Multiple sequence alignment - TraesCS5A01G038300

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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 TraesCS5A01G038300 chr5A 100.000 6946 0 0 1 6946 35626715 35633660 0.000000e+00 12827.0
1 TraesCS5A01G038300 chr5A 92.920 226 15 1 6602 6826 549412445 549412670 1.870000e-85 327.0
2 TraesCS5A01G038300 chr5B 94.273 6635 231 62 1 6541 44776237 44782816 0.000000e+00 10009.0
3 TraesCS5A01G038300 chr5B 86.842 76 3 3 6531 6600 44782839 44782913 2.080000e-10 78.7
4 TraesCS5A01G038300 chr5D 95.050 5353 143 53 1 5275 44907073 44912381 0.000000e+00 8305.0
5 TraesCS5A01G038300 chr5D 91.725 1438 63 27 5179 6602 44912312 44913707 0.000000e+00 1945.0
6 TraesCS5A01G038300 chr7A 93.750 224 13 1 6602 6824 429734705 429734482 1.120000e-87 335.0
7 TraesCS5A01G038300 chr7A 94.091 220 12 1 6602 6820 299325823 299326042 4.020000e-87 333.0
8 TraesCS5A01G038300 chr7A 90.040 251 21 4 6602 6850 717258825 717259073 8.690000e-84 322.0
9 TraesCS5A01G038300 chr7A 80.402 199 39 0 5455 5653 657716928 657716730 1.210000e-32 152.0
10 TraesCS5A01G038300 chr1A 92.672 232 15 2 6596 6825 351584427 351584658 4.020000e-87 333.0
11 TraesCS5A01G038300 chr6A 94.064 219 12 1 6602 6819 117403316 117403098 1.440000e-86 331.0
12 TraesCS5A01G038300 chr3D 91.057 246 19 3 6601 6844 162449772 162449528 5.190000e-86 329.0
13 TraesCS5A01G038300 chr4A 91.489 235 18 2 6597 6830 694753402 694753169 8.690000e-84 322.0
14 TraesCS5A01G038300 chr2D 88.672 256 24 5 6586 6837 320081870 320081616 2.430000e-79 307.0
15 TraesCS5A01G038300 chr2D 85.556 90 13 0 5563 5652 624367336 624367425 2.060000e-15 95.3
16 TraesCS5A01G038300 chr7D 81.407 199 37 0 5455 5653 568949969 568949771 5.570000e-36 163.0
17 TraesCS5A01G038300 chr7B 79.899 199 40 0 5455 5653 625297133 625296935 5.610000e-31 147.0
18 TraesCS5A01G038300 chr2B 85.556 90 13 0 5563 5652 766566860 766566949 2.060000e-15 95.3
19 TraesCS5A01G038300 chr2A 85.556 90 13 0 5563 5652 755774296 755774385 2.060000e-15 95.3
20 TraesCS5A01G038300 chr2A 92.683 41 3 0 6856 6896 593489448 593489488 7.520000e-05 60.2
21 TraesCS5A01G038300 chr3B 100.000 30 0 0 6859 6888 502935541 502935512 1.000000e-03 56.5
22 TraesCS5A01G038300 chr1D 100.000 30 0 0 6856 6885 113877999 113878028 1.000000e-03 56.5
23 TraesCS5A01G038300 chr3A 96.875 32 1 0 6856 6887 623824679 623824710 4.000000e-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 TraesCS5A01G038300 chr5A 35626715 35633660 6945 False 12827.00 12827 100.0000 1 6946 1 chr5A.!!$F1 6945
1 TraesCS5A01G038300 chr5B 44776237 44782913 6676 False 5043.85 10009 90.5575 1 6600 2 chr5B.!!$F1 6599
2 TraesCS5A01G038300 chr5D 44907073 44913707 6634 False 5125.00 8305 93.3875 1 6602 2 chr5D.!!$F1 6601

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
429 441 0.188587 TGTCTGGTCTGGTCTGGTCT 59.811 55.000 0.00 0.00 0.00 3.85 F
675 689 0.328258 CTGTTCACCGGGGAGGATTT 59.672 55.000 6.46 0.00 45.00 2.17 F
1560 1608 0.106015 ATTTCCCACAGGGCCATAGC 60.106 55.000 6.18 0.00 43.94 2.97 F
2094 2152 1.443194 CAAATGACACTGCAGCCGC 60.443 57.895 15.27 3.28 39.24 6.53 F
2764 2824 0.478072 TTTCCTTCTGCCAGCTGGAA 59.522 50.000 37.21 26.78 37.39 3.53 F
3696 3785 0.592637 TCCGCATGCTTCACAGTTTG 59.407 50.000 17.13 0.00 0.00 2.93 F
4446 4535 0.986019 ATAATCCTCCGGCACCACCA 60.986 55.000 0.00 0.00 39.03 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1608 0.037605 AAAACCTACGGACCTGCTCG 60.038 55.000 0.00 0.0 0.00 5.03 R
2219 2279 3.008485 ACTCGATTGGAAGAAAAGGCTCT 59.992 43.478 0.00 0.0 0.00 4.09 R
2764 2824 3.389656 CCAACCAACAAAACCCCACTAAT 59.610 43.478 0.00 0.0 0.00 1.73 R
3696 3785 3.545633 GTTGAACATGTTCTCACGAAGC 58.454 45.455 32.57 14.4 40.14 3.86 R
4446 4535 0.698238 TAACCTGATGCCCTTGCTGT 59.302 50.000 0.00 0.0 38.71 4.40 R
4908 4997 1.133025 CCGTCCTGGAATGCAAATGAC 59.867 52.381 0.00 0.0 42.00 3.06 R
6415 6565 0.107456 ATCATGATCCGGTCCAGCAC 59.893 55.000 1.18 0.0 0.00 4.40 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
85 91 6.364706 CCAAAAACGTAATTCAAGCTATTGCA 59.635 34.615 1.12 0.00 42.74 4.08
426 438 1.121407 TGGTGTCTGGTCTGGTCTGG 61.121 60.000 0.00 0.00 0.00 3.86
427 439 1.122019 GGTGTCTGGTCTGGTCTGGT 61.122 60.000 0.00 0.00 0.00 4.00
429 441 0.188587 TGTCTGGTCTGGTCTGGTCT 59.811 55.000 0.00 0.00 0.00 3.85
437 451 3.626924 GGTCTGGTCTGCCGTGGT 61.627 66.667 0.00 0.00 37.67 4.16
446 460 3.596066 CTGCCGTGGTCTGGTCCTG 62.596 68.421 0.00 0.00 0.00 3.86
447 461 3.311110 GCCGTGGTCTGGTCCTGA 61.311 66.667 0.00 0.00 0.00 3.86
448 462 2.973899 CCGTGGTCTGGTCCTGAG 59.026 66.667 0.00 0.00 0.00 3.35
449 463 2.262915 CGTGGTCTGGTCCTGAGC 59.737 66.667 18.32 18.32 0.00 4.26
554 568 0.612744 ACTTCTGCTTCCTCCTGAGC 59.387 55.000 0.00 0.00 0.00 4.26
616 630 2.590092 GGTGGAATCGGGTCTGGG 59.410 66.667 0.00 0.00 0.00 4.45
675 689 0.328258 CTGTTCACCGGGGAGGATTT 59.672 55.000 6.46 0.00 45.00 2.17
