Multiple sequence alignment - TraesCS2B01G542300

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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 TraesCS2B01G542300 chr2B 100.000 2738 0 0 1 2738 739370619 739367882 0.000000e+00 5057
1 TraesCS2B01G542300 chr2D 86.075 2657 145 113 2 2549 607282695 607285235 0.000000e+00 2649
2 TraesCS2B01G542300 chr2D 91.954 435 23 3 990 1424 603142118 603141696 1.400000e-167 599
3 TraesCS2B01G542300 chr2D 91.473 129 11 0 1474 1602 603141691 603141563 7.790000e-41 178
4 TraesCS2B01G542300 chr2A 88.016 2011 116 60 615 2542 738921381 738923349 0.000000e+00 2263
5 TraesCS2B01G542300 chr6A 81.231 325 32 18 2231 2542 184817907 184817599 4.560000e-58 235
6 TraesCS2B01G542300 chr7D 89.888 178 18 0 1210 1387 79964221 79964398 2.120000e-56 230
7 TraesCS2B01G542300 chr7B 89.888 178 18 0 1210 1387 27067544 27067721 2.120000e-56 230
8 TraesCS2B01G542300 chr7A 89.326 178 19 0 1210 1387 82942459 82942636 9.870000e-55 224
9 TraesCS2B01G542300 chr1D 80.000 185 33 4 1206 1388 475981249 475981067 1.710000e-27 134
10 TraesCS2B01G542300 chr1B 80.000 185 33 4 1206 1388 662193839 662193657 1.710000e-27 134
11 TraesCS2B01G542300 chr1A 80.000 185 33 4 1206 1388 571895377 571895195 1.710000e-27 134


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 TraesCS2B01G542300 chr2B 739367882 739370619 2737 True 5057.0 5057 100.0000 1 2738 1 chr2B.!!$R1 2737
1 TraesCS2B01G542300 chr2D 607282695 607285235 2540 False 2649.0 2649 86.0750 2 2549 1 chr2D.!!$F1 2547
2 TraesCS2B01G542300 chr2D 603141563 603142118 555 True 388.5 599 91.7135 990 1602 2 chr2D.!!$R1 612
3 TraesCS2B01G542300 chr2A 738921381 738923349 1968 False 2263.0 2263 88.0160 615 2542 1 chr2A.!!$F1 1927

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
282 294 0.025001 GATCGAATGTGACGTTGCGG 59.975 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1865 0.320374 TCGACTGGTTGTGGATGACC 59.68 55.0 0.0 0.0 36.45 4.02 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
28 29 4.729227 AAACGTGAGGACAACCATTTTT 57.271 36.364 0.00 0.00 38.94 1.94
75 77 7.716998 GGATAATCTTTTCATTGCCTAGTCAGA 59.283 37.037 0.00 0.00 0.00 3.27
77 79 7.951347 AATCTTTTCATTGCCTAGTCAGATT 57.049 32.000 0.00 0.00 0.00 2.40
81 83 6.500684 TTTCATTGCCTAGTCAGATTTGTC 57.499 37.500 0.00 0.00 0.00 3.18
82 84 5.164620 TCATTGCCTAGTCAGATTTGTCA 57.835 39.130 0.00 0.00 0.00 3.58
136 141 6.869695 TGTCCTTATTGTATACTCAAAGCGA 58.130 36.000 4.17 2.83 0.00 4.93
151 156 1.722011 AGCGATTACTTGTTGACCCG 58.278 50.000 0.00 0.00 0.00 5.28
154 159 2.093783 GCGATTACTTGTTGACCCGAAG 59.906 50.000 0.00 0.00 0.00 3.79
162 169 3.417069 TGTTGACCCGAAGATGTGAAT 57.583 42.857 0.00 0.00 0.00 2.57
175 182 4.728772 AGATGTGAATGGAACTTGGACAA 58.271 39.130 0.00 0.00 0.00 3.18
219 226 4.261447 GGAGGTCAACAAAATTACAGCGTT 60.261 41.667 0.00 0.00 0.00 4.84
262 274 2.373169 TGGTGAGCAACAGAGAAGGATT 59.627 45.455 0.00 0.00 0.00 3.01
263 275 2.746362 GGTGAGCAACAGAGAAGGATTG 59.254 50.000 0.00 0.00 0.00 2.67
264 276 3.557898 GGTGAGCAACAGAGAAGGATTGA 60.558 47.826 0.00 0.00 0.00 2.57
265 277 4.260170 GTGAGCAACAGAGAAGGATTGAT 58.740 43.478 0.00 0.00 0.00 2.57
266 278 4.332268 GTGAGCAACAGAGAAGGATTGATC 59.668 45.833 0.00 0.00 37.84 2.92
269 281 3.935203 GCAACAGAGAAGGATTGATCGAA 59.065 43.478 0.00 0.00 0.00 3.71
275 287 5.233902 CAGAGAAGGATTGATCGAATGTGAC 59.766 44.000 0.00 0.00 0.00 3.67
277 289 3.526931 AGGATTGATCGAATGTGACGT 57.473 42.857 0.00 0.00 0.00 4.34
282 294 0.025001 GATCGAATGTGACGTTGCGG 59.975 55.000 0.00 0.00 0.00 5.69
293 305 1.517276 GACGTTGCGGTCATCTTATCG 59.483 52.381 0.00 0.00 36.91 2.92
297 311 3.734231 CGTTGCGGTCATCTTATCGTAAT 59.266 43.478 0.00 0.00 31.03 1.89
316 330 5.636543 CGTAATTTACCACGAGAAAGAACCT 59.363 40.000 1.04 0.00 40.56 3.50
317 331 6.183360 CGTAATTTACCACGAGAAAGAACCTC 60.183 42.308 1.04 0.00 40.56 3.85
321 335 2.698797 ACCACGAGAAAGAACCTCTCAA 59.301 45.455 0.00 0.00 39.50 3.02
353 371 0.531974 ACCAGCGACAACAACGATGT 60.532 50.000 0.00 0.00 43.90 3.06
361 379 4.361253 ACAACGATGTTGCTCGCT 57.639 50.000 9.45 0.00 42.35 4.93
362 380 2.616969 ACAACGATGTTGCTCGCTT 58.383 47.368 9.45 0.00 42.35 4.68
363 381 0.512952 ACAACGATGTTGCTCGCTTC 59.487 50.000 9.45 0.00 42.35 3.86
387 405 7.962964 CTGTTTCCACAGTGAGAGTAAATAA 57.037 36.000 0.62 0.00 44.96 1.40
388 406 7.724305 TGTTTCCACAGTGAGAGTAAATAAC 57.276 36.000 0.62 0.00 0.00 1.89
389 407 6.422701 TGTTTCCACAGTGAGAGTAAATAACG 59.577 38.462 0.62 0.00 0.00 3.18
396 414 7.952101 CACAGTGAGAGTAAATAACGAATTGTG 59.048 37.037 0.00 0.00 0.00 3.33
402 420 5.938322 AGTAAATAACGAATTGTGCACCAG 58.062 37.500 15.69 3.53 0.00 4.00
408 426 3.407698 ACGAATTGTGCACCAGATACAA 58.592 40.909 15.69 0.00 38.52 2.41
409 427 4.009675 ACGAATTGTGCACCAGATACAAT 58.990 39.130 15.69 2.29 44.39 2.71
410 428 4.142622 ACGAATTGTGCACCAGATACAATG 60.143 41.667 15.69 0.00 42.40 2.82
411 429 3.788333 ATTGTGCACCAGATACAATGC 57.212 42.857 15.69 0.00 41.85 3.56
412 430 2.197283 TGTGCACCAGATACAATGCA 57.803 45.000 15.69 0.00 45.45 3.96
420 438 5.345702 CACCAGATACAATGCAAATTCCAG 58.654 41.667 0.00 0.00 0.00 3.86
