Multiple sequence alignment - TraesCS4B01G294200

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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 TraesCS4B01G294200 chr4B 100.000 2456 0 0 1 2456 579470391 579467936 0.000000e+00 4536.0
1 TraesCS4B01G294200 chr4B 78.997 319 51 7 1991 2294 619220002 619219685 1.150000e-48 204.0
2 TraesCS4B01G294200 chr4D 91.088 1728 95 26 602 2294 464080850 464079147 0.000000e+00 2283.0
3 TraesCS4B01G294200 chr4D 87.469 407 31 7 216 611 464081267 464080870 3.720000e-123 451.0
4 TraesCS4B01G294200 chr4D 88.961 154 12 5 2307 2456 464078994 464078842 4.170000e-43 185.0
5 TraesCS4B01G294200 chr4A 90.164 854 38 18 1153 1975 5972937 5973775 0.000000e+00 1070.0
6 TraesCS4B01G294200 chr4A 91.620 537 25 11 602 1138 5972329 5972845 0.000000e+00 725.0
7 TraesCS4B01G294200 chr4A 85.393 178 19 4 321 498 5971938 5972108 6.980000e-41 178.0
8 TraesCS4B01G294200 chr4A 94.643 112 4 1 502 611 5972198 5972309 3.250000e-39 172.0
9 TraesCS4B01G294200 chr6B 81.098 328 50 2 1974 2289 151292456 151292783 4.050000e-63 252.0
10 TraesCS4B01G294200 chr5D 81.231 325 49 5 1983 2295 515336571 515336247 4.050000e-63 252.0
11 TraesCS4B01G294200 chr1A 80.707 311 48 1 1991 2289 585683704 585683394 5.280000e-57 231.0
12 TraesCS4B01G294200 chr1B 79.618 314 52 1 1988 2289 642092272 642092585 5.320000e-52 215.0
13 TraesCS4B01G294200 chr3B 91.333 150 10 3 2310 2456 640669000 640669149 4.140000e-48 202.0
14 TraesCS4B01G294200 chr3B 79.070 301 53 7 1991 2285 414825852 414825556 5.360000e-47 198.0
15 TraesCS4B01G294200 chr2A 78.549 317 56 8 1991 2295 37385812 37386128 5.360000e-47 198.0
16 TraesCS4B01G294200 chr2A 77.603 317 59 7 1991 2295 37972003 37972319 5.400000e-42 182.0
17 TraesCS4B01G294200 chr3D 87.582 153 15 4 2308 2456 480150727 480150879 9.030000e-40 174.0
18 TraesCS4B01G294200 chr1D 79.051 253 39 8 1974 2214 239550968 239551218 7.030000e-36 161.0
19 TraesCS4B01G294200 chr2D 86.747 83 8 3 173 254 19253672 19253592 3.360000e-14 89.8


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 TraesCS4B01G294200 chr4B 579467936 579470391 2455 True 4536.00 4536 100.000000 1 2456 1 chr4B.!!$R1 2455
1 TraesCS4B01G294200 chr4D 464078842 464081267 2425 True 973.00 2283 89.172667 216 2456 3 chr4D.!!$R1 2240
2 TraesCS4B01G294200 chr4A 5971938 5973775 1837 False 536.25 1070 90.455000 321 1975 4 chr4A.!!$F1 1654

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
106 107 0.187117 TGAACCTGCCAATTCACCCA 59.813 50.0 0.0 0.0 29.89 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2295 0.81361 CCGTCTGAGTTGGTTGCACA 60.814 55.0 0.0 0.0 0.0 4.57 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 3.944476 ACTCTCACATGTGGCTTCC 57.056 52.632 25.16 0.00 0.00 3.46
19 20 1.356124 ACTCTCACATGTGGCTTCCT 58.644 50.000 25.16 1.29 0.00 3.36
20 21 1.701847 ACTCTCACATGTGGCTTCCTT 59.298 47.619 25.16 1.59 0.00 3.36
21 22 2.906389 ACTCTCACATGTGGCTTCCTTA 59.094 45.455 25.16 2.73 0.00 2.69
22 23 3.055530 ACTCTCACATGTGGCTTCCTTAG 60.056 47.826 25.16 12.59 0.00 2.18
23 24 2.237143 TCTCACATGTGGCTTCCTTAGG 59.763 50.000 25.16 0.00 0.00 2.69
31 32 1.664873 GGCTTCCTTAGGCCTAAACG 58.335 55.000 25.14 17.72 44.48 3.60
32 33 1.065636 GGCTTCCTTAGGCCTAAACGT 60.066 52.381 25.14 0.00 44.48 3.99
33 34 2.007608 GCTTCCTTAGGCCTAAACGTG 58.992 52.381 25.14 13.72 0.00 4.49
34 35 2.354403 GCTTCCTTAGGCCTAAACGTGA 60.354 50.000 25.14 15.91 0.00 4.35
35 36 3.867216 GCTTCCTTAGGCCTAAACGTGAA 60.867 47.826 25.14 20.88 0.00 3.18
36 37 3.323751 TCCTTAGGCCTAAACGTGAAC 57.676 47.619 25.14 0.00 0.00 3.18
37 38 2.027837 TCCTTAGGCCTAAACGTGAACC 60.028 50.000 25.14 0.00 0.00 3.62
38 39 1.997606 CTTAGGCCTAAACGTGAACCG 59.002 52.381 25.14 7.38 44.03 4.44
39 40 1.255882 TAGGCCTAAACGTGAACCGA 58.744 50.000 10.98 0.00 40.70 4.69
40 41 0.393820 AGGCCTAAACGTGAACCGAA 59.606 50.000 1.29 0.00 40.70 4.30
41 42 1.202675 AGGCCTAAACGTGAACCGAAA 60.203 47.619 1.29 0.00 40.70 3.46
42 43 1.196127 GGCCTAAACGTGAACCGAAAG 59.804 52.381 0.00 0.00 40.70 2.62
43 44 1.869132 GCCTAAACGTGAACCGAAAGT 59.131 47.619 0.00 0.00 40.70 2.66
44 45 3.059166 GCCTAAACGTGAACCGAAAGTA 58.941 45.455 0.00 0.00 40.70 2.24
