Multiple sequence alignment - TraesCS2D01G039800

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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 TraesCS2D01G039800 chr2D 100.000 2712 0 0 1 2712 14442107 14444818 0.000000e+00 5009.0
1 TraesCS2D01G039800 chr2D 89.058 1645 122 25 1083 2712 14596372 14597973 0.000000e+00 1988.0
2 TraesCS2D01G039800 chr2D 87.500 880 74 17 1839 2712 14648367 14649216 0.000000e+00 983.0
3 TraesCS2D01G039800 chr2D 92.025 652 52 0 1089 1740 14647659 14648310 0.000000e+00 917.0
4 TraesCS2D01G039800 chr2D 91.190 647 57 0 1089 1735 14565705 14566351 0.000000e+00 880.0
5 TraesCS2D01G039800 chr2D 87.474 487 53 5 1955 2440 14567880 14568359 3.050000e-154 555.0
6 TraesCS2D01G039800 chr2D 81.511 622 85 14 1090 1711 14704170 14704761 4.060000e-133 484.0
7 TraesCS2D01G039800 chr2D 99.209 253 2 0 689 941 14565257 14565509 8.850000e-125 457.0
8 TraesCS2D01G039800 chr2D 88.930 271 24 2 2443 2712 14568557 14568822 2.010000e-86 329.0
9 TraesCS2D01G039800 chr2D 81.406 441 34 16 661 1091 14703668 14704070 1.570000e-82 316.0
10 TraesCS2D01G039800 chr2D 91.703 229 10 4 318 543 14564954 14565176 2.620000e-80 309.0
11 TraesCS2D01G039800 chr2D 85.948 306 17 9 408 699 14595802 14596095 1.220000e-78 303.0
12 TraesCS2D01G039800 chr2D 81.470 313 42 11 2 309 20613307 20613608 2.700000e-60 243.0
13 TraesCS2D01G039800 chr2D 94.853 136 3 2 614 748 14647150 14647282 2.740000e-50 209.0
14 TraesCS2D01G039800 chr2D 86.364 198 15 5 863 1058 14647288 14647475 3.540000e-49 206.0
15 TraesCS2D01G039800 chr2D 91.525 59 1 1 1742 1800 36548821 36548767 8.050000e-11 78.7
16 TraesCS2D01G039800 chr2B 94.480 779 37 3 318 1091 26353535 26354312 0.000000e+00 1195.0
17 TraesCS2D01G039800 chr2B 89.908 654 61 3 1083 1735 26354433 26355082 0.000000e+00 837.0
18 TraesCS2D01G039800 chr2B 84.404 109 11 3 1740 1843 32966661 32966554 4.780000e-18 102.0
19 TraesCS2D01G039800 chr2A 86.720 881 72 19 1838 2712 16751890 16752731 0.000000e+00 937.0
20 TraesCS2D01G039800 chr2A 92.214 655 48 1 1089 1740 16751180 16751834 0.000000e+00 924.0
21 TraesCS2D01G039800 chr2A 88.421 570 63 3 1165 1732 16771383 16771951 0.000000e+00 684.0
22 TraesCS2D01G039800 chr2A 89.100 422 26 9 674 1091 16750661 16751066 8.660000e-140 507.0
23 TraesCS2D01G039800 chr2A 81.400 543 78 14 1176 1708 16745994 16746523 3.230000e-114 422.0
24 TraesCS2D01G039800 chr2A 88.841 233 13 7 318 543 16750366 16750592 9.570000e-70 274.0
25 TraesCS2D01G039800 chr2A 79.602 402 45 17 711 1091 16770847 16771232 1.250000e-63 254.0
26 TraesCS2D01G039800 chr3A 88.816 304 31 2 2 303 691820179 691820481 1.190000e-98 370.0
27 TraesCS2D01G039800 chr5B 87.987 308 36 1 2 309 320354424 320354118 1.980000e-96 363.0
28 TraesCS2D01G039800 chr5D 82.372 312 46 7 2 309 524914497 524914803 2.070000e-66 263.0
29 TraesCS2D01G039800 chr7D 81.529 314 41 9 2 309 66505697 66505395 2.700000e-60 243.0
30 TraesCS2D01G039800 chr7D 100.000 43 0 0 1740 1782 487772775 487772733 2.240000e-11 80.5
31 TraesCS2D01G039800 chr7D 92.157 51 4 0 1793 1843 289266235 289266185 3.750000e-09 73.1
32 TraesCS2D01G039800 chr6D 80.696 316 45 11 2 313 149308692 149308995 5.840000e-57 231.0
33 TraesCS2D01G039800 chr6D 100.000 44 0 0 1739 1782 32314824 32314781 6.220000e-12 82.4
34 TraesCS2D01G039800 chr1A 78.457 311 54 8 2 309 12166129 12165829 9.910000e-45 191.0
35 TraesCS2D01G039800 chr1A 95.745 47 2 0 1736 1782 50959911 50959865 2.900000e-10 76.8
36 TraesCS2D01G039800 chr1A 88.710 62 3 1 1782 1843 9792867 9792924 3.750000e-09 73.1
37 TraesCS2D01G039800 chr3B 78.646 192 23 11 115 303 380871943 380871767 7.940000e-21 111.0
38 TraesCS2D01G039800 chr3B 100.000 43 0 0 1740 1782 750405290 750405248 2.240000e-11 80.5
39 TraesCS2D01G039800 chr1B 82.171 129 15 5 184 309 576054845 576054968 1.330000e-18 104.0
40 TraesCS2D01G039800 chr1B 94.118 51 3 0 1793 1843 478897641 478897691 8.050000e-11 78.7
41 TraesCS2D01G039800 chr1B 92.157 51 4 0 1793 1843 645315320 645315270 3.750000e-09 73.1
42 TraesCS2D01G039800 chrUn 84.404 109 11 3 1740 1843 215699668 215699561 4.780000e-18 102.0
43 TraesCS2D01G039800 chrUn 84.404 109 11 3 1740 1843 215705982 215705875 4.780000e-18 102.0
44 TraesCS2D01G039800 chr7A 83.761 117 7 6 1739 1843 8368980 8369096 1.720000e-17 100.0
45 TraesCS2D01G039800 chr5A 96.000 50 2 0 1793 1842 342246409 342246360 6.220000e-12 82.4
46 TraesCS2D01G039800 chr5A 92.857 56 3 1 1728 1783 315321010 315321064 2.240000e-11 80.5
47 TraesCS2D01G039800 chr5A 80.508 118 7 8 1740 1841 150392223 150392106 2.900000e-10 76.8
48 TraesCS2D01G039800 chr4B 97.826 46 1 0 1737 1782 671855435 671855390 2.240000e-11 80.5
