Multiple sequence alignment - TraesCS1D01G238300

Loading Multiple Alignment...

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 TraesCS1D01G238300 chr1D 100.000 4181 0 0 1 4181 327995236 327991056 0.000000e+00 7721.0
1 TraesCS1D01G238300 chr1D 81.560 141 21 5 3668 3803 296363320 296363180 1.230000e-20 111.0
2 TraesCS1D01G238300 chr1B 93.484 2118 106 18 614 2725 442111051 442108960 0.000000e+00 3118.0
3 TraesCS1D01G238300 chr1B 86.693 1503 112 36 2725 4181 442108893 442107433 0.000000e+00 1587.0
4 TraesCS1D01G238300 chr1B 81.429 140 22 4 3668 3803 397818004 397817865 1.230000e-20 111.0
5 TraesCS1D01G238300 chr1A 92.369 2123 113 24 608 2725 407117351 407115273 0.000000e+00 2977.0
6 TraesCS1D01G238300 chr1A 89.900 1198 91 18 2725 3899 407115206 407114016 0.000000e+00 1515.0
7 TraesCS1D01G238300 chr1A 90.998 611 39 12 1 603 407127644 407127042 0.000000e+00 809.0
8 TraesCS1D01G238300 chr1A 89.503 181 11 6 3887 4062 408071201 408071378 5.440000e-54 222.0
9 TraesCS1D01G238300 chr1A 82.857 140 20 4 3668 3803 369087372 369087233 5.680000e-24 122.0
10 TraesCS1D01G238300 chr1A 75.352 142 29 6 3667 3804 368816379 368816240 3.490000e-06 63.9
11 TraesCS1D01G238300 chr5D 75.546 458 65 30 2281 2721 508621335 508621762 9.230000e-42 182.0
12 TraesCS1D01G238300 chr5D 89.600 125 8 2 991 1115 508620163 508620282 2.010000e-33 154.0
13 TraesCS1D01G238300 chr5D 79.091 220 37 5 1552 1764 508620694 508620911 4.360000e-30 143.0
14 TraesCS1D01G238300 chr5D 87.629 97 11 1 3098 3194 508622408 508622503 1.230000e-20 111.0
15 TraesCS1D01G238300 chr5B 82.888 187 27 4 1582 1764 638486378 638486193 3.340000e-36 163.0
16 TraesCS1D01G238300 chr5B 95.789 95 4 0 991 1085 638486956 638486862 2.010000e-33 154.0
17 TraesCS1D01G238300 chr5A 73.987 469 78 27 2268 2721 635958165 635958604 2.600000e-32 150.0
18 TraesCS1D01G238300 chr5A 93.478 92 6 0 991 1082 635957059 635957150 2.030000e-28 137.0
19 TraesCS1D01G238300 chr5A 95.238 42 2 0 3763 3804 79138017 79138058 2.700000e-07 67.6
20 TraesCS1D01G238300 chr7A 79.755 163 28 5 3636 3796 162954310 162954469 3.420000e-21 113.0
21 TraesCS1D01G238300 chr2B 83.333 126 13 4 1647 1764 106119311 106119186 4.420000e-20 110.0
22 TraesCS1D01G238300 chr7D 94.595 37 2 0 3768 3804 459944741 459944777 1.620000e-04 58.4


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 TraesCS1D01G238300 chr1D 327991056 327995236 4180 True 7721.0 7721 100.0000 1 4181 1 chr1D.!!$R2 4180
1 TraesCS1D01G238300 chr1B 442107433 442111051 3618 True 2352.5 3118 90.0885 614 4181 2 chr1B.!!$R2 3567
2 TraesCS1D01G238300 chr1A 407114016 407117351 3335 True 2246.0 2977 91.1345 608 3899 2 chr1A.!!$R4 3291
3 TraesCS1D01G238300 chr1A 407127042 407127644 602 True 809.0 809 90.9980 1 603 1 chr1A.!!$R3 602

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
261 266 0.254747 CCCAAACAAGCCGGGATAGA 59.745 55.000 2.18 0.0 43.21 1.98 F
622 631 0.321564 TGACTGAAAGCCCGGACATG 60.322 55.000 0.73 0.0 37.60 3.21 F
1385 1397 0.110056 GAAATGTGCACGAGCCACTG 60.110 55.000 13.13 0.0 41.13 3.66 F
1386 1398 0.819259 AAATGTGCACGAGCCACTGT 60.819 50.000 13.13 0.0 41.13 3.55 F
2778 2864 1.206610 CCACTGCACTGCTGTATCTCT 59.793 52.381 12.69 0.0 38.59 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1205 0.165944 CGCGCCTTTCGATCAAAACT 59.834 50.000 0.00 0.0 41.67 2.66 R
1665 1680 2.373169 TCCCTTCCATATGATCAGTGCC 59.627 50.000 3.65 0.0 0.00 5.01 R
2780 2866 2.154462 CCTGAAAAGGCAGTTCGTCAT 58.846 47.619 0.00 0.0 34.06 3.06 R
2922 3008 3.036819 TCACTAGCATGAAGGCAGATCT 58.963 45.455 0.00 0.0 35.83 2.75 R
4115 4250 0.615331 TCCCAGACTTTAGCAGGCAG 59.385 55.000 0.00 0.0 29.16 4.85 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
63 64 1.203570 GGGATGGGGGTATAGGTGGAT 60.204 57.143 0.00 0.00 0.00 3.41
67 68 1.677552 GGGGTATAGGTGGATGCGG 59.322 63.158 0.00 0.00 0.00 5.69
68 69 1.125711 GGGGTATAGGTGGATGCGGT 61.126 60.000 0.00 0.00 0.00 5.68
71 72 1.623811 GGTATAGGTGGATGCGGTGAT 59.376 52.381 0.00 0.00 0.00 3.06
