Multiple sequence alignment - TraesCS2D01G088900

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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 TraesCS2D01G088900 chr2D 100.000 3261 0 0 1 3261 38677566 38680826 0.000000e+00 6023.0
1 TraesCS2D01G088900 chr2D 87.110 1668 104 53 526 2114 40903595 40901960 0.000000e+00 1786.0
2 TraesCS2D01G088900 chr2D 85.629 1684 113 59 526 2114 38782989 38781340 0.000000e+00 1650.0
3 TraesCS2D01G088900 chr2D 90.879 1206 72 10 940 2113 38637226 38638425 0.000000e+00 1583.0
4 TraesCS2D01G088900 chr2D 87.489 1167 103 16 2113 3259 40852001 40853144 0.000000e+00 1306.0
5 TraesCS2D01G088900 chr2D 90.899 923 60 10 1186 2093 40849917 40850830 0.000000e+00 1218.0
6 TraesCS2D01G088900 chr2D 91.434 537 35 8 1580 2114 38685831 38685304 0.000000e+00 726.0
7 TraesCS2D01G088900 chr2D 82.473 736 115 13 2529 3261 176159359 176158635 1.650000e-177 632.0
8 TraesCS2D01G088900 chr2D 90.647 417 16 14 527 943 38636795 38637188 1.720000e-147 532.0
9 TraesCS2D01G088900 chr2D 86.777 121 11 4 38 158 38783743 38783628 2.640000e-26 130.0
10 TraesCS2D01G088900 chr2D 86.777 121 11 4 38 158 40904348 40904233 2.640000e-26 130.0
11 TraesCS2D01G088900 chr2D 79.888 179 22 9 2103 2270 38638467 38638642 5.720000e-23 119.0
12 TraesCS2D01G088900 chr2A 89.308 1749 105 45 402 2114 43429056 43430758 0.000000e+00 2119.0
13 TraesCS2D01G088900 chr2A 90.545 1650 81 31 526 2114 43457886 43459521 0.000000e+00 2113.0
14 TraesCS2D01G088900 chr2A 92.941 765 41 3 1350 2114 43484026 43483275 0.000000e+00 1101.0
15 TraesCS2D01G088900 chr2A 88.108 555 38 16 826 1357 43489651 43489102 4.590000e-178 634.0
16 TraesCS2D01G088900 chr2A 98.718 78 1 0 409 486 43456324 43456401 4.390000e-29 139.0
17 TraesCS2D01G088900 chr2A 81.507 146 13 8 2116 2254 43483217 43483079 1.240000e-19 108.0
18 TraesCS2D01G088900 chr2A 93.333 60 3 1 2103 2162 43459563 43459621 1.610000e-13 87.9
19 TraesCS2D01G088900 chr2A 85.714 77 4 2 2359 2429 43463432 43463507 1.250000e-09 75.0
20 TraesCS2D01G088900 chr2A 83.544 79 8 3 38 111 44073985 44073907 5.840000e-08 69.4
21 TraesCS2D01G088900 chr2A 92.857 42 2 1 1 42 44074037 44073997 3.510000e-05 60.2
22 TraesCS2D01G088900 chr2B 87.356 1645 97 49 553 2114 67542327 67540711 0.000000e+00 1783.0
23 TraesCS2D01G088900 chr2B 87.140 1633 113 50 528 2111 67464046 67465630 0.000000e+00 1762.0
24 TraesCS2D01G088900 chr2B 89.985 1338 73 33 826 2114 67659155 67657830 0.000000e+00 1672.0
25 TraesCS2D01G088900 chr2B 90.344 901 55 15 719 1594 67423970 67424863 0.000000e+00 1153.0
26 TraesCS2D01G088900 chr2B 89.826 688 29 10 2113 2785 67425058 67425719 0.000000e+00 845.0
27 TraesCS2D01G088900 chr2B 89.474 114 9 1 607 720 67423518 67423628 1.220000e-29 141.0
28 TraesCS2D01G088900 chr2B 86.777 121 10 3 38 158 67456927 67457041 2.640000e-26 130.0
29 TraesCS2D01G088900 chr2B 89.474 57 1 4 657 712 67659358 67659306 2.100000e-07 67.6
30 TraesCS2D01G088900 chr2B 77.966 118 19 6 300 412 198359613 198359498 2.100000e-07 67.6
31 TraesCS2D01G088900 chr2B 97.143 35 1 0 1 35 67456875 67456909 3.510000e-05 60.2
32 TraesCS2D01G088900 chr2B 96.875 32 1 0 595 626 67423639 67423670 2.000000e-03 54.7
33 TraesCS2D01G088900 chr7B 82.109 749 124 9 2501 3246 120724085 120724826 1.650000e-177 632.0
34 TraesCS2D01G088900 chr7D 81.698 754 118 15 2501 3248 126347402 126348141 7.740000e-171 610.0
35 TraesCS2D01G088900 chr7D 81.432 754 120 15 2501 3248 126297953 126298692 1.670000e-167 599.0
36 TraesCS2D01G088900 chr6D 81.635 746 120 14 2517 3256 471073332 471074066 1.290000e-168 603.0
37 TraesCS2D01G088900 chr3A 81.432 754 124 14 2501 3248 174277677 174276934 1.290000e-168 603.0
38 TraesCS2D01G088900 chr3A 89.506 162 16 1 246 406 724492391 724492230 1.530000e-48 204.0
39 TraesCS2D01G088900 chr6A 81.633 735 125 8 2517 3248 202363392 202362665 4.660000e-168 601.0
40 TraesCS2D01G088900 chr6A 89.820 167 15 2 245 409 73573912 73573746 2.550000e-51 213.0
41 TraesCS2D01G088900 chr4D 81.009 753 122 16 2501 3248 459065643 459064907 2.180000e-161 579.0
42 TraesCS2D01G088900 chr1A 81.132 742 121 13 2517 3248 361075408 361076140 7.850000e-161 577.0
43 TraesCS2D01G088900 chr1A 88.824 170 17 2 246 414 131283459 131283627 1.190000e-49 207.0
44 TraesCS2D01G088900 chr7A 88.136 177 20 1 238 413 728996557 728996381 3.300000e-50 209.0
45 TraesCS2D01G088900 chr7A 88.235 170 19 1 244 412 440649385 440649216 5.520000e-48 202.0
46 TraesCS2D01G088900 chr1B 88.889 171 16 2 244 411 368075902 368076072 1.190000e-49 207.0
47 TraesCS2D01G088900 chr1B 88.235 170 19 1 239 407 389596377 389596546 5.520000e-48 202.0
48 TraesCS2D01G088900 chr5A 88.068 176 18 3 246 420 436098565 436098738 4.260000e-49 206.0
49 TraesCS2D01G088900 chr5B 88.304 171 18 2 246 415 479326965 479327134 1.530000e-48 204.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G088900 chr2D 38677566 38680826 3260 False 6023.000000 6023 100.00000 1 3261 1 chr2D.!!$F1 3260
1 TraesCS2D01G088900 chr2D 40849917 40853144 3227 False 1262.000000 1306 89.19400 1186 3259 2 chr2D.!!$F3 2073
2 TraesCS2D01G088900 chr2D 40901960 40904348 2388 True 958.000000 1786 86.94350 38 2114 2 chr2D.!!$R4 2076
3 TraesCS2D01G088900 chr2D 38781340 38783743 2403 True 890.000000 1650 86.20300 38 2114 2 chr2D.!!$R3 2076
4 TraesCS2D01G088900 chr2D 38636795 38638642 1847 False 744.666667 1583 87.13800 527 2270 3 chr2D.!!$F2 1743
