Multiple sequence alignment - TraesCS3D01G293800

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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 TraesCS3D01G293800 chr3D 100.000 3821 0 0 1 3821 404443213 404439393 0.000000e+00 7057
1 TraesCS3D01G293800 chr3D 86.550 171 18 4 2110 2279 481712973 481712807 2.340000e-42 183
2 TraesCS3D01G293800 chr3D 87.500 160 18 2 2117 2275 582171328 582171486 2.340000e-42 183
3 TraesCS3D01G293800 chr3A 93.211 2077 79 32 75 2115 526866538 526864488 0.000000e+00 2998
4 TraesCS3D01G293800 chr3A 86.162 925 58 43 2311 3179 526864476 526863566 0.000000e+00 935
5 TraesCS3D01G293800 chr3A 91.608 143 6 3 3591 3732 526862965 526862828 3.900000e-45 193
6 TraesCS3D01G293800 chr3B 90.238 2182 91 38 1 2107 530612466 530610332 0.000000e+00 2737
7 TraesCS3D01G293800 chr3B 90.091 1312 59 33 2311 3580 530610311 530609029 0.000000e+00 1637
8 TraesCS3D01G293800 chr3B 85.294 170 22 2 2116 2283 627556013 627555845 5.070000e-39 172
9 TraesCS3D01G293800 chr3B 84.000 150 11 8 3575 3723 530608736 530608599 8.610000e-27 132
10 TraesCS3D01G293800 chr1D 92.285 337 17 7 1781 2115 415141409 415141080 1.610000e-128 470
11 TraesCS3D01G293800 chr1D 83.387 313 37 11 1550 1850 426870193 426869884 3.760000e-70 276
12 TraesCS3D01G293800 chr1D 86.611 239 14 10 2315 2544 415141071 415140842 8.200000e-62 248
13 TraesCS3D01G293800 chr1D 89.542 153 13 3 2112 2261 284241260 284241108 1.400000e-44 191
14 TraesCS3D01G293800 chr1B 82.428 313 40 11 1550 1850 576688122 576687813 3.790000e-65 259
15 TraesCS3D01G293800 chr1B 88.750 160 13 2 2117 2275 566027739 566027894 1.400000e-44 191
16 TraesCS3D01G293800 chr1A 82.109 313 41 11 1550 1850 521877903 521877594 1.760000e-63 254
17 TraesCS3D01G293800 chr2D 89.172 157 16 1 2119 2275 476697544 476697699 1.080000e-45 195
18 TraesCS3D01G293800 chr7D 89.404 151 12 3 2113 2261 77396138 77396286 1.810000e-43 187
19 TraesCS3D01G293800 chr4B 85.311 177 20 3 2109 2283 590632530 590632702 1.090000e-40 178
20 TraesCS3D01G293800 chr2A 84.831 178 21 5 2111 2286 719304499 719304672 1.410000e-39 174


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 TraesCS3D01G293800 chr3D 404439393 404443213 3820 True 7057.000000 7057 100.000000 1 3821 1 chr3D.!!$R1 3820
1 TraesCS3D01G293800 chr3A 526862828 526866538 3710 True 1375.333333 2998 90.327000 75 3732 3 chr3A.!!$R1 3657
2 TraesCS3D01G293800 chr3B 530608599 530612466 3867 True 1502.000000 2737 88.109667 1 3723 3 chr3B.!!$R2 3722
3 TraesCS3D01G293800 chr1D 415140842 415141409 567 True 359.000000 470 89.448000 1781 2544 2 chr1D.!!$R3 763

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
415 451 0.038021 TGCCAAATGGAGCAGTAGCA 59.962 50.0 2.98 0.0 38.42 3.49 F
979 1068 0.163146 CTCTCGATCGCGCATACGTA 59.837 55.0 11.09 0.0 42.83 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1968 0.251832 GTCAGGGTCAGGACTCAGGA 60.252 60.0 1.62 0.0 33.19 3.86 R
2907 3062 0.042448 GTCTTCACGGTGTGCGAAAC 60.042 55.0 8.17 0.0 32.98 2.78 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
48 49 2.133742 GATTGGCCGCCCATCGATTG 62.134 60.000 7.03 0.00 41.78 2.67
57 58 1.095228 CCCATCGATTGTTGACCGGG 61.095 60.000 6.32 0.00 0.00 5.73
88 89 3.132139 CTTCGTCCTCTCGGCGGA 61.132 66.667 7.21 2.06 32.89 5.54
128 136 0.894642 CGCCCCTAGACTAGGTAGGC 60.895 65.000 27.16 27.16 44.87 3.93
160 168 2.998667 CTGAAATCGCGAGACGGC 59.001 61.111 16.66 2.54 46.97 5.68
204 212 6.756074 GTCAATCTCTGAATCATCGTTTCTCT 59.244 38.462 0.00 0.00 35.22 3.10
242 250 5.415221 GCCCACAGATTGACTCTATATAGC 58.585 45.833 4.75 0.00 31.13 2.97
409 445 1.969208 TGTCATTTGCCAAATGGAGCA 59.031 42.857 25.51 19.23 46.40 4.26
411 447 2.028748 GTCATTTGCCAAATGGAGCAGT 60.029 45.455 25.51 0.00 46.40 4.40
412 448 3.193267 GTCATTTGCCAAATGGAGCAGTA 59.807 43.478 25.51 5.94 46.40 2.74
413 449 3.444742 TCATTTGCCAAATGGAGCAGTAG 59.555 43.478 25.51 1.82 46.40 2.57
414 450 1.176527 TTGCCAAATGGAGCAGTAGC 58.823 50.000 2.98 0.00 40.73 3.58
415 451 0.038021 TGCCAAATGGAGCAGTAGCA 59.962 50.000 2.98 0.00 38.42 3.49
428 476 1.317611 CAGTAGCAACGATCGACAACG 59.682 52.381 24.34 5.91 41.26 4.10
