Multiple sequence alignment - TraesCS2A01G573500

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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 TraesCS2A01G573500 chr2A 100.000 3136 0 0 1 3136 769019358 769022493 0.000000e+00 5792.0
1 TraesCS2A01G573500 chr2A 80.966 683 129 1 1491 2173 769003991 769004672 9.890000e-150 540.0
2 TraesCS2A01G573500 chr2A 80.872 596 110 4 1514 2107 769145322 769145915 1.700000e-127 466.0
3 TraesCS2A01G573500 chr2A 84.185 411 51 8 996 1402 769144920 769145320 1.360000e-103 387.0
4 TraesCS2A01G573500 chr2A 78.863 563 113 5 1515 2074 769473476 769472917 2.950000e-100 375.0
5 TraesCS2A01G573500 chr2A 76.341 317 61 13 1092 1401 768306702 768306393 1.160000e-34 158.0
6 TraesCS2A01G573500 chr2B 91.761 1408 99 9 1468 2873 793141625 793140233 0.000000e+00 1941.0
7 TraesCS2A01G573500 chr2B 95.594 522 23 0 880 1401 793142262 793141741 0.000000e+00 837.0
8 TraesCS2A01G573500 chr2B 82.249 676 115 5 1500 2173 793169157 793168485 2.100000e-161 579.0
9 TraesCS2A01G573500 chr2B 92.676 355 25 1 511 864 793143379 793143025 7.760000e-141 510.0
10 TraesCS2A01G573500 chr2B 79.664 595 117 4 1514 2106 793034678 793034086 2.890000e-115 425.0
11 TraesCS2A01G573500 chr2B 84.428 411 50 8 996 1402 793035080 793034680 2.930000e-105 392.0
12 TraesCS2A01G573500 chr2B 78.014 564 116 7 1515 2074 792877160 792877719 6.440000e-92 348.0
13 TraesCS2A01G573500 chr2B 88.298 188 16 3 2951 3136 793140201 793140018 1.460000e-53 220.0
14 TraesCS2A01G573500 chr2B 76.899 316 61 11 1092 1401 793446971 793446662 5.380000e-38 169.0
15 TraesCS2A01G573500 chr2B 80.717 223 31 10 1001 1220 793169821 793169608 2.500000e-36 163.0
16 TraesCS2A01G573500 chr2B 91.429 105 6 2 1 102 793143935 793143831 1.170000e-29 141.0
17 TraesCS2A01G573500 chr2B 92.453 53 4 0 125 177 793143827 793143775 3.350000e-10 76.8
18 TraesCS2A01G573500 chr2D 94.301 930 42 6 1469 2398 643901654 643902572 0.000000e+00 1413.0
19 TraesCS2A01G573500 chr2D 91.881 973 49 9 431 1401 643900548 643901492 0.000000e+00 1332.0
20 TraesCS2A01G573500 chr2D 89.811 687 59 8 2454 3136 643902585 643903264 0.000000e+00 870.0
21 TraesCS2A01G573500 chr2D 80.724 773 128 11 1491 2261 643879079 643879832 1.620000e-162 582.0
22 TraesCS2A01G573500 chr2D 81.711 596 103 6 1514 2106 644016788 644017380 2.810000e-135 492.0
23 TraesCS2A01G573500 chr2D 84.988 413 48 9 996 1404 644016386 644016788 1.050000e-109 407.0
24 TraesCS2A01G573500 chr2D 91.716 169 13 1 1 168 643898364 643898532 1.880000e-57 233.0
25 TraesCS2A01G573500 chr2D 94.853 136 6 1 1 135 643900412 643900547 8.810000e-51 211.0
26 TraesCS2A01G573500 chr2D 77.215 316 60 10 1092 1401 643468532 643468223 1.160000e-39 174.0
27 TraesCS2A01G573500 chr2D 76.899 316 61 11 1092 1401 643640467 643640776 5.380000e-38 169.0
28 TraesCS2A01G573500 chr3B 89.091 55 4 1 903 957 16403702 16403754 2.020000e-07 67.6
29 TraesCS2A01G573500 chr3D 87.273 55 5 1 903 957 11731857 11731909 9.390000e-06 62.1
30 TraesCS2A01G573500 chr1A 92.500 40 0 3 414 453 139633182 139633146 2.000000e-03 54.7


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 TraesCS2A01G573500 chr2A 769019358 769022493 3135 False 5792.000000 5792 100.000000 1 3136 1 chr2A.!!$F2 3135
1 TraesCS2A01G573500 chr2A 769003991 769004672 681 False 540.000000 540 80.966000 1491 2173 1 chr2A.!!$F1 682
2 TraesCS2A01G573500 chr2A 769144920 769145915 995 False 426.500000 466 82.528500 996 2107 2 chr2A.!!$F3 1111
3 TraesCS2A01G573500 chr2A 769472917 769473476 559 True 375.000000 375 78.863000 1515 2074 1 chr2A.!!$R2 559
4 TraesCS2A01G573500 chr2B 793140018 793143935 3917 True 620.966667 1941 92.035167 1 3136 6 chr2B.!!$R3 3135
5 TraesCS2A01G573500 chr2B 793034086 793035080 994 True 408.500000 425 82.046000 996 2106 2 chr2B.!!$R2 1110
6 TraesCS2A01G573500 chr2B 793168485 793169821 1336 True 371.000000 579 81.483000 1001 2173 2 chr2B.!!$R4 1172
7 TraesCS2A01G573500 chr2B 792877160 792877719 559 False 348.000000 348 78.014000 1515 2074 1 chr2B.!!$F1 559
8 TraesCS2A01G573500 chr2D 643898364 643903264 4900 False 811.800000 1413 92.512400 1 3136 5 chr2D.!!$F3 3135
