Multiple sequence alignment - TraesCS5A01G412400

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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 TraesCS5A01G412400 chr5A 100.000 2351 0 0 1 2351 601167961 601165611 0.000000e+00 4342.0
1 TraesCS5A01G412400 chr5A 93.699 857 54 0 1495 2351 398980554 398979698 0.000000e+00 1284.0
2 TraesCS5A01G412400 chr5A 93.240 858 55 2 1494 2351 473215659 473216513 0.000000e+00 1260.0
3 TraesCS5A01G412400 chr5A 95.106 756 32 3 79 833 10721386 10722137 0.000000e+00 1186.0
4 TraesCS5A01G412400 chr5A 91.833 502 39 1 963 1462 600503601 600503100 0.000000e+00 699.0
5 TraesCS5A01G412400 chr5A 88.645 502 40 6 963 1462 601341885 601341399 1.560000e-166 595.0
6 TraesCS5A01G412400 chr5A 86.400 500 50 7 965 1462 601256287 601255804 4.450000e-147 531.0
7 TraesCS5A01G412400 chr5A 84.929 491 50 9 975 1462 601086698 601086229 2.110000e-130 475.0
8 TraesCS5A01G412400 chr7A 94.166 857 50 0 1495 2351 712672737 712671881 0.000000e+00 1306.0
9 TraesCS5A01G412400 chr7A 95.784 759 31 1 79 837 726139468 726138711 0.000000e+00 1223.0
10 TraesCS5A01G412400 chr3A 93.816 857 52 1 1495 2351 557677643 557678498 0.000000e+00 1288.0
11 TraesCS5A01G412400 chr3A 93.787 853 53 0 1494 2346 742883201 742884053 0.000000e+00 1282.0
12 TraesCS5A01G412400 chr4A 93.706 858 54 0 1494 2351 437504000 437503143 0.000000e+00 1286.0
13 TraesCS5A01G412400 chr4A 91.429 70 5 1 858 927 511040513 511040581 6.920000e-16 95.3
14 TraesCS5A01G412400 chr2A 93.706 858 54 0 1494 2351 118452552 118451695 0.000000e+00 1286.0
15 TraesCS5A01G412400 chr2A 93.473 858 55 1 1494 2351 28448621 28447765 0.000000e+00 1273.0
16 TraesCS5A01G412400 chr2A 95.238 63 3 0 860 922 4139274 4139212 1.490000e-17 100.0
17 TraesCS5A01G412400 chr2A 92.857 70 4 1 859 928 722077260 722077192 1.490000e-17 100.0
18 TraesCS5A01G412400 chr1A 93.473 858 55 1 1494 2351 21232228 21231372 0.000000e+00 1273.0
19 TraesCS5A01G412400 chr5B 95.364 755 30 4 79 832 344305591 344304841 0.000000e+00 1195.0
20 TraesCS5A01G412400 chr5B 90.457 503 45 2 963 1462 590183505 590183003 0.000000e+00 660.0
21 TraesCS5A01G412400 chr5B 88.400 500 41 6 965 1462 590806008 590805524 9.360000e-164 586.0
22 TraesCS5A01G412400 chr5B 90.024 421 40 1 963 1381 590256437 590256017 5.710000e-151 544.0
23 TraesCS5A01G412400 chr2B 95.582 747 31 2 79 825 439364688 439365432 0.000000e+00 1195.0
24 TraesCS5A01G412400 chr2B 95.099 755 32 4 79 832 494280382 494281132 0.000000e+00 1184.0
25 TraesCS5A01G412400 chr7B 95.225 754 31 4 80 831 75062721 75063471 0.000000e+00 1188.0
26 TraesCS5A01G412400 chr7B 95.099 755 31 4 79 832 648395600 648394851 0.000000e+00 1184.0
27 TraesCS5A01G412400 chr7B 94.868 760 33 4 79 837 35080161 35079407 0.000000e+00 1182.0
28 TraesCS5A01G412400 chr7B 94.730 759 34 5 79 834 119256634 119255879 0.000000e+00 1175.0
29 TraesCS5A01G412400 chr7B 93.846 65 3 1 858 922 701408238 701408175 1.920000e-16 97.1
30 TraesCS5A01G412400 chr5D 91.650 503 38 4 963 1462 481564262 481563761 0.000000e+00 693.0
31 TraesCS5A01G412400 chr5D 88.845 502 39 6 963 1462 481761152 481760666 3.340000e-168 601.0
32 TraesCS5A01G412400 chr5D 91.289 287 20 2 1186 1472 481749908 481749627 1.020000e-103 387.0
33 TraesCS5A01G412400 chr2D 95.312 64 3 0 858 921 382455997 382455934 4.130000e-18 102.0
34 TraesCS5A01G412400 chr2D 95.385 65 2 1 859 923 643235880 643235817 4.130000e-18 102.0
35 TraesCS5A01G412400 chrUn 94.030 67 3 1 858 924 36436918 36436983 1.490000e-17 100.0
36 TraesCS5A01G412400 chr7D 92.647 68 3 1 858 925 108173772 108173837 1.920000e-16 97.1
37 TraesCS5A01G412400 chr1B 90.141 71 7 0 859 929 678067289 678067359 2.490000e-15 93.5


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 TraesCS5A01G412400 chr5A 601165611 601167961 2350 True 4342 4342 100.000 1 2351 1 chr5A.!!$R4 2350
1 TraesCS5A01G412400 chr5A 398979698 398980554 856 True 1284 1284 93.699 1495 2351 1 chr5A.!!$R1 856
2 TraesCS5A01G412400 chr5A 473215659 473216513 854 False 1260 1260 93.240 1494 2351 1 chr5A.!!$F2 857
