80.963 872 93 41 3743 4573 477736332 477735493 1.630000e-174 623.0
3 TraesCS1D01G279500 chr1A 76.897 290 50 11 4 287 29247523 29247801 1.200000e-31 148.0
4 TraesCS1D01G279500 chr1A 81.622 185 21 7 5134 5314 477735122 477734947 2.010000e-29 141.0
5 TraesCS1D01G279500 chr1B 92.049 2830 133 41 1821 4573 504095960 504093146 0.000000e+00 3895.0
6 TraesCS1D01G279500 chr1B 91.989 1835 101 23 4 1822 504097847 504096043 0.000000e+00 2532.0
7 TraesCS1D01G279500 chr1B 89.506 324 17 8 5037 5343 504092749 504092426 1.390000e-105 394.0
8 TraesCS1D01G279500 chr1B 84.211 418 34 12 4595 4995 504093161 504092759 1.400000e-100 377.0
9 TraesCS1D01G279500 chr3D 74.542 491 78 32 3233 3697 471585648 471586117 2.560000e-38 171.0
10 TraesCS1D01G279500 chr3D 91.304 46 4 0 1 46 64766050 64766005 4.470000e-06 63.9
11 TraesCS1D01G279500 chr2B 80.000 220 36 4 5 222 87518866 87519079 7.160000e-34 156.0
12 TraesCS1D01G279500 chr2B 74.797 246 52 7 14 257 689321154 689321391 9.470000e-18 102.0
13 TraesCS1D01G279500 chr3A 76.325 283 58 5 5 286 691957526 691957800 5.580000e-30 143.0
14 TraesCS1D01G279500 chr3A 83.077 130 21 1 3568 3697 614467860 614467988 3.380000e-22 117.0
15 TraesCS1D01G279500 chr5A 76.494 251 50 6 5 253 443725879 443725636 1.560000e-25 128.0
16 TraesCS1D01G279500 chr3B 73.878 245 54 8 4 246 43585861 43585625 7.370000e-14 89.8
17 TraesCS1D01G279500 chr3B 73.932 234 52 7 14 245 43589087 43588861 9.530000e-13 86.1
18 TraesCS1D01G279500 chr3B 91.111 45 4 0 202 246 43564432 43564388 1.610000e-05 62.1
19 TraesCS1D01G279500 chr3B 91.111 45 4 0 202 246 43570705 43570661 1.610000e-05 62.1
20 TraesCS1D01G279500 chr2A 100.000 28 0 0 6 33 754041261 754041234 1.000000e-02 52.8


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 TraesCS1D01G279500 chr1D 377191084 377196426 5342 True 9867.000000 9867 100.000000 1 5343 1 chr1D.!!$R1 5342
1 TraesCS1D01G279500 chr1A 477734947 477739907 4960 True 1974.666667 5160 85.380333 271 5314 3 chr1A.!!$R1 5043
2 TraesCS1D01G279500 chr1B 504092426 504097847 5421 True 1799.500000 3895 89.438750 4 5343 4 chr1B.!!$R1 5339

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
50 51 0.107703 TGCCCTCTTACAATGCGAGG 60.108 55.000 6.80 6.8 43.11 4.63 F
228 230 0.249868 CCGCGCCTCCATGATTCTAA 60.250 55.000 0.00 0.0 0.00 2.10 F
266 268 0.392998 GGATCGGCAGTGACACCAAT 60.393 55.000 0.84 0.0 0.00 3.16 F
766 788 1.377366 GAGATCCACAGAGCGACGGA 61.377 60.000 0.00 0.0 32.16 4.69 F
1235 1265 1.771073 TTGTGTTTCAGGTGAGCGCG 61.771 55.000 0.00 0.0 0.00 6.86 F
1810 1847 1.795768 ATTGTCGTGTTCTGCATCGT 58.204 45.000 0.00 0.0 0.00 3.73 F
2000 2127 4.318332 TCTTCTCTGTGATTGCATTCGTT 58.682 39.130 4.27 0.0 0.00 3.85 F
3700 3866 1.960689 GTTGTTGTTGCCTGGTATGGT 59.039 47.619 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1247 1277 0.809385 ACACGACGTAGACTGGGATG 59.191 55.000 0.00 0.00 0.00 3.51 R
1632 1666 1.971357 AGGGGCGTACCAGATCATAAG 59.029 52.381 0.00 0.00 42.91 1.73 R
1962 2089 2.092914 AGAAGAAGGTAAAGCCCGATGG 60.093 50.000 0.00 0.00 38.26 3.51 R
2000 2127 3.456644 TGTTGACACTAAAGGAGGGTTCA 59.543 43.478 0.00 0.00 44.07 3.18 R
3098 3254 1.140312 AGTTTGGACCTGGAAGCTGA 58.860 50.000 0.00 0.00 0.00 4.26 R
3383 3540 0.318762 ACTCCTCGAGGAACTGCAAC 59.681 55.000 32.94 0.00 44.91 4.17 R
3753 3991 3.066621 CCTGTGAGCAAAGCAACTGTTAA 59.933 43.478 0.00 0.00 0.00 2.01 R
5095 5454 0.109319 GGTACCCTTGCATGCGTTTG 60.109 55.000 14.09 4.36 0.00 2.93 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
39 40 1.136329 ACACCTCCACATGCCCTCTT 61.136 55.000 0.00 0.00 0.00 2.85
42 43 0.911769 CCTCCACATGCCCTCTTACA 59.088 55.000 0.00 0.00 0.00 2.41
50 51 0.107703 TGCCCTCTTACAATGCGAGG 60.108 55.000 6.80 6.80 43.11 4.63
106 108 7.928706 AGAACCTTATTTCATCTTAGGATGTCG 59.071 37.037 13.92 0.00 46.74 4.35
117 119 4.819761 GATGTCGCCGCTGCCTCA 62.820 66.667 0.00 0.00 0.00 3.86
123 125 4.704833 GCCGCTGCCTCACCTTCA 62.705 66.667 0.00 0.00 0.00 3.02
124 126 2.743928 CCGCTGCCTCACCTTCAC 60.744 66.667 0.00 0.00 0.00 3.18
127 129 1.739562 GCTGCCTCACCTTCACGAG 60.740 63.158 0.00 0.00 0.00 4.18
128 130 1.739562 CTGCCTCACCTTCACGAGC 60.740 63.158 0.00 0.00 0.00 5.03
131 133 1.967535 CCTCACCTTCACGAGCAGA 59.032 57.895 0.00 0.00 0.00 4.26
