Multiple sequence alignment - TraesCS1D01G412400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G412400 chr1D 100.000 4635 0 0 1 4635 473764493 473759859 0.000000e+00 8560.0
1 TraesCS1D01G412400 chr1D 100.000 1288 0 0 4880 6167 473759614 473758327 0.000000e+00 2379.0
2 TraesCS1D01G412400 chr1D 86.429 420 44 10 2021 2438 473736875 473736467 1.220000e-121 448.0
3 TraesCS1D01G412400 chr1D 85.714 98 14 0 1196 1293 473675607 473675510 3.040000e-18 104.0
4 TraesCS1D01G412400 chr1D 97.619 42 0 1 3356 3397 473761100 473761060 3.080000e-08 71.3
5 TraesCS1D01G412400 chr1D 97.619 42 0 1 3394 3434 473761138 473761097 3.080000e-08 71.3
6 TraesCS1D01G412400 chrUn 97.730 1982 36 4 1418 3397 1483388 1485362 0.000000e+00 3402.0
7 TraesCS1D01G412400 chrUn 98.230 1243 14 3 3394 4635 1485328 1486563 0.000000e+00 2167.0
8 TraesCS1D01G412400 chrUn 96.914 1296 22 2 4880 6167 368729110 368727825 0.000000e+00 2156.0
9 TraesCS1D01G412400 chrUn 92.555 685 40 3 168 852 1481341 1482014 0.000000e+00 972.0
10 TraesCS1D01G412400 chrUn 97.028 572 11 4 856 1421 1482531 1483102 0.000000e+00 957.0
11 TraesCS1D01G412400 chrUn 83.077 1040 145 15 3600 4633 346225759 346226773 0.000000e+00 917.0
12 TraesCS1D01G412400 chrUn 96.491 114 4 0 1 114 324766003 324765890 8.160000e-44 189.0
13 TraesCS1D01G412400 chrUn 96.491 114 4 0 1 114 363461791 363461678 8.160000e-44 189.0
14 TraesCS1D01G412400 chrUn 95.614 114 5 0 1 114 403654389 403654502 3.800000e-42 183.0
15 TraesCS1D01G412400 chrUn 79.545 176 36 0 3699 3874 32132988 32132813 6.490000e-25 126.0
16 TraesCS1D01G412400 chrUn 89.130 92 10 0 1210 1301 308941594 308941685 1.400000e-21 115.0
17 TraesCS1D01G412400 chrUn 77.436 195 30 9 1766 1958 308941860 308942042 3.040000e-18 104.0
18 TraesCS1D01G412400 chr1B 83.647 1223 168 16 3419 4635 658737634 658736438 0.000000e+00 1122.0
19 TraesCS1D01G412400 chr1B 85.551 789 100 8 2021 2804 658739066 658738287 0.000000e+00 813.0
20 TraesCS1D01G412400 chr1B 87.253 659 53 10 928 1578 658740551 658739916 0.000000e+00 723.0
21 TraesCS1D01G412400 chr1B 90.079 252 20 3 1759 2006 658739455 658739205 7.710000e-84 322.0
22 TraesCS1D01G412400 chr1B 92.265 181 13 1 1569 1748 658739871 658739691 7.930000e-64 255.0
23 TraesCS1D01G412400 chr1B 89.560 182 19 0 1776 1957 658714742 658714561 1.340000e-56 231.0
24 TraesCS1D01G412400 chr1B 90.164 122 11 1 1419 1540 658715107 658714987 2.300000e-34 158.0
25 TraesCS1D01G412400 chr1B 95.122 82 4 0 1227 1308 658701001 658700920 5.020000e-26 130.0
26 TraesCS1D01G412400 chr1B 100.000 29 0 0 1748 1776 658739674 658739646 3.000000e-03 54.7
27 TraesCS1D01G412400 chr3B 76.625 646 123 21 2038 2666 2485852 2486486 1.280000e-86 331.0
28 TraesCS1D01G412400 chr3B 75.812 554 112 15 2038 2583 2491247 2491786 1.710000e-65 261.0
29 TraesCS1D01G412400 chr3B 82.955 176 30 0 3699 3874 2487196 2487371 6.400000e-35 159.0
30 TraesCS1D01G412400 chr3B 77.436 195 30 9 1766 1958 2474797 2474979 3.040000e-18 104.0
31 TraesCS1D01G412400 chr6D 73.815 928 182 42 1766 2666 13975518 13976411 1.670000e-80 311.0
32 TraesCS1D01G412400 chr6D 97.368 114 3 0 1 114 9374984 9374871 1.750000e-45 195.0
33 TraesCS1D01G412400 chr6A 75.312 640 133 18 2038 2669 14609292 14608670 3.640000e-72 283.0
34 TraesCS1D01G412400 chr6A 86.275 102 13 1 1768 1869 14609572 14609472 6.540000e-20 110.0
35 TraesCS1D01G412400 chr3D 74.648 639 136 16 2038 2666 2983294 2982672 6.130000e-65 259.0
36 TraesCS1D01G412400 chr3D 97.368 114 3 0 1 114 24746644 24746531 1.750000e-45 195.0
37 TraesCS1D01G412400 chr3D 97.368 114 3 0 1 114 306008409 306008296 1.750000e-45 195.0
38 TraesCS1D01G412400 chr3D 78.238 193 28 9 1768 1958 3012457 3012637 1.820000e-20 111.0
39 TraesCS1D01G412400 chr3D 85.417 96 11 2 6075 6167 366237117 366237212 5.090000e-16 97.1
40 TraesCS1D01G412400 chr4A 96.491 114 4 0 1 114 605361589 605361702 8.160000e-44 189.0
41 TraesCS1D01G412400 chr4A 90.217 92 9 0 6076 6167 7126245 7126336 3.020000e-23 121.0
42 TraesCS1D01G412400 chr4A 85.263 95 13 1 6074 6167 190825191 190825097 5.090000e-16 97.1
43 TraesCS1D01G412400 chr4D 89.362 94 10 0 6072 6165 441056607 441056514 1.090000e-22 119.0
44 TraesCS1D01G412400 chr4D 84.375 96 13 2 6074 6167 297383031 297383126 6.580000e-15 93.5
45 TraesCS1D01G412400 chr3A 92.500 80 6 0 1222 1301 17612 17533 1.400000e-21 115.0
46 TraesCS1D01G412400 chr3A 92.500 80 6 0 1222 1301 44641 44562 1.400000e-21 115.0
