Multiple sequence alignment - TraesCS4D01G017400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G017400 chr4D 100.000 4487 0 0 1 4487 7762160 7757674 0.000000e+00 8287
1 TraesCS4D01G017400 chr4A 93.220 2227 106 27 2283 4487 595845260 595847463 0.000000e+00 3234
2 TraesCS4D01G017400 chr4A 85.305 1048 67 40 209 1173 595843244 595844287 0.000000e+00 1002
3 TraesCS4D01G017400 chr4A 96.203 395 14 1 1802 2195 595844865 595845259 0.000000e+00 645
4 TraesCS4D01G017400 chr4A 82.646 582 42 26 1242 1805 595844299 595844839 1.140000e-125 460
5 TraesCS4D01G017400 chr4A 91.729 133 5 2 14 140 595843088 595843220 3.570000e-41 180
6 TraesCS4D01G017400 chr4A 92.523 107 4 3 2172 2278 597739864 597739966 2.800000e-32 150
7 TraesCS4D01G017400 chr4B 93.100 2232 111 24 2283 4487 13975126 13977341 0.000000e+00 3229
8 TraesCS4D01G017400 chr4B 85.699 930 60 30 930 1805 13973796 13974706 0.000000e+00 913
9 TraesCS4D01G017400 chr4B 97.481 397 10 0 1799 2195 13974729 13975125 0.000000e+00 678
10 TraesCS4D01G017400 chr4B 79.587 823 56 41 21 778 13972932 13973707 1.880000e-133 486
11 TraesCS4D01G017400 chr7D 94.059 101 4 2 2186 2285 141292180 141292081 7.770000e-33 152
12 TraesCS4D01G017400 chr7D 90.000 110 10 1 2184 2293 49381992 49381884 1.680000e-29 141
13 TraesCS4D01G017400 chr2A 94.898 98 3 2 2190 2285 456496727 456496630 7.770000e-33 152
14 TraesCS4D01G017400 chr5D 95.745 94 2 2 2186 2278 294640227 294640319 2.800000e-32 150
15 TraesCS4D01G017400 chr3D 93.814 97 6 0 2190 2286 294583565 294583661 3.620000e-31 147
16 TraesCS4D01G017400 chr3D 92.233 103 6 2 2190 2290 411724340 411724442 1.300000e-30 145
17 TraesCS4D01G017400 chr2D 94.681 94 5 0 2189 2282 331544237 331544144 3.620000e-31 147
18 TraesCS4D01G017400 chr1D 93.000 100 7 0 2190 2289 252473234 252473135 3.620000e-31 147


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 TraesCS4D01G017400 chr4D 7757674 7762160 4486 True 8287.0 8287 100.00000 1 4487 1 chr4D.!!$R1 4486
1 TraesCS4D01G017400 chr4A 595843088 595847463 4375 False 1104.2 3234 89.82060 14 4487 5 chr4A.!!$F2 4473
2 TraesCS4D01G017400 chr4B 13972932 13977341 4409 False 1326.5 3229 88.96675 21 4487 4 chr4B.!!$F1 4466

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
826 914 0.106419 GGGAAACGCCAATGGGGATA 60.106 55.0 23.6 0.0 40.01 2.59 F
1631 1813 0.104090 ACTTGGGGTTGGGAGTAGGT 60.104 55.0 0.0 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 2504 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.0 0.0 0.0 0.0 4.00 R
3616 3864 0.668535 GCAGGAACACCAACCAAGTC 59.331 55.0 0.0 0.0 0.0 3.01 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
91 92 3.452627 TGGTTACAAATGTGGCAAAAGGT 59.547 39.130 0.00 0.00 0.00 3.50
92 93 4.055360 GGTTACAAATGTGGCAAAAGGTC 58.945 43.478 0.00 0.00 0.00 3.85
94 95 1.068434 ACAAATGTGGCAAAAGGTCGG 59.932 47.619 0.00 0.00 0.00 4.79
95 96 1.339610 CAAATGTGGCAAAAGGTCGGA 59.660 47.619 0.00 0.00 0.00 4.55
193 209 3.535962 CGCTCTGCTCTCCCCCTC 61.536 72.222 0.00 0.00 0.00 4.30
194 210 2.042025 GCTCTGCTCTCCCCCTCT 60.042 66.667 0.00 0.00 0.00 3.69
195 211 2.133641 GCTCTGCTCTCCCCCTCTC 61.134 68.421 0.00 0.00 0.00 3.20
196 212 1.457455 CTCTGCTCTCCCCCTCTCC 60.457 68.421 0.00 0.00 0.00 3.71
197 213 2.445654 CTGCTCTCCCCCTCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
198 214 2.955246 TGCTCTCCCCCTCTCCCT 60.955 66.667 0.00 0.00 0.00 4.20
199 215 2.123033 GCTCTCCCCCTCTCCCTC 60.123 72.222 0.00 0.00 0.00 4.30
200 216 2.710826 GCTCTCCCCCTCTCCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
201 217 1.541672 CTCTCCCCCTCTCCCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
202 218 2.015726 TCTCCCCCTCTCCCTCTCC 61.016 68.421 0.00 0.00 0.00 3.71
203 219 3.036959 TCCCCCTCTCCCTCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
285 301 1.153289 CGGGAGGACAGCAATGGAG 60.153 63.158 0.00 0.00 0.00 3.86
286 302 1.452833 GGGAGGACAGCAATGGAGC 60.453 63.158 0.00 0.00 0.00 4.70
337 357 2.415843 GCGTGTAGCGGCTATCCA 59.584 61.111 13.60 4.58 41.69 3.41
338 358 1.949631 GCGTGTAGCGGCTATCCAC 60.950 63.158 13.60 15.41 41.69 4.02
339 359 1.657487 CGTGTAGCGGCTATCCACG 60.657 63.158 27.39 27.39 42.19 4.94
399 428 1.373570 GATCGTTTCTTGGCTCCTGG 58.626 55.000 0.00 0.00 0.00 4.45
538 580 1.248486 GGTGGGGTTTCTTGCTCTTC 58.752 55.000 0.00 0.00 0.00 2.87
539 581 1.202940 GGTGGGGTTTCTTGCTCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
547 619 2.867109 TCTTGCTCTTCTTCTTGGGG 57.133 50.000 0.00 0.00 0.00 4.96
557 629 1.073923 TCTTCTTGGGGGCTTCTGTTC 59.926 52.381 0.00 0.00 0.00 3.18
558 630 0.112412 TTCTTGGGGGCTTCTGTTCC 59.888 55.000 0.00 0.00 0.00 3.62
565 638 0.969149 GGGCTTCTGTTCCCCTTTTG 59.031 55.000 0.00 0.00 36.50 2.44
567 640 1.332195 GCTTCTGTTCCCCTTTTGCT 58.668 50.000 0.00 0.00 0.00 3.91
570 643 0.850100 TCTGTTCCCCTTTTGCTCCA 59.150 50.000 0.00 0.00 0.00 3.86
