Multiple sequence alignment - TraesCS2B01G332500

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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 TraesCS2B01G332500 chr2B 100.000 2794 0 0 1 2794 475612012 475609219 0.000000e+00 5160.0
1 TraesCS2B01G332500 chr2D 86.813 1456 53 47 1406 2794 401541675 401540292 0.000000e+00 1496.0
2 TraesCS2B01G332500 chr2D 89.122 1048 57 23 378 1410 401542645 401541640 0.000000e+00 1251.0
3 TraesCS2B01G332500 chr2A 89.521 1002 58 16 377 1359 538368543 538367570 0.000000e+00 1225.0
4 TraesCS2B01G332500 chr2A 91.522 578 23 16 1406 1976 538367563 538367005 0.000000e+00 773.0
5 TraesCS2B01G332500 chr2A 85.938 512 26 20 2012 2500 538367001 538366513 3.210000e-139 505.0
6 TraesCS2B01G332500 chr2A 84.642 293 8 9 2509 2794 538366449 538366187 9.930000e-65 257.0
7 TraesCS2B01G332500 chr2A 92.391 92 3 3 18 105 538368631 538368540 8.120000e-26 128.0
8 TraesCS2B01G332500 chr3B 96.763 278 8 1 102 378 582406007 582405730 1.960000e-126 462.0
9 TraesCS2B01G332500 chr7D 94.000 300 16 2 91 390 42618634 42618337 1.180000e-123 453.0
10 TraesCS2B01G332500 chr7D 88.333 60 4 2 1464 1523 562288384 562288440 4.990000e-08 69.4
11 TraesCS2B01G332500 chr7B 96.043 278 10 1 104 380 274230003 274229726 4.240000e-123 451.0
12 TraesCS2B01G332500 chr7B 95.374 281 12 1 102 381 713698739 713698459 1.970000e-121 446.0
13 TraesCS2B01G332500 chr7B 93.182 44 2 1 1481 1523 612320325 612320282 2.320000e-06 63.9
14 TraesCS2B01G332500 chr5B 95.714 280 11 1 102 380 399955515 399955794 1.530000e-122 449.0
15 TraesCS2B01G332500 chrUn 95.374 281 12 1 102 381 87719880 87719600 1.970000e-121 446.0
16 TraesCS2B01G332500 chr6B 95.374 281 12 1 102 381 417496246 417495966 1.970000e-121 446.0
17 TraesCS2B01G332500 chr6B 94.982 279 13 1 102 379 118216789 118216511 1.190000e-118 436.0
18 TraesCS2B01G332500 chr1B 93.357 286 17 2 99 383 403528582 403528866 3.330000e-114 422.0


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 TraesCS2B01G332500 chr2B 475609219 475612012 2793 True 5160.0 5160 100.0000 1 2794 1 chr2B.!!$R1 2793
1 TraesCS2B01G332500 chr2D 401540292 401542645 2353 True 1373.5 1496 87.9675 378 2794 2 chr2D.!!$R1 2416
2 TraesCS2B01G332500 chr2A 538366187 538368631 2444 True 577.6 1225 88.8028 18 2794 5 chr2A.!!$R1 2776

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
237 242 1.330234 TGGCATGCATGACACAAAGT 58.670 45.0 31.52 0.0 41.84 2.66 F
1309 1352 0.039437 GAACACGAGAGCGGTTGAGA 60.039 55.0 0.00 0.0 43.17 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1415 0.319405 CTGGGGCTTTGCTTTCTTGG 59.681 55.0 0.0 0.0 0.0 3.61 R
2610 2768 0.400670 GGCACCTCTCCCTAATCCCT 60.401 60.0 0.0 0.0 0.0 4.20 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
31 32 7.502120 AATATATTTGCCTCTACAACTGCAG 57.498 36.000 13.48 13.48 34.81 4.41
37 40 2.102252 GCCTCTACAACTGCAGAGCTAT 59.898 50.000 23.35 3.33 37.55 2.97
105 110 4.219288 AGCAGCCACATTTTCTTCTTAAGG 59.781 41.667 1.85 0.00 0.00 2.69
106 111 4.488879 CAGCCACATTTTCTTCTTAAGGC 58.511 43.478 1.85 0.00 39.82 4.35
107 112 4.411013 AGCCACATTTTCTTCTTAAGGCT 58.589 39.130 1.85 0.00 44.51 4.58
108 113 4.488879 GCCACATTTTCTTCTTAAGGCTG 58.511 43.478 1.85 0.00 36.72 4.85
109 114 4.619160 GCCACATTTTCTTCTTAAGGCTGG 60.619 45.833 1.85 0.00 36.72 4.85
110 115 4.524328 CCACATTTTCTTCTTAAGGCTGGT 59.476 41.667 1.85 0.00 0.00 4.00
111 116 5.011023 CCACATTTTCTTCTTAAGGCTGGTT 59.989 40.000 1.85 0.00 0.00 3.67
112 117 5.922544 CACATTTTCTTCTTAAGGCTGGTTG 59.077 40.000 1.85 0.00 0.00 3.77
113 118 5.598417 ACATTTTCTTCTTAAGGCTGGTTGT 59.402 36.000 1.85 0.00 0.00 3.32
114 119 6.775629 ACATTTTCTTCTTAAGGCTGGTTGTA 59.224 34.615 1.85 0.00 0.00 2.41
115 120 7.286775 ACATTTTCTTCTTAAGGCTGGTTGTAA 59.713 33.333 1.85 0.00 0.00 2.41
116 121 7.833285 TTTTCTTCTTAAGGCTGGTTGTAAT 57.167 32.000 1.85 0.00 0.00 1.89
117 122 6.817765 TTCTTCTTAAGGCTGGTTGTAATG 57.182 37.500 1.85 0.00 0.00 1.90
118 123 5.253330 TCTTCTTAAGGCTGGTTGTAATGG 58.747 41.667 1.85 0.00 0.00 3.16
119 124 3.963129 TCTTAAGGCTGGTTGTAATGGG 58.037 45.455 1.85 0.00 0.00 4.00
120 125 3.589735 TCTTAAGGCTGGTTGTAATGGGA 59.410 43.478 1.85 0.00 0.00 4.37
121 126 2.514458 AAGGCTGGTTGTAATGGGAG 57.486 50.000 0.00 0.00 0.00 4.30
122 127 1.372501 AGGCTGGTTGTAATGGGAGT 58.627 50.000 0.00 0.00 0.00 3.85
123 128 2.557869 AGGCTGGTTGTAATGGGAGTA 58.442 47.619 0.00 0.00 0.00 2.59
124 129 3.123273 AGGCTGGTTGTAATGGGAGTAT 58.877 45.455 0.00 0.00 0.00 2.12
125 130 3.136626 AGGCTGGTTGTAATGGGAGTATC 59.863 47.826 0.00 0.00 0.00 2.24
126 131 3.118038 GGCTGGTTGTAATGGGAGTATCA 60.118 47.826 0.00 0.00 36.25 2.15
127 132 4.446311 GGCTGGTTGTAATGGGAGTATCAT 60.446 45.833 0.00 0.00 36.25 2.45
128 133 5.221843 GGCTGGTTGTAATGGGAGTATCATA 60.222 44.000 0.00 0.00 36.25 2.15