45 46 3.122445 GCCTAAACGTGAACCGAAAGTAG 59.878 47.826 0.00 0.00 40.70 2.57
46 47 3.676646 CCTAAACGTGAACCGAAAGTAGG 59.323 47.826 0.00 0.00 40.70 3.18
47 48 2.896745 AACGTGAACCGAAAGTAGGT 57.103 45.000 0.00 0.00 45.29 3.08
56 57 4.929819 ACCGAAAGTAGGTTGCAATTTT 57.070 36.364 0.59 0.00 39.29 1.82
57 58 5.270893 ACCGAAAGTAGGTTGCAATTTTT 57.729 34.783 0.59 0.00 39.29 1.94
80 81 5.538067 TTTATTTTTAAATTGCGCCAGCC 57.462 34.783 4.18 0.00 44.33 4.85
81 82 1.423395 TTTTTAAATTGCGCCAGCCG 58.577 45.000 4.18 0.00 44.33 5.52
82 83 0.389166 TTTTAAATTGCGCCAGCCGG 60.389 50.000 4.18 0.00 44.33 6.13
83 84 2.219325 TTTAAATTGCGCCAGCCGGG 62.219 55.000 4.18 0.00 44.33 5.73
84 85 3.929334 TAAATTGCGCCAGCCGGGT 62.929 57.895 4.18 0.00 44.33 5.28
90 91 4.697756 CGCCAGCCGGGTCTTGAA 62.698 66.667 1.27 0.00 39.65 2.69
91 92 3.056328 GCCAGCCGGGTCTTGAAC 61.056 66.667 1.27 0.00 39.65 3.18
102 103 2.238521 GGTCTTGAACCTGCCAATTCA 58.761 47.619 0.00 0.00 45.45 2.57
103 104 2.029918 GGTCTTGAACCTGCCAATTCAC 60.030 50.000 0.00 0.00 45.45 3.18
104 105 2.029918 GTCTTGAACCTGCCAATTCACC 60.030 50.000 0.00 0.00 34.61 4.02
105 106 1.273327 CTTGAACCTGCCAATTCACCC 59.727 52.381 0.00 0.00 34.61 4.61
106 107 0.187117 TGAACCTGCCAATTCACCCA 59.813 50.000 0.00 0.00 29.89 4.51
107 108 1.337118 GAACCTGCCAATTCACCCAA 58.663 50.000 0.00 0.00 0.00 4.12
108 109 1.691434 GAACCTGCCAATTCACCCAAA 59.309 47.619 0.00 0.00 0.00 3.28
109 110 1.799933 ACCTGCCAATTCACCCAAAA 58.200 45.000 0.00 0.00 0.00 2.44
110 111 2.337849 ACCTGCCAATTCACCCAAAAT 58.662 42.857 0.00 0.00 0.00 1.82
111 112 2.710471 ACCTGCCAATTCACCCAAAATT 59.290 40.909 0.00 0.00 0.00 1.82
112 113 3.138098 ACCTGCCAATTCACCCAAAATTT 59.862 39.130 0.00 0.00 0.00 1.82
113 114 3.752747 CCTGCCAATTCACCCAAAATTTC 59.247 43.478 0.00 0.00 0.00 2.17
114 115 4.387598 CTGCCAATTCACCCAAAATTTCA 58.612 39.130 0.00 0.00 0.00 2.69
115 116 4.785301 TGCCAATTCACCCAAAATTTCAA 58.215 34.783 0.00 0.00 0.00 2.69
116 117 5.195940 TGCCAATTCACCCAAAATTTCAAA 58.804 33.333 0.00 0.00 0.00 2.69
117 118 5.067023 TGCCAATTCACCCAAAATTTCAAAC 59.933 36.000 0.00 0.00 0.00 2.93
118 119 5.299028 GCCAATTCACCCAAAATTTCAAACT 59.701 36.000 0.00 0.00 0.00 2.66
119 120 6.484977 GCCAATTCACCCAAAATTTCAAACTA 59.515 34.615 0.00 0.00 0.00 2.24
120 121 7.307930 GCCAATTCACCCAAAATTTCAAACTAG 60.308 37.037 0.00 0.00 0.00 2.57
121 122 7.714813 CCAATTCACCCAAAATTTCAAACTAGT 59.285 33.333 0.00 0.00 0.00 2.57
122 123 8.550376 CAATTCACCCAAAATTTCAAACTAGTG 58.450 33.333 0.00 0.00 0.00 2.74
123 124 7.411486 TTCACCCAAAATTTCAAACTAGTGA 57.589 32.000 0.00 0.00 0.00 3.41
124 125 7.038154 TCACCCAAAATTTCAAACTAGTGAG 57.962 36.000 0.00 0.00 0.00 3.51
125 126 6.040391 TCACCCAAAATTTCAAACTAGTGAGG 59.960 38.462 0.00 0.00 0.00 3.86
126 127 6.040391 CACCCAAAATTTCAAACTAGTGAGGA 59.960 38.462 0.00 0.00 0.00 3.71
127 128 6.609616 ACCCAAAATTTCAAACTAGTGAGGAA 59.390 34.615 0.00 0.00 0.00 3.36
128 129 7.125053 ACCCAAAATTTCAAACTAGTGAGGAAA 59.875 33.333 15.14 15.14 32.66 3.13
129 130 8.150296 CCCAAAATTTCAAACTAGTGAGGAAAT 58.850 33.333 17.35 17.35 39.21 2.17
130 131 8.981647 CCAAAATTTCAAACTAGTGAGGAAATG 58.018 33.333 21.01 14.36 37.99 2.32
131 132 9.533253 CAAAATTTCAAACTAGTGAGGAAATGT 57.467 29.630 21.01 16.30 37.99 2.71
134 135 7.435068 TTTCAAACTAGTGAGGAAATGTAGC 57.565 36.000 0.00 0.00 0.00 3.58
135 136 6.360370 TCAAACTAGTGAGGAAATGTAGCT 57.640 37.500 0.00 0.00 0.00 3.32
136 137 6.769512 TCAAACTAGTGAGGAAATGTAGCTT 58.230 36.000 0.00 0.00 0.00 3.74
137 138 7.903145 TCAAACTAGTGAGGAAATGTAGCTTA 58.097 34.615 0.00 0.00 0.00 3.09
138 139 8.540388 TCAAACTAGTGAGGAAATGTAGCTTAT 58.460 33.333 0.00 0.00 0.00 1.73
139 140 8.607459 CAAACTAGTGAGGAAATGTAGCTTATG 58.393 37.037 0.00 0.00 0.00 1.90
140 141 6.284459 ACTAGTGAGGAAATGTAGCTTATGC 58.716 40.000 0.00 0.00 40.05 3.14
141 142 5.102953 AGTGAGGAAATGTAGCTTATGCA 57.897 39.130 0.00 0.00 42.74 3.96
142 143 5.688807 AGTGAGGAAATGTAGCTTATGCAT 58.311 37.500 3.79 3.79 42.74 3.96
143 144 6.125029 AGTGAGGAAATGTAGCTTATGCATT 58.875 36.000 3.54 0.00 45.00 3.56
155 156 9.389755 TGTAGCTTATGCATTTATACTTCAACA 57.610 29.630 3.54 0.00 42.74 3.33
158 159 9.573133 AGCTTATGCATTTATACTTCAACAAAC 57.427 29.630 3.54 0.00 42.74 2.93
159 160 9.573133 GCTTATGCATTTATACTTCAACAAACT 57.427 29.630 3.54 0.00 39.41 2.66
