Multiple sequence alignment - TraesCS7A01G111100

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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 TraesCS7A01G111100 chr7A 100.000 3988 0 0 1 3988 68042136 68046123 0.000000e+00 7365
1 TraesCS7A01G111100 chr7A 88.645 3003 309 17 1000 3986 67985132 67988118 0.000000e+00 3627
2 TraesCS7A01G111100 chr7A 86.338 3023 378 22 987 3986 68029169 68032179 0.000000e+00 3262
3 TraesCS7A01G111100 chr7A 81.106 3038 504 50 989 3977 68022487 68025503 0.000000e+00 2366
4 TraesCS7A01G111100 chr7A 91.017 1692 144 4 1000 2684 67592985 67591295 0.000000e+00 2276
5 TraesCS7A01G111100 chr7A 85.056 1887 255 16 2110 3986 68083602 68085471 0.000000e+00 1897
6 TraesCS7A01G111100 chr7A 90.562 890 84 0 998 1887 68077100 68077989 0.000000e+00 1179
7 TraesCS7A01G111100 chr7A 85.410 329 46 2 3658 3985 67584118 67583791 1.370000e-89 340
8 TraesCS7A01G111100 chr7B 88.198 3008 312 20 989 3986 5216548 5219522 0.000000e+00 3548
9 TraesCS7A01G111100 chr7B 85.491 3005 399 21 998 3979 5282138 5285128 0.000000e+00 3099
10 TraesCS7A01G111100 chr7B 85.194 3019 377 36 989 3986 5337076 5340045 0.000000e+00 3035
11 TraesCS7A01G111100 chr7B 83.765 3012 426 35 998 3985 5503194 5506166 0.000000e+00 2795
12 TraesCS7A01G111100 chr7B 90.349 1979 174 7 989 2958 5510156 5512126 0.000000e+00 2580
13 TraesCS7A01G111100 chr7B 84.088 2055 273 32 1966 3986 5196644 5198678 0.000000e+00 1934
14 TraesCS7A01G111100 chr7B 81.576 2030 311 27 2011 3986 5320142 5322162 0.000000e+00 1618
15 TraesCS7A01G111100 chr7B 86.037 931 124 4 987 1914 5195720 5196647 0.000000e+00 994
16 TraesCS7A01G111100 chr7B 88.030 401 24 12 251 643 5502104 5502488 1.690000e-123 453
17 TraesCS7A01G111100 chr7B 91.228 171 11 1 64 234 5501129 5501295 3.100000e-56 230
18 TraesCS7A01G111100 chr7B 79.937 319 48 11 556 864 5195235 5195547 1.870000e-53 220
19 TraesCS7A01G111100 chr7B 88.356 146 15 2 721 864 5509847 5509992 1.470000e-39 174
20 TraesCS7A01G111100 chr7B 87.218 133 14 3 721 850 5336779 5336911 8.930000e-32 148
21 TraesCS7A01G111100 chr7B 92.857 70 5 0 721 790 5216259 5216328 7.050000e-18 102
22 TraesCS7A01G111100 chr7D 87.856 3022 323 22 989 3986 64245424 64248425 0.000000e+00 3507
23 TraesCS7A01G111100 chr7D 85.852 3018 378 34 1000 3985 63943731 63940731 0.000000e+00 3162
24 TraesCS7A01G111100 chr7D 91.040 2299 184 11 974 3255 64222820 64225113 0.000000e+00 3085
25 TraesCS7A01G111100 chr7D 85.238 3028 379 37 989 3986 64265801 64268790 0.000000e+00 3053
26 TraesCS7A01G111100 chr7D 87.717 2076 215 21 1933 3986 59938446 59936389 0.000000e+00 2385
27 TraesCS7A01G111100 chr7D 83.592 579 95 0 3284 3862 64226605 64227183 9.750000e-151 544


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 TraesCS7A01G111100 chr7A 68042136 68046123 3987 False 7365.000000 7365 100.0000 1 3988 1 chr7A.!!$F2 3987
1 TraesCS7A01G111100 chr7A 67985132 67988118 2986 False 3627.000000 3627 88.6450 1000 3986 1 chr7A.!!$F1 2986
2 TraesCS7A01G111100 chr7A 68022487 68032179 9692 False 2814.000000 3262 83.7220 987 3986 2 chr7A.!!$F5 2999
3 TraesCS7A01G111100 chr7A 67591295 67592985 1690 True 2276.000000 2276 91.0170 1000 2684 1 chr7A.!!$R2 1684
4 TraesCS7A01G111100 chr7A 68083602 68085471 1869 False 1897.000000 1897 85.0560 2110 3986 1 chr7A.!!$F4 1876
5 TraesCS7A01G111100 chr7A 68077100 68077989 889 False 1179.000000 1179 90.5620 998 1887 1 chr7A.!!$F3 889
6 TraesCS7A01G111100 chr7B 5282138 5285128 2990 False 3099.000000 3099 85.4910 998 3979 1 chr7B.!!$F1 2981
7 TraesCS7A01G111100 chr7B 5216259 5219522 3263 False 1825.000000 3548 90.5275 721 3986 2 chr7B.!!$F4 3265
8 TraesCS7A01G111100 chr7B 5320142 5322162 2020 False 1618.000000 1618 81.5760 2011 3986 1 chr7B.!!$F2 1975
9 TraesCS7A01G111100 chr7B 5336779 5340045 3266 False 1591.500000 3035 86.2060 721 3986 2 chr7B.!!$F5 3265
10 TraesCS7A01G111100 chr7B 5501129 5512126 10997 False 1246.400000 2795 88.3456 64 3985 5 chr7B.!!$F6 3921
11 TraesCS7A01G111100 chr7B 5195235 5198678 3443 False 1049.333333 1934 83.3540 556 3986 3 chr7B.!!$F3 3430
12 TraesCS7A01G111100 chr7D 64245424 64248425 3001 False 3507.000000 3507 87.8560 989 3986 1 chr7D.!!$F1 2997
