Multiple sequence alignment - TraesCS3D01G300100

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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 TraesCS3D01G300100 chr3D 100.000 2634 0 0 1 2634 414911223 414908590 0.000000e+00 4865
1 TraesCS3D01G300100 chr3A 89.372 1242 58 33 814 2003 535221928 535223147 0.000000e+00 1495
2 TraesCS3D01G300100 chr3A 87.108 574 28 11 2060 2622 535223165 535223703 2.240000e-170 608
3 TraesCS3D01G300100 chr3A 87.824 386 39 7 1 382 535221355 535221736 1.860000e-121 446
4 TraesCS3D01G300100 chr3A 81.877 309 52 4 2 308 567980254 567980560 9.350000e-65 257
5 TraesCS3D01G300100 chr3B 85.574 1324 76 53 880 2141 540733135 540731865 0.000000e+00 1280
6 TraesCS3D01G300100 chr3B 89.818 550 37 10 3 551 540738642 540738111 0.000000e+00 688
7 TraesCS3D01G300100 chr3B 92.255 439 23 7 2185 2622 540731875 540731447 1.730000e-171 612
8 TraesCS3D01G300100 chr7D 98.131 214 4 0 605 818 587546427 587546640 8.900000e-100 374
9 TraesCS3D01G300100 chr6D 98.122 213 3 1 605 816 114768407 114768195 1.150000e-98 370
10 TraesCS3D01G300100 chr6D 98.095 210 4 0 605 814 451070623 451070414 1.490000e-97 366
11 TraesCS3D01G300100 chrUn 98.095 210 4 0 605 814 98338752 98338543 1.490000e-97 366
12 TraesCS3D01G300100 chr2D 98.104 211 3 1 605 814 31669768 31669558 1.490000e-97 366
13 TraesCS3D01G300100 chr2D 95.238 231 8 3 595 824 603126214 603126442 1.930000e-96 363
14 TraesCS3D01G300100 chr5D 97.653 213 4 1 604 815 38981336 38981124 5.360000e-97 364
15 TraesCS3D01G300100 chr5D 97.209 215 3 3 602 815 537667119 537667331 6.930000e-96 361
16 TraesCS3D01G300100 chr5D 96.347 219 6 2 605 822 241421027 241420810 2.490000e-95 359
17 TraesCS3D01G300100 chr5D 83.280 311 50 2 3 312 135093370 135093061 4.290000e-73 285
18 TraesCS3D01G300100 chr4D 81.188 303 54 3 6 307 202363093 202363393 9.420000e-60 241
19 TraesCS3D01G300100 chr4D 79.618 314 60 3 1 312 312918335 312918024 3.410000e-54 222
20 TraesCS3D01G300100 chr4D 79.683 315 59 5 1 312 312938412 312938100 3.410000e-54 222
21 TraesCS3D01G300100 chr4D 79.299 314 63 2 1 312 312941426 312941113 4.410000e-53 219
22 TraesCS3D01G300100 chr1A 78.896 308 58 7 5 309 546017880 546017577 4.450000e-48 202


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 TraesCS3D01G300100 chr3D 414908590 414911223 2633 True 4865.000000 4865 100.000000 1 2634 1 chr3D.!!$R1 2633
1 TraesCS3D01G300100 chr3A 535221355 535223703 2348 False 849.666667 1495 88.101333 1 2622 3 chr3A.!!$F2 2621
2 TraesCS3D01G300100 chr3B 540731447 540733135 1688 True 946.000000 1280 88.914500 880 2622 2 chr3B.!!$R2 1742
3 TraesCS3D01G300100 chr3B 540738111 540738642 531 True 688.000000 688 89.818000 3 551 1 chr3B.!!$R1 548
4 TraesCS3D01G300100 chr4D 312938100 312941426 3326 True 220.500000 222 79.491000 1 312 2 chr4D.!!$R2 311

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
781 3812 0.251916 TAAAGTGGGAGCACGGATGG 59.748 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 5325 0.031585 TTGGGTTCTCGTGTCACTCG 59.968 55.0 0.65 0.0 0.0 4.18 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
34 35 6.857437 AATTTTCTTTGTTATCCCTGAGGG 57.143 37.500 12.53 12.53 46.11 4.30
77 81 9.017509 TCTTAGCAAATCATGATCAAAAGAAGT 57.982 29.630 9.06 0.00 0.00 3.01
273 3293 9.494271 CATCATAAATACCACACAGTTATAGCT 57.506 33.333 0.00 0.00 0.00 3.32
341 3361 1.854434 GCGAACGTGTTTCAGTTGGTG 60.854 52.381 0.00 0.00 33.24 4.17
354 3374 6.377327 TTCAGTTGGTGCTCTTTAGAAAAG 57.623 37.500 0.00 0.00 0.00 2.27
355 3375 5.680619 TCAGTTGGTGCTCTTTAGAAAAGA 58.319 37.500 2.39 2.39 0.00 2.52
405 3425 4.476752 GTTGGGCCGCCGGTATCA 62.477 66.667 4.45 0.00 0.00 2.15
414 3434 3.331293 CCGGTATCAGGCCCCTTT 58.669 61.111 0.00 0.00 0.00 3.11
415 3435 1.152963 CCGGTATCAGGCCCCTTTG 60.153 63.158 0.00 0.00 0.00 2.77
416 3436 1.823899 CGGTATCAGGCCCCTTTGC 60.824 63.158 0.00 0.00 0.00 3.68
417 3437 1.306296 GGTATCAGGCCCCTTTGCA 59.694 57.895 0.00 0.00 0.00 4.08
418 3438 0.324275 GGTATCAGGCCCCTTTGCAA 60.324 55.000 0.00 0.00 0.00 4.08
419 3439 1.555967 GTATCAGGCCCCTTTGCAAA 58.444 50.000 12.14 12.14 0.00 3.68
492 3523 3.648982 CGCTTCGGCACAACTGCA 61.649 61.111 0.00 0.00 46.28 4.41
503 3534 2.732597 GCACAACTGCAAACAAACGGTA 60.733 45.455 0.00 0.00 43.62 4.02
513 3544 7.760340 ACTGCAAACAAACGGTAGAAATTTTAA 59.240 29.630 0.00 0.00 0.00 1.52