422 440 5.481473 ACCAGATACAATGCAAATTCCAGTT 59.519 36.000 0.00 0.00 0.00 3.16
424 442 6.038356 CAGATACAATGCAAATTCCAGTTCC 58.962 40.000 0.00 0.00 0.00 3.62
429 447 0.171231 GCAAATTCCAGTTCCGAGGC 59.829 55.000 0.00 0.00 0.00 4.70
433 451 0.322546 ATTCCAGTTCCGAGGCAACC 60.323 55.000 0.00 0.00 37.17 3.77
437 455 1.247567 CAGTTCCGAGGCAACCAATT 58.752 50.000 0.00 0.00 37.17 2.32
438 456 1.200020 CAGTTCCGAGGCAACCAATTC 59.800 52.381 0.00 0.00 37.17 2.17
445 463 2.804931 GCAACCAATTCGCCACGC 60.805 61.111 0.00 0.00 0.00 5.34
446 464 2.953821 CAACCAATTCGCCACGCT 59.046 55.556 0.00 0.00 0.00 5.07
452 470 0.247814 CAATTCGCCACGCTAGCTTG 60.248 55.000 14.03 14.03 0.00 4.01
453 471 0.673644 AATTCGCCACGCTAGCTTGT 60.674 50.000 18.78 4.97 0.00 3.16
454 472 1.084370 ATTCGCCACGCTAGCTTGTC 61.084 55.000 18.78 6.32 0.00 3.18
455 473 3.188786 CGCCACGCTAGCTTGTCC 61.189 66.667 18.78 9.21 0.00 4.02
456 474 2.047274 GCCACGCTAGCTTGTCCA 60.047 61.111 18.78 0.00 0.00 4.02
457 475 1.450312 GCCACGCTAGCTTGTCCAT 60.450 57.895 18.78 0.00 0.00 3.41
458 476 1.432270 GCCACGCTAGCTTGTCCATC 61.432 60.000 18.78 0.83 0.00 3.51
459 477 0.108186 CCACGCTAGCTTGTCCATCA 60.108 55.000 18.78 0.00 0.00 3.07
460 478 1.284657 CACGCTAGCTTGTCCATCAG 58.715 55.000 13.93 0.00 0.00 2.90
461 479 0.460987 ACGCTAGCTTGTCCATCAGC 60.461 55.000 13.93 0.00 0.00 4.26
462 480 0.179089 CGCTAGCTTGTCCATCAGCT 60.179 55.000 13.93 0.00 40.96 4.24
463 481 1.741732 CGCTAGCTTGTCCATCAGCTT 60.742 52.381 13.93 0.00 38.66 3.74
464 482 1.939255 GCTAGCTTGTCCATCAGCTTC 59.061 52.381 7.70 0.00 38.66 3.86
465 483 2.679059 GCTAGCTTGTCCATCAGCTTCA 60.679 50.000 7.70 0.00 38.66 3.02
466 484 2.110901 AGCTTGTCCATCAGCTTCAG 57.889 50.000 0.00 0.00 33.34 3.02
469 487 2.613133 GCTTGTCCATCAGCTTCAGATC 59.387 50.000 0.00 0.00 0.00 2.75
501 519 3.932580 TTGACGCTAGCTGTGCCGG 62.933 63.158 13.93 0.00 0.00 6.13
503 521 3.642778 GACGCTAGCTGTGCCGGAA 62.643 63.158 13.93 0.00 0.00 4.30
507 525 0.105039 GCTAGCTGTGCCGGAAGTAT 59.895 55.000 5.05 0.00 0.00 2.12
508 526 1.340248 GCTAGCTGTGCCGGAAGTATA 59.660 52.381 5.05 0.00 0.00 1.47
514 532 3.005472 GCTGTGCCGGAAGTATATACAGA 59.995 47.826 15.18 0.00 36.96 3.41
524 542 9.499585 CCGGAAGTATATACAGATACAAATACG 57.500 37.037 15.18 2.60 35.16 3.06
534 553 5.801947 ACAGATACAAATACGTACAACCGAC 59.198 40.000 0.00 0.00 0.00 4.79
535 554 5.230726 CAGATACAAATACGTACAACCGACC 59.769 44.000 0.00 0.00 0.00 4.79
544 563 0.319083 TACAACCGACCGATGTTGCT 59.681 50.000 10.07 3.39 44.38 3.91
546 565 0.165944 CAACCGACCGATGTTGCTTC 59.834 55.000 0.00 0.00 35.87 3.86
547 566 1.289109 AACCGACCGATGTTGCTTCG 61.289 55.000 0.00 0.00 36.38 3.79
563 582 4.109766 TGCTTCGGAGAATTGTACGTATG 58.890 43.478 7.15 0.47 45.90 2.39
564 583 3.060473 GCTTCGGAGAATTGTACGTATGC 60.060 47.826 7.15 6.60 45.90 3.14
590 617 4.803098 ATCGGCTACTGGTCCAATATAC 57.197 45.455 0.00 0.00 0.00 1.47
594 621 4.614535 CGGCTACTGGTCCAATATACGTAC 60.615 50.000 0.00 0.00 0.00 3.67
607 634 3.520290 ATACGTACGGATATGCATGGG 57.480 47.619 21.06 0.00 0.00 4.00
702 755 2.873609 CAGTAGAGTACACTGCTGCTG 58.126 52.381 21.34 14.22 41.78 4.41
705 758 0.037512 AGAGTACACTGCTGCTGCTG 60.038 55.000 18.66 18.66 42.70 4.41
706 759 1.633852 GAGTACACTGCTGCTGCTGC 61.634 60.000 22.51 22.51 41.07 5.25
707 760 2.359107 TACACTGCTGCTGCTGCC 60.359 61.111 25.44 10.66 41.07 4.85
735 788 1.746220 CCGTCGATGTCCTCTTCTCTT 59.254 52.381 3.52 0.00 0.00 2.85
736 789 2.223386 CCGTCGATGTCCTCTTCTCTTC 60.223 54.545 3.52 0.00 0.00 2.87
741 794 3.642141 GATGTCCTCTTCTCTTCTCCCT 58.358 50.000 0.00 0.00 0.00 4.20
747 802 1.064314 TCTTCTCTTCTCCCTCCCGAG 60.064 57.143 0.00 0.00 0.00 4.63
751 806 4.056584 TTCTCCCTCCCGAGCGGA 62.057 66.667 11.05 0.00 38.83 5.54
872 932 1.289530 GGAGGGAGGGAAGAGAGAGAA 59.710 57.143 0.00 0.00 0.00 2.87
886 953 0.767375 AGAGAAACCAGCTCCTGCAA 59.233 50.000 0.00 0.00 42.74 4.08
909 976 2.489722 CCAAAAGCTACTCCTCCTTTGC 59.510 50.000 0.00 0.00 0.00 3.68
1036 1120 2.258591 GCTCGTCGTCTTCCAGCA 59.741 61.111 0.00 0.00 0.00 4.41
1143 1227 1.668151 GGAGGAGCACAACGTGACC 60.668 63.158 0.00 0.95 35.23 4.02
1401 1485 2.051703 GACGAGATCTCCGCGCTC 60.052 66.667 17.13 0.00 41.91 5.03
1515 1599 1.220749 CCGGAAGAAGGCCATCGAA 59.779 57.895 5.01 0.00 0.00 3.71
1557 1641 2.815211 CAGACCGGCATGACCACG 60.815 66.667 0.00 0.00 39.03 4.94
1786 1884 0.036164 CTTCCGGTCATCCACAACCA 59.964 55.000 0.00 0.00 35.13 3.67
1801 1903 2.821366 CCAGTCGACCATGCAGCC 60.821 66.667 13.01 0.00 0.00 4.85
1816 1918 3.071206 GCCAGTCTCCGGAGAGCA 61.071 66.667 34.41 11.24 40.22 4.26
1831 1933 4.443857 GCAGCCAGCGTATGATCA 57.556 55.556 0.00 0.00 0.00 2.92
1833 1935 0.305922 GCAGCCAGCGTATGATCAAC 59.694 55.000 0.00 0.00 0.00 3.18
1868 1971 1.806542 CAACCAACTCAATCCAGTCCG 59.193 52.381 0.00 0.00 0.00 4.79
1871 1974 1.079127 AACTCAATCCAGTCCGCCG 60.079 57.895 0.00 0.00 0.00 6.46
1980 2089 4.379082 GGTGGCGAGATTTTTCAATACGTT 60.379 41.667 0.00 0.00 0.00 3.99
2098 2209 2.749621 ACAATCGCCACCATCTTCTTTC 59.250 45.455 0.00 0.00 0.00 2.62
2106 2217 4.082517 GCCACCATCTTCTTTCTTTTCTCC 60.083 45.833 0.00 0.00 0.00 3.71