129 134 6.476378 GCTGGTTGTAATGGGAGTATCATAT 58.524 40.000 0.00 0.00 36.25 1.78
130 135 7.311046 GGCTGGTTGTAATGGGAGTATCATATA 60.311 40.741 0.00 0.00 36.25 0.86
131 136 7.549488 GCTGGTTGTAATGGGAGTATCATATAC 59.451 40.741 0.00 0.00 36.25 1.47
132 137 8.736097 TGGTTGTAATGGGAGTATCATATACT 57.264 34.615 0.00 0.00 36.25 2.12
133 138 9.831682 TGGTTGTAATGGGAGTATCATATACTA 57.168 33.333 0.00 0.00 36.25 1.82
142 147 9.355916 TGGGAGTATCATATACTAGTATCATGC 57.644 37.037 18.68 12.34 36.25 4.06
143 148 9.355916 GGGAGTATCATATACTAGTATCATGCA 57.644 37.037 18.68 1.71 36.25 3.96
179 184 8.860088 AGTGTATGATACTACATCTGTAATGCA 58.140 33.333 4.03 0.00 34.33 3.96
180 185 9.476202 GTGTATGATACTACATCTGTAATGCAA 57.524 33.333 4.03 0.00 34.33 4.08
192 197 9.565090 ACATCTGTAATGCAAAGTATCATATGT 57.435 29.630 1.90 0.00 0.00 2.29
195 200 8.839343 TCTGTAATGCAAAGTATCATATGTTGG 58.161 33.333 1.90 0.00 0.00 3.77
196 201 8.518430 TGTAATGCAAAGTATCATATGTTGGT 57.482 30.769 1.90 0.00 0.00 3.67
197 202 9.620259 TGTAATGCAAAGTATCATATGTTGGTA 57.380 29.630 1.90 0.00 0.00 3.25
200 205 8.922931 ATGCAAAGTATCATATGTTGGTATCA 57.077 30.769 1.90 0.00 0.00 2.15
201 206 8.922931 TGCAAAGTATCATATGTTGGTATCAT 57.077 30.769 1.90 0.00 0.00 2.45
224 229 9.710900 TCATAGAGTACTACATTTATTGGCATG 57.289 33.333 0.00 0.00 0.00 4.06
225 230 6.867662 AGAGTACTACATTTATTGGCATGC 57.132 37.500 9.90 9.90 0.00 4.06
226 231 6.356556 AGAGTACTACATTTATTGGCATGCA 58.643 36.000 21.36 0.00 0.00 3.96
227 232 7.000472 AGAGTACTACATTTATTGGCATGCAT 59.000 34.615 21.36 7.95 0.00 3.96
228 233 6.973843 AGTACTACATTTATTGGCATGCATG 58.026 36.000 22.70 22.70 0.00 4.06
229 234 6.772233 AGTACTACATTTATTGGCATGCATGA 59.228 34.615 30.64 10.12 0.00 3.07
230 235 5.835257 ACTACATTTATTGGCATGCATGAC 58.165 37.500 30.64 28.54 35.98 3.06
231 236 4.739587 ACATTTATTGGCATGCATGACA 57.260 36.364 31.52 31.52 45.84 3.58
237 242 1.330234 TGGCATGCATGACACAAAGT 58.670 45.000 31.52 0.00 41.84 2.66
238 243 2.512705 TGGCATGCATGACACAAAGTA 58.487 42.857 31.52 6.77 41.84 2.24
239 244 2.488937 TGGCATGCATGACACAAAGTAG 59.511 45.455 31.52 0.00 41.84 2.57
240 245 2.523015 GCATGCATGACACAAAGTAGC 58.477 47.619 30.64 6.16 0.00 3.58
241 246 2.095110 GCATGCATGACACAAAGTAGCA 60.095 45.455 30.64 0.00 37.13 3.49
242 247 3.495193 CATGCATGACACAAAGTAGCAC 58.505 45.455 22.59 0.00 36.06 4.40
243 248 2.570135 TGCATGACACAAAGTAGCACA 58.430 42.857 0.00 0.00 30.65 4.57
244 249 3.148412 TGCATGACACAAAGTAGCACAT 58.852 40.909 0.00 0.00 30.65 3.21
245 250 3.189080 TGCATGACACAAAGTAGCACATC 59.811 43.478 0.00 0.00 30.65 3.06
246 251 3.189080 GCATGACACAAAGTAGCACATCA 59.811 43.478 0.00 0.00 0.00 3.07
247 252 4.142534 GCATGACACAAAGTAGCACATCAT 60.143 41.667 0.00 0.00 0.00 2.45
248 253 5.620654 GCATGACACAAAGTAGCACATCATT 60.621 40.000 0.00 0.00 0.00 2.57
249 254 6.384224 CATGACACAAAGTAGCACATCATTT 58.616 36.000 0.00 0.00 0.00 2.32
250 255 7.529158 CATGACACAAAGTAGCACATCATTTA 58.471 34.615 0.00 0.00 0.00 1.40
251 256 7.503521 TGACACAAAGTAGCACATCATTTAA 57.496 32.000 0.00 0.00 0.00 1.52
252 257 8.109705 TGACACAAAGTAGCACATCATTTAAT 57.890 30.769 0.00 0.00 0.00 1.40
253 258 9.225436 TGACACAAAGTAGCACATCATTTAATA 57.775 29.630 0.00 0.00 0.00 0.98
261 266 9.371136 AGTAGCACATCATTTAATATGATACGG 57.629 33.333 10.72 6.78 36.69 4.02
262 267 9.151471 GTAGCACATCATTTAATATGATACGGT 57.849 33.333 10.72 11.66 36.69 4.83
264 269 9.890629 AGCACATCATTTAATATGATACGGTAT 57.109 29.630 0.00 0.00 36.69 2.73
297 302 9.902684 ATGATACTCAAACATCTCTTTCTTCAT 57.097 29.630 0.00 0.00 0.00 2.57
298 303 9.730705 TGATACTCAAACATCTCTTTCTTCATT 57.269 29.630 0.00 0.00 0.00 2.57
333 338 9.844790 TGTCATCTCATTAAAATTGCTTAGTTG 57.155 29.630 0.00 0.00 0.00 3.16
334 339 9.294030 GTCATCTCATTAAAATTGCTTAGTTGG 57.706 33.333 0.00 0.00 0.00 3.77
335 340 7.975616 TCATCTCATTAAAATTGCTTAGTTGGC 59.024 33.333 0.00 0.00 0.00 4.52
336 341 7.225784 TCTCATTAAAATTGCTTAGTTGGCA 57.774 32.000 0.00 0.00 37.97 4.92
337 342 7.839907 TCTCATTAAAATTGCTTAGTTGGCAT 58.160 30.769 0.00 0.00 39.54 4.40
338 343 7.760794 TCTCATTAAAATTGCTTAGTTGGCATG 59.239 33.333 0.00 0.00 39.54 4.06
339 344 6.313411 TCATTAAAATTGCTTAGTTGGCATGC 59.687 34.615 9.90 9.90 39.54 4.06
340 345 3.681593 AAATTGCTTAGTTGGCATGCA 57.318 38.095 21.36 2.54 39.54 3.96
341 346 3.899052 AATTGCTTAGTTGGCATGCAT 57.101 38.095 21.36 4.57 39.54 3.96
342 347 2.658373 TTGCTTAGTTGGCATGCATG 57.342 45.000 22.70 22.70 39.54 4.06
343 348 1.836802 TGCTTAGTTGGCATGCATGA 58.163 45.000 30.64 7.50 34.56 3.07
344 349 2.380941 TGCTTAGTTGGCATGCATGAT 58.619 42.857 30.64 11.73 34.56 2.45
345 350 3.553904 TGCTTAGTTGGCATGCATGATA 58.446 40.909 30.64 14.66 34.56 2.15
346 351 3.316029 TGCTTAGTTGGCATGCATGATAC 59.684 43.478 30.64 21.28 34.56 2.24