73 74 0.397941 ATAGGTGGATGCGGTGATGG 59.602 55.000 0.00 0.00 0.00 3.51
74 75 0.689412 TAGGTGGATGCGGTGATGGA 60.689 55.000 0.00 0.00 0.00 3.41
83 84 1.087501 GCGGTGATGGAAAAGAGGAC 58.912 55.000 0.00 0.00 0.00 3.85
107 108 2.086869 CTGGTGATGGTAGTGGCAAAG 58.913 52.381 0.00 0.00 0.00 2.77
130 131 5.420421 AGATGAGATGGGAGGTATAATGACG 59.580 44.000 0.00 0.00 0.00 4.35
134 135 4.287067 AGATGGGAGGTATAATGACGCAAT 59.713 41.667 0.00 0.00 0.00 3.56
159 161 4.918810 AGGTCTCCAATTTTCACAACAC 57.081 40.909 0.00 0.00 0.00 3.32
202 204 8.103935 GGGGATGGGTGTTGAAATTTTAATAAA 58.896 33.333 0.00 0.00 0.00 1.40
227 232 2.094734 ACTTTCCAACAACAACGACGAC 59.905 45.455 0.00 0.00 0.00 4.34
230 235 2.281517 TCCAACAACAACGACGACAAT 58.718 42.857 0.00 0.00 0.00 2.71
235 240 2.066262 CAACAACGACGACAATAGCCT 58.934 47.619 0.00 0.00 0.00 4.58
240 245 4.387862 ACAACGACGACAATAGCCTTTTAG 59.612 41.667 0.00 0.00 0.00 1.85
253 258 2.288825 GCCTTTTAGTCCCAAACAAGCC 60.289 50.000 0.00 0.00 0.00 4.35
255 260 1.611519 TTTAGTCCCAAACAAGCCGG 58.388 50.000 0.00 0.00 0.00 6.13
261 266 0.254747 CCCAAACAAGCCGGGATAGA 59.745 55.000 2.18 0.00 43.21 1.98
275 280 4.202131 CCGGGATAGACTAGAGTTGAAACC 60.202 50.000 0.00 0.00 0.00 3.27
281 286 9.059260 GGATAGACTAGAGTTGAAACCTAGTAG 57.941 40.741 17.15 0.00 40.18 2.57
290 295 8.706521 AGAGTTGAAACCTAGTAGAAAGACTTT 58.293 33.333 0.00 0.00 0.00 2.66
294 299 7.974504 TGAAACCTAGTAGAAAGACTTTCCAT 58.025 34.615 21.67 11.92 40.54 3.41
295 300 7.878127 TGAAACCTAGTAGAAAGACTTTCCATG 59.122 37.037 21.67 9.67 40.54 3.66
346 354 5.996669 CAATGTGATCTAGCATTGCTACA 57.003 39.130 14.33 13.19 43.28 2.74
350 358 5.922053 TGTGATCTAGCATTGCTACAATCT 58.078 37.500 23.66 8.26 40.44 2.40
603 612 1.079127 CCTCGTTCGTGGCCAGATT 60.079 57.895 5.11 0.00 0.00 2.40
604 613 1.361668 CCTCGTTCGTGGCCAGATTG 61.362 60.000 5.11 0.00 0.00 2.67
605 614 0.389817 CTCGTTCGTGGCCAGATTGA 60.390 55.000 5.11 0.00 0.00 2.57
606 615 0.669318 TCGTTCGTGGCCAGATTGAC 60.669 55.000 5.11 0.00 0.00 3.18
618 627 0.984230 AGATTGACTGAAAGCCCGGA 59.016 50.000 0.73 0.00 37.60 5.14
620 629 0.400213 ATTGACTGAAAGCCCGGACA 59.600 50.000 0.73 0.00 37.60 4.02
622 631 0.321564 TGACTGAAAGCCCGGACATG 60.322 55.000 0.73 0.00 37.60 3.21
674 683 6.127619 CCAAGATTCAAAGAATGGAACCTACC 60.128 42.308 0.00 0.00 0.00 3.18
707 716 5.276868 CGATCCCAATTCAACGAACAGATAC 60.277 44.000 0.00 0.00 0.00 2.24
719 728 4.278669 ACGAACAGATACGGATTAGCTGAT 59.721 41.667 0.00 0.00 45.65 2.90
721 730 5.795939 CGAACAGATACGGATTAGCTGATAC 59.204 44.000 0.00 0.00 45.65 2.24
724 733 5.472478 ACAGATACGGATTAGCTGATACGAA 59.528 40.000 28.03 0.00 45.65 3.85
750 759 1.058903 GAAACGAGCCGAACGCATC 59.941 57.895 1.50 0.00 41.38 3.91
762 771 1.291877 AACGCATCAACACCGAGCTC 61.292 55.000 2.73 2.73 0.00 4.09
958 967 2.280552 CCTCCCCTCGGACGAAACA 61.281 63.158 0.00 0.00 33.32 2.83
965 974 4.204891 CGGACGAAACATCGCCGC 62.205 66.667 16.48 1.09 42.18 6.53
980 989 2.902846 CGCGAGAGAGATCCCCGT 60.903 66.667 0.00 0.00 0.00 5.28
1108 1118 3.356529 TTTTGCTCTCCCATCTCTTCC 57.643 47.619 0.00 0.00 0.00 3.46
1110 1120 2.260639 TGCTCTCCCATCTCTTCCTT 57.739 50.000 0.00 0.00 0.00 3.36
1121 1131 0.734253 CTCTTCCTTGTCTCCGCGTG 60.734 60.000 4.92 0.00 0.00 5.34
1166 1176 3.499737 GCGGCGGGATTCACAGTG 61.500 66.667 9.78 0.00 0.00 3.66
1194 1205 0.991355 ACCCTGTGGACCAGTTTGGA 60.991 55.000 0.00 0.00 39.74 3.53
1215 1227 2.521733 TTTTGATCGAAAGGCGCGGC 62.522 55.000 27.06 27.06 40.61 6.53
1223 1235 2.786564 GAAAGGCGCGGCTCTGTTTG 62.787 60.000 36.31 0.00 0.00 2.93
1273 1285 1.696884 GAGGCAGGGAGGATCTAAAGG 59.303 57.143 0.00 0.00 33.73 3.11
1281 1293 6.529220 CAGGGAGGATCTAAAGGAAATAGTG 58.471 44.000 0.00 0.00 33.73 2.74
1324 1336 2.436173 GGGGTTCTTGATCTGGTCCTAG 59.564 54.545 0.00 0.00 0.00 3.02
1339 1351 4.406003 TGGTCCTAGGAGCTTTATGAAGTC 59.594 45.833 34.54 10.11 42.49 3.01
1385 1397 0.110056 GAAATGTGCACGAGCCACTG 60.110 55.000 13.13 0.00 41.13 3.66
1386 1398 0.819259 AAATGTGCACGAGCCACTGT 60.819 50.000 13.13 0.00 41.13 3.55