5 TraesCS2D01G088900 chr2D 38685304 38685831 527 True 726.000000 726 91.43400 1580 2114 1 chr2D.!!$R1 534
6 TraesCS2D01G088900 chr2D 176158635 176159359 724 True 632.000000 632 82.47300 2529 3261 1 chr2D.!!$R2 732
7 TraesCS2D01G088900 chr2A 43429056 43430758 1702 False 2119.000000 2119 89.30800 402 2114 1 chr2A.!!$F1 1712
8 TraesCS2D01G088900 chr2A 43489102 43489651 549 True 634.000000 634 88.10800 826 1357 1 chr2A.!!$R1 531
9 TraesCS2D01G088900 chr2A 43483079 43484026 947 True 604.500000 1101 87.22400 1350 2254 2 chr2A.!!$R2 904
10 TraesCS2D01G088900 chr2A 43456324 43463507 7183 False 603.725000 2113 92.07750 409 2429 4 chr2A.!!$F2 2020
11 TraesCS2D01G088900 chr2B 67540711 67542327 1616 True 1783.000000 1783 87.35600 553 2114 1 chr2B.!!$R1 1561
12 TraesCS2D01G088900 chr2B 67464046 67465630 1584 False 1762.000000 1762 87.14000 528 2111 1 chr2B.!!$F1 1583
13 TraesCS2D01G088900 chr2B 67657830 67659358 1528 True 869.800000 1672 89.72950 657 2114 2 chr2B.!!$R3 1457
14 TraesCS2D01G088900 chr2B 67423518 67425719 2201 False 548.425000 1153 91.62975 595 2785 4 chr2B.!!$F2 2190
15 TraesCS2D01G088900 chr7B 120724085 120724826 741 False 632.000000 632 82.10900 2501 3246 1 chr7B.!!$F1 745
16 TraesCS2D01G088900 chr7D 126347402 126348141 739 False 610.000000 610 81.69800 2501 3248 1 chr7D.!!$F2 747
17 TraesCS2D01G088900 chr7D 126297953 126298692 739 False 599.000000 599 81.43200 2501 3248 1 chr7D.!!$F1 747
18 TraesCS2D01G088900 chr6D 471073332 471074066 734 False 603.000000 603 81.63500 2517 3256 1 chr6D.!!$F1 739
19 TraesCS2D01G088900 chr3A 174276934 174277677 743 True 603.000000 603 81.43200 2501 3248 1 chr3A.!!$R1 747
20 TraesCS2D01G088900 chr6A 202362665 202363392 727 True 601.000000 601 81.63300 2517 3248 1 chr6A.!!$R2 731
21 TraesCS2D01G088900 chr4D 459064907 459065643 736 True 579.000000 579 81.00900 2501 3248 1 chr4D.!!$R1 747
22 TraesCS2D01G088900 chr1A 361075408 361076140 732 False 577.000000 577 81.13200 2517 3248 1 chr1A.!!$F2 731

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
33 34 0.036388 ACGGAGACCAATCAATGCGT 60.036 50.0 0.00 0.00 0.00 5.24 F
219 220 0.099082 GTACGCTCACTTCCTCTCCG 59.901 60.0 0.00 0.00 0.00 4.63 F
495 2278 0.173255 GAGACTCTCAGCTGTCAGCC 59.827 60.0 21.32 4.09 43.77 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1128 3475 0.110688 CGGCGGCATTGTTATCGATG 60.111 55.0 8.54 0.00 38.22 3.84 R
2208 6130 0.110373 GACAACGGTTTAAGCGCCAG 60.110 55.0 16.58 8.91 43.79 4.85 R
2371 6317 7.597643 TTCTTTTTACTTAATCGCAAACACG 57.402 32.0 0.00 0.00 0.00 4.49 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
21 22 4.425577 AGCATTTTGATGAAACGGAGAC 57.574 40.909 0.00 0.00 0.00 3.36
22 23 3.191371 AGCATTTTGATGAAACGGAGACC 59.809 43.478 0.00 0.00 0.00 3.85
23 24 3.057596 GCATTTTGATGAAACGGAGACCA 60.058 43.478 0.00 0.00 0.00 4.02
24 25 4.558496 GCATTTTGATGAAACGGAGACCAA 60.558 41.667 0.00 0.00 0.00 3.67
25 26 5.713025 CATTTTGATGAAACGGAGACCAAT 58.287 37.500 0.00 0.00 0.00 3.16
26 27 5.371115 TTTTGATGAAACGGAGACCAATC 57.629 39.130 0.00 0.00 0.00 2.67
27 28 3.694043 TGATGAAACGGAGACCAATCA 57.306 42.857 0.00 0.00 0.00 2.57
28 29 4.014569 TGATGAAACGGAGACCAATCAA 57.985 40.909 0.00 0.00 0.00 2.57
29 30 4.588899 TGATGAAACGGAGACCAATCAAT 58.411 39.130 0.00 0.00 0.00 2.57
30 31 4.395854 TGATGAAACGGAGACCAATCAATG 59.604 41.667 0.00 0.00 0.00 2.82
31 32 2.487762 TGAAACGGAGACCAATCAATGC 59.512 45.455 0.00 0.00 0.00 3.56
32 33 1.086696 AACGGAGACCAATCAATGCG 58.913 50.000 0.00 0.00 0.00 4.73
33 34 0.036388 ACGGAGACCAATCAATGCGT 60.036 50.000 0.00 0.00 0.00 5.24
34 35 1.086696 CGGAGACCAATCAATGCGTT 58.913 50.000 0.00 0.00 0.00 4.84
35 36 1.468520 CGGAGACCAATCAATGCGTTT 59.531 47.619 0.00 0.00 0.00 3.60
36 37 2.476185 CGGAGACCAATCAATGCGTTTC 60.476 50.000 0.00 0.00 0.00 2.78
69 70 0.171903 TAGCTCAAACTACGGACGCC 59.828 55.000 0.00 0.00 0.00 5.68
85 86 3.375922 GGACGCCGGATGATAAAAAGAAA 59.624 43.478 5.05 0.00 0.00 2.52
86 87 4.036380 GGACGCCGGATGATAAAAAGAAAT 59.964 41.667 5.05 0.00 0.00 2.17
111 112 1.144969 GTGCTGCACGCTTGTAGTTA 58.855 50.000 17.93 0.00 37.74 2.24
112 113 1.732259 GTGCTGCACGCTTGTAGTTAT 59.268 47.619 17.93 0.00 37.74 1.89
115 116 3.163594 GCTGCACGCTTGTAGTTATTTG 58.836 45.455 9.91 0.00 37.74 2.32
121 122 4.378616 CACGCTTGTAGTTATTTGTTGCAC 59.621 41.667 0.00 0.00 0.00 4.57
144 145 5.843684 TCAACCGGTTGCAGCTATAGCTC 62.844 52.174 37.21 18.22 43.08 4.09
169 170 3.758023 CTGTTTCAGCTGAGAGAGAGAGA 59.242 47.826 22.76 0.13 0.00 3.10
170 171 3.758023 TGTTTCAGCTGAGAGAGAGAGAG 59.242 47.826 17.43 0.00 0.00 3.20
172 173 3.548745 TCAGCTGAGAGAGAGAGAGAG 57.451 52.381 13.74 0.00 0.00 3.20
173 174 3.106827 TCAGCTGAGAGAGAGAGAGAGA 58.893 50.000 13.74 0.00 0.00 3.10
174 175 3.133542 TCAGCTGAGAGAGAGAGAGAGAG 59.866 52.174 13.74 0.00 0.00 3.20
175 176 3.133542 CAGCTGAGAGAGAGAGAGAGAGA 59.866 52.174 8.42 0.00 0.00 3.10
176 177 3.387374 AGCTGAGAGAGAGAGAGAGAGAG 59.613 52.174 0.00 0.00 0.00 3.20
178 179 4.501229 GCTGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
179 180 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
180 181 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
181 182 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
182 183 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
183 184 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