47 TraesCS1D01G412400 chr3A 92.500 80 6 0 1222 1301 67529 67450 1.400000e-21 115.0
48 TraesCS1D01G412400 chr4B 85.263 95 13 1 6074 6167 368418386 368418480 5.090000e-16 97.1
49 TraesCS1D01G412400 chr6B 83.178 107 14 3 1766 1869 25557570 25557465 1.830000e-15 95.3
50 TraesCS1D01G412400 chr2D 92.857 56 2 2 792 846 35786689 35786743 5.120000e-11 80.5
51 TraesCS1D01G412400 chr1A 91.228 57 5 0 6076 6132 103646932 103646988 1.840000e-10 78.7
52 TraesCS1D01G412400 chr2B 89.796 49 5 0 807 855 108911690 108911642 5.160000e-06 63.9


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 TraesCS1D01G412400 chr1D 473758327 473764493 6166 True 2770.400000 8560 98.809500 1 6167 4 chr1D.!!$R3 6166
1 TraesCS1D01G412400 chrUn 368727825 368729110 1285 True 2156.000000 2156 96.914000 4880 6167 1 chrUn.!!$R4 1287
2 TraesCS1D01G412400 chrUn 1481341 1486563 5222 False 1874.500000 3402 96.385750 168 4635 4 chrUn.!!$F3 4467
3 TraesCS1D01G412400 chrUn 346225759 346226773 1014 False 917.000000 917 83.077000 3600 4633 1 chrUn.!!$F1 1033
4 TraesCS1D01G412400 chr1B 658736438 658740551 4113 True 548.283333 1122 89.799167 928 4635 6 chr1B.!!$R3 3707
5 TraesCS1D01G412400 chr3B 2485852 2491786 5934 False 250.333333 331 78.464000 2038 3874 3 chr3B.!!$F2 1836
6 TraesCS1D01G412400 chr6D 13975518 13976411 893 False 311.000000 311 73.815000 1766 2666 1 chr6D.!!$F1 900
7 TraesCS1D01G412400 chr3D 2982672 2983294 622 True 259.000000 259 74.648000 2038 2666 1 chr3D.!!$R1 628

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
113 114 0.460987 GCCCTTGTGAGACGGAGATG 60.461 60.000 0.00 0.0 0.00 2.90 F
675 676 0.521735 GTCGGTGATTGCTTTGACCC 59.478 55.000 0.00 0.0 0.00 4.46 F
1176 1694 0.388649 CTTGCTTACGTGCTCCGAGT 60.389 55.000 0.00 0.0 40.70 4.18 F
1182 1700 1.171308 TACGTGCTCCGAGTTAGCTT 58.829 50.000 0.00 0.0 40.73 3.74 F
3014 4291 1.271840 ACCCCTACCACGATGCACAT 61.272 55.000 0.00 0.0 0.00 3.21 F
3402 4784 0.032130 CTGCATGCATTGGAGATGCC 59.968 55.000 22.97 0.0 46.09 4.40 F
3439 4821 2.424557 CTCTGCATGCATGGACCTATC 58.575 52.381 27.34 9.8 0.00 2.08 F
3458 4840 3.343941 TCCACACAGCCATAACCTTAC 57.656 47.619 0.00 0.0 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1679 1.132643 AGCTAACTCGGAGCACGTAAG 59.867 52.381 4.58 0.0 42.69 2.34 R
2618 3864 2.109463 CGTGATCACTGTATCGAACGG 58.891 52.381 22.95 0.0 40.63 4.44 R
3136 4484 2.119029 GCCGCCGGGAATAAAGCTT 61.119 57.895 4.77 0.0 34.06 3.74 R
3207 4582 2.494918 GGGTCTCATGTCGTCCGG 59.505 66.667 0.00 0.0 0.00 5.14 R
4351 5738 0.908198 ACCTCCATCTTGACTCCTGC 59.092 55.000 0.00 0.0 0.00 4.85 R
4604 5991 1.770061 TCCTCATCACTGCCATGCATA 59.230 47.619 0.00 0.0 38.13 3.14 R
5083 6845 2.307496 TCCAACCATGCCAACTCATT 57.693 45.000 0.00 0.0 0.00 2.57 R
5495 7257 6.434028 TGATCCAAGTCCAACTAAAATTCAGG 59.566 38.462 0.00 0.0 0.00 3.86 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
26 27 2.261671 CGTAACGCTGCTGAGGGT 59.738 61.111 0.00 0.00 46.90 4.34
27 28 1.805945 CGTAACGCTGCTGAGGGTC 60.806 63.158 0.00 0.00 44.28 4.46
28 29 1.448013 GTAACGCTGCTGAGGGTCC 60.448 63.158 0.00 0.00 44.28 4.46
29 30 1.911269 TAACGCTGCTGAGGGTCCA 60.911 57.895 0.00 0.00 44.28 4.02
30 31 1.888436 TAACGCTGCTGAGGGTCCAG 61.888 60.000 0.00 0.00 44.28 3.86
31 32 3.699894 CGCTGCTGAGGGTCCAGT 61.700 66.667 0.00 0.00 36.57 4.00
32 33 2.046507 GCTGCTGAGGGTCCAGTG 60.047 66.667 0.00 0.00 36.57 3.66
33 34 2.046507 CTGCTGAGGGTCCAGTGC 60.047 66.667 0.00 0.00 36.57 4.40
34 35 3.947132 CTGCTGAGGGTCCAGTGCG 62.947 68.421 0.00 0.00 36.57 5.34
35 36 4.767255 GCTGAGGGTCCAGTGCGG 62.767 72.222 0.00 0.00 36.57 5.69
36 37 4.767255 CTGAGGGTCCAGTGCGGC 62.767 72.222 0.00 0.00 33.14 6.53
51 52 4.710167 GGCCGTGGCGTTAGGGTT 62.710 66.667 4.53 0.00 43.06 4.11
52 53 3.122971 GCCGTGGCGTTAGGGTTC 61.123 66.667 0.00 0.00 0.00 3.62
53 54 2.435410 CCGTGGCGTTAGGGTTCC 60.435 66.667 0.00 0.00 0.00 3.62
54 55 2.812178 CGTGGCGTTAGGGTTCCG 60.812 66.667 0.00 0.00 0.00 4.30
55 56 3.122971 GTGGCGTTAGGGTTCCGC 61.123 66.667 0.00 0.00 46.28 5.54
58 59 4.440127 GCGTTAGGGTTCCGCGGA 62.440 66.667 27.28 27.28 37.89 5.54
59 60 2.202703 CGTTAGGGTTCCGCGGAG 60.203 66.667 29.20 10.37 0.00 4.63
60 61 2.186125 GTTAGGGTTCCGCGGAGG 59.814 66.667 29.20 0.07 42.97 4.30
61 62 3.777910 TTAGGGTTCCGCGGAGGC 61.778 66.667 29.20 23.59 40.77 4.70
66 67 4.699522 GTTCCGCGGAGGCACCTT 62.700 66.667 29.20 0.00 40.77 3.50
67 68 4.697756 TTCCGCGGAGGCACCTTG 62.698 66.667 29.20 0.00 40.77 3.61