1413 1426 4.017808 GACTGACAGCCTTAGAGGACTAA 58.982 47.826 1.25 0.00 37.67 2.24
1422 1435 4.900054 GCCTTAGAGGACTAAACTGGGATA 59.100 45.833 0.00 0.00 37.67 2.59
1447 1460 2.821378 GGCCGTGTTGTTTTTACCCTAT 59.179 45.455 0.00 0.00 0.00 2.57
1453 1466 7.413328 GCCGTGTTGTTTTTACCCTATTACTAG 60.413 40.741 0.00 0.00 0.00 2.57
1454 1467 7.413328 CCGTGTTGTTTTTACCCTATTACTAGC 60.413 40.741 0.00 0.00 0.00 3.42
1457 1470 8.158789 TGTTGTTTTTACCCTATTACTAGCAGT 58.841 33.333 0.00 0.00 0.00 4.40
1458 1471 9.657419 GTTGTTTTTACCCTATTACTAGCAGTA 57.343 33.333 0.00 0.00 0.00 2.74
1459 1472 9.880157 TTGTTTTTACCCTATTACTAGCAGTAG 57.120 33.333 0.00 0.00 31.47 2.57
1460 1473 9.258629 TGTTTTTACCCTATTACTAGCAGTAGA 57.741 33.333 0.00 0.00 31.47 2.59
1497 1510 4.747623 TGCTCCTTGCTTCTGAAAATCAGA 60.748 41.667 5.98 5.98 45.71 3.27
1590 1603 6.095440 GGGTTTTTGCTGCTCTTAGATATTGA 59.905 38.462 0.00 0.00 0.00 2.57
1665 1680 3.131396 GGCAGGTATGATTGTTACCTCG 58.869 50.000 0.00 0.00 44.97 4.63
1669 1684 2.870411 GGTATGATTGTTACCTCGGCAC 59.130 50.000 0.00 0.00 36.88 5.01
1771 1786 5.454613 CCTGGATTTAAAAGGGTTTGTTGCT 60.455 40.000 0.00 0.00 0.00 3.91
1783 1798 2.961522 TTGTTGCTTACTTACGCAGC 57.038 45.000 0.00 0.00 37.46 5.25
1981 1996 7.305763 GGACACACACATTCGTTTTTGTAATTC 60.306 37.037 0.00 0.00 0.00 2.17
2017 2032 6.528537 TGACCAATATGAAATCCCAAAGTG 57.471 37.500 0.00 0.00 0.00 3.16
2104 2119 4.038642 GCTTCCATTGGGTTGTAAGTGAAA 59.961 41.667 2.09 0.00 34.93 2.69
2122 2137 6.069331 AGTGAAAGACTATCCTATCGCCTTA 58.931 40.000 0.00 0.00 30.86 2.69
2166 2181 9.231297 CATCCAAGTTTCCTTTTGAGATTACTA 57.769 33.333 0.00 0.00 0.00 1.82
2264 2280 2.489938 TCATTTGCACTAGTGTCCCC 57.510 50.000 23.44 7.92 0.00 4.81
2560 2579 9.076596 GTGATCAAGGTAATAAAATTGTGAAGC 57.923 33.333 0.00 0.00 0.00 3.86
2619 2638 9.686683 ATACATATTAGACCTGCAAGTCTTTTT 57.313 29.630 22.51 10.62 44.83 1.94
2638 2657 8.491950 GTCTTTTTGTGCTTGTTTTGAGTTTAA 58.508 29.630 0.00 0.00 0.00 1.52
2730 2816 8.249638 TCTGTCATTTTCTGTTTGAATCAACAA 58.750 29.630 0.00 0.00 34.24 2.83
2778 2864 1.206610 CCACTGCACTGCTGTATCTCT 59.793 52.381 12.69 0.00 38.59 3.10
2780 2866 3.118992 CCACTGCACTGCTGTATCTCTAA 60.119 47.826 12.69 0.00 38.59 2.10
2894 2980 2.955881 GCGGGCTGTAGGGTGAGTT 61.956 63.158 0.00 0.00 0.00 3.01
2895 2981 1.677552 CGGGCTGTAGGGTGAGTTT 59.322 57.895 0.00 0.00 0.00 2.66
2898 2984 1.339151 GGGCTGTAGGGTGAGTTTCTG 60.339 57.143 0.00 0.00 0.00 3.02
2903 2989 4.807643 GCTGTAGGGTGAGTTTCTGGAAAT 60.808 45.833 0.00 0.00 32.36 2.17
2936 3022 5.763698 ACATTCACATAGATCTGCCTTCATG 59.236 40.000 5.18 2.28 0.00 3.07
2939 3025 4.590222 TCACATAGATCTGCCTTCATGCTA 59.410 41.667 5.18 0.00 0.00 3.49
2942 3028 3.472283 AGATCTGCCTTCATGCTAGTG 57.528 47.619 0.00 0.00 0.00 2.74
2947 3033 4.005650 TCTGCCTTCATGCTAGTGAAAAG 58.994 43.478 0.00 0.00 37.63 2.27
2965 3051 7.039784 AGTGAAAAGTAATTCAGCTGGCATTAA 60.040 33.333 15.13 0.00 39.84 1.40
2966 3052 7.761249 GTGAAAAGTAATTCAGCTGGCATTAAT 59.239 33.333 15.13 12.83 39.84 1.40
2975 3061 5.713025 TCAGCTGGCATTAATCTTTTGTTC 58.287 37.500 15.13 0.00 0.00 3.18
2976 3062 5.477984 TCAGCTGGCATTAATCTTTTGTTCT 59.522 36.000 15.13 0.00 0.00 3.01
3033 3119 2.479566 TTGTGATGACTGAGAAGCCC 57.520 50.000 0.00 0.00 0.00 5.19
3056 3142 7.232534 GCCCATCATTAAGGTATGTTTATTCCA 59.767 37.037 0.00 0.00 0.00 3.53
3075 3167 3.585289 TCCATTTAAGTACTGACCAGCCA 59.415 43.478 0.00 0.00 0.00 4.75
3077 3169 4.764823 CCATTTAAGTACTGACCAGCCAAA 59.235 41.667 0.00 0.00 0.00 3.28
3083 3176 3.521126 AGTACTGACCAGCCAAATCTGAT 59.479 43.478 0.00 0.00 36.19 2.90
3171 3264 1.331756 GGCCTGCTTGTCATAACATCG 59.668 52.381 0.00 0.00 34.73 3.84
3194 3287 3.567478 AGAGTGAAGCTGTCAACCTTT 57.433 42.857 0.00 0.00 38.23 3.11
3195 3288 4.689612 AGAGTGAAGCTGTCAACCTTTA 57.310 40.909 0.00 0.00 38.23 1.85
3196 3289 4.636249 AGAGTGAAGCTGTCAACCTTTAG 58.364 43.478 0.00 0.00 38.23 1.85
3197 3290 3.142174 AGTGAAGCTGTCAACCTTTAGC 58.858 45.455 0.00 0.00 38.23 3.09
3198 3291 2.878406 GTGAAGCTGTCAACCTTTAGCA 59.122 45.455 0.00 0.00 38.23 3.49
