Multiple sequence alignment - TraesCS3B01G386600

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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 TraesCS3B01G386600 chr3B 100.000 6190 0 0 1 6190 607379125 607385314 0.000000e+00 11431.0
1 TraesCS3B01G386600 chr3B 76.577 1046 163 42 4205 5180 750207916 750206883 3.330000e-137 499.0
2 TraesCS3B01G386600 chr3B 79.661 118 15 5 2354 2471 750209975 750209867 6.650000e-10 76.8
3 TraesCS3B01G386600 chr3B 90.909 55 5 0 2213 2267 730819340 730819394 2.390000e-09 75.0
4 TraesCS3B01G386600 chr3A 94.420 4731 146 42 1518 6190 601560264 601555594 0.000000e+00 7166.0
5 TraesCS3B01G386600 chr3A 90.138 1156 60 13 379 1516 601561412 601560293 0.000000e+00 1454.0
6 TraesCS3B01G386600 chr3A 76.634 719 120 25 4193 4875 697749012 697748306 2.740000e-93 353.0
7 TraesCS3B01G386600 chr3A 81.119 286 32 14 4912 5180 697748175 697747895 6.290000e-50 209.0
8 TraesCS3B01G386600 chr3A 88.776 98 8 3 1305 1402 697751477 697751383 3.920000e-22 117.0
9 TraesCS3B01G386600 chr3A 83.051 118 11 4 2354 2471 697750820 697750712 1.420000e-16 99.0
10 TraesCS3B01G386600 chr3D 93.146 4844 188 50 278 5043 459462603 459467380 0.000000e+00 6974.0
11 TraesCS3B01G386600 chr3D 98.179 1153 19 1 5040 6190 459467451 459468603 0.000000e+00 2012.0
12 TraesCS3B01G386600 chr3D 86.441 118 12 3 118 231 459462206 459462323 6.510000e-25 126.0
13 TraesCS3B01G386600 chr3D 90.909 55 5 0 2213 2267 80261241 80261187 2.390000e-09 75.0
14 TraesCS3B01G386600 chr3D 100.000 34 0 0 5424 5457 459468035 459468068 5.180000e-06 63.9
15 TraesCS3B01G386600 chr6A 89.583 528 49 2 5663 6190 22803754 22804275 0.000000e+00 665.0
16 TraesCS3B01G386600 chr6A 89.831 413 40 2 5779 6190 22695844 22696255 4.250000e-146 529.0
17 TraesCS3B01G386600 chr6A 80.288 416 41 17 5151 5537 22695232 22695635 6.110000e-70 276.0
18 TraesCS3B01G386600 chr6A 77.593 482 47 28 4913 5365 22802944 22803393 1.040000e-57 235.0
19 TraesCS3B01G386600 chr6A 79.387 359 48 17 4900 5247 22694887 22695230 4.830000e-56 230.0
20 TraesCS3B01G386600 chr6A 79.147 211 32 9 2790 2994 204743043 204742839 1.080000e-27 135.0
21 TraesCS3B01G386600 chr6A 81.081 148 19 2 5392 5539 22803498 22803636 6.560000e-20 110.0
22 TraesCS3B01G386600 chr6A 92.105 38 3 0 4925 4962 204739495 204739458 3.000000e-03 54.7
23 TraesCS3B01G386600 chr6D 89.414 529 48 5 5663 6190 24261999 24262520 0.000000e+00 660.0
24 TraesCS3B01G386600 chr6D 90.073 413 39 2 5779 6190 24230796 24231207 9.130000e-148 534.0
25 TraesCS3B01G386600 chr6D 77.370 654 78 41 5151 5753 24230163 24230797 2.150000e-84 324.0
26 TraesCS3B01G386600 chr6D 86.139 202 23 2 5051 5247 24229960 24230161 4.860000e-51 213.0
27 TraesCS3B01G386600 chr6D 81.757 148 18 2 5392 5539 24261743 24261881 1.410000e-21 115.0
28 TraesCS3B01G386600 chr6D 88.462 78 7 2 4780 4856 24229733 24229809 6.610000e-15 93.5
29 TraesCS3B01G386600 chr6D 92.105 38 3 0 4925 4962 143647123 143647160 3.000000e-03 54.7
30 TraesCS3B01G386600 chr6B 89.143 525 54 3 5663 6187 39339167 39339688 0.000000e+00 651.0
31 TraesCS3B01G386600 chr6B 79.612 412 44 21 5153 5537 39197850 39198248 6.160000e-65 259.0
32 TraesCS3B01G386600 chr6B 84.653 202 26 2 5051 5247 39197644 39197845 4.900000e-46 196.0
33 TraesCS3B01G386600 chr6B 81.333 150 15 5 5392 5539 39338911 39339049 6.560000e-20 110.0
34 TraesCS3B01G386600 chr6B 92.105 38 3 0 4925 4962 255672747 255672784 3.000000e-03 54.7
35 TraesCS3B01G386600 chr5A 87.382 531 56 5 5663 6190 465111733 465111211 3.190000e-167 599.0
36 TraesCS3B01G386600 chr5A 82.192 219 31 7 2773 2987 427067831 427068045 1.370000e-41 182.0
37 TraesCS3B01G386600 chr5A 79.253 241 43 6 2818 3053 666232890 666232652 1.790000e-35 161.0
38 TraesCS3B01G386600 chr2A 87.382 531 56 6 5663 6190 425812698 425813220 3.190000e-167 599.0
39 TraesCS3B01G386600 chr1D 78.062 743 129 20 4466 5177 3435358 3434619 7.370000e-119 438.0
40 TraesCS3B01G386600 chr1D 90.000 50 5 0 4339 4388 436190988 436190939 1.440000e-06 65.8
41 TraesCS3B01G386600 chr5D 83.333 204 26 7 2788 2987 329617444 329617245 1.370000e-41 182.0
42 TraesCS3B01G386600 chr4D 79.167 240 45 4 2818 3053 485387036 485386798 1.790000e-35 161.0
43 TraesCS3B01G386600 chr4D 89.362 47 3 2 5151 5196 381837114 381837069 2.410000e-04 58.4
44 TraesCS3B01G386600 chr4B 78.750 240 46 4 2818 3053 618593466 618593228 8.310000e-34 156.0
45 TraesCS3B01G386600 chr1B 90.000 50 5 0 4339 4388 591111305 591111256 1.440000e-06 65.8
46 TraesCS3B01G386600 chr1A 90.000 50 5 0 4339 4388 533449240 533449191 1.440000e-06 65.8
47 TraesCS3B01G386600 chr7B 100.000 28 0 0 5315 5342 47335390 47335417 1.100000e-02 52.8
