Multiple sequence alignment - TraesCS1D01G297500

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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 TraesCS1D01G297500 chr1D 100.000 3191 0 0 1 3191 395883034 395879844 0.000000e+00 5893.0
1 TraesCS1D01G297500 chr1A 91.607 2228 101 40 757 2913 490023797 490021585 0.000000e+00 3000.0
2 TraesCS1D01G297500 chr1A 89.028 957 45 29 2011 2913 490112592 490111642 0.000000e+00 1131.0
3 TraesCS1D01G297500 chr1A 86.702 564 54 7 1 544 490024481 490023919 9.790000e-170 606.0
4 TraesCS1D01G297500 chr1A 78.372 430 44 25 2500 2910 490111176 490110777 1.910000e-57 233.0
5 TraesCS1D01G297500 chr1A 77.958 431 45 25 2500 2910 490021119 490020719 1.150000e-54 224.0
6 TraesCS1D01G297500 chr1A 100.000 33 0 0 2422 2454 490022215 490022183 9.560000e-06 62.1
7 TraesCS1D01G297500 chr1A 100.000 33 0 0 2422 2454 490112268 490112236 9.560000e-06 62.1
8 TraesCS1D01G297500 chr1B 87.491 1327 89 38 1654 2910 526432103 526430784 0.000000e+00 1459.0
9 TraesCS1D01G297500 chr1B 94.553 918 36 13 757 1661 526433046 526432130 0.000000e+00 1406.0
10 TraesCS1D01G297500 chr1B 84.925 796 51 17 1 756 526433779 526433013 0.000000e+00 741.0
11 TraesCS1D01G297500 chr3A 79.614 363 59 11 1117 1470 599528613 599528969 2.460000e-61 246.0
12 TraesCS1D01G297500 chr3D 76.432 454 90 13 1121 1564 456641427 456641873 2.480000e-56 230.0
13 TraesCS1D01G297500 chr3B 76.159 453 93 10 1121 1564 603489684 603490130 1.150000e-54 224.0


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 TraesCS1D01G297500 chr1D 395879844 395883034 3190 True 5893.000000 5893 100.000000 1 3191 1 chr1D.!!$R1 3190
1 TraesCS1D01G297500 chr1A 490020719 490024481 3762 True 973.025000 3000 89.066750 1 2913 4 chr1A.!!$R1 2912
2 TraesCS1D01G297500 chr1A 490110777 490112592 1815 True 475.366667 1131 89.133333 2011 2913 3 chr1A.!!$R2 902
3 TraesCS1D01G297500 chr1B 526430784 526433779 2995 True 1202.000000 1459 88.989667 1 2910 3 chr1B.!!$R1 2909

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
612 652 0.169230 CAGGACTCTCTTCGACACGG 59.831 60.0 0.00 0.0 0.0 4.94 F
770 819 0.390603 TCGTCACGTAGGGCAATTGG 60.391 55.0 7.72 0.0 0.0 3.16 F
780 829 0.620556 GGGCAATTGGAGTCTGGAGA 59.379 55.0 7.72 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1507 1.880340 CTGGAAGTCGGCGATCTGC 60.880 63.158 14.79 10.81 45.38 4.26 R
1753 1850 2.511600 GGCCACGATGAACCTCCG 60.512 66.667 0.00 0.00 0.00 4.63 R
2199 2296 3.321497 CGAAGCTGCAGAACTAGAACTT 58.679 45.455 20.43 8.35 0.00 2.66 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
37 39 1.103398 ACTGTTGCTGCCAAGTGTCC 61.103 55.000 0.00 0.00 0.00 4.02
149 151 6.434028 TCAGATTCAAAACAGGTGATAAAGGG 59.566 38.462 0.00 0.00 0.00 3.95
150 152 5.716703 AGATTCAAAACAGGTGATAAAGGGG 59.283 40.000 0.00 0.00 0.00 4.79
152 154 5.068215 TCAAAACAGGTGATAAAGGGGAA 57.932 39.130 0.00 0.00 0.00 3.97
153 155 4.830600 TCAAAACAGGTGATAAAGGGGAAC 59.169 41.667 0.00 0.00 0.00 3.62
154 156 4.463050 AAACAGGTGATAAAGGGGAACA 57.537 40.909 0.00 0.00 0.00 3.18
155 157 3.721087 ACAGGTGATAAAGGGGAACAG 57.279 47.619 0.00 0.00 0.00 3.16
156 158 2.986728 ACAGGTGATAAAGGGGAACAGT 59.013 45.455 0.00 0.00 0.00 3.55
158 160 4.019591 ACAGGTGATAAAGGGGAACAGTAC 60.020 45.833 0.00 0.00 0.00 2.73
246 267 1.412343 GAGGGGCAAACAAAGAAGCAA 59.588 47.619 0.00 0.00 0.00 3.91
281 302 4.773013 AGTTTACGAACTCTTTGGACCAA 58.227 39.130 1.69 1.69 42.35 3.67
293 314 0.321564 TGGACCAAAGACGCATCCTG 60.322 55.000 0.00 0.00 0.00 3.86
295 316 0.955428 GACCAAAGACGCATCCTGCA 60.955 55.000 0.00 0.00 45.36 4.41
307 328 0.548031 ATCCTGCACATTGATCCGGT 59.452 50.000 0.00 0.00 0.00 5.28
314 335 0.389391 ACATTGATCCGGTAGCGAGG 59.611 55.000 17.33 0.00 0.00 4.63
340 361 0.464735 CTGGTCGAACCACCAAACCA 60.465 55.000 0.00 0.00 44.79 3.67
349 370 2.745968 ACCACCAAACCACACATCTTT 58.254 42.857 0.00 0.00 0.00 2.52
378 400 1.210478 GGAGGTGCTCAGCTTGGATTA 59.790 52.381 0.00 0.00 39.57 1.75
426 448 2.331893 CGGAAATGGCCTCGTGCAA 61.332 57.895 3.32 0.00 43.89 4.08
428 450 0.316841 GGAAATGGCCTCGTGCAAAA 59.683 50.000 3.32 0.00 43.89 2.44
449 471 0.739561 AGTCCTACGATCCGAGCAAC 59.260 55.000 0.00 0.00 0.00 4.17
456 478 1.519719 GATCCGAGCAACTGAGCCT 59.480 57.895 0.00 0.00 34.23 4.58
490 512 5.732647 CCGACTAATAATGCTGAAAAACGTG 59.267 40.000 0.00 0.00 0.00 4.49