3199 3292 2.878406 TGAAGCTGTCAACCTTTAGCAC 59.122 45.455 0.00 0.00 38.59 4.40
3200 3293 2.638480 AGCTGTCAACCTTTAGCACA 57.362 45.000 0.00 0.00 38.59 4.57
3201 3294 3.146104 AGCTGTCAACCTTTAGCACAT 57.854 42.857 0.00 0.00 38.59 3.21
3202 3295 4.286297 AGCTGTCAACCTTTAGCACATA 57.714 40.909 0.00 0.00 38.59 2.29
3203 3296 4.256920 AGCTGTCAACCTTTAGCACATAG 58.743 43.478 0.00 0.00 38.59 2.23
3206 3299 5.048713 GCTGTCAACCTTTAGCACATAGTTT 60.049 40.000 0.00 0.00 36.24 2.66
3323 3430 4.210331 CCTAAACCTGGCTCTTATGCAAT 58.790 43.478 0.00 0.00 34.04 3.56
3327 3434 4.510167 ACCTGGCTCTTATGCAATAGTT 57.490 40.909 0.00 0.00 34.04 2.24
3496 3604 4.526970 TGTTCCTATTTCTGATTGAGCCC 58.473 43.478 0.00 0.00 0.00 5.19
3528 3636 5.048013 GGGAATTGGAACTGGAACTTGTAAG 60.048 44.000 0.00 0.00 0.00 2.34
3536 3644 4.324267 ACTGGAACTTGTAAGTATGTGCC 58.676 43.478 0.00 0.00 38.57 5.01
3540 3648 3.955650 ACTTGTAAGTATGTGCCGTCT 57.044 42.857 0.00 0.00 37.52 4.18
3547 3655 0.796312 GTATGTGCCGTCTTGTGTGG 59.204 55.000 0.00 0.00 0.00 4.17
3555 3664 1.159285 CGTCTTGTGTGGACATGCAT 58.841 50.000 0.00 0.00 33.73 3.96
3557 3666 2.938451 CGTCTTGTGTGGACATGCATAT 59.062 45.455 0.00 0.00 33.73 1.78
3561 3670 5.180117 GTCTTGTGTGGACATGCATATATCC 59.820 44.000 14.22 14.22 34.23 2.59
3584 3693 1.064758 AGTTTGATCTATGCCGGCCAA 60.065 47.619 26.77 16.83 0.00 4.52
3620 3733 1.008327 TGCCCTCATCTCCTGGAAGTA 59.992 52.381 0.00 0.00 0.00 2.24
3637 3750 5.365605 TGGAAGTATACGGTTTCAGATGGAT 59.634 40.000 0.00 0.00 0.00 3.41
3650 3763 7.093771 GGTTTCAGATGGATTTTGATAACCAGT 60.094 37.037 0.00 0.00 35.06 4.00
3659 3772 6.293735 GGATTTTGATAACCAGTGAACGTTCA 60.294 38.462 26.53 26.53 34.20 3.18
3660 3773 6.627395 TTTTGATAACCAGTGAACGTTCAT 57.373 33.333 31.81 18.81 39.73 2.57
3667 3780 3.980646 CAGTGAACGTTCATTGGGAAA 57.019 42.857 33.94 10.62 40.11 3.13
3668 3781 3.888934 CAGTGAACGTTCATTGGGAAAG 58.111 45.455 33.94 16.07 40.11 2.62
3669 3782 2.293399 AGTGAACGTTCATTGGGAAAGC 59.707 45.455 31.81 16.40 38.38 3.51
3670 3783 2.034053 GTGAACGTTCATTGGGAAAGCA 59.966 45.455 31.81 4.02 38.38 3.91
3671 3784 2.890311 TGAACGTTCATTGGGAAAGCAT 59.110 40.909 26.53 0.00 38.38 3.79
3673 3786 1.545582 ACGTTCATTGGGAAAGCATGG 59.454 47.619 0.00 0.00 38.38 3.66
3674 3787 1.736696 CGTTCATTGGGAAAGCATGGC 60.737 52.381 0.00 0.00 37.23 4.40
3676 3789 1.642112 TCATTGGGAAAGCATGGCAA 58.358 45.000 0.00 0.00 0.00 4.52
3677 3790 1.976404 TCATTGGGAAAGCATGGCAAA 59.024 42.857 0.00 0.00 0.00 3.68
3678 3791 2.572556 TCATTGGGAAAGCATGGCAAAT 59.427 40.909 0.00 0.00 0.00 2.32
3679 3792 2.766345 TTGGGAAAGCATGGCAAATC 57.234 45.000 0.00 0.00 0.00 2.17
3680 3793 0.531657 TGGGAAAGCATGGCAAATCG 59.468 50.000 0.00 0.00 0.00 3.34
3682 3795 1.204467 GGGAAAGCATGGCAAATCGAA 59.796 47.619 0.00 0.00 0.00 3.71
3683 3796 2.159057 GGGAAAGCATGGCAAATCGAAT 60.159 45.455 0.00 0.00 0.00 3.34
3684 3797 2.861935 GGAAAGCATGGCAAATCGAATG 59.138 45.455 0.00 0.00 0.00 2.67
3693 3806 6.035866 GCATGGCAAATCGAATGTTTTTCATA 59.964 34.615 0.00 0.00 35.48 2.15
3710 3823 9.000018 GTTTTTCATAGCAATTTATGTCGTCTC 58.000 33.333 0.00 0.00 33.66 3.36
3840 3972 0.104855 GTCATGCCTCGCTGGACATA 59.895 55.000 0.00 0.00 38.35 2.29
3873 4005 7.072076 TGCATGCTGATCAGGAGGATATAATAT 59.928 37.037 29.67 3.52 36.00 1.28
3885 4017 9.720874 AGGAGGATATAATATATCTGCACTCAA 57.279 33.333 17.02 0.00 0.00 3.02
3899 4031 0.178958 ACTCAACTCGTCCAGTCCCT 60.179 55.000 0.00 0.00 32.30 4.20
3900 4032 0.969894 CTCAACTCGTCCAGTCCCTT 59.030 55.000 0.00 0.00 32.30 3.95
3901 4033 0.966920 TCAACTCGTCCAGTCCCTTC 59.033 55.000 0.00 0.00 32.30 3.46
3914 4046 1.221021 CCCTTCTACGGGGTGCTTC 59.779 63.158 0.00 0.00 40.75 3.86
3923 4055 1.906574 ACGGGGTGCTTCATCTTCTTA 59.093 47.619 0.00 0.00 0.00 2.10
3925 4057 3.054361 ACGGGGTGCTTCATCTTCTTATT 60.054 43.478 0.00 0.00 0.00 1.40
3926 4058 3.947834 CGGGGTGCTTCATCTTCTTATTT 59.052 43.478 0.00 0.00 0.00 1.40
3927 4059 4.399303 CGGGGTGCTTCATCTTCTTATTTT 59.601 41.667 0.00 0.00 0.00 1.82
3928 4060 5.588648 CGGGGTGCTTCATCTTCTTATTTTA 59.411 40.000 0.00 0.00 0.00 1.52