571 644 0.961753 CTGTTCCCCTTTTGCTCCAC 59.038 55.000 0.00 0.00 0.00 4.02
574 647 0.555769 TTCCCCTTTTGCTCCACTGT 59.444 50.000 0.00 0.00 0.00 3.55
576 649 0.675633 CCCCTTTTGCTCCACTGTTG 59.324 55.000 0.00 0.00 0.00 3.33
577 650 1.691196 CCCTTTTGCTCCACTGTTGA 58.309 50.000 0.00 0.00 0.00 3.18
578 651 1.338020 CCCTTTTGCTCCACTGTTGAC 59.662 52.381 0.00 0.00 0.00 3.18
579 652 1.002468 CCTTTTGCTCCACTGTTGACG 60.002 52.381 0.00 0.00 0.00 4.35
580 653 0.380378 TTTTGCTCCACTGTTGACGC 59.620 50.000 0.00 0.00 0.00 5.19
582 655 3.414700 GCTCCACTGTTGACGCGG 61.415 66.667 12.47 0.00 0.00 6.46
583 656 3.414700 CTCCACTGTTGACGCGGC 61.415 66.667 12.47 8.67 0.00 6.53
625 703 4.374702 CGCGCGGCTGCATTATCC 62.375 66.667 24.84 0.00 42.97 2.59
674 752 3.830192 GCCCGCCCTGCTGATTTG 61.830 66.667 0.00 0.00 0.00 2.32
686 764 0.454957 CTGATTTGTTCCGGCAAGCG 60.455 55.000 0.00 0.00 0.00 4.68
715 793 2.816958 AATGCGCTCGCTCACAGG 60.817 61.111 9.73 0.00 42.51 4.00
774 860 2.046285 TCAGGAGCGCGTCTGATCA 61.046 57.895 24.56 9.36 35.37 2.92
784 870 0.467384 CGTCTGATCAGATTGGGGCT 59.533 55.000 27.51 0.00 39.97 5.19
787 873 2.172293 GTCTGATCAGATTGGGGCTTCT 59.828 50.000 27.51 0.00 39.97 2.85
803 889 3.382832 CTGCCTTCTCGACCGGGT 61.383 66.667 6.32 0.00 0.00 5.28
811 899 4.304413 TCGACCGGGTCAGGGGAA 62.304 66.667 25.80 2.10 35.02 3.97
826 914 0.106419 GGGAAACGCCAATGGGGATA 60.106 55.000 23.60 0.00 40.01 2.59
835 923 3.560025 CGCCAATGGGGATAGATAGCTTT 60.560 47.826 11.24 0.00 40.01 3.51
836 924 4.013050 GCCAATGGGGATAGATAGCTTTC 58.987 47.826 0.00 0.00 40.01 2.62
853 944 2.524569 TTCCGCGATGATCATAGCAA 57.475 45.000 31.58 20.50 39.02 3.91
859 950 1.723542 CGATGATCATAGCAAGCCGTC 59.276 52.381 8.54 0.00 0.00 4.79
862 953 4.560128 GATGATCATAGCAAGCCGTCTAA 58.440 43.478 8.54 0.00 0.00 2.10
876 967 7.574496 CAAGCCGTCTAATAGTAGTAGTAGTG 58.426 42.308 10.92 6.18 30.33 2.74
877 968 5.700373 AGCCGTCTAATAGTAGTAGTAGTGC 59.300 44.000 10.92 11.58 30.33 4.40
878 969 5.389307 GCCGTCTAATAGTAGTAGTAGTGCG 60.389 48.000 10.92 14.36 30.33 5.34
879 970 5.694006 CCGTCTAATAGTAGTAGTAGTGCGT 59.306 44.000 19.41 0.00 31.31 5.24
880 971 6.346439 CCGTCTAATAGTAGTAGTAGTGCGTG 60.346 46.154 19.41 12.72 31.31 5.34
881 972 6.199908 CGTCTAATAGTAGTAGTAGTGCGTGT 59.800 42.308 10.92 0.00 30.33 4.49
882 973 7.254252 CGTCTAATAGTAGTAGTAGTGCGTGTT 60.254 40.741 10.92 0.00 30.33 3.32
883 974 7.850003 GTCTAATAGTAGTAGTAGTGCGTGTTG 59.150 40.741 10.92 0.00 30.33 3.33
884 975 3.844577 AGTAGTAGTAGTGCGTGTTGG 57.155 47.619 0.00 0.00 0.00 3.77
885 976 3.415212 AGTAGTAGTAGTGCGTGTTGGA 58.585 45.455 0.00 0.00 0.00 3.53
886 977 3.439476 AGTAGTAGTAGTGCGTGTTGGAG 59.561 47.826 0.00 0.00 0.00 3.86
887 978 1.544691 AGTAGTAGTGCGTGTTGGAGG 59.455 52.381 0.00 0.00 0.00 4.30
888 979 0.245539 TAGTAGTGCGTGTTGGAGGC 59.754 55.000 0.00 0.00 35.92 4.70
927 1035 2.750237 GGGTGTTCCGTGGGATGC 60.750 66.667 0.00 0.00 33.83 3.91
932 1051 0.327924 TGTTCCGTGGGATGCTGAAT 59.672 50.000 0.00 0.00 0.00 2.57
935 1054 0.178767 TCCGTGGGATGCTGAATGAG 59.821 55.000 0.00 0.00 0.00 2.90
952 1074 0.659957 GAGCGAATGCAGGTTCATCC 59.340 55.000 0.00 0.00 46.23 3.51
964 1086 3.034635 AGGTTCATCCTCTCAGCGTATT 58.965 45.455 0.00 0.00 44.42 1.89
965 1087 3.452627 AGGTTCATCCTCTCAGCGTATTT 59.547 43.478 0.00 0.00 44.42 1.40
982 1109 2.686558 TTTTTCTGTGACGATGCAGC 57.313 45.000 0.00 0.00 33.09 5.25
998 1125 0.179215 CAGCTGTTTTGATCCGCGAC 60.179 55.000 8.23 0.00 0.00 5.19
999 1126 1.134694 GCTGTTTTGATCCGCGACC 59.865 57.895 8.23 0.00 0.00 4.79
1143 1270 2.278245 TCATCCATCCCTGTGGTTTCT 58.722 47.619 0.00 0.00 40.27 2.52
1151 1278 4.903045 TCCCTGTGGTTTCTAAGTTAGG 57.097 45.455 10.02 0.00 0.00 2.69
1152 1279 4.495565 TCCCTGTGGTTTCTAAGTTAGGA 58.504 43.478 10.02 0.00 0.00 2.94
1157 1284 6.940298 CCTGTGGTTTCTAAGTTAGGATTGAA 59.060 38.462 10.02 0.00 0.00 2.69
1158 1285 7.611855 CCTGTGGTTTCTAAGTTAGGATTGAAT 59.388 37.037 10.02 0.00 0.00 2.57
1161 1288 8.244113 GTGGTTTCTAAGTTAGGATTGAATTGG 58.756 37.037 10.02 0.00 0.00 3.16
1175 1303 5.975693 TTGAATTGGTGATTGTAACCCTC 57.024 39.130 0.00 0.00 36.83 4.30
1182 1310 3.055385 GGTGATTGTAACCCTCTGCTACA 60.055 47.826 0.00 0.00 0.00 2.74
1184 1312 4.572389 GTGATTGTAACCCTCTGCTACATG 59.428 45.833 0.00 0.00 0.00 3.21
1203 1331 5.051816 ACATGTTTCTGCCTTGTTGATTTG 58.948 37.500 0.00 0.00 0.00 2.32
1206 1334 5.108517 TGTTTCTGCCTTGTTGATTTGTTC 58.891 37.500 0.00 0.00 0.00 3.18
1335 1477 5.499004 AGTTGCCACAAATAGGACTAGAA 57.501 39.130 0.00 0.00 0.00 2.10
1443 1596 8.648693 AGTTAAAGTCCTGTTGAACATAGTACT 58.351 33.333 0.00 0.00 0.00 2.73
1444 1597 9.918630 GTTAAAGTCCTGTTGAACATAGTACTA 57.081 33.333 4.77 4.77 0.00 1.82
1445 1598 9.918630 TTAAAGTCCTGTTGAACATAGTACTAC 57.081 33.333 4.31 0.00 0.00 2.73
1446 1599 7.778185 AAGTCCTGTTGAACATAGTACTACT 57.222 36.000 4.31 0.00 0.00 2.57