493 515 7.201149 CGACTAATAATGCTGAAAAACGTGTTG 60.201 37.037 0.00 0.00 0.00 3.33
532 555 5.129815 GGTGGTATAGTTATGTCTTGGTGGA 59.870 44.000 0.00 0.00 0.00 4.02
570 593 3.738830 GGTATGCCGTGTAATAGGACA 57.261 47.619 0.00 0.00 0.00 4.02
571 594 3.650139 GGTATGCCGTGTAATAGGACAG 58.350 50.000 0.00 0.00 0.00 3.51
572 595 2.910688 ATGCCGTGTAATAGGACAGG 57.089 50.000 0.00 0.00 35.46 4.00
573 596 1.563924 TGCCGTGTAATAGGACAGGT 58.436 50.000 0.00 0.00 34.19 4.00
574 597 1.903860 TGCCGTGTAATAGGACAGGTT 59.096 47.619 0.00 0.00 34.19 3.50
575 598 3.098377 TGCCGTGTAATAGGACAGGTTA 58.902 45.455 0.00 0.00 34.19 2.85
612 652 0.169230 CAGGACTCTCTTCGACACGG 59.831 60.000 0.00 0.00 0.00 4.94
621 661 1.068895 TCTTCGACACGGTAAAGCCAA 59.931 47.619 0.00 0.00 36.97 4.52
622 662 2.073816 CTTCGACACGGTAAAGCCAAT 58.926 47.619 0.00 0.00 36.97 3.16
623 663 1.717194 TCGACACGGTAAAGCCAATC 58.283 50.000 0.00 0.00 36.97 2.67
624 664 1.274167 TCGACACGGTAAAGCCAATCT 59.726 47.619 0.00 0.00 36.97 2.40
625 665 2.073816 CGACACGGTAAAGCCAATCTT 58.926 47.619 0.00 0.00 36.97 2.40
626 666 2.482721 CGACACGGTAAAGCCAATCTTT 59.517 45.455 0.00 0.00 46.17 2.52
627 667 3.058501 CGACACGGTAAAGCCAATCTTTT 60.059 43.478 0.00 0.00 42.06 2.27
628 668 4.555906 CGACACGGTAAAGCCAATCTTTTT 60.556 41.667 0.00 0.00 42.06 1.94
682 722 4.912766 CGCGACCATATCTTCTTAGTTCTC 59.087 45.833 0.00 0.00 0.00 2.87
683 723 5.278071 CGCGACCATATCTTCTTAGTTCTCT 60.278 44.000 0.00 0.00 0.00 3.10
756 805 2.690497 GGAGTCTGGAGATCAATCGTCA 59.310 50.000 0.00 0.00 0.00 4.35
757 806 3.490078 GGAGTCTGGAGATCAATCGTCAC 60.490 52.174 0.00 0.00 0.00 3.67
758 807 2.098280 AGTCTGGAGATCAATCGTCACG 59.902 50.000 0.00 0.00 0.00 4.35
759 808 2.092323 TCTGGAGATCAATCGTCACGT 58.908 47.619 0.00 0.00 0.00 4.49
760 809 3.064958 GTCTGGAGATCAATCGTCACGTA 59.935 47.826 0.00 0.00 0.00 3.57
761 810 3.312697 TCTGGAGATCAATCGTCACGTAG 59.687 47.826 0.00 0.00 0.00 3.51
762 811 2.357952 TGGAGATCAATCGTCACGTAGG 59.642 50.000 0.00 0.00 0.00 3.18
763 812 2.287668 GGAGATCAATCGTCACGTAGGG 60.288 54.545 0.00 0.00 0.00 3.53
764 813 1.067212 AGATCAATCGTCACGTAGGGC 59.933 52.381 0.00 0.00 0.00 5.19
765 814 0.821517 ATCAATCGTCACGTAGGGCA 59.178 50.000 0.00 0.00 0.00 5.36
766 815 0.604073 TCAATCGTCACGTAGGGCAA 59.396 50.000 0.00 0.00 0.00 4.52
767 816 1.206132 TCAATCGTCACGTAGGGCAAT 59.794 47.619 0.00 0.00 0.00 3.56
768 817 2.006888 CAATCGTCACGTAGGGCAATT 58.993 47.619 0.00 0.00 0.00 2.32
769 818 1.651987 ATCGTCACGTAGGGCAATTG 58.348 50.000 0.00 0.00 0.00 2.32
770 819 0.390603 TCGTCACGTAGGGCAATTGG 60.391 55.000 7.72 0.00 0.00 3.16
771 820 0.390603 CGTCACGTAGGGCAATTGGA 60.391 55.000 7.72 0.00 0.00 3.53
772 821 1.369625 GTCACGTAGGGCAATTGGAG 58.630 55.000 7.72 0.00 0.00 3.86
773 822 0.981183 TCACGTAGGGCAATTGGAGT 59.019 50.000 7.72 0.00 0.00 3.85
774 823 1.066430 TCACGTAGGGCAATTGGAGTC 60.066 52.381 7.72 0.00 0.00 3.36
775 824 1.066143 CACGTAGGGCAATTGGAGTCT 60.066 52.381 7.72 0.00 0.00 3.24
776 825 1.066143 ACGTAGGGCAATTGGAGTCTG 60.066 52.381 7.72 0.00 0.00 3.51
777 826 1.743772 CGTAGGGCAATTGGAGTCTGG 60.744 57.143 7.72 0.00 0.00 3.86
778 827 1.559682 GTAGGGCAATTGGAGTCTGGA 59.440 52.381 7.72 0.00 0.00 3.86
779 828 0.622665 AGGGCAATTGGAGTCTGGAG 59.377 55.000 7.72 0.00 0.00 3.86
780 829 0.620556 GGGCAATTGGAGTCTGGAGA 59.379 55.000 7.72 0.00 0.00 3.71
781 830 1.213926 GGGCAATTGGAGTCTGGAGAT 59.786 52.381 7.72 0.00 0.00 2.75
782 831 2.295885 GGCAATTGGAGTCTGGAGATG 58.704 52.381 7.72 0.00 0.00 2.90
783 832 2.092753 GGCAATTGGAGTCTGGAGATGA 60.093 50.000 7.72 0.00 0.00 2.92
784 833 3.614092 GCAATTGGAGTCTGGAGATGAA 58.386 45.455 7.72 0.00 0.00 2.57
785 834 4.205587 GCAATTGGAGTCTGGAGATGAAT 58.794 43.478 7.72 0.00 0.00 2.57
786 835 4.275443 GCAATTGGAGTCTGGAGATGAATC 59.725 45.833 7.72 0.00 0.00 2.52
787 836 3.808466 TTGGAGTCTGGAGATGAATCG 57.192 47.619 0.00 0.00 30.36 3.34
788 837 1.410517 TGGAGTCTGGAGATGAATCGC 59.589 52.381 0.00 0.00 30.36 4.58
789 838 1.270041 GGAGTCTGGAGATGAATCGCC 60.270 57.143 6.16 6.16 45.61 5.54
846 895 2.143008 TGAAGCGCAGAGTCGTAAAA 57.857 45.000 11.47 0.00 0.00 1.52
875 924 1.244816 CCGTATCTATCCGCCTCACA 58.755 55.000 0.00 0.00 0.00 3.58
952 1003 2.900546 CCTCCCCTCCGCCATATATATC 59.099 54.545 0.00 0.00 0.00 1.63
956 1007 2.900546 CCCTCCGCCATATATATCCCTC 59.099 54.545 0.00 0.00 0.00 4.30