13 TraesCS7A01G111100 chr7D 63940731 63943731 3000 True 3162.000000 3162 85.8520 1000 3985 1 chr7D.!!$R2 2985
14 TraesCS7A01G111100 chr7D 64265801 64268790 2989 False 3053.000000 3053 85.2380 989 3986 1 chr7D.!!$F2 2997
15 TraesCS7A01G111100 chr7D 59936389 59938446 2057 True 2385.000000 2385 87.7170 1933 3986 1 chr7D.!!$R1 2053
16 TraesCS7A01G111100 chr7D 64222820 64227183 4363 False 1814.500000 3085 87.3160 974 3862 2 chr7D.!!$F3 2888

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
32 33 0.024238 CGAACTTGCGCTCTTGATCG 59.976 55.0 9.73 7.7 0.00 3.69 F
47 48 0.036388 GATCGACCCAAGCAAGGTGA 60.036 55.0 0.00 0.0 37.88 4.02 F
643 1854 0.108945 GCTTTTGCTCATCCTGTGGC 60.109 55.0 0.00 0.0 43.35 5.01 F
925 2180 0.536460 TCGGGTTCTGGTTTTGCTCC 60.536 55.0 0.00 0.0 0.00 4.70 F
1862 9840 0.166814 CGCAGTGCTAGTCCTTTTGC 59.833 55.0 14.33 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 9239 1.229428 TCGTTGGCTTTCTGCTTGAG 58.771 50.000 0.00 0.0 42.39 3.02 R
1473 9443 1.286501 TATGCAGAGCTAAAACGCGG 58.713 50.000 12.47 0.0 34.40 6.46 R
1594 9564 1.892474 CCCACCAACACCAACAATAGG 59.108 52.381 0.00 0.0 0.00 2.57 R
2296 10321 2.366590 AGAGACATGCTTCAGACACACA 59.633 45.455 0.00 0.0 0.00 3.72 R
3848 13387 0.731417 GAACTTGCAGCATCTCGCAT 59.269 50.000 0.00 0.0 46.13 4.73 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
18 19 2.859992 GCAGAGGGAATTGCGAACT 58.140 52.632 0.00 0.00 0.00 3.01
19 20 1.168714 GCAGAGGGAATTGCGAACTT 58.831 50.000 0.00 0.00 0.00 2.66
20 21 1.135575 GCAGAGGGAATTGCGAACTTG 60.136 52.381 0.00 0.00 0.00 3.16
21 22 1.135575 CAGAGGGAATTGCGAACTTGC 60.136 52.381 0.00 0.00 0.00 4.01
22 23 0.179189 GAGGGAATTGCGAACTTGCG 60.179 55.000 0.00 0.00 37.81 4.85
31 32 3.865914 CGAACTTGCGCTCTTGATC 57.134 52.632 9.73 0.00 0.00 2.92
32 33 0.024238 CGAACTTGCGCTCTTGATCG 59.976 55.000 9.73 7.70 0.00 3.69
33 34 1.350193 GAACTTGCGCTCTTGATCGA 58.650 50.000 9.73 0.00 0.00 3.59
34 35 1.059835 GAACTTGCGCTCTTGATCGAC 59.940 52.381 9.73 0.00 0.00 4.20
35 36 0.737715 ACTTGCGCTCTTGATCGACC 60.738 55.000 9.73 0.00 0.00 4.79
36 37 1.424493 CTTGCGCTCTTGATCGACCC 61.424 60.000 9.73 0.00 0.00 4.46
37 38 2.166130 TTGCGCTCTTGATCGACCCA 62.166 55.000 9.73 0.00 0.00 4.51
38 39 1.447838 GCGCTCTTGATCGACCCAA 60.448 57.895 0.00 0.00 0.00 4.12
39 40 1.424493 GCGCTCTTGATCGACCCAAG 61.424 60.000 18.29 18.29 41.63 3.61
40 41 1.424493 CGCTCTTGATCGACCCAAGC 61.424 60.000 19.14 11.75 40.45 4.01
41 42 0.391661 GCTCTTGATCGACCCAAGCA 60.392 55.000 19.14 10.69 40.45 3.91
42 43 1.945819 GCTCTTGATCGACCCAAGCAA 60.946 52.381 19.14 7.28 40.45 3.91
43 44 2.005451 CTCTTGATCGACCCAAGCAAG 58.995 52.381 19.14 8.24 40.45 4.01
44 45 1.089920 CTTGATCGACCCAAGCAAGG 58.910 55.000 14.09 0.00 35.23 3.61
45 46 0.400213 TTGATCGACCCAAGCAAGGT 59.600 50.000 0.00 0.00 41.50 3.50
46 47 0.321564 TGATCGACCCAAGCAAGGTG 60.322 55.000 0.00 0.00 37.88 4.00
47 48 0.036388 GATCGACCCAAGCAAGGTGA 60.036 55.000 0.00 0.00 37.88 4.02
48 49 0.620556 ATCGACCCAAGCAAGGTGAT 59.379 50.000 0.00 0.00 37.88 3.06
49 50 0.321564 TCGACCCAAGCAAGGTGATG 60.322 55.000 0.00 0.00 37.88 3.07
50 51 1.885871 GACCCAAGCAAGGTGATGC 59.114 57.895 0.00 0.00 46.78 3.91
100 101 0.972883 ATCGAGAGCAAGGATAGGGC 59.027 55.000 0.00 0.00 0.00 5.19
103 104 1.063183 GAGAGCAAGGATAGGGCCAT 58.937 55.000 6.18 0.00 0.00 4.40
122 123 3.064545 CCATCTTTTGCTCGATCTGTTCC 59.935 47.826 0.00 0.00 0.00 3.62
123 124 2.699954 TCTTTTGCTCGATCTGTTCCC 58.300 47.619 0.00 0.00 0.00 3.97
142 143 1.279271 CCCCCTCGTCAATCTCTTGTT 59.721 52.381 0.00 0.00 33.87 2.83
202 203 4.806247 GCAACGCTCAGAGTACATCTAAAT 59.194 41.667 0.00 0.00 36.10 1.40
211 212 9.190858 CTCAGAGTACATCTAAATTGCTATGTC 57.809 37.037 0.00 0.00 36.10 3.06
212 213 8.144478 TCAGAGTACATCTAAATTGCTATGTCC 58.856 37.037 0.00 0.00 36.10 4.02
213 214 7.928167 CAGAGTACATCTAAATTGCTATGTCCA 59.072 37.037 0.00 0.00 36.10 4.02
289 1078 4.862641 AGGCACTTATCCCAGTTGTAAT 57.137 40.909 0.00 0.00 27.25 1.89
290 1079 5.968676 AGGCACTTATCCCAGTTGTAATA 57.031 39.130 0.00 0.00 27.25 0.98
291 1080 6.321821 AGGCACTTATCCCAGTTGTAATAA 57.678 37.500 0.00 0.00 27.25 1.40
342 1134 1.203001 GGTCACCAAGAACATCCCCAA 60.203 52.381 0.00 0.00 32.78 4.12
355 1147 3.258123 ACATCCCCAAATTTGACCGAAAG 59.742 43.478 19.86 10.25 0.00 2.62