148 150 4.469657 AGCAGAACACAAACCCTAATCAA 58.530 39.130 0.00 0.00 0.00 2.57
189 191 0.890996 CAAAGTGTGAGCCCTCCCAC 60.891 60.000 3.15 3.15 38.08 4.61
191 193 4.394712 GTGTGAGCCCTCCCACCG 62.395 72.222 0.16 0.00 32.88 4.94
223 225 4.552365 CCACCGCGCCTCCATGAT 62.552 66.667 0.00 0.00 0.00 2.45
225 227 2.203070 ACCGCGCCTCCATGATTC 60.203 61.111 0.00 0.00 0.00 2.52
226 228 2.109799 CCGCGCCTCCATGATTCT 59.890 61.111 0.00 0.00 0.00 2.40
227 229 1.367471 CCGCGCCTCCATGATTCTA 59.633 57.895 0.00 0.00 0.00 2.10
228 230 0.249868 CCGCGCCTCCATGATTCTAA 60.250 55.000 0.00 0.00 0.00 2.10
229 231 1.143305 CGCGCCTCCATGATTCTAAG 58.857 55.000 0.00 0.00 0.00 2.18
230 232 1.517242 GCGCCTCCATGATTCTAAGG 58.483 55.000 0.00 0.00 0.00 2.69
233 235 1.143684 GCCTCCATGATTCTAAGGCCA 59.856 52.381 5.01 0.00 45.45 5.36
237 239 2.173356 TCCATGATTCTAAGGCCACAGG 59.827 50.000 5.01 0.00 0.00 4.00
241 243 3.387962 TGATTCTAAGGCCACAGGAGAT 58.612 45.455 5.01 0.00 0.00 2.75
245 247 1.415659 CTAAGGCCACAGGAGATGAGG 59.584 57.143 5.01 0.00 42.21 3.86
249 251 2.060383 CCACAGGAGATGAGGCGGA 61.060 63.158 0.00 0.00 32.55 5.54
264 266 2.662596 GGATCGGCAGTGACACCA 59.337 61.111 0.84 0.00 0.00 4.17
266 268 0.392998 GGATCGGCAGTGACACCAAT 60.393 55.000 0.84 0.00 0.00 3.16
293 295 2.040679 GGCAGGAAACCCTAAACACCTA 59.959 50.000 0.00 0.00 31.47 3.08
295 297 3.244805 GCAGGAAACCCTAAACACCTAGT 60.245 47.826 0.00 0.00 31.47 2.57
296 298 4.019950 GCAGGAAACCCTAAACACCTAGTA 60.020 45.833 0.00 0.00 31.47 1.82
297 299 5.731591 CAGGAAACCCTAAACACCTAGTAG 58.268 45.833 0.00 0.00 31.47 2.57
336 339 2.230508 GGGGGAAAGAAAACGACAATCC 59.769 50.000 0.00 0.00 0.00 3.01
365 368 6.134535 TGAACCTGGATTTAATACCACTGT 57.865 37.500 0.00 0.00 32.44 3.55
369 372 7.849322 ACCTGGATTTAATACCACTGTTTTT 57.151 32.000 0.00 0.00 32.44 1.94
370 373 7.666623 ACCTGGATTTAATACCACTGTTTTTG 58.333 34.615 0.00 0.00 32.44 2.44
373 376 9.757227 CTGGATTTAATACCACTGTTTTTGAAA 57.243 29.630 0.00 0.00 32.44 2.69
472 476 5.050490 GGGAAAAGAAGAAAGAAAAGCCAC 58.950 41.667 0.00 0.00 0.00 5.01
473 477 4.740205 GGAAAAGAAGAAAGAAAAGCCACG 59.260 41.667 0.00 0.00 0.00 4.94
684 689 3.316573 CTCCCTGCCGACTCCCAAC 62.317 68.421 0.00 0.00 0.00 3.77
688 693 2.203788 TGCCGACTCCCAACTCCT 60.204 61.111 0.00 0.00 0.00 3.69
766 788 1.377366 GAGATCCACAGAGCGACGGA 61.377 60.000 0.00 0.00 32.16 4.69
867 896 2.507992 CGCCGTTCTCTGCTCCAG 60.508 66.667 0.00 0.00 0.00 3.86
1133 1163 3.825908 ATCCCTTCTTTTTGGGCTGTA 57.174 42.857 0.00 0.00 43.04 2.74
1235 1265 1.771073 TTGTGTTTCAGGTGAGCGCG 61.771 55.000 0.00 0.00 0.00 6.86
1236 1266 3.345808 TGTTTCAGGTGAGCGCGC 61.346 61.111 26.66 26.66 0.00 6.86
1326 1356 5.623673 CGCGTTTCAGTATTTAATAATGGCC 59.376 40.000 11.66 0.00 32.13 5.36
1495 1525 5.633182 GCAGATTAGACTACATTCTAGCAGC 59.367 44.000 0.00 0.00 29.67 5.25
1632 1666 3.617263 AGTTTGAACCGCTGATACGATTC 59.383 43.478 0.00 0.00 34.06 2.52
1669 1706 2.223572 CCCCTGATAATTTGTCGCTTGC 60.224 50.000 0.00 0.00 0.00 4.01
1810 1847 1.795768 ATTGTCGTGTTCTGCATCGT 58.204 45.000 0.00 0.00 0.00 3.73
1962 2089 5.391310 CCTGCTCTGTATGTTGTGAATGTTC 60.391 44.000 0.00 0.00 0.00 3.18
2000 2127 4.318332 TCTTCTCTGTGATTGCATTCGTT 58.682 39.130 4.27 0.00 0.00 3.85
2153 2280 4.618920 TGTTTCTTCCCTTAGACTCCAC 57.381 45.455 0.00 0.00 0.00 4.02
2209 2336 9.643693 GACATTTCATTATTGTCCACTTCAAAT 57.356 29.630 0.00 0.00 34.95 2.32
2694 2847 8.897752 AGATTAGTCATTATTTCCTGAGTTTGC 58.102 33.333 0.00 0.00 0.00 3.68
2855 3011 6.607198 CCCCTGTTTTCTATGATGGTGTTAAT 59.393 38.462 0.00 0.00 0.00 1.40
3013 3169 6.409704 CATCCTCCCTAACCATGTATGTATG 58.590 44.000 0.00 0.00 0.00 2.39
3016 3172 5.227569 TCCCTAACCATGTATGTATGCAG 57.772 43.478 0.00 0.00 0.00 4.41
3251 3407 8.467598 TCTATAGCTTTGTATTTATAGGGCTCG 58.532 37.037 0.00 0.00 30.59 5.03
3383 3540 5.181245 ACCATCCAGAACTTTGTATTGTTCG 59.819 40.000 0.00 0.00 44.95 3.95
3439 3596 7.502226 TGTGGTGATCTTATATTTTCATCCCAC 59.498 37.037 0.00 0.00 36.43 4.61
3502 3659 4.864704 TGGCTCAAAAAGGTTATTGTCC 57.135 40.909 0.00 0.00 0.00 4.02
3532 3689 7.066525 CCATGCTTGGCTTGAAATTTATGAATT 59.933 33.333 5.58 0.00 36.06 2.17
3591 3757 4.595781 AGTTGAACTGGTGGACCTTGTATA 59.404 41.667 0.00 0.00 36.82 1.47
