Multiple sequence alignment - TraesCS3D01G473400

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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 TraesCS3D01G473400 chr3D 100.000 4791 0 0 1 4791 574915908 574920698 0.000000e+00 8848.0
1 TraesCS3D01G473400 chr3A 92.819 1852 101 9 1991 3811 710700819 710698969 0.000000e+00 2654.0
2 TraesCS3D01G473400 chr3A 83.982 1798 127 62 195 1934 710702648 710700954 0.000000e+00 1576.0
3 TraesCS3D01G473400 chr3A 77.333 525 59 31 4245 4723 710697721 710697211 6.150000e-64 255.0
4 TraesCS3D01G473400 chr3B 94.297 1473 78 4 2359 3827 765003427 765001957 0.000000e+00 2250.0
5 TraesCS3D01G473400 chr3B 86.966 1780 137 48 64 1781 765006048 765004302 0.000000e+00 1914.0
6 TraesCS3D01G473400 chr3B 91.276 619 33 14 3824 4434 765000398 764999793 0.000000e+00 824.0
7 TraesCS3D01G473400 chr3B 95.014 361 16 2 1991 2350 765003835 765003476 2.500000e-157 566.0
8 TraesCS3D01G473400 chr3B 89.306 346 20 4 4456 4791 764999803 764999465 7.420000e-113 418.0
9 TraesCS3D01G473400 chr3B 83.929 112 11 5 1833 1941 765004059 765003952 3.050000e-17 100.0
10 TraesCS3D01G473400 chr3B 91.071 56 5 0 1720 1775 733749355 733749410 5.140000e-10 76.8
11 TraesCS3D01G473400 chr6D 84.926 1559 161 38 2266 3799 28941500 28939991 0.000000e+00 1509.0
12 TraesCS3D01G473400 chr6D 88.898 1180 114 11 2614 3792 29000269 29001432 0.000000e+00 1437.0
13 TraesCS3D01G473400 chr6D 81.663 1287 146 57 1033 2273 28998667 28999909 0.000000e+00 987.0
14 TraesCS3D01G473400 chr6D 86.408 412 41 11 1522 1933 28942405 28942009 2.050000e-118 436.0
15 TraesCS3D01G473400 chr6D 91.379 290 25 0 1983 2272 28941862 28941573 9.660000e-107 398.0
16 TraesCS3D01G473400 chr6D 90.717 237 22 0 1204 1440 28942789 28942553 2.780000e-82 316.0
17 TraesCS3D01G473400 chr6D 96.721 61 2 0 2266 2326 28999975 29000035 8.480000e-18 102.0
18 TraesCS3D01G473400 chr6B 88.504 1183 116 10 2614 3795 60862196 60861033 0.000000e+00 1413.0
19 TraesCS3D01G473400 chr6B 87.956 1179 127 9 2614 3792 61224936 61226099 0.000000e+00 1376.0
20 TraesCS3D01G473400 chr6B 80.831 1565 209 61 1021 2535 61223415 61224938 0.000000e+00 1144.0
21 TraesCS3D01G473400 chr6B 84.149 776 86 26 1527 2273 60864130 60863363 0.000000e+00 717.0
22 TraesCS3D01G473400 chr6B 82.353 425 56 15 1027 1435 60864553 60864132 7.630000e-93 351.0
23 TraesCS3D01G473400 chr6B 87.755 147 13 3 2394 2535 60862340 60862194 2.970000e-37 167.0
24 TraesCS3D01G473400 chr6B 96.721 61 2 0 2266 2326 60863276 60863216 8.480000e-18 102.0
25 TraesCS3D01G473400 chr6A 88.031 1178 124 11 2616 3792 33541113 33539952 0.000000e+00 1378.0
26 TraesCS3D01G473400 chr6A 87.753 1184 117 20 2614 3793 33584740 33585899 0.000000e+00 1358.0
27 TraesCS3D01G473400 chr6A 81.366 1347 176 52 1015 2326 33583221 33584527 0.000000e+00 1027.0
28 TraesCS3D01G473400 chr6A 90.816 294 25 2 1982 2273 33541726 33541433 4.490000e-105 392.0
29 TraesCS3D01G473400 chr6A 82.338 402 46 21 1051 1435 33542720 33542327 4.620000e-85 326.0
30 TraesCS3D01G473400 chr6A 89.370 254 24 2 1527 1777 33542325 33542072 2.780000e-82 316.0
31 TraesCS3D01G473400 chr6A 96.667 60 2 0 2266 2325 33541363 33541304 3.050000e-17 100.0
32 TraesCS3D01G473400 chr2D 82.273 220 37 2 1218 1436 325364706 325364488 6.330000e-44 189.0
33 TraesCS3D01G473400 chr2A 81.140 228 41 2 2022 2248 497654598 497654372 1.060000e-41 182.0


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 TraesCS3D01G473400 chr3D 574915908 574920698 4790 False 8848.00 8848 100.000000 1 4791 1 chr3D.!!$F1 4790
1 TraesCS3D01G473400 chr3A 710697211 710702648 5437 True 1495.00 2654 84.711333 195 4723 3 chr3A.!!$R1 4528
2 TraesCS3D01G473400 chr3B 764999465 765006048 6583 True 1012.00 2250 90.131333 64 4791 6 chr3B.!!$R1 4727
3 TraesCS3D01G473400 chr6D 28998667 29001432 2765 False 842.00 1437 89.094000 1033 3792 3 chr6D.!!$F1 2759
