Multiple sequence alignment - TraesCS4B01G373700

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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 TraesCS4B01G373700 chr4B 100.000 3803 0 0 1 3803 657994734 657990932 0.000000e+00 7023
1 TraesCS4B01G373700 chr4B 89.315 496 38 4 1 484 603763450 603762958 3.250000e-170 608
2 TraesCS4B01G373700 chr5A 85.012 2562 213 82 512 2993 697878264 697880734 0.000000e+00 2446
3 TraesCS4B01G373700 chr5A 84.762 1726 161 49 2128 3801 697884078 697885753 0.000000e+00 1637
4 TraesCS4B01G373700 chr5A 86.486 666 65 17 1482 2133 697883350 697884004 0.000000e+00 708
5 TraesCS4B01G373700 chr5A 89.818 550 46 7 2980 3526 697880828 697881370 0.000000e+00 697
6 TraesCS4B01G373700 chr5A 80.952 609 61 31 775 1347 697882640 697883229 7.550000e-117 431
7 TraesCS4B01G373700 chr5A 88.626 211 14 8 3587 3790 697881370 697881577 8.160000e-62 248
8 TraesCS4B01G373700 chr4D 86.635 1923 154 52 961 2836 509173162 509175028 0.000000e+00 2032
9 TraesCS4B01G373700 chr4D 89.282 933 70 16 2886 3803 509175028 509175945 0.000000e+00 1142
10 TraesCS4B01G373700 chr2D 91.441 479 39 2 2 480 471987142 471987618 0.000000e+00 656
11 TraesCS4B01G373700 chr6B 91.079 482 39 4 1 480 132893965 132893486 0.000000e+00 649
12 TraesCS4B01G373700 chr6B 89.858 493 35 7 1 480 132888364 132887874 1.500000e-173 619
13 TraesCS4B01G373700 chr6B 89.796 490 35 4 1 478 502267134 502267620 6.980000e-172 614
14 TraesCS4B01G373700 chr7B 89.879 494 36 5 3 485 325876508 325876998 1.160000e-174 623
15 TraesCS4B01G373700 chr7B 89.047 493 40 3 1 481 614477180 614477670 1.960000e-167 599
16 TraesCS4B01G373700 chr5B 89.228 492 30 7 1 480 704493346 704492866 9.100000e-166 593
17 TraesCS4B01G373700 chr5B 89.030 474 33 5 1 462 704784583 704785049 1.530000e-158 569
18 TraesCS4B01G373700 chrUn 86.382 492 54 8 1 481 25881985 25881496 3.370000e-145 525
19 TraesCS4B01G373700 chrUn 86.382 492 54 8 1 481 238576832 238576343 3.370000e-145 525
20 TraesCS4B01G373700 chr6D 87.324 426 39 4 64 477 282529090 282529512 1.240000e-129 473
21 TraesCS4B01G373700 chr7D 83.768 499 61 6 1 482 633442407 633442902 4.480000e-124 455
22 TraesCS4B01G373700 chr7D 83.768 499 61 6 1 482 633457147 633457642 4.480000e-124 455
23 TraesCS4B01G373700 chr1D 83.661 508 53 7 1 480 404624811 404624306 5.790000e-123 451
24 TraesCS4B01G373700 chr2A 83.434 495 46 16 1 479 202039795 202040269 9.760000e-116 427


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 TraesCS4B01G373700 chr4B 657990932 657994734 3802 True 7023.000000 7023 100.000000 1 3803 1 chr4B.!!$R2 3802
1 TraesCS4B01G373700 chr5A 697878264 697885753 7489 False 1027.833333 2446 85.942667 512 3801 6 chr5A.!!$F1 3289
2 TraesCS4B01G373700 chr4D 509173162 509175945 2783 False 1587.000000 2032 87.958500 961 3803 2 chr4D.!!$F1 2842
3 TraesCS4B01G373700 chr1D 404624306 404624811 505 True 451.000000 451 83.661000 1 480 1 chr1D.!!$R1 479

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
783 840 0.105913 GGGGTAGAGGAGGGAGACAG 60.106 65.0 0.00 0.00 0.00 3.51 F
1413 1515 0.026674 CTGCAACATGTATGCGTCCG 59.973 55.0 20.49 10.39 46.76 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1915 0.107800 CAGAGGACACCTGCTCATGG 60.108 60.0 0.0 0.0 37.33 3.66 R
2851 3017 0.318107 ACTGATGTTGCAAAGCACGC 60.318 50.0 0.0 0.0 38.71 5.34 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
26 27 2.159000 AGACGTGGAAACGGAACTTTCT 60.159 45.455 0.00 0.00 37.45 2.52
92 108 6.350110 CCCAACTACCAAAGAATACACAATGG 60.350 42.308 0.00 0.00 0.00 3.16
100 116 4.724074 AGAATACACAATGGCACAATGG 57.276 40.909 0.00 0.00 44.80 3.16
104 120 2.945447 CACAATGGCACAATGGGTAG 57.055 50.000 0.00 0.00 44.80 3.18
117 133 5.359009 CACAATGGGTAGAATGAGCAGAATT 59.641 40.000 0.00 0.00 0.00 2.17
121 137 5.371526 TGGGTAGAATGAGCAGAATTGATC 58.628 41.667 0.00 0.00 40.13 2.92
151 167 4.274214 GGACCAACTTTTACTACCACACAC 59.726 45.833 0.00 0.00 0.00 3.82
152 168 3.872771 ACCAACTTTTACTACCACACACG 59.127 43.478 0.00 0.00 0.00 4.49
162 178 2.973694 ACCACACACGTACTCAACTT 57.026 45.000 0.00 0.00 0.00 2.66
163 179 4.580167 ACTACCACACACGTACTCAACTTA 59.420 41.667 0.00 0.00 0.00 2.24
164 180 4.595762 ACCACACACGTACTCAACTTAT 57.404 40.909 0.00 0.00 0.00 1.73
169 185 4.768968 ACACACGTACTCAACTTATACCCT 59.231 41.667 0.00 0.00 0.00 4.34
213 229 9.589461 ACTACTACAATACTATCCTATGTTGCT 57.411 33.333 0.00 0.00 0.00 3.91
234 250 9.753669 GTTGCTAACATAACCATTTTATTTTGC 57.246 29.630 0.00 0.00 0.00 3.68
237 253 9.150348 GCTAACATAACCATTTTATTTTGCAGT 57.850 29.630 0.00 0.00 0.00 4.40
258 274 9.755804 TGCAGTCATGTTAACAATTTCATAAAA 57.244 25.926 13.23 0.00 0.00 1.52
311 328 9.454859 CTATGATTCAAGGAGGTTTAAAGTTCT 57.545 33.333 0.00 0.00 0.00 3.01
319 336 4.885325 GGAGGTTTAAAGTTCTGGTCAACA 59.115 41.667 0.00 0.00 0.00 3.33
320 337 5.358725 GGAGGTTTAAAGTTCTGGTCAACAA 59.641 40.000 0.00 0.00 0.00 2.83
321 338 6.127563 GGAGGTTTAAAGTTCTGGTCAACAAA 60.128 38.462 0.00 0.00 0.00 2.83
323 340 5.808540 GGTTTAAAGTTCTGGTCAACAAACC 59.191 40.000 0.00 0.00 34.90 3.27
324 341 3.775661 AAAGTTCTGGTCAACAAACCG 57.224 42.857 0.00 0.00 42.62 4.44
356 373 2.226912 GTGTCCGCTCTATATTCGCTCT 59.773 50.000 0.00 0.00 0.00 4.09
367 384 6.266323 TCTATATTCGCTCTGTGTCTGTTTC 58.734 40.000 0.00 0.00 0.00 2.78
373 390 2.927014 GCTCTGTGTCTGTTTCCGGTAG 60.927 54.545 0.00 0.00 0.00 3.18
