Multiple sequence alignment - TraesCS5B01G199400

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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 TraesCS5B01G199400 chr5B 100.000 7352 0 0 1 7352 359315600 359308249 0.000000e+00 13577.0
1 TraesCS5B01G199400 chr5B 97.532 932 19 2 1734 2665 648736964 648737891 0.000000e+00 1591.0
2 TraesCS5B01G199400 chr5B 96.203 79 3 0 6841 6919 698025023 698024945 5.990000e-26 130.0
3 TraesCS5B01G199400 chr5A 94.274 6078 211 46 1130 7145 406672895 406666893 0.000000e+00 9169.0
4 TraesCS5B01G199400 chr5A 94.929 631 24 2 1 624 406692083 406691454 0.000000e+00 981.0
5 TraesCS5B01G199400 chr5A 92.925 424 17 3 661 1084 406673763 406673353 8.160000e-169 604.0
6 TraesCS5B01G199400 chr5A 95.333 150 7 0 7203 7352 406666892 406666743 9.530000e-59 239.0
7 TraesCS5B01G199400 chr5D 92.850 4182 182 45 1 4108 312610320 312606182 0.000000e+00 5958.0
8 TraesCS5B01G199400 chr5D 94.825 3092 84 29 4067 7145 312606190 312603162 0.000000e+00 4754.0
9 TraesCS5B01G199400 chr5D 96.026 151 5 1 7203 7352 312603161 312603011 2.050000e-60 244.0
10 TraesCS5B01G199400 chr5D 80.537 149 23 6 694 838 281224281 281224135 7.800000e-20 110.0
11 TraesCS5B01G199400 chr5D 95.122 41 2 0 7160 7200 428309141 428309181 1.710000e-06 65.8
12 TraesCS5B01G199400 chr7B 96.231 1300 44 3 1365 2663 263150378 263151673 0.000000e+00 2124.0
13 TraesCS5B01G199400 chr1B 93.610 1299 49 5 1368 2665 372098872 372097607 0.000000e+00 1908.0
14 TraesCS5B01G199400 chr1B 96.104 77 3 0 6843 6919 36285226 36285302 7.740000e-25 126.0
15 TraesCS5B01G199400 chr1B 78.182 165 30 5 687 847 15876292 15876454 4.690000e-17 100.0
16 TraesCS5B01G199400 chr7D 97.639 932 18 2 1734 2665 513996145 513995218 0.000000e+00 1596.0
17 TraesCS5B01G199400 chr7D 81.410 156 20 8 686 836 31886212 31886061 1.300000e-22 119.0
18 TraesCS5B01G199400 chr7D 93.671 79 5 0 6841 6919 161971458 161971380 1.300000e-22 119.0
19 TraesCS5B01G199400 chr7D 93.671 79 5 0 6841 6919 567513871 567513949 1.300000e-22 119.0
20 TraesCS5B01G199400 chr7A 97.425 932 20 2 1734 2665 673066056 673066983 0.000000e+00 1585.0
21 TraesCS5B01G199400 chr3D 97.318 932 21 2 1734 2665 208830981 208831908 0.000000e+00 1580.0
22 TraesCS5B01G199400 chr3D 78.065 155 28 5 686 836 561890920 561890768 7.850000e-15 93.5
23 TraesCS5B01G199400 chr6B 96.781 932 26 2 1734 2665 388076508 388075581 0.000000e+00 1552.0
24 TraesCS5B01G199400 chr6B 92.683 82 5 1 6841 6922 40713335 40713255 4.660000e-22 117.0
25 TraesCS5B01G199400 chr6B 97.619 42 1 0 1371 1412 388078259 388078218 1.020000e-08 73.1
26 TraesCS5B01G199400 chr4A 83.898 708 99 11 1348 2053 654360542 654361236 0.000000e+00 662.0
27 TraesCS5B01G199400 chr4A 90.805 87 7 1 6833 6919 681652775 681652690 1.680000e-21 115.0
28 TraesCS5B01G199400 chr6D 93.103 87 5 1 6841 6927 344330737 344330822 7.740000e-25 126.0
29 TraesCS5B01G199400 chr6D 79.861 144 24 4 695 836 463857075 463856935 4.690000e-17 100.0
30 TraesCS5B01G199400 chr3B 82.667 150 18 4 698 843 163361949 163362094 7.740000e-25 126.0
31 TraesCS5B01G199400 chr3B 78.981 157 28 4 686 839 224125406 224125560 1.300000e-17 102.0
32 TraesCS5B01G199400 chr1A 82.031 128 19 3 686 811 560464761 560464886 1.010000e-18 106.0
33 TraesCS5B01G199400 chr1A 95.833 48 2 0 1365 1412 561614310 561614357 2.200000e-10 78.7
34 TraesCS5B01G199400 chr3A 95.833 48 2 0 1365 1412 10617878 10617925 2.200000e-10 78.7
35 TraesCS5B01G199400 chr2A 97.778 45 1 0 1368 1412 37030425 37030381 2.200000e-10 78.7
36 TraesCS5B01G199400 chr2A 93.182 44 2 1 7156 7199 369499501 369499459 6.160000e-06 63.9
37 TraesCS5B01G199400 chr2D 93.182 44 2 1 7156 7199 296850076 296850034 6.160000e-06 63.9
38 TraesCS5B01G199400 chr2B 97.368 38 0 1 7156 7193 364732782 364732818 6.160000e-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 TraesCS5B01G199400 chr5B 359308249 359315600 7351 True 13577.000000 13577 100.000000 1 7352 1 chr5B.!!$R1 7351
1 TraesCS5B01G199400 chr5B 648736964 648737891 927 False 1591.000000 1591 97.532000 1734 2665 1 chr5B.!!$F1 931
2 TraesCS5B01G199400 chr5A 406666743 406673763 7020 True 3337.333333 9169 94.177333 661 7352 3 chr5A.!!$R2 6691
3 TraesCS5B01G199400 chr5A 406691454 406692083 629 True 981.000000 981 94.929000 1 624 1 chr5A.!!$R1 623
4 TraesCS5B01G199400 chr5D 312603011 312610320 7309 True 3652.000000 5958 94.567000 1 7352 3 chr5D.!!$R2 7351
5 TraesCS5B01G199400 chr7B 263150378 263151673 1295 False 2124.000000 2124 96.231000 1365 2663 1 chr7B.!!$F1 1298
6 TraesCS5B01G199400 chr1B 372097607 372098872 1265 True 1908.000000 1908 93.610000 1368 2665 1 chr1B.!!$R1 1297
7 TraesCS5B01G199400 chr7D 513995218 513996145 927 True 1596.000000 1596 97.639000 1734 2665 1 chr7D.!!$R3 931
8 TraesCS5B01G199400 chr7A 673066056 673066983 927 False 1585.000000 1585 97.425000 1734 2665 1 chr7A.!!$F1 931
9 TraesCS5B01G199400 chr3D 208830981 208831908 927 False 1580.000000 1580 97.318000 1734 2665 1 chr3D.!!$F1 931
10 TraesCS5B01G199400 chr6B 388075581 388078259 2678 True 812.550000 1552 97.200000 1371 2665 2 chr6B.!!$R2 1294
11 TraesCS5B01G199400 chr4A 654360542 654361236 694 False 662.000000 662 83.898000 1348 2053 1 chr4A.!!$F1 705

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
