Multiple sequence alignment - TraesCS5D01G237000

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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 TraesCS5D01G237000 chr5D 100.000 3018 0 0 662 3679 345497725 345494708 0.000000e+00 5574
1 TraesCS5D01G237000 chr5D 100.000 304 0 0 1 304 345498386 345498083 2.480000e-156 562
2 TraesCS5D01G237000 chr5D 82.135 459 65 12 997 1451 24570784 24571229 9.640000e-101 377
3 TraesCS5D01G237000 chr5B 97.113 1143 27 3 2537 3679 406172947 406174083 0.000000e+00 1923
4 TraesCS5D01G237000 chr5B 93.333 1305 62 9 662 1943 406171124 406172426 0.000000e+00 1905
5 TraesCS5D01G237000 chr5B 87.611 226 20 3 47 265 406170794 406171018 4.710000e-64 255
6 TraesCS5D01G237000 chr2D 86.023 694 92 4 2987 3679 14897823 14897134 0.000000e+00 739
7 TraesCS5D01G237000 chr2D 84.870 694 103 2 2987 3679 15114906 15115598 0.000000e+00 699
8 TraesCS5D01G237000 chr2D 82.353 612 83 12 997 1588 14899987 14899381 3.280000e-140 508
9 TraesCS5D01G237000 chr2D 75.873 315 63 12 2587 2890 15114353 15114665 8.230000e-32 148
10 TraesCS5D01G237000 chr2A 85.962 691 92 4 2990 3679 17001758 17001072 0.000000e+00 734
11 TraesCS5D01G237000 chr2A 82.997 694 104 8 2987 3679 768732852 768732172 1.880000e-172 616
12 TraesCS5D01G237000 chr2A 80.908 749 95 18 997 1701 17003716 17002972 6.950000e-152 547
13 TraesCS5D01G237000 chr2A 78.170 765 150 13 997 1755 768734748 768733995 4.300000e-129 472
14 TraesCS5D01G237000 chr2B 85.735 694 94 4 2987 3679 26753470 26752781 0.000000e+00 728
15 TraesCS5D01G237000 chr2B 83.502 594 80 7 997 1575 26755152 26754562 4.180000e-149 538
16 TraesCS5D01G237000 chr2B 75.810 463 93 13 997 1442 9887756 9888216 2.220000e-52 217
17 TraesCS5D01G237000 chrUn 83.926 759 119 2 2924 3679 16773122 16773880 0.000000e+00 723
18 TraesCS5D01G237000 chrUn 84.106 755 113 5 2930 3679 270800653 270799901 0.000000e+00 723
19 TraesCS5D01G237000 chrUn 79.161 739 124 22 998 1725 16771149 16771868 5.520000e-133 484
20 TraesCS5D01G237000 chrUn 79.161 739 124 22 998 1725 270802632 270801913 5.520000e-133 484
21 TraesCS5D01G237000 chr7D 80.514 739 123 11 2947 3679 634110481 634109758 6.950000e-152 547
22 TraesCS5D01G237000 chr7B 78.864 440 75 11 1001 1437 742556385 742555961 7.780000e-72 281


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 TraesCS5D01G237000 chr5D 345494708 345498386 3678 True 3068.0 5574 100.000000 1 3679 2 chr5D.!!$R1 3678
1 TraesCS5D01G237000 chr5B 406170794 406174083 3289 False 1361.0 1923 92.685667 47 3679 3 chr5B.!!$F1 3632
2 TraesCS5D01G237000 chr2D 14897134 14899987 2853 True 623.5 739 84.188000 997 3679 2 chr2D.!!$R1 2682
3 TraesCS5D01G237000 chr2D 15114353 15115598 1245 False 423.5 699 80.371500 2587 3679 2 chr2D.!!$F1 1092
4 TraesCS5D01G237000 chr2A 17001072 17003716 2644 True 640.5 734 83.435000 997 3679 2 chr2A.!!$R1 2682
5 TraesCS5D01G237000 chr2A 768732172 768734748 2576 True 544.0 616 80.583500 997 3679 2 chr2A.!!$R2 2682
6 TraesCS5D01G237000 chr2B 26752781 26755152 2371 True 633.0 728 84.618500 997 3679 2 chr2B.!!$R1 2682
7 TraesCS5D01G237000 chrUn 16771149 16773880 2731 False 603.5 723 81.543500 998 3679 2 chrUn.!!$F1 2681
8 TraesCS5D01G237000 chrUn 270799901 270802632 2731 True 603.5 723 81.633500 998 3679 2 chrUn.!!$R1 2681
9 TraesCS5D01G237000 chr7D 634109758 634110481 723 True 547.0 547 80.514000 2947 3679 1 chr7D.!!$R1 732

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
70 71 0.100682 GATGTCGACGAAGCCTAGCA 59.899 55.0 11.62 0.0 0.00 3.49 F
807 845 0.179140 GTCGCCGGGTAACATTACGA 60.179 55.0 2.18 0.0 34.50 3.43 F
2052 2305 0.036765 GTTGGGCTCGTCCACATGTA 60.037 55.0 0.00 0.0 36.38 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2286 0.036765 TACATGTGGACGAGCCCAAC 60.037 55.000 9.11 0.00 38.06 3.77 R
2531 3586 1.242076 GACAGACACTGCATTGGCTT 58.758 50.000 10.19 2.04 41.91 4.35 R
