Multiple sequence alignment - TraesCS5D01G237900

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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 TraesCS5D01G237900 chr5D 100.000 3989 0 0 1 3989 345977100 345981088 0.000000e+00 7367.0
1 TraesCS5D01G237900 chr5B 96.156 2966 71 14 1046 3989 405554618 405551674 0.000000e+00 4806.0
2 TraesCS5D01G237900 chr5B 93.878 49 1 1 972 1018 405554720 405554672 5.530000e-09 73.1
3 TraesCS5D01G237900 chr5A 95.342 2662 84 17 891 3533 445199694 445197054 0.000000e+00 4193.0
4 TraesCS5D01G237900 chr5A 95.051 586 11 7 3407 3989 445197054 445196484 0.000000e+00 905.0
5 TraesCS5D01G237900 chr5A 78.719 437 72 13 406 834 445200505 445200082 5.080000e-69 272.0
6 TraesCS5D01G237900 chr5A 91.549 71 5 1 1 71 445200811 445200742 3.280000e-16 97.1
7 TraesCS5D01G237900 chr6D 77.949 195 37 5 623 815 347162294 347162104 2.520000e-22 117.0
8 TraesCS5D01G237900 chr3A 74.895 239 46 11 624 854 73569876 73570108 3.280000e-16 97.1
9 TraesCS5D01G237900 chr4A 89.091 55 4 2 627 681 43371620 43371568 2.570000e-07 67.6
10 TraesCS5D01G237900 chr2D 94.286 35 1 1 571 605 643161368 643161401 7.000000e-03 52.8


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 TraesCS5D01G237900 chr5D 345977100 345981088 3988 False 7367.000 7367 100.00000 1 3989 1 chr5D.!!$F1 3988
1 TraesCS5D01G237900 chr5B 405551674 405554720 3046 True 2439.550 4806 95.01700 972 3989 2 chr5B.!!$R1 3017
2 TraesCS5D01G237900 chr5A 445196484 445200811 4327 True 1366.775 4193 90.16525 1 3989 4 chr5A.!!$R1 3988

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
690 749 0.107017 CAGGCCTTCCGGTGATTCAT 60.107 55.0 0.0 0.0 37.47 2.57 F
837 897 0.459899 TAGGAGGCAGTGTATGTGCG 59.540 55.0 0.0 0.0 42.19 5.34 F
1911 2358 0.036022 AGGAACTGCTGAAGAGTGGC 59.964 55.0 0.0 0.0 37.18 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2236 1.134907 CATCCCTGTTTGCTTCATGGC 60.135 52.381 0.00 0.0 0.00 4.40 R
2324 2771 1.207811 CATTGGGCTCAATTCCAACCC 59.792 52.381 9.73 0.0 44.64 4.11 R
3412 3885 1.134788 AGCGGTTTAGCGTGCTAGATT 60.135 47.619 1.39 0.0 43.00 2.40 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
91 109 1.076705 GGGAGAAGGCATGGGGTTC 60.077 63.158 0.00 0.00 0.00 3.62
92 110 1.575447 GGGAGAAGGCATGGGGTTCT 61.575 60.000 0.00 0.00 33.14 3.01
93 111 0.394899 GGAGAAGGCATGGGGTTCTG 60.395 60.000 0.00 0.00 30.55 3.02
108 160 3.308530 GGTTCTGAAAAATGGCTCAACG 58.691 45.455 0.00 0.00 0.00 4.10
130 182 1.226945 GCGCCCGGATTCAAATTGG 60.227 57.895 0.73 0.00 0.00 3.16
134 186 1.437160 CCGGATTCAAATTGGGGCG 59.563 57.895 0.00 0.00 0.00 6.13
141 193 1.304052 CAAATTGGGGCGGTCTGGA 60.304 57.895 0.00 0.00 0.00 3.86
145 197 2.270874 ATTGGGGCGGTCTGGATGAC 62.271 60.000 0.00 0.00 44.63 3.06
166 218 1.586154 AAGATGGCACGAAAAGGCGG 61.586 55.000 0.00 0.00 35.12 6.13
187 239 2.268920 CGTGGGAGTGTGGATGGG 59.731 66.667 0.00 0.00 0.00 4.00
189 241 3.338250 TGGGAGTGTGGATGGGGC 61.338 66.667 0.00 0.00 0.00 5.80
224 276 2.354821 GCGTCCTAAAATGTCCATGACC 59.645 50.000 0.00 0.00 0.00 4.02
225 277 3.605634 CGTCCTAAAATGTCCATGACCA 58.394 45.455 0.00 0.00 0.00 4.02
226 278 3.623060 CGTCCTAAAATGTCCATGACCAG 59.377 47.826 0.00 0.00 0.00 4.00
227 279 4.589908 GTCCTAAAATGTCCATGACCAGT 58.410 43.478 0.00 0.00 0.00 4.00
228 280 4.396166 GTCCTAAAATGTCCATGACCAGTG 59.604 45.833 0.00 0.00 0.00 3.66
229 281 3.696051 CCTAAAATGTCCATGACCAGTGG 59.304 47.826 7.91 7.91 38.11 4.00
230 282 1.549203 AAATGTCCATGACCAGTGGC 58.451 50.000 9.78 2.56 36.66 5.01
231 283 0.677731 AATGTCCATGACCAGTGGCG 60.678 55.000 9.78 0.00 36.66 5.69
232 284 2.436646 GTCCATGACCAGTGGCGG 60.437 66.667 9.78 5.08 36.66 6.13
233 285 2.606213 TCCATGACCAGTGGCGGA 60.606 61.111 9.78 7.61 36.66 5.54
249 301 2.147436 CGGAGCTAGCAAAGGATCTC 57.853 55.000 18.83 2.43 0.00 2.75
250 302 1.601663 CGGAGCTAGCAAAGGATCTCG 60.602 57.143 18.83 6.68 0.00 4.04
251 303 1.496934 GAGCTAGCAAAGGATCTCGC 58.503 55.000 18.83 0.00 0.00 5.03
252 304 0.249238 AGCTAGCAAAGGATCTCGCG 60.249 55.000 18.83 0.00 0.00 5.87
253 305 1.826299 GCTAGCAAAGGATCTCGCGC 61.826 60.000 10.63 0.00 0.00 6.86
254 306 1.543941 CTAGCAAAGGATCTCGCGCG 61.544 60.000 26.76 26.76 0.00 6.86
255 307 2.954020 TAGCAAAGGATCTCGCGCGG 62.954 60.000 31.69 20.60 0.00 6.46
256 308 3.929948 CAAAGGATCTCGCGCGGC 61.930 66.667 31.69 16.48 0.00 6.53
279 331 4.382541 GGGTGGGGGAGGGCAAAG 62.383 72.222 0.00 0.00 0.00 2.77
280 332 3.264845 GGTGGGGGAGGGCAAAGA 61.265 66.667 0.00 0.00 0.00 2.52
281 333 2.356667 GTGGGGGAGGGCAAAGAG 59.643 66.667 0.00 0.00 0.00 2.85
282 334 2.209809 TGGGGGAGGGCAAAGAGA 59.790 61.111 0.00 0.00 0.00 3.10
