Multiple sequence alignment - TraesCS6B01G160500

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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 TraesCS6B01G160500 chr6B 100.000 4043 0 0 1 4043 164361924 164365966 0.000000e+00 7467.0
1 TraesCS6B01G160500 chr6B 94.578 166 9 0 285 450 639991492 639991657 1.440000e-64 257.0
2 TraesCS6B01G160500 chr6D 95.208 2567 106 8 570 3124 86720899 86723460 0.000000e+00 4043.0
3 TraesCS6B01G160500 chr6D 90.050 201 9 3 33 233 86715813 86716002 2.410000e-62 250.0
4 TraesCS6B01G160500 chr6D 93.798 129 6 1 447 575 86716032 86716158 4.120000e-45 193.0
5 TraesCS6B01G160500 chr6D 92.188 128 8 1 447 574 86716494 86716619 3.210000e-41 180.0
6 TraesCS6B01G160500 chr6A 91.174 2708 158 34 447 3123 104414427 104411770 0.000000e+00 3602.0
7 TraesCS6B01G160500 chr6A 80.401 449 38 25 448 875 104398086 104398505 3.060000e-76 296.0
8 TraesCS6B01G160500 chr2B 97.306 928 22 1 3119 4043 717923686 717922759 0.000000e+00 1572.0
9 TraesCS6B01G160500 chr2B 97.152 913 25 1 3131 4043 728362653 728361742 0.000000e+00 1541.0
10 TraesCS6B01G160500 chr2B 94.083 169 10 0 284 452 134045912 134045744 1.440000e-64 257.0
11 TraesCS6B01G160500 chr2B 75.306 490 91 20 1985 2466 769031145 769031612 1.470000e-49 207.0
12 TraesCS6B01G160500 chr2B 80.000 135 20 7 1096 1228 243075305 243075176 4.300000e-15 93.5
13 TraesCS6B01G160500 chr3B 97.297 925 24 1 3120 4043 752441726 752442650 0.000000e+00 1568.0
14 TraesCS6B01G160500 chr3B 96.649 925 31 0 3119 4043 548675475 548676399 0.000000e+00 1537.0
15 TraesCS6B01G160500 chr3B 96.448 929 33 0 3115 4043 720177124 720176196 0.000000e+00 1533.0
16 TraesCS6B01G160500 chr3B 72.690 1959 438 70 1083 2997 89357956 89356051 7.590000e-157 564.0
17 TraesCS6B01G160500 chr3B 74.309 1448 306 56 1252 2674 576020925 576022331 1.640000e-153 553.0
18 TraesCS6B01G160500 chr3B 75.000 480 89 20 1099 1555 89059484 89059955 4.120000e-45 193.0
19 TraesCS6B01G160500 chr7B 97.081 925 26 1 3120 4043 192794310 192793386 0.000000e+00 1557.0
20 TraesCS6B01G160500 chr7B 96.537 924 32 0 3120 4043 626387496 626386573 0.000000e+00 1530.0
21 TraesCS6B01G160500 chr4B 96.537 924 31 1 3120 4043 657081324 657080402 0.000000e+00 1528.0
22 TraesCS6B01G160500 chrUn 95.829 935 38 1 3110 4043 34582468 34581534 0.000000e+00 1509.0
23 TraesCS6B01G160500 chr5B 75.384 1759 365 56 1250 2986 586359750 586358038 0.000000e+00 787.0
24 TraesCS6B01G160500 chr2D 73.289 1958 420 67 1096 3006 187109593 187107692 1.230000e-174 623.0
25 TraesCS6B01G160500 chr2D 94.643 168 9 0 285 452 609886955 609886788 1.110000e-65 261.0
26 TraesCS6B01G160500 chr2A 73.047 1959 423 69 1096 3006 199728963 199727062 2.690000e-166 595.0
27 TraesCS6B01G160500 chr5D 74.559 1191 273 25 1806 2986 478594525 478595695 1.010000e-135 494.0
28 TraesCS6B01G160500 chr5D 94.083 169 10 0 285 453 559625769 559625937 1.440000e-64 257.0
29 TraesCS6B01G160500 chr1B 71.853 1716 374 79 1243 2912 266109775 266111427 3.790000e-105 392.0
30 TraesCS6B01G160500 chr1A 71.828 1718 369 86 1243 2912 238671883 238673533 6.340000e-103 385.0
31 TraesCS6B01G160500 chr3A 99.394 165 1 0 285 449 19909391 19909555 2.360000e-77 300.0
32 TraesCS6B01G160500 chr3A 94.578 166 9 0 285 450 529671132 529671297 1.440000e-64 257.0
33 TraesCS6B01G160500 chr7D 93.642 173 10 1 284 455 363148832 363149004 1.440000e-64 257.0
34 TraesCS6B01G160500 chr4D 92.697 178 11 2 279 455 243613267 243613443 5.190000e-64 255.0
35 TraesCS6B01G160500 chr1D 93.529 170 11 0 285 454 9218208 9218377 1.870000e-63 254.0


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 TraesCS6B01G160500 chr6B 164361924 164365966 4042 False 7467.000000 7467 100.000 1 4043 1 chr6B.!!$F1 4042
1 TraesCS6B01G160500 chr6D 86720899 86723460 2561 False 4043.000000 4043 95.208 570 3124 1 chr6D.!!$F1 2554
2 TraesCS6B01G160500 chr6D 86715813 86716619 806 False 207.666667 250 92.012 33 575 3 chr6D.!!$F2 542
3 TraesCS6B01G160500 chr6A 104411770 104414427 2657 True 3602.000000 3602 91.174 447 3123 1 chr6A.!!$R1 2676
4 TraesCS6B01G160500 chr2B 717922759 717923686 927 True 1572.000000 1572 97.306 3119 4043 1 chr2B.!!$R3 924
