Multiple sequence alignment - TraesCS7A01G104100

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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 TraesCS7A01G104100 chr7A 100.000 4616 0 0 1 4616 63447292 63442677 0.000000e+00 8525.0
1 TraesCS7A01G104100 chr4A 91.234 3776 196 47 925 4614 675970094 675966368 0.000000e+00 5014.0
2 TraesCS7A01G104100 chr4A 86.175 217 27 3 242 458 675972719 675972506 9.990000e-57 231.0
3 TraesCS7A01G104100 chr4A 94.118 85 4 1 2763 2847 735552506 735552423 1.350000e-25 128.0
4 TraesCS7A01G104100 chr7D 93.483 1872 83 18 925 2768 58871611 58869751 0.000000e+00 2745.0
5 TraesCS7A01G104100 chr7D 89.458 1015 55 21 3649 4616 58868911 58867902 0.000000e+00 1234.0
6 TraesCS7A01G104100 chr7D 93.711 811 46 4 2845 3651 58869753 58868944 0.000000e+00 1210.0
7 TraesCS7A01G104100 chr7D 86.989 661 66 9 229 876 58872511 58871858 0.000000e+00 726.0
8 TraesCS7A01G104100 chr7D 94.737 57 3 0 168 224 58872609 58872553 6.360000e-14 89.8
9 TraesCS7A01G104100 chr3D 88.372 129 12 2 2642 2767 50123978 50124106 8.000000e-33 152.0
10 TraesCS7A01G104100 chr3D 95.349 86 3 1 2765 2850 558557427 558557511 8.060000e-28 135.0
11 TraesCS7A01G104100 chr3B 96.429 84 2 1 2764 2847 825250026 825250108 2.240000e-28 137.0
12 TraesCS7A01G104100 chr3B 96.386 83 2 1 2767 2849 825250108 825250027 8.060000e-28 135.0
13 TraesCS7A01G104100 chr5B 91.667 96 7 1 2763 2858 63941586 63941680 1.040000e-26 132.0
14 TraesCS7A01G104100 chr2A 96.296 81 1 2 2767 2847 549890388 549890466 1.040000e-26 132.0
15 TraesCS7A01G104100 chr5D 93.182 88 5 1 2767 2854 381397403 381397317 1.350000e-25 128.0
16 TraesCS7A01G104100 chr2B 89.423 104 3 4 2767 2866 782178839 782178740 1.740000e-24 124.0


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 TraesCS7A01G104100 chr7A 63442677 63447292 4615 True 8525.00 8525 100.0000 1 4616 1 chr7A.!!$R1 4615
1 TraesCS7A01G104100 chr4A 675966368 675972719 6351 True 2622.50 5014 88.7045 242 4614 2 chr4A.!!$R2 4372
2 TraesCS7A01G104100 chr7D 58867902 58872609 4707 True 1200.96 2745 91.6756 168 4616 5 chr7D.!!$R1 4448

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
672 1038 0.179234 TCGCCAAACAGGAGTGAACA 59.821 50.0 0.00 0.00 41.22 3.18 F
1554 3798 0.036577 GCCACTCACTGCAGATCTGT 60.037 55.0 23.35 10.43 0.00 3.41 F
1666 3918 0.604578 CCCCAACTGCAGAACATTGG 59.395 55.0 23.35 22.11 37.01 3.16 F
3398 5661 0.737219 GCATGCAGGATGACCTTGAC 59.263 55.0 14.21 0.00 45.36 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2511 4772 0.603065 AAAAGGAAGATTGGCGTGGC 59.397 50.000 0.00 0.0 0.00 5.01 R
3255 5518 1.675310 CAAGGGCATCAACCAGCGA 60.675 57.895 0.00 0.0 0.00 4.93 R
3483 5746 2.233922 ACCATTGAACTAGGGTGACTCG 59.766 50.000 0.00 0.0 31.04 4.18 R
4288 6600 1.002430 GTGCAGTCTGATGGAGGACAA 59.998 52.381 3.32 0.0 35.18 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
61 62 8.911918 ATATTCTACAATATACCGCAAAACCA 57.088 30.769 0.00 0.00 33.99 3.67
62 63 7.817418 ATTCTACAATATACCGCAAAACCAT 57.183 32.000 0.00 0.00 0.00 3.55
63 64 8.911918 ATTCTACAATATACCGCAAAACCATA 57.088 30.769 0.00 0.00 0.00 2.74
64 65 8.734218 TTCTACAATATACCGCAAAACCATAA 57.266 30.769 0.00 0.00 0.00 1.90
65 66 8.145316 TCTACAATATACCGCAAAACCATAAC 57.855 34.615 0.00 0.00 0.00 1.89
66 67 6.139048 ACAATATACCGCAAAACCATAACC 57.861 37.500 0.00 0.00 0.00 2.85
67 68 5.889289 ACAATATACCGCAAAACCATAACCT 59.111 36.000 0.00 0.00 0.00 3.50
68 69 6.378848 ACAATATACCGCAAAACCATAACCTT 59.621 34.615 0.00 0.00 0.00 3.50
69 70 7.093684 ACAATATACCGCAAAACCATAACCTTT 60.094 33.333 0.00 0.00 0.00 3.11
70 71 8.407064 CAATATACCGCAAAACCATAACCTTTA 58.593 33.333 0.00 0.00 0.00 1.85
71 72 8.700439 ATATACCGCAAAACCATAACCTTTAT 57.300 30.769 0.00 0.00 0.00 1.40
72 73 5.731957 ACCGCAAAACCATAACCTTTATT 57.268 34.783 0.00 0.00 0.00 1.40
73 74 6.104146 ACCGCAAAACCATAACCTTTATTT 57.896 33.333 0.00 0.00 0.00 1.40
74 75 6.526526 ACCGCAAAACCATAACCTTTATTTT 58.473 32.000 0.00 0.00 0.00 1.82
75 76 6.647481 ACCGCAAAACCATAACCTTTATTTTC 59.353 34.615 0.00 0.00 0.00 2.29
76 77 6.091577 CCGCAAAACCATAACCTTTATTTTCC 59.908 38.462 0.00 0.00 0.00 3.13
77 78 6.871492 CGCAAAACCATAACCTTTATTTTCCT 59.129 34.615 0.00 0.00 0.00 3.36
78 79 7.062956 CGCAAAACCATAACCTTTATTTTCCTC 59.937 37.037 0.00 0.00 0.00 3.71
79 80 7.875554 GCAAAACCATAACCTTTATTTTCCTCA 59.124 33.333 0.00 0.00 0.00 3.86
80 81 9.942850 CAAAACCATAACCTTTATTTTCCTCAT 57.057 29.630 0.00 0.00 0.00 2.90
81 82 9.942850 AAAACCATAACCTTTATTTTCCTCATG 57.057 29.630 0.00 0.00 0.00 3.07