2114 2225 5.247337 TCTTCTTTCTTTTCTCCCTCTCTCC 59.753 44.000 0.00 0.00 0.00 3.71
2252 2382 9.613428 TTCTGGATTTTGATCTCGTATACAATT 57.387 29.630 3.32 0.00 0.00 2.32
2253 2383 9.045223 TCTGGATTTTGATCTCGTATACAATTG 57.955 33.333 3.24 3.24 0.00 2.32
2278 2408 2.162208 TGATCCAGTGGTTCGTACGTAC 59.838 50.000 15.90 15.90 0.00 3.67
2329 2460 3.677527 CTGGTGGGAGCAGCAAAG 58.322 61.111 0.00 0.00 36.88 2.77
2330 2461 2.598394 TGGTGGGAGCAGCAAAGC 60.598 61.111 0.00 0.00 0.00 3.51
2382 2523 2.438975 CGGCCACCATGCACTCAT 60.439 61.111 2.24 0.00 0.00 2.90
2393 2535 5.124297 CACCATGCACTCATTAATCAGTTGA 59.876 40.000 0.00 0.00 0.00 3.18
2395 2537 5.587443 CCATGCACTCATTAATCAGTTGAGA 59.413 40.000 9.46 0.00 39.36 3.27
2440 2585 2.865308 CTGCATGCGTGTGTCTGG 59.135 61.111 14.09 0.00 0.00 3.86
2444 2589 0.742281 GCATGCGTGTGTCTGGATCT 60.742 55.000 0.00 0.00 0.00 2.75
2448 2593 1.276138 TGCGTGTGTCTGGATCTGAAT 59.724 47.619 0.00 0.00 0.00 2.57
2459 2604 2.040213 GATCTGAATGTGCCGGTGCG 62.040 60.000 1.90 0.00 41.78 5.34
2468 2613 1.522806 TGCCGGTGCGATTATGGAC 60.523 57.895 1.90 0.00 41.78 4.02
2469 2614 2.594962 GCCGGTGCGATTATGGACG 61.595 63.158 1.90 0.00 0.00 4.79
2472 2617 0.939577 CGGTGCGATTATGGACGAGG 60.940 60.000 0.00 0.00 0.00 4.63
2473 2618 0.600255 GGTGCGATTATGGACGAGGG 60.600 60.000 0.00 0.00 0.00 4.30
2474 2619 1.069090 TGCGATTATGGACGAGGGC 59.931 57.895 0.00 0.00 0.00 5.19
2475 2620 2.022129 GCGATTATGGACGAGGGCG 61.022 63.158 0.00 0.00 44.79 6.13
2493 2638 4.015406 TCGTGGCGGATTGGTGCT 62.015 61.111 0.00 0.00 0.00 4.40
2570 2739 0.947244 CCAGTGGCAATTAGGATCGC 59.053 55.000 0.00 0.00 0.00 4.58
2571 2740 1.667236 CAGTGGCAATTAGGATCGCA 58.333 50.000 0.00 0.00 0.00 5.10
2572 2741 1.600957 CAGTGGCAATTAGGATCGCAG 59.399 52.381 0.00 0.00 0.00 5.18
2573 2742 0.947244 GTGGCAATTAGGATCGCAGG 59.053 55.000 0.00 0.00 0.00 4.85
2574 2743 0.546122 TGGCAATTAGGATCGCAGGT 59.454 50.000 0.00 0.00 0.00 4.00
2575 2744 1.765904 TGGCAATTAGGATCGCAGGTA 59.234 47.619 0.00 0.00 0.00 3.08
2576 2745 2.224281 TGGCAATTAGGATCGCAGGTAG 60.224 50.000 0.00 0.00 0.00 3.18
2577 2746 2.037251 GGCAATTAGGATCGCAGGTAGA 59.963 50.000 0.00 0.00 0.00 2.59
2578 2747 3.494398 GGCAATTAGGATCGCAGGTAGAA 60.494 47.826 0.00 0.00 0.00 2.10
2579 2748 4.319177 GCAATTAGGATCGCAGGTAGAAT 58.681 43.478 0.00 0.00 0.00 2.40
2580 2749 4.153117 GCAATTAGGATCGCAGGTAGAATG 59.847 45.833 0.00 0.00 0.00 2.67
2581 2750 3.386768 TTAGGATCGCAGGTAGAATGC 57.613 47.619 0.00 0.00 40.35 3.56
2582 2751 1.418334 AGGATCGCAGGTAGAATGCT 58.582 50.000 0.00 0.00 41.61 3.79
2583 2752 1.069823 AGGATCGCAGGTAGAATGCTG 59.930 52.381 0.00 0.00 41.61 4.41
2584 2753 1.506493 GATCGCAGGTAGAATGCTGG 58.494 55.000 0.00 0.00 41.61 4.85
2585 2754 0.833287 ATCGCAGGTAGAATGCTGGT 59.167 50.000 0.00 0.00 41.61 4.00
2586 2755 0.108186 TCGCAGGTAGAATGCTGGTG 60.108 55.000 0.00 0.00 41.61 4.17
2587 2756 1.709147 CGCAGGTAGAATGCTGGTGC 61.709 60.000 0.00 0.00 41.61 5.01
2596 2765 2.352039 TGCTGGTGCATGCTGCTA 59.648 55.556 20.33 8.85 45.31 3.49
2597 2766 1.747745 TGCTGGTGCATGCTGCTAG 60.748 57.895 20.33 18.37 45.31 3.42
2598 2767 1.748122 GCTGGTGCATGCTGCTAGT 60.748 57.895 20.33 0.00 45.31 2.57
2599 2768 0.462581 GCTGGTGCATGCTGCTAGTA 60.463 55.000 20.33 0.00 45.31 1.82
2600 2769 1.813092 GCTGGTGCATGCTGCTAGTAT 60.813 52.381 20.33 0.00 45.31 2.12
2601 2770 2.548707 GCTGGTGCATGCTGCTAGTATA 60.549 50.000 20.33 0.00 45.31 1.47
2602 2771 3.867600 GCTGGTGCATGCTGCTAGTATAT 60.868 47.826 20.33 0.00 45.31 0.86
2603 2772 3.667360 TGGTGCATGCTGCTAGTATATG 58.333 45.455 20.33 0.00 45.31 1.78
2604 2773 3.071457 TGGTGCATGCTGCTAGTATATGT 59.929 43.478 20.33 0.00 45.31 2.29
2605 2774 4.283212 TGGTGCATGCTGCTAGTATATGTA 59.717 41.667 20.33 0.00 45.31 2.29
2606 2775 4.627467 GGTGCATGCTGCTAGTATATGTAC 59.373 45.833 20.33 13.62 45.31 2.90
2607 2776 4.324669 GTGCATGCTGCTAGTATATGTACG 59.675 45.833 20.33 0.00 45.31 3.67
2608 2777 3.859961 GCATGCTGCTAGTATATGTACGG 59.140 47.826 11.37 0.00 40.96 4.02
2609 2778 4.424626 CATGCTGCTAGTATATGTACGGG 58.575 47.826 0.00 0.00 35.92 5.28
2610 2779 3.493334 TGCTGCTAGTATATGTACGGGT 58.507 45.455 0.00 0.00 35.92 5.28
2611 2780 3.254903 TGCTGCTAGTATATGTACGGGTG 59.745 47.826 0.00 0.00 35.92 4.61
2612 2781 3.504906 GCTGCTAGTATATGTACGGGTGA 59.495 47.826 0.00 0.00 35.92 4.02
2613 2782 4.158025 GCTGCTAGTATATGTACGGGTGAT 59.842 45.833 0.00 0.00 35.92 3.06
2614 2783 5.336531 GCTGCTAGTATATGTACGGGTGATT 60.337 44.000 0.00 0.00 35.92 2.57
2615 2784 6.020971 TGCTAGTATATGTACGGGTGATTG 57.979 41.667 0.00 0.00 35.92 2.67
2616 2785 5.047590 TGCTAGTATATGTACGGGTGATTGG 60.048 44.000 0.00 0.00 35.92 3.16
2617 2786 5.047519 GCTAGTATATGTACGGGTGATTGGT 60.048 44.000 0.00 0.00 35.92 3.67
2618 2787 5.881923 AGTATATGTACGGGTGATTGGTT 57.118 39.130 0.00 0.00 35.92 3.67
2619 2788 6.243216 AGTATATGTACGGGTGATTGGTTT 57.757 37.500 0.00 0.00 35.92 3.27
2620 2789 6.053005 AGTATATGTACGGGTGATTGGTTTG 58.947 40.000 0.00 0.00 35.92 2.93
2621 2790 1.898902 TGTACGGGTGATTGGTTTGG 58.101 50.000 0.00 0.00 0.00 3.28
2622 2791 1.420514 TGTACGGGTGATTGGTTTGGA 59.579 47.619 0.00 0.00 0.00 3.53