5 TraesCS6B01G160500 chr2B 728361742 728362653 911 True 1541.000000 1541 97.152 3131 4043 1 chr2B.!!$R4 912
6 TraesCS6B01G160500 chr3B 752441726 752442650 924 False 1568.000000 1568 97.297 3120 4043 1 chr3B.!!$F4 923
7 TraesCS6B01G160500 chr3B 548675475 548676399 924 False 1537.000000 1537 96.649 3119 4043 1 chr3B.!!$F2 924
8 TraesCS6B01G160500 chr3B 720176196 720177124 928 True 1533.000000 1533 96.448 3115 4043 1 chr3B.!!$R2 928
9 TraesCS6B01G160500 chr3B 89356051 89357956 1905 True 564.000000 564 72.690 1083 2997 1 chr3B.!!$R1 1914
10 TraesCS6B01G160500 chr3B 576020925 576022331 1406 False 553.000000 553 74.309 1252 2674 1 chr3B.!!$F3 1422
11 TraesCS6B01G160500 chr7B 192793386 192794310 924 True 1557.000000 1557 97.081 3120 4043 1 chr7B.!!$R1 923
12 TraesCS6B01G160500 chr7B 626386573 626387496 923 True 1530.000000 1530 96.537 3120 4043 1 chr7B.!!$R2 923
13 TraesCS6B01G160500 chr4B 657080402 657081324 922 True 1528.000000 1528 96.537 3120 4043 1 chr4B.!!$R1 923
14 TraesCS6B01G160500 chrUn 34581534 34582468 934 True 1509.000000 1509 95.829 3110 4043 1 chrUn.!!$R1 933
15 TraesCS6B01G160500 chr5B 586358038 586359750 1712 True 787.000000 787 75.384 1250 2986 1 chr5B.!!$R1 1736
16 TraesCS6B01G160500 chr2D 187107692 187109593 1901 True 623.000000 623 73.289 1096 3006 1 chr2D.!!$R1 1910
17 TraesCS6B01G160500 chr2A 199727062 199728963 1901 True 595.000000 595 73.047 1096 3006 1 chr2A.!!$R1 1910
18 TraesCS6B01G160500 chr5D 478594525 478595695 1170 False 494.000000 494 74.559 1806 2986 1 chr5D.!!$F1 1180
19 TraesCS6B01G160500 chr1B 266109775 266111427 1652 False 392.000000 392 71.853 1243 2912 1 chr1B.!!$F1 1669
20 TraesCS6B01G160500 chr1A 238671883 238673533 1650 False 385.000000 385 71.828 1243 2912 1 chr1A.!!$F1 1669

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
298 299 0.108945 CAACGTACTCCCTCCGTTCC 60.109 60.000 0.0 0.0 42.34 3.62 F
299 300 0.251519 AACGTACTCCCTCCGTTCCT 60.252 55.000 0.0 0.0 40.46 3.36 F
851 863 0.318762 AGCGACTCCCTTTGACTGAC 59.681 55.000 0.0 0.0 0.00 3.51 F
2349 2559 1.299089 GGCCAACGACAAGCACAAC 60.299 57.895 0.0 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1212 1374 2.718073 GGTCGGGTAGATGGCGTGT 61.718 63.158 0.00 0.0 0.00 4.49 R
1245 1407 3.760035 GACGAGAAGGAGCGGCCA 61.760 66.667 2.24 0.0 40.02 5.36 R
2559 2775 0.386838 GGTACCCTATGGTTCCGACG 59.613 60.000 0.00 0.0 44.75 5.12 R
3304 3535 1.490490 AGTTCAGGTCCAGTCTTTGCA 59.510 47.619 0.00 0.0 0.00 4.08 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.559862 ACTCAGTTCGAAAAGATCCCAT 57.440 40.909 0.00 0.00 0.00 4.00
22 23 5.677319 ACTCAGTTCGAAAAGATCCCATA 57.323 39.130 0.00 0.00 0.00 2.74
23 24 6.240549 ACTCAGTTCGAAAAGATCCCATAT 57.759 37.500 0.00 0.00 0.00 1.78
24 25 6.653989 ACTCAGTTCGAAAAGATCCCATATT 58.346 36.000 0.00 0.00 0.00 1.28
25 26 7.792032 ACTCAGTTCGAAAAGATCCCATATTA 58.208 34.615 0.00 0.00 0.00 0.98
26 27 7.928706 ACTCAGTTCGAAAAGATCCCATATTAG 59.071 37.037 0.00 0.00 0.00 1.73
27 28 7.792032 TCAGTTCGAAAAGATCCCATATTAGT 58.208 34.615 0.00 0.00 0.00 2.24
28 29 7.710907 TCAGTTCGAAAAGATCCCATATTAGTG 59.289 37.037 0.00 0.00 0.00 2.74
29 30 6.992715 AGTTCGAAAAGATCCCATATTAGTGG 59.007 38.462 0.00 0.00 39.05 4.00
30 31 5.305585 TCGAAAAGATCCCATATTAGTGGC 58.694 41.667 0.00 0.00 37.96 5.01
31 32 4.152402 CGAAAAGATCCCATATTAGTGGCG 59.848 45.833 0.00 0.00 37.96 5.69
53 54 4.318903 CGGAAACAAAACATGCAGTACGTA 60.319 41.667 0.00 0.00 0.00 3.57
59 60 3.806316 AACATGCAGTACGTAAAGCAC 57.194 42.857 21.10 1.43 40.14 4.40
109 110 3.490933 CGCAGTAGAAAGGATCGGATTCA 60.491 47.826 0.00 0.00 0.00 2.57
119 120 5.646692 AGGATCGGATTCAAAGGGAAATA 57.353 39.130 0.00 0.00 39.39 1.40
160 161 7.040755 ACAACGAAGAACAATGTGGATGAATAA 60.041 33.333 0.00 0.00 0.00 1.40
190 191 7.763172 AGAACTAATTAAGAATGCAGAGACG 57.237 36.000 0.00 0.00 0.00 4.18
216 217 4.472833 AGTAAGGAGATGAACAGGAAGCAT 59.527 41.667 0.00 0.00 0.00 3.79
217 218 5.663106 AGTAAGGAGATGAACAGGAAGCATA 59.337 40.000 0.00 0.00 0.00 3.14
245 246 9.588096 AAAATGATAAACATATAAGGTCCTCCC 57.412 33.333 0.00 0.00 38.38 4.30
246 247 7.888514 ATGATAAACATATAAGGTCCTCCCA 57.111 36.000 0.00 0.00 37.46 4.37
247 248 7.888514 TGATAAACATATAAGGTCCTCCCAT 57.111 36.000 0.00 0.00 34.66 4.00
