Multiple sequence alignment - TraesCS4A01G246900

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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 TraesCS4A01G246900 chr4A 100.000 3701 0 0 1 3701 557871242 557867542 0.000000e+00 6835
1 TraesCS4A01G246900 chr4A 90.698 258 15 1 3453 3701 557793368 557793111 5.920000e-88 335
2 TraesCS4A01G246900 chr4D 93.354 3220 122 34 1 3187 42097715 42100875 0.000000e+00 4676
3 TraesCS4A01G246900 chr4B 94.187 3045 113 29 1 3023 60425720 60428722 0.000000e+00 4584
4 TraesCS4A01G246900 chr4B 91.123 383 28 4 3071 3453 60428884 60429260 7.090000e-142 514
5 TraesCS4A01G246900 chr1B 88.079 1468 114 37 1323 2771 50399766 50398341 0.000000e+00 1685
6 TraesCS4A01G246900 chr1B 85.921 483 31 14 866 1322 50400322 50399851 7.190000e-132 481
7 TraesCS4A01G246900 chr7D 78.030 264 39 10 3452 3701 8811907 8811649 8.280000e-32 148
8 TraesCS4A01G246900 chr7D 77.068 266 44 13 3449 3701 8816970 8816709 1.790000e-28 137
9 TraesCS4A01G246900 chr7A 77.992 259 41 13 3453 3701 332432648 332432396 8.280000e-32 148


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 TraesCS4A01G246900 chr4A 557867542 557871242 3700 True 6835 6835 100.000 1 3701 1 chr4A.!!$R2 3700
1 TraesCS4A01G246900 chr4D 42097715 42100875 3160 False 4676 4676 93.354 1 3187 1 chr4D.!!$F1 3186
2 TraesCS4A01G246900 chr4B 60425720 60429260 3540 False 2549 4584 92.655 1 3453 2 chr4B.!!$F1 3452
3 TraesCS4A01G246900 chr1B 50398341 50400322 1981 True 1083 1685 87.000 866 2771 2 chr1B.!!$R1 1905

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
835 843 0.038251 TGGTCTGAGCATGTCGTGTC 60.038 55.0 5.28 0.00 0.0 3.67 F
2445 2595 0.036858 GAACAGGCAGAGTCCAGGAC 60.037 60.0 12.25 12.25 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 2795 0.035881 CTGTTGCCTTCTCTCCTGCA 59.964 55.0 0.0 0.0 0.0 4.41 R
3506 3774 0.105913 CTCCCTCACCCTCCTACTCC 60.106 65.0 0.0 0.0 0.0 3.85 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
287 288 2.271800 GCCCATCAGTGAACTAACTCG 58.728 52.381 0.00 0.00 0.00 4.18
294 295 5.624344 TCAGTGAACTAACTCGACTAAGG 57.376 43.478 0.00 0.00 0.00 2.69
380 381 1.674322 GAAAGCAAGGCGGCCAGTA 60.674 57.895 23.09 0.00 0.00 2.74
484 485 5.891551 GGAGGATGGAAGGCAAATTAAGTAA 59.108 40.000 0.00 0.00 0.00 2.24
490 491 7.354751 TGGAAGGCAAATTAAGTAAACAGTT 57.645 32.000 0.00 0.00 0.00 3.16
643 649 8.515473 TTATCGTGTTGAACTATTCCATATCG 57.485 34.615 0.00 0.00 0.00 2.92
823 831 5.835280 TCAGATGCACTATTAGATGGTCTGA 59.165 40.000 13.95 13.95 37.73 3.27
832 840 1.189752 AGATGGTCTGAGCATGTCGT 58.810 50.000 25.39 3.26 36.31 4.34
833 841 1.134877 AGATGGTCTGAGCATGTCGTG 60.135 52.381 25.39 0.00 36.31 4.35
835 843 0.038251 TGGTCTGAGCATGTCGTGTC 60.038 55.000 5.28 0.00 0.00 3.67
838 846 1.080501 CTGAGCATGTCGTGTCCGT 60.081 57.895 0.00 0.00 35.01 4.69
840 848 0.249699 TGAGCATGTCGTGTCCGTTT 60.250 50.000 0.00 0.00 35.01 3.60
977 999 6.500684 TGCTGTCTAAACATTTCTTGATCC 57.499 37.500 0.00 0.00 34.13 3.36
1028 1065 8.308851 AGGTTAGTAGTCTTAATTCCTCCTTC 57.691 38.462 0.00 0.00 0.00 3.46
1085 1122 8.752005 ATGCATACTGACTTATTTTGGTATGT 57.248 30.769 0.00 0.00 38.85 2.29
1100 1137 6.533819 TTGGTATGTACGTTTTTCAGAGTG 57.466 37.500 0.00 0.00 0.00 3.51
1239 1283 4.218417 GCATATTTGTTTGGTGTCCTGAGT 59.782 41.667 0.00 0.00 0.00 3.41
1481 1610 5.907207 TGTTGCCTGCTTAAACACAATAAA 58.093 33.333 0.00 0.00 0.00 1.40
1507 1636 6.370166 GCCTAGCTATTGATTTCTACATGGAC 59.630 42.308 0.00 0.00 0.00 4.02
1623 1759 5.873712 CGCTATGATCCAGAGCTAATGAAAT 59.126 40.000 11.12 0.00 45.18 2.17
1821 1957 5.557576 TCACCCTATGATGGATGAAGAAG 57.442 43.478 0.00 0.00 29.99 2.85
1822 1958 5.218959 TCACCCTATGATGGATGAAGAAGA 58.781 41.667 0.00 0.00 29.99 2.87
2087 2225 1.848388 AGATGCCATGGAACAGGATGA 59.152 47.619 18.40 0.00 46.40 2.92
2314 2464 7.704271 ACCTTTTGTAACTCTTTCTAAGTTGC 58.296 34.615 0.00 0.00 39.09 4.17
2403 2553 7.147776 ACGTAATGTGGGAATAGTAAGCTTACT 60.148 37.037 34.85 34.85 45.39 2.24
2425 2575 7.216973 ACTATATGAGTCCAGGACGTTATTC 57.783 40.000 14.32 6.40 37.67 1.75
2433 2583 1.659098 CAGGACGTTATTCGAACAGGC 59.341 52.381 0.00 0.00 42.86 4.85
2434 2584 1.274167 AGGACGTTATTCGAACAGGCA 59.726 47.619 0.00 0.00 42.86 4.75
2435 2585 1.659098 GGACGTTATTCGAACAGGCAG 59.341 52.381 0.00 0.00 42.86 4.85
2436 2586 2.602878 GACGTTATTCGAACAGGCAGA 58.397 47.619 0.00 0.00 42.86 4.26
2437 2587 2.599082 GACGTTATTCGAACAGGCAGAG 59.401 50.000 0.00 0.00 42.86 3.35
2438 2588 2.029290 ACGTTATTCGAACAGGCAGAGT 60.029 45.455 0.00 0.00 42.86 3.24
2439 2589 2.599082 CGTTATTCGAACAGGCAGAGTC 59.401 50.000 0.00 0.00 42.86 3.36
2440 2590 2.930682 GTTATTCGAACAGGCAGAGTCC 59.069 50.000 0.00 0.00 0.00 3.85
2441 2591 0.976641 ATTCGAACAGGCAGAGTCCA 59.023 50.000 0.00 0.00 0.00 4.02
2442 2592 0.318441 TTCGAACAGGCAGAGTCCAG 59.682 55.000 0.00 0.00 0.00 3.86
2443 2593 1.079543 CGAACAGGCAGAGTCCAGG 60.080 63.158 0.00 0.00 0.00 4.45
2444 2594 1.536073 CGAACAGGCAGAGTCCAGGA 61.536 60.000 0.00 0.00 0.00 3.86
2445 2595 0.036858 GAACAGGCAGAGTCCAGGAC 60.037 60.000 12.25 12.25 0.00 3.85