70 71 4.680237 CGCGGAGGCACCTTGACA 62.680 66.667 0.00 0.00 39.92 3.58
71 72 2.743928 GCGGAGGCACCTTGACAG 60.744 66.667 0.00 0.00 39.62 3.51
73 74 2.583441 CGGAGGCACCTTGACAGGA 61.583 63.158 0.00 0.00 44.19 3.86
74 75 1.298014 GGAGGCACCTTGACAGGAG 59.702 63.158 0.00 0.00 44.19 3.69
75 76 1.298014 GAGGCACCTTGACAGGAGG 59.702 63.158 0.00 0.00 44.19 4.30
76 77 2.360475 GGCACCTTGACAGGAGGC 60.360 66.667 0.00 0.00 46.72 4.70
77 78 2.743928 GCACCTTGACAGGAGGCG 60.744 66.667 0.00 0.00 44.19 5.52
78 79 2.046892 CACCTTGACAGGAGGCGG 60.047 66.667 0.00 0.00 44.19 6.13
79 80 4.021925 ACCTTGACAGGAGGCGGC 62.022 66.667 0.00 0.00 44.19 6.53
80 81 4.785453 CCTTGACAGGAGGCGGCC 62.785 72.222 12.11 12.11 44.19 6.13
81 82 4.785453 CTTGACAGGAGGCGGCCC 62.785 72.222 17.02 6.89 0.00 5.80
105 106 4.020617 CTGGCCGCCCTTGTGAGA 62.021 66.667 7.03 0.00 0.00 3.27
106 107 4.329545 TGGCCGCCCTTGTGAGAC 62.330 66.667 7.03 0.00 0.00 3.36
109 110 3.691342 CCGCCCTTGTGAGACGGA 61.691 66.667 0.00 0.00 41.89 4.69
110 111 2.125912 CGCCCTTGTGAGACGGAG 60.126 66.667 0.00 0.00 0.00 4.63
111 112 2.636412 CGCCCTTGTGAGACGGAGA 61.636 63.158 0.00 0.00 0.00 3.71
112 113 1.901085 GCCCTTGTGAGACGGAGAT 59.099 57.895 0.00 0.00 0.00 2.75
113 114 0.460987 GCCCTTGTGAGACGGAGATG 60.461 60.000 0.00 0.00 0.00 2.90
114 115 1.186200 CCCTTGTGAGACGGAGATGA 58.814 55.000 0.00 0.00 0.00 2.92
115 116 1.550524 CCCTTGTGAGACGGAGATGAA 59.449 52.381 0.00 0.00 0.00 2.57
116 117 2.169352 CCCTTGTGAGACGGAGATGAAT 59.831 50.000 0.00 0.00 0.00 2.57
117 118 3.193263 CCTTGTGAGACGGAGATGAATG 58.807 50.000 0.00 0.00 0.00 2.67
118 119 3.368843 CCTTGTGAGACGGAGATGAATGT 60.369 47.826 0.00 0.00 0.00 2.71
119 120 3.510388 TGTGAGACGGAGATGAATGTC 57.490 47.619 0.00 0.00 0.00 3.06
120 121 2.825532 TGTGAGACGGAGATGAATGTCA 59.174 45.455 0.00 0.00 33.83 3.58
121 122 3.182967 GTGAGACGGAGATGAATGTCAC 58.817 50.000 0.00 0.00 33.83 3.67
122 123 3.092301 TGAGACGGAGATGAATGTCACT 58.908 45.455 0.00 0.00 33.83 3.41
123 124 4.096532 GTGAGACGGAGATGAATGTCACTA 59.903 45.833 0.00 0.00 33.83 2.74
124 125 4.096532 TGAGACGGAGATGAATGTCACTAC 59.903 45.833 0.00 0.00 33.83 2.73
125 126 4.274147 AGACGGAGATGAATGTCACTACT 58.726 43.478 0.00 0.00 33.83 2.57
126 127 4.707448 AGACGGAGATGAATGTCACTACTT 59.293 41.667 0.00 0.00 33.83 2.24
127 128 5.000012 ACGGAGATGAATGTCACTACTTC 58.000 43.478 0.00 0.00 0.00 3.01
128 129 4.142138 ACGGAGATGAATGTCACTACTTCC 60.142 45.833 0.00 0.00 0.00 3.46
129 130 4.142160 CGGAGATGAATGTCACTACTTCCA 60.142 45.833 0.00 0.00 0.00 3.53
130 131 5.452496 CGGAGATGAATGTCACTACTTCCAT 60.452 44.000 0.00 0.00 0.00 3.41
131 132 5.757320 GGAGATGAATGTCACTACTTCCATG 59.243 44.000 0.00 0.00 0.00 3.66
132 133 6.407412 GGAGATGAATGTCACTACTTCCATGA 60.407 42.308 0.00 0.00 0.00 3.07
133 134 6.950842 AGATGAATGTCACTACTTCCATGAA 58.049 36.000 0.00 0.00 0.00 2.57
134 135 7.571919 AGATGAATGTCACTACTTCCATGAAT 58.428 34.615 0.00 0.00 0.00 2.57
135 136 6.990341 TGAATGTCACTACTTCCATGAATG 57.010 37.500 0.00 0.00 0.00 2.67
136 137 6.475504 TGAATGTCACTACTTCCATGAATGT 58.524 36.000 0.00 0.00 0.00 2.71
137 138 6.595326 TGAATGTCACTACTTCCATGAATGTC 59.405 38.462 0.00 0.00 0.00 3.06
138 139 4.494484 TGTCACTACTTCCATGAATGTCG 58.506 43.478 0.00 0.00 0.00 4.35
139 140 4.021456 TGTCACTACTTCCATGAATGTCGT 60.021 41.667 0.00 0.00 0.00 4.34
140 141 4.929808 GTCACTACTTCCATGAATGTCGTT 59.070 41.667 0.00 0.00 0.00 3.85
141 142 5.408604 GTCACTACTTCCATGAATGTCGTTT 59.591 40.000 0.00 0.00 0.00 3.60
142 143 5.637810 TCACTACTTCCATGAATGTCGTTTC 59.362 40.000 0.00 0.00 0.00 2.78
143 144 5.408299 CACTACTTCCATGAATGTCGTTTCA 59.592 40.000 0.00 1.82 39.77 2.69
144 145 6.092670 CACTACTTCCATGAATGTCGTTTCAT 59.907 38.462 0.00 5.55 45.03 2.57
145 146 7.277760 CACTACTTCCATGAATGTCGTTTCATA 59.722 37.037 0.00 0.00 42.90 2.15
146 147 7.987458 ACTACTTCCATGAATGTCGTTTCATAT 59.013 33.333 0.00 0.00 42.90 1.78
147 148 7.019774 ACTTCCATGAATGTCGTTTCATATG 57.980 36.000 0.00 0.00 42.90 1.78
148 149 6.038603 ACTTCCATGAATGTCGTTTCATATGG 59.961 38.462 2.13 9.62 42.90 2.74
149 150 5.679601 TCCATGAATGTCGTTTCATATGGA 58.320 37.500 2.13 12.53 42.90 3.41
150 151 6.118852 TCCATGAATGTCGTTTCATATGGAA 58.881 36.000 2.13 0.00 42.90 3.53
151 152 6.038161 TCCATGAATGTCGTTTCATATGGAAC 59.962 38.462 15.88 15.88 42.90 3.62
152 153 6.038603 CCATGAATGTCGTTTCATATGGAACT 59.961 38.462 21.86 5.42 42.90 3.01
153 154 7.415541 CCATGAATGTCGTTTCATATGGAACTT 60.416 37.037 21.86 11.13 42.90 2.66