248 249 8.982471 TGATAAACATATAAGGTCCTCCCATA 57.018 34.615 0.00 0.00 34.66 2.74
249 250 9.046846 TGATAAACATATAAGGTCCTCCCATAG 57.953 37.037 0.00 0.00 34.66 2.23
250 251 8.990693 ATAAACATATAAGGTCCTCCCATAGT 57.009 34.615 0.00 0.00 34.66 2.12
251 252 6.936968 AACATATAAGGTCCTCCCATAGTC 57.063 41.667 0.00 0.00 34.66 2.59
252 253 5.017490 ACATATAAGGTCCTCCCATAGTCG 58.983 45.833 0.00 0.00 34.66 4.18
253 254 3.897657 ATAAGGTCCTCCCATAGTCGA 57.102 47.619 0.00 0.00 34.66 4.20
254 255 2.074729 AAGGTCCTCCCATAGTCGAG 57.925 55.000 0.00 0.00 34.66 4.04
255 256 1.223501 AGGTCCTCCCATAGTCGAGA 58.776 55.000 0.00 0.00 34.66 4.04
256 257 1.569548 AGGTCCTCCCATAGTCGAGAA 59.430 52.381 0.00 0.00 34.66 2.87
257 258 1.682323 GGTCCTCCCATAGTCGAGAAC 59.318 57.143 0.00 0.00 0.00 3.01
260 261 1.683917 CCTCCCATAGTCGAGAACAGG 59.316 57.143 0.00 0.00 0.00 4.00
267 268 5.753921 CCCATAGTCGAGAACAGGAAAATAC 59.246 44.000 0.00 0.00 0.00 1.89
280 281 5.113383 CAGGAAAATACGGCAGTACATACA 58.887 41.667 0.00 0.00 35.39 2.29
282 283 5.583457 AGGAAAATACGGCAGTACATACAAC 59.417 40.000 0.00 0.00 35.39 3.32
283 284 5.459110 AAAATACGGCAGTACATACAACG 57.541 39.130 0.00 0.00 35.39 4.10
284 285 3.788333 ATACGGCAGTACATACAACGT 57.212 42.857 0.00 9.49 35.39 3.99
285 286 4.898829 ATACGGCAGTACATACAACGTA 57.101 40.909 0.00 12.16 38.05 3.57
286 287 2.867429 ACGGCAGTACATACAACGTAC 58.133 47.619 0.00 0.00 39.64 3.67
288 289 3.103738 CGGCAGTACATACAACGTACTC 58.896 50.000 0.00 0.00 44.92 2.59
289 290 3.442100 GGCAGTACATACAACGTACTCC 58.558 50.000 0.00 2.69 44.92 3.85
290 291 3.442100 GCAGTACATACAACGTACTCCC 58.558 50.000 0.00 0.00 44.92 4.30
291 292 3.129988 GCAGTACATACAACGTACTCCCT 59.870 47.826 0.00 0.00 44.92 4.20
292 293 4.732938 GCAGTACATACAACGTACTCCCTC 60.733 50.000 0.00 0.00 44.92 4.30
293 294 3.950395 AGTACATACAACGTACTCCCTCC 59.050 47.826 0.00 0.00 44.92 4.30
294 295 1.747355 ACATACAACGTACTCCCTCCG 59.253 52.381 0.00 0.00 0.00 4.63
295 296 1.747355 CATACAACGTACTCCCTCCGT 59.253 52.381 0.00 0.00 36.17 4.69
296 297 1.909700 TACAACGTACTCCCTCCGTT 58.090 50.000 0.00 0.00 44.81 4.44
297 298 0.600057 ACAACGTACTCCCTCCGTTC 59.400 55.000 0.00 0.00 42.34 3.95
298 299 0.108945 CAACGTACTCCCTCCGTTCC 60.109 60.000 0.00 0.00 42.34 3.62
299 300 0.251519 AACGTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 40.46 3.36
300 301 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
301 302 1.004745 ACGTACTCCCTCCGTTCCTAA 59.995 52.381 0.00 0.00 0.00 2.69
302 303 2.094675 CGTACTCCCTCCGTTCCTAAA 58.905 52.381 0.00 0.00 0.00 1.85
303 304 2.692041 CGTACTCCCTCCGTTCCTAAAT 59.308 50.000 0.00 0.00 0.00 1.40
304 305 3.885297 CGTACTCCCTCCGTTCCTAAATA 59.115 47.826 0.00 0.00 0.00 1.40
305 306 4.522022 CGTACTCCCTCCGTTCCTAAATAT 59.478 45.833 0.00 0.00 0.00 1.28
306 307 5.707298 CGTACTCCCTCCGTTCCTAAATATA 59.293 44.000 0.00 0.00 0.00 0.86
307 308 6.207417 CGTACTCCCTCCGTTCCTAAATATAA 59.793 42.308 0.00 0.00 0.00 0.98
308 309 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
309 310 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
310 311 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
311 312 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
312 313 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
313 314 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
314 315 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
315 316 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
372 373 9.750125 TGTATGTAGACATATTTTAGAGTGCAG 57.250 33.333 5.69 0.00 40.53 4.41
373 374 9.197694 GTATGTAGACATATTTTAGAGTGCAGG 57.802 37.037 5.69 0.00 40.53 4.85
374 375 7.182817 TGTAGACATATTTTAGAGTGCAGGT 57.817 36.000 0.00 0.00 0.00 4.00
375 376 7.620880 TGTAGACATATTTTAGAGTGCAGGTT 58.379 34.615 0.00 0.00 0.00 3.50
376 377 8.100791 TGTAGACATATTTTAGAGTGCAGGTTT 58.899 33.333 0.00 0.00 0.00 3.27
377 378 9.595823 GTAGACATATTTTAGAGTGCAGGTTTA 57.404 33.333 0.00 0.00 0.00 2.01
378 379 8.494016 AGACATATTTTAGAGTGCAGGTTTAC 57.506 34.615 0.00 0.00 0.00 2.01
379 380 8.322091 AGACATATTTTAGAGTGCAGGTTTACT 58.678 33.333 0.00 0.00 0.00 2.24
380 381 8.494016 ACATATTTTAGAGTGCAGGTTTACTC 57.506 34.615 0.00 0.00 42.77 2.59