1447 1600 8.874744 AAGTCCTGTTGAACATAGTACTACTA 57.125 34.615 4.31 0.00 34.82 1.82
1448 1601 8.874744 AGTCCTGTTGAACATAGTACTACTAA 57.125 34.615 4.31 0.00 33.89 2.24
1449 1602 9.476928 AGTCCTGTTGAACATAGTACTACTAAT 57.523 33.333 4.31 0.00 33.89 1.73
1465 1622 9.668497 GTACTACTAATTTTTCCTCTTCACCAT 57.332 33.333 0.00 0.00 0.00 3.55
1534 1709 3.314357 AGTCTGCGAAAGTTTAAACACCC 59.686 43.478 20.06 7.33 0.00 4.61
1541 1716 7.266400 TGCGAAAGTTTAAACACCCTTAAAAT 58.734 30.769 20.06 0.00 33.66 1.82
1543 1718 7.095940 GCGAAAGTTTAAACACCCTTAAAATCC 60.096 37.037 20.06 0.00 33.66 3.01
1546 1721 8.951787 AAGTTTAAACACCCTTAAAATCCAAC 57.048 30.769 20.06 0.00 33.66 3.77
1628 1810 1.854280 ACAAACTTGGGGTTGGGAGTA 59.146 47.619 0.00 0.00 38.29 2.59
1629 1811 2.158519 ACAAACTTGGGGTTGGGAGTAG 60.159 50.000 0.00 0.00 38.29 2.57
1630 1812 1.073098 AACTTGGGGTTGGGAGTAGG 58.927 55.000 0.00 0.00 36.70 3.18
1631 1813 0.104090 ACTTGGGGTTGGGAGTAGGT 60.104 55.000 0.00 0.00 0.00 3.08
1632 1814 0.328258 CTTGGGGTTGGGAGTAGGTG 59.672 60.000 0.00 0.00 0.00 4.00
1633 1815 0.104356 TTGGGGTTGGGAGTAGGTGA 60.104 55.000 0.00 0.00 0.00 4.02
1634 1816 0.838987 TGGGGTTGGGAGTAGGTGAC 60.839 60.000 0.00 0.00 0.00 3.67
1636 1818 1.359168 GGGTTGGGAGTAGGTGACTT 58.641 55.000 0.00 0.00 43.67 3.01
1637 1819 2.543635 GGGTTGGGAGTAGGTGACTTA 58.456 52.381 0.00 0.00 43.67 2.24
1638 1820 2.908351 GGGTTGGGAGTAGGTGACTTAA 59.092 50.000 0.00 0.00 43.67 1.85
1639 1821 3.307269 GGGTTGGGAGTAGGTGACTTAAC 60.307 52.174 0.00 0.00 43.67 2.01
1640 1822 3.307269 GGTTGGGAGTAGGTGACTTAACC 60.307 52.174 0.00 0.00 43.67 2.85
1641 1823 2.173519 TGGGAGTAGGTGACTTAACCG 58.826 52.381 0.00 0.00 45.53 4.44
1642 1824 2.174360 GGGAGTAGGTGACTTAACCGT 58.826 52.381 0.00 0.00 45.53 4.83
1643 1825 3.245229 TGGGAGTAGGTGACTTAACCGTA 60.245 47.826 0.00 0.00 45.53 4.02
1644 1826 3.379688 GGGAGTAGGTGACTTAACCGTAG 59.620 52.174 0.00 0.00 45.53 3.51
1761 1944 1.546029 CCGCTGGCTGCTGTCTATATA 59.454 52.381 14.58 0.00 40.11 0.86
1790 1973 1.608590 CCAGCGTCAACCACTTTTGAT 59.391 47.619 0.00 0.00 37.80 2.57
1869 2112 0.733150 TCACACGGATACTGAGCTCG 59.267 55.000 9.64 6.63 0.00 5.03
1872 2115 1.544691 ACACGGATACTGAGCTCGTTT 59.455 47.619 9.64 5.38 31.35 3.60
2108 2351 5.877012 TGTTGCATCTACAGATCTTTTCTCC 59.123 40.000 0.00 0.00 31.21 3.71
2195 2438 5.093849 TGGCTAACCCTCTTAACATGTAC 57.906 43.478 0.00 0.00 33.59 2.90
2196 2439 4.781087 TGGCTAACCCTCTTAACATGTACT 59.219 41.667 0.00 0.00 33.59 2.73
2197 2440 5.105064 TGGCTAACCCTCTTAACATGTACTC 60.105 44.000 0.00 0.00 33.59 2.59
2198 2441 5.358090 GCTAACCCTCTTAACATGTACTCC 58.642 45.833 0.00 0.00 0.00 3.85
2199 2442 4.838904 AACCCTCTTAACATGTACTCCC 57.161 45.455 0.00 0.00 0.00 4.30
2200 2443 4.076175 ACCCTCTTAACATGTACTCCCT 57.924 45.455 0.00 0.00 0.00 4.20
2201 2444 4.031611 ACCCTCTTAACATGTACTCCCTC 58.968 47.826 0.00 0.00 0.00 4.30
2202 2445 3.388350 CCCTCTTAACATGTACTCCCTCC 59.612 52.174 0.00 0.00 0.00 4.30
2203 2446 3.068307 CCTCTTAACATGTACTCCCTCCG 59.932 52.174 0.00 0.00 0.00 4.63
2204 2447 3.700038 CTCTTAACATGTACTCCCTCCGT 59.300 47.826 0.00 0.00 0.00 4.69
2205 2448 3.698040 TCTTAACATGTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
2206 2449 1.192428 AACATGTACTCCCTCCGTCC 58.808 55.000 0.00 0.00 0.00 4.79
2207 2450 0.686769 ACATGTACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
2208 2451 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
2209 2452 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
2210 2453 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
2211 2454 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
2212 2455 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
2213 2456 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
2214 2457 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2215 2458 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2216 2459 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2217 2460 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2218 2461 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2219 2462 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2220 2463 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2221 2464 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2222 2465 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2223 2466 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2224 2467 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2225 2468 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2226 2469 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2252 2495 9.938280 TTATACTACACTAGTGTCAAAAATGCT 57.062 29.630 31.11 6.17 43.74 3.79
2253 2496 6.787085 ACTACACTAGTGTCAAAAATGCTC 57.213 37.500 31.11 0.00 43.74 4.26
2254 2497 6.525629 ACTACACTAGTGTCAAAAATGCTCT 58.474 36.000 31.11 5.44 43.74 4.09
