Multiple sequence alignment - TraesCS5A01G210100

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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 TraesCS5A01G210100 chr5A 100.000 5495 0 0 1 5495 423255930 423250436 0.000000e+00 10148
1 TraesCS5A01G210100 chr5D 86.401 3243 237 86 1 3124 325097156 325093999 0.000000e+00 3358
2 TraesCS5A01G210100 chr5D 94.011 1269 73 3 4143 5409 325092899 325091632 0.000000e+00 1919
3 TraesCS5A01G210100 chr5D 90.653 674 52 4 3428 4100 325093568 325092905 0.000000e+00 885
4 TraesCS5A01G210100 chr5B 90.342 2630 138 56 554 3125 377546467 377543896 0.000000e+00 3343
5 TraesCS5A01G210100 chr5B 92.700 2000 108 14 3125 5115 377543739 377541769 0.000000e+00 2850
6 TraesCS5A01G210100 chr5B 81.867 375 47 11 174 541 377550042 377549682 4.160000e-76 296
7 TraesCS5A01G210100 chr5B 90.395 177 16 1 1 177 377551029 377550854 1.190000e-56 231


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 TraesCS5A01G210100 chr5A 423250436 423255930 5494 True 10148 10148 100.000 1 5495 1 chr5A.!!$R1 5494
1 TraesCS5A01G210100 chr5D 325091632 325097156 5524 True 2054 3358 90.355 1 5409 3 chr5D.!!$R1 5408
2 TraesCS5A01G210100 chr5B 377541769 377551029 9260 True 1680 3343 88.826 1 5115 4 chr5B.!!$R1 5114

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
218 1033 0.179045 ATGATCTTTCCTTCCGCCCG 60.179 55.0 0.00 0.0 0.00 6.13 F
1270 5356 0.109039 GTTGACTCTCCGTCTGCTCC 60.109 60.0 0.00 0.0 43.25 4.70 F
1668 5771 0.455005 CTCCCGGAGACCGTAAGTTC 59.545 60.0 9.01 0.0 46.80 3.01 F
1671 5774 0.604578 CCGGAGACCGTAAGTTCCAA 59.395 55.0 0.00 0.0 46.80 3.53 F
1956 6068 0.647410 CTGGTCGCTGTATTTGCTCG 59.353 55.0 0.00 0.0 0.00 5.03 F
3861 8248 0.174617 GGAAGAGGAACCTCGCTCTG 59.825 60.0 14.13 0.0 46.90 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 6324 0.320421 AGCGTCAACGGCTACAACAT 60.320 50.000 4.54 0.0 40.23 2.71 R
3106 7270 0.530744 TCTCCACTGGTGCATACGTC 59.469 55.000 0.00 0.0 0.00 4.34 R
3660 8047 5.107109 TGCATCCGAAATTATTGAATCCG 57.893 39.130 0.00 0.0 0.00 4.18 R
3738 8125 1.302907 AAGGGTAGGACTCCTCGGTA 58.697 55.000 0.00 0.0 34.61 4.02 R
4007 8394 2.158871 TCTTGTACTGCCTGAAACCGTT 60.159 45.455 0.00 0.0 0.00 4.44 R
5277 9674 0.029300 CAACAACAGAGGCAACGTGG 59.971 55.000 0.00 0.0 46.39 4.94 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
33 34 4.475944 CCGACAAAACACAAGAATCCATC 58.524 43.478 0.00 0.00 0.00 3.51
39 40 5.443185 AAACACAAGAATCCATCACAGTG 57.557 39.130 0.00 0.00 34.50 3.66
86 87 4.280174 ACTTTGCTGATGTTTCATGCTCTT 59.720 37.500 0.00 0.00 31.41 2.85
88 89 2.094906 TGCTGATGTTTCATGCTCTTGC 60.095 45.455 0.00 0.00 40.20 4.01
106 107 6.020360 GCTCTTGCGATTTTCCATGTTAATTC 60.020 38.462 0.00 0.00 0.00 2.17
111 112 4.499040 CGATTTTCCATGTTAATTCGGTGC 59.501 41.667 10.83 0.00 0.00 5.01
120 121 4.331968 TGTTAATTCGGTGCTCAAGGAAT 58.668 39.130 0.00 0.00 0.00 3.01
126 127 3.270027 TCGGTGCTCAAGGAATGTTATG 58.730 45.455 0.00 0.00 0.00 1.90
215 1030 4.876107 TCAAGTAATGATCTTTCCTTCCGC 59.124 41.667 0.00 0.00 31.50 5.54
216 1031 3.809905 AGTAATGATCTTTCCTTCCGCC 58.190 45.455 0.00 0.00 0.00 6.13
217 1032 2.058593 AATGATCTTTCCTTCCGCCC 57.941 50.000 0.00 0.00 0.00 6.13
218 1033 0.179045 ATGATCTTTCCTTCCGCCCG 60.179 55.000 0.00 0.00 0.00 6.13
255 1070 1.757118 CTAGGGCGAAGAACTCATCCA 59.243 52.381 0.00 0.00 0.00 3.41
338 1157 1.090052 GGGAGAGAAAATCCGGTGCG 61.090 60.000 0.00 0.00 37.75 5.34
387 1227 9.415544 GTTAGAATTTTTGTAGTCTTCGTAGGA 57.584 33.333 0.00 0.00 0.00 2.94
394 1234 2.181954 AGTCTTCGTAGGAGTGACGT 57.818 50.000 11.99 0.00 41.11 4.34
461 1301 6.092807 GGCTTTGATATTTCTCGACTTTGTCT 59.907 38.462 0.00 0.00 0.00 3.41
475 1315 4.461784 GTCTGTCGAGACGAAGCC 57.538 61.111 0.00 0.00 39.44 4.35
492 1332 1.952102 GCCCGGACGTAGATCCAACA 61.952 60.000 0.73 0.00 38.87 3.33
509 1351 2.533266 ACAGTTGCGAGATCTTGTGT 57.467 45.000 11.71 5.11 0.00 3.72
513 1355 2.802816 AGTTGCGAGATCTTGTGTCAAC 59.197 45.455 17.68 17.68 34.31 3.18
514 1356 2.524569 TGCGAGATCTTGTGTCAACA 57.475 45.000 11.71 0.00 0.00 3.33
528 1370 3.305629 GTGTCAACAGCTTCAGATCGATC 59.694 47.826 17.91 17.91 0.00 3.69
543 4587 3.868757 TCGATCCAAGAGTTCAACGAT 57.131 42.857 0.00 0.00 0.00 3.73
549 4593 2.609491 CCAAGAGTTCAACGATGACGGA 60.609 50.000 0.00 0.00 44.46 4.69
552 4596 1.324736 GAGTTCAACGATGACGGATGC 59.675 52.381 0.00 0.00 44.46 3.91
