Multiple sequence alignment - TraesCS1D01G221300

Loading Multiple Alignment...

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 TraesCS1D01G221300 chr1D 100.000 5117 0 0 1 5117 309077862 309072746 0.000000e+00 9450.0
1 TraesCS1D01G221300 chr1B 92.084 4169 238 42 178 4294 418809375 418805247 0.000000e+00 5786.0
2 TraesCS1D01G221300 chr1B 87.037 540 47 13 4594 5117 418804692 418804160 5.710000e-164 588.0
3 TraesCS1D01G221300 chr1B 87.781 311 16 4 4293 4595 418805071 418804775 1.360000e-90 344.0
4 TraesCS1D01G221300 chr1B 95.028 181 9 0 17 197 418809670 418809490 8.390000e-73 285.0
5 TraesCS1D01G221300 chr1B 92.727 55 4 0 2189 2243 665275919 665275973 4.250000e-11 80.5
6 TraesCS1D01G221300 chr1A 93.821 3156 152 20 1 3129 388838136 388834997 0.000000e+00 4708.0
7 TraesCS1D01G221300 chr1A 86.076 2054 164 51 3128 5100 388834915 388832903 0.000000e+00 2097.0
8 TraesCS1D01G221300 chr1A 84.354 294 40 6 4827 5117 482220722 482220432 3.020000e-72 283.0
9 TraesCS1D01G221300 chr1A 84.589 292 36 7 4829 5117 161229192 161229477 1.080000e-71 281.0
10 TraesCS1D01G221300 chr1A 77.778 243 31 10 4518 4745 534763008 534762774 1.500000e-25 128.0
11 TraesCS1D01G221300 chr1A 86.905 84 11 0 4642 4725 497195302 497195385 1.520000e-15 95.3
12 TraesCS1D01G221300 chr2B 86.348 293 31 7 4829 5117 494401711 494401998 1.380000e-80 311.0
13 TraesCS1D01G221300 chr2B 88.608 79 8 1 4518 4595 216292159 216292081 1.520000e-15 95.3
14 TraesCS1D01G221300 chr2D 85.959 292 32 8 4830 5117 422089537 422089823 2.320000e-78 303.0
15 TraesCS1D01G221300 chr2D 82.258 124 15 2 4518 4640 601494380 601494263 3.260000e-17 100.0
16 TraesCS1D01G221300 chr4D 85.522 297 34 8 4826 5117 98888413 98888121 8.330000e-78 302.0
17 TraesCS1D01G221300 chr7D 85.467 289 37 5 4826 5111 274697437 274697723 3.870000e-76 296.0
18 TraesCS1D01G221300 chr4B 84.536 291 39 5 4830 5117 626075716 626075429 3.020000e-72 283.0
19 TraesCS1D01G221300 chr3B 76.886 411 72 16 1848 2243 501420263 501420665 1.440000e-50 211.0
20 TraesCS1D01G221300 chr2A 78.000 250 32 18 4518 4747 177667351 177667597 8.940000e-28 135.0
21 TraesCS1D01G221300 chr6B 91.954 87 7 0 4642 4728 636485975 636485889 6.960000e-24 122.0
22 TraesCS1D01G221300 chr5D 92.593 81 6 0 4648 4728 5560999 5560919 3.240000e-22 117.0
23 TraesCS1D01G221300 chr3A 86.792 106 13 1 4642 4747 241923828 241923932 3.240000e-22 117.0
24 TraesCS1D01G221300 chr3A 76.957 230 25 6 4518 4725 137605081 137605304 7.010000e-19 106.0
25 TraesCS1D01G221300 chr3A 87.805 82 9 1 4648 4729 108744112 108744192 1.520000e-15 95.3
26 TraesCS1D01G221300 chr3A 87.013 77 9 1 4518 4593 745813116 745813192 9.130000e-13 86.1
27 TraesCS1D01G221300 chr5A 89.888 89 8 1 4642 4729 6629112 6629200 4.190000e-21 113.0
28 TraesCS1D01G221300 chr3D 89.024 82 9 0 4648 4729 260598816 260598897 9.060000e-18 102.0
29 TraesCS1D01G221300 chr6D 88.608 79 8 1 4518 4595 272386560 272386638 1.520000e-15 95.3
30 TraesCS1D01G221300 chr7B 80.645 124 17 2 4518 4640 268102268 268102385 7.060000e-14 89.8
31 TraesCS1D01G221300 chrUn 91.667 60 4 1 4667 4725 1084216 1084157 1.180000e-11 82.4


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 TraesCS1D01G221300 chr1D 309072746 309077862 5116 True 9450.00 9450 100.0000 1 5117 1 chr1D.!!$R1 5116
1 TraesCS1D01G221300 chr1B 418804160 418809670 5510 True 1750.75 5786 90.4825 17 5117 4 chr1B.!!$R1 5100
2 TraesCS1D01G221300 chr1A 388832903 388838136 5233 True 3402.50 4708 89.9485 1 5100 2 chr1A.!!$R3 5099

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
880 1023 0.549950 CTGATCCTGGTTGGGCTGAT 59.450 55.000 0.0 0.0 36.20 2.90 F
1959 2114 1.250840 GCAGGAAACCCGCAAAGGAT 61.251 55.000 0.0 0.0 45.00 3.24 F
2660 2822 1.458486 CTGCCAGGGTGGGTTTGTA 59.542 57.895 0.0 0.0 38.19 2.41 F
3736 3989 0.041982 GGTCCCTCCTCTCTCCTGTT 59.958 60.000 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 2692 0.188342 AAGTGTTCCATGGGCCTGTT 59.812 50.0 13.02 0.0 0.00 3.16 R
3001 3168 0.242017 GGGTGCTGCTCAACACATTC 59.758 55.0 0.00 0.0 38.57 2.67 R
4081 4357 0.102120 ACGACATAGCTCTGCTCAGC 59.898 55.0 0.00 0.0 40.44 4.26 R
4819 5392 2.954318 CCAAAGGAGGCCTAATCATGTG 59.046 50.0 4.42 0.0 31.13 3.21 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
