Multiple sequence alignment - TraesCS5B01G468100

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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 TraesCS5B01G468100 chr5B 100.000 3752 0 0 1 3752 641713423 641717174 0.000000e+00 6929
1 TraesCS5B01G468100 chr5B 88.174 1353 115 26 1834 3150 641699145 641700488 0.000000e+00 1570
2 TraesCS5B01G468100 chr5B 84.977 852 97 14 947 1797 641698324 641699145 0.000000e+00 835
3 TraesCS5B01G468100 chr5B 91.566 83 4 2 1 83 641670939 641671018 1.100000e-20 111
4 TraesCS5B01G468100 chr5D 87.585 3085 268 56 77 3103 510655869 510658896 0.000000e+00 3469
5 TraesCS5B01G468100 chr5D 88.388 577 40 9 3186 3751 510658940 510659500 0.000000e+00 669
6 TraesCS5B01G468100 chr5A 88.924 1562 119 12 1406 2950 638817779 638819303 0.000000e+00 1877
7 TraesCS5B01G468100 chr5A 90.180 835 47 19 2947 3751 638819948 638820777 0.000000e+00 1055
8 TraesCS5B01G468100 chr5A 82.854 869 112 20 77 925 638816580 638817431 0.000000e+00 745
9 TraesCS5B01G468100 chr5A 84.437 302 41 2 947 1248 638817486 638817781 3.670000e-75 292
10 TraesCS5B01G468100 chr1D 78.589 1630 293 36 1147 2754 7028149 7029744 0.000000e+00 1026
11 TraesCS5B01G468100 chr1D 81.113 1096 181 22 1672 2754 7050738 7051820 0.000000e+00 854
12 TraesCS5B01G468100 chr2B 81.162 1136 200 11 1626 2754 402556950 402555822 0.000000e+00 900
13 TraesCS5B01G468100 chr6A 83.612 958 154 2 1672 2629 610269603 610270557 0.000000e+00 896
14 TraesCS5B01G468100 chr6B 82.690 959 161 4 1672 2629 706974040 706974994 0.000000e+00 846
15 TraesCS5B01G468100 chr6B 75.806 372 80 10 476 842 706972976 706973342 2.980000e-41 180
16 TraesCS5B01G468100 chr1A 80.633 1074 197 8 1690 2757 9128061 9126993 0.000000e+00 821


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 TraesCS5B01G468100 chr5B 641713423 641717174 3751 False 6929.00 6929 100.00000 1 3752 1 chr5B.!!$F2 3751
1 TraesCS5B01G468100 chr5B 641698324 641700488 2164 False 1202.50 1570 86.57550 947 3150 2 chr5B.!!$F3 2203
2 TraesCS5B01G468100 chr5D 510655869 510659500 3631 False 2069.00 3469 87.98650 77 3751 2 chr5D.!!$F1 3674
3 TraesCS5B01G468100 chr5A 638816580 638820777 4197 False 992.25 1877 86.59875 77 3751 4 chr5A.!!$F1 3674
4 TraesCS5B01G468100 chr1D 7028149 7029744 1595 False 1026.00 1026 78.58900 1147 2754 1 chr1D.!!$F1 1607
5 TraesCS5B01G468100 chr1D 7050738 7051820 1082 False 854.00 854 81.11300 1672 2754 1 chr1D.!!$F2 1082
6 TraesCS5B01G468100 chr2B 402555822 402556950 1128 True 900.00 900 81.16200 1626 2754 1 chr2B.!!$R1 1128
7 TraesCS5B01G468100 chr6A 610269603 610270557 954 False 896.00 896 83.61200 1672 2629 1 chr6A.!!$F1 957
8 TraesCS5B01G468100 chr6B 706972976 706974994 2018 False 513.00 846 79.24800 476 2629 2 chr6B.!!$F1 2153
9 TraesCS5B01G468100 chr1A 9126993 9128061 1068 True 821.00 821 80.63300 1690 2757 1 chr1A.!!$R1 1067

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
68 69 0.106894 CCTTCGCTCCAATACCTCCC 59.893 60.0 0.0 0.0 0.0 4.30 F
1585 1643 0.040058 TAGCCCCTCCAGACGTTACA 59.960 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1659 0.322008 GGGAGCAGAACTGGAGTTGG 60.322 60.0 0.0 0.0 38.56 3.77 R
2758 2841 1.260544 GGAATTTCTTGGCTGCACCT 58.739 50.0 0.5 0.0 40.22 4.00 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
33 34 4.065321 CGCAGGTCTGATAATTTCTCCT 57.935 45.455 1.65 0.00 0.00 3.69
34 35 4.446371 CGCAGGTCTGATAATTTCTCCTT 58.554 43.478 1.65 0.00 0.00 3.36
35 36 5.601662 CGCAGGTCTGATAATTTCTCCTTA 58.398 41.667 1.65 0.00 0.00 2.69
36 37 6.049149 CGCAGGTCTGATAATTTCTCCTTAA 58.951 40.000 1.65 0.00 0.00 1.85
37 38 6.708054 CGCAGGTCTGATAATTTCTCCTTAAT 59.292 38.462 1.65 0.00 0.00 1.40
38 39 7.095439 CGCAGGTCTGATAATTTCTCCTTAATC 60.095 40.741 1.65 0.00 0.00 1.75
39 40 7.936301 GCAGGTCTGATAATTTCTCCTTAATCT 59.064 37.037 1.65 0.00 0.00 2.40
40 41 9.270640 CAGGTCTGATAATTTCTCCTTAATCTG 57.729 37.037 0.00 0.00 0.00 2.90
41 42 7.936301 AGGTCTGATAATTTCTCCTTAATCTGC 59.064 37.037 0.00 0.00 0.00 4.26
42 43 7.716998 GGTCTGATAATTTCTCCTTAATCTGCA 59.283 37.037 0.00 0.00 0.00 4.41
43 44 9.113838 GTCTGATAATTTCTCCTTAATCTGCAA 57.886 33.333 0.00 0.00 0.00 4.08
44 45 9.113838 TCTGATAATTTCTCCTTAATCTGCAAC 57.886 33.333 0.00 0.00 0.00 4.17
45 46 8.225603 TGATAATTTCTCCTTAATCTGCAACC 57.774 34.615 0.00 0.00 0.00 3.77
46 47 5.921962 AATTTCTCCTTAATCTGCAACCC 57.078 39.130 0.00 0.00 0.00 4.11
47 48 4.380843 TTTCTCCTTAATCTGCAACCCA 57.619 40.909 0.00 0.00 0.00 4.51
