Multiple sequence alignment - TraesCS1B01G423200

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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 TraesCS1B01G423200 chr1B 100.000 3899 0 0 1 3899 645885704 645889602 0.000000e+00 7201.0
1 TraesCS1B01G423200 chr1B 90.816 1078 91 6 2206 3277 645906301 645905226 0.000000e+00 1435.0
2 TraesCS1B01G423200 chr1B 87.326 1152 80 26 559 1673 645913639 645912517 0.000000e+00 1258.0
3 TraesCS1B01G423200 chr1B 91.058 917 63 14 1033 1948 645904362 645903464 0.000000e+00 1221.0
4 TraesCS1B01G423200 chr1B 84.615 858 105 12 1058 1905 645896415 645895575 0.000000e+00 828.0
5 TraesCS1B01G423200 chr1B 90.000 460 44 2 2240 2698 645902047 645901589 9.330000e-166 593.0
6 TraesCS1B01G423200 chr1B 80.601 732 126 14 2247 2970 645895366 645894643 5.690000e-153 551.0
7 TraesCS1B01G423200 chr1B 89.306 346 30 4 2731 3076 645901595 645901257 1.000000e-115 427.0
8 TraesCS1B01G423200 chr1B 88.102 353 22 4 1671 2022 645906626 645906293 6.070000e-108 401.0
9 TraesCS1B01G423200 chr1B 96.078 102 4 0 418 519 645913739 645913638 2.410000e-37 167.0
10 TraesCS1B01G423200 chr1B 87.209 86 10 1 1940 2024 645902383 645902298 3.210000e-16 97.1
11 TraesCS1B01G423200 chr1B 94.340 53 3 0 567 619 645886187 645886239 8.980000e-12 82.4
12 TraesCS1B01G423200 chr1B 94.340 53 3 0 484 536 645886270 645886322 8.980000e-12 82.4
13 TraesCS1B01G423200 chr1B 95.455 44 1 1 492 535 645913620 645913578 6.990000e-08 69.4
14 TraesCS1B01G423200 chr1D 94.633 1118 56 2 2217 3330 467849552 467850669 0.000000e+00 1729.0
15 TraesCS1B01G423200 chr1D 94.697 924 47 1 991 1914 467848494 467849415 0.000000e+00 1434.0
16 TraesCS1B01G423200 chr1D 84.908 921 113 10 1000 1895 467863404 467862485 0.000000e+00 907.0
17 TraesCS1B01G423200 chr1D 83.131 990 124 21 925 1895 467852687 467853652 0.000000e+00 863.0
18 TraesCS1B01G423200 chr1D 95.208 480 20 3 3359 3837 467850668 467851145 0.000000e+00 756.0
19 TraesCS1B01G423200 chr1D 85.833 600 26 23 397 953 467847835 467848418 2.020000e-162 582.0
20 TraesCS1B01G423200 chr1D 89.205 176 14 4 180 355 467847550 467847720 8.480000e-52 215.0
21 TraesCS1B01G423200 chr1D 81.667 180 28 4 2029 2206 471759250 471759074 1.130000e-30 145.0
22 TraesCS1B01G423200 chr1D 100.000 37 0 0 582 618 467847971 467848007 6.990000e-08 69.4
23 TraesCS1B01G423200 chr1A 91.819 1149 82 10 2206 3346 560838478 560839622 0.000000e+00 1591.0
24 TraesCS1B01G423200 chr1A 93.282 1042 58 4 991 2022 560837447 560838486 0.000000e+00 1526.0
25 TraesCS1B01G423200 chr1A 85.666 893 102 14 1027 1894 560881594 560880703 0.000000e+00 917.0
26 TraesCS1B01G423200 chr1A 84.740 924 117 11 994 1907 560840385 560841294 0.000000e+00 904.0
27 TraesCS1B01G423200 chr1A 88.945 597 28 17 397 961 560836796 560837386 0.000000e+00 702.0
28 TraesCS1B01G423200 chr1A 81.568 727 130 4 2249 2974 560841477 560842200 7.210000e-167 597.0
29 TraesCS1B01G423200 chr1A 92.857 168 10 1 164 331 560836461 560836626 3.890000e-60 243.0
30 TraesCS1B01G423200 chr1A 91.803 61 5 0 558 618 560836891 560836951 6.940000e-13 86.1
31 TraesCS1B01G423200 chr1A 94.340 53 3 0 484 536 560836983 560837035 8.980000e-12 82.4
32 TraesCS1B01G423200 chr5A 91.367 139 10 2 2013 2151 440939513 440939649 5.140000e-44 189.0
33 TraesCS1B01G423200 chr7D 84.492 187 14 4 2022 2207 619358752 619358580 1.860000e-38 171.0
34 TraesCS1B01G423200 chr7D 83.516 182 24 4 2029 2207 513211731 513211553 8.670000e-37 165.0
35 TraesCS1B01G423200 chr7D 88.710 62 5 2 31 91 32936209 32936269 1.500000e-09 75.0
36 TraesCS1B01G423200 chr2B 94.898 98 5 0 6 103 793907991 793907894 1.880000e-33 154.0
37 TraesCS1B01G423200 chr4B 86.429 140 18 1 7 146 636162035 636162173 6.750000e-33 152.0
38 TraesCS1B01G423200 chr4D 82.123 179 27 4 2029 2205 466669256 466669431 8.730000e-32 148.0
39 TraesCS1B01G423200 chr3D 81.622 185 26 6 2029 2210 83491896 83492075 3.140000e-31 147.0
40 TraesCS1B01G423200 chr5D 80.851 188 28 6 2031 2215 310189286 310189468 1.460000e-29 141.0
41 TraesCS1B01G423200 chr2A 81.421 183 25 6 2029 2206 131713638 131713816 1.460000e-29 141.0
42 TraesCS1B01G423200 chr2A 81.215 181 27 6 2029 2206 216837898 216837722 5.250000e-29 139.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G423200 chr1B 645885704 645889602 3898 False 2455.266667 7201 96.226667 1 3899 3 chr1B.!!$F1 3898
1 TraesCS1B01G423200 chr1B 645901257 645906626 5369 True 695.683333 1435 89.415167 1033 3277 6 chr1B.!!$R2 2244
2 TraesCS1B01G423200 chr1B 645894643 645896415 1772 True 689.500000 828 82.608000 1058 2970 2 chr1B.!!$R1 1912
