Multiple sequence alignment - TraesCS3A01G262400

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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 TraesCS3A01G262400 chr3A 100.000 5016 0 0 1 5016 485016178 485011163 0.000000e+00 9263.0
1 TraesCS3A01G262400 chr3B 90.290 2173 105 46 1046 3205 474031887 474029808 0.000000e+00 2747.0
2 TraesCS3A01G262400 chr3B 93.326 1798 90 17 3230 5016 474029746 474027968 0.000000e+00 2628.0
3 TraesCS3A01G262400 chr3B 87.150 856 47 25 100 918 474032923 474032094 0.000000e+00 913.0
4 TraesCS3A01G262400 chr3B 93.750 128 3 1 928 1055 474032043 474031921 2.380000e-43 187.0
5 TraesCS3A01G262400 chr3D 93.493 1798 80 14 3230 5016 363869861 363868090 0.000000e+00 2638.0
6 TraesCS3A01G262400 chr3D 89.900 1604 70 28 928 2484 363872512 363870954 0.000000e+00 1980.0
7 TraesCS3A01G262400 chr3D 95.087 631 22 4 2575 3205 363870545 363869924 0.000000e+00 985.0
8 TraesCS3A01G262400 chr3D 87.291 716 45 25 100 790 363873302 363872608 0.000000e+00 776.0
9 TraesCS3A01G262400 chr3D 90.667 75 3 4 853 926 363872614 363872543 4.130000e-16 97.1
10 TraesCS3A01G262400 chr1D 81.413 269 48 2 4749 5016 457074694 457074427 8.450000e-53 219.0
11 TraesCS3A01G262400 chr1A 81.648 267 46 3 4752 5016 549712735 549712470 8.450000e-53 219.0
12 TraesCS3A01G262400 chr6B 85.714 126 12 6 1476 1598 238168052 238168174 1.470000e-25 128.0
13 TraesCS3A01G262400 chr6B 91.111 90 8 0 1511 1600 667899833 667899744 6.820000e-24 122.0
14 TraesCS3A01G262400 chr7A 86.207 116 12 4 1485 1598 567456866 567456753 6.820000e-24 122.0
15 TraesCS3A01G262400 chr6D 84.921 126 13 6 1476 1598 138904782 138904904 6.820000e-24 122.0
16 TraesCS3A01G262400 chr6D 85.124 121 17 1 1511 1630 441899540 441899420 6.820000e-24 122.0
17 TraesCS3A01G262400 chr6A 84.921 126 13 6 1476 1598 181563816 181563938 6.820000e-24 122.0
18 TraesCS3A01G262400 chr6A 91.111 90 8 0 1511 1600 591267546 591267457 6.820000e-24 122.0


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 TraesCS3A01G262400 chr3A 485011163 485016178 5015 True 9263.00 9263 100.0000 1 5016 1 chr3A.!!$R1 5015
1 TraesCS3A01G262400 chr3B 474027968 474032923 4955 True 1618.75 2747 91.1290 100 5016 4 chr3B.!!$R1 4916
2 TraesCS3A01G262400 chr3D 363868090 363873302 5212 True 1295.22 2638 91.2876 100 5016 5 chr3D.!!$R1 4916

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
311 317 0.037877 AGGAAACGGACGGAGAGAGA 59.962 55.000 0.00 0.0 0.00 3.10 F
1040 1125 0.107848 ACCCCGAGCTAAATCCAACG 60.108 55.000 0.00 0.0 0.00 4.10 F
1643 1790 0.371645 CGCCTCACTTCGCTTCATTC 59.628 55.000 0.00 0.0 0.00 2.67 F
1916 2073 0.540923 ACTGCTGCAGATCCTCTTCC 59.459 55.000 34.28 0.0 35.18 3.46 F
1917 2074 0.831966 CTGCTGCAGATCCTCTTCCT 59.168 55.000 24.88 0.0 32.44 3.36 F
2529 2703 1.065199 TGCAGACATGGATCCCAAGAC 60.065 52.381 9.90 0.0 36.95 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2046 0.399454 ATCTGCAGCAGTGAAGTGGT 59.601 50.000 22.10 0.0 30.06 4.16 R
2509 2683 1.065199 GTCTTGGGATCCATGTCTGCA 60.065 52.381 15.23 0.0 31.53 4.41 R
3044 3536 1.133809 TCAACAACTCTGGGGAGGGG 61.134 60.000 0.00 0.0 43.46 4.79 R
3750 4285 1.546029 GGCTTTTCAGGAACATCCACC 59.454 52.381 0.00 0.0 39.61 4.61 R
3886 4421 4.692625 ACAGTATGACACAGTTGCTTGATC 59.307 41.667 0.00 0.0 39.69 2.92 R
4525 5064 0.039074 ATGAGCGATCCGACGATTCC 60.039 55.000 0.00 0.0 35.09 3.01 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
23 24 5.685728 GAGAGTTGGCTTGATATAAACCCT 58.314 41.667 0.00 0.00 0.00 4.34
24 25 5.440610 AGAGTTGGCTTGATATAAACCCTG 58.559 41.667 0.00 0.00 0.00 4.45
25 26 5.191722 AGAGTTGGCTTGATATAAACCCTGA 59.808 40.000 0.00 0.00 0.00 3.86
26 27 5.440610 AGTTGGCTTGATATAAACCCTGAG 58.559 41.667 0.00 0.00 0.00 3.35
27 28 5.044846 AGTTGGCTTGATATAAACCCTGAGT 60.045 40.000 0.00 0.00 0.00 3.41
28 29 5.450818 TGGCTTGATATAAACCCTGAGTT 57.549 39.130 0.00 0.00 41.81 3.01
30 31 5.885912 TGGCTTGATATAAACCCTGAGTTTC 59.114 40.000 0.00 0.00 45.85 2.78
31 32 6.122964 GGCTTGATATAAACCCTGAGTTTCT 58.877 40.000 0.00 0.00 45.85 2.52
32 33 6.603599 GGCTTGATATAAACCCTGAGTTTCTT 59.396 38.462 0.00 0.00 45.85 2.52
33 34 7.773690 GGCTTGATATAAACCCTGAGTTTCTTA 59.226 37.037 0.00 0.00 45.85 2.10