2255 2498 6.992715 ACTACACTAGTGTCAAAAATGCTCTT 59.007 34.615 31.11 4.99 43.74 2.85
2256 2499 8.148351 ACTACACTAGTGTCAAAAATGCTCTTA 58.852 33.333 31.11 8.36 43.74 2.10
2257 2500 7.986085 ACACTAGTGTCAAAAATGCTCTTAT 57.014 32.000 22.95 0.00 40.24 1.73
2259 2502 9.672673 ACACTAGTGTCAAAAATGCTCTTATAT 57.327 29.630 22.95 0.00 40.24 0.86
2265 2508 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
2266 2509 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
2267 2510 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
2268 2511 8.783093 TCAAAAATGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
2269 2512 7.687941 AAAATGCTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 0.00 4.79
2270 2513 6.620877 AATGCTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
2271 2514 5.661056 TGCTCTTATATTATGGGACGGAG 57.339 43.478 0.00 0.00 0.00 4.63
2272 2515 4.466370 TGCTCTTATATTATGGGACGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
2273 2516 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2274 2517 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2275 2518 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2276 2519 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2277 2520 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2278 2521 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
2279 2522 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
2280 2523 0.338814 ATGGGACGGAGGGAGTACTT 59.661 55.000 0.00 0.00 0.00 2.24
2281 2524 0.613853 TGGGACGGAGGGAGTACTTG 60.614 60.000 0.00 0.00 0.00 3.16
2291 2534 5.163447 CGGAGGGAGTACTTGTTATGATTGA 60.163 44.000 0.00 0.00 0.00 2.57
2329 2573 8.828644 TGTACTTTTATGCTCGACTTTTGTTTA 58.171 29.630 0.00 0.00 0.00 2.01
2465 2709 8.723365 TGGAATATGTAGGTGACCAAATCTTAT 58.277 33.333 3.63 0.00 0.00 1.73
2559 2803 0.871722 TTGGCAACGATTCGGTTCAG 59.128 50.000 11.29 0.00 42.51 3.02
2564 2808 3.372822 GGCAACGATTCGGTTCAGAATAA 59.627 43.478 11.29 0.00 40.58 1.40
2630 2875 5.008217 GTGACTTGCAACTGTTATGGTTGTA 59.992 40.000 0.00 1.59 43.93 2.41
2686 2931 3.000041 TCTGGTTGCAATAGCTTACACG 59.000 45.455 0.59 0.00 42.74 4.49
2828 3073 7.440523 AATTTCTCCTGTAGTGTTGATTGTC 57.559 36.000 0.00 0.00 0.00 3.18
3047 3294 8.752766 AATTGAAGAACTGCTTTACATTCATG 57.247 30.769 0.00 0.00 36.83 3.07
3159 3406 3.320610 TTTGGTGGTGGGATCTTTTCA 57.679 42.857 0.00 0.00 0.00 2.69
3212 3459 5.047092 CAGGTGGCAAGGATATTTTTGTTCT 60.047 40.000 0.00 0.00 0.00 3.01
3275 3522 8.986991 AGGTACTAGAGATCTTCATTGAAATGT 58.013 33.333 0.00 0.00 36.02 2.71
3338 3585 7.626452 GCCATCTGACACAATTTTACCTACTTC 60.626 40.741 0.00 0.00 0.00 3.01
3440 3687 4.217334 TGTCATGAACGCAATGTGGTTTAT 59.783 37.500 0.00 0.00 0.00 1.40
3459 3706 6.873605 GGTTTATGAAGATTTTGAAAGGGGTG 59.126 38.462 0.00 0.00 0.00 4.61
3483 3730 3.942115 TGAAAACACTGTCGAAATGGTCA 59.058 39.130 0.00 0.00 0.00 4.02
3503 3751 3.578282 TCATAATCGGATTAGGCTCTGCA 59.422 43.478 15.55 0.00 0.00 4.41
3519 3767 1.813092 CTGCAGACCAGAAGTGCAACT 60.813 52.381 8.42 0.00 46.16 3.16
3537 3785 1.774856 ACTTAACTGGGTGTTCCTGCT 59.225 47.619 0.00 0.00 39.89 4.24
3567 3815 0.650512 GCGTGTGACCCGAATATGTG 59.349 55.000 0.00 0.00 0.00 3.21
3616 3864 2.048877 ACCGGAAGTACAACGCCG 60.049 61.111 9.46 2.19 39.46 6.46
3820 4078 2.158755 GCAATCTGTGTATACCAGGCCT 60.159 50.000 0.00 0.00 0.00 5.19
3839 4097 3.005155 GCCTGGAGATAATTCCATTGCAC 59.995 47.826 0.00 0.00 45.80 4.57
3974 4237 3.073209 TGCACATTACCTGTTTCCTGGTA 59.927 43.478 0.00 0.00 42.37 3.25
4000 4263 4.789095 TTTGTTATATTCGCTCTTCGCC 57.211 40.909 0.00 0.00 38.27 5.54
4003 4266 0.312729 TATATTCGCTCTTCGCCGCA 59.687 50.000 0.00 0.00 38.27 5.69
4030 4293 9.872721 AAAAATTGGTTGAAATTTTCTGCAAAT 57.127 22.222 10.33 5.76 44.84 2.32
4066 4333 7.777910 ACTAATCCCATCGAACATAAAATTCCA 59.222 33.333 0.00 0.00 0.00 3.53
4069 4336 5.034152 CCCATCGAACATAAAATTCCAACG 58.966 41.667 0.00 0.00 0.00 4.10
4101 4368 5.814188 TGCAGCTGTATTCTCTGTTGAATAG 59.186 40.000 16.64 0.00 38.93 1.73
4108 4375 7.847096 TGTATTCTCTGTTGAATAGCCTGTTA 58.153 34.615 0.00 0.00 38.93 2.41
4132 4399 7.664082 ACATACTCTCTGAACATCAAACTTG 57.336 36.000 0.00 0.00 0.00 3.16
4135 4402 3.754965 TCTCTGAACATCAAACTTGGGG 58.245 45.455 0.00 0.00 0.00 4.96
4136 4403 3.394274 TCTCTGAACATCAAACTTGGGGA 59.606 43.478 0.00 0.00 0.00 4.81
4137 4404 3.754965 TCTGAACATCAAACTTGGGGAG 58.245 45.455 0.00 0.00 0.00 4.30
4138 4405 2.229784 CTGAACATCAAACTTGGGGAGC 59.770 50.000 0.00 0.00 0.00 4.70
4151 4430 1.271543 TGGGGAGCAGACACAATCAAG 60.272 52.381 0.00 0.00 0.00 3.02
4193 4472 5.712217 CGCTTACGAATTTTGGTATCTCA 57.288 39.130 0.00 0.00 43.93 3.27
4194 4473 5.490213 CGCTTACGAATTTTGGTATCTCAC 58.510 41.667 0.00 0.00 43.93 3.51
4195 4474 5.291128 CGCTTACGAATTTTGGTATCTCACT 59.709 40.000 0.00 0.00 43.93 3.41
4196 4475 6.183360 CGCTTACGAATTTTGGTATCTCACTT 60.183 38.462 0.00 0.00 43.93 3.16
