Multiple sequence alignment - TraesCS2B01G169200

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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 TraesCS2B01G169200 chr2B 100.000 4606 0 0 611 5216 141985749 141990354 0.000000e+00 8506
1 TraesCS2B01G169200 chr2B 100.000 352 0 0 1 352 141985139 141985490 0.000000e+00 651
2 TraesCS2B01G169200 chr2B 99.265 136 1 0 2019 2154 141987025 141987160 4.030000e-61 246
3 TraesCS2B01G169200 chr2B 99.265 136 1 0 1887 2022 141987157 141987292 4.030000e-61 246
4 TraesCS2B01G169200 chr2A 94.357 3119 141 19 2020 5129 89119045 89122137 0.000000e+00 4752
5 TraesCS2B01G169200 chr2A 92.397 947 42 12 1078 2022 89118261 89119179 0.000000e+00 1323
6 TraesCS2B01G169200 chr2A 85.352 355 34 8 1 352 89114369 89114708 8.310000e-93 351
7 TraesCS2B01G169200 chr2A 93.478 92 5 1 873 963 89117691 89117782 9.110000e-28 135
8 TraesCS2B01G169200 chr2A 97.143 70 2 0 5147 5216 89122131 89122200 9.180000e-23 119
9 TraesCS2B01G169200 chr2D 95.507 2404 93 11 2020 4417 89386980 89389374 0.000000e+00 3827
10 TraesCS2B01G169200 chr2D 94.976 1055 50 3 971 2022 89386059 89387113 0.000000e+00 1652
11 TraesCS2B01G169200 chr7D 80.723 166 28 4 2894 3058 60671104 60671266 5.480000e-25 126
12 TraesCS2B01G169200 chr7B 80.723 166 28 4 2894 3058 3174044 3174206 5.480000e-25 126
13 TraesCS2B01G169200 chr7A 80.120 166 29 4 2894 3058 64925934 64926096 2.550000e-23 121
14 TraesCS2B01G169200 chr3D 80.503 159 29 2 2901 3058 225852514 225852357 2.550000e-23 121
15 TraesCS2B01G169200 chr3A 80.503 159 29 2 2901 3058 264025371 264025214 2.550000e-23 121
16 TraesCS2B01G169200 chr3B 79.518 166 30 4 2894 3058 299144094 299144256 1.190000e-21 115
17 TraesCS2B01G169200 chr6B 79.747 158 30 2 2902 3058 51908777 51908621 4.270000e-21 113


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 TraesCS2B01G169200 chr2B 141985139 141990354 5215 False 2412.25 8506 99.6325 1 5216 4 chr2B.!!$F1 5215
1 TraesCS2B01G169200 chr2A 89114369 89122200 7831 False 1336.00 4752 92.5454 1 5216 5 chr2A.!!$F1 5215
2 TraesCS2B01G169200 chr2D 89386059 89389374 3315 False 2739.50 3827 95.2415 971 4417 2 chr2D.!!$F1 3446


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
48 49 0.107456 GTCGCATGAGGGGATGTCAT 59.893 55.000 0.00 0.0 40.92 3.06 F
944 3614 0.107643 GGCCCAGAGCTATTGACCTC 59.892 60.000 0.00 0.0 43.05 3.85 F
1591 4643 0.884704 TCGCTCCAGGTTTGCTGTTC 60.885 55.000 0.00 0.0 0.00 3.18 F
2113 5166 0.917533 AGAACCATGAGGCATGAGCT 59.082 50.000 8.87 0.0 43.81 4.09 F
2116 5169 1.504912 ACCATGAGGCATGAGCTACT 58.495 50.000 8.87 0.0 43.81 2.57 F
2313 5366 1.620323 CATCGATCTGGTATGGCTCCA 59.380 52.381 0.00 0.0 0.00 3.86 F
3547 6604 1.722011 ACTGGTTATTCGGCAACTCG 58.278 50.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 3736 0.255033 AGGCGAGGTGGGGTTTAATC 59.745 55.000 0.00 0.00 0.00 1.75 R
2094 5147 0.917533 AGCTCATGCCTCATGGTTCT 59.082 50.000 6.92 0.43 41.66 3.01 R
2611 5665 1.954927 GAAGGACCTTCCCGCTAATG 58.045 55.000 21.88 0.00 37.19 1.90 R
3959 7016 0.110486 AAATGTTCCAGGTCGCCACT 59.890 50.000 0.00 0.00 0.00 4.00 R
3968 7025 5.629020 CCAAAACATACGTCAAATGTTCCAG 59.371 40.000 13.95 8.16 44.66 3.86 R
4137 7194 3.006323 AGAGTACAAGACAGGACTGCTTG 59.994 47.826 22.81 22.81 43.55 4.01 R
4963 8031 0.037303 CTGGAGCAGGCCTTCAAAGA 59.963 55.000 0.00 0.00 0.00 2.52 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
47 48 1.522092 GTCGCATGAGGGGATGTCA 59.478 57.895 0.00 0.00 40.92 3.58
48 49 0.107456 GTCGCATGAGGGGATGTCAT 59.893 55.000 0.00 0.00 40.92 3.06
58 59 1.325355 GGGATGTCATCATTGGGCAG 58.675 55.000 14.72 0.00 34.06 4.85
59 60 0.672342 GGATGTCATCATTGGGCAGC 59.328 55.000 14.72 0.00 34.06 5.25
60 61 1.395635 GATGTCATCATTGGGCAGCA 58.604 50.000 8.00 0.00 34.06 4.41
61 62 1.961394 GATGTCATCATTGGGCAGCAT 59.039 47.619 8.00 0.00 34.06 3.79
62 63 1.107945 TGTCATCATTGGGCAGCATG 58.892 50.000 0.00 0.00 40.87 4.06
63 64 1.341187 TGTCATCATTGGGCAGCATGA 60.341 47.619 0.00 0.00 39.69 3.07
74 75 2.846039 GCAGCATGACATTGAAGGAG 57.154 50.000 0.00 0.00 39.69 3.69
75 76 2.362736 GCAGCATGACATTGAAGGAGA 58.637 47.619 0.00 0.00 39.69 3.71
76 77 2.950309 GCAGCATGACATTGAAGGAGAT 59.050 45.455 0.00 0.00 39.69 2.75
77 78 3.243101 GCAGCATGACATTGAAGGAGATG 60.243 47.826 0.00 0.00 39.69 2.90
78 79 3.945921 CAGCATGACATTGAAGGAGATGT 59.054 43.478 0.00 0.00 39.69 3.06
79 80 4.398358 CAGCATGACATTGAAGGAGATGTT 59.602 41.667 0.00 0.00 39.69 2.71
80 81 4.398358 AGCATGACATTGAAGGAGATGTTG 59.602 41.667 0.00 0.00 36.67 3.33
81 82 4.397103 GCATGACATTGAAGGAGATGTTGA 59.603 41.667 0.00 0.00 36.67 3.18
86 87 6.072342 TGACATTGAAGGAGATGTTGAATGTG 60.072 38.462 5.55 0.00 40.43 3.21
89 90 5.183530 TGAAGGAGATGTTGAATGTGGAT 57.816 39.130 0.00 0.00 0.00 3.41
99 100 1.106285 GAATGTGGATTGTGGCCTCC 58.894 55.000 3.32 2.38 0.00 4.30
114 115 1.486211 CCTCCCGTTCTCCACTATGT 58.514 55.000 0.00 0.00 0.00 2.29
131 132 0.614979 TGTGTGGAGCCCTCTACCTC 60.615 60.000 8.96 4.02 39.91 3.85
153 154 3.182967 GAGGAGTACGAGTTCAAGCATG 58.817 50.000 0.00 0.00 0.00 4.06
160 161 0.109412 GAGTTCAAGCATGGCAGTGC 60.109 55.000 6.55 6.55 45.38 4.40
173 174 0.108138 GCAGTGCCACCTATCGTCTT 60.108 55.000 2.85 0.00 0.00 3.01
174 175 1.676014 GCAGTGCCACCTATCGTCTTT 60.676 52.381 2.85 0.00 0.00 2.52
175 176 2.002586 CAGTGCCACCTATCGTCTTTG 58.997 52.381 0.00 0.00 0.00 2.77
