Multiple sequence alignment - TraesCS2D01G129000

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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 TraesCS2D01G129000 chr2D 100.000 4055 0 0 1 4055 74990351 74994405 0.000000e+00 7489.0
1 TraesCS2D01G129000 chr2D 84.955 1768 227 25 1329 3088 74995351 74997087 0.000000e+00 1755.0
2 TraesCS2D01G129000 chr2D 86.560 1503 187 9 1614 3108 74999740 75001235 0.000000e+00 1642.0
3 TraesCS2D01G129000 chr2D 86.504 615 69 8 1010 1620 74998916 74999520 0.000000e+00 664.0
4 TraesCS2D01G129000 chr2D 95.122 41 1 1 665 704 74990979 74991019 3.380000e-06 63.9
5 TraesCS2D01G129000 chr2D 95.122 41 1 1 629 669 74991015 74991054 3.380000e-06 63.9
6 TraesCS2D01G129000 chr2A 95.425 3235 122 11 836 4052 74775603 74778829 0.000000e+00 5131.0
7 TraesCS2D01G129000 chr2A 85.264 2158 262 30 933 3061 74765433 74767563 0.000000e+00 2172.0
8 TraesCS2D01G129000 chr2A 85.449 1615 217 14 1482 3088 74780262 74781866 0.000000e+00 1664.0
9 TraesCS2D01G129000 chr2A 91.464 1195 97 3 1928 3119 74643792 74644984 0.000000e+00 1637.0
10 TraesCS2D01G129000 chr2A 86.267 1500 198 6 1614 3108 74785945 74787441 0.000000e+00 1622.0
11 TraesCS2D01G129000 chr2A 85.832 607 71 8 1010 1610 74626625 74627222 7.400000e-177 630.0
12 TraesCS2D01G129000 chr2A 85.065 462 58 7 1010 1470 74784023 74784474 1.030000e-125 460.0
13 TraesCS2D01G129000 chr2A 81.579 342 49 8 1103 1434 74779915 74780252 1.860000e-68 270.0
14 TraesCS2D01G129000 chr2A 84.470 264 30 5 3502 3757 74694729 74694989 2.420000e-62 250.0
15 TraesCS2D01G129000 chr2A 89.744 78 1 3 742 817 74775484 74775556 4.320000e-15 93.5
16 TraesCS2D01G129000 chr2B 96.078 2728 96 6 815 3540 114548763 114551481 0.000000e+00 4434.0
17 TraesCS2D01G129000 chr2B 97.099 1103 26 2 818 1920 114486697 114487793 0.000000e+00 1855.0
18 TraesCS2D01G129000 chr2B 85.999 1507 190 14 1614 3108 114644841 114646338 0.000000e+00 1594.0
19 TraesCS2D01G129000 chr2B 84.625 761 110 7 1362 2120 114501415 114502170 0.000000e+00 750.0
20 TraesCS2D01G129000 chr2B 87.288 590 66 6 1037 1620 114643780 114644366 0.000000e+00 665.0
21 TraesCS2D01G129000 chr2B 86.290 620 66 10 1010 1620 114517931 114518540 0.000000e+00 656.0
22 TraesCS2D01G129000 chr2B 93.810 420 20 1 74 487 114476431 114476850 9.570000e-176 627.0
23 TraesCS2D01G129000 chr2B 86.064 531 52 14 3534 4043 114554191 114554720 5.920000e-153 551.0
24 TraesCS2D01G129000 chr2B 85.824 522 52 13 3543 4043 114500235 114500755 5.970000e-148 534.0
25 TraesCS2D01G129000 chr2B 97.222 252 7 0 566 817 114548485 114548736 1.040000e-115 427.0
26 TraesCS2D01G129000 chr2B 96.795 156 5 0 662 817 114486512 114486667 1.120000e-65 261.0
27 TraesCS2D01G129000 chr2B 84.559 272 28 6 853 1123 114555119 114555377 1.450000e-64 257.0
28 TraesCS2D01G129000 chr2B 78.317 309 36 18 510 817 114500528 114500806 1.940000e-38 171.0
29 TraesCS2D01G129000 chr2B 97.333 75 2 0 604 678 114486423 114486497 1.180000e-25 128.0
30 TraesCS2D01G129000 chr2B 94.805 77 4 0 543 619 114476846 114476922 1.980000e-23 121.0
31 TraesCS2D01G129000 chr2B 93.333 60 4 0 758 817 114475968 114476027 5.580000e-14 89.8
32 TraesCS2D01G129000 chr2B 94.643 56 3 0 758 813 114529369 114529424 2.010000e-13 87.9
33 TraesCS2D01G129000 chr2B 97.500 40 0 1 665 703 114486448 114486487 2.620000e-07 67.6
34 TraesCS2D01G129000 chr2B 95.122 41 1 1 629 669 114486515 114486554 3.380000e-06 63.9
35 TraesCS2D01G129000 chr2B 95.000 40 1 1 665 703 114548548 114548587 1.220000e-05 62.1
36 TraesCS2D01G129000 chr2B 90.244 41 4 0 365 405 593632114 593632154 2.000000e-03 54.7
37 TraesCS2D01G129000 chr1A 85.714 154 16 2 282 435 471785397 471785250 1.510000e-34 158.0
38 TraesCS2D01G129000 chr4A 88.596 114 12 1 331 444 120564410 120564522 1.970000e-28 137.0
39 TraesCS2D01G129000 chr4A 89.552 67 6 1 371 436 23315980 23316046 2.600000e-12 84.2
40 TraesCS2D01G129000 chr4D 87.129 101 13 0 331 431 344857298 344857398 9.210000e-22 115.0
41 TraesCS2D01G129000 chr4B 80.537 149 18 6 254 401 624430132 624429994 1.990000e-18 104.0
42 TraesCS2D01G129000 chr4B 75.207 242 47 7 252 485 494690015 494690251 7.170000e-18 102.0
43 TraesCS2D01G129000 chr3B 81.731 104 18 1 332 434 239733180 239733283 7.220000e-13 86.1
44 TraesCS2D01G129000 chr1B 84.211 76 10 2 87 161 330840181 330840107 5.620000e-09 73.1
45 TraesCS2D01G129000 chr3A 92.683 41 3 0 3767 3807 584765683 584765643 4.380000e-05 60.2


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 TraesCS2D01G129000 chr2D 74990351 74994405 4054 False 2538.933333 7489 96.748000 1 4055 3 chr2D.!!$F1 4054
1 TraesCS2D01G129000 chr2D 74995351 75001235 5884 False 1353.666667 1755 86.006333 1010 3108 3 chr2D.!!$F2 2098