4 TraesCS3D01G473400 chr6D 28939991 28942789 2798 True 664.75 1509 88.357500 1204 3799 4 chr6D.!!$R1 2595
5 TraesCS3D01G473400 chr6B 61223415 61226099 2684 False 1260.00 1376 84.393500 1021 3792 2 chr6B.!!$F1 2771
6 TraesCS3D01G473400 chr6B 60861033 60864553 3520 True 550.00 1413 87.896400 1027 3795 5 chr6B.!!$R1 2768
7 TraesCS3D01G473400 chr6A 33583221 33585899 2678 False 1192.50 1358 84.559500 1015 3793 2 chr6A.!!$F1 2778
8 TraesCS3D01G473400 chr6A 33539952 33542720 2768 True 502.40 1378 89.444400 1051 3792 5 chr6A.!!$R1 2741

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
642 671 0.035630 CTGCTTCTTCTCCCCACTGG 60.036 60.0 0.00 0.00 0.0 4.00 F
1198 1312 0.171903 ACTGTACGTATGTGGGCGAC 59.828 55.0 0.00 0.00 0.0 5.19 F
2134 3024 0.179048 TCATCTTCATCGCCGGCATT 60.179 50.0 28.98 10.21 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 1662 0.451783 GTGCCTCCTAAAATGCCACG 59.548 55.0 0.00 0.00 0.00 4.94 R
2881 4757 0.895530 TGATGGAGAAGACCGTCACC 59.104 55.0 0.40 0.00 46.81 4.02 R
3840 7346 0.032678 ACTAGAGATGGCGCCATTCG 59.967 55.0 40.56 26.87 36.70 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
17 18 4.639824 GTGCCTTCGTCGTGTGTA 57.360 55.556 0.00 0.00 0.00 2.90
18 19 3.117589 GTGCCTTCGTCGTGTGTAT 57.882 52.632 0.00 0.00 0.00 2.29
19 20 2.267188 GTGCCTTCGTCGTGTGTATA 57.733 50.000 0.00 0.00 0.00 1.47
20 21 2.182825 GTGCCTTCGTCGTGTGTATAG 58.817 52.381 0.00 0.00 0.00 1.31
21 22 1.197910 GCCTTCGTCGTGTGTATAGC 58.802 55.000 0.00 0.00 0.00 2.97
22 23 1.468565 GCCTTCGTCGTGTGTATAGCA 60.469 52.381 0.00 0.00 0.00 3.49
23 24 2.451132 CCTTCGTCGTGTGTATAGCAG 58.549 52.381 0.00 0.00 0.00 4.24
24 25 2.159421 CCTTCGTCGTGTGTATAGCAGT 60.159 50.000 0.00 0.00 0.00 4.40
25 26 2.537639 TCGTCGTGTGTATAGCAGTG 57.462 50.000 0.00 0.00 0.00 3.66
26 27 1.808343 TCGTCGTGTGTATAGCAGTGT 59.192 47.619 0.00 0.00 0.00 3.55
27 28 2.159612 TCGTCGTGTGTATAGCAGTGTC 60.160 50.000 0.00 0.00 0.00 3.67
28 29 2.174764 GTCGTGTGTATAGCAGTGTCG 58.825 52.381 0.00 0.00 0.00 4.35
29 30 1.808343 TCGTGTGTATAGCAGTGTCGT 59.192 47.619 0.00 0.00 0.00 4.34
30 31 1.911464 CGTGTGTATAGCAGTGTCGTG 59.089 52.381 0.00 0.00 0.00 4.35
31 32 2.667448 CGTGTGTATAGCAGTGTCGTGT 60.667 50.000 0.00 0.00 0.00 4.49
32 33 3.314553 GTGTGTATAGCAGTGTCGTGTT 58.685 45.455 0.00 0.00 0.00 3.32
33 34 4.478699 GTGTGTATAGCAGTGTCGTGTTA 58.521 43.478 0.00 0.00 0.00 2.41
34 35 5.100259 GTGTGTATAGCAGTGTCGTGTTAT 58.900 41.667 0.00 0.00 0.00 1.89
35 36 6.260377 GTGTGTATAGCAGTGTCGTGTTATA 58.740 40.000 0.00 0.00 0.00 0.98
36 37 6.916387 GTGTGTATAGCAGTGTCGTGTTATAT 59.084 38.462 0.00 0.00 31.30 0.86
37 38 8.071967 GTGTGTATAGCAGTGTCGTGTTATATA 58.928 37.037 0.00 0.00 31.30 0.86
38 39 8.071967 TGTGTATAGCAGTGTCGTGTTATATAC 58.928 37.037 7.31 7.31 38.03 1.47
39 40 8.071967 GTGTATAGCAGTGTCGTGTTATATACA 58.928 37.037 8.64 0.00 37.75 2.29
60 61 6.840780 ACACTTATTTTGGAATGGAAGGAG 57.159 37.500 0.00 0.00 0.00 3.69
61 62 6.314917 ACACTTATTTTGGAATGGAAGGAGT 58.685 36.000 0.00 0.00 0.00 3.85
62 63 7.466804 ACACTTATTTTGGAATGGAAGGAGTA 58.533 34.615 0.00 0.00 0.00 2.59
106 111 3.311322 CGAGTTCCTGTGCAGTTTTAACA 59.689 43.478 0.00 0.00 0.00 2.41
108 113 5.186996 AGTTCCTGTGCAGTTTTAACATG 57.813 39.130 0.00 0.00 0.00 3.21
116 121 2.492088 GCAGTTTTAACATGGTCCCTCC 59.508 50.000 0.00 0.00 0.00 4.30
119 124 5.755849 CAGTTTTAACATGGTCCCTCCTAT 58.244 41.667 0.00 0.00 37.07 2.57
123 128 6.652205 TTTAACATGGTCCCTCCTATTTCT 57.348 37.500 0.00 0.00 37.07 2.52
148 154 3.876274 TCACATGAGAGGCAAGAGTAC 57.124 47.619 0.00 0.00 0.00 2.73
152 158 5.600069 TCACATGAGAGGCAAGAGTACATAT 59.400 40.000 0.00 0.00 0.00 1.78
153 159 5.695363 CACATGAGAGGCAAGAGTACATATG 59.305 44.000 0.00 0.00 0.00 1.78
155 161 6.269538 ACATGAGAGGCAAGAGTACATATGAT 59.730 38.462 10.38 0.00 0.00 2.45
156 162 7.452813 ACATGAGAGGCAAGAGTACATATGATA 59.547 37.037 10.38 0.00 0.00 2.15
