Multiple sequence alignment - TraesCS3D01G115900

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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 TraesCS3D01G115900 chr3D 100.000 4119 0 0 1 4119 69501970 69497852 0.000000e+00 7607.0
1 TraesCS3D01G115900 chr3D 95.294 170 7 1 1369 1538 467283486 467283654 6.790000e-68 268.0
2 TraesCS3D01G115900 chr3A 94.910 3556 143 19 586 4118 80690085 80686545 0.000000e+00 5529.0
3 TraesCS3D01G115900 chr3A 92.256 297 20 3 258 553 504552275 504552569 6.370000e-113 418.0
4 TraesCS3D01G115900 chr3A 91.635 263 15 1 1 263 80690438 80690183 1.410000e-94 357.0
5 TraesCS3D01G115900 chr3A 95.294 170 7 1 1369 1538 609950955 609951123 6.790000e-68 268.0
6 TraesCS3D01G115900 chr3B 94.215 2610 101 26 1542 4119 115397975 115395384 0.000000e+00 3938.0
7 TraesCS3D01G115900 chr3B 93.341 826 47 4 552 1374 115398777 115397957 0.000000e+00 1214.0
8 TraesCS3D01G115900 chr3B 92.692 260 12 1 1 260 115399033 115398781 6.500000e-98 368.0
9 TraesCS3D01G115900 chr3B 96.078 51 2 0 1279 1329 644507506 644507456 2.640000e-12 84.2
10 TraesCS3D01G115900 chr4D 92.739 303 18 3 253 555 319248910 319249208 6.320000e-118 435.0
11 TraesCS3D01G115900 chr4D 92.542 295 19 2 261 553 421335224 421335517 1.770000e-113 420.0
12 TraesCS3D01G115900 chr4B 92.308 299 19 3 261 555 396703714 396704012 4.920000e-114 422.0
13 TraesCS3D01G115900 chr4B 96.450 169 6 0 1372 1540 206802590 206802758 3.140000e-71 279.0
14 TraesCS3D01G115900 chr4B 95.858 169 7 0 1370 1538 386210406 386210238 1.460000e-69 274.0
15 TraesCS3D01G115900 chr7D 92.230 296 21 1 261 554 409099758 409099463 6.370000e-113 418.0
16 TraesCS3D01G115900 chr7D 96.078 51 2 0 1279 1329 634214291 634214341 2.640000e-12 84.2
17 TraesCS3D01G115900 chr7D 92.308 52 4 0 1278 1329 601485840 601485891 1.590000e-09 75.0
18 TraesCS3D01G115900 chrUn 92.230 296 19 3 261 553 289820909 289820615 2.290000e-112 416.0
19 TraesCS3D01G115900 chr5B 92.491 293 19 2 261 550 303229109 303229401 2.290000e-112 416.0
20 TraesCS3D01G115900 chr5B 94.286 175 7 3 1372 1543 87234583 87234409 8.780000e-67 265.0
21 TraesCS3D01G115900 chr5B 95.210 167 8 0 1372 1538 573003545 573003711 8.780000e-67 265.0
22 TraesCS3D01G115900 chr5B 90.196 51 5 0 1279 1329 285502057 285502007 2.660000e-07 67.6
23 TraesCS3D01G115900 chr6A 91.475 305 21 4 253 554 189538776 189538474 8.240000e-112 414.0
24 TraesCS3D01G115900 chr6A 92.727 55 3 1 1498 1552 420830221 420830168 1.230000e-10 78.7
25 TraesCS3D01G115900 chr4A 91.919 297 22 1 261 555 154521415 154521119 8.240000e-112 414.0
26 TraesCS3D01G115900 chr5A 94.350 177 9 1 1373 1549 271053811 271053636 1.890000e-68 270.0
27 TraesCS3D01G115900 chr5A 95.833 48 2 0 1498 1545 596572778 596572825 1.230000e-10 78.7
28 TraesCS3D01G115900 chr7A 95.238 168 7 1 1372 1538 696171915 696172082 8.780000e-67 265.0
29 TraesCS3D01G115900 chr7A 85.714 189 13 5 1373 1548 511110906 511111093 1.950000e-43 187.0
30 TraesCS3D01G115900 chr6D 92.655 177 8 3 1372 1547 202257550 202257722 2.460000e-62 250.0
31 TraesCS3D01G115900 chr6B 91.525 177 10 3 1372 1547 319535674 319535502 5.320000e-59 239.0
32 TraesCS3D01G115900 chr6B 90.909 55 4 1 1498 1552 462028334 462028387 5.710000e-09 73.1
33 TraesCS3D01G115900 chr1B 89.474 76 3 4 1247 1319 633036932 633036859 1.580000e-14 91.6
34 TraesCS3D01G115900 chr1D 86.111 72 8 2 1258 1328 449980345 449980275 4.420000e-10 76.8
35 TraesCS3D01G115900 chr1D 97.674 43 1 0 1287 1329 450055885 450055843 1.590000e-09 75.0


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 TraesCS3D01G115900 chr3D 69497852 69501970 4118 True 7607 7607 100.0000 1 4119 1 chr3D.!!$R1 4118
1 TraesCS3D01G115900 chr3A 80686545 80690438 3893 True 2943 5529 93.2725 1 4118 2 chr3A.!!$R1 4117
2 TraesCS3D01G115900 chr3B 115395384 115399033 3649 True 1840 3938 93.4160 1 4119 3 chr3B.!!$R2 4118

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
52 53 0.026803 GATTGATCGAGCGTTGGTGC 59.973 55.0 0.00 0.0 0.00 5.01 F
437 438 0.034089 GCACTTAGCTCATTGGGGGT 60.034 55.0 0.00 0.0 41.15 4.95 F
444 445 0.040499 GCTCATTGGGGGTTGGGTAA 59.960 55.0 0.00 0.0 0.00 2.85 F
477 478 0.106519 ATGGTGGCTTGCACCTATCC 60.107 55.0 11.31 0.0 42.92 2.59 F
1410 1415 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.0 12.44 0.0 40.80 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1395 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.0 38.40 4.00 R
1458 1463 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.0 0.00 2.71 R
1648 1665 4.497674 GCAGATCAATCAGAGAATGTTGGC 60.498 45.833 0.00 0.0 0.00 4.52 R
2456 2476 0.251922 AGCAACATGGCCTTGGACAT 60.252 50.000 21.67 1.4 0.00 3.06 R
3120 3140 0.027455 TTCAGCTTCGCACACGTTTG 59.973 50.000 0.00 0.0 41.18 2.93 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
52 53 0.026803 GATTGATCGAGCGTTGGTGC 59.973 55.000 0.00 0.00 0.00 5.01
79 80 1.901464 GGCCCTTCCAAACGCTTCA 60.901 57.895 0.00 0.00 34.01 3.02
80 81 1.285950 GCCCTTCCAAACGCTTCAC 59.714 57.895 0.00 0.00 0.00 3.18
148 149 4.918278 TGGTCGGTCCACGGTCCA 62.918 66.667 0.27 0.19 41.93 4.02
149 150 4.368543 GGTCGGTCCACGGTCCAC 62.369 72.222 0.27 0.00 44.45 4.02