2922 4274 3.063997 CAGCTTGGTTAGGTAATTCAGCG 59.936 47.826 0.00 0.00 32.12 5.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.159285 GGTGTAAACAGGTAACGGGC 58.841 55.000 0.00 0.00 46.39 6.13
20 21 1.542987 GGTGTAAACAGGTAACGGGCA 60.543 52.381 0.00 0.00 46.39 5.36
21 22 2.429478 GTGTAAACAGGTAACGGGCAT 58.571 47.619 0.00 0.00 46.39 4.40
22 23 3.598299 GTGTAAACAGGTAACGGGCATA 58.402 45.455 0.00 0.00 46.39 3.14
23 24 4.002316 GTGTAAACAGGTAACGGGCATAA 58.998 43.478 0.00 0.00 46.39 1.90
24 25 4.455190 GTGTAAACAGGTAACGGGCATAAA 59.545 41.667 0.00 0.00 46.39 1.40
25 26 5.124297 GTGTAAACAGGTAACGGGCATAAAT 59.876 40.000 0.00 0.00 46.39 1.40
26 27 4.976224 AAACAGGTAACGGGCATAAATC 57.024 40.909 0.00 0.00 46.39 2.17
27 28 2.927028 ACAGGTAACGGGCATAAATCC 58.073 47.619 0.00 0.00 46.39 3.01
28 29 2.240160 ACAGGTAACGGGCATAAATCCA 59.760 45.455 0.00 0.00 46.39 3.41
29 30 2.616842 CAGGTAACGGGCATAAATCCAC 59.383 50.000 0.00 0.00 46.39 4.02
30 31 1.600485 GGTAACGGGCATAAATCCACG 59.400 52.381 0.00 0.00 0.00 4.94
31 32 2.553086 GTAACGGGCATAAATCCACGA 58.447 47.619 0.00 0.00 0.00 4.35
32 33 2.116827 AACGGGCATAAATCCACGAA 57.883 45.000 0.00 0.00 0.00 3.85
33 34 2.116827 ACGGGCATAAATCCACGAAA 57.883 45.000 0.00 0.00 0.00 3.46
34 35 1.741145 ACGGGCATAAATCCACGAAAC 59.259 47.619 0.00 0.00 0.00 2.78
35 36 1.740585 CGGGCATAAATCCACGAAACA 59.259 47.619 0.00 0.00 0.00 2.83
36 37 2.162608 CGGGCATAAATCCACGAAACAA 59.837 45.455 0.00 0.00 0.00 2.83
37 38 3.366476 CGGGCATAAATCCACGAAACAAA 60.366 43.478 0.00 0.00 0.00 2.83
38 39 3.924073 GGGCATAAATCCACGAAACAAAC 59.076 43.478 0.00 0.00 0.00 2.93
39 40 4.551388 GGCATAAATCCACGAAACAAACA 58.449 39.130 0.00 0.00 0.00 2.83
40 41 4.384547 GGCATAAATCCACGAAACAAACAC 59.615 41.667 0.00 0.00 0.00 3.32
41 42 4.384547 GCATAAATCCACGAAACAAACACC 59.615 41.667 0.00 0.00 0.00 4.16
42 43 5.768317 CATAAATCCACGAAACAAACACCT 58.232 37.500 0.00 0.00 0.00 4.00
43 44 3.982576 AATCCACGAAACAAACACCTC 57.017 42.857 0.00 0.00 0.00 3.85
44 45 2.404923 TCCACGAAACAAACACCTCA 57.595 45.000 0.00 0.00 0.00 3.86
45 46 2.925724 TCCACGAAACAAACACCTCAT 58.074 42.857 0.00 0.00 0.00 2.90
70 71 0.100682 GATGTCGACGAAGCCTAGCA 59.899 55.000 11.62 0.00 0.00 3.49
74 75 1.517257 CGACGAAGCCTAGCACTGG 60.517 63.158 0.00 0.00 0.00 4.00
79 80 0.324943 GAAGCCTAGCACTGGACCAA 59.675 55.000 0.00 0.00 0.00 3.67
88 89 2.978010 CTGGACCAACACCACCGC 60.978 66.667 0.00 0.00 33.57 5.68
109 110 2.345991 CCCGTCGACCACCAACAT 59.654 61.111 10.58 0.00 0.00 2.71
110 111 2.032634 CCCGTCGACCACCAACATG 61.033 63.158 10.58 0.00 0.00 3.21
111 112 1.301401 CCGTCGACCACCAACATGT 60.301 57.895 10.58 0.00 0.00 3.21
142 145 4.612412 GACACGCAACCCCCACGA 62.612 66.667 0.00 0.00 0.00 4.35
150 153 2.437396 AACCCCCACGACGACAACT 61.437 57.895 0.00 0.00 0.00 3.16
156 159 1.127951 CCCACGACGACAACTAAATGC 59.872 52.381 0.00 0.00 0.00 3.56
207 210 1.299926 CCACTATAGCCACGACGCC 60.300 63.158 0.00 0.00 0.00 5.68
217 220 3.998672 ACGACGCCGACCACCAAT 61.999 61.111 0.00 0.00 39.50 3.16
270 288 1.302192 CGTGGAGAAAAAGCCGGGA 60.302 57.895 2.18 0.00 0.00 5.14
298 316 4.529219 CCATAGCACCTCGCCGCA 62.529 66.667 0.00 0.00 44.04 5.69
300 318 2.202932 ATAGCACCTCGCCGCAAG 60.203 61.111 0.00 0.00 44.04 4.01
301 319 2.721167 ATAGCACCTCGCCGCAAGA 61.721 57.895 0.00 0.00 44.04 3.02
682 700 2.956333 GGGTAACTTGCTGAGGTTGTTT 59.044 45.455 0.00 0.00 0.00 2.83
683 701 3.004419 GGGTAACTTGCTGAGGTTGTTTC 59.996 47.826 0.00 0.00 0.00 2.78
692 710 0.955919 GAGGTTGTTTCCTGGGAGCG 60.956 60.000 0.00 0.00 38.02 5.03
693 711 1.971695 GGTTGTTTCCTGGGAGCGG 60.972 63.158 0.00 0.00 0.00 5.52
695 713 3.126703 TTGTTTCCTGGGAGCGGCA 62.127 57.895 1.45 0.00 0.00 5.69
699 717 1.460273 TTTCCTGGGAGCGGCAAAAC 61.460 55.000 1.45 0.00 0.00 2.43
759 791 1.475280 CGACCAGATCAAACGGTAGGA 59.525 52.381 0.00 0.00 31.63 2.94
762 794 3.933332 GACCAGATCAAACGGTAGGAAAG 59.067 47.826 0.00 0.00 31.63 2.62
