Multiple sequence alignment - TraesCS7A01G343700

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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 TraesCS7A01G343700 chr7A 100.000 4083 0 0 1 4083 505014430 505018512 0.000000e+00 7540.0
1 TraesCS7A01G343700 chr7A 85.049 709 94 10 171 877 454464495 454463797 0.000000e+00 712.0
2 TraesCS7A01G343700 chr7A 86.792 159 21 0 6 164 454466346 454466188 1.170000e-40 178.0
3 TraesCS7A01G343700 chr7A 89.362 94 10 0 1 94 631498577 631498484 7.170000e-23 119.0
4 TraesCS7A01G343700 chr7D 93.300 1582 76 7 2510 4083 427630623 427629064 0.000000e+00 2307.0
5 TraesCS7A01G343700 chr7D 89.574 1314 83 25 1185 2477 427631904 427630624 0.000000e+00 1618.0
6 TraesCS7A01G343700 chr7D 81.690 284 19 20 890 1144 427632792 427632513 5.350000e-49 206.0
7 TraesCS7A01G343700 chr7B 92.979 1581 84 9 2507 4083 445422124 445420567 0.000000e+00 2279.0
8 TraesCS7A01G343700 chr7B 89.273 1445 93 35 889 2305 445423786 445422376 0.000000e+00 1753.0
9 TraesCS7A01G343700 chr7B 83.559 888 121 15 1 877 27615471 27616344 0.000000e+00 808.0
10 TraesCS7A01G343700 chr7B 90.341 176 17 0 2302 2477 445422296 445422121 8.830000e-57 231.0
11 TraesCS7A01G343700 chr7B 100.000 29 0 0 3059 3087 688554301 688554329 2.000000e-03 54.7
12 TraesCS7A01G343700 chr2B 85.991 878 113 9 1 877 405283149 405282281 0.000000e+00 931.0
13 TraesCS7A01G343700 chr2B 85.470 117 13 4 3820 3934 477526506 477526620 7.170000e-23 119.0
14 TraesCS7A01G343700 chr6B 85.682 880 101 17 1 877 156222482 156221625 0.000000e+00 904.0
15 TraesCS7A01G343700 chr6B 77.500 120 23 4 3806 3924 2310923 2311039 7.320000e-08 69.4
16 TraesCS7A01G343700 chr1A 84.932 876 116 11 2 877 61263758 61262899 0.000000e+00 872.0
17 TraesCS7A01G343700 chr6A 85.876 793 100 10 87 877 146012713 146011931 0.000000e+00 833.0
18 TraesCS7A01G343700 chr6A 92.718 563 35 6 315 877 431147936 431147380 0.000000e+00 808.0
19 TraesCS7A01G343700 chr6A 94.231 52 3 0 826 877 480809797 480809848 3.380000e-11 80.5
20 TraesCS7A01G343700 chr1B 82.135 890 127 21 1 878 107143410 107142541 0.000000e+00 734.0
21 TraesCS7A01G343700 chrUn 81.278 892 133 24 1 877 8604376 8603504 0.000000e+00 691.0
22 TraesCS7A01G343700 chr2A 86.916 107 11 3 3818 3924 82363426 82363323 2.580000e-22 117.0
23 TraesCS7A01G343700 chr6D 80.769 104 15 5 3841 3942 340461761 340461661 4.380000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G343700 chr7A 505014430 505018512 4082 False 7540 7540 100.000000 1 4083 1 chr7A.!!$F1 4082
1 TraesCS7A01G343700 chr7A 454463797 454466346 2549 True 445 712 85.920500 6 877 2 chr7A.!!$R2 871
2 TraesCS7A01G343700 chr7D 427629064 427632792 3728 True 1377 2307 88.188000 890 4083 3 chr7D.!!$R1 3193
3 TraesCS7A01G343700 chr7B 445420567 445423786 3219 True 1421 2279 90.864333 889 4083 3 chr7B.!!$R1 3194
4 TraesCS7A01G343700 chr7B 27615471 27616344 873 False 808 808 83.559000 1 877 1 chr7B.!!$F1 876
5 TraesCS7A01G343700 chr2B 405282281 405283149 868 True 931 931 85.991000 1 877 1 chr2B.!!$R1 876
6 TraesCS7A01G343700 chr6B 156221625 156222482 857 True 904 904 85.682000 1 877 1 chr6B.!!$R1 876
7 TraesCS7A01G343700 chr1A 61262899 61263758 859 True 872 872 84.932000 2 877 1 chr1A.!!$R1 875
8 TraesCS7A01G343700 chr6A 146011931 146012713 782 True 833 833 85.876000 87 877 1 chr6A.!!$R1 790
9 TraesCS7A01G343700 chr6A 431147380 431147936 556 True 808 808 92.718000 315 877 1 chr6A.!!$R2 562
10 TraesCS7A01G343700 chr1B 107142541 107143410 869 True 734 734 82.135000 1 878 1 chr1B.!!$R1 877
11 TraesCS7A01G343700 chrUn 8603504 8604376 872 True 691 691 81.278000 1 877 1 chrUn.!!$R1 876

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
524 2212 0.036875 CGCCAAGGGAAAGAAGAGGT 59.963 55.0 0.0 0.0 0.00 3.85 F
1543 3858 0.041982 GAGTTCCCTCACCTCCTCCT 59.958 60.0 0.0 0.0 37.67 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 4795 0.109597 GACACTTGCAATTGCTCCCG 60.110 55.0 29.37 17.87 42.66 5.14 R
3510 5944 0.033796 ACCTCTGGGCCATGACATTG 60.034 55.0 6.72 0.00 35.63 2.82 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
44 45 3.055719 CGCGGCAACAACCTGGAT 61.056 61.111 0.00 0.00 0.00 3.41
85 87 3.922893 GCAGCGTCGCATCAGAGC 61.923 66.667 21.09 9.26 0.00 4.09
105 107 2.337532 CCAGCTTGGTGTTGCAGC 59.662 61.111 0.00 0.00 31.35 5.25
111 113 2.132996 TTGGTGTTGCAGCAAGGGG 61.133 57.895 8.49 0.00 45.03 4.79
133 135 1.135915 CGAGGACAAGATCACCTGGAG 59.864 57.143 0.00 0.00 33.89 3.86
164 166 2.986979 TACACGGCGAGGTCAGCA 60.987 61.111 16.62 0.00 36.08 4.41
169 1857 1.878522 CGGCGAGGTCAGCATACAC 60.879 63.158 0.00 0.00 36.08 2.90
187 1875 1.153745 CCTCTCAACTCCCTTCGCG 60.154 63.158 0.00 0.00 0.00 5.87
215 1903 0.388907 CGGCCATGAAAAGCTTGGTG 60.389 55.000 2.24 0.00 42.34 4.17
263 1951 6.838612 AGATCAAGTTCTATCTCTGGCTACTT 59.161 38.462 0.00 0.00 0.00 2.24
278 1966 0.250124 TACTTCACCACAACCGGCTG 60.250 55.000 0.00 0.62 0.00 4.85
