Multiple sequence alignment - TraesCS5D01G025300

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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 TraesCS5D01G025300 chr5D 100.000 4902 0 0 780 5681 22445138 22440237 0.000000e+00 9053.0
1 TraesCS5D01G025300 chr5D 100.000 551 0 0 1 551 22445917 22445367 0.000000e+00 1018.0
2 TraesCS5D01G025300 chr5B 95.837 4108 135 19 885 4977 16037700 16033614 0.000000e+00 6606.0
3 TraesCS5D01G025300 chr5B 88.942 624 41 13 5046 5647 16033619 16033002 0.000000e+00 745.0
4 TraesCS5D01G025300 chr5B 89.737 419 43 0 6 424 593297283 593296865 2.330000e-148 536.0
5 TraesCS5D01G025300 chr5B 78.218 202 26 10 993 1181 641028668 641028472 4.650000e-21 113.0
6 TraesCS5D01G025300 chr5B 87.356 87 10 1 5396 5481 594886827 594886913 1.300000e-16 99.0
7 TraesCS5D01G025300 chr6D 93.390 1543 96 2 3348 4890 68332455 68333991 0.000000e+00 2279.0
8 TraesCS5D01G025300 chr6D 92.721 1360 94 4 1982 3337 68331134 68332492 0.000000e+00 1958.0
9 TraesCS5D01G025300 chr6D 85.646 1045 81 27 968 1986 68330107 68331108 0.000000e+00 1035.0
10 TraesCS5D01G025300 chr6D 88.211 246 21 8 283 527 468557403 468557641 2.590000e-73 287.0
11 TraesCS5D01G025300 chr6D 84.774 243 17 20 303 528 429328557 429328796 5.730000e-55 226.0
12 TraesCS5D01G025300 chr6A 93.260 1543 98 2 3348 4890 85750196 85751732 0.000000e+00 2268.0
13 TraesCS5D01G025300 chr6A 92.721 1360 94 4 1982 3337 85748875 85750233 0.000000e+00 1958.0
14 TraesCS5D01G025300 chr6A 85.824 1044 78 28 968 1986 85747851 85748849 0.000000e+00 1044.0
15 TraesCS5D01G025300 chr6A 90.909 77 7 0 5396 5472 435249454 435249378 2.800000e-18 104.0
16 TraesCS5D01G025300 chr6B 93.195 1543 99 2 3348 4890 143437357 143438893 0.000000e+00 2263.0
17 TraesCS5D01G025300 chr6B 92.212 1361 99 5 1982 3337 143436036 143437394 0.000000e+00 1919.0
18 TraesCS5D01G025300 chr6B 85.153 1044 85 28 968 1986 143435012 143436010 0.000000e+00 1005.0
19 TraesCS5D01G025300 chr6B 82.353 102 15 3 5375 5476 456208204 456208302 1.010000e-12 86.1
20 TraesCS5D01G025300 chr3D 91.981 424 26 1 1 424 159121691 159121276 6.340000e-164 588.0
21 TraesCS5D01G025300 chr3D 85.663 279 17 18 233 511 135170638 135170893 7.250000e-69 272.0
22 TraesCS5D01G025300 chr3D 88.608 79 9 0 5396 5474 185070585 185070507 4.690000e-16 97.1
23 TraesCS5D01G025300 chr3D 86.905 84 9 2 5388 5471 231319099 231319018 6.060000e-15 93.5
24 TraesCS5D01G025300 chr3D 97.436 39 1 0 1 39 135170201 135170239 3.670000e-07 67.6
25 TraesCS5D01G025300 chrUn 91.379 348 22 6 83 424 291715792 291716137 2.400000e-128 470.0
26 TraesCS5D01G025300 chrUn 91.379 348 22 6 83 424 291933329 291933674 2.400000e-128 470.0
27 TraesCS5D01G025300 chrUn 91.379 348 22 6 83 424 302329688 302330033 2.400000e-128 470.0
28 TraesCS5D01G025300 chrUn 96.460 113 4 0 1 113 291715554 291715666 2.700000e-43 187.0
29 TraesCS5D01G025300 chrUn 96.460 113 4 0 1 113 291933091 291933203 2.700000e-43 187.0
30 TraesCS5D01G025300 chrUn 96.460 113 4 0 1 113 302329450 302329562 2.700000e-43 187.0
31 TraesCS5D01G025300 chr7A 90.449 356 26 4 75 424 299411160 299411513 4.010000e-126 462.0
32 TraesCS5D01G025300 chr7A 95.575 113 5 0 1 113 299410930 299411042 1.260000e-41 182.0
33 TraesCS5D01G025300 chr7D 89.474 323 16 8 108 424 366749803 366749493 5.340000e-105 392.0
34 TraesCS5D01G025300 chr7D 89.189 222 17 7 291 511 87177172 87176957 2.610000e-68 270.0
35 TraesCS5D01G025300 chr7D 95.455 132 6 0 1 132 366749940 366749809 1.600000e-50 211.0
36 TraesCS5D01G025300 chr7D 86.667 90 10 2 5382 5471 66823330 66823417 1.300000e-16 99.0
37 TraesCS5D01G025300 chr3B 86.316 95 10 3 5388 5481 771737744 771737652 3.620000e-17 100.0
38 TraesCS5D01G025300 chr1A 87.209 86 9 2 5387 5471 507081757 507081841 4.690000e-16 97.1
39 TraesCS5D01G025300 chr2B 94.286 35 2 0 5538 5572 795575846 795575880 3.000000e-03 54.7


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 TraesCS5D01G025300 chr5D 22440237 22445917 5680 True 5035.500000 9053 100.000000 1 5681 2 chr5D.!!$R1 5680
1 TraesCS5D01G025300 chr5B 16033002 16037700 4698 True 3675.500000 6606 92.389500 885 5647 2 chr5B.!!$R3 4762
2 TraesCS5D01G025300 chr6D 68330107 68333991 3884 False 1757.333333 2279 90.585667 968 4890 3 chr6D.!!$F3 3922
3 TraesCS5D01G025300 chr6A 85747851 85751732 3881 False 1756.666667 2268 90.601667 968 4890 3 chr6A.!!$F1 3922
4 TraesCS5D01G025300 chr6B 143435012 143438893 3881 False 1729.000000 2263 90.186667 968 4890 3 chr6B.!!$F2 3922
5 TraesCS5D01G025300 chrUn 291715554 291716137 583 False 328.500000 470 93.919500 1 424 2 chrUn.!!$F1 423
6 TraesCS5D01G025300 chrUn 291933091 291933674 583 False 328.500000 470 93.919500 1 424 2 chrUn.!!$F2 423
7 TraesCS5D01G025300 chrUn 302329450 302330033 583 False 328.500000 470 93.919500 1 424 2 chrUn.!!$F3 423
