Multiple sequence alignment - TraesCS4B01G225400

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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 TraesCS4B01G225400 chr4B 100.000 3178 0 0 1 3178 471958605 471955428 0.000000e+00 5869
1 TraesCS4B01G225400 chr4A 88.712 2197 129 48 769 2910 66610245 66608113 0.000000e+00 2573
2 TraesCS4B01G225400 chr4A 88.418 1157 83 26 906 2056 66802699 66801588 0.000000e+00 1347
3 TraesCS4B01G225400 chr4A 91.317 1002 56 14 804 1782 66761652 66760659 0.000000e+00 1339
4 TraesCS4B01G225400 chr4A 83.917 771 96 14 1 752 462627284 462628045 0.000000e+00 712
5 TraesCS4B01G225400 chr4A 91.667 276 10 6 1778 2053 66755287 66755025 1.390000e-98 370
6 TraesCS4B01G225400 chr4A 92.000 150 8 2 1904 2053 66772026 66771881 1.160000e-49 207
7 TraesCS4B01G225400 chr4A 92.254 142 7 2 1912 2053 66771136 66770999 6.950000e-47 198
8 TraesCS4B01G225400 chr4D 86.857 1826 133 43 809 2601 384976601 384974850 0.000000e+00 1943
9 TraesCS4B01G225400 chr4D 87.473 455 26 10 2487 2912 384974834 384974382 2.200000e-136 496
10 TraesCS4B01G225400 chr5B 88.462 754 66 9 1 735 120938350 120937599 0.000000e+00 891
11 TraesCS4B01G225400 chr3D 86.093 755 79 15 1 735 506180506 506179758 0.000000e+00 789
12 TraesCS4B01G225400 chr2A 85.885 751 83 10 1 734 753157827 753158571 0.000000e+00 778
13 TraesCS4B01G225400 chr2A 84.780 749 88 13 5 735 235392059 235391319 0.000000e+00 728
14 TraesCS4B01G225400 chr2A 83.936 747 96 11 1 729 720659727 720660467 0.000000e+00 693
15 TraesCS4B01G225400 chr6D 85.602 764 78 17 1 738 412727690 412726933 0.000000e+00 773
16 TraesCS4B01G225400 chr6D 84.530 724 86 13 1 711 142738752 142738042 0.000000e+00 693
17 TraesCS4B01G225400 chr1A 85.545 761 82 15 5 746 25575572 25574821 0.000000e+00 771
18 TraesCS4B01G225400 chr1A 84.109 774 89 19 1 747 315261665 315260899 0.000000e+00 717
19 TraesCS4B01G225400 chr7D 85.411 706 77 14 50 735 104754456 104753757 0.000000e+00 710
20 TraesCS4B01G225400 chr6A 83.554 754 100 15 1 735 169704292 169705040 0.000000e+00 684
21 TraesCS4B01G225400 chr5A 86.796 568 57 11 5 560 578073244 578072683 4.500000e-173 617
22 TraesCS4B01G225400 chr3B 83.537 656 70 15 1 644 422203723 422203094 2.130000e-161 579


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 TraesCS4B01G225400 chr4B 471955428 471958605 3177 True 5869.0 5869 100.000 1 3178 1 chr4B.!!$R1 3177
1 TraesCS4B01G225400 chr4A 66608113 66610245 2132 True 2573.0 2573 88.712 769 2910 1 chr4A.!!$R1 2141
2 TraesCS4B01G225400 chr4A 66801588 66802699 1111 True 1347.0 1347 88.418 906 2056 1 chr4A.!!$R4 1150
3 TraesCS4B01G225400 chr4A 66760659 66761652 993 True 1339.0 1339 91.317 804 1782 1 chr4A.!!$R3 978
4 TraesCS4B01G225400 chr4A 462627284 462628045 761 False 712.0 712 83.917 1 752 1 chr4A.!!$F1 751
5 TraesCS4B01G225400 chr4A 66770999 66772026 1027 True 202.5 207 92.127 1904 2053 2 chr4A.!!$R5 149
6 TraesCS4B01G225400 chr4D 384974382 384976601 2219 True 1219.5 1943 87.165 809 2912 2 chr4D.!!$R1 2103
7 TraesCS4B01G225400 chr5B 120937599 120938350 751 True 891.0 891 88.462 1 735 1 chr5B.!!$R1 734
8 TraesCS4B01G225400 chr3D 506179758 506180506 748 True 789.0 789 86.093 1 735 1 chr3D.!!$R1 734
9 TraesCS4B01G225400 chr2A 753157827 753158571 744 False 778.0 778 85.885 1 734 1 chr2A.!!$F2 733
10 TraesCS4B01G225400 chr2A 235391319 235392059 740 True 728.0 728 84.780 5 735 1 chr2A.!!$R1 730
11 TraesCS4B01G225400 chr2A 720659727 720660467 740 False 693.0 693 83.936 1 729 1 chr2A.!!$F1 728
12 TraesCS4B01G225400 chr6D 412726933 412727690 757 True 773.0 773 85.602 1 738 1 chr6D.!!$R2 737
13 TraesCS4B01G225400 chr6D 142738042 142738752 710 True 693.0 693 84.530 1 711 1 chr6D.!!$R1 710
14 TraesCS4B01G225400 chr1A 25574821 25575572 751 True 771.0 771 85.545 5 746 1 chr1A.!!$R1 741
15 TraesCS4B01G225400 chr1A 315260899 315261665 766 True 717.0 717 84.109 1 747 1 chr1A.!!$R2 746
16 TraesCS4B01G225400 chr7D 104753757 104754456 699 True 710.0 710 85.411 50 735 1 chr7D.!!$R1 685
17 TraesCS4B01G225400 chr6A 169704292 169705040 748 False 684.0 684 83.554 1 735 1 chr6A.!!$F1 734
18 TraesCS4B01G225400 chr5A 578072683 578073244 561 True 617.0 617 86.796 5 560 1 chr5A.!!$R1 555
19 TraesCS4B01G225400 chr3B 422203094 422203723 629 True 579.0 579 83.537 1 644 1 chr3B.!!$R1 643

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
154 161 0.460311 ATGCTACCGAGTTAGCGCTT 59.540 50.0 18.68 0.0 41.92 4.68 F
1460 1537 0.383949 GTTCCGCAGTGCCTTTCAAA 59.616 50.0 10.11 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 3024 0.248907 ACTCGCCGACGGTCATATTG 60.249 55.0 16.73 2.08 40.63 1.9 R
2350 3332 0.036164 TATGCCCGACAAACTGCACT 59.964 50.0 0.00 0.00 36.41 4.4 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
54 59 2.779755 AGCGACACATGTTATGGGAA 57.220 45.000 0.00 0.00 37.07 3.97
59 64 2.958355 GACACATGTTATGGGAATGGGG 59.042 50.000 0.00 0.00 37.07 4.96
154 161 0.460311 ATGCTACCGAGTTAGCGCTT 59.540 50.000 18.68 0.00 41.92 4.68
232 249 4.961585 AGTGACCTCCTAAAGAACCCTAT 58.038 43.478 0.00 0.00 0.00 2.57