183 184 2.271800 CCTATCGTCTTTGCTCACCAC 58.728 52.381 0.00 0.00 0.00 4.16
293 294 2.344535 GCACAAGGCACCATCTGTT 58.655 52.632 0.00 0.00 43.97 3.16
296 297 1.267806 CACAAGGCACCATCTGTTGAC 59.732 52.381 0.00 0.00 0.00 3.18
297 298 1.133823 ACAAGGCACCATCTGTTGACA 60.134 47.619 0.00 0.00 0.00 3.58
306 307 2.224621 CCATCTGTTGACACAAGGGAGT 60.225 50.000 0.00 0.00 30.36 3.85
313 317 4.202223 TGTTGACACAAGGGAGTAGAAGAC 60.202 45.833 0.00 0.00 0.00 3.01
314 318 3.572642 TGACACAAGGGAGTAGAAGACA 58.427 45.455 0.00 0.00 0.00 3.41
317 321 3.967987 ACACAAGGGAGTAGAAGACAACT 59.032 43.478 0.00 0.00 0.00 3.16
318 322 5.145564 ACACAAGGGAGTAGAAGACAACTA 58.854 41.667 0.00 0.00 0.00 2.24
325 329 5.653330 GGGAGTAGAAGACAACTAAGCTACT 59.347 44.000 0.00 0.00 37.87 2.57
338 342 4.654724 ACTAAGCTACTGGAGGGTATTTCC 59.345 45.833 0.00 0.00 35.20 3.13
339 343 3.423058 AGCTACTGGAGGGTATTTCCT 57.577 47.619 0.00 0.00 40.43 3.36
347 351 4.728772 TGGAGGGTATTTCCTAATGCATG 58.271 43.478 0.00 0.00 37.25 4.06
646 2353 7.951591 ACATATATTTGGCTTAAACCCACATC 58.048 34.615 0.00 0.00 30.65 3.06
653 2360 4.947388 TGGCTTAAACCCACATCAATCTAC 59.053 41.667 0.00 0.00 0.00 2.59
674 2381 4.985538 ACACCACATCATCTTGTAAACCT 58.014 39.130 0.00 0.00 0.00 3.50
803 3440 9.883142 ACTTTCTTCCATTCAATGTTTTGTTTA 57.117 25.926 0.00 0.00 34.32 2.01
890 3560 1.759299 AGGCCGGCCTGTAATACGA 60.759 57.895 46.71 0.00 46.22 3.43
893 3563 1.156034 GCCGGCCTGTAATACGAACC 61.156 60.000 18.11 0.00 0.00 3.62
898 3568 1.067516 GCCTGTAATACGAACCCGCTA 59.932 52.381 0.00 0.00 39.95 4.26
944 3614 0.107643 GGCCCAGAGCTATTGACCTC 59.892 60.000 0.00 0.00 43.05 3.85
947 3617 1.694048 CCCAGAGCTATTGACCTCCCT 60.694 57.143 0.00 0.00 0.00 4.20
949 3619 2.676748 CAGAGCTATTGACCTCCCTCT 58.323 52.381 0.00 0.00 0.00 3.69
950 3620 2.627699 CAGAGCTATTGACCTCCCTCTC 59.372 54.545 0.00 0.00 0.00 3.20
951 3621 2.517980 AGAGCTATTGACCTCCCTCTCT 59.482 50.000 0.00 0.00 0.00 3.10
952 3622 2.890945 GAGCTATTGACCTCCCTCTCTC 59.109 54.545 0.00 0.00 0.00 3.20
953 3623 2.517980 AGCTATTGACCTCCCTCTCTCT 59.482 50.000 0.00 0.00 0.00 3.10
954 3624 2.890945 GCTATTGACCTCCCTCTCTCTC 59.109 54.545 0.00 0.00 0.00 3.20
955 3625 3.436470 GCTATTGACCTCCCTCTCTCTCT 60.436 52.174 0.00 0.00 0.00 3.10
956 3626 2.818751 TTGACCTCCCTCTCTCTCTC 57.181 55.000 0.00 0.00 0.00 3.20
957 3627 1.979809 TGACCTCCCTCTCTCTCTCT 58.020 55.000 0.00 0.00 0.00 3.10
958 3628 1.843851 TGACCTCCCTCTCTCTCTCTC 59.156 57.143 0.00 0.00 0.00 3.20
959 3629 2.127708 GACCTCCCTCTCTCTCTCTCT 58.872 57.143 0.00 0.00 0.00 3.10
960 3630 2.104963 GACCTCCCTCTCTCTCTCTCTC 59.895 59.091 0.00 0.00 0.00 3.20
961 3631 2.293856 ACCTCCCTCTCTCTCTCTCTCT 60.294 54.545 0.00 0.00 0.00 3.10
962 3632 2.370189 CCTCCCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
963 3633 3.312890 CTCCCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
964 3634 3.041211 TCCCTCTCTCTCTCTCTCTCTG 58.959 54.545 0.00 0.00 0.00 3.35
1002 3672 2.896443 CTCCACTTCCTCCTCGGC 59.104 66.667 0.00 0.00 0.00 5.54
1036 3706 2.803285 TCTGGCTCATATCTCCCCTT 57.197 50.000 0.00 0.00 0.00 3.95
1053 3723 2.824388 CTTCCCCTCCCCTCCTCGTT 62.824 65.000 0.00 0.00 0.00 3.85
1055 3725 2.764547 CCCTCCCCTCCTCGTTCC 60.765 72.222 0.00 0.00 0.00 3.62
1066 3736 3.685214 CTCGTTCCCCTCAGACGCG 62.685 68.421 3.53 3.53 36.77 6.01
1087 4137 1.360185 TTAAACCCCACCTCGCCTAA 58.640 50.000 0.00 0.00 0.00 2.69
1089 4139 1.848886 AAACCCCACCTCGCCTAAGG 61.849 60.000 0.00 0.00 42.55 2.69
1129 4179 3.219928 GGAGCAGGGATCGAGCGA 61.220 66.667 0.00 0.00 0.00 4.93
1141 4191 3.077556 GAGCGAGCAGAAGGGGGA 61.078 66.667 0.00 0.00 0.00 4.81
1414 4465 3.505464 AGTTTCGGAGATGTTCGGTAG 57.495 47.619 0.00 0.00 35.04 3.18
1483 4535 2.470057 TTTGGGATTCTTATGGGGGC 57.530 50.000 0.00 0.00 0.00 5.80
1585 4637 1.009829 GTGCTATCGCTCCAGGTTTG 58.990 55.000 0.00 0.00 36.97 2.93
1591 4643 0.884704 TCGCTCCAGGTTTGCTGTTC 60.885 55.000 0.00 0.00 0.00 3.18
1626 4678 7.489160 ACTTGCAGTATTGTCAGTTATCGATA 58.511 34.615 0.00 0.00 0.00 2.92
1660 4713 5.352284 TCGCAATCTCTTATTCTCACCTTC 58.648 41.667 0.00 0.00 0.00 3.46
1723 4776 3.502211 GTGACCATACTGACTTTTGTGGG 59.498 47.826 0.00 0.00 0.00 4.61
1736 4789 4.278419 ACTTTTGTGGGAGTGCTGTATTTC 59.722 41.667 0.00 0.00 0.00 2.17
1759 4812 4.957967 CGCGTGTCTGTCAAATTGATTATC 59.042 41.667 0.00 0.00 0.00 1.75
1763 4816 8.338259 GCGTGTCTGTCAAATTGATTATCTATT 58.662 33.333 0.00 0.00 0.00 1.73
1816 4869 3.367395 GCCATTTCCTGTTTGAGTTAGGC 60.367 47.826 0.00 0.00 0.00 3.93
1857 4910 6.701400 GTGGAAATTAACTGTCAACATGCTTT 59.299 34.615 0.00 0.00 0.00 3.51
1888 4941 4.665833 ATGACCAGGAATTGAATGCATG 57.334 40.909 0.00 0.00 0.00 4.06
1890 4943 3.025978 GACCAGGAATTGAATGCATGGA 58.974 45.455 22.75 0.00 0.00 3.41
1904 4957 3.439154 TGCATGGATAACAACAATGGGT 58.561 40.909 0.00 0.00 0.00 4.51
1996 5049 4.034975 GCATGAGCTACTTTGGTGAGATTC 59.965 45.833 0.00 0.00 37.91 2.52
1998 5051 5.227569 TGAGCTACTTTGGTGAGATTCAA 57.772 39.130 0.00 0.00 0.00 2.69
1999 5052 5.620206 TGAGCTACTTTGGTGAGATTCAAA 58.380 37.500 0.00 0.00 0.00 2.69
2000 5053 6.061441 TGAGCTACTTTGGTGAGATTCAAAA 58.939 36.000 0.00 0.00 33.24 2.44
2001 5054 6.545666 TGAGCTACTTTGGTGAGATTCAAAAA 59.454 34.615 0.00 0.00 33.24 1.94
2030 5083 9.967451 TTAATTTCTGACCTATGGATAACAACA 57.033 29.630 0.00 0.00 0.00 3.33
2031 5084 8.877864 AATTTCTGACCTATGGATAACAACAA 57.122 30.769 0.00 0.00 0.00 2.83