49 TraesCS2D01G039800 chr6A 94.118 51 3 0 1793 1843 593347431 593347481 8.050000e-11 78.7


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 TraesCS2D01G039800 chr2D 14442107 14444818 2711 False 5009.00 5009 100.0000 1 2712 1 chr2D.!!$F1 2711
1 TraesCS2D01G039800 chr2D 14595802 14597973 2171 False 1145.50 1988 87.5030 408 2712 2 chr2D.!!$F4 2304
2 TraesCS2D01G039800 chr2D 14647150 14649216 2066 False 578.75 983 90.1855 614 2712 4 chr2D.!!$F5 2098
3 TraesCS2D01G039800 chr2D 14564954 14568822 3868 False 506.00 880 91.7012 318 2712 5 chr2D.!!$F3 2394
4 TraesCS2D01G039800 chr2D 14703668 14704761 1093 False 400.00 484 81.4585 661 1711 2 chr2D.!!$F6 1050
5 TraesCS2D01G039800 chr2B 26353535 26355082 1547 False 1016.00 1195 92.1940 318 1735 2 chr2B.!!$F1 1417
6 TraesCS2D01G039800 chr2A 16745994 16752731 6737 False 612.80 937 87.6550 318 2712 5 chr2A.!!$F1 2394
7 TraesCS2D01G039800 chr2A 16770847 16771951 1104 False 469.00 684 84.0115 711 1732 2 chr2A.!!$F2 1021

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
43 44 0.034896 GGCCCTGGTGGTATACGATG 59.965 60.0 0.0 0.0 36.04 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 6121 0.106569 TCCTCCCATTGAATGCGCAT 60.107 50.0 19.28 19.28 0.0 4.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.722193 ATGAAGTCCAAGCCACGG 57.278 55.556 0.00 0.00 0.00 4.94
18 19 1.761174 ATGAAGTCCAAGCCACGGT 59.239 52.632 0.00 0.00 0.00 4.83
19 20 0.606401 ATGAAGTCCAAGCCACGGTG 60.606 55.000 0.00 0.00 0.00 4.94
20 21 1.966451 GAAGTCCAAGCCACGGTGG 60.966 63.158 22.87 22.87 41.55 4.61
37 38 4.109675 GCGTGGCCCTGGTGGTAT 62.110 66.667 0.00 0.00 36.04 2.73
38 39 2.737881 GCGTGGCCCTGGTGGTATA 61.738 63.158 0.00 0.00 36.04 1.47
39 40 1.145377 CGTGGCCCTGGTGGTATAC 59.855 63.158 0.00 0.00 36.04 1.47
40 41 1.145377 GTGGCCCTGGTGGTATACG 59.855 63.158 0.00 0.00 36.04 3.06
41 42 1.001888 TGGCCCTGGTGGTATACGA 59.998 57.895 0.00 0.00 36.04 3.43
42 43 0.399376 TGGCCCTGGTGGTATACGAT 60.399 55.000 0.00 0.00 36.04 3.73
43 44 0.034896 GGCCCTGGTGGTATACGATG 59.965 60.000 0.00 0.00 36.04 3.84
44 45 1.045407 GCCCTGGTGGTATACGATGA 58.955 55.000 0.00 0.00 36.04 2.92
45 46 1.270147 GCCCTGGTGGTATACGATGAC 60.270 57.143 0.00 0.00 36.04 3.06
46 47 2.036387 CCCTGGTGGTATACGATGACA 58.964 52.381 0.00 0.00 0.00 3.58
47 48 2.632996 CCCTGGTGGTATACGATGACAT 59.367 50.000 0.00 0.00 0.00 3.06
49 50 3.059884 CTGGTGGTATACGATGACATGC 58.940 50.000 0.00 0.00 0.00 4.06
50 51 2.058798 GGTGGTATACGATGACATGCG 58.941 52.381 0.00 0.00 0.00 4.73
53 54 2.359531 TGGTATACGATGACATGCGACA 59.640 45.455 12.27 0.00 0.00 4.35
55 56 2.140065 ATACGATGACATGCGACAGG 57.860 50.000 12.27 0.00 0.00 4.00
56 57 0.815095 TACGATGACATGCGACAGGT 59.185 50.000 12.27 0.00 0.00 4.00
57 58 0.737367 ACGATGACATGCGACAGGTG 60.737 55.000 12.27 0.00 0.00 4.00
58 59 1.423721 CGATGACATGCGACAGGTGG 61.424 60.000 2.06 0.00 0.00 4.61
59 60 0.391661 GATGACATGCGACAGGTGGT 60.392 55.000 2.06 0.00 0.00 4.16
60 61 0.391661 ATGACATGCGACAGGTGGTC 60.392 55.000 2.06 0.00 43.36 4.02
61 62 1.741770 GACATGCGACAGGTGGTCC 60.742 63.158 2.06 0.00 43.95 4.46
63 64 3.311110 ATGCGACAGGTGGTCCGT 61.311 61.111 0.00 0.00 43.95 4.69
64 65 2.879233 ATGCGACAGGTGGTCCGTT 61.879 57.895 0.00 0.00 43.95 4.44
66 67 2.604174 GCGACAGGTGGTCCGTTTG 61.604 63.158 0.00 0.00 43.95 2.93
67 68 1.959226 CGACAGGTGGTCCGTTTGG 60.959 63.158 0.00 0.00 43.95 3.28
68 69 1.147600 GACAGGTGGTCCGTTTGGT 59.852 57.895 0.00 0.00 40.83 3.67
69 70 1.153046 ACAGGTGGTCCGTTTGGTG 60.153 57.895 0.00 0.00 39.05 4.17
70 71 1.147376 CAGGTGGTCCGTTTGGTGA 59.853 57.895 0.00 0.00 39.05 4.02
71 72 0.250727 CAGGTGGTCCGTTTGGTGAT 60.251 55.000 0.00 0.00 39.05 3.06
72 73 0.036306 AGGTGGTCCGTTTGGTGATC 59.964 55.000 0.00 0.00 39.05 2.92
73 74 0.958876 GGTGGTCCGTTTGGTGATCC 60.959 60.000 0.00 0.00 36.30 3.36
74 75 0.036306 GTGGTCCGTTTGGTGATCCT 59.964 55.000 0.00 0.00 36.30 3.24
75 76 0.323629 TGGTCCGTTTGGTGATCCTC 59.676 55.000 0.00 0.00 36.30 3.71
76 77 0.392595 GGTCCGTTTGGTGATCCTCC 60.393 60.000 0.00 0.00 36.30 4.30
78 79 1.189524 TCCGTTTGGTGATCCTCCGT 61.190 55.000 0.00 0.00 36.30 4.69
79 80 1.019278 CCGTTTGGTGATCCTCCGTG 61.019 60.000 0.00 0.00 34.23 4.94
81 82 1.002624 TTTGGTGATCCTCCGTGGC 60.003 57.895 0.00 0.00 35.26 5.01
82 83 2.796483 TTTGGTGATCCTCCGTGGCG 62.796 60.000 0.00 0.00 35.26 5.69
99 100 1.296715 CGCCCACTTGCCTAGTTCT 59.703 57.895 0.00 0.00 33.85 3.01
100 101 0.741221 CGCCCACTTGCCTAGTTCTC 60.741 60.000 0.00 0.00 33.85 2.87
102 103 1.280457 CCCACTTGCCTAGTTCTCCT 58.720 55.000 0.00 0.00 33.85 3.69
104 105 2.355209 CCCACTTGCCTAGTTCTCCTTC 60.355 54.545 0.00 0.00 33.85 3.46
105 106 2.303022 CCACTTGCCTAGTTCTCCTTCA 59.697 50.000 0.00 0.00 33.85 3.02