2446 2596 1.821061 AACAGGCAGAGTCCAGGACG 61.821 60.000 14.32 1.11 37.67 4.79
2447 2597 2.118513 AGGCAGAGTCCAGGACGT 59.881 61.111 14.32 2.66 37.67 4.34
2448 2598 1.534235 AGGCAGAGTCCAGGACGTT 60.534 57.895 14.32 3.48 37.67 3.99
2449 2599 0.251653 AGGCAGAGTCCAGGACGTTA 60.252 55.000 14.32 0.00 37.67 3.18
2450 2600 0.824759 GGCAGAGTCCAGGACGTTAT 59.175 55.000 14.32 0.00 37.67 1.89
2451 2601 1.207329 GGCAGAGTCCAGGACGTTATT 59.793 52.381 14.32 0.00 37.67 1.40
2452 2602 2.541556 GCAGAGTCCAGGACGTTATTC 58.458 52.381 14.32 5.83 37.67 1.75
2453 2603 2.798680 CAGAGTCCAGGACGTTATTCG 58.201 52.381 14.32 0.00 46.00 3.34
2454 2604 2.422479 CAGAGTCCAGGACGTTATTCGA 59.578 50.000 14.32 0.00 42.86 3.71
2455 2605 3.087031 AGAGTCCAGGACGTTATTCGAA 58.913 45.455 14.32 0.00 42.86 3.71
2456 2606 3.119566 AGAGTCCAGGACGTTATTCGAAC 60.120 47.826 14.32 0.00 42.86 3.95
2457 2607 2.559668 AGTCCAGGACGTTATTCGAACA 59.440 45.455 14.32 0.00 42.86 3.18
2458 2608 2.921754 GTCCAGGACGTTATTCGAACAG 59.078 50.000 3.05 0.00 42.86 3.16
2459 2609 1.659098 CCAGGACGTTATTCGAACAGC 59.341 52.381 0.00 0.00 42.86 4.40
2606 2758 0.321653 GTTGAAGATGAGGCCCGTGT 60.322 55.000 0.00 0.00 0.00 4.49
2630 2782 3.093449 GCGAGCTGCAAACAACGC 61.093 61.111 1.02 12.33 45.45 4.84
2643 2795 1.375551 ACAACGCCGAAGACAAAACT 58.624 45.000 0.00 0.00 0.00 2.66
2737 2889 1.041447 GTGGTCGCTAAGCCTAGGGA 61.041 60.000 11.72 5.06 42.96 4.20
2788 2940 1.813513 GCCTGCTCTGTGTGTATTGT 58.186 50.000 0.00 0.00 0.00 2.71
2806 2958 7.329226 GTGTATTGTTGGATCCTTGTTTTCATG 59.671 37.037 14.23 0.00 0.00 3.07
2865 3018 7.820648 TGTTCCTCTTTCTTATTTTGAGATGC 58.179 34.615 0.00 0.00 0.00 3.91
2866 3019 7.094205 TGTTCCTCTTTCTTATTTTGAGATGCC 60.094 37.037 0.00 0.00 0.00 4.40
3002 3155 5.129320 ACAACCCTTGAGCAATTTTTCTTCT 59.871 36.000 0.00 0.00 0.00 2.85
3023 3176 5.494724 TCTTGAGATCATGCTTTACTGCTT 58.505 37.500 0.00 0.00 0.00 3.91
3024 3177 5.353400 TCTTGAGATCATGCTTTACTGCTTG 59.647 40.000 0.00 0.00 38.81 4.01
3031 3198 3.287312 TGCTTTACTGCTTGTGATTGC 57.713 42.857 0.00 0.00 0.00 3.56
3037 3204 0.379669 CTGCTTGTGATTGCGGATCC 59.620 55.000 0.00 0.00 37.75 3.36
3038 3205 0.322366 TGCTTGTGATTGCGGATCCA 60.322 50.000 13.41 0.00 33.60 3.41
3050 3219 4.084011 TGCGGATCCATGATGAACATAA 57.916 40.909 13.41 0.00 37.46 1.90
3051 3220 4.067192 TGCGGATCCATGATGAACATAAG 58.933 43.478 13.41 0.00 37.46 1.73
3053 3222 4.391216 GCGGATCCATGATGAACATAAGAG 59.609 45.833 13.41 0.00 37.46 2.85
3119 3387 0.544833 TCATTGGTTTGCCTGGCCAT 60.545 50.000 17.53 0.00 35.27 4.40
3209 3477 3.058639 GCTCGCTAGGATTTAATGCCAAG 60.059 47.826 0.00 0.00 0.00 3.61
3213 3481 4.450419 CGCTAGGATTTAATGCCAAGAGAG 59.550 45.833 0.00 0.00 0.00 3.20
3217 3485 6.521151 AGGATTTAATGCCAAGAGAGTTTG 57.479 37.500 0.00 0.00 0.00 2.93
3256 3524 8.563732 GTGGTGTAACATTTGGCAAATTAAAAT 58.436 29.630 22.26 9.65 39.98 1.82
3257 3525 9.778741 TGGTGTAACATTTGGCAAATTAAAATA 57.221 25.926 22.26 8.77 39.98 1.40
3280 3548 5.916661 AAGTGATTAGTAGAAAGCTCGGA 57.083 39.130 0.00 0.00 0.00 4.55
3311 3579 3.925688 ACGATGTCGACAATTATGCAC 57.074 42.857 24.13 5.93 43.02 4.57
3390 3658 9.974980 TTTCAGTTAACCAAAATTCATCCTTAC 57.025 29.630 0.88 0.00 0.00 2.34
3393 3661 9.757227 CAGTTAACCAAAATTCATCCTTACAAA 57.243 29.630 0.88 0.00 0.00 2.83
3418 3686 7.595488 AGATAAAATAATTGGTGGATGGAGGT 58.405 34.615 0.00 0.00 0.00 3.85
3420 3688 3.492102 ATAATTGGTGGATGGAGGTCG 57.508 47.619 0.00 0.00 0.00 4.79
3428 3696 1.760613 TGGATGGAGGTCGGTGATTAC 59.239 52.381 0.00 0.00 0.00 1.89
3449 3717 3.381272 ACCGCAAATGATTAGTGGATTGG 59.619 43.478 0.00 0.00 36.76 3.16
3453 3721 5.535333 GCAAATGATTAGTGGATTGGGATG 58.465 41.667 0.00 0.00 0.00 3.51
3454 3722 5.069516 GCAAATGATTAGTGGATTGGGATGT 59.930 40.000 0.00 0.00 0.00 3.06
3455 3723 6.265196 GCAAATGATTAGTGGATTGGGATGTA 59.735 38.462 0.00 0.00 0.00 2.29
3456 3724 7.201902 GCAAATGATTAGTGGATTGGGATGTAA 60.202 37.037 0.00 0.00 0.00 2.41
3457 3725 7.823745 AATGATTAGTGGATTGGGATGTAAC 57.176 36.000 0.00 0.00 0.00 2.50
3458 3726 5.364778 TGATTAGTGGATTGGGATGTAACG 58.635 41.667 0.00 0.00 0.00 3.18
3459 3727 2.038387 AGTGGATTGGGATGTAACGC 57.962 50.000 0.00 0.00 0.00 4.84
3460 3728 1.021968 GTGGATTGGGATGTAACGCC 58.978 55.000 0.00 0.00 0.00 5.68
3461 3729 0.106918 TGGATTGGGATGTAACGCCC 60.107 55.000 0.00 0.00 44.93 6.13
3462 3730 0.822121 GGATTGGGATGTAACGCCCC 60.822 60.000 0.00 0.00 44.03 5.80
3463 3731 1.153046 ATTGGGATGTAACGCCCCG 60.153 57.895 0.00 0.00 44.03 5.73
3464 3732 1.628238 ATTGGGATGTAACGCCCCGA 61.628 55.000 0.00 0.00 44.03 5.14
3465 3733 1.628238 TTGGGATGTAACGCCCCGAT 61.628 55.000 0.00 0.00 44.03 4.18
3466 3734 1.301479 GGGATGTAACGCCCCGATC 60.301 63.158 0.00 0.00 38.45 3.69
3467 3735 1.746517 GGATGTAACGCCCCGATCT 59.253 57.895 0.00 0.00 0.00 2.75
3468 3736 0.600255 GGATGTAACGCCCCGATCTG 60.600 60.000 0.00 0.00 0.00 2.90
3469 3737 0.600255 GATGTAACGCCCCGATCTGG 60.600 60.000 0.00 0.00 37.55 3.86
3470 3738 1.046472 ATGTAACGCCCCGATCTGGA 61.046 55.000 4.46 0.00 42.00 3.86
3471 3739 1.046472 TGTAACGCCCCGATCTGGAT 61.046 55.000 4.46 0.00 42.00 3.41
