Multiple sequence alignment - TraesCS5D01G429600

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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 TraesCS5D01G429600 chr5D 100.000 4968 0 0 1 4968 487003729 487008696 0.000000e+00 9175.0
1 TraesCS5D01G429600 chr5D 89.419 1824 141 13 945 2752 487175357 487173570 0.000000e+00 2252.0
2 TraesCS5D01G429600 chr5D 86.653 1476 129 28 2263 3704 486898247 486896806 0.000000e+00 1572.0
3 TraesCS5D01G429600 chr5D 89.017 1211 100 22 2263 3461 486908834 486907645 0.000000e+00 1469.0
4 TraesCS5D01G429600 chr5D 94.979 717 27 6 2747 3461 487173146 487172437 0.000000e+00 1116.0
5 TraesCS5D01G429600 chr5D 85.133 1056 121 19 933 1959 486910187 486909139 0.000000e+00 1048.0
6 TraesCS5D01G429600 chr5D 84.967 1051 131 14 933 1963 486899595 486898552 0.000000e+00 1040.0
7 TraesCS5D01G429600 chr5D 89.428 577 53 4 3460 4035 487172409 487171840 0.000000e+00 721.0
8 TraesCS5D01G429600 chr5D 82.524 515 48 16 445 930 114628096 114627595 9.950000e-112 414.0
9 TraesCS5D01G429600 chr5D 89.326 178 19 0 3460 3637 486907617 486907440 1.800000e-54 224.0
10 TraesCS5D01G429600 chr5D 83.730 252 22 6 2020 2257 486909131 486908885 2.330000e-53 220.0
11 TraesCS5D01G429600 chr5D 78.800 250 27 14 4066 4310 487171784 487171556 1.440000e-30 145.0
12 TraesCS5D01G429600 chr5B 93.314 4083 174 41 46 4055 598757847 598753791 0.000000e+00 5936.0
13 TraesCS5D01G429600 chr5B 90.082 3176 229 37 936 4055 599124419 599121274 0.000000e+00 4041.0
14 TraesCS5D01G429600 chr5B 88.687 1211 103 22 2263 3461 598659148 598657960 0.000000e+00 1447.0
15 TraesCS5D01G429600 chr5B 84.265 1055 133 14 936 1963 598660497 598659449 0.000000e+00 998.0
16 TraesCS5D01G429600 chr5B 85.598 368 40 5 4053 4409 599121224 599120859 1.690000e-99 374.0
17 TraesCS5D01G429600 chr5B 81.377 494 48 21 459 910 472745893 472745402 3.660000e-96 363.0
18 TraesCS5D01G429600 chr5B 85.950 242 26 3 697 930 82242201 82241960 8.260000e-63 252.0
19 TraesCS5D01G429600 chr5B 88.462 182 21 0 3460 3641 598657932 598657751 2.330000e-53 220.0
20 TraesCS5D01G429600 chr5B 83.730 252 22 6 2020 2257 598659445 598659199 2.330000e-53 220.0
21 TraesCS5D01G429600 chr5B 93.458 107 7 0 4788 4894 598750659 598750553 5.150000e-35 159.0
22 TraesCS5D01G429600 chr5B 91.379 116 7 1 4052 4164 598753743 598753628 6.660000e-34 156.0
23 TraesCS5D01G429600 chr5B 92.553 94 6 1 4681 4773 598752387 598752294 3.120000e-27 134.0
24 TraesCS5D01G429600 chr5B 97.059 68 2 0 4537 4604 598752560 598752493 1.130000e-21 115.0
25 TraesCS5D01G429600 chr5B 94.000 50 3 0 2192 2241 704077644 704077693 5.330000e-10 76.8
26 TraesCS5D01G429600 chr5A 88.970 1786 145 28 2035 3786 607595728 607593961 0.000000e+00 2159.0
27 TraesCS5D01G429600 chr5A 89.348 1211 96 22 2263 3461 607577958 607576769 0.000000e+00 1491.0
28 TraesCS5D01G429600 chr5A 91.848 1055 79 4 936 1988 607596778 607595729 0.000000e+00 1465.0
29 TraesCS5D01G429600 chr5A 78.797 1047 170 30 2399 3418 67521961 67520940 0.000000e+00 656.0
30 TraesCS5D01G429600 chr5A 83.748 603 78 13 944 1527 607588093 607587492 2.020000e-153 553.0
31 TraesCS5D01G429600 chr5A 89.308 318 31 1 1561 1878 607578633 607578319 3.600000e-106 396.0
32 TraesCS5D01G429600 chr5A 84.082 245 28 7 3460 3704 607576741 607576508 5.000000e-55 226.0
33 TraesCS5D01G429600 chr5A 82.143 252 26 9 2020 2257 607578255 607578009 1.090000e-46 198.0
34 TraesCS5D01G429600 chr4B 79.923 1036 168 29 2388 3400 32971846 32972864 0.000000e+00 725.0
35 TraesCS5D01G429600 chr3D 82.106 883 122 24 2284 3145 45931960 45932827 0.000000e+00 723.0
36 TraesCS5D01G429600 chr3D 80.423 189 26 9 3872 4052 114671389 114671204 3.120000e-27 134.0
37 TraesCS5D01G429600 chr6B 78.067 1190 209 40 2389 3557 503007505 503008663 0.000000e+00 704.0
38 TraesCS5D01G429600 chr6B 83.083 532 47 17 438 930 656034316 656033789 1.270000e-120 444.0
39 TraesCS5D01G429600 chr6B 78.120 617 120 12 1227 1834 503005685 503006295 1.310000e-100 377.0
40 TraesCS5D01G429600 chr6B 81.223 458 36 16 377 785 505247880 505248336 1.720000e-84 324.0
41 TraesCS5D01G429600 chr2D 85.476 599 48 17 367 930 547675908 547676502 5.540000e-164 588.0
42 TraesCS5D01G429600 chr7B 79.948 773 136 17 1119 1877 618762319 618761552 7.270000e-153 551.0
43 TraesCS5D01G429600 chr7B 81.784 527 37 22 445 930 26739180 26739688 2.170000e-103 387.0
44 TraesCS5D01G429600 chr2A 86.614 508 45 12 445 930 691231222 691230716 1.570000e-149 540.0
45 TraesCS5D01G429600 chr1A 81.003 658 59 21 262 855 115368863 115368208 3.500000e-126 462.0
46 TraesCS5D01G429600 chr1A 86.168 441 35 13 445 864 296916373 296916808 2.110000e-123 453.0
47 TraesCS5D01G429600 chr1A 86.598 194 20 2 268 461 505536596 505536783 5.040000e-50 209.0
48 TraesCS5D01G429600 chr1D 86.199 442 36 12 445 864 228799472 228799910 5.860000e-124 455.0