348 368 3.452990 TCCATAACGAAGCATGAGGGTTA 59.547 43.478 0.00 0.00 37.33 2.85
507 527 2.079158 GGTGTGTCATGTGATGGTCAG 58.921 52.381 0.00 0.00 0.00 3.51
531 551 2.563261 ATCGCCTCTGCATTGATCAT 57.437 45.000 0.00 0.00 37.32 2.45
566 586 0.909610 GATCAGGTGGACACTGGGGA 60.910 60.000 2.13 0.00 36.62 4.81
633 669 2.301870 TGCCGTGTTGAAATAGAGGACT 59.698 45.455 0.00 0.00 0.00 3.85
677 713 5.308237 AGGTGGAGTCTTTGAGTCATACTTT 59.692 40.000 0.00 0.00 34.00 2.66
678 714 5.639931 GGTGGAGTCTTTGAGTCATACTTTC 59.360 44.000 0.00 0.00 34.00 2.62
715 757 9.422196 GATATTATTAGTTTTCTCACGTTGCAC 57.578 33.333 0.00 0.00 0.00 4.57
735 777 1.280066 CGCATGGGCATTTTTGCTAC 58.720 50.000 0.00 0.00 41.24 3.58
739 781 4.023279 CGCATGGGCATTTTTGCTACTATA 60.023 41.667 0.00 0.00 41.24 1.31
743 786 7.094205 GCATGGGCATTTTTGCTACTATACTAT 60.094 37.037 0.00 0.00 40.72 2.12
767 810 6.456795 AAAAGAAGAACAGAAGAAACAGGG 57.543 37.500 0.00 0.00 0.00 4.45
768 811 5.373812 AAGAAGAACAGAAGAAACAGGGA 57.626 39.130 0.00 0.00 0.00 4.20
769 812 5.373812 AGAAGAACAGAAGAAACAGGGAA 57.626 39.130 0.00 0.00 0.00 3.97
770 813 5.755849 AGAAGAACAGAAGAAACAGGGAAA 58.244 37.500 0.00 0.00 0.00 3.13
771 814 6.187682 AGAAGAACAGAAGAAACAGGGAAAA 58.812 36.000 0.00 0.00 0.00 2.29
772 815 6.319911 AGAAGAACAGAAGAAACAGGGAAAAG 59.680 38.462 0.00 0.00 0.00 2.27
773 816 4.889995 AGAACAGAAGAAACAGGGAAAAGG 59.110 41.667 0.00 0.00 0.00 3.11
774 817 4.251103 ACAGAAGAAACAGGGAAAAGGT 57.749 40.909 0.00 0.00 0.00 3.50
775 818 4.207955 ACAGAAGAAACAGGGAAAAGGTC 58.792 43.478 0.00 0.00 0.00 3.85
780 823 4.145052 AGAAACAGGGAAAAGGTCACATC 58.855 43.478 0.00 0.00 28.68 3.06
801 844 3.798954 GAGATGGGCCTCGGCTTCG 62.799 68.421 4.53 0.00 41.60 3.79
814 857 2.061773 CGGCTTCGCGATCTGAAATAT 58.938 47.619 10.88 0.00 0.00 1.28
902 946 0.679505 CAGACCTGAAGAACACCCGA 59.320 55.000 0.00 0.00 0.00 5.14
991 1053 2.619646 CCACGATCATGGCATGAAATCA 59.380 45.455 31.81 11.20 43.50 2.57
1007 1069 6.174720 TGAAATCACCTCCGCTCTATAAAT 57.825 37.500 0.00 0.00 0.00 1.40
1073 1135 2.464157 AGAACCACTTAGCTGCAGTC 57.536 50.000 16.64 7.83 0.00 3.51
1079 1146 1.472878 CACTTAGCTGCAGTCCGTAGA 59.527 52.381 16.64 0.00 0.00 2.59
1108 1175 3.575630 CTTCCGAGTTTCAACGATCTCA 58.424 45.455 0.00 0.00 0.00 3.27
1110 1179 3.770666 TCCGAGTTTCAACGATCTCATC 58.229 45.455 0.00 0.00 0.00 2.92
1147 1216 6.533819 TTCAATTCTCGAGCGACTTTTAAA 57.466 33.333 7.81 0.00 0.00 1.52
1148 1217 6.153212 TCAATTCTCGAGCGACTTTTAAAG 57.847 37.500 7.81 2.81 0.00 1.85
1149 1218 4.585619 ATTCTCGAGCGACTTTTAAAGC 57.414 40.909 7.81 0.00 0.00 3.51
1172 1249 1.134007 CCTATCTGGTGCAATGGCTGA 60.134 52.381 0.00 0.00 41.91 4.26
1452 1529 2.029844 GTCCTCTGTTCCGCAGTGC 61.030 63.158 4.58 4.58 45.23 4.40
1460 1537 0.383949 GTTCCGCAGTGCCTTTCAAA 59.616 50.000 10.11 0.00 0.00 2.69
1476 1553 6.422100 GCCTTTCAAAGAGAGAAATTTGTTCC 59.578 38.462 0.00 0.00 37.60 3.62
1483 1563 5.684704 AGAGAGAAATTTGTTCCAGTGTGA 58.315 37.500 0.00 0.00 0.00 3.58
1574 1654 2.124983 ACGATGCGGCAGATGCTT 60.125 55.556 9.25 0.00 41.70 3.91
1901 1981 1.286260 GGACGAGTGCGACAAGAGT 59.714 57.895 0.00 0.00 41.64 3.24
1983 2063 1.443702 CGCAAGGTCATCGACGTGA 60.444 57.895 0.00 0.00 32.65 4.35
2000 2080 2.492088 CGTGAAGGTCCAGTGATGAGTA 59.508 50.000 0.00 0.00 0.00 2.59
2004 2084 3.361281 AGGTCCAGTGATGAGTACGTA 57.639 47.619 0.00 0.00 0.00 3.57
2024 2995 0.826256 TGTGCGAGACTGTACCCTGT 60.826 55.000 0.00 0.00 0.00 4.00
2025 2996 0.388649 GTGCGAGACTGTACCCTGTG 60.389 60.000 0.00 0.00 0.00 3.66
2053 3024 3.129462 GGCTTTAAGATTTCAGCTGTCCC 59.871 47.826 14.67 1.95 32.52 4.46
2056 3027 5.105595 GCTTTAAGATTTCAGCTGTCCCAAT 60.106 40.000 14.67 8.11 0.00 3.16
2057 3028 6.095440 GCTTTAAGATTTCAGCTGTCCCAATA 59.905 38.462 14.67 0.00 0.00 1.90
2058 3029 7.201857 GCTTTAAGATTTCAGCTGTCCCAATAT 60.202 37.037 14.67 3.14 0.00 1.28
2059 3030 7.572523 TTAAGATTTCAGCTGTCCCAATATG 57.427 36.000 14.67 0.00 0.00 1.78
2060 3031 5.378230 AGATTTCAGCTGTCCCAATATGA 57.622 39.130 14.67 0.00 0.00 2.15
2061 3032 5.128919 AGATTTCAGCTGTCCCAATATGAC 58.871 41.667 14.67 0.00 0.00 3.06
2063 3034 1.138859 TCAGCTGTCCCAATATGACCG 59.861 52.381 14.67 0.00 31.60 4.79
2064 3035 1.134401 CAGCTGTCCCAATATGACCGT 60.134 52.381 5.25 0.00 31.60 4.83
2065 3036 1.139058 AGCTGTCCCAATATGACCGTC 59.861 52.381 0.00 0.00 31.60 4.79
2066 3037 1.852942 CTGTCCCAATATGACCGTCG 58.147 55.000 0.00 0.00 31.60 5.12
2074 3045 1.099295 ATATGACCGTCGGCGAGTGA 61.099 55.000 12.93 0.90 41.33 3.41
2143 3115 1.818850 GCTCGTTCGCAGAATACGTA 58.181 50.000 0.00 0.00 45.90 3.57
2145 3117 2.538333 GCTCGTTCGCAGAATACGTAGA 60.538 50.000 0.08 0.00 45.90 2.59
2149 3121 3.436496 GTTCGCAGAATACGTAGAGCTT 58.564 45.455 0.08 0.00 45.90 3.74
2227 3203 5.022021 GCACACACTTCGATTAATTACTGC 58.978 41.667 0.00 0.00 0.00 4.40
2235 3211 6.978659 ACTTCGATTAATTACTGCATCGAGAA 59.021 34.615 15.70 6.04 45.98 2.87
2236 3212 7.491372 ACTTCGATTAATTACTGCATCGAGAAA 59.509 33.333 15.70 5.52 45.98 2.52
2237 3213 7.946655 TCGATTAATTACTGCATCGAGAAAT 57.053 32.000 13.39 0.00 41.90 2.17
2259 3235 6.817765 ATATTAGTTCCCTGTTGTGTTGTG 57.182 37.500 0.00 0.00 0.00 3.33