150 151 4.368543 GTCGGTCCACGGTCCACC 62.369 72.222 0.27 0.00 44.45 4.61
151 152 4.608774 TCGGTCCACGGTCCACCT 62.609 66.667 0.27 0.00 44.45 4.00
189 190 6.412072 GCATAAACATCTGTTCATTTAGACGC 59.588 38.462 0.00 0.00 37.25 5.19
220 221 9.979578 ATGATAAGCACAGTTTAAACATCAAAA 57.020 25.926 20.06 1.05 0.00 2.44
227 228 5.979517 ACAGTTTAAACATCAAAAGAGCAGC 59.020 36.000 20.06 0.00 0.00 5.25
267 268 9.265901 CTATTATAGTTTCCATCTTGTCTGGTG 57.734 37.037 0.00 0.00 35.19 4.17
269 270 4.437682 AGTTTCCATCTTGTCTGGTGAA 57.562 40.909 0.00 0.00 35.19 3.18
270 271 4.392940 AGTTTCCATCTTGTCTGGTGAAG 58.607 43.478 0.00 0.00 35.19 3.02
271 272 4.103153 AGTTTCCATCTTGTCTGGTGAAGA 59.897 41.667 0.00 0.00 35.19 2.87
272 273 3.969287 TCCATCTTGTCTGGTGAAGAG 57.031 47.619 0.00 0.00 34.84 2.85
273 274 3.242867 TCCATCTTGTCTGGTGAAGAGT 58.757 45.455 0.00 0.00 34.84 3.24
274 275 3.007290 TCCATCTTGTCTGGTGAAGAGTG 59.993 47.826 0.00 0.00 34.84 3.51
276 277 4.021104 CCATCTTGTCTGGTGAAGAGTGTA 60.021 45.833 0.00 0.00 34.84 2.90
277 278 5.337894 CCATCTTGTCTGGTGAAGAGTGTAT 60.338 44.000 0.00 0.00 34.84 2.29
278 279 6.127338 CCATCTTGTCTGGTGAAGAGTGTATA 60.127 42.308 0.00 0.00 34.84 1.47
279 280 7.418368 CCATCTTGTCTGGTGAAGAGTGTATAT 60.418 40.741 0.00 0.00 34.84 0.86
281 282 7.907389 TCTTGTCTGGTGAAGAGTGTATATTT 58.093 34.615 0.00 0.00 34.84 1.40
284 285 6.212589 TGTCTGGTGAAGAGTGTATATTTGGA 59.787 38.462 0.00 0.00 34.84 3.53
285 286 7.092891 TGTCTGGTGAAGAGTGTATATTTGGAT 60.093 37.037 0.00 0.00 34.84 3.41
288 289 9.613428 CTGGTGAAGAGTGTATATTTGGATTTA 57.387 33.333 0.00 0.00 0.00 1.40
289 290 9.967451 TGGTGAAGAGTGTATATTTGGATTTAA 57.033 29.630 0.00 0.00 0.00 1.52
315 316 6.431198 TTTGTCCACAAAAGAGTGTACTTC 57.569 37.500 2.29 0.00 42.26 3.01
316 317 5.353394 TGTCCACAAAAGAGTGTACTTCT 57.647 39.130 0.00 0.00 37.82 2.85
320 321 7.015292 TGTCCACAAAAGAGTGTACTTCTATCT 59.985 37.037 0.00 0.00 37.82 1.98
321 322 7.873505 GTCCACAAAAGAGTGTACTTCTATCTT 59.126 37.037 0.00 0.00 37.82 2.40
322 323 8.088981 TCCACAAAAGAGTGTACTTCTATCTTC 58.911 37.037 0.00 0.00 37.82 2.87
323 324 7.332182 CCACAAAAGAGTGTACTTCTATCTTCC 59.668 40.741 0.00 0.00 37.82 3.46
324 325 7.332182 CACAAAAGAGTGTACTTCTATCTTCCC 59.668 40.741 0.00 0.00 34.83 3.97
325 326 7.016268 ACAAAAGAGTGTACTTCTATCTTCCCA 59.984 37.037 0.00 0.00 30.16 4.37
327 328 7.741554 AAGAGTGTACTTCTATCTTCCCAAT 57.258 36.000 0.00 0.00 0.00 3.16
328 329 7.118496 AGAGTGTACTTCTATCTTCCCAATG 57.882 40.000 0.00 0.00 0.00 2.82
329 330 5.675538 AGTGTACTTCTATCTTCCCAATGC 58.324 41.667 0.00 0.00 0.00 3.56
331 332 5.294552 GTGTACTTCTATCTTCCCAATGCAC 59.705 44.000 0.00 0.00 0.00 4.57
332 333 4.851639 ACTTCTATCTTCCCAATGCACT 57.148 40.909 0.00 0.00 0.00 4.40
334 335 5.574188 ACTTCTATCTTCCCAATGCACTTT 58.426 37.500 0.00 0.00 0.00 2.66
335 336 6.721318 ACTTCTATCTTCCCAATGCACTTTA 58.279 36.000 0.00 0.00 0.00 1.85
336 337 7.175104 ACTTCTATCTTCCCAATGCACTTTAA 58.825 34.615 0.00 0.00 0.00 1.52
337 338 7.669722 ACTTCTATCTTCCCAATGCACTTTAAA 59.330 33.333 0.00 0.00 0.00 1.52
338 339 7.630242 TCTATCTTCCCAATGCACTTTAAAG 57.370 36.000 13.76 13.76 0.00 1.85
339 340 7.175104 TCTATCTTCCCAATGCACTTTAAAGT 58.825 34.615 15.22 15.22 40.60 2.66
340 341 6.670695 ATCTTCCCAATGCACTTTAAAGTT 57.329 33.333 18.25 1.51 37.08 2.66
342 343 7.589958 TCTTCCCAATGCACTTTAAAGTTAA 57.410 32.000 18.25 9.84 37.08 2.01
343 344 8.012957 TCTTCCCAATGCACTTTAAAGTTAAA 57.987 30.769 18.25 7.40 37.08 1.52
344 345 8.478877 TCTTCCCAATGCACTTTAAAGTTAAAA 58.521 29.630 18.25 4.99 37.08 1.52
345 346 9.103861 CTTCCCAATGCACTTTAAAGTTAAAAA 57.896 29.630 18.25 3.30 37.08 1.94
368 369 6.754702 AAAATGTTCCTCTCTCATCACATG 57.245 37.500 0.00 0.00 0.00 3.21
369 370 3.900966 TGTTCCTCTCTCATCACATGG 57.099 47.619 0.00 0.00 0.00 3.66
370 371 3.176411 TGTTCCTCTCTCATCACATGGT 58.824 45.455 0.00 0.00 0.00 3.55
371 372 4.352893 TGTTCCTCTCTCATCACATGGTA 58.647 43.478 0.00 0.00 0.00 3.25
372 373 4.777366 TGTTCCTCTCTCATCACATGGTAA 59.223 41.667 0.00 0.00 0.00 2.85
373 374 5.426509 TGTTCCTCTCTCATCACATGGTAAT 59.573 40.000 0.00 0.00 0.00 1.89
374 375 5.798125 TCCTCTCTCATCACATGGTAATC 57.202 43.478 0.00 0.00 0.00 1.75
375 376 5.211201 TCCTCTCTCATCACATGGTAATCA 58.789 41.667 0.00 0.00 0.00 2.57
376 377 5.662657 TCCTCTCTCATCACATGGTAATCAA 59.337 40.000 0.00 0.00 0.00 2.57
377 378 5.990386 CCTCTCTCATCACATGGTAATCAAG 59.010 44.000 0.00 0.00 0.00 3.02
378 379 6.183360 CCTCTCTCATCACATGGTAATCAAGA 60.183 42.308 0.00 0.00 0.00 3.02
379 380 6.577103 TCTCTCATCACATGGTAATCAAGAC 58.423 40.000 0.00 0.00 0.00 3.01
380 381 5.674525 TCTCATCACATGGTAATCAAGACC 58.325 41.667 0.00 0.00 37.49 3.85
393 394 9.391006 TGGTAATCAAGACCAATAACATTCTAC 57.609 33.333 0.00 0.00 44.08 2.59
394 395 9.391006 GGTAATCAAGACCAATAACATTCTACA 57.609 33.333 0.00 0.00 36.91 2.74
396 397 8.862325 AATCAAGACCAATAACATTCTACACA 57.138 30.769 0.00 0.00 0.00 3.72
397 398 7.667043 TCAAGACCAATAACATTCTACACAC 57.333 36.000 0.00 0.00 0.00 3.82
398 399 6.367695 TCAAGACCAATAACATTCTACACACG 59.632 38.462 0.00 0.00 0.00 4.49
399 400 5.175859 AGACCAATAACATTCTACACACGG 58.824 41.667 0.00 0.00 0.00 4.94
400 401 4.901868 ACCAATAACATTCTACACACGGT 58.098 39.130 0.00 0.00 0.00 4.83
