Multiple sequence alignment - TraesCS2D01G308700

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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 TraesCS2D01G308700 chr2D 100.000 6028 0 0 1 6028 395634588 395640615 0.000000e+00 11132.0
1 TraesCS2D01G308700 chr2D 87.692 65 3 1 5808 5867 572958365 572958429 3.010000e-08 71.3
2 TraesCS2D01G308700 chr2B 95.908 2737 90 8 382 3116 469188481 469191197 0.000000e+00 4414.0
3 TraesCS2D01G308700 chr2B 94.897 2567 86 19 3113 5659 469191263 469193804 0.000000e+00 3973.0
4 TraesCS2D01G308700 chr2B 91.688 385 22 2 1 385 469188057 469188431 5.350000e-145 525.0
5 TraesCS2D01G308700 chr2B 95.833 48 2 0 5864 5911 469193825 469193872 1.800000e-10 78.7
6 TraesCS2D01G308700 chr2A 95.441 2413 62 15 3113 5518 533944157 533946528 0.000000e+00 3803.0
7 TraesCS2D01G308700 chr2A 96.386 2269 63 7 856 3116 533941832 533944089 0.000000e+00 3718.0
8 TraesCS2D01G308700 chr2A 92.079 303 22 2 1 302 533940556 533940857 5.580000e-115 425.0
9 TraesCS2D01G308700 chr2A 91.342 231 17 3 352 581 533940859 533941087 4.540000e-81 313.0
10 TraesCS2D01G308700 chr2A 93.590 156 8 1 5517 5672 533946670 533946823 1.310000e-56 231.0
11 TraesCS2D01G308700 chr2A 85.455 165 7 10 5871 6027 533946882 533947037 8.090000e-34 156.0
12 TraesCS2D01G308700 chr2A 81.884 138 16 6 5671 5807 759451686 759451815 2.300000e-19 108.0
13 TraesCS2D01G308700 chr2A 89.062 64 2 3 5808 5866 759451784 759451847 2.330000e-09 75.0
14 TraesCS2D01G308700 chr2A 90.741 54 2 3 780 830 533941475 533941528 1.080000e-07 69.4
15 TraesCS2D01G308700 chr2A 86.364 66 4 3 5808 5868 728022246 728022311 3.900000e-07 67.6
16 TraesCS2D01G308700 chr2A 88.462 52 6 0 582 633 9094762 9094813 5.040000e-06 63.9
17 TraesCS2D01G308700 chr1A 84.892 139 16 5 5672 5807 495128997 495129133 1.050000e-27 135.0
18 TraesCS2D01G308700 chr1A 90.323 62 1 4 5808 5864 495129102 495129163 6.480000e-10 76.8
19 TraesCS2D01G308700 chr6D 98.305 59 0 1 3110 3167 126434280 126434338 1.070000e-17 102.0
20 TraesCS2D01G308700 chr6B 98.305 59 0 1 3110 3167 224870718 224870776 1.070000e-17 102.0
21 TraesCS2D01G308700 chr4D 98.305 59 0 1 3110 3167 37038683 37038741 1.070000e-17 102.0
22 TraesCS2D01G308700 chr4D 87.273 55 4 3 581 633 453482653 453482600 6.520000e-05 60.2
23 TraesCS2D01G308700 chr1D 100.000 55 0 0 3113 3167 105967627 105967573 1.070000e-17 102.0
24 TraesCS2D01G308700 chr4B 98.246 57 1 0 3111 3167 179303075 179303019 3.840000e-17 100.0
25 TraesCS2D01G308700 chrUn 92.537 67 3 2 3103 3167 730576 730510 1.790000e-15 95.3
26 TraesCS2D01G308700 chrUn 92.537 67 3 2 3103 3167 229396391 229396457 1.790000e-15 95.3
27 TraesCS2D01G308700 chrUn 88.889 54 2 4 582 631 39599238 39599291 5.040000e-06 63.9
28 TraesCS2D01G308700 chr7A 88.571 70 3 5 569 636 720228157 720228223 5.010000e-11 80.5
29 TraesCS2D01G308700 chr7A 87.692 65 3 4 5808 5867 578430501 578430437 3.010000e-08 71.3
30 TraesCS2D01G308700 chr4A 87.500 72 3 4 5808 5873 148757428 148757357 1.800000e-10 78.7
31 TraesCS2D01G308700 chr3A 86.301 73 5 5 569 639 717425572 717425503 2.330000e-09 75.0
32 TraesCS2D01G308700 chr5A 88.710 62 3 3 5808 5865 521287920 521287981 8.380000e-09 73.1
33 TraesCS2D01G308700 chr5A 83.333 78 8 4 577 651 28312490 28312565 3.900000e-07 67.6
34 TraesCS2D01G308700 chr5D 97.619 42 0 1 577 617 321614926 321614885 3.010000e-08 71.3
35 TraesCS2D01G308700 chr5D 88.710 62 2 4 5808 5864 520249178 520249117 3.010000e-08 71.3
36 TraesCS2D01G308700 chr6A 79.612 103 16 3 5745 5847 47134921 47135018 1.080000e-07 69.4
37 TraesCS2D01G308700 chr6A 91.489 47 2 2 577 623 94180854 94180810 5.040000e-06 63.9


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 TraesCS2D01G308700 chr2D 395634588 395640615 6027 False 11132.000000 11132 100.000000 1 6028 1 chr2D.!!$F1 6027
1 TraesCS2D01G308700 chr2B 469188057 469193872 5815 False 2247.675000 4414 94.581500 1 5911 4 chr2B.!!$F1 5910
2 TraesCS2D01G308700 chr2A 533940556 533947037 6481 False 1245.057143 3803 92.147714 1 6027 7 chr2A.!!$F3 6026

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
148 149 0.923358 AAGTTGTGGGTGAGTTGGGA 59.077 50.000 0.00 0.00 0.0 4.37 F
1167 1710 0.175989 CGAGAGAAGCCCTAACCCAC 59.824 60.000 0.00 0.00 0.0 4.61 F
1315 1858 1.263484 CGGATTGCTCATCTGTGATGC 59.737 52.381 2.93 0.00 33.9 3.91 F
1442 1987 1.471153 GCGGCTACTCTGGGTAAGTTC 60.471 57.143 0.00 0.00 0.0 3.01 F
3153 3777 1.303309 GATAGCAAGCTTCCACGCAT 58.697 50.000 8.96 1.45 0.0 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1252 1795 0.727122 CACGTACGTCCTCGGTGTTC 60.727 60.000 19.94 0.0 41.85 3.18 R