583 4627 2.060980 AGGCTGCCGGTTCCTAGAG 61.061 63.158 13.96 0.00 0.00 2.43
591 4635 1.162698 CGGTTCCTAGAGACACGTGA 58.837 55.000 25.01 0.00 0.00 4.35
635 4680 1.418637 ACAAAGTTAGACCGGCTCCAA 59.581 47.619 0.00 0.00 0.00 3.53
657 4702 6.018098 CCAATAGAAGAGCAGTGACAATGATC 60.018 42.308 12.94 12.94 33.29 2.92
661 4706 5.585445 AGAAGAGCAGTGACAATGATCATTC 59.415 40.000 21.59 19.21 35.55 2.67
711 4777 9.629878 TTTTATTACCAGTGAACTTTTGTAGGA 57.370 29.630 0.00 0.00 0.00 2.94
712 4778 8.842358 TTATTACCAGTGAACTTTTGTAGGAG 57.158 34.615 0.00 0.00 0.00 3.69
766 4834 1.139989 CGATGTTATCGCGCTGGATT 58.860 50.000 5.56 0.00 46.55 3.01
809 4880 7.496747 AGACAAAGAATAATCCTCACTAGAGC 58.503 38.462 0.00 0.00 40.68 4.09
810 4881 7.124901 AGACAAAGAATAATCCTCACTAGAGCA 59.875 37.037 0.00 0.00 40.68 4.26
811 4882 7.271511 ACAAAGAATAATCCTCACTAGAGCAG 58.728 38.462 0.00 0.00 40.68 4.24
812 4883 7.093112 ACAAAGAATAATCCTCACTAGAGCAGT 60.093 37.037 0.00 0.00 40.68 4.40
813 4884 8.417106 CAAAGAATAATCCTCACTAGAGCAGTA 58.583 37.037 0.00 0.00 40.68 2.74
814 4885 7.759489 AGAATAATCCTCACTAGAGCAGTAG 57.241 40.000 0.00 0.00 40.68 2.57
818 4889 1.953686 CCTCACTAGAGCAGTAGGAGC 59.046 57.143 0.00 0.00 40.68 4.70
862 4948 7.590322 GCAGATCACAAATATCTACAGCATTTG 59.410 37.037 0.00 11.48 42.61 2.32
893 4979 2.972505 AAGTGGTCAAGCGTGCCG 60.973 61.111 0.00 0.00 0.00 5.69
1076 5162 3.213402 CGTCGCCTCCTCCTCCTC 61.213 72.222 0.00 0.00 0.00 3.71
1077 5163 2.835895 GTCGCCTCCTCCTCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
1078 5164 3.024356 TCGCCTCCTCCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
1079 5165 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1080 5166 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1081 5167 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1082 5168 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1083 5169 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1084 5170 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1085 5171 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1086 5172 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1087 5173 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1094 5180 2.756283 CTCCTCCTCCTTCGCCGT 60.756 66.667 0.00 0.00 0.00 5.68
1220 5306 2.341101 CCGTCAGGTCCGTGCTACT 61.341 63.158 0.00 0.00 0.00 2.57
1221 5307 1.154016 CGTCAGGTCCGTGCTACTG 60.154 63.158 0.00 0.00 0.00 2.74
1222 5308 1.446272 GTCAGGTCCGTGCTACTGC 60.446 63.158 0.00 0.00 40.20 4.40
1223 5309 1.606601 TCAGGTCCGTGCTACTGCT 60.607 57.895 0.00 0.00 40.48 4.24
1224 5310 0.323087 TCAGGTCCGTGCTACTGCTA 60.323 55.000 0.00 0.00 40.48 3.49
1229 5315 1.153628 CCGTGCTACTGCTACCCAC 60.154 63.158 0.00 0.00 40.48 4.61
1233 5319 1.320344 TGCTACTGCTACCCACTCCG 61.320 60.000 0.00 0.00 40.48 4.63
1234 5320 1.437986 CTACTGCTACCCACTCCGC 59.562 63.158 0.00 0.00 0.00 5.54
1235 5321 1.304630 TACTGCTACCCACTCCGCA 60.305 57.895 0.00 0.00 0.00 5.69
1236 5322 0.901114 TACTGCTACCCACTCCGCAA 60.901 55.000 0.00 0.00 31.24 4.85
1237 5323 1.221840 CTGCTACCCACTCCGCAAT 59.778 57.895 0.00 0.00 31.24 3.56
1238 5324 0.811616 CTGCTACCCACTCCGCAATC 60.812 60.000 0.00 0.00 31.24 2.67
1239 5325 1.523938 GCTACCCACTCCGCAATCC 60.524 63.158 0.00 0.00 0.00 3.01
1240 5326 1.146263 CTACCCACTCCGCAATCCC 59.854 63.158 0.00 0.00 0.00 3.85
1241 5327 2.325393 CTACCCACTCCGCAATCCCC 62.325 65.000 0.00 0.00 0.00 4.81
1242 5328 4.506255 CCCACTCCGCAATCCCCC 62.506 72.222 0.00 0.00 0.00 5.40
1243 5329 4.856801 CCACTCCGCAATCCCCCG 62.857 72.222 0.00 0.00 0.00 5.73
1270 5356 0.109039 GTTGACTCTCCGTCTGCTCC 60.109 60.000 0.00 0.00 43.25 4.70
1273 5359 4.200283 CTCTCCGTCTGCTCCGCC 62.200 72.222 0.00 0.00 0.00 6.13
1303 5406 2.349755 CCCGTTGACATCCCGGTT 59.650 61.111 0.00 0.00 40.10 4.44
1307 5410 1.296056 CGTTGACATCCCGGTTGGTC 61.296 60.000 0.00 5.14 34.77 4.02
1322 5425 1.877165 GGTCCGTTCGATCCGCTTC 60.877 63.158 0.00 0.00 0.00 3.86
1458 5561 3.661745 GGCATCAACCGTACGATCT 57.338 52.632 18.76 0.00 0.00 2.75
1479 5582 1.827399 CGACCATCCCCTAATCCCCG 61.827 65.000 0.00 0.00 0.00 5.73
1530 5633 2.202096 CGCTCGTCGCTTTTGCTG 60.202 61.111 0.00 0.00 44.80 4.41
1531 5634 2.939022 GCTCGTCGCTTTTGCTGT 59.061 55.556 0.00 0.00 44.80 4.40
1532 5635 1.154580 GCTCGTCGCTTTTGCTGTC 60.155 57.895 0.00 0.00 44.80 3.51
1668 5771 0.455005 CTCCCGGAGACCGTAAGTTC 59.545 60.000 9.01 0.00 46.80 3.01