3472 3740 0.319641 GTAACGCCCCGATCTGGATC 60.320 60.000 4.46 0.83 42.00 3.36
3490 3758 1.950828 TCGAAGGCGACTAGAGTAGG 58.049 55.000 0.00 0.00 42.51 3.18
3491 3759 0.308376 CGAAGGCGACTAGAGTAGGC 59.692 60.000 8.07 8.07 42.68 3.93
3495 3763 0.308376 GGCGACTAGAGTAGGCTTCG 59.692 60.000 8.75 0.00 41.61 3.79
3496 3764 0.308376 GCGACTAGAGTAGGCTTCGG 59.692 60.000 0.00 0.00 0.00 4.30
3497 3765 0.945813 CGACTAGAGTAGGCTTCGGG 59.054 60.000 0.00 0.00 0.00 5.14
3498 3766 1.474677 CGACTAGAGTAGGCTTCGGGA 60.475 57.143 0.00 0.00 0.00 5.14
3499 3767 2.223745 GACTAGAGTAGGCTTCGGGAG 58.776 57.143 0.00 0.00 0.00 4.30
3500 3768 1.133730 ACTAGAGTAGGCTTCGGGAGG 60.134 57.143 0.00 0.00 0.00 4.30
3501 3769 0.185416 TAGAGTAGGCTTCGGGAGGG 59.815 60.000 0.00 0.00 0.00 4.30
3502 3770 2.041819 AGTAGGCTTCGGGAGGGG 60.042 66.667 0.00 0.00 0.00 4.79
3503 3771 2.042230 GTAGGCTTCGGGAGGGGA 60.042 66.667 0.00 0.00 0.00 4.81
3504 3772 1.459730 GTAGGCTTCGGGAGGGGAT 60.460 63.158 0.00 0.00 0.00 3.85
3505 3773 1.152312 TAGGCTTCGGGAGGGGATC 60.152 63.158 0.00 0.00 0.00 3.36
3506 3774 2.996470 TAGGCTTCGGGAGGGGATCG 62.996 65.000 0.00 0.00 0.00 3.69
3507 3775 3.930012 GCTTCGGGAGGGGATCGG 61.930 72.222 0.00 0.00 0.00 4.18
3508 3776 2.123425 CTTCGGGAGGGGATCGGA 60.123 66.667 0.00 0.00 0.00 4.55
3509 3777 2.123425 TTCGGGAGGGGATCGGAG 60.123 66.667 0.00 0.00 0.00 4.63
3510 3778 2.930777 CTTCGGGAGGGGATCGGAGT 62.931 65.000 0.00 0.00 0.00 3.85
3511 3779 1.648302 TTCGGGAGGGGATCGGAGTA 61.648 60.000 0.00 0.00 0.00 2.59
3512 3780 1.604023 CGGGAGGGGATCGGAGTAG 60.604 68.421 0.00 0.00 0.00 2.57
3513 3781 1.228925 GGGAGGGGATCGGAGTAGG 60.229 68.421 0.00 0.00 0.00 3.18
3514 3782 1.727215 GGGAGGGGATCGGAGTAGGA 61.727 65.000 0.00 0.00 0.00 2.94
3515 3783 0.251430 GGAGGGGATCGGAGTAGGAG 60.251 65.000 0.00 0.00 0.00 3.69
3516 3784 0.251430 GAGGGGATCGGAGTAGGAGG 60.251 65.000 0.00 0.00 0.00 4.30
3517 3785 1.228925 GGGGATCGGAGTAGGAGGG 60.229 68.421 0.00 0.00 0.00 4.30
3518 3786 1.542679 GGGATCGGAGTAGGAGGGT 59.457 63.158 0.00 0.00 0.00 4.34
3519 3787 0.828343 GGGATCGGAGTAGGAGGGTG 60.828 65.000 0.00 0.00 0.00 4.61
3520 3788 0.185416 GGATCGGAGTAGGAGGGTGA 59.815 60.000 0.00 0.00 0.00 4.02
3521 3789 1.611519 GATCGGAGTAGGAGGGTGAG 58.388 60.000 0.00 0.00 0.00 3.51
3522 3790 0.186386 ATCGGAGTAGGAGGGTGAGG 59.814 60.000 0.00 0.00 0.00 3.86
3523 3791 1.455959 CGGAGTAGGAGGGTGAGGG 60.456 68.421 0.00 0.00 0.00 4.30
3524 3792 1.934459 CGGAGTAGGAGGGTGAGGGA 61.934 65.000 0.00 0.00 0.00 4.20
3525 3793 0.105913 GGAGTAGGAGGGTGAGGGAG 60.106 65.000 0.00 0.00 0.00 4.30
3526 3794 0.927767 GAGTAGGAGGGTGAGGGAGA 59.072 60.000 0.00 0.00 0.00 3.71
3527 3795 1.288335 GAGTAGGAGGGTGAGGGAGAA 59.712 57.143 0.00 0.00 0.00 2.87
3528 3796 1.289530 AGTAGGAGGGTGAGGGAGAAG 59.710 57.143 0.00 0.00 0.00 2.85
3529 3797 0.637195 TAGGAGGGTGAGGGAGAAGG 59.363 60.000 0.00 0.00 0.00 3.46
3530 3798 1.690985 GGAGGGTGAGGGAGAAGGG 60.691 68.421 0.00 0.00 0.00 3.95
3531 3799 1.690985 GAGGGTGAGGGAGAAGGGG 60.691 68.421 0.00 0.00 0.00 4.79
3532 3800 2.692741 GGGTGAGGGAGAAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
3533 3801 2.125225 GGTGAGGGAGAAGGGGGT 59.875 66.667 0.00 0.00 0.00 4.95
3534 3802 2.301738 GGTGAGGGAGAAGGGGGTG 61.302 68.421 0.00 0.00 0.00 4.61
3535 3803 1.229529 GTGAGGGAGAAGGGGGTGA 60.230 63.158 0.00 0.00 0.00 4.02
3536 3804 1.081092 TGAGGGAGAAGGGGGTGAG 59.919 63.158 0.00 0.00 0.00 3.51
3537 3805 2.285743 AGGGAGAAGGGGGTGAGC 60.286 66.667 0.00 0.00 0.00 4.26
3538 3806 3.787001 GGGAGAAGGGGGTGAGCG 61.787 72.222 0.00 0.00 0.00 5.03
3539 3807 2.683933 GGAGAAGGGGGTGAGCGA 60.684 66.667 0.00 0.00 0.00 4.93
3540 3808 2.726351 GGAGAAGGGGGTGAGCGAG 61.726 68.421 0.00 0.00 0.00 5.03
3541 3809 2.685380 AGAAGGGGGTGAGCGAGG 60.685 66.667 0.00 0.00 0.00 4.63
3542 3810 3.787001 GAAGGGGGTGAGCGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
3546 3814 3.327404 GGGGTGAGCGAGGGGAAA 61.327 66.667 0.00 0.00 0.00 3.13
3547 3815 2.269241 GGGTGAGCGAGGGGAAAG 59.731 66.667 0.00 0.00 0.00 2.62
3548 3816 2.593956 GGGTGAGCGAGGGGAAAGT 61.594 63.158 0.00 0.00 0.00 2.66
3549 3817 1.262640 GGGTGAGCGAGGGGAAAGTA 61.263 60.000 0.00 0.00 0.00 2.24
3550 3818 0.175989 GGTGAGCGAGGGGAAAGTAG 59.824 60.000 0.00 0.00 0.00 2.57
3551 3819 0.175989 GTGAGCGAGGGGAAAGTAGG 59.824 60.000 0.00 0.00 0.00 3.18
3552 3820 0.252103 TGAGCGAGGGGAAAGTAGGT 60.252 55.000 0.00 0.00 0.00 3.08
3553 3821 0.175989 GAGCGAGGGGAAAGTAGGTG 59.824 60.000 0.00 0.00 0.00 4.00
3554 3822 0.252103 AGCGAGGGGAAAGTAGGTGA 60.252 55.000 0.00 0.00 0.00 4.02
3555 3823 0.175989 GCGAGGGGAAAGTAGGTGAG 59.824 60.000 0.00 0.00 0.00 3.51
3556 3824 0.824759 CGAGGGGAAAGTAGGTGAGG 59.175 60.000 0.00 0.00 0.00 3.86
3557 3825 1.205055 GAGGGGAAAGTAGGTGAGGG 58.795 60.000 0.00 0.00 0.00 4.30
3558 3826 0.797579 AGGGGAAAGTAGGTGAGGGA 59.202 55.000 0.00 0.00 0.00 4.20
3559 3827 1.153565 AGGGGAAAGTAGGTGAGGGAA 59.846 52.381 0.00 0.00 0.00 3.97
3560 3828 2.206223 GGGGAAAGTAGGTGAGGGAAT 58.794 52.381 0.00 0.00 0.00 3.01
3561 3829 2.581246 GGGGAAAGTAGGTGAGGGAATT 59.419 50.000 0.00 0.00 0.00 2.17
