Multiple sequence alignment - TraesCS7D01G310300

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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 TraesCS7D01G310300 chr7D 100.000 4258 0 0 478 4735 393610469 393614726 0.000000e+00 7864
1 TraesCS7D01G310300 chr7D 100.000 206 0 0 1 206 393609992 393610197 9.620000e-102 381
2 TraesCS7D01G310300 chr7A 92.942 4307 174 49 493 4734 446356998 446361239 0.000000e+00 6150
3 TraesCS7D01G310300 chr7B 93.625 2949 116 24 1834 4734 393394191 393397115 0.000000e+00 4338
4 TraesCS7D01G310300 chr7B 91.186 1214 63 18 605 1783 393392968 393394172 0.000000e+00 1609
5 TraesCS7D01G310300 chr7B 91.765 85 5 1 536 620 393392871 393392953 2.990000e-22 117


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 TraesCS7D01G310300 chr7D 393609992 393614726 4734 False 4122.500000 7864 100.000 1 4735 2 chr7D.!!$F1 4734
1 TraesCS7D01G310300 chr7A 446356998 446361239 4241 False 6150.000000 6150 92.942 493 4734 1 chr7A.!!$F1 4241
2 TraesCS7D01G310300 chr7B 393392871 393397115 4244 False 2021.333333 4338 92.192 536 4734 3 chr7B.!!$F1 4198

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
176 177 0.033504 GGGTCGTATGCATCGGTCAT 59.966 55.0 0.19 0.0 0.0 3.06 F
959 992 0.246910 GACGACTTCCTTCCCACCTC 59.753 60.0 0.00 0.0 0.0 3.85 F
961 994 0.247736 CGACTTCCTTCCCACCTCAG 59.752 60.0 0.00 0.0 0.0 3.35 F
1792 1881 0.311790 ACACAAATGCAGCGTCCTTG 59.688 50.0 0.00 0.0 0.0 3.61 F
3032 3125 0.249868 TTGGTGAACTCAGGACTGCG 60.250 55.0 0.00 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1363 0.104304 AAGAACACGGCGAACAGTCT 59.896 50.0 16.62 5.7 0.0 3.24 R
1894 1983 0.166814 GGACGCTGCATCACAAGAAC 59.833 55.0 0.00 0.0 0.0 3.01 R
2017 2110 0.174845 CCGGATTTGGACAGACGCTA 59.825 55.0 0.00 0.0 0.0 4.26 R
3500 3593 0.522626 TGTGCTGTGCGGATCAAATG 59.477 50.0 0.00 0.0 0.0 2.32 R
4665 4850 0.537143 AGCACCAAGACGCCAAATCA 60.537 50.0 0.00 0.0 0.0 2.57 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
22 23 4.759782 CATATCCTTCTGAAACACGACCT 58.240 43.478 0.00 0.00 0.00 3.85
23 24 2.814280 TCCTTCTGAAACACGACCTC 57.186 50.000 0.00 0.00 0.00 3.85
24 25 2.317040 TCCTTCTGAAACACGACCTCT 58.683 47.619 0.00 0.00 0.00 3.69
25 26 2.035961 TCCTTCTGAAACACGACCTCTG 59.964 50.000 0.00 0.00 0.00 3.35
26 27 2.224066 CCTTCTGAAACACGACCTCTGT 60.224 50.000 0.00 0.00 0.00 3.41
27 28 3.458189 CTTCTGAAACACGACCTCTGTT 58.542 45.455 0.00 0.00 33.09 3.16
28 29 2.821546 TCTGAAACACGACCTCTGTTG 58.178 47.619 0.00 0.00 32.07 3.33
29 30 2.167693 TCTGAAACACGACCTCTGTTGT 59.832 45.455 0.00 0.00 39.82 3.32
30 31 3.382227 TCTGAAACACGACCTCTGTTGTA 59.618 43.478 0.00 0.00 36.96 2.41
31 32 3.713288 TGAAACACGACCTCTGTTGTAG 58.287 45.455 0.00 0.00 36.96 2.74
32 33 3.382227 TGAAACACGACCTCTGTTGTAGA 59.618 43.478 0.00 0.00 36.96 2.59
33 34 4.142116 TGAAACACGACCTCTGTTGTAGAA 60.142 41.667 0.00 0.00 36.96 2.10
34 35 4.395959 AACACGACCTCTGTTGTAGAAA 57.604 40.909 0.00 0.00 36.96 2.52
35 36 3.714391 ACACGACCTCTGTTGTAGAAAC 58.286 45.455 0.00 0.00 36.96 2.78
36 37 3.131577 ACACGACCTCTGTTGTAGAAACA 59.868 43.478 0.00 0.00 36.96 2.83
37 38 4.116961 CACGACCTCTGTTGTAGAAACAA 58.883 43.478 0.00 0.00 43.32 2.83
38 39 4.569162 CACGACCTCTGTTGTAGAAACAAA 59.431 41.667 0.00 0.00 46.84 2.83
39 40 5.064198 CACGACCTCTGTTGTAGAAACAAAA 59.936 40.000 0.00 0.00 46.84 2.44
40 41 5.820947 ACGACCTCTGTTGTAGAAACAAAAT 59.179 36.000 0.00 0.00 46.84 1.82
41 42 6.018180 ACGACCTCTGTTGTAGAAACAAAATC 60.018 38.462 0.00 0.00 46.84 2.17
42 43 6.565999 CGACCTCTGTTGTAGAAACAAAATCC 60.566 42.308 0.00 0.00 46.84 3.01
43 44 5.535030 ACCTCTGTTGTAGAAACAAAATCCC 59.465 40.000 0.00 0.00 46.84 3.85
44 45 5.048013 CCTCTGTTGTAGAAACAAAATCCCC 60.048 44.000 0.00 0.00 46.84 4.81
45 46 5.701224 TCTGTTGTAGAAACAAAATCCCCT 58.299 37.500 0.00 0.00 46.84 4.79
46 47 6.133356 TCTGTTGTAGAAACAAAATCCCCTT 58.867 36.000 0.00 0.00 46.84 3.95
47 48 6.264518 TCTGTTGTAGAAACAAAATCCCCTTC 59.735 38.462 0.00 0.00 46.84 3.46
48 49 5.009210 TGTTGTAGAAACAAAATCCCCTTCG 59.991 40.000 0.00 0.00 46.84 3.79
49 50 3.504520 TGTAGAAACAAAATCCCCTTCGC 59.495 43.478 0.00 0.00 30.91 4.70
50 51 1.893137 AGAAACAAAATCCCCTTCGCC 59.107 47.619 0.00 0.00 0.00 5.54
51 52 1.893137 GAAACAAAATCCCCTTCGCCT 59.107 47.619 0.00 0.00 0.00 5.52
52 53 2.891191 AACAAAATCCCCTTCGCCTA 57.109 45.000 0.00 0.00 0.00 3.93
53 54 2.891191 ACAAAATCCCCTTCGCCTAA 57.109 45.000 0.00 0.00 0.00 2.69
54 55 2.723273 ACAAAATCCCCTTCGCCTAAG 58.277 47.619 0.00 0.00 34.73 2.18
55 56 2.307686 ACAAAATCCCCTTCGCCTAAGA 59.692 45.455 0.00 0.00 37.38 2.10
56 57 3.245122 ACAAAATCCCCTTCGCCTAAGAA 60.245 43.478 0.00 0.00 37.38 2.52
57 58 3.732048 AAATCCCCTTCGCCTAAGAAA 57.268 42.857 0.00 0.00 37.38 2.52
58 59 3.732048 AATCCCCTTCGCCTAAGAAAA 57.268 42.857 0.00 0.00 37.38 2.29