48 49 4.591321 TTCTCCTTAATCTGCAACCCAT 57.409 40.909 0.00 0.00 0.00 4.00
49 50 4.156455 TCTCCTTAATCTGCAACCCATC 57.844 45.455 0.00 0.00 0.00 3.51
50 51 3.117888 TCTCCTTAATCTGCAACCCATCC 60.118 47.826 0.00 0.00 0.00 3.51
51 52 2.852449 TCCTTAATCTGCAACCCATCCT 59.148 45.455 0.00 0.00 0.00 3.24
52 53 3.269381 TCCTTAATCTGCAACCCATCCTT 59.731 43.478 0.00 0.00 0.00 3.36
53 54 3.633986 CCTTAATCTGCAACCCATCCTTC 59.366 47.826 0.00 0.00 0.00 3.46
54 55 1.755179 AATCTGCAACCCATCCTTCG 58.245 50.000 0.00 0.00 0.00 3.79
55 56 0.749454 ATCTGCAACCCATCCTTCGC 60.749 55.000 0.00 0.00 0.00 4.70
56 57 1.377725 CTGCAACCCATCCTTCGCT 60.378 57.895 0.00 0.00 0.00 4.93
57 58 1.372087 CTGCAACCCATCCTTCGCTC 61.372 60.000 0.00 0.00 0.00 5.03
58 59 2.115291 GCAACCCATCCTTCGCTCC 61.115 63.158 0.00 0.00 0.00 4.70
59 60 1.299648 CAACCCATCCTTCGCTCCA 59.700 57.895 0.00 0.00 0.00 3.86
60 61 0.322456 CAACCCATCCTTCGCTCCAA 60.322 55.000 0.00 0.00 0.00 3.53
61 62 0.625849 AACCCATCCTTCGCTCCAAT 59.374 50.000 0.00 0.00 0.00 3.16
62 63 1.507140 ACCCATCCTTCGCTCCAATA 58.493 50.000 0.00 0.00 0.00 1.90
63 64 1.141053 ACCCATCCTTCGCTCCAATAC 59.859 52.381 0.00 0.00 0.00 1.89
64 65 1.543429 CCCATCCTTCGCTCCAATACC 60.543 57.143 0.00 0.00 0.00 2.73
65 66 1.417890 CCATCCTTCGCTCCAATACCT 59.582 52.381 0.00 0.00 0.00 3.08
66 67 2.548920 CCATCCTTCGCTCCAATACCTC 60.549 54.545 0.00 0.00 0.00 3.85
67 68 1.120530 TCCTTCGCTCCAATACCTCC 58.879 55.000 0.00 0.00 0.00 4.30
68 69 0.106894 CCTTCGCTCCAATACCTCCC 59.893 60.000 0.00 0.00 0.00 4.30
69 70 0.249489 CTTCGCTCCAATACCTCCCG 60.249 60.000 0.00 0.00 0.00 5.14
70 71 0.685131 TTCGCTCCAATACCTCCCGA 60.685 55.000 0.00 0.00 0.00 5.14
71 72 1.067582 CGCTCCAATACCTCCCGAC 59.932 63.158 0.00 0.00 0.00 4.79
72 73 1.392710 CGCTCCAATACCTCCCGACT 61.393 60.000 0.00 0.00 0.00 4.18
73 74 0.389757 GCTCCAATACCTCCCGACTC 59.610 60.000 0.00 0.00 0.00 3.36
74 75 1.041437 CTCCAATACCTCCCGACTCC 58.959 60.000 0.00 0.00 0.00 3.85
75 76 0.398098 TCCAATACCTCCCGACTCCC 60.398 60.000 0.00 0.00 0.00 4.30
89 90 3.553508 CCGACTCCCGTTTCTTCTTACAA 60.554 47.826 0.00 0.00 36.31 2.41
95 96 4.758165 TCCCGTTTCTTCTTACAACATTCC 59.242 41.667 0.00 0.00 0.00 3.01
103 104 8.842358 TTCTTCTTACAACATTCCTATTCGTT 57.158 30.769 0.00 0.00 0.00 3.85
109 110 2.550978 ACATTCCTATTCGTTCAGGCG 58.449 47.619 0.00 0.00 0.00 5.52
185 186 2.505777 CGTGCAGAGCCTCGACTG 60.506 66.667 0.00 0.00 37.22 3.51
188 189 2.125753 GCAGAGCCTCGACTGTGG 60.126 66.667 2.93 0.00 36.62 4.17
189 190 2.936912 GCAGAGCCTCGACTGTGGT 61.937 63.158 2.93 0.00 36.62 4.16
196 197 1.535833 CCTCGACTGTGGTGACTACT 58.464 55.000 0.00 0.00 0.00 2.57
203 204 2.092323 CTGTGGTGACTACTCGGATGA 58.908 52.381 0.00 0.00 0.00 2.92
205 206 2.492088 TGTGGTGACTACTCGGATGAAG 59.508 50.000 0.00 0.00 0.00 3.02
206 207 2.492484 GTGGTGACTACTCGGATGAAGT 59.508 50.000 0.00 0.00 0.00 3.01
207 208 3.056749 GTGGTGACTACTCGGATGAAGTT 60.057 47.826 0.00 0.00 0.00 2.66
211 212 4.079970 TGACTACTCGGATGAAGTTCTGT 58.920 43.478 4.17 0.00 0.00 3.41
212 213 4.156190 TGACTACTCGGATGAAGTTCTGTC 59.844 45.833 4.17 2.66 0.00 3.51
220 221 4.568359 CGGATGAAGTTCTGTCGATCAATT 59.432 41.667 4.17 0.00 0.00 2.32
224 225 6.951256 TGAAGTTCTGTCGATCAATTACAG 57.049 37.500 4.17 7.74 41.58 2.74
230 231 1.933853 GTCGATCAATTACAGCGCCTT 59.066 47.619 2.29 0.00 0.00 4.35
234 235 1.737838 TCAATTACAGCGCCTTCCTG 58.262 50.000 2.29 0.00 36.41 3.86
241 242 1.302033 AGCGCCTTCCTGTCAACAG 60.302 57.895 2.29 3.08 43.40 3.16
242 243 1.301716 GCGCCTTCCTGTCAACAGA 60.302 57.895 11.70 0.00 46.59 3.41
255 256 5.939883 CCTGTCAACAGAGTGGATCAATAAA 59.060 40.000 11.70 0.00 46.59 1.40
256 257 6.093219 CCTGTCAACAGAGTGGATCAATAAAG 59.907 42.308 11.70 0.00 46.59 1.85
258 259 7.223584 TGTCAACAGAGTGGATCAATAAAGAA 58.776 34.615 0.00 0.00 0.00 2.52
259 260 7.173218 TGTCAACAGAGTGGATCAATAAAGAAC 59.827 37.037 0.00 0.00 0.00 3.01
266 267 5.104318 AGTGGATCAATAAAGAACTCTCCCC 60.104 44.000 0.00 0.00 0.00 4.81
267 268 4.166144 TGGATCAATAAAGAACTCTCCCCC 59.834 45.833 0.00 0.00 0.00 5.40
270 271 3.451178 TCAATAAAGAACTCTCCCCCTCG 59.549 47.826 0.00 0.00 0.00 4.63
273 274 0.116541 AAGAACTCTCCCCCTCGGAA 59.883 55.000 0.00 0.00 41.40 4.30
275 276 0.615261 GAACTCTCCCCCTCGGAAGT 60.615 60.000 0.00 0.00 41.40 3.01
348 352 2.275380 GGTTGGTGGGCGCTTTCAT 61.275 57.895 7.64 0.00 0.00 2.57
349 353 1.212751 GTTGGTGGGCGCTTTCATC 59.787 57.895 7.64 4.76 0.00 2.92
