Multiple sequence alignment - TraesCS5D01G263900

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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 TraesCS5D01G263900 chr5D 100.000 3562 0 0 1 3562 369139199 369142760 0.000000e+00 6578
1 TraesCS5D01G263900 chr5D 77.955 313 53 12 62 369 445091266 445090965 7.860000e-42 182
2 TraesCS5D01G263900 chr5A 95.493 2685 70 19 897 3560 471299449 471296795 0.000000e+00 4241
3 TraesCS5D01G263900 chr5A 95.480 708 22 4 59 762 471300615 471299914 0.000000e+00 1122
4 TraesCS5D01G263900 chr5A 85.860 587 71 9 2981 3562 674542390 674542969 6.540000e-172 614
5 TraesCS5D01G263900 chr3A 88.034 585 58 10 2979 3560 36081904 36082479 0.000000e+00 682
6 TraesCS5D01G263900 chr3A 86.054 588 72 10 2981 3560 328930940 328930355 1.090000e-174 623
7 TraesCS5D01G263900 chr3A 85.886 581 68 11 2984 3560 96228954 96228384 1.090000e-169 606
8 TraesCS5D01G263900 chr3A 84.536 194 26 3 66 256 552565994 552566186 4.690000e-44 189
9 TraesCS5D01G263900 chr3A 96.610 59 2 0 1 59 654237378 654237320 8.140000e-17 99
10 TraesCS5D01G263900 chr6D 87.223 587 64 7 2976 3560 448819703 448820280 0.000000e+00 658
11 TraesCS5D01G263900 chr6D 78.165 316 53 12 59 369 104068197 104068501 1.690000e-43 187
12 TraesCS5D01G263900 chr7D 86.757 589 67 10 2979 3560 529605341 529604757 0.000000e+00 645
13 TraesCS5D01G263900 chr7D 80.408 245 34 11 116 357 202041167 202041400 1.310000e-39 174
14 TraesCS5D01G263900 chr4A 86.486 592 67 9 2979 3560 712739509 712738921 3.880000e-179 638
15 TraesCS5D01G263900 chr4A 86.125 591 69 10 2979 3560 712768541 712767955 3.020000e-175 625
16 TraesCS5D01G263900 chr4B 86.201 587 68 12 2981 3560 100575330 100574750 1.090000e-174 623
17 TraesCS5D01G263900 chr7A 86.550 342 31 10 59 399 266155803 266156130 2.610000e-96 363
18 TraesCS5D01G263900 chr2D 83.913 230 30 4 430 659 332197320 332197542 2.790000e-51 213
19 TraesCS5D01G263900 chr5B 82.627 236 29 9 153 386 254147461 254147686 7.800000e-47 198
20 TraesCS5D01G263900 chr5B 82.297 209 31 5 56 261 482305017 482305222 3.650000e-40 176
21 TraesCS5D01G263900 chr3B 79.767 257 38 11 116 369 61988584 61988339 1.310000e-39 174


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 TraesCS5D01G263900 chr5D 369139199 369142760 3561 False 6578.0 6578 100.0000 1 3562 1 chr5D.!!$F1 3561
1 TraesCS5D01G263900 chr5A 471296795 471300615 3820 True 2681.5 4241 95.4865 59 3560 2 chr5A.!!$R1 3501
2 TraesCS5D01G263900 chr5A 674542390 674542969 579 False 614.0 614 85.8600 2981 3562 1 chr5A.!!$F1 581
3 TraesCS5D01G263900 chr3A 36081904 36082479 575 False 682.0 682 88.0340 2979 3560 1 chr3A.!!$F1 581
4 TraesCS5D01G263900 chr3A 328930355 328930940 585 True 623.0 623 86.0540 2981 3560 1 chr3A.!!$R2 579
5 TraesCS5D01G263900 chr3A 96228384 96228954 570 True 606.0 606 85.8860 2984 3560 1 chr3A.!!$R1 576
6 TraesCS5D01G263900 chr6D 448819703 448820280 577 False 658.0 658 87.2230 2976 3560 1 chr6D.!!$F2 584
7 TraesCS5D01G263900 chr7D 529604757 529605341 584 True 645.0 645 86.7570 2979 3560 1 chr7D.!!$R1 581
8 TraesCS5D01G263900 chr4A 712738921 712739509 588 True 638.0 638 86.4860 2979 3560 1 chr4A.!!$R1 581
9 TraesCS5D01G263900 chr4A 712767955 712768541 586 True 625.0 625 86.1250 2979 3560 1 chr4A.!!$R2 581
10 TraesCS5D01G263900 chr4B 100574750 100575330 580 True 623.0 623 86.2010 2981 3560 1 chr4B.!!$R1 579

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
30 31 0.179181 GCTACAGCACGCGTACAGTA 60.179 55.0 13.44 13.32 41.59 2.74 F
839 843 0.392595 GAAACGGGCCCTCCTACAAG 60.393 60.0 22.43 3.46 0.00 3.16 F
1514 1855 0.523072 TACGTTGGTACCACTCTCGC 59.477 55.0 16.04 0.08 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 2028 0.173708 GGATCTGACCAGACGTCCAC 59.826 60.000 13.01 1.98 41.18 4.02 R
1695 2036 1.021390 GTGGCGTTGGATCTGACCAG 61.021 60.000 0.00 0.00 41.19 4.00 R
2944 3286 1.445582 GTAACACCGGAGCAGGACG 60.446 63.158 9.46 0.00 34.73 4.79 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
18 19 3.984838 AGATGCTAGCAGCTACAGC 57.015 52.632 32.92 9.92 41.23 4.40
20 21 4.919653 TGCTAGCAGCTACAGCAC 57.080 55.556 14.93 0.00 42.97 4.40
21 22 1.153765 TGCTAGCAGCTACAGCACG 60.154 57.895 14.93 0.00 42.97 5.34
22 23 2.520904 GCTAGCAGCTACAGCACGC 61.521 63.158 10.63 5.81 45.16 5.34
