Multiple sequence alignment - TraesCS6D01G078000

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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 TraesCS6D01G078000 chr6D 100.000 4470 0 0 1 4470 42567808 42563339 0.000000e+00 8255
1 TraesCS6D01G078000 chr6D 90.380 790 62 6 1 777 58745738 58746526 0.000000e+00 1026
2 TraesCS6D01G078000 chr6D 89.975 788 62 10 1 777 68686165 68685384 0.000000e+00 1002
3 TraesCS6D01G078000 chr6D 96.094 128 5 0 2420 2547 422936391 422936518 4.530000e-50 209
4 TraesCS6D01G078000 chr6D 96.094 128 4 1 2420 2547 359354766 359354892 1.630000e-49 207
5 TraesCS6D01G078000 chr6B 94.975 1612 53 13 824 2431 93997572 93999159 0.000000e+00 2503
6 TraesCS6D01G078000 chr6B 89.531 1471 78 24 2556 3989 93999152 94000583 0.000000e+00 1794
7 TraesCS6D01G078000 chr6B 90.102 788 64 7 1 777 152080884 152080100 0.000000e+00 1011
8 TraesCS6D01G078000 chr6B 86.441 354 39 8 4055 4401 94000609 94000960 3.260000e-101 379
9 TraesCS6D01G078000 chr6A 90.574 1411 73 23 2556 3940 58149898 58151274 0.000000e+00 1814
10 TraesCS6D01G078000 chr6A 95.963 966 22 7 824 1784 58148338 58149291 0.000000e+00 1552
11 TraesCS6D01G078000 chr6A 95.922 613 25 0 1822 2434 58149287 58149899 0.000000e+00 994
12 TraesCS6D01G078000 chr6A 86.655 577 23 26 3905 4470 58151354 58151887 1.380000e-164 590
13 TraesCS6D01G078000 chr2D 90.736 788 58 6 1 777 526521610 526520827 0.000000e+00 1037
14 TraesCS6D01G078000 chr2D 88.734 790 75 6 1 777 22417292 22418080 0.000000e+00 953
15 TraesCS6D01G078000 chr2D 98.261 115 2 0 2433 2547 305514869 305514983 7.580000e-48 202
16 TraesCS6D01G078000 chr5D 90.102 788 66 7 1 777 394844258 394843472 0.000000e+00 1013
17 TraesCS6D01G078000 chr5D 89.507 791 66 11 1 777 477840373 477841160 0.000000e+00 985
18 TraesCS6D01G078000 chr7D 89.747 790 68 6 1 777 164484200 164484989 0.000000e+00 998
19 TraesCS6D01G078000 chr7D 96.610 118 4 0 2433 2550 50729915 50729798 3.530000e-46 196
20 TraesCS6D01G078000 chr3A 89.507 791 68 7 1 777 492327240 492328029 0.000000e+00 987
21 TraesCS6D01G078000 chr3D 97.541 122 3 0 2426 2547 410670056 410670177 4.530000e-50 209
22 TraesCS6D01G078000 chr3D 95.312 128 4 2 2420 2547 397162718 397162593 7.580000e-48 202
23 TraesCS6D01G078000 chr7A 95.968 124 5 0 2424 2547 32776500 32776623 7.580000e-48 202
24 TraesCS6D01G078000 chr2A 91.447 152 6 7 2400 2547 460904198 460904050 7.580000e-48 202
25 TraesCS6D01G078000 chr4D 97.458 118 2 1 2430 2547 68663983 68663867 2.730000e-47 200


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 TraesCS6D01G078000 chr6D 42563339 42567808 4469 True 8255.000000 8255 100.000000 1 4470 1 chr6D.!!$R1 4469
1 TraesCS6D01G078000 chr6D 58745738 58746526 788 False 1026.000000 1026 90.380000 1 777 1 chr6D.!!$F1 776
2 TraesCS6D01G078000 chr6D 68685384 68686165 781 True 1002.000000 1002 89.975000 1 777 1 chr6D.!!$R2 776
3 TraesCS6D01G078000 chr6B 93997572 94000960 3388 False 1558.666667 2503 90.315667 824 4401 3 chr6B.!!$F1 3577
4 TraesCS6D01G078000 chr6B 152080100 152080884 784 True 1011.000000 1011 90.102000 1 777 1 chr6B.!!$R1 776
5 TraesCS6D01G078000 chr6A 58148338 58151887 3549 False 1237.500000 1814 92.278500 824 4470 4 chr6A.!!$F1 3646
6 TraesCS6D01G078000 chr2D 526520827 526521610 783 True 1037.000000 1037 90.736000 1 777 1 chr2D.!!$R1 776
7 TraesCS6D01G078000 chr2D 22417292 22418080 788 False 953.000000 953 88.734000 1 777 1 chr2D.!!$F1 776
8 TraesCS6D01G078000 chr5D 394843472 394844258 786 True 1013.000000 1013 90.102000 1 777 1 chr5D.!!$R1 776
9 TraesCS6D01G078000 chr5D 477840373 477841160 787 False 985.000000 985 89.507000 1 777 1 chr5D.!!$F1 776
10 TraesCS6D01G078000 chr7D 164484200 164484989 789 False 998.000000 998 89.747000 1 777 1 chr7D.!!$F1 776
11 TraesCS6D01G078000 chr3A 492327240 492328029 789 False 987.000000 987 89.507000 1 777 1 chr3A.!!$F1 776

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
938 972 0.105913 ATCCTTCCTCCCTCGTCCTC 60.106 60.000 0.00 0.00 0.00 3.71 F
941 975 0.753848 CTTCCTCCCTCGTCCTCCTC 60.754 65.000 0.00 0.00 0.00 3.71 F
1762 1801 1.071699 AGCGCCTAGTTCTTTTGTCCA 59.928 47.619 2.29 0.00 0.00 4.02 F
