Multiple sequence alignment - TraesCS4A01G242800

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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 TraesCS4A01G242800 chr4A 100.000 3401 0 0 1 3401 552815857 552819257 0.000000e+00 6281.0
1 TraesCS4A01G242800 chr4A 94.898 1372 66 2 918 2286 552833195 552831825 0.000000e+00 2143.0
2 TraesCS4A01G242800 chr4A 83.186 113 10 3 497 601 552843583 552843472 1.000000e-15 95.3
3 TraesCS4A01G242800 chr4A 77.976 168 9 12 630 797 552843370 552843231 2.810000e-11 80.5
4 TraesCS4A01G242800 chr4D 90.463 2181 118 49 497 2630 46187875 46185738 0.000000e+00 2793.0
5 TraesCS4A01G242800 chr4D 93.241 1376 84 5 915 2286 46176889 46178259 0.000000e+00 2017.0
6 TraesCS4A01G242800 chr4D 91.837 245 15 5 232 471 3381346 3381102 1.510000e-88 337.0
7 TraesCS4A01G242800 chr4D 86.321 212 17 5 678 886 46176686 46176888 1.590000e-53 220.0
8 TraesCS4A01G242800 chr4B 91.396 1999 96 34 602 2550 67544222 67542250 0.000000e+00 2669.0
9 TraesCS4A01G242800 chr4B 93.440 1631 89 9 674 2298 67354543 67352925 0.000000e+00 2403.0
10 TraesCS4A01G242800 chr4B 93.257 1394 83 7 900 2286 67094932 67096321 0.000000e+00 2043.0
11 TraesCS4A01G242800 chr4B 92.771 1328 91 3 966 2292 67485158 67483835 0.000000e+00 1916.0
12 TraesCS4A01G242800 chr4B 92.614 352 21 3 2280 2630 67352901 67352554 5.070000e-138 501.0
13 TraesCS4A01G242800 chr4B 91.498 247 18 1 2304 2550 67483772 67483529 1.510000e-88 337.0
14 TraesCS4A01G242800 chr4B 82.286 350 19 7 600 924 67491416 67491085 2.600000e-66 263.0
15 TraesCS4A01G242800 chr4B 85.455 275 12 7 630 904 67089680 67089926 9.360000e-66 261.0
16 TraesCS4A01G242800 chr4B 83.621 116 17 2 3282 3397 67535189 67535076 1.290000e-19 108.0
17 TraesCS4A01G242800 chr4B 84.762 105 14 2 3293 3397 67475690 67475588 1.670000e-18 104.0
18 TraesCS4A01G242800 chr4B 90.411 73 3 1 529 601 67491509 67491441 3.610000e-15 93.5
19 TraesCS4A01G242800 chr4B 90.411 73 3 1 529 601 67544323 67544255 3.610000e-15 93.5
20 TraesCS4A01G242800 chr6A 95.860 628 25 1 2624 3250 384583909 384584536 0.000000e+00 1014.0
21 TraesCS4A01G242800 chr6A 95.541 628 27 1 2624 3250 428064089 428064716 0.000000e+00 1003.0
22 TraesCS4A01G242800 chr6A 90.763 249 19 4 226 471 138271035 138271282 2.530000e-86 329.0
23 TraesCS4A01G242800 chr1A 95.534 627 25 2 2627 3250 372284433 372283807 0.000000e+00 1000.0
24 TraesCS4A01G242800 chr1A 97.143 140 3 1 1 139 447114474 447114613 5.670000e-58 235.0
25 TraesCS4A01G242800 chr1A 97.143 140 3 1 1 139 468651643 468651782 5.670000e-58 235.0
26 TraesCS4A01G242800 chr3A 95.382 628 28 1 2624 3250 119292193 119291566 0.000000e+00 998.0
27 TraesCS4A01G242800 chr3A 95.382 628 28 1 2624 3250 454209958 454209331 0.000000e+00 998.0
28 TraesCS4A01G242800 chr3A 92.308 234 16 1 240 471 654557672 654557439 7.030000e-87 331.0
29 TraesCS4A01G242800 chr3A 97.857 140 2 1 1 139 629088537 629088398 1.220000e-59 241.0
30 TraesCS4A01G242800 chr3A 97.857 140 2 1 1 139 696331428 696331567 1.220000e-59 241.0
31 TraesCS4A01G242800 chr3A 97.143 140 2 2 1 139 517388199 517388337 5.670000e-58 235.0
32 TraesCS4A01G242800 chr5A 95.223 628 29 1 2624 3250 162405761 162405134 0.000000e+00 992.0
33 TraesCS4A01G242800 chr5A 94.531 640 30 4 2624 3261 574989803 574990439 0.000000e+00 983.0
34 TraesCS4A01G242800 chr5A 78.495 1116 201 30 1198 2286 69140847 69141950 0.000000e+00 695.0
35 TraesCS4A01G242800 chr5A 91.915 235 17 2 239 471 585634764 585634530 9.100000e-86 327.0
36 TraesCS4A01G242800 chr5A 97.143 140 3 1 1 139 440703631 440703770 5.670000e-58 235.0
37 TraesCS4A01G242800 chr7A 95.223 628 27 2 2625 3249 213819093 213819720 0.000000e+00 990.0
38 TraesCS4A01G242800 chr7A 97.143 140 3 1 1 139 443763773 443763912 5.670000e-58 235.0
39 TraesCS4A01G242800 chr2A 94.679 639 30 4 2620 3255 7640134 7640771 0.000000e+00 989.0
40 TraesCS4A01G242800 chr5B 78.424 1117 200 28 1198 2286 78221084 78219981 0.000000e+00 689.0
41 TraesCS4A01G242800 chr5B 79.528 127 19 4 2294 2416 489987775 489987898 2.170000e-12 84.2
42 TraesCS4A01G242800 chr6D 92.017 238 16 3 239 473 426200958 426200721 7.030000e-87 331.0
43 TraesCS4A01G242800 chr6D 96.154 78 3 0 1265 1342 7294608 7294531 9.910000e-26 128.0
44 TraesCS4A01G242800 chr7D 90.196 255 19 5 226 475 185352208 185351955 9.100000e-86 327.0
45 TraesCS4A01G242800 chr7D 96.154 78 3 0 1265 1342 564687402 564687325 9.910000e-26 128.0
46 TraesCS4A01G242800 chr3D 91.915 235 17 2 239 471 62813845 62813611 9.100000e-86 327.0
47 TraesCS4A01G242800 chr6B 90.688 247 17 5 232 474 579082039 579082283 1.180000e-84 324.0
48 TraesCS4A01G242800 chr6B 86.813 273 34 2 1987 2259 43276036 43275766 1.530000e-78 303.0
49 TraesCS4A01G242800 chr6B 97.143 140 3 1 1 139 663114347 663114486 5.670000e-58 235.0
50 TraesCS4A01G242800 chr2D 88.636 264 20 8 210 466 14087301 14087561 2.550000e-81 313.0
51 TraesCS4A01G242800 chr7B 97.143 140 3 1 1 139 425158773 425158634 5.670000e-58 235.0
52 TraesCS4A01G242800 chr5D 96.000 50 2 0 1262 1311 486832608 486832657 7.820000e-12 82.4


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 TraesCS4A01G242800 chr4A 552815857 552819257 3400 False 6281.00 6281 100.0000 1 3401 1 chr4A.!!$F1 3400
1 TraesCS4A01G242800 chr4A 552831825 552833195 1370 True 2143.00 2143 94.8980 918 2286 1 chr4A.!!$R1 1368
2 TraesCS4A01G242800 chr4D 46185738 46187875 2137 True 2793.00 2793 90.4630 497 2630 1 chr4D.!!$R2 2133