3562 3830 3.371702 GGGGAAAGTAGGTGAGGGAATTC 60.372 52.174 0.00 0.00 0.00 2.17
3563 3831 3.265995 GGGAAAGTAGGTGAGGGAATTCA 59.734 47.826 7.93 0.00 0.00 2.57
3564 3832 4.518249 GGAAAGTAGGTGAGGGAATTCAG 58.482 47.826 7.93 0.00 0.00 3.02
3565 3833 4.225267 GGAAAGTAGGTGAGGGAATTCAGA 59.775 45.833 7.93 0.00 0.00 3.27
3566 3834 5.280521 GGAAAGTAGGTGAGGGAATTCAGAA 60.281 44.000 7.93 0.00 0.00 3.02
3567 3835 6.394345 AAAGTAGGTGAGGGAATTCAGAAT 57.606 37.500 7.93 0.00 0.00 2.40
3568 3836 7.365652 GGAAAGTAGGTGAGGGAATTCAGAATA 60.366 40.741 7.93 0.00 0.00 1.75
3569 3837 7.698163 AAGTAGGTGAGGGAATTCAGAATAT 57.302 36.000 7.93 0.00 0.00 1.28
3570 3838 7.309770 AGTAGGTGAGGGAATTCAGAATATC 57.690 40.000 7.93 0.00 0.00 1.63
3571 3839 7.079048 AGTAGGTGAGGGAATTCAGAATATCT 58.921 38.462 7.93 0.00 0.00 1.98
3572 3840 6.838401 AGGTGAGGGAATTCAGAATATCTT 57.162 37.500 7.93 0.00 0.00 2.40
3573 3841 7.218314 AGGTGAGGGAATTCAGAATATCTTT 57.782 36.000 7.93 0.00 0.00 2.52
3574 3842 7.646884 AGGTGAGGGAATTCAGAATATCTTTT 58.353 34.615 7.93 0.00 0.00 2.27
3575 3843 7.777440 AGGTGAGGGAATTCAGAATATCTTTTC 59.223 37.037 7.93 0.00 0.00 2.29
3576 3844 7.557719 GGTGAGGGAATTCAGAATATCTTTTCA 59.442 37.037 7.93 0.00 0.00 2.69
3577 3845 9.129532 GTGAGGGAATTCAGAATATCTTTTCAT 57.870 33.333 7.93 0.00 0.00 2.57
3578 3846 9.347240 TGAGGGAATTCAGAATATCTTTTCATC 57.653 33.333 7.93 0.00 0.00 2.92
3579 3847 9.347240 GAGGGAATTCAGAATATCTTTTCATCA 57.653 33.333 7.93 0.00 0.00 3.07
3580 3848 9.352191 AGGGAATTCAGAATATCTTTTCATCAG 57.648 33.333 7.93 0.00 0.00 2.90
3581 3849 8.081025 GGGAATTCAGAATATCTTTTCATCAGC 58.919 37.037 7.93 0.00 0.00 4.26
3582 3850 8.627403 GGAATTCAGAATATCTTTTCATCAGCA 58.373 33.333 7.93 0.00 0.00 4.41
3586 3854 9.842775 TTCAGAATATCTTTTCATCAGCATACT 57.157 29.630 0.00 0.00 0.00 2.12
3587 3855 9.842775 TCAGAATATCTTTTCATCAGCATACTT 57.157 29.630 0.00 0.00 0.00 2.24
3588 3856 9.880064 CAGAATATCTTTTCATCAGCATACTTG 57.120 33.333 0.00 0.00 0.00 3.16
3589 3857 9.842775 AGAATATCTTTTCATCAGCATACTTGA 57.157 29.630 0.00 0.00 0.00 3.02
3593 3861 8.969260 ATCTTTTCATCAGCATACTTGATACA 57.031 30.769 0.00 0.00 33.67 2.29
3594 3862 8.791327 TCTTTTCATCAGCATACTTGATACAA 57.209 30.769 0.00 0.00 33.67 2.41
3595 3863 8.668353 TCTTTTCATCAGCATACTTGATACAAC 58.332 33.333 0.00 0.00 33.67 3.32
3596 3864 6.925610 TTCATCAGCATACTTGATACAACC 57.074 37.500 0.00 0.00 33.67 3.77
3597 3865 5.368145 TCATCAGCATACTTGATACAACCC 58.632 41.667 0.00 0.00 33.67 4.11
3598 3866 4.150897 TCAGCATACTTGATACAACCCC 57.849 45.455 0.00 0.00 0.00 4.95
3599 3867 3.780294 TCAGCATACTTGATACAACCCCT 59.220 43.478 0.00 0.00 0.00 4.79
3600 3868 4.130118 CAGCATACTTGATACAACCCCTC 58.870 47.826 0.00 0.00 0.00 4.30
3601 3869 4.040755 AGCATACTTGATACAACCCCTCT 58.959 43.478 0.00 0.00 0.00 3.69
3602 3870 4.101741 AGCATACTTGATACAACCCCTCTC 59.898 45.833 0.00 0.00 0.00 3.20
3603 3871 4.743955 GCATACTTGATACAACCCCTCTCC 60.744 50.000 0.00 0.00 0.00 3.71
3604 3872 2.915869 ACTTGATACAACCCCTCTCCA 58.084 47.619 0.00 0.00 0.00 3.86
3605 3873 2.840651 ACTTGATACAACCCCTCTCCAG 59.159 50.000 0.00 0.00 0.00 3.86
3606 3874 1.879575 TGATACAACCCCTCTCCAGG 58.120 55.000 0.00 0.00 39.98 4.45
3614 3882 4.035843 CCTCTCCAGGGCGTAAGT 57.964 61.111 0.00 0.00 35.89 2.24
3615 3883 3.202548 CCTCTCCAGGGCGTAAGTA 57.797 57.895 0.00 0.00 35.89 2.24
3616 3884 0.745468 CCTCTCCAGGGCGTAAGTAC 59.255 60.000 0.00 0.00 35.89 2.73
3617 3885 1.685491 CCTCTCCAGGGCGTAAGTACT 60.685 57.143 0.00 0.00 35.89 2.73
3618 3886 2.100989 CTCTCCAGGGCGTAAGTACTT 58.899 52.381 13.68 13.68 41.68 2.24
3619 3887 1.822990 TCTCCAGGGCGTAAGTACTTG 59.177 52.381 18.56 3.44 41.68 3.16
3620 3888 0.248289 TCCAGGGCGTAAGTACTTGC 59.752 55.000 18.56 15.76 41.68 4.01
3626 3894 1.986154 CGTAAGTACTTGCGCGACC 59.014 57.895 28.66 0.00 41.24 4.79
3627 3895 1.408474 CGTAAGTACTTGCGCGACCC 61.408 60.000 28.66 0.00 41.24 4.46
3628 3896 0.388907 GTAAGTACTTGCGCGACCCA 60.389 55.000 18.56 0.00 0.00 4.51
3629 3897 0.317799 TAAGTACTTGCGCGACCCAA 59.682 50.000 18.56 3.45 0.00 4.12
3630 3898 1.226030 AAGTACTTGCGCGACCCAAC 61.226 55.000 12.10 1.09 0.00 3.77
3631 3899 2.357760 TACTTGCGCGACCCAACC 60.358 61.111 12.10 0.00 0.00 3.77
3632 3900 3.166490 TACTTGCGCGACCCAACCA 62.166 57.895 12.10 0.00 0.00 3.67
3633 3901 3.726517 CTTGCGCGACCCAACCAG 61.727 66.667 12.10 0.00 0.00 4.00
3638 3906 4.660938 GCGACCCAACCAGCCCTT 62.661 66.667 0.00 0.00 0.00 3.95
3639 3907 2.672996 CGACCCAACCAGCCCTTG 60.673 66.667 0.00 0.00 0.00 3.61
3650 3918 4.887615 GCCCTTGGCCTCTCATAC 57.112 61.111 3.32 0.00 44.06 2.39
3651 3919 1.915228 GCCCTTGGCCTCTCATACA 59.085 57.895 3.32 0.00 44.06 2.29
3652 3920 0.464554 GCCCTTGGCCTCTCATACAC 60.465 60.000 3.32 0.00 44.06 2.90
3653 3921 1.207791 CCCTTGGCCTCTCATACACT 58.792 55.000 3.32 0.00 0.00 3.55
3654 3922 1.561542 CCCTTGGCCTCTCATACACTT 59.438 52.381 3.32 0.00 0.00 3.16
3655 3923 2.771943 CCCTTGGCCTCTCATACACTTA 59.228 50.000 3.32 0.00 0.00 2.24
3656 3924 3.432326 CCCTTGGCCTCTCATACACTTAC 60.432 52.174 3.32 0.00 0.00 2.34