3929 4061 6.238484 CGGGGTGCTTCATCTTCTTATTTTAG 60.238 42.308 0.00 0.00 0.00 1.85
3933 4065 7.905493 GGTGCTTCATCTTCTTATTTTAGTTCG 59.095 37.037 0.00 0.00 0.00 3.95
3949 4081 4.677673 AGTTCGTACACCTGTAACCTTT 57.322 40.909 0.00 0.00 31.52 3.11
3958 4090 3.003689 CACCTGTAACCTTTTGCTCACAG 59.996 47.826 0.00 0.00 34.54 3.66
3971 4103 3.873910 TGCTCACAGTCCTATTTTAGGC 58.126 45.455 0.00 0.00 45.82 3.93
3981 4115 3.567164 TCCTATTTTAGGCGTCGGTAGAG 59.433 47.826 0.00 0.00 45.82 2.43
3997 4131 4.141574 CGGTAGAGGGGGAATAATTTGACA 60.142 45.833 0.00 0.00 0.00 3.58
4003 4137 3.103742 GGGGAATAATTTGACAAGGGCA 58.896 45.455 0.00 0.00 0.00 5.36
4010 4144 0.401738 TTTGACAAGGGCAGAGGGAG 59.598 55.000 0.00 0.00 0.00 4.30
4017 4151 3.934962 GGCAGAGGGAGGATCGGC 61.935 72.222 0.00 0.00 37.18 5.54
4071 4206 3.296854 TGGTGATAGGATAAGACGCTGT 58.703 45.455 0.00 0.00 0.00 4.40
4074 4209 2.693074 TGATAGGATAAGACGCTGTGCA 59.307 45.455 0.00 0.00 0.00 4.57
4082 4217 1.308047 AGACGCTGTGCATGTTGAAA 58.692 45.000 0.00 0.00 0.00 2.69
4115 4250 6.037391 ACGTACTGTCTGATAAGCTAGAACTC 59.963 42.308 0.00 0.00 0.00 3.01
4116 4251 6.259167 CGTACTGTCTGATAAGCTAGAACTCT 59.741 42.308 0.00 0.00 0.00 3.24
4120 4255 4.340950 GTCTGATAAGCTAGAACTCTGCCT 59.659 45.833 0.00 0.00 0.00 4.75
4144 4279 0.181350 AAGTCTGGGAATCCGATGCC 59.819 55.000 0.00 0.00 35.24 4.40
4147 4282 0.690744 TCTGGGAATCCGATGCCTCA 60.691 55.000 5.30 1.47 35.24 3.86
4150 4285 0.533755 GGGAATCCGATGCCTCAGTG 60.534 60.000 5.30 0.00 0.00 3.66
4164 4299 0.682852 TCAGTGGGTCCGTACTTTGG 59.317 55.000 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.466189 CCTTTAGCATCGCCCATGGT 60.466 55.000 11.73 1.05 45.51 3.55
63 64 0.690192 TCCTCTTTTCCATCACCGCA 59.310 50.000 0.00 0.00 0.00 5.69
67 68 2.003301 GCTCGTCCTCTTTTCCATCAC 58.997 52.381 0.00 0.00 0.00 3.06
68 69 1.902508 AGCTCGTCCTCTTTTCCATCA 59.097 47.619 0.00 0.00 0.00 3.07
71 72 0.321671 CCAGCTCGTCCTCTTTTCCA 59.678 55.000 0.00 0.00 0.00 3.53
73 74 1.000955 TCACCAGCTCGTCCTCTTTTC 59.999 52.381 0.00 0.00 0.00 2.29
74 75 1.048601 TCACCAGCTCGTCCTCTTTT 58.951 50.000 0.00 0.00 0.00 2.27
83 84 0.179100 CCACTACCATCACCAGCTCG 60.179 60.000 0.00 0.00 0.00 5.03
107 108 5.655488 CGTCATTATACCTCCCATCTCATC 58.345 45.833 0.00 0.00 0.00 2.92
130 131 6.127647 TGTGAAAATTGGAGACCTATCATTGC 60.128 38.462 0.00 0.00 0.00 3.56
134 135 6.206634 GTGTTGTGAAAATTGGAGACCTATCA 59.793 38.462 0.00 0.00 0.00 2.15
170 172 1.229529 AACACCCATCCCCGTCTCT 60.230 57.895 0.00 0.00 0.00 3.10
172 174 1.131303 TTCAACACCCATCCCCGTCT 61.131 55.000 0.00 0.00 0.00 4.18
173 175 0.250989 TTTCAACACCCATCCCCGTC 60.251 55.000 0.00 0.00 0.00 4.79
174 176 0.407918 ATTTCAACACCCATCCCCGT 59.592 50.000 0.00 0.00 0.00 5.28
202 204 4.670735 CGTCGTTGTTGTTGGAAAGTCTTT 60.671 41.667 0.00 0.00 0.00 2.52
221 226 3.550678 GGACTAAAAGGCTATTGTCGTCG 59.449 47.826 0.00 0.00 0.00 5.12
227 232 5.975693 TGTTTGGGACTAAAAGGCTATTG 57.024 39.130 0.00 0.00 0.00 1.90
230 235 3.824443 GCTTGTTTGGGACTAAAAGGCTA 59.176 43.478 0.00 0.00 0.00 3.93
235 240 1.957877 CCGGCTTGTTTGGGACTAAAA 59.042 47.619 0.00 0.00 0.00 1.52
240 245 2.114411 TCCCGGCTTGTTTGGGAC 59.886 61.111 0.00 0.00 46.96 4.46
253 258 4.645588 AGGTTTCAACTCTAGTCTATCCCG 59.354 45.833 0.00 0.00 0.00 5.14
255 260 7.885009 ACTAGGTTTCAACTCTAGTCTATCC 57.115 40.000 11.86 0.00 37.95 2.59
261 266 8.795513 GTCTTTCTACTAGGTTTCAACTCTAGT 58.204 37.037 17.60 17.60 41.52 2.57
316 323 7.358066 CAATGCTAGATCACATTGTTATGTCC 58.642 38.462 19.87 0.00 45.16 4.02
325 332 6.996879 AGATTGTAGCAATGCTAGATCACATT 59.003 34.615 26.51 16.64 42.11 2.71
332 340 8.792830 AAAGTTTAGATTGTAGCAATGCTAGA 57.207 30.769 16.10 12.02 42.11 2.43
346 354 8.523658 GGTGGAGCATTAAGAAAAGTTTAGATT 58.476 33.333 0.00 0.00 0.00 2.40
350 358 6.071984 TGGGTGGAGCATTAAGAAAAGTTTA 58.928 36.000 0.00 0.00 0.00 2.01
368 376 7.554476 TGTTTTAAAGAAAATTCCTTTGGGTGG 59.446 33.333 13.12 0.00 36.92 4.61
558 567 0.251341 ACAGCTTTAGGCCCTGTTGG 60.251 55.000 0.00 0.00 43.05 3.77