184 185 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
185 186 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
186 187 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
187 188 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
188 189 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
190 191 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
191 192 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
192 193 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
193 194 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
194 195 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
195 196 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
197 198 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
201 202 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
202 203 6.019656 AGAGAGAGAGAGAGAGAGAGAGTA 57.980 45.833 0.00 0.00 0.00 2.59
203 204 5.830991 AGAGAGAGAGAGAGAGAGAGAGTAC 59.169 48.000 0.00 0.00 0.00 2.73
204 205 4.580995 AGAGAGAGAGAGAGAGAGAGTACG 59.419 50.000 0.00 0.00 0.00 3.67
206 207 3.031736 AGAGAGAGAGAGAGAGTACGCT 58.968 50.000 0.00 0.00 0.00 5.07
208 209 2.764010 AGAGAGAGAGAGAGTACGCTCA 59.236 50.000 25.69 0.00 43.57 4.26
209 210 2.864343 GAGAGAGAGAGAGTACGCTCAC 59.136 54.545 25.69 20.15 43.57 3.51
210 211 2.500098 AGAGAGAGAGAGTACGCTCACT 59.500 50.000 25.69 24.11 43.34 3.41
211 212 3.055385 AGAGAGAGAGAGTACGCTCACTT 60.055 47.826 25.69 15.63 41.64 3.16
212 213 3.267483 AGAGAGAGAGTACGCTCACTTC 58.733 50.000 25.69 18.74 41.59 3.01
213 214 2.353579 GAGAGAGAGTACGCTCACTTCC 59.646 54.545 25.69 11.89 41.59 3.46
215 216 2.353579 GAGAGAGTACGCTCACTTCCTC 59.646 54.545 25.69 11.49 41.59 3.71
217 218 2.353579 GAGAGTACGCTCACTTCCTCTC 59.646 54.545 20.26 3.99 44.00 3.20
218 219 1.402613 GAGTACGCTCACTTCCTCTCC 59.597 57.143 0.00 0.00 41.29 3.71
219 220 0.099082 GTACGCTCACTTCCTCTCCG 59.901 60.000 0.00 0.00 0.00 4.63
220 221 0.322277 TACGCTCACTTCCTCTCCGT 60.322 55.000 0.00 0.00 0.00 4.69
221 222 1.137825 CGCTCACTTCCTCTCCGTC 59.862 63.158 0.00 0.00 0.00 4.79
222 223 1.513622 GCTCACTTCCTCTCCGTCC 59.486 63.158 0.00 0.00 0.00 4.79
223 224 1.251527 GCTCACTTCCTCTCCGTCCA 61.252 60.000 0.00 0.00 0.00 4.02
224 225 1.257743 CTCACTTCCTCTCCGTCCAA 58.742 55.000 0.00 0.00 0.00 3.53
225 226 1.827969 CTCACTTCCTCTCCGTCCAAT 59.172 52.381 0.00 0.00 0.00 3.16
226 227 1.825474 TCACTTCCTCTCCGTCCAATC 59.175 52.381 0.00 0.00 0.00 2.67
227 228 1.134670 CACTTCCTCTCCGTCCAATCC 60.135 57.143 0.00 0.00 0.00 3.01
228 229 1.195115 CTTCCTCTCCGTCCAATCCA 58.805 55.000 0.00 0.00 0.00 3.41
229 230 1.765314 CTTCCTCTCCGTCCAATCCAT 59.235 52.381 0.00 0.00 0.00 3.41
230 231 1.123077 TCCTCTCCGTCCAATCCATG 58.877 55.000 0.00 0.00 0.00 3.66
231 232 1.123077 CCTCTCCGTCCAATCCATGA 58.877 55.000 0.00 0.00 0.00 3.07
232 233 1.486310 CCTCTCCGTCCAATCCATGAA 59.514 52.381 0.00 0.00 0.00 2.57
233 234 2.555199 CTCTCCGTCCAATCCATGAAC 58.445 52.381 0.00 0.00 0.00 3.18
234 235 2.169352 CTCTCCGTCCAATCCATGAACT 59.831 50.000 0.00 0.00 0.00 3.01
235 236 2.093500 TCTCCGTCCAATCCATGAACTG 60.093 50.000 0.00 0.00 0.00 3.16
249 250 5.227238 CATGAACTGGATGCAAACTACTC 57.773 43.478 0.00 0.00 0.00 2.59
250 251 3.674997 TGAACTGGATGCAAACTACTCC 58.325 45.455 0.00 0.00 0.00 3.85
251 252 2.789409 ACTGGATGCAAACTACTCCC 57.211 50.000 0.00 0.00 0.00 4.30
252 253 2.269940 ACTGGATGCAAACTACTCCCT 58.730 47.619 0.00 0.00 0.00 4.20
253 254 2.237392 ACTGGATGCAAACTACTCCCTC 59.763 50.000 0.00 0.00 0.00 4.30
254 255 1.559682 TGGATGCAAACTACTCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
255 256 1.559682 GGATGCAAACTACTCCCTCCA 59.440 52.381 0.00 0.00 0.00 3.86
256 257 2.173569 GGATGCAAACTACTCCCTCCAT 59.826 50.000 0.00 0.00 0.00 3.41
257 258 3.372025 GGATGCAAACTACTCCCTCCATT 60.372 47.826 0.00 0.00 0.00 3.16
258 259 3.806949 TGCAAACTACTCCCTCCATTT 57.193 42.857 0.00 0.00 0.00 2.32
259 260 3.686016 TGCAAACTACTCCCTCCATTTC 58.314 45.455 0.00 0.00 0.00 2.17
260 261 3.330701 TGCAAACTACTCCCTCCATTTCT 59.669 43.478 0.00 0.00 0.00 2.52
261 262 4.534500 TGCAAACTACTCCCTCCATTTCTA 59.466 41.667 0.00 0.00 0.00 2.10
262 263 5.013704 TGCAAACTACTCCCTCCATTTCTAA 59.986 40.000 0.00 0.00 0.00 2.10
263 264 5.944007 GCAAACTACTCCCTCCATTTCTAAA 59.056 40.000 0.00 0.00 0.00 1.85
264 265 6.603599 GCAAACTACTCCCTCCATTTCTAAAT 59.396 38.462 0.00 0.00 0.00 1.40
265 266 7.415653 GCAAACTACTCCCTCCATTTCTAAATG 60.416 40.741 8.21 8.21 44.12 2.32
266 267 6.893020 ACTACTCCCTCCATTTCTAAATGT 57.107 37.500 12.99 0.00 43.24 2.71
267 268 7.989947 ACTACTCCCTCCATTTCTAAATGTA 57.010 36.000 12.99 0.00 43.24 2.29
268 269 8.388656 ACTACTCCCTCCATTTCTAAATGTAA 57.611 34.615 12.99 2.38 43.24 2.41
269 270 8.487028 ACTACTCCCTCCATTTCTAAATGTAAG 58.513 37.037 12.99 9.99 43.24 2.34
270 271 7.272144 ACTCCCTCCATTTCTAAATGTAAGT 57.728 36.000 12.99 6.97 43.24 2.24
271 272 7.339482 ACTCCCTCCATTTCTAAATGTAAGTC 58.661 38.462 12.99 0.00 43.24 3.01
272 273 7.182930 ACTCCCTCCATTTCTAAATGTAAGTCT 59.817 37.037 12.99 0.00 43.24 3.24
273 274 7.928873 TCCCTCCATTTCTAAATGTAAGTCTT 58.071 34.615 12.99 0.00 43.24 3.01
274 275 8.390921 TCCCTCCATTTCTAAATGTAAGTCTTT 58.609 33.333 12.99 0.00 43.24 2.52
275 276 8.462016 CCCTCCATTTCTAAATGTAAGTCTTTG 58.538 37.037 12.99 0.00 43.24 2.77
276 277 9.014297 CCTCCATTTCTAAATGTAAGTCTTTGT 57.986 33.333 12.99 0.00 43.24 2.83