3592 3758 5.250774 AGTTGAACTGGTGGACCTTGTATAT 59.749 40.000 0.00 0.00 36.82 0.86
3700 3866 1.960689 GTTGTTGTTGCCTGGTATGGT 59.039 47.619 0.00 0.00 0.00 3.55
3727 3893 4.455606 AGCTTACATTTCACCTATCAGCC 58.544 43.478 0.00 0.00 0.00 4.85
3730 3902 5.049129 GCTTACATTTCACCTATCAGCCATC 60.049 44.000 0.00 0.00 0.00 3.51
3748 3986 3.570550 CCATCTGGCTACTACACTACCTC 59.429 52.174 0.00 0.00 0.00 3.85
3753 3991 4.931914 TGGCTACTACACTACCTCTCTTT 58.068 43.478 0.00 0.00 0.00 2.52
4074 4313 0.179084 ACTGATCGGGTACGGCATTG 60.179 55.000 6.47 0.00 41.39 2.82
4094 4333 1.273606 GGCTCTCAGCACTGAACACTA 59.726 52.381 1.42 0.00 44.75 2.74
4095 4334 2.605030 GCTCTCAGCACTGAACACTAG 58.395 52.381 1.42 0.00 41.89 2.57
4097 4336 3.119173 GCTCTCAGCACTGAACACTAGAT 60.119 47.826 0.00 0.00 41.89 1.98
4098 4337 4.620332 GCTCTCAGCACTGAACACTAGATT 60.620 45.833 0.00 0.00 41.89 2.40
4099 4338 5.474578 TCTCAGCACTGAACACTAGATTT 57.525 39.130 0.00 0.00 39.39 2.17
4102 4341 6.203530 TCTCAGCACTGAACACTAGATTTTTG 59.796 38.462 0.00 0.00 39.39 2.44
4103 4342 6.054941 TCAGCACTGAACACTAGATTTTTGA 58.945 36.000 0.00 0.00 36.53 2.69
4104 4343 6.203530 TCAGCACTGAACACTAGATTTTTGAG 59.796 38.462 0.00 0.00 36.53 3.02
4105 4344 5.049129 AGCACTGAACACTAGATTTTTGAGC 60.049 40.000 0.00 0.00 0.00 4.26
4106 4345 5.049129 GCACTGAACACTAGATTTTTGAGCT 60.049 40.000 0.00 0.00 0.00 4.09
4107 4346 6.369005 CACTGAACACTAGATTTTTGAGCTG 58.631 40.000 0.00 0.00 0.00 4.24
4108 4347 6.017605 CACTGAACACTAGATTTTTGAGCTGT 60.018 38.462 0.00 0.00 0.00 4.40
4109 4348 6.543831 ACTGAACACTAGATTTTTGAGCTGTT 59.456 34.615 0.00 0.00 0.00 3.16
4114 4353 7.945134 ACACTAGATTTTTGAGCTGTTGATTT 58.055 30.769 0.00 0.00 0.00 2.17
4115 4354 8.416329 ACACTAGATTTTTGAGCTGTTGATTTT 58.584 29.630 0.00 0.00 0.00 1.82
4119 4360 8.679288 AGATTTTTGAGCTGTTGATTTTATCG 57.321 30.769 0.00 0.00 0.00 2.92
4172 4442 7.781548 AAAACTCGTACTGTTGTTTATCTGT 57.218 32.000 2.61 0.00 33.07 3.41
4175 4445 5.176958 ACTCGTACTGTTGTTTATCTGTTGC 59.823 40.000 0.00 0.00 0.00 4.17
4214 4484 2.352032 GCCGGACTGCCTGTACTCT 61.352 63.158 5.05 0.00 0.00 3.24
4215 4485 1.889530 GCCGGACTGCCTGTACTCTT 61.890 60.000 5.05 0.00 0.00 2.85
4216 4486 0.608640 CCGGACTGCCTGTACTCTTT 59.391 55.000 0.00 0.00 0.00 2.52
4217 4487 1.404315 CCGGACTGCCTGTACTCTTTC 60.404 57.143 0.00 0.00 0.00 2.62
4219 4489 2.672478 CGGACTGCCTGTACTCTTTCTG 60.672 54.545 0.00 0.00 0.00 3.02
4221 4491 3.580731 GACTGCCTGTACTCTTTCTGTC 58.419 50.000 0.00 0.00 0.00 3.51
4222 4492 2.029828 ACTGCCTGTACTCTTTCTGTCG 60.030 50.000 0.00 0.00 0.00 4.35
4223 4493 1.336887 TGCCTGTACTCTTTCTGTCGC 60.337 52.381 0.00 0.00 0.00 5.19
4224 4494 1.997669 CCTGTACTCTTTCTGTCGCC 58.002 55.000 0.00 0.00 0.00 5.54
4225 4495 1.272490 CCTGTACTCTTTCTGTCGCCA 59.728 52.381 0.00 0.00 0.00 5.69
4227 4497 1.000506 TGTACTCTTTCTGTCGCCACC 59.999 52.381 0.00 0.00 0.00 4.61
4241 4514 2.972505 CACCTTTGGCTGACGCGT 60.973 61.111 13.85 13.85 36.88 6.01
4349 4629 4.107051 GCGGCACATGAGCGCTTT 62.107 61.111 13.26 0.00 33.47 3.51
4356 4636 1.135859 CACATGAGCGCTTTTCCAGTC 60.136 52.381 13.26 0.00 0.00 3.51
4357 4637 0.449388 CATGAGCGCTTTTCCAGTCC 59.551 55.000 13.26 0.00 0.00 3.85
4358 4638 1.021390 ATGAGCGCTTTTCCAGTCCG 61.021 55.000 13.26 0.00 0.00 4.79
4517 4825 2.712709 TCGACAACACCACCAAAAAGA 58.287 42.857 0.00 0.00 0.00 2.52
4518 4826 3.283751 TCGACAACACCACCAAAAAGAT 58.716 40.909 0.00 0.00 0.00 2.40
4559 4871 3.002791 TGTATATATCGTCCGACCGACC 58.997 50.000 0.00 0.00 40.08 4.79
4567 4879 2.497770 CCGACCGACCGGCTTAAT 59.502 61.111 8.55 0.00 43.25 1.40
4568 4880 1.153509 CCGACCGACCGGCTTAATT 60.154 57.895 8.55 0.00 43.25 1.40
4569 4881 1.149964 CCGACCGACCGGCTTAATTC 61.150 60.000 8.55 0.00 43.25 2.17
4570 4882 0.179119 CGACCGACCGGCTTAATTCT 60.179 55.000 8.55 0.00 39.32 2.40
4571 4883 1.066002 CGACCGACCGGCTTAATTCTA 59.934 52.381 8.55 0.00 39.32 2.10
4572 4884 2.288030 CGACCGACCGGCTTAATTCTAT 60.288 50.000 8.55 0.00 39.32 1.98
4573 4885 3.725490 GACCGACCGGCTTAATTCTATT 58.275 45.455 8.55 0.00 39.32 1.73
4574 4886 3.725490 ACCGACCGGCTTAATTCTATTC 58.275 45.455 8.55 0.00 39.32 1.75
4575 4887 3.387050 ACCGACCGGCTTAATTCTATTCT 59.613 43.478 8.55 0.00 39.32 2.40
4576 4888 4.586001 ACCGACCGGCTTAATTCTATTCTA 59.414 41.667 8.55 0.00 39.32 2.10