154 155 7.447374 TGAATGTCGTTTCATATGGAACTTT 57.553 32.000 21.86 11.51 34.56 2.66
155 156 8.554835 TGAATGTCGTTTCATATGGAACTTTA 57.445 30.769 21.86 9.91 34.56 1.85
156 157 9.173021 TGAATGTCGTTTCATATGGAACTTTAT 57.827 29.630 21.86 11.47 34.56 1.40
160 161 8.609176 TGTCGTTTCATATGGAACTTTATAAGC 58.391 33.333 21.86 6.25 34.56 3.09
161 162 8.609176 GTCGTTTCATATGGAACTTTATAAGCA 58.391 33.333 21.86 0.00 34.56 3.91
162 163 9.168451 TCGTTTCATATGGAACTTTATAAGCAA 57.832 29.630 21.86 0.00 34.56 3.91
163 164 9.950680 CGTTTCATATGGAACTTTATAAGCAAT 57.049 29.630 21.86 0.00 34.56 3.56
231 232 3.264947 TGTTCATCCGAGCTCATTTGAG 58.735 45.455 15.40 3.13 44.75 3.02
249 250 6.780706 TTTGAGTCCGAGTTAAGAAACATC 57.219 37.500 0.00 0.00 38.12 3.06
255 256 3.865745 CCGAGTTAAGAAACATCGCATCT 59.134 43.478 0.00 0.00 38.12 2.90
256 257 5.041287 CCGAGTTAAGAAACATCGCATCTA 58.959 41.667 0.00 0.00 38.12 1.98
259 260 6.910972 CGAGTTAAGAAACATCGCATCTACTA 59.089 38.462 0.00 0.00 38.12 1.82
267 268 3.571828 ACATCGCATCTACTACTCTGCAT 59.428 43.478 0.00 0.00 34.29 3.96
308 309 3.658757 GCCATAGCTTTGTTTTGACCA 57.341 42.857 3.39 0.00 35.50 4.02
315 316 3.321968 AGCTTTGTTTTGACCAATCTCCC 59.678 43.478 0.00 0.00 0.00 4.30
370 371 4.133856 GACAACTGTCCAAACTGAATCG 57.866 45.455 0.00 0.00 39.07 3.34
380 381 4.100529 CCAAACTGAATCGTTGATCATGC 58.899 43.478 0.00 0.00 0.00 4.06
393 394 3.620488 TGATCATGCCCTAAGGTGAAAC 58.380 45.455 0.00 0.00 34.57 2.78
404 405 4.515567 CCTAAGGTGAAACAGTGAGGAAAC 59.484 45.833 0.00 0.00 39.98 2.78
410 411 1.949465 AACAGTGAGGAAACGTCACC 58.051 50.000 17.00 0.00 44.65 4.02
419 420 1.264295 GAAACGTCACCTCCCTACCT 58.736 55.000 0.00 0.00 0.00 3.08
481 482 7.078228 CAGTTAAGTTTCCTGACAGCATAAAC 58.922 38.462 13.96 13.96 33.41 2.01
566 567 5.302823 TGATGCATACTCAGCTATGTACACT 59.697 40.000 0.00 0.00 0.00 3.55
675 676 0.521735 GTCGGTGATTGCTTTGACCC 59.478 55.000 0.00 0.00 0.00 4.46
684 685 0.535553 TGCTTTGACCCCCGTGTTAC 60.536 55.000 0.00 0.00 0.00 2.50
701 702 7.799914 CCCGTGTTACTTATTTTAGTTGTTGTC 59.200 37.037 0.00 0.00 0.00 3.18
761 762 4.798882 TCCCCTGTTTCAAAGTGTATGTT 58.201 39.130 0.00 0.00 0.00 2.71
762 763 4.825085 TCCCCTGTTTCAAAGTGTATGTTC 59.175 41.667 0.00 0.00 0.00 3.18
763 764 4.582656 CCCCTGTTTCAAAGTGTATGTTCA 59.417 41.667 0.00 0.00 0.00 3.18
764 765 5.243730 CCCCTGTTTCAAAGTGTATGTTCAT 59.756 40.000 0.00 0.00 0.00 2.57
765 766 6.432783 CCCCTGTTTCAAAGTGTATGTTCATA 59.567 38.462 0.00 0.00 0.00 2.15
766 767 7.122650 CCCCTGTTTCAAAGTGTATGTTCATAT 59.877 37.037 0.00 0.00 0.00 1.78
767 768 8.522830 CCCTGTTTCAAAGTGTATGTTCATATT 58.477 33.333 0.00 0.00 0.00 1.28
768 769 9.912634 CCTGTTTCAAAGTGTATGTTCATATTT 57.087 29.630 0.00 0.00 0.00 1.40
798 799 8.262227 TGTATATCAACGGAAAAATGTACTCCT 58.738 33.333 0.00 0.00 0.00 3.69
806 807 6.080648 GGAAAAATGTACTCCTTCCGTTTT 57.919 37.500 0.00 0.00 0.00 2.43
911 1425 4.180817 TGCGGCATCCATCTATAAATACG 58.819 43.478 0.00 0.00 0.00 3.06
1004 1519 3.753294 AGCTAGGTGAAACGATATGGG 57.247 47.619 0.00 0.00 38.12 4.00
1161 1679 0.516877 TATGCACGCACAACTCTTGC 59.483 50.000 0.00 0.00 36.57 4.01
1176 1694 0.388649 CTTGCTTACGTGCTCCGAGT 60.389 55.000 0.00 0.00 40.70 4.18
1182 1700 1.171308 TACGTGCTCCGAGTTAGCTT 58.829 50.000 0.00 0.00 40.73 3.74
1183 1701 1.171308 ACGTGCTCCGAGTTAGCTTA 58.829 50.000 0.00 0.00 40.73 3.09
1186 1704 2.353889 CGTGCTCCGAGTTAGCTTACTA 59.646 50.000 5.16 0.00 40.73 1.82
1188 1706 4.673580 CGTGCTCCGAGTTAGCTTACTAAA 60.674 45.833 5.16 0.00 38.30 1.85
1556 2371 5.052481 GTCCATCGATTGTCATCATCTCAA 58.948 41.667 0.00 0.00 0.00 3.02
1625 2494 9.309224 CCTAAATAGGTCCCCTTTTTATATTGG 57.691 37.037 6.44 2.47 36.79 3.16
1636 2505 7.981225 CCCCTTTTTATATTGGAACACAAGATG 59.019 37.037 0.00 0.00 40.92 2.90
2009 3110 1.298157 CTTGAACGAATCCGGCAGCA 61.298 55.000 0.00 0.00 40.78 4.41
2482 3725 1.839994 TCCCTGGAAATGAGCGAGAAT 59.160 47.619 0.00 0.00 0.00 2.40
2618 3864 3.309675 CGACCAACATCGATCGCC 58.690 61.111 11.09 0.00 45.13 5.54
2814 4065 2.162408 GGAGCAGTTTCGGAGATTTTGG 59.838 50.000 0.00 0.00 35.04 3.28
2910 4162 6.036470 GGTGCAAATTAGTGATTTCCTTAGC 58.964 40.000 0.00 0.00 35.79 3.09
3014 4291 1.271840 ACCCCTACCACGATGCACAT 61.272 55.000 0.00 0.00 0.00 3.21
3136 4484 1.339055 CCTCTGCAACGATCAAAGGGA 60.339 52.381 0.00 0.00 0.00 4.20
3295 4676 2.546795 CGGAGAGGATGTGCCAATACTC 60.547 54.545 0.56 0.56 40.02 2.59
3376 4758 3.710724 TGGAGATGCCATCCAATTCAAA 58.289 40.909 0.00 0.00 43.87 2.69