381 382 8.100791 ACATATTTTAGAGTGCAGGTTTACTCA 58.899 33.333 7.09 0.00 44.41 3.41
382 383 8.607459 CATATTTTAGAGTGCAGGTTTACTCAG 58.393 37.037 7.09 0.00 44.41 3.35
383 384 5.546621 TTTAGAGTGCAGGTTTACTCAGT 57.453 39.130 7.09 0.00 44.41 3.41
384 385 5.546621 TTAGAGTGCAGGTTTACTCAGTT 57.453 39.130 7.09 0.00 44.41 3.16
385 386 4.423625 AGAGTGCAGGTTTACTCAGTTT 57.576 40.909 7.09 0.00 44.41 2.66
386 387 4.130118 AGAGTGCAGGTTTACTCAGTTTG 58.870 43.478 7.09 0.00 44.41 2.93
387 388 2.618709 AGTGCAGGTTTACTCAGTTTGC 59.381 45.455 0.00 0.00 0.00 3.68
388 389 2.618709 GTGCAGGTTTACTCAGTTTGCT 59.381 45.455 0.00 0.00 0.00 3.91
389 390 2.878406 TGCAGGTTTACTCAGTTTGCTC 59.122 45.455 0.00 0.00 0.00 4.26
390 391 2.226674 GCAGGTTTACTCAGTTTGCTCC 59.773 50.000 0.00 0.00 0.00 4.70
391 392 2.480419 CAGGTTTACTCAGTTTGCTCCG 59.520 50.000 0.00 0.00 0.00 4.63
392 393 2.104281 AGGTTTACTCAGTTTGCTCCGT 59.896 45.455 0.00 0.00 0.00 4.69
393 394 3.322828 AGGTTTACTCAGTTTGCTCCGTA 59.677 43.478 0.00 0.00 0.00 4.02
394 395 4.020485 AGGTTTACTCAGTTTGCTCCGTAT 60.020 41.667 0.00 0.00 0.00 3.06
395 396 4.092968 GGTTTACTCAGTTTGCTCCGTATG 59.907 45.833 0.00 0.00 0.00 2.39
396 397 4.530710 TTACTCAGTTTGCTCCGTATGT 57.469 40.909 0.00 0.00 0.00 2.29
397 398 5.648178 TTACTCAGTTTGCTCCGTATGTA 57.352 39.130 0.00 0.00 0.00 2.29
398 399 4.111375 ACTCAGTTTGCTCCGTATGTAG 57.889 45.455 0.00 0.00 0.00 2.74
399 400 3.510360 ACTCAGTTTGCTCCGTATGTAGT 59.490 43.478 0.00 0.00 0.00 2.73
400 401 4.106029 TCAGTTTGCTCCGTATGTAGTC 57.894 45.455 0.00 0.00 0.00 2.59
401 402 3.508402 TCAGTTTGCTCCGTATGTAGTCA 59.492 43.478 0.00 0.00 0.00 3.41
402 403 3.612860 CAGTTTGCTCCGTATGTAGTCAC 59.387 47.826 0.00 0.00 0.00 3.67
403 404 3.510360 AGTTTGCTCCGTATGTAGTCACT 59.490 43.478 0.00 0.00 0.00 3.41
404 405 3.777465 TTGCTCCGTATGTAGTCACTC 57.223 47.619 0.00 0.00 0.00 3.51
405 406 1.669265 TGCTCCGTATGTAGTCACTCG 59.331 52.381 0.00 0.00 0.00 4.18
406 407 1.669779 GCTCCGTATGTAGTCACTCGT 59.330 52.381 0.00 0.00 0.00 4.18
407 408 2.097142 GCTCCGTATGTAGTCACTCGTT 59.903 50.000 0.00 0.00 0.00 3.85
408 409 3.681855 CTCCGTATGTAGTCACTCGTTG 58.318 50.000 0.00 0.00 0.00 4.10
409 410 2.421073 TCCGTATGTAGTCACTCGTTGG 59.579 50.000 0.00 0.00 0.00 3.77
410 411 2.421073 CCGTATGTAGTCACTCGTTGGA 59.579 50.000 0.00 0.00 0.00 3.53
411 412 3.119743 CCGTATGTAGTCACTCGTTGGAA 60.120 47.826 0.00 0.00 0.00 3.53
412 413 4.439700 CCGTATGTAGTCACTCGTTGGAAT 60.440 45.833 0.00 0.00 0.00 3.01
413 414 4.733887 CGTATGTAGTCACTCGTTGGAATC 59.266 45.833 0.00 0.00 0.00 2.52
414 415 5.448768 CGTATGTAGTCACTCGTTGGAATCT 60.449 44.000 0.00 0.00 0.00 2.40
415 416 4.436242 TGTAGTCACTCGTTGGAATCTC 57.564 45.455 0.00 0.00 0.00 2.75
416 417 4.079970 TGTAGTCACTCGTTGGAATCTCT 58.920 43.478 0.00 0.00 0.00 3.10
417 418 5.250982 TGTAGTCACTCGTTGGAATCTCTA 58.749 41.667 0.00 0.00 0.00 2.43
418 419 5.708697 TGTAGTCACTCGTTGGAATCTCTAA 59.291 40.000 0.00 0.00 0.00 2.10
419 420 5.723672 AGTCACTCGTTGGAATCTCTAAA 57.276 39.130 0.00 0.00 0.00 1.85
420 421 6.097915 AGTCACTCGTTGGAATCTCTAAAA 57.902 37.500 0.00 0.00 0.00 1.52
421 422 6.522054 AGTCACTCGTTGGAATCTCTAAAAA 58.478 36.000 0.00 0.00 0.00 1.94
422 423 6.647067 AGTCACTCGTTGGAATCTCTAAAAAG 59.353 38.462 0.00 0.00 0.00 2.27
423 424 6.645415 GTCACTCGTTGGAATCTCTAAAAAGA 59.355 38.462 0.00 0.00 0.00 2.52
424 425 6.645415 TCACTCGTTGGAATCTCTAAAAAGAC 59.355 38.462 0.00 0.00 0.00 3.01
425 426 6.647067 CACTCGTTGGAATCTCTAAAAAGACT 59.353 38.462 0.00 0.00 0.00 3.24
426 427 7.171678 CACTCGTTGGAATCTCTAAAAAGACTT 59.828 37.037 0.00 0.00 0.00 3.01
427 428 8.365647 ACTCGTTGGAATCTCTAAAAAGACTTA 58.634 33.333 0.00 0.00 0.00 2.24
428 429 9.372369 CTCGTTGGAATCTCTAAAAAGACTTAT 57.628 33.333 0.00 0.00 0.00 1.73
443 444 8.494016 AAAAGACTTATATTTGAGAACGGAGG 57.506 34.615 0.00 0.00 0.00 4.30
444 445 6.163135 AGACTTATATTTGAGAACGGAGGG 57.837 41.667 0.00 0.00 0.00 4.30
445 446 5.897824 AGACTTATATTTGAGAACGGAGGGA 59.102 40.000 0.00 0.00 0.00 4.20
450 451 8.945195 TTATATTTGAGAACGGAGGGAGTATA 57.055 34.615 0.00 0.00 0.00 1.47
575 581 0.520412 CGGCGCAAACGTATCCAAAG 60.520 55.000 10.83 0.00 42.83 2.77
576 582 0.800012 GGCGCAAACGTATCCAAAGA 59.200 50.000 10.83 0.00 42.83 2.52
675 681 2.325082 GCTACGGGTGGCAACTGTG 61.325 63.158 26.87 16.78 37.02 3.66