526 3557 6.614694 AGAAATTTTAATAAAAGGCCCCGT 57.385 33.333 0.00 0.00 33.22 5.28
527 3558 6.403049 AGAAATTTTAATAAAAGGCCCCGTG 58.597 36.000 0.00 0.00 33.22 4.94
551 3582 1.197721 CAGTCACCGCAAAGTCCATTC 59.802 52.381 0.00 0.00 0.00 2.67
560 3591 2.093658 GCAAAGTCCATTCTACCGGAGA 60.094 50.000 9.46 3.59 29.98 3.71
577 3608 1.402613 GAGACGAACTCCTCCAGCTAC 59.597 57.143 0.00 0.00 39.53 3.58
612 3643 3.188786 GTGCGCCATGGACGAGAC 61.189 66.667 26.00 18.42 0.00 3.36
613 3644 3.381983 TGCGCCATGGACGAGACT 61.382 61.111 26.00 0.00 0.00 3.24
614 3645 2.125512 GCGCCATGGACGAGACTT 60.126 61.111 26.00 0.00 0.00 3.01
615 3646 2.456119 GCGCCATGGACGAGACTTG 61.456 63.158 26.00 2.80 0.00 3.16
616 3647 2.456119 CGCCATGGACGAGACTTGC 61.456 63.158 18.40 0.00 0.00 4.01
617 3648 2.109126 GCCATGGACGAGACTTGCC 61.109 63.158 18.40 0.00 0.00 4.52
618 3649 1.599047 CCATGGACGAGACTTGCCT 59.401 57.895 5.56 0.00 0.00 4.75
619 3650 0.742281 CCATGGACGAGACTTGCCTG 60.742 60.000 5.56 2.36 0.00 4.85
620 3651 1.078848 ATGGACGAGACTTGCCTGC 60.079 57.895 0.00 0.00 0.00 4.85
621 3652 1.548357 ATGGACGAGACTTGCCTGCT 61.548 55.000 0.00 0.00 0.00 4.24
622 3653 1.446966 GGACGAGACTTGCCTGCTC 60.447 63.158 0.00 0.00 0.00 4.26
623 3654 1.446966 GACGAGACTTGCCTGCTCC 60.447 63.158 0.00 0.00 0.00 4.70
624 3655 2.125350 CGAGACTTGCCTGCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
625 3656 2.654079 CGAGACTTGCCTGCTCCCT 61.654 63.158 0.00 0.00 0.00 4.20
626 3657 1.682257 GAGACTTGCCTGCTCCCTT 59.318 57.895 0.00 0.00 0.00 3.95
627 3658 0.392327 GAGACTTGCCTGCTCCCTTC 60.392 60.000 0.00 0.00 0.00 3.46
628 3659 1.377856 GACTTGCCTGCTCCCTTCC 60.378 63.158 0.00 0.00 0.00 3.46
629 3660 2.044551 CTTGCCTGCTCCCTTCCC 60.045 66.667 0.00 0.00 0.00 3.97
630 3661 2.858476 TTGCCTGCTCCCTTCCCA 60.858 61.111 0.00 0.00 0.00 4.37
631 3662 2.220786 CTTGCCTGCTCCCTTCCCAT 62.221 60.000 0.00 0.00 0.00 4.00
632 3663 2.123982 GCCTGCTCCCTTCCCATG 60.124 66.667 0.00 0.00 0.00 3.66
633 3664 2.123982 CCTGCTCCCTTCCCATGC 60.124 66.667 0.00 0.00 0.00 4.06
634 3665 2.687610 CCTGCTCCCTTCCCATGCT 61.688 63.158 0.00 0.00 0.00 3.79
635 3666 1.153005 CTGCTCCCTTCCCATGCTC 60.153 63.158 0.00 0.00 0.00 4.26
636 3667 2.194326 GCTCCCTTCCCATGCTCC 59.806 66.667 0.00 0.00 0.00 4.70
637 3668 2.922234 CTCCCTTCCCATGCTCCC 59.078 66.667 0.00 0.00 0.00 4.30
638 3669 2.002977 CTCCCTTCCCATGCTCCCA 61.003 63.158 0.00 0.00 0.00 4.37
639 3670 1.309013 TCCCTTCCCATGCTCCCAT 60.309 57.895 0.00 0.00 0.00 4.00
640 3671 1.152368 CCCTTCCCATGCTCCCATC 59.848 63.158 0.00 0.00 0.00 3.51
641 3672 1.152368 CCTTCCCATGCTCCCATCC 59.848 63.158 0.00 0.00 0.00 3.51
642 3673 1.228063 CTTCCCATGCTCCCATCCG 60.228 63.158 0.00 0.00 0.00 4.18
643 3674 1.987807 CTTCCCATGCTCCCATCCGT 61.988 60.000 0.00 0.00 0.00 4.69
644 3675 2.203252 CCCATGCTCCCATCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
645 3676 2.903855 CCATGCTCCCATCCGTGC 60.904 66.667 0.00 0.00 0.00 5.34
646 3677 2.191375 CATGCTCCCATCCGTGCT 59.809 61.111 0.00 0.00 0.00 4.40
647 3678 1.890979 CATGCTCCCATCCGTGCTC 60.891 63.158 0.00 0.00 0.00 4.26
648 3679 3.112205 ATGCTCCCATCCGTGCTCC 62.112 63.158 0.00 0.00 0.00 4.70
649 3680 4.554036 GCTCCCATCCGTGCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
650 3681 4.227134 CTCCCATCCGTGCTCCCG 62.227 72.222 0.00 0.00 0.00 5.14
660 3691 4.830765 TGCTCCCGCATACGTGGC 62.831 66.667 0.00 0.21 42.25 5.01
661 3692 4.530857 GCTCCCGCATACGTGGCT 62.531 66.667 11.48 0.00 41.87 4.75
662 3693 2.186903 CTCCCGCATACGTGGCTT 59.813 61.111 11.48 0.00 41.87 4.35
663 3694 2.125310 TCCCGCATACGTGGCTTG 60.125 61.111 11.48 3.68 41.87 4.01
664 3695 2.125310 CCCGCATACGTGGCTTGA 60.125 61.111 11.48 0.00 41.87 3.02
665 3696 1.523711 CCCGCATACGTGGCTTGAT 60.524 57.895 11.48 0.00 41.87 2.57
666 3697 1.095228 CCCGCATACGTGGCTTGATT 61.095 55.000 11.48 0.00 41.87 2.57
667 3698 0.732571 CCGCATACGTGGCTTGATTT 59.267 50.000 11.48 0.00 35.59 2.17
668 3699 1.531677 CCGCATACGTGGCTTGATTTG 60.532 52.381 11.48 0.00 35.59 2.32
669 3700 1.396648 CGCATACGTGGCTTGATTTGA 59.603 47.619 11.48 0.00 33.53 2.69
670 3701 2.032054 CGCATACGTGGCTTGATTTGAT 59.968 45.455 11.48 0.00 33.53 2.57
671 3702 3.487376 CGCATACGTGGCTTGATTTGATT 60.487 43.478 11.48 0.00 33.53 2.57
672 3703 3.792956 GCATACGTGGCTTGATTTGATTG 59.207 43.478 0.00 0.00 0.00 2.67