4197 4476 6.961554 GCTTACGAATTTTGGTATCTCACTTG 59.038 38.462 0.00 0.00 0.00 3.16
4198 4477 5.296813 ACGAATTTTGGTATCTCACTTGC 57.703 39.130 0.00 0.00 0.00 4.01
4199 4478 4.142902 ACGAATTTTGGTATCTCACTTGCG 60.143 41.667 0.00 0.00 0.00 4.85
4200 4479 4.092821 CGAATTTTGGTATCTCACTTGCGA 59.907 41.667 0.00 0.00 0.00 5.10
4201 4480 5.220662 CGAATTTTGGTATCTCACTTGCGAT 60.221 40.000 0.00 0.00 0.00 4.58
4202 4481 6.019075 CGAATTTTGGTATCTCACTTGCGATA 60.019 38.462 0.00 0.00 0.00 2.92
4203 4482 7.307396 CGAATTTTGGTATCTCACTTGCGATAT 60.307 37.037 0.00 0.00 0.00 1.63
4204 4483 6.844696 TTTTGGTATCTCACTTGCGATATC 57.155 37.500 0.00 0.00 0.00 1.63
4205 4484 5.791336 TTGGTATCTCACTTGCGATATCT 57.209 39.130 0.34 0.00 0.00 1.98
4206 4485 5.126396 TGGTATCTCACTTGCGATATCTG 57.874 43.478 0.34 0.00 0.00 2.90
4207 4486 4.827284 TGGTATCTCACTTGCGATATCTGA 59.173 41.667 0.34 0.00 0.00 3.27
4208 4487 5.301805 TGGTATCTCACTTGCGATATCTGAA 59.698 40.000 0.34 0.00 0.00 3.02
4209 4488 6.183360 TGGTATCTCACTTGCGATATCTGAAA 60.183 38.462 0.34 0.00 0.00 2.69
4210 4489 6.701841 GGTATCTCACTTGCGATATCTGAAAA 59.298 38.462 0.34 0.00 0.00 2.29
4218 4497 3.565482 TGCGATATCTGAAAAGGCATTCC 59.435 43.478 0.34 0.00 0.00 3.01
4251 4530 4.820284 TTACATGACAAACGCATGAACA 57.180 36.364 10.22 2.26 44.49 3.18
4288 4568 1.877165 GGCACGGTAGCGCTTAGAC 60.877 63.158 18.68 7.97 34.64 2.59
4326 4606 1.003580 AGGATCAAGAGGCGCTTTCAA 59.996 47.619 7.64 0.00 33.60 2.69
4464 4744 2.066999 GGAGAGAACCATCCCCGCT 61.067 63.158 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.647067 CAGTAGTTTAGCACTCTTTAGCAAGT 59.353 38.462 0.00 0.00 36.88 3.16
1 2 6.091441 CCAGTAGTTTAGCACTCTTTAGCAAG 59.909 42.308 0.00 0.00 36.88 4.01
2 3 5.932303 CCAGTAGTTTAGCACTCTTTAGCAA 59.068 40.000 0.00 0.00 36.88 3.91
3 4 5.011738 ACCAGTAGTTTAGCACTCTTTAGCA 59.988 40.000 0.00 0.00 36.88 3.49
4 5 5.480205 ACCAGTAGTTTAGCACTCTTTAGC 58.520 41.667 0.00 0.00 36.88 3.09
5 6 5.800941 CGACCAGTAGTTTAGCACTCTTTAG 59.199 44.000 0.00 0.00 36.88 1.85
6 7 5.474532 TCGACCAGTAGTTTAGCACTCTTTA 59.525 40.000 0.00 0.00 36.88 1.85
7 8 4.280174 TCGACCAGTAGTTTAGCACTCTTT 59.720 41.667 0.00 0.00 36.88 2.52
8 9 3.825014 TCGACCAGTAGTTTAGCACTCTT 59.175 43.478 0.00 0.00 36.88 2.85
9 10 3.190953 GTCGACCAGTAGTTTAGCACTCT 59.809 47.826 3.51 0.00 36.88 3.24
10 11 3.057736 TGTCGACCAGTAGTTTAGCACTC 60.058 47.826 14.12 0.00 36.88 3.51
11 12 2.889045 TGTCGACCAGTAGTTTAGCACT 59.111 45.455 14.12 0.00 39.87 4.40
12 13 2.985139 GTGTCGACCAGTAGTTTAGCAC 59.015 50.000 14.12 0.00 0.00 4.40
91 92 2.374525 CCACCACCCATCCATCCGA 61.375 63.158 0.00 0.00 0.00 4.55
92 93 2.192979 CCACCACCCATCCATCCG 59.807 66.667 0.00 0.00 0.00 4.18
94 95 1.754234 GTGCCACCACCCATCCATC 60.754 63.158 0.00 0.00 35.92 3.51
95 96 2.360191 GTGCCACCACCCATCCAT 59.640 61.111 0.00 0.00 35.92 3.41
186 202 3.036959 GGGAGAGGGAGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
192 208 0.996762 GAGGGAGAGGGAGAGGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
193 209 0.998945 AGAGGGAGAGGGAGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
194 210 0.996762 GAGAGGGAGAGGGAGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
195 211 1.541672 GAGAGGGAGAGGGAGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
196 212 1.541672 GGAGAGGGAGAGGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
197 213 1.541672 GGGAGAGGGAGAGGGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
198 214 2.015726 GGGGAGAGGGAGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
199 215 2.612251 GGGGAGAGGGAGAGGGAG 59.388 72.222 0.00 0.00 0.00 4.30
200 216 3.036959 GGGGGAGAGGGAGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
201 217 3.368501 TGGGGGAGAGGGAGAGGG 61.369 72.222 0.00 0.00 0.00 4.30
202 218 2.041405 GTGGGGGAGAGGGAGAGG 60.041 72.222 0.00 0.00 0.00 3.69
203 219 2.041405 GGTGGGGGAGAGGGAGAG 60.041 72.222 0.00 0.00 0.00 3.20
328 348 3.214250 GAGGGAGCGTGGATAGCCG 62.214 68.421 0.00 0.00 36.79 5.52
331 351 2.210711 GGGGAGGGAGCGTGGATAG 61.211 68.421 0.00 0.00 0.00 2.08
332 352 2.122989 GGGGAGGGAGCGTGGATA 60.123 66.667 0.00 0.00 0.00 2.59
416 445 2.359975 GAGGGGCCGGTCAACAAG 60.360 66.667 9.07 0.00 0.00 3.16
417 446 2.852075 AGAGGGGCCGGTCAACAA 60.852 61.111 9.07 0.00 0.00 2.83
470 499 1.556451 GGAAGCCAGCCAAATCCAAAT 59.444 47.619 0.00 0.00 0.00 2.32
538 580 1.539157 GAACAGAAGCCCCCAAGAAG 58.461 55.000 0.00 0.00 0.00 2.85
539 581 0.112412 GGAACAGAAGCCCCCAAGAA 59.888 55.000 0.00 0.00 0.00 2.52
547 619 0.318441 GCAAAAGGGGAACAGAAGCC 59.682 55.000 0.00 0.00 0.00 4.35
557 629 0.675633 CAACAGTGGAGCAAAAGGGG 59.324 55.000 0.00 0.00 0.00 4.79
558 630 1.338020 GTCAACAGTGGAGCAAAAGGG 59.662 52.381 0.00 0.00 0.00 3.95
560 632 1.597937 GCGTCAACAGTGGAGCAAAAG 60.598 52.381 0.00 0.00 0.00 2.27
565 638 3.414700 CCGCGTCAACAGTGGAGC 61.415 66.667 4.92 0.00 41.54 4.70