162 163 7.636259 TGCATTTATACTTCAACAAACTTGC 57.364 32.000 0.00 0.00 0.00 4.01
163 164 6.362016 TGCATTTATACTTCAACAAACTTGCG 59.638 34.615 0.00 0.00 0.00 4.85
164 165 6.362283 GCATTTATACTTCAACAAACTTGCGT 59.638 34.615 0.00 0.00 0.00 5.24
165 166 7.535940 GCATTTATACTTCAACAAACTTGCGTA 59.464 33.333 0.00 0.00 0.00 4.42
166 167 9.388346 CATTTATACTTCAACAAACTTGCGTAA 57.612 29.630 0.00 0.00 0.00 3.18
167 168 9.953697 ATTTATACTTCAACAAACTTGCGTAAA 57.046 25.926 0.00 0.00 0.00 2.01
168 169 9.953697 TTTATACTTCAACAAACTTGCGTAAAT 57.046 25.926 0.00 0.00 0.00 1.40
169 170 9.953697 TTATACTTCAACAAACTTGCGTAAATT 57.046 25.926 0.00 0.00 0.00 1.82
171 172 9.953697 ATACTTCAACAAACTTGCGTAAATTAA 57.046 25.926 0.00 0.00 0.00 1.40
172 173 8.335256 ACTTCAACAAACTTGCGTAAATTAAG 57.665 30.769 0.00 0.00 0.00 1.85
173 174 7.971722 ACTTCAACAAACTTGCGTAAATTAAGT 59.028 29.630 0.00 0.00 36.29 2.24
174 175 9.440784 CTTCAACAAACTTGCGTAAATTAAGTA 57.559 29.630 0.00 0.00 33.82 2.24
175 176 9.953697 TTCAACAAACTTGCGTAAATTAAGTAT 57.046 25.926 0.00 0.00 33.82 2.12
214 215 9.515226 TTTGCTAAATGGGGTAATATCTATCAC 57.485 33.333 0.00 0.00 0.00 3.06
222 223 8.096621 TGGGGTAATATCTATCACAAAAGTGA 57.903 34.615 0.33 0.33 37.79 3.41
224 225 8.837389 GGGGTAATATCTATCACAAAAGTGAAC 58.163 37.037 2.13 0.00 36.88 3.18
273 284 6.499350 ACTCTACTACTAAAAATGACCCACCA 59.501 38.462 0.00 0.00 0.00 4.17
366 377 5.065731 CCTCTGTTAGATTCCTGAAATGCAC 59.934 44.000 0.00 0.00 0.00 4.57
401 412 5.590663 ACTCTCTTTCTTTGAAGGTTGGTTC 59.409 40.000 0.00 0.00 0.00 3.62
438 449 6.574093 GCTTAACTTTTAAAACTCACTCGAGC 59.426 38.462 13.61 0.00 43.66 5.03
439 450 7.518529 GCTTAACTTTTAAAACTCACTCGAGCT 60.519 37.037 13.61 0.00 43.66 4.09
440 451 5.908916 ACTTTTAAAACTCACTCGAGCTC 57.091 39.130 13.61 2.73 43.66 4.09
441 452 4.444720 ACTTTTAAAACTCACTCGAGCTCG 59.555 41.667 30.03 30.03 43.66 5.03
450 461 2.989253 TCGAGCTCGAGGGTTGCA 60.989 61.111 33.84 10.40 44.22 4.08
451 462 2.507992 CGAGCTCGAGGGTTGCAG 60.508 66.667 32.06 0.00 43.02 4.41
467 478 2.409948 GCAGAGTTGCCTAGGAACAT 57.590 50.000 14.75 4.75 44.74 2.71
469 480 4.078639 GCAGAGTTGCCTAGGAACATAT 57.921 45.455 14.75 0.00 44.74 1.78
485 496 6.939163 AGGAACATATGATCTTGGTCTTATGC 59.061 38.462 10.38 3.07 38.67 3.14
486 497 6.150140 GGAACATATGATCTTGGTCTTATGCC 59.850 42.308 10.38 6.98 38.67 4.40
491 502 0.255890 TCTTGGTCTTATGCCTGGCC 59.744 55.000 17.53 0.00 0.00 5.36
503 514 2.363795 CTGGCCCGGGACAGTAGA 60.364 66.667 43.61 16.43 45.74 2.59
504 515 1.762460 CTGGCCCGGGACAGTAGAT 60.762 63.158 43.61 0.00 45.74 1.98
505 516 2.032860 CTGGCCCGGGACAGTAGATG 62.033 65.000 43.61 22.44 45.74 2.90
529 626 1.879380 CAAAGCGATGTGAAACTGGGA 59.121 47.619 0.00 0.00 38.04 4.37
533 630 3.535561 AGCGATGTGAAACTGGGATTAG 58.464 45.455 0.00 0.00 38.04 1.73
613 712 2.119611 TCCAACAGGGAGCTCGGA 59.880 61.111 7.83 4.57 42.15 4.55
615 714 1.144936 CCAACAGGGAGCTCGGATC 59.855 63.158 7.83 0.00 40.01 3.36
622 721 1.745264 GGAGCTCGGATCCCAAGAG 59.255 63.158 7.83 8.45 35.28 2.85
623 722 1.745264 GAGCTCGGATCCCAAGAGG 59.255 63.158 14.71 0.00 32.96 3.69
666 794 1.594293 CCGTCAGAAGCCACACGTT 60.594 57.895 0.00 0.00 0.00 3.99
667 795 1.157870 CCGTCAGAAGCCACACGTTT 61.158 55.000 0.00 0.00 0.00 3.60
669 797 1.063469 CGTCAGAAGCCACACGTTTTT 59.937 47.619 0.00 0.00 0.00 1.94
670 798 2.285756 CGTCAGAAGCCACACGTTTTTA 59.714 45.455 0.00 0.00 0.00 1.52
671 799 3.614588 GTCAGAAGCCACACGTTTTTAC 58.385 45.455 0.00 0.00 0.00 2.01
672 800 2.285756 TCAGAAGCCACACGTTTTTACG 59.714 45.455 0.00 0.00 39.31 3.18
675 803 0.948678 AGCCACACGTTTTTACGCAT 59.051 45.000 0.00 0.00 36.44 4.73
677 805 1.334239 GCCACACGTTTTTACGCATCA 60.334 47.619 0.00 0.00 36.44 3.07
678 806 2.570169 CCACACGTTTTTACGCATCAG 58.430 47.619 0.00 0.00 36.44 2.90
679 807 2.032377 CCACACGTTTTTACGCATCAGT 60.032 45.455 0.00 0.00 36.44 3.41
680 808 2.964123 CACACGTTTTTACGCATCAGTG 59.036 45.455 0.00 0.00 36.44 3.66
716 844 2.125065 CCCTCTGAGCAGCTGCAG 60.125 66.667 38.24 27.63 45.16 4.41
928 1076 1.203237 AGCCTTCCTCCTCTCTTCACA 60.203 52.381 0.00 0.00 0.00 3.58
934 1082 2.099405 CCTCCTCTCTTCACACTCCTC 58.901 57.143 0.00 0.00 0.00 3.71
935 1083 2.291540 CCTCCTCTCTTCACACTCCTCT 60.292 54.545 0.00 0.00 0.00 3.69