8 TraesCS5D01G025300 chr7A 299410930 299411513 583 False 322.000000 462 93.012000 1 424 2 chr7A.!!$F1 423

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
166 329 0.175989 CTTCCTCCGTAAGTCAGCCC 59.824 60.000 0.00 0.0 0.00 5.19 F
877 1040 0.179001 CCCCAGTTTCCAAGTCGGTT 60.179 55.000 0.00 0.0 35.57 4.44 F
961 1125 0.249868 TCGCCTAATTCCCATCGCTG 60.250 55.000 0.00 0.0 0.00 5.18 F
1548 1746 0.393673 GAGCCAAGGAGAAGAAGGCC 60.394 60.000 0.00 0.0 46.35 5.19 F
2190 2421 1.219664 GTACCAGCCCATACGCACA 59.780 57.895 0.00 0.0 0.00 4.57 F
3729 3960 0.239347 GAGCTGTTGTGAATGCGCTT 59.761 50.000 9.73 0.0 0.00 4.68 F
3870 4101 1.376466 GAAGCAGTGCCAGGAGGAA 59.624 57.895 12.58 0.0 36.89 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 1762 0.040514 CGTTTTGTCAATGCGGCTGA 60.041 50.000 0.00 0.0 0.00 4.26 R
1990 2188 1.004560 TGGCAAGGTTCTCTGCTCG 60.005 57.895 0.00 0.0 0.00 5.03 R
2190 2421 1.152368 AAGCAGCTTCCTTGCAGGT 59.848 52.632 0.21 0.0 43.92 4.00 R
2447 2678 1.217882 CTGCCGAAGTGACGTCTTTT 58.782 50.000 17.92 10.8 0.00 2.27 R
3870 4101 0.620556 CCAGGTGACCCATAAGCTGT 59.379 55.000 0.00 0.0 39.68 4.40 R
4566 4797 0.038744 CATCCTCACAACCCAAGCCT 59.961 55.000 0.00 0.0 0.00 4.58 R
4845 5076 0.803768 CTGGACGGCTGAAGATGTCG 60.804 60.000 0.00 0.0 32.17 4.35 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
139 296 4.266739 CCGTGCTGGTGTTTTTCTTTTTAC 59.733 41.667 0.00 0.00 0.00 2.01
157 314 1.629043 ACAGAACTGCTTCCTCCGTA 58.371 50.000 1.46 0.00 0.00 4.02
166 329 0.175989 CTTCCTCCGTAAGTCAGCCC 59.824 60.000 0.00 0.00 0.00 5.19
251 414 1.566018 CGAAGGTCCAGCCGTTCAAC 61.566 60.000 0.00 0.00 43.70 3.18
268 431 1.080298 AACGCACGAAGAAACACACA 58.920 45.000 0.00 0.00 0.00 3.72
273 436 2.891391 CACGAAGAAACACACATGACG 58.109 47.619 0.00 0.00 0.00 4.35
276 439 3.488310 ACGAAGAAACACACATGACGTAC 59.512 43.478 0.00 0.00 0.00 3.67
289 452 2.033372 TGACGTACCAACAGAAGGACA 58.967 47.619 0.00 0.00 0.00 4.02
315 478 3.371273 GGACCCCAAATTAGTACCACCTC 60.371 52.174 0.00 0.00 0.00 3.85
334 497 9.403583 ACCACCTCGTTTATATTATGATTTTGT 57.596 29.630 0.00 0.00 0.00 2.83
352 515 8.873830 TGATTTTGTCTTTGCAAATCGTAAAAA 58.126 25.926 13.23 14.36 38.05 1.94
424 587 9.950680 CAAAGTCAATCCGTGCTTTATTATTAT 57.049 29.630 0.00 0.00 34.13 1.28
847 1010 9.190858 TGAAATTTGATGTTTGATTTAAGTCGG 57.809 29.630 0.00 0.00 0.00 4.79
848 1011 9.191995 GAAATTTGATGTTTGATTTAAGTCGGT 57.808 29.630 0.00 0.00 0.00 4.69
849 1012 9.541143 AAATTTGATGTTTGATTTAAGTCGGTT 57.459 25.926 0.00 0.00 0.00 4.44
850 1013 8.742554 ATTTGATGTTTGATTTAAGTCGGTTC 57.257 30.769 0.00 0.00 0.00 3.62
851 1014 5.922546 TGATGTTTGATTTAAGTCGGTTCG 58.077 37.500 0.00 0.00 0.00 3.95
852 1015 5.467399 TGATGTTTGATTTAAGTCGGTTCGT 59.533 36.000 0.00 0.00 0.00 3.85
853 1016 5.738118 TGTTTGATTTAAGTCGGTTCGTT 57.262 34.783 0.00 0.00 0.00 3.85
854 1017 5.503498 TGTTTGATTTAAGTCGGTTCGTTG 58.497 37.500 0.00 0.00 0.00 4.10
855 1018 3.799137 TGATTTAAGTCGGTTCGTTGC 57.201 42.857 0.00 0.00 0.00 4.17
856 1019 2.156117 TGATTTAAGTCGGTTCGTTGCG 59.844 45.455 0.00 0.00 0.00 4.85
857 1020 1.569708 TTTAAGTCGGTTCGTTGCGT 58.430 45.000 0.00 0.00 0.00 5.24
858 1021 1.130955 TTAAGTCGGTTCGTTGCGTC 58.869 50.000 0.00 0.00 0.00 5.19
859 1022 0.664166 TAAGTCGGTTCGTTGCGTCC 60.664 55.000 0.00 0.00 0.00 4.79
860 1023 3.408851 GTCGGTTCGTTGCGTCCC 61.409 66.667 0.00 0.00 0.00 4.46
861 1024 4.668118 TCGGTTCGTTGCGTCCCC 62.668 66.667 0.00 0.00 0.00 4.81
862 1025 4.973055 CGGTTCGTTGCGTCCCCA 62.973 66.667 0.00 0.00 0.00 4.96
863 1026 3.047877 GGTTCGTTGCGTCCCCAG 61.048 66.667 0.00 0.00 0.00 4.45
864 1027 2.280592 GTTCGTTGCGTCCCCAGT 60.281 61.111 0.00 0.00 0.00 4.00
865 1028 1.890510 GTTCGTTGCGTCCCCAGTT 60.891 57.895 0.00 0.00 0.00 3.16
866 1029 1.153127 TTCGTTGCGTCCCCAGTTT 60.153 52.632 0.00 0.00 0.00 2.66
867 1030 1.161563 TTCGTTGCGTCCCCAGTTTC 61.162 55.000 0.00 0.00 0.00 2.78
868 1031 2.613506 CGTTGCGTCCCCAGTTTCC 61.614 63.158 0.00 0.00 0.00 3.13
869 1032 1.527380 GTTGCGTCCCCAGTTTCCA 60.527 57.895 0.00 0.00 0.00 3.53
870 1033 1.104577 GTTGCGTCCCCAGTTTCCAA 61.105 55.000 0.00 0.00 0.00 3.53
871 1034 0.821711 TTGCGTCCCCAGTTTCCAAG 60.822 55.000 0.00 0.00 0.00 3.61
872 1035 1.228154 GCGTCCCCAGTTTCCAAGT 60.228 57.895 0.00 0.00 0.00 3.16
873 1036 1.235281 GCGTCCCCAGTTTCCAAGTC 61.235 60.000 0.00 0.00 0.00 3.01
874 1037 0.949105 CGTCCCCAGTTTCCAAGTCG 60.949 60.000 0.00 0.00 0.00 4.18
875 1038 0.605589 GTCCCCAGTTTCCAAGTCGG 60.606 60.000 0.00 0.00 0.00 4.79
876 1039 1.057851 TCCCCAGTTTCCAAGTCGGT 61.058 55.000 0.00 0.00 35.57 4.69
877 1040 0.179001 CCCCAGTTTCCAAGTCGGTT 60.179 55.000 0.00 0.00 35.57 4.44
878 1041 1.235724 CCCAGTTTCCAAGTCGGTTC 58.764 55.000 0.00 0.00 35.57 3.62
879 1042 0.865769 CCAGTTTCCAAGTCGGTTCG 59.134 55.000 0.00 0.00 35.57 3.95
880 1043 1.578583 CAGTTTCCAAGTCGGTTCGT 58.421 50.000 0.00 0.00 35.57 3.85