603 612 0.321564 CATGTCCGGGCTTTCAGTCA 60.322 55.000 7.97 0.00 0.00 3.41
604 613 1.648467 GCATGTCCGGGCTTTCAGTC 61.648 60.000 7.97 0.00 0.00 3.51
605 614 1.675641 GCATGTCCGGGCTTTCAGT 60.676 57.895 7.97 0.00 0.00 3.41
606 615 1.377725 AGCATGTCCGGGCTTTCAG 60.378 57.895 7.97 0.00 36.92 3.02
618 627 0.398696 TGGTGGACCGTAAAGCATGT 59.601 50.000 0.00 0.00 39.43 3.21
620 629 2.279935 TTTGGTGGACCGTAAAGCAT 57.720 45.000 0.00 0.00 39.43 3.79
644 653 7.332678 GGTTCCATTCTTTGAATCTTGGAATTG 59.667 37.037 13.51 0.00 43.10 2.32
647 656 6.077322 AGGTTCCATTCTTTGAATCTTGGAA 58.923 36.000 8.79 8.79 40.08 3.53
648 657 5.644188 AGGTTCCATTCTTTGAATCTTGGA 58.356 37.500 0.00 0.00 27.46 3.53
649 658 5.990120 AGGTTCCATTCTTTGAATCTTGG 57.010 39.130 0.00 0.00 27.46 3.61
650 659 6.660949 AGGTAGGTTCCATTCTTTGAATCTTG 59.339 38.462 0.00 0.00 34.02 3.02
674 683 2.038952 TGAATTGGGATCGGATGGCTAG 59.961 50.000 0.00 0.00 0.00 3.42
707 716 2.316792 CGGTTCGTATCAGCTAATCCG 58.683 52.381 0.00 0.00 0.00 4.18
719 728 3.105157 GTTTCGGCGCGGTTCGTA 61.105 61.111 15.06 0.00 41.07 3.43
750 759 1.021390 GGATGGTGAGCTCGGTGTTG 61.021 60.000 9.64 0.00 0.00 3.33
762 771 3.066900 GGATAGATATCGGACGGATGGTG 59.933 52.174 5.80 0.00 36.55 4.17
958 967 2.622011 GGATCTCTCTCGCGGCGAT 61.622 63.158 26.60 9.84 34.61 4.58
965 974 1.225376 CTCGACGGGGATCTCTCTCG 61.225 65.000 6.21 6.21 0.00 4.04
1108 1118 2.671177 CCAAGCACGCGGAGACAAG 61.671 63.158 12.47 0.00 0.00 3.16
1110 1120 2.486636 CTACCAAGCACGCGGAGACA 62.487 60.000 12.47 0.00 0.00 3.41
1121 1131 5.123344 ACAACCGAAAATACATCTACCAAGC 59.877 40.000 0.00 0.00 0.00 4.01
1194 1205 0.165944 CGCGCCTTTCGATCAAAACT 59.834 50.000 0.00 0.00 41.67 2.66
1215 1227 5.479716 AACACGAAAACTACCAAACAGAG 57.520 39.130 0.00 0.00 0.00 3.35
1223 1235 3.322230 TGCGAAAACACGAAAACTACC 57.678 42.857 0.00 0.00 35.09 3.18
1273 1285 5.452356 CCTTCATGCCCCAAATCACTATTTC 60.452 44.000 0.00 0.00 32.87 2.17
1281 1293 1.197812 AAGCCTTCATGCCCCAAATC 58.802 50.000 0.00 0.00 0.00 2.17
1324 1336 5.864628 AGAAAACGACTTCATAAAGCTCC 57.135 39.130 0.00 0.00 35.81 4.70
1385 1397 4.442192 CCTCTAAGGCTGTCAGTCCAATAC 60.442 50.000 13.61 0.00 0.00 1.89
1386 1398 3.706594 CCTCTAAGGCTGTCAGTCCAATA 59.293 47.826 13.61 7.12 0.00 1.90
1413 1426 0.179056 CACGGCCGAATATCCCAGTT 60.179 55.000 35.90 0.00 0.00 3.16
1422 1435 2.287728 GGTAAAAACAACACGGCCGAAT 60.288 45.455 35.90 16.98 0.00 3.34
1453 1466 7.095439 GGAGCATCAACAAGTAATATCTACTGC 60.095 40.741 0.00 0.00 36.25 4.40
1454 1467 8.147058 AGGAGCATCAACAAGTAATATCTACTG 58.853 37.037 0.00 0.00 36.25 2.74
1457 1470 7.442364 GCAAGGAGCATCAACAAGTAATATCTA 59.558 37.037 0.00 0.00 44.79 1.98
1458 1471 6.261826 GCAAGGAGCATCAACAAGTAATATCT 59.738 38.462 0.00 0.00 44.79 1.98
1459 1472 6.433766 GCAAGGAGCATCAACAAGTAATATC 58.566 40.000 0.00 0.00 44.79 1.63
1460 1473 6.382869 GCAAGGAGCATCAACAAGTAATAT 57.617 37.500 0.00 0.00 44.79 1.28
1462 1475 4.708726 GCAAGGAGCATCAACAAGTAAT 57.291 40.909 0.00 0.00 44.79 1.89
1511 1524 5.305675 TGCTCCCCTCTTTCCCTATATAT 57.694 43.478 0.00 0.00 0.00 0.86
1572 1585 9.565090 AACAATTATCAATATCTAAGAGCAGCA 57.435 29.630 0.00 0.00 0.00 4.41
1609 1622 8.674263 AATCATGAATTCCTCTATGAGAACAC 57.326 34.615 0.00 0.00 33.53 3.32
1665 1680 2.373169 TCCCTTCCATATGATCAGTGCC 59.627 50.000 3.65 0.00 0.00 5.01
1669 1684 5.886474 CCATCAATCCCTTCCATATGATCAG 59.114 44.000 3.65 0.00 0.00 2.90
1717 1732 3.312736 ACCAGAAAGAACCACCACAAT 57.687 42.857 0.00 0.00 0.00 2.71
1783 1798 3.057806 ACAAAATTTAAGGGGTTCTCGCG 60.058 43.478 0.00 0.00 0.00 5.87
1817 1832 4.214986 TGGCCGTCAAGAATCTTATGAA 57.785 40.909 0.00 0.00 0.00 2.57
1822 1837 5.253330 TCTAAAATGGCCGTCAAGAATCTT 58.747 37.500 0.00 0.00 0.00 2.40
1833 1848 3.771577 AGAGGGTATCTAAAATGGCCG 57.228 47.619 0.00 0.00 36.10 6.13
1960 1975 6.961358 TCGAATTACAAAAACGAATGTGTG 57.039 33.333 0.00 0.00 0.00 3.82
2080 2095 2.890311 CACTTACAACCCAATGGAAGCA 59.110 45.455 0.00 0.00 43.77 3.91
2083 2098 5.300792 GTCTTTCACTTACAACCCAATGGAA 59.699 40.000 0.00 0.00 34.81 3.53