106 107 3.054802 CCACTTGCCTAGTTCTCCTTCAT 60.055 47.826 0.00 0.00 33.85 2.57
107 108 4.162320 CCACTTGCCTAGTTCTCCTTCATA 59.838 45.833 0.00 0.00 33.85 2.15
109 110 5.026790 ACTTGCCTAGTTCTCCTTCATAGT 58.973 41.667 0.00 0.00 31.29 2.12
110 111 5.485708 ACTTGCCTAGTTCTCCTTCATAGTT 59.514 40.000 0.00 0.00 31.29 2.24
111 112 6.013293 ACTTGCCTAGTTCTCCTTCATAGTTT 60.013 38.462 0.00 0.00 31.29 2.66
112 113 5.978814 TGCCTAGTTCTCCTTCATAGTTTC 58.021 41.667 0.00 0.00 0.00 2.78
113 114 5.721960 TGCCTAGTTCTCCTTCATAGTTTCT 59.278 40.000 0.00 0.00 0.00 2.52
116 117 6.381420 CCTAGTTCTCCTTCATAGTTTCTCCA 59.619 42.308 0.00 0.00 0.00 3.86
118 119 6.883744 AGTTCTCCTTCATAGTTTCTCCATC 58.116 40.000 0.00 0.00 0.00 3.51
121 122 4.286707 TCCTTCATAGTTTCTCCATCGGA 58.713 43.478 0.00 0.00 0.00 4.55
129 130 2.725008 CTCCATCGGAGTCGGAGC 59.275 66.667 6.55 0.00 44.25 4.70
130 131 1.826054 CTCCATCGGAGTCGGAGCT 60.826 63.158 6.55 0.00 44.25 4.09
132 133 2.279120 CATCGGAGTCGGAGCTGC 60.279 66.667 6.55 0.00 36.95 5.25
136 137 2.279120 GGAGTCGGAGCTGCGATG 60.279 66.667 32.89 2.50 0.00 3.84
137 138 2.492090 GAGTCGGAGCTGCGATGT 59.508 61.111 32.89 22.86 0.00 3.06
138 139 1.587613 GAGTCGGAGCTGCGATGTC 60.588 63.158 32.89 26.23 0.00 3.06
140 141 1.153745 GTCGGAGCTGCGATGTCTT 60.154 57.895 32.89 0.00 0.00 3.01
141 142 1.153765 TCGGAGCTGCGATGTCTTG 60.154 57.895 27.32 0.00 0.00 3.02
142 143 2.806856 CGGAGCTGCGATGTCTTGC 61.807 63.158 24.56 0.00 0.00 4.01
143 144 2.467826 GGAGCTGCGATGTCTTGCC 61.468 63.158 0.00 0.00 0.00 4.52
144 145 1.742880 GAGCTGCGATGTCTTGCCA 60.743 57.895 0.00 0.00 0.00 4.92
145 146 1.975363 GAGCTGCGATGTCTTGCCAC 61.975 60.000 0.00 0.00 0.00 5.01
146 147 2.780643 CTGCGATGTCTTGCCACG 59.219 61.111 0.00 0.00 0.00 4.94
147 148 2.741985 TGCGATGTCTTGCCACGG 60.742 61.111 0.00 0.00 0.00 4.94
148 149 3.499737 GCGATGTCTTGCCACGGG 61.500 66.667 0.00 0.00 0.00 5.28
149 150 2.047274 CGATGTCTTGCCACGGGT 60.047 61.111 0.00 0.00 0.00 5.28
150 151 2.390599 CGATGTCTTGCCACGGGTG 61.391 63.158 0.00 0.00 0.00 4.61
160 161 3.513225 CACGGGTGGATGGCATTC 58.487 61.111 0.00 0.00 0.00 2.67
182 183 1.892209 TCGTGAGAGTGTAGTGCTGA 58.108 50.000 0.00 0.00 34.84 4.26
184 185 2.420372 TCGTGAGAGTGTAGTGCTGATC 59.580 50.000 0.00 0.00 34.84 2.92
185 186 2.421775 CGTGAGAGTGTAGTGCTGATCT 59.578 50.000 0.00 0.00 0.00 2.75
188 189 2.165234 GAGAGTGTAGTGCTGATCTGCA 59.835 50.000 21.87 21.87 41.05 4.41
200 201 2.302445 CTGATCTGCAGCTAATAGGGCT 59.698 50.000 9.47 0.00 37.90 5.19
209 210 3.621558 AGCTAATAGGGCTGTTGTTTCC 58.378 45.455 0.00 0.00 38.73 3.13
210 211 3.267031 AGCTAATAGGGCTGTTGTTTCCT 59.733 43.478 0.00 0.00 38.73 3.36
211 212 4.017126 GCTAATAGGGCTGTTGTTTCCTT 58.983 43.478 0.00 0.00 0.00 3.36
212 213 4.462834 GCTAATAGGGCTGTTGTTTCCTTT 59.537 41.667 0.00 0.00 0.00 3.11
215 216 6.987403 AATAGGGCTGTTGTTTCCTTTTAA 57.013 33.333 0.00 0.00 0.00 1.52
216 217 7.553504 AATAGGGCTGTTGTTTCCTTTTAAT 57.446 32.000 0.00 0.00 0.00 1.40
217 218 5.887214 AGGGCTGTTGTTTCCTTTTAATT 57.113 34.783 0.00 0.00 0.00 1.40
218 219 6.247229 AGGGCTGTTGTTTCCTTTTAATTT 57.753 33.333 0.00 0.00 0.00 1.82
219 220 6.658849 AGGGCTGTTGTTTCCTTTTAATTTT 58.341 32.000 0.00 0.00 0.00 1.82
220 221 7.116075 AGGGCTGTTGTTTCCTTTTAATTTTT 58.884 30.769 0.00 0.00 0.00 1.94
221 222 7.282224 AGGGCTGTTGTTTCCTTTTAATTTTTC 59.718 33.333 0.00 0.00 0.00 2.29
222 223 7.282224 GGGCTGTTGTTTCCTTTTAATTTTTCT 59.718 33.333 0.00 0.00 0.00 2.52
223 224 8.673711 GGCTGTTGTTTCCTTTTAATTTTTCTT 58.326 29.630 0.00 0.00 0.00 2.52
239 240 8.748380 AATTTTTCTTTGATCTTCGAATCCAC 57.252 30.769 0.00 0.00 0.00 4.02
240 241 5.880054 TTTCTTTGATCTTCGAATCCACC 57.120 39.130 0.00 0.00 0.00 4.61
241 242 4.826274 TCTTTGATCTTCGAATCCACCT 57.174 40.909 0.00 0.00 0.00 4.00
243 244 4.222810 TCTTTGATCTTCGAATCCACCTCA 59.777 41.667 0.00 0.00 0.00 3.86
244 245 4.760530 TTGATCTTCGAATCCACCTCAT 57.239 40.909 0.00 0.00 0.00 2.90
245 246 5.869649 TTGATCTTCGAATCCACCTCATA 57.130 39.130 0.00 0.00 0.00 2.15
246 247 6.425210 TTGATCTTCGAATCCACCTCATAT 57.575 37.500 0.00 0.00 0.00 1.78
247 248 6.425210 TGATCTTCGAATCCACCTCATATT 57.575 37.500 0.00 0.00 0.00 1.28
249 250 6.268617 TGATCTTCGAATCCACCTCATATTCT 59.731 38.462 0.00 0.00 0.00 2.40
250 251 6.485830 TCTTCGAATCCACCTCATATTCTT 57.514 37.500 0.00 0.00 0.00 2.52
251 252 6.516718 TCTTCGAATCCACCTCATATTCTTC 58.483 40.000 0.00 0.00 0.00 2.87
252 253 6.325028 TCTTCGAATCCACCTCATATTCTTCT 59.675 38.462 0.00 0.00 0.00 2.85
253 254 6.485830 TCGAATCCACCTCATATTCTTCTT 57.514 37.500 0.00 0.00 0.00 2.52
254 255 6.516718 TCGAATCCACCTCATATTCTTCTTC 58.483 40.000 0.00 0.00 0.00 2.87
256 257 4.672587 TCCACCTCATATTCTTCTTCCG 57.327 45.455 0.00 0.00 0.00 4.30
