Multiple sequence alignment - TraesCS3B01G380200

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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 TraesCS3B01G380200 chr3B 100.000 3661 0 0 1 3661 597785995 597782335 0.000000e+00 6761.0
1 TraesCS3B01G380200 chr3B 85.635 181 20 4 2064 2241 597783755 597783932 6.240000e-43 185.0
2 TraesCS3B01G380200 chr3D 92.094 2669 140 29 336 2968 454897042 454894409 0.000000e+00 3694.0
3 TraesCS3B01G380200 chr3D 88.534 532 19 16 2877 3390 454894599 454894092 1.120000e-169 606.0
4 TraesCS3B01G380200 chr3D 92.941 255 10 5 3412 3660 454894027 454893775 7.470000e-97 364.0
5 TraesCS3B01G380200 chr3D 93.805 113 6 1 204 315 454897145 454897033 6.290000e-38 169.0
6 TraesCS3B01G380200 chr3D 84.971 173 17 7 2064 2232 454895141 454895308 2.260000e-37 167.0
7 TraesCS3B01G380200 chr3D 90.141 71 6 1 1 70 454897255 454897185 1.400000e-14 91.6
8 TraesCS3B01G380200 chr3D 87.838 74 8 1 2099 2172 454895210 454895282 6.510000e-13 86.1
9 TraesCS3B01G380200 chr3D 100.000 28 0 0 2179 2206 454895237 454895210 7.000000e-03 52.8
10 TraesCS3B01G380200 chr3A 93.001 1443 73 15 784 2202 597168226 597166788 0.000000e+00 2080.0
11 TraesCS3B01G380200 chr3A 92.549 1181 47 14 2216 3390 597166733 597165588 0.000000e+00 1655.0
12 TraesCS3B01G380200 chr3A 90.226 399 28 8 206 597 597168954 597168560 9.070000e-141 510.0
13 TraesCS3B01G380200 chr3A 94.779 249 13 0 3412 3660 597165523 597165275 4.430000e-104 388.0
14 TraesCS3B01G380200 chr3A 91.176 170 10 3 619 786 597168425 597168259 3.680000e-55 226.0
15 TraesCS3B01G380200 chr3A 98.551 69 1 0 2173 2241 597166857 597166925 4.960000e-24 122.0
16 TraesCS3B01G380200 chr3A 77.037 135 29 2 2099 2232 597166779 597166646 3.920000e-10 76.8
17 TraesCS3B01G380200 chr3A 75.362 138 26 6 2073 2206 597166646 597166779 3.950000e-05 60.2


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 TraesCS3B01G380200 chr3B 597782335 597785995 3660 True 6761.000000 6761 100.000000 1 3661 1 chr3B.!!$R1 3660
1 TraesCS3B01G380200 chr3D 454893775 454897255 3480 True 829.566667 3694 92.919167 1 3660 6 chr3D.!!$R1 3659
2 TraesCS3B01G380200 chr3A 597165275 597168954 3679 True 822.633333 2080 89.794667 206 3660 6 chr3A.!!$R1 3454

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
605 614 0.035820 TCGGGAACAATACTGCACCC 60.036 55.0 0.0 0.0 37.66 4.61 F
671 793 0.179032 ACCAACAACGACCTGCATCA 60.179 50.0 0.0 0.0 0.00 3.07 F
1555 1736 0.753262 CCGTACATCAAGGAGGAGGG 59.247 60.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1895 0.329261 CCTGCATTCCAGTTCAGGGA 59.671 55.0 0.00 0.0 41.71 4.20 R
1710 1896 0.329261 TCCTGCATTCCAGTTCAGGG 59.671 55.0 7.21 0.0 44.62 4.45 R
3186 3525 0.537188 ATGGAGCCACGGAGTAGTTG 59.463 55.0 0.00 0.0 41.61 3.16 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
39 41 3.758931 GTTGGGCCGGCCATTCAC 61.759 66.667 44.46 29.53 37.98 3.18
53 55 1.460743 CATTCACGAAAGCGCTTCAGA 59.539 47.619 25.24 15.52 42.48 3.27
58 60 1.678269 CGAAAGCGCTTCAGACGAGG 61.678 60.000 25.24 2.90 33.17 4.63
66 68 0.671781 CTTCAGACGAGGCCCAAGTG 60.672 60.000 0.00 0.00 0.00 3.16
78 80 2.159181 CCAAGTGGGTTTCGCTACG 58.841 57.895 0.00 0.00 34.68 3.51
79 81 0.601841 CCAAGTGGGTTTCGCTACGT 60.602 55.000 0.00 0.00 34.68 3.57
80 82 0.511221 CAAGTGGGTTTCGCTACGTG 59.489 55.000 0.00 0.00 34.68 4.49
93 95 2.728922 GCTACGTGCGATATATAGCCC 58.271 52.381 14.32 3.01 33.61 5.19
95 97 2.941453 ACGTGCGATATATAGCCCTG 57.059 50.000 14.32 7.27 0.00 4.45
96 98 2.443416 ACGTGCGATATATAGCCCTGA 58.557 47.619 14.32 0.00 0.00 3.86
97 99 2.163815 ACGTGCGATATATAGCCCTGAC 59.836 50.000 14.32 5.82 0.00 3.51
98 100 2.791503 CGTGCGATATATAGCCCTGACG 60.792 54.545 14.32 12.93 0.00 4.35
100 102 1.134367 GCGATATATAGCCCTGACGCA 59.866 52.381 6.56 0.00 43.35 5.24
101 103 2.223829 GCGATATATAGCCCTGACGCAT 60.224 50.000 6.56 0.00 43.35 4.73
104 106 4.555708 CGATATATAGCCCTGACGCATCTC 60.556 50.000 0.00 0.00 0.00 2.75
105 107 0.881796 TATAGCCCTGACGCATCTCG 59.118 55.000 0.00 0.00 45.38 4.04
114 116 2.655364 CGCATCTCGTACTGGCCG 60.655 66.667 0.00 0.00 0.00 6.13
115 117 2.805546 GCATCTCGTACTGGCCGA 59.194 61.111 0.00 0.00 0.00 5.54
116 118 1.141019 GCATCTCGTACTGGCCGAA 59.859 57.895 0.00 0.00 33.34 4.30
117 119 0.872021 GCATCTCGTACTGGCCGAAG 60.872 60.000 0.00 0.00 33.34 3.79
118 120 0.872021 CATCTCGTACTGGCCGAAGC 60.872 60.000 0.00 0.00 33.34 3.86
119 121 1.320344 ATCTCGTACTGGCCGAAGCA 61.320 55.000 0.00 0.00 42.56 3.91
120 122 1.080093 CTCGTACTGGCCGAAGCAA 60.080 57.895 0.00 0.00 42.56 3.91
