Multiple sequence alignment - TraesCS7D01G272000

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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 TraesCS7D01G272000 chr7D 100.000 3932 0 0 1 3932 262023013 262026944 0.000000e+00 7262.0
1 TraesCS7D01G272000 chr7B 96.343 3035 79 15 511 3532 242357164 242354149 0.000000e+00 4961.0
2 TraesCS7D01G272000 chr7B 91.860 86 7 0 3570 3655 242354141 242354056 1.920000e-23 121.0
3 TraesCS7D01G272000 chr7A 96.346 2928 58 10 510 3409 285056255 285059161 0.000000e+00 4769.0
4 TraesCS7D01G272000 chr7A 96.226 53 2 0 3480 3532 285059168 285059220 1.950000e-13 87.9
5 TraesCS7D01G272000 chr5A 83.996 931 134 9 1000 1918 537353531 537354458 0.000000e+00 880.0
6 TraesCS7D01G272000 chr5D 83.888 931 135 9 1000 1918 423858810 423859737 0.000000e+00 874.0
7 TraesCS7D01G272000 chr5B 83.458 937 142 10 1000 1928 511695296 511696227 0.000000e+00 859.0
8 TraesCS7D01G272000 chr5B 91.176 510 33 8 1 507 158560950 158561450 0.000000e+00 682.0
9 TraesCS7D01G272000 chr6D 95.874 509 14 6 1 509 210138287 210138788 0.000000e+00 817.0
10 TraesCS7D01G272000 chr2B 91.797 512 29 10 1 510 64336942 64336442 0.000000e+00 701.0
11 TraesCS7D01G272000 chr2B 90.891 516 34 10 1 514 12965502 12966006 0.000000e+00 680.0
12 TraesCS7D01G272000 chrUn 91.245 514 32 9 1 512 55786741 55786239 0.000000e+00 688.0
13 TraesCS7D01G272000 chrUn 91.389 511 31 9 1 509 302515016 302515515 0.000000e+00 688.0
14 TraesCS7D01G272000 chr2A 91.211 512 32 9 1 510 733695165 733695665 0.000000e+00 684.0
15 TraesCS7D01G272000 chr4A 91.142 508 33 9 1 505 159497151 159496653 0.000000e+00 678.0
16 TraesCS7D01G272000 chr4A 91.142 508 33 8 1 506 715713345 715713842 0.000000e+00 678.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G272000 chr7D 262023013 262026944 3931 False 7262.00 7262 100.0000 1 3932 1 chr7D.!!$F1 3931
1 TraesCS7D01G272000 chr7B 242354056 242357164 3108 True 2541.00 4961 94.1015 511 3655 2 chr7B.!!$R1 3144
2 TraesCS7D01G272000 chr7A 285056255 285059220 2965 False 2428.45 4769 96.2860 510 3532 2 chr7A.!!$F1 3022
3 TraesCS7D01G272000 chr5A 537353531 537354458 927 False 880.00 880 83.9960 1000 1918 1 chr5A.!!$F1 918
4 TraesCS7D01G272000 chr5D 423858810 423859737 927 False 874.00 874 83.8880 1000 1918 1 chr5D.!!$F1 918
5 TraesCS7D01G272000 chr5B 511695296 511696227 931 False 859.00 859 83.4580 1000 1928 1 chr5B.!!$F2 928
6 TraesCS7D01G272000 chr5B 158560950 158561450 500 False 682.00 682 91.1760 1 507 1 chr5B.!!$F1 506
7 TraesCS7D01G272000 chr6D 210138287 210138788 501 False 817.00 817 95.8740 1 509 1 chr6D.!!$F1 508
8 TraesCS7D01G272000 chr2B 64336442 64336942 500 True 701.00 701 91.7970 1 510 1 chr2B.!!$R1 509
9 TraesCS7D01G272000 chr2B 12965502 12966006 504 False 680.00 680 90.8910 1 514 1 chr2B.!!$F1 513
10 TraesCS7D01G272000 chrUn 55786239 55786741 502 True 688.00 688 91.2450 1 512 1 chrUn.!!$R1 511
11 TraesCS7D01G272000 chr2A 733695165 733695665 500 False 684.00 684 91.2110 1 510 1 chr2A.!!$F1 509

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
550 553 2.179589 GTGCGTTTGAATAGCTGCATG 58.820 47.619 1.02 0.00 34.54 4.06 F
1109 1112 0.322975 GAGTGCCTGGAGCTCAAGAA 59.677 55.000 20.42 4.49 44.23 2.52 F
2217 2250 0.168788 ACATGAAATCCAACGCAGCG 59.831 50.000 14.82 14.82 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1419 2.792947 GGGCTCGTTCTGGGCGATA 61.793 63.158 0.0 0.0 37.74 2.92 R
2625 2658 0.178068 AGTTATCCGTGCAGGCGAAT 59.822 50.000 0.0 0.0 40.77 3.34 R
3803 3845 0.107017 ATGGGGGCAAGACGATGAAG 60.107 55.000 0.0 0.0 0.00 3.02 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
101 102 2.203788 TTCTCAGGGTGGGAGCGT 60.204 61.111 0.00 0.00 32.38 5.07
215 216 2.235402 GGGACTCTTCGTTTATGGTCCA 59.765 50.000 11.25 0.00 43.30 4.02
498 501 7.700022 TTAAGTAATAAAGCGCCCCTTTTTA 57.300 32.000 2.29 2.01 40.85 1.52
499 502 5.830000 AGTAATAAAGCGCCCCTTTTTAG 57.170 39.130 2.29 0.00 40.85 1.85
505 508 4.617253 AAGCGCCCCTTTTTAGAAAAAT 57.383 36.364 2.29 0.00 37.27 1.82
508 511 6.104146 AGCGCCCCTTTTTAGAAAAATAAA 57.896 33.333 2.29 0.00 37.27 1.40
543 546 4.326205 CGAGATTGTGTGCGTTTGAATAG 58.674 43.478 0.00 0.00 0.00 1.73
550 553 2.179589 GTGCGTTTGAATAGCTGCATG 58.820 47.619 1.02 0.00 34.54 4.06
602 605 4.153835 GCAATCAGGTCTCTCTCAAACTTG 59.846 45.833 0.00 0.00 0.00 3.16
617 620 7.335627 TCTCAAACTTGTCCATTATTATCGGT 58.664 34.615 0.00 0.00 0.00 4.69
618 621 7.279981 TCTCAAACTTGTCCATTATTATCGGTG 59.720 37.037 0.00 0.00 0.00 4.94
619 622 6.882140 TCAAACTTGTCCATTATTATCGGTGT 59.118 34.615 0.00 0.00 0.00 4.16
646 649 2.349445 AGAGAGGTTGCCCTAGGTTTT 58.651 47.619 8.29 0.00 42.86 2.43
1109 1112 0.322975 GAGTGCCTGGAGCTCAAGAA 59.677 55.000 20.42 4.49 44.23 2.52
1344 1347 0.970937 TCGGCGACCTCTCTTGGATT 60.971 55.000 4.99 0.00 0.00 3.01
1407 1419 2.284112 CACATTGGCTTGCCCCCT 60.284 61.111 9.35 0.00 0.00 4.79
1737 1749 3.089838 CCCATGAAGGTGCAGGGA 58.910 61.111 0.00 0.00 42.08 4.20
2082 2115 2.031163 ACCAGCTCAAGTGGCGTC 59.969 61.111 0.00 0.00 38.83 5.19
2217 2250 0.168788 ACATGAAATCCAACGCAGCG 59.831 50.000 14.82 14.82 0.00 5.18
2240 2273 2.680913 CGCTGTGCCAGTTAGCCAC 61.681 63.158 4.45 0.00 34.02 5.01
2640 2673 1.656818 CCAAATTCGCCTGCACGGAT 61.657 55.000 6.40 0.00 30.76 4.18