82 83 7.660030 ACCATAACCTTTATTTTCCTCATGG 57.340 36.000 0.00 0.00 36.20 3.66
83 84 7.189087 ACCATAACCTTTATTTTCCTCATGGT 58.811 34.615 0.00 0.00 38.03 3.55
84 85 7.678171 ACCATAACCTTTATTTTCCTCATGGTT 59.322 33.333 0.00 0.00 39.41 3.67
85 86 8.197439 CCATAACCTTTATTTTCCTCATGGTTC 58.803 37.037 0.00 0.00 37.64 3.62
86 87 8.971073 CATAACCTTTATTTTCCTCATGGTTCT 58.029 33.333 0.00 0.00 37.64 3.01
87 88 6.840780 ACCTTTATTTTCCTCATGGTTCTG 57.159 37.500 0.00 0.00 34.23 3.02
88 89 5.716703 ACCTTTATTTTCCTCATGGTTCTGG 59.283 40.000 0.00 0.00 34.23 3.86
89 90 5.394553 CCTTTATTTTCCTCATGGTTCTGGC 60.395 44.000 0.00 0.00 34.23 4.85
90 91 2.673775 TTTTCCTCATGGTTCTGGCA 57.326 45.000 0.00 0.00 34.23 4.92
91 92 2.905415 TTTCCTCATGGTTCTGGCAT 57.095 45.000 0.00 0.00 34.23 4.40
92 93 2.133281 TTCCTCATGGTTCTGGCATG 57.867 50.000 0.00 0.00 34.23 4.06
93 94 0.994247 TCCTCATGGTTCTGGCATGT 59.006 50.000 0.00 0.00 34.23 3.21
94 95 2.195727 TCCTCATGGTTCTGGCATGTA 58.804 47.619 0.00 0.00 34.23 2.29
95 96 2.575735 TCCTCATGGTTCTGGCATGTAA 59.424 45.455 0.00 0.00 34.23 2.41
96 97 2.947652 CCTCATGGTTCTGGCATGTAAG 59.052 50.000 0.00 0.00 0.00 2.34
97 98 2.357009 CTCATGGTTCTGGCATGTAAGC 59.643 50.000 0.00 0.00 0.00 3.09
110 111 5.567138 GCATGTAAGCCACTCACTAAATT 57.433 39.130 0.00 0.00 0.00 1.82
111 112 5.954335 GCATGTAAGCCACTCACTAAATTT 58.046 37.500 0.00 0.00 0.00 1.82
112 113 6.389906 GCATGTAAGCCACTCACTAAATTTT 58.610 36.000 0.00 0.00 0.00 1.82
113 114 6.868339 GCATGTAAGCCACTCACTAAATTTTT 59.132 34.615 0.00 0.00 0.00 1.94
141 142 8.761575 AAGTGGTTAAATTGCAGAATAATGTG 57.238 30.769 0.00 0.00 0.00 3.21
142 143 6.813152 AGTGGTTAAATTGCAGAATAATGTGC 59.187 34.615 0.00 0.00 45.62 4.57
152 153 6.323203 GCAGAATAATGTGCAATATCTGGT 57.677 37.500 12.27 0.00 44.81 4.00
153 154 7.439157 GCAGAATAATGTGCAATATCTGGTA 57.561 36.000 12.27 0.00 44.81 3.25
154 155 7.874940 GCAGAATAATGTGCAATATCTGGTAA 58.125 34.615 12.27 0.00 44.81 2.85
155 156 7.805071 GCAGAATAATGTGCAATATCTGGTAAC 59.195 37.037 12.27 0.00 44.81 2.50
156 157 9.060347 CAGAATAATGTGCAATATCTGGTAACT 57.940 33.333 0.00 0.00 37.61 2.24
161 162 8.613060 AATGTGCAATATCTGGTAACTAGATG 57.387 34.615 0.00 0.00 36.37 2.90
162 163 7.360113 TGTGCAATATCTGGTAACTAGATGA 57.640 36.000 0.00 0.00 36.37 2.92
163 164 7.436933 TGTGCAATATCTGGTAACTAGATGAG 58.563 38.462 0.00 0.00 36.37 2.90
164 165 7.287696 TGTGCAATATCTGGTAACTAGATGAGA 59.712 37.037 0.00 0.00 36.37 3.27
165 166 8.144478 GTGCAATATCTGGTAACTAGATGAGAA 58.856 37.037 0.00 0.00 36.37 2.87
166 167 8.144478 TGCAATATCTGGTAACTAGATGAGAAC 58.856 37.037 0.00 0.00 36.37 3.01
177 178 9.026074 GTAACTAGATGAGAACTTAGATTGTGC 57.974 37.037 0.00 0.00 0.00 4.57
178 179 7.175347 ACTAGATGAGAACTTAGATTGTGCA 57.825 36.000 0.00 0.00 0.00 4.57
179 180 7.615403 ACTAGATGAGAACTTAGATTGTGCAA 58.385 34.615 0.00 0.00 0.00 4.08
224 225 9.762381 AACTCAAGGGTTAAATGTGGATATAAA 57.238 29.630 0.00 0.00 0.00 1.40
225 226 9.185680 ACTCAAGGGTTAAATGTGGATATAAAC 57.814 33.333 0.00 0.00 0.00 2.01
267 305 5.274015 GGTAAAGGGTTGGGGATGAAATTA 58.726 41.667 0.00 0.00 0.00 1.40
291 329 9.941664 TTAGTATTCCTTCGAAAACTATACTCG 57.058 33.333 17.78 0.00 0.00 4.18
412 450 8.169977 AGTCTTGCATTGAAGAATACTCAAAA 57.830 30.769 0.00 0.00 33.73 2.44
453 493 5.287035 GTGCATTTTTCTTAAATGAGGCGAG 59.713 40.000 12.91 0.00 39.36 5.03
458 498 3.802948 TCTTAAATGAGGCGAGAGACC 57.197 47.619 0.00 0.00 43.69 3.85
460 500 4.533815 TCTTAAATGAGGCGAGAGACCTA 58.466 43.478 0.00 0.00 43.69 3.08
463 503 0.820074 ATGAGGCGAGAGACCTACCG 60.820 60.000 0.00 0.00 43.69 4.02
471 511 3.846360 CGAGAGACCTACCGTTTTCATT 58.154 45.455 0.00 0.00 0.00 2.57
476 516 7.464178 CGAGAGACCTACCGTTTTCATTAATTG 60.464 40.741 0.00 0.00 0.00 2.32
481 521 7.813645 ACCTACCGTTTTCATTAATTGAGAAC 58.186 34.615 9.37 9.37 42.93 3.01
499 539 9.751542 ATTGAGAACGTAGTAAGAATTATCTGG 57.248 33.333 0.00 0.00 45.00 3.86
553 595 3.836949 CACACATTACAAGGAACATGGC 58.163 45.455 0.00 0.00 0.00 4.40
554 596 3.507233 CACACATTACAAGGAACATGGCT 59.493 43.478 0.00 0.00 0.00 4.75
574 616 0.475906 ATCATCAGCCAACCTAGCCC 59.524 55.000 0.00 0.00 0.00 5.19
575 617 0.913934 TCATCAGCCAACCTAGCCCA 60.914 55.000 0.00 0.00 0.00 5.36
590 956 1.952102 GCCCAACATGGATGCCACAG 61.952 60.000 0.00 0.00 40.96 3.66
603 969 1.134128 TGCCACAGAGCTGTTGAGAAA 60.134 47.619 5.95 0.00 42.83 2.52
646 1012 2.746904 CCGCAAGTGTCATTCATAACCA 59.253 45.455 0.00 0.00 0.00 3.67
660 1026 0.321741 TAACCAATCGCCTCGCCAAA 60.322 50.000 0.00 0.00 0.00 3.28