283 335 1.465188 TGGGGGAGGGCAAAGAGAA 60.465 57.895 0.00 0.00 0.00 2.87
284 336 1.071314 TGGGGGAGGGCAAAGAGAAA 61.071 55.000 0.00 0.00 0.00 2.52
285 337 0.114364 GGGGGAGGGCAAAGAGAAAA 59.886 55.000 0.00 0.00 0.00 2.29
286 338 1.273267 GGGGGAGGGCAAAGAGAAAAT 60.273 52.381 0.00 0.00 0.00 1.82
287 339 2.024369 GGGGGAGGGCAAAGAGAAAATA 60.024 50.000 0.00 0.00 0.00 1.40
288 340 3.374208 GGGGGAGGGCAAAGAGAAAATAT 60.374 47.826 0.00 0.00 0.00 1.28
289 341 3.638627 GGGGAGGGCAAAGAGAAAATATG 59.361 47.826 0.00 0.00 0.00 1.78
290 342 3.068732 GGGAGGGCAAAGAGAAAATATGC 59.931 47.826 0.00 0.00 36.31 3.14
291 343 3.701040 GGAGGGCAAAGAGAAAATATGCA 59.299 43.478 0.00 0.00 38.73 3.96
292 344 4.160252 GGAGGGCAAAGAGAAAATATGCAA 59.840 41.667 0.00 0.00 38.73 4.08
293 345 5.077134 AGGGCAAAGAGAAAATATGCAAC 57.923 39.130 0.00 0.00 38.73 4.17
294 346 4.774200 AGGGCAAAGAGAAAATATGCAACT 59.226 37.500 0.00 0.00 38.73 3.16
295 347 5.246883 AGGGCAAAGAGAAAATATGCAACTT 59.753 36.000 0.00 0.00 38.73 2.66
296 348 5.934043 GGGCAAAGAGAAAATATGCAACTTT 59.066 36.000 0.00 0.00 38.73 2.66
297 349 6.128472 GGGCAAAGAGAAAATATGCAACTTTG 60.128 38.462 0.00 0.00 42.72 2.77
298 350 6.128472 GGCAAAGAGAAAATATGCAACTTTGG 60.128 38.462 2.54 0.00 41.26 3.28
299 351 6.424812 GCAAAGAGAAAATATGCAACTTTGGT 59.575 34.615 2.54 3.52 41.26 3.67
300 352 7.569957 GCAAAGAGAAAATATGCAACTTTGGTG 60.570 37.037 2.54 0.00 41.26 4.17
301 353 6.029346 AGAGAAAATATGCAACTTTGGTGG 57.971 37.500 0.00 0.00 0.00 4.61
302 354 5.774690 AGAGAAAATATGCAACTTTGGTGGA 59.225 36.000 0.00 0.00 0.00 4.02
303 355 6.029346 AGAAAATATGCAACTTTGGTGGAG 57.971 37.500 0.00 0.00 0.00 3.86
304 356 4.806640 AAATATGCAACTTTGGTGGAGG 57.193 40.909 0.00 0.00 0.00 4.30
305 357 2.214376 TATGCAACTTTGGTGGAGGG 57.786 50.000 0.00 0.00 0.00 4.30
306 358 0.542702 ATGCAACTTTGGTGGAGGGG 60.543 55.000 0.00 0.00 0.00 4.79
307 359 1.908299 GCAACTTTGGTGGAGGGGG 60.908 63.158 0.00 0.00 0.00 5.40
326 378 2.435372 GGGGGTATGAATGCACTCAA 57.565 50.000 0.23 0.00 0.00 3.02
327 379 2.024414 GGGGGTATGAATGCACTCAAC 58.976 52.381 0.23 2.02 0.00 3.18
328 380 2.357154 GGGGGTATGAATGCACTCAACT 60.357 50.000 0.23 0.00 0.00 3.16
329 381 3.118038 GGGGGTATGAATGCACTCAACTA 60.118 47.826 0.23 0.00 0.00 2.24
330 382 4.523083 GGGGTATGAATGCACTCAACTAA 58.477 43.478 0.23 0.00 0.00 2.24
331 383 4.947388 GGGGTATGAATGCACTCAACTAAA 59.053 41.667 0.23 0.00 0.00 1.85
332 384 5.594317 GGGGTATGAATGCACTCAACTAAAT 59.406 40.000 0.23 0.00 0.00 1.40
333 385 6.096846 GGGGTATGAATGCACTCAACTAAATT 59.903 38.462 0.23 0.00 0.00 1.82
334 386 7.363793 GGGGTATGAATGCACTCAACTAAATTT 60.364 37.037 0.23 0.00 0.00 1.82
335 387 8.682710 GGGTATGAATGCACTCAACTAAATTTA 58.317 33.333 0.23 0.00 0.00 1.40
338 390 8.693542 ATGAATGCACTCAACTAAATTTAAGC 57.306 30.769 0.23 0.00 0.00 3.09
339 391 7.090173 TGAATGCACTCAACTAAATTTAAGCC 58.910 34.615 0.00 0.00 0.00 4.35
340 392 6.840780 ATGCACTCAACTAAATTTAAGCCT 57.159 33.333 0.00 0.00 0.00 4.58
341 393 6.648879 TGCACTCAACTAAATTTAAGCCTT 57.351 33.333 0.00 0.00 0.00 4.35
342 394 6.677913 TGCACTCAACTAAATTTAAGCCTTC 58.322 36.000 0.00 0.00 0.00 3.46
343 395 6.264292 TGCACTCAACTAAATTTAAGCCTTCA 59.736 34.615 0.00 0.00 0.00 3.02
344 396 6.582672 GCACTCAACTAAATTTAAGCCTTCAC 59.417 38.462 0.00 0.00 0.00 3.18
345 397 7.648142 CACTCAACTAAATTTAAGCCTTCACA 58.352 34.615 0.00 0.00 0.00 3.58
346 398 8.134895 CACTCAACTAAATTTAAGCCTTCACAA 58.865 33.333 0.00 0.00 0.00 3.33
347 399 8.691797 ACTCAACTAAATTTAAGCCTTCACAAA 58.308 29.630 0.00 0.00 0.00 2.83
348 400 9.528018 CTCAACTAAATTTAAGCCTTCACAAAA 57.472 29.630 0.00 0.00 0.00 2.44
349 401 9.877178 TCAACTAAATTTAAGCCTTCACAAAAA 57.123 25.926 0.00 0.00 0.00 1.94
373 425 8.738645 AAATTCCTTCAGTACTTAAGCTATGG 57.261 34.615 10.76 0.00 0.00 2.74
374 426 5.277857 TCCTTCAGTACTTAAGCTATGGC 57.722 43.478 10.76 0.00 39.06 4.40
397 449 4.175337 GGCAGCGGCATCCCAGTA 62.175 66.667 11.88 0.00 43.71 2.74
398 450 2.590007 GCAGCGGCATCCCAGTAG 60.590 66.667 3.18 0.00 40.72 2.57
399 451 2.903357 CAGCGGCATCCCAGTAGT 59.097 61.111 1.45 0.00 0.00 2.73
400 452 2.028125 GCAGCGGCATCCCAGTAGTA 62.028 60.000 3.18 0.00 40.72 1.82
401 453 0.249489 CAGCGGCATCCCAGTAGTAC 60.249 60.000 1.45 0.00 0.00 2.73
402 454 0.686441 AGCGGCATCCCAGTAGTACA 60.686 55.000 1.45 0.00 0.00 2.90
403 455 0.393077 GCGGCATCCCAGTAGTACAT 59.607 55.000 2.52 0.00 0.00 2.29
404 456 1.873903 GCGGCATCCCAGTAGTACATG 60.874 57.143 2.52 0.00 0.00 3.21
411 463 5.279657 GCATCCCAGTAGTACATGATCATGA 60.280 44.000 36.37 19.94 41.20 3.07
412 464 6.396450 CATCCCAGTAGTACATGATCATGAG 58.604 44.000 36.37 16.05 41.20 2.90
420 472 1.018910 CATGATCATGAGGCGCAACA 58.981 50.000 28.37 9.20 41.20 3.33