3 TraesCS5A01G412400 chr5A 10721386 10722137 751 False 1186 1186 95.106 79 833 1 chr5A.!!$F1 754
4 TraesCS5A01G412400 chr5A 600503100 600503601 501 True 699 699 91.833 963 1462 1 chr5A.!!$R2 499
5 TraesCS5A01G412400 chr7A 712671881 712672737 856 True 1306 1306 94.166 1495 2351 1 chr7A.!!$R1 856
6 TraesCS5A01G412400 chr7A 726138711 726139468 757 True 1223 1223 95.784 79 837 1 chr7A.!!$R2 758
7 TraesCS5A01G412400 chr3A 557677643 557678498 855 False 1288 1288 93.816 1495 2351 1 chr3A.!!$F1 856
8 TraesCS5A01G412400 chr3A 742883201 742884053 852 False 1282 1282 93.787 1494 2346 1 chr3A.!!$F2 852
9 TraesCS5A01G412400 chr4A 437503143 437504000 857 True 1286 1286 93.706 1494 2351 1 chr4A.!!$R1 857
10 TraesCS5A01G412400 chr2A 118451695 118452552 857 True 1286 1286 93.706 1494 2351 1 chr2A.!!$R3 857
11 TraesCS5A01G412400 chr2A 28447765 28448621 856 True 1273 1273 93.473 1494 2351 1 chr2A.!!$R2 857
12 TraesCS5A01G412400 chr1A 21231372 21232228 856 True 1273 1273 93.473 1494 2351 1 chr1A.!!$R1 857
13 TraesCS5A01G412400 chr5B 344304841 344305591 750 True 1195 1195 95.364 79 832 1 chr5B.!!$R1 753
14 TraesCS5A01G412400 chr5B 590183003 590183505 502 True 660 660 90.457 963 1462 1 chr5B.!!$R2 499
15 TraesCS5A01G412400 chr2B 439364688 439365432 744 False 1195 1195 95.582 79 825 1 chr2B.!!$F1 746
16 TraesCS5A01G412400 chr2B 494280382 494281132 750 False 1184 1184 95.099 79 832 1 chr2B.!!$F2 753
17 TraesCS5A01G412400 chr7B 75062721 75063471 750 False 1188 1188 95.225 80 831 1 chr7B.!!$F1 751
18 TraesCS5A01G412400 chr7B 648394851 648395600 749 True 1184 1184 95.099 79 832 1 chr7B.!!$R3 753
19 TraesCS5A01G412400 chr7B 35079407 35080161 754 True 1182 1182 94.868 79 837 1 chr7B.!!$R1 758
20 TraesCS5A01G412400 chr7B 119255879 119256634 755 True 1175 1175 94.730 79 834 1 chr7B.!!$R2 755
21 TraesCS5A01G412400 chr5D 481563761 481564262 501 True 693 693 91.650 963 1462 1 chr5D.!!$R1 499

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
111 112 0.249573 AGAACGCGTCGGAGGAAAAA 60.25 50.0 14.44 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 1471 0.038618 GGCCAAACCGGAACAACATC 60.039 55.0 9.46 0.0 36.56 3.06 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
24 25 7.682787 ATATCCTTGGTCTACTCAAAGATGT 57.317 36.000 0.00 0.00 30.63 3.06
25 26 5.407407 TCCTTGGTCTACTCAAAGATGTC 57.593 43.478 0.00 0.00 0.00 3.06
26 27 5.087323 TCCTTGGTCTACTCAAAGATGTCT 58.913 41.667 0.00 0.00 0.00 3.41
27 28 5.544176 TCCTTGGTCTACTCAAAGATGTCTT 59.456 40.000 0.00 0.00 37.91 3.01
28 29 5.641209 CCTTGGTCTACTCAAAGATGTCTTG 59.359 44.000 0.00 0.00 36.12 3.02
29 30 5.808366 TGGTCTACTCAAAGATGTCTTGT 57.192 39.130 0.00 0.00 36.12 3.16
30 31 5.541845 TGGTCTACTCAAAGATGTCTTGTG 58.458 41.667 0.00 0.00 36.12 3.33
31 32 4.390297 GGTCTACTCAAAGATGTCTTGTGC 59.610 45.833 0.00 0.00 36.12 4.57
32 33 5.233988 GTCTACTCAAAGATGTCTTGTGCT 58.766 41.667 0.00 0.00 36.12 4.40
33 34 5.347364 GTCTACTCAAAGATGTCTTGTGCTC 59.653 44.000 0.00 0.00 36.12 4.26
34 35 3.406764 ACTCAAAGATGTCTTGTGCTCC 58.593 45.455 0.00 0.00 36.12 4.70
35 36 3.181451 ACTCAAAGATGTCTTGTGCTCCA 60.181 43.478 0.00 0.00 36.12 3.86
36 37 4.008330 CTCAAAGATGTCTTGTGCTCCAT 58.992 43.478 0.00 0.00 36.12 3.41
37 38 3.754850 TCAAAGATGTCTTGTGCTCCATG 59.245 43.478 0.00 0.00 36.12 3.66
38 39 2.414994 AGATGTCTTGTGCTCCATGG 57.585 50.000 4.97 4.97 0.00 3.66
39 40 1.632409 AGATGTCTTGTGCTCCATGGT 59.368 47.619 12.58 0.00 0.00 3.55
40 41 2.840038 AGATGTCTTGTGCTCCATGGTA 59.160 45.455 12.58 0.00 0.00 3.25
41 42 3.264193 AGATGTCTTGTGCTCCATGGTAA 59.736 43.478 12.58 0.00 0.00 2.85
42 43 3.719268 TGTCTTGTGCTCCATGGTAAT 57.281 42.857 12.58 0.00 0.00 1.89
43 44 3.346315 TGTCTTGTGCTCCATGGTAATG 58.654 45.455 12.58 2.18 0.00 1.90
56 57 5.489792 CATGGTAATGGTATAGCCTCTGT 57.510 43.478 0.00 0.00 38.35 3.41
57 58 5.482908 CATGGTAATGGTATAGCCTCTGTC 58.517 45.833 0.00 0.00 38.35 3.51
58 59 4.816126 TGGTAATGGTATAGCCTCTGTCT 58.184 43.478 0.00 0.00 38.35 3.41
59 60 5.216622 TGGTAATGGTATAGCCTCTGTCTT 58.783 41.667 0.00 0.00 38.35 3.01
60 61 5.070446 TGGTAATGGTATAGCCTCTGTCTTG 59.930 44.000 0.00 0.00 38.35 3.02
