Multiple sequence alignment - TraesCS3D01G379800

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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 TraesCS3D01G379800 chr3D 100.000 3737 0 0 857 4593 496677359 496673623 0.000000e+00 6902
1 TraesCS3D01G379800 chr3D 100.000 563 0 0 1 563 496678215 496677653 0.000000e+00 1040
2 TraesCS3D01G379800 chr3A 94.778 3543 121 29 940 4454 638206293 638209799 0.000000e+00 5459
3 TraesCS3D01G379800 chr3A 87.204 422 25 8 139 544 638205615 638206023 1.950000e-123 453
4 TraesCS3D01G379800 chr3B 93.958 2764 116 17 1858 4593 655629199 655626459 0.000000e+00 4132
5 TraesCS3D01G379800 chr3B 91.393 1034 57 18 925 1947 655630068 655629056 0.000000e+00 1387
6 TraesCS3D01G379800 chr3B 88.295 393 23 8 165 540 655630874 655630488 2.520000e-122 449


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 TraesCS3D01G379800 chr3D 496673623 496678215 4592 True 3971.000000 6902 100.000000 1 4593 2 chr3D.!!$R1 4592
1 TraesCS3D01G379800 chr3A 638205615 638209799 4184 False 2956.000000 5459 90.991000 139 4454 2 chr3A.!!$F1 4315
2 TraesCS3D01G379800 chr3B 655626459 655630874 4415 True 1989.333333 4132 91.215333 165 4593 3 chr3B.!!$R1 4428

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
468 478 0.251165 ATACAAAACCCAGGTGCGCT 60.251 50.0 9.73 0.0 0.00 5.92 F
1335 1417 0.183971 TTTGGTGGATTGTCCGTGGT 59.816 50.0 0.00 0.0 40.17 4.16 F
2098 2188 0.240945 CAAGATTGGCACGGGTTGTC 59.759 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2128 0.254178 CATCCACCTTCTCCACTGGG 59.746 60.000 0.00 0.00 0.0 4.45 R
2224 2314 0.526211 GAACCTTTGCCCCTTTAGCG 59.474 55.000 0.00 0.00 0.0 4.26 R
3851 3942 1.377725 CACTGGAGTGGACCATGGC 60.378 63.158 13.04 4.47 42.1 4.40 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
35 36 7.237920 TCCGTATTTATTTTAGACTTTCGGC 57.762 36.000 0.00 0.00 34.28 5.54
36 37 6.019640 TCCGTATTTATTTTAGACTTTCGGCG 60.020 38.462 0.00 0.00 34.28 6.46
37 38 6.019640 CCGTATTTATTTTAGACTTTCGGCGA 60.020 38.462 4.99 4.99 0.00 5.54
38 39 7.306983 CCGTATTTATTTTAGACTTTCGGCGAT 60.307 37.037 11.76 0.00 0.00 4.58
39 40 8.060090 CGTATTTATTTTAGACTTTCGGCGATT 58.940 33.333 11.76 0.00 0.00 3.34
40 41 9.712359 GTATTTATTTTAGACTTTCGGCGATTT 57.288 29.630 11.76 0.00 0.00 2.17
42 43 8.663771 TTTATTTTAGACTTTCGGCGATTTTC 57.336 30.769 11.76 7.25 0.00 2.29
43 44 3.984018 TTAGACTTTCGGCGATTTTCG 57.016 42.857 11.76 0.00 43.89 3.46
44 45 1.792006 AGACTTTCGGCGATTTTCGT 58.208 45.000 11.76 3.49 42.81 3.85
45 46 2.140717 AGACTTTCGGCGATTTTCGTT 58.859 42.857 11.76 0.00 42.81 3.85
46 47 2.546789 AGACTTTCGGCGATTTTCGTTT 59.453 40.909 11.76 0.00 42.81 3.60
47 48 3.002965 AGACTTTCGGCGATTTTCGTTTT 59.997 39.130 11.76 0.00 42.81 2.43
48 49 3.697982 ACTTTCGGCGATTTTCGTTTTT 58.302 36.364 11.76 0.00 42.81 1.94
77 78 4.963237 TTGAATTGCGATTTTCGTTTGG 57.037 36.364 0.00 0.00 42.81 3.28
78 79 2.728839 TGAATTGCGATTTTCGTTTGGC 59.271 40.909 0.00 0.00 42.81 4.52
79 80 2.430546 ATTGCGATTTTCGTTTGGCA 57.569 40.000 0.00 0.00 42.81 4.92
80 81 2.430546 TTGCGATTTTCGTTTGGCAT 57.569 40.000 0.00 0.00 42.81 4.40
81 82 1.695813 TGCGATTTTCGTTTGGCATG 58.304 45.000 0.00 0.00 42.81 4.06
82 83 0.991344 GCGATTTTCGTTTGGCATGG 59.009 50.000 0.00 0.00 42.81 3.66
83 84 1.668628 GCGATTTTCGTTTGGCATGGT 60.669 47.619 0.00 0.00 42.81 3.55
84 85 2.250188 CGATTTTCGTTTGGCATGGTC 58.750 47.619 0.00 0.00 34.72 4.02
85 86 2.250188 GATTTTCGTTTGGCATGGTCG 58.750 47.619 0.00 0.00 0.00 4.79
86 87 1.309950 TTTTCGTTTGGCATGGTCGA 58.690 45.000 0.00 0.00 0.00 4.20
87 88 0.589223 TTTCGTTTGGCATGGTCGAC 59.411 50.000 7.13 7.13 0.00 4.20
88 89 0.533085 TTCGTTTGGCATGGTCGACA 60.533 50.000 18.91 3.91 0.00 4.35
89 90 0.321210 TCGTTTGGCATGGTCGACAT 60.321 50.000 18.91 6.28 41.57 3.06
102 103 5.752892 TGGTCGACATGAAGATAGTACTC 57.247 43.478 18.91 0.00 0.00 2.59