52 53 2.543848 TCTGAACTACGCAAGCAACAAG 59.456 45.455 0.00 0.00 45.62 3.16
142 143 4.305539 TCATTCTCAAATCCCAAGCTCA 57.694 40.909 0.00 0.00 0.00 4.26
265 401 4.523943 TGAACTAAAGAAGCATGCCACAAT 59.476 37.500 15.66 0.72 0.00 2.71
272 408 4.018490 AGAAGCATGCCACAATCATGTTA 58.982 39.130 15.66 0.00 42.34 2.41
276 412 6.659745 AGCATGCCACAATCATGTTATATT 57.340 33.333 15.66 0.00 42.34 1.28
278 414 6.492429 AGCATGCCACAATCATGTTATATTCT 59.508 34.615 15.66 0.00 42.34 2.40
303 439 9.522804 CTAGGTCTACAGAAAATATCACAGAAC 57.477 37.037 0.00 0.00 0.00 3.01
304 440 7.907389 AGGTCTACAGAAAATATCACAGAACA 58.093 34.615 0.00 0.00 0.00 3.18
306 442 9.167311 GGTCTACAGAAAATATCACAGAACAAT 57.833 33.333 0.00 0.00 0.00 2.71
329 466 9.357652 CAATTTGTAAAATCAACCATGGTAGAG 57.642 33.333 20.12 11.64 0.00 2.43
342 479 1.687123 TGGTAGAGCTATTTCGCCTCC 59.313 52.381 0.00 0.00 0.00 4.30
354 491 1.741401 CGCCTCCATCGTGCTCAAA 60.741 57.895 0.00 0.00 0.00 2.69
440 577 3.567585 TCATCACAAAATCAGGCACGAAA 59.432 39.130 0.00 0.00 0.00 3.46
448 585 0.948623 TCAGGCACGAAACACATCGG 60.949 55.000 1.59 0.00 46.82 4.18
458 595 2.109425 AACACATCGGAAACTAGGCC 57.891 50.000 0.00 0.00 0.00 5.19
520 657 1.269723 TGTGACAGGACGTAGCAGAAG 59.730 52.381 0.00 0.00 0.00 2.85
582 721 2.096248 AGGGACTTCGTGTCTGAGATC 58.904 52.381 10.13 0.00 44.74 2.75
583 722 1.202200 GGGACTTCGTGTCTGAGATCG 60.202 57.143 10.13 4.19 44.74 3.69
592 731 1.285078 TGTCTGAGATCGGGAGAGGAA 59.715 52.381 0.00 0.00 45.48 3.36
598 737 1.566703 AGATCGGGAGAGGAAGAGTCA 59.433 52.381 0.00 0.00 45.48 3.41
603 742 1.687996 GGGAGAGGAAGAGTCAGGAGG 60.688 61.905 0.00 0.00 0.00 4.30
862 1005 6.365520 CCCAATATAGTCTTTAACTTGGGCT 58.634 40.000 4.64 0.00 40.66 5.19
880 1023 0.549950 CTGATCCTGGTTGGGCTGAT 59.450 55.000 0.00 0.00 36.20 2.90
916 1060 3.884774 TGGGCCAACCGCTCTGTT 61.885 61.111 2.13 0.00 44.64 3.16
1251 1396 4.250464 CTCGCAATAACACCCTAGACAAA 58.750 43.478 0.00 0.00 0.00 2.83
1737 1892 9.998106 ATGTGGGTATACTACTTATCACAAATC 57.002 33.333 2.25 0.00 37.42 2.17
1835 1990 5.534207 TTTCACAAGTTTTGCATCCTCAT 57.466 34.783 0.00 0.00 0.00 2.90
1840 1995 7.669427 TCACAAGTTTTGCATCCTCATTTTAT 58.331 30.769 0.00 0.00 0.00 1.40
1935 2090 3.988976 AGTATCAGCTCTCTTTTGGCA 57.011 42.857 0.00 0.00 0.00 4.92
1959 2114 1.250840 GCAGGAAACCCGCAAAGGAT 61.251 55.000 0.00 0.00 45.00 3.24
2007 2162 4.213694 GCTCTGAATCATGCTTCGATCATT 59.786 41.667 4.92 0.00 0.00 2.57
2106 2262 8.421249 TTGATTTCCTCCTGTATGTTTTTCAT 57.579 30.769 0.00 0.00 40.25 2.57
2109 2265 9.358872 GATTTCCTCCTGTATGTTTTTCATTTC 57.641 33.333 0.00 0.00 37.91 2.17
2168 2324 5.664457 TGTAACCATGAACTGAGATAGCTG 58.336 41.667 0.00 0.00 0.00 4.24
2170 2326 2.502947 ACCATGAACTGAGATAGCTGCA 59.497 45.455 1.02 0.00 0.00 4.41
2180 2336 8.915057 AACTGAGATAGCTGCAAATACAATAT 57.085 30.769 1.02 0.00 0.00 1.28
2211 2367 2.012673 GCAGGTCCAGTTGCTCAATAG 58.987 52.381 0.00 0.00 37.35 1.73
2272 2428 9.748708 TTGTCAAATTTAATTTCCTCACTCAAG 57.251 29.630 0.00 0.00 0.00 3.02
2316 2475 1.936547 GTAGTAGAGGCATGCTTGTGC 59.063 52.381 18.92 12.58 44.31 4.57
2344 2506 3.770263 ATGTCGCACCAAATTCAGATG 57.230 42.857 0.00 0.00 0.00 2.90
2467 2629 9.173021 TGGTCATCGATGATGTTAGTAATTTTT 57.827 29.630 29.53 0.00 40.55 1.94
2518 2680 8.154649 AGTTTCTTAGTGATCGATTTTGTTGT 57.845 30.769 0.00 0.00 0.00 3.32
2530 2692 6.800543 TCGATTTTGTTGTGATTTTCCTTGA 58.199 32.000 0.00 0.00 0.00 3.02
2588 2750 2.125512 GGTGTACCCGAGCTGCTG 60.126 66.667 7.01 0.00 0.00 4.41
2621 2783 4.766891 AGTGGAATTGACATAAGTGTTGGG 59.233 41.667 0.00 0.00 39.09 4.12
2660 2822 1.458486 CTGCCAGGGTGGGTTTGTA 59.542 57.895 0.00 0.00 38.19 2.41
2673 2835 2.423538 GGGTTTGTAGCATGCAGGTAAG 59.576 50.000 21.98 0.00 30.87 2.34
2695 2857 4.772624 AGCAGACACTTAGATCAGGTTGTA 59.227 41.667 0.00 0.00 0.00 2.41
2699 2861 7.251994 CAGACACTTAGATCAGGTTGTAGTAC 58.748 42.308 0.00 0.00 0.00 2.73
2702 2864 6.093771 ACACTTAGATCAGGTTGTAGTACGAG 59.906 42.308 0.00 0.00 0.00 4.18
2740 2902 6.651643 TGTACATTGCGGTACTGATTTTAGTT 59.348 34.615 5.68 0.00 43.17 2.24
2741 2903 6.569179 ACATTGCGGTACTGATTTTAGTTT 57.431 33.333 5.68 0.00 32.19 2.66
2790 2956 4.774124 TCAAGGTTCTGGATCATGTCATC 58.226 43.478 0.00 0.00 0.00 2.92
2862 3028 8.463930 TTCAATGAACAGGAGATAACTTGTTT 57.536 30.769 0.00 0.00 39.49 2.83