937 1085 2.099405 CCTCTCTTCACACTCCTCTCC 58.901 57.143 0.00 0.00 0.00 3.71
938 1086 2.291540 CCTCTCTTCACACTCCTCTCCT 60.292 54.545 0.00 0.00 0.00 3.69
1104 1252 3.424433 GCCACGGTGAGTCTAATTTTTCG 60.424 47.826 10.28 0.00 0.00 3.46
1118 1266 8.365938 GTCTAATTTTTCGCTTCTTATTTGCAC 58.634 33.333 0.00 0.00 0.00 4.57
1138 1286 5.237127 TGCACTGTTCATCTCAAGTTTGTAG 59.763 40.000 0.00 0.00 0.00 2.74
1141 1289 7.042051 GCACTGTTCATCTCAAGTTTGTAGTAA 60.042 37.037 0.00 0.00 0.00 2.24
1167 1392 9.424319 ACATTTATTCAGTCACAAGTAGTAGTG 57.576 33.333 0.00 0.00 37.10 2.74
1202 1427 2.681344 CAGCTGCTCATATGTTGCTTCA 59.319 45.455 18.66 4.40 0.00 3.02
1257 1485 3.955650 TCCTCGTCTGTAAAGAAAGGG 57.044 47.619 11.16 2.50 0.00 3.95
1274 1502 1.907255 AGGGTTACAGCAAGGGAGTAC 59.093 52.381 0.00 0.00 0.00 2.73
1290 1518 1.482182 AGTACCATGAAGCTCGATGCA 59.518 47.619 9.09 0.00 45.94 3.96
1299 1527 1.522580 GCTCGATGCAGGGAAGACC 60.523 63.158 0.00 0.00 42.31 3.85
1309 1537 3.137544 TGCAGGGAAGACCAAGAAAGTTA 59.862 43.478 0.00 0.00 43.89 2.24
1331 1559 0.252284 AACGTGGGAGTGGAGGAGAT 60.252 55.000 0.00 0.00 0.00 2.75
1334 1562 1.685180 CGTGGGAGTGGAGGAGATACA 60.685 57.143 0.00 0.00 0.00 2.29
1446 1674 0.598065 CCAAGCCTCACCCGAAAAAG 59.402 55.000 0.00 0.00 0.00 2.27
1470 1698 1.447314 CTAAGGCACCGTCCGGAAC 60.447 63.158 5.23 0.00 38.96 3.62
1613 1844 7.018235 GCTAGCTAGTTTGCTTTTTAGTTGAG 58.982 38.462 21.62 0.00 43.74 3.02
1623 1854 9.677567 TTTGCTTTTTAGTTGAGCTTGTTATAG 57.322 29.630 0.00 0.00 37.32 1.31
1675 1906 6.448369 TCTCTTTCTTTCATGTTTCCCCTA 57.552 37.500 0.00 0.00 0.00 3.53
1825 2067 8.446599 TTTTAGTCTTCTACTTTTGAAGGGTG 57.553 34.615 0.00 0.00 40.73 4.61
1857 2107 7.675062 TGCATTAAGCCAAAGGAAATCTTAAA 58.325 30.769 0.00 0.00 44.83 1.52
1858 2108 7.602265 TGCATTAAGCCAAAGGAAATCTTAAAC 59.398 33.333 0.00 0.00 44.83 2.01
1859 2109 7.602265 GCATTAAGCCAAAGGAAATCTTAAACA 59.398 33.333 0.00 0.00 34.28 2.83
1860 2110 8.925700 CATTAAGCCAAAGGAAATCTTAAACAC 58.074 33.333 0.00 0.00 34.28 3.32
1867 2118 6.954487 AAGGAAATCTTAAACACGTTCCTT 57.046 33.333 9.20 9.20 45.96 3.36
2020 2277 2.202349 GGTACGAACCGACCGACG 60.202 66.667 0.00 0.00 35.62 5.12
2033 2290 2.880879 CGACGCGGACTCCACATG 60.881 66.667 12.47 0.00 0.00 3.21
2034 2291 2.509336 GACGCGGACTCCACATGG 60.509 66.667 12.47 0.00 0.00 3.66
2035 2292 3.296709 GACGCGGACTCCACATGGT 62.297 63.158 12.47 0.00 36.34 3.55
2036 2293 2.815211 CGCGGACTCCACATGGTG 60.815 66.667 0.00 0.00 36.34 4.17
2037 2294 2.347490 GCGGACTCCACATGGTGT 59.653 61.111 5.32 5.32 43.83 4.16
2038 2295 1.302511 GCGGACTCCACATGGTGTT 60.303 57.895 7.05 0.00 41.50 3.32
2054 2311 1.742831 GTGTTGTGCAACCAACTCAGA 59.257 47.619 17.91 0.00 44.01 3.27
2066 2323 2.146342 CAACTCAGACGGCTTTCATGT 58.854 47.619 0.00 0.00 0.00 3.21
2089 2346 2.389715 GGCAGACACATACTAGAGGGT 58.610 52.381 0.00 0.00 0.00 4.34
2116 2383 3.767131 TCGTCCTACATGAAATCCACTCA 59.233 43.478 0.00 0.00 0.00 3.41
2153 2420 5.358725 GGGGTTGTTTTCAAAGTAGACTTCA 59.641 40.000 0.00 0.00 41.76 3.02
2157 2424 8.406297 GGTTGTTTTCAAAGTAGACTTCAAGAT 58.594 33.333 0.00 0.00 41.76 2.40
2161 2428 5.227569 TCAAAGTAGACTTCAAGATGGCA 57.772 39.130 0.00 0.00 34.61 4.92
2166 2433 5.303971 AGTAGACTTCAAGATGGCATATGC 58.696 41.667 19.79 19.79 41.14 3.14
2189 2456 4.317530 AAGGTTAAATGACCCTTCCTCC 57.682 45.455 0.00 0.00 40.73 4.30
2202 2469 1.899437 TTCCTCCAGCAGGCCTTACG 61.899 60.000 0.00 0.00 43.08 3.18
2212 2479 1.129058 AGGCCTTACGTATGAAGGGG 58.871 55.000 15.65 4.81 43.28 4.79
2217 2484 2.482490 CCTTACGTATGAAGGGGTTCGG 60.482 54.545 9.88 0.00 39.96 4.30
2263 2530 3.118665 AGTCATTTGTGCAAAAAGGCAGT 60.119 39.130 9.16 0.00 45.96 4.40
2264 2531 3.001533 GTCATTTGTGCAAAAAGGCAGTG 59.998 43.478 9.16 1.58 45.96 3.66
2285 2552 7.067494 GCAGTGTAGGGATTAAAGTGAATGATT 59.933 37.037 0.00 0.00 0.00 2.57
2287 2554 9.614792 AGTGTAGGGATTAAAGTGAATGATTAC 57.385 33.333 0.00 0.00 0.00 1.89
2294 2561 9.722056 GGATTAAAGTGAATGATTACACATGTC 57.278 33.333 0.00 0.00 39.18 3.06
2295 2562 9.425893 GATTAAAGTGAATGATTACACATGTCG 57.574 33.333 0.00 0.00 39.18 4.35
2297 2564 7.899178 AAAGTGAATGATTACACATGTCGTA 57.101 32.000 0.00 0.00 39.18 3.43
2298 2565 6.887376 AGTGAATGATTACACATGTCGTAC 57.113 37.500 0.00 0.00 39.18 3.67