23 24 2.202610 TAGCAGCTACAGCACGCG 60.203 61.111 3.53 3.53 43.58 6.01
24 25 2.874010 CTAGCAGCTACAGCACGCGT 62.874 60.000 5.58 5.58 43.58 6.01
25 26 1.650314 TAGCAGCTACAGCACGCGTA 61.650 55.000 13.44 0.00 43.58 4.42
26 27 2.789203 GCAGCTACAGCACGCGTAC 61.789 63.158 13.44 6.32 45.16 3.67
27 28 1.443702 CAGCTACAGCACGCGTACA 60.444 57.895 13.44 0.00 45.16 2.90
28 29 1.154016 AGCTACAGCACGCGTACAG 60.154 57.895 13.44 5.70 45.16 2.74
29 30 1.443872 GCTACAGCACGCGTACAGT 60.444 57.895 13.44 12.79 41.59 3.55
30 31 0.179181 GCTACAGCACGCGTACAGTA 60.179 55.000 13.44 13.32 41.59 2.74
31 32 1.730121 GCTACAGCACGCGTACAGTAA 60.730 52.381 13.44 0.00 41.59 2.24
32 33 2.793933 CTACAGCACGCGTACAGTAAT 58.206 47.619 13.44 0.00 0.00 1.89
33 34 2.925578 ACAGCACGCGTACAGTAATA 57.074 45.000 13.44 0.00 0.00 0.98
34 35 2.793933 ACAGCACGCGTACAGTAATAG 58.206 47.619 13.44 0.00 0.00 1.73
35 36 2.163010 ACAGCACGCGTACAGTAATAGT 59.837 45.455 13.44 0.00 0.00 2.12
36 37 3.176708 CAGCACGCGTACAGTAATAGTT 58.823 45.455 13.44 0.00 0.00 2.24
37 38 3.001070 CAGCACGCGTACAGTAATAGTTG 60.001 47.826 13.44 0.00 0.00 3.16
38 39 2.919229 GCACGCGTACAGTAATAGTTGT 59.081 45.455 13.44 0.00 0.00 3.32
39 40 4.097714 GCACGCGTACAGTAATAGTTGTA 58.902 43.478 13.44 0.00 0.00 2.41
40 41 4.028187 GCACGCGTACAGTAATAGTTGTAC 60.028 45.833 13.44 5.03 43.80 2.90
41 42 5.327091 CACGCGTACAGTAATAGTTGTACT 58.673 41.667 13.44 0.00 44.61 2.73
49 50 6.208988 CAGTAATAGTTGTACTGCAGAGGA 57.791 41.667 23.35 1.69 41.37 3.71
50 51 6.269315 CAGTAATAGTTGTACTGCAGAGGAG 58.731 44.000 23.35 0.00 41.37 3.69
51 52 3.810310 ATAGTTGTACTGCAGAGGAGC 57.190 47.619 23.35 7.46 0.00 4.70
52 53 0.610687 AGTTGTACTGCAGAGGAGCC 59.389 55.000 23.35 3.33 0.00 4.70
53 54 0.737715 GTTGTACTGCAGAGGAGCCG 60.738 60.000 23.35 0.00 0.00 5.52
54 55 0.898326 TTGTACTGCAGAGGAGCCGA 60.898 55.000 23.35 0.00 0.00 5.54
55 56 0.898326 TGTACTGCAGAGGAGCCGAA 60.898 55.000 23.35 0.00 0.00 4.30
56 57 0.458716 GTACTGCAGAGGAGCCGAAC 60.459 60.000 23.35 0.42 0.00 3.95
57 58 1.605058 TACTGCAGAGGAGCCGAACC 61.605 60.000 23.35 0.00 0.00 3.62
83 84 1.615392 GTGAAGCCCATGAAGCAAACT 59.385 47.619 9.90 0.00 0.00 2.66
105 106 6.580963 CTGTAGACAGTGAAGATGCATAAC 57.419 41.667 0.00 0.00 39.09 1.89
106 107 6.286240 TGTAGACAGTGAAGATGCATAACT 57.714 37.500 0.00 0.00 0.00 2.24
107 108 7.404671 TGTAGACAGTGAAGATGCATAACTA 57.595 36.000 0.00 0.00 0.00 2.24
108 109 7.258441 TGTAGACAGTGAAGATGCATAACTAC 58.742 38.462 0.00 0.00 0.00 2.73
109 110 5.344066 AGACAGTGAAGATGCATAACTACG 58.656 41.667 0.00 0.00 0.00 3.51
110 111 4.433615 ACAGTGAAGATGCATAACTACGG 58.566 43.478 0.00 0.83 0.00 4.02
113 114 3.001330 GTGAAGATGCATAACTACGGTGC 59.999 47.826 0.00 0.00 39.26 5.01
114 115 2.240493 AGATGCATAACTACGGTGCC 57.760 50.000 0.00 0.00 38.06 5.01
115 116 1.762957 AGATGCATAACTACGGTGCCT 59.237 47.619 0.00 0.00 38.06 4.75
116 117 2.963101 AGATGCATAACTACGGTGCCTA 59.037 45.455 0.00 0.00 38.06 3.93
117 118 3.578716 AGATGCATAACTACGGTGCCTAT 59.421 43.478 0.00 0.00 38.06 2.57
118 119 3.106242 TGCATAACTACGGTGCCTATG 57.894 47.619 0.00 0.00 38.06 2.23
267 269 7.746475 GGATACAAAAGATTTATGCATAGTCGC 59.254 37.037 6.50 0.00 0.00 5.19
286 288 5.406780 AGTCGCTGAAGTTAAGACAATGAAG 59.593 40.000 0.00 0.00 34.56 3.02
304 306 2.568090 GGGGCAACACGCATCTTG 59.432 61.111 0.00 0.00 45.17 3.02
328 330 9.733556 TTGTCCATAGTAGTACATGTGAAATTT 57.266 29.630 9.11 0.00 0.00 1.82
336 338 8.603304 AGTAGTACATGTGAAATTTAGGGAAGT 58.397 33.333 9.11 0.00 0.00 3.01
377 379 1.157870 AAGAAACGTGACGGCCACAG 61.158 55.000 10.66 0.00 45.98 3.66
502 504 1.611977 TCGGGATAAGCAGATACCACG 59.388 52.381 0.44 0.00 28.97 4.94
546 548 6.883744 TGGAAAGTTTAGAAAAACATTGGCT 58.116 32.000 4.04 0.00 46.18 4.75
547 549 7.334858 TGGAAAGTTTAGAAAAACATTGGCTT 58.665 30.769 4.04 0.00 46.18 4.35
564 566 3.442273 TGGCTTACGATTTTGATGGGTTC 59.558 43.478 0.00 0.00 0.00 3.62
581 583 1.198094 TTCCCTTGGCCGTCAGATCA 61.198 55.000 0.00 0.00 0.00 2.92
616 618 1.676678 CGGAGGATCGGGCTGAAGAA 61.677 60.000 0.00 0.00 34.37 2.52
640 642 4.914504 CGCTACACATCAGACATCTGTATC 59.085 45.833 8.70 0.00 44.12 2.24
718 722 3.634448 ACTCTCAATCGTCGGATCTCAAT 59.366 43.478 0.00 0.00 30.81 2.57
732 736 5.276395 CGGATCTCAATTGTACATCGACAAC 60.276 44.000 5.13 0.00 41.93 3.32
762 766 2.629051 GTCTGGCGCTGGTAGTTTTAT 58.371 47.619 7.64 0.00 0.00 1.40