2032 5085 9.479549 AATTTCTGACCTATGGATAACAACAAT 57.520 29.630 0.00 0.00 0.00 2.71
2033 5086 7.864108 TTCTGACCTATGGATAACAACAATG 57.136 36.000 0.00 0.00 0.00 2.82
2034 5087 6.356556 TCTGACCTATGGATAACAACAATGG 58.643 40.000 0.00 0.00 0.00 3.16
2035 5088 5.445069 TGACCTATGGATAACAACAATGGG 58.555 41.667 0.00 0.00 0.00 4.00
2036 5089 5.044476 TGACCTATGGATAACAACAATGGGT 60.044 40.000 0.00 0.00 0.00 4.51
2037 5090 6.158871 TGACCTATGGATAACAACAATGGGTA 59.841 38.462 0.00 0.00 0.00 3.69
2038 5091 6.601332 ACCTATGGATAACAACAATGGGTAG 58.399 40.000 0.00 0.00 0.00 3.18
2039 5092 6.159751 ACCTATGGATAACAACAATGGGTAGT 59.840 38.462 0.00 0.00 0.00 2.73
2040 5093 7.348801 ACCTATGGATAACAACAATGGGTAGTA 59.651 37.037 0.00 0.00 0.00 1.82
2041 5094 7.878127 CCTATGGATAACAACAATGGGTAGTAG 59.122 40.741 0.00 0.00 0.00 2.57
2042 5095 6.630203 TGGATAACAACAATGGGTAGTAGT 57.370 37.500 0.00 0.00 0.00 2.73
2043 5096 7.023171 TGGATAACAACAATGGGTAGTAGTT 57.977 36.000 0.00 0.00 0.00 2.24
2044 5097 7.463431 TGGATAACAACAATGGGTAGTAGTTT 58.537 34.615 0.00 0.00 0.00 2.66
2045 5098 7.608761 TGGATAACAACAATGGGTAGTAGTTTC 59.391 37.037 0.00 0.00 0.00 2.78
2046 5099 7.066645 GGATAACAACAATGGGTAGTAGTTTCC 59.933 40.741 0.00 0.00 0.00 3.13
2047 5100 4.659115 ACAACAATGGGTAGTAGTTTCCC 58.341 43.478 4.19 4.19 41.41 3.97
2048 5101 4.352893 ACAACAATGGGTAGTAGTTTCCCT 59.647 41.667 10.55 0.00 41.58 4.20
2049 5102 5.163023 ACAACAATGGGTAGTAGTTTCCCTT 60.163 40.000 10.55 3.62 41.58 3.95
2050 5103 5.175388 ACAATGGGTAGTAGTTTCCCTTC 57.825 43.478 10.55 0.00 41.58 3.46
2051 5104 4.600111 ACAATGGGTAGTAGTTTCCCTTCA 59.400 41.667 10.55 0.00 41.58 3.02
2052 5105 4.838904 ATGGGTAGTAGTTTCCCTTCAC 57.161 45.455 10.55 0.00 41.58 3.18
2053 5106 3.865571 TGGGTAGTAGTTTCCCTTCACT 58.134 45.455 10.55 0.00 41.58 3.41
2054 5107 5.014534 TGGGTAGTAGTTTCCCTTCACTA 57.985 43.478 10.55 0.00 41.58 2.74
2055 5108 5.596763 TGGGTAGTAGTTTCCCTTCACTAT 58.403 41.667 10.55 0.00 41.58 2.12
2056 5109 6.027482 TGGGTAGTAGTTTCCCTTCACTATT 58.973 40.000 10.55 0.00 41.58 1.73
2057 5110 6.502863 TGGGTAGTAGTTTCCCTTCACTATTT 59.497 38.462 10.55 0.00 41.58 1.40
2058 5111 6.822170 GGGTAGTAGTTTCCCTTCACTATTTG 59.178 42.308 0.00 0.00 38.29 2.32
2059 5112 7.310858 GGGTAGTAGTTTCCCTTCACTATTTGA 60.311 40.741 0.00 0.00 38.29 2.69
2060 5113 8.098912 GGTAGTAGTTTCCCTTCACTATTTGAA 58.901 37.037 0.00 0.00 42.26 2.69
2069 5122 4.640771 TTCACTATTTGAAGGCTCCTGT 57.359 40.909 0.00 0.00 39.45 4.00
2070 5123 3.942829 TCACTATTTGAAGGCTCCTGTG 58.057 45.455 0.00 0.00 0.00 3.66
2071 5124 3.327757 TCACTATTTGAAGGCTCCTGTGT 59.672 43.478 0.00 0.00 0.00 3.72
2072 5125 4.530553 TCACTATTTGAAGGCTCCTGTGTA 59.469 41.667 0.00 0.00 0.00 2.90
2073 5126 4.631813 CACTATTTGAAGGCTCCTGTGTAC 59.368 45.833 0.00 0.00 0.00 2.90
2074 5127 2.561478 TTTGAAGGCTCCTGTGTACC 57.439 50.000 0.00 0.00 0.00 3.34
2075 5128 1.729586 TTGAAGGCTCCTGTGTACCT 58.270 50.000 0.00 0.00 0.00 3.08
2076 5129 2.615986 TGAAGGCTCCTGTGTACCTA 57.384 50.000 0.00 0.00 0.00 3.08
2077 5130 3.116096 TGAAGGCTCCTGTGTACCTAT 57.884 47.619 0.00 0.00 0.00 2.57
2078 5131 3.031736 TGAAGGCTCCTGTGTACCTATC 58.968 50.000 0.00 0.00 0.00 2.08
2079 5132 3.301274 GAAGGCTCCTGTGTACCTATCT 58.699 50.000 0.00 0.00 0.00 1.98
2080 5133 3.406512 AGGCTCCTGTGTACCTATCTT 57.593 47.619 0.00 0.00 0.00 2.40
2081 5134 3.034635 AGGCTCCTGTGTACCTATCTTG 58.965 50.000 0.00 0.00 0.00 3.02
2082 5135 3.031736 GGCTCCTGTGTACCTATCTTGA 58.968 50.000 0.00 0.00 0.00 3.02
2083 5136 3.643792 GGCTCCTGTGTACCTATCTTGAT 59.356 47.826 0.00 0.00 0.00 2.57
2084 5137 4.262249 GGCTCCTGTGTACCTATCTTGATC 60.262 50.000 0.00 0.00 0.00 2.92
2085 5138 4.557695 GCTCCTGTGTACCTATCTTGATCG 60.558 50.000 0.00 0.00 0.00 3.69
2086 5139 4.788679 TCCTGTGTACCTATCTTGATCGA 58.211 43.478 0.00 0.00 0.00 3.59
2087 5140 5.386060 TCCTGTGTACCTATCTTGATCGAT 58.614 41.667 0.00 0.00 0.00 3.59
2088 5141 5.473846 TCCTGTGTACCTATCTTGATCGATC 59.526 44.000 18.72 18.72 0.00 3.69
2089 5142 5.241728 CCTGTGTACCTATCTTGATCGATCA 59.758 44.000 23.99 23.99 34.44 2.92
2090 5143 6.071672 CCTGTGTACCTATCTTGATCGATCAT 60.072 42.308 27.75 16.13 36.56 2.45
2091 5144 7.290110 TGTGTACCTATCTTGATCGATCATT 57.710 36.000 27.75 17.59 36.56 2.57
2092 5145 7.147976 TGTGTACCTATCTTGATCGATCATTG 58.852 38.462 27.75 21.89 36.56 2.82
2093 5146 7.148641 GTGTACCTATCTTGATCGATCATTGT 58.851 38.462 27.75 17.82 36.56 2.71
2094 5147 8.297426 GTGTACCTATCTTGATCGATCATTGTA 58.703 37.037 27.75 17.97 36.56 2.41
2095 5148 8.515414 TGTACCTATCTTGATCGATCATTGTAG 58.485 37.037 27.75 24.21 36.56 2.74
2096 5149 7.767250 ACCTATCTTGATCGATCATTGTAGA 57.233 36.000 27.75 25.08 36.56 2.59
2097 5150 8.183104 ACCTATCTTGATCGATCATTGTAGAA 57.817 34.615 27.75 15.55 36.56 2.10
2098 5151 8.085296 ACCTATCTTGATCGATCATTGTAGAAC 58.915 37.037 27.75 0.00 36.56 3.01
2099 5152 7.543868 CCTATCTTGATCGATCATTGTAGAACC 59.456 40.741 27.75 0.00 36.56 3.62
2100 5153 6.220726 TCTTGATCGATCATTGTAGAACCA 57.779 37.500 27.75 8.74 36.56 3.67
2101 5154 6.820335 TCTTGATCGATCATTGTAGAACCAT 58.180 36.000 27.75 0.00 36.56 3.55
2102 5155 6.703165 TCTTGATCGATCATTGTAGAACCATG 59.297 38.462 27.75 5.57 36.56 3.66
2103 5156 6.160576 TGATCGATCATTGTAGAACCATGA 57.839 37.500 23.99 0.00 0.00 3.07
2104 5157 6.218746 TGATCGATCATTGTAGAACCATGAG 58.781 40.000 23.99 0.00 0.00 2.90
2105 5158 4.948847 TCGATCATTGTAGAACCATGAGG 58.051 43.478 0.00 0.00 42.21 3.86