347 352 3.567164 GCTTAGTTGGCATGCATGATACT 59.433 43.478 30.64 26.11 0.00 2.12
348 353 4.756642 GCTTAGTTGGCATGCATGATACTA 59.243 41.667 30.64 25.19 0.00 1.82
349 354 5.334414 GCTTAGTTGGCATGCATGATACTAC 60.334 44.000 30.64 22.16 0.00 2.73
350 355 3.133691 AGTTGGCATGCATGATACTACG 58.866 45.455 30.64 1.01 0.00 3.51
351 356 2.872245 GTTGGCATGCATGATACTACGT 59.128 45.455 30.64 0.00 0.00 3.57
352 357 4.055360 GTTGGCATGCATGATACTACGTA 58.945 43.478 30.64 0.00 0.00 3.57
353 358 4.535526 TGGCATGCATGATACTACGTAT 57.464 40.909 30.64 0.00 0.00 3.06
354 359 4.244862 TGGCATGCATGATACTACGTATG 58.755 43.478 30.64 0.23 0.00 2.39
355 360 4.021544 TGGCATGCATGATACTACGTATGA 60.022 41.667 30.64 0.00 0.00 2.15
356 361 5.111989 GGCATGCATGATACTACGTATGAT 58.888 41.667 30.64 0.00 0.00 2.45
357 362 6.127479 TGGCATGCATGATACTACGTATGATA 60.127 38.462 30.64 0.00 0.00 2.15
358 363 6.199154 GGCATGCATGATACTACGTATGATAC 59.801 42.308 30.64 5.71 0.00 2.24
359 364 6.975197 GCATGCATGATACTACGTATGATACT 59.025 38.462 30.64 0.00 0.00 2.12
360 365 8.129211 GCATGCATGATACTACGTATGATACTA 58.871 37.037 30.64 0.00 0.00 1.82
363 368 9.391006 TGCATGATACTACGTATGATACTATCA 57.609 33.333 12.00 12.00 44.55 2.15
375 380 5.386958 TGATACTATCATTACGGTCAGCC 57.613 43.478 0.00 0.00 33.59 4.85
376 381 5.077564 TGATACTATCATTACGGTCAGCCT 58.922 41.667 0.00 0.00 33.59 4.58
393 398 5.180304 GTCAGCCTAAGAAAAGAAACTGAGG 59.820 44.000 0.00 0.00 37.71 3.86
448 453 1.737838 CATGCACATGGTCCGTTACT 58.262 50.000 2.56 0.00 35.24 2.24
553 561 2.695127 ACGTGTTTGAACCACTACCA 57.305 45.000 0.00 0.00 0.00 3.25
777 791 2.680339 GCCATCCTCAAGCACTCTTAAC 59.320 50.000 0.00 0.00 0.00 2.01
882 896 8.301252 TCTACCAACAATTATGAGCTAGTACA 57.699 34.615 0.00 0.00 0.00 2.90
928 945 2.572191 TCGGACAGGTGCGTAATAAG 57.428 50.000 12.88 0.00 44.84 1.73
977 994 5.758784 GCAGGTATGTATAAAGTCACCTTCC 59.241 44.000 0.00 0.00 34.18 3.46
991 1008 2.504367 ACCTTCCGGTGAAACTCAATG 58.496 47.619 0.00 0.00 43.51 2.82
1011 1032 5.557891 ATGCAATTGTCAGTAGCTCTTTC 57.442 39.130 7.40 0.00 0.00 2.62
1012 1033 4.645535 TGCAATTGTCAGTAGCTCTTTCT 58.354 39.130 7.40 0.00 0.00 2.52
1082 1105 1.199097 CCAAAAGACCCACACGTATGC 59.801 52.381 0.00 0.00 0.00 3.14
1179 1202 9.410556 CTAGTCCAGTCCAAACATTTTTAATTG 57.589 33.333 0.00 0.00 0.00 2.32
1254 1297 3.731728 GCACAGCCCATCCCCTGA 61.732 66.667 0.00 0.00 33.40 3.86
1257 1300 3.813724 CAGCCCATCCCCTGACCC 61.814 72.222 0.00 0.00 0.00 4.46
1260 1303 4.455137 CCCATCCCCTGACCCCCT 62.455 72.222 0.00 0.00 0.00 4.79
1261 1304 2.774351 CCATCCCCTGACCCCCTC 60.774 72.222 0.00 0.00 0.00 4.30
1262 1305 2.374342 CATCCCCTGACCCCCTCT 59.626 66.667 0.00 0.00 0.00 3.69
1263 1306 1.768077 CATCCCCTGACCCCCTCTC 60.768 68.421 0.00 0.00 0.00 3.20
1264 1307 3.041297 ATCCCCTGACCCCCTCTCC 62.041 68.421 0.00 0.00 0.00 3.71
1265 1308 3.700350 CCCCTGACCCCCTCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
1266 1309 2.041405 CCCTGACCCCCTCTCCTC 60.041 72.222 0.00 0.00 0.00 3.71
1267 1310 2.041405 CCTGACCCCCTCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
1268 1311 2.641746 CCTGACCCCCTCTCCTCCT 61.642 68.421 0.00 0.00 0.00 3.69
1309 1352 0.039437 GAACACGAGAGCGGTTGAGA 60.039 55.000 0.00 0.00 43.17 3.27
1313 1356 1.192534 CACGAGAGCGGTTGAGAAAAC 59.807 52.381 0.00 0.00 43.17 2.43
1320 1363 3.020984 AGCGGTTGAGAAAACCAGAAAA 58.979 40.909 7.93 0.00 40.28 2.29
1322 1365 3.702330 CGGTTGAGAAAACCAGAAAACC 58.298 45.455 7.93 0.00 40.28 3.27
1325 1368 4.081365 GGTTGAGAAAACCAGAAAACCCAA 60.081 41.667 2.38 0.00 40.03 4.12
1362 1406 4.025858 TGCCTCTGCCTGCAGTCC 62.026 66.667 17.96 3.71 43.96 3.85
1363 1407 3.715097 GCCTCTGCCTGCAGTCCT 61.715 66.667 17.96 0.00 43.96 3.85
1364 1408 2.268280 CCTCTGCCTGCAGTCCTG 59.732 66.667 17.96 7.49 43.96 3.86
1374 1418 2.594303 CAGTCCTGCGCCAACCAA 60.594 61.111 4.18 0.00 0.00 3.67
1375 1419 2.281761 AGTCCTGCGCCAACCAAG 60.282 61.111 4.18 0.00 0.00 3.61
1376 1420 2.281484 GTCCTGCGCCAACCAAGA 60.281 61.111 4.18 0.00 0.00 3.02
1377 1421 1.896660 GTCCTGCGCCAACCAAGAA 60.897 57.895 4.18 0.00 0.00 2.52
1378 1422 1.152860 TCCTGCGCCAACCAAGAAA 60.153 52.632 4.18 0.00 0.00 2.52
1379 1423 1.172180 TCCTGCGCCAACCAAGAAAG 61.172 55.000 4.18 0.00 0.00 2.62
1380 1424 1.372128 CTGCGCCAACCAAGAAAGC 60.372 57.895 4.18 0.00 0.00 3.51
1381 1425 2.074230 CTGCGCCAACCAAGAAAGCA 62.074 55.000 4.18 0.00 0.00 3.91
1382 1426 1.067250 GCGCCAACCAAGAAAGCAA 59.933 52.632 0.00 0.00 0.00 3.91
1383 1427 0.529555 GCGCCAACCAAGAAAGCAAA 60.530 50.000 0.00 0.00 0.00 3.68
1384 1428 1.490621 CGCCAACCAAGAAAGCAAAG 58.509 50.000 0.00 0.00 0.00 2.77
1385 1429 1.220529 GCCAACCAAGAAAGCAAAGC 58.779 50.000 0.00 0.00 0.00 3.51
1386 1430 1.869774 CCAACCAAGAAAGCAAAGCC 58.130 50.000 0.00 0.00 0.00 4.35
1387 1431 1.541015 CCAACCAAGAAAGCAAAGCCC 60.541 52.381 0.00 0.00 0.00 5.19