61 62 4.696479 AATGGTATAGCCTCTGTCTTGG 57.304 45.455 0.00 0.00 38.35 3.61
69 70 2.479566 CCTCTGTCTTGGCAAGCTAA 57.520 50.000 22.31 8.99 0.00 3.09
70 71 2.079925 CCTCTGTCTTGGCAAGCTAAC 58.920 52.381 22.31 15.44 0.00 2.34
71 72 2.550855 CCTCTGTCTTGGCAAGCTAACA 60.551 50.000 22.31 18.94 0.00 2.41
72 73 3.341823 CTCTGTCTTGGCAAGCTAACAT 58.658 45.455 22.31 0.00 0.00 2.71
73 74 4.507710 CTCTGTCTTGGCAAGCTAACATA 58.492 43.478 22.31 12.64 0.00 2.29
74 75 5.102953 TCTGTCTTGGCAAGCTAACATAT 57.897 39.130 22.31 0.00 0.00 1.78
75 76 5.118990 TCTGTCTTGGCAAGCTAACATATC 58.881 41.667 22.31 4.78 0.00 1.63
76 77 4.199310 TGTCTTGGCAAGCTAACATATCC 58.801 43.478 22.31 1.00 0.00 2.59
77 78 4.080356 TGTCTTGGCAAGCTAACATATCCT 60.080 41.667 22.31 0.00 0.00 3.24
78 79 4.513318 GTCTTGGCAAGCTAACATATCCTC 59.487 45.833 22.31 0.00 0.00 3.71
79 80 3.492102 TGGCAAGCTAACATATCCTCC 57.508 47.619 0.00 0.00 0.00 4.30
80 81 2.106511 TGGCAAGCTAACATATCCTCCC 59.893 50.000 0.00 0.00 0.00 4.30
81 82 2.553247 GGCAAGCTAACATATCCTCCCC 60.553 54.545 0.00 0.00 0.00 4.81
82 83 2.553247 GCAAGCTAACATATCCTCCCCC 60.553 54.545 0.00 0.00 0.00 5.40
83 84 2.711009 CAAGCTAACATATCCTCCCCCA 59.289 50.000 0.00 0.00 0.00 4.96
84 85 3.074857 AGCTAACATATCCTCCCCCAA 57.925 47.619 0.00 0.00 0.00 4.12
111 112 0.249573 AGAACGCGTCGGAGGAAAAA 60.250 50.000 14.44 0.00 0.00 1.94
227 228 3.033764 GTCGCGACGCCAAAGACA 61.034 61.111 25.19 0.00 32.57 3.41
229 230 4.072088 CGCGACGCCAAAGACACC 62.072 66.667 15.34 0.00 0.00 4.16
230 231 4.072088 GCGACGCCAAAGACACCG 62.072 66.667 9.14 0.00 0.00 4.94
231 232 2.660552 CGACGCCAAAGACACCGT 60.661 61.111 0.00 0.00 36.53 4.83
290 294 2.531942 GGTGGGGAGTGGAAGGGT 60.532 66.667 0.00 0.00 0.00 4.34
292 296 0.623617 GGTGGGGAGTGGAAGGGTAT 60.624 60.000 0.00 0.00 0.00 2.73
325 329 2.632377 GTCTCCATGAAGAAATCGGCA 58.368 47.619 0.00 0.00 0.00 5.69
577 582 4.451150 GACCAGATCGCCGGCACA 62.451 66.667 28.98 13.13 0.00 4.57
765 770 3.732204 AGATGGAGAGAGAGGGAGGTTAT 59.268 47.826 0.00 0.00 0.00 1.89
839 844 3.449126 GGGAGAGGGAGGGGGCTA 61.449 72.222 0.00 0.00 0.00 3.93
840 845 2.703430 GGAGAGGGAGGGGGCTAA 59.297 66.667 0.00 0.00 0.00 3.09
841 846 1.004361 GGAGAGGGAGGGGGCTAAA 59.996 63.158 0.00 0.00 0.00 1.85
842 847 0.623617 GGAGAGGGAGGGGGCTAAAA 60.624 60.000 0.00 0.00 0.00 1.52
843 848 1.296002 GAGAGGGAGGGGGCTAAAAA 58.704 55.000 0.00 0.00 0.00 1.94
864 869 7.625498 AAAAATGGGGGAGAATTTGTTTAGA 57.375 32.000 0.00 0.00 0.00 2.10
865 870 6.605471 AAATGGGGGAGAATTTGTTTAGAC 57.395 37.500 0.00 0.00 0.00 2.59
866 871 4.042271 TGGGGGAGAATTTGTTTAGACC 57.958 45.455 0.00 0.00 0.00 3.85
867 872 3.399644 TGGGGGAGAATTTGTTTAGACCA 59.600 43.478 0.00 0.00 0.00 4.02
868 873 3.762288 GGGGGAGAATTTGTTTAGACCAC 59.238 47.826 0.00 0.00 0.00 4.16
869 874 4.508584 GGGGGAGAATTTGTTTAGACCACT 60.509 45.833 0.00 0.00 0.00 4.00
870 875 5.280830 GGGGGAGAATTTGTTTAGACCACTA 60.281 44.000 0.00 0.00 0.00 2.74
871 876 6.424032 GGGGAGAATTTGTTTAGACCACTAT 58.576 40.000 0.00 0.00 0.00 2.12
872 877 6.890268 GGGGAGAATTTGTTTAGACCACTATT 59.110 38.462 0.00 0.00 0.00 1.73
873 878 7.396339 GGGGAGAATTTGTTTAGACCACTATTT 59.604 37.037 0.00 0.00 0.00 1.40
874 879 8.803235 GGGAGAATTTGTTTAGACCACTATTTT 58.197 33.333 0.00 0.00 0.00 1.82
909 914 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
910 915 6.522054 TGCTCTTATATTTCTTTACGGAGGG 58.478 40.000 0.00 0.00 0.00 4.30
911 916 6.325545 TGCTCTTATATTTCTTTACGGAGGGA 59.674 38.462 0.00 0.00 0.00 4.20
912 917 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
913 918 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
914 919 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
915 920 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
916 921 8.773033 TTATATTTCTTTACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
917 922 7.672122 ATATTTCTTTACGGAGGGAGTACTT 57.328 36.000 0.00 0.00 0.00 2.24
918 923 8.773033 ATATTTCTTTACGGAGGGAGTACTTA 57.227 34.615 0.00 0.00 0.00 2.24
919 924 7.672122 ATTTCTTTACGGAGGGAGTACTTAT 57.328 36.000 0.00 0.00 0.00 1.73