516 566 6.723977 GTGAGATGAGATAGGGGAAATAGAGT 59.276 42.308 0.00 0.00 0.00 3.24
624 674 2.345760 GCTCCATTGCCACCACAGG 61.346 63.158 0.00 0.00 0.00 4.00
648 698 0.804156 CGAGCGAGAAAAGAGGAGGC 60.804 60.000 0.00 0.00 0.00 4.70
726 776 0.463833 GAGCCAACTAACCCCATCGG 60.464 60.000 0.00 0.00 37.81 4.18
873 953 0.320421 CCCCTACACACACTCCAACG 60.320 60.000 0.00 0.00 0.00 4.10
923 1011 0.458543 CGCTCGCCTCTGCTTCTTTA 60.459 55.000 0.00 0.00 34.43 1.85
924 1012 1.285578 GCTCGCCTCTGCTTCTTTAG 58.714 55.000 0.00 0.00 34.43 1.85
934 1023 5.411053 CCTCTGCTTCTTTAGTTCTTTCCAG 59.589 44.000 0.00 0.00 0.00 3.86
956 1045 2.104729 GCTCTGCTCTGCTCCTCG 59.895 66.667 0.00 0.00 0.00 4.63
961 1050 3.146913 GCTCTGCTCCTCGCCTCT 61.147 66.667 0.00 0.00 38.05 3.69
971 1060 3.571959 CTCGCCTCTCTCGATCGCG 62.572 68.421 11.09 3.99 38.46 5.87
977 1066 0.787540 CTCTCTCGATCGCGCATACG 60.788 60.000 11.09 9.56 44.07 3.06
978 1067 1.082692 CTCTCGATCGCGCATACGT 60.083 57.895 11.09 0.00 42.83 3.57
979 1068 0.163146 CTCTCGATCGCGCATACGTA 59.837 55.000 11.09 0.00 42.83 3.57
990 1079 2.412325 GCGCATACGTACCATATTTGGC 60.412 50.000 0.30 0.00 43.94 4.52
1335 1429 1.435515 GCTCGAGTACCTGCTCCTG 59.564 63.158 15.13 0.00 32.11 3.86
1478 1589 1.060713 CTCACCGAGTGCTTACGTTG 58.939 55.000 0.00 0.00 32.98 4.10
1861 1972 2.109799 CAGGTATGCCCGCTCCTG 59.890 66.667 0.00 10.07 40.83 3.86
1862 1973 2.041922 AGGTATGCCCGCTCCTGA 60.042 61.111 0.00 0.00 38.74 3.86
1863 1974 2.136878 AGGTATGCCCGCTCCTGAG 61.137 63.158 0.00 0.00 38.74 3.35
1904 2015 4.599434 TTTTCGTGCACGCGCCAC 62.599 61.111 33.63 17.53 39.60 5.01
2035 2150 3.121030 GCACGCAGAGCCATCGTT 61.121 61.111 0.00 0.00 38.43 3.85
2036 2151 2.680913 GCACGCAGAGCCATCGTTT 61.681 57.895 0.00 0.00 38.43 3.60
2037 2152 1.133253 CACGCAGAGCCATCGTTTG 59.867 57.895 0.00 0.00 33.84 2.93
2098 2218 4.097286 TCACCCTGAGCAACTAACAAAAAC 59.903 41.667 0.00 0.00 0.00 2.43
2107 2228 7.227116 TGAGCAACTAACAAAAACCGTAGTAAT 59.773 33.333 0.00 0.00 0.00 1.89
2109 2230 9.054922 AGCAACTAACAAAAACCGTAGTAATAA 57.945 29.630 0.00 0.00 0.00 1.40
2110 2231 9.662545 GCAACTAACAAAAACCGTAGTAATAAA 57.337 29.630 0.00 0.00 0.00 1.40
2167 2288 8.934023 TTTTTAAGGATGTCACATCTAACCTT 57.066 30.769 17.46 14.42 39.21 3.50
2168 2289 8.561738 TTTTAAGGATGTCACATCTAACCTTC 57.438 34.615 17.46 0.00 37.44 3.46
2169 2290 4.762289 AGGATGTCACATCTAACCTTCC 57.238 45.455 17.46 0.00 0.00 3.46
2170 2291 4.104086 AGGATGTCACATCTAACCTTCCA 58.896 43.478 17.46 0.00 0.00 3.53
2171 2292 4.080863 AGGATGTCACATCTAACCTTCCAC 60.081 45.833 17.46 0.00 0.00 4.02
2172 2293 4.323485 GGATGTCACATCTAACCTTCCACA 60.323 45.833 17.46 0.00 0.00 4.17
2173 2294 4.698201 TGTCACATCTAACCTTCCACAA 57.302 40.909 0.00 0.00 0.00 3.33
2174 2295 5.042463 TGTCACATCTAACCTTCCACAAA 57.958 39.130 0.00 0.00 0.00 2.83
2175 2296 4.819630 TGTCACATCTAACCTTCCACAAAC 59.180 41.667 0.00 0.00 0.00 2.93
2176 2297 4.819630 GTCACATCTAACCTTCCACAAACA 59.180 41.667 0.00 0.00 0.00 2.83
2177 2298 5.473504 GTCACATCTAACCTTCCACAAACAT 59.526 40.000 0.00 0.00 0.00 2.71
2178 2299 5.473162 TCACATCTAACCTTCCACAAACATG 59.527 40.000 0.00 0.00 0.00 3.21
2179 2300 5.241506 CACATCTAACCTTCCACAAACATGT 59.758 40.000 0.00 0.00 0.00 3.21
2180 2301 6.429692 CACATCTAACCTTCCACAAACATGTA 59.570 38.462 0.00 0.00 0.00 2.29
2181 2302 7.001674 ACATCTAACCTTCCACAAACATGTAA 58.998 34.615 0.00 0.00 0.00 2.41
2182 2303 7.669722 ACATCTAACCTTCCACAAACATGTAAT 59.330 33.333 0.00 0.00 0.00 1.89
2248 2369 9.911788 AGATCATAAATAAAGTGGACATCAGTT 57.088 29.630 0.00 0.00 40.52 3.16
2315 2436 6.093082 ACCGAGAAAACGAAAGAAAGAAAGAA 59.907 34.615 0.00 0.00 35.09 2.52
2316 2437 6.964934 CCGAGAAAACGAAAGAAAGAAAGAAA 59.035 34.615 0.00 0.00 35.09 2.52
2317 2438 7.164335 CCGAGAAAACGAAAGAAAGAAAGAAAG 59.836 37.037 0.00 0.00 35.09 2.62
2318 2439 7.903431 CGAGAAAACGAAAGAAAGAAAGAAAGA 59.097 33.333 0.00 0.00 35.09 2.52
2319 2440 9.556030 GAGAAAACGAAAGAAAGAAAGAAAGAA 57.444 29.630 0.00 0.00 0.00 2.52
2320 2441 9.908152 AGAAAACGAAAGAAAGAAAGAAAGAAA 57.092 25.926 0.00 0.00 0.00 2.52
2322 2443 9.908152 AAAACGAAAGAAAGAAAGAAAGAAAGA 57.092 25.926 0.00 0.00 0.00 2.52