1388 1432 0.758734 AACCAAGAAAGCAAAGCCCC 59.241 50.000 0.00 0.00 0.00 5.80
1389 1433 0.398381 ACCAAGAAAGCAAAGCCCCA 60.398 50.000 0.00 0.00 0.00 4.96
1390 1434 0.319405 CCAAGAAAGCAAAGCCCCAG 59.681 55.000 0.00 0.00 0.00 4.45
1391 1435 1.043022 CAAGAAAGCAAAGCCCCAGT 58.957 50.000 0.00 0.00 0.00 4.00
1392 1436 1.413812 CAAGAAAGCAAAGCCCCAGTT 59.586 47.619 0.00 0.00 0.00 3.16
1393 1437 1.332195 AGAAAGCAAAGCCCCAGTTC 58.668 50.000 0.00 0.00 0.00 3.01
1394 1438 1.039856 GAAAGCAAAGCCCCAGTTCA 58.960 50.000 0.00 0.00 0.00 3.18
1395 1439 1.412343 GAAAGCAAAGCCCCAGTTCAA 59.588 47.619 0.00 0.00 0.00 2.69
1396 1440 1.494960 AAGCAAAGCCCCAGTTCAAA 58.505 45.000 0.00 0.00 0.00 2.69
1397 1441 1.494960 AGCAAAGCCCCAGTTCAAAA 58.505 45.000 0.00 0.00 0.00 2.44
1398 1442 1.836802 AGCAAAGCCCCAGTTCAAAAA 59.163 42.857 0.00 0.00 0.00 1.94
1427 1472 2.071540 GAAAGCAAAGCCCAATCAAGC 58.928 47.619 0.00 0.00 0.00 4.01
1433 1478 1.553706 AAGCCCAATCAAGCAGAAGG 58.446 50.000 0.00 0.00 0.00 3.46
1436 1481 1.340405 GCCCAATCAAGCAGAAGGAGA 60.340 52.381 0.00 0.00 0.00 3.71
1437 1482 2.881403 GCCCAATCAAGCAGAAGGAGAA 60.881 50.000 0.00 0.00 0.00 2.87
1438 1483 3.015327 CCCAATCAAGCAGAAGGAGAAG 58.985 50.000 0.00 0.00 0.00 2.85
1439 1484 3.307975 CCCAATCAAGCAGAAGGAGAAGA 60.308 47.826 0.00 0.00 0.00 2.87
1440 1485 3.940221 CCAATCAAGCAGAAGGAGAAGAG 59.060 47.826 0.00 0.00 0.00 2.85
1817 1863 1.320344 CCTAGCTGGTGACGGTGCTA 61.320 60.000 0.00 0.00 39.64 3.49
1823 1869 2.434359 GTGACGGTGCTACCCTGC 60.434 66.667 0.00 0.00 33.75 4.85
1837 1889 1.487976 ACCCTGCGATCATGAAGACAT 59.512 47.619 0.00 0.00 37.19 3.06
1855 1907 9.914131 TGAAGACATCAGCACTAATGTATATAC 57.086 33.333 5.89 5.89 36.28 1.47
1882 1934 4.029520 ACTCACTACTGCTCAATGGAGAT 58.970 43.478 0.00 0.00 44.26 2.75
1883 1935 4.469227 ACTCACTACTGCTCAATGGAGATT 59.531 41.667 0.00 0.00 44.26 2.40
1884 1936 4.763073 TCACTACTGCTCAATGGAGATTG 58.237 43.478 0.00 0.00 44.26 2.67
1885 1937 3.311871 CACTACTGCTCAATGGAGATTGC 59.688 47.826 0.00 0.00 44.26 3.56
1886 1938 2.502142 ACTGCTCAATGGAGATTGCA 57.498 45.000 0.00 0.00 44.26 4.08
1887 1939 2.366533 ACTGCTCAATGGAGATTGCAG 58.633 47.619 0.00 4.35 44.26 4.41
1888 1940 2.026542 ACTGCTCAATGGAGATTGCAGA 60.027 45.455 14.30 0.00 44.26 4.26
1897 1949 6.765036 TCAATGGAGATTGCAGAAGTAGATTC 59.235 38.462 0.00 0.00 39.16 2.52
1924 1979 2.886587 ACGATTTCTTTTAACCGCGG 57.113 45.000 26.86 26.86 0.00 6.46
1956 2011 5.611796 TTCGTTGATGTCTGAAAATCTGG 57.388 39.130 3.97 0.00 0.00 3.86
1970 2025 5.046878 TGAAAATCTGGAGATTGCATTGCTT 60.047 36.000 10.49 0.00 43.41 3.91
2006 2061 5.588246 GCTCTTTCTCTGGATTTCCTTTAGG 59.412 44.000 0.00 0.00 36.82 2.69
2010 2065 5.941555 TCTCTGGATTTCCTTTAGGTCTC 57.058 43.478 0.00 0.00 36.82 3.36
2066 2128 1.885887 GGCAAGTTTGGTGCTGTATGA 59.114 47.619 0.00 0.00 41.88 2.15
2148 2220 6.824704 GTGATCTAGTGGACTTGAGTAGTACT 59.175 42.308 1.37 1.37 38.64 2.73
2149 2221 7.986320 GTGATCTAGTGGACTTGAGTAGTACTA 59.014 40.741 1.88 0.00 38.64 1.82
2150 2222 8.205512 TGATCTAGTGGACTTGAGTAGTACTAG 58.794 40.741 1.87 15.58 38.64 2.57
2152 2224 8.601047 TCTAGTGGACTTGAGTAGTACTAGTA 57.399 38.462 10.28 0.00 38.64 1.82
2153 2225 9.211410 TCTAGTGGACTTGAGTAGTACTAGTAT 57.789 37.037 10.28 0.00 38.64 2.12
2231 2303 4.956700 TCTCGGAGGATTATGTTGAGAGTT 59.043 41.667 4.96 0.00 0.00 3.01
2314 2402 4.286910 GTGATCGTAAACTGCAAGCAAAA 58.713 39.130 0.00 0.00 37.60 2.44
2400 2489 4.802051 GCCGGCCTCCATTCTGCA 62.802 66.667 18.11 0.00 0.00 4.41
2452 2541 0.901124 AGAGGCAGGAGTGATGTCAC 59.099 55.000 5.01 5.01 46.77 3.67
2500 2599 1.613255 GGAAAGGATTGAAGTCGGGCA 60.613 52.381 0.00 0.00 0.00 5.36
2501 2600 1.740025 GAAAGGATTGAAGTCGGGCAG 59.260 52.381 0.00 0.00 0.00 4.85
2538 2696 4.038162 GCCAACAGGAGATAGACGAGTTAT 59.962 45.833 0.00 0.00 0.00 1.89
2587 2745 0.243365 TTGTTGTCGCCATGAATGCC 59.757 50.000 0.00 0.00 0.00 4.40
2598 2756 2.310945 CCATGAATGCCAGGATAGGGAT 59.689 50.000 0.00 0.00 42.00 3.85
2599 2757 3.524789 CCATGAATGCCAGGATAGGGATA 59.475 47.826 0.00 0.00 38.96 2.59
2600 2758 4.384978 CCATGAATGCCAGGATAGGGATAG 60.385 50.000 0.00 0.00 38.96 2.08
2601 2759 3.184628 TGAATGCCAGGATAGGGATAGG 58.815 50.000 0.00 0.00 38.96 2.57
2602 2760 2.277008 ATGCCAGGATAGGGATAGGG 57.723 55.000 0.00 0.00 38.02 3.53
2603 2761 1.176182 TGCCAGGATAGGGATAGGGA 58.824 55.000 0.00 0.00 0.00 4.20
2604 2762 1.730470 TGCCAGGATAGGGATAGGGAT 59.270 52.381 0.00 0.00 0.00 3.85
2605 2763 2.116158 TGCCAGGATAGGGATAGGGATT 59.884 50.000 0.00 0.00 0.00 3.01
2606 2764 3.193782 GCCAGGATAGGGATAGGGATTT 58.806 50.000 0.00 0.00 0.00 2.17
2607 2765 3.201045 GCCAGGATAGGGATAGGGATTTC 59.799 52.174 0.00 0.00 0.00 2.17
2608 2766 3.783082 CCAGGATAGGGATAGGGATTTCC 59.217 52.174 0.00 0.00 0.00 3.13