3 TraesCS4A01G242800 chr4D 46176686 46178259 1573 False 1118.50 2017 89.7810 678 2286 2 chr4D.!!$F1 1608
4 TraesCS4A01G242800 chr4B 67094932 67096321 1389 False 2043.00 2043 93.2570 900 2286 1 chr4B.!!$F2 1386
5 TraesCS4A01G242800 chr4B 67352554 67354543 1989 True 1452.00 2403 93.0270 674 2630 2 chr4B.!!$R3 1956
6 TraesCS4A01G242800 chr4B 67542250 67544323 2073 True 1381.25 2669 90.9035 529 2550 2 chr4B.!!$R6 2021
7 TraesCS4A01G242800 chr4B 67483529 67485158 1629 True 1126.50 1916 92.1345 966 2550 2 chr4B.!!$R4 1584
8 TraesCS4A01G242800 chr6A 384583909 384584536 627 False 1014.00 1014 95.8600 2624 3250 1 chr6A.!!$F2 626
9 TraesCS4A01G242800 chr6A 428064089 428064716 627 False 1003.00 1003 95.5410 2624 3250 1 chr6A.!!$F3 626
10 TraesCS4A01G242800 chr1A 372283807 372284433 626 True 1000.00 1000 95.5340 2627 3250 1 chr1A.!!$R1 623
11 TraesCS4A01G242800 chr3A 119291566 119292193 627 True 998.00 998 95.3820 2624 3250 1 chr3A.!!$R1 626
12 TraesCS4A01G242800 chr3A 454209331 454209958 627 True 998.00 998 95.3820 2624 3250 1 chr3A.!!$R2 626
13 TraesCS4A01G242800 chr5A 162405134 162405761 627 True 992.00 992 95.2230 2624 3250 1 chr5A.!!$R1 626
14 TraesCS4A01G242800 chr5A 574989803 574990439 636 False 983.00 983 94.5310 2624 3261 1 chr5A.!!$F3 637
15 TraesCS4A01G242800 chr5A 69140847 69141950 1103 False 695.00 695 78.4950 1198 2286 1 chr5A.!!$F1 1088
16 TraesCS4A01G242800 chr7A 213819093 213819720 627 False 990.00 990 95.2230 2625 3249 1 chr7A.!!$F1 624
17 TraesCS4A01G242800 chr2A 7640134 7640771 637 False 989.00 989 94.6790 2620 3255 1 chr2A.!!$F1 635
18 TraesCS4A01G242800 chr5B 78219981 78221084 1103 True 689.00 689 78.4240 1198 2286 1 chr5B.!!$R1 1088

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
238 239 0.036732 TTGCTGCTCCATCCTTCGTT 59.963 50.0 0.0 0.0 0.0 3.85 F
239 240 0.036732 TGCTGCTCCATCCTTCGTTT 59.963 50.0 0.0 0.0 0.0 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1656 1.002502 GTAGCTGGTGGGGTTGACC 60.003 63.158 0.0 0.0 39.11 4.02 R
2718 2892 9.602568 ACCAAAACCGAACTGTATTTTAATTTT 57.397 25.926 0.0 0.0 0.00 1.82 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
114 115 7.462109 GACTTCAGTCAACTCTAATATGCAG 57.538 40.000 1.86 0.00 44.18 4.41
115 116 7.175347 ACTTCAGTCAACTCTAATATGCAGA 57.825 36.000 0.00 0.00 0.00 4.26
116 117 7.264221 ACTTCAGTCAACTCTAATATGCAGAG 58.736 38.462 11.37 11.37 44.28 3.35
132 133 5.873179 TGCAGAGTAAATAAAAACGGAGG 57.127 39.130 0.00 0.00 0.00 4.30
133 134 4.698304 TGCAGAGTAAATAAAAACGGAGGG 59.302 41.667 0.00 0.00 0.00 4.30
134 135 4.939439 GCAGAGTAAATAAAAACGGAGGGA 59.061 41.667 0.00 0.00 0.00 4.20
135 136 5.064834 GCAGAGTAAATAAAAACGGAGGGAG 59.935 44.000 0.00 0.00 0.00 4.30
136 137 6.171213 CAGAGTAAATAAAAACGGAGGGAGT 58.829 40.000 0.00 0.00 0.00 3.85
137 138 7.325694 CAGAGTAAATAAAAACGGAGGGAGTA 58.674 38.462 0.00 0.00 0.00 2.59
138 139 7.277319 CAGAGTAAATAAAAACGGAGGGAGTAC 59.723 40.741 0.00 0.00 0.00 2.73
139 140 6.101997 AGTAAATAAAAACGGAGGGAGTACG 58.898 40.000 0.00 0.00 0.00 3.67
140 141 4.806640 AATAAAAACGGAGGGAGTACGA 57.193 40.909 0.00 0.00 0.00 3.43
141 142 2.738013 AAAAACGGAGGGAGTACGAG 57.262 50.000 0.00 0.00 0.00 4.18
142 143 0.245813 AAAACGGAGGGAGTACGAGC 59.754 55.000 0.00 0.00 0.00 5.03
143 144 1.602327 AAACGGAGGGAGTACGAGCC 61.602 60.000 0.00 0.00 0.00 4.70
144 145 2.124236 CGGAGGGAGTACGAGCCT 60.124 66.667 0.00 0.00 0.00 4.58
145 146 2.482333 CGGAGGGAGTACGAGCCTG 61.482 68.421 0.00 0.00 0.00 4.85
146 147 1.076923 GGAGGGAGTACGAGCCTGA 60.077 63.158 0.00 0.00 0.00 3.86
147 148 1.385756 GGAGGGAGTACGAGCCTGAC 61.386 65.000 0.00 0.00 0.00 3.51
148 149 1.380112 AGGGAGTACGAGCCTGACC 60.380 63.158 0.00 0.00 0.00 4.02
149 150 1.681327 GGGAGTACGAGCCTGACCA 60.681 63.158 0.00 0.00 0.00 4.02
150 151 1.043673 GGGAGTACGAGCCTGACCAT 61.044 60.000 0.00 0.00 0.00 3.55
151 152 0.824759 GGAGTACGAGCCTGACCATT 59.175 55.000 0.00 0.00 0.00 3.16
152 153 2.029623 GGAGTACGAGCCTGACCATTA 58.970 52.381 0.00 0.00 0.00 1.90
153 154 2.223758 GGAGTACGAGCCTGACCATTAC 60.224 54.545 0.00 0.00 0.00 1.89
154 155 2.688958 GAGTACGAGCCTGACCATTACT 59.311 50.000 0.00 0.00 0.00 2.24
155 156 3.881688 GAGTACGAGCCTGACCATTACTA 59.118 47.826 0.00 0.00 0.00 1.82
156 157 3.884091 AGTACGAGCCTGACCATTACTAG 59.116 47.826 0.00 0.00 0.00 2.57
157 158 1.409427 ACGAGCCTGACCATTACTAGC 59.591 52.381 0.00 0.00 0.00 3.42
158 159 1.409064 CGAGCCTGACCATTACTAGCA 59.591 52.381 0.00 0.00 0.00 3.49
159 160 2.544694 CGAGCCTGACCATTACTAGCAG 60.545 54.545 0.00 0.00 0.00 4.24
160 161 2.432510 GAGCCTGACCATTACTAGCAGT 59.567 50.000 0.00 0.00 0.00 4.40
161 162 3.637229 GAGCCTGACCATTACTAGCAGTA 59.363 47.826 0.00 0.00 0.00 2.74
162 163 4.227197 AGCCTGACCATTACTAGCAGTAT 58.773 43.478 0.00 0.00 29.64 2.12
163 164 4.656112 AGCCTGACCATTACTAGCAGTATT 59.344 41.667 0.00 0.00 29.64 1.89
164 165 4.752101 GCCTGACCATTACTAGCAGTATTG 59.248 45.833 0.00 9.41 33.90 1.90
165 166 5.685075 GCCTGACCATTACTAGCAGTATTGT 60.685 44.000 12.77 5.66 32.85 2.71
166 167 6.462487 GCCTGACCATTACTAGCAGTATTGTA 60.462 42.308 12.77 0.00 32.85 2.41
167 168 7.497595 CCTGACCATTACTAGCAGTATTGTAA 58.502 38.462 12.77 0.00 32.85 2.41
168 169 7.438459 CCTGACCATTACTAGCAGTATTGTAAC 59.562 40.741 12.77 7.61 32.85 2.50
169 170 7.270047 TGACCATTACTAGCAGTATTGTAACC 58.730 38.462 12.77 0.00 32.85 2.85