2548 2590 0.739462 TTTGCTCCGCATGTAGTCGG 60.739 55.000 3.35 3.35 46.52 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 2578 1.360551 CTCCCTCCGACTACATGCG 59.639 63.158 0.00 0.0 0.0 4.73 R
2537 2579 1.688772 TACTCCCTCCGACTACATGC 58.311 55.000 0.00 0.0 0.0 4.06 R
3175 3238 0.242825 CCACACGAGCTTCCTACGAA 59.757 55.000 0.00 0.0 0.0 3.85 R
4004 4227 0.037232 CCTTGAAGGTCCTGTCCGAC 60.037 60.000 2.25 0.0 0.0 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
59 60 3.214696 GAACTCCCGGATGGAATTCAT 57.785 47.619 0.73 0.00 46.42 2.57
161 162 1.134965 GTCGGAGTAGAGCATGCAGTT 60.135 52.381 21.98 7.16 0.00 3.16
167 168 1.815003 GTAGAGCATGCAGTTGCCTTT 59.185 47.619 21.98 0.00 43.83 3.11
243 244 0.166814 GCTTTTCATTGCTCGCGAGT 59.833 50.000 34.46 14.96 0.00 4.18
284 285 4.227864 GGACCATGAGATGTTCCTCTTT 57.772 45.455 0.00 0.00 38.67 2.52
309 316 1.682684 GTCGGCTTCCTCCTCCAGA 60.683 63.158 0.00 0.00 0.00 3.86
375 384 1.072505 AAATCGCCGAACACCTGGT 59.927 52.632 0.00 0.00 0.00 4.00
482 494 2.802106 CGGCGAGACCTTCTCTCC 59.198 66.667 0.00 2.59 43.21 3.71
613 632 0.537143 TTTCGCCTGACAATGTGGCT 60.537 50.000 12.08 0.00 44.09 4.75
625 644 1.237285 ATGTGGCTCAGGCGTGTTTC 61.237 55.000 6.26 0.00 39.81 2.78
726 747 1.335506 GGCAAATTTCGGCGTCTTGAA 60.336 47.619 6.85 0.00 0.00 2.69
770 794 3.428282 CCGGCGCGTAAAAAGGCT 61.428 61.111 8.43 0.00 0.00 4.58
777 801 0.608308 GCGTAAAAAGGCTCCTGGGT 60.608 55.000 0.00 0.00 0.00 4.51
778 802 1.905637 CGTAAAAAGGCTCCTGGGTT 58.094 50.000 0.00 0.00 0.00 4.11
779 803 1.539827 CGTAAAAAGGCTCCTGGGTTG 59.460 52.381 0.00 0.00 0.00 3.77
780 804 2.812613 CGTAAAAAGGCTCCTGGGTTGA 60.813 50.000 0.00 0.00 0.00 3.18
781 805 2.702270 AAAAAGGCTCCTGGGTTGAT 57.298 45.000 0.00 0.00 0.00 2.57
782 806 1.928868 AAAAGGCTCCTGGGTTGATG 58.071 50.000 0.00 0.00 0.00 3.07
783 807 0.613012 AAAGGCTCCTGGGTTGATGC 60.613 55.000 0.00 0.00 0.00 3.91
784 808 1.504275 AAGGCTCCTGGGTTGATGCT 61.504 55.000 0.00 0.00 0.00 3.79
785 809 1.452833 GGCTCCTGGGTTGATGCTC 60.453 63.158 0.00 0.00 0.00 4.26
786 810 1.606531 GCTCCTGGGTTGATGCTCT 59.393 57.895 0.00 0.00 0.00 4.09
787 811 0.833287 GCTCCTGGGTTGATGCTCTA 59.167 55.000 0.00 0.00 0.00 2.43
788 812 1.210478 GCTCCTGGGTTGATGCTCTAA 59.790 52.381 0.00 0.00 0.00 2.10
789 813 2.744494 GCTCCTGGGTTGATGCTCTAAG 60.744 54.545 0.00 0.00 0.00 2.18
790 814 1.210478 TCCTGGGTTGATGCTCTAAGC 59.790 52.381 0.00 0.00 42.82 3.09
791 815 1.211457 CCTGGGTTGATGCTCTAAGCT 59.789 52.381 0.11 0.00 42.97 3.74
792 816 2.559440 CTGGGTTGATGCTCTAAGCTC 58.441 52.381 0.11 0.00 42.97 4.09
793 817 2.170187 CTGGGTTGATGCTCTAAGCTCT 59.830 50.000 0.11 0.00 42.97 4.09
794 818 2.169352 TGGGTTGATGCTCTAAGCTCTC 59.831 50.000 0.11 0.00 42.97 3.20
795 819 2.468831 GGTTGATGCTCTAAGCTCTCG 58.531 52.381 0.11 0.00 42.97 4.04
796 820 2.099921 GGTTGATGCTCTAAGCTCTCGA 59.900 50.000 0.11 0.00 42.97 4.04
797 821 3.429547 GGTTGATGCTCTAAGCTCTCGAA 60.430 47.826 0.11 0.00 42.97 3.71
798 822 3.428746 TGATGCTCTAAGCTCTCGAAC 57.571 47.619 0.11 0.00 42.97 3.95
799 823 2.755103 TGATGCTCTAAGCTCTCGAACA 59.245 45.455 0.11 0.00 42.97 3.18
800 824 3.193479 TGATGCTCTAAGCTCTCGAACAA 59.807 43.478 0.11 0.00 42.97 2.83
801 825 3.223423 TGCTCTAAGCTCTCGAACAAG 57.777 47.619 0.11 0.00 42.97 3.16
802 826 1.923864 GCTCTAAGCTCTCGAACAAGC 59.076 52.381 6.10 6.10 38.45 4.01
803 827 2.672478 GCTCTAAGCTCTCGAACAAGCA 60.672 50.000 14.37 0.00 41.06 3.91
804 828 3.579709 CTCTAAGCTCTCGAACAAGCAA 58.420 45.455 14.37 3.91 41.06 3.91
805 829 3.579709 TCTAAGCTCTCGAACAAGCAAG 58.420 45.455 14.37 11.31 41.06 4.01
806 830 2.533266 AAGCTCTCGAACAAGCAAGA 57.467 45.000 14.37 0.00 41.06 3.02
807 831 2.758736 AGCTCTCGAACAAGCAAGAT 57.241 45.000 14.37 0.00 41.06 2.40
808 832 2.615869 AGCTCTCGAACAAGCAAGATC 58.384 47.619 14.37 0.00 41.06 2.75
809 833 1.663135 GCTCTCGAACAAGCAAGATCC 59.337 52.381 8.73 0.00 38.42 3.36
810 834 2.676463 GCTCTCGAACAAGCAAGATCCT 60.676 50.000 8.73 0.00 38.42 3.24
811 835 3.429547 GCTCTCGAACAAGCAAGATCCTA 60.430 47.826 8.73 0.00 38.42 2.94
812 836 4.748892 CTCTCGAACAAGCAAGATCCTAA 58.251 43.478 0.00 0.00 0.00 2.69
813 837 5.147330 TCTCGAACAAGCAAGATCCTAAA 57.853 39.130 0.00 0.00 0.00 1.85