781 819 1.508088 GGTGGGAGCTGCGAAAATG 59.492 57.895 0.00 0.00 0.00 2.32
782 820 1.508088 GTGGGAGCTGCGAAAATGG 59.492 57.895 0.00 0.00 0.00 3.16
789 827 1.862602 GCTGCGAAAATGGGAACGGT 61.863 55.000 0.00 0.00 0.00 4.83
804 842 1.141449 CGGTCGCCGGGTAACATTA 59.859 57.895 2.18 0.00 44.15 1.90
807 845 0.179140 GTCGCCGGGTAACATTACGA 60.179 55.000 2.18 0.00 34.50 3.43
812 850 3.181508 CGCCGGGTAACATTACGATTTTT 60.182 43.478 2.18 0.00 34.50 1.94
865 903 0.911769 TGTGGCCATCTCCTACCTTG 59.088 55.000 9.72 0.00 0.00 3.61
883 921 3.442977 CCTTGGAAATTTCTCTGCTCTGG 59.557 47.826 17.42 5.84 0.00 3.86
893 931 2.853542 TGCTCTGGCCACCCTCAA 60.854 61.111 0.00 0.00 37.74 3.02
895 933 2.596851 GCTCTGGCCACCCTCAAGA 61.597 63.158 0.00 0.00 0.00 3.02
913 951 0.607489 GAGGAAGAAGGCAGCAGCAA 60.607 55.000 2.65 0.00 44.61 3.91
930 968 2.290641 AGCAACAACGAATCCTTGACAC 59.709 45.455 0.00 0.00 0.00 3.67
945 983 4.778415 CACCTCGCTCACCGTCGG 62.778 72.222 10.48 10.48 38.35 4.79
948 986 4.838486 CTCGCTCACCGTCGGCTC 62.838 72.222 12.28 0.00 38.35 4.70
950 988 4.838486 CGCTCACCGTCGGCTCTC 62.838 72.222 12.28 0.00 0.00 3.20
951 989 3.444805 GCTCACCGTCGGCTCTCT 61.445 66.667 12.28 0.00 0.00 3.10
963 1002 3.942748 GTCGGCTCTCTCTTCTTCTTCTA 59.057 47.826 0.00 0.00 0.00 2.10
990 1029 5.355350 CACCAAAATTATCCAGAGACCTCAC 59.645 44.000 0.00 0.00 0.00 3.51
1230 1290 2.580470 GCAGATCCGCGACATCACG 61.580 63.158 8.23 5.47 0.00 4.35
1533 1596 2.633657 CTGCAGCTTGTCGCGTTT 59.366 55.556 5.77 0.00 45.59 3.60
1628 1719 2.361104 GGGAAGACCGCCATTGCA 60.361 61.111 0.00 0.00 37.32 4.08
1805 1896 2.368439 GGTATCACAGCAGCCATCAAA 58.632 47.619 0.00 0.00 0.00 2.69
1809 1900 1.350684 TCACAGCAGCCATCAAAGGTA 59.649 47.619 0.00 0.00 0.00 3.08
1943 2037 2.952310 GGAGCACTTCAAGGAAAACAGT 59.048 45.455 0.00 0.00 0.00 3.55
1950 2044 6.472486 GCACTTCAAGGAAAACAGTTAACTTC 59.528 38.462 5.07 0.64 0.00 3.01
1951 2045 6.687105 CACTTCAAGGAAAACAGTTAACTTCG 59.313 38.462 5.07 0.00 0.00 3.79
1954 2048 7.237920 TCAAGGAAAACAGTTAACTTCGTAC 57.762 36.000 5.07 0.00 0.00 3.67
1955 2049 6.817641 TCAAGGAAAACAGTTAACTTCGTACA 59.182 34.615 5.07 0.00 0.00 2.90
1957 2051 7.008440 AGGAAAACAGTTAACTTCGTACAAC 57.992 36.000 5.07 0.00 0.00 3.32
1958 2052 6.594937 AGGAAAACAGTTAACTTCGTACAACA 59.405 34.615 5.07 0.00 0.00 3.33
1961 2055 9.281075 GAAAACAGTTAACTTCGTACAACAAAT 57.719 29.630 5.07 0.00 0.00 2.32
1966 2060 9.103048 CAGTTAACTTCGTACAACAAATTCATC 57.897 33.333 5.07 0.00 0.00 2.92
1967 2061 8.832521 AGTTAACTTCGTACAACAAATTCATCA 58.167 29.630 1.12 0.00 0.00 3.07
1969 2063 6.241207 ACTTCGTACAACAAATTCATCAGG 57.759 37.500 0.00 0.00 0.00 3.86
1970 2064 5.181245 ACTTCGTACAACAAATTCATCAGGG 59.819 40.000 0.00 0.00 0.00 4.45
1971 2065 4.900684 TCGTACAACAAATTCATCAGGGA 58.099 39.130 0.00 0.00 0.00 4.20
1973 2067 5.353956 TCGTACAACAAATTCATCAGGGATG 59.646 40.000 0.00 0.00 41.00 3.51
1974 2068 4.460948 ACAACAAATTCATCAGGGATGC 57.539 40.909 1.37 0.00 39.63 3.91
1975 2069 3.196254 ACAACAAATTCATCAGGGATGCC 59.804 43.478 0.00 0.00 39.63 4.40
2029 2282 4.858935 ACCGAACATGACAGTTCAATTTG 58.141 39.130 0.00 0.00 46.32 2.32
2033 2286 5.164129 CGAACATGACAGTTCAATTTGCATG 60.164 40.000 0.00 0.00 46.32 4.06
2042 2295 1.067706 TCAATTTGCATGTTGGGCTCG 60.068 47.619 10.56 0.00 0.00 5.03
2044 2297 0.527565 ATTTGCATGTTGGGCTCGTC 59.472 50.000 0.00 0.00 0.00 4.20
2045 2298 1.523154 TTTGCATGTTGGGCTCGTCC 61.523 55.000 0.00 0.00 0.00 4.79
2047 2300 2.690778 GCATGTTGGGCTCGTCCAC 61.691 63.158 0.00 0.00 36.38 4.02
2048 2301 1.302431 CATGTTGGGCTCGTCCACA 60.302 57.895 0.00 0.00 36.38 4.17
2050 2303 0.677731 ATGTTGGGCTCGTCCACATG 60.678 55.000 0.00 0.00 36.38 3.21
2051 2304 1.302511 GTTGGGCTCGTCCACATGT 60.303 57.895 0.00 0.00 36.38 3.21
2052 2305 0.036765 GTTGGGCTCGTCCACATGTA 60.037 55.000 0.00 0.00 36.38 2.29
2053 2306 0.908910 TTGGGCTCGTCCACATGTAT 59.091 50.000 0.00 0.00 36.38 2.29
