Multiple sequence alignment - TraesCS3D01G218200

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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 TraesCS3D01G218200 chr3D 100.000 5188 0 0 1 5188 297490581 297495768 0.000000e+00 9581.0
1 TraesCS3D01G218200 chr3D 89.091 55 2 4 4771 4821 435299794 435299740 1.210000e-06 65.8
2 TraesCS3D01G218200 chr3B 94.314 3957 131 34 878 4788 392294000 392297908 0.000000e+00 5975.0
3 TraesCS3D01G218200 chr3B 86.280 707 66 12 1 680 157904322 157903620 0.000000e+00 739.0
4 TraesCS3D01G218200 chr3B 91.296 517 34 8 1 514 404416400 404416908 0.000000e+00 695.0
5 TraesCS3D01G218200 chr3B 85.822 663 74 13 1 654 705141496 705140845 0.000000e+00 686.0
6 TraesCS3D01G218200 chr3B 96.348 356 8 1 4833 5188 392297906 392298256 9.680000e-162 580.0
7 TraesCS3D01G218200 chr3B 84.800 125 16 3 512 634 431262820 431262943 7.050000e-24 122.0
8 TraesCS3D01G218200 chr3B 95.522 67 2 1 789 854 392293937 392294003 7.100000e-19 106.0
9 TraesCS3D01G218200 chr3B 87.500 56 3 4 4765 4820 672737184 672737235 1.560000e-05 62.1
10 TraesCS3D01G218200 chr3A 96.000 1875 45 6 2922 4788 391474844 391472992 0.000000e+00 3020.0
11 TraesCS3D01G218200 chr3A 92.182 1650 49 27 741 2336 391477095 391475472 0.000000e+00 2259.0
12 TraesCS3D01G218200 chr3A 95.841 553 18 3 2334 2881 391475391 391474839 0.000000e+00 889.0
13 TraesCS3D01G218200 chr3A 84.018 682 88 16 1 672 676921733 676921063 2.040000e-178 636.0
14 TraesCS3D01G218200 chr3A 96.100 359 12 1 4830 5188 391472991 391472635 7.490000e-163 584.0
15 TraesCS3D01G218200 chr5B 86.634 621 67 10 1 617 524326937 524327545 0.000000e+00 673.0
16 TraesCS3D01G218200 chr5B 91.379 58 3 2 4787 4843 562983156 562983212 1.550000e-10 78.7
17 TraesCS3D01G218200 chr5B 95.238 42 2 0 4780 4821 591579748 591579789 3.350000e-07 67.6
18 TraesCS3D01G218200 chr5B 91.489 47 3 1 4775 4821 33191406 33191361 4.340000e-06 63.9
19 TraesCS3D01G218200 chr4D 85.520 663 72 19 1 654 51848806 51849453 0.000000e+00 671.0
20 TraesCS3D01G218200 chr4D 83.988 687 83 18 1 674 363565406 363566078 7.330000e-178 634.0
21 TraesCS3D01G218200 chr6D 84.139 662 83 14 5 654 87469545 87468894 5.710000e-174 621.0
22 TraesCS3D01G218200 chr2B 83.704 675 89 15 1 664 599259930 599260594 7.380000e-173 617.0
23 TraesCS3D01G218200 chr6A 79.643 280 38 10 4052 4315 52719441 52719717 3.190000e-42 183.0
24 TraesCS3D01G218200 chr6A 81.183 186 12 8 4219 4387 615965245 615965424 1.520000e-25 128.0
25 TraesCS3D01G218200 chr5A 76.817 289 38 13 4052 4315 452925341 452925625 9.060000e-28 135.0
26 TraesCS3D01G218200 chr2D 92.157 51 2 1 4785 4835 588887434 588887386 2.590000e-08 71.3
27 TraesCS3D01G218200 chr7A 90.566 53 3 1 4786 4836 22917284 22917232 9.320000e-08 69.4
28 TraesCS3D01G218200 chr2A 95.238 42 2 0 4784 4825 747606265 747606224 3.350000e-07 67.6
29 TraesCS3D01G218200 chr7D 93.333 45 2 1 4785 4828 637938086 637938130 1.210000e-06 65.8
30 TraesCS3D01G218200 chr4A 95.122 41 2 0 2937 2977 580659440 580659400 1.210000e-06 65.8
31 TraesCS3D01G218200 chr5D 90.244 41 4 0 2937 2977 536717391 536717431 3.000000e-03 54.7
32 TraesCS3D01G218200 chr1D 94.118 34 2 0 2973 3006 318118771 318118738 9.000000e-03 52.8


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 TraesCS3D01G218200 chr3D 297490581 297495768 5187 False 9581.000000 9581 100.000000 1 5188 1 chr3D.!!$F1 5187
1 TraesCS3D01G218200 chr3B 392293937 392298256 4319 False 2220.333333 5975 95.394667 789 5188 3 chr3B.!!$F4 4399
2 TraesCS3D01G218200 chr3B 157903620 157904322 702 True 739.000000 739 86.280000 1 680 1 chr3B.!!$R1 679
3 TraesCS3D01G218200 chr3B 404416400 404416908 508 False 695.000000 695 91.296000 1 514 1 chr3B.!!$F1 513
4 TraesCS3D01G218200 chr3B 705140845 705141496 651 True 686.000000 686 85.822000 1 654 1 chr3B.!!$R2 653
5 TraesCS3D01G218200 chr3A 391472635 391477095 4460 True 1688.000000 3020 95.030750 741 5188 4 chr3A.!!$R2 4447
6 TraesCS3D01G218200 chr3A 676921063 676921733 670 True 636.000000 636 84.018000 1 672 1 chr3A.!!$R1 671
7 TraesCS3D01G218200 chr5B 524326937 524327545 608 False 673.000000 673 86.634000 1 617 1 chr5B.!!$F1 616