961 1012 2.755208 CGCCATATATATCCCTCCCCGA 60.755 54.545 0.00 0.00 0.00 5.14
962 1013 2.633481 GCCATATATATCCCTCCCCGAC 59.367 54.545 0.00 0.00 0.00 4.79
963 1014 3.240302 CCATATATATCCCTCCCCGACC 58.760 54.545 0.00 0.00 0.00 4.79
978 1029 1.224592 GACCCCCTCACGCATCAAT 59.775 57.895 0.00 0.00 0.00 2.57
986 1037 2.286008 CCTCACGCATCAATCACAATCG 60.286 50.000 0.00 0.00 0.00 3.34
1407 1471 3.822192 TCCGGCCTCGACGACATG 61.822 66.667 0.00 0.00 35.20 3.21
1416 1480 2.885644 GACGACATGACCGCGCAT 60.886 61.111 8.75 0.00 0.00 4.73
1434 1498 2.509336 GCCGTCATGGTCTCCACG 60.509 66.667 0.00 0.00 41.21 4.94
1567 1631 3.126514 CGTGACCATGAACTACTACGACT 59.873 47.826 0.00 0.00 32.58 4.18
1660 1756 5.075067 TCCTACATCCAGGTCAGATCTATCA 59.925 44.000 0.00 0.00 36.99 2.15
1673 1769 7.255451 GGTCAGATCTATCATCTTCTTCTCGTT 60.255 40.741 0.00 0.00 0.00 3.85
1694 1790 5.395778 CGTTCACTCAGTTCGTGTATATAGC 59.604 44.000 0.00 0.00 34.14 2.97
1706 1803 7.605410 TCGTGTATATAGCACTGATCGATTA 57.395 36.000 0.00 0.00 34.91 1.75
2112 2209 1.317611 CAGTACATGTTCTTCGACGCG 59.682 52.381 2.30 3.53 0.00 6.01
2184 2281 1.133253 CCACATCGCGCAGTTCAAG 59.867 57.895 8.75 0.00 0.00 3.02
2197 2294 6.198403 CGCGCAGTTCAAGAATTAGTTAGATA 59.802 38.462 8.75 0.00 0.00 1.98
2199 2296 9.193133 GCGCAGTTCAAGAATTAGTTAGATATA 57.807 33.333 0.30 0.00 0.00 0.86
2347 2484 8.893219 AATTCGCTGTGATTATTCAGATAGAA 57.107 30.769 0.00 5.29 41.28 2.10
2372 2510 7.710676 TTTAGACTTCAGATCAGCTCTAGTT 57.289 36.000 0.00 0.00 31.13 2.24
2624 2815 2.559698 TTCCGCAAATTCAGAGTCCA 57.440 45.000 0.00 0.00 0.00 4.02
2627 2818 1.446907 CGCAAATTCAGAGTCCAGCT 58.553 50.000 0.00 0.00 0.00 4.24
2704 2896 5.692814 CCATTCGGCATGTGTGAATATAAG 58.307 41.667 8.29 0.00 31.45 1.73
2717 2913 7.071196 TGTGTGAATATAAGGAGAATGCTAGGT 59.929 37.037 0.00 0.00 33.13 3.08
2765 2961 1.900245 ACATGCATGTCTTGACAGCA 58.100 45.000 26.61 20.84 35.87 4.41
2871 3072 6.309737 GCTTTGAGATTTGATCAATTGGTGTC 59.690 38.462 9.40 5.16 36.60 3.67
2917 3118 5.717078 AGAAAATGCTCAATTCTTCTGCA 57.283 34.783 0.00 0.00 38.05 4.41
2919 3120 3.505464 AATGCTCAATTCTTCTGCAGC 57.495 42.857 9.47 0.00 37.07 5.25
2920 3121 2.195741 TGCTCAATTCTTCTGCAGCT 57.804 45.000 9.47 0.00 0.00 4.24
2922 3123 2.486982 TGCTCAATTCTTCTGCAGCTTC 59.513 45.455 9.47 0.00 0.00 3.86
2923 3124 2.748532 GCTCAATTCTTCTGCAGCTTCT 59.251 45.455 9.47 0.00 0.00 2.85
2924 3125 3.426426 GCTCAATTCTTCTGCAGCTTCTG 60.426 47.826 9.47 1.53 34.12 3.02
2925 3126 3.748083 TCAATTCTTCTGCAGCTTCTGT 58.252 40.909 9.47 0.00 33.43 3.41
2926 3127 4.139786 TCAATTCTTCTGCAGCTTCTGTT 58.860 39.130 9.47 0.00 33.43 3.16
2927 3128 4.023450 TCAATTCTTCTGCAGCTTCTGTTG 60.023 41.667 9.47 9.62 33.43 3.33
2928 3129 2.627515 TCTTCTGCAGCTTCTGTTGT 57.372 45.000 9.47 0.00 33.43 3.32
2929 3130 2.216046 TCTTCTGCAGCTTCTGTTGTG 58.784 47.619 9.47 0.00 33.43 3.33
2930 3131 0.664761 TTCTGCAGCTTCTGTTGTGC 59.335 50.000 9.47 0.00 33.43 4.57
2931 3132 1.082300 CTGCAGCTTCTGTTGTGCG 60.082 57.895 0.00 0.00 38.84 5.34
2932 3133 2.428071 GCAGCTTCTGTTGTGCGC 60.428 61.111 0.00 0.00 33.43 6.09
2933 3134 2.253452 CAGCTTCTGTTGTGCGCC 59.747 61.111 4.18 0.00 0.00 6.53
2934 3135 2.111878 AGCTTCTGTTGTGCGCCT 59.888 55.556 4.18 0.00 0.00 5.52
2935 3136 0.950555 CAGCTTCTGTTGTGCGCCTA 60.951 55.000 4.18 0.00 0.00 3.93
2936 3137 0.671781 AGCTTCTGTTGTGCGCCTAG 60.672 55.000 4.18 0.00 0.00 3.02
2937 3138 0.670546 GCTTCTGTTGTGCGCCTAGA 60.671 55.000 4.18 0.00 0.00 2.43
2938 3139 2.009042 GCTTCTGTTGTGCGCCTAGAT 61.009 52.381 4.18 0.00 0.00 1.98
2939 3140 2.738643 GCTTCTGTTGTGCGCCTAGATA 60.739 50.000 4.18 0.00 0.00 1.98
2940 3141 2.871182 TCTGTTGTGCGCCTAGATAG 57.129 50.000 4.18 0.00 0.00 2.08
2941 3142 2.375146 TCTGTTGTGCGCCTAGATAGA 58.625 47.619 4.18 0.00 0.00 1.98
2942 3143 2.359214 TCTGTTGTGCGCCTAGATAGAG 59.641 50.000 4.18 0.00 0.00 2.43
2943 3144 2.359214 CTGTTGTGCGCCTAGATAGAGA 59.641 50.000 4.18 0.00 0.00 3.10
2944 3145 2.758423 TGTTGTGCGCCTAGATAGAGAA 59.242 45.455 4.18 0.00 0.00 2.87
2945 3146 3.194755 TGTTGTGCGCCTAGATAGAGAAA 59.805 43.478 4.18 0.00 0.00 2.52
2946 3147 3.438297 TGTGCGCCTAGATAGAGAAAC 57.562 47.619 4.18 0.00 0.00 2.78
2947 3148 3.024547 TGTGCGCCTAGATAGAGAAACT 58.975 45.455 4.18 0.00 0.00 2.66
2948 3149 4.204799 TGTGCGCCTAGATAGAGAAACTA 58.795 43.478 4.18 0.00 35.42 2.24
2949 3150 4.643334 TGTGCGCCTAGATAGAGAAACTAA 59.357 41.667 4.18 0.00 34.56 2.24
