Multiple sequence alignment - TraesCS7A01G057800

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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 TraesCS7A01G057800 chr7A 100.000 2633 0 0 1 2633 27906387 27903755 0.000000e+00 4863.0
1 TraesCS7A01G057800 chr7A 82.243 642 76 23 1031 1638 27901381 27902018 1.080000e-143 520.0
2 TraesCS7A01G057800 chr7D 81.499 2108 210 75 1 2056 27472374 27470395 0.000000e+00 1567.0
3 TraesCS7A01G057800 chr7D 82.266 1765 195 64 321 2017 27468902 27467188 0.000000e+00 1417.0
4 TraesCS7A01G057800 chr7D 85.490 572 58 13 1031 1591 27453191 27453748 8.170000e-160 573.0
5 TraesCS7A01G057800 chr4A 83.480 1368 142 51 569 1885 704154440 704153106 0.000000e+00 1197.0
6 TraesCS7A01G057800 chr4A 85.488 882 74 27 857 1691 703942165 703941291 0.000000e+00 870.0
7 TraesCS7A01G057800 chr4A 84.385 634 59 28 1028 1638 703932181 703932797 1.050000e-163 586.0
8 TraesCS7A01G057800 chr4A 93.662 142 6 3 341 482 704154646 704154508 2.660000e-50 209.0
9 TraesCS7A01G057800 chr4A 82.323 198 26 5 428 619 704149472 704149278 2.100000e-36 163.0
10 TraesCS7A01G057800 chr4A 75.092 273 36 21 1837 2105 703941009 703940765 6.000000e-17 99.0
11 TraesCS7A01G057800 chr4A 91.379 58 2 2 2008 2062 389252335 389252392 2.810000e-10 76.8
12 TraesCS7A01G057800 chr2D 80.263 608 75 30 1036 1641 7228074 7227510 1.460000e-112 416.0
13 TraesCS7A01G057800 chr5A 82.288 271 41 7 1045 1308 523616336 523616066 7.330000e-56 228.0
14 TraesCS7A01G057800 chr7B 81.102 127 18 3 2008 2128 562391319 562391193 2.160000e-16 97.1
15 TraesCS7A01G057800 chr2A 80.374 107 16 3 2028 2130 1640382 1640277 2.810000e-10 76.8
16 TraesCS7A01G057800 chrUn 100.000 36 0 0 2029 2064 27562676 27562711 1.690000e-07 67.6
17 TraesCS7A01G057800 chrUn 97.222 36 1 0 2029 2064 27632622 27632657 7.870000e-06 62.1
18 TraesCS7A01G057800 chr2B 97.368 38 1 0 2027 2064 209243493 209243456 6.080000e-07 65.8
19 TraesCS7A01G057800 chr2B 97.059 34 1 0 2029 2062 52347946 52347913 1.020000e-04 58.4
20 TraesCS7A01G057800 chr6D 82.051 78 7 6 2008 2080 57512716 57512791 2.830000e-05 60.2
21 TraesCS7A01G057800 chr5D 81.333 75 11 2 1993 2064 424316974 424316900 1.020000e-04 58.4


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 TraesCS7A01G057800 chr7A 27903755 27906387 2632 True 4863.0 4863 100.000000 1 2633 1 chr7A.!!$R1 2632
1 TraesCS7A01G057800 chr7A 27901381 27902018 637 False 520.0 520 82.243000 1031 1638 1 chr7A.!!$F1 607
2 TraesCS7A01G057800 chr7D 27467188 27472374 5186 True 1492.0 1567 81.882500 1 2056 2 chr7D.!!$R1 2055
3 TraesCS7A01G057800 chr7D 27453191 27453748 557 False 573.0 573 85.490000 1031 1591 1 chr7D.!!$F1 560
4 TraesCS7A01G057800 chr4A 703932181 703932797 616 False 586.0 586 84.385000 1028 1638 1 chr4A.!!$F2 610
5 TraesCS7A01G057800 chr4A 704149278 704154646 5368 True 523.0 1197 86.488333 341 1885 3 chr4A.!!$R2 1544
6 TraesCS7A01G057800 chr4A 703940765 703942165 1400 True 484.5 870 80.290000 857 2105 2 chr4A.!!$R1 1248
7 TraesCS7A01G057800 chr2D 7227510 7228074 564 True 416.0 416 80.263000 1036 1641 1 chr2D.!!$R1 605

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
160 165 0.043053 CGCATCTGTTTATGTCGGCG 60.043 55.0 0.0 0.0 37.17 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 4208 0.031994 GCGGCAGTGGTTTGATTGTT 59.968 50.0 0.0 0.0 0.0 2.83 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
42 44 8.729805 TTTTTCCAGTTCAATTTGCTTTGTAT 57.270 26.923 0.00 0.00 0.00 2.29
55 57 7.815398 TTTGCTTTGTATGCAGACAATAATG 57.185 32.000 26.09 16.95 41.71 1.90
56 58 5.893687 TGCTTTGTATGCAGACAATAATGG 58.106 37.500 26.09 14.79 39.04 3.16
63 65 1.867233 GCAGACAATAATGGCGTCGAT 59.133 47.619 0.00 0.00 40.62 3.59
67 69 1.202486 ACAATAATGGCGTCGATCGGT 60.202 47.619 16.41 0.00 40.26 4.69
68 70 2.034939 ACAATAATGGCGTCGATCGGTA 59.965 45.455 16.41 0.00 40.26 4.02
70 72 0.594602 TAATGGCGTCGATCGGTAGG 59.405 55.000 16.41 3.62 40.26 3.18
72 74 1.793134 ATGGCGTCGATCGGTAGGAC 61.793 60.000 16.41 5.29 40.26 3.85
78 83 0.930310 TCGATCGGTAGGACGTAACG 59.070 55.000 16.41 6.27 43.78 3.18
115 120 0.759346 AAAGAGTGCTCGACCAACCT 59.241 50.000 0.00 0.00 34.09 3.50
123 128 2.614983 TGCTCGACCAACCTAAACAAAC 59.385 45.455 0.00 0.00 0.00 2.93
126 131 4.439016 GCTCGACCAACCTAAACAAACAAA 60.439 41.667 0.00 0.00 0.00 2.83
132 137 4.801516 CCAACCTAAACAAACAAAAGACGG 59.198 41.667 0.00 0.00 0.00 4.79
139 144 7.329962 CCTAAACAAACAAAAGACGGAAAAACT 59.670 33.333 0.00 0.00 0.00 2.66
144 149 3.374678 ACAAAAGACGGAAAAACTACGCA 59.625 39.130 0.00 0.00 0.00 5.24
149 154 2.735134 GACGGAAAAACTACGCATCTGT 59.265 45.455 0.00 0.00 32.53 3.41
152 157 4.751098 ACGGAAAAACTACGCATCTGTTTA 59.249 37.500 0.00 0.00 34.09 2.01
153 158 5.410439 ACGGAAAAACTACGCATCTGTTTAT 59.590 36.000 0.00 0.00 34.09 1.40