2870 3036 6.088824 CAGGAGATAACTTGTTTTGCACATC 58.911 40.000 0.00 0.00 34.43 3.06
2909 3075 2.097110 TGGTACTGGACACTGGACTT 57.903 50.000 0.00 0.00 30.67 3.01
2910 3076 1.968493 TGGTACTGGACACTGGACTTC 59.032 52.381 0.00 0.00 30.67 3.01
3022 3189 3.357079 GTGTTGAGCAGCACCCGG 61.357 66.667 6.23 0.00 36.68 5.73
3124 3291 9.174166 GTTCAAGGTAATATTCACAACATACCT 57.826 33.333 0.00 0.00 43.68 3.08
3193 3443 7.199766 GTCTGTCATTGTTGTGTTCCATTTAA 58.800 34.615 0.00 0.00 0.00 1.52
3196 3446 7.720442 TGTCATTGTTGTGTTCCATTTAATGA 58.280 30.769 6.50 0.00 32.68 2.57
3202 3452 5.885230 TGTGTTCCATTTAATGAGCTGAG 57.115 39.130 6.50 0.00 0.00 3.35
3208 3458 4.018506 TCCATTTAATGAGCTGAGGTCCAA 60.019 41.667 9.40 0.00 0.00 3.53
3209 3459 4.891756 CCATTTAATGAGCTGAGGTCCAAT 59.108 41.667 9.40 0.09 0.00 3.16
3210 3460 6.064060 CCATTTAATGAGCTGAGGTCCAATA 58.936 40.000 9.40 0.00 0.00 1.90
3211 3461 6.718454 CCATTTAATGAGCTGAGGTCCAATAT 59.282 38.462 9.40 0.00 0.00 1.28
3212 3462 7.232127 CCATTTAATGAGCTGAGGTCCAATATT 59.768 37.037 9.40 4.85 0.00 1.28
3213 3463 8.636213 CATTTAATGAGCTGAGGTCCAATATTT 58.364 33.333 9.40 0.00 0.00 1.40
3214 3464 9.866655 ATTTAATGAGCTGAGGTCCAATATTTA 57.133 29.630 9.40 0.00 0.00 1.40
3215 3465 9.866655 TTTAATGAGCTGAGGTCCAATATTTAT 57.133 29.630 9.40 0.00 0.00 1.40
3216 3466 9.866655 TTAATGAGCTGAGGTCCAATATTTATT 57.133 29.630 9.40 2.45 0.00 1.40
3217 3467 8.773033 AATGAGCTGAGGTCCAATATTTATTT 57.227 30.769 9.40 0.00 0.00 1.40
3218 3468 7.807977 TGAGCTGAGGTCCAATATTTATTTC 57.192 36.000 9.40 0.00 0.00 2.17
3219 3469 7.577303 TGAGCTGAGGTCCAATATTTATTTCT 58.423 34.615 9.40 0.00 0.00 2.52
3220 3470 8.713971 TGAGCTGAGGTCCAATATTTATTTCTA 58.286 33.333 9.40 0.00 0.00 2.10
3221 3471 9.732130 GAGCTGAGGTCCAATATTTATTTCTAT 57.268 33.333 0.00 0.00 0.00 1.98
3222 3472 9.732130 AGCTGAGGTCCAATATTTATTTCTATC 57.268 33.333 0.00 0.00 0.00 2.08
3223 3473 9.507329 GCTGAGGTCCAATATTTATTTCTATCA 57.493 33.333 0.00 0.00 0.00 2.15
3306 3556 7.552687 TCACATTGGTCAGTAAGAATGATAACC 59.447 37.037 0.00 0.00 31.53 2.85
3309 3559 4.712829 TGGTCAGTAAGAATGATAACCGGA 59.287 41.667 9.46 0.00 0.00 5.14
3369 3619 4.037923 TCAGGGACTTGCATTTTTCTGAAC 59.962 41.667 6.98 0.00 34.60 3.18
3420 3670 2.253392 GCTGTTTTCTGATTCCAGCG 57.747 50.000 7.05 0.00 39.13 5.18
3435 3685 4.819761 GCGGCGCTCCATGTCTCA 62.820 66.667 26.86 0.00 0.00 3.27
3513 3763 8.560374 GCATCCTTGACTAAACTCAATATAACC 58.440 37.037 0.00 0.00 29.71 2.85
3609 3862 6.332630 CAATTTTATTTAGTGCCAGTCTGGG 58.667 40.000 20.72 2.60 38.19 4.45
3700 3953 1.004200 AATTCGACCACCCACCGTC 60.004 57.895 0.00 0.00 0.00 4.79
3728 3981 0.690411 CTCATGCAGGTCCCTCCTCT 60.690 60.000 0.00 0.00 46.24 3.69
3732 3985 1.760480 GCAGGTCCCTCCTCTCTCC 60.760 68.421 0.00 0.00 46.24 3.71
3734 3987 0.396974 CAGGTCCCTCCTCTCTCCTG 60.397 65.000 0.00 0.00 46.24 3.86
3736 3989 0.041982 GGTCCCTCCTCTCTCCTGTT 59.958 60.000 0.00 0.00 0.00 3.16
3761 4014 3.940209 TCAATTTGCAATCCACTGTCC 57.060 42.857 0.00 0.00 0.00 4.02
3762 4015 2.228582 TCAATTTGCAATCCACTGTCCG 59.771 45.455 0.00 0.00 0.00 4.79
3784 4037 4.935205 CGGTCATGAACTTCACCAATCTAA 59.065 41.667 9.52 0.00 0.00 2.10
3796 4049 3.320541 CACCAATCTAAAACCTGCAACCA 59.679 43.478 0.00 0.00 0.00 3.67
3797 4050 3.320826 ACCAATCTAAAACCTGCAACCAC 59.679 43.478 0.00 0.00 0.00 4.16
3823 4082 2.709213 ACTGGACTAGGACTGTACGAC 58.291 52.381 0.00 0.00 0.00 4.34
3824 4083 2.015587 CTGGACTAGGACTGTACGACC 58.984 57.143 0.00 0.00 0.00 4.79
3828 4087 3.341823 GACTAGGACTGTACGACCAAGA 58.658 50.000 0.00 0.00 0.00 3.02
3830 4089 2.289592 AGGACTGTACGACCAAGAGT 57.710 50.000 0.00 0.00 0.00 3.24
3831 4090 1.887198 AGGACTGTACGACCAAGAGTG 59.113 52.381 0.00 0.00 0.00 3.51
3886 4145 3.699779 TTTTGCGTGCACATCTTTGTA 57.300 38.095 18.64 0.00 33.76 2.41
3888 4147 5.363979 TTTTGCGTGCACATCTTTGTATA 57.636 34.783 18.64 0.00 33.76 1.47
3889 4148 4.598406 TTGCGTGCACATCTTTGTATAG 57.402 40.909 18.64 0.00 33.76 1.31
3914 4173 7.987458 AGATGAATTCCTGCTCGATTTTAGTAA 59.013 33.333 2.27 0.00 0.00 2.24
3916 4175 8.506168 TGAATTCCTGCTCGATTTTAGTAAAT 57.494 30.769 2.27 0.00 36.68 1.40
3979 4255 0.744414 TGGCAGGCTGCGAATAACTC 60.744 55.000 31.22 16.20 46.21 3.01
3999 4275 0.610174 TGAGTGCTTCTCATTCGCCT 59.390 50.000 7.81 0.00 46.77 5.52