763 767 2.608090 GTCTGGCGCTGGTAGTTTTATC 59.392 50.000 7.64 0.00 0.00 1.75
764 768 2.235155 TCTGGCGCTGGTAGTTTTATCA 59.765 45.455 7.64 0.00 0.00 2.15
765 769 2.609459 CTGGCGCTGGTAGTTTTATCAG 59.391 50.000 7.64 0.00 40.37 2.90
766 770 2.235155 TGGCGCTGGTAGTTTTATCAGA 59.765 45.455 7.64 0.00 39.90 3.27
767 771 2.608090 GGCGCTGGTAGTTTTATCAGAC 59.392 50.000 7.64 0.00 39.90 3.51
768 772 3.522553 GCGCTGGTAGTTTTATCAGACT 58.477 45.455 0.00 0.00 39.90 3.24
769 773 4.441079 GGCGCTGGTAGTTTTATCAGACTA 60.441 45.833 7.64 0.00 39.90 2.59
770 774 4.503370 GCGCTGGTAGTTTTATCAGACTAC 59.497 45.833 0.00 5.35 44.66 2.73
771 775 5.647589 CGCTGGTAGTTTTATCAGACTACA 58.352 41.667 13.65 2.45 46.30 2.74
772 776 6.273825 CGCTGGTAGTTTTATCAGACTACAT 58.726 40.000 13.65 0.00 46.30 2.29
773 777 7.423199 CGCTGGTAGTTTTATCAGACTACATA 58.577 38.462 13.65 3.87 46.30 2.29
774 778 8.082852 CGCTGGTAGTTTTATCAGACTACATAT 58.917 37.037 13.65 0.00 46.30 1.78
783 787 9.811995 TTTTATCAGACTACATATACAAAGCGT 57.188 29.630 0.00 0.00 0.00 5.07
784 788 9.811995 TTTATCAGACTACATATACAAAGCGTT 57.188 29.630 0.00 0.00 0.00 4.84
785 789 9.811995 TTATCAGACTACATATACAAAGCGTTT 57.188 29.630 0.00 0.00 0.00 3.60
786 790 7.751047 TCAGACTACATATACAAAGCGTTTC 57.249 36.000 0.00 0.00 0.00 2.78
787 791 6.755141 TCAGACTACATATACAAAGCGTTTCC 59.245 38.462 0.00 0.00 0.00 3.13
788 792 6.018994 CAGACTACATATACAAAGCGTTTCCC 60.019 42.308 0.00 0.00 0.00 3.97
789 793 5.736813 ACTACATATACAAAGCGTTTCCCA 58.263 37.500 0.00 0.00 0.00 4.37
790 794 6.174760 ACTACATATACAAAGCGTTTCCCAA 58.825 36.000 0.00 0.00 0.00 4.12
791 795 5.968528 ACATATACAAAGCGTTTCCCAAA 57.031 34.783 0.00 0.00 0.00 3.28
792 796 5.949735 ACATATACAAAGCGTTTCCCAAAG 58.050 37.500 0.00 0.00 0.00 2.77
793 797 5.475564 ACATATACAAAGCGTTTCCCAAAGT 59.524 36.000 0.00 0.00 0.00 2.66
794 798 2.577449 ACAAAGCGTTTCCCAAAGTG 57.423 45.000 0.00 0.00 0.00 3.16
795 799 1.136110 ACAAAGCGTTTCCCAAAGTGG 59.864 47.619 0.00 0.00 37.25 4.00
796 800 1.136110 CAAAGCGTTTCCCAAAGTGGT 59.864 47.619 0.00 0.00 35.17 4.16
797 801 0.744281 AAGCGTTTCCCAAAGTGGTG 59.256 50.000 0.00 0.00 35.17 4.17
798 802 0.395173 AGCGTTTCCCAAAGTGGTGT 60.395 50.000 0.00 0.00 35.17 4.16
799 803 0.458260 GCGTTTCCCAAAGTGGTGTT 59.542 50.000 0.00 0.00 35.17 3.32
800 804 1.134936 GCGTTTCCCAAAGTGGTGTTT 60.135 47.619 0.00 0.00 35.17 2.83
801 805 2.804647 CGTTTCCCAAAGTGGTGTTTC 58.195 47.619 0.00 0.00 35.17 2.78
802 806 2.480587 CGTTTCCCAAAGTGGTGTTTCC 60.481 50.000 0.00 0.00 35.17 3.13
803 807 2.764010 GTTTCCCAAAGTGGTGTTTCCT 59.236 45.455 0.00 0.00 35.17 3.36
804 808 2.838637 TCCCAAAGTGGTGTTTCCTT 57.161 45.000 0.00 0.00 35.17 3.36
805 809 3.108847 TCCCAAAGTGGTGTTTCCTTT 57.891 42.857 0.00 0.00 35.17 3.11
806 810 3.445987 TCCCAAAGTGGTGTTTCCTTTT 58.554 40.909 0.00 0.00 35.17 2.27
807 811 3.841255 TCCCAAAGTGGTGTTTCCTTTTT 59.159 39.130 0.00 0.00 35.17 1.94
835 839 3.395630 GTGAAACGGGCCCTCCTA 58.604 61.111 22.43 0.00 0.00 2.94
836 840 1.078637 GTGAAACGGGCCCTCCTAC 60.079 63.158 22.43 8.74 0.00 3.18
837 841 1.536907 TGAAACGGGCCCTCCTACA 60.537 57.895 22.43 10.71 0.00 2.74
838 842 1.128809 TGAAACGGGCCCTCCTACAA 61.129 55.000 22.43 0.00 0.00 2.41
839 843 0.392595 GAAACGGGCCCTCCTACAAG 60.393 60.000 22.43 3.46 0.00 3.16
840 844 1.131928 AAACGGGCCCTCCTACAAGT 61.132 55.000 22.43 4.23 0.00 3.16
841 845 1.551019 AACGGGCCCTCCTACAAGTC 61.551 60.000 22.43 0.00 0.00 3.01
842 846 2.901042 GGGCCCTCCTACAAGTCG 59.099 66.667 17.04 0.00 0.00 4.18
843 847 1.988406 GGGCCCTCCTACAAGTCGT 60.988 63.158 17.04 0.00 0.00 4.34
844 848 0.685458 GGGCCCTCCTACAAGTCGTA 60.685 60.000 17.04 0.00 0.00 3.43
845 849 1.188863 GGCCCTCCTACAAGTCGTAA 58.811 55.000 0.00 0.00 0.00 3.18
846 850 1.551883 GGCCCTCCTACAAGTCGTAAA 59.448 52.381 0.00 0.00 0.00 2.01
847 851 2.614779 GCCCTCCTACAAGTCGTAAAC 58.385 52.381 0.00 0.00 0.00 2.01
848 852 2.676176 GCCCTCCTACAAGTCGTAAACC 60.676 54.545 0.00 0.00 0.00 3.27
849 853 2.830321 CCCTCCTACAAGTCGTAAACCT 59.170 50.000 0.00 0.00 0.00 3.50
850 854 3.368116 CCCTCCTACAAGTCGTAAACCTG 60.368 52.174 0.00 0.00 0.00 4.00
851 855 3.257624 CCTCCTACAAGTCGTAAACCTGT 59.742 47.826 0.00 0.00 36.50 4.00
852 856 4.262335 CCTCCTACAAGTCGTAAACCTGTT 60.262 45.833 0.00 0.00 34.38 3.16
853 857 4.874970 TCCTACAAGTCGTAAACCTGTTC 58.125 43.478 0.00 0.00 34.38 3.18