4577 4889 5.245526 ACCGACCGGCTTAATTCTATTCTAT 59.754 40.000 8.55 0.00 39.32 1.98
4578 4890 6.164176 CCGACCGGCTTAATTCTATTCTATT 58.836 40.000 0.00 0.00 0.00 1.73
4579 4891 6.649557 CCGACCGGCTTAATTCTATTCTATTT 59.350 38.462 0.00 0.00 0.00 1.40
4580 4892 7.172703 CCGACCGGCTTAATTCTATTCTATTTT 59.827 37.037 0.00 0.00 0.00 1.82
4581 4893 8.221766 CGACCGGCTTAATTCTATTCTATTTTC 58.778 37.037 0.00 0.00 0.00 2.29
4582 4894 9.274206 GACCGGCTTAATTCTATTCTATTTTCT 57.726 33.333 0.00 0.00 0.00 2.52
4583 4895 9.628500 ACCGGCTTAATTCTATTCTATTTTCTT 57.372 29.630 0.00 0.00 0.00 2.52
4628 4940 8.734218 ATTCTATGATCACCTATTGATGCATC 57.266 34.615 20.14 20.14 45.67 3.91
4644 4956 2.094026 TGCATCCATATCGATTCTCCGG 60.094 50.000 1.71 0.00 0.00 5.14
4646 4958 0.895530 TCCATATCGATTCTCCGGCC 59.104 55.000 1.71 0.00 0.00 6.13
4652 4964 4.832608 GATTCTCCGGCCGCCGTT 62.833 66.667 29.21 9.36 46.80 4.44
4691 5014 1.302271 GTTGGGTGGGTCTCGTTCC 60.302 63.158 0.00 0.00 0.00 3.62
4692 5015 2.874664 TTGGGTGGGTCTCGTTCCG 61.875 63.158 0.00 0.00 0.00 4.30
4694 5017 2.739132 GGTGGGTCTCGTTCCGTT 59.261 61.111 0.00 0.00 0.00 4.44
4814 5142 4.509737 GGTGGCGCTCCTACGGAC 62.510 72.222 7.64 0.00 0.00 4.79
4815 5143 3.450115 GTGGCGCTCCTACGGACT 61.450 66.667 7.64 0.00 0.00 3.85
4816 5144 2.117156 GTGGCGCTCCTACGGACTA 61.117 63.158 7.64 0.00 0.00 2.59
4897 5236 3.018019 CCCATGCTCCCCATTGGA 58.982 61.111 3.62 0.00 38.68 3.53
4922 5265 0.107654 CGTGTGATTTCCCTCCCCTC 60.108 60.000 0.00 0.00 0.00 4.30
4965 5308 2.124507 TTTCGTGCTGGGGAGAAGGG 62.125 60.000 0.00 0.00 0.00 3.95
4995 5338 4.060372 CTGCACACTGCTGCTTCT 57.940 55.556 0.00 0.00 45.31 2.85
4997 5340 0.883370 CTGCACACTGCTGCTTCTCA 60.883 55.000 0.00 0.00 45.31 3.27
4998 5341 0.883370 TGCACACTGCTGCTTCTCAG 60.883 55.000 0.00 0.00 45.31 3.35
4999 5342 1.575576 GCACACTGCTGCTTCTCAGG 61.576 60.000 0.00 0.00 43.06 3.86
5001 5344 0.034616 ACACTGCTGCTTCTCAGGTC 59.965 55.000 0.00 0.00 43.06 3.85
5002 5345 0.321021 CACTGCTGCTTCTCAGGTCT 59.679 55.000 0.00 0.00 43.06 3.85
5004 5347 0.607112 CTGCTGCTTCTCAGGTCTCA 59.393 55.000 0.00 0.00 43.06 3.27
5005 5348 0.607112 TGCTGCTTCTCAGGTCTCAG 59.393 55.000 0.00 0.00 43.06 3.35
5006 5349 0.740516 GCTGCTTCTCAGGTCTCAGC 60.741 60.000 0.00 0.00 43.06 4.26
5007 5350 0.607112 CTGCTTCTCAGGTCTCAGCA 59.393 55.000 0.00 0.00 39.15 4.41
5008 5351 1.001746 CTGCTTCTCAGGTCTCAGCAA 59.998 52.381 0.00 0.00 39.92 3.91
5009 5352 1.270518 TGCTTCTCAGGTCTCAGCAAC 60.271 52.381 0.00 0.00 37.54 4.17
5010 5353 1.943507 GCTTCTCAGGTCTCAGCAACC 60.944 57.143 0.00 0.00 37.03 3.77
5011 5354 1.345741 CTTCTCAGGTCTCAGCAACCA 59.654 52.381 0.00 0.00 39.39 3.67
5012 5355 0.972134 TCTCAGGTCTCAGCAACCAG 59.028 55.000 0.00 0.00 39.39 4.00
5013 5356 0.673022 CTCAGGTCTCAGCAACCAGC 60.673 60.000 0.00 0.00 46.19 4.85
5023 5366 2.616969 GCAACCAGCTCTGTTTCGA 58.383 52.632 0.00 0.00 41.15 3.71
5024 5367 1.160137 GCAACCAGCTCTGTTTCGAT 58.840 50.000 0.00 0.00 41.15 3.59
5025 5368 1.135859 GCAACCAGCTCTGTTTCGATG 60.136 52.381 0.00 0.00 41.15 3.84
5026 5369 2.146342 CAACCAGCTCTGTTTCGATGT 58.854 47.619 0.00 0.00 0.00 3.06
5027 5370 1.800805 ACCAGCTCTGTTTCGATGTG 58.199 50.000 0.00 0.00 0.00 3.21
5028 5371 1.070758 ACCAGCTCTGTTTCGATGTGT 59.929 47.619 0.00 0.00 0.00 3.72
5029 5372 1.462283 CCAGCTCTGTTTCGATGTGTG 59.538 52.381 0.00 0.00 0.00 3.82
5030 5373 2.138320 CAGCTCTGTTTCGATGTGTGT 58.862 47.619 0.00 0.00 0.00 3.72
5031 5374 3.317150 CAGCTCTGTTTCGATGTGTGTA 58.683 45.455 0.00 0.00 0.00 2.90
5032 5375 3.928992 CAGCTCTGTTTCGATGTGTGTAT 59.071 43.478 0.00 0.00 0.00 2.29
5035 5378 6.918022 CAGCTCTGTTTCGATGTGTGTATATA 59.082 38.462 0.00 0.00 0.00 0.86
5091 5450 4.554036 GCCGGCCATGGAGAGGAC 62.554 72.222 18.11 7.47 0.00 3.85
5095 5454 2.512515 GCCATGGAGAGGACGCAC 60.513 66.667 18.40 0.00 0.00 5.34
5096 5455 2.981302 CCATGGAGAGGACGCACA 59.019 61.111 5.56 0.00 0.00 4.57
5097 5456 1.296392 CCATGGAGAGGACGCACAA 59.704 57.895 5.56 0.00 0.00 3.33
5098 5457 0.321564 CCATGGAGAGGACGCACAAA 60.322 55.000 5.56 0.00 0.00 2.83
5099 5458 0.798776 CATGGAGAGGACGCACAAAC 59.201 55.000 0.00 0.00 0.00 2.93
5100 5459 0.670546 ATGGAGAGGACGCACAAACG 60.671 55.000 0.00 0.00 39.50 3.60
5162 5522 4.679654 AGCGTTTCAAAATTTTCACCGATC 59.320 37.500 0.00 0.00 0.00 3.69