103 104 4.272748 TGGTCGACATGAAGATAGTACTCG 59.727 45.833 18.91 0.00 0.00 4.18
104 105 4.212911 GTCGACATGAAGATAGTACTCGC 58.787 47.826 11.55 0.00 0.00 5.03
105 106 4.024725 GTCGACATGAAGATAGTACTCGCT 60.025 45.833 11.55 0.00 0.00 4.93
106 107 5.177142 GTCGACATGAAGATAGTACTCGCTA 59.823 44.000 11.55 0.00 0.00 4.26
107 108 5.756833 TCGACATGAAGATAGTACTCGCTAA 59.243 40.000 0.00 0.00 0.00 3.09
108 109 6.427242 TCGACATGAAGATAGTACTCGCTAAT 59.573 38.462 0.00 0.00 0.00 1.73
109 110 7.601508 TCGACATGAAGATAGTACTCGCTAATA 59.398 37.037 0.00 0.00 0.00 0.98
110 111 8.228464 CGACATGAAGATAGTACTCGCTAATAA 58.772 37.037 0.00 0.00 0.00 1.40
117 118 9.962809 AAGATAGTACTCGCTAATAATACTCCT 57.037 33.333 0.00 0.00 0.00 3.69
118 119 9.386010 AGATAGTACTCGCTAATAATACTCCTG 57.614 37.037 0.00 0.00 0.00 3.86
119 120 6.821031 AGTACTCGCTAATAATACTCCTGG 57.179 41.667 0.00 0.00 0.00 4.45
120 121 6.305411 AGTACTCGCTAATAATACTCCTGGT 58.695 40.000 0.00 0.00 0.00 4.00
121 122 5.708877 ACTCGCTAATAATACTCCTGGTC 57.291 43.478 0.00 0.00 0.00 4.02
122 123 4.215827 ACTCGCTAATAATACTCCTGGTCG 59.784 45.833 0.00 0.00 0.00 4.79
123 124 4.392047 TCGCTAATAATACTCCTGGTCGA 58.608 43.478 0.00 0.00 0.00 4.20
124 125 4.214971 TCGCTAATAATACTCCTGGTCGAC 59.785 45.833 7.13 7.13 0.00 4.20
125 126 4.023450 CGCTAATAATACTCCTGGTCGACA 60.023 45.833 18.91 2.63 0.00 4.35
126 127 5.335740 CGCTAATAATACTCCTGGTCGACAT 60.336 44.000 18.91 0.00 0.00 3.06
127 128 5.864474 GCTAATAATACTCCTGGTCGACATG 59.136 44.000 18.91 8.93 0.00 3.21
128 129 4.873746 ATAATACTCCTGGTCGACATGG 57.126 45.455 18.91 17.72 0.00 3.66
129 130 2.454336 ATACTCCTGGTCGACATGGA 57.546 50.000 21.96 21.96 0.00 3.41
130 131 2.225382 TACTCCTGGTCGACATGGAA 57.775 50.000 22.99 11.50 0.00 3.53
131 132 1.348064 ACTCCTGGTCGACATGGAAA 58.652 50.000 22.99 8.20 0.00 3.13
132 133 1.909302 ACTCCTGGTCGACATGGAAAT 59.091 47.619 22.99 14.69 0.00 2.17
133 134 3.104512 ACTCCTGGTCGACATGGAAATA 58.895 45.455 22.99 7.35 0.00 1.40
134 135 3.133003 ACTCCTGGTCGACATGGAAATAG 59.867 47.826 22.99 16.10 0.00 1.73
135 136 3.104512 TCCTGGTCGACATGGAAATAGT 58.895 45.455 21.39 0.00 0.00 2.12
136 137 4.283337 TCCTGGTCGACATGGAAATAGTA 58.717 43.478 21.39 2.77 0.00 1.82
137 138 4.098960 TCCTGGTCGACATGGAAATAGTAC 59.901 45.833 21.39 0.31 0.00 2.73
138 139 4.142026 CCTGGTCGACATGGAAATAGTACA 60.142 45.833 18.91 0.00 0.00 2.90
139 140 5.408880 TGGTCGACATGGAAATAGTACAA 57.591 39.130 18.91 0.00 0.00 2.41
140 141 5.416083 TGGTCGACATGGAAATAGTACAAG 58.584 41.667 18.91 0.00 0.00 3.16
144 145 5.867174 TCGACATGGAAATAGTACAAGTGTG 59.133 40.000 0.00 0.00 0.00 3.82
211 213 0.682855 TTCCCCACATTTCCCGCATC 60.683 55.000 0.00 0.00 0.00 3.91
214 216 1.439353 CCCACATTTCCCGCATCGAG 61.439 60.000 0.00 0.00 0.00 4.04
217 219 2.203209 ATTTCCCGCATCGAGGCC 60.203 61.111 17.46 0.00 0.00 5.19
225 228 2.203126 CATCGAGGCCTGGCTTCC 60.203 66.667 23.17 9.81 30.69 3.46
254 257 3.356290 CCCGTGATTTCTCCCTGATTTT 58.644 45.455 0.00 0.00 0.00 1.82
284 287 2.857748 GCAGTTTGAAACCGAACCTTTG 59.142 45.455 4.14 0.00 0.00 2.77
463 473 0.322322 TCGCGATACAAAACCCAGGT 59.678 50.000 3.71 0.00 0.00 4.00
468 478 0.251165 ATACAAAACCCAGGTGCGCT 60.251 50.000 9.73 0.00 0.00 5.92
544 580 1.512156 GAGCTCCGGCCGTTTCAAAA 61.512 55.000 26.12 0.00 39.73 2.44
545 581 1.081442 GCTCCGGCCGTTTCAAAAG 60.081 57.895 26.12 5.84 0.00 2.27
546 582 1.579429 CTCCGGCCGTTTCAAAAGG 59.421 57.895 26.12 5.01 0.00 3.11
551 587 4.653555 CCGTTTCAAAAGGCAGCC 57.346 55.556 1.84 1.84 0.00 4.85
552 588 1.006220 CCGTTTCAAAAGGCAGCCC 60.006 57.895 8.22 0.00 0.00 5.19
553 589 1.006220 CGTTTCAAAAGGCAGCCCC 60.006 57.895 8.22 0.00 0.00 5.80
554 590 1.371183 GTTTCAAAAGGCAGCCCCC 59.629 57.895 8.22 0.00 0.00 5.40
555 591 1.074926 TTTCAAAAGGCAGCCCCCA 60.075 52.632 8.22 0.00 0.00 4.96
556 592 1.406860 TTTCAAAAGGCAGCCCCCAC 61.407 55.000 8.22 0.00 0.00 4.61