170 171 6.278363 ACCATTACTAGCAGTATTGTAACCG 58.722 40.000 12.77 0.00 32.85 4.44
171 172 6.097270 ACCATTACTAGCAGTATTGTAACCGA 59.903 38.462 12.77 0.00 32.85 4.69
172 173 6.982141 CCATTACTAGCAGTATTGTAACCGAA 59.018 38.462 12.77 0.00 32.85 4.30
173 174 7.656137 CCATTACTAGCAGTATTGTAACCGAAT 59.344 37.037 12.77 0.00 32.85 3.34
174 175 7.997107 TTACTAGCAGTATTGTAACCGAATG 57.003 36.000 0.00 0.00 29.64 2.67
175 176 5.357257 ACTAGCAGTATTGTAACCGAATGG 58.643 41.667 0.00 0.00 42.84 3.16
176 177 7.364056 TTACTAGCAGTATTGTAACCGAATGGT 60.364 37.037 0.00 0.00 39.48 3.55
211 212 7.921786 TTTTATCCAATTGACTACACTCAGG 57.078 36.000 7.12 0.00 0.00 3.86
212 213 6.867519 TTATCCAATTGACTACACTCAGGA 57.132 37.500 7.12 0.00 0.00 3.86
213 214 4.808414 TCCAATTGACTACACTCAGGAG 57.192 45.455 7.12 0.00 0.00 3.69
214 215 4.160329 TCCAATTGACTACACTCAGGAGT 58.840 43.478 7.12 0.00 43.61 3.85
215 216 5.330233 TCCAATTGACTACACTCAGGAGTA 58.670 41.667 7.12 0.00 40.20 2.59
216 217 5.185249 TCCAATTGACTACACTCAGGAGTAC 59.815 44.000 7.12 0.00 40.20 2.73
217 218 5.047306 CCAATTGACTACACTCAGGAGTACA 60.047 44.000 7.12 0.00 40.20 2.90
218 219 5.906113 ATTGACTACACTCAGGAGTACAG 57.094 43.478 0.91 5.00 40.20 2.74
219 220 4.368565 TGACTACACTCAGGAGTACAGT 57.631 45.455 12.38 12.38 40.20 3.55
220 221 4.726583 TGACTACACTCAGGAGTACAGTT 58.273 43.478 13.28 2.50 40.20 3.16
221 222 4.519350 TGACTACACTCAGGAGTACAGTTG 59.481 45.833 13.28 7.17 40.20 3.16
222 223 2.821991 ACACTCAGGAGTACAGTTGC 57.178 50.000 0.91 0.00 40.20 4.17
223 224 2.320781 ACACTCAGGAGTACAGTTGCT 58.679 47.619 0.91 0.00 40.20 3.91
224 225 2.036475 ACACTCAGGAGTACAGTTGCTG 59.964 50.000 0.91 0.00 40.20 4.41
225 226 1.001406 ACTCAGGAGTACAGTTGCTGC 59.999 52.381 0.00 0.00 40.43 5.25
226 227 1.274728 CTCAGGAGTACAGTTGCTGCT 59.725 52.381 0.00 0.00 36.54 4.24
227 228 1.273606 TCAGGAGTACAGTTGCTGCTC 59.726 52.381 0.00 0.00 33.74 4.26
228 229 0.610687 AGGAGTACAGTTGCTGCTCC 59.389 55.000 12.08 12.08 39.44 4.70
229 230 0.321671 GGAGTACAGTTGCTGCTCCA 59.678 55.000 13.99 0.00 39.17 3.86
230 231 1.065854 GGAGTACAGTTGCTGCTCCAT 60.066 52.381 13.99 0.00 39.17 3.41
231 232 2.275318 GAGTACAGTTGCTGCTCCATC 58.725 52.381 0.00 0.00 34.37 3.51
232 233 1.065854 AGTACAGTTGCTGCTCCATCC 60.066 52.381 0.00 0.00 34.37 3.51
233 234 1.065854 GTACAGTTGCTGCTCCATCCT 60.066 52.381 0.00 0.00 34.37 3.24
234 235 0.403271 ACAGTTGCTGCTCCATCCTT 59.597 50.000 0.00 0.00 34.37 3.36
235 236 1.093159 CAGTTGCTGCTCCATCCTTC 58.907 55.000 0.00 0.00 0.00 3.46
236 237 0.392193 AGTTGCTGCTCCATCCTTCG 60.392 55.000 0.00 0.00 0.00 3.79
237 238 0.674895 GTTGCTGCTCCATCCTTCGT 60.675 55.000 0.00 0.00 0.00 3.85
238 239 0.036732 TTGCTGCTCCATCCTTCGTT 59.963 50.000 0.00 0.00 0.00 3.85
239 240 0.036732 TGCTGCTCCATCCTTCGTTT 59.963 50.000 0.00 0.00 0.00 3.60
240 241 1.168714 GCTGCTCCATCCTTCGTTTT 58.831 50.000 0.00 0.00 0.00 2.43
241 242 1.541588 GCTGCTCCATCCTTCGTTTTT 59.458 47.619 0.00 0.00 0.00 1.94
450 451 9.679661 AATAAAATTTGACTTTGACCAAACCTT 57.320 25.926 0.00 0.00 35.42 3.50
455 456 9.927668 AATTTGACTTTGACCAAACCTTATATG 57.072 29.630 0.00 0.00 35.42 1.78
456 457 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
457 458 6.007076 TGACTTTGACCAAACCTTATATGCA 58.993 36.000 0.00 0.00 0.00 3.96
458 459 6.150976 TGACTTTGACCAAACCTTATATGCAG 59.849 38.462 0.00 0.00 0.00 4.41
459 460 6.245408 ACTTTGACCAAACCTTATATGCAGA 58.755 36.000 0.00 0.00 0.00 4.26
460 461 6.151144 ACTTTGACCAAACCTTATATGCAGAC 59.849 38.462 0.00 0.00 0.00 3.51
461 462 5.435686 TGACCAAACCTTATATGCAGACT 57.564 39.130 0.00 0.00 0.00 3.24
462 463 5.815581 TGACCAAACCTTATATGCAGACTT 58.184 37.500 0.00 0.00 0.00 3.01
463 464 6.953101 TGACCAAACCTTATATGCAGACTTA 58.047 36.000 0.00 0.00 0.00 2.24
464 465 7.398829 TGACCAAACCTTATATGCAGACTTAA 58.601 34.615 0.00 0.00 0.00 1.85
465 466 7.885922 TGACCAAACCTTATATGCAGACTTAAA 59.114 33.333 0.00 0.00 0.00 1.52
466 467 8.644374 ACCAAACCTTATATGCAGACTTAAAA 57.356 30.769 0.00 0.00 0.00 1.52
467 468 9.084533 ACCAAACCTTATATGCAGACTTAAAAA 57.915 29.630 0.00 0.00 0.00 1.94
551 553 6.294675 CCATCCAATAATGAACGGCACAATAT 60.295 38.462 0.00 0.00 0.00 1.28
552 554 7.094420 CCATCCAATAATGAACGGCACAATATA 60.094 37.037 0.00 0.00 0.00 0.86
553 555 7.994425 TCCAATAATGAACGGCACAATATAT 57.006 32.000 0.00 0.00 0.00 0.86
554 556 9.679661 ATCCAATAATGAACGGCACAATATATA 57.320 29.630 0.00 0.00 0.00 0.86
566 568 4.245660 CACAATATATAGTCCTGCCACCG 58.754 47.826 0.00 0.00 0.00 4.94
624 664 8.869109 TGACCCATTCCCAATAATGAATAAATC 58.131 33.333 0.00 0.00 38.84 2.17
664 720 4.104102 TCAAGAAAGCAGAACCCTCCTTTA 59.896 41.667 0.00 0.00 0.00 1.85
665 721 4.936685 AGAAAGCAGAACCCTCCTTTAT 57.063 40.909 0.00 0.00 0.00 1.40
666 722 5.262455 AGAAAGCAGAACCCTCCTTTATT 57.738 39.130 0.00 0.00 0.00 1.40
667 723 6.388619 AGAAAGCAGAACCCTCCTTTATTA 57.611 37.500 0.00 0.00 0.00 0.98
668 724 6.790319 AGAAAGCAGAACCCTCCTTTATTAA 58.210 36.000 0.00 0.00 0.00 1.40
669 725 7.238710 AGAAAGCAGAACCCTCCTTTATTAAA 58.761 34.615 0.00 0.00 0.00 1.52
670 726 7.728532 AGAAAGCAGAACCCTCCTTTATTAAAA 59.271 33.333 0.00 0.00 0.00 1.52
671 727 7.468141 AAGCAGAACCCTCCTTTATTAAAAG 57.532 36.000 0.00 0.00 41.57 2.27
707 763 8.699130 GGAAAATAATCAATCAAATCAGACCCT 58.301 33.333 0.00 0.00 0.00 4.34
710 766 5.927281 AATCAATCAAATCAGACCCTTGG 57.073 39.130 0.00 0.00 0.00 3.61
711 767 4.656100 TCAATCAAATCAGACCCTTGGA 57.344 40.909 0.00 0.00 0.00 3.53
712 768 5.197224 TCAATCAAATCAGACCCTTGGAT 57.803 39.130 0.00 0.00 0.00 3.41