2267 3243 3.210227 CCTGTTGTGTTGTGGTGTGATA 58.790 45.455 0.00 0.00 0.00 2.15
2319 3301 9.847706 GAAGCTGATAACTGAATCGAGATATAA 57.152 33.333 0.00 0.00 0.00 0.98
2337 3319 7.961351 AGATATAATATAGGCAGCACATCCTC 58.039 38.462 0.00 0.00 34.02 3.71
2349 3331 5.732528 GCAGCACATCCTCATGAATTTGTAG 60.733 44.000 0.00 0.00 33.72 2.74
2350 3332 5.587443 CAGCACATCCTCATGAATTTGTAGA 59.413 40.000 0.00 0.00 33.72 2.59
2351 3333 5.821470 AGCACATCCTCATGAATTTGTAGAG 59.179 40.000 0.00 0.00 33.72 2.43
2352 3334 5.587844 GCACATCCTCATGAATTTGTAGAGT 59.412 40.000 0.00 0.00 33.72 3.24
2353 3335 6.457934 GCACATCCTCATGAATTTGTAGAGTG 60.458 42.308 0.00 0.00 33.72 3.51
2354 3336 5.587844 ACATCCTCATGAATTTGTAGAGTGC 59.412 40.000 0.00 0.00 33.72 4.40
2355 3337 5.164620 TCCTCATGAATTTGTAGAGTGCA 57.835 39.130 0.00 0.00 0.00 4.57
2356 3338 5.181009 TCCTCATGAATTTGTAGAGTGCAG 58.819 41.667 0.00 0.00 0.00 4.41
2357 3339 4.940046 CCTCATGAATTTGTAGAGTGCAGT 59.060 41.667 0.00 0.00 0.00 4.40
2360 3342 6.671190 TCATGAATTTGTAGAGTGCAGTTTG 58.329 36.000 0.00 0.00 0.00 2.93
2361 3343 6.262944 TCATGAATTTGTAGAGTGCAGTTTGT 59.737 34.615 0.00 0.00 0.00 2.83
2376 3359 4.091365 GCAGTTTGTCGGGCATAAAATTTC 59.909 41.667 0.00 0.00 0.00 2.17
2396 3379 9.840427 AAATTTCAAGAATGTGTTAACGGATAG 57.160 29.630 0.26 0.00 0.00 2.08
2397 3380 6.978343 TTCAAGAATGTGTTAACGGATAGG 57.022 37.500 0.26 0.00 0.00 2.57
2398 3381 6.288941 TCAAGAATGTGTTAACGGATAGGA 57.711 37.500 0.26 0.00 0.00 2.94
2399 3382 6.338146 TCAAGAATGTGTTAACGGATAGGAG 58.662 40.000 0.26 0.00 0.00 3.69
2436 3419 6.483307 TCTTCACTTTTGTTAGTCATGGACAG 59.517 38.462 0.00 0.00 34.60 3.51
2545 3662 1.077212 CCCCTGTAGCTGCAGCAAT 60.077 57.895 38.24 22.64 45.16 3.56
2578 3695 3.954258 ACTTGGTTTTCAGGAGTTCTTGG 59.046 43.478 0.00 0.00 0.00 3.61
2733 3879 1.386533 CAGGATTGCGGCAGAAGAAT 58.613 50.000 1.67 0.00 0.00 2.40
2797 3943 1.692411 GGTGAAAACCCTTGCTGAGT 58.308 50.000 0.00 0.00 0.00 3.41
2836 3982 4.023193 GGCTGTGTAGTATGTTTGCACTTT 60.023 41.667 0.00 0.00 0.00 2.66
2876 4022 4.228567 TGCACGCTCGTTCCACCA 62.229 61.111 0.00 0.00 0.00 4.17
2882 4028 2.741985 CTCGTTCCACCATGCGCA 60.742 61.111 14.96 14.96 0.00 6.09
2902 4048 2.035193 CACCATAGTAGCTCTGCGACAT 59.965 50.000 0.00 0.00 36.66 3.06
2904 4050 2.057316 CATAGTAGCTCTGCGACATGC 58.943 52.381 0.00 0.00 46.70 4.06
2915 4061 2.706760 GCGACATGCATGCAATTTTC 57.293 45.000 26.68 16.42 45.45 2.29
2916 4062 2.264813 GCGACATGCATGCAATTTTCT 58.735 42.857 26.68 3.45 45.45 2.52
2917 4063 3.437428 GCGACATGCATGCAATTTTCTA 58.563 40.909 26.68 0.00 45.45 2.10
2918 4064 3.858812 GCGACATGCATGCAATTTTCTAA 59.141 39.130 26.68 0.00 45.45 2.10
2919 4065 4.027132 GCGACATGCATGCAATTTTCTAAG 60.027 41.667 26.68 10.14 45.45 2.18
2920 4066 4.027132 CGACATGCATGCAATTTTCTAAGC 60.027 41.667 26.68 4.43 0.00 3.09
2921 4067 4.823157 ACATGCATGCAATTTTCTAAGCA 58.177 34.783 26.68 0.00 41.73 3.91
2923 4069 6.575267 ACATGCATGCAATTTTCTAAGCATA 58.425 32.000 26.68 0.00 45.14 3.14
2924 4070 7.042950 ACATGCATGCAATTTTCTAAGCATAA 58.957 30.769 26.68 0.00 45.14 1.90
2925 4071 7.223971 ACATGCATGCAATTTTCTAAGCATAAG 59.776 33.333 26.68 0.00 45.14 1.73
2926 4072 6.044046 TGCATGCAATTTTCTAAGCATAAGG 58.956 36.000 20.30 0.00 45.14 2.69
2927 4073 6.044682 GCATGCAATTTTCTAAGCATAAGGT 58.955 36.000 14.21 0.00 45.14 3.50
2928 4074 7.147932 TGCATGCAATTTTCTAAGCATAAGGTA 60.148 33.333 20.30 0.00 45.14 3.08
2929 4075 7.706179 GCATGCAATTTTCTAAGCATAAGGTAA 59.294 33.333 14.21 0.00 45.14 2.85
2930 4076 9.585099 CATGCAATTTTCTAAGCATAAGGTAAA 57.415 29.630 0.00 0.00 45.14 2.01
2932 4078 9.988815 TGCAATTTTCTAAGCATAAGGTAAAAA 57.011 25.926 0.00 0.00 31.05 1.94
2935 4081 9.634163 AATTTTCTAAGCATAAGGTAAAAACGG 57.366 29.630 0.00 0.00 0.00 4.44
2936 4082 7.748691 TTTCTAAGCATAAGGTAAAAACGGT 57.251 32.000 0.00 0.00 0.00 4.83
2937 4083 6.730960 TCTAAGCATAAGGTAAAAACGGTG 57.269 37.500 0.00 0.00 0.00 4.94
2938 4084 6.465948 TCTAAGCATAAGGTAAAAACGGTGA 58.534 36.000 0.00 0.00 0.00 4.02
2939 4085 5.622770 AAGCATAAGGTAAAAACGGTGAG 57.377 39.130 0.00 0.00 0.00 3.51
2940 4086 3.439129 AGCATAAGGTAAAAACGGTGAGC 59.561 43.478 0.00 0.00 0.00 4.26
2941 4087 3.726782 GCATAAGGTAAAAACGGTGAGCG 60.727 47.826 1.13 1.13 0.00 5.03
2942 4088 1.957668 AAGGTAAAAACGGTGAGCGT 58.042 45.000 2.91 2.91 0.00 5.07
2943 4089 1.223187 AGGTAAAAACGGTGAGCGTG 58.777 50.000 11.46 0.00 0.00 5.34
2944 4090 0.939419 GGTAAAAACGGTGAGCGTGT 59.061 50.000 11.46 0.78 0.00 4.49
2945 4091 1.331447 GGTAAAAACGGTGAGCGTGTT 59.669 47.619 11.46 8.98 0.00 3.32
2946 4092 2.223317 GGTAAAAACGGTGAGCGTGTTT 60.223 45.455 25.59 25.59 37.41 2.83
2947 4093 2.640346 AAAAACGGTGAGCGTGTTTT 57.360 40.000 18.42 17.84 45.00 2.43
2948 4094 2.640346 AAAACGGTGAGCGTGTTTTT 57.360 40.000 11.46 4.89 41.58 1.94
2977 4123 3.458189 GACATCTGGTCATAAAGTCCCG 58.542 50.000 0.00 0.00 46.19 5.14
2978 4124 2.838202 ACATCTGGTCATAAAGTCCCGT 59.162 45.455 0.00 0.00 0.00 5.28
2979 4125 3.263425 ACATCTGGTCATAAAGTCCCGTT 59.737 43.478 0.00 0.00 0.00 4.44
2980 4126 4.261801 CATCTGGTCATAAAGTCCCGTTT 58.738 43.478 0.00 0.00 0.00 3.60
2981 4127 5.046159 ACATCTGGTCATAAAGTCCCGTTTA 60.046 40.000 0.00 0.00 0.00 2.01