49 TraesCS5D01G429600 chr1D 79.228 674 59 29 305 904 409534822 409535488 1.300000e-105 394.0
50 TraesCS5D01G429600 chr1D 81.731 208 26 10 261 459 457873723 457873927 3.980000e-36 163.0
51 TraesCS5D01G429600 chr7A 82.192 584 49 19 385 930 82180190 82180756 7.580000e-123 451.0
52 TraesCS5D01G429600 chr1B 80.728 659 60 23 262 855 167999237 167998581 7.580000e-123 451.0
53 TraesCS5D01G429600 chr1B 90.476 168 15 1 698 864 328103198 328103365 2.330000e-53 220.0
54 TraesCS5D01G429600 chr1B 81.221 213 23 5 262 459 77805609 77805819 6.660000e-34 156.0
55 TraesCS5D01G429600 chr3A 83.333 210 26 7 263 469 94426735 94426938 8.490000e-43 185.0
56 TraesCS5D01G429600 chr3A 82.796 186 21 9 3875 4052 110782885 110782703 6.660000e-34 156.0
57 TraesCS5D01G429600 chr3B 81.283 187 24 9 3874 4052 166160583 166160766 1.860000e-29 141.0


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 TraesCS5D01G429600 chr5D 487003729 487008696 4967 False 9175.00 9175 100.00000 1 4968 1 chr5D.!!$F1 4967
1 TraesCS5D01G429600 chr5D 486896806 486899595 2789 True 1306.00 1572 85.81000 933 3704 2 chr5D.!!$R2 2771
2 TraesCS5D01G429600 chr5D 487171556 487175357 3801 True 1058.50 2252 88.15650 945 4310 4 chr5D.!!$R4 3365
3 TraesCS5D01G429600 chr5D 486907440 486910187 2747 True 740.25 1469 86.80150 933 3637 4 chr5D.!!$R3 2704
4 TraesCS5D01G429600 chr5D 114627595 114628096 501 True 414.00 414 82.52400 445 930 1 chr5D.!!$R1 485
5 TraesCS5D01G429600 chr5B 599120859 599124419 3560 True 2207.50 4041 87.84000 936 4409 2 chr5B.!!$R5 3473
6 TraesCS5D01G429600 chr5B 598750553 598757847 7294 True 1300.00 5936 93.55260 46 4894 5 chr5B.!!$R4 4848
7 TraesCS5D01G429600 chr5B 598657751 598660497 2746 True 721.25 1447 86.28600 936 3641 4 chr5B.!!$R3 2705
8 TraesCS5D01G429600 chr5A 607593961 607596778 2817 True 1812.00 2159 90.40900 936 3786 2 chr5A.!!$R4 2850
9 TraesCS5D01G429600 chr5A 67520940 67521961 1021 True 656.00 656 78.79700 2399 3418 1 chr5A.!!$R1 1019
10 TraesCS5D01G429600 chr5A 607576508 607578633 2125 True 577.75 1491 86.22025 1561 3704 4 chr5A.!!$R3 2143
11 TraesCS5D01G429600 chr5A 607587492 607588093 601 True 553.00 553 83.74800 944 1527 1 chr5A.!!$R2 583
12 TraesCS5D01G429600 chr4B 32971846 32972864 1018 False 725.00 725 79.92300 2388 3400 1 chr4B.!!$F1 1012
13 TraesCS5D01G429600 chr3D 45931960 45932827 867 False 723.00 723 82.10600 2284 3145 1 chr3D.!!$F1 861
14 TraesCS5D01G429600 chr6B 503005685 503008663 2978 False 540.50 704 78.09350 1227 3557 2 chr6B.!!$F2 2330
15 TraesCS5D01G429600 chr6B 656033789 656034316 527 True 444.00 444 83.08300 438 930 1 chr6B.!!$R1 492
16 TraesCS5D01G429600 chr2D 547675908 547676502 594 False 588.00 588 85.47600 367 930 1 chr2D.!!$F1 563
17 TraesCS5D01G429600 chr7B 618761552 618762319 767 True 551.00 551 79.94800 1119 1877 1 chr7B.!!$R1 758
18 TraesCS5D01G429600 chr7B 26739180 26739688 508 False 387.00 387 81.78400 445 930 1 chr7B.!!$F1 485
19 TraesCS5D01G429600 chr2A 691230716 691231222 506 True 540.00 540 86.61400 445 930 1 chr2A.!!$R1 485
20 TraesCS5D01G429600 chr1A 115368208 115368863 655 True 462.00 462 81.00300 262 855 1 chr1A.!!$R1 593
21 TraesCS5D01G429600 chr1D 409534822 409535488 666 False 394.00 394 79.22800 305 904 1 chr1D.!!$F2 599
22 TraesCS5D01G429600 chr7A 82180190 82180756 566 False 451.00 451 82.19200 385 930 1 chr7A.!!$F1 545
23 TraesCS5D01G429600 chr1B 167998581 167999237 656 True 451.00 451 80.72800 262 855 1 chr1B.!!$R1 593

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
35 36 0.106149 GGACACAGACGGTTGGAGTT 59.894 55.0 0.00 0.0 0.00 3.01 F
159 163 0.953960 GTGCCCGTTTCGAACATCCT 60.954 55.0 0.00 0.0 0.00 3.24 F
1078 1260 0.250513 AAGAAGTGTCCTCCATCGCC 59.749 55.0 0.00 0.0 0.00 5.54 F
2276 3269 0.169009 GCGATCTCTGCAAACCCAAC 59.831 55.0 0.00 0.0 0.00 3.77 F
3412 4903 0.764890 ACCCAGTAAGCACAGCTTCA 59.235 50.0 7.62 0.0 46.77 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1209 0.616111 AGGCGATGGAGGACACTTCT 60.616 55.000 0.00 0.00 0.00 2.85 R
1169 1351 1.068083 TAGGTGCGCATAGCTGCTC 59.932 57.895 15.91 0.00 46.65 4.26 R
2493 3529 0.890683 CTTCATCCTGGCCAACAACC 59.109 55.000 7.01 0.00 0.00 3.77 R
3718 5244 0.034380 TAGTGTCACCCTCGCTAGCT 60.034 55.000 13.93 0.00 0.00 3.32 R
4848 8826 0.173708 GACTCCCTCACGTGACCATC 59.826 60.000 15.76 4.56 0.00 3.51 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
20 21 2.900716 TTGTGTGATTCAGACGGACA 57.099 45.000 9.16 0.00 29.81 4.02
21 22 2.148916 TGTGTGATTCAGACGGACAC 57.851 50.000 9.16 0.00 37.92 3.67
22 23 1.410882 TGTGTGATTCAGACGGACACA 59.589 47.619 9.16 0.00 43.44 3.72
23 24 2.061773 GTGTGATTCAGACGGACACAG 58.938 52.381 0.00 0.00 41.09 3.66
24 25 1.960689 TGTGATTCAGACGGACACAGA 59.039 47.619 0.00 0.00 36.72 3.41
25 26 2.288213 TGTGATTCAGACGGACACAGAC 60.288 50.000 0.00 0.00 36.72 3.51
26 27 1.068541 TGATTCAGACGGACACAGACG 60.069 52.381 0.00 0.00 0.00 4.18