2728 2761 1.255667 GGTGTACTTCGGGGAGCAGA 61.256 60.000 0.00 0.00 0.00 4.26
2843 2876 4.329545 GTGGGCGTCCAAGCAGGA 62.330 66.667 12.16 0.00 46.04 3.86
2852 2894 1.073722 CCAAGCAGGAGCAGGACAA 59.926 57.895 0.00 0.00 45.49 3.18
2862 2904 2.612972 GGAGCAGGACAAGTTGATCGAA 60.613 50.000 10.54 0.00 30.78 3.71
2864 2906 3.070018 AGCAGGACAAGTTGATCGAAAG 58.930 45.455 10.54 0.00 0.00 2.62
3157 3199 4.893608 AGGTTGCAAAATGGTTTGTATCC 58.106 39.130 0.00 8.48 45.06 2.59
3353 3395 5.428253 TGTACTCTCATTTCACCCTAATGC 58.572 41.667 0.00 0.00 33.91 3.56
3419 3461 9.897744 TTGTCATGTTTAAATCATGTCTCTTTC 57.102 29.630 20.43 10.55 42.03 2.62
3420 3462 8.229811 TGTCATGTTTAAATCATGTCTCTTTCG 58.770 33.333 20.43 0.00 42.03 3.46
3421 3463 8.230486 GTCATGTTTAAATCATGTCTCTTTCGT 58.770 33.333 20.43 0.00 42.03 3.85
3422 3464 8.783093 TCATGTTTAAATCATGTCTCTTTCGTT 58.217 29.630 20.43 0.00 42.03 3.85
3423 3465 8.843733 CATGTTTAAATCATGTCTCTTTCGTTG 58.156 33.333 16.31 0.00 38.17 4.10
3455 3497 6.038161 CCATTACGAGTATCTCATTTGCCAAA 59.962 38.462 0.00 0.00 0.00 3.28
3466 3508 4.873817 TCATTTGCCAAACTGATCAACTG 58.126 39.130 0.00 0.00 0.00 3.16
3473 3515 5.754406 TGCCAAACTGATCAACTGAAAAATG 59.246 36.000 0.00 0.00 0.00 2.32
3520 3562 9.978044 CTATGTATGATTCTCTCTTGTCAATGA 57.022 33.333 0.00 0.00 0.00 2.57
3526 3568 8.713737 TGATTCTCTCTTGTCAATGACTATTG 57.286 34.615 14.97 3.38 44.03 1.90
3537 3579 5.674525 TCAATGACTATTGATGACTCACCC 58.325 41.667 0.00 0.00 45.77 4.61
3539 3581 2.159099 TGACTATTGATGACTCACCCGC 60.159 50.000 0.00 0.00 0.00 6.13
3540 3582 1.831106 ACTATTGATGACTCACCCGCA 59.169 47.619 0.00 0.00 0.00 5.69
3541 3583 2.236146 ACTATTGATGACTCACCCGCAA 59.764 45.455 0.00 0.00 0.00 4.85
3543 3585 1.974265 TTGATGACTCACCCGCAAAA 58.026 45.000 0.00 0.00 0.00 2.44
3544 3586 1.974265 TGATGACTCACCCGCAAAAA 58.026 45.000 0.00 0.00 0.00 1.94
3601 3643 5.123186 TGCACATGGTTATTTAGACGAAAGG 59.877 40.000 0.00 0.00 0.00 3.11
3604 3646 5.885912 ACATGGTTATTTAGACGAAAGGCAT 59.114 36.000 0.00 0.00 46.78 4.40
3611 3653 5.957842 TTTAGACGAAAGGCATGAACAAT 57.042 34.783 0.00 0.00 46.78 2.71
3628 3670 8.819974 CATGAACAATGCCAACCTTTATAAATC 58.180 33.333 0.00 0.00 0.00 2.17
3655 3697 2.620242 GCCACAACAATAAGGCCAATG 58.380 47.619 5.01 0.00 41.25 2.82
3656 3698 2.233431 GCCACAACAATAAGGCCAATGA 59.767 45.455 5.01 0.00 41.25 2.57
3657 3699 3.306641 GCCACAACAATAAGGCCAATGAA 60.307 43.478 5.01 0.00 41.25 2.57
3658 3700 4.802248 GCCACAACAATAAGGCCAATGAAA 60.802 41.667 5.01 0.00 41.25 2.69
3659 3701 4.690280 CCACAACAATAAGGCCAATGAAAC 59.310 41.667 5.01 0.00 0.00 2.78
3660 3702 5.295950 CACAACAATAAGGCCAATGAAACA 58.704 37.500 5.01 0.00 0.00 2.83
3661 3703 5.757320 CACAACAATAAGGCCAATGAAACAA 59.243 36.000 5.01 0.00 0.00 2.83
3662 3704 6.427547 CACAACAATAAGGCCAATGAAACAAT 59.572 34.615 5.01 0.00 0.00 2.71
3663 3705 6.427547 ACAACAATAAGGCCAATGAAACAATG 59.572 34.615 5.01 0.00 0.00 2.82
3664 3706 4.937015 ACAATAAGGCCAATGAAACAATGC 59.063 37.500 5.01 0.00 0.00 3.56
3665 3707 2.083167 AAGGCCAATGAAACAATGCG 57.917 45.000 5.01 0.00 0.00 4.73
3666 3708 1.255882 AGGCCAATGAAACAATGCGA 58.744 45.000 5.01 0.00 0.00 5.10
3667 3709 1.617850 AGGCCAATGAAACAATGCGAA 59.382 42.857 5.01 0.00 0.00 4.70
3668 3710 1.726248 GGCCAATGAAACAATGCGAAC 59.274 47.619 0.00 0.00 0.00 3.95
3669 3711 2.402305 GCCAATGAAACAATGCGAACA 58.598 42.857 0.00 0.00 0.00 3.18
3670 3712 2.155539 GCCAATGAAACAATGCGAACAC 59.844 45.455 0.00 0.00 0.00 3.32
3671 3713 3.379240 CCAATGAAACAATGCGAACACA 58.621 40.909 0.00 0.00 0.00 3.72
3672 3714 3.801050 CCAATGAAACAATGCGAACACAA 59.199 39.130 0.00 0.00 0.00 3.33
3673 3715 4.269603 CCAATGAAACAATGCGAACACAAA 59.730 37.500 0.00 0.00 0.00 2.83
3674 3716 5.189625 CAATGAAACAATGCGAACACAAAC 58.810 37.500 0.00 0.00 0.00 2.93
3675 3717 3.838120 TGAAACAATGCGAACACAAACA 58.162 36.364 0.00 0.00 0.00 2.83
3676 3718 4.428209 TGAAACAATGCGAACACAAACAT 58.572 34.783 0.00 0.00 0.00 2.71
3677 3719 4.267214 TGAAACAATGCGAACACAAACATG 59.733 37.500 0.00 0.00 0.00 3.21
3678 3720 3.706802 ACAATGCGAACACAAACATGA 57.293 38.095 0.00 0.00 0.00 3.07
3679 3721 3.631144 ACAATGCGAACACAAACATGAG 58.369 40.909 0.00 0.00 0.00 2.90
3680 3722 2.981805 CAATGCGAACACAAACATGAGG 59.018 45.455 0.00 0.00 0.00 3.86
3681 3723 0.310543 TGCGAACACAAACATGAGGC 59.689 50.000 0.00 0.00 0.00 4.70
3682 3724 0.310543 GCGAACACAAACATGAGGCA 59.689 50.000 0.00 0.00 0.00 4.75
3683 3725 1.925946 GCGAACACAAACATGAGGCAC 60.926 52.381 0.00 0.00 0.00 5.01
3684 3726 1.334960 CGAACACAAACATGAGGCACC 60.335 52.381 0.00 0.00 0.00 5.01
3685 3727 1.956477 GAACACAAACATGAGGCACCT 59.044 47.619 0.00 0.00 0.00 4.00
3686 3728 1.609208 ACACAAACATGAGGCACCTC 58.391 50.000 9.88 9.88 43.01 3.85
3687 3729 0.883833 CACAAACATGAGGCACCTCC 59.116 55.000 14.08 0.00 42.09 4.30
3688 3730 0.251341 ACAAACATGAGGCACCTCCC 60.251 55.000 14.08 0.00 42.09 4.30
3689 3731 1.002134 AAACATGAGGCACCTCCCG 60.002 57.895 14.08 7.47 42.09 5.14
3690 3732 3.628646 AACATGAGGCACCTCCCGC 62.629 63.158 14.08 0.00 42.09 6.13
3697 3739 4.162690 GCACCTCCCGCGGATTCT 62.163 66.667 30.73 2.58 0.00 2.40
3698 3740 2.584608 CACCTCCCGCGGATTCTT 59.415 61.111 30.73 3.13 0.00 2.52
3699 3741 1.815421 CACCTCCCGCGGATTCTTG 60.815 63.158 30.73 13.01 0.00 3.02