157 163 7.839680 TGAGAGGCAAGAGTACATATGATAA 57.160 36.000 10.38 0.00 0.00 1.75
158 164 8.250143 TGAGAGGCAAGAGTACATATGATAAA 57.750 34.615 10.38 0.00 0.00 1.40
160 166 9.364989 GAGAGGCAAGAGTACATATGATAAATC 57.635 37.037 10.38 3.51 0.00 2.17
161 167 9.099071 AGAGGCAAGAGTACATATGATAAATCT 57.901 33.333 10.38 5.75 0.00 2.40
298 326 2.306512 ACCTACGGCCAAGATGGTTAAA 59.693 45.455 2.24 0.00 40.46 1.52
367 395 0.703466 CGTCGAAGAAAGAGTCGCAC 59.297 55.000 0.00 0.00 39.69 5.34
376 404 2.563471 AAGAGTCGCACGGTATCTTC 57.437 50.000 0.00 0.00 0.00 2.87
407 435 2.190578 CATGTCCGGCTCCTTCCC 59.809 66.667 0.00 0.00 0.00 3.97
444 473 3.656045 CCACCACCGCGTCCAAAC 61.656 66.667 4.92 0.00 0.00 2.93
445 474 2.590575 CACCACCGCGTCCAAACT 60.591 61.111 4.92 0.00 0.00 2.66
446 475 2.280592 ACCACCGCGTCCAAACTC 60.281 61.111 4.92 0.00 0.00 3.01
642 671 0.035630 CTGCTTCTTCTCCCCACTGG 60.036 60.000 0.00 0.00 0.00 4.00
672 706 2.297701 GTTCAGACCAAGCCTTTCACA 58.702 47.619 0.00 0.00 0.00 3.58
673 707 2.687935 GTTCAGACCAAGCCTTTCACAA 59.312 45.455 0.00 0.00 0.00 3.33
686 720 4.351938 CACAAGGTCGGCCGTCGA 62.352 66.667 27.15 1.97 46.77 4.20
751 785 4.699522 GGCAAGGGAGTCGCCGTT 62.700 66.667 3.13 0.00 45.26 4.44
760 794 4.430423 GTCGCCGTTTGCTGCTCG 62.430 66.667 0.00 3.47 38.05 5.03
786 820 2.427245 CCCGGCGTGAGGAAGATCT 61.427 63.158 6.01 0.00 0.00 2.75
788 822 1.667154 CCGGCGTGAGGAAGATCTGA 61.667 60.000 6.01 0.00 0.00 3.27
789 823 0.248825 CGGCGTGAGGAAGATCTGAG 60.249 60.000 0.00 0.00 0.00 3.35
790 824 0.820871 GGCGTGAGGAAGATCTGAGT 59.179 55.000 0.00 0.00 0.00 3.41
791 825 1.202359 GGCGTGAGGAAGATCTGAGTC 60.202 57.143 0.00 0.00 0.00 3.36
792 826 1.532921 GCGTGAGGAAGATCTGAGTCG 60.533 57.143 0.00 0.00 0.00 4.18
793 827 1.532921 CGTGAGGAAGATCTGAGTCGC 60.533 57.143 0.00 0.00 0.00 5.19
796 830 1.590259 GGAAGATCTGAGTCGCCGC 60.590 63.158 0.00 0.00 0.00 6.53
817 851 0.179073 GCGCCTGCTTCAGATCCTTA 60.179 55.000 0.00 0.00 38.39 2.69
843 896 5.138276 TGCCCGGTATATATGACTATCTCC 58.862 45.833 0.00 0.00 0.00 3.71
856 909 7.690952 ATGACTATCTCCTTACTATTCGTCC 57.309 40.000 0.00 0.00 0.00 4.79
873 926 3.506455 TCGTCCTTGTCTCTCGATTTTCT 59.494 43.478 0.00 0.00 0.00 2.52
910 963 2.008328 CCCGTCGTCGTTGTTGTTT 58.992 52.632 0.71 0.00 35.01 2.83
969 1035 5.848406 ACGAGATCCAAGATCAGTAAATCC 58.152 41.667 7.30 0.00 0.00 3.01
983 1049 5.929992 TCAGTAAATCCGTCTAAAACCTGTG 59.070 40.000 0.00 0.00 0.00 3.66
984 1050 5.929992 CAGTAAATCCGTCTAAAACCTGTGA 59.070 40.000 0.00 0.00 0.00 3.58
988 1054 3.934068 TCCGTCTAAAACCTGTGAATCC 58.066 45.455 0.00 0.00 0.00 3.01
996 1062 2.457366 ACCTGTGAATCCAAGACGAC 57.543 50.000 0.00 0.00 0.00 4.34
1005 1072 5.006746 GTGAATCCAAGACGACATTATGTCC 59.993 44.000 18.33 6.63 44.20 4.02
1008 1075 3.056393 TCCAAGACGACATTATGTCCGTT 60.056 43.478 18.33 7.53 44.20 4.44
1009 1076 3.062099 CCAAGACGACATTATGTCCGTTG 59.938 47.826 18.33 16.94 44.20 4.10
1129 1225 4.765339 GGGTCAGCACCTTAACATAACTTT 59.235 41.667 0.00 0.00 43.22 2.66
1132 1228 6.653740 GGTCAGCACCTTAACATAACTTTACT 59.346 38.462 0.00 0.00 40.00 2.24
1139 1235 8.015658 CACCTTAACATAACTTTACTTGTGCTC 58.984 37.037 0.00 0.00 0.00 4.26
1140 1236 7.095355 ACCTTAACATAACTTTACTTGTGCTCG 60.095 37.037 0.00 0.00 0.00 5.03
1198 1312 0.171903 ACTGTACGTATGTGGGCGAC 59.828 55.000 0.00 0.00 0.00 5.19
1360 1477 2.427245 CGGCGTCCTCTCCCTCATT 61.427 63.158 0.00 0.00 0.00 2.57
1402 1519 2.699954 CCCATGCTCAAGTACGTCTTT 58.300 47.619 0.00 0.00 33.63 2.52
1452 1583 3.498676 GTGAGTCGACACCCTTCTG 57.501 57.895 19.50 0.00 35.07 3.02
1472 1623 5.340803 TCTGTATATCTTGTGTTCGTCTGC 58.659 41.667 0.00 0.00 0.00 4.26
1504 1655 2.261361 CCGGCGTGACATCTGACA 59.739 61.111 6.01 0.00 0.00 3.58
1505 1656 1.153568 CCGGCGTGACATCTGACAT 60.154 57.895 6.01 0.00 0.00 3.06
1506 1657 1.423721 CCGGCGTGACATCTGACATG 61.424 60.000 6.01 0.00 0.00 3.21
1507 1658 0.458370 CGGCGTGACATCTGACATGA 60.458 55.000 0.00 0.00 0.00 3.07