665 1031 2.463589 AATCGCCTCGCCAAACAGGA 62.464 55.000 0.00 0.00 41.22 3.86
669 1035 1.371183 CCTCGCCAAACAGGAGTGA 59.629 57.895 0.00 0.00 41.22 3.41
670 1036 0.250295 CCTCGCCAAACAGGAGTGAA 60.250 55.000 0.00 0.00 41.22 3.18
671 1037 0.868406 CTCGCCAAACAGGAGTGAAC 59.132 55.000 0.00 0.00 41.22 3.18
672 1038 0.179234 TCGCCAAACAGGAGTGAACA 59.821 50.000 0.00 0.00 41.22 3.18
682 1055 7.416213 CCAAACAGGAGTGAACAAAGACATAAA 60.416 37.037 0.00 0.00 41.22 1.40
707 1080 6.436261 ACTAACGATTATGTCATAGACACCG 58.564 40.000 1.43 6.73 45.65 4.94
745 1118 4.859245 CGACGAATGATGACGATCCATTAT 59.141 41.667 0.00 0.00 0.00 1.28
771 1144 0.250793 TCGGGTTTGTCCACGCATAT 59.749 50.000 0.00 0.00 38.11 1.78
790 1163 1.372872 GTTTTCATTTGGCGGCGCT 60.373 52.632 32.30 9.02 0.00 5.92
791 1164 1.080839 TTTTCATTTGGCGGCGCTC 60.081 52.632 32.30 21.54 0.00 5.03
792 1165 1.523154 TTTTCATTTGGCGGCGCTCT 61.523 50.000 32.30 10.94 0.00 4.09
793 1166 0.675208 TTTCATTTGGCGGCGCTCTA 60.675 50.000 32.30 16.77 0.00 2.43
805 1178 2.288579 CGGCGCTCTAAACATACCCATA 60.289 50.000 7.64 0.00 0.00 2.74
806 1179 3.735591 GGCGCTCTAAACATACCCATAA 58.264 45.455 7.64 0.00 0.00 1.90
812 1185 7.386848 GCGCTCTAAACATACCCATAATTTCTA 59.613 37.037 0.00 0.00 0.00 2.10
860 1233 1.878953 ACCACTTACAAGCCAAGTCG 58.121 50.000 0.00 0.00 33.99 4.18
870 1243 4.192317 ACAAGCCAAGTCGATTCTATTCC 58.808 43.478 0.00 0.00 0.00 3.01
873 1246 2.803492 GCCAAGTCGATTCTATTCCGCT 60.803 50.000 0.00 0.00 0.00 5.52
896 3096 1.533753 CCAAAAGCTTGCAGGGGGA 60.534 57.895 0.00 0.00 0.00 4.81
918 3118 2.847441 GGGGGAAAATCGTATGAGACC 58.153 52.381 0.00 0.00 0.00 3.85
919 3119 2.171870 GGGGGAAAATCGTATGAGACCA 59.828 50.000 0.00 0.00 0.00 4.02
920 3120 3.467803 GGGGAAAATCGTATGAGACCAG 58.532 50.000 0.00 0.00 0.00 4.00
921 3121 3.467803 GGGAAAATCGTATGAGACCAGG 58.532 50.000 0.00 0.00 0.00 4.45
922 3122 3.118371 GGGAAAATCGTATGAGACCAGGT 60.118 47.826 0.00 0.00 0.00 4.00
923 3123 4.514401 GGAAAATCGTATGAGACCAGGTT 58.486 43.478 0.00 0.00 0.00 3.50
932 3132 3.868757 TGAGACCAGGTTATTCAGTCG 57.131 47.619 0.00 0.00 32.70 4.18
937 3137 2.009774 CCAGGTTATTCAGTCGCAAGG 58.990 52.381 0.00 0.00 38.47 3.61
959 3159 2.417933 AGCGAGCAAATAGTGAAAGCAG 59.582 45.455 0.00 0.00 0.00 4.24
992 3192 4.995058 TTTCGGAGGCCACCCCCT 62.995 66.667 14.25 0.00 38.12 4.79
1159 3392 1.512310 CCTCTTCTGCGTCGACGTC 60.512 63.158 35.48 27.35 42.22 4.34
1194 3427 2.956964 CGAGATGAAGGTCGCCGC 60.957 66.667 0.00 0.00 0.00 6.53
1195 3428 2.586357 GAGATGAAGGTCGCCGCC 60.586 66.667 0.00 0.00 0.00 6.13
1196 3429 4.514577 AGATGAAGGTCGCCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
1416 3649 1.254954 GACACCGTCTCCTTGGTAGT 58.745 55.000 0.00 0.00 36.50 2.73
1437 3670 0.827368 CTCTACTGCCCTCCTTGTCC 59.173 60.000 0.00 0.00 0.00 4.02
1452 3685 1.755008 GTCCCCTCACTCTCTCGGG 60.755 68.421 0.00 0.00 36.42 5.14
1529 3773 2.096268 CGTTTCAGTTCATGTGTGCGAT 60.096 45.455 0.00 0.00 0.00 4.58
1554 3798 0.036577 GCCACTCACTGCAGATCTGT 60.037 55.000 23.35 10.43 0.00 3.41
1622 3866 6.260714 CGGATACATGAAGAAATGGACATGAA 59.739 38.462 0.00 0.00 41.45 2.57
1643 3887 5.186021 TGAAAACTGAGTAGTTGCCCAAAAA 59.814 36.000 0.00 0.00 46.14 1.94
1646 3890 5.869649 ACTGAGTAGTTGCCCAAAAATTT 57.130 34.783 0.00 0.00 31.66 1.82
1656 3900 2.503331 CCCAAAAATTTCCCCAACTGC 58.497 47.619 0.00 0.00 0.00 4.40
1666 3918 0.604578 CCCCAACTGCAGAACATTGG 59.395 55.000 23.35 22.11 37.01 3.16
1674 3926 1.470996 GCAGAACATTGGCCCCACAA 61.471 55.000 0.00 0.00 34.41 3.33
1679 3931 3.906846 AGAACATTGGCCCCACAAAATTA 59.093 39.130 0.00 0.00 33.48 1.40
1741 3993 2.693074 AGTTTGCCTTTAGTGTTGTGGG 59.307 45.455 0.00 0.00 0.00 4.61
1766 4018 8.141268 GGTTAATGAATTCCAGAAGTTGTTTCA 58.859 33.333 2.27 0.00 38.31 2.69
1871 4130 7.573710 TGTGGGTTACTCTCATATATTGCTTT 58.426 34.615 0.00 0.00 0.00 3.51
1872 4131 7.715249 TGTGGGTTACTCTCATATATTGCTTTC 59.285 37.037 0.00 0.00 0.00 2.62
1873 4132 7.934120 GTGGGTTACTCTCATATATTGCTTTCT 59.066 37.037 0.00 0.00 0.00 2.52
1874 4133 7.933577 TGGGTTACTCTCATATATTGCTTTCTG 59.066 37.037 0.00 0.00 0.00 3.02
1967 4226 3.748083 TGCTGCTTCTTCAATTGAGACT 58.252 40.909 8.41 0.00 0.00 3.24
1991 4250 1.219393 GTCCCTGGCTGCTACTGAC 59.781 63.158 0.00 0.00 0.00 3.51
2112 4371 4.553323 CTTGCTGCAAGTTGCTCTAATTT 58.447 39.130 29.38 0.00 45.31 1.82
2314 4575 3.157087 GTTGGTCATCCACAATTCCACT 58.843 45.455 0.00 0.00 44.22 4.00
2511 4772 5.163622 GGGTCATCTGTTGATTGTTGTATGG 60.164 44.000 0.00 0.00 36.54 2.74