2106 5159 3.496130 CGATCATTGTAGAACCATGAGGC 59.504 47.826 0.00 0.00 39.06 4.70
2107 5160 3.998913 TCATTGTAGAACCATGAGGCA 57.001 42.857 0.00 0.00 39.06 4.75
2108 5161 4.508551 TCATTGTAGAACCATGAGGCAT 57.491 40.909 0.00 0.00 39.06 4.40
2109 5162 4.201657 TCATTGTAGAACCATGAGGCATG 58.798 43.478 0.00 0.00 41.10 4.06
2110 5163 3.998913 TTGTAGAACCATGAGGCATGA 57.001 42.857 8.87 0.00 43.81 3.07
2111 5164 3.548745 TGTAGAACCATGAGGCATGAG 57.451 47.619 8.87 2.46 43.81 2.90
2112 5165 2.216898 GTAGAACCATGAGGCATGAGC 58.783 52.381 8.87 0.00 43.81 4.26
2113 5166 0.917533 AGAACCATGAGGCATGAGCT 59.082 50.000 8.87 0.00 43.81 4.09
2114 5167 2.121948 AGAACCATGAGGCATGAGCTA 58.878 47.619 8.87 0.00 43.81 3.32
2115 5168 2.158842 AGAACCATGAGGCATGAGCTAC 60.159 50.000 8.87 0.00 43.81 3.58
2116 5169 1.504912 ACCATGAGGCATGAGCTACT 58.495 50.000 8.87 0.00 43.81 2.57
2117 5170 1.842562 ACCATGAGGCATGAGCTACTT 59.157 47.619 8.87 0.00 43.81 2.24
2118 5171 2.240667 ACCATGAGGCATGAGCTACTTT 59.759 45.455 8.87 0.00 43.81 2.66
2119 5172 2.617308 CCATGAGGCATGAGCTACTTTG 59.383 50.000 8.87 0.00 43.81 2.77
2120 5173 2.408271 TGAGGCATGAGCTACTTTGG 57.592 50.000 0.00 0.00 41.70 3.28
2121 5174 1.630369 TGAGGCATGAGCTACTTTGGT 59.370 47.619 0.00 0.00 41.70 3.67
2122 5175 2.012673 GAGGCATGAGCTACTTTGGTG 58.987 52.381 0.00 0.00 41.70 4.17
2123 5176 1.630369 AGGCATGAGCTACTTTGGTGA 59.370 47.619 0.00 0.00 41.70 4.02
2124 5177 2.012673 GGCATGAGCTACTTTGGTGAG 58.987 52.381 0.00 0.00 41.70 3.51
2125 5178 2.355108 GGCATGAGCTACTTTGGTGAGA 60.355 50.000 0.00 0.00 41.70 3.27
2126 5179 3.539604 GCATGAGCTACTTTGGTGAGAT 58.460 45.455 0.00 0.00 37.91 2.75
2127 5180 3.944015 GCATGAGCTACTTTGGTGAGATT 59.056 43.478 0.00 0.00 37.91 2.40
2164 5217 3.146847 CTGACCTGTGGTTACCCTTTTC 58.853 50.000 0.00 0.00 35.25 2.29
2169 5222 4.352893 ACCTGTGGTTACCCTTTTCTATGT 59.647 41.667 0.00 0.00 27.29 2.29
2213 5266 6.515832 TCGTACAGTCATGAGCATATTTGAT 58.484 36.000 0.00 0.00 0.00 2.57
2313 5366 1.620323 CATCGATCTGGTATGGCTCCA 59.380 52.381 0.00 0.00 0.00 3.86
2339 5392 3.071023 TGAGAGGTAAACACTTCACCTGG 59.929 47.826 0.00 0.00 42.78 4.45
2362 5415 5.183904 GGCTAACCATGGTCATTCATTATCC 59.816 44.000 20.07 6.24 35.26 2.59
2367 5420 6.617538 ACCATGGTCATTCATTATCCTGATT 58.382 36.000 13.00 0.00 0.00 2.57
2432 5485 4.197750 GAGGTTCTCTAGGTGTCGATGTA 58.802 47.826 0.00 0.00 0.00 2.29
2473 5527 9.696917 ATTTTCTAAATGAACATGACTTTGACC 57.303 29.630 0.00 0.00 33.88 4.02
2611 5665 6.142817 CCTTGTACATGTTGCAAAGACTAAC 58.857 40.000 2.30 0.00 0.00 2.34
2750 5804 8.017418 TGGTTTACCTCATTTTCAAGACAATT 57.983 30.769 0.00 0.00 36.82 2.32
2759 5813 9.459640 CTCATTTTCAAGACAATTATGCTATGG 57.540 33.333 0.00 0.00 0.00 2.74
2760 5814 7.922278 TCATTTTCAAGACAATTATGCTATGGC 59.078 33.333 0.00 0.00 39.26 4.40
2829 5885 6.176896 TCCTCGTGATTGATTTGTGGATTTA 58.823 36.000 0.00 0.00 0.00 1.40
2834 5890 7.324856 TCGTGATTGATTTGTGGATTTAAAACG 59.675 33.333 0.00 0.00 0.00 3.60
2836 5892 7.116233 GTGATTGATTTGTGGATTTAAAACGCT 59.884 33.333 0.00 0.00 0.00 5.07
2961 6017 2.298729 TGAAGCTTTTGTTGGTATGGGC 59.701 45.455 0.00 0.00 0.00 5.36
3186 6243 4.376146 TGTCATTCTTCACGACATGTTGA 58.624 39.130 20.26 8.15 34.83 3.18
3366 6423 9.241919 TCAATCTGGAAGCTCAATAATGTTTAA 57.758 29.630 0.00 0.00 0.00 1.52
3395 6452 9.738832 CTAGCTCAATTTCTAGGTTAGACTTAC 57.261 37.037 0.00 0.00 33.84 2.34
3412 6469 6.027749 AGACTTACGTTTTTGCAAAGAACAG 58.972 36.000 24.05 20.20 0.00 3.16
3547 6604 1.722011 ACTGGTTATTCGGCAACTCG 58.278 50.000 0.00 0.00 0.00 4.18
3814 6871 4.336713 AGGAAGAAGTTTGCTCACAAAGAC 59.663 41.667 0.00 0.00 46.17 3.01
3829 6886 2.469274 AAGACGAGGAGTACGACTCA 57.531 50.000 16.54 0.00 46.79 3.41
3959 7016 6.826231 TCGTAGGGATGCTTTGATTTTGATAA 59.174 34.615 0.00 0.00 0.00 1.75
3968 7025 4.695217 TTGATTTTGATAAGTGGCGACC 57.305 40.909 0.00 0.00 0.00 4.79
4137 7194 5.611796 TCTGTATGAAGTGCACATTGTTC 57.388 39.130 21.04 14.17 0.00 3.18
4150 7207 2.880890 ACATTGTTCAAGCAGTCCTGTC 59.119 45.455 0.00 0.00 0.00 3.51
4206 7263 8.254508 TCTGTTTGTTTTTAAATGGCTTACAGT 58.745 29.630 0.00 0.00 0.00 3.55
4272 7329 3.297134 TTGGCTTCCCTAATGATCACC 57.703 47.619 0.00 0.00 0.00 4.02
4279 7336 6.352137 GGCTTCCCTAATGATCACCAAATTTT 60.352 38.462 0.00 0.00 0.00 1.82
4306 7363 4.163336 ACATCGGCAATGTTGAAACATGC 61.163 43.478 9.34 13.40 46.73 4.06
4417 7485 9.760660 GTTGTGAATACTAGATTTTAGCAACTG 57.239 33.333 0.00 0.00 0.00 3.16
4418 7486 8.492673 TGTGAATACTAGATTTTAGCAACTGG 57.507 34.615 0.00 0.00 0.00 4.00
4419 7487 8.318412 TGTGAATACTAGATTTTAGCAACTGGA 58.682 33.333 0.00 0.00 0.00 3.86
4420 7488 8.821894 GTGAATACTAGATTTTAGCAACTGGAG 58.178 37.037 0.00 0.00 0.00 3.86
4421 7489 8.540388 TGAATACTAGATTTTAGCAACTGGAGT 58.460 33.333 0.00 0.00 0.00 3.85
4434 7502 7.524717 AGCAACTGGAGTATTTACAAAATGT 57.475 32.000 0.00 0.00 0.00 2.71
4457 7525 7.148641 TGTTGTTTACTTGTTTTGTGATGTGT 58.851 30.769 0.00 0.00 0.00 3.72
4458 7526 8.297426 TGTTGTTTACTTGTTTTGTGATGTGTA 58.703 29.630 0.00 0.00 0.00 2.90
4512 7580 7.806409 AAGTTATATGCATGCTGTGTTGATA 57.194 32.000 20.33 6.67 0.00 2.15
4518 7586 3.506844 TGCATGCTGTGTTGATATTGTGT 59.493 39.130 20.33 0.00 0.00 3.72
4527 7595 9.787532 GCTGTGTTGATATTGTGTACATTTATT 57.212 29.630 0.00 0.00 0.00 1.40
4583 7651 6.018669 GCTAAGTATGCTTTTACTGCACTAGG 60.019 42.308 0.00 0.00 43.59 3.02
4603 7671 2.821969 GGACACCTCAGCAACATGATTT 59.178 45.455 0.00 0.00 0.00 2.17