814 838 5.734720 TCTCGAACAAGCAAGATCCTAAAT 58.265 37.500 0.00 0.00 0.00 1.40
815 839 6.873997 TCTCGAACAAGCAAGATCCTAAATA 58.126 36.000 0.00 0.00 0.00 1.40
816 840 7.327975 TCTCGAACAAGCAAGATCCTAAATAA 58.672 34.615 0.00 0.00 0.00 1.40
817 841 7.822334 TCTCGAACAAGCAAGATCCTAAATAAA 59.178 33.333 0.00 0.00 0.00 1.40
818 842 8.330466 TCGAACAAGCAAGATCCTAAATAAAA 57.670 30.769 0.00 0.00 0.00 1.52
819 843 8.788806 TCGAACAAGCAAGATCCTAAATAAAAA 58.211 29.630 0.00 0.00 0.00 1.94
838 862 3.443099 AAAGCTCTCCAACAAGCAAAC 57.557 42.857 0.00 0.00 41.06 2.93
844 868 1.045911 TCCAACAAGCAAACCACCCC 61.046 55.000 0.00 0.00 0.00 4.95
930 964 0.924226 TTTCCCCCATCCTTCCTCCC 60.924 60.000 0.00 0.00 0.00 4.30
931 965 1.848835 TTCCCCCATCCTTCCTCCCT 61.849 60.000 0.00 0.00 0.00 4.20
933 967 2.143419 CCCCATCCTTCCTCCCTCG 61.143 68.421 0.00 0.00 0.00 4.63
934 968 1.383248 CCCATCCTTCCTCCCTCGT 60.383 63.158 0.00 0.00 0.00 4.18
935 969 1.403687 CCCATCCTTCCTCCCTCGTC 61.404 65.000 0.00 0.00 0.00 4.20
936 970 1.403687 CCATCCTTCCTCCCTCGTCC 61.404 65.000 0.00 0.00 0.00 4.79
937 971 0.397816 CATCCTTCCTCCCTCGTCCT 60.398 60.000 0.00 0.00 0.00 3.85
938 972 0.105913 ATCCTTCCTCCCTCGTCCTC 60.106 60.000 0.00 0.00 0.00 3.71
939 973 1.758906 CCTTCCTCCCTCGTCCTCC 60.759 68.421 0.00 0.00 0.00 4.30
940 974 1.308326 CTTCCTCCCTCGTCCTCCT 59.692 63.158 0.00 0.00 0.00 3.69
941 975 0.753848 CTTCCTCCCTCGTCCTCCTC 60.754 65.000 0.00 0.00 0.00 3.71
942 976 1.506907 TTCCTCCCTCGTCCTCCTCA 61.507 60.000 0.00 0.00 0.00 3.86
1071 1105 2.125229 TCGTCCTCGTCCTCCTCG 60.125 66.667 0.00 0.00 38.33 4.63
1357 1393 6.109359 CAGAGATCTAGGGTTTGTTAGTTGG 58.891 44.000 0.00 0.00 0.00 3.77
1573 1609 5.013568 ACATTATGATTGGTTGGTGCATG 57.986 39.130 0.00 0.00 0.00 4.06
1582 1618 2.223595 TGGTTGGTGCATGTTTTACACG 60.224 45.455 0.00 0.00 35.11 4.49
1641 1680 5.654650 ACAGTTAGGTCTTGAGTAGATGGAG 59.345 44.000 0.00 0.00 34.79 3.86
1727 1766 4.460263 AGCACCTGTCACTGTAATTTTGA 58.540 39.130 0.00 0.00 0.00 2.69
1728 1767 4.275936 AGCACCTGTCACTGTAATTTTGAC 59.724 41.667 0.00 0.00 40.14 3.18
1729 1768 4.036262 GCACCTGTCACTGTAATTTTGACA 59.964 41.667 3.79 3.79 45.71 3.58
1756 1795 2.633488 GATGGAAGCGCCTAGTTCTTT 58.367 47.619 2.29 0.00 37.63 2.52
1762 1801 1.071699 AGCGCCTAGTTCTTTTGTCCA 59.928 47.619 2.29 0.00 0.00 4.02
1794 1833 2.844946 TCTTGTTGACTTGAATGCCGA 58.155 42.857 0.00 0.00 0.00 5.54
1805 1844 6.992123 TGACTTGAATGCCGATTCTATGTTAT 59.008 34.615 0.00 0.00 39.10 1.89
1966 2008 4.462834 TGTTATGTTTGGTGGTGTTGTCAA 59.537 37.500 0.00 0.00 0.00 3.18
1982 2024 7.308529 GGTGTTGTCAATGAATCATGTTCTGTA 60.309 37.037 0.00 0.00 0.00 2.74
1994 2036 6.149129 TCATGTTCTGTATAGTGCTGTAGG 57.851 41.667 0.00 0.00 0.00 3.18
2020 2062 7.360946 GCAGAGTCACTTTAACCAACGATTAAT 60.361 37.037 0.00 0.00 0.00 1.40
2041 2083 1.815003 GGTAGCAGCAAAAGCACATCT 59.185 47.619 0.00 0.00 0.00 2.90
2079 2121 5.405797 GCTTTAATTTTGCAAGAGGAGAGG 58.594 41.667 0.00 0.00 0.00 3.69
2123 2165 9.294030 GAAAGTAGCTATGGAATCAAACAAATG 57.706 33.333 0.00 0.00 0.00 2.32
2142 2184 2.747460 TCCACCTTGCTCGCATGC 60.747 61.111 7.91 7.91 0.00 4.06
2407 2449 7.653311 GCAGAAAAAGTTGGATGTAAGTTTCAT 59.347 33.333 0.00 0.00 33.33 2.57
2432 2474 9.920946 ATGTTTAGAATGGTTCCATTATGTACT 57.079 29.630 18.29 12.57 36.86 2.73
2437 2479 7.736893 AGAATGGTTCCATTATGTACTACTCC 58.263 38.462 15.81 1.37 36.86 3.85
2438 2480 5.881923 TGGTTCCATTATGTACTACTCCC 57.118 43.478 0.00 0.00 0.00 4.30
2439 2481 5.535029 TGGTTCCATTATGTACTACTCCCT 58.465 41.667 0.00 0.00 0.00 4.20
2440 2482 5.601313 TGGTTCCATTATGTACTACTCCCTC 59.399 44.000 0.00 0.00 0.00 4.30
2441 2483 5.011840 GGTTCCATTATGTACTACTCCCTCC 59.988 48.000 0.00 0.00 0.00 4.30
2442 2484 4.404640 TCCATTATGTACTACTCCCTCCG 58.595 47.826 0.00 0.00 0.00 4.63
2443 2485 4.141088 TCCATTATGTACTACTCCCTCCGT 60.141 45.833 0.00 0.00 0.00 4.69
2444 2486 4.587684 CCATTATGTACTACTCCCTCCGTT 59.412 45.833 0.00 0.00 0.00 4.44
2445 2487 5.278858 CCATTATGTACTACTCCCTCCGTTC 60.279 48.000 0.00 0.00 0.00 3.95
2446 2488 2.134789 TGTACTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
2447 2489 1.637553 TGTACTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