2516 4777 2.227626 TGTTGATTGTTGTATGGCCACG 59.772 45.455 8.16 0.00 0.00 4.94
2722 4983 8.299570 CAGTACAATTCTAAACTGAAAAGGCAT 58.700 33.333 0.00 0.00 41.47 4.40
2731 4992 6.819397 AAACTGAAAAGGCATAGTAGGTTC 57.181 37.500 0.00 0.00 0.00 3.62
2759 5020 5.830000 AACAGAGGGTTGACAAAACTTAC 57.170 39.130 0.00 0.00 38.60 2.34
2776 5037 5.836024 ACTTACAAAATGTACTCCCTCCA 57.164 39.130 0.00 0.00 31.69 3.86
2779 5040 4.236527 ACAAAATGTACTCCCTCCATCC 57.763 45.455 0.00 0.00 0.00 3.51
2790 5051 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
2791 5052 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
2792 5053 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
2793 5054 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
2840 5101 5.611374 ACATCTTACATTTATGGGACGGAG 58.389 41.667 0.00 0.00 0.00 4.63
2847 5108 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2855 5116 3.119209 GGACGGAGGGAGTACAAGTTTAG 60.119 52.174 0.00 0.00 0.00 1.85
2858 5119 3.676324 CGGAGGGAGTACAAGTTTAGCAG 60.676 52.174 0.00 0.00 0.00 4.24
2890 5151 5.930837 AAACTGTTTTTGGTGGAGAATGA 57.069 34.783 0.00 0.00 0.00 2.57
2958 5221 7.578852 CATCTCACGACATGTATAAAATGCAT 58.421 34.615 0.00 0.00 35.94 3.96
2983 5246 4.677182 ACAATTCTAAACTGGAATGGCCT 58.323 39.130 3.32 0.00 37.63 5.19
3022 5285 7.064134 TGCACAGAAGGTTAACAATACGAATAG 59.936 37.037 8.10 0.00 0.00 1.73
3031 5294 7.306399 GGTTAACAATACGAATAGGATGTGTCG 60.306 40.741 8.10 0.00 39.37 4.35
3060 5323 1.670811 ACAGTACTGCTTTGTGTGTGC 59.329 47.619 22.90 0.00 0.00 4.57
3061 5324 1.670295 CAGTACTGCTTTGTGTGTGCA 59.330 47.619 10.54 0.00 35.30 4.57
3104 5367 3.131223 TGCGACTTGGTTTTGATTTCCAA 59.869 39.130 0.00 0.00 38.65 3.53
3111 5374 5.529581 TGGTTTTGATTTCCAAGAGAACC 57.470 39.130 0.00 0.00 40.80 3.62
3255 5518 1.877443 GCCCACAAAACGTGTATGACT 59.123 47.619 0.00 0.00 44.78 3.41
3398 5661 0.737219 GCATGCAGGATGACCTTGAC 59.263 55.000 14.21 0.00 45.36 3.18
3401 5664 2.885135 TGCAGGATGACCTTGACATT 57.115 45.000 0.00 0.00 45.36 2.71
3483 5746 1.153469 GTCTCCAGCAGCCAGTAGC 60.153 63.158 0.00 0.00 44.25 3.58
3552 5816 1.838112 TGTAAAGGGCCAAGCAGATG 58.162 50.000 6.18 0.00 0.00 2.90
3619 5883 9.585099 TTGTATAAATTGCTCCTTTATTTGCAG 57.415 29.630 0.00 0.00 36.75 4.41
3627 5891 5.360429 TGCTCCTTTATTTGCAGCATATCAA 59.640 36.000 1.05 0.00 35.17 2.57
3651 5915 7.944729 ATCACTGCAATCTACCTTGTATTTT 57.055 32.000 0.00 0.00 0.00 1.82
3653 5917 7.168219 TCACTGCAATCTACCTTGTATTTTCT 58.832 34.615 0.00 0.00 0.00 2.52
3667 5966 1.202203 TTTTCTCGGTGTCGTGAACG 58.798 50.000 0.00 0.00 44.84 3.95
3718 6017 2.151202 CCGGTTTCTGTATTGTGCAGT 58.849 47.619 0.00 0.00 35.60 4.40
3723 6022 4.069304 GTTTCTGTATTGTGCAGTGGGTA 58.931 43.478 0.00 0.00 35.60 3.69
3766 6065 5.338708 GCCATGCATCTGGTTAGGTAGATAT 60.339 44.000 8.13 0.00 38.63 1.63
3872 6172 4.970662 ATCTCAAATTCATCGTTGTGGG 57.029 40.909 0.00 0.00 0.00 4.61
3931 6231 1.455849 CACCACTCTGGGGCAAAGA 59.544 57.895 0.00 0.00 43.37 2.52
3991 6291 6.423905 GTCCTTCGAATCGATCCATAATTTCA 59.576 38.462 6.06 0.00 35.23 2.69
4028 6328 3.051392 CTGGCCGCCATTTTCGACC 62.051 63.158 13.86 0.00 30.82 4.79
4029 6329 3.059386 GGCCGCCATTTTCGACCA 61.059 61.111 3.91 0.00 29.63 4.02
4052 6352 1.668419 GAGCTAATGTTGCCGGTGAT 58.332 50.000 1.90 0.00 0.00 3.06
4069 6369 2.118679 TGATGGTCCCGACAAGATGAT 58.881 47.619 0.00 0.00 0.00 2.45
4090 6390 1.077716 CCCCTCCTAGCCGGTTTTG 60.078 63.158 1.90 0.00 0.00 2.44
4120 6420 2.036004 CGATCCGTTGACGTCGTTTATG 60.036 50.000 11.62 1.89 34.56 1.90
4158 6458 2.753966 CGAGAACATGCCGCCCTTG 61.754 63.158 0.00 0.00 0.00 3.61
4288 6600 2.733956 CTCTCTTGGAGCTGTACCTCT 58.266 52.381 0.00 0.00 35.08 3.69
4344 6679 3.982437 GGAATTTTACCGACGAACGAAG 58.018 45.455 0.00 0.00 45.77 3.79
4345 6680 3.674753 GGAATTTTACCGACGAACGAAGA 59.325 43.478 0.00 0.00 45.77 2.87
4346 6681 4.150451 GGAATTTTACCGACGAACGAAGAA 59.850 41.667 0.00 0.14 45.77 2.52
4347 6682 4.635961 ATTTTACCGACGAACGAAGAAC 57.364 40.909 0.00 0.00 45.77 3.01
4348 6683 1.673760 TTACCGACGAACGAAGAACG 58.326 50.000 0.00 0.00 45.77 3.95
4461 6796 3.047877 GGGACGGCGTTGAACTGG 61.048 66.667 16.19 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.999660 TGGTTTTGCGGTATATTGTAGAATATA 57.000 29.630 7.97 7.97 36.38 0.86
36 37 8.911918 TGGTTTTGCGGTATATTGTAGAATAT 57.088 30.769 9.80 9.80 38.20 1.28
37 38 8.911918 ATGGTTTTGCGGTATATTGTAGAATA 57.088 30.769 0.00 0.00 0.00 1.75
38 39 7.817418 ATGGTTTTGCGGTATATTGTAGAAT 57.183 32.000 0.00 0.00 0.00 2.40
39 40 8.614346 GTTATGGTTTTGCGGTATATTGTAGAA 58.386 33.333 0.00 0.00 0.00 2.10