48 TraesCS3B01G386600 chr7B 100.000 28 0 0 5315 5342 47595189 47595216 1.100000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G386600 chr3B 607379125 607385314 6189 False 11431.000000 11431 100.000000 1 6190 1 chr3B.!!$F1 6189
1 TraesCS3B01G386600 chr3B 750206883 750209975 3092 True 287.900000 499 78.119000 2354 5180 2 chr3B.!!$R1 2826
2 TraesCS3B01G386600 chr3A 601555594 601561412 5818 True 4310.000000 7166 92.279000 379 6190 2 chr3A.!!$R1 5811
3 TraesCS3B01G386600 chr3D 459462206 459468603 6397 False 2293.975000 6974 94.441500 118 6190 4 chr3D.!!$F1 6072
4 TraesCS3B01G386600 chr6A 22694887 22696255 1368 False 345.000000 529 83.168667 4900 6190 3 chr6A.!!$F1 1290
5 TraesCS3B01G386600 chr6A 22802944 22804275 1331 False 336.666667 665 82.752333 4913 6190 3 chr6A.!!$F2 1277
6 TraesCS3B01G386600 chr6D 24261743 24262520 777 False 387.500000 660 85.585500 5392 6190 2 chr6D.!!$F3 798
7 TraesCS3B01G386600 chr6D 24229733 24231207 1474 False 291.125000 534 85.511000 4780 6190 4 chr6D.!!$F2 1410
8 TraesCS3B01G386600 chr6B 39338911 39339688 777 False 380.500000 651 85.238000 5392 6187 2 chr6B.!!$F3 795
9 TraesCS3B01G386600 chr6B 39197644 39198248 604 False 227.500000 259 82.132500 5051 5537 2 chr6B.!!$F2 486
10 TraesCS3B01G386600 chr5A 465111211 465111733 522 True 599.000000 599 87.382000 5663 6190 1 chr5A.!!$R1 527
11 TraesCS3B01G386600 chr2A 425812698 425813220 522 False 599.000000 599 87.382000 5663 6190 1 chr2A.!!$F1 527
12 TraesCS3B01G386600 chr1D 3434619 3435358 739 True 438.000000 438 78.062000 4466 5177 1 chr1D.!!$R1 711

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
96 97 0.035881 TGAGAGGCTGGCAGTTTGAG 59.964 55.000 17.16 0.00 0.00 3.02 F
97 98 0.036022 GAGAGGCTGGCAGTTTGAGT 59.964 55.000 17.16 0.00 0.00 3.41 F
99 100 0.036022 GAGGCTGGCAGTTTGAGTCT 59.964 55.000 17.16 0.00 0.00 3.24 F
1415 1675 0.104120 GGTGAGCACCCAAACCAAAC 59.896 55.000 8.48 0.00 45.68 2.93 F
1418 1678 0.104120 GAGCACCCAAACCAAACCAC 59.896 55.000 0.00 0.00 0.00 4.16 F
2513 2827 0.108992 GTAGTGGTCGCCATGTCGAA 60.109 55.000 0.00 0.00 40.43 3.71 F
2515 2829 0.670546 AGTGGTCGCCATGTCGAAAG 60.671 55.000 0.00 0.00 40.43 2.62 F
2715 3490 0.692476 CACCAGGACCATGGACTTCA 59.308 55.000 21.47 0.00 43.57 3.02 F
3527 4304 1.064946 CTTCTACGCCTGCGAGAGG 59.935 63.158 19.52 12.42 46.13 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1671 0.249955 GATGCATTGGGGGTGGTTTG 59.750 55.000 0.00 0.00 0.00 2.93 R
1889 2186 0.334676 GTTTGGGGGATCCATGGACA 59.665 55.000 18.99 7.31 46.52 4.02 R
1918 2215 1.933021 AGTGATTAGTCCACCGACCA 58.067 50.000 0.00 0.00 40.12 4.02 R
2715 3490 0.108615 CGCTTCCAGTTCTCGTGGAT 60.109 55.000 0.00 0.00 43.78 3.41 R
3311 4086 1.480212 AATGCACCACGAGGAGGACA 61.480 55.000 5.68 0.00 38.69 4.02 R
3950 4798 0.250338 ACTGACCTTCCCGAACAAGC 60.250 55.000 0.00 0.00 0.00 4.01 R
4448 5796 6.582636 TCAGTTATGTTACCTCCATTAGCTG 58.417 40.000 0.00 0.00 0.00 4.24 R
4663 6020 6.595326 TGCGACTAGACAAAGATGAAATTGAT 59.405 34.615 0.00 0.00 0.00 2.57 R
5292 6918 1.196127 GTACTTTGTACAACCCAGCGC 59.804 52.381 8.07 0.00 0.00 5.92 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
20 21 3.769739 TGTTCATCAAGCACAGTACCT 57.230 42.857 0.00 0.00 0.00 3.08
21 22 3.402110 TGTTCATCAAGCACAGTACCTG 58.598 45.455 0.00 0.00 37.52 4.00
22 23 2.099141 TCATCAAGCACAGTACCTGC 57.901 50.000 5.19 5.19 34.37 4.85
23 24 1.347378 TCATCAAGCACAGTACCTGCA 59.653 47.619 14.00 0.00 37.08 4.41
24 25 2.026915 TCATCAAGCACAGTACCTGCAT 60.027 45.455 14.00 1.17 37.08 3.96
25 26 3.197549 TCATCAAGCACAGTACCTGCATA 59.802 43.478 14.00 1.62 37.08 3.14
26 27 2.972625 TCAAGCACAGTACCTGCATAC 58.027 47.619 14.00 0.00 37.08 2.39
27 28 1.660607 CAAGCACAGTACCTGCATACG 59.339 52.381 14.00 0.00 37.08 3.06
28 29 0.175760 AGCACAGTACCTGCATACGG 59.824 55.000 14.00 0.00 37.08 4.02
29 30 0.174845 GCACAGTACCTGCATACGGA 59.825 55.000 8.01 0.00 34.37 4.69
30 31 1.202533 GCACAGTACCTGCATACGGAT 60.203 52.381 8.01 0.00 34.37 4.18
31 32 2.035449 GCACAGTACCTGCATACGGATA 59.965 50.000 8.01 0.00 34.37 2.59
32 33 3.639538 CACAGTACCTGCATACGGATAC 58.360 50.000 4.87 1.43 34.37 2.24
58 59 2.504032 CCATGTGGCGTACGGGAT 59.496 61.111 18.39 0.00 0.00 3.85
59 60 1.594293 CCATGTGGCGTACGGGATC 60.594 63.158 18.39 0.00 0.00 3.36
60 61 1.441729 CATGTGGCGTACGGGATCT 59.558 57.895 18.39 0.00 0.00 2.75
61 62 0.179084 CATGTGGCGTACGGGATCTT 60.179 55.000 18.39 0.00 0.00 2.40
62 63 0.179084 ATGTGGCGTACGGGATCTTG 60.179 55.000 18.39 0.00 0.00 3.02
63 64 1.520787 GTGGCGTACGGGATCTTGG 60.521 63.158 18.39 0.00 0.00 3.61
64 65 1.985662 TGGCGTACGGGATCTTGGT 60.986 57.895 18.39 0.00 0.00 3.67
65 66 1.227176 GGCGTACGGGATCTTGGTC 60.227 63.158 18.39 0.00 0.00 4.02
66 67 1.588139 GCGTACGGGATCTTGGTCG 60.588 63.158 18.39 0.00 0.00 4.79
67 68 1.805254 CGTACGGGATCTTGGTCGT 59.195 57.895 7.57 0.00 39.30 4.34
68 69 0.524816 CGTACGGGATCTTGGTCGTG 60.525 60.000 7.57 0.00 37.10 4.35