1671 5774 0.604578 CCGGAGACCGTAAGTTCCAA 59.395 55.000 0.00 0.00 46.80 3.53
1672 5775 1.206371 CCGGAGACCGTAAGTTCCAAT 59.794 52.381 0.00 0.00 46.80 3.16
1678 5781 5.122869 GGAGACCGTAAGTTCCAATTTTACC 59.877 44.000 0.00 0.00 0.00 2.85
1682 5785 5.049474 ACCGTAAGTTCCAATTTTACCGTTC 60.049 40.000 0.00 0.00 0.00 3.95
1691 5794 6.289834 TCCAATTTTACCGTTCACTTACTCA 58.710 36.000 0.00 0.00 0.00 3.41
1695 5798 8.450964 CAATTTTACCGTTCACTTACTCATCAT 58.549 33.333 0.00 0.00 0.00 2.45
1696 5799 7.591006 TTTTACCGTTCACTTACTCATCATC 57.409 36.000 0.00 0.00 0.00 2.92
1697 5800 4.801330 ACCGTTCACTTACTCATCATCA 57.199 40.909 0.00 0.00 0.00 3.07
1698 5801 4.495422 ACCGTTCACTTACTCATCATCAC 58.505 43.478 0.00 0.00 0.00 3.06
1700 5803 4.564372 CCGTTCACTTACTCATCATCACAG 59.436 45.833 0.00 0.00 0.00 3.66
1703 5809 5.588958 TCACTTACTCATCATCACAGGAG 57.411 43.478 0.00 0.00 0.00 3.69
1719 5825 1.704070 AGGAGATCCCATCAAGGCATC 59.296 52.381 0.00 0.00 37.41 3.91
1720 5826 1.422781 GGAGATCCCATCAAGGCATCA 59.577 52.381 0.00 0.00 35.39 3.07
1721 5827 2.158564 GGAGATCCCATCAAGGCATCAA 60.159 50.000 0.00 0.00 35.39 2.57
1726 5834 4.090761 TCCCATCAAGGCATCAAGTATC 57.909 45.455 0.00 0.00 35.39 2.24
1731 5839 5.008415 CCATCAAGGCATCAAGTATCAACTC 59.992 44.000 0.00 0.00 33.75 3.01
1759 5867 1.599667 CGTAGCTGCGTACCCTGTATG 60.600 57.143 16.66 0.00 0.00 2.39
1760 5868 1.407979 GTAGCTGCGTACCCTGTATGT 59.592 52.381 0.00 0.00 0.00 2.29
1761 5869 1.771565 AGCTGCGTACCCTGTATGTA 58.228 50.000 0.00 0.00 0.00 2.29
1762 5870 2.317040 AGCTGCGTACCCTGTATGTAT 58.683 47.619 0.00 0.00 0.00 2.29
1764 5872 2.800544 GCTGCGTACCCTGTATGTATTG 59.199 50.000 0.00 0.00 0.00 1.90
1765 5873 2.800544 CTGCGTACCCTGTATGTATTGC 59.199 50.000 0.00 0.00 0.00 3.56
1766 5874 2.168728 TGCGTACCCTGTATGTATTGCA 59.831 45.455 0.00 0.00 33.14 4.08
1767 5875 3.199677 GCGTACCCTGTATGTATTGCAA 58.800 45.455 0.00 0.00 0.00 4.08
1789 5897 2.724977 TCAGTAACGGTTGCTGAGAG 57.275 50.000 29.71 11.48 45.48 3.20
1811 5920 3.782443 CAGGGCCCCGTGGTCTAC 61.782 72.222 21.43 0.00 36.12 2.59
1874 5986 7.404671 AAAATCCACCTTATCTAATTTGCGT 57.595 32.000 0.00 0.00 0.00 5.24
1875 5987 7.404671 AAATCCACCTTATCTAATTTGCGTT 57.595 32.000 0.00 0.00 0.00 4.84
1876 5988 7.404671 AATCCACCTTATCTAATTTGCGTTT 57.595 32.000 0.00 0.00 0.00 3.60
1877 5989 6.431198 TCCACCTTATCTAATTTGCGTTTC 57.569 37.500 0.00 0.00 0.00 2.78
1878 5990 5.941058 TCCACCTTATCTAATTTGCGTTTCA 59.059 36.000 0.00 0.00 0.00 2.69
1879 5991 6.431543 TCCACCTTATCTAATTTGCGTTTCAA 59.568 34.615 0.00 0.00 0.00 2.69
1880 5992 6.526674 CCACCTTATCTAATTTGCGTTTCAAC 59.473 38.462 0.00 0.00 33.73 3.18
1956 6068 0.647410 CTGGTCGCTGTATTTGCTCG 59.353 55.000 0.00 0.00 0.00 5.03
2132 6247 3.531538 TGATCGCCTGTTTGTAAGGATC 58.468 45.455 0.00 0.00 36.91 3.36
2135 6250 1.448985 GCCTGTTTGTAAGGATCGCA 58.551 50.000 0.00 0.00 36.91 5.10
2144 6259 4.071961 TGTAAGGATCGCAGCACAATAT 57.928 40.909 0.00 0.00 0.00 1.28
2194 6309 7.609760 TGGTTGTGCTAATTAAGACTGTATG 57.390 36.000 0.00 0.00 0.00 2.39
2209 6324 8.885693 AAGACTGTATGGCATAGACTATATCA 57.114 34.615 7.61 0.00 0.00 2.15
2257 6372 2.401583 AGTATTGTGCCGCTTGATCA 57.598 45.000 0.00 0.00 0.00 2.92
2628 6770 1.303643 GGGCCACAGACCAAAGAGG 60.304 63.158 4.39 0.00 45.67 3.69
2819 6979 7.194607 TGAGATCTTTTTCATCAGACACAAC 57.805 36.000 0.00 0.00 0.00 3.32
2864 7024 9.369904 GTTCAACAATGGATTAAAATACTGCAT 57.630 29.630 0.00 0.00 0.00 3.96
2968 7132 2.498644 TCAGTTGGTGTTTGGTGACA 57.501 45.000 0.00 0.00 39.83 3.58
2993 7157 1.340017 GCTATCTTGTGGGGCTTGTCA 60.340 52.381 0.00 0.00 0.00 3.58
3106 7270 8.723942 AGTTATAGTTCCAAATGAAGCTAGTG 57.276 34.615 0.00 0.00 32.37 2.74
3129 7496 2.224137 CGTATGCACCAGTGGAGATCAT 60.224 50.000 18.40 14.34 33.50 2.45
3243 7626 4.441913 GGGATTGGGTGTGATTTAAGCATG 60.442 45.833 0.00 0.00 0.00 4.06
3357 7743 9.250624 CCTAGCTACAAGTAAAATGACAGATAC 57.749 37.037 0.00 0.00 0.00 2.24
3361 7747 7.043325 GCTACAAGTAAAATGACAGATACCGAG 60.043 40.741 0.00 0.00 0.00 4.63
3486 7873 9.770097 TTATCAATCGAGAAGATAGCTCATTTT 57.230 29.630 0.00 0.00 38.98 1.82
3660 8047 3.357079 CTGGTTGACTGTGCCGGC 61.357 66.667 22.73 22.73 0.00 6.13
3738 8125 5.567037 TCAAATACAATGGAGGGATCGAT 57.433 39.130 0.00 0.00 0.00 3.59
3822 8209 3.244112 CCGTAGTTCAGGTTTTGGACTCT 60.244 47.826 0.00 0.00 42.20 3.24
3861 8248 0.174617 GGAAGAGGAACCTCGCTCTG 59.825 60.000 14.13 0.00 46.90 3.35