2323 2444 9.908152 AAACGAAAGAAAGAAAGAAAGAAAGAA 57.092 25.926 0.00 0.00 0.00 2.52
2324 2445 9.908152 AACGAAAGAAAGAAAGAAAGAAAGAAA 57.092 25.926 0.00 0.00 0.00 2.52
2325 2446 9.561270 ACGAAAGAAAGAAAGAAAGAAAGAAAG 57.439 29.630 0.00 0.00 0.00 2.62
2326 2447 9.774742 CGAAAGAAAGAAAGAAAGAAAGAAAGA 57.225 29.630 0.00 0.00 0.00 2.52
2341 2462 4.025040 AGAAAGAGATGGTTGTGATGCA 57.975 40.909 0.00 0.00 0.00 3.96
2347 2468 0.320334 ATGGTTGTGATGCACGTCGA 60.320 50.000 0.00 0.00 37.14 4.20
2465 2592 0.025898 CACATGAGCTTCGCGTGATG 59.974 55.000 5.77 3.04 0.00 3.07
2489 2621 4.060900 CTGCATGGCATCTTACTAATCGT 58.939 43.478 0.00 0.00 38.13 3.73
2510 2642 0.465097 AGCTGTGTGTTCTTGCTGCT 60.465 50.000 0.00 0.00 32.32 4.24
2552 2692 4.307443 TGCCTTGATCTCATGTACTACG 57.693 45.455 0.00 0.00 0.00 3.51
2565 2705 8.723311 TCTCATGTACTACGGTTTTATTTTTGG 58.277 33.333 0.00 0.00 0.00 3.28
2573 2728 5.293560 ACGGTTTTATTTTTGGGATGTGTG 58.706 37.500 0.00 0.00 0.00 3.82
2577 2732 6.018343 GGTTTTATTTTTGGGATGTGTGTGTG 60.018 38.462 0.00 0.00 0.00 3.82
2822 2977 0.321671 GCTCAGTTCCACAGGTAGCA 59.678 55.000 0.00 0.00 0.00 3.49
2877 3032 0.253044 TTACCAAGCCAGCCAGCTAG 59.747 55.000 0.00 0.00 44.11 3.42
2882 3037 0.980231 AAGCCAGCCAGCTAGCTAGT 60.980 55.000 18.86 1.42 44.11 2.57
2883 3038 0.105964 AGCCAGCCAGCTAGCTAGTA 60.106 55.000 18.86 0.00 42.61 1.82
2884 3039 0.316841 GCCAGCCAGCTAGCTAGTAG 59.683 60.000 18.86 13.87 42.61 2.57
2905 3060 1.040893 TAGCTAGCTGCCGTGGCTTA 61.041 55.000 27.68 0.00 44.23 3.09
2907 3062 1.502163 GCTAGCTGCCGTGGCTTATG 61.502 60.000 12.84 1.37 42.51 1.90
2912 3070 0.096976 CTGCCGTGGCTTATGTTTCG 59.903 55.000 12.84 0.00 42.51 3.46
2918 3076 0.878416 TGGCTTATGTTTCGCACACC 59.122 50.000 0.00 0.00 38.61 4.16
2919 3077 0.179200 GGCTTATGTTTCGCACACCG 60.179 55.000 0.00 0.00 38.61 4.94
2921 3079 1.724654 GCTTATGTTTCGCACACCGTG 60.725 52.381 0.00 0.00 38.61 4.94
2922 3080 1.795872 CTTATGTTTCGCACACCGTGA 59.204 47.619 5.28 0.00 38.61 4.35
2923 3081 1.867166 TATGTTTCGCACACCGTGAA 58.133 45.000 5.28 0.00 42.36 3.18
2924 3082 0.586319 ATGTTTCGCACACCGTGAAG 59.414 50.000 5.28 0.00 44.64 3.02
2925 3083 0.460459 TGTTTCGCACACCGTGAAGA 60.460 50.000 5.28 0.00 44.64 2.87
2926 3084 0.042448 GTTTCGCACACCGTGAAGAC 60.042 55.000 5.28 0.00 44.64 3.01
2927 3085 1.484227 TTTCGCACACCGTGAAGACG 61.484 55.000 5.28 3.48 44.64 4.18
2946 3104 4.952957 AGACGAAGATGAAGATGAAGAGGA 59.047 41.667 0.00 0.00 0.00 3.71
2947 3105 5.420421 AGACGAAGATGAAGATGAAGAGGAA 59.580 40.000 0.00 0.00 0.00 3.36
2948 3106 6.042638 ACGAAGATGAAGATGAAGAGGAAA 57.957 37.500 0.00 0.00 0.00 3.13
2965 3134 8.840833 AAGAGGAAAGCTACTAGAAAAGAAAG 57.159 34.615 0.00 0.00 0.00 2.62
2966 3135 7.390823 AGAGGAAAGCTACTAGAAAAGAAAGG 58.609 38.462 0.00 0.00 0.00 3.11
2974 3143 6.935208 GCTACTAGAAAAGAAAGGGAAACAGA 59.065 38.462 0.00 0.00 0.00 3.41
2998 3167 8.945057 AGAGCTAAAAGAAGATGATTTCAAGAC 58.055 33.333 0.00 0.00 0.00 3.01
2999 3168 8.627208 AGCTAAAAGAAGATGATTTCAAGACA 57.373 30.769 0.00 0.00 0.00 3.41
3005 3179 7.142306 AGAAGATGATTTCAAGACACATGTG 57.858 36.000 24.25 24.25 0.00 3.21
3019 3193 0.807667 CATGTGGTAGAGCTGCGGAC 60.808 60.000 0.00 0.00 0.00 4.79
3034 3215 2.224233 TGCGGACGTAGCTAGTAGATCT 60.224 50.000 15.17 0.00 35.28 2.75
3035 3216 2.807392 GCGGACGTAGCTAGTAGATCTT 59.193 50.000 0.00 0.00 0.00 2.40
3039 3220 5.908499 CGGACGTAGCTAGTAGATCTTTTTC 59.092 44.000 0.00 0.00 0.00 2.29
3041 3222 6.434018 ACGTAGCTAGTAGATCTTTTTCGT 57.566 37.500 0.00 0.00 0.00 3.85
3042 3223 6.256686 ACGTAGCTAGTAGATCTTTTTCGTG 58.743 40.000 0.00 0.00 0.00 4.35
3126 3307 2.822701 GGGAATGCCGGACGAACC 60.823 66.667 5.05 0.46 33.83 3.62
3208 3437 9.948964 TCTGATCTTTTCTCAAATTCATGAGTA 57.051 29.630 6.96 0.00 45.65 2.59
3223 3458 3.266510 TGAGTATTAGTGGCTGGCTTG 57.733 47.619 2.00 0.00 0.00 4.01
3302 3733 2.168936 TGTACACGTGGACCTTCTGTTT 59.831 45.455 27.68 0.00 0.00 2.83
3303 3734 3.384146 TGTACACGTGGACCTTCTGTTTA 59.616 43.478 27.68 2.88 0.00 2.01
3631 4396 3.026879 CGCTGCTGATCCGCTACG 61.027 66.667 10.62 9.80 0.00 3.51
3732 4497 2.685897 ACCAAGTTTTTCGCTGCTGTTA 59.314 40.909 0.00 0.00 0.00 2.41