378 407 5.011329 TCTGTGTCTGTTTCCGGTAGTATTT 59.989 40.000 0.00 0.00 0.00 1.40
412 441 6.698766 GGTTTCTATATTCGTTTCCGCTTCTA 59.301 38.462 0.00 0.00 0.00 2.10
480 509 1.300233 GCGCCGTTCTCATCCCTAG 60.300 63.158 0.00 0.00 0.00 3.02
481 510 2.017559 GCGCCGTTCTCATCCCTAGT 62.018 60.000 0.00 0.00 0.00 2.57
482 511 0.460311 CGCCGTTCTCATCCCTAGTT 59.540 55.000 0.00 0.00 0.00 2.24
483 512 1.679680 CGCCGTTCTCATCCCTAGTTA 59.320 52.381 0.00 0.00 0.00 2.24
484 513 2.543238 CGCCGTTCTCATCCCTAGTTAC 60.543 54.545 0.00 0.00 0.00 2.50
485 514 2.223994 GCCGTTCTCATCCCTAGTTACC 60.224 54.545 0.00 0.00 0.00 2.85
486 515 3.028850 CCGTTCTCATCCCTAGTTACCA 58.971 50.000 0.00 0.00 0.00 3.25
487 516 3.181478 CCGTTCTCATCCCTAGTTACCAC 60.181 52.174 0.00 0.00 0.00 4.16
488 517 3.181478 CGTTCTCATCCCTAGTTACCACC 60.181 52.174 0.00 0.00 0.00 4.61
489 518 3.769189 TCTCATCCCTAGTTACCACCA 57.231 47.619 0.00 0.00 0.00 4.17
490 519 3.371965 TCTCATCCCTAGTTACCACCAC 58.628 50.000 0.00 0.00 0.00 4.16
491 520 3.104512 CTCATCCCTAGTTACCACCACA 58.895 50.000 0.00 0.00 0.00 4.17
492 521 3.517901 CTCATCCCTAGTTACCACCACAA 59.482 47.826 0.00 0.00 0.00 3.33
493 522 3.517901 TCATCCCTAGTTACCACCACAAG 59.482 47.826 0.00 0.00 0.00 3.16
494 523 1.626825 TCCCTAGTTACCACCACAAGC 59.373 52.381 0.00 0.00 0.00 4.01
495 524 1.349688 CCCTAGTTACCACCACAAGCA 59.650 52.381 0.00 0.00 0.00 3.91
496 525 2.423577 CCTAGTTACCACCACAAGCAC 58.576 52.381 0.00 0.00 0.00 4.40
497 526 2.423577 CTAGTTACCACCACAAGCACC 58.576 52.381 0.00 0.00 0.00 5.01
498 527 0.179001 AGTTACCACCACAAGCACCC 60.179 55.000 0.00 0.00 0.00 4.61
499 528 1.151908 TTACCACCACAAGCACCCC 59.848 57.895 0.00 0.00 0.00 4.95
500 529 1.357272 TTACCACCACAAGCACCCCT 61.357 55.000 0.00 0.00 0.00 4.79
501 530 0.474079 TACCACCACAAGCACCCCTA 60.474 55.000 0.00 0.00 0.00 3.53
502 531 1.140134 ACCACCACAAGCACCCCTAT 61.140 55.000 0.00 0.00 0.00 2.57
503 532 0.394352 CCACCACAAGCACCCCTATC 60.394 60.000 0.00 0.00 0.00 2.08
504 533 0.620556 CACCACAAGCACCCCTATCT 59.379 55.000 0.00 0.00 0.00 1.98
505 534 1.004745 CACCACAAGCACCCCTATCTT 59.995 52.381 0.00 0.00 0.00 2.40
506 535 1.282157 ACCACAAGCACCCCTATCTTC 59.718 52.381 0.00 0.00 0.00 2.87
507 536 1.281867 CCACAAGCACCCCTATCTTCA 59.718 52.381 0.00 0.00 0.00 3.02
508 537 2.092212 CCACAAGCACCCCTATCTTCAT 60.092 50.000 0.00 0.00 0.00 2.57
509 538 3.624777 CACAAGCACCCCTATCTTCATT 58.375 45.455 0.00 0.00 0.00 2.57
510 539 4.385199 CCACAAGCACCCCTATCTTCATTA 60.385 45.833 0.00 0.00 0.00 1.90
515 544 6.966534 AGCACCCCTATCTTCATTAATTTG 57.033 37.500 0.00 0.00 0.00 2.32
541 570 7.307751 GCTGTCACATAAGCAAACTAACTTGTA 60.308 37.037 0.00 0.00 39.31 2.41
562 591 9.444600 CTTGTATTAGGGTGTGTTATGTTACTT 57.555 33.333 0.00 0.00 0.00 2.24
580 613 2.952978 ACTTCCACTATGACTAGCCTCG 59.047 50.000 0.00 0.00 0.00 4.63
582 615 3.014304 TCCACTATGACTAGCCTCGTT 57.986 47.619 0.00 0.00 0.00 3.85
583 616 4.160642 TCCACTATGACTAGCCTCGTTA 57.839 45.455 0.00 0.00 0.00 3.18
584 617 4.135306 TCCACTATGACTAGCCTCGTTAG 58.865 47.826 0.00 0.00 0.00 2.34
585 618 3.304794 CCACTATGACTAGCCTCGTTAGC 60.305 52.174 0.00 0.00 0.00 3.09
586 619 3.315470 CACTATGACTAGCCTCGTTAGCA 59.685 47.826 0.00 0.00 0.00 3.49
587 620 3.566322 ACTATGACTAGCCTCGTTAGCAG 59.434 47.826 0.00 0.00 0.00 4.24
602 643 1.944177 AGCAGAAAGAGGAGGCACTA 58.056 50.000 0.00 0.00 41.55 2.74
609 650 1.770294 AGAGGAGGCACTAGTAGCAC 58.230 55.000 15.90 10.43 41.55 4.40
612 653 3.053544 AGAGGAGGCACTAGTAGCACTAA 60.054 47.826 15.90 0.00 41.55 2.24
613 654 3.292460 AGGAGGCACTAGTAGCACTAAG 58.708 50.000 15.90 0.00 41.55 2.18
614 655 2.362717 GGAGGCACTAGTAGCACTAAGG 59.637 54.545 15.90 0.00 41.55 2.69
643 686 3.655810 GAGCACAGGAGGACAGGCG 62.656 68.421 0.00 0.00 0.00 5.52
650 693 4.154347 GAGGACAGGCGCCTCCAG 62.154 72.222 30.35 21.54 44.96 3.86
651 694 4.704103 AGGACAGGCGCCTCCAGA 62.704 66.667 30.35 0.00 37.29 3.86
652 695 4.154347 GGACAGGCGCCTCCAGAG 62.154 72.222 30.29 18.37 37.29 3.35
665 708 1.274728 CTCCAGAGTCCAGACACAAGG 59.725 57.143 0.00 1.13 0.00 3.61
677 720 2.829120 AGACACAAGGAGAAGGTAGAGC 59.171 50.000 0.00 0.00 0.00 4.09
678 721 1.903183 ACACAAGGAGAAGGTAGAGCC 59.097 52.381 0.00 0.00 37.58 4.70
691 734 3.737850 GGTAGAGCCTTCCATCATCTTG 58.262 50.000 0.00 0.00 0.00 3.02
692 735 3.495806 GGTAGAGCCTTCCATCATCTTGG 60.496 52.174 0.00 0.00 38.18 3.61
693 736 1.493871 AGAGCCTTCCATCATCTTGGG 59.506 52.381 0.00 0.00 37.37 4.12
694 737 1.492176 GAGCCTTCCATCATCTTGGGA 59.508 52.381 0.00 0.00 37.37 4.37
695 738 1.213926 AGCCTTCCATCATCTTGGGAC 59.786 52.381 0.00 0.00 37.37 4.46
696 739 1.959042 CCTTCCATCATCTTGGGACG 58.041 55.000 0.00 0.00 37.37 4.79
697 740 1.210478 CCTTCCATCATCTTGGGACGT 59.790 52.381 0.00 0.00 37.37 4.34
725 768 0.545171 CCATGCATGTCACCTCCTCT 59.455 55.000 24.58 0.00 0.00 3.69
726 769 1.764723 CCATGCATGTCACCTCCTCTA 59.235 52.381 24.58 0.00 0.00 2.43
728 771 3.201290 CATGCATGTCACCTCCTCTAAC 58.799 50.000 18.91 0.00 0.00 2.34
730 773 2.637382 TGCATGTCACCTCCTCTAACAA 59.363 45.455 0.00 0.00 0.00 2.83
731 774 3.003480 GCATGTCACCTCCTCTAACAAC 58.997 50.000 0.00 0.00 0.00 3.32
733 776 2.972348 TGTCACCTCCTCTAACAACCT 58.028 47.619 0.00 0.00 0.00 3.50
734 777 2.897969 TGTCACCTCCTCTAACAACCTC 59.102 50.000 0.00 0.00 0.00 3.85
735 778 2.234168 GTCACCTCCTCTAACAACCTCC 59.766 54.545 0.00 0.00 0.00 4.30
736 779 1.555533 CACCTCCTCTAACAACCTCCC 59.444 57.143 0.00 0.00 0.00 4.30