2623 2792 2.040545 TGTACGGGTGATTGGTTTGGAT 59.959 45.455 0.00 0.00 0.00 3.41
2624 2793 1.544724 ACGGGTGATTGGTTTGGATG 58.455 50.000 0.00 0.00 0.00 3.51
2625 2794 0.817013 CGGGTGATTGGTTTGGATGG 59.183 55.000 0.00 0.00 0.00 3.51
2626 2795 1.194218 GGGTGATTGGTTTGGATGGG 58.806 55.000 0.00 0.00 0.00 4.00
2627 2796 1.552254 GGGTGATTGGTTTGGATGGGT 60.552 52.381 0.00 0.00 0.00 4.51
2628 2797 1.550072 GGTGATTGGTTTGGATGGGTG 59.450 52.381 0.00 0.00 0.00 4.61
2629 2798 2.247358 GTGATTGGTTTGGATGGGTGT 58.753 47.619 0.00 0.00 0.00 4.16
2630 2799 2.632512 GTGATTGGTTTGGATGGGTGTT 59.367 45.455 0.00 0.00 0.00 3.32
2631 2800 3.829601 GTGATTGGTTTGGATGGGTGTTA 59.170 43.478 0.00 0.00 0.00 2.41
2632 2801 4.082245 GTGATTGGTTTGGATGGGTGTTAG 60.082 45.833 0.00 0.00 0.00 2.34
2633 2802 2.595750 TGGTTTGGATGGGTGTTAGG 57.404 50.000 0.00 0.00 0.00 2.69
2634 2803 1.182667 GGTTTGGATGGGTGTTAGGC 58.817 55.000 0.00 0.00 0.00 3.93
2635 2804 1.182667 GTTTGGATGGGTGTTAGGCC 58.817 55.000 0.00 0.00 0.00 5.19
2636 2805 0.780637 TTTGGATGGGTGTTAGGCCA 59.219 50.000 5.01 0.00 0.00 5.36
2637 2806 0.039035 TTGGATGGGTGTTAGGCCAC 59.961 55.000 5.01 0.00 34.52 5.01
2644 2813 2.466867 GTGTTAGGCCACCACATCG 58.533 57.895 5.01 0.00 0.00 3.84
2645 2814 1.024579 GTGTTAGGCCACCACATCGG 61.025 60.000 5.01 0.00 42.50 4.18
2646 2815 1.195442 TGTTAGGCCACCACATCGGA 61.195 55.000 5.01 0.00 38.63 4.55
2647 2816 0.180406 GTTAGGCCACCACATCGGAT 59.820 55.000 5.01 0.00 38.63 4.18
2648 2817 0.180171 TTAGGCCACCACATCGGATG 59.820 55.000 16.20 16.20 38.63 3.51
2649 2818 0.689412 TAGGCCACCACATCGGATGA 60.689 55.000 23.98 0.00 38.63 2.92
2650 2819 1.819632 GGCCACCACATCGGATGAC 60.820 63.158 23.98 6.25 38.63 3.06
2651 2820 1.819632 GCCACCACATCGGATGACC 60.820 63.158 23.98 2.55 38.63 4.02
2663 2832 1.982612 GGATGACCGAAAAGCAAAGC 58.017 50.000 0.00 0.00 0.00 3.51
2664 2833 1.402852 GGATGACCGAAAAGCAAAGCC 60.403 52.381 0.00 0.00 0.00 4.35
2665 2834 1.269448 GATGACCGAAAAGCAAAGCCA 59.731 47.619 0.00 0.00 0.00 4.75
2666 2835 0.667993 TGACCGAAAAGCAAAGCCAG 59.332 50.000 0.00 0.00 0.00 4.85
2667 2836 0.664466 GACCGAAAAGCAAAGCCAGC 60.664 55.000 0.00 0.00 0.00 4.85
2668 2837 1.109323 ACCGAAAAGCAAAGCCAGCT 61.109 50.000 0.00 0.00 45.97 4.24
2669 2838 0.387750 CCGAAAAGCAAAGCCAGCTC 60.388 55.000 0.00 0.00 42.53 4.09
2670 2839 0.387750 CGAAAAGCAAAGCCAGCTCC 60.388 55.000 0.00 0.00 42.53 4.70
2671 2840 0.675633 GAAAAGCAAAGCCAGCTCCA 59.324 50.000 0.00 0.00 42.53 3.86
2672 2841 0.677842 AAAAGCAAAGCCAGCTCCAG 59.322 50.000 0.00 0.00 42.53 3.86
2673 2842 1.813728 AAAGCAAAGCCAGCTCCAGC 61.814 55.000 0.00 0.00 42.53 4.85
2685 2854 4.776322 TCCAGCGCGGTGGATTGG 62.776 66.667 46.16 27.56 41.99 3.16
2687 2856 3.803082 CAGCGCGGTGGATTGGTG 61.803 66.667 29.65 1.57 0.00 4.17
2688 2857 4.015406 AGCGCGGTGGATTGGTGA 62.015 61.111 11.39 0.00 0.00 4.02
2689 2858 2.824041 GCGCGGTGGATTGGTGAT 60.824 61.111 8.83 0.00 0.00 3.06
2690 2859 3.101209 CGCGGTGGATTGGTGATG 58.899 61.111 0.00 0.00 0.00 3.07
2691 2860 1.449423 CGCGGTGGATTGGTGATGA 60.449 57.895 0.00 0.00 0.00 2.92
2692 2861 0.815213 CGCGGTGGATTGGTGATGAT 60.815 55.000 0.00 0.00 0.00 2.45
2693 2862 1.392589 GCGGTGGATTGGTGATGATT 58.607 50.000 0.00 0.00 0.00 2.57
2694 2863 1.066002 GCGGTGGATTGGTGATGATTG 59.934 52.381 0.00 0.00 0.00 2.67
2695 2864 1.066002 CGGTGGATTGGTGATGATTGC 59.934 52.381 0.00 0.00 0.00 3.56
2696 2865 1.066002 GGTGGATTGGTGATGATTGCG 59.934 52.381 0.00 0.00 0.00 4.85
2697 2866 1.066002 GTGGATTGGTGATGATTGCGG 59.934 52.381 0.00 0.00 0.00 5.69
2698 2867 1.340893 TGGATTGGTGATGATTGCGGT 60.341 47.619 0.00 0.00 0.00 5.68
2699 2868 1.750778 GGATTGGTGATGATTGCGGTT 59.249 47.619 0.00 0.00 0.00 4.44
2700 2869 2.166254 GGATTGGTGATGATTGCGGTTT 59.834 45.455 0.00 0.00 0.00 3.27
2701 2870 3.368323 GGATTGGTGATGATTGCGGTTTT 60.368 43.478 0.00 0.00 0.00 2.43
2702 2871 3.296322 TTGGTGATGATTGCGGTTTTC 57.704 42.857 0.00 0.00 0.00 2.29
2703 2872 1.198867 TGGTGATGATTGCGGTTTTCG 59.801 47.619 0.00 0.00 42.76 3.46
2712 2881 3.711842 CGGTTTTCGCGCTCTGCA 61.712 61.111 5.56 0.00 46.97 4.41
2713 2882 2.870372 GGTTTTCGCGCTCTGCAT 59.130 55.556 5.56 0.00 46.97 3.96
2714 2883 1.512734 GGTTTTCGCGCTCTGCATG 60.513 57.895 5.56 0.00 46.97 4.06
2715 2884 2.148365 GTTTTCGCGCTCTGCATGC 61.148 57.895 11.82 11.82 46.97 4.06
2721 2890 3.270092 CGCTCTGCATGCGCTGAT 61.270 61.111 18.57 0.00 46.72 2.90
2722 2891 2.632541 GCTCTGCATGCGCTGATC 59.367 61.111 14.09 3.40 44.07 2.92
2723 2892 2.929116 CTCTGCATGCGCTGATCG 59.071 61.111 14.09 0.00 44.07 3.69
2724 2893 2.586914 TCTGCATGCGCTGATCGG 60.587 61.111 14.09 0.00 40.74 4.18
2725 2894 4.309347 CTGCATGCGCTGATCGGC 62.309 66.667 17.01 17.01 39.30 5.54
2728 2897 3.204119 CATGCGCTGATCGGCCAA 61.204 61.111 20.82 9.52 38.94 4.52
2729 2898 2.898840 ATGCGCTGATCGGCCAAG 60.899 61.111 20.82 8.19 38.94 3.61
2730 2899 3.687321 ATGCGCTGATCGGCCAAGT 62.687 57.895 20.82 3.50 38.94 3.16
2731 2900 2.202878 GCGCTGATCGGCCAAGTA 60.203 61.111 20.82 0.00 38.94 2.24
2732 2901 2.526120 GCGCTGATCGGCCAAGTAC 61.526 63.158 20.82 0.17 38.94 2.73
2733 2902 1.141881 CGCTGATCGGCCAAGTACT 59.858 57.895 20.82 0.00 33.78 2.73