281 1969 3.964875 CACCACAACCGGCTGTGC 61.965 66.667 28.75 0.00 44.47 4.57
305 1993 1.226575 CGATCGCCTGCAACGTAGA 60.227 57.895 0.26 0.00 0.00 2.59
308 1996 1.605058 ATCGCCTGCAACGTAGAGGT 61.605 55.000 8.47 0.00 0.00 3.85
313 2001 0.673644 CTGCAACGTAGAGGTTGGGG 60.674 60.000 14.87 0.00 45.72 4.96
338 2026 2.041620 TCCCTATTTCTGCCAGCTTTGT 59.958 45.455 0.00 0.00 0.00 2.83
410 2098 0.885879 GGGAAGTTTGGGTAAAGGCG 59.114 55.000 0.00 0.00 0.00 5.52
418 2106 2.437895 GGTAAAGGCGGCCACCTC 60.438 66.667 23.09 0.00 39.93 3.85
463 2151 2.674380 CTCCTGGGGTGCAAGCAC 60.674 66.667 16.46 16.46 45.49 4.40
477 2165 1.135257 CAAGCACCACAACAACCGAAA 60.135 47.619 0.00 0.00 0.00 3.46
524 2212 0.036875 CGCCAAGGGAAAGAAGAGGT 59.963 55.000 0.00 0.00 0.00 3.85
556 2244 4.319133 GGCTTTGATCGCCTGGAA 57.681 55.556 0.00 0.00 44.17 3.53
642 2330 2.586792 GCCTGCCGGAGAGACATT 59.413 61.111 5.05 0.00 0.00 2.71
781 2473 3.488363 CCTCCTACTACGCCTCTGTAAT 58.512 50.000 0.00 0.00 0.00 1.89
784 2476 3.562973 TCCTACTACGCCTCTGTAATTCG 59.437 47.826 0.00 0.00 0.00 3.34
803 2505 6.780457 ATTCGTTTTCCCTTCATTGATCAT 57.220 33.333 0.00 0.00 0.00 2.45
829 2541 9.950680 TTTGATCACAAATTTTGTAACTCTCTC 57.049 29.630 14.13 5.18 43.23 3.20
830 2542 8.908786 TGATCACAAATTTTGTAACTCTCTCT 57.091 30.769 14.13 0.00 43.23 3.10
855 2567 2.232208 GCTAAGCCAATGAAAAGCCAGT 59.768 45.455 0.00 0.00 0.00 4.00
877 2589 7.513968 CAGTAAGTCTGGATCTTTCGAAAAAG 58.486 38.462 12.41 0.89 40.42 2.27
878 2590 5.948992 AAGTCTGGATCTTTCGAAAAAGG 57.051 39.130 12.41 0.48 41.88 3.11
879 2591 5.228945 AGTCTGGATCTTTCGAAAAAGGA 57.771 39.130 12.41 6.42 41.88 3.36
880 2592 5.810095 AGTCTGGATCTTTCGAAAAAGGAT 58.190 37.500 12.41 11.05 41.88 3.24
881 2593 5.877564 AGTCTGGATCTTTCGAAAAAGGATC 59.122 40.000 21.58 21.58 41.88 3.36
882 2594 5.065346 GTCTGGATCTTTCGAAAAAGGATCC 59.935 44.000 31.58 31.58 42.33 3.36
883 2595 3.938963 TGGATCTTTCGAAAAAGGATCCG 59.061 43.478 31.72 14.65 43.37 4.18
884 2596 3.939592 GGATCTTTCGAAAAAGGATCCGT 59.060 43.478 28.01 0.00 41.88 4.69
885 2597 4.034163 GGATCTTTCGAAAAAGGATCCGTC 59.966 45.833 28.01 14.79 41.88 4.79
886 2598 3.997762 TCTTTCGAAAAAGGATCCGTCA 58.002 40.909 12.41 0.00 41.88 4.35
887 2599 3.744426 TCTTTCGAAAAAGGATCCGTCAC 59.256 43.478 12.41 0.00 41.88 3.67
916 2628 2.701107 TCGAATAACGGATTTGCCACA 58.299 42.857 0.00 0.00 42.82 4.17
933 2645 3.316308 GCCACATGTTACCTCAATGATCC 59.684 47.826 0.00 0.00 0.00 3.36
995 2708 5.074102 TGCATAATTCCTGATGATTCCTCCT 59.926 40.000 0.00 0.00 0.00 3.69
1002 2715 4.347292 TCCTGATGATTCCTCCTTCTCATG 59.653 45.833 0.00 0.00 0.00 3.07
1006 2719 4.750021 TGATTCCTCCTTCTCATGACAG 57.250 45.455 0.00 0.00 0.00 3.51
1039 2752 4.919168 CACCACATGACACAAAGCAATTAG 59.081 41.667 0.00 0.00 0.00 1.73
1040 2753 4.022068 ACCACATGACACAAAGCAATTAGG 60.022 41.667 0.00 0.00 0.00 2.69
1041 2754 4.218200 CCACATGACACAAAGCAATTAGGA 59.782 41.667 0.00 0.00 0.00 2.94
1042 2755 5.278907 CCACATGACACAAAGCAATTAGGAA 60.279 40.000 0.00 0.00 0.00 3.36
1043 2756 5.630680 CACATGACACAAAGCAATTAGGAAC 59.369 40.000 0.00 0.00 0.00 3.62
1044 2757 4.481930 TGACACAAAGCAATTAGGAACG 57.518 40.909 0.00 0.00 0.00 3.95
1045 2758 3.234386 GACACAAAGCAATTAGGAACGC 58.766 45.455 0.00 0.00 0.00 4.84
1047 2760 3.067461 ACACAAAGCAATTAGGAACGCAA 59.933 39.130 0.00 0.00 0.00 4.85
1053 2799 4.072131 AGCAATTAGGAACGCAAAGAGAA 58.928 39.130 0.00 0.00 0.00 2.87
1064 2810 6.237835 GGAACGCAAAGAGAAAAAGAAAAAGG 60.238 38.462 0.00 0.00 0.00 3.11
1068 2814 7.148639 ACGCAAAGAGAAAAAGAAAAAGGAAAC 60.149 33.333 0.00 0.00 0.00 2.78
1069 2815 7.464358 GCAAAGAGAAAAAGAAAAAGGAAACC 58.536 34.615 0.00 0.00 0.00 3.27
1070 2816 7.414098 GCAAAGAGAAAAAGAAAAAGGAAACCC 60.414 37.037 0.00 0.00 0.00 4.11
1074 2820 7.824289 AGAGAAAAAGAAAAAGGAAACCCAAAG 59.176 33.333 0.00 0.00 0.00 2.77
1075 2821 7.685481 AGAAAAAGAAAAAGGAAACCCAAAGA 58.315 30.769 0.00 0.00 0.00 2.52
1080 2826 7.921786 AGAAAAAGGAAACCCAAAGAAAAAG 57.078 32.000 0.00 0.00 0.00 2.27
1082 2828 5.772393 AAAGGAAACCCAAAGAAAAAGGT 57.228 34.783 0.00 0.00 0.00 3.50
1091 2837 8.500753 AACCCAAAGAAAAAGGTTATTTTGTC 57.499 30.769 0.00 0.00 40.79 3.18
1092 2838 7.625469 ACCCAAAGAAAAAGGTTATTTTGTCA 58.375 30.769 0.00 0.00 32.85 3.58
1093 2839 8.103935 ACCCAAAGAAAAAGGTTATTTTGTCAA 58.896 29.630 0.00 0.00 32.85 3.18
1094 2840 8.394877 CCCAAAGAAAAAGGTTATTTTGTCAAC 58.605 33.333 0.00 0.00 32.85 3.18
1096 2842 9.971744 CAAAGAAAAAGGTTATTTTGTCAACAG 57.028 29.630 0.00 0.00 32.85 3.16
1098 2844 9.936759 AAGAAAAAGGTTATTTTGTCAACAGAA 57.063 25.926 0.00 0.00 32.85 3.02
1099 2845 9.586435 AGAAAAAGGTTATTTTGTCAACAGAAG 57.414 29.630 0.00 0.00 32.85 2.85
1521 3836 1.376037 CCACCTCCACTTCCTTCGC 60.376 63.158 0.00 0.00 0.00 4.70
1543 3858 0.041982 GAGTTCCCTCACCTCCTCCT 59.958 60.000 0.00 0.00 37.67 3.69
1545 3860 0.978667 GTTCCCTCACCTCCTCCTCC 60.979 65.000 0.00 0.00 0.00 4.30
1546 3861 1.156322 TTCCCTCACCTCCTCCTCCT 61.156 60.000 0.00 0.00 0.00 3.69
1547 3862 1.075600 CCCTCACCTCCTCCTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