737 780 1.151413 ACCTCCTCTAACAACCTCCCA 59.849 52.381 0.00 0.00 0.00 4.37
738 781 2.266279 CCTCCTCTAACAACCTCCCAA 58.734 52.381 0.00 0.00 0.00 4.12
742 785 3.913799 TCCTCTAACAACCTCCCAAATGA 59.086 43.478 0.00 0.00 0.00 2.57
748 791 2.299867 ACAACCTCCCAAATGAATGCAC 59.700 45.455 0.00 0.00 0.00 4.57
754 797 0.179166 CCAAATGAATGCACGACGGG 60.179 55.000 0.00 0.00 0.00 5.28
783 840 0.105913 GGGGTAGAGGAGGGAGACAG 60.106 65.000 0.00 0.00 0.00 3.51
804 861 2.025321 GGGCAGAAAAGATTACCTGGGA 60.025 50.000 0.00 0.00 0.00 4.37
821 878 1.592223 GACTCACTTGTCCCCCTCG 59.408 63.158 0.00 0.00 0.00 4.63
846 903 2.279385 TCGATCGCGCATGCATCA 60.279 55.556 19.57 0.00 42.97 3.07
855 912 1.378124 CGCATGCATCACCATCACCA 61.378 55.000 19.57 0.00 0.00 4.17
857 914 1.000607 GCATGCATCACCATCACCATC 60.001 52.381 14.21 0.00 0.00 3.51
858 915 2.303175 CATGCATCACCATCACCATCA 58.697 47.619 0.00 0.00 0.00 3.07
860 917 1.027357 GCATCACCATCACCATCACC 58.973 55.000 0.00 0.00 0.00 4.02
861 918 1.682702 GCATCACCATCACCATCACCA 60.683 52.381 0.00 0.00 0.00 4.17
862 919 2.940158 CATCACCATCACCATCACCAT 58.060 47.619 0.00 0.00 0.00 3.55
863 920 3.748348 GCATCACCATCACCATCACCATA 60.748 47.826 0.00 0.00 0.00 2.74
864 921 3.558931 TCACCATCACCATCACCATAC 57.441 47.619 0.00 0.00 0.00 2.39
865 922 2.843113 TCACCATCACCATCACCATACA 59.157 45.455 0.00 0.00 0.00 2.29
866 923 3.459227 TCACCATCACCATCACCATACAT 59.541 43.478 0.00 0.00 0.00 2.29
867 924 4.079844 TCACCATCACCATCACCATACATT 60.080 41.667 0.00 0.00 0.00 2.71
868 925 4.037089 CACCATCACCATCACCATACATTG 59.963 45.833 0.00 0.00 0.00 2.82
869 926 3.005050 CCATCACCATCACCATACATTGC 59.995 47.826 0.00 0.00 0.00 3.56
870 927 3.362870 TCACCATCACCATACATTGCA 57.637 42.857 0.00 0.00 0.00 4.08
871 928 3.281158 TCACCATCACCATACATTGCAG 58.719 45.455 0.00 0.00 0.00 4.41
872 929 3.054508 TCACCATCACCATACATTGCAGA 60.055 43.478 0.00 0.00 0.00 4.26
873 930 3.887110 CACCATCACCATACATTGCAGAT 59.113 43.478 0.00 0.00 0.00 2.90
891 948 1.530013 ATTTGCAGCTGACCCTGTGC 61.530 55.000 20.43 0.00 35.28 4.57
903 960 2.183811 CTGTGCTCTGCTCCTCCG 59.816 66.667 0.00 0.00 0.00 4.63
914 972 3.024356 TCCTCCGCTCCCTCCTCT 61.024 66.667 0.00 0.00 0.00 3.69
922 980 3.011821 TCCGCTCCCTCCTCTCATATAAT 59.988 47.826 0.00 0.00 0.00 1.28
923 981 4.229812 TCCGCTCCCTCCTCTCATATAATA 59.770 45.833 0.00 0.00 0.00 0.98
924 982 5.103473 TCCGCTCCCTCCTCTCATATAATAT 60.103 44.000 0.00 0.00 0.00 1.28
925 983 6.102762 TCCGCTCCCTCCTCTCATATAATATA 59.897 42.308 0.00 0.00 0.00 0.86
926 984 6.778069 CCGCTCCCTCCTCTCATATAATATAA 59.222 42.308 0.00 0.00 0.00 0.98
927 985 7.255660 CCGCTCCCTCCTCTCATATAATATAAC 60.256 44.444 0.00 0.00 0.00 1.89
928 986 7.504238 CGCTCCCTCCTCTCATATAATATAACT 59.496 40.741 0.00 0.00 0.00 2.24
942 1000 7.663043 ATAATATAACTCTGGCTAGCCTACC 57.337 40.000 33.07 8.57 36.94 3.18
943 1001 1.688772 TAACTCTGGCTAGCCTACCG 58.311 55.000 33.07 20.31 36.94 4.02
971 1029 2.213499 CCAACAAGGACACTCACACTC 58.787 52.381 0.00 0.00 41.22 3.51
972 1030 2.158900 CCAACAAGGACACTCACACTCT 60.159 50.000 0.00 0.00 41.22 3.24
973 1031 2.868583 CAACAAGGACACTCACACTCTG 59.131 50.000 0.00 0.00 0.00 3.35
974 1032 1.202580 ACAAGGACACTCACACTCTGC 60.203 52.381 0.00 0.00 0.00 4.26
975 1033 1.069823 CAAGGACACTCACACTCTGCT 59.930 52.381 0.00 0.00 0.00 4.24
976 1034 0.678395 AGGACACTCACACTCTGCTG 59.322 55.000 0.00 0.00 0.00 4.41
1023 1087 3.006247 GGAGATGGAGAGAGTTTGCAAC 58.994 50.000 0.00 0.00 0.00 4.17
1029 1093 2.545952 GGAGAGAGTTTGCAACAGACGA 60.546 50.000 0.00 0.00 0.00 4.20
1030 1094 2.728839 GAGAGAGTTTGCAACAGACGAG 59.271 50.000 0.00 0.00 0.00 4.18
1081 1145 3.440415 ACGGCATCGACGAGCAGA 61.440 61.111 19.71 0.00 35.20 4.26
1082 1146 2.026734 CGGCATCGACGAGCAGAT 59.973 61.111 17.11 0.00 35.20 2.90
1199 1275 2.759114 CCTGCTGCTCAAAGGGGA 59.241 61.111 0.00 0.00 0.00 4.81
1242 1318 2.881352 GCCGACGCTCTTCTTCCG 60.881 66.667 0.00 0.00 0.00 4.30
1246 1322 1.153549 GACGCTCTTCTTCCGCCAT 60.154 57.895 0.00 0.00 0.00 4.40
1249 1331 1.524849 GCTCTTCTTCCGCCATCCC 60.525 63.158 0.00 0.00 0.00 3.85
1254 1336 2.203394 CTTCCGCCATCCCCCATG 60.203 66.667 0.00 0.00 0.00 3.66
1260 1342 4.275508 CCATCCCCCATGCCGGAG 62.276 72.222 5.05 0.00 36.56 4.63
1314 1396 2.270205 CCCGCAGCTTCCAGTCAT 59.730 61.111 0.00 0.00 0.00 3.06
1317 1399 0.463295 CCGCAGCTTCCAGTCATCAT 60.463 55.000 0.00 0.00 0.00 2.45
1319 1401 1.741394 CGCAGCTTCCAGTCATCATCA 60.741 52.381 0.00 0.00 0.00 3.07
1320 1402 1.941294 GCAGCTTCCAGTCATCATCAG 59.059 52.381 0.00 0.00 0.00 2.90
1321 1403 2.419713 GCAGCTTCCAGTCATCATCAGA 60.420 50.000 0.00 0.00 0.00 3.27
1322 1404 3.744846 GCAGCTTCCAGTCATCATCAGAT 60.745 47.826 0.00 0.00 33.87 2.90
1323 1405 4.452825 CAGCTTCCAGTCATCATCAGATT 58.547 43.478 0.00 0.00 30.20 2.40
1325 1407 4.163649 AGCTTCCAGTCATCATCAGATTCA 59.836 41.667 0.00 0.00 30.20 2.57
1329 1411 3.875727 CCAGTCATCATCAGATTCACCAC 59.124 47.826 0.00 0.00 30.20 4.16
1338 1424 3.148412 TCAGATTCACCACCAACATGTG 58.852 45.455 0.00 0.00 35.98 3.21
1362 1457 4.651045 ACCAATCACTTGCTTCCTTCTTTT 59.349 37.500 0.00 0.00 0.00 2.27
1365 1460 5.702349 ATCACTTGCTTCCTTCTTTTCTG 57.298 39.130 0.00 0.00 0.00 3.02
1371 1466 4.936891 TGCTTCCTTCTTTTCTGCTTTTC 58.063 39.130 0.00 0.00 0.00 2.29
1374 1469 5.452496 GCTTCCTTCTTTTCTGCTTTTCCTT 60.452 40.000 0.00 0.00 0.00 3.36
1375 1470 5.520376 TCCTTCTTTTCTGCTTTTCCTTG 57.480 39.130 0.00 0.00 0.00 3.61
1376 1471 4.053983 CCTTCTTTTCTGCTTTTCCTTGC 58.946 43.478 0.00 0.00 0.00 4.01