870 911 2.439104 GCGGAGGATGGAGGAGCTT 61.439 63.158 0.00 0.00 0.00 3.74
871 912 1.745264 CGGAGGATGGAGGAGCTTC 59.255 63.158 0.00 0.00 0.00 3.86
890 931 3.847602 CTGGGCGCAGAGGGAGAG 61.848 72.222 25.55 0.00 0.00 3.20
950 991 2.345244 CAGCTGCTTCGTGTCCCT 59.655 61.111 0.00 0.00 0.00 4.20
1113 1159 6.203723 AGCTGTTCAATTCTCAACTTGTACTC 59.796 38.462 0.00 0.00 0.00 2.59
1196 1242 4.082787 ACCACCGAAGATGCTAAACAAATG 60.083 41.667 0.00 0.00 0.00 2.32
1209 1255 4.816786 AAACAAATGTGCAAATTCAGCC 57.183 36.364 1.67 0.00 0.00 4.85
1248 1294 3.996363 TGATTGATCGCATACATGTAGCC 59.004 43.478 11.91 3.81 0.00 3.93
1283 1330 2.544686 TGCACAAACAAATGCTTGCATC 59.455 40.909 8.64 0.00 42.55 3.91
1308 1356 9.658475 TCGGTTGCTTTTATTATTTATTCATCG 57.342 29.630 0.00 0.00 0.00 3.84
1355 1403 3.322466 CTGTGCCTCCTCCCCGTT 61.322 66.667 0.00 0.00 0.00 4.44
1545 1593 2.158813 TGGAAGCCGGGTCATCTATTTC 60.159 50.000 6.62 0.00 0.00 2.17
1560 1608 0.106015 ATTTCCCACAGGGCCATAGC 60.106 55.000 6.18 0.00 43.94 2.97
1778 1836 9.904198 TGAAGGTGTCATTATATGAAGAATCAA 57.096 29.630 0.00 0.00 41.69 2.57
1798 1856 5.366460 TCAATTTTGTTGCATGGATGTTGT 58.634 33.333 0.00 0.00 0.00 3.32
2094 2152 1.443194 CAAATGACACTGCAGCCGC 60.443 57.895 15.27 3.28 39.24 6.53
2219 2279 4.214310 TCCAATGACAGGAAGAGCAAAAA 58.786 39.130 0.00 0.00 30.71 1.94
2589 2649 7.819900 GGTATGTACTCAAGTTGTCTCAGATTT 59.180 37.037 2.11 0.00 0.00 2.17
2764 2824 0.478072 TTTCCTTCTGCCAGCTGGAA 59.522 50.000 37.21 26.78 37.39 3.53
2783 2844 3.644265 GGAATTAGTGGGGTTTTGTTGGT 59.356 43.478 0.00 0.00 0.00 3.67
2804 2865 4.532126 GGTTGGGGAATTTCTCTGGAAAAT 59.468 41.667 0.00 0.00 43.51 1.82
2843 2917 2.949447 AGTTCCCATGTTGCAGAGTTT 58.051 42.857 0.00 0.00 0.00 2.66
2852 2926 6.392354 CCATGTTGCAGAGTTTTTGATGTAT 58.608 36.000 0.00 0.00 0.00 2.29
3054 3132 6.948886 TCCTAACCAATTTTATGCTGTTACCA 59.051 34.615 0.00 0.00 0.00 3.25
3064 3142 7.987750 TTTATGCTGTTACCATAGTTGTTCA 57.012 32.000 0.00 0.00 0.00 3.18
3102 3180 6.734137 TCACACATAACACTTTTCCATGTTC 58.266 36.000 0.00 0.00 39.67 3.18
3284 3362 6.961131 TCTATAACCCCCGGTATATTCATCAA 59.039 38.462 0.00 0.00 33.12 2.57
3378 3456 4.789807 CCCTTCTGAGTTCATCATTCCAT 58.210 43.478 0.00 0.00 37.28 3.41
3638 3717 6.879400 GGTAACTAGTCATGATTCCAGAGTT 58.121 40.000 0.00 4.09 0.00 3.01
3653 3732 4.081420 TCCAGAGTTCCTGCTGTTATCTTC 60.081 45.833 0.00 0.00 41.57 2.87
3657 3736 7.099764 CAGAGTTCCTGCTGTTATCTTCTTTA 58.900 38.462 0.00 0.00 35.89 1.85
3696 3785 0.592637 TCCGCATGCTTCACAGTTTG 59.407 50.000 17.13 0.00 0.00 2.93
3700 3789 2.056577 GCATGCTTCACAGTTTGCTTC 58.943 47.619 11.37 0.00 31.13 3.86
3822 3911 3.135348 CACTCTGGGAGATTGAGCCATTA 59.865 47.826 1.31 0.00 33.32 1.90
3834 3923 2.817258 TGAGCCATTAACAACCTTTCCG 59.183 45.455 0.00 0.00 0.00 4.30
3919 4008 2.897271 TGGCATGTTCAATGGTAGGT 57.103 45.000 0.00 0.00 0.00 3.08
3925 4014 4.496341 GCATGTTCAATGGTAGGTTGATCG 60.496 45.833 0.00 0.00 35.68 3.69
3982 4071 7.865385 TGCTTTTATACAATTCAACCAAGTGTC 59.135 33.333 0.00 0.00 39.05 3.67
4026 4115 2.106477 TCATATGCGCAGGTGTCAAA 57.894 45.000 18.32 0.00 0.00 2.69
4404 4493 5.077564 GGTAATCCTGGGTTTCTTCAAAGT 58.922 41.667 0.00 0.00 0.00 2.66
4446 4535 0.986019 ATAATCCTCCGGCACCACCA 60.986 55.000 0.00 0.00 39.03 4.17
4470 4559 2.880890 GCAAGGGCATCAGGTTATACAG 59.119 50.000 0.00 0.00 40.72 2.74
4614 4703 6.937465 AGAACCTCTTAGAAGGAAACAATGAC 59.063 38.462 5.06 0.00 38.87 3.06
4629 4718 2.424601 CAATGACCCATCGTTGCATCTT 59.575 45.455 0.00 0.00 43.21 2.40
4827 4916 3.737559 AATATGTCCCACTTTGCTGGA 57.262 42.857 0.00 0.00 32.30 3.86
4896 4985 2.234661 TGGTGCAAATGTTGACAACCAA 59.765 40.909 15.59 0.00 0.00 3.67
4908 4997 4.747540 TGACAACCAATTTCTGTCATCG 57.252 40.909 9.05 0.00 43.36 3.84
5251 5353 7.844779 AGAGGTAAAGAGTTCATATTAGGTGGA 59.155 37.037 0.00 0.00 0.00 4.02
5340 5471 2.064434 TGAGCACAATTGTTGGGTCA 57.936 45.000 20.63 20.63 36.14 4.02
5405 5536 9.570468 CCAGCTAATCCATCTTATTATGCATAT 57.430 33.333 7.36 0.82 0.00 1.78
5499 5635 0.383590 AGATCGCTCGACATCACCAG 59.616 55.000 0.00 0.00 0.00 4.00
5515 5651 3.963374 TCACCAGATTCAGCAGCTACTAT 59.037 43.478 0.00 0.00 0.00 2.12
5676 5812 3.055312 ACCTAGAAAAACCATCTCCGGTC 60.055 47.826 0.00 0.00 38.76 4.79
5679 5815 2.148768 GAAAAACCATCTCCGGTCGTT 58.851 47.619 0.00 0.00 38.76 3.85
5707 5843 7.171508 GCACATACAATAAATTCGATCTCCTCA 59.828 37.037 0.00 0.00 0.00 3.86
5949 6088 1.270094 CGCCACTGGACTACTGAAACA 60.270 52.381 0.00 0.00 0.00 2.83
5977 6118 1.066358 CCGGAGTCCAGAACTAAACCC 60.066 57.143 10.49 0.00 38.74 4.11
5978 6119 1.621814 CGGAGTCCAGAACTAAACCCA 59.378 52.381 10.49 0.00 38.74 4.51
5979 6120 2.353803 CGGAGTCCAGAACTAAACCCAG 60.354 54.545 10.49 0.00 38.74 4.45
5980 6121 2.615747 GGAGTCCAGAACTAAACCCAGC 60.616 54.545 3.60 0.00 38.74 4.85
5981 6122 2.038557 GAGTCCAGAACTAAACCCAGCA 59.961 50.000 0.00 0.00 38.74 4.41
5983 6124 2.054799 TCCAGAACTAAACCCAGCACT 58.945 47.619 0.00 0.00 0.00 4.40