881 1044 1.937899 CAGTTTCCAAGTCGGTTCGTT 59.062 47.619 0.00 0.00 35.57 3.85
882 1045 2.353579 CAGTTTCCAAGTCGGTTCGTTT 59.646 45.455 0.00 0.00 35.57 3.60
883 1046 3.011818 AGTTTCCAAGTCGGTTCGTTTT 58.988 40.909 0.00 0.00 35.57 2.43
896 1059 9.985730 AGTCGGTTCGTTTTATATATAATCCAA 57.014 29.630 6.01 0.00 0.00 3.53
923 1086 1.005332 TGGGATTTGCCTGATCCGAAA 59.995 47.619 0.00 0.00 43.28 3.46
931 1094 1.886655 GCCTGATCCGAAACCCAAACT 60.887 52.381 0.00 0.00 0.00 2.66
936 1100 1.151908 CCGAAACCCAAACTCCCCA 59.848 57.895 0.00 0.00 0.00 4.96
955 1119 3.287222 CCAAAATCTCGCCTAATTCCCA 58.713 45.455 0.00 0.00 0.00 4.37
961 1125 0.249868 TCGCCTAATTCCCATCGCTG 60.250 55.000 0.00 0.00 0.00 5.18
962 1126 1.845809 CGCCTAATTCCCATCGCTGC 61.846 60.000 0.00 0.00 0.00 5.25
981 1145 4.090588 CCCCGCGAAACCCTAGCA 62.091 66.667 8.23 0.00 0.00 3.49
1350 1548 3.885521 GAGGACGACTACCGCCGG 61.886 72.222 0.00 0.00 43.32 6.13
1513 1711 4.339814 GGGAGATCGCTAAGAAGAAGAAGA 59.660 45.833 0.00 0.00 0.00 2.87
1548 1746 0.393673 GAGCCAAGGAGAAGAAGGCC 60.394 60.000 0.00 0.00 46.35 5.19
1614 1812 2.060980 GGATCAGTCGCAGGAGGGT 61.061 63.158 0.00 0.00 0.00 4.34
1796 1994 1.454976 CAGGGAGGATGGCTGATGG 59.545 63.158 0.00 0.00 0.00 3.51
1878 2076 2.042464 TGGGATGCTACTCCTAAGCTG 58.958 52.381 0.00 0.00 40.73 4.24
1879 2077 1.270571 GGGATGCTACTCCTAAGCTGC 60.271 57.143 0.00 0.00 40.73 5.25
1880 2078 1.691434 GGATGCTACTCCTAAGCTGCT 59.309 52.381 0.00 0.00 40.73 4.24
1990 2188 2.325082 ACGGCAGCGACACCATTTC 61.325 57.895 0.00 0.00 0.00 2.17
2039 2270 2.113774 CCACCTTGCTGCTGTCCA 59.886 61.111 0.00 0.00 0.00 4.02
2072 2303 3.511477 AGTATTACCATCTCCTGCGGAT 58.489 45.455 0.00 0.00 0.00 4.18
2160 2391 4.191544 CGCAGGGATACAAGATTCTTGAA 58.808 43.478 28.60 0.00 39.74 2.69
2169 2400 3.181440 ACAAGATTCTTGAACCTCCAGCA 60.181 43.478 28.60 0.00 0.00 4.41
2190 2421 1.219664 GTACCAGCCCATACGCACA 59.780 57.895 0.00 0.00 0.00 4.57
2982 3213 7.493971 CACCTTAAGAACCTAGTTGAGATCATG 59.506 40.741 3.36 0.00 0.00 3.07
3343 3574 5.453567 TGATTATATCCGGAGTCAGTGTG 57.546 43.478 11.34 0.00 0.00 3.82
3371 3602 3.324846 AGCACACAGTGTTTAGATCCTGA 59.675 43.478 2.45 0.00 35.75 3.86
3383 3614 5.984695 TTAGATCCTGATTGTATCCGGAG 57.015 43.478 11.34 0.00 44.30 4.63
3389 3620 3.491619 CCTGATTGTATCCGGAGTCACAG 60.492 52.174 11.34 14.39 35.89 3.66
3390 3621 3.361786 TGATTGTATCCGGAGTCACAGA 58.638 45.455 11.34 5.78 0.00 3.41
3513 3744 3.890147 AGGTGGGAGTTACTGATATCGTC 59.110 47.826 0.00 0.00 0.00 4.20
3604 3835 0.694196 GGTGGTGGCTAACTTGGGTA 59.306 55.000 0.00 0.00 0.00 3.69
3729 3960 0.239347 GAGCTGTTGTGAATGCGCTT 59.761 50.000 9.73 0.00 0.00 4.68
3870 4101 1.376466 GAAGCAGTGCCAGGAGGAA 59.624 57.895 12.58 0.00 36.89 3.36
3954 4185 1.470098 CTGGGTTCAATTCTTGGAGCG 59.530 52.381 0.00 0.00 37.53 5.03
3966 4197 2.027192 TCTTGGAGCGTTGAAGGCTATT 60.027 45.455 12.75 0.00 39.71 1.73
3969 4200 2.084546 GGAGCGTTGAAGGCTATTGTT 58.915 47.619 12.75 0.00 39.71 2.83
4024 4255 5.181748 CAATCAAGGATCTTCTTCCTCGTT 58.818 41.667 0.00 0.00 45.63 3.85
4041 4272 2.158593 TCGTTTGACCCCCATCTTGAAA 60.159 45.455 0.00 0.00 0.00 2.69
4056 4287 7.364056 CCCATCTTGAAAAATAGGCATGAGAAA 60.364 37.037 0.00 0.00 0.00 2.52
4193 4424 5.333581 TCACAAGAAGGGTATCAGAAGAGA 58.666 41.667 0.00 0.00 0.00 3.10
4356 4587 1.733526 GCCGTTCACAGTTTTGCCT 59.266 52.632 0.00 0.00 0.00 4.75
4470 4701 7.177184 AGATGGGCAAAGATTACATATATGCA 58.823 34.615 12.79 0.00 34.14 3.96
4485 4716 2.359230 GCAGTCGCTCCCTTGCTT 60.359 61.111 0.00 0.00 33.88 3.91
4566 4797 2.224378 GCATATGGCTCTAGGAGTTGCA 60.224 50.000 4.56 0.00 40.25 4.08
4662 4893 4.149511 TCTCATAAATGCCGTCATGGAA 57.850 40.909 0.00 0.00 42.00 3.53
4678 4909 1.343069 GGAAGCTATCGAGGGGATGT 58.657 55.000 0.00 0.00 36.55 3.06
4822 5053 3.084786 GCACTTGTGGCTTCTTATCCTT 58.915 45.455 2.81 0.00 0.00 3.36
4824 5055 3.691609 CACTTGTGGCTTCTTATCCTTCC 59.308 47.826 0.00 0.00 0.00 3.46
4996 5228 9.745880 ATCAGTATTCTGTTATAACACTTACGG 57.254 33.333 14.35 14.65 41.91 4.02
4997 5229 8.742777 TCAGTATTCTGTTATAACACTTACGGT 58.257 33.333 14.35 1.31 41.91 4.83
5000 5232 9.787532 GTATTCTGTTATAACACTTACGGTACA 57.212 33.333 14.35 0.00 34.70 2.90
5002 5234 9.880157 ATTCTGTTATAACACTTACGGTACAAT 57.120 29.630 14.35 0.00 34.70 2.71
5003 5235 8.915871 TCTGTTATAACACTTACGGTACAATC 57.084 34.615 14.35 0.00 34.70 2.67
5004 5236 8.522003 TCTGTTATAACACTTACGGTACAATCA 58.478 33.333 14.35 0.00 34.70 2.57
5005 5237 8.692110 TGTTATAACACTTACGGTACAATCAG 57.308 34.615 14.35 0.00 33.17 2.90
5006 5238 7.276218 TGTTATAACACTTACGGTACAATCAGC 59.724 37.037 14.35 0.00 33.17 4.26
5007 5239 3.955650 ACACTTACGGTACAATCAGCT 57.044 42.857 0.00 0.00 0.00 4.24
5008 5240 5.395682 AACACTTACGGTACAATCAGCTA 57.604 39.130 0.00 0.00 0.00 3.32
5009 5241 4.995124 ACACTTACGGTACAATCAGCTAG 58.005 43.478 0.00 0.00 0.00 3.42