854 858 3.671928 CCTACAAGTCGTAAACCTGTTCG 59.328 47.826 0.00 0.00 34.38 3.95
855 859 2.476821 ACAAGTCGTAAACCTGTTCGG 58.523 47.619 0.00 0.00 27.59 4.30
866 870 1.617357 ACCTGTTCGGTTGTCTCTACC 59.383 52.381 0.00 0.00 46.37 3.18
867 871 1.893801 CCTGTTCGGTTGTCTCTACCT 59.106 52.381 0.00 0.00 33.35 3.08
868 872 2.352814 CCTGTTCGGTTGTCTCTACCTG 60.353 54.545 0.00 0.00 33.35 4.00
869 873 2.296471 CTGTTCGGTTGTCTCTACCTGT 59.704 50.000 0.00 0.00 33.35 4.00
870 874 2.696707 TGTTCGGTTGTCTCTACCTGTT 59.303 45.455 0.00 0.00 33.35 3.16
871 875 3.243636 TGTTCGGTTGTCTCTACCTGTTC 60.244 47.826 0.00 0.00 33.35 3.18
872 876 2.589720 TCGGTTGTCTCTACCTGTTCA 58.410 47.619 0.00 0.00 33.35 3.18
873 877 2.557056 TCGGTTGTCTCTACCTGTTCAG 59.443 50.000 0.00 0.00 33.35 3.02
874 878 2.689646 GGTTGTCTCTACCTGTTCAGC 58.310 52.381 0.00 0.00 32.75 4.26
875 879 2.300437 GGTTGTCTCTACCTGTTCAGCT 59.700 50.000 0.00 0.00 32.75 4.24
876 880 3.244249 GGTTGTCTCTACCTGTTCAGCTT 60.244 47.826 0.00 0.00 32.75 3.74
877 881 3.944055 TGTCTCTACCTGTTCAGCTTC 57.056 47.619 0.00 0.00 0.00 3.86
878 882 2.229062 TGTCTCTACCTGTTCAGCTTCG 59.771 50.000 0.00 0.00 0.00 3.79
879 883 2.488545 GTCTCTACCTGTTCAGCTTCGA 59.511 50.000 0.00 0.00 0.00 3.71
880 884 3.057456 GTCTCTACCTGTTCAGCTTCGAA 60.057 47.826 0.00 0.00 0.00 3.71
881 885 3.191581 TCTCTACCTGTTCAGCTTCGAAG 59.808 47.826 21.02 21.02 0.00 3.79
882 886 2.891580 TCTACCTGTTCAGCTTCGAAGT 59.108 45.455 25.24 10.34 0.00 3.01
883 887 2.156343 ACCTGTTCAGCTTCGAAGTC 57.844 50.000 25.24 17.29 0.00 3.01
884 888 1.063806 CCTGTTCAGCTTCGAAGTCG 58.936 55.000 25.24 16.60 41.45 4.18
885 889 1.063806 CTGTTCAGCTTCGAAGTCGG 58.936 55.000 25.24 17.43 40.29 4.79
886 890 0.671796 TGTTCAGCTTCGAAGTCGGA 59.328 50.000 25.24 19.18 40.29 4.55
887 891 1.067974 TGTTCAGCTTCGAAGTCGGAA 59.932 47.619 25.24 22.93 40.29 4.30
888 892 1.721926 GTTCAGCTTCGAAGTCGGAAG 59.278 52.381 25.24 9.92 40.29 3.46
889 893 1.244816 TCAGCTTCGAAGTCGGAAGA 58.755 50.000 25.24 11.84 40.29 2.87
890 894 1.819288 TCAGCTTCGAAGTCGGAAGAT 59.181 47.619 25.24 0.00 45.19 2.40
891 895 3.014623 TCAGCTTCGAAGTCGGAAGATA 58.985 45.455 25.24 1.52 45.19 1.98
892 896 3.442625 TCAGCTTCGAAGTCGGAAGATAA 59.557 43.478 25.24 0.90 45.19 1.75
893 897 4.082408 TCAGCTTCGAAGTCGGAAGATAAA 60.082 41.667 25.24 0.28 45.19 1.40
894 898 4.625742 CAGCTTCGAAGTCGGAAGATAAAA 59.374 41.667 25.24 0.00 45.19 1.52
895 899 5.292101 CAGCTTCGAAGTCGGAAGATAAAAT 59.708 40.000 25.24 0.00 45.19 1.82
954 1295 2.693591 CCTAACTCACAGATCCGCCTTA 59.306 50.000 0.00 0.00 0.00 2.69
957 1298 3.695830 ACTCACAGATCCGCCTTAAAA 57.304 42.857 0.00 0.00 0.00 1.52
1125 1466 2.736144 TACACGGGTTACTGCTTCTG 57.264 50.000 0.00 0.00 0.00 3.02
1511 1852 4.774200 ACCTAATTACGTTGGTACCACTCT 59.226 41.667 16.04 1.58 0.00 3.24
1513 1854 2.995466 TTACGTTGGTACCACTCTCG 57.005 50.000 16.04 18.24 0.00 4.04
1514 1855 0.523072 TACGTTGGTACCACTCTCGC 59.477 55.000 16.04 0.08 0.00 5.03
1515 1856 1.445582 CGTTGGTACCACTCTCGCC 60.446 63.158 16.04 0.00 0.00 5.54
1517 1858 1.604308 TTGGTACCACTCTCGCCGA 60.604 57.895 16.04 0.00 0.00 5.54
1518 1859 1.592400 TTGGTACCACTCTCGCCGAG 61.592 60.000 16.04 8.05 45.56 4.63
1519 1860 2.772691 GGTACCACTCTCGCCGAGG 61.773 68.421 15.08 7.64 44.33 4.63
1520 1861 1.748122 GTACCACTCTCGCCGAGGA 60.748 63.158 15.08 0.11 44.33 3.71
1521 1862 1.748122 TACCACTCTCGCCGAGGAC 60.748 63.158 15.08 0.00 44.33 3.85
1563 1904 4.994217 TCAGAAACACATTACGAGCATGAA 59.006 37.500 0.00 0.00 0.00 2.57
1629 1970 2.604855 CGTGCAAGTCTACTCGTCAAGT 60.605 50.000 0.00 0.00 42.33 3.16
1643 1984 2.528378 AAGTACCGGGCAGTGGGT 60.528 61.111 6.32 0.00 40.35 4.51
1652 1993 1.380302 GGCAGTGGGTTGACAGGAT 59.620 57.895 0.00 0.00 0.00 3.24
1661 2002 2.030274 GGGTTGACAGGATTTTTGTCCG 60.030 50.000 3.24 0.00 43.32 4.79
1695 2036 4.926207 GGTACCATGGTGGACGTC 57.074 61.111 28.17 7.13 40.96 4.34
1785 2126 1.874562 GCTCTACGTCCACTGTCGT 59.125 57.895 0.00 0.00 42.82 4.34
1858 2199 1.428448 TTTGTCTCGTCCTTGATGCG 58.572 50.000 0.00 0.00 0.00 4.73
1936 2278 7.675161 TGTCATTAGTGGAGGAGATTTATCA 57.325 36.000 0.00 0.00 0.00 2.15
1975 2317 3.878103 AGACTACATGTAGCCGAGTACAG 59.122 47.826 28.88 7.98 36.36 2.74
1979 2321 0.663688 ATGTAGCCGAGTACAGCGAG 59.336 55.000 9.37 2.15 36.36 5.03
2303 2645 5.605908 TGCTGATATGGAAGAAGAGGAGATT 59.394 40.000 0.00 0.00 0.00 2.40