711 718 1.234821 GACATTGCCCGTCAAAGACA 58.765 50.000 0.00 0.00 38.34 3.41
731 738 1.916697 GCAGCGAAACTTCCTGCCTC 61.917 60.000 16.07 0.00 41.48 4.70
778 786 5.048013 TCTCTCACATGTTGTTGTCGAGTAT 60.048 40.000 0.00 0.00 31.96 2.12
783 791 5.003496 CACATGTTGTTGTCGAGTATACGAG 59.997 44.000 0.00 0.00 42.88 4.18
820 831 6.219473 CAGCAAGGACATAAGGACATAGTAG 58.781 44.000 0.00 0.00 0.00 2.57
851 863 0.318762 AGCGACTCCCTTTGACTGAC 59.681 55.000 0.00 0.00 0.00 3.51
859 871 4.040584 ACTCCCTTTGACTGACTAAGGTTC 59.959 45.833 15.85 0.00 45.39 3.62
862 874 4.202367 CCCTTTGACTGACTAAGGTTCAGT 60.202 45.833 15.85 4.70 45.39 3.41
899 915 3.618594 GCTCGATGATTTGTGCAACTCTA 59.381 43.478 0.00 0.00 38.04 2.43
1212 1374 3.311110 ACGCTCCGCCAGAAAGGA 61.311 61.111 0.00 0.00 41.22 3.36
1605 1797 2.494445 CACGAGGCGATGCAGGTA 59.506 61.111 0.00 0.00 0.00 3.08
1755 1950 2.687805 CGGCTTCTCGTCCTCGACA 61.688 63.158 0.00 0.00 41.35 4.35
1801 1996 1.448540 CTTGGATGGAGCTTCGCGT 60.449 57.895 5.77 0.00 0.00 6.01
1911 2109 2.517875 CTGCCCATAGCCACTGCC 60.518 66.667 0.00 0.00 42.71 4.85
2091 2289 2.517798 GGGGGTAGGAGGATTCGGC 61.518 68.421 0.00 0.00 0.00 5.54
2349 2559 1.299089 GGCCAACGACAAGCACAAC 60.299 57.895 0.00 0.00 0.00 3.32
2559 2775 2.105128 CCGGAGACCTCGCATGTC 59.895 66.667 0.00 0.00 0.00 3.06
2562 2778 1.226717 GGAGACCTCGCATGTCGTC 60.227 63.158 8.91 3.27 37.80 4.20
2997 3216 3.632604 ACGTCATGTCGTATCCTTCATCT 59.367 43.478 16.28 0.00 42.35 2.90
3044 3263 1.202463 CCTTGTGCACGAGAGATAGGG 60.202 57.143 31.88 13.13 0.00 3.53
3304 3535 4.554363 CGAAGCGTCGCCGGAGAT 62.554 66.667 12.23 0.00 41.08 2.75
3519 3750 0.456312 GGAGACGTTGTCGCAGTAGG 60.456 60.000 3.23 0.00 41.18 3.18
3525 3756 0.319555 GTTGTCGCAGTAGGTGAGCA 60.320 55.000 0.00 0.00 36.51 4.26
3615 3846 3.741029 GCCACTGCTCGATACTCAA 57.259 52.632 0.00 0.00 33.53 3.02
3654 3885 4.680237 CGGTGGGCTGTCGCTTGA 62.680 66.667 0.00 0.00 36.09 3.02
3953 4184 1.134098 CCCACAATGGAGCGGTAGAAT 60.134 52.381 0.00 0.00 40.96 2.40
3956 4187 1.210478 ACAATGGAGCGGTAGAATGCT 59.790 47.619 0.00 0.00 45.90 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.559862 ATGGGATCTTTTCGAACTGAGT 57.440 40.909 0.00 0.00 0.00 3.41
2 3 7.710907 CACTAATATGGGATCTTTTCGAACTGA 59.289 37.037 0.00 0.00 0.00 3.41
3 4 7.041780 CCACTAATATGGGATCTTTTCGAACTG 60.042 40.741 0.00 0.00 35.95 3.16
4 5 6.992715 CCACTAATATGGGATCTTTTCGAACT 59.007 38.462 0.00 0.00 35.95 3.01
6 7 5.763204 GCCACTAATATGGGATCTTTTCGAA 59.237 40.000 0.00 0.00 40.43 3.71
8 9 4.152402 CGCCACTAATATGGGATCTTTTCG 59.848 45.833 0.00 0.00 40.43 3.46
9 10 4.455877 CCGCCACTAATATGGGATCTTTTC 59.544 45.833 0.00 0.00 40.43 2.29
10 11 4.104102 TCCGCCACTAATATGGGATCTTTT 59.896 41.667 0.00 0.00 40.43 2.27
11 12 3.650942 TCCGCCACTAATATGGGATCTTT 59.349 43.478 0.00 0.00 40.43 2.52
12 13 3.248024 TCCGCCACTAATATGGGATCTT 58.752 45.455 0.00 0.00 40.43 2.40
13 14 2.902608 TCCGCCACTAATATGGGATCT 58.097 47.619 0.00 0.00 40.43 2.75
14 15 3.695830 TTCCGCCACTAATATGGGATC 57.304 47.619 0.00 0.00 40.43 3.36
15 16 3.137544 TGTTTCCGCCACTAATATGGGAT 59.862 43.478 0.00 0.00 40.43 3.85
16 17 2.506231 TGTTTCCGCCACTAATATGGGA 59.494 45.455 0.00 0.00 40.43 4.37
17 18 2.925724 TGTTTCCGCCACTAATATGGG 58.074 47.619 0.00 0.00 40.43 4.00
18 19 4.974368 TTTGTTTCCGCCACTAATATGG 57.026 40.909 0.00 0.00 43.26 2.74
19 20 5.704888 TGTTTTGTTTCCGCCACTAATATG 58.295 37.500 0.00 0.00 0.00 1.78
20 21 5.968528 TGTTTTGTTTCCGCCACTAATAT 57.031 34.783 0.00 0.00 0.00 1.28
21 22 5.704888 CATGTTTTGTTTCCGCCACTAATA 58.295 37.500 0.00 0.00 0.00 0.98
22 23 4.555262 CATGTTTTGTTTCCGCCACTAAT 58.445 39.130 0.00 0.00 0.00 1.73
23 24 3.797184 GCATGTTTTGTTTCCGCCACTAA 60.797 43.478 0.00 0.00 0.00 2.24
24 25 2.287909 GCATGTTTTGTTTCCGCCACTA 60.288 45.455 0.00 0.00 0.00 2.74
25 26 1.537990 GCATGTTTTGTTTCCGCCACT 60.538 47.619 0.00 0.00 0.00 4.00
26 27 0.858583 GCATGTTTTGTTTCCGCCAC 59.141 50.000 0.00 0.00 0.00 5.01
27 28 0.461548 TGCATGTTTTGTTTCCGCCA 59.538 45.000 0.00 0.00 0.00 5.69
28 29 1.139163 CTGCATGTTTTGTTTCCGCC 58.861 50.000 0.00 0.00 0.00 6.13
29 30 1.851658 ACTGCATGTTTTGTTTCCGC 58.148 45.000 0.00 0.00 0.00 5.54
30 31 2.970609 CGTACTGCATGTTTTGTTTCCG 59.029 45.455 0.00 0.00 0.00 4.30