3 TraesCS1B01G423200 chr1B 645912517 645913739 1222 True 498.133333 1258 92.953000 418 1673 3 chr1B.!!$R3 1255
4 TraesCS1B01G423200 chr1D 467862485 467863404 919 True 907.000000 907 84.908000 1000 1895 1 chr1D.!!$R1 895
5 TraesCS1B01G423200 chr1D 467847550 467853652 6102 False 806.914286 1729 91.815286 180 3837 7 chr1D.!!$F1 3657
6 TraesCS1B01G423200 chr1A 560880703 560881594 891 True 917.000000 917 85.666000 1027 1894 1 chr1A.!!$R1 867
7 TraesCS1B01G423200 chr1A 560836461 560842200 5739 False 716.437500 1591 89.919250 164 3346 8 chr1A.!!$F1 3182

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
996 1240 0.032615 AAGGATCACCGGAGAGAGCT 60.033 55.0 9.46 0.0 41.83 4.09 F
2072 4460 0.097150 TCGCGAAGTCTCAGTCGATG 59.903 55.0 6.20 0.0 39.64 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 4570 0.037734 TGTGGCTAGGTCTCAGTCGA 59.962 55.0 0.0 0.0 0.0 4.20 R
3771 6466 0.367887 CATCGTGTCATGCTGTGTCG 59.632 55.0 0.0 0.0 0.0 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
44 45 0.595310 GTATGCCTCGTCGGAAGAGC 60.595 60.000 14.44 10.73 43.49 4.09
47 48 2.202676 CCTCGTCGGAAGAGCAGC 60.203 66.667 14.44 0.00 43.49 5.25
48 49 2.568612 CTCGTCGGAAGAGCAGCA 59.431 61.111 7.99 0.00 43.49 4.41
49 50 1.515952 CTCGTCGGAAGAGCAGCAG 60.516 63.158 7.99 0.00 43.49 4.24
153 154 4.634133 GTGTCGCCCGTGTCGTCA 62.634 66.667 0.00 0.00 0.00 4.35
154 155 3.676605 TGTCGCCCGTGTCGTCAT 61.677 61.111 0.00 0.00 0.00 3.06
155 156 2.879462 GTCGCCCGTGTCGTCATC 60.879 66.667 0.00 0.00 0.00 2.92
156 157 3.060000 TCGCCCGTGTCGTCATCT 61.060 61.111 0.00 0.00 0.00 2.90
157 158 2.579787 CGCCCGTGTCGTCATCTC 60.580 66.667 0.00 0.00 0.00 2.75
158 159 2.571757 GCCCGTGTCGTCATCTCA 59.428 61.111 0.00 0.00 0.00 3.27
159 160 1.805945 GCCCGTGTCGTCATCTCAC 60.806 63.158 0.00 0.00 0.00 3.51
160 161 1.883732 CCCGTGTCGTCATCTCACT 59.116 57.895 0.00 0.00 0.00 3.41
161 162 0.179161 CCCGTGTCGTCATCTCACTC 60.179 60.000 0.00 0.00 0.00 3.51
162 163 0.179161 CCGTGTCGTCATCTCACTCC 60.179 60.000 0.00 0.00 0.00 3.85
263 264 9.575783 GAACATAACGGCATTTTATCCTAAAAA 57.424 29.630 0.00 0.00 33.15 1.94
334 335 4.754667 GGGTTCGTCGTGGGAGGC 62.755 72.222 0.00 0.00 0.00 4.70
336 337 4.353437 GTTCGTCGTGGGAGGCGT 62.353 66.667 0.00 0.00 0.00 5.68
337 338 3.608662 TTCGTCGTGGGAGGCGTT 61.609 61.111 0.00 0.00 0.00 4.84
356 357 1.380524 TTTTTCCAGCGAACGAACCA 58.619 45.000 0.00 0.00 0.00 3.67
368 385 2.973082 GAACCATTGCACCCCTGC 59.027 61.111 0.00 0.00 44.52 4.85
370 387 3.164610 AACCATTGCACCCCTGCCT 62.165 57.895 0.00 0.00 43.51 4.75
371 388 2.284112 CCATTGCACCCCTGCCTT 60.284 61.111 0.00 0.00 43.51 4.35
372 389 1.914764 CCATTGCACCCCTGCCTTT 60.915 57.895 0.00 0.00 43.51 3.11
373 390 1.294138 CATTGCACCCCTGCCTTTG 59.706 57.895 0.00 0.00 43.51 2.77
374 391 2.586293 ATTGCACCCCTGCCTTTGC 61.586 57.895 0.00 0.00 43.51 3.68
379 396 1.383803 ACCCCTGCCTTTGCCAAAA 60.384 52.632 0.00 0.00 36.33 2.44
641 816 0.767998 TATCCGGCCCATGTTGCATA 59.232 50.000 0.00 0.00 0.00 3.14
809 991 2.614057 CAAGATGTCTAAATGGCCGACC 59.386 50.000 0.00 0.00 0.00 4.79
888 1070 3.873952 GACCATGCAGTCCTATCTTGAAC 59.126 47.826 0.00 0.00 0.00 3.18
912 1103 2.100631 CACGCCGAGGTTGTGATCC 61.101 63.158 9.90 0.00 35.66 3.36
940 1131 6.674694 AATTTCAGTTGAGATCGGATTGAG 57.325 37.500 0.00 0.00 0.00 3.02
942 1133 2.159043 TCAGTTGAGATCGGATTGAGCC 60.159 50.000 0.00 0.00 31.78 4.70
954 1145 2.227388 GGATTGAGCCACTCACAACTTG 59.773 50.000 0.00 0.00 40.46 3.16
958 1149 1.405105 GAGCCACTCACAACTTGCAAA 59.595 47.619 0.00 0.00 0.00 3.68
959 1150 1.134946 AGCCACTCACAACTTGCAAAC 59.865 47.619 0.00 0.00 0.00 2.93
960 1151 1.135141 GCCACTCACAACTTGCAAACA 60.135 47.619 0.00 0.00 0.00 2.83
961 1152 2.481795 GCCACTCACAACTTGCAAACAT 60.482 45.455 0.00 0.00 0.00 2.71
962 1153 3.243367 GCCACTCACAACTTGCAAACATA 60.243 43.478 0.00 0.00 0.00 2.29
987 1216 0.905357 AGTGGAAGGAAGGATCACCG 59.095 55.000 0.00 0.00 41.83 4.94
989 1233 0.252513 TGGAAGGAAGGATCACCGGA 60.253 55.000 9.46 0.00 41.83 5.14
996 1240 0.032615 AAGGATCACCGGAGAGAGCT 60.033 55.000 9.46 0.00 41.83 4.09
1242 2494 4.711949 CTGCAGCTCGGCCAGGTT 62.712 66.667 2.24 0.00 0.00 3.50
1485 2737 3.386237 GAGGAGGTCGCCACAGCT 61.386 66.667 0.00 0.00 36.60 4.24
1629 2881 2.128507 GTTCCTCCGGGAGCTCGAT 61.129 63.158 18.91 0.00 43.29 3.59
1683 2935 2.173669 CGACATGTGGCCATCGTCC 61.174 63.158 9.72 0.00 31.23 4.79
1891 3155 3.063997 CGTCAAAGCCATCATCTTGGTAC 59.936 47.826 0.00 0.00 39.11 3.34
2005 4393 4.275936 ACACTGCTTGCTAAGTTAAAGTGG 59.724 41.667 16.80 1.79 0.00 4.00
2017 4405 7.278203 GCTAAGTTAAAGTGGACAGAGTTATCC 59.722 40.741 0.00 0.00 35.37 2.59