59 60 2.484742 TCCCCTTCGCCTAAGAAAAC 57.515 50.000 0.00 0.00 37.38 2.43
60 61 1.700739 TCCCCTTCGCCTAAGAAAACA 59.299 47.619 0.00 0.00 37.38 2.83
61 62 2.084546 CCCCTTCGCCTAAGAAAACAG 58.915 52.381 0.00 0.00 37.38 3.16
62 63 2.290071 CCCCTTCGCCTAAGAAAACAGA 60.290 50.000 0.00 0.00 37.38 3.41
63 64 3.003480 CCCTTCGCCTAAGAAAACAGAG 58.997 50.000 0.00 0.00 37.38 3.35
64 65 3.557264 CCCTTCGCCTAAGAAAACAGAGT 60.557 47.826 0.00 0.00 37.38 3.24
65 66 4.065789 CCTTCGCCTAAGAAAACAGAGTT 58.934 43.478 0.00 0.00 37.38 3.01
66 67 4.083802 CCTTCGCCTAAGAAAACAGAGTTG 60.084 45.833 0.00 0.00 37.38 3.16
67 68 3.399330 TCGCCTAAGAAAACAGAGTTGG 58.601 45.455 0.00 0.00 0.00 3.77
68 69 2.484264 CGCCTAAGAAAACAGAGTTGGG 59.516 50.000 0.00 0.00 0.00 4.12
69 70 2.820197 GCCTAAGAAAACAGAGTTGGGG 59.180 50.000 0.00 0.00 0.00 4.96
70 71 3.497942 GCCTAAGAAAACAGAGTTGGGGA 60.498 47.826 0.00 0.00 0.00 4.81
71 72 4.327680 CCTAAGAAAACAGAGTTGGGGAG 58.672 47.826 0.00 0.00 0.00 4.30
72 73 2.959465 AGAAAACAGAGTTGGGGAGG 57.041 50.000 0.00 0.00 0.00 4.30
73 74 2.136026 AGAAAACAGAGTTGGGGAGGT 58.864 47.619 0.00 0.00 0.00 3.85
74 75 2.106684 AGAAAACAGAGTTGGGGAGGTC 59.893 50.000 0.00 0.00 0.00 3.85
75 76 1.821088 AAACAGAGTTGGGGAGGTCT 58.179 50.000 0.00 0.00 0.00 3.85
76 77 1.353091 AACAGAGTTGGGGAGGTCTC 58.647 55.000 0.00 0.00 0.00 3.36
102 103 2.047179 GGGACCTGTGCCTTCGTC 60.047 66.667 0.00 0.00 38.15 4.20
103 104 2.432628 GGACCTGTGCCTTCGTCG 60.433 66.667 0.00 0.00 0.00 5.12
104 105 2.338984 GACCTGTGCCTTCGTCGT 59.661 61.111 0.00 0.00 0.00 4.34
105 106 1.300697 GACCTGTGCCTTCGTCGTT 60.301 57.895 0.00 0.00 0.00 3.85
106 107 1.557443 GACCTGTGCCTTCGTCGTTG 61.557 60.000 0.00 0.00 0.00 4.10
107 108 1.594293 CCTGTGCCTTCGTCGTTGT 60.594 57.895 0.00 0.00 0.00 3.32
108 109 1.557443 CCTGTGCCTTCGTCGTTGTC 61.557 60.000 0.00 0.00 0.00 3.18
109 110 1.876453 CTGTGCCTTCGTCGTTGTCG 61.876 60.000 0.00 0.00 38.55 4.35
110 111 1.947642 GTGCCTTCGTCGTTGTCGT 60.948 57.895 0.00 0.00 38.33 4.34
111 112 1.947146 TGCCTTCGTCGTTGTCGTG 60.947 57.895 0.00 0.00 38.33 4.35
112 113 2.654912 GCCTTCGTCGTTGTCGTGG 61.655 63.158 0.00 0.00 38.33 4.94
113 114 1.008194 CCTTCGTCGTTGTCGTGGA 60.008 57.895 0.00 0.00 38.33 4.02
114 115 1.002250 CCTTCGTCGTTGTCGTGGAG 61.002 60.000 0.00 0.00 38.33 3.86
115 116 0.040692 CTTCGTCGTTGTCGTGGAGA 60.041 55.000 0.00 0.00 38.33 3.71
116 117 0.594602 TTCGTCGTTGTCGTGGAGAT 59.405 50.000 0.00 0.00 38.33 2.75
117 118 0.167470 TCGTCGTTGTCGTGGAGATC 59.833 55.000 0.00 0.00 38.33 2.75
118 119 0.168348 CGTCGTTGTCGTGGAGATCT 59.832 55.000 0.00 0.00 38.33 2.75
119 120 1.395954 CGTCGTTGTCGTGGAGATCTA 59.604 52.381 0.00 0.00 38.33 1.98
120 121 2.783333 GTCGTTGTCGTGGAGATCTAC 58.217 52.381 0.00 0.00 38.33 2.59
127 128 2.580729 CGTGGAGATCTACGTCGATC 57.419 55.000 19.48 19.48 44.21 3.69
128 129 1.136584 CGTGGAGATCTACGTCGATCG 60.137 57.143 20.52 9.36 44.21 3.69
137 138 4.057615 CGTCGATCGTCACCACTG 57.942 61.111 15.94 0.00 34.52 3.66
138 139 2.152699 CGTCGATCGTCACCACTGC 61.153 63.158 15.94 0.00 34.52 4.40
139 140 1.080772 GTCGATCGTCACCACTGCA 60.081 57.895 15.94 0.00 0.00 4.41
140 141 1.073216 GTCGATCGTCACCACTGCAG 61.073 60.000 15.94 13.48 0.00 4.41
141 142 1.807165 CGATCGTCACCACTGCAGG 60.807 63.158 19.93 4.24 0.00 4.85
142 143 1.293498 GATCGTCACCACTGCAGGT 59.707 57.895 19.93 5.02 44.48 4.00
143 144 0.737715 GATCGTCACCACTGCAGGTC 60.738 60.000 19.93 0.00 40.77 3.85
144 145 2.172483 ATCGTCACCACTGCAGGTCC 62.172 60.000 19.93 0.16 40.77 4.46
145 146 2.828868 GTCACCACTGCAGGTCCA 59.171 61.111 19.93 0.00 40.77 4.02
146 147 1.302033 GTCACCACTGCAGGTCCAG 60.302 63.158 19.93 3.88 40.77 3.86
147 148 2.670934 CACCACTGCAGGTCCAGC 60.671 66.667 19.93 0.00 40.77 4.85
148 149 3.958860 ACCACTGCAGGTCCAGCC 61.959 66.667 19.93 0.00 37.28 4.85
150 151 4.320456 CACTGCAGGTCCAGCCGT 62.320 66.667 19.93 0.14 43.70 5.68
151 152 3.560251 ACTGCAGGTCCAGCCGTT 61.560 61.111 19.93 0.00 43.70 4.44
152 153 3.052082 CTGCAGGTCCAGCCGTTG 61.052 66.667 5.57 0.00 43.70 4.10
153 154 3.535629 CTGCAGGTCCAGCCGTTGA 62.536 63.158 5.57 0.00 43.70 3.18
154 155 3.050275 GCAGGTCCAGCCGTTGAC 61.050 66.667 0.00 0.00 43.70 3.18
155 156 2.738521 CAGGTCCAGCCGTTGACG 60.739 66.667 0.00 0.00 43.70 4.35
156 157 4.681978 AGGTCCAGCCGTTGACGC 62.682 66.667 0.00 0.00 43.70 5.19
171 172 3.394874 CGCGGGTCGTATGCATCG 61.395 66.667 0.19 7.36 0.00 3.84
172 173 3.036084 GCGGGTCGTATGCATCGG 61.036 66.667 0.19 0.00 0.00 4.18
173 174 2.415843 CGGGTCGTATGCATCGGT 59.584 61.111 0.19 0.00 0.00 4.69
174 175 1.660575 CGGGTCGTATGCATCGGTC 60.661 63.158 0.19 4.63 0.00 4.79
175 176 1.440060 GGGTCGTATGCATCGGTCA 59.560 57.895 0.19 0.00 0.00 4.02
176 177 0.033504 GGGTCGTATGCATCGGTCAT 59.966 55.000 0.19 0.00 0.00 3.06
177 178 1.419374 GGTCGTATGCATCGGTCATC 58.581 55.000 0.19 0.00 0.00 2.92