3733 4498 3.042887 CCAAGTTTTTCGCTGCTGTTAC 58.957 45.455 0.00 0.00 0.00 2.50
3734 4499 3.042887 CAAGTTTTTCGCTGCTGTTACC 58.957 45.455 0.00 0.00 0.00 2.85
3735 4500 1.607148 AGTTTTTCGCTGCTGTTACCC 59.393 47.619 0.00 0.00 0.00 3.69
3736 4501 1.335496 GTTTTTCGCTGCTGTTACCCA 59.665 47.619 0.00 0.00 0.00 4.51
3737 4502 0.948678 TTTTCGCTGCTGTTACCCAC 59.051 50.000 0.00 0.00 0.00 4.61
3738 4503 0.107831 TTTCGCTGCTGTTACCCACT 59.892 50.000 0.00 0.00 0.00 4.00
3739 4504 0.320421 TTCGCTGCTGTTACCCACTC 60.320 55.000 0.00 0.00 0.00 3.51
3740 4505 1.741770 CGCTGCTGTTACCCACTCC 60.742 63.158 0.00 0.00 0.00 3.85
3741 4506 1.679898 GCTGCTGTTACCCACTCCT 59.320 57.895 0.00 0.00 0.00 3.69
3742 4507 0.902531 GCTGCTGTTACCCACTCCTA 59.097 55.000 0.00 0.00 0.00 2.94
3743 4508 1.405661 GCTGCTGTTACCCACTCCTAC 60.406 57.143 0.00 0.00 0.00 3.18
3744 4509 1.207329 CTGCTGTTACCCACTCCTACC 59.793 57.143 0.00 0.00 0.00 3.18
3745 4510 1.272807 GCTGTTACCCACTCCTACCA 58.727 55.000 0.00 0.00 0.00 3.25
3746 4511 1.626825 GCTGTTACCCACTCCTACCAA 59.373 52.381 0.00 0.00 0.00 3.67
3747 4512 2.039348 GCTGTTACCCACTCCTACCAAA 59.961 50.000 0.00 0.00 0.00 3.28
3748 4513 3.497227 GCTGTTACCCACTCCTACCAAAA 60.497 47.826 0.00 0.00 0.00 2.44
3749 4514 4.809691 GCTGTTACCCACTCCTACCAAAAT 60.810 45.833 0.00 0.00 0.00 1.82
3750 4515 4.658063 TGTTACCCACTCCTACCAAAATG 58.342 43.478 0.00 0.00 0.00 2.32
3751 4516 4.351407 TGTTACCCACTCCTACCAAAATGA 59.649 41.667 0.00 0.00 0.00 2.57
3752 4517 3.721087 ACCCACTCCTACCAAAATGAG 57.279 47.619 0.00 0.00 0.00 2.90
3753 4518 2.986728 ACCCACTCCTACCAAAATGAGT 59.013 45.455 0.00 0.00 38.56 3.41
3757 4522 3.753272 CACTCCTACCAAAATGAGTGTGG 59.247 47.826 9.69 0.00 46.02 4.17
3758 4523 4.746702 CACTCCTACCAAAATGAGTGTGGT 60.747 45.833 0.00 0.00 46.02 4.16
3759 4524 4.141251 ACTCCTACCAAAATGAGTGTGGTT 60.141 41.667 0.00 0.00 43.19 3.67
3760 4525 4.141287 TCCTACCAAAATGAGTGTGGTTG 58.859 43.478 0.00 0.00 43.19 3.77
3761 4526 4.141287 CCTACCAAAATGAGTGTGGTTGA 58.859 43.478 0.00 0.00 43.19 3.18
3762 4527 4.766891 CCTACCAAAATGAGTGTGGTTGAT 59.233 41.667 0.00 0.00 43.19 2.57
3763 4528 5.243730 CCTACCAAAATGAGTGTGGTTGATT 59.756 40.000 0.00 0.00 43.19 2.57
3764 4529 5.612725 ACCAAAATGAGTGTGGTTGATTT 57.387 34.783 0.00 0.00 43.19 2.17
3765 4530 6.723298 ACCAAAATGAGTGTGGTTGATTTA 57.277 33.333 0.00 0.00 43.19 1.40
3766 4531 6.748132 ACCAAAATGAGTGTGGTTGATTTAG 58.252 36.000 0.00 0.00 43.19 1.85
3767 4532 6.323739 ACCAAAATGAGTGTGGTTGATTTAGT 59.676 34.615 0.00 0.00 43.19 2.24
3768 4533 7.504238 ACCAAAATGAGTGTGGTTGATTTAGTA 59.496 33.333 0.00 0.00 43.19 1.82
3769 4534 7.807907 CCAAAATGAGTGTGGTTGATTTAGTAC 59.192 37.037 0.00 0.00 0.00 2.73
3770 4535 8.349245 CAAAATGAGTGTGGTTGATTTAGTACA 58.651 33.333 0.00 0.00 0.00 2.90
3771 4536 8.458573 AAATGAGTGTGGTTGATTTAGTACAA 57.541 30.769 0.00 0.00 0.00 2.41
3772 4537 8.635765 AATGAGTGTGGTTGATTTAGTACAAT 57.364 30.769 0.00 0.00 0.00 2.71
3773 4538 8.635765 ATGAGTGTGGTTGATTTAGTACAATT 57.364 30.769 0.00 0.00 0.00 2.32
3774 4539 8.458573 TGAGTGTGGTTGATTTAGTACAATTT 57.541 30.769 0.00 0.00 0.00 1.82
3775 4540 8.908903 TGAGTGTGGTTGATTTAGTACAATTTT 58.091 29.630 0.00 0.00 0.00 1.82
3790 4555 8.561738 AGTACAATTTTAGTACACTGGATTGG 57.438 34.615 7.17 0.00 43.24 3.16
3791 4556 6.834168 ACAATTTTAGTACACTGGATTGGG 57.166 37.500 0.00 0.00 31.34 4.12
3792 4557 6.311735 ACAATTTTAGTACACTGGATTGGGT 58.688 36.000 0.00 0.00 31.34 4.51
3793 4558 6.433093 ACAATTTTAGTACACTGGATTGGGTC 59.567 38.462 0.00 0.00 31.34 4.46
3803 4568 1.668419 GGATTGGGTCCTCGAACATG 58.332 55.000 0.00 0.00 44.16 3.21
3804 4569 1.017387 GATTGGGTCCTCGAACATGC 58.983 55.000 0.00 0.00 0.00 4.06
3805 4570 0.620556 ATTGGGTCCTCGAACATGCT 59.379 50.000 0.00 0.00 0.00 3.79
3806 4571 0.321564 TTGGGTCCTCGAACATGCTG 60.322 55.000 0.00 0.00 0.00 4.41
3807 4572 1.191489 TGGGTCCTCGAACATGCTGA 61.191 55.000 0.00 0.00 0.00 4.26
3808 4573 0.179000 GGGTCCTCGAACATGCTGAT 59.821 55.000 0.00 0.00 0.00 2.90
3809 4574 1.576356 GGTCCTCGAACATGCTGATC 58.424 55.000 0.00 0.00 0.00 2.92
3810 4575 1.137872 GGTCCTCGAACATGCTGATCT 59.862 52.381 0.00 0.00 0.00 2.75