356 1148 1.616374 TCCCCAAATTTGACCGAAAGC 59.384 47.619 19.86 0.00 0.00 3.51
359 1151 2.094752 CCCAAATTTGACCGAAAGCGAT 60.095 45.455 19.86 0.00 40.82 4.58
360 1152 3.574614 CCAAATTTGACCGAAAGCGATT 58.425 40.909 19.86 0.00 40.82 3.34
361 1153 3.987220 CCAAATTTGACCGAAAGCGATTT 59.013 39.130 19.86 0.00 40.82 2.17
362 1154 5.157781 CCAAATTTGACCGAAAGCGATTTA 58.842 37.500 19.86 0.00 40.82 1.40
363 1155 5.060446 CCAAATTTGACCGAAAGCGATTTAC 59.940 40.000 19.86 0.00 40.82 2.01
364 1156 3.443054 TTTGACCGAAAGCGATTTACG 57.557 42.857 0.00 4.88 45.66 3.18
387 1179 8.581253 ACGTTTACCCTAATACTAACTACAGT 57.419 34.615 0.00 0.00 0.00 3.55
409 1201 6.850823 CAGTTTCGTCGAAATCTTGAAAATCA 59.149 34.615 22.28 0.00 33.97 2.57
410 1202 6.851330 AGTTTCGTCGAAATCTTGAAAATCAC 59.149 34.615 22.28 6.59 33.97 3.06
411 1203 5.915812 TCGTCGAAATCTTGAAAATCACA 57.084 34.783 0.00 0.00 0.00 3.58
412 1204 6.480524 TCGTCGAAATCTTGAAAATCACAT 57.519 33.333 0.00 0.00 0.00 3.21
422 1214 3.433343 TGAAAATCACATGCATGGGACT 58.567 40.909 33.16 21.49 44.07 3.85
436 1228 2.662596 GACTGTGGGATGCGGTGA 59.337 61.111 0.00 0.00 0.00 4.02
439 1231 1.820906 CTGTGGGATGCGGTGATGG 60.821 63.158 0.00 0.00 0.00 3.51
440 1232 2.256072 CTGTGGGATGCGGTGATGGA 62.256 60.000 0.00 0.00 0.00 3.41
441 1233 1.819632 GTGGGATGCGGTGATGGAC 60.820 63.158 0.00 0.00 0.00 4.02
442 1234 1.995066 TGGGATGCGGTGATGGACT 60.995 57.895 0.00 0.00 0.00 3.85
443 1235 1.524621 GGGATGCGGTGATGGACTG 60.525 63.158 0.00 0.00 0.00 3.51
447 1239 1.561769 ATGCGGTGATGGACTGGGAA 61.562 55.000 0.00 0.00 0.00 3.97
448 1240 1.224592 GCGGTGATGGACTGGGAAT 59.775 57.895 0.00 0.00 0.00 3.01
507 1303 1.695813 TGTTGCAAAAATCATCGGCG 58.304 45.000 0.00 0.00 0.00 6.46
540 1336 5.152623 TGGTTCAGCCTCTATATATGCAC 57.847 43.478 0.00 0.00 38.35 4.57
546 1342 5.954752 TCAGCCTCTATATATGCACTAGCTT 59.045 40.000 0.00 0.00 42.74 3.74
575 1371 3.763360 TGGTTGCTACTCCATTGATTTGG 59.237 43.478 0.00 0.00 38.18 3.28
643 1854 0.108945 GCTTTTGCTCATCCTGTGGC 60.109 55.000 0.00 0.00 43.35 5.01
647 1858 0.694771 TTGCTCATCCTGTGGCTCTT 59.305 50.000 0.00 0.00 0.00 2.85
653 1864 3.415212 TCATCCTGTGGCTCTTTGAAAG 58.585 45.455 0.00 0.00 0.00 2.62
664 1875 6.969473 GTGGCTCTTTGAAAGCAATTAGTATC 59.031 38.462 0.00 0.00 41.66 2.24
665 1876 6.886459 TGGCTCTTTGAAAGCAATTAGTATCT 59.114 34.615 0.00 0.00 41.66 1.98
667 1878 7.912773 GGCTCTTTGAAAGCAATTAGTATCTTC 59.087 37.037 0.00 0.00 41.66 2.87
668 1879 7.637907 GCTCTTTGAAAGCAATTAGTATCTTCG 59.362 37.037 0.00 0.00 39.61 3.79
669 1880 8.771920 TCTTTGAAAGCAATTAGTATCTTCGA 57.228 30.769 0.00 0.00 33.25 3.71
670 1881 8.873830 TCTTTGAAAGCAATTAGTATCTTCGAG 58.126 33.333 0.00 0.00 33.25 4.04
671 1882 6.589830 TGAAAGCAATTAGTATCTTCGAGC 57.410 37.500 0.00 0.00 0.00 5.03
672 1883 6.341316 TGAAAGCAATTAGTATCTTCGAGCT 58.659 36.000 0.00 0.00 0.00 4.09
673 1884 7.489160 TGAAAGCAATTAGTATCTTCGAGCTA 58.511 34.615 0.00 0.00 0.00 3.32
681 1901 5.499004 AGTATCTTCGAGCTATCTCCTCT 57.501 43.478 0.00 0.00 35.94 3.69
691 1911 3.074538 AGCTATCTCCTCTTCCTCCTCTC 59.925 52.174 0.00 0.00 0.00 3.20
698 1918 3.594232 TCCTCTTCCTCCTCTCTACAACT 59.406 47.826 0.00 0.00 0.00 3.16
704 1924 5.986501 TCCTCCTCTCTACAACTTTCTTC 57.013 43.478 0.00 0.00 0.00 2.87
707 1927 6.209788 TCCTCCTCTCTACAACTTTCTTCTTC 59.790 42.308 0.00 0.00 0.00 2.87
710 1930 6.551601 TCCTCTCTACAACTTTCTTCTTCTGT 59.448 38.462 0.00 0.00 0.00 3.41
712 1932 7.713073 CCTCTCTACAACTTTCTTCTTCTGTTT 59.287 37.037 0.00 0.00 0.00 2.83
713 1933 8.425577 TCTCTACAACTTTCTTCTTCTGTTTG 57.574 34.615 0.00 0.00 0.00 2.93
715 1935 9.314321 CTCTACAACTTTCTTCTTCTGTTTGTA 57.686 33.333 0.00 0.00 0.00 2.41
716 1936 9.661563 TCTACAACTTTCTTCTTCTGTTTGTAA 57.338 29.630 0.00 0.00 0.00 2.41
765 1985 3.639672 ATGATGTGCAGAACTGGATCA 57.360 42.857 3.99 3.47 32.40 2.92
794 2014 2.567615 ACTAGTTCACCTTGGGTAGCTG 59.432 50.000 0.00 0.00 32.11 4.24
824 2057 3.190118 GGACTCTGCAAGTTGGATTTGAG 59.810 47.826 4.75 7.69 38.74 3.02
825 2059 2.555757 ACTCTGCAAGTTGGATTTGAGC 59.444 45.455 10.73 0.00 33.03 4.26
830 2064 2.670509 GCAAGTTGGATTTGAGCAGCTC 60.671 50.000 16.21 16.21 0.00 4.09
869 2104 8.919661 CATTCTTCTATTTCTGCTTTGGAAAAC 58.080 33.333 0.00 0.00 36.47 2.43
870 2105 7.823745 TCTTCTATTTCTGCTTTGGAAAACT 57.176 32.000 0.00 0.00 36.47 2.66