2448 2490 2.846206 TGTACTACTCCCTCCGTTCCTA 59.154 50.000 0.00 0.00 0.00 2.94
2449 2491 3.266772 TGTACTACTCCCTCCGTTCCTAA 59.733 47.826 0.00 0.00 0.00 2.69
2450 2492 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2451 2493 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2452 2494 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2453 2495 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2454 2496 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2455 2497 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2456 2498 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2457 2499 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2458 2500 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2459 2501 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2460 2502 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2461 2503 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2462 2504 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2463 2505 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2479 2521 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
2480 2522 6.897966 AGTCTTTGTAGAGATTCCACTATGGA 59.102 38.462 0.00 0.00 46.61 3.41
2490 2532 2.036387 TCCACTATGGACCACATACGG 58.964 52.381 0.00 0.00 42.67 4.02
2491 2533 2.036387 CCACTATGGACCACATACGGA 58.964 52.381 0.00 0.00 40.96 4.69
2492 2534 2.632996 CCACTATGGACCACATACGGAT 59.367 50.000 0.00 0.00 40.96 4.18
2493 2535 3.554960 CCACTATGGACCACATACGGATG 60.555 52.174 5.94 5.94 40.96 3.51
2494 2536 6.014967 CCACTATGGACCACATACGGATGT 62.015 50.000 7.68 7.68 43.21 3.06
2495 2537 4.279922 CACTATGGACCACATACGGATGTA 59.720 45.833 14.23 0.00 44.82 2.29
2496 2538 5.047306 CACTATGGACCACATACGGATGTAT 60.047 44.000 14.23 4.48 44.82 2.29
2497 2539 6.152154 CACTATGGACCACATACGGATGTATA 59.848 42.308 14.23 6.48 44.82 1.47
2498 2540 6.895756 ACTATGGACCACATACGGATGTATAT 59.104 38.462 14.23 1.16 44.82 0.86
2499 2541 8.057011 ACTATGGACCACATACGGATGTATATA 58.943 37.037 14.23 7.10 44.82 0.86
2500 2542 6.769134 TGGACCACATACGGATGTATATAG 57.231 41.667 14.23 0.00 44.82 1.31
2501 2543 6.486941 TGGACCACATACGGATGTATATAGA 58.513 40.000 14.23 0.00 44.82 1.98
2502 2544 7.123383 TGGACCACATACGGATGTATATAGAT 58.877 38.462 14.23 0.00 44.82 1.98
2503 2545 7.068226 TGGACCACATACGGATGTATATAGATG 59.932 40.741 14.23 0.00 44.82 2.90
2504 2546 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
2505 2547 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
2506 2548 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
2507 2549 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
2508 2550 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
2509 2551 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2513 2555 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
2514 2556 9.809096 CGGATGTATATAGATGCATTTTAGAGT 57.191 33.333 11.19 0.00 38.38 3.24
2524 2566 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
2535 2577 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2536 2578 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2537 2579 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2538 2580 2.421424 AGATTCACTCATTTTGCTCCGC 59.579 45.455 0.00 0.00 0.00 5.54
2539 2581 1.603456 TTCACTCATTTTGCTCCGCA 58.397 45.000 0.00 0.00 36.47 5.69
2540 2582 1.825090 TCACTCATTTTGCTCCGCAT 58.175 45.000 0.00 0.00 38.76 4.73
2541 2583 1.469703 TCACTCATTTTGCTCCGCATG 59.530 47.619 0.00 0.00 38.76 4.06
2542 2584 1.200716 CACTCATTTTGCTCCGCATGT 59.799 47.619 0.00 0.00 38.76 3.21
2543 2585 2.419673 CACTCATTTTGCTCCGCATGTA 59.580 45.455 0.00 0.00 38.76 2.29
2544 2586 2.679837 ACTCATTTTGCTCCGCATGTAG 59.320 45.455 0.00 0.00 38.76 2.74
2545 2587 2.679837 CTCATTTTGCTCCGCATGTAGT 59.320 45.455 0.00 0.00 38.76 2.73
2546 2588 2.677836 TCATTTTGCTCCGCATGTAGTC 59.322 45.455 0.00 0.00 38.76 2.59
2547 2589 1.075542 TTTTGCTCCGCATGTAGTCG 58.924 50.000 0.00 0.00 38.76 4.18
2548 2590 0.739462 TTTGCTCCGCATGTAGTCGG 60.739 55.000 3.35 3.35 46.52 4.79
2553 2595 3.521605 CGCATGTAGTCGGAGGGA 58.478 61.111 0.00 0.00 0.00 4.20
2554 2596 1.360551 CGCATGTAGTCGGAGGGAG 59.639 63.158 0.00 0.00 0.00 4.30