40 41 7.227116 GGTTATGGTTTTGCGGTATATTGTAGA 59.773 37.037 0.00 0.00 0.00 2.59
41 42 7.227910 AGGTTATGGTTTTGCGGTATATTGTAG 59.772 37.037 0.00 0.00 0.00 2.74
42 43 7.055378 AGGTTATGGTTTTGCGGTATATTGTA 58.945 34.615 0.00 0.00 0.00 2.41
43 44 5.889289 AGGTTATGGTTTTGCGGTATATTGT 59.111 36.000 0.00 0.00 0.00 2.71
44 45 6.385649 AGGTTATGGTTTTGCGGTATATTG 57.614 37.500 0.00 0.00 0.00 1.90
45 46 7.412853 AAAGGTTATGGTTTTGCGGTATATT 57.587 32.000 0.00 0.00 0.00 1.28
46 47 8.700439 ATAAAGGTTATGGTTTTGCGGTATAT 57.300 30.769 0.00 0.00 0.00 0.86
47 48 8.522542 AATAAAGGTTATGGTTTTGCGGTATA 57.477 30.769 0.00 0.00 0.00 1.47
48 49 7.412853 AATAAAGGTTATGGTTTTGCGGTAT 57.587 32.000 0.00 0.00 0.00 2.73
49 50 6.837471 AATAAAGGTTATGGTTTTGCGGTA 57.163 33.333 0.00 0.00 0.00 4.02
50 51 5.731957 AATAAAGGTTATGGTTTTGCGGT 57.268 34.783 0.00 0.00 0.00 5.68
51 52 6.091577 GGAAAATAAAGGTTATGGTTTTGCGG 59.908 38.462 0.00 0.00 0.00 5.69
52 53 6.871492 AGGAAAATAAAGGTTATGGTTTTGCG 59.129 34.615 0.00 0.00 33.83 4.85
53 54 7.875554 TGAGGAAAATAAAGGTTATGGTTTTGC 59.124 33.333 0.00 0.00 0.00 3.68
54 55 9.942850 ATGAGGAAAATAAAGGTTATGGTTTTG 57.057 29.630 0.00 0.00 0.00 2.44
55 56 9.942850 CATGAGGAAAATAAAGGTTATGGTTTT 57.057 29.630 0.00 0.00 0.00 2.43
56 57 8.539544 CCATGAGGAAAATAAAGGTTATGGTTT 58.460 33.333 0.00 0.00 36.89 3.27
57 58 7.678171 ACCATGAGGAAAATAAAGGTTATGGTT 59.322 33.333 0.00 0.00 41.06 3.67
58 59 7.189087 ACCATGAGGAAAATAAAGGTTATGGT 58.811 34.615 0.00 0.00 39.59 3.55
59 60 7.660030 ACCATGAGGAAAATAAAGGTTATGG 57.340 36.000 0.00 0.00 38.69 2.74
60 61 8.971073 AGAACCATGAGGAAAATAAAGGTTATG 58.029 33.333 0.00 0.00 38.16 1.90
61 62 8.971073 CAGAACCATGAGGAAAATAAAGGTTAT 58.029 33.333 0.00 0.00 38.16 1.89
62 63 7.396055 CCAGAACCATGAGGAAAATAAAGGTTA 59.604 37.037 0.00 0.00 38.16 2.85
63 64 6.211384 CCAGAACCATGAGGAAAATAAAGGTT 59.789 38.462 0.00 0.00 40.52 3.50
64 65 5.716703 CCAGAACCATGAGGAAAATAAAGGT 59.283 40.000 0.00 0.00 38.69 3.50
65 66 5.394553 GCCAGAACCATGAGGAAAATAAAGG 60.395 44.000 0.00 0.00 38.69 3.11
66 67 5.185635 TGCCAGAACCATGAGGAAAATAAAG 59.814 40.000 0.00 0.00 38.69 1.85
67 68 5.083122 TGCCAGAACCATGAGGAAAATAAA 58.917 37.500 0.00 0.00 38.69 1.40
68 69 4.671831 TGCCAGAACCATGAGGAAAATAA 58.328 39.130 0.00 0.00 38.69 1.40
69 70 4.314522 TGCCAGAACCATGAGGAAAATA 57.685 40.909 0.00 0.00 38.69 1.40
70 71 3.173953 TGCCAGAACCATGAGGAAAAT 57.826 42.857 0.00 0.00 38.69 1.82
71 72 2.673775 TGCCAGAACCATGAGGAAAA 57.326 45.000 0.00 0.00 38.69 2.29
72 73 2.225091 ACATGCCAGAACCATGAGGAAA 60.225 45.455 8.22 0.00 41.97 3.13
73 74 1.355381 ACATGCCAGAACCATGAGGAA 59.645 47.619 8.22 0.00 41.97 3.36
74 75 0.994247 ACATGCCAGAACCATGAGGA 59.006 50.000 8.22 0.00 41.97 3.71
75 76 2.715749 TACATGCCAGAACCATGAGG 57.284 50.000 8.22 0.00 41.97 3.86
76 77 2.357009 GCTTACATGCCAGAACCATGAG 59.643 50.000 8.22 0.00 41.97 2.90
77 78 2.368439 GCTTACATGCCAGAACCATGA 58.632 47.619 8.22 0.00 41.97 3.07
78 79 2.857592 GCTTACATGCCAGAACCATG 57.142 50.000 0.00 0.00 44.28 3.66
88 89 5.567138 AATTTAGTGAGTGGCTTACATGC 57.433 39.130 0.00 0.00 0.00 4.06
115 116 9.206870 CACATTATTCTGCAATTTAACCACTTT 57.793 29.630 0.00 0.00 0.00 2.66
116 117 7.331687 GCACATTATTCTGCAATTTAACCACTT 59.668 33.333 0.00 0.00 33.31 3.16
117 118 6.813152 GCACATTATTCTGCAATTTAACCACT 59.187 34.615 0.00 0.00 33.31 4.00
118 119 6.589523 TGCACATTATTCTGCAATTTAACCAC 59.410 34.615 0.00 0.00 40.45 4.16
119 120 6.695429 TGCACATTATTCTGCAATTTAACCA 58.305 32.000 0.00 0.00 40.45 3.67
120 121 7.593875 TTGCACATTATTCTGCAATTTAACC 57.406 32.000 0.99 0.00 46.07 2.85
128 129 5.829391 ACCAGATATTGCACATTATTCTGCA 59.171 36.000 0.00 0.00 41.68 4.41
129 130 6.323203 ACCAGATATTGCACATTATTCTGC 57.677 37.500 0.00 0.00 0.00 4.26
130 131 9.060347 AGTTACCAGATATTGCACATTATTCTG 57.940 33.333 0.00 0.00 0.00 3.02
135 136 9.710900 CATCTAGTTACCAGATATTGCACATTA 57.289 33.333 0.00 0.00 31.48 1.90
136 137 8.432013 TCATCTAGTTACCAGATATTGCACATT 58.568 33.333 0.00 0.00 31.48 2.71
137 138 7.966812 TCATCTAGTTACCAGATATTGCACAT 58.033 34.615 0.00 0.00 31.48 3.21
138 139 7.287696 TCTCATCTAGTTACCAGATATTGCACA 59.712 37.037 0.00 0.00 31.48 4.57
139 140 7.661968 TCTCATCTAGTTACCAGATATTGCAC 58.338 38.462 0.00 0.00 31.48 4.57
140 141 7.839680 TCTCATCTAGTTACCAGATATTGCA 57.160 36.000 0.00 0.00 31.48 4.08
141 142 8.364142 AGTTCTCATCTAGTTACCAGATATTGC 58.636 37.037 0.00 0.00 31.48 3.56
146 147 9.875708 ATCTAAGTTCTCATCTAGTTACCAGAT 57.124 33.333 0.00 0.00 32.90 2.90