69 70 0.804933 GTACGGGATCTTGGTCGTGC 60.805 60.000 0.00 0.00 37.10 5.34
70 71 1.952102 TACGGGATCTTGGTCGTGCC 61.952 60.000 0.00 0.00 37.10 5.01
71 72 2.990479 GGGATCTTGGTCGTGCCT 59.010 61.111 0.00 0.00 38.35 4.75
72 73 1.672854 CGGGATCTTGGTCGTGCCTA 61.673 60.000 0.00 0.00 38.35 3.93
73 74 0.179081 GGGATCTTGGTCGTGCCTAC 60.179 60.000 0.00 0.00 38.35 3.18
74 75 0.824759 GGATCTTGGTCGTGCCTACT 59.175 55.000 0.00 0.00 38.35 2.57
75 76 1.202428 GGATCTTGGTCGTGCCTACTC 60.202 57.143 0.00 0.00 38.35 2.59
76 77 0.456221 ATCTTGGTCGTGCCTACTCG 59.544 55.000 1.06 0.00 38.35 4.18
77 78 0.892358 TCTTGGTCGTGCCTACTCGT 60.892 55.000 1.06 0.00 38.35 4.18
78 79 0.732880 CTTGGTCGTGCCTACTCGTG 60.733 60.000 1.06 0.00 38.35 4.35
79 80 1.174078 TTGGTCGTGCCTACTCGTGA 61.174 55.000 0.00 0.00 38.35 4.35
80 81 1.136984 GGTCGTGCCTACTCGTGAG 59.863 63.158 0.00 0.00 34.50 3.51
81 82 1.303799 GGTCGTGCCTACTCGTGAGA 61.304 60.000 3.44 0.00 39.12 3.27
91 92 2.601666 TCGTGAGAGGCTGGCAGT 60.602 61.111 17.16 0.00 34.84 4.40
92 93 2.210013 TCGTGAGAGGCTGGCAGTT 61.210 57.895 17.16 4.76 34.84 3.16
93 94 1.302033 CGTGAGAGGCTGGCAGTTT 60.302 57.895 17.16 4.36 0.00 2.66
94 95 1.572085 CGTGAGAGGCTGGCAGTTTG 61.572 60.000 17.16 0.00 0.00 2.93
95 96 0.250467 GTGAGAGGCTGGCAGTTTGA 60.250 55.000 17.16 0.00 0.00 2.69
96 97 0.035881 TGAGAGGCTGGCAGTTTGAG 59.964 55.000 17.16 0.00 0.00 3.02
97 98 0.036022 GAGAGGCTGGCAGTTTGAGT 59.964 55.000 17.16 0.00 0.00 3.41
98 99 0.036022 AGAGGCTGGCAGTTTGAGTC 59.964 55.000 17.16 4.33 0.00 3.36
99 100 0.036022 GAGGCTGGCAGTTTGAGTCT 59.964 55.000 17.16 0.00 0.00 3.24
100 101 0.250640 AGGCTGGCAGTTTGAGTCTG 60.251 55.000 17.16 0.00 36.18 3.51
101 102 1.239968 GGCTGGCAGTTTGAGTCTGG 61.240 60.000 17.16 0.00 33.98 3.86
106 107 1.242076 GCAGTTTGAGTCTGGCATGT 58.758 50.000 0.00 0.00 33.98 3.21
107 108 1.610522 GCAGTTTGAGTCTGGCATGTT 59.389 47.619 0.00 0.00 33.98 2.71
108 109 2.035066 GCAGTTTGAGTCTGGCATGTTT 59.965 45.455 0.00 0.00 33.98 2.83
109 110 3.253188 GCAGTTTGAGTCTGGCATGTTTA 59.747 43.478 0.00 0.00 33.98 2.01
110 111 4.261572 GCAGTTTGAGTCTGGCATGTTTAA 60.262 41.667 0.00 0.00 33.98 1.52
111 112 5.455392 CAGTTTGAGTCTGGCATGTTTAAG 58.545 41.667 0.00 0.00 0.00 1.85
112 113 4.520492 AGTTTGAGTCTGGCATGTTTAAGG 59.480 41.667 0.00 0.00 0.00 2.69
113 114 3.788227 TGAGTCTGGCATGTTTAAGGT 57.212 42.857 0.00 0.00 0.00 3.50
114 115 3.411446 TGAGTCTGGCATGTTTAAGGTG 58.589 45.455 0.00 0.00 0.00 4.00
115 116 2.162408 GAGTCTGGCATGTTTAAGGTGC 59.838 50.000 0.00 0.00 38.12 5.01
122 123 4.096732 GCATGTTTAAGGTGCCTACTTG 57.903 45.455 0.00 0.00 32.88 3.16
165 166 0.894835 GTTGCCCCACCTTAACCATG 59.105 55.000 0.00 0.00 0.00 3.66
166 167 0.485099 TTGCCCCACCTTAACCATGT 59.515 50.000 0.00 0.00 0.00 3.21
168 169 1.711375 TGCCCCACCTTAACCATGTTA 59.289 47.619 0.00 0.00 0.00 2.41
170 171 2.693074 GCCCCACCTTAACCATGTTATG 59.307 50.000 0.00 0.00 0.00 1.90
171 172 2.693074 CCCCACCTTAACCATGTTATGC 59.307 50.000 0.00 0.00 0.00 3.14
172 173 2.357637 CCCACCTTAACCATGTTATGCG 59.642 50.000 0.00 0.00 0.00 4.73
174 175 2.357637 CACCTTAACCATGTTATGCGGG 59.642 50.000 0.00 0.00 0.00 6.13
175 176 1.336755 CCTTAACCATGTTATGCGGGC 59.663 52.381 0.00 0.00 0.00 6.13
176 177 1.002900 CTTAACCATGTTATGCGGGCG 60.003 52.381 0.00 0.00 0.00 6.13
177 178 0.178301 TAACCATGTTATGCGGGCGA 59.822 50.000 0.00 0.00 0.00 5.54
178 179 1.373590 AACCATGTTATGCGGGCGAC 61.374 55.000 0.00 0.00 0.00 5.19
179 180 1.817520 CCATGTTATGCGGGCGACA 60.818 57.895 0.00 0.00 0.00 4.35
180 181 1.351707 CATGTTATGCGGGCGACAC 59.648 57.895 0.00 0.00 0.00 3.67
198 202 4.678574 CGACACTAATGTAATCCCCGTCAA 60.679 45.833 0.00 0.00 39.95 3.18
213 217 3.169207 CGTCAACGGTTCAGATTTCAC 57.831 47.619 0.00 0.00 35.37 3.18
236 277 2.749621 GTTCACCAGGACATTAAGCAGG 59.250 50.000 0.00 0.00 0.00 4.85
240 419 1.341383 CCAGGACATTAAGCAGGCCTT 60.341 52.381 0.00 0.00 37.57 4.35
277 456 9.927668 AACATTTAAGCAAACATATTAAGCAGT 57.072 25.926 0.00 0.00 0.00 4.40
305 542 7.553881 TTTGAAAATGATAGCTAGTACTGGC 57.446 36.000 22.57 22.57 37.33 4.85
306 543 5.611374 TGAAAATGATAGCTAGTACTGGCC 58.389 41.667 25.75 12.55 37.85 5.36
307 544 5.366768 TGAAAATGATAGCTAGTACTGGCCT 59.633 40.000 25.75 14.76 37.85 5.19
308 545 4.881019 AATGATAGCTAGTACTGGCCTG 57.119 45.455 25.75 8.29 37.85 4.85
309 546 1.964223 TGATAGCTAGTACTGGCCTGC 59.036 52.381 25.75 15.75 37.85 4.85
314 551 2.040412 AGCTAGTACTGGCCTGCTTTTT 59.960 45.455 25.75 3.63 37.85 1.94
325 562 3.936653 GCTTTTTGCAACGAGGCC 58.063 55.556 0.00 0.00 42.31 5.19
371 608 1.484240 CTTCTCTGCCCTCCGATTTCT 59.516 52.381 0.00 0.00 0.00 2.52
372 609 1.115467 TCTCTGCCCTCCGATTTCTC 58.885 55.000 0.00 0.00 0.00 2.87
373 610 0.249238 CTCTGCCCTCCGATTTCTCG 60.249 60.000 0.00 0.00 44.62 4.04