1548 3863 1.075600 CCTCACCTCCTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1549 3864 1.589399 CCTCACCTCCTCCTCCTCCT 61.589 65.000 0.00 0.00 0.00 3.69
1550 3865 0.106217 CTCACCTCCTCCTCCTCCTC 60.106 65.000 0.00 0.00 0.00 3.71
1551 3866 1.075600 CACCTCCTCCTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1552 3867 1.230819 ACCTCCTCCTCCTCCTCCT 60.231 63.158 0.00 0.00 0.00 3.69
1553 3868 1.293683 ACCTCCTCCTCCTCCTCCTC 61.294 65.000 0.00 0.00 0.00 3.71
1554 3869 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1555 3870 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1556 3871 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1557 3872 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1558 3873 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1568 3883 1.215679 TCCTCCTCCTCCTCCTCGTT 61.216 60.000 0.00 0.00 0.00 3.85
1576 3891 2.310945 TCCTCCTCCTCGTTTTCCTCTA 59.689 50.000 0.00 0.00 0.00 2.43
1577 3892 2.691011 CCTCCTCCTCGTTTTCCTCTAG 59.309 54.545 0.00 0.00 0.00 2.43
1594 3914 3.681593 TCTAGGTTGAAAAATCCGTGGG 58.318 45.455 0.00 0.00 0.00 4.61
1603 3923 3.337694 AAAATCCGTGGGTCGTTGATA 57.662 42.857 0.00 0.00 37.94 2.15
1604 3924 2.304751 AATCCGTGGGTCGTTGATAC 57.695 50.000 0.00 0.00 37.94 2.24
1620 3940 3.902162 TACCGCGTGCGAGAACCAC 62.902 63.158 16.91 0.00 42.83 4.16
1627 3947 1.837051 TGCGAGAACCACCTCCAGT 60.837 57.895 0.00 0.00 0.00 4.00
1628 3948 1.371558 GCGAGAACCACCTCCAGTT 59.628 57.895 0.00 0.00 0.00 3.16
1629 3949 0.951040 GCGAGAACCACCTCCAGTTG 60.951 60.000 0.00 0.00 0.00 3.16
1643 3965 4.080919 CCTCCAGTTGATGATACAGTGGAA 60.081 45.833 0.00 0.00 35.66 3.53
1644 3966 5.089970 TCCAGTTGATGATACAGTGGAAG 57.910 43.478 0.00 0.00 34.23 3.46
1645 3967 4.777366 TCCAGTTGATGATACAGTGGAAGA 59.223 41.667 0.00 0.00 34.23 2.87
1646 3968 5.105187 TCCAGTTGATGATACAGTGGAAGAG 60.105 44.000 0.00 0.00 34.23 2.85
1647 3969 5.114780 CAGTTGATGATACAGTGGAAGAGG 58.885 45.833 0.00 0.00 0.00 3.69
1648 3970 4.780021 AGTTGATGATACAGTGGAAGAGGT 59.220 41.667 0.00 0.00 0.00 3.85
1649 3971 5.249393 AGTTGATGATACAGTGGAAGAGGTT 59.751 40.000 0.00 0.00 0.00 3.50
1650 3972 5.089970 TGATGATACAGTGGAAGAGGTTG 57.910 43.478 0.00 0.00 0.00 3.77
1663 3985 4.702131 GGAAGAGGTTGTTGTTATCATGCT 59.298 41.667 0.00 0.00 0.00 3.79
1680 4002 1.332195 GCTTTTGCTTCCTCCCTTGT 58.668 50.000 0.00 0.00 43.35 3.16
1688 4010 2.424956 GCTTCCTCCCTTGTGCAATTAG 59.575 50.000 0.00 0.00 0.00 1.73
1689 4011 3.873801 GCTTCCTCCCTTGTGCAATTAGA 60.874 47.826 0.00 0.00 0.00 2.10
1705 4042 7.166473 GTGCAATTAGACAGTTTGTTCTCTTTG 59.834 37.037 0.00 0.00 0.00 2.77
1706 4043 7.148086 TGCAATTAGACAGTTTGTTCTCTTTGT 60.148 33.333 0.00 0.00 0.00 2.83
1707 4044 7.166473 GCAATTAGACAGTTTGTTCTCTTTGTG 59.834 37.037 0.00 0.00 0.00 3.33
1708 4045 6.677781 TTAGACAGTTTGTTCTCTTTGTGG 57.322 37.500 0.00 0.00 0.00 4.17
1710 4047 3.023832 ACAGTTTGTTCTCTTTGTGGGG 58.976 45.455 0.00 0.00 0.00 4.96
1711 4048 2.031870 AGTTTGTTCTCTTTGTGGGGC 58.968 47.619 0.00 0.00 0.00 5.80
1712 4049 2.031870 GTTTGTTCTCTTTGTGGGGCT 58.968 47.619 0.00 0.00 0.00 5.19
1735 4072 1.888436 GACTCCACCGTGCTGATCCA 61.888 60.000 0.00 0.00 0.00 3.41
1764 4101 8.812513 ATCCAGATTCAGATGAACAATTGTTA 57.187 30.769 23.33 12.30 38.56 2.41
1768 4105 7.484007 CAGATTCAGATGAACAATTGTTACTGC 59.516 37.037 28.34 20.95 38.56 4.40
1774 4111 7.385752 CAGATGAACAATTGTTACTGCCATTTT 59.614 33.333 23.33 11.32 38.56 1.82
1780 4117 9.723601 AACAATTGTTACTGCCATTTTCATTAT 57.276 25.926 22.10 0.00 36.32 1.28
1781 4118 9.723601 ACAATTGTTACTGCCATTTTCATTATT 57.276 25.926 4.92 0.00 0.00 1.40
1813 4150 6.121590 TGAGCATACATCTTATTCAGGCAAA 58.878 36.000 0.00 0.00 0.00 3.68
1831 4168 0.896226 AACTAGGTCGGCCTTCTCAC 59.104 55.000 17.04 0.00 44.18 3.51
1879 4216 4.023707 GTCCACAGATGTTCCTTGTTTGAG 60.024 45.833 0.00 0.00 0.00 3.02
1959 4303 5.163513 AGCTTTGTTTGTTTGTCTCTGTTG 58.836 37.500 0.00 0.00 0.00 3.33
1966 4310 5.957842 TTGTTTGTCTCTGTTGTGTTTCT 57.042 34.783 0.00 0.00 0.00 2.52
1989 4333 8.268850 TCTTTATCACAAGCCTTTGTATTCTC 57.731 34.615 0.00 0.00 45.53 2.87
1992 4336 2.084546 ACAAGCCTTTGTATTCTCCGC 58.915 47.619 0.00 0.00 45.45 5.54
2006 4350 0.447801 CTCCGCCAATTTTGTCCTCG 59.552 55.000 0.00 0.00 0.00 4.63
2036 4380 1.277557 AGTGCCAGATTCACTCCTGTC 59.722 52.381 0.00 0.00 40.47 3.51
2050 4394 1.737735 CTGTCGGCATGCGTCTTCA 60.738 57.895 12.44 5.65 0.00 3.02
2054 4398 2.792290 CGGCATGCGTCTTCACTCG 61.792 63.158 12.44 1.95 0.00 4.18
2061 4405 3.132629 TGCGTCTTCACTCGATAGTTC 57.867 47.619 0.00 0.00 31.97 3.01
2117 4461 1.477295 GGACCTCTCGTTCCCTTGTAG 59.523 57.143 0.00 0.00 0.00 2.74
2120 4464 0.179134 CTCTCGTTCCCTTGTAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
2123 4467 1.679680 CTCGTTCCCTTGTAGCCGATA 59.320 52.381 0.00 0.00 0.00 2.92
2141 4485 3.481028 CGATAATGGTACGAAGACACACG 59.519 47.826 0.00 0.00 0.00 4.49
2147 4491 2.325761 GTACGAAGACACACGATTGCT 58.674 47.619 0.00 0.00 0.00 3.91
