Multiple sequence alignment - TraesCS2D01G110600

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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 TraesCS2D01G110600 chr2D 100.000 2508 0 0 1 2508 61313908 61311401 0.000000e+00 4632.0
1 TraesCS2D01G110600 chr2B 88.417 1554 114 33 152 1690 96081610 96080108 0.000000e+00 1812.0
2 TraesCS2D01G110600 chr2B 83.866 595 35 22 721 1293 96025833 96025278 6.190000e-141 510.0
3 TraesCS2D01G110600 chr2B 87.007 431 37 16 1815 2235 96079784 96079363 3.780000e-128 468.0
4 TraesCS2D01G110600 chr2A 90.731 917 52 19 848 1749 61804654 61803756 0.000000e+00 1192.0
5 TraesCS2D01G110600 chr2A 89.666 629 34 15 1813 2415 61801241 61800618 0.000000e+00 773.0
6 TraesCS2D01G110600 chr2A 86.807 667 49 11 223 855 61805337 61804676 0.000000e+00 708.0
7 TraesCS2D01G110600 chr2A 100.000 31 0 0 1690 1720 513868700 513868730 9.690000e-05 58.4
8 TraesCS2D01G110600 chr5D 100.000 36 0 0 1690 1725 313155944 313155979 1.610000e-07 67.6


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 TraesCS2D01G110600 chr2D 61311401 61313908 2507 True 4632 4632 100.000 1 2508 1 chr2D.!!$R1 2507
1 TraesCS2D01G110600 chr2B 96079363 96081610 2247 True 1140 1812 87.712 152 2235 2 chr2B.!!$R2 2083
2 TraesCS2D01G110600 chr2B 96025278 96025833 555 True 510 510 83.866 721 1293 1 chr2B.!!$R1 572
3 TraesCS2D01G110600 chr2A 61800618 61805337 4719 True 891 1192 89.068 223 2415 3 chr2A.!!$R1 2192

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
673 682 0.108992 GACGCACTAACGACCATGGA 60.109 55.0 21.47 0.0 36.7 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1618 0.179134 GAGATGGTTGGACCGACGAG 60.179 60.0 5.75 0.0 42.58 4.18 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
33 34 2.185867 GCATCGGTCGGCCAGTTA 59.814 61.111 6.96 0.00 34.09 2.24
34 35 1.883084 GCATCGGTCGGCCAGTTAG 60.883 63.158 6.96 0.00 34.09 2.34
35 36 1.813859 CATCGGTCGGCCAGTTAGA 59.186 57.895 6.96 0.00 34.09 2.10
36 37 0.249073 CATCGGTCGGCCAGTTAGAG 60.249 60.000 6.96 0.00 34.09 2.43
37 38 0.683504 ATCGGTCGGCCAGTTAGAGT 60.684 55.000 6.96 0.00 34.09 3.24
38 39 0.896940 TCGGTCGGCCAGTTAGAGTT 60.897 55.000 6.96 0.00 34.09 3.01
39 40 0.736325 CGGTCGGCCAGTTAGAGTTG 60.736 60.000 6.96 0.00 34.09 3.16
40 41 0.391263 GGTCGGCCAGTTAGAGTTGG 60.391 60.000 0.00 0.00 37.53 3.77
41 42 0.320697 GTCGGCCAGTTAGAGTTGGT 59.679 55.000 2.24 0.00 36.81 3.67
42 43 0.606604 TCGGCCAGTTAGAGTTGGTC 59.393 55.000 2.24 0.00 36.81 4.02
43 44 0.608640 CGGCCAGTTAGAGTTGGTCT 59.391 55.000 2.24 0.00 36.93 3.85
44 45 1.404315 CGGCCAGTTAGAGTTGGTCTC 60.404 57.143 2.24 0.00 43.05 3.36
45 46 1.066071 GGCCAGTTAGAGTTGGTCTCC 60.066 57.143 0.00 0.00 43.71 3.71
46 47 1.623811 GCCAGTTAGAGTTGGTCTCCA 59.376 52.381 0.00 0.00 43.71 3.86
47 48 2.038557 GCCAGTTAGAGTTGGTCTCCAA 59.961 50.000 0.00 0.00 43.71 3.53
60 61 1.474077 GTCTCCAACCAATGTGGATGC 59.526 52.381 0.18 0.00 40.96 3.91
61 62 1.355381 TCTCCAACCAATGTGGATGCT 59.645 47.619 0.18 0.00 40.96 3.79
62 63 1.747355 CTCCAACCAATGTGGATGCTC 59.253 52.381 0.18 0.00 40.96 4.26
63 64 1.355381 TCCAACCAATGTGGATGCTCT 59.645 47.619 0.18 0.00 40.96 4.09
64 65 2.575735 TCCAACCAATGTGGATGCTCTA 59.424 45.455 0.18 0.00 40.96 2.43