2054 2307 0.177836 TGGGCTCGTCCACATGTATG 59.822 55.000 0.00 0.00 36.21 2.39
2055 2308 0.178068 GGGCTCGTCCACATGTATGT 59.822 55.000 0.00 0.00 42.84 2.29
2075 2328 9.435688 TGTATGTGCATCATTAATATGTACTCC 57.564 33.333 17.83 11.10 39.71 3.85
2076 2329 9.658799 GTATGTGCATCATTAATATGTACTCCT 57.341 33.333 17.83 10.70 39.71 3.69
2078 2331 9.658799 ATGTGCATCATTAATATGTACTCCTAC 57.341 33.333 17.83 0.00 39.71 3.18
2079 2332 8.870116 TGTGCATCATTAATATGTACTCCTACT 58.130 33.333 17.83 0.00 39.71 2.57
2080 2333 9.360093 GTGCATCATTAATATGTACTCCTACTC 57.640 37.037 13.58 0.00 37.10 2.59
2081 2334 9.088987 TGCATCATTAATATGTACTCCTACTCA 57.911 33.333 0.00 0.00 33.34 3.41
2082 2335 9.579768 GCATCATTAATATGTACTCCTACTCAG 57.420 37.037 0.00 0.00 33.34 3.35
2090 2343 9.509956 AATATGTACTCCTACTCAGATAGTGAC 57.490 37.037 0.00 0.00 39.39 3.67
2091 2344 6.309389 TGTACTCCTACTCAGATAGTGACA 57.691 41.667 0.00 0.00 39.39 3.58
2092 2345 6.350103 TGTACTCCTACTCAGATAGTGACAG 58.650 44.000 0.00 0.00 39.39 3.51
2093 2346 5.444744 ACTCCTACTCAGATAGTGACAGT 57.555 43.478 0.00 0.00 39.39 3.55
2118 2371 8.993121 GTCAACATAATTGACATATACTCCCTG 58.007 37.037 13.53 0.00 45.89 4.45
2186 2870 8.014322 TCTGACTTCATGTTCGTATTTTGTAC 57.986 34.615 0.00 0.00 0.00 2.90
2189 2873 8.227119 TGACTTCATGTTCGTATTTTGTACATG 58.773 33.333 0.00 0.00 42.79 3.21
2294 3009 7.148018 ACGTCTAATATTTCGTTACAGAGGGAA 60.148 37.037 0.00 0.00 32.62 3.97
2300 3015 9.543783 AATATTTCGTTACAGAGGGAATACTTC 57.456 33.333 0.00 0.00 28.96 3.01
2301 3016 5.988310 TTCGTTACAGAGGGAATACTTCA 57.012 39.130 0.00 0.00 0.00 3.02
2308 3023 6.739331 ACAGAGGGAATACTTCAGAATAGG 57.261 41.667 0.00 0.00 0.00 2.57
2356 3254 8.370493 TCTATTGAGCAGTTTAAGATATGTGC 57.630 34.615 0.00 0.00 0.00 4.57
2369 3267 5.981088 AGATATGTGCAAATTGGTTGTGA 57.019 34.783 0.00 0.00 39.63 3.58
2371 3269 6.158598 AGATATGTGCAAATTGGTTGTGAAC 58.841 36.000 0.00 0.00 39.63 3.18
2383 3281 2.547007 GGTTGTGAACCCCATTTTTCGG 60.547 50.000 0.00 0.00 46.12 4.30
2384 3282 2.074729 TGTGAACCCCATTTTTCGGT 57.925 45.000 0.00 0.00 0.00 4.69
2385 3283 1.683917 TGTGAACCCCATTTTTCGGTG 59.316 47.619 0.00 0.00 0.00 4.94
2386 3284 1.684450 GTGAACCCCATTTTTCGGTGT 59.316 47.619 0.00 0.00 0.00 4.16
2387 3285 2.101750 GTGAACCCCATTTTTCGGTGTT 59.898 45.455 0.00 0.00 0.00 3.32
2389 3443 2.074729 ACCCCATTTTTCGGTGTTCA 57.925 45.000 0.00 0.00 0.00 3.18
2391 3445 2.298729 ACCCCATTTTTCGGTGTTCATG 59.701 45.455 0.00 0.00 0.00 3.07
2394 3448 3.987220 CCCATTTTTCGGTGTTCATGTTC 59.013 43.478 0.00 0.00 0.00 3.18
2395 3449 4.500545 CCCATTTTTCGGTGTTCATGTTCA 60.501 41.667 0.00 0.00 0.00 3.18
2396 3450 4.444056 CCATTTTTCGGTGTTCATGTTCAC 59.556 41.667 12.18 12.18 0.00 3.18
2409 3463 2.151881 TGTTCACCAATTGCATGCAC 57.848 45.000 22.58 6.01 0.00 4.57
2411 3465 2.063266 GTTCACCAATTGCATGCACAG 58.937 47.619 22.58 12.93 0.00 3.66
2413 3467 1.687660 TCACCAATTGCATGCACAGTT 59.312 42.857 22.58 12.93 0.00 3.16
2418 3472 5.179742 CACCAATTGCATGCACAGTTTTATT 59.820 36.000 22.58 12.76 0.00 1.40
2420 3474 6.081049 CCAATTGCATGCACAGTTTTATTTG 58.919 36.000 22.58 7.73 0.00 2.32
2421 3475 5.866335 ATTGCATGCACAGTTTTATTTGG 57.134 34.783 22.58 0.00 0.00 3.28
2422 3476 4.333913 TGCATGCACAGTTTTATTTGGT 57.666 36.364 18.46 0.00 0.00 3.67
2423 3477 4.056740 TGCATGCACAGTTTTATTTGGTG 58.943 39.130 18.46 0.00 0.00 4.17
2424 3478 4.202192 TGCATGCACAGTTTTATTTGGTGA 60.202 37.500 18.46 0.00 0.00 4.02
2425 3479 4.150451 GCATGCACAGTTTTATTTGGTGAC 59.850 41.667 14.21 0.00 0.00 3.67
2426 3480 5.531634 CATGCACAGTTTTATTTGGTGACT 58.468 37.500 0.00 0.00 0.00 3.41
2427 3481 6.676950 CATGCACAGTTTTATTTGGTGACTA 58.323 36.000 0.00 0.00 0.00 2.59
2428 3482 6.312399 TGCACAGTTTTATTTGGTGACTAG 57.688 37.500 0.00 0.00 0.00 2.57
2429 3483 6.058833 TGCACAGTTTTATTTGGTGACTAGA 58.941 36.000 0.00 0.00 0.00 2.43
2430 3484 6.544197 TGCACAGTTTTATTTGGTGACTAGAA 59.456 34.615 0.00 0.00 0.00 2.10