9 TraesCS2A01G573500 chr2D 643879079 643879832 753 False 582.000000 582 80.724000 1491 2261 1 chr2D.!!$F2 770
10 TraesCS2A01G573500 chr2D 644016386 644017380 994 False 449.500000 492 83.349500 996 2106 2 chr2D.!!$F4 1110

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
352 387 0.107993 TGGGCGAAGAAGAGCTCATG 60.108 55.0 17.77 0.0 39.18 3.07 F
398 982 0.110644 GCTTGGTCGCGTCTTCTTTG 60.111 55.0 5.77 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 4385 0.169672 CCGGAGTCGACGCTAAGAAA 59.830 55.0 18.88 0.0 39.0 2.52 R
2261 5318 0.761187 TCTTGCTCTGCTGACCACTT 59.239 50.0 0.00 0.0 0.0 3.16 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
41 44 4.025647 GTGACCGCAGCAGTTAGATTATTC 60.026 45.833 0.00 0.00 0.00 1.75
114 118 2.939103 GCACATCCTCTAGCGACAAAAT 59.061 45.455 0.00 0.00 0.00 1.82
121 125 7.606456 ACATCCTCTAGCGACAAAATCTAAAAA 59.394 33.333 0.00 0.00 0.00 1.94
123 127 8.197988 TCCTCTAGCGACAAAATCTAAAAATC 57.802 34.615 0.00 0.00 0.00 2.17
180 215 1.733399 GAACTCGGTCGACAGCCAC 60.733 63.158 18.91 0.00 0.00 5.01
181 216 3.222354 AACTCGGTCGACAGCCACC 62.222 63.158 18.91 0.00 0.00 4.61
182 217 3.680786 CTCGGTCGACAGCCACCA 61.681 66.667 18.91 0.00 32.33 4.17
183 218 3.916392 CTCGGTCGACAGCCACCAC 62.916 68.421 18.91 0.00 32.33 4.16
186 221 2.357517 GTCGACAGCCACCACCAG 60.358 66.667 11.55 0.00 0.00 4.00
187 222 2.842462 TCGACAGCCACCACCAGT 60.842 61.111 0.00 0.00 0.00 4.00
188 223 1.532078 TCGACAGCCACCACCAGTA 60.532 57.895 0.00 0.00 0.00 2.74
189 224 1.116536 TCGACAGCCACCACCAGTAA 61.117 55.000 0.00 0.00 0.00 2.24
192 227 1.303317 CAGCCACCACCAGTAACCC 60.303 63.158 0.00 0.00 0.00 4.11
193 228 1.772567 AGCCACCACCAGTAACCCA 60.773 57.895 0.00 0.00 0.00 4.51
195 230 1.074248 CCACCACCAGTAACCCACC 59.926 63.158 0.00 0.00 0.00 4.61
196 231 1.710996 CCACCACCAGTAACCCACCA 61.711 60.000 0.00 0.00 0.00 4.17
199 234 1.074248 CACCAGTAACCCACCACCC 59.926 63.158 0.00 0.00 0.00 4.61
200 235 2.158130 ACCAGTAACCCACCACCCC 61.158 63.158 0.00 0.00 0.00 4.95
201 236 2.761160 CAGTAACCCACCACCCCC 59.239 66.667 0.00 0.00 0.00 5.40
215 250 3.072468 CCCCCGCGGTAAGTGAGA 61.072 66.667 26.12 0.00 0.00 3.27
216 251 2.183555 CCCCGCGGTAAGTGAGAC 59.816 66.667 26.12 0.00 0.00 3.36
225 260 2.877335 GGTAAGTGAGACCGACATGAC 58.123 52.381 0.00 0.00 0.00 3.06
226 261 2.416972 GGTAAGTGAGACCGACATGACC 60.417 54.545 0.00 0.00 0.00 4.02
227 262 1.338107 AAGTGAGACCGACATGACCA 58.662 50.000 0.00 0.00 0.00 4.02
228 263 1.561643 AGTGAGACCGACATGACCAT 58.438 50.000 0.00 0.00 0.00 3.55
229 264 2.735151 AGTGAGACCGACATGACCATA 58.265 47.619 0.00 0.00 0.00 2.74
230 265 3.300388 AGTGAGACCGACATGACCATAT 58.700 45.455 0.00 0.00 0.00 1.78
231 266 3.706594 AGTGAGACCGACATGACCATATT 59.293 43.478 0.00 0.00 0.00 1.28
234 269 3.038280 AGACCGACATGACCATATTCCA 58.962 45.455 0.00 0.00 0.00 3.53
235 270 3.648067 AGACCGACATGACCATATTCCAT 59.352 43.478 0.00 0.00 0.00 3.41
236 271 3.743521 ACCGACATGACCATATTCCATG 58.256 45.455 0.00 0.00 42.32 3.66
237 272 3.076621 CCGACATGACCATATTCCATGG 58.923 50.000 4.97 4.97 41.28 3.66
249 284 5.997746 CCATATTCCATGGTTGTACCTACAG 59.002 44.000 12.58 0.00 39.58 2.74
250 285 6.409234 CCATATTCCATGGTTGTACCTACAGT 60.409 42.308 12.58 0.00 39.58 3.55
251 286 4.986054 TTCCATGGTTGTACCTACAGTT 57.014 40.909 12.58 0.00 39.58 3.16
252 287 4.986054 TCCATGGTTGTACCTACAGTTT 57.014 40.909 12.58 0.00 39.58 2.66
253 288 4.901868 TCCATGGTTGTACCTACAGTTTC 58.098 43.478 12.58 0.00 39.58 2.78
254 289 4.007659 CCATGGTTGTACCTACAGTTTCC 58.992 47.826 2.57 0.00 39.58 3.13
255 290 4.505918 CCATGGTTGTACCTACAGTTTCCA 60.506 45.833 2.57 0.00 39.58 3.53
256 291 4.345859 TGGTTGTACCTACAGTTTCCAG 57.654 45.455 0.00 0.00 39.58 3.86
257 292 3.712733 TGGTTGTACCTACAGTTTCCAGT 59.287 43.478 0.00 0.00 39.58 4.00
259 294 4.062991 GTTGTACCTACAGTTTCCAGTGG 58.937 47.826 1.40 1.40 37.52 4.00
260 295 3.578978 TGTACCTACAGTTTCCAGTGGA 58.421 45.455 8.12 8.12 0.00 4.02
261 296 4.164981 TGTACCTACAGTTTCCAGTGGAT 58.835 43.478 14.00 0.00 0.00 3.41
262 297 3.983044 ACCTACAGTTTCCAGTGGATC 57.017 47.619 14.00 9.62 0.00 3.36
263 298 3.248024 ACCTACAGTTTCCAGTGGATCA 58.752 45.455 14.00 0.00 0.00 2.92