65 66 3.010027 TCCAACCAATGTGGATGCTCTAA 59.990 43.478 0.18 0.00 40.96 2.10
66 67 3.379372 CCAACCAATGTGGATGCTCTAAG 59.621 47.826 0.18 0.00 40.96 2.18
67 68 2.648059 ACCAATGTGGATGCTCTAAGC 58.352 47.619 0.18 0.00 40.96 3.09
68 69 1.952296 CCAATGTGGATGCTCTAAGCC 59.048 52.381 0.00 0.00 40.96 4.35
69 70 1.952296 CAATGTGGATGCTCTAAGCCC 59.048 52.381 0.00 0.00 41.51 5.19
70 71 1.516110 ATGTGGATGCTCTAAGCCCT 58.484 50.000 0.00 0.00 41.51 5.19
71 72 1.289160 TGTGGATGCTCTAAGCCCTT 58.711 50.000 0.00 0.00 41.51 3.95
72 73 1.635487 TGTGGATGCTCTAAGCCCTTT 59.365 47.619 0.00 0.00 41.51 3.11
73 74 2.843730 TGTGGATGCTCTAAGCCCTTTA 59.156 45.455 0.00 0.00 41.51 1.85
74 75 3.206964 GTGGATGCTCTAAGCCCTTTAC 58.793 50.000 0.00 0.00 41.51 2.01
75 76 2.843730 TGGATGCTCTAAGCCCTTTACA 59.156 45.455 0.00 0.00 41.51 2.41
76 77 3.265737 TGGATGCTCTAAGCCCTTTACAA 59.734 43.478 0.00 0.00 41.51 2.41
77 78 3.628032 GGATGCTCTAAGCCCTTTACAAC 59.372 47.826 0.00 0.00 41.51 3.32
78 79 3.780804 TGCTCTAAGCCCTTTACAACA 57.219 42.857 0.00 0.00 41.51 3.33
79 80 3.408634 TGCTCTAAGCCCTTTACAACAC 58.591 45.455 0.00 0.00 41.51 3.32
80 81 3.181449 TGCTCTAAGCCCTTTACAACACA 60.181 43.478 0.00 0.00 41.51 3.72
81 82 3.818773 GCTCTAAGCCCTTTACAACACAA 59.181 43.478 0.00 0.00 34.48 3.33
82 83 4.083271 GCTCTAAGCCCTTTACAACACAAG 60.083 45.833 0.00 0.00 34.48 3.16
83 84 4.394729 TCTAAGCCCTTTACAACACAAGG 58.605 43.478 0.00 0.00 39.58 3.61
84 85 2.748209 AGCCCTTTACAACACAAGGT 57.252 45.000 0.00 0.00 38.37 3.50
85 86 2.306847 AGCCCTTTACAACACAAGGTG 58.693 47.619 0.00 0.00 38.37 4.00
86 87 1.269569 GCCCTTTACAACACAAGGTGC 60.270 52.381 0.00 0.00 38.37 5.01
87 88 2.306847 CCCTTTACAACACAAGGTGCT 58.693 47.619 0.00 0.00 38.37 4.40
88 89 2.693074 CCCTTTACAACACAAGGTGCTT 59.307 45.455 0.00 0.00 38.37 3.91
89 90 3.886505 CCCTTTACAACACAAGGTGCTTA 59.113 43.478 0.00 0.00 38.37 3.09
90 91 4.522789 CCCTTTACAACACAAGGTGCTTAT 59.477 41.667 0.00 0.00 38.37 1.73
91 92 5.460646 CCTTTACAACACAAGGTGCTTATG 58.539 41.667 0.00 0.00 36.98 1.90
92 93 5.240623 CCTTTACAACACAAGGTGCTTATGA 59.759 40.000 0.00 0.00 36.98 2.15
93 94 5.940192 TTACAACACAAGGTGCTTATGAG 57.060 39.130 0.00 0.00 36.98 2.90
94 95 4.085357 ACAACACAAGGTGCTTATGAGA 57.915 40.909 0.00 0.00 36.98 3.27
95 96 4.067896 ACAACACAAGGTGCTTATGAGAG 58.932 43.478 0.00 0.00 36.98 3.20
96 97 3.340814 ACACAAGGTGCTTATGAGAGG 57.659 47.619 0.00 0.00 36.98 3.69
97 98 2.639839 ACACAAGGTGCTTATGAGAGGT 59.360 45.455 0.00 0.00 36.98 3.85
98 99 3.005554 CACAAGGTGCTTATGAGAGGTG 58.994 50.000 0.00 0.00 0.00 4.00
99 100 2.639839 ACAAGGTGCTTATGAGAGGTGT 59.360 45.455 0.00 0.00 0.00 4.16
100 101 3.073062 ACAAGGTGCTTATGAGAGGTGTT 59.927 43.478 0.00 0.00 0.00 3.32
101 102 4.074970 CAAGGTGCTTATGAGAGGTGTTT 58.925 43.478 0.00 0.00 0.00 2.83
102 103 5.221843 ACAAGGTGCTTATGAGAGGTGTTTA 60.222 40.000 0.00 0.00 0.00 2.01
103 104 5.091261 AGGTGCTTATGAGAGGTGTTTAG 57.909 43.478 0.00 0.00 0.00 1.85
104 105 4.777896 AGGTGCTTATGAGAGGTGTTTAGA 59.222 41.667 0.00 0.00 0.00 2.10
105 106 5.248477 AGGTGCTTATGAGAGGTGTTTAGAA 59.752 40.000 0.00 0.00 0.00 2.10
106 107 5.938125 GGTGCTTATGAGAGGTGTTTAGAAA 59.062 40.000 0.00 0.00 0.00 2.52