557 593 3.313524 CAAAAGGCAGCCCCCACC 61.314 66.667 8.22 0.00 0.00 4.61
558 594 4.638895 AAAAGGCAGCCCCCACCC 62.639 66.667 8.22 0.00 0.00 4.61
906 942 4.179599 CCCCTCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
907 943 4.179599 CCCTCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
908 944 4.179599 CCTCTCCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
909 945 4.179599 CTCTCCCCTCCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
1211 1291 4.468689 CGGTCCGGGCCTTCCTTC 62.469 72.222 25.54 0.00 0.00 3.46
1212 1292 4.468689 GGTCCGGGCCTTCCTTCG 62.469 72.222 20.78 0.00 0.00 3.79
1213 1293 3.703127 GTCCGGGCCTTCCTTCGT 61.703 66.667 0.84 0.00 0.00 3.85
1214 1294 2.037687 TCCGGGCCTTCCTTCGTA 59.962 61.111 0.84 0.00 0.00 3.43
1229 1310 1.676746 TCGTATCTCTTCCGTCCTGG 58.323 55.000 0.00 0.00 40.09 4.45
1247 1329 1.000955 TGGACTCTGAAGTTTCGCCTC 59.999 52.381 0.00 0.00 35.28 4.70
1248 1330 1.341606 GACTCTGAAGTTTCGCCTCG 58.658 55.000 0.00 0.00 35.28 4.63
1249 1331 0.959553 ACTCTGAAGTTTCGCCTCGA 59.040 50.000 0.00 0.00 28.74 4.04
1251 1333 1.923204 CTCTGAAGTTTCGCCTCGATG 59.077 52.381 0.00 0.00 35.23 3.84
1252 1334 1.544246 TCTGAAGTTTCGCCTCGATGA 59.456 47.619 0.00 0.00 35.23 2.92
1335 1417 0.183971 TTTGGTGGATTGTCCGTGGT 59.816 50.000 0.00 0.00 40.17 4.16
1340 1422 0.762418 TGGATTGTCCGTGGTTGTCT 59.238 50.000 0.00 0.00 40.17 3.41
1345 1427 2.110213 TCCGTGGTTGTCTGTGGC 59.890 61.111 0.00 0.00 0.00 5.01
1434 1523 0.524862 CTTGATCACAGGTTGCTGGC 59.475 55.000 0.00 0.00 0.00 4.85
1438 1527 0.892358 ATCACAGGTTGCTGGCTGTG 60.892 55.000 0.00 0.00 45.88 3.66
1495 1585 3.864003 GTGTCCTAGATTTACTGAACGCC 59.136 47.826 0.00 0.00 0.00 5.68
1518 1608 7.035612 GCCCCTGTCATCAGTTTTTAAATAAG 58.964 38.462 0.00 0.00 39.82 1.73
1836 1926 1.552337 TGATCTGTCAGAAGGTCAGGC 59.448 52.381 6.64 0.00 32.27 4.85
1892 1982 0.610687 CCTGTCAGAAGGTCAGGGTC 59.389 60.000 0.00 0.00 43.30 4.46
2026 2116 5.813383 AGTCCTCATCTGACAAACATTGAT 58.187 37.500 0.00 0.00 35.15 2.57
2033 2123 8.032952 TCATCTGACAAACATTGATTCTGTAC 57.967 34.615 0.00 0.00 0.00 2.90
2038 2128 6.204688 TGACAAACATTGATTCTGTACCTCAC 59.795 38.462 0.00 0.00 0.00 3.51
2043 2133 2.902608 TGATTCTGTACCTCACCCAGT 58.097 47.619 0.00 0.00 0.00 4.00
2098 2188 0.240945 CAAGATTGGCACGGGTTGTC 59.759 55.000 0.00 0.00 0.00 3.18
2110 2200 1.984020 GGTTGTCCCTCCTGGTCTC 59.016 63.158 0.00 0.00 34.77 3.36
2224 2314 3.377172 AGTTGTACAATTATGCTTCGGCC 59.623 43.478 12.26 0.00 40.91 6.13
2278 2368 2.973082 GCCAAAGGCGCTTCCAAT 59.027 55.556 7.64 0.00 39.62 3.16
2332 2422 4.101448 CCTTGCTCCGTGGAGGGG 62.101 72.222 17.29 0.00 45.86 4.79
2545 2635 1.077716 GCCAAAGTGGGCGAGGTAT 60.078 57.895 0.00 0.00 45.40 2.73
2599 2689 3.002791 TGCAAGCTATTGTACACTGAGC 58.997 45.455 12.75 12.75 38.76 4.26
2614 2704 2.238144 ACTGAGCATGCTTGAGGTGTAT 59.762 45.455 23.61 2.05 0.00 2.29
2664 2754 4.624882 CGAGAACTTGATTCCAGTTGAGAG 59.375 45.833 7.79 0.00 38.16 3.20
2667 2757 7.067496 AGAACTTGATTCCAGTTGAGAGTAA 57.933 36.000 7.79 0.00 38.16 2.24
2701 2791 1.594862 GATGACAAATCGAAGGAGCCG 59.405 52.381 0.00 0.00 0.00 5.52
3135 3225 9.914834 TGCTATTGTTACCCTTAATTTCTGTAT 57.085 29.630 0.00 0.00 0.00 2.29
3215 3305 0.687354 GGAAGTCAGTTGCCTCCTCA 59.313 55.000 0.00 0.00 0.00 3.86
3245 3335 4.998051 ACCAACTTGTCCTGGATAATGTT 58.002 39.130 6.33 9.87 36.49 2.71
3449 3539 6.418057 TCCTGTGTTTTATTTTTGGATGCT 57.582 33.333 0.00 0.00 0.00 3.79
3724 3814 6.709281 ACAGATTATCTAGCCTCATCATTGG 58.291 40.000 0.00 0.00 0.00 3.16
3737 3827 5.186409 CCTCATCATTGGTCTCAAATTTGGT 59.814 40.000 17.90 0.00 36.36 3.67
3747 3837 3.645687 TCTCAAATTTGGTGGGAAAAGGG 59.354 43.478 17.90 0.00 0.00 3.95
3851 3942 2.513204 CTGCTCTGGTCCATGCCG 60.513 66.667 12.65 4.78 0.00 5.69
3934 4025 1.070758 GAGCCGGCAATCATAGAAGGA 59.929 52.381 31.54 0.00 0.00 3.36