5169 5529 5.701750 TCAAAATTTTCACCGATCCTCGTTA 59.298 36.000 0.00 0.00 38.40 3.18
5244 5604 0.532573 GCTCTGCTACTACCACTGCA 59.467 55.000 0.00 0.00 0.00 4.41
5245 5605 1.137872 GCTCTGCTACTACCACTGCAT 59.862 52.381 0.00 0.00 34.79 3.96
5246 5606 2.362397 GCTCTGCTACTACCACTGCATA 59.638 50.000 0.00 0.00 34.79 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.446616 TGTCTCCGACGAATCTCACG 59.553 55.000 0.00 0.00 34.95 4.35
2 3 1.199327 TGTGTCTCCGACGAATCTCAC 59.801 52.381 0.00 0.11 34.95 3.51
3 4 1.199327 GTGTGTCTCCGACGAATCTCA 59.801 52.381 0.00 0.00 34.95 3.27
4 5 1.467713 GGTGTGTCTCCGACGAATCTC 60.468 57.143 0.00 0.00 34.95 2.75
5 6 0.526662 GGTGTGTCTCCGACGAATCT 59.473 55.000 0.00 0.00 34.95 2.40
6 7 0.526662 AGGTGTGTCTCCGACGAATC 59.473 55.000 0.00 0.00 34.95 2.52
7 8 0.526662 GAGGTGTGTCTCCGACGAAT 59.473 55.000 0.00 0.00 34.95 3.34
8 9 1.521450 GGAGGTGTGTCTCCGACGAA 61.521 60.000 0.00 0.00 43.19 3.85
29 30 1.600957 CTCGCATTGTAAGAGGGCATG 59.399 52.381 0.00 0.00 0.00 4.06
30 31 1.475751 CCTCGCATTGTAAGAGGGCAT 60.476 52.381 13.57 0.00 45.77 4.40
31 32 0.107703 CCTCGCATTGTAAGAGGGCA 60.108 55.000 13.57 0.00 45.77 5.36
32 33 2.695314 CCTCGCATTGTAAGAGGGC 58.305 57.895 13.57 0.00 45.77 5.19
67 68 2.509561 GTTCTCTTCGCCTCGCCC 60.510 66.667 0.00 0.00 0.00 6.13
71 72 4.504858 TGAAATAAGGTTCTCTTCGCCTC 58.495 43.478 0.00 0.00 36.93 4.70
106 108 4.704833 TGAAGGTGAGGCAGCGGC 62.705 66.667 0.00 0.00 36.92 6.53
116 118 0.861837 GTGTTCTGCTCGTGAAGGTG 59.138 55.000 0.00 0.00 0.00 4.00
117 119 0.464036 TGTGTTCTGCTCGTGAAGGT 59.536 50.000 0.00 0.00 0.00 3.50
122 124 0.307760 GGGTTTGTGTTCTGCTCGTG 59.692 55.000 0.00 0.00 0.00 4.35
123 125 0.180406 AGGGTTTGTGTTCTGCTCGT 59.820 50.000 0.00 0.00 0.00 4.18
124 126 2.163818 TAGGGTTTGTGTTCTGCTCG 57.836 50.000 0.00 0.00 0.00 5.03
127 129 4.846779 TTGATTAGGGTTTGTGTTCTGC 57.153 40.909 0.00 0.00 0.00 4.26
128 130 6.391227 AGTTTGATTAGGGTTTGTGTTCTG 57.609 37.500 0.00 0.00 0.00 3.02
158 160 5.221244 GGCTCACACTTTGATTTTAGGTGTT 60.221 40.000 0.00 0.00 38.79 3.32
159 161 4.278419 GGCTCACACTTTGATTTTAGGTGT 59.722 41.667 0.00 0.00 41.03 4.16
170 172 1.455849 TGGGAGGGCTCACACTTTG 59.544 57.895 0.00 0.00 38.24 2.77
189 191 4.626081 GATCCCGACCCATGCCGG 62.626 72.222 0.00 0.00 44.94 6.13
191 193 3.488569 TGGATCCCGACCCATGCC 61.489 66.667 9.90 0.00 0.00 4.40
215 217 3.474600 CTGTGGCCTTAGAATCATGGAG 58.525 50.000 3.32 0.00 0.00 3.86
223 225 2.768527 CTCATCTCCTGTGGCCTTAGAA 59.231 50.000 3.32 0.00 0.00 2.10
225 227 1.415659 CCTCATCTCCTGTGGCCTTAG 59.584 57.143 3.32 1.53 32.08 2.18
226 228 1.500474 CCTCATCTCCTGTGGCCTTA 58.500 55.000 3.32 0.00 32.08 2.69
227 229 2.305095 CCTCATCTCCTGTGGCCTT 58.695 57.895 3.32 0.00 32.08 4.35
228 230 4.063335 CCTCATCTCCTGTGGCCT 57.937 61.111 3.32 0.00 32.08 5.19
233 235 1.459455 CGATCCGCCTCATCTCCTGT 61.459 60.000 0.00 0.00 0.00 4.00
237 239 2.048690 GCCGATCCGCCTCATCTC 60.049 66.667 0.00 0.00 0.00 2.75
241 243 4.147449 CACTGCCGATCCGCCTCA 62.147 66.667 3.52 0.00 0.00 3.86
245 247 3.188786 GTGTCACTGCCGATCCGC 61.189 66.667 0.00 0.00 0.00 5.54
249 251 0.740868 CGATTGGTGTCACTGCCGAT 60.741 55.000 2.35 0.00 0.00 4.18
255 257 0.247736 GCCTCTCGATTGGTGTCACT 59.752 55.000 2.35 0.00 0.00 3.41
257 259 0.247460 CTGCCTCTCGATTGGTGTCA 59.753 55.000 5.85 0.00 0.00 3.58
259 261 0.904865 TCCTGCCTCTCGATTGGTGT 60.905 55.000 5.85 0.00 0.00 4.16
264 266 0.253327 GGGTTTCCTGCCTCTCGATT 59.747 55.000 0.00 0.00 0.00 3.34
266 268 0.040646 TAGGGTTTCCTGCCTCTCGA 59.959 55.000 0.00 0.00 44.61 4.04
293 295 4.959839 CCTAGAAAGAAGGAGGCTTCTACT 59.040 45.833 0.00 0.99 42.26 2.57
295 297 4.290942 CCCTAGAAAGAAGGAGGCTTCTA 58.709 47.826 0.00 0.00 42.26 2.10
296 298 3.111484 CCCTAGAAAGAAGGAGGCTTCT 58.889 50.000 0.00 0.00 44.69 2.85
297 299 2.171659 CCCCTAGAAAGAAGGAGGCTTC 59.828 54.545 0.00 0.00 36.08 3.86
336 339 8.621286 GTGGTATTAAATCCAGGTTCAGTTATG 58.379 37.037 2.79 0.00 34.16 1.90
365 368 9.477484 TTGTGTAGCTTTACAACTTTTCAAAAA 57.523 25.926 10.38 0.00 32.30 1.94
369 372 7.594714 TGTTTGTGTAGCTTTACAACTTTTCA 58.405 30.769 13.15 7.07 36.61 2.69
370 373 8.455598 TTGTTTGTGTAGCTTTACAACTTTTC 57.544 30.769 13.15 5.27 36.61 2.29