107 108 6.430000 GGTGCTTATGAGAGGTGTTTAGAAAA 59.570 38.462 0.00 0.00 0.00 2.29
108 109 7.040686 GGTGCTTATGAGAGGTGTTTAGAAAAA 60.041 37.037 0.00 0.00 0.00 1.94
109 110 8.515414 GTGCTTATGAGAGGTGTTTAGAAAAAT 58.485 33.333 0.00 0.00 0.00 1.82
110 111 9.733556 TGCTTATGAGAGGTGTTTAGAAAAATA 57.266 29.630 0.00 0.00 0.00 1.40
115 116 8.754991 TGAGAGGTGTTTAGAAAAATAAACCA 57.245 30.769 6.84 0.00 42.45 3.67
116 117 8.846211 TGAGAGGTGTTTAGAAAAATAAACCAG 58.154 33.333 6.84 0.00 42.45 4.00
117 118 8.762481 AGAGGTGTTTAGAAAAATAAACCAGT 57.238 30.769 6.84 0.00 42.45 4.00
118 119 9.197306 AGAGGTGTTTAGAAAAATAAACCAGTT 57.803 29.630 6.84 0.00 42.45 3.16
119 120 9.811995 GAGGTGTTTAGAAAAATAAACCAGTTT 57.188 29.630 0.86 0.86 42.45 2.66
153 154 5.296151 CCAATGCTTATTGGTAGAGGAGA 57.704 43.478 10.20 0.00 44.56 3.71
154 155 5.303971 CCAATGCTTATTGGTAGAGGAGAG 58.696 45.833 10.20 0.00 44.56 3.20
155 156 5.070981 CCAATGCTTATTGGTAGAGGAGAGA 59.929 44.000 10.20 0.00 44.56 3.10
156 157 5.799827 ATGCTTATTGGTAGAGGAGAGAC 57.200 43.478 0.00 0.00 0.00 3.36
157 158 4.610333 TGCTTATTGGTAGAGGAGAGACA 58.390 43.478 0.00 0.00 0.00 3.41
158 159 5.023452 TGCTTATTGGTAGAGGAGAGACAA 58.977 41.667 0.00 0.00 0.00 3.18
159 160 5.483937 TGCTTATTGGTAGAGGAGAGACAAA 59.516 40.000 0.00 0.00 0.00 2.83
160 161 6.013725 TGCTTATTGGTAGAGGAGAGACAAAA 60.014 38.462 0.00 0.00 0.00 2.44
167 168 7.786030 TGGTAGAGGAGAGACAAAATAATCAG 58.214 38.462 0.00 0.00 0.00 2.90
168 169 7.147655 TGGTAGAGGAGAGACAAAATAATCAGG 60.148 40.741 0.00 0.00 0.00 3.86
171 172 5.435291 AGGAGAGACAAAATAATCAGGCAG 58.565 41.667 0.00 0.00 0.00 4.85
180 181 1.289160 TAATCAGGCAGCCCTCTTGT 58.711 50.000 8.22 0.00 40.33 3.16
181 182 0.323178 AATCAGGCAGCCCTCTTGTG 60.323 55.000 8.22 0.00 40.33 3.33
182 183 2.833604 ATCAGGCAGCCCTCTTGTGC 62.834 60.000 8.22 0.00 40.33 4.57
205 206 3.055240 AGAGCTAAGCACTGAAGCATCTT 60.055 43.478 7.71 0.00 38.75 2.40
241 242 4.083271 GCCTAAGCAAACTCGATCTTTTGT 60.083 41.667 13.01 0.00 39.53 2.83
275 276 1.860676 TAGTTGTGTCAGACGGTTGC 58.139 50.000 0.00 0.00 0.00 4.17
435 439 1.135402 CGCAAGTGGGAATAAACAGGC 60.135 52.381 0.00 0.00 0.00 4.85
488 492 2.124942 GCTGCCAGCTACTGACCC 60.125 66.667 10.04 0.00 38.45 4.46
502 506 2.032426 ACTGACCCTTTTTGTTAACGCG 59.968 45.455 3.53 3.53 0.00 6.01
506 510 2.224784 ACCCTTTTTGTTAACGCGCTAG 59.775 45.455 5.73 0.00 0.00 3.42
508 512 2.239201 CTTTTTGTTAACGCGCTAGGC 58.761 47.619 5.73 0.00 38.69 3.93
542 547 2.560244 CGAGAGCTCGTCGAACATG 58.440 57.895 22.93 0.00 46.99 3.21
544 549 1.540407 GAGAGCTCGTCGAACATGTC 58.460 55.000 8.37 0.00 0.00 3.06
587 592 3.630148 GACATGGCACGCCGATCG 61.630 66.667 8.51 8.51 45.38 3.69
618 627 7.240674 TCGATACATCATTTCCGTTTCTTTTG 58.759 34.615 0.00 0.00 0.00 2.44
623 632 4.942852 TCATTTCCGTTTCTTTTGCACAT 58.057 34.783 0.00 0.00 0.00 3.21
638 647 0.464373 CACATCACTAAGCCCGGCAT 60.464 55.000 13.15 1.26 0.00 4.40
665 674 2.741122 TGTTTTTGGACGCACTAACG 57.259 45.000 0.00 0.00 39.50 3.18
673 682 0.108992 GACGCACTAACGACCATGGA 60.109 55.000 21.47 0.00 36.70 3.41
715 724 2.362668 AGCGCGCGTAATGATTTTAC 57.637 45.000 32.35 9.71 0.00 2.01
745 755 3.872560 AAAGCGTAAAGGTTCTTCGTG 57.127 42.857 0.00 0.00 40.06 4.35
779 812 3.308438 TCTTTGTAACACTACTCCGGC 57.692 47.619 0.00 0.00 0.00 6.13