992 1010 0.109597 CCACACGTACGTACTCCCAC 60.110 60.000 22.34 0.0 0.00 4.61 F
2835 4833 0.108138 AGACCCTTGCGCACTGTATC 60.108 55.000 11.12 4.5 0.00 2.24 F
3401 5400 1.109609 CTACCTCCCGAGTTACCCAC 58.890 60.000 0.00 0.0 0.00 4.61 F
3561 5568 1.668419 ACACACCTGTTGCTGTCTTC 58.332 50.000 0.00 0.0 0.00 2.87 F
5119 7165 1.135944 GCTACTTGCTGGTTTTCTCGC 60.136 52.381 0.00 0.0 38.95 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2846 4844 0.865639 GTTGCAACACAAGTGCGGAC 60.866 55.0 24.52 0.00 39.50 4.79 R
4109 6152 0.622665 CAGCTCTGGTTCCCTGGAAT 59.377 55.0 1.26 0.00 36.45 3.01 R
5119 7165 0.914644 TCTTCAGATCAAGGGCCTGG 59.085 55.0 6.92 3.14 0.00 4.45 R
5266 7312 1.428869 CTCCCCTCATCTTACCTGGG 58.571 60.0 0.00 0.00 37.68 4.45 R
6512 8571 0.322322 TGTTAAGTGTGTAGGCCCGG 59.678 55.0 0.00 0.00 0.00 5.73 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
50 51 7.887381 TGTCTCTCCCTCTTTTCGATATATTC 58.113 38.462 0.00 0.00 0.00 1.75
90 91 3.933861 AGATGGACCCATAAGTTCCAC 57.066 47.619 0.82 0.00 36.70 4.02
149 151 8.925338 ACACCTAACCATTTTATTACAAACCAA 58.075 29.630 0.00 0.00 0.00 3.67
293 295 6.475402 GCCATACTTGCCAATTGTATTTACAC 59.525 38.462 4.43 0.00 35.64 2.90
297 299 5.772672 ACTTGCCAATTGTATTTACACCTCA 59.227 36.000 4.43 0.00 35.64 3.86
303 305 4.374689 TTGTATTTACACCTCAAGCCCA 57.625 40.909 0.00 0.00 35.64 5.36
332 334 3.525199 AGGCTTGGTAGACTTGATCCATT 59.475 43.478 0.00 0.00 35.73 3.16
334 336 5.059833 GGCTTGGTAGACTTGATCCATTAG 58.940 45.833 0.00 0.00 0.00 1.73
393 395 7.510407 AGATCCACCCTAAATTCTTTAGTAGC 58.490 38.462 6.04 0.00 40.76 3.58
445 447 8.926374 AGCCATATGAAATTACCATTTGAATCA 58.074 29.630 3.65 0.00 32.35 2.57
531 542 5.771469 CCACAACTCTTGTTTATGCATCAA 58.229 37.500 0.19 0.08 43.23 2.57
684 695 5.419542 TCGTACTCTCTTCATCCCAAAATG 58.580 41.667 0.00 0.00 0.00 2.32
759 770 8.440833 ACTACATACGAAGCAAAATGAGTAAAC 58.559 33.333 0.00 0.00 0.00 2.01
763 774 6.476243 ACGAAGCAAAATGAGTAAACGTAT 57.524 33.333 0.00 0.00 0.00 3.06
768 779 8.950403 AAGCAAAATGAGTAAACGTATTCTTC 57.050 30.769 0.00 0.00 0.00 2.87
938 949 3.515316 CTGACGTGGCACCCGTTCT 62.515 63.158 12.86 0.00 38.92 3.01
992 1010 0.109597 CCACACGTACGTACTCCCAC 60.110 60.000 22.34 0.00 0.00 4.61
1014 1032 1.745115 CAAAGCCGATTCCTCGCCA 60.745 57.895 0.00 0.00 43.66 5.69
1090 1108 0.173255 ATTTCAAAATCCCGCAGCCG 59.827 50.000 0.00 0.00 0.00 5.52
1116 1134 3.493303 GCCTCCATCCTCCCCCAC 61.493 72.222 0.00 0.00 0.00 4.61
1117 1135 2.374342 CCTCCATCCTCCCCCACT 59.626 66.667 0.00 0.00 0.00 4.00
1584 2025 3.449227 CTGGACACCGGCGAGCTA 61.449 66.667 9.30 0.00 0.00 3.32
1633 2074 3.120338 TCGCGATTTTGTGATCTGGTTTC 60.120 43.478 3.71 0.00 0.00 2.78
1668 2109 3.249091 CTTGGAGTCATTCGTCAGACTG 58.751 50.000 10.23 0.00 44.61 3.51
1962 3862 4.808414 ATACTTGACTGCTAGACTGCAA 57.192 40.909 0.00 0.00 42.83 4.08
2032 3937 2.128035 CGTGAGGAAGACACACTGAAC 58.872 52.381 0.00 0.00 38.04 3.18
2095 4000 5.736207 GCTTCTTGGAAAACTCGGTTCATTT 60.736 40.000 0.00 0.00 0.00 2.32
2320 4227 7.776107 TCTTTGTGTCATTGATTGTTTGGTTA 58.224 30.769 0.00 0.00 0.00 2.85
2400 4307 6.753180 TGTTGATAACAAAGGCTGCATTAAA 58.247 32.000 0.00 0.00 38.72 1.52
2635 4616 1.614903 ACCTGTGTGCATGAAACATGG 59.385 47.619 12.56 9.19 33.20 3.66
2665 4646 2.364002 GTTTGGTTCCAAGCAGGCTTAA 59.636 45.455 6.16 0.00 37.74 1.85
2666 4647 2.603075 TGGTTCCAAGCAGGCTTAAT 57.397 45.000 6.16 0.00 37.29 1.40
2670 4651 3.258123 GGTTCCAAGCAGGCTTAATCAAA 59.742 43.478 6.16 0.00 37.29 2.69
2671 4652 4.262420 GGTTCCAAGCAGGCTTAATCAAAA 60.262 41.667 6.16 0.00 37.29 2.44
2672 4653 5.482006 GTTCCAAGCAGGCTTAATCAAAAT 58.518 37.500 6.16 0.00 37.29 1.82
2673 4654 6.350949 GGTTCCAAGCAGGCTTAATCAAAATA 60.351 38.462 6.16 0.00 37.29 1.40
2674 4655 6.455360 TCCAAGCAGGCTTAATCAAAATAG 57.545 37.500 6.16 0.00 37.29 1.73
2675 4656 5.360714 TCCAAGCAGGCTTAATCAAAATAGG 59.639 40.000 6.16 0.18 37.29 2.57
2678 4659 6.645790 AGCAGGCTTAATCAAAATAGGATG 57.354 37.500 0.00 0.00 0.00 3.51
2679 4660 5.537674 AGCAGGCTTAATCAAAATAGGATGG 59.462 40.000 0.00 0.00 0.00 3.51
2680 4661 5.302823 GCAGGCTTAATCAAAATAGGATGGT 59.697 40.000 0.00 0.00 0.00 3.55
2681 4662 6.515696 GCAGGCTTAATCAAAATAGGATGGTC 60.516 42.308 0.00 0.00 0.00 4.02
2682 4663 6.015940 CAGGCTTAATCAAAATAGGATGGTCC 60.016 42.308 0.00 0.00 36.58 4.46
2683 4664 5.243954 GGCTTAATCAAAATAGGATGGTCCC 59.756 44.000 0.00 0.00 37.19 4.46
2684 4665 5.833131 GCTTAATCAAAATAGGATGGTCCCA 59.167 40.000 0.00 0.00 37.19 4.37
2685 4666 6.015940 GCTTAATCAAAATAGGATGGTCCCAG 60.016 42.308 0.00 0.00 37.19 4.45
2686 4667 3.951563 TCAAAATAGGATGGTCCCAGG 57.048 47.619 0.00 0.00 37.19 4.45
2688 4669 2.513738 CAAAATAGGATGGTCCCAGGGA 59.486 50.000 3.01 3.01 37.19 4.20
2708 4700 5.077564 GGGATAACAAAATAGGATGGTCCC 58.922 45.833 0.00 0.00 37.19 4.46
2723 4715 4.396357 TGGTCCCAAGGATAACATGTTT 57.604 40.909 17.78 4.68 32.73 2.83
2724 4716 4.085733 TGGTCCCAAGGATAACATGTTTG 58.914 43.478 17.78 8.31 32.73 2.93
2737 4729 5.738619 AACATGTTTGTTATTTCCCCCTC 57.261 39.130 4.92 0.00 44.22 4.30
2752 4744 2.024414 CCCCTCTTATTTTCTTGCGGG 58.976 52.381 0.00 0.00 0.00 6.13
2760 4752 6.416415 TCTTATTTTCTTGCGGGGTAACATA 58.584 36.000 0.00 0.00 39.74 2.29
2761 4753 7.057894 TCTTATTTTCTTGCGGGGTAACATAT 58.942 34.615 0.00 0.00 39.74 1.78
2762 4754 4.974368 TTTTCTTGCGGGGTAACATATG 57.026 40.909 0.00 0.00 39.74 1.78