121 123 0.669318 CTCGTACTGGCCGAAGCAAA 60.669 55.000 0.00 0.00 42.56 3.68
122 124 0.669318 TCGTACTGGCCGAAGCAAAG 60.669 55.000 0.00 0.00 42.56 2.77
123 125 1.635663 CGTACTGGCCGAAGCAAAGG 61.636 60.000 0.00 0.00 42.56 3.11
124 126 0.605589 GTACTGGCCGAAGCAAAGGT 60.606 55.000 0.00 0.00 42.56 3.50
125 127 0.109723 TACTGGCCGAAGCAAAGGTT 59.890 50.000 0.00 0.00 42.56 3.50
126 128 0.755327 ACTGGCCGAAGCAAAGGTTT 60.755 50.000 0.00 0.00 42.56 3.27
127 129 0.318955 CTGGCCGAAGCAAAGGTTTG 60.319 55.000 0.00 0.00 42.56 2.93
135 137 4.607024 CAAAGGTTTGCGTCACGG 57.393 55.556 0.00 0.00 0.00 4.94
136 138 2.018544 CAAAGGTTTGCGTCACGGA 58.981 52.632 0.00 0.00 0.00 4.69
137 139 0.378962 CAAAGGTTTGCGTCACGGAA 59.621 50.000 0.00 0.00 35.06 4.30
138 140 0.379316 AAAGGTTTGCGTCACGGAAC 59.621 50.000 2.55 0.00 36.85 3.62
159 161 5.562298 ACGGAAGTGGGCATATATAGTTT 57.438 39.130 0.00 0.00 46.97 2.66
160 162 5.548406 ACGGAAGTGGGCATATATAGTTTC 58.452 41.667 0.00 0.00 46.97 2.78
161 163 5.071250 ACGGAAGTGGGCATATATAGTTTCA 59.929 40.000 0.00 0.00 46.97 2.69
162 164 5.995282 CGGAAGTGGGCATATATAGTTTCAA 59.005 40.000 0.00 0.00 0.00 2.69
163 165 6.485313 CGGAAGTGGGCATATATAGTTTCAAA 59.515 38.462 0.00 0.00 0.00 2.69
164 166 7.307989 CGGAAGTGGGCATATATAGTTTCAAAG 60.308 40.741 0.00 0.00 0.00 2.77
165 167 7.719633 GGAAGTGGGCATATATAGTTTCAAAGA 59.280 37.037 0.00 0.00 0.00 2.52
166 168 9.120538 GAAGTGGGCATATATAGTTTCAAAGAA 57.879 33.333 0.00 0.00 0.00 2.52
167 169 9.474313 AAGTGGGCATATATAGTTTCAAAGAAA 57.526 29.630 0.00 0.00 0.00 2.52
168 170 9.474313 AGTGGGCATATATAGTTTCAAAGAAAA 57.526 29.630 0.00 0.00 0.00 2.29
234 236 1.143183 ACTCGTTGTTGCCGTGTCT 59.857 52.632 0.00 0.00 0.00 3.41
265 269 4.907879 ATCGAAATTCTGGAAGGATTGC 57.092 40.909 0.00 0.00 42.77 3.56
285 289 2.151202 CATGCTACAAGTTCCAACGGT 58.849 47.619 0.00 0.00 0.00 4.83
310 314 1.040339 AACTTGCGCTTTGTCCCCAA 61.040 50.000 9.73 0.00 0.00 4.12
325 329 2.604079 CAAGCATGGCCAACCCCA 60.604 61.111 10.96 0.00 39.65 4.96
354 358 2.525248 CCAATCCATCGACACGGCG 61.525 63.158 4.80 4.80 0.00 6.46
382 386 1.076777 CCGCCAAATCCACCATCCT 60.077 57.895 0.00 0.00 0.00 3.24
401 405 0.911769 TTCCCATCAGAAGTCGGCAT 59.088 50.000 0.00 0.00 0.00 4.40
423 428 1.459209 CAGATACAGTTTGTCGCGCAA 59.541 47.619 8.75 6.55 34.87 4.85
516 525 1.469703 TGGATCAGCAGAACATTTGCG 59.530 47.619 0.00 0.00 45.98 4.85
529 538 6.526325 CAGAACATTTGCGATCCGATTAAAAA 59.474 34.615 0.00 0.00 0.00 1.94
575 584 1.672881 GTACGCTCCTAGTTCGGCTAA 59.327 52.381 0.00 0.00 0.00 3.09
576 585 1.180029 ACGCTCCTAGTTCGGCTAAA 58.820 50.000 0.00 0.00 0.00 1.85
601 610 1.941325 CTCCTCGGGAACAATACTGC 58.059 55.000 0.00 0.00 0.00 4.40
603 612 1.066430 TCCTCGGGAACAATACTGCAC 60.066 52.381 0.00 0.00 0.00 4.57
604 613 1.369625 CTCGGGAACAATACTGCACC 58.630 55.000 0.00 0.00 0.00 5.01
605 614 0.035820 TCGGGAACAATACTGCACCC 60.036 55.000 0.00 0.00 37.66 4.61
606 615 1.029947 CGGGAACAATACTGCACCCC 61.030 60.000 0.00 0.00 37.72 4.95
608 617 1.341976 GGGAACAATACTGCACCCCAT 60.342 52.381 0.00 0.00 36.05 4.00
611 620 3.356290 GAACAATACTGCACCCCATTCT 58.644 45.455 0.00 0.00 0.00 2.40
612 621 2.726821 ACAATACTGCACCCCATTCTG 58.273 47.619 0.00 0.00 0.00 3.02
613 622 1.406539 CAATACTGCACCCCATTCTGC 59.593 52.381 0.00 0.00 0.00 4.26
624 746 1.952296 CCCATTCTGCATGTTAGCTCC 59.048 52.381 0.00 0.00 34.99 4.70
671 793 0.179032 ACCAACAACGACCTGCATCA 60.179 50.000 0.00 0.00 0.00 3.07
696 818 1.003233 CACCCCACAAGGAGTAGGTTC 59.997 57.143 0.00 0.00 38.24 3.62
746 870 3.721575 ACATCATGGGCCAGTAATAAGGA 59.278 43.478 13.78 0.00 0.00 3.36
747 871 4.202503 ACATCATGGGCCAGTAATAAGGAG 60.203 45.833 13.78 0.00 0.00 3.69
748 872 3.393687 TCATGGGCCAGTAATAAGGAGT 58.606 45.455 13.78 0.00 0.00 3.85
787 915 6.550163 AGATAAGGATTTCCATTAGCAGCAT 58.450 36.000 0.00 0.00 38.89 3.79
803 966 4.070716 GCAGCATCTTATTAGTGCAGGAT 58.929 43.478 0.00 0.00 41.19 3.24
918 1096 8.267183 TGGATCTTTTGCAGAGTTATTATCAGA 58.733 33.333 0.00 0.00 33.87 3.27
996 1174 2.747855 GCCCAGGCAAGAACCTCG 60.748 66.667 3.12 0.00 38.26 4.63
1013 1191 3.480133 GCCCATGGCGTACCCTCT 61.480 66.667 6.09 0.00 39.62 3.69
1015 1193 2.808206 CCCATGGCGTACCCTCTCC 61.808 68.421 6.09 0.00 33.59 3.71
1017 1195 1.338136 CCATGGCGTACCCTCTCCTT 61.338 60.000 0.00 0.00 33.59 3.36
1023 1201 1.960953 GCGTACCCTCTCCTTCTCCTT 60.961 57.143 0.00 0.00 0.00 3.36
1027 1205 1.719378 ACCCTCTCCTTCTCCTTCTCA 59.281 52.381 0.00 0.00 0.00 3.27
1031 1209 3.373830 CTCTCCTTCTCCTTCTCATGGT 58.626 50.000 0.00 0.00 0.00 3.55
1077 1258 4.338879 CCATTTCATCCACCAAGAGAACT 58.661 43.478 0.00 0.00 0.00 3.01