2561 3113 1.318576 ACAACCAGCCAAGTAACAGC 58.681 50.000 0.00 0.0 0.00 4.40 R
3078 3630 4.400884 TGCGGCCATAATCTTTACAACATT 59.599 37.500 2.24 0.0 0.00 2.71 R
3345 3969 4.447724 GGAATAGAAATACGCGCAGAATCA 59.552 41.667 5.73 0.0 0.00 2.57 R
5070 5701 0.035343 AGCCCTCGCTTTTTCCCTAC 60.035 55.000 0.00 0.0 45.55 3.18 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
53 54 5.104527 TCCGACTATTGATCCTTCCAACAAT 60.105 40.000 0.00 0.00 36.94 2.71
73 74 3.906720 TGGTGAGTAGGCCAAGATAAC 57.093 47.619 5.01 0.00 0.00 1.89
148 149 0.923358 AAGTTGTGGGTGAGTTGGGA 59.077 50.000 0.00 0.00 0.00 4.37
158 159 3.610911 GGTGAGTTGGGACTGAAATAGG 58.389 50.000 0.00 0.00 35.88 2.57
161 162 5.280317 GGTGAGTTGGGACTGAAATAGGTAA 60.280 44.000 0.00 0.00 35.88 2.85
186 187 8.546597 AAACTTTTGCTCTTGTTAACACATTT 57.453 26.923 8.07 0.00 31.06 2.32
187 188 8.546597 AACTTTTGCTCTTGTTAACACATTTT 57.453 26.923 8.07 0.00 31.06 1.82
194 195 6.642707 TCTTGTTAACACATTTTTCCCGAT 57.357 33.333 8.07 0.00 31.06 4.18
203 204 1.378531 TTTTTCCCGATGCATCTCCG 58.621 50.000 23.73 11.90 0.00 4.63
295 297 3.953612 TGAGTGAAAAGCAAGTGGTTCAT 59.046 39.130 0.00 0.00 34.26 2.57
336 338 6.986817 GCTTGCTCTAATACCTCTATCAACAA 59.013 38.462 0.00 0.00 0.00 2.83
339 341 9.905713 TTGCTCTAATACCTCTATCAACAAAAT 57.094 29.630 0.00 0.00 0.00 1.82
441 496 1.248486 GCCCCTCAAAGGAGTGAAAC 58.752 55.000 0.00 0.00 37.67 2.78
503 558 7.374754 CGAACTGACGAAAACACATTTCATAAA 59.625 33.333 0.00 0.00 46.42 1.40
535 590 4.024133 CCAAATTTACACAAAAGCCAAGCC 60.024 41.667 0.00 0.00 0.00 4.35
600 655 1.271379 ACGAAAAAGAATTTCCCCCGC 59.729 47.619 0.00 0.00 37.28 6.13
638 693 1.136363 CGACCACAACACAAGCATACG 60.136 52.381 0.00 0.00 0.00 3.06
646 701 2.346803 ACACAAGCATACGGTAGCAAG 58.653 47.619 10.66 6.25 0.00 4.01
647 702 2.028476 ACACAAGCATACGGTAGCAAGA 60.028 45.455 10.66 0.00 0.00 3.02
750 850 9.340695 GCAGAAATAAAAATTATGCCCAAAAAC 57.659 29.630 0.00 0.00 0.00 2.43
755 855 9.579932 AATAAAAATTATGCCCAAAAACCTTCA 57.420 25.926 0.00 0.00 0.00 3.02
760 860 2.745968 TGCCCAAAAACCTTCACTCTT 58.254 42.857 0.00 0.00 0.00 2.85
910 1452 4.775780 TCTCTTTCTCCATTTCCCTTCGTA 59.224 41.667 0.00 0.00 0.00 3.43
916 1458 4.130118 CTCCATTTCCCTTCGTATTCTGG 58.870 47.826 0.00 0.00 0.00 3.86
930 1473 3.697747 CTGGGGTTCGCCGTACCA 61.698 66.667 14.96 3.75 37.40 3.25
1065 1608 1.378778 CGAACCGTCCTCCTCCTCT 60.379 63.158 0.00 0.00 0.00 3.69
1138 1681 2.352032 CCCACCCGTCTCCTCACTC 61.352 68.421 0.00 0.00 0.00 3.51
1167 1710 0.175989 CGAGAGAAGCCCTAACCCAC 59.824 60.000 0.00 0.00 0.00 4.61
1204 1747 2.813908 CTCCACAAGTACGCGCCC 60.814 66.667 5.73 0.00 0.00 6.13
1305 1848 2.643551 GGGAATTTCTCGGATTGCTCA 58.356 47.619 0.00 0.00 0.00 4.26
1315 1858 1.263484 CGGATTGCTCATCTGTGATGC 59.737 52.381 2.93 0.00 33.90 3.91
1356 1899 3.066760 GTGTTCCTTTTGGGTTCTCTGTG 59.933 47.826 0.00 0.00 40.87 3.66
1357 1900 3.288092 GTTCCTTTTGGGTTCTCTGTGT 58.712 45.455 0.00 0.00 40.87 3.72
1442 1987 1.471153 GCGGCTACTCTGGGTAAGTTC 60.471 57.143 0.00 0.00 0.00 3.01
1643 2194 3.756434 AGCTAAATTTCTAAAGCACCGCA 59.244 39.130 12.08 0.00 37.44 5.69
1820 2371 7.733402 TTATTGTTTCTGTTTTAGGCGTACT 57.267 32.000 0.00 0.00 0.00 2.73
1821 2372 5.412526 TTGTTTCTGTTTTAGGCGTACTG 57.587 39.130 0.00 0.00 0.00 2.74
1822 2373 4.695396 TGTTTCTGTTTTAGGCGTACTGA 58.305 39.130 0.00 0.00 0.00 3.41
1823 2374 5.117584 TGTTTCTGTTTTAGGCGTACTGAA 58.882 37.500 0.00 0.00 0.00 3.02
1824 2375 5.006941 TGTTTCTGTTTTAGGCGTACTGAAC 59.993 40.000 0.00 1.40 32.06 3.18
1825 2376 4.325028 TCTGTTTTAGGCGTACTGAACA 57.675 40.909 8.18 8.18 36.11 3.18
1826 2377 4.304110 TCTGTTTTAGGCGTACTGAACAG 58.696 43.478 19.95 19.95 45.80 3.16
1827 2378 4.056050 CTGTTTTAGGCGTACTGAACAGT 58.944 43.478 18.79 12.10 42.94 3.55
1828 2379 4.444536 TGTTTTAGGCGTACTGAACAGTT 58.555 39.130 12.66 0.00 42.54 3.16
1829 2380 4.877251 TGTTTTAGGCGTACTGAACAGTTT 59.123 37.500 12.66 0.00 42.54 2.66
1980 2531 7.432252 GCTTATTGCTCACATTGGTATGTTTAC 59.568 37.037 0.00 0.00 39.72 2.01
2209 2760 4.431416 TGCTTCTTGACCTTGACCTTTA 57.569 40.909 0.00 0.00 0.00 1.85
2216 2767 6.349300 TCTTGACCTTGACCTTTATCTATGC 58.651 40.000 0.00 0.00 0.00 3.14
2407 2958 6.607600 AGTTCTAGTCAGTGGACATATTAGCA 59.392 38.462 0.00 0.00 46.80 3.49
2426 2977 7.806680 TTAGCATGATATATCCCTTGGTACA 57.193 36.000 10.25 4.71 0.00 2.90
2512 3064 6.464895 TTCCACGGTTATAAAACTAACACG 57.535 37.500 0.00 0.00 35.81 4.49
2670 3222 2.569404 AGTGATCCACTCTTTGACCTCC 59.431 50.000 0.00 0.00 41.21 4.30
2996 3548 6.798482 TCATGCCATTTCAGCTTTAAGTATG 58.202 36.000 0.00 0.00 0.00 2.39
3078 3630 8.673711 CACTTGATTTTCGGAAGTATGGATTTA 58.326 33.333 0.00 0.00 0.00 1.40