4607 7675 6.350445 GGACACCTCAGCAACATGATTTATTT 60.350 38.462 0.00 0.00 0.00 1.40
4666 7734 5.269991 ACTACCTCTGACCAATAGCAGTAA 58.730 41.667 0.00 0.00 33.90 2.24
4755 7823 4.758251 TGCTCCACCGCCATGTCG 62.758 66.667 0.00 0.00 0.00 4.35
4847 7915 3.139469 GGTCCTCCCCTCGTCGAC 61.139 72.222 5.18 5.18 0.00 4.20
4945 8013 2.809601 CGTCACCGCCGAAGAAGG 60.810 66.667 0.00 0.00 0.00 3.46
4966 8034 2.586792 GGCCATCCGAGCACTCTT 59.413 61.111 0.00 0.00 0.00 2.85
4967 8035 1.078143 GGCCATCCGAGCACTCTTT 60.078 57.895 0.00 0.00 0.00 2.52
4976 8044 1.163554 GAGCACTCTTTGAAGGCCTG 58.836 55.000 5.69 0.00 0.00 4.85
4983 8051 0.251077 CTTTGAAGGCCTGCTCCAGT 60.251 55.000 13.40 0.00 0.00 4.00
5040 8108 2.024871 CGCTCCTCCTAAGTCGCG 59.975 66.667 0.00 0.00 34.47 5.87
5061 8129 4.856801 ATCATGACGCGGCCCCAC 62.857 66.667 10.82 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.501128 CCCTCATGCGACCATCGT 59.499 61.111 0.00 0.00 42.81 3.73
47 48 2.082140 ATGTCATGCTGCCCAATGAT 57.918 45.000 4.71 0.00 0.00 2.45
48 49 1.478916 CAATGTCATGCTGCCCAATGA 59.521 47.619 0.00 0.00 0.00 2.57
58 59 4.397103 TCAACATCTCCTTCAATGTCATGC 59.603 41.667 0.00 0.00 35.10 4.06
59 60 6.505044 TTCAACATCTCCTTCAATGTCATG 57.495 37.500 0.00 0.00 35.10 3.07
60 61 6.662234 ACATTCAACATCTCCTTCAATGTCAT 59.338 34.615 0.00 0.00 35.10 3.06
61 62 6.005823 ACATTCAACATCTCCTTCAATGTCA 58.994 36.000 0.00 0.00 35.10 3.58
62 63 6.320171 CACATTCAACATCTCCTTCAATGTC 58.680 40.000 0.00 0.00 35.10 3.06
63 64 5.184479 CCACATTCAACATCTCCTTCAATGT 59.816 40.000 0.00 0.00 37.71 2.71
65 66 5.573219 TCCACATTCAACATCTCCTTCAAT 58.427 37.500 0.00 0.00 0.00 2.57
66 67 4.984295 TCCACATTCAACATCTCCTTCAA 58.016 39.130 0.00 0.00 0.00 2.69
67 68 4.639078 TCCACATTCAACATCTCCTTCA 57.361 40.909 0.00 0.00 0.00 3.02
68 69 5.416952 ACAATCCACATTCAACATCTCCTTC 59.583 40.000 0.00 0.00 0.00 3.46
69 70 5.184479 CACAATCCACATTCAACATCTCCTT 59.816 40.000 0.00 0.00 0.00 3.36
70 71 4.703575 CACAATCCACATTCAACATCTCCT 59.296 41.667 0.00 0.00 0.00 3.69
71 72 4.142315 CCACAATCCACATTCAACATCTCC 60.142 45.833 0.00 0.00 0.00 3.71
72 73 4.676196 GCCACAATCCACATTCAACATCTC 60.676 45.833 0.00 0.00 0.00 2.75
73 74 3.194116 GCCACAATCCACATTCAACATCT 59.806 43.478 0.00 0.00 0.00 2.90
74 75 3.514645 GCCACAATCCACATTCAACATC 58.485 45.455 0.00 0.00 0.00 3.06
75 76 2.234414 GGCCACAATCCACATTCAACAT 59.766 45.455 0.00 0.00 0.00 2.71
76 77 1.617850 GGCCACAATCCACATTCAACA 59.382 47.619 0.00 0.00 0.00 3.33
77 78 1.895131 AGGCCACAATCCACATTCAAC 59.105 47.619 5.01 0.00 0.00 3.18
78 79 2.170166 GAGGCCACAATCCACATTCAA 58.830 47.619 5.01 0.00 0.00 2.69
79 80 1.616725 GGAGGCCACAATCCACATTCA 60.617 52.381 5.01 0.00 35.54 2.57
80 81 1.106285 GGAGGCCACAATCCACATTC 58.894 55.000 5.01 0.00 35.54 2.67
81 82 0.324645 GGGAGGCCACAATCCACATT 60.325 55.000 5.01 0.00 37.33 2.71
86 87 1.749258 GAACGGGAGGCCACAATCC 60.749 63.158 5.01 2.03 34.64 3.01
89 90 2.747686 GAGAACGGGAGGCCACAA 59.252 61.111 5.01 0.00 0.00 3.33
114 115 1.379977 CGAGGTAGAGGGCTCCACA 60.380 63.158 0.00 0.00 0.00 4.17
131 132 1.199327 TGCTTGAACTCGTACTCCTCG 59.801 52.381 0.00 0.00 0.00 4.63
153 154 1.521681 GACGATAGGTGGCACTGCC 60.522 63.158 18.45 13.68 46.43 4.85
160 161 2.271800 GTGAGCAAAGACGATAGGTGG 58.728 52.381 0.00 0.00 43.77 4.61
162 163 1.899814 TGGTGAGCAAAGACGATAGGT 59.100 47.619 0.00 0.00 43.77 3.08
167 168 0.531974 GTGGTGGTGAGCAAAGACGA 60.532 55.000 0.00 0.00 0.00 4.20
168 169 1.831389 CGTGGTGGTGAGCAAAGACG 61.831 60.000 0.00 0.00 0.00 4.18
169 170 0.531974 TCGTGGTGGTGAGCAAAGAC 60.532 55.000 0.00 0.00 0.00 3.01
173 174 0.753867 TAACTCGTGGTGGTGAGCAA 59.246 50.000 0.00 0.00 35.61 3.91
174 175 0.973632 ATAACTCGTGGTGGTGAGCA 59.026 50.000 0.00 0.00 35.61 4.26
175 176 1.204941 AGATAACTCGTGGTGGTGAGC 59.795 52.381 0.00 0.00 35.61 4.26
290 291 3.964688 TCTTCTACTCCCTTGTGTCAACA 59.035 43.478 0.00 0.00 0.00 3.33
293 294 3.572642 TGTCTTCTACTCCCTTGTGTCA 58.427 45.455 0.00 0.00 0.00 3.58
296 297 4.608948 AGTTGTCTTCTACTCCCTTGTG 57.391 45.455 0.00 0.00 0.00 3.33
297 298 5.279556 GCTTAGTTGTCTTCTACTCCCTTGT 60.280 44.000 0.00 0.00 32.55 3.16
306 307 5.652891 CCTCCAGTAGCTTAGTTGTCTTCTA 59.347 44.000 0.00 0.00 0.00 2.10
313 317 5.615925 AATACCCTCCAGTAGCTTAGTTG 57.384 43.478 0.00 0.00 0.00 3.16
314 318 5.130643 GGAAATACCCTCCAGTAGCTTAGTT 59.869 44.000 0.00 0.00 32.77 2.24
317 321 4.892198 AGGAAATACCCTCCAGTAGCTTA 58.108 43.478 0.00 0.00 40.05 3.09
318 322 3.737263 AGGAAATACCCTCCAGTAGCTT 58.263 45.455 0.00 0.00 40.05 3.74
325 329 4.728772 CATGCATTAGGAAATACCCTCCA 58.271 43.478 0.00 0.00 40.05 3.86
631 2338 4.947388 TGTAGATTGATGTGGGTTTAAGCC 59.053 41.667 6.20 6.20 36.00 4.35
635 2342 5.221945 TGTGGTGTAGATTGATGTGGGTTTA 60.222 40.000 0.00 0.00 0.00 2.01
646 2353 7.848223 TTACAAGATGATGTGGTGTAGATTG 57.152 36.000 0.00 0.00 34.75 2.67
653 2360 4.396166 GGAGGTTTACAAGATGATGTGGTG 59.604 45.833 0.00 0.00 34.75 4.17
760 2467 8.689061 GGAAGAAAGTTTCCTTAAAAACACCTA 58.311 33.333 12.05 0.00 42.73 3.08
761 2468 7.179516 TGGAAGAAAGTTTCCTTAAAAACACCT 59.820 33.333 12.05 0.00 45.59 4.00
762 2469 7.324935 TGGAAGAAAGTTTCCTTAAAAACACC 58.675 34.615 12.05 3.32 45.59 4.16
763 2470 8.942338 ATGGAAGAAAGTTTCCTTAAAAACAC 57.058 30.769 12.05 0.00 45.59 3.32
764 2471 9.594478 GAATGGAAGAAAGTTTCCTTAAAAACA 57.406 29.630 12.05 1.77 45.59 2.83
765 2472 9.594478 TGAATGGAAGAAAGTTTCCTTAAAAAC 57.406 29.630 12.05 0.00 45.59 2.43