178 179 1.053048 GTCGTATGCATCGGTCATCG 58.947 55.000 0.19 0.00 40.90 3.84
179 180 0.663269 TCGTATGCATCGGTCATCGC 60.663 55.000 0.19 0.00 39.05 4.58
180 181 1.617755 CGTATGCATCGGTCATCGCC 61.618 60.000 0.19 0.00 39.05 5.54
495 496 2.954611 GGTTGGCCGAGTGAAAGC 59.045 61.111 0.00 0.00 0.00 3.51
496 497 1.896660 GGTTGGCCGAGTGAAAGCA 60.897 57.895 0.00 0.00 0.00 3.91
497 498 1.244019 GGTTGGCCGAGTGAAAGCAT 61.244 55.000 0.00 0.00 0.00 3.79
498 499 0.598065 GTTGGCCGAGTGAAAGCATT 59.402 50.000 0.00 0.00 0.00 3.56
499 500 1.000274 GTTGGCCGAGTGAAAGCATTT 60.000 47.619 0.00 0.00 43.98 2.32
526 527 7.454225 CGATAATTTATTCTTCTTCCCCCTCT 58.546 38.462 0.00 0.00 0.00 3.69
638 668 9.927668 AAAAGAAATTCCGAAATGAACATACAT 57.072 25.926 0.00 0.00 0.00 2.29
642 672 5.811399 TTCCGAAATGAACATACATGACC 57.189 39.130 0.00 0.00 0.00 4.02
700 730 1.739049 CACCACGCCAAAACACCAT 59.261 52.632 0.00 0.00 0.00 3.55
758 788 0.462759 GTTCATTCCCCTCCAGAGCG 60.463 60.000 0.00 0.00 0.00 5.03
782 812 1.983224 CACCTGTCTCCCGATTGGT 59.017 57.895 0.00 0.00 34.77 3.67
815 845 2.586293 CGTTACCCCCGAACCCACT 61.586 63.158 0.00 0.00 0.00 4.00
954 987 2.125633 GGCGACGACTTCCTTCCC 60.126 66.667 0.00 0.00 0.00 3.97
955 988 2.654877 GCGACGACTTCCTTCCCA 59.345 61.111 0.00 0.00 0.00 4.37
958 991 1.533469 CGACGACTTCCTTCCCACCT 61.533 60.000 0.00 0.00 0.00 4.00
959 992 0.246910 GACGACTTCCTTCCCACCTC 59.753 60.000 0.00 0.00 0.00 3.85
960 993 0.471211 ACGACTTCCTTCCCACCTCA 60.471 55.000 0.00 0.00 0.00 3.86
961 994 0.247736 CGACTTCCTTCCCACCTCAG 59.752 60.000 0.00 0.00 0.00 3.35
1408 1472 2.002977 CCCTGGAATCTGGAGCCCA 61.003 63.158 0.00 0.00 34.32 5.36
1501 1581 5.750067 GTGGGATCATTTCGAATGATTTTGG 59.250 40.000 18.06 0.00 38.73 3.28
1502 1582 5.655974 TGGGATCATTTCGAATGATTTTGGA 59.344 36.000 18.06 2.77 38.73 3.53
1510 1590 8.642020 CATTTCGAATGATTTTGGAAGAAAGAC 58.358 33.333 0.00 0.00 31.26 3.01
1644 1727 3.199946 TGATTGGAGTCCTACCATTCACC 59.800 47.826 11.33 0.00 40.48 4.02
1682 1765 4.402474 TCTTATCACTCGATTCTTGCCTCA 59.598 41.667 0.00 0.00 32.73 3.86
1715 1798 5.300286 AGCTTGCTGTTTCTGAATTGTAACT 59.700 36.000 0.00 0.00 0.00 2.24
1783 1872 4.661222 TCCCAGAATAGAACACAAATGCA 58.339 39.130 0.00 0.00 0.00 3.96
1784 1873 4.701651 TCCCAGAATAGAACACAAATGCAG 59.298 41.667 0.00 0.00 0.00 4.41
1786 1875 4.093514 CAGAATAGAACACAAATGCAGCG 58.906 43.478 0.00 0.00 0.00 5.18
1787 1876 3.753272 AGAATAGAACACAAATGCAGCGT 59.247 39.130 0.00 0.00 0.00 5.07
1788 1877 3.747099 ATAGAACACAAATGCAGCGTC 57.253 42.857 0.00 0.00 0.00 5.19
1789 1878 0.593128 AGAACACAAATGCAGCGTCC 59.407 50.000 0.00 0.00 0.00 4.79
1790 1879 0.593128 GAACACAAATGCAGCGTCCT 59.407 50.000 0.00 0.00 0.00 3.85
1791 1880 1.001378 GAACACAAATGCAGCGTCCTT 60.001 47.619 0.00 0.00 0.00 3.36
1792 1881 0.311790 ACACAAATGCAGCGTCCTTG 59.688 50.000 0.00 0.00 0.00 3.61
1793 1882 0.311790 CACAAATGCAGCGTCCTTGT 59.688 50.000 0.00 0.00 0.00 3.16
1794 1883 0.311790 ACAAATGCAGCGTCCTTGTG 59.688 50.000 4.20 0.00 0.00 3.33
1795 1884 0.592637 CAAATGCAGCGTCCTTGTGA 59.407 50.000 0.00 0.00 0.00 3.58
1796 1885 1.200716 CAAATGCAGCGTCCTTGTGAT 59.799 47.619 0.00 0.00 0.00 3.06
1797 1886 0.806868 AATGCAGCGTCCTTGTGATG 59.193 50.000 0.00 0.00 0.00 3.07
1820 1909 2.998670 AGCGTCACATGAAGAATGACTG 59.001 45.455 0.00 0.86 40.51 3.51
1822 1911 3.187227 GCGTCACATGAAGAATGACTGTT 59.813 43.478 0.00 0.00 40.51 3.16
1823 1912 4.319766 GCGTCACATGAAGAATGACTGTTT 60.320 41.667 0.00 0.00 40.51 2.83
1830 1919 3.376859 TGAAGAATGACTGTTTTGTGCGT 59.623 39.130 0.00 0.00 0.00 5.24
1870 1959 5.975693 AAATCCGTTTGGCTATTTCTTCA 57.024 34.783 0.00 0.00 34.14 3.02
1891 1980 7.555195 TCTTCATGTGATGTGCTAATTGATCTT 59.445 33.333 0.00 0.00 0.00 2.40
1894 1983 6.185852 TGTGATGTGCTAATTGATCTTGTG 57.814 37.500 0.00 0.00 0.00 3.33
2061 2154 4.147449 TCGCTCTGCCGGACCATG 62.147 66.667 5.05 0.00 0.00 3.66
2076 2169 3.132289 GGACCATGTTCTCGTAATCCTCA 59.868 47.826 0.00 0.00 0.00 3.86
2180 2273 2.974489 CTCAGTTGCTGCCTTGCCG 61.974 63.158 0.00 0.00 0.00 5.69
2216 2309 4.738998 CATTGCCCTGCCGGACCA 62.739 66.667 5.05 0.00 0.00 4.02
2539 2632 4.044426 GGAAACATCAACAGAAACAGTGC 58.956 43.478 0.00 0.00 0.00 4.40
2623 2716 1.597854 CGCAACCAGAGCCACTTCA 60.598 57.895 0.00 0.00 0.00 3.02
2727 2820 2.406616 CGGTTCTTGCGGGAATGGG 61.407 63.158 0.00 0.00 0.00 4.00
2807 2900 6.549763 GATGATGGCATCGAGGAAGTCCTT 62.550 50.000 21.65 0.00 43.04 3.36
2963 3056 1.303643 GTTCCTGCACTTCCCTGGG 60.304 63.158 6.33 6.33 0.00 4.45
3032 3125 0.249868 TTGGTGAACTCAGGACTGCG 60.250 55.000 0.00 0.00 0.00 5.18
3056 3149 0.773644 ACAGCTTTGGTCCATCAGGT 59.226 50.000 0.00 0.00 35.89 4.00
3150 3243 1.135199 CAATTGTCAGGCCAGATGCAC 60.135 52.381 5.01 0.00 43.89 4.57
3216 3309 4.593206 AGGAAGGGATGAAGTATGCGAATA 59.407 41.667 0.00 0.00 0.00 1.75