2561 2603 3.418995 TGTAGTCGGAGGGAGTATATGC 58.581 50.000 0.00 0.00 33.26 3.14
2606 2648 7.012989 TGGTAGCTAACTTTTCAGAACCTTTTC 59.987 37.037 10.78 0.00 0.00 2.29
2698 2741 6.915544 TCTAAGCATCTATGAGCAACAAAG 57.084 37.500 0.00 0.00 0.00 2.77
2710 2753 4.067896 GAGCAACAAAGACCTGATGAGAA 58.932 43.478 0.00 0.00 0.00 2.87
2772 2831 8.055986 GCTTCTGTTTTTGTGTAAAAATAGTGC 58.944 33.333 16.24 16.49 40.33 4.40
2796 2855 3.165071 ACTGGCAATTTTAGTGGAAGGG 58.835 45.455 0.00 0.00 0.00 3.95
2816 2875 5.458595 AGGGTTCTTTGTTCTTGGAAGAAT 58.541 37.500 5.16 0.00 45.83 2.40
2881 2944 7.994425 TTGGATGCTTATTGAAAGTGTTCTA 57.006 32.000 0.00 0.00 34.60 2.10
3045 3108 5.482878 AGGAATGGAGTCTTCAATGCAAAAT 59.517 36.000 0.00 0.00 0.00 1.82
3109 3172 6.549364 TGATGTTGTGGTAAGAAATTGTCCTT 59.451 34.615 0.00 0.00 0.00 3.36
3199 3262 2.280797 GAAGCTCGTGTGGCACCA 60.281 61.111 16.26 0.00 0.00 4.17
3340 3403 7.201857 GCTGATAAATGGCTATCTTGGTTTCTT 60.202 37.037 0.00 0.00 30.80 2.52
3353 3416 1.543871 GGTTTCTTCCACGGCTAACCA 60.544 52.381 0.00 0.00 36.06 3.67
3508 3581 2.672651 TGCCAACTCCATGCCGTG 60.673 61.111 0.00 0.00 0.00 4.94
3509 3582 2.359850 GCCAACTCCATGCCGTGA 60.360 61.111 0.00 0.00 0.00 4.35
3510 3583 2.690778 GCCAACTCCATGCCGTGAC 61.691 63.158 0.00 0.00 0.00 3.67
3511 3584 1.302431 CCAACTCCATGCCGTGACA 60.302 57.895 0.00 0.00 0.00 3.58
3512 3585 1.300971 CCAACTCCATGCCGTGACAG 61.301 60.000 0.00 0.00 0.00 3.51
3513 3586 1.672356 AACTCCATGCCGTGACAGC 60.672 57.895 0.00 0.00 0.00 4.40
3514 3587 2.046988 CTCCATGCCGTGACAGCA 60.047 61.111 0.00 0.00 45.94 4.41
3654 3727 0.040942 TTGCACTAATGTGGGCCCAT 59.959 50.000 31.45 15.75 43.97 4.00
3715 3794 6.154445 GGCTGAATATTTGTAATGCCTGATG 58.846 40.000 0.00 0.00 36.52 3.07
3716 3795 6.016024 GGCTGAATATTTGTAATGCCTGATGA 60.016 38.462 0.00 0.00 36.52 2.92
3722 3801 4.880886 TTGTAATGCCTGATGATTGTCG 57.119 40.909 0.00 0.00 0.00 4.35
3729 3808 2.555199 CCTGATGATTGTCGGAGGAAC 58.445 52.381 0.00 0.00 0.00 3.62
3747 3826 1.696063 ACAGTGAATGCTGGCTTTGT 58.304 45.000 0.00 0.00 40.59 2.83
3755 3834 4.810491 TGAATGCTGGCTTTGTTTTTCTTC 59.190 37.500 0.00 0.00 0.00 2.87
3762 3841 2.034685 GCTTTGTTTTTCTTCGCTCCCT 59.965 45.455 0.00 0.00 0.00 4.20
3813 3908 4.171754 GCTGAAGCCAATGTTCATCTTTC 58.828 43.478 0.00 0.00 33.49 2.62
3880 3988 4.697352 ACTGAAGAGTGTATGTCAAATGGC 59.303 41.667 0.00 0.00 0.00 4.40
3955 4178 4.092529 CAGAGCATGTTGTAGCTACTGTTG 59.907 45.833 23.84 16.06 42.04 3.33
4003 4226 1.376466 TGAGGTTGAAGCTCAGGGC 59.624 57.895 21.77 0.00 46.53 5.19
4004 4227 2.454832 TGAGGTTGAAGCTCAGGGCG 62.455 60.000 21.77 0.00 46.53 6.13
4029 4253 0.251634 CAGGACCTTCAAGGAGAGGC 59.748 60.000 11.59 0.00 37.67 4.70
4088 4314 3.569701 TGGAGAGCAATTTGACTGAAACC 59.430 43.478 0.00 0.00 0.00 3.27
4145 4374 6.713450 CCCCATAAATTTATGTAGTTAGCCGT 59.287 38.462 28.10 0.00 39.04 5.68
4186 4415 4.136796 TGCATTGCTGTTTACAAGTCTCT 58.863 39.130 10.49 0.00 0.00 3.10
4189 4418 5.409826 GCATTGCTGTTTACAAGTCTCTACT 59.590 40.000 0.16 0.00 37.65 2.57
4204 4433 7.646548 AGTCTCTACTAACATGTAATGCTGA 57.353 36.000 0.00 0.00 40.71 4.26
4215 4444 6.803154 CATGTAATGCTGATCATCATGAGT 57.197 37.500 12.58 0.64 38.60 3.41
4220 4449 2.367894 TGCTGATCATCATGAGTCTCCC 59.632 50.000 0.09 0.00 0.00 4.30
4240 4469 1.455786 CGCGATCTTCGTTTGTTCTGT 59.544 47.619 0.00 0.00 42.81 3.41
4264 4496 4.758251 TGTCGGGCAGGTGCATCG 62.758 66.667 4.01 7.38 44.36 3.84
4303 4535 3.247006 TGTTCATCTTAGAACCGGAGC 57.753 47.619 9.46 0.00 45.62 4.70
4318 4555 2.952978 CCGGAGCTCTACTTGACATAGT 59.047 50.000 14.64 0.00 0.00 2.12
4349 4587 5.559148 TCAATGCCCTTTAAATGGTTTGT 57.441 34.783 17.96 1.72 0.00 2.83
4358 4596 6.708054 CCCTTTAAATGGTTTGTTAACATGCA 59.292 34.615 9.56 0.00 35.92 3.96
4363 4601 6.542574 AATGGTTTGTTAACATGCATTGTG 57.457 33.333 9.56 0.00 38.99 3.33
4448 4686 4.816925 CCTACTAATTTGACCTAGGCAAGC 59.183 45.833 9.30 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.901114 TCCATCCGGGAGTTCGACAA 60.901 55.000 0.00 0.00 42.15 3.18
59 60 4.261801 CCGAAAGCTTTTCCTCAGGATTA 58.738 43.478 14.05 0.00 0.00 1.75
161 162 1.741401 CGGCATCGTCTGAAAGGCA 60.741 57.895 1.31 0.00 39.79 4.75