3657 3925 3.197766 CCTTGGCCTCTCATACACTTACA 59.802 47.826 3.32 0.00 0.00 2.41
3658 3926 4.323485 CCTTGGCCTCTCATACACTTACAA 60.323 45.833 3.32 0.00 0.00 2.41
3659 3927 4.471904 TGGCCTCTCATACACTTACAAG 57.528 45.455 3.32 0.00 0.00 3.16
3660 3928 3.838317 TGGCCTCTCATACACTTACAAGT 59.162 43.478 3.32 0.00 40.60 3.16
3678 3946 4.382320 GGAACCCACGCACGCCTA 62.382 66.667 0.00 0.00 0.00 3.93
3679 3947 3.116531 GAACCCACGCACGCCTAC 61.117 66.667 0.00 0.00 0.00 3.18
3680 3948 3.869473 GAACCCACGCACGCCTACA 62.869 63.158 0.00 0.00 0.00 2.74
3681 3949 4.675029 ACCCACGCACGCCTACAC 62.675 66.667 0.00 0.00 0.00 2.90
3682 3950 4.373116 CCCACGCACGCCTACACT 62.373 66.667 0.00 0.00 0.00 3.55
3683 3951 2.357034 CCACGCACGCCTACACTT 60.357 61.111 0.00 0.00 0.00 3.16
3684 3952 2.667318 CCACGCACGCCTACACTTG 61.667 63.158 0.00 0.00 0.00 3.16
3685 3953 2.357034 ACGCACGCCTACACTTGG 60.357 61.111 0.00 0.00 0.00 3.61
3686 3954 3.788766 CGCACGCCTACACTTGGC 61.789 66.667 0.00 0.00 46.42 4.52
3691 3959 4.542075 GCCTACACTTGGCTAGGC 57.458 61.111 9.85 9.85 46.40 3.93
3692 3960 1.153147 GCCTACACTTGGCTAGGCC 60.153 63.158 14.58 0.00 46.60 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 7.953158 AAGATGGAATGACTGTATTACGATG 57.047 36.000 0.00 0.00 0.00 3.84
258 259 0.738975 CACTGATGGGCATGCTTCAG 59.261 55.000 28.38 28.38 41.06 3.02
287 288 2.762745 TCAACAAAGACGGCCTTAGTC 58.237 47.619 0.00 0.24 38.81 2.59
294 295 1.533129 GGTGTGTTCAACAAAGACGGC 60.533 52.381 0.00 0.00 41.57 5.68
380 381 2.221169 TGCACAATTTCTCTTCGCTGT 58.779 42.857 0.00 0.00 0.00 4.40
484 485 1.152963 AGGGCTGCACGAAACTGTT 60.153 52.632 0.50 0.00 0.00 3.16
490 491 2.669569 GCAAGAGGGCTGCACGAA 60.670 61.111 0.50 0.00 0.00 3.85
823 831 0.531974 ACAAACGGACACGACATGCT 60.532 50.000 0.00 0.00 44.60 3.79
832 840 1.092921 GCCACTGTGACAAACGGACA 61.093 55.000 9.86 0.00 38.65 4.02
833 841 1.092921 TGCCACTGTGACAAACGGAC 61.093 55.000 9.86 0.00 38.65 4.79
835 843 1.355210 GTGCCACTGTGACAAACGG 59.645 57.895 9.86 0.00 41.37 4.44
838 846 1.378531 GAGTGTGCCACTGTGACAAA 58.621 50.000 9.86 0.00 45.44 2.83
840 848 1.146041 GGAGTGTGCCACTGTGACA 59.854 57.895 9.86 0.00 45.44 3.58
875 890 5.803020 AGAGTAAATCGAACAAAGATGCC 57.197 39.130 0.00 0.00 0.00 4.40
977 999 6.791887 TGCTTTAAGTTTCTGATGAGTGAG 57.208 37.500 0.00 0.00 0.00 3.51
1028 1065 9.322776 CTTTCAAACAGTTTCTTATTGATCTCG 57.677 33.333 0.00 0.00 30.81 4.04
1056 1093 8.297470 ACCAAAATAAGTCAGTATGCATCATT 57.703 30.769 0.19 0.00 34.76 2.57
1085 1122 9.450807 GTACTAACTAACACTCTGAAAAACGTA 57.549 33.333 0.00 0.00 0.00 3.57
1453 1582 2.483877 TGTTTAAGCAGGCAACAGATCG 59.516 45.455 0.00 0.00 41.41 3.69
1481 1610 6.270927 TCCATGTAGAAATCAATAGCTAGGCT 59.729 38.462 0.00 0.00 43.41 4.58
1575 1704 0.789601 ATTTGCGCCAAAAACATCGC 59.210 45.000 4.18 0.00 46.78 4.58
1623 1759 2.857186 TATGCAGCCAGTTCAGTTGA 57.143 45.000 0.00 0.00 0.00 3.18
1706 1842 1.375396 CCACTTCACGCGATGGGAA 60.375 57.895 15.93 9.99 0.00 3.97
2087 2225 4.042187 ACTGAGAAAGAAGCTACCAACCAT 59.958 41.667 0.00 0.00 0.00 3.55
2393 2543 7.573469 CGTCCTGGACTCATATAGTAAGCTTAC 60.573 44.444 26.04 26.04 39.07 2.34
2403 2553 5.999600 TCGAATAACGTCCTGGACTCATATA 59.000 40.000 23.49 10.00 43.13 0.86
2406 2556 3.021695 TCGAATAACGTCCTGGACTCAT 58.978 45.455 23.49 12.16 43.13 2.90
2425 2575 1.079543 CCTGGACTCTGCCTGTTCG 60.080 63.158 0.00 0.00 0.00 3.95
2433 2583 2.422479 TCGAATAACGTCCTGGACTCTG 59.578 50.000 23.49 11.44 43.13 3.35
2434 2584 2.719739 TCGAATAACGTCCTGGACTCT 58.280 47.619 23.49 12.99 43.13 3.24
2435 2585 3.177487 GTTCGAATAACGTCCTGGACTC 58.823 50.000 23.49 13.09 43.13 3.36
2436 2586 2.559668 TGTTCGAATAACGTCCTGGACT 59.440 45.455 23.49 9.38 43.13 3.85
2437 2587 2.921754 CTGTTCGAATAACGTCCTGGAC 59.078 50.000 16.99 16.99 43.13 4.02
2438 2588 2.673043 GCTGTTCGAATAACGTCCTGGA 60.673 50.000 0.00 0.00 43.13 3.86
2439 2589 1.659098 GCTGTTCGAATAACGTCCTGG 59.341 52.381 0.00 0.00 43.13 4.45
2440 2590 1.659098 GGCTGTTCGAATAACGTCCTG 59.341 52.381 0.00 0.00 43.13 3.86
2441 2591 1.274167 TGGCTGTTCGAATAACGTCCT 59.726 47.619 0.00 0.00 43.13 3.85
2442 2592 1.659098 CTGGCTGTTCGAATAACGTCC 59.341 52.381 0.00 0.00 43.13 4.79
2443 2593 2.092211 CACTGGCTGTTCGAATAACGTC 59.908 50.000 0.00 0.00 43.13 4.34
2444 2594 2.066262 CACTGGCTGTTCGAATAACGT 58.934 47.619 0.00 0.00 43.13 3.99
2445 2595 2.333926 TCACTGGCTGTTCGAATAACG 58.666 47.619 0.00 0.00 44.09 3.18
2446 2596 5.523916 ACATATCACTGGCTGTTCGAATAAC 59.476 40.000 0.00 0.00 0.00 1.89
2447 2597 5.670485 ACATATCACTGGCTGTTCGAATAA 58.330 37.500 0.00 0.00 0.00 1.40
2448 2598 5.276461 ACATATCACTGGCTGTTCGAATA 57.724 39.130 0.00 0.00 0.00 1.75
2449 2599 4.142609 ACATATCACTGGCTGTTCGAAT 57.857 40.909 0.00 0.00 0.00 3.34
2450 2600 3.610040 ACATATCACTGGCTGTTCGAA 57.390 42.857 0.00 0.00 0.00 3.71
2451 2601 3.610040 AACATATCACTGGCTGTTCGA 57.390 42.857 0.00 0.00 0.00 3.71
2452 2602 3.181507 CCAAACATATCACTGGCTGTTCG 60.182 47.826 0.00 0.00 31.73 3.95
2453 2603 3.758554 ACCAAACATATCACTGGCTGTTC 59.241 43.478 0.00 0.00 31.73 3.18
2454 2604 3.507233 CACCAAACATATCACTGGCTGTT 59.493 43.478 0.00 0.00 33.45 3.16
