Multiple sequence alignment - TraesCS2A01G138200

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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 TraesCS2A01G138200 chr2A 100.000 3214 0 0 689 3902 83825862 83829075 0.000000e+00 5936
1 TraesCS2A01G138200 chr2A 100.000 159 0 0 1 159 83825174 83825332 1.060000e-75 294
2 TraesCS2A01G138200 chr2B 88.926 1788 145 16 742 2479 135004931 135006715 0.000000e+00 2156
3 TraesCS2A01G138200 chr2B 84.966 592 47 19 3318 3902 135007734 135008290 2.630000e-156 562
4 TraesCS2A01G138200 chr2B 82.553 235 24 9 3003 3223 135007431 135007662 1.430000e-44 191
5 TraesCS2A01G138200 chr2D 91.684 1419 94 10 988 2389 83138162 83139573 0.000000e+00 1945
6 TraesCS2A01G138200 chr2D 88.854 314 23 2 689 990 83137689 83138002 3.680000e-100 375
7 TraesCS2A01G138200 chr2D 87.225 227 24 3 3678 3902 83141678 83141901 1.800000e-63 254


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 TraesCS2A01G138200 chr2A 83825174 83829075 3901 False 3115.000000 5936 100.000000 1 3902 2 chr2A.!!$F1 3901
1 TraesCS2A01G138200 chr2B 135004931 135008290 3359 False 969.666667 2156 85.481667 742 3902 3 chr2B.!!$F1 3160
2 TraesCS2A01G138200 chr2D 83137689 83141901 4212 False 858.000000 1945 89.254333 689 3902 3 chr2D.!!$F1 3213

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
155 156 0.040351 CCTCCCTCACTCCTCAGACA 59.960 60.0 0.00 0.0 0.00 3.41 F
1541 1737 0.037790 GCAAGGATAGAGCCGCTAGG 60.038 60.0 0.00 0.0 41.62 3.02 F
1655 1881 0.106708 GCCGATCCTTGGATGCTACA 59.893 55.0 6.92 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 2304 0.178068 TCTCGGCAATGGCTCTTACC 59.822 55.0 5.02 0.0 40.87 2.85 R
2506 3104 0.391130 TCCACGGCATGAGCTTGTAC 60.391 55.0 0.00 0.0 41.70 2.90 R
3543 4923 0.108945 GCCTTTTGTGCTCTCCATGC 60.109 55.0 0.00 0.0 0.00 4.06 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
17 18 2.688538 AGTCCGGTACTCCTCCCC 59.311 66.667 0.00 0.00 30.33 4.81
18 19 2.443577 GTCCGGTACTCCTCCCCC 60.444 72.222 0.00 0.00 0.00 5.40
34 35 4.851252 CCCTCCCCTGCCCTGGAT 62.851 72.222 0.00 0.00 0.00 3.41
35 36 2.697644 CCTCCCCTGCCCTGGATT 60.698 66.667 0.00 0.00 0.00 3.01
36 37 2.761465 CCTCCCCTGCCCTGGATTC 61.761 68.421 0.00 0.00 0.00 2.52
37 38 2.696125 TCCCCTGCCCTGGATTCC 60.696 66.667 0.00 0.00 0.00 3.01
38 39 3.825623 CCCCTGCCCTGGATTCCC 61.826 72.222 0.00 0.00 0.00 3.97
39 40 3.023116 CCCTGCCCTGGATTCCCA 61.023 66.667 0.00 0.00 40.95 4.37
40 41 2.625460 CCCTGCCCTGGATTCCCAA 61.625 63.158 0.00 0.00 42.98 4.12
41 42 1.622499 CCTGCCCTGGATTCCCAAT 59.378 57.895 0.00 0.00 42.98 3.16
42 43 0.468771 CCTGCCCTGGATTCCCAATC 60.469 60.000 0.00 0.00 42.98 2.67
51 52 2.773525 GATTCCCAATCCCAATCCCA 57.226 50.000 0.00 0.00 31.60 4.37
52 53 3.264922 GATTCCCAATCCCAATCCCAT 57.735 47.619 0.00 0.00 31.60 4.00
53 54 2.773525 TTCCCAATCCCAATCCCATC 57.226 50.000 0.00 0.00 0.00 3.51
54 55 1.925623 TCCCAATCCCAATCCCATCT 58.074 50.000 0.00 0.00 0.00 2.90
55 56 1.500303 TCCCAATCCCAATCCCATCTG 59.500 52.381 0.00 0.00 0.00 2.90
56 57 1.335145 CCAATCCCAATCCCATCTGC 58.665 55.000 0.00 0.00 0.00 4.26
57 58 1.335145 CAATCCCAATCCCATCTGCC 58.665 55.000 0.00 0.00 0.00 4.85
58 59 0.189327 AATCCCAATCCCATCTGCCC 59.811 55.000 0.00 0.00 0.00 5.36
59 60 1.733387 ATCCCAATCCCATCTGCCCC 61.733 60.000 0.00 0.00 0.00 5.80
60 61 2.199535 CCAATCCCATCTGCCCCC 59.800 66.667 0.00 0.00 0.00 5.40
61 62 2.203394 CAATCCCATCTGCCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
62 63 4.209866 AATCCCATCTGCCCCCGC 62.210 66.667 0.00 0.00 0.00 6.13
98 99 4.500116 GCCGTCTCTCCGAGCCAC 62.500 72.222 0.00 0.00 0.00 5.01
99 100 3.827898 CCGTCTCTCCGAGCCACC 61.828 72.222 0.00 0.00 0.00 4.61
100 101 4.180946 CGTCTCTCCGAGCCACCG 62.181 72.222 0.00 0.00 0.00 4.94
101 102 4.500116 GTCTCTCCGAGCCACCGC 62.500 72.222 0.00 0.00 0.00 5.68
125 126 4.944372 CGCCGCCCGTCAGGTATC 62.944 72.222 0.00 0.00 38.26 2.24
126 127 3.845259 GCCGCCCGTCAGGTATCA 61.845 66.667 0.00 0.00 38.26 2.15
127 128 2.106332 CCGCCCGTCAGGTATCAC 59.894 66.667 0.00 0.00 38.26 3.06
128 129 2.106332 CGCCCGTCAGGTATCACC 59.894 66.667 0.00 0.00 38.99 4.02
129 130 2.504519 GCCCGTCAGGTATCACCC 59.495 66.667 0.00 0.00 39.75 4.61
130 131 3.103091 GCCCGTCAGGTATCACCCC 62.103 68.421 0.00 0.00 39.75 4.95
131 132 2.440817 CCCGTCAGGTATCACCCCC 61.441 68.421 0.00 0.00 39.75 5.40
132 133 2.792947 CCGTCAGGTATCACCCCCG 61.793 68.421 0.00 0.00 39.75 5.73
133 134 2.056223 CGTCAGGTATCACCCCCGT 61.056 63.158 0.00 0.00 39.75 5.28
134 135 1.821258 GTCAGGTATCACCCCCGTC 59.179 63.158 0.00 0.00 39.75 4.79