265 300 4.256920 CCTACAGTTTCCAGTGGATCAAG 58.743 47.826 14.00 6.67 0.00 3.02
267 302 4.170468 ACAGTTTCCAGTGGATCAAGTT 57.830 40.909 14.00 0.00 0.00 2.66
268 303 5.304686 ACAGTTTCCAGTGGATCAAGTTA 57.695 39.130 14.00 0.00 0.00 2.24
270 305 4.455877 CAGTTTCCAGTGGATCAAGTTACC 59.544 45.833 14.00 0.00 0.00 2.85
271 306 4.351111 AGTTTCCAGTGGATCAAGTTACCT 59.649 41.667 14.00 0.00 0.00 3.08
273 308 2.027192 TCCAGTGGATCAAGTTACCTGC 60.027 50.000 8.12 0.00 0.00 4.85
275 310 3.614092 CAGTGGATCAAGTTACCTGCAT 58.386 45.455 0.00 0.00 0.00 3.96
276 311 3.376234 CAGTGGATCAAGTTACCTGCATG 59.624 47.826 0.00 0.00 0.00 4.06
277 312 2.098117 GTGGATCAAGTTACCTGCATGC 59.902 50.000 11.82 11.82 0.00 4.06
280 315 3.181493 GGATCAAGTTACCTGCATGCTTG 60.181 47.826 20.33 12.84 38.20 4.01
294 329 2.658373 TGCTTGCTTGCATTGTATGG 57.342 45.000 0.00 0.00 38.12 2.74
295 330 2.169330 TGCTTGCTTGCATTGTATGGA 58.831 42.857 0.00 0.00 38.12 3.41
296 331 2.561858 TGCTTGCTTGCATTGTATGGAA 59.438 40.909 0.00 0.00 38.12 3.53
309 344 9.134055 TGCATTGTATGGAAGAATATGATTTCA 57.866 29.630 0.00 0.00 0.00 2.69
337 372 9.741647 CTTCTATTTTATTTTTGAGAGATGGGC 57.258 33.333 0.00 0.00 0.00 5.36
339 374 6.773976 ATTTTATTTTTGAGAGATGGGCGA 57.226 33.333 0.00 0.00 0.00 5.54
341 376 5.818136 TTATTTTTGAGAGATGGGCGAAG 57.182 39.130 0.00 0.00 0.00 3.79
342 377 3.417069 TTTTTGAGAGATGGGCGAAGA 57.583 42.857 0.00 0.00 0.00 2.87
344 379 2.680312 TTGAGAGATGGGCGAAGAAG 57.320 50.000 0.00 0.00 0.00 2.85
346 381 1.753649 TGAGAGATGGGCGAAGAAGAG 59.246 52.381 0.00 0.00 0.00 2.85
347 382 0.463620 AGAGATGGGCGAAGAAGAGC 59.536 55.000 0.00 0.00 0.00 4.09
348 383 0.463620 GAGATGGGCGAAGAAGAGCT 59.536 55.000 0.00 0.00 0.00 4.09
349 384 0.463620 AGATGGGCGAAGAAGAGCTC 59.536 55.000 5.27 5.27 0.00 4.09
350 385 3.791640 TGGGCGAAGAAGAGCTCA 58.208 55.556 17.77 0.00 42.22 4.26
351 386 2.290847 TGGGCGAAGAAGAGCTCAT 58.709 52.632 17.77 2.97 39.18 2.90
352 387 0.107993 TGGGCGAAGAAGAGCTCATG 60.108 55.000 17.77 0.00 39.18 3.07
354 389 1.677217 GGGCGAAGAAGAGCTCATGTT 60.677 52.381 17.77 9.04 33.25 2.71
355 390 2.079925 GGCGAAGAAGAGCTCATGTTT 58.920 47.619 17.77 0.20 0.00 2.83
357 392 3.057946 GGCGAAGAAGAGCTCATGTTTTT 60.058 43.478 17.77 3.02 0.00 1.94
374 409 3.859411 TTTTTCTTTTGGTCGTGCTGT 57.141 38.095 0.00 0.00 0.00 4.40
375 410 3.859411 TTTTCTTTTGGTCGTGCTGTT 57.141 38.095 0.00 0.00 0.00 3.16
376 411 3.859411 TTTCTTTTGGTCGTGCTGTTT 57.141 38.095 0.00 0.00 0.00 2.83
377 412 3.859411 TTCTTTTGGTCGTGCTGTTTT 57.141 38.095 0.00 0.00 0.00 2.43
378 413 3.143807 TCTTTTGGTCGTGCTGTTTTG 57.856 42.857 0.00 0.00 0.00 2.44
380 415 0.179124 TTTGGTCGTGCTGTTTTGGC 60.179 50.000 0.00 0.00 0.00 4.52
382 417 1.034838 TGGTCGTGCTGTTTTGGCTT 61.035 50.000 0.00 0.00 0.00 4.35
383 418 0.594796 GGTCGTGCTGTTTTGGCTTG 60.595 55.000 0.00 0.00 0.00 4.01
384 419 0.594796 GTCGTGCTGTTTTGGCTTGG 60.595 55.000 0.00 0.00 0.00 3.61
386 421 0.594796 CGTGCTGTTTTGGCTTGGTC 60.595 55.000 0.00 0.00 0.00 4.02
387 422 0.594796 GTGCTGTTTTGGCTTGGTCG 60.595 55.000 0.00 0.00 0.00 4.79
388 423 1.661509 GCTGTTTTGGCTTGGTCGC 60.662 57.895 0.00 0.00 0.00 5.19
390 425 2.058829 CTGTTTTGGCTTGGTCGCGT 62.059 55.000 5.77 0.00 0.00 6.01
391 426 1.370051 GTTTTGGCTTGGTCGCGTC 60.370 57.895 5.77 0.00 0.00 5.19
395 979 2.048127 GGCTTGGTCGCGTCTTCT 60.048 61.111 5.77 0.00 0.00 2.85
398 982 0.110644 GCTTGGTCGCGTCTTCTTTG 60.111 55.000 5.77 0.00 0.00 2.77
401 985 1.428448 TGGTCGCGTCTTCTTTGATG 58.572 50.000 5.77 0.00 0.00 3.07
402 986 1.000394 TGGTCGCGTCTTCTTTGATGA 60.000 47.619 5.77 0.00 0.00 2.92
404 988 2.673368 GGTCGCGTCTTCTTTGATGAAT 59.327 45.455 5.77 0.00 0.00 2.57
408 992 6.345882 GGTCGCGTCTTCTTTGATGAATATAC 60.346 42.308 5.77 0.00 0.00 1.47
411 995 6.199154 CGCGTCTTCTTTGATGAATATACACT 59.801 38.462 0.00 0.00 0.00 3.55
421 1005 9.558396 TTTGATGAATATACACTCATACATGCA 57.442 29.630 0.00 0.00 32.40 3.96
422 1006 8.767478 TGATGAATATACACTCATACATGCAG 57.233 34.615 0.00 0.00 32.40 4.41
423 1007 7.332678 TGATGAATATACACTCATACATGCAGC 59.667 37.037 0.00 0.00 32.40 5.25
424 1008 6.762333 TGAATATACACTCATACATGCAGCT 58.238 36.000 0.00 0.00 0.00 4.24
425 1009 6.870439 TGAATATACACTCATACATGCAGCTC 59.130 38.462 0.00 0.00 0.00 4.09