2 TraesCS2D01G129000 chr2A 74765433 74767563 2130 False 2172.000000 2172 85.264000 933 3061 1 chr2A.!!$F4 2128
3 TraesCS2D01G129000 chr2A 74643792 74644984 1192 False 1637.000000 1637 91.464000 1928 3119 1 chr2A.!!$F2 1191
4 TraesCS2D01G129000 chr2A 74775484 74787441 11957 False 1540.083333 5131 87.254833 742 4052 6 chr2A.!!$F5 3310
5 TraesCS2D01G129000 chr2A 74626625 74627222 597 False 630.000000 630 85.832000 1010 1610 1 chr2A.!!$F1 600
6 TraesCS2D01G129000 chr2B 114548485 114555377 6892 False 1146.220000 4434 91.784600 566 4043 5 chr2B.!!$F7 3477
7 TraesCS2D01G129000 chr2B 114643780 114646338 2558 False 1129.500000 1594 86.643500 1037 3108 2 chr2B.!!$F8 2071
8 TraesCS2D01G129000 chr2B 114517931 114518540 609 False 656.000000 656 86.290000 1010 1620 1 chr2B.!!$F1 610
9 TraesCS2D01G129000 chr2B 114500235 114502170 1935 False 485.000000 750 82.922000 510 4043 3 chr2B.!!$F6 3533
10 TraesCS2D01G129000 chr2B 114486423 114487793 1370 False 475.100000 1855 96.769800 604 1920 5 chr2B.!!$F5 1316
11 TraesCS2D01G129000 chr2B 114475968 114476922 954 False 279.266667 627 93.982667 74 817 3 chr2B.!!$F4 743

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
488 489 0.037326 GCTGCGCATGGCTAGGTATA 60.037 55.000 12.24 0.00 44.05 1.47 F
493 494 1.204941 CGCATGGCTAGGTATACTCCC 59.795 57.143 2.25 0.00 0.00 4.30 F
1259 4336 1.728426 GTTCCACCACGACGACGAG 60.728 63.158 15.32 5.96 42.66 4.18 F
2138 5883 1.808945 CAGAGGATTGCTTTCTGCGTT 59.191 47.619 0.00 0.00 46.63 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2138 5883 0.958091 CACCGCAACCTCCAAATTGA 59.042 50.000 0.00 0.0 0.00 2.57 R
2372 6117 2.616960 CGACACCTTTGATGATCCGAA 58.383 47.619 0.00 0.0 0.00 4.30 R
2644 6389 0.107508 CCACATGCGACCTCAAGGAT 60.108 55.000 2.30 0.0 38.94 3.24 R
3243 6992 0.682209 TACACCTCGCCAGGGACTAC 60.682 60.000 1.31 0.0 45.53 2.73 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
25 26 2.751688 GTGGGCCCCTTACGTCAA 59.248 61.111 22.27 0.00 0.00 3.18
26 27 1.073548 GTGGGCCCCTTACGTCAAA 59.926 57.895 22.27 0.00 0.00 2.69
27 28 0.537828 GTGGGCCCCTTACGTCAAAA 60.538 55.000 22.27 0.00 0.00 2.44
29 30 1.634459 TGGGCCCCTTACGTCAAAATA 59.366 47.619 22.27 0.00 0.00 1.40
66 67 7.586714 ACTTCTTACGTAAATAGAAAACGGG 57.413 36.000 18.19 6.70 40.81 5.28
67 68 6.091305 ACTTCTTACGTAAATAGAAAACGGGC 59.909 38.462 18.19 0.00 40.81 6.13
68 69 4.869861 TCTTACGTAAATAGAAAACGGGCC 59.130 41.667 9.68 0.00 40.81 5.80
69 70 2.358957 ACGTAAATAGAAAACGGGCCC 58.641 47.619 13.57 13.57 40.81 5.80
70 71 1.328374 CGTAAATAGAAAACGGGCCCG 59.672 52.381 42.17 42.17 46.03 6.13
83 84 1.152312 GGCCCGATCTTCCCTCCTA 60.152 63.158 0.00 0.00 0.00 2.94
85 86 0.470268 GCCCGATCTTCCCTCCTAGT 60.470 60.000 0.00 0.00 0.00 2.57
88 89 2.491825 CCCGATCTTCCCTCCTAGTGAT 60.492 54.545 0.00 0.00 0.00 3.06
89 90 2.823154 CCGATCTTCCCTCCTAGTGATC 59.177 54.545 0.00 0.00 0.00 2.92
90 91 2.823154 CGATCTTCCCTCCTAGTGATCC 59.177 54.545 0.00 0.00 0.00 3.36
92 93 3.776731 TCTTCCCTCCTAGTGATCCAA 57.223 47.619 0.00 0.00 0.00 3.53
95 96 5.788430 TCTTCCCTCCTAGTGATCCAATAA 58.212 41.667 0.00 0.00 0.00 1.40
96 97 6.393897 TCTTCCCTCCTAGTGATCCAATAAT 58.606 40.000 0.00 0.00 0.00 1.28
97 98 7.544650 TCTTCCCTCCTAGTGATCCAATAATA 58.455 38.462 0.00 0.00 0.00 0.98
99 100 8.757307 TTCCCTCCTAGTGATCCAATAATAAT 57.243 34.615 0.00 0.00 0.00 1.28
101 102 7.403231 TCCCTCCTAGTGATCCAATAATAATCC 59.597 40.741 0.00 0.00 0.00 3.01
103 104 8.482128 CCTCCTAGTGATCCAATAATAATCCTC 58.518 40.741 0.00 0.00 0.00 3.71
105 106 7.961431 TCCTAGTGATCCAATAATAATCCTCCA 59.039 37.037 0.00 0.00 0.00 3.86
106 107 8.263640 CCTAGTGATCCAATAATAATCCTCCAG 58.736 40.741 0.00 0.00 0.00 3.86
107 108 7.025520 AGTGATCCAATAATAATCCTCCAGG 57.974 40.000 0.00 0.00 0.00 4.45
108 109 6.012157 AGTGATCCAATAATAATCCTCCAGGG 60.012 42.308 0.00 0.00 35.41 4.45
110 111 7.028760 TGATCCAATAATAATCCTCCAGGGTA 58.971 38.462 0.00 0.00 36.25 3.69
111 112 6.697641 TCCAATAATAATCCTCCAGGGTAC 57.302 41.667 0.00 0.00 36.25 3.34
114 115 7.017254 TCCAATAATAATCCTCCAGGGTACTTC 59.983 40.741 0.00 0.00 36.25 3.01
117 118 9.684702 AATAATAATCCTCCAGGGTACTTCTTA 57.315 33.333 0.00 0.00 36.25 2.10
120 121 2.042162 TCCTCCAGGGTACTTCTTACGT 59.958 50.000 0.00 0.00 36.25 3.57
122 123 4.019174 CCTCCAGGGTACTTCTTACGTAA 58.981 47.826 7.94 7.94 0.00 3.18
123 124 4.463891 CCTCCAGGGTACTTCTTACGTAAA 59.536 45.833 9.68 0.00 0.00 2.01
125 126 6.212888 TCCAGGGTACTTCTTACGTAAATC 57.787 41.667 9.68 0.00 0.00 2.17
126 127 5.716228 TCCAGGGTACTTCTTACGTAAATCA 59.284 40.000 9.68 0.00 0.00 2.57
149 150 4.798574 CGTACCAAACTTTACGTAGGTCT 58.201 43.478 5.30 0.00 37.02 3.85
150 151 5.938322 CGTACCAAACTTTACGTAGGTCTA 58.062 41.667 5.30 0.00 37.02 2.59