135 136 1.382146 TCAGGTATCACCCCCGTCC 60.382 63.158 0.00 0.00 39.75 4.79
136 137 2.041197 AGGTATCACCCCCGTCCC 60.041 66.667 0.00 0.00 39.75 4.46
137 138 3.166394 GGTATCACCCCCGTCCCC 61.166 72.222 0.00 0.00 30.04 4.81
138 139 2.041197 GTATCACCCCCGTCCCCT 60.041 66.667 0.00 0.00 0.00 4.79
139 140 2.138831 GTATCACCCCCGTCCCCTC 61.139 68.421 0.00 0.00 0.00 4.30
140 141 3.399911 TATCACCCCCGTCCCCTCC 62.400 68.421 0.00 0.00 0.00 4.30
146 147 4.400251 CCCGTCCCCTCCCTCACT 62.400 72.222 0.00 0.00 0.00 3.41
147 148 2.760385 CCGTCCCCTCCCTCACTC 60.760 72.222 0.00 0.00 0.00 3.51
148 149 2.760385 CGTCCCCTCCCTCACTCC 60.760 72.222 0.00 0.00 0.00 3.85
149 150 2.781406 GTCCCCTCCCTCACTCCT 59.219 66.667 0.00 0.00 0.00 3.69
150 151 1.382009 GTCCCCTCCCTCACTCCTC 60.382 68.421 0.00 0.00 0.00 3.71
151 152 1.862138 TCCCCTCCCTCACTCCTCA 60.862 63.158 0.00 0.00 0.00 3.86
152 153 1.382420 CCCCTCCCTCACTCCTCAG 60.382 68.421 0.00 0.00 0.00 3.35
153 154 1.700368 CCCTCCCTCACTCCTCAGA 59.300 63.158 0.00 0.00 0.00 3.27
154 155 0.686112 CCCTCCCTCACTCCTCAGAC 60.686 65.000 0.00 0.00 0.00 3.51
155 156 0.040351 CCTCCCTCACTCCTCAGACA 59.960 60.000 0.00 0.00 0.00 3.41
156 157 1.473258 CTCCCTCACTCCTCAGACAG 58.527 60.000 0.00 0.00 0.00 3.51
157 158 1.005332 CTCCCTCACTCCTCAGACAGA 59.995 57.143 0.00 0.00 0.00 3.41
158 159 1.181786 CCCTCACTCCTCAGACAGAC 58.818 60.000 0.00 0.00 0.00 3.51
710 711 0.386352 CGACGGCGTCTGAAACACTA 60.386 55.000 33.90 0.00 0.00 2.74
712 713 2.476686 CGACGGCGTCTGAAACACTATA 60.477 50.000 33.90 0.00 0.00 1.31
713 714 3.504863 GACGGCGTCTGAAACACTATAA 58.495 45.455 31.15 0.00 0.00 0.98
728 729 3.306166 CACTATAACACTTTCTTCCGCCG 59.694 47.826 0.00 0.00 0.00 6.46
807 808 2.829003 CCCTAGAGCTCGCCGTCA 60.829 66.667 8.37 0.00 0.00 4.35
812 813 0.748367 TAGAGCTCGCCGTCACATCT 60.748 55.000 8.37 0.00 0.00 2.90
817 818 0.383590 CTCGCCGTCACATCTCATCT 59.616 55.000 0.00 0.00 0.00 2.90
866 867 1.811266 CGGGTCTGCATCCACTTCG 60.811 63.158 9.72 1.59 0.00 3.79
876 877 0.390866 ATCCACTTCGCAGCACTCAG 60.391 55.000 0.00 0.00 0.00 3.35
882 883 1.128136 CTTCGCAGCACTCAGTGATTG 59.872 52.381 9.70 7.19 35.23 2.67
884 885 1.571215 CGCAGCACTCAGTGATTGCA 61.571 55.000 30.14 0.00 41.90 4.08
961 978 2.096013 CACTCTGCTGCACATCAATCAG 59.904 50.000 0.00 0.00 0.00 2.90
1009 1202 5.917462 TGTATGTTGTAGTGATGGATCAGG 58.083 41.667 0.00 0.00 37.51 3.86
1102 1295 4.980592 TGGTCAGGGCCCTCTGCA 62.981 66.667 25.77 4.09 43.89 4.41
1225 1418 1.838112 CATAAAAGCCAGCCCTCACA 58.162 50.000 0.00 0.00 0.00 3.58
1321 1514 1.985116 GACGGCTCCAGGAAGGTCT 60.985 63.158 6.86 0.00 39.02 3.85
1367 1560 1.071605 GAGTACTGCAAAGTGAGCCG 58.928 55.000 0.00 0.00 0.00 5.52
1377 1571 3.628017 CAAAGTGAGCCGGTTTTAGTTG 58.372 45.455 1.90 0.00 0.00 3.16
1394 1588 1.932511 GTTGGTGTTGTTGGCATTGTG 59.067 47.619 0.00 0.00 0.00 3.33
1396 1590 1.408340 TGGTGTTGTTGGCATTGTGAG 59.592 47.619 0.00 0.00 0.00 3.51
1397 1591 1.408702 GGTGTTGTTGGCATTGTGAGT 59.591 47.619 0.00 0.00 0.00 3.41
1428 1624 5.168526 TGTGATGTGTCTTTGTAGTTTGC 57.831 39.130 0.00 0.00 0.00 3.68
1505 1701 3.536570 TCCATTTCCGCATTTCGATGTA 58.463 40.909 0.00 0.00 41.67 2.29
1541 1737 0.037790 GCAAGGATAGAGCCGCTAGG 60.038 60.000 0.00 0.00 41.62 3.02
1618 1844 0.249114 GAAGCGGAGGAAGATCGGAC 60.249 60.000 0.00 0.00 0.00 4.79
1655 1881 0.106708 GCCGATCCTTGGATGCTACA 59.893 55.000 6.92 0.00 0.00 2.74
1658 1884 2.037641 CCGATCCTTGGATGCTACATCA 59.962 50.000 6.92 0.00 0.00 3.07
1660 1886 3.496130 CGATCCTTGGATGCTACATCAAC 59.504 47.826 6.92 0.00 0.00 3.18
1707 1933 1.354101 TGGCGGTAAAAGGAAGAGGA 58.646 50.000 0.00 0.00 0.00 3.71
1730 1956 2.027285 TGAATCGAATTGCCTGTCTCCA 60.027 45.455 0.00 0.00 0.00 3.86
1793 2019 2.100031 GCATGTCGACACGATGGCA 61.100 57.895 22.71 0.00 38.42 4.92
1820 2046 2.189594 TGGAGCTGTTCAAGGATGTG 57.810 50.000 0.00 0.00 0.00 3.21
1832 2058 0.320771 AGGATGTGCACCGTCACTTC 60.321 55.000 15.69 0.28 39.19 3.01
1856 2082 1.528076 TGTTGTTCAGCATGCCGGT 60.528 52.632 15.66 0.00 34.76 5.28
1888 2114 0.960364 GCAATGGAGGCGTTCAAGGA 60.960 55.000 0.00 0.00 0.00 3.36
1889 2115 1.755179 CAATGGAGGCGTTCAAGGAT 58.245 50.000 0.00 0.00 0.00 3.24
1893 2119 1.648467 GGAGGCGTTCAAGGATGCAC 61.648 60.000 0.00 0.00 0.00 4.57
1895 2121 1.210155 GGCGTTCAAGGATGCACAC 59.790 57.895 0.00 0.00 0.00 3.82
1901 2127 2.014335 TCAAGGATGCACACGATCAG 57.986 50.000 0.00 0.00 0.00 2.90
1924 2150 5.882557 AGTTTCAGAGTGTTGTTCAGAATGT 59.117 36.000 0.00 0.00 37.40 2.71
1935 2161 2.434884 AGAATGTGAGCACCGCCG 60.435 61.111 0.00 0.00 0.00 6.46
2045 2271 2.167075 TCATGCTGATCTGCGAGAAAGA 59.833 45.455 18.32 7.86 35.36 2.52