2780 4778 2.758089 GCTGCAGTGCCAATCCTCG 61.758 63.158 16.64 0.00 0.00 4.63
2830 4828 1.600916 GGAAAGACCCTTGCGCACT 60.601 57.895 11.12 0.00 0.00 4.40
2835 4833 0.108138 AGACCCTTGCGCACTGTATC 60.108 55.000 11.12 4.50 0.00 2.24
2845 4843 4.441792 TGCGCACTGTATCATTGATAACT 58.558 39.130 5.66 0.00 0.00 2.24
2846 4844 4.270808 TGCGCACTGTATCATTGATAACTG 59.729 41.667 5.66 8.90 0.00 3.16
2854 4852 3.610040 TCATTGATAACTGTCCGCACT 57.390 42.857 0.00 0.00 0.00 4.40
2856 4854 3.684305 TCATTGATAACTGTCCGCACTTG 59.316 43.478 0.00 0.00 0.00 3.16
2908 4906 3.062639 CGCCTGCTACAACTTTATCTGTG 59.937 47.826 0.00 0.00 0.00 3.66
2913 4911 7.227512 GCCTGCTACAACTTTATCTGTGATTAT 59.772 37.037 0.00 0.00 0.00 1.28
2942 4940 7.509141 TGTCATGATTTATTTGTCACTGTGT 57.491 32.000 7.79 0.00 0.00 3.72
2943 4941 7.361894 TGTCATGATTTATTTGTCACTGTGTG 58.638 34.615 7.79 0.00 34.45 3.82
2944 4942 7.013178 TGTCATGATTTATTTGTCACTGTGTGT 59.987 33.333 7.79 0.00 34.79 3.72
2960 4958 4.626042 TGTGTGTTTTCTTTGTGCAAGTT 58.374 34.783 0.00 0.00 33.66 2.66
2976 4974 4.771577 TGCAAGTTATTCCCATGTCAATGT 59.228 37.500 0.00 0.00 31.27 2.71
3104 5102 3.064820 GGGCATACCTTGTATGTGAAACG 59.935 47.826 13.93 0.00 36.19 3.60
3131 5129 7.214467 TCCAGTACTTTATTTCTTGCCTTTG 57.786 36.000 0.00 0.00 0.00 2.77
3146 5144 6.827762 TCTTGCCTTTGTTTTTGAATTTGGAT 59.172 30.769 0.00 0.00 0.00 3.41
3152 5150 6.432403 TTGTTTTTGAATTTGGATAGGCCT 57.568 33.333 11.78 11.78 37.63 5.19
3153 5151 6.432403 TGTTTTTGAATTTGGATAGGCCTT 57.568 33.333 12.58 0.00 37.63 4.35
3154 5152 6.836242 TGTTTTTGAATTTGGATAGGCCTTT 58.164 32.000 12.58 1.34 37.63 3.11
3255 5254 7.454260 AATGCTAAAAGTTTCCCTACTTCAG 57.546 36.000 0.00 0.00 37.37 3.02
3258 5257 5.181433 GCTAAAAGTTTCCCTACTTCAGTGG 59.819 44.000 0.00 0.00 37.37 4.00
3342 5341 9.357161 CTATCCACTAGACCACTACTAGATTTT 57.643 37.037 0.00 0.00 39.48 1.82
3390 5389 5.453480 GGTCAGAACAATATGTCTACCTCCC 60.453 48.000 0.00 0.00 0.00 4.30
3401 5400 1.109609 CTACCTCCCGAGTTACCCAC 58.890 60.000 0.00 0.00 0.00 4.61
3551 5558 9.681062 ATTTGTAGCTTTAATATACACACCTGT 57.319 29.630 0.00 0.00 0.00 4.00
3552 5559 9.509956 TTTGTAGCTTTAATATACACACCTGTT 57.490 29.630 0.00 0.00 0.00 3.16
3553 5560 8.487313 TGTAGCTTTAATATACACACCTGTTG 57.513 34.615 0.00 0.00 0.00 3.33
3554 5561 6.436843 AGCTTTAATATACACACCTGTTGC 57.563 37.500 0.00 0.00 0.00 4.17
3555 5562 6.180472 AGCTTTAATATACACACCTGTTGCT 58.820 36.000 0.00 0.00 0.00 3.91
3556 5563 6.094048 AGCTTTAATATACACACCTGTTGCTG 59.906 38.462 0.00 0.00 0.00 4.41
3557 5564 6.128007 GCTTTAATATACACACCTGTTGCTGT 60.128 38.462 0.00 0.00 0.00 4.40
3558 5565 6.978343 TTAATATACACACCTGTTGCTGTC 57.022 37.500 0.00 0.00 0.00 3.51
3559 5566 4.826274 ATATACACACCTGTTGCTGTCT 57.174 40.909 0.00 0.00 0.00 3.41
3560 5567 3.492102 ATACACACCTGTTGCTGTCTT 57.508 42.857 0.00 0.00 0.00 3.01
3561 5568 1.668419 ACACACCTGTTGCTGTCTTC 58.332 50.000 0.00 0.00 0.00 2.87
3564 5571 2.620115 CACACCTGTTGCTGTCTTCAAT 59.380 45.455 0.00 0.00 0.00 2.57
3577 5584 6.994496 TGCTGTCTTCAATAGATTCTTATGGG 59.006 38.462 0.00 0.00 34.79 4.00
3728 5736 2.294195 TGATCCCCACCCTTCCAATCTA 60.294 50.000 0.00 0.00 0.00 1.98
3882 5891 8.531622 TGGTTATTCATTGCACTAACAAAATG 57.468 30.769 0.00 0.00 32.27 2.32
3950 5959 5.689031 GCACCCACCAATACCTGAACATATA 60.689 44.000 0.00 0.00 0.00 0.86
3984 5993 6.098017 GCTAAAGATTTTCTGCTGAAATGCT 58.902 36.000 18.05 14.82 41.24 3.79
4108 6151 5.626142 TCTGTTGCTGTGGGTAATTTTCTA 58.374 37.500 0.00 0.00 0.00 2.10
4109 6152 6.065374 TCTGTTGCTGTGGGTAATTTTCTAA 58.935 36.000 0.00 0.00 0.00 2.10
4164 6207 7.201609 GCGTCAGATTTATTGAAGGTACATTCA 60.202 37.037 18.42 18.42 37.41 2.57
4316 6359 2.464865 GGCAGCTACTCAATCGTACTG 58.535 52.381 0.00 0.00 0.00 2.74
4344 6387 2.961062 AGGTTGGATTGCTGGCATAATC 59.039 45.455 13.30 13.30 33.58 1.75
4380 6423 6.472887 TCAGCTTGTTTGGCTTAGTACTAAT 58.527 36.000 15.57 0.00 38.03 1.73
4414 6457 3.430042 ACAATGACACAGGATGCTTCT 57.570 42.857 0.00 0.00 42.53 2.85
4484 6527 4.421131 AGTAACTCCTGTGATTCCTGAGT 58.579 43.478 0.00 0.00 37.88 3.41
4487 6530 3.242867 ACTCCTGTGATTCCTGAGTTCA 58.757 45.455 0.00 0.00 32.61 3.18
4597 6641 7.173047 GGCAACTGGTCAACAATTAATTCAAAT 59.827 33.333 0.00 0.00 0.00 2.32
4642 6686 2.746375 GGAGGGTGGCGGTGATGAT 61.746 63.158 0.00 0.00 0.00 2.45
5039 7083 9.850628 TCAAAAATAGAAGCATTTCTTGATGAG 57.149 29.630 0.00 0.00 40.79 2.90
5119 7165 1.135944 GCTACTTGCTGGTTTTCTCGC 60.136 52.381 0.00 0.00 38.95 5.03
5266 7312 2.434359 CCTCGTGGAAAGTCGCCC 60.434 66.667 0.00 0.00 34.57 6.13
5368 7414 3.280295 CAGCAGGCAATTCTCAAGAGAT 58.720 45.455 0.00 0.00 37.29 2.75
5501 7547 3.244422 ACCTAAACCTTGCTTCGATGACA 60.244 43.478 1.89 0.00 0.00 3.58
5508 7554 4.154918 ACCTTGCTTCGATGACAGAAATTC 59.845 41.667 1.89 0.00 0.00 2.17
5510 7556 5.582269 CCTTGCTTCGATGACAGAAATTCTA 59.418 40.000 1.89 0.00 0.00 2.10
5530 7576 2.880963 TGCAAAAACCTTAGGTGCAC 57.119 45.000 8.80 8.80 35.34 4.57
5842 7889 1.860950 CAACACTCGTTCCACAGTGAG 59.139 52.381 0.62 0.00 42.37 3.51
5934 7983 1.202855 ACAGTGCATATCCAGATGGCC 60.203 52.381 0.00 0.00 34.44 5.36
6048 8097 1.872679 GCGACGCTACCCGAAGAAG 60.873 63.158 13.73 0.00 41.02 2.85
6102 8151 0.032615 TTTCCTGCCAAGGGTTGTGT 60.033 50.000 0.00 0.00 44.62 3.72
6135 8184 4.228097 GCGGTGCTATGCGTGCTG 62.228 66.667 0.00 0.00 0.00 4.41