673 3704 4.353737 CATACGTGGCTTGATTTGATTGG 58.646 43.478 0.00 0.00 0.00 3.16
674 3705 2.513753 ACGTGGCTTGATTTGATTGGA 58.486 42.857 0.00 0.00 0.00 3.53
675 3706 2.890311 ACGTGGCTTGATTTGATTGGAA 59.110 40.909 0.00 0.00 0.00 3.53
676 3707 3.320541 ACGTGGCTTGATTTGATTGGAAA 59.679 39.130 0.00 0.00 0.00 3.13
677 3708 4.202202 ACGTGGCTTGATTTGATTGGAAAA 60.202 37.500 0.00 0.00 0.00 2.29
678 3709 4.749099 CGTGGCTTGATTTGATTGGAAAAA 59.251 37.500 0.00 0.00 0.00 1.94
705 3736 4.293671 CGGCCCCACCCCTGAAAA 62.294 66.667 0.00 0.00 33.26 2.29
706 3737 2.449777 GGCCCCACCCCTGAAAAT 59.550 61.111 0.00 0.00 0.00 1.82
707 3738 1.685765 GGCCCCACCCCTGAAAATC 60.686 63.158 0.00 0.00 0.00 2.17
708 3739 1.078347 GCCCCACCCCTGAAAATCA 59.922 57.895 0.00 0.00 0.00 2.57
709 3740 0.972471 GCCCCACCCCTGAAAATCAG 60.972 60.000 0.32 0.32 43.91 2.90
736 3767 7.978925 GGGGGAGATGATTAGATTAGAAAAGA 58.021 38.462 0.00 0.00 0.00 2.52
737 3768 8.440771 GGGGGAGATGATTAGATTAGAAAAGAA 58.559 37.037 0.00 0.00 0.00 2.52
738 3769 9.853177 GGGGAGATGATTAGATTAGAAAAGAAA 57.147 33.333 0.00 0.00 0.00 2.52
759 3790 4.830826 AAAAGGAAAAGAACAGCCGTAG 57.169 40.909 0.00 0.00 0.00 3.51
775 3806 2.822764 CGTAGGATAAAGTGGGAGCAC 58.177 52.381 0.00 0.00 0.00 4.40
776 3807 2.798499 CGTAGGATAAAGTGGGAGCACG 60.798 54.545 0.00 0.00 0.00 5.34
777 3808 0.541863 AGGATAAAGTGGGAGCACGG 59.458 55.000 0.00 0.00 0.00 4.94
778 3809 0.539986 GGATAAAGTGGGAGCACGGA 59.460 55.000 0.00 0.00 0.00 4.69
779 3810 1.141053 GGATAAAGTGGGAGCACGGAT 59.859 52.381 0.00 0.00 0.00 4.18
780 3811 2.213499 GATAAAGTGGGAGCACGGATG 58.787 52.381 0.00 0.00 0.00 3.51
781 3812 0.251916 TAAAGTGGGAGCACGGATGG 59.748 55.000 0.00 0.00 0.00 3.51
782 3813 2.484287 AAAGTGGGAGCACGGATGGG 62.484 60.000 0.00 0.00 0.00 4.00
783 3814 3.399181 GTGGGAGCACGGATGGGA 61.399 66.667 0.00 0.00 0.00 4.37
784 3815 3.083349 TGGGAGCACGGATGGGAG 61.083 66.667 0.00 0.00 0.00 4.30
785 3816 4.554036 GGGAGCACGGATGGGAGC 62.554 72.222 0.00 0.00 0.00 4.70
786 3817 3.785859 GGAGCACGGATGGGAGCA 61.786 66.667 0.00 0.00 0.00 4.26
787 3818 2.507944 GAGCACGGATGGGAGCAT 59.492 61.111 0.00 0.00 0.00 3.79
788 3819 1.890979 GAGCACGGATGGGAGCATG 60.891 63.158 0.00 0.00 0.00 4.06
789 3820 2.903855 GCACGGATGGGAGCATGG 60.904 66.667 0.00 0.00 0.00 3.66
790 3821 2.910360 CACGGATGGGAGCATGGA 59.090 61.111 0.00 0.00 0.00 3.41
791 3822 1.227764 CACGGATGGGAGCATGGAG 60.228 63.158 0.00 0.00 0.00 3.86
792 3823 1.383109 ACGGATGGGAGCATGGAGA 60.383 57.895 0.00 0.00 0.00 3.71
793 3824 1.370437 CGGATGGGAGCATGGAGAG 59.630 63.158 0.00 0.00 0.00 3.20
794 3825 1.759881 GGATGGGAGCATGGAGAGG 59.240 63.158 0.00 0.00 0.00 3.69
795 3826 1.759881 GATGGGAGCATGGAGAGGG 59.240 63.158 0.00 0.00 0.00 4.30
796 3827 0.765903 GATGGGAGCATGGAGAGGGA 60.766 60.000 0.00 0.00 0.00 4.20
797 3828 0.767446 ATGGGAGCATGGAGAGGGAG 60.767 60.000 0.00 0.00 0.00 4.30
798 3829 2.817056 GGGAGCATGGAGAGGGAGC 61.817 68.421 0.00 0.00 0.00 4.70
799 3830 2.068821 GGAGCATGGAGAGGGAGCA 61.069 63.158 0.00 0.00 0.00 4.26
800 3831 1.446791 GAGCATGGAGAGGGAGCAG 59.553 63.158 0.00 0.00 0.00 4.24
801 3832 2.042404 GAGCATGGAGAGGGAGCAGG 62.042 65.000 0.00 0.00 0.00 4.85
802 3833 2.509916 CATGGAGAGGGAGCAGGC 59.490 66.667 0.00 0.00 0.00 4.85
803 3834 2.041762 ATGGAGAGGGAGCAGGCA 59.958 61.111 0.00 0.00 0.00 4.75
804 3835 1.617536 ATGGAGAGGGAGCAGGCAA 60.618 57.895 0.00 0.00 0.00 4.52
805 3836 1.633915 ATGGAGAGGGAGCAGGCAAG 61.634 60.000 0.00 0.00 0.00 4.01
806 3837 2.124778 GAGAGGGAGCAGGCAAGC 60.125 66.667 0.00 0.00 0.00 4.01
807 3838 3.695747 GAGAGGGAGCAGGCAAGCC 62.696 68.421 2.02 2.02 34.23 4.35
811 3842 4.496336 GGAGCAGGCAAGCCGGAT 62.496 66.667 15.46 8.74 41.95 4.18
812 3843 2.899339 GAGCAGGCAAGCCGGATC 60.899 66.667 15.46 14.32 39.23 3.36
813 3844 4.496336 AGCAGGCAAGCCGGATCC 62.496 66.667 15.46 0.00 41.95 3.36
815 3846 4.473520 CAGGCAAGCCGGATCCGT 62.474 66.667 31.22 12.64 41.95 4.69
816 3847 4.473520 AGGCAAGCCGGATCCGTG 62.474 66.667 31.22 23.53 41.95 4.94
903 3936 4.402583 CATATGTTTGTTACCGTGTGCTG 58.597 43.478 0.00 0.00 0.00 4.41
914 3947 3.286751 TGTGCTGGCCGCTTGTTC 61.287 61.111 18.14 6.69 40.11 3.18
915 3948 4.389576 GTGCTGGCCGCTTGTTCG 62.390 66.667 18.14 0.00 40.11 3.95
1117 4168 0.955919 CGACAAGAAGAACTGGGCCC 60.956 60.000 17.59 17.59 0.00 5.80
1218 4277 3.170717 TCCATACTTTCCACCGTCTTCT 58.829 45.455 0.00 0.00 0.00 2.85