34 35 9.343539 GCTTGATATAAACCCTGAGTTTCTTAT 57.656 33.333 0.00 0.00 45.85 1.73
39 40 9.901172 ATATAAACCCTGAGTTTCTTATTTCGT 57.099 29.630 0.00 0.00 45.85 3.85
40 41 5.941948 AACCCTGAGTTTCTTATTTCGTG 57.058 39.130 0.00 0.00 33.89 4.35
41 42 3.751698 ACCCTGAGTTTCTTATTTCGTGC 59.248 43.478 0.00 0.00 0.00 5.34
42 43 3.127030 CCCTGAGTTTCTTATTTCGTGCC 59.873 47.826 0.00 0.00 0.00 5.01
43 44 3.127030 CCTGAGTTTCTTATTTCGTGCCC 59.873 47.826 0.00 0.00 0.00 5.36
44 45 3.745799 TGAGTTTCTTATTTCGTGCCCA 58.254 40.909 0.00 0.00 0.00 5.36
45 46 3.500680 TGAGTTTCTTATTTCGTGCCCAC 59.499 43.478 0.00 0.00 0.00 4.61
58 59 3.697747 CCCACGGGCGGACTGTAA 61.698 66.667 0.00 0.00 36.76 2.41
59 60 2.433664 CCACGGGCGGACTGTAAC 60.434 66.667 0.00 0.00 36.76 2.50
60 61 2.340809 CACGGGCGGACTGTAACA 59.659 61.111 0.00 0.00 36.76 2.41
61 62 2.025418 CACGGGCGGACTGTAACAC 61.025 63.158 0.00 0.00 36.76 3.32
62 63 2.340809 CGGGCGGACTGTAACACA 59.659 61.111 0.00 0.00 0.00 3.72
63 64 1.301087 CGGGCGGACTGTAACACAA 60.301 57.895 0.00 0.00 0.00 3.33
64 65 0.881159 CGGGCGGACTGTAACACAAA 60.881 55.000 0.00 0.00 0.00 2.83
65 66 0.872388 GGGCGGACTGTAACACAAAG 59.128 55.000 0.00 0.00 0.00 2.77
66 67 0.872388 GGCGGACTGTAACACAAAGG 59.128 55.000 0.00 0.00 0.00 3.11
67 68 1.541670 GGCGGACTGTAACACAAAGGA 60.542 52.381 0.00 0.00 0.00 3.36
68 69 1.798813 GCGGACTGTAACACAAAGGAG 59.201 52.381 0.00 0.00 0.00 3.69
69 70 1.798813 CGGACTGTAACACAAAGGAGC 59.201 52.381 0.00 0.00 0.00 4.70
70 71 2.548067 CGGACTGTAACACAAAGGAGCT 60.548 50.000 0.00 0.00 0.00 4.09
71 72 3.067833 GGACTGTAACACAAAGGAGCTC 58.932 50.000 4.71 4.71 0.00 4.09
72 73 3.067833 GACTGTAACACAAAGGAGCTCC 58.932 50.000 26.22 26.22 0.00 4.70
73 74 2.438021 ACTGTAACACAAAGGAGCTCCA 59.562 45.455 33.90 8.39 38.89 3.86
74 75 2.808543 CTGTAACACAAAGGAGCTCCAC 59.191 50.000 33.90 20.30 38.89 4.02
75 76 2.438021 TGTAACACAAAGGAGCTCCACT 59.562 45.455 33.90 18.18 38.89 4.00
76 77 3.644265 TGTAACACAAAGGAGCTCCACTA 59.356 43.478 33.90 11.18 38.89 2.74
77 78 4.286032 TGTAACACAAAGGAGCTCCACTAT 59.714 41.667 33.90 14.29 38.89 2.12
78 79 5.482526 TGTAACACAAAGGAGCTCCACTATA 59.517 40.000 33.90 14.20 38.89 1.31
79 80 4.744795 ACACAAAGGAGCTCCACTATAG 57.255 45.455 33.90 20.05 38.89 1.31
80 81 4.097418 ACACAAAGGAGCTCCACTATAGT 58.903 43.478 33.90 20.67 38.89 2.12
81 82 5.269991 ACACAAAGGAGCTCCACTATAGTA 58.730 41.667 33.90 0.00 38.89 1.82
82 83 5.127356 ACACAAAGGAGCTCCACTATAGTAC 59.873 44.000 33.90 3.23 38.89 2.73
83 84 5.127194 CACAAAGGAGCTCCACTATAGTACA 59.873 44.000 33.90 0.00 38.89 2.90
84 85 5.720041 ACAAAGGAGCTCCACTATAGTACAA 59.280 40.000 33.90 0.00 38.89 2.41
85 86 6.212791 ACAAAGGAGCTCCACTATAGTACAAA 59.787 38.462 33.90 0.00 38.89 2.83
86 87 6.869206 AAGGAGCTCCACTATAGTACAAAA 57.131 37.500 33.90 0.00 38.89 2.44
87 88 7.439108 AAGGAGCTCCACTATAGTACAAAAT 57.561 36.000 33.90 4.78 38.89 1.82
88 89 8.548880 AAGGAGCTCCACTATAGTACAAAATA 57.451 34.615 33.90 0.00 38.89 1.40
89 90 8.728596 AGGAGCTCCACTATAGTACAAAATAT 57.271 34.615 33.90 3.98 38.89 1.28
90 91 9.160412 AGGAGCTCCACTATAGTACAAAATATT 57.840 33.333 33.90 3.63 38.89 1.28
104 105 9.720769 AGTACAAAATATTAGTGCACTTGTAGT 57.279 29.630 27.06 22.54 30.69 2.73
123 124 3.195661 AGTATTTTGACGGGAGAATCGC 58.804 45.455 0.00 0.00 45.73 4.58
144 145 2.106938 TAGAAGGCGCGGCAGATG 59.893 61.111 34.94 0.00 0.00 2.90
145 146 2.721167 TAGAAGGCGCGGCAGATGT 61.721 57.895 34.94 20.02 0.00 3.06
214 220 4.181010 CCTGGTCTCCCATGCCCG 62.181 72.222 0.00 0.00 40.90 6.13
310 316 0.452585 GAGGAAACGGACGGAGAGAG 59.547 60.000 0.00 0.00 0.00 3.20
311 317 0.037877 AGGAAACGGACGGAGAGAGA 59.962 55.000 0.00 0.00 0.00 3.10
312 318 0.452585 GGAAACGGACGGAGAGAGAG 59.547 60.000 0.00 0.00 0.00 3.20
313 319 1.451067 GAAACGGACGGAGAGAGAGA 58.549 55.000 0.00 0.00 0.00 3.10
341 348 1.024579 CACCGATTGGACTTTCCCCG 61.025 60.000 5.81 0.00 39.21 5.73
380 387 2.488952 GCAGGAGGGAAAAGATCGATC 58.511 52.381 17.91 17.91 0.00 3.69
381 388 2.103941 GCAGGAGGGAAAAGATCGATCT 59.896 50.000 22.32 22.32 39.22 2.75
479 496 2.418333 CGTCGTGTCTGCTCGTTCG 61.418 63.158 0.00 0.00 33.82 3.95
480 497 1.370172 GTCGTGTCTGCTCGTTCGT 60.370 57.895 0.00 0.00 33.82 3.85
481 498 0.933509 GTCGTGTCTGCTCGTTCGTT 60.934 55.000 0.00 0.00 33.82 3.85