3700 3742 2.897350 CCTCCCGCGGATTCTTGC 60.897 66.667 30.73 0.00 0.00 4.01
3701 3743 2.187946 CTCCCGCGGATTCTTGCT 59.812 61.111 30.73 0.00 0.00 3.91
3702 3744 1.884926 CTCCCGCGGATTCTTGCTC 60.885 63.158 30.73 0.00 0.00 4.26
3703 3745 2.897350 CCCGCGGATTCTTGCTCC 60.897 66.667 30.73 0.00 0.00 4.70
3704 3746 2.187946 CCGCGGATTCTTGCTCCT 59.812 61.111 24.07 0.00 0.00 3.69
3705 3747 1.441729 CCGCGGATTCTTGCTCCTA 59.558 57.895 24.07 0.00 0.00 2.94
3706 3748 0.598680 CCGCGGATTCTTGCTCCTAG 60.599 60.000 24.07 0.00 0.00 3.02
3707 3749 1.218230 CGCGGATTCTTGCTCCTAGC 61.218 60.000 0.00 0.00 42.82 3.42
3708 3750 0.882484 GCGGATTCTTGCTCCTAGCC 60.882 60.000 0.00 0.00 41.51 3.93
3709 3751 0.755686 CGGATTCTTGCTCCTAGCCT 59.244 55.000 0.00 0.00 41.51 4.58
3710 3752 1.270041 CGGATTCTTGCTCCTAGCCTC 60.270 57.143 0.00 0.00 41.51 4.70
3711 3753 2.046292 GGATTCTTGCTCCTAGCCTCT 58.954 52.381 0.00 0.00 41.51 3.69
3712 3754 2.037121 GGATTCTTGCTCCTAGCCTCTC 59.963 54.545 0.00 0.00 41.51 3.20
3713 3755 1.490574 TTCTTGCTCCTAGCCTCTCC 58.509 55.000 0.00 0.00 41.51 3.71
3714 3756 0.633921 TCTTGCTCCTAGCCTCTCCT 59.366 55.000 0.00 0.00 41.51 3.69
3715 3757 0.752054 CTTGCTCCTAGCCTCTCCTG 59.248 60.000 0.00 0.00 41.51 3.86
3716 3758 1.333636 TTGCTCCTAGCCTCTCCTGC 61.334 60.000 0.00 0.00 41.51 4.85
3717 3759 2.855514 GCTCCTAGCCTCTCCTGCG 61.856 68.421 0.00 0.00 34.48 5.18
3718 3760 2.835431 TCCTAGCCTCTCCTGCGC 60.835 66.667 0.00 0.00 0.00 6.09
3719 3761 3.922640 CCTAGCCTCTCCTGCGCC 61.923 72.222 4.18 0.00 0.00 6.53
3720 3762 4.277593 CTAGCCTCTCCTGCGCCG 62.278 72.222 4.18 0.00 0.00 6.46
3753 3795 4.451150 GCGACGGCCACCATCTCA 62.451 66.667 2.24 0.00 0.00 3.27
3754 3796 2.509336 CGACGGCCACCATCTCAC 60.509 66.667 2.24 0.00 0.00 3.51
3755 3797 2.509336 GACGGCCACCATCTCACG 60.509 66.667 2.24 0.00 0.00 4.35
3756 3798 2.994995 ACGGCCACCATCTCACGA 60.995 61.111 2.24 0.00 0.00 4.35
3757 3799 2.509336 CGGCCACCATCTCACGAC 60.509 66.667 2.24 0.00 0.00 4.34
3758 3800 2.662596 GGCCACCATCTCACGACA 59.337 61.111 0.00 0.00 0.00 4.35
3759 3801 1.448540 GGCCACCATCTCACGACAG 60.449 63.158 0.00 0.00 0.00 3.51
3760 3802 2.103042 GCCACCATCTCACGACAGC 61.103 63.158 0.00 0.00 0.00 4.40
3761 3803 1.807165 CCACCATCTCACGACAGCG 60.807 63.158 0.00 0.00 44.79 5.18
3762 3804 1.212751 CACCATCTCACGACAGCGA 59.787 57.895 0.00 0.00 41.64 4.93
3763 3805 1.073216 CACCATCTCACGACAGCGAC 61.073 60.000 0.00 0.00 41.64 5.19
3764 3806 1.517257 CCATCTCACGACAGCGACC 60.517 63.158 0.00 0.00 41.64 4.79
3765 3807 1.212751 CATCTCACGACAGCGACCA 59.787 57.895 0.00 0.00 41.64 4.02
3766 3808 1.073216 CATCTCACGACAGCGACCAC 61.073 60.000 0.00 0.00 41.64 4.16
3767 3809 1.244697 ATCTCACGACAGCGACCACT 61.245 55.000 0.00 0.00 41.64 4.00
3768 3810 1.442857 CTCACGACAGCGACCACTC 60.443 63.158 0.00 0.00 41.64 3.51
3769 3811 2.430921 CACGACAGCGACCACTCC 60.431 66.667 0.00 0.00 41.64 3.85
3770 3812 4.039357 ACGACAGCGACCACTCCG 62.039 66.667 0.00 0.00 41.64 4.63
3771 3813 4.778415 CGACAGCGACCACTCCGG 62.778 72.222 0.00 0.00 40.82 5.14
3778 3820 4.681978 GACCACTCCGGCGCTGTT 62.682 66.667 16.49 0.00 39.03 3.16
3779 3821 4.988598 ACCACTCCGGCGCTGTTG 62.989 66.667 16.49 9.76 39.03 3.33
3781 3823 4.988598 CACTCCGGCGCTGTTGGT 62.989 66.667 16.49 7.78 0.00 3.67
3782 3824 4.681978 ACTCCGGCGCTGTTGGTC 62.682 66.667 16.49 0.00 0.00 4.02
3783 3825 4.680237 CTCCGGCGCTGTTGGTCA 62.680 66.667 16.49 0.00 0.00 4.02
3784 3826 4.243008 TCCGGCGCTGTTGGTCAA 62.243 61.111 16.49 0.00 0.00 3.18
3785 3827 3.726517 CCGGCGCTGTTGGTCAAG 61.727 66.667 16.49 0.00 0.00 3.02
3786 3828 4.389576 CGGCGCTGTTGGTCAAGC 62.390 66.667 8.45 0.00 0.00 4.01
3787 3829 3.286751 GGCGCTGTTGGTCAAGCA 61.287 61.111 7.64 0.00 33.49 3.91
3788 3830 2.629656 GGCGCTGTTGGTCAAGCAT 61.630 57.895 7.64 0.00 33.49 3.79
3789 3831 1.154150 GCGCTGTTGGTCAAGCATC 60.154 57.895 0.00 0.00 32.59 3.91
3790 3832 1.580845 GCGCTGTTGGTCAAGCATCT 61.581 55.000 0.00 0.00 32.59 2.90
3791 3833 0.445436 CGCTGTTGGTCAAGCATCTC 59.555 55.000 0.00 0.00 0.00 2.75
3792 3834 0.807496 GCTGTTGGTCAAGCATCTCC 59.193 55.000 0.00 0.00 0.00 3.71
3793 3835 1.612726 GCTGTTGGTCAAGCATCTCCT 60.613 52.381 0.00 0.00 0.00 3.69
3794 3836 2.787994 CTGTTGGTCAAGCATCTCCTT 58.212 47.619 0.00 0.00 0.00 3.36
3795 3837 2.746362 CTGTTGGTCAAGCATCTCCTTC 59.254 50.000 0.00 0.00 0.00 3.46
3796 3838 2.106338 TGTTGGTCAAGCATCTCCTTCA 59.894 45.455 0.00 0.00 0.00 3.02
3797 3839 2.479566 TGGTCAAGCATCTCCTTCAC 57.520 50.000 0.00 0.00 0.00 3.18
3798 3840 1.980765 TGGTCAAGCATCTCCTTCACT 59.019 47.619 0.00 0.00 0.00 3.41
3799 3841 2.027745 TGGTCAAGCATCTCCTTCACTC 60.028 50.000 0.00 0.00 0.00 3.51
3800 3842 2.027745 GGTCAAGCATCTCCTTCACTCA 60.028 50.000 0.00 0.00 0.00 3.41
3801 3843 3.260740 GTCAAGCATCTCCTTCACTCAG 58.739 50.000 0.00 0.00 0.00 3.35
3802 3844 2.235650 TCAAGCATCTCCTTCACTCAGG 59.764 50.000 0.00 0.00 34.86 3.86
3803 3845 0.540923 AGCATCTCCTTCACTCAGGC 59.459 55.000 0.00 0.00 33.35 4.85
3804 3846 0.540923 GCATCTCCTTCACTCAGGCT 59.459 55.000 0.00 0.00 33.35 4.58
3805 3847 1.065564 GCATCTCCTTCACTCAGGCTT 60.066 52.381 0.00 0.00 33.35 4.35
3806 3848 2.903798 CATCTCCTTCACTCAGGCTTC 58.096 52.381 0.00 0.00 33.35 3.86
3807 3849 2.015456 TCTCCTTCACTCAGGCTTCA 57.985 50.000 0.00 0.00 33.35 3.02
