Multiple sequence alignment - TraesCS1A01G287200

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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 TraesCS1A01G287200 chr1A 100.000 2921 0 0 1 2921 483929913 483926993 0.000000e+00 5395.0
1 TraesCS1A01G287200 chr1D 91.151 2814 142 55 168 2921 384148866 384146100 0.000000e+00 3718.0
2 TraesCS1A01G287200 chr1B 91.396 1906 79 44 379 2237 515456458 515454591 0.000000e+00 2532.0
3 TraesCS1A01G287200 chr1B 88.391 603 39 11 163 760 515457132 515456556 0.000000e+00 697.0
4 TraesCS1A01G287200 chr5A 96.970 165 5 0 1 165 305183413 305183249 7.970000e-71 278.0
5 TraesCS1A01G287200 chr5A 96.951 164 5 0 1 164 332643726 332643889 2.870000e-70 276.0
6 TraesCS1A01G287200 chr3B 96.341 164 6 0 1 164 463205018 463204855 1.330000e-68 270.0
7 TraesCS1A01G287200 chr3B 95.238 168 8 0 1 168 18858957 18858790 1.730000e-67 267.0
8 TraesCS1A01G287200 chr6A 95.266 169 6 1 1 169 569702635 569702469 1.730000e-67 267.0
9 TraesCS1A01G287200 chr4A 94.737 171 9 0 1 171 464567435 464567605 1.730000e-67 267.0
10 TraesCS1A01G287200 chr4A 93.750 176 9 2 1 175 464113015 464112841 2.230000e-66 263.0
11 TraesCS1A01G287200 chr4A 95.745 47 2 0 1689 1735 114142613 114142659 3.120000e-10 76.8
12 TraesCS1A01G287200 chr2B 95.238 168 8 0 1 168 710833392 710833225 1.730000e-67 267.0
13 TraesCS1A01G287200 chr3A 94.737 171 8 1 1 171 370245892 370246061 6.210000e-67 265.0
14 TraesCS1A01G287200 chr4D 100.000 44 0 0 1692 1735 350831289 350831246 6.710000e-12 82.4
15 TraesCS1A01G287200 chr4B 97.727 44 1 0 1692 1735 434193843 434193800 3.120000e-10 76.8


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 TraesCS1A01G287200 chr1A 483926993 483929913 2920 True 5395.0 5395 100.0000 1 2921 1 chr1A.!!$R1 2920
1 TraesCS1A01G287200 chr1D 384146100 384148866 2766 True 3718.0 3718 91.1510 168 2921 1 chr1D.!!$R1 2753
2 TraesCS1A01G287200 chr1B 515454591 515457132 2541 True 1614.5 2532 89.8935 163 2237 2 chr1B.!!$R1 2074

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
780 1273 0.109597 GGTGAAGTTTCAGCGCCATG 60.11 55.0 2.29 0.0 44.45 3.66 F
1154 1660 0.029567 GTAGATCAGAGGTGTCCGCG 59.97 60.0 0.00 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 2381 0.329261 TGGACATAAGCAGCAGCCTT 59.671 50.0 0.0 0.0 43.56 4.35 R
2832 3373 1.302383 TTGCCCTGCAACCGTATTCG 61.302 55.0 0.0 0.0 43.99 3.34 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
23 24 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
25 26 7.628501 ACTCCCTCCGTTCCTAAATATTTAT 57.371 36.000 8.34 0.00 0.00 1.40
26 27 7.677892 ACTCCCTCCGTTCCTAAATATTTATC 58.322 38.462 8.34 0.61 0.00 1.75
27 28 7.513091 ACTCCCTCCGTTCCTAAATATTTATCT 59.487 37.037 8.34 0.00 0.00 1.98
28 29 8.271398 TCCCTCCGTTCCTAAATATTTATCTT 57.729 34.615 8.34 0.00 0.00 2.40
29 30 8.720537 TCCCTCCGTTCCTAAATATTTATCTTT 58.279 33.333 8.34 0.00 0.00 2.52
30 31 9.000486 CCCTCCGTTCCTAAATATTTATCTTTC 58.000 37.037 8.34 0.00 0.00 2.62
31 32 9.780186 CCTCCGTTCCTAAATATTTATCTTTCT 57.220 33.333 8.34 0.00 0.00 2.52
58 59 9.302345 AGACATTTCAAATGACTACTACATACG 57.698 33.333 17.30 0.00 0.00 3.06
59 60 8.420374 ACATTTCAAATGACTACTACATACGG 57.580 34.615 17.30 0.00 0.00 4.02
60 61 8.255206 ACATTTCAAATGACTACTACATACGGA 58.745 33.333 17.30 0.00 0.00 4.69
61 62 9.261180 CATTTCAAATGACTACTACATACGGAT 57.739 33.333 3.82 0.00 0.00 4.18
62 63 8.642908 TTTCAAATGACTACTACATACGGATG 57.357 34.615 5.94 5.94 39.16 3.51
64 65 8.454570 TCAAATGACTACTACATACGGATGTA 57.545 34.615 19.32 19.32 44.77 2.29
65 66 9.074576 TCAAATGACTACTACATACGGATGTAT 57.925 33.333 20.64 13.02 45.42 2.29
107 108 8.850156 AGTGTAGATTCACTTATTTTGCTTTGT 58.150 29.630 0.00 0.00 44.92 2.83
111 112 8.693542 AGATTCACTTATTTTGCTTTGTATGC 57.306 30.769 0.00 0.00 0.00 3.14
112 113 8.306038 AGATTCACTTATTTTGCTTTGTATGCA 58.694 29.630 0.00 0.00 38.80 3.96
113 114 7.872163 TTCACTTATTTTGCTTTGTATGCAG 57.128 32.000 0.00 0.00 41.71 4.41
114 115 6.980593 TCACTTATTTTGCTTTGTATGCAGT 58.019 32.000 0.00 0.00 41.71 4.40
115 116 7.083858 TCACTTATTTTGCTTTGTATGCAGTC 58.916 34.615 0.00 0.00 41.71 3.51