1219 4278 3.194968 TCCATACTTTCCACCGTCTTCTC 59.805 47.826 0.00 0.00 0.00 2.87
1220 4279 3.179830 CATACTTTCCACCGTCTTCTCG 58.820 50.000 0.00 0.00 0.00 4.04
1221 4280 1.325355 ACTTTCCACCGTCTTCTCGA 58.675 50.000 0.00 0.00 0.00 4.04
1262 4321 3.781307 CCCGGCCAACTGATCCGA 61.781 66.667 2.24 0.00 45.53 4.55
1308 4367 1.202592 TGCAGAGTTCAACTACGCCAA 60.203 47.619 7.94 0.00 0.00 4.52
1311 4370 1.002087 AGAGTTCAACTACGCCAAGGG 59.998 52.381 0.00 0.00 0.00 3.95
1421 4480 1.871080 CTTCGTGTTCCAGCTCAACT 58.129 50.000 6.62 0.00 0.00 3.16
1658 4721 2.126307 CGTGTGTGAGCGGAGAGG 60.126 66.667 0.00 0.00 0.00 3.69
1659 4722 2.262915 GTGTGTGAGCGGAGAGGG 59.737 66.667 0.00 0.00 0.00 4.30
1660 4723 2.117423 TGTGTGAGCGGAGAGGGA 59.883 61.111 0.00 0.00 0.00 4.20
1661 4724 1.533033 TGTGTGAGCGGAGAGGGAA 60.533 57.895 0.00 0.00 0.00 3.97
1860 4955 0.593128 ACAGGCTGCAAATCGTGAAC 59.407 50.000 15.89 0.00 0.00 3.18
1937 5034 7.031372 CAGGTTTGTGATAACTGATGGAAATG 58.969 38.462 0.00 0.00 0.00 2.32
1938 5035 6.721208 AGGTTTGTGATAACTGATGGAAATGT 59.279 34.615 0.00 0.00 0.00 2.71
1941 5038 7.523293 TTGTGATAACTGATGGAAATGTGTT 57.477 32.000 0.00 0.00 0.00 3.32
1942 5039 8.628630 TTGTGATAACTGATGGAAATGTGTTA 57.371 30.769 0.00 0.00 0.00 2.41
1962 5059 1.002087 AGTGTCTTAAAGGGACTGGCG 59.998 52.381 0.00 0.00 40.86 5.69
1996 5125 3.788227 TGGTGGTGCTCATAACTCTTT 57.212 42.857 0.00 0.00 0.00 2.52
2003 5132 6.595716 GTGGTGCTCATAACTCTTTACAATCT 59.404 38.462 0.00 0.00 0.00 2.40
2004 5133 6.595326 TGGTGCTCATAACTCTTTACAATCTG 59.405 38.462 0.00 0.00 0.00 2.90
2005 5134 6.595716 GGTGCTCATAACTCTTTACAATCTGT 59.404 38.462 0.00 0.00 0.00 3.41
2006 5135 7.413438 GGTGCTCATAACTCTTTACAATCTGTG 60.413 40.741 0.00 0.00 0.00 3.66
2007 5136 6.092670 TGCTCATAACTCTTTACAATCTGTGC 59.907 38.462 0.00 0.00 0.00 4.57
2008 5137 6.647212 TCATAACTCTTTACAATCTGTGCG 57.353 37.500 0.00 0.00 0.00 5.34
2009 5138 5.580691 TCATAACTCTTTACAATCTGTGCGG 59.419 40.000 0.00 0.00 0.00 5.69
2010 5139 3.402628 ACTCTTTACAATCTGTGCGGT 57.597 42.857 0.00 0.00 0.00 5.68
2011 5140 3.067106 ACTCTTTACAATCTGTGCGGTG 58.933 45.455 0.00 0.00 0.00 4.94
2012 5141 3.067106 CTCTTTACAATCTGTGCGGTGT 58.933 45.455 0.00 0.00 0.00 4.16
2013 5142 2.805671 TCTTTACAATCTGTGCGGTGTG 59.194 45.455 0.00 0.00 0.00 3.82
2016 5145 0.106708 ACAATCTGTGCGGTGTGAGT 59.893 50.000 0.00 0.00 0.00 3.41
2025 5154 2.033151 GTGCGGTGTGAGTAAACTTCAC 60.033 50.000 9.41 9.41 33.60 3.18
2052 5181 4.957759 AAACAATACAGTAATCACCCGC 57.042 40.909 0.00 0.00 0.00 6.13
2053 5182 3.620427 ACAATACAGTAATCACCCGCA 57.380 42.857 0.00 0.00 0.00 5.69
2054 5183 3.945346 ACAATACAGTAATCACCCGCAA 58.055 40.909 0.00 0.00 0.00 4.85
2055 5184 4.328536 ACAATACAGTAATCACCCGCAAA 58.671 39.130 0.00 0.00 0.00 3.68
2056 5185 4.762765 ACAATACAGTAATCACCCGCAAAA 59.237 37.500 0.00 0.00 0.00 2.44
2057 5186 4.957759 ATACAGTAATCACCCGCAAAAC 57.042 40.909 0.00 0.00 0.00 2.43
2058 5187 2.577700 ACAGTAATCACCCGCAAAACA 58.422 42.857 0.00 0.00 0.00 2.83
2059 5188 2.952978 ACAGTAATCACCCGCAAAACAA 59.047 40.909 0.00 0.00 0.00 2.83
2060 5189 3.381908 ACAGTAATCACCCGCAAAACAAA 59.618 39.130 0.00 0.00 0.00 2.83
2061 5190 4.142138 ACAGTAATCACCCGCAAAACAAAA 60.142 37.500 0.00 0.00 0.00 2.44
2062 5191 4.806247 CAGTAATCACCCGCAAAACAAAAA 59.194 37.500 0.00 0.00 0.00 1.94
2119 5251 1.687494 GAGGCACGATGTGAGCGAAC 61.687 60.000 0.24 0.00 35.23 3.95
2143 5275 4.399303 CCTCCTGCGGTTGATTTTAGATTT 59.601 41.667 0.00 0.00 0.00 2.17
2145 5277 5.949735 TCCTGCGGTTGATTTTAGATTTTC 58.050 37.500 0.00 0.00 0.00 2.29
2151 5283 8.547069 TGCGGTTGATTTTAGATTTTCTTTTTG 58.453 29.630 0.00 0.00 0.00 2.44
2170 5302 8.919145 TCTTTTTGAGGCAAGGTTTATTTTAGA 58.081 29.630 0.00 0.00 0.00 2.10
2171 5303 9.710900 CTTTTTGAGGCAAGGTTTATTTTAGAT 57.289 29.630 0.00 0.00 0.00 1.98
2174 5306 9.528489 TTTGAGGCAAGGTTTATTTTAGATACT 57.472 29.630 0.00 0.00 0.00 2.12
2176 5308 9.832445 TGAGGCAAGGTTTATTTTAGATACTAG 57.168 33.333 0.00 0.00 0.00 2.57
2177 5309 8.678593 AGGCAAGGTTTATTTTAGATACTAGC 57.321 34.615 0.00 0.00 0.00 3.42
2178 5310 8.272173 AGGCAAGGTTTATTTTAGATACTAGCA 58.728 33.333 0.00 0.00 0.00 3.49
2179 5311 8.560374 GGCAAGGTTTATTTTAGATACTAGCAG 58.440 37.037 0.00 0.00 0.00 4.24
2180 5312 8.560374 GCAAGGTTTATTTTAGATACTAGCAGG 58.440 37.037 0.00 0.00 0.00 4.85