2435 2777 5.185249 TGCCTACTACCTAGACAACTCAAAG 59.815 44.000 0.00 0.00 0.00 2.77
2724 3066 2.239654 TGGGACCATTTCTTAGGCTCTG 59.760 50.000 0.00 0.00 0.00 3.35
2754 3096 3.678056 AGGCTCATCAACGTTGTTCTA 57.322 42.857 26.47 9.01 0.00 2.10
2770 3112 8.922676 ACGTTGTTCTATACTTTTGACATACAG 58.077 33.333 0.00 0.00 0.00 2.74
2855 3197 3.904717 TGGCCAAAGAAGAAGGTAACAA 58.095 40.909 0.61 0.00 41.41 2.83
2862 3204 4.625607 AGAAGAAGGTAACAAGTCCTGG 57.374 45.455 0.00 0.00 41.41 4.45
2899 3241 7.328404 TGGCTTCCAATTCAGTATATATCCA 57.672 36.000 0.00 0.00 0.00 3.41
2900 3242 7.932134 TGGCTTCCAATTCAGTATATATCCAT 58.068 34.615 0.00 0.00 0.00 3.41
2901 3243 7.830697 TGGCTTCCAATTCAGTATATATCCATG 59.169 37.037 0.00 0.00 0.00 3.66
2902 3244 7.831193 GGCTTCCAATTCAGTATATATCCATGT 59.169 37.037 0.00 0.00 0.00 3.21
2903 3245 8.671921 GCTTCCAATTCAGTATATATCCATGTG 58.328 37.037 0.00 0.00 0.00 3.21
2904 3246 9.730705 CTTCCAATTCAGTATATATCCATGTGT 57.269 33.333 0.00 0.00 0.00 3.72
2944 3286 1.202463 ACATCTGACGGTGATGCTAGC 60.202 52.381 8.10 8.10 43.53 3.42
3329 3698 2.267351 CGCAGTGATTTGGTGGGCA 61.267 57.895 0.00 0.00 0.00 5.36
3356 3727 4.034394 CGTGGTGTCATTCCATGTTATCTG 59.966 45.833 0.00 0.00 37.25 2.90
3439 3810 4.502105 TGCTACAATATCACATGGTGGT 57.498 40.909 0.00 0.00 33.87 4.16
3445 3817 3.650281 ATATCACATGGTGGTGCTTCA 57.350 42.857 0.00 0.00 38.66 3.02
3450 3822 3.061322 CACATGGTGGTGCTTCATTTTG 58.939 45.455 0.00 0.00 31.10 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.117994 TGCTGTAGCTGCTAGCATCT 58.882 50.000 23.43 23.43 45.56 2.90
1 2 3.675086 TGCTGTAGCTGCTAGCATC 57.325 52.632 19.72 14.91 45.56 3.91
3 4 1.153765 CGTGCTGTAGCTGCTAGCA 60.154 57.895 20.13 20.13 45.56 3.49
4 5 2.520904 GCGTGCTGTAGCTGCTAGC 61.521 63.158 15.73 15.73 42.84 3.42
5 6 2.226896 CGCGTGCTGTAGCTGCTAG 61.227 63.158 10.13 1.96 42.66 3.42
6 7 1.650314 TACGCGTGCTGTAGCTGCTA 61.650 55.000 24.59 5.02 42.66 3.49
7 8 2.989881 TACGCGTGCTGTAGCTGCT 61.990 57.895 24.59 7.57 42.66 4.24
8 9 2.506217 TACGCGTGCTGTAGCTGC 60.506 61.111 24.59 8.26 42.66 5.25
9 10 1.406219 CTGTACGCGTGCTGTAGCTG 61.406 60.000 27.18 5.98 42.66 4.24
10 11 1.154016 CTGTACGCGTGCTGTAGCT 60.154 57.895 27.18 0.00 42.66 3.32
11 12 0.179181 TACTGTACGCGTGCTGTAGC 60.179 55.000 31.94 12.12 42.50 3.58
12 13 2.251869 TTACTGTACGCGTGCTGTAG 57.748 50.000 32.76 23.18 33.10 2.74
13 14 2.925578 ATTACTGTACGCGTGCTGTA 57.074 45.000 31.94 31.94 0.00 2.74
14 15 2.163010 ACTATTACTGTACGCGTGCTGT 59.837 45.455 33.73 33.73 0.00 4.40
15 16 2.793933 ACTATTACTGTACGCGTGCTG 58.206 47.619 27.34 27.34 0.00 4.41
16 17 3.176708 CAACTATTACTGTACGCGTGCT 58.823 45.455 27.18 11.46 0.00 4.40
17 18 2.919229 ACAACTATTACTGTACGCGTGC 59.081 45.455 24.59 22.71 0.00 5.34
18 19 5.595724 GTACAACTATTACTGTACGCGTG 57.404 43.478 24.59 7.93 38.77 5.34
23 24 6.973474 CCTCTGCAGTACAACTATTACTGTAC 59.027 42.308 14.67 4.56 45.62 2.90
24 25 6.888088 TCCTCTGCAGTACAACTATTACTGTA 59.112 38.462 14.67 5.92 45.62 2.74
25 26 5.715279 TCCTCTGCAGTACAACTATTACTGT 59.285 40.000 14.67 0.00 45.62 3.55
26 27 6.208988 TCCTCTGCAGTACAACTATTACTG 57.791 41.667 14.67 5.34 46.31 2.74
27 28 5.163499 GCTCCTCTGCAGTACAACTATTACT 60.163 44.000 14.67 0.00 0.00 2.24
28 29 5.044558 GCTCCTCTGCAGTACAACTATTAC 58.955 45.833 14.67 0.00 0.00 1.89
29 30 4.099573 GGCTCCTCTGCAGTACAACTATTA 59.900 45.833 14.67 0.00 34.04 0.98
30 31 3.118592 GGCTCCTCTGCAGTACAACTATT 60.119 47.826 14.67 0.00 34.04 1.73
31 32 2.432510 GGCTCCTCTGCAGTACAACTAT 59.567 50.000 14.67 0.00 34.04 2.12
32 33 1.825474 GGCTCCTCTGCAGTACAACTA 59.175 52.381 14.67 0.00 34.04 2.24
33 34 0.610687 GGCTCCTCTGCAGTACAACT 59.389 55.000 14.67 0.00 34.04 3.16
34 35 0.737715 CGGCTCCTCTGCAGTACAAC 60.738 60.000 14.67 1.94 34.04 3.32
35 36 0.898326 TCGGCTCCTCTGCAGTACAA 60.898 55.000 14.67 0.00 34.04 2.41
36 37 0.898326 TTCGGCTCCTCTGCAGTACA 60.898 55.000 14.67 0.00 34.04 2.90
37 38 0.458716 GTTCGGCTCCTCTGCAGTAC 60.459 60.000 14.67 0.00 34.04 2.73
38 39 1.605058 GGTTCGGCTCCTCTGCAGTA 61.605 60.000 14.67 0.00 34.04 2.74
39 40 2.659610 GTTCGGCTCCTCTGCAGT 59.340 61.111 14.67 0.00 34.04 4.40
40 41 2.125350 GGTTCGGCTCCTCTGCAG 60.125 66.667 7.63 7.63 34.04 4.41
41 42 3.706373 GGGTTCGGCTCCTCTGCA 61.706 66.667 0.00 0.00 34.04 4.41
42 43 2.543067 ATTGGGTTCGGCTCCTCTGC 62.543 60.000 0.00 0.00 0.00 4.26