257 258 4.030913 TCCACCTCATATTCTTCTTCCGT 58.969 43.478 0.00 0.00 0.00 4.69
258 259 4.469945 TCCACCTCATATTCTTCTTCCGTT 59.530 41.667 0.00 0.00 0.00 4.44
259 260 4.572389 CCACCTCATATTCTTCTTCCGTTG 59.428 45.833 0.00 0.00 0.00 4.10
263 264 5.355350 CCTCATATTCTTCTTCCGTTGCTTT 59.645 40.000 0.00 0.00 0.00 3.51
265 266 6.173339 TCATATTCTTCTTCCGTTGCTTTCT 58.827 36.000 0.00 0.00 0.00 2.52
266 267 4.756084 ATTCTTCTTCCGTTGCTTTCTG 57.244 40.909 0.00 0.00 0.00 3.02
269 270 2.831685 TCTTCCGTTGCTTTCTGCTA 57.168 45.000 0.00 0.00 43.37 3.49
270 271 3.120321 TCTTCCGTTGCTTTCTGCTAA 57.880 42.857 0.00 0.00 43.37 3.09
272 273 4.072131 TCTTCCGTTGCTTTCTGCTAAAT 58.928 39.130 0.00 0.00 43.37 1.40
274 275 3.674997 TCCGTTGCTTTCTGCTAAATCT 58.325 40.909 0.00 0.00 43.37 2.40
275 276 4.827692 TCCGTTGCTTTCTGCTAAATCTA 58.172 39.130 0.00 0.00 43.37 1.98
276 277 5.242434 TCCGTTGCTTTCTGCTAAATCTAA 58.758 37.500 0.00 0.00 43.37 2.10
277 278 5.703592 TCCGTTGCTTTCTGCTAAATCTAAA 59.296 36.000 0.00 0.00 43.37 1.85
278 279 6.374333 TCCGTTGCTTTCTGCTAAATCTAAAT 59.626 34.615 0.00 0.00 43.37 1.40
281 282 7.750458 CGTTGCTTTCTGCTAAATCTAAATCAA 59.250 33.333 0.00 0.00 43.37 2.57
283 284 7.253422 TGCTTTCTGCTAAATCTAAATCAAGC 58.747 34.615 0.00 0.00 43.37 4.01
284 285 6.694844 GCTTTCTGCTAAATCTAAATCAAGCC 59.305 38.462 0.00 0.00 38.95 4.35
285 286 7.629222 GCTTTCTGCTAAATCTAAATCAAGCCA 60.629 37.037 0.00 0.00 38.95 4.75
286 287 6.932356 TCTGCTAAATCTAAATCAAGCCAG 57.068 37.500 0.00 0.00 0.00 4.85
287 288 5.297776 TCTGCTAAATCTAAATCAAGCCAGC 59.702 40.000 0.00 0.00 0.00 4.85
288 289 4.949238 TGCTAAATCTAAATCAAGCCAGCA 59.051 37.500 0.00 0.00 33.24 4.41
289 290 5.418524 TGCTAAATCTAAATCAAGCCAGCAA 59.581 36.000 0.00 0.00 32.77 3.91
290 291 6.097270 TGCTAAATCTAAATCAAGCCAGCAAT 59.903 34.615 0.00 0.00 32.77 3.56
291 292 6.982724 GCTAAATCTAAATCAAGCCAGCAATT 59.017 34.615 0.00 0.00 0.00 2.32
292 293 7.493645 GCTAAATCTAAATCAAGCCAGCAATTT 59.506 33.333 0.00 0.00 0.00 1.82
294 295 4.497300 TCTAAATCAAGCCAGCAATTTGC 58.503 39.130 13.55 13.55 45.46 3.68
346 4402 4.083003 GGATCACACCAACAAAAGCGATAA 60.083 41.667 0.00 0.00 0.00 1.75
511 4574 4.560108 GCATGATCATGATTAGGGGCAAAC 60.560 45.833 34.65 11.72 41.20 2.93
602 4670 6.285990 GCTTCATTCAAAATAGGCATGGAAT 58.714 36.000 0.00 0.00 0.00 3.01
685 4763 1.915769 AGCACCTTCGAGGGAGCTT 60.916 57.895 28.51 15.28 44.78 3.74
936 5032 8.477419 AAATTTCCTTCTAATTTGTCAGACCA 57.523 30.769 0.00 0.00 34.75 4.02
1222 5506 3.404141 GAGCAGCGGAGAGACGGTC 62.404 68.421 0.00 0.00 43.39 4.79
1453 5737 0.895530 CGGTGCTCAACTTCCCTCTA 59.104 55.000 0.00 0.00 0.00 2.43
1458 5742 1.827969 GCTCAACTTCCCTCTAGAGCA 59.172 52.381 14.73 0.00 45.67 4.26
1573 5857 2.436646 CGCAGCAAGGTCGGGATT 60.437 61.111 0.00 0.00 0.00 3.01
1745 6029 3.103738 CAGTACTACACATACGCGAACC 58.896 50.000 15.93 0.00 0.00 3.62
1746 6030 2.749076 AGTACTACACATACGCGAACCA 59.251 45.455 15.93 0.00 0.00 3.67
1747 6031 2.728690 ACTACACATACGCGAACCAA 57.271 45.000 15.93 0.00 0.00 3.67
1748 6032 2.331194 ACTACACATACGCGAACCAAC 58.669 47.619 15.93 0.00 0.00 3.77
1749 6033 2.029649 ACTACACATACGCGAACCAACT 60.030 45.455 15.93 0.00 0.00 3.16
1750 6034 1.873698 ACACATACGCGAACCAACTT 58.126 45.000 15.93 0.00 0.00 2.66
1751 6035 1.529438 ACACATACGCGAACCAACTTG 59.471 47.619 15.93 0.78 0.00 3.16
1752 6036 1.529438 CACATACGCGAACCAACTTGT 59.471 47.619 15.93 1.11 0.00 3.16
1773 6057 3.053619 GTGGTTGGATGGTTAGAGGGATT 60.054 47.826 0.00 0.00 0.00 3.01
1784 6091 4.202367 GGTTAGAGGGATTGTGGTATCTGG 60.202 50.000 0.00 0.00 0.00 3.86
1800 6107 4.989279 ATCTGGTGCTCGCATTTATTTT 57.011 36.364 0.00 0.00 0.00 1.82
1802 6109 5.484173 TCTGGTGCTCGCATTTATTTTAG 57.516 39.130 0.00 0.00 0.00 1.85
1803 6110 5.182487 TCTGGTGCTCGCATTTATTTTAGA 58.818 37.500 0.00 0.00 0.00 2.10
1804 6111 5.645929 TCTGGTGCTCGCATTTATTTTAGAA 59.354 36.000 0.00 0.00 0.00 2.10
1805 6112 6.318648 TCTGGTGCTCGCATTTATTTTAGAAT 59.681 34.615 0.00 0.00 0.00 2.40
1806 6113 6.862209 TGGTGCTCGCATTTATTTTAGAATT 58.138 32.000 0.00 0.00 0.00 2.17
1807 6114 7.319646 TGGTGCTCGCATTTATTTTAGAATTT 58.680 30.769 0.00 0.00 0.00 1.82
1808 6115 7.487829 TGGTGCTCGCATTTATTTTAGAATTTC 59.512 33.333 0.00 0.00 0.00 2.17
1809 6116 7.043391 GGTGCTCGCATTTATTTTAGAATTTCC 60.043 37.037 0.00 0.00 0.00 3.13
1810 6117 6.690957 TGCTCGCATTTATTTTAGAATTTCCG 59.309 34.615 0.00 0.00 0.00 4.30
1811 6118 6.142320 GCTCGCATTTATTTTAGAATTTCCGG 59.858 38.462 0.00 0.00 0.00 5.14
1812 6119 7.090953 TCGCATTTATTTTAGAATTTCCGGT 57.909 32.000 0.00 0.00 0.00 5.28
1813 6120 6.970043 TCGCATTTATTTTAGAATTTCCGGTG 59.030 34.615 0.00 0.00 0.00 4.94
1814 6121 6.970043 CGCATTTATTTTAGAATTTCCGGTGA 59.030 34.615 0.00 0.00 0.00 4.02