2018 4406 6.936968 AGTTAAAGTGGACAGAGTTATCCT 57.063 37.500 0.00 0.00 35.86 3.24
2019 4407 8.431910 AAGTTAAAGTGGACAGAGTTATCCTA 57.568 34.615 0.00 0.00 35.86 2.94
2020 4408 8.431910 AGTTAAAGTGGACAGAGTTATCCTAA 57.568 34.615 0.00 0.00 35.86 2.69
2021 4409 8.877195 AGTTAAAGTGGACAGAGTTATCCTAAA 58.123 33.333 0.00 0.00 35.86 1.85
2022 4410 8.933807 GTTAAAGTGGACAGAGTTATCCTAAAC 58.066 37.037 0.00 0.00 35.86 2.01
2023 4411 5.326200 AGTGGACAGAGTTATCCTAAACG 57.674 43.478 0.00 0.00 35.86 3.60
2024 4412 4.159879 AGTGGACAGAGTTATCCTAAACGG 59.840 45.833 0.00 0.00 35.86 4.44
2025 4413 4.081807 GTGGACAGAGTTATCCTAAACGGT 60.082 45.833 0.00 0.00 35.86 4.83
2026 4414 4.081862 TGGACAGAGTTATCCTAAACGGTG 60.082 45.833 0.00 0.00 35.86 4.94
2027 4415 3.858247 ACAGAGTTATCCTAAACGGTGC 58.142 45.455 0.00 0.00 34.46 5.01
2028 4416 3.514309 ACAGAGTTATCCTAAACGGTGCT 59.486 43.478 0.00 0.00 34.46 4.40
2029 4417 3.865745 CAGAGTTATCCTAAACGGTGCTG 59.134 47.826 0.00 0.00 34.46 4.41
2030 4418 2.608090 GAGTTATCCTAAACGGTGCTGC 59.392 50.000 0.00 0.00 34.46 5.25
2031 4419 2.236395 AGTTATCCTAAACGGTGCTGCT 59.764 45.455 0.00 0.00 34.46 4.24
2032 4420 3.449737 AGTTATCCTAAACGGTGCTGCTA 59.550 43.478 0.00 0.00 34.46 3.49
2033 4421 4.081309 AGTTATCCTAAACGGTGCTGCTAA 60.081 41.667 0.00 0.00 34.46 3.09
2034 4422 2.843401 TCCTAAACGGTGCTGCTAAA 57.157 45.000 0.00 0.00 0.00 1.85
2035 4423 3.343941 TCCTAAACGGTGCTGCTAAAT 57.656 42.857 0.00 0.00 0.00 1.40
2036 4424 3.267483 TCCTAAACGGTGCTGCTAAATC 58.733 45.455 0.00 0.00 0.00 2.17
2037 4425 3.055385 TCCTAAACGGTGCTGCTAAATCT 60.055 43.478 0.00 0.00 0.00 2.40
2038 4426 3.309954 CCTAAACGGTGCTGCTAAATCTC 59.690 47.826 0.00 0.00 0.00 2.75
2039 4427 2.472695 AACGGTGCTGCTAAATCTCA 57.527 45.000 0.00 0.00 0.00 3.27
2040 4428 2.015736 ACGGTGCTGCTAAATCTCAG 57.984 50.000 0.00 0.00 0.00 3.35
2041 4429 1.276421 ACGGTGCTGCTAAATCTCAGT 59.724 47.619 0.00 0.00 33.09 3.41
2042 4430 1.929836 CGGTGCTGCTAAATCTCAGTC 59.070 52.381 0.00 0.00 33.09 3.51
2043 4431 1.929836 GGTGCTGCTAAATCTCAGTCG 59.070 52.381 0.00 0.00 33.09 4.18
2044 4432 2.417379 GGTGCTGCTAAATCTCAGTCGA 60.417 50.000 0.00 0.00 33.09 4.20
2045 4433 2.600867 GTGCTGCTAAATCTCAGTCGAC 59.399 50.000 7.70 7.70 33.09 4.20
2046 4434 2.493675 TGCTGCTAAATCTCAGTCGACT 59.506 45.455 13.58 13.58 33.09 4.18
2047 4435 2.857152 GCTGCTAAATCTCAGTCGACTG 59.143 50.000 34.76 34.76 45.08 3.51
2057 4445 4.044024 GTCGACTGAGACTTCGCG 57.956 61.111 8.70 0.00 38.09 5.87
2058 4446 1.496393 GTCGACTGAGACTTCGCGA 59.504 57.895 3.71 3.71 38.09 5.87
2059 4447 0.110328 GTCGACTGAGACTTCGCGAA 60.110 55.000 22.01 22.01 38.09 4.70
2060 4448 0.166161 TCGACTGAGACTTCGCGAAG 59.834 55.000 39.55 39.55 43.79 3.79
2069 4457 2.631303 CTTCGCGAAGTCTCAGTCG 58.369 57.895 34.97 12.16 40.24 4.18
2070 4458 0.166161 CTTCGCGAAGTCTCAGTCGA 59.834 55.000 34.97 4.60 39.64 4.20
2071 4459 0.803117 TTCGCGAAGTCTCAGTCGAT 59.197 50.000 19.38 0.00 39.64 3.59
2072 4460 0.097150 TCGCGAAGTCTCAGTCGATG 59.903 55.000 6.20 0.00 39.64 3.84
2073 4461 0.179187 CGCGAAGTCTCAGTCGATGT 60.179 55.000 0.00 0.00 39.64 3.06
2074 4462 1.729472 CGCGAAGTCTCAGTCGATGTT 60.729 52.381 0.00 0.00 39.64 2.71
2075 4463 2.475685 CGCGAAGTCTCAGTCGATGTTA 60.476 50.000 0.00 0.00 39.64 2.41
2076 4464 3.696898 GCGAAGTCTCAGTCGATGTTAT 58.303 45.455 0.00 0.00 39.64 1.89
2077 4465 4.552184 CGCGAAGTCTCAGTCGATGTTATA 60.552 45.833 0.00 0.00 39.64 0.98
2078 4466 5.453648 GCGAAGTCTCAGTCGATGTTATAT 58.546 41.667 0.00 0.00 39.64 0.86
2079 4467 5.915758 GCGAAGTCTCAGTCGATGTTATATT 59.084 40.000 0.00 0.00 39.64 1.28
2080 4468 6.087028 GCGAAGTCTCAGTCGATGTTATATTC 59.913 42.308 0.00 0.00 39.64 1.75
2081 4469 6.579292 CGAAGTCTCAGTCGATGTTATATTCC 59.421 42.308 0.00 0.00 39.64 3.01
2082 4470 7.520776 CGAAGTCTCAGTCGATGTTATATTCCT 60.521 40.741 0.00 0.00 39.64 3.36
2083 4471 7.589958 AGTCTCAGTCGATGTTATATTCCTT 57.410 36.000 0.00 0.00 0.00 3.36
2084 4472 8.012957 AGTCTCAGTCGATGTTATATTCCTTT 57.987 34.615 0.00 0.00 0.00 3.11
2085 4473 7.923344 AGTCTCAGTCGATGTTATATTCCTTTG 59.077 37.037 0.00 0.00 0.00 2.77
2086 4474 7.921214 GTCTCAGTCGATGTTATATTCCTTTGA 59.079 37.037 0.00 0.00 0.00 2.69
2087 4475 8.642432 TCTCAGTCGATGTTATATTCCTTTGAT 58.358 33.333 0.00 0.00 0.00 2.57
2088 4476 9.265901 CTCAGTCGATGTTATATTCCTTTGATT 57.734 33.333 0.00 0.00 0.00 2.57
2089 4477 9.613428 TCAGTCGATGTTATATTCCTTTGATTT 57.387 29.630 0.00 0.00 0.00 2.17
2106 4494 5.375417 TGATTTTTCATGCAGATTCGTGT 57.625 34.783 0.00 0.00 0.00 4.49
2108 4496 6.907741 TGATTTTTCATGCAGATTCGTGTAA 58.092 32.000 0.00 0.00 0.00 2.41
2115 4503 6.734137 TCATGCAGATTCGTGTAAAGTTTTT 58.266 32.000 0.00 0.00 0.00 1.94