1377 1472 4.202192 CCTTCTTTTCTGCTTTTCCTTGCT 60.202 41.667 0.00 0.00 0.00 3.91
1378 1473 5.010012 CCTTCTTTTCTGCTTTTCCTTGCTA 59.990 40.000 0.00 0.00 0.00 3.49
1379 1474 5.695851 TCTTTTCTGCTTTTCCTTGCTAG 57.304 39.130 0.00 0.00 0.00 3.42
1380 1475 3.923017 TTTCTGCTTTTCCTTGCTAGC 57.077 42.857 8.10 8.10 0.00 3.42
1381 1476 2.867109 TCTGCTTTTCCTTGCTAGCT 57.133 45.000 17.23 0.00 34.77 3.32
1382 1477 3.981071 TCTGCTTTTCCTTGCTAGCTA 57.019 42.857 17.23 7.59 34.77 3.32
1383 1478 3.866651 TCTGCTTTTCCTTGCTAGCTAG 58.133 45.455 16.84 16.84 34.77 3.42
1384 1479 3.261897 TCTGCTTTTCCTTGCTAGCTAGT 59.738 43.478 21.62 0.00 34.77 2.57
1385 1480 4.006319 CTGCTTTTCCTTGCTAGCTAGTT 58.994 43.478 21.62 0.00 34.77 2.24
1386 1481 3.753272 TGCTTTTCCTTGCTAGCTAGTTG 59.247 43.478 21.62 10.07 34.77 3.16
1387 1482 3.753797 GCTTTTCCTTGCTAGCTAGTTGT 59.246 43.478 21.62 0.00 0.00 3.32
1388 1483 4.216472 GCTTTTCCTTGCTAGCTAGTTGTT 59.784 41.667 21.62 0.00 0.00 2.83
1389 1484 5.411669 GCTTTTCCTTGCTAGCTAGTTGTTA 59.588 40.000 21.62 3.18 0.00 2.41
1390 1485 6.620949 GCTTTTCCTTGCTAGCTAGTTGTTAC 60.621 42.308 21.62 4.84 0.00 2.50
1391 1486 5.740290 TTCCTTGCTAGCTAGTTGTTACT 57.260 39.130 21.62 0.00 38.44 2.24
1408 1510 4.631377 TGTTACTCTCTGCAACATGTATGC 59.369 41.667 19.66 19.66 44.08 3.14
1412 1514 1.328680 CTCTGCAACATGTATGCGTCC 59.671 52.381 20.49 3.80 46.76 4.79
1413 1515 0.026674 CTGCAACATGTATGCGTCCG 59.973 55.000 20.49 10.39 46.76 4.79
1424 1526 0.670546 ATGCGTCCGTCAAGTTGGAG 60.671 55.000 2.34 0.00 34.21 3.86
1426 1528 1.009389 GCGTCCGTCAAGTTGGAGAG 61.009 60.000 2.34 0.00 34.21 3.20
1450 1572 6.425721 AGAACAAATTGAGATGCAAAACCATG 59.574 34.615 0.00 0.00 40.48 3.66
1451 1573 4.998672 ACAAATTGAGATGCAAAACCATGG 59.001 37.500 11.19 11.19 40.48 3.66
1457 1579 2.835764 AGATGCAAAACCATGGCTGATT 59.164 40.909 13.04 0.00 0.00 2.57
1469 1591 3.117589 GCTGATTTGCCTGCTGTTG 57.882 52.632 0.00 0.00 0.00 3.33
1514 1640 1.213926 AGCTAGATGCAAAAGGGAGGG 59.786 52.381 0.00 0.00 45.94 4.30
1555 1681 1.293498 CTCCAACTCGGTGACCAGG 59.707 63.158 1.11 0.00 35.57 4.45
1577 1703 1.339151 GGTACTTCCAGCACAAGGAGG 60.339 57.143 0.00 0.00 38.16 4.30
1834 1960 3.220658 TCTGCGGTCGGTGTCACA 61.221 61.111 5.12 0.00 0.00 3.58
1840 1966 3.936203 GTCGGTGTCACAGGCCCA 61.936 66.667 0.00 0.00 0.00 5.36
1909 2035 5.192927 TCCCCATAAATTGTCATCACACTC 58.807 41.667 0.00 0.00 29.76 3.51
1927 2070 6.656270 TCACACTCAAATTCATCTGCTGTTAT 59.344 34.615 0.00 0.00 0.00 1.89
1928 2071 7.823799 TCACACTCAAATTCATCTGCTGTTATA 59.176 33.333 0.00 0.00 0.00 0.98
1929 2072 8.618677 CACACTCAAATTCATCTGCTGTTATAT 58.381 33.333 0.00 0.00 0.00 0.86
1930 2073 8.618677 ACACTCAAATTCATCTGCTGTTATATG 58.381 33.333 0.00 0.00 0.00 1.78
1931 2074 8.833493 CACTCAAATTCATCTGCTGTTATATGA 58.167 33.333 0.00 0.00 0.00 2.15
1932 2075 9.570468 ACTCAAATTCATCTGCTGTTATATGAT 57.430 29.630 0.00 0.00 0.00 2.45
1939 2082 8.272545 TCATCTGCTGTTATATGATAAATGGC 57.727 34.615 0.00 0.00 0.00 4.40
1940 2083 8.105197 TCATCTGCTGTTATATGATAAATGGCT 58.895 33.333 0.00 0.00 0.00 4.75
1941 2084 7.677454 TCTGCTGTTATATGATAAATGGCTG 57.323 36.000 0.00 0.00 0.00 4.85
1942 2085 7.452562 TCTGCTGTTATATGATAAATGGCTGA 58.547 34.615 0.00 0.00 0.00 4.26
1943 2086 7.605309 TCTGCTGTTATATGATAAATGGCTGAG 59.395 37.037 0.00 0.00 0.00 3.35
1953 2096 1.181098 AATGGCTGAGTTGTGTGCCC 61.181 55.000 0.00 0.00 44.32 5.36
2019 2162 3.296709 GAAGAGGGTCCAGCGCGAA 62.297 63.158 12.10 0.00 34.93 4.70
2020 2163 2.579684 GAAGAGGGTCCAGCGCGAAT 62.580 60.000 12.10 0.00 34.93 3.34
2049 2192 1.668419 ATGCCAGCGTCATTCCTTAC 58.332 50.000 0.00 0.00 0.00 2.34
2125 2268 3.729217 GCTAAAACGCACAAGAAAAGGTC 59.271 43.478 0.00 0.00 0.00 3.85
2135 2278 4.450419 CACAAGAAAAGGTCAGAGCTACTG 59.550 45.833 1.60 6.79 46.97 2.74
2172 2316 7.756722 AGCATTTAATTACATTCTGCTGACAAC 59.243 33.333 0.00 0.00 37.13 3.32
2195 2339 6.675987 ACAAAATCTGAACTTCTGAAGCATC 58.324 36.000 17.00 15.15 0.00 3.91
2298 2443 2.092323 GGTCACAGGTAGGGCAATTTC 58.908 52.381 0.00 0.00 0.00 2.17
2310 2455 2.456577 GGCAATTTCCCTCCAAAGCTA 58.543 47.619 0.00 0.00 0.00 3.32
2311 2456 2.831526 GGCAATTTCCCTCCAAAGCTAA 59.168 45.455 0.00 0.00 0.00 3.09
2324 2469 9.136323 CCCTCCAAAGCTAAATTTGTAATAGAT 57.864 33.333 0.00 0.00 38.28 1.98
2358 2516 2.027192 TCTGGCCAGTTCTGGTGAATAC 60.027 50.000 31.58 2.72 34.40 1.89
2363 2521 3.758554 GCCAGTTCTGGTGAATACATGTT 59.241 43.478 18.42 0.00 34.40 2.71
2368 2526 7.309377 CCAGTTCTGGTGAATACATGTTCATTT 60.309 37.037 2.30 0.00 39.99 2.32
2369 2527 8.729756 CAGTTCTGGTGAATACATGTTCATTTA 58.270 33.333 2.30 0.00 39.99 1.40
2370 2528 9.466497 AGTTCTGGTGAATACATGTTCATTTAT 57.534 29.630 2.30 0.00 39.99 1.40
2499 2657 8.709308 AGTAGGTTTAGCTGTTTCATATCTCAT 58.291 33.333 0.00 0.00 0.00 2.90
2526 2684 4.679373 AATACCTGATGTCGATGCTTCT 57.321 40.909 0.00 0.00 0.00 2.85
2530 2688 2.864946 CCTGATGTCGATGCTTCTTGAG 59.135 50.000 0.00 0.00 0.00 3.02
2693 2851 1.530293 GTTCAAGTGTGAGAGCAGCAG 59.470 52.381 0.00 0.00 34.49 4.24
2847 3005 3.178046 TGCAGGACAGAGGGTGTATTAA 58.822 45.455 0.00 0.00 40.56 1.40
2851 3017 3.700038 AGGACAGAGGGTGTATTAAGACG 59.300 47.826 0.00 0.00 40.56 4.18
2852 3018 3.445857 GACAGAGGGTGTATTAAGACGC 58.554 50.000 5.21 5.21 40.56 5.19
2857 3023 1.636988 GGTGTATTAAGACGCGTGCT 58.363 50.000 20.70 11.30 0.00 4.40
2863 3029 0.658368 TTAAGACGCGTGCTTTGCAA 59.342 45.000 20.70 8.56 41.47 4.08