3808 3850 2.544721 TCTCCTTCACTCAGGCTTCAT 58.455 47.619 0.00 0.00 33.35 2.57
3809 3851 2.499289 TCTCCTTCACTCAGGCTTCATC 59.501 50.000 0.00 0.00 33.35 2.92
3810 3852 1.205655 TCCTTCACTCAGGCTTCATCG 59.794 52.381 0.00 0.00 33.35 3.84
3811 3853 1.066573 CCTTCACTCAGGCTTCATCGT 60.067 52.381 0.00 0.00 0.00 3.73
3812 3854 2.266554 CTTCACTCAGGCTTCATCGTC 58.733 52.381 0.00 0.00 0.00 4.20
3813 3855 1.550327 TCACTCAGGCTTCATCGTCT 58.450 50.000 0.00 0.00 0.00 4.18
3814 3856 1.895798 TCACTCAGGCTTCATCGTCTT 59.104 47.619 0.00 0.00 0.00 3.01
3815 3857 1.998315 CACTCAGGCTTCATCGTCTTG 59.002 52.381 0.00 0.00 0.00 3.02
3816 3858 1.005340 CTCAGGCTTCATCGTCTTGC 58.995 55.000 0.00 0.00 0.00 4.01
3817 3859 0.391661 TCAGGCTTCATCGTCTTGCC 60.392 55.000 0.00 0.00 43.52 4.52
3818 3860 1.078143 AGGCTTCATCGTCTTGCCC 60.078 57.895 0.00 0.00 44.19 5.36
3819 3861 2.115291 GGCTTCATCGTCTTGCCCC 61.115 63.158 0.00 0.00 37.81 5.80
3820 3862 2.115291 GCTTCATCGTCTTGCCCCC 61.115 63.158 0.00 0.00 0.00 5.40
3821 3863 1.299648 CTTCATCGTCTTGCCCCCA 59.700 57.895 0.00 0.00 0.00 4.96
3822 3864 0.107017 CTTCATCGTCTTGCCCCCAT 60.107 55.000 0.00 0.00 0.00 4.00
3823 3865 0.394216 TTCATCGTCTTGCCCCCATG 60.394 55.000 0.00 0.00 0.00 3.66
3824 3866 1.825191 CATCGTCTTGCCCCCATGG 60.825 63.158 4.14 4.14 37.09 3.66
3833 3875 3.554342 CCCCCATGGCTCTCTCGG 61.554 72.222 6.09 0.00 0.00 4.63
3834 3876 2.444706 CCCCATGGCTCTCTCGGA 60.445 66.667 6.09 0.00 0.00 4.55
3835 3877 1.840650 CCCCATGGCTCTCTCGGAT 60.841 63.158 6.09 0.00 0.00 4.18
3836 3878 1.670590 CCCATGGCTCTCTCGGATC 59.329 63.158 6.09 0.00 0.00 3.36
3837 3879 0.831288 CCCATGGCTCTCTCGGATCT 60.831 60.000 6.09 0.00 0.00 2.75
3838 3880 0.602562 CCATGGCTCTCTCGGATCTC 59.397 60.000 0.00 0.00 0.00 2.75
3839 3881 1.326328 CATGGCTCTCTCGGATCTCA 58.674 55.000 0.00 0.00 0.00 3.27
3840 3882 1.685517 CATGGCTCTCTCGGATCTCAA 59.314 52.381 0.00 0.00 0.00 3.02
3841 3883 1.397672 TGGCTCTCTCGGATCTCAAG 58.602 55.000 0.00 0.00 0.00 3.02
3842 3884 1.341482 TGGCTCTCTCGGATCTCAAGT 60.341 52.381 0.00 0.00 0.00 3.16
3843 3885 1.754226 GGCTCTCTCGGATCTCAAGTT 59.246 52.381 0.00 0.00 0.00 2.66
3844 3886 2.167487 GGCTCTCTCGGATCTCAAGTTT 59.833 50.000 0.00 0.00 0.00 2.66
3845 3887 3.186119 GCTCTCTCGGATCTCAAGTTTG 58.814 50.000 0.00 0.00 0.00 2.93
3846 3888 3.119316 GCTCTCTCGGATCTCAAGTTTGA 60.119 47.826 0.00 0.00 35.57 2.69
3847 3889 4.619394 GCTCTCTCGGATCTCAAGTTTGAA 60.619 45.833 0.00 0.00 36.64 2.69
3848 3890 4.810790 TCTCTCGGATCTCAAGTTTGAAC 58.189 43.478 0.00 0.00 36.64 3.18
3849 3891 4.524714 TCTCTCGGATCTCAAGTTTGAACT 59.475 41.667 0.00 0.00 42.04 3.01
3850 3892 5.710567 TCTCTCGGATCTCAAGTTTGAACTA 59.289 40.000 0.00 0.00 38.57 2.24
3851 3893 5.955488 TCTCGGATCTCAAGTTTGAACTAG 58.045 41.667 0.00 0.00 38.57 2.57
3852 3894 5.073311 TCGGATCTCAAGTTTGAACTAGG 57.927 43.478 0.00 0.00 38.57 3.02
3853 3895 4.527038 TCGGATCTCAAGTTTGAACTAGGT 59.473 41.667 0.00 0.00 38.57 3.08
3854 3896 4.865365 CGGATCTCAAGTTTGAACTAGGTC 59.135 45.833 0.00 0.00 38.57 3.85
3855 3897 5.336849 CGGATCTCAAGTTTGAACTAGGTCT 60.337 44.000 9.68 0.00 38.57 3.85
3856 3898 5.872070 GGATCTCAAGTTTGAACTAGGTCTG 59.128 44.000 9.68 0.00 38.57 3.51
3857 3899 5.215252 TCTCAAGTTTGAACTAGGTCTGG 57.785 43.478 9.68 0.00 38.57 3.86
3858 3900 3.740115 TCAAGTTTGAACTAGGTCTGGC 58.260 45.455 9.68 0.00 38.57 4.85
3859 3901 3.391296 TCAAGTTTGAACTAGGTCTGGCT 59.609 43.478 9.68 1.22 38.57 4.75
3860 3902 4.137543 CAAGTTTGAACTAGGTCTGGCTT 58.862 43.478 9.68 7.32 38.57 4.35
3861 3903 4.439253 AGTTTGAACTAGGTCTGGCTTT 57.561 40.909 9.68 0.00 37.52 3.51
3862 3904 4.390264 AGTTTGAACTAGGTCTGGCTTTC 58.610 43.478 9.68 0.00 37.52 2.62
3863 3905 2.743636 TGAACTAGGTCTGGCTTTCG 57.256 50.000 9.68 0.00 0.00 3.46
3864 3906 2.244695 TGAACTAGGTCTGGCTTTCGA 58.755 47.619 9.68 0.00 0.00 3.71
3865 3907 2.231478 TGAACTAGGTCTGGCTTTCGAG 59.769 50.000 9.68 0.00 0.00 4.04
3866 3908 1.187087 ACTAGGTCTGGCTTTCGAGG 58.813 55.000 0.00 0.00 0.00 4.63
3867 3909 0.179097 CTAGGTCTGGCTTTCGAGGC 60.179 60.000 4.21 4.21 0.00 4.70
3870 3912 3.985041 AGGTCTGGCTTTCGAGGCCTA 62.985 57.143 24.80 14.48 42.75 3.93
3874 3916 2.993539 GGCTTTCGAGGCCTACATC 58.006 57.895 19.80 0.00 45.57 3.06
3875 3917 0.533085 GGCTTTCGAGGCCTACATCC 60.533 60.000 19.80 0.00 45.57 3.51
3876 3918 0.876342 GCTTTCGAGGCCTACATCCG 60.876 60.000 4.42 4.45 0.00 4.18
3877 3919 0.744874 CTTTCGAGGCCTACATCCGA 59.255 55.000 4.42 7.46 0.00 4.55
3878 3920 1.136305 CTTTCGAGGCCTACATCCGAA 59.864 52.381 19.09 19.09 37.45 4.30
3879 3921 1.187974 TTCGAGGCCTACATCCGAAA 58.812 50.000 20.30 7.42 36.49 3.46
3880 3922 0.744874 TCGAGGCCTACATCCGAAAG 59.255 55.000 4.42 0.00 0.00 2.62
3881 3923 0.460311 CGAGGCCTACATCCGAAAGT 59.540 55.000 4.42 0.00 0.00 2.66
3882 3924 1.679680 CGAGGCCTACATCCGAAAGTA 59.320 52.381 4.42 0.00 0.00 2.24
3883 3925 2.287668 CGAGGCCTACATCCGAAAGTAG 60.288 54.545 4.42 0.00 37.92 2.57
3884 3926 2.694109 GAGGCCTACATCCGAAAGTAGT 59.306 50.000 4.42 0.00 36.77 2.73
3885 3927 3.105283 AGGCCTACATCCGAAAGTAGTT 58.895 45.455 1.29 0.00 36.77 2.24
3886 3928 3.132467 AGGCCTACATCCGAAAGTAGTTC 59.868 47.826 1.29 3.57 36.77 3.01
3897 3939 3.509740 GAAAGTAGTTCGGAGTACCAGC 58.490 50.000 5.01 0.00 33.03 4.85
3898 3940 2.510928 AGTAGTTCGGAGTACCAGCT 57.489 50.000 5.01 0.00 33.03 4.24