579 652 4.404654 CCAAAAGGAGCACGCCGC 62.405 66.667 0.00 0.00 42.91 6.53
580 653 4.404654 GCCAAAAGGAGCACGCCG 62.405 66.667 0.00 0.00 0.00 6.46
582 655 4.404654 CGGCCAAAAGGAGCACGC 62.405 66.667 2.24 0.00 0.00 5.34
583 656 2.070654 AAACGGCCAAAAGGAGCACG 62.071 55.000 2.24 0.00 0.00 5.34
584 657 0.597377 CAAACGGCCAAAAGGAGCAC 60.597 55.000 2.24 0.00 0.00 4.40
585 658 1.739049 CAAACGGCCAAAAGGAGCA 59.261 52.632 2.24 0.00 0.00 4.26
589 667 0.038618 GCTACCAAACGGCCAAAAGG 60.039 55.000 2.24 0.95 0.00 3.11
668 746 1.578926 CGCTTGCCGGAACAAATCA 59.421 52.632 5.05 0.00 0.00 2.57
692 770 2.432456 AGCGAGCGCATTGACGAA 60.432 55.556 17.68 0.00 44.88 3.85
747 833 1.148157 CGCGCTCCTGACAAATCGAT 61.148 55.000 5.56 0.00 0.00 3.59
756 842 1.997928 CTGATCAGACGCGCTCCTGA 61.998 60.000 24.08 24.08 42.78 3.86
784 870 2.646175 CCCGGTCGAGAAGGCAGAA 61.646 63.158 0.00 0.00 0.00 3.02
787 873 3.379445 GACCCGGTCGAGAAGGCA 61.379 66.667 0.65 0.00 0.00 4.75
803 889 1.304052 CCATTGGCGTTTCCCCTGA 60.304 57.895 0.00 0.00 0.00 3.86
811 899 2.290323 GCTATCTATCCCCATTGGCGTT 60.290 50.000 0.00 0.00 0.00 4.84
826 914 2.297315 TGATCATCGCGGAAAGCTATCT 59.703 45.455 6.13 0.00 45.59 1.98
835 923 1.936656 GCTTGCTATGATCATCGCGGA 60.937 52.381 22.78 14.86 32.80 5.54
836 924 0.441533 GCTTGCTATGATCATCGCGG 59.558 55.000 22.78 18.89 32.80 6.46
853 944 5.700373 GCACTACTACTACTATTAGACGGCT 59.300 44.000 0.00 0.00 0.00 5.52
859 950 7.011763 TCCAACACGCACTACTACTACTATTAG 59.988 40.741 0.00 0.00 0.00 1.73
862 953 5.188434 TCCAACACGCACTACTACTACTAT 58.812 41.667 0.00 0.00 0.00 2.12
910 1018 2.750237 GCATCCCACGGAACACCC 60.750 66.667 0.00 0.00 34.34 4.61
927 1035 1.376543 ACCTGCATTCGCTCATTCAG 58.623 50.000 0.00 0.00 39.64 3.02
932 1051 1.372582 GATGAACCTGCATTCGCTCA 58.627 50.000 0.00 0.00 39.64 4.26
952 1074 4.201532 CGTCACAGAAAAATACGCTGAGAG 60.202 45.833 0.00 0.00 31.60 3.20
964 1086 1.532437 CAGCTGCATCGTCACAGAAAA 59.468 47.619 0.00 0.00 35.90 2.29
965 1087 1.150827 CAGCTGCATCGTCACAGAAA 58.849 50.000 0.00 0.00 35.90 2.52
982 1109 1.086696 ATGGTCGCGGATCAAAACAG 58.913 50.000 6.13 0.00 0.00 3.16
999 1126 4.624364 TAGGCCGCCATCGCCATG 62.624 66.667 13.15 0.00 35.38 3.66
1143 1270 8.877864 ACAATCACCAATTCAATCCTAACTTA 57.122 30.769 0.00 0.00 0.00 2.24
1151 1278 6.378280 AGAGGGTTACAATCACCAATTCAATC 59.622 38.462 0.00 0.00 35.80 2.67
1152 1279 6.153340 CAGAGGGTTACAATCACCAATTCAAT 59.847 38.462 0.00 0.00 35.80 2.57
1157 1284 3.010584 AGCAGAGGGTTACAATCACCAAT 59.989 43.478 0.00 0.00 35.80 3.16
1158 1285 2.375174 AGCAGAGGGTTACAATCACCAA 59.625 45.455 0.00 0.00 35.80 3.67
1161 1288 4.202245 TGTAGCAGAGGGTTACAATCAC 57.798 45.455 0.00 0.00 39.80 3.06
1175 1303 2.816087 ACAAGGCAGAAACATGTAGCAG 59.184 45.455 0.00 0.00 0.00 4.24
1182 1310 5.280654 ACAAATCAACAAGGCAGAAACAT 57.719 34.783 0.00 0.00 0.00 2.71
1184 1312 5.108517 TGAACAAATCAACAAGGCAGAAAC 58.891 37.500 0.00 0.00 34.30 2.78
1206 1334 6.128822 CGATATAACCAACCGATGTTCTCATG 60.129 42.308 0.00 0.00 34.06 3.07
1256 1393 3.054576 TCCTAGGGGTGTGGTGTAAAAA 58.945 45.455 9.46 0.00 0.00 1.94
1448 1601 9.927081 AGAATATGTATGGTGAAGAGGAAAAAT 57.073 29.630 0.00 0.00 0.00 1.82
1449 1602 9.753674 AAGAATATGTATGGTGAAGAGGAAAAA 57.246 29.630 0.00 0.00 0.00 1.94
1501 1658 6.743575 ACTTTCGCAGACTTATTAAAGCAT 57.256 33.333 0.00 0.00 36.05 3.79
1502 1659 6.554334 AACTTTCGCAGACTTATTAAAGCA 57.446 33.333 0.00 0.00 36.05 3.91
1503 1660 8.944212 TTAAACTTTCGCAGACTTATTAAAGC 57.056 30.769 0.00 0.00 36.05 3.51
1515 1690 3.982576 AGGGTGTTTAAACTTTCGCAG 57.017 42.857 18.72 0.00 0.00 5.18
1541 1716 8.868522 ATTCAACTTGAGAGATATTTGTTGGA 57.131 30.769 0.00 0.00 35.46 3.53
1623 1805 3.379688 CCTACGGTTAAGTCACCTACTCC 59.620 52.174 0.00 0.00 37.50 3.85
1628 1810 2.560105 GTCACCTACGGTTAAGTCACCT 59.440 50.000 0.00 0.00 31.02 4.00
1629 1811 2.560105 AGTCACCTACGGTTAAGTCACC 59.440 50.000 0.00 0.00 31.02 4.02
1630 1812 3.254166 TGAGTCACCTACGGTTAAGTCAC 59.746 47.826 0.00 0.00 31.02 3.67
1631 1813 3.489355 TGAGTCACCTACGGTTAAGTCA 58.511 45.455 0.00 0.00 31.02 3.41
1632 1814 4.233005 GTTGAGTCACCTACGGTTAAGTC 58.767 47.826 0.00 0.00 31.02 3.01
1633 1815 3.006217 GGTTGAGTCACCTACGGTTAAGT 59.994 47.826 0.00 0.00 31.02 2.24
1634 1816 3.257624 AGGTTGAGTCACCTACGGTTAAG 59.742 47.826 11.26 0.00 46.14 1.85
1635 1817 3.233507 AGGTTGAGTCACCTACGGTTAA 58.766 45.455 11.26 0.00 46.14 2.01
1636 1818 2.880443 AGGTTGAGTCACCTACGGTTA 58.120 47.619 11.26 0.00 46.14 2.85
1637 1819 1.713297 AGGTTGAGTCACCTACGGTT 58.287 50.000 11.26 0.00 46.14 4.44
1638 1820 3.452098 AGGTTGAGTCACCTACGGT 57.548 52.632 11.26 0.00 46.14 4.83
1644 1826 2.341846 TGGTTGAAGGTTGAGTCACC 57.658 50.000 0.00 0.00 37.04 4.02
1761 1944 2.952978 TGGTTGACGCTGGTGTAAATTT 59.047 40.909 0.00 0.00 0.00 1.82
1790 1973 1.754226 GGAAGAAACTGGTTTGTGGCA 59.246 47.619 3.30 0.00 32.11 4.92
1869 2112 7.689446 AGAAGAATAGCCCTTGAAGTAAAAC 57.311 36.000 0.00 0.00 0.00 2.43