27 28 0.243907 ATTCAGACGGACACAGACGG 59.756 55.000 0.00 0.00 0.00 4.79
28 29 1.105167 TTCAGACGGACACAGACGGT 61.105 55.000 0.00 0.00 0.00 4.83
29 30 1.105167 TCAGACGGACACAGACGGTT 61.105 55.000 0.00 0.00 0.00 4.44
30 31 0.939577 CAGACGGACACAGACGGTTG 60.940 60.000 0.00 0.00 0.00 3.77
31 32 1.663702 GACGGACACAGACGGTTGG 60.664 63.158 0.00 0.00 0.00 3.77
32 33 2.079020 GACGGACACAGACGGTTGGA 62.079 60.000 0.00 0.00 0.00 3.53
33 34 1.372997 CGGACACAGACGGTTGGAG 60.373 63.158 0.00 0.00 0.00 3.86
34 35 1.746517 GGACACAGACGGTTGGAGT 59.253 57.895 0.00 0.00 0.00 3.85
35 36 0.106149 GGACACAGACGGTTGGAGTT 59.894 55.000 0.00 0.00 0.00 3.01
36 37 1.342174 GGACACAGACGGTTGGAGTTA 59.658 52.381 0.00 0.00 0.00 2.24
37 38 2.401351 GACACAGACGGTTGGAGTTAC 58.599 52.381 0.00 0.00 0.00 2.50
38 39 2.035576 GACACAGACGGTTGGAGTTACT 59.964 50.000 0.00 0.00 0.00 2.24
39 40 2.035576 ACACAGACGGTTGGAGTTACTC 59.964 50.000 3.36 3.36 0.00 2.59
40 41 2.296471 CACAGACGGTTGGAGTTACTCT 59.704 50.000 12.41 0.00 0.00 3.24
41 42 2.963782 ACAGACGGTTGGAGTTACTCTT 59.036 45.455 12.41 0.00 0.00 2.85
42 43 4.022589 CACAGACGGTTGGAGTTACTCTTA 60.023 45.833 12.41 0.00 0.00 2.10
43 44 4.022503 ACAGACGGTTGGAGTTACTCTTAC 60.023 45.833 12.41 9.96 0.00 2.34
44 45 3.190118 AGACGGTTGGAGTTACTCTTACG 59.810 47.826 12.41 13.28 0.00 3.18
76 80 8.925161 ACAAATCAATTGAAAGTTTTCTCGAA 57.075 26.923 13.09 0.00 41.85 3.71
91 95 3.309388 TCTCGAAAAGAAAGACGCAGAG 58.691 45.455 0.00 0.00 0.00 3.35
159 163 0.953960 GTGCCCGTTTCGAACATCCT 60.954 55.000 0.00 0.00 0.00 3.24
204 212 3.825908 AAAAAGTATCAAGCCTCCCCA 57.174 42.857 0.00 0.00 0.00 4.96
230 238 1.453379 CGAGCTTCCCTCCCGAGTA 60.453 63.158 0.00 0.00 37.27 2.59
263 271 2.183555 CGCGACAGTAGGGTTCCC 59.816 66.667 0.00 0.00 0.00 3.97
755 877 9.995003 AAAGATTAAATTGTTTTATCTGCACCA 57.005 25.926 5.13 0.00 0.00 4.17
773 895 2.827921 ACCATCTTGGCCTGAAATCAAC 59.172 45.455 3.32 0.00 42.67 3.18
912 1058 8.736097 ATGATTGGGAATATAGTGGTACTGTA 57.264 34.615 0.00 0.00 0.00 2.74
913 1059 7.959175 TGATTGGGAATATAGTGGTACTGTAC 58.041 38.462 9.46 9.46 0.00 2.90
941 1087 9.151471 GCTTTGTTGTTGATTATGTACTCTCTA 57.849 33.333 0.00 0.00 0.00 2.43
1078 1260 0.250513 AAGAAGTGTCCTCCATCGCC 59.749 55.000 0.00 0.00 0.00 5.54
1101 1283 2.755103 GTCTTTGATTTGGCGAGGGATT 59.245 45.455 0.00 0.00 0.00 3.01
1110 1292 1.203001 TGGCGAGGGATTGAACCTTTT 60.203 47.619 0.00 0.00 38.79 2.27
1113 1295 2.296190 GCGAGGGATTGAACCTTTTGTT 59.704 45.455 0.00 0.00 38.79 2.83
1885 2178 8.915036 GTTTCTAGAGGTGATTAGGATACAGAA 58.085 37.037 0.00 0.00 41.41 3.02
1886 2179 8.466617 TTCTAGAGGTGATTAGGATACAGAAC 57.533 38.462 0.00 0.00 41.41 3.01
1892 2189 6.551601 AGGTGATTAGGATACAGAACTACAGG 59.448 42.308 0.00 0.00 41.41 4.00
1908 2205 4.821805 ACTACAGGTGATCTTTTGTGGTTG 59.178 41.667 0.00 0.00 32.33 3.77
2008 2916 4.285260 GGGAAAGAATATTAGAGCCCCGTA 59.715 45.833 0.00 0.00 0.00 4.02
2109 3020 4.882842 TTGATAGTGTAACCTGCACTGA 57.117 40.909 7.54 0.00 45.59 3.41
2132 3044 9.364989 CTGAAAATTTTCCTTTATGCCGAATAA 57.635 29.630 24.51 3.06 36.36 1.40
2155 3067 2.108075 ACCCATGAGTGTCAACAATGGA 59.892 45.455 12.03 0.00 41.79 3.41
2156 3068 3.245371 ACCCATGAGTGTCAACAATGGAT 60.245 43.478 12.03 0.00 41.79 3.41
2193 3141 3.343617 TGTTGCTGTCTTTACCATAGGC 58.656 45.455 0.00 0.00 0.00 3.93
2271 3264 1.168714 AAAGGGCGATCTCTGCAAAC 58.831 50.000 0.00 0.00 0.00 2.93
2276 3269 0.169009 GCGATCTCTGCAAACCCAAC 59.831 55.000 0.00 0.00 0.00 3.77
2277 3270 1.522668 CGATCTCTGCAAACCCAACA 58.477 50.000 0.00 0.00 0.00 3.33
2439 3475 4.248859 CTGGAATTCCTGTCTGTACACTG 58.751 47.826 24.73 0.00 36.82 3.66
2466 3502 9.389755 GAGCAAGAAGAGAAGGATAAGTTAATT 57.610 33.333 0.00 0.00 0.00 1.40
2652 3689 2.827383 AAGCTCTCGCCGAACAGCTC 62.827 60.000 17.78 0.00 41.48 4.09
2804 4284 9.672086 CTTAGTCTGTAGCTTGATTGATACTAC 57.328 37.037 0.00 0.00 35.00 2.73
2806 4286 8.982091 AGTCTGTAGCTTGATTGATACTACTA 57.018 34.615 0.00 0.00 35.38 1.82
3146 4629 1.620819 CTAGACTGCTGGTGTGAAGGT 59.379 52.381 0.00 0.00 0.00 3.50
3155 4638 3.243201 GCTGGTGTGAAGGTTCAGAAAAG 60.243 47.826 0.00 0.00 37.98 2.27
3171 4656 7.251704 TCAGAAAAGACTTAAAGCTTGAGTG 57.748 36.000 17.62 2.99 0.00 3.51
3385 4873 5.535783 TGCATTGGATGTCATTTTATCGGAT 59.464 36.000 0.00 0.00 0.00 4.18
3412 4903 0.764890 ACCCAGTAAGCACAGCTTCA 59.235 50.000 7.62 0.00 46.77 3.02
3458 4949 8.965986 CATGATTAGGCTCATGTTTTCATATG 57.034 34.615 6.97 0.00 44.86 1.78
3585 5108 1.586564 GAAGGCTCGACGATCACCG 60.587 63.158 0.00 0.00 45.44 4.94
3607 5130 1.269102 CGGTGCTACGGATAACAGGAG 60.269 57.143 0.00 0.00 0.00 3.69
3712 5238 5.047377 TGGTGAGTCCCATAAAAAGAATTGC 60.047 40.000 0.00 0.00 34.77 3.56
3718 5244 5.418840 GTCCCATAAAAAGAATTGCCTCTCA 59.581 40.000 0.00 0.00 0.00 3.27
3720 5246 5.346522 CCATAAAAAGAATTGCCTCTCAGC 58.653 41.667 0.00 0.00 0.00 4.26
3741 5267 1.339097 AGCGAGGGTGACACTAAAGT 58.661 50.000 5.39 0.00 0.00 2.66