3153 3777 1.303309 GATAGCAAGCTTCCACGCAT 58.697 50.000 8.96 1.45 0.00 4.73
3244 3868 9.487790 CAAGTGGAATTCTTATAAAAAGCCAAA 57.512 29.630 5.23 0.00 0.00 3.28
3438 4062 3.809832 ACGTAATGCATGCCTGTATCTTC 59.190 43.478 16.68 0.00 0.00 2.87
3517 4141 8.887264 TTTGGGTGACTAAATATATTGGTGTT 57.113 30.769 0.00 0.00 35.71 3.32
3617 4241 9.289782 ACCTGATTATGGTCTTTATGCTATTTC 57.710 33.333 0.00 0.00 31.03 2.17
3852 4476 7.654022 TCTTGTTGGTTTTGGAAATACTTCT 57.346 32.000 0.00 0.00 0.00 2.85
3920 4544 8.190784 GCACATAAATGCTTCTGTTTTAGGTAT 58.809 33.333 0.00 0.00 42.62 2.73
4040 4664 8.379161 CAGTCTGAGAAACTCTATTTTCATTCG 58.621 37.037 0.00 0.00 37.86 3.34
4051 4675 3.965292 TTTTCATTCGTTACCGTTGCA 57.035 38.095 0.00 0.00 35.01 4.08
4077 4701 2.360801 TGGCTTGTGCTAAAACCTTCAC 59.639 45.455 0.00 0.00 39.59 3.18
4109 4733 3.792401 TGTGCTATTCATTTCCGATCGT 58.208 40.909 15.09 0.00 0.00 3.73
4123 4747 7.598189 TTTCCGATCGTTTGTTATCATTGTA 57.402 32.000 15.09 0.00 0.00 2.41
4410 5035 4.949238 TGCAGGAAAGTATGTGTAATGCAT 59.051 37.500 0.00 0.00 36.33 3.96
4710 5335 9.863845 TCATCTACTGATTGTTGTTCGTTATTA 57.136 29.630 0.00 0.00 0.00 0.98
4844 5469 7.428020 TGAAAACTTCATTTCAGGAAGATGTG 58.572 34.615 8.96 0.00 42.68 3.21
4962 5587 6.092533 CCATTTCCAAATATTTGCTTCGCTTT 59.907 34.615 20.67 0.00 36.86 3.51
4973 5598 3.146066 TGCTTCGCTTTCCAACTAATGT 58.854 40.909 0.00 0.00 0.00 2.71
5070 5701 2.362736 ACTGCCAACATCAGCACTATG 58.637 47.619 0.00 0.00 35.04 2.23
5076 5707 3.134623 CCAACATCAGCACTATGTAGGGA 59.865 47.826 9.33 0.00 36.56 4.20
5106 5737 0.739813 GCTCGTATCGGTGCCTGTTT 60.740 55.000 0.00 0.00 0.00 2.83
5155 5786 4.442375 TGTGCCAAAAAGAAAGACGAAA 57.558 36.364 0.00 0.00 0.00 3.46
5157 5788 4.170256 GTGCCAAAAAGAAAGACGAAACA 58.830 39.130 0.00 0.00 0.00 2.83
5251 5882 9.592720 GTGCCATTTGTAAATAAATTTTCACAC 57.407 29.630 0.00 0.00 28.84 3.82
5425 6057 5.843969 TGAGCCTTGGAGACCATATTATACA 59.156 40.000 0.00 0.00 31.53 2.29
5437 6069 5.633601 ACCATATTATACACAGTCGAATGCG 59.366 40.000 13.64 5.98 39.35 4.73
5457 6089 6.641176 TGCGTAGTGTACATACAAGATTTG 57.359 37.500 0.00 0.00 38.04 2.32
5458 6090 5.062934 TGCGTAGTGTACATACAAGATTTGC 59.937 40.000 0.00 1.68 38.04 3.68
5459 6091 5.062934 GCGTAGTGTACATACAAGATTTGCA 59.937 40.000 0.00 0.00 38.04 4.08
5460 6092 6.466812 CGTAGTGTACATACAAGATTTGCAC 58.533 40.000 0.00 0.00 38.04 4.57
5461 6093 6.310467 CGTAGTGTACATACAAGATTTGCACT 59.690 38.462 0.00 0.00 38.04 4.40
5462 6094 7.148639 CGTAGTGTACATACAAGATTTGCACTT 60.149 37.037 0.00 0.00 38.04 3.16
5463 6095 7.510549 AGTGTACATACAAGATTTGCACTTT 57.489 32.000 0.00 0.00 38.04 2.66
5513 6145 7.702348 AGATTTTGTTGTTGTTGAAGCTAAGAC 59.298 33.333 0.00 0.00 0.00 3.01
5597 6372 5.751243 ACGGCATGATATTTTACTGGTTC 57.249 39.130 0.00 0.00 0.00 3.62
5672 6456 6.025539 ACATATGAGAGGGGATATAACTGCA 58.974 40.000 10.38 0.00 0.00 4.41
5673 6457 4.899352 ATGAGAGGGGATATAACTGCAC 57.101 45.455 0.00 0.00 0.00 4.57
5674 6458 3.653164 TGAGAGGGGATATAACTGCACA 58.347 45.455 0.00 0.00 0.00 4.57
5675 6459 4.234550 TGAGAGGGGATATAACTGCACAT 58.765 43.478 0.00 0.00 0.00 3.21
5676 6460 4.284490 TGAGAGGGGATATAACTGCACATC 59.716 45.833 0.00 0.00 0.00 3.06
5677 6461 4.497516 AGAGGGGATATAACTGCACATCT 58.502 43.478 0.00 0.00 0.00 2.90
5678 6462 5.655394 AGAGGGGATATAACTGCACATCTA 58.345 41.667 0.00 0.00 0.00 1.98
5679 6463 5.719085 AGAGGGGATATAACTGCACATCTAG 59.281 44.000 0.00 0.00 0.00 2.43
5680 6464 5.655394 AGGGGATATAACTGCACATCTAGA 58.345 41.667 0.00 0.00 0.00 2.43
5681 6465 5.482175 AGGGGATATAACTGCACATCTAGAC 59.518 44.000 0.00 0.00 0.00 2.59
5682 6466 5.403246 GGGATATAACTGCACATCTAGACG 58.597 45.833 0.00 0.00 0.00 4.18
5683 6467 5.047943 GGGATATAACTGCACATCTAGACGT 60.048 44.000 0.00 0.00 0.00 4.34
5684 6468 5.859114 GGATATAACTGCACATCTAGACGTG 59.141 44.000 14.50 14.50 36.18 4.49
5685 6469 4.720649 ATAACTGCACATCTAGACGTGT 57.279 40.909 19.27 6.97 35.51 4.49
5686 6470 2.638556 ACTGCACATCTAGACGTGTC 57.361 50.000 19.27 12.33 35.51 3.67
5687 6471 2.163509 ACTGCACATCTAGACGTGTCT 58.836 47.619 19.27 7.77 43.40 3.41
5688 6472 2.558795 ACTGCACATCTAGACGTGTCTT 59.441 45.455 19.27 2.17 40.93 3.01
5689 6473 3.756963 ACTGCACATCTAGACGTGTCTTA 59.243 43.478 19.27 4.45 40.93 2.10
5690 6474 4.217767 ACTGCACATCTAGACGTGTCTTAA 59.782 41.667 19.27 1.56 40.93 1.85
5691 6475 5.105716 ACTGCACATCTAGACGTGTCTTAAT 60.106 40.000 19.27 0.00 40.93 1.40
5692 6476 5.720202 TGCACATCTAGACGTGTCTTAATT 58.280 37.500 19.27 0.00 40.93 1.40
5693 6477 6.859017 TGCACATCTAGACGTGTCTTAATTA 58.141 36.000 19.27 0.00 40.93 1.40
5694 6478 7.489160 TGCACATCTAGACGTGTCTTAATTAT 58.511 34.615 19.27 0.00 40.93 1.28