298 299 8.683550 TTGTAGAGATTACACTATGAAACACG 57.316 34.615 0.00 0.00 0.00 4.49
299 300 7.823665 TGTAGAGATTACACTATGAAACACGT 58.176 34.615 0.00 0.00 0.00 4.49
300 301 8.949177 TGTAGAGATTACACTATGAAACACGTA 58.051 33.333 0.00 0.00 0.00 3.57
301 302 9.219497 GTAGAGATTACACTATGAAACACGTAC 57.781 37.037 0.00 0.00 0.00 3.67
302 303 6.965500 AGAGATTACACTATGAAACACGTACG 59.035 38.462 15.01 15.01 0.00 3.67
303 304 6.032094 AGATTACACTATGAAACACGTACGG 58.968 40.000 21.06 11.05 0.00 4.02
304 305 3.921119 ACACTATGAAACACGTACGGA 57.079 42.857 21.06 0.00 0.00 4.69
305 306 4.445452 ACACTATGAAACACGTACGGAT 57.555 40.909 21.06 3.70 0.00 4.18
306 307 4.171005 ACACTATGAAACACGTACGGATG 58.829 43.478 21.06 12.24 0.00 3.51
307 308 4.171005 CACTATGAAACACGTACGGATGT 58.829 43.478 21.06 12.94 0.00 3.06
308 309 5.106197 ACACTATGAAACACGTACGGATGTA 60.106 40.000 21.06 1.43 0.00 2.29
309 310 5.975344 CACTATGAAACACGTACGGATGTAT 59.025 40.000 21.06 8.76 32.11 2.29
310 311 7.134163 CACTATGAAACACGTACGGATGTATA 58.866 38.462 21.06 9.38 32.11 1.47
311 312 7.112565 CACTATGAAACACGTACGGATGTATAC 59.887 40.741 21.06 10.56 32.11 1.47
312 313 5.307926 TGAAACACGTACGGATGTATACA 57.692 39.130 21.06 8.27 32.11 2.29
313 314 5.707931 TGAAACACGTACGGATGTATACAA 58.292 37.500 21.06 0.00 32.11 2.41
314 315 6.155136 TGAAACACGTACGGATGTATACAAA 58.845 36.000 21.06 0.00 32.11 2.83
315 316 6.812656 TGAAACACGTACGGATGTATACAAAT 59.187 34.615 21.06 0.00 32.11 2.32
316 317 6.578020 AACACGTACGGATGTATACAAATG 57.422 37.500 21.06 6.18 32.11 2.32
317 318 4.505191 ACACGTACGGATGTATACAAATGC 59.495 41.667 21.06 0.00 32.11 3.56
318 319 4.504826 CACGTACGGATGTATACAAATGCA 59.495 41.667 21.06 0.00 32.11 3.96
319 320 5.176774 CACGTACGGATGTATACAAATGCAT 59.823 40.000 21.06 0.00 40.65 3.96
320 321 5.756347 ACGTACGGATGTATACAAATGCATT 59.244 36.000 21.06 5.99 38.39 3.56
321 322 6.259167 ACGTACGGATGTATACAAATGCATTT 59.741 34.615 18.99 18.99 38.39 2.32
322 323 7.129622 CGTACGGATGTATACAAATGCATTTT 58.870 34.615 21.95 15.06 38.39 1.82
323 324 8.277018 CGTACGGATGTATACAAATGCATTTTA 58.723 33.333 21.95 16.54 38.39 1.52
324 325 9.594038 GTACGGATGTATACAAATGCATTTTAG 57.406 33.333 21.95 14.13 38.39 1.85
325 326 7.138736 ACGGATGTATACAAATGCATTTTAGC 58.861 34.615 21.95 10.97 38.39 3.09
326 327 7.013274 ACGGATGTATACAAATGCATTTTAGCT 59.987 33.333 21.95 9.68 38.39 3.32
327 328 7.535258 CGGATGTATACAAATGCATTTTAGCTC 59.465 37.037 21.95 12.70 38.39 4.09
328 329 8.571336 GGATGTATACAAATGCATTTTAGCTCT 58.429 33.333 21.95 4.91 38.39 4.09
335 336 8.284945 ACAAATGCATTTTAGCTCTAGATTCA 57.715 30.769 21.95 0.00 34.99 2.57
337 338 8.404000 CAAATGCATTTTAGCTCTAGATTCACT 58.596 33.333 21.95 0.00 34.99 3.41
339 340 6.643388 TGCATTTTAGCTCTAGATTCACTCA 58.357 36.000 0.00 0.00 34.99 3.41
346 347 5.743117 AGCTCTAGATTCACTCATTTTGCT 58.257 37.500 0.00 0.00 0.00 3.91
352 353 9.453572 TCTAGATTCACTCATTTTGCTTTGTAT 57.546 29.630 0.00 0.00 0.00 2.29
353 354 9.499585 CTAGATTCACTCATTTTGCTTTGTATG 57.500 33.333 0.00 0.00 0.00 2.39
355 356 9.013229 AGATTCACTCATTTTGCTTTGTATGTA 57.987 29.630 0.00 0.00 0.00 2.29
356 357 9.282247 GATTCACTCATTTTGCTTTGTATGTAG 57.718 33.333 0.00 0.00 0.00 2.74
359 360 7.023575 CACTCATTTTGCTTTGTATGTAGTCC 58.976 38.462 0.00 0.00 0.00 3.85
360 361 6.714810 ACTCATTTTGCTTTGTATGTAGTCCA 59.285 34.615 0.00 0.00 0.00 4.02
362 363 8.800370 TCATTTTGCTTTGTATGTAGTCCATA 57.200 30.769 0.00 0.00 34.86 2.74
367 368 6.941857 TGCTTTGTATGTAGTCCATAGTGAA 58.058 36.000 0.00 0.00 36.71 3.18
369 370 8.046708 TGCTTTGTATGTAGTCCATAGTGAAAT 58.953 33.333 0.00 0.00 36.71 2.17
370 371 8.552034 GCTTTGTATGTAGTCCATAGTGAAATC 58.448 37.037 0.00 0.00 36.71 2.17
371 372 8.958119 TTTGTATGTAGTCCATAGTGAAATCC 57.042 34.615 0.00 0.00 36.71 3.01
372 373 7.062749 TGTATGTAGTCCATAGTGAAATCCC 57.937 40.000 0.00 0.00 36.71 3.85
374 375 8.008332 TGTATGTAGTCCATAGTGAAATCCCTA 58.992 37.037 0.00 0.00 36.71 3.53
375 376 6.726490 TGTAGTCCATAGTGAAATCCCTAC 57.274 41.667 0.00 0.00 0.00 3.18
376 377 6.199376 TGTAGTCCATAGTGAAATCCCTACA 58.801 40.000 0.00 0.00 32.27 2.74
377 378 6.670464 TGTAGTCCATAGTGAAATCCCTACAA 59.330 38.462 0.00 0.00 31.91 2.41
378 379 6.636454 AGTCCATAGTGAAATCCCTACAAA 57.364 37.500 0.00 0.00 0.00 2.83
379 380 6.653989 AGTCCATAGTGAAATCCCTACAAAG 58.346 40.000 0.00 0.00 0.00 2.77
381 382 6.539103 GTCCATAGTGAAATCCCTACAAAGAC 59.461 42.308 0.00 0.00 0.00 3.01
385 386 9.838339 CATAGTGAAATCCCTACAAAGACTTAT 57.162 33.333 0.00 0.00 0.00 1.73
400 401 9.379791 ACAAAGACTTATATTTAGAAACGGAGG 57.620 33.333 0.00 0.00 0.00 4.30
403 404 9.819267 AAGACTTATATTTAGAAACGGAGGAAG 57.181 33.333 0.00 0.00 0.00 3.46
479 2262 3.708403 ATCCAAACTGCTCACATGAGA 57.292 42.857 13.15 0.00 44.74 3.27
480 2263 2.771089 TCCAAACTGCTCACATGAGAC 58.229 47.619 13.15 4.94 44.74 3.36
481 2264 2.369860 TCCAAACTGCTCACATGAGACT 59.630 45.455 13.15 0.00 44.74 3.24
484 2267 3.591196 AACTGCTCACATGAGACTCTC 57.409 47.619 13.15 0.00 44.74 3.20
485 2268 2.523245 ACTGCTCACATGAGACTCTCA 58.477 47.619 13.15 11.24 44.74 3.27
486 2269 2.492881 ACTGCTCACATGAGACTCTCAG 59.507 50.000 14.12 11.42 44.08 3.35
487 2270 1.204231 TGCTCACATGAGACTCTCAGC 59.796 52.381 14.12 11.48 44.08 4.26
488 2271 1.477700 GCTCACATGAGACTCTCAGCT 59.522 52.381 14.12 0.00 44.08 4.24
489 2272 2.736081 GCTCACATGAGACTCTCAGCTG 60.736 54.545 14.12 7.63 44.08 4.24
490 2273 2.492881 CTCACATGAGACTCTCAGCTGT 59.507 50.000 14.67 11.27 44.08 4.40