116 117 6.862608 CACTTATTTTGCTTTGTATGCAGTCA 59.137 34.615 0.00 0.00 41.71 3.41
117 118 7.543172 CACTTATTTTGCTTTGTATGCAGTCAT 59.457 33.333 0.00 0.00 41.71 3.06
118 119 8.090214 ACTTATTTTGCTTTGTATGCAGTCATT 58.910 29.630 0.00 0.00 41.71 2.57
119 120 8.830201 TTATTTTGCTTTGTATGCAGTCATTT 57.170 26.923 0.00 0.00 41.71 2.32
120 121 9.920133 TTATTTTGCTTTGTATGCAGTCATTTA 57.080 25.926 0.00 0.00 41.71 1.40
122 123 8.830201 TTTTGCTTTGTATGCAGTCATTTATT 57.170 26.923 0.00 0.00 41.71 1.40
123 124 7.815398 TTGCTTTGTATGCAGTCATTTATTG 57.185 32.000 0.00 0.00 41.71 1.90
124 125 7.155655 TGCTTTGTATGCAGTCATTTATTGA 57.844 32.000 0.00 0.00 35.31 2.57
125 126 7.600960 TGCTTTGTATGCAGTCATTTATTGAA 58.399 30.769 0.00 0.00 33.95 2.69
126 127 8.087136 TGCTTTGTATGCAGTCATTTATTGAAA 58.913 29.630 0.00 0.00 33.95 2.69
127 128 9.090692 GCTTTGTATGCAGTCATTTATTGAAAT 57.909 29.630 0.00 0.00 35.70 2.17
141 142 9.859427 CATTTATTGAAATGCCTAGAAAGACAA 57.141 29.630 0.00 0.00 44.05 3.18
143 144 8.635765 TTATTGAAATGCCTAGAAAGACAAGT 57.364 30.769 0.00 0.00 0.00 3.16
144 145 9.733556 TTATTGAAATGCCTAGAAAGACAAGTA 57.266 29.630 0.00 0.00 0.00 2.24
145 146 8.814038 ATTGAAATGCCTAGAAAGACAAGTAT 57.186 30.769 0.00 0.00 0.00 2.12
146 147 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
147 148 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
148 149 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
150 151 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
151 152 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
152 153 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
153 154 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
154 155 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
155 156 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
156 157 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
157 158 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
158 159 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
159 160 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
160 161 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
161 162 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
162 163 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
163 164 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
164 165 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
165 166 2.449137 TTAGGAACGGAGGGAGTAGG 57.551 55.000 0.00 0.00 0.00 3.18
246 247 1.256812 CGAAAATGTGGGGCTCCTTT 58.743 50.000 3.07 0.00 0.00 3.11
270 271 1.318576 CAAACGACCAAGAAAGGCCT 58.681 50.000 0.00 0.00 0.00 5.19
318 333 2.232298 CTCCTCACTCCTGCCGGTTC 62.232 65.000 1.90 0.00 0.00 3.62
319 334 2.286523 CCTCACTCCTGCCGGTTCT 61.287 63.158 1.90 0.00 0.00 3.01
320 335 0.970937 CCTCACTCCTGCCGGTTCTA 60.971 60.000 1.90 0.00 0.00 2.10
335 350 6.070653 TGCCGGTTCTACTAGAAAGGAAAATA 60.071 38.462 18.81 3.97 36.80 1.40
339 354 9.765795 CGGTTCTACTAGAAAGGAAAATATCAT 57.234 33.333 0.00 0.00 35.75 2.45
347 362 9.213799 CTAGAAAGGAAAATATCATGGTAGAGC 57.786 37.037 0.00 0.00 0.00 4.09
377 392 7.982354 ACAAAAGCACTAGTGGAATAGATAGAC 59.018 37.037 23.95 3.02 0.00 2.59
426 444 2.896685 AGAACTCAGGTCTCCTCACAAG 59.103 50.000 0.00 0.00 0.00 3.16
429 447 2.896685 ACTCAGGTCTCCTCACAAGAAG 59.103 50.000 0.00 0.00 0.00 2.85
431 449 2.158310 TCAGGTCTCCTCACAAGAAGGA 60.158 50.000 0.00 0.00 0.00 3.36
581 1058 3.003480 CAGCTCCTTCCCTTTAGAAACG 58.997 50.000 0.00 0.00 0.00 3.60
582 1059 2.904434 AGCTCCTTCCCTTTAGAAACGA 59.096 45.455 0.00 0.00 0.00 3.85
615 1092 1.007336 AGACACGATGAAACGCGGAC 61.007 55.000 12.47 1.26 36.70 4.79
647 1126 5.519927 CCTGTCAAACCTCAAATTTTCACAC 59.480 40.000 0.00 0.00 0.00 3.82
648 1127 6.030548 TGTCAAACCTCAAATTTTCACACA 57.969 33.333 0.00 0.00 0.00 3.72
649 1128 6.098679 TGTCAAACCTCAAATTTTCACACAG 58.901 36.000 0.00 0.00 0.00 3.66
652 1131 7.117667 GTCAAACCTCAAATTTTCACACAGTTT 59.882 33.333 0.00 0.00 0.00 2.66
653 1132 7.659390 TCAAACCTCAAATTTTCACACAGTTTT 59.341 29.630 0.00 0.00 0.00 2.43
654 1133 6.966435 ACCTCAAATTTTCACACAGTTTTG 57.034 33.333 0.00 0.00 0.00 2.44