427 431 6.174720 TCTCTGTCTTCATTGTAACCAACT 57.825 37.500 0.00 0.00 32.26 3.16
429 433 5.680619 TCTGTCTTCATTGTAACCAACTGT 58.319 37.500 0.00 0.00 32.26 3.55
446 456 0.760567 TGTGGCCTCTCTGACACTGT 60.761 55.000 3.32 0.00 35.02 3.55
451 461 3.265791 GGCCTCTCTGACACTGTATTTG 58.734 50.000 0.00 0.00 0.00 2.32
453 463 3.265791 CCTCTCTGACACTGTATTTGGC 58.734 50.000 0.00 0.00 0.00 4.52
461 477 2.224185 ACACTGTATTTGGCACGTCAGA 60.224 45.455 12.70 0.00 0.00 3.27
469 485 1.069090 GGCACGTCAGAACCACAGA 59.931 57.895 0.00 0.00 0.00 3.41
561 577 2.202756 GTCCTCCGTGATGCCGAC 60.203 66.667 0.00 0.00 0.00 4.79
620 636 0.818445 GTGGCTGGCATGGAGATCAG 60.818 60.000 7.33 0.00 0.00 2.90
659 675 6.005823 TGGTGATGTTTGATCAGAAGAATGT 58.994 36.000 0.00 0.00 0.00 2.71
739 755 1.555075 TGGAAGGTATGAGGCTCACAC 59.445 52.381 21.37 19.28 0.00 3.82
746 762 5.140747 GGTATGAGGCTCACACCTAATAG 57.859 47.826 32.52 0.00 40.68 1.73
789 805 5.862924 AGAATCAGTTTTATGTGACCGTG 57.137 39.130 0.00 0.00 0.00 4.94
793 809 2.066262 AGTTTTATGTGACCGTGCTCG 58.934 47.619 0.14 0.14 0.00 5.03
856 872 5.050126 ACTCTACTTCTCATATCCACCGA 57.950 43.478 0.00 0.00 0.00 4.69
862 878 5.605534 ACTTCTCATATCCACCGATGAAAG 58.394 41.667 0.00 0.00 31.83 2.62
865 881 5.787380 TCTCATATCCACCGATGAAAGATG 58.213 41.667 0.00 0.00 31.83 2.90
866 882 5.305386 TCTCATATCCACCGATGAAAGATGT 59.695 40.000 0.00 0.00 31.83 3.06
870 886 7.990314 TCATATCCACCGATGAAAGATGTTAAA 59.010 33.333 0.00 0.00 0.00 1.52
876 892 6.578545 CACCGATGAAAGATGTTAAAACTGTG 59.421 38.462 0.00 0.00 0.00 3.66
893 909 2.227388 CTGTGAGTGATCCAACAAAGGC 59.773 50.000 0.00 0.00 0.00 4.35
928 944 2.544267 GGCAGCCTTCGTATCATTGTAC 59.456 50.000 3.29 0.00 0.00 2.90
931 947 4.682787 CAGCCTTCGTATCATTGTACAGA 58.317 43.478 0.00 0.00 0.00 3.41
932 948 5.109210 CAGCCTTCGTATCATTGTACAGAA 58.891 41.667 0.00 0.00 0.00 3.02
933 949 5.233050 CAGCCTTCGTATCATTGTACAGAAG 59.767 44.000 10.34 10.34 36.33 2.85
934 950 4.508124 GCCTTCGTATCATTGTACAGAAGG 59.492 45.833 23.63 23.63 45.42 3.46
940 956 5.974158 CGTATCATTGTACAGAAGGAGACAG 59.026 44.000 7.50 0.00 29.45 3.51
941 957 4.193826 TCATTGTACAGAAGGAGACAGC 57.806 45.455 0.00 0.00 0.00 4.40
943 959 3.667497 TTGTACAGAAGGAGACAGCTG 57.333 47.619 13.48 13.48 39.00 4.24
944 960 2.876581 TGTACAGAAGGAGACAGCTGA 58.123 47.619 23.35 0.00 37.25 4.26
951 1000 3.509575 AGAAGGAGACAGCTGAGTACTTG 59.490 47.826 23.35 0.00 0.00 3.16
953 1002 1.404851 GGAGACAGCTGAGTACTTGGC 60.405 57.143 23.35 11.48 0.00 4.52
955 1004 1.974236 AGACAGCTGAGTACTTGGCTT 59.026 47.619 23.35 10.95 32.30 4.35
958 1007 4.040461 AGACAGCTGAGTACTTGGCTTTTA 59.960 41.667 23.35 0.00 32.30 1.52
961 1010 5.770162 ACAGCTGAGTACTTGGCTTTTATTT 59.230 36.000 23.35 0.00 32.30 1.40
984 1033 8.696043 TTTATTATATCAAGCTGCCAACATCT 57.304 30.769 0.00 0.00 0.00 2.90
987 1036 2.275134 TCAAGCTGCCAACATCTCAA 57.725 45.000 0.00 0.00 0.00 3.02
1066 1115 5.319140 TGATGATGAAAATCAGTGGCTTG 57.681 39.130 0.00 0.00 33.59 4.01
1095 1144 4.902443 TGTAATGGAGATCTCTCGTCAC 57.098 45.455 21.81 13.45 43.76 3.67
1104 1153 4.206375 AGATCTCTCGTCACTGTGATGAT 58.794 43.478 27.60 16.14 41.15 2.45
1106 1155 4.362932 TCTCTCGTCACTGTGATGATTC 57.637 45.455 27.60 8.88 41.15 2.52
1109 1158 1.135112 TCGTCACTGTGATGATTCCCG 60.135 52.381 24.77 16.16 37.48 5.14
1112 1161 2.932614 GTCACTGTGATGATTCCCGAAG 59.067 50.000 14.37 0.00 0.00 3.79
1122 1171 2.521958 ATTCCCGAAGACCGTGCTGG 62.522 60.000 0.00 0.00 46.41 4.85
1139 1188 1.762957 CTGGTCGAATGGGGAGTACAT 59.237 52.381 0.00 0.00 0.00 2.29
1143 1192 3.393800 GTCGAATGGGGAGTACATGATG 58.606 50.000 0.00 0.00 0.00 3.07
1166 1215 2.890311 CTGGTGATTGTGCTTACCCAAA 59.110 45.455 0.00 0.00 32.20 3.28
1254 1303 8.154856 ACTAATTCAAACTACTTCAAGCCAGTA 58.845 33.333 0.00 0.00 0.00 2.74
1360 1409 9.679661 TGCTTACAGATGTTTCCTATTTTGATA 57.320 29.630 0.00 0.00 0.00 2.15
1503 1561 4.131596 TCTGGGTAACAAAGGTTTTCTCG 58.868 43.478 0.00 0.00 38.45 4.04
1563 1621 2.417933 CACTGCTTATCTCAAGGTGCAC 59.582 50.000 8.80 8.80 0.00 4.57
1577 1635 2.300967 TGCACCTTAGCCCCTCCAG 61.301 63.158 0.00 0.00 0.00 3.86
1578 1636 1.995626 GCACCTTAGCCCCTCCAGA 60.996 63.158 0.00 0.00 0.00 3.86
1579 1637 1.908483 CACCTTAGCCCCTCCAGAC 59.092 63.158 0.00 0.00 0.00 3.51
1580 1638 1.686110 ACCTTAGCCCCTCCAGACG 60.686 63.158 0.00 0.00 0.00 4.18
1581 1639 1.686110 CCTTAGCCCCTCCAGACGT 60.686 63.158 0.00 0.00 0.00 4.34
1582 1640 1.265454 CCTTAGCCCCTCCAGACGTT 61.265 60.000 0.00 0.00 0.00 3.99