5010 5242 4.461781 ACACTTACGGTACAATCAGCTAGT 59.538 41.667 0.00 0.00 0.00 2.57
5011 5243 4.798907 CACTTACGGTACAATCAGCTAGTG 59.201 45.833 0.00 0.00 0.00 2.74
5012 5244 4.461781 ACTTACGGTACAATCAGCTAGTGT 59.538 41.667 0.00 0.00 40.15 3.55
5013 5245 3.232213 ACGGTACAATCAGCTAGTGTG 57.768 47.619 6.41 0.00 36.94 3.82
5014 5246 2.823747 ACGGTACAATCAGCTAGTGTGA 59.176 45.455 6.41 0.09 36.94 3.58
5015 5247 3.179830 CGGTACAATCAGCTAGTGTGAC 58.820 50.000 6.41 2.35 36.94 3.67
5016 5248 3.522553 GGTACAATCAGCTAGTGTGACC 58.477 50.000 6.41 6.48 36.94 4.02
5017 5249 3.056107 GGTACAATCAGCTAGTGTGACCA 60.056 47.826 6.41 0.00 36.94 4.02
5018 5250 3.045601 ACAATCAGCTAGTGTGACCAC 57.954 47.619 0.00 0.00 42.17 4.16
5019 5251 2.368548 ACAATCAGCTAGTGTGACCACA 59.631 45.455 0.00 0.00 44.39 4.17
5020 5252 3.008375 ACAATCAGCTAGTGTGACCACAT 59.992 43.478 6.10 0.00 44.39 3.21
5021 5253 2.749280 TCAGCTAGTGTGACCACATG 57.251 50.000 6.10 0.00 44.39 3.21
5022 5254 1.970640 TCAGCTAGTGTGACCACATGT 59.029 47.619 6.10 0.00 44.39 3.21
5023 5255 2.029020 TCAGCTAGTGTGACCACATGTC 60.029 50.000 6.10 0.00 44.39 3.06
5036 5268 5.953183 GACCACATGTCATTTTAGCATTCA 58.047 37.500 0.00 0.00 43.85 2.57
5037 5269 6.343716 ACCACATGTCATTTTAGCATTCAA 57.656 33.333 0.00 0.00 0.00 2.69
5038 5270 6.392354 ACCACATGTCATTTTAGCATTCAAG 58.608 36.000 0.00 0.00 0.00 3.02
5039 5271 5.290158 CCACATGTCATTTTAGCATTCAAGC 59.710 40.000 0.00 0.00 0.00 4.01
5040 5272 5.865013 CACATGTCATTTTAGCATTCAAGCA 59.135 36.000 0.00 0.00 36.85 3.91
5041 5273 6.034577 CACATGTCATTTTAGCATTCAAGCAG 59.965 38.462 0.00 0.00 36.85 4.24
5042 5274 5.710513 TGTCATTTTAGCATTCAAGCAGT 57.289 34.783 0.00 0.00 36.85 4.40
5043 5275 6.816134 TGTCATTTTAGCATTCAAGCAGTA 57.184 33.333 0.00 0.00 36.85 2.74
5044 5276 6.845302 TGTCATTTTAGCATTCAAGCAGTAG 58.155 36.000 0.00 0.00 36.85 2.57
5050 5282 2.486982 AGCATTCAAGCAGTAGCAAGTG 59.513 45.455 0.00 0.00 45.49 3.16
5053 5285 2.638480 TCAAGCAGTAGCAAGTGGTT 57.362 45.000 0.00 0.00 45.38 3.67
5059 5291 6.040391 TCAAGCAGTAGCAAGTGGTTTTTAAT 59.960 34.615 0.00 0.00 42.66 1.40
5062 5294 5.858581 GCAGTAGCAAGTGGTTTTTAATCTG 59.141 40.000 0.00 0.00 41.58 2.90
5077 5309 5.825593 TTAATCTGTCTTGTCACCTTCCT 57.174 39.130 0.00 0.00 0.00 3.36
5079 5311 4.713792 ATCTGTCTTGTCACCTTCCTTT 57.286 40.909 0.00 0.00 0.00 3.11
5110 5345 3.753294 TTTGGTGTGGTGTGTTTTTGT 57.247 38.095 0.00 0.00 0.00 2.83
5174 5413 3.517602 GCAGGATGTACATGTTCACGTA 58.482 45.455 14.43 0.00 39.31 3.57
5176 5415 4.570772 GCAGGATGTACATGTTCACGTATT 59.429 41.667 14.43 0.00 39.31 1.89
5306 5547 3.305813 CCTGGTGTTACTTCTTGCGTCTA 60.306 47.826 0.00 0.00 0.00 2.59
5307 5548 4.495422 CTGGTGTTACTTCTTGCGTCTAT 58.505 43.478 0.00 0.00 0.00 1.98
5308 5549 4.491676 TGGTGTTACTTCTTGCGTCTATC 58.508 43.478 0.00 0.00 0.00 2.08
5523 5771 6.449635 AAAGTATTGCTAAAATCCGATGCA 57.550 33.333 0.00 0.00 0.00 3.96
5526 5774 3.763097 TTGCTAAAATCCGATGCACTG 57.237 42.857 0.00 0.00 33.13 3.66
5529 5777 2.939103 GCTAAAATCCGATGCACTGACT 59.061 45.455 0.00 0.00 0.00 3.41
5534 5782 1.795768 TCCGATGCACTGACTGTTTC 58.204 50.000 0.00 0.00 0.00 2.78
5535 5783 0.439985 CCGATGCACTGACTGTTTCG 59.560 55.000 0.00 0.00 0.00 3.46
5539 5787 1.295792 TGCACTGACTGTTTCGGAAC 58.704 50.000 0.00 0.00 34.26 3.62
5542 5790 1.261619 CACTGACTGTTTCGGAACTGC 59.738 52.381 12.96 7.07 38.01 4.40
5544 5792 1.795286 CTGACTGTTTCGGAACTGCTC 59.205 52.381 12.96 10.17 38.01 4.26
5556 5804 2.294512 GGAACTGCTCTGTTTTTCAGGG 59.705 50.000 0.00 0.00 46.73 4.45
5562 5810 3.513515 TGCTCTGTTTTTCAGGGTGTTTT 59.486 39.130 0.00 0.00 45.80 2.43
5568 5816 2.534042 TTTCAGGGTGTTTTGGTCCA 57.466 45.000 0.00 0.00 0.00 4.02
5584 5832 0.033504 TCCAAGTGTGCCGAAGAGTC 59.966 55.000 0.00 0.00 0.00 3.36
5586 5834 1.541233 CCAAGTGTGCCGAAGAGTCTT 60.541 52.381 4.68 4.68 0.00 3.01
5595 5843 3.706594 TGCCGAAGAGTCTTATCTGGATT 59.293 43.478 5.09 0.00 0.00 3.01
5609 5857 1.381191 GGATTTGGGACCGGGCATT 60.381 57.895 11.00 0.00 0.00 3.56
5625 5877 3.210012 ATTGCAAGGGCCGAGTGGT 62.210 57.895 4.94 0.00 40.13 4.16
5639 5891 2.470257 CGAGTGGTGTGTTTACTTCGTC 59.530 50.000 0.00 0.00 0.00 4.20
5642 5894 1.210870 GGTGTGTTTACTTCGTCGCA 58.789 50.000 0.00 0.00 0.00 5.10
5643 5895 1.191647 GGTGTGTTTACTTCGTCGCAG 59.808 52.381 0.00 0.00 0.00 5.18
5644 5896 1.856597 GTGTGTTTACTTCGTCGCAGT 59.143 47.619 2.49 2.49 0.00 4.40
5645 5897 1.855978 TGTGTTTACTTCGTCGCAGTG 59.144 47.619 7.84 0.00 0.00 3.66
5646 5898 1.856597 GTGTTTACTTCGTCGCAGTGT 59.143 47.619 7.84 0.00 0.00 3.55
5647 5899 3.044986 GTGTTTACTTCGTCGCAGTGTA 58.955 45.455 7.84 0.00 0.00 2.90
5648 5900 3.486841 GTGTTTACTTCGTCGCAGTGTAA 59.513 43.478 7.84 0.00 0.00 2.41
5649 5901 3.486841 TGTTTACTTCGTCGCAGTGTAAC 59.513 43.478 7.84 11.50 0.00 2.50
5650 5902 2.336554 TACTTCGTCGCAGTGTAACC 57.663 50.000 7.84 0.00 37.80 2.85