2455 2605 3.084039 CACCAAACATATCACTGGCTGT 58.916 45.455 0.00 0.00 31.74 4.40
2456 2606 3.084039 ACACCAAACATATCACTGGCTG 58.916 45.455 0.00 0.00 31.74 4.85
2457 2607 3.439857 ACACCAAACATATCACTGGCT 57.560 42.857 0.00 0.00 31.74 4.75
2458 2608 3.505680 TGAACACCAAACATATCACTGGC 59.494 43.478 0.00 0.00 31.74 4.85
2459 2609 5.643664 CATGAACACCAAACATATCACTGG 58.356 41.667 0.00 0.00 34.95 4.00
2562 2714 0.251354 ATCCAGTGCGCATCAGTTCT 59.749 50.000 15.91 0.54 0.00 3.01
2606 2758 0.518636 GTTTGCAGCTCGCTCATTCA 59.481 50.000 9.12 0.00 43.06 2.57
2630 2782 1.532868 CTCCTGCAGTTTTGTCTTCGG 59.467 52.381 13.81 0.00 0.00 4.30
2643 2795 0.035881 CTGTTGCCTTCTCTCCTGCA 59.964 55.000 0.00 0.00 0.00 4.41
2704 2856 4.579869 AGCGACCACAGAATTCACTTTAT 58.420 39.130 8.44 0.00 0.00 1.40
2705 2857 4.002906 AGCGACCACAGAATTCACTTTA 57.997 40.909 8.44 0.00 0.00 1.85
2737 2889 2.152016 GCTCCCGCTTAGTTGAACTTT 58.848 47.619 1.97 0.00 0.00 2.66
2788 2940 3.237746 TGGCATGAAAACAAGGATCCAA 58.762 40.909 15.82 0.00 0.00 3.53
2806 2958 3.209410 ACAGAAAATCATCCGATCTGGC 58.791 45.455 6.11 0.00 37.80 4.85
2865 3018 2.043980 ACCATTTTAGGCACCGCGG 61.044 57.895 26.86 26.86 0.00 6.46
2866 3019 1.136565 CACCATTTTAGGCACCGCG 59.863 57.895 0.00 0.00 0.00 6.46
3002 3155 5.005740 ACAAGCAGTAAAGCATGATCTCAA 58.994 37.500 0.00 0.00 36.75 3.02
3023 3176 2.158784 TCATCATGGATCCGCAATCACA 60.159 45.455 7.39 0.00 35.96 3.58
3024 3177 2.497138 TCATCATGGATCCGCAATCAC 58.503 47.619 7.39 0.00 35.96 3.06
3031 3198 5.545588 ACTCTTATGTTCATCATGGATCCG 58.454 41.667 7.39 0.00 37.91 4.18
3037 3204 8.400186 TGTGCAATAACTCTTATGTTCATCATG 58.600 33.333 0.00 0.00 37.91 3.07
3038 3205 8.510243 TGTGCAATAACTCTTATGTTCATCAT 57.490 30.769 0.00 0.00 40.25 2.45
3076 3344 7.552687 TGAACTACTGAACTGAACAATGAAAGT 59.447 33.333 0.00 0.00 0.00 2.66
3119 3387 8.267183 TCTCATATTCTCATAAGCTGTTTCCAA 58.733 33.333 0.00 0.00 0.00 3.53
3209 3477 1.583054 AGGTGTGCGTTCAAACTCTC 58.417 50.000 0.00 0.00 31.03 3.20
3213 3481 1.544686 CACAAGGTGTGCGTTCAAAC 58.455 50.000 0.00 0.00 41.89 2.93
3256 3524 7.400599 TCCGAGCTTTCTACTAATCACTTTA 57.599 36.000 0.00 0.00 0.00 1.85
3257 3525 6.282199 TCCGAGCTTTCTACTAATCACTTT 57.718 37.500 0.00 0.00 0.00 2.66
3263 3531 2.950309 TCGCTCCGAGCTTTCTACTAAT 59.050 45.455 18.14 0.00 39.60 1.73
3280 3548 3.064408 TGTCGACATCGTATAACTTCGCT 59.936 43.478 15.76 0.00 40.80 4.93
3290 3558 4.678622 AGTGCATAATTGTCGACATCGTA 58.321 39.130 20.80 11.99 40.80 3.43
3292 3560 4.520743 AAGTGCATAATTGTCGACATCG 57.479 40.909 20.80 7.40 41.45 3.84
3367 3635 9.757227 TTTGTAAGGATGAATTTTGGTTAACTG 57.243 29.630 5.42 0.00 0.00 3.16
3390 3658 9.754382 CTCCATCCACCAATTATTTTATCTTTG 57.246 33.333 0.00 0.00 0.00 2.77
3393 3661 7.595488 ACCTCCATCCACCAATTATTTTATCT 58.405 34.615 0.00 0.00 0.00 1.98
3396 3664 5.825679 CGACCTCCATCCACCAATTATTTTA 59.174 40.000 0.00 0.00 0.00 1.52
3399 3667 3.435026 CCGACCTCCATCCACCAATTATT 60.435 47.826 0.00 0.00 0.00 1.40
3400 3668 2.106511 CCGACCTCCATCCACCAATTAT 59.893 50.000 0.00 0.00 0.00 1.28
3401 3669 1.488812 CCGACCTCCATCCACCAATTA 59.511 52.381 0.00 0.00 0.00 1.40
3402 3670 0.255890 CCGACCTCCATCCACCAATT 59.744 55.000 0.00 0.00 0.00 2.32
3403 3671 0.914417 ACCGACCTCCATCCACCAAT 60.914 55.000 0.00 0.00 0.00 3.16
3420 3688 5.505654 CCACTAATCATTTGCGGTAATCACC 60.506 44.000 0.00 0.00 41.93 4.02
3428 3696 3.243501 CCCAATCCACTAATCATTTGCGG 60.244 47.826 0.00 0.00 0.00 5.69
3431 3699 6.720112 ACATCCCAATCCACTAATCATTTG 57.280 37.500 0.00 0.00 0.00 2.32
3432 3700 7.013274 CGTTACATCCCAATCCACTAATCATTT 59.987 37.037 0.00 0.00 0.00 2.32
3440 3708 1.408266 GGCGTTACATCCCAATCCACT 60.408 52.381 0.00 0.00 0.00 4.00
3449 3717 0.600255 CAGATCGGGGCGTTACATCC 60.600 60.000 0.00 0.00 0.00 3.51
3453 3721 0.319641 GATCCAGATCGGGGCGTTAC 60.320 60.000 12.28 0.00 34.36 2.50
3454 3722 2.046938 GATCCAGATCGGGGCGTTA 58.953 57.895 12.28 0.00 34.36 3.18
3455 3723 2.822399 GATCCAGATCGGGGCGTT 59.178 61.111 12.28 0.00 34.36 4.84
3471 3739 1.950828 CCTACTCTAGTCGCCTTCGA 58.049 55.000 0.00 0.00 43.28 3.71
3472 3740 0.308376 GCCTACTCTAGTCGCCTTCG 59.692 60.000 0.00 0.00 0.00 3.79
3473 3741 1.682740 AGCCTACTCTAGTCGCCTTC 58.317 55.000 0.00 0.00 0.00 3.46
3474 3742 2.025898 GAAGCCTACTCTAGTCGCCTT 58.974 52.381 0.00 0.00 0.00 4.35
3475 3743 1.682740 GAAGCCTACTCTAGTCGCCT 58.317 55.000 0.00 0.00 0.00 5.52
3476 3744 0.308376 CGAAGCCTACTCTAGTCGCC 59.692 60.000 0.00 0.00 0.00 5.54
3477 3745 0.308376 CCGAAGCCTACTCTAGTCGC 59.692 60.000 0.00 0.00 0.00 5.19
3478 3746 0.945813 CCCGAAGCCTACTCTAGTCG 59.054 60.000 0.00 0.00 0.00 4.18
3479 3747 2.223745 CTCCCGAAGCCTACTCTAGTC 58.776 57.143 0.00 0.00 0.00 2.59
3480 3748 1.133730 CCTCCCGAAGCCTACTCTAGT 60.134 57.143 0.00 0.00 0.00 2.57
3481 3749 1.611519 CCTCCCGAAGCCTACTCTAG 58.388 60.000 0.00 0.00 0.00 2.43
3482 3750 0.185416 CCCTCCCGAAGCCTACTCTA 59.815 60.000 0.00 0.00 0.00 2.43
3483 3751 1.075896 CCCTCCCGAAGCCTACTCT 60.076 63.158 0.00 0.00 0.00 3.24
3484 3752 2.134933 CCCCTCCCGAAGCCTACTC 61.135 68.421 0.00 0.00 0.00 2.59