1509 1660 1.002366 GCGTGACATCTGACATGACC 58.998 55.000 0.00 0.00 0.00 4.02
1511 1662 1.002366 GTGACATCTGACATGACCGC 58.998 55.000 0.00 0.00 0.00 5.68
1514 1665 0.737367 ACATCTGACATGACCGCGTG 60.737 55.000 4.92 0.00 37.07 5.34
1791 2123 7.914427 TCTCTGGTACCTATGTTACATTGAT 57.086 36.000 14.36 0.00 0.00 2.57
1803 2135 6.558771 TGTTACATTGATCAAGTTCCACAG 57.441 37.500 14.54 0.00 0.00 3.66
1804 2136 6.295249 TGTTACATTGATCAAGTTCCACAGA 58.705 36.000 14.54 0.00 0.00 3.41
1805 2137 6.770303 TGTTACATTGATCAAGTTCCACAGAA 59.230 34.615 14.54 0.09 0.00 3.02
1806 2138 5.954296 ACATTGATCAAGTTCCACAGAAG 57.046 39.130 14.54 0.00 30.91 2.85
1808 2140 6.243900 ACATTGATCAAGTTCCACAGAAGAT 58.756 36.000 14.54 0.00 30.91 2.40
1810 2142 4.582869 TGATCAAGTTCCACAGAAGATGG 58.417 43.478 0.00 0.00 38.71 3.51
1817 2343 6.126863 AGTTCCACAGAAGATGGACATAAA 57.873 37.500 0.00 0.00 46.09 1.40
1821 2347 8.956426 GTTCCACAGAAGATGGACATAAATAAA 58.044 33.333 0.00 0.00 46.09 1.40
1863 2411 4.756642 GCTAATCGAATGTTGATGGATGGA 59.243 41.667 0.00 0.00 0.00 3.41
1870 2422 5.585390 GAATGTTGATGGATGGATGTGTTC 58.415 41.667 0.00 0.00 0.00 3.18
1881 2433 1.068748 GGATGTGTTCTTGCAGTGCTG 60.069 52.381 17.60 9.42 0.00 4.41
1939 2505 2.899976 TGACCCAATGTACGTATGCTG 58.100 47.619 0.00 0.00 0.00 4.41
1943 2581 3.123804 CCCAATGTACGTATGCTGTCTC 58.876 50.000 0.00 0.00 0.00 3.36
1944 2582 2.789339 CCAATGTACGTATGCTGTCTCG 59.211 50.000 0.00 0.00 0.00 4.04
1950 2588 0.907837 CGTATGCTGTCTCGTTGTCG 59.092 55.000 0.00 0.00 38.55 4.35
1952 2590 1.912110 GTATGCTGTCTCGTTGTCGAC 59.088 52.381 9.11 9.11 41.35 4.20
1979 2744 1.151668 AGCGTGTCATCTTGTTCTGC 58.848 50.000 0.00 0.00 0.00 4.26
1981 2746 1.264020 GCGTGTCATCTTGTTCTGCAA 59.736 47.619 0.00 0.00 35.50 4.08
1989 2855 6.430616 TGTCATCTTGTTCTGCAATGAATGTA 59.569 34.615 0.00 0.00 36.36 2.29
2134 3024 0.179048 TCATCTTCATCGCCGGCATT 60.179 50.000 28.98 10.21 0.00 3.56
2338 3344 1.133790 CAGGTTCGGTTCCGTACTAGG 59.866 57.143 17.45 6.77 31.97 3.02
2339 3345 1.177401 GGTTCGGTTCCGTACTAGGT 58.823 55.000 17.45 0.00 31.97 3.08
2340 3346 1.135286 GGTTCGGTTCCGTACTAGGTG 60.135 57.143 17.45 0.00 31.97 4.00
2342 3348 0.322816 TCGGTTCCGTACTAGGTGCT 60.323 55.000 11.04 0.00 0.00 4.40
2372 3940 2.168621 CACAAACGCAGACGCTCG 59.831 61.111 0.00 0.00 45.53 5.03
2389 4243 1.330829 CTCGCATACAGAGCACGACTA 59.669 52.381 0.00 0.00 0.00 2.59
2391 4245 2.357952 TCGCATACAGAGCACGACTAAT 59.642 45.455 0.00 0.00 0.00 1.73
2425 4285 2.282040 GGCCTGTTGCAGCTGAGT 60.282 61.111 20.43 0.00 43.89 3.41
2446 4306 2.649742 TCACCTTCATCCTCTTCCCT 57.350 50.000 0.00 0.00 0.00 4.20
2452 4312 1.952621 TCATCCTCTTCCCTTCCGTT 58.047 50.000 0.00 0.00 0.00 4.44
2509 4369 2.444700 AATTCCCGCAAGACGTCGGT 62.445 55.000 10.46 0.00 43.87 4.69
2553 4414 0.872388 GGTCGGCAGTACAACCTTTG 59.128 55.000 0.00 0.00 0.00 2.77
2779 4655 0.544595 AGAAGTACTCGGGGCAGGTT 60.545 55.000 0.00 0.00 0.00 3.50
2881 4757 2.754648 CGCCTATGGGATATGCGTG 58.245 57.895 0.00 0.00 42.38 5.34
2971 4847 0.460311 CCTTCGTCGTGGCCTTCTAT 59.540 55.000 3.32 0.00 0.00 1.98
3109 4985 2.731341 GCACTACGTCTATGTCAAGCGT 60.731 50.000 0.00 0.00 39.23 5.07
3286 5162 2.325082 GGTGCATGCCGTCTTCGTT 61.325 57.895 16.68 0.00 35.01 3.85
3460 5336 1.907739 CCTCATCGAGGGCCTCAAA 59.092 57.895 31.69 19.96 45.43 2.69
3490 5366 1.053264 ATGATGAGGCGGCCTTCTCT 61.053 55.000 24.71 8.12 31.76 3.10
3538 5426 3.750639 AACAACAACAACGACAACGAT 57.249 38.095 0.00 0.00 42.66 3.73
3787 5675 2.494073 GGTCGGGATCACCTATGAGATC 59.506 54.545 0.00 0.00 38.57 2.75
3840 7346 2.052237 CTTGACAACACGCCGCAC 60.052 61.111 0.00 0.00 0.00 5.34
3863 7759 2.489938 TGGCGCCATCTCTAGTTTTT 57.510 45.000 29.03 0.00 0.00 1.94
3892 7790 1.518286 GCTAACGAGTCGTACGTGAC 58.482 55.000 20.23 7.10 43.16 3.67
3899 7797 3.376078 TCGTACGTGACCCTGGCC 61.376 66.667 16.05 0.00 0.00 5.36