5985 6126 2.427506 CAGAACTAAACCCAGCACTCC 58.572 52.381 0.00 0.00 0.00 3.85
5986 6127 2.054799 AGAACTAAACCCAGCACTCCA 58.945 47.619 0.00 0.00 0.00 3.86
6060 6205 0.103937 CCTCTCCTCGCCATGAACTC 59.896 60.000 0.00 0.00 0.00 3.01
6281 6431 4.425520 CGACTGGAGACCTAAAACTGATC 58.574 47.826 0.00 0.00 0.00 2.92
6284 6434 6.380079 ACTGGAGACCTAAAACTGATCATT 57.620 37.500 0.00 0.00 0.00 2.57
6334 6484 1.623811 ACTAAGTGTGGTTGATCCGCT 59.376 47.619 0.00 0.00 46.10 5.52
6337 6487 0.973632 AGTGTGGTTGATCCGCTGTA 59.026 50.000 0.00 0.00 46.10 2.74
6391 6541 5.070001 AGCTTTGACCTGTAAAGTTGCATA 58.930 37.500 0.00 0.00 37.44 3.14
6413 6563 2.166254 GGGTGGTTGTTTGATATGCTGG 59.834 50.000 0.00 0.00 0.00 4.85
6414 6564 3.088532 GGTGGTTGTTTGATATGCTGGA 58.911 45.455 0.00 0.00 0.00 3.86
6415 6565 3.129287 GGTGGTTGTTTGATATGCTGGAG 59.871 47.826 0.00 0.00 0.00 3.86
6416 6566 3.758554 GTGGTTGTTTGATATGCTGGAGT 59.241 43.478 0.00 0.00 0.00 3.85
6417 6567 3.758023 TGGTTGTTTGATATGCTGGAGTG 59.242 43.478 0.00 0.00 0.00 3.51
6418 6568 3.428045 GGTTGTTTGATATGCTGGAGTGC 60.428 47.826 0.00 0.00 0.00 4.40
6419 6569 3.354948 TGTTTGATATGCTGGAGTGCT 57.645 42.857 0.00 0.00 0.00 4.40
6420 6570 3.011818 TGTTTGATATGCTGGAGTGCTG 58.988 45.455 0.00 0.00 0.00 4.41
6435 6585 1.344438 GTGCTGGACCGGATCATGATA 59.656 52.381 9.46 0.00 0.00 2.15
6436 6586 2.046292 TGCTGGACCGGATCATGATAA 58.954 47.619 9.46 0.00 0.00 1.75
6461 6611 1.533625 GTGCCAAAGTGCAGACCATA 58.466 50.000 0.00 0.00 43.02 2.74
6491 6641 2.814336 GACTTTTTGAGAGGCCATTCGT 59.186 45.455 5.01 0.00 0.00 3.85
6497 6647 0.253327 GAGAGGCCATTCGTTTCCCT 59.747 55.000 5.01 0.00 0.00 4.20
6498 6648 0.035056 AGAGGCCATTCGTTTCCCTG 60.035 55.000 5.01 0.00 0.00 4.45
6521 6673 2.017782 TGCTTGGCACGTCAAAAGTTA 58.982 42.857 0.00 0.00 31.71 2.24
6535 6719 6.570058 CGTCAAAAGTTATGTTCACGAAGAAG 59.430 38.462 0.00 0.00 36.78 2.85
6541 6725 5.930569 AGTTATGTTCACGAAGAAGTAACCC 59.069 40.000 16.86 2.00 38.26 4.11
6551 6735 5.126707 ACGAAGAAGTAACCCTCGAACATAT 59.873 40.000 0.00 0.00 0.00 1.78
6602 6792 8.595362 TGAGATTCTGAGGTGTTTCTCTTATA 57.405 34.615 0.00 0.00 34.98 0.98
6603 6793 8.470805 TGAGATTCTGAGGTGTTTCTCTTATAC 58.529 37.037 0.00 0.00 34.98 1.47
6604 6794 8.602472 AGATTCTGAGGTGTTTCTCTTATACT 57.398 34.615 0.00 0.00 34.98 2.12
6605 6795 8.691797 AGATTCTGAGGTGTTTCTCTTATACTC 58.308 37.037 0.00 0.00 34.98 2.59
6606 6796 6.777213 TCTGAGGTGTTTCTCTTATACTCC 57.223 41.667 0.00 0.00 34.98 3.85
6607 6797 5.657302 TCTGAGGTGTTTCTCTTATACTCCC 59.343 44.000 0.00 0.00 34.98 4.30
6608 6798 5.590818 TGAGGTGTTTCTCTTATACTCCCT 58.409 41.667 0.00 0.00 34.98 4.20
6609 6799 5.657302 TGAGGTGTTTCTCTTATACTCCCTC 59.343 44.000 0.00 0.00 34.98 4.30
6610 6800 5.844601 AGGTGTTTCTCTTATACTCCCTCT 58.155 41.667 0.00 0.00 0.00 3.69
6611 6801 5.894964 AGGTGTTTCTCTTATACTCCCTCTC 59.105 44.000 0.00 0.00 0.00 3.20
6612 6802 5.894964 GGTGTTTCTCTTATACTCCCTCTCT 59.105 44.000 0.00 0.00 0.00 3.10
6613 6803 6.040054 GGTGTTTCTCTTATACTCCCTCTCTC 59.960 46.154 0.00 0.00 0.00 3.20
6614 6804 6.831868 GTGTTTCTCTTATACTCCCTCTCTCT 59.168 42.308 0.00 0.00 0.00 3.10
6615 6805 7.340999 GTGTTTCTCTTATACTCCCTCTCTCTT 59.659 40.741 0.00 0.00 0.00 2.85
6616 6806 8.558312 TGTTTCTCTTATACTCCCTCTCTCTTA 58.442 37.037 0.00 0.00 0.00 2.10
6617 6807 9.063615 GTTTCTCTTATACTCCCTCTCTCTTAG 57.936 40.741 0.00 0.00 0.00 2.18
6618 6808 7.941053 TCTCTTATACTCCCTCTCTCTTAGT 57.059 40.000 0.00 0.00 0.00 2.24
6619 6809 8.339720 TCTCTTATACTCCCTCTCTCTTAGTT 57.660 38.462 0.00 0.00 0.00 2.24
6620 6810 8.783903 TCTCTTATACTCCCTCTCTCTTAGTTT 58.216 37.037 0.00 0.00 0.00 2.66
6626 6816 6.616577 ACTCCCTCTCTCTTAGTTTATAGGG 58.383 44.000 0.00 0.00 43.23 3.53
6627 6817 5.395611 TCCCTCTCTCTTAGTTTATAGGGC 58.604 45.833 0.00 0.00 41.88 5.19
6628 6818 4.218852 CCCTCTCTCTTAGTTTATAGGGCG 59.781 50.000 0.00 0.00 36.30 6.13
6629 6819 4.828387 CCTCTCTCTTAGTTTATAGGGCGT 59.172 45.833 0.00 0.00 0.00 5.68
6630 6820 5.278561 CCTCTCTCTTAGTTTATAGGGCGTG 60.279 48.000 0.00 0.00 0.00 5.34
6631 6821 4.037684 TCTCTCTTAGTTTATAGGGCGTGC 59.962 45.833 0.00 0.00 0.00 5.34
6632 6822 3.050619 CTCTTAGTTTATAGGGCGTGCG 58.949 50.000 0.00 0.00 0.00 5.34
6633 6823 1.525619 CTTAGTTTATAGGGCGTGCGC 59.474 52.381 8.17 8.17 41.06 6.09
6634 6824 0.595567 TAGTTTATAGGGCGTGCGCG 60.596 55.000 16.86 16.86 43.06 6.86
6635 6825 2.169146 GTTTATAGGGCGTGCGCGT 61.169 57.895 22.18 3.77 43.06 6.01
6636 6826 0.871163 GTTTATAGGGCGTGCGCGTA 60.871 55.000 22.18 0.00 43.06 4.42
6637 6827 0.871163 TTTATAGGGCGTGCGCGTAC 60.871 55.000 22.18 17.94 43.06 3.67
6638 6828 1.727511 TTATAGGGCGTGCGCGTACT 61.728 55.000 24.56 20.32 43.06 2.73
6639 6829 2.121564 TATAGGGCGTGCGCGTACTC 62.122 60.000 24.56 17.22 43.06 2.59
6642 6832 4.183686 GGCGTGCGCGTACTCCTA 62.184 66.667 26.13 0.00 43.06 2.94
6643 6833 2.651232 GCGTGCGCGTACTCCTAG 60.651 66.667 24.56 10.08 40.81 3.02
6644 6834 3.095911 CGTGCGCGTACTCCTAGA 58.904 61.111 24.56 0.00 0.00 2.43