147 148 9.702253 AATCTAAGTTCTCATCTAGTTACCAGA 57.298 33.333 0.00 0.00 0.00 3.86
148 149 9.743057 CAATCTAAGTTCTCATCTAGTTACCAG 57.257 37.037 0.00 0.00 0.00 4.00
149 150 9.256228 ACAATCTAAGTTCTCATCTAGTTACCA 57.744 33.333 0.00 0.00 0.00 3.25
150 151 9.522804 CACAATCTAAGTTCTCATCTAGTTACC 57.477 37.037 0.00 0.00 0.00 2.85
151 152 9.026074 GCACAATCTAAGTTCTCATCTAGTTAC 57.974 37.037 0.00 0.00 0.00 2.50
152 153 8.749354 TGCACAATCTAAGTTCTCATCTAGTTA 58.251 33.333 0.00 0.00 0.00 2.24
153 154 7.615403 TGCACAATCTAAGTTCTCATCTAGTT 58.385 34.615 0.00 0.00 0.00 2.24
154 155 7.175347 TGCACAATCTAAGTTCTCATCTAGT 57.825 36.000 0.00 0.00 0.00 2.57
155 156 7.010923 GGTTGCACAATCTAAGTTCTCATCTAG 59.989 40.741 0.00 0.00 0.00 2.43
156 157 6.818644 GGTTGCACAATCTAAGTTCTCATCTA 59.181 38.462 0.00 0.00 0.00 1.98
157 158 5.645497 GGTTGCACAATCTAAGTTCTCATCT 59.355 40.000 0.00 0.00 0.00 2.90
158 159 5.645497 AGGTTGCACAATCTAAGTTCTCATC 59.355 40.000 0.00 0.00 28.20 2.92
159 160 5.564550 AGGTTGCACAATCTAAGTTCTCAT 58.435 37.500 0.00 0.00 28.20 2.90
160 161 4.973168 AGGTTGCACAATCTAAGTTCTCA 58.027 39.130 0.00 0.00 28.20 3.27
161 162 5.948992 AAGGTTGCACAATCTAAGTTCTC 57.051 39.130 0.00 0.00 30.24 2.87
162 163 5.827797 TCAAAGGTTGCACAATCTAAGTTCT 59.172 36.000 0.00 0.00 30.24 3.01
163 164 6.072112 TCAAAGGTTGCACAATCTAAGTTC 57.928 37.500 0.00 0.00 30.24 3.01
164 165 6.655078 ATCAAAGGTTGCACAATCTAAGTT 57.345 33.333 0.00 0.00 30.24 2.66
165 166 6.714810 TGTATCAAAGGTTGCACAATCTAAGT 59.285 34.615 0.00 0.00 30.24 2.24
166 167 7.144722 TGTATCAAAGGTTGCACAATCTAAG 57.855 36.000 0.00 0.00 30.24 2.18
177 178 5.415701 AGTTGCCACTATGTATCAAAGGTTG 59.584 40.000 0.00 0.00 0.00 3.77
178 179 5.570320 AGTTGCCACTATGTATCAAAGGTT 58.430 37.500 0.00 0.00 0.00 3.50
179 180 5.179452 AGTTGCCACTATGTATCAAAGGT 57.821 39.130 0.00 0.00 0.00 3.50
224 225 3.392285 ACCCTTTGTCCTACCGTTTAAGT 59.608 43.478 0.00 0.00 0.00 2.24
225 226 4.011966 ACCCTTTGTCCTACCGTTTAAG 57.988 45.455 0.00 0.00 0.00 1.85
228 229 4.392047 CTTTACCCTTTGTCCTACCGTTT 58.608 43.478 0.00 0.00 0.00 3.60
231 232 2.355412 CCCTTTACCCTTTGTCCTACCG 60.355 54.545 0.00 0.00 0.00 4.02
236 274 2.244695 CCAACCCTTTACCCTTTGTCC 58.755 52.381 0.00 0.00 0.00 4.02
267 305 6.916932 GCGAGTATAGTTTTCGAAGGAATACT 59.083 38.462 17.31 17.31 43.73 2.12
291 329 9.675553 GCATAAGAATTTAATGTTCTTTTTCGC 57.324 29.630 16.74 12.20 41.75 4.70
397 435 8.303876 GCCTTTATTGGTTTTGAGTATTCTTCA 58.696 33.333 0.00 0.00 0.00 3.02
429 467 5.160641 TCGCCTCATTTAAGAAAAATGCAC 58.839 37.500 5.74 0.00 37.50 4.57
432 470 6.963805 GTCTCTCGCCTCATTTAAGAAAAATG 59.036 38.462 4.46 4.46 38.60 2.32
453 493 7.548075 TCTCAATTAATGAAAACGGTAGGTCTC 59.452 37.037 0.00 0.00 37.67 3.36
476 516 9.968870 AATCCAGATAATTCTTACTACGTTCTC 57.031 33.333 0.00 0.00 0.00 2.87
524 566 3.073209 TCCTTGTAATGTGTGCAGGGTTA 59.927 43.478 0.00 0.00 39.71 2.85
530 572 3.255395 CCATGTTCCTTGTAATGTGTGCA 59.745 43.478 0.00 0.00 0.00 4.57
553 595 2.289945 GGGCTAGGTTGGCTGATGATAG 60.290 54.545 0.00 0.00 0.00 2.08
554 596 1.699634 GGGCTAGGTTGGCTGATGATA 59.300 52.381 0.00 0.00 0.00 2.15
574 616 0.454600 GCTCTGTGGCATCCATGTTG 59.545 55.000 0.00 0.00 35.28 3.33
575 617 0.330604 AGCTCTGTGGCATCCATGTT 59.669 50.000 0.00 0.00 35.28 2.71
590 956 7.078228 ACGAATGTTATTTTTCTCAACAGCTC 58.922 34.615 0.00 0.00 35.77 4.09
603 969 3.267483 CCACCCTCGACGAATGTTATTT 58.733 45.455 0.00 0.00 0.00 1.40
646 1012 2.040544 CCTGTTTGGCGAGGCGATT 61.041 57.895 0.00 0.00 0.00 3.34
660 1026 6.828785 AGTTTTATGTCTTTGTTCACTCCTGT 59.171 34.615 0.00 0.00 0.00 4.00
665 1031 8.428186 TCGTTAGTTTTATGTCTTTGTTCACT 57.572 30.769 0.00 0.00 0.00 3.41
682 1055 6.916387 CGGTGTCTATGACATAATCGTTAGTT 59.084 38.462 3.65 0.00 44.63 2.24
707 1080 0.710567 CGTCGCACTCAAGATCACAC 59.289 55.000 0.00 0.00 0.00 3.82
745 1118 2.422591 GACAAACCCGACCCGACA 59.577 61.111 0.00 0.00 0.00 4.35
771 1144 1.663074 GCGCCGCCAAATGAAAACA 60.663 52.632 0.00 0.00 0.00 2.83
823 1196 9.623000 GTAAGTGGTATAGAAAACCCATACATT 57.377 33.333 0.00 0.00 36.06 2.71
825 1198 8.148437 TGTAAGTGGTATAGAAAACCCATACA 57.852 34.615 0.00 0.00 36.06 2.29
860 1233 6.445357 TTTTGGGTAAAGCGGAATAGAATC 57.555 37.500 0.00 0.00 0.00 2.52
873 1246 1.691434 CCCTGCAAGCTTTTGGGTAAA 59.309 47.619 16.20 0.00 33.49 2.01
903 3103 7.335627 TGAATAACCTGGTCTCATACGATTTT 58.664 34.615 0.00 0.00 0.00 1.82
905 3105 6.098409 ACTGAATAACCTGGTCTCATACGATT 59.902 38.462 0.00 0.00 0.00 3.34
907 3107 4.954202 ACTGAATAACCTGGTCTCATACGA 59.046 41.667 0.00 0.00 0.00 3.43