920 925 7.486407 TTTCTTTACGGAGGGAGTACTTATT 57.514 36.000 0.00 0.00 0.00 1.40
921 926 7.486407 TTCTTTACGGAGGGAGTACTTATTT 57.514 36.000 0.00 0.00 0.00 1.40
922 927 7.486407 TCTTTACGGAGGGAGTACTTATTTT 57.514 36.000 0.00 0.00 0.00 1.82
923 928 7.325694 TCTTTACGGAGGGAGTACTTATTTTG 58.674 38.462 0.00 0.00 0.00 2.44
924 929 6.610075 TTACGGAGGGAGTACTTATTTTGT 57.390 37.500 0.00 0.00 0.00 2.83
925 930 5.494390 ACGGAGGGAGTACTTATTTTGTT 57.506 39.130 0.00 0.00 0.00 2.83
926 931 5.872963 ACGGAGGGAGTACTTATTTTGTTT 58.127 37.500 0.00 0.00 0.00 2.83
927 932 5.704053 ACGGAGGGAGTACTTATTTTGTTTG 59.296 40.000 0.00 0.00 0.00 2.93
928 933 5.123344 CGGAGGGAGTACTTATTTTGTTTGG 59.877 44.000 0.00 0.00 0.00 3.28
929 934 6.243148 GGAGGGAGTACTTATTTTGTTTGGA 58.757 40.000 0.00 0.00 0.00 3.53
930 935 6.717997 GGAGGGAGTACTTATTTTGTTTGGAA 59.282 38.462 0.00 0.00 0.00 3.53
931 936 7.396339 GGAGGGAGTACTTATTTTGTTTGGAAT 59.604 37.037 0.00 0.00 0.00 3.01
932 937 9.457436 GAGGGAGTACTTATTTTGTTTGGAATA 57.543 33.333 0.00 0.00 0.00 1.75
933 938 9.816787 AGGGAGTACTTATTTTGTTTGGAATAA 57.183 29.630 0.00 0.00 0.00 1.40
934 939 9.850628 GGGAGTACTTATTTTGTTTGGAATAAC 57.149 33.333 0.00 0.00 0.00 1.89
938 943 9.850628 GTACTTATTTTGTTTGGAATAACTCCC 57.149 33.333 0.00 0.00 44.69 4.30
939 944 8.721133 ACTTATTTTGTTTGGAATAACTCCCT 57.279 30.769 0.00 0.00 44.69 4.20
940 945 9.816787 ACTTATTTTGTTTGGAATAACTCCCTA 57.183 29.630 0.00 0.00 44.69 3.53
942 947 9.816787 TTATTTTGTTTGGAATAACTCCCTAGT 57.183 29.630 0.00 0.00 44.69 2.57
944 949 9.990868 ATTTTGTTTGGAATAACTCCCTAGTAT 57.009 29.630 0.00 0.00 44.69 2.12
945 950 9.816787 TTTTGTTTGGAATAACTCCCTAGTATT 57.183 29.630 0.00 0.00 44.69 1.89
946 951 9.816787 TTTGTTTGGAATAACTCCCTAGTATTT 57.183 29.630 0.00 0.00 44.69 1.40
947 952 9.816787 TTGTTTGGAATAACTCCCTAGTATTTT 57.183 29.630 0.00 0.00 44.69 1.82
958 963 9.833917 AACTCCCTAGTATTTTAGAAGTATTGC 57.166 33.333 0.00 0.00 33.75 3.56
959 964 8.430431 ACTCCCTAGTATTTTAGAAGTATTGCC 58.570 37.037 0.00 0.00 32.84 4.52
960 965 8.562949 TCCCTAGTATTTTAGAAGTATTGCCT 57.437 34.615 0.00 0.00 0.00 4.75
961 966 9.664777 TCCCTAGTATTTTAGAAGTATTGCCTA 57.335 33.333 0.00 0.00 0.00 3.93
975 980 3.475566 TTGCCTATATCTGGTGACTGC 57.524 47.619 0.00 0.00 0.00 4.40
979 984 4.061596 GCCTATATCTGGTGACTGCTTTC 58.938 47.826 0.00 0.00 0.00 2.62
1017 1022 2.369860 TCTGATGTTTCCAGACTGTGCT 59.630 45.455 0.93 0.00 35.89 4.40
1040 1045 5.444663 AAGCAATTCAAAGAGGTCAAGAC 57.555 39.130 0.00 0.00 0.00 3.01
1076 1081 7.327214 GGTGAAGAAACAGAGAAGAGTATCAT 58.673 38.462 0.00 0.00 37.82 2.45
1099 1104 5.964958 AGAGATGCTGATAGAAGAGCTAC 57.035 43.478 0.00 0.00 36.11 3.58
1101 1106 5.832595 AGAGATGCTGATAGAAGAGCTACAA 59.167 40.000 0.00 0.00 36.11 2.41
1122 1127 1.206849 CAGAGAGAGGAGGAAGCAACC 59.793 57.143 0.00 0.00 0.00 3.77
1212 1217 1.610522 GCTGACAAATGCAGTTCAGGT 59.389 47.619 15.47 3.32 35.81 4.00
1239 1244 5.163301 GGATACATGTGAAGAAGCTAGGGAA 60.163 44.000 9.11 0.00 0.00 3.97
1254 1259 2.050144 AGGGAAAAGTCAGCAGAGTCA 58.950 47.619 0.00 0.00 0.00 3.41
1266 1271 0.109365 CAGAGTCACTGCTCGGTCAG 60.109 60.000 0.00 3.78 39.86 3.51
1280 1285 4.822026 CTCGGTCAGAGGAAATTAACTGT 58.178 43.478 0.00 0.00 43.20 3.55
1284 1289 7.218614 TCGGTCAGAGGAAATTAACTGTTTTA 58.781 34.615 0.00 0.00 0.00 1.52
1308 1313 0.252558 AGGAAAGGGCTCGGGAACTA 60.253 55.000 0.00 0.00 0.00 2.24
1335 1340 0.481128 AACCCGGGAATGTCAAACCT 59.519 50.000 32.02 0.00 0.00 3.50
1347 1352 2.158740 TGTCAAACCTCACCGGAATCAA 60.159 45.455 9.46 0.00 36.31 2.57
1361 1366 4.640201 CCGGAATCAATAATGAACACTGGT 59.360 41.667 0.00 0.00 39.49 4.00
1385 1392 3.348647 TGGTGATGGACAACATACCAG 57.651 47.619 0.00 0.00 41.68 4.00
1386 1393 2.642311 TGGTGATGGACAACATACCAGT 59.358 45.455 0.00 0.00 41.68 4.00
1403 1410 8.366401 ACATACCAGTCAATAGAGATCTCATTG 58.634 37.037 25.94 25.94 33.50 2.82
1417 1424 2.158475 TCTCATTGCAAACACCCTTCCT 60.158 45.455 1.71 0.00 0.00 3.36
1428 1435 2.176247 ACCCTTCCTCGGTGATACAT 57.824 50.000 0.00 0.00 30.39 2.29
1432 1439 3.578716 CCCTTCCTCGGTGATACATGTAT 59.421 47.826 18.31 18.31 0.00 2.29