482 499 0.659417 TCGTGTCTGCTCGTTCGTTC 60.659 55.000 0.00 0.00 33.82 3.95
483 500 1.606350 CGTGTCTGCTCGTTCGTTCC 61.606 60.000 0.00 0.00 0.00 3.62
491 508 2.097954 TGCTCGTTCGTTCCGTATATGT 59.902 45.455 0.00 0.00 0.00 2.29
511 533 5.493133 TGTGTGTAGGTTTACTTTTGCTG 57.507 39.130 0.00 0.00 0.00 4.41
526 548 3.348647 TTGCTGGAGCTGTGCTAATTA 57.651 42.857 0.00 0.00 39.88 1.40
586 608 2.815211 GCACCGATGAAGCGCAGA 60.815 61.111 11.47 0.00 0.00 4.26
596 618 4.842911 CGATGAAGCGCAGATAAATAAAGC 59.157 41.667 11.47 0.00 0.00 3.51
628 650 3.185797 CGACGGGTTCTTTACAAAAGGAG 59.814 47.826 0.00 0.00 0.00 3.69
669 691 1.338579 TGGTATGCTGCAATCGTCACA 60.339 47.619 6.36 0.00 0.00 3.58
693 716 4.385310 CCTTTACACCCCCATCCTAAAGAG 60.385 50.000 0.00 0.00 29.46 2.85
695 718 2.482494 ACACCCCCATCCTAAAGAGAG 58.518 52.381 0.00 0.00 0.00 3.20
727 751 7.392393 TCTTTTATCGGGAAACTAAAAAGGGAG 59.608 37.037 0.00 0.00 35.60 4.30
730 754 1.816835 GGGAAACTAAAAAGGGAGCCG 59.183 52.381 0.00 0.00 0.00 5.52
756 780 1.419374 CCACGTTCTCTCCTTCAACG 58.581 55.000 2.07 2.07 46.57 4.10
799 843 3.115390 AGCCTAAACCATCTCTAGCCAA 58.885 45.455 0.00 0.00 0.00 4.52
809 853 5.103940 ACCATCTCTAGCCAACCATTTACAT 60.104 40.000 0.00 0.00 0.00 2.29
812 856 5.918608 TCTCTAGCCAACCATTTACATCTC 58.081 41.667 0.00 0.00 0.00 2.75
813 857 5.036117 TCTAGCCAACCATTTACATCTCC 57.964 43.478 0.00 0.00 0.00 3.71
816 860 2.354821 GCCAACCATTTACATCTCCGAC 59.645 50.000 0.00 0.00 0.00 4.79
831 875 5.984233 TCTCCGACGATCCATTTTAATTG 57.016 39.130 0.00 0.00 0.00 2.32
833 877 4.519213 TCCGACGATCCATTTTAATTGGT 58.481 39.130 0.00 0.00 0.00 3.67
834 878 4.944930 TCCGACGATCCATTTTAATTGGTT 59.055 37.500 0.00 0.00 0.00 3.67
835 879 5.065474 TCCGACGATCCATTTTAATTGGTTC 59.935 40.000 0.00 6.39 0.00 3.62
836 880 5.065988 CCGACGATCCATTTTAATTGGTTCT 59.934 40.000 12.32 3.63 0.00 3.01
841 885 8.987890 ACGATCCATTTTAATTGGTTCTTTTTG 58.012 29.630 12.32 3.18 0.00 2.44
861 905 4.255833 TGTTGTTGAGGCAAATCCATTC 57.744 40.909 0.00 0.00 37.29 2.67
865 909 3.760151 TGTTGAGGCAAATCCATTCTGAG 59.240 43.478 0.00 0.00 37.29 3.35
874 918 7.669722 AGGCAAATCCATTCTGAGTAGTAAAAA 59.330 33.333 0.00 0.00 37.29 1.94
875 919 7.970614 GGCAAATCCATTCTGAGTAGTAAAAAG 59.029 37.037 0.00 0.00 34.01 2.27
876 920 8.730680 GCAAATCCATTCTGAGTAGTAAAAAGA 58.269 33.333 0.00 0.00 0.00 2.52
881 925 9.712305 TCCATTCTGAGTAGTAAAAAGAGAAAG 57.288 33.333 0.00 0.00 0.00 2.62
923 975 2.189521 GGCCACCCACCATAGACG 59.810 66.667 0.00 0.00 0.00 4.18
924 976 2.363975 GGCCACCCACCATAGACGA 61.364 63.158 0.00 0.00 0.00 4.20
925 977 1.153429 GCCACCCACCATAGACGAC 60.153 63.158 0.00 0.00 0.00 4.34
926 978 1.141019 CCACCCACCATAGACGACG 59.859 63.158 0.00 0.00 0.00 5.12
1008 1093 2.961526 TCGCTCCTTTCGCTAAATCT 57.038 45.000 0.00 0.00 0.00 2.40
1009 1094 4.360563 CTTCGCTCCTTTCGCTAAATCTA 58.639 43.478 0.00 0.00 0.00 1.98
1010 1095 4.380841 TCGCTCCTTTCGCTAAATCTAA 57.619 40.909 0.00 0.00 0.00 2.10
1011 1096 4.751060 TCGCTCCTTTCGCTAAATCTAAA 58.249 39.130 0.00 0.00 0.00 1.85
1012 1097 4.804139 TCGCTCCTTTCGCTAAATCTAAAG 59.196 41.667 0.00 0.00 0.00 1.85
1040 1125 0.107848 ACCCCGAGCTAAATCCAACG 60.108 55.000 0.00 0.00 0.00 4.10
1051 1136 7.254319 CGAGCTAAATCCAACGCTAGAATTAAA 60.254 37.037 0.00 0.00 31.96 1.52
1055 1140 4.914312 TCCAACGCTAGAATTAAACACG 57.086 40.909 0.00 0.00 0.00 4.49
1065 1193 1.632046 ATTAAACACGCTCGCCACGG 61.632 55.000 0.00 0.00 34.00 4.94
1153 1300 1.490574 CTCCGATCCAAACCCTCTCT 58.509 55.000 0.00 0.00 0.00 3.10
1166 1313 1.588403 CTCTCTCACCTCGCATGCG 60.588 63.158 33.61 33.61 41.35 4.73
1399 1546 4.779733 GGCGGGGACTCCTCCTCA 62.780 72.222 0.00 0.00 36.73 3.86
1402 1549 2.781406 GGGGACTCCTCCTCAGGT 59.219 66.667 0.00 0.00 41.28 4.00
1403 1550 1.687493 GGGGACTCCTCCTCAGGTG 60.687 68.421 0.00 0.00 41.28 4.00
1404 1551 2.363172 GGGACTCCTCCTCAGGTGC 61.363 68.421 0.00 0.00 41.28 5.01
1643 1790 0.371645 CGCCTCACTTCGCTTCATTC 59.628 55.000 0.00 0.00 0.00 2.67
1663 1819 2.163815 TCTTACTTCTTCGAAGCCGGAG 59.836 50.000 20.56 15.85 42.73 4.63
1740 1896 1.005215 AGGTGCGTACTGGGTAGTAGT 59.995 52.381 3.01 0.00 39.96 2.73
1745 1901 4.509600 GTGCGTACTGGGTAGTAGTAGTAG 59.490 50.000 0.00 0.00 39.96 2.57
1746 1902 4.061596 GCGTACTGGGTAGTAGTAGTAGG 58.938 52.174 0.00 0.00 39.96 3.18