154 155 5.046807 ACCAAACTTTACGTAGGTCTAGCAT 60.047 40.000 0.00 0.00 30.80 3.79
156 157 7.037438 CCAAACTTTACGTAGGTCTAGCATTA 58.963 38.462 0.00 0.00 0.00 1.90
157 158 7.009907 CCAAACTTTACGTAGGTCTAGCATTAC 59.990 40.741 0.00 0.00 0.00 1.89
158 159 7.401955 AACTTTACGTAGGTCTAGCATTACT 57.598 36.000 0.00 0.00 0.00 2.24
160 161 6.039159 ACTTTACGTAGGTCTAGCATTACTCC 59.961 42.308 0.00 0.00 0.00 3.85
163 164 1.705873 AGGTCTAGCATTACTCCCCG 58.294 55.000 0.00 0.00 0.00 5.73
164 165 1.063114 AGGTCTAGCATTACTCCCCGT 60.063 52.381 0.00 0.00 0.00 5.28
165 166 1.761198 GGTCTAGCATTACTCCCCGTT 59.239 52.381 0.00 0.00 0.00 4.44
166 167 2.169978 GGTCTAGCATTACTCCCCGTTT 59.830 50.000 0.00 0.00 0.00 3.60
168 169 2.433239 TCTAGCATTACTCCCCGTTTCC 59.567 50.000 0.00 0.00 0.00 3.13
169 170 0.255033 AGCATTACTCCCCGTTTCCC 59.745 55.000 0.00 0.00 0.00 3.97
172 173 1.134189 CATTACTCCCCGTTTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
173 174 0.117742 TTACTCCCCGTTTCCCTCCT 59.882 55.000 0.00 0.00 0.00 3.69
175 176 2.285144 TCCCCGTTTCCCTCCTCC 60.285 66.667 0.00 0.00 0.00 4.30
176 177 3.408853 CCCCGTTTCCCTCCTCCC 61.409 72.222 0.00 0.00 0.00 4.30
177 178 2.609610 CCCGTTTCCCTCCTCCCA 60.610 66.667 0.00 0.00 0.00 4.37
178 179 2.228480 CCCGTTTCCCTCCTCCCAA 61.228 63.158 0.00 0.00 0.00 4.12
180 181 1.489560 CCGTTTCCCTCCTCCCAACT 61.490 60.000 0.00 0.00 0.00 3.16
181 182 1.272807 CGTTTCCCTCCTCCCAACTA 58.727 55.000 0.00 0.00 0.00 2.24
184 185 3.181468 CGTTTCCCTCCTCCCAACTATAC 60.181 52.174 0.00 0.00 0.00 1.47
186 187 2.233178 TCCCTCCTCCCAACTATACCT 58.767 52.381 0.00 0.00 0.00 3.08
187 188 2.090719 TCCCTCCTCCCAACTATACCTG 60.091 54.545 0.00 0.00 0.00 4.00
188 189 2.330216 CCTCCTCCCAACTATACCTGG 58.670 57.143 0.00 0.00 0.00 4.45
198 199 4.821805 CCAACTATACCTGGGCATAACTTG 59.178 45.833 0.00 0.98 0.00 3.16
199 200 4.706842 ACTATACCTGGGCATAACTTGG 57.293 45.455 0.00 0.00 0.00 3.61
200 201 3.394606 ACTATACCTGGGCATAACTTGGG 59.605 47.826 0.00 0.00 0.00 4.12
201 202 0.257616 TACCTGGGCATAACTTGGGC 59.742 55.000 0.00 0.00 0.00 5.36
205 206 2.274104 GGCATAACTTGGGCCGGA 59.726 61.111 5.05 0.00 38.04 5.14
206 207 2.119029 GGCATAACTTGGGCCGGAC 61.119 63.158 5.05 0.00 38.04 4.79
208 209 1.817941 CATAACTTGGGCCGGACCG 60.818 63.158 24.84 11.51 40.62 4.79
218 219 4.821589 CCGGACCGAGCTTCAGGC 62.822 72.222 17.49 0.00 42.19 4.85
219 220 4.821589 CGGACCGAGCTTCAGGCC 62.822 72.222 8.64 0.00 43.05 5.19
220 221 3.706373 GGACCGAGCTTCAGGCCA 61.706 66.667 5.01 0.00 43.05 5.36
221 222 2.125350 GACCGAGCTTCAGGCCAG 60.125 66.667 5.01 0.00 43.05 4.85
234 235 2.568003 GGCCAGGCCTAACAAAGAC 58.432 57.895 24.99 0.00 46.69 3.01
235 236 0.965866 GGCCAGGCCTAACAAAGACC 60.966 60.000 24.99 0.00 46.69 3.85
237 238 0.323629 CCAGGCCTAACAAAGACCGA 59.676 55.000 3.98 0.00 0.00 4.69
243 244 2.870435 GCCTAACAAAGACCGAAGCAGA 60.870 50.000 0.00 0.00 0.00 4.26
244 245 3.399330 CCTAACAAAGACCGAAGCAGAA 58.601 45.455 0.00 0.00 0.00 3.02
245 246 3.813166 CCTAACAAAGACCGAAGCAGAAA 59.187 43.478 0.00 0.00 0.00 2.52
255 256 1.464734 GAAGCAGAAAACCTAGGCCC 58.535 55.000 9.30 0.00 0.00 5.80
256 257 0.322546 AAGCAGAAAACCTAGGCCCG 60.323 55.000 9.30 0.00 0.00 6.13
260 261 1.077930 GAAAACCTAGGCCCGTCCC 60.078 63.158 9.30 0.00 34.51 4.46
261 262 2.864378 GAAAACCTAGGCCCGTCCCG 62.864 65.000 9.30 0.00 34.51 5.14
281 282 1.604604 GCTGTGTGGCCTAGTTTTCA 58.395 50.000 3.32 0.00 0.00 2.69
282 283 1.537202 GCTGTGTGGCCTAGTTTTCAG 59.463 52.381 3.32 4.46 0.00 3.02
283 284 2.154462 CTGTGTGGCCTAGTTTTCAGG 58.846 52.381 3.32 0.00 36.16 3.86
300 301 4.956932 GCCCAAGCCCGGCCTATC 62.957 72.222 5.55 0.00 40.78 2.08
302 303 2.111878 CCAAGCCCGGCCTATCAG 59.888 66.667 5.55 0.00 0.00 2.90
303 304 2.443394 CCAAGCCCGGCCTATCAGA 61.443 63.158 5.55 0.00 0.00 3.27
304 305 1.227674 CAAGCCCGGCCTATCAGAC 60.228 63.158 5.55 0.00 0.00 3.51
305 306 1.689233 AAGCCCGGCCTATCAGACA 60.689 57.895 5.55 0.00 0.00 3.41
306 307 1.271840 AAGCCCGGCCTATCAGACAA 61.272 55.000 5.55 0.00 0.00 3.18
307 308 1.223487 GCCCGGCCTATCAGACAAA 59.777 57.895 0.00 0.00 0.00 2.83
308 309 0.393808 GCCCGGCCTATCAGACAAAA 60.394 55.000 0.00 0.00 0.00 2.44
310 311 2.017049 CCCGGCCTATCAGACAAAAAG 58.983 52.381 0.00 0.00 0.00 2.27
311 312 1.401905 CCGGCCTATCAGACAAAAAGC 59.598 52.381 0.00 0.00 0.00 3.51
312 313 1.401905 CGGCCTATCAGACAAAAAGCC 59.598 52.381 0.00 0.00 35.78 4.35
314 315 2.446435 GCCTATCAGACAAAAAGCCCA 58.554 47.619 0.00 0.00 0.00 5.36
315 316 3.026694 GCCTATCAGACAAAAAGCCCAT 58.973 45.455 0.00 0.00 0.00 4.00
316 317 3.448660 GCCTATCAGACAAAAAGCCCATT 59.551 43.478 0.00 0.00 0.00 3.16
318 319 3.967332 ATCAGACAAAAAGCCCATTGG 57.033 42.857 0.00 0.00 0.00 3.16
345 346 3.866703 GGCTAGGCCTCTTCCTTAAAT 57.133 47.619 9.68 0.00 46.69 1.40