1583 1641 1.481871 CTTAGCCCCTCCAGACGTTA 58.518 55.000 0.00 0.00 0.00 3.18
1584 1642 1.136500 CTTAGCCCCTCCAGACGTTAC 59.864 57.143 0.00 0.00 0.00 2.50
1585 1643 0.040058 TAGCCCCTCCAGACGTTACA 59.960 55.000 0.00 0.00 0.00 2.41
1586 1644 0.834687 AGCCCCTCCAGACGTTACAA 60.835 55.000 0.00 0.00 0.00 2.41
1587 1645 0.672711 GCCCCTCCAGACGTTACAAC 60.673 60.000 0.00 0.00 0.00 3.32
1588 1646 0.974383 CCCCTCCAGACGTTACAACT 59.026 55.000 0.00 0.00 0.00 3.16
1589 1647 1.067071 CCCCTCCAGACGTTACAACTC 60.067 57.143 0.00 0.00 0.00 3.01
1590 1648 1.893801 CCCTCCAGACGTTACAACTCT 59.106 52.381 0.00 0.00 0.00 3.24
1591 1649 3.087031 CCCTCCAGACGTTACAACTCTA 58.913 50.000 0.00 0.00 0.00 2.43
1592 1650 3.119566 CCCTCCAGACGTTACAACTCTAC 60.120 52.174 0.00 0.00 0.00 2.59
1593 1651 3.757493 CCTCCAGACGTTACAACTCTACT 59.243 47.826 0.00 0.00 0.00 2.57
1594 1652 4.379603 CCTCCAGACGTTACAACTCTACTG 60.380 50.000 0.00 0.00 0.00 2.74
1595 1653 3.057736 TCCAGACGTTACAACTCTACTGC 60.058 47.826 0.00 0.00 0.00 4.40
1596 1654 3.305131 CCAGACGTTACAACTCTACTGCA 60.305 47.826 0.00 0.00 0.00 4.41
1597 1655 4.486090 CAGACGTTACAACTCTACTGCAT 58.514 43.478 0.00 0.00 0.00 3.96
1598 1656 5.392703 CCAGACGTTACAACTCTACTGCATA 60.393 44.000 0.00 0.00 0.00 3.14
1599 1657 5.512082 CAGACGTTACAACTCTACTGCATAC 59.488 44.000 0.00 0.00 0.00 2.39
1600 1658 5.415077 AGACGTTACAACTCTACTGCATACT 59.585 40.000 0.00 0.00 0.00 2.12
1601 1659 5.638783 ACGTTACAACTCTACTGCATACTC 58.361 41.667 0.00 0.00 0.00 2.59
1602 1660 5.035443 CGTTACAACTCTACTGCATACTCC 58.965 45.833 0.00 0.00 0.00 3.85
1657 1721 7.396540 AGGAAGGTCATTTTAGCAATTACAG 57.603 36.000 0.00 0.00 0.00 2.74
1759 1827 6.478016 CAGCGATGAAGACTCTGAATTTGATA 59.522 38.462 0.00 0.00 0.00 2.15
1761 1829 7.714377 AGCGATGAAGACTCTGAATTTGATAAT 59.286 33.333 0.00 0.00 0.00 1.28
1780 1848 8.888836 TGATAATTTATCATCAGGAATGCCAT 57.111 30.769 13.83 0.00 40.09 4.40
1816 1884 3.071457 TGAGAAGTTGAGAGAATGCACCA 59.929 43.478 0.00 0.00 0.00 4.17
1828 1896 3.319122 AGAATGCACCAAAGGTTTCAGTC 59.681 43.478 0.00 7.25 33.76 3.51
1851 1919 1.272554 AACTCGGGGGAGGTGGATTC 61.273 60.000 0.00 0.00 0.00 2.52
1875 1943 5.109210 GGTTCTGTTTTTGAAGGGAAACTG 58.891 41.667 0.00 0.00 36.84 3.16
2074 2151 5.958380 TCACTTGATAGGTGGATCTACAACT 59.042 40.000 11.67 3.17 42.10 3.16
2175 2252 0.603065 AAGGGTGCAGGCGAAAAATC 59.397 50.000 0.00 0.00 0.00 2.17
2202 2279 5.814705 TCATTTGGACATCAAACCACAAAAC 59.185 36.000 0.00 0.00 46.72 2.43
2208 2285 6.048509 GGACATCAAACCACAAAACATTCTT 58.951 36.000 0.00 0.00 0.00 2.52
2225 2302 7.644986 ACATTCTTTTAGACGAGAACTTCAG 57.355 36.000 0.00 0.00 34.96 3.02
2319 2396 0.462047 GAACACCTGGGTATCTGGCG 60.462 60.000 0.00 0.00 37.94 5.69
2499 2579 5.541953 ATCAGTGGATTGATCTGATCGAA 57.458 39.130 11.46 8.03 42.81 3.71
2629 2709 3.244770 GGTGATCAAGGTGTTGGAAGGTA 60.245 47.826 0.00 0.00 34.09 3.08
2644 2724 5.657474 TGGAAGGTACTATAAGCGTTGAAG 58.343 41.667 0.00 0.00 38.49 3.02
2679 2759 4.215827 CAGAGCTTTCTCAATGCAAACTCT 59.784 41.667 0.00 0.00 41.81 3.24
2700 2780 5.181009 TCTGCCATGTCTGTTCAAGATAAG 58.819 41.667 0.00 0.00 37.23 1.73
2758 2841 1.529713 GGCCCACGGTGAAAAAGGA 60.530 57.895 10.28 0.00 0.00 3.36
2788 2875 3.318839 CCAAGAAATTCCACACTGCAGAA 59.681 43.478 23.35 3.93 0.00 3.02
2791 2878 5.382618 AGAAATTCCACACTGCAGAATTC 57.617 39.130 23.35 5.62 38.85 2.17
2805 2892 4.445052 TGCAGAATTCGATTTTTGCAACTG 59.555 37.500 26.41 14.36 38.95 3.16
2823 2910 7.145985 TGCAACTGATCTTTATCGTATCCTAC 58.854 38.462 0.00 0.00 34.60 3.18
2960 3706 8.638629 AGTGAGTAGTATAAGTGAAGTCTGTT 57.361 34.615 0.00 0.00 0.00 3.16
2961 3707 8.516234 AGTGAGTAGTATAAGTGAAGTCTGTTG 58.484 37.037 0.00 0.00 0.00 3.33
2967 3713 3.864789 AAGTGAAGTCTGTTGGGTGAT 57.135 42.857 0.00 0.00 0.00 3.06
3105 3893 4.682787 TCATATTGACGTAAGCAGGTGAG 58.317 43.478 0.00 0.00 45.62 3.51
3165 3961 0.823460 AATTGGCATGGGCTAAACCG 59.177 50.000 0.00 0.00 44.04 4.44
3181 3977 1.204146 ACCGTCTATCAGCACCCAAT 58.796 50.000 0.00 0.00 0.00 3.16
3182 3978 1.139058 ACCGTCTATCAGCACCCAATC 59.861 52.381 0.00 0.00 0.00 2.67
3184 3980 2.205074 CGTCTATCAGCACCCAATCAC 58.795 52.381 0.00 0.00 0.00 3.06
3419 4241 9.804977 AGTAAGAGACAGTACTAAAAGGAAGTA 57.195 33.333 0.00 0.00 0.00 2.24
3472 4294 4.196971 GGCAGTTACCATACCTCGAAAAT 58.803 43.478 0.00 0.00 0.00 1.82
3552 4379 9.030452 TGCACCTTCACCTTTAACATAATAATT 57.970 29.630 0.00 0.00 0.00 1.40
3585 4412 5.169295 AGTAATGACTGTAGCCTCGTTTTC 58.831 41.667 0.00 0.00 33.41 2.29