2157 4545 9.787435 TTTCCTTTTATACACTATGTGTCACTT 57.213 29.630 6.62 0.17 43.92 3.16
2158 4546 8.771920 TCCTTTTATACACTATGTGTCACTTG 57.228 34.615 6.62 0.00 43.92 3.16
2159 4547 8.590204 TCCTTTTATACACTATGTGTCACTTGA 58.410 33.333 6.62 0.00 43.92 3.02
2163 4551 9.936759 TTTATACACTATGTGTCACTTGATTGA 57.063 29.630 6.62 0.00 43.92 2.57
2165 4553 6.101650 ACACTATGTGTCACTTGATTGAGA 57.898 37.500 4.27 0.00 43.92 3.27
2166 4554 5.928839 ACACTATGTGTCACTTGATTGAGAC 59.071 40.000 4.27 0.00 43.92 3.36
2168 4556 6.648310 CACTATGTGTCACTTGATTGAGACTT 59.352 38.462 4.27 0.00 39.84 3.01
2169 4557 7.172190 CACTATGTGTCACTTGATTGAGACTTT 59.828 37.037 4.27 0.00 39.84 2.66
2171 4559 4.035558 TGTGTCACTTGATTGAGACTTTGC 59.964 41.667 4.27 0.00 39.84 3.68
2172 4560 3.248363 TGTCACTTGATTGAGACTTTGCG 59.752 43.478 0.00 0.00 32.41 4.85
2173 4561 3.494626 GTCACTTGATTGAGACTTTGCGA 59.505 43.478 0.00 0.00 0.00 5.10
2174 4562 4.024893 GTCACTTGATTGAGACTTTGCGAA 60.025 41.667 0.00 0.00 0.00 4.70
2175 4563 4.212004 TCACTTGATTGAGACTTTGCGAAG 59.788 41.667 12.41 12.41 38.87 3.79
2184 4572 1.772182 ACTTTGCGAAGTCTCAGTCG 58.228 50.000 13.90 0.00 42.35 4.18
2185 4573 1.337071 ACTTTGCGAAGTCTCAGTCGA 59.663 47.619 13.90 0.00 42.35 4.20
2186 4574 1.716581 CTTTGCGAAGTCTCAGTCGAC 59.283 52.381 7.70 7.70 39.64 4.20
2187 4575 0.952280 TTGCGAAGTCTCAGTCGACT 59.048 50.000 13.58 13.58 45.73 4.18
2188 4576 0.238553 TGCGAAGTCTCAGTCGACTG 59.761 55.000 34.76 34.76 43.14 3.51
2198 4586 0.736053 CAGTCGACTGAGACCTAGCC 59.264 60.000 36.73 0.00 46.59 3.93
2199 4587 0.328592 AGTCGACTGAGACCTAGCCA 59.671 55.000 19.30 0.00 41.83 4.75
2200 4588 0.452585 GTCGACTGAGACCTAGCCAC 59.547 60.000 8.70 0.00 35.22 5.01
2201 4589 0.037734 TCGACTGAGACCTAGCCACA 59.962 55.000 0.00 0.00 0.00 4.17
2202 4590 0.171455 CGACTGAGACCTAGCCACAC 59.829 60.000 0.00 0.00 0.00 3.82
2203 4591 0.533032 GACTGAGACCTAGCCACACC 59.467 60.000 0.00 0.00 0.00 4.16
2204 4592 0.905337 ACTGAGACCTAGCCACACCC 60.905 60.000 0.00 0.00 0.00 4.61
2205 4593 0.616111 CTGAGACCTAGCCACACCCT 60.616 60.000 0.00 0.00 0.00 4.34
2206 4594 0.708209 TGAGACCTAGCCACACCCTA 59.292 55.000 0.00 0.00 0.00 3.53
2207 4595 1.291033 TGAGACCTAGCCACACCCTAT 59.709 52.381 0.00 0.00 0.00 2.57
2208 4596 1.964933 GAGACCTAGCCACACCCTATC 59.035 57.143 0.00 0.00 0.00 2.08
2209 4597 1.049402 GACCTAGCCACACCCTATCC 58.951 60.000 0.00 0.00 0.00 2.59
2231 4623 6.112734 TCCTAAAACGCATGTTATCTCATGT 58.887 36.000 8.17 0.00 44.68 3.21
2334 4963 1.419387 GAGTGGGCCATATCAGAGCTT 59.581 52.381 10.70 0.00 0.00 3.74
2347 4976 2.009774 CAGAGCTTATCAACAACCCGG 58.990 52.381 0.00 0.00 0.00 5.73
2493 5122 2.791868 GCCCCTGCCGTTGTTGTTT 61.792 57.895 0.00 0.00 0.00 2.83
2569 5198 1.039856 GGTGTTGGTCAATGCTTGGT 58.960 50.000 0.00 0.00 0.00 3.67
2571 5200 1.956477 GTGTTGGTCAATGCTTGGTCT 59.044 47.619 0.00 0.00 0.00 3.85
2655 5285 1.817447 GAAGAAGCAGCAAAGGCAGAT 59.183 47.619 0.00 0.00 44.61 2.90
2902 5532 4.710324 ACCTATTCTCGGAGTCTAGTCAG 58.290 47.826 4.69 0.00 0.00 3.51
2989 5623 8.693542 AAATTGCAAAGTTCTACTATTGCATC 57.306 30.769 19.77 3.05 43.94 3.91
3008 5642 5.142265 GCATCACATCATTAGTATTGTGCG 58.858 41.667 0.00 0.00 39.39 5.34
3017 5651 9.411801 CATCATTAGTATTGTGCGATAACTAGT 57.588 33.333 0.00 0.00 0.00 2.57
3024 5658 3.766151 TGTGCGATAACTAGTGTAGTGC 58.234 45.455 0.00 0.00 39.39 4.40
3209 5849 5.549159 TGTGTTTAGTTTTCACAACGTACG 58.451 37.500 15.01 15.01 38.80 3.67
3222 5862 0.170561 ACGTACGGCAGCTCAACTAG 59.829 55.000 21.06 0.00 0.00 2.57
3324 5964 8.763356 CAAAGACAAAATTTGCAGCAACTATAA 58.237 29.630 7.54 0.00 31.46 0.98
3329 5969 9.054922 ACAAAATTTGCAGCAACTATAATTGTT 57.945 25.926 7.54 0.40 31.83 2.83
3330 5970 9.532697 CAAAATTTGCAGCAACTATAATTGTTC 57.467 29.630 7.54 0.00 31.83 3.18
3331 5971 8.830201 AAATTTGCAGCAACTATAATTGTTCA 57.170 26.923 7.54 0.00 31.83 3.18
3334 5974 6.756299 TGCAGCAACTATAATTGTTCATGA 57.244 33.333 0.00 0.00 31.83 3.07
3341 5981 7.433131 GCAACTATAATTGTTCATGACATGTGG 59.567 37.037 14.98 0.00 38.26 4.17
3520 6213 4.313277 TCGATGATGAGCAGGTTAGAAG 57.687 45.455 0.00 0.00 0.00 2.85
3589 6283 5.997746 CCCATGAAAAGTTCAGAACTACTCA 59.002 40.000 21.31 21.31 43.98 3.41
3640 6334 7.310113 CCTTATATCTGACGGAAAGGAGCTAAT 60.310 40.741 7.27 0.00 33.48 1.73
3724 6419 2.169330 GAGGTTGAACGACTCCTACCT 58.831 52.381 10.61 10.61 39.55 3.08
3726 6421 1.891150 GGTTGAACGACTCCTACCTGA 59.109 52.381 0.00 0.00 0.00 3.86
3727 6422 2.094649 GGTTGAACGACTCCTACCTGAG 60.095 54.545 0.00 0.00 38.37 3.35
3756 6451 5.012664 TGAAGGTCTACATTAACCTGCAAGA 59.987 40.000 0.00 0.00 46.28 3.02
3771 6466 4.083431 CCTGCAAGATCAAATCCATCGATC 60.083 45.833 0.00 0.00 34.07 3.69