768 2475 9.762933 CATTGAATGGAAGAAAGTTTCCTTAAA 57.237 29.630 12.05 0.00 45.59 1.52
770 2477 8.477419 ACATTGAATGGAAGAAAGTTTCCTTA 57.523 30.769 12.05 0.00 45.59 2.69
772 2479 6.983906 ACATTGAATGGAAGAAAGTTTCCT 57.016 33.333 12.05 0.00 45.59 3.36
773 2480 8.337532 CAAAACATTGAATGGAAGAAAGTTTCC 58.662 33.333 12.05 0.00 45.59 3.13
774 2481 8.882736 ACAAAACATTGAATGGAAGAAAGTTTC 58.117 29.630 10.27 7.57 33.60 2.78
776 2483 8.791327 AACAAAACATTGAATGGAAGAAAGTT 57.209 26.923 10.27 2.66 33.60 2.66
849 3490 7.168905 CCTGGTAGGAAGAATACTCAGTTTTT 58.831 38.462 0.00 0.00 37.67 1.94
852 3493 4.162509 GCCTGGTAGGAAGAATACTCAGTT 59.837 45.833 0.00 0.00 37.67 3.16
854 3495 3.070302 GGCCTGGTAGGAAGAATACTCAG 59.930 52.174 0.00 0.00 37.67 3.35
856 3497 2.036089 CGGCCTGGTAGGAAGAATACTC 59.964 54.545 0.00 0.00 37.67 2.59
857 3498 2.040178 CGGCCTGGTAGGAAGAATACT 58.960 52.381 0.00 0.00 37.67 2.12
858 3499 1.070289 CCGGCCTGGTAGGAAGAATAC 59.930 57.143 0.00 0.00 37.67 1.89
863 3519 4.176752 GGCCGGCCTGGTAGGAAG 62.177 72.222 38.76 0.00 37.67 3.46
882 3552 3.698029 TGACTAGCGGGTTCGTATTAC 57.302 47.619 0.00 0.00 38.89 1.89
890 3560 0.107831 TTGCTGTTGACTAGCGGGTT 59.892 50.000 0.00 0.00 44.01 4.11
893 3563 1.639298 GCCTTGCTGTTGACTAGCGG 61.639 60.000 0.00 0.00 44.01 5.52
898 3568 0.896940 CATGGGCCTTGCTGTTGACT 60.897 55.000 4.53 0.00 0.00 3.41
944 3614 2.774234 ACAGAGAGAGAGAGAGAGAGGG 59.226 54.545 0.00 0.00 0.00 4.30
947 3617 4.614475 AGAGACAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
949 3619 4.614475 AGAGAGACAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
950 3620 4.648762 AGAGAGAGACAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
951 3621 4.614475 AGAGAGAGACAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
952 3622 4.648762 AGAGAGAGAGACAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
953 3623 4.614475 AGAGAGAGAGACAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
954 3624 4.648762 AGAGAGAGAGAGACAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
955 3625 4.614475 AGAGAGAGAGAGACAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
956 3626 4.202202 GGAGAGAGAGAGAGACAGAGAGAG 60.202 54.167 0.00 0.00 0.00 3.20
957 3627 3.706594 GGAGAGAGAGAGAGACAGAGAGA 59.293 52.174 0.00 0.00 0.00 3.10
958 3628 3.181461 GGGAGAGAGAGAGAGACAGAGAG 60.181 56.522 0.00 0.00 0.00 3.20
959 3629 2.771943 GGGAGAGAGAGAGAGACAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
960 3630 2.483714 CGGGAGAGAGAGAGAGACAGAG 60.484 59.091 0.00 0.00 0.00 3.35
961 3631 1.484653 CGGGAGAGAGAGAGAGACAGA 59.515 57.143 0.00 0.00 0.00 3.41
962 3632 1.953559 CGGGAGAGAGAGAGAGACAG 58.046 60.000 0.00 0.00 0.00 3.51
963 3633 0.107410 GCGGGAGAGAGAGAGAGACA 60.107 60.000 0.00 0.00 0.00 3.41
964 3634 0.107410 TGCGGGAGAGAGAGAGAGAC 60.107 60.000 0.00 0.00 0.00 3.36
1002 3672 1.651240 CCAGAAGACAATGGCTGCGG 61.651 60.000 0.00 0.00 0.00 5.69
1036 3706 3.281787 AACGAGGAGGGGAGGGGA 61.282 66.667 0.00 0.00 0.00 4.81
1053 3723 1.134907 GTTTAATCGCGTCTGAGGGGA 60.135 52.381 17.48 17.48 0.00 4.81
1055 3725 1.287425 GGTTTAATCGCGTCTGAGGG 58.713 55.000 5.77 0.00 0.00 4.30
1066 3736 0.255033 AGGCGAGGTGGGGTTTAATC 59.745 55.000 0.00 0.00 0.00 1.75
1129 4179 1.005215 CATGTCTTTCCCCCTTCTGCT 59.995 52.381 0.00 0.00 0.00 4.24
1141 4191 1.562672 CCGAGGGTCCCCATGTCTTT 61.563 60.000 3.51 0.00 38.92 2.52
1414 4465 1.406614 CCCTGAGTCAACCTGATCTGC 60.407 57.143 0.00 0.00 0.00 4.26
1483 4535 7.538575 ACCAATTTCTATTCCAGTTTCATTCG 58.461 34.615 0.00 0.00 0.00 3.34
1585 4637 2.854185 GCAAGTCAACAAACAGAACAGC 59.146 45.455 0.00 0.00 0.00 4.40
1635 4687 6.656632 AGGTGAGAATAAGAGATTGCGATA 57.343 37.500 0.00 0.00 0.00 2.92
1699 4752 4.133820 CACAAAAGTCAGTATGGTCACCA 58.866 43.478 0.00 0.00 38.19 4.17
1723 4776 1.059264 GACACGCGAAATACAGCACTC 59.941 52.381 15.93 0.00 0.00 3.51
1736 4789 2.880822 ATCAATTTGACAGACACGCG 57.119 45.000 3.53 3.53 0.00 6.01
1816 4869 1.837439 TCCACCAACTATAGCACTGGG 59.163 52.381 16.49 7.31 32.94 4.45
1888 4941 7.066645 GGAAACTACTACCCATTGTTGTTATCC 59.933 40.741 0.00 0.00 34.66 2.59
1890 4943 6.888088 GGGAAACTACTACCCATTGTTGTTAT 59.112 38.462 0.00 0.00 42.81 1.89
2004 5057 9.967451 TGTTGTTATCCATAGGTCAGAAATTAA 57.033 29.630 0.00 0.00 0.00 1.40
2005 5058 9.967451 TTGTTGTTATCCATAGGTCAGAAATTA 57.033 29.630 0.00 0.00 0.00 1.40
2006 5059 8.877864 TTGTTGTTATCCATAGGTCAGAAATT 57.122 30.769 0.00 0.00 0.00 1.82
2007 5060 8.906867 CATTGTTGTTATCCATAGGTCAGAAAT 58.093 33.333 0.00 0.00 0.00 2.17
2008 5061 7.339212 CCATTGTTGTTATCCATAGGTCAGAAA 59.661 37.037 0.00 0.00 0.00 2.52
2009 5062 6.828273 CCATTGTTGTTATCCATAGGTCAGAA 59.172 38.462 0.00 0.00 0.00 3.02
2010 5063 6.356556 CCATTGTTGTTATCCATAGGTCAGA 58.643 40.000 0.00 0.00 0.00 3.27
2011 5064 5.532406 CCCATTGTTGTTATCCATAGGTCAG 59.468 44.000 0.00 0.00 0.00 3.51
2012 5065 5.044476 ACCCATTGTTGTTATCCATAGGTCA 60.044 40.000 0.00 0.00 0.00 4.02
2013 5066 5.445964 ACCCATTGTTGTTATCCATAGGTC 58.554 41.667 0.00 0.00 0.00 3.85
2014 5067 5.466127 ACCCATTGTTGTTATCCATAGGT 57.534 39.130 0.00 0.00 0.00 3.08
2015 5068 6.601332 ACTACCCATTGTTGTTATCCATAGG 58.399 40.000 0.00 0.00 27.90 2.57
2016 5069 8.429641 ACTACTACCCATTGTTGTTATCCATAG 58.570 37.037 0.00 0.00 34.66 2.23
2017 5070 8.326765 ACTACTACCCATTGTTGTTATCCATA 57.673 34.615 0.00 0.00 34.66 2.74