1344 1525 2.342648 GGGGTGAACTTCGCGTCT 59.657 61.111 5.77 0.00 0.00 4.18
1410 1591 2.125310 CCATTGTCGGCGCAGGTA 60.125 61.111 10.83 0.00 0.00 3.08
1497 1678 3.007723 GGATCATTGCCAGCTCTCTGATA 59.992 47.826 0.00 0.00 42.95 2.15
1500 1681 5.045012 TCATTGCCAGCTCTCTGATATTT 57.955 39.130 0.00 0.00 42.95 1.40
1509 1690 7.440198 CCAGCTCTCTGATATTTATCAACTCA 58.560 38.462 2.18 0.00 41.72 3.41
1545 1726 6.762702 TTCACTCATTACTACCGTACATCA 57.237 37.500 0.00 0.00 0.00 3.07
1555 1736 0.753262 CCGTACATCAAGGAGGAGGG 59.247 60.000 0.00 0.00 0.00 4.30
1618 1799 3.810373 CGTGCTCATGTCAAGGTAAAAC 58.190 45.455 0.00 0.00 0.00 2.43
1769 1955 0.457443 GGCAGTTTATCTTGGCAGGC 59.543 55.000 0.00 0.00 0.00 4.85
1878 2064 3.815401 CCAGGTCTACAACTCCAAACTTG 59.185 47.826 0.00 0.00 0.00 3.16
1882 2068 4.991687 GGTCTACAACTCCAAACTTGAGAG 59.008 45.833 0.00 6.46 34.07 3.20
1887 2073 2.576615 ACTCCAAACTTGAGAGGTTGC 58.423 47.619 0.00 0.00 46.95 4.17
1891 2077 2.031682 CCAAACTTGAGAGGTTGCTTCG 60.032 50.000 0.00 0.00 46.95 3.79
1898 2084 2.807967 TGAGAGGTTGCTTCGAACATTG 59.192 45.455 0.00 0.00 0.00 2.82
1912 2098 1.985473 ACATTGCAAGGCTCACTCAA 58.015 45.000 11.69 0.00 0.00 3.02
1940 2126 4.681025 AGCAAAATTGTGTACTTGAATGCG 59.319 37.500 0.00 0.00 35.37 4.73
1968 2154 1.734465 CTTTCACGGTGATCCTTCAGC 59.266 52.381 12.26 0.00 45.00 4.26
2023 2210 8.641498 AATGTCATGATTCCCAACTTATATCC 57.359 34.615 0.00 0.00 0.00 2.59
2046 2233 3.833070 AGTAACAGTGGACACCTCTAAGG 59.167 47.826 0.00 0.00 42.49 2.69
2139 2328 9.692749 TTTATTCAGAACTAACTACACTGAGTG 57.307 33.333 11.70 11.70 38.52 3.51
2156 2345 9.003658 ACACTGAGTGGTTAATTCTGAATAAAG 57.996 33.333 17.92 0.00 37.94 1.85
2158 2347 9.442047 ACTGAGTGGTTAATTCTGAATAAAGAG 57.558 33.333 2.85 0.00 0.00 2.85
2290 2520 5.708697 CCAAGATTGCATCATAATCCTAGCA 59.291 40.000 0.00 0.00 35.62 3.49
2300 2530 7.859875 GCATCATAATCCTAGCAAAAGAAGAAC 59.140 37.037 0.00 0.00 0.00 3.01
2317 2547 7.617041 AGAAGAACTATTAAAGCATGGTGAC 57.383 36.000 0.00 0.00 0.00 3.67
2399 2629 1.069364 GCAGAAAGCAGAGTTGACAGC 60.069 52.381 0.00 0.00 44.79 4.40
2477 2707 3.256631 AGTTTGCCATGACAACAGGATTC 59.743 43.478 0.00 0.00 0.00 2.52
2539 2769 3.686016 AGGTCGGAATACTTTGCAACAT 58.314 40.909 0.00 0.00 0.00 2.71
2574 2804 4.901250 TCTGCAGGAATGTGTCATCCTATA 59.099 41.667 15.13 0.00 44.26 1.31
2749 2981 8.816640 TGATTCAATCTTTTGGCTTTTACTTC 57.183 30.769 0.00 0.00 33.44 3.01
2789 3021 1.195448 GAGTCACTGGCATGTGTTTCG 59.805 52.381 14.00 0.00 38.90 3.46
2790 3022 0.944386 GTCACTGGCATGTGTTTCGT 59.056 50.000 14.00 0.00 38.90 3.85
2791 3023 1.333619 GTCACTGGCATGTGTTTCGTT 59.666 47.619 14.00 0.00 38.90 3.85
2792 3024 2.020720 TCACTGGCATGTGTTTCGTTT 58.979 42.857 14.00 0.00 38.90 3.60
2793 3025 2.118683 CACTGGCATGTGTTTCGTTTG 58.881 47.619 8.37 0.00 33.61 2.93
2794 3026 1.748493 ACTGGCATGTGTTTCGTTTGT 59.252 42.857 0.00 0.00 0.00 2.83
2795 3027 2.165437 ACTGGCATGTGTTTCGTTTGTT 59.835 40.909 0.00 0.00 0.00 2.83
2796 3028 3.378742 ACTGGCATGTGTTTCGTTTGTTA 59.621 39.130 0.00 0.00 0.00 2.41
2797 3029 4.037446 ACTGGCATGTGTTTCGTTTGTTAT 59.963 37.500 0.00 0.00 0.00 1.89
2798 3030 5.239744 ACTGGCATGTGTTTCGTTTGTTATA 59.760 36.000 0.00 0.00 0.00 0.98
2799 3031 6.072175 ACTGGCATGTGTTTCGTTTGTTATAT 60.072 34.615 0.00 0.00 0.00 0.86
2800 3032 6.682746 TGGCATGTGTTTCGTTTGTTATATT 58.317 32.000 0.00 0.00 0.00 1.28
2801 3033 7.817641 TGGCATGTGTTTCGTTTGTTATATTA 58.182 30.769 0.00 0.00 0.00 0.98
2802 3034 8.462811 TGGCATGTGTTTCGTTTGTTATATTAT 58.537 29.630 0.00 0.00 0.00 1.28
2803 3035 9.938670 GGCATGTGTTTCGTTTGTTATATTATA 57.061 29.630 0.00 0.00 0.00 0.98
2824 3056 9.948964 ATTATACACAATATGATAAGCTCAGCA 57.051 29.630 0.00 0.00 37.28 4.41
2825 3057 9.948964 TTATACACAATATGATAAGCTCAGCAT 57.051 29.630 0.00 0.00 37.28 3.79
2826 3058 8.859236 ATACACAATATGATAAGCTCAGCATT 57.141 30.769 0.00 0.00 37.28 3.56
2827 3059 7.199541 ACACAATATGATAAGCTCAGCATTC 57.800 36.000 0.00 0.00 37.28 2.67
2828 3060 6.996879 ACACAATATGATAAGCTCAGCATTCT 59.003 34.615 0.00 0.00 37.28 2.40
2829 3061 7.172875 ACACAATATGATAAGCTCAGCATTCTC 59.827 37.037 0.00 0.00 37.28 2.87
2830 3062 7.172703 CACAATATGATAAGCTCAGCATTCTCA 59.827 37.037 0.00 0.00 37.28 3.27
2831 3063 7.388224 ACAATATGATAAGCTCAGCATTCTCAG 59.612 37.037 0.00 0.00 37.28 3.35
2832 3064 5.548181 ATGATAAGCTCAGCATTCTCAGA 57.452 39.130 0.00 0.00 37.28 3.27
2833 3065 5.349061 TGATAAGCTCAGCATTCTCAGAA 57.651 39.130 0.00 0.00 0.00 3.02
2834 3066 5.737860 TGATAAGCTCAGCATTCTCAGAAA 58.262 37.500 0.00 0.00 0.00 2.52
2835 3067 6.354938 TGATAAGCTCAGCATTCTCAGAAAT 58.645 36.000 0.00 0.00 0.00 2.17