154 159 5.732647 CGGAAAAACTACGCATCTGTTTATG 59.267 40.000 0.00 0.00 34.09 1.90
155 160 6.608610 GGAAAAACTACGCATCTGTTTATGT 58.391 36.000 0.00 0.00 34.09 2.29
156 161 6.741358 GGAAAAACTACGCATCTGTTTATGTC 59.259 38.462 0.00 0.00 34.09 3.06
157 162 5.450376 AAACTACGCATCTGTTTATGTCG 57.550 39.130 0.00 0.00 32.92 4.35
158 163 3.444916 ACTACGCATCTGTTTATGTCGG 58.555 45.455 0.00 0.00 33.58 4.79
159 164 1.006832 ACGCATCTGTTTATGTCGGC 58.993 50.000 0.00 0.00 33.58 5.54
160 165 0.043053 CGCATCTGTTTATGTCGGCG 60.043 55.000 0.00 0.00 37.17 6.46
161 166 0.316196 GCATCTGTTTATGTCGGCGC 60.316 55.000 0.00 0.00 0.00 6.53
162 167 0.043053 CATCTGTTTATGTCGGCGCG 60.043 55.000 0.00 0.00 0.00 6.86
163 168 0.459585 ATCTGTTTATGTCGGCGCGT 60.460 50.000 8.43 1.17 0.00 6.01
164 169 1.058748 CTGTTTATGTCGGCGCGTG 59.941 57.895 8.43 0.00 0.00 5.34
165 170 2.291508 CTGTTTATGTCGGCGCGTGG 62.292 60.000 8.43 0.00 0.00 4.94
179 184 2.181584 CGTGGGAGTCGCTCTAACT 58.818 57.895 8.82 0.00 0.00 2.24
182 187 0.612174 TGGGAGTCGCTCTAACTGCT 60.612 55.000 8.82 0.00 35.62 4.24
183 188 0.179124 GGGAGTCGCTCTAACTGCTG 60.179 60.000 0.00 0.00 35.62 4.41
184 189 0.811915 GGAGTCGCTCTAACTGCTGA 59.188 55.000 0.00 0.00 32.85 4.26
185 190 1.468395 GGAGTCGCTCTAACTGCTGAC 60.468 57.143 0.00 0.00 35.71 3.51
186 191 1.470890 GAGTCGCTCTAACTGCTGACT 59.529 52.381 0.00 10.87 42.25 3.41
187 192 1.889829 AGTCGCTCTAACTGCTGACTT 59.110 47.619 0.00 0.00 39.35 3.01
188 193 2.094957 AGTCGCTCTAACTGCTGACTTC 60.095 50.000 0.00 0.00 39.35 3.01
189 194 1.886542 TCGCTCTAACTGCTGACTTCA 59.113 47.619 0.00 0.00 0.00 3.02
190 195 2.296190 TCGCTCTAACTGCTGACTTCAA 59.704 45.455 0.00 0.00 0.00 2.69
191 196 2.410053 CGCTCTAACTGCTGACTTCAAC 59.590 50.000 0.00 0.00 0.00 3.18
192 197 2.410053 GCTCTAACTGCTGACTTCAACG 59.590 50.000 0.00 0.00 0.00 4.10
193 198 2.404215 TCTAACTGCTGACTTCAACGC 58.596 47.619 0.00 0.00 0.00 4.84
208 213 2.661537 CGCAACACAGAGTCGCCA 60.662 61.111 0.00 0.00 0.00 5.69
215 220 1.202440 ACACAGAGTCGCCACGTTAAA 60.202 47.619 0.00 0.00 0.00 1.52
312 317 1.674359 TCAAAGAGCACGCAAAAGGA 58.326 45.000 0.00 0.00 0.00 3.36
313 318 2.020720 TCAAAGAGCACGCAAAAGGAA 58.979 42.857 0.00 0.00 0.00 3.36
314 319 2.425312 TCAAAGAGCACGCAAAAGGAAA 59.575 40.909 0.00 0.00 0.00 3.13
315 320 3.119316 TCAAAGAGCACGCAAAAGGAAAA 60.119 39.130 0.00 0.00 0.00 2.29
316 321 2.781945 AGAGCACGCAAAAGGAAAAG 57.218 45.000 0.00 0.00 0.00 2.27
317 322 1.131771 GAGCACGCAAAAGGAAAAGC 58.868 50.000 0.00 0.00 0.00 3.51
336 341 0.163788 CGCAAGGTTAAGCTGACGTG 59.836 55.000 8.16 3.85 0.00 4.49
337 342 0.110192 GCAAGGTTAAGCTGACGTGC 60.110 55.000 8.16 10.41 0.00 5.34
338 343 0.163788 CAAGGTTAAGCTGACGTGCG 59.836 55.000 8.16 0.00 38.13 5.34
339 344 1.566018 AAGGTTAAGCTGACGTGCGC 61.566 55.000 8.16 0.00 38.13 6.09
553 563 4.090057 GCCGCACGTGCTTTCCTC 62.090 66.667 35.27 15.16 39.32 3.71
559 569 1.272781 CACGTGCTTTCCTCGAGATC 58.727 55.000 15.71 0.00 34.71 2.75
580 608 1.848652 GGAGCTCTACCAGTACACCA 58.151 55.000 14.64 0.00 0.00 4.17
590 618 3.097614 ACCAGTACACCATAGTCTGACC 58.902 50.000 3.76 0.00 0.00 4.02
605 633 0.671796 TGACCCACTGACACAGTACG 59.328 55.000 4.08 0.95 43.43 3.67
634 662 1.260544 GGCCAAGACCAGCAGAAAAT 58.739 50.000 0.00 0.00 0.00 1.82
642 671 1.339151 ACCAGCAGAAAATCCCGTCTC 60.339 52.381 0.00 0.00 0.00 3.36
734 764 5.810080 AACTCTTCTAGTTGTAGCCTTGT 57.190 39.130 0.00 0.00 46.90 3.16
735 765 6.912951 AACTCTTCTAGTTGTAGCCTTGTA 57.087 37.500 0.00 0.00 46.90 2.41
736 766 6.518208 ACTCTTCTAGTTGTAGCCTTGTAG 57.482 41.667 0.00 0.00 33.35 2.74
737 767 5.419471 ACTCTTCTAGTTGTAGCCTTGTAGG 59.581 44.000 0.00 0.00 33.35 3.18
759 789 0.385723 GGATGAGATCGCGACGTACC 60.386 60.000 12.93 7.05 0.00 3.34
775 805 0.942410 TACCGACGACTGCTTTGCAC 60.942 55.000 0.00 0.00 33.79 4.57
891 939 3.508762 CGGCCGAATCCTATATACACAC 58.491 50.000 24.07 0.00 0.00 3.82
916 971 3.801068 CTCCTCGCTCCCTCCCGAT 62.801 68.421 0.00 0.00 32.52 4.18
954 1012 2.030007 ACAAGCCAACACCATTGATTCG 60.030 45.455 0.00 0.00 0.00 3.34
955 1013 0.527565 AGCCAACACCATTGATTCGC 59.472 50.000 0.00 0.00 0.00 4.70
956 1014 0.527565 GCCAACACCATTGATTCGCT 59.472 50.000 0.00 0.00 0.00 4.93
957 1015 1.742831 GCCAACACCATTGATTCGCTA 59.257 47.619 0.00 0.00 0.00 4.26
958 1016 2.223340 GCCAACACCATTGATTCGCTAG 60.223 50.000 0.00 0.00 0.00 3.42
959 1017 2.223340 CCAACACCATTGATTCGCTAGC 60.223 50.000 4.06 4.06 0.00 3.42
960 1018 2.679837 CAACACCATTGATTCGCTAGCT 59.320 45.455 13.93 0.00 0.00 3.32
961 1019 3.819564 ACACCATTGATTCGCTAGCTA 57.180 42.857 13.93 0.00 0.00 3.32
962 1020 3.458189 ACACCATTGATTCGCTAGCTAC 58.542 45.455 13.93 1.99 0.00 3.58
964 1022 3.492383 CACCATTGATTCGCTAGCTACAG 59.508 47.826 13.93 0.00 0.00 2.74