2734 2903 0.872021 CGCTGATCGGCCAAGTACTC 60.872 60.000 20.82 0.00 33.78 2.59
2735 2904 0.530870 GCTGATCGGCCAAGTACTCC 60.531 60.000 16.13 0.00 0.00 3.85
2736 2905 1.115467 CTGATCGGCCAAGTACTCCT 58.885 55.000 2.24 0.00 0.00 3.69
2737 2906 0.824109 TGATCGGCCAAGTACTCCTG 59.176 55.000 2.24 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.772384 TACCCCCGCAAAAGGAAGAA 59.228 50.000 0.00 0.00 0.00 2.52
29 30 0.772384 TTACCCCCGCAAAAGGAAGA 59.228 50.000 0.00 0.00 0.00 2.87
30 31 1.173913 CTTACCCCCGCAAAAGGAAG 58.826 55.000 0.00 0.00 0.00 3.46
34 35 2.721425 TATCCTTACCCCCGCAAAAG 57.279 50.000 0.00 0.00 0.00 2.27
35 36 3.203487 AGATTATCCTTACCCCCGCAAAA 59.797 43.478 0.00 0.00 0.00 2.44
36 37 2.781174 AGATTATCCTTACCCCCGCAAA 59.219 45.455 0.00 0.00 0.00 3.68
37 38 2.414612 AGATTATCCTTACCCCCGCAA 58.585 47.619 0.00 0.00 0.00 4.85
114 119 9.472361 GTAATCGCTTTGAGTATACAATAAGGA 57.528 33.333 5.50 5.47 28.63 3.36
130 135 2.482721 CGGGTCAACAAGTAATCGCTTT 59.517 45.455 0.00 0.00 0.00 3.51
136 141 4.695455 CACATCTTCGGGTCAACAAGTAAT 59.305 41.667 0.00 0.00 0.00 1.89
151 156 4.761739 TGTCCAAGTTCCATTCACATCTTC 59.238 41.667 0.00 0.00 0.00 2.87
154 159 4.761739 TCTTGTCCAAGTTCCATTCACATC 59.238 41.667 6.90 0.00 39.38 3.06
162 169 3.951680 GGTTTCTTCTTGTCCAAGTTCCA 59.048 43.478 6.90 0.00 39.38 3.53
175 182 0.108585 TTGCCGCTCTGGTTTCTTCT 59.891 50.000 0.00 0.00 41.21 2.85
262 274 0.713329 CGCAACGTCACATTCGATCA 59.287 50.000 0.00 0.00 0.00 2.92
263 275 0.025001 CCGCAACGTCACATTCGATC 59.975 55.000 0.00 0.00 0.00 3.69
264 276 0.669318 ACCGCAACGTCACATTCGAT 60.669 50.000 0.00 0.00 0.00 3.59
265 277 1.279527 GACCGCAACGTCACATTCGA 61.280 55.000 0.00 0.00 32.74 3.71
266 278 1.129809 GACCGCAACGTCACATTCG 59.870 57.895 0.00 0.00 32.74 3.34
269 281 0.037326 AGATGACCGCAACGTCACAT 60.037 50.000 0.00 0.00 45.19 3.21
275 287 1.556564 ACGATAAGATGACCGCAACG 58.443 50.000 0.00 0.00 0.00 4.10
277 289 6.201425 GGTAAATTACGATAAGATGACCGCAA 59.799 38.462 0.00 0.00 0.00 4.85
282 294 7.859377 TCTCGTGGTAAATTACGATAAGATGAC 59.141 37.037 1.91 0.00 46.66 3.06
288 300 8.863049 GTTCTTTCTCGTGGTAAATTACGATAA 58.137 33.333 1.91 0.00 46.66 1.75
293 305 6.872547 AGAGGTTCTTTCTCGTGGTAAATTAC 59.127 38.462 0.00 0.00 36.45 1.89
297 311 4.342951 TGAGAGGTTCTTTCTCGTGGTAAA 59.657 41.667 0.00 0.00 43.16 2.01
328 342 0.179234 TTGTTGTCGCTGGTCCAAGA 59.821 50.000 0.00 0.00 0.00 3.02
329 343 0.307760 GTTGTTGTCGCTGGTCCAAG 59.692 55.000 0.00 0.00 0.00 3.61
353 371 0.944386 GTGGAAACAGAAGCGAGCAA 59.056 50.000 0.00 0.00 44.46 3.91
354 372 0.179059 TGTGGAAACAGAAGCGAGCA 60.179 50.000 0.00 0.00 44.46 4.26
355 373 0.514691 CTGTGGAAACAGAAGCGAGC 59.485 55.000 0.00 0.00 44.46 5.03
356 374 1.528586 CACTGTGGAAACAGAAGCGAG 59.471 52.381 12.57 0.00 44.46 5.03
357 375 1.138069 TCACTGTGGAAACAGAAGCGA 59.862 47.619 12.57 1.52 44.46 4.93
358 376 1.528586 CTCACTGTGGAAACAGAAGCG 59.471 52.381 12.57 0.00 44.46 4.68
359 377 2.805099 CTCTCACTGTGGAAACAGAAGC 59.195 50.000 12.57 0.00 44.46 3.86
360 378 4.065321 ACTCTCACTGTGGAAACAGAAG 57.935 45.455 12.57 9.10 44.46 2.85
361 379 5.607939 TTACTCTCACTGTGGAAACAGAA 57.392 39.130 12.57 0.24 44.46 3.02
362 380 5.607939 TTTACTCTCACTGTGGAAACAGA 57.392 39.130 12.57 2.12 44.46 3.41
363 381 7.359264 CGTTATTTACTCTCACTGTGGAAACAG 60.359 40.741 8.11 4.36 44.46 3.16
375 393 6.128391 GGTGCACAATTCGTTATTTACTCTCA 60.128 38.462 20.43 0.00 0.00 3.27
376 394 6.128391 TGGTGCACAATTCGTTATTTACTCTC 60.128 38.462 20.43 0.00 0.00 3.20
381 399 6.751514 ATCTGGTGCACAATTCGTTATTTA 57.248 33.333 20.43 0.00 0.00 1.40
384 402 5.182487 TGTATCTGGTGCACAATTCGTTAT 58.818 37.500 20.43 2.89 0.00 1.89
385 403 4.570930 TGTATCTGGTGCACAATTCGTTA 58.429 39.130 20.43 0.00 0.00 3.18
386 404 3.407698 TGTATCTGGTGCACAATTCGTT 58.592 40.909 20.43 0.00 0.00 3.85
387 405 3.052455 TGTATCTGGTGCACAATTCGT 57.948 42.857 20.43 1.59 0.00 3.85
388 406 4.345288 CATTGTATCTGGTGCACAATTCG 58.655 43.478 20.43 0.00 40.09 3.34
389 407 4.107622 GCATTGTATCTGGTGCACAATTC 58.892 43.478 20.43 7.39 40.09 2.17
396 414 4.114794 GGAATTTGCATTGTATCTGGTGC 58.885 43.478 0.00 0.00 38.05 5.01
402 420 5.036737 CGGAACTGGAATTTGCATTGTATC 58.963 41.667 0.00 0.00 0.00 2.24
408 426 2.094675 CCTCGGAACTGGAATTTGCAT 58.905 47.619 0.00 0.00 0.00 3.96
409 427 1.533625 CCTCGGAACTGGAATTTGCA 58.466 50.000 0.00 0.00 0.00 4.08
410 428 0.171231 GCCTCGGAACTGGAATTTGC 59.829 55.000 0.00 0.00 0.00 3.68
411 429 1.533625 TGCCTCGGAACTGGAATTTG 58.466 50.000 0.00 0.00 0.00 2.32
412 430 1.886542 GTTGCCTCGGAACTGGAATTT 59.113 47.619 0.00 0.00 0.00 1.82
420 438 0.168128 CGAATTGGTTGCCTCGGAAC 59.832 55.000 0.00 0.00 0.00 3.62
422 440 2.038269 GCGAATTGGTTGCCTCGGA 61.038 57.895 0.00 0.00 0.00 4.55
424 442 2.485122 GGCGAATTGGTTGCCTCG 59.515 61.111 0.00 0.00 45.40 4.63
429 447 0.096976 CTAGCGTGGCGAATTGGTTG 59.903 55.000 0.00 0.00 0.00 3.77
433 451 0.247814 CAAGCTAGCGTGGCGAATTG 60.248 55.000 21.34 8.52 34.52 2.32
437 455 2.126071 GACAAGCTAGCGTGGCGA 60.126 61.111 29.97 0.00 34.52 5.54
438 456 3.188786 GGACAAGCTAGCGTGGCG 61.189 66.667 29.97 9.90 34.24 5.69
443 461 0.179089 AGCTGATGGACAAGCTAGCG 60.179 55.000 9.55 0.00 36.36 4.26