3377 4759 4.095211 TGGAGATGCCATCCAATTCAAAA 58.905 39.130 0.00 0.00 43.87 2.44
3379 4761 4.081531 GGAGATGCCATCCAATTCAAAACA 60.082 41.667 0.00 0.00 36.79 2.83
3380 4762 5.080969 AGATGCCATCCAATTCAAAACAG 57.919 39.130 0.00 0.00 0.00 3.16
3381 4763 3.042871 TGCCATCCAATTCAAAACAGC 57.957 42.857 0.00 0.00 0.00 4.40
3382 4764 2.633967 TGCCATCCAATTCAAAACAGCT 59.366 40.909 0.00 0.00 0.00 4.24
3383 4765 3.256558 GCCATCCAATTCAAAACAGCTC 58.743 45.455 0.00 0.00 0.00 4.09
3384 4766 3.056322 GCCATCCAATTCAAAACAGCTCT 60.056 43.478 0.00 0.00 0.00 4.09
3385 4767 4.491676 CCATCCAATTCAAAACAGCTCTG 58.508 43.478 0.00 0.00 0.00 3.35
3386 4768 3.648339 TCCAATTCAAAACAGCTCTGC 57.352 42.857 0.00 0.00 0.00 4.26
3387 4769 2.957680 TCCAATTCAAAACAGCTCTGCA 59.042 40.909 0.00 0.00 0.00 4.41
3388 4770 3.575256 TCCAATTCAAAACAGCTCTGCAT 59.425 39.130 0.00 0.00 0.00 3.96
3389 4771 3.678072 CCAATTCAAAACAGCTCTGCATG 59.322 43.478 0.00 0.00 0.00 4.06
3390 4772 2.427232 TTCAAAACAGCTCTGCATGC 57.573 45.000 11.82 11.82 0.00 4.06
3391 4773 1.320507 TCAAAACAGCTCTGCATGCA 58.679 45.000 21.29 21.29 0.00 3.96
3392 4774 1.890489 TCAAAACAGCTCTGCATGCAT 59.110 42.857 22.97 2.59 0.00 3.96
3393 4775 2.297880 TCAAAACAGCTCTGCATGCATT 59.702 40.909 22.97 8.63 0.00 3.56
3394 4776 2.363788 AAACAGCTCTGCATGCATTG 57.636 45.000 22.97 18.38 0.00 2.82
3395 4777 0.530744 AACAGCTCTGCATGCATTGG 59.469 50.000 22.97 14.77 0.00 3.16
3396 4778 0.323087 ACAGCTCTGCATGCATTGGA 60.323 50.000 22.97 14.31 0.00 3.53
3397 4779 0.382158 CAGCTCTGCATGCATTGGAG 59.618 55.000 22.97 23.63 44.66 3.86
3401 4783 1.029681 TCTGCATGCATTGGAGATGC 58.970 50.000 22.97 7.56 46.62 3.91
3402 4784 0.032130 CTGCATGCATTGGAGATGCC 59.968 55.000 22.97 0.00 46.09 4.40
3403 4785 2.631561 CTGCATGCATTGGAGATGCCA 61.632 52.381 22.97 0.00 46.09 4.92
3413 4795 3.385314 TGGAGATGCCATCCAATTCAA 57.615 42.857 0.00 0.00 43.87 2.69
3414 4796 3.710724 TGGAGATGCCATCCAATTCAAA 58.289 40.909 0.00 0.00 43.87 2.69
3415 4797 4.095211 TGGAGATGCCATCCAATTCAAAA 58.905 39.130 0.00 0.00 43.87 2.44
3439 4821 2.424557 CTCTGCATGCATGGACCTATC 58.575 52.381 27.34 9.80 0.00 2.08
3453 4835 3.467803 GACCTATCCACACAGCCATAAC 58.532 50.000 0.00 0.00 0.00 1.89
3458 4840 3.343941 TCCACACAGCCATAACCTTAC 57.656 47.619 0.00 0.00 0.00 2.34
3952 5338 6.417044 GCATCAAATTCATAGTTCATGCACTC 59.583 38.462 0.00 0.00 36.29 3.51
3993 5380 7.280876 TGCTTAATTTGTTGGTTTTGCATGTTA 59.719 29.630 0.00 0.00 0.00 2.41
4351 5738 4.463879 CCGCAGTCCAGAGCCCAG 62.464 72.222 0.00 0.00 0.00 4.45
4557 5944 5.597813 AAGAATTCTACTGAGTTGTTGCG 57.402 39.130 8.75 0.00 27.47 4.85
4604 5991 8.177119 TCCACACTTAACAATAAAAAGCAGAT 57.823 30.769 0.00 0.00 0.00 2.90
4921 6308 4.479786 AGAGGAATTGAGCTCCAGTTAC 57.520 45.455 12.15 4.13 35.20 2.50
5065 6827 5.007626 GTCTGTAGTGAAATGACAGTGCAAA 59.992 40.000 0.00 0.00 41.14 3.68
5139 6901 8.853077 ACACTAAGAAATGTGATCAAGATTCA 57.147 30.769 14.47 2.69 37.59 2.57
5207 6969 8.988060 TCTGGTTTCTAAGGTGTATGATCATAA 58.012 33.333 16.97 5.41 0.00 1.90
5435 7197 5.888161 AGGCAAATCAGGTAACAATAGGAAG 59.112 40.000 0.00 0.00 41.41 3.46
5519 7281 6.127619 CCCTGAATTTTAGTTGGACTTGGATC 60.128 42.308 0.00 0.00 0.00 3.36
5676 7831 2.609459 CCGAATATGCTCTCGCTGTTTT 59.391 45.455 0.00 0.00 36.97 2.43
5855 10604 7.652727 AGTATACATAGTAGCATGTGACACTG 58.347 38.462 7.20 4.12 39.46 3.66
5875 10624 8.255111 ACACTGATATTGATCCTTCATCACTA 57.745 34.615 0.00 0.00 41.56 2.74
5876 10625 8.147058 ACACTGATATTGATCCTTCATCACTAC 58.853 37.037 0.00 0.00 41.56 2.73
5877 10626 8.146412 CACTGATATTGATCCTTCATCACTACA 58.854 37.037 0.00 0.00 41.56 2.74
5878 10627 8.878211 ACTGATATTGATCCTTCATCACTACAT 58.122 33.333 0.00 0.00 41.56 2.29
5882 10631 7.918536 ATTGATCCTTCATCACTACATATGC 57.081 36.000 1.58 0.00 41.56 3.14
5883 10632 6.423776 TGATCCTTCATCACTACATATGCA 57.576 37.500 1.58 0.00 36.51 3.96
5884 10633 7.012661 TGATCCTTCATCACTACATATGCAT 57.987 36.000 3.79 3.79 36.51 3.96
6162 10911 0.610687 ACACCTAGCCTCTGCAGAAC 59.389 55.000 18.85 12.90 41.13 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.805945 GACCCTCAGCAGCGTTACG 60.806 63.158 0.00 0.00 0.00 3.18
10 11 1.448013 GGACCCTCAGCAGCGTTAC 60.448 63.158 0.00 0.00 0.00 2.50
11 12 1.888436 CTGGACCCTCAGCAGCGTTA 61.888 60.000 0.00 0.00 0.00 3.18
12 13 3.241530 TGGACCCTCAGCAGCGTT 61.242 61.111 0.00 0.00 0.00 4.84
13 14 3.699894 CTGGACCCTCAGCAGCGT 61.700 66.667 0.00 0.00 0.00 5.07
14 15 3.699894 ACTGGACCCTCAGCAGCG 61.700 66.667 0.00 0.00 38.26 5.18