2078 2304 2.043652 CCCCAACAGGATGCCAGG 60.044 66.667 0.00 0.00 42.53 4.45
2151 2377 1.887242 AGCGCTGCGAGTGTTTTCA 60.887 52.632 28.07 0.00 0.00 2.69
2240 2466 5.948162 ACTCAAGATGCTCAATGGTATGTTT 59.052 36.000 0.00 0.00 0.00 2.83
2251 2477 6.280643 TCAATGGTATGTTTACTGATCCTCG 58.719 40.000 0.00 0.00 0.00 4.63
2256 2482 6.323996 TGGTATGTTTACTGATCCTCGAATCT 59.676 38.462 0.00 0.00 0.00 2.40
2263 2489 5.207110 ACTGATCCTCGAATCTTGTATGG 57.793 43.478 0.00 0.00 0.00 2.74
2281 2507 0.455410 GGGCGCATTGCACTTCATTA 59.545 50.000 10.83 0.00 46.33 1.90
2376 2602 5.305644 AGAACCTGTAGCCTACATTCCTATG 59.694 44.000 4.77 0.00 38.15 2.23
2437 2968 5.425577 GCTATTAGCTTTTGTTCTAGGCC 57.574 43.478 8.47 0.00 38.45 5.19
2460 2994 6.979817 GCCTGCATATTTATTCATGTTTGTCA 59.020 34.615 0.00 0.00 0.00 3.58
2521 3119 1.134995 TCTCTGTACAAGCTCATGCCG 60.135 52.381 0.00 0.00 40.80 5.69
2541 3139 2.221055 CGTGGAACTGCTGAACAACTAC 59.779 50.000 0.00 0.00 31.75 2.73
2547 3145 5.122396 GGAACTGCTGAACAACTACCATAAG 59.878 44.000 0.00 0.00 0.00 1.73
2555 3153 6.908825 TGAACAACTACCATAAGCAACATTC 58.091 36.000 0.00 0.00 0.00 2.67
2575 3178 6.973474 ACATTCGTGCTAGTTTCTACTATGAC 59.027 38.462 0.00 0.00 36.32 3.06
2621 3226 3.118629 TCAGCAAGAACACACTCTGTCTT 60.119 43.478 0.00 0.00 30.29 3.01
2633 3238 5.294306 CACACTCTGTCTTGCTTGTTCTTAA 59.706 40.000 0.00 0.00 0.00 1.85
2646 3251 5.463724 GCTTGTTCTTAAGCGTAGATAGCAT 59.536 40.000 0.00 0.00 43.02 3.79
2649 3254 5.213675 GTTCTTAAGCGTAGATAGCATCGT 58.786 41.667 0.00 0.00 37.01 3.73
2700 3342 4.569966 CCATCTGATAACTCTGTGCTTGTC 59.430 45.833 0.00 0.00 0.00 3.18
2711 3353 2.039084 CTGTGCTTGTCTAGAAGGGGTT 59.961 50.000 0.00 0.00 0.00 4.11
2719 3361 3.589735 TGTCTAGAAGGGGTTAAATGGCA 59.410 43.478 0.00 0.00 0.00 4.92
2723 3365 3.099141 AGAAGGGGTTAAATGGCATGTG 58.901 45.455 0.00 0.00 0.00 3.21
2735 3380 2.373224 TGGCATGTGTCTGTTTGTCAA 58.627 42.857 0.00 0.00 0.00 3.18
2786 3431 8.736751 TTCCTCGTTTTGTTTATATTTTCTGC 57.263 30.769 0.00 0.00 0.00 4.26
2790 3435 9.139174 CTCGTTTTGTTTATATTTTCTGCCAAT 57.861 29.630 0.00 0.00 0.00 3.16
2805 3483 4.019411 TCTGCCAATCTTATTGTCCAGACA 60.019 41.667 12.43 0.00 39.98 3.41
2810 3488 6.318648 GCCAATCTTATTGTCCAGACATAACA 59.681 38.462 0.48 0.00 41.52 2.41
2811 3489 7.013655 GCCAATCTTATTGTCCAGACATAACAT 59.986 37.037 0.48 0.00 41.52 2.71
2844 3522 6.433716 TGATCTGAAATGTTATGCTTTGTCCA 59.566 34.615 0.00 0.00 0.00 4.02
2873 3551 4.387598 CTGATTCATGTCTCATCCCCTTC 58.612 47.826 0.00 0.00 0.00 3.46
2923 3601 3.006967 GCTTAAAGCGATATGGGAGGAGA 59.993 47.826 0.00 0.00 0.00 3.71
2948 3626 7.264947 AGAAGCTCTAGAAGTTCTAATTCAGC 58.735 38.462 13.51 15.86 0.00 4.26
2982 3660 5.334028 GCAATGGCAGTTGAAATTTTGGTAC 60.334 40.000 11.99 0.00 40.72 3.34
3018 3804 8.472413 TGTAAATGGTTATATATCTAGCGTCCC 58.528 37.037 0.00 0.00 0.00 4.46
3022 3808 5.886474 TGGTTATATATCTAGCGTCCCTCTG 59.114 44.000 0.00 0.00 0.00 3.35
3045 3831 3.659786 AGTGTTCTAATGCGCTGTGTTA 58.340 40.909 9.73 2.07 0.00 2.41
3051 3837 2.455674 AATGCGCTGTGTTAGTGAGA 57.544 45.000 9.73 0.00 39.30 3.27
3082 3911 0.404040 ATTCCTTTCCTTGCACCGGA 59.596 50.000 9.46 0.00 0.00 5.14
3086 3915 1.291877 CTTTCCTTGCACCGGACTCG 61.292 60.000 9.46 0.00 0.00 4.18
3105 3983 1.249407 GGTGGAAAATTGTACGGCCA 58.751 50.000 2.24 0.00 0.00 5.36
3145 4029 0.378257 CCGATTCCAACAGCATTCCG 59.622 55.000 0.00 0.00 0.00 4.30
3149 4033 0.871722 TTCCAACAGCATTCCGAACG 59.128 50.000 0.00 0.00 0.00 3.95
3151 4035 0.165944 CCAACAGCATTCCGAACGAC 59.834 55.000 0.00 0.00 0.00 4.34
3158 4042 1.260206 CATTCCGAACGACTCTGACG 58.740 55.000 0.00 0.00 0.00 4.35
3159 4043 0.879765 ATTCCGAACGACTCTGACGT 59.120 50.000 0.00 0.00 45.89 4.34
3161 4045 0.881600 TCCGAACGACTCTGACGTCA 60.882 55.000 18.88 18.88 43.16 4.35
3162 4046 0.725118 CCGAACGACTCTGACGTCAC 60.725 60.000 15.76 3.76 43.16 3.67
3163 4047 0.041576 CGAACGACTCTGACGTCACA 60.042 55.000 15.76 3.17 43.16 3.58
3196 4548 2.687935 ACAACAGCCACCTAAAACTGTG 59.312 45.455 0.00 0.00 42.34 3.66
3208 4560 2.684001 AAACTGTGGTTCGTCAGACA 57.316 45.000 0.41 0.00 34.14 3.41
3217 4569 4.344668 CGTCAGACACGTAGCGAG 57.655 61.111 0.41 0.00 44.07 5.03
3218 4570 1.226046 CGTCAGACACGTAGCGAGG 60.226 63.158 0.41 0.00 44.07 4.63
3219 4571 1.632948 CGTCAGACACGTAGCGAGGA 61.633 60.000 0.41 0.00 44.07 3.71
3220 4572 0.520404 GTCAGACACGTAGCGAGGAA 59.480 55.000 0.00 0.00 0.00 3.36
3221 4573 1.068748 GTCAGACACGTAGCGAGGAAA 60.069 52.381 0.00 0.00 0.00 3.13
3222 4574 1.816835 TCAGACACGTAGCGAGGAAAT 59.183 47.619 0.00 0.00 0.00 2.17