427 1011 3.176552 ACACTCATACATGCAGCTCTC 57.823 47.619 0.00 0.00 0.00 3.20
428 1012 2.158986 ACACTCATACATGCAGCTCTCC 60.159 50.000 0.00 0.00 0.00 3.71
443 2200 0.820226 TCTCCTGCATGGTTCGAGAG 59.180 55.000 0.00 0.00 37.07 3.20
480 2566 4.974645 TTGGAAGAAAAGAGCTAGACCA 57.025 40.909 0.00 0.00 0.00 4.02
538 2625 1.216930 TGATCCGATCCAGGTAGGTCA 59.783 52.381 5.91 0.00 39.02 4.02
615 2702 5.526115 CAACTTGCATTGGATGTCATATCC 58.474 41.667 0.00 0.00 38.66 2.59
642 2729 6.618287 TCCTAAATTATGTCAAATCCAGCG 57.382 37.500 0.00 0.00 0.00 5.18
708 2795 1.747774 GTTGTTGGGTGCAAGGCAT 59.252 52.632 0.00 0.00 41.91 4.40
710 2797 1.550072 GTTGTTGGGTGCAAGGCATAT 59.450 47.619 0.00 0.00 41.91 1.78
732 2819 8.534496 CATATGGAAAGTTCTGGGAAATTTCTT 58.466 33.333 22.88 16.51 31.96 2.52
740 2827 5.920193 TCTGGGAAATTTCTTGGCATTAG 57.080 39.130 17.42 5.52 0.00 1.73
758 2845 4.921470 TTAGTTAACAAGCAGCATCGAC 57.079 40.909 8.61 0.00 0.00 4.20
789 2876 0.115745 ACCGTTCTCCCCTCACCTTA 59.884 55.000 0.00 0.00 0.00 2.69
792 2879 1.066358 CGTTCTCCCCTCACCTTAACC 60.066 57.143 0.00 0.00 0.00 2.85
840 2927 4.121317 ACAATTGCACATGTTTTCCACTG 58.879 39.130 5.05 0.00 0.00 3.66
872 3711 5.709631 TCTCTGATCATATCGAGCTAAGCTT 59.290 40.000 3.48 3.48 39.88 3.74
873 3712 5.707931 TCTGATCATATCGAGCTAAGCTTG 58.292 41.667 9.86 0.01 39.88 4.01
874 3713 4.814147 TGATCATATCGAGCTAAGCTTGG 58.186 43.478 9.86 7.48 39.88 3.61
875 3714 3.667497 TCATATCGAGCTAAGCTTGGG 57.333 47.619 9.86 2.93 39.88 4.12
876 3715 2.300152 TCATATCGAGCTAAGCTTGGGG 59.700 50.000 9.86 0.22 39.88 4.96
877 3716 1.048601 TATCGAGCTAAGCTTGGGGG 58.951 55.000 9.86 0.00 39.88 5.40
878 3717 0.983378 ATCGAGCTAAGCTTGGGGGT 60.983 55.000 9.86 4.77 39.88 4.95
986 3825 2.608546 GCAGAAAGCTCAGCTACATCTG 59.391 50.000 23.38 23.38 41.99 2.90
990 3829 0.179078 AGCTCAGCTACATCTGCAGC 60.179 55.000 9.47 0.00 36.99 5.25
1269 4229 1.237285 ACAACACCGAGCTGAATGCC 61.237 55.000 0.00 0.00 44.23 4.40
1410 4370 2.256461 GCCCTCGTCAACGTACGT 59.744 61.111 16.72 16.72 43.31 3.57
1411 4371 1.501741 GCCCTCGTCAACGTACGTA 59.498 57.895 23.12 3.61 43.31 3.57
1412 4372 0.794605 GCCCTCGTCAACGTACGTAC 60.795 60.000 23.12 16.04 43.31 3.67
1414 4374 1.069296 CCCTCGTCAACGTACGTACAA 60.069 52.381 23.12 7.28 43.31 2.41
1416 4376 3.236816 CCTCGTCAACGTACGTACAATT 58.763 45.455 23.12 15.16 43.31 2.32
1417 4377 4.402583 CCTCGTCAACGTACGTACAATTA 58.597 43.478 23.12 5.28 43.31 1.40
1418 4378 5.030295 CCTCGTCAACGTACGTACAATTAT 58.970 41.667 23.12 0.10 43.31 1.28
1419 4379 5.512788 CCTCGTCAACGTACGTACAATTATT 59.487 40.000 23.12 0.00 43.31 1.40
1420 4380 6.290748 CCTCGTCAACGTACGTACAATTATTC 60.291 42.308 23.12 10.58 43.31 1.75
1421 4381 6.314018 TCGTCAACGTACGTACAATTATTCT 58.686 36.000 23.12 0.00 43.31 2.40
1425 4385 8.642020 GTCAACGTACGTACAATTATTCTTTCT 58.358 33.333 23.12 0.00 0.00 2.52
1443 4478 1.129998 TCTTTCTTAGCGTCGACTCCG 59.870 52.381 14.70 1.20 37.07 4.63
1444 4479 0.169672 TTTCTTAGCGTCGACTCCGG 59.830 55.000 14.70 0.00 36.24 5.14
1445 4480 2.262471 TTCTTAGCGTCGACTCCGGC 62.262 60.000 14.70 9.54 36.98 6.13
1446 4481 3.753070 CTTAGCGTCGACTCCGGCC 62.753 68.421 14.70 0.00 37.02 6.13
1479 4534 9.362539 GTTACTCTCAACAGAACCGATTAATTA 57.637 33.333 0.00 0.00 0.00 1.40
1775 4830 0.456628 TCATCGACCCGTTATTCGCA 59.543 50.000 0.00 0.00 38.35 5.10
1776 4831 0.575390 CATCGACCCGTTATTCGCAC 59.425 55.000 0.00 0.00 38.35 5.34
1937 4992 2.786495 CCTCATCGACCACCCCGAG 61.786 68.421 0.00 0.00 39.55 4.63
1961 5016 1.172812 GGCTCTTGGCTTCACGGTTT 61.173 55.000 0.00 0.00 41.46 3.27
1973 5028 1.599518 ACGGTTTGCGCTCATCCAA 60.600 52.632 9.73 0.00 0.00 3.53
1986 5041 1.134098 TCATCCAATCCGCCTTCTTCC 60.134 52.381 0.00 0.00 0.00 3.46
2078 5133 4.344865 AACTGCGCCGTCCCCAAT 62.345 61.111 4.51 0.00 0.00 3.16
2123 5178 4.657824 AACGACGAGGGCCACACG 62.658 66.667 6.18 11.31 0.00 4.49
2141 5196 1.596477 GGCCGCCATGTGAGAGATC 60.596 63.158 3.91 0.00 0.00 2.75
2142 5197 1.144716 GCCGCCATGTGAGAGATCA 59.855 57.895 0.00 0.00 0.00 2.92
2227 5284 3.059800 GTGTCCTTGTGCTAGTCGTTTTC 60.060 47.826 0.00 0.00 0.00 2.29
2261 5318 8.849490 GTCGTACGTGTTGTAATAAAATGAGTA 58.151 33.333 16.05 0.00 34.07 2.59