5651 5903 0.672342 ACTTCGTCGCAGTGTAACCT 59.328 50.000 0.00 0.00 37.80 3.50
5652 5904 1.068127 ACTTCGTCGCAGTGTAACCTT 59.932 47.619 0.00 0.00 37.80 3.50
5653 5905 2.132762 CTTCGTCGCAGTGTAACCTTT 58.867 47.619 0.00 0.00 37.80 3.11
5654 5906 1.774639 TCGTCGCAGTGTAACCTTTC 58.225 50.000 0.00 0.00 37.80 2.62
5655 5907 1.067364 TCGTCGCAGTGTAACCTTTCA 59.933 47.619 0.00 0.00 37.80 2.69
5656 5908 2.066262 CGTCGCAGTGTAACCTTTCAT 58.934 47.619 0.00 0.00 37.80 2.57
5657 5909 3.057386 TCGTCGCAGTGTAACCTTTCATA 60.057 43.478 0.00 0.00 37.80 2.15
5658 5910 3.676172 CGTCGCAGTGTAACCTTTCATAA 59.324 43.478 0.00 0.00 37.80 1.90
5659 5911 4.328983 CGTCGCAGTGTAACCTTTCATAAT 59.671 41.667 0.00 0.00 37.80 1.28
5660 5912 5.500290 CGTCGCAGTGTAACCTTTCATAATC 60.500 44.000 0.00 0.00 37.80 1.75
5661 5913 4.873827 TCGCAGTGTAACCTTTCATAATCC 59.126 41.667 0.00 0.00 37.80 3.01
5662 5914 4.876107 CGCAGTGTAACCTTTCATAATCCT 59.124 41.667 0.00 0.00 37.80 3.24
5663 5915 6.046593 CGCAGTGTAACCTTTCATAATCCTA 58.953 40.000 0.00 0.00 37.80 2.94
5664 5916 6.018994 CGCAGTGTAACCTTTCATAATCCTAC 60.019 42.308 0.00 0.00 37.80 3.18
5665 5917 7.048512 GCAGTGTAACCTTTCATAATCCTACT 58.951 38.462 0.00 0.00 37.80 2.57
5666 5918 7.553044 GCAGTGTAACCTTTCATAATCCTACTT 59.447 37.037 0.00 0.00 37.80 2.24
5667 5919 9.449719 CAGTGTAACCTTTCATAATCCTACTTT 57.550 33.333 0.00 0.00 37.80 2.66
5668 5920 9.449719 AGTGTAACCTTTCATAATCCTACTTTG 57.550 33.333 0.00 0.00 37.80 2.77
5669 5921 9.444600 GTGTAACCTTTCATAATCCTACTTTGA 57.555 33.333 0.00 0.00 0.00 2.69
5672 5924 8.581253 AACCTTTCATAATCCTACTTTGAAGG 57.419 34.615 0.00 0.00 35.26 3.46
5673 5925 7.119387 ACCTTTCATAATCCTACTTTGAAGGG 58.881 38.462 9.68 9.68 44.57 3.95
5674 5926 7.119387 CCTTTCATAATCCTACTTTGAAGGGT 58.881 38.462 0.00 0.00 38.22 4.34
5675 5927 7.067494 CCTTTCATAATCCTACTTTGAAGGGTG 59.933 40.741 0.00 0.00 38.22 4.61
5676 5928 6.884472 TCATAATCCTACTTTGAAGGGTGA 57.116 37.500 0.00 0.00 34.66 4.02
5677 5929 7.265599 TCATAATCCTACTTTGAAGGGTGAA 57.734 36.000 0.00 0.00 34.66 3.18
5678 5930 7.338710 TCATAATCCTACTTTGAAGGGTGAAG 58.661 38.462 0.00 0.00 34.66 3.02
5679 5931 5.843019 AATCCTACTTTGAAGGGTGAAGA 57.157 39.130 0.00 0.00 34.66 2.87
5680 5932 5.843019 ATCCTACTTTGAAGGGTGAAGAA 57.157 39.130 0.00 0.00 34.66 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 247 0.955178 CTCCTCGATGCCTACGACAT 59.045 55.000 0.00 0.00 35.88 3.06
124 281 7.812309 AGCAGTTCTGTAAAAAGAAAAACAC 57.188 32.000 1.78 0.00 37.90 3.32
128 285 7.404671 AGGAAGCAGTTCTGTAAAAAGAAAA 57.595 32.000 1.78 0.00 37.90 2.29
139 296 2.028930 ACTTACGGAGGAAGCAGTTCTG 60.029 50.000 0.00 0.00 32.72 3.02
157 314 4.335647 CGTGGGCTGGGCTGACTT 62.336 66.667 0.00 0.00 0.00 3.01
166 329 2.241880 ACGTTTCGTTCGTGGGCTG 61.242 57.895 0.00 0.00 36.35 4.85
203 366 1.468565 GGCCCTTTCCGCGAAAAATAC 60.469 52.381 8.23 0.00 30.84 1.89
238 401 2.970324 GTGCGTTGAACGGCTGGA 60.970 61.111 20.01 0.00 42.82 3.86
251 414 1.260297 TCATGTGTGTTTCTTCGTGCG 59.740 47.619 0.00 0.00 0.00 5.34
268 431 2.631062 TGTCCTTCTGTTGGTACGTCAT 59.369 45.455 0.00 0.00 0.00 3.06
273 436 1.732259 CGCATGTCCTTCTGTTGGTAC 59.268 52.381 0.00 0.00 0.00 3.34
276 439 0.321564 TCCGCATGTCCTTCTGTTGG 60.322 55.000 0.00 0.00 0.00 3.77
289 452 2.422377 GGTACTAATTTGGGGTCCGCAT 60.422 50.000 9.81 0.00 0.00 4.73
326 489 7.993821 TTTACGATTTGCAAAGACAAAATCA 57.006 28.000 18.19 0.00 42.45 2.57
332 495 5.333513 ACGTTTTTACGATTTGCAAAGACA 58.666 33.333 18.19 0.00 36.85 3.41
334 497 9.828852 ATAATACGTTTTTACGATTTGCAAAGA 57.171 25.926 18.19 0.00 36.85 2.52
339 502 8.590339 TGTCATAATACGTTTTTACGATTTGC 57.410 30.769 4.55 0.00 36.85 3.68
352 515 7.544566 ACGTTTTCTTCTCATGTCATAATACGT 59.455 33.333 0.00 0.00 0.00 3.57
375 538 1.606224 GGGTTCACCGTCACAATACGT 60.606 52.381 0.00 0.00 41.27 3.57
396 559 3.626028 AAAGCACGGATTGACTTTGTC 57.374 42.857 0.00 0.00 33.18 3.18
821 984 9.190858 CCGACTTAAATCAAACATCAAATTTCA 57.809 29.630 0.00 0.00 0.00 2.69
822 985 9.191995 ACCGACTTAAATCAAACATCAAATTTC 57.808 29.630 0.00 0.00 0.00 2.17
823 986 9.541143 AACCGACTTAAATCAAACATCAAATTT 57.459 25.926 0.00 0.00 0.00 1.82
824 987 9.191995 GAACCGACTTAAATCAAACATCAAATT 57.808 29.630 0.00 0.00 0.00 1.82
825 988 7.537306 CGAACCGACTTAAATCAAACATCAAAT 59.463 33.333 0.00 0.00 0.00 2.32
826 989 6.853872 CGAACCGACTTAAATCAAACATCAAA 59.146 34.615 0.00 0.00 0.00 2.69
827 990 6.017770 ACGAACCGACTTAAATCAAACATCAA 60.018 34.615 0.00 0.00 0.00 2.57
828 991 5.467399 ACGAACCGACTTAAATCAAACATCA 59.533 36.000 0.00 0.00 0.00 3.07
829 992 5.923665 ACGAACCGACTTAAATCAAACATC 58.076 37.500 0.00 0.00 0.00 3.06
830 993 5.934935 ACGAACCGACTTAAATCAAACAT 57.065 34.783 0.00 0.00 0.00 2.71
831 994 5.503498 CAACGAACCGACTTAAATCAAACA 58.497 37.500 0.00 0.00 0.00 2.83
832 995 4.377738 GCAACGAACCGACTTAAATCAAAC 59.622 41.667 0.00 0.00 0.00 2.93