2950 3151 5.216648 GTGCGCCTAGATAGAGAAACTAAG 58.783 45.833 4.18 0.00 34.56 2.18
2951 3152 4.231439 GCGCCTAGATAGAGAAACTAAGC 58.769 47.826 0.00 0.00 34.56 3.09
2952 3153 4.022676 GCGCCTAGATAGAGAAACTAAGCT 60.023 45.833 0.00 0.00 34.56 3.74
2953 3154 5.695818 CGCCTAGATAGAGAAACTAAGCTC 58.304 45.833 0.00 0.00 34.56 4.09
2954 3155 5.615984 CGCCTAGATAGAGAAACTAAGCTCG 60.616 48.000 0.00 0.00 36.29 5.03
2955 3156 5.239963 GCCTAGATAGAGAAACTAAGCTCGT 59.760 44.000 0.00 0.00 36.29 4.18
2956 3157 6.238814 GCCTAGATAGAGAAACTAAGCTCGTT 60.239 42.308 0.00 0.00 36.29 3.85
2957 3158 7.136119 CCTAGATAGAGAAACTAAGCTCGTTG 58.864 42.308 2.52 0.00 36.29 4.10
2958 3159 6.761099 AGATAGAGAAACTAAGCTCGTTGA 57.239 37.500 2.52 0.00 36.29 3.18
2959 3160 7.341445 AGATAGAGAAACTAAGCTCGTTGAT 57.659 36.000 2.52 0.00 36.29 2.57
2960 3161 8.453238 AGATAGAGAAACTAAGCTCGTTGATA 57.547 34.615 2.52 0.00 36.29 2.15
2961 3162 8.564574 AGATAGAGAAACTAAGCTCGTTGATAG 58.435 37.037 2.52 0.00 36.29 2.08
2962 3163 6.761099 AGAGAAACTAAGCTCGTTGATAGA 57.239 37.500 2.52 0.00 36.29 1.98
2963 3164 7.341445 AGAGAAACTAAGCTCGTTGATAGAT 57.659 36.000 2.52 0.00 36.29 1.98
2964 3165 8.453238 AGAGAAACTAAGCTCGTTGATAGATA 57.547 34.615 2.52 0.00 36.29 1.98
2965 3166 8.347035 AGAGAAACTAAGCTCGTTGATAGATAC 58.653 37.037 2.52 0.00 36.29 2.24
2966 3167 7.997482 AGAAACTAAGCTCGTTGATAGATACA 58.003 34.615 2.52 0.00 0.00 2.29
2967 3168 8.132362 AGAAACTAAGCTCGTTGATAGATACAG 58.868 37.037 2.52 0.00 0.00 2.74
2968 3169 6.320494 ACTAAGCTCGTTGATAGATACAGG 57.680 41.667 0.00 0.00 0.00 4.00
2969 3170 6.062749 ACTAAGCTCGTTGATAGATACAGGA 58.937 40.000 0.00 0.00 0.00 3.86
2970 3171 6.717540 ACTAAGCTCGTTGATAGATACAGGAT 59.282 38.462 0.00 0.00 0.00 3.24
2971 3172 6.412362 AAGCTCGTTGATAGATACAGGATT 57.588 37.500 0.00 0.00 0.00 3.01
2972 3173 7.526142 AAGCTCGTTGATAGATACAGGATTA 57.474 36.000 0.00 0.00 0.00 1.75
2973 3174 7.710676 AGCTCGTTGATAGATACAGGATTAT 57.289 36.000 0.00 0.00 0.00 1.28
2974 3175 8.128322 AGCTCGTTGATAGATACAGGATTATT 57.872 34.615 0.00 0.00 0.00 1.40
2975 3176 9.244292 AGCTCGTTGATAGATACAGGATTATTA 57.756 33.333 0.00 0.00 0.00 0.98
2976 3177 9.856488 GCTCGTTGATAGATACAGGATTATTAA 57.144 33.333 0.00 0.00 0.00 1.40
3001 3202 9.696572 AACAGAGTAGATTAGGTATACAGTTCA 57.303 33.333 5.01 0.00 0.00 3.18
3002 3203 9.344772 ACAGAGTAGATTAGGTATACAGTTCAG 57.655 37.037 5.01 0.00 0.00 3.02
3003 3204 9.562408 CAGAGTAGATTAGGTATACAGTTCAGA 57.438 37.037 5.01 0.00 0.00 3.27
3013 3214 8.498054 AGGTATACAGTTCAGATGAAAATGTG 57.502 34.615 18.15 8.50 37.06 3.21
3014 3215 7.066284 AGGTATACAGTTCAGATGAAAATGTGC 59.934 37.037 18.15 11.33 37.06 4.57
3015 3216 7.066284 GGTATACAGTTCAGATGAAAATGTGCT 59.934 37.037 18.15 11.34 37.06 4.40
3016 3217 5.779529 ACAGTTCAGATGAAAATGTGCTT 57.220 34.783 11.74 0.00 35.91 3.91
3017 3218 5.766222 ACAGTTCAGATGAAAATGTGCTTC 58.234 37.500 11.74 0.00 35.91 3.86
3018 3219 5.300034 ACAGTTCAGATGAAAATGTGCTTCA 59.700 36.000 11.74 0.00 35.91 3.02
3019 3220 6.015688 ACAGTTCAGATGAAAATGTGCTTCAT 60.016 34.615 11.74 0.00 44.34 2.57
3020 3221 7.175467 ACAGTTCAGATGAAAATGTGCTTCATA 59.825 33.333 11.74 0.00 42.27 2.15
3021 3222 7.484007 CAGTTCAGATGAAAATGTGCTTCATAC 59.516 37.037 0.00 0.00 42.27 2.39
3022 3223 7.175467 AGTTCAGATGAAAATGTGCTTCATACA 59.825 33.333 0.00 0.00 42.27 2.29
3023 3224 7.634671 TCAGATGAAAATGTGCTTCATACAT 57.365 32.000 0.00 0.00 42.27 2.29
3024 3225 8.735692 TCAGATGAAAATGTGCTTCATACATA 57.264 30.769 0.00 0.00 42.27 2.29
3025 3226 9.346005 TCAGATGAAAATGTGCTTCATACATAT 57.654 29.630 0.00 0.79 42.27 1.78
3026 3227 9.608617 CAGATGAAAATGTGCTTCATACATATC 57.391 33.333 0.00 0.00 42.27 1.63
3027 3228 9.346005 AGATGAAAATGTGCTTCATACATATCA 57.654 29.630 0.00 0.00 42.27 2.15
3028 3229 9.955208 GATGAAAATGTGCTTCATACATATCAA 57.045 29.630 0.00 0.00 42.27 2.57
3029 3230 9.740239 ATGAAAATGTGCTTCATACATATCAAC 57.260 29.630 0.00 0.00 40.82 3.18
3030 3231 8.738106 TGAAAATGTGCTTCATACATATCAACA 58.262 29.630 0.00 0.00 37.77 3.33
3031 3232 8.915871 AAAATGTGCTTCATACATATCAACAC 57.084 30.769 0.00 0.00 37.77 3.32
3032 3233 7.628769 AATGTGCTTCATACATATCAACACA 57.371 32.000 0.00 0.00 37.77 3.72
3033 3234 7.628769 ATGTGCTTCATACATATCAACACAA 57.371 32.000 0.00 0.00 38.80 3.33
3034 3235 7.075674 TGTGCTTCATACATATCAACACAAG 57.924 36.000 0.00 0.00 32.99 3.16