445 463 3.118847 TCTGAAGCTGATGGACAAGCTAG 60.119 47.826 0.00 0.00 34.45 3.42
446 464 2.833943 TCTGAAGCTGATGGACAAGCTA 59.166 45.455 0.00 0.00 34.45 3.32
452 470 2.613133 GCTTGATCTGAAGCTGATGGAC 59.387 50.000 9.86 0.00 44.26 4.02
453 471 2.915349 GCTTGATCTGAAGCTGATGGA 58.085 47.619 9.86 0.00 44.26 3.41
461 479 2.614520 CTCATGGCTGCTTGATCTGAAG 59.385 50.000 0.00 0.00 0.00 3.02
462 480 2.026542 ACTCATGGCTGCTTGATCTGAA 60.027 45.455 0.00 0.00 0.00 3.02
463 481 1.558294 ACTCATGGCTGCTTGATCTGA 59.442 47.619 0.00 0.00 0.00 3.27
464 482 2.039818 ACTCATGGCTGCTTGATCTG 57.960 50.000 0.00 0.00 0.00 2.90
465 483 2.026542 TCAACTCATGGCTGCTTGATCT 60.027 45.455 0.00 0.00 0.00 2.75
466 484 2.097142 GTCAACTCATGGCTGCTTGATC 59.903 50.000 0.00 0.00 0.00 2.92
469 487 0.167470 CGTCAACTCATGGCTGCTTG 59.833 55.000 0.00 0.00 0.00 4.01
473 491 1.284657 CTAGCGTCAACTCATGGCTG 58.715 55.000 0.00 0.00 35.28 4.85
507 525 8.835439 TCGGTTGTACGTATTTGTATCTGTATA 58.165 33.333 0.00 0.00 34.94 1.47
508 526 7.645340 GTCGGTTGTACGTATTTGTATCTGTAT 59.355 37.037 0.00 0.00 34.94 2.29
514 532 4.104776 CGGTCGGTTGTACGTATTTGTAT 58.895 43.478 0.00 0.00 34.94 2.29
524 542 0.441145 GCAACATCGGTCGGTTGTAC 59.559 55.000 11.77 0.00 44.70 2.90
525 543 0.319083 AGCAACATCGGTCGGTTGTA 59.681 50.000 11.77 0.00 44.70 2.41
526 544 0.534203 AAGCAACATCGGTCGGTTGT 60.534 50.000 11.77 4.85 44.70 3.32
535 554 2.416547 ACAATTCTCCGAAGCAACATCG 59.583 45.455 0.00 0.00 39.92 3.84
544 563 3.861113 GTGCATACGTACAATTCTCCGAA 59.139 43.478 0.00 0.00 0.00 4.30
546 565 2.215587 CGTGCATACGTACAATTCTCCG 59.784 50.000 0.00 0.00 44.99 4.63
547 566 3.836229 CGTGCATACGTACAATTCTCC 57.164 47.619 0.00 0.00 44.99 3.71
563 582 0.594284 GACCAGTAGCCGATACGTGC 60.594 60.000 0.00 0.00 39.55 5.34
564 583 0.030369 GGACCAGTAGCCGATACGTG 59.970 60.000 0.00 0.00 39.55 4.49
568 587 4.397103 CGTATATTGGACCAGTAGCCGATA 59.603 45.833 10.71 0.00 35.54 2.92
571 590 2.295349 ACGTATATTGGACCAGTAGCCG 59.705 50.000 13.28 13.28 0.00 5.52
573 592 4.470462 CGTACGTATATTGGACCAGTAGC 58.530 47.826 7.22 0.00 0.00 3.58
590 617 1.019278 GGCCCATGCATATCCGTACG 61.019 60.000 8.69 8.69 40.13 3.67
594 621 0.675837 CAGAGGCCCATGCATATCCG 60.676 60.000 0.00 0.00 40.13 4.18
649 702 2.835431 AGCCTGACCCGATCCGAG 60.835 66.667 0.00 0.00 0.00 4.63
710 763 3.356639 GAGGACATCGACGGCAGCA 62.357 63.158 0.00 0.00 0.00 4.41
713 766 0.965866 AGAAGAGGACATCGACGGCA 60.966 55.000 0.00 0.00 0.00 5.69
741 794 0.394762 TAAACTAGCTCCGCTCGGGA 60.395 55.000 8.59 0.00 44.68 5.14
747 802 4.870991 GGGATAATCATAAACTAGCTCCGC 59.129 45.833 0.00 0.00 0.00 5.54
751 806 7.149202 TGGTTGGGATAATCATAAACTAGCT 57.851 36.000 0.00 0.00 0.00 3.32
872 932 0.396974 TTGGTTTGCAGGAGCTGGTT 60.397 50.000 0.00 0.00 42.74 3.67
886 953 4.145052 CAAAGGAGGAGTAGCTTTTGGTT 58.855 43.478 0.00 0.00 0.00 3.67
919 990 2.441901 CTCGGCTGCTCTCTCCCT 60.442 66.667 0.00 0.00 0.00 4.20
1436 1520 3.554342 CCATCTCCCCTCCGGCAG 61.554 72.222 0.00 0.00 0.00 4.85
1772 1865 0.320374 TCGACTGGTTGTGGATGACC 59.680 55.000 0.00 0.00 36.45 4.02
1786 1884 2.267006 CTGGCTGCATGGTCGACT 59.733 61.111 16.46 0.00 0.00 4.18
1801 1903 2.493973 GCTGCTCTCCGGAGACTG 59.506 66.667 30.49 26.25 41.86 3.51
1816 1918 0.541392 TGGTTGATCATACGCTGGCT 59.459 50.000 0.00 0.00 0.00 4.75
1823 1925 5.761726 TGCTGAATCTGATGGTTGATCATAC 59.238 40.000 0.00 0.00 40.46 2.39
1824 1926 5.761726 GTGCTGAATCTGATGGTTGATCATA 59.238 40.000 0.00 0.00 40.46 2.15
1825 1927 4.579340 GTGCTGAATCTGATGGTTGATCAT 59.421 41.667 0.00 0.00 40.46 2.45
1826 1928 3.943381 GTGCTGAATCTGATGGTTGATCA 59.057 43.478 0.00 0.00 38.87 2.92
1828 1930 3.959293 TGTGCTGAATCTGATGGTTGAT 58.041 40.909 0.00 0.00 0.00 2.57
1829 1931 3.421919 TGTGCTGAATCTGATGGTTGA 57.578 42.857 0.00 0.00 0.00 3.18
1830 1932 3.366679 GGTTGTGCTGAATCTGATGGTTG 60.367 47.826 0.00 0.00 0.00 3.77
1831 1933 2.821969 GGTTGTGCTGAATCTGATGGTT 59.178 45.455 0.00 0.00 0.00 3.67
1833 1935 2.439409 TGGTTGTGCTGAATCTGATGG 58.561 47.619 0.00 0.00 0.00 3.51
1868 1971 3.654173 GAACGGTAGGTGGGTCGGC 62.654 68.421 0.00 0.00 0.00 5.54
1963 2072 7.581476 TCCAGAACAACGTATTGAAAAATCTC 58.419 34.615 0.00 0.00 39.30 2.75
1964 2073 7.504924 TCCAGAACAACGTATTGAAAAATCT 57.495 32.000 0.00 0.00 39.30 2.40
2098 2209 1.836802 CCAGGGAGAGAGGGAGAAAAG 59.163 57.143 0.00 0.00 0.00 2.27
2106 2217 1.691434 GATAACAGCCAGGGAGAGAGG 59.309 57.143 0.00 0.00 0.00 3.69
2114 2225 5.704888 CTTATCTACTCGATAACAGCCAGG 58.295 45.833 0.00 0.00 39.16 4.45
2156 2277 6.258160 CAACTGGGCGATTAATTAAGACAAG 58.742 40.000 3.94 0.00 0.00 3.16
2159 2281 5.169836 CCAACTGGGCGATTAATTAAGAC 57.830 43.478 3.94 0.34 0.00 3.01
2252 2382 3.417069 ACGAACCACTGGATCAATTCA 57.583 42.857 0.71 0.00 0.00 2.57
2253 2383 3.306166 CGTACGAACCACTGGATCAATTC 59.694 47.826 10.44 0.00 0.00 2.17
2279 2409 1.741327 TAAGCCCAGCGACGGGATAC 61.741 60.000 13.47 0.00 46.85 2.24
2280 2410 1.044231 TTAAGCCCAGCGACGGGATA 61.044 55.000 13.47 3.16 46.85 2.59
2285 2415 2.237751 CGGATTAAGCCCAGCGACG 61.238 63.158 3.70 0.00 0.00 5.12
2286 2416 1.887707 CCGGATTAAGCCCAGCGAC 60.888 63.158 3.70 0.00 0.00 5.19