1872 2115 7.390718 GTCAAAGAAGAATAGCCCTTGAAGTAA 59.609 37.037 0.00 0.00 0.00 2.24
2108 2351 3.594603 ATAGGCCCATTAAGTCGATCG 57.405 47.619 9.36 9.36 0.00 3.69
2195 2438 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2196 2439 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2197 2440 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2198 2441 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2199 2442 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2200 2443 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2201 2444 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2202 2445 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2226 2469 9.938280 AGCATTTTTGACACTAGTGTAGTATAA 57.062 29.630 27.98 17.60 45.05 0.98
2227 2470 9.582431 GAGCATTTTTGACACTAGTGTAGTATA 57.418 33.333 27.98 14.06 45.05 1.47
2228 2471 8.314751 AGAGCATTTTTGACACTAGTGTAGTAT 58.685 33.333 27.98 13.96 45.05 2.12
2229 2472 7.667557 AGAGCATTTTTGACACTAGTGTAGTA 58.332 34.615 27.98 14.71 45.05 1.82
2230 2473 6.525629 AGAGCATTTTTGACACTAGTGTAGT 58.474 36.000 27.98 6.32 45.05 2.73
2231 2474 7.426929 AAGAGCATTTTTGACACTAGTGTAG 57.573 36.000 27.98 12.67 45.05 2.74
2239 2482 9.683069 CCCATAATATAAGAGCATTTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
2240 2483 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
2241 2484 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
2242 2485 8.783093 CGTCCCATAATATAAGAGCATTTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
2243 2486 8.023128 CCGTCCCATAATATAAGAGCATTTTTG 58.977 37.037 0.00 0.00 0.00 2.44
2244 2487 7.942341 TCCGTCCCATAATATAAGAGCATTTTT 59.058 33.333 0.00 0.00 0.00 1.94
2245 2488 7.458397 TCCGTCCCATAATATAAGAGCATTTT 58.542 34.615 0.00 0.00 0.00 1.82
2246 2489 7.016153 TCCGTCCCATAATATAAGAGCATTT 57.984 36.000 0.00 0.00 0.00 2.32
2247 2490 6.352222 CCTCCGTCCCATAATATAAGAGCATT 60.352 42.308 0.00 0.00 0.00 3.56
2248 2491 5.129485 CCTCCGTCCCATAATATAAGAGCAT 59.871 44.000 0.00 0.00 0.00 3.79
2249 2492 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
2250 2493 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2251 2494 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2252 2495 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2253 2496 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2254 2497 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2255 2498 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2256 2499 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2257 2500 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2258 2501 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2259 2502 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2260 2503 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2261 2504 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2262 2505 0.613853 CAAGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2263 2506 0.614134 ACAAGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2264 2507 1.264295 AACAAGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2265 2508 3.698040 TCATAACAAGTACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
2266 2509 3.705051 TCATAACAAGTACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
2267 2510 4.939052 ATCATAACAAGTACTCCCTCCG 57.061 45.455 0.00 0.00 0.00 4.63
2268 2511 6.235231 TCAATCATAACAAGTACTCCCTCC 57.765 41.667 0.00 0.00 0.00 4.30
2269 2512 7.439655 GTGATCAATCATAACAAGTACTCCCTC 59.560 40.741 0.00 0.00 39.30 4.30
2270 2513 7.126421 AGTGATCAATCATAACAAGTACTCCCT 59.874 37.037 0.00 0.00 39.30 4.20
2271 2514 7.275920 AGTGATCAATCATAACAAGTACTCCC 58.724 38.462 0.00 0.00 39.30 4.30
2272 2515 9.817809 TTAGTGATCAATCATAACAAGTACTCC 57.182 33.333 0.00 0.00 39.30 3.85
2304 2547 9.654417 TTAAACAAAAGTCGAGCATAAAAGTAC 57.346 29.630 0.00 0.00 0.00 2.73
2312 2555 5.772521 AGCAATTAAACAAAAGTCGAGCAT 58.227 33.333 0.00 0.00 0.00 3.79
2313 2556 5.181690 AGCAATTAAACAAAAGTCGAGCA 57.818 34.783 0.00 0.00 0.00 4.26
2314 2557 5.212194 TGAGCAATTAAACAAAAGTCGAGC 58.788 37.500 0.00 0.00 0.00 5.03
2315 2558 7.858052 ATTGAGCAATTAAACAAAAGTCGAG 57.142 32.000 0.00 0.00 0.00 4.04
2316 2559 7.918033 TGAATTGAGCAATTAAACAAAAGTCGA 59.082 29.630 8.31 0.00 40.77 4.20
2317 2560 7.998212 GTGAATTGAGCAATTAAACAAAAGTCG 59.002 33.333 8.31 0.00 40.77 4.18
2521 2765 9.480053 GTTGCCAAATTATAGCATATGAACATT 57.520 29.630 6.97 0.00 36.20 2.71
2523 2767 7.012799 TCGTTGCCAAATTATAGCATATGAACA 59.987 33.333 6.97 0.00 36.20 3.18
2526 2770 7.686438 ATCGTTGCCAAATTATAGCATATGA 57.314 32.000 6.97 0.00 36.20 2.15
2564 2808 8.827177 TTCGAGACTGTTGACAAGTAATAATT 57.173 30.769 0.00 0.00 0.00 1.40
2572 2816 4.672413 GCAAATTTCGAGACTGTTGACAAG 59.328 41.667 0.00 0.00 0.00 3.16
2630 2875 5.255397 TGGAGTACCTGAAATGGAAACAT 57.745 39.130 0.00 0.00 45.07 2.71