491 2274 2.491298 TCACATGAGACTCTCAGCTGTC 59.509 50.000 14.67 3.54 44.08 3.51
492 2275 2.230750 CACATGAGACTCTCAGCTGTCA 59.769 50.000 14.67 9.29 44.08 3.58
493 2276 2.492881 ACATGAGACTCTCAGCTGTCAG 59.507 50.000 14.67 12.88 44.08 3.51
494 2277 0.887247 TGAGACTCTCAGCTGTCAGC 59.113 55.000 17.48 17.48 42.84 4.26
495 2278 0.173255 GAGACTCTCAGCTGTCAGCC 59.827 60.000 21.32 4.09 43.77 4.85
496 2279 0.541530 AGACTCTCAGCTGTCAGCCA 60.542 55.000 21.32 7.53 43.77 4.75
497 2280 0.389687 GACTCTCAGCTGTCAGCCAC 60.390 60.000 21.32 2.05 43.77 5.01
498 2281 1.445754 CTCTCAGCTGTCAGCCACG 60.446 63.158 21.32 10.40 43.77 4.94
499 2282 2.433838 CTCAGCTGTCAGCCACGG 60.434 66.667 21.32 8.90 43.77 4.94
500 2283 2.917227 TCAGCTGTCAGCCACGGA 60.917 61.111 21.32 11.06 43.77 4.69
501 2284 2.031012 CAGCTGTCAGCCACGGAA 59.969 61.111 21.32 0.00 43.77 4.30
502 2285 1.597854 CAGCTGTCAGCCACGGAAA 60.598 57.895 21.32 0.00 43.77 3.13
503 2286 1.302033 AGCTGTCAGCCACGGAAAG 60.302 57.895 21.32 0.00 43.77 2.62
504 2287 1.301716 GCTGTCAGCCACGGAAAGA 60.302 57.895 14.27 0.00 34.48 2.52
505 2288 0.674895 GCTGTCAGCCACGGAAAGAT 60.675 55.000 14.27 0.00 34.48 2.40
506 2289 1.081892 CTGTCAGCCACGGAAAGATG 58.918 55.000 0.00 0.00 32.23 2.90
507 2290 0.955428 TGTCAGCCACGGAAAGATGC 60.955 55.000 0.00 0.00 0.00 3.91
508 2291 0.674895 GTCAGCCACGGAAAGATGCT 60.675 55.000 0.00 0.00 0.00 3.79
509 2292 0.391661 TCAGCCACGGAAAGATGCTC 60.392 55.000 0.00 0.00 0.00 4.26
510 2293 1.448540 AGCCACGGAAAGATGCTCG 60.449 57.895 0.00 0.00 0.00 5.03
522 2305 2.914777 GATGCTCGAGGGTCCAGTGC 62.915 65.000 15.58 0.00 0.00 4.40
524 2344 3.023949 GCTCGAGGGTCCAGTGCAT 62.024 63.158 15.58 0.00 0.00 3.96
782 3011 1.300156 GCATACATCGCTCTCGCCA 60.300 57.895 0.00 0.00 35.26 5.69
1052 3386 0.391528 TCACACATCATCACCCGCAG 60.392 55.000 0.00 0.00 0.00 5.18
1148 3507 1.227999 ATCGATAACAATGCCGCCGG 61.228 55.000 0.00 0.00 0.00 6.13
1182 3553 2.346365 CAGCAGCAGCACAGGAGA 59.654 61.111 3.17 0.00 45.49 3.71
1209 3580 2.047274 AAGGTGGCCATCGTCACG 60.047 61.111 9.72 0.00 34.93 4.35
1440 3811 1.956170 CGTCCTCTGCAACAACGCT 60.956 57.895 0.00 0.00 0.00 5.07
2046 4471 2.488153 CGTCATCGGCCTGTGATAGATA 59.512 50.000 9.76 0.00 0.00 1.98
2094 4535 1.722636 GGAGGGTAGTACGTGCTCCG 61.723 65.000 10.21 0.00 44.03 4.63
2129 5759 1.724545 ACAGGTTGGCACTAGTGGTA 58.275 50.000 23.95 0.00 0.00 3.25
2208 6130 3.070878 TGGATTTGCCTGGTTTTTCTTCC 59.929 43.478 0.00 0.00 37.63 3.46
2240 6163 2.281139 TTGTCGTGCCGCATGGAA 60.281 55.556 12.66 3.65 37.49 3.53
2393 6344 5.818181 GCGTGTTTGCGATTAAGTAAAAAG 58.182 37.500 0.00 0.00 0.00 2.27
2507 6487 5.890424 GAGAATCTATAGCTAGACGCCTT 57.110 43.478 0.00 0.00 36.81 4.35
2581 6563 2.203294 GGCGGATATGGGGCGTTT 60.203 61.111 0.00 0.00 0.00 3.60
2675 6671 1.338136 CCGGACCCAACTCTAGCCAT 61.338 60.000 0.00 0.00 0.00 4.40
2680 6676 3.372025 GGACCCAACTCTAGCCATTTCAT 60.372 47.826 0.00 0.00 0.00 2.57
2721 6717 4.742201 CACCACCCGAGCTCACCG 62.742 72.222 15.40 0.00 0.00 4.94
2789 6786 1.843368 AACTCCGACCAGTCCGAATA 58.157 50.000 0.00 0.00 0.00 1.75
2809 6807 2.184322 CGACTGGGGTGTCATCCG 59.816 66.667 0.00 0.00 36.82 4.18
2885 6883 1.177256 ATAACGCCTAGCCGACGGAT 61.177 55.000 20.50 15.58 0.00 4.18
2907 6905 4.436998 CTGTCCGGCGTGACTCCC 62.437 72.222 22.60 4.20 36.21 4.30
2962 6962 2.762043 TGGATCATCGCGGTCCCA 60.762 61.111 6.13 3.02 0.00 4.37
2964 6964 2.797278 GGATCATCGCGGTCCCAGT 61.797 63.158 6.13 0.00 0.00 4.00
2968 6971 2.442272 ATCGCGGTCCCAGTAGCT 60.442 61.111 6.13 0.00 0.00 3.32
2985 6988 7.388460 CAGTAGCTGGAAAATTTCTCATTCT 57.612 36.000 5.65 5.45 0.00 2.40
3000 7005 1.482182 CATTCTCCATCACCAGTCGGA 59.518 52.381 0.00 0.00 35.59 4.55
3054 7060 2.016905 CCGTGGGAAGGAGAGGATAT 57.983 55.000 0.00 0.00 0.00 1.63
3203 10115 2.772691 CGCCCTCACCCGAGAGTAC 61.773 68.421 0.00 0.00 42.34 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.057596 TGGTCTCCGTTTCATCAAAATGC 60.058 43.478 0.00 0.00 33.28 3.56
3 4 5.476599 TGATTGGTCTCCGTTTCATCAAAAT 59.523 36.000 0.00 0.00 0.00 1.82
5 6 4.393834 TGATTGGTCTCCGTTTCATCAAA 58.606 39.130 0.00 0.00 0.00 2.69
6 7 4.014569 TGATTGGTCTCCGTTTCATCAA 57.985 40.909 0.00 0.00 0.00 2.57
7 8 3.694043 TGATTGGTCTCCGTTTCATCA 57.306 42.857 0.00 0.00 0.00 3.07
8 9 4.731773 GCATTGATTGGTCTCCGTTTCATC 60.732 45.833 0.00 0.00 0.00 2.92
9 10 3.129287 GCATTGATTGGTCTCCGTTTCAT 59.871 43.478 0.00 0.00 0.00 2.57
10 11 2.487762 GCATTGATTGGTCTCCGTTTCA 59.512 45.455 0.00 0.00 0.00 2.69
11 12 2.476185 CGCATTGATTGGTCTCCGTTTC 60.476 50.000 0.00 0.00 0.00 2.78
12 13 1.468520 CGCATTGATTGGTCTCCGTTT 59.531 47.619 0.00 0.00 0.00 3.60
13 14 1.086696 CGCATTGATTGGTCTCCGTT 58.913 50.000 0.00 0.00 0.00 4.44
14 15 0.036388 ACGCATTGATTGGTCTCCGT 60.036 50.000 0.00 0.00 0.00 4.69
15 16 1.086696 AACGCATTGATTGGTCTCCG 58.913 50.000 0.00 0.00 0.00 4.63
16 17 2.487762 TGAAACGCATTGATTGGTCTCC 59.512 45.455 0.00 0.00 0.00 3.71
17 18 3.829886 TGAAACGCATTGATTGGTCTC 57.170 42.857 0.00 0.00 0.00 3.36
18 19 3.507233 ACATGAAACGCATTGATTGGTCT 59.493 39.130 0.00 0.00 34.15 3.85
19 20 3.609373 CACATGAAACGCATTGATTGGTC 59.391 43.478 0.00 0.00 34.15 4.02
20 21 3.577667 CACATGAAACGCATTGATTGGT 58.422 40.909 0.00 0.00 34.15 3.67
21 22 2.924926 CCACATGAAACGCATTGATTGG 59.075 45.455 0.00 0.00 34.15 3.16
22 23 2.924926 CCCACATGAAACGCATTGATTG 59.075 45.455 0.00 0.00 34.15 2.67
23 24 2.674747 GCCCACATGAAACGCATTGATT 60.675 45.455 0.00 0.00 34.15 2.57