6334 8383 2.619013 AATTTTCTTCAGGCGCTTCG 57.381 45.000 7.64 0.00 0.00 3.79
6335 8384 1.808411 ATTTTCTTCAGGCGCTTCGA 58.192 45.000 7.64 0.00 0.00 3.71
6383 8435 5.392380 GCAGCTGTAATACTGAAAACATGCT 60.392 40.000 16.64 0.00 35.90 3.79
6468 8527 7.071698 AGGATATGATTGGCTTCTTTCTCACTA 59.928 37.037 0.00 0.00 0.00 2.74
6503 8562 0.111832 ACATCAGGGCCTGCATATGG 59.888 55.000 29.02 14.99 0.00 2.74
6504 8563 0.611062 CATCAGGGCCTGCATATGGG 60.611 60.000 29.02 8.37 0.00 4.00
6505 8564 1.070127 ATCAGGGCCTGCATATGGGT 61.070 55.000 29.02 0.00 0.00 4.51
6506 8565 1.231068 CAGGGCCTGCATATGGGTT 59.769 57.895 22.68 0.00 0.00 4.11
6509 8568 1.573376 AGGGCCTGCATATGGGTTTAA 59.427 47.619 4.50 0.00 0.00 1.52
6510 8569 1.686587 GGGCCTGCATATGGGTTTAAC 59.313 52.381 0.84 0.00 0.00 2.01
6511 8570 1.336755 GGCCTGCATATGGGTTTAACG 59.663 52.381 4.56 0.00 0.00 3.18
6512 8571 1.269051 GCCTGCATATGGGTTTAACGC 60.269 52.381 4.56 5.16 0.00 4.84
6513 8572 1.336755 CCTGCATATGGGTTTAACGCC 59.663 52.381 9.60 3.02 0.00 5.68
6514 8573 1.002900 CTGCATATGGGTTTAACGCCG 60.003 52.381 9.60 0.00 0.00 6.46
6515 8574 0.309612 GCATATGGGTTTAACGCCGG 59.690 55.000 9.60 0.00 0.00 6.13
6516 8575 0.948678 CATATGGGTTTAACGCCGGG 59.051 55.000 2.18 0.00 0.00 5.73
6517 8576 0.820482 ATATGGGTTTAACGCCGGGC 60.820 55.000 9.54 9.54 0.00 6.13
6620 8681 3.066064 CGAGTAGACAGGATCACAGGAAG 59.934 52.174 0.00 0.00 0.00 3.46
6624 8685 2.043664 AGACAGGATCACAGGAAGGAGA 59.956 50.000 0.00 0.00 0.00 3.71
6694 8755 2.766828 CTGTTTAGGGGAGGGAGTACAG 59.233 54.545 0.00 0.00 0.00 2.74
6704 8765 3.010250 GGAGGGAGTACAGAAAAATGGGT 59.990 47.826 0.00 0.00 0.00 4.51
6718 8779 5.447624 AAAATGGGTTTAACGACTTGAGG 57.552 39.130 0.00 0.00 0.00 3.86
6762 8824 0.179070 GACCGAGGGATCTTCCAAGC 60.179 60.000 0.00 0.00 38.64 4.01
6885 8947 6.016610 GCTTAGTCTCTTCTATCAGATCGGTT 60.017 42.308 0.00 0.00 0.00 4.44
6916 8978 3.733077 GCATTGGTTAGAGCATGCACTTC 60.733 47.826 22.83 15.30 33.54 3.01
6917 8979 3.423539 TTGGTTAGAGCATGCACTTCT 57.576 42.857 22.83 17.00 0.00 2.85
6918 8980 4.551702 TTGGTTAGAGCATGCACTTCTA 57.448 40.909 22.83 15.97 0.00 2.10
6919 8981 4.128925 TGGTTAGAGCATGCACTTCTAG 57.871 45.455 22.83 0.00 0.00 2.43
6920 8982 3.769300 TGGTTAGAGCATGCACTTCTAGA 59.231 43.478 22.83 1.48 0.00 2.43
6921 8983 4.222810 TGGTTAGAGCATGCACTTCTAGAA 59.777 41.667 22.83 8.00 0.00 2.10
6975 9037 1.891150 AGATCTTGCCCTGCTTGTTTG 59.109 47.619 0.00 0.00 0.00 2.93
6996 9058 1.065418 GGCTTTAGGCTGGCAAGTCTA 60.065 52.381 0.00 0.00 39.69 2.59
6997 9059 2.618045 GGCTTTAGGCTGGCAAGTCTAA 60.618 50.000 11.28 11.28 46.48 2.10
7006 9068 2.724977 GGCAAGTCTAAAGCCCAAAC 57.275 50.000 0.00 0.00 42.58 2.93
7007 9069 1.960689 GGCAAGTCTAAAGCCCAAACA 59.039 47.619 0.00 0.00 42.58 2.83
7008 9070 2.364002 GGCAAGTCTAAAGCCCAAACAA 59.636 45.455 0.00 0.00 42.58 2.83
7009 9071 3.552890 GGCAAGTCTAAAGCCCAAACAAG 60.553 47.826 0.00 0.00 42.58 3.16
7010 9072 3.642705 CAAGTCTAAAGCCCAAACAAGC 58.357 45.455 0.00 0.00 0.00 4.01
7011 9073 2.944129 AGTCTAAAGCCCAAACAAGCA 58.056 42.857 0.00 0.00 0.00 3.91
7012 9074 2.887152 AGTCTAAAGCCCAAACAAGCAG 59.113 45.455 0.00 0.00 0.00 4.24
7013 9075 2.029918 GTCTAAAGCCCAAACAAGCAGG 60.030 50.000 0.00 0.00 0.00 4.85
7014 9076 1.273327 CTAAAGCCCAAACAAGCAGGG 59.727 52.381 0.00 0.00 45.68 4.45
7017 9079 3.548488 CCCAAACAAGCAGGGCAA 58.452 55.556 0.00 0.00 35.44 4.52
7021 9083 1.134431 CCAAACAAGCAGGGCAAGTTT 60.134 47.619 5.57 5.57 37.93 2.66
7045 9107 2.997485 AAAAACAGATTCTCGCAGGC 57.003 45.000 0.00 0.00 0.00 4.85
7049 9111 2.119801 ACAGATTCTCGCAGGCAAAT 57.880 45.000 0.00 0.00 0.00 2.32
7072 9134 6.131544 TCTAGAAGCTGAAACAAAACAACC 57.868 37.500 0.00 0.00 0.00 3.77
7093 9155 4.186159 CCATTTGGAATTAGCTTTGCCAG 58.814 43.478 0.00 0.00 37.39 4.85
7111 9173 3.876320 GCCAGAGAAGGTGAATCTGAATC 59.124 47.826 3.09 0.00 42.48 2.52
7113 9175 4.450053 CAGAGAAGGTGAATCTGAATCCC 58.550 47.826 0.00 0.00 42.48 3.85
7137 9199 5.066968 ACCATTTTTAGTGCAATTACCCG 57.933 39.130 0.00 0.00 0.00 5.28
7145 9207 2.028748 AGTGCAATTACCCGAAGTACGT 60.029 45.455 0.00 0.00 40.78 3.57
7146 9208 2.346545 GTGCAATTACCCGAAGTACGTC 59.653 50.000 0.00 0.00 40.78 4.34
7147 9209 1.585214 GCAATTACCCGAAGTACGTCG 59.415 52.381 22.07 22.07 40.78 5.12
7148 9210 2.731968 GCAATTACCCGAAGTACGTCGA 60.732 50.000 28.92 12.10 43.86 4.20
7149 9211 3.500982 CAATTACCCGAAGTACGTCGAA 58.499 45.455 28.92 17.21 43.86 3.71
7150 9212 3.848272 ATTACCCGAAGTACGTCGAAA 57.152 42.857 28.92 19.82 43.86 3.46
7151 9213 3.634568 TTACCCGAAGTACGTCGAAAA 57.365 42.857 28.92 17.35 43.86 2.29
7152 9214 1.770957 ACCCGAAGTACGTCGAAAAC 58.229 50.000 28.92 0.00 43.86 2.43
7153 9215 1.063031 CCCGAAGTACGTCGAAAACC 58.937 55.000 28.92 0.00 43.86 3.27
7154 9216 1.063031 CCGAAGTACGTCGAAAACCC 58.937 55.000 28.92 0.00 43.86 4.11
7155 9217 1.602668 CCGAAGTACGTCGAAAACCCA 60.603 52.381 28.92 0.00 43.86 4.51
7156 9218 1.453148 CGAAGTACGTCGAAAACCCAC 59.547 52.381 24.20 0.00 43.86 4.61
7157 9219 2.472816 GAAGTACGTCGAAAACCCACA 58.527 47.619 0.00 0.00 0.00 4.17
7158 9220 1.856802 AGTACGTCGAAAACCCACAC 58.143 50.000 0.00 0.00 0.00 3.82
7159 9221 0.503961 GTACGTCGAAAACCCACACG 59.496 55.000 0.00 0.00 36.54 4.49
7160 9222 0.597118 TACGTCGAAAACCCACACGG 60.597 55.000 0.00 0.00 34.75 4.94