346 347 4.171878 GGCTAGGCCTCTTCCTTAAATT 57.828 45.455 9.68 0.00 46.69 1.82
347 348 3.885901 GGCTAGGCCTCTTCCTTAAATTG 59.114 47.826 9.68 0.00 46.69 2.32
348 349 3.316588 GCTAGGCCTCTTCCTTAAATTGC 59.683 47.826 9.68 0.00 37.66 3.56
349 350 3.456380 AGGCCTCTTCCTTAAATTGCA 57.544 42.857 0.00 0.00 30.82 4.08
350 351 3.778265 AGGCCTCTTCCTTAAATTGCAA 58.222 40.909 0.00 0.00 30.82 4.08
351 352 4.159557 AGGCCTCTTCCTTAAATTGCAAA 58.840 39.130 1.71 0.00 30.82 3.68
353 354 5.957774 AGGCCTCTTCCTTAAATTGCAAATA 59.042 36.000 1.71 0.00 30.82 1.40
354 355 6.042777 GGCCTCTTCCTTAAATTGCAAATAC 58.957 40.000 1.71 0.00 0.00 1.89
355 356 5.743872 GCCTCTTCCTTAAATTGCAAATACG 59.256 40.000 1.71 0.00 0.00 3.06
356 357 6.404293 GCCTCTTCCTTAAATTGCAAATACGA 60.404 38.462 1.71 0.00 0.00 3.43
361 362 6.090129 TCCTTAAATTGCAAATACGACAAGC 58.910 36.000 1.71 0.00 0.00 4.01
362 363 6.072175 TCCTTAAATTGCAAATACGACAAGCT 60.072 34.615 1.71 0.00 0.00 3.74
363 364 6.251376 CCTTAAATTGCAAATACGACAAGCTC 59.749 38.462 1.71 0.00 0.00 4.09
365 366 2.073117 TGCAAATACGACAAGCTCGA 57.927 45.000 0.37 0.00 46.14 4.04
367 368 1.267087 GCAAATACGACAAGCTCGAGC 60.267 52.381 30.01 30.01 46.14 5.03
368 369 1.324736 CAAATACGACAAGCTCGAGCC 59.675 52.381 32.94 16.98 46.14 4.70
370 371 2.337749 ATACGACAAGCTCGAGCCCG 62.338 60.000 32.94 28.92 46.14 6.13
388 389 3.145551 GCCAAGCCCAGCCATCAG 61.146 66.667 0.00 0.00 0.00 2.90
389 390 2.441532 CCAAGCCCAGCCATCAGG 60.442 66.667 0.00 0.00 38.23 3.86
408 409 3.133141 GGCTCAAAATCTAGGCCTAGG 57.867 52.381 34.43 20.53 39.68 3.02
431 432 4.820744 CCCATGGGCAAGGTCGGG 62.821 72.222 20.41 0.00 0.00 5.14
432 433 4.047125 CCATGGGCAAGGTCGGGT 62.047 66.667 2.85 0.00 0.00 5.28
445 446 2.746277 CGGGTCGGCCTCTTTTGG 60.746 66.667 5.77 0.00 34.45 3.28
446 447 2.434774 GGGTCGGCCTCTTTTGGT 59.565 61.111 5.77 0.00 34.45 3.67
448 449 1.674651 GGTCGGCCTCTTTTGGTCC 60.675 63.158 0.00 0.00 0.00 4.46
449 450 2.033194 GTCGGCCTCTTTTGGTCCG 61.033 63.158 0.00 9.09 43.23 4.79
450 451 3.431725 CGGCCTCTTTTGGTCCGC 61.432 66.667 0.00 0.00 38.89 5.54
452 453 2.668550 GCCTCTTTTGGTCCGCGT 60.669 61.111 4.92 0.00 0.00 6.01
453 454 2.677979 GCCTCTTTTGGTCCGCGTC 61.678 63.158 4.92 0.00 0.00 5.19
486 487 2.108976 GCTGCGCATGGCTAGGTA 59.891 61.111 12.24 0.00 44.05 3.08
488 489 0.037326 GCTGCGCATGGCTAGGTATA 60.037 55.000 12.24 0.00 44.05 1.47
489 490 1.714794 CTGCGCATGGCTAGGTATAC 58.285 55.000 12.24 0.00 44.05 1.47
490 491 1.273606 CTGCGCATGGCTAGGTATACT 59.726 52.381 12.24 0.00 44.05 2.12
492 493 1.404315 GCGCATGGCTAGGTATACTCC 60.404 57.143 0.30 0.60 39.11 3.85
493 494 1.204941 CGCATGGCTAGGTATACTCCC 59.795 57.143 2.25 0.00 0.00 4.30
494 495 2.257207 GCATGGCTAGGTATACTCCCA 58.743 52.381 2.25 5.04 35.83 4.37
495 496 2.637872 GCATGGCTAGGTATACTCCCAA 59.362 50.000 2.25 0.00 35.25 4.12
497 498 3.700863 TGGCTAGGTATACTCCCAACT 57.299 47.619 2.25 0.00 30.43 3.16
499 500 5.349738 TGGCTAGGTATACTCCCAACTAT 57.650 43.478 2.25 0.00 30.43 2.12
500 501 5.723355 TGGCTAGGTATACTCCCAACTATT 58.277 41.667 2.25 0.00 30.43 1.73
501 502 5.542635 TGGCTAGGTATACTCCCAACTATTG 59.457 44.000 2.25 0.00 30.43 1.90
502 503 5.480205 GCTAGGTATACTCCCAACTATTGC 58.520 45.833 2.25 0.00 0.00 3.56
503 504 5.246429 GCTAGGTATACTCCCAACTATTGCT 59.754 44.000 2.25 0.00 0.00 3.91
504 505 6.436532 GCTAGGTATACTCCCAACTATTGCTA 59.563 42.308 2.25 0.00 0.00 3.49
505 506 6.919775 AGGTATACTCCCAACTATTGCTAG 57.080 41.667 2.25 0.00 0.00 3.42
506 507 5.246429 AGGTATACTCCCAACTATTGCTAGC 59.754 44.000 8.10 8.10 0.00 3.42
507 508 5.011738 GGTATACTCCCAACTATTGCTAGCA 59.988 44.000 14.93 14.93 0.00 3.49
509 510 2.092914 ACTCCCAACTATTGCTAGCACC 60.093 50.000 19.17 0.00 0.00 5.01
510 511 1.912731 TCCCAACTATTGCTAGCACCA 59.087 47.619 19.17 3.75 0.00 4.17
511 512 2.307392 TCCCAACTATTGCTAGCACCAA 59.693 45.455 19.17 2.85 0.00 3.67
512 513 2.423538 CCCAACTATTGCTAGCACCAAC 59.576 50.000 19.17 0.00 0.00 3.77
513 514 3.347216 CCAACTATTGCTAGCACCAACT 58.653 45.455 19.17 0.00 0.00 3.16
530 531 3.865929 CTTCCACCTGACACGCGCT 62.866 63.158 5.73 0.00 0.00 5.92
534 535 2.356313 ACCTGACACGCGCTTCAG 60.356 61.111 23.98 23.98 39.25 3.02
551 552 4.742138 GCTTCAGCCTATTGAGGTAGAAGG 60.742 50.000 19.73 0.00 45.87 3.46
692 724 2.846039 AGTACGAGGCAGACGTATTG 57.154 50.000 12.72 0.00 45.42 1.90
1232 4291 4.379243 CGCGCCACTCCAGTTCCT 62.379 66.667 0.00 0.00 0.00 3.36
1259 4336 1.728426 GTTCCACCACGACGACGAG 60.728 63.158 15.32 5.96 42.66 4.18
2138 5883 1.808945 CAGAGGATTGCTTTCTGCGTT 59.191 47.619 0.00 0.00 46.63 4.84
2331 6076 9.485206 GAAAATGGTAGTCTTGACAAGTACTTA 57.515 33.333 18.92 9.25 0.00 2.24
2332 6077 8.828688 AAATGGTAGTCTTGACAAGTACTTAC 57.171 34.615 18.92 14.30 0.00 2.34