2671 2829 2.906897 CAGTTGTGCACCGCCCTT 60.907 61.111 15.69 0.00 0.00 3.95
2673 2831 2.594592 GTTGTGCACCGCCCTTCT 60.595 61.111 15.69 0.00 0.00 2.85
2749 2913 1.741401 CTCATCGACGCCAGCCAAA 60.741 57.895 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.748412 TGCAGTTGTAGAGGCAAATATATTTTT 58.252 29.630 8.01 0.00 32.54 1.94
5 6 8.292444 TGCAGTTGTAGAGGCAAATATATTTT 57.708 30.769 8.01 0.00 32.54 1.82
6 7 7.775093 TCTGCAGTTGTAGAGGCAAATATATTT 59.225 33.333 14.67 4.81 35.59 1.40
7 8 7.282585 TCTGCAGTTGTAGAGGCAAATATATT 58.717 34.615 14.67 0.00 35.59 1.28
8 9 6.830912 TCTGCAGTTGTAGAGGCAAATATAT 58.169 36.000 14.67 0.00 35.59 0.86
9 10 6.233905 TCTGCAGTTGTAGAGGCAAATATA 57.766 37.500 14.67 0.00 35.59 0.86
10 11 5.102953 TCTGCAGTTGTAGAGGCAAATAT 57.897 39.130 14.67 0.00 35.59 1.28
11 12 4.507710 CTCTGCAGTTGTAGAGGCAAATA 58.492 43.478 14.67 0.00 46.67 1.40
12 13 3.341823 CTCTGCAGTTGTAGAGGCAAAT 58.658 45.455 14.67 0.00 46.67 2.32
13 14 2.771089 CTCTGCAGTTGTAGAGGCAAA 58.229 47.619 14.67 0.00 46.67 3.68
14 15 2.462456 CTCTGCAGTTGTAGAGGCAA 57.538 50.000 14.67 0.00 46.67 4.52
31 32 5.297776 TGCCTCTGCAGAAATTAAATAGCTC 59.702 40.000 18.85 0.00 44.23 4.09
63 68 3.282021 GCTTGGATGTATCAGGCTTCAA 58.718 45.455 0.00 0.00 34.89 2.69
105 110 4.150897 TGATACTCCCATTACAACCAGC 57.849 45.455 0.00 0.00 0.00 4.85
106 111 8.816894 AGTATATGATACTCCCATTACAACCAG 58.183 37.037 0.00 0.00 0.00 4.00
107 112 8.736097 AGTATATGATACTCCCATTACAACCA 57.264 34.615 0.00 0.00 0.00 3.67
116 121 9.355916 GCATGATACTAGTATATGATACTCCCA 57.644 37.037 22.89 12.81 0.00 4.37
117 122 9.355916 TGCATGATACTAGTATATGATACTCCC 57.644 37.037 22.89 9.00 0.00 4.30
153 158 8.860088 TGCATTACAGATGTAGTATCATACACT 58.140 33.333 0.00 0.00 38.43 3.55
154 159 9.476202 TTGCATTACAGATGTAGTATCATACAC 57.524 33.333 0.00 0.00 38.43 2.90
166 171 9.565090 ACATATGATACTTTGCATTACAGATGT 57.435 29.630 10.38 0.00 35.13 3.06
169 174 8.839343 CCAACATATGATACTTTGCATTACAGA 58.161 33.333 10.38 0.00 0.00 3.41
170 175 8.623903 ACCAACATATGATACTTTGCATTACAG 58.376 33.333 10.38 0.00 0.00 2.74
171 176 8.518430 ACCAACATATGATACTTTGCATTACA 57.482 30.769 10.38 0.00 0.00 2.41
174 179 9.353431 TGATACCAACATATGATACTTTGCATT 57.647 29.630 10.38 0.00 0.00 3.56
175 180 8.922931 TGATACCAACATATGATACTTTGCAT 57.077 30.769 10.38 0.00 0.00 3.96
176 181 8.922931 ATGATACCAACATATGATACTTTGCA 57.077 30.769 10.38 0.00 0.00 4.08
198 203 9.710900 CATGCCAATAAATGTAGTACTCTATGA 57.289 33.333 0.00 0.00 0.00 2.15
199 204 8.446273 GCATGCCAATAAATGTAGTACTCTATG 58.554 37.037 6.36 0.00 0.00 2.23
200 205 8.156820 TGCATGCCAATAAATGTAGTACTCTAT 58.843 33.333 16.68 0.00 0.00 1.98
201 206 7.505258 TGCATGCCAATAAATGTAGTACTCTA 58.495 34.615 16.68 0.00 0.00 2.43
202 207 6.356556 TGCATGCCAATAAATGTAGTACTCT 58.643 36.000 16.68 0.00 0.00 3.24
203 208 6.618287 TGCATGCCAATAAATGTAGTACTC 57.382 37.500 16.68 0.00 0.00 2.59
204 209 6.772233 TCATGCATGCCAATAAATGTAGTACT 59.228 34.615 22.25 0.00 0.00 2.73
205 210 6.857964 GTCATGCATGCCAATAAATGTAGTAC 59.142 38.462 22.25 5.12 0.00 2.73
206 211 6.545298 TGTCATGCATGCCAATAAATGTAGTA 59.455 34.615 22.25 0.00 0.00 1.82
207 212 5.360429 TGTCATGCATGCCAATAAATGTAGT 59.640 36.000 22.25 0.00 0.00 2.73
208 213 5.688621 GTGTCATGCATGCCAATAAATGTAG 59.311 40.000 22.25 0.00 0.00 2.74
209 214 5.126707 TGTGTCATGCATGCCAATAAATGTA 59.873 36.000 22.25 0.00 0.00 2.29
210 215 4.081586 TGTGTCATGCATGCCAATAAATGT 60.082 37.500 22.25 0.00 0.00 2.71
211 216 4.434520 TGTGTCATGCATGCCAATAAATG 58.565 39.130 22.25 11.06 0.00 2.32
212 217 4.739587 TGTGTCATGCATGCCAATAAAT 57.260 36.364 22.25 0.00 0.00 1.40
213 218 4.532314 TTGTGTCATGCATGCCAATAAA 57.468 36.364 22.25 9.43 0.00 1.40
214 219 4.021280 ACTTTGTGTCATGCATGCCAATAA 60.021 37.500 22.25 12.50 0.00 1.40
215 220 3.510753 ACTTTGTGTCATGCATGCCAATA 59.489 39.130 22.25 6.82 0.00 1.90
216 221 2.300723 ACTTTGTGTCATGCATGCCAAT 59.699 40.909 22.25 0.00 0.00 3.16
217 222 1.687660 ACTTTGTGTCATGCATGCCAA 59.312 42.857 22.25 19.09 0.00 4.52
218 223 1.330234 ACTTTGTGTCATGCATGCCA 58.670 45.000 22.25 14.83 0.00 4.92
219 224 2.733227 GCTACTTTGTGTCATGCATGCC 60.733 50.000 22.25 11.84 0.00 4.40
220 225 2.095110 TGCTACTTTGTGTCATGCATGC 60.095 45.455 22.25 11.82 0.00 4.06
221 226 3.058085 TGTGCTACTTTGTGTCATGCATG 60.058 43.478 21.07 21.07 34.18 4.06
222 227 3.148412 TGTGCTACTTTGTGTCATGCAT 58.852 40.909 0.00 0.00 34.18 3.96
223 228 2.570135 TGTGCTACTTTGTGTCATGCA 58.430 42.857 0.00 0.00 0.00 3.96
224 229 3.189080 TGATGTGCTACTTTGTGTCATGC 59.811 43.478 0.00 0.00 0.00 4.06
225 230 5.556355 ATGATGTGCTACTTTGTGTCATG 57.444 39.130 0.00 0.00 0.00 3.07
226 231 6.579666 AAATGATGTGCTACTTTGTGTCAT 57.420 33.333 0.00 0.00 0.00 3.06
227 232 7.503521 TTAAATGATGTGCTACTTTGTGTCA 57.496 32.000 0.00 0.00 0.00 3.58