3223 4575 1.920574 CAGACACGTAGCGAGGAAATG 59.079 52.381 0.00 0.00 0.00 2.32
3224 4576 1.135083 AGACACGTAGCGAGGAAATGG 60.135 52.381 0.00 0.00 0.00 3.16
3229 4581 1.867233 CGTAGCGAGGAAATGGAATGG 59.133 52.381 0.00 0.00 0.00 3.16
3234 4586 3.694566 AGCGAGGAAATGGAATGGTTTAC 59.305 43.478 0.00 0.00 0.00 2.01
3235 4587 3.442273 GCGAGGAAATGGAATGGTTTACA 59.558 43.478 0.00 0.00 0.00 2.41
3237 4589 5.394115 GCGAGGAAATGGAATGGTTTACAAT 60.394 40.000 0.00 0.00 0.00 2.71
3238 4590 6.035843 CGAGGAAATGGAATGGTTTACAATG 58.964 40.000 0.00 0.00 0.00 2.82
3241 4593 6.155049 AGGAAATGGAATGGTTTACAATGGAG 59.845 38.462 0.00 0.00 0.00 3.86
3242 4594 5.343307 AATGGAATGGTTTACAATGGAGC 57.657 39.130 0.00 0.00 0.00 4.70
3243 4595 3.096092 TGGAATGGTTTACAATGGAGCC 58.904 45.455 0.00 0.00 0.00 4.70
3248 4600 2.109128 TGGTTTACAATGGAGCCCAAGA 59.891 45.455 0.00 0.00 36.95 3.02
3293 4672 6.365970 AAGAACTGTTCAGTATCCTGATGT 57.634 37.500 21.50 0.00 46.80 3.06
3295 4674 6.773638 AGAACTGTTCAGTATCCTGATGTTT 58.226 36.000 21.50 0.00 46.80 2.83
3296 4675 7.227156 AGAACTGTTCAGTATCCTGATGTTTT 58.773 34.615 21.50 0.00 46.80 2.43
3297 4676 7.721399 AGAACTGTTCAGTATCCTGATGTTTTT 59.279 33.333 21.50 0.00 46.80 1.94
3298 4677 7.440523 ACTGTTCAGTATCCTGATGTTTTTC 57.559 36.000 3.47 0.00 46.80 2.29
3299 4678 7.227156 ACTGTTCAGTATCCTGATGTTTTTCT 58.773 34.615 3.47 0.00 46.80 2.52
3300 4679 7.721399 ACTGTTCAGTATCCTGATGTTTTTCTT 59.279 33.333 3.47 0.00 46.80 2.52
3301 4680 8.463930 TGTTCAGTATCCTGATGTTTTTCTTT 57.536 30.769 0.00 0.00 46.80 2.52
3302 4681 8.912988 TGTTCAGTATCCTGATGTTTTTCTTTT 58.087 29.630 0.00 0.00 46.80 2.27
3305 4684 9.231297 TCAGTATCCTGATGTTTTTCTTTTAGG 57.769 33.333 0.00 0.00 42.80 2.69
3306 4685 9.231297 CAGTATCCTGATGTTTTTCTTTTAGGA 57.769 33.333 0.00 0.00 41.50 2.94
3307 4686 9.807921 AGTATCCTGATGTTTTTCTTTTAGGAA 57.192 29.630 0.00 0.00 36.74 3.36
3312 4691 8.579863 CCTGATGTTTTTCTTTTAGGAAGTCAT 58.420 33.333 0.00 0.00 0.00 3.06
3341 4720 4.756084 GCTTGAGCTAATTGTGTCACTT 57.244 40.909 4.27 0.00 38.21 3.16
3342 4721 4.470462 GCTTGAGCTAATTGTGTCACTTG 58.530 43.478 4.27 0.00 38.21 3.16
3367 4746 6.237648 GCTTTGTCAAGAAAGTTCACACAATG 60.238 38.462 2.15 3.60 35.67 2.82
3370 4749 3.044986 CAAGAAAGTTCACACAATGCCG 58.955 45.455 0.00 0.00 0.00 5.69
3377 4756 2.177394 TCACACAATGCCGCTAGAAA 57.823 45.000 0.00 0.00 0.00 2.52
3379 4758 2.225491 TCACACAATGCCGCTAGAAAAC 59.775 45.455 0.00 0.00 0.00 2.43
3391 4770 3.730715 CGCTAGAAAACAACAAAGCCTTG 59.269 43.478 0.00 0.00 38.61 3.61
3411 4790 6.259608 GCCTTGCAATATATAAGCTCGATGAT 59.740 38.462 0.00 0.00 0.00 2.45
3416 4795 8.253113 TGCAATATATAAGCTCGATGATCTCAA 58.747 33.333 10.38 0.00 0.00 3.02
3417 4796 8.754096 GCAATATATAAGCTCGATGATCTCAAG 58.246 37.037 0.00 0.00 0.00 3.02
3424 4803 4.642437 AGCTCGATGATCTCAAGTTACTCA 59.358 41.667 0.00 0.00 0.00 3.41
3428 4807 7.812191 GCTCGATGATCTCAAGTTACTCAATAT 59.188 37.037 0.00 0.00 0.00 1.28
3452 4831 8.985315 ATATTTTGAGATGCAACTAATCAGGA 57.015 30.769 0.00 0.00 35.91 3.86
3474 4853 5.048713 GGATTTCAACCTCAAACTGTGTAGG 60.049 44.000 2.72 2.72 33.26 3.18
3483 4862 5.284861 TCAAACTGTGTAGGAACTTGCTA 57.715 39.130 0.00 0.00 41.75 3.49
3484 4863 5.676552 TCAAACTGTGTAGGAACTTGCTAA 58.323 37.500 0.00 0.00 41.75 3.09
3498 4877 7.668052 AGGAACTTGCTAAATACCATACAAACA 59.332 33.333 0.00 0.00 27.25 2.83
3500 4879 9.685828 GAACTTGCTAAATACCATACAAACAAA 57.314 29.630 0.00 0.00 0.00 2.83
3526 4906 4.874970 GTGAATTCACACAGGCAAGAAAT 58.125 39.130 29.43 0.00 45.75 2.17
3531 4911 6.594788 ATTCACACAGGCAAGAAATTATGT 57.405 33.333 0.00 0.00 0.00 2.29
3543 4923 4.530388 AGAAATTATGTCATGAATGCGCG 58.470 39.130 0.00 0.00 0.00 6.86
3548 4928 1.656263 GTCATGAATGCGCGCATGG 60.656 57.895 43.67 31.16 41.60 3.66
3549 4929 1.818785 TCATGAATGCGCGCATGGA 60.819 52.632 43.67 32.65 41.60 3.41
3551 4931 1.524393 ATGAATGCGCGCATGGAGA 60.524 52.632 43.67 27.69 36.68 3.71
3557 4937 3.120385 CGCGCATGGAGAGCACAA 61.120 61.111 8.75 0.00 43.95 3.33
3559 4939 1.580942 GCGCATGGAGAGCACAAAA 59.419 52.632 0.30 0.00 43.16 2.44
3564 4946 1.822990 CATGGAGAGCACAAAAGGCAT 59.177 47.619 0.00 0.00 0.00 4.40
3574 4959 3.492011 GCACAAAAGGCATCAGTTGAAAG 59.508 43.478 0.00 0.00 0.00 2.62
3579 4964 4.590850 AAGGCATCAGTTGAAAGGAAAC 57.409 40.909 0.00 0.00 0.00 2.78
3586 4971 5.026038 TCAGTTGAAAGGAAACCGTAGAA 57.974 39.130 0.00 0.00 0.00 2.10
3587 4972 5.430007 TCAGTTGAAAGGAAACCGTAGAAA 58.570 37.500 0.00 0.00 0.00 2.52
3589 4974 6.374894 TCAGTTGAAAGGAAACCGTAGAAAAA 59.625 34.615 0.00 0.00 0.00 1.94
3698 5083 8.934825 CAAATATCCACAAATACCAACAAAAGG 58.065 33.333 0.00 0.00 0.00 3.11