7168 9230 3.462169 ACCCACACGGTGATTCGA 58.538 55.556 16.29 0.00 46.09 3.71
7169 9231 1.749665 ACCCACACGGTGATTCGAA 59.250 52.632 16.29 0.00 46.09 3.71
7170 9232 0.320421 ACCCACACGGTGATTCGAAG 60.320 55.000 16.29 0.00 46.09 3.79
7171 9233 1.635663 CCCACACGGTGATTCGAAGC 61.636 60.000 16.29 6.43 35.23 3.86
7172 9234 1.635663 CCACACGGTGATTCGAAGCC 61.636 60.000 16.29 8.39 35.23 4.35
7173 9235 0.948623 CACACGGTGATTCGAAGCCA 60.949 55.000 16.29 4.93 35.23 4.75
7174 9236 0.250124 ACACGGTGATTCGAAGCCAA 60.250 50.000 16.29 0.00 0.00 4.52
7175 9237 0.165944 CACGGTGATTCGAAGCCAAC 59.834 55.000 11.45 9.42 0.00 3.77
7176 9238 0.034896 ACGGTGATTCGAAGCCAACT 59.965 50.000 11.45 0.00 0.00 3.16
7177 9239 0.443869 CGGTGATTCGAAGCCAACTG 59.556 55.000 11.45 4.64 0.00 3.16
7178 9240 1.808411 GGTGATTCGAAGCCAACTGA 58.192 50.000 11.45 0.00 0.00 3.41
7179 9241 2.151202 GGTGATTCGAAGCCAACTGAA 58.849 47.619 11.45 0.00 0.00 3.02
7180 9242 2.160417 GGTGATTCGAAGCCAACTGAAG 59.840 50.000 11.45 0.00 0.00 3.02
7181 9243 1.806542 TGATTCGAAGCCAACTGAAGC 59.193 47.619 11.45 0.00 0.00 3.86
7182 9244 2.079925 GATTCGAAGCCAACTGAAGCT 58.920 47.619 0.88 0.00 42.40 3.74
7183 9245 1.229428 TTCGAAGCCAACTGAAGCTG 58.771 50.000 0.00 0.00 39.87 4.24
7184 9246 0.392706 TCGAAGCCAACTGAAGCTGA 59.607 50.000 0.00 0.00 39.87 4.26
7185 9247 1.202639 TCGAAGCCAACTGAAGCTGAA 60.203 47.619 0.00 0.00 39.87 3.02
7186 9248 1.603802 CGAAGCCAACTGAAGCTGAAA 59.396 47.619 0.00 0.00 39.87 2.69
7187 9249 2.603173 CGAAGCCAACTGAAGCTGAAAC 60.603 50.000 0.00 0.00 39.87 2.78
7188 9250 2.057137 AGCCAACTGAAGCTGAAACA 57.943 45.000 0.00 0.00 38.11 2.83
7189 9251 2.378038 AGCCAACTGAAGCTGAAACAA 58.622 42.857 0.00 0.00 38.11 2.83
7190 9252 2.760092 AGCCAACTGAAGCTGAAACAAA 59.240 40.909 0.00 0.00 38.11 2.83
7191 9253 2.860136 GCCAACTGAAGCTGAAACAAAC 59.140 45.455 0.00 0.00 0.00 2.93
7192 9254 3.675775 GCCAACTGAAGCTGAAACAAACA 60.676 43.478 0.00 0.00 0.00 2.83
7193 9255 4.685924 CCAACTGAAGCTGAAACAAACAT 58.314 39.130 0.00 0.00 0.00 2.71
7194 9256 4.505191 CCAACTGAAGCTGAAACAAACATG 59.495 41.667 0.00 0.00 0.00 3.21
7195 9257 5.342433 CAACTGAAGCTGAAACAAACATGA 58.658 37.500 0.00 0.00 0.00 3.07
7196 9258 4.925068 ACTGAAGCTGAAACAAACATGAC 58.075 39.130 0.00 0.00 0.00 3.06
7197 9259 4.202050 ACTGAAGCTGAAACAAACATGACC 60.202 41.667 0.00 0.00 0.00 4.02
7198 9260 3.953612 TGAAGCTGAAACAAACATGACCT 59.046 39.130 0.00 0.00 0.00 3.85
7199 9261 5.129634 TGAAGCTGAAACAAACATGACCTA 58.870 37.500 0.00 0.00 0.00 3.08
7200 9262 5.239306 TGAAGCTGAAACAAACATGACCTAG 59.761 40.000 0.00 0.00 0.00 3.02
7201 9263 4.973168 AGCTGAAACAAACATGACCTAGA 58.027 39.130 0.00 0.00 0.00 2.43
7242 9305 0.464452 CCCCTCGAATCCCACACTAC 59.536 60.000 0.00 0.00 0.00 2.73
7336 9399 4.955450 ACACAAATTATGCATGCCCTTAGA 59.045 37.500 16.68 0.00 0.00 2.10
7340 9403 7.175467 CACAAATTATGCATGCCCTTAGAGATA 59.825 37.037 16.68 0.28 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.726291 AGAATATATCGAAAAGAGGGAGAGACA 59.274 37.037 0.00 0.00 0.00 3.41
117 119 9.742144 TGTAATAAAATGGTTAGGTGTGTACAT 57.258 29.630 0.00 0.00 0.00 2.29
207 209 7.664731 GGTACATGATCATCAAGAAATCATCCT 59.335 37.037 4.86 2.13 37.90 3.24
219 221 5.243730 TCATAAGAGCGGTACATGATCATCA 59.756 40.000 4.86 0.00 0.00 3.07
245 247 3.494398 CCACCATATTACTTGGGGACTCG 60.494 52.174 0.00 0.00 40.29 4.18
283 285 4.584638 ATGGGCTTGAGGTGTAAATACA 57.415 40.909 0.00 0.00 0.00 2.29
293 295 0.034059 CCTAGCGTATGGGCTTGAGG 59.966 60.000 0.00 0.00 41.39 3.86
303 305 2.946785 AGTCTACCAAGCCTAGCGTAT 58.053 47.619 0.00 0.00 0.00 3.06
332 334 4.541648 GCCCGCTCCCCTCCTCTA 62.542 72.222 0.00 0.00 0.00 2.43
359 361 7.499232 AGAATTTAGGGTGGATCTAATTTCGTG 59.501 37.037 0.00 0.00 39.50 4.35
392 394 3.691049 TTGCTTAGTATTCCATTGCGC 57.309 42.857 0.00 0.00 0.00 6.09
393 395 7.362662 ACATATTTGCTTAGTATTCCATTGCG 58.637 34.615 0.00 0.00 0.00 4.85
445 447 9.772973 CCATGGATTCAATGTGAAAATATCAAT 57.227 29.630 5.56 0.00 40.12 2.57
460 471 6.879993 CACATTTCAATTTCCCATGGATTCAA 59.120 34.615 15.22 0.00 0.00 2.69
467 478 9.439500 AACTTATTCACATTTCAATTTCCCATG 57.561 29.630 0.00 0.00 0.00 3.66
506 517 2.031245 TGCATAAACAAGAGTTGTGGCG 60.031 45.455 0.00 0.00 44.59 5.69
566 577 8.333908 GTGAGAAAGTAGACATGAATAATGCAG 58.666 37.037 0.00 0.00 40.22 4.41
575 586 4.176271 CGCATGTGAGAAAGTAGACATGA 58.824 43.478 13.70 0.00 45.66 3.07
684 695 5.981915 ACTTATATTTAAGAACGGACGGAGC 59.018 40.000 9.58 0.00 38.56 4.70
716 727 8.007716 CGTATGTAGTTCACGTTGAAATCTTTT 58.992 33.333 4.43 0.00 38.22 2.27
732 743 8.542497 TTACTCATTTTGCTTCGTATGTAGTT 57.458 30.769 0.00 0.00 0.00 2.24
836 847 2.283145 AATCAGCCACACTTGCTTCT 57.717 45.000 0.00 0.00 36.81 2.85
841 852 5.185454 TCCATACTAAATCAGCCACACTTG 58.815 41.667 0.00 0.00 0.00 3.16
992 1010 1.453928 GAGGAATCGGCTTTGGGGG 60.454 63.158 0.00 0.00 0.00 5.40
1090 1108 4.959596 GATGGAGGCGCCGCTCTC 62.960 72.222 29.50 20.98 40.66 3.20
1518 1959 2.861101 GCCGGAGCCGATCATCTCA 61.861 63.158 5.05 0.00 42.83 3.27
1539 1980 4.809513 AGGTAGACCTGCCCGAAT 57.190 55.556 0.00 0.00 46.55 3.34
1584 2025 0.951040 GCACCTGCTTTACTGCGAGT 60.951 55.000 0.00 0.00 38.21 4.18
1620 2061 4.021104 CCAGACAGTAGAAACCAGATCACA 60.021 45.833 0.00 0.00 0.00 3.58
1633 2074 5.049459 TGACTCCAAGTCTCCAGACAGTAG 61.049 50.000 9.39 3.82 45.27 2.57