31 32 3.959943 ACGTACTGCATGTTTTGTTTCC 58.040 40.909 0.00 0.00 0.00 3.13
53 54 5.043248 CACAATTTCTTTCCTTCGTGCTTT 58.957 37.500 0.00 0.00 0.00 3.51
59 60 5.455525 GTGTTCACACAATTTCTTTCCTTCG 59.544 40.000 5.16 0.00 45.75 3.79
129 130 4.970003 CCACATTGTTCTTCGTTGTTCTTC 59.030 41.667 0.00 0.00 0.00 2.87
130 131 4.638421 TCCACATTGTTCTTCGTTGTTCTT 59.362 37.500 0.00 0.00 0.00 2.52
131 132 4.196193 TCCACATTGTTCTTCGTTGTTCT 58.804 39.130 0.00 0.00 0.00 3.01
132 133 4.545823 TCCACATTGTTCTTCGTTGTTC 57.454 40.909 0.00 0.00 0.00 3.18
133 134 4.578516 TCATCCACATTGTTCTTCGTTGTT 59.421 37.500 0.00 0.00 0.00 2.83
134 135 4.133820 TCATCCACATTGTTCTTCGTTGT 58.866 39.130 0.00 0.00 0.00 3.32
135 136 4.747540 TCATCCACATTGTTCTTCGTTG 57.252 40.909 0.00 0.00 0.00 4.10
136 137 5.964958 ATTCATCCACATTGTTCTTCGTT 57.035 34.783 0.00 0.00 0.00 3.85
137 138 7.447374 TTTATTCATCCACATTGTTCTTCGT 57.553 32.000 0.00 0.00 0.00 3.85
138 139 8.741101 TTTTTATTCATCCACATTGTTCTTCG 57.259 30.769 0.00 0.00 0.00 3.79
180 181 2.428890 CTCCTTACTTCCGTCTCTGCAT 59.571 50.000 0.00 0.00 0.00 3.96
190 191 5.422214 TTCCTGTTCATCTCCTTACTTCC 57.578 43.478 0.00 0.00 0.00 3.46
233 234 3.398292 TCTCGACTATGGGAGGACCTTAT 59.602 47.826 0.00 0.00 41.11 1.73
236 237 1.223501 TCTCGACTATGGGAGGACCT 58.776 55.000 0.00 0.00 41.11 3.85
237 238 1.682323 GTTCTCGACTATGGGAGGACC 59.318 57.143 0.00 0.00 33.49 4.46
238 239 2.359531 CTGTTCTCGACTATGGGAGGAC 59.640 54.545 0.00 0.00 38.92 3.85
239 240 2.656002 CTGTTCTCGACTATGGGAGGA 58.344 52.381 0.00 0.00 0.00 3.71
240 241 1.683917 CCTGTTCTCGACTATGGGAGG 59.316 57.143 0.00 0.00 0.00 4.30
241 242 2.656002 TCCTGTTCTCGACTATGGGAG 58.344 52.381 0.00 0.00 0.00 4.30
242 243 2.820728 TCCTGTTCTCGACTATGGGA 57.179 50.000 0.00 0.00 0.00 4.37
243 244 3.887621 TTTCCTGTTCTCGACTATGGG 57.112 47.619 0.00 0.00 0.00 4.00
244 245 5.459107 CGTATTTTCCTGTTCTCGACTATGG 59.541 44.000 0.00 0.00 0.00 2.74
245 246 5.459107 CCGTATTTTCCTGTTCTCGACTATG 59.541 44.000 0.00 0.00 0.00 2.23
246 247 5.589192 CCGTATTTTCCTGTTCTCGACTAT 58.411 41.667 0.00 0.00 0.00 2.12
247 248 4.676196 GCCGTATTTTCCTGTTCTCGACTA 60.676 45.833 0.00 0.00 0.00 2.59
248 249 3.846360 CCGTATTTTCCTGTTCTCGACT 58.154 45.455 0.00 0.00 0.00 4.18
249 250 2.347755 GCCGTATTTTCCTGTTCTCGAC 59.652 50.000 0.00 0.00 0.00 4.20
250 251 2.028839 TGCCGTATTTTCCTGTTCTCGA 60.029 45.455 0.00 0.00 0.00 4.04
251 252 2.343101 TGCCGTATTTTCCTGTTCTCG 58.657 47.619 0.00 0.00 0.00 4.04
252 253 3.335579 ACTGCCGTATTTTCCTGTTCTC 58.664 45.455 0.00 0.00 0.00 2.87
253 254 3.418684 ACTGCCGTATTTTCCTGTTCT 57.581 42.857 0.00 0.00 0.00 3.01
254 255 3.998341 TGTACTGCCGTATTTTCCTGTTC 59.002 43.478 0.00 0.00 0.00 3.18
255 256 4.010667 TGTACTGCCGTATTTTCCTGTT 57.989 40.909 0.00 0.00 0.00 3.16
256 257 3.688694 TGTACTGCCGTATTTTCCTGT 57.311 42.857 0.00 0.00 0.00 4.00
257 258 5.113383 TGTATGTACTGCCGTATTTTCCTG 58.887 41.667 0.00 0.00 0.00 3.86
260 261 5.062558 ACGTTGTATGTACTGCCGTATTTTC 59.937 40.000 0.00 0.00 0.00 2.29
267 268 3.141002 AGTACGTTGTATGTACTGCCG 57.859 47.619 10.13 0.00 46.11 5.69
282 283 1.755179 TTAGGAACGGAGGGAGTACG 58.245 55.000 0.00 0.00 0.00 3.67
283 284 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
284 285 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
285 286 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
286 287 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
287 288 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
288 289 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
289 290 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
322 323 9.607988 ACATCCGTATGTTATAGTCAATTTGAA 57.392 29.630 0.00 0.00 44.07 2.69
346 347 9.750125 CTGCACTCTAAAATATGTCTACATACA 57.250 33.333 4.98 0.00 41.15 2.29
347 348 9.197694 CCTGCACTCTAAAATATGTCTACATAC 57.802 37.037 4.98 0.00 41.15 2.39
348 349 8.924303 ACCTGCACTCTAAAATATGTCTACATA 58.076 33.333 5.33 5.33 42.38 2.29
349 350 7.796054 ACCTGCACTCTAAAATATGTCTACAT 58.204 34.615 0.63 0.63 40.22 2.29
350 351 7.182817 ACCTGCACTCTAAAATATGTCTACA 57.817 36.000 0.00 0.00 0.00 2.74
351 352 8.494016 AAACCTGCACTCTAAAATATGTCTAC 57.506 34.615 0.00 0.00 0.00 2.59