2372 6117 2.503356 CTCTACATTGGCCTGAGAGGTT 59.497 50.000 3.32 0.00 37.80 3.50
2644 6389 3.128764 TGTGTTCGCATTTGGTGTGTTTA 59.871 39.130 0.00 0.00 39.38 2.01
2666 6411 3.918253 TTGAGGTCGCATGTGGGCC 62.918 63.158 6.39 9.32 0.00 5.80
2670 6415 2.731571 GGTCGCATGTGGGCCTAGA 61.732 63.158 4.53 0.00 0.00 2.43
2884 6629 3.270027 CGAAAGGTCATGCAATACCTGA 58.730 45.455 20.62 3.55 45.51 3.86
2971 6719 5.050490 AGAATGAAGGGTTCGATTCATACG 58.950 41.667 11.34 0.00 43.56 3.06
3067 6815 7.182060 AGAGGGAAGGTGAATGCTTTTAATTA 58.818 34.615 0.00 0.00 0.00 1.40
3111 6860 7.661847 TCTTCTCTCAATGTTCCTTTAAGAACC 59.338 37.037 5.43 0.00 44.55 3.62
3169 6918 7.381948 GTGAACTAGTTCTATCTCATGCATGAG 59.618 40.741 39.57 39.57 45.40 2.90
3206 6955 9.280174 CAGTAACACTTTTGGTAAGGAAATAGA 57.720 33.333 0.00 0.00 0.00 1.98
3285 7034 9.627123 TGTAAGCTTAGTTATGGATTTGCTTAT 57.373 29.630 6.38 0.00 41.60 1.73
3361 7111 5.774690 ACAATATAGGGCAGAAGAGAGAGAG 59.225 44.000 0.00 0.00 0.00 3.20
3526 7277 0.963225 GTCTCCCCTAATCTCTCCGC 59.037 60.000 0.00 0.00 0.00 5.54
3624 10118 8.091449 TCAATAATTTTGTGTATGGTTTGGACC 58.909 33.333 0.00 0.00 46.71 4.46
3639 10133 1.210967 TGGACCGAAACCAGTTTCTGT 59.789 47.619 16.92 16.92 45.32 3.41
3640 10134 2.294979 GGACCGAAACCAGTTTCTGTT 58.705 47.619 17.67 5.23 43.63 3.16
3816 10314 3.899052 TCACACCCTTTAAGTATCCGG 57.101 47.619 0.00 0.00 0.00 5.14
3822 10320 5.221986 ACACCCTTTAAGTATCCGGTTCTTT 60.222 40.000 0.00 0.00 0.00 2.52
3824 10322 5.250082 ACCCTTTAAGTATCCGGTTCTTTCT 59.750 40.000 0.00 0.00 0.00 2.52
3841 10344 5.611374 TCTTTCTACCAACTTTCACCTGAG 58.389 41.667 0.00 0.00 0.00 3.35
3842 10345 4.351874 TTCTACCAACTTTCACCTGAGG 57.648 45.455 0.00 0.00 0.00 3.86
3843 10346 3.583228 TCTACCAACTTTCACCTGAGGA 58.417 45.455 4.99 0.00 0.00 3.71
3844 10347 2.640316 ACCAACTTTCACCTGAGGAC 57.360 50.000 4.99 0.00 0.00 3.85
3845 10348 1.843851 ACCAACTTTCACCTGAGGACA 59.156 47.619 4.99 0.00 0.00 4.02
3846 10349 2.443255 ACCAACTTTCACCTGAGGACAT 59.557 45.455 4.99 0.00 0.00 3.06
3847 10350 3.650942 ACCAACTTTCACCTGAGGACATA 59.349 43.478 4.99 0.00 0.00 2.29
3848 10351 4.003648 CCAACTTTCACCTGAGGACATAC 58.996 47.826 4.99 0.00 0.00 2.39
3849 10352 4.504864 CCAACTTTCACCTGAGGACATACA 60.505 45.833 4.99 0.00 0.00 2.29
3882 10390 5.117584 AGAAGACATACATAGACGACGAGT 58.882 41.667 0.00 0.00 0.00 4.18
3941 10451 3.006967 AGTGTCACGGGCCTATCATATTC 59.993 47.826 0.84 0.00 0.00 1.75
3952 10469 4.440802 GCCTATCATATTCTACGAGGCAGG 60.441 50.000 5.16 0.00 45.91 4.85
3961 10478 1.607628 CTACGAGGCAGGCGTATTACT 59.392 52.381 7.53 0.00 42.52 2.24
3973 10490 6.607689 CAGGCGTATTACTTTGAATTCAACA 58.392 36.000 20.35 10.79 35.28 3.33
4043 10796 1.862242 GAGGTACCCTCCCCCTTACTA 59.138 57.143 8.74 0.00 44.36 1.82
4044 10797 1.577729 AGGTACCCTCCCCCTTACTAC 59.422 57.143 8.74 0.00 0.00 2.73
4046 10799 1.577729 GTACCCTCCCCCTTACTACCT 59.422 57.143 0.00 0.00 0.00 3.08
4047 10800 0.641048 ACCCTCCCCCTTACTACCTC 59.359 60.000 0.00 0.00 0.00 3.85
4048 10801 0.942721 CCCTCCCCCTTACTACCTCT 59.057 60.000 0.00 0.00 0.00 3.69
4049 10802 1.413227 CCCTCCCCCTTACTACCTCTG 60.413 61.905 0.00 0.00 0.00 3.35
4051 10804 2.668625 CTCCCCCTTACTACCTCTGTC 58.331 57.143 0.00 0.00 0.00 3.51
4053 10806 1.291335 CCCCCTTACTACCTCTGTCCT 59.709 57.143 0.00 0.00 0.00 3.85
4054 10807 2.389715 CCCCTTACTACCTCTGTCCTG 58.610 57.143 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.414658 TTTGACGTAAGGGGCCCACC 62.415 60.000 27.72 7.11 46.39 4.61
8 9 0.537828 TTTTGACGTAAGGGGCCCAC 60.538 55.000 27.72 14.67 46.39 4.61
9 10 0.406361 ATTTTGACGTAAGGGGCCCA 59.594 50.000 27.72 0.43 46.39 5.36
10 11 2.019249 GTATTTTGACGTAAGGGGCCC 58.981 52.381 17.12 17.12 46.39 5.80
40 41 8.587111 CCCGTTTTCTATTTACGTAAGAAGTAC 58.413 37.037 8.23 9.45 43.62 2.73
41 42 7.275560 GCCCGTTTTCTATTTACGTAAGAAGTA 59.724 37.037 8.23 1.76 43.62 2.24
50 51 1.328374 CGGGCCCGTTTTCTATTTACG 59.672 52.381 36.64 4.77 35.20 3.18
51 52 2.631267 TCGGGCCCGTTTTCTATTTAC 58.369 47.619 41.57 0.00 40.74 2.01
52 53 3.135167 AGATCGGGCCCGTTTTCTATTTA 59.865 43.478 41.57 20.64 40.74 1.40
53 54 2.092592 AGATCGGGCCCGTTTTCTATTT 60.093 45.455 41.57 20.30 40.74 1.40
58 59 1.374343 GGAAGATCGGGCCCGTTTTC 61.374 60.000 41.57 35.36 40.74 2.29
60 61 2.271173 GGAAGATCGGGCCCGTTT 59.729 61.111 41.57 31.75 40.74 3.60
61 62 3.793888 GGGAAGATCGGGCCCGTT 61.794 66.667 41.57 34.87 40.74 4.44
63 64 3.930012 GAGGGAAGATCGGGCCCG 61.930 72.222 39.13 39.13 46.68 6.13
65 66 1.152312 TAGGAGGGAAGATCGGGCC 60.152 63.158 0.00 0.00 0.00 5.80
66 67 0.470268 ACTAGGAGGGAAGATCGGGC 60.470 60.000 0.00 0.00 0.00 6.13
67 68 1.133450 TCACTAGGAGGGAAGATCGGG 60.133 57.143 0.00 0.00 0.00 5.14
68 69 2.366640 TCACTAGGAGGGAAGATCGG 57.633 55.000 0.00 0.00 0.00 4.18