818 852 6.373774 GTGACAGAAGATTTTCATGACTGGAT 59.626 38.462 10.81 0.00 35.70 3.41
869 932 7.856415 AGCTGATCCAGATTAAGTTTAACTCT 58.144 34.615 0.00 0.00 32.44 3.24
905 973 3.418675 CGCTGGTAGTACAGTGGTG 57.581 57.895 2.06 0.00 43.43 4.17
1190 1283 0.238289 CAAATCCTGGCGACACACAC 59.762 55.000 0.00 0.00 35.60 3.82
1198 1291 2.319707 CGACACACACGCACACAC 59.680 61.111 0.00 0.00 0.00 3.82
1199 1292 2.448705 CGACACACACGCACACACA 61.449 57.895 0.00 0.00 0.00 3.72
1201 1294 1.631144 GACACACACGCACACACACA 61.631 55.000 0.00 0.00 0.00 3.72
1202 1295 1.225991 CACACACGCACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
1203 1296 1.669437 ACACACGCACACACACACA 60.669 52.632 0.00 0.00 0.00 3.72
1204 1297 1.024046 ACACACGCACACACACACAT 61.024 50.000 0.00 0.00 0.00 3.21
1205 1298 0.933796 CACACGCACACACACACATA 59.066 50.000 0.00 0.00 0.00 2.29
1206 1299 0.934496 ACACGCACACACACACATAC 59.066 50.000 0.00 0.00 0.00 2.39
1214 1307 3.000041 ACACACACACATACGGCTAATG 59.000 45.455 0.00 0.00 0.00 1.90
1499 1592 2.125512 CCGGCTTCTCCTTCCACG 60.126 66.667 0.00 0.00 0.00 4.94
1504 1597 3.665675 CTTCTCCTTCCACGGCCGG 62.666 68.421 31.76 18.27 0.00 6.13
1514 1607 3.899395 ACGGCCGGTGAAAATAGC 58.101 55.556 31.76 0.00 0.00 2.97
1571 1667 6.638610 ACTGAGATCTTGTTAATCACCTCTG 58.361 40.000 0.00 0.00 0.00 3.35
1593 1690 8.190326 TCTGTCTTGTCTATCTTTAGTTTGGA 57.810 34.615 0.00 0.00 0.00 3.53
1667 1768 6.350906 AGTGTTGTTGTAAGTTGGCTAAGTA 58.649 36.000 0.00 0.00 0.00 2.24
1675 1776 3.336138 AGTTGGCTAAGTAGAGCAACC 57.664 47.619 0.00 0.00 44.76 3.77
1705 1806 2.334971 TCGTTTCTCGAATACGCACA 57.665 45.000 8.30 0.00 45.98 4.57
1708 1809 2.759038 GTTTCTCGAATACGCACAAGC 58.241 47.619 0.00 0.00 39.58 4.01
1755 2176 8.014322 TGGATAATCGTATTTCGTAAATCTGC 57.986 34.615 0.00 0.00 40.80 4.26
1767 2188 4.449743 TCGTAAATCTGCGTGCTAAAGTTT 59.550 37.500 0.00 0.00 31.87 2.66
1768 2189 4.781528 CGTAAATCTGCGTGCTAAAGTTTC 59.218 41.667 0.00 0.00 0.00 2.78
1781 2202 7.020010 GTGCTAAAGTTTCAGTGAAGATCATG 58.980 38.462 5.56 0.00 0.00 3.07
1783 2204 7.877612 TGCTAAAGTTTCAGTGAAGATCATGTA 59.122 33.333 5.56 0.00 0.00 2.29
1794 4410 1.210478 AGATCATGTAAGCAAGCCGGT 59.790 47.619 1.90 0.00 0.00 5.28
1801 4417 1.669265 GTAAGCAAGCCGGTATTGACC 59.331 52.381 21.31 7.97 43.03 4.02
1803 4419 2.469516 GCAAGCCGGTATTGACCCG 61.470 63.158 21.31 0.00 43.64 5.28
1811 4427 1.202604 CGGTATTGACCCGGTATTGCT 60.203 52.381 0.00 0.00 43.64 3.91
1847 4481 3.270027 TGTCAGTGTCTTCCAAAGTGTG 58.730 45.455 0.00 0.00 0.00 3.82
1858 4492 2.231478 TCCAAAGTGTGACGATCCTCTC 59.769 50.000 0.00 0.00 0.00 3.20
1896 4530 0.179000 ATGATGACGCTTGTCCCTCC 59.821 55.000 0.00 0.00 42.17 4.30
1929 4563 6.763135 TGCATAACAATCCTCTAATGTGAGTC 59.237 38.462 0.00 0.00 32.50 3.36
1934 4568 7.482169 ACAATCCTCTAATGTGAGTCTTACA 57.518 36.000 0.00 0.00 32.50 2.41
1935 4569 7.551585 ACAATCCTCTAATGTGAGTCTTACAG 58.448 38.462 3.63 0.00 32.50 2.74
1936 4570 7.397476 ACAATCCTCTAATGTGAGTCTTACAGA 59.603 37.037 3.63 0.00 32.50 3.41
1937 4571 8.420222 CAATCCTCTAATGTGAGTCTTACAGAT 58.580 37.037 3.63 0.00 32.50 2.90
1938 4572 7.962995 TCCTCTAATGTGAGTCTTACAGATT 57.037 36.000 3.63 0.00 35.83 2.40