374 611 1.884926 CTGCCCTCCGATTTCTCGC 60.885 63.158 0.00 0.00 43.66 5.03
375 612 2.962253 GCCCTCCGATTTCTCGCG 60.962 66.667 0.00 0.00 43.66 5.87
376 613 2.962253 CCCTCCGATTTCTCGCGC 60.962 66.667 0.00 0.00 43.66 6.86
377 614 3.323136 CCTCCGATTTCTCGCGCG 61.323 66.667 26.76 26.76 43.66 6.86
522 765 2.654877 CCGCACCTAACGTCCACT 59.345 61.111 0.00 0.00 0.00 4.00
527 770 2.537401 GCACCTAACGTCCACTATCAC 58.463 52.381 0.00 0.00 0.00 3.06
538 781 0.245539 CACTATCACCAACCGTCGGT 59.754 55.000 12.23 12.23 37.65 4.69
542 785 0.601841 ATCACCAACCGTCGGTTCAC 60.602 55.000 26.61 0.00 43.05 3.18
553 796 2.660802 GGTTCACCATCCGACGGT 59.339 61.111 14.79 0.00 37.16 4.83
554 797 1.004200 GGTTCACCATCCGACGGTT 60.004 57.895 14.79 1.91 33.25 4.44
555 798 1.017701 GGTTCACCATCCGACGGTTC 61.018 60.000 14.79 0.00 33.25 3.62
705 951 1.141019 GCTAGCCGTTCATCCACGA 59.859 57.895 2.29 0.00 43.15 4.35
710 956 1.736645 CCGTTCATCCACGACGCTT 60.737 57.895 0.00 0.00 43.15 4.68
758 1009 2.717485 GCGACGGCAGTATACGGA 59.283 61.111 7.24 0.00 39.62 4.69
896 1152 2.877383 TCCACCCCACCTCCCCTA 60.877 66.667 0.00 0.00 0.00 3.53
897 1153 2.366972 CCACCCCACCTCCCCTAG 60.367 72.222 0.00 0.00 0.00 3.02
1413 1673 4.268720 GGTGAGCACCCAAACCAA 57.731 55.556 8.48 0.00 45.68 3.67
1414 1674 2.510664 GGTGAGCACCCAAACCAAA 58.489 52.632 8.48 0.00 45.68 3.28
1415 1675 0.104120 GGTGAGCACCCAAACCAAAC 59.896 55.000 8.48 0.00 45.68 2.93
1416 1676 0.104120 GTGAGCACCCAAACCAAACC 59.896 55.000 0.00 0.00 0.00 3.27
1417 1677 0.324738 TGAGCACCCAAACCAAACCA 60.325 50.000 0.00 0.00 0.00 3.67
1418 1678 0.104120 GAGCACCCAAACCAAACCAC 59.896 55.000 0.00 0.00 0.00 4.16
1419 1679 1.145156 GCACCCAAACCAAACCACC 59.855 57.895 0.00 0.00 0.00 4.61
1420 1680 1.826709 CACCCAAACCAAACCACCC 59.173 57.895 0.00 0.00 0.00 4.61
1421 1681 1.383386 ACCCAAACCAAACCACCCC 60.383 57.895 0.00 0.00 0.00 4.95
1422 1682 2.144078 CCCAAACCAAACCACCCCC 61.144 63.158 0.00 0.00 0.00 5.40
1423 1683 1.383248 CCAAACCAAACCACCCCCA 60.383 57.895 0.00 0.00 0.00 4.96
1424 1684 0.983378 CCAAACCAAACCACCCCCAA 60.983 55.000 0.00 0.00 0.00 4.12
1444 1704 2.517450 GCATCGACTGCGTGCTACC 61.517 63.158 0.73 0.00 41.97 3.18
1475 1737 8.742554 TTCTCTTTCTTTCAAACAAAACTGTC 57.257 30.769 0.00 0.00 0.00 3.51
1477 1739 8.356657 TCTCTTTCTTTCAAACAAAACTGTCAA 58.643 29.630 0.00 0.00 0.00 3.18
1485 1747 8.909708 TTCAAACAAAACTGTCAACTAATCTG 57.090 30.769 0.00 0.00 0.00 2.90
1494 1756 4.503910 TGTCAACTAATCTGGTTCGATGG 58.496 43.478 0.00 0.00 0.00 3.51
1496 1758 2.614057 CAACTAATCTGGTTCGATGGCC 59.386 50.000 0.00 0.00 0.00 5.36
1513 1775 2.290641 TGGCCGTGTGATTAAGAATGGT 60.291 45.455 0.00 0.00 0.00 3.55
1516 1778 3.002348 GCCGTGTGATTAAGAATGGTAGC 59.998 47.826 0.00 0.00 0.00 3.58
1566 1855 0.532862 CTGACAAAGTGGCCACGAGT 60.533 55.000 29.68 26.70 36.20 4.18
1589 1878 9.310449 GAGTATGGGGAATCTTATGTAGTTCTA 57.690 37.037 0.00 0.00 0.00 2.10
1607 1896 1.410153 CTATTGGGGGCATCTTGTTGC 59.590 52.381 0.00 0.00 42.01 4.17
1610 1899 1.607467 GGGGGCATCTTGTTGCTGT 60.607 57.895 4.06 0.00 42.38 4.40
1631 1920 6.219417 TGTATCCACCATTTTTATGCTTGG 57.781 37.500 0.00 0.00 35.31 3.61
1653 1942 3.463944 CCACAGTCGTTTGAAGTTACCT 58.536 45.455 0.00 0.00 0.00 3.08
1678 1967 5.606505 GAACTGTTCCTATTTGCCCAAAAA 58.393 37.500 9.38 0.00 33.56 1.94
1679 1968 5.213891 ACTGTTCCTATTTGCCCAAAAAG 57.786 39.130 0.00 0.00 33.56 2.27
1680 1969 4.898861 ACTGTTCCTATTTGCCCAAAAAGA 59.101 37.500 0.00 0.00 33.56 2.52
1681 1970 5.011023 ACTGTTCCTATTTGCCCAAAAAGAG 59.989 40.000 0.00 0.00 33.56 2.85
1682 1971 4.898861 TGTTCCTATTTGCCCAAAAAGAGT 59.101 37.500 0.00 0.00 33.56 3.24
1718 2007 0.666913 CGTACCGAACCGAGATCCAT 59.333 55.000 0.00 0.00 0.00 3.41
1790 2083 3.030291 TGCCTGGTCAGAACACAAAATT 58.970 40.909 0.00 0.00 0.00 1.82
1800 2093 8.403236 GGTCAGAACACAAAATTAAGTACAGTT 58.597 33.333 0.00 0.00 0.00 3.16
1826 2119 2.301738 GCACCCCCACTCCTAGCTT 61.302 63.158 0.00 0.00 0.00 3.74
1827 2120 1.604378 CACCCCCACTCCTAGCTTG 59.396 63.158 0.00 0.00 0.00 4.01
1828 2121 2.301738 ACCCCCACTCCTAGCTTGC 61.302 63.158 0.00 0.00 0.00 4.01
1870 2167 9.932207 CAATTATAATGCCCATGATACAATGTT 57.068 29.630 0.00 0.00 0.00 2.71
1889 2186 8.730680 ACAATGTTCGCTCAAAAGAAGTAATAT 58.269 29.630 0.00 0.00 0.00 1.28
2015 2315 1.370051 CTGTTCGTGACGCTGTCGA 60.370 57.895 0.00 0.00 39.41 4.20
2161 2462 6.240894 AGGTTCAGTCTGATTTTAGCATCAA 58.759 36.000 2.68 0.00 32.63 2.57
2175 2476 1.470098 GCATCAACGTTGGAGCTCATT 59.530 47.619 27.02 0.00 0.00 2.57
2177 2478 3.126858 GCATCAACGTTGGAGCTCATTAA 59.873 43.478 27.02 4.97 0.00 1.40
2178 2479 4.651994 CATCAACGTTGGAGCTCATTAAC 58.348 43.478 27.02 15.39 0.00 2.01
2210 2515 3.509184 TGATGGATGAAATTTGGCACGAA 59.491 39.130 0.00 0.00 0.00 3.85
2293 2598 4.753516 TTCTTTTGCTCGATGGGATCTA 57.246 40.909 0.00 0.00 0.00 1.98