1445 1453 7.093509 GGTGATACATGTATGGAAAAAGGGTTT 60.094 37.037 22.93 0.00 0.00 3.27
1448 1456 6.096673 ACATGTATGGAAAAAGGGTTTCAC 57.903 37.500 0.00 0.00 0.00 3.18
1469 1477 5.505173 ACTTCTGGTGACTTTTGATGTTG 57.495 39.130 0.00 0.00 0.00 3.33
1470 1478 4.949856 ACTTCTGGTGACTTTTGATGTTGT 59.050 37.500 0.00 0.00 0.00 3.32
1471 1479 5.418840 ACTTCTGGTGACTTTTGATGTTGTT 59.581 36.000 0.00 0.00 0.00 2.83
1472 1480 5.499139 TCTGGTGACTTTTGATGTTGTTC 57.501 39.130 0.00 0.00 0.00 3.18
1473 1481 4.338118 TCTGGTGACTTTTGATGTTGTTCC 59.662 41.667 0.00 0.00 0.00 3.62
1474 1482 3.066064 TGGTGACTTTTGATGTTGTTCCG 59.934 43.478 0.00 0.00 0.00 4.30
1475 1483 3.550030 GGTGACTTTTGATGTTGTTCCGG 60.550 47.826 0.00 0.00 0.00 5.14
1476 1484 3.066203 GTGACTTTTGATGTTGTTCCGGT 59.934 43.478 0.00 0.00 0.00 5.28
1477 1485 3.697045 TGACTTTTGATGTTGTTCCGGTT 59.303 39.130 0.00 0.00 0.00 4.44
1478 1486 4.158764 TGACTTTTGATGTTGTTCCGGTTT 59.841 37.500 0.00 0.00 0.00 3.27
1479 1487 4.429108 ACTTTTGATGTTGTTCCGGTTTG 58.571 39.130 0.00 0.00 0.00 2.93
1480 1488 3.444703 TTTGATGTTGTTCCGGTTTGG 57.555 42.857 0.00 0.00 40.09 3.28
1481 1489 0.671251 TGATGTTGTTCCGGTTTGGC 59.329 50.000 0.00 0.00 37.80 4.52
1482 1490 0.038618 GATGTTGTTCCGGTTTGGCC 60.039 55.000 0.00 0.00 37.80 5.36
1483 1491 0.757188 ATGTTGTTCCGGTTTGGCCA 60.757 50.000 0.00 0.00 37.80 5.36
1484 1492 0.970937 TGTTGTTCCGGTTTGGCCAA 60.971 50.000 16.05 16.05 37.80 4.52
1485 1493 0.249280 GTTGTTCCGGTTTGGCCAAG 60.249 55.000 19.48 7.23 37.80 3.61
1486 1494 1.395826 TTGTTCCGGTTTGGCCAAGG 61.396 55.000 19.48 16.81 37.80 3.61
1487 1495 1.830847 GTTCCGGTTTGGCCAAGGT 60.831 57.895 19.48 0.00 37.80 3.50
1488 1496 0.537828 GTTCCGGTTTGGCCAAGGTA 60.538 55.000 19.48 7.88 37.80 3.08
1489 1497 0.250989 TTCCGGTTTGGCCAAGGTAG 60.251 55.000 19.48 11.32 37.80 3.18
1490 1498 1.128809 TCCGGTTTGGCCAAGGTAGA 61.129 55.000 19.48 11.86 37.80 2.59
1491 1499 0.676782 CCGGTTTGGCCAAGGTAGAG 60.677 60.000 19.48 8.19 36.97 2.43
1492 1500 0.323629 CGGTTTGGCCAAGGTAGAGA 59.676 55.000 19.48 0.00 36.97 3.10
1568 1576 1.689582 GGGGTCCTCATCCGTCCTT 60.690 63.158 0.00 0.00 0.00 3.36
1581 1589 3.684628 TCCTTCCCTCCCTCCGCT 61.685 66.667 0.00 0.00 0.00 5.52
1654 1662 1.302832 CTTCCCTCTTGCCTGCGTT 60.303 57.895 0.00 0.00 0.00 4.84
1778 1786 4.028490 GCGGTGATGGTGGGGTGA 62.028 66.667 0.00 0.00 0.00 4.02
1846 1854 3.587933 GGGTTTGCGGCGACACAA 61.588 61.111 12.98 1.95 0.00 3.33
1995 2003 4.969196 AGCGACCCGTGCACACAG 62.969 66.667 18.64 6.94 33.85 3.66
2225 2234 3.093278 CGTCATTCTTGGAGGCGC 58.907 61.111 0.00 0.00 0.00 6.53
2325 2334 2.280797 GCGTGGTGCAGTGGAGAA 60.281 61.111 0.00 0.00 45.45 2.87
2328 2337 0.320683 CGTGGTGCAGTGGAGAATCA 60.321 55.000 0.00 0.00 36.25 2.57
2334 2343 0.674895 GCAGTGGAGAATCAACGCCT 60.675 55.000 0.00 0.00 46.19 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.566879 AGACATCTTTGAGTAGACCAAGGATAT 59.433 37.037 0.00 0.00 37.97 1.63
1 2 6.897966 AGACATCTTTGAGTAGACCAAGGATA 59.102 38.462 0.00 0.00 37.97 2.59
2 3 5.723887 AGACATCTTTGAGTAGACCAAGGAT 59.276 40.000 0.00 0.00 39.78 3.24
3 4 5.087323 AGACATCTTTGAGTAGACCAAGGA 58.913 41.667 0.00 0.00 34.80 3.36
5 6 6.146837 CACAAGACATCTTTGAGTAGACCAAG 59.853 42.308 0.00 0.00 33.11 3.61
6 7 5.991606 CACAAGACATCTTTGAGTAGACCAA 59.008 40.000 0.00 0.00 33.11 3.67
7 8 5.541845 CACAAGACATCTTTGAGTAGACCA 58.458 41.667 0.00 0.00 33.11 4.02
8 9 4.390297 GCACAAGACATCTTTGAGTAGACC 59.610 45.833 0.00 0.00 33.11 3.85
9 10 5.233988 AGCACAAGACATCTTTGAGTAGAC 58.766 41.667 0.00 0.00 33.11 2.59
10 11 5.473931 GAGCACAAGACATCTTTGAGTAGA 58.526 41.667 0.00 0.00 33.11 2.59
11 12 4.629200 GGAGCACAAGACATCTTTGAGTAG 59.371 45.833 0.00 0.00 33.11 2.57
12 13 4.040339 TGGAGCACAAGACATCTTTGAGTA 59.960 41.667 0.00 0.00 33.11 2.59
13 14 3.181451 TGGAGCACAAGACATCTTTGAGT 60.181 43.478 0.00 0.00 33.11 3.41
14 15 3.405831 TGGAGCACAAGACATCTTTGAG 58.594 45.455 0.00 0.00 33.11 3.02
15 16 3.490439 TGGAGCACAAGACATCTTTGA 57.510 42.857 0.00 0.00 33.11 2.69
16 17 3.119602 CCATGGAGCACAAGACATCTTTG 60.120 47.826 5.56 0.00 33.11 2.77
17 18 3.087031 CCATGGAGCACAAGACATCTTT 58.913 45.455 5.56 0.00 33.11 2.52