3818 6513 3.084039 GTGGAAACATGCAGAGGATGAA 58.916 45.455 5.50 0.00 46.14 2.57
3824 6519 3.542648 ACATGCAGAGGATGAACATGAG 58.457 45.455 0.00 0.00 40.39 2.90
3826 6521 2.190538 TGCAGAGGATGAACATGAGGA 58.809 47.619 0.00 0.00 0.00 3.71
3830 6525 4.685302 GCAGAGGATGAACATGAGGATGAA 60.685 45.833 0.00 0.00 33.36 2.57
3832 6527 4.472470 AGAGGATGAACATGAGGATGAACA 59.528 41.667 0.00 0.00 33.36 3.18
3833 6528 5.132312 AGAGGATGAACATGAGGATGAACAT 59.868 40.000 0.00 0.00 34.36 2.71
3834 6529 5.131067 AGGATGAACATGAGGATGAACATG 58.869 41.667 0.00 0.00 33.04 3.21
3835 6530 4.261489 GGATGAACATGAGGATGAACATGC 60.261 45.833 0.00 0.00 33.86 4.06
3837 6532 3.692593 TGAACATGAGGATGAACATGCAG 59.307 43.478 0.00 0.00 33.36 4.41
3838 6533 3.361281 ACATGAGGATGAACATGCAGT 57.639 42.857 0.00 0.00 33.36 4.40
3839 6534 3.014623 ACATGAGGATGAACATGCAGTG 58.985 45.455 0.00 6.57 33.36 3.66
3840 6535 2.865119 TGAGGATGAACATGCAGTGT 57.135 45.000 8.79 0.00 44.84 3.55
3841 6536 2.703416 TGAGGATGAACATGCAGTGTC 58.297 47.619 8.79 0.00 41.14 3.67
3842 6537 2.303890 TGAGGATGAACATGCAGTGTCT 59.696 45.455 8.79 0.00 41.14 3.41
3843 6538 2.935201 GAGGATGAACATGCAGTGTCTC 59.065 50.000 8.79 0.00 41.14 3.36
3844 6539 2.570752 AGGATGAACATGCAGTGTCTCT 59.429 45.455 8.79 0.00 41.14 3.10
3845 6540 3.771479 AGGATGAACATGCAGTGTCTCTA 59.229 43.478 8.79 0.00 41.14 2.43
3846 6541 4.408270 AGGATGAACATGCAGTGTCTCTAT 59.592 41.667 8.79 0.00 41.14 1.98
3847 6542 5.600069 AGGATGAACATGCAGTGTCTCTATA 59.400 40.000 8.79 0.00 41.14 1.31
3848 6543 6.098838 AGGATGAACATGCAGTGTCTCTATAA 59.901 38.462 8.79 0.00 41.14 0.98
3849 6544 6.763135 GGATGAACATGCAGTGTCTCTATAAA 59.237 38.462 0.00 0.00 41.14 1.40
3851 6546 5.874810 TGAACATGCAGTGTCTCTATAAACC 59.125 40.000 0.00 0.00 41.14 3.27
3853 6548 5.665459 ACATGCAGTGTCTCTATAAACCTC 58.335 41.667 0.00 0.00 35.77 3.85
3854 6549 5.423610 ACATGCAGTGTCTCTATAAACCTCT 59.576 40.000 0.00 0.00 35.77 3.69
3855 6550 5.584253 TGCAGTGTCTCTATAAACCTCTC 57.416 43.478 0.00 0.00 0.00 3.20
3858 6553 5.128008 GCAGTGTCTCTATAAACCTCTCCTT 59.872 44.000 0.00 0.00 0.00 3.36
3859 6554 6.321690 GCAGTGTCTCTATAAACCTCTCCTTA 59.678 42.308 0.00 0.00 0.00 2.69
3861 6556 8.356657 CAGTGTCTCTATAAACCTCTCCTTATG 58.643 40.741 0.00 0.00 0.00 1.90
3863 6558 8.697292 GTGTCTCTATAAACCTCTCCTTATGTT 58.303 37.037 0.00 0.00 0.00 2.71
3864 6559 9.268282 TGTCTCTATAAACCTCTCCTTATGTTT 57.732 33.333 0.00 0.00 35.32 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.582959 GAGGCATACTCGTTCAGCG 58.417 57.895 0.00 0.00 43.01 5.18
24 25 1.025812 CTCTTCCGACGAGGCATACT 58.974 55.000 0.00 0.00 40.77 2.12
25 26 0.595310 GCTCTTCCGACGAGGCATAC 60.595 60.000 0.00 0.00 40.77 2.39
27 28 2.290122 CTGCTCTTCCGACGAGGCAT 62.290 60.000 0.00 0.00 40.77 4.40
28 29 2.989253 TGCTCTTCCGACGAGGCA 60.989 61.111 0.00 0.00 40.77 4.75
29 30 2.202676 CTGCTCTTCCGACGAGGC 60.203 66.667 0.00 0.00 40.77 4.70
30 31 2.202676 GCTGCTCTTCCGACGAGG 60.203 66.667 0.00 0.00 42.97 4.63
32 33 2.568612 CTGCTGCTCTTCCGACGA 59.431 61.111 0.00 0.00 0.00 4.20
33 34 3.184683 GCTGCTGCTCTTCCGACG 61.185 66.667 8.53 0.00 36.03 5.12
34 35 3.184683 CGCTGCTGCTCTTCCGAC 61.185 66.667 14.03 0.00 36.97 4.79
56 57 4.517703 GTCTCCGACCTCGCGACG 62.518 72.222 3.71 7.83 38.18 5.12
57 58 4.517703 CGTCTCCGACCTCGCGAC 62.518 72.222 3.71 0.00 38.18 5.19
58 59 4.747529 TCGTCTCCGACCTCGCGA 62.748 66.667 9.26 9.26 38.40 5.87
60 61 3.878519 CCTCGTCTCCGACCTCGC 61.879 72.222 0.00 0.00 38.40 5.03
61 62 2.436292 ACCTCGTCTCCGACCTCG 60.436 66.667 0.00 0.00 38.40 4.63
62 63 3.053849 GCACCTCGTCTCCGACCTC 62.054 68.421 0.00 0.00 38.40 3.85
64 65 4.477975 CGCACCTCGTCTCCGACC 62.478 72.222 0.00 0.00 38.40 4.79
123 124 4.729856 GACACGGGTCGGTTCGGG 62.730 72.222 0.00 0.00 33.68 5.14
136 137 3.909258 ATGACGACACGGGCGACAC 62.909 63.158 8.45 1.18 36.40 3.67
137 138 3.620300 GATGACGACACGGGCGACA 62.620 63.158 8.45 8.56 37.75 4.35
138 139 2.879462 GATGACGACACGGGCGAC 60.879 66.667 8.45 3.06 0.00 5.19
141 142 1.805945 GTGAGATGACGACACGGGC 60.806 63.158 0.00 0.00 0.00 6.13
142 143 0.179161 GAGTGAGATGACGACACGGG 60.179 60.000 0.00 0.00 39.19 5.28
143 144 0.179161 GGAGTGAGATGACGACACGG 60.179 60.000 0.00 0.00 39.19 4.94
144 145 0.521735 TGGAGTGAGATGACGACACG 59.478 55.000 0.00 0.00 39.19 4.49
145 146 1.402984 GGTGGAGTGAGATGACGACAC 60.403 57.143 0.00 0.00 35.15 3.67
146 147 0.888619 GGTGGAGTGAGATGACGACA 59.111 55.000 0.00 0.00 0.00 4.35
148 149 0.039764 AGGGTGGAGTGAGATGACGA 59.960 55.000 0.00 0.00 0.00 4.20
149 150 1.405821 GTAGGGTGGAGTGAGATGACG 59.594 57.143 0.00 0.00 0.00 4.35