2170 4514 3.244911 ACAGGTTGTTAGCCATGTAGCTT 60.245 43.478 1.62 0.00 41.41 3.74
2283 4627 0.958822 GTTGCCGTGTCCCTCATTTT 59.041 50.000 0.00 0.00 0.00 1.82
2288 4632 2.357952 GCCGTGTCCCTCATTTTATTCC 59.642 50.000 0.00 0.00 0.00 3.01
2291 4635 4.644685 CCGTGTCCCTCATTTTATTCCAAT 59.355 41.667 0.00 0.00 0.00 3.16
2296 4640 8.137437 GTGTCCCTCATTTTATTCCAATGTATG 58.863 37.037 0.00 0.00 33.91 2.39
2344 4771 2.366533 TCGAGTCTTAGCCGAATGAGT 58.633 47.619 0.00 0.00 0.00 3.41
2347 4774 3.190874 GAGTCTTAGCCGAATGAGTTGG 58.809 50.000 0.00 0.00 0.00 3.77
2356 4783 3.065371 GCCGAATGAGTTGGGAACATAAG 59.935 47.826 0.00 0.00 42.32 1.73
2367 4794 3.953612 TGGGAACATAAGGCTGCTTTATG 59.046 43.478 30.95 30.95 41.85 1.90
2368 4795 3.243535 GGGAACATAAGGCTGCTTTATGC 60.244 47.826 31.91 21.44 40.50 3.14
2369 4796 3.548818 GGAACATAAGGCTGCTTTATGCG 60.549 47.826 31.91 17.79 46.63 4.73
2390 4817 2.608752 GGGAGCAATTGCAAGTGTCAAG 60.609 50.000 30.89 2.82 45.16 3.02
2453 4880 3.025287 ACATGATTTTGTTTGACGGGC 57.975 42.857 0.00 0.00 0.00 6.13
2463 4890 1.990160 TTTGACGGGCCACTTCACCT 61.990 55.000 4.39 0.00 0.00 4.00
2477 4904 5.450965 CCACTTCACCTTGATCATTTATGCC 60.451 44.000 0.00 0.00 0.00 4.40
2478 4905 5.125900 CACTTCACCTTGATCATTTATGCCA 59.874 40.000 0.00 0.00 0.00 4.92
2479 4906 5.716228 ACTTCACCTTGATCATTTATGCCAA 59.284 36.000 0.00 0.00 0.00 4.52
2480 4907 6.211184 ACTTCACCTTGATCATTTATGCCAAA 59.789 34.615 0.00 0.00 0.00 3.28
2481 4908 5.964758 TCACCTTGATCATTTATGCCAAAC 58.035 37.500 0.00 0.00 0.00 2.93
2482 4909 5.479724 TCACCTTGATCATTTATGCCAAACA 59.520 36.000 0.00 0.00 0.00 2.83
2483 4910 6.154877 TCACCTTGATCATTTATGCCAAACAT 59.845 34.615 0.00 0.00 43.18 2.71
2484 4911 7.341512 TCACCTTGATCATTTATGCCAAACATA 59.658 33.333 0.00 0.00 40.38 2.29
2572 4999 8.519492 AACAATATGTTGCTTATTTGTGTCAC 57.481 30.769 1.57 0.00 39.45 3.67
2574 5001 8.306038 ACAATATGTTGCTTATTTGTGTCACAT 58.694 29.630 6.48 0.00 38.96 3.21
2595 5022 0.807496 GGCTTGCAGGATGTTCAGTC 59.193 55.000 0.00 0.00 39.31 3.51
2613 5040 3.112075 ACAACAGCGTGCCGATCG 61.112 61.111 8.51 8.51 0.00 3.69
2647 5074 0.320771 CTAGGGTGCAGCAAAGTCGT 60.321 55.000 19.06 0.00 0.00 4.34
2719 5146 2.470057 TTGAGGAAGCCTTGGGTTTT 57.530 45.000 5.53 0.00 31.76 2.43
2746 5173 0.321919 ATGTGCGTGACAAGAGCCAT 60.322 50.000 0.00 0.00 38.36 4.40
2758 5185 0.678048 AGAGCCATTTTGTCTCGCCC 60.678 55.000 0.00 0.00 32.42 6.13
2775 5202 1.072331 GCCCGAAGATGTGTATGGGAT 59.928 52.381 0.00 0.00 39.03 3.85
2806 5233 1.582624 TCAGGGGAAGATGAGGAGGAT 59.417 52.381 0.00 0.00 0.00 3.24
2884 5311 8.864024 GCTTTAGCCAAGAACATTTTAAGATTC 58.136 33.333 0.00 0.00 33.80 2.52
2889 5316 6.743172 GCCAAGAACATTTTAAGATTCGAGAC 59.257 38.462 0.00 0.00 0.00 3.36
2899 5326 2.933573 AGATTCGAGACGATGGGTAGT 58.066 47.619 0.00 0.00 35.23 2.73
2979 5406 4.837860 TCAATTGGCCTCTGGTAAACAAAT 59.162 37.500 3.32 0.00 0.00 2.32
2986 5413 1.539388 TCTGGTAAACAAATGCCAGCG 59.461 47.619 6.56 0.00 45.86 5.18
2992 5419 1.526575 AACAAATGCCAGCGGTCCAG 61.527 55.000 0.00 0.00 0.00 3.86
3002 5429 2.307768 CAGCGGTCCAGTATAGGAGAA 58.692 52.381 0.00 0.00 38.64 2.87
3012 5439 4.099573 CCAGTATAGGAGAACCGACAATGT 59.900 45.833 0.00 0.00 41.83 2.71
3019 5446 3.680458 GGAGAACCGACAATGTTTCTCTC 59.320 47.826 19.57 13.36 0.00 3.20
3042 5469 3.142174 CTGGAGGGTCAAGAAAAGACAC 58.858 50.000 0.00 0.00 39.70 3.67
3056 5483 7.208225 AGAAAAGACACTAAAGGAAAGCATC 57.792 36.000 0.00 0.00 0.00 3.91
3283 5710 0.875059 CTGCAAGTCGGTTCCCTTTC 59.125 55.000 0.00 0.00 0.00 2.62
3342 5769 1.414181 CATATCTCGTTCTGGGGCTGT 59.586 52.381 0.00 0.00 0.00 4.40
3460 5894 0.627451 AGCTGGGGATGCAAATCAGA 59.373 50.000 11.99 0.00 0.00 3.27
3488 5922 4.202080 ACATTGCGATGCTATGCTTCATTT 60.202 37.500 14.18 0.00 43.36 2.32
3499 5933 4.612264 ATGCTTCATTTGTTTGCCTCTT 57.388 36.364 0.00 0.00 0.00 2.85
3510 5944 2.987821 GTTTGCCTCTTCGACTAGTGTC 59.012 50.000 0.00 0.00 39.70 3.67
3511 5945 1.905637 TGCCTCTTCGACTAGTGTCA 58.094 50.000 0.00 0.00 43.06 3.58
3512 5946 2.235891 TGCCTCTTCGACTAGTGTCAA 58.764 47.619 0.00 0.00 43.06 3.18
3513 5947 2.826128 TGCCTCTTCGACTAGTGTCAAT 59.174 45.455 0.00 0.00 43.06 2.57
3514 5948 3.182967 GCCTCTTCGACTAGTGTCAATG 58.817 50.000 0.00 0.00 43.06 2.82
3515 5949 3.367498 GCCTCTTCGACTAGTGTCAATGT 60.367 47.826 0.00 0.00 43.06 2.71
3631 6065 3.191162 TGCATGTGTCATAGCCTTCAAAC 59.809 43.478 0.00 0.00 0.00 2.93
3632 6066 3.191162 GCATGTGTCATAGCCTTCAAACA 59.809 43.478 0.00 0.00 0.00 2.83
3677 6111 1.064758 TGTGCCTTGTTCTTCACACCT 60.065 47.619 0.00 0.00 33.98 4.00
3736 6170 1.471119 TCGGAGATGCGAGTTAGGTT 58.529 50.000 0.00 0.00 0.00 3.50
3737 6171 1.134367 TCGGAGATGCGAGTTAGGTTG 59.866 52.381 0.00 0.00 0.00 3.77
3738 6172 1.135083 CGGAGATGCGAGTTAGGTTGT 60.135 52.381 0.00 0.00 0.00 3.32
3739 6173 2.674177 CGGAGATGCGAGTTAGGTTGTT 60.674 50.000 0.00 0.00 0.00 2.83
3740 6174 2.673368 GGAGATGCGAGTTAGGTTGTTG 59.327 50.000 0.00 0.00 0.00 3.33