3935 4026 1.071385 AGCCGGCAATCATAGAAGGAG 59.929 52.381 31.54 0.00 0.00 3.69
3936 4027 1.517242 CCGGCAATCATAGAAGGAGC 58.483 55.000 0.00 0.00 0.00 4.70
3937 4028 1.517242 CGGCAATCATAGAAGGAGCC 58.483 55.000 0.00 0.00 37.32 4.70
3938 4029 1.202687 CGGCAATCATAGAAGGAGCCA 60.203 52.381 0.00 0.00 40.58 4.75
3939 4030 2.551721 CGGCAATCATAGAAGGAGCCAT 60.552 50.000 0.00 0.00 40.58 4.40
3941 4032 2.818432 GCAATCATAGAAGGAGCCATGG 59.182 50.000 7.63 7.63 0.00 3.66
3942 4033 2.818432 CAATCATAGAAGGAGCCATGGC 59.182 50.000 30.12 30.12 42.33 4.40
3943 4034 1.510492 TCATAGAAGGAGCCATGGCA 58.490 50.000 37.18 16.40 44.88 4.92
3944 4035 1.419012 TCATAGAAGGAGCCATGGCAG 59.581 52.381 37.18 14.96 44.88 4.85
3945 4036 0.769873 ATAGAAGGAGCCATGGCAGG 59.230 55.000 37.18 0.00 44.88 4.85
3946 4037 0.326522 TAGAAGGAGCCATGGCAGGA 60.327 55.000 37.18 12.90 44.88 3.86
3947 4038 1.452833 GAAGGAGCCATGGCAGGAC 60.453 63.158 37.18 22.90 44.88 3.85
3984 4075 2.754552 TGCTTCCTTGTATGATTGCCAC 59.245 45.455 0.00 0.00 0.00 5.01
3985 4076 3.019564 GCTTCCTTGTATGATTGCCACT 58.980 45.455 0.00 0.00 0.00 4.00
3986 4077 3.445096 GCTTCCTTGTATGATTGCCACTT 59.555 43.478 0.00 0.00 0.00 3.16
3987 4078 4.676196 GCTTCCTTGTATGATTGCCACTTG 60.676 45.833 0.00 0.00 0.00 3.16
3988 4079 2.754552 TCCTTGTATGATTGCCACTTGC 59.245 45.455 0.00 0.00 41.77 4.01
3989 4080 2.159198 CCTTGTATGATTGCCACTTGCC 60.159 50.000 0.00 0.00 40.16 4.52
3990 4081 2.212812 TGTATGATTGCCACTTGCCA 57.787 45.000 0.00 0.00 40.16 4.92
4128 4236 2.757868 TGTGTTGCTTACAAGGCAGTTT 59.242 40.909 0.00 0.00 40.90 2.66
4130 4238 4.180817 GTGTTGCTTACAAGGCAGTTTTT 58.819 39.130 0.00 0.00 40.90 1.94
4167 4275 1.545582 CCACAATGGAAGGCGTCATTT 59.454 47.619 2.23 0.00 40.96 2.32
4168 4276 2.415893 CCACAATGGAAGGCGTCATTTC 60.416 50.000 2.23 0.00 40.96 2.17
4169 4277 2.228582 CACAATGGAAGGCGTCATTTCA 59.771 45.455 2.23 0.00 31.95 2.69
4170 4278 3.091545 ACAATGGAAGGCGTCATTTCAT 58.908 40.909 2.23 0.00 31.95 2.57
4172 4280 2.488204 TGGAAGGCGTCATTTCATCA 57.512 45.000 2.23 0.00 0.00 3.07
4173 4281 2.358957 TGGAAGGCGTCATTTCATCAG 58.641 47.619 2.23 0.00 0.00 2.90
4181 4290 4.201822 GGCGTCATTTCATCAGTAACTTCC 60.202 45.833 0.00 0.00 0.00 3.46
4186 4295 7.148423 CGTCATTTCATCAGTAACTTCCATTGA 60.148 37.037 0.00 0.00 0.00 2.57
4249 4359 1.134128 CCCTGCACAGCCACATATGTA 60.134 52.381 8.32 0.00 0.00 2.29
4250 4360 2.216046 CCTGCACAGCCACATATGTAG 58.784 52.381 8.32 1.85 0.00 2.74
4251 4361 1.600957 CTGCACAGCCACATATGTAGC 59.399 52.381 17.28 17.28 32.82 3.58
4262 4372 3.310774 CACATATGTAGCACAGCTGTTCC 59.689 47.826 18.94 11.50 40.10 3.62
4277 4387 3.306364 GCTGTTCCTAGCAGTTGAGAGAA 60.306 47.826 0.00 0.00 43.17 2.87
4279 4389 5.486526 CTGTTCCTAGCAGTTGAGAGAATT 58.513 41.667 0.00 0.00 0.00 2.17
4282 4392 6.428159 TGTTCCTAGCAGTTGAGAGAATTTTC 59.572 38.462 0.00 0.00 0.00 2.29
4296 4407 8.658609 TGAGAGAATTTTCTTTTTGCAAGTTTG 58.341 29.630 0.00 0.00 37.73 2.93
4396 4527 9.956640 ATTTCATGGATAGATTCATAGAAGGAC 57.043 33.333 0.00 0.00 0.00 3.85
4419 4550 5.694458 ACGGCATTGAAAAATACTTTTGTCC 59.306 36.000 0.00 0.00 34.83 4.02
4440 4571 1.067821 GCGACATCTGGTTAGCTAGCT 59.932 52.381 23.12 23.12 32.78 3.32
4445 4576 5.220710 ACATCTGGTTAGCTAGCTAATGG 57.779 43.478 33.67 25.43 40.18 3.16
4491 4622 1.003355 CCTGCTCGGTTGACCATGT 60.003 57.895 0.51 0.00 35.14 3.21
4496 4627 3.215151 TGCTCGGTTGACCATGTTTTAA 58.785 40.909 0.51 0.00 35.14 1.52
4498 4629 4.279671 TGCTCGGTTGACCATGTTTTAAAT 59.720 37.500 0.51 0.00 35.14 1.40
4507 4638 7.798596 TGACCATGTTTTAAATTGTGCAAAT 57.201 28.000 0.00 0.00 0.00 2.32
4548 4679 2.167693 GGATATCCACAGTTCCACACGA 59.832 50.000 17.34 0.00 35.64 4.35
4549 4680 3.448686 GATATCCACAGTTCCACACGAG 58.551 50.000 0.00 0.00 0.00 4.18
4552 4683 2.521126 TCCACAGTTCCACACGAGATA 58.479 47.619 0.00 0.00 0.00 1.98
4553 4684 3.096852 TCCACAGTTCCACACGAGATAT 58.903 45.455 0.00 0.00 0.00 1.63