401 402 4.933400 ACCAATAACATTCTACACACGGTC 59.067 41.667 0.00 0.00 0.00 4.79
402 403 5.175859 CCAATAACATTCTACACACGGTCT 58.824 41.667 0.00 0.00 0.00 3.85
403 404 5.642063 CCAATAACATTCTACACACGGTCTT 59.358 40.000 0.00 0.00 0.00 3.01
404 405 6.183360 CCAATAACATTCTACACACGGTCTTC 60.183 42.308 0.00 0.00 0.00 2.87
405 406 4.602340 AACATTCTACACACGGTCTTCT 57.398 40.909 0.00 0.00 0.00 2.85
406 407 4.602340 ACATTCTACACACGGTCTTCTT 57.398 40.909 0.00 0.00 0.00 2.52
407 408 5.717078 ACATTCTACACACGGTCTTCTTA 57.283 39.130 0.00 0.00 0.00 2.10
408 409 6.092955 ACATTCTACACACGGTCTTCTTAA 57.907 37.500 0.00 0.00 0.00 1.85
409 410 6.698380 ACATTCTACACACGGTCTTCTTAAT 58.302 36.000 0.00 0.00 0.00 1.40
410 411 7.159372 ACATTCTACACACGGTCTTCTTAATT 58.841 34.615 0.00 0.00 0.00 1.40
411 412 7.660208 ACATTCTACACACGGTCTTCTTAATTT 59.340 33.333 0.00 0.00 0.00 1.82
412 413 7.647907 TTCTACACACGGTCTTCTTAATTTC 57.352 36.000 0.00 0.00 0.00 2.17
413 414 6.989659 TCTACACACGGTCTTCTTAATTTCT 58.010 36.000 0.00 0.00 0.00 2.52
414 415 8.114331 TCTACACACGGTCTTCTTAATTTCTA 57.886 34.615 0.00 0.00 0.00 2.10
415 416 8.025445 TCTACACACGGTCTTCTTAATTTCTAC 58.975 37.037 0.00 0.00 0.00 2.59
416 417 6.518493 ACACACGGTCTTCTTAATTTCTACA 58.482 36.000 0.00 0.00 0.00 2.74
417 418 7.159372 ACACACGGTCTTCTTAATTTCTACAT 58.841 34.615 0.00 0.00 0.00 2.29
418 419 7.117812 ACACACGGTCTTCTTAATTTCTACATG 59.882 37.037 0.00 0.00 0.00 3.21
419 420 6.092259 ACACGGTCTTCTTAATTTCTACATGC 59.908 38.462 0.00 0.00 0.00 4.06
420 421 6.092122 CACGGTCTTCTTAATTTCTACATGCA 59.908 38.462 0.00 0.00 0.00 3.96
421 422 6.092259 ACGGTCTTCTTAATTTCTACATGCAC 59.908 38.462 0.00 0.00 0.00 4.57
422 423 6.313905 CGGTCTTCTTAATTTCTACATGCACT 59.686 38.462 0.00 0.00 0.00 4.40
423 424 7.148407 CGGTCTTCTTAATTTCTACATGCACTT 60.148 37.037 0.00 0.00 0.00 3.16
424 425 9.162764 GGTCTTCTTAATTTCTACATGCACTTA 57.837 33.333 0.00 0.00 0.00 2.24
426 427 8.883731 TCTTCTTAATTTCTACATGCACTTAGC 58.116 33.333 0.00 0.00 45.96 3.09
427 428 8.792830 TTCTTAATTTCTACATGCACTTAGCT 57.207 30.769 0.00 0.00 45.94 3.32
428 429 8.425577 TCTTAATTTCTACATGCACTTAGCTC 57.574 34.615 0.00 0.00 45.94 4.09
429 430 8.040727 TCTTAATTTCTACATGCACTTAGCTCA 58.959 33.333 0.00 0.00 45.94 4.26
430 431 8.737168 TTAATTTCTACATGCACTTAGCTCAT 57.263 30.769 0.00 0.00 45.94 2.90
431 432 7.636150 AATTTCTACATGCACTTAGCTCATT 57.364 32.000 0.00 0.00 45.94 2.57
432 433 6.426980 TTTCTACATGCACTTAGCTCATTG 57.573 37.500 0.00 0.00 45.94 2.82
433 434 4.445453 TCTACATGCACTTAGCTCATTGG 58.555 43.478 0.00 0.00 45.94 3.16
434 435 2.372264 ACATGCACTTAGCTCATTGGG 58.628 47.619 0.00 0.00 45.94 4.12
435 436 1.679680 CATGCACTTAGCTCATTGGGG 59.320 52.381 0.00 0.00 45.94 4.96
436 437 0.034186 TGCACTTAGCTCATTGGGGG 60.034 55.000 0.00 0.00 45.94 5.40
437 438 0.034089 GCACTTAGCTCATTGGGGGT 60.034 55.000 0.00 0.00 41.15 4.95
438 439 1.616994 GCACTTAGCTCATTGGGGGTT 60.617 52.381 0.00 0.00 41.15 4.11
439 440 2.094675 CACTTAGCTCATTGGGGGTTG 58.905 52.381 0.00 0.00 0.00 3.77
440 441 1.005924 ACTTAGCTCATTGGGGGTTGG 59.994 52.381 0.00 0.00 0.00 3.77
441 442 0.334676 TTAGCTCATTGGGGGTTGGG 59.665 55.000 0.00 0.00 0.00 4.12
442 443 0.849094 TAGCTCATTGGGGGTTGGGT 60.849 55.000 0.00 0.00 0.00 4.51
443 444 0.849094 AGCTCATTGGGGGTTGGGTA 60.849 55.000 0.00 0.00 0.00 3.69
444 445 0.040499 GCTCATTGGGGGTTGGGTAA 59.960 55.000 0.00 0.00 0.00 2.85
445 446 1.342975 GCTCATTGGGGGTTGGGTAAT 60.343 52.381 0.00 0.00 0.00 1.89
446 447 2.892301 GCTCATTGGGGGTTGGGTAATT 60.892 50.000 0.00 0.00 0.00 1.40
447 448 3.628769 GCTCATTGGGGGTTGGGTAATTA 60.629 47.826 0.00 0.00 0.00 1.40
448 449 4.615513 CTCATTGGGGGTTGGGTAATTAA 58.384 43.478 0.00 0.00 0.00 1.40
449 450 5.024803 TCATTGGGGGTTGGGTAATTAAA 57.975 39.130 0.00 0.00 0.00 1.52
450 451 5.026790 TCATTGGGGGTTGGGTAATTAAAG 58.973 41.667 0.00 0.00 0.00 1.85
451 452 4.761591 TTGGGGGTTGGGTAATTAAAGA 57.238 40.909 0.00 0.00 0.00 2.52
452 453 4.325084 TGGGGGTTGGGTAATTAAAGAG 57.675 45.455 0.00 0.00 0.00 2.85
453 454 3.011934 TGGGGGTTGGGTAATTAAAGAGG 59.988 47.826 0.00 0.00 0.00 3.69
454 455 3.270169 GGGGGTTGGGTAATTAAAGAGGA 59.730 47.826 0.00 0.00 0.00 3.71
455 456 4.533815 GGGGTTGGGTAATTAAAGAGGAG 58.466 47.826 0.00 0.00 0.00 3.69
456 457 4.228895 GGGGTTGGGTAATTAAAGAGGAGA 59.771 45.833 0.00 0.00 0.00 3.71
457 458 5.437946 GGGTTGGGTAATTAAAGAGGAGAG 58.562 45.833 0.00 0.00 0.00 3.20
458 459 5.191124 GGGTTGGGTAATTAAAGAGGAGAGA 59.809 44.000 0.00 0.00 0.00 3.10
459 460 6.126449 GGGTTGGGTAATTAAAGAGGAGAGAT 60.126 42.308 0.00 0.00 0.00 2.75
460 461 6.768381 GGTTGGGTAATTAAAGAGGAGAGATG 59.232 42.308 0.00 0.00 0.00 2.90
461 462 6.500589 TGGGTAATTAAAGAGGAGAGATGG 57.499 41.667 0.00 0.00 0.00 3.51
462 463 5.970640 TGGGTAATTAAAGAGGAGAGATGGT 59.029 40.000 0.00 0.00 0.00 3.55
463 464 6.126768 TGGGTAATTAAAGAGGAGAGATGGTG 60.127 42.308 0.00 0.00 0.00 4.17
464 465 6.292150 GGTAATTAAAGAGGAGAGATGGTGG 58.708 44.000 0.00 0.00 0.00 4.61
465 466 3.914426 TTAAAGAGGAGAGATGGTGGC 57.086 47.619 0.00 0.00 0.00 5.01
466 467 1.963985 AAAGAGGAGAGATGGTGGCT 58.036 50.000 0.00 0.00 0.00 4.75
467 468 1.963985 AAGAGGAGAGATGGTGGCTT 58.036 50.000 0.00 0.00 0.00 4.35
468 469 1.202330 AGAGGAGAGATGGTGGCTTG 58.798 55.000 0.00 0.00 0.00 4.01