965 1023 3.133003 ACCATTGATTCGCTAGCTACAGT 59.867 43.478 13.93 1.79 0.00 3.55
967 1025 5.011125 ACCATTGATTCGCTAGCTACAGTAT 59.989 40.000 13.93 0.00 0.00 2.12
970 1028 5.363979 TGATTCGCTAGCTACAGTATCTG 57.636 43.478 13.93 0.00 37.52 2.90
971 1029 3.627732 TTCGCTAGCTACAGTATCTGC 57.372 47.619 13.93 0.00 34.37 4.26
972 1030 2.572290 TCGCTAGCTACAGTATCTGCA 58.428 47.619 13.93 0.00 34.37 4.41
989 1058 2.860136 CTGCAGATAAGCAAACGATCGA 59.140 45.455 24.34 0.00 45.13 3.59
990 1059 3.457234 TGCAGATAAGCAAACGATCGAT 58.543 40.909 24.34 7.21 42.46 3.59
993 1068 3.120286 CAGATAAGCAAACGATCGATCCG 59.880 47.826 24.34 16.00 0.00 4.18
1006 1081 0.460109 CGATCCGTGCAAGATGGACA 60.460 55.000 0.00 0.00 42.98 4.02
1008 1083 1.398390 GATCCGTGCAAGATGGACAAC 59.602 52.381 0.00 0.00 42.98 3.32
1010 1085 0.798776 CCGTGCAAGATGGACAACTC 59.201 55.000 0.00 0.00 38.73 3.01
1018 1093 2.501223 GATGGACAACTCCGGCGTGA 62.501 60.000 6.01 1.65 39.88 4.35
1019 1094 1.899437 ATGGACAACTCCGGCGTGAT 61.899 55.000 6.01 0.00 39.88 3.06
1021 1096 1.215647 GACAACTCCGGCGTGATCT 59.784 57.895 6.01 0.00 0.00 2.75
1026 1101 1.693627 ACTCCGGCGTGATCTTCTAT 58.306 50.000 6.01 0.00 0.00 1.98
1034 1121 1.300931 TGATCTTCTATGGCGGCGC 60.301 57.895 26.17 26.17 0.00 6.53
1176 1263 4.645921 GTGCGCCAGCCCAACAAC 62.646 66.667 4.18 0.00 44.33 3.32
1506 1642 4.344865 GGCTTGGCGGACCTGGAA 62.345 66.667 0.00 0.00 36.63 3.53
1577 1719 2.341257 GAGCATCTCACACATGAACGT 58.659 47.619 0.00 0.00 33.30 3.99
1578 1720 2.341257 AGCATCTCACACATGAACGTC 58.659 47.619 0.00 0.00 33.30 4.34
1649 1803 3.303938 ACTGATCGAGTGGGATTGATCT 58.696 45.455 0.00 0.00 39.79 2.75
1665 1819 1.881973 GATCTGGCAGTTTGTTGAGCA 59.118 47.619 15.27 0.00 0.00 4.26
1673 1827 2.032894 CAGTTTGTTGAGCACGATTCGT 60.033 45.455 5.75 5.75 42.36 3.85
1697 1851 1.410882 CTCCTGAGTCCTCCGAAATCC 59.589 57.143 0.00 0.00 0.00 3.01
1739 2036 1.581934 ATGGACGCACACCATATTCG 58.418 50.000 0.00 0.00 44.96 3.34
1740 2037 1.087202 TGGACGCACACCATATTCGC 61.087 55.000 0.00 0.00 32.03 4.70
1741 2038 1.087202 GGACGCACACCATATTCGCA 61.087 55.000 0.00 0.00 0.00 5.10
1756 2053 4.871993 ATTCGCATGAGCTAGTTTCAAG 57.128 40.909 0.00 1.44 39.10 3.02
1762 2064 0.093705 GAGCTAGTTTCAAGCACGCG 59.906 55.000 3.53 3.53 42.62 6.01
1770 2072 0.666274 TTCAAGCACGCGTACTCTGG 60.666 55.000 13.44 7.43 0.00 3.86
1771 2073 1.372997 CAAGCACGCGTACTCTGGT 60.373 57.895 13.44 0.91 0.00 4.00
1804 2116 6.320494 TCTTGAAAATTGGCGCTAAAACTA 57.680 33.333 11.18 0.00 0.00 2.24
1810 2122 1.141645 TGGCGCTAAAACTACACACG 58.858 50.000 7.64 0.00 0.00 4.49
1829 2141 2.028385 ACGTGAGCTAGTTTTGGTAGGG 60.028 50.000 0.00 0.00 0.00 3.53
1838 2150 4.498894 AGTTTTGGTAGGGGTATAGTGC 57.501 45.455 0.00 0.00 0.00 4.40
1839 2151 4.109320 AGTTTTGGTAGGGGTATAGTGCT 58.891 43.478 0.00 0.00 0.00 4.40
1846 2158 5.092259 GGTAGGGGTATAGTGCTAGGAAAT 58.908 45.833 0.00 0.00 0.00 2.17
1854 2166 7.928706 GGGTATAGTGCTAGGAAATATATGCAG 59.071 40.741 0.00 0.00 0.00 4.41
1876 2189 1.195448 CAGTTTGCTGAGCGGTTACAG 59.805 52.381 0.00 0.00 45.28 2.74
1882 3970 2.076863 GCTGAGCGGTTACAGACAATT 58.923 47.619 7.44 0.00 36.38 2.32
1885 3973 4.332819 GCTGAGCGGTTACAGACAATTTAT 59.667 41.667 7.44 0.00 36.38 1.40
1888 3976 5.813672 TGAGCGGTTACAGACAATTTATACC 59.186 40.000 0.00 0.00 0.00 2.73
1894 3982 7.222224 CGGTTACAGACAATTTATACCTCACTC 59.778 40.741 0.00 0.00 0.00 3.51
1895 3983 7.222224 GGTTACAGACAATTTATACCTCACTCG 59.778 40.741 0.00 0.00 0.00 4.18
1896 3984 6.525578 ACAGACAATTTATACCTCACTCGA 57.474 37.500 0.00 0.00 0.00 4.04
1897 3985 6.565234 ACAGACAATTTATACCTCACTCGAG 58.435 40.000 11.84 11.84 39.16 4.04
1898 3986 6.377429 ACAGACAATTTATACCTCACTCGAGA 59.623 38.462 21.68 0.00 42.34 4.04
1899 3987 7.068839 ACAGACAATTTATACCTCACTCGAGAT 59.931 37.037 21.68 3.10 42.34 2.75
1900 3988 7.923344 CAGACAATTTATACCTCACTCGAGATT 59.077 37.037 21.68 0.86 42.34 2.40
1936 4025 7.168219 TCCATGTAAATAGCTCTGTCAAAAGT 58.832 34.615 0.00 0.00 0.00 2.66
1966 4055 7.425224 ACTCTACCTTGTAAATACTGCAGAT 57.575 36.000 23.35 6.78 0.00 2.90
1967 4056 7.493367 ACTCTACCTTGTAAATACTGCAGATC 58.507 38.462 23.35 4.35 0.00 2.75
2026 4117 9.727627 GAGAGCAATTATAAAGATTCACCAAAG 57.272 33.333 0.00 0.00 0.00 2.77
2071 4210 6.910536 AAAACTACATCGAGATCCATGAAC 57.089 37.500 0.00 0.00 0.00 3.18
2072 4211 5.598416 AACTACATCGAGATCCATGAACA 57.402 39.130 0.00 0.00 0.00 3.18
2076 4215 5.027293 ACATCGAGATCCATGAACAATCA 57.973 39.130 0.00 0.00 40.57 2.57
2100 4239 4.277593 TGCCGCCGCCAAAACAAG 62.278 61.111 0.00 0.00 0.00 3.16
2102 4241 2.415426 CCGCCGCCAAAACAAGTT 59.585 55.556 0.00 0.00 0.00 2.66
2104 4243 1.226831 CGCCGCCAAAACAAGTTGT 60.227 52.632 1.64 1.64 0.00 3.32
2111 4250 3.303461 CGCCAAAACAAGTTGTCGACATA 60.303 43.478 20.80 7.70 31.84 2.29
2128 4267 2.011741 ATATCGTTGTCGCCGCTCCA 62.012 55.000 0.00 0.00 36.96 3.86