5695 6479 7.979537 TGCACATCTAGACGTGTCTTAATTATT 59.020 33.333 19.27 0.00 40.93 1.40
5696 6480 8.269424 GCACATCTAGACGTGTCTTAATTATTG 58.731 37.037 19.27 0.00 40.93 1.90
5697 6481 9.302345 CACATCTAGACGTGTCTTAATTATTGT 57.698 33.333 10.77 0.00 40.93 2.71
5720 6504 9.534565 TTGTATATCTAAGTGACTCAATCAAGC 57.465 33.333 0.00 0.00 39.72 4.01
5721 6505 8.695456 TGTATATCTAAGTGACTCAATCAAGCA 58.305 33.333 0.00 0.00 39.72 3.91
5722 6506 9.703892 GTATATCTAAGTGACTCAATCAAGCAT 57.296 33.333 0.00 0.00 39.72 3.79
5726 6510 8.846943 TCTAAGTGACTCAATCAAGCATAAAA 57.153 30.769 0.00 0.00 39.72 1.52
5727 6511 9.283768 TCTAAGTGACTCAATCAAGCATAAAAA 57.716 29.630 0.00 0.00 39.72 1.94
5755 6539 9.374711 AGATAAAGAAAAAGGAAAATACCCACA 57.625 29.630 0.00 0.00 0.00 4.17
5757 6541 9.942850 ATAAAGAAAAAGGAAAATACCCACATG 57.057 29.630 0.00 0.00 0.00 3.21
5758 6542 7.610580 AAGAAAAAGGAAAATACCCACATGA 57.389 32.000 0.00 0.00 0.00 3.07
5759 6543 7.610580 AGAAAAAGGAAAATACCCACATGAA 57.389 32.000 0.00 0.00 0.00 2.57
5760 6544 8.206126 AGAAAAAGGAAAATACCCACATGAAT 57.794 30.769 0.00 0.00 0.00 2.57
5761 6545 8.314021 AGAAAAAGGAAAATACCCACATGAATC 58.686 33.333 0.00 0.00 0.00 2.52
5762 6546 7.797121 AAAAGGAAAATACCCACATGAATCT 57.203 32.000 0.00 0.00 0.00 2.40
5763 6547 7.410120 AAAGGAAAATACCCACATGAATCTC 57.590 36.000 0.00 0.00 0.00 2.75
5764 6548 5.449553 AGGAAAATACCCACATGAATCTCC 58.550 41.667 0.00 0.00 0.00 3.71
5765 6549 4.275936 GGAAAATACCCACATGAATCTCCG 59.724 45.833 0.00 0.00 0.00 4.63
5766 6550 4.503714 AAATACCCACATGAATCTCCGT 57.496 40.909 0.00 0.00 0.00 4.69
5767 6551 2.979814 TACCCACATGAATCTCCGTG 57.020 50.000 0.00 0.00 0.00 4.94
5768 6552 0.984230 ACCCACATGAATCTCCGTGT 59.016 50.000 0.00 0.00 36.78 4.49
5769 6553 2.184533 ACCCACATGAATCTCCGTGTA 58.815 47.619 0.00 0.00 34.76 2.90
5770 6554 2.569853 ACCCACATGAATCTCCGTGTAA 59.430 45.455 0.00 0.00 34.76 2.41
5771 6555 3.008594 ACCCACATGAATCTCCGTGTAAA 59.991 43.478 0.00 0.00 34.76 2.01
5772 6556 4.006989 CCCACATGAATCTCCGTGTAAAA 58.993 43.478 0.00 0.00 34.76 1.52
5773 6557 4.640201 CCCACATGAATCTCCGTGTAAAAT 59.360 41.667 0.00 0.00 34.76 1.82
5774 6558 5.220854 CCCACATGAATCTCCGTGTAAAATC 60.221 44.000 0.00 0.00 34.76 2.17
5775 6559 5.353956 CCACATGAATCTCCGTGTAAAATCA 59.646 40.000 0.00 0.00 34.76 2.57
5776 6560 6.128035 CCACATGAATCTCCGTGTAAAATCAA 60.128 38.462 0.00 0.00 34.76 2.57
5777 6561 7.415541 CCACATGAATCTCCGTGTAAAATCAAT 60.416 37.037 0.00 0.00 34.76 2.57
5778 6562 8.611757 CACATGAATCTCCGTGTAAAATCAATA 58.388 33.333 0.00 0.00 34.76 1.90
5779 6563 9.173021 ACATGAATCTCCGTGTAAAATCAATAA 57.827 29.630 0.00 0.00 34.76 1.40
5780 6564 9.438291 CATGAATCTCCGTGTAAAATCAATAAC 57.562 33.333 0.00 0.00 0.00 1.89
5781 6565 8.554835 TGAATCTCCGTGTAAAATCAATAACA 57.445 30.769 0.00 0.00 0.00 2.41
5782 6566 9.173021 TGAATCTCCGTGTAAAATCAATAACAT 57.827 29.630 0.00 0.00 0.00 2.71
5786 6570 9.051679 TCTCCGTGTAAAATCAATAACATATGG 57.948 33.333 7.80 0.00 0.00 2.74
5787 6571 7.644490 TCCGTGTAAAATCAATAACATATGGC 58.356 34.615 7.80 0.00 0.00 4.40
5788 6572 7.500892 TCCGTGTAAAATCAATAACATATGGCT 59.499 33.333 7.80 0.00 0.00 4.75
5789 6573 8.134895 CCGTGTAAAATCAATAACATATGGCTT 58.865 33.333 7.80 0.00 0.00 4.35
5797 6581 7.439157 TCAATAACATATGGCTTAGATGTGC 57.561 36.000 7.80 0.00 40.18 4.57
5798 6582 6.997476 TCAATAACATATGGCTTAGATGTGCA 59.003 34.615 7.80 0.00 40.18 4.57
5799 6583 7.501892 TCAATAACATATGGCTTAGATGTGCAA 59.498 33.333 7.80 0.00 40.18 4.08
5800 6584 8.301720 CAATAACATATGGCTTAGATGTGCAAT 58.698 33.333 7.80 0.00 40.18 3.56
5801 6585 9.519191 AATAACATATGGCTTAGATGTGCAATA 57.481 29.630 7.80 0.00 40.18 1.90
5802 6586 6.808008 ACATATGGCTTAGATGTGCAATAC 57.192 37.500 7.80 0.00 39.63 1.89
5803 6587 6.537355 ACATATGGCTTAGATGTGCAATACT 58.463 36.000 7.80 0.00 39.63 2.12
5804 6588 7.000472 ACATATGGCTTAGATGTGCAATACTT 59.000 34.615 7.80 0.00 39.63 2.24
5805 6589 8.156820 ACATATGGCTTAGATGTGCAATACTTA 58.843 33.333 7.80 0.00 39.63 2.24
5806 6590 9.170734 CATATGGCTTAGATGTGCAATACTTAT 57.829 33.333 0.00 0.00 29.08 1.73
5809 6593 9.745018 ATGGCTTAGATGTGCAATACTTATAAT 57.255 29.630 0.00 0.00 0.00 1.28
5810 6594 9.002600 TGGCTTAGATGTGCAATACTTATAATG 57.997 33.333 0.00 0.00 0.00 1.90
5811 6595 9.219603 GGCTTAGATGTGCAATACTTATAATGA 57.780 33.333 0.00 0.00 0.00 2.57
5817 6601 9.958285 GATGTGCAATACTTATAATGACATACG 57.042 33.333 0.00 0.00 0.00 3.06
5818 6602 8.305441 TGTGCAATACTTATAATGACATACGG 57.695 34.615 0.00 0.00 0.00 4.02
5819 6603 7.095397 TGTGCAATACTTATAATGACATACGGC 60.095 37.037 0.00 0.00 0.00 5.68
5820 6604 7.117812 GTGCAATACTTATAATGACATACGGCT 59.882 37.037 0.00 0.00 0.00 5.52