713 769 4.951715 TCAATCAAATCAGACCCTTGGATG 59.048 41.667 0.00 0.00 0.00 3.51
735 795 2.494918 CGGATCCACCTGTCGGAC 59.505 66.667 13.41 0.00 34.69 4.79
764 824 2.659897 CCACGGCATAGCTCTCGC 60.660 66.667 0.00 0.00 0.00 5.03
860 943 1.305887 TCCTCCTCCCTTTCGGTCC 60.306 63.158 0.00 0.00 0.00 4.46
861 944 2.368011 CCTCCTCCCTTTCGGTCCC 61.368 68.421 0.00 0.00 0.00 4.46
862 945 2.682494 TCCTCCCTTTCGGTCCCG 60.682 66.667 0.00 0.00 41.35 5.14
863 946 3.782443 CCTCCCTTTCGGTCCCGG 61.782 72.222 5.80 0.00 40.25 5.73
864 947 4.468689 CTCCCTTTCGGTCCCGGC 62.469 72.222 5.80 0.00 40.25 6.13
1455 1551 4.778143 GGCCGCATCTTCACCGGT 62.778 66.667 0.00 0.00 43.70 5.28
1560 1656 1.226717 GGACTACCTCAAGAGCGCG 60.227 63.158 0.00 0.00 0.00 6.86
2576 2750 0.893727 GTGGTGGTGGCCGAAATCTT 60.894 55.000 0.00 0.00 0.00 2.40
2660 2834 5.163972 CGTTCGGTTTATTCGGTTTACATGA 60.164 40.000 0.00 0.00 0.00 3.07
2745 2919 9.602568 AAATTAAAATACAGTTCGGTTTTGGTT 57.397 25.926 0.00 0.00 0.00 3.67
2784 2958 5.048083 TCGGTATGGTTTCGGTATATACCAC 60.048 44.000 27.58 18.99 46.80 4.16
2810 2984 2.356382 ACCAAAGTTGACGCGAATTTGA 59.644 40.909 15.93 0.00 33.69 2.69
2865 3039 8.997621 TGACTCAAAACACATACTATTCTACC 57.002 34.615 0.00 0.00 0.00 3.18
2866 3040 7.758076 TGACTCAAAACACATACTATTCTACCG 59.242 37.037 0.00 0.00 0.00 4.02
2948 3128 2.987413 TGGACGTGCTTAGCATTTTG 57.013 45.000 11.03 3.73 41.91 2.44
2955 3135 6.033513 GGACGTGCTTAGCATTTTGAAAATAC 59.966 38.462 11.03 0.00 41.91 1.89
3051 3232 7.424803 CAACTTGTATGGTTGTTCATCTCAAA 58.575 34.615 0.00 0.00 39.14 2.69
3165 3347 5.168647 AGTTCATACCATACCGAAACCAA 57.831 39.130 0.00 0.00 0.00 3.67
3223 3407 7.083230 GGTTTATTTTCGGTATGGTTTTTCGA 58.917 34.615 0.00 0.00 0.00 3.71
3251 3435 6.415867 CAGTTTTTAAATGCACAGAGTGAGTG 59.584 38.462 0.58 0.00 39.92 3.51
3252 3436 6.318648 AGTTTTTAAATGCACAGAGTGAGTGA 59.681 34.615 0.58 0.00 39.30 3.41
3253 3437 5.929697 TTTAAATGCACAGAGTGAGTGAG 57.070 39.130 0.58 0.00 39.30 3.51
3257 3441 0.965439 GCACAGAGTGAGTGAGAGGT 59.035 55.000 0.58 0.00 39.30 3.85
3267 3451 3.471620 TGAGAGGTCACAGGCCAC 58.528 61.111 5.01 0.00 0.00 5.01
3268 3452 2.262915 GAGAGGTCACAGGCCACG 59.737 66.667 5.01 0.00 0.00 4.94
3269 3453 2.524394 AGAGGTCACAGGCCACGT 60.524 61.111 5.01 0.00 0.00 4.49
3270 3454 2.048127 GAGGTCACAGGCCACGTC 60.048 66.667 5.01 1.09 0.00 4.34
3271 3455 2.842462 AGGTCACAGGCCACGTCA 60.842 61.111 5.01 0.00 0.00 4.35
3272 3456 2.110213 GGTCACAGGCCACGTCAA 59.890 61.111 5.01 0.00 0.00 3.18
3273 3457 1.525077 GGTCACAGGCCACGTCAAA 60.525 57.895 5.01 0.00 0.00 2.69
3274 3458 0.889186 GGTCACAGGCCACGTCAAAT 60.889 55.000 5.01 0.00 0.00 2.32
3275 3459 0.951558 GTCACAGGCCACGTCAAATT 59.048 50.000 5.01 0.00 0.00 1.82
3276 3460 1.069227 GTCACAGGCCACGTCAAATTC 60.069 52.381 5.01 0.00 0.00 2.17
3277 3461 0.110238 CACAGGCCACGTCAAATTCG 60.110 55.000 5.01 0.00 0.00 3.34
3278 3462 1.234615 ACAGGCCACGTCAAATTCGG 61.235 55.000 5.01 0.00 0.00 4.30
3279 3463 1.072505 AGGCCACGTCAAATTCGGT 59.927 52.632 5.01 0.00 0.00 4.69
3280 3464 0.536460 AGGCCACGTCAAATTCGGTT 60.536 50.000 5.01 0.00 0.00 4.44
3281 3465 0.386731 GGCCACGTCAAATTCGGTTG 60.387 55.000 0.00 0.00 0.00 3.77
3282 3466 0.589223 GCCACGTCAAATTCGGTTGA 59.411 50.000 0.00 0.00 35.14 3.18
3289 3473 3.762407 TCAAATTCGGTTGACAGAGGA 57.238 42.857 0.00 0.00 32.56 3.71
3290 3474 4.079980 TCAAATTCGGTTGACAGAGGAA 57.920 40.909 0.00 0.00 32.56 3.36
3291 3475 4.065088 TCAAATTCGGTTGACAGAGGAAG 58.935 43.478 0.00 0.00 32.56 3.46
3292 3476 2.770164 ATTCGGTTGACAGAGGAAGG 57.230 50.000 0.00 0.00 0.00 3.46
3293 3477 1.712056 TTCGGTTGACAGAGGAAGGA 58.288 50.000 0.00 0.00 0.00 3.36
3294 3478 1.712056 TCGGTTGACAGAGGAAGGAA 58.288 50.000 0.00 0.00 0.00 3.36
3295 3479 2.043992 TCGGTTGACAGAGGAAGGAAA 58.956 47.619 0.00 0.00 0.00 3.13
3296 3480 2.436542 TCGGTTGACAGAGGAAGGAAAA 59.563 45.455 0.00 0.00 0.00 2.29
3297 3481 3.072476 TCGGTTGACAGAGGAAGGAAAAT 59.928 43.478 0.00 0.00 0.00 1.82
3298 3482 3.189287 CGGTTGACAGAGGAAGGAAAATG 59.811 47.826 0.00 0.00 0.00 2.32
3299 3483 3.507622 GGTTGACAGAGGAAGGAAAATGG 59.492 47.826 0.00 0.00 0.00 3.16
3300 3484 4.145052 GTTGACAGAGGAAGGAAAATGGT 58.855 43.478 0.00 0.00 0.00 3.55
3301 3485 4.453480 TGACAGAGGAAGGAAAATGGTT 57.547 40.909 0.00 0.00 0.00 3.67
3302 3486 4.803452 TGACAGAGGAAGGAAAATGGTTT 58.197 39.130 0.00 0.00 0.00 3.27
3303 3487 5.208121 TGACAGAGGAAGGAAAATGGTTTT 58.792 37.500 0.00 0.00 35.12 2.43
3304 3488 5.068987 TGACAGAGGAAGGAAAATGGTTTTG 59.931 40.000 0.00 0.00 31.94 2.44
3305 3489 4.962362 ACAGAGGAAGGAAAATGGTTTTGT 59.038 37.500 0.00 0.00 31.94 2.83
3306 3490 5.163416 ACAGAGGAAGGAAAATGGTTTTGTG 60.163 40.000 0.00 0.00 31.94 3.33
3307 3491 4.344968 AGAGGAAGGAAAATGGTTTTGTGG 59.655 41.667 0.00 0.00 31.94 4.17
3308 3492 3.390967 AGGAAGGAAAATGGTTTTGTGGG 59.609 43.478 0.00 0.00 31.94 4.61
3309 3493 3.135712 GGAAGGAAAATGGTTTTGTGGGT 59.864 43.478 0.00 0.00 31.94 4.51
3310 3494 3.836365 AGGAAAATGGTTTTGTGGGTG 57.164 42.857 0.00 0.00 31.94 4.61
3311 3495 3.379452 AGGAAAATGGTTTTGTGGGTGA 58.621 40.909 0.00 0.00 31.94 4.02
3312 3496 3.973305 AGGAAAATGGTTTTGTGGGTGAT 59.027 39.130 0.00 0.00 31.94 3.06
3313 3497 4.411869 AGGAAAATGGTTTTGTGGGTGATT 59.588 37.500 0.00 0.00 31.94 2.57
3314 3498 5.104151 AGGAAAATGGTTTTGTGGGTGATTT 60.104 36.000 0.00 0.00 31.94 2.17
3315 3499 5.592282 GGAAAATGGTTTTGTGGGTGATTTT 59.408 36.000 0.00 0.00 31.94 1.82