424 476 1.162181 ATCATGAGGCGCAACATCCG 61.162 55.000 10.83 3.57 0.00 4.18
434 486 2.349817 GCGCAACATCCGAATATGAAGG 60.350 50.000 0.30 0.00 0.00 3.46
438 490 4.335315 GCAACATCCGAATATGAAGGTTCA 59.665 41.667 0.00 0.00 42.14 3.18
441 493 3.173668 TCCGAATATGAAGGTTCACGG 57.826 47.619 11.38 11.38 41.61 4.94
442 494 2.159014 TCCGAATATGAAGGTTCACGGG 60.159 50.000 15.51 5.35 41.01 5.28
458 510 1.808343 ACGGGTTGGATTTAAAGCGTC 59.192 47.619 0.00 0.00 0.00 5.19
486 538 7.986085 AAAAATATTATATGGCGAGTGAGCT 57.014 32.000 0.00 0.00 37.29 4.09
507 559 4.800914 GCTCAGGATGACAACTGTGTTAGT 60.801 45.833 9.51 0.00 42.56 2.24
508 560 4.631131 TCAGGATGACAACTGTGTTAGTG 58.369 43.478 9.51 0.00 42.56 2.74
516 568 4.189231 ACAACTGTGTTAGTGTGGTCTTC 58.811 43.478 0.00 0.00 40.26 2.87
529 582 5.471456 AGTGTGGTCTTCTCATCAAAATCAC 59.529 40.000 0.00 0.00 0.00 3.06
550 603 9.719355 AATCACTGTACTAACAATTACATGACA 57.281 29.630 0.00 0.00 34.49 3.58
555 614 9.277565 CTGTACTAACAATTACATGACAATTGC 57.722 33.333 24.58 14.56 43.90 3.56
560 619 6.689178 ACAATTACATGACAATTGCGAAAC 57.311 33.333 24.58 0.00 43.90 2.78
580 639 7.464444 GCGAAACAATTTATGATTGGATGGTTG 60.464 37.037 8.07 0.00 33.56 3.77
584 643 6.098695 ACAATTTATGATTGGATGGTTGGGAG 59.901 38.462 8.07 0.00 33.56 4.30
585 644 5.464588 TTTATGATTGGATGGTTGGGAGA 57.535 39.130 0.00 0.00 0.00 3.71
591 650 1.073763 TGGATGGTTGGGAGAACAGTG 59.926 52.381 0.00 0.00 0.00 3.66
597 656 2.572104 GGTTGGGAGAACAGTGGTATCT 59.428 50.000 2.28 0.00 0.00 1.98
602 661 3.769844 GGGAGAACAGTGGTATCTTCAGA 59.230 47.826 2.28 0.00 0.00 3.27
604 663 4.382147 GGAGAACAGTGGTATCTTCAGACC 60.382 50.000 2.28 0.00 36.17 3.85
613 672 6.566079 TGGTATCTTCAGACCATCAGAATT 57.434 37.500 0.00 0.00 40.87 2.17
614 673 6.962182 TGGTATCTTCAGACCATCAGAATTT 58.038 36.000 0.00 0.00 40.87 1.82
615 674 8.089625 TGGTATCTTCAGACCATCAGAATTTA 57.910 34.615 0.00 0.00 40.87 1.40
616 675 8.548025 TGGTATCTTCAGACCATCAGAATTTAA 58.452 33.333 0.00 0.00 40.87 1.52
617 676 9.050601 GGTATCTTCAGACCATCAGAATTTAAG 57.949 37.037 0.00 0.00 35.65 1.85
618 677 9.606631 GTATCTTCAGACCATCAGAATTTAAGT 57.393 33.333 0.00 0.00 0.00 2.24
619 678 7.912056 TCTTCAGACCATCAGAATTTAAGTG 57.088 36.000 0.00 0.00 0.00 3.16
648 707 5.958083 AAGTGCTAGACTTGACACTGGTGT 61.958 45.833 6.04 6.04 43.71 4.16
650 709 3.060602 GCTAGACTTGACACTGGTGTTC 58.939 50.000 7.82 2.03 45.05 3.18
657 716 2.020720 TGACACTGGTGTTCGCATTTT 58.979 42.857 7.82 0.00 45.05 1.82
658 717 2.032799 TGACACTGGTGTTCGCATTTTC 59.967 45.455 7.82 0.00 45.05 2.29
661 720 1.608590 ACTGGTGTTCGCATTTTCCTG 59.391 47.619 0.00 0.00 0.00 3.86
662 721 1.608590 CTGGTGTTCGCATTTTCCTGT 59.391 47.619 0.00 0.00 0.00 4.00
667 726 5.473846 TGGTGTTCGCATTTTCCTGTATTTA 59.526 36.000 0.00 0.00 0.00 1.40
670 729 8.185505 GGTGTTCGCATTTTCCTGTATTTATTA 58.814 33.333 0.00 0.00 0.00 0.98
683 742 3.945640 ATTTATTACAGGCCTTCCGGT 57.054 42.857 0.00 0.00 43.31 5.28
685 744 1.868713 TATTACAGGCCTTCCGGTGA 58.131 50.000 0.00 0.00 40.99 4.02
689 748 1.299648 CAGGCCTTCCGGTGATTCA 59.700 57.895 0.00 0.00 37.47 2.57
690 749 0.107017 CAGGCCTTCCGGTGATTCAT 60.107 55.000 0.00 0.00 37.47 2.57
696 755 3.081061 CCTTCCGGTGATTCATGTTCAA 58.919 45.455 0.00 0.00 0.00 2.69
700 759 4.331108 TCCGGTGATTCATGTTCAATGAA 58.669 39.130 0.00 3.43 41.59 2.57
703 762 5.097529 CGGTGATTCATGTTCAATGAAAGG 58.902 41.667 0.00 0.00 40.84 3.11
707 766 7.147949 GGTGATTCATGTTCAATGAAAGGAGAT 60.148 37.037 0.00 0.00 40.84 2.75
708 767 7.914346 GTGATTCATGTTCAATGAAAGGAGATC 59.086 37.037 0.00 0.78 40.84 2.75
710 769 7.621428 TTCATGTTCAATGAAAGGAGATCTC 57.379 36.000 14.75 14.75 35.35 2.75
711 770 6.600822 TTCATGTTCAATGAAAGGAGATCTCC 59.399 38.462 31.27 31.27 40.11 3.71
727 787 6.664816 GGAGATCTCCTGTCATCTATGAAGAT 59.335 42.308 31.11 5.10 46.16 2.40
743 803 5.605564 TGAAGATGTATGTGACGGTTTTG 57.394 39.130 0.00 0.00 0.00 2.44
760 820 6.025896 CGGTTTTGTCAATCTCAAGATGATG 58.974 40.000 0.00 0.00 34.49 3.07
762 822 7.148423 CGGTTTTGTCAATCTCAAGATGATGTA 60.148 37.037 0.00 0.00 34.49 2.29
763 823 7.965107 GGTTTTGTCAATCTCAAGATGATGTAC 59.035 37.037 0.00 0.00 34.49 2.90
764 824 7.615582 TTTGTCAATCTCAAGATGATGTACC 57.384 36.000 0.00 0.00 34.49 3.34
766 826 6.343703 TGTCAATCTCAAGATGATGTACCAG 58.656 40.000 0.00 0.00 34.49 4.00
776 836 4.900652 AGATGATGTACCAGCTCAATCTCT 59.099 41.667 0.00 0.00 0.00 3.10
777 837 5.366186 AGATGATGTACCAGCTCAATCTCTT 59.634 40.000 0.00 0.00 0.00 2.85
778 838 6.552725 AGATGATGTACCAGCTCAATCTCTTA 59.447 38.462 0.00 0.00 0.00 2.10
779 839 6.544928 TGATGTACCAGCTCAATCTCTTAA 57.455 37.500 0.00 0.00 0.00 1.85
780 840 6.946340 TGATGTACCAGCTCAATCTCTTAAA 58.054 36.000 0.00 0.00 0.00 1.52