1815 6122 7.647715 CGCATTTATTTTAGAATTTCCGGTGAT 59.352 33.333 0.00 0.00 0.00 3.06
1816 6123 8.755018 GCATTTATTTTAGAATTTCCGGTGATG 58.245 33.333 0.00 0.00 0.00 3.07
1817 6124 8.755018 CATTTATTTTAGAATTTCCGGTGATGC 58.245 33.333 0.00 0.00 0.00 3.91
1818 6125 4.349663 TTTTAGAATTTCCGGTGATGCG 57.650 40.909 0.00 0.00 0.00 4.73
1819 6126 1.295792 TAGAATTTCCGGTGATGCGC 58.704 50.000 0.00 0.00 0.00 6.09
1820 6127 0.676466 AGAATTTCCGGTGATGCGCA 60.676 50.000 14.96 14.96 0.00 6.09
1821 6128 0.381801 GAATTTCCGGTGATGCGCAT 59.618 50.000 25.66 25.66 0.00 4.73
1822 6129 0.817013 AATTTCCGGTGATGCGCATT 59.183 45.000 26.12 8.31 0.00 3.56
1823 6130 0.381801 ATTTCCGGTGATGCGCATTC 59.618 50.000 26.12 19.54 0.00 2.67
1824 6131 0.957888 TTTCCGGTGATGCGCATTCA 60.958 50.000 26.12 19.83 0.00 2.57
1825 6132 0.957888 TTCCGGTGATGCGCATTCAA 60.958 50.000 26.12 10.83 0.00 2.69
1826 6133 0.747644 TCCGGTGATGCGCATTCAAT 60.748 50.000 26.12 0.98 0.00 2.57
1827 6134 0.593008 CCGGTGATGCGCATTCAATG 60.593 55.000 26.12 16.81 0.00 2.82
1830 6137 0.740149 GTGATGCGCATTCAATGGGA 59.260 50.000 26.12 4.11 45.09 4.37
1860 6167 7.915930 ACATTCCCATGAATTTTGTCCATTTA 58.084 30.769 0.00 0.00 39.20 1.40
1893 6200 6.515272 TTAATGAGAAGATTTGCCTTGGTC 57.485 37.500 0.00 0.00 0.00 4.02
1962 7620 6.055231 TGGAACAATGTTTCGTTAACTCAG 57.945 37.500 0.00 0.00 34.32 3.35
1972 7630 1.201921 CGTTAACTCAGAATGCCGCAC 60.202 52.381 3.71 0.00 34.76 5.34
2090 7749 2.972625 TGACATTTAGAAGTCCCGCAG 58.027 47.619 0.00 0.00 33.89 5.18
2127 7789 5.718724 TGCAACATCCATTGACATTAACA 57.281 34.783 0.00 0.00 0.00 2.41
2133 7795 7.994425 ACATCCATTGACATTAACAACTACA 57.006 32.000 0.00 0.00 0.00 2.74
2136 7798 9.859427 CATCCATTGACATTAACAACTACAAAT 57.141 29.630 0.00 0.00 0.00 2.32
2209 7871 4.000988 AGGAAATAATGTGCTTTCGTCGT 58.999 39.130 0.00 0.00 33.19 4.34
2227 7889 1.455773 TCGTCGCCAGATCCATCCT 60.456 57.895 0.00 0.00 0.00 3.24
2290 7952 5.819901 GCAAACTCTAGAGAATGCCTACAAT 59.180 40.000 28.62 4.74 37.48 2.71
2331 7995 2.619849 CCACCAATGCAGGTCAGATCTT 60.620 50.000 0.00 0.00 40.77 2.40
2351 8019 1.073284 TGAGTTTCCAAGCTGGGGTAC 59.927 52.381 7.48 5.87 38.32 3.34
2352 8020 0.036306 AGTTTCCAAGCTGGGGTACG 59.964 55.000 7.48 0.00 38.32 3.67
2353 8021 0.250597 GTTTCCAAGCTGGGGTACGT 60.251 55.000 7.48 0.00 38.32 3.57
2354 8022 1.002315 GTTTCCAAGCTGGGGTACGTA 59.998 52.381 7.48 0.00 38.32 3.57
2404 8072 6.863126 AGCAAACTTAAGTCACAATGTATTGC 59.137 34.615 20.41 20.41 41.38 3.56
2458 8321 3.497332 ACAGCCTACAAGTCTGACTGTA 58.503 45.455 11.71 13.72 35.27 2.74
2470 8333 2.426024 TCTGACTGTAATGCCTCGGTAC 59.574 50.000 0.00 0.00 0.00 3.34
2477 8347 1.760192 AATGCCTCGGTACTCGTACT 58.240 50.000 7.12 0.00 40.32 2.73
2478 8348 1.760192 ATGCCTCGGTACTCGTACTT 58.240 50.000 7.12 0.00 40.32 2.24
2479 8349 1.089920 TGCCTCGGTACTCGTACTTC 58.910 55.000 7.12 0.00 40.32 3.01
2480 8350 0.027324 GCCTCGGTACTCGTACTTCG 59.973 60.000 7.12 3.93 40.32 3.79
2481 8351 1.363744 CCTCGGTACTCGTACTTCGT 58.636 55.000 7.12 0.00 40.80 3.85
2519 8389 4.019792 TGTAGACATTGCCACTCAACAT 57.980 40.909 0.00 0.00 37.53 2.71
2559 8429 0.593128 AGCAAAACGGAGCATGTCAC 59.407 50.000 0.00 0.00 0.00 3.67
2566 8436 1.002430 ACGGAGCATGTCACTGATTGT 59.998 47.619 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.606401 CACCGTGGCTTGGACTTCAT 60.606 55.000 2.55 0.00 0.00 2.57
1 2 1.227823 CACCGTGGCTTGGACTTCA 60.228 57.895 2.55 0.00 0.00 3.02
3 4 2.113139 CCACCGTGGCTTGGACTT 59.887 61.111 4.16 0.00 34.46 3.01
20 21 2.737881 TATACCACCAGGGCCACGC 61.738 63.158 6.18 0.00 42.05 5.34
21 22 1.145377 GTATACCACCAGGGCCACG 59.855 63.158 6.18 0.00 42.05 4.94
22 23 1.145377 CGTATACCACCAGGGCCAC 59.855 63.158 6.18 0.00 42.05 5.01
23 24 0.399376 ATCGTATACCACCAGGGCCA 60.399 55.000 6.18 0.00 42.05 5.36
25 26 1.045407 TCATCGTATACCACCAGGGC 58.955 55.000 0.00 0.00 42.05 5.19
27 28 3.653344 CATGTCATCGTATACCACCAGG 58.347 50.000 0.00 0.00 42.21 4.45
28 29 3.059884 GCATGTCATCGTATACCACCAG 58.940 50.000 0.00 0.00 0.00 4.00
29 30 2.544903 CGCATGTCATCGTATACCACCA 60.545 50.000 0.00 0.00 0.00 4.17
30 31 2.058798 CGCATGTCATCGTATACCACC 58.941 52.381 0.00 0.00 0.00 4.61
33 34 2.980476 CTGTCGCATGTCATCGTATACC 59.020 50.000 0.00 0.00 0.00 2.73
35 36 2.621526 ACCTGTCGCATGTCATCGTATA 59.378 45.455 0.00 0.00 0.00 1.47
36 37 1.409064 ACCTGTCGCATGTCATCGTAT 59.591 47.619 0.00 0.00 0.00 3.06
37 38 0.815095 ACCTGTCGCATGTCATCGTA 59.185 50.000 0.00 0.00 0.00 3.43
38 39 0.737367 CACCTGTCGCATGTCATCGT 60.737 55.000 0.00 0.00 0.00 3.73
39 40 1.423721 CCACCTGTCGCATGTCATCG 61.424 60.000 0.00 0.00 0.00 3.84
40 41 0.391661 ACCACCTGTCGCATGTCATC 60.392 55.000 0.00 0.00 0.00 2.92
41 42 0.391661 GACCACCTGTCGCATGTCAT 60.392 55.000 0.00 0.00 33.49 3.06