3637 4464 2.165437 TGTTTGGTTGTCTGAAACAGGC 59.835 45.455 0.00 0.00 39.58 4.85
3707 4534 9.230122 TGAATCATTAAAACTGCAAGACATAGA 57.770 29.630 0.00 0.00 37.43 1.98
3715 4543 3.507622 ACTGCAAGACATAGAAAAAGGCC 59.492 43.478 0.00 0.00 37.43 5.19
3730 4558 4.961438 AAAGGCCAAACAACAATCTGAT 57.039 36.364 5.01 0.00 0.00 2.90
3751 4579 4.281525 TGACCACGCAGAAAACTTTAAC 57.718 40.909 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.532155 AGACCTGCGGATCGGAGC 61.532 66.667 4.16 1.98 43.66 4.70
4 5 1.459455 ATCAGACCTGCGGATCGGAG 61.459 60.000 4.16 1.90 44.57 4.63
5 6 0.179001 TATCAGACCTGCGGATCGGA 60.179 55.000 4.16 0.00 33.37 4.55
6 7 0.673985 TTATCAGACCTGCGGATCGG 59.326 55.000 0.00 0.00 33.37 4.18
7 8 2.732412 ATTATCAGACCTGCGGATCG 57.268 50.000 0.00 0.00 33.37 3.69
8 9 4.636249 AGAAATTATCAGACCTGCGGATC 58.364 43.478 0.00 0.00 33.37 3.36
9 10 4.503991 GGAGAAATTATCAGACCTGCGGAT 60.504 45.833 0.00 0.00 35.53 4.18
10 11 3.181465 GGAGAAATTATCAGACCTGCGGA 60.181 47.826 0.00 0.00 0.00 5.54
11 12 3.134458 GGAGAAATTATCAGACCTGCGG 58.866 50.000 0.00 0.00 0.00 5.69
12 13 4.065321 AGGAGAAATTATCAGACCTGCG 57.935 45.455 0.00 0.00 30.84 5.18
13 14 7.936301 AGATTAAGGAGAAATTATCAGACCTGC 59.064 37.037 0.00 0.00 31.85 4.85
14 15 9.270640 CAGATTAAGGAGAAATTATCAGACCTG 57.729 37.037 0.00 0.00 31.85 4.00
15 16 7.936301 GCAGATTAAGGAGAAATTATCAGACCT 59.064 37.037 0.00 0.00 32.45 3.85
16 17 7.716998 TGCAGATTAAGGAGAAATTATCAGACC 59.283 37.037 0.00 0.00 0.00 3.85
17 18 8.668510 TGCAGATTAAGGAGAAATTATCAGAC 57.331 34.615 0.00 0.00 0.00 3.51
18 19 9.113838 GTTGCAGATTAAGGAGAAATTATCAGA 57.886 33.333 0.00 0.00 0.00 3.27
19 20 8.348507 GGTTGCAGATTAAGGAGAAATTATCAG 58.651 37.037 0.00 0.00 0.00 2.90
20 21 7.285401 GGGTTGCAGATTAAGGAGAAATTATCA 59.715 37.037 0.00 0.00 0.00 2.15
21 22 7.285401 TGGGTTGCAGATTAAGGAGAAATTATC 59.715 37.037 0.00 0.00 0.00 1.75
22 23 7.125391 TGGGTTGCAGATTAAGGAGAAATTAT 58.875 34.615 0.00 0.00 0.00 1.28
23 24 6.489603 TGGGTTGCAGATTAAGGAGAAATTA 58.510 36.000 0.00 0.00 0.00 1.40
24 25 5.332743 TGGGTTGCAGATTAAGGAGAAATT 58.667 37.500 0.00 0.00 0.00 1.82
25 26 4.934356 TGGGTTGCAGATTAAGGAGAAAT 58.066 39.130 0.00 0.00 0.00 2.17
26 27 4.380843 TGGGTTGCAGATTAAGGAGAAA 57.619 40.909 0.00 0.00 0.00 2.52
27 28 4.526970 GATGGGTTGCAGATTAAGGAGAA 58.473 43.478 0.00 0.00 0.00 2.87
28 29 3.117888 GGATGGGTTGCAGATTAAGGAGA 60.118 47.826 0.00 0.00 0.00 3.71
29 30 3.117738 AGGATGGGTTGCAGATTAAGGAG 60.118 47.826 0.00 0.00 0.00 3.69
30 31 2.852449 AGGATGGGTTGCAGATTAAGGA 59.148 45.455 0.00 0.00 0.00 3.36
31 32 3.303351 AGGATGGGTTGCAGATTAAGG 57.697 47.619 0.00 0.00 0.00 2.69
32 33 3.313526 CGAAGGATGGGTTGCAGATTAAG 59.686 47.826 0.00 0.00 0.00 1.85
33 34 3.278574 CGAAGGATGGGTTGCAGATTAA 58.721 45.455 0.00 0.00 0.00 1.40
34 35 2.917933 CGAAGGATGGGTTGCAGATTA 58.082 47.619 0.00 0.00 0.00 1.75
35 36 1.755179 CGAAGGATGGGTTGCAGATT 58.245 50.000 0.00 0.00 0.00 2.40
36 37 0.749454 GCGAAGGATGGGTTGCAGAT 60.749 55.000 0.00 0.00 0.00 2.90
37 38 1.377202 GCGAAGGATGGGTTGCAGA 60.377 57.895 0.00 0.00 0.00 4.26
38 39 1.372087 GAGCGAAGGATGGGTTGCAG 61.372 60.000 0.00 0.00 0.00 4.41
39 40 1.377202 GAGCGAAGGATGGGTTGCA 60.377 57.895 0.00 0.00 0.00 4.08
40 41 2.115291 GGAGCGAAGGATGGGTTGC 61.115 63.158 0.00 0.00 0.00 4.17
41 42 0.322456 TTGGAGCGAAGGATGGGTTG 60.322 55.000 0.00 0.00 0.00 3.77
42 43 0.625849 ATTGGAGCGAAGGATGGGTT 59.374 50.000 0.00 0.00 0.00 4.11
43 44 1.141053 GTATTGGAGCGAAGGATGGGT 59.859 52.381 0.00 0.00 0.00 4.51
44 45 1.543429 GGTATTGGAGCGAAGGATGGG 60.543 57.143 0.00 0.00 0.00 4.00
45 46 1.417890 AGGTATTGGAGCGAAGGATGG 59.582 52.381 0.00 0.00 0.00 3.51
46 47 2.548920 GGAGGTATTGGAGCGAAGGATG 60.549 54.545 0.00 0.00 0.00 3.51
47 48 1.694696 GGAGGTATTGGAGCGAAGGAT 59.305 52.381 0.00 0.00 0.00 3.24
48 49 1.120530 GGAGGTATTGGAGCGAAGGA 58.879 55.000 0.00 0.00 0.00 3.36
49 50 0.106894 GGGAGGTATTGGAGCGAAGG 59.893 60.000 0.00 0.00 0.00 3.46
50 51 0.249489 CGGGAGGTATTGGAGCGAAG 60.249 60.000 0.00 0.00 0.00 3.79
51 52 0.685131 TCGGGAGGTATTGGAGCGAA 60.685 55.000 0.00 0.00 0.00 4.70
52 53 1.076559 TCGGGAGGTATTGGAGCGA 60.077 57.895 0.00 0.00 0.00 4.93
53 54 1.067582 GTCGGGAGGTATTGGAGCG 59.932 63.158 0.00 0.00 0.00 5.03
54 55 0.389757 GAGTCGGGAGGTATTGGAGC 59.610 60.000 0.00 0.00 0.00 4.70
55 56 1.041437 GGAGTCGGGAGGTATTGGAG 58.959 60.000 0.00 0.00 0.00 3.86
56 57 0.398098 GGGAGTCGGGAGGTATTGGA 60.398 60.000 0.00 0.00 0.00 3.53
57 58 1.745320 CGGGAGTCGGGAGGTATTGG 61.745 65.000 0.00 0.00 34.75 3.16