3744 5270 4.275810 AGCGAGGGTGACACTAAAGTATA 58.724 43.478 5.39 0.00 0.00 1.47
3749 5275 6.039493 CGAGGGTGACACTAAAGTATACTGAT 59.961 42.308 6.06 1.37 0.00 2.90
3783 5309 5.409890 CAAGACCTTGTAACGGGAGTCGT 62.410 52.174 1.75 0.00 43.66 4.34
3846 5372 7.011016 CACGGTACAACTAATATGAGCAATTCA 59.989 37.037 0.00 0.00 40.85 2.57
3932 5463 3.074412 AGTTCAACCTATGCGGAAGTTG 58.926 45.455 10.32 10.32 40.72 3.16
3974 5515 5.283457 ACAGTCTGGTATCTAGGAATTGC 57.717 43.478 4.53 0.00 0.00 3.56
3983 5524 7.577303 TGGTATCTAGGAATTGCAATTCTCTT 58.423 34.615 37.77 28.25 43.33 2.85
3988 5529 5.143376 AGGAATTGCAATTCTCTTGTTGG 57.857 39.130 37.77 0.00 43.33 3.77
4002 5543 4.541705 TCTTGTTGGGTTCATCTTTTGGA 58.458 39.130 0.00 0.00 0.00 3.53
4041 5582 4.541973 ATTTGAAATCCAACTGCCTTCC 57.458 40.909 0.00 0.00 33.85 3.46
4167 5780 5.426689 AGTAGATCTTGCTCACAATCCAA 57.573 39.130 0.00 0.00 34.61 3.53
4182 5795 7.337938 TCACAATCCAATCATAGAGCAAGTAA 58.662 34.615 0.00 0.00 0.00 2.24
4201 5814 9.797473 GCAAGTAAATTTGTGAAAGAAAATAGC 57.203 29.630 0.00 0.00 30.79 2.97
4218 5832 9.880157 AGAAAATAGCGAACTTAATGGTAGTAA 57.120 29.630 0.00 0.00 0.00 2.24
4224 5838 5.522824 GCGAACTTAATGGTAGTAAGAAGGG 59.477 44.000 3.41 0.00 33.57 3.95
4234 5848 3.902881 AGTAAGAAGGGCATCACTCTG 57.097 47.619 0.00 0.00 0.00 3.35
4277 5901 1.003580 ACCTCGTGAATCTGGCACATT 59.996 47.619 0.00 0.00 38.20 2.71
4435 6176 2.127708 AGGGCTCGGACCTAAATCAAT 58.872 47.619 0.00 0.00 40.73 2.57
4459 6200 5.811399 TTGAATCAACAAAGTCGTCAACT 57.189 34.783 0.00 0.00 41.10 3.16
4460 6201 5.403897 TGAATCAACAAAGTCGTCAACTC 57.596 39.130 0.00 0.00 37.17 3.01
4473 6214 3.810941 TCGTCAACTCGCCAAAATTAAGT 59.189 39.130 0.00 0.00 0.00 2.24
4479 6220 5.622770 ACTCGCCAAAATTAAGTAACCTG 57.377 39.130 0.00 0.00 0.00 4.00
4499 6240 4.697352 CCTGTCAACTCATAGTCTTTTGGG 59.303 45.833 0.00 0.00 0.00 4.12
4501 6242 3.440522 GTCAACTCATAGTCTTTTGGGGC 59.559 47.826 0.00 0.00 0.00 5.80
4512 6253 1.484240 CTTTTGGGGCTGTTGGTCAAA 59.516 47.619 0.00 0.00 0.00 2.69
4517 6258 1.273327 GGGGCTGTTGGTCAAAGAATG 59.727 52.381 0.00 0.00 0.00 2.67
4521 6262 2.224018 GCTGTTGGTCAAAGAATGGCAA 60.224 45.455 0.00 0.00 34.42 4.52
4523 6264 4.634199 CTGTTGGTCAAAGAATGGCAATT 58.366 39.130 0.00 0.00 34.42 2.32
4529 6270 7.099266 TGGTCAAAGAATGGCAATTACTATG 57.901 36.000 0.00 0.00 34.42 2.23
4531 6272 7.178274 TGGTCAAAGAATGGCAATTACTATGTT 59.822 33.333 0.00 0.00 34.42 2.71
4532 6273 7.489113 GGTCAAAGAATGGCAATTACTATGTTG 59.511 37.037 0.00 0.00 34.42 3.33
4533 6274 8.243426 GTCAAAGAATGGCAATTACTATGTTGA 58.757 33.333 0.00 0.00 32.41 3.18
4542 6850 7.998383 TGGCAATTACTATGTTGATATTGTCCT 59.002 33.333 0.00 0.00 29.14 3.85
4582 6890 0.665835 GTTGATGAACCGTGGTGCAA 59.334 50.000 3.26 0.00 37.20 4.08
4604 6912 2.419673 CGCTTGTAGTGCATGGATTTGA 59.580 45.455 0.00 0.00 0.00 2.69
4606 6914 4.604976 GCTTGTAGTGCATGGATTTGATC 58.395 43.478 0.00 0.00 0.00 2.92
4607 6915 4.096833 GCTTGTAGTGCATGGATTTGATCA 59.903 41.667 0.00 0.00 0.00 2.92
4608 6916 5.221185 GCTTGTAGTGCATGGATTTGATCAT 60.221 40.000 0.00 0.00 0.00 2.45
4609 6917 6.016860 GCTTGTAGTGCATGGATTTGATCATA 60.017 38.462 0.00 0.00 0.00 2.15
4610 6918 7.309012 GCTTGTAGTGCATGGATTTGATCATAT 60.309 37.037 0.00 0.00 0.00 1.78
4611 6919 7.443259 TGTAGTGCATGGATTTGATCATATG 57.557 36.000 3.15 0.00 0.00 1.78
4612 6920 6.999871 TGTAGTGCATGGATTTGATCATATGT 59.000 34.615 3.15 0.00 31.83 2.29
4613 6921 8.156165 TGTAGTGCATGGATTTGATCATATGTA 58.844 33.333 3.15 0.00 31.83 2.29
4614 6922 7.683437 AGTGCATGGATTTGATCATATGTAG 57.317 36.000 3.15 0.00 31.83 2.74
4615 6923 7.229308 AGTGCATGGATTTGATCATATGTAGT 58.771 34.615 3.15 1.49 31.83 2.73
4616 6924 8.377799 AGTGCATGGATTTGATCATATGTAGTA 58.622 33.333 3.15 0.00 31.83 1.82
4617 6925 8.663025 GTGCATGGATTTGATCATATGTAGTAG 58.337 37.037 3.15 0.00 31.83 2.57
4618 6926 8.377799 TGCATGGATTTGATCATATGTAGTAGT 58.622 33.333 3.15 0.00 31.83 2.73
4619 6927 9.875691 GCATGGATTTGATCATATGTAGTAGTA 57.124 33.333 3.15 0.00 31.83 1.82
4643 6951 1.080298 GAAGTGCATGTTGGCTGCC 60.080 57.895 12.87 12.87 38.89 4.85
4654 6962 0.820871 TTGGCTGCCTTTTGTCGTTT 59.179 45.000 21.03 0.00 0.00 3.60
4658 6966 1.838913 CTGCCTTTTGTCGTTTGGTG 58.161 50.000 0.00 0.00 0.00 4.17
4659 6967 0.179124 TGCCTTTTGTCGTTTGGTGC 60.179 50.000 0.00 0.00 0.00 5.01
4662 6970 1.923864 CCTTTTGTCGTTTGGTGCAAC 59.076 47.619 0.00 0.00 0.00 4.17
4663 6971 1.581602 CTTTTGTCGTTTGGTGCAACG 59.418 47.619 0.00 0.00 38.12 4.10
4664 6972 0.522180 TTTGTCGTTTGGTGCAACGT 59.478 45.000 8.38 0.00 38.12 3.99
4666 6974 0.741574 TGTCGTTTGGTGCAACGTCT 60.742 50.000 8.38 0.00 38.12 4.18
4667 6975 0.315869 GTCGTTTGGTGCAACGTCTG 60.316 55.000 8.38 0.00 38.12 3.51
4668 6976 0.741574 TCGTTTGGTGCAACGTCTGT 60.742 50.000 8.38 0.00 38.12 3.41
4669 6977 0.588730 CGTTTGGTGCAACGTCTGTG 60.589 55.000 0.00 0.00 38.12 3.66
4670 6978 0.450184 GTTTGGTGCAACGTCTGTGT 59.550 50.000 0.00 0.00 38.12 3.72