2299 2566 5.810587 AGTGAATGATTACACATGTCGTACC 59.189 40.000 0.00 0.00 39.18 3.34
2300 2567 5.006358 GTGAATGATTACACATGTCGTACCC 59.994 44.000 0.00 0.00 37.05 3.69
2302 2569 4.118093 TGATTACACATGTCGTACCCTG 57.882 45.455 0.00 0.00 0.00 4.45
2303 2570 3.512329 TGATTACACATGTCGTACCCTGT 59.488 43.478 0.00 0.00 0.00 4.00
2304 2571 3.581024 TTACACATGTCGTACCCTGTC 57.419 47.619 0.00 0.00 0.00 3.51
2305 2572 0.606604 ACACATGTCGTACCCTGTCC 59.393 55.000 0.00 0.00 0.00 4.02
2310 2717 0.963962 TGTCGTACCCTGTCCTTGTC 59.036 55.000 0.00 0.00 0.00 3.18
2324 2731 6.229936 TGTCCTTGTCCATACTACAATACC 57.770 41.667 0.00 0.00 36.33 2.73
2325 2732 5.962031 TGTCCTTGTCCATACTACAATACCT 59.038 40.000 0.00 0.00 36.33 3.08
2326 2733 6.127168 TGTCCTTGTCCATACTACAATACCTG 60.127 42.308 0.00 0.00 36.33 4.00
2327 2734 6.097839 GTCCTTGTCCATACTACAATACCTGA 59.902 42.308 0.00 0.00 36.33 3.86
2328 2735 6.097839 TCCTTGTCCATACTACAATACCTGAC 59.902 42.308 0.00 0.00 36.33 3.51
2333 2741 5.066893 TCCATACTACAATACCTGACGACAC 59.933 44.000 0.00 0.00 0.00 3.67
2344 2752 9.093970 CAATACCTGACGACACTATTATTTTCA 57.906 33.333 0.00 0.00 0.00 2.69
2369 2777 5.241506 TGGAACAAGATTTGACAAAGGCTAG 59.758 40.000 6.77 0.00 31.92 3.42
2401 2809 2.995466 TGTGCTATGCTTGTTTGAGC 57.005 45.000 0.00 0.00 43.00 4.26
2417 2826 2.302260 TGAGCAATTGTCGGGTTGAAA 58.698 42.857 7.40 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.356124 AGGAAGCCACATGTGAGAGT 58.644 50.000 27.46 9.07 0.00 3.24
1 2 2.486472 AAGGAAGCCACATGTGAGAG 57.514 50.000 27.46 11.65 0.00 3.20
2 3 2.237143 CCTAAGGAAGCCACATGTGAGA 59.763 50.000 27.46 2.16 0.00 3.27
3 4 2.636830 CCTAAGGAAGCCACATGTGAG 58.363 52.381 27.46 17.31 0.00 3.51
4 5 1.340017 GCCTAAGGAAGCCACATGTGA 60.340 52.381 27.46 3.36 0.00 3.58
5 6 1.098050 GCCTAAGGAAGCCACATGTG 58.902 55.000 19.31 19.31 0.00 3.21
6 7 3.577389 GCCTAAGGAAGCCACATGT 57.423 52.632 0.00 0.00 0.00 3.21
13 14 2.007608 CACGTTTAGGCCTAAGGAAGC 58.992 52.381 23.96 7.50 0.00 3.86
14 15 3.604875 TCACGTTTAGGCCTAAGGAAG 57.395 47.619 23.96 15.41 0.00 3.46
15 16 3.557686 GGTTCACGTTTAGGCCTAAGGAA 60.558 47.826 23.96 20.93 0.00 3.36
16 17 2.027837 GGTTCACGTTTAGGCCTAAGGA 60.028 50.000 23.96 16.99 0.00 3.36
17 18 2.353323 GGTTCACGTTTAGGCCTAAGG 58.647 52.381 23.96 21.09 0.00 2.69
18 19 1.997606 CGGTTCACGTTTAGGCCTAAG 59.002 52.381 23.96 16.44 37.93 2.18
19 20 1.617850 TCGGTTCACGTTTAGGCCTAA 59.382 47.619 21.68 21.68 44.69 2.69
20 21 1.255882 TCGGTTCACGTTTAGGCCTA 58.744 50.000 8.91 8.91 44.69 3.93
21 22 0.393820 TTCGGTTCACGTTTAGGCCT 59.606 50.000 11.78 11.78 44.69 5.19
22 23 1.196127 CTTTCGGTTCACGTTTAGGCC 59.804 52.381 0.00 0.00 44.69 5.19
23 24 1.869132 ACTTTCGGTTCACGTTTAGGC 59.131 47.619 0.00 0.00 44.69 3.93
24 25 3.676646 CCTACTTTCGGTTCACGTTTAGG 59.323 47.826 0.00 0.00 44.69 2.69
25 26 4.301628 ACCTACTTTCGGTTCACGTTTAG 58.698 43.478 0.00 0.00 44.69 1.85
26 27 4.320608 ACCTACTTTCGGTTCACGTTTA 57.679 40.909 0.00 0.00 44.69 2.01
27 28 3.183793 ACCTACTTTCGGTTCACGTTT 57.816 42.857 0.00 0.00 44.69 3.60
28 29 2.867975 CAACCTACTTTCGGTTCACGTT 59.132 45.455 0.00 0.00 42.63 3.99
29 30 2.476821 CAACCTACTTTCGGTTCACGT 58.523 47.619 0.00 0.00 42.63 4.49
30 31 1.193874 GCAACCTACTTTCGGTTCACG 59.806 52.381 0.00 0.00 42.63 4.35
31 32 2.215196 TGCAACCTACTTTCGGTTCAC 58.785 47.619 0.00 0.00 42.63 3.18
32 33 2.623878 TGCAACCTACTTTCGGTTCA 57.376 45.000 0.00 0.00 42.63 3.18
33 34 4.499037 AATTGCAACCTACTTTCGGTTC 57.501 40.909 0.00 0.00 42.63 3.62
34 35 4.929819 AAATTGCAACCTACTTTCGGTT 57.070 36.364 0.00 0.00 45.26 4.44
35 36 4.929819 AAAATTGCAACCTACTTTCGGT 57.070 36.364 0.00 0.00 35.97 4.69
56 57 6.374578 GGCTGGCGCAATTTAAAAATAAAAA 58.625 32.000 10.83 0.00 38.10 1.94
57 58 5.389935 CGGCTGGCGCAATTTAAAAATAAAA 60.390 36.000 11.55 0.00 38.10 1.52
58 59 4.092091 CGGCTGGCGCAATTTAAAAATAAA 59.908 37.500 11.55 0.00 38.10 1.40
59 60 3.614616 CGGCTGGCGCAATTTAAAAATAA 59.385 39.130 11.55 0.00 38.10 1.40
60 61 3.182967 CGGCTGGCGCAATTTAAAAATA 58.817 40.909 11.55 0.00 38.10 1.40
61 62 1.999024 CGGCTGGCGCAATTTAAAAAT 59.001 42.857 11.55 0.00 38.10 1.82
62 63 1.423395 CGGCTGGCGCAATTTAAAAA 58.577 45.000 11.55 0.00 38.10 1.94
63 64 0.389166 CCGGCTGGCGCAATTTAAAA 60.389 50.000 18.95 0.00 38.10 1.52