3316 3500 6.448207 AAAATGGTTTTGTGGGTGATTTTG 57.552 33.333 0.00 0.00 0.00 2.44
3317 3501 4.769345 ATGGTTTTGTGGGTGATTTTGT 57.231 36.364 0.00 0.00 0.00 2.83
3318 3502 4.559862 TGGTTTTGTGGGTGATTTTGTT 57.440 36.364 0.00 0.00 0.00 2.83
3319 3503 4.911390 TGGTTTTGTGGGTGATTTTGTTT 58.089 34.783 0.00 0.00 0.00 2.83
3320 3504 4.697352 TGGTTTTGTGGGTGATTTTGTTTG 59.303 37.500 0.00 0.00 0.00 2.93
3321 3505 4.697828 GGTTTTGTGGGTGATTTTGTTTGT 59.302 37.500 0.00 0.00 0.00 2.83
3322 3506 5.875359 GGTTTTGTGGGTGATTTTGTTTGTA 59.125 36.000 0.00 0.00 0.00 2.41
3323 3507 6.371825 GGTTTTGTGGGTGATTTTGTTTGTAA 59.628 34.615 0.00 0.00 0.00 2.41
3324 3508 6.969828 TTTGTGGGTGATTTTGTTTGTAAC 57.030 33.333 0.00 0.00 0.00 2.50
3325 3509 5.012328 TGTGGGTGATTTTGTTTGTAACC 57.988 39.130 0.00 0.00 0.00 2.85
3326 3510 4.466370 TGTGGGTGATTTTGTTTGTAACCA 59.534 37.500 0.00 0.00 0.00 3.67
3327 3511 5.129485 TGTGGGTGATTTTGTTTGTAACCAT 59.871 36.000 0.00 0.00 0.00 3.55
3328 3512 6.052360 GTGGGTGATTTTGTTTGTAACCATT 58.948 36.000 0.00 0.00 0.00 3.16
3329 3513 6.018343 GTGGGTGATTTTGTTTGTAACCATTG 60.018 38.462 0.00 0.00 0.00 2.82
3330 3514 6.127054 TGGGTGATTTTGTTTGTAACCATTGA 60.127 34.615 0.00 0.00 0.00 2.57
3331 3515 6.423604 GGGTGATTTTGTTTGTAACCATTGAG 59.576 38.462 0.00 0.00 0.00 3.02
3332 3516 7.206687 GGTGATTTTGTTTGTAACCATTGAGA 58.793 34.615 0.00 0.00 0.00 3.27
3333 3517 7.872483 GGTGATTTTGTTTGTAACCATTGAGAT 59.128 33.333 0.00 0.00 0.00 2.75
3334 3518 9.906660 GTGATTTTGTTTGTAACCATTGAGATA 57.093 29.630 0.00 0.00 0.00 1.98
3341 3525 8.739039 TGTTTGTAACCATTGAGATAGATTTGG 58.261 33.333 0.00 0.00 0.00 3.28
3342 3526 8.739972 GTTTGTAACCATTGAGATAGATTTGGT 58.260 33.333 0.00 0.00 39.07 3.67
3343 3527 7.864108 TGTAACCATTGAGATAGATTTGGTG 57.136 36.000 0.00 0.00 37.52 4.17
3344 3528 5.841957 AACCATTGAGATAGATTTGGTGC 57.158 39.130 0.00 0.00 37.52 5.01
3345 3529 4.858850 ACCATTGAGATAGATTTGGTGCA 58.141 39.130 0.00 0.00 36.18 4.57
3346 3530 5.263599 ACCATTGAGATAGATTTGGTGCAA 58.736 37.500 0.00 0.00 36.18 4.08
3347 3531 5.126061 ACCATTGAGATAGATTTGGTGCAAC 59.874 40.000 0.00 0.00 36.18 4.17
3348 3532 5.125900 CCATTGAGATAGATTTGGTGCAACA 59.874 40.000 0.00 0.00 39.98 3.33
3349 3533 6.350361 CCATTGAGATAGATTTGGTGCAACAA 60.350 38.462 14.57 14.57 39.98 2.83
3350 3534 5.885230 TGAGATAGATTTGGTGCAACAAG 57.115 39.130 18.10 0.00 39.98 3.16
3351 3535 4.701651 TGAGATAGATTTGGTGCAACAAGG 59.298 41.667 18.10 0.00 39.98 3.61
3352 3536 4.666512 AGATAGATTTGGTGCAACAAGGT 58.333 39.130 18.10 10.70 39.98 3.50
3353 3537 4.460382 AGATAGATTTGGTGCAACAAGGTG 59.540 41.667 18.10 0.00 39.98 4.00
3354 3538 2.387757 AGATTTGGTGCAACAAGGTGT 58.612 42.857 18.10 6.53 39.98 4.16
3355 3539 2.101249 AGATTTGGTGCAACAAGGTGTG 59.899 45.455 18.10 0.00 39.98 3.82
3356 3540 0.108424 TTTGGTGCAACAAGGTGTGC 60.108 50.000 18.10 0.00 39.98 4.57
3357 3541 1.253593 TTGGTGCAACAAGGTGTGCA 61.254 50.000 14.57 0.00 39.98 4.57
3358 3542 1.042003 TGGTGCAACAAGGTGTGCAT 61.042 50.000 0.00 0.00 39.98 3.96
3359 3543 0.104671 GGTGCAACAAGGTGTGCATT 59.895 50.000 0.00 0.00 39.98 3.56
3360 3544 1.339610 GGTGCAACAAGGTGTGCATTA 59.660 47.619 0.00 0.00 39.98 1.90
3361 3545 2.223923 GGTGCAACAAGGTGTGCATTAA 60.224 45.455 0.00 0.00 39.98 1.40
3362 3546 3.452474 GTGCAACAAGGTGTGCATTAAA 58.548 40.909 1.20 0.00 37.00 1.52
3363 3547 3.490526 GTGCAACAAGGTGTGCATTAAAG 59.509 43.478 1.20 0.00 37.00 1.85
3364 3548 3.059166 GCAACAAGGTGTGCATTAAAGG 58.941 45.455 0.00 0.00 0.00 3.11
3365 3549 3.492482 GCAACAAGGTGTGCATTAAAGGT 60.492 43.478 0.00 0.00 0.00 3.50
3366 3550 4.692228 CAACAAGGTGTGCATTAAAGGTT 58.308 39.130 0.00 0.00 0.00 3.50
3367 3551 4.320608 ACAAGGTGTGCATTAAAGGTTG 57.679 40.909 0.00 0.00 0.00 3.77
3368 3552 3.059166 CAAGGTGTGCATTAAAGGTTGC 58.941 45.455 0.00 0.00 39.33 4.17
3369 3553 2.597455 AGGTGTGCATTAAAGGTTGCT 58.403 42.857 0.00 0.00 39.60 3.91
3370 3554 2.558359 AGGTGTGCATTAAAGGTTGCTC 59.442 45.455 0.00 0.00 39.60 4.26
3371 3555 2.295909 GGTGTGCATTAAAGGTTGCTCA 59.704 45.455 0.00 0.75 39.30 4.26
3372 3556 3.568538 GTGTGCATTAAAGGTTGCTCAG 58.431 45.455 4.28 0.00 41.40 3.35
3373 3557 3.253188 GTGTGCATTAAAGGTTGCTCAGA 59.747 43.478 4.28 0.00 41.40 3.27
3374 3558 3.888323 TGTGCATTAAAGGTTGCTCAGAA 59.112 39.130 0.00 0.00 37.41 3.02
3375 3559 4.340666 TGTGCATTAAAGGTTGCTCAGAAA 59.659 37.500 0.00 0.00 37.41 2.52
3376 3560 5.163468 TGTGCATTAAAGGTTGCTCAGAAAA 60.163 36.000 0.00 0.00 37.41 2.29
3377 3561 5.752955 GTGCATTAAAGGTTGCTCAGAAAAA 59.247 36.000 0.00 0.00 39.60 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 7.261325 TCTGCATATTAGAGTTGACTGAAGTC 58.739 38.462 3.41 3.41 44.97 3.01
91 92 7.175347 TCTGCATATTAGAGTTGACTGAAGT 57.825 36.000 0.00 0.00 0.00 3.01
92 93 7.697352 CTCTGCATATTAGAGTTGACTGAAG 57.303 40.000 5.84 0.00 37.48 3.02
106 107 8.621286 CCTCCGTTTTTATTTACTCTGCATATT 58.379 33.333 0.00 0.00 0.00 1.28
107 108 7.228706 CCCTCCGTTTTTATTTACTCTGCATAT 59.771 37.037 0.00 0.00 0.00 1.78
108 109 6.540914 CCCTCCGTTTTTATTTACTCTGCATA 59.459 38.462 0.00 0.00 0.00 3.14
109 110 5.357032 CCCTCCGTTTTTATTTACTCTGCAT 59.643 40.000 0.00 0.00 0.00 3.96
110 111 4.698304 CCCTCCGTTTTTATTTACTCTGCA 59.302 41.667 0.00 0.00 0.00 4.41
111 112 4.939439 TCCCTCCGTTTTTATTTACTCTGC 59.061 41.667 0.00 0.00 0.00 4.26
112 113 6.171213 ACTCCCTCCGTTTTTATTTACTCTG 58.829 40.000 0.00 0.00 0.00 3.35
113 114 6.370186 ACTCCCTCCGTTTTTATTTACTCT 57.630 37.500 0.00 0.00 0.00 3.24