8 TraesCS3D01G218200 chr4D 51848806 51849453 647 False 671.000000 671 85.520000 1 654 1 chr4D.!!$F1 653
9 TraesCS3D01G218200 chr4D 363565406 363566078 672 False 634.000000 634 83.988000 1 674 1 chr4D.!!$F2 673
10 TraesCS3D01G218200 chr6D 87468894 87469545 651 True 621.000000 621 84.139000 5 654 1 chr6D.!!$R1 649
11 TraesCS3D01G218200 chr2B 599259930 599260594 664 False 617.000000 617 83.704000 1 664 1 chr2B.!!$F1 663

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
892 983 0.108138 CCGCTCAGTTTCCTTCCGAT 60.108 55.000 0.00 0.0 0.00 4.18 F
1688 1827 1.002773 GGAACCGTGGCCTTTTCTCTA 59.997 52.381 3.32 0.0 0.00 2.43 F
2096 2235 0.326264 AGTCAACTGTGATGGGGCTC 59.674 55.000 0.00 0.0 35.80 4.70 F
2516 2745 0.843309 TGGACTGCTCAGGGTTTTCA 59.157 50.000 1.66 0.0 0.00 2.69 F
3621 3857 0.868406 GCAGAAGGTGGTCAAAGACG 59.132 55.000 0.00 0.0 32.65 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2170 1.470805 GCCATTATTTCCCGGTGCAAC 60.471 52.381 0.0 0.0 0.00 4.17 R
3379 3615 1.514014 CCGCACAATTACCGCTTGC 60.514 57.895 0.0 0.0 0.00 4.01 R
3884 4129 1.072159 GCAGCTCCCACTGTCACTT 59.928 57.895 0.0 0.0 39.96 3.16 R
4017 4262 1.273327 TGCCTGATACGATGATGCGAT 59.727 47.619 0.0 0.0 34.83 4.58 R
4812 5066 0.841289 TCCCTCTGTCCCAAAAACGT 59.159 50.000 0.0 0.0 0.00 3.99 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
67 69 3.820467 AGAACAAATGAACGCCTTCATGA 59.180 39.130 11.07 0.00 44.93 3.07
144 146 2.267324 GAGGCGGAGAAGCAAGCT 59.733 61.111 0.00 0.00 39.27 3.74
196 198 1.416401 AGACCAAGGCGAAAGAAGTGA 59.584 47.619 0.00 0.00 0.00 3.41
220 222 1.748403 GCTAGCATGATGACGGGGA 59.252 57.895 10.63 0.00 0.00 4.81
365 370 2.753055 TTATGCCGACAAGTGTGCTA 57.247 45.000 0.00 0.00 0.00 3.49
399 413 1.736645 CGATGGCGTGGTCGAACTT 60.737 57.895 0.33 0.00 40.11 2.66
400 414 1.787847 GATGGCGTGGTCGAACTTG 59.212 57.895 0.33 0.00 39.71 3.16
404 418 1.282930 GGCGTGGTCGAACTTGAGTC 61.283 60.000 0.33 0.00 39.71 3.36
405 419 0.318784 GCGTGGTCGAACTTGAGTCT 60.319 55.000 0.33 0.00 39.71 3.24
411 425 1.340248 GTCGAACTTGAGTCTCACCCA 59.660 52.381 0.78 0.00 0.00 4.51
549 609 1.293179 CATGATCTATGGCCGCGGA 59.707 57.895 33.48 9.86 32.95 5.54
618 681 1.076332 GCGCACTGTCGACCTAAATT 58.924 50.000 14.12 0.00 0.00 1.82
628 691 6.016213 TGTCGACCTAAATTTTAAAAGGGC 57.984 37.500 14.12 3.19 33.44 5.19
629 692 5.535406 TGTCGACCTAAATTTTAAAAGGGCA 59.465 36.000 14.12 2.05 36.92 5.36
631 694 6.005198 TCGACCTAAATTTTAAAAGGGCAGA 58.995 36.000 10.54 6.30 36.92 4.26
655 722 1.824272 CGAACGACCGACCCAAACAC 61.824 60.000 0.00 0.00 0.00 3.32
664 731 1.268335 CGACCCAAACACACGAAAAGG 60.268 52.381 0.00 0.00 0.00 3.11
668 735 1.960689 CCAAACACACGAAAAGGGGAT 59.039 47.619 0.00 0.00 0.00 3.85
674 741 2.081462 ACACGAAAAGGGGATAAAGCG 58.919 47.619 0.00 0.00 0.00 4.68
677 744 1.375551 GAAAAGGGGATAAAGCGCGA 58.624 50.000 12.10 0.00 0.00 5.87
678 745 1.947456 GAAAAGGGGATAAAGCGCGAT 59.053 47.619 12.10 0.00 0.00 4.58
679 746 1.594331 AAAGGGGATAAAGCGCGATC 58.406 50.000 12.10 3.09 0.00 3.69
680 747 0.468226 AAGGGGATAAAGCGCGATCA 59.532 50.000 12.10 0.00 0.00 2.92
681 748 0.249911 AGGGGATAAAGCGCGATCAC 60.250 55.000 12.10 15.16 0.00 3.06
682 749 1.228657 GGGGATAAAGCGCGATCACC 61.229 60.000 20.69 20.69 38.45 4.02
683 750 1.228657 GGGATAAAGCGCGATCACCC 61.229 60.000 12.10 11.41 0.00 4.61
684 751 1.228657 GGATAAAGCGCGATCACCCC 61.229 60.000 12.10 0.00 0.00 4.95
685 752 1.557443 GATAAAGCGCGATCACCCCG 61.557 60.000 12.10 0.00 0.00 5.73
686 753 2.306255 ATAAAGCGCGATCACCCCGT 62.306 55.000 12.10 0.00 0.00 5.28
687 754 2.510064 TAAAGCGCGATCACCCCGTT 62.510 55.000 12.10 0.00 0.00 4.44
690 757 2.433491 CGCGATCACCCCGTTGAA 60.433 61.111 0.00 0.00 0.00 2.69
691 758 2.452813 CGCGATCACCCCGTTGAAG 61.453 63.158 0.00 0.00 0.00 3.02
692 759 1.375523 GCGATCACCCCGTTGAAGT 60.376 57.895 0.00 0.00 0.00 3.01
693 760 0.953960 GCGATCACCCCGTTGAAGTT 60.954 55.000 0.00 0.00 0.00 2.66
694 761 0.796312 CGATCACCCCGTTGAAGTTG 59.204 55.000 0.00 0.00 0.00 3.16
695 762 1.876416 CGATCACCCCGTTGAAGTTGT 60.876 52.381 0.00 0.00 0.00 3.32
696 763 2.227194 GATCACCCCGTTGAAGTTGTT 58.773 47.619 0.00 0.00 0.00 2.83