1668 2109 6.442112 CAAAAATCAAACAAGGGAGAGAGTC 58.558 40.000 0.00 0.00 0.00 3.36
1962 3862 5.880901 ACCACAGGAAGTAGATCAAACAAT 58.119 37.500 0.00 0.00 0.00 2.71
2032 3937 1.815003 GGAACAAACTCCAGCAGGATG 59.185 52.381 0.00 0.00 44.70 3.51
2095 4000 1.188863 GGTTACTTACTGCCTCCGGA 58.811 55.000 2.93 2.93 0.00 5.14
2251 4157 8.833231 TCAGAGTTTTTACCTTAATGTCTCTG 57.167 34.615 14.88 14.88 44.05 3.35
2320 4227 8.333984 TCCCATGATCATCAAGATAATTAGCAT 58.666 33.333 4.86 0.00 37.00 3.79
2400 4307 3.376546 GCCCCAAAATCGGCAAGT 58.623 55.556 0.00 0.00 45.01 3.16
2635 4616 3.489229 GCTTGGAACCAAACTCACACTTC 60.489 47.826 7.68 0.00 35.33 3.01
2665 4646 3.140895 CCCTGGGACCATCCTATTTTGAT 59.859 47.826 7.01 0.00 36.57 2.57
2666 4647 2.513738 CCCTGGGACCATCCTATTTTGA 59.486 50.000 7.01 0.00 36.57 2.69
2670 4651 2.843909 ATCCCTGGGACCATCCTATT 57.156 50.000 19.82 0.00 36.57 1.73
2671 4652 3.115962 TGTTATCCCTGGGACCATCCTAT 60.116 47.826 19.82 1.48 36.57 2.57
2672 4653 2.251605 TGTTATCCCTGGGACCATCCTA 59.748 50.000 19.82 2.02 36.57 2.94
2673 4654 1.010793 TGTTATCCCTGGGACCATCCT 59.989 52.381 19.82 3.16 36.57 3.24
2674 4655 1.518367 TGTTATCCCTGGGACCATCC 58.482 55.000 19.82 5.21 32.98 3.51
2675 4656 3.662759 TTTGTTATCCCTGGGACCATC 57.337 47.619 19.82 9.60 32.98 3.51
2678 4659 4.167307 TCCTATTTTGTTATCCCTGGGACC 59.833 45.833 19.82 9.72 32.98 4.46
2679 4660 5.382664 TCCTATTTTGTTATCCCTGGGAC 57.617 43.478 19.82 6.86 32.98 4.46
2680 4661 5.162991 CCATCCTATTTTGTTATCCCTGGGA 60.163 44.000 19.69 19.69 35.55 4.37
2681 4662 5.079643 CCATCCTATTTTGTTATCCCTGGG 58.920 45.833 6.33 6.33 0.00 4.45
2682 4663 5.705400 ACCATCCTATTTTGTTATCCCTGG 58.295 41.667 0.00 0.00 0.00 4.45
2683 4664 5.770162 GGACCATCCTATTTTGTTATCCCTG 59.230 44.000 0.00 0.00 32.53 4.45
2684 4665 5.162980 GGGACCATCCTATTTTGTTATCCCT 60.163 44.000 0.00 0.00 39.23 4.20
2685 4666 5.077564 GGGACCATCCTATTTTGTTATCCC 58.922 45.833 0.00 0.00 36.57 3.85
2686 4667 5.701224 TGGGACCATCCTATTTTGTTATCC 58.299 41.667 0.00 0.00 36.57 2.59
2688 4669 6.068498 TCCTTGGGACCATCCTATTTTGTTAT 60.068 38.462 0.00 0.00 36.57 1.89
2708 4700 7.763985 GGGGAAATAACAAACATGTTATCCTTG 59.236 37.037 12.39 8.57 42.24 3.61
2723 4715 7.093509 GCAAGAAAATAAGAGGGGGAAATAACA 60.094 37.037 0.00 0.00 0.00 2.41
2724 4716 7.265673 GCAAGAAAATAAGAGGGGGAAATAAC 58.734 38.462 0.00 0.00 0.00 1.89
2726 4718 5.592688 CGCAAGAAAATAAGAGGGGGAAATA 59.407 40.000 0.00 0.00 43.02 1.40
2727 4719 4.402474 CGCAAGAAAATAAGAGGGGGAAAT 59.598 41.667 0.00 0.00 43.02 2.17
2728 4720 3.761752 CGCAAGAAAATAAGAGGGGGAAA 59.238 43.478 0.00 0.00 43.02 3.13
2729 4721 3.352648 CGCAAGAAAATAAGAGGGGGAA 58.647 45.455 0.00 0.00 43.02 3.97
2730 4722 2.356741 CCGCAAGAAAATAAGAGGGGGA 60.357 50.000 0.00 0.00 43.02 4.81
2736 4728 4.653868 TGTTACCCCGCAAGAAAATAAGA 58.346 39.130 0.00 0.00 43.02 2.10
2737 4729 5.576447 ATGTTACCCCGCAAGAAAATAAG 57.424 39.130 0.00 0.00 43.02 1.73
2752 4744 1.334869 GGCACTGCAGCATATGTTACC 59.665 52.381 15.27 0.00 35.83 2.85
2760 4752 1.000019 AGGATTGGCACTGCAGCAT 60.000 52.632 15.27 0.00 35.83 3.79
2761 4753 1.676635 GAGGATTGGCACTGCAGCA 60.677 57.895 15.27 0.06 35.83 4.41
2762 4754 2.758089 CGAGGATTGGCACTGCAGC 61.758 63.158 15.27 0.33 0.00 5.25
2802 4800 4.021192 GCAAGGGTCTTTCCATGAAATTGA 60.021 41.667 0.00 0.00 38.11 2.57
2803 4801 4.248058 GCAAGGGTCTTTCCATGAAATTG 58.752 43.478 0.00 0.00 38.11 2.32
2830 4828 4.808895 GTGCGGACAGTTATCAATGATACA 59.191 41.667 0.63 0.00 0.00 2.29
2835 4833 3.436704 ACAAGTGCGGACAGTTATCAATG 59.563 43.478 10.52 0.00 37.34 2.82
2845 4843 1.308783 TTGCAACACAAGTGCGGACA 61.309 50.000 10.52 0.00 33.24 4.02
2846 4844 0.865639 GTTGCAACACAAGTGCGGAC 60.866 55.000 24.52 0.00 39.50 4.79
2854 4852 9.786105 CTTATATACAATGATGTTGCAACACAA 57.214 29.630 33.29 23.85 42.51 3.33
2856 4854 9.787532 AACTTATATACAATGATGTTGCAACAC 57.212 29.630 33.29 24.93 42.51 3.32
2884 4882 1.940613 GATAAAGTTGTAGCAGGCGGG 59.059 52.381 0.00 0.00 0.00 6.13
2921 4919 8.578308 AAACACACAGTGACAAATAAATCATG 57.422 30.769 7.81 0.00 36.96 3.07
2928 4926 7.540400 CACAAAGAAAACACACAGTGACAAATA 59.460 33.333 7.81 0.00 36.96 1.40
2942 4940 6.045955 GGGAATAACTTGCACAAAGAAAACA 58.954 36.000 0.00 0.00 39.38 2.83
2943 4941 6.045955 TGGGAATAACTTGCACAAAGAAAAC 58.954 36.000 0.00 0.00 39.38 2.43
2944 4942 6.227298 TGGGAATAACTTGCACAAAGAAAA 57.773 33.333 0.00 0.00 39.38 2.29
2960 4958 7.493320 GTCGTTAAGTACATTGACATGGGAATA 59.507 37.037 0.00 0.00 34.27 1.75
2976 4974 6.795098 AGCATTGAACATTGTCGTTAAGTA 57.205 33.333 0.00 0.00 0.00 2.24
3104 5102 5.416013 AGGCAAGAAATAAAGTACTGGAAGC 59.584 40.000 0.00 0.00 37.60 3.86
3131 5129 6.348458 GCAAAGGCCTATCCAAATTCAAAAAC 60.348 38.462 5.16 0.00 37.29 2.43
3173 5172 9.004231 AGAACTAAAATATGGTACTCTGGGATT 57.996 33.333 0.00 0.00 0.00 3.01
3342 5341 1.896660 GTGCTTTCGTGCTTCCCCA 60.897 57.895 0.00 0.00 0.00 4.96
3390 5389 0.035439 AAGGCCATGTGGGTAACTCG 60.035 55.000 5.01 0.00 39.65 4.18
3452 5451 1.002033 CAGCTTGTTCTGTGCTTGGTC 60.002 52.381 0.00 0.00 34.51 4.02
3453 5452 1.027357 CAGCTTGTTCTGTGCTTGGT 58.973 50.000 0.00 0.00 34.51 3.67
3546 5553 4.623932 TCTATTGAAGACAGCAACAGGT 57.376 40.909 0.00 0.00 0.00 4.00
3547 5554 5.879223 AGAATCTATTGAAGACAGCAACAGG 59.121 40.000 0.00 0.00 36.93 4.00
3548 5555 6.981762 AGAATCTATTGAAGACAGCAACAG 57.018 37.500 0.00 0.00 36.93 3.16