2864 3030 0.041663 TAAGACGCGTGCTTTGCAAC 60.042 50.000 20.70 0.00 41.47 4.17
2873 3039 2.032117 CGTGCTTTGCAACATCAGTGTA 60.032 45.455 0.00 0.00 41.47 2.90
2874 3040 3.300009 GTGCTTTGCAACATCAGTGTAC 58.700 45.455 0.00 0.00 41.47 2.90
2879 3045 1.943340 TGCAACATCAGTGTACGCAAA 59.057 42.857 9.48 0.00 41.30 3.68
2880 3046 2.551887 TGCAACATCAGTGTACGCAAAT 59.448 40.909 9.48 0.00 41.30 2.32
2883 3049 5.150683 GCAACATCAGTGTACGCAAATAAA 58.849 37.500 9.48 0.00 37.67 1.40
2884 3050 5.799936 GCAACATCAGTGTACGCAAATAAAT 59.200 36.000 9.48 0.00 37.67 1.40
2950 3116 9.107177 ACTGCTTGATTATTCTCATAAGTTCAG 57.893 33.333 0.00 0.00 0.00 3.02
3037 3312 9.129209 GCTAGTTTTGGAAAAAGAATACACATC 57.871 33.333 0.00 0.00 0.00 3.06
3167 3442 3.745458 GCTTCTCAAGGTTCTCAGACTTG 59.255 47.826 0.00 0.00 42.14 3.16
3236 3511 4.879104 CATCAGATGCAAAGGAGAAGAC 57.121 45.455 0.00 0.00 0.00 3.01
3239 3514 5.682234 TCAGATGCAAAGGAGAAGACATA 57.318 39.130 0.00 0.00 0.00 2.29
3243 3518 7.025963 CAGATGCAAAGGAGAAGACATAAAAC 58.974 38.462 0.00 0.00 0.00 2.43
3330 3613 4.212143 TGTGCATCTTCACTAAGCAGAT 57.788 40.909 0.00 0.00 37.81 2.90
3334 3617 6.481313 TGTGCATCTTCACTAAGCAGATTATC 59.519 38.462 0.00 0.00 37.81 1.75
3442 3725 8.705048 AATGATAAAGAACGTCCTAAAGAGAC 57.295 34.615 0.00 0.00 0.00 3.36
3464 3747 4.403113 ACGTTAACCCAAGTTGGTGAAAAT 59.597 37.500 20.54 2.89 39.05 1.82
3478 3761 5.226396 TGGTGAAAATAAAGCAATTCCACG 58.774 37.500 0.00 0.00 0.00 4.94
3486 3770 1.238439 AGCAATTCCACGTTGACTGG 58.762 50.000 0.00 0.00 0.00 4.00
3528 3812 7.538678 CCAAACTATCATTAAAACTGAGCACAC 59.461 37.037 0.00 0.00 0.00 3.82
3556 7953 9.349713 AGGAGTTTGTAAATGACAGATAAACAA 57.650 29.630 0.00 0.00 39.88 2.83
3653 8050 5.488341 TCTGGAGTAACAAAATGGCTAGTC 58.512 41.667 0.00 0.00 0.00 2.59
3710 8107 7.062255 GCCTGAAAGAAGTTACATAATTTGCAC 59.938 37.037 0.00 0.00 34.07 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 96 3.195396 ACCCATTGTGCCATTGTGTATTC 59.805 43.478 0.00 0.00 0.00 1.75
83 99 2.300956 ACCCATTGTGCCATTGTGTA 57.699 45.000 0.00 0.00 0.00 2.90
92 108 2.357009 CTGCTCATTCTACCCATTGTGC 59.643 50.000 0.00 0.00 0.00 4.57
100 116 7.507733 AATGATCAATTCTGCTCATTCTACC 57.492 36.000 0.00 0.00 42.13 3.18
104 120 6.918569 CCTCAAATGATCAATTCTGCTCATTC 59.081 38.462 0.00 0.00 44.01 2.67
117 133 7.004086 AGTAAAAGTTGGTCCTCAAATGATCA 58.996 34.615 0.00 0.00 37.08 2.92
121 137 6.488683 TGGTAGTAAAAGTTGGTCCTCAAATG 59.511 38.462 0.00 0.00 37.08 2.32
151 167 6.835914 CCGTATAGGGTATAAGTTGAGTACG 58.164 44.000 3.14 0.00 35.97 3.67
169 185 7.938490 TGTAGTAGTACATGACAATCCCGTATA 59.062 37.037 6.31 0.00 34.02 1.47
298 315 6.350696 GGTTTGTTGACCAGAACTTTAAACCT 60.351 38.462 0.00 0.00 36.92 3.50
301 318 5.183522 ACGGTTTGTTGACCAGAACTTTAAA 59.816 36.000 0.00 0.00 39.78 1.52
304 321 3.086282 ACGGTTTGTTGACCAGAACTTT 58.914 40.909 0.00 0.00 39.78 2.66
319 336 2.415759 GGACACGGAAACAAAACGGTTT 60.416 45.455 0.00 0.00 43.30 3.27
320 337 1.132834 GGACACGGAAACAAAACGGTT 59.867 47.619 0.00 0.00 0.00 4.44
321 338 0.734309 GGACACGGAAACAAAACGGT 59.266 50.000 0.00 0.00 0.00 4.83
323 340 0.926628 GCGGACACGGAAACAAAACG 60.927 55.000 0.00 0.00 41.36 3.60
324 341 0.379316 AGCGGACACGGAAACAAAAC 59.621 50.000 0.00 0.00 41.36 2.43
356 373 4.877378 AATACTACCGGAAACAGACACA 57.123 40.909 9.46 0.00 0.00 3.72
373 390 7.812690 ATATAGAAACCCCGGAAACAAATAC 57.187 36.000 0.73 0.00 0.00 1.89
378 407 4.080975 ACGAATATAGAAACCCCGGAAACA 60.081 41.667 0.73 0.00 0.00 2.83
420 449 9.090103 TGGGTGTTACCATATTTGTTTTCATAA 57.910 29.630 0.00 0.00 41.02 1.90
425 454 7.880713 GGAATTGGGTGTTACCATATTTGTTTT 59.119 33.333 0.00 0.00 41.02 2.43
440 469 0.179012 AAACGGACGGAATTGGGTGT 60.179 50.000 0.00 0.00 0.00 4.16
470 499 3.104512 TGTGGTGGTAACTAGGGATGAG 58.895 50.000 0.00 0.00 37.61 2.90
480 509 1.176619 GGGGTGCTTGTGGTGGTAAC 61.177 60.000 0.00 0.00 0.00 2.50
481 510 1.151908 GGGGTGCTTGTGGTGGTAA 59.848 57.895 0.00 0.00 0.00 2.85
482 511 0.474079 TAGGGGTGCTTGTGGTGGTA 60.474 55.000 0.00 0.00 0.00 3.25
483 512 1.140134 ATAGGGGTGCTTGTGGTGGT 61.140 55.000 0.00 0.00 0.00 4.16
484 513 0.394352 GATAGGGGTGCTTGTGGTGG 60.394 60.000 0.00 0.00 0.00 4.61
485 514 0.620556 AGATAGGGGTGCTTGTGGTG 59.379 55.000 0.00 0.00 0.00 4.17
486 515 1.282157 GAAGATAGGGGTGCTTGTGGT 59.718 52.381 0.00 0.00 0.00 4.16
487 516 1.281867 TGAAGATAGGGGTGCTTGTGG 59.718 52.381 0.00 0.00 0.00 4.17
488 517 2.787473 TGAAGATAGGGGTGCTTGTG 57.213 50.000 0.00 0.00 0.00 3.33
489 518 5.450818 TTAATGAAGATAGGGGTGCTTGT 57.549 39.130 0.00 0.00 0.00 3.16
490 519 6.966534 AATTAATGAAGATAGGGGTGCTTG 57.033 37.500 0.00 0.00 0.00 4.01
491 520 6.183360 GCAAATTAATGAAGATAGGGGTGCTT 60.183 38.462 0.00 0.00 0.00 3.91
492 521 5.302823 GCAAATTAATGAAGATAGGGGTGCT 59.697 40.000 0.00 0.00 0.00 4.40
493 522 5.302823 AGCAAATTAATGAAGATAGGGGTGC 59.697 40.000 0.00 0.00 0.00 5.01
494 523 6.322201 ACAGCAAATTAATGAAGATAGGGGTG 59.678 38.462 0.00 0.00 0.00 4.61
495 524 6.435164 ACAGCAAATTAATGAAGATAGGGGT 58.565 36.000 0.00 0.00 0.00 4.95
496 525 6.547141 TGACAGCAAATTAATGAAGATAGGGG 59.453 38.462 0.00 0.00 0.00 4.79
497 526 7.067372 TGTGACAGCAAATTAATGAAGATAGGG 59.933 37.037 0.00 0.00 0.00 3.53
498 527 7.988737 TGTGACAGCAAATTAATGAAGATAGG 58.011 34.615 0.00 0.00 0.00 2.57
502 531 7.970061 GCTTATGTGACAGCAAATTAATGAAGA 59.030 33.333 0.00 0.00 35.95 2.87
503 532 7.756272 TGCTTATGTGACAGCAAATTAATGAAG 59.244 33.333 0.00 0.00 43.14 3.02