4554 4685 3.130516 TCCACAGTTCCACACGAGATATC 59.869 47.826 0.00 0.00 0.00 1.63
4559 4690 1.605753 TCCACACGAGATATCCTCCG 58.394 55.000 0.00 3.80 38.71 4.63
4572 4703 0.820226 TCCTCCGATGTCAGCTTCAG 59.180 55.000 0.00 0.00 0.00 3.02
4575 4706 0.390340 TCCGATGTCAGCTTCAGCAC 60.390 55.000 0.75 0.00 45.16 4.40
4579 4710 1.923204 GATGTCAGCTTCAGCACTACG 59.077 52.381 0.75 0.00 45.16 3.51
4584 4715 1.457303 CAGCTTCAGCACTACGTTGAC 59.543 52.381 3.44 0.00 45.16 3.18
4589 4720 3.120321 TCAGCACTACGTTGACCATTT 57.880 42.857 3.44 0.00 28.60 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.177013 GCCGAAAGTCTAAAATAAATACGGAAA 58.823 33.333 0.00 0.00 38.09 3.13
10 11 7.464444 CGCCGAAAGTCTAAAATAAATACGGAA 60.464 37.037 0.00 0.00 38.09 4.30
11 12 6.019640 CGCCGAAAGTCTAAAATAAATACGGA 60.020 38.462 0.00 0.00 38.09 4.69
12 13 6.019640 TCGCCGAAAGTCTAAAATAAATACGG 60.020 38.462 0.00 0.00 38.72 4.02
13 14 6.925600 TCGCCGAAAGTCTAAAATAAATACG 58.074 36.000 0.00 0.00 0.00 3.06
14 15 9.712359 AAATCGCCGAAAGTCTAAAATAAATAC 57.288 29.630 0.00 0.00 0.00 1.89
16 17 9.285770 GAAAATCGCCGAAAGTCTAAAATAAAT 57.714 29.630 0.00 0.00 0.00 1.40
17 18 7.479291 CGAAAATCGCCGAAAGTCTAAAATAAA 59.521 33.333 0.00 0.00 31.14 1.40
18 19 6.957077 CGAAAATCGCCGAAAGTCTAAAATAA 59.043 34.615 0.00 0.00 31.14 1.40
19 20 6.091169 ACGAAAATCGCCGAAAGTCTAAAATA 59.909 34.615 0.00 0.00 45.12 1.40
20 21 5.106830 ACGAAAATCGCCGAAAGTCTAAAAT 60.107 36.000 0.00 0.00 45.12 1.82
21 22 4.211794 ACGAAAATCGCCGAAAGTCTAAAA 59.788 37.500 0.00 0.00 45.12 1.52
22 23 3.742369 ACGAAAATCGCCGAAAGTCTAAA 59.258 39.130 0.00 0.00 45.12 1.85
23 24 3.319755 ACGAAAATCGCCGAAAGTCTAA 58.680 40.909 0.00 0.00 45.12 2.10
24 25 2.950433 ACGAAAATCGCCGAAAGTCTA 58.050 42.857 0.00 0.00 45.12 2.59
25 26 1.792006 ACGAAAATCGCCGAAAGTCT 58.208 45.000 0.00 0.00 45.12 3.24
26 27 2.589338 AACGAAAATCGCCGAAAGTC 57.411 45.000 0.00 0.00 45.12 3.01
27 28 3.343380 AAAACGAAAATCGCCGAAAGT 57.657 38.095 0.00 0.00 45.12 2.66
53 54 6.188175 CCAAACGAAAATCGCAATTCAAAAA 58.812 32.000 0.00 0.00 45.12 1.94
54 55 5.732288 CCAAACGAAAATCGCAATTCAAAA 58.268 33.333 0.00 0.00 45.12 2.44
55 56 4.318404 GCCAAACGAAAATCGCAATTCAAA 60.318 37.500 0.00 0.00 45.12 2.69
56 57 3.183373 GCCAAACGAAAATCGCAATTCAA 59.817 39.130 0.00 0.00 45.12 2.69
57 58 2.728839 GCCAAACGAAAATCGCAATTCA 59.271 40.909 0.00 0.00 45.12 2.57
58 59 2.728839 TGCCAAACGAAAATCGCAATTC 59.271 40.909 0.00 0.00 45.12 2.17
59 60 2.748605 TGCCAAACGAAAATCGCAATT 58.251 38.095 0.00 0.00 45.12 2.32
60 61 2.430546 TGCCAAACGAAAATCGCAAT 57.569 40.000 0.00 0.00 45.12 3.56
61 62 2.057316 CATGCCAAACGAAAATCGCAA 58.943 42.857 0.00 0.00 45.12 4.85
62 63 1.668337 CCATGCCAAACGAAAATCGCA 60.668 47.619 0.00 0.00 45.12 5.10
63 64 0.991344 CCATGCCAAACGAAAATCGC 59.009 50.000 0.00 0.00 45.12 4.58
64 65 2.250188 GACCATGCCAAACGAAAATCG 58.750 47.619 0.00 0.00 46.93 3.34
65 66 2.095466 TCGACCATGCCAAACGAAAATC 60.095 45.455 0.00 0.00 0.00 2.17
66 67 1.883275 TCGACCATGCCAAACGAAAAT 59.117 42.857 0.00 0.00 0.00 1.82
67 68 1.002251 GTCGACCATGCCAAACGAAAA 60.002 47.619 3.51 0.00 34.91 2.29
68 69 0.589223 GTCGACCATGCCAAACGAAA 59.411 50.000 3.51 0.00 34.91 3.46
69 70 0.533085 TGTCGACCATGCCAAACGAA 60.533 50.000 14.12 0.00 34.91 3.85
70 71 0.321210 ATGTCGACCATGCCAAACGA 60.321 50.000 14.12 0.00 30.69 3.85
71 72 0.179192 CATGTCGACCATGCCAAACG 60.179 55.000 14.12 0.00 44.21 3.60
72 73 3.700577 CATGTCGACCATGCCAAAC 57.299 52.632 14.12 0.00 44.21 2.93
79 80 5.049336 CGAGTACTATCTTCATGTCGACCAT 60.049 44.000 14.12 3.85 0.00 3.55
80 81 4.272748 CGAGTACTATCTTCATGTCGACCA 59.727 45.833 14.12 1.26 0.00 4.02
81 82 4.774586 CGAGTACTATCTTCATGTCGACC 58.225 47.826 14.12 0.00 0.00 4.79
82 83 4.024725 AGCGAGTACTATCTTCATGTCGAC 60.025 45.833 9.11 9.11 0.00 4.20
83 84 4.127907 AGCGAGTACTATCTTCATGTCGA 58.872 43.478 0.00 0.00 0.00 4.20