2104 2119 7.179269 AGATCTTTAAGGCGATAGGATAGTCT 58.821 38.462 0.00 0.00 0.00 3.24
2166 2181 3.290710 GAGAACATGGCATGGTGGTAAT 58.709 45.455 29.49 7.83 33.60 1.89
2368 2384 8.753175 GCTTACAAAGTACAATAATCGAGTAGG 58.247 37.037 0.00 0.00 0.00 3.18
2369 2385 8.753175 GGCTTACAAAGTACAATAATCGAGTAG 58.247 37.037 0.00 0.00 0.00 2.57
2593 2612 9.686683 AAAAAGACTTGCAGGTCTAATATGTAT 57.313 29.630 29.30 10.48 44.67 2.29
2606 2625 3.514645 ACAAGCACAAAAAGACTTGCAG 58.485 40.909 0.00 0.00 42.55 4.41
2643 2662 5.509840 GCCGTTCATGAACCTATACAGAGAT 60.510 44.000 28.40 0.00 38.03 2.75
2765 2851 5.358442 AGTTCGTCATTAGAGATACAGCAGT 59.642 40.000 0.00 0.00 0.00 4.40
2778 2864 3.751175 CCTGAAAAGGCAGTTCGTCATTA 59.249 43.478 0.00 0.00 34.06 1.90
2780 2866 2.154462 CCTGAAAAGGCAGTTCGTCAT 58.846 47.619 0.00 0.00 34.06 3.06
2894 2980 8.637099 TGTGAATGTGATACAAAATTTCCAGAA 58.363 29.630 0.00 0.00 0.00 3.02
2895 2981 8.175925 TGTGAATGTGATACAAAATTTCCAGA 57.824 30.769 0.00 0.00 0.00 3.86
2903 2989 8.615211 GCAGATCTATGTGAATGTGATACAAAA 58.385 33.333 0.00 0.00 0.00 2.44
2922 3008 3.036819 TCACTAGCATGAAGGCAGATCT 58.963 45.455 0.00 0.00 35.83 2.75
2923 3009 3.465742 TCACTAGCATGAAGGCAGATC 57.534 47.619 0.00 0.00 35.83 2.75
2924 3010 3.920231 TTCACTAGCATGAAGGCAGAT 57.080 42.857 0.00 0.00 33.62 2.90
2936 3022 5.674820 GCCAGCTGAATTACTTTTCACTAGC 60.675 44.000 17.39 0.00 32.39 3.42
2939 3025 4.144297 TGCCAGCTGAATTACTTTTCACT 58.856 39.130 17.39 0.00 32.39 3.41
2942 3028 8.193438 AGATTAATGCCAGCTGAATTACTTTTC 58.807 33.333 17.39 11.82 0.00 2.29
2947 3033 7.761249 ACAAAAGATTAATGCCAGCTGAATTAC 59.239 33.333 17.39 8.14 0.00 1.89
2966 3052 9.587772 GTAGATAGCTGTTCATAGAACAAAAGA 57.412 33.333 12.94 1.30 0.00 2.52
2975 3061 9.363763 CAACATATGGTAGATAGCTGTTCATAG 57.636 37.037 7.80 0.00 0.00 2.23
2976 3062 8.314021 CCAACATATGGTAGATAGCTGTTCATA 58.686 37.037 7.80 0.00 44.85 2.15
3056 3142 6.375455 CAGATTTGGCTGGTCAGTACTTAAAT 59.625 38.462 0.00 0.00 32.26 1.40
3075 3167 5.713389 TCATCAGTGCTTCCAAATCAGATTT 59.287 36.000 2.20 2.20 0.00 2.17
3077 3169 4.851843 TCATCAGTGCTTCCAAATCAGAT 58.148 39.130 0.00 0.00 0.00 2.90
3083 3176 3.575256 AGCATTTCATCAGTGCTTCCAAA 59.425 39.130 0.00 0.00 46.29 3.28
3156 3249 5.348724 TCACTCTTTCGATGTTATGACAAGC 59.651 40.000 0.00 0.00 39.66 4.01
3171 3264 3.471680 AGGTTGACAGCTTCACTCTTTC 58.528 45.455 0.00 0.00 32.26 2.62
3194 3287 9.678941 CTCGATTACAAGATAAACTATGTGCTA 57.321 33.333 0.00 0.00 0.00 3.49
3195 3288 7.653713 CCTCGATTACAAGATAAACTATGTGCT 59.346 37.037 0.00 0.00 0.00 4.40
3196 3289 7.095607 CCCTCGATTACAAGATAAACTATGTGC 60.096 40.741 0.00 0.00 0.00 4.57
3197 3290 7.095607 GCCCTCGATTACAAGATAAACTATGTG 60.096 40.741 0.00 0.00 0.00 3.21
3198 3291 6.929606 GCCCTCGATTACAAGATAAACTATGT 59.070 38.462 0.00 0.00 0.00 2.29
3199 3292 6.929049 TGCCCTCGATTACAAGATAAACTATG 59.071 38.462 0.00 0.00 0.00 2.23
3200 3293 7.015292 TCTGCCCTCGATTACAAGATAAACTAT 59.985 37.037 0.00 0.00 0.00 2.12
3201 3294 6.322969 TCTGCCCTCGATTACAAGATAAACTA 59.677 38.462 0.00 0.00 0.00 2.24
3202 3295 5.128827 TCTGCCCTCGATTACAAGATAAACT 59.871 40.000 0.00 0.00 0.00 2.66
3203 3296 5.357257 TCTGCCCTCGATTACAAGATAAAC 58.643 41.667 0.00 0.00 0.00 2.01
3206 3299 4.404394 TGTTCTGCCCTCGATTACAAGATA 59.596 41.667 0.00 0.00 0.00 1.98
3364 3471 5.182950 TCAACTGTTACACCCAATGCAATAG 59.817 40.000 0.00 0.00 30.90 1.73
3496 3604 3.256631 CCAGTTCCAATTCCCAAACTCTG 59.743 47.826 0.00 0.00 29.78 3.35
3528 3636 0.796312 CCACACAAGACGGCACATAC 59.204 55.000 0.00 0.00 0.00 2.39
3536 3644 1.159285 ATGCATGTCCACACAAGACG 58.841 50.000 0.00 0.00 37.04 4.18
3540 3648 5.046288 TGGATATATGCATGTCCACACAA 57.954 39.130 20.06 4.23 44.84 3.33
3547 3655 6.866010 TCAAACTGTGGATATATGCATGTC 57.134 37.500 10.16 4.77 0.00 3.06
3555 3664 6.398095 CGGCATAGATCAAACTGTGGATATA 58.602 40.000 0.00 1.26 31.36 0.86
3557 3666 4.503123 CCGGCATAGATCAAACTGTGGATA 60.503 45.833 0.00 0.00 31.36 2.59
3561 3670 1.331756 GCCGGCATAGATCAAACTGTG 59.668 52.381 24.80 0.00 33.30 3.66
3604 3713 4.145807 ACCGTATACTTCCAGGAGATGAG 58.854 47.826 0.56 0.00 0.00 2.90