871 2106 8.918202 TCTTCTATTTCTGCTTTGGAAAACTA 57.082 30.769 0.00 0.00 36.47 2.24
878 2114 6.834168 TCTGCTTTGGAAAACTATAAAGGG 57.166 37.500 0.00 0.00 32.30 3.95
879 2115 6.311735 TCTGCTTTGGAAAACTATAAAGGGT 58.688 36.000 0.00 0.00 32.30 4.34
898 2153 1.091197 TGCACTGCATATCCGCACAG 61.091 55.000 0.00 0.00 36.86 3.66
899 2154 1.091771 GCACTGCATATCCGCACAGT 61.092 55.000 0.00 0.00 43.92 3.55
902 2157 3.133691 CACTGCATATCCGCACAGTAAT 58.866 45.455 0.00 0.00 41.28 1.89
908 2163 4.434725 GCATATCCGCACAGTAATCAATCG 60.435 45.833 0.00 0.00 0.00 3.34
914 2169 3.270877 GCACAGTAATCAATCGGGTTCT 58.729 45.455 0.00 0.00 0.00 3.01
925 2180 0.536460 TCGGGTTCTGGTTTTGCTCC 60.536 55.000 0.00 0.00 0.00 4.70
929 2184 1.266989 GGTTCTGGTTTTGCTCCTTCG 59.733 52.381 0.00 0.00 0.00 3.79
935 2190 1.266989 GGTTTTGCTCCTTCGGTCTTG 59.733 52.381 0.00 0.00 0.00 3.02
940 2206 0.868406 GCTCCTTCGGTCTTGTTGTG 59.132 55.000 0.00 0.00 0.00 3.33
970 2236 1.341209 GAGTTTCAACCCAAGGGCAAG 59.659 52.381 4.70 0.00 39.32 4.01
994 2279 4.261656 CGAGAGCAGATACGGATAAAGGTT 60.262 45.833 0.00 0.00 0.00 3.50
996 2281 4.406003 AGAGCAGATACGGATAAAGGTTGT 59.594 41.667 0.00 0.00 0.00 3.32
1044 2329 2.356780 CCCCGTCCTCCGTAAGCTT 61.357 63.158 3.48 3.48 33.66 3.74
1135 9105 1.153309 CTGGAGATGATGCACGCCA 60.153 57.895 0.00 0.00 35.03 5.69
1150 9120 1.066716 ACGCCATACTTCGCAAGGTTA 60.067 47.619 1.84 0.00 38.47 2.85
1305 9275 2.881074 ACGAACATGAGGAATCGAGTG 58.119 47.619 0.00 0.00 38.59 3.51
1335 9305 3.142174 CCTCAAGAAGACCACCAAACTC 58.858 50.000 0.00 0.00 0.00 3.01
1402 9372 1.461559 AGCTCAAGATCTTGCCAAGC 58.538 50.000 27.87 27.87 40.24 4.01
1425 9395 1.375013 GGCGGACCTGCGTAAAAGA 60.375 57.895 2.88 0.00 35.06 2.52
1448 9418 1.260825 CGAGCTTGACATGCATAGCAG 59.739 52.381 18.82 10.06 43.65 4.24
1452 9422 3.118482 AGCTTGACATGCATAGCAGTAGT 60.118 43.478 18.82 2.84 43.65 2.73
1473 9443 1.688811 TGGTGCTACCATTGACCCC 59.311 57.895 4.16 0.00 44.79 4.95
1479 9449 2.530958 CTACCATTGACCCCCGCGTT 62.531 60.000 4.92 0.00 0.00 4.84
1491 9461 1.369091 CCCGCGTTTTAGCTCTGCAT 61.369 55.000 4.92 0.00 34.40 3.96
1587 9557 5.010282 GGGAGTTCTAAGGAGCAATTGAAA 58.990 41.667 10.34 0.00 0.00 2.69
1594 9564 4.440839 AAGGAGCAATTGAAAACGATCC 57.559 40.909 10.34 0.00 37.40 3.36
1687 9657 4.734398 TTTGATTGTGTGGCTTTTGTCT 57.266 36.364 0.00 0.00 0.00 3.41
1862 9840 0.166814 CGCAGTGCTAGTCCTTTTGC 59.833 55.000 14.33 0.00 0.00 3.68
1871 9849 8.408601 CAGTGCTAGTCCTTTTGCATATATTTT 58.591 33.333 0.00 0.00 37.76 1.82
2080 10066 7.894753 TTTTTGCATCCATATCATTAGTGGA 57.105 32.000 0.00 0.00 45.37 4.02
2296 10321 0.102120 CACAACAACCCGCAATGTGT 59.898 50.000 0.00 0.00 37.27 3.72
2539 10564 6.488715 AGGATAAAGCAGAAAGAAGAATGGT 58.511 36.000 0.00 0.00 0.00 3.55
2670 10695 6.095440 AGCCTTGTTTGTTATACCTAAGCATG 59.905 38.462 0.00 0.00 0.00 4.06
2722 10747 1.133668 GGCTGATATGGAGGTGGCTTT 60.134 52.381 0.00 0.00 0.00 3.51
2745 10770 6.078456 TCTGAAGGGTTTATCCAATGTGAT 57.922 37.500 0.00 0.00 38.11 3.06
2797 10822 5.507315 GGAGAGAGCTACTACAATGAGCTTC 60.507 48.000 0.00 0.00 46.42 3.86
2821 10846 0.183014 CAGGAGCTTGATCCAGCCAT 59.817 55.000 14.83 2.33 42.26 4.40
2947 10972 3.762288 GGATAATGATGAGTGGCATGCAT 59.238 43.478 21.36 3.18 37.34 3.96
2953 10978 3.818773 TGATGAGTGGCATGCATCTAATG 59.181 43.478 21.36 0.00 39.24 1.90
3026 11051 8.388484 GTTCAGAACCATCAATTAGATAGCAT 57.612 34.615 1.29 0.00 34.43 3.79
3046 11071 4.884164 GCATTAGCCTATCAAAAGTGAGGT 59.116 41.667 0.00 0.00 33.69 3.85
3138 11163 3.091545 GCTGGATCTTGGAAATTGTGGA 58.908 45.455 0.00 0.00 0.00 4.02
3141 11166 4.739793 TGGATCTTGGAAATTGTGGAAGT 58.260 39.130 0.00 0.00 0.00 3.01
3142 11167 4.523943 TGGATCTTGGAAATTGTGGAAGTG 59.476 41.667 0.00 0.00 0.00 3.16
3154 11188 1.834263 GTGGAAGTGGCTCTGGTATCT 59.166 52.381 0.00 0.00 0.00 1.98
3168 11202 6.701145 TCTGGTATCTGTCTCAAGTATGTC 57.299 41.667 0.00 0.00 0.00 3.06
3208 11242 2.795960 AGGTACCTAGGGCTCAGGAATA 59.204 50.000 14.41 0.00 36.61 1.75
3211 11245 3.130734 ACCTAGGGCTCAGGAATACAA 57.869 47.619 14.81 0.00 36.61 2.41
3237 11271 1.062587 CGCGAACTCCCAATTGACATC 59.937 52.381 7.12 0.00 0.00 3.06
3375 12878 2.190538 CTGCCAAAAGGAATGGGGAAT 58.809 47.619 0.00 0.00 38.44 3.01
3379 12882 3.873410 GCCAAAAGGAATGGGGAATTTGG 60.873 47.826 10.01 10.01 40.28 3.28