3905 7803 2.688902 ACGTGACCCTGGCCTATATA 57.311 50.000 3.32 0.00 0.00 0.86
3932 7830 2.951458 GGCCCGTTTTCTTCGGTG 59.049 61.111 0.00 0.00 45.63 4.94
3957 7855 2.600731 CTCTAGCAGAACAGTTGACCG 58.399 52.381 0.00 0.00 0.00 4.79
4097 7996 7.563906 AGATTTTGAAAACATTGGTCCTGAAA 58.436 30.769 0.00 0.00 0.00 2.69
4172 8071 8.463456 AAAATGTTTGCCAAAGTTTTCAAATG 57.537 26.923 13.00 0.00 32.07 2.32
4174 8073 6.566197 TGTTTGCCAAAGTTTTCAAATGTT 57.434 29.167 13.00 0.00 32.07 2.71
4175 8074 6.606768 TGTTTGCCAAAGTTTTCAAATGTTC 58.393 32.000 13.00 4.78 32.07 3.18
4176 8075 6.205464 TGTTTGCCAAAGTTTTCAAATGTTCA 59.795 30.769 13.00 6.57 32.07 3.18
4178 8077 6.360844 TGCCAAAGTTTTCAAATGTTCATG 57.639 33.333 0.00 0.00 0.00 3.07
4180 8079 6.596888 TGCCAAAGTTTTCAAATGTTCATGAA 59.403 30.769 3.38 3.38 33.93 2.57
4310 8210 8.884124 TCTGAAAGAAATATGTTTTCCCAGAT 57.116 30.769 0.00 0.00 42.31 2.90
4311 8211 8.742777 TCTGAAAGAAATATGTTTTCCCAGATG 58.257 33.333 0.00 0.00 42.31 2.90
4316 8216 8.293699 AGAAATATGTTTTCCCAGATGTTACC 57.706 34.615 0.00 0.00 0.00 2.85
4317 8217 6.693315 AATATGTTTTCCCAGATGTTACCG 57.307 37.500 0.00 0.00 0.00 4.02
4451 8354 8.486210 TGGCACTCTTATAGATTGTGTTCTATT 58.514 33.333 0.00 0.00 39.21 1.73
4487 8406 3.094572 CCTGCAGGGAAAATTCATGAGT 58.905 45.455 26.14 0.00 37.23 3.41
4488 8407 4.018506 TCCTGCAGGGAAAATTCATGAGTA 60.019 41.667 32.23 4.08 41.91 2.59
4489 8408 4.337555 CCTGCAGGGAAAATTCATGAGTAG 59.662 45.833 26.14 0.00 37.23 2.57
4490 8409 5.178096 TGCAGGGAAAATTCATGAGTAGA 57.822 39.130 0.00 0.00 0.00 2.59
4491 8410 5.188434 TGCAGGGAAAATTCATGAGTAGAG 58.812 41.667 0.00 0.00 0.00 2.43
4631 8567 9.696917 ATCAAATATTCTCAAACAACTTTGGAC 57.303 29.630 0.00 0.00 37.87 4.02
4655 8591 3.259625 AGACCCTCTCAGTTTGCTAACTC 59.740 47.826 10.73 0.00 42.67 3.01
4666 8612 7.492524 TCAGTTTGCTAACTCTCCATATACAG 58.507 38.462 10.73 0.00 42.67 2.74
4673 8619 6.869388 GCTAACTCTCCATATACAGCCTAAAC 59.131 42.308 0.00 0.00 0.00 2.01
4674 8620 7.256012 GCTAACTCTCCATATACAGCCTAAACT 60.256 40.741 0.00 0.00 0.00 2.66
4707 8653 6.018507 GCATGATAAAACAGCCAAAATGGATC 60.019 38.462 0.00 0.00 40.96 3.36
4712 8658 3.756082 ACAGCCAAAATGGATCCCTAA 57.244 42.857 9.90 0.00 40.96 2.69
4733 8679 5.432885 AAACGGTGAATACACTTTTCCAG 57.567 39.130 0.00 0.00 45.32 3.86
4753 8699 6.710278 TCCAGATTCACACAATGTAATGAGA 58.290 36.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.182825 CTATACACACGACGAAGGCAC 58.817 52.381 0.00 0.00 0.00 5.01
1 2 1.468565 GCTATACACACGACGAAGGCA 60.469 52.381 0.00 0.00 0.00 4.75
2 3 1.197910 GCTATACACACGACGAAGGC 58.802 55.000 0.00 0.00 0.00 4.35
3 4 2.159421 ACTGCTATACACACGACGAAGG 60.159 50.000 0.00 0.00 0.00 3.46
4 5 2.846550 CACTGCTATACACACGACGAAG 59.153 50.000 0.00 0.00 0.00 3.79
5 6 2.227149 ACACTGCTATACACACGACGAA 59.773 45.455 0.00 0.00 0.00 3.85
6 7 1.808343 ACACTGCTATACACACGACGA 59.192 47.619 0.00 0.00 0.00 4.20
7 8 2.174764 GACACTGCTATACACACGACG 58.825 52.381 0.00 0.00 0.00 5.12
8 9 2.174764 CGACACTGCTATACACACGAC 58.825 52.381 0.00 0.00 0.00 4.34
9 10 1.808343 ACGACACTGCTATACACACGA 59.192 47.619 0.00 0.00 0.00 4.35
10 11 1.911464 CACGACACTGCTATACACACG 59.089 52.381 0.00 0.00 0.00 4.49
11 12 2.942710 ACACGACACTGCTATACACAC 58.057 47.619 0.00 0.00 0.00 3.82
12 13 3.653539 AACACGACACTGCTATACACA 57.346 42.857 0.00 0.00 0.00 3.72
13 14 8.071967 TGTATATAACACGACACTGCTATACAC 58.928 37.037 0.00 0.00 31.43 2.90
14 15 8.156994 TGTATATAACACGACACTGCTATACA 57.843 34.615 0.00 0.00 31.43 2.29
34 35 9.627123 CTCCTTCCATTCCAAAATAAGTGTATA 57.373 33.333 0.00 0.00 0.00 1.47
35 36 8.116026 ACTCCTTCCATTCCAAAATAAGTGTAT 58.884 33.333 0.00 0.00 0.00 2.29
36 37 7.466804 ACTCCTTCCATTCCAAAATAAGTGTA 58.533 34.615 0.00 0.00 0.00 2.90
37 38 6.314917 ACTCCTTCCATTCCAAAATAAGTGT 58.685 36.000 0.00 0.00 0.00 3.55
38 39 6.840780 ACTCCTTCCATTCCAAAATAAGTG 57.159 37.500 0.00 0.00 0.00 3.16