697 764 1.670791 TCACCCCGTTGAAGTTGTTC 58.329 50.000 0.00 0.00 0.00 3.18
698 765 1.210967 TCACCCCGTTGAAGTTGTTCT 59.789 47.619 0.00 0.00 33.38 3.01
699 766 2.021457 CACCCCGTTGAAGTTGTTCTT 58.979 47.619 0.00 0.00 39.32 2.52
700 767 3.118334 TCACCCCGTTGAAGTTGTTCTTA 60.118 43.478 0.00 0.00 36.40 2.10
701 768 3.250040 CACCCCGTTGAAGTTGTTCTTAG 59.750 47.826 0.00 0.00 36.40 2.18
702 769 3.135167 ACCCCGTTGAAGTTGTTCTTAGA 59.865 43.478 0.00 0.00 36.40 2.10
703 770 3.746492 CCCCGTTGAAGTTGTTCTTAGAG 59.254 47.826 0.00 0.00 36.40 2.43
704 771 4.377897 CCCGTTGAAGTTGTTCTTAGAGT 58.622 43.478 0.00 0.00 36.40 3.24
705 772 4.211374 CCCGTTGAAGTTGTTCTTAGAGTG 59.789 45.833 0.00 0.00 36.40 3.51
706 773 4.809426 CCGTTGAAGTTGTTCTTAGAGTGT 59.191 41.667 0.00 0.00 36.40 3.55
707 774 5.050972 CCGTTGAAGTTGTTCTTAGAGTGTC 60.051 44.000 0.00 0.00 36.40 3.67
708 775 5.518847 CGTTGAAGTTGTTCTTAGAGTGTCA 59.481 40.000 0.00 0.00 36.40 3.58
709 776 6.201044 CGTTGAAGTTGTTCTTAGAGTGTCAT 59.799 38.462 0.00 0.00 36.40 3.06
710 777 7.381408 CGTTGAAGTTGTTCTTAGAGTGTCATA 59.619 37.037 0.00 0.00 36.40 2.15
711 778 9.209175 GTTGAAGTTGTTCTTAGAGTGTCATAT 57.791 33.333 0.00 0.00 36.40 1.78
712 779 9.778741 TTGAAGTTGTTCTTAGAGTGTCATATT 57.221 29.630 0.00 0.00 36.40 1.28
713 780 9.778741 TGAAGTTGTTCTTAGAGTGTCATATTT 57.221 29.630 0.00 0.00 36.40 1.40
715 782 8.034058 AGTTGTTCTTAGAGTGTCATATTTGC 57.966 34.615 0.00 0.00 0.00 3.68
716 783 7.880195 AGTTGTTCTTAGAGTGTCATATTTGCT 59.120 33.333 0.00 0.00 0.00 3.91
717 784 9.151471 GTTGTTCTTAGAGTGTCATATTTGCTA 57.849 33.333 0.00 0.00 0.00 3.49
718 785 9.719355 TTGTTCTTAGAGTGTCATATTTGCTAA 57.281 29.630 0.00 0.00 0.00 3.09
719 786 9.371136 TGTTCTTAGAGTGTCATATTTGCTAAG 57.629 33.333 0.00 0.00 36.38 2.18
720 787 9.372369 GTTCTTAGAGTGTCATATTTGCTAAGT 57.628 33.333 0.00 0.00 36.42 2.24
721 788 9.587772 TTCTTAGAGTGTCATATTTGCTAAGTC 57.412 33.333 0.00 0.00 36.42 3.01
722 789 8.198109 TCTTAGAGTGTCATATTTGCTAAGTCC 58.802 37.037 0.00 0.00 36.42 3.85
723 790 5.352284 AGAGTGTCATATTTGCTAAGTCCG 58.648 41.667 0.00 0.00 0.00 4.79
724 791 4.442706 AGTGTCATATTTGCTAAGTCCGG 58.557 43.478 0.00 0.00 0.00 5.14
725 792 4.081087 AGTGTCATATTTGCTAAGTCCGGT 60.081 41.667 0.00 0.00 0.00 5.28
726 793 4.270325 GTGTCATATTTGCTAAGTCCGGTC 59.730 45.833 0.00 0.00 0.00 4.79
727 794 4.081365 TGTCATATTTGCTAAGTCCGGTCA 60.081 41.667 0.00 0.00 0.00 4.02
728 795 5.057149 GTCATATTTGCTAAGTCCGGTCAT 58.943 41.667 0.00 0.00 0.00 3.06
729 796 6.183360 TGTCATATTTGCTAAGTCCGGTCATA 60.183 38.462 0.00 0.00 0.00 2.15
730 797 6.704493 GTCATATTTGCTAAGTCCGGTCATAA 59.296 38.462 0.00 0.00 0.00 1.90
731 798 7.225931 GTCATATTTGCTAAGTCCGGTCATAAA 59.774 37.037 0.00 0.00 0.00 1.40
732 799 7.936847 TCATATTTGCTAAGTCCGGTCATAAAT 59.063 33.333 0.00 4.00 0.00 1.40
733 800 5.811399 TTTGCTAAGTCCGGTCATAAATG 57.189 39.130 0.00 0.00 0.00 2.32
734 801 3.202906 TGCTAAGTCCGGTCATAAATGC 58.797 45.455 0.00 0.00 0.00 3.56
735 802 3.118408 TGCTAAGTCCGGTCATAAATGCT 60.118 43.478 0.00 0.00 0.00 3.79
736 803 3.495001 GCTAAGTCCGGTCATAAATGCTC 59.505 47.826 0.00 0.00 0.00 4.26
737 804 2.622064 AGTCCGGTCATAAATGCTCC 57.378 50.000 0.00 0.00 0.00 4.70
738 805 2.119495 AGTCCGGTCATAAATGCTCCT 58.881 47.619 0.00 0.00 0.00 3.69
739 806 3.305720 AGTCCGGTCATAAATGCTCCTA 58.694 45.455 0.00 0.00 0.00 2.94
746 813 6.455647 CGGTCATAAATGCTCCTAGTATTGA 58.544 40.000 0.00 0.00 30.89 2.57
757 824 2.205074 CTAGTATTGACCAGCCGCAAG 58.795 52.381 0.00 0.00 0.00 4.01
771 838 1.524849 GCAAGGGCCTACTAGCAGC 60.525 63.158 6.41 0.00 0.00 5.25
776 843 2.586357 GCCTACTAGCAGCCACGC 60.586 66.667 0.00 0.00 0.00 5.34
823 890 1.520342 GAGATGCAGCGAGTCCACC 60.520 63.158 0.00 0.00 0.00 4.61
892 983 0.108138 CCGCTCAGTTTCCTTCCGAT 60.108 55.000 0.00 0.00 0.00 4.18
893 984 1.676014 CCGCTCAGTTTCCTTCCGATT 60.676 52.381 0.00 0.00 0.00 3.34
894 985 1.661112 CGCTCAGTTTCCTTCCGATTC 59.339 52.381 0.00 0.00 0.00 2.52
895 986 2.010497 GCTCAGTTTCCTTCCGATTCC 58.990 52.381 0.00 0.00 0.00 3.01
896 987 2.271800 CTCAGTTTCCTTCCGATTCCG 58.728 52.381 0.00 0.00 0.00 4.30
897 988 1.897133 TCAGTTTCCTTCCGATTCCGA 59.103 47.619 0.00 0.00 38.22 4.55