3811 4576 2.362397 GGTCCTCGAACATGCTGATCTA 59.638 50.000 0.00 0.00 0.00 1.98
3812 4577 3.376540 GTCCTCGAACATGCTGATCTAC 58.623 50.000 0.00 0.00 0.00 2.59
3813 4578 3.067461 GTCCTCGAACATGCTGATCTACT 59.933 47.826 0.00 0.00 0.00 2.57
3814 4579 3.701542 TCCTCGAACATGCTGATCTACTT 59.298 43.478 0.00 0.00 0.00 2.24
3815 4580 3.801050 CCTCGAACATGCTGATCTACTTG 59.199 47.826 0.00 0.00 0.00 3.16
3816 4581 3.785486 TCGAACATGCTGATCTACTTGG 58.215 45.455 0.00 0.00 0.00 3.61
3817 4582 2.868583 CGAACATGCTGATCTACTTGGG 59.131 50.000 0.00 0.00 0.00 4.12
3818 4583 3.209410 GAACATGCTGATCTACTTGGGG 58.791 50.000 0.00 0.00 0.00 4.96
3819 4584 1.133976 ACATGCTGATCTACTTGGGGC 60.134 52.381 0.00 0.00 0.00 5.80
3820 4585 1.134007 CATGCTGATCTACTTGGGGCA 60.134 52.381 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.268076 AATCACGGGGCAACTGCAC 61.268 57.895 3.76 0.00 45.53 4.57
48 49 0.893727 AACAATGCCTCCCGGTCAAC 60.894 55.000 0.00 0.00 0.00 3.18
57 58 1.390463 GACGAAGACGAACAATGCCTC 59.610 52.381 0.00 0.00 42.66 4.70
88 89 2.654863 CGGCATTGGGAACTAGGAAAT 58.345 47.619 0.00 0.00 0.00 2.17
128 136 1.351430 TTCAGCTGAATTCGCGGTCG 61.351 55.000 25.16 0.13 0.00 4.79
160 168 2.885644 CGACCATTGTCCGGCTCG 60.886 66.667 0.00 0.00 38.32 5.03
204 212 0.545787 TGGGCGAGTAAAGAAGGGGA 60.546 55.000 0.00 0.00 0.00 4.81
304 338 1.777461 CGATAGTACGCGTTGGTTAGC 59.223 52.381 20.78 7.11 0.00 3.09
318 352 2.739932 GCCTGATGCTTCACACGATAGT 60.740 50.000 0.00 0.00 45.10 2.12
340 374 2.410774 GCAATGCGCTCGATTAGATCAC 60.411 50.000 9.73 0.00 37.77 3.06
409 445 1.614385 CGTTGTCGATCGTTGCTACT 58.386 50.000 15.94 0.00 39.71 2.57
411 447 0.522626 TCCGTTGTCGATCGTTGCTA 59.477 50.000 15.94 1.40 39.71 3.49
412 448 0.732880 CTCCGTTGTCGATCGTTGCT 60.733 55.000 15.94 0.00 39.71 3.91
413 449 1.007336 ACTCCGTTGTCGATCGTTGC 61.007 55.000 15.94 7.51 39.71 4.17
414 450 0.708370 CACTCCGTTGTCGATCGTTG 59.292 55.000 15.94 1.70 39.71 4.10
415 451 0.594602 TCACTCCGTTGTCGATCGTT 59.405 50.000 15.94 0.00 39.71 3.85
428 476 1.620822 AGGTTGTGCCAAATCACTCC 58.379 50.000 0.00 0.00 40.61 3.85
624 674 1.691215 CTCTTTTCTCGCTCGCTGGC 61.691 60.000 0.00 0.00 0.00 4.85
630 680 0.461163 GGCCTCCTCTTTTCTCGCTC 60.461 60.000 0.00 0.00 0.00 5.03
697 747 0.390340 TAGTTGGCTCGCTGCTTCAG 60.390 55.000 0.00 0.00 42.39 3.02
715 765 2.364579 ACGAGGCCGATGGGGTTA 60.365 61.111 0.00 0.00 39.50 2.85
858 936 0.462375 ACTGCGTTGGAGTGTGTGTA 59.538 50.000 0.00 0.00 0.00 2.90
873 953 1.505353 GAGATGCTGTTGCCACTGC 59.495 57.895 12.18 12.18 45.68 4.40
916 1004 4.390297 CCGCTCTGGAAAGAACTAAAGAAG 59.610 45.833 0.00 0.00 42.00 2.85
923 1011 0.036858 GAGCCGCTCTGGAAAGAACT 60.037 55.000 13.42 0.00 42.00 3.01
924 1012 0.036858 AGAGCCGCTCTGGAAAGAAC 60.037 55.000 22.32 0.00 39.62 3.01
948 1037 3.330992 TCGAGAGAGGCGAGGAGCA 62.331 63.158 0.00 0.00 41.58 4.26
961 1050 0.110956 GTACGTATGCGCGATCGAGA 60.111 55.000 23.47 8.16 42.83 4.04
1089 1183 3.462678 GGGCTGGAGAGGTCGACC 61.463 72.222 27.67 27.67 0.00 4.79
1421 1532 0.305922 GTATCGCAGTGGCTTGCATC 59.694 55.000 13.44 0.00 44.28 3.91
1482 1593 1.359833 CTGCAAACACACGCCATGT 59.640 52.632 0.00 0.00 44.81 3.21
1605 1716 4.530857 CCTCCGCCGTCACCATCC 62.531 72.222 0.00 0.00 0.00 3.51
1857 1968 0.251832 GTCAGGGTCAGGACTCAGGA 60.252 60.000 1.62 0.00 33.19 3.86
1859 1970 0.605589 GTGTCAGGGTCAGGACTCAG 59.394 60.000 1.62 0.00 33.19 3.35
1861 1972 1.179814 ACGTGTCAGGGTCAGGACTC 61.180 60.000 0.00 0.00 35.11 3.36
1862 1973 1.152525 ACGTGTCAGGGTCAGGACT 60.153 57.895 0.00 0.00 35.11 3.85
1863 1974 1.006102 CACGTGTCAGGGTCAGGAC 60.006 63.158 7.58 0.00 34.63 3.85
1904 2015 9.777575 GCTAGTAGTAGTAGAAAAAGAACAGAG 57.222 37.037 15.07 0.00 0.00 3.35
2033 2148 1.539388 TGGTGATGATGCGAACCAAAC 59.461 47.619 0.00 0.00 39.71 2.93
2034 2149 1.811965 CTGGTGATGATGCGAACCAAA 59.188 47.619 0.00 0.00 41.98 3.28
2035 2150 1.271325 ACTGGTGATGATGCGAACCAA 60.271 47.619 0.00 0.00 41.98 3.67
2036 2151 0.324614 ACTGGTGATGATGCGAACCA 59.675 50.000 0.00 0.00 40.36 3.67
2037 2152 2.309528 TACTGGTGATGATGCGAACC 57.690 50.000 0.00 0.00 0.00 3.62