3042 3243 9.030301 TCATACATATCAACACAAGTCAATACG 57.970 33.333 0.00 0.00 0.00 3.06
3053 3254 6.371548 ACACAAGTCAATACGCTGTAATCATT 59.628 34.615 0.00 0.00 0.00 2.57
3080 3281 8.243426 CAGATATAGTTCAGATCAGCTTCTACC 58.757 40.741 0.00 0.00 0.00 3.18
3094 3295 4.164988 AGCTTCTACCCACAAATAGCAGAT 59.835 41.667 0.00 0.00 0.00 2.90
3103 3304 4.365723 CACAAATAGCAGATTGGATTGGC 58.634 43.478 0.00 0.00 0.00 4.52
3106 3307 3.870538 ATAGCAGATTGGATTGGCTCA 57.129 42.857 0.00 0.00 36.10 4.26
3107 3308 2.054232 AGCAGATTGGATTGGCTCAG 57.946 50.000 0.00 0.00 0.00 3.35
3108 3309 1.562942 AGCAGATTGGATTGGCTCAGA 59.437 47.619 0.00 0.00 0.00 3.27
3110 3311 2.957006 GCAGATTGGATTGGCTCAGATT 59.043 45.455 0.00 0.00 0.00 2.40
3111 3312 4.139786 GCAGATTGGATTGGCTCAGATTA 58.860 43.478 0.00 0.00 0.00 1.75
3112 3313 4.765856 GCAGATTGGATTGGCTCAGATTAT 59.234 41.667 0.00 0.00 0.00 1.28
3113 3314 5.243283 GCAGATTGGATTGGCTCAGATTATT 59.757 40.000 0.00 0.00 0.00 1.40
3116 3317 8.202137 CAGATTGGATTGGCTCAGATTATTTTT 58.798 33.333 0.00 0.00 0.00 1.94
3158 3550 8.668510 AGTATAACAGCATTCTACAAATGGAG 57.331 34.615 0.45 0.00 0.00 3.86
3160 3552 9.109393 GTATAACAGCATTCTACAAATGGAGAA 57.891 33.333 10.38 10.38 36.18 2.87
3166 3558 8.084073 CAGCATTCTACAAATGGAGAAGAAAAA 58.916 33.333 13.21 0.00 35.24 1.94
3167 3559 8.810041 AGCATTCTACAAATGGAGAAGAAAAAT 58.190 29.630 13.21 0.00 35.24 1.82
3181 3573 9.455847 GGAGAAGAAAAATAAATCATCGATTGG 57.544 33.333 0.00 0.00 32.14 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 1.101049 ACGTTTGGGACACTTGGCAG 61.101 55.000 0.00 0.00 39.29 4.85
31 33 1.594293 CTGCGACGTTTGGGACACT 60.594 57.895 0.00 0.00 39.29 3.55
37 39 1.442520 CCAATGCTGCGACGTTTGG 60.443 57.895 0.00 0.00 0.00 3.28
149 151 4.009675 TGATGATGCAAAGGTACTGTTCC 58.990 43.478 0.00 0.00 40.86 3.62
150 152 5.392380 CCTTGATGATGCAAAGGTACTGTTC 60.392 44.000 6.03 0.00 40.86 3.18
152 154 4.012374 CCTTGATGATGCAAAGGTACTGT 58.988 43.478 6.03 0.00 40.86 3.55
153 155 4.264253 TCCTTGATGATGCAAAGGTACTG 58.736 43.478 12.70 0.00 40.86 2.74
154 156 5.104193 ATCTCCTTGATGATGCAAAGGTACT 60.104 40.000 12.70 0.00 34.74 2.73
155 157 4.517285 TCTCCTTGATGATGCAAAGGTAC 58.483 43.478 12.70 0.00 0.00 3.34
156 158 4.842531 TCTCCTTGATGATGCAAAGGTA 57.157 40.909 12.70 2.06 0.00 3.08
179 200 3.313526 TGAAGAAAGTTGCTCAGTGCTTC 59.686 43.478 0.00 0.00 43.37 3.86
186 207 9.598517 AAATTTACAATTGAAGAAAGTTGCTCA 57.401 25.926 13.59 0.00 0.00 4.26
188 209 9.598517 TCAAATTTACAATTGAAGAAAGTTGCT 57.401 25.926 24.03 2.78 37.00 3.91
246 267 8.468399 AGAGTTCGTAAACTTAGCTAAGCTATT 58.532 33.333 29.39 22.99 45.80 1.73
293 314 0.529773 TCGCTACCGGATCAATGTGC 60.530 55.000 9.46 0.00 34.56 4.57
295 316 0.389391 CCTCGCTACCGGATCAATGT 59.611 55.000 9.46 0.00 34.56 2.71
349 370 0.260230 TGAGCACCTCCCACCAAAAA 59.740 50.000 0.00 0.00 0.00 1.94
378 400 1.341080 CAACCTCCTTTGCACCCAAT 58.659 50.000 0.00 0.00 0.00 3.16
426 448 3.220110 TGCTCGGATCGTAGGACTATTT 58.780 45.455 0.00 0.00 0.00 1.40
428 450 2.553172 GTTGCTCGGATCGTAGGACTAT 59.447 50.000 0.00 0.00 0.00 2.12
449 471 0.745845 CGGAATGTGGGAAGGCTCAG 60.746 60.000 0.00 0.00 0.00 3.35
456 478 4.819630 GCATTATTAGTCGGAATGTGGGAA 59.180 41.667 0.00 0.00 33.88 3.97
490 512 4.202111 ACCACCTCTGTAACAAAATGCAAC 60.202 41.667 0.00 0.00 0.00 4.17
493 515 5.897377 ATACCACCTCTGTAACAAAATGC 57.103 39.130 0.00 0.00 0.00 3.56
567 590 8.986847 GTTAAGTTTAACTTCCTCTAACCTGTC 58.013 37.037 14.03 0.00 39.51 3.51
570 593 8.155510 CCTGTTAAGTTTAACTTCCTCTAACCT 58.844 37.037 14.03 0.00 42.61 3.50
571 594 8.152898 TCCTGTTAAGTTTAACTTCCTCTAACC 58.847 37.037 14.03 0.00 42.61 2.85
572 595 8.986847 GTCCTGTTAAGTTTAACTTCCTCTAAC 58.013 37.037 14.03 12.42 42.61 2.34
573 596 8.931568 AGTCCTGTTAAGTTTAACTTCCTCTAA 58.068 33.333 14.03 0.00 42.61 2.10
574 597 8.488308 AGTCCTGTTAAGTTTAACTTCCTCTA 57.512 34.615 14.03 0.00 42.61 2.43
575 598 7.290481 AGAGTCCTGTTAAGTTTAACTTCCTCT 59.710 37.037 14.03 10.61 42.61 3.69
635 675 0.950116 GACGGGGAAGATCGTACGAT 59.050 55.000 29.79 29.79 39.88 3.73
636 676 1.097547 GGACGGGGAAGATCGTACGA 61.098 60.000 21.93 21.93 39.88 3.43
637 677 1.099879 AGGACGGGGAAGATCGTACG 61.100 60.000 9.53 9.53 44.20 3.67
638 678 1.109609 AAGGACGGGGAAGATCGTAC 58.890 55.000 0.00 0.00 39.88 3.67
639 679 1.108776 CAAGGACGGGGAAGATCGTA 58.891 55.000 0.00 0.00 39.88 3.43