1939 4573 8.001881 TCCTCTAATGTGAGTCTTACAGATTC 57.998 38.462 3.63 0.00 34.16 2.52
1940 4574 7.836685 TCCTCTAATGTGAGTCTTACAGATTCT 59.163 37.037 3.63 0.00 32.82 2.40
1957 4598 7.833786 ACAGATTCTTTCGTTAGTGGTGTATA 58.166 34.615 0.00 0.00 0.00 1.47
1987 4628 9.561069 AACATGTATAATGACCTTCATAAGACC 57.439 33.333 0.00 0.00 35.76 3.85
1988 4629 8.938883 ACATGTATAATGACCTTCATAAGACCT 58.061 33.333 0.00 0.00 35.76 3.85
2037 4692 4.988598 AGGTGCGCAAGTGGTCCG 62.989 66.667 14.00 0.00 41.68 4.79
2096 4754 0.464036 TGAACTCTTCAGTGTGCCGT 59.536 50.000 0.00 0.00 34.08 5.68
2118 4776 5.488341 GTCCATGCCTAACTTTAGTTCTGA 58.512 41.667 0.00 0.00 39.31 3.27
2138 4796 7.133133 TCTGATTTTCATCATCTCATCTCCA 57.867 36.000 0.00 0.00 38.81 3.86
2161 4819 1.670811 GGCTTGACCAATACATCCACG 59.329 52.381 0.00 0.00 38.86 4.94
2186 4844 0.389687 CCGCGGCAAAATGGAAATGT 60.390 50.000 14.67 0.00 0.00 2.71
2247 4907 2.488347 GGTGACTAAGGGCAACTCCAAA 60.488 50.000 0.00 0.00 36.21 3.28
2258 4918 1.069022 CAACTCCAAAGTGCGGACATG 60.069 52.381 10.52 7.87 35.36 3.21
2271 4931 2.732289 GACATGTTTGGCCAGTGGT 58.268 52.632 11.74 0.94 0.00 4.16
2273 4933 0.827507 ACATGTTTGGCCAGTGGTCC 60.828 55.000 12.24 13.23 0.00 4.46
2297 4964 2.185004 ATTTGTTCAGACCGGTCCTG 57.815 50.000 30.82 25.18 0.00 3.86
2366 5033 1.807165 CAGATGTCTGCCACGTCGG 60.807 63.158 0.00 0.00 44.81 4.79
2393 5060 2.366533 TGTTTACAAGCGAAACCCACA 58.633 42.857 0.00 0.00 36.20 4.17
2415 5083 0.398381 TTTTTGTTGCCTCTGCCCCT 60.398 50.000 0.00 0.00 36.33 4.79
2416 5084 0.480690 TTTTGTTGCCTCTGCCCCTA 59.519 50.000 0.00 0.00 36.33 3.53
2417 5085 0.704076 TTTGTTGCCTCTGCCCCTAT 59.296 50.000 0.00 0.00 36.33 2.57
2418 5086 0.255890 TTGTTGCCTCTGCCCCTATC 59.744 55.000 0.00 0.00 36.33 2.08
2419 5087 1.227674 GTTGCCTCTGCCCCTATCG 60.228 63.158 0.00 0.00 36.33 2.92
2420 5088 1.382557 TTGCCTCTGCCCCTATCGA 60.383 57.895 0.00 0.00 36.33 3.59
2421 5089 1.686325 TTGCCTCTGCCCCTATCGAC 61.686 60.000 0.00 0.00 36.33 4.20
2422 5090 2.873525 GCCTCTGCCCCTATCGACC 61.874 68.421 0.00 0.00 0.00 4.79
2423 5091 2.210711 CCTCTGCCCCTATCGACCC 61.211 68.421 0.00 0.00 0.00 4.46
2424 5092 2.122989 TCTGCCCCTATCGACCCC 60.123 66.667 0.00 0.00 0.00 4.95
2425 5093 3.242291 CTGCCCCTATCGACCCCC 61.242 72.222 0.00 0.00 0.00 5.40
2444 5112 3.878667 CCCCCTCTCATTCCGGCC 61.879 72.222 0.00 0.00 0.00 6.13
2445 5113 3.878667 CCCCTCTCATTCCGGCCC 61.879 72.222 0.00 0.00 0.00 5.80
2446 5114 3.089874 CCCTCTCATTCCGGCCCA 61.090 66.667 0.00 0.00 0.00 5.36
2447 5115 2.455565 CCCTCTCATTCCGGCCCAT 61.456 63.158 0.00 0.00 0.00 4.00
2448 5116 1.072159 CCTCTCATTCCGGCCCATC 59.928 63.158 0.00 0.00 0.00 3.51
2449 5117 1.301244 CTCTCATTCCGGCCCATCG 60.301 63.158 0.00 0.00 0.00 3.84
2450 5118 2.032860 CTCTCATTCCGGCCCATCGT 62.033 60.000 0.00 0.00 0.00 3.73
2451 5119 1.595382 CTCATTCCGGCCCATCGTC 60.595 63.158 0.00 0.00 0.00 4.20
2452 5120 2.967076 CATTCCGGCCCATCGTCG 60.967 66.667 0.00 0.00 0.00 5.12
2453 5121 3.467226 ATTCCGGCCCATCGTCGT 61.467 61.111 0.00 0.00 0.00 4.34
2454 5122 3.441011 ATTCCGGCCCATCGTCGTC 62.441 63.158 0.00 0.00 0.00 4.20
2458 5126 4.832608 GGCCCATCGTCGTCCACC 62.833 72.222 0.00 0.00 0.00 4.61
2460 5128 3.445687 CCCATCGTCGTCCACCGA 61.446 66.667 0.00 0.00 45.00 4.69