84 85 4.475763 AGCGAGTACTATCTTCATGTCG 57.524 45.455 0.00 0.00 0.00 4.35
91 92 9.962809 AGGAGTATTATTAGCGAGTACTATCTT 57.037 33.333 0.00 0.00 0.00 2.40
92 93 9.386010 CAGGAGTATTATTAGCGAGTACTATCT 57.614 37.037 0.00 0.00 0.00 1.98
93 94 8.614346 CCAGGAGTATTATTAGCGAGTACTATC 58.386 40.741 0.00 0.00 0.00 2.08
94 95 8.108364 ACCAGGAGTATTATTAGCGAGTACTAT 58.892 37.037 0.00 0.00 0.00 2.12
95 96 7.456725 ACCAGGAGTATTATTAGCGAGTACTA 58.543 38.462 0.00 0.00 0.00 1.82
96 97 6.305411 ACCAGGAGTATTATTAGCGAGTACT 58.695 40.000 0.00 0.00 0.00 2.73
97 98 6.572167 ACCAGGAGTATTATTAGCGAGTAC 57.428 41.667 0.00 0.00 0.00 2.73
98 99 5.410746 CGACCAGGAGTATTATTAGCGAGTA 59.589 44.000 0.00 0.00 0.00 2.59
99 100 4.215827 CGACCAGGAGTATTATTAGCGAGT 59.784 45.833 0.00 0.00 0.00 4.18
100 101 4.454847 TCGACCAGGAGTATTATTAGCGAG 59.545 45.833 0.00 0.00 0.00 5.03
101 102 4.214971 GTCGACCAGGAGTATTATTAGCGA 59.785 45.833 3.51 0.00 0.00 4.93
102 103 4.023450 TGTCGACCAGGAGTATTATTAGCG 60.023 45.833 14.12 0.00 0.00 4.26
103 104 5.449107 TGTCGACCAGGAGTATTATTAGC 57.551 43.478 14.12 0.00 0.00 3.09
104 105 6.208797 TCCATGTCGACCAGGAGTATTATTAG 59.791 42.308 18.84 0.00 0.00 1.73
105 106 6.072649 TCCATGTCGACCAGGAGTATTATTA 58.927 40.000 18.84 0.00 0.00 0.98
106 107 4.899457 TCCATGTCGACCAGGAGTATTATT 59.101 41.667 18.84 0.00 0.00 1.40
107 108 4.480115 TCCATGTCGACCAGGAGTATTAT 58.520 43.478 18.84 0.00 0.00 1.28
108 109 3.905968 TCCATGTCGACCAGGAGTATTA 58.094 45.455 18.84 0.20 0.00 0.98
109 110 2.747177 TCCATGTCGACCAGGAGTATT 58.253 47.619 18.84 0.00 0.00 1.89
110 111 2.454336 TCCATGTCGACCAGGAGTAT 57.546 50.000 18.84 0.00 0.00 2.12
111 112 2.225382 TTCCATGTCGACCAGGAGTA 57.775 50.000 20.87 9.16 0.00 2.59
112 113 1.348064 TTTCCATGTCGACCAGGAGT 58.652 50.000 20.87 0.00 0.00 3.85
113 114 2.698855 ATTTCCATGTCGACCAGGAG 57.301 50.000 20.87 4.46 0.00 3.69
114 115 3.104512 ACTATTTCCATGTCGACCAGGA 58.895 45.455 18.84 18.84 0.00 3.86
115 116 3.543680 ACTATTTCCATGTCGACCAGG 57.456 47.619 14.12 14.75 0.00 4.45
116 117 5.006153 TGTACTATTTCCATGTCGACCAG 57.994 43.478 14.12 5.17 0.00 4.00
117 118 5.046878 ACTTGTACTATTTCCATGTCGACCA 60.047 40.000 14.12 1.26 0.00 4.02
118 119 5.291128 CACTTGTACTATTTCCATGTCGACC 59.709 44.000 14.12 0.00 0.00 4.79
119 120 5.867716 ACACTTGTACTATTTCCATGTCGAC 59.132 40.000 9.11 9.11 0.00 4.20
120 121 5.867174 CACACTTGTACTATTTCCATGTCGA 59.133 40.000 0.00 0.00 0.00 4.20
121 122 5.063438 CCACACTTGTACTATTTCCATGTCG 59.937 44.000 0.00 0.00 0.00 4.35
122 123 5.163754 GCCACACTTGTACTATTTCCATGTC 60.164 44.000 0.00 0.00 0.00 3.06
123 124 4.700213 GCCACACTTGTACTATTTCCATGT 59.300 41.667 0.00 0.00 0.00 3.21
124 125 4.699735 TGCCACACTTGTACTATTTCCATG 59.300 41.667 0.00 0.00 0.00 3.66
125 126 4.917385 TGCCACACTTGTACTATTTCCAT 58.083 39.130 0.00 0.00 0.00 3.41
126 127 4.359434 TGCCACACTTGTACTATTTCCA 57.641 40.909 0.00 0.00 0.00 3.53
127 128 5.393027 CCATTGCCACACTTGTACTATTTCC 60.393 44.000 0.00 0.00 0.00 3.13
128 129 5.414454 TCCATTGCCACACTTGTACTATTTC 59.586 40.000 0.00 0.00 0.00 2.17
129 130 5.183140 GTCCATTGCCACACTTGTACTATTT 59.817 40.000 0.00 0.00 0.00 1.40
130 131 4.700213 GTCCATTGCCACACTTGTACTATT 59.300 41.667 0.00 0.00 0.00 1.73
131 132 4.261801 GTCCATTGCCACACTTGTACTAT 58.738 43.478 0.00 0.00 0.00 2.12
132 133 3.071747 TGTCCATTGCCACACTTGTACTA 59.928 43.478 0.00 0.00 0.00 1.82
133 134 2.158682 TGTCCATTGCCACACTTGTACT 60.159 45.455 0.00 0.00 0.00 2.73
134 135 2.031157 GTGTCCATTGCCACACTTGTAC 60.031 50.000 8.95 0.00 39.92 2.90
135 136 2.226330 GTGTCCATTGCCACACTTGTA 58.774 47.619 8.95 0.00 39.92 2.41
136 137 1.032014 GTGTCCATTGCCACACTTGT 58.968 50.000 8.95 0.00 39.92 3.16
137 138 0.040157 CGTGTCCATTGCCACACTTG 60.040 55.000 12.61 0.00 40.74 3.16
138 139 1.172180 CCGTGTCCATTGCCACACTT 61.172 55.000 12.61 0.00 40.74 3.16
139 140 1.600636 CCGTGTCCATTGCCACACT 60.601 57.895 12.61 0.00 40.74 3.55