2836 3068 6.827251 TGATAAGCTCAGCATTCTCAGAAATT 59.173 34.615 0.00 0.00 0.00 1.82
2837 3069 7.989170 TGATAAGCTCAGCATTCTCAGAAATTA 59.011 33.333 0.00 0.00 0.00 1.40
2838 3070 8.743085 ATAAGCTCAGCATTCTCAGAAATTAA 57.257 30.769 0.00 0.00 0.00 1.40
2839 3071 7.642082 AAGCTCAGCATTCTCAGAAATTAAT 57.358 32.000 0.00 0.00 0.00 1.40
2840 3072 7.642082 AGCTCAGCATTCTCAGAAATTAATT 57.358 32.000 0.00 0.00 0.00 1.40
2841 3073 8.064336 AGCTCAGCATTCTCAGAAATTAATTT 57.936 30.769 13.24 13.24 0.00 1.82
2842 3074 9.182214 AGCTCAGCATTCTCAGAAATTAATTTA 57.818 29.630 13.34 0.00 0.00 1.40
2843 3075 9.793252 GCTCAGCATTCTCAGAAATTAATTTAA 57.207 29.630 13.34 4.69 0.00 1.52
2868 3100 7.157347 AGAAAGGAAATCAAGAAATCAAAGGC 58.843 34.615 0.00 0.00 0.00 4.35
2869 3101 6.423776 AAGGAAATCAAGAAATCAAAGGCA 57.576 33.333 0.00 0.00 0.00 4.75
2870 3102 6.616237 AGGAAATCAAGAAATCAAAGGCAT 57.384 33.333 0.00 0.00 0.00 4.40
2871 3103 7.722949 AGGAAATCAAGAAATCAAAGGCATA 57.277 32.000 0.00 0.00 0.00 3.14
2872 3104 8.137745 AGGAAATCAAGAAATCAAAGGCATAA 57.862 30.769 0.00 0.00 0.00 1.90
2873 3105 8.037166 AGGAAATCAAGAAATCAAAGGCATAAC 58.963 33.333 0.00 0.00 0.00 1.89
2874 3106 7.818930 GGAAATCAAGAAATCAAAGGCATAACA 59.181 33.333 0.00 0.00 0.00 2.41
2875 3107 8.538409 AAATCAAGAAATCAAAGGCATAACAC 57.462 30.769 0.00 0.00 0.00 3.32
2876 3108 5.698832 TCAAGAAATCAAAGGCATAACACG 58.301 37.500 0.00 0.00 0.00 4.49
2877 3109 5.240623 TCAAGAAATCAAAGGCATAACACGT 59.759 36.000 0.00 0.00 0.00 4.49
2878 3110 5.046910 AGAAATCAAAGGCATAACACGTG 57.953 39.130 15.48 15.48 0.00 4.49
2879 3111 4.518970 AGAAATCAAAGGCATAACACGTGT 59.481 37.500 17.22 17.22 0.00 4.49
2880 3112 4.846779 AATCAAAGGCATAACACGTGTT 57.153 36.364 33.99 33.99 41.73 3.32
2881 3113 4.846779 ATCAAAGGCATAACACGTGTTT 57.153 36.364 36.26 21.60 39.31 2.83
2882 3114 4.640789 TCAAAGGCATAACACGTGTTTT 57.359 36.364 36.26 26.60 39.31 2.43
2883 3115 4.355437 TCAAAGGCATAACACGTGTTTTG 58.645 39.130 36.26 34.83 39.10 2.44
2971 3297 8.347004 TCAAGAAATCAAAGGCATAACATGTA 57.653 30.769 0.00 0.00 0.00 2.29
3011 3350 2.022195 CACAATATGGCAAGCTCAGCT 58.978 47.619 0.00 0.00 42.56 4.24
3135 3474 5.355350 GGAGTAACCATTCTCACCTCAAATG 59.645 44.000 0.00 0.00 38.79 2.32
3138 3477 4.371624 ACCATTCTCACCTCAAATGACA 57.628 40.909 0.00 0.00 33.22 3.58
3182 3521 0.979665 TGGAGCTCTCAAGTCCCAAG 59.020 55.000 14.64 0.00 0.00 3.61
3186 3525 0.035915 GCTCTCAAGTCCCAAGTCCC 60.036 60.000 0.00 0.00 0.00 4.46
3187 3526 1.352083 CTCTCAAGTCCCAAGTCCCA 58.648 55.000 0.00 0.00 0.00 4.37
3188 3527 1.699634 CTCTCAAGTCCCAAGTCCCAA 59.300 52.381 0.00 0.00 0.00 4.12
3189 3528 1.420138 TCTCAAGTCCCAAGTCCCAAC 59.580 52.381 0.00 0.00 0.00 3.77
3191 3530 2.637872 CTCAAGTCCCAAGTCCCAACTA 59.362 50.000 0.00 0.00 33.48 2.24
3193 3532 2.372172 CAAGTCCCAAGTCCCAACTACT 59.628 50.000 0.00 0.00 33.48 2.57
3194 3533 2.258109 AGTCCCAAGTCCCAACTACTC 58.742 52.381 0.00 0.00 33.48 2.59
3195 3534 1.278413 GTCCCAAGTCCCAACTACTCC 59.722 57.143 0.00 0.00 33.48 3.85
3196 3535 0.249398 CCCAAGTCCCAACTACTCCG 59.751 60.000 0.00 0.00 33.48 4.63
3197 3536 0.974383 CCAAGTCCCAACTACTCCGT 59.026 55.000 0.00 0.00 33.48 4.69
3198 3537 1.337823 CCAAGTCCCAACTACTCCGTG 60.338 57.143 0.00 0.00 33.48 4.94
3199 3538 0.974383 AAGTCCCAACTACTCCGTGG 59.026 55.000 0.00 0.00 33.48 4.94
3200 3539 1.079336 GTCCCAACTACTCCGTGGC 60.079 63.158 0.00 0.00 0.00 5.01
3201 3540 1.229082 TCCCAACTACTCCGTGGCT 60.229 57.895 0.00 0.00 0.00 4.75
3202 3541 1.218316 CCCAACTACTCCGTGGCTC 59.782 63.158 0.00 0.00 0.00 4.70
3203 3542 1.218316 CCAACTACTCCGTGGCTCC 59.782 63.158 0.00 0.00 0.00 4.70
3204 3543 1.541310 CCAACTACTCCGTGGCTCCA 61.541 60.000 0.00 0.00 0.00 3.86
3205 3544 0.537188 CAACTACTCCGTGGCTCCAT 59.463 55.000 0.00 0.00 0.00 3.41
3206 3545 0.537188 AACTACTCCGTGGCTCCATG 59.463 55.000 1.13 1.13 0.00 3.66
3207 3546 1.227380 CTACTCCGTGGCTCCATGC 60.227 63.158 2.60 0.00 41.94 4.06
3208 3547 1.960040 CTACTCCGTGGCTCCATGCA 61.960 60.000 2.60 0.00 45.15 3.96
3209 3548 1.549243 TACTCCGTGGCTCCATGCAA 61.549 55.000 2.60 0.00 45.15 4.08
3210 3549 2.046023 TCCGTGGCTCCATGCAAG 60.046 61.111 2.60 0.00 45.15 4.01
3211 3550 3.818787 CCGTGGCTCCATGCAAGC 61.819 66.667 9.24 9.24 45.15 4.01
3212 3551 3.057548 CGTGGCTCCATGCAAGCA 61.058 61.111 17.06 0.00 45.15 3.91
3330 3673 6.099341 AGAATGAGTTCAAAACAAACCACAC 58.901 36.000 0.00 0.00 36.79 3.82
3390 3761 3.379372 TCACCTACGTGGCACTAAGATAC 59.621 47.826 16.72 0.00 40.65 2.24
3403 3774 7.093068 TGGCACTAAGATACTCCAAAATAGTGA 60.093 37.037 12.71 0.00 40.56 3.41
3413 3784 5.827797 ACTCCAAAATAGTGAACAAGCTCAA 59.172 36.000 0.00 0.00 0.00 3.02