58 59 1.041447 ACGGGAGTCGGGAGGTATTG 61.041 60.000 0.00 0.00 40.62 1.90
59 60 0.325016 AACGGGAGTCGGGAGGTATT 60.325 55.000 0.00 0.00 46.69 1.89
60 61 0.325016 AAACGGGAGTCGGGAGGTAT 60.325 55.000 0.00 0.00 46.69 2.73
61 62 0.967380 GAAACGGGAGTCGGGAGGTA 60.967 60.000 0.00 0.00 46.69 3.08
62 63 2.203743 AAACGGGAGTCGGGAGGT 60.204 61.111 0.00 0.00 46.69 3.85
63 64 1.542187 AAGAAACGGGAGTCGGGAGG 61.542 60.000 0.00 0.00 46.69 4.30
64 65 0.108756 GAAGAAACGGGAGTCGGGAG 60.109 60.000 0.00 0.00 46.69 4.30
65 66 0.541296 AGAAGAAACGGGAGTCGGGA 60.541 55.000 0.00 0.00 46.69 5.14
66 67 0.320697 AAGAAGAAACGGGAGTCGGG 59.679 55.000 0.00 0.00 46.69 5.14
67 68 2.029649 TGTAAGAAGAAACGGGAGTCGG 60.030 50.000 0.00 0.00 46.69 4.79
68 69 3.293311 TGTAAGAAGAAACGGGAGTCG 57.707 47.619 0.00 0.00 46.69 4.18
69 70 4.374399 TGTTGTAAGAAGAAACGGGAGTC 58.626 43.478 0.00 0.00 46.69 3.36
71 72 5.106673 GGAATGTTGTAAGAAGAAACGGGAG 60.107 44.000 0.00 0.00 0.00 4.30
72 73 4.758165 GGAATGTTGTAAGAAGAAACGGGA 59.242 41.667 0.00 0.00 0.00 5.14
73 74 4.760204 AGGAATGTTGTAAGAAGAAACGGG 59.240 41.667 0.00 0.00 0.00 5.28
74 75 5.941948 AGGAATGTTGTAAGAAGAAACGG 57.058 39.130 0.00 0.00 0.00 4.44
75 76 7.898309 CGAATAGGAATGTTGTAAGAAGAAACG 59.102 37.037 0.00 0.00 0.00 3.60
89 90 2.550978 CGCCTGAACGAATAGGAATGT 58.449 47.619 7.58 0.00 36.11 2.71
95 96 0.583438 CATGGCGCCTGAACGAATAG 59.417 55.000 29.70 2.17 34.06 1.73
103 104 3.329889 AGAACCCATGGCGCCTGA 61.330 61.111 29.70 8.87 0.00 3.86
109 110 1.187567 AAACTGGCAGAACCCATGGC 61.188 55.000 23.66 0.00 43.16 4.40
175 176 0.251209 TAGTCACCACAGTCGAGGCT 60.251 55.000 0.00 0.00 0.00 4.58
185 186 2.492484 ACTTCATCCGAGTAGTCACCAC 59.508 50.000 0.00 0.00 0.00 4.16
188 189 4.082679 ACAGAACTTCATCCGAGTAGTCAC 60.083 45.833 0.00 0.00 0.00 3.67
189 190 4.079970 ACAGAACTTCATCCGAGTAGTCA 58.920 43.478 0.00 0.00 0.00 3.41
196 197 2.752903 TGATCGACAGAACTTCATCCGA 59.247 45.455 0.00 0.00 0.00 4.55
203 204 4.327357 CGCTGTAATTGATCGACAGAACTT 59.673 41.667 16.61 0.00 42.65 2.66
205 206 3.542291 GCGCTGTAATTGATCGACAGAAC 60.542 47.826 16.61 7.16 42.65 3.01
206 207 2.603110 GCGCTGTAATTGATCGACAGAA 59.397 45.455 16.61 0.00 42.65 3.02
207 208 2.193447 GCGCTGTAATTGATCGACAGA 58.807 47.619 16.61 0.00 42.65 3.41
211 212 2.201732 GAAGGCGCTGTAATTGATCGA 58.798 47.619 7.64 0.00 0.00 3.59
212 213 1.261619 GGAAGGCGCTGTAATTGATCG 59.738 52.381 7.64 0.00 0.00 3.69
220 221 0.320421 GTTGACAGGAAGGCGCTGTA 60.320 55.000 7.64 0.00 0.00 2.74
224 225 1.294659 CTCTGTTGACAGGAAGGCGC 61.295 60.000 10.97 0.00 43.91 6.53
230 231 2.608623 TGATCCACTCTGTTGACAGGA 58.391 47.619 10.97 2.22 43.91 3.86
234 235 7.389053 AGTTCTTTATTGATCCACTCTGTTGAC 59.611 37.037 0.00 0.00 0.00 3.18
241 242 6.052360 GGGAGAGTTCTTTATTGATCCACTC 58.948 44.000 0.00 0.00 0.00 3.51
242 243 5.104318 GGGGAGAGTTCTTTATTGATCCACT 60.104 44.000 0.00 0.00 0.00 4.00
255 256 3.521810 TCCGAGGGGGAGAGTTCT 58.478 61.111 0.00 0.00 40.94 3.01
266 267 4.441634 CCTTGTACCTGAATACTTCCGAGG 60.442 50.000 0.00 0.00 0.00 4.63
267 268 4.401519 TCCTTGTACCTGAATACTTCCGAG 59.598 45.833 0.00 0.00 0.00 4.63
270 271 4.430908 CGTCCTTGTACCTGAATACTTCC 58.569 47.826 0.00 0.00 0.00 3.46
273 274 3.438183 ACCGTCCTTGTACCTGAATACT 58.562 45.455 0.00 0.00 0.00 2.12
275 276 4.343231 TGTACCGTCCTTGTACCTGAATA 58.657 43.478 0.00 0.00 38.21 1.75
281 285 2.084610 GGTTGTACCGTCCTTGTACC 57.915 55.000 0.00 0.00 38.21 3.34
313 317 1.215647 CCCTTGTCGAACGGAGGAG 59.784 63.158 11.41 0.00 0.00 3.69
348 352 2.975799 GCGCCAAAAGACCACCGA 60.976 61.111 0.00 0.00 0.00 4.69
349 353 3.254014 CTGCGCCAAAAGACCACCG 62.254 63.158 4.18 0.00 0.00 4.94
394 398 4.757799 TGAAGACAGAGAAGACGAAGAG 57.242 45.455 0.00 0.00 0.00 2.85
408 412 4.578516 CCACAGTTGGTTACAATGAAGACA 59.421 41.667 0.00 0.00 39.13 3.41
427 431 0.760567 ACAGTGTCAGAGAGGCCACA 60.761 55.000 5.01 0.00 0.00 4.17
429 433 2.238084 ATACAGTGTCAGAGAGGCCA 57.762 50.000 5.01 0.00 0.00 5.36
432 436 3.265791 GCCAAATACAGTGTCAGAGAGG 58.734 50.000 0.00 0.00 0.00 3.69
433 437 3.681897 GTGCCAAATACAGTGTCAGAGAG 59.318 47.826 0.00 0.00 0.00 3.20
437 441 2.143122 ACGTGCCAAATACAGTGTCAG 58.857 47.619 0.00 0.00 0.00 3.51
446 456 2.147958 GTGGTTCTGACGTGCCAAATA 58.852 47.619 0.00 0.00 32.26 1.40
451 461 0.320771 ATCTGTGGTTCTGACGTGCC 60.321 55.000 0.00 0.00 0.00 5.01
453 463 2.221749 CACAATCTGTGGTTCTGACGTG 59.778 50.000 0.00 0.00 44.27 4.49