5821 6605 7.659799 TGCAATACTTATAATGACATACGGCTT 59.340 33.333 0.00 0.00 0.00 4.35
5822 6606 9.146984 GCAATACTTATAATGACATACGGCTTA 57.853 33.333 0.00 0.00 0.00 3.09
5826 6610 8.988064 ACTTATAATGACATACGGCTTAGATG 57.012 34.615 0.00 0.00 0.00 2.90
5827 6611 8.585881 ACTTATAATGACATACGGCTTAGATGT 58.414 33.333 0.00 0.00 36.52 3.06
5828 6612 8.757164 TTATAATGACATACGGCTTAGATGTG 57.243 34.615 0.00 0.00 33.99 3.21
5829 6613 2.821546 TGACATACGGCTTAGATGTGC 58.178 47.619 0.00 0.00 33.99 4.57
5830 6614 2.167487 TGACATACGGCTTAGATGTGCA 59.833 45.455 0.00 0.00 33.99 4.57
5831 6615 3.194861 GACATACGGCTTAGATGTGCAA 58.805 45.455 0.00 0.00 33.99 4.08
5832 6616 3.808728 ACATACGGCTTAGATGTGCAAT 58.191 40.909 0.00 0.00 32.62 3.56
5833 6617 4.956085 ACATACGGCTTAGATGTGCAATA 58.044 39.130 0.00 0.00 32.62 1.90
5834 6618 4.750098 ACATACGGCTTAGATGTGCAATAC 59.250 41.667 0.00 0.00 32.62 1.89
5835 6619 3.543680 ACGGCTTAGATGTGCAATACT 57.456 42.857 0.00 0.00 0.00 2.12
5836 6620 3.873910 ACGGCTTAGATGTGCAATACTT 58.126 40.909 0.00 0.00 0.00 2.24
5837 6621 5.018539 ACGGCTTAGATGTGCAATACTTA 57.981 39.130 0.00 0.00 0.00 2.24
5838 6622 5.611374 ACGGCTTAGATGTGCAATACTTAT 58.389 37.500 0.00 0.00 0.00 1.73
5839 6623 5.466728 ACGGCTTAGATGTGCAATACTTATG 59.533 40.000 0.00 0.00 0.00 1.90
5840 6624 5.106948 CGGCTTAGATGTGCAATACTTATGG 60.107 44.000 0.00 0.00 0.00 2.74
5841 6625 5.335191 GGCTTAGATGTGCAATACTTATGGC 60.335 44.000 0.00 0.00 33.16 4.40
5842 6626 5.239306 GCTTAGATGTGCAATACTTATGGCA 59.761 40.000 0.00 0.00 40.19 4.92
5858 6642 3.808466 TGGCACATTGTGTTTTAGCAA 57.192 38.095 17.64 0.00 35.75 3.91
5859 6643 4.128925 TGGCACATTGTGTTTTAGCAAA 57.871 36.364 17.64 0.00 35.75 3.68
5860 6644 4.507710 TGGCACATTGTGTTTTAGCAAAA 58.492 34.783 17.64 0.00 35.75 2.44
5862 6646 7.130014 ATGGCACATTGTGTTTTAGCAAAACT 61.130 34.615 17.64 3.56 46.91 2.66
5919 6703 8.744652 AGAGATAGTTGTACATACATCATAGCC 58.255 37.037 0.00 0.00 35.89 3.93
5920 6704 8.422577 AGATAGTTGTACATACATCATAGCCA 57.577 34.615 0.00 0.00 35.89 4.75
5921 6705 8.526978 AGATAGTTGTACATACATCATAGCCAG 58.473 37.037 0.00 0.00 35.89 4.85
5936 6777 2.229792 AGCCAGCACGATTCTGAAAAA 58.770 42.857 0.00 0.00 33.54 1.94
5982 6824 3.560068 GGCAGTACATACAACATAGGCAC 59.440 47.826 0.00 0.00 0.00 5.01
5983 6825 4.442706 GCAGTACATACAACATAGGCACT 58.557 43.478 0.00 0.00 46.37 4.40
5984 6826 4.876107 GCAGTACATACAACATAGGCACTT 59.124 41.667 0.00 0.00 41.75 3.16
5985 6827 6.046593 GCAGTACATACAACATAGGCACTTA 58.953 40.000 0.00 0.00 41.75 2.24
5986 6828 6.201044 GCAGTACATACAACATAGGCACTTAG 59.799 42.308 0.00 0.00 41.75 2.18
5987 6829 6.701841 CAGTACATACAACATAGGCACTTAGG 59.298 42.308 0.00 0.00 41.75 2.69
5988 6830 4.451900 ACATACAACATAGGCACTTAGGC 58.548 43.478 0.00 0.00 41.75 3.93
5997 6839 0.902531 GGCACTTAGGCAGTAGGTGA 59.097 55.000 10.64 0.00 40.42 4.02
6013 6855 7.497249 GCAGTAGGTGATTACAAGATTCTGAAT 59.503 37.037 1.81 1.81 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.167693 CGTTATCTTGGCCTACTCACCA 59.832 50.000 3.32 0.00 0.00 4.17
63 64 4.617223 GCTTTTTCAGAACGTTATCTTGGC 59.383 41.667 0.00 0.00 0.00 4.52
73 74 2.618709 AGGTGGAAGCTTTTTCAGAACG 59.381 45.455 0.00 0.00 46.63 3.95
148 149 8.465273 AGAGCAAAAGTTTTACCTATTTCAGT 57.535 30.769 0.00 0.00 0.00 3.41
158 159 8.455598 TGTGTTAACAAGAGCAAAAGTTTTAC 57.544 30.769 10.51 0.00 31.82 2.01
161 162 8.546597 AAATGTGTTAACAAGAGCAAAAGTTT 57.453 26.923 10.51 0.00 40.46 2.66
186 187 1.116308 TACGGAGATGCATCGGGAAA 58.884 50.000 20.67 5.60 0.00 3.13
187 188 1.116308 TTACGGAGATGCATCGGGAA 58.884 50.000 20.67 13.87 0.00 3.97
194 195 1.760613 CTAGGGGTTTACGGAGATGCA 59.239 52.381 0.00 0.00 0.00 3.96
203 204 5.367060 ACTCAATGAGATCCTAGGGGTTTAC 59.633 44.000 18.20 0.00 33.32 2.01
405 460 3.322466 CCCTCGGCAAGGTGACCT 61.322 66.667 0.00 0.00 44.56 3.85
441 496 5.327091 CGTGAATGAAGAATTGCTACCTTG 58.673 41.667 0.00 0.00 0.00 3.61
503 558 7.224557 GCTTTTGTGTAAATTTGGTGAGATTGT 59.775 33.333 0.00 0.00 0.00 2.71
600 655 8.373048 TGTGGTCGGTGCTTTATAATATAAAG 57.627 34.615 22.11 22.11 37.53 1.85
638 693 8.296713 TCAAACTCAAATACAAATCTTGCTACC 58.703 33.333 0.00 0.00 0.00 3.18
690 790 6.825610 TGCCCTAAAACTTTCAAACATGAAT 58.174 32.000 0.00 0.00 0.00 2.57
750 850 7.334671 GTGATTTTTAGGGTAGAAGAGTGAAGG 59.665 40.741 0.00 0.00 0.00 3.46
760 860 9.856162 AGTGTTTTTAGTGATTTTTAGGGTAGA 57.144 29.630 0.00 0.00 0.00 2.59
799 901 4.873817 TCTTCAACACATGATGCAAAAGG 58.126 39.130 0.00 0.00 38.03 3.11
910 1452 1.219935 GTACGGCGAACCCCAGAAT 59.780 57.895 16.62 0.00 0.00 2.40
916 1458 2.584143 CGATGGTACGGCGAACCC 60.584 66.667 16.62 10.70 36.06 4.11