3711 5096 4.100808 CCAACAAAAGGGAACTGGAAATGA 59.899 41.667 0.00 0.00 42.68 2.57
3755 5141 9.306280 CAATATTATTTGCATACGAAGAAGACG 57.694 33.333 0.00 0.00 0.00 4.18
3767 5153 3.427638 CGAAGAAGACGTCATAGCTTGGA 60.428 47.826 19.50 0.00 0.00 3.53
3788 5174 4.269523 TATCCCTGCCATGCCGCC 62.270 66.667 0.00 0.00 0.00 6.13
3820 5206 6.067217 AGATACTAGCAAAACCCACAGAAT 57.933 37.500 0.00 0.00 0.00 2.40
3837 5223 5.068987 CACAGAATTTCACTCCTTTTTCCCA 59.931 40.000 0.00 0.00 0.00 4.37
3887 5274 1.073284 ACCCTGTTTGTTAGCCACGAT 59.927 47.619 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.688538 GGGGAGGAGTACCGGACT 59.311 66.667 9.46 7.46 42.90 3.85
1 2 2.443577 GGGGGAGGAGTACCGGAC 60.444 72.222 9.46 1.42 41.83 4.79
17 18 4.851252 ATCCAGGGCAGGGGAGGG 62.851 72.222 0.00 0.00 36.45 4.30
18 19 2.697644 AATCCAGGGCAGGGGAGG 60.698 66.667 0.00 0.00 36.45 4.30
19 20 2.761465 GGAATCCAGGGCAGGGGAG 61.761 68.421 0.00 0.00 36.45 4.30
20 21 2.696125 GGAATCCAGGGCAGGGGA 60.696 66.667 0.00 0.00 37.64 4.81
21 22 3.825623 GGGAATCCAGGGCAGGGG 61.826 72.222 0.09 0.00 0.00 4.79
22 23 1.953100 ATTGGGAATCCAGGGCAGGG 61.953 60.000 0.09 0.00 45.04 4.45
23 24 0.468771 GATTGGGAATCCAGGGCAGG 60.469 60.000 0.09 0.00 45.04 4.85
24 25 3.122369 GATTGGGAATCCAGGGCAG 57.878 57.895 0.09 0.00 45.04 4.85
32 33 2.773525 TGGGATTGGGATTGGGAATC 57.226 50.000 0.00 0.00 37.17 2.52
33 34 2.799576 AGATGGGATTGGGATTGGGAAT 59.200 45.455 0.00 0.00 0.00 3.01
34 35 2.091166 CAGATGGGATTGGGATTGGGAA 60.091 50.000 0.00 0.00 0.00 3.97
35 36 1.500303 CAGATGGGATTGGGATTGGGA 59.500 52.381 0.00 0.00 0.00 4.37
36 37 2.005370 CAGATGGGATTGGGATTGGG 57.995 55.000 0.00 0.00 0.00 4.12
37 38 1.335145 GCAGATGGGATTGGGATTGG 58.665 55.000 0.00 0.00 0.00 3.16
38 39 1.335145 GGCAGATGGGATTGGGATTG 58.665 55.000 0.00 0.00 0.00 2.67
39 40 0.189327 GGGCAGATGGGATTGGGATT 59.811 55.000 0.00 0.00 0.00 3.01
40 41 1.733387 GGGGCAGATGGGATTGGGAT 61.733 60.000 0.00 0.00 0.00 3.85
41 42 2.394506 GGGGCAGATGGGATTGGGA 61.395 63.158 0.00 0.00 0.00 4.37
42 43 2.199535 GGGGCAGATGGGATTGGG 59.800 66.667 0.00 0.00 0.00 4.12
43 44 2.199535 GGGGGCAGATGGGATTGG 59.800 66.667 0.00 0.00 0.00 3.16
44 45 2.203394 CGGGGGCAGATGGGATTG 60.203 66.667 0.00 0.00 0.00 2.67
45 46 4.209866 GCGGGGGCAGATGGGATT 62.210 66.667 0.00 0.00 0.00 3.01
108 109 4.944372 GATACCTGACGGGCGGCG 62.944 72.222 0.51 0.51 39.10 6.46
109 110 3.845259 TGATACCTGACGGGCGGC 61.845 66.667 0.00 0.00 39.10 6.53
110 111 2.106332 GTGATACCTGACGGGCGG 59.894 66.667 0.00 0.00 39.10 6.13
111 112 2.106332 GGTGATACCTGACGGGCG 59.894 66.667 0.00 0.00 39.10 6.13
112 113 2.504519 GGGTGATACCTGACGGGC 59.495 66.667 0.00 0.00 38.64 6.13
113 114 2.440817 GGGGGTGATACCTGACGGG 61.441 68.421 0.00 0.00 38.64 5.28
114 115 2.792947 CGGGGGTGATACCTGACGG 61.793 68.421 0.00 0.00 38.64 4.79
115 116 2.012902 GACGGGGGTGATACCTGACG 62.013 65.000 0.00 3.54 38.64 4.35
116 117 1.683418 GGACGGGGGTGATACCTGAC 61.683 65.000 0.00 0.00 38.64 3.51
117 118 1.382146 GGACGGGGGTGATACCTGA 60.382 63.158 0.00 0.00 38.64 3.86
118 119 2.440817 GGGACGGGGGTGATACCTG 61.441 68.421 0.00 0.00 38.64 4.00
119 120 2.041197 GGGACGGGGGTGATACCT 60.041 66.667 0.00 0.00 38.64 3.08
120 121 3.166394 GGGGACGGGGGTGATACC 61.166 72.222 0.00 0.00 37.60 2.73
121 122 2.041197 AGGGGACGGGGGTGATAC 60.041 66.667 0.00 0.00 0.00 2.24
122 123 2.284493 GAGGGGACGGGGGTGATA 59.716 66.667 0.00 0.00 0.00 2.15
123 124 4.817909 GGAGGGGACGGGGGTGAT 62.818 72.222 0.00 0.00 0.00 3.06
129 130 4.400251 AGTGAGGGAGGGGACGGG 62.400 72.222 0.00 0.00 0.00 5.28
130 131 2.760385 GAGTGAGGGAGGGGACGG 60.760 72.222 0.00 0.00 0.00 4.79
131 132 2.760385 GGAGTGAGGGAGGGGACG 60.760 72.222 0.00 0.00 0.00 4.79
132 133 1.382009 GAGGAGTGAGGGAGGGGAC 60.382 68.421 0.00 0.00 0.00 4.46
133 134 1.862138 TGAGGAGTGAGGGAGGGGA 60.862 63.158 0.00 0.00 0.00 4.81
134 135 1.382420 CTGAGGAGTGAGGGAGGGG 60.382 68.421 0.00 0.00 0.00 4.79
135 136 0.686112 GTCTGAGGAGTGAGGGAGGG 60.686 65.000 0.00 0.00 0.00 4.30
136 137 0.040351 TGTCTGAGGAGTGAGGGAGG 59.960 60.000 0.00 0.00 0.00 4.30
137 138 1.005332 TCTGTCTGAGGAGTGAGGGAG 59.995 57.143 0.00 0.00 0.00 4.30
138 139 1.076438 TCTGTCTGAGGAGTGAGGGA 58.924 55.000 0.00 0.00 0.00 4.20
139 140 1.181786 GTCTGTCTGAGGAGTGAGGG 58.818 60.000 0.00 0.00 0.00 4.30
697 698 7.639162 AGAAAGTGTTATAGTGTTTCAGACG 57.361 36.000 0.00 0.00 30.92 4.18
710 711 1.084289 GCGGCGGAAGAAAGTGTTAT 58.916 50.000 9.78 0.00 0.00 1.89
712 713 2.604174 CGCGGCGGAAGAAAGTGTT 61.604 57.895 15.84 0.00 0.00 3.32
713 714 3.041940 CGCGGCGGAAGAAAGTGT 61.042 61.111 15.84 0.00 0.00 3.55