2982 4128 5.080969 TCTGGTCATAAAGTCCCGTTTAG 57.919 43.478 0.00 0.00 0.00 1.85
2983 4129 4.773674 TCTGGTCATAAAGTCCCGTTTAGA 59.226 41.667 0.00 0.00 0.00 2.10
2984 4130 5.246656 TCTGGTCATAAAGTCCCGTTTAGAA 59.753 40.000 0.00 0.00 0.00 2.10
2985 4131 5.240121 TGGTCATAAAGTCCCGTTTAGAAC 58.760 41.667 0.00 0.00 0.00 3.01
2986 4132 5.221682 TGGTCATAAAGTCCCGTTTAGAACA 60.222 40.000 0.00 0.00 0.00 3.18
2987 4133 5.702209 GGTCATAAAGTCCCGTTTAGAACAA 59.298 40.000 0.00 0.00 0.00 2.83
2988 4134 6.128363 GGTCATAAAGTCCCGTTTAGAACAAG 60.128 42.308 0.00 0.00 0.00 3.16
2989 4135 5.935789 TCATAAAGTCCCGTTTAGAACAAGG 59.064 40.000 0.00 0.00 0.00 3.61
2990 4136 2.853235 AGTCCCGTTTAGAACAAGGG 57.147 50.000 0.00 0.00 43.32 3.95
2994 4140 3.412237 CCCGTTTAGAACAAGGGAAGA 57.588 47.619 0.00 0.00 44.70 2.87
2995 4141 3.746940 CCCGTTTAGAACAAGGGAAGAA 58.253 45.455 0.00 0.00 44.70 2.52
2996 4142 4.139038 CCCGTTTAGAACAAGGGAAGAAA 58.861 43.478 0.00 0.00 44.70 2.52
2997 4143 4.581409 CCCGTTTAGAACAAGGGAAGAAAA 59.419 41.667 0.00 0.00 44.70 2.29
2998 4144 5.068067 CCCGTTTAGAACAAGGGAAGAAAAA 59.932 40.000 0.00 0.00 44.70 1.94
2999 4145 5.975344 CCGTTTAGAACAAGGGAAGAAAAAC 59.025 40.000 0.00 0.00 34.15 2.43
3000 4146 6.404954 CCGTTTAGAACAAGGGAAGAAAAACA 60.405 38.462 0.00 0.00 34.15 2.83
3001 4147 7.200455 CGTTTAGAACAAGGGAAGAAAAACAT 58.800 34.615 0.00 0.00 0.00 2.71
3002 4148 8.347035 CGTTTAGAACAAGGGAAGAAAAACATA 58.653 33.333 0.00 0.00 0.00 2.29
3003 4149 9.678941 GTTTAGAACAAGGGAAGAAAAACATAG 57.321 33.333 0.00 0.00 0.00 2.23
3004 4150 6.901081 AGAACAAGGGAAGAAAAACATAGG 57.099 37.500 0.00 0.00 0.00 2.57
3005 4151 6.373759 AGAACAAGGGAAGAAAAACATAGGT 58.626 36.000 0.00 0.00 0.00 3.08
3006 4152 7.523415 AGAACAAGGGAAGAAAAACATAGGTA 58.477 34.615 0.00 0.00 0.00 3.08
3007 4153 8.170730 AGAACAAGGGAAGAAAAACATAGGTAT 58.829 33.333 0.00 0.00 0.00 2.73
3008 4154 8.721133 AACAAGGGAAGAAAAACATAGGTATT 57.279 30.769 0.00 0.00 0.00 1.89
3009 4155 8.721133 ACAAGGGAAGAAAAACATAGGTATTT 57.279 30.769 0.00 0.00 0.00 1.40
3010 4156 9.154632 ACAAGGGAAGAAAAACATAGGTATTTT 57.845 29.630 1.81 1.81 0.00 1.82
3011 4157 9.423061 CAAGGGAAGAAAAACATAGGTATTTTG 57.577 33.333 5.55 0.00 0.00 2.44
3012 4158 8.134202 AGGGAAGAAAAACATAGGTATTTTGG 57.866 34.615 5.55 0.00 0.00 3.28
3013 4159 7.953493 AGGGAAGAAAAACATAGGTATTTTGGA 59.047 33.333 5.55 0.00 0.00 3.53
3014 4160 8.251026 GGGAAGAAAAACATAGGTATTTTGGAG 58.749 37.037 5.55 0.00 0.00 3.86
3015 4161 7.759886 GGAAGAAAAACATAGGTATTTTGGAGC 59.240 37.037 5.55 0.00 0.00 4.70
3016 4162 7.775053 AGAAAAACATAGGTATTTTGGAGCA 57.225 32.000 5.55 0.00 0.00 4.26
3017 4163 8.366359 AGAAAAACATAGGTATTTTGGAGCAT 57.634 30.769 5.55 0.00 0.00 3.79
3018 4164 9.474313 AGAAAAACATAGGTATTTTGGAGCATA 57.526 29.630 5.55 0.00 0.00 3.14
3028 4174 9.780186 AGGTATTTTGGAGCATATAGTTTCTAC 57.220 33.333 0.00 0.00 0.00 2.59
3029 4175 9.555727 GGTATTTTGGAGCATATAGTTTCTACA 57.444 33.333 0.00 0.00 0.00 2.74
3060 4206 9.720769 ATAATTTTCTGGTACCAATATCCTACG 57.279 33.333 17.11 0.52 0.00 3.51
3061 4207 6.549433 TTTTCTGGTACCAATATCCTACGT 57.451 37.500 17.11 0.00 0.00 3.57
3062 4208 6.549433 TTTCTGGTACCAATATCCTACGTT 57.451 37.500 17.11 0.00 0.00 3.99
3063 4209 5.779529 TCTGGTACCAATATCCTACGTTC 57.220 43.478 17.11 0.00 0.00 3.95
3064 4210 4.586001 TCTGGTACCAATATCCTACGTTCC 59.414 45.833 17.11 0.00 0.00 3.62
3065 4211 4.549668 TGGTACCAATATCCTACGTTCCT 58.450 43.478 13.60 0.00 0.00 3.36
3066 4212 4.964262 TGGTACCAATATCCTACGTTCCTT 59.036 41.667 13.60 0.00 0.00 3.36
3067 4213 5.426185 TGGTACCAATATCCTACGTTCCTTT 59.574 40.000 13.60 0.00 0.00 3.11
3068 4214 5.756833 GGTACCAATATCCTACGTTCCTTTG 59.243 44.000 7.15 0.00 0.00 2.77
3069 4215 4.777463 ACCAATATCCTACGTTCCTTTGG 58.223 43.478 0.00 3.26 38.61 3.28
3070 4216 4.472108 ACCAATATCCTACGTTCCTTTGGA 59.528 41.667 16.52 6.98 36.67 3.53
3071 4217 5.045432 ACCAATATCCTACGTTCCTTTGGAA 60.045 40.000 16.52 0.00 39.66 3.53
3072 4218 6.062095 CCAATATCCTACGTTCCTTTGGAAT 58.938 40.000 0.00 0.00 44.04 3.01
3073 4219 6.546034 CCAATATCCTACGTTCCTTTGGAATT 59.454 38.462 0.00 0.00 44.04 2.17
3074 4220 7.068226 CCAATATCCTACGTTCCTTTGGAATTT 59.932 37.037 0.00 0.00 44.04 1.82
3075 4221 7.803279 ATATCCTACGTTCCTTTGGAATTTC 57.197 36.000 0.00 0.00 44.04 2.17
3076 4222 5.237236 TCCTACGTTCCTTTGGAATTTCT 57.763 39.130 0.00 0.00 44.04 2.52
3077 4223 6.363167 TCCTACGTTCCTTTGGAATTTCTA 57.637 37.500 0.00 0.00 44.04 2.10
3078 4224 6.954232 TCCTACGTTCCTTTGGAATTTCTAT 58.046 36.000 0.00 0.00 44.04 1.98
3079 4225 8.081517 TCCTACGTTCCTTTGGAATTTCTATA 57.918 34.615 0.00 0.00 44.04 1.31
3080 4226 8.711170 TCCTACGTTCCTTTGGAATTTCTATAT 58.289 33.333 0.00 0.00 44.04 0.86
3081 4227 9.991906 CCTACGTTCCTTTGGAATTTCTATATA 57.008 33.333 0.00 0.00 44.04 0.86
3106 4252 7.578310 ATCCACTCATTTCACTTGGATTATG 57.422 36.000 0.00 0.00 43.23 1.90
3107 4253 5.887598 TCCACTCATTTCACTTGGATTATGG 59.112 40.000 0.00 0.00 31.19 2.74
3108 4254 5.887598 CCACTCATTTCACTTGGATTATGGA 59.112 40.000 0.00 0.00 0.00 3.41
3109 4255 6.039047 CCACTCATTTCACTTGGATTATGGAG 59.961 42.308 0.00 0.00 0.00 3.86