4007 8394 2.158623 AGTGTTGCCTTTGAGGTGATCA 60.159 45.455 0.00 0.00 37.80 2.92
4041 8428 3.921021 CAGTACAAGAGCGGAGTTTACAG 59.079 47.826 0.00 0.00 0.00 2.74
4054 8441 3.000727 AGTTTACAGTAGCGACCATTGC 58.999 45.455 0.00 0.00 0.00 3.56
4167 8554 4.979197 GTGCTTCCTATCTCTTGTATCACG 59.021 45.833 0.00 0.00 0.00 4.35
4185 8572 8.396390 TGTATCACGACACTCTTCTACTATTTC 58.604 37.037 0.00 0.00 0.00 2.17
4412 8799 1.858041 CTCTTCATGCCATAGCGCG 59.142 57.895 0.00 0.00 44.31 6.86
4416 8803 2.921692 TTCATGCCATAGCGCGCTCA 62.922 55.000 40.23 29.16 44.31 4.26
4418 8805 1.015607 CATGCCATAGCGCGCTCATA 61.016 55.000 40.23 22.30 44.31 2.15
4485 8873 1.076850 TGCGTCCTACCCCATCGTA 60.077 57.895 0.00 0.00 0.00 3.43
4513 8904 0.949105 AAGCGCCAAATCGACGAGTT 60.949 50.000 2.29 4.45 0.00 3.01
4541 8933 4.871513 TCGCTTCGCTAGACATGAATAAT 58.128 39.130 0.00 0.00 0.00 1.28
4789 9184 2.501723 ACCGAGGCATCATCTTACTGTT 59.498 45.455 0.00 0.00 0.00 3.16
4794 9189 5.403766 CGAGGCATCATCTTACTGTTGATAC 59.596 44.000 0.00 0.00 34.39 2.24
4809 9204 5.252547 TGTTGATACTAGCAGGAAATTGCA 58.747 37.500 0.52 0.00 46.47 4.08
4830 9225 2.454538 TGCCACACATGAATATTGCCA 58.545 42.857 0.00 0.00 0.00 4.92
4842 9237 8.614814 ACATGAATATTGCCATATACTTAGGGT 58.385 33.333 0.00 0.00 31.71 4.34
5048 9444 6.189859 TCTCCAATCCTATGAAGCAAATGTT 58.810 36.000 0.00 0.00 0.00 2.71
5062 9458 6.152932 AGCAAATGTTATGCATAGGGAAAG 57.847 37.500 6.50 0.00 46.22 2.62
5077 9474 5.443230 AGGGAAAGAAATGAGGGTAAGAG 57.557 43.478 0.00 0.00 0.00 2.85
5079 9476 5.313506 AGGGAAAGAAATGAGGGTAAGAGTT 59.686 40.000 0.00 0.00 0.00 3.01
5135 9532 1.324736 CATTAACTCAAGCGCGACTCC 59.675 52.381 12.10 0.00 0.00 3.85
5145 9542 0.172803 GCGCGACTCCCTCTTCTTTA 59.827 55.000 12.10 0.00 0.00 1.85
5152 9549 5.404096 CGACTCCCTCTTCTTTACTTCTTC 58.596 45.833 0.00 0.00 0.00 2.87
5179 9576 1.271102 GCGTGAGTCTCTTCTTGGTCT 59.729 52.381 0.65 0.00 0.00 3.85
5184 9581 4.747605 GTGAGTCTCTTCTTGGTCTTGAAC 59.252 45.833 0.65 0.00 0.00 3.18
5208 9605 1.685355 GCTGGCTTCTCCCCTCTCTC 61.685 65.000 0.00 0.00 0.00 3.20
5214 9611 1.000496 TTCTCCCCTCTCTCCTTCGA 59.000 55.000 0.00 0.00 0.00 3.71
5215 9612 0.256464 TCTCCCCTCTCTCCTTCGAC 59.744 60.000 0.00 0.00 0.00 4.20
5251 9648 5.755375 GTGCTTGCTATTGTAGATAAGCTCA 59.245 40.000 18.42 5.74 42.68 4.26
5277 9674 7.074502 CGCTAGAGCTCCAAATGAAAATTATC 58.925 38.462 10.93 0.00 39.32 1.75
5280 9677 7.105241 AGAGCTCCAAATGAAAATTATCCAC 57.895 36.000 10.93 0.00 0.00 4.02
5289 9686 4.331968 TGAAAATTATCCACGTTGCCTCT 58.668 39.130 0.00 0.00 0.00 3.69
5298 9695 1.101049 ACGTTGCCTCTGTTGTTGGG 61.101 55.000 0.00 0.00 0.00 4.12
5331 9728 4.034285 AGTCAAATCAAGATTTCCCCGT 57.966 40.909 5.11 0.00 38.84 5.28
5354 9751 2.410730 GCATCATGTTTCAACAAGCTGC 59.589 45.455 7.68 7.68 40.74 5.25
5364 9761 3.013219 TCAACAAGCTGCAAGTGTGTAA 58.987 40.909 1.02 0.00 32.96 2.41
5389 9786 2.546368 TGTTTGTTGTGTATCCACGAGC 59.454 45.455 0.00 0.00 44.92 5.03
5399 9796 1.361668 ATCCACGAGCGACATGTTGC 61.362 55.000 27.71 27.71 40.27 4.17
5409 9806 5.060816 CGAGCGACATGTTGCAAATATTTTT 59.939 36.000 34.07 14.50 42.40 1.94
5410 9807 6.155691 AGCGACATGTTGCAAATATTTTTG 57.844 33.333 34.07 4.44 44.18 2.44
5411 9808 5.695816 AGCGACATGTTGCAAATATTTTTGT 59.304 32.000 34.07 10.93 43.43 2.83
5412 9809 6.202570 AGCGACATGTTGCAAATATTTTTGTT 59.797 30.769 34.07 10.74 43.43 2.83
5413 9810 7.383572 AGCGACATGTTGCAAATATTTTTGTTA 59.616 29.630 34.07 0.00 43.43 2.41
5414 9811 7.683676 GCGACATGTTGCAAATATTTTTGTTAG 59.316 33.333 29.49 0.00 43.43 2.34
5415 9812 8.910666 CGACATGTTGCAAATATTTTTGTTAGA 58.089 29.630 0.00 0.00 43.43 2.10
5417 9814 9.762933 ACATGTTGCAAATATTTTTGTTAGAGT 57.237 25.926 0.00 1.44 43.43 3.24
5444 9841 5.858475 ACGAAAGTAAAGCGAGATTGAATG 58.142 37.500 0.00 0.00 46.88 2.67
5445 9842 5.408604 ACGAAAGTAAAGCGAGATTGAATGT 59.591 36.000 0.00 0.00 46.88 2.71
5446 9843 5.729883 CGAAAGTAAAGCGAGATTGAATGTG 59.270 40.000 0.00 0.00 0.00 3.21
5447 9844 6.401047 CGAAAGTAAAGCGAGATTGAATGTGA 60.401 38.462 0.00 0.00 0.00 3.58
5448 9845 6.801539 AAGTAAAGCGAGATTGAATGTGAA 57.198 33.333 0.00 0.00 0.00 3.18
5449 9846 6.992063 AGTAAAGCGAGATTGAATGTGAAT 57.008 33.333 0.00 0.00 0.00 2.57
5450 9847 6.779117 AGTAAAGCGAGATTGAATGTGAATG 58.221 36.000 0.00 0.00 0.00 2.67
5451 9848 4.627611 AAGCGAGATTGAATGTGAATGG 57.372 40.909 0.00 0.00 0.00 3.16
5452 9849 3.877559 AGCGAGATTGAATGTGAATGGA 58.122 40.909 0.00 0.00 0.00 3.41