781 841 7.394016 TGATGTACCAGCTCAATCTCTTAAAA 58.606 34.615 0.00 0.00 0.00 1.52
785 845 5.869579 ACCAGCTCAATCTCTTAAAAGTGA 58.130 37.500 0.00 0.00 33.61 3.41
787 847 6.597280 ACCAGCTCAATCTCTTAAAAGTGATC 59.403 38.462 7.52 0.00 38.05 2.92
795 855 9.790344 CAATCTCTTAAAAGTGATCATAGGGAT 57.210 33.333 0.00 0.00 38.05 3.85
804 864 6.172350 AGTGATCATAGGGATAGGGTATGT 57.828 41.667 0.00 0.00 36.00 2.29
822 882 6.407639 GGGTATGTGTATGTGTGTTCATAGGA 60.408 42.308 0.00 0.00 32.01 2.94
824 884 5.084818 TGTGTATGTGTGTTCATAGGAGG 57.915 43.478 0.00 0.00 32.01 4.30
825 885 3.871594 GTGTATGTGTGTTCATAGGAGGC 59.128 47.826 0.00 0.00 32.01 4.70
828 888 1.977854 TGTGTGTTCATAGGAGGCAGT 59.022 47.619 0.00 0.00 0.00 4.40
829 889 2.289631 TGTGTGTTCATAGGAGGCAGTG 60.290 50.000 0.00 0.00 0.00 3.66
830 890 1.977854 TGTGTTCATAGGAGGCAGTGT 59.022 47.619 0.00 0.00 0.00 3.55
831 891 3.056107 GTGTGTTCATAGGAGGCAGTGTA 60.056 47.826 0.00 0.00 0.00 2.90
832 892 3.774766 TGTGTTCATAGGAGGCAGTGTAT 59.225 43.478 0.00 0.00 0.00 2.29
833 893 4.122776 GTGTTCATAGGAGGCAGTGTATG 58.877 47.826 0.00 0.00 0.00 2.39
834 894 3.774766 TGTTCATAGGAGGCAGTGTATGT 59.225 43.478 0.00 0.00 0.00 2.29
835 895 4.122776 GTTCATAGGAGGCAGTGTATGTG 58.877 47.826 0.00 0.00 0.00 3.21
836 896 2.103094 TCATAGGAGGCAGTGTATGTGC 59.897 50.000 0.00 0.00 40.42 4.57
837 897 0.459899 TAGGAGGCAGTGTATGTGCG 59.540 55.000 0.00 0.00 42.19 5.34
838 898 2.464459 GGAGGCAGTGTATGTGCGC 61.464 63.158 0.00 0.00 42.19 6.09
839 899 1.741401 GAGGCAGTGTATGTGCGCA 60.741 57.895 5.66 5.66 42.19 6.09
845 905 2.348872 GCAGTGTATGTGCGCATGTATC 60.349 50.000 22.84 0.00 36.58 2.24
851 911 1.358877 TGTGCGCATGTATCAGTGTC 58.641 50.000 15.91 0.00 0.00 3.67
854 914 1.204467 TGCGCATGTATCAGTGTCTGA 59.796 47.619 5.66 1.92 44.99 3.27
855 915 7.922555 ATGTGCGCATGTATCAGTGTCTGAT 62.923 44.000 15.91 15.08 42.49 2.90
1023 1440 2.703798 CCTTGCCCAACCGCATCAG 61.704 63.158 0.00 0.00 38.87 2.90
1025 1442 4.657408 TGCCCAACCGCATCAGCA 62.657 61.111 0.00 0.00 42.27 4.41
1026 1443 3.372730 GCCCAACCGCATCAGCAA 61.373 61.111 0.00 0.00 42.27 3.91
1027 1444 2.879907 CCCAACCGCATCAGCAAG 59.120 61.111 0.00 0.00 42.27 4.01
1029 1446 2.338015 CCAACCGCATCAGCAAGCT 61.338 57.895 0.00 0.00 42.27 3.74
1030 1447 1.154093 CAACCGCATCAGCAAGCTG 60.154 57.895 15.67 15.67 44.86 4.24
1074 1517 2.749621 GCAGTCAAATTCCCAGTCGAAT 59.250 45.455 0.00 0.00 33.84 3.34
1095 1542 0.810823 GGAGCAGAGCAGCACAGATC 60.811 60.000 0.00 0.00 36.85 2.75
1132 1579 2.224159 AACCCCATGCCACTCTCGT 61.224 57.895 0.00 0.00 0.00 4.18
1683 2130 1.000396 GGCTTGGCAGGTCTGGAAT 60.000 57.895 0.00 0.00 0.00 3.01
1766 2213 2.046023 TGACGAGGGCTGCATTGG 60.046 61.111 0.50 0.00 0.00 3.16
1778 2225 2.437180 CATTGGCGAGGCTGAGCA 60.437 61.111 6.82 0.00 34.54 4.26
1872 2319 3.209410 CTGCAAGAGGGATGGTATCAAC 58.791 50.000 0.00 0.00 34.07 3.18
1911 2358 0.036022 AGGAACTGCTGAAGAGTGGC 59.964 55.000 0.00 0.00 37.18 5.01
2112 2559 7.679638 GCATTAACAGTTTATGAGGACATGACC 60.680 40.741 15.08 6.05 37.87 4.02
2324 2771 3.861113 GCAACATGCACAATAATGAGTGG 59.139 43.478 0.00 0.00 44.26 4.00
2352 2799 0.888736 TTGAGCCCAATGTGGTGACG 60.889 55.000 0.00 0.00 35.17 4.35
2481 2928 1.442526 CGGCTCTGATTCATGGCCAC 61.443 60.000 8.16 0.00 42.56 5.01
2669 3116 2.430694 AGCATGCTGACATTCGTACCTA 59.569 45.455 21.98 0.00 32.87 3.08
2775 3222 1.993369 GCCAATACCGTGAAGCTGGC 61.993 60.000 0.00 0.00 42.28 4.85
2847 3294 4.158025 ACTTACTCACTACTGATTCGTGGG 59.842 45.833 0.00 0.00 35.32 4.61
3104 3551 5.182001 ACAATGAAGAACCATTCTGCTACAC 59.818 40.000 0.00 0.00 40.59 2.90
3412 3885 3.326836 TGACCGATTGACAGTAATGCA 57.673 42.857 0.00 0.00 0.00 3.96
3477 4076 1.609061 GCTTGTGTTCTGAGCTAGCCA 60.609 52.381 12.13 8.40 33.72 4.75
3494 4093 1.464734 CCAAGCTCGGAGTAGAGACA 58.535 55.000 6.90 0.00 40.57 3.41
3497 4096 2.948979 CAAGCTCGGAGTAGAGACAGAT 59.051 50.000 6.90 0.00 40.57 2.90
3528 4127 4.623814 GCACATGCTGCACTAGGA 57.376 55.556 3.57 0.00 46.29 2.94
3529 4128 2.093216 GCACATGCTGCACTAGGAC 58.907 57.895 3.57 0.00 46.29 3.85
3530 4129 0.392193 GCACATGCTGCACTAGGACT 60.392 55.000 3.57 0.00 46.29 3.85
3531 4130 1.134699 GCACATGCTGCACTAGGACTA 60.135 52.381 3.57 0.00 46.29 2.59
3532 4131 2.484417 GCACATGCTGCACTAGGACTAT 60.484 50.000 3.57 0.00 46.29 2.12
3800 4400 5.572896 GGCACAGAAATCAGTTTTTAATCGG 59.427 40.000 0.00 0.00 0.00 4.18
3828 4428 8.415950 TTGTTAATAATGTGTGAACCCATCTT 57.584 30.769 0.00 0.00 0.00 2.40
3866 4469 6.815089 TCAAATTAGTCTGGTGTTGCAAAAT 58.185 32.000 0.00 0.00 0.00 1.82
3950 4554 0.673437 CGAGATCCTTGAGCCTCCTC 59.327 60.000 0.00 0.00 38.62 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 90 2.573893 GAACCCCATGCCTTCTCCCC 62.574 65.000 0.00 0.00 0.00 4.81