1014 1557 2.036414 TCCTGCAGCGAGGAGAGT 59.964 61.111 8.66 0.00 37.20 3.24
1051 1594 3.151022 GGCAGAGGAGGAGGACGG 61.151 72.222 0.00 0.00 0.00 4.79
1167 1710 2.357517 AGTGGCTGCGAAGGAACG 60.358 61.111 0.00 0.00 0.00 3.95
1204 1747 1.144057 GTAGGCCGACCAGTCCATG 59.856 63.158 4.34 0.00 39.06 3.66
1252 1795 0.727122 CACGTACGTCCTCGGTGTTC 60.727 60.000 19.94 0.00 41.85 3.18
1253 1796 1.283793 CACGTACGTCCTCGGTGTT 59.716 57.895 19.94 0.00 41.85 3.32
1305 1848 2.429971 AGTCAGATCACGCATCACAGAT 59.570 45.455 0.00 0.00 33.29 2.90
1315 1858 4.748892 ACACTTCCAATAGTCAGATCACG 58.251 43.478 0.00 0.00 0.00 4.35
1356 1899 6.366315 TGTACACATTGAAAACCTACACAC 57.634 37.500 0.00 0.00 0.00 3.82
1357 1900 6.016693 CCATGTACACATTGAAAACCTACACA 60.017 38.462 0.00 0.00 33.61 3.72
1442 1987 3.246226 GCTCATTGTAACCGTAGCATCTG 59.754 47.826 0.00 0.00 0.00 2.90
1643 2194 3.525199 CCTAAGGCCATAATAGCTGGGAT 59.475 47.826 5.01 0.00 34.16 3.85
1823 2374 9.535878 TTGTCTTTAAAAACTGTTCAAAACTGT 57.464 25.926 0.00 0.00 44.10 3.55
1824 2375 9.791838 GTTGTCTTTAAAAACTGTTCAAAACTG 57.208 29.630 0.00 0.00 36.53 3.16
1825 2376 9.535878 TGTTGTCTTTAAAAACTGTTCAAAACT 57.464 25.926 0.00 0.00 0.00 2.66
1980 2531 4.769345 AAGCCTAAGGAAGATTGAGGAG 57.231 45.455 0.00 0.00 0.00 3.69
2209 2760 7.478322 CAGTTGCAAATAACAAGAGCATAGAT 58.522 34.615 0.00 0.00 34.87 1.98
2407 2958 5.547666 TGCACTGTACCAAGGGATATATCAT 59.452 40.000 14.60 0.00 0.00 2.45
2541 3093 7.483580 ACAGCAGAGTAACTAAAGGTAGAAT 57.516 36.000 0.00 0.00 0.00 2.40
2552 3104 3.325135 AGCCAAGTAACAGCAGAGTAACT 59.675 43.478 0.00 0.00 0.00 2.24
2561 3113 1.318576 ACAACCAGCCAAGTAACAGC 58.681 50.000 0.00 0.00 0.00 4.40
3078 3630 4.400884 TGCGGCCATAATCTTTACAACATT 59.599 37.500 2.24 0.00 0.00 2.71
3249 3873 7.177878 AGGGTGAAGGATATATTTTAGCATGG 58.822 38.462 0.00 0.00 0.00 3.66
3345 3969 4.447724 GGAATAGAAATACGCGCAGAATCA 59.552 41.667 5.73 0.00 0.00 2.57
3438 4062 5.947228 TTTCTCTAACCACATTGAGCTTG 57.053 39.130 0.00 0.00 0.00 4.01
3464 4088 5.301551 TGGTCAATGTCAAGTAAATGCACTT 59.698 36.000 0.00 0.00 39.34 3.16
3517 4141 6.636705 ACGGTATGTATAGCTGAAACAAAGA 58.363 36.000 0.00 0.00 0.00 2.52
3617 4241 7.229907 ACATGGTTTTAGTAAAAGTGGTGGTAG 59.770 37.037 8.33 0.00 0.00 3.18
3768 4392 6.899393 TGTTTCAATCCATTCAACTAGCTT 57.101 33.333 0.00 0.00 0.00 3.74
3831 4455 7.411486 TTCAGAAGTATTTCCAAAACCAACA 57.589 32.000 0.00 0.00 33.64 3.33
3861 4485 6.489700 TCAACCAATCACAGAAAAGATAAGCA 59.510 34.615 0.00 0.00 0.00 3.91
4051 4675 1.066454 GTTTTAGCACAAGCCAACCGT 59.934 47.619 0.00 0.00 43.56 4.83
4077 4701 6.992063 AATGAATAGCACAGAGTTAACTGG 57.008 37.500 14.14 7.58 41.59 4.00
4109 4733 7.807433 GTGCAACTGACATACAATGATAACAAA 59.193 33.333 0.00 0.00 0.00 2.83
4208 4833 4.695396 TGGTTGTTAGTGCGAGTCTAAAA 58.305 39.130 0.00 0.00 0.00 1.52
4218 4843 5.479306 TCTTGATAGTCTGGTTGTTAGTGC 58.521 41.667 0.00 0.00 0.00 4.40
4367 4992 3.750130 GCATGGGCTATGAAGTGATACAG 59.250 47.826 15.66 0.00 39.21 2.74
4410 5035 4.099266 AGCTCTGCAAAACATGTTAACCAA 59.901 37.500 12.39 0.00 0.00 3.67
4537 5162 1.541588 AGCGAAAACATCCAAGCCTTC 59.458 47.619 0.00 0.00 0.00 3.46
4844 5469 3.248266 GTGTGATGCAAATTCTTCAGGC 58.752 45.455 0.00 0.00 0.00 4.85
5024 5649 2.023501 ACTGCTCCTCCTTCCAGTCTAT 60.024 50.000 0.00 0.00 33.57 1.98
5027 5652 1.478916 GTACTGCTCCTCCTTCCAGTC 59.521 57.143 0.00 0.00 39.15 3.51
5029 5654 0.827368 GGTACTGCTCCTCCTTCCAG 59.173 60.000 0.00 0.00 0.00 3.86
5070 5701 0.035343 AGCCCTCGCTTTTTCCCTAC 60.035 55.000 0.00 0.00 45.55 3.18
5097 5728 5.181690 TGAGAAACACAATAAACAGGCAC 57.818 39.130 0.00 0.00 0.00 5.01
5155 5786 6.386927 TGAGTGGTAAATCTCATCCCTATTGT 59.613 38.462 0.00 0.00 36.04 2.71
5157 5788 6.617371 ACTGAGTGGTAAATCTCATCCCTATT 59.383 38.462 0.00 0.00 39.48 1.73
5251 5882 0.251297 TTCATGGGTCAGCACTTGGG 60.251 55.000 0.00 0.00 0.00 4.12
5259 5890 4.115516 CACGAATCTAGTTCATGGGTCAG 58.884 47.826 0.00 0.00 36.60 3.51
5425 6057 2.227149 TGTACACTACGCATTCGACTGT 59.773 45.455 4.58 0.00 39.41 3.55
5437 6069 7.596749 AGTGCAAATCTTGTATGTACACTAC 57.403 36.000 0.00 3.26 35.64 2.73
5513 6145 6.350949 CCACCCCCACTTGAAAATAACATTAG 60.351 42.308 0.00 0.00 0.00 1.73
5526 6301 0.539669 GGTTTCTCCACCCCCACTTG 60.540 60.000 0.00 0.00 35.97 3.16
5597 6372 1.207089 TGGAATGAAGCTACTCACGGG 59.793 52.381 0.00 0.00 0.00 5.28
5651 6431 5.402630 TGTGCAGTTATATCCCCTCTCATA 58.597 41.667 0.00 0.00 0.00 2.15
5653 6433 3.653164 TGTGCAGTTATATCCCCTCTCA 58.347 45.455 0.00 0.00 0.00 3.27
5659 6443 5.047943 ACGTCTAGATGTGCAGTTATATCCC 60.048 44.000 16.90 0.00 0.00 3.85
5694 6478 9.534565 GCTTGATTGAGTCACTTAGATATACAA 57.465 33.333 0.00 0.00 36.32 2.41