792 793 0.317436 GATGTGACGGCGAGCTCTAG 60.317 60.000 16.62 5.31 0.00 2.43
807 808 1.590932 GCCGCAATGAGATGAGATGT 58.409 50.000 0.00 0.00 0.00 3.06
812 813 3.264159 CGCGCCGCAATGAGATGA 61.264 61.111 10.75 0.00 0.00 2.92
831 832 2.501492 CGTAGGTGGAGGACGGATT 58.499 57.895 0.00 0.00 33.01 3.01
882 883 1.136984 GCAGAGCAGAGCAATGTGC 59.863 57.895 0.00 0.00 45.46 4.57
884 885 0.036448 ACAGCAGAGCAGAGCAATGT 59.964 50.000 0.00 0.00 0.00 2.71
961 978 9.107367 CATGAAAGACGAGAAACTTAATTTGAC 57.893 33.333 0.00 0.00 0.00 3.18
1023 1216 1.448119 CTCTGCCTCGCACGATCCTA 61.448 60.000 0.00 0.00 33.79 2.94
1209 1402 0.962356 CGATGTGAGGGCTGGCTTTT 60.962 55.000 0.00 0.00 0.00 2.27
1212 1405 2.685017 TCGATGTGAGGGCTGGCT 60.685 61.111 0.00 0.00 0.00 4.75
1221 1414 2.362503 AGCCGGGAGTCGATGTGA 60.363 61.111 2.18 0.00 42.43 3.58
1225 1418 2.427245 CCTTGAGCCGGGAGTCGAT 61.427 63.158 2.18 0.00 42.43 3.59
1321 1514 2.048222 CTGCTTCTCGCACCGGAA 60.048 61.111 9.46 0.00 45.47 4.30
1367 1560 3.191669 GCCAACAACACCAACTAAAACC 58.808 45.455 0.00 0.00 0.00 3.27
1377 1571 1.408702 ACTCACAATGCCAACAACACC 59.591 47.619 0.00 0.00 0.00 4.16
1394 1588 6.610741 AGACACATCACAAAAGAAAGACTC 57.389 37.500 0.00 0.00 0.00 3.36
1396 1590 7.029563 ACAAAGACACATCACAAAAGAAAGAC 58.970 34.615 0.00 0.00 0.00 3.01
1397 1591 7.156876 ACAAAGACACATCACAAAAGAAAGA 57.843 32.000 0.00 0.00 0.00 2.52
1428 1624 1.528586 CAGAGGCGAAACAAGTCAGTG 59.471 52.381 0.00 0.00 0.00 3.66
1505 1701 1.761449 TGCCATACACCGCATCAAAT 58.239 45.000 0.00 0.00 0.00 2.32
1541 1737 0.602905 CGGACACTTCCACCACTTCC 60.603 60.000 0.00 0.00 43.00 3.46
1567 1763 0.828022 ATTCTCCATGTCGGCGGTTA 59.172 50.000 7.21 0.00 33.14 2.85
1568 1764 0.744414 CATTCTCCATGTCGGCGGTT 60.744 55.000 7.21 0.00 33.14 4.44
1707 1933 3.265791 GAGACAGGCAATTCGATTCAGT 58.734 45.455 0.00 0.00 0.00 3.41
1730 1956 1.512926 GCACATCCTTCAACGTGTCT 58.487 50.000 0.00 0.00 0.00 3.41
1793 2019 0.610174 TGAACAGCTCCATCGCTTCT 59.390 50.000 0.00 0.00 38.41 2.85
1820 2046 1.367840 ACTCTGGAAGTGACGGTGC 59.632 57.895 0.00 0.00 36.65 5.01
1832 2058 1.068748 GCATGCTGAACAACACTCTGG 60.069 52.381 11.37 0.00 0.00 3.86
1888 2114 2.998670 CTCTGAAACTGATCGTGTGCAT 59.001 45.455 0.00 0.00 0.00 3.96
1889 2115 2.224042 ACTCTGAAACTGATCGTGTGCA 60.224 45.455 0.00 0.00 0.00 4.57
1893 2119 3.804325 ACAACACTCTGAAACTGATCGTG 59.196 43.478 0.00 0.00 0.00 4.35
1895 2121 4.507756 TGAACAACACTCTGAAACTGATCG 59.492 41.667 0.00 0.00 0.00 3.69
1901 2127 5.967674 CACATTCTGAACAACACTCTGAAAC 59.032 40.000 0.00 0.00 35.31 2.78
1935 2161 1.530013 AACTGCTCCATGGCTGTTGC 61.530 55.000 6.96 6.71 46.87 4.17
2045 2271 2.045926 GGCACCTCAGGCGACAAT 60.046 61.111 0.00 0.00 0.00 2.71
2078 2304 0.178068 TCTCGGCAATGGCTCTTACC 59.822 55.000 5.02 0.00 40.87 2.85
2151 2377 1.960689 CATTTGGTCCGGTTCCTTTGT 59.039 47.619 16.54 1.95 0.00 2.83
2240 2466 5.243954 CCCATACAAGATTCGAGGATCAGTA 59.756 44.000 0.00 3.29 33.17 2.74
2251 2477 2.859806 GCAATGCGCCCATACAAGATTC 60.860 50.000 4.18 0.00 32.94 2.52
2256 2482 0.964860 AGTGCAATGCGCCCATACAA 60.965 50.000 15.78 0.00 40.23 2.41
2263 2489 2.497107 ATAATGAAGTGCAATGCGCC 57.503 45.000 15.78 1.42 40.23 6.53
2351 2577 3.452627 AGGAATGTAGGCTACAGGTTCTG 59.547 47.826 29.14 0.00 42.77 3.02
2435 2966 6.979817 TGACAAACATGAATAAATATGCAGGC 59.020 34.615 0.00 0.00 0.00 4.85
2506 3104 0.391130 TCCACGGCATGAGCTTGTAC 60.391 55.000 0.00 0.00 41.70 2.90
2521 3119 2.548480 GGTAGTTGTTCAGCAGTTCCAC 59.452 50.000 0.00 0.00 0.00 4.02
2541 3139 3.623060 ACTAGCACGAATGTTGCTTATGG 59.377 43.478 2.58 0.00 39.79 2.74
2547 3145 3.813529 AGAAACTAGCACGAATGTTGC 57.186 42.857 0.00 0.00 0.00 4.17
2555 3153 4.201891 ACCGTCATAGTAGAAACTAGCACG 60.202 45.833 10.10 10.10 41.46 5.34
2575 3178 4.871513 AGCATACACATACACAGATACCG 58.128 43.478 0.00 0.00 0.00 4.02
2633 3238 1.267261 GGTGACGATGCTATCTACGCT 59.733 52.381 0.00 0.00 0.00 5.07
2635 3240 2.333389 GGGTGACGATGCTATCTACG 57.667 55.000 0.00 0.00 0.00 3.51
2649 3254 3.545124 AATCCGTGCAAGCGGGTGA 62.545 57.895 15.02 0.00 45.77 4.02
2673 3278 1.135046 CAGAGTTATCAGATGGCGCG 58.865 55.000 0.00 0.00 0.00 6.86
2700 3342 4.339247 CACATGCCATTTAACCCCTTCTAG 59.661 45.833 0.00 0.00 0.00 2.43
2711 3353 4.582240 TGACAAACAGACACATGCCATTTA 59.418 37.500 0.00 0.00 0.00 1.40
2719 3361 5.028549 AGAGTCTTGACAAACAGACACAT 57.971 39.130 8.18 0.00 32.89 3.21
2723 3365 5.988561 AGAATGAGAGTCTTGACAAACAGAC 59.011 40.000 0.00 0.00 0.00 3.51
2735 3380 3.387374 CCCTATGCACAGAATGAGAGTCT 59.613 47.826 0.00 0.00 39.69 3.24
2786 3431 7.864108 TGTTATGTCTGGACAATAAGATTGG 57.136 36.000 7.53 0.00 45.41 3.16