2181 5313 9.832445 CAAGGTTTATTTTAGATACTAGCAGGA 57.168 33.333 0.00 0.00 0.00 3.86
2189 5321 9.905713 ATTTTAGATACTAGCAGGAATTTGACA 57.094 29.630 0.00 0.00 0.00 3.58
2190 5322 8.948631 TTTAGATACTAGCAGGAATTTGACAG 57.051 34.615 0.00 0.00 0.00 3.51
2191 5323 5.363939 AGATACTAGCAGGAATTTGACAGC 58.636 41.667 0.00 0.00 0.00 4.40
2192 5324 3.710209 ACTAGCAGGAATTTGACAGCT 57.290 42.857 0.00 0.00 36.20 4.24
2193 5325 3.604582 ACTAGCAGGAATTTGACAGCTC 58.395 45.455 0.00 0.00 33.83 4.09
2194 5326 1.446907 AGCAGGAATTTGACAGCTCG 58.553 50.000 0.00 0.00 0.00 5.03
2195 5327 1.002430 AGCAGGAATTTGACAGCTCGA 59.998 47.619 0.00 0.00 0.00 4.04
2196 5328 1.396301 GCAGGAATTTGACAGCTCGAG 59.604 52.381 8.45 8.45 0.00 4.04
2237 5369 2.576615 GGCAGTCTTGTCACTTTTCCT 58.423 47.619 0.00 0.00 0.00 3.36
2332 5472 6.735678 TTGTGAGATTACATTTATGTGCGT 57.264 33.333 5.64 0.00 41.89 5.24
2335 5475 6.183360 TGTGAGATTACATTTATGTGCGTGTC 60.183 38.462 5.64 1.35 41.89 3.67
2350 5490 0.532573 GTGTCTTCTCCCTGCATCGA 59.467 55.000 0.00 0.00 0.00 3.59
2368 5508 2.105821 TCGACACCCTCAAAACCTCATT 59.894 45.455 0.00 0.00 0.00 2.57
2423 5563 3.716872 TCCCAGGAGGAAGGAAACATATC 59.283 47.826 0.00 0.00 43.78 1.63
2622 5764 5.398169 TGCCATTCGTGACATTACATTTTC 58.602 37.500 0.00 0.00 0.00 2.29
2623 5765 4.798387 GCCATTCGTGACATTACATTTTCC 59.202 41.667 0.00 0.00 0.00 3.13
2624 5766 5.393027 GCCATTCGTGACATTACATTTTCCT 60.393 40.000 0.00 0.00 0.00 3.36
2625 5767 6.029607 CCATTCGTGACATTACATTTTCCTG 58.970 40.000 0.00 0.00 0.00 3.86
2626 5768 5.621197 TTCGTGACATTACATTTTCCTGG 57.379 39.130 0.00 0.00 0.00 4.45
2627 5769 4.006989 TCGTGACATTACATTTTCCTGGG 58.993 43.478 0.00 0.00 0.00 4.45
2628 5770 3.756434 CGTGACATTACATTTTCCTGGGT 59.244 43.478 0.00 0.00 0.00 4.51
2629 5771 4.379394 CGTGACATTACATTTTCCTGGGTG 60.379 45.833 0.00 0.00 0.00 4.61
2630 5772 3.509575 TGACATTACATTTTCCTGGGTGC 59.490 43.478 0.00 0.00 0.00 5.01
2631 5773 3.505386 ACATTACATTTTCCTGGGTGCA 58.495 40.909 0.00 0.00 0.00 4.57
2632 5774 3.258123 ACATTACATTTTCCTGGGTGCAC 59.742 43.478 8.80 8.80 0.00 4.57
2633 5775 1.917872 TACATTTTCCTGGGTGCACC 58.082 50.000 28.57 28.57 40.81 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.334552 TCATGATTTGCTAAGAGGCACAA 58.665 39.130 0.00 0.00 42.27 3.33
51 52 9.017509 ACTTCTTTTGATCATGATTTGCTAAGA 57.982 29.630 10.14 11.38 0.00 2.10
77 81 7.836685 TGGGATTTGTTAAGCTAAATGTGGATA 59.163 33.333 0.00 0.00 0.00 2.59
109 3128 5.536497 AAATTGAAGGATGGGGTAGACTT 57.464 39.130 0.00 0.00 0.00 3.01
110 3129 5.536497 AAAATTGAAGGATGGGGTAGACT 57.464 39.130 0.00 0.00 0.00 3.24
117 3136 6.101997 GCAAGTAGAAAAATTGAAGGATGGG 58.898 40.000 0.00 0.00 0.00 4.00
273 3293 1.123077 AGAATGCACGGGAGCTGATA 58.877 50.000 0.00 0.00 34.99 2.15
404 3424 2.344872 GCTTTGCAAAGGGGCCTG 59.655 61.111 34.02 13.59 36.53 4.85
405 3425 2.092904 TAGGCTTTGCAAAGGGGCCT 62.093 55.000 33.20 33.20 45.20 5.19
408 3428 1.595093 CCGTAGGCTTTGCAAAGGGG 61.595 60.000 34.02 15.64 46.14 4.79
409 3429 1.883021 CCGTAGGCTTTGCAAAGGG 59.117 57.895 34.02 24.04 46.14 3.95
503 3534 6.014070 ACACGGGGCCTTTTATTAAAATTTCT 60.014 34.615 0.84 0.00 0.00 2.52
513 3544 0.621609 TGCTACACGGGGCCTTTTAT 59.378 50.000 0.84 0.00 0.00 1.40
526 3557 0.105964 ACTTTGCGGTGACTGCTACA 59.894 50.000 18.25 0.00 0.00 2.74
527 3558 0.790814 GACTTTGCGGTGACTGCTAC 59.209 55.000 18.25 1.07 0.00 3.58
560 3591 0.608582 ACGTAGCTGGAGGAGTTCGT 60.609 55.000 0.00 0.00 0.00 3.85
563 3594 1.465794 GAGACGTAGCTGGAGGAGTT 58.534 55.000 0.00 0.00 0.00 3.01
564 3595 0.394625 GGAGACGTAGCTGGAGGAGT 60.395 60.000 0.00 0.00 0.00 3.85
565 3596 2.410466 GGAGACGTAGCTGGAGGAG 58.590 63.158 0.00 0.00 0.00 3.69
566 3597 4.659986 GGAGACGTAGCTGGAGGA 57.340 61.111 0.00 0.00 0.00 3.71
605 3636 1.446966 GGAGCAGGCAAGTCTCGTC 60.447 63.158 0.00 0.00 0.00 4.20
606 3637 2.659610 GGAGCAGGCAAGTCTCGT 59.340 61.111 0.00 0.00 0.00 4.18
608 3639 0.392327 GAAGGGAGCAGGCAAGTCTC 60.392 60.000 0.00 0.00 0.00 3.36
609 3640 1.682257 GAAGGGAGCAGGCAAGTCT 59.318 57.895 0.00 0.00 0.00 3.24
610 3641 1.377856 GGAAGGGAGCAGGCAAGTC 60.378 63.158 0.00 0.00 0.00 3.01
611 3642 2.759795 GGAAGGGAGCAGGCAAGT 59.240 61.111 0.00 0.00 0.00 3.16
612 3643 2.044551 GGGAAGGGAGCAGGCAAG 60.045 66.667 0.00 0.00 0.00 4.01
613 3644 2.240918 ATGGGAAGGGAGCAGGCAA 61.241 57.895 0.00 0.00 0.00 4.52
614 3645 2.614969 ATGGGAAGGGAGCAGGCA 60.615 61.111 0.00 0.00 0.00 4.75