4672 6980 0.391793 TTGGTGCAACGTCTGTGTGA 60.392 50.000 0.00 0.00 38.12 3.58
4674 6982 0.235665 GGTGCAACGTCTGTGTGATG 59.764 55.000 0.00 0.00 38.12 3.07
4675 6983 0.235665 GTGCAACGTCTGTGTGATGG 59.764 55.000 0.00 0.00 36.05 3.51
4676 6984 0.105778 TGCAACGTCTGTGTGATGGA 59.894 50.000 0.00 0.00 36.05 3.41
4677 6985 0.792640 GCAACGTCTGTGTGATGGAG 59.207 55.000 0.00 0.00 36.05 3.86
4678 6986 1.873903 GCAACGTCTGTGTGATGGAGT 60.874 52.381 0.00 0.00 36.05 3.85
4679 6987 2.609491 GCAACGTCTGTGTGATGGAGTA 60.609 50.000 0.00 0.00 36.05 2.59
4686 7043 5.527951 CGTCTGTGTGATGGAGTATACTACT 59.472 44.000 16.20 1.95 42.86 2.57
4724 7081 4.467795 CCTAGGTCCTGATTCAAACAGAGA 59.532 45.833 0.00 0.00 37.54 3.10
4727 7084 4.020662 AGGTCCTGATTCAAACAGAGACTC 60.021 45.833 12.70 0.00 36.63 3.36
4738 7095 5.652452 TCAAACAGAGACTCGGAGATGAATA 59.348 40.000 12.86 0.00 33.89 1.75
4739 7096 5.766150 AACAGAGACTCGGAGATGAATAG 57.234 43.478 12.86 0.00 33.89 1.73
4759 7116 8.217799 TGAATAGATTCCTTGGACCGAATTAAT 58.782 33.333 0.00 0.00 35.97 1.40
4761 7118 6.699575 AGATTCCTTGGACCGAATTAATTG 57.300 37.500 5.17 0.00 0.00 2.32
4762 7119 4.712122 TTCCTTGGACCGAATTAATTGC 57.288 40.909 5.17 0.00 0.00 3.56
4764 7121 2.223479 CCTTGGACCGAATTAATTGCCG 60.223 50.000 5.17 3.90 0.00 5.69
4765 7122 2.404923 TGGACCGAATTAATTGCCGA 57.595 45.000 5.17 0.00 0.00 5.54
4766 7123 2.925724 TGGACCGAATTAATTGCCGAT 58.074 42.857 5.17 0.00 0.00 4.18
4767 7124 2.875933 TGGACCGAATTAATTGCCGATC 59.124 45.455 5.17 0.16 0.00 3.69
4772 7170 3.243035 CCGAATTAATTGCCGATCAAGCA 60.243 43.478 5.17 3.37 38.22 3.91
4795 7193 7.041644 AGCATTGTTTGTTGATGGAAAATGAAG 60.042 33.333 0.00 0.00 0.00 3.02
4797 7195 6.477053 TGTTTGTTGATGGAAAATGAAGGA 57.523 33.333 0.00 0.00 0.00 3.36
4798 7196 7.065120 TGTTTGTTGATGGAAAATGAAGGAT 57.935 32.000 0.00 0.00 0.00 3.24
4811 8789 9.411801 GGAAAATGAAGGATACACTTTTTCTTC 57.588 33.333 17.22 0.00 42.07 2.87
4843 8821 1.383799 CCCACCATTGCTTCCTCCA 59.616 57.895 0.00 0.00 0.00 3.86
4848 8826 0.101759 CCATTGCTTCCTCCATTGCG 59.898 55.000 0.00 0.00 0.00 4.85
4864 8842 3.001902 GCGATGGTCACGTGAGGGA 62.002 63.158 20.73 5.99 44.68 4.20
4913 8891 3.077556 CCCTCCCCTGTCGTCCAG 61.078 72.222 0.00 0.00 41.15 3.86
4914 8892 2.283966 CCTCCCCTGTCGTCCAGT 60.284 66.667 4.59 0.00 39.74 4.00
4915 8893 2.352032 CCTCCCCTGTCGTCCAGTC 61.352 68.421 4.59 0.00 39.74 3.51
4916 8894 1.304547 CTCCCCTGTCGTCCAGTCT 60.305 63.158 4.59 0.00 39.74 3.24
4917 8895 1.599606 CTCCCCTGTCGTCCAGTCTG 61.600 65.000 0.00 0.00 39.74 3.51
4918 8896 1.908793 CCCCTGTCGTCCAGTCTGT 60.909 63.158 0.00 0.00 39.74 3.41
4919 8897 1.290324 CCCTGTCGTCCAGTCTGTG 59.710 63.158 0.00 0.00 39.74 3.66
4920 8898 1.464376 CCCTGTCGTCCAGTCTGTGT 61.464 60.000 0.00 0.00 39.74 3.72
4921 8899 0.319040 CCTGTCGTCCAGTCTGTGTG 60.319 60.000 0.00 0.00 39.74 3.82
4922 8900 0.385751 CTGTCGTCCAGTCTGTGTGT 59.614 55.000 0.00 0.00 36.37 3.72
4923 8901 0.384309 TGTCGTCCAGTCTGTGTGTC 59.616 55.000 0.00 0.00 0.00 3.67
4924 8902 0.318784 GTCGTCCAGTCTGTGTGTCC 60.319 60.000 0.00 0.00 0.00 4.02
4925 8903 1.006102 CGTCCAGTCTGTGTGTCCC 60.006 63.158 0.00 0.00 0.00 4.46
4926 8904 1.371558 GTCCAGTCTGTGTGTCCCC 59.628 63.158 0.00 0.00 0.00 4.81
4927 8905 1.841556 TCCAGTCTGTGTGTCCCCC 60.842 63.158 0.00 0.00 0.00 5.40
4928 8906 2.146724 CCAGTCTGTGTGTCCCCCA 61.147 63.158 0.00 0.00 0.00 4.96
4929 8907 1.705002 CCAGTCTGTGTGTCCCCCAA 61.705 60.000 0.00 0.00 0.00 4.12
4930 8908 0.401738 CAGTCTGTGTGTCCCCCAAT 59.598 55.000 0.00 0.00 0.00 3.16
4931 8909 0.693049 AGTCTGTGTGTCCCCCAATC 59.307 55.000 0.00 0.00 0.00 2.67
4932 8910 0.322546 GTCTGTGTGTCCCCCAATCC 60.323 60.000 0.00 0.00 0.00 3.01
4933 8911 1.000896 CTGTGTGTCCCCCAATCCC 60.001 63.158 0.00 0.00 0.00 3.85
4934 8912 2.359011 GTGTGTCCCCCAATCCCC 59.641 66.667 0.00 0.00 0.00 4.81
4935 8913 2.944390 TGTGTCCCCCAATCCCCC 60.944 66.667 0.00 0.00 0.00 5.40
4936 8914 2.944390 GTGTCCCCCAATCCCCCA 60.944 66.667 0.00 0.00 0.00 4.96
4937 8915 2.120807 TGTCCCCCAATCCCCCAA 60.121 61.111 0.00 0.00 0.00 4.12
4938 8916 1.784743 TGTCCCCCAATCCCCCAAA 60.785 57.895 0.00 0.00 0.00 3.28
4939 8917 1.380280 TGTCCCCCAATCCCCCAAAA 61.380 55.000 0.00 0.00 0.00 2.44
4940 8918 0.178888 GTCCCCCAATCCCCCAAAAA 60.179 55.000 0.00 0.00 0.00 1.94
4958 8936 3.864789 AAAAGCCACCTTCTCTCTTGA 57.135 42.857 0.00 0.00 0.00 3.02
4959 8937 3.864789 AAAGCCACCTTCTCTCTTGAA 57.135 42.857 0.00 0.00 0.00 2.69
4960 8938 3.415457 AAGCCACCTTCTCTCTTGAAG 57.585 47.619 0.00 0.00 42.10 3.02
4961 8939 2.614259 AGCCACCTTCTCTCTTGAAGA 58.386 47.619 5.90 0.00 44.40 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.869801 GTGTCCGTCTGAATCACACAAA 59.130 45.455 8.58 0.00 37.81 2.83
2 3 1.410882 TGTGTCCGTCTGAATCACACA 59.589 47.619 11.04 11.04 43.87 3.72
3 4 2.061773 CTGTGTCCGTCTGAATCACAC 58.938 52.381 7.12 7.12 38.28 3.82
5 6 2.329379 GTCTGTGTCCGTCTGAATCAC 58.671 52.381 0.00 0.00 0.00 3.06