3620 3733 8.621286 GTTATCAAAATCCATCTGAAACCGTAT 58.379 33.333 0.00 0.00 0.00 3.06
3637 3750 6.627395 ATGAACGTTCACTGGTTATCAAAA 57.373 33.333 31.87 5.40 40.49 2.44
3650 3763 2.302260 TGCTTTCCCAATGAACGTTCA 58.698 42.857 31.41 31.41 42.14 3.18
3659 3772 2.419021 CGATTTGCCATGCTTTCCCAAT 60.419 45.455 0.00 0.00 0.00 3.16
3660 3773 1.067000 CGATTTGCCATGCTTTCCCAA 60.067 47.619 0.00 0.00 0.00 4.12
3663 3776 2.652941 TTCGATTTGCCATGCTTTCC 57.347 45.000 0.00 0.00 0.00 3.13
3665 3778 3.598019 ACATTCGATTTGCCATGCTTT 57.402 38.095 0.00 0.00 0.00 3.51
3667 3780 3.598019 AAACATTCGATTTGCCATGCT 57.402 38.095 0.00 0.00 0.00 3.79
3668 3781 4.152045 TGAAAAACATTCGATTTGCCATGC 59.848 37.500 0.00 0.00 0.00 4.06
3669 3782 5.842619 TGAAAAACATTCGATTTGCCATG 57.157 34.783 0.00 0.00 0.00 3.66
3670 3783 6.256321 GCTATGAAAAACATTCGATTTGCCAT 59.744 34.615 0.00 0.00 40.07 4.40
3671 3784 5.576384 GCTATGAAAAACATTCGATTTGCCA 59.424 36.000 0.00 0.00 40.07 4.92
3673 3786 6.630676 TGCTATGAAAAACATTCGATTTGC 57.369 33.333 0.00 0.00 40.07 3.68
3678 3791 9.853555 ACATAAATTGCTATGAAAAACATTCGA 57.146 25.926 4.50 0.00 40.07 3.71
3682 3795 9.289303 GACGACATAAATTGCTATGAAAAACAT 57.711 29.630 4.50 0.00 42.39 2.71
3683 3796 8.511321 AGACGACATAAATTGCTATGAAAAACA 58.489 29.630 4.50 0.00 34.07 2.83
3684 3797 8.895932 AGACGACATAAATTGCTATGAAAAAC 57.104 30.769 4.50 0.00 34.07 2.43
3693 3806 4.471904 TCCTGAGACGACATAAATTGCT 57.528 40.909 0.00 0.00 0.00 3.91
3703 3816 2.029838 AATTGCCATCCTGAGACGAC 57.970 50.000 0.00 0.00 0.00 4.34
3705 3818 3.855689 AAAAATTGCCATCCTGAGACG 57.144 42.857 0.00 0.00 0.00 4.18
3776 3890 5.726980 TGACAAATTCCTTTAGCAAGCAT 57.273 34.783 0.00 0.00 0.00 3.79
3840 3972 3.958147 TCCTGATCAGCATGCAATTTCAT 59.042 39.130 21.98 1.56 34.76 2.57
3873 4005 2.167662 TGGACGAGTTGAGTGCAGATA 58.832 47.619 0.00 0.00 35.06 1.98
3885 4017 1.836802 GTAGAAGGGACTGGACGAGT 58.163 55.000 0.00 0.00 40.86 4.18
3899 4031 1.568504 AGATGAAGCACCCCGTAGAA 58.431 50.000 0.00 0.00 0.00 2.10
3900 4032 1.480954 GAAGATGAAGCACCCCGTAGA 59.519 52.381 0.00 0.00 0.00 2.59
3901 4033 1.482593 AGAAGATGAAGCACCCCGTAG 59.517 52.381 0.00 0.00 0.00 3.51
3914 4046 9.367444 AGGTGTACGAACTAAAATAAGAAGATG 57.633 33.333 0.00 0.00 0.00 2.90
3923 4055 6.762333 AGGTTACAGGTGTACGAACTAAAAT 58.238 36.000 0.00 0.00 0.00 1.82
3925 4057 5.789643 AGGTTACAGGTGTACGAACTAAA 57.210 39.130 0.00 0.00 0.00 1.85
3926 4058 5.789643 AAGGTTACAGGTGTACGAACTAA 57.210 39.130 0.00 0.00 0.00 2.24
3927 4059 5.789643 AAAGGTTACAGGTGTACGAACTA 57.210 39.130 0.00 0.00 0.00 2.24
3928 4060 4.677673 AAAGGTTACAGGTGTACGAACT 57.322 40.909 0.00 0.00 0.00 3.01
3929 4061 4.553351 GCAAAAGGTTACAGGTGTACGAAC 60.553 45.833 0.00 0.00 0.00 3.95
3933 4065 4.024302 GTGAGCAAAAGGTTACAGGTGTAC 60.024 45.833 0.00 0.00 0.00 2.90
3971 4103 1.696063 TTATTCCCCCTCTACCGACG 58.304 55.000 0.00 0.00 0.00 5.12
3981 4115 2.434336 GCCCTTGTCAAATTATTCCCCC 59.566 50.000 0.00 0.00 0.00 5.40
3997 4131 1.764054 CGATCCTCCCTCTGCCCTT 60.764 63.158 0.00 0.00 0.00 3.95
4003 4137 0.692419 ATTGTGCCGATCCTCCCTCT 60.692 55.000 0.00 0.00 0.00 3.69
4010 4144 2.948979 TGGTCAAATATTGTGCCGATCC 59.051 45.455 0.00 0.00 32.44 3.36
4017 4151 4.711721 CACGACACTGGTCAAATATTGTG 58.288 43.478 0.00 0.00 44.54 3.33
4071 4206 3.051327 CGTGCTTGATTTTCAACATGCA 58.949 40.909 0.00 0.00 42.05 3.96
4074 4209 5.008613 ACAGTACGTGCTTGATTTTCAACAT 59.991 36.000 2.37 0.00 32.21 2.71
4082 4217 3.660501 TCAGACAGTACGTGCTTGATT 57.339 42.857 2.37 0.00 0.00 2.57
4115 4250 0.615331 TCCCAGACTTTAGCAGGCAG 59.385 55.000 0.00 0.00 29.16 4.85
4116 4251 1.064003 TTCCCAGACTTTAGCAGGCA 58.936 50.000 0.00 0.00 29.16 4.75
4120 4255 2.184533 TCGGATTCCCAGACTTTAGCA 58.815 47.619 0.00 0.00 0.00 3.49
4144 4279 1.337823 CCAAAGTACGGACCCACTGAG 60.338 57.143 0.00 0.00 0.00 3.35
4147 4282 1.125711 AGCCAAAGTACGGACCCACT 61.126 55.000 0.00 0.00 0.00 4.00
4150 4285 1.208776 ACATAGCCAAAGTACGGACCC 59.791 52.381 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.