5453 9850 3.624861 AGCGAGATTGAATGTGAATGGAC 59.375 43.478 0.00 0.00 0.00 4.02
5454 9851 3.242870 GCGAGATTGAATGTGAATGGACC 60.243 47.826 0.00 0.00 0.00 4.46
5455 9852 3.940852 CGAGATTGAATGTGAATGGACCA 59.059 43.478 0.00 0.00 0.00 4.02
5456 9853 4.577693 CGAGATTGAATGTGAATGGACCAT 59.422 41.667 0.00 0.00 0.00 3.55
5457 9854 5.066893 CGAGATTGAATGTGAATGGACCATT 59.933 40.000 19.92 19.92 36.72 3.16
5458 9855 6.260714 CGAGATTGAATGTGAATGGACCATTA 59.739 38.462 19.84 5.14 33.90 1.90
5459 9856 7.519488 CGAGATTGAATGTGAATGGACCATTAG 60.519 40.741 19.84 0.00 33.90 1.73
5460 9857 7.121382 AGATTGAATGTGAATGGACCATTAGT 58.879 34.615 19.84 3.87 33.90 2.24
5461 9858 6.757897 TTGAATGTGAATGGACCATTAGTC 57.242 37.500 19.84 13.25 45.51 2.59
5471 9868 3.329929 GACCATTAGTCCTCGTGGTTT 57.670 47.619 2.99 0.00 44.56 3.27
5472 9869 3.671716 GACCATTAGTCCTCGTGGTTTT 58.328 45.455 2.99 0.00 44.56 2.43
5473 9870 3.408634 ACCATTAGTCCTCGTGGTTTTG 58.591 45.455 2.99 0.00 42.03 2.44
5474 9871 3.071892 ACCATTAGTCCTCGTGGTTTTGA 59.928 43.478 2.99 0.00 42.03 2.69
5475 9872 3.435671 CCATTAGTCCTCGTGGTTTTGAC 59.564 47.826 2.99 0.00 34.23 3.18
5476 9873 4.315803 CATTAGTCCTCGTGGTTTTGACT 58.684 43.478 2.99 1.94 39.47 3.41
5477 9874 2.528041 AGTCCTCGTGGTTTTGACTC 57.472 50.000 2.99 0.00 30.81 3.36
5478 9875 1.137513 GTCCTCGTGGTTTTGACTCG 58.862 55.000 2.99 0.00 34.23 4.18
5479 9876 0.599204 TCCTCGTGGTTTTGACTCGC 60.599 55.000 2.99 0.00 34.23 5.03
5480 9877 0.600255 CCTCGTGGTTTTGACTCGCT 60.600 55.000 0.00 0.00 0.00 4.93
5481 9878 0.784778 CTCGTGGTTTTGACTCGCTC 59.215 55.000 0.00 0.00 0.00 5.03
5482 9879 0.103390 TCGTGGTTTTGACTCGCTCA 59.897 50.000 0.00 0.00 0.00 4.26
5483 9880 0.232303 CGTGGTTTTGACTCGCTCAC 59.768 55.000 0.00 0.00 0.00 3.51
5484 9881 1.583054 GTGGTTTTGACTCGCTCACT 58.417 50.000 0.00 0.00 0.00 3.41
5485 9882 1.527311 GTGGTTTTGACTCGCTCACTC 59.473 52.381 0.00 0.00 0.00 3.51
5486 9883 1.412710 TGGTTTTGACTCGCTCACTCT 59.587 47.619 0.00 0.00 0.00 3.24
5487 9884 2.062519 GGTTTTGACTCGCTCACTCTC 58.937 52.381 0.00 0.00 0.00 3.20
5488 9885 2.545952 GGTTTTGACTCGCTCACTCTCA 60.546 50.000 0.00 0.00 0.00 3.27
5489 9886 3.321497 GTTTTGACTCGCTCACTCTCAT 58.679 45.455 0.00 0.00 0.00 2.90
5490 9887 2.929531 TTGACTCGCTCACTCTCATC 57.070 50.000 0.00 0.00 0.00 2.92
5491 9888 1.826385 TGACTCGCTCACTCTCATCA 58.174 50.000 0.00 0.00 0.00 3.07
5492 9889 1.470494 TGACTCGCTCACTCTCATCAC 59.530 52.381 0.00 0.00 0.00 3.06
5493 9890 1.742831 GACTCGCTCACTCTCATCACT 59.257 52.381 0.00 0.00 0.00 3.41
5494 9891 2.939756 GACTCGCTCACTCTCATCACTA 59.060 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.947244 GTTTGGAGGAGTGCACTGTG 59.053 55.000 27.27 2.76 0.00 3.66
39 40 1.578206 GGCTTCGTTTGGAGGAGTGC 61.578 60.000 0.00 0.00 0.00 4.40
86 87 4.156922 ACCGAATTAACATGGAAAATCGCA 59.843 37.500 11.96 0.00 0.00 5.10
88 89 4.499040 GCACCGAATTAACATGGAAAATCG 59.501 41.667 10.94 10.94 0.00 3.34
106 107 3.270027 TCATAACATTCCTTGAGCACCG 58.730 45.455 0.00 0.00 0.00 4.94
111 112 9.270640 CTCCTAATCTTCATAACATTCCTTGAG 57.729 37.037 0.00 0.00 0.00 3.02
204 1019 3.127533 CAGCGGGCGGAAGGAAAG 61.128 66.667 0.00 0.00 0.00 2.62
255 1070 0.834612 TCACCAACGGAACCTGAAGT 59.165 50.000 0.00 0.00 0.00 3.01
313 1128 0.530870 GGATTTTCTCTCCCCGCGAG 60.531 60.000 8.23 0.00 40.30 5.03
315 1130 1.883084 CGGATTTTCTCTCCCCGCG 60.883 63.158 0.00 0.00 33.47 6.46
338 1157 1.065851 GAACTACTAGCTGGAGCCGAC 59.934 57.143 3.17 0.00 43.38 4.79
387 1227 0.320421 CCATTCACCCGAACGTCACT 60.320 55.000 0.00 0.00 32.81 3.41
461 1301 3.744719 CCGGGCTTCGTCTCGACA 61.745 66.667 0.00 0.00 34.89 4.35
470 1310 1.363080 GGATCTACGTCCGGGCTTC 59.637 63.158 3.66 0.00 0.00 3.86
475 1315 0.815734 ACTGTTGGATCTACGTCCGG 59.184 55.000 0.00 0.00 41.35 5.14
492 1332 2.802816 GTTGACACAAGATCTCGCAACT 59.197 45.455 0.00 0.00 33.38 3.16
509 1351 2.497273 TGGATCGATCTGAAGCTGTTGA 59.503 45.455 23.96 0.00 0.00 3.18
513 1355 3.181477 ACTCTTGGATCGATCTGAAGCTG 60.181 47.826 23.96 19.86 0.00 4.24
514 1356 3.030291 ACTCTTGGATCGATCTGAAGCT 58.970 45.455 23.96 11.70 0.00 3.74
528 1370 1.726791 CCGTCATCGTTGAACTCTTGG 59.273 52.381 0.00 0.00 32.48 3.61
543 4587 2.580815 CTGGAGCTGCATCCGTCA 59.419 61.111 8.91 0.00 42.77 4.35
569 4613 1.592400 CGTGTCTCTAGGAACCGGCA 61.592 60.000 0.00 0.00 0.00 5.69
572 4616 1.162698 TCACGTGTCTCTAGGAACCG 58.837 55.000 16.51 0.00 0.00 4.44
