Multiple sequence alignment - TraesCS4A01G052400

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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 TraesCS4A01G052400 chr4A 100.000 4799 0 0 1 4799 43361765 43366563 0.000000e+00 8863.0
1 TraesCS4A01G052400 chr4A 85.322 729 78 19 88 813 335732580 335731878 0.000000e+00 726.0
2 TraesCS4A01G052400 chr4A 91.429 105 9 0 709 813 43355257 43355153 1.390000e-30 145.0
3 TraesCS4A01G052400 chr4A 89.394 66 6 1 4468 4533 428145786 428145722 1.110000e-11 82.4
4 TraesCS4A01G052400 chr4A 84.615 65 9 1 4469 4533 615883560 615883497 4.010000e-06 63.9
5 TraesCS4A01G052400 chr4A 84.615 65 9 1 4469 4533 615890294 615890231 4.010000e-06 63.9
6 TraesCS4A01G052400 chr4A 84.615 65 9 1 4469 4533 615892984 615892921 4.010000e-06 63.9
7 TraesCS4A01G052400 chr4A 84.615 65 9 1 4469 4533 615895677 615895614 4.010000e-06 63.9
8 TraesCS4A01G052400 chr4D 91.768 3134 149 35 906 3987 420139319 420142395 0.000000e+00 4257.0
9 TraesCS4A01G052400 chr4D 88.859 736 59 12 79 813 15059518 15060231 0.000000e+00 883.0
10 TraesCS4A01G052400 chr4D 98.925 93 1 0 5 97 169112455 169112547 2.970000e-37 167.0
11 TraesCS4A01G052400 chr4D 88.636 88 8 2 4389 4476 420143037 420143122 6.570000e-19 106.0
12 TraesCS4A01G052400 chr4D 95.238 42 2 0 533 574 15059990 15060031 3.100000e-07 67.6
13 TraesCS4A01G052400 chr4B 90.827 1886 96 24 865 2714 517965674 517963830 0.000000e+00 2453.0
14 TraesCS4A01G052400 chr4B 93.619 909 44 7 2842 3742 517960637 517959735 0.000000e+00 1345.0
15 TraesCS4A01G052400 chr4B 87.371 483 32 13 4049 4523 517959549 517959088 1.180000e-145 527.0
16 TraesCS4A01G052400 chr4B 94.709 189 5 1 4611 4799 517957462 517957279 6.080000e-74 289.0
17 TraesCS4A01G052400 chr4B 95.808 167 7 0 3774 3940 517959736 517959570 2.200000e-68 270.0
18 TraesCS4A01G052400 chr4B 94.891 137 7 0 2712 2848 517963664 517963528 1.050000e-51 215.0
19 TraesCS4A01G052400 chr4B 93.750 96 5 1 4532 4626 517958947 517958852 5.010000e-30 143.0
20 TraesCS4A01G052400 chr7A 95.868 726 29 1 88 813 538241587 538240863 0.000000e+00 1173.0
21 TraesCS4A01G052400 chr7A 90.260 154 14 1 2580 2732 201987155 201987002 2.930000e-47 200.0
22 TraesCS4A01G052400 chr7A 88.889 153 17 0 2577 2729 206959856 206960008 6.340000e-44 189.0
23 TraesCS4A01G052400 chr7A 95.960 99 2 2 1 98 437690351 437690254 4.970000e-35 159.0
24 TraesCS4A01G052400 chr7A 92.381 105 8 0 709 813 538244066 538244170 2.990000e-32 150.0
25 TraesCS4A01G052400 chr1D 89.669 726 54 11 88 813 458344356 458343652 0.000000e+00 905.0
26 TraesCS4A01G052400 chr1D 92.727 55 4 0 4479 4533 335585993 335586047 3.980000e-11 80.5
27 TraesCS4A01G052400 chr1D 97.297 37 1 0 537 573 458343888 458343852 4.010000e-06 63.9
28 TraesCS4A01G052400 chr6D 88.995 736 59 11 79 813 384360055 384360769 0.000000e+00 891.0
29 TraesCS4A01G052400 chr6D 95.238 42 2 0 533 574 384360528 384360569 3.100000e-07 67.6
30 TraesCS4A01G052400 chr5A 90.446 157 14 1 2580 2735 86662171 86662015 6.300000e-49 206.0
31 TraesCS4A01G052400 chr5A 88.050 159 18 1 2579 2736 283308704 283308546 2.280000e-43 187.0
32 TraesCS4A01G052400 chr5A 96.875 96 3 0 1 96 626054202 626054297 1.380000e-35 161.0
33 TraesCS4A01G052400 chr5D 88.535 157 18 0 659 815 33446603 33446447 1.760000e-44 191.0
34 TraesCS4A01G052400 chr5D 93.478 46 3 0 4473 4518 485057864 485057909 8.620000e-08 69.4
35 TraesCS4A01G052400 chr7D 88.889 153 17 0 2577 2729 197927005 197927157 6.340000e-44 189.0
36 TraesCS4A01G052400 chr7D 88.961 154 16 1 2580 2732 436961795 436961948 6.340000e-44 189.0
37 TraesCS4A01G052400 chr7B 88.961 154 16 1 2580 2732 453623290 453623443 6.340000e-44 189.0
38 TraesCS4A01G052400 chr7B 89.474 57 6 0 4477 4533 734291097 734291041 6.660000e-09 73.1
39 TraesCS4A01G052400 chr2D 88.961 154 16 1 2580 2732 88290055 88290208 6.340000e-44 189.0
40 TraesCS4A01G052400 chr3D 87.097 155 19 1 659 813 16639158 16639311 1.780000e-39 174.0
41 TraesCS4A01G052400 chr6A 97.872 94 2 0 5 98 4965619 4965526 3.840000e-36 163.0
42 TraesCS4A01G052400 chr6A 96.000 100 2 2 1 100 612083818 612083915 1.380000e-35 161.0
43 TraesCS4A01G052400 chr3A 98.901 91 1 0 1 91 647720502 647720412 3.840000e-36 163.0
44 TraesCS4A01G052400 chr3A 97.849 93 2 0 1 93 691549851 691549759 1.380000e-35 161.0
45 TraesCS4A01G052400 chr2A 94.231 104 4 2 1 103 642218165 642218267 1.790000e-34 158.0
46 TraesCS4A01G052400 chr1A 97.802 91 2 0 1 91 297761500 297761590 1.790000e-34 158.0
47 TraesCS4A01G052400 chr1A 90.909 55 5 0 4479 4533 386427668 386427614 1.850000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G052400 chr4A 43361765 43366563 4798 False 8863.000000 8863 100.000000 1 4799 1 chr4A.!!$F1 4798