24 25 1.135024 GCCCACATGAAACGCATTGAT 60.135 47.619 0.00 0.00 34.15 2.57
25 26 0.243365 GCCCACATGAAACGCATTGA 59.757 50.000 0.00 0.00 34.15 2.57
26 27 0.038435 TGCCCACATGAAACGCATTG 60.038 50.000 0.00 0.00 34.15 2.82
27 28 0.896923 ATGCCCACATGAAACGCATT 59.103 45.000 0.00 0.00 36.82 3.56
28 29 2.582272 ATGCCCACATGAAACGCAT 58.418 47.368 0.00 4.11 37.85 4.73
29 30 4.093966 ATGCCCACATGAAACGCA 57.906 50.000 0.00 1.58 34.35 5.24
69 70 5.065988 ACGACCCATTTCTTTTTATCATCCG 59.934 40.000 0.00 0.00 0.00 4.18
71 72 5.743872 GCACGACCCATTTCTTTTTATCATC 59.256 40.000 0.00 0.00 0.00 2.92
72 73 5.418840 AGCACGACCCATTTCTTTTTATCAT 59.581 36.000 0.00 0.00 0.00 2.45
73 74 4.764823 AGCACGACCCATTTCTTTTTATCA 59.235 37.500 0.00 0.00 0.00 2.15
74 75 5.095490 CAGCACGACCCATTTCTTTTTATC 58.905 41.667 0.00 0.00 0.00 1.75
75 76 4.618227 GCAGCACGACCCATTTCTTTTTAT 60.618 41.667 0.00 0.00 0.00 1.40
76 77 3.305064 GCAGCACGACCCATTTCTTTTTA 60.305 43.478 0.00 0.00 0.00 1.52
77 78 2.545742 GCAGCACGACCCATTTCTTTTT 60.546 45.455 0.00 0.00 0.00 1.94
121 122 2.205074 CTATAGCTGCAACCGGTTGAG 58.795 52.381 43.76 34.72 42.93 3.02
158 159 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
159 160 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
160 161 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
162 163 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
163 164 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
164 165 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
165 166 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
166 167 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
167 168 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
169 170 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
170 171 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
172 173 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
173 174 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
174 175 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
175 176 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
176 177 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
178 179 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
179 180 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
180 181 5.278071 CGTACTCTCTCTCTCTCTCTCTCTC 60.278 52.000 0.00 0.00 0.00 3.20
181 182 4.580995 CGTACTCTCTCTCTCTCTCTCTCT 59.419 50.000 0.00 0.00 0.00 3.10
182 183 4.793353 GCGTACTCTCTCTCTCTCTCTCTC 60.793 54.167 0.00 0.00 0.00 3.20
183 184 3.068307 GCGTACTCTCTCTCTCTCTCTCT 59.932 52.174 0.00 0.00 0.00 3.10
184 185 3.068307 AGCGTACTCTCTCTCTCTCTCTC 59.932 52.174 0.00 0.00 0.00 3.20
185 186 3.031736 AGCGTACTCTCTCTCTCTCTCT 58.968 50.000 0.00 0.00 0.00 3.10
186 187 3.181479 TGAGCGTACTCTCTCTCTCTCTC 60.181 52.174 13.72 0.00 43.85 3.20
187 188 2.764010 TGAGCGTACTCTCTCTCTCTCT 59.236 50.000 13.72 0.00 43.85 3.10
188 189 2.864343 GTGAGCGTACTCTCTCTCTCTC 59.136 54.545 13.72 0.00 43.85 3.20
190 191 2.901249 AGTGAGCGTACTCTCTCTCTC 58.099 52.381 13.72 3.19 41.77 3.20
191 192 3.267483 GAAGTGAGCGTACTCTCTCTCT 58.733 50.000 15.65 10.28 44.08 3.10
192 193 2.353579 GGAAGTGAGCGTACTCTCTCTC 59.646 54.545 15.65 10.25 44.08 3.20
193 194 2.026636 AGGAAGTGAGCGTACTCTCTCT 60.027 50.000 13.72 12.21 44.08 3.10
194 195 2.353579 GAGGAAGTGAGCGTACTCTCTC 59.646 54.545 13.72 10.18 44.08 3.20
195 196 2.026636 AGAGGAAGTGAGCGTACTCTCT 60.027 50.000 13.72 8.05 46.20 3.10
197 198 2.361789 GAGAGGAAGTGAGCGTACTCT 58.638 52.381 0.00 0.00 43.85 3.24
201 202 0.322277 ACGGAGAGGAAGTGAGCGTA 60.322 55.000 0.00 0.00 0.00 4.42
202 203 1.587933 GACGGAGAGGAAGTGAGCGT 61.588 60.000 0.00 0.00 0.00 5.07
203 204 1.137825 GACGGAGAGGAAGTGAGCG 59.862 63.158 0.00 0.00 0.00 5.03
204 205 1.251527 TGGACGGAGAGGAAGTGAGC 61.252 60.000 0.00 0.00 0.00 4.26
206 207 1.825474 GATTGGACGGAGAGGAAGTGA 59.175 52.381 0.00 0.00 0.00 3.41
208 209 1.196012 GGATTGGACGGAGAGGAAGT 58.804 55.000 0.00 0.00 0.00 3.01
209 210 1.195115 TGGATTGGACGGAGAGGAAG 58.805 55.000 0.00 0.00 0.00 3.46
210 211 1.486310 CATGGATTGGACGGAGAGGAA 59.514 52.381 0.00 0.00 0.00 3.36
211 212 1.123077 CATGGATTGGACGGAGAGGA 58.877 55.000 0.00 0.00 0.00 3.71
212 213 1.123077 TCATGGATTGGACGGAGAGG 58.877 55.000 0.00 0.00 0.00 3.69
213 214 2.169352 AGTTCATGGATTGGACGGAGAG 59.831 50.000 0.00 0.00 39.03 3.20
215 216 2.283298 CAGTTCATGGATTGGACGGAG 58.717 52.381 0.00 0.00 39.03 4.63
227 228 4.095483 GGAGTAGTTTGCATCCAGTTCATG 59.905 45.833 0.00 0.00 0.00 3.07
228 229 4.265073 GGAGTAGTTTGCATCCAGTTCAT 58.735 43.478 0.00 0.00 0.00 2.57
229 230 3.559171 GGGAGTAGTTTGCATCCAGTTCA 60.559 47.826 4.26 0.00 33.24 3.18
230 231 3.010420 GGGAGTAGTTTGCATCCAGTTC 58.990 50.000 4.26 0.00 33.24 3.01
231 232 2.644798 AGGGAGTAGTTTGCATCCAGTT 59.355 45.455 4.26 0.00 33.24 3.16
232 233 2.237392 GAGGGAGTAGTTTGCATCCAGT 59.763 50.000 4.26 0.00 33.24 4.00
233 234 2.420687 GGAGGGAGTAGTTTGCATCCAG 60.421 54.545 4.26 0.00 38.93 3.86
234 235 1.559682 GGAGGGAGTAGTTTGCATCCA 59.440 52.381 4.26 0.00 38.93 3.41
235 236 1.559682 TGGAGGGAGTAGTTTGCATCC 59.440 52.381 0.00 0.00 39.46 3.51
236 237 3.567478 ATGGAGGGAGTAGTTTGCATC 57.433 47.619 0.00 0.00 0.00 3.91
237 238 4.018050 AGAAATGGAGGGAGTAGTTTGCAT 60.018 41.667 0.00 0.00 0.00 3.96
238 239 3.330701 AGAAATGGAGGGAGTAGTTTGCA 59.669 43.478 0.00 0.00 0.00 4.08