167 168 0.320374 AAAGAACCGGCATCGTCTGA 59.680 50.000 0.00 0.00 33.95 3.27
284 285 2.282958 AGGAAGCCGACGTCCAGA 60.283 61.111 10.58 0.00 45.99 3.86
471 482 0.108089 GCCGGAAAGGAGAGAAGGTC 60.108 60.000 5.05 0.00 45.00 3.85
562 575 1.923395 AGATTCGCCTTCCACCCCA 60.923 57.895 0.00 0.00 0.00 4.96
570 585 1.656652 CAATCGTCCAGATTCGCCTT 58.343 50.000 0.00 0.00 45.95 4.35
606 625 1.228245 AAACACGCCTGAGCCACAT 60.228 52.632 0.00 0.00 34.57 3.21
710 731 0.521735 GCCTTCAAGACGCCGAAATT 59.478 50.000 0.00 0.00 0.00 1.82
726 747 3.785122 AAAAACCCCACTCGCGCCT 62.785 57.895 0.00 0.00 0.00 5.52
770 794 1.210478 GCTTAGAGCATCAACCCAGGA 59.790 52.381 0.00 0.00 41.89 3.86
777 801 3.193479 TGTTCGAGAGCTTAGAGCATCAA 59.807 43.478 2.47 0.00 45.56 2.57
778 802 2.755103 TGTTCGAGAGCTTAGAGCATCA 59.245 45.455 2.47 0.00 45.56 3.07
779 803 3.428746 TGTTCGAGAGCTTAGAGCATC 57.571 47.619 2.47 0.00 45.56 3.91
780 804 3.779759 CTTGTTCGAGAGCTTAGAGCAT 58.220 45.455 2.47 0.00 45.56 3.79
781 805 2.672478 GCTTGTTCGAGAGCTTAGAGCA 60.672 50.000 9.45 0.00 45.56 4.26
782 806 1.923864 GCTTGTTCGAGAGCTTAGAGC 59.076 52.381 9.45 0.00 42.84 4.09
783 807 3.223423 TGCTTGTTCGAGAGCTTAGAG 57.777 47.619 15.47 0.00 39.60 2.43
784 808 3.255888 TCTTGCTTGTTCGAGAGCTTAGA 59.744 43.478 15.47 14.30 39.60 2.10
785 809 3.579709 TCTTGCTTGTTCGAGAGCTTAG 58.420 45.455 15.47 12.85 39.60 2.18
786 810 3.660501 TCTTGCTTGTTCGAGAGCTTA 57.339 42.857 15.47 6.13 39.60 3.09
787 811 2.533266 TCTTGCTTGTTCGAGAGCTT 57.467 45.000 15.47 0.00 39.60 3.74
788 812 2.615869 GATCTTGCTTGTTCGAGAGCT 58.384 47.619 15.47 0.00 39.60 4.09
789 813 1.663135 GGATCTTGCTTGTTCGAGAGC 59.337 52.381 9.70 9.70 39.33 4.09
790 814 3.244033 AGGATCTTGCTTGTTCGAGAG 57.756 47.619 0.00 0.00 30.55 3.20
791 815 4.801330 TTAGGATCTTGCTTGTTCGAGA 57.199 40.909 0.00 0.00 0.00 4.04
792 816 7.539712 TTATTTAGGATCTTGCTTGTTCGAG 57.460 36.000 0.00 0.00 0.00 4.04
793 817 7.915293 TTTATTTAGGATCTTGCTTGTTCGA 57.085 32.000 0.00 0.00 0.00 3.71
794 818 8.964420 TTTTTATTTAGGATCTTGCTTGTTCG 57.036 30.769 0.00 0.00 0.00 3.95
816 840 4.183865 GTTTGCTTGTTGGAGAGCTTTTT 58.816 39.130 0.00 0.00 39.60 1.94
817 841 3.430790 GGTTTGCTTGTTGGAGAGCTTTT 60.431 43.478 0.00 0.00 39.60 2.27
818 842 2.101415 GGTTTGCTTGTTGGAGAGCTTT 59.899 45.455 0.00 0.00 39.60 3.51
819 843 1.683385 GGTTTGCTTGTTGGAGAGCTT 59.317 47.619 0.00 0.00 39.60 3.74
820 844 1.322442 GGTTTGCTTGTTGGAGAGCT 58.678 50.000 0.00 0.00 39.60 4.09
821 845 1.032014 TGGTTTGCTTGTTGGAGAGC 58.968 50.000 0.00 0.00 39.33 4.09
822 846 1.338020 GGTGGTTTGCTTGTTGGAGAG 59.662 52.381 0.00 0.00 0.00 3.20
827 851 1.445518 GGGGGTGGTTTGCTTGTTG 59.554 57.895 0.00 0.00 0.00 3.33
844 868 3.281727 TTCGGAATTTCAGATGGAGGG 57.718 47.619 0.00 0.00 0.00 4.30
930 964 1.231221 CGGTAGATGAGGAGGACGAG 58.769 60.000 0.00 0.00 0.00 4.18
931 965 0.818445 GCGGTAGATGAGGAGGACGA 60.818 60.000 0.00 0.00 0.00 4.20
933 967 1.797211 CGGCGGTAGATGAGGAGGAC 61.797 65.000 0.00 0.00 0.00 3.85
934 968 1.528542 CGGCGGTAGATGAGGAGGA 60.529 63.158 0.00 0.00 0.00 3.71
935 969 3.043419 CGGCGGTAGATGAGGAGG 58.957 66.667 0.00 0.00 0.00 4.30
936 970 2.336809 GCGGCGGTAGATGAGGAG 59.663 66.667 9.78 0.00 0.00 3.69
937 971 3.592814 CGCGGCGGTAGATGAGGA 61.593 66.667 15.84 0.00 0.00 3.71
1357 1393 1.782028 AAACGTCAGAACCGCAAGCC 61.782 55.000 0.00 0.00 0.00 4.35
1573 1609 2.351350 CCAATGTCAGCCCGTGTAAAAC 60.351 50.000 0.00 0.00 0.00 2.43
1582 1618 0.883833 CACAGAACCAATGTCAGCCC 59.116 55.000 0.00 0.00 0.00 5.19
1641 1680 6.426980 TGTCATTTGATATGTCTCACAAGC 57.573 37.500 0.00 0.00 0.00 4.01
1727 1766 0.527565 GCGCTTCCATCCATTGTTGT 59.472 50.000 0.00 0.00 0.00 3.32
1728 1767 0.179129 GGCGCTTCCATCCATTGTTG 60.179 55.000 7.64 0.00 34.01 3.33
1729 1768 0.323725 AGGCGCTTCCATCCATTGTT 60.324 50.000 7.64 0.00 37.29 2.83
1756 1795 8.637099 TCAACAAGAACAATATCAATTGGACAA 58.363 29.630 5.42 0.00 45.72 3.18
1824 1864 8.522830 TCAAAAGAAAAACTCAAGTCAATCTGT 58.477 29.630 0.00 0.00 0.00 3.41
1883 1925 2.289320 GCAAACACAAATACATGGGCCA 60.289 45.455 9.61 9.61 0.00 5.36
1966 2008 7.278135 ACAGCACTATACAGAACATGATTCAT 58.722 34.615 0.00 0.00 0.00 2.57
1994 2036 3.128349 TCGTTGGTTAAAGTGACTCTGC 58.872 45.455 0.00 0.00 0.00 4.26