1747 1903 4.202264 GCGTACTGGGTAGTAGTAGTAGGA 60.202 50.000 0.00 0.00 39.96 2.94
1748 1904 5.537188 CGTACTGGGTAGTAGTAGTAGGAG 58.463 50.000 0.00 0.00 39.96 3.69
1749 1905 5.069781 CGTACTGGGTAGTAGTAGTAGGAGT 59.930 48.000 0.00 0.00 39.96 3.85
1763 1919 7.575505 AGTAGTAGGAGTATATGGATATGCGT 58.424 38.462 0.00 0.00 31.71 5.24
1808 1964 5.680619 AGATTCCGTGTGCCTATTTATGAA 58.319 37.500 0.00 0.00 0.00 2.57
1888 2045 7.873505 GGCGAAAGATCATCTTATTTAGGTAGT 59.126 37.037 0.00 0.00 35.27 2.73
1889 2046 9.909644 GCGAAAGATCATCTTATTTAGGTAGTA 57.090 33.333 0.00 0.00 35.27 1.82
1915 2072 1.206610 TCACTGCTGCAGATCCTCTTC 59.793 52.381 34.28 0.00 35.18 2.87
1916 2073 0.540923 ACTGCTGCAGATCCTCTTCC 59.459 55.000 34.28 0.00 35.18 3.46
1917 2074 0.831966 CTGCTGCAGATCCTCTTCCT 59.168 55.000 24.88 0.00 32.44 3.36
1925 2082 4.128643 GCAGATCCTCTTCCTCTCAAATG 58.871 47.826 0.00 0.00 0.00 2.32
1960 2117 7.684428 GCACACAAGATAAGGAAAAAGAACCTT 60.684 37.037 0.00 0.00 46.45 3.50
1964 2121 8.197439 ACAAGATAAGGAAAAAGAACCTTGTTG 58.803 33.333 0.00 0.13 44.77 3.33
1999 2156 5.122519 TGCGGATGAAATTCAGCTGTATTA 58.877 37.500 19.51 5.16 40.99 0.98
2074 2242 7.833682 TCTGTCCAGCCATGAAAATTATCTTTA 59.166 33.333 0.00 0.00 0.00 1.85
2178 2348 6.653740 CCATTAGTTTAGAAAACCTCGACCTT 59.346 38.462 0.00 0.00 0.00 3.50
2289 2462 4.439253 AATATAGTTCCAGTTCCAGGCC 57.561 45.455 0.00 0.00 0.00 5.19
2305 2478 4.081087 TCCAGGCCATCTCTTGTTAGTTAC 60.081 45.833 5.01 0.00 0.00 2.50
2435 2609 6.593382 AGAAACTTTTCGAATGATGAGGAGAG 59.407 38.462 0.00 0.00 41.92 3.20
2509 2683 8.006564 ACCAATGTACCTGATGATTGGAATTAT 58.993 33.333 21.13 2.40 45.26 1.28
2529 2703 1.065199 TGCAGACATGGATCCCAAGAC 60.065 52.381 9.90 0.00 36.95 3.01
2555 2729 2.595095 CCACACCACCCACACACT 59.405 61.111 0.00 0.00 0.00 3.55
2569 2743 3.436704 CCACACACTCGCTTGATTTATGT 59.563 43.478 0.00 0.00 0.00 2.29
2699 3191 4.398044 AGGGAAGGTATATTTGTGTTTGCG 59.602 41.667 0.00 0.00 0.00 4.85
2947 3439 1.609208 ATTTGCGAGCTGTGGTTCTT 58.391 45.000 0.00 0.00 0.00 2.52
3022 3514 7.880713 ACTTTTTGGTTTGACATTTACAAGGTT 59.119 29.630 0.00 0.00 0.00 3.50
3032 3524 9.834628 TTGACATTTACAAGGTTAATTCGATTC 57.165 29.630 0.00 0.00 0.00 2.52
3033 3525 8.455682 TGACATTTACAAGGTTAATTCGATTCC 58.544 33.333 0.00 0.00 0.00 3.01
3063 3555 1.133809 CCCCTCCCCAGAGTTGTTGA 61.134 60.000 0.00 0.00 38.58 3.18
3080 3572 8.523915 AGTTGTTGATGATAAATGGCTGATAA 57.476 30.769 0.00 0.00 0.00 1.75
3112 3604 6.072728 CCTCCATTTTGTAGAATGTCGACAAA 60.073 38.462 24.13 9.96 45.55 2.83
3119 3611 4.391830 TGTAGAATGTCGACAAAATCAGCC 59.608 41.667 24.13 12.37 29.16 4.85
3124 3616 1.197721 GTCGACAAAATCAGCCTGGTG 59.802 52.381 11.55 0.00 0.00 4.17
3242 3772 4.759183 GGGATAATGGATTGAGAAGCTGAC 59.241 45.833 0.00 0.00 0.00 3.51
3259 3790 8.622157 AGAAGCTGACAATAGATGATTCATTTG 58.378 33.333 0.00 4.53 0.00 2.32
3291 3822 7.362574 GCTCACCAAGCCAAGTATGTAAAAATA 60.363 37.037 0.00 0.00 45.92 1.40
3326 3857 8.113173 TGAATCAAATGAACAATCAGATGTCA 57.887 30.769 0.00 0.00 39.39 3.58
3344 3875 3.153919 GTCAAAGTTGCTGGGGTGATAA 58.846 45.455 0.00 0.00 0.00 1.75
3345 3876 3.763897 GTCAAAGTTGCTGGGGTGATAAT 59.236 43.478 0.00 0.00 0.00 1.28
3346 3877 4.016444 TCAAAGTTGCTGGGGTGATAATC 58.984 43.478 0.00 0.00 0.00 1.75
3349 3884 5.450818 AAGTTGCTGGGGTGATAATCTAA 57.549 39.130 0.00 0.00 0.00 2.10
3353 3888 3.780294 TGCTGGGGTGATAATCTAACACT 59.220 43.478 0.00 0.00 35.28 3.55
3355 3890 5.070446 TGCTGGGGTGATAATCTAACACTAG 59.930 44.000 0.00 0.00 35.28 2.57
3361 3896 7.927092 GGGGTGATAATCTAACACTAGAGTTTC 59.073 40.741 10.91 2.55 37.58 2.78
3389 3924 3.197265 ACAATTTTGGTGCTTCAGTTGC 58.803 40.909 0.00 0.00 0.00 4.17
3390 3925 2.531522 ATTTTGGTGCTTCAGTTGCC 57.468 45.000 0.00 0.00 0.00 4.52
3391 3926 1.189752 TTTTGGTGCTTCAGTTGCCA 58.810 45.000 0.00 0.00 0.00 4.92
3392 3927 1.412079 TTTGGTGCTTCAGTTGCCAT 58.588 45.000 0.00 0.00 0.00 4.40
3393 3928 2.284754 TTGGTGCTTCAGTTGCCATA 57.715 45.000 0.00 0.00 0.00 2.74
3394 3929 2.284754 TGGTGCTTCAGTTGCCATAA 57.715 45.000 0.00 0.00 0.00 1.90
3395 3930 2.161855 TGGTGCTTCAGTTGCCATAAG 58.838 47.619 0.00 0.00 0.00 1.73
3396 3931 1.135286 GGTGCTTCAGTTGCCATAAGC 60.135 52.381 0.00 0.00 43.62 3.09