2431 3485 7.078228 GCACAGTTTTATTTGGTGACTAGAAG 58.922 38.462 0.00 0.00 0.00 2.85
2432 3486 7.584987 CACAGTTTTATTTGGTGACTAGAAGG 58.415 38.462 0.00 0.00 0.00 3.46
2433 3487 7.444183 CACAGTTTTATTTGGTGACTAGAAGGA 59.556 37.037 0.00 0.00 0.00 3.36
2434 3488 7.444487 ACAGTTTTATTTGGTGACTAGAAGGAC 59.556 37.037 0.00 0.00 0.00 3.85
2435 3489 7.444183 CAGTTTTATTTGGTGACTAGAAGGACA 59.556 37.037 0.00 0.00 0.00 4.02
2436 3490 7.444487 AGTTTTATTTGGTGACTAGAAGGACAC 59.556 37.037 0.00 0.00 0.00 3.67
2437 3491 6.681729 TTATTTGGTGACTAGAAGGACACT 57.318 37.500 0.00 0.00 34.28 3.55
2438 3492 4.336889 TTTGGTGACTAGAAGGACACTG 57.663 45.455 0.00 0.00 34.28 3.66
2439 3493 3.238788 TGGTGACTAGAAGGACACTGA 57.761 47.619 0.00 0.00 34.28 3.41
2440 3494 3.572642 TGGTGACTAGAAGGACACTGAA 58.427 45.455 0.00 0.00 34.28 3.02
2441 3495 3.964688 TGGTGACTAGAAGGACACTGAAA 59.035 43.478 0.00 0.00 34.28 2.69
2442 3496 4.407621 TGGTGACTAGAAGGACACTGAAAA 59.592 41.667 0.00 0.00 34.28 2.29
2443 3497 5.071788 TGGTGACTAGAAGGACACTGAAAAT 59.928 40.000 0.00 0.00 34.28 1.82
2511 3566 8.041143 TCATTATATAAACCCTAAGCACTGGT 57.959 34.615 0.00 0.00 0.00 4.00
2545 3600 5.476599 TCAGTAATTTAAGCCAATGCAGTGT 59.523 36.000 13.82 0.00 41.13 3.55
2546 3601 5.801947 CAGTAATTTAAGCCAATGCAGTGTC 59.198 40.000 13.82 0.00 41.13 3.67
2641 3801 5.784177 TGGACAGTTACTTGATCTCACTTC 58.216 41.667 0.00 0.00 0.00 3.01
2644 3804 7.397476 TGGACAGTTACTTGATCTCACTTCTAT 59.603 37.037 0.00 0.00 0.00 1.98
3675 5265 2.304761 TGGAATTGTACAGGTCCTGGAC 59.695 50.000 25.55 25.55 44.96 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.159285 GCCCGTTACCTGTTTACACC 58.841 55.000 0.00 0.00 0.00 4.16
1 2 1.881591 TGCCCGTTACCTGTTTACAC 58.118 50.000 0.00 0.00 0.00 2.90
2 3 2.863132 ATGCCCGTTACCTGTTTACA 57.137 45.000 0.00 0.00 0.00 2.41
3 4 5.220912 GGATTTATGCCCGTTACCTGTTTAC 60.221 44.000 0.00 0.00 0.00 2.01
4 5 4.883006 GGATTTATGCCCGTTACCTGTTTA 59.117 41.667 0.00 0.00 0.00 2.01
5 6 3.697542 GGATTTATGCCCGTTACCTGTTT 59.302 43.478 0.00 0.00 0.00 2.83
6 7 3.284617 GGATTTATGCCCGTTACCTGTT 58.715 45.455 0.00 0.00 0.00 3.16
7 8 2.240160 TGGATTTATGCCCGTTACCTGT 59.760 45.455 0.00 0.00 0.00 4.00
8 9 2.616842 GTGGATTTATGCCCGTTACCTG 59.383 50.000 0.00 0.00 0.00 4.00
9 10 2.743838 CGTGGATTTATGCCCGTTACCT 60.744 50.000 0.00 0.00 0.00 3.08
10 11 1.600485 CGTGGATTTATGCCCGTTACC 59.400 52.381 0.00 0.00 0.00 2.85
11 12 2.553086 TCGTGGATTTATGCCCGTTAC 58.447 47.619 0.00 0.00 0.00 2.50
12 13 2.983907 TCGTGGATTTATGCCCGTTA 57.016 45.000 0.00 0.00 0.00 3.18
13 14 2.116827 TTCGTGGATTTATGCCCGTT 57.883 45.000 0.00 0.00 0.00 4.44
14 15 1.741145 GTTTCGTGGATTTATGCCCGT 59.259 47.619 0.00 0.00 0.00 5.28
15 16 1.740585 TGTTTCGTGGATTTATGCCCG 59.259 47.619 0.00 0.00 0.00 6.13
16 17 3.859411 TTGTTTCGTGGATTTATGCCC 57.141 42.857 0.00 0.00 0.00 5.36
17 18 4.384547 GTGTTTGTTTCGTGGATTTATGCC 59.615 41.667 0.00 0.00 0.00 4.40
18 19 4.384547 GGTGTTTGTTTCGTGGATTTATGC 59.615 41.667 0.00 0.00 0.00 3.14
19 20 5.768317 AGGTGTTTGTTTCGTGGATTTATG 58.232 37.500 0.00 0.00 0.00 1.90
20 21 5.533154 TGAGGTGTTTGTTTCGTGGATTTAT 59.467 36.000 0.00 0.00 0.00 1.40
21 22 4.882427 TGAGGTGTTTGTTTCGTGGATTTA 59.118 37.500 0.00 0.00 0.00 1.40
22 23 3.697045 TGAGGTGTTTGTTTCGTGGATTT 59.303 39.130 0.00 0.00 0.00 2.17
23 24 3.283751 TGAGGTGTTTGTTTCGTGGATT 58.716 40.909 0.00 0.00 0.00 3.01
24 25 2.925724 TGAGGTGTTTGTTTCGTGGAT 58.074 42.857 0.00 0.00 0.00 3.41
25 26 2.404923 TGAGGTGTTTGTTTCGTGGA 57.595 45.000 0.00 0.00 0.00 4.02
26 27 4.320202 CCTTATGAGGTGTTTGTTTCGTGG 60.320 45.833 0.00 0.00 38.32 4.94
27 28 4.513692 TCCTTATGAGGTGTTTGTTTCGTG 59.486 41.667 3.04 0.00 43.97 4.35
28 29 4.710324 TCCTTATGAGGTGTTTGTTTCGT 58.290 39.130 3.04 0.00 43.97 3.85
29 30 4.994852 TCTCCTTATGAGGTGTTTGTTTCG 59.005 41.667 3.04 0.00 43.97 3.46
30 31 6.846350 CATCTCCTTATGAGGTGTTTGTTTC 58.154 40.000 3.04 0.00 45.58 2.78