3383 12886 6.385467 CCAAAAGGAATGGGGAATTTGGTATA 59.615 38.462 6.87 0.00 34.58 1.47
3388 12891 4.741928 ATGGGGAATTTGGTATACCTCC 57.258 45.455 22.41 19.03 36.82 4.30
3461 12964 2.497675 TGAGCCATCTGACAGAGGTTAC 59.502 50.000 15.47 5.35 0.00 2.50
3464 12967 2.094182 GCCATCTGACAGAGGTTACGAA 60.094 50.000 15.47 0.00 0.00 3.85
3480 12983 5.005490 GGTTACGAAGCTCATACTTTACTGC 59.995 44.000 0.00 0.00 0.00 4.40
3483 12986 3.240861 CGAAGCTCATACTTTACTGCGAC 59.759 47.826 0.00 0.00 0.00 5.19
3493 12996 4.890088 ACTTTACTGCGACAATAAGGACA 58.110 39.130 0.00 0.00 0.00 4.02
3495 12998 5.938125 ACTTTACTGCGACAATAAGGACATT 59.062 36.000 0.00 0.00 0.00 2.71
3502 13005 4.024556 GCGACAATAAGGACATTGATCTGG 60.025 45.833 3.01 0.00 38.01 3.86
3580 13083 4.799564 TGGATTAATTTTGGTGGCAGAC 57.200 40.909 0.00 0.00 0.00 3.51
3599 13108 1.814394 ACTGAATGATTGCATGCGTGT 59.186 42.857 14.09 0.46 32.23 4.49
3634 13143 5.515886 CCCCCTCCACAACTTCATACTTTTA 60.516 44.000 0.00 0.00 0.00 1.52
3646 13179 7.398024 ACTTCATACTTTTAAGTCATGGAGCT 58.602 34.615 14.04 0.00 40.37 4.09
3649 13185 7.394016 TCATACTTTTAAGTCATGGAGCTTCA 58.606 34.615 0.00 0.00 40.37 3.02
3650 13186 7.882791 TCATACTTTTAAGTCATGGAGCTTCAA 59.117 33.333 0.00 0.00 40.37 2.69
3651 13187 6.959639 ACTTTTAAGTCATGGAGCTTCAAA 57.040 33.333 0.00 0.00 32.86 2.69
3652 13188 6.974965 ACTTTTAAGTCATGGAGCTTCAAAG 58.025 36.000 19.01 19.01 39.69 2.77
3704 13243 2.809601 CTCAACGTCGCTTCCCCG 60.810 66.667 0.00 0.00 0.00 5.73
3751 13290 0.329596 AGAACTGCAAGGGGATGACC 59.670 55.000 0.00 0.00 39.30 4.02
3790 13329 1.882989 GCCTGCTCTTCGGTCTCTGT 61.883 60.000 0.00 0.00 0.00 3.41
3844 13383 1.451927 GTGAGGGCCGATGCATTCA 60.452 57.895 0.00 0.00 40.13 2.57
3845 13384 1.153107 TGAGGGCCGATGCATTCAG 60.153 57.895 0.00 0.00 40.13 3.02
3848 13387 1.002430 GAGGGCCGATGCATTCAGATA 59.998 52.381 0.00 0.00 40.13 1.98
3986 13525 0.321919 GAGGTTGACTGCAGCATGGA 60.322 55.000 15.27 0.00 35.86 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135575 CAAGTTCGCAATTCCCTCTGC 60.136 52.381 0.00 0.00 35.14 4.26
1 2 1.135575 GCAAGTTCGCAATTCCCTCTG 60.136 52.381 0.00 0.00 0.00 3.35
15 16 1.071605 GTCGATCAAGAGCGCAAGTT 58.928 50.000 11.47 0.00 40.42 2.66
16 17 0.737715 GGTCGATCAAGAGCGCAAGT 60.738 55.000 11.47 0.00 40.42 3.16
17 18 1.424493 GGGTCGATCAAGAGCGCAAG 61.424 60.000 11.47 0.00 40.42 4.01
18 19 1.447838 GGGTCGATCAAGAGCGCAA 60.448 57.895 11.47 0.00 40.42 4.85
19 20 2.166130 TTGGGTCGATCAAGAGCGCA 62.166 55.000 11.47 0.00 40.42 6.09
20 21 1.424493 CTTGGGTCGATCAAGAGCGC 61.424 60.000 20.07 0.00 42.94 5.92
21 22 1.424493 GCTTGGGTCGATCAAGAGCG 61.424 60.000 25.57 0.65 42.94 5.03
22 23 0.391661 TGCTTGGGTCGATCAAGAGC 60.392 55.000 25.57 18.24 42.94 4.09
23 24 2.005451 CTTGCTTGGGTCGATCAAGAG 58.995 52.381 25.57 15.65 42.94 2.85
24 25 1.339055 CCTTGCTTGGGTCGATCAAGA 60.339 52.381 25.57 13.57 42.94 3.02
25 26 1.089920 CCTTGCTTGGGTCGATCAAG 58.910 55.000 20.29 20.29 43.10 3.02
26 27 0.400213 ACCTTGCTTGGGTCGATCAA 59.600 50.000 0.00 0.88 30.15 2.57
27 28 0.321564 CACCTTGCTTGGGTCGATCA 60.322 55.000 0.00 0.00 34.44 2.92
28 29 0.036388 TCACCTTGCTTGGGTCGATC 60.036 55.000 0.00 0.00 34.44 3.69
29 30 0.620556 ATCACCTTGCTTGGGTCGAT 59.379 50.000 0.00 0.00 34.44 3.59
30 31 0.321564 CATCACCTTGCTTGGGTCGA 60.322 55.000 1.00 0.00 34.44 4.20
31 32 1.926511 GCATCACCTTGCTTGGGTCG 61.927 60.000 1.00 0.00 39.57 4.79
32 33 1.885871 GCATCACCTTGCTTGGGTC 59.114 57.895 1.00 0.00 39.57 4.46
33 34 4.102113 GCATCACCTTGCTTGGGT 57.898 55.556 1.00 0.00 39.57 4.51
39 40 1.000060 TGAGCAAAAGCATCACCTTGC 60.000 47.619 0.00 0.00 43.56 4.01
40 41 3.057104 TGATGAGCAAAAGCATCACCTTG 60.057 43.478 0.00 0.00 44.17 3.61
41 42 3.159472 TGATGAGCAAAAGCATCACCTT 58.841 40.909 0.00 0.00 44.17 3.50
42 43 2.799017 TGATGAGCAAAAGCATCACCT 58.201 42.857 0.00 0.00 44.17 4.00
46 47 3.517602 TGCAATGATGAGCAAAAGCATC 58.482 40.909 0.00 0.00 40.92 3.91
47 48 3.056107 ACTGCAATGATGAGCAAAAGCAT 60.056 39.130 0.00 0.00 40.73 3.79
48 49 2.297880 ACTGCAATGATGAGCAAAAGCA 59.702 40.909 0.00 0.00 40.73 3.91
49 50 2.921754 GACTGCAATGATGAGCAAAAGC 59.078 45.455 0.00 0.00 40.73 3.51
50 51 3.168963 CGACTGCAATGATGAGCAAAAG 58.831 45.455 0.00 0.00 40.73 2.27
51 52 2.553602 ACGACTGCAATGATGAGCAAAA 59.446 40.909 0.00 0.00 40.73 2.44