3397 3932 1.135286 GTGCTTCAGTTGCCATAAGCC 60.135 52.381 0.00 0.00 42.87 4.35
3444 3979 1.524002 CCAGGGCACGTCAGATGAT 59.476 57.895 0.00 0.00 0.00 2.45
3501 4036 2.472488 GCTTTGCAAGGTGAAACATTCG 59.528 45.455 10.54 0.00 39.78 3.34
3906 4441 3.375299 GGGATCAAGCAACTGTGTCATAC 59.625 47.826 0.00 0.00 0.00 2.39
3983 4520 7.040478 TGTGTTAAATGTGGGAGAAGAAGAATG 60.040 37.037 0.00 0.00 0.00 2.67
4079 4617 0.251608 GTATTGCAACCCCCAGTGGT 60.252 55.000 8.74 0.00 41.55 4.16
4153 4691 5.501156 GAGGGACAAGGATAGAACATTTGT 58.499 41.667 0.00 0.00 34.91 2.83
4164 4702 1.866601 GAACATTTGTGGCCACTTTGC 59.133 47.619 34.75 10.58 0.00 3.68
4253 4791 5.531634 AGTGTTCATATGTTTTGTGGCTTG 58.468 37.500 1.90 0.00 0.00 4.01
4293 4832 1.532437 TGCGTCTTTCTGCACTTCATG 59.468 47.619 0.00 0.00 35.90 3.07
4352 4891 1.216064 TGGGGCTGCAGAATAGACAT 58.784 50.000 20.43 0.00 0.00 3.06
4359 4898 5.118990 GGCTGCAGAATAGACATAACTCAA 58.881 41.667 20.43 0.00 0.00 3.02
4367 4906 8.420222 CAGAATAGACATAACTCAAGATCAGGT 58.580 37.037 0.00 0.00 0.00 4.00
4371 4910 7.192852 AGACATAACTCAAGATCAGGTGAAT 57.807 36.000 0.00 0.00 0.00 2.57
4372 4911 7.271511 AGACATAACTCAAGATCAGGTGAATC 58.728 38.462 0.00 0.00 0.00 2.52
4374 4913 3.922171 ACTCAAGATCAGGTGAATCCC 57.078 47.619 0.00 0.00 36.75 3.85
4376 4915 3.588842 ACTCAAGATCAGGTGAATCCCAA 59.411 43.478 0.00 0.00 36.75 4.12
4434 4973 0.107456 AGTTCAGCACACCACTCCAG 59.893 55.000 0.00 0.00 0.00 3.86
4435 4974 1.227943 TTCAGCACACCACTCCAGC 60.228 57.895 0.00 0.00 0.00 4.85
4443 4982 0.455633 CACCACTCCAGCGTACGTAC 60.456 60.000 17.90 15.90 0.00 3.67
4469 5008 7.168972 CGTAGTATGTACAGTACTGTCTCTACC 59.831 44.444 31.11 15.66 43.74 3.18
4516 5055 2.806945 TTTACATCAGCTGGAAGGGG 57.193 50.000 15.13 0.00 0.00 4.79
4517 5056 0.918983 TTACATCAGCTGGAAGGGGG 59.081 55.000 15.13 0.00 0.00 5.40
4567 5109 2.163010 CACGGCAAGCAAATCTCTCAAT 59.837 45.455 0.00 0.00 0.00 2.57
4574 5116 6.484643 GGCAAGCAAATCTCTCAATAGTGATA 59.515 38.462 0.00 0.00 35.42 2.15
4610 5152 0.727398 GGCCGCAAACACTGATCTAC 59.273 55.000 0.00 0.00 0.00 2.59
4611 5153 1.676014 GGCCGCAAACACTGATCTACT 60.676 52.381 0.00 0.00 0.00 2.57
4612 5154 2.418197 GGCCGCAAACACTGATCTACTA 60.418 50.000 0.00 0.00 0.00 1.82
4643 5189 2.064242 GCTGGTGTTAGGGGTGGTGT 62.064 60.000 0.00 0.00 0.00 4.16
4738 5284 1.230635 CGTCTTTGTGACCCAGGCAG 61.231 60.000 0.00 0.00 42.49 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.529060 CAGGGTTTATATCAAGCCAACTCTC 59.471 44.000 17.79 0.00 45.37 3.20
1 2 5.191722 TCAGGGTTTATATCAAGCCAACTCT 59.808 40.000 17.79 0.00 45.37 3.24
2 3 5.437060 TCAGGGTTTATATCAAGCCAACTC 58.563 41.667 17.79 0.00 45.37 3.01
7 8 6.122964 AGAAACTCAGGGTTTATATCAAGCC 58.877 40.000 9.43 9.43 46.77 4.35
8 9 7.631717 AAGAAACTCAGGGTTTATATCAAGC 57.368 36.000 0.00 0.00 46.77 4.01
13 14 9.901172 ACGAAATAAGAAACTCAGGGTTTATAT 57.099 29.630 0.00 0.00 46.77 0.86
14 15 9.158233 CACGAAATAAGAAACTCAGGGTTTATA 57.842 33.333 0.00 0.00 46.77 0.98
15 16 7.361799 GCACGAAATAAGAAACTCAGGGTTTAT 60.362 37.037 0.00 0.00 46.77 1.40
16 17 6.072893 GCACGAAATAAGAAACTCAGGGTTTA 60.073 38.462 0.00 0.00 46.77 2.01
18 19 4.215613 GCACGAAATAAGAAACTCAGGGTT 59.784 41.667 0.00 0.00 40.28 4.11
19 20 3.751698 GCACGAAATAAGAAACTCAGGGT 59.248 43.478 0.00 0.00 0.00 4.34
20 21 3.127030 GGCACGAAATAAGAAACTCAGGG 59.873 47.826 0.00 0.00 0.00 4.45
21 22 3.127030 GGGCACGAAATAAGAAACTCAGG 59.873 47.826 0.00 0.00 0.00 3.86
22 23 3.751175 TGGGCACGAAATAAGAAACTCAG 59.249 43.478 0.00 0.00 0.00 3.35
23 24 3.500680 GTGGGCACGAAATAAGAAACTCA 59.499 43.478 0.00 0.00 0.00 3.41
24 25 4.079665 GTGGGCACGAAATAAGAAACTC 57.920 45.455 0.00 0.00 0.00 3.01
41 42 3.697747 TTACAGTCCGCCCGTGGG 61.698 66.667 0.00 0.00 38.57 4.61
42 43 2.433664 GTTACAGTCCGCCCGTGG 60.434 66.667 0.00 0.00 0.00 4.94
43 44 2.025418 GTGTTACAGTCCGCCCGTG 61.025 63.158 0.00 0.00 0.00 4.94
44 45 2.030490 TTGTGTTACAGTCCGCCCGT 62.030 55.000 0.00 0.00 0.00 5.28
45 46 0.881159 TTTGTGTTACAGTCCGCCCG 60.881 55.000 0.00 0.00 0.00 6.13
46 47 0.872388 CTTTGTGTTACAGTCCGCCC 59.128 55.000 0.00 0.00 0.00 6.13
47 48 0.872388 CCTTTGTGTTACAGTCCGCC 59.128 55.000 0.00 0.00 0.00 6.13
48 49 1.798813 CTCCTTTGTGTTACAGTCCGC 59.201 52.381 0.00 0.00 0.00 5.54
49 50 1.798813 GCTCCTTTGTGTTACAGTCCG 59.201 52.381 0.00 0.00 0.00 4.79