2142 2263 8.934023 AAGGTTAGATGTGACATCCTTAAAAA 57.066 30.769 21.05 4.81 32.96 1.94
2143 2264 7.610305 GGAAGGTTAGATGTGACATCCTTAAAA 59.390 37.037 21.05 6.42 34.55 1.52
2144 2265 7.110155 GGAAGGTTAGATGTGACATCCTTAAA 58.890 38.462 21.05 8.69 34.55 1.52
2145 2266 6.214615 TGGAAGGTTAGATGTGACATCCTTAA 59.785 38.462 21.05 11.73 34.55 1.85
2146 2267 5.724370 TGGAAGGTTAGATGTGACATCCTTA 59.276 40.000 21.05 6.22 34.55 2.69
2147 2268 4.536090 TGGAAGGTTAGATGTGACATCCTT 59.464 41.667 21.05 17.24 36.67 3.36
2148 2269 4.080863 GTGGAAGGTTAGATGTGACATCCT 60.081 45.833 21.05 9.66 0.00 3.24
2149 2270 4.192317 GTGGAAGGTTAGATGTGACATCC 58.808 47.826 21.05 7.40 0.00 3.51
2150 2271 4.832248 TGTGGAAGGTTAGATGTGACATC 58.168 43.478 17.46 17.46 0.00 3.06
2151 2272 4.908601 TGTGGAAGGTTAGATGTGACAT 57.091 40.909 0.00 0.00 0.00 3.06
2152 2273 4.698201 TTGTGGAAGGTTAGATGTGACA 57.302 40.909 0.00 0.00 0.00 3.58
2153 2274 4.819630 TGTTTGTGGAAGGTTAGATGTGAC 59.180 41.667 0.00 0.00 0.00 3.67
2154 2275 5.042463 TGTTTGTGGAAGGTTAGATGTGA 57.958 39.130 0.00 0.00 0.00 3.58
2155 2276 5.241506 ACATGTTTGTGGAAGGTTAGATGTG 59.758 40.000 0.00 0.00 33.85 3.21
2156 2277 5.385198 ACATGTTTGTGGAAGGTTAGATGT 58.615 37.500 0.00 0.00 33.85 3.06
2157 2278 5.964958 ACATGTTTGTGGAAGGTTAGATG 57.035 39.130 0.00 0.00 33.85 2.90
2158 2279 7.669722 ACATTACATGTTTGTGGAAGGTTAGAT 59.330 33.333 2.30 0.00 41.63 1.98
2159 2280 7.001674 ACATTACATGTTTGTGGAAGGTTAGA 58.998 34.615 2.30 0.00 41.63 2.10
2160 2281 7.214467 ACATTACATGTTTGTGGAAGGTTAG 57.786 36.000 2.30 0.00 41.63 2.34
2161 2282 7.094549 GCTACATTACATGTTTGTGGAAGGTTA 60.095 37.037 21.40 3.89 41.63 2.85
2162 2283 6.294508 GCTACATTACATGTTTGTGGAAGGTT 60.295 38.462 21.40 1.26 41.63 3.50
2163 2284 5.183140 GCTACATTACATGTTTGTGGAAGGT 59.817 40.000 21.40 12.23 41.63 3.50
2164 2285 5.182950 TGCTACATTACATGTTTGTGGAAGG 59.817 40.000 21.40 7.72 41.63 3.46
2165 2286 6.252967 TGCTACATTACATGTTTGTGGAAG 57.747 37.500 21.40 13.56 41.63 3.46
2166 2287 6.039829 TGTTGCTACATTACATGTTTGTGGAA 59.960 34.615 21.40 12.88 41.63 3.53
2167 2288 5.532779 TGTTGCTACATTACATGTTTGTGGA 59.467 36.000 21.40 12.01 41.63 4.02
2168 2289 5.767269 TGTTGCTACATTACATGTTTGTGG 58.233 37.500 19.06 17.50 41.63 4.17
2169 2290 7.691430 TTTGTTGCTACATTACATGTTTGTG 57.309 32.000 19.06 11.94 41.63 3.33
2170 2291 8.709386 TTTTTGTTGCTACATTACATGTTTGT 57.291 26.923 2.30 11.32 41.63 2.83
2222 2343 9.911788 AACTGATGTCCACTTTATTTATGATCT 57.088 29.630 0.00 0.00 0.00 2.75
2267 2388 8.504005 CGGTTTGTTTATTTTATGAGTCTGTCT 58.496 33.333 0.00 0.00 0.00 3.41
2268 2389 8.500773 TCGGTTTGTTTATTTTATGAGTCTGTC 58.499 33.333 0.00 0.00 0.00 3.51
2269 2390 8.385898 TCGGTTTGTTTATTTTATGAGTCTGT 57.614 30.769 0.00 0.00 0.00 3.41
2270 2391 8.717821 TCTCGGTTTGTTTATTTTATGAGTCTG 58.282 33.333 0.00 0.00 0.00 3.51
2271 2392 8.842358 TCTCGGTTTGTTTATTTTATGAGTCT 57.158 30.769 0.00 0.00 0.00 3.24
2272 2393 9.887406 TTTCTCGGTTTGTTTATTTTATGAGTC 57.113 29.630 0.00 0.00 0.00 3.36
2275 2396 9.171701 CGTTTTCTCGGTTTGTTTATTTTATGA 57.828 29.630 0.00 0.00 0.00 2.15
2276 2397 9.171701 TCGTTTTCTCGGTTTGTTTATTTTATG 57.828 29.630 0.00 0.00 0.00 1.90
2277 2398 9.733219 TTCGTTTTCTCGGTTTGTTTATTTTAT 57.267 25.926 0.00 0.00 0.00 1.40
2278 2399 9.565213 TTTCGTTTTCTCGGTTTGTTTATTTTA 57.435 25.926 0.00 0.00 0.00 1.52
2279 2400 8.463456 TTTCGTTTTCTCGGTTTGTTTATTTT 57.537 26.923 0.00 0.00 0.00 1.82
2287 2408 5.565695 TCTTTCTTTCGTTTTCTCGGTTTG 58.434 37.500 0.00 0.00 0.00 2.93
2315 2436 6.294397 GCATCACAACCATCTCTTTCTTTCTT 60.294 38.462 0.00 0.00 0.00 2.52
2316 2437 5.182760 GCATCACAACCATCTCTTTCTTTCT 59.817 40.000 0.00 0.00 0.00 2.52
2317 2438 5.048504 TGCATCACAACCATCTCTTTCTTTC 60.049 40.000 0.00 0.00 0.00 2.62
2318 2439 4.828939 TGCATCACAACCATCTCTTTCTTT 59.171 37.500 0.00 0.00 0.00 2.52
2319 2440 4.217118 GTGCATCACAACCATCTCTTTCTT 59.783 41.667 0.00 0.00 34.08 2.52
2320 2441 3.755378 GTGCATCACAACCATCTCTTTCT 59.245 43.478 0.00 0.00 34.08 2.52
2321 2442 3.425359 CGTGCATCACAACCATCTCTTTC 60.425 47.826 0.00 0.00 33.40 2.62
2322 2443 2.485426 CGTGCATCACAACCATCTCTTT 59.515 45.455 0.00 0.00 33.40 2.52