3899 3941 3.641434 AGTAGTTCGGAGTACCAGCTA 57.359 47.619 5.01 0.00 33.03 3.32
3900 3942 3.960571 AGTAGTTCGGAGTACCAGCTAA 58.039 45.455 5.01 0.00 33.03 3.09
3901 3943 4.534797 AGTAGTTCGGAGTACCAGCTAAT 58.465 43.478 5.01 0.00 33.03 1.73
3902 3944 4.579753 AGTAGTTCGGAGTACCAGCTAATC 59.420 45.833 5.01 0.00 33.03 1.75
3903 3945 3.362706 AGTTCGGAGTACCAGCTAATCA 58.637 45.455 0.00 0.00 35.59 2.57
3904 3946 3.130693 AGTTCGGAGTACCAGCTAATCAC 59.869 47.826 0.00 0.00 35.59 3.06
3905 3947 3.014304 TCGGAGTACCAGCTAATCACT 57.986 47.619 0.00 0.00 35.59 3.41
3906 3948 3.362706 TCGGAGTACCAGCTAATCACTT 58.637 45.455 0.00 0.00 35.59 3.16
3907 3949 3.767673 TCGGAGTACCAGCTAATCACTTT 59.232 43.478 0.00 0.00 35.59 2.66
3908 3950 3.865745 CGGAGTACCAGCTAATCACTTTG 59.134 47.826 0.00 0.00 35.59 2.77
3909 3951 4.381612 CGGAGTACCAGCTAATCACTTTGA 60.382 45.833 0.00 0.00 35.59 2.69
3910 3952 5.112686 GGAGTACCAGCTAATCACTTTGAG 58.887 45.833 0.00 0.00 35.97 3.02
3911 3953 5.091261 AGTACCAGCTAATCACTTTGAGG 57.909 43.478 0.00 0.00 0.00 3.86
3912 3954 3.356529 ACCAGCTAATCACTTTGAGGG 57.643 47.619 0.00 0.00 0.00 4.30
3913 3955 2.644798 ACCAGCTAATCACTTTGAGGGT 59.355 45.455 0.00 0.00 0.00 4.34
3914 3956 3.012518 CCAGCTAATCACTTTGAGGGTG 58.987 50.000 0.00 0.00 36.17 4.61
3915 3957 3.307691 CCAGCTAATCACTTTGAGGGTGA 60.308 47.826 0.00 0.00 45.84 4.02
3916 3958 3.686726 CAGCTAATCACTTTGAGGGTGAC 59.313 47.826 0.00 0.00 44.82 3.67
3917 3959 3.327757 AGCTAATCACTTTGAGGGTGACA 59.672 43.478 0.00 0.00 44.82 3.58
3918 3960 4.018960 AGCTAATCACTTTGAGGGTGACAT 60.019 41.667 0.00 0.00 44.82 3.06
3919 3961 4.333926 GCTAATCACTTTGAGGGTGACATC 59.666 45.833 0.00 0.00 44.82 3.06
3920 3962 2.859165 TCACTTTGAGGGTGACATCC 57.141 50.000 0.00 0.00 41.42 3.51
3921 3963 2.054021 TCACTTTGAGGGTGACATCCA 58.946 47.619 7.68 0.00 41.42 3.41
3922 3964 2.644299 TCACTTTGAGGGTGACATCCAT 59.356 45.455 7.68 0.00 41.42 3.41
3923 3965 3.012518 CACTTTGAGGGTGACATCCATC 58.987 50.000 7.68 4.78 41.42 3.51
3924 3966 2.283298 CTTTGAGGGTGACATCCATCG 58.717 52.381 7.68 0.00 41.42 3.84
3925 3967 0.541392 TTGAGGGTGACATCCATCGG 59.459 55.000 7.68 0.00 41.42 4.18
3926 3968 1.337384 TGAGGGTGACATCCATCGGG 61.337 60.000 7.68 0.00 41.42 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 216 0.956633 TTCTCCACGCGTTGTAGAGT 59.043 50.000 10.22 0.00 37.56 3.24
403 406 6.312426 CAGTCAAATAAGATCCTCTCACACAC 59.688 42.308 0.00 0.00 0.00 3.82
498 501 6.208599 TCGCTGAAATGGACCTTTATTTTTCT 59.791 34.615 0.00 0.00 0.00 2.52
499 502 6.386654 TCGCTGAAATGGACCTTTATTTTTC 58.613 36.000 0.00 0.00 0.00 2.29
505 508 3.973206 TCTCGCTGAAATGGACCTTTA 57.027 42.857 0.00 0.00 0.00 1.85
508 511 2.026822 ACAATCTCGCTGAAATGGACCT 60.027 45.455 0.00 0.00 0.00 3.85
519 522 0.235665 CAAACGCACACAATCTCGCT 59.764 50.000 0.00 0.00 0.00 4.93
543 546 0.961019 TTTTCAGTCCACCATGCAGC 59.039 50.000 0.00 0.00 0.00 5.25
550 553 4.821805 TGAGTCAAGAATTTTCAGTCCACC 59.178 41.667 0.00 0.00 0.00 4.61
602 605 8.885722 TCTTTTAACACACCGATAATAATGGAC 58.114 33.333 0.00 0.00 0.00 4.02
646 649 6.228258 GTTTGATTGGAGGCCGTTAGATATA 58.772 40.000 0.00 0.00 0.00 0.86
1344 1347 1.582968 GTAGTTGGACACGCGGAGA 59.417 57.895 12.47 0.00 0.00 3.71
1407 1419 2.792947 GGGCTCGTTCTGGGCGATA 61.793 63.158 0.00 0.00 37.74 2.92
1602 1614 3.706373 GCGTTCTCCTGGCCCTCA 61.706 66.667 0.00 0.00 0.00 3.86
2014 2029 4.382320 GTTACCACCGGCAGCGGA 62.382 66.667 8.49 0.00 0.00 5.54
2625 2658 0.178068 AGTTATCCGTGCAGGCGAAT 59.822 50.000 0.00 0.00 40.77 3.34
2640 2673 1.203038 TGGTCCACGTGGAGGTAGTTA 60.203 52.381 37.04 11.18 46.49 2.24
2843 2876 2.839486 TTCGATCAACTTGTCCTGCT 57.161 45.000 0.00 0.00 0.00 4.24
2852 2894 2.030805 GGCAACAAGCTTTCGATCAACT 60.031 45.455 0.00 0.00 44.79 3.16
3157 3199 6.029607 CCAAAAGATGTTAATCACACGGATG 58.970 40.000 0.00 0.00 38.61 3.51
3399 3441 6.855914 GCAACGAAAGAGACATGATTTAAACA 59.144 34.615 0.00 0.00 0.00 2.83
3409 3451 2.159653 GCAATCGCAACGAAAGAGACAT 60.160 45.455 0.00 0.00 39.99 3.06
3419 3461 0.371989 TCGTAATGGCAATCGCAACG 59.628 50.000 0.00 0.00 41.24 4.10
3420 3462 1.396996 ACTCGTAATGGCAATCGCAAC 59.603 47.619 0.00 0.00 41.24 4.17
3421 3463 1.732941 ACTCGTAATGGCAATCGCAA 58.267 45.000 0.00 0.00 41.24 4.85
3422 3464 2.588027 TACTCGTAATGGCAATCGCA 57.412 45.000 0.00 0.00 41.24 5.10
3423 3465 3.318017 AGATACTCGTAATGGCAATCGC 58.682 45.455 0.00 0.00 37.44 4.58
3455 3497 7.572523 TTCAGTCATTTTTCAGTTGATCAGT 57.427 32.000 0.00 0.00 0.00 3.41
3473 3515 8.252417 ACATAGATATGCAGAGATGATTCAGTC 58.748 37.037 7.44 0.00 37.19 3.51
3520 3562 1.831106 TGCGGGTGAGTCATCAATAGT 59.169 47.619 5.60 0.00 37.14 2.12
3557 3599 3.914364 GCAAAATCGAATTGGTCAGTGAC 59.086 43.478 15.24 15.24 0.00 3.67
3558 3600 3.567585 TGCAAAATCGAATTGGTCAGTGA 59.432 39.130 14.02 0.00 0.00 3.41
3559 3601 3.670055 GTGCAAAATCGAATTGGTCAGTG 59.330 43.478 14.02 0.00 0.00 3.66
3560 3602 3.317711 TGTGCAAAATCGAATTGGTCAGT 59.682 39.130 14.02 0.00 0.00 3.41
3561 3603 3.899734 TGTGCAAAATCGAATTGGTCAG 58.100 40.909 14.02 0.00 0.00 3.51
3562 3604 3.998099 TGTGCAAAATCGAATTGGTCA 57.002 38.095 14.02 4.27 0.00 4.02
3563 3605 3.613737 CCATGTGCAAAATCGAATTGGTC 59.386 43.478 14.02 2.15 0.00 4.02
3564 3606 3.006752 ACCATGTGCAAAATCGAATTGGT 59.993 39.130 14.02 1.44 0.00 3.67