114 115 6.254373 CGTACTCCCTCCGTTTTTATTTACTC 59.746 42.308 0.00 0.00 0.00 2.59
115 116 6.071391 TCGTACTCCCTCCGTTTTTATTTACT 60.071 38.462 0.00 0.00 0.00 2.24
116 117 6.099341 TCGTACTCCCTCCGTTTTTATTTAC 58.901 40.000 0.00 0.00 0.00 2.01
117 118 6.279513 TCGTACTCCCTCCGTTTTTATTTA 57.720 37.500 0.00 0.00 0.00 1.40
118 119 5.151297 TCGTACTCCCTCCGTTTTTATTT 57.849 39.130 0.00 0.00 0.00 1.40
119 120 4.752146 CTCGTACTCCCTCCGTTTTTATT 58.248 43.478 0.00 0.00 0.00 1.40
120 121 3.429960 GCTCGTACTCCCTCCGTTTTTAT 60.430 47.826 0.00 0.00 0.00 1.40
121 122 2.094545 GCTCGTACTCCCTCCGTTTTTA 60.095 50.000 0.00 0.00 0.00 1.52
122 123 1.337541 GCTCGTACTCCCTCCGTTTTT 60.338 52.381 0.00 0.00 0.00 1.94
123 124 0.245813 GCTCGTACTCCCTCCGTTTT 59.754 55.000 0.00 0.00 0.00 2.43
124 125 1.602327 GGCTCGTACTCCCTCCGTTT 61.602 60.000 0.00 0.00 0.00 3.60
125 126 2.050934 GGCTCGTACTCCCTCCGTT 61.051 63.158 0.00 0.00 0.00 4.44
126 127 2.439883 GGCTCGTACTCCCTCCGT 60.440 66.667 0.00 0.00 0.00 4.69
127 128 2.124236 AGGCTCGTACTCCCTCCG 60.124 66.667 0.00 0.00 0.00 4.63
128 129 1.076923 TCAGGCTCGTACTCCCTCC 60.077 63.158 0.00 0.00 0.00 4.30
129 130 1.385756 GGTCAGGCTCGTACTCCCTC 61.386 65.000 0.00 0.00 0.00 4.30
130 131 1.380112 GGTCAGGCTCGTACTCCCT 60.380 63.158 0.00 0.00 0.00 4.20
131 132 1.043673 ATGGTCAGGCTCGTACTCCC 61.044 60.000 0.00 0.00 0.00 4.30
132 133 0.824759 AATGGTCAGGCTCGTACTCC 59.175 55.000 0.00 0.00 0.00 3.85
133 134 2.688958 AGTAATGGTCAGGCTCGTACTC 59.311 50.000 0.00 0.00 0.00 2.59
134 135 2.736347 AGTAATGGTCAGGCTCGTACT 58.264 47.619 0.00 0.00 0.00 2.73
135 136 3.550436 GCTAGTAATGGTCAGGCTCGTAC 60.550 52.174 0.00 0.00 0.00 3.67
136 137 2.621998 GCTAGTAATGGTCAGGCTCGTA 59.378 50.000 0.00 0.00 0.00 3.43
137 138 1.409427 GCTAGTAATGGTCAGGCTCGT 59.591 52.381 0.00 0.00 0.00 4.18
138 139 1.409064 TGCTAGTAATGGTCAGGCTCG 59.591 52.381 0.00 0.00 0.00 5.03
139 140 2.432510 ACTGCTAGTAATGGTCAGGCTC 59.567 50.000 0.00 0.00 0.00 4.70
140 141 2.472029 ACTGCTAGTAATGGTCAGGCT 58.528 47.619 0.00 0.00 0.00 4.58
141 142 2.990066 ACTGCTAGTAATGGTCAGGC 57.010 50.000 0.00 0.00 0.00 4.85
142 143 5.918608 ACAATACTGCTAGTAATGGTCAGG 58.081 41.667 12.80 0.00 36.23 3.86
143 144 7.438459 GGTTACAATACTGCTAGTAATGGTCAG 59.562 40.741 12.80 0.00 36.23 3.51
144 145 7.270047 GGTTACAATACTGCTAGTAATGGTCA 58.730 38.462 12.80 0.00 36.23 4.02
145 146 6.420008 CGGTTACAATACTGCTAGTAATGGTC 59.580 42.308 12.80 5.81 36.23 4.02
146 147 6.097270 TCGGTTACAATACTGCTAGTAATGGT 59.903 38.462 12.80 8.49 36.23 3.55
147 148 6.509656 TCGGTTACAATACTGCTAGTAATGG 58.490 40.000 12.80 4.64 36.23 3.16
148 149 7.997107 TTCGGTTACAATACTGCTAGTAATG 57.003 36.000 8.79 8.79 37.55 1.90
149 150 7.656137 CCATTCGGTTACAATACTGCTAGTAAT 59.344 37.037 0.00 0.00 33.89 1.89
150 151 6.982141 CCATTCGGTTACAATACTGCTAGTAA 59.018 38.462 0.00 0.00 33.89 2.24
151 152 6.097270 ACCATTCGGTTACAATACTGCTAGTA 59.903 38.462 0.00 0.00 46.31 1.82
152 153 5.105064 ACCATTCGGTTACAATACTGCTAGT 60.105 40.000 0.00 0.00 46.31 2.57
153 154 5.357257 ACCATTCGGTTACAATACTGCTAG 58.643 41.667 0.00 0.00 46.31 3.42
154 155 5.347620 ACCATTCGGTTACAATACTGCTA 57.652 39.130 0.00 0.00 46.31 3.49
155 156 4.216411 ACCATTCGGTTACAATACTGCT 57.784 40.909 0.00 0.00 46.31 4.24
186 187 8.160765 TCCTGAGTGTAGTCAATTGGATAAAAA 58.839 33.333 5.42 0.00 0.00 1.94
187 188 7.685481 TCCTGAGTGTAGTCAATTGGATAAAA 58.315 34.615 5.42 0.00 0.00 1.52
188 189 7.038302 ACTCCTGAGTGTAGTCAATTGGATAAA 60.038 37.037 5.42 0.00 40.75 1.40
189 190 6.440647 ACTCCTGAGTGTAGTCAATTGGATAA 59.559 38.462 5.42 0.00 40.75 1.75
190 191 5.958380 ACTCCTGAGTGTAGTCAATTGGATA 59.042 40.000 5.42 0.00 40.75 2.59
191 192 4.780021 ACTCCTGAGTGTAGTCAATTGGAT 59.220 41.667 5.42 0.00 40.75 3.41
192 193 4.160329 ACTCCTGAGTGTAGTCAATTGGA 58.840 43.478 5.42 0.00 40.75 3.53
193 194 4.543590 ACTCCTGAGTGTAGTCAATTGG 57.456 45.455 5.42 0.00 40.75 3.16
194 195 6.025749 TGTACTCCTGAGTGTAGTCAATTG 57.974 41.667 10.02 0.00 42.52 2.32
195 196 5.775701 ACTGTACTCCTGAGTGTAGTCAATT 59.224 40.000 10.02 0.00 42.52 2.32
196 197 5.326069 ACTGTACTCCTGAGTGTAGTCAAT 58.674 41.667 10.02 0.00 42.52 2.57
197 198 4.726583 ACTGTACTCCTGAGTGTAGTCAA 58.273 43.478 10.02 0.00 42.52 3.18
198 199 4.368565 ACTGTACTCCTGAGTGTAGTCA 57.631 45.455 10.02 1.77 42.52 3.41
199 200 4.616373 GCAACTGTACTCCTGAGTGTAGTC 60.616 50.000 10.02 0.99 42.52 2.59
200 201 3.256136 GCAACTGTACTCCTGAGTGTAGT 59.744 47.826 10.02 10.35 42.52 2.73
201 202 3.508012 AGCAACTGTACTCCTGAGTGTAG 59.492 47.826 10.02 9.79 42.52 2.74
202 203 3.255888 CAGCAACTGTACTCCTGAGTGTA 59.744 47.826 10.02 0.00 42.52 2.90
203 204 2.036475 CAGCAACTGTACTCCTGAGTGT 59.964 50.000 10.02 0.00 42.52 3.55
204 205 2.681706 CAGCAACTGTACTCCTGAGTG 58.318 52.381 10.02 0.00 42.52 3.51
205 206 1.001406 GCAGCAACTGTACTCCTGAGT 59.999 52.381 5.01 5.01 37.42 3.41
206 207 1.274728 AGCAGCAACTGTACTCCTGAG 59.725 52.381 0.00 0.00 33.43 3.35
207 208 1.273606 GAGCAGCAACTGTACTCCTGA 59.726 52.381 0.00 0.00 33.43 3.86
208 209 1.674221 GGAGCAGCAACTGTACTCCTG 60.674 57.143 11.73 0.00 37.59 3.86
209 210 0.610687 GGAGCAGCAACTGTACTCCT 59.389 55.000 11.73 0.00 37.59 3.69
210 211 0.321671 TGGAGCAGCAACTGTACTCC 59.678 55.000 11.98 11.98 39.53 3.85
211 212 2.275318 GATGGAGCAGCAACTGTACTC 58.725 52.381 0.00 0.00 33.43 2.59
212 213 1.065854 GGATGGAGCAGCAACTGTACT 60.066 52.381 0.00 0.00 33.43 2.73
213 214 1.065854 AGGATGGAGCAGCAACTGTAC 60.066 52.381 0.00 0.00 33.43 2.90