1 TraesCS4A01G052400 chr4A 335731878 335732580 702 True 726.000000 726 85.322000 88 813 1 chr4A.!!$R2 725
2 TraesCS4A01G052400 chr4D 420139319 420143122 3803 False 2181.500000 4257 90.202000 906 4476 2 chr4D.!!$F3 3570
3 TraesCS4A01G052400 chr4D 15059518 15060231 713 False 475.300000 883 92.048500 79 813 2 chr4D.!!$F2 734
4 TraesCS4A01G052400 chr4B 517957279 517965674 8395 True 748.857143 2453 92.996429 865 4799 7 chr4B.!!$R1 3934
5 TraesCS4A01G052400 chr7A 538240863 538241587 724 True 1173.000000 1173 95.868000 88 813 1 chr7A.!!$R3 725
6 TraesCS4A01G052400 chr1D 458343652 458344356 704 True 484.450000 905 93.483000 88 813 2 chr1D.!!$R1 725
7 TraesCS4A01G052400 chr6D 384360055 384360769 714 False 479.300000 891 92.116500 79 813 2 chr6D.!!$F1 734

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
592 593 0.036294 GGCGAACCCTAGCTCTGTTT 60.036 55.0 0.00 0.0 0.00 2.83 F
848 849 0.104671 CCCACCAAACAAACAGCCAG 59.895 55.0 0.00 0.0 0.00 4.85 F
2122 2185 0.179073 CGATTTGGATCTGGCTCCGT 60.179 55.0 0.00 0.0 38.21 4.69 F
2391 2456 0.114168 ATGGGGTTAGCAAGCACCAA 59.886 50.0 4.27 0.0 34.50 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1972 0.031178 GCCACAAAGCAACCACTGAG 59.969 55.0 0.00 0.0 0.00 3.35 R
2317 2382 1.048601 GACCTCAACAGACCCAGTGA 58.951 55.0 0.00 0.0 0.00 3.41 R
3023 6163 0.455005 GGGAATTCAGAAGCAGCAGC 59.545 55.0 7.93 0.0 42.56 5.25 R
3958 7106 0.466739 GAACCAAGGGACCGGTGTTT 60.467 55.0 14.63 0.0 34.62 2.83 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
19 20 1.028905 GATCACACTCTCCCCTCTCG 58.971 60.000 0.00 0.00 0.00 4.04
20 21 0.333312 ATCACACTCTCCCCTCTCGT 59.667 55.000 0.00 0.00 0.00 4.18
21 22 0.112606 TCACACTCTCCCCTCTCGTT 59.887 55.000 0.00 0.00 0.00 3.85
22 23 0.244994 CACACTCTCCCCTCTCGTTG 59.755 60.000 0.00 0.00 0.00 4.10
23 24 1.216710 CACTCTCCCCTCTCGTTGC 59.783 63.158 0.00 0.00 0.00 4.17
24 25 1.077625 ACTCTCCCCTCTCGTTGCT 59.922 57.895 0.00 0.00 0.00 3.91
25 26 0.331954 ACTCTCCCCTCTCGTTGCTA 59.668 55.000 0.00 0.00 0.00 3.49
26 27 1.063567 ACTCTCCCCTCTCGTTGCTAT 60.064 52.381 0.00 0.00 0.00 2.97
27 28 1.339610 CTCTCCCCTCTCGTTGCTATG 59.660 57.143 0.00 0.00 0.00 2.23
28 29 0.249657 CTCCCCTCTCGTTGCTATGC 60.250 60.000 0.00 0.00 0.00 3.14
29 30 0.975556 TCCCCTCTCGTTGCTATGCA 60.976 55.000 0.00 0.00 36.47 3.96
30 31 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
31 32 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
32 33 1.202568 CCCTCTCGTTGCTATGCATCA 60.203 52.381 0.19 0.00 38.76 3.07
33 34 1.863454 CCTCTCGTTGCTATGCATCAC 59.137 52.381 0.19 0.00 38.76 3.06
34 35 1.863454 CTCTCGTTGCTATGCATCACC 59.137 52.381 0.19 0.00 38.76 4.02
35 36 1.206849 TCTCGTTGCTATGCATCACCA 59.793 47.619 0.19 0.00 38.76 4.17
36 37 2.158914 TCTCGTTGCTATGCATCACCAT 60.159 45.455 0.19 0.00 38.76 3.55
37 38 1.941975 TCGTTGCTATGCATCACCATG 59.058 47.619 0.19 0.00 38.76 3.66
38 39 1.941975 CGTTGCTATGCATCACCATGA 59.058 47.619 0.19 0.00 38.76 3.07
39 40 2.551032 CGTTGCTATGCATCACCATGAT 59.449 45.455 0.19 0.00 38.76 2.45
40 41 3.364664 CGTTGCTATGCATCACCATGATC 60.365 47.826 0.19 0.00 38.76 2.92
41 42 3.782656 TGCTATGCATCACCATGATCT 57.217 42.857 0.19 0.00 34.28 2.75
42 43 4.094830 TGCTATGCATCACCATGATCTT 57.905 40.909 0.19 0.00 34.28 2.40
43 44 3.818773 TGCTATGCATCACCATGATCTTG 59.181 43.478 0.19 1.60 34.28 3.02
44 45 3.366070 GCTATGCATCACCATGATCTTGC 60.366 47.826 0.19 0.00 34.28 4.01
45 46 1.018910 TGCATCACCATGATCTTGCG 58.981 50.000 3.07 0.30 34.28 4.85
46 47 1.019673 GCATCACCATGATCTTGCGT 58.980 50.000 3.07 0.87 34.28 5.24
47 48 1.268386 GCATCACCATGATCTTGCGTG 60.268 52.381 17.02 17.02 34.28 5.34
48 49 2.011947 CATCACCATGATCTTGCGTGT 58.988 47.619 19.89 6.63 34.28 4.49
49 50 1.441738 TCACCATGATCTTGCGTGTG 58.558 50.000 19.89 14.96 0.00 3.82
50 51 0.179181 CACCATGATCTTGCGTGTGC 60.179 55.000 15.81 0.00 43.20 4.57
83 84 6.956202 TTTTTGAAATTACTACGTTCCCCA 57.044 33.333 0.00 0.00 0.00 4.96
84 85 6.956202 TTTTGAAATTACTACGTTCCCCAA 57.044 33.333 0.00 0.00 0.00 4.12
85 86 5.945466 TTGAAATTACTACGTTCCCCAAC 57.055 39.130 0.00 0.00 0.00 3.77
86 87 4.970711 TGAAATTACTACGTTCCCCAACA 58.029 39.130 0.00 0.00 32.14 3.33
125 126 1.556911 AGATCTCCAAGCAATCCACGT 59.443 47.619 0.00 0.00 0.00 4.49
279 280 5.415701 TCAAAGAAATTGGACAGCATACCTC 59.584 40.000 0.00 0.00 39.62 3.85
592 593 0.036294 GGCGAACCCTAGCTCTGTTT 60.036 55.000 0.00 0.00 0.00 2.83
596 597 0.992695 AACCCTAGCTCTGTTTCCCC 59.007 55.000 0.00 0.00 0.00 4.81
715 716 2.937873 GCATTAAGGTGGCTAACGACCA 60.938 50.000 0.00 0.00 34.36 4.02