3428 3815 2.099141 CTCAAAAGGAGCATCGGTCA 57.901 50.000 0.00 0.00 36.69 4.02
3583 3974 8.489489 AGCATCAAGTGATTAATTTAGAGAGGA 58.511 33.333 0.00 0.00 31.21 3.71
3628 4019 0.675633 GGCATGCTTCCACAAACAGT 59.324 50.000 18.92 0.00 0.00 3.55
3648 4039 3.561503 GTGCAAAATTGTACTCCGTTCC 58.438 45.455 7.06 0.00 40.10 3.62
3649 4040 3.003897 GTGCAAAATTGTACTCCGTTCCA 59.996 43.478 7.06 0.00 40.10 3.53
3660 4051 5.467399 TGTACTCCGTTCCAAAATAAGTGTG 59.533 40.000 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.461127 GTCTGAAGCGCTTTCGTGAAT 59.539 47.619 25.84 0.00 38.71 2.57
39 41 1.678269 CCTCGTCTGAAGCGCTTTCG 61.678 60.000 25.84 23.45 38.71 3.46
41 43 2.029844 GCCTCGTCTGAAGCGCTTT 61.030 57.895 25.84 8.06 0.00 3.51
73 75 2.358267 AGGGCTATATATCGCACGTAGC 59.642 50.000 11.00 2.67 37.60 3.58
74 76 3.626217 TCAGGGCTATATATCGCACGTAG 59.374 47.826 11.00 4.02 33.99 3.51
75 77 3.376234 GTCAGGGCTATATATCGCACGTA 59.624 47.826 11.00 0.00 33.99 3.57
78 80 2.798680 CGTCAGGGCTATATATCGCAC 58.201 52.381 11.00 7.42 0.00 5.34
79 81 1.134367 GCGTCAGGGCTATATATCGCA 59.866 52.381 11.00 0.00 41.59 5.10
80 82 1.134367 TGCGTCAGGGCTATATATCGC 59.866 52.381 0.61 0.61 42.17 4.58
83 85 3.316588 CGAGATGCGTCAGGGCTATATAT 59.683 47.826 8.99 0.00 34.64 0.86
84 86 2.683362 CGAGATGCGTCAGGGCTATATA 59.317 50.000 8.99 0.00 34.64 0.86
85 87 1.474478 CGAGATGCGTCAGGGCTATAT 59.526 52.381 8.99 0.00 34.64 0.86
86 88 0.881796 CGAGATGCGTCAGGGCTATA 59.118 55.000 8.99 0.00 34.64 1.31
88 90 3.120105 CGAGATGCGTCAGGGCTA 58.880 61.111 8.99 0.00 34.64 3.93
98 100 0.872021 CTTCGGCCAGTACGAGATGC 60.872 60.000 2.24 0.00 41.81 3.91
100 102 1.320344 TGCTTCGGCCAGTACGAGAT 61.320 55.000 2.24 0.00 41.81 2.75
101 103 1.529152 TTGCTTCGGCCAGTACGAGA 61.529 55.000 2.24 0.00 41.81 4.04
104 106 1.635663 CCTTTGCTTCGGCCAGTACG 61.636 60.000 2.24 0.00 40.91 3.67
105 107 0.605589 ACCTTTGCTTCGGCCAGTAC 60.606 55.000 2.24 0.00 40.91 2.73
107 109 0.755327 AAACCTTTGCTTCGGCCAGT 60.755 50.000 2.24 0.00 40.91 4.00
108 110 0.318955 CAAACCTTTGCTTCGGCCAG 60.319 55.000 2.24 0.00 40.91 4.85
109 111 1.739049 CAAACCTTTGCTTCGGCCA 59.261 52.632 2.24 0.00 40.91 5.36
110 112 4.653555 CAAACCTTTGCTTCGGCC 57.346 55.556 0.00 0.00 40.91 6.13
118 120 0.378962 TTCCGTGACGCAAACCTTTG 59.621 50.000 0.00 0.00 41.03 2.77
119 121 0.379316 GTTCCGTGACGCAAACCTTT 59.621 50.000 0.00 0.00 0.00 3.11
120 122 1.768112 CGTTCCGTGACGCAAACCTT 61.768 55.000 13.32 0.00 36.12 3.50
121 123 2.241880 CGTTCCGTGACGCAAACCT 61.242 57.895 13.32 0.00 36.12 3.50
122 124 2.247267 CGTTCCGTGACGCAAACC 59.753 61.111 13.32 0.00 36.12 3.27
123 125 1.764180 TTCCGTTCCGTGACGCAAAC 61.764 55.000 0.00 5.44 41.50 2.93
124 126 1.492319 CTTCCGTTCCGTGACGCAAA 61.492 55.000 0.00 0.00 41.50 3.68
125 127 1.952133 CTTCCGTTCCGTGACGCAA 60.952 57.895 0.00 0.00 41.50 4.85
126 128 2.355363 CTTCCGTTCCGTGACGCA 60.355 61.111 0.00 0.00 41.50 5.24
127 129 2.355481 ACTTCCGTTCCGTGACGC 60.355 61.111 0.00 0.00 41.50 5.19
128 130 2.019951 CCACTTCCGTTCCGTGACG 61.020 63.158 0.00 0.00 42.43 4.35
129 131 1.666872 CCCACTTCCGTTCCGTGAC 60.667 63.158 0.00 0.00 0.00 3.67
130 132 2.738480 CCCACTTCCGTTCCGTGA 59.262 61.111 0.00 0.00 0.00 4.35
131 133 3.047877 GCCCACTTCCGTTCCGTG 61.048 66.667 0.00 0.00 0.00 4.94
132 134 1.546589 TATGCCCACTTCCGTTCCGT 61.547 55.000 0.00 0.00 0.00 4.69
133 135 0.179056 ATATGCCCACTTCCGTTCCG 60.179 55.000 0.00 0.00 0.00 4.30
134 136 2.922740 TATATGCCCACTTCCGTTCC 57.077 50.000 0.00 0.00 0.00 3.62
135 137 5.148651 ACTATATATGCCCACTTCCGTTC 57.851 43.478 0.00 0.00 0.00 3.95
136 138 5.562298 AACTATATATGCCCACTTCCGTT 57.438 39.130 0.00 0.00 0.00 4.44
137 139 5.071250 TGAAACTATATATGCCCACTTCCGT 59.929 40.000 0.00 0.00 0.00 4.69
138 140 5.547465 TGAAACTATATATGCCCACTTCCG 58.453 41.667 0.00 0.00 0.00 4.30
139 141 7.719633 TCTTTGAAACTATATATGCCCACTTCC 59.280 37.037 0.00 0.00 0.00 3.46
140 142 8.677148 TCTTTGAAACTATATATGCCCACTTC 57.323 34.615 0.00 0.00 0.00 3.01
141 143 9.474313 TTTCTTTGAAACTATATATGCCCACTT 57.526 29.630 0.00 0.00 0.00 3.16
142 144 9.474313 TTTTCTTTGAAACTATATATGCCCACT 57.526 29.630 0.00 0.00 0.00 4.00
192 194 2.813042 GCAGAGGAGTGCACGAGC 60.813 66.667 12.01 6.81 43.41 5.03
193 195 2.125753 GGCAGAGGAGTGCACGAG 60.126 66.667 12.01 0.15 45.93 4.18
194 196 4.056125 CGGCAGAGGAGTGCACGA 62.056 66.667 12.01 0.00 45.93 4.35
196 198 3.537206 AACCGGCAGAGGAGTGCAC 62.537 63.158 9.40 9.40 45.93 4.57
197 199 3.240134 GAACCGGCAGAGGAGTGCA 62.240 63.158 0.00 0.00 45.93 4.57
198 200 2.435059 GAACCGGCAGAGGAGTGC 60.435 66.667 0.00 0.00 43.19 4.40