2321 2626 9.897744 TGTATTCTGAAACAATGAGAAATGAAC 57.102 29.630 0.00 0.00 29.78 3.18
2341 2649 9.612066 AATGAACAATCAACCTGTTGTTTTTAT 57.388 25.926 9.65 0.00 45.59 1.40
2482 2790 3.216800 ACATCGAGGTACGGCAGTAATA 58.783 45.455 0.00 0.00 42.82 0.98
2513 2827 0.108992 GTAGTGGTCGCCATGTCGAA 60.109 55.000 0.00 0.00 40.43 3.71
2515 2829 0.670546 AGTGGTCGCCATGTCGAAAG 60.671 55.000 0.00 0.00 40.43 2.62
2516 2830 0.949105 GTGGTCGCCATGTCGAAAGT 60.949 55.000 0.00 0.00 40.43 2.66
2579 2921 0.990374 AGATTTGGCAGCTGGAGACT 59.010 50.000 17.12 0.00 0.00 3.24
2585 2927 1.304509 GGCAGCTGGAGACTTTGCTC 61.305 60.000 17.12 0.00 35.23 4.26
2715 3490 0.692476 CACCAGGACCATGGACTTCA 59.308 55.000 21.47 0.00 43.57 3.02
3060 3835 3.706373 GCGACTTCCCCAGGCTCA 61.706 66.667 0.00 0.00 0.00 4.26
3311 4086 1.326213 ACCTGCTGCTGCTCGTCTAT 61.326 55.000 17.00 0.00 40.48 1.98
3353 4128 5.777449 TCCTACTTCATATTCCTCACCAGA 58.223 41.667 0.00 0.00 0.00 3.86
3382 4157 7.613585 TGGTACAAGAAGACGGTAATTAATCA 58.386 34.615 0.00 0.00 31.92 2.57
3435 4210 7.231519 GCCACCTATATAATGCTTTTCTTTCCT 59.768 37.037 0.00 0.00 0.00 3.36
3436 4211 8.571336 CCACCTATATAATGCTTTTCTTTCCTG 58.429 37.037 0.00 0.00 0.00 3.86
3437 4212 9.125026 CACCTATATAATGCTTTTCTTTCCTGT 57.875 33.333 0.00 0.00 0.00 4.00
3458 4233 8.729756 TCCTGTATGTAAATTCAAGTGTTGATG 58.270 33.333 0.00 0.00 39.84 3.07
3465 4240 8.349245 TGTAAATTCAAGTGTTGATGATCGTTT 58.651 29.630 0.00 0.00 39.84 3.60
3527 4304 1.064946 CTTCTACGCCTGCGAGAGG 59.935 63.158 19.52 12.42 46.13 3.69
3548 4325 5.175859 AGGATTATCAGAAAAGTTCGCGAA 58.824 37.500 19.38 19.38 34.02 4.70
3848 4690 5.168569 CGAGGTTCTTGCTTACAGTTGATA 58.831 41.667 0.00 0.00 0.00 2.15
3849 4691 5.289675 CGAGGTTCTTGCTTACAGTTGATAG 59.710 44.000 0.00 0.00 0.00 2.08
3950 4798 2.830923 ACTGGACATCTGAACTCAGGAG 59.169 50.000 6.87 0.00 43.91 3.69
4037 4891 6.071278 AGGAGAGTAGAACAAATGTGGACTAC 60.071 42.308 11.40 11.40 37.56 2.73
4416 5763 8.149647 AGTCCAATGATGTAAATTTCTTTTGCA 58.850 29.630 0.00 0.00 42.89 4.08
4418 5765 8.366401 TCCAATGATGTAAATTTCTTTTGCAGA 58.634 29.630 0.00 0.00 42.16 4.26
4659 6016 4.095185 ACAGCGTACTTATCTCACTCTGAC 59.905 45.833 0.00 0.00 31.22 3.51
4663 6020 6.542735 AGCGTACTTATCTCACTCTGACATTA 59.457 38.462 0.00 0.00 0.00 1.90
4695 6068 7.811653 TCATCTTTGTCTAGTCGCATCTATAG 58.188 38.462 0.00 0.00 0.00 1.31
4727 6110 8.997323 AGCTAAAGTAATATGCAGAATGTCATC 58.003 33.333 0.00 0.00 39.31 2.92
4832 6215 4.148128 TGCCAAAAATGGTGTTGACATT 57.852 36.364 0.00 0.00 40.07 2.71
4886 6275 6.670902 TCTGCATTCTCATCTGATCCCATATA 59.329 38.462 0.00 0.00 0.00 0.86
4910 6321 0.944386 TGCTTCCTTTTCTGACACGC 59.056 50.000 0.00 0.00 0.00 5.34
5056 6554 9.429359 GCAGATTTATACTAGACAGTGCAATAT 57.571 33.333 0.00 0.00 36.14 1.28
5629 7382 1.552337 TGGAGGTCTGCATCTTCAGTC 59.448 52.381 0.00 0.00 35.63 3.51
5658 7411 2.740981 CCTGACAGTCTCTGCATTTGAC 59.259 50.000 1.31 0.00 34.37 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.396328 TGCGTATCCGTATGCAGGTACTG 62.396 52.174 0.00 0.00 45.42 2.74
14 15 1.268899 GCGTATCCGTATGCAGGTACT 59.731 52.381 0.00 0.00 41.50 2.73
15 16 1.001048 TGCGTATCCGTATGCAGGTAC 60.001 52.381 0.00 0.00 45.42 3.34
16 17 1.320507 TGCGTATCCGTATGCAGGTA 58.679 50.000 0.00 0.00 45.42 3.08
17 18 2.120765 TGCGTATCCGTATGCAGGT 58.879 52.632 0.00 0.00 45.42 4.00
21 22 1.324718 CGTACTGCGTATCCGTATGC 58.675 55.000 0.00 0.00 42.09 3.14
22 23 1.324718 GCGTACTGCGTATCCGTATG 58.675 55.000 0.00 0.00 43.66 2.39
23 24 3.761481 GCGTACTGCGTATCCGTAT 57.239 52.632 0.00 0.00 43.66 3.06
41 42 1.594293 GATCCCGTACGCCACATGG 60.594 63.158 10.49 4.58 38.53 3.66
42 43 0.179084 AAGATCCCGTACGCCACATG 60.179 55.000 10.49 0.00 0.00 3.21
43 44 0.179084 CAAGATCCCGTACGCCACAT 60.179 55.000 10.49 0.00 0.00 3.21
44 45 1.216977 CAAGATCCCGTACGCCACA 59.783 57.895 10.49 0.00 0.00 4.17
45 46 1.520787 CCAAGATCCCGTACGCCAC 60.521 63.158 10.49 0.85 0.00 5.01
46 47 1.952102 GACCAAGATCCCGTACGCCA 61.952 60.000 10.49 0.00 0.00 5.69
47 48 1.227176 GACCAAGATCCCGTACGCC 60.227 63.158 10.49 0.00 0.00 5.68
48 49 1.588139 CGACCAAGATCCCGTACGC 60.588 63.158 10.49 0.00 0.00 4.42
49 50 0.524816 CACGACCAAGATCCCGTACG 60.525 60.000 8.69 8.69 33.62 3.67
50 51 0.804933 GCACGACCAAGATCCCGTAC 60.805 60.000 0.00 0.00 33.62 3.67
51 52 1.514087 GCACGACCAAGATCCCGTA 59.486 57.895 0.00 0.00 33.62 4.02
52 53 2.264794 GCACGACCAAGATCCCGT 59.735 61.111 0.00 0.00 35.46 5.28
53 54 1.672854 TAGGCACGACCAAGATCCCG 61.673 60.000 0.00 0.00 43.14 5.14
54 55 0.179081 GTAGGCACGACCAAGATCCC 60.179 60.000 0.00 0.00 43.14 3.85
55 56 0.824759 AGTAGGCACGACCAAGATCC 59.175 55.000 0.00 0.00 43.14 3.36
56 57 1.534175 CGAGTAGGCACGACCAAGATC 60.534 57.143 0.00 0.00 43.14 2.75
57 58 0.456221 CGAGTAGGCACGACCAAGAT 59.544 55.000 0.00 0.00 43.14 2.40