722 723 2.093341 GGTGGCTAACGACCAGGATTAA 60.093 50.000 0.00 0.00 38.04 1.40
724 725 4.004982 GTGGCTAACGACCAGGATTAAAA 58.995 43.478 0.00 0.00 38.04 1.52
737 738 5.081032 CAGGATTAAAAAGTTGGGGGTGTA 58.919 41.667 0.00 0.00 0.00 2.90
768 769 4.534500 GGGATTTGGAGTTTGGGGTTTAAT 59.466 41.667 0.00 0.00 0.00 1.40
783 784 6.068670 GGGGTTTAATACAGACAAGCCATAT 58.931 40.000 0.00 0.00 38.34 1.78
793 794 3.776969 AGACAAGCCATATGAGTTCAGGA 59.223 43.478 3.65 0.00 0.00 3.86
823 824 8.673456 AAATAGACTTTACTCTCTCCTTTCCT 57.327 34.615 0.00 0.00 0.00 3.36
824 825 8.673456 AATAGACTTTACTCTCTCCTTTCCTT 57.327 34.615 0.00 0.00 0.00 3.36
825 826 8.673456 ATAGACTTTACTCTCTCCTTTCCTTT 57.327 34.615 0.00 0.00 0.00 3.11
826 827 7.381789 AGACTTTACTCTCTCCTTTCCTTTT 57.618 36.000 0.00 0.00 0.00 2.27
827 828 7.446769 AGACTTTACTCTCTCCTTTCCTTTTC 58.553 38.462 0.00 0.00 0.00 2.29
828 829 7.291416 AGACTTTACTCTCTCCTTTCCTTTTCT 59.709 37.037 0.00 0.00 0.00 2.52
829 830 7.446769 ACTTTACTCTCTCCTTTCCTTTTCTC 58.553 38.462 0.00 0.00 0.00 2.87
830 831 4.901197 ACTCTCTCCTTTCCTTTTCTCC 57.099 45.455 0.00 0.00 0.00 3.71
831 832 3.585289 ACTCTCTCCTTTCCTTTTCTCCC 59.415 47.826 0.00 0.00 0.00 4.30
832 833 3.584848 CTCTCTCCTTTCCTTTTCTCCCA 59.415 47.826 0.00 0.00 0.00 4.37
833 834 3.328050 TCTCTCCTTTCCTTTTCTCCCAC 59.672 47.826 0.00 0.00 0.00 4.61
834 835 2.375509 TCTCCTTTCCTTTTCTCCCACC 59.624 50.000 0.00 0.00 0.00 4.61
835 836 2.108250 CTCCTTTCCTTTTCTCCCACCA 59.892 50.000 0.00 0.00 0.00 4.17
836 837 2.516277 TCCTTTCCTTTTCTCCCACCAA 59.484 45.455 0.00 0.00 0.00 3.67
837 838 3.052490 TCCTTTCCTTTTCTCCCACCAAA 60.052 43.478 0.00 0.00 0.00 3.28
838 839 3.069586 CCTTTCCTTTTCTCCCACCAAAC 59.930 47.826 0.00 0.00 0.00 2.93
839 840 3.390175 TTCCTTTTCTCCCACCAAACA 57.610 42.857 0.00 0.00 0.00 2.83
840 841 3.390175 TCCTTTTCTCCCACCAAACAA 57.610 42.857 0.00 0.00 0.00 2.83
841 842 3.714144 TCCTTTTCTCCCACCAAACAAA 58.286 40.909 0.00 0.00 0.00 2.83
842 843 3.449377 TCCTTTTCTCCCACCAAACAAAC 59.551 43.478 0.00 0.00 0.00 2.93
843 844 3.196685 CCTTTTCTCCCACCAAACAAACA 59.803 43.478 0.00 0.00 0.00 2.83
844 845 4.432712 CTTTTCTCCCACCAAACAAACAG 58.567 43.478 0.00 0.00 0.00 3.16
845 846 1.398692 TCTCCCACCAAACAAACAGC 58.601 50.000 0.00 0.00 0.00 4.40
846 847 0.389025 CTCCCACCAAACAAACAGCC 59.611 55.000 0.00 0.00 0.00 4.85
847 848 0.324738 TCCCACCAAACAAACAGCCA 60.325 50.000 0.00 0.00 0.00 4.75
848 849 0.104671 CCCACCAAACAAACAGCCAG 59.895 55.000 0.00 0.00 0.00 4.85
849 850 0.530431 CCACCAAACAAACAGCCAGC 60.530 55.000 0.00 0.00 0.00 4.85
850 851 0.530431 CACCAAACAAACAGCCAGCC 60.530 55.000 0.00 0.00 0.00 4.85
851 852 1.069596 CCAAACAAACAGCCAGCCC 59.930 57.895 0.00 0.00 0.00 5.19
852 853 1.300080 CAAACAAACAGCCAGCCCG 60.300 57.895 0.00 0.00 0.00 6.13
853 854 3.150647 AAACAAACAGCCAGCCCGC 62.151 57.895 0.00 0.00 0.00 6.13
854 855 4.892965 ACAAACAGCCAGCCCGCA 62.893 61.111 0.00 0.00 0.00 5.69
855 856 4.347453 CAAACAGCCAGCCCGCAC 62.347 66.667 0.00 0.00 0.00 5.34
1171 1174 0.613292 ACATCTCGGTCAGTGCTCCT 60.613 55.000 3.43 0.00 0.00 3.69
1218 1255 2.405892 CCTTCGTGGCTTTGTTCTTG 57.594 50.000 0.00 0.00 0.00 3.02
1232 1269 3.130633 TGTTCTTGTTCGTCATGGTGAG 58.869 45.455 0.00 0.00 0.00 3.51
1270 1307 2.108168 TGAATCTCTTGGACCGGGTAG 58.892 52.381 6.32 0.00 0.00 3.18
1279 1316 1.227176 GACCGGGTAGAATGCCGTC 60.227 63.158 6.32 0.00 44.50 4.79
1367 1408 3.565902 GGATGGATGGACGGATTCTTTTC 59.434 47.826 0.00 0.00 0.00 2.29
1369 1410 5.454755 GGATGGATGGACGGATTCTTTTCTA 60.455 44.000 0.00 0.00 0.00 2.10
1392 1433 3.013921 TGCTCGGTGTTCTGTTTTTCTT 58.986 40.909 0.00 0.00 0.00 2.52
1410 1451 7.880160 TTTTCTTGTCCTCATCTTTTTCTGA 57.120 32.000 0.00 0.00 0.00 3.27
1506 1553 9.940166 GAAAATTTTGAGTTCTTGAATGCATTT 57.060 25.926 14.33 0.00 0.00 2.32
1677 1726 1.001974 ACTTCTGCATTCGCTGTACCA 59.998 47.619 0.00 0.00 39.64 3.25
1697 1746 8.517878 TGTACCAACTCAGTAGTAGTACATTTC 58.482 37.037 10.33 0.00 43.59 2.17
1772 1835 5.593909 AGTGGTTCAGTTCATCATTCACAAA 59.406 36.000 0.00 0.00 0.00 2.83
1778 1841 7.274603 TCAGTTCATCATTCACAAATCACAA 57.725 32.000 0.00 0.00 0.00 3.33
1792 1855 5.067936 ACAAATCACAACGAATAACCCAACA 59.932 36.000 0.00 0.00 0.00 3.33
1871 1934 4.082895 TCGAGAAGCTCAAAGGTACTGTAC 60.083 45.833 9.46 9.46 40.86 2.90
1891 1954 0.593618 TATCGATCGCTCTGCTCCAC 59.406 55.000 11.09 0.00 0.00 4.02
1892 1955 1.106351 ATCGATCGCTCTGCTCCACT 61.106 55.000 11.09 0.00 0.00 4.00
1907 1970 5.819991 TGCTCCACTATTTCTCCAATTTCT 58.180 37.500 0.00 0.00 0.00 2.52
1909 1972 5.449725 GCTCCACTATTTCTCCAATTTCTGC 60.450 44.000 0.00 0.00 0.00 4.26
1964 2027 6.336566 CAGTTAGTCTGAAGCTACATGTCAT 58.663 40.000 0.00 0.00 46.27 3.06