50 51 3.067833 GAGCTCCTTTGTGTTACAGTCC 58.932 50.000 0.87 0.00 0.00 3.85
51 52 3.067833 GGAGCTCCTTTGTGTTACAGTC 58.932 50.000 26.25 0.00 0.00 3.51
52 53 2.438021 TGGAGCTCCTTTGTGTTACAGT 59.562 45.455 32.28 0.00 36.82 3.55
53 54 2.808543 GTGGAGCTCCTTTGTGTTACAG 59.191 50.000 32.28 0.00 36.82 2.74
54 55 2.438021 AGTGGAGCTCCTTTGTGTTACA 59.562 45.455 32.28 6.14 36.82 2.41
55 56 3.127425 AGTGGAGCTCCTTTGTGTTAC 57.873 47.619 32.28 19.32 36.82 2.50
56 57 5.720041 ACTATAGTGGAGCTCCTTTGTGTTA 59.280 40.000 32.28 14.18 36.82 2.41
57 58 4.532521 ACTATAGTGGAGCTCCTTTGTGTT 59.467 41.667 32.28 13.48 36.82 3.32
58 59 4.097418 ACTATAGTGGAGCTCCTTTGTGT 58.903 43.478 32.28 19.93 36.82 3.72
59 60 4.744795 ACTATAGTGGAGCTCCTTTGTG 57.255 45.455 32.28 19.34 36.82 3.33
60 61 5.269991 TGTACTATAGTGGAGCTCCTTTGT 58.730 41.667 32.28 21.86 36.82 2.83
61 62 5.854010 TGTACTATAGTGGAGCTCCTTTG 57.146 43.478 32.28 17.89 36.82 2.77
62 63 6.869206 TTTGTACTATAGTGGAGCTCCTTT 57.131 37.500 32.28 21.92 36.82 3.11
63 64 6.869206 TTTTGTACTATAGTGGAGCTCCTT 57.131 37.500 32.28 22.26 36.82 3.36
64 65 8.728596 ATATTTTGTACTATAGTGGAGCTCCT 57.271 34.615 32.28 16.77 36.82 3.69
78 79 9.720769 ACTACAAGTGCACTAATATTTTGTACT 57.279 29.630 22.01 9.00 37.75 2.73
87 88 8.865978 CGTCAAAATACTACAAGTGCACTAATA 58.134 33.333 22.01 14.26 0.00 0.98
88 89 7.148474 CCGTCAAAATACTACAAGTGCACTAAT 60.148 37.037 22.01 13.84 0.00 1.73
89 90 6.146510 CCGTCAAAATACTACAAGTGCACTAA 59.853 38.462 22.01 8.05 0.00 2.24
90 91 5.636121 CCGTCAAAATACTACAAGTGCACTA 59.364 40.000 22.01 2.96 0.00 2.74
91 92 4.451096 CCGTCAAAATACTACAAGTGCACT 59.549 41.667 15.25 15.25 0.00 4.40
92 93 4.378046 CCCGTCAAAATACTACAAGTGCAC 60.378 45.833 9.40 9.40 0.00 4.57
93 94 3.749088 CCCGTCAAAATACTACAAGTGCA 59.251 43.478 0.00 0.00 0.00 4.57
94 95 3.998341 TCCCGTCAAAATACTACAAGTGC 59.002 43.478 0.00 0.00 0.00 4.40
95 96 5.475719 TCTCCCGTCAAAATACTACAAGTG 58.524 41.667 0.00 0.00 0.00 3.16
96 97 5.733620 TCTCCCGTCAAAATACTACAAGT 57.266 39.130 0.00 0.00 0.00 3.16
97 98 6.019801 CGATTCTCCCGTCAAAATACTACAAG 60.020 42.308 0.00 0.00 0.00 3.16
98 99 5.808540 CGATTCTCCCGTCAAAATACTACAA 59.191 40.000 0.00 0.00 0.00 2.41
99 100 5.345702 CGATTCTCCCGTCAAAATACTACA 58.654 41.667 0.00 0.00 0.00 2.74
100 101 4.208666 GCGATTCTCCCGTCAAAATACTAC 59.791 45.833 0.00 0.00 0.00 2.73
101 102 4.365723 GCGATTCTCCCGTCAAAATACTA 58.634 43.478 0.00 0.00 0.00 1.82
102 103 3.195661 GCGATTCTCCCGTCAAAATACT 58.804 45.455 0.00 0.00 0.00 2.12
103 104 2.034001 CGCGATTCTCCCGTCAAAATAC 60.034 50.000 0.00 0.00 0.00 1.89
104 105 2.198406 CGCGATTCTCCCGTCAAAATA 58.802 47.619 0.00 0.00 0.00 1.40
105 106 1.006832 CGCGATTCTCCCGTCAAAAT 58.993 50.000 0.00 0.00 0.00 1.82
111 112 3.465296 CTACGCGCGATTCTCCCGT 62.465 63.158 39.36 13.47 36.07 5.28
144 145 1.200948 GCTTGCTGGGAAGAATCACAC 59.799 52.381 6.05 0.00 32.81 3.82
145 146 1.074405 AGCTTGCTGGGAAGAATCACA 59.926 47.619 6.05 0.00 36.35 3.58
228 234 3.259902 CAGGAGATGTGGCATCATATCG 58.740 50.000 11.12 3.55 43.49 2.92
311 317 3.918328 AATCGGTGGACGGGGGTCT 62.918 63.158 0.00 0.00 44.45 3.85
312 318 3.396570 AATCGGTGGACGGGGGTC 61.397 66.667 0.00 0.00 44.45 4.46
313 319 3.712907 CAATCGGTGGACGGGGGT 61.713 66.667 0.00 0.00 44.45 4.95
341 348 1.004918 CGGTTGGATAGGGATCGGC 60.005 63.158 0.00 0.00 32.28 5.54
428 440 2.534019 CCAGGCACACACACACGTC 61.534 63.158 0.00 0.00 0.00 4.34
429 441 2.513666 CCAGGCACACACACACGT 60.514 61.111 0.00 0.00 0.00 4.49
479 496 7.260603 AGTAAACCTACACACATATACGGAAC 58.739 38.462 0.00 0.00 0.00 3.62
480 497 7.408756 AGTAAACCTACACACATATACGGAA 57.591 36.000 0.00 0.00 0.00 4.30
481 498 7.408756 AAGTAAACCTACACACATATACGGA 57.591 36.000 0.00 0.00 0.00 4.69
482 499 8.385111 CAAAAGTAAACCTACACACATATACGG 58.615 37.037 0.00 0.00 0.00 4.02
483 500 7.901377 GCAAAAGTAAACCTACACACATATACG 59.099 37.037 0.00 0.00 0.00 3.06
491 508 4.783055 TCCAGCAAAAGTAAACCTACACA 58.217 39.130 0.00 0.00 0.00 3.72
511 533 5.294552 CCTACACTTTAATTAGCACAGCTCC 59.705 44.000 0.00 0.00 40.44 4.70
596 618 3.230522 AACCCGTCGGTCTTTCCCG 62.231 63.158 11.06 0.00 43.71 5.14
620 642 2.821969 ACAAGCTGTATGGCTCCTTTTG 59.178 45.455 0.00 0.00 42.24 2.44
628 650 3.310774 CAGTACATGACAAGCTGTATGGC 59.689 47.826 0.00 0.00 31.06 4.40