352 353 9.595823 GTAAACCTGCACTCTAAAATATGTCTA 57.404 33.333 0.00 0.00 0.00 2.59
353 354 8.322091 AGTAAACCTGCACTCTAAAATATGTCT 58.678 33.333 0.00 0.00 0.00 3.41
354 355 8.494016 AGTAAACCTGCACTCTAAAATATGTC 57.506 34.615 0.00 0.00 0.00 3.06
355 356 8.100791 TGAGTAAACCTGCACTCTAAAATATGT 58.899 33.333 3.65 0.00 41.46 2.29
356 357 8.492673 TGAGTAAACCTGCACTCTAAAATATG 57.507 34.615 3.65 0.00 41.46 1.78
357 358 8.322091 ACTGAGTAAACCTGCACTCTAAAATAT 58.678 33.333 3.65 0.00 41.46 1.28
358 359 7.676947 ACTGAGTAAACCTGCACTCTAAAATA 58.323 34.615 3.65 0.00 41.46 1.40
359 360 6.534634 ACTGAGTAAACCTGCACTCTAAAAT 58.465 36.000 3.65 0.00 41.46 1.82
360 361 5.925509 ACTGAGTAAACCTGCACTCTAAAA 58.074 37.500 3.65 0.00 41.46 1.52
361 362 5.546621 ACTGAGTAAACCTGCACTCTAAA 57.453 39.130 3.65 0.00 41.46 1.85
362 363 5.546621 AACTGAGTAAACCTGCACTCTAA 57.453 39.130 3.65 0.00 41.46 2.10
363 364 5.297547 CAAACTGAGTAAACCTGCACTCTA 58.702 41.667 3.65 0.00 41.46 2.43
364 365 4.130118 CAAACTGAGTAAACCTGCACTCT 58.870 43.478 3.65 0.00 41.46 3.24
365 366 3.304057 GCAAACTGAGTAAACCTGCACTC 60.304 47.826 0.00 0.00 41.31 3.51
366 367 2.618709 GCAAACTGAGTAAACCTGCACT 59.381 45.455 0.00 0.00 0.00 4.40
367 368 2.618709 AGCAAACTGAGTAAACCTGCAC 59.381 45.455 0.00 0.00 0.00 4.57
368 369 2.878406 GAGCAAACTGAGTAAACCTGCA 59.122 45.455 0.00 0.00 0.00 4.41
369 370 2.226674 GGAGCAAACTGAGTAAACCTGC 59.773 50.000 0.00 0.00 0.00 4.85
370 371 2.480419 CGGAGCAAACTGAGTAAACCTG 59.520 50.000 0.00 0.00 0.00 4.00
371 372 2.104281 ACGGAGCAAACTGAGTAAACCT 59.896 45.455 0.00 0.00 0.00 3.50
372 373 2.490991 ACGGAGCAAACTGAGTAAACC 58.509 47.619 0.00 0.00 0.00 3.27
373 374 4.689345 ACATACGGAGCAAACTGAGTAAAC 59.311 41.667 0.00 0.00 0.00 2.01
374 375 4.890088 ACATACGGAGCAAACTGAGTAAA 58.110 39.130 0.00 0.00 0.00 2.01
375 376 4.530710 ACATACGGAGCAAACTGAGTAA 57.469 40.909 0.00 0.00 0.00 2.24
376 377 4.703575 ACTACATACGGAGCAAACTGAGTA 59.296 41.667 0.00 0.00 0.00 2.59
377 378 3.510360 ACTACATACGGAGCAAACTGAGT 59.490 43.478 0.00 0.00 0.00 3.41
378 379 4.106197 GACTACATACGGAGCAAACTGAG 58.894 47.826 0.00 0.00 0.00 3.35
379 380 3.508402 TGACTACATACGGAGCAAACTGA 59.492 43.478 0.00 0.00 0.00 3.41
380 381 3.612860 GTGACTACATACGGAGCAAACTG 59.387 47.826 0.00 0.00 0.00 3.16
381 382 3.510360 AGTGACTACATACGGAGCAAACT 59.490 43.478 0.00 0.00 0.00 2.66
382 383 3.846360 AGTGACTACATACGGAGCAAAC 58.154 45.455 0.00 0.00 0.00 2.93
383 384 3.427098 CGAGTGACTACATACGGAGCAAA 60.427 47.826 0.00 0.00 0.00 3.68
384 385 2.096980 CGAGTGACTACATACGGAGCAA 59.903 50.000 0.00 0.00 0.00 3.91
385 386 1.669265 CGAGTGACTACATACGGAGCA 59.331 52.381 0.00 0.00 0.00 4.26
386 387 1.669779 ACGAGTGACTACATACGGAGC 59.330 52.381 0.00 0.00 34.15 4.70
387 388 3.487042 CCAACGAGTGACTACATACGGAG 60.487 52.174 0.00 0.00 34.15 4.63
388 389 2.421073 CCAACGAGTGACTACATACGGA 59.579 50.000 0.00 0.00 34.15 4.69
389 390 2.421073 TCCAACGAGTGACTACATACGG 59.579 50.000 0.00 0.00 34.15 4.02
390 391 3.752412 TCCAACGAGTGACTACATACG 57.248 47.619 0.00 0.00 35.21 3.06
391 392 5.892568 AGATTCCAACGAGTGACTACATAC 58.107 41.667 0.00 0.00 0.00 2.39
392 393 5.886474 AGAGATTCCAACGAGTGACTACATA 59.114 40.000 0.00 0.00 0.00 2.29
393 394 4.707448 AGAGATTCCAACGAGTGACTACAT 59.293 41.667 0.00 0.00 0.00 2.29
394 395 4.079970 AGAGATTCCAACGAGTGACTACA 58.920 43.478 0.00 0.00 0.00 2.74
395 396 4.705337 AGAGATTCCAACGAGTGACTAC 57.295 45.455 0.00 0.00 0.00 2.73
396 397 6.829229 TTTAGAGATTCCAACGAGTGACTA 57.171 37.500 0.00 0.00 0.00 2.59
397 398 5.723672 TTTAGAGATTCCAACGAGTGACT 57.276 39.130 0.00 0.00 0.00 3.41
398 399 6.645415 TCTTTTTAGAGATTCCAACGAGTGAC 59.355 38.462 0.00 0.00 0.00 3.67
399 400 6.645415 GTCTTTTTAGAGATTCCAACGAGTGA 59.355 38.462 0.00 0.00 0.00 3.41
400 401 6.647067 AGTCTTTTTAGAGATTCCAACGAGTG 59.353 38.462 0.00 0.00 0.00 3.51
401 402 6.760291 AGTCTTTTTAGAGATTCCAACGAGT 58.240 36.000 0.00 0.00 0.00 4.18
402 403 7.659652 AAGTCTTTTTAGAGATTCCAACGAG 57.340 36.000 0.00 0.00 0.00 4.18
417 418 8.947115 CCTCCGTTCTCAAATATAAGTCTTTTT 58.053 33.333 0.00 0.00 0.00 1.94
418 419 7.553044 CCCTCCGTTCTCAAATATAAGTCTTTT 59.447 37.037 0.00 0.00 0.00 2.27
419 420 7.048512 CCCTCCGTTCTCAAATATAAGTCTTT 58.951 38.462 0.00 0.00 0.00 2.52