1974 2037 5.521906 AGCTACATGTCATGTCGTCTTAT 57.478 39.130 21.65 0.00 43.67 1.73
1998 2061 2.161808 ACATCTTCAGTACACTCGTCCG 59.838 50.000 0.00 0.00 0.00 4.79
2030 2093 2.475200 ACGCTGTTTTTCTTGCTGAC 57.525 45.000 0.00 0.00 0.00 3.51
2053 2116 3.553917 GCGTAACACCAAAGCAAAACAAT 59.446 39.130 0.00 0.00 0.00 2.71
2054 2117 4.033472 GCGTAACACCAAAGCAAAACAATT 59.967 37.500 0.00 0.00 0.00 2.32
2074 2137 8.094798 ACAATTGAGTGCTTTCTTTAATACGA 57.905 30.769 13.59 0.00 0.00 3.43
2094 2157 3.579709 GACTGTATCCATCCACATAGCG 58.420 50.000 0.00 0.00 0.00 4.26
2122 2185 0.179073 CGATTTGGATCTGGCTCCGT 60.179 55.000 0.00 0.00 38.21 4.69
2165 2228 4.739046 ACTCTTTTCGATCTGCAAAGTG 57.261 40.909 6.46 6.71 0.00 3.16
2169 2232 4.152402 TCTTTTCGATCTGCAAAGTGCTAC 59.848 41.667 6.46 0.00 45.31 3.58
2170 2233 1.629013 TCGATCTGCAAAGTGCTACG 58.371 50.000 1.43 2.96 45.31 3.51
2236 2299 1.601914 GGTCCAATGTTTGTTGACGCC 60.602 52.381 0.00 0.00 0.00 5.68
2317 2382 8.947055 ACATCTTGTTTTACTTGCAATCTTTT 57.053 26.923 0.00 0.00 0.00 2.27
2391 2456 0.114168 ATGGGGTTAGCAAGCACCAA 59.886 50.000 4.27 0.00 34.50 3.67
2414 2479 4.286032 ACCAGCTGATTTGGTAGTCTGTAA 59.714 41.667 17.39 0.00 46.80 2.41
2421 2486 7.173907 GCTGATTTGGTAGTCTGTAATGCATAT 59.826 37.037 0.00 0.00 0.00 1.78
2551 2616 0.438830 GCGCGGAAAGACAGTAGTTG 59.561 55.000 8.83 0.00 0.00 3.16
2658 2732 3.300009 GCCTGAAATGAGTGAACAAACG 58.700 45.455 0.00 0.00 0.00 3.60
2659 2733 3.243068 GCCTGAAATGAGTGAACAAACGT 60.243 43.478 0.00 0.00 0.00 3.99
2666 2740 8.332464 TGAAATGAGTGAACAAACGTACTAAAG 58.668 33.333 0.00 0.00 0.00 1.85
2707 2824 8.528643 TCCGATTCAGAAAAGAGTTAGAACATA 58.471 33.333 0.00 0.00 0.00 2.29
2758 3000 9.123709 GTTCGTTAAATAAAATGTGAATGCTCA 57.876 29.630 0.00 0.00 0.00 4.26
2924 6064 7.273381 CGTATGAATTTCCCATTTTCACACTTC 59.727 37.037 0.00 0.00 32.61 3.01
2987 6127 7.394641 TGGGCATTTACACTTTACATACATCAA 59.605 33.333 0.00 0.00 0.00 2.57
3023 6163 1.461127 ACTTTGCTAAAGCGCTCGAAG 59.539 47.619 12.06 15.91 45.83 3.79
3193 6333 6.468543 AGTGACTGACCCTATTTCTTTCTTC 58.531 40.000 0.00 0.00 0.00 2.87
3248 6388 2.967397 CGCGAGTACAACCTCCCA 59.033 61.111 0.00 0.00 0.00 4.37
3287 6427 4.320567 CGGAACATCATCTGCTACGAGTAT 60.321 45.833 0.00 0.00 0.00 2.12
3530 6670 2.498167 GTGAAGAAGCTGAGGCAGAAA 58.502 47.619 0.00 0.00 41.70 2.52
3593 6733 4.841422 AGTTCTGAACCTTGATCTGATGG 58.159 43.478 16.48 0.00 0.00 3.51
3700 6848 1.350684 TGAATTGGTGTGCTGAGGCTA 59.649 47.619 0.00 0.00 39.59 3.93
3732 6880 5.640147 TGTACATTGGATTTGGTTCTTCCT 58.360 37.500 0.00 0.00 37.07 3.36
3743 6891 2.095461 GGTTCTTCCTGATGAAAGGCC 58.905 52.381 0.00 0.00 37.24 5.19
3747 6895 1.145900 TTCCTGATGAAAGGCCCCCA 61.146 55.000 0.00 0.00 37.24 4.96
3760 6908 1.105759 GCCCCCATGCATGTTCTCTC 61.106 60.000 24.58 5.67 0.00 3.20
3822 6970 1.603678 GCATGTGTTCTGGCTTTGTGG 60.604 52.381 0.00 0.00 0.00 4.17
3828 6976 0.106769 TTCTGGCTTTGTGGTGCTCA 60.107 50.000 0.00 0.00 0.00 4.26
3930 7078 6.183360 CCGAAATAATTGTTTCAGCAAGCTTC 60.183 38.462 22.54 0.00 37.84 3.86
3931 7079 6.363088 CGAAATAATTGTTTCAGCAAGCTTCA 59.637 34.615 22.54 0.00 37.84 3.02
3955 7103 6.409524 AGACATTTGGAATTTTTCTGCTCA 57.590 33.333 0.00 0.00 0.00 4.26
3956 7104 7.001099 AGACATTTGGAATTTTTCTGCTCAT 57.999 32.000 0.00 0.00 0.00 2.90
3958 7106 8.587608 AGACATTTGGAATTTTTCTGCTCATAA 58.412 29.630 0.00 0.00 0.00 1.90
3960 7108 9.558396 ACATTTGGAATTTTTCTGCTCATAAAA 57.442 25.926 0.00 0.00 0.00 1.52
3961 7109 9.815936 CATTTGGAATTTTTCTGCTCATAAAAC 57.184 29.630 0.00 0.00 0.00 2.43
3964 7112 6.928492 TGGAATTTTTCTGCTCATAAAACACC 59.072 34.615 0.00 0.00 0.00 4.16
3968 7116 2.695359 TCTGCTCATAAAACACCGGTC 58.305 47.619 2.59 0.00 0.00 4.79
3980 7128 2.033602 CCGGTCCCTTGGTTCACC 59.966 66.667 0.00 0.00 0.00 4.02
3987 7135 3.499745 GGTCCCTTGGTTCACCATAAACT 60.500 47.826 0.00 0.00 46.97 2.66
3992 7178 5.514136 CCCTTGGTTCACCATAAACTACTGA 60.514 44.000 0.00 0.00 46.97 3.41
4003 7189 6.070194 ACCATAAACTACTGAGCTAACCATGT 60.070 38.462 0.00 0.00 0.00 3.21
4004 7190 6.258727 CCATAAACTACTGAGCTAACCATGTG 59.741 42.308 0.00 0.00 0.00 3.21
4017 7204 0.238289 CCATGTGCACGTTGAAGACC 59.762 55.000 18.28 0.00 0.00 3.85
4020 7207 2.535012 TGTGCACGTTGAAGACCATA 57.465 45.000 13.13 0.00 0.00 2.74
4027 7214 5.703592 TGCACGTTGAAGACCATAAAACTAT 59.296 36.000 0.00 0.00 0.00 2.12
4030 7217 7.593644 GCACGTTGAAGACCATAAAACTATTTT 59.406 33.333 0.00 0.00 36.67 1.82
4031 7218 8.901748 CACGTTGAAGACCATAAAACTATTTTG 58.098 33.333 0.00 0.00 34.19 2.44
4032 7219 8.626526 ACGTTGAAGACCATAAAACTATTTTGT 58.373 29.630 0.00 0.00 34.19 2.83
4109 7373 5.762179 AACACATGACTGAGAAATCCCTA 57.238 39.130 0.00 0.00 0.00 3.53