151 152 4.417183 AGATAGTAGGGTGGAGTGAGATGA 59.583 45.833 0.00 0.00 0.00 2.92
152 153 4.735369 AGATAGTAGGGTGGAGTGAGATG 58.265 47.826 0.00 0.00 0.00 2.90
153 154 5.144100 CAAGATAGTAGGGTGGAGTGAGAT 58.856 45.833 0.00 0.00 0.00 2.75
154 155 4.537751 CAAGATAGTAGGGTGGAGTGAGA 58.462 47.826 0.00 0.00 0.00 3.27
155 156 3.639094 CCAAGATAGTAGGGTGGAGTGAG 59.361 52.174 0.00 0.00 0.00 3.51
156 157 3.012502 ACCAAGATAGTAGGGTGGAGTGA 59.987 47.826 0.00 0.00 33.39 3.41
157 158 3.375699 ACCAAGATAGTAGGGTGGAGTG 58.624 50.000 0.00 0.00 33.39 3.51
158 159 3.775316 CAACCAAGATAGTAGGGTGGAGT 59.225 47.826 0.00 0.00 36.47 3.85
159 160 3.775316 ACAACCAAGATAGTAGGGTGGAG 59.225 47.826 0.00 0.00 44.42 3.86
160 161 3.798515 ACAACCAAGATAGTAGGGTGGA 58.201 45.455 0.00 0.00 44.42 4.02
161 162 4.569719 AACAACCAAGATAGTAGGGTGG 57.430 45.455 0.00 0.00 44.42 4.61
162 163 6.264518 ACAAAAACAACCAAGATAGTAGGGTG 59.735 38.462 0.00 0.00 45.61 4.61
228 229 4.418013 TGCCGTTATGTTCAACAAGATG 57.582 40.909 0.00 0.00 0.00 2.90
229 230 5.643379 AATGCCGTTATGTTCAACAAGAT 57.357 34.783 0.00 0.00 0.00 2.40
337 338 1.380524 TGGTTCGTTCGCTGGAAAAA 58.619 45.000 0.00 0.00 33.05 1.94
355 356 1.294138 CAAAGGCAGGGGTGCAATG 59.706 57.895 0.00 0.00 36.33 2.82
356 357 2.586293 GCAAAGGCAGGGGTGCAAT 61.586 57.895 0.00 0.00 40.72 3.56
368 385 3.730715 GCGATCGATTATTTTGGCAAAGG 59.269 43.478 21.57 0.64 0.00 3.11
370 387 4.350346 CTGCGATCGATTATTTTGGCAAA 58.650 39.130 21.57 8.93 0.00 3.68
371 388 3.243035 CCTGCGATCGATTATTTTGGCAA 60.243 43.478 21.57 0.00 0.00 4.52
372 389 2.290367 CCTGCGATCGATTATTTTGGCA 59.710 45.455 21.57 1.59 0.00 4.92
373 390 2.548057 TCCTGCGATCGATTATTTTGGC 59.452 45.455 21.57 0.00 0.00 4.52
374 391 3.058914 GGTCCTGCGATCGATTATTTTGG 60.059 47.826 21.57 7.89 0.00 3.28
375 392 3.559655 TGGTCCTGCGATCGATTATTTTG 59.440 43.478 21.57 0.00 0.00 2.44
379 396 2.230025 CTCTGGTCCTGCGATCGATTAT 59.770 50.000 21.57 0.00 0.00 1.28
697 872 7.820872 CCAAGAAATTTCAAGCTTTATGGTGAT 59.179 33.333 19.99 0.00 0.00 3.06
809 991 0.525668 GACGCCATCACTAGACACGG 60.526 60.000 0.00 0.00 0.00 4.94
938 1129 1.024271 TTGCAAGTTGTGAGTGGCTC 58.976 50.000 4.48 0.00 0.00 4.70
940 1131 1.135141 TGTTTGCAAGTTGTGAGTGGC 60.135 47.619 4.48 0.00 0.00 5.01
942 1133 4.919206 TGTATGTTTGCAAGTTGTGAGTG 58.081 39.130 4.48 0.00 0.00 3.51
954 1145 5.428253 TCCTTCCACTAGATGTATGTTTGC 58.572 41.667 0.00 0.00 0.00 3.68
958 1149 5.529289 TCCTTCCTTCCACTAGATGTATGT 58.471 41.667 0.00 0.00 0.00 2.29
959 1150 6.268617 TGATCCTTCCTTCCACTAGATGTATG 59.731 42.308 0.00 0.00 0.00 2.39
960 1151 6.268847 GTGATCCTTCCTTCCACTAGATGTAT 59.731 42.308 0.00 0.00 0.00 2.29
961 1152 5.598830 GTGATCCTTCCTTCCACTAGATGTA 59.401 44.000 0.00 0.00 0.00 2.29
962 1153 4.407296 GTGATCCTTCCTTCCACTAGATGT 59.593 45.833 0.00 0.00 0.00 3.06
987 1216 2.114616 TCCTCCATTTGAGCTCTCTCC 58.885 52.381 16.19 0.00 39.98 3.71
989 1233 1.480137 CGTCCTCCATTTGAGCTCTCT 59.520 52.381 16.19 0.00 39.98 3.10
996 1240 1.271856 TGTAGGCGTCCTCCATTTGA 58.728 50.000 1.46 0.00 34.61 2.69
1032 1276 1.581402 CAGCGACACGAGAGCTACG 60.581 63.158 10.54 10.54 39.48 3.51
1033 1277 1.870016 GCAGCGACACGAGAGCTAC 60.870 63.158 7.15 0.00 39.48 3.58
1034 1278 1.983196 GAGCAGCGACACGAGAGCTA 61.983 60.000 7.15 0.00 39.48 3.32
1036 1280 2.878520 GAGCAGCGACACGAGAGC 60.879 66.667 0.00 0.00 0.00 4.09
1464 2716 2.680352 GTGGCGACCTCCTCCTCA 60.680 66.667 0.00 0.00 0.00 3.86
1538 2790 3.406361 CGAGCGTGGACAGCACAC 61.406 66.667 0.00 0.00 37.01 3.82
1539 2791 3.911698 ACGAGCGTGGACAGCACA 61.912 61.111 0.00 0.00 37.01 4.57
1687 2939 4.373116 ACTGAACCACGCGGCGAT 62.373 61.111 30.94 10.64 34.57 4.58
1891 3155 4.613448 GCTATGCGAAGAGAATACTGTACG 59.387 45.833 0.00 0.00 0.00 3.67
1945 4327 8.355169 AGATGTTTTTATGCATTGCCTATAGTG 58.645 33.333 3.54 0.00 0.00 2.74
1947 4329 8.025445 GGAGATGTTTTTATGCATTGCCTATAG 58.975 37.037 3.54 0.00 0.00 1.31
1952 4334 3.798337 CGGAGATGTTTTTATGCATTGCC 59.202 43.478 3.54 0.00 0.00 4.52
2005 4393 3.864003 GCACCGTTTAGGATAACTCTGTC 59.136 47.826 0.00 0.00 45.00 3.51
2017 4405 3.932710 TGAGATTTAGCAGCACCGTTTAG 59.067 43.478 0.00 0.00 0.00 1.85
2018 4406 3.932710 CTGAGATTTAGCAGCACCGTTTA 59.067 43.478 0.00 0.00 0.00 2.01
2019 4407 2.744202 CTGAGATTTAGCAGCACCGTTT 59.256 45.455 0.00 0.00 0.00 3.60
2020 4408 2.289694 ACTGAGATTTAGCAGCACCGTT 60.290 45.455 0.00 0.00 35.57 4.44
2021 4409 1.276421 ACTGAGATTTAGCAGCACCGT 59.724 47.619 0.00 0.00 35.57 4.83
2022 4410 1.929836 GACTGAGATTTAGCAGCACCG 59.070 52.381 0.00 0.00 35.57 4.94
2023 4411 1.929836 CGACTGAGATTTAGCAGCACC 59.070 52.381 0.00 0.00 35.57 5.01
2024 4412 2.600867 GTCGACTGAGATTTAGCAGCAC 59.399 50.000 8.70 0.00 35.57 4.40