5695 6479 8.695456 TGCTTGATTGAGTCACTTAGATATACA 58.305 33.333 0.00 0.00 36.32 2.29
5696 6480 9.703892 ATGCTTGATTGAGTCACTTAGATATAC 57.296 33.333 0.00 0.00 36.32 1.47
5700 6484 9.453572 TTTTATGCTTGATTGAGTCACTTAGAT 57.546 29.630 0.00 0.00 36.32 1.98
5701 6485 8.846943 TTTTATGCTTGATTGAGTCACTTAGA 57.153 30.769 0.00 0.00 36.32 2.10
5729 6513 9.374711 TGTGGGTATTTTCCTTTTTCTTTATCT 57.625 29.630 0.00 0.00 0.00 1.98
5731 6515 9.942850 CATGTGGGTATTTTCCTTTTTCTTTAT 57.057 29.630 0.00 0.00 0.00 1.40
5732 6516 9.148879 TCATGTGGGTATTTTCCTTTTTCTTTA 57.851 29.630 0.00 0.00 0.00 1.85
5733 6517 8.028652 TCATGTGGGTATTTTCCTTTTTCTTT 57.971 30.769 0.00 0.00 0.00 2.52
5734 6518 7.610580 TCATGTGGGTATTTTCCTTTTTCTT 57.389 32.000 0.00 0.00 0.00 2.52
5735 6519 7.610580 TTCATGTGGGTATTTTCCTTTTTCT 57.389 32.000 0.00 0.00 0.00 2.52
5736 6520 8.314021 AGATTCATGTGGGTATTTTCCTTTTTC 58.686 33.333 0.00 0.00 0.00 2.29
5737 6521 8.206126 AGATTCATGTGGGTATTTTCCTTTTT 57.794 30.769 0.00 0.00 0.00 1.94
5738 6522 7.093333 GGAGATTCATGTGGGTATTTTCCTTTT 60.093 37.037 0.00 0.00 0.00 2.27
5739 6523 6.381133 GGAGATTCATGTGGGTATTTTCCTTT 59.619 38.462 0.00 0.00 0.00 3.11
5740 6524 5.893824 GGAGATTCATGTGGGTATTTTCCTT 59.106 40.000 0.00 0.00 0.00 3.36
5741 6525 5.449553 GGAGATTCATGTGGGTATTTTCCT 58.550 41.667 0.00 0.00 0.00 3.36
5742 6526 4.275936 CGGAGATTCATGTGGGTATTTTCC 59.724 45.833 0.00 0.00 0.00 3.13
5743 6527 4.881850 ACGGAGATTCATGTGGGTATTTTC 59.118 41.667 0.00 0.00 0.00 2.29
5744 6528 4.640201 CACGGAGATTCATGTGGGTATTTT 59.360 41.667 0.00 0.00 0.00 1.82
5745 6529 4.199310 CACGGAGATTCATGTGGGTATTT 58.801 43.478 0.00 0.00 0.00 1.40
5746 6530 3.199946 ACACGGAGATTCATGTGGGTATT 59.800 43.478 0.00 0.00 36.67 1.89
5747 6531 2.771943 ACACGGAGATTCATGTGGGTAT 59.228 45.455 0.00 0.00 36.67 2.73
5748 6532 2.184533 ACACGGAGATTCATGTGGGTA 58.815 47.619 0.00 0.00 36.67 3.69
5749 6533 0.984230 ACACGGAGATTCATGTGGGT 59.016 50.000 0.00 0.00 36.67 4.51
5750 6534 2.979814 TACACGGAGATTCATGTGGG 57.020 50.000 0.00 0.00 36.67 4.61
5751 6535 5.353956 TGATTTTACACGGAGATTCATGTGG 59.646 40.000 0.00 0.00 36.67 4.17
5752 6536 6.421377 TGATTTTACACGGAGATTCATGTG 57.579 37.500 0.00 2.58 38.28 3.21
5753 6537 7.630242 ATTGATTTTACACGGAGATTCATGT 57.370 32.000 0.00 0.00 0.00 3.21
5754 6538 9.438291 GTTATTGATTTTACACGGAGATTCATG 57.562 33.333 0.00 0.00 0.00 3.07
5755 6539 9.173021 TGTTATTGATTTTACACGGAGATTCAT 57.827 29.630 0.00 0.00 0.00 2.57
5756 6540 8.554835 TGTTATTGATTTTACACGGAGATTCA 57.445 30.769 0.00 0.00 0.00 2.57
5760 6544 9.051679 CCATATGTTATTGATTTTACACGGAGA 57.948 33.333 1.24 0.00 0.00 3.71
5761 6545 7.803189 GCCATATGTTATTGATTTTACACGGAG 59.197 37.037 1.24 0.00 0.00 4.63
5762 6546 7.500892 AGCCATATGTTATTGATTTTACACGGA 59.499 33.333 1.24 0.00 0.00 4.69
5763 6547 7.648142 AGCCATATGTTATTGATTTTACACGG 58.352 34.615 1.24 0.00 0.00 4.94
5771 6555 8.517878 GCACATCTAAGCCATATGTTATTGATT 58.482 33.333 1.24 0.00 31.60 2.57
5772 6556 7.666804 TGCACATCTAAGCCATATGTTATTGAT 59.333 33.333 1.24 0.00 31.60 2.57
5773 6557 6.997476 TGCACATCTAAGCCATATGTTATTGA 59.003 34.615 1.24 0.00 31.60 2.57
5774 6558 7.205737 TGCACATCTAAGCCATATGTTATTG 57.794 36.000 1.24 0.00 31.60 1.90
5775 6559 7.822161 TTGCACATCTAAGCCATATGTTATT 57.178 32.000 1.24 0.00 31.60 1.40
5776 6560 8.950210 GTATTGCACATCTAAGCCATATGTTAT 58.050 33.333 1.24 0.00 31.60 1.89
5777 6561 8.156820 AGTATTGCACATCTAAGCCATATGTTA 58.843 33.333 1.24 0.00 31.60 2.41
5778 6562 7.000472 AGTATTGCACATCTAAGCCATATGTT 59.000 34.615 1.24 0.00 31.60 2.71
5779 6563 6.537355 AGTATTGCACATCTAAGCCATATGT 58.463 36.000 1.24 0.00 34.22 2.29
5780 6564 7.444629 AAGTATTGCACATCTAAGCCATATG 57.555 36.000 0.00 0.00 0.00 1.78
5783 6567 9.745018 ATTATAAGTATTGCACATCTAAGCCAT 57.255 29.630 0.00 0.00 0.00 4.40
5784 6568 9.002600 CATTATAAGTATTGCACATCTAAGCCA 57.997 33.333 0.00 0.00 0.00 4.75
5785 6569 9.219603 TCATTATAAGTATTGCACATCTAAGCC 57.780 33.333 0.00 0.00 0.00 4.35
5791 6575 9.958285 CGTATGTCATTATAAGTATTGCACATC 57.042 33.333 0.00 0.00 0.00 3.06
5792 6576 8.935844 CCGTATGTCATTATAAGTATTGCACAT 58.064 33.333 0.00 0.00 0.00 3.21
5793 6577 7.095397 GCCGTATGTCATTATAAGTATTGCACA 60.095 37.037 0.00 0.00 0.00 4.57
5794 6578 7.117812 AGCCGTATGTCATTATAAGTATTGCAC 59.882 37.037 0.00 0.00 0.00 4.57
5795 6579 7.158697 AGCCGTATGTCATTATAAGTATTGCA 58.841 34.615 0.00 0.00 0.00 4.08
5796 6580 7.596749 AGCCGTATGTCATTATAAGTATTGC 57.403 36.000 0.00 0.00 0.00 3.56
5801 6585 8.585881 ACATCTAAGCCGTATGTCATTATAAGT 58.414 33.333 0.00 0.00 0.00 2.24
5802 6586 8.864024 CACATCTAAGCCGTATGTCATTATAAG 58.136 37.037 0.00 0.00 31.60 1.73