4110 7374 5.965033 ACACATGACTGAGAAATCCCTAT 57.035 39.130 0.00 0.00 0.00 2.57
4211 7577 2.601240 TCAGGTGCATCATCCCAAAA 57.399 45.000 0.00 0.00 0.00 2.44
4222 7588 5.743714 GCATCATCCCAAAATGCCAATGTAT 60.744 40.000 0.00 0.00 39.87 2.29
4263 7630 1.083489 TGATTAAGCGGCAGGTTTCG 58.917 50.000 6.60 0.00 39.10 3.46
4349 7747 4.406648 CTGTATACAGGCTCCACATTCA 57.593 45.455 22.95 0.00 40.20 2.57
4403 7841 9.162793 CGAAAAATCACATGCTAAACATATCTC 57.837 33.333 0.00 0.00 36.64 2.75
4412 7850 8.486210 ACATGCTAAACATATCTCAACTAGGAA 58.514 33.333 0.00 0.00 36.64 3.36
4470 7908 8.100508 AGTTCTTGTAAGAGCTGGTTTTAATC 57.899 34.615 9.73 0.00 43.67 1.75
4486 7924 7.832187 TGGTTTTAATCAATATTTCCTCCGTCT 59.168 33.333 0.00 0.00 0.00 4.18
4500 7938 3.612860 CCTCCGTCTCAAAATAAGTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
4508 7946 6.140737 GTCTCAAAATAAGTGTCGCAACTTTG 59.859 38.462 7.70 1.84 40.77 2.77
4520 7958 7.278424 AGTGTCGCAACTTTGTACTAACTTTAA 59.722 33.333 0.00 0.00 0.00 1.52
4563 8134 2.937799 GCCTTCTCTTCATGAGCTCTTG 59.062 50.000 20.70 20.70 42.38 3.02
4572 8143 1.211457 CATGAGCTCTTGGCCTAGGTT 59.789 52.381 19.36 3.24 43.05 3.50
4574 8145 0.179097 GAGCTCTTGGCCTAGGTTCG 60.179 60.000 14.51 2.40 43.05 3.95
4577 8148 0.895530 CTCTTGGCCTAGGTTCGTGA 59.104 55.000 14.51 2.38 0.00 4.35
4597 8168 5.293079 CGTGAAATTTCCACACAAAAACCAT 59.707 36.000 15.48 0.00 34.36 3.55
4674 9650 2.435693 GCTCCATGTAGCCCTCGGT 61.436 63.158 0.00 0.00 36.45 4.69
4695 9671 4.545610 GTTTCATCTTCAACATCGCCAAA 58.454 39.130 0.00 0.00 0.00 3.28
4699 9675 4.278170 TCATCTTCAACATCGCCAAAAGTT 59.722 37.500 0.00 0.00 0.00 2.66
4700 9676 4.647424 TCTTCAACATCGCCAAAAGTTT 57.353 36.364 0.00 0.00 0.00 2.66
4701 9677 4.358851 TCTTCAACATCGCCAAAAGTTTG 58.641 39.130 0.00 0.00 37.90 2.93
4765 9741 5.188948 TGGCACCACTCATATTTACTGTAGT 59.811 40.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.028905 CGAGAGGGGAGAGTGTGATC 58.971 60.000 0.00 0.00 0.00 2.92
1 2 0.333312 ACGAGAGGGGAGAGTGTGAT 59.667 55.000 0.00 0.00 0.00 3.06
2 3 0.112606 AACGAGAGGGGAGAGTGTGA 59.887 55.000 0.00 0.00 0.00 3.58
3 4 0.244994 CAACGAGAGGGGAGAGTGTG 59.755 60.000 0.00 0.00 0.00 3.82
4 5 1.536943 GCAACGAGAGGGGAGAGTGT 61.537 60.000 0.00 0.00 0.00 3.55
7 8 1.339610 CATAGCAACGAGAGGGGAGAG 59.660 57.143 0.00 0.00 0.00 3.20
8 9 1.403814 CATAGCAACGAGAGGGGAGA 58.596 55.000 0.00 0.00 0.00 3.71
9 10 0.249657 GCATAGCAACGAGAGGGGAG 60.250 60.000 0.00 0.00 0.00 4.30
10 11 0.975556 TGCATAGCAACGAGAGGGGA 60.976 55.000 0.00 0.00 34.76 4.81
11 12 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
12 13 1.202568 TGATGCATAGCAACGAGAGGG 60.203 52.381 0.00 0.00 43.62 4.30
13 14 1.863454 GTGATGCATAGCAACGAGAGG 59.137 52.381 0.00 0.00 43.62 3.69
14 15 1.863454 GGTGATGCATAGCAACGAGAG 59.137 52.381 0.00 0.00 43.62 3.20
15 16 1.206849 TGGTGATGCATAGCAACGAGA 59.793 47.619 0.00 0.00 43.62 4.04
16 17 1.655484 TGGTGATGCATAGCAACGAG 58.345 50.000 0.00 0.00 43.62 4.18
17 18 1.941975 CATGGTGATGCATAGCAACGA 59.058 47.619 0.00 0.00 43.62 3.85
18 19 1.941975 TCATGGTGATGCATAGCAACG 59.058 47.619 0.00 1.35 43.62 4.10
19 20 3.819337 AGATCATGGTGATGCATAGCAAC 59.181 43.478 0.00 0.00 43.62 4.17
20 21 4.094830 AGATCATGGTGATGCATAGCAA 57.905 40.909 0.00 0.00 43.62 3.91
21 22 3.782656 AGATCATGGTGATGCATAGCA 57.217 42.857 0.00 4.86 44.86 3.49
22 23 3.366070 GCAAGATCATGGTGATGCATAGC 60.366 47.826 0.00 0.00 37.20 2.97
23 24 3.120304 CGCAAGATCATGGTGATGCATAG 60.120 47.826 0.00 0.00 37.20 2.23
24 25 2.809696 CGCAAGATCATGGTGATGCATA 59.190 45.455 0.00 0.00 37.20 3.14
25 26 1.607148 CGCAAGATCATGGTGATGCAT 59.393 47.619 0.00 0.00 37.20 3.96
26 27 1.018910 CGCAAGATCATGGTGATGCA 58.981 50.000 11.83 0.00 37.20 3.96
27 28 1.019673 ACGCAAGATCATGGTGATGC 58.980 50.000 0.00 3.06 37.20 3.91
28 29 2.011947 ACACGCAAGATCATGGTGATG 58.988 47.619 19.56 8.58 37.20 3.07
29 30 2.011947 CACACGCAAGATCATGGTGAT 58.988 47.619 19.56 0.00 40.34 3.06
30 31 1.441738 CACACGCAAGATCATGGTGA 58.558 50.000 19.56 0.00 43.62 4.02
31 32 0.179181 GCACACGCAAGATCATGGTG 60.179 55.000 14.17 14.17 43.62 4.17
32 33 1.638388 CGCACACGCAAGATCATGGT 61.638 55.000 0.00 0.00 43.62 3.55
33 34 1.061411 CGCACACGCAAGATCATGG 59.939 57.895 0.00 0.00 43.62 3.66
34 35 0.998669 TACGCACACGCAAGATCATG 59.001 50.000 0.00 0.00 45.53 3.07
35 36 1.135112 TCTACGCACACGCAAGATCAT 60.135 47.619 0.00 0.00 45.53 2.45
36 37 0.242555 TCTACGCACACGCAAGATCA 59.757 50.000 0.00 0.00 45.53 2.92
37 38 1.346365 TTCTACGCACACGCAAGATC 58.654 50.000 0.00 0.00 45.53 2.75
38 39 1.790755 TTTCTACGCACACGCAAGAT 58.209 45.000 0.00 0.00 45.53 2.40