214 215 1.279496 AGGATGGAGCAGCAACTGTA 58.721 50.000 0.00 0.00 33.43 2.74
215 216 0.403271 AAGGATGGAGCAGCAACTGT 59.597 50.000 0.00 0.00 33.43 3.55
216 217 1.093159 GAAGGATGGAGCAGCAACTG 58.907 55.000 0.00 0.00 34.12 3.16
217 218 0.392193 CGAAGGATGGAGCAGCAACT 60.392 55.000 0.00 0.00 0.00 3.16
218 219 0.674895 ACGAAGGATGGAGCAGCAAC 60.675 55.000 0.00 0.00 0.00 4.17
219 220 0.036732 AACGAAGGATGGAGCAGCAA 59.963 50.000 0.00 0.00 0.00 3.91
220 221 0.036732 AAACGAAGGATGGAGCAGCA 59.963 50.000 0.00 0.00 0.00 4.41
221 222 1.168714 AAAACGAAGGATGGAGCAGC 58.831 50.000 0.00 0.00 0.00 5.25
424 425 9.679661 AAGGTTTGGTCAAAGTCAAATTTTATT 57.320 25.926 0.00 0.00 35.66 1.40
429 430 9.927668 CATATAAGGTTTGGTCAAAGTCAAATT 57.072 29.630 0.00 0.00 35.66 1.82
430 431 8.034804 GCATATAAGGTTTGGTCAAAGTCAAAT 58.965 33.333 0.00 0.00 35.66 2.32
431 432 7.014711 TGCATATAAGGTTTGGTCAAAGTCAAA 59.985 33.333 0.00 0.00 0.00 2.69
432 433 6.491745 TGCATATAAGGTTTGGTCAAAGTCAA 59.508 34.615 0.00 0.00 0.00 3.18
433 434 6.007076 TGCATATAAGGTTTGGTCAAAGTCA 58.993 36.000 0.00 0.00 0.00 3.41
434 435 6.374333 TCTGCATATAAGGTTTGGTCAAAGTC 59.626 38.462 0.00 0.00 0.00 3.01
435 436 6.151144 GTCTGCATATAAGGTTTGGTCAAAGT 59.849 38.462 0.00 0.00 0.00 2.66
436 437 6.375455 AGTCTGCATATAAGGTTTGGTCAAAG 59.625 38.462 0.00 0.00 0.00 2.77
437 438 6.245408 AGTCTGCATATAAGGTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
438 439 5.815581 AGTCTGCATATAAGGTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
439 440 5.435686 AGTCTGCATATAAGGTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
440 441 7.859325 TTAAGTCTGCATATAAGGTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
441 442 8.644374 TTTTAAGTCTGCATATAAGGTTTGGT 57.356 30.769 0.00 0.00 0.00 3.67
501 502 8.437742 GGTTTCGTCACTTCGATTTATTCTTAA 58.562 33.333 0.00 0.00 39.57 1.85
508 509 4.628333 GGATGGTTTCGTCACTTCGATTTA 59.372 41.667 0.00 0.00 39.57 1.40
514 515 5.873179 TTATTGGATGGTTTCGTCACTTC 57.127 39.130 0.00 0.00 0.00 3.01
551 553 0.750850 GCTTCGGTGGCAGGACTATA 59.249 55.000 0.00 0.00 0.00 1.31
552 554 1.264749 TGCTTCGGTGGCAGGACTAT 61.265 55.000 0.00 0.00 34.56 2.12
553 555 1.911269 TGCTTCGGTGGCAGGACTA 60.911 57.895 0.00 0.00 34.56 2.59
554 556 3.241530 TGCTTCGGTGGCAGGACT 61.242 61.111 0.00 0.00 34.56 3.85
595 635 2.838637 TTATTGGGAATGGGTCACCC 57.161 50.000 5.63 5.63 45.71 4.61
596 636 3.909732 TCATTATTGGGAATGGGTCACC 58.090 45.455 0.00 0.00 37.41 4.02
597 637 7.595819 TTATTCATTATTGGGAATGGGTCAC 57.404 36.000 0.00 0.00 37.41 3.67
598 638 8.795899 ATTTATTCATTATTGGGAATGGGTCA 57.204 30.769 0.00 0.00 37.41 4.02
600 640 8.795899 TGATTTATTCATTATTGGGAATGGGT 57.204 30.769 0.00 0.00 37.41 4.51
624 664 8.003784 GCTTTCTTGATTTTGTCGGTTTATTTG 58.996 33.333 0.00 0.00 0.00 2.32
670 726 9.270707 TGATTGATTATTTTCCTTCCATTTCCT 57.729 29.630 0.00 0.00 0.00 3.36
671 727 9.889128 TTGATTGATTATTTTCCTTCCATTTCC 57.111 29.630 0.00 0.00 0.00 3.13
687 743 6.730447 TCCAAGGGTCTGATTTGATTGATTA 58.270 36.000 0.00 0.00 0.00 1.75
813 875 1.176619 TGCGAGGTTGGAGAAGACGA 61.177 55.000 0.00 0.00 0.00 4.20
1432 1528 3.554692 GAAGATGCGGCCGTCGTG 61.555 66.667 28.70 0.00 41.72 4.35
1455 1551 2.847234 ACCTTGCCGTCCTGGTGA 60.847 61.111 0.00 0.00 41.21 4.02
1533 1629 3.259374 TCTTGAGGTAGTCCTTGAGCTTG 59.741 47.826 0.00 0.00 45.24 4.01
1560 1656 1.002502 GTAGCTGGTGGGGTTGACC 60.003 63.158 0.00 0.00 39.11 4.02
2718 2892 9.602568 ACCAAAACCGAACTGTATTTTAATTTT 57.397 25.926 0.00 0.00 0.00 1.82
2750 2924 6.374894 ACCGAAACCATACCGAAATAATTTGA 59.625 34.615 0.00 0.00 0.00 2.69
2784 2958 2.520979 TCGCGTCAACTTTGGTTTTTG 58.479 42.857 5.77 0.00 32.73 2.44
3223 3407 7.715657 TCACTCTGTGCATTTAAAAACTGAAT 58.284 30.769 0.00 0.00 32.98 2.57
3251 3435 2.262915 CGTGGCCTGTGACCTCTC 59.737 66.667 3.32 0.00 0.00 3.20
3252 3436 2.524394 ACGTGGCCTGTGACCTCT 60.524 61.111 3.32 0.00 0.00 3.69
3253 3437 2.048127 GACGTGGCCTGTGACCTC 60.048 66.667 3.32 0.00 0.00 3.85
3257 3441 1.234821 GAATTTGACGTGGCCTGTGA 58.765 50.000 3.32 0.00 0.00 3.58
3261 3445 0.536460 AACCGAATTTGACGTGGCCT 60.536 50.000 3.32 0.00 0.00 5.19
3262 3446 0.386731 CAACCGAATTTGACGTGGCC 60.387 55.000 0.00 0.00 0.00 5.36
3263 3447 0.589223 TCAACCGAATTTGACGTGGC 59.411 50.000 0.00 0.00 30.29 5.01
3264 3448 2.309898 GTCAACCGAATTTGACGTGG 57.690 50.000 0.00 0.00 44.41 4.94
3269 3453 3.762407 TCCTCTGTCAACCGAATTTGA 57.238 42.857 0.00 0.00 32.94 2.69
3270 3454 3.189287 CCTTCCTCTGTCAACCGAATTTG 59.811 47.826 0.00 0.00 0.00 2.32
3271 3455 3.072476 TCCTTCCTCTGTCAACCGAATTT 59.928 43.478 0.00 0.00 0.00 1.82
3272 3456 2.637872 TCCTTCCTCTGTCAACCGAATT 59.362 45.455 0.00 0.00 0.00 2.17
3273 3457 2.257207 TCCTTCCTCTGTCAACCGAAT 58.743 47.619 0.00 0.00 0.00 3.34
3274 3458 1.712056 TCCTTCCTCTGTCAACCGAA 58.288 50.000 0.00 0.00 0.00 4.30
3275 3459 1.712056 TTCCTTCCTCTGTCAACCGA 58.288 50.000 0.00 0.00 0.00 4.69
3276 3460 2.543777 TTTCCTTCCTCTGTCAACCG 57.456 50.000 0.00 0.00 0.00 4.44
3277 3461 3.507622 CCATTTTCCTTCCTCTGTCAACC 59.492 47.826 0.00 0.00 0.00 3.77
3278 3462 4.145052 ACCATTTTCCTTCCTCTGTCAAC 58.855 43.478 0.00 0.00 0.00 3.18
3279 3463 4.453480 ACCATTTTCCTTCCTCTGTCAA 57.547 40.909 0.00 0.00 0.00 3.18
3280 3464 4.453480 AACCATTTTCCTTCCTCTGTCA 57.547 40.909 0.00 0.00 0.00 3.58
3281 3465 5.069119 ACAAAACCATTTTCCTTCCTCTGTC 59.931 40.000 0.00 0.00 0.00 3.51