4011 4287 3.608796 TCATTCGCCTGATGACATCAAA 58.391 40.909 18.49 10.57 39.11 2.69
4030 4306 4.819761 GGCTGGTCGATGCGCTCA 62.820 66.667 9.73 0.00 0.00 4.26
4031 4307 2.815211 GCTGGTCGATGCGCTCAA 60.815 61.111 9.73 0.00 0.00 3.02
4046 4322 1.696336 GCTCAATCCCTGGCTATCTGA 59.304 52.381 0.00 0.00 0.00 3.27
4065 4341 1.610522 GACAAACATGCCAAGCAGAGT 59.389 47.619 0.00 0.00 43.65 3.24
4074 4350 1.333619 GCCAAGCAGAGTTTTGTCGAA 59.666 47.619 0.00 0.00 0.00 3.71
4081 4357 2.095567 CAGAGTTTTGTCGAAGGGCATG 60.096 50.000 0.00 0.00 0.00 4.06
4100 4376 0.102120 GCTGAGCAGAGCTATGTCGT 59.898 55.000 10.55 0.00 39.88 4.34
4101 4377 1.837648 CTGAGCAGAGCTATGTCGTG 58.162 55.000 10.55 0.96 39.88 4.35
4113 4389 3.119849 GCTATGTCGTGGCATCAAAACTT 60.120 43.478 0.00 0.00 33.92 2.66
4121 4397 3.429881 GTGGCATCAAAACTTTAAGCAGC 59.570 43.478 0.00 0.00 0.00 5.25
4178 4454 5.716228 TGTGCTGGATTACATTGGAGAAAAT 59.284 36.000 0.00 0.00 0.00 1.82
4184 4460 5.070847 GGATTACATTGGAGAAAATGCCCAT 59.929 40.000 0.00 0.00 40.54 4.00
4193 4470 3.575687 GAGAAAATGCCCATGGGGAATAG 59.424 47.826 30.57 3.78 41.15 1.73
4194 4471 1.720781 AAATGCCCATGGGGAATAGC 58.279 50.000 30.57 15.24 41.15 2.97
4206 4483 2.633481 GGGGAATAGCTCGGTAGATGTT 59.367 50.000 0.00 0.00 0.00 2.71
4210 4487 4.202121 GGAATAGCTCGGTAGATGTTGACA 60.202 45.833 0.00 0.00 0.00 3.58
4218 4495 5.917462 TCGGTAGATGTTGACATGATCATT 58.083 37.500 5.16 0.00 37.11 2.57
4219 4496 5.985530 TCGGTAGATGTTGACATGATCATTC 59.014 40.000 5.16 8.03 37.11 2.67
4220 4497 5.754890 CGGTAGATGTTGACATGATCATTCA 59.245 40.000 5.16 10.47 37.11 2.57
4226 4503 9.000486 AGATGTTGACATGATCATTCATATCAC 58.000 33.333 24.22 18.22 43.63 3.06
4227 4504 8.685838 ATGTTGACATGATCATTCATATCACA 57.314 30.769 5.16 13.22 43.63 3.58
4228 4505 7.922837 TGTTGACATGATCATTCATATCACAC 58.077 34.615 5.16 7.92 43.63 3.82
4229 4506 7.553402 TGTTGACATGATCATTCATATCACACA 59.447 33.333 5.16 10.01 43.63 3.72
4231 4508 6.201425 TGACATGATCATTCATATCACACACG 59.799 38.462 5.16 0.00 40.10 4.49
4232 4509 6.282930 ACATGATCATTCATATCACACACGA 58.717 36.000 5.16 0.00 40.70 4.35
4233 4510 6.201615 ACATGATCATTCATATCACACACGAC 59.798 38.462 5.16 0.00 40.70 4.34
4234 4511 5.659463 TGATCATTCATATCACACACGACA 58.341 37.500 0.00 0.00 0.00 4.35
4247 4529 4.031201 CACACACGACAAAAATGTTTCCAC 59.969 41.667 0.00 0.00 0.00 4.02
4256 4539 8.003224 CGACAAAAATGTTTCCACAATTGTATG 58.997 33.333 11.53 5.86 37.90 2.39
4266 4549 9.722056 GTTTCCACAATTGTATGTATGATCTTC 57.278 33.333 11.53 0.00 30.84 2.87
4323 4783 4.600062 AGACATGGATTTGGGTAGTTTCC 58.400 43.478 0.00 0.00 0.00 3.13
4340 4800 4.228210 AGTTTCCATATTGGGAGCTTGAGA 59.772 41.667 0.00 0.00 31.95 3.27
4393 4853 2.288273 GCCATGTAAGTAGAGGCTACCG 60.288 54.545 0.00 0.00 42.01 4.02
4422 4890 2.428890 TGGTAAACAACAGCCTGTTTGG 59.571 45.455 7.51 0.00 46.42 3.28
4424 4892 3.131400 GGTAAACAACAGCCTGTTTGGAA 59.869 43.478 7.51 0.00 46.42 3.53
4425 4893 4.202212 GGTAAACAACAGCCTGTTTGGAAT 60.202 41.667 7.51 0.00 46.42 3.01
4426 4894 3.457610 AACAACAGCCTGTTTGGAATG 57.542 42.857 7.51 0.00 38.77 2.67
4427 4895 1.069049 ACAACAGCCTGTTTGGAATGC 59.931 47.619 7.51 0.00 38.77 3.56
4428 4896 1.068895 CAACAGCCTGTTTGGAATGCA 59.931 47.619 7.51 0.00 38.77 3.96
4437 4905 5.600908 CTGTTTGGAATGCAGGAATTTTG 57.399 39.130 0.00 0.00 0.00 2.44
4438 4906 5.287674 TGTTTGGAATGCAGGAATTTTGA 57.712 34.783 0.00 0.00 0.00 2.69
4439 4907 5.299148 TGTTTGGAATGCAGGAATTTTGAG 58.701 37.500 0.00 0.00 0.00 3.02
4440 4908 4.540359 TTGGAATGCAGGAATTTTGAGG 57.460 40.909 0.00 0.00 0.00 3.86
4441 4909 2.833338 TGGAATGCAGGAATTTTGAGGG 59.167 45.455 0.00 0.00 0.00 4.30
4442 4910 2.169144 GGAATGCAGGAATTTTGAGGGG 59.831 50.000 0.00 0.00 0.00 4.79
4460 4928 4.082125 AGGGGATTTCACATGAAACTGTC 58.918 43.478 9.16 3.96 45.55 3.51
4486 4954 1.933853 CGCATAACTAGTGGCCTGTTC 59.066 52.381 3.32 0.00 0.00 3.18
4559 5035 4.957684 AGGAATAGGAAACCATAGGACG 57.042 45.455 0.00 0.00 0.00 4.79
4560 5036 4.296056 AGGAATAGGAAACCATAGGACGT 58.704 43.478 0.00 0.00 0.00 4.34
4564 5040 1.831736 AGGAAACCATAGGACGTGAGG 59.168 52.381 0.00 0.00 0.00 3.86
4565 5041 1.553704 GGAAACCATAGGACGTGAGGT 59.446 52.381 0.00 0.00 0.00 3.85
4568 5044 1.475403 ACCATAGGACGTGAGGTGAG 58.525 55.000 0.00 0.00 0.00 3.51