6 7 1.068541 CGTCTGTGTCCGTCTGAATCA 60.069 52.381 0.00 0.00 0.00 2.57
7 8 1.618861 CGTCTGTGTCCGTCTGAATC 58.381 55.000 0.00 0.00 0.00 2.52
8 9 0.243907 CCGTCTGTGTCCGTCTGAAT 59.756 55.000 0.00 0.00 0.00 2.57
9 10 1.105167 ACCGTCTGTGTCCGTCTGAA 61.105 55.000 0.00 0.00 0.00 3.02
10 11 1.105167 AACCGTCTGTGTCCGTCTGA 61.105 55.000 0.00 0.00 0.00 3.27
11 12 0.939577 CAACCGTCTGTGTCCGTCTG 60.940 60.000 0.00 0.00 0.00 3.51
12 13 1.362717 CAACCGTCTGTGTCCGTCT 59.637 57.895 0.00 0.00 0.00 4.18
13 14 1.663702 CCAACCGTCTGTGTCCGTC 60.664 63.158 0.00 0.00 0.00 4.79
14 15 2.083835 CTCCAACCGTCTGTGTCCGT 62.084 60.000 0.00 0.00 0.00 4.69
15 16 1.372997 CTCCAACCGTCTGTGTCCG 60.373 63.158 0.00 0.00 0.00 4.79
16 17 0.106149 AACTCCAACCGTCTGTGTCC 59.894 55.000 0.00 0.00 0.00 4.02
17 18 2.035576 AGTAACTCCAACCGTCTGTGTC 59.964 50.000 0.00 0.00 0.00 3.67
18 19 2.035576 GAGTAACTCCAACCGTCTGTGT 59.964 50.000 0.00 0.00 0.00 3.72
19 20 2.296471 AGAGTAACTCCAACCGTCTGTG 59.704 50.000 0.00 0.00 0.00 3.66
20 21 2.595238 AGAGTAACTCCAACCGTCTGT 58.405 47.619 0.00 0.00 0.00 3.41
21 22 3.662247 AAGAGTAACTCCAACCGTCTG 57.338 47.619 0.00 0.00 0.00 3.51
22 23 3.190118 CGTAAGAGTAACTCCAACCGTCT 59.810 47.826 0.00 0.00 43.02 4.18
23 24 3.057946 ACGTAAGAGTAACTCCAACCGTC 60.058 47.826 0.00 0.00 43.62 4.79
24 25 2.887152 ACGTAAGAGTAACTCCAACCGT 59.113 45.455 0.00 0.00 43.62 4.83
25 26 3.240069 CACGTAAGAGTAACTCCAACCG 58.760 50.000 0.00 0.00 43.62 4.44
26 27 4.248691 ACACGTAAGAGTAACTCCAACC 57.751 45.455 0.00 0.00 40.15 3.77
27 28 5.284079 TGAACACGTAAGAGTAACTCCAAC 58.716 41.667 0.00 0.00 41.43 3.77
28 29 5.518848 TGAACACGTAAGAGTAACTCCAA 57.481 39.130 0.00 0.00 41.43 3.53
29 30 5.163530 TGTTGAACACGTAAGAGTAACTCCA 60.164 40.000 0.00 0.00 41.43 3.86
30 31 5.284079 TGTTGAACACGTAAGAGTAACTCC 58.716 41.667 0.00 0.00 41.43 3.85
31 32 6.817270 TTGTTGAACACGTAAGAGTAACTC 57.183 37.500 0.00 0.00 41.43 3.01
32 33 7.493320 TGATTTGTTGAACACGTAAGAGTAACT 59.507 33.333 0.00 0.00 41.43 2.24
33 34 7.623770 TGATTTGTTGAACACGTAAGAGTAAC 58.376 34.615 0.00 0.00 41.43 2.50
34 35 7.773864 TGATTTGTTGAACACGTAAGAGTAA 57.226 32.000 0.00 0.00 41.43 2.24
35 36 7.773864 TTGATTTGTTGAACACGTAAGAGTA 57.226 32.000 0.00 0.00 41.43 2.59
36 37 6.671614 TTGATTTGTTGAACACGTAAGAGT 57.328 33.333 0.00 0.00 45.27 3.24
37 38 7.855409 TCAATTGATTTGTTGAACACGTAAGAG 59.145 33.333 3.38 0.00 37.42 2.85
38 39 7.698628 TCAATTGATTTGTTGAACACGTAAGA 58.301 30.769 3.38 0.00 37.42 2.10
39 40 7.906611 TCAATTGATTTGTTGAACACGTAAG 57.093 32.000 3.38 0.00 39.03 2.34
40 41 8.689251 TTTCAATTGATTTGTTGAACACGTAA 57.311 26.923 9.40 0.00 42.24 3.18
41 42 7.971168 ACTTTCAATTGATTTGTTGAACACGTA 59.029 29.630 9.40 0.00 42.24 3.57
42 43 6.811170 ACTTTCAATTGATTTGTTGAACACGT 59.189 30.769 9.40 0.00 42.24 4.49
43 44 7.220599 ACTTTCAATTGATTTGTTGAACACG 57.779 32.000 9.40 0.00 42.24 4.49
44 45 9.824534 AAAACTTTCAATTGATTTGTTGAACAC 57.175 25.926 9.40 0.00 42.24 3.32
76 80 2.510768 ACGTCTCTGCGTCTTTCTTT 57.489 45.000 0.00 0.00 41.71 2.52
87 91 1.359848 CGGGATTTTGGACGTCTCTG 58.640 55.000 16.46 0.00 0.00 3.35
91 95 2.030958 ACGCGGGATTTTGGACGTC 61.031 57.895 12.47 7.13 0.00 4.34
230 238 3.764466 CGCTCGGGGACTCTGCTT 61.764 66.667 0.00 0.00 0.00 3.91
755 877 1.474077 GCGTTGATTTCAGGCCAAGAT 59.526 47.619 5.01 0.00 0.00 2.40
773 895 3.680642 ATTGCATGTTACTGCTAAGCG 57.319 42.857 0.00 0.00 42.75 4.68
813 942 3.985019 TTCGGCCAGTATAACCAAGAA 57.015 42.857 2.24 0.00 0.00 2.52
912 1058 4.846779 ACATAATCAACAACAAAGCGGT 57.153 36.364 0.00 0.00 0.00 5.68
913 1059 5.938322 AGTACATAATCAACAACAAAGCGG 58.062 37.500 0.00 0.00 0.00 5.52
1045 1191 2.031333 CACTTCTTTGCACAAGAGCTCC 60.031 50.000 10.93 0.00 34.99 4.70
1051 1197 2.291741 GGAGGACACTTCTTTGCACAAG 59.708 50.000 0.00 0.00 0.00 3.16
1060 1209 0.616111 AGGCGATGGAGGACACTTCT 60.616 55.000 0.00 0.00 0.00 2.85
1078 1260 1.470098 CCCTCGCCAAATCAAAGACAG 59.530 52.381 0.00 0.00 0.00 3.51
1101 1283 4.382577 GCTCCAAGGAAAACAAAAGGTTCA 60.383 41.667 0.00 0.00 39.29 3.18
1110 1292 1.321474 CAGCTGCTCCAAGGAAAACA 58.679 50.000 0.00 0.00 0.00 2.83
1113 1295 1.321474 CAACAGCTGCTCCAAGGAAA 58.679 50.000 15.27 0.00 0.00 3.13
1169 1351 1.068083 TAGGTGCGCATAGCTGCTC 59.932 57.895 15.91 0.00 46.65 4.26
1493 1681 5.528690 TCAATGAAGAGAATTATCTTGCCGG 59.471 40.000 19.59 0.00 39.63 6.13
1880 2173 5.760253 CACAAAAGATCACCTGTAGTTCTGT 59.240 40.000 0.00 0.00 0.00 3.41
1881 2174 5.180117 CCACAAAAGATCACCTGTAGTTCTG 59.820 44.000 0.00 0.00 0.00 3.02
1885 2178 4.706842 ACCACAAAAGATCACCTGTAGT 57.293 40.909 0.00 0.00 0.00 2.73
1886 2179 4.821805 ACAACCACAAAAGATCACCTGTAG 59.178 41.667 0.00 0.00 0.00 2.74
1892 2189 5.036737 CAGACAACAACCACAAAAGATCAC 58.963 41.667 0.00 0.00 0.00 3.06
1908 2205 2.369394 CCTTAAGATGGGGCAGACAAC 58.631 52.381 3.36 0.00 0.00 3.32
2008 2916 2.944349 CAATGCAACAAAAGGGTGCTTT 59.056 40.909 5.89 2.93 0.00 3.51
2069 2980 5.756195 TCAATTTATATGCACAGGACAGC 57.244 39.130 0.00 0.00 0.00 4.40