69 70 2.823154 GGATCACTAGGAGGGAAGATCG 59.177 54.545 0.00 0.00 34.27 3.69
70 71 3.850752 TGGATCACTAGGAGGGAAGATC 58.149 50.000 0.00 0.00 27.39 2.75
73 74 6.694445 ATTATTGGATCACTAGGAGGGAAG 57.306 41.667 0.00 0.00 27.39 3.46
74 75 8.757307 ATTATTATTGGATCACTAGGAGGGAA 57.243 34.615 0.00 0.00 27.39 3.97
76 77 7.404396 AGGATTATTATTGGATCACTAGGAGGG 59.596 40.741 0.00 0.00 0.00 4.30
83 84 6.012157 CCCTGGAGGATTATTATTGGATCACT 60.012 42.308 0.00 0.00 38.24 3.41
85 86 5.857283 ACCCTGGAGGATTATTATTGGATCA 59.143 40.000 0.00 0.00 39.89 2.92
88 89 6.399013 AGTACCCTGGAGGATTATTATTGGA 58.601 40.000 0.00 0.00 39.89 3.53
89 90 6.704056 AGTACCCTGGAGGATTATTATTGG 57.296 41.667 0.00 0.00 39.89 3.16
90 91 7.978925 AGAAGTACCCTGGAGGATTATTATTG 58.021 38.462 0.00 0.00 39.89 1.90
92 93 9.102453 GTAAGAAGTACCCTGGAGGATTATTAT 57.898 37.037 0.00 0.00 39.89 1.28
95 96 5.539193 CGTAAGAAGTACCCTGGAGGATTAT 59.461 44.000 0.00 0.00 38.58 1.28
96 97 4.891756 CGTAAGAAGTACCCTGGAGGATTA 59.108 45.833 0.00 0.00 38.58 1.75
97 98 3.705072 CGTAAGAAGTACCCTGGAGGATT 59.295 47.826 0.00 0.00 38.58 3.01
99 100 2.042162 ACGTAAGAAGTACCCTGGAGGA 59.958 50.000 0.00 0.00 39.44 3.71
101 102 5.649782 TTTACGTAAGAAGTACCCTGGAG 57.350 43.478 8.23 0.00 43.62 3.86
103 104 5.809051 GTGATTTACGTAAGAAGTACCCTGG 59.191 44.000 8.23 0.00 43.62 4.45
128 129 5.802451 GCTAGACCTACGTAAAGTTTGGTAC 59.198 44.000 2.23 0.00 38.15 3.34
129 130 5.476599 TGCTAGACCTACGTAAAGTTTGGTA 59.523 40.000 2.23 0.23 38.15 3.25
132 133 6.963049 AATGCTAGACCTACGTAAAGTTTG 57.037 37.500 0.00 0.00 0.00 2.93
134 135 7.401955 AGTAATGCTAGACCTACGTAAAGTT 57.598 36.000 0.00 0.00 0.00 2.66
136 137 6.437094 GGAGTAATGCTAGACCTACGTAAAG 58.563 44.000 0.00 0.00 0.00 1.85
140 141 3.220940 GGGAGTAATGCTAGACCTACGT 58.779 50.000 0.00 0.00 0.00 3.57
141 142 2.557490 GGGGAGTAATGCTAGACCTACG 59.443 54.545 0.00 0.00 0.00 3.51
144 145 1.063114 ACGGGGAGTAATGCTAGACCT 60.063 52.381 0.00 0.00 0.00 3.85
145 146 1.411041 ACGGGGAGTAATGCTAGACC 58.589 55.000 0.00 0.00 0.00 3.85
147 148 2.433239 GGAAACGGGGAGTAATGCTAGA 59.567 50.000 0.00 0.00 0.00 2.43
148 149 2.484947 GGGAAACGGGGAGTAATGCTAG 60.485 54.545 0.00 0.00 0.00 3.42
149 150 1.487558 GGGAAACGGGGAGTAATGCTA 59.512 52.381 0.00 0.00 0.00 3.49
150 151 0.255033 GGGAAACGGGGAGTAATGCT 59.745 55.000 0.00 0.00 0.00 3.79
154 155 0.117742 AGGAGGGAAACGGGGAGTAA 59.882 55.000 0.00 0.00 0.00 2.24
156 157 1.612739 GAGGAGGGAAACGGGGAGT 60.613 63.158 0.00 0.00 0.00 3.85
157 158 2.368011 GGAGGAGGGAAACGGGGAG 61.368 68.421 0.00 0.00 0.00 4.30
158 159 2.285144 GGAGGAGGGAAACGGGGA 60.285 66.667 0.00 0.00 0.00 4.81
160 161 2.228480 TTGGGAGGAGGGAAACGGG 61.228 63.158 0.00 0.00 0.00 5.28
163 164 3.136077 GGTATAGTTGGGAGGAGGGAAAC 59.864 52.174 0.00 0.00 0.00 2.78
164 165 3.014807 AGGTATAGTTGGGAGGAGGGAAA 59.985 47.826 0.00 0.00 0.00 3.13
165 166 2.595380 AGGTATAGTTGGGAGGAGGGAA 59.405 50.000 0.00 0.00 0.00 3.97
166 167 2.090719 CAGGTATAGTTGGGAGGAGGGA 60.091 54.545 0.00 0.00 0.00 4.20
168 169 2.330216 CCAGGTATAGTTGGGAGGAGG 58.670 57.143 0.00 0.00 0.00 4.30
175 176 4.706842 AGTTATGCCCAGGTATAGTTGG 57.293 45.455 0.00 0.00 0.00 3.77
176 177 4.821805 CCAAGTTATGCCCAGGTATAGTTG 59.178 45.833 9.90 9.90 0.00 3.16
177 178 4.141251 CCCAAGTTATGCCCAGGTATAGTT 60.141 45.833 0.00 0.00 0.00 2.24
178 179 3.394606 CCCAAGTTATGCCCAGGTATAGT 59.605 47.826 0.00 0.00 0.00 2.12
180 181 2.107552 GCCCAAGTTATGCCCAGGTATA 59.892 50.000 0.00 0.00 0.00 1.47
181 182 1.133482 GCCCAAGTTATGCCCAGGTAT 60.133 52.381 0.00 0.00 0.00 2.73
184 185 1.758122 GGCCCAAGTTATGCCCAGG 60.758 63.158 0.00 0.00 39.30 4.45
186 187 2.044451 CGGCCCAAGTTATGCCCA 60.044 61.111 0.00 0.00 42.29 5.36
187 188 2.833121 CCGGCCCAAGTTATGCCC 60.833 66.667 0.00 0.00 42.29 5.36
188 189 2.119029 GTCCGGCCCAAGTTATGCC 61.119 63.158 0.00 5.02 41.85 4.40
192 193 2.604079 TCGGTCCGGCCCAAGTTA 60.604 61.111 12.29 0.00 0.00 2.24
193 194 4.016706 CTCGGTCCGGCCCAAGTT 62.017 66.667 12.29 0.00 0.00 2.66
199 200 4.821589 CTGAAGCTCGGTCCGGCC 62.822 72.222 12.29 0.00 0.00 6.13
200 201 4.821589 CCTGAAGCTCGGTCCGGC 62.822 72.222 12.29 13.71 0.00 6.13
201 202 4.821589 GCCTGAAGCTCGGTCCGG 62.822 72.222 12.29 0.00 38.99 5.14
203 204 3.672295 CTGGCCTGAAGCTCGGTCC 62.672 68.421 3.32 0.00 43.05 4.46
205 206 3.710722 CCTGGCCTGAAGCTCGGT 61.711 66.667 11.88 0.00 43.05 4.69
221 222 0.803117 GCTTCGGTCTTTGTTAGGCC 59.197 55.000 0.00 0.00 45.75 5.19
223 224 3.040147 TCTGCTTCGGTCTTTGTTAGG 57.960 47.619 0.00 0.00 0.00 2.69
227 228 2.357952 GGTTTTCTGCTTCGGTCTTTGT 59.642 45.455 0.00 0.00 0.00 2.83
228 229 2.618709 AGGTTTTCTGCTTCGGTCTTTG 59.381 45.455 0.00 0.00 0.00 2.77
230 231 2.640316 AGGTTTTCTGCTTCGGTCTT 57.360 45.000 0.00 0.00 0.00 3.01