6645 6835 1.647629 CGTGCGCGTACTCCTAGAT 59.352 57.895 24.56 0.00 0.00 1.98
6646 6836 0.029035 CGTGCGCGTACTCCTAGATT 59.971 55.000 24.56 0.00 0.00 2.40
6647 6837 1.478137 GTGCGCGTACTCCTAGATTG 58.522 55.000 20.55 0.00 0.00 2.67
6648 6838 1.100510 TGCGCGTACTCCTAGATTGT 58.899 50.000 8.43 0.00 0.00 2.71
6649 6839 1.065102 TGCGCGTACTCCTAGATTGTC 59.935 52.381 8.43 0.00 0.00 3.18
6650 6840 1.065102 GCGCGTACTCCTAGATTGTCA 59.935 52.381 8.43 0.00 0.00 3.58
6651 6841 2.479049 GCGCGTACTCCTAGATTGTCAA 60.479 50.000 8.43 0.00 0.00 3.18
6652 6842 3.795826 GCGCGTACTCCTAGATTGTCAAT 60.796 47.826 8.43 0.00 0.00 2.57
6653 6843 4.360563 CGCGTACTCCTAGATTGTCAATT 58.639 43.478 0.00 0.00 0.00 2.32
6654 6844 4.804139 CGCGTACTCCTAGATTGTCAATTT 59.196 41.667 0.00 0.00 0.00 1.82
6655 6845 5.276395 CGCGTACTCCTAGATTGTCAATTTG 60.276 44.000 0.00 0.00 0.00 2.32
6656 6846 5.810587 GCGTACTCCTAGATTGTCAATTTGA 59.189 40.000 0.00 0.00 0.00 2.69
6781 6971 8.114301 AGGGTGATAAAATTGATAACCTAGGT 57.886 34.615 9.21 9.21 0.00 3.08
6782 6972 9.232882 AGGGTGATAAAATTGATAACCTAGGTA 57.767 33.333 16.67 4.12 0.00 3.08
6788 6978 7.647907 AAAATTGATAACCTAGGTATACGCG 57.352 36.000 16.67 3.53 0.00 6.01
6789 6979 5.972107 ATTGATAACCTAGGTATACGCGT 57.028 39.130 19.17 19.17 0.00 6.01
6790 6980 7.452880 AATTGATAACCTAGGTATACGCGTA 57.547 36.000 22.94 22.94 0.00 4.42
6791 6981 6.486253 TTGATAACCTAGGTATACGCGTAG 57.514 41.667 24.78 11.28 0.00 3.51
6792 6982 4.937620 TGATAACCTAGGTATACGCGTAGG 59.062 45.833 24.78 21.85 46.64 3.18
6793 6983 3.492102 AACCTAGGTATACGCGTAGGA 57.508 47.619 25.95 14.03 45.08 2.94
6794 6984 2.772287 ACCTAGGTATACGCGTAGGAC 58.228 52.381 25.95 22.99 45.08 3.85
6795 6985 2.370189 ACCTAGGTATACGCGTAGGACT 59.630 50.000 25.95 22.11 45.08 3.85
6796 6986 3.181450 ACCTAGGTATACGCGTAGGACTT 60.181 47.826 25.95 21.88 45.08 3.01
6797 6987 3.188048 CCTAGGTATACGCGTAGGACTTG 59.812 52.174 24.78 19.23 45.08 3.16
6798 6988 2.648059 AGGTATACGCGTAGGACTTGT 58.352 47.619 24.78 8.30 0.00 3.16
6799 6989 3.808728 AGGTATACGCGTAGGACTTGTA 58.191 45.455 24.78 7.25 0.00 2.41
6800 6990 4.199310 AGGTATACGCGTAGGACTTGTAA 58.801 43.478 24.78 0.00 0.00 2.41
6801 6991 4.640201 AGGTATACGCGTAGGACTTGTAAA 59.360 41.667 24.78 0.00 0.00 2.01
6802 6992 4.735338 GGTATACGCGTAGGACTTGTAAAC 59.265 45.833 24.78 6.78 0.00 2.01
6803 6993 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
6804 6994 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
6805 6995 2.035066 ACGCGTAGGACTTGTAAACTGT 59.965 45.455 11.67 0.00 0.00 3.55
6806 6996 2.407361 CGCGTAGGACTTGTAAACTGTG 59.593 50.000 0.00 0.00 0.00 3.66
6807 6997 3.645884 GCGTAGGACTTGTAAACTGTGA 58.354 45.455 0.00 0.00 0.00 3.58
6808 6998 3.427863 GCGTAGGACTTGTAAACTGTGAC 59.572 47.826 0.00 0.00 0.00 3.67
6809 6999 3.667261 CGTAGGACTTGTAAACTGTGACG 59.333 47.826 0.00 0.00 0.00 4.35
6810 7000 3.107642 AGGACTTGTAAACTGTGACGG 57.892 47.619 0.00 0.00 0.00 4.79
6811 7001 2.696707 AGGACTTGTAAACTGTGACGGA 59.303 45.455 0.00 0.00 0.00 4.69
6812 7002 3.057734 GGACTTGTAAACTGTGACGGAG 58.942 50.000 0.00 0.00 0.00 4.63
6813 7003 3.057734 GACTTGTAAACTGTGACGGAGG 58.942 50.000 0.00 0.00 0.00 4.30
6814 7004 2.224209 ACTTGTAAACTGTGACGGAGGG 60.224 50.000 0.00 0.00 0.00 4.30
6815 7005 1.707106 TGTAAACTGTGACGGAGGGA 58.293 50.000 0.00 0.00 0.00 4.20
6816 7006 1.616865 TGTAAACTGTGACGGAGGGAG 59.383 52.381 0.00 0.00 0.00 4.30
6817 7007 1.617357 GTAAACTGTGACGGAGGGAGT 59.383 52.381 0.00 0.00 0.00 3.85
6818 7008 2.005370 AAACTGTGACGGAGGGAGTA 57.995 50.000 0.00 0.00 0.00 2.59
6819 7009 2.233305 AACTGTGACGGAGGGAGTAT 57.767 50.000 0.00 0.00 0.00 2.12
6820 7010 2.233305 ACTGTGACGGAGGGAGTATT 57.767 50.000 0.00 0.00 0.00 1.89
6821 7011 3.377253 ACTGTGACGGAGGGAGTATTA 57.623 47.619 0.00 0.00 0.00 0.98
6822 7012 3.705051 ACTGTGACGGAGGGAGTATTAA 58.295 45.455 0.00 0.00 0.00 1.40
6823 7013 4.091549 ACTGTGACGGAGGGAGTATTAAA 58.908 43.478 0.00 0.00 0.00 1.52
6824 7014 4.529377 ACTGTGACGGAGGGAGTATTAAAA 59.471 41.667 0.00 0.00 0.00 1.52
6825 7015 5.012354 ACTGTGACGGAGGGAGTATTAAAAA 59.988 40.000 0.00 0.00 0.00 1.94
6866 7056 8.688747 AGGCTTTAATTCTAGATGAGGATTTG 57.311 34.615 0.00 0.00 34.88 2.32
6867 7057 8.277918 AGGCTTTAATTCTAGATGAGGATTTGT 58.722 33.333 0.00 0.00 34.88 2.83
6868 7058 8.348507 GGCTTTAATTCTAGATGAGGATTTGTG 58.651 37.037 0.00 0.00 34.88 3.33
6869 7059 8.348507 GCTTTAATTCTAGATGAGGATTTGTGG 58.651 37.037 0.00 0.00 34.88 4.17
6870 7060 7.807977 TTAATTCTAGATGAGGATTTGTGGC 57.192 36.000 0.00 0.00 34.88 5.01
6871 7061 5.643421 ATTCTAGATGAGGATTTGTGGCT 57.357 39.130 0.00 0.00 0.00 4.75
6872 7062 4.679373 TCTAGATGAGGATTTGTGGCTC 57.321 45.455 0.00 0.00 0.00 4.70
6873 7063 4.293494 TCTAGATGAGGATTTGTGGCTCT 58.707 43.478 0.00 0.00 0.00 4.09
6874 7064 4.718774 TCTAGATGAGGATTTGTGGCTCTT 59.281 41.667 0.00 0.00 0.00 2.85
6875 7065 3.618351 AGATGAGGATTTGTGGCTCTTG 58.382 45.455 0.00 0.00 0.00 3.02