43 44 0.035056 AATTGGGTTCGGCTCCTCTG 60.035 55.000 0.00 0.00 0.00 3.35
44 45 0.035056 CAATTGGGTTCGGCTCCTCT 60.035 55.000 0.00 0.00 0.00 3.69
45 46 0.322546 ACAATTGGGTTCGGCTCCTC 60.323 55.000 10.83 0.00 0.00 3.71
46 47 0.609131 CACAATTGGGTTCGGCTCCT 60.609 55.000 10.83 0.00 0.00 3.69
47 48 0.608035 TCACAATTGGGTTCGGCTCC 60.608 55.000 7.75 0.00 0.00 4.70
48 49 1.200020 CTTCACAATTGGGTTCGGCTC 59.800 52.381 7.75 0.00 0.00 4.70
49 50 1.247567 CTTCACAATTGGGTTCGGCT 58.752 50.000 7.75 0.00 0.00 5.52
50 51 0.388520 GCTTCACAATTGGGTTCGGC 60.389 55.000 7.75 4.60 0.00 5.54
51 52 0.243636 GGCTTCACAATTGGGTTCGG 59.756 55.000 7.75 0.00 0.00 4.30
52 53 0.243636 GGGCTTCACAATTGGGTTCG 59.756 55.000 7.75 0.00 0.00 3.95
53 54 1.337118 TGGGCTTCACAATTGGGTTC 58.663 50.000 7.75 0.00 0.00 3.62
54 55 1.624813 CATGGGCTTCACAATTGGGTT 59.375 47.619 7.75 0.00 0.00 4.11
55 56 1.203162 TCATGGGCTTCACAATTGGGT 60.203 47.619 7.75 0.00 0.00 4.51
56 57 1.559368 TCATGGGCTTCACAATTGGG 58.441 50.000 10.83 5.72 0.00 4.12
57 58 2.675889 GCTTCATGGGCTTCACAATTGG 60.676 50.000 10.83 0.00 0.00 3.16
83 84 6.286240 AGTTATGCATCTTCACTGTCTACA 57.714 37.500 0.19 0.00 0.00 2.74
104 105 1.191535 TTGCTCATAGGCACCGTAGT 58.808 50.000 0.00 0.00 42.27 2.73
105 106 1.933853 GTTTGCTCATAGGCACCGTAG 59.066 52.381 0.00 0.00 42.27 3.51
106 107 1.406341 GGTTTGCTCATAGGCACCGTA 60.406 52.381 0.00 0.00 42.27 4.02
107 108 0.676782 GGTTTGCTCATAGGCACCGT 60.677 55.000 0.00 0.00 42.27 4.83
108 109 0.392998 AGGTTTGCTCATAGGCACCG 60.393 55.000 0.00 0.00 42.27 4.94
109 110 1.474077 CAAGGTTTGCTCATAGGCACC 59.526 52.381 0.00 0.00 42.27 5.01
110 111 2.927553 CAAGGTTTGCTCATAGGCAC 57.072 50.000 0.00 0.00 42.27 5.01
267 269 4.702131 CCCCCTTCATTGTCTTAACTTCAG 59.298 45.833 0.00 0.00 0.00 3.02
286 288 2.676471 AAGATGCGTGTTGCCCCC 60.676 61.111 0.00 0.00 45.60 5.40
351 353 3.910170 GGCCGTCACGTTTCTTTTTAATC 59.090 43.478 0.00 0.00 0.00 1.75
352 354 3.315749 TGGCCGTCACGTTTCTTTTTAAT 59.684 39.130 0.00 0.00 0.00 1.40
377 379 0.106708 TCGTCTCCATGCCTATTGCC 59.893 55.000 0.00 0.00 40.16 4.52
388 390 0.609957 TTCTACCGCCTTCGTCTCCA 60.610 55.000 0.00 0.00 0.00 3.86
447 449 0.180406 CCAAACCGACCCCATCTAGG 59.820 60.000 0.00 0.00 37.03 3.02
502 504 0.394565 ATCTTCACGCCTATGCTCCC 59.605 55.000 0.00 0.00 34.43 4.30
521 523 7.334858 AGCCAATGTTTTTCTAAACTTTCCAA 58.665 30.769 0.00 0.00 43.25 3.53
564 566 0.322456 TTTGATCTGACGGCCAAGGG 60.322 55.000 2.24 0.00 0.00 3.95
581 583 2.009774 CTCCGCCGTTGATTCATCTTT 58.990 47.619 0.00 0.00 0.00 2.52
616 618 2.493675 ACAGATGTCTGATGTGTAGCGT 59.506 45.455 16.41 0.00 46.59 5.07
718 722 3.503363 AGTCCTACGTTGTCGATGTACAA 59.497 43.478 0.00 0.00 40.62 2.41
732 736 2.490217 CGCCAGACCAGTCCTACG 59.510 66.667 0.00 0.00 0.00 3.51
762 766 6.755141 GGAAACGCTTTGTATATGTAGTCTGA 59.245 38.462 0.00 0.00 0.00 3.27
763 767 6.018994 GGGAAACGCTTTGTATATGTAGTCTG 60.019 42.308 0.00 0.00 0.00 3.51
764 768 6.047231 GGGAAACGCTTTGTATATGTAGTCT 58.953 40.000 0.00 0.00 0.00 3.24
765 769 5.813672 TGGGAAACGCTTTGTATATGTAGTC 59.186 40.000 0.00 0.00 0.00 2.59
766 770 5.736813 TGGGAAACGCTTTGTATATGTAGT 58.263 37.500 0.00 0.00 0.00 2.73
767 771 6.671614 TTGGGAAACGCTTTGTATATGTAG 57.328 37.500 0.00 0.00 0.00 2.74
768 772 6.655848 ACTTTGGGAAACGCTTTGTATATGTA 59.344 34.615 0.00 0.00 0.00 2.29
769 773 5.475564 ACTTTGGGAAACGCTTTGTATATGT 59.524 36.000 0.00 0.00 0.00 2.29
770 774 5.799936 CACTTTGGGAAACGCTTTGTATATG 59.200 40.000 0.00 0.00 0.00 1.78
771 775 5.105917 CCACTTTGGGAAACGCTTTGTATAT 60.106 40.000 0.00 0.00 32.67 0.86
772 776 4.216687 CCACTTTGGGAAACGCTTTGTATA 59.783 41.667 0.00 0.00 32.67 1.47
773 777 3.005367 CCACTTTGGGAAACGCTTTGTAT 59.995 43.478 0.00 0.00 32.67 2.29
774 778 2.359531 CCACTTTGGGAAACGCTTTGTA 59.640 45.455 0.00 0.00 32.67 2.41
775 779 1.136110 CCACTTTGGGAAACGCTTTGT 59.864 47.619 0.00 0.00 32.67 2.83
776 780 1.136110 ACCACTTTGGGAAACGCTTTG 59.864 47.619 0.00 0.00 43.37 2.77
777 781 1.136110 CACCACTTTGGGAAACGCTTT 59.864 47.619 0.00 0.00 43.37 3.51
778 782 0.744281 CACCACTTTGGGAAACGCTT 59.256 50.000 0.00 0.00 43.37 4.68
779 783 0.395173 ACACCACTTTGGGAAACGCT 60.395 50.000 0.00 0.00 43.37 5.07
780 784 0.458260 AACACCACTTTGGGAAACGC 59.542 50.000 0.00 0.00 43.37 4.84
781 785 2.480587 GGAAACACCACTTTGGGAAACG 60.481 50.000 0.00 0.00 43.37 3.60