2305 2436 2.046507 GCTCCCACCAGCAGACAG 60.047 66.667 0.00 0.00 39.43 3.51
2328 2459 1.867233 CTAACGCGGATATGCTTTGCT 59.133 47.619 12.47 0.00 0.00 3.91
2329 2460 1.069906 CCTAACGCGGATATGCTTTGC 60.070 52.381 12.47 0.00 0.00 3.68
2330 2461 2.210116 ACCTAACGCGGATATGCTTTG 58.790 47.619 12.47 0.00 0.00 2.77
2371 2504 5.587443 TCTCAACTGATTAATGAGTGCATGG 59.413 40.000 8.41 0.00 41.04 3.66
2373 2506 7.052248 TCATCTCAACTGATTAATGAGTGCAT 58.948 34.615 8.41 0.00 41.04 3.96
2374 2507 6.408869 TCATCTCAACTGATTAATGAGTGCA 58.591 36.000 8.41 0.00 41.04 4.57
2378 2519 8.945481 AAGTCTCATCTCAACTGATTAATGAG 57.055 34.615 14.65 14.65 41.49 2.90
2379 2520 9.730705 AAAAGTCTCATCTCAACTGATTAATGA 57.269 29.630 0.00 0.00 0.00 2.57
2440 2585 1.723870 GCACCGGCACATTCAGATC 59.276 57.895 0.00 0.00 40.72 2.75
2444 2589 0.391793 TAATCGCACCGGCACATTCA 60.392 50.000 0.00 0.00 41.24 2.57
2448 2593 1.817520 CCATAATCGCACCGGCACA 60.818 57.895 0.00 0.00 41.24 4.57
2474 2619 3.487202 CACCAATCCGCCACGACG 61.487 66.667 0.00 0.00 0.00 5.12
2475 2620 3.799755 GCACCAATCCGCCACGAC 61.800 66.667 0.00 0.00 0.00 4.34
2476 2621 4.015406 AGCACCAATCCGCCACGA 62.015 61.111 0.00 0.00 0.00 4.35
2477 2622 3.803082 CAGCACCAATCCGCCACG 61.803 66.667 0.00 0.00 0.00 4.94
2478 2623 3.443045 CCAGCACCAATCCGCCAC 61.443 66.667 0.00 0.00 0.00 5.01
2479 2624 3.965258 ACCAGCACCAATCCGCCA 61.965 61.111 0.00 0.00 0.00 5.69
2480 2625 3.443045 CACCAGCACCAATCCGCC 61.443 66.667 0.00 0.00 0.00 6.13
2481 2626 3.443045 CCACCAGCACCAATCCGC 61.443 66.667 0.00 0.00 0.00 5.54
2482 2627 3.443045 GCCACCAGCACCAATCCG 61.443 66.667 0.00 0.00 42.97 4.18
2551 2720 0.947244 GCGATCCTAATTGCCACTGG 59.053 55.000 0.00 0.00 36.43 4.00
2552 2721 1.600957 CTGCGATCCTAATTGCCACTG 59.399 52.381 0.00 0.00 41.03 3.66
2553 2722 1.475751 CCTGCGATCCTAATTGCCACT 60.476 52.381 0.00 0.00 41.03 4.00
2554 2723 0.947244 CCTGCGATCCTAATTGCCAC 59.053 55.000 0.00 0.00 41.03 5.01
2555 2724 0.546122 ACCTGCGATCCTAATTGCCA 59.454 50.000 0.00 0.00 41.03 4.92
2556 2725 2.037251 TCTACCTGCGATCCTAATTGCC 59.963 50.000 0.00 0.00 41.03 4.52
2557 2726 3.386768 TCTACCTGCGATCCTAATTGC 57.613 47.619 0.00 0.00 41.94 3.56
2558 2727 4.153117 GCATTCTACCTGCGATCCTAATTG 59.847 45.833 0.00 0.00 0.00 2.32
2559 2728 4.040952 AGCATTCTACCTGCGATCCTAATT 59.959 41.667 0.00 0.00 44.38 1.40
2560 2729 3.580458 AGCATTCTACCTGCGATCCTAAT 59.420 43.478 0.00 0.00 44.38 1.73
2561 2730 2.965831 AGCATTCTACCTGCGATCCTAA 59.034 45.455 0.00 0.00 44.38 2.69
2562 2731 2.297315 CAGCATTCTACCTGCGATCCTA 59.703 50.000 0.00 0.00 44.38 2.94
2563 2732 1.069823 CAGCATTCTACCTGCGATCCT 59.930 52.381 0.00 0.00 44.38 3.24
2564 2733 1.506493 CAGCATTCTACCTGCGATCC 58.494 55.000 0.00 0.00 44.38 3.36
2565 2734 1.202580 ACCAGCATTCTACCTGCGATC 60.203 52.381 0.00 0.00 44.38 3.69
2566 2735 0.833287 ACCAGCATTCTACCTGCGAT 59.167 50.000 0.00 0.00 44.38 4.58
2567 2736 0.108186 CACCAGCATTCTACCTGCGA 60.108 55.000 0.00 0.00 44.38 5.10
2568 2737 1.709147 GCACCAGCATTCTACCTGCG 61.709 60.000 0.00 0.00 44.38 5.18
2569 2738 2.101700 GCACCAGCATTCTACCTGC 58.898 57.895 0.00 0.00 41.58 4.85
2587 2756 4.082190 ACCCGTACATATACTAGCAGCATG 60.082 45.833 0.00 0.00 40.87 4.06
2588 2757 4.082190 CACCCGTACATATACTAGCAGCAT 60.082 45.833 0.00 0.00 0.00 3.79
2589 2758 3.254903 CACCCGTACATATACTAGCAGCA 59.745 47.826 0.00 0.00 0.00 4.41
2590 2759 3.504906 TCACCCGTACATATACTAGCAGC 59.495 47.826 0.00 0.00 0.00 5.25
2591 2760 5.899120 ATCACCCGTACATATACTAGCAG 57.101 43.478 0.00 0.00 0.00 4.24
2592 2761 5.047590 CCAATCACCCGTACATATACTAGCA 60.048 44.000 0.00 0.00 0.00 3.49
2593 2762 5.047519 ACCAATCACCCGTACATATACTAGC 60.048 44.000 0.00 0.00 0.00 3.42
2594 2763 6.585695 ACCAATCACCCGTACATATACTAG 57.414 41.667 0.00 0.00 0.00 2.57
2595 2764 6.982160 AACCAATCACCCGTACATATACTA 57.018 37.500 0.00 0.00 0.00 1.82
2596 2765 5.881923 AACCAATCACCCGTACATATACT 57.118 39.130 0.00 0.00 0.00 2.12
2597 2766 5.237779 CCAAACCAATCACCCGTACATATAC 59.762 44.000 0.00 0.00 0.00 1.47
2598 2767 5.130643 TCCAAACCAATCACCCGTACATATA 59.869 40.000 0.00 0.00 0.00 0.86
2599 2768 4.080243 TCCAAACCAATCACCCGTACATAT 60.080 41.667 0.00 0.00 0.00 1.78
2600 2769 3.263681 TCCAAACCAATCACCCGTACATA 59.736 43.478 0.00 0.00 0.00 2.29
2601 2770 2.040545 TCCAAACCAATCACCCGTACAT 59.959 45.455 0.00 0.00 0.00 2.29
2602 2771 1.420514 TCCAAACCAATCACCCGTACA 59.579 47.619 0.00 0.00 0.00 2.90
2603 2772 2.188062 TCCAAACCAATCACCCGTAC 57.812 50.000 0.00 0.00 0.00 3.67
2604 2773 2.619332 CCATCCAAACCAATCACCCGTA 60.619 50.000 0.00 0.00 0.00 4.02
2605 2774 1.544724 CATCCAAACCAATCACCCGT 58.455 50.000 0.00 0.00 0.00 5.28
2606 2775 0.817013 CCATCCAAACCAATCACCCG 59.183 55.000 0.00 0.00 0.00 5.28
2607 2776 1.194218 CCCATCCAAACCAATCACCC 58.806 55.000 0.00 0.00 0.00 4.61
2608 2777 1.550072 CACCCATCCAAACCAATCACC 59.450 52.381 0.00 0.00 0.00 4.02
2609 2778 2.247358 ACACCCATCCAAACCAATCAC 58.753 47.619 0.00 0.00 0.00 3.06
2610 2779 2.692709 ACACCCATCCAAACCAATCA 57.307 45.000 0.00 0.00 0.00 2.57
2611 2780 3.447229 CCTAACACCCATCCAAACCAATC 59.553 47.826 0.00 0.00 0.00 2.67
2612 2781 3.440127 CCTAACACCCATCCAAACCAAT 58.560 45.455 0.00 0.00 0.00 3.16