235 240 9.371136 CCGTATCATATTAAATGATGTGCTACT 57.629 33.333 16.73 0.65 38.98 2.57
236 241 9.151471 ACCGTATCATATTAAATGATGTGCTAC 57.849 33.333 16.73 9.67 38.98 3.58
238 243 9.890629 ATACCGTATCATATTAAATGATGTGCT 57.109 29.630 16.73 5.80 38.98 4.40
307 312 9.844790 CAACTAAGCAATTTTAATGAGATGACA 57.155 29.630 0.00 0.00 0.00 3.58
308 313 9.294030 CCAACTAAGCAATTTTAATGAGATGAC 57.706 33.333 0.00 0.00 0.00 3.06
309 314 7.975616 GCCAACTAAGCAATTTTAATGAGATGA 59.024 33.333 0.00 0.00 0.00 2.92
310 315 7.760794 TGCCAACTAAGCAATTTTAATGAGATG 59.239 33.333 0.00 0.00 37.28 2.90
311 316 7.839907 TGCCAACTAAGCAATTTTAATGAGAT 58.160 30.769 0.00 0.00 37.28 2.75
312 317 7.225784 TGCCAACTAAGCAATTTTAATGAGA 57.774 32.000 0.00 0.00 37.28 3.27
313 318 7.464977 GCATGCCAACTAAGCAATTTTAATGAG 60.465 37.037 6.36 0.00 44.83 2.90
314 319 6.313411 GCATGCCAACTAAGCAATTTTAATGA 59.687 34.615 6.36 0.00 44.83 2.57
315 320 6.092396 TGCATGCCAACTAAGCAATTTTAATG 59.908 34.615 16.68 0.00 44.83 1.90
316 321 6.171921 TGCATGCCAACTAAGCAATTTTAAT 58.828 32.000 16.68 0.00 44.83 1.40
317 322 5.545588 TGCATGCCAACTAAGCAATTTTAA 58.454 33.333 16.68 0.00 44.83 1.52
318 323 5.144692 TGCATGCCAACTAAGCAATTTTA 57.855 34.783 16.68 0.00 44.83 1.52
319 324 4.005487 TGCATGCCAACTAAGCAATTTT 57.995 36.364 16.68 0.00 44.83 1.82
320 325 3.681593 TGCATGCCAACTAAGCAATTT 57.318 38.095 16.68 0.00 44.83 1.82
321 326 3.196039 TCATGCATGCCAACTAAGCAATT 59.804 39.130 22.25 0.00 44.83 2.32
322 327 2.761767 TCATGCATGCCAACTAAGCAAT 59.238 40.909 22.25 0.00 44.83 3.56
323 328 2.169330 TCATGCATGCCAACTAAGCAA 58.831 42.857 22.25 0.00 44.83 3.91
324 329 1.836802 TCATGCATGCCAACTAAGCA 58.163 45.000 22.25 0.00 45.94 3.91
325 330 3.567164 AGTATCATGCATGCCAACTAAGC 59.433 43.478 22.25 4.42 0.00 3.09
326 331 5.107337 CGTAGTATCATGCATGCCAACTAAG 60.107 44.000 24.68 23.10 0.00 2.18
327 332 4.749598 CGTAGTATCATGCATGCCAACTAA 59.250 41.667 24.68 9.84 0.00 2.24
328 333 4.202212 ACGTAGTATCATGCATGCCAACTA 60.202 41.667 22.25 21.88 41.94 2.24
329 334 3.133691 CGTAGTATCATGCATGCCAACT 58.866 45.455 22.25 22.78 0.00 3.16
330 335 2.872245 ACGTAGTATCATGCATGCCAAC 59.128 45.455 22.25 17.59 41.94 3.77
331 336 3.192541 ACGTAGTATCATGCATGCCAA 57.807 42.857 22.25 5.34 41.94 4.52
332 337 2.908688 ACGTAGTATCATGCATGCCA 57.091 45.000 22.25 8.84 41.94 4.92
350 355 7.148052 AGGCTGACCGTAATGATAGTATCATAC 60.148 40.741 22.95 18.54 44.79 2.39
351 356 6.890268 AGGCTGACCGTAATGATAGTATCATA 59.110 38.462 22.95 10.82 44.79 2.15
352 357 5.717178 AGGCTGACCGTAATGATAGTATCAT 59.283 40.000 18.22 18.22 46.34 2.45
353 358 5.077564 AGGCTGACCGTAATGATAGTATCA 58.922 41.667 15.10 15.10 42.09 2.15
354 359 5.646577 AGGCTGACCGTAATGATAGTATC 57.353 43.478 2.97 2.97 42.76 2.24
355 360 6.946583 TCTTAGGCTGACCGTAATGATAGTAT 59.053 38.462 0.00 0.00 42.76 2.12
356 361 6.301486 TCTTAGGCTGACCGTAATGATAGTA 58.699 40.000 0.00 0.00 42.76 1.82
357 362 5.138276 TCTTAGGCTGACCGTAATGATAGT 58.862 41.667 0.00 0.00 42.76 2.12
358 363 5.707242 TCTTAGGCTGACCGTAATGATAG 57.293 43.478 0.00 0.00 42.76 2.08
359 364 6.474140 TTTCTTAGGCTGACCGTAATGATA 57.526 37.500 0.00 0.00 42.76 2.15
360 365 5.353394 TTTCTTAGGCTGACCGTAATGAT 57.647 39.130 0.00 0.00 42.76 2.45
361 366 4.811969 TTTCTTAGGCTGACCGTAATGA 57.188 40.909 0.00 0.00 42.76 2.57
362 367 5.175859 TCTTTTCTTAGGCTGACCGTAATG 58.824 41.667 0.00 0.00 42.76 1.90
363 368 5.416271 TCTTTTCTTAGGCTGACCGTAAT 57.584 39.130 0.00 0.00 42.76 1.89
364 369 4.877378 TCTTTTCTTAGGCTGACCGTAA 57.123 40.909 0.00 0.00 42.76 3.18
365 370 4.877378 TTCTTTTCTTAGGCTGACCGTA 57.123 40.909 0.00 0.00 42.76 4.02
366 371 3.764237 TTCTTTTCTTAGGCTGACCGT 57.236 42.857 0.00 0.00 42.76 4.83
367 372 4.065789 AGTTTCTTTTCTTAGGCTGACCG 58.934 43.478 0.00 0.00 42.76 4.79
368 373 5.063880 TCAGTTTCTTTTCTTAGGCTGACC 58.936 41.667 0.00 0.00 0.00 4.02
369 374 5.180304 CCTCAGTTTCTTTTCTTAGGCTGAC 59.820 44.000 0.00 0.00 0.00 3.51
370 375 5.163195 ACCTCAGTTTCTTTTCTTAGGCTGA 60.163 40.000 0.00 0.00 30.68 4.26
371 376 5.049129 CACCTCAGTTTCTTTTCTTAGGCTG 60.049 44.000 0.00 0.00 30.68 4.85
372 377 5.066593 CACCTCAGTTTCTTTTCTTAGGCT 58.933 41.667 0.00 0.00 30.68 4.58
373 378 4.822350 ACACCTCAGTTTCTTTTCTTAGGC 59.178 41.667 0.00 0.00 30.68 3.93
374 379 5.239525 CCACACCTCAGTTTCTTTTCTTAGG 59.760 44.000 0.00 0.00 32.98 2.69
375 380 5.823045 ACCACACCTCAGTTTCTTTTCTTAG 59.177 40.000 0.00 0.00 0.00 2.18
376 381 5.751586 ACCACACCTCAGTTTCTTTTCTTA 58.248 37.500 0.00 0.00 0.00 2.10
393 398 4.619437 TTTTCCTTTTGTACGACCACAC 57.381 40.909 0.00 0.00 0.00 3.82
457 463 4.639135 AAGAAAGAAACGAAAAGCTGCT 57.361 36.364 0.00 0.00 0.00 4.24
458 464 5.516696 AGAAAAGAAAGAAACGAAAAGCTGC 59.483 36.000 0.00 0.00 0.00 5.25
459 465 6.197282 GGAGAAAAGAAAGAAACGAAAAGCTG 59.803 38.462 0.00 0.00 0.00 4.24
460 466 6.266323 GGAGAAAAGAAAGAAACGAAAAGCT 58.734 36.000 0.00 0.00 0.00 3.74