18 19 2.040813 ACCATGGAGCACAAGACATCTT 59.959 45.455 21.47 0.00 36.45 2.40
19 20 1.632409 ACCATGGAGCACAAGACATCT 59.368 47.619 21.47 0.00 0.00 2.90
20 21 2.119801 ACCATGGAGCACAAGACATC 57.880 50.000 21.47 0.00 0.00 3.06
21 22 3.719268 TTACCATGGAGCACAAGACAT 57.281 42.857 21.47 0.00 0.00 3.06
22 23 3.346315 CATTACCATGGAGCACAAGACA 58.654 45.455 21.47 0.00 0.00 3.41
34 35 5.247110 AGACAGAGGCTATACCATTACCATG 59.753 44.000 0.00 0.00 43.14 3.66
35 36 5.407049 AGACAGAGGCTATACCATTACCAT 58.593 41.667 0.00 0.00 43.14 3.55
36 37 4.816126 AGACAGAGGCTATACCATTACCA 58.184 43.478 0.00 0.00 43.14 3.25
37 38 5.511545 CCAAGACAGAGGCTATACCATTACC 60.512 48.000 0.00 0.00 43.14 2.85
38 39 5.542779 CCAAGACAGAGGCTATACCATTAC 58.457 45.833 0.00 0.00 43.14 1.89
39 40 5.808366 CCAAGACAGAGGCTATACCATTA 57.192 43.478 0.00 0.00 43.14 1.90
40 41 4.696479 CCAAGACAGAGGCTATACCATT 57.304 45.455 0.00 0.00 43.14 3.16
50 51 2.079925 GTTAGCTTGCCAAGACAGAGG 58.920 52.381 9.04 0.00 0.00 3.69
51 52 2.771089 TGTTAGCTTGCCAAGACAGAG 58.229 47.619 9.04 0.00 0.00 3.35
52 53 2.928801 TGTTAGCTTGCCAAGACAGA 57.071 45.000 9.04 0.00 0.00 3.41
53 54 4.274459 GGATATGTTAGCTTGCCAAGACAG 59.726 45.833 9.04 0.00 0.00 3.51
54 55 4.080356 AGGATATGTTAGCTTGCCAAGACA 60.080 41.667 9.04 4.21 0.00 3.41
55 56 4.455606 AGGATATGTTAGCTTGCCAAGAC 58.544 43.478 9.04 0.00 0.00 3.01
56 57 4.444876 GGAGGATATGTTAGCTTGCCAAGA 60.445 45.833 9.04 0.00 0.00 3.02
57 58 3.817647 GGAGGATATGTTAGCTTGCCAAG 59.182 47.826 0.00 0.00 0.00 3.61
58 59 3.435026 GGGAGGATATGTTAGCTTGCCAA 60.435 47.826 0.00 0.00 32.04 4.52
59 60 2.106511 GGGAGGATATGTTAGCTTGCCA 59.893 50.000 0.00 0.00 32.04 4.92
60 61 2.553247 GGGGAGGATATGTTAGCTTGCC 60.553 54.545 0.00 0.00 30.95 4.52
61 62 2.553247 GGGGGAGGATATGTTAGCTTGC 60.553 54.545 0.00 0.00 0.00 4.01
62 63 2.711009 TGGGGGAGGATATGTTAGCTTG 59.289 50.000 0.00 0.00 0.00 4.01
63 64 3.074857 TGGGGGAGGATATGTTAGCTT 57.925 47.619 0.00 0.00 0.00 3.74
64 65 2.815357 TGGGGGAGGATATGTTAGCT 57.185 50.000 0.00 0.00 0.00 3.32
65 66 2.979678 TCTTGGGGGAGGATATGTTAGC 59.020 50.000 0.00 0.00 0.00 3.09
66 67 4.493618 TCTCTTGGGGGAGGATATGTTAG 58.506 47.826 0.00 0.00 34.39 2.34
67 68 4.569676 TCTCTTGGGGGAGGATATGTTA 57.430 45.455 0.00 0.00 34.39 2.41
68 69 3.438131 TCTCTTGGGGGAGGATATGTT 57.562 47.619 0.00 0.00 34.39 2.71
69 70 3.049344 GTTCTCTTGGGGGAGGATATGT 58.951 50.000 0.00 0.00 34.39 2.29
70 71 2.373502 GGTTCTCTTGGGGGAGGATATG 59.626 54.545 0.00 0.00 34.39 1.78
71 72 2.021042 TGGTTCTCTTGGGGGAGGATAT 60.021 50.000 0.00 0.00 34.39 1.63
72 73 1.368203 TGGTTCTCTTGGGGGAGGATA 59.632 52.381 0.00 0.00 34.39 2.59
73 74 0.121197 TGGTTCTCTTGGGGGAGGAT 59.879 55.000 0.00 0.00 34.39 3.24
74 75 0.547712 CTGGTTCTCTTGGGGGAGGA 60.548 60.000 0.00 0.00 34.39 3.71
75 76 0.547712 TCTGGTTCTCTTGGGGGAGG 60.548 60.000 0.00 0.00 34.39 4.30
76 77 1.003696 GTTCTGGTTCTCTTGGGGGAG 59.996 57.143 0.00 0.00 34.88 4.30
77 78 1.064825 GTTCTGGTTCTCTTGGGGGA 58.935 55.000 0.00 0.00 0.00 4.81
78 79 0.321653 CGTTCTGGTTCTCTTGGGGG 60.322 60.000 0.00 0.00 0.00 5.40
79 80 0.955919 GCGTTCTGGTTCTCTTGGGG 60.956 60.000 0.00 0.00 0.00 4.96
80 81 1.291877 CGCGTTCTGGTTCTCTTGGG 61.292 60.000 0.00 0.00 0.00 4.12
81 82 0.600255 ACGCGTTCTGGTTCTCTTGG 60.600 55.000 5.58 0.00 0.00 3.61
82 83 0.784778 GACGCGTTCTGGTTCTCTTG 59.215 55.000 15.53 0.00 0.00 3.02
83 84 0.663568 CGACGCGTTCTGGTTCTCTT 60.664 55.000 15.53 0.00 0.00 2.85
84 85 1.081376 CGACGCGTTCTGGTTCTCT 60.081 57.895 15.53 0.00 0.00 3.10
111 112 4.394712 CTTCGCCCAAGCCTCCGT 62.395 66.667 0.00 0.00 34.57 4.69
216 217 2.660552 CGACGGTGTCTTTGGCGT 60.661 61.111 0.00 0.00 0.00 5.68
511 516 4.451150 CCTCGCGTGGCTGCCTTA 62.451 66.667 21.03 0.00 0.00 2.69
840 845 7.450074 GTCTAAACAAATTCTCCCCCATTTTT 58.550 34.615 0.00 0.00 0.00 1.94
841 846 6.013725 GGTCTAAACAAATTCTCCCCCATTTT 60.014 38.462 0.00 0.00 0.00 1.82
842 847 5.483937 GGTCTAAACAAATTCTCCCCCATTT 59.516 40.000 0.00 0.00 0.00 2.32
843 848 5.023452 GGTCTAAACAAATTCTCCCCCATT 58.977 41.667 0.00 0.00 0.00 3.16
844 849 4.045334 TGGTCTAAACAAATTCTCCCCCAT 59.955 41.667 0.00 0.00 0.00 4.00