39 40 1.790755 ATTTCTACGCACACGCAAGA 58.209 45.000 0.00 0.00 45.53 3.02
40 41 2.594529 AATTTCTACGCACACGCAAG 57.405 45.000 0.00 0.00 45.53 4.01
41 42 3.341857 AAAATTTCTACGCACACGCAA 57.658 38.095 0.00 0.00 45.53 4.85
42 43 3.341857 AAAAATTTCTACGCACACGCA 57.658 38.095 0.00 0.00 45.53 5.24
60 61 6.956202 TGGGGAACGTAGTAATTTCAAAAA 57.044 33.333 0.00 0.00 45.00 1.94
61 62 6.320672 TGTTGGGGAACGTAGTAATTTCAAAA 59.679 34.615 0.00 0.00 45.00 2.44
62 63 5.826737 TGTTGGGGAACGTAGTAATTTCAAA 59.173 36.000 0.00 0.00 45.00 2.69
63 64 5.239087 GTGTTGGGGAACGTAGTAATTTCAA 59.761 40.000 0.00 0.00 45.00 2.69
64 65 4.756135 GTGTTGGGGAACGTAGTAATTTCA 59.244 41.667 0.00 0.00 45.00 2.69
65 66 4.999311 AGTGTTGGGGAACGTAGTAATTTC 59.001 41.667 0.00 0.00 45.00 2.17
66 67 4.976864 AGTGTTGGGGAACGTAGTAATTT 58.023 39.130 0.00 0.00 45.00 1.82
67 68 4.564199 GGAGTGTTGGGGAACGTAGTAATT 60.564 45.833 0.00 0.00 45.00 1.40
68 69 3.055602 GGAGTGTTGGGGAACGTAGTAAT 60.056 47.826 0.00 0.00 45.00 1.89
69 70 2.299867 GGAGTGTTGGGGAACGTAGTAA 59.700 50.000 0.00 0.00 45.00 2.24
70 71 1.895131 GGAGTGTTGGGGAACGTAGTA 59.105 52.381 0.00 0.00 45.00 1.82
72 73 0.682852 TGGAGTGTTGGGGAACGTAG 59.317 55.000 0.00 0.00 0.00 3.51
73 74 1.354101 ATGGAGTGTTGGGGAACGTA 58.646 50.000 0.00 0.00 0.00 3.57
74 75 1.002773 GTATGGAGTGTTGGGGAACGT 59.997 52.381 0.00 0.00 0.00 3.99
75 76 1.278127 AGTATGGAGTGTTGGGGAACG 59.722 52.381 0.00 0.00 0.00 3.95
76 77 3.434940 AAGTATGGAGTGTTGGGGAAC 57.565 47.619 0.00 0.00 0.00 3.62
77 78 5.339695 GGATAAAGTATGGAGTGTTGGGGAA 60.340 44.000 0.00 0.00 0.00 3.97
78 79 4.165372 GGATAAAGTATGGAGTGTTGGGGA 59.835 45.833 0.00 0.00 0.00 4.81
79 80 4.461198 GGATAAAGTATGGAGTGTTGGGG 58.539 47.826 0.00 0.00 0.00 4.96
80 81 4.461198 GGGATAAAGTATGGAGTGTTGGG 58.539 47.826 0.00 0.00 0.00 4.12
81 82 4.127171 CGGGATAAAGTATGGAGTGTTGG 58.873 47.826 0.00 0.00 0.00 3.77
82 83 5.018539 TCGGGATAAAGTATGGAGTGTTG 57.981 43.478 0.00 0.00 0.00 3.33
83 84 5.424252 TCTTCGGGATAAAGTATGGAGTGTT 59.576 40.000 0.00 0.00 0.00 3.32
84 85 4.960469 TCTTCGGGATAAAGTATGGAGTGT 59.040 41.667 0.00 0.00 0.00 3.55
85 86 5.531122 TCTTCGGGATAAAGTATGGAGTG 57.469 43.478 0.00 0.00 0.00 3.51
86 87 6.078664 AGATCTTCGGGATAAAGTATGGAGT 58.921 40.000 0.00 0.00 34.33 3.85
125 126 1.140161 CCCGACGACGCCATTTCTA 59.860 57.895 0.64 0.00 38.29 2.10
279 280 2.621338 ACTATTCGTGTGTGGATGCTG 58.379 47.619 0.00 0.00 0.00 4.41
619 620 1.891811 TCTCTGCCTGTCTCTCTGTTG 59.108 52.381 0.00 0.00 0.00 3.33
715 716 4.207698 ACACCCCCAACTTTTTAATCCT 57.792 40.909 0.00 0.00 0.00 3.24
722 723 4.810345 TGAAATCTACACCCCCAACTTTT 58.190 39.130 0.00 0.00 0.00 2.27
724 725 3.245264 CCTGAAATCTACACCCCCAACTT 60.245 47.826 0.00 0.00 0.00 2.66
737 738 4.774200 CCAAACTCCAAATCCCTGAAATCT 59.226 41.667 0.00 0.00 0.00 2.40
768 769 5.395657 CCTGAACTCATATGGCTTGTCTGTA 60.396 44.000 2.13 0.00 0.00 2.74
813 814 2.375509 GGTGGGAGAAAAGGAAAGGAGA 59.624 50.000 0.00 0.00 0.00 3.71
814 815 2.108250 TGGTGGGAGAAAAGGAAAGGAG 59.892 50.000 0.00 0.00 0.00 3.69
815 816 2.140224 TGGTGGGAGAAAAGGAAAGGA 58.860 47.619 0.00 0.00 0.00 3.36
816 817 2.675658 TGGTGGGAGAAAAGGAAAGG 57.324 50.000 0.00 0.00 0.00 3.11
817 818 3.704061 TGTTTGGTGGGAGAAAAGGAAAG 59.296 43.478 0.00 0.00 0.00 2.62
818 819 3.714144 TGTTTGGTGGGAGAAAAGGAAA 58.286 40.909 0.00 0.00 0.00 3.13
819 820 3.390175 TGTTTGGTGGGAGAAAAGGAA 57.610 42.857 0.00 0.00 0.00 3.36
820 821 3.390175 TTGTTTGGTGGGAGAAAAGGA 57.610 42.857 0.00 0.00 0.00 3.36
821 822 3.196685 TGTTTGTTTGGTGGGAGAAAAGG 59.803 43.478 0.00 0.00 0.00 3.11
822 823 4.432712 CTGTTTGTTTGGTGGGAGAAAAG 58.567 43.478 0.00 0.00 0.00 2.27
823 824 3.368948 GCTGTTTGTTTGGTGGGAGAAAA 60.369 43.478 0.00 0.00 0.00 2.29
824 825 2.167487 GCTGTTTGTTTGGTGGGAGAAA 59.833 45.455 0.00 0.00 0.00 2.52
825 826 1.754226 GCTGTTTGTTTGGTGGGAGAA 59.246 47.619 0.00 0.00 0.00 2.87
826 827 1.398692 GCTGTTTGTTTGGTGGGAGA 58.601 50.000 0.00 0.00 0.00 3.71
827 828 0.389025 GGCTGTTTGTTTGGTGGGAG 59.611 55.000 0.00 0.00 0.00 4.30
828 829 0.324738 TGGCTGTTTGTTTGGTGGGA 60.325 50.000 0.00 0.00 0.00 4.37
829 830 0.104671 CTGGCTGTTTGTTTGGTGGG 59.895 55.000 0.00 0.00 0.00 4.61
830 831 0.530431 GCTGGCTGTTTGTTTGGTGG 60.530 55.000 0.00 0.00 0.00 4.61
831 832 0.530431 GGCTGGCTGTTTGTTTGGTG 60.530 55.000 0.00 0.00 0.00 4.17
832 833 1.685355 GGGCTGGCTGTTTGTTTGGT 61.685 55.000 0.00 0.00 0.00 3.67
833 834 1.069596 GGGCTGGCTGTTTGTTTGG 59.930 57.895 0.00 0.00 0.00 3.28
834 835 1.300080 CGGGCTGGCTGTTTGTTTG 60.300 57.895 1.18 0.00 0.00 2.93
835 836 3.128375 CGGGCTGGCTGTTTGTTT 58.872 55.556 1.18 0.00 0.00 2.83
836 837 3.605664 GCGGGCTGGCTGTTTGTT 61.606 61.111 11.96 0.00 0.00 2.83