2109 3020 8.931775 GTGTTATTCGGCATAAAGGAAAATTTT 58.068 29.630 2.28 2.28 0.00 1.82
2276 3269 1.537202 GTACAACAGCTGCTCCCTTTG 59.463 52.381 15.27 12.13 0.00 2.77
2277 3270 1.545651 GGTACAACAGCTGCTCCCTTT 60.546 52.381 15.27 0.00 0.00 3.11
2439 3475 5.351948 ACTTATCCTTCTCTTCTTGCTCC 57.648 43.478 0.00 0.00 0.00 4.70
2466 3502 2.280835 CAGCCTGTCTGCTAGGTGA 58.719 57.895 0.00 0.00 40.32 4.02
2493 3529 0.890683 CTTCATCCTGGCCAACAACC 59.109 55.000 7.01 0.00 0.00 3.77
2652 3689 4.053295 CCAACATCTTTTCACTGCCAAAG 58.947 43.478 0.00 0.00 0.00 2.77
3146 4629 7.336931 ACACTCAAGCTTTAAGTCTTTTCTGAA 59.663 33.333 8.05 0.00 0.00 3.02
3155 4638 5.928839 TGATGAGACACTCAAGCTTTAAGTC 59.071 40.000 8.05 8.60 44.04 3.01
3171 4656 7.219535 GCACAAACAATGTCATAATGATGAGAC 59.780 37.037 0.00 0.00 42.87 3.36
3385 4873 4.323417 CTGTGCTTACTGGGTTGTATGAA 58.677 43.478 0.00 0.00 0.00 2.57
3458 4949 1.875514 TGTGAGAGACAAAGCATGCAC 59.124 47.619 21.98 5.47 0.00 4.57
3585 5108 1.535437 CCTGTTATCCGTAGCACCGAC 60.535 57.143 0.00 0.00 0.00 4.79
3607 5130 5.579718 TCGCTACTTCATACTTGAGCTTAC 58.420 41.667 0.00 0.00 32.27 2.34
3718 5244 0.034380 TAGTGTCACCCTCGCTAGCT 60.034 55.000 13.93 0.00 0.00 3.32
3720 5246 2.492484 ACTTTAGTGTCACCCTCGCTAG 59.508 50.000 0.00 0.00 31.13 3.42
3741 5267 1.121407 AGCGCAGGCCCATCAGTATA 61.121 55.000 11.47 0.00 41.24 1.47
3744 5270 4.479993 GAGCGCAGGCCCATCAGT 62.480 66.667 11.47 0.00 41.24 3.41
3749 5275 4.704833 GTCTTGAGCGCAGGCCCA 62.705 66.667 11.47 0.00 41.24 5.36
3932 5463 7.549488 AGACTGTAATAAAGATACAACCACAGC 59.451 37.037 0.00 0.00 35.43 4.40
3974 5515 5.972107 AGATGAACCCAACAAGAGAATTG 57.028 39.130 0.00 0.00 0.00 2.32
3983 5524 5.423886 GTTTTCCAAAAGATGAACCCAACA 58.576 37.500 0.00 0.00 0.00 3.33
4002 5543 6.790232 TCAAATTCCAAGAGACTTGGTTTT 57.210 33.333 23.82 20.73 40.40 2.43
4131 5744 5.534207 AGATCTACTTCAATCTGCCTCTG 57.466 43.478 0.00 0.00 31.09 3.35
4182 5795 8.871686 AAGTTCGCTATTTTCTTTCACAAATT 57.128 26.923 0.00 0.00 0.00 1.82
4200 5813 5.522824 CCCTTCTTACTACCATTAAGTTCGC 59.477 44.000 0.00 0.00 0.00 4.70
4201 5814 5.522824 GCCCTTCTTACTACCATTAAGTTCG 59.477 44.000 0.00 0.00 0.00 3.95
4218 5832 2.641815 AGTTTCAGAGTGATGCCCTTCT 59.358 45.455 0.00 0.00 0.00 2.85
4224 5838 6.560253 TTTTTAGGAGTTTCAGAGTGATGC 57.440 37.500 0.00 0.00 0.00 3.91
4234 5848 9.286170 AGGTCTCAAACTATTTTTAGGAGTTTC 57.714 33.333 0.00 0.00 40.54 2.78
4277 5901 4.263462 ACAGCCAGACATGTAATTCTTGGA 60.263 41.667 0.00 0.00 0.00 3.53
4332 5956 8.936070 TTCTTGCGCTAGATTAACTTTACATA 57.064 30.769 21.87 0.00 0.00 2.29
4338 5962 5.223225 GCTTTCTTGCGCTAGATTAACTT 57.777 39.130 21.87 0.00 0.00 2.66
4370 5994 8.594687 ACTGAAATTTTGTTGAATTTTCTGTCG 58.405 29.630 0.00 0.00 41.10 4.35
4419 6160 7.761409 TGATTCAAAATTGATTTAGGTCCGAG 58.239 34.615 0.00 0.00 37.00 4.63
4420 6161 7.695480 TGATTCAAAATTGATTTAGGTCCGA 57.305 32.000 0.00 0.00 37.00 4.55
4430 6171 7.920151 TGACGACTTTGTTGATTCAAAATTGAT 59.080 29.630 0.00 0.00 36.96 2.57
4435 6176 6.616947 AGTTGACGACTTTGTTGATTCAAAA 58.383 32.000 0.00 0.00 36.96 2.44
4453 6194 5.854866 GGTTACTTAATTTTGGCGAGTTGAC 59.145 40.000 0.00 0.00 0.00 3.18
4459 6200 5.064558 TGACAGGTTACTTAATTTTGGCGA 58.935 37.500 0.00 0.00 0.00 5.54
4460 6201 5.365403 TGACAGGTTACTTAATTTTGGCG 57.635 39.130 0.00 0.00 0.00 5.69
4473 6214 6.934645 CCAAAAGACTATGAGTTGACAGGTTA 59.065 38.462 0.00 0.00 0.00 2.85
4479 6220 3.440522 GCCCCAAAAGACTATGAGTTGAC 59.559 47.826 0.00 0.00 0.00 3.18
4499 6240 1.337167 GCCATTCTTTGACCAACAGCC 60.337 52.381 0.00 0.00 0.00 4.85
4501 6242 3.731652 TTGCCATTCTTTGACCAACAG 57.268 42.857 0.00 0.00 0.00 3.16
4517 6258 8.396272 AGGACAATATCAACATAGTAATTGCC 57.604 34.615 0.00 0.00 0.00 4.52
4521 6262 9.784531 CTCCAAGGACAATATCAACATAGTAAT 57.215 33.333 0.00 0.00 0.00 1.89
4523 6264 8.319057 ACTCCAAGGACAATATCAACATAGTA 57.681 34.615 0.00 0.00 0.00 1.82
4529 6270 6.879458 AGTGTTACTCCAAGGACAATATCAAC 59.121 38.462 0.00 0.00 0.00 3.18
4531 6272 6.013725 ACAGTGTTACTCCAAGGACAATATCA 60.014 38.462 0.00 0.00 0.00 2.15
4532 6273 6.407202 ACAGTGTTACTCCAAGGACAATATC 58.593 40.000 0.00 0.00 0.00 1.63
4533 6274 6.374417 ACAGTGTTACTCCAAGGACAATAT 57.626 37.500 0.00 0.00 0.00 1.28
4535 6276 4.706842 ACAGTGTTACTCCAAGGACAAT 57.293 40.909 0.00 0.00 0.00 2.71
4542 6850 6.722590 TCAACCTATCTACAGTGTTACTCCAA 59.277 38.462 0.00 0.00 0.00 3.53
4582 6890 2.113860 AATCCATGCACTACAAGCGT 57.886 45.000 0.00 0.00 33.85 5.07
4606 6914 9.313118 TGCACTTCACAAATACTACTACATATG 57.687 33.333 0.00 0.00 0.00 1.78
4608 6916 9.313118 CATGCACTTCACAAATACTACTACATA 57.687 33.333 0.00 0.00 0.00 2.29
4609 6917 7.824289 ACATGCACTTCACAAATACTACTACAT 59.176 33.333 0.00 0.00 0.00 2.29
4610 6918 7.158697 ACATGCACTTCACAAATACTACTACA 58.841 34.615 0.00 0.00 0.00 2.74
4611 6919 7.596749 ACATGCACTTCACAAATACTACTAC 57.403 36.000 0.00 0.00 0.00 2.73