3777 6211 3.181467 TGCTTGCAATGGCTTTACTTGTT 60.181 39.130 11.46 0.00 41.91 2.83
3783 6217 4.217550 GCAATGGCTTTACTTGTTACCAGA 59.782 41.667 0.00 0.00 36.96 3.86
3785 6219 6.555315 CAATGGCTTTACTTGTTACCAGATC 58.445 40.000 0.00 0.00 0.00 2.75
3790 6224 0.981183 ACTTGTTACCAGATCGGGCA 59.019 50.000 12.27 0.00 40.22 5.36
3796 6230 0.673985 TACCAGATCGGGCATTCTCG 59.326 55.000 12.27 0.00 40.22 4.04
3814 6248 5.013568 TCTCGTGTAAAGTTTGAAGGACA 57.986 39.130 0.00 0.00 0.00 4.02
3831 6265 2.668457 GGACAGCACTACAAATCTGACG 59.332 50.000 0.00 0.00 0.00 4.35
3880 6317 6.276847 TGAACGTCTTTTATGGCAATTTGTT 58.723 32.000 0.00 0.00 0.00 2.83
3894 6331 4.036616 GCAATTTGTTTTTGCCAAGGATGT 59.963 37.500 0.00 0.00 42.84 3.06
3895 6332 5.450274 GCAATTTGTTTTTGCCAAGGATGTT 60.450 36.000 0.00 0.00 42.84 2.71
3925 6362 1.630223 TGGCAAGCATGTCAAATCCA 58.370 45.000 0.00 0.00 38.47 3.41
3931 6368 3.014304 AGCATGTCAAATCCAGCTCAT 57.986 42.857 0.00 0.00 0.00 2.90
3958 6395 8.870160 TCGATTTTCCATGCTTAAAAATATGG 57.130 30.769 0.00 0.00 41.09 2.74
3966 6403 7.560991 TCCATGCTTAAAAATATGGTGTCAGAT 59.439 33.333 0.00 0.00 40.68 2.90
3979 6416 6.176975 TGGTGTCAGATTTTTAGCATTACG 57.823 37.500 0.00 0.00 0.00 3.18
3989 6426 8.237267 AGATTTTTAGCATTACGGAAGTTTGAG 58.763 33.333 0.00 0.00 46.40 3.02
4021 6458 3.380004 AGTGAAATCTTTGGCGAAACACA 59.620 39.130 12.23 0.00 0.00 3.72
4022 6459 4.109050 GTGAAATCTTTGGCGAAACACAA 58.891 39.130 6.90 0.00 0.00 3.33
4023 6460 4.207019 GTGAAATCTTTGGCGAAACACAAG 59.793 41.667 6.90 0.00 0.00 3.16
4052 6489 3.834489 GATGCTCCTTTCATCCTCTGA 57.166 47.619 0.00 0.00 35.49 3.27
4053 6490 4.148128 GATGCTCCTTTCATCCTCTGAA 57.852 45.455 0.00 0.00 42.15 3.02
4054 6491 3.623906 TGCTCCTTTCATCCTCTGAAG 57.376 47.619 0.00 0.00 44.48 3.02
4055 6492 2.909006 TGCTCCTTTCATCCTCTGAAGT 59.091 45.455 0.00 0.00 44.48 3.01
4056 6493 3.269178 GCTCCTTTCATCCTCTGAAGTG 58.731 50.000 0.00 0.00 44.48 3.16
4057 6494 3.871485 CTCCTTTCATCCTCTGAAGTGG 58.129 50.000 0.00 0.00 44.48 4.00
4063 6500 3.099905 TCATCCTCTGAAGTGGTACTGG 58.900 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.653234 AAGGTCCATGATCCATCTGC 57.347 50.000 0.00 0.00 0.00 4.26
44 45 1.407656 GCACGACCTGGGGGATGATA 61.408 60.000 0.00 0.00 36.25 2.15
74 76 2.186125 CTGGCTGCTCTGATGCGA 59.814 61.111 0.00 0.00 35.36 5.10
85 87 2.337532 GCAACACCAAGCTGGCTG 59.662 61.111 0.00 0.00 42.67 4.85
105 107 0.905357 ATCTTGTCCTCGACCCCTTG 59.095 55.000 0.00 0.00 0.00 3.61
111 113 1.134965 CCAGGTGATCTTGTCCTCGAC 60.135 57.143 0.00 0.00 0.00 4.20
164 166 2.761208 CGAAGGGAGTTGAGAGGTGTAT 59.239 50.000 0.00 0.00 0.00 2.29
169 1857 1.153745 CGCGAAGGGAGTTGAGAGG 60.154 63.158 0.00 0.00 46.37 3.69
187 1875 0.608035 TTTCATGGCCGAGGTTGGTC 60.608 55.000 0.00 0.00 0.00 4.02
215 1903 0.393537 CAGGTGCCCAGATCTTCCAC 60.394 60.000 0.00 0.39 0.00 4.02
263 1951 2.203139 CACAGCCGGTTGTGGTGA 60.203 61.111 35.96 0.00 43.65 4.02
278 1966 3.121030 AGGCGATCGTTGCAGCAC 61.121 61.111 17.81 0.00 0.00 4.40
281 1969 3.120385 TGCAGGCGATCGTTGCAG 61.120 61.111 31.47 14.94 42.41 4.41
313 2001 2.158549 AGCTGGCAGAAATAGGGATTCC 60.159 50.000 20.86 0.00 0.00 3.01
338 2026 2.357034 GACTCGAGGTTGCGGCAA 60.357 61.111 18.41 12.11 0.00 4.52
453 2141 0.805711 GTTGTTGTGGTGCTTGCACC 60.806 55.000 31.20 31.20 45.20 5.01
463 2151 1.267832 CGACAGTTTCGGTTGTTGTGG 60.268 52.381 0.00 0.00 44.60 4.17
477 2165 1.792949 GTTGAGAATTGCGACGACAGT 59.207 47.619 0.00 0.00 0.00 3.55
484 2172 1.351430 CGCGGAGTTGAGAATTGCGA 61.351 55.000 0.00 0.00 46.29 5.10
555 2243 6.877236 TCTGTTTCTTTCAAGCCAGATTTTT 58.123 32.000 0.00 0.00 0.00 1.94
556 2244 6.469782 TCTGTTTCTTTCAAGCCAGATTTT 57.530 33.333 0.00 0.00 0.00 1.82
642 2330 1.219124 GGCGAGTCTCCATTGCTCA 59.781 57.895 0.00 0.00 0.00 4.26
695 2383 5.121380 ACCTAGGTCTATTCCTCACGTTA 57.879 43.478 9.21 0.00 38.86 3.18
724 2412 2.817258 CTCTCTCCCTCCGCTGTTATAG 59.183 54.545 0.00 0.00 0.00 1.31
725 2413 2.489255 CCTCTCTCCCTCCGCTGTTATA 60.489 54.545 0.00 0.00 0.00 0.98
726 2414 1.698506 CTCTCTCCCTCCGCTGTTAT 58.301 55.000 0.00 0.00 0.00 1.89
727 2415 0.395862 CCTCTCTCCCTCCGCTGTTA 60.396 60.000 0.00 0.00 0.00 2.41
728 2416 1.684049 CCTCTCTCCCTCCGCTGTT 60.684 63.158 0.00 0.00 0.00 3.16
781 2473 6.588719 AATGATCAATGAAGGGAAAACGAA 57.411 33.333 0.00 0.00 0.00 3.85
803 2505 9.950680 GAGAGAGTTACAAAATTTGTGATCAAA 57.049 29.630 20.40 4.43 45.03 2.69
828 2540 3.719268 TTTCATTGGCTTAGCAGGAGA 57.281 42.857 6.53 0.00 0.00 3.71
829 2541 3.428589 GCTTTTCATTGGCTTAGCAGGAG 60.429 47.826 6.53 0.00 0.00 3.69
830 2542 2.493278 GCTTTTCATTGGCTTAGCAGGA 59.507 45.455 6.53 0.00 0.00 3.86
855 2567 6.765403 TCCTTTTTCGAAAGATCCAGACTTA 58.235 36.000 10.98 0.00 41.60 2.24
897 2609 3.181501 ACATGTGGCAAATCCGTTATTCG 60.182 43.478 0.00 0.00 37.80 3.34
916 2628 5.745227 ACTTTCGGATCATTGAGGTAACAT 58.255 37.500 0.00 0.00 41.41 2.71
933 2645 7.908193 ATGCAAGTTTTTACTTGTACTTTCG 57.092 32.000 16.67 0.00 46.36 3.46
1002 2715 1.089920 GTGGTGGTGATGATGCTGTC 58.910 55.000 0.00 0.00 0.00 3.51