461 467 5.459107 GGGAGAAAAGAAAGAAACGAAAAGC 59.541 40.000 0.00 0.00 0.00 3.51
462 468 6.796426 AGGGAGAAAAGAAAGAAACGAAAAG 58.204 36.000 0.00 0.00 0.00 2.27
696 710 3.954258 AGCCACACTTATCCCAATTAAGC 59.046 43.478 0.00 0.00 0.00 3.09
791 805 8.049117 TCCTAATTGCATTTGTTCTAGTCTCAT 58.951 33.333 4.11 0.00 0.00 2.90
796 810 6.127619 GGCTTCCTAATTGCATTTGTTCTAGT 60.128 38.462 4.11 0.00 0.00 2.57
977 994 3.641648 ACAATTGCATTGAGTTTCACCG 58.358 40.909 5.05 0.00 42.83 4.94
989 1006 5.251764 AGAAAGAGCTACTGACAATTGCAT 58.748 37.500 5.05 0.00 0.00 3.96
991 1008 6.727824 TTAGAAAGAGCTACTGACAATTGC 57.272 37.500 5.05 0.00 0.00 3.56
997 1014 6.448006 TGTGTCTTTAGAAAGAGCTACTGAC 58.552 40.000 4.94 0.00 45.01 3.51
1011 1032 4.573900 AGGCAGTTCAGATGTGTCTTTAG 58.426 43.478 0.00 0.00 30.42 1.85
1012 1033 4.040339 TGAGGCAGTTCAGATGTGTCTTTA 59.960 41.667 0.00 0.00 30.42 1.85
1082 1105 5.634896 CATGAACGAATCTTGGGAAAAGAG 58.365 41.667 0.00 0.00 31.30 2.85
1188 1211 9.074576 TGCATAGCTCTTGATGAAATGAAATAT 57.925 29.630 0.00 0.00 0.00 1.28
1190 1213 7.147966 TGTGCATAGCTCTTGATGAAATGAAAT 60.148 33.333 0.00 0.00 0.00 2.17
1228 1252 3.977244 GGGCTGTGCGTTTGGTGG 61.977 66.667 0.00 0.00 0.00 4.61
1253 1296 2.284151 GGAGGAGGAGAGGGGGTC 59.716 72.222 0.00 0.00 0.00 4.46
1254 1297 3.369388 GGGAGGAGGAGAGGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
1257 1300 0.341609 AAAGAGGGAGGAGGAGAGGG 59.658 60.000 0.00 0.00 0.00 4.30
1258 1301 3.628832 ATAAAGAGGGAGGAGGAGAGG 57.371 52.381 0.00 0.00 0.00 3.69
1259 1302 6.192044 GGTATATAAAGAGGGAGGAGGAGAG 58.808 48.000 0.00 0.00 0.00 3.20
1260 1303 5.620021 TGGTATATAAAGAGGGAGGAGGAGA 59.380 44.000 0.00 0.00 0.00 3.71
1261 1304 5.717654 GTGGTATATAAAGAGGGAGGAGGAG 59.282 48.000 0.00 0.00 0.00 3.69
1262 1305 5.137255 TGTGGTATATAAAGAGGGAGGAGGA 59.863 44.000 0.00 0.00 0.00 3.71
1263 1306 5.246429 GTGTGGTATATAAAGAGGGAGGAGG 59.754 48.000 0.00 0.00 0.00 4.30
1264 1307 5.047943 CGTGTGGTATATAAAGAGGGAGGAG 60.048 48.000 0.00 0.00 0.00 3.69
1265 1308 4.831155 CGTGTGGTATATAAAGAGGGAGGA 59.169 45.833 0.00 0.00 0.00 3.71
1266 1309 4.560919 GCGTGTGGTATATAAAGAGGGAGG 60.561 50.000 0.00 0.00 0.00 4.30
1267 1310 4.557205 GCGTGTGGTATATAAAGAGGGAG 58.443 47.826 0.00 0.00 0.00 4.30
1268 1311 3.005050 CGCGTGTGGTATATAAAGAGGGA 59.995 47.826 0.00 0.00 0.00 4.20
1309 1352 2.159156 GCTCGTTGGGTTTTCTGGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
1313 1356 0.593128 CAGCTCGTTGGGTTTTCTGG 59.407 55.000 0.00 0.00 0.00 3.86
1320 1363 1.609501 TAGGCTCAGCTCGTTGGGT 60.610 57.895 0.00 0.00 0.00 4.51
1322 1365 0.459237 CAGTAGGCTCAGCTCGTTGG 60.459 60.000 0.00 0.00 0.00 3.77
1325 1368 1.096416 GTACAGTAGGCTCAGCTCGT 58.904 55.000 0.00 0.00 0.00 4.18
1359 1403 1.452145 TTTCTTGGTTGGCGCAGGAC 61.452 55.000 10.83 3.87 0.00 3.85
1360 1404 1.152860 TTTCTTGGTTGGCGCAGGA 60.153 52.632 10.83 0.00 0.00 3.86
1361 1405 1.286880 CTTTCTTGGTTGGCGCAGG 59.713 57.895 10.83 0.00 0.00 4.85
1362 1406 1.372128 GCTTTCTTGGTTGGCGCAG 60.372 57.895 10.83 0.00 0.00 5.18
1363 1407 1.670949 TTGCTTTCTTGGTTGGCGCA 61.671 50.000 10.83 0.00 0.00 6.09
1364 1408 0.529555 TTTGCTTTCTTGGTTGGCGC 60.530 50.000 0.00 0.00 0.00 6.53
1365 1409 1.490621 CTTTGCTTTCTTGGTTGGCG 58.509 50.000 0.00 0.00 0.00 5.69
1366 1410 1.220529 GCTTTGCTTTCTTGGTTGGC 58.779 50.000 0.00 0.00 0.00 4.52
1367 1411 1.541015 GGGCTTTGCTTTCTTGGTTGG 60.541 52.381 0.00 0.00 0.00 3.77
1368 1412 1.541015 GGGGCTTTGCTTTCTTGGTTG 60.541 52.381 0.00 0.00 0.00 3.77
1369 1413 0.758734 GGGGCTTTGCTTTCTTGGTT 59.241 50.000 0.00 0.00 0.00 3.67
1370 1414 0.398381 TGGGGCTTTGCTTTCTTGGT 60.398 50.000 0.00 0.00 0.00 3.67
1371 1415 0.319405 CTGGGGCTTTGCTTTCTTGG 59.681 55.000 0.00 0.00 0.00 3.61
1372 1416 1.043022 ACTGGGGCTTTGCTTTCTTG 58.957 50.000 0.00 0.00 0.00 3.02
1373 1417 1.688735 GAACTGGGGCTTTGCTTTCTT 59.311 47.619 0.00 0.00 0.00 2.52
1374 1418 1.332195 GAACTGGGGCTTTGCTTTCT 58.668 50.000 0.00 0.00 0.00 2.52
1375 1419 1.039856 TGAACTGGGGCTTTGCTTTC 58.960 50.000 0.00 0.00 0.00 2.62
1376 1420 1.494960 TTGAACTGGGGCTTTGCTTT 58.505 45.000 0.00 0.00 0.00 3.51
1377 1421 1.494960 TTTGAACTGGGGCTTTGCTT 58.505 45.000 0.00 0.00 0.00 3.91
1378 1422 1.494960 TTTTGAACTGGGGCTTTGCT 58.505 45.000 0.00 0.00 0.00 3.91
1379 1423 2.323968 TTTTTGAACTGGGGCTTTGC 57.676 45.000 0.00 0.00 0.00 3.68
1396 1440 5.709631 TGGGCTTTGCTTTCTTTTTCTTTTT 59.290 32.000 0.00 0.00 0.00 1.94
1397 1441 5.252547 TGGGCTTTGCTTTCTTTTTCTTTT 58.747 33.333 0.00 0.00 0.00 2.27
1398 1442 4.842574 TGGGCTTTGCTTTCTTTTTCTTT 58.157 34.783 0.00 0.00 0.00 2.52
1399 1443 4.486125 TGGGCTTTGCTTTCTTTTTCTT 57.514 36.364 0.00 0.00 0.00 2.52
1400 1444 4.486125 TTGGGCTTTGCTTTCTTTTTCT 57.514 36.364 0.00 0.00 0.00 2.52