52 53 2.095617 CACGACTGCAATGATGAGCAAA 60.096 45.455 0.00 0.00 40.73 3.68
53 54 1.465777 CACGACTGCAATGATGAGCAA 59.534 47.619 0.00 0.00 40.73 3.91
54 55 1.081094 CACGACTGCAATGATGAGCA 58.919 50.000 0.00 0.00 39.25 4.26
55 56 1.081892 ACACGACTGCAATGATGAGC 58.918 50.000 0.00 0.00 0.00 4.26
56 57 2.071540 ACACACGACTGCAATGATGAG 58.928 47.619 0.00 0.00 0.00 2.90
57 58 1.799994 CACACACGACTGCAATGATGA 59.200 47.619 0.00 0.00 0.00 2.92
58 59 1.532437 ACACACACGACTGCAATGATG 59.468 47.619 0.00 0.00 0.00 3.07
59 60 1.882912 ACACACACGACTGCAATGAT 58.117 45.000 0.00 0.00 0.00 2.45
60 61 2.035321 TCTACACACACGACTGCAATGA 59.965 45.455 0.00 0.00 0.00 2.57
61 62 2.403259 TCTACACACACGACTGCAATG 58.597 47.619 0.00 0.00 0.00 2.82
62 63 2.812358 TCTACACACACGACTGCAAT 57.188 45.000 0.00 0.00 0.00 3.56
63 64 2.672714 GATCTACACACACGACTGCAA 58.327 47.619 0.00 0.00 0.00 4.08
64 65 1.401018 CGATCTACACACACGACTGCA 60.401 52.381 0.00 0.00 0.00 4.41
65 66 1.135774 TCGATCTACACACACGACTGC 60.136 52.381 0.00 0.00 0.00 4.40
66 67 2.415512 TCTCGATCTACACACACGACTG 59.584 50.000 0.00 0.00 0.00 3.51
67 68 2.673862 CTCTCGATCTACACACACGACT 59.326 50.000 0.00 0.00 0.00 4.18
68 69 2.788407 GCTCTCGATCTACACACACGAC 60.788 54.545 0.00 0.00 0.00 4.34
100 101 3.064545 GGAACAGATCGAGCAAAAGATGG 59.935 47.826 2.38 0.00 0.00 3.51
103 104 2.615493 GGGGAACAGATCGAGCAAAAGA 60.615 50.000 2.38 0.00 0.00 2.52
122 123 0.905357 ACAAGAGATTGACGAGGGGG 59.095 55.000 0.00 0.00 0.00 5.40
123 124 2.350522 CAACAAGAGATTGACGAGGGG 58.649 52.381 0.00 0.00 0.00 4.79
151 152 3.756117 CAAAAGTCTTTGTAGCTCCCCT 58.244 45.455 0.00 0.00 37.69 4.79
202 203 4.508551 AATCTGACCATGGACATAGCAA 57.491 40.909 21.47 2.50 0.00 3.91
276 1065 8.107095 TCTTAGCTTGTTTATTACAACTGGGAT 58.893 33.333 0.00 0.00 41.73 3.85
290 1079 8.669243 GCACTACTCATAAATCTTAGCTTGTTT 58.331 33.333 0.00 0.00 0.00 2.83
291 1080 7.824289 TGCACTACTCATAAATCTTAGCTTGTT 59.176 33.333 0.00 0.00 0.00 2.83
305 1094 4.562757 GGTGACCAAAGTGCACTACTCATA 60.563 45.833 22.01 3.12 39.18 2.15
308 1097 2.143925 GGTGACCAAAGTGCACTACTC 58.856 52.381 22.01 12.27 39.18 2.59
342 1134 4.083696 ACGTAAATCGCTTTCGGTCAAATT 60.084 37.500 0.00 0.00 44.19 1.82
355 1147 8.480066 GTTAGTATTAGGGTAAACGTAAATCGC 58.520 37.037 0.00 0.00 44.19 4.58
356 1148 9.736023 AGTTAGTATTAGGGTAAACGTAAATCG 57.264 33.333 0.00 0.00 46.00 3.34
361 1153 9.681062 ACTGTAGTTAGTATTAGGGTAAACGTA 57.319 33.333 0.00 0.00 0.00 3.57
362 1154 8.581253 ACTGTAGTTAGTATTAGGGTAAACGT 57.419 34.615 0.00 0.00 0.00 3.99
363 1155 9.860898 AAACTGTAGTTAGTATTAGGGTAAACG 57.139 33.333 0.00 0.00 37.25 3.60
383 1175 5.728351 TTTCAAGATTTCGACGAAACTGT 57.272 34.783 24.21 9.80 34.23 3.55
386 1178 6.631238 TGTGATTTTCAAGATTTCGACGAAAC 59.369 34.615 24.21 17.21 34.23 2.78
387 1179 6.720343 TGTGATTTTCAAGATTTCGACGAAA 58.280 32.000 23.98 23.98 35.94 3.46
391 1183 5.858049 TGCATGTGATTTTCAAGATTTCGAC 59.142 36.000 0.00 0.00 0.00 4.20
409 1201 1.000521 CCCACAGTCCCATGCATGT 60.001 57.895 24.58 4.09 0.00 3.21
410 1202 0.106369 ATCCCACAGTCCCATGCATG 60.106 55.000 20.19 20.19 0.00 4.06
411 1203 0.106369 CATCCCACAGTCCCATGCAT 60.106 55.000 0.00 0.00 0.00 3.96
412 1204 1.303948 CATCCCACAGTCCCATGCA 59.696 57.895 0.00 0.00 0.00 3.96
422 1214 2.271821 CCATCACCGCATCCCACA 59.728 61.111 0.00 0.00 0.00 4.17
436 1228 2.219216 ATCCCAGATTCCCAGTCCAT 57.781 50.000 0.00 0.00 0.00 3.41
439 1231 1.344763 CGGTATCCCAGATTCCCAGTC 59.655 57.143 0.00 0.00 0.00 3.51
440 1232 1.062428 TCGGTATCCCAGATTCCCAGT 60.062 52.381 0.00 0.00 0.00 4.00
441 1233 1.717032 TCGGTATCCCAGATTCCCAG 58.283 55.000 0.00 0.00 0.00 4.45
442 1234 2.257207 GATCGGTATCCCAGATTCCCA 58.743 52.381 0.00 0.00 0.00 4.37
443 1235 2.028020 GTGATCGGTATCCCAGATTCCC 60.028 54.545 0.00 0.00 0.00 3.97
447 1239 2.251818 CTGGTGATCGGTATCCCAGAT 58.748 52.381 13.38 0.00 44.85 2.90
448 1240 1.063190 ACTGGTGATCGGTATCCCAGA 60.063 52.381 20.40 0.00 44.85 3.86
485 1281 2.799412 GCCGATGATTTTTGCAACAACA 59.201 40.909 0.00 0.87 0.00 3.33
525 1321 6.039616 GTGAAGCTAGTGCATATATAGAGGC 58.960 44.000 0.00 0.00 42.74 4.70
540 1336 2.498167 AGCAACCACAAGTGAAGCTAG 58.502 47.619 0.94 0.00 32.83 3.42
546 1342 1.765904 TGGAGTAGCAACCACAAGTGA 59.234 47.619 0.94 0.00 0.00 3.41
575 1371 3.026694 AGCTCCCAAATGCATTACCTTC 58.973 45.455 13.39 1.17 0.00 3.46