615 3646 2.123982 CATGGGAAGGGAGCAGGC 60.124 66.667 0.00 0.00 0.00 4.85
616 3647 2.123982 GCATGGGAAGGGAGCAGG 60.124 66.667 0.00 0.00 0.00 4.85
617 3648 1.153005 GAGCATGGGAAGGGAGCAG 60.153 63.158 0.00 0.00 0.00 4.24
618 3649 2.683465 GGAGCATGGGAAGGGAGCA 61.683 63.158 0.00 0.00 0.00 4.26
619 3650 2.194326 GGAGCATGGGAAGGGAGC 59.806 66.667 0.00 0.00 0.00 4.70
620 3651 1.358830 ATGGGAGCATGGGAAGGGAG 61.359 60.000 0.00 0.00 0.00 4.30
621 3652 1.309013 ATGGGAGCATGGGAAGGGA 60.309 57.895 0.00 0.00 0.00 4.20
622 3653 1.152368 GATGGGAGCATGGGAAGGG 59.848 63.158 0.00 0.00 0.00 3.95
623 3654 1.152368 GGATGGGAGCATGGGAAGG 59.848 63.158 0.00 0.00 0.00 3.46
624 3655 1.228063 CGGATGGGAGCATGGGAAG 60.228 63.158 0.00 0.00 0.00 3.46
625 3656 2.000701 ACGGATGGGAGCATGGGAA 61.001 57.895 0.00 0.00 0.00 3.97
626 3657 2.366837 ACGGATGGGAGCATGGGA 60.367 61.111 0.00 0.00 0.00 4.37
627 3658 2.203252 CACGGATGGGAGCATGGG 60.203 66.667 0.00 0.00 0.00 4.00
628 3659 2.903855 GCACGGATGGGAGCATGG 60.904 66.667 0.00 0.00 0.00 3.66
629 3660 1.890979 GAGCACGGATGGGAGCATG 60.891 63.158 0.00 0.00 0.00 4.06
630 3661 2.507944 GAGCACGGATGGGAGCAT 59.492 61.111 0.00 0.00 0.00 3.79
631 3662 3.785859 GGAGCACGGATGGGAGCA 61.786 66.667 0.00 0.00 0.00 4.26
632 3663 4.554036 GGGAGCACGGATGGGAGC 62.554 72.222 0.00 0.00 0.00 4.70
633 3664 4.227134 CGGGAGCACGGATGGGAG 62.227 72.222 0.00 0.00 0.00 4.30
645 3676 2.173669 CAAGCCACGTATGCGGGAG 61.174 63.158 7.15 0.00 45.97 4.30
646 3677 1.966901 ATCAAGCCACGTATGCGGGA 61.967 55.000 7.15 6.11 45.97 5.14
647 3678 1.095228 AATCAAGCCACGTATGCGGG 61.095 55.000 8.39 2.48 43.45 6.13
648 3679 0.732571 AAATCAAGCCACGTATGCGG 59.267 50.000 8.39 0.00 43.45 5.69
649 3680 1.396648 TCAAATCAAGCCACGTATGCG 59.603 47.619 0.19 0.19 44.93 4.73
650 3681 3.698029 ATCAAATCAAGCCACGTATGC 57.302 42.857 1.17 1.17 0.00 3.14
651 3682 4.096231 TCCAATCAAATCAAGCCACGTATG 59.904 41.667 0.00 0.00 0.00 2.39
652 3683 4.269183 TCCAATCAAATCAAGCCACGTAT 58.731 39.130 0.00 0.00 0.00 3.06
653 3684 3.680490 TCCAATCAAATCAAGCCACGTA 58.320 40.909 0.00 0.00 0.00 3.57
654 3685 2.513753 TCCAATCAAATCAAGCCACGT 58.486 42.857 0.00 0.00 0.00 4.49
655 3686 3.574284 TTCCAATCAAATCAAGCCACG 57.426 42.857 0.00 0.00 0.00 4.94
688 3719 3.600410 ATTTTCAGGGGTGGGGCCG 62.600 63.158 0.00 0.00 38.44 6.13
689 3720 1.685765 GATTTTCAGGGGTGGGGCC 60.686 63.158 0.00 0.00 0.00 5.80
690 3721 0.972471 CTGATTTTCAGGGGTGGGGC 60.972 60.000 0.00 0.00 40.71 5.80
691 3722 3.288099 CTGATTTTCAGGGGTGGGG 57.712 57.895 0.00 0.00 40.71 4.96
711 3742 7.978925 TCTTTTCTAATCTAATCATCTCCCCC 58.021 38.462 0.00 0.00 0.00 5.40
712 3743 9.853177 TTTCTTTTCTAATCTAATCATCTCCCC 57.147 33.333 0.00 0.00 0.00 4.81
737 3768 4.037565 CCTACGGCTGTTCTTTTCCTTTTT 59.962 41.667 1.99 0.00 0.00 1.94
738 3769 3.568430 CCTACGGCTGTTCTTTTCCTTTT 59.432 43.478 1.99 0.00 0.00 2.27
739 3770 3.146847 CCTACGGCTGTTCTTTTCCTTT 58.853 45.455 1.99 0.00 0.00 3.11
740 3771 2.370849 TCCTACGGCTGTTCTTTTCCTT 59.629 45.455 1.99 0.00 0.00 3.36
741 3772 1.975680 TCCTACGGCTGTTCTTTTCCT 59.024 47.619 1.99 0.00 0.00 3.36
742 3773 2.467566 TCCTACGGCTGTTCTTTTCC 57.532 50.000 1.99 0.00 0.00 3.13
743 3774 5.642491 ACTTTATCCTACGGCTGTTCTTTTC 59.358 40.000 1.99 0.00 0.00 2.29
744 3775 5.411669 CACTTTATCCTACGGCTGTTCTTTT 59.588 40.000 1.99 0.00 0.00 2.27
745 3776 4.935808 CACTTTATCCTACGGCTGTTCTTT 59.064 41.667 1.99 0.00 0.00 2.52
746 3777 4.504858 CACTTTATCCTACGGCTGTTCTT 58.495 43.478 1.99 0.00 0.00 2.52
747 3778 3.118738 CCACTTTATCCTACGGCTGTTCT 60.119 47.826 1.99 0.00 0.00 3.01
748 3779 3.195661 CCACTTTATCCTACGGCTGTTC 58.804 50.000 1.99 0.00 0.00 3.18
749 3780 2.093128 CCCACTTTATCCTACGGCTGTT 60.093 50.000 1.99 0.00 0.00 3.16
750 3781 1.485066 CCCACTTTATCCTACGGCTGT 59.515 52.381 2.42 2.42 0.00 4.40
751 3782 1.760613 TCCCACTTTATCCTACGGCTG 59.239 52.381 0.00 0.00 0.00 4.85
752 3783 2.040178 CTCCCACTTTATCCTACGGCT 58.960 52.381 0.00 0.00 0.00 5.52
753 3784 1.540580 GCTCCCACTTTATCCTACGGC 60.541 57.143 0.00 0.00 0.00 5.68
754 3785 1.760613 TGCTCCCACTTTATCCTACGG 59.239 52.381 0.00 0.00 0.00 4.02
755 3786 2.798499 CGTGCTCCCACTTTATCCTACG 60.798 54.545 0.00 0.00 39.86 3.51
756 3787 2.483188 CCGTGCTCCCACTTTATCCTAC 60.483 54.545 0.00 0.00 39.86 3.18
757 3788 1.760613 CCGTGCTCCCACTTTATCCTA 59.239 52.381 0.00 0.00 39.86 2.94