231 232 2.028020 CCTAGGTTTTCTGCTTCGGTCT 60.028 50.000 0.00 0.00 0.00 3.85
233 234 1.610886 GCCTAGGTTTTCTGCTTCGGT 60.611 52.381 11.31 0.00 0.00 4.69
234 235 1.087501 GCCTAGGTTTTCTGCTTCGG 58.912 55.000 11.31 0.00 0.00 4.30
235 236 1.087501 GGCCTAGGTTTTCTGCTTCG 58.912 55.000 11.31 0.00 0.00 3.79
237 238 0.322546 CGGGCCTAGGTTTTCTGCTT 60.323 55.000 11.31 0.00 0.00 3.91
243 244 3.084304 GGGACGGGCCTAGGTTTT 58.916 61.111 11.31 0.00 36.66 2.43
264 265 2.270352 CCTGAAAACTAGGCCACACA 57.730 50.000 5.01 0.00 0.00 3.72
271 272 1.177401 GCTTGGGCCTGAAAACTAGG 58.823 55.000 4.53 0.00 38.39 3.02
287 288 1.271840 TTGTCTGATAGGCCGGGCTT 61.272 55.000 37.40 23.03 0.00 4.35
289 290 0.393808 TTTTGTCTGATAGGCCGGGC 60.394 55.000 22.67 22.67 0.00 6.13
291 292 1.401905 GCTTTTTGTCTGATAGGCCGG 59.598 52.381 0.00 0.00 0.00 6.13
292 293 1.401905 GGCTTTTTGTCTGATAGGCCG 59.598 52.381 0.00 0.00 0.00 6.13
295 296 4.142093 CCAATGGGCTTTTTGTCTGATAGG 60.142 45.833 0.00 0.00 0.00 2.57
299 300 1.969923 CCCAATGGGCTTTTTGTCTGA 59.030 47.619 4.89 0.00 35.35 3.27
300 301 2.460757 CCCAATGGGCTTTTTGTCTG 57.539 50.000 4.89 0.00 35.35 3.51
326 327 3.316588 GCAATTTAAGGAAGAGGCCTAGC 59.683 47.826 4.42 0.00 37.26 3.42
327 328 4.526970 TGCAATTTAAGGAAGAGGCCTAG 58.473 43.478 4.42 0.00 37.26 3.02
330 331 4.535526 TTTGCAATTTAAGGAAGAGGCC 57.464 40.909 0.00 0.00 0.00 5.19
331 332 5.743872 CGTATTTGCAATTTAAGGAAGAGGC 59.256 40.000 0.00 0.00 0.00 4.70
332 333 6.967199 GTCGTATTTGCAATTTAAGGAAGAGG 59.033 38.462 0.00 0.00 0.00 3.69
333 334 7.526608 TGTCGTATTTGCAATTTAAGGAAGAG 58.473 34.615 0.00 0.00 0.00 2.85
334 335 7.441890 TGTCGTATTTGCAATTTAAGGAAGA 57.558 32.000 0.00 0.00 0.00 2.87
335 336 7.201350 GCTTGTCGTATTTGCAATTTAAGGAAG 60.201 37.037 0.00 0.14 0.00 3.46
336 337 6.584563 GCTTGTCGTATTTGCAATTTAAGGAA 59.415 34.615 0.00 0.00 0.00 3.36
337 338 6.072175 AGCTTGTCGTATTTGCAATTTAAGGA 60.072 34.615 0.00 0.00 0.00 3.36
339 340 6.022251 CGAGCTTGTCGTATTTGCAATTTAAG 60.022 38.462 0.00 0.00 44.20 1.85
340 341 5.792962 CGAGCTTGTCGTATTTGCAATTTAA 59.207 36.000 0.00 0.00 44.20 1.52
341 342 5.320723 CGAGCTTGTCGTATTTGCAATTTA 58.679 37.500 0.00 0.00 44.20 1.40
344 345 3.389687 CGAGCTTGTCGTATTTGCAAT 57.610 42.857 0.00 0.00 44.20 3.56
345 346 2.873170 CGAGCTTGTCGTATTTGCAA 57.127 45.000 0.00 0.00 44.20 4.08
371 372 3.145551 CTGATGGCTGGGCTTGGC 61.146 66.667 0.00 0.00 0.00 4.52
372 373 2.441532 CCTGATGGCTGGGCTTGG 60.442 66.667 0.00 0.00 0.00 3.61
382 383 2.883386 GCCTAGATTTTGAGCCTGATGG 59.117 50.000 0.00 0.00 0.00 3.51
383 384 2.883386 GGCCTAGATTTTGAGCCTGATG 59.117 50.000 0.00 0.00 40.57 3.07
384 385 3.220674 GGCCTAGATTTTGAGCCTGAT 57.779 47.619 0.00 0.00 40.57 2.90
385 386 2.717639 GGCCTAGATTTTGAGCCTGA 57.282 50.000 0.00 0.00 40.57 3.86
388 389 2.812243 GCCTAGGCCTAGATTTTGAGCC 60.812 54.545 36.80 13.08 44.20 4.70
389 390 2.499197 GCCTAGGCCTAGATTTTGAGC 58.501 52.381 36.80 25.68 35.21 4.26
414 415 4.820744 CCCGACCTTGCCCATGGG 62.821 72.222 27.87 27.87 38.57 4.00
416 417 2.438434 GACCCGACCTTGCCCATG 60.438 66.667 0.00 0.00 0.00 3.66
417 418 4.096003 CGACCCGACCTTGCCCAT 62.096 66.667 0.00 0.00 0.00 4.00
422 423 4.452733 GAGGCCGACCCGACCTTG 62.453 72.222 0.00 0.00 40.37 3.61
424 425 4.698625 AAGAGGCCGACCCGACCT 62.699 66.667 0.00 0.00 43.55 3.85
425 426 3.249837 AAAAGAGGCCGACCCGACC 62.250 63.158 0.00 0.00 39.21 4.79
427 428 2.345991 CAAAAGAGGCCGACCCGA 59.654 61.111 0.00 0.00 39.21 5.14
429 430 1.674651 GACCAAAAGAGGCCGACCC 60.675 63.158 0.00 0.00 36.11 4.46
430 431 1.674651 GGACCAAAAGAGGCCGACC 60.675 63.158 0.00 0.00 0.00 4.79
431 432 2.033194 CGGACCAAAAGAGGCCGAC 61.033 63.158 0.00 0.00 45.20 4.79
432 433 2.345991 CGGACCAAAAGAGGCCGA 59.654 61.111 0.00 0.00 45.20 5.54
435 436 2.668550 ACGCGGACCAAAAGAGGC 60.669 61.111 12.47 0.00 0.00 4.70
436 437 2.380410 CGACGCGGACCAAAAGAGG 61.380 63.158 12.47 0.00 0.00 3.69
471 472 1.272490 GAGTATACCTAGCCATGCGCA 59.728 52.381 14.96 14.96 41.38 6.09
473 474 1.204941 GGGAGTATACCTAGCCATGCG 59.795 57.143 0.00 0.00 0.00 4.73
474 475 2.257207 TGGGAGTATACCTAGCCATGC 58.743 52.381 0.00 0.00 0.00 4.06
476 477 4.214993 AGTTGGGAGTATACCTAGCCAT 57.785 45.455 0.00 0.00 0.00 4.40
477 478 3.700863 AGTTGGGAGTATACCTAGCCA 57.299 47.619 0.00 0.00 0.00 4.75
478 479 5.569026 GCAATAGTTGGGAGTATACCTAGCC 60.569 48.000 0.00 0.00 0.00 3.93
479 480 5.246429 AGCAATAGTTGGGAGTATACCTAGC 59.754 44.000 0.00 0.00 0.00 3.42
481 482 6.436532 GCTAGCAATAGTTGGGAGTATACCTA 59.563 42.308 10.63 0.00 0.00 3.08
482 483 5.246429 GCTAGCAATAGTTGGGAGTATACCT 59.754 44.000 10.63 0.00 0.00 3.08
483 484 5.011738 TGCTAGCAATAGTTGGGAGTATACC 59.988 44.000 16.84 0.00 0.00 2.73
484 485 5.927115 GTGCTAGCAATAGTTGGGAGTATAC 59.073 44.000 21.29 0.00 0.00 1.47