907 998 1.153628 CGATTCCGAGGGCGAGTTT 60.154 57.895 0.00 0.00 40.82 2.66
919 1010 2.383527 CGAGTTTCTGCCGCTGGAC 61.384 63.158 0.00 0.00 0.00 4.02
960 1060 2.285024 TAACCACCCCGTCCTTCCG 61.285 63.158 0.00 0.00 0.00 4.30
1279 1403 4.227134 CCTCTCATCGGCCACGGG 62.227 72.222 2.24 0.00 41.39 5.28
1334 1458 1.837538 CGCTTTCGAGCCAAACGGAA 61.838 55.000 0.00 0.00 38.10 4.30
1458 1593 4.466567 TGTGAACACGCTTTCATACTTG 57.533 40.909 2.87 0.00 37.80 3.16
1459 1594 3.874543 TGTGAACACGCTTTCATACTTGT 59.125 39.130 2.87 0.00 37.80 3.16
1469 1604 7.490079 CACGCTTTCATACTTGTATACTTGGTA 59.510 37.037 4.17 5.26 0.00 3.25
1547 1686 7.013942 AGGTCATAAAAGTAACTCCACAAAACC 59.986 37.037 0.00 0.00 0.00 3.27
1555 1694 3.926058 ACTCCACAAAACCTACACACT 57.074 42.857 0.00 0.00 0.00 3.55
1630 1769 1.403679 GAGGAGATCATCGGCCTATCG 59.596 57.143 0.00 0.00 0.00 2.92
1688 1827 1.002773 GGAACCGTGGCCTTTTCTCTA 59.997 52.381 3.32 0.00 0.00 2.43
1894 2033 4.020128 ACTCCCATGGTTTAGTCTTCTCAC 60.020 45.833 11.73 0.00 0.00 3.51
2096 2235 0.326264 AGTCAACTGTGATGGGGCTC 59.674 55.000 0.00 0.00 35.80 4.70
2131 2270 3.306225 GGAAACATTTCATGGCAGCTGAA 60.306 43.478 20.43 4.69 38.92 3.02
2238 2377 5.106712 TGTTCCTTCGCTAATTCATTCACAC 60.107 40.000 0.00 0.00 0.00 3.82
2477 2706 3.669251 AGAACAGCACCTAACTCAGTC 57.331 47.619 0.00 0.00 0.00 3.51
2483 2712 2.499289 AGCACCTAACTCAGTCATCCAG 59.501 50.000 0.00 0.00 0.00 3.86
2516 2745 0.843309 TGGACTGCTCAGGGTTTTCA 59.157 50.000 1.66 0.00 0.00 2.69
2565 2794 6.071952 GGAGGCAAAATCAAGTCAAACTATCA 60.072 38.462 0.00 0.00 0.00 2.15
2574 2803 7.812309 TCAAGTCAAACTATCAGTGATTACG 57.188 36.000 11.68 3.27 0.00 3.18
2616 2845 4.397417 AGCCATCAAGCATCTTGTTTACTC 59.603 41.667 6.47 0.00 34.23 2.59
2668 2897 4.906618 TGGACTGAAAAGTATCCTGGTTC 58.093 43.478 0.00 0.00 32.06 3.62
2721 2950 1.586028 CCTCCAAAATGGTGGCGTG 59.414 57.895 4.68 0.00 43.34 5.34
2728 2959 5.165234 CCAAAATGGTGGCGTGAAGCTAA 62.165 47.826 0.00 0.00 38.34 3.09
2868 3104 6.538263 AGTCTTGTTTAGCTCTTGAATCCTT 58.462 36.000 0.00 0.00 0.00 3.36
2946 3182 8.488668 GGTAATTGGTAAAGTTATACTCCCTCA 58.511 37.037 0.00 0.00 0.00 3.86
2964 3200 2.755103 CTCAGCCCCAAAATAAGTGTCC 59.245 50.000 0.00 0.00 0.00 4.02
3090 3326 3.865745 GCAATGCTACACGAGAAGTATGT 59.134 43.478 0.00 0.00 0.00 2.29
3379 3615 3.569277 TCCAACTCATTGTCATTGTGGTG 59.431 43.478 7.53 7.53 33.60 4.17
3610 3846 2.096248 CTCCGAGTTAGAGCAGAAGGT 58.904 52.381 0.00 0.00 0.00 3.50
3620 3856 2.262423 AGCAGAAGGTGGTCAAAGAC 57.738 50.000 0.00 0.00 27.31 3.01
3621 3857 0.868406 GCAGAAGGTGGTCAAAGACG 59.132 55.000 0.00 0.00 32.65 4.18
3622 3858 1.810412 GCAGAAGGTGGTCAAAGACGT 60.810 52.381 0.00 0.00 32.65 4.34
3623 3859 2.135933 CAGAAGGTGGTCAAAGACGTC 58.864 52.381 7.70 7.70 32.65 4.34
3768 4013 3.145286 GGCTCTTCCATATTGCCTCTTC 58.855 50.000 0.00 0.00 40.36 2.87
3809 4054 1.133253 CTCATTTCACGGCGCACAG 59.867 57.895 10.83 1.82 0.00 3.66
4017 4262 5.278463 GCTCAAGACAAATTGCCAGTAGAAA 60.278 40.000 0.00 0.00 0.00 2.52
4315 4561 8.933807 CAAGTTTATACTCAGATGCATATGGAG 58.066 37.037 20.58 18.03 31.99 3.86
4408 4654 7.770897 AGTGAGAACTGCCCTTAACTTTATATG 59.229 37.037 0.00 0.00 0.00 1.78
4409 4655 6.542370 TGAGAACTGCCCTTAACTTTATATGC 59.458 38.462 0.00 0.00 0.00 3.14
4788 5042 0.110823 CGGCAGCAACAGAAACGTAC 60.111 55.000 0.00 0.00 0.00 3.67
4789 5043 0.237498 GGCAGCAACAGAAACGTACC 59.763 55.000 0.00 0.00 0.00 3.34
4790 5044 0.237498 GCAGCAACAGAAACGTACCC 59.763 55.000 0.00 0.00 0.00 3.69
4791 5045 0.872388 CAGCAACAGAAACGTACCCC 59.128 55.000 0.00 0.00 0.00 4.95
4792 5046 0.250597 AGCAACAGAAACGTACCCCC 60.251 55.000 0.00 0.00 0.00 5.40
4793 5047 0.250597 GCAACAGAAACGTACCCCCT 60.251 55.000 0.00 0.00 0.00 4.79
4794 5048 1.804601 CAACAGAAACGTACCCCCTC 58.195 55.000 0.00 0.00 0.00 4.30
4795 5049 0.689055 AACAGAAACGTACCCCCTCC 59.311 55.000 0.00 0.00 0.00 4.30
4796 5050 1.217244 CAGAAACGTACCCCCTCCG 59.783 63.158 0.00 0.00 0.00 4.63
4797 5051 1.228988 AGAAACGTACCCCCTCCGT 60.229 57.895 0.00 0.00 36.17 4.69
4798 5052 1.216444 GAAACGTACCCCCTCCGTC 59.784 63.158 0.00 0.00 32.95 4.79
4799 5053 2.230994 GAAACGTACCCCCTCCGTCC 62.231 65.000 0.00 0.00 32.95 4.79