1401 1445 4.815846 TGATTGGGCTTTGCTTTCTTTTTC 59.184 37.500 0.00 0.00 0.00 2.29
1402 1446 4.779696 TGATTGGGCTTTGCTTTCTTTTT 58.220 34.783 0.00 0.00 0.00 1.94
1403 1447 4.420522 TGATTGGGCTTTGCTTTCTTTT 57.579 36.364 0.00 0.00 0.00 2.27
1404 1448 4.383173 CTTGATTGGGCTTTGCTTTCTTT 58.617 39.130 0.00 0.00 0.00 2.52
1427 1472 4.383989 CCCATTCTTCCTCTTCTCCTTCTG 60.384 50.000 0.00 0.00 0.00 3.02
1433 1478 2.437651 CTCCCCCATTCTTCCTCTTCTC 59.562 54.545 0.00 0.00 0.00 2.87
1436 1481 1.601248 CCTCCCCCATTCTTCCTCTT 58.399 55.000 0.00 0.00 0.00 2.85
1437 1482 0.990818 GCCTCCCCCATTCTTCCTCT 60.991 60.000 0.00 0.00 0.00 3.69
1438 1483 1.534203 GCCTCCCCCATTCTTCCTC 59.466 63.158 0.00 0.00 0.00 3.71
1439 1484 2.378634 CGCCTCCCCCATTCTTCCT 61.379 63.158 0.00 0.00 0.00 3.36
1440 1485 2.193248 CGCCTCCCCCATTCTTCC 59.807 66.667 0.00 0.00 0.00 3.46
1817 1863 0.904649 TGTCTTCATGATCGCAGGGT 59.095 50.000 0.00 0.00 0.00 4.34
1823 1869 3.455327 AGTGCTGATGTCTTCATGATCG 58.545 45.455 0.00 0.00 34.06 3.69
1837 1889 8.935614 AGTAGTGGTATATACATTAGTGCTGA 57.064 34.615 14.70 0.00 0.00 4.26
1855 1907 4.428209 CATTGAGCAGTAGTGAGTAGTGG 58.572 47.826 0.42 0.00 33.16 4.00
1882 1934 8.194769 TCGTTACATATGAATCTACTTCTGCAA 58.805 33.333 10.38 0.00 34.75 4.08
1883 1935 7.712797 TCGTTACATATGAATCTACTTCTGCA 58.287 34.615 10.38 0.00 34.75 4.41
1884 1936 8.749841 ATCGTTACATATGAATCTACTTCTGC 57.250 34.615 10.38 0.00 34.75 4.26
1897 1949 7.109668 CGCGGTTAAAAGAAATCGTTACATATG 59.890 37.037 0.00 0.00 35.41 1.78
1912 1967 0.454452 GCTTGAGCCGCGGTTAAAAG 60.454 55.000 28.70 25.87 34.31 2.27
1924 1979 1.394917 ACATCAACGAATCGCTTGAGC 59.605 47.619 19.21 0.00 33.42 4.26
1956 2011 4.500375 GGGGAATGTAAGCAATGCAATCTC 60.500 45.833 8.35 0.00 0.00 2.75
1970 2025 2.505819 GAGAAAGAGCAGGGGGAATGTA 59.494 50.000 0.00 0.00 0.00 2.29
2030 2092 1.901591 TGCCTCTGCTTTGGAAGAAG 58.098 50.000 0.00 0.00 38.71 2.85
2032 2094 1.143684 ACTTGCCTCTGCTTTGGAAGA 59.856 47.619 0.00 0.00 38.71 2.87
2148 2220 7.041848 TCGCTTCGCAGTAGTACAAATATACTA 60.042 37.037 2.52 0.00 36.74 1.82
2149 2221 5.913514 CGCTTCGCAGTAGTACAAATATACT 59.086 40.000 2.52 0.00 38.89 2.12
2150 2222 5.911280 TCGCTTCGCAGTAGTACAAATATAC 59.089 40.000 2.52 0.00 0.00 1.47
2152 2224 4.928601 TCGCTTCGCAGTAGTACAAATAT 58.071 39.130 2.52 0.00 0.00 1.28
2153 2225 4.359971 TCGCTTCGCAGTAGTACAAATA 57.640 40.909 2.52 0.00 0.00 1.40
2154 2226 3.226346 TCGCTTCGCAGTAGTACAAAT 57.774 42.857 2.52 0.00 0.00 2.32
2155 2227 2.710220 TCGCTTCGCAGTAGTACAAA 57.290 45.000 2.52 0.00 0.00 2.83
2156 2228 2.933495 ATCGCTTCGCAGTAGTACAA 57.067 45.000 2.52 0.00 0.00 2.41
2157 2229 3.376234 ACTTATCGCTTCGCAGTAGTACA 59.624 43.478 2.52 0.00 0.00 2.90
2158 2230 3.724751 CACTTATCGCTTCGCAGTAGTAC 59.275 47.826 0.00 0.00 0.00 2.73
2159 2231 3.624410 TCACTTATCGCTTCGCAGTAGTA 59.376 43.478 0.00 0.00 0.00 1.82
2160 2232 2.422479 TCACTTATCGCTTCGCAGTAGT 59.578 45.455 0.00 0.00 0.00 2.73
2161 2233 3.066369 TCACTTATCGCTTCGCAGTAG 57.934 47.619 0.00 0.00 0.00 2.57
2178 2250 1.429148 GGCACGGAATCACGGATCAC 61.429 60.000 0.00 0.00 38.39 3.06
2314 2402 2.226330 TGCAACAACTTTGCCGACTAT 58.774 42.857 6.53 0.00 44.32 2.12
2452 2541 3.626680 TTTCTGCGAGAGACGGGCG 62.627 63.158 0.00 0.00 42.83 6.13
2474 2563 4.082733 CCGACTTCAATCCTTTCCTTTTCC 60.083 45.833 0.00 0.00 0.00 3.13
2483 2582 0.693049 ACTGCCCGACTTCAATCCTT 59.307 50.000 0.00 0.00 0.00 3.36
2500 2599 2.048127 GGCTCGGCTTCGTTCACT 60.048 61.111 0.00 0.00 35.06 3.41
2501 2600 1.959226 TTGGCTCGGCTTCGTTCAC 60.959 57.895 0.00 0.00 35.06 3.18
2538 2696 4.758251 CATGCGTGCTCCACCCGA 62.758 66.667 0.00 0.00 0.00 5.14
2587 2745 4.704403 AGGAAATCCCTATCCCTATCCTG 58.296 47.826 0.00 0.00 45.48 3.86
2607 2765 2.896039 CACCTCTCCCTAATCCCTAGG 58.104 57.143 0.06 0.06 46.33 3.02
2608 2766 2.252714 GCACCTCTCCCTAATCCCTAG 58.747 57.143 0.00 0.00 0.00 3.02
2609 2767 1.132817 GGCACCTCTCCCTAATCCCTA 60.133 57.143 0.00 0.00 0.00 3.53
2610 2768 0.400670 GGCACCTCTCCCTAATCCCT 60.401 60.000 0.00 0.00 0.00 4.20
2611 2769 2.146779 GGCACCTCTCCCTAATCCC 58.853 63.158 0.00 0.00 0.00 3.85
2656 2814 2.594592 AGAAGGGCGGTGCACAAC 60.595 61.111 20.43 9.60 32.33 3.32
2657 2815 2.281484 GAGAAGGGCGGTGCACAA 60.281 61.111 20.43 0.00 32.33 3.33
2658 2816 3.241530 AGAGAAGGGCGGTGCACA 61.242 61.111 20.43 0.00 32.33 4.57
2659 2817 2.743928 CAGAGAAGGGCGGTGCAC 60.744 66.667 8.80 8.80 0.00 4.57
2660 2818 4.704833 GCAGAGAAGGGCGGTGCA 62.705 66.667 0.00 0.00 34.18 4.57
2661 2819 4.400961 AGCAGAGAAGGGCGGTGC 62.401 66.667 0.00 0.00 34.54 5.01
2662 2820 2.435586 CAGCAGAGAAGGGCGGTG 60.436 66.667 0.00 0.00 34.54 4.94
2663 2821 4.400961 GCAGCAGAGAAGGGCGGT 62.401 66.667 0.00 0.00 34.54 5.68
2749 2913 2.385803 CCGTGATGAGGGTAGTAGGTT 58.614 52.381 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.