4597 5157 6.515512 TCTCAATTCTTATAGGGAAAGGGG 57.484 41.667 0.00 0.00 0.00 4.79
4616 5176 4.290722 AGGGGAAGAGATGTCACTTGATTT 59.709 41.667 0.00 0.00 0.00 2.17
4617 5177 4.637977 GGGGAAGAGATGTCACTTGATTTC 59.362 45.833 0.00 0.00 0.00 2.17
4627 5187 4.469945 TGTCACTTGATTTCTAGGGTAGGG 59.530 45.833 0.00 0.00 0.00 3.53
4665 5225 7.607607 GGCCTTTGAAATGTGAAGGATTAATTT 59.392 33.333 0.00 0.00 41.97 1.82
4666 5226 8.659491 GCCTTTGAAATGTGAAGGATTAATTTC 58.341 33.333 5.59 0.00 41.97 2.17
4749 5309 9.705290 TTGCCTACAAAATTTCTATCCTTTTTC 57.295 29.630 0.00 0.00 31.21 2.29
4782 5355 4.702131 CCAAAGGAGGTCTGGACTTATTTG 59.298 45.833 12.07 12.07 32.19 2.32
4819 5392 7.201835 TGTAAAAACACCGGAATAGGAAAAAC 58.798 34.615 9.46 0.00 34.73 2.43
4844 5417 2.505819 TGATTAGGCCTCCTTTGGTCTC 59.494 50.000 9.68 0.00 41.77 3.36
4864 5437 5.644206 GTCTCTAGGAATTTTGTGGGAGTTC 59.356 44.000 0.00 0.00 0.00 3.01
4874 5447 9.495572 GAATTTTGTGGGAGTTCTATAGGATAG 57.504 37.037 0.00 0.00 0.00 2.08
4878 5451 8.423906 TTGTGGGAGTTCTATAGGATAGAATC 57.576 38.462 11.13 9.62 36.16 2.52
4908 5482 1.839424 AATTCCTTCGGAGCCCTTTG 58.161 50.000 0.00 0.00 31.21 2.77
4909 5483 0.034089 ATTCCTTCGGAGCCCTTTGG 60.034 55.000 0.00 0.00 31.21 3.28
4916 5490 1.353022 TCGGAGCCCTTTGGTTTGTAT 59.647 47.619 0.00 0.00 0.00 2.29
4926 5500 6.710278 CCCTTTGGTTTGTATGAATGGATTT 58.290 36.000 0.00 0.00 0.00 2.17
4955 5529 6.935240 CCTATGTAGGATAGGAACCAATCA 57.065 41.667 0.00 0.00 46.63 2.57
4959 5533 6.823286 TGTAGGATAGGAACCAATCATTCA 57.177 37.500 0.00 0.00 0.00 2.57
4973 5547 7.682628 ACCAATCATTCACATTTCAAAGGAAT 58.317 30.769 0.00 0.00 31.93 3.01
5026 5601 5.745312 TTCCTATCCTATGCATCGAATGT 57.255 39.130 0.19 0.00 0.00 2.71
5043 5618 7.295322 TCGAATGTCATCTCTTTCTCCATAT 57.705 36.000 0.00 0.00 0.00 1.78
5050 5625 9.770097 TGTCATCTCTTTCTCCATATAATTGAC 57.230 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 3.084039 TGATTGCTTTTCTTCGAGCCAT 58.916 40.909 0.00 0.00 38.11 4.40
251 387 2.953466 ACATGATTGTGGCATGCTTC 57.047 45.000 18.92 11.37 45.32 3.86
276 412 9.475620 TTCTGTGATATTTTCTGTAGACCTAGA 57.524 33.333 0.00 0.00 0.00 2.43
278 414 9.031537 TGTTCTGTGATATTTTCTGTAGACCTA 57.968 33.333 0.00 0.00 0.00 3.08
303 439 9.357652 CTCTACCATGGTTGATTTTACAAATTG 57.642 33.333 26.07 8.95 30.44 2.32
304 440 8.034804 GCTCTACCATGGTTGATTTTACAAATT 58.965 33.333 26.07 0.00 30.44 1.82
306 442 6.719370 AGCTCTACCATGGTTGATTTTACAAA 59.281 34.615 26.07 2.58 30.44 2.83
307 443 6.245408 AGCTCTACCATGGTTGATTTTACAA 58.755 36.000 26.07 3.10 30.44 2.41
315 451 4.693283 CGAAATAGCTCTACCATGGTTGA 58.307 43.478 25.38 24.96 0.00 3.18
318 454 2.224305 GGCGAAATAGCTCTACCATGGT 60.224 50.000 23.55 23.55 37.29 3.55
319 455 2.037772 AGGCGAAATAGCTCTACCATGG 59.962 50.000 11.19 11.19 37.29 3.66
329 466 0.861837 CACGATGGAGGCGAAATAGC 59.138 55.000 0.00 0.00 0.00 2.97
342 479 3.734902 GCCCCTTTATTTTGAGCACGATG 60.735 47.826 0.00 0.00 0.00 3.84
354 491 3.832490 GGTTTCAGTTCAGCCCCTTTATT 59.168 43.478 0.00 0.00 0.00 1.40
440 577 3.855159 GGCCTAGTTTCCGATGTGT 57.145 52.632 0.00 0.00 0.00 3.72
448 585 0.035739 TGGTGTTCCGGCCTAGTTTC 59.964 55.000 0.00 0.00 36.30 2.78
520 657 1.467920 AGCCTCTGTTTATGCTTGGC 58.532 50.000 0.00 0.00 39.19 4.52
582 721 0.033991 TCCTGACTCTTCCTCTCCCG 60.034 60.000 0.00 0.00 0.00 5.14
583 722 1.687996 CCTCCTGACTCTTCCTCTCCC 60.688 61.905 0.00 0.00 0.00 4.30
592 731 1.077068 CTCTCGCCCTCCTGACTCT 60.077 63.158 0.00 0.00 0.00 3.24
598 737 4.851214 GAGCCCTCTCGCCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
862 1005 0.256752 CATCAGCCCAACCAGGATCA 59.743 55.000 0.00 0.00 41.22 2.92
916 1060 2.232941 GGACACGGAGAAAGGTCACATA 59.767 50.000 0.00 0.00 32.00 2.29
997 1141 2.114670 CGTCCCATTGCGCCATTCT 61.115 57.895 4.18 0.00 0.00 2.40
1068 1212 4.853142 AGGGAGATGGGCCGCGTA 62.853 66.667 4.92 0.00 0.00 4.42
1212 1356 2.536365 CGAGCAAGTGAGCGGTATTAA 58.464 47.619 0.00 0.00 40.15 1.40
1218 1363 1.083806 TATTGCGAGCAAGTGAGCGG 61.084 55.000 15.90 0.00 39.47 5.52
1251 1396 4.697352 ACACGCAGAAAGAATTAAGCAGAT 59.303 37.500 0.00 0.00 0.00 2.90
1737 1892 0.394216 TGCCAATGATTCCTCCACCG 60.394 55.000 0.00 0.00 0.00 4.94
1944 2099 1.740025 CTCTCATCCTTTGCGGGTTTC 59.260 52.381 0.00 0.00 0.00 2.78