1006 2719 1.402968 GTCATGTGGTGGTGATGATGC 59.597 52.381 0.00 0.00 0.00 3.91
1039 2752 6.237835 CCTTTTTCTTTTTCTCTTTGCGTTCC 60.238 38.462 0.00 0.00 0.00 3.62
1040 2753 6.530181 TCCTTTTTCTTTTTCTCTTTGCGTTC 59.470 34.615 0.00 0.00 0.00 3.95
1041 2754 6.394809 TCCTTTTTCTTTTTCTCTTTGCGTT 58.605 32.000 0.00 0.00 0.00 4.84
1042 2755 5.961272 TCCTTTTTCTTTTTCTCTTTGCGT 58.039 33.333 0.00 0.00 0.00 5.24
1043 2756 6.885735 TTCCTTTTTCTTTTTCTCTTTGCG 57.114 33.333 0.00 0.00 0.00 4.85
1044 2757 7.414098 GGGTTTCCTTTTTCTTTTTCTCTTTGC 60.414 37.037 0.00 0.00 0.00 3.68
1045 2758 7.606073 TGGGTTTCCTTTTTCTTTTTCTCTTTG 59.394 33.333 0.00 0.00 0.00 2.77
1047 2760 7.252612 TGGGTTTCCTTTTTCTTTTTCTCTT 57.747 32.000 0.00 0.00 0.00 2.85
1053 2799 8.698973 TTTTCTTTGGGTTTCCTTTTTCTTTT 57.301 26.923 0.00 0.00 0.00 2.27
1064 2810 8.952278 ACAAAATAACCTTTTTCTTTGGGTTTC 58.048 29.630 0.00 0.00 41.54 2.78
1068 2814 8.394877 GTTGACAAAATAACCTTTTTCTTTGGG 58.605 33.333 0.00 0.00 0.00 4.12
1069 2815 8.940952 TGTTGACAAAATAACCTTTTTCTTTGG 58.059 29.630 0.00 0.00 0.00 3.28
1070 2816 9.971744 CTGTTGACAAAATAACCTTTTTCTTTG 57.028 29.630 0.00 0.00 0.00 2.77
1074 2820 8.817100 CCTTCTGTTGACAAAATAACCTTTTTC 58.183 33.333 0.00 0.00 0.00 2.29
1075 2821 7.768582 CCCTTCTGTTGACAAAATAACCTTTTT 59.231 33.333 0.00 0.00 0.00 1.94
1080 2826 4.830600 TCCCCTTCTGTTGACAAAATAACC 59.169 41.667 0.00 0.00 0.00 2.85
1082 2828 5.076873 CCTCCCCTTCTGTTGACAAAATAA 58.923 41.667 0.00 0.00 0.00 1.40
1091 2837 2.260822 TCTTCTCCTCCCCTTCTGTTG 58.739 52.381 0.00 0.00 0.00 3.33
1092 2838 2.723530 TCTTCTCCTCCCCTTCTGTT 57.276 50.000 0.00 0.00 0.00 3.16
1093 2839 2.723530 TTCTTCTCCTCCCCTTCTGT 57.276 50.000 0.00 0.00 0.00 3.41
1094 2840 3.871851 GCTTTTCTTCTCCTCCCCTTCTG 60.872 52.174 0.00 0.00 0.00 3.02
1096 2842 2.307392 AGCTTTTCTTCTCCTCCCCTTC 59.693 50.000 0.00 0.00 0.00 3.46
1098 2844 1.912731 GAGCTTTTCTTCTCCTCCCCT 59.087 52.381 0.00 0.00 0.00 4.79
1099 2845 1.065053 GGAGCTTTTCTTCTCCTCCCC 60.065 57.143 0.00 0.00 44.19 4.81
1177 2924 1.219393 GCCGTTGGAGAGAAGAGGG 59.781 63.158 0.00 0.00 0.00 4.30
1178 2925 1.153745 CGCCGTTGGAGAGAAGAGG 60.154 63.158 0.00 0.00 0.00 3.69
1381 3696 3.801997 CCGCTGCCCCTTGAGGAT 61.802 66.667 0.00 0.00 38.24 3.24
1543 3858 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1545 3860 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1546 3861 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1547 3862 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1548 3863 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1549 3864 1.215679 AACGAGGAGGAGGAGGAGGA 61.216 60.000 0.00 0.00 0.00 3.71
1550 3865 0.324830 AAACGAGGAGGAGGAGGAGG 60.325 60.000 0.00 0.00 0.00 4.30
1551 3866 1.478916 GAAAACGAGGAGGAGGAGGAG 59.521 57.143 0.00 0.00 0.00 3.69
1552 3867 1.558233 GAAAACGAGGAGGAGGAGGA 58.442 55.000 0.00 0.00 0.00 3.71
1553 3868 0.537653 GGAAAACGAGGAGGAGGAGG 59.462 60.000 0.00 0.00 0.00 4.30
1554 3869 1.478916 GAGGAAAACGAGGAGGAGGAG 59.521 57.143 0.00 0.00 0.00 3.69
1555 3870 1.077334 AGAGGAAAACGAGGAGGAGGA 59.923 52.381 0.00 0.00 0.00 3.71
1556 3871 1.562783 AGAGGAAAACGAGGAGGAGG 58.437 55.000 0.00 0.00 0.00 4.30
1557 3872 2.691011 CCTAGAGGAAAACGAGGAGGAG 59.309 54.545 0.00 0.00 37.39 3.69
1558 3873 2.042706 ACCTAGAGGAAAACGAGGAGGA 59.957 50.000 1.60 0.00 38.94 3.71
1568 3883 5.472137 CACGGATTTTTCAACCTAGAGGAAA 59.528 40.000 1.60 0.00 38.94 3.13
1576 3891 2.235891 GACCCACGGATTTTTCAACCT 58.764 47.619 0.00 0.00 0.00 3.50
1577 3892 1.068816 CGACCCACGGATTTTTCAACC 60.069 52.381 0.00 0.00 38.46 3.77
1594 3914 2.693285 GCACGCGGTATCAACGAC 59.307 61.111 12.47 0.00 0.00 4.34
1620 3940 3.452264 TCCACTGTATCATCAACTGGAGG 59.548 47.826 0.00 0.00 0.00 4.30
1627 3947 5.013079 ACAACCTCTTCCACTGTATCATCAA 59.987 40.000 0.00 0.00 0.00 2.57
1628 3948 4.532126 ACAACCTCTTCCACTGTATCATCA 59.468 41.667 0.00 0.00 0.00 3.07
1629 3949 5.091261 ACAACCTCTTCCACTGTATCATC 57.909 43.478 0.00 0.00 0.00 2.92
1643 3965 6.449698 CAAAAGCATGATAACAACAACCTCT 58.550 36.000 0.00 0.00 0.00 3.69
1644 3966 5.119125 GCAAAAGCATGATAACAACAACCTC 59.881 40.000 0.00 0.00 0.00 3.85
1645 3967 4.990426 GCAAAAGCATGATAACAACAACCT 59.010 37.500 0.00 0.00 0.00 3.50
1646 3968 4.990426 AGCAAAAGCATGATAACAACAACC 59.010 37.500 0.00 0.00 0.00 3.77
1647 3969 6.346838 GGAAGCAAAAGCATGATAACAACAAC 60.347 38.462 0.00 0.00 0.00 3.32
1648 3970 5.695816 GGAAGCAAAAGCATGATAACAACAA 59.304 36.000 0.00 0.00 0.00 2.83
1649 3971 5.010922 AGGAAGCAAAAGCATGATAACAACA 59.989 36.000 0.00 0.00 0.00 3.33
1650 3972 5.473039 AGGAAGCAAAAGCATGATAACAAC 58.527 37.500 0.00 0.00 0.00 3.32
1663 3985 1.039856 GCACAAGGGAGGAAGCAAAA 58.960 50.000 0.00 0.00 0.00 2.44
1680 4002 6.942532 AAGAGAACAAACTGTCTAATTGCA 57.057 33.333 0.00 0.00 0.00 4.08
1688 4010 3.066760 CCCCACAAAGAGAACAAACTGTC 59.933 47.826 0.00 0.00 0.00 3.51
1689 4011 3.023832 CCCCACAAAGAGAACAAACTGT 58.976 45.455 0.00 0.00 0.00 3.55