845 850 3.399644 TGGTCTAAACAAATTCTCCCCCA 59.600 43.478 0.00 0.00 0.00 4.96
846 851 3.762288 GTGGTCTAAACAAATTCTCCCCC 59.238 47.826 0.00 0.00 0.00 5.40
847 852 4.663334 AGTGGTCTAAACAAATTCTCCCC 58.337 43.478 0.00 0.00 0.00 4.81
848 853 7.939784 AATAGTGGTCTAAACAAATTCTCCC 57.060 36.000 0.00 0.00 0.00 4.30
883 888 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
884 889 7.661847 CCCTCCGTAAAGAAATATAAGAGCATT 59.338 37.037 0.00 0.00 0.00 3.56
885 890 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
886 891 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
887 892 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
888 893 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
889 894 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
890 895 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
891 896 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
892 897 8.773033 AAGTACTCCCTCCGTAAAGAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
893 898 7.672122 AAGTACTCCCTCCGTAAAGAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
894 899 8.773033 ATAAGTACTCCCTCCGTAAAGAAATA 57.227 34.615 0.00 0.00 0.00 1.40
895 900 7.672122 ATAAGTACTCCCTCCGTAAAGAAAT 57.328 36.000 0.00 0.00 0.00 2.17
896 901 7.486407 AATAAGTACTCCCTCCGTAAAGAAA 57.514 36.000 0.00 0.00 0.00 2.52
897 902 7.486407 AAATAAGTACTCCCTCCGTAAAGAA 57.514 36.000 0.00 0.00 0.00 2.52
898 903 7.038799 ACAAAATAAGTACTCCCTCCGTAAAGA 60.039 37.037 0.00 0.00 0.00 2.52
899 904 7.101700 ACAAAATAAGTACTCCCTCCGTAAAG 58.898 38.462 0.00 0.00 0.00 1.85
900 905 7.008021 ACAAAATAAGTACTCCCTCCGTAAA 57.992 36.000 0.00 0.00 0.00 2.01
901 906 6.610075 ACAAAATAAGTACTCCCTCCGTAA 57.390 37.500 0.00 0.00 0.00 3.18
902 907 6.610075 AACAAAATAAGTACTCCCTCCGTA 57.390 37.500 0.00 0.00 0.00 4.02
903 908 5.494390 AACAAAATAAGTACTCCCTCCGT 57.506 39.130 0.00 0.00 0.00 4.69
904 909 5.123344 CCAAACAAAATAAGTACTCCCTCCG 59.877 44.000 0.00 0.00 0.00 4.63
905 910 6.243148 TCCAAACAAAATAAGTACTCCCTCC 58.757 40.000 0.00 0.00 0.00 4.30
906 911 7.754851 TTCCAAACAAAATAAGTACTCCCTC 57.245 36.000 0.00 0.00 0.00 4.30
907 912 9.816787 TTATTCCAAACAAAATAAGTACTCCCT 57.183 29.630 0.00 0.00 0.00 4.20
908 913 9.850628 GTTATTCCAAACAAAATAAGTACTCCC 57.149 33.333 0.00 0.00 30.22 4.30
932 937 9.833917 GCAATACTTCTAAAATACTAGGGAGTT 57.166 33.333 0.00 0.00 37.10 3.01
933 938 8.430431 GGCAATACTTCTAAAATACTAGGGAGT 58.570 37.037 0.00 0.00 39.92 3.85
934 939 8.652290 AGGCAATACTTCTAAAATACTAGGGAG 58.348 37.037 0.00 0.00 0.00 4.30
935 940 8.562949 AGGCAATACTTCTAAAATACTAGGGA 57.437 34.615 0.00 0.00 0.00 4.20
944 949 9.778741 CACCAGATATAGGCAATACTTCTAAAA 57.221 33.333 0.00 0.00 0.00 1.52
945 950 9.154632 TCACCAGATATAGGCAATACTTCTAAA 57.845 33.333 0.00 0.00 0.00 1.85
946 951 8.585881 GTCACCAGATATAGGCAATACTTCTAA 58.414 37.037 0.00 0.00 0.00 2.10
947 952 7.950684 AGTCACCAGATATAGGCAATACTTCTA 59.049 37.037 0.00 0.00 0.00 2.10
948 953 6.784969 AGTCACCAGATATAGGCAATACTTCT 59.215 38.462 0.00 0.00 0.00 2.85
949 954 6.870965 CAGTCACCAGATATAGGCAATACTTC 59.129 42.308 0.00 0.00 0.00 3.01
950 955 6.742644 GCAGTCACCAGATATAGGCAATACTT 60.743 42.308 0.00 0.00 0.00 2.24
951 956 5.279708 GCAGTCACCAGATATAGGCAATACT 60.280 44.000 0.00 0.00 0.00 2.12
952 957 4.932200 GCAGTCACCAGATATAGGCAATAC 59.068 45.833 0.00 0.00 0.00 1.89
953 958 4.840680 AGCAGTCACCAGATATAGGCAATA 59.159 41.667 0.00 0.00 0.00 1.90
954 959 3.649981 AGCAGTCACCAGATATAGGCAAT 59.350 43.478 0.00 0.00 0.00 3.56
955 960 3.041211 AGCAGTCACCAGATATAGGCAA 58.959 45.455 0.00 0.00 0.00 4.52
956 961 2.682594 AGCAGTCACCAGATATAGGCA 58.317 47.619 0.00 0.00 0.00 4.75
957 962 3.760580 AAGCAGTCACCAGATATAGGC 57.239 47.619 0.00 0.00 0.00 3.93
958 963 5.053145 GTGAAAGCAGTCACCAGATATAGG 58.947 45.833 8.25 0.00 41.79 2.57
975 980 8.044060 TCAGAAGCAATAATAACCAGTGAAAG 57.956 34.615 0.00 0.00 0.00 2.62
979 984 7.325660 ACATCAGAAGCAATAATAACCAGTG 57.674 36.000 0.00 0.00 0.00 3.66
1017 1022 6.299141 AGTCTTGACCTCTTTGAATTGCTTA 58.701 36.000 0.00 0.00 0.00 3.09