3282 3466 4.962362 ACAAAACCATTTTCCTTCCTCTGT 59.038 37.500 0.00 0.00 0.00 3.41
3283 3467 5.291971 CACAAAACCATTTTCCTTCCTCTG 58.708 41.667 0.00 0.00 0.00 3.35
3284 3468 4.344968 CCACAAAACCATTTTCCTTCCTCT 59.655 41.667 0.00 0.00 0.00 3.69
3285 3469 4.503123 CCCACAAAACCATTTTCCTTCCTC 60.503 45.833 0.00 0.00 0.00 3.71
3286 3470 3.390967 CCCACAAAACCATTTTCCTTCCT 59.609 43.478 0.00 0.00 0.00 3.36
3287 3471 3.135712 ACCCACAAAACCATTTTCCTTCC 59.864 43.478 0.00 0.00 0.00 3.46
3288 3472 4.126437 CACCCACAAAACCATTTTCCTTC 58.874 43.478 0.00 0.00 0.00 3.46
3289 3473 3.777522 TCACCCACAAAACCATTTTCCTT 59.222 39.130 0.00 0.00 0.00 3.36
3290 3474 3.379452 TCACCCACAAAACCATTTTCCT 58.621 40.909 0.00 0.00 0.00 3.36
3291 3475 3.828875 TCACCCACAAAACCATTTTCC 57.171 42.857 0.00 0.00 0.00 3.13
3292 3476 6.094742 ACAAAATCACCCACAAAACCATTTTC 59.905 34.615 0.00 0.00 0.00 2.29
3293 3477 5.948758 ACAAAATCACCCACAAAACCATTTT 59.051 32.000 0.00 0.00 0.00 1.82
3294 3478 5.504853 ACAAAATCACCCACAAAACCATTT 58.495 33.333 0.00 0.00 0.00 2.32
3295 3479 5.109500 ACAAAATCACCCACAAAACCATT 57.891 34.783 0.00 0.00 0.00 3.16
3296 3480 4.769345 ACAAAATCACCCACAAAACCAT 57.231 36.364 0.00 0.00 0.00 3.55
3297 3481 4.559862 AACAAAATCACCCACAAAACCA 57.440 36.364 0.00 0.00 0.00 3.67
3298 3482 4.697828 ACAAACAAAATCACCCACAAAACC 59.302 37.500 0.00 0.00 0.00 3.27
3299 3483 5.871465 ACAAACAAAATCACCCACAAAAC 57.129 34.783 0.00 0.00 0.00 2.43
3300 3484 6.371825 GGTTACAAACAAAATCACCCACAAAA 59.628 34.615 0.00 0.00 0.00 2.44
3301 3485 5.875359 GGTTACAAACAAAATCACCCACAAA 59.125 36.000 0.00 0.00 0.00 2.83
3302 3486 5.046591 TGGTTACAAACAAAATCACCCACAA 60.047 36.000 0.00 0.00 0.00 3.33
3303 3487 4.466370 TGGTTACAAACAAAATCACCCACA 59.534 37.500 0.00 0.00 0.00 4.17
3304 3488 5.012328 TGGTTACAAACAAAATCACCCAC 57.988 39.130 0.00 0.00 0.00 4.61
3305 3489 5.878406 ATGGTTACAAACAAAATCACCCA 57.122 34.783 0.00 0.00 0.00 4.51
3306 3490 6.284459 TCAATGGTTACAAACAAAATCACCC 58.716 36.000 0.00 0.00 0.00 4.61
3307 3491 7.206687 TCTCAATGGTTACAAACAAAATCACC 58.793 34.615 0.00 0.00 0.00 4.02
3308 3492 8.816640 ATCTCAATGGTTACAAACAAAATCAC 57.183 30.769 0.00 0.00 0.00 3.06
3315 3499 8.739039 CCAAATCTATCTCAATGGTTACAAACA 58.261 33.333 0.00 0.00 0.00 2.83
3316 3500 8.739972 ACCAAATCTATCTCAATGGTTACAAAC 58.260 33.333 0.00 0.00 37.92 2.93
3317 3501 8.739039 CACCAAATCTATCTCAATGGTTACAAA 58.261 33.333 0.00 0.00 39.05 2.83
3318 3502 7.148086 GCACCAAATCTATCTCAATGGTTACAA 60.148 37.037 0.00 0.00 39.05 2.41
3319 3503 6.318648 GCACCAAATCTATCTCAATGGTTACA 59.681 38.462 0.00 0.00 39.05 2.41
3320 3504 6.318648 TGCACCAAATCTATCTCAATGGTTAC 59.681 38.462 0.00 0.00 39.05 2.50
3321 3505 6.422333 TGCACCAAATCTATCTCAATGGTTA 58.578 36.000 0.00 0.00 39.05 2.85
3322 3506 5.263599 TGCACCAAATCTATCTCAATGGTT 58.736 37.500 0.00 0.00 39.05 3.67
3323 3507 4.858850 TGCACCAAATCTATCTCAATGGT 58.141 39.130 0.00 0.00 41.65 3.55
3324 3508 5.125900 TGTTGCACCAAATCTATCTCAATGG 59.874 40.000 0.00 0.00 0.00 3.16
3325 3509 6.198650 TGTTGCACCAAATCTATCTCAATG 57.801 37.500 0.00 0.00 0.00 2.82
3326 3510 6.127535 CCTTGTTGCACCAAATCTATCTCAAT 60.128 38.462 0.00 0.00 0.00 2.57
3327 3511 5.183713 CCTTGTTGCACCAAATCTATCTCAA 59.816 40.000 0.00 0.00 0.00 3.02
3328 3512 4.701651 CCTTGTTGCACCAAATCTATCTCA 59.298 41.667 0.00 0.00 0.00 3.27
3329 3513 4.702131 ACCTTGTTGCACCAAATCTATCTC 59.298 41.667 0.00 0.00 0.00 2.75
3330 3514 4.460382 CACCTTGTTGCACCAAATCTATCT 59.540 41.667 0.00 0.00 0.00 1.98
3331 3515 4.218417 ACACCTTGTTGCACCAAATCTATC 59.782 41.667 0.00 0.00 0.00 2.08
3332 3516 4.022068 CACACCTTGTTGCACCAAATCTAT 60.022 41.667 0.00 0.00 0.00 1.98
3333 3517 3.317711 CACACCTTGTTGCACCAAATCTA 59.682 43.478 0.00 0.00 0.00 1.98
3334 3518 2.101249 CACACCTTGTTGCACCAAATCT 59.899 45.455 0.00 0.00 0.00 2.40
3335 3519 2.472816 CACACCTTGTTGCACCAAATC 58.527 47.619 0.00 0.00 0.00 2.17
3336 3520 1.473080 GCACACCTTGTTGCACCAAAT 60.473 47.619 0.00 0.00 0.00 2.32
3337 3521 0.108424 GCACACCTTGTTGCACCAAA 60.108 50.000 0.00 0.00 0.00 3.28
3338 3522 1.253593 TGCACACCTTGTTGCACCAA 61.254 50.000 0.00 0.00 32.45 3.67
3339 3523 1.042003 ATGCACACCTTGTTGCACCA 61.042 50.000 0.00 0.00 37.28 4.17
3340 3524 0.104671 AATGCACACCTTGTTGCACC 59.895 50.000 0.00 0.00 37.28 5.01
3341 3525 2.791383 TAATGCACACCTTGTTGCAC 57.209 45.000 0.00 0.00 37.28 4.57
3342 3526 3.492309 CCTTTAATGCACACCTTGTTGCA 60.492 43.478 0.00 0.00 38.21 4.08
3343 3527 3.059166 CCTTTAATGCACACCTTGTTGC 58.941 45.455 0.00 0.00 0.00 4.17
3344 3528 4.320608 ACCTTTAATGCACACCTTGTTG 57.679 40.909 0.00 0.00 0.00 3.33
3345 3529 4.692228 CAACCTTTAATGCACACCTTGTT 58.308 39.130 0.00 0.00 0.00 2.83
3346 3530 3.492482 GCAACCTTTAATGCACACCTTGT 60.492 43.478 0.00 0.00 42.12 3.16
3347 3531 3.059166 GCAACCTTTAATGCACACCTTG 58.941 45.455 0.00 0.00 42.12 3.61
3348 3532 2.965147 AGCAACCTTTAATGCACACCTT 59.035 40.909 0.00 0.00 44.95 3.50
3349 3533 2.558359 GAGCAACCTTTAATGCACACCT 59.442 45.455 0.00 0.00 44.95 4.00
3350 3534 2.295909 TGAGCAACCTTTAATGCACACC 59.704 45.455 0.00 0.00 44.95 4.16
3351 3535 3.253188 TCTGAGCAACCTTTAATGCACAC 59.747 43.478 0.00 0.00 44.95 3.82
3352 3536 3.485394 TCTGAGCAACCTTTAATGCACA 58.515 40.909 0.00 0.98 44.95 4.57
3353 3537 4.503741 TTCTGAGCAACCTTTAATGCAC 57.496 40.909 0.00 0.00 44.95 4.57
3354 3538 5.528043 TTTTCTGAGCAACCTTTAATGCA 57.472 34.783 1.90 0.00 44.95 3.96


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

AutoCloner maintained by Alex Coulton.