4800 5054 4.766632 ACGTACCCCCTCCGTCCC 62.767 72.222 0.00 0.00 0.00 4.46
4801 5055 4.764771 CGTACCCCCTCCGTCCCA 62.765 72.222 0.00 0.00 0.00 4.37
4802 5056 2.041197 GTACCCCCTCCGTCCCAT 60.041 66.667 0.00 0.00 0.00 4.00
4803 5057 1.233949 GTACCCCCTCCGTCCCATA 59.766 63.158 0.00 0.00 0.00 2.74
4804 5058 0.398948 GTACCCCCTCCGTCCCATAA 60.399 60.000 0.00 0.00 0.00 1.90
4805 5059 0.569204 TACCCCCTCCGTCCCATAAT 59.431 55.000 0.00 0.00 0.00 1.28
4806 5060 0.569204 ACCCCCTCCGTCCCATAATA 59.431 55.000 0.00 0.00 0.00 0.98
4807 5061 1.153565 ACCCCCTCCGTCCCATAATAT 59.846 52.381 0.00 0.00 0.00 1.28
4808 5062 2.387861 ACCCCCTCCGTCCCATAATATA 59.612 50.000 0.00 0.00 0.00 0.86
4809 5063 3.181392 ACCCCCTCCGTCCCATAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
4810 5064 3.454812 CCCCCTCCGTCCCATAATATAAG 59.545 52.174 0.00 0.00 0.00 1.73
4811 5065 4.359105 CCCCTCCGTCCCATAATATAAGA 58.641 47.826 0.00 0.00 0.00 2.10
4812 5066 4.781087 CCCCTCCGTCCCATAATATAAGAA 59.219 45.833 0.00 0.00 0.00 2.52
4813 5067 5.338137 CCCCTCCGTCCCATAATATAAGAAC 60.338 48.000 0.00 0.00 0.00 3.01
4814 5068 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
4815 5069 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
4816 5070 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
4817 5071 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
4818 5072 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
4819 5073 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
4820 5074 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
4821 5075 7.853929 CGTCCCATAATATAAGAACGTTTTTGG 59.146 37.037 13.87 5.54 0.00 3.28
4822 5076 8.132995 GTCCCATAATATAAGAACGTTTTTGGG 58.867 37.037 13.87 13.75 0.00 4.12
4823 5077 8.053963 TCCCATAATATAAGAACGTTTTTGGGA 58.946 33.333 16.96 16.96 36.17 4.37
4824 5078 8.132995 CCCATAATATAAGAACGTTTTTGGGAC 58.867 37.037 14.35 0.00 0.00 4.46
4825 5079 8.679100 CCATAATATAAGAACGTTTTTGGGACA 58.321 33.333 13.87 0.00 0.00 4.02
4826 5080 9.716507 CATAATATAAGAACGTTTTTGGGACAG 57.283 33.333 13.87 0.00 42.39 3.51
4827 5081 7.989416 AATATAAGAACGTTTTTGGGACAGA 57.011 32.000 13.87 0.00 42.39 3.41
4828 5082 5.941948 ATAAGAACGTTTTTGGGACAGAG 57.058 39.130 13.87 0.00 42.39 3.35
4862 5116 8.609617 TTATATGCTGCCCATATAGAACTACT 57.390 34.615 11.64 0.00 45.42 2.57
4863 5117 9.709387 TTATATGCTGCCCATATAGAACTACTA 57.291 33.333 11.64 0.00 45.42 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.107366 CTTCTCCTCCCTTGAGTCCTC 58.893 57.143 0.00 0.00 36.86 3.71
67 69 1.978361 AGCCTCCTCCTTTGGATCTT 58.022 50.000 0.00 0.00 35.30 2.40
144 146 3.085533 GGCCTCGATCTCTAGCATCTTA 58.914 50.000 0.00 0.00 0.00 2.10
196 198 1.001924 CGTCATCATGCTAGCGAGAGT 60.002 52.381 10.77 0.00 0.00 3.24
220 222 4.241151 AGATCCACCTTCATGATCTCCAT 58.759 43.478 0.00 0.00 40.88 3.41
346 351 2.739913 GTTAGCACACTTGTCGGCATAA 59.260 45.455 0.00 0.00 0.00 1.90
354 359 1.247567 GGCCATGTTAGCACACTTGT 58.752 50.000 0.00 0.00 35.03 3.16
399 413 3.631686 CACACAAAAATGGGTGAGACTCA 59.368 43.478 5.28 0.00 45.49 3.41
400 414 3.550842 GCACACAAAAATGGGTGAGACTC 60.551 47.826 14.95 0.00 45.49 3.36
404 418 2.546373 CCAGCACACAAAAATGGGTGAG 60.546 50.000 14.95 6.31 45.49 3.51
405 419 1.411977 CCAGCACACAAAAATGGGTGA 59.588 47.619 14.95 0.00 45.49 4.02
411 425 2.158928 ACACATGCCAGCACACAAAAAT 60.159 40.909 0.00 0.00 0.00 1.82
503 525 0.674581 CATGTCGTCACCATGCCAGT 60.675 55.000 0.00 0.00 33.90 4.00
613 676 5.618195 CGCTCGTCTGCCCTTTTAAAATTTA 60.618 40.000 0.09 0.00 0.00 1.40
618 681 1.153353 CGCTCGTCTGCCCTTTTAAA 58.847 50.000 0.00 0.00 0.00 1.52
628 691 2.870161 CGGTCGTTCGCTCGTCTG 60.870 66.667 0.00 0.00 0.00 3.51
629 692 3.046087 TCGGTCGTTCGCTCGTCT 61.046 61.111 6.82 0.00 0.00 4.18
631 694 4.395583 GGTCGGTCGTTCGCTCGT 62.396 66.667 6.82 0.00 0.00 4.18
655 722 1.202143 GCGCTTTATCCCCTTTTCGTG 60.202 52.381 0.00 0.00 0.00 4.35
664 731 1.228657 GGGTGATCGCGCTTTATCCC 61.229 60.000 15.49 8.46 0.00 3.85
668 735 2.202824 CGGGGTGATCGCGCTTTA 60.203 61.111 21.01 0.00 44.45 1.85
674 741 0.953960 AACTTCAACGGGGTGATCGC 60.954 55.000 0.00 0.00 0.00 4.58