1986 2141 5.362263 TCAATGATCGAAGCATGATTCAGA 58.638 37.500 22.50 19.12 0.00 3.27
2007 2162 3.743521 CTCAATAAGGCGAATCCCATCA 58.256 45.455 0.00 0.00 34.51 3.07
2049 2204 4.450976 TGTCACAGTGCTTGTAGACAAAT 58.549 39.130 16.46 0.00 41.00 2.32
2150 2306 3.189618 TGCAGCTATCTCAGTTCATGG 57.810 47.619 0.00 0.00 0.00 3.66
2168 2324 9.338291 CTGCACAGATAATGATATTGTATTTGC 57.662 33.333 0.00 0.00 0.00 3.68
2170 2326 9.578576 ACCTGCACAGATAATGATATTGTATTT 57.421 29.630 0.00 0.00 0.00 1.40
2180 2336 2.840038 ACTGGACCTGCACAGATAATGA 59.160 45.455 8.88 0.00 38.09 2.57
2188 2344 1.227943 GAGCAACTGGACCTGCACA 60.228 57.895 6.94 0.00 41.17 4.57
2211 2367 7.857885 CCTATCTGTGACAACAACTTTCTTTTC 59.142 37.037 0.00 0.00 35.37 2.29
2248 2404 9.965824 TTCTTGAGTGAGGAAATTAAATTTGAC 57.034 29.630 0.00 0.00 31.47 3.18
2289 2445 3.131933 AGCATGCCTCTACTACTTCACAG 59.868 47.826 15.66 0.00 0.00 3.66
2316 2475 2.847959 TTGGTGCGACATTATGCATG 57.152 45.000 10.16 0.00 43.96 4.06
2344 2506 5.065731 AGCTGCAGTGTATCAATAAAAGAGC 59.934 40.000 16.64 0.00 0.00 4.09
2467 2629 6.430864 TGCAAAAATGTATCAGAGGGGATAA 58.569 36.000 0.00 0.00 31.90 1.75
2469 2631 4.870636 TGCAAAAATGTATCAGAGGGGAT 58.129 39.130 0.00 0.00 0.00 3.85
2477 2639 9.066892 ACTAAGAAACTCTGCAAAAATGTATCA 57.933 29.630 0.00 0.00 0.00 2.15
2484 2646 6.481976 TCGATCACTAAGAAACTCTGCAAAAA 59.518 34.615 0.00 0.00 0.00 1.94
2494 2656 8.067784 TCACAACAAAATCGATCACTAAGAAAC 58.932 33.333 0.00 0.00 0.00 2.78
2530 2692 0.188342 AAGTGTTCCATGGGCCTGTT 59.812 50.000 13.02 0.00 0.00 3.16
2588 2750 4.326826 TGTCAATTCCACTCTCACATTCC 58.673 43.478 0.00 0.00 0.00 3.01
2660 2822 0.325933 TGTCTGCTTACCTGCATGCT 59.674 50.000 20.33 0.40 42.48 3.79
2673 2835 3.931578 ACAACCTGATCTAAGTGTCTGC 58.068 45.455 0.00 0.00 0.00 4.26
2702 2864 3.849645 GCAATGTACAGAAGTGTGTGCAC 60.850 47.826 10.75 10.75 44.43 4.57
2714 2876 5.545658 AAAATCAGTACCGCAATGTACAG 57.454 39.130 0.33 3.51 42.84 2.74
2825 2991 7.428020 TCCTGTTCATTGAATTATAAGCATGC 58.572 34.615 10.51 10.51 0.00 4.06
2870 3036 9.982651 AGTACCATAAACTATATAGTGTTGCAG 57.017 33.333 16.11 6.80 36.50 4.41
2880 3046 7.787904 TCCAGTGTCCAGTACCATAAACTATAT 59.212 37.037 0.00 0.00 0.00 0.86
2885 3051 4.020485 AGTCCAGTGTCCAGTACCATAAAC 60.020 45.833 0.00 0.00 0.00 2.01
2909 3075 2.107366 TGTGGAGTGCTGATATTCCGA 58.893 47.619 0.00 0.00 32.27 4.55
2910 3076 2.159043 AGTGTGGAGTGCTGATATTCCG 60.159 50.000 0.00 0.00 32.27 4.30
2995 3162 2.796593 GCTGCTCAACACATTCCAAAAC 59.203 45.455 0.00 0.00 0.00 2.43
2996 3163 2.429971 TGCTGCTCAACACATTCCAAAA 59.570 40.909 0.00 0.00 0.00 2.44
3001 3168 0.242017 GGGTGCTGCTCAACACATTC 59.758 55.000 0.00 0.00 38.57 2.67
3022 3189 4.434330 CGCGACTGAATTAAACTCTTCCAC 60.434 45.833 0.00 0.00 0.00 4.02
3193 3443 8.223330 AGAAATAAATATTGGACCTCAGCTCAT 58.777 33.333 0.00 0.00 0.00 2.90
3196 3446 9.732130 GATAGAAATAAATATTGGACCTCAGCT 57.268 33.333 0.00 0.00 0.00 4.24
3214 3464 9.566432 AAGGCGAGAGAAAATAATGATAGAAAT 57.434 29.630 0.00 0.00 0.00 2.17
3215 3465 8.964476 AAGGCGAGAGAAAATAATGATAGAAA 57.036 30.769 0.00 0.00 0.00 2.52
3216 3466 8.424918 AGAAGGCGAGAGAAAATAATGATAGAA 58.575 33.333 0.00 0.00 0.00 2.10
3217 3467 7.957002 AGAAGGCGAGAGAAAATAATGATAGA 58.043 34.615 0.00 0.00 0.00 1.98
3218 3468 8.600449 AAGAAGGCGAGAGAAAATAATGATAG 57.400 34.615 0.00 0.00 0.00 2.08
3219 3469 8.964476 AAAGAAGGCGAGAGAAAATAATGATA 57.036 30.769 0.00 0.00 0.00 2.15
3220 3470 7.872113 AAAGAAGGCGAGAGAAAATAATGAT 57.128 32.000 0.00 0.00 0.00 2.45
3221 3471 7.390440 TGAAAAGAAGGCGAGAGAAAATAATGA 59.610 33.333 0.00 0.00 0.00 2.57
3222 3472 7.530010 TGAAAAGAAGGCGAGAGAAAATAATG 58.470 34.615 0.00 0.00 0.00 1.90
3223 3473 7.687941 TGAAAAGAAGGCGAGAGAAAATAAT 57.312 32.000 0.00 0.00 0.00 1.28
3224 3474 7.687941 ATGAAAAGAAGGCGAGAGAAAATAA 57.312 32.000 0.00 0.00 0.00 1.40
3235 3485 4.800471 GCATTTCCTAATGAAAAGAAGGCG 59.200 41.667 2.25 0.00 45.67 5.52
3236 3486 5.970592 AGCATTTCCTAATGAAAAGAAGGC 58.029 37.500 2.25 0.00 45.67 4.35
3270 3520 4.202357 ACTGACCAATGTGAAAGCACTAGA 60.202 41.667 0.00 0.00 45.36 2.43
3306 3556 4.495422 ACTAGCTGAAGTGTTTGTATCCG 58.505 43.478 0.00 0.00 0.00 4.18
3309 3559 9.555727 TTCTTAAACTAGCTGAAGTGTTTGTAT 57.444 29.630 0.00 0.00 34.88 2.29
3351 3601 5.095691 TCTCGTTCAGAAAAATGCAAGTC 57.904 39.130 0.00 0.00 0.00 3.01