583 4627 4.143094 GCCAAGAACTATTCTTCACGTGTC 60.143 45.833 16.51 1.99 46.62 3.67
635 4680 6.231258 TGATCATTGTCACTGCTCTTCTAT 57.769 37.500 0.00 0.00 0.00 1.98
661 4706 3.320879 ATCGAGGCCAGCACCACTG 62.321 63.158 5.01 0.00 46.77 3.66
670 4717 6.829298 TGGTAATAAAAATTACATCGAGGCCA 59.171 34.615 5.01 0.00 38.43 5.36
722 4788 7.021196 GTGCACATGTTTATTTCAATACGACT 58.979 34.615 13.17 0.00 0.00 4.18
766 4834 4.214310 TGTCTCAATCTTCAAGGCCAAAA 58.786 39.130 5.01 0.00 0.00 2.44
809 4880 9.509956 AGTAAGTATAATCTACTGCTCCTACTG 57.490 37.037 0.00 0.00 0.00 2.74
810 4881 9.509956 CAGTAAGTATAATCTACTGCTCCTACT 57.490 37.037 8.52 0.00 32.93 2.57
818 4889 9.619316 GTGATCTGCAGTAAGTATAATCTACTG 57.381 37.037 14.67 13.48 40.59 2.74
862 4948 3.181465 TGACCACTTGTTTGAGACTCTCC 60.181 47.826 3.68 0.00 0.00 3.71
897 4983 0.788391 GTTTTATATCGGGGAGCGCG 59.212 55.000 0.00 0.00 41.10 6.86
1076 5162 3.532155 CGGCGAAGGAGGAGGAGG 61.532 72.222 0.00 0.00 0.00 4.30
1077 5163 2.756283 ACGGCGAAGGAGGAGGAG 60.756 66.667 16.62 0.00 0.00 3.69
1078 5164 2.754658 GACGGCGAAGGAGGAGGA 60.755 66.667 16.62 0.00 0.00 3.71
1079 5165 2.756283 AGACGGCGAAGGAGGAGG 60.756 66.667 16.62 0.00 0.00 4.30
1080 5166 2.776913 GGAGACGGCGAAGGAGGAG 61.777 68.421 16.62 0.00 0.00 3.69
1081 5167 2.754658 GGAGACGGCGAAGGAGGA 60.755 66.667 16.62 0.00 0.00 3.71
1082 5168 2.646175 TTGGAGACGGCGAAGGAGG 61.646 63.158 16.62 0.00 0.00 4.30
1083 5169 1.446272 GTTGGAGACGGCGAAGGAG 60.446 63.158 16.62 0.00 0.00 3.69
1084 5170 2.654877 GTTGGAGACGGCGAAGGA 59.345 61.111 16.62 0.00 0.00 3.36
1085 5171 2.434359 GGTTGGAGACGGCGAAGG 60.434 66.667 16.62 0.00 0.00 3.46
1086 5172 2.434359 GGGTTGGAGACGGCGAAG 60.434 66.667 16.62 0.00 0.00 3.79
1087 5173 4.367023 CGGGTTGGAGACGGCGAA 62.367 66.667 16.62 0.00 0.00 4.70
1220 5306 1.220749 GATTGCGGAGTGGGTAGCA 59.779 57.895 0.00 0.00 37.89 3.49
1221 5307 1.523938 GGATTGCGGAGTGGGTAGC 60.524 63.158 0.00 0.00 0.00 3.58
1222 5308 1.146263 GGGATTGCGGAGTGGGTAG 59.854 63.158 0.00 0.00 0.00 3.18
1223 5309 2.372074 GGGGATTGCGGAGTGGGTA 61.372 63.158 0.00 0.00 0.00 3.69
1224 5310 3.728373 GGGGATTGCGGAGTGGGT 61.728 66.667 0.00 0.00 0.00 4.51
1283 5374 2.125269 CGGGATGTCAACGGGGAC 60.125 66.667 2.15 2.15 38.29 4.46
1289 5380 0.958876 GGACCAACCGGGATGTCAAC 60.959 60.000 17.64 2.26 41.15 3.18
1290 5381 1.377229 GGACCAACCGGGATGTCAA 59.623 57.895 17.64 0.00 41.15 3.18
1303 5406 2.552585 GAAGCGGATCGAACGGACCA 62.553 60.000 13.59 0.00 0.00 4.02
1307 5410 2.954868 CGGAAGCGGATCGAACGG 60.955 66.667 13.59 5.53 0.00 4.44
1458 5561 0.473117 GGGATTAGGGGATGGTCGGA 60.473 60.000 0.00 0.00 0.00 4.55
1502 5605 0.937699 CGACGAGCGTTTTGAGGACA 60.938 55.000 0.00 0.00 34.64 4.02
1668 5771 6.548441 TGAGTAAGTGAACGGTAAAATTGG 57.452 37.500 0.00 0.00 0.00 3.16
1671 5774 7.822334 TGATGATGAGTAAGTGAACGGTAAAAT 59.178 33.333 0.00 0.00 0.00 1.82
1672 5775 7.117236 GTGATGATGAGTAAGTGAACGGTAAAA 59.883 37.037 0.00 0.00 0.00 1.52
1678 5781 4.564372 CCTGTGATGATGAGTAAGTGAACG 59.436 45.833 0.00 0.00 0.00 3.95
1682 5785 5.588958 TCTCCTGTGATGATGAGTAAGTG 57.411 43.478 0.00 0.00 0.00 3.16
1691 5794 3.595021 TGATGGGATCTCCTGTGATGAT 58.405 45.455 0.00 0.00 36.20 2.45
1695 5798 2.121948 CCTTGATGGGATCTCCTGTGA 58.878 52.381 0.00 0.00 36.20 3.58
1696 5799 1.476471 GCCTTGATGGGATCTCCTGTG 60.476 57.143 0.00 0.00 36.20 3.66
1697 5800 0.842635 GCCTTGATGGGATCTCCTGT 59.157 55.000 0.00 0.00 36.20 4.00
1698 5801 0.841961 TGCCTTGATGGGATCTCCTG 59.158 55.000 0.00 0.00 36.20 3.86
1719 5825 4.177026 ACGCTAGCAAGAGTTGATACTTG 58.823 43.478 16.45 0.00 44.05 3.16
1720 5826 4.457834 ACGCTAGCAAGAGTTGATACTT 57.542 40.909 16.45 0.00 30.81 2.24
1721 5827 5.176407 CTACGCTAGCAAGAGTTGATACT 57.824 43.478 16.45 0.00 37.01 2.12
1810 5919 9.593134 GAACAGAGTATGATATCTGAAACTTGT 57.407 33.333 9.06 6.74 44.68 3.16
1811 5920 8.750416 CGAACAGAGTATGATATCTGAAACTTG 58.250 37.037 9.06 6.27 44.68 3.16
1862 5974 8.539674 GTTTGAAAGTTGAAACGCAAATTAGAT 58.460 29.630 11.90 0.00 43.30 1.98
1863 5975 7.009723 GGTTTGAAAGTTGAAACGCAAATTAGA 59.990 33.333 11.90 0.00 43.30 2.10
1874 5986 4.644685 AGCTAGCTGGTTTGAAAGTTGAAA 59.355 37.500 18.57 0.00 0.00 2.69
1875 5987 4.036734 CAGCTAGCTGGTTTGAAAGTTGAA 59.963 41.667 33.06 0.00 40.17 2.69
1876 5988 3.565482 CAGCTAGCTGGTTTGAAAGTTGA 59.435 43.478 33.06 0.00 40.17 3.18
1877 5989 3.893720 CAGCTAGCTGGTTTGAAAGTTG 58.106 45.455 33.06 7.08 40.17 3.16