640 680 1.898154 CAAGGACGGGGAAGATCGT 59.102 57.895 0.00 0.00 42.67 3.73
641 681 1.521681 GCAAGGACGGGGAAGATCG 60.522 63.158 0.00 0.00 0.00 3.69
642 682 1.521681 CGCAAGGACGGGGAAGATC 60.522 63.158 0.00 0.00 0.00 2.75
756 805 1.066143 CAGACTCCAATTGCCCTACGT 60.066 52.381 0.00 0.00 0.00 3.57
757 806 1.656652 CAGACTCCAATTGCCCTACG 58.343 55.000 0.00 0.00 0.00 3.51
758 807 1.559682 TCCAGACTCCAATTGCCCTAC 59.440 52.381 0.00 0.00 0.00 3.18
759 808 1.839994 CTCCAGACTCCAATTGCCCTA 59.160 52.381 0.00 0.00 0.00 3.53
760 809 0.622665 CTCCAGACTCCAATTGCCCT 59.377 55.000 0.00 0.00 0.00 5.19
761 810 0.620556 TCTCCAGACTCCAATTGCCC 59.379 55.000 0.00 0.00 0.00 5.36
762 811 2.092753 TCATCTCCAGACTCCAATTGCC 60.093 50.000 0.00 0.00 0.00 4.52
763 812 3.272574 TCATCTCCAGACTCCAATTGC 57.727 47.619 0.00 0.00 0.00 3.56
764 813 4.510711 CGATTCATCTCCAGACTCCAATTG 59.489 45.833 0.00 0.00 0.00 2.32
765 814 4.701765 CGATTCATCTCCAGACTCCAATT 58.298 43.478 0.00 0.00 0.00 2.32
766 815 3.494048 GCGATTCATCTCCAGACTCCAAT 60.494 47.826 0.00 0.00 0.00 3.16
767 816 2.159043 GCGATTCATCTCCAGACTCCAA 60.159 50.000 0.00 0.00 0.00 3.53
768 817 1.410517 GCGATTCATCTCCAGACTCCA 59.589 52.381 0.00 0.00 0.00 3.86
769 818 1.270041 GGCGATTCATCTCCAGACTCC 60.270 57.143 0.00 0.00 32.04 3.85
770 819 1.270041 GGGCGATTCATCTCCAGACTC 60.270 57.143 0.00 0.00 33.37 3.36
771 820 0.755686 GGGCGATTCATCTCCAGACT 59.244 55.000 0.00 0.00 33.37 3.24
772 821 0.465705 TGGGCGATTCATCTCCAGAC 59.534 55.000 0.00 0.00 33.37 3.51
773 822 0.755079 CTGGGCGATTCATCTCCAGA 59.245 55.000 15.52 0.00 42.87 3.86
774 823 0.755079 TCTGGGCGATTCATCTCCAG 59.245 55.000 14.88 14.88 42.24 3.86
775 824 1.134401 GTTCTGGGCGATTCATCTCCA 60.134 52.381 0.00 0.00 33.37 3.86
776 825 1.587547 GTTCTGGGCGATTCATCTCC 58.412 55.000 0.00 0.00 0.00 3.71
777 826 1.587547 GGTTCTGGGCGATTCATCTC 58.412 55.000 0.00 0.00 0.00 2.75
778 827 0.179073 CGGTTCTGGGCGATTCATCT 60.179 55.000 0.00 0.00 0.00 2.90
779 828 0.462047 ACGGTTCTGGGCGATTCATC 60.462 55.000 0.00 0.00 0.00 2.92
780 829 0.035439 AACGGTTCTGGGCGATTCAT 60.035 50.000 0.00 0.00 0.00 2.57
781 830 0.609151 TAACGGTTCTGGGCGATTCA 59.391 50.000 0.00 0.00 0.00 2.57
782 831 1.004595 GTAACGGTTCTGGGCGATTC 58.995 55.000 0.00 0.00 0.00 2.52
783 832 0.322322 TGTAACGGTTCTGGGCGATT 59.678 50.000 0.00 0.00 0.00 3.34
784 833 0.108329 CTGTAACGGTTCTGGGCGAT 60.108 55.000 0.00 0.00 0.00 4.58
785 834 1.180456 TCTGTAACGGTTCTGGGCGA 61.180 55.000 0.00 0.00 0.00 5.54
786 835 0.108329 ATCTGTAACGGTTCTGGGCG 60.108 55.000 0.00 0.00 0.00 6.13
787 836 2.429610 TCTATCTGTAACGGTTCTGGGC 59.570 50.000 0.00 0.00 0.00 5.36
788 837 4.730949 TTCTATCTGTAACGGTTCTGGG 57.269 45.455 0.00 0.00 0.00 4.45
789 838 7.611213 AATTTTCTATCTGTAACGGTTCTGG 57.389 36.000 0.00 0.00 0.00 3.86
846 895 2.352814 GGATAGATACGGCTGCAACGAT 60.353 50.000 16.24 6.35 34.93 3.73
875 924 4.872124 AGGTTTGAAGTTTAAACGACGACT 59.128 37.500 14.84 5.50 38.57 4.18
961 1012 1.224592 GATTGATGCGTGAGGGGGT 59.775 57.895 0.00 0.00 0.00 4.95
962 1013 1.097547 GTGATTGATGCGTGAGGGGG 61.098 60.000 0.00 0.00 0.00 5.40
963 1014 0.392863 TGTGATTGATGCGTGAGGGG 60.393 55.000 0.00 0.00 0.00 4.79
973 1024 2.742774 TCGATCGCGATTGTGATTGAT 58.257 42.857 30.40 3.61 46.01 2.57
1263 1327 1.375908 GGTGATGAGCTTGCCGTCA 60.376 57.895 0.00 0.00 0.00 4.35
1416 1480 2.662596 GTGGAGACCATGACGGCA 59.337 61.111 0.00 0.00 39.03 5.69
1434 1498 3.290619 GCGATCTGCGACGAGAAC 58.709 61.111 0.00 0.00 44.57 3.01
1443 1507 1.880340 CTGGAAGTCGGCGATCTGC 60.880 63.158 14.79 10.81 45.38 4.26
1660 1756 5.461032 AACTGAGTGAACGAGAAGAAGAT 57.539 39.130 0.00 0.00 0.00 2.40
1673 1769 5.589050 AGTGCTATATACACGAACTGAGTGA 59.411 40.000 3.20 0.00 42.94 3.41
1694 1790 5.536554 AGTTGCTTGTTAATCGATCAGTG 57.463 39.130 0.00 0.00 0.00 3.66
1706 1803 5.415389 TGCATGTCATGTATAGTTGCTTGTT 59.585 36.000 14.26 0.00 0.00 2.83
1753 1850 2.511600 GGCCACGATGAACCTCCG 60.512 66.667 0.00 0.00 0.00 4.63
2197 2294 5.105752 CGAAGCTGCAGAACTAGAACTTAT 58.894 41.667 20.43 0.00 0.00 1.73
2199 2296 3.321497 CGAAGCTGCAGAACTAGAACTT 58.679 45.455 20.43 8.35 0.00 2.66
2318 2436 8.668510 ATCTGAATAATCACAGCGAATTAACT 57.331 30.769 0.00 0.00 34.57 2.24
2347 2484 7.896383 ACTAGAGCTGATCTGAAGTCTAAAT 57.104 36.000 5.55 0.00 39.20 1.40
2372 2510 8.659527 TCTGAACCAATCCAATCTGCTATTATA 58.340 33.333 0.00 0.00 0.00 0.98