2686 2931 1.609783 CCCCTCCCCTGACAACATC 59.390 63.158 0.00 0.00 0.00 3.06
2793 3038 9.311916 CACTACAGGAGAAATTATTTCAGAGAG 57.688 37.037 18.37 10.26 42.10 3.20
3067 3314 8.340618 ACTTTGTCAATGCAACTATATGACTT 57.659 30.769 13.45 0.00 0.00 3.01
3159 3406 8.216423 AGAAGTAGACCAATGCTATGATCAAAT 58.784 33.333 0.00 0.00 0.00 2.32
3223 3470 5.235186 GCTGTAGTGCAAATAGATGTGGTAG 59.765 44.000 0.00 0.00 0.00 3.18
3275 3522 7.934665 TGTGTACTAAGGAAAACTGAATTAGCA 59.065 33.333 0.00 0.00 0.00 3.49
3440 3687 5.392995 TCATCACCCCTTTCAAAATCTTCA 58.607 37.500 0.00 0.00 0.00 3.02
3459 3706 5.108385 ACCATTTCGACAGTGTTTTCATC 57.892 39.130 0.00 0.00 0.00 2.92
3483 3730 3.834813 TCTGCAGAGCCTAATCCGATTAT 59.165 43.478 13.74 0.00 0.00 1.28
3503 3751 4.130118 CAGTTAAGTTGCACTTCTGGTCT 58.870 43.478 5.04 0.00 39.51 3.85
3519 3767 1.493022 ACAGCAGGAACACCCAGTTAA 59.507 47.619 0.00 0.00 41.51 2.01
3616 3864 0.668535 GCAGGAACACCAACCAAGTC 59.331 55.000 0.00 0.00 0.00 3.01
3882 4142 6.964464 TCCCAGGAATAACAACAGCTTATAA 58.036 36.000 0.00 0.00 0.00 0.98
3974 4237 8.104222 GCGAAGAGCGAATATAACAAAATTTT 57.896 30.769 0.00 0.00 44.57 1.82
4030 4293 6.740944 TCGATGGGATTAGTTTGGAGAATA 57.259 37.500 0.00 0.00 0.00 1.75
4031 4294 5.630415 TCGATGGGATTAGTTTGGAGAAT 57.370 39.130 0.00 0.00 0.00 2.40
4032 4295 5.183228 GTTCGATGGGATTAGTTTGGAGAA 58.817 41.667 0.00 0.00 0.00 2.87
4043 4306 7.264947 GTTGGAATTTTATGTTCGATGGGATT 58.735 34.615 0.00 0.00 0.00 3.01
4101 4368 5.073311 TGTTCAGAGAGTATGTAACAGGC 57.927 43.478 0.00 0.00 0.00 4.85
4108 4375 6.652481 CCAAGTTTGATGTTCAGAGAGTATGT 59.348 38.462 0.00 0.00 0.00 2.29
4132 4399 1.457346 CTTGATTGTGTCTGCTCCCC 58.543 55.000 0.00 0.00 0.00 4.81
4135 4402 1.198637 GTGGCTTGATTGTGTCTGCTC 59.801 52.381 0.00 0.00 0.00 4.26
4136 4403 1.202855 AGTGGCTTGATTGTGTCTGCT 60.203 47.619 0.00 0.00 0.00 4.24
4137 4404 1.242076 AGTGGCTTGATTGTGTCTGC 58.758 50.000 0.00 0.00 0.00 4.26
4138 4405 3.551454 CCAAAGTGGCTTGATTGTGTCTG 60.551 47.826 0.00 0.00 0.00 3.51
4151 4430 2.701107 GAGAGTTACCTCCAAAGTGGC 58.299 52.381 0.00 0.00 38.58 5.01
4172 4451 6.663944 AGTGAGATACCAAAATTCGTAAGC 57.336 37.500 0.00 0.00 37.18 3.09
4177 4456 4.092821 TCGCAAGTGAGATACCAAAATTCG 59.907 41.667 0.00 0.00 39.48 3.34
4180 4459 7.172190 CAGATATCGCAAGTGAGATACCAAAAT 59.828 37.037 6.87 0.00 39.10 1.82
4181 4460 6.479990 CAGATATCGCAAGTGAGATACCAAAA 59.520 38.462 6.87 0.00 39.10 2.44
4183 4462 5.301805 TCAGATATCGCAAGTGAGATACCAA 59.698 40.000 6.87 0.00 39.10 3.67
4186 4465 7.095857 CCTTTTCAGATATCGCAAGTGAGATAC 60.096 40.741 6.87 2.93 39.10 2.24
4187 4466 6.925718 CCTTTTCAGATATCGCAAGTGAGATA 59.074 38.462 7.13 7.13 40.23 1.98
4188 4467 5.757320 CCTTTTCAGATATCGCAAGTGAGAT 59.243 40.000 3.04 3.04 38.17 2.75
4189 4468 5.111989 CCTTTTCAGATATCGCAAGTGAGA 58.888 41.667 0.00 0.00 39.48 3.27
4190 4469 4.260538 GCCTTTTCAGATATCGCAAGTGAG 60.261 45.833 0.00 0.00 39.48 3.51
4191 4470 3.623060 GCCTTTTCAGATATCGCAAGTGA 59.377 43.478 0.00 0.00 39.48 3.41
4192 4471 3.374988 TGCCTTTTCAGATATCGCAAGTG 59.625 43.478 0.00 0.00 39.48 3.16
4193 4472 3.609853 TGCCTTTTCAGATATCGCAAGT 58.390 40.909 0.00 0.00 39.48 3.16
4194 4473 4.825546 ATGCCTTTTCAGATATCGCAAG 57.174 40.909 3.78 2.48 0.00 4.01
4195 4474 4.036734 GGAATGCCTTTTCAGATATCGCAA 59.963 41.667 3.78 0.00 0.00 4.85
4196 4475 3.565482 GGAATGCCTTTTCAGATATCGCA 59.435 43.478 0.00 0.00 0.00 5.10
4197 4476 3.565482 TGGAATGCCTTTTCAGATATCGC 59.435 43.478 0.00 0.00 34.31 4.58
4198 4477 4.818546 ACTGGAATGCCTTTTCAGATATCG 59.181 41.667 10.84 0.00 34.31 2.92
4199 4478 7.094463 CCATACTGGAATGCCTTTTCAGATATC 60.094 40.741 10.84 0.00 40.96 1.63
4200 4479 6.718454 CCATACTGGAATGCCTTTTCAGATAT 59.282 38.462 10.84 4.05 40.96 1.63
4201 4480 6.064060 CCATACTGGAATGCCTTTTCAGATA 58.936 40.000 10.84 2.31 40.96 1.98
4202 4481 4.891756 CCATACTGGAATGCCTTTTCAGAT 59.108 41.667 10.84 0.10 40.96 2.90
4203 4482 4.272489 CCATACTGGAATGCCTTTTCAGA 58.728 43.478 10.84 0.00 40.96 3.27
4204 4483 3.382546 CCCATACTGGAATGCCTTTTCAG 59.617 47.826 3.78 3.78 40.96 3.02
4205 4484 3.364549 CCCATACTGGAATGCCTTTTCA 58.635 45.455 0.00 0.00 40.96 2.69
4206 4485 2.101415 GCCCATACTGGAATGCCTTTTC 59.899 50.000 0.00 0.00 40.96 2.29
4207 4486 2.110578 GCCCATACTGGAATGCCTTTT 58.889 47.619 0.00 0.00 40.96 2.27
4208 4487 1.006998 TGCCCATACTGGAATGCCTTT 59.993 47.619 0.00 0.00 40.96 3.11
4209 4488 0.630673 TGCCCATACTGGAATGCCTT 59.369 50.000 0.00 0.00 40.96 4.35
4210 4489 0.855598 ATGCCCATACTGGAATGCCT 59.144 50.000 0.00 0.00 40.96 4.75
4218 4497 5.833406 TTGTCATGTAAATGCCCATACTG 57.167 39.130 0.00 0.00 0.00 2.74
4288 4568 7.415592 TGATCCTGTGCCTTATCTGATATAG 57.584 40.000 0.00 0.13 0.00 1.31
4326 4606 5.300792 GGAGAGGAATCTCGACAAACTATCT 59.699 44.000 0.00 0.00 44.47 1.98


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

AutoCloner maintained by Alex Coulton.