420 421 6.383147 TCCCTCCGTTCTCAAATATAAGTCTT 59.617 38.462 0.00 0.00 0.00 3.01
421 422 5.897824 TCCCTCCGTTCTCAAATATAAGTCT 59.102 40.000 0.00 0.00 0.00 3.24
422 423 6.158023 TCCCTCCGTTCTCAAATATAAGTC 57.842 41.667 0.00 0.00 0.00 3.01
423 424 5.661759 ACTCCCTCCGTTCTCAAATATAAGT 59.338 40.000 0.00 0.00 0.00 2.24
424 425 6.163135 ACTCCCTCCGTTCTCAAATATAAG 57.837 41.667 0.00 0.00 0.00 1.73
425 426 7.850935 ATACTCCCTCCGTTCTCAAATATAA 57.149 36.000 0.00 0.00 0.00 0.98
426 427 8.967918 CATATACTCCCTCCGTTCTCAAATATA 58.032 37.037 0.00 0.00 0.00 0.86
427 428 7.455008 ACATATACTCCCTCCGTTCTCAAATAT 59.545 37.037 0.00 0.00 0.00 1.28
428 429 6.781014 ACATATACTCCCTCCGTTCTCAAATA 59.219 38.462 0.00 0.00 0.00 1.40
429 430 5.602978 ACATATACTCCCTCCGTTCTCAAAT 59.397 40.000 0.00 0.00 0.00 2.32
430 431 4.960469 ACATATACTCCCTCCGTTCTCAAA 59.040 41.667 0.00 0.00 0.00 2.69
431 432 4.543689 ACATATACTCCCTCCGTTCTCAA 58.456 43.478 0.00 0.00 0.00 3.02
432 433 4.180377 ACATATACTCCCTCCGTTCTCA 57.820 45.455 0.00 0.00 0.00 3.27
433 434 5.068636 TGTACATATACTCCCTCCGTTCTC 58.931 45.833 0.00 0.00 32.00 2.87
434 435 5.057843 TGTACATATACTCCCTCCGTTCT 57.942 43.478 0.00 0.00 32.00 3.01
435 436 5.068198 TGTTGTACATATACTCCCTCCGTTC 59.932 44.000 0.00 0.00 32.00 3.95
436 437 4.957954 TGTTGTACATATACTCCCTCCGTT 59.042 41.667 0.00 0.00 32.00 4.44
437 438 4.340381 GTGTTGTACATATACTCCCTCCGT 59.660 45.833 0.00 0.00 32.00 4.69
438 439 4.261909 GGTGTTGTACATATACTCCCTCCG 60.262 50.000 0.00 0.00 32.00 4.63
439 440 4.652421 TGGTGTTGTACATATACTCCCTCC 59.348 45.833 12.48 3.13 32.00 4.30
440 441 5.864418 TGGTGTTGTACATATACTCCCTC 57.136 43.478 12.48 0.00 32.00 4.30
441 442 5.486063 TGTTGGTGTTGTACATATACTCCCT 59.514 40.000 12.48 0.00 32.00 4.20
442 443 5.736813 TGTTGGTGTTGTACATATACTCCC 58.263 41.667 12.48 6.65 32.00 4.30
443 444 6.821665 ACATGTTGGTGTTGTACATATACTCC 59.178 38.462 9.39 9.39 31.64 3.85
444 445 7.843490 ACATGTTGGTGTTGTACATATACTC 57.157 36.000 0.00 0.00 31.64 2.59
450 451 7.831690 TCCAATATACATGTTGGTGTTGTACAT 59.168 33.333 2.30 0.00 45.77 2.29
486 492 9.656040 AGGTAATGTTTGTACGTTATGAATACA 57.344 29.630 0.00 0.00 37.88 2.29
575 581 2.161486 GTCATGCTCACTCCGCGTC 61.161 63.158 4.92 0.00 0.00 5.19
576 582 2.125912 GTCATGCTCACTCCGCGT 60.126 61.111 4.92 0.00 0.00 6.01
675 681 1.079405 TCCAAAGTCGTCGATGGGC 60.079 57.895 12.30 0.00 33.66 5.36
711 718 1.968540 GGCAGGAAGTTTCGCTGCT 60.969 57.895 22.66 0.90 44.10 4.24
778 786 5.705609 TGCTGCTCATCAATATACTCGTA 57.294 39.130 0.00 0.00 0.00 3.43
783 791 5.059161 TGTCCTTGCTGCTCATCAATATAC 58.941 41.667 0.00 0.00 0.00 1.47
820 831 3.695556 AGGGAGTCGCTTAGTCTAACTTC 59.304 47.826 3.41 0.00 0.00 3.01
851 863 8.502387 CATCAGAAGAGAAAAACTGAACCTTAG 58.498 37.037 0.00 0.00 41.57 2.18
859 871 4.687948 TCGAGCATCAGAAGAGAAAAACTG 59.312 41.667 0.00 0.00 33.17 3.16
862 874 5.482006 TCATCGAGCATCAGAAGAGAAAAA 58.518 37.500 0.00 0.00 33.17 1.94
899 915 1.315981 TTGATGCTCTCGCCGAGACT 61.316 55.000 13.77 0.45 42.62 3.24
1024 1186 0.822532 CCCACGAGTAGGAGGCGTAT 60.823 60.000 0.00 0.00 36.37 3.06
1164 1326 4.067512 TCCAGGAGGCCGCTCTCT 62.068 66.667 6.40 0.00 34.39 3.10
1212 1374 2.718073 GGTCGGGTAGATGGCGTGT 61.718 63.158 0.00 0.00 0.00 4.49
1245 1407 3.760035 GACGAGAAGGAGCGGCCA 61.760 66.667 2.24 0.00 40.02 5.36
1605 1797 2.718073 GCCGTCGTAGTCCACCCAT 61.718 63.158 0.00 0.00 0.00 4.00
1911 2109 4.421479 ACGAAGAGGACCAGCGCG 62.421 66.667 0.00 0.00 0.00 6.86
2091 2289 4.991687 GGAAGAACTCCTCTGTACACTTTG 59.008 45.833 0.00 0.00 41.61 2.77
2349 2559 3.328382 TGAACCCAATTCAGAGTACCG 57.672 47.619 0.00 0.00 42.62 4.02
2559 2775 0.386838 GGTACCCTATGGTTCCGACG 59.613 60.000 0.00 0.00 44.75 5.12
2997 3216 1.630369 AGGCTGTTAATGCTCTCCACA 59.370 47.619 0.00 0.00 0.00 4.17
3044 3263 9.349145 GAATACAAACCAATGTTAACACCATAC 57.651 33.333 11.22 0.00 34.75 2.39
3304 3535 1.490490 AGTTCAGGTCCAGTCTTTGCA 59.510 47.619 0.00 0.00 0.00 4.08
3519 3750 2.426522 TGTTCACAAGGCTATGCTCAC 58.573 47.619 0.00 0.00 0.00 3.51
3654 3885 2.234908 CGTCCCTGATCTCTTGGTCTTT 59.765 50.000 0.00 0.00 0.00 2.52
3915 4146 1.604378 GTGCCCTGCAGTACCTGAT 59.396 57.895 13.81 0.00 40.08 2.90


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

AutoCloner maintained by Alex Coulton.