83 101 2.833943 GAGCCATTTTTCAGAACCCCAT 59.166 45.455 0.00 0.00 0.00 4.00
91 109 2.095059 CCTCCGTTGAGCCATTTTTCAG 60.095 50.000 0.00 0.00 37.29 3.02
92 110 1.885887 CCTCCGTTGAGCCATTTTTCA 59.114 47.619 0.00 0.00 37.29 2.69
93 111 1.402852 GCCTCCGTTGAGCCATTTTTC 60.403 52.381 0.00 0.00 37.29 2.29
108 160 3.987954 TTTGAATCCGGGCGCCTCC 62.988 63.158 28.56 9.89 0.00 4.30
115 167 1.822615 GCCCCAATTTGAATCCGGG 59.177 57.895 0.00 0.72 36.59 5.73
122 174 1.304052 CCAGACCGCCCCAATTTGA 60.304 57.895 0.00 0.00 0.00 2.69
123 175 0.684153 ATCCAGACCGCCCCAATTTG 60.684 55.000 0.00 0.00 0.00 2.32
141 193 3.057315 CCTTTTCGTGCCATCTTTGTCAT 60.057 43.478 0.00 0.00 0.00 3.06
145 197 1.701704 GCCTTTTCGTGCCATCTTTG 58.298 50.000 0.00 0.00 0.00 2.77
146 198 0.240945 CGCCTTTTCGTGCCATCTTT 59.759 50.000 0.00 0.00 0.00 2.52
152 204 4.404654 CTGCCGCCTTTTCGTGCC 62.405 66.667 0.00 0.00 0.00 5.01
157 209 4.404654 CCACGCTGCCGCCTTTTC 62.405 66.667 0.00 0.00 38.22 2.29
166 218 3.612247 ATCCACACTCCCACGCTGC 62.612 63.158 0.00 0.00 0.00 5.25
170 222 2.268920 CCCATCCACACTCCCACG 59.731 66.667 0.00 0.00 0.00 4.94
177 229 2.034999 TTTCGGCCCCATCCACAC 59.965 61.111 0.00 0.00 0.00 3.82
187 239 3.056328 GCACACTCCCTTTCGGCC 61.056 66.667 0.00 0.00 0.00 6.13
189 241 2.027625 GACGCACACTCCCTTTCGG 61.028 63.158 0.00 0.00 0.00 4.30
198 250 2.224426 TGGACATTTTAGGACGCACACT 60.224 45.455 0.00 0.00 0.00 3.55
200 252 2.552599 TGGACATTTTAGGACGCACA 57.447 45.000 0.00 0.00 0.00 4.57
202 254 3.006940 GTCATGGACATTTTAGGACGCA 58.993 45.455 0.00 0.00 32.09 5.24
203 255 2.354821 GGTCATGGACATTTTAGGACGC 59.645 50.000 0.00 0.00 33.68 5.19
206 258 4.567537 CCACTGGTCATGGACATTTTAGGA 60.568 45.833 0.00 0.00 39.87 2.94
224 276 1.364626 CTTTGCTAGCTCCGCCACTG 61.365 60.000 17.23 0.00 0.00 3.66
225 277 1.078848 CTTTGCTAGCTCCGCCACT 60.079 57.895 17.23 0.00 0.00 4.00
226 278 2.109126 CCTTTGCTAGCTCCGCCAC 61.109 63.158 17.23 0.00 0.00 5.01
227 279 1.626356 ATCCTTTGCTAGCTCCGCCA 61.626 55.000 17.23 0.00 0.00 5.69
228 280 0.882484 GATCCTTTGCTAGCTCCGCC 60.882 60.000 17.23 0.00 0.00 6.13
229 281 0.105778 AGATCCTTTGCTAGCTCCGC 59.894 55.000 17.23 0.00 0.00 5.54
230 282 1.601663 CGAGATCCTTTGCTAGCTCCG 60.602 57.143 17.23 6.16 0.00 4.63
231 283 1.871822 GCGAGATCCTTTGCTAGCTCC 60.872 57.143 17.23 0.00 31.29 4.70
232 284 1.496934 GCGAGATCCTTTGCTAGCTC 58.503 55.000 17.23 3.63 31.29 4.09
233 285 0.249238 CGCGAGATCCTTTGCTAGCT 60.249 55.000 17.23 0.00 31.70 3.32
235 287 1.543941 CGCGCGAGATCCTTTGCTAG 61.544 60.000 28.94 0.00 0.00 3.42
236 288 1.588932 CGCGCGAGATCCTTTGCTA 60.589 57.895 28.94 0.00 0.00 3.49
237 289 2.887568 CGCGCGAGATCCTTTGCT 60.888 61.111 28.94 0.00 0.00 3.91
238 290 3.929948 CCGCGCGAGATCCTTTGC 61.930 66.667 34.63 0.00 0.00 3.68
239 291 3.929948 GCCGCGCGAGATCCTTTG 61.930 66.667 34.63 12.35 0.00 2.77
262 314 4.382541 CTTTGCCCTCCCCCACCC 62.383 72.222 0.00 0.00 0.00 4.61
263 315 3.264845 TCTTTGCCCTCCCCCACC 61.265 66.667 0.00 0.00 0.00 4.61
264 316 1.789576 TTCTCTTTGCCCTCCCCCAC 61.790 60.000 0.00 0.00 0.00 4.61
265 317 1.071314 TTTCTCTTTGCCCTCCCCCA 61.071 55.000 0.00 0.00 0.00 4.96
266 318 0.114364 TTTTCTCTTTGCCCTCCCCC 59.886 55.000 0.00 0.00 0.00 5.40
267 319 2.238084 ATTTTCTCTTTGCCCTCCCC 57.762 50.000 0.00 0.00 0.00 4.81
268 320 3.068732 GCATATTTTCTCTTTGCCCTCCC 59.931 47.826 0.00 0.00 0.00 4.30
269 321 3.701040 TGCATATTTTCTCTTTGCCCTCC 59.299 43.478 0.00 0.00 32.39 4.30
270 322 4.989279 TGCATATTTTCTCTTTGCCCTC 57.011 40.909 0.00 0.00 32.39 4.30
271 323 4.774200 AGTTGCATATTTTCTCTTTGCCCT 59.226 37.500 0.00 0.00 32.39 5.19
272 324 5.077134 AGTTGCATATTTTCTCTTTGCCC 57.923 39.130 0.00 0.00 32.39 5.36
273 325 6.128472 CCAAAGTTGCATATTTTCTCTTTGCC 60.128 38.462 0.00 0.00 38.94 4.52
274 326 6.424812 ACCAAAGTTGCATATTTTCTCTTTGC 59.575 34.615 0.00 0.00 38.94 3.68
275 327 7.095523 CCACCAAAGTTGCATATTTTCTCTTTG 60.096 37.037 0.00 0.00 39.53 2.77
276 328 6.930722 CCACCAAAGTTGCATATTTTCTCTTT 59.069 34.615 0.00 0.00 0.00 2.52
277 329 6.267471 TCCACCAAAGTTGCATATTTTCTCTT 59.733 34.615 0.00 0.00 0.00 2.85
278 330 5.774690 TCCACCAAAGTTGCATATTTTCTCT 59.225 36.000 0.00 0.00 0.00 3.10
279 331 6.024552 TCCACCAAAGTTGCATATTTTCTC 57.975 37.500 0.00 0.00 0.00 2.87
280 332 5.047092 CCTCCACCAAAGTTGCATATTTTCT 60.047 40.000 0.00 0.00 0.00 2.52
281 333 5.170748 CCTCCACCAAAGTTGCATATTTTC 58.829 41.667 0.00 0.00 0.00 2.29
282 334 4.020307 CCCTCCACCAAAGTTGCATATTTT 60.020 41.667 0.00 0.00 0.00 1.82
283 335 3.515104 CCCTCCACCAAAGTTGCATATTT 59.485 43.478 0.00 0.00 0.00 1.40
284 336 3.099141 CCCTCCACCAAAGTTGCATATT 58.901 45.455 0.00 0.00 0.00 1.28