2833 3511 1.884579 CAGCTTCACTGGACAAAGCAT 59.115 47.619 8.80 0.00 46.11 3.79
2835 3513 7.059418 ATGAATCAGCTTCACTGGACAAAGC 62.059 44.000 0.00 0.00 46.37 3.51
2837 3515 4.216902 CATGAATCAGCTTCACTGGACAAA 59.783 41.667 0.00 0.00 46.37 2.83
2844 3522 4.548451 TGAGACATGAATCAGCTTCACT 57.452 40.909 0.00 0.00 46.37 3.41
2873 3551 1.407989 GGAGAGATTGCCCACCTGAAG 60.408 57.143 0.00 0.00 0.00 3.02
2912 3590 3.984090 TCTAGAGCTTCTCTCCTCCCATA 59.016 47.826 0.00 0.00 40.34 2.74
2923 3601 7.264947 GCTGAATTAGAACTTCTAGAGCTTCT 58.735 38.462 14.95 14.95 33.39 2.85
2948 3626 0.454600 CTGCCATTGCTGCAACTAGG 59.545 55.000 18.51 19.39 38.46 3.02
2991 3669 9.865321 GGACGCTAGATATATAACCATTTACAA 57.135 33.333 0.00 0.00 0.00 2.41
3018 3804 3.061831 CAGCGCATTAGAACACTTCAGAG 59.938 47.826 11.47 0.00 0.00 3.35
3022 3808 2.480419 ACACAGCGCATTAGAACACTTC 59.520 45.455 11.47 0.00 0.00 3.01
3045 3831 1.577736 ATGCCAAGGCTACTCTCACT 58.422 50.000 12.96 0.00 42.51 3.41
3051 3837 2.621668 GGAAAGGAATGCCAAGGCTACT 60.622 50.000 12.96 0.00 42.51 2.57
3082 3911 2.419667 CCGTACAATTTTCCACCGAGT 58.580 47.619 0.00 0.00 0.00 4.18
3086 3915 1.249407 TGGCCGTACAATTTTCCACC 58.751 50.000 0.00 0.00 0.00 4.61
3093 3971 2.883122 TACCCTTTGGCCGTACAATT 57.117 45.000 0.00 0.00 33.59 2.32
3096 3974 1.340211 CCATTACCCTTTGGCCGTACA 60.340 52.381 0.00 0.00 33.59 2.90
3105 3983 1.149077 ACAGGTTGCCCATTACCCTTT 59.851 47.619 0.00 0.00 34.90 3.11
3145 4029 2.333389 ATGTGACGTCAGAGTCGTTC 57.667 50.000 20.73 4.95 43.70 3.95
3149 4033 3.497118 CTCAGAATGTGACGTCAGAGTC 58.503 50.000 29.15 29.15 36.87 3.36
3151 4035 2.257894 GCTCAGAATGTGACGTCAGAG 58.742 52.381 20.73 20.37 37.40 3.35
3158 4042 4.671377 TGTTGTTTTGCTCAGAATGTGAC 58.329 39.130 0.00 0.00 37.40 3.67
3159 4043 4.734402 GCTGTTGTTTTGCTCAGAATGTGA 60.734 41.667 0.00 0.00 37.40 3.58
3161 4045 3.491447 GGCTGTTGTTTTGCTCAGAATGT 60.491 43.478 0.00 0.00 37.40 2.71
3162 4046 3.054878 GGCTGTTGTTTTGCTCAGAATG 58.945 45.455 0.00 0.00 37.54 2.67
3163 4047 2.694628 TGGCTGTTGTTTTGCTCAGAAT 59.305 40.909 0.00 0.00 0.00 2.40
3201 4553 0.520404 TTCCTCGCTACGTGTCTGAC 59.480 55.000 0.00 0.00 0.00 3.51
3208 4560 2.550978 CATTCCATTTCCTCGCTACGT 58.449 47.619 0.00 0.00 0.00 3.57
3214 4566 5.637006 TTGTAAACCATTCCATTTCCTCG 57.363 39.130 0.00 0.00 0.00 4.63
3217 4569 6.293004 TCCATTGTAAACCATTCCATTTCC 57.707 37.500 0.00 0.00 0.00 3.13
3218 4570 5.812127 GCTCCATTGTAAACCATTCCATTTC 59.188 40.000 0.00 0.00 0.00 2.17
3219 4571 5.338300 GGCTCCATTGTAAACCATTCCATTT 60.338 40.000 0.00 0.00 0.00 2.32
3220 4572 4.162131 GGCTCCATTGTAAACCATTCCATT 59.838 41.667 0.00 0.00 0.00 3.16
3221 4573 3.706086 GGCTCCATTGTAAACCATTCCAT 59.294 43.478 0.00 0.00 0.00 3.41
3222 4574 3.096092 GGCTCCATTGTAAACCATTCCA 58.904 45.455 0.00 0.00 0.00 3.53
3223 4575 2.430694 GGGCTCCATTGTAAACCATTCC 59.569 50.000 0.00 0.00 0.00 3.01
3224 4576 3.096092 TGGGCTCCATTGTAAACCATTC 58.904 45.455 0.00 0.00 0.00 2.67
3229 4581 4.864704 TTTCTTGGGCTCCATTGTAAAC 57.135 40.909 0.00 0.00 31.53 2.01
3234 4586 5.420104 AGAGTAATTTTCTTGGGCTCCATTG 59.580 40.000 0.00 0.00 31.53 2.82
3235 4587 5.583932 AGAGTAATTTTCTTGGGCTCCATT 58.416 37.500 0.00 0.00 31.53 3.16
3237 4589 4.289672 AGAGAGTAATTTTCTTGGGCTCCA 59.710 41.667 0.00 0.00 0.00 3.86
3238 4590 4.849518 AGAGAGTAATTTTCTTGGGCTCC 58.150 43.478 0.00 0.00 0.00 4.70
3241 4593 6.657117 AGAAAGAGAGAGTAATTTTCTTGGGC 59.343 38.462 0.00 0.00 35.25 5.36
3242 4594 9.726438 TTAGAAAGAGAGAGTAATTTTCTTGGG 57.274 33.333 3.48 0.00 38.58 4.12
3284 4663 8.712228 ACTTCCTAAAAGAAAAACATCAGGAT 57.288 30.769 0.00 0.00 31.32 3.24
3293 4672 8.990163 ACCAGTATGACTTCCTAAAAGAAAAA 57.010 30.769 0.00 0.00 39.69 1.94
3295 4674 7.822822 GCTACCAGTATGACTTCCTAAAAGAAA 59.177 37.037 0.00 0.00 39.69 2.52
3296 4675 7.180408 AGCTACCAGTATGACTTCCTAAAAGAA 59.820 37.037 0.00 0.00 39.69 2.52
3297 4676 6.668283 AGCTACCAGTATGACTTCCTAAAAGA 59.332 38.462 0.00 0.00 39.69 2.52
3298 4677 6.879400 AGCTACCAGTATGACTTCCTAAAAG 58.121 40.000 0.00 0.00 39.69 2.27
3299 4678 6.869206 AGCTACCAGTATGACTTCCTAAAA 57.131 37.500 0.00 0.00 39.69 1.52
3300 4679 6.439375 TCAAGCTACCAGTATGACTTCCTAAA 59.561 38.462 0.00 0.00 39.69 1.85
3301 4680 5.955959 TCAAGCTACCAGTATGACTTCCTAA 59.044 40.000 0.00 0.00 39.69 2.69
3302 4681 5.516044 TCAAGCTACCAGTATGACTTCCTA 58.484 41.667 0.00 0.00 39.69 2.94
3303 4682 4.353777 TCAAGCTACCAGTATGACTTCCT 58.646 43.478 0.00 0.00 39.69 3.36
3304 4683 4.688021 CTCAAGCTACCAGTATGACTTCC 58.312 47.826 0.00 0.00 39.69 3.46
3305 4684 4.116238 GCTCAAGCTACCAGTATGACTTC 58.884 47.826 0.00 0.00 36.60 3.01