669 691 2.672703 TAGGATGGGGGTGTAAAGGT 57.327 50.000 0.00 0.00 0.00 3.50
693 716 5.183331 AGTTTCCCGATAAAAGAAAAGGCTC 59.817 40.000 0.00 0.00 31.71 4.70
695 718 5.386958 AGTTTCCCGATAAAAGAAAAGGC 57.613 39.130 0.00 0.00 31.71 4.35
730 754 1.153997 GAGAGAACGTGGCGAGGTC 60.154 63.158 0.00 0.00 0.00 3.85
756 780 3.281158 AGGCGAAGAGAACTAGGAGTAC 58.719 50.000 0.00 0.00 0.00 2.73
799 843 3.243771 GGATCGTCGGAGATGTAAATGGT 60.244 47.826 0.00 0.00 45.22 3.55
809 853 4.814234 CCAATTAAAATGGATCGTCGGAGA 59.186 41.667 4.98 0.00 40.56 3.71
812 856 4.893424 ACCAATTAAAATGGATCGTCGG 57.107 40.909 15.47 0.00 40.56 4.79
813 857 6.119144 AGAACCAATTAAAATGGATCGTCG 57.881 37.500 15.47 0.00 42.68 5.12
816 860 8.987890 ACAAAAAGAACCAATTAAAATGGATCG 58.012 29.630 15.47 5.07 42.68 3.69
831 875 3.855858 TGCCTCAACAACAAAAAGAACC 58.144 40.909 0.00 0.00 0.00 3.62
833 877 5.584251 GGATTTGCCTCAACAACAAAAAGAA 59.416 36.000 0.00 0.00 36.90 2.52
834 878 5.115480 GGATTTGCCTCAACAACAAAAAGA 58.885 37.500 0.00 0.00 36.90 2.52
835 879 4.874966 TGGATTTGCCTCAACAACAAAAAG 59.125 37.500 0.00 0.00 36.90 2.27
836 880 4.836825 TGGATTTGCCTCAACAACAAAAA 58.163 34.783 0.00 0.00 36.90 1.94
841 885 4.022068 TCAGAATGGATTTGCCTCAACAAC 60.022 41.667 0.00 0.00 37.63 3.32
861 905 8.940952 CCCATTCTTTCTCTTTTTACTACTCAG 58.059 37.037 0.00 0.00 0.00 3.35
865 909 9.503399 TTCTCCCATTCTTTCTCTTTTTACTAC 57.497 33.333 0.00 0.00 0.00 2.73
874 918 9.183368 GTGAAATATTTCTCCCATTCTTTCTCT 57.817 33.333 24.77 0.00 38.02 3.10
875 919 9.183368 AGTGAAATATTTCTCCCATTCTTTCTC 57.817 33.333 24.77 1.30 38.02 2.87
880 924 9.401058 CAACTAGTGAAATATTTCTCCCATTCT 57.599 33.333 24.77 14.51 38.02 2.40
881 925 8.624776 CCAACTAGTGAAATATTTCTCCCATTC 58.375 37.037 24.77 9.60 38.02 2.67
883 927 6.547510 GCCAACTAGTGAAATATTTCTCCCAT 59.452 38.462 24.77 11.22 38.02 4.00
884 928 5.885912 GCCAACTAGTGAAATATTTCTCCCA 59.114 40.000 24.77 13.30 38.02 4.37
894 938 1.427368 TGGGTGGCCAACTAGTGAAAT 59.573 47.619 22.79 0.00 0.00 2.17
1008 1093 3.328637 AGCTCGGGGTTTCCTTTACTTTA 59.671 43.478 0.00 0.00 0.00 1.85
1009 1094 2.107726 AGCTCGGGGTTTCCTTTACTTT 59.892 45.455 0.00 0.00 0.00 2.66
1010 1095 1.703513 AGCTCGGGGTTTCCTTTACTT 59.296 47.619 0.00 0.00 0.00 2.24
1011 1096 1.359168 AGCTCGGGGTTTCCTTTACT 58.641 50.000 0.00 0.00 0.00 2.24
1012 1097 3.339253 TTAGCTCGGGGTTTCCTTTAC 57.661 47.619 0.00 0.00 0.00 2.01
1040 1125 2.285660 GGCGAGCGTGTTTAATTCTAGC 60.286 50.000 0.00 0.00 0.00 3.42
1051 1136 4.595538 TTTCCGTGGCGAGCGTGT 62.596 61.111 0.00 0.00 0.00 4.49
1055 1140 2.442188 CGTACTTTCCGTGGCGAGC 61.442 63.158 0.00 0.00 0.00 5.03
1411 1558 4.067512 TCCTCCTCCTCGGCTGCT 62.068 66.667 0.00 0.00 0.00 4.24
1643 1790 2.094649 ACTCCGGCTTCGAAGAAGTAAG 60.095 50.000 28.95 18.38 45.90 2.34
1740 1896 7.832685 ACAACGCATATCCATATACTCCTACTA 59.167 37.037 0.00 0.00 0.00 1.82
1745 1901 4.330074 GCACAACGCATATCCATATACTCC 59.670 45.833 0.00 0.00 41.79 3.85
1746 1902 5.456192 GCACAACGCATATCCATATACTC 57.544 43.478 0.00 0.00 41.79 2.59
1761 1917 8.547894 TCTAATACTGCTAATAAATGCACAACG 58.452 33.333 0.00 0.00 35.20 4.10
1778 1934 4.060038 AGGCACACGGAATCTAATACTG 57.940 45.455 0.00 0.00 0.00 2.74
1854 2010 8.682936 ATAAGATGATCTTTCGCCAATTTACT 57.317 30.769 13.54 0.00 37.89 2.24
1862 2019 7.873505 ACTACCTAAATAAGATGATCTTTCGCC 59.126 37.037 13.54 0.00 37.89 5.54
1888 2045 1.047801 TCTGCAGCAGTGAAGTGGTA 58.952 50.000 22.10 0.00 30.06 3.25
1889 2046 0.399454 ATCTGCAGCAGTGAAGTGGT 59.601 50.000 22.10 0.00 30.06 4.16
1890 2047 1.085091 GATCTGCAGCAGTGAAGTGG 58.915 55.000 22.10 0.00 30.06 4.00
1891 2048 1.085091 GGATCTGCAGCAGTGAAGTG 58.915 55.000 22.10 0.00 30.06 3.16
1915 2072 5.176223 GTGTGCAATTCAAACATTTGAGAGG 59.824 40.000 7.10 2.98 46.68 3.69
1916 2073 5.749588 TGTGTGCAATTCAAACATTTGAGAG 59.250 36.000 7.10 3.60 46.68 3.20
1917 2074 5.658468 TGTGTGCAATTCAAACATTTGAGA 58.342 33.333 7.10 0.73 46.68 3.27
1925 2082 6.446318 TCCTTATCTTGTGTGCAATTCAAAC 58.554 36.000 0.00 0.00 33.65 2.93
2044 2212 5.841957 ATTTTCATGGCTGGACAGATTAC 57.158 39.130 3.00 0.00 0.00 1.89
2074 2242 1.094785 GCCGTGTTGGACAGCAATAT 58.905 50.000 0.00 0.00 42.00 1.28
2289 2462 9.017669 GTATAACGGTGTAACTAACAAGAGATG 57.982 37.037 0.00 0.00 40.63 2.90