2018 5071 7.208064 ACTACTACCCATTGTTGTTATCCAT 57.792 36.000 0.00 0.00 34.66 3.41
2019 5072 6.630203 ACTACTACCCATTGTTGTTATCCA 57.370 37.500 0.00 0.00 34.66 3.41
2020 5073 7.066645 GGAAACTACTACCCATTGTTGTTATCC 59.933 40.741 0.00 0.00 34.66 2.59
2021 5074 7.066645 GGGAAACTACTACCCATTGTTGTTATC 59.933 40.741 0.00 0.00 42.81 1.75
2022 5075 6.888088 GGGAAACTACTACCCATTGTTGTTAT 59.112 38.462 0.00 0.00 42.81 1.89
2023 5076 6.044637 AGGGAAACTACTACCCATTGTTGTTA 59.955 38.462 0.00 0.00 45.43 2.41
2024 5077 5.074804 GGGAAACTACTACCCATTGTTGTT 58.925 41.667 0.00 0.00 42.81 2.83
2025 5078 4.352893 AGGGAAACTACTACCCATTGTTGT 59.647 41.667 0.00 0.00 45.43 3.32
2026 5079 4.918588 AGGGAAACTACTACCCATTGTTG 58.081 43.478 0.00 0.00 45.43 3.33
2027 5080 5.073965 TGAAGGGAAACTACTACCCATTGTT 59.926 40.000 0.00 0.00 45.43 2.83
2028 5081 4.600111 TGAAGGGAAACTACTACCCATTGT 59.400 41.667 0.00 0.00 45.43 2.71
2029 5082 4.941873 GTGAAGGGAAACTACTACCCATTG 59.058 45.833 0.00 0.00 45.43 2.82
2030 5083 4.850386 AGTGAAGGGAAACTACTACCCATT 59.150 41.667 0.00 0.00 45.43 3.16
2031 5084 4.436079 AGTGAAGGGAAACTACTACCCAT 58.564 43.478 0.00 0.00 45.43 4.00
2032 5085 3.865571 AGTGAAGGGAAACTACTACCCA 58.134 45.455 0.00 0.00 45.43 4.51
2033 5086 6.556974 AATAGTGAAGGGAAACTACTACCC 57.443 41.667 0.00 0.00 43.55 3.69
2034 5087 7.618137 TCAAATAGTGAAGGGAAACTACTACC 58.382 38.462 0.00 0.00 31.93 3.18
2048 5101 4.202461 ACACAGGAGCCTTCAAATAGTGAA 60.202 41.667 7.61 0.00 44.20 3.18
2049 5102 3.327757 ACACAGGAGCCTTCAAATAGTGA 59.672 43.478 7.61 0.00 0.00 3.41
2050 5103 3.679389 ACACAGGAGCCTTCAAATAGTG 58.321 45.455 0.00 0.00 0.00 2.74
2051 5104 4.323562 GGTACACAGGAGCCTTCAAATAGT 60.324 45.833 0.00 0.00 0.00 2.12
2052 5105 4.080863 AGGTACACAGGAGCCTTCAAATAG 60.081 45.833 0.00 0.00 0.00 1.73
2053 5106 3.844211 AGGTACACAGGAGCCTTCAAATA 59.156 43.478 0.00 0.00 0.00 1.40
2054 5107 2.644798 AGGTACACAGGAGCCTTCAAAT 59.355 45.455 0.00 0.00 0.00 2.32
2055 5108 2.054799 AGGTACACAGGAGCCTTCAAA 58.945 47.619 0.00 0.00 0.00 2.69
2056 5109 1.729586 AGGTACACAGGAGCCTTCAA 58.270 50.000 0.00 0.00 0.00 2.69
2057 5110 2.615986 TAGGTACACAGGAGCCTTCA 57.384 50.000 0.00 0.00 32.90 3.02
2058 5111 3.301274 AGATAGGTACACAGGAGCCTTC 58.699 50.000 0.00 0.00 32.90 3.46
2059 5112 3.406512 AGATAGGTACACAGGAGCCTT 57.593 47.619 0.00 0.00 32.90 4.35
2060 5113 3.034635 CAAGATAGGTACACAGGAGCCT 58.965 50.000 0.00 0.00 35.28 4.58
2061 5114 3.031736 TCAAGATAGGTACACAGGAGCC 58.968 50.000 0.00 0.00 0.00 4.70
2062 5115 4.557695 CGATCAAGATAGGTACACAGGAGC 60.558 50.000 0.00 0.00 0.00 4.70
2063 5116 4.822350 TCGATCAAGATAGGTACACAGGAG 59.178 45.833 0.00 0.00 0.00 3.69
2064 5117 4.788679 TCGATCAAGATAGGTACACAGGA 58.211 43.478 0.00 0.00 0.00 3.86
2065 5118 5.241728 TGATCGATCAAGATAGGTACACAGG 59.758 44.000 25.44 0.00 33.08 4.00
2066 5119 6.319141 TGATCGATCAAGATAGGTACACAG 57.681 41.667 25.44 0.00 33.08 3.66
2067 5120 6.901081 ATGATCGATCAAGATAGGTACACA 57.099 37.500 30.41 4.18 40.69 3.72
2068 5121 7.148641 ACAATGATCGATCAAGATAGGTACAC 58.851 38.462 30.41 0.00 40.69 2.90
2069 5122 7.290110 ACAATGATCGATCAAGATAGGTACA 57.710 36.000 30.41 4.85 40.69 2.90
2070 5123 8.731605 TCTACAATGATCGATCAAGATAGGTAC 58.268 37.037 30.41 0.00 40.69 3.34
2071 5124 8.863872 TCTACAATGATCGATCAAGATAGGTA 57.136 34.615 30.41 21.51 40.69 3.08
2072 5125 7.767250 TCTACAATGATCGATCAAGATAGGT 57.233 36.000 30.41 21.54 40.69 3.08
2073 5126 7.543868 GGTTCTACAATGATCGATCAAGATAGG 59.456 40.741 30.41 18.24 40.69 2.57
2074 5127 8.084684 TGGTTCTACAATGATCGATCAAGATAG 58.915 37.037 30.41 26.40 40.69 2.08
2075 5128 7.951591 TGGTTCTACAATGATCGATCAAGATA 58.048 34.615 30.41 19.97 40.69 1.98
2076 5129 6.820335 TGGTTCTACAATGATCGATCAAGAT 58.180 36.000 30.41 19.92 40.69 2.40
2077 5130 6.220726 TGGTTCTACAATGATCGATCAAGA 57.779 37.500 30.41 24.07 40.69 3.02
2078 5131 6.703165 TCATGGTTCTACAATGATCGATCAAG 59.297 38.462 30.41 25.79 40.69 3.02
2079 5132 6.581712 TCATGGTTCTACAATGATCGATCAA 58.418 36.000 30.41 14.16 40.69 2.57
2080 5133 6.160576 TCATGGTTCTACAATGATCGATCA 57.839 37.500 29.09 29.09 41.70 2.92
2081 5134 5.636965 CCTCATGGTTCTACAATGATCGATC 59.363 44.000 18.72 18.72 0.00 3.69
2082 5135 5.545588 CCTCATGGTTCTACAATGATCGAT 58.454 41.667 0.00 0.00 0.00 3.59
2083 5136 4.740634 GCCTCATGGTTCTACAATGATCGA 60.741 45.833 0.00 0.00 35.27 3.59
2084 5137 3.496130 GCCTCATGGTTCTACAATGATCG 59.504 47.826 0.00 0.00 35.27 3.69
2085 5138 4.454678 TGCCTCATGGTTCTACAATGATC 58.545 43.478 0.00 0.00 35.27 2.92
2086 5139 4.508551 TGCCTCATGGTTCTACAATGAT 57.491 40.909 0.00 0.00 35.27 2.45
2087 5140 3.998913 TGCCTCATGGTTCTACAATGA 57.001 42.857 0.00 0.00 35.27 2.57
2088 5141 4.201657 TCATGCCTCATGGTTCTACAATG 58.798 43.478 6.92 0.00 41.66 2.82
2089 5142 4.458397 CTCATGCCTCATGGTTCTACAAT 58.542 43.478 6.92 0.00 41.66 2.71
2090 5143 3.877559 CTCATGCCTCATGGTTCTACAA 58.122 45.455 6.92 0.00 41.66 2.41
2091 5144 2.420547 GCTCATGCCTCATGGTTCTACA 60.421 50.000 6.92 0.00 41.66 2.74
2092 5145 2.158842 AGCTCATGCCTCATGGTTCTAC 60.159 50.000 6.92 0.00 41.66 2.59
2093 5146 2.121948 AGCTCATGCCTCATGGTTCTA 58.878 47.619 6.92 0.00 41.66 2.10
2094 5147 0.917533 AGCTCATGCCTCATGGTTCT 59.082 50.000 6.92 0.43 41.66 3.01
2095 5148 2.158842 AGTAGCTCATGCCTCATGGTTC 60.159 50.000 6.92 0.00 41.66 3.62
2096 5149 1.842562 AGTAGCTCATGCCTCATGGTT 59.157 47.619 6.92 0.16 41.66 3.67
2097 5150 1.504912 AGTAGCTCATGCCTCATGGT 58.495 50.000 6.92 0.00 41.66 3.55