64 65 1.214062 CCGGCTGGCGCAATTTAAA 59.786 52.632 18.95 0.00 38.10 1.52
65 66 2.705821 CCCGGCTGGCGCAATTTAA 61.706 57.895 18.95 0.00 38.10 1.52
66 67 3.137459 CCCGGCTGGCGCAATTTA 61.137 61.111 18.95 0.00 38.10 1.40
73 74 4.697756 TTCAAGACCCGGCTGGCG 62.698 66.667 17.39 17.39 37.83 5.69
74 75 3.056328 GTTCAAGACCCGGCTGGC 61.056 66.667 5.85 0.00 37.83 4.85
75 76 2.359975 GGTTCAAGACCCGGCTGG 60.360 66.667 3.88 3.88 43.06 4.85
83 84 2.029918 GGTGAATTGGCAGGTTCAAGAC 60.030 50.000 15.89 8.41 36.23 3.01
84 85 2.238521 GGTGAATTGGCAGGTTCAAGA 58.761 47.619 15.89 0.00 36.23 3.02
85 86 1.273327 GGGTGAATTGGCAGGTTCAAG 59.727 52.381 15.89 0.00 36.23 3.02
86 87 1.337118 GGGTGAATTGGCAGGTTCAA 58.663 50.000 15.89 2.40 36.23 2.69
87 88 0.187117 TGGGTGAATTGGCAGGTTCA 59.813 50.000 11.78 11.78 32.31 3.18
88 89 1.337118 TTGGGTGAATTGGCAGGTTC 58.663 50.000 7.51 7.51 0.00 3.62
89 90 1.799933 TTTGGGTGAATTGGCAGGTT 58.200 45.000 0.00 0.00 0.00 3.50
90 91 1.799933 TTTTGGGTGAATTGGCAGGT 58.200 45.000 0.00 0.00 0.00 4.00
91 92 3.421919 AATTTTGGGTGAATTGGCAGG 57.578 42.857 0.00 0.00 0.00 4.85
92 93 4.387598 TGAAATTTTGGGTGAATTGGCAG 58.612 39.130 0.00 0.00 0.00 4.85
93 94 4.428294 TGAAATTTTGGGTGAATTGGCA 57.572 36.364 0.00 0.00 0.00 4.92
94 95 5.299028 AGTTTGAAATTTTGGGTGAATTGGC 59.701 36.000 0.00 0.00 0.00 4.52
95 96 6.940831 AGTTTGAAATTTTGGGTGAATTGG 57.059 33.333 0.00 0.00 0.00 3.16
96 97 8.550376 CACTAGTTTGAAATTTTGGGTGAATTG 58.450 33.333 0.00 0.00 0.00 2.32
97 98 8.482128 TCACTAGTTTGAAATTTTGGGTGAATT 58.518 29.630 0.00 0.00 0.00 2.17
98 99 8.017418 TCACTAGTTTGAAATTTTGGGTGAAT 57.983 30.769 0.00 0.00 0.00 2.57
99 100 7.411486 TCACTAGTTTGAAATTTTGGGTGAA 57.589 32.000 0.00 0.00 0.00 3.18
100 101 6.040391 CCTCACTAGTTTGAAATTTTGGGTGA 59.960 38.462 0.00 0.00 0.00 4.02
101 102 6.040391 TCCTCACTAGTTTGAAATTTTGGGTG 59.960 38.462 0.00 0.00 0.00 4.61
102 103 6.133356 TCCTCACTAGTTTGAAATTTTGGGT 58.867 36.000 0.00 0.00 0.00 4.51
103 104 6.648879 TCCTCACTAGTTTGAAATTTTGGG 57.351 37.500 0.00 0.00 0.00 4.12
104 105 8.981647 CATTTCCTCACTAGTTTGAAATTTTGG 58.018 33.333 16.00 6.69 34.38 3.28
105 106 9.533253 ACATTTCCTCACTAGTTTGAAATTTTG 57.467 29.630 16.00 11.78 34.38 2.44
108 109 8.515414 GCTACATTTCCTCACTAGTTTGAAATT 58.485 33.333 16.00 12.05 34.38 1.82
109 110 7.885399 AGCTACATTTCCTCACTAGTTTGAAAT 59.115 33.333 14.08 14.08 36.39 2.17
110 111 7.224297 AGCTACATTTCCTCACTAGTTTGAAA 58.776 34.615 11.53 11.53 0.00 2.69
111 112 6.769512 AGCTACATTTCCTCACTAGTTTGAA 58.230 36.000 0.00 0.00 0.00 2.69
112 113 6.360370 AGCTACATTTCCTCACTAGTTTGA 57.640 37.500 0.00 0.00 0.00 2.69
113 114 8.607459 CATAAGCTACATTTCCTCACTAGTTTG 58.393 37.037 0.00 0.00 0.00 2.93
114 115 7.281100 GCATAAGCTACATTTCCTCACTAGTTT 59.719 37.037 0.00 0.00 37.91 2.66
115 116 6.763610 GCATAAGCTACATTTCCTCACTAGTT 59.236 38.462 0.00 0.00 37.91 2.24
116 117 6.127054 TGCATAAGCTACATTTCCTCACTAGT 60.127 38.462 0.00 0.00 42.74 2.57
117 118 6.283694 TGCATAAGCTACATTTCCTCACTAG 58.716 40.000 0.00 0.00 42.74 2.57
118 119 6.233905 TGCATAAGCTACATTTCCTCACTA 57.766 37.500 0.00 0.00 42.74 2.74
119 120 5.102953 TGCATAAGCTACATTTCCTCACT 57.897 39.130 0.00 0.00 42.74 3.41
120 121 6.382869 AATGCATAAGCTACATTTCCTCAC 57.617 37.500 0.00 0.00 42.74 3.51
121 122 8.696043 ATAAATGCATAAGCTACATTTCCTCA 57.304 30.769 15.86 4.58 41.70 3.86
123 124 9.799106 AGTATAAATGCATAAGCTACATTTCCT 57.201 29.630 15.86 10.33 41.70 3.36
129 130 9.389755 TGTTGAAGTATAAATGCATAAGCTACA 57.610 29.630 0.00 0.00 42.74 2.74
132 133 9.573133 GTTTGTTGAAGTATAAATGCATAAGCT 57.427 29.630 0.00 0.00 42.74 3.74
133 134 9.573133 AGTTTGTTGAAGTATAAATGCATAAGC 57.427 29.630 0.00 0.00 42.57 3.09
136 137 9.352784 GCAAGTTTGTTGAAGTATAAATGCATA 57.647 29.630 0.00 0.00 0.00 3.14
137 138 7.062138 CGCAAGTTTGTTGAAGTATAAATGCAT 59.938 33.333 0.00 0.00 0.00 3.96
138 139 6.362016 CGCAAGTTTGTTGAAGTATAAATGCA 59.638 34.615 0.00 0.00 0.00 3.96
139 140 6.741500 CGCAAGTTTGTTGAAGTATAAATGC 58.258 36.000 0.00 0.00 0.00 3.56
188 189 9.515226 GTGATAGATATTACCCCATTTAGCAAA 57.485 33.333 0.00 0.00 0.00 3.68
189 190 8.664992 TGTGATAGATATTACCCCATTTAGCAA 58.335 33.333 0.00 0.00 0.00 3.91
190 191 8.213489 TGTGATAGATATTACCCCATTTAGCA 57.787 34.615 0.00 0.00 0.00 3.49