908 3108 5.263968 ACTGAATAACCTGGTCTCATACG 57.736 43.478 0.00 0.00 0.00 3.06
909 3109 5.282510 CGACTGAATAACCTGGTCTCATAC 58.717 45.833 0.00 1.08 0.00 2.39
910 3110 4.202121 GCGACTGAATAACCTGGTCTCATA 60.202 45.833 0.00 0.00 0.00 2.15
911 3111 3.430929 GCGACTGAATAACCTGGTCTCAT 60.431 47.826 0.00 0.00 0.00 2.90
913 3113 2.094182 TGCGACTGAATAACCTGGTCTC 60.094 50.000 0.00 0.00 0.00 3.36
914 3114 1.899814 TGCGACTGAATAACCTGGTCT 59.100 47.619 0.00 0.00 0.00 3.85
915 3115 2.380084 TGCGACTGAATAACCTGGTC 57.620 50.000 0.00 0.00 0.00 4.02
917 3117 2.009774 CCTTGCGACTGAATAACCTGG 58.990 52.381 0.00 0.00 0.00 4.45
918 3118 2.932614 CTCCTTGCGACTGAATAACCTG 59.067 50.000 0.00 0.00 0.00 4.00
919 3119 2.678190 GCTCCTTGCGACTGAATAACCT 60.678 50.000 0.00 0.00 0.00 3.50
920 3120 1.666189 GCTCCTTGCGACTGAATAACC 59.334 52.381 0.00 0.00 0.00 2.85
932 3132 1.063174 CACTATTTGCTCGCTCCTTGC 59.937 52.381 0.00 0.00 38.57 4.01
937 3137 2.416547 TGCTTTCACTATTTGCTCGCTC 59.583 45.455 0.00 0.00 0.00 5.03
992 3192 3.726558 ATGGTCGTCGGGATCGGGA 62.727 63.158 0.00 0.00 36.95 5.14
1327 3560 0.907486 TGTGGAGGAAGAGCATGAGG 59.093 55.000 0.00 0.00 0.00 3.86
1416 3649 2.623502 GGACAAGGAGGGCAGTAGAGTA 60.624 54.545 0.00 0.00 0.00 2.59
1452 3685 3.243134 GCACTCCTCGTCTGGTTATCTAC 60.243 52.174 0.00 0.00 0.00 2.59
1478 3711 0.746923 GAAATCAGGGGGCGTGTACC 60.747 60.000 0.00 0.00 0.00 3.34
1508 3741 1.260297 TCGCACACATGAACTGAAACG 59.740 47.619 0.00 0.00 0.00 3.60
1554 3798 6.529829 GGCAACATCATAAATCGTTAAGCAAA 59.470 34.615 0.00 0.00 0.00 3.68
1599 3843 9.294030 GTTTTCATGTCCATTTCTTCATGTATC 57.706 33.333 0.00 0.00 38.78 2.24
1622 3866 5.869649 ATTTTTGGGCAACTACTCAGTTT 57.130 34.783 0.00 0.00 42.51 2.66
1643 3887 2.380064 TGTTCTGCAGTTGGGGAAAT 57.620 45.000 14.67 0.00 0.00 2.17
1646 3890 1.619654 CAATGTTCTGCAGTTGGGGA 58.380 50.000 14.67 0.00 0.00 4.81
1656 3900 1.047002 TTTGTGGGGCCAATGTTCTG 58.953 50.000 4.39 0.00 0.00 3.02
1666 3918 4.898861 TCAATAGGGATAATTTTGTGGGGC 59.101 41.667 0.00 0.00 0.00 5.80
1679 3931 8.686739 ACTAGCATAGGTTAATCAATAGGGAT 57.313 34.615 0.00 0.00 44.97 3.85
1722 3974 2.741145 ACCCACAACACTAAAGGCAAA 58.259 42.857 0.00 0.00 0.00 3.68
1741 3993 9.185192 CTGAAACAACTTCTGGAATTCATTAAC 57.815 33.333 7.93 0.00 34.86 2.01
1766 4018 4.012374 CCTCAGTTCATTACCACATTGCT 58.988 43.478 0.00 0.00 0.00 3.91
1824 4083 7.652909 CCACAAAGCTCAAATCAAAGTATCAAA 59.347 33.333 0.00 0.00 0.00 2.69
1825 4084 7.147312 CCACAAAGCTCAAATCAAAGTATCAA 58.853 34.615 0.00 0.00 0.00 2.57
1826 4085 6.294675 CCCACAAAGCTCAAATCAAAGTATCA 60.295 38.462 0.00 0.00 0.00 2.15
1827 4086 6.095377 CCCACAAAGCTCAAATCAAAGTATC 58.905 40.000 0.00 0.00 0.00 2.24
1828 4087 5.539955 ACCCACAAAGCTCAAATCAAAGTAT 59.460 36.000 0.00 0.00 0.00 2.12
1829 4088 4.892934 ACCCACAAAGCTCAAATCAAAGTA 59.107 37.500 0.00 0.00 0.00 2.24
1830 4089 3.706086 ACCCACAAAGCTCAAATCAAAGT 59.294 39.130 0.00 0.00 0.00 2.66
1831 4090 4.326504 ACCCACAAAGCTCAAATCAAAG 57.673 40.909 0.00 0.00 0.00 2.77
1871 4130 2.815503 CAGTTCACCATCACATTGCAGA 59.184 45.455 0.00 0.00 0.00 4.26
1872 4131 2.094906 CCAGTTCACCATCACATTGCAG 60.095 50.000 0.00 0.00 0.00 4.41
1873 4132 1.887854 CCAGTTCACCATCACATTGCA 59.112 47.619 0.00 0.00 0.00 4.08
1874 4133 1.203052 CCCAGTTCACCATCACATTGC 59.797 52.381 0.00 0.00 0.00 3.56
1967 4226 2.306715 TAGCAGCCAGGGACCGGATA 62.307 60.000 9.46 0.00 0.00 2.59
1991 4250 1.202452 TCAGCCACTGCATATCTCGTG 60.202 52.381 0.00 0.00 41.13 4.35
2112 4371 5.376625 AGCAAGACAGAAAATGTTACCAGA 58.623 37.500 0.00 0.00 44.17 3.86
2314 4575 5.013079 AGGACATTAGATGACAAGTGGTGAA 59.987 40.000 0.00 0.00 0.00 3.18
2511 4772 0.603065 AAAAGGAAGATTGGCGTGGC 59.397 50.000 0.00 0.00 0.00 5.01
2516 4777 7.010460 GCATTGTTATACAAAAGGAAGATTGGC 59.990 37.037 0.00 0.00 41.96 4.52
2722 4983 3.504906 CCTCTGTTGACACGAACCTACTA 59.495 47.826 0.00 0.00 0.00 1.82
2759 5020 3.053693 TGGGATGGAGGGAGTACATTTTG 60.054 47.826 0.00 0.00 0.00 2.44
2813 5074 7.394923 TCCGTCCCATAAATGTAAGATGTTTTT 59.605 33.333 0.00 0.00 0.00 1.94
2814 5075 6.887545 TCCGTCCCATAAATGTAAGATGTTTT 59.112 34.615 0.00 0.00 0.00 2.43
2815 5076 6.419791 TCCGTCCCATAAATGTAAGATGTTT 58.580 36.000 0.00 0.00 0.00 2.83
2816 5077 5.996644 TCCGTCCCATAAATGTAAGATGTT 58.003 37.500 0.00 0.00 0.00 2.71
2817 5078 5.454755 CCTCCGTCCCATAAATGTAAGATGT 60.455 44.000 0.00 0.00 0.00 3.06
2818 5079 4.997395 CCTCCGTCCCATAAATGTAAGATG 59.003 45.833 0.00 0.00 0.00 2.90
2819 5080 4.041691 CCCTCCGTCCCATAAATGTAAGAT 59.958 45.833 0.00 0.00 0.00 2.40