373 376 6.033966 GCTTGTTTGTGTAGCTTTACAACTT 58.966 36.000 13.15 0.00 36.61 2.66
450 454 4.740205 CGTGGCTTTTCTTTCTTCTTTTCC 59.260 41.667 0.00 0.00 0.00 3.13
472 476 2.253758 CGTGATATTGGCCTGCCCG 61.254 63.158 3.32 0.00 35.87 6.13
473 477 1.152963 ACGTGATATTGGCCTGCCC 60.153 57.895 3.32 0.00 34.56 5.36
482 486 1.227556 GGCGAGGGCACGTGATATT 60.228 57.895 22.23 0.20 42.47 1.28
754 776 0.039074 CTGAAAGTCCGTCGCTCTGT 60.039 55.000 0.00 0.00 0.00 3.41
766 788 1.575447 GGATGGGGGAGGCTGAAAGT 61.575 60.000 0.00 0.00 35.30 2.66
791 813 4.704103 AGTCCTCCGGCAGGCAGA 62.704 66.667 13.41 0.00 43.08 4.26
842 871 2.583593 GAGAACGGCGCTAGGCAG 60.584 66.667 6.90 4.17 46.16 4.85
843 872 3.068691 AGAGAACGGCGCTAGGCA 61.069 61.111 6.90 0.00 46.16 4.75
847 876 2.490217 GAGCAGAGAACGGCGCTA 59.510 61.111 6.90 0.00 41.73 4.26
867 896 4.754667 GAGGGGTCGCCGGTTGAC 62.755 72.222 17.53 17.53 35.60 3.18
1133 1163 1.909302 CACACCTTCCTCCATACCTGT 59.091 52.381 0.00 0.00 0.00 4.00
1235 1265 4.650377 GGGATGCTGGATCGGGGC 62.650 72.222 2.99 0.00 30.87 5.80
1236 1266 3.170672 TGGGATGCTGGATCGGGG 61.171 66.667 2.99 0.00 30.87 5.73
1247 1277 0.809385 ACACGACGTAGACTGGGATG 59.191 55.000 0.00 0.00 0.00 3.51
1326 1356 9.607988 TGTTATGACAAGTACCCATATTAACAG 57.392 33.333 0.00 0.00 31.49 3.16
1495 1525 2.995466 TTTTCTGCCGATCAGCAAAG 57.005 45.000 4.92 0.00 43.52 2.77
1632 1666 1.971357 AGGGGCGTACCAGATCATAAG 59.029 52.381 0.00 0.00 42.91 1.73
1669 1706 3.135225 TCAATTATTCCCGCCATACACG 58.865 45.455 0.00 0.00 0.00 4.49
1962 2089 2.092914 AGAAGAAGGTAAAGCCCGATGG 60.093 50.000 0.00 0.00 38.26 3.51
2000 2127 3.456644 TGTTGACACTAAAGGAGGGTTCA 59.543 43.478 0.00 0.00 44.07 3.18
2132 2259 4.232091 AGTGGAGTCTAAGGGAAGAAACA 58.768 43.478 0.00 0.00 0.00 2.83
2146 2273 8.850007 AAAAGGAAAAGATAGTAAGTGGAGTC 57.150 34.615 0.00 0.00 0.00 3.36
2685 2838 5.128205 TGGAATCATAGATGGCAAACTCAG 58.872 41.667 0.00 0.00 0.00 3.35
2694 2847 6.780457 ACCTTTTGTTGGAATCATAGATGG 57.220 37.500 0.00 0.00 0.00 3.51
2855 3011 2.189676 TCCTTGTAATACCCGCCTTGA 58.810 47.619 0.00 0.00 0.00 3.02
2933 3089 2.596904 TTAGGATGGTGTAGAAGCGC 57.403 50.000 0.00 0.00 0.00 5.92
3013 3169 1.477700 TCTGGGCATGCAAAATACTGC 59.522 47.619 21.36 0.00 42.95 4.40
3016 3172 5.520376 ACTTATCTGGGCATGCAAAATAC 57.480 39.130 21.36 0.00 0.00 1.89
3056 3212 2.029918 CCTTAAAACCTGTGAAGCCTGC 60.030 50.000 0.00 0.00 0.00 4.85
3098 3254 1.140312 AGTTTGGACCTGGAAGCTGA 58.860 50.000 0.00 0.00 0.00 4.26
3251 3407 2.092429 TGGTGGAAGAGTGGCCATATTC 60.092 50.000 9.72 13.63 36.41 1.75
3383 3540 0.318762 ACTCCTCGAGGAACTGCAAC 59.681 55.000 32.94 0.00 44.91 4.17
3439 3596 7.356719 CGAACGAAAACAAGAGTGAAAATCATG 60.357 37.037 0.00 0.00 35.55 3.07
3566 3732 3.394606 ACAAGGTCCACCAGTTCAACTAT 59.605 43.478 0.00 0.00 38.89 2.12
3591 3757 5.394553 GCAAGGAGCTTAATAAACCTGCAAT 60.395 40.000 0.00 0.00 41.15 3.56
3592 3758 4.082245 GCAAGGAGCTTAATAAACCTGCAA 60.082 41.667 0.00 0.00 41.15 4.08
3700 3866 6.953101 TGATAGGTGAAATGTAAGCTACCAA 58.047 36.000 1.12 0.00 0.00 3.67
3727 3893 4.465886 AGAGGTAGTGTAGTAGCCAGATG 58.534 47.826 0.00 0.00 0.00 2.90
3730 3902 4.159244 AGAGAGGTAGTGTAGTAGCCAG 57.841 50.000 0.00 0.00 0.00 4.85
3736 3908 7.836479 ACTGTTAAAAGAGAGGTAGTGTAGT 57.164 36.000 0.00 0.00 0.00 2.73
3740 3912 5.992217 AGCAACTGTTAAAAGAGAGGTAGTG 59.008 40.000 0.00 0.00 0.00 2.74
3742 3914 7.355778 CAAAGCAACTGTTAAAAGAGAGGTAG 58.644 38.462 0.00 0.00 0.00 3.18
3748 3986 5.456822 GTGAGCAAAGCAACTGTTAAAAGAG 59.543 40.000 0.00 0.00 0.00 2.85
3753 3991 3.066621 CCTGTGAGCAAAGCAACTGTTAA 59.933 43.478 0.00 0.00 0.00 2.01
3834 4072 9.690913 AACAAATCATATACTATATGCCTGCAT 57.309 29.630 9.87 9.87 40.19 3.96
3835 4073 8.949177 CAACAAATCATATACTATATGCCTGCA 58.051 33.333 10.24 0.00 0.00 4.41
3836 4074 8.950210 ACAACAAATCATATACTATATGCCTGC 58.050 33.333 10.24 0.00 0.00 4.85
3879 4117 6.128007 CCACAAAGACTCTTGTTACAAAGTGT 60.128 38.462 14.24 9.60 37.43 3.55
4054 4293 0.539986 AATGCCGTACCCGATCAGTT 59.460 50.000 0.00 0.00 35.63 3.16
4074 4313 0.034616 AGTGTTCAGTGCTGAGAGCC 59.965 55.000 1.98 0.00 41.51 4.70
4094 4333 8.514594 TCGATAAAATCAACAGCTCAAAAATCT 58.485 29.630 0.00 0.00 0.00 2.40
4095 4334 8.673626 TCGATAAAATCAACAGCTCAAAAATC 57.326 30.769 0.00 0.00 0.00 2.17