3380 3630 6.375174 ACAGCACAGATATTTGAAGCAATGTA 59.625 34.615 14.30 0.00 0.00 2.29
3420 3670 1.817099 CCTTGAGACATGGAGCGCC 60.817 63.158 2.29 0.00 31.33 6.53
3435 3685 1.078426 CCGCCATCGTTCCTTCCTT 60.078 57.895 0.00 0.00 0.00 3.36
3513 3763 8.314751 CCTACTACTATGGAAATTATGGGACTG 58.685 40.741 0.00 0.00 0.00 3.51
3558 3808 1.062121 AGAGATAACCTGCCAGCCCTA 60.062 52.381 0.00 0.00 0.00 3.53
3641 3894 3.117491 TCTTAGCATATGCCTGCAGTC 57.883 47.619 23.96 0.00 44.77 3.51
3700 3953 3.136123 CTGCATGAGTTGGGCGGG 61.136 66.667 0.00 0.00 0.00 6.13
3742 3995 2.598589 CGGACAGTGGATTGCAAATTG 58.401 47.619 1.71 0.00 0.00 2.32
3743 3996 1.545582 CCGGACAGTGGATTGCAAATT 59.454 47.619 1.71 0.00 0.00 1.82
3744 3997 1.176527 CCGGACAGTGGATTGCAAAT 58.823 50.000 1.71 0.00 0.00 2.32
3756 4009 2.069273 GTGAAGTTCATGACCGGACAG 58.931 52.381 9.46 2.48 0.00 3.51
3761 4014 3.338249 AGATTGGTGAAGTTCATGACCG 58.662 45.455 9.18 0.00 0.00 4.79
3762 4015 6.817765 TTTAGATTGGTGAAGTTCATGACC 57.182 37.500 9.18 6.45 0.00 4.02
3784 4037 1.944709 GTTACTCGTGGTTGCAGGTTT 59.055 47.619 0.00 0.00 0.00 3.27
3796 4049 3.244840 ACAGTCCTAGTCCAGTTACTCGT 60.245 47.826 0.00 0.00 0.00 4.18
3797 4050 3.345414 ACAGTCCTAGTCCAGTTACTCG 58.655 50.000 0.00 0.00 0.00 4.18
3865 4124 2.886081 ACAAAGATGTGCACGCAAAAA 58.114 38.095 13.13 0.00 38.69 1.94
3867 4126 3.913548 ATACAAAGATGTGCACGCAAA 57.086 38.095 13.13 0.00 40.84 3.68
3868 4127 4.249661 TCTATACAAAGATGTGCACGCAA 58.750 39.130 13.13 0.00 40.84 4.85
3869 4128 3.855858 TCTATACAAAGATGTGCACGCA 58.144 40.909 13.13 0.00 40.84 5.24
3870 4129 4.766007 CATCTATACAAAGATGTGCACGC 58.234 43.478 13.13 6.90 45.19 5.34
3878 4137 7.601886 CGAGCAGGAATTCATCTATACAAAGAT 59.398 37.037 7.93 0.00 36.64 2.40
3882 4141 6.405278 TCGAGCAGGAATTCATCTATACAA 57.595 37.500 7.93 0.00 0.00 2.41
3884 4143 7.897575 AAATCGAGCAGGAATTCATCTATAC 57.102 36.000 7.93 0.00 0.00 1.47
3886 4145 8.153550 ACTAAAATCGAGCAGGAATTCATCTAT 58.846 33.333 7.93 0.00 0.00 1.98
3888 4147 6.352516 ACTAAAATCGAGCAGGAATTCATCT 58.647 36.000 7.93 0.41 0.00 2.90
3889 4148 6.610741 ACTAAAATCGAGCAGGAATTCATC 57.389 37.500 7.93 0.00 0.00 2.92
3926 4185 7.252612 TGGTCAGTTAATCTTGATCAAGGTA 57.747 36.000 30.33 20.93 38.88 3.08
3928 4187 6.825213 TCATGGTCAGTTAATCTTGATCAAGG 59.175 38.462 30.33 15.43 38.88 3.61
3929 4188 7.854557 TCATGGTCAGTTAATCTTGATCAAG 57.145 36.000 26.56 26.56 39.71 3.02
3930 4189 8.812513 ATTCATGGTCAGTTAATCTTGATCAA 57.187 30.769 8.12 8.12 0.00 2.57
3931 4190 8.270030 AGATTCATGGTCAGTTAATCTTGATCA 58.730 33.333 0.00 0.00 34.12 2.92
3934 4210 7.855375 AGAGATTCATGGTCAGTTAATCTTGA 58.145 34.615 5.36 0.00 37.10 3.02
3996 4272 2.097825 AGCCTTTTGATGTCATCAGGC 58.902 47.619 26.22 26.22 45.16 4.85
3997 4273 2.426024 CCAGCCTTTTGATGTCATCAGG 59.574 50.000 14.98 13.89 40.94 3.86
3999 4275 3.084039 GACCAGCCTTTTGATGTCATCA 58.916 45.455 11.62 11.62 37.55 3.07
4011 4287 4.087892 AGCGCATCGACCAGCCTT 62.088 61.111 11.47 0.00 0.00 4.35
4030 4306 3.266772 TGTTTGTCAGATAGCCAGGGATT 59.733 43.478 0.00 0.00 0.00 3.01
4031 4307 2.846206 TGTTTGTCAGATAGCCAGGGAT 59.154 45.455 0.00 0.00 0.00 3.85
4046 4322 1.696063 ACTCTGCTTGGCATGTTTGT 58.304 45.000 2.12 0.00 38.13 2.83
4065 4341 0.597568 CAGCATGCCCTTCGACAAAA 59.402 50.000 15.66 0.00 0.00 2.44
4074 4350 2.590645 CTCTGCTCAGCATGCCCT 59.409 61.111 15.66 0.00 38.13 5.19
4081 4357 0.102120 ACGACATAGCTCTGCTCAGC 59.898 55.000 0.00 0.00 40.44 4.26
4100 4376 3.652274 GCTGCTTAAAGTTTTGATGCCA 58.348 40.909 0.00 0.00 0.00 4.92
4101 4377 2.663119 CGCTGCTTAAAGTTTTGATGCC 59.337 45.455 0.00 0.00 0.00 4.40
4113 4389 2.813754 AGCTTCAATTCACGCTGCTTAA 59.186 40.909 0.00 0.00 0.00 1.85
4121 4397 2.474526 CGCCTACAAGCTTCAATTCACG 60.475 50.000 0.00 0.00 0.00 4.35
4166 4442 2.158871 CCCATGGGCATTTTCTCCAATG 60.159 50.000 20.41 0.00 37.23 2.82
4167 4443 2.121129 CCCATGGGCATTTTCTCCAAT 58.879 47.619 20.41 0.00 33.90 3.16
4169 4445 0.325484 CCCCATGGGCATTTTCTCCA 60.325 55.000 26.87 0.00 35.35 3.86
4178 4454 1.846261 GAGCTATTCCCCATGGGCA 59.154 57.895 26.87 8.21 43.94 5.36
4184 4460 2.248248 CATCTACCGAGCTATTCCCCA 58.752 52.381 0.00 0.00 0.00 4.96
4193 4470 3.165058 TCATGTCAACATCTACCGAGC 57.835 47.619 0.00 0.00 33.61 5.03
4194 4471 4.936891 TGATCATGTCAACATCTACCGAG 58.063 43.478 0.00 0.00 33.61 4.63