655 1134 6.696411 ACCTCAAATTTTCACACAGTTTTGA 58.304 32.000 0.00 0.00 33.47 2.69
662 1141 7.814264 ATTTTCACACAGTTTTGAGAGAGAT 57.186 32.000 0.00 0.00 0.00 2.75
664 1143 8.731275 TTTTCACACAGTTTTGAGAGAGATAA 57.269 30.769 0.00 0.00 0.00 1.75
668 1147 8.830580 TCACACAGTTTTGAGAGAGATAAAAAG 58.169 33.333 0.00 0.00 0.00 2.27
705 1187 5.813672 TGACATACCAGCCGTTAATTTCTAC 59.186 40.000 0.00 0.00 0.00 2.59
780 1273 0.109597 GGTGAAGTTTCAGCGCCATG 60.110 55.000 2.29 0.00 44.45 3.66
843 1336 1.078567 CTCCAGCCACAGAAGAGCC 60.079 63.158 0.00 0.00 0.00 4.70
1036 1540 4.735132 GCGTCAGCACGGCACCTA 62.735 66.667 0.00 0.00 46.80 3.08
1067 1571 2.746375 ATCCACCATGGGCGACTCC 61.746 63.158 18.09 0.00 38.32 3.85
1068 1572 3.402681 CCACCATGGGCGACTCCT 61.403 66.667 18.09 0.00 32.67 3.69
1069 1573 2.187946 CACCATGGGCGACTCCTC 59.812 66.667 18.09 0.00 34.39 3.71
1101 1605 6.239600 GGCTTCCTACATCAGAATGGTATGTA 60.240 42.308 0.00 0.00 37.19 2.29
1102 1606 6.647067 GCTTCCTACATCAGAATGGTATGTAC 59.353 42.308 0.00 0.00 37.19 2.90
1114 1618 3.517602 TGGTATGTACAGCTAGCGTTTG 58.482 45.455 15.48 8.90 0.00 2.93
1115 1619 3.193903 TGGTATGTACAGCTAGCGTTTGA 59.806 43.478 15.48 0.03 0.00 2.69
1119 1623 5.880054 ATGTACAGCTAGCGTTTGAATTT 57.120 34.783 15.48 0.00 0.00 1.82
1120 1624 5.277601 TGTACAGCTAGCGTTTGAATTTC 57.722 39.130 15.48 0.00 0.00 2.17
1122 1626 4.410492 ACAGCTAGCGTTTGAATTTCTG 57.590 40.909 9.55 0.00 0.00 3.02
1125 1629 3.120060 AGCTAGCGTTTGAATTTCTGCTG 60.120 43.478 9.55 0.00 34.08 4.41
1142 1648 0.384309 CTGTAAGCGCGGGTAGATCA 59.616 55.000 8.83 0.00 0.00 2.92
1145 1651 0.952280 TAAGCGCGGGTAGATCAGAG 59.048 55.000 8.83 0.00 0.00 3.35
1149 1655 1.384989 CGCGGGTAGATCAGAGGTGT 61.385 60.000 0.00 0.00 0.00 4.16
1150 1656 0.386113 GCGGGTAGATCAGAGGTGTC 59.614 60.000 0.00 0.00 0.00 3.67
1151 1657 1.033574 CGGGTAGATCAGAGGTGTCC 58.966 60.000 0.00 0.00 0.00 4.02
1153 1659 0.386113 GGTAGATCAGAGGTGTCCGC 59.614 60.000 0.00 0.00 0.00 5.54
1154 1660 0.029567 GTAGATCAGAGGTGTCCGCG 59.970 60.000 0.00 0.00 0.00 6.46
1155 1661 1.725557 TAGATCAGAGGTGTCCGCGC 61.726 60.000 0.00 0.00 0.00 6.86
1164 1670 3.662153 TGTCCGCGCGTGTGTCTA 61.662 61.111 29.95 4.51 0.00 2.59
1165 1671 2.202570 GTCCGCGCGTGTGTCTAT 60.203 61.111 29.95 0.00 0.00 1.98
1166 1672 2.101575 TCCGCGCGTGTGTCTATC 59.898 61.111 29.95 0.00 0.00 2.08
1167 1673 2.202557 CCGCGCGTGTGTCTATCA 60.203 61.111 29.95 0.00 0.00 2.15
1169 1675 1.348538 CCGCGCGTGTGTCTATCAAA 61.349 55.000 29.95 0.00 0.00 2.69
1170 1676 0.246757 CGCGCGTGTGTCTATCAAAC 60.247 55.000 24.19 0.00 0.00 2.93
1171 1677 0.787787 GCGCGTGTGTCTATCAAACA 59.212 50.000 8.43 0.00 34.11 2.83
1172 1678 1.193650 GCGCGTGTGTCTATCAAACAA 59.806 47.619 8.43 0.00 34.11 2.83
1173 1679 2.159707 GCGCGTGTGTCTATCAAACAAT 60.160 45.455 8.43 0.00 34.11 2.71
1174 1680 3.061563 GCGCGTGTGTCTATCAAACAATA 59.938 43.478 8.43 0.00 34.11 1.90
1175 1681 4.260212 GCGCGTGTGTCTATCAAACAATAT 60.260 41.667 8.43 0.00 34.11 1.28
1176 1682 5.051307 GCGCGTGTGTCTATCAAACAATATA 60.051 40.000 8.43 0.00 34.11 0.86
1177 1683 6.346598 GCGCGTGTGTCTATCAAACAATATAT 60.347 38.462 8.43 0.00 34.11 0.86
1178 1684 7.148869 GCGCGTGTGTCTATCAAACAATATATA 60.149 37.037 8.43 0.00 34.11 0.86
1179 1685 8.860128 CGCGTGTGTCTATCAAACAATATATAT 58.140 33.333 0.00 0.00 34.11 0.86
1207 1718 1.691434 GGAATCTTTGTGGGTTGCCAA 59.309 47.619 0.00 0.00 0.00 4.52
1227 1738 6.838090 TGCCAATAATTGATTGATTCCAGGTA 59.162 34.615 0.00 0.00 46.94 3.08
1337 1848 3.317149 GTCGTCACTGCCACTGGTATATA 59.683 47.826 0.00 0.00 0.00 0.86
1338 1849 4.022242 GTCGTCACTGCCACTGGTATATAT 60.022 45.833 0.00 0.00 0.00 0.86
1339 1850 5.182570 GTCGTCACTGCCACTGGTATATATA 59.817 44.000 0.00 0.00 0.00 0.86
1340 1851 5.949952 TCGTCACTGCCACTGGTATATATAT 59.050 40.000 0.00 0.00 0.00 0.86
1407 1918 6.072119 GGGTGTATTTTAAGACAAAGGAGGTG 60.072 42.308 0.00 0.00 31.17 4.00
1472 1985 7.821359 TGCCTAATTAGATCTTCATGCTATGAC 59.179 37.037 14.28 0.00 39.39 3.06
1479 1992 3.826466 TCTTCATGCTATGACGCTATCG 58.174 45.455 0.00 0.00 39.39 2.92
1541 2055 2.416547 GCGCTTCAGCTCAATTGACTTA 59.583 45.455 3.38 0.00 39.32 2.24