782 786 2.764010 AGGAAACACCACTTTGGGAAAC 59.236 45.455 0.00 0.00 43.37 2.78
783 787 3.108847 AGGAAACACCACTTTGGGAAA 57.891 42.857 0.00 0.00 43.37 3.13
784 788 2.838637 AGGAAACACCACTTTGGGAA 57.161 45.000 0.00 0.00 43.37 3.97
785 789 2.838637 AAGGAAACACCACTTTGGGA 57.161 45.000 0.00 0.00 43.37 4.37
786 790 3.904800 AAAAGGAAACACCACTTTGGG 57.095 42.857 0.00 0.00 43.37 4.12
807 811 1.671845 CCCGTTTCACGAGTCCAAAAA 59.328 47.619 0.00 0.00 46.05 1.94
808 812 1.301423 CCCGTTTCACGAGTCCAAAA 58.699 50.000 0.00 0.00 46.05 2.44
809 813 1.161563 GCCCGTTTCACGAGTCCAAA 61.162 55.000 0.00 0.00 46.05 3.28
810 814 1.595929 GCCCGTTTCACGAGTCCAA 60.596 57.895 0.00 0.00 46.05 3.53
811 815 2.029964 GCCCGTTTCACGAGTCCA 59.970 61.111 0.00 0.00 46.05 4.02
812 816 2.741211 GGCCCGTTTCACGAGTCC 60.741 66.667 0.00 0.00 46.05 3.85
813 817 2.741211 GGGCCCGTTTCACGAGTC 60.741 66.667 5.69 0.00 46.05 3.36
814 818 3.236003 GAGGGCCCGTTTCACGAGT 62.236 63.158 18.44 0.00 46.05 4.18
815 819 2.434359 GAGGGCCCGTTTCACGAG 60.434 66.667 18.44 0.00 46.05 4.18
816 820 4.011517 GGAGGGCCCGTTTCACGA 62.012 66.667 18.44 0.00 46.05 4.35
817 821 2.652095 TAGGAGGGCCCGTTTCACG 61.652 63.158 18.44 0.00 42.11 4.35
818 822 1.078637 GTAGGAGGGCCCGTTTCAC 60.079 63.158 18.44 8.52 40.87 3.18
819 823 1.128809 TTGTAGGAGGGCCCGTTTCA 61.129 55.000 18.44 10.80 40.87 2.69
820 824 0.392595 CTTGTAGGAGGGCCCGTTTC 60.393 60.000 18.44 8.82 40.87 2.78
821 825 1.131928 ACTTGTAGGAGGGCCCGTTT 61.132 55.000 18.44 8.27 40.87 3.60
822 826 1.538135 ACTTGTAGGAGGGCCCGTT 60.538 57.895 18.44 8.68 40.87 4.44
823 827 1.988406 GACTTGTAGGAGGGCCCGT 60.988 63.158 18.44 5.03 40.87 5.28
824 828 2.901042 GACTTGTAGGAGGGCCCG 59.099 66.667 18.44 0.95 40.87 6.13
825 829 0.685458 TACGACTTGTAGGAGGGCCC 60.685 60.000 16.46 16.46 33.31 5.80
826 830 1.188863 TTACGACTTGTAGGAGGGCC 58.811 55.000 0.00 0.00 33.75 5.80
827 831 2.614779 GTTTACGACTTGTAGGAGGGC 58.385 52.381 0.00 0.00 33.75 5.19
828 832 2.830321 AGGTTTACGACTTGTAGGAGGG 59.170 50.000 0.00 0.00 33.75 4.30
829 833 3.257624 ACAGGTTTACGACTTGTAGGAGG 59.742 47.826 0.00 0.00 45.62 4.30
830 834 4.516365 ACAGGTTTACGACTTGTAGGAG 57.484 45.455 0.00 0.00 45.62 3.69
831 835 4.557296 CGAACAGGTTTACGACTTGTAGGA 60.557 45.833 0.00 0.00 46.61 2.94
832 836 3.671928 CGAACAGGTTTACGACTTGTAGG 59.328 47.826 0.00 0.00 46.61 3.18
833 837 3.671928 CCGAACAGGTTTACGACTTGTAG 59.328 47.826 0.00 0.00 46.61 2.74
834 838 3.641648 CCGAACAGGTTTACGACTTGTA 58.358 45.455 0.00 0.00 46.61 2.41
848 852 2.296471 ACAGGTAGAGACAACCGAACAG 59.704 50.000 0.00 0.00 42.15 3.16
849 853 2.313317 ACAGGTAGAGACAACCGAACA 58.687 47.619 0.00 0.00 42.15 3.18
850 854 3.243636 TGAACAGGTAGAGACAACCGAAC 60.244 47.826 0.00 0.00 42.15 3.95
851 855 2.960384 TGAACAGGTAGAGACAACCGAA 59.040 45.455 0.00 0.00 42.15 4.30
852 856 2.557056 CTGAACAGGTAGAGACAACCGA 59.443 50.000 0.00 0.00 42.15 4.69
853 857 2.927014 GCTGAACAGGTAGAGACAACCG 60.927 54.545 3.99 0.00 42.15 4.44
854 858 2.300437 AGCTGAACAGGTAGAGACAACC 59.700 50.000 4.67 0.00 37.39 3.77
855 859 3.669251 AGCTGAACAGGTAGAGACAAC 57.331 47.619 4.67 0.00 37.39 3.32
856 860 3.305403 CGAAGCTGAACAGGTAGAGACAA 60.305 47.826 6.94 0.00 38.35 3.18
857 861 2.229062 CGAAGCTGAACAGGTAGAGACA 59.771 50.000 6.94 0.00 38.35 3.41
858 862 2.488545 TCGAAGCTGAACAGGTAGAGAC 59.511 50.000 6.94 0.00 38.35 3.36
859 863 2.791655 TCGAAGCTGAACAGGTAGAGA 58.208 47.619 6.94 4.85 38.35 3.10
860 864 3.057174 ACTTCGAAGCTGAACAGGTAGAG 60.057 47.826 24.86 0.00 38.35 2.43
861 865 2.891580 ACTTCGAAGCTGAACAGGTAGA 59.108 45.455 24.86 7.32 38.35 2.59
862 866 3.246619 GACTTCGAAGCTGAACAGGTAG 58.753 50.000 24.86 0.00 38.35 3.18
863 867 2.351447 CGACTTCGAAGCTGAACAGGTA 60.351 50.000 24.86 0.00 43.02 3.08
864 868 1.603172 CGACTTCGAAGCTGAACAGGT 60.603 52.381 24.86 2.65 43.02 4.00
865 869 1.063806 CGACTTCGAAGCTGAACAGG 58.936 55.000 24.86 0.00 43.02 4.00
866 870 1.063806 CCGACTTCGAAGCTGAACAG 58.936 55.000 24.86 8.29 43.02 3.16
867 871 0.671796 TCCGACTTCGAAGCTGAACA 59.328 50.000 24.86 1.67 43.02 3.18
868 872 1.721926 CTTCCGACTTCGAAGCTGAAC 59.278 52.381 24.86 10.25 43.02 3.18
869 873 1.611977 TCTTCCGACTTCGAAGCTGAA 59.388 47.619 24.86 20.74 43.02 3.02
870 874 1.244816 TCTTCCGACTTCGAAGCTGA 58.755 50.000 24.86 15.28 43.02 4.26
871 875 2.285827 ATCTTCCGACTTCGAAGCTG 57.714 50.000 24.86 16.55 43.02 4.24