504 533 7.600960 TGCTTATGTGACAGCAAATTAATGAA 58.399 30.769 0.00 0.00 43.14 2.57
505 534 7.155655 TGCTTATGTGACAGCAAATTAATGA 57.844 32.000 0.00 0.00 43.14 2.57
515 544 5.613358 AGTTAGTTTGCTTATGTGACAGC 57.387 39.130 0.00 0.00 36.49 4.40
530 559 9.444600 CATAACACACCCTAATACAAGTTAGTT 57.555 33.333 0.00 0.00 31.24 2.24
531 560 8.599792 ACATAACACACCCTAATACAAGTTAGT 58.400 33.333 0.00 0.00 31.24 2.24
532 561 9.444600 AACATAACACACCCTAATACAAGTTAG 57.555 33.333 0.00 0.00 0.00 2.34
541 570 6.882678 GTGGAAGTAACATAACACACCCTAAT 59.117 38.462 0.00 0.00 0.00 1.73
562 591 2.730934 ACGAGGCTAGTCATAGTGGA 57.269 50.000 0.00 0.00 0.00 4.02
580 613 2.027653 AGTGCCTCCTCTTTCTGCTAAC 60.028 50.000 0.00 0.00 0.00 2.34
582 615 1.944177 AGTGCCTCCTCTTTCTGCTA 58.056 50.000 0.00 0.00 0.00 3.49
583 616 1.830477 CTAGTGCCTCCTCTTTCTGCT 59.170 52.381 0.00 0.00 0.00 4.24
584 617 1.552792 ACTAGTGCCTCCTCTTTCTGC 59.447 52.381 0.00 0.00 0.00 4.26
585 618 3.181480 GCTACTAGTGCCTCCTCTTTCTG 60.181 52.174 5.39 0.00 0.00 3.02
586 619 3.028130 GCTACTAGTGCCTCCTCTTTCT 58.972 50.000 5.39 0.00 0.00 2.52
587 620 2.761208 TGCTACTAGTGCCTCCTCTTTC 59.239 50.000 5.39 0.00 0.00 2.62
602 643 2.832733 GGTCAACCTCCTTAGTGCTACT 59.167 50.000 0.00 0.00 0.00 2.57
609 650 0.175989 GCTCCGGTCAACCTCCTTAG 59.824 60.000 0.00 0.00 0.00 2.18
612 653 2.203788 TGCTCCGGTCAACCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
613 654 2.047179 GTGCTCCGGTCAACCTCC 60.047 66.667 0.00 0.00 0.00 4.30
614 655 1.374758 CTGTGCTCCGGTCAACCTC 60.375 63.158 0.00 0.00 0.00 3.85
643 686 1.188219 TGTGTCTGGACTCTGGAGGC 61.188 60.000 2.58 0.00 35.10 4.70
646 689 1.133167 TCCTTGTGTCTGGACTCTGGA 60.133 52.381 2.38 7.75 0.00 3.86
647 690 1.274728 CTCCTTGTGTCTGGACTCTGG 59.725 57.143 2.38 5.91 0.00 3.86
648 691 2.242926 TCTCCTTGTGTCTGGACTCTG 58.757 52.381 2.38 0.00 0.00 3.35
649 692 2.685106 TCTCCTTGTGTCTGGACTCT 57.315 50.000 2.38 0.00 0.00 3.24
650 693 2.028567 CCTTCTCCTTGTGTCTGGACTC 60.029 54.545 2.38 0.00 0.00 3.36
651 694 1.974236 CCTTCTCCTTGTGTCTGGACT 59.026 52.381 2.38 0.00 0.00 3.85
652 695 1.694696 ACCTTCTCCTTGTGTCTGGAC 59.305 52.381 0.00 0.00 0.00 4.02
677 720 1.210478 ACGTCCCAAGATGATGGAAGG 59.790 52.381 0.00 0.00 43.54 3.46
678 721 2.093500 TCACGTCCCAAGATGATGGAAG 60.093 50.000 0.00 0.00 43.54 3.46
679 722 1.905894 TCACGTCCCAAGATGATGGAA 59.094 47.619 0.00 0.00 43.54 3.53
680 723 1.207089 GTCACGTCCCAAGATGATGGA 59.793 52.381 0.00 0.00 43.54 3.41
681 724 1.656652 GTCACGTCCCAAGATGATGG 58.343 55.000 0.00 0.00 40.35 3.51
683 726 0.175760 CCGTCACGTCCCAAGATGAT 59.824 55.000 0.00 0.00 32.93 2.45
685 728 1.447838 CCCGTCACGTCCCAAGATG 60.448 63.158 0.00 0.00 34.96 2.90
686 729 1.608336 TCCCGTCACGTCCCAAGAT 60.608 57.895 0.00 0.00 0.00 2.40
687 730 2.203523 TCCCGTCACGTCCCAAGA 60.204 61.111 0.00 0.00 0.00 3.02
688 731 2.048503 GTCCCGTCACGTCCCAAG 60.049 66.667 0.00 0.00 0.00 3.61
689 732 3.618750 GGTCCCGTCACGTCCCAA 61.619 66.667 0.00 0.00 0.00 4.12
692 735 3.387947 ATGGGTCCCGTCACGTCC 61.388 66.667 2.65 0.00 0.00 4.79
693 736 2.125673 CATGGGTCCCGTCACGTC 60.126 66.667 0.00 0.00 0.00 4.34
694 737 4.388499 GCATGGGTCCCGTCACGT 62.388 66.667 0.00 0.00 0.00 4.49
695 738 3.680620 ATGCATGGGTCCCGTCACG 62.681 63.158 0.00 0.00 0.00 4.35
696 739 2.114670 CATGCATGGGTCCCGTCAC 61.115 63.158 19.40 0.00 0.00 3.67
697 740 2.271821 CATGCATGGGTCCCGTCA 59.728 61.111 19.40 2.21 0.00 4.35
725 768 4.021544 GTGCATTCATTTGGGAGGTTGTTA 60.022 41.667 0.00 0.00 0.00 2.41
726 769 2.971330 TGCATTCATTTGGGAGGTTGTT 59.029 40.909 0.00 0.00 0.00 2.83
728 771 2.671914 CGTGCATTCATTTGGGAGGTTG 60.672 50.000 0.00 0.00 0.00 3.77
730 773 1.176527 CGTGCATTCATTTGGGAGGT 58.823 50.000 0.00 0.00 0.00 3.85
731 774 1.133025 GTCGTGCATTCATTTGGGAGG 59.867 52.381 0.00 0.00 0.00 4.30
733 776 0.801872 CGTCGTGCATTCATTTGGGA 59.198 50.000 0.00 0.00 0.00 4.37
734 777 0.179166 CCGTCGTGCATTCATTTGGG 60.179 55.000 0.00 0.00 0.00 4.12
735 778 0.179166 CCCGTCGTGCATTCATTTGG 60.179 55.000 0.00 0.00 0.00 3.28
736 779 0.521291 ACCCGTCGTGCATTCATTTG 59.479 50.000 0.00 0.00 0.00 2.32
737 780 1.243902 AACCCGTCGTGCATTCATTT 58.756 45.000 0.00 0.00 0.00 2.32
738 781 2.102070 TAACCCGTCGTGCATTCATT 57.898 45.000 0.00 0.00 0.00 2.57
742 785 0.250381 TGGTTAACCCGTCGTGCATT 60.250 50.000 21.97 0.00 35.15 3.56
748 791 2.028733 CCCGTTGGTTAACCCGTCG 61.029 63.158 21.97 20.35 35.15 5.12
774 829 0.695347 CTTTTCTGCCCTGTCTCCCT 59.305 55.000 0.00 0.00 0.00 4.20
783 840 2.025321 TCCCAGGTAATCTTTTCTGCCC 60.025 50.000 0.00 0.00 0.00 5.36
804 861 1.152312 ACGAGGGGGACAAGTGAGT 60.152 57.895 0.00 0.00 0.00 3.41
846 903 4.209538 CAATGTATGGTGATGGTGATGGT 58.790 43.478 0.00 0.00 0.00 3.55
869 926 0.809385 CAGGGTCAGCTGCAAATCTG 59.191 55.000 9.47 8.23 0.00 2.90
870 927 0.403271 ACAGGGTCAGCTGCAAATCT 59.597 50.000 9.47 0.00 0.00 2.40
871 928 0.524862 CACAGGGTCAGCTGCAAATC 59.475 55.000 9.47 0.00 0.00 2.17
872 929 1.530013 GCACAGGGTCAGCTGCAAAT 61.530 55.000 9.47 0.00 0.00 2.32
873 930 2.195567 GCACAGGGTCAGCTGCAAA 61.196 57.895 9.47 0.00 0.00 3.68
891 948 3.535962 GGGAGCGGAGGAGCAGAG 61.536 72.222 0.00 0.00 40.15 3.35
903 960 8.776061 AGTTATATTATATGAGAGGAGGGAGC 57.224 38.462 0.00 0.00 0.00 4.70
922 980 3.418995 CGGTAGGCTAGCCAGAGTTATA 58.581 50.000 34.70 14.22 38.92 0.98
923 981 2.240279 CGGTAGGCTAGCCAGAGTTAT 58.760 52.381 34.70 15.31 38.92 1.89
924 982 1.688772 CGGTAGGCTAGCCAGAGTTA 58.311 55.000 34.70 15.73 38.92 2.24