3440 3533 7.397892 TGACACTGGTTTGAAAGATTTTGTA 57.602 32.000 0.00 0.00 0.00 2.41
3495 3588 3.973973 TCTTCCATGGTAGATGGGTAAGG 59.026 47.826 16.51 0.00 39.60 2.69
3500 3593 0.391966 GGTAGATGGGTAAGGACGGC 59.608 60.000 0.00 0.00 0.00 5.68
3515 3608 1.063006 CGGCATTTGATCCGCACAG 59.937 57.895 0.00 0.00 39.14 3.66
3530 3623 1.725641 CACAGCACACGGTACATGAT 58.274 50.000 0.00 0.00 0.00 2.45
3598 3691 1.477923 GGTGGTAGAGTGGGTTTTGCA 60.478 52.381 0.00 0.00 0.00 4.08
3769 3883 5.863935 GCATAGATTGTTTCCCTGTGTTTTC 59.136 40.000 0.00 0.00 0.00 2.29
3778 3892 3.934068 TCCCTGTGTTTTCGTCTAATCC 58.066 45.455 0.00 0.00 0.00 3.01
3863 3978 4.334203 TGCGCAAATTCGTTATGGAGTTAT 59.666 37.500 8.16 0.00 0.00 1.89
3864 3979 4.670621 GCGCAAATTCGTTATGGAGTTATG 59.329 41.667 0.30 0.00 0.00 1.90
3865 3980 5.204833 CGCAAATTCGTTATGGAGTTATGG 58.795 41.667 0.00 0.00 0.00 2.74
3866 3981 5.519722 GCAAATTCGTTATGGAGTTATGGG 58.480 41.667 0.00 0.00 0.00 4.00
3867 3982 5.507315 GCAAATTCGTTATGGAGTTATGGGG 60.507 44.000 0.00 0.00 0.00 4.96
3868 3983 5.640158 AATTCGTTATGGAGTTATGGGGA 57.360 39.130 0.00 0.00 0.00 4.81
3869 3984 4.682778 TTCGTTATGGAGTTATGGGGAG 57.317 45.455 0.00 0.00 0.00 4.30
3870 3985 3.649843 TCGTTATGGAGTTATGGGGAGT 58.350 45.455 0.00 0.00 0.00 3.85
3907 4022 4.322801 GGTACACCTTGCTTGATGTAGTCT 60.323 45.833 0.00 0.00 0.00 3.24
3910 4025 4.067896 CACCTTGCTTGATGTAGTCTTGT 58.932 43.478 0.00 0.00 0.00 3.16
3991 4110 9.502091 TTTCTATATACATGATGGCAACCTTAC 57.498 33.333 0.00 0.00 0.00 2.34
4093 4216 8.398665 ACAAATAGAGAAATCAAATCTAACGCC 58.601 33.333 0.00 0.00 0.00 5.68
4236 4378 4.337274 ACTTAACCAGTTAACCTTGCACAC 59.663 41.667 0.88 0.00 32.26 3.82
4281 4423 5.785940 AGACCTAGGCTTCTTTTCCTCTTTA 59.214 40.000 9.30 0.00 34.02 1.85
4314 4482 9.343539 ACTGCCTTCTTACTTTATCCATTTATC 57.656 33.333 0.00 0.00 0.00 1.75
4315 4483 9.342308 CTGCCTTCTTACTTTATCCATTTATCA 57.658 33.333 0.00 0.00 0.00 2.15
4316 4484 9.866655 TGCCTTCTTACTTTATCCATTTATCAT 57.133 29.630 0.00 0.00 0.00 2.45
4338 4506 8.704849 TCATCATTTAAAGTTTCTTGAAGGGA 57.295 30.769 0.00 0.00 0.00 4.20
4339 4507 9.312904 TCATCATTTAAAGTTTCTTGAAGGGAT 57.687 29.630 0.00 0.00 0.00 3.85
4376 4544 3.324268 TCCAACGGTTCCAGTTGTGTATA 59.676 43.478 17.69 4.10 45.31 1.47
4377 4545 4.020039 TCCAACGGTTCCAGTTGTGTATAT 60.020 41.667 17.69 0.00 45.31 0.86
4379 4547 5.875910 CCAACGGTTCCAGTTGTGTATATTA 59.124 40.000 17.69 0.00 45.31 0.98
4380 4548 6.540914 CCAACGGTTCCAGTTGTGTATATTAT 59.459 38.462 17.69 0.00 45.31 1.28
4381 4549 7.066525 CCAACGGTTCCAGTTGTGTATATTATT 59.933 37.037 17.69 0.00 45.31 1.40
4382 4550 7.781548 ACGGTTCCAGTTGTGTATATTATTC 57.218 36.000 0.00 0.00 0.00 1.75
4383 4551 7.562135 ACGGTTCCAGTTGTGTATATTATTCT 58.438 34.615 0.00 0.00 0.00 2.40
4384 4552 8.698210 ACGGTTCCAGTTGTGTATATTATTCTA 58.302 33.333 0.00 0.00 0.00 2.10
4385 4553 8.975439 CGGTTCCAGTTGTGTATATTATTCTAC 58.025 37.037 0.00 0.00 0.00 2.59
4386 4554 9.269453 GGTTCCAGTTGTGTATATTATTCTACC 57.731 37.037 0.00 0.00 0.00 3.18
4387 4555 9.826574 GTTCCAGTTGTGTATATTATTCTACCA 57.173 33.333 0.00 0.00 0.00 3.25
4414 4584 6.446451 ACCACTACCACTATCCCTATGTTTA 58.554 40.000 0.00 0.00 0.00 2.01
4415 4585 6.325804 ACCACTACCACTATCCCTATGTTTAC 59.674 42.308 0.00 0.00 0.00 2.01
4416 4586 6.325545 CCACTACCACTATCCCTATGTTTACA 59.674 42.308 0.00 0.00 0.00 2.41
4417 4587 7.434492 CACTACCACTATCCCTATGTTTACAG 58.566 42.308 0.00 0.00 0.00 2.74
4418 4588 5.888982 ACCACTATCCCTATGTTTACAGG 57.111 43.478 0.00 0.00 0.00 4.00
4419 4589 5.535029 ACCACTATCCCTATGTTTACAGGA 58.465 41.667 0.00 0.00 33.42 3.86
4420 4590 5.365895 ACCACTATCCCTATGTTTACAGGAC 59.634 44.000 0.00 0.00 33.42 3.85
4421 4591 5.365605 CCACTATCCCTATGTTTACAGGACA 59.634 44.000 0.00 0.00 33.42 4.02
4459 4639 8.257306 AGTTAAAAGTCAAAGCAAGGAATCAAA 58.743 29.630 0.00 0.00 0.00 2.69
4464 4644 5.009410 AGTCAAAGCAAGGAATCAAACAGAG 59.991 40.000 0.00 0.00 0.00 3.35
4465 4645 5.009010 GTCAAAGCAAGGAATCAAACAGAGA 59.991 40.000 0.00 0.00 0.00 3.10
4469 4649 5.836347 AGCAAGGAATCAAACAGAGAAAAC 58.164 37.500 0.00 0.00 0.00 2.43
4563 4743 2.329267 TCAAGGAGAGCTCTGGACAAA 58.671 47.619 23.91 0.00 0.00 2.83
4564 4744 2.037772 TCAAGGAGAGCTCTGGACAAAC 59.962 50.000 23.91 4.15 0.00 2.93
4665 4850 6.765989 TGAGTAAACTACACATTTTGAGCTGT 59.234 34.615 0.00 0.00 0.00 4.40
4690 4875 3.357079 CGTCTTGGTGCTGGTGCC 61.357 66.667 0.00 0.00 38.71 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.759782 AGGTCGTGTTTCAGAAGGATATG 58.240 43.478 0.00 0.00 0.00 1.78
2 3 4.082190 CAGAGGTCGTGTTTCAGAAGGATA 60.082 45.833 0.00 0.00 0.00 2.59
3 4 2.900546 AGAGGTCGTGTTTCAGAAGGAT 59.099 45.455 0.00 0.00 0.00 3.24
4 5 2.035961 CAGAGGTCGTGTTTCAGAAGGA 59.964 50.000 0.00 0.00 0.00 3.36
5 6 2.224066 ACAGAGGTCGTGTTTCAGAAGG 60.224 50.000 0.00 0.00 0.00 3.46
6 7 3.099267 ACAGAGGTCGTGTTTCAGAAG 57.901 47.619 0.00 0.00 0.00 2.85