638 1849 4.584325 ACTAATTGCTTTCAAAGAGCCACA 59.416 37.500 0.00 0.00 39.38 4.17
643 1854 8.873830 TCGAAGATACTAATTGCTTTCAAAGAG 58.126 33.333 0.00 0.00 35.56 2.85
647 1858 6.818644 AGCTCGAAGATACTAATTGCTTTCAA 59.181 34.615 0.00 0.00 33.89 2.69
653 1864 6.750039 GGAGATAGCTCGAAGATACTAATTGC 59.250 42.308 1.16 0.00 42.25 3.56
664 1875 3.486383 AGGAAGAGGAGATAGCTCGAAG 58.514 50.000 1.16 0.00 42.25 3.79
665 1876 3.482436 GAGGAAGAGGAGATAGCTCGAA 58.518 50.000 1.16 0.00 42.25 3.71
667 1878 2.159382 GGAGGAAGAGGAGATAGCTCG 58.841 57.143 1.16 0.00 42.25 5.03
668 1879 3.074538 AGAGGAGGAAGAGGAGATAGCTC 59.925 52.174 0.00 0.00 40.54 4.09
669 1880 3.063650 AGAGGAGGAAGAGGAGATAGCT 58.936 50.000 0.00 0.00 0.00 3.32
670 1881 3.074538 AGAGAGGAGGAAGAGGAGATAGC 59.925 52.174 0.00 0.00 0.00 2.97
671 1882 5.309543 TGTAGAGAGGAGGAAGAGGAGATAG 59.690 48.000 0.00 0.00 0.00 2.08
672 1883 5.228383 TGTAGAGAGGAGGAAGAGGAGATA 58.772 45.833 0.00 0.00 0.00 1.98
673 1884 4.051478 TGTAGAGAGGAGGAAGAGGAGAT 58.949 47.826 0.00 0.00 0.00 2.75
681 1901 6.078664 AGAAGAAAGTTGTAGAGAGGAGGAA 58.921 40.000 0.00 0.00 0.00 3.36
731 1951 6.038936 TCTGCACATCATAAATTCACATCAGG 59.961 38.462 0.00 0.00 0.00 3.86
765 1985 4.263506 CCCAAGGTGAACTAGTGGAGAATT 60.264 45.833 0.00 0.00 0.00 2.17
813 2046 1.831580 AGGAGCTGCTCAAATCCAAC 58.168 50.000 28.95 10.61 34.08 3.77
852 2087 8.314021 CCCTTTATAGTTTTCCAAAGCAGAAAT 58.686 33.333 0.00 0.00 33.45 2.17
869 2104 4.697352 GGATATGCAGTGCACCCTTTATAG 59.303 45.833 22.44 0.00 43.04 1.31
870 2105 4.651778 GGATATGCAGTGCACCCTTTATA 58.348 43.478 22.44 7.42 43.04 0.98
871 2106 3.490348 GGATATGCAGTGCACCCTTTAT 58.510 45.455 22.44 13.88 43.04 1.40
874 2110 0.464373 CGGATATGCAGTGCACCCTT 60.464 55.000 22.44 7.12 43.04 3.95
878 2114 3.812203 TGCGGATATGCAGTGCAC 58.188 55.556 22.44 9.40 43.04 4.57
898 2153 5.399013 CAAAACCAGAACCCGATTGATTAC 58.601 41.667 0.00 0.00 0.00 1.89
899 2154 4.082463 GCAAAACCAGAACCCGATTGATTA 60.082 41.667 0.00 0.00 0.00 1.75
902 2157 1.611491 GCAAAACCAGAACCCGATTGA 59.389 47.619 0.00 0.00 0.00 2.57
908 2163 1.613925 GAAGGAGCAAAACCAGAACCC 59.386 52.381 0.00 0.00 0.00 4.11
925 2180 1.013596 TGCACACAACAAGACCGAAG 58.986 50.000 0.00 0.00 0.00 3.79
929 2184 1.202394 TGCAATGCACACAACAAGACC 60.202 47.619 2.72 0.00 31.71 3.85
935 2190 2.497107 AACTCTGCAATGCACACAAC 57.503 45.000 2.72 0.00 33.79 3.32
940 2206 2.397549 GGTTGAAACTCTGCAATGCAC 58.602 47.619 2.72 0.00 33.79 4.57
970 2236 2.991434 TTATCCGTATCTGCTCTCGC 57.009 50.000 0.00 0.00 0.00 5.03
979 2264 7.383687 TCCATATCACAACCTTTATCCGTATC 58.616 38.462 0.00 0.00 0.00 2.24
981 2266 6.239487 CCTCCATATCACAACCTTTATCCGTA 60.239 42.308 0.00 0.00 0.00 4.02
984 2269 5.941788 ACCTCCATATCACAACCTTTATCC 58.058 41.667 0.00 0.00 0.00 2.59
994 2279 0.463654 GCGGCAACCTCCATATCACA 60.464 55.000 0.00 0.00 0.00 3.58
996 2281 0.179048 CAGCGGCAACCTCCATATCA 60.179 55.000 1.45 0.00 0.00 2.15
1150 9120 2.581354 GTCTGATGGCACCTCGCT 59.419 61.111 0.00 0.00 41.91 4.93
1269 9239 1.229428 TCGTTGGCTTTCTGCTTGAG 58.771 50.000 0.00 0.00 42.39 3.02
1305 9275 5.644206 GGTGGTCTTCTTGAGGAACTTATTC 59.356 44.000 0.00 0.00 41.55 1.75
1335 9305 1.963515 AGTGCCTTGCCTTTACCAAAG 59.036 47.619 0.00 0.00 38.24 2.77
1350 9320 4.978083 ATCACAGATTTGATGAAGTGCC 57.022 40.909 0.00 0.00 34.79 5.01
1402 9372 3.583276 TACGCAGGTCCGCCAACTG 62.583 63.158 0.00 0.00 37.19 3.16
1425 9395 3.062763 GCTATGCATGTCAAGCTCGTAT 58.937 45.455 10.16 0.00 32.18 3.06
1473 9443 1.286501 TATGCAGAGCTAAAACGCGG 58.713 50.000 12.47 0.00 34.40 6.46
1479 9449 6.291377 CCCTACATCTTTATGCAGAGCTAAA 58.709 40.000 0.00 0.00 36.50 1.85
1491 9461 4.324254 CCAACAAGCTCCCCTACATCTTTA 60.324 45.833 0.00 0.00 0.00 1.85
1587 9557 3.713826 ACACCAACAATAGGGATCGTT 57.286 42.857 0.00 0.00 0.00 3.85
1594 9564 1.892474 CCCACCAACACCAACAATAGG 59.108 52.381 0.00 0.00 0.00 2.57
1852 9827 9.603921 CATTTCCAAAATATATGCAAAAGGACT 57.396 29.630 0.00 0.00 0.00 3.85
1871 9849 5.545063 TCTCACTACTTCACACATTTCCA 57.455 39.130 0.00 0.00 0.00 3.53
2100 10109 9.715121 TGTAACAAGGATAAACTGGTACTAAAG 57.285 33.333 0.00 0.00 0.00 1.85
2103 10112 9.492973 GTTTGTAACAAGGATAAACTGGTACTA 57.507 33.333 0.00 0.00 0.00 1.82
2104 10113 8.215736 AGTTTGTAACAAGGATAAACTGGTACT 58.784 33.333 0.00 0.00 39.37 2.73