42 43 1.005037 GACCACCTGTCGCATGTCA 60.005 57.895 0.00 0.00 33.49 3.58
43 44 1.741770 GGACCACCTGTCGCATGTC 60.742 63.158 0.00 0.00 45.46 3.06
44 45 2.347490 GGACCACCTGTCGCATGT 59.653 61.111 0.00 0.00 45.46 3.21
45 46 2.815211 CGGACCACCTGTCGCATG 60.815 66.667 0.00 0.00 45.46 4.06
46 47 2.391724 AAACGGACCACCTGTCGCAT 62.392 55.000 0.00 0.00 45.46 4.73
47 48 3.096633 AAACGGACCACCTGTCGCA 62.097 57.895 0.00 0.00 45.46 5.10
49 50 1.959226 CCAAACGGACCACCTGTCG 60.959 63.158 0.00 0.00 45.46 4.35
50 51 1.147600 ACCAAACGGACCACCTGTC 59.852 57.895 0.00 0.00 43.67 3.51
53 54 0.036306 GATCACCAAACGGACCACCT 59.964 55.000 0.00 0.00 0.00 4.00
55 56 0.036306 AGGATCACCAAACGGACCAC 59.964 55.000 0.00 0.00 38.94 4.16
56 57 0.323629 GAGGATCACCAAACGGACCA 59.676 55.000 0.00 0.00 38.94 4.02
57 58 0.392595 GGAGGATCACCAAACGGACC 60.393 60.000 0.00 0.00 38.94 4.46
58 59 0.739813 CGGAGGATCACCAAACGGAC 60.740 60.000 8.52 0.00 38.94 4.79
59 60 1.189524 ACGGAGGATCACCAAACGGA 61.190 55.000 8.52 0.00 38.94 4.69
60 61 1.019278 CACGGAGGATCACCAAACGG 61.019 60.000 8.52 0.00 38.94 4.44
61 62 1.019278 CCACGGAGGATCACCAAACG 61.019 60.000 8.52 0.00 41.22 3.60
63 64 1.002624 GCCACGGAGGATCACCAAA 60.003 57.895 8.52 0.00 41.22 3.28
64 65 2.668632 GCCACGGAGGATCACCAA 59.331 61.111 8.52 0.00 41.22 3.67
82 83 0.393132 GGAGAACTAGGCAAGTGGGC 60.393 60.000 0.00 0.00 38.88 5.36
83 84 1.280457 AGGAGAACTAGGCAAGTGGG 58.720 55.000 0.00 0.00 38.88 4.61
84 85 2.303022 TGAAGGAGAACTAGGCAAGTGG 59.697 50.000 0.00 0.00 38.88 4.00
86 87 5.026790 ACTATGAAGGAGAACTAGGCAAGT 58.973 41.667 0.00 0.00 41.49 3.16
88 89 6.213600 AGAAACTATGAAGGAGAACTAGGCAA 59.786 38.462 0.00 0.00 0.00 4.52
89 90 5.721960 AGAAACTATGAAGGAGAACTAGGCA 59.278 40.000 0.00 0.00 0.00 4.75
91 92 6.381420 TGGAGAAACTATGAAGGAGAACTAGG 59.619 42.308 0.00 0.00 0.00 3.02
92 93 7.411486 TGGAGAAACTATGAAGGAGAACTAG 57.589 40.000 0.00 0.00 0.00 2.57
94 95 6.406400 CGATGGAGAAACTATGAAGGAGAACT 60.406 42.308 0.00 0.00 0.00 3.01
95 96 5.751028 CGATGGAGAAACTATGAAGGAGAAC 59.249 44.000 0.00 0.00 0.00 3.01
96 97 5.163405 CCGATGGAGAAACTATGAAGGAGAA 60.163 44.000 0.00 0.00 0.00 2.87
99 100 4.286707 TCCGATGGAGAAACTATGAAGGA 58.713 43.478 0.00 0.00 0.00 3.36
100 101 4.672587 TCCGATGGAGAAACTATGAAGG 57.327 45.455 0.00 0.00 0.00 3.46
113 114 2.121538 CAGCTCCGACTCCGATGGA 61.122 63.158 0.00 0.00 38.22 3.41
116 117 3.893763 CGCAGCTCCGACTCCGAT 61.894 66.667 0.00 0.00 38.22 4.18
118 119 3.893763 ATCGCAGCTCCGACTCCG 61.894 66.667 0.00 0.00 40.40 4.63
121 122 1.599606 AAGACATCGCAGCTCCGACT 61.600 55.000 0.00 0.00 40.40 4.18
122 123 1.153745 AAGACATCGCAGCTCCGAC 60.154 57.895 0.00 0.00 40.40 4.79
123 124 1.153765 CAAGACATCGCAGCTCCGA 60.154 57.895 0.27 0.27 41.98 4.55
124 125 2.806856 GCAAGACATCGCAGCTCCG 61.807 63.158 0.00 0.00 0.00 4.63
126 127 1.742880 TGGCAAGACATCGCAGCTC 60.743 57.895 0.00 0.00 0.00 4.09
127 128 2.037136 GTGGCAAGACATCGCAGCT 61.037 57.895 0.00 0.00 0.00 4.24
128 129 2.482374 GTGGCAAGACATCGCAGC 59.518 61.111 0.00 0.00 0.00 5.25
129 130 2.743752 CCGTGGCAAGACATCGCAG 61.744 63.158 0.76 0.00 0.00 5.18
130 131 2.741985 CCGTGGCAAGACATCGCA 60.742 61.111 0.76 0.00 0.00 5.10
132 133 2.047274 ACCCGTGGCAAGACATCG 60.047 61.111 0.76 0.00 0.00 3.84
133 134 2.040544 CCACCCGTGGCAAGACATC 61.041 63.158 0.76 0.00 44.73 3.06
134 135 2.034066 CCACCCGTGGCAAGACAT 59.966 61.111 0.76 0.00 44.73 3.06
143 144 2.120909 GGAATGCCATCCACCCGTG 61.121 63.158 0.19 0.00 39.42 4.94
144 145 2.275418 GGAATGCCATCCACCCGT 59.725 61.111 0.19 0.00 39.42 5.28
145 146 2.275089 TGGAATGCCATCCACCCG 59.725 61.111 3.56 0.00 44.52 5.28
155 156 2.015736 ACACTCTCACGATGGAATGC 57.984 50.000 0.00 0.00 0.00 3.56
156 157 4.108336 CACTACACTCTCACGATGGAATG 58.892 47.826 0.00 0.00 0.00 2.67
157 158 3.429547 GCACTACACTCTCACGATGGAAT 60.430 47.826 0.00 0.00 0.00 3.01
158 159 2.094700 GCACTACACTCTCACGATGGAA 60.095 50.000 0.00 0.00 0.00 3.53
159 160 1.472878 GCACTACACTCTCACGATGGA 59.527 52.381 0.00 0.00 0.00 3.41
160 161 1.474478 AGCACTACACTCTCACGATGG 59.526 52.381 0.00 0.00 0.00 3.51
162 163 2.437413 TCAGCACTACACTCTCACGAT 58.563 47.619 0.00 0.00 0.00 3.73
163 164 1.892209 TCAGCACTACACTCTCACGA 58.108 50.000 0.00 0.00 0.00 4.35
164 165 2.421775 AGATCAGCACTACACTCTCACG 59.578 50.000 0.00 0.00 0.00 4.35
165 166 3.768406 CAGATCAGCACTACACTCTCAC 58.232 50.000 0.00 0.00 0.00 3.51
166 167 2.165234 GCAGATCAGCACTACACTCTCA 59.835 50.000 5.05 0.00 0.00 3.27
168 169 2.166050 CTGCAGATCAGCACTACACTCT 59.834 50.000 8.42 0.00 40.11 3.24
169 170 2.538437 CTGCAGATCAGCACTACACTC 58.462 52.381 8.42 0.00 40.11 3.51
170 171 2.669300 CTGCAGATCAGCACTACACT 57.331 50.000 8.42 0.00 40.11 3.55
180 181 2.333069 AGCCCTATTAGCTGCAGATCA 58.667 47.619 20.43 1.98 39.69 2.92