3485 3753 1.962570 ATCCCCTCCCGAAGCCTACT 61.963 60.000 0.00 0.00 0.00 2.57
3486 3754 1.459730 ATCCCCTCCCGAAGCCTAC 60.460 63.158 0.00 0.00 0.00 3.18
3487 3755 1.152312 GATCCCCTCCCGAAGCCTA 60.152 63.158 0.00 0.00 0.00 3.93
3488 3756 2.446802 GATCCCCTCCCGAAGCCT 60.447 66.667 0.00 0.00 0.00 4.58
3489 3757 3.930012 CGATCCCCTCCCGAAGCC 61.930 72.222 0.00 0.00 0.00 4.35
3490 3758 3.930012 CCGATCCCCTCCCGAAGC 61.930 72.222 0.00 0.00 0.00 3.86
3491 3759 2.123425 TCCGATCCCCTCCCGAAG 60.123 66.667 0.00 0.00 0.00 3.79
3492 3760 1.648302 TACTCCGATCCCCTCCCGAA 61.648 60.000 0.00 0.00 0.00 4.30
3493 3761 2.065470 CTACTCCGATCCCCTCCCGA 62.065 65.000 0.00 0.00 0.00 5.14
3494 3762 1.604023 CTACTCCGATCCCCTCCCG 60.604 68.421 0.00 0.00 0.00 5.14
3495 3763 1.228925 CCTACTCCGATCCCCTCCC 60.229 68.421 0.00 0.00 0.00 4.30
3496 3764 0.251430 CTCCTACTCCGATCCCCTCC 60.251 65.000 0.00 0.00 0.00 4.30
3497 3765 0.251430 CCTCCTACTCCGATCCCCTC 60.251 65.000 0.00 0.00 0.00 4.30
3498 3766 1.731324 CCCTCCTACTCCGATCCCCT 61.731 65.000 0.00 0.00 0.00 4.79
3499 3767 1.228925 CCCTCCTACTCCGATCCCC 60.229 68.421 0.00 0.00 0.00 4.81
3500 3768 0.828343 CACCCTCCTACTCCGATCCC 60.828 65.000 0.00 0.00 0.00 3.85
3501 3769 0.185416 TCACCCTCCTACTCCGATCC 59.815 60.000 0.00 0.00 0.00 3.36
3502 3770 1.611519 CTCACCCTCCTACTCCGATC 58.388 60.000 0.00 0.00 0.00 3.69
3503 3771 0.186386 CCTCACCCTCCTACTCCGAT 59.814 60.000 0.00 0.00 0.00 4.18
3504 3772 1.613610 CCTCACCCTCCTACTCCGA 59.386 63.158 0.00 0.00 0.00 4.55
3505 3773 1.455959 CCCTCACCCTCCTACTCCG 60.456 68.421 0.00 0.00 0.00 4.63
3506 3774 0.105913 CTCCCTCACCCTCCTACTCC 60.106 65.000 0.00 0.00 0.00 3.85
3507 3775 0.927767 TCTCCCTCACCCTCCTACTC 59.072 60.000 0.00 0.00 0.00 2.59
3508 3776 1.289530 CTTCTCCCTCACCCTCCTACT 59.710 57.143 0.00 0.00 0.00 2.57
3509 3777 1.689892 CCTTCTCCCTCACCCTCCTAC 60.690 61.905 0.00 0.00 0.00 3.18
3510 3778 0.637195 CCTTCTCCCTCACCCTCCTA 59.363 60.000 0.00 0.00 0.00 2.94
3511 3779 1.394151 CCTTCTCCCTCACCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
3512 3780 1.690985 CCCTTCTCCCTCACCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
3513 3781 1.690985 CCCCTTCTCCCTCACCCTC 60.691 68.421 0.00 0.00 0.00 4.30
3514 3782 2.456840 CCCCTTCTCCCTCACCCT 59.543 66.667 0.00 0.00 0.00 4.34
3515 3783 2.692741 CCCCCTTCTCCCTCACCC 60.693 72.222 0.00 0.00 0.00 4.61
3516 3784 2.125225 ACCCCCTTCTCCCTCACC 59.875 66.667 0.00 0.00 0.00 4.02
3517 3785 1.229529 TCACCCCCTTCTCCCTCAC 60.230 63.158 0.00 0.00 0.00 3.51
3518 3786 1.081092 CTCACCCCCTTCTCCCTCA 59.919 63.158 0.00 0.00 0.00 3.86
3519 3787 2.371259 GCTCACCCCCTTCTCCCTC 61.371 68.421 0.00 0.00 0.00 4.30
3520 3788 2.285743 GCTCACCCCCTTCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
3521 3789 3.787001 CGCTCACCCCCTTCTCCC 61.787 72.222 0.00 0.00 0.00 4.30
3522 3790 2.683933 TCGCTCACCCCCTTCTCC 60.684 66.667 0.00 0.00 0.00 3.71
3523 3791 2.726351 CCTCGCTCACCCCCTTCTC 61.726 68.421 0.00 0.00 0.00 2.87
3524 3792 2.685380 CCTCGCTCACCCCCTTCT 60.685 66.667 0.00 0.00 0.00 2.85
3525 3793 3.787001 CCCTCGCTCACCCCCTTC 61.787 72.222 0.00 0.00 0.00 3.46
3529 3797 3.327404 TTTCCCCTCGCTCACCCC 61.327 66.667 0.00 0.00 0.00 4.95
3530 3798 1.262640 TACTTTCCCCTCGCTCACCC 61.263 60.000 0.00 0.00 0.00 4.61
3531 3799 0.175989 CTACTTTCCCCTCGCTCACC 59.824 60.000 0.00 0.00 0.00 4.02
3532 3800 0.175989 CCTACTTTCCCCTCGCTCAC 59.824 60.000 0.00 0.00 0.00 3.51
3533 3801 0.252103 ACCTACTTTCCCCTCGCTCA 60.252 55.000 0.00 0.00 0.00 4.26
3534 3802 0.175989 CACCTACTTTCCCCTCGCTC 59.824 60.000 0.00 0.00 0.00 5.03
3535 3803 0.252103 TCACCTACTTTCCCCTCGCT 60.252 55.000 0.00 0.00 0.00 4.93
3536 3804 0.175989 CTCACCTACTTTCCCCTCGC 59.824 60.000 0.00 0.00 0.00 5.03
3537 3805 0.824759 CCTCACCTACTTTCCCCTCG 59.175 60.000 0.00 0.00 0.00 4.63
3538 3806 1.205055 CCCTCACCTACTTTCCCCTC 58.795 60.000 0.00 0.00 0.00 4.30
3539 3807 0.797579 TCCCTCACCTACTTTCCCCT 59.202 55.000 0.00 0.00 0.00 4.79
3540 3808 1.665137 TTCCCTCACCTACTTTCCCC 58.335 55.000 0.00 0.00 0.00 4.81
3541 3809 3.265995 TGAATTCCCTCACCTACTTTCCC 59.734 47.826 2.27 0.00 0.00 3.97
3542 3810 4.225267 TCTGAATTCCCTCACCTACTTTCC 59.775 45.833 2.27 0.00 0.00 3.13
3543 3811 5.422214 TCTGAATTCCCTCACCTACTTTC 57.578 43.478 2.27 0.00 0.00 2.62
3544 3812 5.843019 TTCTGAATTCCCTCACCTACTTT 57.157 39.130 2.27 0.00 0.00 2.66
3545 3813 7.570607 AGATATTCTGAATTCCCTCACCTACTT 59.429 37.037 8.38 0.00 0.00 2.24
3546 3814 7.079048 AGATATTCTGAATTCCCTCACCTACT 58.921 38.462 8.38 0.00 0.00 2.57
3547 3815 7.309770 AGATATTCTGAATTCCCTCACCTAC 57.690 40.000 8.38 0.00 0.00 3.18
3548 3816 7.937700 AAGATATTCTGAATTCCCTCACCTA 57.062 36.000 8.38 0.00 0.00 3.08
3549 3817 6.838401 AAGATATTCTGAATTCCCTCACCT 57.162 37.500 8.38 0.00 0.00 4.00
3550 3818 7.557719 TGAAAAGATATTCTGAATTCCCTCACC 59.442 37.037 8.38 0.00 0.00 4.02
3551 3819 8.511604 TGAAAAGATATTCTGAATTCCCTCAC 57.488 34.615 8.38 0.00 0.00 3.51
3552 3820 9.347240 GATGAAAAGATATTCTGAATTCCCTCA 57.653 33.333 8.38 5.39 0.00 3.86
3553 3821 9.347240 TGATGAAAAGATATTCTGAATTCCCTC 57.653 33.333 8.38 1.81 0.00 4.30