2025 4413 2.493675 AGTCGACTGAGATTTAGCAGCA 59.506 45.455 19.30 0.00 35.57 4.41
2026 4414 2.857152 CAGTCGACTGAGATTTAGCAGC 59.143 50.000 36.73 0.00 46.59 5.25
2038 4426 0.791238 CGCGAAGTCTCAGTCGACTG 60.791 60.000 34.76 34.76 43.14 3.51
2039 4427 0.949588 TCGCGAAGTCTCAGTCGACT 60.950 55.000 13.58 13.58 45.73 4.18
2040 4428 0.110328 TTCGCGAAGTCTCAGTCGAC 60.110 55.000 19.38 7.70 39.64 4.20
2041 4429 0.166161 CTTCGCGAAGTCTCAGTCGA 59.834 55.000 34.97 4.60 39.64 4.20
2042 4430 2.631303 CTTCGCGAAGTCTCAGTCG 58.369 57.895 34.97 12.16 40.24 4.18
2051 4439 0.166161 TCGACTGAGACTTCGCGAAG 59.834 55.000 39.55 39.55 43.79 3.79
2052 4440 0.803117 ATCGACTGAGACTTCGCGAA 59.197 50.000 22.01 22.01 35.15 4.70
2053 4441 0.097150 CATCGACTGAGACTTCGCGA 59.903 55.000 3.71 3.71 35.15 5.87
2054 4442 0.179187 ACATCGACTGAGACTTCGCG 60.179 55.000 0.00 0.00 35.15 5.87
2055 4443 1.983972 AACATCGACTGAGACTTCGC 58.016 50.000 0.00 0.00 35.15 4.70
2056 4444 6.579292 GGAATATAACATCGACTGAGACTTCG 59.421 42.308 0.00 0.00 36.55 3.79
2057 4445 7.653647 AGGAATATAACATCGACTGAGACTTC 58.346 38.462 0.00 0.00 0.00 3.01
2058 4446 7.589958 AGGAATATAACATCGACTGAGACTT 57.410 36.000 0.00 0.00 0.00 3.01
2059 4447 7.589958 AAGGAATATAACATCGACTGAGACT 57.410 36.000 0.00 0.00 0.00 3.24
2060 4448 7.921214 TCAAAGGAATATAACATCGACTGAGAC 59.079 37.037 0.00 0.00 0.00 3.36
2061 4449 8.007405 TCAAAGGAATATAACATCGACTGAGA 57.993 34.615 0.00 0.00 0.00 3.27
2062 4450 8.824159 ATCAAAGGAATATAACATCGACTGAG 57.176 34.615 0.00 0.00 0.00 3.35
2063 4451 9.613428 AAATCAAAGGAATATAACATCGACTGA 57.387 29.630 0.00 0.00 0.00 3.41
2076 4464 9.590451 GAATCTGCATGAAAAATCAAAGGAATA 57.410 29.630 0.00 0.00 0.00 1.75
2077 4465 7.277098 CGAATCTGCATGAAAAATCAAAGGAAT 59.723 33.333 0.00 0.00 0.00 3.01
2078 4466 6.587226 CGAATCTGCATGAAAAATCAAAGGAA 59.413 34.615 0.00 0.00 0.00 3.36
2079 4467 6.094719 CGAATCTGCATGAAAAATCAAAGGA 58.905 36.000 0.00 0.00 0.00 3.36
2080 4468 5.865552 ACGAATCTGCATGAAAAATCAAAGG 59.134 36.000 0.00 0.00 0.00 3.11
2081 4469 6.364165 ACACGAATCTGCATGAAAAATCAAAG 59.636 34.615 0.00 0.00 0.00 2.77
2082 4470 6.215121 ACACGAATCTGCATGAAAAATCAAA 58.785 32.000 0.00 0.00 0.00 2.69
2083 4471 5.771469 ACACGAATCTGCATGAAAAATCAA 58.229 33.333 0.00 0.00 0.00 2.57
2084 4472 5.375417 ACACGAATCTGCATGAAAAATCA 57.625 34.783 0.00 0.00 0.00 2.57
2085 4473 7.538678 ACTTTACACGAATCTGCATGAAAAATC 59.461 33.333 0.00 0.00 0.00 2.17
2086 4474 7.370383 ACTTTACACGAATCTGCATGAAAAAT 58.630 30.769 0.00 0.00 0.00 1.82
2087 4475 6.734137 ACTTTACACGAATCTGCATGAAAAA 58.266 32.000 0.00 0.00 0.00 1.94
2088 4476 6.312399 ACTTTACACGAATCTGCATGAAAA 57.688 33.333 0.00 0.00 0.00 2.29
2089 4477 5.940192 ACTTTACACGAATCTGCATGAAA 57.060 34.783 0.00 0.00 0.00 2.69
2090 4478 5.940192 AACTTTACACGAATCTGCATGAA 57.060 34.783 0.00 0.00 0.00 2.57
2091 4479 5.940192 AAACTTTACACGAATCTGCATGA 57.060 34.783 0.00 0.00 0.00 3.07
2092 4480 6.991485 AAAAACTTTACACGAATCTGCATG 57.009 33.333 0.00 0.00 0.00 4.06
2144 4532 6.352016 AGTCTCAATCAAGTGACACATAGT 57.648 37.500 8.59 0.00 35.17 2.12
2145 4533 7.516481 CAAAGTCTCAATCAAGTGACACATAG 58.484 38.462 8.59 0.00 35.17 2.23
2149 4537 4.531332 GCAAAGTCTCAATCAAGTGACAC 58.469 43.478 0.00 0.00 35.17 3.67
2152 4540 3.727726 TCGCAAAGTCTCAATCAAGTGA 58.272 40.909 0.00 0.00 0.00 3.41
2153 4541 4.024556 ACTTCGCAAAGTCTCAATCAAGTG 60.025 41.667 0.00 0.00 42.10 3.16
2154 4542 4.130118 ACTTCGCAAAGTCTCAATCAAGT 58.870 39.130 0.00 0.00 42.10 3.16
2155 4543 4.739046 ACTTCGCAAAGTCTCAATCAAG 57.261 40.909 0.00 0.00 42.10 3.02
2166 4554 1.716581 GTCGACTGAGACTTCGCAAAG 59.283 52.381 8.70 0.00 38.09 2.77
2168 4556 3.474007 GTCGACTGAGACTTCGCAA 57.526 52.632 8.70 0.00 38.09 4.85
2180 4568 0.328592 TGGCTAGGTCTCAGTCGACT 59.671 55.000 13.58 13.58 34.38 4.18
2181 4569 0.452585 GTGGCTAGGTCTCAGTCGAC 59.547 60.000 7.70 7.70 0.00 4.20
2182 4570 0.037734 TGTGGCTAGGTCTCAGTCGA 59.962 55.000 0.00 0.00 0.00 4.20
2183 4571 0.171455 GTGTGGCTAGGTCTCAGTCG 59.829 60.000 0.00 0.00 0.00 4.18
2184 4572 0.533032 GGTGTGGCTAGGTCTCAGTC 59.467 60.000 0.00 0.00 0.00 3.51
2185 4573 0.905337 GGGTGTGGCTAGGTCTCAGT 60.905 60.000 0.00 0.00 0.00 3.41
2186 4574 0.616111 AGGGTGTGGCTAGGTCTCAG 60.616 60.000 0.00 0.00 0.00 3.35
2187 4575 0.708209 TAGGGTGTGGCTAGGTCTCA 59.292 55.000 0.00 0.00 0.00 3.27
2188 4576 1.964933 GATAGGGTGTGGCTAGGTCTC 59.035 57.143 0.00 0.00 0.00 3.36
2189 4577 1.413227 GGATAGGGTGTGGCTAGGTCT 60.413 57.143 0.00 0.00 0.00 3.85
2190 4578 1.049402 GGATAGGGTGTGGCTAGGTC 58.951 60.000 0.00 0.00 0.00 3.85
2191 4579 0.642710 AGGATAGGGTGTGGCTAGGT 59.357 55.000 0.00 0.00 0.00 3.08