486 487 4.202367 GGTGCTAGCAATAGTTGGGAGTAT 60.202 45.833 21.29 0.00 0.00 2.12
488 489 2.092914 GGTGCTAGCAATAGTTGGGAGT 60.093 50.000 21.29 0.00 0.00 3.85
489 490 2.092968 TGGTGCTAGCAATAGTTGGGAG 60.093 50.000 21.29 0.00 0.00 4.30
490 491 1.912731 TGGTGCTAGCAATAGTTGGGA 59.087 47.619 21.29 0.00 0.00 4.37
492 493 3.347216 AGTTGGTGCTAGCAATAGTTGG 58.653 45.455 21.29 0.00 37.94 3.77
493 494 4.142600 GGAAGTTGGTGCTAGCAATAGTTG 60.143 45.833 21.29 0.00 37.94 3.16
494 495 4.010349 GGAAGTTGGTGCTAGCAATAGTT 58.990 43.478 21.29 15.70 37.94 2.24
495 496 3.009033 TGGAAGTTGGTGCTAGCAATAGT 59.991 43.478 21.29 7.71 37.94 2.12
497 498 3.343617 GTGGAAGTTGGTGCTAGCAATA 58.656 45.455 21.29 8.65 37.94 1.90
499 500 1.604604 GTGGAAGTTGGTGCTAGCAA 58.395 50.000 21.29 0.91 32.60 3.91
500 501 0.250727 GGTGGAAGTTGGTGCTAGCA 60.251 55.000 14.93 14.93 0.00 3.49
501 502 0.036875 AGGTGGAAGTTGGTGCTAGC 59.963 55.000 8.10 8.10 0.00 3.42
502 503 1.347707 TCAGGTGGAAGTTGGTGCTAG 59.652 52.381 0.00 0.00 0.00 3.42
503 504 1.071699 GTCAGGTGGAAGTTGGTGCTA 59.928 52.381 0.00 0.00 0.00 3.49
504 505 0.179018 GTCAGGTGGAAGTTGGTGCT 60.179 55.000 0.00 0.00 0.00 4.40
505 506 0.465460 TGTCAGGTGGAAGTTGGTGC 60.465 55.000 0.00 0.00 0.00 5.01
506 507 1.308998 GTGTCAGGTGGAAGTTGGTG 58.691 55.000 0.00 0.00 0.00 4.17
507 508 0.179056 CGTGTCAGGTGGAAGTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
509 510 1.831389 CGCGTGTCAGGTGGAAGTTG 61.831 60.000 0.00 0.00 0.00 3.16
510 511 1.594293 CGCGTGTCAGGTGGAAGTT 60.594 57.895 0.00 0.00 0.00 2.66
511 512 2.029073 CGCGTGTCAGGTGGAAGT 59.971 61.111 0.00 0.00 0.00 3.01
512 513 3.414700 GCGCGTGTCAGGTGGAAG 61.415 66.667 8.43 0.00 0.00 3.46
513 514 3.454587 AAGCGCGTGTCAGGTGGAA 62.455 57.895 8.43 0.00 0.00 3.53
551 552 2.918616 GACCTCGTCGTCTATGTATGC 58.081 52.381 0.00 0.00 0.00 3.14
668 669 3.191078 ACGTCTGCCTCGTACTACTAT 57.809 47.619 0.00 0.00 39.78 2.12
762 804 3.004734 ACGTGGAAGAAAGCAGGAAAATG 59.995 43.478 0.00 0.00 0.00 2.32
1230 4289 0.685097 TGGTGGAACTTTCGAGGAGG 59.315 55.000 3.38 0.00 36.74 4.30
1231 4290 1.797025 GTGGTGGAACTTTCGAGGAG 58.203 55.000 0.00 0.00 36.74 3.69
1232 4291 0.032952 CGTGGTGGAACTTTCGAGGA 59.967 55.000 0.00 0.00 36.74 3.71
2138 5883 0.958091 CACCGCAACCTCCAAATTGA 59.042 50.000 0.00 0.00 0.00 2.57
2331 6076 5.749462 AGAGCTGGCTTATTTTGAGTATGT 58.251 37.500 0.00 0.00 0.00 2.29
2332 6077 6.763135 TGTAGAGCTGGCTTATTTTGAGTATG 59.237 38.462 0.00 0.00 0.00 2.39
2372 6117 2.616960 CGACACCTTTGATGATCCGAA 58.383 47.619 0.00 0.00 0.00 4.30
2644 6389 0.107508 CCACATGCGACCTCAAGGAT 60.108 55.000 2.30 0.00 38.94 3.24
2666 6411 4.872691 CCTTGCTACTGTTGATTGGTCTAG 59.127 45.833 0.00 0.00 0.00 2.43
2670 6415 3.788227 TCCTTGCTACTGTTGATTGGT 57.212 42.857 0.00 0.00 0.00 3.67
2735 6480 1.429463 GTCGAGAATTGAGCCGTTGT 58.571 50.000 0.00 0.00 0.00 3.32
2884 6629 0.953960 GGAATTGACTGGTCGCGGTT 60.954 55.000 6.13 0.00 0.00 4.44
2971 6719 4.297299 TCGATGAAGGGTACGACATTAC 57.703 45.455 0.00 0.00 0.00 1.89
3169 6918 8.403236 ACCAAAAGTGTTACTGATTACTGAAAC 58.597 33.333 0.00 0.00 0.00 2.78
3206 6955 4.012138 GGCAAATGGCGGTTACCT 57.988 55.556 0.00 0.00 46.16 3.08
3243 6992 0.682209 TACACCTCGCCAGGGACTAC 60.682 60.000 1.31 0.00 45.53 2.73
3285 7034 6.265422 TGTTTGAGATGCTCTTAGGATATCGA 59.735 38.462 0.00 0.00 37.13 3.59
3361 7111 1.721487 CCGTGGCGGTGATGAATTC 59.279 57.895 0.00 0.00 42.73 2.17
3383 7133 6.857964 CACTTTTACCACATCTGTTAAAGCAG 59.142 38.462 0.00 0.00 37.81 4.24
3526 7277 2.063425 GGGGGATTAGGGGAGGTTTAG 58.937 57.143 0.00 0.00 0.00 1.85
3553 10047 4.408904 AGGCAGCATAAATTCCCCATAT 57.591 40.909 0.00 0.00 0.00 1.78
3630 10124 5.621228 GCTCGTACAAATTCAACAGAAACTG 59.379 40.000 0.00 0.00 37.52 3.16
3639 10133 4.260579 CGCCATATGCTCGTACAAATTCAA 60.261 41.667 0.00 0.00 38.05 2.69
3640 10134 3.247411 CGCCATATGCTCGTACAAATTCA 59.753 43.478 0.00 0.00 38.05 2.57
3816 10314 5.820947 TCAGGTGAAAGTTGGTAGAAAGAAC 59.179 40.000 0.00 0.00 0.00 3.01
3822 10320 3.323979 GTCCTCAGGTGAAAGTTGGTAGA 59.676 47.826 0.00 0.00 0.00 2.59
3824 10322 3.042682 TGTCCTCAGGTGAAAGTTGGTA 58.957 45.455 0.00 0.00 0.00 3.25
3841 10344 7.952671 TGTCTTCTACCTCAATATGTATGTCC 58.047 38.462 0.00 0.00 0.00 4.02
3882 10390 2.038952 CCACAGAGTCCATGGTCTCAAA 59.961 50.000 31.93 3.14 33.79 2.69
3925 10435 3.693807 TCGTAGAATATGATAGGCCCGT 58.306 45.455 0.00 0.00 30.14 5.28
3941 10451 1.607628 AGTAATACGCCTGCCTCGTAG 59.392 52.381 7.93 0.00 44.22 3.51
3952 10469 9.123709 TGAAATGTTGAATTCAAAGTAATACGC 57.876 29.630 22.07 7.47 37.63 4.42
3961 10478 6.256104 CAGTGTGCTGAAATGTTGAATTCAAA 59.744 34.615 22.07 12.81 45.28 2.69
4007 10524 1.212751 CTCATGGACACAGCGACGA 59.787 57.895 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.