199 201 1.374758 GTGAACCGGCAGAGGAGTG 60.375 63.158 0.00 0.00 34.73 3.51
200 202 1.534235 AGTGAACCGGCAGAGGAGT 60.534 57.895 0.00 0.00 34.73 3.85
201 203 1.216710 GAGTGAACCGGCAGAGGAG 59.783 63.158 0.00 0.00 34.73 3.69
202 204 2.636412 CGAGTGAACCGGCAGAGGA 61.636 63.158 0.00 0.00 34.73 3.71
234 236 4.098807 TCCAGAATTTCGATACGTGATGGA 59.901 41.667 0.00 0.00 0.00 3.41
247 249 4.117685 GCATGCAATCCTTCCAGAATTTC 58.882 43.478 14.21 0.00 0.00 2.17
265 269 2.151202 ACCGTTGGAACTTGTAGCATG 58.849 47.619 0.00 0.00 0.00 4.06
267 271 1.541670 GGACCGTTGGAACTTGTAGCA 60.542 52.381 0.00 0.00 0.00 3.49
285 289 1.092921 ACAAAGCGCAAGTTCACGGA 61.093 50.000 11.47 0.00 41.68 4.69
310 314 2.042639 GATGGGGTTGGCCATGCT 60.043 61.111 6.09 0.00 36.17 3.79
316 320 1.380380 CAGGGAAGATGGGGTTGGC 60.380 63.158 0.00 0.00 0.00 4.52
325 329 1.146566 GATGGATTGGGCAGGGAAGAT 59.853 52.381 0.00 0.00 0.00 2.40
363 367 1.379843 GGATGGTGGATTTGGCGGT 60.380 57.895 0.00 0.00 0.00 5.68
382 386 0.911769 ATGCCGACTTCTGATGGGAA 59.088 50.000 0.00 0.00 0.00 3.97
401 405 2.256174 GCGCGACAAACTGTATCTGTA 58.744 47.619 12.10 0.00 0.00 2.74
423 428 0.392461 ACGTGCAGACCAGTGTTTGT 60.392 50.000 0.00 0.00 0.00 2.83
529 538 1.098869 TGTGGTTGTGCGTGACAATT 58.901 45.000 5.59 0.00 46.34 2.32
534 543 0.306228 CGAAATGTGGTTGTGCGTGA 59.694 50.000 0.00 0.00 0.00 4.35
575 584 0.472471 TGTTCCCGAGGAGCAACTTT 59.528 50.000 6.94 0.00 39.86 2.66
576 585 0.472471 TTGTTCCCGAGGAGCAACTT 59.528 50.000 14.93 0.00 45.39 2.66
601 610 1.406539 GCTAACATGCAGAATGGGGTG 59.593 52.381 0.00 0.00 40.94 4.61
603 612 1.952296 GAGCTAACATGCAGAATGGGG 59.048 52.381 0.00 0.00 40.94 4.96
604 613 1.952296 GGAGCTAACATGCAGAATGGG 59.048 52.381 0.00 0.00 40.94 4.00
605 614 1.600957 CGGAGCTAACATGCAGAATGG 59.399 52.381 0.00 0.00 40.94 3.16
606 615 2.031314 CACGGAGCTAACATGCAGAATG 59.969 50.000 0.00 0.00 42.48 2.67
608 617 1.725641 CACGGAGCTAACATGCAGAA 58.274 50.000 0.00 0.00 34.99 3.02
611 620 1.745115 GGCACGGAGCTAACATGCA 60.745 57.895 10.50 0.00 44.79 3.96
612 621 1.305219 TTGGCACGGAGCTAACATGC 61.305 55.000 0.74 0.74 44.79 4.06
613 622 1.135689 GTTTGGCACGGAGCTAACATG 60.136 52.381 0.61 0.00 43.90 3.21
624 746 1.106944 AAAGTGGGGAGTTTGGCACG 61.107 55.000 0.00 0.00 0.00 5.34
696 818 2.205022 TTGGCAGGATTGGAGACTTG 57.795 50.000 0.00 0.00 0.00 3.16
737 861 8.986929 TTCTGGGTACTACTACTCCTTATTAC 57.013 38.462 0.00 0.00 0.00 1.89
746 870 7.880623 TCCTTATCTTTCTGGGTACTACTACT 58.119 38.462 0.00 0.00 0.00 2.57
747 871 8.709272 ATCCTTATCTTTCTGGGTACTACTAC 57.291 38.462 0.00 0.00 0.00 2.73
748 872 9.725206 AAATCCTTATCTTTCTGGGTACTACTA 57.275 33.333 0.00 0.00 0.00 1.82
870 1038 4.450419 CAGCTGATTCGTTCATATCTTCCC 59.550 45.833 8.42 0.00 32.72 3.97
957 1135 1.488393 GAGGTTCTAGGCCTCTGCAAT 59.512 52.381 9.68 0.00 46.71 3.56
996 1174 3.462199 GAGAGGGTACGCCATGGGC 62.462 68.421 15.13 4.92 46.75 5.36
1006 1184 2.927007 TGAGAAGGAGAAGGAGAGGGTA 59.073 50.000 0.00 0.00 0.00 3.69
1012 1190 2.419851 GCACCATGAGAAGGAGAAGGAG 60.420 54.545 0.00 0.00 0.00 3.69
1013 1191 1.556911 GCACCATGAGAAGGAGAAGGA 59.443 52.381 0.00 0.00 0.00 3.36
1015 1193 2.419851 GGAGCACCATGAGAAGGAGAAG 60.420 54.545 0.00 0.00 35.97 2.85
1017 1195 1.198713 GGAGCACCATGAGAAGGAGA 58.801 55.000 0.00 0.00 35.97 3.71
1023 1201 0.689080 GGAGGAGGAGCACCATGAGA 60.689 60.000 2.07 0.00 38.94 3.27
1027 1205 1.760086 CGAGGAGGAGGAGCACCAT 60.760 63.158 2.07 0.00 38.94 3.55
1031 1209 4.067512 AGGCGAGGAGGAGGAGCA 62.068 66.667 0.00 0.00 0.00 4.26
1077 1258 1.600636 CGGGAACTTTGGCTGCTGA 60.601 57.895 0.00 0.00 0.00 4.26
1321 1502 1.666872 CGAAGTTCACCCCCGTCAC 60.667 63.158 3.32 0.00 0.00 3.67
1497 1678 8.599624 AATCATTGGTTCCTGAGTTGATAAAT 57.400 30.769 0.00 0.00 0.00 1.40
1500 1681 7.121168 GTGAAATCATTGGTTCCTGAGTTGATA 59.879 37.037 0.00 0.00 30.58 2.15
1509 1690 7.177878 AGTAATGAGTGAAATCATTGGTTCCT 58.822 34.615 14.45 2.49 46.70 3.36
1545 1726 1.544917 AATGCCCACCCTCCTCCTT 60.545 57.895 0.00 0.00 0.00 3.36
1618 1799 2.568623 ACAAACCCAGAACTGCCTAG 57.431 50.000 0.00 0.00 0.00 3.02
1709 1895 0.329261 CCTGCATTCCAGTTCAGGGA 59.671 55.000 0.00 0.00 41.71 4.20
1710 1896 0.329261 TCCTGCATTCCAGTTCAGGG 59.671 55.000 7.21 0.00 44.62 4.45
1757 1943 3.027533 AGGAAGGCCTGCCAAGATA 57.972 52.632 32.76 0.00 44.90 1.98
1769 1955 0.612732 TGCAGCCAAATGGAGGAAGG 60.613 55.000 2.98 0.00 37.39 3.46
1878 2064 2.413371 GCAATGTTCGAAGCAACCTCTC 60.413 50.000 0.00 0.00 0.00 3.20
1882 2068 2.053627 CTTGCAATGTTCGAAGCAACC 58.946 47.619 15.98 0.00 41.55 3.77
1887 2073 1.536766 TGAGCCTTGCAATGTTCGAAG 59.463 47.619 12.48 0.00 0.00 3.79