6876 7066 2.205022 TGAGGATTTGTGGCTCTTGG 57.795 50.000 0.00 0.00 0.00 3.61
6877 7067 1.272092 TGAGGATTTGTGGCTCTTGGG 60.272 52.381 0.00 0.00 0.00 4.12
6878 7068 0.779997 AGGATTTGTGGCTCTTGGGT 59.220 50.000 0.00 0.00 0.00 4.51
6879 7069 0.890683 GGATTTGTGGCTCTTGGGTG 59.109 55.000 0.00 0.00 0.00 4.61
6880 7070 0.244721 GATTTGTGGCTCTTGGGTGC 59.755 55.000 0.00 0.00 0.00 5.01
6886 7076 2.203337 GCTCTTGGGTGCCACACA 60.203 61.111 0.00 0.00 35.86 3.72
6894 7084 3.725819 GTGCCACACACGCTTGTA 58.274 55.556 0.00 0.00 40.07 2.41
6895 7085 2.244000 GTGCCACACACGCTTGTAT 58.756 52.632 0.00 0.00 40.07 2.29
6896 7086 0.165944 GTGCCACACACGCTTGTATC 59.834 55.000 0.00 0.00 40.07 2.24
6897 7087 0.034756 TGCCACACACGCTTGTATCT 59.965 50.000 0.00 0.00 33.30 1.98
6898 7088 0.721718 GCCACACACGCTTGTATCTC 59.278 55.000 0.00 0.00 33.30 2.75
6899 7089 0.992072 CCACACACGCTTGTATCTCG 59.008 55.000 0.00 0.00 33.30 4.04
6900 7090 0.992072 CACACACGCTTGTATCTCGG 59.008 55.000 0.00 0.00 33.30 4.63
6901 7091 0.108804 ACACACGCTTGTATCTCGGG 60.109 55.000 0.00 0.00 33.30 5.14
6902 7092 0.172578 CACACGCTTGTATCTCGGGA 59.827 55.000 0.00 0.00 33.30 5.14
6903 7093 0.456221 ACACGCTTGTATCTCGGGAG 59.544 55.000 0.00 0.00 32.60 4.30
6904 7094 0.872021 CACGCTTGTATCTCGGGAGC 60.872 60.000 0.00 0.00 0.00 4.70
6905 7095 1.300233 CGCTTGTATCTCGGGAGCC 60.300 63.158 0.00 0.00 0.00 4.70
6915 7105 2.357517 CGGGAGCCGTGATATGCC 60.358 66.667 0.00 0.00 42.73 4.40
6916 7106 2.032681 GGGAGCCGTGATATGCCC 59.967 66.667 0.00 0.00 0.00 5.36
6917 7107 2.357517 GGAGCCGTGATATGCCCG 60.358 66.667 0.00 0.00 0.00 6.13
6918 7108 2.357517 GAGCCGTGATATGCCCGG 60.358 66.667 0.00 0.00 44.46 5.73
6919 7109 3.161450 AGCCGTGATATGCCCGGT 61.161 61.111 0.00 0.00 43.56 5.28
6920 7110 2.972505 GCCGTGATATGCCCGGTG 60.973 66.667 0.00 0.00 43.56 4.94
6921 7111 2.280797 CCGTGATATGCCCGGTGG 60.281 66.667 0.00 0.00 37.00 4.61
6940 7130 4.814294 GGCGGCGTGGATCGAACT 62.814 66.667 9.37 0.00 42.86 3.01
6941 7131 3.255379 GCGGCGTGGATCGAACTC 61.255 66.667 9.37 0.00 42.86 3.01
6942 7132 2.582498 CGGCGTGGATCGAACTCC 60.582 66.667 0.00 0.00 42.86 3.85
6943 7133 2.202892 GGCGTGGATCGAACTCCC 60.203 66.667 2.62 0.00 42.86 4.30
6944 7134 2.722201 GGCGTGGATCGAACTCCCT 61.722 63.158 2.62 0.00 42.86 4.20
6945 7135 1.389609 GGCGTGGATCGAACTCCCTA 61.390 60.000 2.62 0.00 42.86 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.575694 TCCACACACACACAATTTGC 57.424 45.000 0.00 0.00 0.00 3.68
85 91 1.417517 CTTTTTCTGCTTTGCCCCCTT 59.582 47.619 0.00 0.00 0.00 3.95
407 419 1.121407 CCAGACCAGACCAGACACCA 61.121 60.000 0.00 0.00 0.00 4.17
426 438 2.048127 GACCAGACCACGGCAGAC 60.048 66.667 0.00 0.00 0.00 3.51
427 439 3.311110 GGACCAGACCACGGCAGA 61.311 66.667 0.00 0.00 0.00 4.26
429 441 3.625897 CAGGACCAGACCACGGCA 61.626 66.667 0.00 0.00 0.00 5.69
437 451 3.443925 CGCTCGCTCAGGACCAGA 61.444 66.667 0.00 0.00 0.00 3.86
554 568 2.587194 CGGCCCGAGCTCATTCAG 60.587 66.667 15.40 0.00 39.73 3.02
634 648 4.038080 GAAGCGCCAACCAACCCG 62.038 66.667 2.29 0.00 0.00 5.28
636 650 1.578206 GAGAGAAGCGCCAACCAACC 61.578 60.000 2.29 0.00 0.00 3.77
637 651 1.578206 GGAGAGAAGCGCCAACCAAC 61.578 60.000 2.29 0.00 36.33 3.77
638 652 1.302511 GGAGAGAAGCGCCAACCAA 60.303 57.895 2.29 0.00 36.33 3.67
639 653 2.217038 AGGAGAGAAGCGCCAACCA 61.217 57.895 2.29 0.00 39.21 3.67
729 770 1.811266 CCATTGCCGACTCACCTCG 60.811 63.158 0.00 0.00 0.00 4.63
821 862 1.431243 TCCAACCTGTTATTGCCCCTT 59.569 47.619 0.00 0.00 0.00 3.95
1113 1159 0.107800 CCACTGGAGATGCAGACAGG 60.108 60.000 8.45 3.55 35.34 4.00
1196 1242 1.269936 ACAAGCAGGCTGAATTTGCAC 60.270 47.619 20.86 0.00 40.22 4.57
1209 1255 0.318022 TCATGCGCAAACACAAGCAG 60.318 50.000 17.11 0.00 43.20 4.24
1248 1294 2.361992 TGCAGGCCAGCAATGGAG 60.362 61.111 21.95 0.00 42.46 3.86
1283 1330 9.445786 ACGATGAATAAATAATAAAAGCAACCG 57.554 29.630 0.00 0.00 0.00 4.44
1308 1356 7.645340 GTGACAATAATGCCATAACATGAGAAC 59.355 37.037 0.00 0.00 0.00 3.01
1355 1403 6.142916 TTGGGACACAGACAAGAAGTCACA 62.143 45.833 0.00 0.00 45.13 3.58
1560 1608 0.037605 AAAACCTACGGACCTGCTCG 60.038 55.000 0.00 0.00 0.00 5.03
1704 1762 3.531538 AGAATCGCAAACCGTATGATGT 58.468 40.909 0.00 0.00 38.35 3.06
1752 1810 9.904198 TTGATTCTTCATATAATGACACCTTCA 57.096 29.630 0.00 0.00 39.39 3.02
2094 2152 3.469008 TGTGATTAATACCGGGCTCAG 57.531 47.619 6.32 0.00 0.00 3.35
2219 2279 3.008485 ACTCGATTGGAAGAAAAGGCTCT 59.992 43.478 0.00 0.00 0.00 4.09
2671 2731 8.485976 AAAGCTGCAAAATGTACTTTTTGTTA 57.514 26.923 31.36 23.88 44.62 2.41
2683 2743 6.530534 CCTTCTCATCTAAAAGCTGCAAAATG 59.469 38.462 1.02 0.00 0.00 2.32
2692 2752 6.036626 GTGCTAGAACCTTCTCATCTAAAAGC 59.963 42.308 0.00 0.00 38.70 3.51
2764 2824 3.389656 CCAACCAACAAAACCCCACTAAT 59.610 43.478 0.00 0.00 0.00 1.73
2783 2844 5.154418 ACATTTTCCAGAGAAATTCCCCAA 58.846 37.500 0.00 0.00 41.55 4.12
2804 2865 9.967451 TGGGAACTATAAAAGATGAATACAACA 57.033 29.630 0.00 0.00 0.00 3.33