2275 5332 3.883830 ATGAGTAAGTGGTCAGCAGAG 57.116 47.619 0.00 0.00 0.00 3.35
2324 5381 4.634443 CCGTAAGAGGTTCCATTTGGTTAG 59.366 45.833 0.00 0.00 43.02 2.34
2379 5438 1.902508 TCCATTCTTCGTCTTGGAGCT 59.097 47.619 0.00 0.00 33.40 4.09
2380 5439 3.096852 TCCATTCTTCGTCTTGGAGCTA 58.903 45.455 0.00 0.00 33.40 3.32
2381 5440 3.131223 TCCATTCTTCGTCTTGGAGCTAG 59.869 47.826 0.00 0.00 33.40 3.42
2382 5441 2.656560 TTCTTCGTCTTGGAGCTAGC 57.343 50.000 6.62 6.62 0.00 3.42
2414 5473 8.203937 AGTTTTGTTAAGTTAAATGTTTGGCC 57.796 30.769 0.00 0.00 0.00 5.36
2513 5572 8.789762 ACATATAAATATAGTTGTTTTCCCCGC 58.210 33.333 0.00 0.00 0.00 6.13
2515 5574 5.986501 AAATATAGTTGTTTTCCCCGCAA 57.013 34.783 0.00 0.00 0.00 4.85
2517 5576 3.934457 ATAGTTGTTTTCCCCGCAAAG 57.066 42.857 0.00 0.00 0.00 2.77
2518 5577 1.770294 AGTTGTTTTCCCCGCAAAGA 58.230 45.000 0.00 0.00 0.00 2.52
2519 5578 2.104170 AGTTGTTTTCCCCGCAAAGAA 58.896 42.857 0.00 0.00 0.00 2.52
2520 5579 2.498078 AGTTGTTTTCCCCGCAAAGAAA 59.502 40.909 0.00 0.00 0.00 2.52
2521 5580 2.588027 TGTTTTCCCCGCAAAGAAAC 57.412 45.000 0.00 0.00 31.93 2.78
2522 5581 1.825474 TGTTTTCCCCGCAAAGAAACA 59.175 42.857 0.00 0.00 31.93 2.83
2523 5582 2.432510 TGTTTTCCCCGCAAAGAAACAT 59.567 40.909 0.00 0.00 31.93 2.71
2524 5583 3.637229 TGTTTTCCCCGCAAAGAAACATA 59.363 39.130 0.00 0.00 31.93 2.29
2525 5584 4.234574 GTTTTCCCCGCAAAGAAACATAG 58.765 43.478 0.00 0.00 31.93 2.23
2526 5585 2.871096 TCCCCGCAAAGAAACATAGT 57.129 45.000 0.00 0.00 0.00 2.12
2528 5587 4.289238 TCCCCGCAAAGAAACATAGTAA 57.711 40.909 0.00 0.00 0.00 2.24
2529 5588 4.850680 TCCCCGCAAAGAAACATAGTAAT 58.149 39.130 0.00 0.00 0.00 1.89
2530 5589 5.991861 TCCCCGCAAAGAAACATAGTAATA 58.008 37.500 0.00 0.00 0.00 0.98
2531 5590 6.053005 TCCCCGCAAAGAAACATAGTAATAG 58.947 40.000 0.00 0.00 0.00 1.73
2532 5591 5.820947 CCCCGCAAAGAAACATAGTAATAGT 59.179 40.000 0.00 0.00 0.00 2.12
2533 5592 6.987992 CCCCGCAAAGAAACATAGTAATAGTA 59.012 38.462 0.00 0.00 0.00 1.82
2615 5675 6.432783 TCCATAGTAATTGTTGGTCAAACCTG 59.567 38.462 0.00 0.00 39.58 4.00
2627 5687 2.478894 GTCAAACCTGTACGTGGTGATG 59.521 50.000 10.55 12.12 37.93 3.07
2647 5707 3.011818 TGAAGTGCAGCATAACCAGATG 58.988 45.455 0.00 0.00 0.00 2.90
2767 5827 5.171337 GCATAAGCAACAACGCAATACATAC 59.829 40.000 0.00 0.00 41.58 2.39
2863 5923 5.059833 ACCTAGAGCAAAAATCCATCGATC 58.940 41.667 0.00 0.00 0.00 3.69
2902 5963 0.461961 GGAGAAGGACAGACGGATGG 59.538 60.000 0.00 0.00 0.00 3.51
2913 5974 2.749076 CAGACGGATGGCAATTTCTTCA 59.251 45.455 0.00 0.00 0.00 3.02
2922 5983 7.387673 CGGATGGCAATTTCTTCATGTAGTATA 59.612 37.037 0.00 0.00 0.00 1.47
2949 6012 9.950680 GTATATGCATTGTTTTAAGTAGCATGT 57.049 29.630 3.54 0.00 40.92 3.21
2962 6025 3.555956 AGTAGCATGTTATAGTGTTGCGC 59.444 43.478 0.00 0.00 38.32 6.09
2984 6047 3.662247 AAGAGACTTTGGTCCTACACG 57.338 47.619 0.00 0.00 43.05 4.49
2986 6049 0.320697 AGACTTTGGTCCTACACGGC 59.679 55.000 0.00 0.00 43.05 5.68
3001 6064 8.667463 GTCCTACACGGCAAGTAAAATTTTATA 58.333 33.333 13.54 0.00 0.00 0.98
3002 6065 8.885722 TCCTACACGGCAAGTAAAATTTTATAG 58.114 33.333 13.54 7.84 0.00 1.31
3007 6070 6.025280 CGGCAAGTAAAATTTTATAGCGTGT 58.975 36.000 13.54 0.00 0.00 4.49
3125 6190 1.407979 TCGCTAGCTAGCCACCTTTAC 59.592 52.381 34.27 9.29 46.34 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 53 6.970613 ACACGACAATTCTTTGGTTTCTTTAC 59.029 34.615 0.00 0.00 37.15 2.01
59 62 3.249799 TGTAGCACACGACAATTCTTTGG 59.750 43.478 0.00 0.00 37.15 3.28
114 118 7.595819 ATCTTTTGTGGTGGTGATTTTTAGA 57.404 32.000 0.00 0.00 0.00 2.10
121 125 6.122277 CACCTATATCTTTTGTGGTGGTGAT 58.878 40.000 0.00 0.00 43.39 3.06
123 127 5.818136 CACCTATATCTTTTGTGGTGGTG 57.182 43.478 0.00 0.00 40.65 4.17
164 168 3.681835 GGTGGCTGTCGACCGAGT 61.682 66.667 14.12 0.00 0.00 4.18
175 210 1.772567 TGGGTTACTGGTGGTGGCT 60.773 57.895 0.00 0.00 0.00 4.75
180 215 1.074248 GGTGGTGGGTTACTGGTGG 59.926 63.158 0.00 0.00 0.00 4.61
181 216 1.074248 GGGTGGTGGGTTACTGGTG 59.926 63.158 0.00 0.00 0.00 4.17
182 217 2.158130 GGGGTGGTGGGTTACTGGT 61.158 63.158 0.00 0.00 0.00 4.00
183 218 2.761160 GGGGTGGTGGGTTACTGG 59.239 66.667 0.00 0.00 0.00 4.00
199 234 2.183555 GTCTCACTTACCGCGGGG 59.816 66.667 31.76 18.33 40.11 5.73