1705 4042 1.078143 GTGGAGTCATCAGCCCCAC 60.078 63.158 0.00 0.00 40.20 4.61
1706 4043 2.300967 GGTGGAGTCATCAGCCCCA 61.301 63.158 0.00 0.00 0.00 4.96
1707 4044 2.592308 GGTGGAGTCATCAGCCCC 59.408 66.667 0.00 0.00 0.00 5.80
1708 4045 2.187946 CGGTGGAGTCATCAGCCC 59.812 66.667 0.00 0.00 0.00 5.19
1710 4047 2.103042 GCACGGTGGAGTCATCAGC 61.103 63.158 10.60 0.00 0.00 4.26
1711 4048 0.738762 CAGCACGGTGGAGTCATCAG 60.739 60.000 10.60 0.00 0.00 2.90
1712 4049 1.184970 TCAGCACGGTGGAGTCATCA 61.185 55.000 10.60 0.00 0.00 3.07
1764 4101 9.537192 CATGACAATAATAATGAAAATGGCAGT 57.463 29.630 0.00 0.00 0.00 4.40
1768 4105 9.752961 TGCTCATGACAATAATAATGAAAATGG 57.247 29.630 0.00 0.00 0.00 3.16
1782 4119 8.913487 TGAATAAGATGTATGCTCATGACAAT 57.087 30.769 0.00 0.00 0.00 2.71
1783 4120 7.443272 CCTGAATAAGATGTATGCTCATGACAA 59.557 37.037 0.00 0.00 0.00 3.18
1784 4121 6.932960 CCTGAATAAGATGTATGCTCATGACA 59.067 38.462 0.00 0.00 0.00 3.58
1785 4122 6.128336 GCCTGAATAAGATGTATGCTCATGAC 60.128 42.308 0.00 0.00 0.00 3.06
1786 4123 5.936372 GCCTGAATAAGATGTATGCTCATGA 59.064 40.000 0.00 0.00 0.00 3.07
1787 4124 5.704053 TGCCTGAATAAGATGTATGCTCATG 59.296 40.000 0.00 0.00 0.00 3.07
1788 4125 5.872963 TGCCTGAATAAGATGTATGCTCAT 58.127 37.500 0.00 0.00 0.00 2.90
1795 4132 7.195374 ACCTAGTTTGCCTGAATAAGATGTA 57.805 36.000 0.00 0.00 0.00 2.29
1796 4133 6.067217 ACCTAGTTTGCCTGAATAAGATGT 57.933 37.500 0.00 0.00 0.00 3.06
1831 4168 6.364165 CCAAAACACAGAACAGCAATAATGAG 59.636 38.462 0.00 0.00 0.00 2.90
1879 4216 0.798776 CTTTCCACATGGACGCACTC 59.201 55.000 0.00 0.00 45.39 3.51
1898 4235 7.138736 ACAAATATGTGGCTTAATATCGTTGC 58.861 34.615 0.00 0.00 38.69 4.17
1959 4303 6.273071 ACAAAGGCTTGTGATAAAGAAACAC 58.727 36.000 0.00 0.00 44.28 3.32
1966 4310 6.093495 CGGAGAATACAAAGGCTTGTGATAAA 59.907 38.462 0.00 0.00 45.53 1.40
1989 4333 0.109781 CACGAGGACAAAATTGGCGG 60.110 55.000 0.00 0.00 36.95 6.13
1992 4336 4.503741 AATCACACGAGGACAAAATTGG 57.496 40.909 0.00 0.00 0.00 3.16
2006 4350 3.503363 TGAATCTGGCACTCAAATCACAC 59.497 43.478 0.00 0.00 0.00 3.82
2031 4375 2.434884 AAGACGCATGCCGACAGG 60.435 61.111 13.15 0.00 41.02 4.00
2036 4380 2.792290 CGAGTGAAGACGCATGCCG 61.792 63.158 13.15 10.04 44.21 5.69
2050 4394 5.008415 CCGGTGTATGTTAGAACTATCGAGT 59.992 44.000 0.00 0.00 37.59 4.18
2054 4398 5.533903 TCTCCCGGTGTATGTTAGAACTATC 59.466 44.000 0.00 0.00 0.00 2.08
2061 4405 4.939052 AGATTCTCCCGGTGTATGTTAG 57.061 45.455 0.00 0.00 0.00 2.34
2117 4461 2.793232 GTGTCTTCGTACCATTATCGGC 59.207 50.000 0.00 0.00 0.00 5.54
2120 4464 4.665212 TCGTGTGTCTTCGTACCATTATC 58.335 43.478 0.00 0.00 0.00 1.75
2123 4467 3.587797 ATCGTGTGTCTTCGTACCATT 57.412 42.857 0.00 0.00 0.00 3.16
2141 4485 3.343617 TGGCTAACAACCTGTAGCAATC 58.656 45.455 5.17 0.00 37.30 2.67
2147 4491 3.517901 AGCTACATGGCTAACAACCTGTA 59.482 43.478 0.00 0.00 41.16 2.74
2170 4514 5.269991 ACTACCATTAGCCAGAAGACAGTA 58.730 41.667 0.00 0.00 0.00 2.74
2250 4594 6.238239 GGACACGGCAACAATTTTAACAATTT 60.238 34.615 0.00 0.00 0.00 1.82
2291 4635 9.679661 ATGGTAAGAAATTGTACATCACATACA 57.320 29.630 0.00 0.00 36.90 2.29
2296 4640 9.935682 CATGTATGGTAAGAAATTGTACATCAC 57.064 33.333 0.00 0.00 31.14 3.06
2310 4737 6.804295 GCTAAGACTCGATCATGTATGGTAAG 59.196 42.308 0.00 0.00 0.00 2.34
2325 4752 2.853731 ACTCATTCGGCTAAGACTCG 57.146 50.000 0.00 0.00 0.00 4.18
2344 4771 2.603075 AAGCAGCCTTATGTTCCCAA 57.397 45.000 0.00 0.00 0.00 4.12
2347 4774 3.548818 CGCATAAAGCAGCCTTATGTTCC 60.549 47.826 20.32 7.41 46.13 3.62
2356 4783 2.838974 GCTCCCGCATAAAGCAGCC 61.839 63.158 0.00 0.00 46.13 4.85
2367 4794 1.444895 CACTTGCAATTGCTCCCGC 60.445 57.895 29.37 4.05 42.66 6.13
2368 4795 0.109597 GACACTTGCAATTGCTCCCG 60.110 55.000 29.37 17.87 42.66 5.14
2369 4796 0.961019 TGACACTTGCAATTGCTCCC 59.039 50.000 29.37 13.59 42.66 4.30
2379 4806 4.508662 AGGTAGCTTATCTTGACACTTGC 58.491 43.478 0.00 0.00 0.00 4.01
2390 4817 7.447238 ACAGATGTAGAGAGAAGGTAGCTTATC 59.553 40.741 19.12 19.12 0.00 1.75
2453 4880 5.450965 GGCATAAATGATCAAGGTGAAGTGG 60.451 44.000 0.00 0.00 0.00 4.00
2501 4928 9.581289 GGTACCAGATATCTAGCTACATCATAT 57.419 37.037 7.15 0.00 0.00 1.78
2502 4929 8.557450 TGGTACCAGATATCTAGCTACATCATA 58.443 37.037 11.60 0.00 0.00 2.15
2503 4930 7.414266 TGGTACCAGATATCTAGCTACATCAT 58.586 38.462 11.60 0.00 0.00 2.45
2504 4931 6.790319 TGGTACCAGATATCTAGCTACATCA 58.210 40.000 11.60 0.00 0.00 3.07
2505 4932 7.704578 TTGGTACCAGATATCTAGCTACATC 57.295 40.000 15.65 0.00 0.00 3.06
2506 4933 8.671987 ATTTGGTACCAGATATCTAGCTACAT 57.328 34.615 16.07 0.00 0.00 2.29
2507 4934 9.769677 ATATTTGGTACCAGATATCTAGCTACA 57.230 33.333 25.29 6.02 30.87 2.74
2517 4944 7.888514 ATCAGGGAATATTTGGTACCAGATA 57.111 36.000 23.38 23.38 0.00 1.98
2524 4951 9.094578 TGTTTTTCAATCAGGGAATATTTGGTA 57.905 29.630 0.00 0.00 0.00 3.25
2572 4999 1.546923 TGAACATCCTGCAAGCCAATG 59.453 47.619 0.00 0.00 0.00 2.82
2574 5001 1.250328 CTGAACATCCTGCAAGCCAA 58.750 50.000 0.00 0.00 0.00 4.52