3110 4256 6.039047 CACTCATTTCACTTGGATTATGGAGG 59.961 42.308 0.00 0.00 0.00 4.30
3111 4257 6.069440 ACTCATTTCACTTGGATTATGGAGGA 60.069 38.462 0.00 0.00 0.00 3.71
3112 4258 6.730447 TCATTTCACTTGGATTATGGAGGAA 58.270 36.000 0.00 0.00 0.00 3.36
3113 4259 6.830324 TCATTTCACTTGGATTATGGAGGAAG 59.170 38.462 0.00 0.00 0.00 3.46
3114 4260 4.778213 TCACTTGGATTATGGAGGAAGG 57.222 45.455 0.00 0.00 0.00 3.46
3115 4261 4.370776 TCACTTGGATTATGGAGGAAGGA 58.629 43.478 0.00 0.00 0.00 3.36
3116 4262 4.788075 TCACTTGGATTATGGAGGAAGGAA 59.212 41.667 0.00 0.00 0.00 3.36
3117 4263 5.252863 TCACTTGGATTATGGAGGAAGGAAA 59.747 40.000 0.00 0.00 0.00 3.13
3118 4264 5.951747 CACTTGGATTATGGAGGAAGGAAAA 59.048 40.000 0.00 0.00 0.00 2.29
3119 4265 5.952347 ACTTGGATTATGGAGGAAGGAAAAC 59.048 40.000 0.00 0.00 0.00 2.43
3120 4266 5.528600 TGGATTATGGAGGAAGGAAAACA 57.471 39.130 0.00 0.00 0.00 2.83
3121 4267 6.091076 TGGATTATGGAGGAAGGAAAACAT 57.909 37.500 0.00 0.00 0.00 2.71
3122 4268 5.893255 TGGATTATGGAGGAAGGAAAACATG 59.107 40.000 0.00 0.00 0.00 3.21
3123 4269 6.129179 GGATTATGGAGGAAGGAAAACATGA 58.871 40.000 0.00 0.00 0.00 3.07
3124 4270 6.264067 GGATTATGGAGGAAGGAAAACATGAG 59.736 42.308 0.00 0.00 0.00 2.90
3125 4271 3.439857 TGGAGGAAGGAAAACATGAGG 57.560 47.619 0.00 0.00 0.00 3.86
3126 4272 2.716424 TGGAGGAAGGAAAACATGAGGT 59.284 45.455 0.00 0.00 0.00 3.85
3127 4273 3.244911 TGGAGGAAGGAAAACATGAGGTC 60.245 47.826 0.00 0.00 0.00 3.85
3128 4274 3.009584 GGAGGAAGGAAAACATGAGGTCT 59.990 47.826 0.00 0.00 0.00 3.85
3129 4275 4.006319 GAGGAAGGAAAACATGAGGTCTG 58.994 47.826 0.00 0.00 0.00 3.51
3130 4276 3.652869 AGGAAGGAAAACATGAGGTCTGA 59.347 43.478 0.00 0.00 0.00 3.27
3131 4277 3.753797 GGAAGGAAAACATGAGGTCTGAC 59.246 47.826 0.00 0.00 0.00 3.51
3132 4278 3.425162 AGGAAAACATGAGGTCTGACC 57.575 47.619 19.20 19.20 38.99 4.02
3145 4291 4.846168 GGTCTGACCTTATTCCCTCTTT 57.154 45.455 19.53 0.00 34.73 2.52
3146 4292 5.180810 GGTCTGACCTTATTCCCTCTTTT 57.819 43.478 19.53 0.00 34.73 2.27
3147 4293 5.186942 GGTCTGACCTTATTCCCTCTTTTC 58.813 45.833 19.53 0.00 34.73 2.29
3148 4294 4.870991 GTCTGACCTTATTCCCTCTTTTCG 59.129 45.833 0.00 0.00 0.00 3.46
3149 4295 4.775780 TCTGACCTTATTCCCTCTTTTCGA 59.224 41.667 0.00 0.00 0.00 3.71
3150 4296 5.247564 TCTGACCTTATTCCCTCTTTTCGAA 59.752 40.000 0.00 0.00 0.00 3.71
3151 4297 5.871834 TGACCTTATTCCCTCTTTTCGAAA 58.128 37.500 6.47 6.47 0.00 3.46
3152 4298 6.481643 TGACCTTATTCCCTCTTTTCGAAAT 58.518 36.000 12.12 0.00 0.00 2.17
3153 4299 6.946009 TGACCTTATTCCCTCTTTTCGAAATT 59.054 34.615 12.12 0.00 0.00 1.82
3154 4300 8.104566 TGACCTTATTCCCTCTTTTCGAAATTA 58.895 33.333 12.12 2.00 0.00 1.40
3155 4301 8.873186 ACCTTATTCCCTCTTTTCGAAATTAA 57.127 30.769 12.12 0.00 0.00 1.40
3156 4302 9.304335 ACCTTATTCCCTCTTTTCGAAATTAAA 57.696 29.630 12.12 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 64 2.910688 TGACGATTCTAAGGGATGCC 57.089 50.000 0.00 0.00 0.00 4.40
154 161 4.708421 GGACACTTACCTACTACCACATGA 59.292 45.833 0.00 0.00 0.00 3.07
254 273 6.350949 GGGTTACGGTCCAAGTACTAATGTAA 60.351 42.308 0.00 0.00 0.00 2.41
266 285 0.397564 GGAACTGGGTTACGGTCCAA 59.602 55.000 0.00 0.00 37.84 3.53
348 368 3.746751 GCTCCATACAATGTCTCCTGCAT 60.747 47.826 0.00 0.00 0.00 3.96
384 404 2.513435 GCTAGCTGCCCTCTGTGC 60.513 66.667 7.70 0.00 35.15 4.57
519 539 7.668525 ATGTATGTAGACATGATCAATGCAG 57.331 36.000 0.00 0.00 40.22 4.41
531 551 7.508977 TCCACCTGATCATAATGTATGTAGACA 59.491 37.037 0.00 0.00 37.45 3.41
566 586 3.991051 CGCCCTCACTGACGGTGT 61.991 66.667 14.06 0.00 45.50 4.16
633 669 3.353600 CATGCCGTGCAAGTCCAA 58.646 55.556 2.68 0.00 43.62 3.53
699 741 0.928451 GCGGTGCAACGTGAGAAAAC 60.928 55.000 27.13 1.63 38.12 2.43
715 757 0.175302 TAGCAAAAATGCCCATGCGG 59.825 50.000 0.00 0.00 43.39 5.69
743 786 7.343357 TCCCTGTTTCTTCTGTTCTTCTTTTA 58.657 34.615 0.00 0.00 0.00 1.52
752 795 4.610333 ACCTTTTCCCTGTTTCTTCTGTT 58.390 39.130 0.00 0.00 0.00 3.16
753 796 4.207955 GACCTTTTCCCTGTTTCTTCTGT 58.792 43.478 0.00 0.00 0.00 3.41
754 797 4.036852 GTGACCTTTTCCCTGTTTCTTCTG 59.963 45.833 0.00 0.00 0.00 3.02
755 798 4.207955 GTGACCTTTTCCCTGTTTCTTCT 58.792 43.478 0.00 0.00 0.00 2.85
756 799 3.951680 TGTGACCTTTTCCCTGTTTCTTC 59.048 43.478 0.00 0.00 0.00 2.87
757 800 3.976015 TGTGACCTTTTCCCTGTTTCTT 58.024 40.909 0.00 0.00 0.00 2.52
758 801 3.662759 TGTGACCTTTTCCCTGTTTCT 57.337 42.857 0.00 0.00 0.00 2.52
759 802 3.888930 TGATGTGACCTTTTCCCTGTTTC 59.111 43.478 0.00 0.00 0.00 2.78
760 803 3.636764 GTGATGTGACCTTTTCCCTGTTT 59.363 43.478 0.00 0.00 0.00 2.83
761 804 3.222603 GTGATGTGACCTTTTCCCTGTT 58.777 45.455 0.00 0.00 0.00 3.16
762 805 2.810400 CGTGATGTGACCTTTTCCCTGT 60.810 50.000 0.00 0.00 0.00 4.00
763 806 1.806542 CGTGATGTGACCTTTTCCCTG 59.193 52.381 0.00 0.00 0.00 4.45
764 807 1.697432 TCGTGATGTGACCTTTTCCCT 59.303 47.619 0.00 0.00 0.00 4.20
765 808 2.076863 CTCGTGATGTGACCTTTTCCC 58.923 52.381 0.00 0.00 0.00 3.97
766 809 3.040147 TCTCGTGATGTGACCTTTTCC 57.960 47.619 0.00 0.00 0.00 3.13
767 810 3.372206 CCATCTCGTGATGTGACCTTTTC 59.628 47.826 22.15 0.00 46.38 2.29