200 235 2.183555 GGTCTCACTTACCGCGGG 59.816 66.667 31.76 14.78 0.00 6.13
205 240 2.416972 GGTCATGTCGGTCTCACTTACC 60.417 54.545 0.00 0.00 0.00 2.85
208 243 1.338107 TGGTCATGTCGGTCTCACTT 58.662 50.000 0.00 0.00 0.00 3.16
209 244 1.561643 ATGGTCATGTCGGTCTCACT 58.438 50.000 0.00 0.00 0.00 3.41
210 245 3.735237 ATATGGTCATGTCGGTCTCAC 57.265 47.619 0.00 0.00 0.00 3.51
211 246 3.069586 GGAATATGGTCATGTCGGTCTCA 59.930 47.826 0.00 0.00 0.00 3.27
212 247 3.069586 TGGAATATGGTCATGTCGGTCTC 59.930 47.826 0.00 0.00 0.00 3.36
214 249 3.469008 TGGAATATGGTCATGTCGGTC 57.531 47.619 0.00 0.00 0.00 4.79
215 250 3.496692 CCATGGAATATGGTCATGTCGGT 60.497 47.826 5.56 0.00 37.24 4.69
216 251 3.076621 CCATGGAATATGGTCATGTCGG 58.923 50.000 5.56 0.00 37.24 4.79
225 260 5.935945 TGTAGGTACAACCATGGAATATGG 58.064 41.667 21.47 4.45 41.95 2.74
226 261 6.591935 ACTGTAGGTACAACCATGGAATATG 58.408 40.000 21.47 13.71 41.95 1.78
227 262 6.824958 ACTGTAGGTACAACCATGGAATAT 57.175 37.500 21.47 3.15 41.95 1.28
228 263 6.630203 AACTGTAGGTACAACCATGGAATA 57.370 37.500 21.47 4.43 41.95 1.75
229 264 5.514500 AACTGTAGGTACAACCATGGAAT 57.486 39.130 21.47 3.48 41.95 3.01
230 265 4.986054 AACTGTAGGTACAACCATGGAA 57.014 40.909 21.47 0.00 41.95 3.53
231 266 4.263156 GGAAACTGTAGGTACAACCATGGA 60.263 45.833 21.47 0.00 41.95 3.41
234 269 4.349930 ACTGGAAACTGTAGGTACAACCAT 59.650 41.667 0.00 0.00 41.13 3.55
235 270 3.712733 ACTGGAAACTGTAGGTACAACCA 59.287 43.478 0.00 0.00 41.13 3.67
236 271 4.062991 CACTGGAAACTGTAGGTACAACC 58.937 47.826 0.00 0.00 40.96 3.77
237 272 4.062991 CCACTGGAAACTGTAGGTACAAC 58.937 47.826 0.00 0.00 40.96 3.32
239 274 3.578978 TCCACTGGAAACTGTAGGTACA 58.421 45.455 0.00 0.00 40.96 2.90
242 277 3.248024 TGATCCACTGGAAACTGTAGGT 58.752 45.455 0.66 0.00 40.96 3.08
243 278 3.981071 TGATCCACTGGAAACTGTAGG 57.019 47.619 0.66 0.00 40.96 3.18
244 279 4.899502 ACTTGATCCACTGGAAACTGTAG 58.100 43.478 0.66 0.00 40.96 2.74
246 281 3.864789 ACTTGATCCACTGGAAACTGT 57.135 42.857 0.66 0.00 44.07 3.55
247 282 4.455877 GGTAACTTGATCCACTGGAAACTG 59.544 45.833 0.66 0.00 34.34 3.16
276 311 2.945447 TCCATACAATGCAAGCAAGC 57.055 45.000 0.00 0.00 0.00 4.01
277 312 4.707030 TCTTCCATACAATGCAAGCAAG 57.293 40.909 0.00 0.00 0.00 4.01
280 315 6.973843 TCATATTCTTCCATACAATGCAAGC 58.026 36.000 0.00 0.00 0.00 4.01
281 316 9.976511 AAATCATATTCTTCCATACAATGCAAG 57.023 29.630 0.00 0.00 0.00 4.01
282 317 9.970395 GAAATCATATTCTTCCATACAATGCAA 57.030 29.630 0.00 0.00 0.00 4.08
283 318 9.134055 TGAAATCATATTCTTCCATACAATGCA 57.866 29.630 0.00 0.00 0.00 3.96
313 348 7.773224 TCGCCCATCTCTCAAAAATAAAATAGA 59.227 33.333 0.00 0.00 0.00 1.98
314 349 7.930217 TCGCCCATCTCTCAAAAATAAAATAG 58.070 34.615 0.00 0.00 0.00 1.73
315 350 7.873719 TCGCCCATCTCTCAAAAATAAAATA 57.126 32.000 0.00 0.00 0.00 1.40
317 352 6.432783 TCTTCGCCCATCTCTCAAAAATAAAA 59.567 34.615 0.00 0.00 0.00 1.52
318 353 5.943416 TCTTCGCCCATCTCTCAAAAATAAA 59.057 36.000 0.00 0.00 0.00 1.40
319 354 5.496556 TCTTCGCCCATCTCTCAAAAATAA 58.503 37.500 0.00 0.00 0.00 1.40
320 355 5.097742 TCTTCGCCCATCTCTCAAAAATA 57.902 39.130 0.00 0.00 0.00 1.40
323 358 3.007940 TCTTCTTCGCCCATCTCTCAAAA 59.992 43.478 0.00 0.00 0.00 2.44
325 360 2.167281 CTCTTCTTCGCCCATCTCTCAA 59.833 50.000 0.00 0.00 0.00 3.02
326 361 1.753649 CTCTTCTTCGCCCATCTCTCA 59.246 52.381 0.00 0.00 0.00 3.27
327 362 1.537990 GCTCTTCTTCGCCCATCTCTC 60.538 57.143 0.00 0.00 0.00 3.20
329 364 0.463620 AGCTCTTCTTCGCCCATCTC 59.536 55.000 0.00 0.00 0.00 2.75
331 366 0.176680 TGAGCTCTTCTTCGCCCATC 59.823 55.000 16.19 0.00 0.00 3.51
333 368 0.107993 CATGAGCTCTTCTTCGCCCA 60.108 55.000 16.19 0.00 0.00 5.36
334 369 0.107945 ACATGAGCTCTTCTTCGCCC 60.108 55.000 16.19 0.00 0.00 6.13
335 370 1.731720 AACATGAGCTCTTCTTCGCC 58.268 50.000 16.19 0.00 0.00 5.54
336 371 3.820777 AAAACATGAGCTCTTCTTCGC 57.179 42.857 16.19 0.00 0.00 4.70
354 389 3.859411 ACAGCACGACCAAAAGAAAAA 57.141 38.095 0.00 0.00 0.00 1.94
355 390 3.859411 AACAGCACGACCAAAAGAAAA 57.141 38.095 0.00 0.00 0.00 2.29
357 392 3.506810 CAAAACAGCACGACCAAAAGAA 58.493 40.909 0.00 0.00 0.00 2.52
360 395 1.737363 GCCAAAACAGCACGACCAAAA 60.737 47.619 0.00 0.00 0.00 2.44