15 16 2.046507 CACTGGACCCTCAGCAGC 60.047 66.667 0.00 0.00 38.26 5.25
16 17 2.046507 GCACTGGACCCTCAGCAG 60.047 66.667 0.00 0.00 38.26 4.24
17 18 4.007644 CGCACTGGACCCTCAGCA 62.008 66.667 0.00 0.00 38.26 4.41
18 19 4.767255 CCGCACTGGACCCTCAGC 62.767 72.222 0.00 0.00 42.00 4.26
19 20 4.767255 GCCGCACTGGACCCTCAG 62.767 72.222 0.00 0.00 42.00 3.35
34 35 4.710167 AACCCTAACGCCACGGCC 62.710 66.667 1.63 0.00 37.98 6.13
35 36 3.122971 GAACCCTAACGCCACGGC 61.123 66.667 0.00 0.00 37.85 5.68
36 37 2.435410 GGAACCCTAACGCCACGG 60.435 66.667 0.00 0.00 0.00 4.94
37 38 2.812178 CGGAACCCTAACGCCACG 60.812 66.667 0.00 0.00 0.00 4.94
38 39 3.122971 GCGGAACCCTAACGCCAC 61.123 66.667 0.00 0.00 46.92 5.01
42 43 2.202703 CTCCGCGGAACCCTAACG 60.203 66.667 30.53 11.08 0.00 3.18
43 44 2.186125 CCTCCGCGGAACCCTAAC 59.814 66.667 30.53 0.00 33.16 2.34
44 45 3.777910 GCCTCCGCGGAACCCTAA 61.778 66.667 30.53 4.52 33.16 2.69
49 50 4.699522 AAGGTGCCTCCGCGGAAC 62.700 66.667 30.53 23.77 41.10 3.62
50 51 4.697756 CAAGGTGCCTCCGCGGAA 62.698 66.667 30.53 12.32 41.99 4.30
53 54 4.680237 TGTCAAGGTGCCTCCGCG 62.680 66.667 0.00 0.00 41.99 6.46
54 55 2.743928 CTGTCAAGGTGCCTCCGC 60.744 66.667 0.00 0.00 41.99 5.54
55 56 2.046892 CCTGTCAAGGTGCCTCCG 60.047 66.667 0.00 0.00 41.99 4.63
56 57 1.298014 CTCCTGTCAAGGTGCCTCC 59.702 63.158 0.00 0.00 44.82 4.30
57 58 1.298014 CCTCCTGTCAAGGTGCCTC 59.702 63.158 0.00 0.00 44.82 4.70
58 59 2.900106 GCCTCCTGTCAAGGTGCCT 61.900 63.158 0.00 0.00 44.82 4.75
59 60 2.360475 GCCTCCTGTCAAGGTGCC 60.360 66.667 0.00 0.00 44.82 5.01
60 61 2.743928 CGCCTCCTGTCAAGGTGC 60.744 66.667 0.00 0.00 44.82 5.01
61 62 2.046892 CCGCCTCCTGTCAAGGTG 60.047 66.667 0.00 0.00 44.82 4.00
62 63 4.021925 GCCGCCTCCTGTCAAGGT 62.022 66.667 0.00 0.00 44.82 3.50
63 64 4.785453 GGCCGCCTCCTGTCAAGG 62.785 72.222 0.71 0.00 46.06 3.61
64 65 4.785453 GGGCCGCCTCCTGTCAAG 62.785 72.222 9.86 0.00 0.00 3.02
88 89 4.020617 TCTCACAAGGGCGGCCAG 62.021 66.667 31.59 23.68 0.00 4.85
89 90 4.329545 GTCTCACAAGGGCGGCCA 62.330 66.667 31.59 7.93 0.00 5.36
92 93 3.649277 CTCCGTCTCACAAGGGCGG 62.649 68.421 0.00 0.00 40.41 6.13
93 94 1.949847 ATCTCCGTCTCACAAGGGCG 61.950 60.000 0.00 0.00 0.00 6.13
94 95 0.460987 CATCTCCGTCTCACAAGGGC 60.461 60.000 0.00 0.00 0.00 5.19
95 96 1.186200 TCATCTCCGTCTCACAAGGG 58.814 55.000 0.00 0.00 0.00 3.95
96 97 3.193263 CATTCATCTCCGTCTCACAAGG 58.807 50.000 0.00 0.00 0.00 3.61
97 98 3.854666 ACATTCATCTCCGTCTCACAAG 58.145 45.455 0.00 0.00 0.00 3.16
98 99 3.258123 TGACATTCATCTCCGTCTCACAA 59.742 43.478 0.00 0.00 0.00 3.33
99 100 2.825532 TGACATTCATCTCCGTCTCACA 59.174 45.455 0.00 0.00 0.00 3.58
100 101 3.119316 AGTGACATTCATCTCCGTCTCAC 60.119 47.826 0.00 0.00 0.00 3.51
101 102 3.092301 AGTGACATTCATCTCCGTCTCA 58.908 45.455 0.00 0.00 0.00 3.27
102 103 3.791973 AGTGACATTCATCTCCGTCTC 57.208 47.619 0.00 0.00 0.00 3.36
103 104 4.274147 AGTAGTGACATTCATCTCCGTCT 58.726 43.478 0.00 0.00 0.00 4.18
104 105 4.640789 AGTAGTGACATTCATCTCCGTC 57.359 45.455 0.00 0.00 0.00 4.79
105 106 4.142138 GGAAGTAGTGACATTCATCTCCGT 60.142 45.833 0.00 0.00 0.00 4.69
106 107 4.142160 TGGAAGTAGTGACATTCATCTCCG 60.142 45.833 0.00 0.00 0.00 4.63
107 108 5.344743 TGGAAGTAGTGACATTCATCTCC 57.655 43.478 0.00 0.00 0.00 3.71
108 109 6.577103 TCATGGAAGTAGTGACATTCATCTC 58.423 40.000 0.00 0.00 0.00 2.75
109 110 6.550938 TCATGGAAGTAGTGACATTCATCT 57.449 37.500 0.00 0.00 0.00 2.90
110 111 7.281774 ACATTCATGGAAGTAGTGACATTCATC 59.718 37.037 0.00 0.00 0.00 2.92
111 112 7.114754 ACATTCATGGAAGTAGTGACATTCAT 58.885 34.615 0.00 0.00 0.00 2.57
112 113 6.475504 ACATTCATGGAAGTAGTGACATTCA 58.524 36.000 0.00 0.00 0.00 2.57
113 114 6.237942 CGACATTCATGGAAGTAGTGACATTC 60.238 42.308 0.00 0.00 0.00 2.67
114 115 5.582269 CGACATTCATGGAAGTAGTGACATT 59.418 40.000 0.00 0.00 0.00 2.71
115 116 5.111989 CGACATTCATGGAAGTAGTGACAT 58.888 41.667 0.00 0.00 0.00 3.06
116 117 4.021456 ACGACATTCATGGAAGTAGTGACA 60.021 41.667 0.00 0.00 0.00 3.58
117 118 4.495422 ACGACATTCATGGAAGTAGTGAC 58.505 43.478 0.00 0.00 0.00 3.67
118 119 4.801330 ACGACATTCATGGAAGTAGTGA 57.199 40.909 0.00 0.00 0.00 3.41
119 120 5.408299 TGAAACGACATTCATGGAAGTAGTG 59.592 40.000 0.00 0.00 34.50 2.74
120 121 5.547465 TGAAACGACATTCATGGAAGTAGT 58.453 37.500 0.00 0.00 34.50 2.73
121 122 6.668541 ATGAAACGACATTCATGGAAGTAG 57.331 37.500 12.60 0.00 45.76 2.57
122 123 7.226523 CCATATGAAACGACATTCATGGAAGTA 59.773 37.037 18.97 5.47 46.63 2.24