3054 3132 7.882791 TGATCAAGGTGTAACATGAACAACTAT 59.117 33.333 19.17 12.44 44.04 2.12
3064 3142 6.939730 TGTTATGTGTGATCAAGGTGTAACAT 59.060 34.615 0.00 2.42 39.98 2.71
3102 3180 7.062957 AGAAGTTGGTTATTATCATTCCTGGG 58.937 38.462 0.00 0.00 0.00 4.45
3331 3409 6.992715 GCTAGCCCTGATAAAAGACAAAGATA 59.007 38.462 2.29 0.00 0.00 1.98
3378 3456 7.759489 AAACAGATTTGACATACTTAGCCAA 57.241 32.000 0.00 0.00 0.00 4.52
3638 3717 9.601217 GAATAACTAAAGAAGATAACAGCAGGA 57.399 33.333 0.00 0.00 0.00 3.86
3653 3732 9.110502 GGAATAGGTTGAGGTGAATAACTAAAG 57.889 37.037 0.00 0.00 0.00 1.85
3657 3736 5.671493 CGGAATAGGTTGAGGTGAATAACT 58.329 41.667 0.00 0.00 0.00 2.24
3696 3785 3.545633 GTTGAACATGTTCTCACGAAGC 58.454 45.455 32.57 14.40 40.14 3.86
3700 3789 5.666969 TTAAGGTTGAACATGTTCTCACG 57.333 39.130 32.57 0.00 40.14 4.35
3822 3911 4.295141 TGGATACATCGGAAAGGTTGTT 57.705 40.909 0.00 0.00 46.17 2.83
3919 4008 5.418676 TGCTATTCTTGTCACATCGATCAA 58.581 37.500 0.00 0.00 0.00 2.57
3925 4014 6.918569 ACGTATACTGCTATTCTTGTCACATC 59.081 38.462 0.56 0.00 0.00 3.06
4026 4115 9.294030 GAAGAATAACGAGCAAAATCATCATTT 57.706 29.630 0.00 0.00 33.27 2.32
4404 4493 1.612676 AATGCAGCTGCTGAAACTGA 58.387 45.000 36.61 16.61 42.66 3.41
4446 4535 0.698238 TAACCTGATGCCCTTGCTGT 59.302 50.000 0.00 0.00 38.71 4.40
4614 4703 1.452110 TGTGAAGATGCAACGATGGG 58.548 50.000 0.00 0.00 0.00 4.00
4629 4718 6.053005 AGAGAAGTTACGAAAACCATTGTGA 58.947 36.000 0.00 0.00 0.00 3.58
4839 4928 2.270047 GATGAGTCTCTTGCTGACTGC 58.730 52.381 0.65 0.00 43.88 4.40
4896 4985 5.571784 ATGCAAATGACGATGACAGAAAT 57.428 34.783 0.00 0.00 0.00 2.17
4908 4997 1.133025 CCGTCCTGGAATGCAAATGAC 59.867 52.381 0.00 0.00 42.00 3.06
5249 5351 4.642429 TGAACTCTTTGCCTCTTAAGTCC 58.358 43.478 1.63 0.00 0.00 3.85
5251 5353 7.624549 TGATATGAACTCTTTGCCTCTTAAGT 58.375 34.615 1.63 0.00 0.00 2.24
5340 5471 6.349611 GCACTCATCAAAATGGTGTCATTAGT 60.350 38.462 0.00 0.00 42.29 2.24
5405 5536 3.254166 GCCTTCAGTTCATGCAGAAGAAA 59.746 43.478 11.54 1.98 39.78 2.52
5499 5635 5.627367 CGTAACTCATAGTAGCTGCTGAATC 59.373 44.000 15.31 0.31 0.00 2.52
5515 5651 2.747989 CTCCAGCTCACTACGTAACTCA 59.252 50.000 0.00 0.00 0.00 3.41
5676 5812 7.639850 AGATCGAATTTATTGTATGTGCAAACG 59.360 33.333 0.00 0.00 31.63 3.60
5679 5815 7.498900 AGGAGATCGAATTTATTGTATGTGCAA 59.501 33.333 0.00 0.00 0.00 4.08
5707 5843 4.319046 GCATTCGAAGATGTTATGCACGAT 60.319 41.667 11.65 0.00 40.86 3.73
5829 5968 3.699894 CGCTCCAGGTGCAGAGGT 61.700 66.667 13.92 0.00 0.00 3.85
5831 5970 2.183811 CTCGCTCCAGGTGCAGAG 59.816 66.667 13.92 15.13 0.00 3.35
5949 6088 0.699399 TCTGGACTCCGGTCTTCTCT 59.301 55.000 0.00 0.00 41.82 3.10
5977 6118 2.743928 GCGGTCCTTGGAGTGCTG 60.744 66.667 5.98 0.00 0.00 4.41
5978 6119 3.241530 TGCGGTCCTTGGAGTGCT 61.242 61.111 12.34 0.00 0.00 4.40
5979 6120 2.743928 CTGCGGTCCTTGGAGTGC 60.744 66.667 6.21 6.21 0.00 4.40
5980 6121 2.743928 GCTGCGGTCCTTGGAGTG 60.744 66.667 0.00 0.00 0.00 3.51
5981 6122 2.527951 GATGCTGCGGTCCTTGGAGT 62.528 60.000 0.00 0.00 0.00 3.85
5983 6124 2.268920 GATGCTGCGGTCCTTGGA 59.731 61.111 0.00 0.00 0.00 3.53
5985 6126 2.743752 CGTGATGCTGCGGTCCTTG 61.744 63.158 0.00 0.00 0.00 3.61
5986 6127 2.434884 CGTGATGCTGCGGTCCTT 60.435 61.111 0.00 0.00 0.00 3.36
6090 6239 6.111382 ACATATCCATGATCGGAATGATGTC 58.889 40.000 0.00 0.00 38.95 3.06
6245 6395 2.165030 TCCAGTCGGAATACTCGGTTTC 59.835 50.000 0.00 0.00 38.83 2.78
6334 6484 8.328758 AGAACATAATCTTTGACTCCCAATACA 58.671 33.333 0.00 0.00 34.23 2.29
6337 6487 7.177878 ACAGAACATAATCTTTGACTCCCAAT 58.822 34.615 0.00 0.00 34.23 3.16
6391 6541 3.091545 CAGCATATCAAACAACCACCCT 58.908 45.455 0.00 0.00 0.00 4.34
6413 6563 0.531532 CATGATCCGGTCCAGCACTC 60.532 60.000 0.00 0.00 0.00 3.51
6414 6564 0.977627 TCATGATCCGGTCCAGCACT 60.978 55.000 0.00 0.00 0.00 4.40
6415 6565 0.107456 ATCATGATCCGGTCCAGCAC 59.893 55.000 1.18 0.00 0.00 4.40
6416 6566 1.715785 TATCATGATCCGGTCCAGCA 58.284 50.000 12.53 0.00 0.00 4.41
6417 6567 2.224281 TGTTATCATGATCCGGTCCAGC 60.224 50.000 12.53 0.00 0.00 4.85
6418 6568 3.751479 TGTTATCATGATCCGGTCCAG 57.249 47.619 12.53 0.00 0.00 3.86
6435 6585 1.300080 GCACTTTGGCACGCATGTT 60.300 52.632 0.00 0.00 0.00 2.71
6436 6586 2.336088 GCACTTTGGCACGCATGT 59.664 55.556 0.00 0.00 0.00 3.21
6461 6611 3.197983 CCTCTCAAAAAGTCGGTATCCCT 59.802 47.826 0.00 0.00 0.00 4.20
6491 6641 0.823356 GTGCCAAGCAGACAGGGAAA 60.823 55.000 0.00 0.00 40.08 3.13
6497 6647 0.746204 TTTGACGTGCCAAGCAGACA 60.746 50.000 0.00 0.00 40.08 3.41
6498 6648 0.380378 TTTTGACGTGCCAAGCAGAC 59.620 50.000 0.00 0.00 40.08 3.51
6521 6673 4.566987 GAGGGTTACTTCTTCGTGAACAT 58.433 43.478 0.00 0.00 0.00 2.71
6551 6735 7.994334 AGATTACCAACCACACTTTTAACACTA 59.006 33.333 0.00 0.00 0.00 2.74
6564 6748 5.734720 TCAGAATCTCAGATTACCAACCAC 58.265 41.667 0.00 0.00 0.00 4.16
6602 6792 6.616577 CCCTATAAACTAAGAGAGAGGGAGT 58.383 44.000 0.00 0.00 44.48 3.85