2005 2047 5.065474 GCTGCTACCATTAATCGTTGGTTAA 59.935 40.000 3.87 0.00 43.73 2.01
2041 2083 1.848652 AAAGCCTAGTGACCTCGCTA 58.151 50.000 0.00 0.00 37.87 4.26
2109 2151 3.259123 AGGTGGAGCATTTGTTTGATTCC 59.741 43.478 0.00 0.00 0.00 3.01
2123 2165 2.437359 ATGCGAGCAAGGTGGAGC 60.437 61.111 0.57 0.00 0.00 4.70
2142 2184 7.715686 ACCTGCATGCAGATAATATGATATCAG 59.284 37.037 42.21 23.92 46.30 2.90
2432 2474 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2434 2476 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2436 2478 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2437 2479 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2438 2480 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
2453 2495 8.696374 CCATAGTGGAATCTCTACAAAGACTTA 58.304 37.037 0.00 0.00 40.96 2.24
2454 2496 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
2455 2497 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
2456 2498 7.113658 TCCATAGTGGAATCTCTACAAAGAC 57.886 40.000 0.00 0.00 45.00 3.01
2470 2512 2.036387 CCGTATGTGGTCCATAGTGGA 58.964 52.381 0.00 0.00 45.98 4.02
2471 2513 2.036387 TCCGTATGTGGTCCATAGTGG 58.964 52.381 0.00 0.00 36.71 4.00
2472 2514 3.069586 ACATCCGTATGTGGTCCATAGTG 59.930 47.826 0.00 0.00 44.79 2.74
2473 2515 3.305720 ACATCCGTATGTGGTCCATAGT 58.694 45.455 0.00 0.00 44.79 2.12
2474 2516 5.661056 ATACATCCGTATGTGGTCCATAG 57.339 43.478 3.56 0.00 45.99 2.23
2475 2517 8.276477 TCTATATACATCCGTATGTGGTCCATA 58.724 37.037 3.56 0.00 45.99 2.74
2476 2518 7.123383 TCTATATACATCCGTATGTGGTCCAT 58.877 38.462 3.56 0.00 45.99 3.41
2477 2519 6.486941 TCTATATACATCCGTATGTGGTCCA 58.513 40.000 3.56 0.00 45.99 4.02
2478 2520 7.426410 CATCTATATACATCCGTATGTGGTCC 58.574 42.308 3.56 0.00 45.99 4.46
2479 2521 6.918569 GCATCTATATACATCCGTATGTGGTC 59.081 42.308 3.56 0.00 45.99 4.02
2480 2522 6.379988 TGCATCTATATACATCCGTATGTGGT 59.620 38.462 3.56 0.00 45.99 4.16
2481 2523 6.805713 TGCATCTATATACATCCGTATGTGG 58.194 40.000 3.56 0.00 45.99 4.17
2482 2524 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
2487 2529 9.809096 CTCTAAAATGCATCTATATACATCCGT 57.191 33.333 0.00 0.00 0.00 4.69
2488 2530 9.809096 ACTCTAAAATGCATCTATATACATCCG 57.191 33.333 0.00 0.00 0.00 4.18
2498 2540 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
2499 2541 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
2500 2542 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
2513 2555 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2514 2556 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2515 2557 5.149054 CGGAGCAAAATGAGTGAATCTAC 57.851 43.478 0.00 0.00 0.00 2.59
2536 2578 1.360551 CTCCCTCCGACTACATGCG 59.639 63.158 0.00 0.00 0.00 4.73
2537 2579 1.688772 TACTCCCTCCGACTACATGC 58.311 55.000 0.00 0.00 0.00 4.06
2538 2580 4.142359 GCATATACTCCCTCCGACTACATG 60.142 50.000 0.00 0.00 0.00 3.21
2539 2581 4.017808 GCATATACTCCCTCCGACTACAT 58.982 47.826 0.00 0.00 0.00 2.29
2540 2582 3.181437 TGCATATACTCCCTCCGACTACA 60.181 47.826 0.00 0.00 0.00 2.74
2541 2583 3.418995 TGCATATACTCCCTCCGACTAC 58.581 50.000 0.00 0.00 0.00 2.73
2542 2584 3.801307 TGCATATACTCCCTCCGACTA 57.199 47.619 0.00 0.00 0.00 2.59
2543 2585 2.677542 TGCATATACTCCCTCCGACT 57.322 50.000 0.00 0.00 0.00 4.18
2544 2586 3.746045 TTTGCATATACTCCCTCCGAC 57.254 47.619 0.00 0.00 0.00 4.79
2545 2587 3.056821 CGATTTGCATATACTCCCTCCGA 60.057 47.826 0.00 0.00 0.00 4.55
2546 2588 3.056821 TCGATTTGCATATACTCCCTCCG 60.057 47.826 0.00 0.00 0.00 4.63
2547 2589 4.021016 AGTCGATTTGCATATACTCCCTCC 60.021 45.833 0.00 0.00 0.00 4.30
2548 2590 5.047660 AGAGTCGATTTGCATATACTCCCTC 60.048 44.000 13.36 5.56 35.13 4.30
2549 2591 4.835615 AGAGTCGATTTGCATATACTCCCT 59.164 41.667 13.36 0.00 35.13 4.20
2550 2592 4.926238 CAGAGTCGATTTGCATATACTCCC 59.074 45.833 13.36 0.00 35.13 4.30
2551 2593 5.533482 ACAGAGTCGATTTGCATATACTCC 58.467 41.667 13.36 1.42 35.13 3.85
2552 2594 6.697455 TCAACAGAGTCGATTTGCATATACTC 59.303 38.462 10.44 10.44 34.85 2.59
2553 2595 6.573434 TCAACAGAGTCGATTTGCATATACT 58.427 36.000 0.00 0.00 0.00 2.12
2554 2596 6.828502 TCAACAGAGTCGATTTGCATATAC 57.171 37.500 0.00 0.00 0.00 1.47