1891 2077 1.881973 TGAGTGAGCCTTGCAATGTTC 59.118 47.619 10.84 10.84 0.00 3.18
1898 2084 1.538950 CTTCCTTTGAGTGAGCCTTGC 59.461 52.381 0.00 0.00 0.00 4.01
1912 2098 6.463995 TCAAGTACACAATTTTGCTTCCTT 57.536 33.333 0.00 0.00 0.00 3.36
1940 2126 1.774639 TCACCGTGAAAGCTTCGTAC 58.225 50.000 0.00 0.00 0.00 3.67
1991 2177 5.039920 TGGGAATCATGACATTACTGGAG 57.960 43.478 0.00 0.00 0.00 3.86
2023 2210 4.322049 CCTTAGAGGTGTCCACTGTTACTG 60.322 50.000 0.00 0.00 0.00 2.74
2046 2233 3.631227 AGCTACCGTGGAGTATTAGTGAC 59.369 47.826 0.00 0.00 0.00 3.67
2139 2328 7.391148 TGGTGCTCTTTATTCAGAATTAACC 57.609 36.000 0.00 0.00 0.00 2.85
2144 2333 7.576477 GCTTTCTTGGTGCTCTTTATTCAGAAT 60.576 37.037 0.20 0.20 0.00 2.40
2156 2345 2.739379 GACTACTGCTTTCTTGGTGCTC 59.261 50.000 0.00 0.00 0.00 4.26
2158 2347 2.481952 CTGACTACTGCTTTCTTGGTGC 59.518 50.000 0.00 0.00 0.00 5.01
2290 2520 9.077885 TCACCATGCTTTAATAGTTCTTCTTTT 57.922 29.630 0.00 0.00 0.00 2.27
2317 2547 5.670485 TCTAGTTGTACATGGCCAAGTATG 58.330 41.667 22.73 13.12 0.00 2.39
2394 2624 5.493735 GCGATAAGAATAACACAAGCTGTC 58.506 41.667 0.00 0.00 30.29 3.51
2395 2625 4.332819 GGCGATAAGAATAACACAAGCTGT 59.667 41.667 0.00 0.00 32.89 4.40
2399 2629 5.465724 GGTAGGGCGATAAGAATAACACAAG 59.534 44.000 0.00 0.00 0.00 3.16
2477 2707 2.224378 ACATCCCAGTGTTGTCTCTGTG 60.224 50.000 0.00 0.00 34.54 3.66
2539 2769 5.610982 ACATTCCTGCAGATAGGGGTAAATA 59.389 40.000 17.39 0.00 38.42 1.40
2574 2804 3.255642 GGGTGCACCGCATCATAAAATAT 59.744 43.478 29.08 0.00 42.13 1.28
2597 2827 5.775701 TGCTATCCTATAAACCCTCTCTGTC 59.224 44.000 0.00 0.00 0.00 3.51
2698 2929 6.721321 ACGCATTAGGTTAATTCGTTAATGG 58.279 36.000 1.67 6.52 43.45 3.16
2726 2957 9.264719 CTTGAAGTAAAAGCCAAAAGATTGAAT 57.735 29.630 0.00 0.00 38.94 2.57
2764 2996 1.808945 CACATGCCAGTGACTCTTTCC 59.191 52.381 0.00 0.00 42.05 3.13
2798 3030 9.948964 TGCTGAGCTTATCATATTGTGTATAAT 57.051 29.630 5.83 0.00 37.28 1.28
2799 3031 9.948964 ATGCTGAGCTTATCATATTGTGTATAA 57.051 29.630 5.83 0.00 37.28 0.98
2800 3032 9.948964 AATGCTGAGCTTATCATATTGTGTATA 57.051 29.630 5.83 0.00 37.28 1.47
2801 3033 8.859236 AATGCTGAGCTTATCATATTGTGTAT 57.141 30.769 5.83 0.00 37.28 2.29
2802 3034 8.152898 AGAATGCTGAGCTTATCATATTGTGTA 58.847 33.333 5.83 0.00 37.28 2.90
2803 3035 6.996879 AGAATGCTGAGCTTATCATATTGTGT 59.003 34.615 5.83 0.00 37.28 3.72
2804 3036 7.172703 TGAGAATGCTGAGCTTATCATATTGTG 59.827 37.037 5.83 0.00 37.28 3.33
2805 3037 7.222161 TGAGAATGCTGAGCTTATCATATTGT 58.778 34.615 5.83 0.00 37.28 2.71
2806 3038 7.603024 TCTGAGAATGCTGAGCTTATCATATTG 59.397 37.037 5.83 0.11 37.28 1.90
2807 3039 7.677892 TCTGAGAATGCTGAGCTTATCATATT 58.322 34.615 5.83 0.00 37.28 1.28
2808 3040 7.242322 TCTGAGAATGCTGAGCTTATCATAT 57.758 36.000 5.83 0.00 37.28 1.78
2809 3041 6.661304 TCTGAGAATGCTGAGCTTATCATA 57.339 37.500 5.83 1.23 37.28 2.15
2810 3042 5.548181 TCTGAGAATGCTGAGCTTATCAT 57.452 39.130 5.83 0.00 37.28 2.45
2811 3043 5.349061 TTCTGAGAATGCTGAGCTTATCA 57.651 39.130 5.83 9.48 36.21 2.15
2812 3044 6.864360 ATTTCTGAGAATGCTGAGCTTATC 57.136 37.500 5.83 5.26 0.00 1.75
2813 3045 8.743085 TTAATTTCTGAGAATGCTGAGCTTAT 57.257 30.769 5.83 0.00 0.00 1.73
2814 3046 8.743085 ATTAATTTCTGAGAATGCTGAGCTTA 57.257 30.769 5.83 0.00 0.00 3.09
2815 3047 7.642082 ATTAATTTCTGAGAATGCTGAGCTT 57.358 32.000 5.83 0.00 0.00 3.74
2816 3048 7.642082 AATTAATTTCTGAGAATGCTGAGCT 57.358 32.000 5.83 0.00 0.00 4.09
2817 3049 9.793252 TTAAATTAATTTCTGAGAATGCTGAGC 57.207 29.630 16.56 0.00 0.00 4.26
2842 3074 7.658982 GCCTTTGATTTCTTGATTTCCTTTCTT 59.341 33.333 0.00 0.00 0.00 2.52
2843 3075 7.157347 GCCTTTGATTTCTTGATTTCCTTTCT 58.843 34.615 0.00 0.00 0.00 2.52
2844 3076 6.930722 TGCCTTTGATTTCTTGATTTCCTTTC 59.069 34.615 0.00 0.00 0.00 2.62
2845 3077 6.829849 TGCCTTTGATTTCTTGATTTCCTTT 58.170 32.000 0.00 0.00 0.00 3.11
2846 3078 6.423776 TGCCTTTGATTTCTTGATTTCCTT 57.576 33.333 0.00 0.00 0.00 3.36
2847 3079 6.616237 ATGCCTTTGATTTCTTGATTTCCT 57.384 33.333 0.00 0.00 0.00 3.36
2848 3080 7.818930 TGTTATGCCTTTGATTTCTTGATTTCC 59.181 33.333 0.00 0.00 0.00 3.13
2849 3081 8.650714 GTGTTATGCCTTTGATTTCTTGATTTC 58.349 33.333 0.00 0.00 0.00 2.17
2850 3082 7.329226 CGTGTTATGCCTTTGATTTCTTGATTT 59.671 33.333 0.00 0.00 0.00 2.17
2851 3083 6.808212 CGTGTTATGCCTTTGATTTCTTGATT 59.192 34.615 0.00 0.00 0.00 2.57
2852 3084 6.071952 ACGTGTTATGCCTTTGATTTCTTGAT 60.072 34.615 0.00 0.00 0.00 2.57
2853 3085 5.240623 ACGTGTTATGCCTTTGATTTCTTGA 59.759 36.000 0.00 0.00 0.00 3.02
2854 3086 5.343058 CACGTGTTATGCCTTTGATTTCTTG 59.657 40.000 7.58 0.00 0.00 3.02