837 838 4.892965 TGCGGGCTGGCTGTTTGT 62.893 61.111 11.96 0.00 0.00 2.83
838 839 4.347453 GTGCGGGCTGGCTGTTTG 62.347 66.667 11.96 0.00 0.00 2.93
858 859 4.899239 GGATCCCCTGCGAGCGTG 62.899 72.222 0.00 0.00 0.00 5.34
1057 1060 3.854669 ATCCTTCCTCGGCGCCAG 61.855 66.667 28.98 21.57 0.00 4.85
1058 1061 4.161295 CATCCTTCCTCGGCGCCA 62.161 66.667 28.98 12.94 0.00 5.69
1171 1174 2.926242 GACGGGGAAGGGTGTGGA 60.926 66.667 0.00 0.00 0.00 4.02
1213 1250 3.069586 AGACTCACCATGACGAACAAGAA 59.930 43.478 0.00 0.00 0.00 2.52
1214 1251 2.628178 AGACTCACCATGACGAACAAGA 59.372 45.455 0.00 0.00 0.00 3.02
1215 1252 2.989840 GAGACTCACCATGACGAACAAG 59.010 50.000 0.00 0.00 0.00 3.16
1216 1253 2.628178 AGAGACTCACCATGACGAACAA 59.372 45.455 5.02 0.00 0.00 2.83
1217 1254 2.239400 AGAGACTCACCATGACGAACA 58.761 47.619 5.02 0.00 0.00 3.18
1218 1255 3.057174 AGAAGAGACTCACCATGACGAAC 60.057 47.826 5.02 0.00 0.00 3.95
1232 1269 3.644884 TCACCAAGAACGAGAAGAGAC 57.355 47.619 0.00 0.00 0.00 3.36
1270 1307 1.025041 GGAAATCAGGGACGGCATTC 58.975 55.000 0.00 0.00 0.00 2.67
1279 1316 2.112815 GCGAACCGGGAAATCAGGG 61.113 63.158 6.32 0.00 0.00 4.45
1367 1408 4.749245 AAAACAGAACACCGAGCAATAG 57.251 40.909 0.00 0.00 0.00 1.73
1369 1410 3.632145 AGAAAAACAGAACACCGAGCAAT 59.368 39.130 0.00 0.00 0.00 3.56
1410 1451 0.465460 TTTCTGAACTGCAACGGCCT 60.465 50.000 0.00 0.00 40.13 5.19
1437 1478 2.616376 TGAACCACGAAATGTTGTCAGG 59.384 45.455 0.00 0.00 0.00 3.86
1441 1482 3.380004 ACATGTGAACCACGAAATGTTGT 59.620 39.130 0.00 0.00 37.14 3.32
1539 1586 3.528532 ACGAATCTAACCCGGCTTAAAG 58.471 45.455 0.00 0.00 0.00 1.85
1544 1591 0.177373 GGAACGAATCTAACCCGGCT 59.823 55.000 0.00 0.00 0.00 5.52
1677 1726 7.091443 GCACAGAAATGTACTACTACTGAGTT 58.909 38.462 0.00 0.00 37.10 3.01
1730 1793 4.595781 ACCACTTGGATGTTGGAACTACTA 59.404 41.667 1.14 0.00 38.94 1.82
1731 1794 3.394606 ACCACTTGGATGTTGGAACTACT 59.605 43.478 1.14 0.00 38.94 2.57
1732 1795 3.751518 ACCACTTGGATGTTGGAACTAC 58.248 45.455 1.14 0.00 38.94 2.73
1772 1835 5.975693 ATTGTTGGGTTATTCGTTGTGAT 57.024 34.783 0.00 0.00 0.00 3.06
1778 1841 6.659242 AGATCAGAAATTGTTGGGTTATTCGT 59.341 34.615 0.00 0.00 0.00 3.85
1792 1855 1.456296 TGCGCTGCAGATCAGAAATT 58.544 45.000 20.43 0.00 45.72 1.82
1871 1934 0.877743 TGGAGCAGAGCGATCGATAG 59.122 55.000 21.57 10.24 0.00 2.08
1891 1954 6.183360 CCACTGAGCAGAAATTGGAGAAATAG 60.183 42.308 4.21 0.00 0.00 1.73
1892 1955 5.649395 CCACTGAGCAGAAATTGGAGAAATA 59.351 40.000 4.21 0.00 0.00 1.40
1907 1970 0.740149 CACAAAGCAACCACTGAGCA 59.260 50.000 0.00 0.00 0.00 4.26
1909 1972 0.031178 GCCACAAAGCAACCACTGAG 59.969 55.000 0.00 0.00 0.00 3.35
1964 2027 6.025749 ACTGAAGATGTTGATAAGACGACA 57.974 37.500 0.00 0.00 38.34 4.35
1974 2037 4.321008 GGACGAGTGTACTGAAGATGTTGA 60.321 45.833 0.00 0.00 0.00 3.18
2030 2093 1.515221 GTTTTGCTTTGGTGTTACGCG 59.485 47.619 3.53 3.53 0.00 6.01
2053 2116 6.704493 ACAGTCGTATTAAAGAAAGCACTCAA 59.296 34.615 0.00 0.00 0.00 3.02
2054 2117 6.220930 ACAGTCGTATTAAAGAAAGCACTCA 58.779 36.000 0.00 0.00 0.00 3.41
2094 2157 4.672801 GCCAGATCCAAATCGTGAAGAAAC 60.673 45.833 0.00 0.00 36.97 2.78
2122 2185 2.293586 ACTTGGATTAGGGCTACAGGGA 60.294 50.000 0.00 0.00 0.00 4.20
2132 2195 7.436673 CAGATCGAAAAGAGTACTTGGATTAGG 59.563 40.741 0.00 0.00 36.39 2.69
2165 2228 3.061139 GCGTCACTCATTGTATTCGTAGC 60.061 47.826 0.00 0.00 0.00 3.58
2169 2232 3.179048 TCAGCGTCACTCATTGTATTCG 58.821 45.455 0.00 0.00 0.00 3.34
2170 2233 4.551603 GCATCAGCGTCACTCATTGTATTC 60.552 45.833 0.00 0.00 0.00 1.75
2236 2299 5.688500 TCCTCCTAGGAGCTTTTGCATAATG 60.689 44.000 30.56 13.68 40.06 1.90
2317 2382 1.048601 GACCTCAACAGACCCAGTGA 58.951 55.000 0.00 0.00 0.00 3.41
2565 2630 3.994392 GCGGAAGTACTTCAGAACATTCA 59.006 43.478 31.75 0.00 41.20 2.57
2658 2732 6.690528 GGAAGTATGTAGACGCACTTTAGTAC 59.309 42.308 0.00 0.00 31.57 2.73
2659 2733 6.457392 CGGAAGTATGTAGACGCACTTTAGTA 60.457 42.308 0.00 0.00 31.57 1.82
2666 2740 2.838386 TCGGAAGTATGTAGACGCAC 57.162 50.000 0.00 0.00 0.00 5.34
2721 2963 6.855763 TTATTTAACGAACTACTCCCTCCA 57.144 37.500 0.00 0.00 0.00 3.86
2758 3000 1.686355 TGCCAACGGATCTGTTTTGT 58.314 45.000 17.47 0.00 0.00 2.83
2763 3005 1.981256 AAACTTGCCAACGGATCTGT 58.019 45.000 0.00 0.00 0.00 3.41
2852 5992 6.975196 AGATGTCTCAGAGCAATGTATACT 57.025 37.500 4.17 0.00 0.00 2.12
2899 6039 7.273381 CGAAGTGTGAAAATGGGAAATTCATAC 59.727 37.037 6.53 6.53 42.18 2.39
2924 6064 1.197721 GACTGGAATTGCAGTGGAACG 59.802 52.381 33.75 7.89 45.86 3.95
2962 6102 7.328277 TGATGTATGTAAAGTGTAAATGCCC 57.672 36.000 0.00 0.00 0.00 5.36
2991 6131 7.643764 GCGCTTTAGCAAAGTTCAAATATATGA 59.356 33.333 0.00 0.00 42.21 2.15