469 470 0.463474 GAGGAGAGATGGTGGCTTGC 60.463 60.000 0.00 0.00 0.00 4.01
470 471 1.203441 AGGAGAGATGGTGGCTTGCA 61.203 55.000 0.00 0.00 0.00 4.08
471 472 1.028868 GGAGAGATGGTGGCTTGCAC 61.029 60.000 0.00 0.00 0.00 4.57
472 473 1.001641 AGAGATGGTGGCTTGCACC 60.002 57.895 3.83 3.83 42.80 5.01
473 474 1.001641 GAGATGGTGGCTTGCACCT 60.002 57.895 11.31 0.00 42.92 4.00
474 475 0.253044 GAGATGGTGGCTTGCACCTA 59.747 55.000 11.31 0.12 42.92 3.08
475 476 0.921896 AGATGGTGGCTTGCACCTAT 59.078 50.000 11.31 4.36 42.92 2.57
476 477 1.133976 AGATGGTGGCTTGCACCTATC 60.134 52.381 11.31 11.42 42.92 2.08
477 478 0.106519 ATGGTGGCTTGCACCTATCC 60.107 55.000 11.31 0.00 42.92 2.59
478 479 1.302949 GGTGGCTTGCACCTATCCA 59.697 57.895 3.58 0.00 39.52 3.41
479 480 0.323360 GGTGGCTTGCACCTATCCAA 60.323 55.000 3.58 0.00 39.52 3.53
480 481 1.686115 GGTGGCTTGCACCTATCCAAT 60.686 52.381 3.58 0.00 39.52 3.16
481 482 1.406539 GTGGCTTGCACCTATCCAATG 59.593 52.381 0.00 0.00 0.00 2.82
482 483 0.386838 GGCTTGCACCTATCCAATGC 59.613 55.000 0.00 0.00 39.88 3.56
488 489 4.822685 TGCACCTATCCAATGCATTTTT 57.177 36.364 9.83 0.00 44.17 1.94
510 511 6.844097 TTTACCCCACTTCATAATTTGTCC 57.156 37.500 0.00 0.00 0.00 4.02
511 512 4.675063 ACCCCACTTCATAATTTGTCCT 57.325 40.909 0.00 0.00 0.00 3.85
512 513 5.789574 ACCCCACTTCATAATTTGTCCTA 57.210 39.130 0.00 0.00 0.00 2.94
513 514 6.147437 ACCCCACTTCATAATTTGTCCTAA 57.853 37.500 0.00 0.00 0.00 2.69
514 515 6.557568 ACCCCACTTCATAATTTGTCCTAAA 58.442 36.000 0.00 0.00 0.00 1.85
515 516 7.013834 ACCCCACTTCATAATTTGTCCTAAAA 58.986 34.615 0.00 0.00 0.00 1.52
516 517 7.678171 ACCCCACTTCATAATTTGTCCTAAAAT 59.322 33.333 0.00 0.00 0.00 1.82
517 518 8.539544 CCCCACTTCATAATTTGTCCTAAAATT 58.460 33.333 1.08 1.08 41.45 1.82
518 519 9.942850 CCCACTTCATAATTTGTCCTAAAATTT 57.057 29.630 0.70 0.00 39.73 1.82
540 541 7.837202 TTTCTATATGTACACTTTTCACCGG 57.163 36.000 0.00 0.00 0.00 5.28
541 542 6.778834 TCTATATGTACACTTTTCACCGGA 57.221 37.500 9.46 0.00 0.00 5.14
542 543 6.567050 TCTATATGTACACTTTTCACCGGAC 58.433 40.000 9.46 0.00 0.00 4.79
543 544 1.855513 TGTACACTTTTCACCGGACG 58.144 50.000 9.46 0.00 0.00 4.79
544 545 1.142474 GTACACTTTTCACCGGACGG 58.858 55.000 9.46 9.56 42.03 4.79
545 546 1.039068 TACACTTTTCACCGGACGGA 58.961 50.000 18.80 0.00 38.96 4.69
546 547 0.249741 ACACTTTTCACCGGACGGAG 60.250 55.000 18.80 10.03 38.96 4.63
547 548 0.949105 CACTTTTCACCGGACGGAGG 60.949 60.000 18.80 9.15 38.96 4.30
548 549 1.375523 CTTTTCACCGGACGGAGGG 60.376 63.158 18.80 6.62 38.96 4.30
549 550 1.823169 CTTTTCACCGGACGGAGGGA 61.823 60.000 18.80 8.89 38.96 4.20
550 551 1.823169 TTTTCACCGGACGGAGGGAG 61.823 60.000 18.80 2.08 38.96 4.30
572 573 7.860872 GGGAGTACAAATTTGAACTAAACACTG 59.139 37.037 24.64 0.00 0.00 3.66
629 632 9.646522 AATTGAGGTTGCTGATATTTAATACCT 57.353 29.630 0.00 0.00 37.46 3.08
650 653 2.166870 TCTGTTAATGTGGCGGTCGTAT 59.833 45.455 0.00 0.00 0.00 3.06
660 663 3.122948 GTGGCGGTCGTATTTGCATATAG 59.877 47.826 0.00 0.00 0.00 1.31
662 665 2.093783 GCGGTCGTATTTGCATATAGGC 59.906 50.000 1.55 1.55 0.00 3.93
741 744 5.013079 TCTGTGGTTGGTGATCTGAGTTTAT 59.987 40.000 0.00 0.00 0.00 1.40
814 817 7.042658 CCTTACATTAGAGCTTCCGTGATAAAC 60.043 40.741 0.00 0.00 0.00 2.01
884 887 9.502091 TTTGTATCTTATGTCTTTACTTGTGCT 57.498 29.630 0.00 0.00 0.00 4.40
890 893 8.799367 TCTTATGTCTTTACTTGTGCTACAGTA 58.201 33.333 0.00 0.00 0.00 2.74
921 924 1.074248 TTGTTTCCTCTTCCGCCCC 59.926 57.895 0.00 0.00 0.00 5.80
1136 1140 5.882557 ACTGTTCAATCACATATGGAGTTCC 59.117 40.000 7.80 0.00 0.00 3.62
1269 1274 7.418378 ACATACTCCCTCCATCCAAAAATAAA 58.582 34.615 0.00 0.00 0.00 1.40
1273 1278 6.730507 ACTCCCTCCATCCAAAAATAAATGTT 59.269 34.615 0.00 0.00 0.00 2.71
1277 1282 6.119240 TCCATCCAAAAATAAATGTTGCCA 57.881 33.333 0.00 0.00 0.00 4.92
1321 1326 6.549912 AAACTACGACACTTATTTTGGGAC 57.450 37.500 0.00 0.00 0.00 4.46
1325 1330 2.671396 CGACACTTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
1360 1365 6.119144 TGTTGTTTTCTTCTGTGCTTCTAC 57.881 37.500 0.00 0.00 0.00 2.59
1366 1371 5.474578 TTCTTCTGTGCTTCTACTCACAT 57.525 39.130 0.00 0.00 41.69 3.21
1410 1415 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
1513 1530 3.621805 TCGGACCCTTCGCAAGCA 61.622 61.111 0.00 0.00 37.18 3.91
1648 1665 2.011947 TCAAGCAGCATTCGATCCTTG 58.988 47.619 0.00 0.00 0.00 3.61
1779 1796 6.271566 CCTTTAGGGTATCGTCTAACTTGTC 58.728 44.000 0.00 0.00 0.00 3.18
1794 1811 7.797123 GTCTAACTTGTCACATTAAGGTTTTCG 59.203 37.037 0.00 0.00 0.00 3.46
1982 2001 7.288810 TCCACAAAGATGTAGCAAGAATTTT 57.711 32.000 0.00 0.00 37.82 1.82
1986 2005 6.421801 ACAAAGATGTAGCAAGAATTTTGTGC 59.578 34.615 5.83 1.79 38.24 4.57
1989 2008 5.945784 AGATGTAGCAAGAATTTTGTGCCTA 59.054 36.000 5.59 0.00 39.13 3.93
2034 2053 5.359756 TCATGAAGTACACTGATATGCACC 58.640 41.667 0.00 0.00 0.00 5.01
2039 2058 4.759782 AGTACACTGATATGCACCAGTTC 58.240 43.478 13.55 8.77 41.26 3.01
2260 2280 0.745845 AGCCGCTTGATGGTGCTAAG 60.746 55.000 0.00 0.00 0.00 2.18
2320 2340 1.216977 CCCGAGTGTTGCCACGATA 59.783 57.895 0.00 0.00 46.56 2.92
2456 2476 0.250234 CTCAATCGGAAGGAGGCACA 59.750 55.000 2.35 0.00 0.00 4.57
2734 2754 0.966920 ACAACCTCGTCCACTACCAG 59.033 55.000 0.00 0.00 0.00 4.00