2855 3087 5.009610 ACACGTGTTATGCCTTTGATTTCTT 59.990 36.000 17.22 0.00 0.00 2.52
2856 3088 4.518970 ACACGTGTTATGCCTTTGATTTCT 59.481 37.500 17.22 0.00 0.00 2.52
2857 3089 4.794169 ACACGTGTTATGCCTTTGATTTC 58.206 39.130 17.22 0.00 0.00 2.17
2858 3090 4.846779 ACACGTGTTATGCCTTTGATTT 57.153 36.364 17.22 0.00 0.00 2.17
2859 3091 4.846779 AACACGTGTTATGCCTTTGATT 57.153 36.364 31.49 3.27 36.32 2.57
2860 3092 4.846779 AAACACGTGTTATGCCTTTGAT 57.153 36.364 32.47 11.49 37.25 2.57
2861 3093 4.142359 ACAAAACACGTGTTATGCCTTTGA 60.142 37.500 32.14 0.00 37.25 2.69
2862 3094 4.109050 ACAAAACACGTGTTATGCCTTTG 58.891 39.130 32.47 29.39 37.25 2.77
2863 3095 4.379339 ACAAAACACGTGTTATGCCTTT 57.621 36.364 32.47 19.43 37.25 3.11
2864 3096 4.379339 AACAAAACACGTGTTATGCCTT 57.621 36.364 32.47 20.13 37.44 4.35
2865 3097 4.109050 CAAACAAAACACGTGTTATGCCT 58.891 39.130 32.47 15.24 38.24 4.75
2866 3098 3.860536 ACAAACAAAACACGTGTTATGCC 59.139 39.130 32.47 0.00 38.24 4.40
2867 3099 5.443142 AACAAACAAAACACGTGTTATGC 57.557 34.783 32.47 0.00 38.24 3.14
2869 3101 8.690680 AACATAACAAACAAAACACGTGTTAT 57.309 26.923 32.47 19.73 42.98 1.89
2870 3102 9.784680 ATAACATAACAAACAAAACACGTGTTA 57.215 25.926 32.47 15.11 38.24 2.41
2871 3103 8.690680 ATAACATAACAAACAAAACACGTGTT 57.309 26.923 27.70 27.70 40.92 3.32
2872 3104 9.224058 GTATAACATAACAAACAAAACACGTGT 57.776 29.630 17.22 17.22 0.00 4.49
2873 3105 9.222916 TGTATAACATAACAAACAAAACACGTG 57.777 29.630 15.48 15.48 0.00 4.49
2874 3106 9.224058 GTGTATAACATAACAAACAAAACACGT 57.776 29.630 0.00 0.00 0.00 4.49
2875 3107 9.222916 TGTGTATAACATAACAAACAAAACACG 57.777 29.630 0.00 0.00 36.12 4.49
2906 3138 2.625737 GCTGAGAATGCTGAGCTTACA 58.374 47.619 4.65 0.83 46.27 2.41
3047 3386 2.422597 TCACGGTGTTATGCCTTTGAG 58.577 47.619 8.17 0.00 0.00 3.02
3078 3417 4.439563 CCCTTCTCTAGCTTCTCGAGTTTC 60.440 50.000 13.13 2.50 0.00 2.78
3135 3474 7.332926 ACATTCACAAGTTACAGATCTGATGTC 59.667 37.037 29.27 14.90 32.02 3.06
3138 3477 9.322773 CATACATTCACAAGTTACAGATCTGAT 57.677 33.333 29.27 15.19 0.00 2.90
3182 3521 1.079336 GCCACGGAGTAGTTGGGAC 60.079 63.158 0.00 0.00 41.61 4.46
3186 3525 0.537188 ATGGAGCCACGGAGTAGTTG 59.463 55.000 0.00 0.00 41.61 3.16
3187 3526 0.537188 CATGGAGCCACGGAGTAGTT 59.463 55.000 0.00 0.00 41.61 2.24
3188 3527 1.961180 GCATGGAGCCACGGAGTAGT 61.961 60.000 0.00 0.00 41.61 2.73
3189 3528 1.227380 GCATGGAGCCACGGAGTAG 60.227 63.158 0.00 0.00 41.61 2.57
3191 3530 2.809861 CTTGCATGGAGCCACGGAGT 62.810 60.000 0.00 0.00 44.83 3.85
3193 3532 2.046023 CTTGCATGGAGCCACGGA 60.046 61.111 0.00 0.00 44.83 4.69
3194 3533 3.818787 GCTTGCATGGAGCCACGG 61.819 66.667 1.34 0.00 44.83 4.94
3195 3534 1.940883 ATTGCTTGCATGGAGCCACG 61.941 55.000 6.42 0.00 44.83 4.94
3196 3535 1.105457 TATTGCTTGCATGGAGCCAC 58.895 50.000 6.42 0.00 44.83 5.01
3197 3536 2.076207 ATATTGCTTGCATGGAGCCA 57.924 45.000 6.42 0.00 44.83 4.75
3198 3537 4.589216 TTTATATTGCTTGCATGGAGCC 57.411 40.909 6.42 0.00 44.83 4.70
3199 3538 5.835257 TCTTTTATATTGCTTGCATGGAGC 58.165 37.500 1.77 1.77 45.96 4.70
3200 3539 6.263842 TCCTCTTTTATATTGCTTGCATGGAG 59.736 38.462 1.34 0.00 0.00 3.86
3201 3540 6.128486 TCCTCTTTTATATTGCTTGCATGGA 58.872 36.000 1.34 0.00 0.00 3.41
3202 3541 6.395426 TCCTCTTTTATATTGCTTGCATGG 57.605 37.500 1.34 0.00 0.00 3.66
3203 3542 7.924412 ACATTCCTCTTTTATATTGCTTGCATG 59.076 33.333 0.00 0.00 0.00 4.06
3204 3543 7.924412 CACATTCCTCTTTTATATTGCTTGCAT 59.076 33.333 0.00 0.00 0.00 3.96
3205 3544 7.259882 CACATTCCTCTTTTATATTGCTTGCA 58.740 34.615 0.00 0.00 0.00 4.08
3206 3545 6.698766 CCACATTCCTCTTTTATATTGCTTGC 59.301 38.462 0.00 0.00 0.00 4.01
3207 3546 7.775120 ACCACATTCCTCTTTTATATTGCTTG 58.225 34.615 0.00 0.00 0.00 4.01
3208 3547 7.961326 ACCACATTCCTCTTTTATATTGCTT 57.039 32.000 0.00 0.00 0.00 3.91
3209 3548 9.289782 GATACCACATTCCTCTTTTATATTGCT 57.710 33.333 0.00 0.00 0.00 3.91
3210 3549 8.515414 GGATACCACATTCCTCTTTTATATTGC 58.485 37.037 0.00 0.00 0.00 3.56
3211 3550 9.573166 TGGATACCACATTCCTCTTTTATATTG 57.427 33.333 0.00 0.00 32.95 1.90
3212 3551 9.799106 CTGGATACCACATTCCTCTTTTATATT 57.201 33.333 0.00 0.00 32.95 1.28
3390 3761 5.947228 TGAGCTTGTTCACTATTTTGGAG 57.053 39.130 0.00 0.00 0.00 3.86
3581 3972 2.558359 CCCTTGAATGACTGGTGTTTCC 59.442 50.000 0.00 0.00 0.00 3.13
3583 3974 3.222603 GACCCTTGAATGACTGGTGTTT 58.777 45.455 0.00 0.00 0.00 2.83
3628 4019 3.215151 TGGAACGGAGTACAATTTTGCA 58.785 40.909 0.00 0.00 45.00 4.08


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

AutoCloner maintained by Alex Coulton.