58 59 0.892358 ACGAGTAGGCACGACCAAGA 60.892 55.000 0.00 0.00 43.14 3.02
59 60 0.732880 CACGAGTAGGCACGACCAAG 60.733 60.000 0.00 0.00 43.14 3.61
60 61 1.174078 TCACGAGTAGGCACGACCAA 61.174 55.000 0.00 0.00 43.14 3.67
61 62 1.583495 CTCACGAGTAGGCACGACCA 61.583 60.000 0.00 0.00 43.14 4.02
62 63 1.136984 CTCACGAGTAGGCACGACC 59.863 63.158 0.00 0.00 33.33 4.79
63 64 0.097325 CTCTCACGAGTAGGCACGAC 59.903 60.000 0.00 0.00 32.47 4.34
64 65 1.025113 CCTCTCACGAGTAGGCACGA 61.025 60.000 0.00 0.00 35.43 4.35
65 66 1.429825 CCTCTCACGAGTAGGCACG 59.570 63.158 0.00 0.00 35.43 5.34
66 67 1.139947 GCCTCTCACGAGTAGGCAC 59.860 63.158 22.21 4.61 44.17 5.01
67 68 1.000771 AGCCTCTCACGAGTAGGCA 60.001 57.895 25.81 0.00 45.65 4.75
68 69 1.435515 CAGCCTCTCACGAGTAGGC 59.564 63.158 20.74 20.74 44.63 3.93
69 70 2.010582 GCCAGCCTCTCACGAGTAGG 62.011 65.000 0.00 7.71 35.43 3.18
70 71 1.315981 TGCCAGCCTCTCACGAGTAG 61.316 60.000 0.00 0.00 35.43 2.57
71 72 1.304134 TGCCAGCCTCTCACGAGTA 60.304 57.895 0.00 0.00 35.43 2.59
72 73 2.601666 TGCCAGCCTCTCACGAGT 60.602 61.111 0.00 0.00 35.43 4.18
73 74 2.164865 AACTGCCAGCCTCTCACGAG 62.165 60.000 0.00 0.00 37.01 4.18
74 75 1.758440 AAACTGCCAGCCTCTCACGA 61.758 55.000 0.00 0.00 0.00 4.35
75 76 1.302033 AAACTGCCAGCCTCTCACG 60.302 57.895 0.00 0.00 0.00 4.35
76 77 0.250467 TCAAACTGCCAGCCTCTCAC 60.250 55.000 0.00 0.00 0.00 3.51
77 78 0.035881 CTCAAACTGCCAGCCTCTCA 59.964 55.000 0.00 0.00 0.00 3.27
78 79 0.036022 ACTCAAACTGCCAGCCTCTC 59.964 55.000 0.00 0.00 0.00 3.20
79 80 0.036022 GACTCAAACTGCCAGCCTCT 59.964 55.000 0.00 0.00 0.00 3.69
80 81 0.036022 AGACTCAAACTGCCAGCCTC 59.964 55.000 0.00 0.00 0.00 4.70
81 82 0.250640 CAGACTCAAACTGCCAGCCT 60.251 55.000 0.00 0.00 0.00 4.58
82 83 1.239968 CCAGACTCAAACTGCCAGCC 61.240 60.000 0.00 0.00 34.47 4.85
83 84 1.860484 GCCAGACTCAAACTGCCAGC 61.860 60.000 0.00 0.00 34.47 4.85
84 85 0.535780 TGCCAGACTCAAACTGCCAG 60.536 55.000 0.00 0.00 34.47 4.85
85 86 0.111061 ATGCCAGACTCAAACTGCCA 59.889 50.000 0.00 0.00 34.47 4.92
86 87 0.524862 CATGCCAGACTCAAACTGCC 59.475 55.000 0.00 0.00 34.47 4.85
87 88 1.242076 ACATGCCAGACTCAAACTGC 58.758 50.000 0.00 0.00 34.47 4.40
88 89 3.996150 AAACATGCCAGACTCAAACTG 57.004 42.857 0.00 0.00 35.43 3.16
89 90 4.520492 CCTTAAACATGCCAGACTCAAACT 59.480 41.667 0.00 0.00 0.00 2.66
90 91 4.278419 ACCTTAAACATGCCAGACTCAAAC 59.722 41.667 0.00 0.00 0.00 2.93
91 92 4.278170 CACCTTAAACATGCCAGACTCAAA 59.722 41.667 0.00 0.00 0.00 2.69
92 93 3.820467 CACCTTAAACATGCCAGACTCAA 59.180 43.478 0.00 0.00 0.00 3.02
93 94 3.411446 CACCTTAAACATGCCAGACTCA 58.589 45.455 0.00 0.00 0.00 3.41
94 95 2.162408 GCACCTTAAACATGCCAGACTC 59.838 50.000 0.00 0.00 0.00 3.36
95 96 2.162681 GCACCTTAAACATGCCAGACT 58.837 47.619 0.00 0.00 0.00 3.24
96 97 1.202348 GGCACCTTAAACATGCCAGAC 59.798 52.381 15.90 0.00 0.00 3.51
97 98 1.075374 AGGCACCTTAAACATGCCAGA 59.925 47.619 20.59 0.00 0.00 3.86
98 99 1.549203 AGGCACCTTAAACATGCCAG 58.451 50.000 20.59 0.00 0.00 4.85
99 100 2.041081 AGTAGGCACCTTAAACATGCCA 59.959 45.455 20.59 8.70 0.00 4.92
100 101 2.723273 AGTAGGCACCTTAAACATGCC 58.277 47.619 13.85 13.85 0.00 4.40
101 102 3.506067 ACAAGTAGGCACCTTAAACATGC 59.494 43.478 0.00 0.00 0.00 4.06
102 103 4.518970 ACACAAGTAGGCACCTTAAACATG 59.481 41.667 0.00 0.00 0.00 3.21
103 104 4.725490 ACACAAGTAGGCACCTTAAACAT 58.275 39.130 0.00 0.00 0.00 2.71
104 105 4.131596 GACACAAGTAGGCACCTTAAACA 58.868 43.478 0.00 0.00 0.00 2.83
105 106 4.024302 GTGACACAAGTAGGCACCTTAAAC 60.024 45.833 0.00 0.00 0.00 2.01
106 107 4.131596 GTGACACAAGTAGGCACCTTAAA 58.868 43.478 0.00 0.00 0.00 1.52
107 108 3.495453 GGTGACACAAGTAGGCACCTTAA 60.495 47.826 10.84 0.00 44.23 1.85
108 109 2.038033 GGTGACACAAGTAGGCACCTTA 59.962 50.000 10.84 0.00 44.23 2.69
109 110 1.202770 GGTGACACAAGTAGGCACCTT 60.203 52.381 10.84 0.00 44.23 3.50
110 111 0.396811 GGTGACACAAGTAGGCACCT 59.603 55.000 10.84 0.00 44.23 4.00
111 112 0.107831 TGGTGACACAAGTAGGCACC 59.892 55.000 11.18 11.18 46.97 5.01
112 113 1.961793 TTGGTGACACAAGTAGGCAC 58.038 50.000 8.08 0.00 42.67 5.01
113 114 2.294074 GTTTGGTGACACAAGTAGGCA 58.706 47.619 8.08 0.00 42.67 4.75
114 115 2.290641 CTGTTTGGTGACACAAGTAGGC 59.709 50.000 8.08 0.00 42.67 3.93
115 116 2.290641 GCTGTTTGGTGACACAAGTAGG 59.709 50.000 8.08 0.00 42.67 3.18
116 117 2.032894 CGCTGTTTGGTGACACAAGTAG 60.033 50.000 8.08 0.35 42.67 2.57
117 118 1.937223 CGCTGTTTGGTGACACAAGTA 59.063 47.619 8.08 0.00 42.67 2.24
118 119 0.732571 CGCTGTTTGGTGACACAAGT 59.267 50.000 8.08 0.00 42.67 3.16
119 120 0.029300 CCGCTGTTTGGTGACACAAG 59.971 55.000 8.08 0.00 42.67 3.16
120 121 1.380403 CCCGCTGTTTGGTGACACAA 61.380 55.000 8.08 0.00 42.67 3.33
121 122 1.821759 CCCGCTGTTTGGTGACACA 60.822 57.895 8.08 0.00 42.67 3.72
122 123 3.030652 CCCGCTGTTTGGTGACAC 58.969 61.111 0.00 0.00 42.67 3.67