285 337 2.624029 CCCCTCCACCAAAGTTGCATAT 60.624 50.000 0.00 0.00 0.00 1.78
286 338 1.272425 CCCCTCCACCAAAGTTGCATA 60.272 52.381 0.00 0.00 0.00 3.14
287 339 0.542702 CCCCTCCACCAAAGTTGCAT 60.543 55.000 0.00 0.00 0.00 3.96
288 340 1.152567 CCCCTCCACCAAAGTTGCA 60.153 57.895 0.00 0.00 0.00 4.08
289 341 1.908299 CCCCCTCCACCAAAGTTGC 60.908 63.158 0.00 0.00 0.00 4.17
290 342 4.519610 CCCCCTCCACCAAAGTTG 57.480 61.111 0.00 0.00 0.00 3.16
307 359 2.024414 GTTGAGTGCATTCATACCCCC 58.976 52.381 13.14 0.00 0.00 5.40
308 360 3.004752 AGTTGAGTGCATTCATACCCC 57.995 47.619 13.14 0.00 0.00 4.95
309 361 6.699575 ATTTAGTTGAGTGCATTCATACCC 57.300 37.500 13.14 2.16 0.00 3.69
312 364 9.787532 GCTTAAATTTAGTTGAGTGCATTCATA 57.212 29.630 13.14 0.51 0.00 2.15
313 365 7.761249 GGCTTAAATTTAGTTGAGTGCATTCAT 59.239 33.333 13.14 1.54 0.00 2.57
314 366 7.039784 AGGCTTAAATTTAGTTGAGTGCATTCA 60.040 33.333 7.97 7.97 0.00 2.57
315 367 7.315890 AGGCTTAAATTTAGTTGAGTGCATTC 58.684 34.615 1.56 1.56 0.00 2.67
316 368 7.232118 AGGCTTAAATTTAGTTGAGTGCATT 57.768 32.000 0.00 0.00 0.00 3.56
317 369 6.840780 AGGCTTAAATTTAGTTGAGTGCAT 57.159 33.333 0.00 0.00 0.00 3.96
318 370 6.264292 TGAAGGCTTAAATTTAGTTGAGTGCA 59.736 34.615 0.00 0.00 0.00 4.57
319 371 6.582672 GTGAAGGCTTAAATTTAGTTGAGTGC 59.417 38.462 0.00 0.00 0.00 4.40
320 372 7.648142 TGTGAAGGCTTAAATTTAGTTGAGTG 58.352 34.615 0.00 0.00 0.00 3.51
321 373 7.817418 TGTGAAGGCTTAAATTTAGTTGAGT 57.183 32.000 0.00 0.00 0.00 3.41
322 374 9.528018 TTTTGTGAAGGCTTAAATTTAGTTGAG 57.472 29.630 0.00 0.00 0.00 3.02
323 375 9.877178 TTTTTGTGAAGGCTTAAATTTAGTTGA 57.123 25.926 0.00 0.00 0.00 3.18
347 399 9.178758 CCATAGCTTAAGTACTGAAGGAATTTT 57.821 33.333 19.78 0.00 0.00 1.82
348 400 7.283354 GCCATAGCTTAAGTACTGAAGGAATTT 59.717 37.037 19.78 0.00 35.50 1.82
349 401 6.768381 GCCATAGCTTAAGTACTGAAGGAATT 59.232 38.462 19.78 0.00 35.50 2.17
350 402 6.292150 GCCATAGCTTAAGTACTGAAGGAAT 58.708 40.000 19.78 0.00 35.50 3.01
351 403 5.671493 GCCATAGCTTAAGTACTGAAGGAA 58.329 41.667 19.78 0.00 35.50 3.36
352 404 5.277857 GCCATAGCTTAAGTACTGAAGGA 57.722 43.478 19.78 0.00 35.50 3.36
367 419 2.520260 CTGCCCCCAAGCCATAGC 60.520 66.667 0.00 0.00 40.32 2.97
368 420 2.520260 GCTGCCCCCAAGCCATAG 60.520 66.667 0.00 0.00 0.00 2.23
369 421 4.504596 CGCTGCCCCCAAGCCATA 62.505 66.667 0.00 0.00 0.00 2.74
380 432 4.175337 TACTGGGATGCCGCTGCC 62.175 66.667 0.00 0.00 36.33 4.85
381 433 2.028125 TACTACTGGGATGCCGCTGC 62.028 60.000 0.00 0.00 38.26 5.25
382 434 0.249489 GTACTACTGGGATGCCGCTG 60.249 60.000 0.00 0.00 0.00 5.18
383 435 0.686441 TGTACTACTGGGATGCCGCT 60.686 55.000 0.00 0.00 0.00 5.52
384 436 0.393077 ATGTACTACTGGGATGCCGC 59.607 55.000 0.00 0.00 0.00 6.53
385 437 1.686587 TCATGTACTACTGGGATGCCG 59.313 52.381 0.00 0.00 0.00 5.69
386 438 3.324846 TGATCATGTACTACTGGGATGCC 59.675 47.826 0.00 0.00 0.00 4.40
387 439 4.607293 TGATCATGTACTACTGGGATGC 57.393 45.455 0.00 0.00 0.00 3.91
388 440 6.350629 TCATGATCATGTACTACTGGGATG 57.649 41.667 30.01 6.25 39.72 3.51
389 441 5.483231 CCTCATGATCATGTACTACTGGGAT 59.517 44.000 30.01 0.00 39.72 3.85
390 442 4.835056 CCTCATGATCATGTACTACTGGGA 59.165 45.833 30.01 10.20 39.72 4.37
391 443 4.562347 GCCTCATGATCATGTACTACTGGG 60.562 50.000 30.01 20.06 39.72 4.45
392 444 4.564041 GCCTCATGATCATGTACTACTGG 58.436 47.826 30.01 21.18 39.72 4.00
393 445 4.233005 CGCCTCATGATCATGTACTACTG 58.767 47.826 30.01 15.06 39.72 2.74
394 446 3.305676 GCGCCTCATGATCATGTACTACT 60.306 47.826 30.01 0.00 39.72 2.57
395 447 2.989840 GCGCCTCATGATCATGTACTAC 59.010 50.000 30.01 16.94 39.72 2.73
396 448 2.627699 TGCGCCTCATGATCATGTACTA 59.372 45.455 30.01 13.82 39.72 1.82
397 449 1.413812 TGCGCCTCATGATCATGTACT 59.586 47.619 30.01 0.00 39.72 2.73
398 450 1.869774 TGCGCCTCATGATCATGTAC 58.130 50.000 30.01 20.37 39.72 2.90
399 451 2.212652 GTTGCGCCTCATGATCATGTA 58.787 47.619 30.01 18.04 39.72 2.29
400 452 1.019673 GTTGCGCCTCATGATCATGT 58.980 50.000 30.01 0.00 39.72 3.21
401 453 1.018910 TGTTGCGCCTCATGATCATG 58.981 50.000 26.79 26.79 40.09 3.07
402 454 1.878088 GATGTTGCGCCTCATGATCAT 59.122 47.619 16.87 1.18 0.00 2.45
403 455 1.302366 GATGTTGCGCCTCATGATCA 58.698 50.000 16.87 0.00 0.00 2.92
404 456 0.590195 GGATGTTGCGCCTCATGATC 59.410 55.000 16.87 5.97 0.00 2.92
411 463 1.202639 TCATATTCGGATGTTGCGCCT 60.203 47.619 4.18 0.00 0.00 5.52
412 464 1.225855 TCATATTCGGATGTTGCGCC 58.774 50.000 4.18 0.00 0.00 6.53
420 472 3.494398 CCCGTGAACCTTCATATTCGGAT 60.494 47.826 13.57 0.00 42.35 4.18
424 476 3.377172 CCAACCCGTGAACCTTCATATTC 59.623 47.826 0.00 0.00 39.73 1.75
434 486 3.571571 GCTTTAAATCCAACCCGTGAAC 58.428 45.455 0.00 0.00 0.00 3.18
438 490 1.808343 GACGCTTTAAATCCAACCCGT 59.192 47.619 0.00 0.00 0.00 5.28