4097 4336 8.514594 AGATCGATAAAATCAACAGCTCAAAAA 58.485 29.630 0.00 0.00 0.00 1.94
4098 4337 8.044060 AGATCGATAAAATCAACAGCTCAAAA 57.956 30.769 0.00 0.00 0.00 2.44
4099 4338 7.615582 AGATCGATAAAATCAACAGCTCAAA 57.384 32.000 0.00 0.00 0.00 2.69
4156 4420 4.062293 AGCGCAACAGATAAACAACAGTA 58.938 39.130 11.47 0.00 0.00 2.74
4162 4432 3.187637 GGTACAAGCGCAACAGATAAACA 59.812 43.478 11.47 0.00 0.00 2.83
4166 4436 1.276705 TGGGTACAAGCGCAACAGATA 59.723 47.619 11.47 0.00 0.00 1.98
4168 4438 0.036164 ATGGGTACAAGCGCAACAGA 59.964 50.000 11.47 0.00 35.01 3.41
4170 4440 1.240641 CCATGGGTACAAGCGCAACA 61.241 55.000 11.47 0.00 35.01 3.33
4171 4441 0.958382 TCCATGGGTACAAGCGCAAC 60.958 55.000 13.02 1.43 35.01 4.17
4172 4442 0.676466 CTCCATGGGTACAAGCGCAA 60.676 55.000 13.02 0.00 35.01 4.85
4175 4445 1.819632 GCCTCCATGGGTACAAGCG 60.820 63.158 13.02 0.00 36.00 4.68
4201 4471 2.029828 CGACAGAAAGAGTACAGGCAGT 60.030 50.000 0.00 0.00 0.00 4.40
4214 4484 2.714259 CCAAAGGTGGCGACAGAAA 58.286 52.632 0.00 0.00 44.46 2.52
4215 4485 4.473643 CCAAAGGTGGCGACAGAA 57.526 55.556 0.00 0.00 44.46 3.02
4224 4494 2.954753 GACGCGTCAGCCAAAGGTG 61.955 63.158 33.09 0.00 43.07 4.00
4225 4495 2.665185 GACGCGTCAGCCAAAGGT 60.665 61.111 33.09 0.00 41.18 3.50
4227 4497 1.891060 GACAGACGCGTCAGCCAAAG 61.891 60.000 37.85 20.42 41.18 2.77
4336 4616 0.877071 ACTGGAAAAGCGCTCATGTG 59.123 50.000 12.06 2.30 0.00 3.21
4356 4636 3.361977 CAAAACTCCCGGTGGCGG 61.362 66.667 0.00 0.00 0.00 6.13
4357 4637 2.593436 ACAAAACTCCCGGTGGCG 60.593 61.111 0.00 0.00 0.00 5.69
4358 4638 2.265904 GGACAAAACTCCCGGTGGC 61.266 63.158 0.00 0.00 0.00 5.01
4450 4733 2.184579 GGGGCTTCTTCGGTCTCG 59.815 66.667 0.00 0.00 37.82 4.04
4451 4734 1.079057 GTGGGGCTTCTTCGGTCTC 60.079 63.158 0.00 0.00 0.00 3.36
4452 4735 2.593956 GGTGGGGCTTCTTCGGTCT 61.594 63.158 0.00 0.00 0.00 3.85
4453 4736 2.046217 GGTGGGGCTTCTTCGGTC 60.046 66.667 0.00 0.00 0.00 4.79
4499 4807 5.004922 TCAATCTTTTTGGTGGTGTTGTC 57.995 39.130 0.00 0.00 0.00 3.18
4517 4825 5.263599 ACATGTACACCCACATTCATCAAT 58.736 37.500 0.00 0.00 37.02 2.57
4518 4826 4.661222 ACATGTACACCCACATTCATCAA 58.339 39.130 0.00 0.00 37.02 2.57
4570 4882 9.567848 GGTGATTCGCAAAAAGAAAATAGAATA 57.432 29.630 0.00 0.00 0.00 1.75
4571 4883 8.087750 TGGTGATTCGCAAAAAGAAAATAGAAT 58.912 29.630 0.00 0.00 0.00 2.40
4572 4884 7.429633 TGGTGATTCGCAAAAAGAAAATAGAA 58.570 30.769 0.00 0.00 0.00 2.10
4573 4885 6.976088 TGGTGATTCGCAAAAAGAAAATAGA 58.024 32.000 0.00 0.00 0.00 1.98
4574 4886 6.183360 GCTGGTGATTCGCAAAAAGAAAATAG 60.183 38.462 0.00 0.00 0.00 1.73
4575 4887 5.633182 GCTGGTGATTCGCAAAAAGAAAATA 59.367 36.000 0.00 0.00 0.00 1.40
4576 4888 4.448732 GCTGGTGATTCGCAAAAAGAAAAT 59.551 37.500 0.00 0.00 0.00 1.82
4577 4889 3.801594 GCTGGTGATTCGCAAAAAGAAAA 59.198 39.130 0.00 0.00 0.00 2.29
4578 4890 3.068024 AGCTGGTGATTCGCAAAAAGAAA 59.932 39.130 0.00 0.00 0.00 2.52
4579 4891 2.622942 AGCTGGTGATTCGCAAAAAGAA 59.377 40.909 0.00 0.00 0.00 2.52
4580 4892 2.229792 AGCTGGTGATTCGCAAAAAGA 58.770 42.857 0.00 0.00 0.00 2.52
4581 4893 2.712057 AGCTGGTGATTCGCAAAAAG 57.288 45.000 0.00 0.00 0.00 2.27
4582 4894 4.576216 TTAAGCTGGTGATTCGCAAAAA 57.424 36.364 0.00 0.00 0.00 1.94
4583 4895 4.782019 ATTAAGCTGGTGATTCGCAAAA 57.218 36.364 0.00 0.00 0.00 2.44
4584 4896 4.458989 AGAATTAAGCTGGTGATTCGCAAA 59.541 37.500 0.00 0.00 34.54 3.68
4585 4897 4.009675 AGAATTAAGCTGGTGATTCGCAA 58.990 39.130 0.00 0.00 34.54 4.85
4586 4898 3.609853 AGAATTAAGCTGGTGATTCGCA 58.390 40.909 0.00 0.00 34.54 5.10
4587 4899 5.466728 TCATAGAATTAAGCTGGTGATTCGC 59.533 40.000 0.00 0.00 34.54 4.70
4588 4900 7.386025 TGATCATAGAATTAAGCTGGTGATTCG 59.614 37.037 0.00 0.00 34.54 3.34
4589 4901 8.502387 GTGATCATAGAATTAAGCTGGTGATTC 58.498 37.037 0.00 7.67 0.00 2.52
4590 4902 7.446625 GGTGATCATAGAATTAAGCTGGTGATT 59.553 37.037 0.00 0.00 0.00 2.57
4591 4903 6.939163 GGTGATCATAGAATTAAGCTGGTGAT 59.061 38.462 0.00 8.94 0.00 3.06
4592 4904 6.100279 AGGTGATCATAGAATTAAGCTGGTGA 59.900 38.462 0.00 0.00 0.00 4.02
4593 4905 6.294473 AGGTGATCATAGAATTAAGCTGGTG 58.706 40.000 0.00 0.00 0.00 4.17
4628 4940 0.458543 CGGCCGGAGAATCGATATGG 60.459 60.000 20.10 0.00 34.37 2.74
4644 4956 3.667429 GACAAGCATGAACGGCGGC 62.667 63.158 13.24 4.07 36.08 6.53