2192 4580 2.696526 TAGGATAGGGTGTGGCTAGG 57.303 55.000 0.00 0.00 0.00 3.02
2193 4581 4.704965 GTTTTAGGATAGGGTGTGGCTAG 58.295 47.826 0.00 0.00 0.00 3.42
2194 4582 3.133362 CGTTTTAGGATAGGGTGTGGCTA 59.867 47.826 0.00 0.00 0.00 3.93
2195 4583 2.093128 CGTTTTAGGATAGGGTGTGGCT 60.093 50.000 0.00 0.00 0.00 4.75
2196 4584 2.285977 CGTTTTAGGATAGGGTGTGGC 58.714 52.381 0.00 0.00 0.00 5.01
2197 4585 2.285977 GCGTTTTAGGATAGGGTGTGG 58.714 52.381 0.00 0.00 0.00 4.17
2198 4586 2.980568 TGCGTTTTAGGATAGGGTGTG 58.019 47.619 0.00 0.00 0.00 3.82
2199 4587 3.054655 ACATGCGTTTTAGGATAGGGTGT 60.055 43.478 0.00 0.00 0.00 4.16
2200 4588 3.541632 ACATGCGTTTTAGGATAGGGTG 58.458 45.455 0.00 0.00 0.00 4.61
2201 4589 3.926058 ACATGCGTTTTAGGATAGGGT 57.074 42.857 0.00 0.00 0.00 4.34
2202 4590 6.231211 AGATAACATGCGTTTTAGGATAGGG 58.769 40.000 0.00 0.00 36.52 3.53
2203 4591 6.929049 TGAGATAACATGCGTTTTAGGATAGG 59.071 38.462 0.00 0.00 36.52 2.57
2204 4592 7.946655 TGAGATAACATGCGTTTTAGGATAG 57.053 36.000 0.00 0.00 36.52 2.08
2205 4593 8.310406 CATGAGATAACATGCGTTTTAGGATA 57.690 34.615 0.00 0.00 40.54 2.59
2206 4594 7.194607 CATGAGATAACATGCGTTTTAGGAT 57.805 36.000 0.00 0.00 40.54 3.24
2207 4595 6.603237 CATGAGATAACATGCGTTTTAGGA 57.397 37.500 0.00 0.00 40.54 2.94
2231 4623 9.919416 TGAGATTTTTAGATGAATAATGACCCA 57.081 29.630 0.00 0.00 0.00 4.51
2334 4963 1.001887 GGCCACCGGGTTGTTGATA 60.002 57.895 6.32 0.00 36.17 2.15
2347 4976 3.818787 CGCCTTCTGCATGGCCAC 61.819 66.667 8.16 0.00 45.90 5.01
2493 5122 4.373116 GGTTCCTGGCACTCGCGA 62.373 66.667 9.26 9.26 39.92 5.87
2569 5198 2.556459 GCTCATCGCGGCCTAGAGA 61.556 63.158 6.13 0.00 0.00 3.10
2655 5285 1.490574 CAAAGTCACCACCCCCAAAA 58.509 50.000 0.00 0.00 0.00 2.44
2909 5539 8.430801 ACAGTATGCATTCATTTCTTAGAGTC 57.569 34.615 3.54 0.00 42.53 3.36
2982 5616 7.143340 GCACAATACTAATGATGTGATGCAAT 58.857 34.615 8.78 0.00 44.52 3.56
2989 5623 8.076714 AGTTATCGCACAATACTAATGATGTG 57.923 34.615 0.00 0.00 44.55 3.21
3008 5642 3.712091 AGCCGCACTACACTAGTTATC 57.288 47.619 0.00 0.00 36.76 1.75
3017 5651 4.280929 ACATATTGATCTAGCCGCACTACA 59.719 41.667 0.00 0.00 0.00 2.74
3024 5658 3.997021 GGAACCACATATTGATCTAGCCG 59.003 47.826 0.00 0.00 0.00 5.52
3084 5718 9.787532 ATGTATCAATTGAAATAAAACGTCCAG 57.212 29.630 13.09 0.00 0.00 3.86
3147 5785 7.906160 TGTTTCTATAATTTTCGCTGTAGAGC 58.094 34.615 0.76 0.76 42.37 4.09
3209 5849 2.481289 AGGAAACTAGTTGAGCTGCC 57.519 50.000 9.34 4.59 40.61 4.85
3298 5938 5.473796 AGTTGCTGCAAATTTTGTCTTTG 57.526 34.783 17.80 0.00 36.81 2.77
3324 5964 4.458989 GGTACACCACATGTCATGAACAAT 59.541 41.667 19.77 4.65 42.09 2.71
3329 5969 2.265367 AGGGTACACCACATGTCATGA 58.735 47.619 19.77 0.00 42.09 3.07
3330 5970 2.749076 CAAGGGTACACCACATGTCATG 59.251 50.000 11.41 11.41 42.09 3.07
3331 5971 2.375174 ACAAGGGTACACCACATGTCAT 59.625 45.455 0.00 0.00 42.09 3.06
3334 5974 1.817740 GCACAAGGGTACACCACATGT 60.818 52.381 0.00 0.00 46.06 3.21
3341 5981 5.240844 AGTTAAAATGAGCACAAGGGTACAC 59.759 40.000 0.00 0.00 0.00 2.90
3398 6049 6.370593 TGATGACTTTCTTTTGTGAATACGC 58.629 36.000 0.00 0.00 0.00 4.42
3520 6213 3.505680 AGATGCTAGATGATCCTGACGTC 59.494 47.826 9.11 9.11 0.00 4.34
3589 6283 7.174426 GGCATCACCTAAACTTTACACTAACTT 59.826 37.037 0.00 0.00 34.51 2.66
3626 6320 4.608948 ATCTACCATTAGCTCCTTTCCG 57.391 45.455 0.00 0.00 0.00 4.30
3640 6334 5.949952 TGTGCTCTGTCTTAACTATCTACCA 59.050 40.000 0.00 0.00 0.00 3.25
3724 6419 1.632589 TGTAGACCTTCAGCTGCTCA 58.367 50.000 9.47 0.00 0.00 4.26
3726 6421 4.508662 GTTAATGTAGACCTTCAGCTGCT 58.491 43.478 9.47 0.00 0.00 4.24
3727 6422 3.623510 GGTTAATGTAGACCTTCAGCTGC 59.376 47.826 9.47 0.00 33.08 5.25
3756 6451 4.053983 CTGTGTCGATCGATGGATTTGAT 58.946 43.478 22.50 0.00 31.51 2.57
3771 6466 0.367887 CATCGTGTCATGCTGTGTCG 59.632 55.000 0.00 0.00 0.00 4.35
3818 6513 3.014623 CACTGCATGTTCATCCTCATGT 58.985 45.455 0.00 0.00 42.09 3.21
3824 6519 2.983229 AGAGACACTGCATGTTCATCC 58.017 47.619 0.00 0.00 43.56 3.51
3826 6521 6.540189 GGTTTATAGAGACACTGCATGTTCAT 59.460 38.462 0.00 0.00 43.56 2.57
3832 6527 5.069781 GGAGAGGTTTATAGAGACACTGCAT 59.930 44.000 0.00 0.00 0.00 3.96
3833 6528 4.402793 GGAGAGGTTTATAGAGACACTGCA 59.597 45.833 0.00 0.00 0.00 4.41
3834 6529 4.647399 AGGAGAGGTTTATAGAGACACTGC 59.353 45.833 0.00 0.00 0.00 4.40
3835 6530 6.783708 AAGGAGAGGTTTATAGAGACACTG 57.216 41.667 0.00 0.00 0.00 3.66
3837 6532 8.240267 ACATAAGGAGAGGTTTATAGAGACAC 57.760 38.462 0.00 0.00 0.00 3.67
3838 6533 8.840200 AACATAAGGAGAGGTTTATAGAGACA 57.160 34.615 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.