441 493 5.632244 TTTAGGACGCTTTAAATCCAACC 57.368 39.130 8.64 1.22 34.73 3.77
466 518 5.163468 CCTGAGCTCACTCGCCATATAATAT 60.163 44.000 13.74 0.00 46.69 1.28
469 521 2.297315 CCTGAGCTCACTCGCCATATAA 59.703 50.000 13.74 0.00 46.69 0.98
475 527 1.227205 CATCCTGAGCTCACTCGCC 60.227 63.158 13.74 0.00 46.69 5.54
480 532 2.289320 ACAGTTGTCATCCTGAGCTCAC 60.289 50.000 13.74 2.16 32.93 3.51
485 537 4.687948 CACTAACACAGTTGTCATCCTGAG 59.312 45.833 6.95 2.59 34.26 3.35
486 538 4.100963 ACACTAACACAGTTGTCATCCTGA 59.899 41.667 6.95 0.00 34.26 3.86
507 559 5.471116 CAGTGATTTTGATGAGAAGACCACA 59.529 40.000 0.00 0.00 0.00 4.17
508 560 5.471456 ACAGTGATTTTGATGAGAAGACCAC 59.529 40.000 0.00 0.00 0.00 4.16
529 582 9.277565 GCAATTGTCATGTAATTGTTAGTACAG 57.722 33.333 24.90 9.20 43.80 2.74
555 614 7.010367 CCAACCATCCAATCATAAATTGTTTCG 59.990 37.037 0.00 0.00 0.00 3.46
560 619 6.324512 TCTCCCAACCATCCAATCATAAATTG 59.675 38.462 0.00 0.00 0.00 2.32
564 623 5.200483 GTTCTCCCAACCATCCAATCATAA 58.800 41.667 0.00 0.00 0.00 1.90
566 625 3.011595 TGTTCTCCCAACCATCCAATCAT 59.988 43.478 0.00 0.00 0.00 2.45
569 628 2.379907 ACTGTTCTCCCAACCATCCAAT 59.620 45.455 0.00 0.00 0.00 3.16
573 632 1.073923 ACCACTGTTCTCCCAACCATC 59.926 52.381 0.00 0.00 0.00 3.51
580 639 3.769844 TCTGAAGATACCACTGTTCTCCC 59.230 47.826 0.00 0.00 0.00 4.30
584 643 4.537135 TGGTCTGAAGATACCACTGTTC 57.463 45.455 0.00 0.00 40.84 3.18
591 650 8.964476 TTAAATTCTGATGGTCTGAAGATACC 57.036 34.615 5.69 0.00 37.66 2.73
597 656 6.778821 TCCACTTAAATTCTGATGGTCTGAA 58.221 36.000 2.48 2.48 38.41 3.02
602 661 7.671398 ACTTGAATCCACTTAAATTCTGATGGT 59.329 33.333 0.00 0.00 33.86 3.55
604 663 7.487189 GCACTTGAATCCACTTAAATTCTGATG 59.513 37.037 0.00 0.00 33.86 3.07
606 665 6.716628 AGCACTTGAATCCACTTAAATTCTGA 59.283 34.615 0.00 0.00 33.86 3.27
609 668 8.178313 GTCTAGCACTTGAATCCACTTAAATTC 58.822 37.037 0.00 0.00 33.42 2.17
610 669 7.885399 AGTCTAGCACTTGAATCCACTTAAATT 59.115 33.333 0.00 0.00 26.56 1.82
611 670 7.398024 AGTCTAGCACTTGAATCCACTTAAAT 58.602 34.615 0.00 0.00 26.56 1.40
612 671 6.769512 AGTCTAGCACTTGAATCCACTTAAA 58.230 36.000 0.00 0.00 26.56 1.52
613 672 6.360370 AGTCTAGCACTTGAATCCACTTAA 57.640 37.500 0.00 0.00 26.56 1.85
614 673 6.360370 AAGTCTAGCACTTGAATCCACTTA 57.640 37.500 6.74 0.00 44.28 2.24
615 674 4.899352 AGTCTAGCACTTGAATCCACTT 57.101 40.909 0.00 0.00 26.56 3.16
616 675 4.899352 AAGTCTAGCACTTGAATCCACT 57.101 40.909 6.74 0.00 44.28 4.00
683 742 7.832685 AGATCTCCTTTCATTGAACATGAATCA 59.167 33.333 0.00 0.13 37.79 2.57
685 744 7.284944 GGAGATCTCCTTTCATTGAACATGAAT 59.715 37.037 31.11 0.00 46.16 2.57
700 759 6.380414 TTCATAGATGACAGGAGATCTCCTT 58.620 40.000 37.06 27.56 46.42 3.36
703 762 7.707624 ATCTTCATAGATGACAGGAGATCTC 57.292 40.000 14.75 14.75 39.66 2.75
716 775 6.656632 ACCGTCACATACATCTTCATAGAT 57.343 37.500 0.00 0.00 41.89 1.98
717 776 6.465439 AACCGTCACATACATCTTCATAGA 57.535 37.500 0.00 0.00 34.21 1.98
718 777 7.064609 ACAAAACCGTCACATACATCTTCATAG 59.935 37.037 0.00 0.00 0.00 2.23
719 778 6.876789 ACAAAACCGTCACATACATCTTCATA 59.123 34.615 0.00 0.00 0.00 2.15
720 779 5.705441 ACAAAACCGTCACATACATCTTCAT 59.295 36.000 0.00 0.00 0.00 2.57
721 780 5.060506 ACAAAACCGTCACATACATCTTCA 58.939 37.500 0.00 0.00 0.00 3.02
722 781 5.178623 TGACAAAACCGTCACATACATCTTC 59.821 40.000 0.00 0.00 40.94 2.87
727 787 5.060506 AGATTGACAAAACCGTCACATACA 58.939 37.500 0.00 0.00 45.36 2.29
743 803 5.236047 GCTGGTACATCATCTTGAGATTGAC 59.764 44.000 0.00 0.00 38.20 3.18
760 820 6.874134 TCACTTTTAAGAGATTGAGCTGGTAC 59.126 38.462 0.00 0.00 0.00 3.34
762 822 5.869579 TCACTTTTAAGAGATTGAGCTGGT 58.130 37.500 0.00 0.00 0.00 4.00
763 823 6.596888 TGATCACTTTTAAGAGATTGAGCTGG 59.403 38.462 0.00 0.00 36.65 4.85
764 824 7.606858 TGATCACTTTTAAGAGATTGAGCTG 57.393 36.000 0.00 0.00 36.65 4.24
766 826 8.772705 CCTATGATCACTTTTAAGAGATTGAGC 58.227 37.037 0.00 0.00 36.65 4.26
776 836 7.947782 ACCCTATCCCTATGATCACTTTTAA 57.052 36.000 0.00 0.00 34.76 1.52
777 837 9.046846 CATACCCTATCCCTATGATCACTTTTA 57.953 37.037 0.00 0.00 34.76 1.52
778 838 7.517604 ACATACCCTATCCCTATGATCACTTTT 59.482 37.037 0.00 0.00 34.76 2.27
779 839 7.025620 ACATACCCTATCCCTATGATCACTTT 58.974 38.462 0.00 0.00 34.76 2.66
780 840 6.441924 CACATACCCTATCCCTATGATCACTT 59.558 42.308 0.00 0.00 34.76 3.16
781 841 5.960811 CACATACCCTATCCCTATGATCACT 59.039 44.000 0.00 0.00 34.76 3.41
785 845 7.345653 CACATACACATACCCTATCCCTATGAT 59.654 40.741 0.00 0.00 37.49 2.45
787 847 6.440647 ACACATACACATACCCTATCCCTATG 59.559 42.308 0.00 0.00 0.00 2.23
795 855 6.553953 ATGAACACACATACACATACCCTA 57.446 37.500 0.00 0.00 0.00 3.53