2770 2790 2.283966 CTGGTGGAGACCCCGTCT 60.284 66.667 0.00 0.00 46.42 4.18
2866 2886 2.583593 GAGCGGACCAGCGACATC 60.584 66.667 0.00 0.00 43.00 3.06
2941 2961 1.227263 CCATCCGTACCTGAAGGCG 60.227 63.158 0.00 0.00 39.32 5.52
3016 3036 2.266055 GGGACCAAGGAGCTCGTG 59.734 66.667 10.16 9.30 0.00 4.35
3112 3132 6.408206 CGTTCCTATGGTTAATCCCTTCTCTT 60.408 42.308 0.00 0.00 34.77 2.85
3120 3140 7.565680 TGGTTAATCCCTTCTCTTAAGTGATC 58.434 38.462 8.00 0.00 34.77 2.92
3166 3187 5.008980 GGCGTGTACCTATATCCTAGAACT 58.991 45.833 0.00 0.00 0.00 3.01
3284 3309 2.535331 GGTCGTTGCATGTGTTTGTTT 58.465 42.857 0.00 0.00 0.00 2.83
3285 3310 2.926838 GGTCGTTGCATGTGTTTGTTTT 59.073 40.909 0.00 0.00 0.00 2.43
3345 3375 6.485648 GGACAAAGTTGTATTACAGGTTCTGT 59.514 38.462 5.84 5.84 43.79 3.41
3389 3419 2.144952 AGGTGCCAGTGACACATGA 58.855 52.632 11.90 0.00 39.87 3.07
3390 3420 0.035881 AGGTGCCAGTGACACATGAG 59.964 55.000 11.90 0.00 39.87 2.90
3394 3424 0.604780 GCCAGTGACACATGAGCAGT 60.605 55.000 8.59 0.00 0.00 4.40
3395 3425 1.888215 CCAGTGACACATGAGCAGTT 58.112 50.000 8.59 0.00 0.00 3.16
3404 3434 5.301551 TGACACATGAGCAGTTTATTTGGTT 59.698 36.000 0.00 0.00 0.00 3.67
3406 3436 5.301551 ACACATGAGCAGTTTATTTGGTTGA 59.698 36.000 0.00 0.00 0.00 3.18
3428 3458 2.455674 TATCTGTGTGGCAGTGACAC 57.544 50.000 22.88 22.88 45.23 3.67
3532 3563 2.094700 CGGTCAGGAATTCAGAAGTCGA 60.095 50.000 7.93 0.00 0.00 4.20
3541 3572 5.927115 GGAATTCAGAAGTCGAAAGTGTAGT 59.073 40.000 7.93 0.00 0.00 2.73
3553 3584 1.817357 AGTGTAGTCGTGTCCATCGA 58.183 50.000 0.00 0.00 34.91 3.59
3554 3585 2.156917 AGTGTAGTCGTGTCCATCGAA 58.843 47.619 0.00 0.00 39.01 3.71
3555 3586 2.095364 AGTGTAGTCGTGTCCATCGAAC 60.095 50.000 0.00 0.00 39.01 3.95
3556 3587 1.135888 TGTAGTCGTGTCCATCGAACG 60.136 52.381 0.20 0.20 39.01 3.95
3621 3653 2.740055 GGTGCAGCCACTCTGTCG 60.740 66.667 4.03 0.00 44.66 4.35
3631 3663 3.639094 AGCCACTCTGTCGAATATAAGCT 59.361 43.478 0.00 0.00 0.00 3.74
3672 3710 0.389948 GAGATCAACCCAACGCGTCT 60.390 55.000 14.44 0.48 0.00 4.18
3707 3745 1.005215 CATTCCCCACTTTCTCAGGCT 59.995 52.381 0.00 0.00 0.00 4.58
3709 3747 1.573108 TCCCCACTTTCTCAGGCTAG 58.427 55.000 0.00 0.00 0.00 3.42
3735 3775 2.491621 CACCAGCTCGATCTCGCA 59.508 61.111 5.98 0.00 39.60 5.10
4025 4081 2.664081 CCTCGGGAAGCTGAGCCTT 61.664 63.158 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.026803 GCACCAACGCTCGATCAATC 59.973 55.000 0.00 0.00 0.00 2.67
52 53 2.513897 GGAAGGGCCACGGAATCG 60.514 66.667 6.18 0.00 43.02 3.34
150 151 2.689983 GTTTATGCACATCCCCTGGAAG 59.310 50.000 0.00 0.00 34.34 3.46
151 152 2.042297 TGTTTATGCACATCCCCTGGAA 59.958 45.455 0.00 0.00 34.34 3.53
189 190 7.592938 TGTTTAAACTGTGCTTATCATTGGAG 58.407 34.615 18.72 0.00 0.00 3.86
220 221 1.672881 GAAAATATGGCACGCTGCTCT 59.327 47.619 9.31 1.66 44.28 4.09
260 261 6.640518 TCCAAATATACACTCTTCACCAGAC 58.359 40.000 0.00 0.00 0.00 3.51
263 264 9.967451 TTAAATCCAAATATACACTCTTCACCA 57.033 29.630 0.00 0.00 0.00 4.17
281 282 9.323985 CTCTTTTGTGGACAAATTTTAAATCCA 57.676 29.630 5.80 3.79 44.30 3.41
284 285 9.665719 ACACTCTTTTGTGGACAAATTTTAAAT 57.334 25.926 5.80 0.00 44.30 1.40
296 297 7.540474 AGATAGAAGTACACTCTTTTGTGGA 57.460 36.000 3.13 0.00 41.84 4.02
297 298 7.332182 GGAAGATAGAAGTACACTCTTTTGTGG 59.668 40.741 3.13 0.00 41.84 4.17
298 299 7.332182 GGGAAGATAGAAGTACACTCTTTTGTG 59.668 40.741 3.13 0.00 43.07 3.33
299 300 7.016268 TGGGAAGATAGAAGTACACTCTTTTGT 59.984 37.037 3.13 0.00 0.00 2.83
300 301 7.386851 TGGGAAGATAGAAGTACACTCTTTTG 58.613 38.462 3.13 0.00 0.00 2.44
301 302 7.554959 TGGGAAGATAGAAGTACACTCTTTT 57.445 36.000 3.13 0.00 0.00 2.27
302 303 7.554959 TTGGGAAGATAGAAGTACACTCTTT 57.445 36.000 3.13 0.00 0.00 2.52
303 304 7.560368 CATTGGGAAGATAGAAGTACACTCTT 58.440 38.462 3.13 0.20 0.00 2.85
304 305 6.407525 GCATTGGGAAGATAGAAGTACACTCT 60.408 42.308 0.00 0.00 0.00 3.24
305 306 5.755861 GCATTGGGAAGATAGAAGTACACTC 59.244 44.000 0.00 0.00 0.00 3.51
306 307 5.189736 TGCATTGGGAAGATAGAAGTACACT 59.810 40.000 0.00 0.00 0.00 3.55
308 309 5.189736 AGTGCATTGGGAAGATAGAAGTACA 59.810 40.000 0.00 0.00 0.00 2.90
309 310 5.675538 AGTGCATTGGGAAGATAGAAGTAC 58.324 41.667 0.00 0.00 0.00 2.73
310 311 5.957771 AGTGCATTGGGAAGATAGAAGTA 57.042 39.130 0.00 0.00 0.00 2.24
311 312 4.851639 AGTGCATTGGGAAGATAGAAGT 57.148 40.909 0.00 0.00 0.00 3.01
312 313 7.630242 TTAAAGTGCATTGGGAAGATAGAAG 57.370 36.000 0.00 0.00 0.00 2.85
313 314 7.669722 ACTTTAAAGTGCATTGGGAAGATAGAA 59.330 33.333 19.94 0.00 37.98 2.10
315 316 7.396540 ACTTTAAAGTGCATTGGGAAGATAG 57.603 36.000 19.94 0.00 37.98 2.08
316 317 7.775053 AACTTTAAAGTGCATTGGGAAGATA 57.225 32.000 21.22 0.00 39.66 1.98
344 345 6.152323 CCATGTGATGAGAGAGGAACATTTTT 59.848 38.462 0.00 0.00 0.00 1.94
345 346 5.651139 CCATGTGATGAGAGAGGAACATTTT 59.349 40.000 0.00 0.00 0.00 1.82
346 347 5.191426 CCATGTGATGAGAGAGGAACATTT 58.809 41.667 0.00 0.00 0.00 2.32
347 348 4.226846 ACCATGTGATGAGAGAGGAACATT 59.773 41.667 0.00 0.00 0.00 2.71
349 350 3.176411 ACCATGTGATGAGAGAGGAACA 58.824 45.455 0.00 0.00 0.00 3.18
350 351 3.902881 ACCATGTGATGAGAGAGGAAC 57.097 47.619 0.00 0.00 0.00 3.62