361 396 0.179124 GCCAAAACAGCACGACCAAA 60.179 50.000 0.00 0.00 0.00 3.28
362 397 1.034838 AGCCAAAACAGCACGACCAA 61.035 50.000 0.00 0.00 0.00 3.67
363 398 1.034838 AAGCCAAAACAGCACGACCA 61.035 50.000 0.00 0.00 0.00 4.02
364 399 0.594796 CAAGCCAAAACAGCACGACC 60.595 55.000 0.00 0.00 0.00 4.79
366 401 1.034838 ACCAAGCCAAAACAGCACGA 61.035 50.000 0.00 0.00 0.00 4.35
368 403 0.594796 CGACCAAGCCAAAACAGCAC 60.595 55.000 0.00 0.00 0.00 4.40
369 404 1.732917 CGACCAAGCCAAAACAGCA 59.267 52.632 0.00 0.00 0.00 4.41
372 407 2.054140 GACGCGACCAAGCCAAAACA 62.054 55.000 15.93 0.00 0.00 2.83
373 408 1.370051 GACGCGACCAAGCCAAAAC 60.370 57.895 15.93 0.00 0.00 2.43
374 409 1.098712 AAGACGCGACCAAGCCAAAA 61.099 50.000 15.93 0.00 0.00 2.44
375 410 1.503818 GAAGACGCGACCAAGCCAAA 61.504 55.000 15.93 0.00 0.00 3.28
376 411 1.959226 GAAGACGCGACCAAGCCAA 60.959 57.895 15.93 0.00 0.00 4.52
377 412 2.357034 GAAGACGCGACCAAGCCA 60.357 61.111 15.93 0.00 0.00 4.75
378 413 1.228657 AAAGAAGACGCGACCAAGCC 61.229 55.000 15.93 0.00 0.00 4.35
380 415 1.497991 TCAAAGAAGACGCGACCAAG 58.502 50.000 15.93 0.00 0.00 3.61
382 417 1.000394 TCATCAAAGAAGACGCGACCA 60.000 47.619 15.93 0.00 0.00 4.02
383 418 1.710013 TCATCAAAGAAGACGCGACC 58.290 50.000 15.93 3.72 0.00 4.79
384 419 3.999229 ATTCATCAAAGAAGACGCGAC 57.001 42.857 15.93 6.86 0.00 5.19
386 421 6.199154 AGTGTATATTCATCAAAGAAGACGCG 59.801 38.462 3.53 3.53 30.63 6.01
387 422 7.222805 TGAGTGTATATTCATCAAAGAAGACGC 59.777 37.037 0.00 0.00 0.00 5.19
388 423 8.634475 TGAGTGTATATTCATCAAAGAAGACG 57.366 34.615 0.00 0.00 0.00 4.18
395 979 9.558396 TGCATGTATGAGTGTATATTCATCAAA 57.442 29.630 0.65 0.00 35.26 2.69
398 982 7.548427 AGCTGCATGTATGAGTGTATATTCATC 59.452 37.037 1.02 0.00 35.26 2.92
401 985 7.095910 AGAGCTGCATGTATGAGTGTATATTC 58.904 38.462 1.02 0.00 0.00 1.75
402 986 7.002250 AGAGCTGCATGTATGAGTGTATATT 57.998 36.000 1.02 0.00 0.00 1.28
404 988 5.047731 GGAGAGCTGCATGTATGAGTGTATA 60.048 44.000 1.02 0.00 0.00 1.47
408 992 2.102757 AGGAGAGCTGCATGTATGAGTG 59.897 50.000 1.02 0.00 0.00 3.51
411 995 1.202615 GCAGGAGAGCTGCATGTATGA 60.203 52.381 1.02 0.00 46.19 2.15
420 1004 1.088340 CGAACCATGCAGGAGAGCTG 61.088 60.000 0.00 0.00 41.22 4.24
421 1005 1.220206 CGAACCATGCAGGAGAGCT 59.780 57.895 0.00 0.00 41.22 4.09
422 1006 0.809241 CTCGAACCATGCAGGAGAGC 60.809 60.000 0.00 0.00 41.22 4.09
423 1007 0.820226 TCTCGAACCATGCAGGAGAG 59.180 55.000 0.00 9.57 41.22 3.20
424 1008 0.820226 CTCTCGAACCATGCAGGAGA 59.180 55.000 0.00 0.30 41.22 3.71
425 1009 0.820226 TCTCTCGAACCATGCAGGAG 59.180 55.000 0.00 0.00 41.22 3.69
427 1011 1.205655 TCTTCTCTCGAACCATGCAGG 59.794 52.381 0.00 0.00 45.67 4.85
428 1012 2.662006 TCTTCTCTCGAACCATGCAG 57.338 50.000 0.00 0.00 0.00 4.41
448 2205 6.371548 GCTCTTTTCTTCCAAACAACCTTTTT 59.628 34.615 0.00 0.00 0.00 1.94
449 2206 5.874810 GCTCTTTTCTTCCAAACAACCTTTT 59.125 36.000 0.00 0.00 0.00 2.27
455 2212 5.531287 GGTCTAGCTCTTTTCTTCCAAACAA 59.469 40.000 0.00 0.00 0.00 2.83
459 2216 4.974645 TGGTCTAGCTCTTTTCTTCCAA 57.025 40.909 0.00 0.00 0.00 3.53
462 2219 6.533367 CACACTATGGTCTAGCTCTTTTCTTC 59.467 42.308 0.00 0.00 0.00 2.87
538 2625 0.475906 ACGTACCCCGAGCTAGGTAT 59.524 55.000 12.29 1.82 40.64 2.73
551 2638 5.104374 TGGAATCATTTAGAACGACGTACC 58.896 41.667 0.00 0.00 0.00 3.34
615 2702 8.295288 GCTGGATTTGACATAATTTAGGATCAG 58.705 37.037 0.00 0.00 0.00 2.90
642 2729 3.485947 TGTTAACTCCATTTGCGCATC 57.514 42.857 12.75 0.00 0.00 3.91
708 2795 7.039082 CCAAGAAATTTCCCAGAACTTTCCATA 60.039 37.037 14.61 0.00 0.00 2.74
710 2797 5.070313 CCAAGAAATTTCCCAGAACTTTCCA 59.930 40.000 14.61 0.00 0.00 3.53
732 2819 3.153130 TGCTGCTTGTTAACTAATGCCA 58.847 40.909 7.22 0.00 0.00 4.92
740 2827 1.804151 TGGTCGATGCTGCTTGTTAAC 59.196 47.619 0.00 0.00 0.00 2.01
758 2845 0.246635 AGAACGGTCGGTGAGAATGG 59.753 55.000 0.00 0.00 0.00 3.16
789 2876 3.684788 GTCGCATTGACTAATGACTGGTT 59.315 43.478 4.33 0.00 45.21 3.67
818 2905 4.121317 CAGTGGAAAACATGTGCAATTGT 58.879 39.130 7.40 0.00 0.00 2.71
819 2906 4.025563 CACAGTGGAAAACATGTGCAATTG 60.026 41.667 0.00 0.00 34.37 2.32
822 2909 2.495270 ACACAGTGGAAAACATGTGCAA 59.505 40.909 5.31 0.00 39.79 4.08