191 192 9.515226 TTTGTGATAGATATTACCCCATTTAGC 57.485 33.333 0.00 0.00 0.00 3.09
194 195 9.936329 ACTTTTGTGATAGATATTACCCCATTT 57.064 29.630 0.00 0.00 0.00 2.32
213 214 5.899631 TTACCCCTAGAGTTCACTTTTGT 57.100 39.130 0.00 0.00 0.00 2.83
214 215 7.576861 TTTTTACCCCTAGAGTTCACTTTTG 57.423 36.000 0.00 0.00 0.00 2.44
295 306 3.701664 AGGAGGAAGGGCAAATTTGTAG 58.298 45.455 19.03 0.00 0.00 2.74
343 354 5.645067 TGTGCATTTCAGGAATCTAACAGAG 59.355 40.000 0.00 0.00 0.00 3.35
374 385 7.116736 ACCAACCTTCAAAGAAAGAGAGTTTA 58.883 34.615 0.00 0.00 0.00 2.01
385 396 3.818773 GGAATCGAACCAACCTTCAAAGA 59.181 43.478 7.06 0.00 0.00 2.52
386 397 3.821033 AGGAATCGAACCAACCTTCAAAG 59.179 43.478 13.17 0.00 0.00 2.77
401 412 8.964420 TTTAAAAGTTAAGCATTCAGGAATCG 57.036 30.769 0.00 0.00 0.00 3.34
438 449 2.832931 CAACTCTGCAACCCTCGAG 58.167 57.895 5.13 5.13 0.00 4.04
467 478 4.505566 GCCAGGCATAAGACCAAGATCATA 60.506 45.833 6.55 0.00 0.00 2.15
469 480 2.421952 GCCAGGCATAAGACCAAGATCA 60.422 50.000 6.55 0.00 0.00 2.92
485 496 3.470888 CTACTGTCCCGGGCCAGG 61.471 72.222 33.50 16.13 32.90 4.45
486 497 1.762460 ATCTACTGTCCCGGGCCAG 60.762 63.158 29.62 29.62 34.82 4.85
491 502 1.704641 TGATCCATCTACTGTCCCGG 58.295 55.000 0.00 0.00 0.00 5.73
498 509 4.100035 TCACATCGCTTTGATCCATCTACT 59.900 41.667 0.00 0.00 34.13 2.57
500 511 4.670896 TCACATCGCTTTGATCCATCTA 57.329 40.909 0.00 0.00 34.13 1.98
501 512 3.548745 TCACATCGCTTTGATCCATCT 57.451 42.857 0.00 0.00 34.13 2.90
502 513 4.095483 AGTTTCACATCGCTTTGATCCATC 59.905 41.667 0.00 0.00 34.13 3.51
503 514 4.012374 AGTTTCACATCGCTTTGATCCAT 58.988 39.130 0.00 0.00 34.13 3.41
504 515 3.189080 CAGTTTCACATCGCTTTGATCCA 59.811 43.478 0.00 0.00 34.13 3.41
505 516 3.426695 CCAGTTTCACATCGCTTTGATCC 60.427 47.826 0.00 0.00 34.13 3.36
529 626 0.802494 CACGGCGCCAGTTTTCTAAT 59.198 50.000 28.98 0.00 0.00 1.73
533 630 4.700365 GCCACGGCGCCAGTTTTC 62.700 66.667 28.98 11.87 0.00 2.29
649 777 0.655733 AAAACGTGTGGCTTCTGACG 59.344 50.000 0.00 0.00 37.82 4.35
716 844 9.131416 GAGTGTAAGCTTTCTCTCTTTTACTAC 57.869 37.037 21.14 4.15 0.00 2.73
797 945 5.702670 TGGTCAAAGCTCAGATTTCTTACAG 59.297 40.000 0.00 0.00 0.00 2.74
840 988 7.225011 ACACTGGTAGTCAGATATAGATCGAA 58.775 38.462 0.00 0.00 46.18 3.71
928 1076 0.031616 GGGGTGATGAGGAGAGGAGT 60.032 60.000 0.00 0.00 0.00 3.85
934 1082 0.543749 GGTGAAGGGGTGATGAGGAG 59.456 60.000 0.00 0.00 0.00 3.69
935 1083 0.178876 TGGTGAAGGGGTGATGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
937 1085 0.393537 GCTGGTGAAGGGGTGATGAG 60.394 60.000 0.00 0.00 0.00 2.90
938 1086 1.685224 GCTGGTGAAGGGGTGATGA 59.315 57.895 0.00 0.00 0.00 2.92
980 1128 4.458989 TCATGGTGAACTCCAATTAACTGC 59.541 41.667 0.00 0.00 41.09 4.40
1104 1252 5.947443 AGATGAACAGTGCAAATAAGAAGC 58.053 37.500 0.00 0.00 0.00 3.86
1118 1266 8.365399 TGTTACTACAAACTTGAGATGAACAG 57.635 34.615 0.00 0.00 0.00 3.16
1141 1289 9.424319 CACTACTACTTGTGACTGAATAAATGT 57.576 33.333 0.00 0.00 36.38 2.71
1167 1392 1.198637 GCAGCTGGTGAGATCAACAAC 59.801 52.381 17.12 0.00 43.85 3.32
1202 1427 3.222354 GACGGGTCCTTCACTGCGT 62.222 63.158 0.00 0.00 0.00 5.24
1257 1485 3.055385 TCATGGTACTCCCTTGCTGTAAC 60.055 47.826 0.00 0.00 38.09 2.50
1274 1502 1.164662 CCCTGCATCGAGCTTCATGG 61.165 60.000 7.69 0.00 45.94 3.66
1290 1518 6.183360 CGTTTTTAACTTTCTTGGTCTTCCCT 60.183 38.462 0.00 0.00 0.00 4.20
1299 1527 5.741982 CACTCCCACGTTTTTAACTTTCTTG 59.258 40.000 0.00 0.00 0.00 3.02
1309 1537 0.841289 TCCTCCACTCCCACGTTTTT 59.159 50.000 0.00 0.00 0.00 1.94
1331 1559 3.073798 TGGTTCAGCAGATCCCTTTTGTA 59.926 43.478 3.96 0.00 33.46 2.41
1334 1562 2.978156 TGGTTCAGCAGATCCCTTTT 57.022 45.000 3.96 0.00 33.46 2.27
1382 1610 1.207089 CGGCCACCTTATCAGACTCAA 59.793 52.381 2.24 0.00 0.00 3.02
1446 1674 1.574702 GGACGGTGCCTTAGTTGTGC 61.575 60.000 0.00 0.00 0.00 4.57
1638 1869 7.287005 TGAAAGAAAGAGAACTACCACTACTCA 59.713 37.037 0.00 0.00 0.00 3.41
1675 1906 4.141111 CCTAGAAACTAGCTAGAGAGGGGT 60.141 50.000 27.45 0.27 38.03 4.95
1805 2047 6.017026 CCTTTCACCCTTCAAAAGTAGAAGAC 60.017 42.308 4.61 0.00 44.00 3.01
1825 2067 4.160252 TCCTTTGGCTTAATGCATCCTTTC 59.840 41.667 0.00 0.00 45.15 2.62