2561 2603 4.248859 ACCAGATCAACAGAGTCGATTTG 58.751 43.478 0.00 0.00 0.00 2.32
2772 2831 4.082571 CCTTCCACTAAAATTGCCAGTCTG 60.083 45.833 0.00 0.00 0.00 3.51
2796 2855 9.965824 TGAATTATTCTTCCAAGAACAAAGAAC 57.034 29.630 6.50 0.84 46.80 3.01
2941 3004 3.631686 ACAGCAAGAGCAACAACATGTAA 59.368 39.130 0.00 0.00 45.49 2.41
2942 3005 3.213506 ACAGCAAGAGCAACAACATGTA 58.786 40.909 0.00 0.00 45.49 2.29
2944 3007 2.787601 ACAGCAAGAGCAACAACATG 57.212 45.000 0.00 0.00 45.49 3.21
2945 3008 2.689471 TCAACAGCAAGAGCAACAACAT 59.311 40.909 0.00 0.00 45.49 2.71
2946 3009 2.090760 TCAACAGCAAGAGCAACAACA 58.909 42.857 0.00 0.00 45.49 3.33
2947 3010 2.159393 TGTCAACAGCAAGAGCAACAAC 60.159 45.455 0.00 0.00 45.49 3.32
2948 3011 2.090760 TGTCAACAGCAAGAGCAACAA 58.909 42.857 0.00 0.00 45.49 2.83
3045 3108 8.800370 AGATCTCGTCAATAAGAGCATATAGA 57.200 34.615 0.00 0.00 34.66 1.98
3109 3172 4.330944 AAGTACATGAACGACAAGTGGA 57.669 40.909 0.00 0.00 32.58 4.02
3173 3236 1.920574 CACACGAGCTTCCTACGAATG 59.079 52.381 0.00 0.00 0.00 2.67
3174 3237 1.135083 CCACACGAGCTTCCTACGAAT 60.135 52.381 0.00 0.00 0.00 3.34
3175 3238 0.242825 CCACACGAGCTTCCTACGAA 59.757 55.000 0.00 0.00 0.00 3.85
3176 3239 1.880894 CCACACGAGCTTCCTACGA 59.119 57.895 0.00 0.00 0.00 3.43
3177 3240 1.805945 GCCACACGAGCTTCCTACG 60.806 63.158 0.00 0.00 0.00 3.51
3199 3262 3.327757 TGAACCTGCCTATCTTGTTGTCT 59.672 43.478 0.00 0.00 0.00 3.41
3303 3366 4.676196 GCCATTTATCAGCACAGGAACAAG 60.676 45.833 0.00 0.00 0.00 3.16
3306 3369 3.019564 AGCCATTTATCAGCACAGGAAC 58.980 45.455 0.00 0.00 0.00 3.62
3340 3403 1.377987 GCCAATGGTTAGCCGTGGA 60.378 57.895 18.84 0.00 42.24 4.02
3353 3416 5.163416 GCAACAGTAAGGAAATATGGCCAAT 60.163 40.000 10.96 1.41 0.00 3.16
3513 3586 3.354089 AACGAAAACCAAGCACAGATG 57.646 42.857 0.00 0.00 0.00 2.90
3514 3587 3.705604 CAAACGAAAACCAAGCACAGAT 58.294 40.909 0.00 0.00 0.00 2.90
3515 3588 2.733858 GCAAACGAAAACCAAGCACAGA 60.734 45.455 0.00 0.00 0.00 3.41
3606 3679 3.525537 GATCTCAAGTGCGGAGAATTCA 58.474 45.455 8.44 0.00 44.01 2.57
3618 3691 5.564550 AGTGCAAACATTAGGATCTCAAGT 58.435 37.500 0.00 0.00 0.00 3.16
3715 3794 2.743636 TCACTGTTCCTCCGACAATC 57.256 50.000 0.00 0.00 0.00 2.67
3716 3795 3.338249 CATTCACTGTTCCTCCGACAAT 58.662 45.455 0.00 0.00 0.00 2.71
3722 3801 1.457346 CCAGCATTCACTGTTCCTCC 58.543 55.000 0.00 0.00 35.83 4.30
3729 3808 2.806608 AACAAAGCCAGCATTCACTG 57.193 45.000 0.00 0.00 37.42 3.66
3747 3826 5.127491 TGACTAAAAGGGAGCGAAGAAAAA 58.873 37.500 0.00 0.00 0.00 1.94
3755 3834 3.254892 GTTCTCTGACTAAAAGGGAGCG 58.745 50.000 0.00 0.00 0.00 5.03
3813 3908 9.321562 CAAGGGGAAAATGAATGAGAATAATTG 57.678 33.333 0.00 0.00 0.00 2.32
3880 3988 2.309764 GAAGTGCCTATGCGTTGCCG 62.310 60.000 0.00 0.00 41.78 5.69
3955 4178 1.006922 GCCAGCCACAGCAAACTTC 60.007 57.895 0.00 0.00 43.56 3.01
4003 4226 0.388649 CTTGAAGGTCCTGTCCGACG 60.389 60.000 0.00 0.00 33.30 5.12
4004 4227 0.037232 CCTTGAAGGTCCTGTCCGAC 60.037 60.000 2.25 0.00 0.00 4.79
4005 4228 0.178944 TCCTTGAAGGTCCTGTCCGA 60.179 55.000 11.60 0.00 36.53 4.55
4029 4253 2.906691 ATCTTCTTCGCCATCCTCAG 57.093 50.000 0.00 0.00 0.00 3.35
4099 4325 3.243907 GGCAGACTATTACAGATTCGCCT 60.244 47.826 0.00 0.00 33.03 5.52
4102 4328 3.069586 TGGGGCAGACTATTACAGATTCG 59.930 47.826 0.00 0.00 0.00 3.34
4145 4374 2.325583 AAGTGCTCGAAACTTGACCA 57.674 45.000 11.33 0.00 36.52 4.02
4186 4415 9.211485 CATGATGATCAGCATTACATGTTAGTA 57.789 33.333 23.38 0.00 34.88 1.82
4189 4418 7.935210 ACTCATGATGATCAGCATTACATGTTA 59.065 33.333 23.38 0.00 38.95 2.41
4199 4428 2.367894 GGGAGACTCATGATGATCAGCA 59.632 50.000 17.22 17.22 0.00 4.41
4204 4433 0.316522 CGCGGGAGACTCATGATGAT 59.683 55.000 4.53 0.00 0.00 2.45
4215 4444 0.457853 CAAACGAAGATCGCGGGAGA 60.458 55.000 6.13 0.00 45.12 3.71
4220 4449 1.455786 ACAGAACAAACGAAGATCGCG 59.544 47.619 0.00 0.00 45.12 5.87
4240 4469 1.028905 CACCTGCCCGACAAAAAGAA 58.971 50.000 0.00 0.00 0.00 2.52
4303 4535 4.404073 AGGCTGGAACTATGTCAAGTAGAG 59.596 45.833 0.00 0.00 0.00 2.43
4318 4555 0.114954 AAGGGCATTGAAGGCTGGAA 59.885 50.000 0.72 0.00 0.00 3.53
4381 4619 9.547753 GTATTCATTTACATCACTACACAGGAT 57.452 33.333 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.