188 189 3.267031 AGGAAACAACAGCCCTATTAGCT 59.733 43.478 0.00 0.00 42.70 3.32
189 190 3.621558 AGGAAACAACAGCCCTATTAGC 58.378 45.455 0.00 0.00 0.00 3.09
191 192 8.658840 ATTAAAAGGAAACAACAGCCCTATTA 57.341 30.769 0.00 0.00 0.00 0.98
192 193 6.987403 TTAAAAGGAAACAACAGCCCTATT 57.013 33.333 0.00 0.00 0.00 1.73
193 194 7.553504 AATTAAAAGGAAACAACAGCCCTAT 57.446 32.000 0.00 0.00 0.00 2.57
194 195 6.987403 AATTAAAAGGAAACAACAGCCCTA 57.013 33.333 0.00 0.00 0.00 3.53
195 196 5.887214 AATTAAAAGGAAACAACAGCCCT 57.113 34.783 0.00 0.00 0.00 5.19
196 197 6.935741 AAAATTAAAAGGAAACAACAGCCC 57.064 33.333 0.00 0.00 0.00 5.19
215 216 7.177392 AGGTGGATTCGAAGATCAAAGAAAAAT 59.823 33.333 3.35 0.00 35.04 1.82
216 217 6.490040 AGGTGGATTCGAAGATCAAAGAAAAA 59.510 34.615 3.35 0.00 35.04 1.94
217 218 6.003950 AGGTGGATTCGAAGATCAAAGAAAA 58.996 36.000 3.35 0.00 35.04 2.29
218 219 5.560724 AGGTGGATTCGAAGATCAAAGAAA 58.439 37.500 3.35 0.00 35.04 2.52
219 220 5.165961 AGGTGGATTCGAAGATCAAAGAA 57.834 39.130 3.35 0.00 35.04 2.52
220 221 4.222810 TGAGGTGGATTCGAAGATCAAAGA 59.777 41.667 3.35 0.00 35.04 2.52
221 222 4.507710 TGAGGTGGATTCGAAGATCAAAG 58.492 43.478 3.35 0.00 35.04 2.77
222 223 4.551702 TGAGGTGGATTCGAAGATCAAA 57.448 40.909 3.35 0.00 35.04 2.69
223 224 4.760530 ATGAGGTGGATTCGAAGATCAA 57.239 40.909 3.35 0.00 35.04 2.57
224 225 6.268617 AGAATATGAGGTGGATTCGAAGATCA 59.731 38.462 3.35 1.95 35.23 2.92
226 227 6.678568 AGAATATGAGGTGGATTCGAAGAT 57.321 37.500 3.35 0.00 35.23 2.40
227 228 6.325028 AGAAGAATATGAGGTGGATTCGAAGA 59.675 38.462 3.35 0.00 35.23 2.87
230 231 6.463049 GGAAGAAGAATATGAGGTGGATTCGA 60.463 42.308 0.00 0.00 35.23 3.71
231 232 5.698545 GGAAGAAGAATATGAGGTGGATTCG 59.301 44.000 0.00 0.00 35.23 3.34
232 233 5.698545 CGGAAGAAGAATATGAGGTGGATTC 59.301 44.000 0.00 0.00 0.00 2.52
233 234 5.131142 ACGGAAGAAGAATATGAGGTGGATT 59.869 40.000 0.00 0.00 0.00 3.01
234 235 4.656112 ACGGAAGAAGAATATGAGGTGGAT 59.344 41.667 0.00 0.00 0.00 3.41
235 236 4.030913 ACGGAAGAAGAATATGAGGTGGA 58.969 43.478 0.00 0.00 0.00 4.02
236 237 4.408182 ACGGAAGAAGAATATGAGGTGG 57.592 45.455 0.00 0.00 0.00 4.61
238 239 4.080863 AGCAACGGAAGAAGAATATGAGGT 60.081 41.667 0.00 0.00 0.00 3.85
239 240 4.446371 AGCAACGGAAGAAGAATATGAGG 58.554 43.478 0.00 0.00 0.00 3.86
240 241 6.314896 AGAAAGCAACGGAAGAAGAATATGAG 59.685 38.462 0.00 0.00 0.00 2.90
241 242 6.092670 CAGAAAGCAACGGAAGAAGAATATGA 59.907 38.462 0.00 0.00 0.00 2.15
243 244 5.163713 GCAGAAAGCAACGGAAGAAGAATAT 60.164 40.000 0.00 0.00 44.79 1.28
244 245 4.154195 GCAGAAAGCAACGGAAGAAGAATA 59.846 41.667 0.00 0.00 44.79 1.75
245 246 3.057946 GCAGAAAGCAACGGAAGAAGAAT 60.058 43.478 0.00 0.00 44.79 2.40
246 247 2.290641 GCAGAAAGCAACGGAAGAAGAA 59.709 45.455 0.00 0.00 44.79 2.52
247 248 1.873591 GCAGAAAGCAACGGAAGAAGA 59.126 47.619 0.00 0.00 44.79 2.87
259 260 6.694844 GGCTTGATTTAGATTTAGCAGAAAGC 59.305 38.462 0.00 0.00 46.19 3.51
263 264 5.297776 GCTGGCTTGATTTAGATTTAGCAGA 59.702 40.000 0.00 0.00 0.00 4.26
265 266 4.949238 TGCTGGCTTGATTTAGATTTAGCA 59.051 37.500 0.00 0.00 35.36 3.49
266 267 5.505173 TGCTGGCTTGATTTAGATTTAGC 57.495 39.130 0.00 0.00 0.00 3.09
269 270 6.093082 GCAAATTGCTGGCTTGATTTAGATTT 59.907 34.615 11.19 0.00 40.96 2.17
270 271 5.583457 GCAAATTGCTGGCTTGATTTAGATT 59.417 36.000 11.19 0.00 40.96 2.40
272 273 4.497300 GCAAATTGCTGGCTTGATTTAGA 58.503 39.130 11.19 0.00 40.96 2.10
304 305 4.527509 TCCATTGTGTGTGTGTGTTTTT 57.472 36.364 0.00 0.00 0.00 1.94
305 306 4.159321 TGATCCATTGTGTGTGTGTGTTTT 59.841 37.500 0.00 0.00 0.00 2.43
307 308 3.066621 GTGATCCATTGTGTGTGTGTGTT 59.933 43.478 0.00 0.00 0.00 3.32
308 309 2.618241 GTGATCCATTGTGTGTGTGTGT 59.382 45.455 0.00 0.00 0.00 3.72
309 310 2.617774 TGTGATCCATTGTGTGTGTGTG 59.382 45.455 0.00 0.00 0.00 3.82
310 311 2.618241 GTGTGATCCATTGTGTGTGTGT 59.382 45.455 0.00 0.00 0.00 3.72
311 312 2.030893 GGTGTGATCCATTGTGTGTGTG 60.031 50.000 0.00 0.00 0.00 3.82
315 316 2.622470 TGTTGGTGTGATCCATTGTGTG 59.378 45.455 0.00 0.00 37.33 3.82
316 317 2.942804 TGTTGGTGTGATCCATTGTGT 58.057 42.857 0.00 0.00 37.33 3.72
346 4402 8.006298 TCTGATGAGTTTATGTTGGTGTTTTT 57.994 30.769 0.00 0.00 0.00 1.94
602 4670 2.723322 CTGAATCCATCCAGCCTTGA 57.277 50.000 0.00 0.00 0.00 3.02
685 4763 1.642037 CCTCCTAGCGTTGACGTCGA 61.642 60.000 11.62 6.16 42.22 4.20
988 5088 2.111384 CTCCTCTGTGGGCTAGCTAAA 58.889 52.381 15.72 0.00 36.20 1.85
1437 5721 1.827969 GCTCTAGAGGGAAGTTGAGCA 59.172 52.381 21.23 0.00 44.19 4.26
1453 5737 2.336478 CGACTCCTGGACGTGCTCT 61.336 63.158 8.99 0.00 0.00 4.09
1458 5742 3.063084 GGAGCGACTCCTGGACGT 61.063 66.667 15.90 0.00 46.41 4.34
1640 5924 1.760086 CGAGGTCCTCCAGCTCCAT 60.760 63.158 13.54 0.00 45.57 3.41