1879 2130 8.740123 TCTTGTGTACATAAAGAAAAACCTCA 57.260 30.769 17.12 0.00 0.00 3.86
1892 2143 4.647399 TGACCATCCGATCTTGTGTACATA 59.353 41.667 0.00 0.00 0.00 2.29
1893 2144 3.450817 TGACCATCCGATCTTGTGTACAT 59.549 43.478 0.00 0.00 0.00 2.29
1894 2145 2.829120 TGACCATCCGATCTTGTGTACA 59.171 45.455 0.00 0.00 0.00 2.90
1895 2146 3.187700 GTGACCATCCGATCTTGTGTAC 58.812 50.000 0.00 0.00 0.00 2.90
1896 2147 2.829120 TGTGACCATCCGATCTTGTGTA 59.171 45.455 0.00 0.00 0.00 2.90
1995 2252 2.056577 GTCGGTTCGTACCAACTTCAG 58.943 52.381 12.05 0.00 45.31 3.02
1997 2254 1.422388 GGTCGGTTCGTACCAACTTC 58.578 55.000 12.05 0.00 45.31 3.01
2016 2273 2.880879 CATGTGGAGTCCGCGTCG 60.881 66.667 14.75 7.15 36.72 5.12
2020 2277 1.302511 AACACCATGTGGAGTCCGC 60.303 57.895 16.21 16.21 38.05 5.54
2037 2294 1.013596 CGTCTGAGTTGGTTGCACAA 58.986 50.000 0.00 0.00 0.00 3.33
2038 2295 0.813610 CCGTCTGAGTTGGTTGCACA 60.814 55.000 0.00 0.00 0.00 4.57
2054 2311 2.746277 GCCCGACATGAAAGCCGT 60.746 61.111 0.00 0.00 0.00 5.68
2066 2323 2.298610 CTCTAGTATGTGTCTGCCCGA 58.701 52.381 0.00 0.00 0.00 5.14
2089 2346 4.250464 GGATTTCATGTAGGACGACAACA 58.750 43.478 0.00 0.00 31.83 3.33
2134 2401 7.468631 GCCATCTTGAAGTCTACTTTGAAAACA 60.469 37.037 0.00 0.00 36.11 2.83
2153 2420 7.725397 TCATTTAACCTTAGCATATGCCATCTT 59.275 33.333 23.96 7.84 43.38 2.40
2157 2424 5.534654 GGTCATTTAACCTTAGCATATGCCA 59.465 40.000 23.96 8.09 37.82 4.92
2161 2428 7.004691 GGAAGGGTCATTTAACCTTAGCATAT 58.995 38.462 0.00 0.00 44.25 1.78
2166 2433 5.045140 TGGAGGAAGGGTCATTTAACCTTAG 60.045 44.000 0.00 0.00 44.25 2.18
2189 2456 2.205074 CTTCATACGTAAGGCCTGCTG 58.795 52.381 5.69 0.40 46.39 4.41
2202 2469 2.052782 ATTGCCGAACCCCTTCATAC 57.947 50.000 0.00 0.00 0.00 2.39
2212 2479 0.035439 TCCTCCAGGAATTGCCGAAC 60.035 55.000 0.00 0.00 42.18 3.95
2236 2503 4.207019 CCTTTTTGCACAAATGACTCGAAC 59.793 41.667 0.00 0.00 0.00 3.95
2237 2504 4.358851 CCTTTTTGCACAAATGACTCGAA 58.641 39.130 0.00 0.00 0.00 3.71
2240 2507 3.456280 TGCCTTTTTGCACAAATGACTC 58.544 40.909 4.98 0.00 36.04 3.36
2263 2530 9.391006 GTGTAATCATTCACTTTAATCCCTACA 57.609 33.333 0.00 0.00 0.00 2.74
2264 2531 9.391006 TGTGTAATCATTCACTTTAATCCCTAC 57.609 33.333 0.00 0.00 35.82 3.18
2285 2552 1.820519 GGACAGGGTACGACATGTGTA 59.179 52.381 1.15 3.46 0.00 2.90
2287 2554 0.895530 AGGACAGGGTACGACATGTG 59.104 55.000 1.15 0.00 0.00 3.21
2294 2561 0.902531 ATGGACAAGGACAGGGTACG 59.097 55.000 0.00 0.00 0.00 3.67
2295 2562 3.105283 AGTATGGACAAGGACAGGGTAC 58.895 50.000 0.00 0.00 0.00 3.34
2297 2564 2.344093 AGTATGGACAAGGACAGGGT 57.656 50.000 0.00 0.00 0.00 4.34
2298 2565 3.104512 TGTAGTATGGACAAGGACAGGG 58.895 50.000 0.00 0.00 0.00 4.45
2299 2566 4.819105 TTGTAGTATGGACAAGGACAGG 57.181 45.455 0.00 0.00 33.03 4.00
2300 2567 6.098409 AGGTATTGTAGTATGGACAAGGACAG 59.902 42.308 0.00 0.00 40.01 3.51
2302 2569 6.097839 TCAGGTATTGTAGTATGGACAAGGAC 59.902 42.308 0.00 0.00 40.01 3.85
2303 2570 6.097839 GTCAGGTATTGTAGTATGGACAAGGA 59.902 42.308 0.00 0.00 40.01 3.36
2304 2571 6.281405 GTCAGGTATTGTAGTATGGACAAGG 58.719 44.000 0.00 0.00 40.01 3.61
2305 2572 5.977725 CGTCAGGTATTGTAGTATGGACAAG 59.022 44.000 0.00 0.00 40.01 3.16
2310 2717 5.067413 AGTGTCGTCAGGTATTGTAGTATGG 59.933 44.000 0.00 0.00 0.00 2.74
2324 2731 7.770801 TCCATGAAAATAATAGTGTCGTCAG 57.229 36.000 0.00 0.00 0.00 3.51
2325 2732 7.604545 TGTTCCATGAAAATAATAGTGTCGTCA 59.395 33.333 0.00 0.00 0.00 4.35
2326 2733 7.970384 TGTTCCATGAAAATAATAGTGTCGTC 58.030 34.615 0.00 0.00 0.00 4.20
2327 2734 7.915293 TGTTCCATGAAAATAATAGTGTCGT 57.085 32.000 0.00 0.00 0.00 4.34
2328 2735 8.664798 TCTTGTTCCATGAAAATAATAGTGTCG 58.335 33.333 0.00 0.00 0.00 4.35
2344 2752 4.590222 AGCCTTTGTCAAATCTTGTTCCAT 59.410 37.500 0.00 0.00 0.00 3.41
2351 2759 9.466497 TCATATTTCTAGCCTTTGTCAAATCTT 57.534 29.630 0.00 0.00 0.00 2.40
2352 2760 9.466497 TTCATATTTCTAGCCTTTGTCAAATCT 57.534 29.630 0.00 2.44 0.00 2.40
2353 2761 9.727627 CTTCATATTTCTAGCCTTTGTCAAATC 57.272 33.333 0.00 0.00 0.00 2.17
2359 2767 6.660949 ACAAGCTTCATATTTCTAGCCTTTGT 59.339 34.615 0.00 0.00 34.19 2.83
2426 2835 7.401080 CCAAAGCAGAACAATTTACTTTGTTG 58.599 34.615 7.25 0.00 46.84 3.33


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

AutoCloner maintained by Alex Coulton.