8 9 2.167693 ACAACAGAGGTCGTGTTTCAGA 59.832 45.455 0.00 0.00 35.93 3.27
9 10 2.550978 ACAACAGAGGTCGTGTTTCAG 58.449 47.619 0.00 0.00 35.93 3.02
10 11 2.684001 ACAACAGAGGTCGTGTTTCA 57.316 45.000 0.00 0.00 35.93 2.69
12 13 4.395959 TTCTACAACAGAGGTCGTGTTT 57.604 40.909 0.00 0.00 35.93 2.83
13 14 4.117685 GTTTCTACAACAGAGGTCGTGTT 58.882 43.478 0.00 0.00 38.71 3.32
14 15 3.131577 TGTTTCTACAACAGAGGTCGTGT 59.868 43.478 0.00 0.00 33.83 4.49
15 16 3.713288 TGTTTCTACAACAGAGGTCGTG 58.287 45.455 0.00 0.00 33.83 4.35
16 17 4.395959 TTGTTTCTACAACAGAGGTCGT 57.604 40.909 0.00 0.00 39.29 4.34
17 18 5.728351 TTTTGTTTCTACAACAGAGGTCG 57.272 39.130 0.00 0.00 43.66 4.79
18 19 6.294010 GGGATTTTGTTTCTACAACAGAGGTC 60.294 42.308 0.00 0.00 43.66 3.85
19 20 5.535030 GGGATTTTGTTTCTACAACAGAGGT 59.465 40.000 0.00 0.00 43.66 3.85
20 21 5.048013 GGGGATTTTGTTTCTACAACAGAGG 60.048 44.000 0.00 0.00 43.66 3.69
21 22 5.770162 AGGGGATTTTGTTTCTACAACAGAG 59.230 40.000 0.00 0.00 43.66 3.35
22 23 5.701224 AGGGGATTTTGTTTCTACAACAGA 58.299 37.500 0.00 0.00 43.66 3.41
23 24 6.405278 AAGGGGATTTTGTTTCTACAACAG 57.595 37.500 0.00 0.00 43.66 3.16
24 25 5.009210 CGAAGGGGATTTTGTTTCTACAACA 59.991 40.000 0.00 0.00 43.66 3.33
25 26 5.458015 CGAAGGGGATTTTGTTTCTACAAC 58.542 41.667 0.00 0.00 43.66 3.32
26 27 4.022676 GCGAAGGGGATTTTGTTTCTACAA 60.023 41.667 0.00 0.00 42.34 2.41
27 28 3.504520 GCGAAGGGGATTTTGTTTCTACA 59.495 43.478 0.00 0.00 0.00 2.74
28 29 3.119602 GGCGAAGGGGATTTTGTTTCTAC 60.120 47.826 0.00 0.00 0.00 2.59
29 30 3.086282 GGCGAAGGGGATTTTGTTTCTA 58.914 45.455 0.00 0.00 0.00 2.10
30 31 1.893137 GGCGAAGGGGATTTTGTTTCT 59.107 47.619 0.00 0.00 0.00 2.52
31 32 1.893137 AGGCGAAGGGGATTTTGTTTC 59.107 47.619 0.00 0.00 0.00 2.78
32 33 2.009681 AGGCGAAGGGGATTTTGTTT 57.990 45.000 0.00 0.00 0.00 2.83
33 34 2.891191 TAGGCGAAGGGGATTTTGTT 57.109 45.000 0.00 0.00 0.00 2.83
34 35 2.307686 TCTTAGGCGAAGGGGATTTTGT 59.692 45.455 7.53 0.00 35.67 2.83
35 36 2.999331 TCTTAGGCGAAGGGGATTTTG 58.001 47.619 7.53 0.00 35.67 2.44
36 37 3.732048 TTCTTAGGCGAAGGGGATTTT 57.268 42.857 7.53 0.00 35.67 1.82
37 38 3.732048 TTTCTTAGGCGAAGGGGATTT 57.268 42.857 7.53 0.00 35.67 2.17
38 39 3.245122 TGTTTTCTTAGGCGAAGGGGATT 60.245 43.478 7.53 0.00 35.67 3.01
39 40 2.307686 TGTTTTCTTAGGCGAAGGGGAT 59.692 45.455 7.53 0.00 35.67 3.85
40 41 1.700739 TGTTTTCTTAGGCGAAGGGGA 59.299 47.619 7.53 0.00 35.67 4.81
41 42 2.084546 CTGTTTTCTTAGGCGAAGGGG 58.915 52.381 7.53 0.00 35.67 4.79
42 43 3.003480 CTCTGTTTTCTTAGGCGAAGGG 58.997 50.000 7.53 0.00 35.67 3.95
43 44 3.665190 ACTCTGTTTTCTTAGGCGAAGG 58.335 45.455 7.53 0.00 35.67 3.46
44 45 4.083802 CCAACTCTGTTTTCTTAGGCGAAG 60.084 45.833 0.37 0.37 36.38 3.79
45 46 3.813166 CCAACTCTGTTTTCTTAGGCGAA 59.187 43.478 0.00 0.00 0.00 4.70
46 47 3.399330 CCAACTCTGTTTTCTTAGGCGA 58.601 45.455 0.00 0.00 0.00 5.54
47 48 2.484264 CCCAACTCTGTTTTCTTAGGCG 59.516 50.000 0.00 0.00 0.00 5.52
48 49 2.820197 CCCCAACTCTGTTTTCTTAGGC 59.180 50.000 0.00 0.00 0.00 3.93
49 50 4.327680 CTCCCCAACTCTGTTTTCTTAGG 58.672 47.826 0.00 0.00 0.00 2.69
50 51 4.202472 ACCTCCCCAACTCTGTTTTCTTAG 60.202 45.833 0.00 0.00 0.00 2.18
51 52 3.720002 ACCTCCCCAACTCTGTTTTCTTA 59.280 43.478 0.00 0.00 0.00 2.10
52 53 2.514160 ACCTCCCCAACTCTGTTTTCTT 59.486 45.455 0.00 0.00 0.00 2.52
53 54 2.106684 GACCTCCCCAACTCTGTTTTCT 59.893 50.000 0.00 0.00 0.00 2.52
54 55 2.106684 AGACCTCCCCAACTCTGTTTTC 59.893 50.000 0.00 0.00 0.00 2.29
55 56 2.106684 GAGACCTCCCCAACTCTGTTTT 59.893 50.000 0.00 0.00 0.00 2.43
56 57 1.700186 GAGACCTCCCCAACTCTGTTT 59.300 52.381 0.00 0.00 0.00 2.83
57 58 1.353091 GAGACCTCCCCAACTCTGTT 58.647 55.000 0.00 0.00 0.00 3.16
58 59 0.545548 GGAGACCTCCCCAACTCTGT 60.546 60.000 4.72 0.00 43.94 3.41
59 60 2.291856 GGAGACCTCCCCAACTCTG 58.708 63.158 4.72 0.00 43.94 3.35
60 61 4.899243 GGAGACCTCCCCAACTCT 57.101 61.111 4.72 0.00 43.94 3.24
69 70 3.450115 CCCGTCGGTGGAGACCTC 61.450 72.222 11.06 0.00 40.58 3.85
72 73 3.756727 GTCCCCGTCGGTGGAGAC 61.757 72.222 18.50 11.94 37.76 3.36
77 78 4.373116 CACAGGTCCCCGTCGGTG 62.373 72.222 11.06 3.79 0.00 4.94
81 82 3.607370 GAAGGCACAGGTCCCCGTC 62.607 68.421 0.00 0.00 0.00 4.79
82 83 3.637273 GAAGGCACAGGTCCCCGT 61.637 66.667 0.00 0.00 0.00 5.28
83 84 4.760047 CGAAGGCACAGGTCCCCG 62.760 72.222 0.00 0.00 0.00 5.73
84 85 3.607370 GACGAAGGCACAGGTCCCC 62.607 68.421 0.00 0.00 0.00 4.81
85 86 2.047179 GACGAAGGCACAGGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
86 87 2.432628 CGACGAAGGCACAGGTCC 60.433 66.667 0.00 0.00 0.00 4.46
87 88 1.300697 AACGACGAAGGCACAGGTC 60.301 57.895 0.00 0.00 0.00 3.85
88 89 1.594293 CAACGACGAAGGCACAGGT 60.594 57.895 0.00 0.00 0.00 4.00
89 90 1.557443 GACAACGACGAAGGCACAGG 61.557 60.000 0.00 0.00 0.00 4.00