1746 6030 4.398319 CTCTAACCATCCAACCACAAGTT 58.602 43.478 0.00 0.00 40.16 2.66
1747 6031 3.244911 CCTCTAACCATCCAACCACAAGT 60.245 47.826 0.00 0.00 0.00 3.16
1748 6032 3.347216 CCTCTAACCATCCAACCACAAG 58.653 50.000 0.00 0.00 0.00 3.16
1749 6033 2.041081 CCCTCTAACCATCCAACCACAA 59.959 50.000 0.00 0.00 0.00 3.33
1750 6034 1.633432 CCCTCTAACCATCCAACCACA 59.367 52.381 0.00 0.00 0.00 4.17
1751 6035 1.913419 TCCCTCTAACCATCCAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
1752 6036 2.352561 TCCCTCTAACCATCCAACCA 57.647 50.000 0.00 0.00 0.00 3.67
1766 6050 2.746472 GCACCAGATACCACAATCCCTC 60.746 54.545 0.00 0.00 0.00 4.30
1773 6057 1.218047 GCGAGCACCAGATACCACA 59.782 57.895 0.00 0.00 0.00 4.17
1784 6091 7.305418 CGGAAATTCTAAAATAAATGCGAGCAC 60.305 37.037 0.00 0.00 0.00 4.40
1800 6107 1.295792 GCGCATCACCGGAAATTCTA 58.704 50.000 9.46 0.00 0.00 2.10
1802 6109 0.381801 ATGCGCATCACCGGAAATTC 59.618 50.000 19.28 0.00 30.90 2.17
1803 6110 0.817013 AATGCGCATCACCGGAAATT 59.183 45.000 25.53 0.76 30.90 1.82
1804 6111 0.381801 GAATGCGCATCACCGGAAAT 59.618 50.000 25.53 3.87 30.90 2.17
1805 6112 0.957888 TGAATGCGCATCACCGGAAA 60.958 50.000 25.53 2.10 30.90 3.13
1806 6113 0.957888 TTGAATGCGCATCACCGGAA 60.958 50.000 25.53 8.72 30.90 4.30
1807 6114 0.747644 ATTGAATGCGCATCACCGGA 60.748 50.000 25.53 8.62 0.00 5.14
1808 6115 0.593008 CATTGAATGCGCATCACCGG 60.593 55.000 25.53 10.05 0.00 5.28
1809 6116 0.593008 CCATTGAATGCGCATCACCG 60.593 55.000 25.53 14.79 0.00 4.94
1810 6117 0.249155 CCCATTGAATGCGCATCACC 60.249 55.000 25.53 16.03 0.00 4.02
1811 6118 0.740149 TCCCATTGAATGCGCATCAC 59.260 50.000 25.53 20.34 0.00 3.06
1812 6119 1.026584 CTCCCATTGAATGCGCATCA 58.973 50.000 25.53 19.52 0.00 3.07
1813 6120 0.313043 CCTCCCATTGAATGCGCATC 59.687 55.000 25.53 17.12 0.00 3.91
1814 6121 0.106569 TCCTCCCATTGAATGCGCAT 60.107 50.000 19.28 19.28 0.00 4.73
1815 6122 0.749091 CTCCTCCCATTGAATGCGCA 60.749 55.000 14.96 14.96 0.00 6.09
1816 6123 0.464373 TCTCCTCCCATTGAATGCGC 60.464 55.000 0.00 0.00 0.00 6.09
1817 6124 1.303309 GTCTCCTCCCATTGAATGCG 58.697 55.000 0.00 0.00 0.00 4.73
1818 6125 2.425143 TGTCTCCTCCCATTGAATGC 57.575 50.000 0.00 0.00 0.00 3.56
1819 6126 3.887716 GGAATGTCTCCTCCCATTGAATG 59.112 47.826 0.00 0.00 41.61 2.67
1820 6127 4.176120 GGAATGTCTCCTCCCATTGAAT 57.824 45.455 0.00 0.00 41.61 2.57
1821 6128 3.652057 GGAATGTCTCCTCCCATTGAA 57.348 47.619 0.00 0.00 41.61 2.69
1830 6137 5.336102 ACAAAATTCATGGGAATGTCTCCT 58.664 37.500 0.00 0.00 42.87 3.69
1893 6200 3.018423 AGGCAAGCTAATTAAGGGTGG 57.982 47.619 0.00 0.00 0.00 4.61
1930 6496 6.208644 ACGAAACATTGTTCCATTTTGAGAG 58.791 36.000 1.83 0.00 0.00 3.20
1939 6505 5.818336 TCTGAGTTAACGAAACATTGTTCCA 59.182 36.000 1.83 0.00 40.83 3.53
1952 7610 1.075542 TGCGGCATTCTGAGTTAACG 58.924 50.000 0.00 0.00 0.00 3.18
1953 7611 2.076863 AGTGCGGCATTCTGAGTTAAC 58.923 47.619 5.72 0.00 0.00 2.01
1962 7620 3.621268 TGTATTACTTCAGTGCGGCATTC 59.379 43.478 5.72 0.00 0.00 2.67
2068 7726 4.404394 TCTGCGGGACTTCTAAATGTCATA 59.596 41.667 0.00 0.00 35.11 2.15
2077 7735 1.919240 TTCACTCTGCGGGACTTCTA 58.081 50.000 0.00 0.00 0.00 2.10
2112 7774 9.072375 TCATTTGTAGTTGTTAATGTCAATGGA 57.928 29.630 0.00 0.00 31.59 3.41
2127 7789 6.347079 CCGTTCGTATGTTGTCATTTGTAGTT 60.347 38.462 0.00 0.00 35.70 2.24
2133 7795 2.809119 TGCCGTTCGTATGTTGTCATTT 59.191 40.909 0.00 0.00 35.70 2.32
2136 7798 1.795872 CTTGCCGTTCGTATGTTGTCA 59.204 47.619 0.00 0.00 0.00 3.58
2190 7852 3.430895 ACGACGACGAAAGCACATTATTT 59.569 39.130 15.32 0.00 42.66 1.40
2209 7871 1.455773 AGGATGGATCTGGCGACGA 60.456 57.895 0.00 0.00 0.00 4.20
2227 7889 1.343075 ACCCAAGATCTAGCTTCCCGA 60.343 52.381 0.00 0.00 0.00 5.14
2290 7952 5.586155 TGGTGTTTTCCACTATTCCCTTA 57.414 39.130 0.00 0.00 43.94 2.69
2331 7995 1.073284 GTACCCCAGCTTGGAAACTCA 59.927 52.381 5.14 0.00 40.96 3.41
2351 8019 3.562973 TCTTAAGCATAGGGTCTCGTACG 59.437 47.826 9.53 9.53 0.00 3.67
2352 8020 5.110940 CTCTTAAGCATAGGGTCTCGTAC 57.889 47.826 0.00 0.00 0.00 3.67
2380 8048 6.089417 GGCAATACATTGTGACTTAAGTTTGC 59.911 38.462 20.06 20.06 39.88 3.68
2404 8072 5.165961 TCTTCATCTAAAAGTGAGGGTGG 57.834 43.478 0.00 0.00 0.00 4.61
2458 8321 1.760192 AGTACGAGTACCGAGGCATT 58.240 50.000 9.53 0.00 41.76 3.56
2477 8347 4.993905 CATCAGGTATGTGAGTGTACGAA 58.006 43.478 0.00 0.00 0.00 3.85
2478 8348 4.632538 CATCAGGTATGTGAGTGTACGA 57.367 45.455 0.00 0.00 0.00 3.43
2519 8389 1.136891 CCTCGCATCTGTGGTATGTCA 59.863 52.381 0.00 0.00 0.00 3.58
2559 8429 9.786105 TTATGTTTGTATGTTGCATACAATCAG 57.214 29.630 29.15 0.00 42.47 2.90
2566 8436 6.261859 CGCCTTTATGTTTGTATGTTGCATA 58.738 36.000 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.