758 3789 0.541863 CCGTGCTCCCACTTTATCCT 59.458 55.000 0.00 0.00 39.86 3.24
759 3790 0.539986 TCCGTGCTCCCACTTTATCC 59.460 55.000 0.00 0.00 39.86 2.59
760 3791 2.213499 CATCCGTGCTCCCACTTTATC 58.787 52.381 0.00 0.00 39.86 1.75
761 3792 1.134098 CCATCCGTGCTCCCACTTTAT 60.134 52.381 0.00 0.00 39.86 1.40
762 3793 0.251916 CCATCCGTGCTCCCACTTTA 59.748 55.000 0.00 0.00 39.86 1.85
763 3794 1.002134 CCATCCGTGCTCCCACTTT 60.002 57.895 0.00 0.00 39.86 2.66
764 3795 2.671070 CCATCCGTGCTCCCACTT 59.329 61.111 0.00 0.00 39.86 3.16
765 3796 3.402681 CCCATCCGTGCTCCCACT 61.403 66.667 0.00 0.00 39.86 4.00
766 3797 3.391665 CTCCCATCCGTGCTCCCAC 62.392 68.421 0.00 0.00 38.62 4.61
767 3798 3.083349 CTCCCATCCGTGCTCCCA 61.083 66.667 0.00 0.00 0.00 4.37
768 3799 4.554036 GCTCCCATCCGTGCTCCC 62.554 72.222 0.00 0.00 0.00 4.30
769 3800 3.112205 ATGCTCCCATCCGTGCTCC 62.112 63.158 0.00 0.00 0.00 4.70
770 3801 1.890979 CATGCTCCCATCCGTGCTC 60.891 63.158 0.00 0.00 0.00 4.26
771 3802 2.191375 CATGCTCCCATCCGTGCT 59.809 61.111 0.00 0.00 0.00 4.40
772 3803 2.903855 CCATGCTCCCATCCGTGC 60.904 66.667 0.00 0.00 0.00 5.34
773 3804 1.227764 CTCCATGCTCCCATCCGTG 60.228 63.158 0.00 0.00 0.00 4.94
774 3805 1.383109 TCTCCATGCTCCCATCCGT 60.383 57.895 0.00 0.00 0.00 4.69
775 3806 1.370437 CTCTCCATGCTCCCATCCG 59.630 63.158 0.00 0.00 0.00 4.18
776 3807 1.759881 CCTCTCCATGCTCCCATCC 59.240 63.158 0.00 0.00 0.00 3.51
777 3808 0.765903 TCCCTCTCCATGCTCCCATC 60.766 60.000 0.00 0.00 0.00 3.51
778 3809 0.767446 CTCCCTCTCCATGCTCCCAT 60.767 60.000 0.00 0.00 0.00 4.00
779 3810 1.383664 CTCCCTCTCCATGCTCCCA 60.384 63.158 0.00 0.00 0.00 4.37
780 3811 2.817056 GCTCCCTCTCCATGCTCCC 61.817 68.421 0.00 0.00 0.00 4.30
781 3812 2.042404 CTGCTCCCTCTCCATGCTCC 62.042 65.000 0.00 0.00 0.00 4.70
782 3813 1.446791 CTGCTCCCTCTCCATGCTC 59.553 63.158 0.00 0.00 0.00 4.26
783 3814 2.071262 CCTGCTCCCTCTCCATGCT 61.071 63.158 0.00 0.00 0.00 3.79
784 3815 2.509916 CCTGCTCCCTCTCCATGC 59.490 66.667 0.00 0.00 0.00 4.06
785 3816 1.918467 TTGCCTGCTCCCTCTCCATG 61.918 60.000 0.00 0.00 0.00 3.66
786 3817 1.617536 TTGCCTGCTCCCTCTCCAT 60.618 57.895 0.00 0.00 0.00 3.41
787 3818 2.203983 TTGCCTGCTCCCTCTCCA 60.204 61.111 0.00 0.00 0.00 3.86
788 3819 2.588989 CTTGCCTGCTCCCTCTCC 59.411 66.667 0.00 0.00 0.00 3.71
789 3820 2.124778 GCTTGCCTGCTCCCTCTC 60.125 66.667 0.00 0.00 0.00 3.20
790 3821 3.726144 GGCTTGCCTGCTCCCTCT 61.726 66.667 4.11 0.00 0.00 3.69
794 3825 4.496336 ATCCGGCTTGCCTGCTCC 62.496 66.667 10.12 0.00 0.00 4.70
795 3826 2.899339 GATCCGGCTTGCCTGCTC 60.899 66.667 10.12 0.76 0.00 4.26
796 3827 4.496336 GGATCCGGCTTGCCTGCT 62.496 66.667 10.12 0.00 0.00 4.24
798 3829 4.473520 ACGGATCCGGCTTGCCTG 62.474 66.667 35.87 7.52 44.69 4.85
799 3830 4.473520 CACGGATCCGGCTTGCCT 62.474 66.667 35.87 12.31 44.69 4.75
1117 4168 1.223187 GTGGTGTAGTTGACGTTGGG 58.777 55.000 0.00 0.00 0.00 4.12
1189 4240 3.375699 GTGGAAAGTATGGAGGAGGAGA 58.624 50.000 0.00 0.00 0.00 3.71
1221 4280 3.119459 CGGGAAATGGTAGATCGATCGAT 60.119 47.826 29.76 29.76 37.59 3.59
1283 4342 1.462670 GTAGTTGAACTCTGCAGCAGC 59.537 52.381 18.43 4.10 42.57 5.25
1284 4343 1.723542 CGTAGTTGAACTCTGCAGCAG 59.276 52.381 17.10 17.10 0.00 4.24
1308 4367 2.280552 ACCACGTCGTACATGCCCT 61.281 57.895 0.00 0.00 0.00 5.19
1311 4370 1.955529 CTGCACCACGTCGTACATGC 61.956 60.000 16.58 16.58 0.00 4.06
1421 4480 0.680921 AAGTAGTAGCGGCCCGTGTA 60.681 55.000 4.45 0.00 0.00 2.90
1656 4719 1.151361 ACCCATTGGTCCCTTCCCT 60.151 57.895 1.20 0.00 43.06 4.20
1744 4810 2.427095 ACTTCCAAAGCACGCTTTCTTT 59.573 40.909 13.93 0.00 43.56 2.52
1937 5034 4.995487 CCAGTCCCTTTAAGACACTAACAC 59.005 45.833 0.00 0.00 36.68 3.32
1938 5035 4.504340 GCCAGTCCCTTTAAGACACTAACA 60.504 45.833 0.00 0.00 36.68 2.41
1941 5038 2.232941 CGCCAGTCCCTTTAAGACACTA 59.767 50.000 0.00 0.00 36.68 2.74
1942 5039 1.002087 CGCCAGTCCCTTTAAGACACT 59.998 52.381 0.00 0.00 36.68 3.55
1996 5125 1.343142 ACTCACACCGCACAGATTGTA 59.657 47.619 0.00 0.00 0.00 2.41
2003 5132 2.206750 GAAGTTTACTCACACCGCACA 58.793 47.619 0.00 0.00 0.00 4.57
2004 5133 2.033151 GTGAAGTTTACTCACACCGCAC 60.033 50.000 0.00 0.00 34.77 5.34
2005 5134 2.206750 GTGAAGTTTACTCACACCGCA 58.793 47.619 0.00 0.00 34.77 5.69
2006 5135 1.529865 GGTGAAGTTTACTCACACCGC 59.470 52.381 17.12 3.69 40.53 5.68