2613 5040 1.287730 CCTAGCAATCGCGGCATCTC 61.288 60.000 6.13 0.00 45.49 2.75
2719 5146 1.596752 GTCACGCACATCACCCACA 60.597 57.895 0.00 0.00 0.00 4.17
2746 5173 1.270625 ACATCTTCGGGCGAGACAAAA 60.271 47.619 0.00 0.00 0.00 2.44
2758 5185 2.545526 GTGCATCCCATACACATCTTCG 59.454 50.000 0.00 0.00 34.43 3.79
2775 5202 2.036098 CCCCTGATTGGCTGTGCA 59.964 61.111 0.00 0.00 0.00 4.57
2806 5233 4.424711 GAACCATGCCCCCTGCGA 62.425 66.667 0.00 0.00 45.60 5.10
2884 5311 0.525668 GCACACTACCCATCGTCTCG 60.526 60.000 0.00 0.00 0.00 4.04
2889 5316 1.153369 CCCAGCACACTACCCATCG 60.153 63.158 0.00 0.00 0.00 3.84
2899 5326 1.628340 ACAGTAGCATTACCCAGCACA 59.372 47.619 0.00 0.00 0.00 4.57
2979 5406 1.399744 CCTATACTGGACCGCTGGCA 61.400 60.000 0.00 0.00 0.00 4.92
2986 5413 2.622470 GTCGGTTCTCCTATACTGGACC 59.378 54.545 0.00 0.00 31.94 4.46
2992 5419 6.338937 AGAAACATTGTCGGTTCTCCTATAC 58.661 40.000 0.00 0.00 0.00 1.47
3002 5429 3.306364 CCAGAGAGAGAAACATTGTCGGT 60.306 47.826 0.00 0.00 0.00 4.69
3012 5439 3.169099 CTTGACCCTCCAGAGAGAGAAA 58.831 50.000 0.00 0.00 43.39 2.52
3019 5446 3.071602 TGTCTTTTCTTGACCCTCCAGAG 59.928 47.826 0.00 0.00 33.83 3.35
3042 5469 5.006386 ACACTTCCAGATGCTTTCCTTTAG 58.994 41.667 0.00 0.00 0.00 1.85
3056 5483 6.472686 ACCTCTAGCTAATAACACTTCCAG 57.527 41.667 0.00 0.00 0.00 3.86
3255 5682 1.347707 ACCGACTTGCAGATTCTTCCA 59.652 47.619 0.00 0.00 0.00 3.53
3283 5710 5.901552 ACAATTGTTGTGGTTAGTTGAAGG 58.098 37.500 4.92 0.00 43.48 3.46
3342 5769 6.638610 ACCAAACAAACAGATTCAAATGTCA 58.361 32.000 0.00 0.00 0.00 3.58
3378 5805 6.611236 TCTCCAAGTTCATCACCATAGATGTA 59.389 38.462 0.00 0.00 44.46 2.29
3410 5837 0.244721 GTGAGGGAACATTGGCTTGC 59.755 55.000 0.00 0.00 0.00 4.01
3460 5894 2.216046 CATAGCATCGCAATGTCCAGT 58.784 47.619 0.00 0.00 35.18 4.00
3488 5922 2.364324 ACACTAGTCGAAGAGGCAAACA 59.636 45.455 0.00 0.00 36.95 2.83
3510 5944 0.033796 ACCTCTGGGCCATGACATTG 60.034 55.000 6.72 0.00 35.63 2.82
3511 5945 0.706433 AACCTCTGGGCCATGACATT 59.294 50.000 6.72 0.00 35.63 2.71
3512 5946 0.257039 GAACCTCTGGGCCATGACAT 59.743 55.000 6.72 0.00 35.63 3.06
3513 5947 0.842030 AGAACCTCTGGGCCATGACA 60.842 55.000 6.72 0.00 35.63 3.58
3514 5948 0.329596 AAGAACCTCTGGGCCATGAC 59.670 55.000 6.72 0.00 35.63 3.06
3515 5949 1.075601 AAAGAACCTCTGGGCCATGA 58.924 50.000 6.72 6.07 35.63 3.07
3631 6065 4.825546 AGAGCAATTCACAACTCAACTG 57.174 40.909 0.00 0.00 0.00 3.16
3632 6066 5.591877 AGAAAGAGCAATTCACAACTCAACT 59.408 36.000 0.00 0.00 0.00 3.16
3677 6111 1.975660 AGAAAAAGCGGTGCCTAACA 58.024 45.000 0.00 0.00 0.00 2.41
3701 6135 3.197116 TCTCCGAAAGAAGGGGAACATAC 59.803 47.826 0.00 0.00 0.00 2.39
3736 6170 4.136796 AGCAGCAATAGAGAACAACAACA 58.863 39.130 0.00 0.00 0.00 3.33
3737 6171 4.756084 AGCAGCAATAGAGAACAACAAC 57.244 40.909 0.00 0.00 0.00 3.32
3738 6172 4.557296 GCAAGCAGCAATAGAGAACAACAA 60.557 41.667 0.00 0.00 44.79 2.83
3739 6173 3.058016 GCAAGCAGCAATAGAGAACAACA 60.058 43.478 0.00 0.00 44.79 3.33
3740 6174 3.496155 GCAAGCAGCAATAGAGAACAAC 58.504 45.455 0.00 0.00 44.79 3.32
3777 6211 0.673985 CGAGAATGCCCGATCTGGTA 59.326 55.000 4.97 0.14 35.15 3.25
3783 6217 2.093658 ACTTTACACGAGAATGCCCGAT 60.094 45.455 0.00 0.00 0.00 4.18
3785 6219 1.722011 ACTTTACACGAGAATGCCCG 58.278 50.000 0.00 0.00 0.00 6.13
3790 6224 6.053005 TGTCCTTCAAACTTTACACGAGAAT 58.947 36.000 0.00 0.00 0.00 2.40
3796 6230 4.335594 AGTGCTGTCCTTCAAACTTTACAC 59.664 41.667 0.00 0.00 0.00 2.90
3814 6248 3.579709 CTGACGTCAGATTTGTAGTGCT 58.420 45.455 36.73 0.00 46.59 4.40
3844 6278 2.238521 AGACGTTCAATTTGCCATGGT 58.761 42.857 14.67 0.00 0.00 3.55
3856 6293 5.837437 ACAAATTGCCATAAAAGACGTTCA 58.163 33.333 0.00 0.00 0.00 3.18
3880 6317 4.751767 AACTTGAACATCCTTGGCAAAA 57.248 36.364 0.00 0.00 0.00 2.44
3887 6324 4.892934 TGCCAACTAAACTTGAACATCCTT 59.107 37.500 0.00 0.00 0.00 3.36
3894 6331 4.099266 ACATGCTTGCCAACTAAACTTGAA 59.901 37.500 0.00 0.00 0.00 2.69
3895 6332 3.636300 ACATGCTTGCCAACTAAACTTGA 59.364 39.130 0.00 0.00 0.00 3.02
3925 6362 3.698040 AGCATGGAAAATCGAAATGAGCT 59.302 39.130 0.00 0.00 0.00 4.09
3958 6395 6.417191 TCCGTAATGCTAAAAATCTGACAC 57.583 37.500 0.00 0.00 0.00 3.67
3966 6403 7.012515 TGACTCAAACTTCCGTAATGCTAAAAA 59.987 33.333 0.00 0.00 0.00 1.94
3979 6416 5.815740 TCACTGTAAACTGACTCAAACTTCC 59.184 40.000 0.00 0.00 0.00 3.46
3989 6426 5.915196 GCCAAAGATTTCACTGTAAACTGAC 59.085 40.000 0.00 0.00 0.00 3.51
4051 6488 3.629142 AACCATAGCCAGTACCACTTC 57.371 47.619 0.00 0.00 0.00 3.01
4052 6489 4.079253 CAAAACCATAGCCAGTACCACTT 58.921 43.478 0.00 0.00 0.00 3.16
4053 6490 3.561313 CCAAAACCATAGCCAGTACCACT 60.561 47.826 0.00 0.00 0.00 4.00
4054 6491 2.752903 CCAAAACCATAGCCAGTACCAC 59.247 50.000 0.00 0.00 0.00 4.16
4055 6492 2.882229 GCCAAAACCATAGCCAGTACCA 60.882 50.000 0.00 0.00 0.00 3.25
4056 6493 1.749063 GCCAAAACCATAGCCAGTACC 59.251 52.381 0.00 0.00 0.00 3.34
4057 6494 2.442413 TGCCAAAACCATAGCCAGTAC 58.558 47.619 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.