31 32 6.824305 CATCTCCTTATGAGGTGTTTGTTT 57.176 37.500 3.04 0.00 45.58 2.83
39 40 2.619177 CGTCGACATCTCCTTATGAGGT 59.381 50.000 17.16 0.00 43.97 3.85
40 41 2.879026 TCGTCGACATCTCCTTATGAGG 59.121 50.000 17.16 0.00 45.02 3.86
41 42 4.532276 CTTCGTCGACATCTCCTTATGAG 58.468 47.826 17.16 0.00 42.90 2.90
42 43 3.243101 GCTTCGTCGACATCTCCTTATGA 60.243 47.826 17.16 0.00 0.00 2.15
43 44 3.046390 GCTTCGTCGACATCTCCTTATG 58.954 50.000 17.16 0.00 0.00 1.90
44 45 2.034812 GGCTTCGTCGACATCTCCTTAT 59.965 50.000 17.16 0.00 0.00 1.73
45 46 1.404391 GGCTTCGTCGACATCTCCTTA 59.596 52.381 17.16 0.00 0.00 2.69
60 61 0.324943 TTGGTCCAGTGCTAGGCTTC 59.675 55.000 0.00 0.00 0.00 3.86
62 63 1.127567 TGTTGGTCCAGTGCTAGGCT 61.128 55.000 0.00 0.00 0.00 4.58
70 71 2.508928 CGGTGGTGTTGGTCCAGT 59.491 61.111 0.00 0.00 35.49 4.00
90 91 4.692475 GTTGGTGGTCGACGGGGG 62.692 72.222 9.92 0.00 0.00 5.40
142 145 1.796459 GGTCGTGCATTTAGTTGTCGT 59.204 47.619 0.00 0.00 0.00 4.34
150 153 0.250945 TGGCAAGGGTCGTGCATTTA 60.251 50.000 7.95 0.00 44.07 1.40
156 159 2.978010 GTGGTGGCAAGGGTCGTG 60.978 66.667 0.00 0.00 0.00 4.35
193 196 2.717485 GTCGGCGTCGTGGCTATA 59.283 61.111 10.18 0.00 42.02 1.31
204 207 2.888534 CGGTATTGGTGGTCGGCG 60.889 66.667 0.00 0.00 0.00 6.46
207 210 1.520787 GAGGCGGTATTGGTGGTCG 60.521 63.158 0.00 0.00 0.00 4.79
212 215 2.499685 GCTCGAGGCGGTATTGGT 59.500 61.111 15.58 0.00 0.00 3.67
270 288 4.996434 GCTATGGCGGCAGCGGAT 62.996 66.667 19.29 1.93 46.35 4.18
283 301 2.202932 CTTGCGGCGAGGTGCTAT 60.203 61.111 12.98 0.00 45.43 2.97
669 687 0.178992 CCCAGGAAACAACCTCAGCA 60.179 55.000 0.00 0.00 38.32 4.41
678 696 2.632602 TTTGCCGCTCCCAGGAAACA 62.633 55.000 0.00 0.00 0.00 2.83
682 700 2.282180 GTTTTGCCGCTCCCAGGA 60.282 61.111 0.00 0.00 0.00 3.86
683 701 2.282462 AGTTTTGCCGCTCCCAGG 60.282 61.111 0.00 0.00 0.00 4.45
693 711 2.302929 CCGATTCGTTCGCAGTTTTGC 61.303 52.381 5.20 0.00 46.71 3.68
695 713 1.070175 CACCGATTCGTTCGCAGTTTT 60.070 47.619 5.20 0.00 46.71 2.43
699 717 0.787787 TTTCACCGATTCGTTCGCAG 59.212 50.000 5.20 0.00 46.71 5.18
718 736 2.490903 GCAATCTTGAAGCCACATCAGT 59.509 45.455 0.00 0.00 0.00 3.41
759 791 2.351924 TTTCGCAGCTCCCACCCTTT 62.352 55.000 0.00 0.00 0.00 3.11
762 794 1.678970 ATTTTCGCAGCTCCCACCC 60.679 57.895 0.00 0.00 0.00 4.61
782 820 4.067913 TTACCCGGCGACCGTTCC 62.068 66.667 9.30 0.00 46.80 3.62
789 827 0.746063 ATCGTAATGTTACCCGGCGA 59.254 50.000 9.30 0.00 0.00 5.54
838 876 0.529378 GAGATGGCCACAGCTTTTGG 59.471 55.000 8.16 6.75 44.73 3.28
850 888 3.584733 ATTTCCAAGGTAGGAGATGGC 57.415 47.619 0.00 0.00 39.25 4.40
865 903 1.747924 GGCCAGAGCAGAGAAATTTCC 59.252 52.381 14.61 6.57 42.56 3.13
883 921 0.693049 TTCTTCCTCTTGAGGGTGGC 59.307 55.000 15.81 0.00 0.00 5.01
893 931 1.299321 GCTGCTGCCTTCTTCCTCT 59.701 57.895 3.85 0.00 0.00 3.69
895 933 0.892814 GTTGCTGCTGCCTTCTTCCT 60.893 55.000 13.47 0.00 38.71 3.36
903 941 0.730494 GATTCGTTGTTGCTGCTGCC 60.730 55.000 13.47 0.00 38.71 4.85
906 944 1.267806 CAAGGATTCGTTGTTGCTGCT 59.732 47.619 10.26 0.00 0.00 4.24
913 951 2.767505 GAGGTGTCAAGGATTCGTTGT 58.232 47.619 16.31 0.05 32.10 3.32
945 983 5.221244 GGTGGATAGAAGAAGAAGAGAGAGC 60.221 48.000 0.00 0.00 0.00 4.09
946 984 5.890985 TGGTGGATAGAAGAAGAAGAGAGAG 59.109 44.000 0.00 0.00 0.00 3.20
947 985 5.832221 TGGTGGATAGAAGAAGAAGAGAGA 58.168 41.667 0.00 0.00 0.00 3.10
948 986 6.537453 TTGGTGGATAGAAGAAGAAGAGAG 57.463 41.667 0.00 0.00 0.00 3.20
949 987 6.935240 TTTGGTGGATAGAAGAAGAAGAGA 57.065 37.500 0.00 0.00 0.00 3.10
950 988 8.572855 AATTTTGGTGGATAGAAGAAGAAGAG 57.427 34.615 0.00 0.00 0.00 2.85
963 1002 5.194537 AGGTCTCTGGATAATTTTGGTGGAT 59.805 40.000 0.00 0.00 0.00 3.41
1088 1127 4.003788 CGCCGTTGACTCCCCTGT 62.004 66.667 0.00 0.00 0.00 4.00
1095 1134 2.915659 TGGAGGTCGCCGTTGACT 60.916 61.111 4.54 0.00 38.91 3.41
1230 1290 3.000674 CGATGCAGTCTTCAATGTCGTAC 60.001 47.826 0.00 0.00 0.00 3.67