2473 2622 3.435566 TCGATGATGAGCGTTTCAGTAC 58.564 45.455 0.00 0.00 39.68 2.73
2627 2818 5.755375 GCTAACAATGAAGTAGCAGCTGATA 59.245 40.000 20.43 14.08 34.22 2.15
2729 2925 7.975616 ACATGCATGTCATACTTTGATTTTACC 59.024 33.333 26.61 0.00 35.87 2.85
2765 2961 4.240096 CTGATTTTTCTTGCCGCAATCTT 58.760 39.130 6.19 0.00 0.00 2.40
2850 3046 4.395854 CCGACACCAATTGATCAAATCTCA 59.604 41.667 13.09 0.00 0.00 3.27
2851 3047 4.396166 ACCGACACCAATTGATCAAATCTC 59.604 41.667 13.09 1.21 0.00 2.75
2852 3048 4.156556 CACCGACACCAATTGATCAAATCT 59.843 41.667 13.09 0.00 0.00 2.40
2853 3049 4.155826 TCACCGACACCAATTGATCAAATC 59.844 41.667 13.09 3.17 0.00 2.17
2854 3050 4.078537 TCACCGACACCAATTGATCAAAT 58.921 39.130 13.09 0.02 0.00 2.32
2871 3072 6.925610 TCTTTTCCTGAAATATCATCACCG 57.074 37.500 0.00 0.00 34.37 4.94
2913 3114 1.082300 CGCACAACAGAAGCTGCAG 60.082 57.895 10.11 10.11 34.37 4.41
2914 3115 3.024784 CGCACAACAGAAGCTGCA 58.975 55.556 1.02 0.00 34.37 4.41
2915 3116 2.428071 GCGCACAACAGAAGCTGC 60.428 61.111 0.30 0.00 34.37 5.25
2916 3117 0.950555 TAGGCGCACAACAGAAGCTG 60.951 55.000 10.83 0.00 37.52 4.24
2917 3118 0.671781 CTAGGCGCACAACAGAAGCT 60.672 55.000 10.83 0.00 0.00 3.74
2919 3120 2.015736 ATCTAGGCGCACAACAGAAG 57.984 50.000 10.83 0.00 0.00 2.85
2920 3121 2.758423 TCTATCTAGGCGCACAACAGAA 59.242 45.455 10.83 0.00 0.00 3.02
2922 3123 2.359214 TCTCTATCTAGGCGCACAACAG 59.641 50.000 10.83 0.00 0.00 3.16
2923 3124 2.375146 TCTCTATCTAGGCGCACAACA 58.625 47.619 10.83 0.00 0.00 3.33
2924 3125 3.438297 TTCTCTATCTAGGCGCACAAC 57.562 47.619 10.83 0.00 0.00 3.32
2925 3126 3.447586 AGTTTCTCTATCTAGGCGCACAA 59.552 43.478 10.83 0.00 0.00 3.33
2926 3127 3.024547 AGTTTCTCTATCTAGGCGCACA 58.975 45.455 10.83 0.00 0.00 4.57
2927 3128 3.719173 AGTTTCTCTATCTAGGCGCAC 57.281 47.619 10.83 0.00 0.00 5.34
2928 3129 4.261656 GCTTAGTTTCTCTATCTAGGCGCA 60.262 45.833 10.83 0.00 29.98 6.09
2929 3130 4.022676 AGCTTAGTTTCTCTATCTAGGCGC 60.023 45.833 0.00 0.00 40.18 6.53
2930 3131 5.615984 CGAGCTTAGTTTCTCTATCTAGGCG 60.616 48.000 0.00 0.00 40.18 5.52
2931 3132 5.239963 ACGAGCTTAGTTTCTCTATCTAGGC 59.760 44.000 0.00 0.00 37.15 3.93
2932 3133 6.870971 ACGAGCTTAGTTTCTCTATCTAGG 57.129 41.667 0.00 0.00 0.00 3.02
2933 3134 7.921787 TCAACGAGCTTAGTTTCTCTATCTAG 58.078 38.462 5.88 0.00 0.00 2.43
2934 3135 7.860918 TCAACGAGCTTAGTTTCTCTATCTA 57.139 36.000 5.88 0.00 0.00 1.98
2935 3136 6.761099 TCAACGAGCTTAGTTTCTCTATCT 57.239 37.500 5.88 0.00 0.00 1.98
2936 3137 8.561212 TCTATCAACGAGCTTAGTTTCTCTATC 58.439 37.037 5.88 0.00 0.00 2.08
2937 3138 8.453238 TCTATCAACGAGCTTAGTTTCTCTAT 57.547 34.615 5.88 0.33 0.00 1.98
2938 3139 7.860918 TCTATCAACGAGCTTAGTTTCTCTA 57.139 36.000 5.88 0.00 0.00 2.43
2939 3140 6.761099 TCTATCAACGAGCTTAGTTTCTCT 57.239 37.500 5.88 0.00 0.00 3.10
2940 3141 8.129840 TGTATCTATCAACGAGCTTAGTTTCTC 58.870 37.037 5.88 0.00 0.00 2.87
2941 3142 7.997482 TGTATCTATCAACGAGCTTAGTTTCT 58.003 34.615 5.88 0.74 0.00 2.52
2942 3143 7.380065 CCTGTATCTATCAACGAGCTTAGTTTC 59.620 40.741 5.88 0.00 0.00 2.78
2943 3144 7.068348 TCCTGTATCTATCAACGAGCTTAGTTT 59.932 37.037 5.88 0.00 0.00 2.66
2944 3145 6.546403 TCCTGTATCTATCAACGAGCTTAGTT 59.454 38.462 3.10 3.10 0.00 2.24
2945 3146 6.062749 TCCTGTATCTATCAACGAGCTTAGT 58.937 40.000 0.00 0.00 0.00 2.24
2946 3147 6.561737 TCCTGTATCTATCAACGAGCTTAG 57.438 41.667 0.00 0.00 0.00 2.18
2947 3148 7.526142 AATCCTGTATCTATCAACGAGCTTA 57.474 36.000 0.00 0.00 0.00 3.09
2948 3149 6.412362 AATCCTGTATCTATCAACGAGCTT 57.588 37.500 0.00 0.00 0.00 3.74
2949 3150 7.710676 ATAATCCTGTATCTATCAACGAGCT 57.289 36.000 0.00 0.00 0.00 4.09
2950 3151 9.856488 TTAATAATCCTGTATCTATCAACGAGC 57.144 33.333 0.00 0.00 0.00 5.03
2975 3176 9.696572 TGAACTGTATACCTAATCTACTCTGTT 57.303 33.333 0.00 0.00 0.00 3.16
2976 3177 9.344772 CTGAACTGTATACCTAATCTACTCTGT 57.655 37.037 0.00 0.00 0.00 3.41
2977 3178 9.562408 TCTGAACTGTATACCTAATCTACTCTG 57.438 37.037 0.00 0.00 0.00 3.35
2987 3188 9.599866 CACATTTTCATCTGAACTGTATACCTA 57.400 33.333 0.00 0.00 32.30 3.08
2988 3189 7.066284 GCACATTTTCATCTGAACTGTATACCT 59.934 37.037 0.00 0.00 32.30 3.08
2989 3190 7.066284 AGCACATTTTCATCTGAACTGTATACC 59.934 37.037 0.00 0.00 32.30 2.73
2990 3191 7.978982 AGCACATTTTCATCTGAACTGTATAC 58.021 34.615 0.00 0.00 32.30 1.47
2991 3192 8.565896 AAGCACATTTTCATCTGAACTGTATA 57.434 30.769 6.89 0.00 32.30 1.47