1546 2060 6.615088 GCTTCAGCTCAATTGACTTAATTCA 58.385 36.000 3.38 0.00 36.08 2.57
1555 2069 6.595326 TCAATTGACTTAATTCATCGCAGACT 59.405 34.615 3.38 0.00 36.59 3.24
1558 2072 5.348986 TGACTTAATTCATCGCAGACTACC 58.651 41.667 0.00 0.00 42.51 3.18
1559 2073 4.694339 ACTTAATTCATCGCAGACTACCC 58.306 43.478 0.00 0.00 42.51 3.69
1561 2075 5.597182 ACTTAATTCATCGCAGACTACCCTA 59.403 40.000 0.00 0.00 42.51 3.53
1564 2084 1.613925 TCATCGCAGACTACCCTATGC 59.386 52.381 0.00 0.00 42.51 3.14
1565 2085 1.341209 CATCGCAGACTACCCTATGCA 59.659 52.381 0.00 0.00 42.51 3.96
1573 2093 2.614057 GACTACCCTATGCATGCACAAC 59.386 50.000 25.37 3.58 0.00 3.32
1574 2094 2.239654 ACTACCCTATGCATGCACAACT 59.760 45.455 25.37 9.96 0.00 3.16
1575 2095 1.755179 ACCCTATGCATGCACAACTC 58.245 50.000 25.37 0.00 0.00 3.01
1580 2100 3.441222 CCTATGCATGCACAACTCTTTGA 59.559 43.478 25.37 0.00 36.48 2.69
1581 2101 4.097437 CCTATGCATGCACAACTCTTTGAT 59.903 41.667 25.37 4.75 36.48 2.57
1583 2103 2.885894 TGCATGCACAACTCTTTGATGA 59.114 40.909 18.46 0.00 36.48 2.92
1587 2107 1.873591 GCACAACTCTTTGATGACGGT 59.126 47.619 0.00 0.00 36.48 4.83
1594 2114 7.330946 CACAACTCTTTGATGACGGTTAGATTA 59.669 37.037 0.00 0.00 36.48 1.75
1595 2115 8.041323 ACAACTCTTTGATGACGGTTAGATTAT 58.959 33.333 0.00 0.00 36.48 1.28
1596 2116 9.529325 CAACTCTTTGATGACGGTTAGATTATA 57.471 33.333 0.00 0.00 34.24 0.98
1625 2150 8.488668 ACTAGCTAGCTAGAGTAGTACTTCTTT 58.511 37.037 43.93 22.37 46.56 2.52
1664 2191 9.813826 TGAATATATGTCAGAGGATGTAAGAGA 57.186 33.333 0.00 0.00 0.00 3.10
1851 2379 2.034472 GACGACGACGAGGGCTAGAC 62.034 65.000 15.32 0.00 42.66 2.59
1852 2380 2.708255 GACGACGAGGGCTAGACG 59.292 66.667 0.00 0.00 0.00 4.18
1853 2381 1.812922 GACGACGAGGGCTAGACGA 60.813 63.158 0.00 0.00 0.00 4.20
2237 2772 2.242564 CGTCTACACGCCGATCATATG 58.757 52.381 0.00 0.00 39.69 1.78
2240 2780 4.049186 GTCTACACGCCGATCATATGTTT 58.951 43.478 1.90 0.00 0.00 2.83
2264 2804 7.462109 TTTTCTTGTCATGGTTCGAAAAATG 57.538 32.000 12.85 12.85 30.28 2.32
2268 2808 7.304735 TCTTGTCATGGTTCGAAAAATGTATG 58.695 34.615 16.66 8.75 0.00 2.39
2302 2842 9.383519 GTTATTCTCCACATGATTCAGAGTAAA 57.616 33.333 0.00 0.00 0.00 2.01
2305 2845 7.912056 TCTCCACATGATTCAGAGTAAAAAG 57.088 36.000 0.00 0.00 0.00 2.27
2307 2847 5.415701 TCCACATGATTCAGAGTAAAAAGCC 59.584 40.000 0.00 0.00 0.00 4.35
2315 2856 8.474025 TGATTCAGAGTAAAAAGCCAAAAAGAA 58.526 29.630 0.00 0.00 0.00 2.52
2319 2860 7.123547 TCAGAGTAAAAAGCCAAAAAGAAAGGA 59.876 33.333 0.00 0.00 0.00 3.36
2328 2869 7.047460 AGCCAAAAAGAAAGGATGCATATAG 57.953 36.000 0.00 0.00 0.00 1.31
2346 2887 8.690884 TGCATATAGAGAGATTAATAGAGTGCC 58.309 37.037 0.00 0.00 0.00 5.01
2347 2888 8.912988 GCATATAGAGAGATTAATAGAGTGCCT 58.087 37.037 0.00 0.00 0.00 4.75
2421 2962 4.318974 GCAAAACATTTGCGCTGAATCTTT 60.319 37.500 9.73 6.72 35.58 2.52
2432 2973 3.058983 CGCTGAATCTTTGTGCACAGTTA 60.059 43.478 20.59 9.50 0.00 2.24
2433 2974 4.470462 GCTGAATCTTTGTGCACAGTTAG 58.530 43.478 20.59 17.57 0.00 2.34
2435 2976 3.882288 TGAATCTTTGTGCACAGTTAGCA 59.118 39.130 20.59 12.21 40.19 3.49
2436 2977 4.520111 TGAATCTTTGTGCACAGTTAGCAT 59.480 37.500 20.59 10.28 44.79 3.79
2437 2978 5.704978 TGAATCTTTGTGCACAGTTAGCATA 59.295 36.000 20.59 0.00 44.79 3.14
2438 2979 5.551760 ATCTTTGTGCACAGTTAGCATAC 57.448 39.130 20.59 0.00 44.79 2.39
2439 2980 3.431912 TCTTTGTGCACAGTTAGCATACG 59.568 43.478 20.59 0.18 44.79 3.06
2440 2981 2.448926 TGTGCACAGTTAGCATACGT 57.551 45.000 17.42 0.00 44.79 3.57
2441 2982 3.579335 TGTGCACAGTTAGCATACGTA 57.421 42.857 17.42 0.00 44.79 3.57
2471 3012 4.081697 TCTCCGTCTGACATTAGCAAATGA 60.082 41.667 8.73 0.00 44.50 2.57
2475 3016 5.136250 GTCTGACATTAGCAAATGAGACG 57.864 43.478 2.24 0.00 44.50 4.18
2494 3035 2.167900 ACGTGACTATGGGTTAGAAGGC 59.832 50.000 0.00 0.00 0.00 4.35
2515 3056 2.096466 CGCACGTCACTCTTTTTATGCA 60.096 45.455 0.00 0.00 0.00 3.96
2516 3057 3.226347 GCACGTCACTCTTTTTATGCAC 58.774 45.455 0.00 0.00 0.00 4.57
2522 3063 5.178623 CGTCACTCTTTTTATGCACTAACCA 59.821 40.000 0.00 0.00 0.00 3.67
2535 3076 5.666462 TGCACTAACCAGAATTATCGCTAA 58.334 37.500 0.00 0.00 0.00 3.09