39 40 9.190317 GAATACTCCTTCCATTCCAAAATAAGT 57.810 33.333 0.00 0.00 0.00 2.24
40 41 9.189156 TGAATACTCCTTCCATTCCAAAATAAG 57.811 33.333 0.00 0.00 0.00 1.73
41 42 9.540538 TTGAATACTCCTTCCATTCCAAAATAA 57.459 29.630 0.00 0.00 0.00 1.40
42 43 8.966868 GTTGAATACTCCTTCCATTCCAAAATA 58.033 33.333 0.00 0.00 0.00 1.40
43 44 7.675619 AGTTGAATACTCCTTCCATTCCAAAAT 59.324 33.333 0.00 0.00 28.23 1.82
44 45 7.010160 AGTTGAATACTCCTTCCATTCCAAAA 58.990 34.615 0.00 0.00 28.23 2.44
45 46 6.552008 AGTTGAATACTCCTTCCATTCCAAA 58.448 36.000 0.00 0.00 28.23 3.28
46 47 6.139679 AGTTGAATACTCCTTCCATTCCAA 57.860 37.500 0.00 0.00 28.23 3.53
47 48 5.779241 AGTTGAATACTCCTTCCATTCCA 57.221 39.130 0.00 0.00 28.23 3.53
48 49 6.763610 CACTAGTTGAATACTCCTTCCATTCC 59.236 42.308 0.00 0.00 38.33 3.01
49 50 7.556844 TCACTAGTTGAATACTCCTTCCATTC 58.443 38.462 0.00 0.00 38.33 2.67
50 51 7.496346 TCACTAGTTGAATACTCCTTCCATT 57.504 36.000 0.00 0.00 38.33 3.16
51 52 7.496346 TTCACTAGTTGAATACTCCTTCCAT 57.504 36.000 0.00 0.00 39.45 3.41
52 53 6.928348 TTCACTAGTTGAATACTCCTTCCA 57.072 37.500 0.00 0.00 39.45 3.53
53 54 7.387643 AGTTTCACTAGTTGAATACTCCTTCC 58.612 38.462 0.00 0.00 43.99 3.46
54 55 8.088981 TGAGTTTCACTAGTTGAATACTCCTTC 58.911 37.037 23.83 14.26 43.99 3.46
55 56 7.963532 TGAGTTTCACTAGTTGAATACTCCTT 58.036 34.615 23.83 9.98 43.99 3.36
56 57 7.540474 TGAGTTTCACTAGTTGAATACTCCT 57.460 36.000 23.83 12.89 43.99 3.69
57 58 7.148787 CGTTGAGTTTCACTAGTTGAATACTCC 60.149 40.741 23.83 17.28 43.99 3.85
58 59 7.619571 GCGTTGAGTTTCACTAGTTGAATACTC 60.620 40.741 22.37 22.37 43.99 2.59
59 60 6.145696 GCGTTGAGTTTCACTAGTTGAATACT 59.854 38.462 0.00 7.39 43.99 2.12
60 61 6.297353 GCGTTGAGTTTCACTAGTTGAATAC 58.703 40.000 0.00 3.33 43.99 1.89
61 62 5.118050 CGCGTTGAGTTTCACTAGTTGAATA 59.882 40.000 0.00 0.00 43.99 1.75
62 63 4.084537 CGCGTTGAGTTTCACTAGTTGAAT 60.085 41.667 0.00 0.00 43.99 2.57
80 81 1.956170 CTGCACAGGAACTCGCGTT 60.956 57.895 5.77 0.00 36.76 4.84
81 82 2.356313 CTGCACAGGAACTCGCGT 60.356 61.111 5.77 0.00 36.76 6.01
90 91 3.305335 GGACCATGTTAAAACTGCACAGG 60.305 47.826 2.21 0.00 0.00 4.00
91 92 3.305335 GGGACCATGTTAAAACTGCACAG 60.305 47.826 0.00 0.00 0.00 3.66
94 95 3.153919 GAGGGACCATGTTAAAACTGCA 58.846 45.455 0.00 0.00 0.00 4.41
95 96 2.492088 GGAGGGACCATGTTAAAACTGC 59.508 50.000 0.00 0.00 38.79 4.40
162 168 8.584157 CCTACTACTTCATGAGATCATTAGCTT 58.416 37.037 0.00 0.00 33.61 3.74
164 170 7.891561 ACCTACTACTTCATGAGATCATTAGC 58.108 38.462 0.00 0.00 33.61 3.09
165 171 9.295825 AGACCTACTACTTCATGAGATCATTAG 57.704 37.037 0.00 0.00 33.61 1.73
167 173 9.647918 TTAGACCTACTACTTCATGAGATCATT 57.352 33.333 0.00 0.00 33.61 2.57
168 174 9.295825 CTTAGACCTACTACTTCATGAGATCAT 57.704 37.037 0.00 0.00 36.96 2.45
169 175 8.275758 ACTTAGACCTACTACTTCATGAGATCA 58.724 37.037 0.00 0.00 0.00 2.92
245 251 3.557595 CGAGGAGCAATTCTAACATGGTC 59.442 47.826 0.00 0.00 40.03 4.02
246 252 3.055094 ACGAGGAGCAATTCTAACATGGT 60.055 43.478 0.00 0.00 0.00 3.55
255 264 4.742438 TTGTTTGTACGAGGAGCAATTC 57.258 40.909 0.00 0.00 0.00 2.17
329 357 2.351726 ACGGATCTTACCACGTACGTAC 59.648 50.000 22.34 15.90 37.85 3.67
330 358 2.607635 GACGGATCTTACCACGTACGTA 59.392 50.000 22.34 4.43 39.95 3.57
331 359 1.398390 GACGGATCTTACCACGTACGT 59.602 52.381 16.72 16.72 39.95 3.57
332 360 1.593070 CGACGGATCTTACCACGTACG 60.593 57.143 15.01 15.01 39.95 3.67
376 404 4.935495 CATGCCCACGGGATCGGG 62.935 72.222 6.21 0.00 46.15 5.14
407 435 2.008329 GAACTCATCTTCAGCCAGCAG 58.992 52.381 0.00 0.00 0.00 4.24
444 473 2.543777 TTCTGTTTTGGACTCGGGAG 57.456 50.000 0.00 0.00 0.00 4.30
445 474 3.284793 TTTTCTGTTTTGGACTCGGGA 57.715 42.857 0.00 0.00 0.00 5.14
642 671 1.860676 TGGTCTGAACACTACGTTGC 58.139 50.000 0.00 0.00 38.19 4.17
672 706 3.745803 GACTCGACGGCCGACCTT 61.746 66.667 35.90 9.58 43.23 3.50
677 711 4.873129 CCATGGACTCGACGGCCG 62.873 72.222 26.86 26.86 40.25 6.13