561 577 3.450115 GACCAGACCCTCGTCCCG 61.450 72.222 0.00 0.00 40.12 5.14
566 582 1.293498 CCACTTGACCAGACCCTCG 59.707 63.158 0.00 0.00 0.00 4.63
569 585 1.600916 GTGCCACTTGACCAGACCC 60.601 63.158 0.00 0.00 0.00 4.46
620 636 3.365265 CCAGGTTGCCGTGCTTCC 61.365 66.667 0.00 1.05 0.00 3.46
659 675 3.004629 GTCAAATGACTGCCACACAATGA 59.995 43.478 6.30 0.00 41.65 2.57
739 755 7.225538 AGTCGAATTTGTTGCAGATCTATTAGG 59.774 37.037 0.00 0.00 0.00 2.69
746 762 6.408858 TCTTAGTCGAATTTGTTGCAGATC 57.591 37.500 0.00 0.00 0.00 2.75
789 805 2.492484 ACCGTATAATCCATCTCCGAGC 59.508 50.000 0.00 0.00 0.00 5.03
793 809 6.034591 CGACATAACCGTATAATCCATCTCC 58.965 44.000 0.00 0.00 0.00 3.71
856 872 8.450578 TCACTCACAGTTTTAACATCTTTCAT 57.549 30.769 0.00 0.00 0.00 2.57
862 878 6.801539 TGGATCACTCACAGTTTTAACATC 57.198 37.500 0.00 0.00 0.00 3.06
865 881 6.371809 TGTTGGATCACTCACAGTTTTAAC 57.628 37.500 0.00 0.00 0.00 2.01
866 882 7.397892 TTTGTTGGATCACTCACAGTTTTAA 57.602 32.000 0.00 0.00 0.00 1.52
870 886 3.885297 CCTTTGTTGGATCACTCACAGTT 59.115 43.478 0.00 0.00 0.00 3.16
876 892 3.674997 TGTAGCCTTTGTTGGATCACTC 58.325 45.455 0.00 0.00 0.00 3.51
893 909 1.952296 GGCTGCCATTCTGGAATGTAG 59.048 52.381 15.17 16.29 44.97 2.74
916 932 5.891451 TGTCTCCTTCTGTACAATGATACG 58.109 41.667 0.00 0.00 0.00 3.06
928 944 3.088532 AGTACTCAGCTGTCTCCTTCTG 58.911 50.000 14.67 0.00 0.00 3.02
931 947 2.564947 CCAAGTACTCAGCTGTCTCCTT 59.435 50.000 14.67 9.31 0.00 3.36
932 948 2.175202 CCAAGTACTCAGCTGTCTCCT 58.825 52.381 14.67 3.32 0.00 3.69
933 949 1.404851 GCCAAGTACTCAGCTGTCTCC 60.405 57.143 14.67 0.86 0.00 3.71
934 950 1.548269 AGCCAAGTACTCAGCTGTCTC 59.452 52.381 14.67 3.41 33.41 3.36
951 1000 9.358872 GGCAGCTTGATATAATAAATAAAAGCC 57.641 33.333 0.00 0.00 39.62 4.35
958 1007 9.305555 AGATGTTGGCAGCTTGATATAATAAAT 57.694 29.630 2.28 0.00 38.31 1.40
961 1010 7.452562 TGAGATGTTGGCAGCTTGATATAATA 58.547 34.615 2.28 0.00 42.00 0.98
967 1016 2.502142 TGAGATGTTGGCAGCTTGAT 57.498 45.000 2.28 0.00 42.00 2.57
979 1028 9.140874 TCTCATATACTGACTGAATTGAGATGT 57.859 33.333 0.00 0.00 34.89 3.06
1048 1097 4.699257 AGACTCAAGCCACTGATTTTCATC 59.301 41.667 0.00 0.00 0.00 2.92
1064 1113 6.838090 AGAGATCTCCATTACATCAGACTCAA 59.162 38.462 19.30 0.00 0.00 3.02
1066 1115 6.348458 CGAGAGATCTCCATTACATCAGACTC 60.348 46.154 19.30 4.17 39.79 3.36
1095 1144 2.555199 GGTCTTCGGGAATCATCACAG 58.445 52.381 0.00 0.00 0.00 3.66
1122 1171 3.181465 ACATCATGTACTCCCCATTCGAC 60.181 47.826 0.00 0.00 0.00 4.20
1123 1172 3.038280 ACATCATGTACTCCCCATTCGA 58.962 45.455 0.00 0.00 0.00 3.71
1124 1173 3.070159 AGACATCATGTACTCCCCATTCG 59.930 47.826 0.00 0.00 0.00 3.34
1128 1177 2.118679 CCAGACATCATGTACTCCCCA 58.881 52.381 0.00 0.00 0.00 4.96
1129 1178 2.119495 ACCAGACATCATGTACTCCCC 58.881 52.381 0.00 0.00 0.00 4.81
1139 1188 2.865119 AGCACAATCACCAGACATCA 57.135 45.000 0.00 0.00 0.00 3.07
1143 1192 2.084546 GGGTAAGCACAATCACCAGAC 58.915 52.381 0.00 0.00 32.42 3.51
1166 1215 2.654877 CGTACTCCCCGCACACTT 59.345 61.111 0.00 0.00 0.00 3.16
1254 1303 3.356529 AGATTTGCTTTCCGGTCATCT 57.643 42.857 0.00 0.00 0.00 2.90
1360 1409 1.832883 TTCACAACGGCATGGCTATT 58.167 45.000 18.09 8.69 0.00 1.73
1362 1411 1.832883 AATTCACAACGGCATGGCTA 58.167 45.000 18.09 0.00 0.00 3.93
1368 1417 4.744570 TGTTTGTTAAATTCACAACGGCA 58.255 34.783 3.25 1.94 33.81 5.69
1503 1561 5.928264 AGCTTCAGGTTTTATTGATTGCAAC 59.072 36.000 0.00 0.00 36.72 4.17
1563 1621 1.265454 AACGTCTGGAGGGGCTAAGG 61.265 60.000 0.00 0.00 0.00 2.69
1577 1635 5.638783 AGTATGCAGTAGAGTTGTAACGTC 58.361 41.667 0.00 0.00 0.00 4.34
1578 1636 5.392811 GGAGTATGCAGTAGAGTTGTAACGT 60.393 44.000 0.00 0.00 0.00 3.99
1579 1637 5.035443 GGAGTATGCAGTAGAGTTGTAACG 58.965 45.833 0.00 0.00 0.00 3.18
1580 1638 5.962433 TGGAGTATGCAGTAGAGTTGTAAC 58.038 41.667 0.00 0.00 0.00 2.50
1581 1639 6.210784 AGTTGGAGTATGCAGTAGAGTTGTAA 59.789 38.462 0.00 0.00 38.09 2.41
1582 1640 5.715279 AGTTGGAGTATGCAGTAGAGTTGTA 59.285 40.000 0.00 0.00 38.09 2.41
1583 1641 4.528596 AGTTGGAGTATGCAGTAGAGTTGT 59.471 41.667 0.00 0.00 38.09 3.32
1584 1642 5.078411 AGTTGGAGTATGCAGTAGAGTTG 57.922 43.478 0.00 0.00 38.09 3.16
1585 1643 4.160626 GGAGTTGGAGTATGCAGTAGAGTT 59.839 45.833 0.00 0.00 38.09 3.01
1586 1644 3.702045 GGAGTTGGAGTATGCAGTAGAGT 59.298 47.826 0.00 0.00 38.09 3.24
1587 1645 3.701542 TGGAGTTGGAGTATGCAGTAGAG 59.298 47.826 0.00 0.00 38.09 2.43
1588 1646 3.701542 CTGGAGTTGGAGTATGCAGTAGA 59.298 47.826 0.00 0.00 38.09 2.59