2613 2782 2.883026 CCTAACACCCATCCAAACCAA 58.117 47.619 0.00 0.00 0.00 3.67
2614 2783 1.549037 GCCTAACACCCATCCAAACCA 60.549 52.381 0.00 0.00 0.00 3.67
2615 2784 1.182667 GCCTAACACCCATCCAAACC 58.817 55.000 0.00 0.00 0.00 3.27
2616 2785 1.182667 GGCCTAACACCCATCCAAAC 58.817 55.000 0.00 0.00 0.00 2.93
2617 2786 0.780637 TGGCCTAACACCCATCCAAA 59.219 50.000 3.32 0.00 0.00 3.28
2618 2787 0.039035 GTGGCCTAACACCCATCCAA 59.961 55.000 3.32 0.00 35.34 3.53
2619 2788 1.688811 GTGGCCTAACACCCATCCA 59.311 57.895 3.32 0.00 35.34 3.41
2620 2789 4.657952 GTGGCCTAACACCCATCC 57.342 61.111 3.32 0.00 35.34 3.51
2626 2795 1.024579 CCGATGTGGTGGCCTAACAC 61.025 60.000 14.31 14.31 40.60 3.32
2627 2796 1.195442 TCCGATGTGGTGGCCTAACA 61.195 55.000 3.32 6.22 39.52 2.41
2628 2797 0.180406 ATCCGATGTGGTGGCCTAAC 59.820 55.000 3.32 0.00 39.52 2.34
2629 2798 0.180171 CATCCGATGTGGTGGCCTAA 59.820 55.000 3.32 0.00 39.52 2.69
2630 2799 0.689412 TCATCCGATGTGGTGGCCTA 60.689 55.000 3.32 0.00 39.52 3.93
2631 2800 1.995066 TCATCCGATGTGGTGGCCT 60.995 57.895 3.32 0.00 39.52 5.19
2632 2801 1.819632 GTCATCCGATGTGGTGGCC 60.820 63.158 8.24 0.00 39.52 5.36
2633 2802 1.819632 GGTCATCCGATGTGGTGGC 60.820 63.158 8.24 0.00 39.52 5.01
2634 2803 4.540153 GGTCATCCGATGTGGTGG 57.460 61.111 8.24 0.00 39.52 4.61
2644 2813 1.402852 GGCTTTGCTTTTCGGTCATCC 60.403 52.381 0.00 0.00 0.00 3.51
2645 2814 1.269448 TGGCTTTGCTTTTCGGTCATC 59.731 47.619 0.00 0.00 0.00 2.92
2646 2815 1.270550 CTGGCTTTGCTTTTCGGTCAT 59.729 47.619 0.00 0.00 0.00 3.06
2647 2816 0.667993 CTGGCTTTGCTTTTCGGTCA 59.332 50.000 0.00 0.00 0.00 4.02
2648 2817 0.664466 GCTGGCTTTGCTTTTCGGTC 60.664 55.000 0.00 0.00 0.00 4.79
2649 2818 1.109323 AGCTGGCTTTGCTTTTCGGT 61.109 50.000 0.00 0.00 37.52 4.69
2650 2819 0.387750 GAGCTGGCTTTGCTTTTCGG 60.388 55.000 0.00 0.00 41.30 4.30
2651 2820 0.387750 GGAGCTGGCTTTGCTTTTCG 60.388 55.000 0.00 0.00 41.30 3.46
2652 2821 0.675633 TGGAGCTGGCTTTGCTTTTC 59.324 50.000 0.00 0.00 41.30 2.29
2653 2822 0.677842 CTGGAGCTGGCTTTGCTTTT 59.322 50.000 0.00 0.00 41.30 2.27
2654 2823 1.813728 GCTGGAGCTGGCTTTGCTTT 61.814 55.000 0.00 0.00 41.30 3.51
2655 2824 2.273912 GCTGGAGCTGGCTTTGCTT 61.274 57.895 0.00 0.00 41.30 3.91
2656 2825 2.675772 GCTGGAGCTGGCTTTGCT 60.676 61.111 0.00 0.38 44.24 3.91
2657 2826 4.112341 CGCTGGAGCTGGCTTTGC 62.112 66.667 0.00 1.58 39.32 3.68
2658 2827 4.112341 GCGCTGGAGCTGGCTTTG 62.112 66.667 0.00 0.00 39.32 2.77
2667 2836 3.197790 CAATCCACCGCGCTGGAG 61.198 66.667 26.00 11.67 43.82 3.86
2668 2837 4.776322 CCAATCCACCGCGCTGGA 62.776 66.667 24.55 24.55 44.72 3.86
2670 2839 3.803082 CACCAATCCACCGCGCTG 61.803 66.667 5.56 0.00 0.00 5.18
2671 2840 3.329542 ATCACCAATCCACCGCGCT 62.330 57.895 5.56 0.00 0.00 5.92
2672 2841 2.824041 ATCACCAATCCACCGCGC 60.824 61.111 0.00 0.00 0.00 6.86
2673 2842 0.815213 ATCATCACCAATCCACCGCG 60.815 55.000 0.00 0.00 0.00 6.46
2674 2843 1.066002 CAATCATCACCAATCCACCGC 59.934 52.381 0.00 0.00 0.00 5.68
2675 2844 1.066002 GCAATCATCACCAATCCACCG 59.934 52.381 0.00 0.00 0.00 4.94
2676 2845 1.066002 CGCAATCATCACCAATCCACC 59.934 52.381 0.00 0.00 0.00 4.61
2677 2846 1.066002 CCGCAATCATCACCAATCCAC 59.934 52.381 0.00 0.00 0.00 4.02
2678 2847 1.340893 ACCGCAATCATCACCAATCCA 60.341 47.619 0.00 0.00 0.00 3.41
2679 2848 1.392589 ACCGCAATCATCACCAATCC 58.607 50.000 0.00 0.00 0.00 3.01
2680 2849 3.508744 AAACCGCAATCATCACCAATC 57.491 42.857 0.00 0.00 0.00 2.67
2681 2850 3.673052 CGAAAACCGCAATCATCACCAAT 60.673 43.478 0.00 0.00 0.00 3.16
2682 2851 2.351253 CGAAAACCGCAATCATCACCAA 60.351 45.455 0.00 0.00 0.00 3.67
2683 2852 1.198867 CGAAAACCGCAATCATCACCA 59.801 47.619 0.00 0.00 0.00 4.17
2684 2853 1.895051 CGAAAACCGCAATCATCACC 58.105 50.000 0.00 0.00 0.00 4.02
2695 2864 3.027170 ATGCAGAGCGCGAAAACCG 62.027 57.895 12.10 0.00 46.97 4.44
2696 2865 1.512734 CATGCAGAGCGCGAAAACC 60.513 57.895 12.10 0.00 46.97 3.27
2697 2866 2.148365 GCATGCAGAGCGCGAAAAC 61.148 57.895 12.10 0.00 46.97 2.43
2698 2867 2.176546 GCATGCAGAGCGCGAAAA 59.823 55.556 12.10 0.00 46.97 2.29
2705 2874 2.632541 GATCAGCGCATGCAGAGC 59.367 61.111 19.57 13.28 46.23 4.09
2706 2875 2.595878 CCGATCAGCGCATGCAGAG 61.596 63.158 19.57 6.20 46.23 3.35
2707 2876 2.586914 CCGATCAGCGCATGCAGA 60.587 61.111 19.57 12.56 46.23 4.26
2708 2877 4.309347 GCCGATCAGCGCATGCAG 62.309 66.667 19.57 11.69 46.23 4.41
2711 2880 3.177272 CTTGGCCGATCAGCGCATG 62.177 63.158 11.47 5.22 39.11 4.06
2712 2881 2.310327 TACTTGGCCGATCAGCGCAT 62.310 55.000 11.47 0.00 39.11 4.73
2713 2882 3.012859 TACTTGGCCGATCAGCGCA 62.013 57.895 11.47 0.00 39.11 6.09
2714 2883 2.202878 TACTTGGCCGATCAGCGC 60.203 61.111 0.00 0.00 39.11 5.92
2715 2884 0.872021 GAGTACTTGGCCGATCAGCG 60.872 60.000 0.00 0.00 40.47 5.18
2716 2885 0.530870 GGAGTACTTGGCCGATCAGC 60.531 60.000 0.00 0.00 0.00 4.26
2717 2886 1.115467 AGGAGTACTTGGCCGATCAG 58.885 55.000 0.00 0.00 0.00 2.90
2718 2887 0.824109 CAGGAGTACTTGGCCGATCA 59.176 55.000 0.00 0.00 0.00 2.92
2719 2888 3.669354 CAGGAGTACTTGGCCGATC 57.331 57.895 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.