2007 5136 2.140717 GGGTGAAGTTTACTCACACCG 58.859 52.381 21.48 0.00 45.44 4.94
2008 5137 3.202829 TGGGTGAAGTTTACTCACACC 57.797 47.619 20.80 20.80 44.64 4.16
2009 5138 5.570234 TTTTGGGTGAAGTTTACTCACAC 57.430 39.130 0.00 2.00 38.20 3.82
2034 5163 4.955925 TTTGCGGGTGATTACTGTATTG 57.044 40.909 0.00 0.00 0.00 1.90
2035 5164 4.762765 TGTTTTGCGGGTGATTACTGTATT 59.237 37.500 0.00 0.00 0.00 1.89
2036 5165 4.328536 TGTTTTGCGGGTGATTACTGTAT 58.671 39.130 0.00 0.00 0.00 2.29
2037 5166 3.741249 TGTTTTGCGGGTGATTACTGTA 58.259 40.909 0.00 0.00 0.00 2.74
2038 5167 2.577700 TGTTTTGCGGGTGATTACTGT 58.422 42.857 0.00 0.00 0.00 3.55
2039 5168 3.634568 TTGTTTTGCGGGTGATTACTG 57.365 42.857 0.00 0.00 0.00 2.74
2040 5169 4.657436 TTTTGTTTTGCGGGTGATTACT 57.343 36.364 0.00 0.00 0.00 2.24
2059 5188 7.644490 TGCTTCACGATTACTGTATTGTTTTT 58.356 30.769 0.00 0.00 0.00 1.94
2060 5189 7.197071 TGCTTCACGATTACTGTATTGTTTT 57.803 32.000 0.00 0.00 0.00 2.43
2061 5190 6.795098 TGCTTCACGATTACTGTATTGTTT 57.205 33.333 0.00 0.00 0.00 2.83
2062 5191 6.795098 TTGCTTCACGATTACTGTATTGTT 57.205 33.333 0.00 0.00 0.00 2.83
2063 5192 6.795098 TTTGCTTCACGATTACTGTATTGT 57.205 33.333 0.00 0.00 0.00 2.71
2064 5193 6.688385 CCATTTGCTTCACGATTACTGTATTG 59.312 38.462 0.00 0.00 0.00 1.90
2065 5194 6.677920 GCCATTTGCTTCACGATTACTGTATT 60.678 38.462 0.00 0.00 36.87 1.89
2066 5195 5.220854 GCCATTTGCTTCACGATTACTGTAT 60.221 40.000 0.00 0.00 36.87 2.29
2067 5196 4.094294 GCCATTTGCTTCACGATTACTGTA 59.906 41.667 0.00 0.00 36.87 2.74
2107 5239 0.460987 CAGGAGGGTTCGCTCACATC 60.461 60.000 16.40 2.15 0.00 3.06
2143 5275 9.541143 CTAAAATAAACCTTGCCTCAAAAAGAA 57.459 29.630 0.00 0.00 0.00 2.52
2145 5277 9.710900 ATCTAAAATAAACCTTGCCTCAAAAAG 57.289 29.630 0.00 0.00 0.00 2.27
2151 5283 8.775527 GCTAGTATCTAAAATAAACCTTGCCTC 58.224 37.037 0.00 0.00 0.00 4.70
2170 5302 5.363939 GAGCTGTCAAATTCCTGCTAGTAT 58.636 41.667 0.00 0.00 36.21 2.12
2171 5303 4.678044 CGAGCTGTCAAATTCCTGCTAGTA 60.678 45.833 0.00 0.00 36.21 1.82
2172 5304 3.604582 GAGCTGTCAAATTCCTGCTAGT 58.395 45.455 0.00 0.00 36.21 2.57
2173 5305 2.606725 CGAGCTGTCAAATTCCTGCTAG 59.393 50.000 0.00 0.00 36.21 3.42
2174 5306 2.233676 TCGAGCTGTCAAATTCCTGCTA 59.766 45.455 0.00 0.00 36.21 3.49
2175 5307 1.002430 TCGAGCTGTCAAATTCCTGCT 59.998 47.619 0.00 4.51 38.39 4.24
2176 5308 1.396301 CTCGAGCTGTCAAATTCCTGC 59.604 52.381 0.00 0.00 0.00 4.85
2177 5309 2.414481 CACTCGAGCTGTCAAATTCCTG 59.586 50.000 13.61 0.00 0.00 3.86
2178 5310 2.300152 TCACTCGAGCTGTCAAATTCCT 59.700 45.455 13.61 0.00 0.00 3.36
2179 5311 2.413453 GTCACTCGAGCTGTCAAATTCC 59.587 50.000 13.61 0.00 0.00 3.01
2180 5312 3.059884 TGTCACTCGAGCTGTCAAATTC 58.940 45.455 13.61 0.00 0.00 2.17
2181 5313 2.802816 GTGTCACTCGAGCTGTCAAATT 59.197 45.455 13.61 0.00 0.00 1.82
2182 5314 2.408050 GTGTCACTCGAGCTGTCAAAT 58.592 47.619 13.61 0.00 0.00 2.32
2183 5315 1.852942 GTGTCACTCGAGCTGTCAAA 58.147 50.000 13.61 0.00 0.00 2.69
2184 5316 0.317854 CGTGTCACTCGAGCTGTCAA 60.318 55.000 13.61 0.00 0.00 3.18
2185 5317 1.164041 TCGTGTCACTCGAGCTGTCA 61.164 55.000 13.61 10.98 33.38 3.58
2186 5318 0.453615 CTCGTGTCACTCGAGCTGTC 60.454 60.000 15.77 8.57 45.77 3.51
2187 5319 1.576920 CTCGTGTCACTCGAGCTGT 59.423 57.895 15.77 0.00 45.77 4.40
2188 5320 4.449158 CTCGTGTCACTCGAGCTG 57.551 61.111 15.77 10.35 45.77 4.24
2192 5324 0.820482 TGGGTTCTCGTGTCACTCGA 60.820 55.000 1.42 1.42 35.96 4.04
2193 5325 0.031585 TTGGGTTCTCGTGTCACTCG 59.968 55.000 0.65 0.00 0.00 4.18
2194 5326 1.068741 ACTTGGGTTCTCGTGTCACTC 59.931 52.381 0.65 0.00 0.00 3.51
2195 5327 1.120530 ACTTGGGTTCTCGTGTCACT 58.879 50.000 0.65 0.00 0.00 3.41
2196 5328 1.217882 CACTTGGGTTCTCGTGTCAC 58.782 55.000 0.00 0.00 0.00 3.67
2237 5369 0.521291 GCAAACAGAGCACGGCATTA 59.479 50.000 0.00 0.00 0.00 1.90
2321 5461 3.055094 AGGGAGAAGACACGCACATAAAT 60.055 43.478 0.00 0.00 0.00 1.40
2332 5472 0.532573 GTCGATGCAGGGAGAAGACA 59.467 55.000 0.00 0.00 0.00 3.41
2335 5475 0.460987 GGTGTCGATGCAGGGAGAAG 60.461 60.000 0.00 0.00 0.00 2.85
2350 5490 4.546674 AGAAAATGAGGTTTTGAGGGTGT 58.453 39.130 0.00 0.00 40.04 4.16
2452 5593 5.393787 CCATGTGCAAAAGCAACAGATCTAT 60.394 40.000 0.00 0.00 0.00 1.98
2545 5687 3.003480 GACCAATTCCTTTCTGGACTCG 58.997 50.000 0.00 0.00 46.14 4.18


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

AutoCloner maintained by Alex Coulton.