2737 3278 7.712205 TGGTTCTCATATGATTGTGTGTATCTG 59.288 37.037 5.72 0.00 0.00 2.90
2799 3340 7.497249 GCTATCAAACATTATTGGTCTCTCAGT 59.503 37.037 0.00 0.00 0.00 3.41
2832 3373 2.756760 TCAAAGATTCCATTGCTCCAGC 59.243 45.455 0.00 0.00 42.50 4.85
2833 3374 1.386533 AAGATTCCATTGCTCCAGCG 58.613 50.000 0.00 0.00 45.83 5.18
2834 3375 0.543277 AGATTCCATTGCTCCAGCGA 59.457 50.000 0.00 0.00 45.83 4.93
2835 3376 1.065199 AGATTCCATTGCTCCAGCGAA 60.065 47.619 0.00 0.00 45.83 4.70
2863 3404 0.675083 CAGGGCAATGCTTTCACACA 59.325 50.000 4.82 0.00 0.00 3.72
2869 3410 2.096119 GCAATGCTTTCACACATTTGGC 60.096 45.455 0.00 0.00 34.32 4.52
2870 3411 3.132160 CAATGCTTTCACACATTTGGCA 58.868 40.909 0.00 0.00 34.32 4.92
2916 3457 4.718940 ATGCGGGTAAATGGAGAAAAAG 57.281 40.909 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.908453 AGATAAATATTTAGGAACGGAGGGAG 58.092 38.462 13.15 0.00 0.00 4.30
4 5 8.919777 AAAGATAAATATTTAGGAACGGAGGG 57.080 34.615 13.15 0.00 0.00 4.30
5 6 9.780186 AGAAAGATAAATATTTAGGAACGGAGG 57.220 33.333 13.15 0.00 0.00 4.30
32 33 9.302345 CGTATGTAGTAGTCATTTGAAATGTCT 57.698 33.333 18.62 18.62 0.00 3.41
33 34 8.540492 CCGTATGTAGTAGTCATTTGAAATGTC 58.460 37.037 16.62 11.74 0.00 3.06
34 35 8.255206 TCCGTATGTAGTAGTCATTTGAAATGT 58.745 33.333 16.62 2.38 0.00 2.71
35 36 8.642908 TCCGTATGTAGTAGTCATTTGAAATG 57.357 34.615 11.54 11.54 0.00 2.32
36 37 9.261180 CATCCGTATGTAGTAGTCATTTGAAAT 57.739 33.333 0.00 0.00 0.00 2.17
37 38 8.255206 ACATCCGTATGTAGTAGTCATTTGAAA 58.745 33.333 0.00 0.00 44.66 2.69
38 39 7.778083 ACATCCGTATGTAGTAGTCATTTGAA 58.222 34.615 0.00 0.00 44.66 2.69
39 40 7.342769 ACATCCGTATGTAGTAGTCATTTGA 57.657 36.000 0.00 0.00 44.66 2.69
85 86 9.787532 GCATACAAAGCAAAATAAGTGAATCTA 57.212 29.630 0.00 0.00 0.00 1.98
86 87 8.306038 TGCATACAAAGCAAAATAAGTGAATCT 58.694 29.630 0.00 0.00 39.39 2.40
87 88 8.464770 TGCATACAAAGCAAAATAAGTGAATC 57.535 30.769 0.00 0.00 39.39 2.52
88 89 8.090214 ACTGCATACAAAGCAAAATAAGTGAAT 58.910 29.630 0.00 0.00 42.17 2.57
89 90 7.432869 ACTGCATACAAAGCAAAATAAGTGAA 58.567 30.769 0.00 0.00 42.17 3.18
90 91 6.980593 ACTGCATACAAAGCAAAATAAGTGA 58.019 32.000 0.00 0.00 42.17 3.41
91 92 6.862608 TGACTGCATACAAAGCAAAATAAGTG 59.137 34.615 0.00 0.00 42.17 3.16
92 93 6.980593 TGACTGCATACAAAGCAAAATAAGT 58.019 32.000 0.00 0.00 42.17 2.24
93 94 8.470040 AATGACTGCATACAAAGCAAAATAAG 57.530 30.769 0.00 0.00 42.17 1.73
94 95 8.830201 AAATGACTGCATACAAAGCAAAATAA 57.170 26.923 0.00 0.00 42.17 1.40
96 97 9.439500 AATAAATGACTGCATACAAAGCAAAAT 57.561 25.926 0.00 0.00 42.17 1.82
97 98 8.710551 CAATAAATGACTGCATACAAAGCAAAA 58.289 29.630 0.00 0.00 42.17 2.44
98 99 8.087136 TCAATAAATGACTGCATACAAAGCAAA 58.913 29.630 0.00 0.00 35.72 3.68
99 100 7.600960 TCAATAAATGACTGCATACAAAGCAA 58.399 30.769 0.00 0.00 35.72 3.91
100 101 7.155655 TCAATAAATGACTGCATACAAAGCA 57.844 32.000 0.00 0.00 35.18 3.91
101 102 8.464770 TTTCAATAAATGACTGCATACAAAGC 57.535 30.769 0.00 0.00 37.92 3.51
117 118 9.077885 ACTTGTCTTTCTAGGCATTTCAATAAA 57.922 29.630 0.00 0.00 35.56 1.40
118 119 8.635765 ACTTGTCTTTCTAGGCATTTCAATAA 57.364 30.769 0.00 0.00 35.56 1.40
119 120 9.905713 ATACTTGTCTTTCTAGGCATTTCAATA 57.094 29.630 0.00 0.00 35.56 1.90
120 121 8.814038 ATACTTGTCTTTCTAGGCATTTCAAT 57.186 30.769 0.00 0.00 35.56 2.57
121 122 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
122 123 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
124 125 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
125 126 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
126 127 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
127 128 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
128 129 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
129 130 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
130 131 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
131 132 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
132 133 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
133 134 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
134 135 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