872 876 4.451629 TTTATCTTCCGACTTCGAAGCT 57.548 40.909 24.86 12.14 43.02 3.74
873 877 5.720261 ATTTTATCTTCCGACTTCGAAGC 57.280 39.130 24.86 15.90 43.02 3.86
874 878 7.988904 AGTATTTTATCTTCCGACTTCGAAG 57.011 36.000 23.43 23.43 43.02 3.79
882 886 9.459640 GCGCATATATAGTATTTTATCTTCCGA 57.540 33.333 0.30 0.00 0.00 4.55
883 887 8.700644 GGCGCATATATAGTATTTTATCTTCCG 58.299 37.037 10.83 0.00 0.00 4.30
884 888 9.542462 TGGCGCATATATAGTATTTTATCTTCC 57.458 33.333 10.83 0.00 0.00 3.46
886 890 9.031360 CGTGGCGCATATATAGTATTTTATCTT 57.969 33.333 10.83 0.00 0.00 2.40
887 891 8.575565 CGTGGCGCATATATAGTATTTTATCT 57.424 34.615 10.83 0.00 0.00 1.98
962 1303 1.444933 TCAGTGGATCTGTGGGGTTT 58.555 50.000 0.00 0.00 43.97 3.27
965 1306 2.584835 TTTTCAGTGGATCTGTGGGG 57.415 50.000 0.00 0.00 43.97 4.96
990 1331 2.438392 GGGAAGATCCATCGGGTTAGTT 59.562 50.000 0.00 0.00 38.64 2.24
991 1332 2.047830 GGGAAGATCCATCGGGTTAGT 58.952 52.381 0.00 0.00 38.64 2.24
1143 1484 2.983402 TGTAGTTGACGAAGAGACCG 57.017 50.000 0.00 0.00 0.00 4.79
1396 1737 3.127352 GACGGCGGTAGAGAGGCTG 62.127 68.421 13.24 0.00 38.97 4.85
1563 1904 3.244215 CCATCGAGCTGGTGGTGTTATAT 60.244 47.826 0.00 0.00 0.00 0.86
1615 1956 1.399791 CCCGGTACTTGACGAGTAGAC 59.600 57.143 0.00 0.00 41.41 2.59
1629 1970 2.527123 TCAACCCACTGCCCGGTA 60.527 61.111 0.00 0.00 0.00 4.02
1643 1984 4.079980 TCTCGGACAAAAATCCTGTCAA 57.920 40.909 5.42 0.00 44.16 3.18
1652 1993 2.955660 ACATTGCCTTCTCGGACAAAAA 59.044 40.909 0.00 0.00 34.20 1.94
1661 2002 0.321653 ACCCGTCACATTGCCTTCTC 60.322 55.000 0.00 0.00 0.00 2.87
1687 2028 0.173708 GGATCTGACCAGACGTCCAC 59.826 60.000 13.01 1.98 41.18 4.02
1695 2036 1.021390 GTGGCGTTGGATCTGACCAG 61.021 60.000 0.00 0.00 41.19 4.00
1785 2126 4.160065 CCATGCCTCATAACAAAATCACCA 59.840 41.667 0.00 0.00 0.00 4.17
1836 2177 3.725895 CGCATCAAGGACGAGACAAAATG 60.726 47.826 0.00 0.00 0.00 2.32
1858 2199 3.190535 ACATGTTGGTTAGATTGAACGCC 59.809 43.478 0.00 0.00 0.00 5.68
1889 2230 8.635765 ACAACCTAGTGTATGACATGAAAATT 57.364 30.769 0.00 0.00 0.00 1.82
1890 2231 7.882791 TGACAACCTAGTGTATGACATGAAAAT 59.117 33.333 0.00 0.00 0.00 1.82
1936 2278 4.184649 AGTCTTGGGGTTTTGATCACTT 57.815 40.909 0.00 0.00 0.00 3.16
1975 2317 2.224885 GCATCGTCGTCTTCCTCGC 61.225 63.158 0.00 0.00 0.00 5.03
1979 2321 2.347755 GGTTTTAGCATCGTCGTCTTCC 59.652 50.000 0.00 0.00 0.00 3.46
2303 2645 1.927487 TGTAGCCCTCGAGGTTGTTA 58.073 50.000 29.25 14.56 38.26 2.41
2435 2777 7.986562 GGAAAAGTGATCCCAAATACTCTAAC 58.013 38.462 0.00 0.00 0.00 2.34
2573 2915 5.047802 GGAGTGCAGATGAATTTCCTTTGAA 60.048 40.000 0.00 0.00 0.00 2.69
2724 3066 4.154918 ACGTTGATGAGCCTTGAGAAATTC 59.845 41.667 0.00 0.00 0.00 2.17
2754 3096 5.726793 AGGGACTCCTGTATGTCAAAAGTAT 59.273 40.000 0.00 0.00 42.98 2.12
2770 3112 4.348168 TCTGCTAATTAATCCAGGGACTCC 59.652 45.833 9.50 0.00 34.60 3.85
2855 3197 3.054802 CCAATAGAGAAACTGCCAGGACT 60.055 47.826 0.00 0.00 0.00 3.85
2862 3204 3.347216 TGGAAGCCAATAGAGAAACTGC 58.653 45.455 0.00 0.00 0.00 4.40
2899 3241 3.132925 GCAAAAAGCACATGGAACACAT 58.867 40.909 0.00 0.00 43.30 3.21
2900 3242 2.168106 AGCAAAAAGCACATGGAACACA 59.832 40.909 0.00 0.00 45.94 3.72
2901 3243 2.540931 CAGCAAAAAGCACATGGAACAC 59.459 45.455 0.00 0.00 45.94 3.32
2902 3244 6.761671 GTCCAGCAAAAAGCACATGGAACA 62.762 45.833 0.00 0.00 44.00 3.18
2903 3245 4.346787 GTCCAGCAAAAAGCACATGGAAC 61.347 47.826 0.00 0.00 44.00 3.62
2904 3246 2.224018 GTCCAGCAAAAAGCACATGGAA 60.224 45.455 0.00 0.00 44.00 3.53
2944 3286 1.445582 GTAACACCGGAGCAGGACG 60.446 63.158 9.46 0.00 34.73 4.79
2955 3297 5.681639 AGCAACCCTTCTATATGTAACACC 58.318 41.667 0.00 0.00 0.00 4.16
3057 3416 8.721019 TTTCTCTGCAAATTTGATCAAACTTT 57.279 26.923 22.71 18.76 32.51 2.66
3160 3524 9.591792 TCAGAGCAAAAATATCGATATCCATAG 57.408 33.333 18.01 8.88 0.00 2.23
3162 3526 8.725148 GTTCAGAGCAAAAATATCGATATCCAT 58.275 33.333 18.01 5.58 0.00 3.41
3168 3532 6.375455 ACCAAGTTCAGAGCAAAAATATCGAT 59.625 34.615 2.16 2.16 0.00 3.59
3356 3727 8.983702 TCCCACATAAATATAGGTTGGTTAAC 57.016 34.615 0.00 0.00 32.19 2.01
3439 3810 4.202202 CCACCACCTAAACAAAATGAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
3445 3817 3.901222 CCCTTCCACCACCTAAACAAAAT 59.099 43.478 0.00 0.00 0.00 1.82
3450 3822 1.905637 CACCCTTCCACCACCTAAAC 58.094 55.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.