2476 5144 4.077184 GACCACCGCCGTGATGGA 62.077 66.667 6.77 0.00 43.14 3.41
2477 5145 4.082523 ACCACCGCCGTGATGGAG 62.083 66.667 6.77 0.00 43.14 3.86
2484 5152 4.873129 CCGTGATGGAGCCGTCGG 62.873 72.222 6.99 6.99 42.00 4.79
2485 5153 3.822192 CGTGATGGAGCCGTCGGA 61.822 66.667 17.49 0.00 34.87 4.55
2486 5154 2.105128 GTGATGGAGCCGTCGGAG 59.895 66.667 17.49 0.00 34.87 4.63
2487 5155 3.147595 TGATGGAGCCGTCGGAGG 61.148 66.667 17.49 0.00 34.87 4.30
2488 5156 2.833582 GATGGAGCCGTCGGAGGA 60.834 66.667 17.49 0.00 0.00 3.71
2489 5157 2.835431 ATGGAGCCGTCGGAGGAG 60.835 66.667 17.49 0.00 0.00 3.69
2490 5158 3.663815 ATGGAGCCGTCGGAGGAGT 62.664 63.158 17.49 0.00 0.00 3.85
2491 5159 3.519930 GGAGCCGTCGGAGGAGTC 61.520 72.222 17.49 2.53 0.00 3.36
2492 5160 3.878519 GAGCCGTCGGAGGAGTCG 61.879 72.222 17.49 0.00 0.00 4.18
2493 5161 4.405671 AGCCGTCGGAGGAGTCGA 62.406 66.667 17.49 0.00 0.00 4.20
2494 5162 3.210528 GCCGTCGGAGGAGTCGAT 61.211 66.667 17.49 0.00 38.93 3.59
2495 5163 1.890979 GCCGTCGGAGGAGTCGATA 60.891 63.158 17.49 0.00 38.93 2.92
2496 5164 1.442526 GCCGTCGGAGGAGTCGATAA 61.443 60.000 17.49 0.00 38.93 1.75
2497 5165 0.307146 CCGTCGGAGGAGTCGATAAC 59.693 60.000 4.91 0.00 38.93 1.89
2498 5166 1.012086 CGTCGGAGGAGTCGATAACA 58.988 55.000 0.00 0.00 38.93 2.41
2499 5167 1.399440 CGTCGGAGGAGTCGATAACAA 59.601 52.381 0.00 0.00 38.93 2.83
2500 5168 2.033049 CGTCGGAGGAGTCGATAACAAT 59.967 50.000 0.00 0.00 38.93 2.71
2501 5169 3.249320 CGTCGGAGGAGTCGATAACAATA 59.751 47.826 0.00 0.00 38.93 1.90
2502 5170 4.083431 CGTCGGAGGAGTCGATAACAATAT 60.083 45.833 0.00 0.00 38.93 1.28
2503 5171 5.562307 CGTCGGAGGAGTCGATAACAATATT 60.562 44.000 0.00 0.00 38.93 1.28
2504 5172 5.857517 GTCGGAGGAGTCGATAACAATATTC 59.142 44.000 0.00 0.00 38.93 1.75
2505 5173 5.533528 TCGGAGGAGTCGATAACAATATTCA 59.466 40.000 0.00 0.00 0.00 2.57
2506 5174 6.208797 TCGGAGGAGTCGATAACAATATTCAT 59.791 38.462 0.00 0.00 0.00 2.57
2507 5175 6.528423 CGGAGGAGTCGATAACAATATTCATC 59.472 42.308 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.709880 TAACTGGCCGACCGATGCG 62.710 63.158 0.00 0.00 39.70 4.73
16 17 1.883084 CTAACTGGCCGACCGATGC 60.883 63.158 0.00 0.00 39.70 3.91
17 18 0.249073 CTCTAACTGGCCGACCGATG 60.249 60.000 0.00 0.00 39.70 3.84
18 19 0.683504 ACTCTAACTGGCCGACCGAT 60.684 55.000 0.00 0.00 39.70 4.18
19 20 0.896940 AACTCTAACTGGCCGACCGA 60.897 55.000 0.00 0.00 39.70 4.69
20 21 0.736325 CAACTCTAACTGGCCGACCG 60.736 60.000 0.00 0.00 39.70 4.79
21 22 0.391263 CCAACTCTAACTGGCCGACC 60.391 60.000 0.00 0.00 0.00 4.79
22 23 0.320697 ACCAACTCTAACTGGCCGAC 59.679 55.000 0.00 0.00 36.03 4.79
23 24 0.606604 GACCAACTCTAACTGGCCGA 59.393 55.000 0.00 0.00 36.03 5.54
24 25 0.608640 AGACCAACTCTAACTGGCCG 59.391 55.000 0.00 0.00 36.03 6.13
25 26 1.066071 GGAGACCAACTCTAACTGGCC 60.066 57.143 0.00 0.00 44.37 5.36
26 27 1.623811 TGGAGACCAACTCTAACTGGC 59.376 52.381 0.00 0.00 44.37 4.85
40 41 1.474077 GCATCCACATTGGTTGGAGAC 59.526 52.381 5.61 0.00 37.62 3.36
41 42 1.355381 AGCATCCACATTGGTTGGAGA 59.645 47.619 5.61 0.00 37.62 3.71
42 43 1.747355 GAGCATCCACATTGGTTGGAG 59.253 52.381 5.61 0.00 37.62 3.86
43 44 1.355381 AGAGCATCCACATTGGTTGGA 59.645 47.619 5.61 0.00 37.62 3.53