165 166 1.260561 CATTAGTGTCGCCCGCATAAC 59.739 52.381 0.00 0.00 0.00 1.89
166 167 1.134640 ACATTAGTGTCGCCCGCATAA 60.135 47.619 0.00 0.00 31.41 1.90
168 169 0.462375 TACATTAGTGTCGCCCGCAT 59.538 50.000 0.00 0.00 39.77 4.73
170 171 1.525619 GATTACATTAGTGTCGCCCGC 59.474 52.381 0.00 0.00 39.77 6.13
171 172 2.132762 GGATTACATTAGTGTCGCCCG 58.867 52.381 0.00 0.00 39.77 6.13
172 173 2.490991 GGGATTACATTAGTGTCGCCC 58.509 52.381 0.00 0.94 39.77 6.13
174 175 2.132762 CGGGGATTACATTAGTGTCGC 58.867 52.381 0.00 0.00 39.77 5.19
175 176 3.181484 TGACGGGGATTACATTAGTGTCG 60.181 47.826 0.00 0.00 39.77 4.35
176 177 4.395959 TGACGGGGATTACATTAGTGTC 57.604 45.455 0.00 0.00 39.77 3.67
177 178 4.510571 GTTGACGGGGATTACATTAGTGT 58.489 43.478 0.00 0.00 42.39 3.55
178 179 3.554324 CGTTGACGGGGATTACATTAGTG 59.446 47.826 0.00 0.00 35.37 2.74
179 180 3.788937 CGTTGACGGGGATTACATTAGT 58.211 45.455 0.00 0.00 35.37 2.24
198 202 3.560068 GTGAACAGTGAAATCTGAACCGT 59.440 43.478 0.00 0.00 38.63 4.83
207 211 3.576078 TGTCCTGGTGAACAGTGAAAT 57.424 42.857 0.00 0.00 46.06 2.17
284 521 5.698545 CAGGCCAGTACTAGCTATCATTTTC 59.301 44.000 13.09 0.00 0.00 2.29
289 526 1.964223 GCAGGCCAGTACTAGCTATCA 59.036 52.381 13.09 0.00 0.00 2.15
290 527 2.243810 AGCAGGCCAGTACTAGCTATC 58.756 52.381 13.09 2.78 0.00 2.08
292 529 2.160721 AAGCAGGCCAGTACTAGCTA 57.839 50.000 13.09 0.00 0.00 3.32
298 535 3.496898 GCAAAAAGCAGGCCAGTAC 57.503 52.632 5.01 0.00 44.79 2.73
308 545 2.016165 CGGCCTCGTTGCAAAAAGC 61.016 57.895 0.00 1.75 45.96 3.51
309 546 1.371635 CCGGCCTCGTTGCAAAAAG 60.372 57.895 0.00 1.03 33.95 2.27
350 587 1.482593 GAAATCGGAGGGCAGAGAAGA 59.517 52.381 0.00 0.00 0.00 2.87
522 765 0.967662 TGAACCGACGGTTGGTGATA 59.032 50.000 35.60 12.22 46.95 2.15
527 770 1.296056 GATGGTGAACCGACGGTTGG 61.296 60.000 35.60 13.03 46.95 3.77
538 781 1.294138 GGAACCGTCGGATGGTGAA 59.706 57.895 22.06 0.00 37.61 3.18
572 815 0.318107 TCGTGTCGTTCTTCCCGAAC 60.318 55.000 0.00 0.00 46.78 3.95
630 874 1.600107 CGAGATTTTGGGTCGGGGA 59.400 57.895 0.00 0.00 0.00 4.81
689 935 1.138036 CGTCGTGGATGAACGGCTA 59.862 57.895 0.00 0.00 45.74 3.93
690 936 2.126071 CGTCGTGGATGAACGGCT 60.126 61.111 0.00 0.00 45.74 5.52
695 941 1.640428 GATGAAGCGTCGTGGATGAA 58.360 50.000 0.00 0.00 0.00 2.57
698 944 0.385751 ATCGATGAAGCGTCGTGGAT 59.614 50.000 12.35 12.35 42.61 3.41
705 951 2.417516 CGGGGATCGATGAAGCGT 59.582 61.111 0.54 0.00 42.43 5.07
743 991 1.009222 CCGTCCGTATACTGCCGTC 60.009 63.158 0.56 0.00 0.00 4.79
744 992 3.113745 CCGTCCGTATACTGCCGT 58.886 61.111 0.56 0.00 0.00 5.68
896 1152 1.733402 CTGCTGCGAGGTAGCTAGCT 61.733 60.000 24.94 24.94 41.66 3.32
897 1153 1.299773 CTGCTGCGAGGTAGCTAGC 60.300 63.158 18.70 18.70 41.66 3.42
1408 1668 1.414866 GCATTGGGGGTGGTTTGGTT 61.415 55.000 0.00 0.00 0.00 3.67
1409 1669 1.841103 GCATTGGGGGTGGTTTGGT 60.841 57.895 0.00 0.00 0.00 3.67
1410 1670 1.200092 ATGCATTGGGGGTGGTTTGG 61.200 55.000 0.00 0.00 0.00 3.28
1411 1671 0.249955 GATGCATTGGGGGTGGTTTG 59.750 55.000 0.00 0.00 0.00 2.93
1412 1672 1.257055 CGATGCATTGGGGGTGGTTT 61.257 55.000 5.98 0.00 0.00 3.27
1413 1673 1.682005 CGATGCATTGGGGGTGGTT 60.682 57.895 5.98 0.00 0.00 3.67
1414 1674 2.044053 CGATGCATTGGGGGTGGT 60.044 61.111 5.98 0.00 0.00 4.16
1415 1675 2.120909 GTCGATGCATTGGGGGTGG 61.121 63.158 14.12 0.00 0.00 4.61
1416 1676 1.077501 AGTCGATGCATTGGGGGTG 60.078 57.895 14.12 0.00 0.00 4.61
1417 1677 1.077501 CAGTCGATGCATTGGGGGT 60.078 57.895 14.12 0.00 0.00 4.95
1418 1678 3.831883 CAGTCGATGCATTGGGGG 58.168 61.111 14.12 0.15 0.00 5.40
1436 1696 4.932200 AGAAAGAGAAAGATTGGTAGCACG 59.068 41.667 0.00 0.00 0.00 5.34
1472 1734 4.503910 CCATCGAACCAGATTAGTTGACA 58.496 43.478 0.00 0.00 0.00 3.58
1475 1737 2.614057 GGCCATCGAACCAGATTAGTTG 59.386 50.000 0.00 0.00 0.00 3.16
1477 1739 1.202533 CGGCCATCGAACCAGATTAGT 60.203 52.381 2.24 0.00 42.43 2.24
1485 1747 1.024579 AATCACACGGCCATCGAACC 61.025 55.000 2.24 0.00 42.43 3.62
1494 1756 3.002348 GCTACCATTCTTAATCACACGGC 59.998 47.826 0.00 0.00 0.00 5.68
1496 1758 5.109210 TCAGCTACCATTCTTAATCACACG 58.891 41.667 0.00 0.00 0.00 4.49
1513 1775 7.222805 CGTGCAGTTCTAATTAGAAATCAGCTA 59.777 37.037 25.73 14.18 43.30 3.32
1516 1778 7.525688 TCGTGCAGTTCTAATTAGAAATCAG 57.474 36.000 25.73 16.18 43.30 2.90
1589 1878 2.289840 GCAACAAGATGCCCCCAAT 58.710 52.632 0.00 0.00 40.49 3.16
1610 1899 4.100808 GGCCAAGCATAAAAATGGTGGATA 59.899 41.667 0.00 0.00 35.34 2.59
1631 1920 2.032290 GGTAACTTCAAACGACTGTGGC 60.032 50.000 0.00 0.00 0.00 5.01
1653 1942 2.039216 TGGGCAAATAGGAACAGTTCGA 59.961 45.455 7.22 0.00 0.00 3.71
1678 1967 0.535102 CGACCCTGCCAACAAACTCT 60.535 55.000 0.00 0.00 0.00 3.24
1679 1968 1.515521 CCGACCCTGCCAACAAACTC 61.516 60.000 0.00 0.00 0.00 3.01