140 141 2.953821 CCGTGTCCATTGCCACAC 59.046 61.111 6.93 6.93 39.70 3.82
144 145 0.458370 GATTTGCCGTGTCCATTGCC 60.458 55.000 0.00 0.00 0.00 4.52
156 157 4.549458 CGGGTCAATGATAATGATTTGCC 58.451 43.478 0.00 0.00 0.00 4.52
157 158 3.983344 GCGGGTCAATGATAATGATTTGC 59.017 43.478 0.00 0.00 0.00 3.68
211 213 1.821332 GAATGGAAGCCAGGCCTCG 60.821 63.158 8.22 0.00 36.75 4.63
214 216 0.466372 GGTAGAATGGAAGCCAGGCC 60.466 60.000 8.22 0.00 36.75 5.19
217 219 0.179045 CGGGGTAGAATGGAAGCCAG 60.179 60.000 0.00 0.00 36.75 4.85
225 228 3.467803 GGAGAAATCACGGGGTAGAATG 58.532 50.000 0.00 0.00 0.00 2.67
254 257 2.098443 GGTTTCAAACTGCGAAGTTCCA 59.902 45.455 9.83 0.00 0.00 3.53
284 287 2.031683 CCGTTGTCACTGTCAAAACTCC 59.968 50.000 0.00 0.00 0.00 3.85
468 478 2.610859 GAGGTGGAGGCCAGGGAA 60.611 66.667 5.01 0.00 32.34 3.97
889 925 4.179599 GAGGGGAGGGGAGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
890 926 4.179599 GGAGGGGAGGGGAGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
891 927 4.179599 GGGAGGGGAGGGGAGAGG 62.180 77.778 0.00 0.00 0.00 3.69
892 928 4.179599 GGGGAGGGGAGGGGAGAG 62.180 77.778 0.00 0.00 0.00 3.20
918 954 2.822701 GGGCACCGAACGGAATCC 60.823 66.667 20.14 15.16 40.86 3.01
1208 1288 2.033550 CCAGGACGGAAGAGATACGAAG 59.966 54.545 0.00 0.00 37.68 3.79
1210 1290 1.211212 TCCAGGACGGAAGAGATACGA 59.789 52.381 0.00 0.00 42.52 3.43
1211 1291 1.676746 TCCAGGACGGAAGAGATACG 58.323 55.000 0.00 0.00 42.52 3.06
1229 1310 1.068472 TCGAGGCGAAACTTCAGAGTC 60.068 52.381 0.00 0.00 34.21 3.36
1247 1329 6.371825 ACAGGATTCATTCATCATCATCATCG 59.628 38.462 0.00 0.00 0.00 3.84
1248 1330 7.530863 CACAGGATTCATTCATCATCATCATC 58.469 38.462 0.00 0.00 0.00 2.92
1249 1331 6.071896 GCACAGGATTCATTCATCATCATCAT 60.072 38.462 0.00 0.00 0.00 2.45
1251 1333 5.335740 GGCACAGGATTCATTCATCATCATC 60.336 44.000 0.00 0.00 0.00 2.92
1252 1334 4.523173 GGCACAGGATTCATTCATCATCAT 59.477 41.667 0.00 0.00 0.00 2.45
1518 1608 1.064952 CCAGTCAACACGGAACCAAAC 59.935 52.381 0.00 0.00 0.00 2.93
1836 1926 4.261031 CCTTGGTTACAGTTTGTTCTTCGG 60.261 45.833 0.00 0.00 0.00 4.30
1892 1982 0.397941 TTGGTCAGAGCACCTTCCTG 59.602 55.000 0.48 0.00 37.34 3.86
2026 2116 1.132977 TCCACTGGGTGAGGTACAGAA 60.133 52.381 0.00 0.00 35.23 3.02
2033 2123 0.838122 ACCTTCTCCACTGGGTGAGG 60.838 60.000 0.00 2.99 37.92 3.86
2038 2128 0.254178 CATCCACCTTCTCCACTGGG 59.746 60.000 0.00 0.00 0.00 4.45
2043 2133 1.280133 CTTCAGCATCCACCTTCTCCA 59.720 52.381 0.00 0.00 0.00 3.86
2098 2188 1.418334 ATTCATCGAGACCAGGAGGG 58.582 55.000 0.00 0.00 44.81 4.30
2110 2200 3.182182 TGCTCTCGTCTTGAATTCATCG 58.818 45.455 9.40 14.00 0.00 3.84
2224 2314 0.526211 GAACCTTTGCCCCTTTAGCG 59.474 55.000 0.00 0.00 0.00 4.26
2332 2422 9.486497 TCAGAAAGCTCTATGATGACATATTTC 57.514 33.333 0.00 0.00 38.17 2.17
2422 2512 3.911661 AGACTGCTCAGCATTTCAAAC 57.088 42.857 0.00 0.00 38.13 2.93
2511 2601 2.214376 TGGCTCGGGAAATGTGAAAT 57.786 45.000 0.00 0.00 0.00 2.17
2545 2635 5.911752 TGGCTTAGCAAATTGAACTTCAAA 58.088 33.333 6.53 0.00 40.12 2.69
2599 2689 3.317149 CCATTCCATACACCTCAAGCATG 59.683 47.826 0.00 0.00 0.00 4.06
2614 2704 2.601240 TTTCCACAGCATCCATTCCA 57.399 45.000 0.00 0.00 0.00 3.53
2664 2754 8.746922 TTTGTCATCAGATTCAGCATTTTTAC 57.253 30.769 0.00 0.00 0.00 2.01
2667 2757 6.750501 CGATTTGTCATCAGATTCAGCATTTT 59.249 34.615 0.00 0.00 0.00 1.82
2701 2791 3.305608 CCTTCAAAGGTGGTTGCTCAATC 60.306 47.826 0.32 0.00 41.41 2.67
3099 3189 7.539034 AGGGTAACAATAGCAGAAACAAAAT 57.461 32.000 0.00 0.00 39.74 1.82
3149 3239 2.676076 GCCTGAAAACATGAAACGCAT 58.324 42.857 0.00 0.00 37.85 4.73
3150 3240 1.599171 CGCCTGAAAACATGAAACGCA 60.599 47.619 0.00 0.00 0.00 5.24
3153 3243 3.498397 TCTCTCGCCTGAAAACATGAAAC 59.502 43.478 0.00 0.00 0.00 2.78
3158 3248 5.674525 TCAATATCTCTCGCCTGAAAACAT 58.325 37.500 0.00 0.00 0.00 2.71