677 744 2.158667 AGAACAACTTCAACGGGGTGAT 60.159 45.455 0.00 0.00 0.00 3.06
678 745 1.210967 AGAACAACTTCAACGGGGTGA 59.789 47.619 0.00 0.00 0.00 4.02
679 746 1.675552 AGAACAACTTCAACGGGGTG 58.324 50.000 0.00 0.00 0.00 4.61
680 747 2.430248 AAGAACAACTTCAACGGGGT 57.570 45.000 0.00 0.00 32.91 4.95
681 748 3.735591 TCTAAGAACAACTTCAACGGGG 58.264 45.455 0.00 0.00 39.72 5.73
682 749 4.211374 CACTCTAAGAACAACTTCAACGGG 59.789 45.833 0.00 0.00 39.72 5.28
683 750 4.809426 ACACTCTAAGAACAACTTCAACGG 59.191 41.667 0.00 0.00 39.72 4.44
684 751 5.518847 TGACACTCTAAGAACAACTTCAACG 59.481 40.000 0.00 0.00 39.72 4.10
685 752 6.903883 TGACACTCTAAGAACAACTTCAAC 57.096 37.500 0.00 0.00 39.72 3.18
686 753 9.778741 AATATGACACTCTAAGAACAACTTCAA 57.221 29.630 0.00 0.00 39.72 2.69
687 754 9.778741 AAATATGACACTCTAAGAACAACTTCA 57.221 29.630 0.00 0.00 39.72 3.02
689 756 8.507249 GCAAATATGACACTCTAAGAACAACTT 58.493 33.333 0.00 0.00 42.04 2.66
690 757 7.880195 AGCAAATATGACACTCTAAGAACAACT 59.120 33.333 0.00 0.00 0.00 3.16
691 758 8.034058 AGCAAATATGACACTCTAAGAACAAC 57.966 34.615 0.00 0.00 0.00 3.32
692 759 9.719355 TTAGCAAATATGACACTCTAAGAACAA 57.281 29.630 0.00 0.00 0.00 2.83
693 760 9.371136 CTTAGCAAATATGACACTCTAAGAACA 57.629 33.333 0.00 0.00 35.71 3.18
694 761 9.372369 ACTTAGCAAATATGACACTCTAAGAAC 57.628 33.333 11.59 0.00 36.62 3.01
695 762 9.587772 GACTTAGCAAATATGACACTCTAAGAA 57.412 33.333 11.59 0.00 36.62 2.52
696 763 8.198109 GGACTTAGCAAATATGACACTCTAAGA 58.802 37.037 11.59 0.00 36.62 2.10
697 764 7.168302 CGGACTTAGCAAATATGACACTCTAAG 59.832 40.741 0.00 0.00 38.15 2.18
698 765 6.978659 CGGACTTAGCAAATATGACACTCTAA 59.021 38.462 0.00 0.00 0.00 2.10
699 766 6.461092 CCGGACTTAGCAAATATGACACTCTA 60.461 42.308 0.00 0.00 0.00 2.43
700 767 5.352284 CGGACTTAGCAAATATGACACTCT 58.648 41.667 0.00 0.00 0.00 3.24
701 768 4.508124 CCGGACTTAGCAAATATGACACTC 59.492 45.833 0.00 0.00 0.00 3.51
702 769 4.081087 ACCGGACTTAGCAAATATGACACT 60.081 41.667 9.46 0.00 0.00 3.55
703 770 4.189231 ACCGGACTTAGCAAATATGACAC 58.811 43.478 9.46 0.00 0.00 3.67
704 771 4.081365 TGACCGGACTTAGCAAATATGACA 60.081 41.667 9.46 0.00 0.00 3.58
705 772 4.439057 TGACCGGACTTAGCAAATATGAC 58.561 43.478 9.46 0.00 0.00 3.06
706 773 4.746535 TGACCGGACTTAGCAAATATGA 57.253 40.909 9.46 0.00 0.00 2.15
707 774 7.490962 TTTATGACCGGACTTAGCAAATATG 57.509 36.000 9.46 0.00 0.00 1.78
708 775 7.308589 GCATTTATGACCGGACTTAGCAAATAT 60.309 37.037 9.46 0.00 0.00 1.28
709 776 6.017440 GCATTTATGACCGGACTTAGCAAATA 60.017 38.462 9.46 0.00 0.00 1.40
710 777 5.221048 GCATTTATGACCGGACTTAGCAAAT 60.221 40.000 9.46 0.84 0.00 2.32
711 778 4.095782 GCATTTATGACCGGACTTAGCAAA 59.904 41.667 9.46 0.00 0.00 3.68
712 779 3.625764 GCATTTATGACCGGACTTAGCAA 59.374 43.478 9.46 0.00 0.00 3.91
713 780 3.118408 AGCATTTATGACCGGACTTAGCA 60.118 43.478 9.46 0.00 0.00 3.49
714 781 3.467803 AGCATTTATGACCGGACTTAGC 58.532 45.455 9.46 4.98 0.00 3.09
715 782 4.058817 GGAGCATTTATGACCGGACTTAG 58.941 47.826 9.46 0.00 0.00 2.18
716 783 3.709653 AGGAGCATTTATGACCGGACTTA 59.290 43.478 9.46 0.95 33.35 2.24
717 784 2.505819 AGGAGCATTTATGACCGGACTT 59.494 45.455 9.46 2.19 33.35 3.01
718 785 2.119495 AGGAGCATTTATGACCGGACT 58.881 47.619 9.46 0.00 33.35 3.85
719 786 2.622064 AGGAGCATTTATGACCGGAC 57.378 50.000 9.46 1.07 33.35 4.79
720 787 3.305720 ACTAGGAGCATTTATGACCGGA 58.694 45.455 9.46 0.00 33.35 5.14
721 788 3.753294 ACTAGGAGCATTTATGACCGG 57.247 47.619 0.00 0.00 33.35 5.28
722 789 6.366332 GTCAATACTAGGAGCATTTATGACCG 59.634 42.308 0.00 0.00 33.35 4.79
723 790 6.651225 GGTCAATACTAGGAGCATTTATGACC 59.349 42.308 0.00 0.00 33.89 4.02
724 791 7.217200 TGGTCAATACTAGGAGCATTTATGAC 58.783 38.462 0.00 0.00 36.68 3.06
725 792 7.373617 TGGTCAATACTAGGAGCATTTATGA 57.626 36.000 0.00 0.00 36.68 2.15
726 793 6.148480 GCTGGTCAATACTAGGAGCATTTATG 59.852 42.308 0.00 0.00 40.35 1.90
727 794 6.234177 GCTGGTCAATACTAGGAGCATTTAT 58.766 40.000 0.00 0.00 40.35 1.40
728 795 5.454755 GGCTGGTCAATACTAGGAGCATTTA 60.455 44.000 0.00 0.00 40.35 1.40
729 796 4.455606 GCTGGTCAATACTAGGAGCATTT 58.544 43.478 0.00 0.00 40.35 2.32
730 797 3.181450 GGCTGGTCAATACTAGGAGCATT 60.181 47.826 0.00 0.00 40.35 3.56