3565 3607 3.587923 ACCATGTGCAAAATCGAATTGG 58.412 40.909 14.02 0.06 0.00 3.16
3566 3608 6.890663 ATAACCATGTGCAAAATCGAATTG 57.109 33.333 9.32 9.32 0.00 2.32
3567 3609 7.903995 AAATAACCATGTGCAAAATCGAATT 57.096 28.000 0.00 0.00 0.00 2.17
3568 3610 8.465999 TCTAAATAACCATGTGCAAAATCGAAT 58.534 29.630 0.00 0.00 0.00 3.34
3569 3611 7.753132 GTCTAAATAACCATGTGCAAAATCGAA 59.247 33.333 0.00 0.00 0.00 3.71
3570 3612 7.247728 GTCTAAATAACCATGTGCAAAATCGA 58.752 34.615 0.00 0.00 0.00 3.59
3571 3613 6.194508 CGTCTAAATAACCATGTGCAAAATCG 59.805 38.462 0.00 0.00 0.00 3.34
3572 3614 7.247728 TCGTCTAAATAACCATGTGCAAAATC 58.752 34.615 0.00 0.00 0.00 2.17
3604 3646 7.901029 TGATTTATAAAGGTTGGCATTGTTCA 58.099 30.769 3.94 0.00 0.00 3.18
3611 3653 7.984617 GGCTTTAATGATTTATAAAGGTTGGCA 59.015 33.333 3.94 0.00 32.03 4.92
3617 3659 9.868277 TGTTGTGGCTTTAATGATTTATAAAGG 57.132 29.630 3.94 0.00 32.03 3.11
3628 3670 4.869861 GGCCTTATTGTTGTGGCTTTAATG 59.130 41.667 0.00 0.00 44.36 1.90
3633 3675 2.008242 TGGCCTTATTGTTGTGGCTT 57.992 45.000 3.32 0.00 44.36 4.35
3655 3697 4.502282 TCATGTTTGTGTTCGCATTGTTTC 59.498 37.500 0.00 0.00 0.00 2.78
3656 3698 4.428209 TCATGTTTGTGTTCGCATTGTTT 58.572 34.783 0.00 0.00 0.00 2.83
3657 3699 4.039151 TCATGTTTGTGTTCGCATTGTT 57.961 36.364 0.00 0.00 0.00 2.83
3658 3700 3.550639 CCTCATGTTTGTGTTCGCATTGT 60.551 43.478 0.00 0.00 0.00 2.71
3659 3701 2.981805 CCTCATGTTTGTGTTCGCATTG 59.018 45.455 0.00 0.00 0.00 2.82
3660 3702 2.607771 GCCTCATGTTTGTGTTCGCATT 60.608 45.455 0.00 0.00 0.00 3.56
3661 3703 1.068333 GCCTCATGTTTGTGTTCGCAT 60.068 47.619 0.00 0.00 0.00 4.73
3662 3704 0.310543 GCCTCATGTTTGTGTTCGCA 59.689 50.000 0.00 0.00 0.00 5.10
3663 3705 0.310543 TGCCTCATGTTTGTGTTCGC 59.689 50.000 0.00 0.00 0.00 4.70
3664 3706 1.334960 GGTGCCTCATGTTTGTGTTCG 60.335 52.381 0.00 0.00 0.00 3.95
3665 3707 1.956477 AGGTGCCTCATGTTTGTGTTC 59.044 47.619 0.00 0.00 0.00 3.18
3666 3708 1.956477 GAGGTGCCTCATGTTTGTGTT 59.044 47.619 13.00 0.00 42.31 3.32
3667 3709 1.609208 GAGGTGCCTCATGTTTGTGT 58.391 50.000 13.00 0.00 42.31 3.72
3668 3710 0.883833 GGAGGTGCCTCATGTTTGTG 59.116 55.000 18.75 0.00 44.40 3.33
3669 3711 0.251341 GGGAGGTGCCTCATGTTTGT 60.251 55.000 18.75 0.00 44.40 2.83
3670 3712 1.308069 CGGGAGGTGCCTCATGTTTG 61.308 60.000 18.75 0.00 44.40 2.93
3671 3713 1.002134 CGGGAGGTGCCTCATGTTT 60.002 57.895 18.75 0.00 44.40 2.83
3672 3714 2.671070 CGGGAGGTGCCTCATGTT 59.329 61.111 18.75 0.00 44.40 2.71
3673 3715 4.101448 GCGGGAGGTGCCTCATGT 62.101 66.667 18.75 0.00 44.40 3.21
3680 3722 3.682292 AAGAATCCGCGGGAGGTGC 62.682 63.158 27.83 7.99 34.05 5.01
3681 3723 1.815421 CAAGAATCCGCGGGAGGTG 60.815 63.158 27.83 13.51 34.05 4.00
3682 3724 2.584608 CAAGAATCCGCGGGAGGT 59.415 61.111 27.83 8.01 34.05 3.85
3683 3725 2.897350 GCAAGAATCCGCGGGAGG 60.897 66.667 27.83 10.41 34.05 4.30
3684 3726 1.884926 GAGCAAGAATCCGCGGGAG 60.885 63.158 27.83 10.02 34.05 4.30
3685 3727 2.186903 GAGCAAGAATCCGCGGGA 59.813 61.111 27.83 12.89 35.55 5.14
3686 3728 2.028125 TAGGAGCAAGAATCCGCGGG 62.028 60.000 27.83 9.14 42.02 6.13
3687 3729 0.598680 CTAGGAGCAAGAATCCGCGG 60.599 60.000 22.12 22.12 42.02 6.46
3688 3730 1.218230 GCTAGGAGCAAGAATCCGCG 61.218 60.000 0.00 0.00 41.89 6.46
3689 3731 0.882484 GGCTAGGAGCAAGAATCCGC 60.882 60.000 0.21 0.00 44.75 5.54
3690 3732 0.755686 AGGCTAGGAGCAAGAATCCG 59.244 55.000 0.21 0.00 44.75 4.18
3691 3733 2.037121 GAGAGGCTAGGAGCAAGAATCC 59.963 54.545 0.21 0.00 44.75 3.01
3692 3734 2.037121 GGAGAGGCTAGGAGCAAGAATC 59.963 54.545 0.21 0.00 44.75 2.52
3693 3735 2.046292 GGAGAGGCTAGGAGCAAGAAT 58.954 52.381 0.21 0.00 44.75 2.40
3694 3736 1.007721 AGGAGAGGCTAGGAGCAAGAA 59.992 52.381 0.21 0.00 44.75 2.52
3695 3737 0.633921 AGGAGAGGCTAGGAGCAAGA 59.366 55.000 0.21 0.00 44.75 3.02
3696 3738 0.752054 CAGGAGAGGCTAGGAGCAAG 59.248 60.000 0.21 0.00 44.75 4.01
3697 3739 1.333636 GCAGGAGAGGCTAGGAGCAA 61.334 60.000 0.21 0.00 44.75 3.91
3698 3740 1.760086 GCAGGAGAGGCTAGGAGCA 60.760 63.158 0.21 0.00 44.75 4.26
3699 3741 2.855514 CGCAGGAGAGGCTAGGAGC 61.856 68.421 0.00 0.00 41.46 4.70
3700 3742 2.855514 GCGCAGGAGAGGCTAGGAG 61.856 68.421 0.30 0.00 0.00 3.69
3701 3743 2.835431 GCGCAGGAGAGGCTAGGA 60.835 66.667 0.30 0.00 0.00 2.94
3702 3744 3.922640 GGCGCAGGAGAGGCTAGG 61.923 72.222 10.83 0.00 37.15 3.02
3703 3745 4.277593 CGGCGCAGGAGAGGCTAG 62.278 72.222 10.83 0.00 37.97 3.42
3736 3778 4.451150 TGAGATGGTGGCCGTCGC 62.451 66.667 0.00 4.51 43.76 5.19
3737 3779 2.509336 GTGAGATGGTGGCCGTCG 60.509 66.667 0.00 0.00 43.76 5.12
3738 3780 2.509336 CGTGAGATGGTGGCCGTC 60.509 66.667 0.00 0.00 39.68 4.79
3739 3781 2.994995 TCGTGAGATGGTGGCCGT 60.995 61.111 0.00 0.00 33.31 5.68
3740 3782 2.509336 GTCGTGAGATGGTGGCCG 60.509 66.667 0.00 0.00 45.19 6.13
3741 3783 1.448540 CTGTCGTGAGATGGTGGCC 60.449 63.158 0.00 0.00 45.19 5.36
3742 3784 2.103042 GCTGTCGTGAGATGGTGGC 61.103 63.158 0.00 0.00 45.19 5.01
3743 3785 1.807165 CGCTGTCGTGAGATGGTGG 60.807 63.158 0.00 0.00 45.19 4.61
3744 3786 1.073216 GTCGCTGTCGTGAGATGGTG 61.073 60.000 0.00 0.00 45.19 4.17
3745 3787 1.213013 GTCGCTGTCGTGAGATGGT 59.787 57.895 0.00 0.00 45.19 3.55
3746 3788 1.517257 GGTCGCTGTCGTGAGATGG 60.517 63.158 0.00 0.00 45.19 3.51