3549 5556 8.886719 CATAAGAATCTATTGAAGACAGCAACA 58.113 33.333 0.00 0.00 36.93 3.33
3550 5557 8.341173 CCATAAGAATCTATTGAAGACAGCAAC 58.659 37.037 0.00 0.00 36.93 4.17
3551 5558 7.500227 CCCATAAGAATCTATTGAAGACAGCAA 59.500 37.037 0.00 0.00 36.93 3.91
3552 5559 6.994496 CCCATAAGAATCTATTGAAGACAGCA 59.006 38.462 0.00 0.00 36.93 4.41
3553 5560 6.995091 ACCCATAAGAATCTATTGAAGACAGC 59.005 38.462 0.00 0.00 36.93 4.40
3554 5561 7.989741 ACACCCATAAGAATCTATTGAAGACAG 59.010 37.037 0.00 0.00 36.93 3.51
3555 5562 7.861629 ACACCCATAAGAATCTATTGAAGACA 58.138 34.615 0.00 0.00 36.93 3.41
3556 5563 8.738645 AACACCCATAAGAATCTATTGAAGAC 57.261 34.615 0.00 0.00 36.93 3.01
3559 5566 9.403583 GGTAAACACCCATAAGAATCTATTGAA 57.596 33.333 0.00 0.00 0.00 2.69
3560 5567 8.778059 AGGTAAACACCCATAAGAATCTATTGA 58.222 33.333 0.00 0.00 0.00 2.57
3561 5568 8.980481 AGGTAAACACCCATAAGAATCTATTG 57.020 34.615 0.00 0.00 0.00 1.90
3728 5736 3.508426 TCCAGATATCTGCAGAGCTGAT 58.492 45.455 30.31 18.92 46.11 2.90
3877 5886 3.530535 AGCGCAACCTGAAAAACATTTT 58.469 36.364 11.47 0.00 0.00 1.82
3882 5891 2.492019 AGAAGCGCAACCTGAAAAAC 57.508 45.000 11.47 0.00 0.00 2.43
3950 5959 5.884792 CAGAAAATCTTTAGCCTCTGGTGAT 59.115 40.000 0.00 0.00 0.00 3.06
3984 5993 2.862541 ACAACAGGCATACTTCTGCAA 58.137 42.857 0.00 0.00 44.12 4.08
4108 6151 1.005215 CAGCTCTGGTTCCCTGGAATT 59.995 52.381 1.26 0.00 36.45 2.17
4109 6152 0.622665 CAGCTCTGGTTCCCTGGAAT 59.377 55.000 1.26 0.00 36.45 3.01
4164 6207 9.158233 CATGTTTAAGATGCAGGAAATCAAATT 57.842 29.630 0.00 0.00 0.00 1.82
4316 6359 1.068055 CAGCAATCCAACCTTCTGTGC 60.068 52.381 0.00 0.00 0.00 4.57
4380 6423 7.297936 TGTGTCATTGTTTAGAGAGGTTAGA 57.702 36.000 0.00 0.00 0.00 2.10
4484 6527 5.499313 TGAGATTGTGTAGAATGGCATGAA 58.501 37.500 0.00 0.00 0.00 2.57
4487 6530 7.414222 AAAATGAGATTGTGTAGAATGGCAT 57.586 32.000 0.00 0.00 0.00 4.40
4524 6568 7.037797 GCAATTAAATAAGTTGCAGTGTCAC 57.962 36.000 5.97 0.00 45.57 3.67
4642 6686 3.251487 CAGCAAACTCACACATGTCATCA 59.749 43.478 0.00 0.00 0.00 3.07
4806 6850 1.003580 GCTCTGGAATTGACAGACCCA 59.996 52.381 5.55 0.00 39.87 4.51
5119 7165 0.914644 TCTTCAGATCAAGGGCCTGG 59.085 55.000 6.92 3.14 0.00 4.45
5266 7312 1.428869 CTCCCCTCATCTTACCTGGG 58.571 60.000 0.00 0.00 37.68 4.45
5368 7414 1.441729 GCTGCTATCTACACCGCCA 59.558 57.895 0.00 0.00 0.00 5.69
5483 7529 3.126001 TCTGTCATCGAAGCAAGGTTT 57.874 42.857 0.00 0.00 0.00 3.27
5501 7547 8.306761 CACCTAAGGTTTTTGCATAGAATTTCT 58.693 33.333 4.03 4.03 31.02 2.52
5508 7554 4.218417 AGTGCACCTAAGGTTTTTGCATAG 59.782 41.667 14.63 0.00 34.35 2.23
5510 7556 2.965147 AGTGCACCTAAGGTTTTTGCAT 59.035 40.909 14.63 0.00 34.35 3.96
5530 7576 2.168106 ACCAGTTCTAGCAGAGATGCAG 59.832 50.000 2.73 0.00 37.25 4.41
5545 7591 6.270231 GTCCCCTATTAGATCATGTACCAGTT 59.730 42.308 0.00 0.00 0.00 3.16
5842 7889 4.167554 AGCACTGTATAGCTATCTTCGC 57.832 45.455 10.16 8.09 39.78 4.70
5934 7983 2.361610 ACCAGGCTGATTTGGGCG 60.362 61.111 17.94 0.00 38.82 6.13
6048 8097 0.685458 TCTCCCAGGTTAGTACGCCC 60.685 60.000 1.45 0.00 0.00 6.13
6102 8151 3.740321 GCACCGCAAAGAATGAAAAATGA 59.260 39.130 0.00 0.00 0.00 2.57
6135 8184 0.593128 AAGCCATGCGACTGAAACAC 59.407 50.000 0.00 0.00 0.00 3.32
6320 8369 0.740868 CCAATCGAAGCGCCTGAAGA 60.741 55.000 2.29 0.00 0.00 2.87
6334 8383 5.527582 ACAGAGTGTAACAACTTCACCAATC 59.472 40.000 0.00 0.00 41.43 2.67
6335 8384 5.296780 CACAGAGTGTAACAACTTCACCAAT 59.703 40.000 0.00 0.00 41.43 3.16
6394 8446 9.029368 TGAGAGAGAGAATCAAACTATCAAGAA 57.971 33.333 0.00 0.00 37.82 2.52
6468 8527 3.216800 TGATGTTGCTTTGTTCAGCTCT 58.783 40.909 0.00 0.00 40.79 4.09
6503 8562 2.108514 GTAGGCCCGGCGTTAAACC 61.109 63.158 10.44 0.00 0.00 3.27
6504 8563 1.375780 TGTAGGCCCGGCGTTAAAC 60.376 57.895 10.44 3.23 0.00 2.01
6505 8564 1.375780 GTGTAGGCCCGGCGTTAAA 60.376 57.895 10.44 0.00 0.00 1.52
6506 8565 2.265424 GTGTAGGCCCGGCGTTAA 59.735 61.111 10.44 0.00 0.00 2.01
6510 8569 2.510064 TTAAGTGTGTAGGCCCGGCG 62.510 60.000 0.00 0.00 0.00 6.46
6511 8570 1.022982 GTTAAGTGTGTAGGCCCGGC 61.023 60.000 0.00 0.00 0.00 6.13
6512 8571 0.322322 TGTTAAGTGTGTAGGCCCGG 59.678 55.000 0.00 0.00 0.00 5.73
6513 8572 2.396590 ATGTTAAGTGTGTAGGCCCG 57.603 50.000 0.00 0.00 0.00 6.13
6514 8573 2.163613 GCAATGTTAAGTGTGTAGGCCC 59.836 50.000 0.00 0.00 0.00 5.80
6515 8574 3.081804 AGCAATGTTAAGTGTGTAGGCC 58.918 45.455 0.00 0.00 0.00 5.19
6516 8575 3.751175 TCAGCAATGTTAAGTGTGTAGGC 59.249 43.478 0.00 0.00 0.00 3.93
6517 8576 5.700832 TCTTCAGCAATGTTAAGTGTGTAGG 59.299 40.000 0.00 0.00 0.00 3.18
6620 8681 6.072783 CCTTCTCTGTTTTCTCATTGTTCTCC 60.073 42.308 0.00 0.00 0.00 3.71
6624 8685 5.694995 TCCCTTCTCTGTTTTCTCATTGTT 58.305 37.500 0.00 0.00 0.00 2.83
6694 8755 5.918576 CCTCAAGTCGTTAAACCCATTTTTC 59.081 40.000 0.00 0.00 0.00 2.29
6746 8808 1.147153 GGGCTTGGAAGATCCCTCG 59.853 63.158 0.00 0.00 35.03 4.63
6755 8817 2.708861 TCTCTTGTACAAGGGCTTGGAA 59.291 45.455 30.35 11.41 44.45 3.53
6762 8824 1.625818 AGCACCTCTCTTGTACAAGGG 59.374 52.381 30.35 28.63 40.24 3.95
6799 8861 8.608844 AAGTTCTTTATGTCACCTCTTGTAAG 57.391 34.615 0.00 0.00 0.00 2.34
6885 8947 4.141846 TGCTCTAACCAATGCAACCAAAAA 60.142 37.500 0.00 0.00 32.12 1.94
6901 8963 5.667539 AGTTCTAGAAGTGCATGCTCTAA 57.332 39.130 21.70 9.85 0.00 2.10