135 136 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
136 137 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
137 138 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
138 139 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
139 140 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
140 141 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
141 142 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
142 143 4.280425 CCTACTCCCTCCGTTCCTAAATAC 59.720 50.000 0.00 0.00 0.00 1.89
143 144 4.078980 ACCTACTCCCTCCGTTCCTAAATA 60.079 45.833 0.00 0.00 0.00 1.40
144 145 3.306613 CCTACTCCCTCCGTTCCTAAAT 58.693 50.000 0.00 0.00 0.00 1.40
145 146 2.043526 ACCTACTCCCTCCGTTCCTAAA 59.956 50.000 0.00 0.00 0.00 1.85
146 147 1.642762 ACCTACTCCCTCCGTTCCTAA 59.357 52.381 0.00 0.00 0.00 2.69
147 148 1.302907 ACCTACTCCCTCCGTTCCTA 58.697 55.000 0.00 0.00 0.00 2.94
148 149 0.412640 AACCTACTCCCTCCGTTCCT 59.587 55.000 0.00 0.00 0.00 3.36
149 150 0.535797 CAACCTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
150 151 0.108281 GCAACCTACTCCCTCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
151 152 0.544595 AGCAACCTACTCCCTCCGTT 60.545 55.000 0.00 0.00 0.00 4.44
152 153 0.544595 AAGCAACCTACTCCCTCCGT 60.545 55.000 0.00 0.00 0.00 4.69
153 154 0.108138 CAAGCAACCTACTCCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
154 155 0.253327 CCAAGCAACCTACTCCCTCC 59.747 60.000 0.00 0.00 0.00 4.30
155 156 0.984995 ACCAAGCAACCTACTCCCTC 59.015 55.000 0.00 0.00 0.00 4.30
156 157 1.446016 AACCAAGCAACCTACTCCCT 58.554 50.000 0.00 0.00 0.00 4.20
157 158 1.886542 CAAACCAAGCAACCTACTCCC 59.113 52.381 0.00 0.00 0.00 4.30
158 159 2.583143 ACAAACCAAGCAACCTACTCC 58.417 47.619 0.00 0.00 0.00 3.85
159 160 4.386711 AGTACAAACCAAGCAACCTACTC 58.613 43.478 0.00 0.00 0.00 2.59
160 161 4.432980 AGTACAAACCAAGCAACCTACT 57.567 40.909 0.00 0.00 0.00 2.57
161 162 4.337274 ACAAGTACAAACCAAGCAACCTAC 59.663 41.667 0.00 0.00 0.00 3.18
162 163 4.336993 CACAAGTACAAACCAAGCAACCTA 59.663 41.667 0.00 0.00 0.00 3.08
163 164 3.130340 CACAAGTACAAACCAAGCAACCT 59.870 43.478 0.00 0.00 0.00 3.50
164 165 3.443976 CACAAGTACAAACCAAGCAACC 58.556 45.455 0.00 0.00 0.00 3.77
165 166 3.443976 CCACAAGTACAAACCAAGCAAC 58.556 45.455 0.00 0.00 0.00 4.17
227 228 1.256812 AAAGGAGCCCCACATTTTCG 58.743 50.000 0.00 0.00 33.88 3.46
246 247 3.429684 GCCTTTCTTGGTCGTTTGGAAAA 60.430 43.478 0.00 0.00 0.00 2.29
270 271 6.974048 CGCATTTTCATTGGATAGTTGAATCA 59.026 34.615 0.00 0.00 0.00 2.57
305 306 1.284198 TCTAGTAGAACCGGCAGGAGT 59.716 52.381 10.86 0.00 41.02 3.85
347 362 4.647424 TTCCACTAGTGCTTTTGTTTGG 57.353 40.909 17.86 0.00 0.00 3.28
349 364 9.167311 CTATCTATTCCACTAGTGCTTTTGTTT 57.833 33.333 17.86 1.35 0.00 2.83
426 444 8.988064 ACTTGAGTTCTTTTTCTTTTTCCTTC 57.012 30.769 0.00 0.00 0.00 3.46
429 447 8.244113 TCAGACTTGAGTTCTTTTTCTTTTTCC 58.756 33.333 0.00 0.00 0.00 3.13
431 449 9.411801 GTTCAGACTTGAGTTCTTTTTCTTTTT 57.588 29.630 0.00 0.00 34.15 1.94
581 1058 3.313526 TCGTGTCTATTAGGCCTACGTTC 59.686 47.826 13.46 3.21 0.00 3.95
582 1059 3.282021 TCGTGTCTATTAGGCCTACGTT 58.718 45.455 13.46 2.98 0.00 3.99
615 1092 2.027625 GGTTTGACAGGGCTCGTCG 61.028 63.158 4.52 0.00 36.11 5.12
647 1126 8.839310 TCTCCTTTTTATCTCTCTCAAAACTG 57.161 34.615 0.00 0.00 0.00 3.16
648 1127 8.100164 CCTCTCCTTTTTATCTCTCTCAAAACT 58.900 37.037 0.00 0.00 0.00 2.66
649 1128 8.097662 TCCTCTCCTTTTTATCTCTCTCAAAAC 58.902 37.037 0.00 0.00 0.00 2.43
652 1131 7.676043 TCTTCCTCTCCTTTTTATCTCTCTCAA 59.324 37.037 0.00 0.00 0.00 3.02
653 1132 7.185565 TCTTCCTCTCCTTTTTATCTCTCTCA 58.814 38.462 0.00 0.00 0.00 3.27
654 1133 7.654022 TCTTCCTCTCCTTTTTATCTCTCTC 57.346 40.000 0.00 0.00 0.00 3.20
655 1134 8.442660 TTTCTTCCTCTCCTTTTTATCTCTCT 57.557 34.615 0.00 0.00 0.00 3.10
662 1141 9.449719 GTATGTCATTTCTTCCTCTCCTTTTTA 57.550 33.333 0.00 0.00 0.00 1.52
664 1143 6.887002 GGTATGTCATTTCTTCCTCTCCTTTT 59.113 38.462 0.00 0.00 0.00 2.27
668 1147 5.359194 TGGTATGTCATTTCTTCCTCTCC 57.641 43.478 0.00 0.00 0.00 3.71