6603 6793 5.479027 GCCCTATAAACTAAGAGAGAGGGAG 59.521 48.000 7.83 0.00 44.48 4.30
6604 6794 5.395611 GCCCTATAAACTAAGAGAGAGGGA 58.604 45.833 7.83 0.00 44.48 4.20
6605 6795 4.218852 CGCCCTATAAACTAAGAGAGAGGG 59.781 50.000 0.00 0.00 44.52 4.30
6606 6796 4.828387 ACGCCCTATAAACTAAGAGAGAGG 59.172 45.833 0.00 0.00 0.00 3.69
6607 6797 5.764131 CACGCCCTATAAACTAAGAGAGAG 58.236 45.833 0.00 0.00 0.00 3.20
6608 6798 4.037684 GCACGCCCTATAAACTAAGAGAGA 59.962 45.833 0.00 0.00 0.00 3.10
6609 6799 4.299978 GCACGCCCTATAAACTAAGAGAG 58.700 47.826 0.00 0.00 0.00 3.20
6610 6800 3.243301 CGCACGCCCTATAAACTAAGAGA 60.243 47.826 0.00 0.00 0.00 3.10
6611 6801 3.050619 CGCACGCCCTATAAACTAAGAG 58.949 50.000 0.00 0.00 0.00 2.85
6612 6802 2.800629 GCGCACGCCCTATAAACTAAGA 60.801 50.000 0.30 0.00 34.56 2.10
6613 6803 1.525619 GCGCACGCCCTATAAACTAAG 59.474 52.381 0.30 0.00 34.56 2.18
6614 6804 1.574134 GCGCACGCCCTATAAACTAA 58.426 50.000 0.30 0.00 34.56 2.24
6615 6805 0.595567 CGCGCACGCCCTATAAACTA 60.596 55.000 8.75 0.00 37.98 2.24
6616 6806 1.881252 CGCGCACGCCCTATAAACT 60.881 57.895 8.75 0.00 37.98 2.66
6617 6807 0.871163 TACGCGCACGCCCTATAAAC 60.871 55.000 5.73 0.00 45.53 2.01
6618 6808 0.871163 GTACGCGCACGCCCTATAAA 60.871 55.000 5.73 0.00 45.53 1.40
6619 6809 1.299316 GTACGCGCACGCCCTATAA 60.299 57.895 5.73 0.00 45.53 0.98
6620 6810 2.121564 GAGTACGCGCACGCCCTATA 62.122 60.000 5.73 0.00 45.53 1.31
6621 6811 3.480225 GAGTACGCGCACGCCCTAT 62.480 63.158 5.73 0.00 45.53 2.57
6622 6812 4.183686 GAGTACGCGCACGCCCTA 62.184 66.667 5.73 0.00 45.53 3.53
6625 6815 4.183686 TAGGAGTACGCGCACGCC 62.184 66.667 22.99 22.99 45.53 5.68
6626 6816 2.389866 ATCTAGGAGTACGCGCACGC 62.390 60.000 5.73 4.99 45.53 5.34
6628 6818 1.202268 ACAATCTAGGAGTACGCGCAC 60.202 52.381 5.73 2.54 0.00 5.34
6629 6819 1.065102 GACAATCTAGGAGTACGCGCA 59.935 52.381 5.73 0.00 0.00 6.09
6630 6820 1.065102 TGACAATCTAGGAGTACGCGC 59.935 52.381 5.73 0.00 0.00 6.86
6631 6821 3.416119 TTGACAATCTAGGAGTACGCG 57.584 47.619 3.53 3.53 0.00 6.01
6632 6822 5.810587 TCAAATTGACAATCTAGGAGTACGC 59.189 40.000 0.05 0.00 0.00 4.42
6633 6823 7.223058 GTCAAATTGACAATCTAGGAGTACG 57.777 40.000 20.08 0.00 46.22 3.67
6755 6945 9.232882 ACCTAGGTTATCAATTTTATCACCCTA 57.767 33.333 9.21 0.00 0.00 3.53
6756 6946 8.114301 ACCTAGGTTATCAATTTTATCACCCT 57.886 34.615 9.21 0.00 0.00 4.34
6762 6952 9.362539 CGCGTATACCTAGGTTATCAATTTTAT 57.637 33.333 22.11 5.71 0.00 1.40
6763 6953 8.359642 ACGCGTATACCTAGGTTATCAATTTTA 58.640 33.333 22.11 0.00 0.00 1.52
6764 6954 7.212274 ACGCGTATACCTAGGTTATCAATTTT 58.788 34.615 22.11 0.00 0.00 1.82
6765 6955 6.752168 ACGCGTATACCTAGGTTATCAATTT 58.248 36.000 22.11 0.00 0.00 1.82
6766 6956 6.336842 ACGCGTATACCTAGGTTATCAATT 57.663 37.500 22.11 0.00 0.00 2.32
6767 6957 5.972107 ACGCGTATACCTAGGTTATCAAT 57.028 39.130 22.11 9.64 0.00 2.57
6768 6958 5.412594 CCTACGCGTATACCTAGGTTATCAA 59.587 44.000 22.11 0.75 0.00 2.57
6769 6959 4.937620 CCTACGCGTATACCTAGGTTATCA 59.062 45.833 22.11 1.21 0.00 2.15
6770 6960 5.064071 GTCCTACGCGTATACCTAGGTTATC 59.936 48.000 22.11 9.56 0.00 1.75
6771 6961 4.938226 GTCCTACGCGTATACCTAGGTTAT 59.062 45.833 22.11 13.54 0.00 1.89
6772 6962 4.040461 AGTCCTACGCGTATACCTAGGTTA 59.960 45.833 22.11 9.58 0.00 2.85
6773 6963 3.142174 GTCCTACGCGTATACCTAGGTT 58.858 50.000 22.11 10.62 0.00 3.50
6774 6964 2.370189 AGTCCTACGCGTATACCTAGGT 59.630 50.000 20.91 20.57 0.00 3.08
6775 6965 3.051081 AGTCCTACGCGTATACCTAGG 57.949 52.381 20.91 18.03 0.00 3.02
6776 6966 3.812053 ACAAGTCCTACGCGTATACCTAG 59.188 47.826 20.91 8.56 0.00 3.02
6777 6967 3.808728 ACAAGTCCTACGCGTATACCTA 58.191 45.455 20.91 0.00 0.00 3.08
6778 6968 2.648059 ACAAGTCCTACGCGTATACCT 58.352 47.619 20.91 12.19 0.00 3.08
6779 6969 4.552166 TTACAAGTCCTACGCGTATACC 57.448 45.455 20.91 10.04 0.00 2.73
6780 6970 5.453587 CAGTTTACAAGTCCTACGCGTATAC 59.546 44.000 20.91 19.74 0.00 1.47
6781 6971 5.123820 ACAGTTTACAAGTCCTACGCGTATA 59.876 40.000 20.91 8.44 0.00 1.47
6782 6972 4.082571 ACAGTTTACAAGTCCTACGCGTAT 60.083 41.667 20.91 5.41 0.00 3.06
6783 6973 3.253188 ACAGTTTACAAGTCCTACGCGTA 59.747 43.478 19.40 19.40 0.00 4.42
6784 6974 2.035066 ACAGTTTACAAGTCCTACGCGT 59.965 45.455 19.17 19.17 0.00 6.01
6785 6975 2.407361 CACAGTTTACAAGTCCTACGCG 59.593 50.000 3.53 3.53 0.00 6.01
6786 6976 3.427863 GTCACAGTTTACAAGTCCTACGC 59.572 47.826 0.00 0.00 0.00 4.42
6787 6977 3.667261 CGTCACAGTTTACAAGTCCTACG 59.333 47.826 0.00 0.00 0.00 3.51
6788 6978 3.985925 CCGTCACAGTTTACAAGTCCTAC 59.014 47.826 0.00 0.00 0.00 3.18
6789 6979 3.890756 TCCGTCACAGTTTACAAGTCCTA 59.109 43.478 0.00 0.00 0.00 2.94
6790 6980 2.696707 TCCGTCACAGTTTACAAGTCCT 59.303 45.455 0.00 0.00 0.00 3.85
6791 6981 3.057734 CTCCGTCACAGTTTACAAGTCC 58.942 50.000 0.00 0.00 0.00 3.85
6792 6982 3.057734 CCTCCGTCACAGTTTACAAGTC 58.942 50.000 0.00 0.00 0.00 3.01
6793 6983 2.224209 CCCTCCGTCACAGTTTACAAGT 60.224 50.000 0.00 0.00 0.00 3.16