3554 3822 9.352191 CTGATGAAAAGATATTCTGAATTCCCT 57.648 33.333 8.38 1.23 0.00 4.20
3555 3823 8.081025 GCTGATGAAAAGATATTCTGAATTCCC 58.919 37.037 8.38 0.00 0.00 3.97
3556 3824 8.627403 TGCTGATGAAAAGATATTCTGAATTCC 58.373 33.333 8.38 1.33 0.00 3.01
3560 3828 9.842775 AGTATGCTGATGAAAAGATATTCTGAA 57.157 29.630 0.00 0.00 0.00 3.02
3561 3829 9.842775 AAGTATGCTGATGAAAAGATATTCTGA 57.157 29.630 0.00 0.00 0.00 3.27
3562 3830 9.880064 CAAGTATGCTGATGAAAAGATATTCTG 57.120 33.333 0.00 0.00 0.00 3.02
3563 3831 9.842775 TCAAGTATGCTGATGAAAAGATATTCT 57.157 29.630 0.00 0.00 0.00 2.40
3568 3836 8.969260 TGTATCAAGTATGCTGATGAAAAGAT 57.031 30.769 6.18 0.00 0.00 2.40
3569 3837 8.668353 GTTGTATCAAGTATGCTGATGAAAAGA 58.332 33.333 6.18 0.00 0.00 2.52
3570 3838 7.912250 GGTTGTATCAAGTATGCTGATGAAAAG 59.088 37.037 6.18 0.00 0.00 2.27
3571 3839 7.148086 GGGTTGTATCAAGTATGCTGATGAAAA 60.148 37.037 6.18 0.00 0.00 2.29
3572 3840 6.318648 GGGTTGTATCAAGTATGCTGATGAAA 59.681 38.462 6.18 0.37 0.00 2.69
3573 3841 5.822519 GGGTTGTATCAAGTATGCTGATGAA 59.177 40.000 6.18 0.00 0.00 2.57
3574 3842 5.368145 GGGTTGTATCAAGTATGCTGATGA 58.632 41.667 6.18 0.00 0.00 2.92
3575 3843 4.516698 GGGGTTGTATCAAGTATGCTGATG 59.483 45.833 6.18 0.00 0.00 3.07
3576 3844 4.413520 AGGGGTTGTATCAAGTATGCTGAT 59.586 41.667 0.00 0.00 0.00 2.90
3577 3845 3.780294 AGGGGTTGTATCAAGTATGCTGA 59.220 43.478 0.00 0.00 0.00 4.26
3578 3846 4.130118 GAGGGGTTGTATCAAGTATGCTG 58.870 47.826 0.00 0.00 0.00 4.41
3579 3847 4.040755 AGAGGGGTTGTATCAAGTATGCT 58.959 43.478 0.00 0.00 0.00 3.79
3580 3848 4.381411 GAGAGGGGTTGTATCAAGTATGC 58.619 47.826 0.00 0.00 0.00 3.14
3581 3849 4.408921 TGGAGAGGGGTTGTATCAAGTATG 59.591 45.833 0.00 0.00 0.00 2.39
3582 3850 4.631234 TGGAGAGGGGTTGTATCAAGTAT 58.369 43.478 0.00 0.00 0.00 2.12
3583 3851 4.030913 CTGGAGAGGGGTTGTATCAAGTA 58.969 47.826 0.00 0.00 0.00 2.24
3584 3852 2.840651 CTGGAGAGGGGTTGTATCAAGT 59.159 50.000 0.00 0.00 0.00 3.16
3585 3853 2.171448 CCTGGAGAGGGGTTGTATCAAG 59.829 54.545 0.00 0.00 35.40 3.02
3586 3854 2.196595 CCTGGAGAGGGGTTGTATCAA 58.803 52.381 0.00 0.00 35.40 2.57
3587 3855 1.879575 CCTGGAGAGGGGTTGTATCA 58.120 55.000 0.00 0.00 35.40 2.15
3597 3865 0.745468 GTACTTACGCCCTGGAGAGG 59.255 60.000 0.00 0.00 39.42 3.69
3598 3866 1.765230 AGTACTTACGCCCTGGAGAG 58.235 55.000 0.00 0.00 0.00 3.20
3599 3867 1.822990 CAAGTACTTACGCCCTGGAGA 59.177 52.381 8.04 0.00 0.00 3.71
3600 3868 1.739371 GCAAGTACTTACGCCCTGGAG 60.739 57.143 8.04 0.00 0.00 3.86
3601 3869 0.248289 GCAAGTACTTACGCCCTGGA 59.752 55.000 8.04 0.00 0.00 3.86
3602 3870 1.082117 CGCAAGTACTTACGCCCTGG 61.082 60.000 14.89 0.00 0.00 4.45
3603 3871 1.693083 GCGCAAGTACTTACGCCCTG 61.693 60.000 33.30 12.24 46.35 4.45
3604 3872 1.447314 GCGCAAGTACTTACGCCCT 60.447 57.895 33.30 0.00 46.35 5.19
3605 3873 3.087176 GCGCAAGTACTTACGCCC 58.913 61.111 33.30 14.27 46.35 6.13
3608 3876 1.408474 GGGTCGCGCAAGTACTTACG 61.408 60.000 21.39 21.39 41.68 3.18
3609 3877 0.388907 TGGGTCGCGCAAGTACTTAC 60.389 55.000 8.04 1.09 41.68 2.34
3610 3878 0.317799 TTGGGTCGCGCAAGTACTTA 59.682 50.000 8.04 0.00 41.68 2.24
3611 3879 1.070105 TTGGGTCGCGCAAGTACTT 59.930 52.632 8.75 1.12 41.68 2.24
3612 3880 1.666872 GTTGGGTCGCGCAAGTACT 60.667 57.895 8.75 0.00 36.99 2.73
3613 3881 2.674084 GGTTGGGTCGCGCAAGTAC 61.674 63.158 8.75 0.00 36.99 2.73
3614 3882 2.357760 GGTTGGGTCGCGCAAGTA 60.358 61.111 8.75 0.00 36.99 2.24
3615 3883 4.555709 TGGTTGGGTCGCGCAAGT 62.556 61.111 8.75 0.00 36.99 3.16
3616 3884 3.726517 CTGGTTGGGTCGCGCAAG 61.727 66.667 8.75 0.00 36.99 4.01
3621 3889 4.660938 AAGGGCTGGTTGGGTCGC 62.661 66.667 0.00 0.00 0.00 5.19
3622 3890 2.672996 CAAGGGCTGGTTGGGTCG 60.673 66.667 0.00 0.00 0.00 4.79
3623 3891 2.283173 CCAAGGGCTGGTTGGGTC 60.283 66.667 6.07 0.00 40.83 4.46
3634 3902 1.207791 AGTGTATGAGAGGCCAAGGG 58.792 55.000 5.01 0.00 0.00 3.95
3635 3903 3.197766 TGTAAGTGTATGAGAGGCCAAGG 59.802 47.826 5.01 0.00 0.00 3.61
3636 3904 4.471904 TGTAAGTGTATGAGAGGCCAAG 57.528 45.455 5.01 0.00 0.00 3.61
3637 3905 4.286032 ACTTGTAAGTGTATGAGAGGCCAA 59.714 41.667 5.01 0.00 37.98 4.52
3638 3906 3.838317 ACTTGTAAGTGTATGAGAGGCCA 59.162 43.478 5.01 0.00 37.98 5.36
3639 3907 4.473477 ACTTGTAAGTGTATGAGAGGCC 57.527 45.455 0.00 0.00 37.98 5.19
3661 3929 4.382320 TAGGCGTGCGTGGGTTCC 62.382 66.667 0.00 0.00 0.00 3.62
3662 3930 3.116531 GTAGGCGTGCGTGGGTTC 61.117 66.667 0.00 0.00 0.00 3.62
3663 3931 3.931247 TGTAGGCGTGCGTGGGTT 61.931 61.111 0.00 0.00 0.00 4.11
3664 3932 4.675029 GTGTAGGCGTGCGTGGGT 62.675 66.667 0.00 0.00 0.00 4.51
3665 3933 3.876589 AAGTGTAGGCGTGCGTGGG 62.877 63.158 0.00 0.00 0.00 4.61
3666 3934 2.357034 AAGTGTAGGCGTGCGTGG 60.357 61.111 0.00 0.00 0.00 4.94
3667 3935 2.667318 CCAAGTGTAGGCGTGCGTG 61.667 63.158 0.00 0.00 0.00 5.34
3668 3936 2.357034 CCAAGTGTAGGCGTGCGT 60.357 61.111 0.00 0.00 0.00 5.24
3669 3937 3.788766 GCCAAGTGTAGGCGTGCG 61.789 66.667 0.00 0.00 43.15 5.34


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

AutoCloner maintained by Alex Coulton.