2143 4300 1.350193 CTCCACCGTGTCGATGAAAG 58.650 55.000 0.00 0.00 0.00 2.62
2148 4305 1.011968 CCGTGTCGATGAAAGCCGAA 61.012 55.000 0.00 0.00 36.50 4.30
2149 4306 0.093026 CGTGTCGATGAAAGCCGAAC 59.907 55.000 0.00 0.00 36.50 3.95
2156 4313 2.092838 CGATGAAAGCCGAACAGTCTTC 59.907 50.000 0.00 0.00 0.00 2.87
2159 4316 2.034939 TGAAAGCCGAACAGTCTTCGTA 59.965 45.455 0.00 0.00 40.04 3.43
2171 4328 4.512944 ACAGTCTTCGTACACGTTTCTCTA 59.487 41.667 1.19 0.00 40.80 2.43
2175 4332 4.756642 TCTTCGTACACGTTTCTCTAAGGA 59.243 41.667 1.19 0.00 40.80 3.36
2178 4335 2.719426 ACACGTTTCTCTAAGGACCG 57.281 50.000 0.00 0.00 0.00 4.79
2188 4345 0.247736 CTAAGGACCGAGCTGCACTT 59.752 55.000 1.02 0.00 0.00 3.16
2208 4383 5.354234 CACTTGTAGCCGTTGAATCCTTTAT 59.646 40.000 0.00 0.00 0.00 1.40
2211 4386 6.189677 TGTAGCCGTTGAATCCTTTATTTG 57.810 37.500 0.00 0.00 0.00 2.32
2214 4389 7.771361 TGTAGCCGTTGAATCCTTTATTTGATA 59.229 33.333 0.00 0.00 0.00 2.15
2235 4410 8.357796 TGATATGAAGAATCTGACACGAAATC 57.642 34.615 0.00 0.00 0.00 2.17
2247 4422 1.340465 CGAAATCTCGTCGTTGCGG 59.660 57.895 0.00 0.00 40.33 5.69
2255 4430 4.025401 GTCGTTGCGGGTGCCTTG 62.025 66.667 0.00 0.00 41.78 3.61
2260 4435 3.429372 TTGCGGGTGCCTTGACCTT 62.429 57.895 0.00 0.00 41.78 3.50
2261 4436 3.365265 GCGGGTGCCTTGACCTTG 61.365 66.667 0.00 0.00 36.14 3.61
2263 4438 2.116125 GGGTGCCTTGACCTTGCT 59.884 61.111 0.00 0.00 36.14 3.91
2266 4441 2.598394 TGCCTTGACCTTGCTGCC 60.598 61.111 0.00 0.00 0.00 4.85
2276 4451 3.767816 TTGCTGCCCAAGAAGCTG 58.232 55.556 0.00 0.00 40.21 4.24
2277 4452 1.904865 TTGCTGCCCAAGAAGCTGG 60.905 57.895 0.00 0.00 40.21 4.85
2278 4453 3.756727 GCTGCCCAAGAAGCTGGC 61.757 66.667 5.08 5.08 45.56 4.85
2281 4456 2.034687 GCCCAAGAAGCTGGCAGA 59.965 61.111 20.86 0.00 44.70 4.26
2282 4457 1.604593 GCCCAAGAAGCTGGCAGAA 60.605 57.895 20.86 0.00 44.70 3.02
2283 4458 1.871126 GCCCAAGAAGCTGGCAGAAC 61.871 60.000 20.86 8.27 44.70 3.01
2304 4483 3.887716 ACATGCCCAAGCTTCATCTAATC 59.112 43.478 0.00 0.00 40.80 1.75
2305 4484 2.936202 TGCCCAAGCTTCATCTAATCC 58.064 47.619 0.00 0.00 40.80 3.01
2306 4485 2.241941 TGCCCAAGCTTCATCTAATCCA 59.758 45.455 0.00 0.00 40.80 3.41
2307 4486 3.117398 TGCCCAAGCTTCATCTAATCCAT 60.117 43.478 0.00 0.00 40.80 3.41
2308 4487 3.505293 GCCCAAGCTTCATCTAATCCATC 59.495 47.826 0.00 0.00 35.50 3.51
2310 4489 4.446745 CCCAAGCTTCATCTAATCCATCCA 60.447 45.833 0.00 0.00 0.00 3.41
2313 4492 6.239396 CAAGCTTCATCTAATCCATCCAGAT 58.761 40.000 0.00 0.00 0.00 2.90
2327 4506 2.525368 TCCAGATGGACGAACTTGAGA 58.475 47.619 0.00 0.00 39.78 3.27
2328 4507 2.493675 TCCAGATGGACGAACTTGAGAG 59.506 50.000 0.00 0.00 39.78 3.20
2332 4511 1.938585 TGGACGAACTTGAGAGGGAT 58.061 50.000 0.00 0.00 0.00 3.85
2333 4512 2.257207 TGGACGAACTTGAGAGGGATT 58.743 47.619 0.00 0.00 0.00 3.01
2337 4516 4.315803 GACGAACTTGAGAGGGATTGAAA 58.684 43.478 0.00 0.00 0.00 2.69
2340 4519 3.059352 ACTTGAGAGGGATTGAAACCG 57.941 47.619 0.00 0.00 0.00 4.44
2368 4547 2.647529 TAATCGAAGAAGCAGCGTCA 57.352 45.000 11.18 0.00 43.58 4.35
2371 4550 0.528017 TCGAAGAAGCAGCGTCATCT 59.472 50.000 11.18 0.00 0.00 2.90
2372 4551 0.644331 CGAAGAAGCAGCGTCATCTG 59.356 55.000 11.18 1.80 37.15 2.90
2373 4552 1.719600 GAAGAAGCAGCGTCATCTGT 58.280 50.000 11.18 0.00 36.49 3.41
2376 4558 0.390340 GAAGCAGCGTCATCTGTCCA 60.390 55.000 3.11 0.00 36.49 4.02
2382 4564 1.291877 GCGTCATCTGTCCAAGCGTT 61.292 55.000 0.00 0.00 0.00 4.84
2383 4565 0.716108 CGTCATCTGTCCAAGCGTTC 59.284 55.000 0.00 0.00 0.00 3.95
2390 4572 1.376037 GTCCAAGCGTTCCTCCTGG 60.376 63.158 0.00 0.00 0.00 4.45
2448 4630 0.977395 GGTATCAGGATTCCCCTCCG 59.023 60.000 0.00 0.00 45.60 4.63
2450 4632 1.185618 TATCAGGATTCCCCTCCGCG 61.186 60.000 0.00 0.00 45.60 6.46
2451 4633 3.470888 CAGGATTCCCCTCCGCGT 61.471 66.667 4.92 0.00 45.60 6.01
2452 4634 3.155167 AGGATTCCCCTCCGCGTC 61.155 66.667 4.92 0.00 43.31 5.19
2459 4641 4.003788 CCCTCCGCGTCACCAACT 62.004 66.667 4.92 0.00 0.00 3.16
2470 4652 0.685097 TCACCAACTACCAGAGTGGC 59.315 55.000 0.00 0.00 42.67 5.01
2471 4653 0.670546 CACCAACTACCAGAGTGGCG 60.671 60.000 0.00 0.00 42.67 5.69
2479 4661 1.379977 CCAGAGTGGCGGGTAGAGA 60.380 63.158 0.00 0.00 0.00 3.10
2480 4662 1.388065 CCAGAGTGGCGGGTAGAGAG 61.388 65.000 0.00 0.00 0.00 3.20
2485 4667 2.363925 GGCGGGTAGAGAGGTGGT 60.364 66.667 0.00 0.00 0.00 4.16
2486 4668 2.722201 GGCGGGTAGAGAGGTGGTG 61.722 68.421 0.00 0.00 0.00 4.17
2500 4682 1.836391 TGGTGAATCCATAGGGCCG 59.164 57.895 0.00 0.00 41.93 6.13
2505 4687 3.537206 AATCCATAGGGCCGCGAGC 62.537 63.158 8.23 9.71 42.60 5.03
2523 4705 1.202806 AGCTGAGATCGAGAGGAGGAG 60.203 57.143 0.00 0.00 0.00 3.69
2529 4711 0.031616 ATCGAGAGGAGGAGGGCTTT 60.032 55.000 0.00 0.00 0.00 3.51