731 798 2.370189 GGCTGGTCAATACTAGGAGCAT 59.630 50.000 0.00 0.00 40.35 3.79
732 799 1.762957 GGCTGGTCAATACTAGGAGCA 59.237 52.381 0.00 0.00 39.03 4.26
733 800 1.269831 CGGCTGGTCAATACTAGGAGC 60.270 57.143 0.00 0.00 34.89 4.70
734 801 1.269831 GCGGCTGGTCAATACTAGGAG 60.270 57.143 0.00 0.00 34.89 3.69
735 802 0.750850 GCGGCTGGTCAATACTAGGA 59.249 55.000 0.00 0.00 34.89 2.94
736 803 0.464036 TGCGGCTGGTCAATACTAGG 59.536 55.000 0.00 0.00 34.89 3.02
737 804 2.205074 CTTGCGGCTGGTCAATACTAG 58.795 52.381 0.00 0.00 37.27 2.57
738 805 1.134521 CCTTGCGGCTGGTCAATACTA 60.135 52.381 0.00 0.00 0.00 1.82
739 806 0.392998 CCTTGCGGCTGGTCAATACT 60.393 55.000 0.00 0.00 0.00 2.12
757 824 2.506472 GTGGCTGCTAGTAGGCCC 59.494 66.667 27.46 15.71 44.71 5.80
760 827 0.807667 CTTGCGTGGCTGCTAGTAGG 60.808 60.000 10.06 0.00 33.81 3.18
762 829 1.218047 CCTTGCGTGGCTGCTAGTA 59.782 57.895 0.00 0.00 36.21 1.82
763 830 2.046892 CCTTGCGTGGCTGCTAGT 60.047 61.111 0.00 0.00 36.21 2.57
771 838 2.572095 TACCATCGAGCCTTGCGTGG 62.572 60.000 0.00 0.00 36.61 4.94
776 843 0.811616 GTGCCTACCATCGAGCCTTG 60.812 60.000 0.00 0.00 0.00 3.61
785 852 1.153706 GCGTGTACGTGCCTACCAT 60.154 57.895 0.00 0.00 42.22 3.55
787 854 1.804326 CAGCGTGTACGTGCCTACC 60.804 63.158 0.00 0.00 42.22 3.18
823 890 2.789092 GCAGGAATTTCTCGCAATCGTG 60.789 50.000 3.99 0.00 36.96 4.35
892 983 1.292223 CAGAAACTCGCCCTCGGAA 59.708 57.895 0.00 0.00 36.13 4.30
893 984 2.970639 CAGAAACTCGCCCTCGGA 59.029 61.111 0.00 0.00 36.13 4.55
894 985 2.815647 GCAGAAACTCGCCCTCGG 60.816 66.667 0.00 0.00 36.13 4.63
895 986 2.815647 GGCAGAAACTCGCCCTCG 60.816 66.667 0.00 0.00 42.82 4.63
896 987 2.815647 CGGCAGAAACTCGCCCTC 60.816 66.667 0.00 0.00 46.04 4.30
907 998 4.373116 GGTTCGTCCAGCGGCAGA 62.373 66.667 1.45 0.00 41.72 4.26
960 1060 5.231702 AGAGGAAGAGTTTTTCGAGTAAGC 58.768 41.667 0.00 0.00 0.00 3.09
1190 1304 2.811317 GTCAAGTCAGGAGGCGCG 60.811 66.667 0.00 0.00 0.00 6.86
1334 1458 0.462047 GGAATGATCCACGCGAAGGT 60.462 55.000 15.93 0.00 45.79 3.50
1412 1536 2.163613 CAGCAGCAGCAATGAGAATTGA 59.836 45.455 3.17 0.00 45.49 2.57
1458 1593 7.868415 CACCTTATTCTCTGCTACCAAGTATAC 59.132 40.741 0.00 0.00 0.00 1.47
1459 1594 7.783119 TCACCTTATTCTCTGCTACCAAGTATA 59.217 37.037 0.00 0.00 0.00 1.47
1469 1604 5.543507 ATCGATTCACCTTATTCTCTGCT 57.456 39.130 0.00 0.00 0.00 4.24
1547 1686 1.346395 TGTTGGGGCACTAGTGTGTAG 59.654 52.381 23.44 0.00 45.44 2.74
1555 1694 1.423541 ACTTGTGATGTTGGGGCACTA 59.576 47.619 0.00 0.00 33.83 2.74
1688 1827 2.126071 CCCGTCACGCAACGAGAT 60.126 61.111 11.32 0.00 45.37 2.75
1862 2001 8.170730 AGACTAAACCATGGGAGTTAAAGAAAT 58.829 33.333 18.09 0.00 0.00 2.17
1894 2033 3.490439 AAAATGGCAGGGTGAAAAAGG 57.510 42.857 0.00 0.00 0.00 3.11
2031 2170 1.470805 GCCATTATTTCCCGGTGCAAC 60.471 52.381 0.00 0.00 0.00 4.17
2096 2235 5.408299 TGAAATGTTTCCTGACAGTACATCG 59.592 40.000 12.66 0.00 36.36 3.84
2131 2270 6.620877 TCTCATTACTAAGTGGACCAACAT 57.379 37.500 0.00 0.00 0.00 2.71
2238 2377 4.337555 CCATGAGAATTAAACAGCTCCAGG 59.662 45.833 0.00 0.00 0.00 4.45
2477 2706 1.905215 AGGACTGGACTTGACTGGATG 59.095 52.381 0.00 0.00 0.00 3.51
2516 2745 2.238084 TGGTCTGGCTGATGTAGACT 57.762 50.000 0.00 0.00 40.43 3.24
2565 2794 3.367087 GCCGATACATAGGCGTAATCACT 60.367 47.826 0.00 0.00 44.22 3.41
2616 2845 1.954528 CAGTTGCTGGAGCCAACAG 59.045 57.895 13.05 1.21 41.18 3.16
2668 2897 8.166066 TGACACATTCATATAAAGAACGAAACG 58.834 33.333 0.00 0.00 0.00 3.60
2946 3182 1.716503 AGGGACACTTATTTTGGGGCT 59.283 47.619 0.00 0.00 0.00 5.19
3299 3535 9.547279 ACCTGATGGATATACATTACATAGTCA 57.453 33.333 0.86 0.00 37.04 3.41
3305 3541 6.556874 TGGTCACCTGATGGATATACATTACA 59.443 38.462 0.86 0.00 37.04 2.41
3379 3615 1.514014 CCGCACAATTACCGCTTGC 60.514 57.895 0.00 0.00 0.00 4.01
3610 3846 2.129823 GTCTTCGACGTCTTTGACCA 57.870 50.000 14.70 0.00 0.00 4.02
3768 4013 3.316029 TGACTCTTGTGCTTTCCATTGTG 59.684 43.478 0.00 0.00 0.00 3.33
3809 4054 6.963049 TTAAAGACCGTAATGCTTTCTCTC 57.037 37.500 0.00 0.00 34.12 3.20
3884 4129 1.072159 GCAGCTCCCACTGTCACTT 59.928 57.895 0.00 0.00 39.96 3.16
3977 4222 3.650281 TGAGCTTCCTTGGCAATATCA 57.350 42.857 0.00 0.00 0.00 2.15