90 91 1.853319 GACAACGACGAAGGCACAG 59.147 57.895 0.00 0.00 0.00 3.66
91 92 1.947146 CGACAACGACGAAGGCACA 60.947 57.895 0.00 0.00 42.66 4.57
92 93 1.947642 ACGACAACGACGAAGGCAC 60.948 57.895 0.00 0.00 42.66 5.01
93 94 1.947146 CACGACAACGACGAAGGCA 60.947 57.895 0.00 0.00 42.66 4.75
94 95 2.654912 CCACGACAACGACGAAGGC 61.655 63.158 0.00 0.00 42.66 4.35
95 96 1.002250 CTCCACGACAACGACGAAGG 61.002 60.000 0.00 0.00 42.66 3.46
96 97 0.040692 TCTCCACGACAACGACGAAG 60.041 55.000 0.00 0.00 42.66 3.79
97 98 0.594602 ATCTCCACGACAACGACGAA 59.405 50.000 0.00 0.00 42.66 3.85
98 99 0.167470 GATCTCCACGACAACGACGA 59.833 55.000 0.00 0.00 42.66 4.20
99 100 0.168348 AGATCTCCACGACAACGACG 59.832 55.000 0.00 0.00 42.66 5.12
100 101 2.783333 GTAGATCTCCACGACAACGAC 58.217 52.381 0.00 0.00 42.66 4.34
101 102 1.395954 CGTAGATCTCCACGACAACGA 59.604 52.381 11.79 0.00 40.56 3.85
102 103 1.129998 ACGTAGATCTCCACGACAACG 59.870 52.381 21.70 15.09 40.56 4.10
103 104 2.783333 GACGTAGATCTCCACGACAAC 58.217 52.381 21.70 1.86 40.56 3.32
104 105 1.395954 CGACGTAGATCTCCACGACAA 59.604 52.381 21.70 0.00 40.56 3.18
105 106 1.004595 CGACGTAGATCTCCACGACA 58.995 55.000 21.70 0.00 40.56 4.35
106 107 1.284657 TCGACGTAGATCTCCACGAC 58.715 55.000 21.70 15.38 40.56 4.34
107 108 2.133553 GATCGACGTAGATCTCCACGA 58.866 52.381 25.75 17.23 42.68 4.35
108 109 1.136584 CGATCGACGTAGATCTCCACG 60.137 57.143 28.44 16.51 43.52 4.94
109 110 2.580729 CGATCGACGTAGATCTCCAC 57.419 55.000 28.44 9.84 43.52 4.02
121 122 1.073216 CTGCAGTGGTGACGATCGAC 61.073 60.000 24.34 17.11 0.00 4.20
122 123 1.212751 CTGCAGTGGTGACGATCGA 59.787 57.895 24.34 0.00 0.00 3.59
123 124 1.807165 CCTGCAGTGGTGACGATCG 60.807 63.158 14.88 14.88 0.00 3.69
124 125 0.737715 GACCTGCAGTGGTGACGATC 60.738 60.000 13.81 0.00 41.00 3.69
125 126 1.293498 GACCTGCAGTGGTGACGAT 59.707 57.895 13.81 0.00 41.00 3.73
126 127 2.734591 GACCTGCAGTGGTGACGA 59.265 61.111 13.81 0.00 41.00 4.20
127 128 2.357517 GGACCTGCAGTGGTGACG 60.358 66.667 13.81 0.00 41.00 4.35
128 129 1.302033 CTGGACCTGCAGTGGTGAC 60.302 63.158 13.81 1.47 41.00 3.67
129 130 3.150949 CTGGACCTGCAGTGGTGA 58.849 61.111 13.81 0.00 41.00 4.02
130 131 2.670934 GCTGGACCTGCAGTGGTG 60.671 66.667 17.78 0.00 41.00 4.17
131 132 3.958860 GGCTGGACCTGCAGTGGT 61.959 66.667 23.12 4.91 44.10 4.16
133 134 3.832237 AACGGCTGGACCTGCAGTG 62.832 63.158 25.30 16.11 36.94 3.66
134 135 3.560251 AACGGCTGGACCTGCAGT 61.560 61.111 23.12 21.82 38.15 4.40
135 136 3.052082 CAACGGCTGGACCTGCAG 61.052 66.667 23.12 21.19 35.61 4.41
136 137 3.555324 TCAACGGCTGGACCTGCA 61.555 61.111 23.12 1.12 35.61 4.41
137 138 3.050275 GTCAACGGCTGGACCTGC 61.050 66.667 14.68 14.68 35.61 4.85
138 139 2.738521 CGTCAACGGCTGGACCTG 60.739 66.667 0.00 0.00 35.61 4.00
139 140 4.681978 GCGTCAACGGCTGGACCT 62.682 66.667 4.54 0.00 40.23 3.85
155 156 3.036084 CCGATGCATACGACCCGC 61.036 66.667 16.69 0.00 0.00 6.13
156 157 1.660575 GACCGATGCATACGACCCG 60.661 63.158 16.69 7.92 0.00 5.28
157 158 0.033504 ATGACCGATGCATACGACCC 59.966 55.000 16.69 8.18 0.00 4.46
158 159 1.419374 GATGACCGATGCATACGACC 58.581 55.000 16.69 9.98 0.00 4.79
159 160 1.053048 CGATGACCGATGCATACGAC 58.947 55.000 16.69 11.71 41.76 4.34
160 161 0.663269 GCGATGACCGATGCATACGA 60.663 55.000 16.69 1.86 41.76 3.43
161 162 1.617755 GGCGATGACCGATGCATACG 61.618 60.000 0.00 5.34 41.76 3.06
162 163 2.153913 GGCGATGACCGATGCATAC 58.846 57.895 0.00 0.00 41.76 2.39
163 164 4.673403 GGCGATGACCGATGCATA 57.327 55.556 0.00 0.00 41.76 3.14
478 479 1.244019 ATGCTTTCACTCGGCCAACC 61.244 55.000 2.24 0.00 0.00 3.77
479 480 0.598065 AATGCTTTCACTCGGCCAAC 59.402 50.000 2.24 0.00 0.00 3.77
480 481 1.269448 GAAATGCTTTCACTCGGCCAA 59.731 47.619 2.24 0.00 39.45 4.52
481 482 0.881118 GAAATGCTTTCACTCGGCCA 59.119 50.000 2.24 0.00 39.45 5.36
482 483 0.171231 GGAAATGCTTTCACTCGGCC 59.829 55.000 0.00 0.00 41.43 6.13
483 484 0.179189 CGGAAATGCTTTCACTCGGC 60.179 55.000 9.75 0.00 41.43 5.54
484 485 1.438651 TCGGAAATGCTTTCACTCGG 58.561 50.000 9.75 0.00 41.43 4.63
485 486 4.857871 TTATCGGAAATGCTTTCACTCG 57.142 40.909 9.75 5.66 41.43 4.18
486 487 9.736023 AATAAATTATCGGAAATGCTTTCACTC 57.264 29.630 9.75 0.00 41.43 3.51
487 488 9.736023 GAATAAATTATCGGAAATGCTTTCACT 57.264 29.630 9.75 0.00 41.43 3.41
488 489 9.736023 AGAATAAATTATCGGAAATGCTTTCAC 57.264 29.630 9.75 0.00 41.43 3.18
494 495 9.399403 GGAAGAAGAATAAATTATCGGAAATGC 57.601 33.333 0.00 0.00 0.00 3.56
495 496 9.899226 GGGAAGAAGAATAAATTATCGGAAATG 57.101 33.333 0.00 0.00 0.00 2.32
496 497 9.078990 GGGGAAGAAGAATAAATTATCGGAAAT 57.921 33.333 0.00 0.00 0.00 2.17
497 498 7.504574 GGGGGAAGAAGAATAAATTATCGGAAA 59.495 37.037 0.00 0.00 0.00 3.13
498 499 7.002276 GGGGGAAGAAGAATAAATTATCGGAA 58.998 38.462 0.00 0.00 0.00 4.30
499 500 6.331837 AGGGGGAAGAAGAATAAATTATCGGA 59.668 38.462 0.00 0.00 0.00 4.55