2323 2444 2.079158 CGTGCATCACAACCATCTCTT 58.921 47.619 0.00 0.00 33.40 2.85
2324 2445 1.002430 ACGTGCATCACAACCATCTCT 59.998 47.619 0.00 0.00 33.40 3.10
2325 2446 1.394917 GACGTGCATCACAACCATCTC 59.605 52.381 0.00 0.00 33.40 2.75
2326 2447 1.442769 GACGTGCATCACAACCATCT 58.557 50.000 0.00 0.00 33.40 2.90
2465 2592 2.260844 TAGTAAGATGCCATGCAGCC 57.739 50.000 0.05 0.00 46.90 4.85
2489 2621 1.603802 GCAGCAAGAACACACAGCTAA 59.396 47.619 0.00 0.00 33.59 3.09
2510 2642 8.593492 AGGCATATATACGATACGATACGTAA 57.407 34.615 0.00 0.00 45.39 3.18
2552 2692 6.018343 CACACACACATCCCAAAAATAAAACC 60.018 38.462 0.00 0.00 0.00 3.27
2565 2705 1.156736 GCACCTACACACACACATCC 58.843 55.000 0.00 0.00 0.00 3.51
2573 2728 1.226746 GTTGGTCAGCACCTACACAC 58.773 55.000 3.45 0.00 45.11 3.82
2577 2732 1.375523 CCCGTTGGTCAGCACCTAC 60.376 63.158 0.00 0.00 44.17 3.18
2885 3040 2.279784 GCCACGGCAGCTAGCTAG 60.280 66.667 18.86 16.84 44.79 3.42
2886 3041 1.040893 TAAGCCACGGCAGCTAGCTA 61.041 55.000 18.86 0.00 44.88 3.32
2887 3042 1.690219 ATAAGCCACGGCAGCTAGCT 61.690 55.000 12.68 12.68 44.88 3.32
2888 3043 1.227674 ATAAGCCACGGCAGCTAGC 60.228 57.895 6.62 6.62 44.88 3.42
2889 3044 0.179073 ACATAAGCCACGGCAGCTAG 60.179 55.000 11.35 0.00 44.88 3.42
2890 3045 0.251916 AACATAAGCCACGGCAGCTA 59.748 50.000 11.35 0.00 44.88 3.32
2891 3046 0.609131 AAACATAAGCCACGGCAGCT 60.609 50.000 11.35 0.00 44.88 4.24
2892 3047 0.179163 GAAACATAAGCCACGGCAGC 60.179 55.000 11.35 0.00 44.88 5.25
2905 3060 0.586319 CTTCACGGTGTGCGAAACAT 59.414 50.000 8.17 0.00 41.97 2.71
2907 3062 0.042448 GTCTTCACGGTGTGCGAAAC 60.042 55.000 8.17 0.00 32.98 2.78
2912 3070 0.596600 TCTTCGTCTTCACGGTGTGC 60.597 55.000 8.17 0.00 46.70 4.57
2919 3077 6.096036 TCTTCATCTTCATCTTCGTCTTCAC 58.904 40.000 0.00 0.00 0.00 3.18
2921 3079 5.748152 CCTCTTCATCTTCATCTTCGTCTTC 59.252 44.000 0.00 0.00 0.00 2.87
2922 3080 5.420421 TCCTCTTCATCTTCATCTTCGTCTT 59.580 40.000 0.00 0.00 0.00 3.01
2923 3081 4.952957 TCCTCTTCATCTTCATCTTCGTCT 59.047 41.667 0.00 0.00 0.00 4.18
2924 3082 5.255710 TCCTCTTCATCTTCATCTTCGTC 57.744 43.478 0.00 0.00 0.00 4.20
2925 3083 5.667539 TTCCTCTTCATCTTCATCTTCGT 57.332 39.130 0.00 0.00 0.00 3.85
2926 3084 5.006552 GCTTTCCTCTTCATCTTCATCTTCG 59.993 44.000 0.00 0.00 0.00 3.79
2927 3085 6.114767 AGCTTTCCTCTTCATCTTCATCTTC 58.885 40.000 0.00 0.00 0.00 2.87
2928 3086 6.064735 AGCTTTCCTCTTCATCTTCATCTT 57.935 37.500 0.00 0.00 0.00 2.40
2929 3087 5.697082 AGCTTTCCTCTTCATCTTCATCT 57.303 39.130 0.00 0.00 0.00 2.90
2946 3104 7.778382 TGTTTCCCTTTCTTTTCTAGTAGCTTT 59.222 33.333 0.00 0.00 0.00 3.51
2947 3105 7.287810 TGTTTCCCTTTCTTTTCTAGTAGCTT 58.712 34.615 0.00 0.00 0.00 3.74
2948 3106 6.838382 TGTTTCCCTTTCTTTTCTAGTAGCT 58.162 36.000 0.00 0.00 0.00 3.32
2965 3134 5.940470 TCATCTTCTTTTAGCTCTGTTTCCC 59.060 40.000 0.00 0.00 0.00 3.97
2966 3135 7.622893 ATCATCTTCTTTTAGCTCTGTTTCC 57.377 36.000 0.00 0.00 0.00 3.13
2974 3143 8.510505 GTGTCTTGAAATCATCTTCTTTTAGCT 58.489 33.333 0.00 0.00 0.00 3.32
2998 3167 1.086067 CCGCAGCTCTACCACATGTG 61.086 60.000 19.31 19.31 0.00 3.21
2999 3168 1.219124 CCGCAGCTCTACCACATGT 59.781 57.895 0.00 0.00 0.00 3.21
3002 3171 2.970639 GTCCGCAGCTCTACCACA 59.029 61.111 0.00 0.00 0.00 4.17
3005 3179 1.355916 CTACGTCCGCAGCTCTACC 59.644 63.158 0.00 0.00 0.00 3.18
3019 3193 6.194876 CACACGAAAAAGATCTACTAGCTACG 59.805 42.308 0.00 0.00 0.00 3.51
3034 3215 1.581402 CGCACACGCACACGAAAAA 60.581 52.632 0.00 0.00 43.93 1.94
3035 3216 2.022069 CGCACACGCACACGAAAA 59.978 55.556 0.00 0.00 43.93 2.29
3053 3234 4.918060 CGCACACGCACACACACG 62.918 66.667 0.00 0.00 38.40 4.49
3057 3238 3.858989 CACACGCACACGCACACA 61.859 61.111 0.00 0.00 45.53 3.72
3064 3245 1.864711 ACTATGAACACACACGCACAC 59.135 47.619 0.00 0.00 0.00 3.82
3065 3246 2.232756 ACTATGAACACACACGCACA 57.767 45.000 0.00 0.00 0.00 4.57
3066 3247 2.903678 CAACTATGAACACACACGCAC 58.096 47.619 0.00 0.00 0.00 5.34
3067 3248 1.262950 GCAACTATGAACACACACGCA 59.737 47.619 0.00 0.00 0.00 5.24
3068 3249 1.531149 AGCAACTATGAACACACACGC 59.469 47.619 0.00 0.00 0.00 5.34
3154 3335 8.414778 GCTATATCTGGTTCACACTAACTAACT 58.585 37.037 0.00 0.00 0.00 2.24