4017 4262 1.273327 TGCCTGATACGATGATGCGAT 59.727 47.619 0.00 0.00 34.83 4.58
4315 4561 4.791088 GCAAGAAGAAGAAACAGAACCAGC 60.791 45.833 0.00 0.00 0.00 4.85
4408 4654 2.559440 TGGCAAAACAAAATGACAGGC 58.441 42.857 0.00 0.00 29.35 4.85
4409 4655 5.754543 ATTTGGCAAAACAAAATGACAGG 57.245 34.783 17.70 0.00 42.91 4.00
4611 4857 7.905604 TGCTAATTGGAGTTTATCATATCCG 57.094 36.000 0.00 0.00 34.39 4.18
4788 5042 1.966845 ATATTATGGGACGGAGGGGG 58.033 55.000 0.00 0.00 0.00 5.40
4789 5043 4.359105 TCTTATATTATGGGACGGAGGGG 58.641 47.826 0.00 0.00 0.00 4.79
4790 5044 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
4791 5045 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
4792 5046 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
4793 5047 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
4794 5048 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
4795 5049 7.853929 CCAAAAACGTTCTTATATTATGGGACG 59.146 37.037 0.00 9.33 0.00 4.79
4796 5050 8.132995 CCCAAAAACGTTCTTATATTATGGGAC 58.867 37.037 0.00 0.00 44.24 4.46
4797 5051 8.053963 TCCCAAAAACGTTCTTATATTATGGGA 58.946 33.333 17.64 17.64 46.92 4.37
4798 5052 8.132995 GTCCCAAAAACGTTCTTATATTATGGG 58.867 37.037 0.00 10.66 43.13 4.00
4799 5053 8.679100 TGTCCCAAAAACGTTCTTATATTATGG 58.321 33.333 0.00 2.50 0.00 2.74
4800 5054 9.716507 CTGTCCCAAAAACGTTCTTATATTATG 57.283 33.333 0.00 0.00 0.00 1.90
4801 5055 9.675464 TCTGTCCCAAAAACGTTCTTATATTAT 57.325 29.630 0.00 0.00 0.00 1.28
4802 5056 9.158233 CTCTGTCCCAAAAACGTTCTTATATTA 57.842 33.333 0.00 0.00 0.00 0.98
4803 5057 7.120726 CCTCTGTCCCAAAAACGTTCTTATATT 59.879 37.037 0.00 0.00 0.00 1.28
4804 5058 6.598064 CCTCTGTCCCAAAAACGTTCTTATAT 59.402 38.462 0.00 0.00 0.00 0.86
4805 5059 5.935789 CCTCTGTCCCAAAAACGTTCTTATA 59.064 40.000 0.00 0.00 0.00 0.98
4806 5060 4.760204 CCTCTGTCCCAAAAACGTTCTTAT 59.240 41.667 0.00 0.00 0.00 1.73
4807 5061 4.131596 CCTCTGTCCCAAAAACGTTCTTA 58.868 43.478 0.00 0.00 0.00 2.10
4808 5062 2.949644 CCTCTGTCCCAAAAACGTTCTT 59.050 45.455 0.00 0.00 0.00 2.52
4809 5063 2.572290 CCTCTGTCCCAAAAACGTTCT 58.428 47.619 0.00 0.00 0.00 3.01
4810 5064 1.607148 CCCTCTGTCCCAAAAACGTTC 59.393 52.381 0.00 0.00 0.00 3.95
4811 5065 1.213430 TCCCTCTGTCCCAAAAACGTT 59.787 47.619 0.00 0.00 0.00 3.99
4812 5066 0.841289 TCCCTCTGTCCCAAAAACGT 59.159 50.000 0.00 0.00 0.00 3.99
4813 5067 1.202770 ACTCCCTCTGTCCCAAAAACG 60.203 52.381 0.00 0.00 0.00 3.60
4814 5068 2.658807 ACTCCCTCTGTCCCAAAAAC 57.341 50.000 0.00 0.00 0.00 2.43
4815 5069 5.333566 AATTACTCCCTCTGTCCCAAAAA 57.666 39.130 0.00 0.00 0.00 1.94
4816 5070 5.333566 AAATTACTCCCTCTGTCCCAAAA 57.666 39.130 0.00 0.00 0.00 2.44
4817 5071 6.652205 ATAAATTACTCCCTCTGTCCCAAA 57.348 37.500 0.00 0.00 0.00 3.28
4818 5072 7.691791 GCATATAAATTACTCCCTCTGTCCCAA 60.692 40.741 0.00 0.00 0.00 4.12
4819 5073 6.239887 GCATATAAATTACTCCCTCTGTCCCA 60.240 42.308 0.00 0.00 0.00 4.37
4820 5074 6.013293 AGCATATAAATTACTCCCTCTGTCCC 60.013 42.308 0.00 0.00 0.00 4.46
4821 5075 6.876257 CAGCATATAAATTACTCCCTCTGTCC 59.124 42.308 0.00 0.00 0.00 4.02
4822 5076 6.370166 GCAGCATATAAATTACTCCCTCTGTC 59.630 42.308 0.00 0.00 0.00 3.51
4823 5077 6.234177 GCAGCATATAAATTACTCCCTCTGT 58.766 40.000 0.00 0.00 0.00 3.41
4824 5078 5.645497 GGCAGCATATAAATTACTCCCTCTG 59.355 44.000 0.00 0.00 0.00 3.35
4825 5079 5.280727 GGGCAGCATATAAATTACTCCCTCT 60.281 44.000 0.00 0.00 0.00 3.69
4826 5080 4.944317 GGGCAGCATATAAATTACTCCCTC 59.056 45.833 0.00 0.00 0.00 4.30
4827 5081 4.353788 TGGGCAGCATATAAATTACTCCCT 59.646 41.667 0.00 0.00 0.00 4.20
4828 5082 4.662278 TGGGCAGCATATAAATTACTCCC 58.338 43.478 0.00 0.00 0.00 4.30
4862 5116 8.553153 TCACACCATTCCCAAGAGTTTATTATA 58.447 33.333 0.00 0.00 0.00 0.98
4863 5117 7.410174 TCACACCATTCCCAAGAGTTTATTAT 58.590 34.615 0.00 0.00 0.00 1.28
4880 5134 1.356124 AGTCCTTCAGCTCACACCAT 58.644 50.000 0.00 0.00 0.00 3.55
4883 5137 3.702045 AGGTATAGTCCTTCAGCTCACAC 59.298 47.826 0.00 0.00 33.52 3.82
5053 5307 2.922503 TGAAGAGCCCGAGCCACA 60.923 61.111 0.00 0.00 41.25 4.17


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

AutoCloner maintained by Alex Coulton.