2435 2609 3.537580 TGCCTCGAAATACAACATACCC 58.462 45.455 0.00 0.00 0.00 3.69
2491 2665 5.533903 GTCTGCATAATTCCAATCATCAGGT 59.466 40.000 0.00 0.00 0.00 4.00
2494 2668 6.015772 CCATGTCTGCATAATTCCAATCATCA 60.016 38.462 0.00 0.00 33.30 3.07
2509 2683 1.065199 GTCTTGGGATCCATGTCTGCA 60.065 52.381 15.23 0.00 31.53 4.41
2555 2729 8.094798 ACTAACTTTGAACATAAATCAAGCGA 57.905 30.769 0.00 0.00 38.01 4.93
2569 2743 9.856162 ATTCTTTTGTAGGGTACTAACTTTGAA 57.144 29.630 0.00 0.00 0.00 2.69
2633 3125 5.333339 GCATAATCATACCTGCAACACGTAG 60.333 44.000 0.00 0.00 34.77 3.51
2699 3191 8.450964 TGCTATGTAAGTTAAAGATGAAACAGC 58.549 33.333 0.00 0.00 0.00 4.40
3044 3536 1.133809 TCAACAACTCTGGGGAGGGG 61.134 60.000 0.00 0.00 43.46 4.79
3080 3572 9.710900 GACATTCTACAAAATGGAGGAAAATTT 57.289 29.630 2.11 0.00 40.28 1.82
3112 3604 2.225091 TGGACAATTCACCAGGCTGATT 60.225 45.455 17.94 4.58 0.00 2.57
3124 3616 6.317789 TGAATGACAAGAACTGGACAATTC 57.682 37.500 0.00 0.00 0.00 2.17
3326 3857 4.322057 AGATTATCACCCCAGCAACTTT 57.678 40.909 0.00 0.00 0.00 2.66
3355 3890 8.135529 AGCACCAAAATTGTAAAGTAGAAACTC 58.864 33.333 0.00 0.00 33.75 3.01
3361 3896 7.425606 ACTGAAGCACCAAAATTGTAAAGTAG 58.574 34.615 0.00 0.00 0.00 2.57
3365 3900 5.293079 GCAACTGAAGCACCAAAATTGTAAA 59.707 36.000 0.00 0.00 0.00 2.01
3367 3902 4.367450 GCAACTGAAGCACCAAAATTGTA 58.633 39.130 0.00 0.00 0.00 2.41
3369 3904 2.545106 GGCAACTGAAGCACCAAAATTG 59.455 45.455 0.00 0.00 0.00 2.32
3389 3924 5.913137 TTGTTTCAGTTATGGGCTTATGG 57.087 39.130 0.00 0.00 0.00 2.74
3441 3976 3.235750 TGGGACCAATCAACAACATCA 57.764 42.857 0.00 0.00 0.00 3.07
3444 3979 2.158400 TCCATGGGACCAATCAACAACA 60.158 45.455 13.02 0.00 0.00 3.33
3603 4138 5.820947 TGGTAACTCTTTCAAGTCAGGTTTC 59.179 40.000 0.00 0.00 37.61 2.78
3750 4285 1.546029 GGCTTTTCAGGAACATCCACC 59.454 52.381 0.00 0.00 39.61 4.61
3886 4421 4.692625 ACAGTATGACACAGTTGCTTGATC 59.307 41.667 0.00 0.00 39.69 2.92
3983 4520 1.134670 AGCTTATTCACCAGCGTCCTC 60.135 52.381 0.00 0.00 41.24 3.71
4079 4617 7.339212 CACTTTTACATGATGGAAATCCTACCA 59.661 37.037 3.26 0.00 40.57 3.25
4164 4702 0.716108 CAAGACTTTAGACTGCGCCG 59.284 55.000 4.18 0.00 0.00 6.46
4170 4708 5.221722 TGTGATTGCTCCAAGACTTTAGACT 60.222 40.000 0.00 0.00 0.00 3.24
4293 4832 7.365741 AGTAACATACAGTACAGTGTACACAC 58.634 38.462 30.09 16.54 46.77 3.82
4352 4891 4.782691 TGGGATTCACCTGATCTTGAGTTA 59.217 41.667 0.00 0.00 38.98 2.24
4359 4898 3.270433 ACCATTTGGGATTCACCTGATCT 59.730 43.478 0.96 0.00 41.15 2.75
4367 4906 7.456269 ACATAGGTTTTTACCATTTGGGATTCA 59.544 33.333 0.96 0.00 41.15 2.57
4371 4910 8.903059 ATTACATAGGTTTTTACCATTTGGGA 57.097 30.769 0.96 0.00 41.15 4.37
4372 4911 8.754080 TGATTACATAGGTTTTTACCATTTGGG 58.246 33.333 0.96 0.00 44.81 4.12
4403 4942 5.008019 GGTGTGCTGAACTGGTTATATGATG 59.992 44.000 0.00 0.00 0.00 3.07
4435 4974 7.563473 CAGTACTGTACATACTACGTACGTACG 60.563 44.444 38.49 38.49 44.00 3.67
4443 4982 7.168972 GGTAGAGACAGTACTGTACATACTACG 59.831 44.444 27.98 0.00 45.05 3.51
4445 4984 7.147828 ACGGTAGAGACAGTACTGTACATACTA 60.148 40.741 27.98 20.46 45.05 1.82
4447 4986 5.814705 ACGGTAGAGACAGTACTGTACATAC 59.185 44.000 27.98 25.01 45.05 2.39
4486 5025 5.066893 CCAGCTGATGTAAATATGTGCTTGT 59.933 40.000 17.39 0.00 0.00 3.16
4490 5029 5.278169 CCTTCCAGCTGATGTAAATATGTGC 60.278 44.000 17.39 0.00 0.00 4.57
4524 5063 1.101635 TGAGCGATCCGACGATTCCT 61.102 55.000 0.00 0.00 35.09 3.36
4525 5064 0.039074 ATGAGCGATCCGACGATTCC 60.039 55.000 0.00 0.00 35.09 3.01
4567 5109 6.037391 CCGGCCGAGTTTTTATTTTATCACTA 59.963 38.462 30.73 0.00 0.00 2.74
4574 5116 1.067425 GGCCGGCCGAGTTTTTATTTT 60.067 47.619 33.60 0.00 0.00 1.82
4610 5152 5.599999 AACACCAGCCAGTAGTAGATTAG 57.400 43.478 0.00 0.00 0.00 1.73
4611 5153 5.597182 CCTAACACCAGCCAGTAGTAGATTA 59.403 44.000 0.00 0.00 0.00 1.75
4612 5154 4.406003 CCTAACACCAGCCAGTAGTAGATT 59.594 45.833 0.00 0.00 0.00 2.40
4678 5224 2.680352 TTCGCCGAGCCCTTCTCT 60.680 61.111 0.00 0.00 39.70 3.10
4693 5239 1.270826 GGCAAAGGCAAGAAGGACTTC 59.729 52.381 3.91 3.91 43.71 3.01
4738 5284 1.150081 CAGGGCCATCCAGGATGAC 59.850 63.158 28.79 18.68 42.09 3.06


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

AutoCloner maintained by Alex Coulton.