2079 6191 6.835488 AGGTTCATTGGCTGATTTGTACATAT 59.165 34.615 0.00 0.00 32.72 1.78
2132 6247 4.095410 TGGAAAGAAATATTGTGCTGCG 57.905 40.909 0.00 0.00 0.00 5.18
2183 6298 9.975218 TGATATAGTCTATGCCATACAGTCTTA 57.025 33.333 2.37 0.00 0.00 2.10
2184 6299 8.885693 TGATATAGTCTATGCCATACAGTCTT 57.114 34.615 2.37 0.00 0.00 3.01
2185 6300 8.911965 CATGATATAGTCTATGCCATACAGTCT 58.088 37.037 2.37 0.00 0.00 3.24
2194 6309 6.758886 GGCTACAACATGATATAGTCTATGCC 59.241 42.308 0.00 0.00 0.00 4.40
2209 6324 0.320421 AGCGTCAACGGCTACAACAT 60.320 50.000 4.54 0.00 40.23 2.71
2257 6372 2.222027 GTACACCAACTCTGCTTGCTT 58.778 47.619 0.00 0.00 0.00 3.91
2568 6710 2.758979 TCGACCATTCTACTTCCTGTCC 59.241 50.000 0.00 0.00 0.00 4.02
2628 6770 4.036734 TCAGGGCGATGATTGAATTAAAGC 59.963 41.667 0.00 0.00 0.00 3.51
2722 6882 2.808315 CGATCTGTCGGTCCCCAG 59.192 66.667 0.00 0.00 44.00 4.45
2864 7024 8.760103 TTATTTATTTAGTAGCGTGTCACACA 57.240 30.769 9.06 0.00 33.40 3.72
2968 7132 1.132500 GCCCCACAAGATAGCTACCT 58.868 55.000 0.00 0.00 0.00 3.08
2993 7157 4.646492 GTGGAATTAATGAACAGGAGGCAT 59.354 41.667 0.00 0.00 0.00 4.40
3090 7254 3.678056 ACGTCACTAGCTTCATTTGGA 57.322 42.857 0.00 0.00 0.00 3.53
3106 7270 0.530744 TCTCCACTGGTGCATACGTC 59.469 55.000 0.00 0.00 0.00 4.34
3243 7626 9.720667 AAAAAGTCACACGGTAAGTTTATTAAC 57.279 29.630 0.00 0.00 34.36 2.01
3357 7743 7.866393 ACTTCGGAATAATTAGTGTAATCTCGG 59.134 37.037 0.00 0.00 0.00 4.63
3660 8047 5.107109 TGCATCCGAAATTATTGAATCCG 57.893 39.130 0.00 0.00 0.00 4.18
3738 8125 1.302907 AAGGGTAGGACTCCTCGGTA 58.697 55.000 0.00 0.00 34.61 4.02
3822 8209 5.554437 TCCTTACCAGTGTGATGTTAACA 57.446 39.130 11.41 11.41 0.00 2.41
4007 8394 2.158871 TCTTGTACTGCCTGAAACCGTT 60.159 45.455 0.00 0.00 0.00 4.44
4126 8513 5.931441 AGCACATTAACTGAAGACTGAAC 57.069 39.130 0.00 0.00 0.00 3.18
4167 8554 7.528307 TCAGAACGAAATAGTAGAAGAGTGTC 58.472 38.462 0.00 0.00 0.00 3.67
4185 8572 4.680934 CACAACTTGCATTTTCAGAACG 57.319 40.909 0.00 0.00 0.00 3.95
4370 8757 2.867624 ACACAAGATGGAAGTGCACAT 58.132 42.857 21.04 7.05 36.76 3.21
4412 8799 2.974536 GAGTCAGTATCGCGTTATGAGC 59.025 50.000 5.77 2.69 0.00 4.26
4416 8803 2.871022 AGTCGAGTCAGTATCGCGTTAT 59.129 45.455 5.77 0.00 39.98 1.89
4418 8805 1.085091 AGTCGAGTCAGTATCGCGTT 58.915 50.000 5.77 0.00 39.98 4.84
4467 8855 1.076850 TACGATGGGGTAGGACGCA 60.077 57.895 0.00 0.00 37.72 5.24
4522 8914 6.834959 ACACATTATTCATGTCTAGCGAAG 57.165 37.500 0.00 0.00 43.17 3.79
4541 8933 1.748493 GTCTTGTGGGCTGAAAACACA 59.252 47.619 0.00 0.00 42.77 3.72
4738 9133 4.080638 TGAATGGGCCATTTTATTTGTCCC 60.081 41.667 31.17 15.35 33.90 4.46
4789 9184 4.276678 GCATGCAATTTCCTGCTAGTATCA 59.723 41.667 14.21 0.00 43.07 2.15
4794 9189 1.752498 TGGCATGCAATTTCCTGCTAG 59.248 47.619 21.36 0.00 43.07 3.42
4809 9204 3.032459 TGGCAATATTCATGTGTGGCAT 58.968 40.909 0.00 0.00 39.53 4.40
4830 9225 8.707449 TGTAAACGGAATGAACCCTAAGTATAT 58.293 33.333 0.00 0.00 0.00 0.86
4842 9237 5.239351 TCGAAATCCTGTAAACGGAATGAA 58.761 37.500 0.00 0.00 33.55 2.57
4941 9336 9.403583 GATTCCCAACAATTCTTACCATTAGTA 57.596 33.333 0.00 0.00 0.00 1.82
5022 9418 6.837568 ACATTTGCTTCATAGGATTGGAGATT 59.162 34.615 0.00 0.00 0.00 2.40
5048 9444 5.134339 ACCCTCATTTCTTTCCCTATGCATA 59.866 40.000 6.20 6.20 0.00 3.14
5062 9458 5.422214 TGGAGAACTCTTACCCTCATTTC 57.578 43.478 1.86 0.00 0.00 2.17
5120 9517 2.992114 AGGGAGTCGCGCTTGAGT 60.992 61.111 5.56 0.00 36.16 3.41
5135 9532 5.044428 TCGTCGAAGAAGTAAAGAAGAGG 57.956 43.478 0.00 0.00 39.69 3.69
5145 9542 0.309922 TCACGCTTCGTCGAAGAAGT 59.690 50.000 33.52 27.35 46.82 3.01
5152 9549 0.110147 AAGAGACTCACGCTTCGTCG 60.110 55.000 5.02 0.00 38.32 5.12
5187 9584 4.847444 GAGGGGAGAAGCCAGCGC 62.847 72.222 0.00 0.00 38.95 5.92
5208 9605 3.441290 ACGAGCTCCCGTCGAAGG 61.441 66.667 10.80 10.80 38.56 3.46
5215 9612 4.379243 AAGCACCACGAGCTCCCG 62.379 66.667 8.47 0.00 42.53 5.14
5228 9625 5.755375 GTGAGCTTATCTACAATAGCAAGCA 59.245 40.000 17.17 0.00 41.75 3.91
5277 9674 0.029300 CAACAACAGAGGCAACGTGG 59.971 55.000 0.00 0.00 46.39 4.94
5280 9677 1.654220 CCCAACAACAGAGGCAACG 59.346 57.895 0.00 0.00 46.39 4.10
5289 9686 3.448093 TGCATCTTATCCCCAACAACA 57.552 42.857 0.00 0.00 0.00 3.33
5298 9695 7.325660 TCTTGATTTGACTTGCATCTTATCC 57.674 36.000 0.00 0.00 0.00 2.59
5331 9728 4.052608 CAGCTTGTTGAAACATGATGCAA 58.947 39.130 12.46 0.00 41.36 4.08