768 811 3.338249 CCATCTCGTGATGTGACCTTTT 58.662 45.455 22.15 0.00 46.38 2.27
769 812 2.355108 CCCATCTCGTGATGTGACCTTT 60.355 50.000 22.15 0.00 46.38 3.11
770 813 1.208052 CCCATCTCGTGATGTGACCTT 59.792 52.381 22.15 0.00 46.38 3.50
771 814 0.826715 CCCATCTCGTGATGTGACCT 59.173 55.000 22.15 0.00 46.38 3.85
772 815 0.811616 GCCCATCTCGTGATGTGACC 60.812 60.000 22.15 7.23 46.38 4.02
773 816 0.811616 GGCCCATCTCGTGATGTGAC 60.812 60.000 22.15 12.53 46.38 3.67
774 817 0.977627 AGGCCCATCTCGTGATGTGA 60.978 55.000 22.15 0.00 46.38 3.58
775 818 0.531532 GAGGCCCATCTCGTGATGTG 60.532 60.000 22.15 14.50 46.38 3.21
801 844 9.121517 CCAACATGAAAATATATTTCAGATCGC 57.878 33.333 11.08 0.00 41.13 4.58
804 847 8.370182 GGCCCAACATGAAAATATATTTCAGAT 58.630 33.333 11.08 1.82 41.13 2.90
814 857 3.011144 TCAGGAGGCCCAACATGAAAATA 59.989 43.478 0.00 0.00 33.88 1.40
885 929 0.670854 GCTCGGGTGTTCTTCAGGTC 60.671 60.000 0.00 0.00 0.00 3.85
902 946 1.258445 CGTACCTGGTTGGAGAGGCT 61.258 60.000 3.84 0.00 39.71 4.58
991 1053 1.348036 GCCCATTTATAGAGCGGAGGT 59.652 52.381 0.00 0.00 46.54 3.85
1108 1175 3.917329 TTGAAACGAGAGAGTGTCGAT 57.083 42.857 0.00 0.00 39.92 3.59
1110 1179 4.230657 AGAATTGAAACGAGAGAGTGTCG 58.769 43.478 0.00 0.00 43.25 4.35
1147 1216 1.142465 CATTGCACCAGATAGGGAGCT 59.858 52.381 3.46 0.00 43.89 4.09
1148 1217 1.602311 CATTGCACCAGATAGGGAGC 58.398 55.000 0.00 0.00 43.89 4.70
1149 1218 1.816961 GCCATTGCACCAGATAGGGAG 60.817 57.143 0.00 0.00 43.89 4.30
1452 1529 7.491682 TGGAACAAATTTCTCTCTTTGAAAGG 58.508 34.615 4.94 0.00 34.18 3.11
1460 1537 5.684704 TCACACTGGAACAAATTTCTCTCT 58.315 37.500 0.00 0.00 38.70 3.10
1476 1553 1.672441 GGCTCTGCTTCTCTCACACTG 60.672 57.143 0.00 0.00 0.00 3.66
1483 1563 0.897863 ACGTCAGGCTCTGCTTCTCT 60.898 55.000 0.00 0.00 0.00 3.10
1524 1604 2.531483 ATCGGGTCCACTAGCCCTGT 62.531 60.000 2.14 0.00 43.31 4.00
1574 1654 2.994995 AGCCGGTCCATCGTGTCA 60.995 61.111 1.90 0.00 0.00 3.58
1983 2063 2.526432 ACGTACTCATCACTGGACCTT 58.474 47.619 0.00 0.00 0.00 3.50
2000 2080 1.131883 GGTACAGTCTCGCACATACGT 59.868 52.381 0.00 0.00 0.00 3.57
2004 2084 0.532573 CAGGGTACAGTCTCGCACAT 59.467 55.000 0.00 0.00 0.00 3.21
2024 2995 4.697352 GCTGAAATCTTAAAGCCTCAGACA 59.303 41.667 1.21 0.00 33.65 3.41
2025 2996 4.940654 AGCTGAAATCTTAAAGCCTCAGAC 59.059 41.667 1.21 0.00 36.28 3.51
2053 3024 0.248907 ACTCGCCGACGGTCATATTG 60.249 55.000 16.73 2.08 40.63 1.90
2056 3027 1.712018 CTCACTCGCCGACGGTCATA 61.712 60.000 16.73 0.00 40.63 2.15
2057 3028 3.052620 CTCACTCGCCGACGGTCAT 62.053 63.158 16.73 0.00 40.63 3.06
2058 3029 3.733960 CTCACTCGCCGACGGTCA 61.734 66.667 16.73 0.90 40.63 4.02
2059 3030 3.735029 ACTCACTCGCCGACGGTC 61.735 66.667 16.73 7.00 40.63 4.79
2060 3031 4.039357 CACTCACTCGCCGACGGT 62.039 66.667 16.73 0.00 40.63 4.83
2063 3034 2.479412 AAGAGCACTCACTCGCCGAC 62.479 60.000 0.00 0.00 41.77 4.79
2064 3035 1.806461 AAAGAGCACTCACTCGCCGA 61.806 55.000 0.00 0.00 41.77 5.54
2065 3036 1.373497 AAAGAGCACTCACTCGCCG 60.373 57.895 0.00 0.00 41.77 6.46
2066 3037 0.601311 ACAAAGAGCACTCACTCGCC 60.601 55.000 0.00 0.00 41.77 5.54
2074 3045 1.893801 ACTACGCCTACAAAGAGCACT 59.106 47.619 0.00 0.00 0.00 4.40
2140 3112 8.540492 CCAAGTACATTTACATAAAGCTCTACG 58.460 37.037 0.00 0.00 0.00 3.51
2143 3115 6.884295 TGCCAAGTACATTTACATAAAGCTCT 59.116 34.615 0.00 0.00 0.00 4.09
2145 3117 7.461182 TTGCCAAGTACATTTACATAAAGCT 57.539 32.000 0.00 0.00 0.00 3.74
2205 3178 6.164408 TGCAGTAATTAATCGAAGTGTGTG 57.836 37.500 0.00 0.00 0.00 3.82
2207 3180 6.019881 TCGATGCAGTAATTAATCGAAGTGTG 60.020 38.462 14.53 0.00 45.59 3.82
2227 3203 7.495934 ACAACAGGGAACTAATATTTCTCGATG 59.504 37.037 0.00 0.00 40.21 3.84
2235 3211 6.208599 CCACAACACAACAGGGAACTAATATT 59.791 38.462 0.00 0.00 40.21 1.28
2236 3212 5.710099 CCACAACACAACAGGGAACTAATAT 59.290 40.000 0.00 0.00 40.21 1.28
2237 3213 5.067273 CCACAACACAACAGGGAACTAATA 58.933 41.667 0.00 0.00 40.21 0.98
2259 3235 6.595326 TCTGAAAGAACACATCATATCACACC 59.405 38.462 0.00 0.00 42.31 4.16
2286 3265 2.168521 TCAGTTATCAGCTTCTTCCGGG 59.831 50.000 0.00 0.00 0.00 5.73
2287 3266 3.526931 TCAGTTATCAGCTTCTTCCGG 57.473 47.619 0.00 0.00 0.00 5.14
2319 3301 3.842436 TCATGAGGATGTGCTGCCTATAT 59.158 43.478 0.00 0.00 33.84 0.86
2337 3319 6.441274 ACAAACTGCACTCTACAAATTCATG 58.559 36.000 0.00 0.00 0.00 3.07
2349 3331 1.237285 ATGCCCGACAAACTGCACTC 61.237 55.000 0.00 0.00 36.41 3.51
2350 3332 0.036164 TATGCCCGACAAACTGCACT 59.964 50.000 0.00 0.00 36.41 4.40
2351 3333 0.878416 TTATGCCCGACAAACTGCAC 59.122 50.000 0.00 0.00 36.41 4.57
2352 3334 1.610363 TTTATGCCCGACAAACTGCA 58.390 45.000 0.00 0.00 38.23 4.41
2353 3335 2.715737 TTTTATGCCCGACAAACTGC 57.284 45.000 0.00 0.00 0.00 4.40
2354 3336 5.226396 TGAAATTTTATGCCCGACAAACTG 58.774 37.500 0.00 0.00 0.00 3.16
2355 3337 5.461032 TGAAATTTTATGCCCGACAAACT 57.539 34.783 0.00 0.00 0.00 2.66
2356 3338 5.923684 TCTTGAAATTTTATGCCCGACAAAC 59.076 36.000 0.00 0.00 0.00 2.93
2357 3339 6.090483 TCTTGAAATTTTATGCCCGACAAA 57.910 33.333 0.00 0.00 0.00 2.83
2360 3342 6.034898 CACATTCTTGAAATTTTATGCCCGAC 59.965 38.462 0.00 0.00 0.00 4.79