239 240 3.956744 AGAAATGGAGGGAGTAGTTTGC 58.043 45.455 0.00 0.00 0.00 3.68
240 241 7.989826 CATTTAGAAATGGAGGGAGTAGTTTG 58.010 38.462 7.03 0.00 41.54 2.93
272 273 9.135843 CGTGTTTCATAGTGTAATCTCTACAAA 57.864 33.333 0.00 0.00 0.00 2.83
273 274 8.301720 ACGTGTTTCATAGTGTAATCTCTACAA 58.698 33.333 0.00 0.00 0.00 2.41
274 275 7.823665 ACGTGTTTCATAGTGTAATCTCTACA 58.176 34.615 0.00 0.00 0.00 2.74
275 276 9.219497 GTACGTGTTTCATAGTGTAATCTCTAC 57.781 37.037 0.00 0.00 0.00 2.59
276 277 8.118607 CGTACGTGTTTCATAGTGTAATCTCTA 58.881 37.037 7.22 0.00 0.00 2.43
277 278 6.965500 CGTACGTGTTTCATAGTGTAATCTCT 59.035 38.462 7.22 0.00 0.00 3.10
278 279 6.195983 CCGTACGTGTTTCATAGTGTAATCTC 59.804 42.308 15.21 0.00 0.00 2.75
279 280 6.032094 CCGTACGTGTTTCATAGTGTAATCT 58.968 40.000 15.21 0.00 0.00 2.40
280 281 6.029607 TCCGTACGTGTTTCATAGTGTAATC 58.970 40.000 15.21 0.00 0.00 1.75
281 282 5.953183 TCCGTACGTGTTTCATAGTGTAAT 58.047 37.500 15.21 0.00 0.00 1.89
282 283 5.369685 TCCGTACGTGTTTCATAGTGTAA 57.630 39.130 15.21 0.00 0.00 2.41
283 284 5.106197 ACATCCGTACGTGTTTCATAGTGTA 60.106 40.000 15.21 0.00 0.00 2.90
284 285 3.921119 TCCGTACGTGTTTCATAGTGT 57.079 42.857 15.21 0.00 0.00 3.55
285 286 4.171005 ACATCCGTACGTGTTTCATAGTG 58.829 43.478 15.21 0.00 0.00 2.74
286 287 4.445452 ACATCCGTACGTGTTTCATAGT 57.555 40.909 15.21 0.00 0.00 2.12
287 288 7.134163 TGTATACATCCGTACGTGTTTCATAG 58.866 38.462 15.54 0.00 0.00 2.23
288 289 7.025485 TGTATACATCCGTACGTGTTTCATA 57.975 36.000 15.54 6.41 0.00 2.15
289 290 5.893687 TGTATACATCCGTACGTGTTTCAT 58.106 37.500 15.54 7.25 0.00 2.57
290 291 5.307926 TGTATACATCCGTACGTGTTTCA 57.692 39.130 15.54 10.20 0.00 2.69
291 292 6.630676 TTTGTATACATCCGTACGTGTTTC 57.369 37.500 15.54 8.22 0.00 2.78
292 293 6.455913 GCATTTGTATACATCCGTACGTGTTT 60.456 38.462 15.54 10.96 0.00 2.83
293 294 5.005971 GCATTTGTATACATCCGTACGTGTT 59.994 40.000 15.54 7.56 0.00 3.32
294 295 4.505191 GCATTTGTATACATCCGTACGTGT 59.495 41.667 15.21 15.00 0.00 4.49
295 296 4.504826 TGCATTTGTATACATCCGTACGTG 59.495 41.667 15.21 9.44 0.00 4.49
296 297 4.684877 TGCATTTGTATACATCCGTACGT 58.315 39.130 15.21 0.00 0.00 3.57
297 298 5.839262 ATGCATTTGTATACATCCGTACG 57.161 39.130 8.69 8.69 0.00 3.67
298 299 9.594038 CTAAAATGCATTTGTATACATCCGTAC 57.406 33.333 24.74 0.00 32.27 3.67
299 300 8.286800 GCTAAAATGCATTTGTATACATCCGTA 58.713 33.333 24.74 8.25 32.27 4.02
300 301 7.013274 AGCTAAAATGCATTTGTATACATCCGT 59.987 33.333 24.74 7.53 34.99 4.69
301 302 7.362662 AGCTAAAATGCATTTGTATACATCCG 58.637 34.615 24.74 3.86 34.99 4.18
302 303 8.571336 AGAGCTAAAATGCATTTGTATACATCC 58.429 33.333 24.74 8.68 34.99 3.51
305 306 9.830975 TCTAGAGCTAAAATGCATTTGTATACA 57.169 29.630 24.74 0.08 34.99 2.29
309 310 9.394767 TGAATCTAGAGCTAAAATGCATTTGTA 57.605 29.630 24.74 16.55 34.99 2.41
310 311 8.186821 GTGAATCTAGAGCTAAAATGCATTTGT 58.813 33.333 24.74 16.33 34.99 2.83
311 312 8.404000 AGTGAATCTAGAGCTAAAATGCATTTG 58.596 33.333 24.74 14.39 34.99 2.32
312 313 8.517062 AGTGAATCTAGAGCTAAAATGCATTT 57.483 30.769 18.99 18.99 34.99 2.32
313 314 7.772292 TGAGTGAATCTAGAGCTAAAATGCATT 59.228 33.333 5.99 5.99 34.99 3.56
314 315 7.278135 TGAGTGAATCTAGAGCTAAAATGCAT 58.722 34.615 0.00 0.00 34.99 3.96
315 316 6.643388 TGAGTGAATCTAGAGCTAAAATGCA 58.357 36.000 0.00 0.00 34.99 3.96
316 317 7.727331 ATGAGTGAATCTAGAGCTAAAATGC 57.273 36.000 0.00 0.00 0.00 3.56
319 320 8.454106 GCAAAATGAGTGAATCTAGAGCTAAAA 58.546 33.333 0.00 0.00 0.00 1.52
320 321 7.826252 AGCAAAATGAGTGAATCTAGAGCTAAA 59.174 33.333 0.00 0.00 0.00 1.85
321 322 7.334090 AGCAAAATGAGTGAATCTAGAGCTAA 58.666 34.615 0.00 0.00 0.00 3.09
322 323 6.882656 AGCAAAATGAGTGAATCTAGAGCTA 58.117 36.000 0.00 0.00 0.00 3.32
323 324 5.743117 AGCAAAATGAGTGAATCTAGAGCT 58.257 37.500 0.00 0.00 0.00 4.09
324 325 6.434018 AAGCAAAATGAGTGAATCTAGAGC 57.566 37.500 0.00 0.00 0.00 4.09
325 326 7.814642 ACAAAGCAAAATGAGTGAATCTAGAG 58.185 34.615 0.00 0.00 0.00 2.43
326 327 7.750229 ACAAAGCAAAATGAGTGAATCTAGA 57.250 32.000 0.00 0.00 0.00 2.43
327 328 9.499585 CATACAAAGCAAAATGAGTGAATCTAG 57.500 33.333 0.00 0.00 0.00 2.43
328 329 9.013229 ACATACAAAGCAAAATGAGTGAATCTA 57.987 29.630 0.00 0.00 0.00 1.98
329 330 7.889469 ACATACAAAGCAAAATGAGTGAATCT 58.111 30.769 0.00 0.00 0.00 2.40
332 333 8.165239 ACTACATACAAAGCAAAATGAGTGAA 57.835 30.769 0.00 0.00 0.00 3.18
334 335 7.023575 GGACTACATACAAAGCAAAATGAGTG 58.976 38.462 0.00 0.00 0.00 3.51
335 336 6.714810 TGGACTACATACAAAGCAAAATGAGT 59.285 34.615 0.00 0.00 0.00 3.41
337 338 7.701539 ATGGACTACATACAAAGCAAAATGA 57.298 32.000 0.00 0.00 38.26 2.57
339 340 8.677300 CACTATGGACTACATACAAAGCAAAAT 58.323 33.333 0.00 0.00 41.03 1.82
344 345 7.843490 TTTCACTATGGACTACATACAAAGC 57.157 36.000 0.00 0.00 41.03 3.51
346 347 7.990886 GGGATTTCACTATGGACTACATACAAA 59.009 37.037 0.00 0.00 41.03 2.83
352 353 6.199376 TGTAGGGATTTCACTATGGACTACA 58.801 40.000 0.00 0.00 33.90 2.74
353 354 6.726490 TGTAGGGATTTCACTATGGACTAC 57.274 41.667 0.00 0.00 33.90 2.73
355 356 6.443849 TCTTTGTAGGGATTTCACTATGGACT 59.556 38.462 0.00 0.00 33.90 3.85
356 357 6.539103 GTCTTTGTAGGGATTTCACTATGGAC 59.461 42.308 0.00 0.00 33.90 4.02
359 360 9.838339 ATAAGTCTTTGTAGGGATTTCACTATG 57.162 33.333 0.00 0.00 33.90 2.23
374 375 9.379791 CCTCCGTTTCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
375 376 9.595823 TCCTCCGTTTCTAAATATAAGTCTTTG 57.404 33.333 0.00 0.00 0.00 2.77