4612 6920 7.119116 CCAACATGCACTTCACAAATACTACTA 59.881 37.037 0.00 0.00 0.00 1.82
4613 6921 6.072508 CCAACATGCACTTCACAAATACTACT 60.073 38.462 0.00 0.00 0.00 2.57
4614 6922 6.086222 CCAACATGCACTTCACAAATACTAC 58.914 40.000 0.00 0.00 0.00 2.73
4615 6923 5.335583 GCCAACATGCACTTCACAAATACTA 60.336 40.000 0.00 0.00 0.00 1.82
4616 6924 4.559300 GCCAACATGCACTTCACAAATACT 60.559 41.667 0.00 0.00 0.00 2.12
4617 6925 3.674753 GCCAACATGCACTTCACAAATAC 59.325 43.478 0.00 0.00 0.00 1.89
4618 6926 3.573538 AGCCAACATGCACTTCACAAATA 59.426 39.130 0.00 0.00 0.00 1.40
4619 6927 2.366266 AGCCAACATGCACTTCACAAAT 59.634 40.909 0.00 0.00 0.00 2.32
4620 6928 1.755959 AGCCAACATGCACTTCACAAA 59.244 42.857 0.00 0.00 0.00 2.83
4621 6929 1.067364 CAGCCAACATGCACTTCACAA 59.933 47.619 0.00 0.00 0.00 3.33
4622 6930 0.669619 CAGCCAACATGCACTTCACA 59.330 50.000 0.00 0.00 0.00 3.58
4623 6931 0.665369 GCAGCCAACATGCACTTCAC 60.665 55.000 0.00 0.00 43.31 3.18
4624 6932 1.661480 GCAGCCAACATGCACTTCA 59.339 52.632 0.00 0.00 43.31 3.02
4625 6933 1.080298 GGCAGCCAACATGCACTTC 60.080 57.895 6.55 0.00 45.68 3.01
4654 6962 0.179059 ATCACACAGACGTTGCACCA 60.179 50.000 0.00 0.00 0.00 4.17
4658 6966 0.792640 CTCCATCACACAGACGTTGC 59.207 55.000 0.00 0.00 0.00 4.17
4659 6967 2.154854 ACTCCATCACACAGACGTTG 57.845 50.000 0.00 0.00 0.00 4.10
4662 6970 4.902443 AGTATACTCCATCACACAGACG 57.098 45.455 0.00 0.00 0.00 4.18
4686 7043 5.900123 AGGACCTAGGTTCTACTACGTACTA 59.100 44.000 22.21 0.00 30.97 1.82
4724 7081 5.011533 CCAAGGAATCTATTCATCTCCGAGT 59.988 44.000 5.15 0.00 38.53 4.18
4727 7084 5.233988 GTCCAAGGAATCTATTCATCTCCG 58.766 45.833 5.15 0.00 38.53 4.63
4738 7095 5.067805 GCAATTAATTCGGTCCAAGGAATCT 59.932 40.000 0.00 0.00 31.95 2.40
4739 7096 5.281727 GCAATTAATTCGGTCCAAGGAATC 58.718 41.667 0.00 0.00 31.95 2.52
4759 7116 2.035704 ACAAACAATGCTTGATCGGCAA 59.964 40.909 15.33 2.34 43.14 4.52
4761 7118 2.352503 ACAAACAATGCTTGATCGGC 57.647 45.000 3.15 3.88 0.00 5.54
4762 7119 3.899734 TCAACAAACAATGCTTGATCGG 58.100 40.909 3.15 0.00 29.80 4.18
4764 7121 5.472148 TCCATCAACAAACAATGCTTGATC 58.528 37.500 3.15 0.00 37.52 2.92
4765 7122 5.471556 TCCATCAACAAACAATGCTTGAT 57.528 34.783 3.15 0.00 38.84 2.57
4766 7123 4.933505 TCCATCAACAAACAATGCTTGA 57.066 36.364 3.15 0.00 35.24 3.02
4767 7124 5.987777 TTTCCATCAACAAACAATGCTTG 57.012 34.783 0.00 0.00 0.00 4.01
4772 7170 7.507829 TCCTTCATTTTCCATCAACAAACAAT 58.492 30.769 0.00 0.00 0.00 2.71
4795 7193 5.920840 GCAAAGTGGAAGAAAAAGTGTATCC 59.079 40.000 0.00 0.00 0.00 2.59
4797 7195 6.321181 TCAGCAAAGTGGAAGAAAAAGTGTAT 59.679 34.615 0.00 0.00 0.00 2.29
4798 7196 5.650266 TCAGCAAAGTGGAAGAAAAAGTGTA 59.350 36.000 0.00 0.00 0.00 2.90
4811 8789 1.588082 GTGGGCATCAGCAAAGTGG 59.412 57.895 0.00 0.00 44.61 4.00
4843 8821 0.740868 CCTCACGTGACCATCGCAAT 60.741 55.000 15.76 0.00 0.00 3.56
4848 8826 0.173708 GACTCCCTCACGTGACCATC 59.826 60.000 15.76 4.56 0.00 3.51
4896 8874 3.077556 CTGGACGACAGGGGAGGG 61.078 72.222 0.00 0.00 43.70 4.30
4904 8882 0.384309 GACACACAGACTGGACGACA 59.616 55.000 7.51 0.00 0.00 4.35
4905 8883 0.318784 GGACACACAGACTGGACGAC 60.319 60.000 7.51 0.00 0.00 4.34
4906 8884 1.461091 GGGACACACAGACTGGACGA 61.461 60.000 7.51 0.00 0.00 4.20
4907 8885 1.006102 GGGACACACAGACTGGACG 60.006 63.158 7.51 0.00 0.00 4.79
4908 8886 1.371558 GGGGACACACAGACTGGAC 59.628 63.158 7.51 0.00 0.00 4.02
4909 8887 1.841556 GGGGGACACACAGACTGGA 60.842 63.158 7.51 0.00 0.00 3.86
4910 8888 1.705002 TTGGGGGACACACAGACTGG 61.705 60.000 7.51 0.00 0.00 4.00
4911 8889 0.401738 ATTGGGGGACACACAGACTG 59.598 55.000 0.00 0.00 0.00 3.51
4912 8890 0.693049 GATTGGGGGACACACAGACT 59.307 55.000 0.00 0.00 0.00 3.24
4913 8891 0.322546 GGATTGGGGGACACACAGAC 60.323 60.000 0.00 0.00 0.00 3.51
4914 8892 1.497309 GGGATTGGGGGACACACAGA 61.497 60.000 0.00 0.00 0.00 3.41
4915 8893 1.000896 GGGATTGGGGGACACACAG 60.001 63.158 0.00 0.00 0.00 3.66
4916 8894 2.543797 GGGGATTGGGGGACACACA 61.544 63.158 0.00 0.00 0.00 3.72
4917 8895 2.359011 GGGGATTGGGGGACACAC 59.641 66.667 0.00 0.00 0.00 3.82
4918 8896 2.944390 GGGGGATTGGGGGACACA 60.944 66.667 0.00 0.00 0.00 3.72
4919 8897 2.100525 TTTGGGGGATTGGGGGACAC 62.101 60.000 0.00 0.00 0.00 3.67
4920 8898 1.380280 TTTTGGGGGATTGGGGGACA 61.380 55.000 0.00 0.00 0.00 4.02
4921 8899 0.178888 TTTTTGGGGGATTGGGGGAC 60.179 55.000 0.00 0.00 0.00 4.46
4922 8900 2.276077 TTTTTGGGGGATTGGGGGA 58.724 52.632 0.00 0.00 0.00 4.81
4937 8915 4.170468 TCAAGAGAGAAGGTGGCTTTTT 57.830 40.909 0.00 0.00 0.00 1.94
4938 8916 3.864789 TCAAGAGAGAAGGTGGCTTTT 57.135 42.857 0.00 0.00 0.00 2.27
4939 8917 3.392616 TCTTCAAGAGAGAAGGTGGCTTT 59.607 43.478 4.11 0.00 44.01 3.51
4940 8918 2.975489 TCTTCAAGAGAGAAGGTGGCTT 59.025 45.455 4.11 0.00 44.01 4.35
4941 8919 2.614259 TCTTCAAGAGAGAAGGTGGCT 58.386 47.619 4.11 0.00 44.01 4.75


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

AutoCloner maintained by Alex Coulton.