3023 6163 0.455005 GGGAATTCAGAAGCAGCAGC 59.545 55.000 7.93 0.00 42.56 5.25
3193 6333 3.447742 GACTTGTTTGGTTTGCCTGAAG 58.552 45.455 0.00 0.00 35.27 3.02
3287 6427 2.041115 CCTCGAGCTCGTCTGGTCA 61.041 63.158 33.33 13.31 40.80 4.02
3530 6670 3.221222 GGCACCTCATAGGCGTCT 58.779 61.111 0.00 0.00 39.63 4.18
3593 6733 5.507650 GGACACTATGGATAAGAAGACGGAC 60.508 48.000 0.00 0.00 0.00 4.79
3700 6848 3.939740 ATCCAATGTACAGACATGCCT 57.060 42.857 0.33 0.00 45.93 4.75
3732 6880 1.381599 GCATGGGGGCCTTTCATCA 60.382 57.895 0.84 0.00 0.00 3.07
3743 6891 2.228059 GATGAGAGAACATGCATGGGG 58.772 52.381 29.41 6.29 0.00 4.96
3747 6895 4.261072 GCGAAATGATGAGAGAACATGCAT 60.261 41.667 0.00 0.00 0.00 3.96
3760 6908 1.105457 ACCACCCATGCGAAATGATG 58.895 50.000 0.44 0.00 0.00 3.07
3822 6970 1.153549 GTCCCCGACAGATGAGCAC 60.154 63.158 0.00 0.00 32.09 4.40
3828 6976 0.836400 AACACAGGTCCCCGACAGAT 60.836 55.000 0.00 0.00 33.68 2.90
3930 7078 6.702723 TGAGCAGAAAAATTCCAAATGTCTTG 59.297 34.615 0.00 0.00 0.00 3.02
3931 7079 6.819284 TGAGCAGAAAAATTCCAAATGTCTT 58.181 32.000 0.00 0.00 0.00 3.01
3955 7103 1.426215 ACCAAGGGACCGGTGTTTTAT 59.574 47.619 14.63 0.00 33.00 1.40
3956 7104 0.845337 ACCAAGGGACCGGTGTTTTA 59.155 50.000 14.63 0.00 33.00 1.52
3958 7106 0.466739 GAACCAAGGGACCGGTGTTT 60.467 55.000 14.63 0.00 34.62 2.83
3960 7108 2.073716 TGAACCAAGGGACCGGTGT 61.074 57.895 14.63 0.00 34.62 4.16
3961 7109 1.599797 GTGAACCAAGGGACCGGTG 60.600 63.158 14.63 0.00 34.62 4.94
3964 7112 2.833227 TGGTGAACCAAGGGACCG 59.167 61.111 0.00 0.00 44.35 4.79
3980 7128 6.238211 GCACATGGTTAGCTCAGTAGTTTATG 60.238 42.308 0.00 0.00 0.00 1.90
3987 7135 2.673893 CGTGCACATGGTTAGCTCAGTA 60.674 50.000 18.64 0.00 0.00 2.74
3992 7178 0.874390 CAACGTGCACATGGTTAGCT 59.126 50.000 18.64 0.00 0.00 3.32
4003 7189 3.880490 AGTTTTATGGTCTTCAACGTGCA 59.120 39.130 0.00 0.00 0.00 4.57
4004 7190 4.483476 AGTTTTATGGTCTTCAACGTGC 57.517 40.909 0.00 0.00 0.00 5.34
4170 7536 9.480053 CCTGATTTTGTAGTCATTGTTTTCATT 57.520 29.630 0.00 0.00 0.00 2.57
4222 7588 6.176896 TCATACAAAGAATTCCGTGATCCAA 58.823 36.000 11.82 0.00 0.00 3.53
4230 7596 6.136071 CCGCTTAATCATACAAAGAATTCCG 58.864 40.000 0.65 0.00 0.00 4.30
4263 7630 0.962356 CTGCCTGGGTCATGTTCCAC 60.962 60.000 10.68 2.78 0.00 4.02
4349 7747 7.383572 CAGAAACTCGTAGCAAGCTATATGATT 59.616 37.037 4.93 0.00 0.00 2.57
4403 7841 5.661056 TCACCACTGATAGTTCCTAGTTG 57.339 43.478 0.00 0.00 0.00 3.16
4412 7850 6.231211 AGAATTTTCGTTCACCACTGATAGT 58.769 36.000 0.00 0.00 0.00 2.12
4416 7854 5.607477 AGTAGAATTTTCGTTCACCACTGA 58.393 37.500 0.00 0.00 0.00 3.41
4457 7895 7.201821 CGGAGGAAATATTGATTAAAACCAGCT 60.202 37.037 0.00 0.00 0.00 4.24
4470 7908 8.893727 ACTTATTTTGAGACGGAGGAAATATTG 58.106 33.333 0.00 0.00 0.00 1.90
4476 7914 5.223449 ACACTTATTTTGAGACGGAGGAA 57.777 39.130 0.00 0.00 0.00 3.36
4477 7915 4.617530 CGACACTTATTTTGAGACGGAGGA 60.618 45.833 0.00 0.00 0.00 3.71
4486 7924 5.885881 ACAAAGTTGCGACACTTATTTTGA 58.114 33.333 16.80 0.00 35.87 2.69
4520 7958 7.712537 AGGCCCAAATCCATATAACTTCATAT 58.287 34.615 0.00 0.00 0.00 1.78
4523 7961 5.402054 AGGCCCAAATCCATATAACTTCA 57.598 39.130 0.00 0.00 0.00 3.02
4524 7962 6.071320 AGAAGGCCCAAATCCATATAACTTC 58.929 40.000 0.00 0.00 0.00 3.01
4527 7965 5.635120 AGAGAAGGCCCAAATCCATATAAC 58.365 41.667 0.00 0.00 0.00 1.89
4530 7968 4.168675 TGAAGAGAAGGCCCAAATCCATAT 59.831 41.667 0.00 0.00 0.00 1.78
4533 7971 1.710244 TGAAGAGAAGGCCCAAATCCA 59.290 47.619 0.00 0.00 0.00 3.41
4534 7972 2.514458 TGAAGAGAAGGCCCAAATCC 57.486 50.000 0.00 0.00 0.00 3.01
4535 7973 3.624777 TCATGAAGAGAAGGCCCAAATC 58.375 45.455 0.00 0.00 0.00 2.17
4563 8134 2.422479 GGAAATTTCACGAACCTAGGCC 59.578 50.000 19.49 0.00 0.00 5.19
4572 8143 4.865365 GGTTTTTGTGTGGAAATTTCACGA 59.135 37.500 19.49 7.34 37.91 4.35
4574 8145 6.538381 AGATGGTTTTTGTGTGGAAATTTCAC 59.462 34.615 19.49 14.90 35.82 3.18
4577 8148 7.280652 CAGAAGATGGTTTTTGTGTGGAAATTT 59.719 33.333 0.00 0.00 0.00 1.82
4597 8168 1.406069 GGCTTGGAGCGATTCAGAAGA 60.406 52.381 0.00 0.00 43.62 2.87
4674 9650 4.844998 TTTGGCGATGTTGAAGATGAAA 57.155 36.364 0.00 0.00 0.00 2.69
4699 9675 0.825425 TGGCTTTTGGTGATCGCCAA 60.825 50.000 32.12 32.12 46.76 4.52
4700 9676 3.680156 GGCTTTTGGTGATCGCCA 58.320 55.556 24.20 24.20 40.41 5.69
4701 9677 0.179129 CATGGCTTTTGGTGATCGCC 60.179 55.000 18.84 18.84 41.06 5.54
4702 9678 0.527565 ACATGGCTTTTGGTGATCGC 59.472 50.000 0.00 0.00 0.00 4.58
4703 9679 4.165779 GTTTACATGGCTTTTGGTGATCG 58.834 43.478 0.00 0.00 0.00 3.69
4733 9709 1.067295 TGAGTGGTGCCAGAAATCCT 58.933 50.000 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.