123 124 6.038603 CCATATGAAACGACATTCATGGAAGT 59.961 38.462 18.97 0.00 46.63 3.01
124 125 6.260714 TCCATATGAAACGACATTCATGGAAG 59.739 38.462 18.97 9.87 46.63 3.46
125 126 6.118852 TCCATATGAAACGACATTCATGGAA 58.881 36.000 18.97 6.49 46.63 3.53
126 127 5.679601 TCCATATGAAACGACATTCATGGA 58.320 37.500 18.97 17.02 46.63 3.41
127 128 6.038603 AGTTCCATATGAAACGACATTCATGG 59.961 38.462 18.97 15.65 46.63 3.66
128 129 7.019774 AGTTCCATATGAAACGACATTCATG 57.980 36.000 18.97 9.78 46.63 3.07
130 131 7.447374 AAAGTTCCATATGAAACGACATTCA 57.553 32.000 3.65 0.00 43.03 2.57
134 135 8.609176 GCTTATAAAGTTCCATATGAAACGACA 58.391 33.333 3.65 0.00 33.94 4.35
135 136 8.609176 TGCTTATAAAGTTCCATATGAAACGAC 58.391 33.333 3.65 0.00 33.94 4.34
136 137 8.725405 TGCTTATAAAGTTCCATATGAAACGA 57.275 30.769 3.65 0.00 33.94 3.85
137 138 9.950680 ATTGCTTATAAAGTTCCATATGAAACG 57.049 29.630 3.65 0.00 33.94 3.60
199 200 5.536538 AGCTCGGATGAACAGTATAATCTGA 59.463 40.000 0.65 0.00 38.63 3.27
201 202 5.536538 TGAGCTCGGATGAACAGTATAATCT 59.463 40.000 9.64 0.00 0.00 2.40
206 207 4.679373 AATGAGCTCGGATGAACAGTAT 57.321 40.909 9.64 0.00 0.00 2.12
207 208 4.081697 TCAAATGAGCTCGGATGAACAGTA 60.082 41.667 9.64 0.00 0.00 2.74
219 220 2.663826 ACTCGGACTCAAATGAGCTC 57.336 50.000 6.82 6.82 45.79 4.09
231 232 2.991190 TGCGATGTTTCTTAACTCGGAC 59.009 45.455 0.00 0.00 36.41 4.79
249 250 3.361794 ACATGCAGAGTAGTAGATGCG 57.638 47.619 0.00 0.00 41.58 4.73
255 256 6.462487 GGCTTGGTATAACATGCAGAGTAGTA 60.462 42.308 25.01 0.00 41.67 1.82
256 257 5.360591 GCTTGGTATAACATGCAGAGTAGT 58.639 41.667 20.54 0.00 40.19 2.73
259 260 3.200825 AGGCTTGGTATAACATGCAGAGT 59.799 43.478 25.01 8.14 41.67 3.24
267 268 3.056891 GCTTGCAAAGGCTTGGTATAACA 60.057 43.478 0.00 0.00 46.35 2.41
304 305 1.153349 GCCGTCAGGGAGATTGGTC 60.153 63.158 0.00 0.00 38.47 4.02
315 316 1.890979 GGATGGATGCTGCCGTCAG 60.891 63.158 16.15 0.00 44.19 3.51
370 371 3.281727 TCACCTTAGGGCATGATCAAC 57.718 47.619 2.32 0.00 35.63 3.18
380 381 2.637872 TCCTCACTGTTTCACCTTAGGG 59.362 50.000 2.32 0.00 38.88 3.53
393 394 1.784525 GAGGTGACGTTTCCTCACTG 58.215 55.000 25.00 0.00 46.59 3.66
404 405 0.397254 ATCCAGGTAGGGAGGTGACG 60.397 60.000 0.00 0.00 41.08 4.35
410 411 2.777459 AGTGGTATCCAGGTAGGGAG 57.223 55.000 0.00 0.00 41.08 4.30
450 451 6.677781 TGTCAGGAAACTTAACTGTCAAAG 57.322 37.500 0.00 2.35 40.21 2.77
542 543 5.302823 AGTGTACATAGCTGAGTATGCATCA 59.697 40.000 0.19 0.00 34.24 3.07
566 567 7.038017 ACTCATCTAAGAAAGAGAATGGGTGAA 60.038 37.037 5.50 0.00 37.74 3.18
628 629 3.028130 TCTATATCCTGTGCACGGTTGA 58.972 45.455 23.77 15.15 0.00 3.18
675 676 7.641760 ACAACAACTAAAATAAGTAACACGGG 58.358 34.615 0.00 0.00 0.00 5.28
732 733 4.159506 CACTTTGAAACAGGGGAAAAGTCA 59.840 41.667 0.00 0.00 38.63 3.41
733 734 4.159693 ACACTTTGAAACAGGGGAAAAGTC 59.840 41.667 0.00 0.00 38.63 3.01
771 772 8.885722 GGAGTACATTTTTCCGTTGATATACAA 58.114 33.333 0.00 0.00 36.02 2.41
778 779 4.758165 GGAAGGAGTACATTTTTCCGTTGA 59.242 41.667 0.00 0.00 36.11 3.18
843 844 4.393062 ACCACGCTCATCAAGTTTATCAAG 59.607 41.667 0.00 0.00 0.00 3.02
852 853 1.811266 CCCGACCACGCTCATCAAG 60.811 63.158 0.00 0.00 38.29 3.02
1004 1519 3.065095 GGAAGAAGAGCACATCTGCAATC 59.935 47.826 0.00 0.00 46.97 2.67
1058 1576 4.082523 GCAGCGGTAGGAGCACCA 62.083 66.667 2.07 0.00 38.61 4.17
1161 1679 1.132643 AGCTAACTCGGAGCACGTAAG 59.867 52.381 4.58 0.00 42.69 2.34
1182 1700 9.219603 GAAGCAGATATGCATGGTTATTTAGTA 57.780 33.333 15.82 0.00 37.27 1.82
1183 1701 7.941238 AGAAGCAGATATGCATGGTTATTTAGT 59.059 33.333 15.82 0.00 37.27 2.24
1186 1704 7.286087 TGAAGAAGCAGATATGCATGGTTATTT 59.714 33.333 15.82 4.43 38.15 1.40
1188 1706 6.301486 TGAAGAAGCAGATATGCATGGTTAT 58.699 36.000 15.82 0.00 37.27 1.89
2009 3110 5.242434 TGATCAGTTATTAGTTGGTTGCGT 58.758 37.500 0.00 0.00 0.00 5.24
2482 3725 3.489568 CCGCATGTAGTGTACCGTATGAA 60.490 47.826 0.00 0.00 0.00 2.57
2618 3864 2.109463 CGTGATCACTGTATCGAACGG 58.891 52.381 22.95 0.00 40.63 4.44
2836 4087 4.859304 TTGCTGAGGTCGTTAGAGTTTA 57.141 40.909 0.00 0.00 0.00 2.01
2910 4162 7.951530 TGAACTAAAAAGAGTTAAGGGTACG 57.048 36.000 0.00 0.00 39.79 3.67
3014 4291 2.300956 TTTGGATTGCTGGGCTGTTA 57.699 45.000 0.00 0.00 0.00 2.41
3136 4484 2.119029 GCCGCCGGGAATAAAGCTT 61.119 57.895 4.77 0.00 34.06 3.74
3207 4582 2.494918 GGGTCTCATGTCGTCCGG 59.505 66.667 0.00 0.00 0.00 5.14
3295 4676 1.607251 GGTTGTACCTTGTGTCCTCGG 60.607 57.143 0.00 0.00 34.73 4.63
3372 4754 1.320507 TGCATGCAGAGCTGTTTTGA 58.679 45.000 18.46 0.00 0.00 2.69