6946 9008 5.588845 AGCAGGGCAAGATCTAGATAGTAT 58.411 41.667 4.89 0.00 0.00 2.12
6951 9013 2.776536 ACAAGCAGGGCAAGATCTAGAT 59.223 45.455 4.47 4.47 0.00 1.98
6975 9037 1.304464 ACTTGCCAGCCTAAAGCCC 60.304 57.895 0.00 0.00 45.47 5.19
6996 9058 2.135890 CCCTGCTTGTTTGGGCTTT 58.864 52.632 0.00 0.00 33.88 3.51
6997 9059 3.875390 CCCTGCTTGTTTGGGCTT 58.125 55.556 0.00 0.00 33.88 4.35
7003 9065 4.479786 TTTAAACTTGCCCTGCTTGTTT 57.520 36.364 11.99 11.99 37.89 2.83
7004 9066 4.479786 TTTTAAACTTGCCCTGCTTGTT 57.520 36.364 0.00 0.00 0.00 2.83
7005 9067 4.479786 TTTTTAAACTTGCCCTGCTTGT 57.520 36.364 0.00 0.00 0.00 3.16
7039 9101 1.329906 CAGCTTCTAGATTTGCCTGCG 59.670 52.381 0.00 0.00 0.00 5.18
7045 9107 8.534778 GTTGTTTTGTTTCAGCTTCTAGATTTG 58.465 33.333 0.00 0.00 0.00 2.32
7049 9111 5.650266 TGGTTGTTTTGTTTCAGCTTCTAGA 59.350 36.000 0.00 0.00 0.00 2.43
7072 9134 5.075858 TCTGGCAAAGCTAATTCCAAATG 57.924 39.130 0.00 0.00 0.00 2.32
7093 9155 3.133003 TCGGGATTCAGATTCACCTTCTC 59.867 47.826 0.00 0.00 0.00 2.87
7111 9173 3.866883 ATTGCACTAAAAATGGTCGGG 57.133 42.857 0.00 0.00 0.00 5.14
7113 9175 5.099575 GGGTAATTGCACTAAAAATGGTCG 58.900 41.667 0.00 0.00 0.00 4.79
7137 9199 2.219445 GTGTGGGTTTTCGACGTACTTC 59.781 50.000 0.00 0.00 0.00 3.01
7152 9214 1.635663 GCTTCGAATCACCGTGTGGG 61.636 60.000 0.00 0.00 40.75 4.61
7153 9215 1.635663 GGCTTCGAATCACCGTGTGG 61.636 60.000 0.00 0.00 42.84 4.17
7154 9216 0.948623 TGGCTTCGAATCACCGTGTG 60.949 55.000 0.00 0.00 34.45 3.82
7155 9217 0.250124 TTGGCTTCGAATCACCGTGT 60.250 50.000 0.00 0.00 0.00 4.49
7156 9218 0.165944 GTTGGCTTCGAATCACCGTG 59.834 55.000 0.00 0.00 0.00 4.94
7157 9219 0.034896 AGTTGGCTTCGAATCACCGT 59.965 50.000 0.00 0.00 0.00 4.83
7158 9220 0.443869 CAGTTGGCTTCGAATCACCG 59.556 55.000 0.00 0.00 0.00 4.94
7159 9221 1.808411 TCAGTTGGCTTCGAATCACC 58.192 50.000 0.00 1.39 0.00 4.02
7160 9222 2.413371 GCTTCAGTTGGCTTCGAATCAC 60.413 50.000 0.00 0.00 0.00 3.06
7161 9223 1.806542 GCTTCAGTTGGCTTCGAATCA 59.193 47.619 0.00 0.00 0.00 2.57
7162 9224 2.079925 AGCTTCAGTTGGCTTCGAATC 58.920 47.619 0.00 0.00 34.96 2.52
7163 9225 1.808945 CAGCTTCAGTTGGCTTCGAAT 59.191 47.619 0.00 0.00 36.59 3.34
7164 9226 1.202639 TCAGCTTCAGTTGGCTTCGAA 60.203 47.619 0.00 0.00 36.59 3.71
7165 9227 0.392706 TCAGCTTCAGTTGGCTTCGA 59.607 50.000 0.00 0.00 36.59 3.71
7166 9228 1.229428 TTCAGCTTCAGTTGGCTTCG 58.771 50.000 0.00 0.00 36.59 3.79
7167 9229 2.358898 TGTTTCAGCTTCAGTTGGCTTC 59.641 45.455 0.00 0.00 36.59 3.86
7168 9230 2.378038 TGTTTCAGCTTCAGTTGGCTT 58.622 42.857 0.00 0.00 36.59 4.35
7169 9231 2.057137 TGTTTCAGCTTCAGTTGGCT 57.943 45.000 0.00 0.00 39.60 4.75
7170 9232 2.860136 GTTTGTTTCAGCTTCAGTTGGC 59.140 45.455 0.00 0.00 0.00 4.52
7171 9233 4.108699 TGTTTGTTTCAGCTTCAGTTGG 57.891 40.909 0.00 0.00 0.00 3.77
7172 9234 5.230726 GTCATGTTTGTTTCAGCTTCAGTTG 59.769 40.000 0.00 0.00 0.00 3.16
7173 9235 5.343249 GTCATGTTTGTTTCAGCTTCAGTT 58.657 37.500 0.00 0.00 0.00 3.16
7174 9236 4.202050 GGTCATGTTTGTTTCAGCTTCAGT 60.202 41.667 0.00 0.00 0.00 3.41
7175 9237 4.037208 AGGTCATGTTTGTTTCAGCTTCAG 59.963 41.667 0.00 0.00 0.00 3.02
7176 9238 3.953612 AGGTCATGTTTGTTTCAGCTTCA 59.046 39.130 0.00 0.00 0.00 3.02
7177 9239 4.574599 AGGTCATGTTTGTTTCAGCTTC 57.425 40.909 0.00 0.00 0.00 3.86
7178 9240 5.376625 TCTAGGTCATGTTTGTTTCAGCTT 58.623 37.500 0.00 0.00 0.00 3.74
7179 9241 4.973168 TCTAGGTCATGTTTGTTTCAGCT 58.027 39.130 0.00 0.00 0.00 4.24
7180 9242 5.689383 TTCTAGGTCATGTTTGTTTCAGC 57.311 39.130 0.00 0.00 0.00 4.26
7181 9243 6.127897 GGGATTCTAGGTCATGTTTGTTTCAG 60.128 42.308 0.00 0.00 0.00 3.02
7182 9244 5.710099 GGGATTCTAGGTCATGTTTGTTTCA 59.290 40.000 0.00 0.00 0.00 2.69
7183 9245 5.710099 TGGGATTCTAGGTCATGTTTGTTTC 59.290 40.000 0.00 0.00 0.00 2.78
7184 9246 5.476945 GTGGGATTCTAGGTCATGTTTGTTT 59.523 40.000 0.00 0.00 0.00 2.83
7185 9247 5.010282 GTGGGATTCTAGGTCATGTTTGTT 58.990 41.667 0.00 0.00 0.00 2.83
7186 9248 4.289672 AGTGGGATTCTAGGTCATGTTTGT 59.710 41.667 0.00 0.00 0.00 2.83
7187 9249 4.848357 AGTGGGATTCTAGGTCATGTTTG 58.152 43.478 0.00 0.00 0.00 2.93
7188 9250 6.595682 CATAGTGGGATTCTAGGTCATGTTT 58.404 40.000 0.00 0.00 0.00 2.83
7189 9251 5.455326 GCATAGTGGGATTCTAGGTCATGTT 60.455 44.000 0.00 0.00 0.00 2.71
7190 9252 4.040952 GCATAGTGGGATTCTAGGTCATGT 59.959 45.833 0.00 0.00 0.00 3.21
7191 9253 4.573900 GCATAGTGGGATTCTAGGTCATG 58.426 47.826 0.00 0.00 0.00 3.07
7192 9254 3.259374 CGCATAGTGGGATTCTAGGTCAT 59.741 47.826 0.00 0.00 31.21 3.06
7193 9255 2.628178 CGCATAGTGGGATTCTAGGTCA 59.372 50.000 0.00 0.00 31.21 4.02
7194 9256 2.628657 ACGCATAGTGGGATTCTAGGTC 59.371 50.000 0.81 0.00 34.12 3.85
7195 9257 2.679082 ACGCATAGTGGGATTCTAGGT 58.321 47.619 0.81 0.00 34.12 3.08
7196 9258 3.753294 AACGCATAGTGGGATTCTAGG 57.247 47.619 0.81 0.00 34.12 3.02
7197 9259 4.238514 GCTAACGCATAGTGGGATTCTAG 58.761 47.826 0.81 0.00 34.12 2.43
7198 9260 3.639561 TGCTAACGCATAGTGGGATTCTA 59.360 43.478 0.81 0.00 42.25 2.10
7199 9261 2.434336 TGCTAACGCATAGTGGGATTCT 59.566 45.455 0.81 0.00 42.25 2.40
7200 9262 2.833794 TGCTAACGCATAGTGGGATTC 58.166 47.619 0.81 0.00 42.25 2.52
7242 9305 3.060602 ACGGTGGTTTTGTGTTTTTGTG 58.939 40.909 0.00 0.00 0.00 3.33
7292 9355 4.956700 TGTTTTGGTTTAGTGTGGGATTCA 59.043 37.500 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.