2105 10114 8.387190 AGTTTGTAACAAGGATAAACTGGTAC 57.613 34.615 0.00 0.00 39.37 3.34
2106 10115 8.983702 AAGTTTGTAACAAGGATAAACTGGTA 57.016 30.769 0.00 0.00 40.35 3.25
2107 10116 7.558444 TGAAGTTTGTAACAAGGATAAACTGGT 59.442 33.333 0.00 0.00 40.35 4.00
2108 10117 7.936584 TGAAGTTTGTAACAAGGATAAACTGG 58.063 34.615 0.00 0.00 40.35 4.00
2178 10203 5.554070 TCGATTACGATGAGGTACCTATGA 58.446 41.667 16.29 1.88 43.81 2.15
2296 10321 2.366590 AGAGACATGCTTCAGACACACA 59.633 45.455 0.00 0.00 0.00 3.72
2481 10506 8.935614 TGACTAGAAGGCTAGCTATTGTAATA 57.064 34.615 15.72 0.67 46.55 0.98
2670 10695 7.607250 TCTTAATCTCAGAGTCTTCAGGAAAC 58.393 38.462 0.00 0.00 0.00 2.78
2722 10747 5.512942 TCACATTGGATAAACCCTTCAGA 57.487 39.130 0.00 0.00 38.00 3.27
2745 10770 5.197451 TCAAACAGCCTGGTTTCTTCTTTA 58.803 37.500 0.00 0.00 38.86 1.85
2786 10811 3.672808 CTCCTGTTCAGAAGCTCATTGT 58.327 45.455 1.00 0.00 0.00 2.71
2797 10822 2.630158 CTGGATCAAGCTCCTGTTCAG 58.370 52.381 0.00 0.00 36.20 3.02
2821 10846 4.024387 CGTTCCTTCCTCGTTGATTTTTGA 60.024 41.667 0.00 0.00 0.00 2.69
2947 10972 7.082700 TGCGAAATTTTCTATGCACATTAGA 57.917 32.000 7.50 0.00 0.00 2.10
2953 10978 4.096732 ACCTGCGAAATTTTCTATGCAC 57.903 40.909 7.50 0.00 0.00 4.57
3018 11043 7.739825 TCACTTTTGATAGGCTAATGCTATCT 58.260 34.615 0.00 0.00 39.59 1.98
3026 11051 4.783227 AGGACCTCACTTTTGATAGGCTAA 59.217 41.667 0.00 0.00 0.00 3.09
3138 11163 2.763448 GAGACAGATACCAGAGCCACTT 59.237 50.000 0.00 0.00 0.00 3.16
3141 11166 2.532250 TGAGACAGATACCAGAGCCA 57.468 50.000 0.00 0.00 0.00 4.75
3142 11167 2.763448 ACTTGAGACAGATACCAGAGCC 59.237 50.000 0.00 0.00 0.00 4.70
3154 11188 8.786826 ATTAAATTTCCGACATACTTGAGACA 57.213 30.769 0.00 0.00 0.00 3.41
3168 11202 7.555195 AGGTACCTTAGGTGAATTAAATTTCCG 59.445 37.037 15.13 0.00 36.19 4.30
3208 11242 0.872388 GGGAGTTCGCGAACATTTGT 59.128 50.000 42.89 28.05 43.47 2.83
3211 11245 1.821216 ATTGGGAGTTCGCGAACATT 58.179 45.000 42.89 29.41 43.47 2.71
3237 11271 2.218934 CAAAAGCTGCAACTTGCCG 58.781 52.632 11.29 6.07 44.23 5.69
3343 12846 1.725641 TTTGGCAGCATCACTCTACG 58.274 50.000 0.00 0.00 0.00 3.51
3379 12882 6.370718 ACTCGTTTCAACATTTGGAGGTATAC 59.629 38.462 0.00 0.00 0.00 1.47
3383 12886 3.551846 ACTCGTTTCAACATTTGGAGGT 58.448 40.909 0.00 0.00 0.00 3.85
3388 12891 8.169268 GGATAAGTCTACTCGTTTCAACATTTG 58.831 37.037 0.00 0.00 0.00 2.32
3391 12894 7.093902 TGAGGATAAGTCTACTCGTTTCAACAT 60.094 37.037 0.00 0.00 32.76 2.71
3461 12964 3.240861 GTCGCAGTAAAGTATGAGCTTCG 59.759 47.826 0.00 0.00 0.00 3.79
3464 12967 3.868757 TGTCGCAGTAAAGTATGAGCT 57.131 42.857 0.00 0.00 0.00 4.09
3470 12973 6.028146 TGTCCTTATTGTCGCAGTAAAGTA 57.972 37.500 0.00 0.00 0.00 2.24
3480 12983 5.118990 ACCAGATCAATGTCCTTATTGTCG 58.881 41.667 0.00 0.00 38.77 4.35
3516 13019 4.844884 AGTTGCCTAGGGACTCAATTAAC 58.155 43.478 11.72 0.00 41.75 2.01
3551 13054 7.147915 TGCCACCAAAATTAATCCATAGACTTC 60.148 37.037 0.00 0.00 0.00 3.01
3554 13057 6.321181 TCTGCCACCAAAATTAATCCATAGAC 59.679 38.462 0.00 0.00 0.00 2.59
3558 13061 5.025453 AGTCTGCCACCAAAATTAATCCAT 58.975 37.500 0.00 0.00 0.00 3.41
3561 13064 5.643379 TCAGTCTGCCACCAAAATTAATC 57.357 39.130 0.00 0.00 0.00 1.75
3580 13083 2.554806 ACACGCATGCAATCATTCAG 57.445 45.000 19.57 0.00 0.00 3.02
3621 13130 7.398024 AGCTCCATGACTTAAAAGTATGAAGT 58.602 34.615 0.00 0.00 39.88 3.01
3634 13143 4.077822 CCTTCTTTGAAGCTCCATGACTT 58.922 43.478 0.00 0.00 0.00 3.01
3646 13179 4.127171 CTCAAGAACGACCCTTCTTTGAA 58.873 43.478 0.00 0.00 38.24 2.69
3649 13185 3.388350 AGTCTCAAGAACGACCCTTCTTT 59.612 43.478 0.00 0.00 38.24 2.52
3650 13186 2.966516 AGTCTCAAGAACGACCCTTCTT 59.033 45.455 0.00 0.00 40.47 2.52
3651 13187 2.599677 AGTCTCAAGAACGACCCTTCT 58.400 47.619 0.00 0.00 31.41 2.85
3652 13188 3.318886 GAAGTCTCAAGAACGACCCTTC 58.681 50.000 0.00 0.00 0.00 3.46
3751 13290 3.255149 GGCAGCATCCCAATTATCTGAAG 59.745 47.826 0.00 0.00 0.00 3.02
3844 13383 2.224233 ACTTGCAGCATCTCGCATATCT 60.224 45.455 0.00 0.00 46.13 1.98
3845 13384 2.141517 ACTTGCAGCATCTCGCATATC 58.858 47.619 0.00 0.00 46.13 1.63
3848 13387 0.731417 GAACTTGCAGCATCTCGCAT 59.269 50.000 0.00 0.00 46.13 4.73


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

AutoCloner maintained by Alex Coulton.