6794 6984 2.036733 TCCCTCCGTCACAGTTTACAAG 59.963 50.000 0.00 0.00 0.00 3.16
6795 6985 2.036733 CTCCCTCCGTCACAGTTTACAA 59.963 50.000 0.00 0.00 0.00 2.41
6796 6986 1.616865 CTCCCTCCGTCACAGTTTACA 59.383 52.381 0.00 0.00 0.00 2.41
6797 6987 1.617357 ACTCCCTCCGTCACAGTTTAC 59.383 52.381 0.00 0.00 0.00 2.01
6798 6988 2.005370 ACTCCCTCCGTCACAGTTTA 57.995 50.000 0.00 0.00 0.00 2.01
6799 6989 2.005370 TACTCCCTCCGTCACAGTTT 57.995 50.000 0.00 0.00 0.00 2.66
6800 6990 2.233305 ATACTCCCTCCGTCACAGTT 57.767 50.000 0.00 0.00 0.00 3.16
6801 6991 2.233305 AATACTCCCTCCGTCACAGT 57.767 50.000 0.00 0.00 0.00 3.55
6802 6992 4.730949 TTTAATACTCCCTCCGTCACAG 57.269 45.455 0.00 0.00 0.00 3.66
6803 6993 5.486735 TTTTTAATACTCCCTCCGTCACA 57.513 39.130 0.00 0.00 0.00 3.58
6840 7030 9.784531 CAAATCCTCATCTAGAATTAAAGCCTA 57.215 33.333 0.00 0.00 0.00 3.93
6841 7031 8.277918 ACAAATCCTCATCTAGAATTAAAGCCT 58.722 33.333 0.00 0.00 0.00 4.58
6842 7032 8.348507 CACAAATCCTCATCTAGAATTAAAGCC 58.651 37.037 0.00 0.00 0.00 4.35
6843 7033 8.348507 CCACAAATCCTCATCTAGAATTAAAGC 58.651 37.037 0.00 0.00 0.00 3.51
6844 7034 8.348507 GCCACAAATCCTCATCTAGAATTAAAG 58.651 37.037 0.00 0.00 0.00 1.85
6845 7035 8.055181 AGCCACAAATCCTCATCTAGAATTAAA 58.945 33.333 0.00 0.00 0.00 1.52
6846 7036 7.577303 AGCCACAAATCCTCATCTAGAATTAA 58.423 34.615 0.00 0.00 0.00 1.40
6847 7037 7.071698 AGAGCCACAAATCCTCATCTAGAATTA 59.928 37.037 0.00 0.00 0.00 1.40
6848 7038 6.011122 AGCCACAAATCCTCATCTAGAATT 57.989 37.500 0.00 0.00 0.00 2.17
6849 7039 5.369110 AGAGCCACAAATCCTCATCTAGAAT 59.631 40.000 0.00 0.00 0.00 2.40
6850 7040 4.718774 AGAGCCACAAATCCTCATCTAGAA 59.281 41.667 0.00 0.00 0.00 2.10
6851 7041 4.293494 AGAGCCACAAATCCTCATCTAGA 58.707 43.478 0.00 0.00 0.00 2.43
6852 7042 4.686191 AGAGCCACAAATCCTCATCTAG 57.314 45.455 0.00 0.00 0.00 2.43
6853 7043 4.384537 CCAAGAGCCACAAATCCTCATCTA 60.385 45.833 0.00 0.00 0.00 1.98
6854 7044 3.618351 CAAGAGCCACAAATCCTCATCT 58.382 45.455 0.00 0.00 0.00 2.90
6855 7045 2.686915 CCAAGAGCCACAAATCCTCATC 59.313 50.000 0.00 0.00 0.00 2.92
6856 7046 2.622452 CCCAAGAGCCACAAATCCTCAT 60.622 50.000 0.00 0.00 0.00 2.90
6857 7047 1.272092 CCCAAGAGCCACAAATCCTCA 60.272 52.381 0.00 0.00 0.00 3.86
6858 7048 1.272147 ACCCAAGAGCCACAAATCCTC 60.272 52.381 0.00 0.00 0.00 3.71
6859 7049 0.779997 ACCCAAGAGCCACAAATCCT 59.220 50.000 0.00 0.00 0.00 3.24
6860 7050 0.890683 CACCCAAGAGCCACAAATCC 59.109 55.000 0.00 0.00 0.00 3.01
6861 7051 0.244721 GCACCCAAGAGCCACAAATC 59.755 55.000 0.00 0.00 0.00 2.17
6862 7052 2.354902 GCACCCAAGAGCCACAAAT 58.645 52.632 0.00 0.00 0.00 2.32
6863 7053 3.854856 GCACCCAAGAGCCACAAA 58.145 55.556 0.00 0.00 0.00 2.83
6869 7059 2.203337 TGTGTGGCACCCAAGAGC 60.203 61.111 16.26 0.00 34.18 4.09
6870 7060 2.253758 CGTGTGTGGCACCCAAGAG 61.254 63.158 16.26 1.16 44.97 2.85
6871 7061 2.203139 CGTGTGTGGCACCCAAGA 60.203 61.111 16.26 0.00 44.97 3.02
6872 7062 3.964875 GCGTGTGTGGCACCCAAG 61.965 66.667 16.26 13.50 44.97 3.61
6873 7063 4.497984 AGCGTGTGTGGCACCCAA 62.498 61.111 16.26 0.00 44.97 4.12
6874 7064 4.497984 AAGCGTGTGTGGCACCCA 62.498 61.111 16.26 7.00 44.97 4.51
6875 7065 3.964875 CAAGCGTGTGTGGCACCC 61.965 66.667 16.26 3.63 44.97 4.61
6876 7066 1.234615 ATACAAGCGTGTGTGGCACC 61.235 55.000 15.96 7.17 44.97 5.01
6877 7067 0.165944 GATACAAGCGTGTGTGGCAC 59.834 55.000 15.96 11.55 44.36 5.01
6878 7068 0.034756 AGATACAAGCGTGTGTGGCA 59.965 50.000 15.96 0.00 38.82 4.92
6879 7069 0.721718 GAGATACAAGCGTGTGTGGC 59.278 55.000 15.96 0.00 38.82 5.01
6880 7070 0.992072 CGAGATACAAGCGTGTGTGG 59.008 55.000 15.96 0.00 38.82 4.17
6881 7071 0.992072 CCGAGATACAAGCGTGTGTG 59.008 55.000 15.96 0.00 38.82 3.82
6882 7072 0.108804 CCCGAGATACAAGCGTGTGT 60.109 55.000 15.96 8.85 38.82 3.72
6883 7073 0.172578 TCCCGAGATACAAGCGTGTG 59.827 55.000 15.96 0.00 38.82 3.82
6884 7074 0.456221 CTCCCGAGATACAAGCGTGT 59.544 55.000 10.83 10.83 42.09 4.49
6885 7075 0.872021 GCTCCCGAGATACAAGCGTG 60.872 60.000 0.00 0.00 0.00 5.34
6886 7076 1.437986 GCTCCCGAGATACAAGCGT 59.562 57.895 0.00 0.00 0.00 5.07
6887 7077 1.300233 GGCTCCCGAGATACAAGCG 60.300 63.158 0.00 0.00 33.77 4.68
6888 7078 4.760757 GGCTCCCGAGATACAAGC 57.239 61.111 0.00 0.00 0.00 4.01
6899 7089 2.032681 GGGCATATCACGGCTCCC 59.967 66.667 0.00 0.00 0.00 4.30
6900 7090 2.357517 CGGGCATATCACGGCTCC 60.358 66.667 0.00 0.00 0.00 4.70
6901 7091 2.357517 CCGGGCATATCACGGCTC 60.358 66.667 0.00 0.00 41.23 4.70
6923 7113 4.814294 AGTTCGATCCACGCCGCC 62.814 66.667 0.00 0.00 42.26 6.13
6924 7114 3.255379 GAGTTCGATCCACGCCGC 61.255 66.667 0.00 0.00 42.26 6.53
6925 7115 2.582498 GGAGTTCGATCCACGCCG 60.582 66.667 0.00 0.00 42.26 6.46
6926 7116 1.389609 TAGGGAGTTCGATCCACGCC 61.390 60.000 7.35 3.83 41.52 5.68
6927 7117 2.112898 TAGGGAGTTCGATCCACGC 58.887 57.895 7.35 3.05 41.52 5.34


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

AutoCloner maintained by Alex Coulton.