1485 1548 3.033764 TTGTCAGCGGCGTCGAAC 61.034 61.111 16.53 8.49 39.00 3.95
1533 1596 3.944411 ACCCCCACCGGACCCTTA 61.944 66.667 9.46 0.00 0.00 2.69
1805 1896 2.317040 CTGATGTGACCCCGTATACCT 58.683 52.381 0.00 0.00 0.00 3.08
1809 1900 1.830145 GGCTGATGTGACCCCGTAT 59.170 57.895 0.00 0.00 0.00 3.06
1877 1968 1.301677 GCTTTGCCCTGTCTTCCTCG 61.302 60.000 0.00 0.00 0.00 4.63
1943 2037 8.286800 CCTGATGAATTTGTTGTACGAAGTTAA 58.713 33.333 0.00 0.00 37.78 2.01
1950 2044 5.572211 CATCCCTGATGAATTTGTTGTACG 58.428 41.667 0.00 0.00 42.09 3.67
1951 2045 5.343249 GCATCCCTGATGAATTTGTTGTAC 58.657 41.667 8.21 0.00 42.09 2.90
1954 2048 3.735820 CGGCATCCCTGATGAATTTGTTG 60.736 47.826 8.21 0.00 42.09 3.33
1955 2049 2.428171 CGGCATCCCTGATGAATTTGTT 59.572 45.455 8.21 0.00 42.09 2.83
1957 2051 1.338973 CCGGCATCCCTGATGAATTTG 59.661 52.381 8.21 0.00 42.09 2.32
1958 2052 1.215173 TCCGGCATCCCTGATGAATTT 59.785 47.619 8.21 0.00 42.09 1.82
1961 2055 1.728323 TATCCGGCATCCCTGATGAA 58.272 50.000 8.21 0.00 42.09 2.57
1966 2060 0.037303 AGCATTATCCGGCATCCCTG 59.963 55.000 0.00 0.00 0.00 4.45
1967 2061 0.037303 CAGCATTATCCGGCATCCCT 59.963 55.000 0.00 0.00 0.00 4.20
1969 2063 1.160137 GTCAGCATTATCCGGCATCC 58.840 55.000 0.00 0.00 0.00 3.51
1970 2064 1.160137 GGTCAGCATTATCCGGCATC 58.840 55.000 0.00 0.00 0.00 3.91
1971 2065 0.767375 AGGTCAGCATTATCCGGCAT 59.233 50.000 0.00 0.00 0.00 4.40
1973 2067 0.179045 ACAGGTCAGCATTATCCGGC 60.179 55.000 0.00 0.00 0.00 6.13
1974 2068 2.332063 AACAGGTCAGCATTATCCGG 57.668 50.000 0.00 0.00 0.00 5.14
1975 2069 2.355756 CCAAACAGGTCAGCATTATCCG 59.644 50.000 0.00 0.00 0.00 4.18
2009 2221 4.289342 TGCAAATTGAACTGTCATGTTCG 58.711 39.130 0.00 0.00 46.59 3.95
2029 2282 2.359850 TGGACGAGCCCAACATGC 60.360 61.111 0.00 0.00 34.97 4.06
2033 2286 0.036765 TACATGTGGACGAGCCCAAC 60.037 55.000 9.11 0.00 38.06 3.77
2044 2297 8.517056 ACATATTAATGATGCACATACATGTGG 58.483 33.333 20.76 2.98 45.23 4.17
2050 2303 9.658799 AGGAGTACATATTAATGATGCACATAC 57.341 33.333 0.00 0.00 38.38 2.39
2052 2305 9.658799 GTAGGAGTACATATTAATGATGCACAT 57.341 33.333 0.00 0.00 41.45 3.21
2053 2306 8.870116 AGTAGGAGTACATATTAATGATGCACA 58.130 33.333 0.00 0.00 36.54 4.57
2054 2307 9.360093 GAGTAGGAGTACATATTAATGATGCAC 57.640 37.037 0.00 0.29 36.54 4.57
2055 2308 9.088987 TGAGTAGGAGTACATATTAATGATGCA 57.911 33.333 0.00 0.00 36.54 3.96
2056 2309 9.579768 CTGAGTAGGAGTACATATTAATGATGC 57.420 37.037 0.00 0.00 36.54 3.91
2064 2317 9.509956 GTCACTATCTGAGTAGGAGTACATATT 57.490 37.037 0.00 0.00 35.64 1.28
2065 2318 8.661345 TGTCACTATCTGAGTAGGAGTACATAT 58.339 37.037 0.00 0.00 35.64 1.78
2066 2319 8.030913 TGTCACTATCTGAGTAGGAGTACATA 57.969 38.462 0.00 0.00 35.64 2.29
2067 2320 6.901300 TGTCACTATCTGAGTAGGAGTACAT 58.099 40.000 0.00 0.00 35.64 2.29
2068 2321 6.070136 ACTGTCACTATCTGAGTAGGAGTACA 60.070 42.308 0.00 0.00 35.64 2.90
2069 2322 6.350906 ACTGTCACTATCTGAGTAGGAGTAC 58.649 44.000 0.00 0.00 35.64 2.73
2070 2323 6.156429 TGACTGTCACTATCTGAGTAGGAGTA 59.844 42.308 6.36 0.00 35.64 2.59
2071 2324 5.045505 TGACTGTCACTATCTGAGTAGGAGT 60.046 44.000 6.36 0.00 35.64 3.85
2072 2325 5.432645 TGACTGTCACTATCTGAGTAGGAG 58.567 45.833 6.36 0.00 35.64 3.69
2073 2326 5.437191 TGACTGTCACTATCTGAGTAGGA 57.563 43.478 6.36 0.00 35.64 2.94
2074 2327 5.416013 TGTTGACTGTCACTATCTGAGTAGG 59.584 44.000 10.56 0.00 35.64 3.18
2075 2328 6.502136 TGTTGACTGTCACTATCTGAGTAG 57.498 41.667 10.56 0.00 35.64 2.57
2076 2329 8.575649 TTATGTTGACTGTCACTATCTGAGTA 57.424 34.615 10.56 0.00 35.64 2.59
2077 2330 5.991933 ATGTTGACTGTCACTATCTGAGT 57.008 39.130 10.56 0.00 39.82 3.41
2078 2331 8.815189 CAATTATGTTGACTGTCACTATCTGAG 58.185 37.037 10.56 0.00 0.00 3.35
2079 2332 8.531146 TCAATTATGTTGACTGTCACTATCTGA 58.469 33.333 10.56 8.66 0.00 3.27
2080 2333 8.598924 GTCAATTATGTTGACTGTCACTATCTG 58.401 37.037 10.56 6.82 43.91 2.90
2081 2334 8.314021 TGTCAATTATGTTGACTGTCACTATCT 58.686 33.333 10.56 0.00 46.53 1.98