1680 1969 1.528309 CCGACCCTGCCAACAAACT 60.528 57.895 0.00 0.00 0.00 2.66
1681 1970 3.039134 CCGACCCTGCCAACAAAC 58.961 61.111 0.00 0.00 0.00 2.93
1682 1971 2.909965 GCCGACCCTGCCAACAAA 60.910 61.111 0.00 0.00 0.00 2.83
1701 1990 5.294356 CAAATAATGGATCTCGGTTCGGTA 58.706 41.667 0.00 0.00 0.00 4.02
1718 2007 4.019771 GGGAAATTCTTGTGGGCCAAATAA 60.020 41.667 8.40 0.25 31.20 1.40
1790 2083 3.399330 GTGCTGGCAGAAACTGTACTTA 58.601 45.455 20.86 0.00 33.43 2.24
1800 2093 4.284550 GTGGGGGTGCTGGCAGAA 62.285 66.667 20.86 4.21 0.00 3.02
1848 2145 6.128035 GCGAACATTGTATCATGGGCATTATA 60.128 38.462 0.00 0.00 0.00 0.98
1849 2146 5.335897 GCGAACATTGTATCATGGGCATTAT 60.336 40.000 0.00 0.00 0.00 1.28
1850 2147 4.023279 GCGAACATTGTATCATGGGCATTA 60.023 41.667 0.00 0.00 0.00 1.90
1870 2167 6.403049 TGGACATATTACTTCTTTTGAGCGA 58.597 36.000 0.00 0.00 0.00 4.93
1889 2186 0.334676 GTTTGGGGGATCCATGGACA 59.665 55.000 18.99 7.31 46.52 4.02
1917 2214 2.467880 AGTGATTAGTCCACCGACCAT 58.532 47.619 0.00 0.00 40.12 3.55
1918 2215 1.933021 AGTGATTAGTCCACCGACCA 58.067 50.000 0.00 0.00 40.12 4.02
2015 2315 3.222855 CTCGATGCTCCTCCGCCT 61.223 66.667 0.00 0.00 0.00 5.52
2161 2462 1.274167 TCGGTTAATGAGCTCCAACGT 59.726 47.619 12.15 0.00 0.00 3.99
2175 2476 1.271856 TCCATCAGCAGGTTCGGTTA 58.728 50.000 0.00 0.00 0.00 2.85
2177 2478 0.107508 CATCCATCAGCAGGTTCGGT 60.108 55.000 0.00 0.00 0.00 4.69
2178 2479 0.178767 TCATCCATCAGCAGGTTCGG 59.821 55.000 0.00 0.00 0.00 4.30
2210 2515 1.594293 CCGTTCTTGTCGCACCTGT 60.594 57.895 0.00 0.00 0.00 4.00
2293 2598 9.288576 TCATTTCTCATTGTTTCAGAATACAGT 57.711 29.630 0.00 0.00 0.00 3.55
2321 2626 6.420604 AGCGAATAAAAACAACAGGTTGATTG 59.579 34.615 18.28 2.24 42.93 2.67
2341 2649 2.472695 AATAACCTGTCAGCAGCGAA 57.527 45.000 0.00 0.00 41.26 4.70
2482 2790 5.062528 GGCGACCACTACTAGTAGTCTATT 58.937 45.833 28.86 15.11 43.98 1.73
2513 2827 0.389948 CGCGCCCTCTGAAGTTACTT 60.390 55.000 0.00 0.00 0.00 2.24
2515 2829 0.802607 CTCGCGCCCTCTGAAGTTAC 60.803 60.000 0.00 0.00 0.00 2.50
2516 2830 1.248785 ACTCGCGCCCTCTGAAGTTA 61.249 55.000 0.00 0.00 0.00 2.24
2715 3490 0.108615 CGCTTCCAGTTCTCGTGGAT 60.109 55.000 0.00 0.00 43.78 3.41
3060 3835 3.532155 GTCGCTCGGGCAGGAGAT 61.532 66.667 8.62 0.00 38.60 2.75
3152 3927 4.741239 AGGATGCCGGTGACCCCT 62.741 66.667 1.90 0.00 0.00 4.79
3311 4086 1.480212 AATGCACCACGAGGAGGACA 61.480 55.000 5.68 0.00 38.69 4.02
3353 4128 5.733620 TTACCGTCTTCTTGTACCAGATT 57.266 39.130 0.00 0.00 0.00 2.40
3382 4157 3.051940 TCATCAGTAAGGAGGGCAGAT 57.948 47.619 0.00 0.00 0.00 2.90
3436 4211 9.425893 CGATCATCAACACTTGAATTTACATAC 57.574 33.333 0.00 0.00 43.95 2.39
3437 4212 9.161629 ACGATCATCAACACTTGAATTTACATA 57.838 29.630 0.00 0.00 43.95 2.29
3438 4213 8.044060 ACGATCATCAACACTTGAATTTACAT 57.956 30.769 0.00 0.00 43.95 2.29
3450 4225 6.236941 GCGAACAAATAAACGATCATCAACAC 60.237 38.462 0.00 0.00 0.00 3.32
3458 4233 5.163992 TGTCTGAGCGAACAAATAAACGATC 60.164 40.000 0.00 0.00 40.65 3.69
3465 4240 4.200838 TCCATGTCTGAGCGAACAAATA 57.799 40.909 0.00 0.00 0.00 1.40
3527 4304 6.795114 TGTTTTCGCGAACTTTTCTGATAATC 59.205 34.615 23.33 2.11 0.00 1.75
3548 4325 4.879545 AGAATGTTCACGTGGTAGTTGTTT 59.120 37.500 17.00 0.00 0.00 2.83
3594 4371 7.900352 CAGTCAGAAAGAAGTAATAAATCGTGC 59.100 37.037 0.00 0.00 0.00 5.34
3848 4690 1.001641 GGATGCCTGCAAGACCACT 60.002 57.895 0.00 0.00 34.07 4.00
3849 4691 2.401766 CGGATGCCTGCAAGACCAC 61.402 63.158 0.00 0.00 34.07 4.16
3950 4798 0.250338 ACTGACCTTCCCGAACAAGC 60.250 55.000 0.00 0.00 0.00 4.01
4448 5796 6.582636 TCAGTTATGTTACCTCCATTAGCTG 58.417 40.000 0.00 0.00 0.00 4.24
4663 6020 6.595326 TGCGACTAGACAAAGATGAAATTGAT 59.405 34.615 0.00 0.00 0.00 2.57
4695 6068 8.425577 TTCTGCATATTACTTTAGCTCAGTTC 57.574 34.615 3.89 0.00 0.00 3.01
4727 6110 2.609459 GGTGAGGTAATTGTGCATCTCG 59.391 50.000 0.00 0.00 0.00 4.04
4832 6215 1.568504 ATACCTTGCTTCCGGAGACA 58.431 50.000 3.34 4.01 0.00 3.41
4886 6275 4.023707 CGTGTCAGAAAAGGAAGCAAAGAT 60.024 41.667 0.00 0.00 0.00 2.40
4910 6321 3.868757 TGTGTCCGAATCTACAAGAGG 57.131 47.619 0.00 0.00 0.00 3.69
5070 6570 7.942341 TCCACAATAGAAAACACCTGTAGATTT 59.058 33.333 0.00 0.00 0.00 2.17
5190 6702 3.358111 TGAAATTCTTCGGGTATGGCA 57.642 42.857 0.00 0.00 33.94 4.92
5292 6918 1.196127 GTACTTTGTACAACCCAGCGC 59.804 52.381 8.07 0.00 0.00 5.92
5525 7230 9.416794 GAACTATATCAGTATCAGGTGACATTG 57.583 37.037 0.00 0.00 36.04 2.82
5629 7382 1.622811 AGAGACTGTCAGGGCAGAAAG 59.377 52.381 8.06 0.00 39.62 2.62
5658 7411 4.697756 TTGCTTCAGGCGTCCCCG 62.698 66.667 0.00 0.00 45.43 5.73
5741 7497 4.746535 TCATCGCAAGGAACTAATGGTA 57.253 40.909 0.00 0.00 38.49 3.25
6136 7916 3.072211 CAGACACTGCATCTGTTGTCAT 58.928 45.455 7.51 0.00 39.04 3.06


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

AutoCloner maintained by Alex Coulton.