833 996 4.529446 GCAACGAACCGACTTAAATCAAA 58.471 39.130 0.00 0.00 0.00 2.69
834 997 3.363182 CGCAACGAACCGACTTAAATCAA 60.363 43.478 0.00 0.00 0.00 2.57
835 998 2.156117 CGCAACGAACCGACTTAAATCA 59.844 45.455 0.00 0.00 0.00 2.57
836 999 2.156310 ACGCAACGAACCGACTTAAATC 59.844 45.455 0.00 0.00 0.00 2.17
837 1000 2.137523 ACGCAACGAACCGACTTAAAT 58.862 42.857 0.00 0.00 0.00 1.40
838 1001 1.522258 GACGCAACGAACCGACTTAAA 59.478 47.619 0.00 0.00 0.00 1.52
839 1002 1.130955 GACGCAACGAACCGACTTAA 58.869 50.000 0.00 0.00 0.00 1.85
840 1003 0.664166 GGACGCAACGAACCGACTTA 60.664 55.000 0.00 0.00 0.00 2.24
841 1004 1.952635 GGACGCAACGAACCGACTT 60.953 57.895 0.00 0.00 0.00 3.01
842 1005 2.355481 GGACGCAACGAACCGACT 60.355 61.111 0.00 0.00 0.00 4.18
843 1006 3.408851 GGGACGCAACGAACCGAC 61.409 66.667 0.00 0.00 0.00 4.79
844 1007 4.668118 GGGGACGCAACGAACCGA 62.668 66.667 0.00 0.00 0.00 4.69
845 1008 4.973055 TGGGGACGCAACGAACCG 62.973 66.667 0.00 0.00 0.00 4.44
846 1009 3.047877 CTGGGGACGCAACGAACC 61.048 66.667 0.00 0.00 0.00 3.62
847 1010 1.441732 AAACTGGGGACGCAACGAAC 61.442 55.000 0.00 0.00 0.00 3.95
848 1011 1.153127 AAACTGGGGACGCAACGAA 60.153 52.632 0.00 0.00 0.00 3.85
849 1012 1.595929 GAAACTGGGGACGCAACGA 60.596 57.895 0.00 0.00 0.00 3.85
850 1013 2.613506 GGAAACTGGGGACGCAACG 61.614 63.158 0.00 0.00 0.00 4.10
851 1014 1.104577 TTGGAAACTGGGGACGCAAC 61.105 55.000 0.00 0.00 0.00 4.17
852 1015 0.821711 CTTGGAAACTGGGGACGCAA 60.822 55.000 0.00 0.00 0.00 4.85
853 1016 1.228124 CTTGGAAACTGGGGACGCA 60.228 57.895 0.00 0.00 0.00 5.24
854 1017 1.228154 ACTTGGAAACTGGGGACGC 60.228 57.895 0.00 0.00 0.00 5.19
855 1018 0.949105 CGACTTGGAAACTGGGGACG 60.949 60.000 0.00 0.00 0.00 4.79
856 1019 0.605589 CCGACTTGGAAACTGGGGAC 60.606 60.000 0.00 0.00 42.00 4.46
857 1020 1.057851 ACCGACTTGGAAACTGGGGA 61.058 55.000 0.00 0.00 42.00 4.81
858 1021 0.179001 AACCGACTTGGAAACTGGGG 60.179 55.000 0.00 0.00 42.00 4.96
859 1022 1.235724 GAACCGACTTGGAAACTGGG 58.764 55.000 0.00 0.00 42.00 4.45
860 1023 0.865769 CGAACCGACTTGGAAACTGG 59.134 55.000 0.00 0.00 42.00 4.00
861 1024 1.578583 ACGAACCGACTTGGAAACTG 58.421 50.000 0.00 0.00 42.00 3.16
862 1025 2.320745 AACGAACCGACTTGGAAACT 57.679 45.000 0.00 0.00 42.00 2.66
863 1026 3.409851 AAAACGAACCGACTTGGAAAC 57.590 42.857 0.00 0.00 42.00 2.78
864 1027 8.721019 ATATATAAAACGAACCGACTTGGAAA 57.279 30.769 0.00 0.00 42.00 3.13
865 1028 9.814899 TTATATATAAAACGAACCGACTTGGAA 57.185 29.630 2.56 0.00 42.00 3.53
866 1029 9.985730 ATTATATATAAAACGAACCGACTTGGA 57.014 29.630 9.20 0.00 42.00 3.53
869 1032 9.985730 TGGATTATATATAAAACGAACCGACTT 57.014 29.630 9.20 0.00 0.00 3.01
870 1033 9.985730 TTGGATTATATATAAAACGAACCGACT 57.014 29.630 9.20 0.00 0.00 4.18
881 1044 9.852784 TCCCACCTCTCTTGGATTATATATAAA 57.147 33.333 9.20 0.00 36.02 1.40
896 1059 0.622665 CAGGCAAATCCCACCTCTCT 59.377 55.000 0.00 0.00 34.51 3.10
904 1067 1.405463 GTTTCGGATCAGGCAAATCCC 59.595 52.381 11.28 0.00 39.71 3.85
905 1068 1.405463 GGTTTCGGATCAGGCAAATCC 59.595 52.381 7.83 7.83 39.51 3.01
923 1086 2.817839 CGAGATTTTGGGGAGTTTGGGT 60.818 50.000 0.00 0.00 0.00 4.51
931 1094 3.551846 GAATTAGGCGAGATTTTGGGGA 58.448 45.455 0.00 0.00 0.00 4.81
936 1100 3.815401 CGATGGGAATTAGGCGAGATTTT 59.185 43.478 0.00 0.00 0.00 1.82
1224 1419 4.814294 GCGTGGCCCGTGTAGGAG 62.814 72.222 13.97 0.00 45.00 3.69
1513 1711 0.261696 GCTCTCTCCTCCTCCTCCTT 59.738 60.000 0.00 0.00 0.00 3.36
1564 1762 0.040514 CGTTTTGTCAATGCGGCTGA 60.041 50.000 0.00 0.00 0.00 4.26
1572 1770 2.415357 CCTATTGCGCCGTTTTGTCAAT 60.415 45.455 4.18 0.00 0.00 2.57
1574 1772 0.519519 CCTATTGCGCCGTTTTGTCA 59.480 50.000 4.18 0.00 0.00 3.58
1639 1837 2.301583 AGTCTGTCTTGGCCTTCTTCTC 59.698 50.000 3.32 0.00 0.00 2.87
1652 1850 2.170187 GCATCCCAATCTGAGTCTGTCT 59.830 50.000 0.00 0.00 0.00 3.41
1796 1994 2.467826 GCTGCCGGAGTTGCATCTC 61.468 63.158 15.21 15.21 38.22 2.75
1986 2184 2.079925 GCAAGGTTCTCTGCTCGAAAT 58.920 47.619 0.00 0.00 0.00 2.17
1990 2188 1.004560 TGGCAAGGTTCTCTGCTCG 60.005 57.895 0.00 0.00 0.00 5.03
2039 2270 4.180377 TGGTAATACTCCGGAGTCATCT 57.820 45.455 39.49 23.23 42.54 2.90
2072 2303 1.612146 TCCTCAATGTCCCGCTCCA 60.612 57.895 0.00 0.00 0.00 3.86
2160 2391 1.961180 GCTGGTACGATGCTGGAGGT 61.961 60.000 0.00 0.00 0.00 3.85
2169 2400 1.366366 GCGTATGGGCTGGTACGAT 59.634 57.895 16.61 0.00 44.67 3.73
2190 2421 1.152368 AAGCAGCTTCCTTGCAGGT 59.848 52.632 0.21 0.00 43.92 4.00
2447 2678 1.217882 CTGCCGAAGTGACGTCTTTT 58.782 50.000 17.92 10.80 0.00 2.27
2982 3213 3.386078 TCTCATCAGTTAGACCATGCTCC 59.614 47.826 0.00 0.00 0.00 4.70
3122 3353 2.222027 CAAGGACCTTTCCACTGTGAC 58.778 52.381 9.86 0.00 45.72 3.67
3343 3574 4.058124 TCTAAACACTGTGTGCTGATGAC 58.942 43.478 15.11 0.00 36.98 3.06
3355 3586 6.422100 CGGATACAATCAGGATCTAAACACTG 59.578 42.308 0.00 0.00 0.00 3.66