352 353 5.211201 TGATTACCATGTGATGAGAGAGGA 58.789 41.667 0.00 0.00 0.00 3.71
353 354 5.541953 TGATTACCATGTGATGAGAGAGG 57.458 43.478 0.00 0.00 0.00 3.69
355 356 6.407412 GGTCTTGATTACCATGTGATGAGAGA 60.407 42.308 0.00 0.00 36.96 3.10
356 357 5.757320 GGTCTTGATTACCATGTGATGAGAG 59.243 44.000 0.00 0.00 36.96 3.20
358 359 5.430886 TGGTCTTGATTACCATGTGATGAG 58.569 41.667 0.00 0.00 42.10 2.90
359 360 5.434182 TGGTCTTGATTACCATGTGATGA 57.566 39.130 0.00 0.00 42.10 2.92
360 361 6.704289 ATTGGTCTTGATTACCATGTGATG 57.296 37.500 0.00 0.00 46.16 3.07
361 362 7.833682 TGTTATTGGTCTTGATTACCATGTGAT 59.166 33.333 0.00 0.00 46.16 3.06
362 363 7.171653 TGTTATTGGTCTTGATTACCATGTGA 58.828 34.615 0.00 0.00 46.16 3.58
363 364 7.389803 TGTTATTGGTCTTGATTACCATGTG 57.610 36.000 0.00 0.00 46.16 3.21
364 365 8.593945 AATGTTATTGGTCTTGATTACCATGT 57.406 30.769 0.00 0.00 46.16 3.21
365 366 8.906867 AGAATGTTATTGGTCTTGATTACCATG 58.093 33.333 0.00 0.00 46.16 3.66
367 368 9.391006 GTAGAATGTTATTGGTCTTGATTACCA 57.609 33.333 0.00 0.00 45.26 3.25
368 369 9.391006 TGTAGAATGTTATTGGTCTTGATTACC 57.609 33.333 0.00 0.00 37.53 2.85
370 371 9.952030 TGTGTAGAATGTTATTGGTCTTGATTA 57.048 29.630 0.00 0.00 0.00 1.75
371 372 8.730680 GTGTGTAGAATGTTATTGGTCTTGATT 58.269 33.333 0.00 0.00 0.00 2.57
372 373 7.064609 CGTGTGTAGAATGTTATTGGTCTTGAT 59.935 37.037 0.00 0.00 0.00 2.57
373 374 6.367695 CGTGTGTAGAATGTTATTGGTCTTGA 59.632 38.462 0.00 0.00 0.00 3.02
374 375 6.402118 CCGTGTGTAGAATGTTATTGGTCTTG 60.402 42.308 0.00 0.00 0.00 3.02
375 376 5.642063 CCGTGTGTAGAATGTTATTGGTCTT 59.358 40.000 0.00 0.00 0.00 3.01
376 377 5.175859 CCGTGTGTAGAATGTTATTGGTCT 58.824 41.667 0.00 0.00 0.00 3.85
377 378 4.933400 ACCGTGTGTAGAATGTTATTGGTC 59.067 41.667 0.00 0.00 0.00 4.02
378 379 4.901868 ACCGTGTGTAGAATGTTATTGGT 58.098 39.130 0.00 0.00 0.00 3.67
379 380 5.175859 AGACCGTGTGTAGAATGTTATTGG 58.824 41.667 0.00 0.00 0.00 3.16
380 381 6.590292 AGAAGACCGTGTGTAGAATGTTATTG 59.410 38.462 0.00 0.00 0.00 1.90
381 382 6.698380 AGAAGACCGTGTGTAGAATGTTATT 58.302 36.000 0.00 0.00 0.00 1.40
382 383 6.282199 AGAAGACCGTGTGTAGAATGTTAT 57.718 37.500 0.00 0.00 0.00 1.89
383 384 5.717078 AGAAGACCGTGTGTAGAATGTTA 57.283 39.130 0.00 0.00 0.00 2.41
384 385 4.602340 AGAAGACCGTGTGTAGAATGTT 57.398 40.909 0.00 0.00 0.00 2.71
385 386 4.602340 AAGAAGACCGTGTGTAGAATGT 57.398 40.909 0.00 0.00 0.00 2.71
386 387 7.596749 AATTAAGAAGACCGTGTGTAGAATG 57.403 36.000 0.00 0.00 0.00 2.67
387 388 8.095169 AGAAATTAAGAAGACCGTGTGTAGAAT 58.905 33.333 0.00 0.00 0.00 2.40
388 389 7.439381 AGAAATTAAGAAGACCGTGTGTAGAA 58.561 34.615 0.00 0.00 0.00 2.10
389 390 6.989659 AGAAATTAAGAAGACCGTGTGTAGA 58.010 36.000 0.00 0.00 0.00 2.59
390 391 7.811236 TGTAGAAATTAAGAAGACCGTGTGTAG 59.189 37.037 0.00 0.00 0.00 2.74
391 392 7.660112 TGTAGAAATTAAGAAGACCGTGTGTA 58.340 34.615 0.00 0.00 0.00 2.90
392 393 6.518493 TGTAGAAATTAAGAAGACCGTGTGT 58.482 36.000 0.00 0.00 0.00 3.72
393 394 7.456253 CATGTAGAAATTAAGAAGACCGTGTG 58.544 38.462 0.00 0.00 0.00 3.82
394 395 6.092259 GCATGTAGAAATTAAGAAGACCGTGT 59.908 38.462 0.00 0.00 0.00 4.49
395 396 6.092122 TGCATGTAGAAATTAAGAAGACCGTG 59.908 38.462 0.00 0.00 0.00 4.94
396 397 6.092259 GTGCATGTAGAAATTAAGAAGACCGT 59.908 38.462 0.00 0.00 0.00 4.83
397 398 6.313905 AGTGCATGTAGAAATTAAGAAGACCG 59.686 38.462 0.00 0.00 0.00 4.79
398 399 7.617041 AGTGCATGTAGAAATTAAGAAGACC 57.383 36.000 0.00 0.00 0.00 3.85
400 401 8.883731 GCTAAGTGCATGTAGAAATTAAGAAGA 58.116 33.333 10.04 0.00 42.31 2.87
401 402 8.887717 AGCTAAGTGCATGTAGAAATTAAGAAG 58.112 33.333 10.04 0.00 45.94 2.85
402 403 8.792830 AGCTAAGTGCATGTAGAAATTAAGAA 57.207 30.769 10.04 0.00 45.94 2.52
403 404 8.040727 TGAGCTAAGTGCATGTAGAAATTAAGA 58.959 33.333 10.04 0.00 45.94 2.10
404 405 8.201554 TGAGCTAAGTGCATGTAGAAATTAAG 57.798 34.615 10.04 0.00 45.94 1.85
405 406 8.737168 ATGAGCTAAGTGCATGTAGAAATTAA 57.263 30.769 10.04 0.00 45.94 1.40
406 407 8.615211 CAATGAGCTAAGTGCATGTAGAAATTA 58.385 33.333 10.04 0.00 45.94 1.40
407 408 7.415989 CCAATGAGCTAAGTGCATGTAGAAATT 60.416 37.037 10.04 4.39 45.94 1.82
408 409 6.039047 CCAATGAGCTAAGTGCATGTAGAAAT 59.961 38.462 10.04 0.00 45.94 2.17
409 410 5.355071 CCAATGAGCTAAGTGCATGTAGAAA 59.645 40.000 10.04 0.00 45.94 2.52
410 411 4.877823 CCAATGAGCTAAGTGCATGTAGAA 59.122 41.667 10.04 0.00 45.94 2.10
411 412 4.445453 CCAATGAGCTAAGTGCATGTAGA 58.555 43.478 10.04 0.00 45.94 2.59
412 413 3.562973 CCCAATGAGCTAAGTGCATGTAG 59.437 47.826 0.00 0.00 45.94 2.74
413 414 3.544684 CCCAATGAGCTAAGTGCATGTA 58.455 45.455 0.00 0.00 45.94 2.29
414 415 2.372264 CCCAATGAGCTAAGTGCATGT 58.628 47.619 0.00 0.00 45.94 3.21
415 416 1.679680 CCCCAATGAGCTAAGTGCATG 59.320 52.381 0.00 0.00 45.94 4.06
416 417 1.410648 CCCCCAATGAGCTAAGTGCAT 60.411 52.381 0.00 0.00 45.94 3.96
417 418 0.034186 CCCCCAATGAGCTAAGTGCA 60.034 55.000 0.00 0.00 45.94 4.57
418 419 0.034089 ACCCCCAATGAGCTAAGTGC 60.034 55.000 0.00 0.00 43.29 4.40
419 420 2.094675 CAACCCCCAATGAGCTAAGTG 58.905 52.381 0.00 0.00 0.00 3.16
420 421 1.005924 CCAACCCCCAATGAGCTAAGT 59.994 52.381 0.00 0.00 0.00 2.24
421 422 1.686115 CCCAACCCCCAATGAGCTAAG 60.686 57.143 0.00 0.00 0.00 2.18
422 423 0.334676 CCCAACCCCCAATGAGCTAA 59.665 55.000 0.00 0.00 0.00 3.09