2098 5151 2.617308 CAAAGTAGCTCATGCCTCATGG 59.383 50.000 6.92 0.34 41.66 3.66
2099 5152 2.617308 CCAAAGTAGCTCATGCCTCATG 59.383 50.000 0.00 0.59 42.60 3.07
2100 5153 2.240667 ACCAAAGTAGCTCATGCCTCAT 59.759 45.455 0.00 0.00 40.80 2.90
2101 5154 1.630369 ACCAAAGTAGCTCATGCCTCA 59.370 47.619 0.00 0.00 40.80 3.86
2102 5155 2.012673 CACCAAAGTAGCTCATGCCTC 58.987 52.381 0.00 0.00 40.80 4.70
2103 5156 1.630369 TCACCAAAGTAGCTCATGCCT 59.370 47.619 0.00 0.00 40.80 4.75
2104 5157 2.012673 CTCACCAAAGTAGCTCATGCC 58.987 52.381 0.00 0.00 40.80 4.40
2105 5158 2.977914 TCTCACCAAAGTAGCTCATGC 58.022 47.619 0.00 0.00 40.05 4.06
2106 5159 5.181009 TGAATCTCACCAAAGTAGCTCATG 58.819 41.667 0.00 0.00 0.00 3.07
2107 5160 5.426689 TGAATCTCACCAAAGTAGCTCAT 57.573 39.130 0.00 0.00 0.00 2.90
2108 5161 4.890158 TGAATCTCACCAAAGTAGCTCA 57.110 40.909 0.00 0.00 0.00 4.26
2109 5162 6.560253 TTTTGAATCTCACCAAAGTAGCTC 57.440 37.500 0.00 0.00 34.29 4.09
2110 5163 6.959639 TTTTTGAATCTCACCAAAGTAGCT 57.040 33.333 0.00 0.00 34.29 3.32
2164 5217 6.108687 TGCCTTGACACTGATAAAGACATAG 58.891 40.000 0.00 0.00 0.00 2.23
2169 5222 4.183865 CGATGCCTTGACACTGATAAAGA 58.816 43.478 0.00 0.00 0.00 2.52
2213 5266 4.042809 TCTTTGTTGATCCTTGGCTCCTTA 59.957 41.667 0.00 0.00 0.00 2.69
2313 5366 6.263168 CAGGTGAAGTGTTTACCTCTCAAAAT 59.737 38.462 0.30 0.00 42.72 1.82
2339 5392 6.006449 AGGATAATGAATGACCATGGTTAGC 58.994 40.000 20.85 11.79 0.00 3.09
2362 5415 7.521529 TGCGAACAAGAGAAGAAAATAATCAG 58.478 34.615 0.00 0.00 0.00 2.90
2367 5420 7.433708 TTGATGCGAACAAGAGAAGAAAATA 57.566 32.000 0.00 0.00 0.00 1.40
2415 5468 8.913487 TTATGTAATACATCGACACCTAGAGA 57.087 34.615 9.43 0.00 39.88 3.10
2473 5527 2.602257 TCCATTCTGAGCACCATACG 57.398 50.000 0.00 0.00 0.00 3.06
2611 5665 1.954927 GAAGGACCTTCCCGCTAATG 58.045 55.000 21.88 0.00 37.19 1.90
2750 5804 6.685527 TTTTGTAAATGACGCCATAGCATA 57.314 33.333 0.00 0.00 39.83 3.14
2829 5885 4.044426 GACAAAATGAAGCTCAGCGTTTT 58.956 39.130 0.00 7.78 0.00 2.43
2834 5890 4.494350 TCAAGACAAAATGAAGCTCAGC 57.506 40.909 0.00 0.00 0.00 4.26
2836 5892 6.829229 ATCATCAAGACAAAATGAAGCTCA 57.171 33.333 0.00 0.00 33.44 4.26
2961 6017 2.175184 CTCCGTCAAGCAAAGTGGCG 62.175 60.000 0.00 0.00 43.57 5.69
3186 6243 6.328672 AGCCAGGAGTATGACAATCTTCTAAT 59.671 38.462 0.00 0.00 0.00 1.73
3366 6423 9.649316 AGTCTAACCTAGAAATTGAGCTAGTAT 57.351 33.333 0.00 0.00 36.40 2.12
3412 6469 7.018235 GCTCATAAAGAGTTCTAACAGCAAAC 58.982 38.462 0.00 0.00 46.47 2.93
3417 6474 6.870965 ACTGTGCTCATAAAGAGTTCTAACAG 59.129 38.462 0.00 0.00 46.47 3.16
3547 6604 6.749923 ATAAAGCTGAACATCCTTGTCTTC 57.250 37.500 0.00 0.00 34.06 2.87
3814 6871 1.402259 AGCATTGAGTCGTACTCCTCG 59.598 52.381 11.01 0.00 44.44 4.63
3959 7016 0.110486 AAATGTTCCAGGTCGCCACT 59.890 50.000 0.00 0.00 0.00 4.00
3968 7025 5.629020 CCAAAACATACGTCAAATGTTCCAG 59.371 40.000 13.95 8.16 44.66 3.86
4137 7194 3.006323 AGAGTACAAGACAGGACTGCTTG 59.994 47.826 22.81 22.81 43.55 4.01
4150 7207 9.029243 CAATTAAGATGCACTCTAGAGTACAAG 57.971 37.037 25.85 15.09 38.13 3.16
4174 7231 7.768120 AGCCATTTAAAAACAAACAGATCACAA 59.232 29.630 0.00 0.00 0.00 3.33
4206 7263 5.829924 GGGGCAAAGATAGAAGATTGAATCA 59.170 40.000 8.03 0.00 0.00 2.57
4272 7329 6.324819 ACATTGCCGATGTCTCTAAAATTTG 58.675 36.000 0.00 0.00 45.88 2.32
4306 7363 7.647907 ACTGAAAATTGAAATTTAGCAGCAG 57.352 32.000 20.17 15.21 40.63 4.24
4487 7555 7.806409 ATCAACACAGCATGCATATAACTTA 57.194 32.000 21.98 0.00 42.53 2.24
4556 7624 5.882557 AGTGCAGTAAAAGCATACTTAGCAT 59.117 36.000 0.00 2.22 44.79 3.79
4563 7631 5.063564 GTGTCCTAGTGCAGTAAAAGCATAC 59.936 44.000 2.26 0.00 44.79 2.39
4574 7642 0.108424 GCTGAGGTGTCCTAGTGCAG 60.108 60.000 0.00 0.00 31.76 4.41
4583 7651 5.824904 ATAAATCATGTTGCTGAGGTGTC 57.175 39.130 0.00 0.00 0.00 3.67
4603 7671 9.730420 GTTTTGTGTAAGAAAAGAGAGCAAATA 57.270 29.630 0.00 0.00 39.92 1.40
4607 7675 8.500753 TTAGTTTTGTGTAAGAAAAGAGAGCA 57.499 30.769 0.00 0.00 39.92 4.26
4636 7704 5.762179 ATTGGTCAGAGGTAGTTGAATGA 57.238 39.130 0.00 0.00 0.00 2.57
4639 7707 4.530553 TGCTATTGGTCAGAGGTAGTTGAA 59.469 41.667 0.00 0.00 0.00 2.69
4666 7734 2.026729 GGGGCTTGAGAGTTTAGAGCTT 60.027 50.000 0.00 0.00 33.96 3.74
4830 7898 3.139469 GTCGACGAGGGGAGGACC 61.139 72.222 0.00 0.00 39.11 4.46
4853 7921 3.723348 GGAGGTTGTTCGGCGTGC 61.723 66.667 6.85 1.22 0.00 5.34
4873 7941 2.048127 GTTCTGGTTCGAGGCGCT 60.048 61.111 7.64 0.00 0.00 5.92
4949 8017 1.078143 AAAGAGTGCTCGGATGGCC 60.078 57.895 0.00 0.00 34.09 5.36
4950 8018 0.391661 TCAAAGAGTGCTCGGATGGC 60.392 55.000 0.00 0.00 34.09 4.40
4951 8019 2.005451 CTTCAAAGAGTGCTCGGATGG 58.995 52.381 0.00 0.00 34.09 3.51
4952 8020 2.005451 CCTTCAAAGAGTGCTCGGATG 58.995 52.381 0.00 0.00 34.09 3.51
4953 8021 1.677217 GCCTTCAAAGAGTGCTCGGAT 60.677 52.381 0.00 0.00 34.09 4.18
4963 8031 0.037303 CTGGAGCAGGCCTTCAAAGA 59.963 55.000 0.00 0.00 0.00 2.52
4965 8033 0.250901 GACTGGAGCAGGCCTTCAAA 60.251 55.000 0.00 0.00 32.43 2.69
4966 8034 1.376466 GACTGGAGCAGGCCTTCAA 59.624 57.895 0.00 0.00 32.43 2.69
4967 8035 2.947532 CGACTGGAGCAGGCCTTCA 61.948 63.158 0.00 0.00 35.82 3.02
5033 8101 1.815421 GTCATGATGGCCGCGACTT 60.815 57.895 8.23 0.00 0.00 3.01
5034 8102 2.202932 GTCATGATGGCCGCGACT 60.203 61.111 8.23 0.00 0.00 4.18



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

AutoCloner maintained by Alex Coulton.