705 1187 2.225727 GCTCGTGGTCTTTTTACTTGGG 59.774 50.000 0.00 0.00 0.00 4.12
1036 1540 1.780309 TGGTGGATGAACTTGGAAGGT 59.220 47.619 0.00 0.00 0.00 3.50
1067 1571 1.403814 TGTAGGAAGCCGAGGATGAG 58.596 55.000 0.00 0.00 0.00 2.90
1068 1572 1.964223 GATGTAGGAAGCCGAGGATGA 59.036 52.381 0.00 0.00 0.00 2.92
1069 1573 1.688735 TGATGTAGGAAGCCGAGGATG 59.311 52.381 0.00 0.00 0.00 3.51
1101 1605 3.365364 GCAGAAATTCAAACGCTAGCTGT 60.365 43.478 13.93 9.71 0.00 4.40
1102 1606 3.120060 AGCAGAAATTCAAACGCTAGCTG 60.120 43.478 13.93 9.03 0.00 4.24
1114 1618 1.529826 CCGCGCTTACAGCAGAAATTC 60.530 52.381 5.56 0.00 42.58 2.17
1115 1619 0.447801 CCGCGCTTACAGCAGAAATT 59.552 50.000 5.56 0.00 42.58 1.82
1119 1623 2.279502 CTACCCGCGCTTACAGCAGA 62.280 60.000 5.56 0.00 42.58 4.26
1120 1624 1.878522 CTACCCGCGCTTACAGCAG 60.879 63.158 5.56 0.00 42.58 4.24
1122 1626 0.940047 GATCTACCCGCGCTTACAGC 60.940 60.000 5.56 0.00 38.02 4.40
1125 1629 0.666913 TCTGATCTACCCGCGCTTAC 59.333 55.000 5.56 0.00 0.00 2.34
1133 1639 1.033574 CGGACACCTCTGATCTACCC 58.966 60.000 0.00 0.00 0.00 3.69
1134 1640 0.386113 GCGGACACCTCTGATCTACC 59.614 60.000 0.00 0.00 0.00 3.18
1135 1641 0.029567 CGCGGACACCTCTGATCTAC 59.970 60.000 0.00 0.00 0.00 2.59
1149 1655 2.101575 GATAGACACACGCGCGGA 59.898 61.111 35.22 10.00 0.00 5.54
1150 1656 1.348538 TTTGATAGACACACGCGCGG 61.349 55.000 35.22 24.36 0.00 6.46
1151 1657 0.246757 GTTTGATAGACACACGCGCG 60.247 55.000 30.96 30.96 0.00 6.86
1153 1659 3.722555 ATTGTTTGATAGACACACGCG 57.277 42.857 3.53 3.53 32.50 6.01
1175 1681 9.116080 ACCCACAAAGATTCCATCATCTATATA 57.884 33.333 0.00 0.00 32.84 0.86
1176 1682 7.993416 ACCCACAAAGATTCCATCATCTATAT 58.007 34.615 0.00 0.00 32.84 0.86
1177 1683 7.392766 ACCCACAAAGATTCCATCATCTATA 57.607 36.000 0.00 0.00 32.84 1.31
1178 1684 6.271585 ACCCACAAAGATTCCATCATCTAT 57.728 37.500 0.00 0.00 32.84 1.98
1179 1685 5.715439 ACCCACAAAGATTCCATCATCTA 57.285 39.130 0.00 0.00 32.84 1.98
1180 1686 4.598036 ACCCACAAAGATTCCATCATCT 57.402 40.909 0.00 0.00 34.78 2.90
1181 1687 4.678840 GCAACCCACAAAGATTCCATCATC 60.679 45.833 0.00 0.00 0.00 2.92
1182 1688 3.196254 GCAACCCACAAAGATTCCATCAT 59.804 43.478 0.00 0.00 0.00 2.45
1183 1689 2.562298 GCAACCCACAAAGATTCCATCA 59.438 45.455 0.00 0.00 0.00 3.07
1184 1690 2.094026 GGCAACCCACAAAGATTCCATC 60.094 50.000 0.00 0.00 0.00 3.51
1185 1691 1.901833 GGCAACCCACAAAGATTCCAT 59.098 47.619 0.00 0.00 0.00 3.41
1186 1692 1.337118 GGCAACCCACAAAGATTCCA 58.663 50.000 0.00 0.00 0.00 3.53
1187 1693 1.337118 TGGCAACCCACAAAGATTCC 58.663 50.000 0.00 0.00 35.79 3.01
1199 1710 6.347696 TGGAATCAATCAATTATTGGCAACC 58.652 36.000 0.00 0.00 44.42 3.77
1207 1718 7.353525 TGGTGTACCTGGAATCAATCAATTAT 58.646 34.615 0.00 0.00 36.82 1.28
1227 1738 3.771479 TGCACTTCTCTATCAGATGGTGT 59.229 43.478 0.00 0.00 37.46 4.16
1337 1848 5.688807 ACTTGCATGCAGTAAGGAAGATAT 58.311 37.500 21.50 0.00 43.37 1.63
1338 1849 5.102953 ACTTGCATGCAGTAAGGAAGATA 57.897 39.130 21.50 0.00 43.37 1.98
1339 1850 3.960571 ACTTGCATGCAGTAAGGAAGAT 58.039 40.909 21.50 2.04 43.37 2.40
1340 1851 3.423539 ACTTGCATGCAGTAAGGAAGA 57.576 42.857 21.50 1.24 43.37 2.87
1393 1904 0.178990 GGCACCACCTCCTTTGTCTT 60.179 55.000 0.00 0.00 34.51 3.01
1419 1932 7.067008 GGACGTATATATATGCTTTGCCCAAAT 59.933 37.037 11.23 0.00 0.00 2.32
1434 1947 9.869667 AGATCTAATTAGGCAGGACGTATATAT 57.130 33.333 12.54 0.00 0.00 0.86
1435 1948 9.696572 AAGATCTAATTAGGCAGGACGTATATA 57.303 33.333 12.54 0.00 0.00 0.86
1436 1949 8.596781 AAGATCTAATTAGGCAGGACGTATAT 57.403 34.615 12.54 0.00 0.00 0.86
1437 1950 7.668469 TGAAGATCTAATTAGGCAGGACGTATA 59.332 37.037 12.54 0.00 0.00 1.47
1457 1970 4.419280 CGATAGCGTCATAGCATGAAGAT 58.581 43.478 13.26 10.45 41.69 2.40
1472 1985 8.425491 CCTTTTATGTGTCTAAATACGATAGCG 58.575 37.037 0.00 0.00 44.79 4.26
1518 2031 9.888496 AATTAAGTCAATTGAGCTGAAGCGCTG 62.888 40.741 12.58 0.00 39.67 5.18
1519 2032 8.009389 AATTAAGTCAATTGAGCTGAAGCGCT 62.009 38.462 8.80 2.64 39.67 5.92
1520 2033 5.901300 AATTAAGTCAATTGAGCTGAAGCGC 60.901 40.000 8.80 0.00 39.67 5.92
1521 2034 5.634896 AATTAAGTCAATTGAGCTGAAGCG 58.365 37.500 8.80 0.00 39.67 4.68