3371 3602 3.366396 ACTCTGTGACTCCGGATACAAT 58.634 45.455 3.57 0.00 0.00 2.71
3383 3614 1.269831 ACGCTGAAAGGACTCTGTGAC 60.270 52.381 0.00 0.00 0.00 3.67
3389 3620 2.755650 TGAAGAACGCTGAAAGGACTC 58.244 47.619 0.00 0.00 0.00 3.36
3390 3621 2.910688 TGAAGAACGCTGAAAGGACT 57.089 45.000 0.00 0.00 0.00 3.85
3513 3744 3.118629 TCAGATCCTCAACAATCTTCCCG 60.119 47.826 0.00 0.00 29.77 5.14
3729 3960 3.650950 GGCTTGACCCTCTGGCCA 61.651 66.667 4.71 4.71 42.08 5.36
3870 4101 0.620556 CCAGGTGACCCATAAGCTGT 59.379 55.000 0.00 0.00 39.68 4.40
3954 4185 9.301153 CCAATAACATTAACAATAGCCTTCAAC 57.699 33.333 0.00 0.00 0.00 3.18
3966 4197 8.800370 TCTTAGTCATGCCAATAACATTAACA 57.200 30.769 0.00 0.00 0.00 2.41
3969 4200 9.056005 GTCATCTTAGTCATGCCAATAACATTA 57.944 33.333 0.00 0.00 0.00 1.90
4024 4255 5.022787 CCTATTTTTCAAGATGGGGGTCAA 58.977 41.667 0.00 0.00 0.00 3.18
4041 4272 5.819991 TCTTGGACTTTCTCATGCCTATTT 58.180 37.500 0.00 0.00 0.00 1.40
4056 4287 3.777106 TCAATGCAGTTCTCTTGGACT 57.223 42.857 0.00 0.00 0.00 3.85
4193 4424 7.759489 ATATAACCAAATGTGTTCACAGTGT 57.241 32.000 11.24 0.00 0.00 3.55
4470 4701 0.321122 CTTCAAGCAAGGGAGCGACT 60.321 55.000 0.00 0.00 40.15 4.18
4485 4716 2.355412 CCTGTCCATCAGTGCATCTTCA 60.355 50.000 0.00 0.00 42.19 3.02
4566 4797 0.038744 CATCCTCACAACCCAAGCCT 59.961 55.000 0.00 0.00 0.00 4.58
4662 4893 1.133325 ACTCACATCCCCTCGATAGCT 60.133 52.381 0.00 0.00 0.00 3.32
4678 4909 1.216444 CTGCGCCTAGAGCAACTCA 59.784 57.895 4.18 1.34 44.67 3.41
4822 5053 1.485066 GTTTCCAAGATCGCCTAGGGA 59.515 52.381 11.72 6.66 0.00 4.20
4824 5055 2.678336 GTTGTTTCCAAGATCGCCTAGG 59.322 50.000 3.67 3.67 0.00 3.02
4845 5076 0.803768 CTGGACGGCTGAAGATGTCG 60.804 60.000 0.00 0.00 32.17 4.35
4916 5147 8.005192 TCAATAGCCATTGCACATATTAACAA 57.995 30.769 0.00 0.00 41.21 2.83
4918 5149 8.870160 TTTCAATAGCCATTGCACATATTAAC 57.130 30.769 0.00 0.00 41.21 2.01
4970 5202 9.745880 CCGTAAGTGTTATAACAGAATACTGAT 57.254 33.333 18.56 1.45 46.03 2.90
4974 5206 9.787532 TGTACCGTAAGTGTTATAACAGAATAC 57.212 33.333 18.56 17.84 40.05 1.89
4976 5208 9.880157 ATTGTACCGTAAGTGTTATAACAGAAT 57.120 29.630 18.56 10.12 40.05 2.40
4977 5209 9.357652 GATTGTACCGTAAGTGTTATAACAGAA 57.642 33.333 18.56 4.63 40.05 3.02
4978 5210 8.522003 TGATTGTACCGTAAGTGTTATAACAGA 58.478 33.333 18.56 4.77 40.05 3.41
4979 5211 8.692110 TGATTGTACCGTAAGTGTTATAACAG 57.308 34.615 18.56 8.43 40.05 3.16
4980 5212 7.276218 GCTGATTGTACCGTAAGTGTTATAACA 59.724 37.037 14.35 14.35 36.38 2.41
4981 5213 7.490402 AGCTGATTGTACCGTAAGTGTTATAAC 59.510 37.037 8.75 8.75 0.00 1.89
4982 5214 7.549839 AGCTGATTGTACCGTAAGTGTTATAA 58.450 34.615 0.00 0.00 0.00 0.98
4983 5215 7.104043 AGCTGATTGTACCGTAAGTGTTATA 57.896 36.000 0.00 0.00 0.00 0.98
4984 5216 5.974108 AGCTGATTGTACCGTAAGTGTTAT 58.026 37.500 0.00 0.00 0.00 1.89
4985 5217 5.395682 AGCTGATTGTACCGTAAGTGTTA 57.604 39.130 0.00 0.00 0.00 2.41
4986 5218 4.267349 AGCTGATTGTACCGTAAGTGTT 57.733 40.909 0.00 0.00 0.00 3.32
4987 5219 3.955650 AGCTGATTGTACCGTAAGTGT 57.044 42.857 0.00 0.00 0.00 3.55
4988 5220 4.798907 CACTAGCTGATTGTACCGTAAGTG 59.201 45.833 0.00 0.00 0.00 3.16
4989 5221 4.461781 ACACTAGCTGATTGTACCGTAAGT 59.538 41.667 0.00 0.00 0.00 2.24
4990 5222 4.798907 CACACTAGCTGATTGTACCGTAAG 59.201 45.833 0.00 0.00 0.00 2.34
4991 5223 4.460034 TCACACTAGCTGATTGTACCGTAA 59.540 41.667 0.00 0.00 0.00 3.18
4992 5224 4.011698 TCACACTAGCTGATTGTACCGTA 58.988 43.478 0.00 0.00 0.00 4.02
4993 5225 2.823747 TCACACTAGCTGATTGTACCGT 59.176 45.455 0.00 0.00 0.00 4.83
4994 5226 3.179830 GTCACACTAGCTGATTGTACCG 58.820 50.000 0.00 0.00 0.00 4.02
4995 5227 3.056107 TGGTCACACTAGCTGATTGTACC 60.056 47.826 0.00 6.26 0.00 3.34
4996 5228 3.927142 GTGGTCACACTAGCTGATTGTAC 59.073 47.826 0.00 0.00 44.29 2.90
4997 5229 4.188247 GTGGTCACACTAGCTGATTGTA 57.812 45.455 0.00 0.00 44.29 2.41
4998 5230 3.045601 GTGGTCACACTAGCTGATTGT 57.954 47.619 0.00 0.00 44.29 2.71
5014 5246 5.981088 TGAATGCTAAAATGACATGTGGT 57.019 34.783 1.15 0.00 0.00 4.16
5015 5247 5.290158 GCTTGAATGCTAAAATGACATGTGG 59.710 40.000 1.15 0.00 0.00 4.17
5016 5248 5.865013 TGCTTGAATGCTAAAATGACATGTG 59.135 36.000 1.15 0.00 0.00 3.21
5017 5249 6.028146 TGCTTGAATGCTAAAATGACATGT 57.972 33.333 0.00 0.00 0.00 3.21
5018 5250 6.097356 ACTGCTTGAATGCTAAAATGACATG 58.903 36.000 0.00 0.00 0.00 3.21
5019 5251 6.276832 ACTGCTTGAATGCTAAAATGACAT 57.723 33.333 0.00 0.00 0.00 3.06
5020 5252 5.710513 ACTGCTTGAATGCTAAAATGACA 57.289 34.783 0.00 0.00 0.00 3.58
5021 5253 5.741040 GCTACTGCTTGAATGCTAAAATGAC 59.259 40.000 0.00 0.00 36.03 3.06
5022 5254 5.415389 TGCTACTGCTTGAATGCTAAAATGA 59.585 36.000 0.00 0.00 40.48 2.57
5023 5255 5.643664 TGCTACTGCTTGAATGCTAAAATG 58.356 37.500 0.00 0.00 40.48 2.32
5024 5256 5.902613 TGCTACTGCTTGAATGCTAAAAT 57.097 34.783 0.00 0.00 40.48 1.82