3747 3789 1.073216 GTGGTCGCTGTCGTGAGATG 61.073 60.000 0.00 0.00 45.19 2.90
3748 3790 1.213013 GTGGTCGCTGTCGTGAGAT 59.787 57.895 0.00 0.00 45.19 2.75
3749 3791 1.853114 GAGTGGTCGCTGTCGTGAGA 61.853 60.000 0.00 0.00 36.96 3.27
3750 3792 1.442857 GAGTGGTCGCTGTCGTGAG 60.443 63.158 0.00 0.00 36.96 3.51
3751 3793 2.643272 GAGTGGTCGCTGTCGTGA 59.357 61.111 0.00 0.00 36.96 4.35
3752 3794 2.430921 GGAGTGGTCGCTGTCGTG 60.431 66.667 0.00 0.00 36.96 4.35
3753 3795 4.039357 CGGAGTGGTCGCTGTCGT 62.039 66.667 0.00 0.00 36.96 4.34
3754 3796 4.778415 CCGGAGTGGTCGCTGTCG 62.778 72.222 0.00 0.00 0.00 4.35
3761 3803 4.681978 AACAGCGCCGGAGTGGTC 62.682 66.667 5.05 0.00 41.21 4.02
3762 3804 4.988598 CAACAGCGCCGGAGTGGT 62.989 66.667 5.05 0.92 41.21 4.16
3764 3806 4.988598 ACCAACAGCGCCGGAGTG 62.989 66.667 5.05 5.88 0.00 3.51
3765 3807 4.681978 GACCAACAGCGCCGGAGT 62.682 66.667 5.05 0.00 0.00 3.85
3766 3808 4.680237 TGACCAACAGCGCCGGAG 62.680 66.667 5.05 1.55 0.00 4.63
3767 3809 4.243008 TTGACCAACAGCGCCGGA 62.243 61.111 5.05 0.00 0.00 5.14
3768 3810 3.726517 CTTGACCAACAGCGCCGG 61.727 66.667 2.29 0.00 0.00 6.13
3769 3811 4.389576 GCTTGACCAACAGCGCCG 62.390 66.667 2.29 0.00 0.00 6.46
3770 3812 2.533391 GATGCTTGACCAACAGCGCC 62.533 60.000 2.29 0.00 0.00 6.53
3771 3813 1.154150 GATGCTTGACCAACAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
3772 3814 0.445436 GAGATGCTTGACCAACAGCG 59.555 55.000 0.00 0.00 0.00 5.18
3773 3815 0.807496 GGAGATGCTTGACCAACAGC 59.193 55.000 0.00 0.00 0.00 4.40
3774 3816 2.486472 AGGAGATGCTTGACCAACAG 57.514 50.000 0.00 0.00 0.00 3.16
3775 3817 2.106338 TGAAGGAGATGCTTGACCAACA 59.894 45.455 0.00 0.00 0.00 3.33
3776 3818 2.485814 GTGAAGGAGATGCTTGACCAAC 59.514 50.000 0.00 0.00 0.00 3.77
3777 3819 2.373169 AGTGAAGGAGATGCTTGACCAA 59.627 45.455 0.40 0.00 0.00 3.67
3778 3820 1.980765 AGTGAAGGAGATGCTTGACCA 59.019 47.619 0.40 0.00 0.00 4.02
3779 3821 2.027745 TGAGTGAAGGAGATGCTTGACC 60.028 50.000 0.40 0.00 0.00 4.02
3780 3822 3.260740 CTGAGTGAAGGAGATGCTTGAC 58.739 50.000 0.00 0.00 0.00 3.18
3781 3823 2.235650 CCTGAGTGAAGGAGATGCTTGA 59.764 50.000 0.00 0.00 40.02 3.02
3782 3824 2.630158 CCTGAGTGAAGGAGATGCTTG 58.370 52.381 0.00 0.00 40.02 4.01
3783 3825 1.065564 GCCTGAGTGAAGGAGATGCTT 60.066 52.381 0.00 0.00 40.02 3.91
3784 3826 0.540923 GCCTGAGTGAAGGAGATGCT 59.459 55.000 0.00 0.00 40.02 3.79
3785 3827 0.540923 AGCCTGAGTGAAGGAGATGC 59.459 55.000 0.00 0.00 40.02 3.91
3786 3828 2.235650 TGAAGCCTGAGTGAAGGAGATG 59.764 50.000 0.00 0.00 40.02 2.90
3787 3829 2.544721 TGAAGCCTGAGTGAAGGAGAT 58.455 47.619 0.00 0.00 40.02 2.75
3788 3830 2.015456 TGAAGCCTGAGTGAAGGAGA 57.985 50.000 0.00 0.00 40.02 3.71
3789 3831 2.738000 CGATGAAGCCTGAGTGAAGGAG 60.738 54.545 0.00 0.00 40.02 3.69
3790 3832 1.205655 CGATGAAGCCTGAGTGAAGGA 59.794 52.381 0.00 0.00 40.02 3.36
3791 3833 1.066573 ACGATGAAGCCTGAGTGAAGG 60.067 52.381 0.00 0.00 40.63 3.46
3792 3834 2.094286 AGACGATGAAGCCTGAGTGAAG 60.094 50.000 0.00 0.00 0.00 3.02
3793 3835 1.895798 AGACGATGAAGCCTGAGTGAA 59.104 47.619 0.00 0.00 0.00 3.18
3794 3836 1.550327 AGACGATGAAGCCTGAGTGA 58.450 50.000 0.00 0.00 0.00 3.41
3795 3837 1.998315 CAAGACGATGAAGCCTGAGTG 59.002 52.381 0.00 0.00 0.00 3.51
3796 3838 1.674221 GCAAGACGATGAAGCCTGAGT 60.674 52.381 0.00 0.00 0.00 3.41
3797 3839 1.005340 GCAAGACGATGAAGCCTGAG 58.995 55.000 0.00 0.00 0.00 3.35
3798 3840 0.391661 GGCAAGACGATGAAGCCTGA 60.392 55.000 0.00 0.00 42.01 3.86
3799 3841 1.372087 GGGCAAGACGATGAAGCCTG 61.372 60.000 0.00 0.00 44.60 4.85
3800 3842 1.078143 GGGCAAGACGATGAAGCCT 60.078 57.895 0.00 0.00 44.60 4.58
3801 3843 2.115291 GGGGCAAGACGATGAAGCC 61.115 63.158 0.00 0.00 44.48 4.35
3802 3844 2.115291 GGGGGCAAGACGATGAAGC 61.115 63.158 0.00 0.00 0.00 3.86
3803 3845 0.107017 ATGGGGGCAAGACGATGAAG 60.107 55.000 0.00 0.00 0.00 3.02
3804 3846 0.394216 CATGGGGGCAAGACGATGAA 60.394 55.000 0.00 0.00 0.00 2.57
3805 3847 1.224315 CATGGGGGCAAGACGATGA 59.776 57.895 0.00 0.00 0.00 2.92
3806 3848 1.825191 CCATGGGGGCAAGACGATG 60.825 63.158 2.85 0.00 0.00 3.84
3807 3849 2.597340 CCATGGGGGCAAGACGAT 59.403 61.111 2.85 0.00 0.00 3.73
3816 3858 3.554342 CCGAGAGAGCCATGGGGG 61.554 72.222 15.13 0.00 40.85 5.40
3817 3859 1.825281 GATCCGAGAGAGCCATGGGG 61.825 65.000 15.13 4.07 37.18 4.96
3818 3860 0.831288 AGATCCGAGAGAGCCATGGG 60.831 60.000 15.13 0.00 0.00 4.00
3819 3861 0.602562 GAGATCCGAGAGAGCCATGG 59.397 60.000 7.63 7.63 0.00 3.66
3820 3862 1.326328 TGAGATCCGAGAGAGCCATG 58.674 55.000 0.00 0.00 0.00 3.66
3821 3863 1.962807 CTTGAGATCCGAGAGAGCCAT 59.037 52.381 0.00 0.00 0.00 4.40
3822 3864 1.341482 ACTTGAGATCCGAGAGAGCCA 60.341 52.381 5.68 0.00 0.00 4.75
3823 3865 1.398692 ACTTGAGATCCGAGAGAGCC 58.601 55.000 5.68 0.00 0.00 4.70
3824 3866 3.119316 TCAAACTTGAGATCCGAGAGAGC 60.119 47.826 5.68 0.00 32.50 4.09
3825 3867 4.710423 TCAAACTTGAGATCCGAGAGAG 57.290 45.455 5.68 0.00 32.50 3.20
3826 3868 4.524714 AGTTCAAACTTGAGATCCGAGAGA 59.475 41.667 5.68 0.03 38.61 3.10
3827 3869 4.815269 AGTTCAAACTTGAGATCCGAGAG 58.185 43.478 5.68 0.00 38.61 3.20
3828 3870 4.873746 AGTTCAAACTTGAGATCCGAGA 57.126 40.909 5.68 0.00 38.61 4.04
3829 3871 5.105752 CCTAGTTCAAACTTGAGATCCGAG 58.894 45.833 0.00 0.00 40.37 4.63