423 424 0.849094 ACCCAACCCCCAATGAGCTA 60.849 55.000 0.00 0.00 0.00 3.32
424 425 0.849094 TACCCAACCCCCAATGAGCT 60.849 55.000 0.00 0.00 0.00 4.09
425 426 0.040499 TTACCCAACCCCCAATGAGC 59.960 55.000 0.00 0.00 0.00 4.26
426 427 2.846665 ATTACCCAACCCCCAATGAG 57.153 50.000 0.00 0.00 0.00 2.90
427 428 4.694280 TTAATTACCCAACCCCCAATGA 57.306 40.909 0.00 0.00 0.00 2.57
428 429 5.026790 TCTTTAATTACCCAACCCCCAATG 58.973 41.667 0.00 0.00 0.00 2.82
429 430 5.277250 CTCTTTAATTACCCAACCCCCAAT 58.723 41.667 0.00 0.00 0.00 3.16
430 431 4.511294 CCTCTTTAATTACCCAACCCCCAA 60.511 45.833 0.00 0.00 0.00 4.12
431 432 3.011934 CCTCTTTAATTACCCAACCCCCA 59.988 47.826 0.00 0.00 0.00 4.96
432 433 3.270169 TCCTCTTTAATTACCCAACCCCC 59.730 47.826 0.00 0.00 0.00 5.40
433 434 4.228895 TCTCCTCTTTAATTACCCAACCCC 59.771 45.833 0.00 0.00 0.00 4.95
434 435 5.191124 TCTCTCCTCTTTAATTACCCAACCC 59.809 44.000 0.00 0.00 0.00 4.11
435 436 6.309389 TCTCTCCTCTTTAATTACCCAACC 57.691 41.667 0.00 0.00 0.00 3.77
436 437 6.768381 CCATCTCTCCTCTTTAATTACCCAAC 59.232 42.308 0.00 0.00 0.00 3.77
437 438 6.447084 ACCATCTCTCCTCTTTAATTACCCAA 59.553 38.462 0.00 0.00 0.00 4.12
438 439 5.970640 ACCATCTCTCCTCTTTAATTACCCA 59.029 40.000 0.00 0.00 0.00 4.51
439 440 6.292150 CACCATCTCTCCTCTTTAATTACCC 58.708 44.000 0.00 0.00 0.00 3.69
440 441 6.292150 CCACCATCTCTCCTCTTTAATTACC 58.708 44.000 0.00 0.00 0.00 2.85
441 442 5.760743 GCCACCATCTCTCCTCTTTAATTAC 59.239 44.000 0.00 0.00 0.00 1.89
442 443 5.667626 AGCCACCATCTCTCCTCTTTAATTA 59.332 40.000 0.00 0.00 0.00 1.40
443 444 4.476479 AGCCACCATCTCTCCTCTTTAATT 59.524 41.667 0.00 0.00 0.00 1.40
444 445 4.043596 AGCCACCATCTCTCCTCTTTAAT 58.956 43.478 0.00 0.00 0.00 1.40
445 446 3.454858 AGCCACCATCTCTCCTCTTTAA 58.545 45.455 0.00 0.00 0.00 1.52
446 447 3.121929 AGCCACCATCTCTCCTCTTTA 57.878 47.619 0.00 0.00 0.00 1.85
447 448 1.963985 AGCCACCATCTCTCCTCTTT 58.036 50.000 0.00 0.00 0.00 2.52
448 449 1.558756 CAAGCCACCATCTCTCCTCTT 59.441 52.381 0.00 0.00 0.00 2.85
449 450 1.202330 CAAGCCACCATCTCTCCTCT 58.798 55.000 0.00 0.00 0.00 3.69
450 451 0.463474 GCAAGCCACCATCTCTCCTC 60.463 60.000 0.00 0.00 0.00 3.71
451 452 1.203441 TGCAAGCCACCATCTCTCCT 61.203 55.000 0.00 0.00 0.00 3.69
452 453 1.028868 GTGCAAGCCACCATCTCTCC 61.029 60.000 0.00 0.00 38.55 3.71
453 454 2.475666 GTGCAAGCCACCATCTCTC 58.524 57.895 0.00 0.00 38.55 3.20
454 455 4.730487 GTGCAAGCCACCATCTCT 57.270 55.556 0.00 0.00 38.55 3.10
461 462 1.406539 CATTGGATAGGTGCAAGCCAC 59.593 52.381 0.00 0.00 39.12 5.01
462 463 1.766494 CATTGGATAGGTGCAAGCCA 58.234 50.000 0.00 0.00 39.12 4.75
463 464 0.386838 GCATTGGATAGGTGCAAGCC 59.613 55.000 0.00 0.00 39.12 4.35
464 465 1.105457 TGCATTGGATAGGTGCAAGC 58.895 50.000 0.00 0.00 44.99 4.01
485 486 7.511028 AGGACAAATTATGAAGTGGGGTAAAAA 59.489 33.333 0.00 0.00 0.00 1.94
486 487 7.013834 AGGACAAATTATGAAGTGGGGTAAAA 58.986 34.615 0.00 0.00 0.00 1.52
487 488 6.557568 AGGACAAATTATGAAGTGGGGTAAA 58.442 36.000 0.00 0.00 0.00 2.01
488 489 6.147437 AGGACAAATTATGAAGTGGGGTAA 57.853 37.500 0.00 0.00 0.00 2.85
489 490 5.789574 AGGACAAATTATGAAGTGGGGTA 57.210 39.130 0.00 0.00 0.00 3.69
490 491 4.675063 AGGACAAATTATGAAGTGGGGT 57.325 40.909 0.00 0.00 0.00 4.95
491 492 7.475137 TTTTAGGACAAATTATGAAGTGGGG 57.525 36.000 0.00 0.00 0.00 4.96
492 493 9.942850 AAATTTTAGGACAAATTATGAAGTGGG 57.057 29.630 0.00 0.00 35.67 4.61
514 515 8.889717 CCGGTGAAAAGTGTACATATAGAAATT 58.110 33.333 0.00 0.00 0.00 1.82
515 516 8.262227 TCCGGTGAAAAGTGTACATATAGAAAT 58.738 33.333 0.00 0.00 0.00 2.17
516 517 7.546667 GTCCGGTGAAAAGTGTACATATAGAAA 59.453 37.037 0.00 0.00 0.00 2.52
517 518 7.037438 GTCCGGTGAAAAGTGTACATATAGAA 58.963 38.462 0.00 0.00 0.00 2.10
518 519 6.567050 GTCCGGTGAAAAGTGTACATATAGA 58.433 40.000 0.00 0.00 0.00 1.98
519 520 5.457799 CGTCCGGTGAAAAGTGTACATATAG 59.542 44.000 0.00 0.00 0.00 1.31
520 521 5.342433 CGTCCGGTGAAAAGTGTACATATA 58.658 41.667 0.00 0.00 0.00 0.86
521 522 4.178540 CGTCCGGTGAAAAGTGTACATAT 58.821 43.478 0.00 0.00 0.00 1.78
522 523 3.577667 CGTCCGGTGAAAAGTGTACATA 58.422 45.455 0.00 0.00 0.00 2.29
523 524 2.409975 CGTCCGGTGAAAAGTGTACAT 58.590 47.619 0.00 0.00 0.00 2.29
524 525 1.538634 CCGTCCGGTGAAAAGTGTACA 60.539 52.381 0.00 0.00 0.00 2.90
525 526 1.142474 CCGTCCGGTGAAAAGTGTAC 58.858 55.000 0.00 0.00 0.00 2.90
526 527 1.000060 CTCCGTCCGGTGAAAAGTGTA 60.000 52.381 0.00 0.00 36.47 2.90
527 528 0.249741 CTCCGTCCGGTGAAAAGTGT 60.250 55.000 0.00 0.00 36.47 3.55
528 529 0.949105 CCTCCGTCCGGTGAAAAGTG 60.949 60.000 0.00 0.00 36.47 3.16
529 530 1.370064 CCTCCGTCCGGTGAAAAGT 59.630 57.895 0.00 0.00 36.47 2.66
530 531 1.375523 CCCTCCGTCCGGTGAAAAG 60.376 63.158 0.00 0.00 36.47 2.27
531 532 1.823169 CTCCCTCCGTCCGGTGAAAA 61.823 60.000 0.00 0.00 36.47 2.29
532 533 2.203669 TCCCTCCGTCCGGTGAAA 60.204 61.111 0.00 0.00 36.47 2.69
533 534 2.141011 TACTCCCTCCGTCCGGTGAA 62.141 60.000 0.00 0.00 36.47 3.18
534 535 2.605607 TACTCCCTCCGTCCGGTGA 61.606 63.158 0.00 0.00 36.47 4.02
535 536 2.044650 TACTCCCTCCGTCCGGTG 60.045 66.667 0.00 3.10 36.47 4.94
536 537 2.044551 GTACTCCCTCCGTCCGGT 60.045 66.667 0.00 0.00 36.47 5.28
537 538 1.252904 TTTGTACTCCCTCCGTCCGG 61.253 60.000 0.00 0.00 0.00 5.14