925 983 1.677637 GCGGTAGGCTAGCCAGAGTT 61.678 60.000 34.70 16.83 39.11 3.01
926 984 2.128507 GCGGTAGGCTAGCCAGAGT 61.129 63.158 34.70 17.23 39.11 3.24
927 985 2.731374 GCGGTAGGCTAGCCAGAG 59.269 66.667 34.70 22.32 39.11 3.35
971 1029 2.561956 AACCAAGCAGCAGCAGCAG 61.562 57.895 12.92 3.98 45.49 4.24
972 1030 2.520020 AACCAAGCAGCAGCAGCA 60.520 55.556 12.92 0.00 45.49 4.41
973 1031 2.049433 CAACCAAGCAGCAGCAGC 60.049 61.111 3.17 0.46 45.49 5.25
974 1032 2.049433 GCAACCAAGCAGCAGCAG 60.049 61.111 3.17 0.00 45.49 4.24
975 1033 3.608662 GGCAACCAAGCAGCAGCA 61.609 61.111 3.17 0.00 45.49 4.41
976 1034 2.444700 AATGGCAACCAAGCAGCAGC 62.445 55.000 0.00 0.00 36.95 5.25
1081 1145 4.038521 CGATGACGCAGGCATCAT 57.961 55.556 19.64 2.08 41.66 2.45
1110 1186 3.017581 GGCTCCATGGGGGTCTGT 61.018 66.667 15.13 0.00 38.11 3.41
1170 1246 1.177256 GCAGCAGGGCCTTGGATATG 61.177 60.000 17.71 0.00 0.00 1.78
1231 1307 1.524849 GGGATGGCGGAAGAAGAGC 60.525 63.158 0.00 0.00 0.00 4.09
1249 1331 2.280389 CATCGTCTCCGGCATGGG 60.280 66.667 0.00 0.00 38.76 4.00
1254 1336 2.413765 GAGGTCATCGTCTCCGGC 59.586 66.667 0.00 0.00 33.95 6.13
1260 1342 0.106419 AGGAGGAGGAGGTCATCGTC 60.106 60.000 5.92 5.92 41.23 4.20
1264 1346 1.144093 CTCGTAGGAGGAGGAGGTCAT 59.856 57.143 4.45 0.00 36.61 3.06
1265 1347 0.547075 CTCGTAGGAGGAGGAGGTCA 59.453 60.000 4.45 0.00 36.61 4.02
1268 1350 0.536460 GAGCTCGTAGGAGGAGGAGG 60.536 65.000 14.00 0.00 40.80 4.30
1269 1351 0.536460 GGAGCTCGTAGGAGGAGGAG 60.536 65.000 14.00 0.00 40.80 3.69
1270 1352 0.989212 AGGAGCTCGTAGGAGGAGGA 60.989 60.000 7.25 0.00 40.80 3.71
1299 1381 0.935898 GATGATGACTGGAAGCTGCG 59.064 55.000 0.00 0.00 37.60 5.18
1302 1384 4.163649 TGAATCTGATGATGACTGGAAGCT 59.836 41.667 0.00 0.00 32.13 3.74
1309 1391 3.520721 TGGTGGTGAATCTGATGATGACT 59.479 43.478 0.00 0.00 32.44 3.41
1314 1396 3.786368 TGTTGGTGGTGAATCTGATGA 57.214 42.857 0.00 0.00 0.00 2.92
1317 1399 3.148412 CACATGTTGGTGGTGAATCTGA 58.852 45.455 0.00 0.00 35.13 3.27
1319 1401 3.149196 GTCACATGTTGGTGGTGAATCT 58.851 45.455 0.00 0.00 42.59 2.40
1320 1402 2.228822 GGTCACATGTTGGTGGTGAATC 59.771 50.000 0.00 0.00 42.59 2.52
1321 1403 2.238521 GGTCACATGTTGGTGGTGAAT 58.761 47.619 0.00 0.00 42.59 2.57
1322 1404 1.064389 TGGTCACATGTTGGTGGTGAA 60.064 47.619 0.00 0.00 42.59 3.18
1323 1405 0.548510 TGGTCACATGTTGGTGGTGA 59.451 50.000 0.00 0.00 39.27 4.02
1325 1407 2.238521 GATTGGTCACATGTTGGTGGT 58.761 47.619 0.00 0.00 39.27 4.16
1338 1424 3.416156 AGAAGGAAGCAAGTGATTGGTC 58.584 45.455 0.00 0.00 0.00 4.02
1347 1433 4.581077 AAGCAGAAAAGAAGGAAGCAAG 57.419 40.909 0.00 0.00 0.00 4.01
1349 1435 4.202151 GGAAAAGCAGAAAAGAAGGAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
1350 1436 4.038522 AGGAAAAGCAGAAAAGAAGGAAGC 59.961 41.667 0.00 0.00 0.00 3.86
1354 1449 4.053983 GCAAGGAAAAGCAGAAAAGAAGG 58.946 43.478 0.00 0.00 0.00 3.46
1362 1457 2.867109 AGCTAGCAAGGAAAAGCAGA 57.133 45.000 18.83 0.00 37.44 4.26
1365 1460 3.753797 ACAACTAGCTAGCAAGGAAAAGC 59.246 43.478 20.91 0.00 35.16 3.51
1371 1466 5.126384 AGAGAGTAACAACTAGCTAGCAAGG 59.874 44.000 20.91 9.92 0.00 3.61
1374 1469 4.142359 GCAGAGAGTAACAACTAGCTAGCA 60.142 45.833 20.91 1.89 0.00 3.49
1375 1470 4.142359 TGCAGAGAGTAACAACTAGCTAGC 60.142 45.833 20.91 6.62 0.00 3.42
1376 1471 5.568685 TGCAGAGAGTAACAACTAGCTAG 57.431 43.478 19.44 19.44 0.00 3.42
1377 1472 5.710984 GTTGCAGAGAGTAACAACTAGCTA 58.289 41.667 0.00 0.00 41.77 3.32
1378 1473 4.561105 GTTGCAGAGAGTAACAACTAGCT 58.439 43.478 0.00 0.00 41.77 3.32
1379 1474 4.912528 GTTGCAGAGAGTAACAACTAGC 57.087 45.455 0.00 0.00 41.77 3.42
1386 1481 4.259970 CGCATACATGTTGCAGAGAGTAAC 60.260 45.833 23.47 0.00 42.40 2.50
1387 1482 3.865164 CGCATACATGTTGCAGAGAGTAA 59.135 43.478 23.47 0.00 40.14 2.24
1388 1483 3.119137 ACGCATACATGTTGCAGAGAGTA 60.119 43.478 23.47 0.00 40.14 2.59
1389 1484 2.274437 CGCATACATGTTGCAGAGAGT 58.726 47.619 23.47 0.00 40.14 3.24
1390 1485 2.274437 ACGCATACATGTTGCAGAGAG 58.726 47.619 23.47 14.01 40.14 3.20
1391 1486 2.270923 GACGCATACATGTTGCAGAGA 58.729 47.619 23.47 0.12 40.14 3.10
1408 1510 0.596577 TCTCTCCAACTTGACGGACG 59.403 55.000 0.00 0.00 0.00 4.79
1412 1514 5.007626 TCAATTTGTTCTCTCCAACTTGACG 59.992 40.000 0.00 0.00 36.89 4.35
1413 1515 6.260936 TCTCAATTTGTTCTCTCCAACTTGAC 59.739 38.462 0.00 0.00 36.89 3.18
1424 1526 5.984926 TGGTTTTGCATCTCAATTTGTTCTC 59.015 36.000 0.00 0.00 34.12 2.87
1426 1528 6.347888 CCATGGTTTTGCATCTCAATTTGTTC 60.348 38.462 2.57 0.00 34.12 3.18
1435 1537 1.820519 TCAGCCATGGTTTTGCATCTC 59.179 47.619 14.67 0.00 0.00 2.75
1451 1573 1.012486 GCAACAGCAGGCAAATCAGC 61.012 55.000 0.00 0.00 0.00 4.26
1457 1579 1.178534 GGGTAAGCAACAGCAGGCAA 61.179 55.000 0.00 0.00 0.00 4.52
1672 1798 2.111669 CTGGTGGCTGCTGTGACA 59.888 61.111 0.00 0.00 0.00 3.58
1691 1817 2.507886 TCTTGGAGTCCTGGTTGTCAAA 59.492 45.455 11.33 0.00 0.00 2.69
1692 1818 2.123589 TCTTGGAGTCCTGGTTGTCAA 58.876 47.619 11.33 0.00 0.00 3.18
1693 1819 1.801242 TCTTGGAGTCCTGGTTGTCA 58.199 50.000 11.33 0.00 0.00 3.58
1739 1865 3.426568 GTGCGAGGCCAGCAACTC 61.427 66.667 24.45 11.13 46.97 3.01
1789 1915 0.107800 CAGAGGACACCTGCTCATGG 60.108 60.000 0.00 0.00 37.33 3.66
1834 1960 0.326904 TCATCAGATCACCTGGGCCT 60.327 55.000 4.53 0.00 43.12 5.19
1840 1966 1.135915 GTGAGCGTCATCAGATCACCT 59.864 52.381 3.55 0.00 45.89 4.00