3306 4685 4.130286 GCTCAAGCTACCAGTATGACTT 57.870 45.455 0.00 0.00 36.60 3.01
3307 4686 3.810310 GCTCAAGCTACCAGTATGACT 57.190 47.619 0.00 0.00 36.60 3.41
3333 4712 4.355543 TTCTTGACAAAGCAAGTGACAC 57.644 40.909 0.00 0.00 44.30 3.67
3337 4716 5.287035 GTGAACTTTCTTGACAAAGCAAGTG 59.713 40.000 4.64 0.00 45.42 3.16
3340 4719 5.160641 GTGTGAACTTTCTTGACAAAGCAA 58.839 37.500 0.00 0.00 36.93 3.91
3341 4720 4.217334 TGTGTGAACTTTCTTGACAAAGCA 59.783 37.500 0.00 0.00 36.93 3.91
3342 4721 4.732784 TGTGTGAACTTTCTTGACAAAGC 58.267 39.130 0.00 0.00 36.93 3.51
3356 4735 1.438651 TCTAGCGGCATTGTGTGAAC 58.561 50.000 1.45 0.00 0.00 3.18
3367 4746 2.051423 GCTTTGTTGTTTTCTAGCGGC 58.949 47.619 0.00 0.00 0.00 6.53
3370 4749 3.490896 GCAAGGCTTTGTTGTTTTCTAGC 59.509 43.478 10.54 0.00 36.65 3.42
3377 4756 7.492344 GCTTATATATTGCAAGGCTTTGTTGTT 59.508 33.333 10.54 0.00 36.65 2.83
3379 4758 7.205297 AGCTTATATATTGCAAGGCTTTGTTG 58.795 34.615 10.54 0.00 36.65 3.33
3391 4770 8.640091 TTGAGATCATCGAGCTTATATATTGC 57.360 34.615 0.00 0.00 0.00 3.56
3428 4807 8.985315 ATCCTGATTAGTTGCATCTCAAAATA 57.015 30.769 0.00 0.00 36.26 1.40
3429 4808 7.893124 ATCCTGATTAGTTGCATCTCAAAAT 57.107 32.000 0.00 0.00 36.26 1.82
3430 4809 7.707624 AATCCTGATTAGTTGCATCTCAAAA 57.292 32.000 0.00 0.00 36.26 2.44
3431 4810 7.394077 TGAAATCCTGATTAGTTGCATCTCAAA 59.606 33.333 0.00 0.00 36.26 2.69
3432 4811 6.885918 TGAAATCCTGATTAGTTGCATCTCAA 59.114 34.615 0.00 0.00 0.00 3.02
3433 4812 6.417258 TGAAATCCTGATTAGTTGCATCTCA 58.583 36.000 0.00 0.00 0.00 3.27
3434 4813 6.932356 TGAAATCCTGATTAGTTGCATCTC 57.068 37.500 0.00 0.00 0.00 2.75
3435 4814 6.096001 GGTTGAAATCCTGATTAGTTGCATCT 59.904 38.462 2.28 2.28 0.00 2.90
3436 4815 6.096001 AGGTTGAAATCCTGATTAGTTGCATC 59.904 38.462 0.00 0.00 33.62 3.91
3446 4825 5.242393 CACAGTTTGAGGTTGAAATCCTGAT 59.758 40.000 0.00 0.00 35.20 2.90
3451 4830 5.763204 TCCTACACAGTTTGAGGTTGAAATC 59.237 40.000 0.00 0.00 0.00 2.17
3452 4831 5.690865 TCCTACACAGTTTGAGGTTGAAAT 58.309 37.500 0.00 0.00 0.00 2.17
3474 4853 9.685828 TTTGTTTGTATGGTATTTAGCAAGTTC 57.314 29.630 0.00 0.00 37.24 3.01
3483 4862 7.589958 TCACCAGTTTGTTTGTATGGTATTT 57.410 32.000 0.00 0.00 42.29 1.40
3484 4863 7.589958 TTCACCAGTTTGTTTGTATGGTATT 57.410 32.000 0.00 0.00 42.29 1.89
3498 4877 2.362077 GCCTGTGTGAATTCACCAGTTT 59.638 45.455 32.36 0.00 45.88 2.66
3500 4879 1.133823 TGCCTGTGTGAATTCACCAGT 60.134 47.619 32.36 0.00 45.88 4.00
3515 4894 6.200286 GCATTCATGACATAATTTCTTGCCTG 59.800 38.462 0.00 0.00 0.00 4.85
3517 4897 5.174398 CGCATTCATGACATAATTTCTTGCC 59.826 40.000 0.00 0.00 0.00 4.52
3526 4906 1.012841 TGCGCGCATTCATGACATAA 58.987 45.000 33.09 1.22 0.00 1.90
3531 4911 1.778027 CTCCATGCGCGCATTCATGA 61.778 55.000 41.73 30.48 41.82 3.07
3543 4923 0.108945 GCCTTTTGTGCTCTCCATGC 60.109 55.000 0.00 0.00 0.00 4.06
3548 4928 2.157738 ACTGATGCCTTTTGTGCTCTC 58.842 47.619 0.00 0.00 0.00 3.20
3549 4929 2.283145 ACTGATGCCTTTTGTGCTCT 57.717 45.000 0.00 0.00 0.00 4.09
3551 4931 2.309613 TCAACTGATGCCTTTTGTGCT 58.690 42.857 0.00 0.00 0.00 4.40
3557 4937 4.202253 GGTTTCCTTTCAACTGATGCCTTT 60.202 41.667 0.00 0.00 0.00 3.11
3559 4939 2.893489 GGTTTCCTTTCAACTGATGCCT 59.107 45.455 0.00 0.00 0.00 4.75
3564 4946 4.675976 TCTACGGTTTCCTTTCAACTGA 57.324 40.909 0.00 0.00 34.95 3.41
3589 4974 5.457473 CCTTTCAGTTAATTGCGACGTTTTT 59.543 36.000 0.00 0.00 0.00 1.94
3593 4978 3.395639 TCCTTTCAGTTAATTGCGACGT 58.604 40.909 0.00 0.00 0.00 4.34
3594 4979 4.600012 ATCCTTTCAGTTAATTGCGACG 57.400 40.909 0.00 0.00 0.00 5.12
3595 4980 7.693952 TCATTATCCTTTCAGTTAATTGCGAC 58.306 34.615 0.00 0.00 0.00 5.19
3596 4981 7.857734 TCATTATCCTTTCAGTTAATTGCGA 57.142 32.000 0.00 0.00 0.00 5.10
3654 5039 7.924412 GGATATTTGATGTCAGCAAATTGATGT 59.076 33.333 28.47 11.33 41.71 3.06
3698 5083 4.646572 AGACTCAGTTCATTTCCAGTTCC 58.353 43.478 0.00 0.00 0.00 3.62
3751 5137 0.456221 CCGTCCAAGCTATGACGTCT 59.544 55.000 26.53 4.95 39.14 4.18
3755 5141 3.027974 GGATACCGTCCAAGCTATGAC 57.972 52.381 5.65 5.65 46.96 3.06
3788 5174 3.604065 TTGCTAGTATCTCAGTACGCG 57.396 47.619 3.53 3.53 0.00 6.01
3789 5175 4.503370 GGTTTTGCTAGTATCTCAGTACGC 59.497 45.833 0.00 0.00 0.00 4.42
3790 5176 5.041940 GGGTTTTGCTAGTATCTCAGTACG 58.958 45.833 0.00 0.00 0.00 3.67
3791 5177 5.811100 GTGGGTTTTGCTAGTATCTCAGTAC 59.189 44.000 0.00 0.00 0.00 2.73
3820 5206 3.901222 GGGATTGGGAAAAAGGAGTGAAA 59.099 43.478 0.00 0.00 0.00 2.69
3837 5223 5.670792 TCTACAACATGTCTAACGGGATT 57.329 39.130 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.