797 857 5.758296 CCTATGAACACACATACACATACCC 59.242 44.000 0.00 0.00 0.00 3.69
804 864 3.517500 TGCCTCCTATGAACACACATACA 59.482 43.478 0.00 0.00 0.00 2.29
822 882 1.078214 ATGCGCACATACACTGCCT 60.078 52.632 14.90 0.00 33.67 4.75
824 884 1.006086 TACATGCGCACATACACTGC 58.994 50.000 14.90 0.00 33.67 4.40
825 885 2.865551 TGATACATGCGCACATACACTG 59.134 45.455 14.90 8.00 33.67 3.66
828 888 2.865551 CACTGATACATGCGCACATACA 59.134 45.455 14.90 9.09 33.67 2.29
829 889 2.866156 ACACTGATACATGCGCACATAC 59.134 45.455 14.90 4.21 33.67 2.39
830 890 3.123050 GACACTGATACATGCGCACATA 58.877 45.455 14.90 8.86 33.67 2.29
831 891 1.935873 GACACTGATACATGCGCACAT 59.064 47.619 14.90 6.44 36.79 3.21
832 892 1.066929 AGACACTGATACATGCGCACA 60.067 47.619 14.90 4.51 0.00 4.57
833 893 1.325640 CAGACACTGATACATGCGCAC 59.674 52.381 14.90 0.00 32.44 5.34
834 894 1.204467 TCAGACACTGATACATGCGCA 59.796 47.619 14.96 14.96 35.39 6.09
835 895 1.926561 TCAGACACTGATACATGCGC 58.073 50.000 0.00 0.00 35.39 6.09
873 933 1.807886 CATGCAAGAGGCCAAGAGC 59.192 57.895 5.01 4.15 43.89 4.09
874 934 0.963856 TGCATGCAAGAGGCCAAGAG 60.964 55.000 20.30 0.00 43.89 2.85
876 936 0.179111 CATGCATGCAAGAGGCCAAG 60.179 55.000 26.68 2.53 43.89 3.61
878 938 3.610976 CATGCATGCAAGAGGCCA 58.389 55.556 26.68 0.00 43.89 5.36
889 949 1.138859 TGCCGTTAGTCTAGCATGCAT 59.861 47.619 21.98 7.68 0.00 3.96
1029 1446 1.540363 GGTTTTCTCGGTGAGCACTCA 60.540 52.381 0.00 0.00 37.24 3.41
1030 1447 1.149148 GGTTTTCTCGGTGAGCACTC 58.851 55.000 0.16 0.00 0.00 3.51
1031 1448 0.250338 GGGTTTTCTCGGTGAGCACT 60.250 55.000 0.16 0.00 0.00 4.40
1032 1449 0.534203 TGGGTTTTCTCGGTGAGCAC 60.534 55.000 0.00 0.00 0.00 4.40
1033 1450 0.250295 CTGGGTTTTCTCGGTGAGCA 60.250 55.000 0.00 0.00 0.00 4.26
1074 1517 0.613012 TCTGTGCTGCTCTGCTCCTA 60.613 55.000 0.00 0.00 0.00 2.94
1132 1579 2.359169 GGATGAGGCGGAGTGGTGA 61.359 63.158 0.00 0.00 0.00 4.02
1523 1970 3.633094 CTCACCAGCACGTCGAGGG 62.633 68.421 10.27 0.00 0.00 4.30
1669 2116 3.087343 TCTGATTCCAGACCTGCCA 57.913 52.632 0.00 0.00 44.01 4.92
1683 2130 4.193334 CGTCTCGCCGCCATCTGA 62.193 66.667 0.00 0.00 0.00 3.27
1731 2178 3.302675 CGTCACAAAGTGCGGATATCATG 60.303 47.826 4.83 0.00 32.98 3.07
1778 2225 1.542492 CTTCATGGCAAGGAACAGCT 58.458 50.000 0.00 0.00 0.00 4.24
1789 2236 1.134907 CATCCCTGTTTGCTTCATGGC 60.135 52.381 0.00 0.00 0.00 4.40
1860 2307 1.212935 AGTGCCCTGTTGATACCATCC 59.787 52.381 0.00 0.00 0.00 3.51
2037 2484 4.337555 GCTCCATCAATCAAGCTGTTGTAT 59.662 41.667 0.00 0.00 34.98 2.29
2112 2559 2.750237 GGGCACAAACCTAGGCGG 60.750 66.667 9.30 0.45 39.35 6.13
2292 2739 1.980772 GCATGTTGCCAGGGCTTCT 60.981 57.895 12.19 0.00 42.51 2.85
2324 2771 1.207811 CATTGGGCTCAATTCCAACCC 59.792 52.381 9.73 0.00 44.64 4.11
2352 2799 3.259625 GCCCATCTATCAAGGAGGAGTAC 59.740 52.174 0.00 0.00 0.00 2.73
2669 3116 5.046591 TCCTCAGTTGTGGAGTTCGATAAAT 60.047 40.000 0.00 0.00 33.24 1.40
2745 3192 5.547465 TCACGGTATTGGCCATCTAAATAG 58.453 41.667 6.09 0.00 0.00 1.73
2775 3222 5.236282 TCTCTCATGCAAGAGAAGAACTTG 58.764 41.667 21.07 9.01 46.76 3.16
3104 3551 1.986413 CCCTCAGTTCTGTCCCAGG 59.014 63.158 0.00 0.00 31.51 4.45
3412 3885 1.134788 AGCGGTTTAGCGTGCTAGATT 60.135 47.619 1.39 0.00 43.00 2.40
3477 4076 2.791347 TCTGTCTCTACTCCGAGCTT 57.209 50.000 0.00 0.00 0.00 3.74
3523 4122 9.621629 CCATTATAGTCCTAGTGATAGTCCTAG 57.378 40.741 0.00 0.00 0.00 3.02
3524 4123 9.347777 TCCATTATAGTCCTAGTGATAGTCCTA 57.652 37.037 0.00 0.00 0.00 2.94
3525 4124 8.110908 GTCCATTATAGTCCTAGTGATAGTCCT 58.889 40.741 0.00 0.00 0.00 3.85
3526 4125 7.066043 CGTCCATTATAGTCCTAGTGATAGTCC 59.934 44.444 0.00 0.00 0.00 3.85
3527 4126 7.823310 TCGTCCATTATAGTCCTAGTGATAGTC 59.177 40.741 0.00 0.00 0.00 2.59
3528 4127 7.687388 TCGTCCATTATAGTCCTAGTGATAGT 58.313 38.462 0.00 0.00 0.00 2.12
3529 4128 8.740123 ATCGTCCATTATAGTCCTAGTGATAG 57.260 38.462 0.00 0.00 0.00 2.08
3531 4130 9.126151 CATATCGTCCATTATAGTCCTAGTGAT 57.874 37.037 0.00 0.00 0.00 3.06
3532 4131 8.326529 TCATATCGTCCATTATAGTCCTAGTGA 58.673 37.037 0.00 0.00 0.00 3.41
3756 4355 8.929827 TGTGCCATAATCAATAAAACAGAATG 57.070 30.769 0.00 0.00 46.00 2.67
3757 4356 8.970020 TCTGTGCCATAATCAATAAAACAGAAT 58.030 29.630 0.00 0.00 38.73 2.40
3758 4357 8.347004 TCTGTGCCATAATCAATAAAACAGAA 57.653 30.769 0.00 0.00 38.73 3.02
3800 4400 7.209471 TGGGTTCACACATTATTAACAAGTC 57.791 36.000 0.00 0.00 0.00 3.01
3866 4469 7.019254 TCCTAGGGACAGATTGTACATCCTATA 59.981 40.741 9.46 5.51 31.17 1.31
3950 4554 3.698289 TGACCTTGAGTACTACCAGGAG 58.302 50.000 17.56 0.41 0.00 3.69


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

AutoCloner maintained by Alex Coulton.