377 378 9.819267 CTTCCTCCGTTTCTAAATATAAGTCTT 57.181 33.333 0.00 0.00 0.00 3.01
378 379 8.979534 ACTTCCTCCGTTTCTAAATATAAGTCT 58.020 33.333 0.00 0.00 0.00 3.24
443 786 7.530010 CAGTTTGGATACCACTTTAACATGAG 58.470 38.462 0.00 0.00 30.78 2.90
479 2262 1.670590 GTGGCTGACAGCTGAGAGT 59.329 57.895 25.92 0.00 41.99 3.24
480 2263 1.445754 CGTGGCTGACAGCTGAGAG 60.446 63.158 25.92 15.95 41.99 3.20
481 2264 2.653115 CGTGGCTGACAGCTGAGA 59.347 61.111 25.92 4.88 41.99 3.27
484 2267 1.572085 CTTTCCGTGGCTGACAGCTG 61.572 60.000 25.92 13.48 41.99 4.24
485 2268 1.302033 CTTTCCGTGGCTGACAGCT 60.302 57.895 25.92 0.00 41.99 4.24
486 2269 0.674895 ATCTTTCCGTGGCTGACAGC 60.675 55.000 19.55 19.55 41.46 4.40
487 2270 1.081892 CATCTTTCCGTGGCTGACAG 58.918 55.000 0.00 0.00 0.00 3.51
488 2271 0.955428 GCATCTTTCCGTGGCTGACA 60.955 55.000 0.00 0.00 0.00 3.58
489 2272 0.674895 AGCATCTTTCCGTGGCTGAC 60.675 55.000 0.00 0.00 32.76 3.51
490 2273 0.391661 GAGCATCTTTCCGTGGCTGA 60.392 55.000 0.00 0.00 34.44 4.26
491 2274 1.699656 CGAGCATCTTTCCGTGGCTG 61.700 60.000 0.00 0.00 34.44 4.85
492 2275 1.448540 CGAGCATCTTTCCGTGGCT 60.449 57.895 0.00 0.00 37.56 4.75
493 2276 1.424493 CTCGAGCATCTTTCCGTGGC 61.424 60.000 0.00 0.00 0.00 5.01
494 2277 0.807667 CCTCGAGCATCTTTCCGTGG 60.808 60.000 6.99 0.00 0.00 4.94
495 2278 0.807667 CCCTCGAGCATCTTTCCGTG 60.808 60.000 6.99 0.00 0.00 4.94
496 2279 1.258445 ACCCTCGAGCATCTTTCCGT 61.258 55.000 6.99 0.00 0.00 4.69
497 2280 0.528684 GACCCTCGAGCATCTTTCCG 60.529 60.000 6.99 0.00 0.00 4.30
498 2281 0.179070 GGACCCTCGAGCATCTTTCC 60.179 60.000 6.99 1.90 0.00 3.13
499 2282 0.537188 TGGACCCTCGAGCATCTTTC 59.463 55.000 6.99 0.00 0.00 2.62
500 2283 0.539051 CTGGACCCTCGAGCATCTTT 59.461 55.000 6.99 0.00 0.00 2.52
501 2284 0.616111 ACTGGACCCTCGAGCATCTT 60.616 55.000 6.99 0.00 0.00 2.40
502 2285 1.000993 ACTGGACCCTCGAGCATCT 59.999 57.895 6.99 0.00 0.00 2.90
503 2286 1.142748 CACTGGACCCTCGAGCATC 59.857 63.158 6.99 6.25 0.00 3.91
504 2287 3.023949 GCACTGGACCCTCGAGCAT 62.024 63.158 6.99 0.00 0.00 3.79
505 2288 3.695606 GCACTGGACCCTCGAGCA 61.696 66.667 6.99 0.00 0.00 4.26
506 2289 2.527951 AATGCACTGGACCCTCGAGC 62.528 60.000 6.99 0.00 0.00 5.03
507 2290 0.824109 TAATGCACTGGACCCTCGAG 59.176 55.000 5.13 5.13 0.00 4.04
508 2291 1.066430 GTTAATGCACTGGACCCTCGA 60.066 52.381 0.00 0.00 0.00 4.04
509 2292 1.066143 AGTTAATGCACTGGACCCTCG 60.066 52.381 0.00 0.00 0.00 4.63
510 2293 2.789409 AGTTAATGCACTGGACCCTC 57.211 50.000 0.00 0.00 0.00 4.30
782 3011 0.821517 TCACCTACGTTCATGGCGAT 59.178 50.000 15.39 4.89 0.00 4.58
951 3275 2.764572 CGTCTTTATATAGGGGCCGGAT 59.235 50.000 5.05 0.00 0.00 4.18
985 3309 1.305046 ACGGGAGTGGGACGAGATT 60.305 57.895 0.00 0.00 44.82 2.40
1056 3390 2.440247 ATGGCTAAAGGGCGGTGC 60.440 61.111 0.00 0.00 44.11 5.01
1057 3391 1.077787 TCATGGCTAAAGGGCGGTG 60.078 57.895 0.00 0.00 44.11 4.94
1058 3392 1.077716 GTCATGGCTAAAGGGCGGT 60.078 57.895 0.00 0.00 44.11 5.68
1059 3393 1.823899 GGTCATGGCTAAAGGGCGG 60.824 63.158 0.00 0.00 44.11 6.13
1065 3401 0.179111 CGAGAGCGGTCATGGCTAAA 60.179 55.000 18.15 0.00 41.72 1.85
1128 3475 0.110688 CGGCGGCATTGTTATCGATG 60.111 55.000 8.54 0.00 38.22 3.84
1129 3476 1.227999 CCGGCGGCATTGTTATCGAT 61.228 55.000 15.42 2.16 0.00 3.59
1133 3480 2.770589 GCACCGGCGGCATTGTTAT 61.771 57.895 28.71 0.00 0.00 1.89
1134 3481 3.436055 GCACCGGCGGCATTGTTA 61.436 61.111 28.71 0.00 0.00 2.41
1182 3553 2.936032 GCCACCTTCCCCTCCAGT 60.936 66.667 0.00 0.00 0.00 4.00
1413 3784 3.374402 CAGAGGACGTCCAGCCGT 61.374 66.667 35.00 15.47 45.18 5.68
1612 4007 4.082523 CACGATGGTCCCACCGCT 62.083 66.667 0.00 0.00 42.58 5.52
1622 4023 4.429212 TCGCCACCGACACGATGG 62.429 66.667 0.00 0.00 38.82 3.51
2046 4471 4.336889 TCTCAATCGGTTTGACTTCACT 57.663 40.909 0.00 0.00 39.44 3.41
2094 4535 1.732259 CCTGTACTTGATTGCGACACC 59.268 52.381 0.00 0.00 0.00 4.16
2129 5759 5.189934 ACCAGCAGCTAATTACTCCTACTTT 59.810 40.000 0.00 0.00 0.00 2.66
2208 6130 0.110373 GACAACGGTTTAAGCGCCAG 60.110 55.000 16.58 8.91 43.79 4.85
2371 6317 7.597643 TTCTTTTTACTTAATCGCAAACACG 57.402 32.000 0.00 0.00 0.00 4.49
2581 6563 1.509463 GACATGACGGACGCACCTA 59.491 57.895 0.00 0.00 36.31 3.08
2675 6671 1.561542 GGAGGGAAGAGGAGCATGAAA 59.438 52.381 0.00 0.00 0.00 2.69
2680 6676 0.616111 GAGTGGAGGGAAGAGGAGCA 60.616 60.000 0.00 0.00 0.00 4.26
2721 6717 1.067582 CGGGAATCGCCAGAGGTAC 59.932 63.158 0.00 0.00 38.95 3.34
2789 6786 1.258445 GGATGACACCCCAGTCGACT 61.258 60.000 13.58 13.58 41.41 4.18
2809 6807 1.973812 GCCTCCTCCAACTTGCACC 60.974 63.158 0.00 0.00 0.00 5.01
2865 6863 4.724022 CGTCGGCTAGGCGTTATT 57.276 55.556 34.02 0.00 44.05 1.40
2885 6883 2.678580 TCACGCCGGACAGATCCA 60.679 61.111 5.05 0.00 46.67 3.41
2962 6962 6.601217 GGAGAATGAGAAATTTTCCAGCTACT 59.399 38.462 5.52 0.05 33.80 2.57
2964 6964 6.484288 TGGAGAATGAGAAATTTTCCAGCTA 58.516 36.000 5.52 0.00 37.37 3.32
2968 6971 6.153340 GGTGATGGAGAATGAGAAATTTTCCA 59.847 38.462 11.43 11.43 43.50 3.53
2976 6979 3.118992 CGACTGGTGATGGAGAATGAGAA 60.119 47.826 0.00 0.00 0.00 2.87
2981 6984 1.482593 GTCCGACTGGTGATGGAGAAT 59.517 52.381 0.00 0.00 36.30 2.40
2985 6988 0.251608 TCTGTCCGACTGGTGATGGA 60.252 55.000 5.66 0.00 36.30 3.41
3000 7005 2.311463 CCGATGGGACTCATAGTCTGT 58.689 52.381 6.99 0.00 44.46 3.41
3203 10115 1.209127 GGCACAAACCGTCCGATTG 59.791 57.895 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.