44 45 1.843368 AGAGCATCCACATTGGTTGG 58.157 50.000 5.61 0.00 37.62 3.77
45 46 3.181493 GCTTAGAGCATCCACATTGGTTG 60.181 47.826 0.00 0.00 41.89 3.77
46 47 3.019564 GCTTAGAGCATCCACATTGGTT 58.980 45.455 0.00 0.00 41.89 3.67
47 48 2.648059 GCTTAGAGCATCCACATTGGT 58.352 47.619 0.00 0.00 41.89 3.67
48 49 1.952296 GGCTTAGAGCATCCACATTGG 59.048 52.381 2.04 0.00 44.75 3.16
49 50 1.952296 GGGCTTAGAGCATCCACATTG 59.048 52.381 2.04 0.00 44.75 2.82
50 51 1.849039 AGGGCTTAGAGCATCCACATT 59.151 47.619 2.04 0.00 44.75 2.71
51 52 1.516110 AGGGCTTAGAGCATCCACAT 58.484 50.000 2.04 0.00 44.75 3.21
52 53 1.289160 AAGGGCTTAGAGCATCCACA 58.711 50.000 2.04 0.00 44.75 4.17
53 54 2.426842 AAAGGGCTTAGAGCATCCAC 57.573 50.000 2.04 0.00 44.75 4.02
54 55 2.843730 TGTAAAGGGCTTAGAGCATCCA 59.156 45.455 2.04 0.00 44.75 3.41
55 56 3.560636 TGTAAAGGGCTTAGAGCATCC 57.439 47.619 2.04 0.00 44.75 3.51
56 57 4.095036 GTGTTGTAAAGGGCTTAGAGCATC 59.905 45.833 2.04 0.00 44.75 3.91
57 58 4.010349 GTGTTGTAAAGGGCTTAGAGCAT 58.990 43.478 2.04 0.00 44.75 3.79
58 59 3.181449 TGTGTTGTAAAGGGCTTAGAGCA 60.181 43.478 2.04 0.00 44.75 4.26
59 60 3.408634 TGTGTTGTAAAGGGCTTAGAGC 58.591 45.455 0.00 0.00 41.46 4.09
60 61 4.455877 CCTTGTGTTGTAAAGGGCTTAGAG 59.544 45.833 0.00 0.00 39.49 2.43
61 62 4.141344 ACCTTGTGTTGTAAAGGGCTTAGA 60.141 41.667 6.42 0.00 46.12 2.10
62 63 4.023193 CACCTTGTGTTGTAAAGGGCTTAG 60.023 45.833 6.42 0.00 46.12 2.18
63 64 3.886505 CACCTTGTGTTGTAAAGGGCTTA 59.113 43.478 6.42 0.00 46.12 3.09
64 65 2.693074 CACCTTGTGTTGTAAAGGGCTT 59.307 45.455 6.42 0.00 46.12 4.35
65 66 2.306847 CACCTTGTGTTGTAAAGGGCT 58.693 47.619 6.42 0.00 46.12 5.19
66 67 1.269569 GCACCTTGTGTTGTAAAGGGC 60.270 52.381 6.42 3.48 46.12 5.19
67 68 2.306847 AGCACCTTGTGTTGTAAAGGG 58.693 47.619 6.42 0.00 46.12 3.95
69 70 6.204688 TCTCATAAGCACCTTGTGTTGTAAAG 59.795 38.462 2.44 0.00 34.84 1.85
70 71 6.058833 TCTCATAAGCACCTTGTGTTGTAAA 58.941 36.000 2.44 0.00 34.84 2.01
71 72 5.616270 TCTCATAAGCACCTTGTGTTGTAA 58.384 37.500 2.44 0.00 34.84 2.41
72 73 5.222079 TCTCATAAGCACCTTGTGTTGTA 57.778 39.130 2.44 0.00 34.84 2.41
73 74 4.067896 CTCTCATAAGCACCTTGTGTTGT 58.932 43.478 2.44 0.00 34.84 3.32
74 75 3.438087 CCTCTCATAAGCACCTTGTGTTG 59.562 47.826 2.44 0.00 34.84 3.33
75 76 3.073062 ACCTCTCATAAGCACCTTGTGTT 59.927 43.478 2.44 0.00 34.84 3.32
76 77 2.639839 ACCTCTCATAAGCACCTTGTGT 59.360 45.455 2.44 0.00 34.84 3.72
77 78 3.005554 CACCTCTCATAAGCACCTTGTG 58.994 50.000 0.00 0.00 34.61 3.33
78 79 2.639839 ACACCTCTCATAAGCACCTTGT 59.360 45.455 0.00 0.00 0.00 3.16
79 80 3.340814 ACACCTCTCATAAGCACCTTG 57.659 47.619 0.00 0.00 0.00 3.61
80 81 4.373156 AAACACCTCTCATAAGCACCTT 57.627 40.909 0.00 0.00 0.00 3.50
81 82 4.777896 TCTAAACACCTCTCATAAGCACCT 59.222 41.667 0.00 0.00 0.00 4.00
82 83 5.086104 TCTAAACACCTCTCATAAGCACC 57.914 43.478 0.00 0.00 0.00 5.01
83 84 7.435068 TTTTCTAAACACCTCTCATAAGCAC 57.565 36.000 0.00 0.00 0.00 4.40
84 85 8.635765 ATTTTTCTAAACACCTCTCATAAGCA 57.364 30.769 0.00 0.00 0.00 3.91
89 90 9.362151 TGGTTTATTTTTCTAAACACCTCTCAT 57.638 29.630 8.47 0.00 41.36 2.90
90 91 8.754991 TGGTTTATTTTTCTAAACACCTCTCA 57.245 30.769 8.47 0.00 41.36 3.27