4218 4495 6.552859 ACATTTTTGTCGTGTGTGATATGA 57.447 33.333 0.00 0.00 0.00 2.15
4219 4496 7.148983 GGAAACATTTTTGTCGTGTGTGATATG 60.149 37.037 0.00 0.00 0.00 1.78
4220 4497 6.861055 GGAAACATTTTTGTCGTGTGTGATAT 59.139 34.615 0.00 0.00 0.00 1.63
4225 4502 4.170256 GTGGAAACATTTTTGTCGTGTGT 58.830 39.130 0.00 0.00 46.14 3.72
4226 4503 4.169508 TGTGGAAACATTTTTGTCGTGTG 58.830 39.130 0.00 0.00 46.14 3.82
4227 4504 4.442375 TGTGGAAACATTTTTGTCGTGT 57.558 36.364 0.00 0.00 46.14 4.49
4228 4505 5.964887 ATTGTGGAAACATTTTTGTCGTG 57.035 34.783 0.00 0.00 46.14 4.35
4229 4506 5.872070 ACAATTGTGGAAACATTTTTGTCGT 59.128 32.000 11.07 0.00 46.14 4.34
4231 4508 8.825745 ACATACAATTGTGGAAACATTTTTGTC 58.174 29.630 21.42 0.00 46.14 3.18
4232 4509 8.729805 ACATACAATTGTGGAAACATTTTTGT 57.270 26.923 21.42 0.00 46.14 2.83
4247 4529 9.276590 TGCCTTAGAAGATCATACATACAATTG 57.723 33.333 3.24 3.24 0.00 2.32
4256 4539 7.397761 AGGGTAGTATGCCTTAGAAGATCATAC 59.602 40.741 17.55 17.55 42.40 2.39
4266 4549 5.871396 TCTTTCAGGGTAGTATGCCTTAG 57.129 43.478 0.00 0.00 42.40 2.18
4268 4551 5.905913 AGTATCTTTCAGGGTAGTATGCCTT 59.094 40.000 0.00 0.00 42.40 4.35
4323 4783 4.148128 ACAGTCTCAAGCTCCCAATATG 57.852 45.455 0.00 0.00 0.00 1.78
4340 4800 5.063880 GGATGTTTCCAGTTACAGAACAGT 58.936 41.667 0.00 0.00 42.12 3.55
4393 4853 3.003378 GGCTGTTGTTTACCAGACAGTTC 59.997 47.826 4.52 0.00 41.11 3.01
4422 4890 3.099141 TCCCCTCAAAATTCCTGCATTC 58.901 45.455 0.00 0.00 0.00 2.67
4424 4892 2.925966 TCCCCTCAAAATTCCTGCAT 57.074 45.000 0.00 0.00 0.00 3.96
4425 4893 2.925966 ATCCCCTCAAAATTCCTGCA 57.074 45.000 0.00 0.00 0.00 4.41
4426 4894 3.515104 TGAAATCCCCTCAAAATTCCTGC 59.485 43.478 0.00 0.00 0.00 4.85
4427 4895 4.527816 TGTGAAATCCCCTCAAAATTCCTG 59.472 41.667 0.00 0.00 0.00 3.86
4428 4896 4.750941 TGTGAAATCCCCTCAAAATTCCT 58.249 39.130 0.00 0.00 0.00 3.36
4430 4898 6.284891 TCATGTGAAATCCCCTCAAAATTC 57.715 37.500 0.00 0.00 0.00 2.17
4431 4899 6.684897 TTCATGTGAAATCCCCTCAAAATT 57.315 33.333 0.00 0.00 0.00 1.82
4432 4900 6.270695 AGTTTCATGTGAAATCCCCTCAAAAT 59.729 34.615 10.98 0.00 44.69 1.82
4433 4901 5.602145 AGTTTCATGTGAAATCCCCTCAAAA 59.398 36.000 10.98 0.00 44.69 2.44
4434 4902 5.010922 CAGTTTCATGTGAAATCCCCTCAAA 59.989 40.000 10.98 0.00 44.69 2.69
4435 4903 4.523943 CAGTTTCATGTGAAATCCCCTCAA 59.476 41.667 10.98 0.00 44.69 3.02
4436 4904 4.081406 CAGTTTCATGTGAAATCCCCTCA 58.919 43.478 10.98 0.00 44.69 3.86
4437 4905 4.082125 ACAGTTTCATGTGAAATCCCCTC 58.918 43.478 10.98 0.00 44.69 4.30
4438 4906 4.082125 GACAGTTTCATGTGAAATCCCCT 58.918 43.478 10.98 1.84 44.69 4.79
4439 4907 3.193479 GGACAGTTTCATGTGAAATCCCC 59.807 47.826 10.98 7.22 44.69 4.81
4440 4908 3.119849 CGGACAGTTTCATGTGAAATCCC 60.120 47.826 15.66 11.51 44.69 3.85
4441 4909 3.751175 TCGGACAGTTTCATGTGAAATCC 59.249 43.478 10.98 12.21 44.69 3.01
4442 4910 5.551760 ATCGGACAGTTTCATGTGAAATC 57.448 39.130 10.98 5.50 44.69 2.17
4460 4928 1.792949 GCCACTAGTTATGCGAATCGG 59.207 52.381 4.35 0.00 0.00 4.18
4486 4954 2.682856 CCCACAATATTCCTGTGTTCCG 59.317 50.000 5.52 0.00 42.18 4.30
4582 5058 5.608860 ACATCTCTTCCCCTTTCCCTATAAG 59.391 44.000 0.00 0.00 0.00 1.73
4583 5059 5.548573 ACATCTCTTCCCCTTTCCCTATAA 58.451 41.667 0.00 0.00 0.00 0.98
4597 5157 6.760770 CCCTAGAAATCAAGTGACATCTCTTC 59.239 42.308 0.00 0.00 0.00 2.87
4616 5176 5.103686 CCAATGGAAAAATCCCTACCCTAGA 60.104 44.000 0.00 0.00 0.00 2.43
4617 5177 5.140454 CCAATGGAAAAATCCCTACCCTAG 58.860 45.833 0.00 0.00 0.00 3.02
4627 5187 6.207221 ACATTTCAAAGGCCAATGGAAAAATC 59.793 34.615 13.35 0.00 33.00 2.17
4670 5230 5.832539 ATGGATTCCTATTCCTGTGTAGG 57.167 43.478 3.95 0.00 46.06 3.18
4769 5342 5.427378 TCATGCGAATCAAATAAGTCCAGA 58.573 37.500 0.00 0.00 0.00 3.86
4782 5355 5.003402 CGGTGTTTTTACAATCATGCGAATC 59.997 40.000 0.00 0.00 0.00 2.52
4819 5392 2.954318 CCAAAGGAGGCCTAATCATGTG 59.046 50.000 4.42 0.00 31.13 3.21
4844 5417 7.934120 CCTATAGAACTCCCACAAAATTCCTAG 59.066 40.741 0.00 0.00 0.00 3.02
4908 5482 9.136323 AGGAATAGAAATCCATTCATACAAACC 57.864 33.333 4.41 0.00 40.72 3.27
5086 5661 9.132923 GGTTCATAGGATATGAATATCGTAGGA 57.867 37.037 17.05 17.05 43.29 2.94


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

AutoCloner maintained by Alex Coulton.