3830 3872 4.527038 ACCTAGTTCAAACTTGAGATCCGA 59.473 41.667 0.00 0.00 40.37 4.55
3831 3873 4.822026 ACCTAGTTCAAACTTGAGATCCG 58.178 43.478 0.00 0.00 40.37 4.18
3832 3874 5.872070 CAGACCTAGTTCAAACTTGAGATCC 59.128 44.000 0.00 0.00 40.37 3.36
3833 3875 5.872070 CCAGACCTAGTTCAAACTTGAGATC 59.128 44.000 0.00 0.00 40.37 2.75
3834 3876 5.799213 CCAGACCTAGTTCAAACTTGAGAT 58.201 41.667 0.00 0.00 40.37 2.75
3835 3877 4.503296 GCCAGACCTAGTTCAAACTTGAGA 60.503 45.833 0.00 0.00 40.37 3.27
3836 3878 3.748568 GCCAGACCTAGTTCAAACTTGAG 59.251 47.826 0.00 0.00 40.37 3.02
3837 3879 3.391296 AGCCAGACCTAGTTCAAACTTGA 59.609 43.478 0.00 0.00 40.37 3.02
3838 3880 3.744660 AGCCAGACCTAGTTCAAACTTG 58.255 45.455 0.00 0.00 40.37 3.16
3839 3881 4.439253 AAGCCAGACCTAGTTCAAACTT 57.561 40.909 0.00 0.00 40.37 2.66
3840 3882 4.390264 GAAAGCCAGACCTAGTTCAAACT 58.610 43.478 0.46 0.46 42.91 2.66
3841 3883 3.186613 CGAAAGCCAGACCTAGTTCAAAC 59.813 47.826 0.00 0.00 0.00 2.93
3842 3884 3.070446 TCGAAAGCCAGACCTAGTTCAAA 59.930 43.478 0.00 0.00 0.00 2.69
3843 3885 2.631062 TCGAAAGCCAGACCTAGTTCAA 59.369 45.455 0.00 0.00 0.00 2.69
3844 3886 2.231478 CTCGAAAGCCAGACCTAGTTCA 59.769 50.000 0.00 0.00 0.00 3.18
3845 3887 2.417515 CCTCGAAAGCCAGACCTAGTTC 60.418 54.545 0.00 0.00 0.00 3.01
3846 3888 1.550976 CCTCGAAAGCCAGACCTAGTT 59.449 52.381 0.00 0.00 0.00 2.24
3847 3889 1.187087 CCTCGAAAGCCAGACCTAGT 58.813 55.000 0.00 0.00 0.00 2.57
3848 3890 0.179097 GCCTCGAAAGCCAGACCTAG 60.179 60.000 0.00 0.00 0.00 3.02
3849 3891 1.898154 GCCTCGAAAGCCAGACCTA 59.102 57.895 0.00 0.00 0.00 3.08
3850 3892 2.665603 GCCTCGAAAGCCAGACCT 59.334 61.111 0.00 0.00 0.00 3.85
3857 3899 0.876342 CGGATGTAGGCCTCGAAAGC 60.876 60.000 9.68 0.00 0.00 3.51
3858 3900 0.744874 TCGGATGTAGGCCTCGAAAG 59.255 55.000 9.68 0.00 0.00 2.62
3859 3901 1.187974 TTCGGATGTAGGCCTCGAAA 58.812 50.000 20.30 7.42 36.99 3.46
3860 3902 1.136305 CTTTCGGATGTAGGCCTCGAA 59.864 52.381 19.09 19.09 37.94 3.71
3861 3903 0.744874 CTTTCGGATGTAGGCCTCGA 59.255 55.000 9.68 9.42 0.00 4.04
3862 3904 0.460311 ACTTTCGGATGTAGGCCTCG 59.540 55.000 9.68 6.47 0.00 4.63
3863 3905 2.694109 ACTACTTTCGGATGTAGGCCTC 59.306 50.000 9.68 1.02 40.11 4.70
3864 3906 2.748388 ACTACTTTCGGATGTAGGCCT 58.252 47.619 18.29 11.78 40.11 5.19
3865 3907 3.455327 GAACTACTTTCGGATGTAGGCC 58.545 50.000 18.29 0.00 40.11 5.19
3876 3918 3.193056 AGCTGGTACTCCGAACTACTTTC 59.807 47.826 0.00 0.00 36.30 2.62
3877 3919 3.163467 AGCTGGTACTCCGAACTACTTT 58.837 45.455 0.00 0.00 36.30 2.66
3878 3920 2.805194 AGCTGGTACTCCGAACTACTT 58.195 47.619 0.00 0.00 36.30 2.24
3879 3921 2.510928 AGCTGGTACTCCGAACTACT 57.489 50.000 0.00 0.00 36.30 2.57
3880 3922 4.337555 TGATTAGCTGGTACTCCGAACTAC 59.662 45.833 0.00 0.00 36.30 2.73
3881 3923 4.337555 GTGATTAGCTGGTACTCCGAACTA 59.662 45.833 0.00 0.00 36.30 2.24
3882 3924 3.130693 GTGATTAGCTGGTACTCCGAACT 59.869 47.826 0.00 0.00 36.30 3.01
3883 3925 3.130693 AGTGATTAGCTGGTACTCCGAAC 59.869 47.826 0.00 0.00 36.30 3.95
3884 3926 3.362706 AGTGATTAGCTGGTACTCCGAA 58.637 45.455 0.00 0.00 36.30 4.30
3885 3927 3.014304 AGTGATTAGCTGGTACTCCGA 57.986 47.619 0.00 0.00 36.30 4.55
3886 3928 3.802948 AAGTGATTAGCTGGTACTCCG 57.197 47.619 0.00 0.00 36.30 4.63
3887 3929 5.086104 TCAAAGTGATTAGCTGGTACTCC 57.914 43.478 0.00 0.00 0.00 3.85
3888 3930 5.112686 CCTCAAAGTGATTAGCTGGTACTC 58.887 45.833 0.00 0.00 0.00 2.59
3889 3931 4.080863 CCCTCAAAGTGATTAGCTGGTACT 60.081 45.833 0.00 0.00 0.00 2.73
3890 3932 4.192317 CCCTCAAAGTGATTAGCTGGTAC 58.808 47.826 0.00 0.00 0.00 3.34
3891 3933 3.844211 ACCCTCAAAGTGATTAGCTGGTA 59.156 43.478 0.00 0.00 0.00 3.25
3892 3934 2.644798 ACCCTCAAAGTGATTAGCTGGT 59.355 45.455 0.00 0.00 0.00 4.00
3893 3935 3.012518 CACCCTCAAAGTGATTAGCTGG 58.987 50.000 0.00 0.00 37.42 4.85
3894 3936 3.686726 GTCACCCTCAAAGTGATTAGCTG 59.313 47.826 0.00 0.00 45.45 4.24
3895 3937 3.327757 TGTCACCCTCAAAGTGATTAGCT 59.672 43.478 0.00 0.00 45.45 3.32
3896 3938 3.674997 TGTCACCCTCAAAGTGATTAGC 58.325 45.455 0.00 0.00 45.45 3.09
3897 3939 4.878397 GGATGTCACCCTCAAAGTGATTAG 59.122 45.833 0.00 0.00 45.45 1.73
3898 3940 4.288366 TGGATGTCACCCTCAAAGTGATTA 59.712 41.667 0.00 0.00 45.45 1.75
3899 3941 3.074390 TGGATGTCACCCTCAAAGTGATT 59.926 43.478 0.00 0.00 45.45 2.57
3900 3942 2.644299 TGGATGTCACCCTCAAAGTGAT 59.356 45.455 0.00 0.00 45.45 3.06
3901 3943 2.054021 TGGATGTCACCCTCAAAGTGA 58.946 47.619 0.00 0.00 41.84 3.41
3902 3944 2.566833 TGGATGTCACCCTCAAAGTG 57.433 50.000 0.00 0.00 36.54 3.16
3903 3945 2.355108 CGATGGATGTCACCCTCAAAGT 60.355 50.000 0.00 0.00 0.00 2.66
3904 3946 2.283298 CGATGGATGTCACCCTCAAAG 58.717 52.381 0.00 0.00 0.00 2.77
3905 3947 1.065491 CCGATGGATGTCACCCTCAAA 60.065 52.381 0.00 0.00 0.00 2.69
3906 3948 0.541392 CCGATGGATGTCACCCTCAA 59.459 55.000 0.00 0.00 0.00 3.02
3907 3949 1.337384 CCCGATGGATGTCACCCTCA 61.337 60.000 0.00 0.00 0.00 3.86
3908 3950 1.048724 TCCCGATGGATGTCACCCTC 61.049 60.000 0.00 0.00 35.03 4.30
3909 3951 0.620410 TTCCCGATGGATGTCACCCT 60.620 55.000 0.00 0.00 41.40 4.34
3910 3952 0.474184 ATTCCCGATGGATGTCACCC 59.526 55.000 0.00 0.00 41.40 4.61
3911 3953 2.222027 GAATTCCCGATGGATGTCACC 58.778 52.381 0.00 0.00 41.40 4.02


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

AutoCloner maintained by Alex Coulton.