2992 3193 7.175467 TGAAGCACATTTTCATCTGAACTGTAT 59.825 33.333 6.89 0.00 32.30 2.29
2993 3194 6.486320 TGAAGCACATTTTCATCTGAACTGTA 59.514 34.615 6.89 0.00 32.30 2.74
2994 3195 5.300034 TGAAGCACATTTTCATCTGAACTGT 59.700 36.000 0.00 0.00 33.18 3.55
2995 3196 5.765176 TGAAGCACATTTTCATCTGAACTG 58.235 37.500 0.00 0.00 33.13 3.16
2996 3197 6.585695 ATGAAGCACATTTTCATCTGAACT 57.414 33.333 0.00 0.00 40.31 3.01
2997 3198 7.307694 TGTATGAAGCACATTTTCATCTGAAC 58.692 34.615 3.95 0.00 42.58 3.18
2998 3199 7.451501 TGTATGAAGCACATTTTCATCTGAA 57.548 32.000 3.95 0.00 42.58 3.02
2999 3200 7.634671 ATGTATGAAGCACATTTTCATCTGA 57.365 32.000 3.95 0.00 42.58 3.27
3000 3201 9.608617 GATATGTATGAAGCACATTTTCATCTG 57.391 33.333 3.95 0.00 42.58 2.90
3001 3202 9.346005 TGATATGTATGAAGCACATTTTCATCT 57.654 29.630 3.95 0.41 42.58 2.90
3002 3203 9.955208 TTGATATGTATGAAGCACATTTTCATC 57.045 29.630 3.95 0.00 42.58 2.92
3003 3204 9.740239 GTTGATATGTATGAAGCACATTTTCAT 57.260 29.630 5.86 5.86 44.86 2.57
3004 3205 8.738106 TGTTGATATGTATGAAGCACATTTTCA 58.262 29.630 2.03 0.00 40.07 2.69
3005 3206 9.013490 GTGTTGATATGTATGAAGCACATTTTC 57.987 33.333 2.03 0.00 40.07 2.29
3006 3207 8.522003 TGTGTTGATATGTATGAAGCACATTTT 58.478 29.630 2.03 0.00 40.07 1.82
3007 3208 8.054152 TGTGTTGATATGTATGAAGCACATTT 57.946 30.769 2.03 0.00 40.07 2.32
3008 3209 7.628769 TGTGTTGATATGTATGAAGCACATT 57.371 32.000 2.03 0.00 40.07 2.71
3009 3210 7.337689 ACTTGTGTTGATATGTATGAAGCACAT 59.662 33.333 0.00 2.31 42.39 3.21
3010 3211 6.654582 ACTTGTGTTGATATGTATGAAGCACA 59.345 34.615 0.00 0.00 33.33 4.57
3011 3212 7.076842 ACTTGTGTTGATATGTATGAAGCAC 57.923 36.000 0.00 0.00 0.00 4.40
3012 3213 6.878389 TGACTTGTGTTGATATGTATGAAGCA 59.122 34.615 0.00 0.00 0.00 3.91
3013 3214 7.307493 TGACTTGTGTTGATATGTATGAAGC 57.693 36.000 0.00 0.00 0.00 3.86
3016 3217 9.030301 CGTATTGACTTGTGTTGATATGTATGA 57.970 33.333 0.00 0.00 0.00 2.15
3017 3218 7.793888 GCGTATTGACTTGTGTTGATATGTATG 59.206 37.037 0.00 0.00 0.00 2.39
3018 3219 7.710907 AGCGTATTGACTTGTGTTGATATGTAT 59.289 33.333 0.00 0.00 0.00 2.29
3019 3220 7.010091 CAGCGTATTGACTTGTGTTGATATGTA 59.990 37.037 0.00 0.00 0.00 2.29
3020 3221 5.874810 AGCGTATTGACTTGTGTTGATATGT 59.125 36.000 0.00 0.00 0.00 2.29
3021 3222 6.183360 ACAGCGTATTGACTTGTGTTGATATG 60.183 38.462 0.00 0.00 0.00 1.78
3022 3223 5.874810 ACAGCGTATTGACTTGTGTTGATAT 59.125 36.000 0.00 0.00 0.00 1.63
3023 3224 5.234752 ACAGCGTATTGACTTGTGTTGATA 58.765 37.500 0.00 0.00 0.00 2.15
3024 3225 4.065088 ACAGCGTATTGACTTGTGTTGAT 58.935 39.130 0.00 0.00 0.00 2.57
3025 3226 3.462982 ACAGCGTATTGACTTGTGTTGA 58.537 40.909 0.00 0.00 0.00 3.18
3026 3227 3.878086 ACAGCGTATTGACTTGTGTTG 57.122 42.857 0.00 0.00 0.00 3.33
3027 3228 5.699001 TGATTACAGCGTATTGACTTGTGTT 59.301 36.000 0.00 0.00 0.00 3.32
3028 3229 5.234752 TGATTACAGCGTATTGACTTGTGT 58.765 37.500 0.00 0.00 0.00 3.72
3029 3230 5.778161 TGATTACAGCGTATTGACTTGTG 57.222 39.130 0.00 0.00 0.00 3.33
3030 3231 6.593770 TGAATGATTACAGCGTATTGACTTGT 59.406 34.615 0.00 0.00 0.00 3.16
3031 3232 7.003939 TGAATGATTACAGCGTATTGACTTG 57.996 36.000 0.00 0.00 0.00 3.16
3032 3233 7.041721 TCTGAATGATTACAGCGTATTGACTT 58.958 34.615 0.00 0.00 34.57 3.01
3033 3234 6.573434 TCTGAATGATTACAGCGTATTGACT 58.427 36.000 0.00 0.00 34.57 3.41
3034 3235 6.828502 TCTGAATGATTACAGCGTATTGAC 57.171 37.500 0.00 0.00 34.57 3.18
3040 3241 8.360390 TGAACTATATCTGAATGATTACAGCGT 58.640 33.333 0.00 0.00 36.65 5.07
3042 3243 9.920133 TCTGAACTATATCTGAATGATTACAGC 57.080 33.333 0.00 0.00 36.65 4.40
3053 3254 9.008965 GTAGAAGCTGATCTGAACTATATCTGA 57.991 37.037 3.42 0.00 0.00 3.27
3080 3281 4.738541 GCCAATCCAATCTGCTATTTGTGG 60.739 45.833 0.00 0.00 0.00 4.17
3133 3379 8.486210 TCTCCATTTGTAGAATGCTGTTATACT 58.514 33.333 8.10 0.00 0.00 2.12
3135 3381 9.330063 CTTCTCCATTTGTAGAATGCTGTTATA 57.670 33.333 0.00 0.00 31.60 0.98
3136 3382 8.049117 TCTTCTCCATTTGTAGAATGCTGTTAT 58.951 33.333 0.00 0.00 31.60 1.89
3139 3385 5.809001 TCTTCTCCATTTGTAGAATGCTGT 58.191 37.500 0.00 0.00 31.60 4.40
3141 3387 7.765695 TTTTCTTCTCCATTTGTAGAATGCT 57.234 32.000 0.00 0.00 31.60 3.79
3142 3388 8.992835 ATTTTTCTTCTCCATTTGTAGAATGC 57.007 30.769 0.00 0.00 31.60 3.56


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

AutoCloner maintained by Alex Coulton.