2532 4714 1.681486 GAGAGGAGGAGGGCTTTCCG 61.681 65.000 3.52 0.00 42.29 4.30
2539 4721 1.302511 GAGGGCTTTCCGCTTGTCA 60.303 57.895 0.00 0.00 41.52 3.58
2541 4723 1.896660 GGGCTTTCCGCTTGTCACA 60.897 57.895 0.00 0.00 39.13 3.58
2544 4726 1.000274 GGCTTTCCGCTTGTCACATTT 60.000 47.619 0.00 0.00 39.13 2.32
2570 4752 6.018994 CACCATAGTTATTTCCGCTACACTTC 60.019 42.308 0.00 0.00 0.00 3.01
2593 4776 3.001514 GCCTCCCATCAGCCTCAA 58.998 61.111 0.00 0.00 0.00 3.02
2596 4779 1.153289 CTCCCATCAGCCTCAACCG 60.153 63.158 0.00 0.00 0.00 4.44
2597 4780 1.903877 CTCCCATCAGCCTCAACCGT 61.904 60.000 0.00 0.00 0.00 4.83
2598 4781 1.450312 CCCATCAGCCTCAACCGTC 60.450 63.158 0.00 0.00 0.00 4.79
2599 4782 1.450312 CCATCAGCCTCAACCGTCC 60.450 63.158 0.00 0.00 0.00 4.79
2602 4785 1.194781 ATCAGCCTCAACCGTCCACT 61.195 55.000 0.00 0.00 0.00 4.00
2603 4786 1.374758 CAGCCTCAACCGTCCACTC 60.375 63.158 0.00 0.00 0.00 3.51
2604 4787 1.837051 AGCCTCAACCGTCCACTCA 60.837 57.895 0.00 0.00 0.00 3.41
2605 4788 1.374758 GCCTCAACCGTCCACTCAG 60.375 63.158 0.00 0.00 0.00 3.35
2606 4789 1.374758 CCTCAACCGTCCACTCAGC 60.375 63.158 0.00 0.00 0.00 4.26
2607 4790 1.734477 CTCAACCGTCCACTCAGCG 60.734 63.158 0.00 0.00 0.00 5.18
2608 4791 3.414700 CAACCGTCCACTCAGCGC 61.415 66.667 0.00 0.00 0.00 5.92
2609 4792 3.616721 AACCGTCCACTCAGCGCT 61.617 61.111 2.64 2.64 0.00 5.92
2610 4793 2.273179 AACCGTCCACTCAGCGCTA 61.273 57.895 10.99 0.00 0.00 4.26
2611 4794 1.605058 AACCGTCCACTCAGCGCTAT 61.605 55.000 10.99 0.00 0.00 2.97
2612 4795 0.750546 ACCGTCCACTCAGCGCTATA 60.751 55.000 10.99 0.00 0.00 1.31
2613 4796 0.039978 CCGTCCACTCAGCGCTATAG 60.040 60.000 10.99 13.83 0.00 1.31
2614 4797 0.039978 CGTCCACTCAGCGCTATAGG 60.040 60.000 10.99 10.46 0.00 2.57
2615 4798 1.319541 GTCCACTCAGCGCTATAGGA 58.680 55.000 10.99 12.89 0.00 2.94
2616 4799 1.001158 GTCCACTCAGCGCTATAGGAC 60.001 57.143 24.94 24.94 37.50 3.85
2617 4800 0.315568 CCACTCAGCGCTATAGGACC 59.684 60.000 10.99 0.00 0.00 4.46
2618 4801 0.039978 CACTCAGCGCTATAGGACCG 60.040 60.000 10.99 0.00 0.00 4.79
2622 4805 4.675404 GCGCTATAGGACCGCAAT 57.325 55.556 15.54 0.00 46.32 3.56
2623 4806 2.446341 GCGCTATAGGACCGCAATC 58.554 57.895 15.54 0.00 46.32 2.67
2624 4807 0.319555 GCGCTATAGGACCGCAATCA 60.320 55.000 15.54 0.00 46.32 2.57
2625 4808 1.419374 CGCTATAGGACCGCAATCAC 58.581 55.000 1.04 0.00 0.00 3.06
2626 4809 1.797025 GCTATAGGACCGCAATCACC 58.203 55.000 1.04 0.00 0.00 4.02
2627 4810 1.070134 GCTATAGGACCGCAATCACCA 59.930 52.381 1.04 0.00 0.00 4.17
2628 4811 2.755650 CTATAGGACCGCAATCACCAC 58.244 52.381 0.00 0.00 0.00 4.16
2629 4812 1.204146 ATAGGACCGCAATCACCACT 58.796 50.000 0.00 0.00 0.00 4.00
2630 4813 0.981183 TAGGACCGCAATCACCACTT 59.019 50.000 0.00 0.00 0.00 3.16
2631 4814 0.606401 AGGACCGCAATCACCACTTG 60.606 55.000 0.00 0.00 0.00 3.16
2632 4815 0.605319 GGACCGCAATCACCACTTGA 60.605 55.000 0.00 0.00 39.11 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.921976 TCTGCATACAAAGCAAATTGAACTG 59.078 36.000 0.00 0.00 42.17 3.16
28 30 6.715344 ATTGTCTGCATACAAAGCAAATTG 57.285 33.333 19.93 0.00 42.33 2.32
42 44 1.006086 CGACGCCATTATTGTCTGCA 58.994 50.000 0.00 0.00 0.00 4.41
55 57 2.330745 GTCCTACCGATCGACGCC 59.669 66.667 18.66 0.00 41.07 5.68
56 58 2.052414 CGTCCTACCGATCGACGC 60.052 66.667 18.66 0.00 42.37 5.19
63 65 1.358725 CGTCCGTTACGTCCTACCGA 61.359 60.000 3.52 0.00 46.72 4.69
78 83 0.899720 TTGTCCATCTGTACCCGTCC 59.100 55.000 0.00 0.00 0.00 4.79
84 89 3.929610 GAGCACTCTTTGTCCATCTGTAC 59.070 47.826 0.00 0.00 0.00 2.90
85 90 3.367395 CGAGCACTCTTTGTCCATCTGTA 60.367 47.826 0.00 0.00 0.00 2.74
87 92 1.998315 CGAGCACTCTTTGTCCATCTG 59.002 52.381 0.00 0.00 0.00 2.90
115 120 9.127006 GTAGTTTTTCCGTCTTTTGTTTGTTTA 57.873 29.630 0.00 0.00 0.00 2.01
123 128 3.942739 TGCGTAGTTTTTCCGTCTTTTG 58.057 40.909 0.00 0.00 0.00 2.44
126 131 3.432252 CAGATGCGTAGTTTTTCCGTCTT 59.568 43.478 0.00 0.00 0.00 3.01
132 137 6.461698 CGACATAAACAGATGCGTAGTTTTTC 59.538 38.462 12.53 7.72 36.85 2.29
139 144 2.198406 GCCGACATAAACAGATGCGTA 58.802 47.619 0.00 0.00 0.00 4.42
144 149 0.459585 ACGCGCCGACATAAACAGAT 60.460 50.000 5.73 0.00 0.00 2.90
149 154 2.816083 CCCACGCGCCGACATAAA 60.816 61.111 5.73 0.00 0.00 1.40
161 166 0.179161 CAGTTAGAGCGACTCCCACG 60.179 60.000 3.66 0.00 0.00 4.94
162 167 0.458716 GCAGTTAGAGCGACTCCCAC 60.459 60.000 3.66 1.94 0.00 4.61
163 168 0.612174 AGCAGTTAGAGCGACTCCCA 60.612 55.000 3.66 0.00 37.01 4.37
164 169 0.179124 CAGCAGTTAGAGCGACTCCC 60.179 60.000 3.66 0.00 37.01 4.30
165 170 0.811915 TCAGCAGTTAGAGCGACTCC 59.188 55.000 3.66 0.00 37.01 3.85
170 175 2.354109 TGAAGTCAGCAGTTAGAGCG 57.646 50.000 0.00 0.00 37.01 5.03
179 184 0.376852 GTGTTGCGTTGAAGTCAGCA 59.623 50.000 0.00 0.00 37.89 4.41
182 187 1.933181 CTCTGTGTTGCGTTGAAGTCA 59.067 47.619 0.00 0.00 0.00 3.41