840 2927 6.546972 TCGATATGATCAGAGACTGTACAC 57.453 41.667 0.09 0.00 32.61 2.90
875 3714 1.848400 AACCTGGGTTGGTACACCC 59.152 57.895 13.42 13.42 45.59 4.61
1116 3955 3.461773 CCCGCGATGTCCTCCAGT 61.462 66.667 8.23 0.00 0.00 4.00
1269 4229 4.988598 AGCGTCTGGTTGGGCACG 62.989 66.667 0.00 0.00 35.32 5.34
1411 4371 8.169268 CGACGCTAAGAAAGAAAGAATAATTGT 58.831 33.333 0.00 0.00 0.00 2.71
1412 4372 8.380644 TCGACGCTAAGAAAGAAAGAATAATTG 58.619 33.333 0.00 0.00 0.00 2.32
1414 4374 7.760340 AGTCGACGCTAAGAAAGAAAGAATAAT 59.240 33.333 10.46 0.00 0.00 1.28
1416 4376 6.618811 AGTCGACGCTAAGAAAGAAAGAATA 58.381 36.000 10.46 0.00 0.00 1.75
1417 4377 5.471257 AGTCGACGCTAAGAAAGAAAGAAT 58.529 37.500 10.46 0.00 0.00 2.40
1418 4378 4.868067 AGTCGACGCTAAGAAAGAAAGAA 58.132 39.130 10.46 0.00 0.00 2.52
1419 4379 4.474113 GAGTCGACGCTAAGAAAGAAAGA 58.526 43.478 12.41 0.00 0.00 2.52
1420 4380 3.608939 GGAGTCGACGCTAAGAAAGAAAG 59.391 47.826 18.88 0.00 0.00 2.62
1421 4381 3.572584 GGAGTCGACGCTAAGAAAGAAA 58.427 45.455 18.88 0.00 0.00 2.52
1425 4385 0.169672 CCGGAGTCGACGCTAAGAAA 59.830 55.000 18.88 0.00 39.00 2.52
1443 4478 4.358810 AGAGTAACTCTCCCGGCC 57.641 61.111 0.00 0.00 43.71 6.13
1451 4486 4.500603 TCGGTTCTGTTGAGAGTAACTC 57.499 45.455 0.00 0.00 45.11 3.01
1463 4515 9.998106 ATATGCTAGTTAATTAATCGGTTCTGT 57.002 29.630 0.31 0.00 0.00 3.41
1490 4545 1.044231 TCCACCACGTACCCGCATAT 61.044 55.000 0.00 0.00 37.70 1.78
1491 4546 1.044231 ATCCACCACGTACCCGCATA 61.044 55.000 0.00 0.00 37.70 3.14
1492 4547 2.363975 ATCCACCACGTACCCGCAT 61.364 57.895 0.00 0.00 37.70 4.73
1493 4548 2.998480 ATCCACCACGTACCCGCA 60.998 61.111 0.00 0.00 37.70 5.69
1703 4758 1.613630 GGAGAAGGAGGGGCAGTGA 60.614 63.158 0.00 0.00 0.00 3.41
1855 4910 5.008019 TCGAAGTAGTACTTGTTGTCGAACT 59.992 40.000 20.21 0.00 38.80 3.01
1937 4992 1.016653 GTGAAGCCAAGAGCCTCGTC 61.017 60.000 0.00 0.00 45.47 4.20
1961 5016 2.896854 GCGGATTGGATGAGCGCA 60.897 61.111 11.47 0.00 0.00 6.09
2048 5103 1.219124 GCAGTTCTGCCGGATCTCA 59.781 57.895 5.05 0.00 0.00 3.27
2123 5178 1.596477 GATCTCTCACATGGCGGCC 60.596 63.158 13.32 13.32 0.00 6.13
2141 5196 5.627367 GTGAGCTAGCATCGATAACTAACTG 59.373 44.000 18.83 3.08 0.00 3.16
2142 5197 5.561145 CGTGAGCTAGCATCGATAACTAACT 60.561 44.000 18.83 3.99 0.00 2.24
2227 5284 1.071502 CAACACGTACGACAACTGCAG 60.072 52.381 24.41 13.48 0.00 4.41
2261 5318 0.761187 TCTTGCTCTGCTGACCACTT 59.239 50.000 0.00 0.00 0.00 3.16
2275 5332 5.245075 AGGAAGCATATACTCCTACTCTTGC 59.755 44.000 0.00 0.00 0.00 4.01
2507 5566 2.871096 ACTATGTTTCTTTGCGGGGA 57.129 45.000 0.00 0.00 0.00 4.81
2508 5567 5.820947 ACTATTACTATGTTTCTTTGCGGGG 59.179 40.000 0.00 0.00 0.00 5.73
2509 5568 6.920569 ACTATTACTATGTTTCTTTGCGGG 57.079 37.500 0.00 0.00 0.00 6.13
2589 5648 7.007723 AGGTTTGACCAACAATTACTATGGAA 58.992 34.615 0.00 0.00 41.95 3.53
2590 5649 6.432783 CAGGTTTGACCAACAATTACTATGGA 59.567 38.462 0.00 0.00 41.95 3.41
2615 5675 1.726791 CTGCACTTCATCACCACGTAC 59.273 52.381 0.00 0.00 0.00 3.67
2627 5687 3.273434 TCATCTGGTTATGCTGCACTTC 58.727 45.455 3.57 0.00 0.00 3.01
2647 5707 0.101579 GGTAGCAGTTCTCCGAGCTC 59.898 60.000 2.73 2.73 38.47 4.09
2941 6004 3.555956 AGCGCAACACTATAACATGCTAC 59.444 43.478 11.47 0.00 34.93 3.58
2946 6009 5.749109 GTCTCTTAGCGCAACACTATAACAT 59.251 40.000 11.47 0.00 0.00 2.71
2947 6010 5.100259 GTCTCTTAGCGCAACACTATAACA 58.900 41.667 11.47 0.00 0.00 2.41
2948 6011 5.341617 AGTCTCTTAGCGCAACACTATAAC 58.658 41.667 11.47 0.00 0.00 1.89
2949 6012 5.578005 AGTCTCTTAGCGCAACACTATAA 57.422 39.130 11.47 0.00 0.00 0.98
2955 6018 2.143122 CCAAAGTCTCTTAGCGCAACA 58.857 47.619 11.47 0.00 0.00 3.33
2962 6025 4.380655 CCGTGTAGGACCAAAGTCTCTTAG 60.381 50.000 0.00 0.00 45.00 2.18
2984 6047 7.201401 CCAACACGCTATAAAATTTTACTTGCC 60.201 37.037 12.74 0.57 0.00 4.52
2986 6049 7.460896 CGCCAACACGCTATAAAATTTTACTTG 60.461 37.037 12.74 7.24 0.00 3.16
3007 6070 4.600692 TCTCTAAATGCTATAGCGCCAA 57.399 40.909 19.55 2.47 45.83 4.52
3072 6137 6.866248 GGTGGTTAATTAGTTGGTGAAACATG 59.134 38.462 0.00 0.00 41.61 3.21


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

AutoCloner maintained by Alex Coulton.