2820 5081 3.389983 CCCTCCGTCCCATAAATGTAAGA 59.610 47.826 0.00 0.00 0.00 2.10
2821 5082 3.389983 TCCCTCCGTCCCATAAATGTAAG 59.610 47.826 0.00 0.00 0.00 2.34
2822 5083 3.386063 TCCCTCCGTCCCATAAATGTAA 58.614 45.455 0.00 0.00 0.00 2.41
2823 5084 2.969950 CTCCCTCCGTCCCATAAATGTA 59.030 50.000 0.00 0.00 0.00 2.29
2824 5085 1.768870 CTCCCTCCGTCCCATAAATGT 59.231 52.381 0.00 0.00 0.00 2.71
2825 5086 1.768870 ACTCCCTCCGTCCCATAAATG 59.231 52.381 0.00 0.00 0.00 2.32
2826 5087 2.191981 ACTCCCTCCGTCCCATAAAT 57.808 50.000 0.00 0.00 0.00 1.40
2827 5088 2.292389 TGTACTCCCTCCGTCCCATAAA 60.292 50.000 0.00 0.00 0.00 1.40
2840 5101 5.143376 TGTACTGCTAAACTTGTACTCCC 57.857 43.478 0.00 0.00 36.98 4.30
2855 5116 7.704899 ACCAAAAACAGTTTAGAATTGTACTGC 59.295 33.333 0.00 0.00 41.22 4.40
2858 5119 8.192110 TCCACCAAAAACAGTTTAGAATTGTAC 58.808 33.333 0.00 0.00 0.00 2.90
2912 5173 3.951037 TGCAGTAAGCCTTCTGACAAAAA 59.049 39.130 7.73 0.00 44.83 1.94
2913 5174 3.550820 TGCAGTAAGCCTTCTGACAAAA 58.449 40.909 7.73 0.00 44.83 2.44
2919 5180 2.935201 GTGAGATGCAGTAAGCCTTCTG 59.065 50.000 0.00 0.00 44.83 3.02
2958 5221 5.417580 GGCCATTCCAGTTTAGAATTGTACA 59.582 40.000 0.00 0.00 31.56 2.90
2983 5246 4.322725 CCTTCTGTGCACATCAACCTACTA 60.323 45.833 22.00 0.00 0.00 1.82
3022 5285 8.441608 CAGTACTGTACTATATACGACACATCC 58.558 40.741 19.32 0.00 37.23 3.51
3031 5294 9.234384 CACACAAAGCAGTACTGTACTATATAC 57.766 37.037 23.44 7.79 37.23 1.47
3060 5323 5.163933 GCAATCCACAAATAACAACAGCATG 60.164 40.000 0.00 0.00 46.00 4.06
3061 5324 4.931002 GCAATCCACAAATAACAACAGCAT 59.069 37.500 0.00 0.00 0.00 3.79
3104 5367 5.209659 AGTACCTGGAATAATCGGTTCTCT 58.790 41.667 0.00 0.00 0.00 3.10
3111 5374 7.309177 CAGTAGATGAGTACCTGGAATAATCG 58.691 42.308 0.00 0.00 0.00 3.34
3179 5442 5.491982 ACTATGTCCATGGTGAAGTTCTTC 58.508 41.667 12.58 5.70 31.01 2.87
3255 5518 1.675310 CAAGGGCATCAACCAGCGA 60.675 57.895 0.00 0.00 0.00 4.93
3398 5661 5.452078 TCTTAACAACTTGCTTGGGAATG 57.548 39.130 0.00 0.00 33.66 2.67
3401 5664 5.923733 TTTTCTTAACAACTTGCTTGGGA 57.076 34.783 0.00 0.00 33.66 4.37
3483 5746 2.233922 ACCATTGAACTAGGGTGACTCG 59.766 50.000 0.00 0.00 31.04 4.18
3552 5816 3.728845 TCTCCACAGCAGTAAAAGTGTC 58.271 45.455 0.00 0.00 0.00 3.67
3619 5883 5.704515 AGGTAGATTGCAGTGATTGATATGC 59.295 40.000 0.00 0.00 39.14 3.14
3627 5891 7.831193 AGAAAATACAAGGTAGATTGCAGTGAT 59.169 33.333 0.00 0.00 33.28 3.06
3651 5915 2.640989 CCGTTCACGACACCGAGA 59.359 61.111 0.00 0.00 43.02 4.04
3653 5917 3.218470 ACCCGTTCACGACACCGA 61.218 61.111 0.00 0.00 43.02 4.69
3667 5966 3.318275 TGCTAGTATCAGATTCGTCACCC 59.682 47.826 0.00 0.00 0.00 4.61
3696 5995 0.878416 GCACAATACAGAAACCGGCA 59.122 50.000 0.00 0.00 0.00 5.69
3699 5998 2.095768 CCACTGCACAATACAGAAACCG 60.096 50.000 0.00 0.00 38.55 4.44
3718 6017 7.572523 CATTTCTCTATGCAAAAGATACCCA 57.427 36.000 0.00 0.00 0.00 4.51
3743 6042 4.630644 ATCTACCTAACCAGATGCATGG 57.369 45.455 2.46 3.82 46.47 3.66
3766 6065 8.426569 ACAGGTTAAACTCATGTAAGGTACTA 57.573 34.615 0.00 0.00 38.49 1.82
3841 6140 9.559958 AACGATGAATTTGAGATTTATGTGAAC 57.440 29.630 0.00 0.00 0.00 3.18
3848 6147 6.624861 GCCCACAACGATGAATTTGAGATTTA 60.625 38.462 0.00 0.00 0.00 1.40
3872 6172 2.794350 CCTTTTTGGTCACAAATGTCGC 59.206 45.455 0.00 0.00 45.31 5.19
3991 6291 4.323868 GCCAGAGACAGGAAAAGGAAGTAT 60.324 45.833 0.00 0.00 0.00 2.12
4028 6328 1.003545 CCGGCAACATTAGCTCGAATG 60.004 52.381 7.53 7.53 41.69 2.67
4029 6329 1.299541 CCGGCAACATTAGCTCGAAT 58.700 50.000 0.00 0.00 0.00 3.34
4052 6352 1.207089 GTGATCATCTTGTCGGGACCA 59.793 52.381 0.00 0.00 0.00 4.02
4069 6369 2.758852 AAACCGGCTAGGAGGGGTGA 62.759 60.000 0.00 0.00 45.00 4.02
4105 6405 3.427528 TGCTCTTCATAAACGACGTCAAC 59.572 43.478 17.16 0.00 0.00 3.18
4113 6413 1.667724 CCCTGCTGCTCTTCATAAACG 59.332 52.381 0.00 0.00 0.00 3.60
4120 6420 1.823041 GGATGCCCTGCTGCTCTTC 60.823 63.158 0.00 0.00 0.00 2.87
4288 6600 1.002430 GTGCAGTCTGATGGAGGACAA 59.998 52.381 3.32 0.00 35.18 3.18
4340 6675 3.989705 TTACATCATGCACGTTCTTCG 57.010 42.857 0.00 0.00 46.00 3.79
4350 6685 4.661125 TGTTCTTTCGCATTACATCATGC 58.339 39.130 0.00 0.00 45.34 4.06
4351 6686 7.022979 TCTTTGTTCTTTCGCATTACATCATG 58.977 34.615 0.00 0.00 0.00 3.07
4352 6687 7.144722 TCTTTGTTCTTTCGCATTACATCAT 57.855 32.000 0.00 0.00 0.00 2.45
4353 6688 6.552859 TCTTTGTTCTTTCGCATTACATCA 57.447 33.333 0.00 0.00 0.00 3.07
4354 6689 7.059945 CACTTCTTTGTTCTTTCGCATTACATC 59.940 37.037 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.