1076 1081 6.538263 TGTAGCTCTTCTATCAGCATCTCTA 58.462 40.000 0.00 0.00 38.18 2.43
1099 1104 1.898472 TGCTTCCTCCTCTCTCTGTTG 59.102 52.381 0.00 0.00 0.00 3.33
1101 1106 1.899142 GTTGCTTCCTCCTCTCTCTGT 59.101 52.381 0.00 0.00 0.00 3.41
1122 1127 1.208614 GGCTTGTTGCTGAGCTTCG 59.791 57.895 5.83 0.00 42.39 3.79
1175 1180 2.305635 TCAGCCTCCTTTTGATACTGCA 59.694 45.455 0.00 0.00 0.00 4.41
1212 1217 6.014242 CCCTAGCTTCTTCACATGTATCCATA 60.014 42.308 0.00 0.00 0.00 2.74
1254 1259 1.270907 ATTTCCTCTGACCGAGCAGT 58.729 50.000 4.74 0.00 38.49 4.40
1266 1271 7.614192 TCCTCCCATAAAACAGTTAATTTCCTC 59.386 37.037 0.00 0.00 0.00 3.71
1280 1285 2.356741 CGAGCCCTTTCCTCCCATAAAA 60.357 50.000 0.00 0.00 0.00 1.52
1284 1289 2.378634 CCGAGCCCTTTCCTCCCAT 61.379 63.158 0.00 0.00 0.00 4.00
1308 1313 0.258774 CATTCCCGGGTTTCCATCCT 59.741 55.000 22.86 0.00 0.00 3.24
1335 1340 5.353956 CAGTGTTCATTATTGATTCCGGTGA 59.646 40.000 0.00 0.00 0.00 4.02
1347 1352 4.018506 TCACCATCCACCAGTGTTCATTAT 60.019 41.667 0.00 0.00 33.21 1.28
1361 1366 3.371487 GGTATGTTGTCCATCACCATCCA 60.371 47.826 0.00 0.00 34.86 3.41
1381 1388 5.129980 TGCAATGAGATCTCTATTGACTGGT 59.870 40.000 30.96 8.62 33.77 4.00
1385 1392 7.185453 GTGTTTGCAATGAGATCTCTATTGAC 58.815 38.462 30.96 24.47 33.77 3.18
1386 1393 6.317140 GGTGTTTGCAATGAGATCTCTATTGA 59.683 38.462 30.96 20.93 33.77 2.57
1403 1410 1.228154 ACCGAGGAAGGGTGTTTGC 60.228 57.895 0.00 0.00 36.14 3.68
1417 1424 5.820423 CCTTTTTCCATACATGTATCACCGA 59.180 40.000 15.60 6.41 0.00 4.69
1426 1433 6.345096 AGTGAAACCCTTTTTCCATACATG 57.655 37.500 0.00 0.00 37.80 3.21
1428 1435 6.040391 CAGAAGTGAAACCCTTTTTCCATACA 59.960 38.462 0.00 0.00 37.80 2.29
1432 1439 3.704061 CCAGAAGTGAAACCCTTTTTCCA 59.296 43.478 0.00 0.00 37.80 3.53
1448 1456 5.505173 ACAACATCAAAAGTCACCAGAAG 57.495 39.130 0.00 0.00 0.00 2.85
1459 1467 3.786635 CCAAACCGGAACAACATCAAAA 58.213 40.909 9.46 0.00 36.56 2.44
1462 1470 0.671251 GCCAAACCGGAACAACATCA 59.329 50.000 9.46 0.00 36.56 3.07
1463 1471 0.038618 GGCCAAACCGGAACAACATC 60.039 55.000 9.46 0.00 36.56 3.06
1464 1472 0.757188 TGGCCAAACCGGAACAACAT 60.757 50.000 9.46 0.00 43.94 2.71
1465 1473 0.970937 TTGGCCAAACCGGAACAACA 60.971 50.000 17.98 0.00 43.94 3.33
1466 1474 0.249280 CTTGGCCAAACCGGAACAAC 60.249 55.000 20.91 0.00 43.94 3.32
1467 1475 1.395826 CCTTGGCCAAACCGGAACAA 61.396 55.000 20.91 2.79 43.94 2.83
1468 1476 1.830408 CCTTGGCCAAACCGGAACA 60.830 57.895 20.91 0.00 43.94 3.18
1469 1477 0.537828 TACCTTGGCCAAACCGGAAC 60.538 55.000 24.96 0.00 43.94 3.62
1470 1478 0.250989 CTACCTTGGCCAAACCGGAA 60.251 55.000 24.96 0.00 43.94 4.30
1471 1479 1.128809 TCTACCTTGGCCAAACCGGA 61.129 55.000 24.96 15.56 43.94 5.14
1472 1480 0.676782 CTCTACCTTGGCCAAACCGG 60.677 60.000 20.91 19.45 43.94 5.28
1473 1481 0.323629 TCTCTACCTTGGCCAAACCG 59.676 55.000 20.91 12.19 43.94 4.44
1474 1482 1.613520 GGTCTCTACCTTGGCCAAACC 60.614 57.143 20.91 17.89 43.08 3.27
1475 1483 1.613520 GGGTCTCTACCTTGGCCAAAC 60.614 57.143 20.91 12.54 45.95 2.93
1476 1484 0.696501 GGGTCTCTACCTTGGCCAAA 59.303 55.000 20.91 3.58 45.95 3.28
1477 1485 1.205460 GGGGTCTCTACCTTGGCCAA 61.205 60.000 19.25 19.25 45.95 4.52
1478 1486 1.615424 GGGGTCTCTACCTTGGCCA 60.615 63.158 0.00 0.00 45.95 5.36
1479 1487 2.376165 GGGGGTCTCTACCTTGGCC 61.376 68.421 0.00 0.00 45.95 5.36
1480 1488 3.321445 GGGGGTCTCTACCTTGGC 58.679 66.667 0.00 0.00 45.95 4.52
1527 1535 1.416772 GCGGCTAGGGTTTTAGATCCT 59.583 52.381 0.00 0.00 34.85 3.24
1635 1643 2.437359 CGCAGGCAAGAGGGAAGG 60.437 66.667 0.00 0.00 0.00 3.46
1765 1773 2.531428 TGCCTCACCCCACCATCA 60.531 61.111 0.00 0.00 0.00 3.07
1833 1841 1.596752 AGATGTTGTGTCGCCGCAA 60.597 52.632 0.00 0.00 38.70 4.85
1846 1854 1.739338 GCCGATCCGAGGTCAGATGT 61.739 60.000 0.00 0.00 0.00 3.06
1978 1986 4.969196 CTGTGTGCACGGGTCGCT 62.969 66.667 13.13 0.00 34.12 4.93
1995 2003 3.829948 TCGAAGAACCTTCATCACGTAC 58.170 45.455 7.38 0.00 0.00 3.67
2005 2013 0.175989 GGATCCGCTCGAAGAACCTT 59.824 55.000 0.00 0.00 34.09 3.50
2225 2234 1.599797 GGTCCCTTGAACCCGTGTG 60.600 63.158 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.