3155 3336 8.414778 AGCTATATCTGGTTCACACTAACTAAC 58.585 37.037 0.00 0.00 0.00 2.34
3156 3337 8.534954 AGCTATATCTGGTTCACACTAACTAA 57.465 34.615 0.00 0.00 0.00 2.24
3208 3437 1.849039 AGATCCAAGCCAGCCACTAAT 59.151 47.619 0.00 0.00 0.00 1.73
3209 3438 1.289160 AGATCCAAGCCAGCCACTAA 58.711 50.000 0.00 0.00 0.00 2.24
3214 3443 1.260544 AAACAAGATCCAAGCCAGCC 58.739 50.000 0.00 0.00 0.00 4.85
3215 3444 2.560105 AGAAAACAAGATCCAAGCCAGC 59.440 45.455 0.00 0.00 0.00 4.85
3223 3458 5.235516 TCGGAAGTACAGAAAACAAGATCC 58.764 41.667 0.00 0.00 0.00 3.36
3302 3733 4.133820 CGTTGGATCATTGGCAGGTTATA 58.866 43.478 0.00 0.00 0.00 0.98
3303 3734 2.951642 CGTTGGATCATTGGCAGGTTAT 59.048 45.455 0.00 0.00 0.00 1.89
3631 4396 0.593128 AAAGATGTCACAGGCAACGC 59.407 50.000 0.00 0.00 46.39 4.84
3654 4419 3.587498 TCCAGGACTCCAGAAGAGAAAA 58.413 45.455 0.00 0.00 46.50 2.29
3732 4497 2.986728 ACTCATTTTGGTAGGAGTGGGT 59.013 45.455 0.00 0.00 39.04 4.51
3733 4498 3.721087 ACTCATTTTGGTAGGAGTGGG 57.279 47.619 0.00 0.00 39.04 4.61
3736 4501 3.394606 ACCACACTCATTTTGGTAGGAGT 59.605 43.478 0.00 0.00 42.04 3.85
3737 4502 4.021102 ACCACACTCATTTTGGTAGGAG 57.979 45.455 0.00 0.00 42.04 3.69
3738 4503 4.141287 CAACCACACTCATTTTGGTAGGA 58.859 43.478 0.00 0.00 43.08 2.94
3739 4504 4.141287 TCAACCACACTCATTTTGGTAGG 58.859 43.478 0.00 0.00 43.08 3.18
3740 4505 5.964958 ATCAACCACACTCATTTTGGTAG 57.035 39.130 0.00 0.00 43.08 3.18
3741 4506 6.723298 AAATCAACCACACTCATTTTGGTA 57.277 33.333 0.00 0.00 43.08 3.25
3742 4507 5.612725 AAATCAACCACACTCATTTTGGT 57.387 34.783 0.00 0.00 45.95 3.67
3743 4508 6.748132 ACTAAATCAACCACACTCATTTTGG 58.252 36.000 0.00 0.00 36.39 3.28
3744 4509 8.349245 TGTACTAAATCAACCACACTCATTTTG 58.651 33.333 0.00 0.00 0.00 2.44
3745 4510 8.458573 TGTACTAAATCAACCACACTCATTTT 57.541 30.769 0.00 0.00 0.00 1.82
3746 4511 8.458573 TTGTACTAAATCAACCACACTCATTT 57.541 30.769 0.00 0.00 0.00 2.32
3747 4512 8.635765 ATTGTACTAAATCAACCACACTCATT 57.364 30.769 0.00 0.00 0.00 2.57
3748 4513 8.635765 AATTGTACTAAATCAACCACACTCAT 57.364 30.769 0.00 0.00 0.00 2.90
3749 4514 8.458573 AAATTGTACTAAATCAACCACACTCA 57.541 30.769 0.00 0.00 0.00 3.41
3764 4529 9.661563 CCAATCCAGTGTACTAAAATTGTACTA 57.338 33.333 6.24 0.00 40.44 1.82
3765 4530 7.610305 CCCAATCCAGTGTACTAAAATTGTACT 59.390 37.037 6.24 0.00 40.44 2.73
3766 4531 7.392393 ACCCAATCCAGTGTACTAAAATTGTAC 59.608 37.037 0.00 0.00 40.27 2.90
3767 4532 7.463431 ACCCAATCCAGTGTACTAAAATTGTA 58.537 34.615 0.00 0.00 0.00 2.41
3768 4533 6.311735 ACCCAATCCAGTGTACTAAAATTGT 58.688 36.000 0.00 0.00 0.00 2.71
3769 4534 6.834168 ACCCAATCCAGTGTACTAAAATTG 57.166 37.500 0.00 0.00 0.00 2.32
3785 4550 1.017387 GCATGTTCGAGGACCCAATC 58.983 55.000 0.00 0.00 0.00 2.67
3786 4551 0.620556 AGCATGTTCGAGGACCCAAT 59.379 50.000 0.00 0.00 0.00 3.16
3787 4552 0.321564 CAGCATGTTCGAGGACCCAA 60.322 55.000 0.00 0.00 0.00 4.12
3788 4553 1.191489 TCAGCATGTTCGAGGACCCA 61.191 55.000 0.00 0.00 37.40 4.51
3789 4554 0.179000 ATCAGCATGTTCGAGGACCC 59.821 55.000 0.00 0.00 37.40 4.46
3790 4555 1.137872 AGATCAGCATGTTCGAGGACC 59.862 52.381 0.00 0.00 39.72 4.46
3791 4556 2.593346 AGATCAGCATGTTCGAGGAC 57.407 50.000 0.00 0.00 39.72 3.85
3792 4557 3.291584 AGTAGATCAGCATGTTCGAGGA 58.708 45.455 0.00 0.00 39.72 3.71
3793 4558 3.724508 AGTAGATCAGCATGTTCGAGG 57.275 47.619 0.00 0.00 39.72 4.63
3794 4559 3.801050 CCAAGTAGATCAGCATGTTCGAG 59.199 47.826 0.00 0.00 39.72 4.04
3795 4560 3.430790 CCCAAGTAGATCAGCATGTTCGA 60.431 47.826 0.00 0.00 39.72 3.71
3796 4561 2.868583 CCCAAGTAGATCAGCATGTTCG 59.131 50.000 0.00 0.00 39.72 3.95
3797 4562 3.209410 CCCCAAGTAGATCAGCATGTTC 58.791 50.000 0.00 0.00 37.40 3.18
3798 4563 2.684927 GCCCCAAGTAGATCAGCATGTT 60.685 50.000 0.00 0.00 37.40 2.71
3799 4564 1.133976 GCCCCAAGTAGATCAGCATGT 60.134 52.381 0.00 0.00 37.40 3.21
3800 4565 1.134007 TGCCCCAAGTAGATCAGCATG 60.134 52.381 0.00 0.00 37.54 4.06
3801 4566 1.216064 TGCCCCAAGTAGATCAGCAT 58.784 50.000 0.00 0.00 0.00 3.79
3802 4567 2.695561 TGCCCCAAGTAGATCAGCA 58.304 52.632 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.