2361 3343 6.098679 CACATTCTTGAAATTTTATGCCCGA 58.901 36.000 0.00 0.00 0.00 5.14
2376 3359 6.106673 ACTCCTATCCGTTAACACATTCTTG 58.893 40.000 6.39 0.00 0.00 3.02
2394 3377 9.847224 AAAGTGAAGAAAAGAATTGTACTCCTA 57.153 29.630 0.00 0.00 0.00 2.94
2395 3378 8.753497 AAAGTGAAGAAAAGAATTGTACTCCT 57.247 30.769 0.00 0.00 0.00 3.69
2396 3379 9.237846 CAAAAGTGAAGAAAAGAATTGTACTCC 57.762 33.333 0.00 0.00 0.00 3.85
2397 3380 9.788960 ACAAAAGTGAAGAAAAGAATTGTACTC 57.211 29.630 0.00 0.00 0.00 2.59
2527 3644 1.077212 ATTGCTGCAGCTACAGGGG 60.077 57.895 36.61 0.00 42.66 4.79
2531 3648 0.321830 TGCTCATTGCTGCAGCTACA 60.322 50.000 36.61 21.28 43.37 2.74
2545 3662 4.206375 TGAAAACCAAGTTCATCTGCTCA 58.794 39.130 0.00 0.00 30.08 4.26
2554 3671 5.450550 CCAAGAACTCCTGAAAACCAAGTTC 60.451 44.000 5.62 5.62 40.44 3.01
2716 3862 2.019984 AGAATTCTTCTGCCGCAATCC 58.980 47.619 0.88 0.00 38.91 3.01
2726 3872 3.823304 GCAACCAAGGTCAGAATTCTTCT 59.177 43.478 4.86 1.12 41.70 2.85
2733 3879 0.823356 GCCAGCAACCAAGGTCAGAA 60.823 55.000 0.00 0.00 0.00 3.02
2813 3959 3.074412 AGTGCAAACATACTACACAGCC 58.926 45.455 0.00 0.00 33.69 4.85
2836 3982 2.027325 CAACAGCAGCAGCAGTCAA 58.973 52.632 3.17 0.00 45.49 3.18
2876 4022 1.043816 AGAGCTACTATGGTGCGCAT 58.956 50.000 15.91 0.00 0.00 4.73
2882 4028 1.763968 TGTCGCAGAGCTACTATGGT 58.236 50.000 0.00 0.00 36.95 3.55
2902 4048 6.044046 CCTTATGCTTAGAAAATTGCATGCA 58.956 36.000 18.46 18.46 44.52 3.96
2904 4050 9.585099 TTTACCTTATGCTTAGAAAATTGCATG 57.415 29.630 9.21 0.00 44.52 4.06
2912 4058 7.444792 TCACCGTTTTTACCTTATGCTTAGAAA 59.555 33.333 0.00 0.00 0.00 2.52
2913 4059 6.935771 TCACCGTTTTTACCTTATGCTTAGAA 59.064 34.615 0.00 0.00 0.00 2.10
2914 4060 6.465948 TCACCGTTTTTACCTTATGCTTAGA 58.534 36.000 0.00 0.00 0.00 2.10
2915 4061 6.674760 GCTCACCGTTTTTACCTTATGCTTAG 60.675 42.308 0.00 0.00 0.00 2.18
2916 4062 5.122711 GCTCACCGTTTTTACCTTATGCTTA 59.877 40.000 0.00 0.00 0.00 3.09
2917 4063 4.082949 GCTCACCGTTTTTACCTTATGCTT 60.083 41.667 0.00 0.00 0.00 3.91
2918 4064 3.439129 GCTCACCGTTTTTACCTTATGCT 59.561 43.478 0.00 0.00 0.00 3.79
2919 4065 3.726782 CGCTCACCGTTTTTACCTTATGC 60.727 47.826 0.00 0.00 0.00 3.14
2920 4066 3.998522 CGCTCACCGTTTTTACCTTATG 58.001 45.455 0.00 0.00 0.00 1.90
2956 4102 3.118738 ACGGGACTTTATGACCAGATGTC 60.119 47.826 0.00 0.00 44.72 3.06
2957 4103 2.838202 ACGGGACTTTATGACCAGATGT 59.162 45.455 0.00 0.00 32.09 3.06
2958 4104 3.543680 ACGGGACTTTATGACCAGATG 57.456 47.619 0.00 0.00 32.09 2.90
2959 4105 4.569719 AAACGGGACTTTATGACCAGAT 57.430 40.909 0.00 0.00 32.09 2.90
2960 4106 4.773674 TCTAAACGGGACTTTATGACCAGA 59.226 41.667 0.00 0.00 32.09 3.86
2961 4107 5.080969 TCTAAACGGGACTTTATGACCAG 57.919 43.478 0.00 0.00 32.09 4.00
2962 4108 5.221682 TGTTCTAAACGGGACTTTATGACCA 60.222 40.000 0.00 0.00 32.09 4.02
2963 4109 5.240121 TGTTCTAAACGGGACTTTATGACC 58.760 41.667 0.00 0.00 0.00 4.02
2964 4110 6.128363 CCTTGTTCTAAACGGGACTTTATGAC 60.128 42.308 0.00 0.00 0.00 3.06
2965 4111 5.935789 CCTTGTTCTAAACGGGACTTTATGA 59.064 40.000 0.00 0.00 0.00 2.15
2966 4112 5.123344 CCCTTGTTCTAAACGGGACTTTATG 59.877 44.000 0.00 0.00 37.05 1.90
2967 4113 5.013391 TCCCTTGTTCTAAACGGGACTTTAT 59.987 40.000 0.00 0.00 38.95 1.40
2968 4114 4.347583 TCCCTTGTTCTAAACGGGACTTTA 59.652 41.667 0.00 0.00 38.95 1.85
2969 4115 3.136992 TCCCTTGTTCTAAACGGGACTTT 59.863 43.478 0.00 0.00 38.95 2.66
2970 4116 2.707257 TCCCTTGTTCTAAACGGGACTT 59.293 45.455 0.00 0.00 38.95 3.01
2971 4117 2.332117 TCCCTTGTTCTAAACGGGACT 58.668 47.619 0.00 0.00 38.95 3.85
2972 4118 2.845363 TCCCTTGTTCTAAACGGGAC 57.155 50.000 0.00 0.00 38.95 4.46
2973 4119 2.974099 TCTTCCCTTGTTCTAAACGGGA 59.026 45.455 0.00 0.00 41.99 5.14
2974 4120 3.412237 TCTTCCCTTGTTCTAAACGGG 57.588 47.619 0.00 0.00 36.21 5.28
2975 4121 5.761165 TTTTCTTCCCTTGTTCTAAACGG 57.239 39.130 0.00 0.00 0.00 4.44
2976 4122 6.557110 TGTTTTTCTTCCCTTGTTCTAAACG 58.443 36.000 0.00 0.00 0.00 3.60
2977 4123 9.678941 CTATGTTTTTCTTCCCTTGTTCTAAAC 57.321 33.333 0.00 0.00 0.00 2.01
2978 4124 8.856103 CCTATGTTTTTCTTCCCTTGTTCTAAA 58.144 33.333 0.00 0.00 0.00 1.85
2979 4125 8.002459 ACCTATGTTTTTCTTCCCTTGTTCTAA 58.998 33.333 0.00 0.00 0.00 2.10
2980 4126 7.523415 ACCTATGTTTTTCTTCCCTTGTTCTA 58.477 34.615 0.00 0.00 0.00 2.10
2981 4127 6.373759 ACCTATGTTTTTCTTCCCTTGTTCT 58.626 36.000 0.00 0.00 0.00 3.01
2982 4128 6.650427 ACCTATGTTTTTCTTCCCTTGTTC 57.350 37.500 0.00 0.00 0.00 3.18
2983 4129 8.721133 AATACCTATGTTTTTCTTCCCTTGTT 57.279 30.769 0.00 0.00 0.00 2.83
2984 4130 8.721133 AAATACCTATGTTTTTCTTCCCTTGT 57.279 30.769 0.00 0.00 0.00 3.16
2985 4131 9.423061 CAAAATACCTATGTTTTTCTTCCCTTG 57.577 33.333 0.00 0.00 27.53 3.61
2986 4132 8.593679 CCAAAATACCTATGTTTTTCTTCCCTT 58.406 33.333 0.00 0.00 27.53 3.95
2987 4133 7.953493 TCCAAAATACCTATGTTTTTCTTCCCT 59.047 33.333 0.00 0.00 27.53 4.20
2988 4134 8.129496 TCCAAAATACCTATGTTTTTCTTCCC 57.871 34.615 0.00 0.00 27.53 3.97
2989 4135 7.759886 GCTCCAAAATACCTATGTTTTTCTTCC 59.240 37.037 0.00 0.00 27.53 3.46
2990 4136 8.303876 TGCTCCAAAATACCTATGTTTTTCTTC 58.696 33.333 0.00 0.00 27.53 2.87
2991 4137 8.189119 TGCTCCAAAATACCTATGTTTTTCTT 57.811 30.769 0.00 0.00 27.53 2.52