3317 3407 9.823647 ATGATTCACAAAGTTAGAATCGTATCT 57.176 29.630 14.06 0.00 46.56 1.98
3724 3814 4.503123 CCCTTTTCCCACCAAATTTGAGAC 60.503 45.833 19.86 0.00 0.00 3.36
3737 3827 3.304829 CTTTGTTCCTTCCCTTTTCCCA 58.695 45.455 0.00 0.00 0.00 4.37
3747 3837 2.024414 AGGTGCACACTTTGTTCCTTC 58.976 47.619 20.43 0.00 29.93 3.46
3823 3914 4.830046 TGGACCAGAGCAGAGATAATCTAC 59.170 45.833 0.00 0.00 36.10 2.59
3851 3942 1.377725 CACTGGAGTGGACCATGGC 60.378 63.158 13.04 4.47 42.10 4.40
3936 4027 2.125326 CATGCCAGTCCTGCCATGG 61.125 63.158 7.63 7.63 41.21 3.66
3937 4028 2.125326 CCATGCCAGTCCTGCCATG 61.125 63.158 10.45 10.45 43.59 3.66
3938 4029 2.277737 CCATGCCAGTCCTGCCAT 59.722 61.111 0.00 0.00 0.00 4.40
3939 4030 3.259314 ACCATGCCAGTCCTGCCA 61.259 61.111 0.00 0.00 0.00 4.92
3945 4036 4.247781 CATGGGACCATGCCAGTC 57.752 61.111 17.57 0.00 42.59 3.51
3984 4075 2.503895 ACATTTCTCTCCCTGGCAAG 57.496 50.000 0.00 0.00 0.00 4.01
3985 4076 2.912956 AGTACATTTCTCTCCCTGGCAA 59.087 45.455 0.00 0.00 0.00 4.52
3986 4077 2.237143 CAGTACATTTCTCTCCCTGGCA 59.763 50.000 0.00 0.00 0.00 4.92
3987 4078 2.501723 TCAGTACATTTCTCTCCCTGGC 59.498 50.000 0.00 0.00 0.00 4.85
3988 4079 4.826274 TTCAGTACATTTCTCTCCCTGG 57.174 45.455 0.00 0.00 0.00 4.45
3989 4080 7.816995 GCTATATTCAGTACATTTCTCTCCCTG 59.183 40.741 0.00 0.00 0.00 4.45
3990 4081 7.510685 TGCTATATTCAGTACATTTCTCTCCCT 59.489 37.037 0.00 0.00 0.00 4.20
4128 4236 6.042638 TGTGGAAAGTGGAAACAAATGAAA 57.957 33.333 0.00 0.00 46.06 2.69
4130 4238 5.667539 TTGTGGAAAGTGGAAACAAATGA 57.332 34.783 0.00 0.00 46.06 2.57
4161 4269 8.044060 TCAATGGAAGTTACTGATGAAATGAC 57.956 34.615 0.00 0.00 0.00 3.06
4162 4270 8.812513 ATCAATGGAAGTTACTGATGAAATGA 57.187 30.769 0.00 0.00 0.00 2.57
4167 4275 9.383519 GAAACTATCAATGGAAGTTACTGATGA 57.616 33.333 1.02 0.00 33.24 2.92
4168 4276 9.166173 TGAAACTATCAATGGAAGTTACTGATG 57.834 33.333 1.02 0.00 34.30 3.07
4169 4277 9.739276 TTGAAACTATCAATGGAAGTTACTGAT 57.261 29.630 2.49 0.00 43.08 2.90
4186 4295 7.899973 AGCCATTGACTTCATTTTGAAACTAT 58.100 30.769 0.00 0.00 35.73 2.12
4249 4359 0.036577 CTGCTAGGAACAGCTGTGCT 60.037 55.000 24.24 17.89 42.30 4.40
4250 4360 2.464682 CTGCTAGGAACAGCTGTGC 58.535 57.895 22.49 19.82 42.30 4.57
4262 4372 9.178427 CAAAAAGAAAATTCTCTCAACTGCTAG 57.822 33.333 0.00 0.00 36.28 3.42
4279 4389 7.548780 AGCAATAGACAAACTTGCAAAAAGAAA 59.451 29.630 0.00 0.00 45.93 2.52
4282 4392 6.833342 AGCAATAGACAAACTTGCAAAAAG 57.167 33.333 0.00 0.00 45.93 2.27
4296 4407 1.952296 CTGGGCATGGAAGCAATAGAC 59.048 52.381 0.00 0.00 35.83 2.59
4419 4550 1.759994 CTAGCTAACCAGATGTCGCG 58.240 55.000 0.00 0.00 0.00 5.87
4440 4571 5.695818 GTTTTAAGAAACGAGCTGCCATTA 58.304 37.500 0.00 0.00 36.16 1.90
4480 4611 5.525378 TGCACAATTTAAAACATGGTCAACC 59.475 36.000 0.00 0.00 0.00 3.77
4491 4622 5.741388 ACCGCAATTTGCACAATTTAAAA 57.259 30.435 20.56 0.00 45.36 1.52
4496 4627 3.876320 AGAAAACCGCAATTTGCACAATT 59.124 34.783 20.56 10.01 45.36 2.32
4498 4629 2.898705 AGAAAACCGCAATTTGCACAA 58.101 38.095 20.56 0.00 45.36 3.33
4507 4638 1.000385 CATCCAGCAAGAAAACCGCAA 60.000 47.619 0.00 0.00 0.00 4.85
4541 4672 1.605753 TCGGAGGATATCTCGTGTGG 58.394 55.000 2.05 0.00 43.34 4.17
4545 4676 3.078097 CTGACATCGGAGGATATCTCGT 58.922 50.000 2.05 0.00 43.34 4.18
4548 4679 3.168035 AGCTGACATCGGAGGATATCT 57.832 47.619 2.05 0.00 27.30 1.98
4549 4680 3.256879 TGAAGCTGACATCGGAGGATATC 59.743 47.826 0.00 0.00 0.00 1.63
4552 4683 1.411977 CTGAAGCTGACATCGGAGGAT 59.588 52.381 0.00 0.00 0.00 3.24
4553 4684 0.820226 CTGAAGCTGACATCGGAGGA 59.180 55.000 0.00 0.00 0.00 3.71
4554 4685 0.809241 GCTGAAGCTGACATCGGAGG 60.809 60.000 0.00 0.00 38.21 4.30
4559 4690 1.923204 CGTAGTGCTGAAGCTGACATC 59.077 52.381 3.61 0.00 42.66 3.06


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

AutoCloner maintained by Alex Coulton.