770 804 0.248825 CTCAGATCTTCCTCACGCCG 60.249 60.000 0.00 0.00 0.00 6.46
796 830 3.267860 GATCTGAAGCAGGCGCGG 61.268 66.667 8.83 0.00 45.49 6.46
801 835 2.941720 GCAAGTAAGGATCTGAAGCAGG 59.058 50.000 0.00 0.00 31.51 4.85
809 843 2.170012 TACCGGGCAAGTAAGGATCT 57.830 50.000 6.32 0.00 0.00 2.75
817 851 6.195700 AGATAGTCATATATACCGGGCAAGT 58.804 40.000 6.32 0.00 0.00 3.16
843 896 5.293814 TCGAGAGACAAGGACGAATAGTAAG 59.706 44.000 0.00 0.00 33.31 2.34
849 902 4.457834 AAATCGAGAGACAAGGACGAAT 57.542 40.909 0.00 0.00 46.97 3.34
852 905 3.839293 AGAAAATCGAGAGACAAGGACG 58.161 45.455 0.00 0.00 46.97 4.79
873 926 1.719709 CACGACCGATGAGCTCGTA 59.280 57.895 8.83 0.00 46.18 3.43
910 963 2.542550 TCGGAAGGGTGGTTTCAGATA 58.457 47.619 0.00 0.00 0.00 1.98
969 1035 4.994852 TCTTGGATTCACAGGTTTTAGACG 59.005 41.667 0.00 0.00 0.00 4.18
996 1062 2.276201 TCGGCTTCAACGGACATAATG 58.724 47.619 0.00 0.00 0.00 1.90
1129 1225 2.736995 GCCGTGCGAGCACAAGTA 60.737 61.111 25.18 0.00 46.47 2.24
1139 1235 1.011242 CATTAACATCGGCCGTGCG 60.011 57.895 27.15 16.90 0.00 5.34
1140 1236 1.355210 CCATTAACATCGGCCGTGC 59.645 57.895 27.15 0.00 0.00 5.34
1285 1399 1.196354 GTGCTCGAGTACACGTACAGT 59.804 52.381 26.19 0.00 38.48 3.55
1360 1477 2.133520 AGGAGGACGAGGGTGTAGATA 58.866 52.381 0.00 0.00 0.00 1.98
1452 1583 5.340803 TGAGCAGACGAACACAAGATATAC 58.659 41.667 0.00 0.00 0.00 1.47
1499 1650 3.490759 GCCACGCGGTCATGTCAG 61.491 66.667 12.47 0.00 33.28 3.51
1500 1651 3.604129 ATGCCACGCGGTCATGTCA 62.604 57.895 12.47 0.00 30.70 3.58
1501 1652 1.922135 AAATGCCACGCGGTCATGTC 61.922 55.000 12.47 0.00 31.81 3.06
1504 1655 0.732571 CTAAAATGCCACGCGGTCAT 59.267 50.000 12.47 7.66 32.47 3.06
1505 1656 1.302383 CCTAAAATGCCACGCGGTCA 61.302 55.000 12.47 5.24 33.28 4.02
1506 1657 1.022451 TCCTAAAATGCCACGCGGTC 61.022 55.000 12.47 0.00 33.28 4.79
1507 1658 1.003112 TCCTAAAATGCCACGCGGT 60.003 52.632 12.47 0.00 33.28 5.68
1509 1660 1.721487 CCTCCTAAAATGCCACGCG 59.279 57.895 3.53 3.53 0.00 6.01
1511 1662 0.451783 GTGCCTCCTAAAATGCCACG 59.548 55.000 0.00 0.00 0.00 4.94
1514 1665 1.132453 GAACGTGCCTCCTAAAATGCC 59.868 52.381 0.00 0.00 0.00 4.40
1573 1887 1.273327 GCCTGTTGGTTTGGGATCAAG 59.727 52.381 0.00 0.00 33.98 3.02
1574 1888 1.337118 GCCTGTTGGTTTGGGATCAA 58.663 50.000 0.00 0.00 35.27 2.57
1582 1896 1.228154 GTCCTCGGCCTGTTGGTTT 60.228 57.895 0.00 0.00 35.27 3.27
1791 2123 3.390967 TGTCCATCTTCTGTGGAACTTGA 59.609 43.478 0.00 0.00 46.67 3.02
1828 2354 7.975866 ACATTCGATTAGCATTCAAATGTTC 57.024 32.000 4.76 0.00 38.65 3.18
1830 2356 7.537715 TCAACATTCGATTAGCATTCAAATGT 58.462 30.769 4.76 0.00 38.65 2.71
1831 2357 7.974243 TCAACATTCGATTAGCATTCAAATG 57.026 32.000 0.00 0.00 39.40 2.32
1847 2395 5.359009 AGAACACATCCATCCATCAACATTC 59.641 40.000 0.00 0.00 0.00 2.67
1848 2396 5.266788 AGAACACATCCATCCATCAACATT 58.733 37.500 0.00 0.00 0.00 2.71
1863 2411 1.605710 GACAGCACTGCAAGAACACAT 59.394 47.619 3.30 0.00 37.43 3.21
1881 2433 4.148825 ATCCCGCTCACCGCAGAC 62.149 66.667 0.00 0.00 39.08 3.51
1943 2581 2.407361 ACGCTAAAATCTGTCGACAACG 59.593 45.455 20.49 9.16 41.26 4.10
1944 2582 3.183775 ACACGCTAAAATCTGTCGACAAC 59.816 43.478 20.49 0.00 0.00 3.32
1950 2588 5.120830 ACAAGATGACACGCTAAAATCTGTC 59.879 40.000 0.00 0.00 34.74 3.51
1952 2590 5.536554 ACAAGATGACACGCTAAAATCTG 57.463 39.130 0.00 0.00 0.00 2.90
1979 2744 8.867935 TGTTTTCACAACAAACTACATTCATTG 58.132 29.630 0.00 0.00 35.50 2.82
1981 2746 7.222611 GCTGTTTTCACAACAAACTACATTCAT 59.777 33.333 0.00 0.00 35.50 2.57
1989 2855 2.490115 TCCGCTGTTTTCACAACAAACT 59.510 40.909 0.00 0.00 35.50 2.66
2350 3918 1.368019 CGTCTGCGTTTGTGCTGTG 60.368 57.895 0.00 0.00 35.55 3.66
2372 3940 5.470845 AAAATTAGTCGTGCTCTGTATGC 57.529 39.130 0.00 0.00 0.00 3.14
2397 4251 1.533625 CAACAGGCCGGAAATCAAGA 58.466 50.000 10.86 0.00 0.00 3.02
2400 4254 1.228398 TGCAACAGGCCGGAAATCA 60.228 52.632 10.86 0.00 43.89 2.57