183 188 1.933853 ACTCTGTGTTGCGTTGAAGTC 59.066 47.619 0.00 0.00 0.00 3.01
184 189 1.933853 GACTCTGTGTTGCGTTGAAGT 59.066 47.619 0.00 0.00 0.00 3.01
185 190 1.071239 CGACTCTGTGTTGCGTTGAAG 60.071 52.381 0.00 0.00 0.00 3.02
186 191 0.927537 CGACTCTGTGTTGCGTTGAA 59.072 50.000 0.00 0.00 0.00 2.69
187 192 1.487452 GCGACTCTGTGTTGCGTTGA 61.487 55.000 6.35 0.00 45.05 3.18
188 193 1.083401 GCGACTCTGTGTTGCGTTG 60.083 57.895 6.35 0.00 45.05 4.10
189 194 3.319904 GCGACTCTGTGTTGCGTT 58.680 55.556 6.35 0.00 45.05 4.84
193 198 1.151777 AACGTGGCGACTCTGTGTTG 61.152 55.000 0.00 0.00 0.00 3.33
293 298 1.674359 TCCTTTTGCGTGCTCTTTGA 58.326 45.000 0.00 0.00 0.00 2.69
312 317 1.953686 TCAGCTTAACCTTGCGCTTTT 59.046 42.857 9.73 0.00 0.00 2.27
313 318 1.266989 GTCAGCTTAACCTTGCGCTTT 59.733 47.619 9.73 0.00 0.00 3.51
314 319 0.875059 GTCAGCTTAACCTTGCGCTT 59.125 50.000 9.73 0.00 0.00 4.68
315 320 1.291877 CGTCAGCTTAACCTTGCGCT 61.292 55.000 9.73 0.00 0.00 5.92
316 321 1.132640 CGTCAGCTTAACCTTGCGC 59.867 57.895 0.00 0.00 0.00 6.09
317 322 0.163788 CACGTCAGCTTAACCTTGCG 59.836 55.000 0.00 0.00 0.00 4.85
553 563 0.535328 TGGTAGAGCTCCGGATCTCG 60.535 60.000 25.41 6.86 39.16 4.04
559 569 0.739561 GTGTACTGGTAGAGCTCCGG 59.260 60.000 10.93 3.33 37.36 5.14
580 608 2.828520 CTGTGTCAGTGGGTCAGACTAT 59.171 50.000 0.00 0.00 34.36 2.12
590 618 1.350193 GCATCGTACTGTGTCAGTGG 58.650 55.000 11.92 4.96 45.01 4.00
616 644 1.203287 GGATTTTCTGCTGGTCTTGGC 59.797 52.381 0.00 0.00 0.00 4.52
621 649 1.087501 GACGGGATTTTCTGCTGGTC 58.912 55.000 0.00 0.00 0.00 4.02
626 654 2.003301 GACAGAGACGGGATTTTCTGC 58.997 52.381 0.59 0.00 40.47 4.26
730 760 1.336332 CGATCTCATCCGGCCTACAAG 60.336 57.143 0.00 0.00 0.00 3.16
732 762 1.806461 GCGATCTCATCCGGCCTACA 61.806 60.000 0.00 0.00 0.00 2.74
733 763 1.080434 GCGATCTCATCCGGCCTAC 60.080 63.158 0.00 0.00 0.00 3.18
734 764 2.626780 CGCGATCTCATCCGGCCTA 61.627 63.158 0.00 0.00 0.00 3.93
735 765 3.983494 CGCGATCTCATCCGGCCT 61.983 66.667 0.00 0.00 0.00 5.19
736 766 3.978491 TCGCGATCTCATCCGGCC 61.978 66.667 3.71 0.00 0.00 6.13
737 767 2.731348 GTCGCGATCTCATCCGGC 60.731 66.667 14.06 0.00 0.00 6.13
738 768 1.838568 TACGTCGCGATCTCATCCGG 61.839 60.000 14.06 0.00 0.00 5.14
759 789 2.551270 GGTGCAAAGCAGTCGTCG 59.449 61.111 0.00 0.00 40.08 5.12
891 939 4.244802 GGAGCGAGGAGAGCGACG 62.245 72.222 0.00 0.00 40.04 5.12
916 971 3.932710 GCTTGTGATCGAGGTTTGTATGA 59.067 43.478 0.00 0.00 0.00 2.15
954 1012 4.782019 ATCTGCAGATACTGTAGCTAGC 57.218 45.455 27.73 6.62 42.46 3.42
955 1013 6.072230 TGCTTATCTGCAGATACTGTAGCTAG 60.072 42.308 35.46 27.41 42.46 3.42
956 1014 5.770162 TGCTTATCTGCAGATACTGTAGCTA 59.230 40.000 35.46 26.33 42.46 3.32
957 1015 4.586421 TGCTTATCTGCAGATACTGTAGCT 59.414 41.667 35.46 18.13 42.46 3.32
958 1016 4.876125 TGCTTATCTGCAGATACTGTAGC 58.124 43.478 32.64 32.64 42.46 3.58
959 1017 6.074623 CGTTTGCTTATCTGCAGATACTGTAG 60.075 42.308 31.46 25.81 43.73 2.74
960 1018 5.748630 CGTTTGCTTATCTGCAGATACTGTA 59.251 40.000 31.46 23.22 44.27 2.74
961 1019 4.568359 CGTTTGCTTATCTGCAGATACTGT 59.432 41.667 31.46 13.52 44.27 3.55
962 1020 4.805719 TCGTTTGCTTATCTGCAGATACTG 59.194 41.667 31.46 26.12 44.27 2.74
964 1022 5.387855 CGATCGTTTGCTTATCTGCAGATAC 60.388 44.000 31.46 22.36 44.27 2.24
965 1023 4.681483 CGATCGTTTGCTTATCTGCAGATA 59.319 41.667 28.69 28.69 44.27 1.98
967 1025 2.860136 CGATCGTTTGCTTATCTGCAGA 59.140 45.455 20.79 20.79 44.27 4.26
970 1028 3.120854 GGATCGATCGTTTGCTTATCTGC 60.121 47.826 18.81 0.00 0.00 4.26
971 1029 3.120286 CGGATCGATCGTTTGCTTATCTG 59.880 47.826 18.81 9.77 0.00 2.90
972 1030 3.243434 ACGGATCGATCGTTTGCTTATCT 60.243 43.478 18.81 0.00 37.61 1.98
989 1058 1.003580 AGTTGTCCATCTTGCACGGAT 59.996 47.619 0.00 0.00 0.00 4.18
990 1059 0.396435 AGTTGTCCATCTTGCACGGA 59.604 50.000 0.00 0.00 0.00 4.69
993 1068 0.798776 CGGAGTTGTCCATCTTGCAC 59.201 55.000 0.00 0.00 44.18 4.57
1006 1081 1.471119 TAGAAGATCACGCCGGAGTT 58.529 50.000 8.62 0.00 0.00 3.01
1008 1083 1.336332 CCATAGAAGATCACGCCGGAG 60.336 57.143 5.05 3.72 0.00 4.63
1010 1085 0.946221 GCCATAGAAGATCACGCCGG 60.946 60.000 0.00 0.00 0.00 6.13
1018 1093 0.608130 TATGCGCCGCCATAGAAGAT 59.392 50.000 6.63 0.00 0.00 2.40
1019 1094 0.319555 GTATGCGCCGCCATAGAAGA 60.320 55.000 6.63 0.00 0.00 2.87
1021 1096 1.663388 CGTATGCGCCGCCATAGAA 60.663 57.895 6.63 0.00 0.00 2.10
1034 1121 2.204491 GACATCACCGTCGCGTATG 58.796 57.895 5.77 4.56 0.00 2.39
1649 1803 0.746204 TCGTGCTCAACAAACTGCCA 60.746 50.000 0.00 0.00 0.00 4.92
1665 1819 1.000955 ACTCAGGAGCAAACGAATCGT 59.999 47.619 0.96 0.96 43.97 3.73
1673 1827 0.541998 TCGGAGGACTCAGGAGCAAA 60.542 55.000 1.32 0.00 0.00 3.68
1697 1851 1.267261 GACACTCCCCTATCGATCGTG 59.733 57.143 15.94 5.01 0.00 4.35