5025 5257 5.241506 ACTTGCTACTGCTTGAATGCTAAAA 59.758 36.000 0.00 0.00 40.48 1.52
5026 5258 4.761739 ACTTGCTACTGCTTGAATGCTAAA 59.238 37.500 0.00 0.00 40.48 1.85
5027 5259 4.154737 CACTTGCTACTGCTTGAATGCTAA 59.845 41.667 0.00 0.00 40.48 3.09
5028 5260 3.686241 CACTTGCTACTGCTTGAATGCTA 59.314 43.478 0.00 0.00 40.48 3.49
5029 5261 2.486982 CACTTGCTACTGCTTGAATGCT 59.513 45.455 0.00 0.00 40.48 3.79
5030 5262 2.415090 CCACTTGCTACTGCTTGAATGC 60.415 50.000 0.00 0.00 40.48 3.56
5031 5263 2.816087 ACCACTTGCTACTGCTTGAATG 59.184 45.455 0.00 0.00 40.48 2.67
5032 5264 3.146104 ACCACTTGCTACTGCTTGAAT 57.854 42.857 0.00 0.00 40.48 2.57
5033 5265 2.638480 ACCACTTGCTACTGCTTGAA 57.362 45.000 0.00 0.00 40.48 2.69
5034 5266 2.638480 AACCACTTGCTACTGCTTGA 57.362 45.000 0.00 0.00 40.48 3.02
5035 5267 3.715628 AAAACCACTTGCTACTGCTTG 57.284 42.857 0.00 0.00 40.48 4.01
5036 5268 5.845391 TTAAAAACCACTTGCTACTGCTT 57.155 34.783 0.00 0.00 40.48 3.91
5037 5269 5.770162 AGATTAAAAACCACTTGCTACTGCT 59.230 36.000 0.00 0.00 40.48 4.24
5038 5270 5.858581 CAGATTAAAAACCACTTGCTACTGC 59.141 40.000 0.00 0.00 40.20 4.40
5039 5271 6.970484 ACAGATTAAAAACCACTTGCTACTG 58.030 36.000 0.00 0.00 0.00 2.74
5040 5272 6.998673 AGACAGATTAAAAACCACTTGCTACT 59.001 34.615 0.00 0.00 0.00 2.57
5041 5273 7.203255 AGACAGATTAAAAACCACTTGCTAC 57.797 36.000 0.00 0.00 0.00 3.58
5042 5274 7.284489 ACAAGACAGATTAAAAACCACTTGCTA 59.716 33.333 0.00 0.00 36.65 3.49
5043 5275 6.096846 ACAAGACAGATTAAAAACCACTTGCT 59.903 34.615 0.00 0.00 36.65 3.91
5044 5276 6.273071 ACAAGACAGATTAAAAACCACTTGC 58.727 36.000 0.00 0.00 36.65 4.01
5050 5282 6.635030 AGGTGACAAGACAGATTAAAAACC 57.365 37.500 0.00 0.00 0.00 3.27
5053 5285 6.601332 AGGAAGGTGACAAGACAGATTAAAA 58.399 36.000 0.00 0.00 0.00 1.52
5059 5291 4.503714 AAAAGGAAGGTGACAAGACAGA 57.496 40.909 0.00 0.00 0.00 3.41
5096 5331 1.476488 AGAGCCACAAAAACACACCAC 59.524 47.619 0.00 0.00 0.00 4.16
5110 5345 5.367937 AGATCCTTGCTTTTATAGAGAGCCA 59.632 40.000 0.00 0.00 35.59 4.75
5174 5413 4.198530 TCCAATGCATGTGTATGACGAAT 58.801 39.130 0.00 0.00 36.36 3.34
5176 5415 3.258971 TCCAATGCATGTGTATGACGA 57.741 42.857 0.00 0.00 36.36 4.20
5285 5526 2.755650 AGACGCAAGAAGTAACACCAG 58.244 47.619 0.00 0.00 43.62 4.00
5436 5684 9.569167 CTGTGAAGTAATGTAAGATCGTTTAGA 57.431 33.333 0.00 0.00 0.00 2.10
5437 5685 9.569167 TCTGTGAAGTAATGTAAGATCGTTTAG 57.431 33.333 0.00 0.00 0.00 1.85
5446 5694 6.287589 ACTCCCTCTGTGAAGTAATGTAAG 57.712 41.667 0.00 0.00 0.00 2.34
5519 5767 1.873591 GTTCCGAAACAGTCAGTGCAT 59.126 47.619 0.00 0.00 35.36 3.96
5523 5771 1.139058 AGCAGTTCCGAAACAGTCAGT 59.861 47.619 0.00 0.00 37.88 3.41
5526 5774 1.795286 CAGAGCAGTTCCGAAACAGTC 59.205 52.381 0.00 0.00 37.88 3.51
5529 5777 2.325583 AACAGAGCAGTTCCGAAACA 57.674 45.000 0.00 0.00 37.88 2.83
5544 5792 4.180817 GACCAAAACACCCTGAAAAACAG 58.819 43.478 0.00 0.00 45.36 3.16
5556 5804 1.470805 GGCACACTTGGACCAAAACAC 60.471 52.381 8.59 0.00 0.00 3.32
5562 5810 1.227823 CTTCGGCACACTTGGACCA 60.228 57.895 0.00 0.00 0.00 4.02
5568 5816 3.511934 AGATAAGACTCTTCGGCACACTT 59.488 43.478 0.00 0.00 0.00 3.16
5584 5832 2.487265 CCCGGTCCCAAATCCAGATAAG 60.487 54.545 0.00 0.00 0.00 1.73
5586 5834 1.136828 CCCGGTCCCAAATCCAGATA 58.863 55.000 0.00 0.00 0.00 1.98
5595 5843 3.817210 TTGCAATGCCCGGTCCCAA 62.817 57.895 1.53 0.00 0.00 4.12
5609 5857 4.641645 CACCACTCGGCCCTTGCA 62.642 66.667 0.00 0.00 40.13 4.08
5639 5891 4.876107 AGGATTATGAAAGGTTACACTGCG 59.124 41.667 0.00 0.00 0.00 5.18
5642 5894 9.449719 CAAAGTAGGATTATGAAAGGTTACACT 57.550 33.333 0.00 0.00 0.00 3.55
5643 5895 9.444600 TCAAAGTAGGATTATGAAAGGTTACAC 57.555 33.333 0.00 0.00 0.00 2.90
5646 5898 9.681062 CCTTCAAAGTAGGATTATGAAAGGTTA 57.319 33.333 0.00 0.00 34.56 2.85
5647 5899 7.615757 CCCTTCAAAGTAGGATTATGAAAGGTT 59.384 37.037 0.00 0.00 34.56 3.50
5648 5900 7.119387 CCCTTCAAAGTAGGATTATGAAAGGT 58.881 38.462 0.00 0.00 34.56 3.50
5649 5901 7.067494 CACCCTTCAAAGTAGGATTATGAAAGG 59.933 40.741 0.00 0.00 37.53 3.11
5650 5902 7.829211 TCACCCTTCAAAGTAGGATTATGAAAG 59.171 37.037 0.00 0.00 34.56 2.62
5651 5903 7.695055 TCACCCTTCAAAGTAGGATTATGAAA 58.305 34.615 0.00 0.00 34.56 2.69
5652 5904 7.265599 TCACCCTTCAAAGTAGGATTATGAA 57.734 36.000 0.00 0.00 34.56 2.57
5653 5905 6.884472 TCACCCTTCAAAGTAGGATTATGA 57.116 37.500 0.00 0.00 34.56 2.15
5654 5906 7.338710 TCTTCACCCTTCAAAGTAGGATTATG 58.661 38.462 0.00 0.00 34.56 1.90
5655 5907 7.510675 TCTTCACCCTTCAAAGTAGGATTAT 57.489 36.000 0.00 0.00 34.56 1.28
5656 5908 6.945636 TCTTCACCCTTCAAAGTAGGATTA 57.054 37.500 0.00 0.00 34.56 1.75
5657 5909 5.843019 TCTTCACCCTTCAAAGTAGGATT 57.157 39.130 0.00 0.00 34.56 3.01
5658 5910 5.843019 TTCTTCACCCTTCAAAGTAGGAT 57.157 39.130 0.00 0.00 34.56 3.24


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

AutoCloner maintained by Alex Coulton.