1541 2055 4.800914 GCATAGGGTAGTCTGCGATGAATT 60.801 45.833 0.00 0.00 0.00 2.17
1546 2060 1.704641 TGCATAGGGTAGTCTGCGAT 58.295 50.000 0.00 0.00 37.44 4.58
1555 2069 2.505407 AGAGTTGTGCATGCATAGGGTA 59.495 45.455 25.64 2.61 0.00 3.69
1558 2072 3.441222 TCAAAGAGTTGTGCATGCATAGG 59.559 43.478 25.64 6.46 36.07 2.57
1559 2073 4.690184 TCAAAGAGTTGTGCATGCATAG 57.310 40.909 25.64 7.46 36.07 2.23
1561 2075 3.508402 TCATCAAAGAGTTGTGCATGCAT 59.492 39.130 25.64 7.59 36.07 3.96
1564 2084 3.485633 CGTCATCAAAGAGTTGTGCATG 58.514 45.455 0.00 0.00 36.07 4.06
1565 2085 2.485426 CCGTCATCAAAGAGTTGTGCAT 59.515 45.455 0.00 0.00 36.07 3.96
1573 2093 9.529325 TGTTATAATCTAACCGTCATCAAAGAG 57.471 33.333 0.00 0.00 0.00 2.85
1574 2094 9.309516 GTGTTATAATCTAACCGTCATCAAAGA 57.690 33.333 0.00 0.00 0.00 2.52
1575 2095 9.314321 AGTGTTATAATCTAACCGTCATCAAAG 57.686 33.333 0.00 0.00 0.00 2.77
1580 2100 8.179509 AGCTAGTGTTATAATCTAACCGTCAT 57.820 34.615 0.00 0.00 0.00 3.06
1581 2101 7.578310 AGCTAGTGTTATAATCTAACCGTCA 57.422 36.000 0.00 0.00 0.00 4.35
1583 2103 7.447853 AGCTAGCTAGTGTTATAATCTAACCGT 59.552 37.037 17.69 0.00 0.00 4.83
1594 2114 8.873144 AGTACTACTCTAGCTAGCTAGTGTTAT 58.127 37.037 41.90 34.26 45.41 1.89
1595 2115 8.248904 AGTACTACTCTAGCTAGCTAGTGTTA 57.751 38.462 41.90 32.08 45.41 2.41
1596 2116 7.128234 AGTACTACTCTAGCTAGCTAGTGTT 57.872 40.000 41.90 32.84 45.41 3.32
1649 2174 6.040729 AGTGATCACATCTCTTACATCCTCTG 59.959 42.308 27.02 0.00 29.46 3.35
1653 2178 8.948631 TTTTAGTGATCACATCTCTTACATCC 57.051 34.615 27.02 0.00 35.08 3.51
1664 2191 8.950210 CAGTAAGGTTCATTTTAGTGATCACAT 58.050 33.333 27.02 14.51 33.88 3.21
1681 2209 1.136828 TCCACACTGCCAGTAAGGTT 58.863 50.000 12.76 0.00 40.61 3.50
1851 2379 0.654683 GACATAAGCAGCAGCCTTCG 59.345 55.000 0.00 0.00 43.56 3.79
1852 2380 1.020437 GGACATAAGCAGCAGCCTTC 58.980 55.000 0.00 0.00 43.56 3.46
1853 2381 0.329261 TGGACATAAGCAGCAGCCTT 59.671 50.000 0.00 0.00 43.56 4.35
2240 2780 7.038659 ACATTTTTCGAACCATGACAAGAAAA 58.961 30.769 18.43 11.98 36.29 2.29
2244 2784 6.033831 GCATACATTTTTCGAACCATGACAAG 59.966 38.462 18.43 9.01 0.00 3.16
2264 2804 6.919721 TGTGGAGAATAACCTTTTTGCATAC 58.080 36.000 0.00 0.00 0.00 2.39
2268 2808 6.024552 TCATGTGGAGAATAACCTTTTTGC 57.975 37.500 0.00 0.00 0.00 3.68
2302 2842 4.420522 TGCATCCTTTCTTTTTGGCTTT 57.579 36.364 0.00 0.00 0.00 3.51
2305 2845 7.013655 TCTCTATATGCATCCTTTCTTTTTGGC 59.986 37.037 0.19 0.00 0.00 4.52
2307 2847 9.334947 TCTCTCTATATGCATCCTTTCTTTTTG 57.665 33.333 0.19 0.00 0.00 2.44
2342 2883 6.837992 TCGTTTAAAGACAATTATGAGGCAC 58.162 36.000 0.00 0.00 0.00 5.01
2343 2884 7.389330 TCTTCGTTTAAAGACAATTATGAGGCA 59.611 33.333 0.00 0.00 30.38 4.75
2344 2885 7.748847 TCTTCGTTTAAAGACAATTATGAGGC 58.251 34.615 0.00 0.00 30.38 4.70
2346 2887 7.905493 GGCTCTTCGTTTAAAGACAATTATGAG 59.095 37.037 0.00 0.00 32.03 2.90
2347 2888 7.389330 TGGCTCTTCGTTTAAAGACAATTATGA 59.611 33.333 0.00 0.00 32.03 2.15
2348 2889 7.526608 TGGCTCTTCGTTTAAAGACAATTATG 58.473 34.615 0.00 0.00 32.03 1.90
2349 2890 7.626452 GCTGGCTCTTCGTTTAAAGACAATTAT 60.626 37.037 0.00 0.00 32.03 1.28
2401 2942 4.209703 CACAAAGATTCAGCGCAAATGTTT 59.790 37.500 18.63 18.63 31.85 2.83
2421 2962 2.448926 ACGTATGCTAACTGTGCACA 57.551 45.000 20.37 20.37 43.59 4.57
2471 3012 3.700038 CCTTCTAACCCATAGTCACGTCT 59.300 47.826 0.00 0.00 33.08 4.18
2475 3016 2.822764 CGCCTTCTAACCCATAGTCAC 58.177 52.381 0.00 0.00 33.08 3.67
2494 3035 2.096466 TGCATAAAAAGAGTGACGTGCG 60.096 45.455 0.00 0.00 34.28 5.34
2515 3056 9.561069 AATGAATTAGCGATAATTCTGGTTAGT 57.439 29.630 33.67 17.99 43.34 2.24
2709 3250 5.809001 ACACACAATCATATGAGAACCAGT 58.191 37.500 11.78 3.51 0.00 4.00
2737 3278 6.691508 AGCAAACTTGATTTTGGAATAGTCC 58.308 36.000 1.18 1.18 45.21 3.85
2832 3373 1.302383 TTGCCCTGCAACCGTATTCG 61.302 55.000 0.00 0.00 43.99 3.34
2833 3374 2.562125 TTGCCCTGCAACCGTATTC 58.438 52.632 0.00 0.00 43.99 1.75
2834 3375 4.832741 TTGCCCTGCAACCGTATT 57.167 50.000 0.00 0.00 43.99 1.89


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

AutoCloner maintained by Alex Coulton.