1730 2027 4.342862 AACTAGCTCATGCGAATATGGT 57.657 40.909 0.00 0.00 45.42 3.55
1734 2031 4.271049 GCTTGAAACTAGCTCATGCGAATA 59.729 41.667 13.97 0.00 45.42 1.75
1736 2033 2.416547 GCTTGAAACTAGCTCATGCGAA 59.583 45.455 13.97 0.00 45.42 4.70
1737 2034 2.002586 GCTTGAAACTAGCTCATGCGA 58.997 47.619 13.97 0.00 45.42 5.10
1739 2036 2.475187 CGTGCTTGAAACTAGCTCATGC 60.475 50.000 18.94 18.94 41.78 4.06
1740 2037 2.475187 GCGTGCTTGAAACTAGCTCATG 60.475 50.000 0.00 0.00 39.38 3.07
1741 2038 1.734465 GCGTGCTTGAAACTAGCTCAT 59.266 47.619 0.00 0.00 39.38 2.90
1756 2053 0.163146 GAAAACCAGAGTACGCGTGC 59.837 55.000 24.59 22.34 0.00 5.34
1762 2064 5.763204 TCAAGAACATGGAAAACCAGAGTAC 59.237 40.000 0.00 0.00 0.00 2.73
1770 2072 6.429624 GCCAATTTTCAAGAACATGGAAAAC 58.570 36.000 8.41 0.00 41.62 2.43
1771 2073 5.236047 CGCCAATTTTCAAGAACATGGAAAA 59.764 36.000 8.60 8.60 42.60 2.29
1777 2084 3.665745 AGCGCCAATTTTCAAGAACAT 57.334 38.095 2.29 0.00 0.00 2.71
1790 2097 1.527736 CGTGTGTAGTTTTAGCGCCAA 59.472 47.619 2.29 0.00 0.00 4.52
1804 2116 2.210116 CCAAAACTAGCTCACGTGTGT 58.790 47.619 16.51 6.68 0.00 3.72
1810 2122 2.305052 ACCCCTACCAAAACTAGCTCAC 59.695 50.000 0.00 0.00 0.00 3.51
1829 2141 7.439655 GCTGCATATATTTCCTAGCACTATACC 59.560 40.741 0.00 0.00 0.00 2.73
1838 2150 6.569226 GCAAACTGGCTGCATATATTTCCTAG 60.569 42.308 0.50 0.00 39.69 3.02
1839 2151 5.241506 GCAAACTGGCTGCATATATTTCCTA 59.758 40.000 0.50 0.00 39.69 2.94
1854 2166 1.234615 TAACCGCTCAGCAAACTGGC 61.235 55.000 0.00 0.00 44.59 4.85
1868 2181 7.039882 AGTGAGGTATAAATTGTCTGTAACCG 58.960 38.462 0.00 0.00 0.00 4.44
1876 2189 8.649973 AAATCTCGAGTGAGGTATAAATTGTC 57.350 34.615 13.13 0.00 42.79 3.18
1943 4032 6.926272 GGATCTGCAGTATTTACAAGGTAGAG 59.074 42.308 14.67 0.00 0.00 2.43
1944 4033 6.611642 AGGATCTGCAGTATTTACAAGGTAGA 59.388 38.462 14.67 0.00 0.00 2.59
1945 4034 6.821388 AGGATCTGCAGTATTTACAAGGTAG 58.179 40.000 14.67 0.00 0.00 3.18
1946 4035 6.808321 AGGATCTGCAGTATTTACAAGGTA 57.192 37.500 14.67 0.00 0.00 3.08
1947 4036 5.700402 AGGATCTGCAGTATTTACAAGGT 57.300 39.130 14.67 0.00 0.00 3.50
1948 4037 8.682936 ATTAAGGATCTGCAGTATTTACAAGG 57.317 34.615 14.67 0.00 0.00 3.61
1996 4085 9.060347 GGTGAATCTTTATAATTGCTCTCATCA 57.940 33.333 0.00 0.00 0.00 3.07
2002 4091 7.975616 TGCTTTGGTGAATCTTTATAATTGCTC 59.024 33.333 0.00 0.00 0.00 4.26
2004 4093 8.477984 TTGCTTTGGTGAATCTTTATAATTGC 57.522 30.769 0.00 0.00 0.00 3.56
2017 4108 1.408702 GAGGTGCTTTGCTTTGGTGAA 59.591 47.619 0.00 0.00 0.00 3.18
2021 4112 2.204237 GTTTGAGGTGCTTTGCTTTGG 58.796 47.619 0.00 0.00 0.00 3.28
2026 4117 7.650834 TTTTATTATGTTTGAGGTGCTTTGC 57.349 32.000 0.00 0.00 0.00 3.68
2059 4198 5.416952 AGTGGTTTGATTGTTCATGGATCTC 59.583 40.000 0.00 0.00 0.00 2.75
2062 4201 4.322198 GCAGTGGTTTGATTGTTCATGGAT 60.322 41.667 0.00 0.00 0.00 3.41
2069 4208 0.031994 GCGGCAGTGGTTTGATTGTT 59.968 50.000 0.00 0.00 0.00 2.83
2071 4210 1.080569 GGCGGCAGTGGTTTGATTG 60.081 57.895 3.07 0.00 0.00 2.67
2072 4211 2.625823 CGGCGGCAGTGGTTTGATT 61.626 57.895 10.53 0.00 0.00 2.57
2111 4250 4.063967 TGGAGCGGCGACAACGAT 62.064 61.111 12.98 0.00 42.66 3.73
2128 4267 1.736645 CGGCTTTCATCGACACGGT 60.737 57.895 0.00 0.00 0.00 4.83
2131 4288 1.126846 CTGTTCGGCTTTCATCGACAC 59.873 52.381 0.00 0.00 34.99 3.67
2133 4290 1.390463 GACTGTTCGGCTTTCATCGAC 59.610 52.381 0.00 0.00 34.99 4.20
2143 4300 1.058404 GTGTACGAAGACTGTTCGGC 58.942 55.000 12.48 5.91 45.34 5.54
2148 4305 3.314635 AGAGAAACGTGTACGAAGACTGT 59.685 43.478 11.79 1.44 43.02 3.55
2149 4306 3.886549 AGAGAAACGTGTACGAAGACTG 58.113 45.455 11.79 0.00 43.02 3.51
2156 4313 3.496155 GGTCCTTAGAGAAACGTGTACG 58.504 50.000 2.43 2.43 46.33 3.67
2159 4316 2.228343 CTCGGTCCTTAGAGAAACGTGT 59.772 50.000 0.00 0.00 36.65 4.49
2171 4328 1.302033 CAAGTGCAGCTCGGTCCTT 60.302 57.895 0.00 0.00 0.00 3.36
2175 4332 1.374758 GCTACAAGTGCAGCTCGGT 60.375 57.895 0.00 0.00 34.86 4.69
2178 4335 0.951040 AACGGCTACAAGTGCAGCTC 60.951 55.000 3.63 0.00 37.91 4.09
2188 4345 5.941058 TCAAATAAAGGATTCAACGGCTACA 59.059 36.000 0.00 0.00 0.00 2.74
2208 4383 8.546597 TTTCGTGTCAGATTCTTCATATCAAA 57.453 30.769 0.00 0.00 0.00 2.69
2211 4386 8.586570 AGATTTCGTGTCAGATTCTTCATATC 57.413 34.615 0.00 0.00 0.00 1.63
2214 4389 5.518128 CGAGATTTCGTGTCAGATTCTTCAT 59.482 40.000 0.00 0.00 41.84 2.57
2230 4405 1.012486 ACCCGCAACGACGAGATTTC 61.012 55.000 0.00 0.00 34.06 2.17
2239 4414 4.243008 TCAAGGCACCCGCAACGA 62.243 61.111 0.00 0.00 41.24 3.85
2247 4422 2.924105 GCAGCAAGGTCAAGGCACC 61.924 63.158 0.00 0.00 36.58 5.01
2253 4428 0.106268 TTCTTGGGCAGCAAGGTCAA 60.106 50.000 0.00 0.00 0.00 3.18
2255 4430 1.871126 GCTTCTTGGGCAGCAAGGTC 61.871 60.000 0.00 0.00 35.95 3.85
2260 4435 2.282674 CCAGCTTCTTGGGCAGCA 60.283 61.111 0.00 0.00 38.61 4.41