1927 2070 5.066375 GCACACAACTCAGCCATTTATCATA 59.934 40.000 0.00 0.00 0.00 2.15
1928 2071 4.142315 GCACACAACTCAGCCATTTATCAT 60.142 41.667 0.00 0.00 0.00 2.45
1929 2072 3.191162 GCACACAACTCAGCCATTTATCA 59.809 43.478 0.00 0.00 0.00 2.15
1930 2073 3.428045 GGCACACAACTCAGCCATTTATC 60.428 47.826 0.00 0.00 46.26 1.75
1931 2074 2.493278 GGCACACAACTCAGCCATTTAT 59.507 45.455 0.00 0.00 46.26 1.40
1932 2075 1.885887 GGCACACAACTCAGCCATTTA 59.114 47.619 0.00 0.00 46.26 1.40
1933 2076 0.675633 GGCACACAACTCAGCCATTT 59.324 50.000 0.00 0.00 46.26 2.32
1934 2077 2.344535 GGCACACAACTCAGCCATT 58.655 52.632 0.00 0.00 46.26 3.16
1935 2078 4.085876 GGCACACAACTCAGCCAT 57.914 55.556 0.00 0.00 46.26 4.40
1937 2080 2.985847 GGGGCACACAACTCAGCC 60.986 66.667 0.00 0.00 46.28 4.85
1938 2081 2.985847 GGGGGCACACAACTCAGC 60.986 66.667 0.00 0.00 0.00 4.26
1939 2082 1.601759 CAGGGGGCACACAACTCAG 60.602 63.158 0.00 0.00 0.00 3.35
1940 2083 1.426251 ATCAGGGGGCACACAACTCA 61.426 55.000 0.00 0.00 0.00 3.41
1941 2084 0.962356 CATCAGGGGGCACACAACTC 60.962 60.000 0.00 0.00 0.00 3.01
1942 2085 1.075482 CATCAGGGGGCACACAACT 59.925 57.895 0.00 0.00 0.00 3.16
1943 2086 0.323725 ATCATCAGGGGGCACACAAC 60.324 55.000 0.00 0.00 0.00 3.32
1953 2096 4.735578 GCTTTGCACACAATATCATCAGGG 60.736 45.833 0.00 0.00 35.21 4.45
2019 2162 1.434622 CGCTGGCATTGCTTCTCGAT 61.435 55.000 8.82 0.00 0.00 3.59
2020 2163 2.102438 CGCTGGCATTGCTTCTCGA 61.102 57.895 8.82 0.00 0.00 4.04
2063 2206 3.056962 CCAGATATCAGGACTCCATGACG 60.057 52.174 8.45 0.00 0.00 4.35
2067 2210 2.636893 GCACCAGATATCAGGACTCCAT 59.363 50.000 20.19 0.00 0.00 3.41
2125 2268 5.163571 TGCTCTCAATAGTTCAGTAGCTCTG 60.164 44.000 0.00 0.00 44.85 3.35
2172 2316 6.675026 TGATGCTTCAGAAGTTCAGATTTTG 58.325 36.000 11.94 0.00 0.00 2.44
2195 2339 1.337167 TGCGTGTCAGGTCTCTTGATG 60.337 52.381 0.00 0.00 0.00 3.07
2298 2443 8.519799 TCTATTACAAATTTAGCTTTGGAGGG 57.480 34.615 0.00 0.00 39.83 4.30
2324 2469 3.327757 ACTGGCCAGAGTTTAGATGAACA 59.672 43.478 39.19 0.00 31.94 3.18
2326 2471 4.287067 AGAACTGGCCAGAGTTTAGATGAA 59.713 41.667 39.19 0.00 36.27 2.57
2327 2472 3.840666 AGAACTGGCCAGAGTTTAGATGA 59.159 43.478 39.19 0.00 36.27 2.92
2328 2473 3.937706 CAGAACTGGCCAGAGTTTAGATG 59.062 47.826 39.19 19.35 36.27 2.90
2330 2475 2.303022 CCAGAACTGGCCAGAGTTTAGA 59.697 50.000 39.19 0.00 44.73 2.10
2331 2476 2.704572 CCAGAACTGGCCAGAGTTTAG 58.295 52.381 39.19 20.87 44.73 1.85
2332 2477 2.859165 CCAGAACTGGCCAGAGTTTA 57.141 50.000 39.19 0.00 44.73 2.01
2333 2478 3.733709 CCAGAACTGGCCAGAGTTT 57.266 52.632 39.19 22.97 44.73 2.66
2402 2560 7.387948 GCTTCAATATGACCTGTAATTATCCGT 59.612 37.037 0.00 0.00 0.00 4.69
2403 2561 7.604164 AGCTTCAATATGACCTGTAATTATCCG 59.396 37.037 0.00 0.00 0.00 4.18
2526 2684 7.615403 AGCATAAAGTCAGTATTCAGACTCAA 58.385 34.615 0.00 0.00 43.88 3.02
2530 2688 7.834068 TGAAGCATAAAGTCAGTATTCAGAC 57.166 36.000 0.00 0.00 35.02 3.51
2544 2702 9.073475 ACACCTGTAAGTATTTTGAAGCATAAA 57.927 29.630 0.00 0.00 0.00 1.40
2553 2711 7.005380 CGTAAACGACACCTGTAAGTATTTTG 58.995 38.462 0.00 0.00 43.02 2.44
2693 2851 1.807142 GAACCCAGCTCTGTTTACTGC 59.193 52.381 0.00 0.00 0.00 4.40
2847 3005 1.785041 ATGTTGCAAAGCACGCGTCT 61.785 50.000 9.86 7.13 38.71 4.18
2851 3017 0.318107 ACTGATGTTGCAAAGCACGC 60.318 50.000 0.00 0.00 38.71 5.34
2852 3018 1.268692 ACACTGATGTTGCAAAGCACG 60.269 47.619 0.00 0.00 38.71 5.34
2857 3023 1.943340 TGCGTACACTGATGTTGCAAA 59.057 42.857 0.00 0.00 42.56 3.68
2863 3029 6.148645 TGACATTTATTTGCGTACACTGATGT 59.851 34.615 0.00 0.00 43.30 3.06
2864 3030 6.541969 TGACATTTATTTGCGTACACTGATG 58.458 36.000 0.00 0.00 0.00 3.07
2873 3039 5.229423 ACATGCTTTGACATTTATTTGCGT 58.771 33.333 0.00 0.00 0.00 5.24
2874 3040 5.766702 ACATGCTTTGACATTTATTTGCG 57.233 34.783 0.00 0.00 0.00 4.85
2901 3067 2.380084 ACTGTTACATACCACCTGCG 57.620 50.000 0.00 0.00 0.00 5.18
2950 3116 4.765813 TTAGGTGTATCTTAACCTGGGC 57.234 45.455 4.61 0.00 46.42 5.36
3167 3442 6.314784 GGACACATTACATAGCTTTGTTGTC 58.685 40.000 21.80 21.80 34.86 3.18
3236 3511 4.082125 AGCTGGGAGTTGGAAGTTTTATG 58.918 43.478 0.00 0.00 0.00 1.90
3239 3514 2.310538 CAGCTGGGAGTTGGAAGTTTT 58.689 47.619 5.57 0.00 0.00 2.43
3330 3613 6.007076 TCACATTAAAACTGCTGTGGGATAA 58.993 36.000 0.00 0.00 39.51 1.75
3334 3617 4.582701 TTCACATTAAAACTGCTGTGGG 57.417 40.909 0.00 0.00 39.51 4.61
3442 3725 4.373348 TTTTCACCAACTTGGGTTAACG 57.627 40.909 12.62 0.00 43.37 3.18
3464 3747 3.252215 CCAGTCAACGTGGAATTGCTTTA 59.748 43.478 0.00 0.00 37.23 1.85
3478 3761 6.017400 ACATGAATCAAATCACCAGTCAAC 57.983 37.500 0.00 0.00 30.82 3.18
3486 3770 8.461222 TGATAGTTTGGACATGAATCAAATCAC 58.539 33.333 0.00 0.00 33.72 3.06
3514 3798 5.546621 AACTCCTAGTGTGCTCAGTTTTA 57.453 39.130 0.73 0.00 0.00 1.52
3559 7956 7.027161 CGCATAATGTTTAACTTAAGTGCCTT 58.973 34.615 9.34 0.00 0.00 4.35
3560 7957 6.373216 TCGCATAATGTTTAACTTAAGTGCCT 59.627 34.615 9.34 0.00 0.00 4.75
3611 8008 1.135721 GAACTTGATGCTGGGCCAATC 59.864 52.381 8.04 9.64 0.00 2.67
3653 8050 0.240945 GGGTGAAGTTGATTGGTGCG 59.759 55.000 0.00 0.00 0.00 5.34
3716 8117 9.750125 AACCTAATCTGATTTTTCTGTTGTTTC 57.250 29.630 8.38 0.00 0.00 2.78
3720 8121 8.352201 TGTGAACCTAATCTGATTTTTCTGTTG 58.648 33.333 8.38 0.00 0.00 3.33
3753 8155 9.268282 AGTCCTTCTAGACAGGTATTGAAATTA 57.732 33.333 16.04 0.00 39.34 1.40


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

AutoCloner maintained by Alex Coulton.