5803 6587 7.330946 GCACATCTAAGCCGTATGTCATTATAA 59.669 37.037 0.00 0.00 31.60 0.98
5804 6588 6.811665 GCACATCTAAGCCGTATGTCATTATA 59.188 38.462 0.00 0.00 31.60 0.98
5805 6589 5.639506 GCACATCTAAGCCGTATGTCATTAT 59.360 40.000 0.00 0.00 31.60 1.28
5806 6590 4.988540 GCACATCTAAGCCGTATGTCATTA 59.011 41.667 0.00 0.00 31.60 1.90
5807 6591 3.809832 GCACATCTAAGCCGTATGTCATT 59.190 43.478 0.00 0.00 31.60 2.57
5808 6592 3.181466 TGCACATCTAAGCCGTATGTCAT 60.181 43.478 0.00 0.00 31.60 3.06
5809 6593 2.167487 TGCACATCTAAGCCGTATGTCA 59.833 45.455 0.00 0.00 31.60 3.58
5810 6594 2.821546 TGCACATCTAAGCCGTATGTC 58.178 47.619 0.00 0.00 31.60 3.06
5811 6595 2.979814 TGCACATCTAAGCCGTATGT 57.020 45.000 0.00 0.00 34.22 2.29
5812 6596 4.991056 AGTATTGCACATCTAAGCCGTATG 59.009 41.667 0.00 0.00 0.00 2.39
5813 6597 5.215252 AGTATTGCACATCTAAGCCGTAT 57.785 39.130 0.00 0.00 0.00 3.06
5814 6598 4.665833 AGTATTGCACATCTAAGCCGTA 57.334 40.909 0.00 0.00 0.00 4.02
5815 6599 3.543680 AGTATTGCACATCTAAGCCGT 57.456 42.857 0.00 0.00 0.00 5.68
5816 6600 5.106948 CCATAAGTATTGCACATCTAAGCCG 60.107 44.000 0.00 0.00 0.00 5.52
5817 6601 5.335191 GCCATAAGTATTGCACATCTAAGCC 60.335 44.000 0.00 0.00 0.00 4.35
5818 6602 5.239306 TGCCATAAGTATTGCACATCTAAGC 59.761 40.000 0.00 0.00 30.49 3.09
5819 6603 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
5827 6611 4.462132 ACACAATGTGCCATAAGTATTGCA 59.538 37.500 14.01 0.00 36.98 4.08
5828 6612 4.997565 ACACAATGTGCCATAAGTATTGC 58.002 39.130 14.01 0.00 36.98 3.56
5829 6613 7.887996 AAAACACAATGTGCCATAAGTATTG 57.112 32.000 14.01 0.00 36.98 1.90
5830 6614 7.759433 GCTAAAACACAATGTGCCATAAGTATT 59.241 33.333 14.01 0.00 36.98 1.89
5831 6615 7.093988 TGCTAAAACACAATGTGCCATAAGTAT 60.094 33.333 14.01 0.00 36.98 2.12
5832 6616 6.207614 TGCTAAAACACAATGTGCCATAAGTA 59.792 34.615 14.01 2.05 36.98 2.24
5833 6617 5.010516 TGCTAAAACACAATGTGCCATAAGT 59.989 36.000 14.01 0.00 36.98 2.24
5834 6618 5.468592 TGCTAAAACACAATGTGCCATAAG 58.531 37.500 14.01 6.18 36.98 1.73
5835 6619 5.459536 TGCTAAAACACAATGTGCCATAA 57.540 34.783 14.01 0.00 36.98 1.90
5836 6620 5.459536 TTGCTAAAACACAATGTGCCATA 57.540 34.783 14.01 3.12 36.98 2.74
5837 6621 4.333913 TTGCTAAAACACAATGTGCCAT 57.666 36.364 14.01 2.01 36.98 4.40
5838 6622 3.808466 TTGCTAAAACACAATGTGCCA 57.192 38.095 14.01 0.00 36.98 4.92
5852 6636 9.906660 CCAGATTTATTGTTACAGTTTTGCTAA 57.093 29.630 0.00 0.00 0.00 3.09
5853 6637 8.026607 GCCAGATTTATTGTTACAGTTTTGCTA 58.973 33.333 0.00 0.00 0.00 3.49
5854 6638 6.868339 GCCAGATTTATTGTTACAGTTTTGCT 59.132 34.615 0.00 0.00 0.00 3.91
5855 6639 6.868339 AGCCAGATTTATTGTTACAGTTTTGC 59.132 34.615 0.00 0.00 0.00 3.68
5858 6642 9.686683 AGATAGCCAGATTTATTGTTACAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
5859 6643 9.331282 GAGATAGCCAGATTTATTGTTACAGTT 57.669 33.333 0.00 0.00 0.00 3.16
5860 6644 8.486210 TGAGATAGCCAGATTTATTGTTACAGT 58.514 33.333 0.00 0.00 0.00 3.55
5861 6645 8.893219 TGAGATAGCCAGATTTATTGTTACAG 57.107 34.615 0.00 0.00 0.00 2.74
5862 6646 9.679661 TTTGAGATAGCCAGATTTATTGTTACA 57.320 29.630 0.00 0.00 0.00 2.41
5902 6686 4.631131 GTGCTGGCTATGATGTATGTACA 58.369 43.478 0.00 0.00 40.98 2.90
5906 6690 3.030668 TCGTGCTGGCTATGATGTATG 57.969 47.619 0.00 0.00 0.00 2.39
5912 6696 1.756538 TCAGAATCGTGCTGGCTATGA 59.243 47.619 0.00 0.00 34.20 2.15
5914 6698 2.988010 TTCAGAATCGTGCTGGCTAT 57.012 45.000 0.00 0.00 34.20 2.97
5915 6699 2.760634 TTTCAGAATCGTGCTGGCTA 57.239 45.000 0.00 0.00 34.20 3.93
5916 6700 1.896220 TTTTCAGAATCGTGCTGGCT 58.104 45.000 0.00 0.00 34.20 4.75
5917 6701 2.030805 AGTTTTTCAGAATCGTGCTGGC 60.031 45.455 0.00 0.00 34.20 4.85
5918 6702 3.558505 CAGTTTTTCAGAATCGTGCTGG 58.441 45.455 0.00 0.00 34.20 4.85
5919 6703 3.003689 ACCAGTTTTTCAGAATCGTGCTG 59.996 43.478 0.00 0.00 34.71 4.41
5920 6704 3.214328 ACCAGTTTTTCAGAATCGTGCT 58.786 40.909 0.00 0.00 0.00 4.40
5921 6705 3.626028 ACCAGTTTTTCAGAATCGTGC 57.374 42.857 0.00 0.00 0.00 5.34
5936 6777 9.350951 GCCTATTTATTTTACCAGATTACCAGT 57.649 33.333 0.00 0.00 0.00 4.00
5982 6824 6.222038 TCTTGTAATCACCTACTGCCTAAG 57.778 41.667 0.00 0.00 0.00 2.18
5983 6825 6.808321 ATCTTGTAATCACCTACTGCCTAA 57.192 37.500 0.00 0.00 0.00 2.69
5984 6826 6.611642 AGAATCTTGTAATCACCTACTGCCTA 59.388 38.462 0.00 0.00 0.00 3.93
5985 6827 5.426833 AGAATCTTGTAATCACCTACTGCCT 59.573 40.000 0.00 0.00 0.00 4.75
5986 6828 5.525378 CAGAATCTTGTAATCACCTACTGCC 59.475 44.000 0.00 0.00 0.00 4.85
5987 6829 6.341316 TCAGAATCTTGTAATCACCTACTGC 58.659 40.000 0.00 0.00 0.00 4.40
5988 6830 8.954950 ATTCAGAATCTTGTAATCACCTACTG 57.045 34.615 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.