5354 9751 6.751425 ACACAACAAACATCATTACACACTTG 59.249 34.615 0.00 0.00 0.00 3.16
5409 9806 7.434897 TCGCTTTACTTTCGTTTTACTCTAACA 59.565 33.333 0.00 0.00 0.00 2.41
5410 9807 7.777425 TCGCTTTACTTTCGTTTTACTCTAAC 58.223 34.615 0.00 0.00 0.00 2.34
5411 9808 7.862372 TCTCGCTTTACTTTCGTTTTACTCTAA 59.138 33.333 0.00 0.00 0.00 2.10
5412 9809 7.362662 TCTCGCTTTACTTTCGTTTTACTCTA 58.637 34.615 0.00 0.00 0.00 2.43
5413 9810 6.211515 TCTCGCTTTACTTTCGTTTTACTCT 58.788 36.000 0.00 0.00 0.00 3.24
5414 9811 6.443876 TCTCGCTTTACTTTCGTTTTACTC 57.556 37.500 0.00 0.00 0.00 2.59
5415 9812 7.170320 TCAATCTCGCTTTACTTTCGTTTTACT 59.830 33.333 0.00 0.00 0.00 2.24
5416 9813 7.285788 TCAATCTCGCTTTACTTTCGTTTTAC 58.714 34.615 0.00 0.00 0.00 2.01
5417 9814 7.410800 TCAATCTCGCTTTACTTTCGTTTTA 57.589 32.000 0.00 0.00 0.00 1.52
5418 9815 6.295039 TCAATCTCGCTTTACTTTCGTTTT 57.705 33.333 0.00 0.00 0.00 2.43
5419 9816 5.917541 TCAATCTCGCTTTACTTTCGTTT 57.082 34.783 0.00 0.00 0.00 3.60
5420 9817 5.917541 TTCAATCTCGCTTTACTTTCGTT 57.082 34.783 0.00 0.00 0.00 3.85
5421 9818 5.408604 ACATTCAATCTCGCTTTACTTTCGT 59.591 36.000 0.00 0.00 0.00 3.85
5422 9819 5.729883 CACATTCAATCTCGCTTTACTTTCG 59.270 40.000 0.00 0.00 0.00 3.46
5423 9820 6.831769 TCACATTCAATCTCGCTTTACTTTC 58.168 36.000 0.00 0.00 0.00 2.62
5424 9821 6.801539 TCACATTCAATCTCGCTTTACTTT 57.198 33.333 0.00 0.00 0.00 2.66
5425 9822 6.801539 TTCACATTCAATCTCGCTTTACTT 57.198 33.333 0.00 0.00 0.00 2.24
5426 9823 6.183360 CCATTCACATTCAATCTCGCTTTACT 60.183 38.462 0.00 0.00 0.00 2.24
5427 9824 5.967674 CCATTCACATTCAATCTCGCTTTAC 59.032 40.000 0.00 0.00 0.00 2.01
5428 9825 5.879777 TCCATTCACATTCAATCTCGCTTTA 59.120 36.000 0.00 0.00 0.00 1.85
5429 9826 4.701651 TCCATTCACATTCAATCTCGCTTT 59.298 37.500 0.00 0.00 0.00 3.51
5430 9827 4.095483 GTCCATTCACATTCAATCTCGCTT 59.905 41.667 0.00 0.00 0.00 4.68
5431 9828 3.624861 GTCCATTCACATTCAATCTCGCT 59.375 43.478 0.00 0.00 0.00 4.93
5432 9829 3.242870 GGTCCATTCACATTCAATCTCGC 60.243 47.826 0.00 0.00 0.00 5.03
5433 9830 3.940852 TGGTCCATTCACATTCAATCTCG 59.059 43.478 0.00 0.00 0.00 4.04
5434 9831 6.461110 AATGGTCCATTCACATTCAATCTC 57.539 37.500 11.59 0.00 29.38 2.75
5435 9832 7.121382 ACTAATGGTCCATTCACATTCAATCT 58.879 34.615 20.65 0.00 35.54 2.40
5436 9833 7.338800 ACTAATGGTCCATTCACATTCAATC 57.661 36.000 20.65 0.00 35.54 2.67
5437 9834 7.338800 GACTAATGGTCCATTCACATTCAAT 57.661 36.000 20.65 0.00 38.93 2.57
5438 9835 6.757897 GACTAATGGTCCATTCACATTCAA 57.242 37.500 20.65 0.00 38.93 2.69
5451 9848 3.329929 AAACCACGAGGACTAATGGTC 57.670 47.619 5.68 0.00 44.80 4.02
5453 9850 3.435671 GTCAAAACCACGAGGACTAATGG 59.564 47.826 5.68 0.00 38.69 3.16
5454 9851 4.315803 AGTCAAAACCACGAGGACTAATG 58.684 43.478 5.68 0.00 37.08 1.90
5455 9852 4.566987 GAGTCAAAACCACGAGGACTAAT 58.433 43.478 5.68 0.00 38.82 1.73
5456 9853 3.551454 CGAGTCAAAACCACGAGGACTAA 60.551 47.826 5.68 0.00 38.82 2.24
5457 9854 2.030540 CGAGTCAAAACCACGAGGACTA 60.031 50.000 5.68 0.00 38.82 2.59
5458 9855 1.269621 CGAGTCAAAACCACGAGGACT 60.270 52.381 5.68 0.00 41.22 3.85
5459 9856 1.137513 CGAGTCAAAACCACGAGGAC 58.862 55.000 5.68 0.00 38.69 3.85
5460 9857 0.599204 GCGAGTCAAAACCACGAGGA 60.599 55.000 5.68 0.00 38.69 3.71
5461 9858 0.600255 AGCGAGTCAAAACCACGAGG 60.600 55.000 0.00 0.00 42.21 4.63
5462 9859 0.784778 GAGCGAGTCAAAACCACGAG 59.215 55.000 0.00 0.00 0.00 4.18
5463 9860 0.103390 TGAGCGAGTCAAAACCACGA 59.897 50.000 0.00 0.00 29.64 4.35
5464 9861 0.232303 GTGAGCGAGTCAAAACCACG 59.768 55.000 0.00 0.00 36.74 4.94
5465 9862 1.527311 GAGTGAGCGAGTCAAAACCAC 59.473 52.381 0.00 0.00 36.74 4.16
5466 9863 1.412710 AGAGTGAGCGAGTCAAAACCA 59.587 47.619 0.00 0.00 36.74 3.67
5467 9864 2.062519 GAGAGTGAGCGAGTCAAAACC 58.937 52.381 0.00 0.00 36.74 3.27
5468 9865 2.743938 TGAGAGTGAGCGAGTCAAAAC 58.256 47.619 0.00 0.00 36.74 2.43
5469 9866 3.005791 TGATGAGAGTGAGCGAGTCAAAA 59.994 43.478 0.00 0.00 36.74 2.44
5470 9867 2.558359 TGATGAGAGTGAGCGAGTCAAA 59.442 45.455 0.00 0.00 36.74 2.69
5471 9868 2.095008 GTGATGAGAGTGAGCGAGTCAA 60.095 50.000 0.00 0.00 36.74 3.18
5472 9869 1.470494 GTGATGAGAGTGAGCGAGTCA 59.530 52.381 0.00 0.00 0.00 3.41
5473 9870 1.742831 AGTGATGAGAGTGAGCGAGTC 59.257 52.381 0.00 0.00 0.00 3.36
5474 9871 1.832883 AGTGATGAGAGTGAGCGAGT 58.167 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.