3376 4758 0.530744 CCAATGCATGCAGAGCTGTT 59.469 50.000 26.69 11.37 0.00 3.16
3377 4759 0.323087 TCCAATGCATGCAGAGCTGT 60.323 50.000 26.69 4.78 0.00 4.40
3379 4761 0.255033 TCTCCAATGCATGCAGAGCT 59.745 50.000 26.69 6.06 0.00 4.09
3380 4762 1.001268 CATCTCCAATGCATGCAGAGC 60.001 52.381 26.69 6.96 0.00 4.09
3381 4763 1.001268 GCATCTCCAATGCATGCAGAG 60.001 52.381 26.69 24.52 44.00 3.35
3382 4764 1.029681 GCATCTCCAATGCATGCAGA 58.970 50.000 26.69 17.23 44.00 4.26
3383 4765 0.032130 GGCATCTCCAATGCATGCAG 59.968 55.000 26.69 13.25 46.21 4.41
3384 4766 0.684805 TGGCATCTCCAATGCATGCA 60.685 50.000 25.04 25.04 46.21 3.96
3385 4767 2.120765 TGGCATCTCCAATGCATGC 58.879 52.632 11.82 11.82 46.21 4.06
3394 4776 4.081531 TGTTTTGAATTGGATGGCATCTCC 60.082 41.667 25.48 13.57 0.00 3.71
3395 4777 5.075858 TGTTTTGAATTGGATGGCATCTC 57.924 39.130 25.48 15.92 0.00 2.75
3396 4778 4.622220 GCTGTTTTGAATTGGATGGCATCT 60.622 41.667 25.48 7.06 0.00 2.90
3397 4779 3.619929 GCTGTTTTGAATTGGATGGCATC 59.380 43.478 19.23 19.23 0.00 3.91
3398 4780 3.262405 AGCTGTTTTGAATTGGATGGCAT 59.738 39.130 0.00 0.00 0.00 4.40
3399 4781 2.633967 AGCTGTTTTGAATTGGATGGCA 59.366 40.909 0.00 0.00 0.00 4.92
3400 4782 3.056322 AGAGCTGTTTTGAATTGGATGGC 60.056 43.478 0.00 0.00 0.00 4.40
3401 4783 4.491676 CAGAGCTGTTTTGAATTGGATGG 58.508 43.478 0.00 0.00 0.00 3.51
3402 4784 3.924686 GCAGAGCTGTTTTGAATTGGATG 59.075 43.478 0.00 0.00 0.00 3.51
3403 4785 3.575256 TGCAGAGCTGTTTTGAATTGGAT 59.425 39.130 0.00 0.00 0.00 3.41
3404 4786 2.957680 TGCAGAGCTGTTTTGAATTGGA 59.042 40.909 0.00 0.00 0.00 3.53
3405 4787 3.374220 TGCAGAGCTGTTTTGAATTGG 57.626 42.857 0.00 0.00 0.00 3.16
3406 4788 3.122948 GCATGCAGAGCTGTTTTGAATTG 59.877 43.478 14.21 0.00 0.00 2.32
3407 4789 3.243941 TGCATGCAGAGCTGTTTTGAATT 60.244 39.130 18.46 0.00 0.00 2.17
3408 4790 2.297880 TGCATGCAGAGCTGTTTTGAAT 59.702 40.909 18.46 0.00 0.00 2.57
3409 4791 1.682323 TGCATGCAGAGCTGTTTTGAA 59.318 42.857 18.46 0.00 0.00 2.69
3410 4792 1.320507 TGCATGCAGAGCTGTTTTGA 58.679 45.000 18.46 0.00 0.00 2.69
3411 4793 1.992667 CATGCATGCAGAGCTGTTTTG 59.007 47.619 26.69 11.96 0.00 2.44
3412 4794 1.067142 CCATGCATGCAGAGCTGTTTT 60.067 47.619 26.69 2.26 0.00 2.43
3413 4795 0.530744 CCATGCATGCAGAGCTGTTT 59.469 50.000 26.69 3.09 0.00 2.83
3414 4796 0.323087 TCCATGCATGCAGAGCTGTT 60.323 50.000 26.69 3.94 0.00 3.16
3415 4797 1.030488 GTCCATGCATGCAGAGCTGT 61.030 55.000 26.69 4.78 0.00 4.40
3439 4821 2.006888 CGTAAGGTTATGGCTGTGTGG 58.993 52.381 0.00 0.00 0.00 4.17
3453 4835 2.276201 TCAATGGCATCGAACGTAAGG 58.724 47.619 0.00 0.00 46.39 2.69
3458 4840 3.500982 ACAAAATCAATGGCATCGAACG 58.499 40.909 0.00 0.00 0.00 3.95
3952 5338 5.607119 ATTAAGCAGAGGTAAACAACACG 57.393 39.130 0.00 0.00 0.00 4.49
3993 5380 8.532819 TCGGTTACATGGGCTTAATTTATTTTT 58.467 29.630 0.00 0.00 0.00 1.94
4351 5738 0.908198 ACCTCCATCTTGACTCCTGC 59.092 55.000 0.00 0.00 0.00 4.85
4604 5991 1.770061 TCCTCATCACTGCCATGCATA 59.230 47.619 0.00 0.00 38.13 3.14
5039 6707 4.084328 GCACTGTCATTTCACTACAGACAC 60.084 45.833 8.57 0.00 42.59 3.67
5083 6845 2.307496 TCCAACCATGCCAACTCATT 57.693 45.000 0.00 0.00 0.00 2.57
5495 7257 6.434028 TGATCCAAGTCCAACTAAAATTCAGG 59.566 38.462 0.00 0.00 0.00 3.86
5676 7831 0.976641 CAGAGGGAGTAACTGTGCCA 59.023 55.000 0.00 0.00 0.00 4.92
5875 10624 7.069702 TGTTCCCATTTTGTATCATGCATATGT 59.930 33.333 0.00 0.00 35.73 2.29
5876 10625 7.435305 TGTTCCCATTTTGTATCATGCATATG 58.565 34.615 0.00 0.00 35.57 1.78
5877 10626 7.600231 TGTTCCCATTTTGTATCATGCATAT 57.400 32.000 0.00 0.00 0.00 1.78
5878 10627 7.415592 TTGTTCCCATTTTGTATCATGCATA 57.584 32.000 0.00 0.00 0.00 3.14
5879 10628 5.936187 TGTTCCCATTTTGTATCATGCAT 57.064 34.783 0.00 0.00 0.00 3.96
5880 10629 5.735285 TTGTTCCCATTTTGTATCATGCA 57.265 34.783 0.00 0.00 0.00 3.96
5881 10630 5.931146 TGTTTGTTCCCATTTTGTATCATGC 59.069 36.000 0.00 0.00 0.00 4.06
5882 10631 7.959689 TTGTTTGTTCCCATTTTGTATCATG 57.040 32.000 0.00 0.00 0.00 3.07
5883 10632 9.218440 GAATTGTTTGTTCCCATTTTGTATCAT 57.782 29.630 0.00 0.00 0.00 2.45
5884 10633 7.383572 CGAATTGTTTGTTCCCATTTTGTATCA 59.616 33.333 0.00 0.00 0.00 2.15
6013 10762 4.178545 AGGCAACATCCAATTCTTTTCG 57.821 40.909 0.00 0.00 41.41 3.46
6028 10777 3.649073 GGAAACCACAAACATAGGCAAC 58.351 45.455 0.00 0.00 0.00 4.17
6121 10870 8.680903 GGTGTCTTCATGATGATTGTATTTTCT 58.319 33.333 13.82 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.