538 539 0.822164 ATTTGTACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
539 540 3.007635 CAAATTTGTACTCCCTCCGTCC 58.992 50.000 10.15 0.00 0.00 4.79
540 541 3.934068 TCAAATTTGTACTCCCTCCGTC 58.066 45.455 17.47 0.00 0.00 4.79
541 542 4.070009 GTTCAAATTTGTACTCCCTCCGT 58.930 43.478 17.47 0.00 0.00 4.69
542 543 4.324267 AGTTCAAATTTGTACTCCCTCCG 58.676 43.478 20.89 0.00 34.29 4.63
543 544 7.229907 TGTTTAGTTCAAATTTGTACTCCCTCC 59.770 37.037 27.39 15.43 39.18 4.30
544 545 8.074370 GTGTTTAGTTCAAATTTGTACTCCCTC 58.926 37.037 27.39 18.14 39.18 4.30
545 546 7.778382 AGTGTTTAGTTCAAATTTGTACTCCCT 59.222 33.333 27.39 16.34 39.18 4.20
546 547 7.860872 CAGTGTTTAGTTCAAATTTGTACTCCC 59.139 37.037 27.39 18.33 39.18 4.30
547 548 8.617809 TCAGTGTTTAGTTCAAATTTGTACTCC 58.382 33.333 27.39 18.60 39.18 3.85
548 549 9.997482 TTCAGTGTTTAGTTCAAATTTGTACTC 57.003 29.630 27.39 16.95 39.18 2.59
550 551 8.743099 GCTTCAGTGTTTAGTTCAAATTTGTAC 58.257 33.333 17.43 17.43 0.00 2.90
591 594 4.574013 GCAACCTCAATTACCAGATCTCTG 59.426 45.833 0.00 0.00 43.40 3.35
592 595 4.472833 AGCAACCTCAATTACCAGATCTCT 59.527 41.667 0.00 0.00 0.00 3.10
626 629 0.690762 ACCGCCACATTAACAGAGGT 59.309 50.000 0.00 0.00 0.00 3.85
629 632 0.319083 ACGACCGCCACATTAACAGA 59.681 50.000 0.00 0.00 0.00 3.41
639 642 2.248280 ATATGCAAATACGACCGCCA 57.752 45.000 0.00 0.00 0.00 5.69
814 817 4.068640 AGGGAGGAGTGCCTTTTGAATTG 61.069 47.826 0.00 0.00 43.40 2.32
1136 1140 5.639506 CCCATAACTAAGTTGAGTGACTGTG 59.360 44.000 0.00 0.00 0.00 3.66
1302 1307 3.257873 TCCGTCCCAAAATAAGTGTCGTA 59.742 43.478 0.00 0.00 0.00 3.43
1321 1326 0.964358 AACAGTACTCCGTCCCTCCG 60.964 60.000 0.00 0.00 0.00 4.63
1325 1330 2.538512 AAACAACAGTACTCCGTCCC 57.461 50.000 0.00 0.00 0.00 4.46
1338 1343 6.037172 TGAGTAGAAGCACAGAAGAAAACAAC 59.963 38.462 0.00 0.00 0.00 3.32
1360 1365 3.495806 GGCTCCCCTTCAGAATATGTGAG 60.496 52.174 0.00 0.00 0.00 3.51
1390 1395 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
1426 1431 2.034685 GCTGTTTCCAGGACTTGAAACC 59.965 50.000 19.88 7.59 46.13 3.27
1428 1433 2.091885 AGGCTGTTTCCAGGACTTGAAA 60.092 45.455 0.00 0.00 39.22 2.69
1456 1461 1.818674 CGCAGCCTTTCCCTACATTTT 59.181 47.619 0.00 0.00 0.00 1.82
1458 1463 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
1648 1665 4.497674 GCAGATCAATCAGAGAATGTTGGC 60.498 45.833 0.00 0.00 0.00 4.52
1779 1796 9.458374 AAGTTCAATAACGAAAACCTTAATGTG 57.542 29.630 0.00 0.00 40.73 3.21
1939 1958 7.028926 TGTGGAAGCGTTCAAATAGTTTTAA 57.971 32.000 0.00 0.00 0.00 1.52
1941 1960 5.508200 TGTGGAAGCGTTCAAATAGTTTT 57.492 34.783 0.00 0.00 0.00 2.43
1982 2001 6.118852 TGACACAAATGCTAATATAGGCACA 58.881 36.000 4.92 0.00 41.39 4.57
1989 2008 9.908152 CATGAATCATGACACAAATGCTAATAT 57.092 29.630 17.76 0.00 43.81 1.28
2056 2076 6.834168 TTCATCCCAACAGAATTAACTTCC 57.166 37.500 0.00 0.00 34.11 3.46
2456 2476 0.251922 AGCAACATGGCCTTGGACAT 60.252 50.000 21.67 1.40 0.00 3.06
2578 2598 5.200368 AGACATCCACCAAAATGTGTTTC 57.800 39.130 0.00 0.00 36.28 2.78
2647 2667 4.416738 GGCTCTGCCCACACCTCC 62.417 72.222 0.00 0.00 44.06 4.30
2734 2754 3.304928 CCAGACAATTGAACTTCTGGTGC 60.305 47.826 24.67 0.00 46.94 5.01
2770 2790 1.788229 TGACCCTTATGAGATCGCCA 58.212 50.000 0.00 0.00 0.00 5.69
2866 2886 2.045340 AACAGCCCGAATTCCCCG 60.045 61.111 0.00 0.00 0.00 5.73
3112 3132 2.745102 TCGCACACGTTTGATCACTTA 58.255 42.857 5.75 0.00 41.18 2.24
3120 3140 0.027455 TTCAGCTTCGCACACGTTTG 59.973 50.000 0.00 0.00 41.18 2.93
3166 3187 4.399483 AGTTAGGGAGTTCAGAGTACCA 57.601 45.455 0.00 0.00 30.73 3.25
3299 3326 2.740981 CAAAAACACAAGCCAGTTGCAA 59.259 40.909 0.00 0.00 44.83 4.08
3345 3375 1.075601 AGGAGGGAGAATGGCAAACA 58.924 50.000 0.00 0.00 0.00 2.83
3389 3419 7.394359 ACAGATATGTCAACCAAATAAACTGCT 59.606 33.333 0.00 0.00 0.00 4.24
3390 3420 7.485913 CACAGATATGTCAACCAAATAAACTGC 59.514 37.037 0.00 0.00 0.00 4.40
3394 3424 7.576666 GCCACACAGATATGTCAACCAAATAAA 60.577 37.037 0.00 0.00 0.00 1.40
3395 3425 6.127758 GCCACACAGATATGTCAACCAAATAA 60.128 38.462 0.00 0.00 0.00 1.40
3428 3458 1.004610 CGCGGAAATACACTGCTGATG 60.005 52.381 0.00 0.00 37.48 3.07
3429 3459 1.134818 TCGCGGAAATACACTGCTGAT 60.135 47.619 6.13 0.00 37.48 2.90
3430 3460 0.245266 TCGCGGAAATACACTGCTGA 59.755 50.000 6.13 0.00 37.48 4.26
3431 3461 1.075542 TTCGCGGAAATACACTGCTG 58.924 50.000 6.13 0.00 37.48 4.41
3455 3485 8.340757 ACCAAATTACTCCTGGGAAATTACATA 58.659 33.333 0.00 0.00 34.31 2.29
3456 3486 7.189087 ACCAAATTACTCCTGGGAAATTACAT 58.811 34.615 0.00 0.00 34.31 2.29
3461 3492 6.322931 AGAAACCAAATTACTCCTGGGAAAT 58.677 36.000 0.00 0.00 34.31 2.17
3463 3494 5.333566 AGAAACCAAATTACTCCTGGGAA 57.666 39.130 0.00 0.00 34.31 3.97
3532 3563 2.555325 TCGATGGACACGACTACACTTT 59.445 45.455 0.00 0.00 34.85 2.66
3541 3572 0.726787 CGTTCGTTCGATGGACACGA 60.727 55.000 5.24 5.24 41.05 4.35
3631 3663 0.104120 CACGGGATGAGATGCGGTTA 59.896 55.000 0.00 0.00 32.13 2.85
3672 3710 1.352114 GAATGGCTACGCACGTGTTA 58.648 50.000 18.38 8.06 0.00 2.41
3707 3745 4.457496 GCTGGTGCTGCCGCTCTA 62.457 66.667 0.70 0.00 41.21 2.43


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

AutoCloner maintained by Alex Coulton.