500 501 6.543735 AGGGGGAAGAAGAATAAATTATCGG 58.456 40.000 0.00 0.00 0.00 4.18
501 502 7.389053 CAGAGGGGGAAGAAGAATAAATTATCG 59.611 40.741 0.00 0.00 0.00 2.92
502 503 8.221251 ACAGAGGGGGAAGAAGAATAAATTATC 58.779 37.037 0.00 0.00 0.00 1.75
503 504 8.119062 ACAGAGGGGGAAGAAGAATAAATTAT 57.881 34.615 0.00 0.00 0.00 1.28
504 505 7.525158 ACAGAGGGGGAAGAAGAATAAATTA 57.475 36.000 0.00 0.00 0.00 1.40
505 506 6.408770 ACAGAGGGGGAAGAAGAATAAATT 57.591 37.500 0.00 0.00 0.00 1.82
542 544 4.860022 TGGGAATTTCTTGGAGGAGAATC 58.140 43.478 0.00 0.00 35.70 2.52
603 605 9.209297 CATTTCGGAATTTCTTTTTGTTGTTTC 57.791 29.630 0.00 0.00 0.00 2.78
607 637 8.386606 TGTTCATTTCGGAATTTCTTTTTGTTG 58.613 29.630 0.00 0.00 0.00 3.33
657 687 1.550072 AGCAATTATTGGGGTGCACAC 59.450 47.619 20.43 16.45 39.50 3.82
758 788 2.027625 CGGGAGACAGGTGCGTTTC 61.028 63.158 0.00 0.00 0.00 2.78
815 845 2.214216 CGGGACCCCTCACTGACAA 61.214 63.158 4.46 0.00 0.00 3.18
954 987 2.639286 GTGGTTTGCGCTGAGGTG 59.361 61.111 9.73 0.00 0.00 4.00
955 988 2.594592 GGTGGTTTGCGCTGAGGT 60.595 61.111 9.73 0.00 0.00 3.85
958 991 4.927782 AGCGGTGGTTTGCGCTGA 62.928 61.111 9.73 0.00 36.28 4.26
959 992 3.879351 GAAGCGGTGGTTTGCGCTG 62.879 63.158 9.73 0.00 37.78 5.18
960 993 3.660111 GAAGCGGTGGTTTGCGCT 61.660 61.111 9.73 0.00 39.55 5.92
1211 1269 1.481901 TTACCGCCTTACCACTGCCA 61.482 55.000 0.00 0.00 0.00 4.92
1299 1363 0.104304 AAGAACACGGCGAACAGTCT 59.896 50.000 16.62 5.70 0.00 3.24
1301 1365 1.213094 CGAAGAACACGGCGAACAGT 61.213 55.000 16.62 3.29 0.00 3.55
1408 1472 0.105778 CAAACCAATTTGGCCCACGT 59.894 50.000 15.49 0.00 42.67 4.49
1464 1534 0.546598 ATCCCACCACGAGATTTCCC 59.453 55.000 0.00 0.00 0.00 3.97
1644 1727 6.381801 AGTGATAAGAACTGCAATTTTTCCG 58.618 36.000 0.00 0.00 0.00 4.30
1698 1781 6.530120 TGGCTAGAGTTACAATTCAGAAACA 58.470 36.000 0.00 0.00 0.00 2.83
1715 1798 2.103373 GTGACTGACTGGATGGCTAGA 58.897 52.381 0.00 0.00 0.00 2.43
1783 1872 2.037136 GCTGCATCACAAGGACGCT 61.037 57.895 0.00 0.00 0.00 5.07
1784 1873 2.482374 GCTGCATCACAAGGACGC 59.518 61.111 0.00 0.00 0.00 5.19
1786 1875 0.950555 TGACGCTGCATCACAAGGAC 60.951 55.000 0.00 0.00 0.00 3.85
1787 1876 0.950555 GTGACGCTGCATCACAAGGA 60.951 55.000 22.34 0.00 44.87 3.36
1788 1877 1.499056 GTGACGCTGCATCACAAGG 59.501 57.895 22.34 0.00 44.87 3.61
1792 1881 0.798159 TTCATGTGACGCTGCATCAC 59.202 50.000 20.76 20.76 45.58 3.06
1793 1882 1.081094 CTTCATGTGACGCTGCATCA 58.919 50.000 0.00 0.00 0.00 3.07
1794 1883 1.362768 TCTTCATGTGACGCTGCATC 58.637 50.000 0.00 0.00 0.00 3.91
1795 1884 1.812235 TTCTTCATGTGACGCTGCAT 58.188 45.000 0.00 0.00 0.00 3.96
1796 1885 1.465777 CATTCTTCATGTGACGCTGCA 59.534 47.619 0.00 0.00 0.00 4.41
1797 1886 1.733912 TCATTCTTCATGTGACGCTGC 59.266 47.619 0.00 0.00 34.06 5.25
1798 1887 2.998670 AGTCATTCTTCATGTGACGCTG 59.001 45.455 7.51 0.61 45.17 5.18
1799 1888 2.998670 CAGTCATTCTTCATGTGACGCT 59.001 45.455 7.51 0.00 45.17 5.07
1800 1889 2.738846 ACAGTCATTCTTCATGTGACGC 59.261 45.455 7.51 0.00 45.17 5.19
1820 1909 3.231160 CCTAAATTCGGACGCACAAAAC 58.769 45.455 0.00 0.00 0.00 2.43
1822 1911 1.198178 GCCTAAATTCGGACGCACAAA 59.802 47.619 0.00 0.00 0.00 2.83
1823 1912 0.800012 GCCTAAATTCGGACGCACAA 59.200 50.000 0.00 0.00 0.00 3.33
1830 1919 2.676632 TTAGCGTGCCTAAATTCGGA 57.323 45.000 0.00 0.00 33.18 4.55
1870 1959 6.376299 ACACAAGATCAATTAGCACATCACAT 59.624 34.615 0.00 0.00 0.00 3.21
1891 1980 0.587768 CGCTGCATCACAAGAACACA 59.412 50.000 0.00 0.00 0.00 3.72
1894 1983 0.166814 GGACGCTGCATCACAAGAAC 59.833 55.000 0.00 0.00 0.00 3.01
1955 2048 1.453379 CTCCGAGGAGAGGGCGTTA 60.453 63.158 13.69 0.00 44.53 3.18
2006 2099 1.070105 AGACGCTAAAACGGTGCCA 59.930 52.632 0.00 0.00 37.37 4.92
2017 2110 0.174845 CCGGATTTGGACAGACGCTA 59.825 55.000 0.00 0.00 0.00 4.26
2061 2154 3.427243 CGTCACTGAGGATTACGAGAAC 58.573 50.000 0.00 0.00 35.66 3.01
2076 2169 0.745845 GGCAGCAATGATCCGTCACT 60.746 55.000 0.00 0.00 37.14 3.41
2150 2243 1.977544 AACTGAGAGGGGACGACGG 60.978 63.158 0.00 0.00 0.00 4.79
2180 2273 3.083997 ACGAGGCTGGGTCCATCC 61.084 66.667 0.51 1.81 32.79 3.51
2189 2282 3.818787 GGGCAATGCACGAGGCTG 61.819 66.667 7.79 0.00 45.15 4.85
2216 2309 0.835941 GGGACACAGCCATCTCAGAT 59.164 55.000 0.00 0.00 0.00 2.90
2623 2716 2.903784 TGCCGATGCCTGTTATACCTAT 59.096 45.455 0.00 0.00 36.33 2.57
2727 2820 3.306088 CCGATATGGGAGTGGTACATGAC 60.306 52.174 0.00 0.00 44.52 3.06
2963 3056 3.756963 GGACATCTTGTAGGGTTTGGTTC 59.243 47.826 0.00 0.00 0.00 3.62
3032 3125 1.181098 ATGGACCAAAGCTGTGGCAC 61.181 55.000 23.74 16.07 43.00 5.01
3074 3167 2.251642 GCCTGTCGTGACGCCTTTT 61.252 57.895 0.00 0.00 0.00 2.27
3150 3243 4.033702 CACGTTGATCAGTGATGGATTCAG 59.966 45.833 11.20 0.00 40.56 3.02
3216 3309 1.076485 GCATCACTCCCTGGCCAAT 60.076 57.895 7.01 0.00 0.00 3.16