1589 1647 3.449018 ACTGGAGTTGGAGTATGCAGTAG 59.551 47.826 0.00 0.00 42.82 2.57
1590 1648 3.441101 ACTGGAGTTGGAGTATGCAGTA 58.559 45.455 0.00 0.00 42.82 2.74
1591 1649 2.260822 ACTGGAGTTGGAGTATGCAGT 58.739 47.619 0.00 0.00 38.09 4.40
1592 1650 3.055530 AGAACTGGAGTTGGAGTATGCAG 60.056 47.826 0.00 0.00 38.09 4.41
1593 1651 2.906389 AGAACTGGAGTTGGAGTATGCA 59.094 45.455 0.00 0.00 38.56 3.96
1594 1652 3.265791 CAGAACTGGAGTTGGAGTATGC 58.734 50.000 0.00 0.00 38.56 3.14
1595 1653 3.055530 AGCAGAACTGGAGTTGGAGTATG 60.056 47.826 0.00 0.00 38.56 2.39
1596 1654 3.177228 AGCAGAACTGGAGTTGGAGTAT 58.823 45.455 0.00 0.00 38.56 2.12
1597 1655 2.563179 GAGCAGAACTGGAGTTGGAGTA 59.437 50.000 0.00 0.00 38.56 2.59
1598 1656 1.346068 GAGCAGAACTGGAGTTGGAGT 59.654 52.381 0.00 0.00 38.56 3.85
1599 1657 1.338579 GGAGCAGAACTGGAGTTGGAG 60.339 57.143 0.00 0.00 38.56 3.86
1600 1658 0.687354 GGAGCAGAACTGGAGTTGGA 59.313 55.000 0.00 0.00 38.56 3.53
1601 1659 0.322008 GGGAGCAGAACTGGAGTTGG 60.322 60.000 0.00 0.00 38.56 3.77
1602 1660 0.397941 TGGGAGCAGAACTGGAGTTG 59.602 55.000 0.00 0.00 38.56 3.16
1759 1827 7.256190 CCTCAATGGCATTCCTGATGATAAATT 60.256 37.037 10.36 0.00 38.03 1.82
1761 1829 5.537295 CCTCAATGGCATTCCTGATGATAAA 59.463 40.000 10.36 0.00 38.03 1.40
1780 1848 7.393234 TCTCAACTTCTCAAAAGAAAACCTCAA 59.607 33.333 0.00 0.00 40.95 3.02
1816 1884 4.142249 CCCGAGTTTTTGACTGAAACCTTT 60.142 41.667 0.00 0.00 39.19 3.11
1828 1896 0.893727 CCACCTCCCCCGAGTTTTTG 60.894 60.000 0.00 0.00 33.93 2.44
1851 1919 4.109766 GTTTCCCTTCAAAAACAGAACCG 58.890 43.478 0.00 0.00 35.83 4.44
1875 1943 3.056250 TCACTGCAACTCTCTCTTCATCC 60.056 47.826 0.00 0.00 0.00 3.51
1941 2009 2.159517 GCTGCCAATAGTTTCAACCTCG 60.160 50.000 0.00 0.00 0.00 4.63
1987 2055 7.768120 AGATTTCTCTACACAGAAGCCAATAAG 59.232 37.037 0.00 0.00 33.85 1.73
2074 2151 7.418827 CCAATCAAAAGGGGCATTATTATGACA 60.419 37.037 0.00 0.00 41.94 3.58
2175 2252 2.228582 TGGTTTGATGTCCAAATGAGCG 59.771 45.455 0.00 0.00 45.48 5.03
2202 2279 7.505646 CACTGAAGTTCTCGTCTAAAAGAATG 58.494 38.462 4.17 0.00 34.26 2.67
2208 2285 3.069016 TGGCACTGAAGTTCTCGTCTAAA 59.931 43.478 4.17 0.00 0.00 1.85
2319 2396 1.742831 TGCGATGTTAACCATTCAGGC 59.257 47.619 2.48 0.00 43.14 4.85
2499 2579 9.645059 CGTGAGACCATATCATCACTATTATTT 57.355 33.333 3.06 0.00 39.89 1.40
2553 2633 2.043625 CAGGCACCACATTGCAAGT 58.956 52.632 4.94 0.17 44.94 3.16
2629 2709 4.188247 TGTCAGCTTCAACGCTTATAGT 57.812 40.909 0.00 0.00 38.41 2.12
2644 2724 5.583854 TGAGAAAGCTCTGAATTATGTCAGC 59.416 40.000 0.00 0.00 44.01 4.26
2679 2759 3.691118 GCTTATCTTGAACAGACATGGCA 59.309 43.478 0.00 0.00 32.83 4.92
2700 2780 2.073816 CGAACCGAATATGGGTATGGC 58.926 52.381 0.00 0.00 36.57 4.40
2758 2841 1.260544 GGAATTTCTTGGCTGCACCT 58.739 50.000 0.50 0.00 40.22 4.00
2788 2875 9.294030 GATAAAGATCAGTTGCAAAAATCGAAT 57.706 29.630 0.00 1.92 31.78 3.34
2791 2878 6.742718 ACGATAAAGATCAGTTGCAAAAATCG 59.257 34.615 0.00 8.09 37.81 3.34
2823 2910 5.583061 ACATGCTTCCAATGCACAAATATTG 59.417 36.000 0.00 0.00 43.59 1.90
2935 3031 8.516234 CAACAGACTTCACTTATACTACTCACT 58.484 37.037 0.00 0.00 0.00 3.41
3105 3893 6.199393 ACAACTGCAAAAGAGACGAAATTAC 58.801 36.000 0.00 0.00 0.00 1.89
3165 3961 3.550437 AGTGATTGGGTGCTGATAGAC 57.450 47.619 0.00 0.00 0.00 2.59
3181 3977 6.213397 TCACCATCCAAGAAGAGAAATAGTGA 59.787 38.462 0.00 0.00 0.00 3.41
3182 3978 6.409704 TCACCATCCAAGAAGAGAAATAGTG 58.590 40.000 0.00 0.00 0.00 2.74
3184 3980 7.391554 TGTTTCACCATCCAAGAAGAGAAATAG 59.608 37.037 0.00 0.00 0.00 1.73
3393 4215 8.709272 ACTTCCTTTTAGTACTGTCTCTTACT 57.291 34.615 5.39 0.00 33.11 2.24
3552 4379 6.763135 GGCTACAGTCATTACTCATCATGAAA 59.237 38.462 0.00 0.00 31.97 2.69
3554 4381 5.600069 AGGCTACAGTCATTACTCATCATGA 59.400 40.000 0.00 0.00 31.97 3.07
3585 4412 1.354368 ACAGTTCTACACCATTGGGGG 59.646 52.381 10.34 2.38 46.04 5.40
3637 4464 5.565592 TGTTAATAGCAGGCACAAATCTG 57.434 39.130 0.00 0.00 0.00 2.90
3697 4524 5.841810 TGTTTGGCCTTTTTCTATGTCTTG 58.158 37.500 3.32 0.00 0.00 3.02
3699 4526 5.362430 TGTTGTTTGGCCTTTTTCTATGTCT 59.638 36.000 3.32 0.00 0.00 3.41
3707 4534 5.096443 TCAGATTGTTGTTTGGCCTTTTT 57.904 34.783 3.32 0.00 0.00 1.94
3708 4535 4.751767 TCAGATTGTTGTTTGGCCTTTT 57.248 36.364 3.32 0.00 0.00 2.27
3715 4543 4.221342 CGTGGTCATCAGATTGTTGTTTG 58.779 43.478 0.00 0.00 0.00 2.93
3730 4558 4.281525 GTTAAAGTTTTCTGCGTGGTCA 57.718 40.909 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.