2992 4138 7.775053 TGCTCCAAAATACCTATGTTTTTCT 57.225 32.000 0.00 0.00 27.53 2.52
3002 4148 9.780186 GTAGAAACTATATGCTCCAAAATACCT 57.220 33.333 0.00 0.00 0.00 3.08
3003 4149 9.555727 TGTAGAAACTATATGCTCCAAAATACC 57.444 33.333 0.00 0.00 0.00 2.73
3034 4180 9.720769 CGTAGGATATTGGTACCAGAAAATTAT 57.279 33.333 15.65 6.46 0.00 1.28
3035 4181 8.707449 ACGTAGGATATTGGTACCAGAAAATTA 58.293 33.333 15.65 0.00 0.00 1.40
3036 4182 7.571025 ACGTAGGATATTGGTACCAGAAAATT 58.429 34.615 15.65 4.14 0.00 1.82
3037 4183 7.133133 ACGTAGGATATTGGTACCAGAAAAT 57.867 36.000 15.65 8.37 0.00 1.82
3038 4184 6.549433 ACGTAGGATATTGGTACCAGAAAA 57.451 37.500 15.65 0.00 0.00 2.29
3039 4185 6.407299 GGAACGTAGGATATTGGTACCAGAAA 60.407 42.308 15.65 0.01 0.00 2.52
3040 4186 5.069516 GGAACGTAGGATATTGGTACCAGAA 59.930 44.000 15.65 7.73 0.00 3.02
3041 4187 4.586001 GGAACGTAGGATATTGGTACCAGA 59.414 45.833 15.65 7.90 0.00 3.86
3042 4188 4.587684 AGGAACGTAGGATATTGGTACCAG 59.412 45.833 15.65 2.44 0.00 4.00
3043 4189 4.549668 AGGAACGTAGGATATTGGTACCA 58.450 43.478 11.60 11.60 0.00 3.25
3044 4190 5.541953 AAGGAACGTAGGATATTGGTACC 57.458 43.478 4.43 4.43 0.00 3.34
3045 4191 5.756833 CCAAAGGAACGTAGGATATTGGTAC 59.243 44.000 0.00 0.00 33.18 3.34
3046 4192 5.662208 TCCAAAGGAACGTAGGATATTGGTA 59.338 40.000 13.80 3.47 37.80 3.25
3047 4193 4.472108 TCCAAAGGAACGTAGGATATTGGT 59.528 41.667 13.80 0.00 37.80 3.67
3048 4194 5.031066 TCCAAAGGAACGTAGGATATTGG 57.969 43.478 9.99 9.99 37.90 3.16
3049 4195 7.568199 AATTCCAAAGGAACGTAGGATATTG 57.432 36.000 0.00 0.00 45.07 1.90
3050 4196 8.053355 AGAAATTCCAAAGGAACGTAGGATATT 58.947 33.333 0.00 0.00 45.07 1.28
3051 4197 7.574607 AGAAATTCCAAAGGAACGTAGGATAT 58.425 34.615 0.00 0.00 45.07 1.63
3052 4198 6.954232 AGAAATTCCAAAGGAACGTAGGATA 58.046 36.000 0.00 0.00 45.07 2.59
3053 4199 5.816682 AGAAATTCCAAAGGAACGTAGGAT 58.183 37.500 0.00 0.00 45.07 3.24
3054 4200 5.237236 AGAAATTCCAAAGGAACGTAGGA 57.763 39.130 0.00 0.00 45.07 2.94
3055 4201 8.904099 ATATAGAAATTCCAAAGGAACGTAGG 57.096 34.615 0.00 0.00 45.07 3.18
3083 4229 5.887598 CCATAATCCAAGTGAAATGAGTGGA 59.112 40.000 0.00 0.00 42.38 4.02
3084 4230 5.887598 TCCATAATCCAAGTGAAATGAGTGG 59.112 40.000 0.00 0.00 0.00 4.00
3085 4231 6.039047 CCTCCATAATCCAAGTGAAATGAGTG 59.961 42.308 0.00 0.00 0.00 3.51
3086 4232 6.069440 TCCTCCATAATCCAAGTGAAATGAGT 60.069 38.462 0.00 0.00 0.00 3.41
3087 4233 6.359804 TCCTCCATAATCCAAGTGAAATGAG 58.640 40.000 0.00 0.00 0.00 2.90
3088 4234 6.325993 TCCTCCATAATCCAAGTGAAATGA 57.674 37.500 0.00 0.00 0.00 2.57
3089 4235 6.040166 CCTTCCTCCATAATCCAAGTGAAATG 59.960 42.308 0.00 0.00 0.00 2.32
3090 4236 6.068853 TCCTTCCTCCATAATCCAAGTGAAAT 60.069 38.462 0.00 0.00 0.00 2.17
3091 4237 5.252863 TCCTTCCTCCATAATCCAAGTGAAA 59.747 40.000 0.00 0.00 0.00 2.69
3092 4238 4.788075 TCCTTCCTCCATAATCCAAGTGAA 59.212 41.667 0.00 0.00 0.00 3.18
3093 4239 4.370776 TCCTTCCTCCATAATCCAAGTGA 58.629 43.478 0.00 0.00 0.00 3.41
3094 4240 4.778213 TCCTTCCTCCATAATCCAAGTG 57.222 45.455 0.00 0.00 0.00 3.16
3095 4241 5.796502 TTTCCTTCCTCCATAATCCAAGT 57.203 39.130 0.00 0.00 0.00 3.16
3096 4242 5.951747 TGTTTTCCTTCCTCCATAATCCAAG 59.048 40.000 0.00 0.00 0.00 3.61
3097 4243 5.898120 TGTTTTCCTTCCTCCATAATCCAA 58.102 37.500 0.00 0.00 0.00 3.53
3098 4244 5.528600 TGTTTTCCTTCCTCCATAATCCA 57.471 39.130 0.00 0.00 0.00 3.41
3099 4245 6.129179 TCATGTTTTCCTTCCTCCATAATCC 58.871 40.000 0.00 0.00 0.00 3.01
3100 4246 6.264067 CCTCATGTTTTCCTTCCTCCATAATC 59.736 42.308 0.00 0.00 0.00 1.75
3101 4247 6.131961 CCTCATGTTTTCCTTCCTCCATAAT 58.868 40.000 0.00 0.00 0.00 1.28
3102 4248 5.015178 ACCTCATGTTTTCCTTCCTCCATAA 59.985 40.000 0.00 0.00 0.00 1.90
3103 4249 4.540099 ACCTCATGTTTTCCTTCCTCCATA 59.460 41.667 0.00 0.00 0.00 2.74
3104 4250 3.334881 ACCTCATGTTTTCCTTCCTCCAT 59.665 43.478 0.00 0.00 0.00 3.41
3105 4251 2.716424 ACCTCATGTTTTCCTTCCTCCA 59.284 45.455 0.00 0.00 0.00 3.86
3106 4252 3.009584 AGACCTCATGTTTTCCTTCCTCC 59.990 47.826 0.00 0.00 0.00 4.30
3107 4253 4.006319 CAGACCTCATGTTTTCCTTCCTC 58.994 47.826 0.00 0.00 0.00 3.71
3108 4254 3.652869 TCAGACCTCATGTTTTCCTTCCT 59.347 43.478 0.00 0.00 0.00 3.36
3109 4255 3.753797 GTCAGACCTCATGTTTTCCTTCC 59.246 47.826 0.00 0.00 0.00 3.46
3110 4256 3.753797 GGTCAGACCTCATGTTTTCCTTC 59.246 47.826 12.94 0.00 34.73 3.46
3111 4257 3.756117 GGTCAGACCTCATGTTTTCCTT 58.244 45.455 12.94 0.00 34.73 3.36
3112 4258 3.425162 GGTCAGACCTCATGTTTTCCT 57.575 47.619 12.94 0.00 34.73 3.36
3124 4270 4.846168 AAAGAGGGAATAAGGTCAGACC 57.154 45.455 12.25 12.25 38.99 3.85
3125 4271 4.870991 CGAAAAGAGGGAATAAGGTCAGAC 59.129 45.833 0.00 0.00 0.00 3.51
3126 4272 4.775780 TCGAAAAGAGGGAATAAGGTCAGA 59.224 41.667 0.00 0.00 0.00 3.27
3127 4273 5.086104 TCGAAAAGAGGGAATAAGGTCAG 57.914 43.478 0.00 0.00 0.00 3.51
3128 4274 5.492855 TTCGAAAAGAGGGAATAAGGTCA 57.507 39.130 0.00 0.00 0.00 4.02
3129 4275 7.392494 AATTTCGAAAAGAGGGAATAAGGTC 57.608 36.000 15.66 0.00 0.00 3.85
3130 4276 8.873186 TTAATTTCGAAAAGAGGGAATAAGGT 57.127 30.769 15.66 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.