3440 3533 5.132502 TGTGGATCTGTGAATTCTTTGTGT 58.867 37.500 7.05 0.00 0.00 3.72
3500 3593 0.522626 TGTGCTGTGCGGATCAAATG 59.477 50.000 0.00 0.00 0.00 2.32
3510 3603 0.948623 TCATGTACCGTGTGCTGTGC 60.949 55.000 0.00 0.00 0.00 4.57
3515 3608 3.059884 CTCCATATCATGTACCGTGTGC 58.940 50.000 0.00 0.00 0.00 4.57
3530 3623 9.151471 CTTTCGTTATCTGTTTTTCTCTCCATA 57.849 33.333 0.00 0.00 0.00 2.74
3598 3691 8.943002 CAACAAGGTCTAAAAATATACCGAAGT 58.057 33.333 0.00 0.00 37.09 3.01
3732 3829 6.841443 ACAATCTATGCATTCTCTCTTTCG 57.159 37.500 3.54 0.00 0.00 3.46
3769 3883 2.799917 GCAGCCACAGTAGGATTAGACG 60.800 54.545 0.00 0.00 0.00 4.18
3778 3892 1.374631 TTGCTCGCAGCCACAGTAG 60.375 57.895 5.82 0.00 41.51 2.57
3823 3937 1.672881 CGCAGATTTCAGATTGGGGAC 59.327 52.381 0.00 0.00 0.00 4.46
3863 3978 0.699577 TCTTTGTCCCCAACTCCCCA 60.700 55.000 0.00 0.00 0.00 4.96
3864 3979 0.704664 ATCTTTGTCCCCAACTCCCC 59.295 55.000 0.00 0.00 0.00 4.81
3865 3980 1.616994 CCATCTTTGTCCCCAACTCCC 60.617 57.143 0.00 0.00 0.00 4.30
3866 3981 1.075536 ACCATCTTTGTCCCCAACTCC 59.924 52.381 0.00 0.00 0.00 3.85
3867 3982 2.586648 ACCATCTTTGTCCCCAACTC 57.413 50.000 0.00 0.00 0.00 3.01
3868 3983 2.714250 TGTACCATCTTTGTCCCCAACT 59.286 45.455 0.00 0.00 0.00 3.16
3869 3984 2.817844 GTGTACCATCTTTGTCCCCAAC 59.182 50.000 0.00 0.00 0.00 3.77
3870 3985 2.224917 GGTGTACCATCTTTGTCCCCAA 60.225 50.000 0.00 0.00 35.64 4.12
3934 4050 0.947244 CAGGCGGCATAGGTCATTTC 59.053 55.000 13.08 0.00 0.00 2.17
4093 4216 3.875727 GTGATCTTGATGTGGATCCAGTG 59.124 47.826 16.81 2.07 37.96 3.66
4236 4378 3.650070 TGACTAGAGTGTGCTTGTCTG 57.350 47.619 0.00 0.00 40.01 3.51
4281 4423 8.957466 GGATAAAGTAAGAAGGCAGTACATTTT 58.043 33.333 0.00 0.00 0.00 1.82
4314 4482 9.362539 CATCCCTTCAAGAAACTTTAAATGATG 57.637 33.333 0.00 0.00 0.00 3.07
4315 4483 8.534496 CCATCCCTTCAAGAAACTTTAAATGAT 58.466 33.333 0.00 0.00 0.00 2.45
4316 4484 7.525360 GCCATCCCTTCAAGAAACTTTAAATGA 60.525 37.037 0.00 0.00 0.00 2.57
4317 4485 6.591448 GCCATCCCTTCAAGAAACTTTAAATG 59.409 38.462 0.00 0.00 0.00 2.32
4318 4486 6.295859 GGCCATCCCTTCAAGAAACTTTAAAT 60.296 38.462 0.00 0.00 0.00 1.40
4319 4487 5.011635 GGCCATCCCTTCAAGAAACTTTAAA 59.988 40.000 0.00 0.00 0.00 1.52
4320 4488 4.526650 GGCCATCCCTTCAAGAAACTTTAA 59.473 41.667 0.00 0.00 0.00 1.52
4321 4489 4.086457 GGCCATCCCTTCAAGAAACTTTA 58.914 43.478 0.00 0.00 0.00 1.85
4322 4490 2.899900 GGCCATCCCTTCAAGAAACTTT 59.100 45.455 0.00 0.00 0.00 2.66
4323 4491 2.110721 AGGCCATCCCTTCAAGAAACTT 59.889 45.455 5.01 0.00 43.06 2.66
4324 4492 1.713078 AGGCCATCCCTTCAAGAAACT 59.287 47.619 5.01 0.00 43.06 2.66
4325 4493 2.222227 AGGCCATCCCTTCAAGAAAC 57.778 50.000 5.01 0.00 43.06 2.78
4335 4503 2.835156 GGAGAGTAGATAAGGCCATCCC 59.165 54.545 5.01 0.00 0.00 3.85
4336 4504 3.511477 TGGAGAGTAGATAAGGCCATCC 58.489 50.000 5.01 0.00 0.00 3.51
4337 4505 4.559704 CGTTGGAGAGTAGATAAGGCCATC 60.560 50.000 5.01 0.00 0.00 3.51
4338 4506 3.322254 CGTTGGAGAGTAGATAAGGCCAT 59.678 47.826 5.01 0.00 0.00 4.40
4339 4507 2.693591 CGTTGGAGAGTAGATAAGGCCA 59.306 50.000 5.01 0.00 0.00 5.36
4376 4544 7.130775 AGTGGTAGTGGTAGTGGTAGAATAAT 58.869 38.462 0.00 0.00 0.00 1.28
4377 4545 6.496743 AGTGGTAGTGGTAGTGGTAGAATAA 58.503 40.000 0.00 0.00 0.00 1.40
4379 4547 4.944177 AGTGGTAGTGGTAGTGGTAGAAT 58.056 43.478 0.00 0.00 0.00 2.40
4380 4548 4.393239 AGTGGTAGTGGTAGTGGTAGAA 57.607 45.455 0.00 0.00 0.00 2.10
4381 4549 5.398353 GGATAGTGGTAGTGGTAGTGGTAGA 60.398 48.000 0.00 0.00 0.00 2.59
4382 4550 4.826183 GGATAGTGGTAGTGGTAGTGGTAG 59.174 50.000 0.00 0.00 0.00 3.18
4383 4551 4.386761 GGGATAGTGGTAGTGGTAGTGGTA 60.387 50.000 0.00 0.00 0.00 3.25
4384 4552 3.629282 GGGATAGTGGTAGTGGTAGTGGT 60.629 52.174 0.00 0.00 0.00 4.16
4385 4553 2.963782 GGGATAGTGGTAGTGGTAGTGG 59.036 54.545 0.00 0.00 0.00 4.00
4386 4554 3.912248 AGGGATAGTGGTAGTGGTAGTG 58.088 50.000 0.00 0.00 0.00 2.74
4387 4555 5.135705 ACATAGGGATAGTGGTAGTGGTAGT 59.864 44.000 0.00 0.00 0.00 2.73
4398 4566 6.463049 CCTGTCCTGTAAACATAGGGATAGTG 60.463 46.154 10.61 2.67 34.80 2.74
4417 4587 5.431179 TTTAACTATGAGGAACCCTGTCC 57.569 43.478 0.00 0.00 38.03 4.02
4418 4588 6.473758 ACTTTTAACTATGAGGAACCCTGTC 58.526 40.000 0.00 0.00 31.76 3.51
4419 4589 6.043938 TGACTTTTAACTATGAGGAACCCTGT 59.956 38.462 0.00 0.00 31.76 4.00
4420 4590 6.472887 TGACTTTTAACTATGAGGAACCCTG 58.527 40.000 0.00 0.00 31.76 4.45
4421 4591 6.697641 TGACTTTTAACTATGAGGAACCCT 57.302 37.500 0.00 0.00 36.03 4.34
4478 4658 1.282738 GGGGTCGGGATTAGGAAACAA 59.717 52.381 0.00 0.00 0.00 2.83
4563 4743 3.570212 AGCCGGCTCTTGGGTTGT 61.570 61.111 27.08 0.00 32.04 3.32
4564 4744 3.058160 CAGCCGGCTCTTGGGTTG 61.058 66.667 30.29 10.27 34.30 3.77
4665 4850 0.537143 AGCACCAAGACGCCAAATCA 60.537 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.