2082 2335 8.479313 TGTCAATTATGTTGACTGTCACTATC 57.521 34.615 10.56 2.67 46.53 2.08
2089 2342 9.547753 GGAGTATATGTCAATTATGTTGACTGT 57.452 33.333 19.90 13.75 46.53 3.55
2090 2343 8.993121 GGGAGTATATGTCAATTATGTTGACTG 58.007 37.037 19.90 0.00 46.53 3.51
2091 2344 8.938883 AGGGAGTATATGTCAATTATGTTGACT 58.061 33.333 19.90 11.83 46.53 3.41
2092 2345 8.993121 CAGGGAGTATATGTCAATTATGTTGAC 58.007 37.037 15.15 15.15 46.57 3.18
2093 2346 8.713971 ACAGGGAGTATATGTCAATTATGTTGA 58.286 33.333 0.00 0.00 0.00 3.18
2164 2848 7.692291 CCATGTACAAAATACGAACATGAAGTC 59.308 37.037 13.72 0.00 46.57 3.01
2211 2896 9.543783 CCTACATTTTGTTAGAGGGAGTATTAC 57.456 37.037 0.00 0.00 0.00 1.89
2274 2989 9.543783 GAAGTATTCCCTCTGTAACGAAATATT 57.456 33.333 0.00 0.00 39.83 1.28
2280 2995 5.258841 TCTGAAGTATTCCCTCTGTAACGA 58.741 41.667 0.00 0.00 46.93 3.85
2281 2996 5.578005 TCTGAAGTATTCCCTCTGTAACG 57.422 43.478 0.00 0.00 46.93 3.18
2283 2998 7.290248 CCCTATTCTGAAGTATTCCCTCTGTAA 59.710 40.741 0.00 0.00 46.93 2.41
2284 2999 6.782988 CCCTATTCTGAAGTATTCCCTCTGTA 59.217 42.308 0.00 0.00 46.93 2.74
2287 3002 5.793967 ACCCTATTCTGAAGTATTCCCTCT 58.206 41.667 0.00 0.00 46.93 3.69
2300 3015 9.847224 AACATAGGTACAAATAACCCTATTCTG 57.153 33.333 0.00 0.00 38.03 3.02
2371 3269 2.298729 ACATGAACACCGAAAAATGGGG 59.701 45.455 0.00 0.00 35.42 4.96
2383 3281 3.715495 TGCAATTGGTGAACATGAACAC 58.285 40.909 7.72 9.00 36.44 3.32
2384 3282 4.308265 CATGCAATTGGTGAACATGAACA 58.692 39.130 14.35 0.00 40.39 3.18
2385 3283 3.123959 GCATGCAATTGGTGAACATGAAC 59.876 43.478 20.50 6.20 40.39 3.18
2386 3284 3.244112 TGCATGCAATTGGTGAACATGAA 60.244 39.130 20.30 11.61 40.39 2.57
2387 3285 2.299297 TGCATGCAATTGGTGAACATGA 59.701 40.909 20.30 8.24 40.39 3.07
2389 3443 2.037381 TGTGCATGCAATTGGTGAACAT 59.963 40.909 24.58 0.00 0.00 2.71
2391 3445 2.063266 CTGTGCATGCAATTGGTGAAC 58.937 47.619 24.58 7.10 0.00 3.18
2394 3448 2.157834 AACTGTGCATGCAATTGGTG 57.842 45.000 24.58 11.12 0.00 4.17
2395 3449 2.914695 AAACTGTGCATGCAATTGGT 57.085 40.000 24.58 15.24 0.00 3.67
2396 3450 5.866335 AATAAAACTGTGCATGCAATTGG 57.134 34.783 24.58 14.59 0.00 3.16
2400 3454 4.510711 CACCAAATAAAACTGTGCATGCAA 59.489 37.500 24.58 11.95 0.00 4.08
2402 3456 4.150451 GTCACCAAATAAAACTGTGCATGC 59.850 41.667 11.82 11.82 0.00 4.06
2403 3457 5.531634 AGTCACCAAATAAAACTGTGCATG 58.468 37.500 0.00 0.00 0.00 4.06
2409 3463 7.444183 TGTCCTTCTAGTCACCAAATAAAACTG 59.556 37.037 0.00 0.00 0.00 3.16
2411 3465 7.444487 AGTGTCCTTCTAGTCACCAAATAAAAC 59.556 37.037 0.00 0.00 0.00 2.43
2413 3467 6.934645 CAGTGTCCTTCTAGTCACCAAATAAA 59.065 38.462 0.00 0.00 0.00 1.40
2418 3472 3.572642 TCAGTGTCCTTCTAGTCACCAA 58.427 45.455 0.00 0.00 0.00 3.67
2420 3474 4.602340 TTTCAGTGTCCTTCTAGTCACC 57.398 45.455 0.00 0.00 0.00 4.02
2421 3475 7.226720 TGAAATTTTCAGTGTCCTTCTAGTCAC 59.773 37.037 7.74 0.00 34.08 3.67
2422 3476 7.279615 TGAAATTTTCAGTGTCCTTCTAGTCA 58.720 34.615 7.74 0.00 34.08 3.41
2423 3477 7.730364 TGAAATTTTCAGTGTCCTTCTAGTC 57.270 36.000 7.74 0.00 34.08 2.59
2462 3517 9.868277 TGAAATAATGTCAAAAACTGAACTTGT 57.132 25.926 0.00 0.00 35.22 3.16
2499 3554 3.914426 ATTCCAGTACCAGTGCTTAGG 57.086 47.619 0.00 0.00 0.00 2.69
2500 3555 5.245531 TGAAATTCCAGTACCAGTGCTTAG 58.754 41.667 0.00 0.00 0.00 2.18
2511 3566 8.871629 TGGCTTAAATTACTGAAATTCCAGTA 57.128 30.769 0.00 0.00 44.82 2.74
2531 3586 1.242076 GACAGACACTGCATTGGCTT 58.758 50.000 10.19 2.04 41.91 4.35
2545 3600 5.480422 TGTAATTCTACTCTGCAAGGACAGA 59.520 40.000 0.00 0.00 44.32 3.41
2546 3601 5.724328 TGTAATTCTACTCTGCAAGGACAG 58.276 41.667 0.00 0.00 39.12 3.51
2644 3804 9.301153 GATCAAGTAACTGCAAAGAAAAGAAAA 57.699 29.630 0.00 0.00 0.00 2.29
2922 4274 3.063997 CAGCTTGGTTAGGTAATTCAGCG 59.936 47.826 0.00 0.00 32.12 5.18


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

AutoCloner maintained by Alex Coulton.