2261 4436 3.756727 GCCAGCTTCTTGGGCAGC 61.757 66.667 7.12 0.00 46.92 5.25
2266 4441 1.201647 CATGTTCTGCCAGCTTCTTGG 59.798 52.381 0.00 0.00 41.35 3.61
2278 4453 1.250328 TGAAGCTTGGGCATGTTCTG 58.750 50.000 2.10 0.00 41.70 3.02
2279 4454 2.097825 GATGAAGCTTGGGCATGTTCT 58.902 47.619 2.10 0.00 41.70 3.01
2280 4455 2.097825 AGATGAAGCTTGGGCATGTTC 58.902 47.619 2.10 0.00 41.70 3.18
2281 4456 2.226962 AGATGAAGCTTGGGCATGTT 57.773 45.000 2.10 0.00 41.70 2.71
2282 4457 3.370840 TTAGATGAAGCTTGGGCATGT 57.629 42.857 2.10 2.35 41.70 3.21
2283 4458 3.255149 GGATTAGATGAAGCTTGGGCATG 59.745 47.826 2.10 0.00 41.70 4.06
2289 4468 5.618236 TCTGGATGGATTAGATGAAGCTTG 58.382 41.667 2.10 0.00 0.00 4.01
2307 4486 2.493675 CTCTCAAGTTCGTCCATCTGGA 59.506 50.000 0.00 0.00 43.08 3.86
2308 4487 2.417924 CCTCTCAAGTTCGTCCATCTGG 60.418 54.545 0.00 0.00 0.00 3.86
2310 4489 1.827969 CCCTCTCAAGTTCGTCCATCT 59.172 52.381 0.00 0.00 0.00 2.90
2313 4492 1.938585 ATCCCTCTCAAGTTCGTCCA 58.061 50.000 0.00 0.00 0.00 4.02
2316 4495 4.065789 GTTTCAATCCCTCTCAAGTTCGT 58.934 43.478 0.00 0.00 0.00 3.85
2317 4496 3.437049 GGTTTCAATCCCTCTCAAGTTCG 59.563 47.826 0.00 0.00 0.00 3.95
2347 4526 3.322369 TGACGCTGCTTCTTCGATTAAA 58.678 40.909 7.67 0.00 0.00 1.52
2349 4528 2.647529 TGACGCTGCTTCTTCGATTA 57.352 45.000 7.67 0.00 0.00 1.75
2361 4540 1.690283 CGCTTGGACAGATGACGCTG 61.690 60.000 0.00 0.00 41.63 5.18
2368 4547 0.250513 GGAGGAACGCTTGGACAGAT 59.749 55.000 0.00 0.00 0.00 2.90
2371 4550 1.371183 CAGGAGGAACGCTTGGACA 59.629 57.895 0.00 0.00 30.60 4.02
2372 4551 4.285851 CAGGAGGAACGCTTGGAC 57.714 61.111 0.00 0.00 30.60 4.02
2376 4558 3.393360 CTCCCAGGAGGAACGCTT 58.607 61.111 5.74 0.00 46.94 4.68
2390 4572 9.156940 AGTAAATAGGTAGGATTTTAGTCCTCC 57.843 37.037 0.00 1.77 45.51 4.30
2412 4594 9.488762 TCCTGATACCTTGATTCTTTCTAGTAA 57.511 33.333 0.00 0.00 0.00 2.24
2419 4601 6.368805 GGGAATCCTGATACCTTGATTCTTT 58.631 40.000 0.00 0.00 41.65 2.52
2420 4602 5.163045 GGGGAATCCTGATACCTTGATTCTT 60.163 44.000 0.00 0.00 41.65 2.52
2424 4606 3.959920 AGGGGAATCCTGATACCTTGAT 58.040 45.455 0.00 0.00 46.07 2.57
2448 4630 0.317479 ACTCTGGTAGTTGGTGACGC 59.683 55.000 0.00 0.00 33.35 5.19
2450 4632 1.608283 GCCACTCTGGTAGTTGGTGAC 60.608 57.143 0.00 0.00 40.46 3.67
2451 4633 0.685097 GCCACTCTGGTAGTTGGTGA 59.315 55.000 0.00 0.00 40.46 4.02
2452 4634 0.670546 CGCCACTCTGGTAGTTGGTG 60.671 60.000 0.00 0.00 40.46 4.17
2458 4640 2.116383 CTACCCGCCACTCTGGTAG 58.884 63.158 0.00 0.00 43.24 3.18
2459 4641 0.395311 CTCTACCCGCCACTCTGGTA 60.395 60.000 0.00 0.00 40.46 3.25
2470 4652 1.409427 GATTCACCACCTCTCTACCCG 59.591 57.143 0.00 0.00 0.00 5.28
2471 4653 1.763545 GGATTCACCACCTCTCTACCC 59.236 57.143 0.00 0.00 38.79 3.69
2485 4667 2.099652 CTCGCGGCCCTATGGATTCA 62.100 60.000 6.13 0.00 0.00 2.57
2486 4668 1.374758 CTCGCGGCCCTATGGATTC 60.375 63.158 6.13 0.00 0.00 2.52
2497 4679 4.257510 TCGATCTCAGCTCGCGGC 62.258 66.667 6.13 9.11 42.19 6.53
2498 4680 2.051435 CTCGATCTCAGCTCGCGG 60.051 66.667 6.13 0.00 36.11 6.46
2500 4682 1.163420 TCCTCTCGATCTCAGCTCGC 61.163 60.000 0.00 0.00 36.11 5.03
2505 4687 1.545428 CCCTCCTCCTCTCGATCTCAG 60.545 61.905 0.00 0.00 0.00 3.35
2506 4688 0.476338 CCCTCCTCCTCTCGATCTCA 59.524 60.000 0.00 0.00 0.00 3.27
2513 4695 1.681486 CGGAAAGCCCTCCTCCTCTC 61.681 65.000 0.53 0.00 32.82 3.20
2529 4711 1.234821 GGTGAAATGTGACAAGCGGA 58.765 50.000 0.00 0.00 0.00 5.54
2532 4714 5.376854 AACTATGGTGAAATGTGACAAGC 57.623 39.130 0.00 0.00 0.00 4.01
2539 4721 5.885912 AGCGGAAATAACTATGGTGAAATGT 59.114 36.000 0.00 0.00 0.00 2.71
2541 4723 7.012044 GTGTAGCGGAAATAACTATGGTGAAAT 59.988 37.037 0.00 0.00 0.00 2.17
2544 4726 5.128171 AGTGTAGCGGAAATAACTATGGTGA 59.872 40.000 0.00 0.00 0.00 4.02
2593 4776 0.750546 TATAGCGCTGAGTGGACGGT 60.751 55.000 22.90 0.00 40.97 4.83
2596 4779 1.001158 GTCCTATAGCGCTGAGTGGAC 60.001 57.143 25.88 25.88 36.23 4.02
2597 4780 1.319541 GTCCTATAGCGCTGAGTGGA 58.680 55.000 22.90 18.45 0.00 4.02
2598 4781 0.315568 GGTCCTATAGCGCTGAGTGG 59.684 60.000 22.90 16.41 0.00 4.00
2599 4782 0.039978 CGGTCCTATAGCGCTGAGTG 60.040 60.000 22.90 11.04 42.92 3.51
2607 4790 1.070134 TGGTGATTGCGGTCCTATAGC 59.930 52.381 0.00 0.00 0.00 2.97
2608 4791 2.365617 AGTGGTGATTGCGGTCCTATAG 59.634 50.000 0.00 0.00 0.00 1.31
2609 4792 2.394632 AGTGGTGATTGCGGTCCTATA 58.605 47.619 0.00 0.00 0.00 1.31
2610 4793 1.204146 AGTGGTGATTGCGGTCCTAT 58.796 50.000 0.00 0.00 0.00 2.57
2611 4794 0.981183 AAGTGGTGATTGCGGTCCTA 59.019 50.000 0.00 0.00 0.00 2.94
2612 4795 0.606401 CAAGTGGTGATTGCGGTCCT 60.606 55.000 0.00 0.00 0.00 3.85
2613 4796 0.605319 TCAAGTGGTGATTGCGGTCC 60.605 55.000 0.00 0.00 0.00 4.46
2614 4797 2.927004 TCAAGTGGTGATTGCGGTC 58.073 52.632 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.