4646 4958 2.096406 CGACAAGCATGAACGGCG 59.904 61.111 4.80 4.80 36.08 6.46
4650 4962 1.154413 CCACGCGACAAGCATGAAC 60.154 57.895 15.93 0.00 42.45 3.18
4651 4963 2.965147 GCCACGCGACAAGCATGAA 61.965 57.895 15.93 0.00 42.45 2.57
4652 4964 3.422303 GCCACGCGACAAGCATGA 61.422 61.111 15.93 0.00 42.45 3.07
4814 5142 3.474007 CGGCCACACGCTACTATAG 57.526 57.895 2.24 0.00 37.74 1.31
4878 5217 2.042741 CAATGGGGAGCATGGGCA 60.043 61.111 0.00 0.00 44.61 5.36
4887 5226 0.893270 CACGCAAACTCCAATGGGGA 60.893 55.000 5.97 0.00 45.89 4.81
4897 5236 1.880027 GAGGGAAATCACACGCAAACT 59.120 47.619 0.00 0.00 0.00 2.66
4934 5277 3.340814 AGCACGAAATGGTGAATCTCT 57.659 42.857 0.00 0.00 40.38 3.10
4984 5327 0.607620 GAGACCTGAGAAGCAGCAGT 59.392 55.000 0.00 0.00 43.50 4.40
4995 5338 1.372683 GCTGGTTGCTGAGACCTGA 59.627 57.895 9.73 0.00 38.09 3.86
5005 5348 1.135859 CATCGAAACAGAGCTGGTTGC 60.136 52.381 5.36 0.00 41.20 4.17
5006 5349 2.096069 CACATCGAAACAGAGCTGGTTG 60.096 50.000 5.36 0.00 41.20 3.77
5007 5350 2.146342 CACATCGAAACAGAGCTGGTT 58.854 47.619 0.00 0.00 44.30 3.67
5008 5351 1.070758 ACACATCGAAACAGAGCTGGT 59.929 47.619 0.00 0.00 34.19 4.00
5009 5352 1.462283 CACACATCGAAACAGAGCTGG 59.538 52.381 0.00 0.00 34.19 4.85
5010 5353 2.138320 ACACACATCGAAACAGAGCTG 58.862 47.619 0.00 0.00 0.00 4.24
5011 5354 2.533266 ACACACATCGAAACAGAGCT 57.467 45.000 0.00 0.00 0.00 4.09
5012 5355 7.875316 ATATATACACACATCGAAACAGAGC 57.125 36.000 0.00 0.00 0.00 4.09
5013 5356 8.703336 CCAATATATACACACATCGAAACAGAG 58.297 37.037 0.00 0.00 0.00 3.35
5014 5357 8.201464 ACCAATATATACACACATCGAAACAGA 58.799 33.333 0.00 0.00 0.00 3.41
5015 5358 8.365399 ACCAATATATACACACATCGAAACAG 57.635 34.615 0.00 0.00 0.00 3.16
5016 5359 9.471084 CTACCAATATATACACACATCGAAACA 57.529 33.333 0.00 0.00 0.00 2.83
5017 5360 8.922676 CCTACCAATATATACACACATCGAAAC 58.077 37.037 0.00 0.00 0.00 2.78
5018 5361 8.092068 CCCTACCAATATATACACACATCGAAA 58.908 37.037 0.00 0.00 0.00 3.46
5019 5362 7.233962 ACCCTACCAATATATACACACATCGAA 59.766 37.037 0.00 0.00 0.00 3.71
5020 5363 6.722590 ACCCTACCAATATATACACACATCGA 59.277 38.462 0.00 0.00 0.00 3.59
5021 5364 6.931838 ACCCTACCAATATATACACACATCG 58.068 40.000 0.00 0.00 0.00 3.84
5022 5365 9.569122 AAAACCCTACCAATATATACACACATC 57.431 33.333 0.00 0.00 0.00 3.06
5023 5366 9.569122 GAAAACCCTACCAATATATACACACAT 57.431 33.333 0.00 0.00 0.00 3.21
5024 5367 7.711772 CGAAAACCCTACCAATATATACACACA 59.288 37.037 0.00 0.00 0.00 3.72
5025 5368 7.307573 GCGAAAACCCTACCAATATATACACAC 60.308 40.741 0.00 0.00 0.00 3.82
5026 5369 6.707161 GCGAAAACCCTACCAATATATACACA 59.293 38.462 0.00 0.00 0.00 3.72
5027 5370 6.932960 AGCGAAAACCCTACCAATATATACAC 59.067 38.462 0.00 0.00 0.00 2.90
5028 5371 7.069877 AGCGAAAACCCTACCAATATATACA 57.930 36.000 0.00 0.00 0.00 2.29
5029 5372 7.876582 AGAAGCGAAAACCCTACCAATATATAC 59.123 37.037 0.00 0.00 0.00 1.47
5030 5373 7.876068 CAGAAGCGAAAACCCTACCAATATATA 59.124 37.037 0.00 0.00 0.00 0.86
5031 5374 6.710744 CAGAAGCGAAAACCCTACCAATATAT 59.289 38.462 0.00 0.00 0.00 0.86
5032 5375 6.053005 CAGAAGCGAAAACCCTACCAATATA 58.947 40.000 0.00 0.00 0.00 0.86
5035 5378 3.081804 CAGAAGCGAAAACCCTACCAAT 58.918 45.455 0.00 0.00 0.00 3.16
5081 5440 0.670546 CGTTTGTGCGTCCTCTCCAT 60.671 55.000 0.00 0.00 0.00 3.41
5091 5450 2.366584 CCTTGCATGCGTTTGTGCG 61.367 57.895 14.09 0.00 44.11 5.34
5092 5451 2.023223 CCCTTGCATGCGTTTGTGC 61.023 57.895 14.09 0.00 41.61 4.57
5093 5452 0.595588 TACCCTTGCATGCGTTTGTG 59.404 50.000 14.09 1.71 0.00 3.33
5095 5454 0.109319 GGTACCCTTGCATGCGTTTG 60.109 55.000 14.09 4.36 0.00 2.93
5096 5455 0.251165 AGGTACCCTTGCATGCGTTT 60.251 50.000 14.09 0.00 0.00 3.60
5097 5456 0.676782 GAGGTACCCTTGCATGCGTT 60.677 55.000 14.09 0.00 31.76 4.84
5098 5457 1.078426 GAGGTACCCTTGCATGCGT 60.078 57.895 14.09 7.21 31.76 5.24
5099 5458 0.811616 GAGAGGTACCCTTGCATGCG 60.812 60.000 14.09 0.35 31.76 4.73
5100 5459 0.253044 TGAGAGGTACCCTTGCATGC 59.747 55.000 11.82 11.82 31.76 4.06
5162 5522 3.433615 GCCAGCTATAAATGCTAACGAGG 59.566 47.826 0.00 0.00 38.92 4.63
5169 5529 2.283145 CTGGGCCAGCTATAAATGCT 57.717 50.000 22.68 0.00 42.06 3.79


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

AutoCloner maintained by Alex Coulton.