2402 4256 2.639327 GCTGCAACAGGCCGGAAAT 61.639 57.895 10.86 0.00 43.89 2.17
2425 4285 3.260205 AGGGAAGAGGATGAAGGTGAAA 58.740 45.455 0.00 0.00 0.00 2.69
2446 4306 2.029815 TAGCACAGCGCAACGGAA 59.970 55.556 11.47 0.00 46.13 4.30
2452 4312 2.436469 CCCATGTAGCACAGCGCA 60.436 61.111 11.47 0.00 46.13 6.09
2509 4369 5.724370 TGGGATAGATTTGTAGAAGGTGTCA 59.276 40.000 0.00 0.00 0.00 3.58
2553 4414 3.186409 TCGATCTTGTTGCAGCTGTAAAC 59.814 43.478 19.29 20.27 0.00 2.01
2612 4488 2.504681 CCAAAACATCGCCGCTGC 60.505 61.111 0.00 0.00 0.00 5.25
2779 4655 1.946984 AGTTCACCTCCGGGATGTAA 58.053 50.000 0.00 0.00 36.25 2.41
2869 4745 1.142965 CGTCACCACGCATATCCCA 59.857 57.895 0.00 0.00 39.69 4.37
2881 4757 0.895530 TGATGGAGAAGACCGTCACC 59.104 55.000 0.40 0.00 46.81 4.02
2971 4847 2.184322 GCGAGCCCGAAGATGACA 59.816 61.111 0.00 0.00 38.22 3.58
3109 4985 1.089920 GGTCGAGCTCGTACCAGTAA 58.910 55.000 33.67 16.38 38.50 2.24
3286 5162 4.335416 GGAGGTTCTTGATGGACATGAAA 58.665 43.478 0.00 0.00 41.80 2.69
3460 5336 2.292267 GCCTCATCATGGACGAACAAT 58.708 47.619 0.00 0.00 0.00 2.71
3490 5366 3.529341 ATCGTCGGTGTGCTGGCAA 62.529 57.895 0.00 0.00 0.00 4.52
3538 5426 4.221422 GCTACCCGCCGAGCATCA 62.221 66.667 0.00 0.00 38.62 3.07
3787 5675 8.994429 AGAACACTGAATACAAACTGATCTAG 57.006 34.615 0.00 0.00 0.00 2.43
3840 7346 0.032678 ACTAGAGATGGCGCCATTCG 59.967 55.000 40.56 26.87 36.70 3.34
3863 7759 0.601558 ACTCGTTAGCCAGCGAAGAA 59.398 50.000 0.00 0.00 36.93 2.52
3865 7761 1.134530 CGACTCGTTAGCCAGCGAAG 61.135 60.000 0.00 0.00 36.93 3.79
3866 7762 1.154093 CGACTCGTTAGCCAGCGAA 60.154 57.895 0.00 0.00 36.93 4.70
3867 7763 1.020861 TACGACTCGTTAGCCAGCGA 61.021 55.000 9.84 0.00 41.54 4.93
3868 7764 0.860618 GTACGACTCGTTAGCCAGCG 60.861 60.000 9.84 0.00 41.54 5.18
3869 7765 0.860618 CGTACGACTCGTTAGCCAGC 60.861 60.000 10.44 0.00 41.54 4.85
3870 7766 0.445436 ACGTACGACTCGTTAGCCAG 59.555 55.000 24.41 0.00 41.54 4.85
3871 7767 0.166597 CACGTACGACTCGTTAGCCA 59.833 55.000 24.41 0.00 41.54 4.75
3873 7769 1.518286 GTCACGTACGACTCGTTAGC 58.482 55.000 24.41 0.35 41.54 3.09
3874 7770 1.201965 GGGTCACGTACGACTCGTTAG 60.202 57.143 24.41 6.90 41.54 2.34
3899 7797 3.194968 ACGGGCCGAAACTGGATATATAG 59.805 47.826 35.78 0.00 0.00 1.31
3905 7803 0.538746 AAAACGGGCCGAAACTGGAT 60.539 50.000 35.78 3.72 0.00 3.41
3957 7855 2.152078 GGCATAACGCGCTTTGTGC 61.152 57.895 31.20 31.20 43.84 4.57
4071 7969 6.748132 TCAGGACCAATGTTTTCAAAATCTC 58.252 36.000 0.00 0.00 0.00 2.75
4286 8186 8.526147 ACATCTGGGAAAACATATTTCTTTCAG 58.474 33.333 1.47 6.88 31.93 3.02
4306 8206 5.605564 TTGTGAACATTCGGTAACATCTG 57.394 39.130 0.00 0.00 0.00 2.90
4310 8210 9.751542 AATAAAATTTGTGAACATTCGGTAACA 57.248 25.926 0.00 0.00 0.00 2.41
4451 8354 4.099633 CCTGCAGGAGATTCCCATAGATA 58.900 47.826 29.88 0.00 37.19 1.98
4487 8406 3.159213 TGGTGGAACGTTACTCCTCTA 57.841 47.619 27.26 10.32 38.12 2.43
4488 8407 2.005370 TGGTGGAACGTTACTCCTCT 57.995 50.000 27.26 0.00 38.12 3.69
4489 8408 4.460948 TTATGGTGGAACGTTACTCCTC 57.539 45.455 27.26 14.14 38.12 3.71
4490 8409 4.529377 TCTTTATGGTGGAACGTTACTCCT 59.471 41.667 27.26 17.14 38.12 3.69
4491 8410 4.824289 TCTTTATGGTGGAACGTTACTCC 58.176 43.478 22.19 22.19 38.12 3.85
4631 8567 0.605589 AGCAAACTGAGAGGGTCTCG 59.394 55.000 0.00 0.00 46.25 4.04
4655 8591 9.561069 AAAACATAGTTTAGGCTGTATATGGAG 57.439 33.333 0.00 0.00 0.00 3.86
4666 8612 8.925161 TTTATCATGCAAAACATAGTTTAGGC 57.075 30.769 0.00 10.42 36.64 3.93
4695 8641 2.100749 CCGTTTAGGGATCCATTTTGGC 59.899 50.000 15.23 0.00 35.03 4.52
4707 8653 5.106436 GGAAAAGTGTATTCACCGTTTAGGG 60.106 44.000 0.00 0.00 46.96 3.53
4712 8658 4.710324 TCTGGAAAAGTGTATTCACCGTT 58.290 39.130 0.00 0.00 44.83 4.44
4733 8679 9.708222 GTGTATTCTCATTACATTGTGTGAATC 57.292 33.333 0.00 0.00 38.63 2.52


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

AutoCloner maintained by Alex Coulton.