91 92 8.847196 ACTGGTTTATTTTTCTAAACACCTCTC 58.153 33.333 8.47 0.00 41.36 3.20
92 93 8.762481 ACTGGTTTATTTTTCTAAACACCTCT 57.238 30.769 8.47 0.00 41.36 3.69
93 94 9.811995 AAACTGGTTTATTTTTCTAAACACCTC 57.188 29.630 8.47 0.00 41.36 3.85
132 133 5.988561 GTCTCTCCTCTACCAATAAGCATTG 59.011 44.000 0.00 0.00 41.13 2.82
133 134 5.663106 TGTCTCTCCTCTACCAATAAGCATT 59.337 40.000 0.00 0.00 0.00 3.56
134 135 5.211973 TGTCTCTCCTCTACCAATAAGCAT 58.788 41.667 0.00 0.00 0.00 3.79
135 136 4.610333 TGTCTCTCCTCTACCAATAAGCA 58.390 43.478 0.00 0.00 0.00 3.91
136 137 5.599999 TTGTCTCTCCTCTACCAATAAGC 57.400 43.478 0.00 0.00 0.00 3.09
140 141 8.772250 TGATTATTTTGTCTCTCCTCTACCAAT 58.228 33.333 0.00 0.00 0.00 3.16
141 142 8.146053 TGATTATTTTGTCTCTCCTCTACCAA 57.854 34.615 0.00 0.00 0.00 3.67
142 143 7.147655 CCTGATTATTTTGTCTCTCCTCTACCA 60.148 40.741 0.00 0.00 0.00 3.25
143 144 7.213678 CCTGATTATTTTGTCTCTCCTCTACC 58.786 42.308 0.00 0.00 0.00 3.18
144 145 6.704050 GCCTGATTATTTTGTCTCTCCTCTAC 59.296 42.308 0.00 0.00 0.00 2.59
145 146 6.384015 TGCCTGATTATTTTGTCTCTCCTCTA 59.616 38.462 0.00 0.00 0.00 2.43
146 147 5.190528 TGCCTGATTATTTTGTCTCTCCTCT 59.809 40.000 0.00 0.00 0.00 3.69
147 148 5.431765 TGCCTGATTATTTTGTCTCTCCTC 58.568 41.667 0.00 0.00 0.00 3.71
148 149 5.435291 CTGCCTGATTATTTTGTCTCTCCT 58.565 41.667 0.00 0.00 0.00 3.69
149 150 4.036144 GCTGCCTGATTATTTTGTCTCTCC 59.964 45.833 0.00 0.00 0.00 3.71
150 151 4.036144 GGCTGCCTGATTATTTTGTCTCTC 59.964 45.833 12.43 0.00 0.00 3.20
151 152 3.950395 GGCTGCCTGATTATTTTGTCTCT 59.050 43.478 12.43 0.00 0.00 3.10
152 153 3.067320 GGGCTGCCTGATTATTTTGTCTC 59.933 47.826 19.68 0.00 0.00 3.36
153 154 3.026694 GGGCTGCCTGATTATTTTGTCT 58.973 45.455 19.68 0.00 0.00 3.41
154 155 3.026694 AGGGCTGCCTGATTATTTTGTC 58.973 45.455 19.68 0.00 0.00 3.18
155 156 3.026694 GAGGGCTGCCTGATTATTTTGT 58.973 45.455 19.68 0.00 0.00 2.83
156 157 3.294214 AGAGGGCTGCCTGATTATTTTG 58.706 45.455 19.68 0.00 0.00 2.44
157 158 3.677156 AGAGGGCTGCCTGATTATTTT 57.323 42.857 19.68 0.00 0.00 1.82
158 159 3.294214 CAAGAGGGCTGCCTGATTATTT 58.706 45.455 19.68 1.38 0.00 1.40
159 160 2.243221 ACAAGAGGGCTGCCTGATTATT 59.757 45.455 19.68 3.12 0.00 1.40
160 161 1.849039 ACAAGAGGGCTGCCTGATTAT 59.151 47.619 19.68 0.00 0.00 1.28
167 168 3.060615 CTGCACAAGAGGGCTGCC 61.061 66.667 11.05 11.05 0.00 4.85
168 169 2.033141 TCTGCACAAGAGGGCTGC 59.967 61.111 0.00 0.00 0.00 5.25
180 181 1.943046 GCTTCAGTGCTTAGCTCTGCA 60.943 52.381 25.75 17.34 45.87 4.41
181 182 0.726256 GCTTCAGTGCTTAGCTCTGC 59.274 55.000 25.75 14.35 45.87 4.26
219 220 5.613358 ACAAAAGATCGAGTTTGCTTAGG 57.387 39.130 15.23 3.17 38.10 2.69
220 221 6.575201 GTGAACAAAAGATCGAGTTTGCTTAG 59.425 38.462 15.23 3.69 38.10 2.18
230 231 2.224090 TGGACCGTGAACAAAAGATCGA 60.224 45.455 0.00 0.00 0.00 3.59
231 232 2.139917 TGGACCGTGAACAAAAGATCG 58.860 47.619 0.00 0.00 0.00 3.69
241 242 3.623960 CACAACTAAAACTGGACCGTGAA 59.376 43.478 0.00 0.00 0.00 3.18
275 276 5.828747 ACGTAGCACATAGTTACATAGGTG 58.171 41.667 0.00 0.00 39.74 4.00
329 333 1.671845 CGTGACTAGGAGTAGCTGGAC 59.328 57.143 0.00 0.00 0.00 4.02
332 336 1.332375 GCTCGTGACTAGGAGTAGCTG 59.668 57.143 0.00 0.00 40.17 4.24
435 439 1.258982 GATCGAGCTTATGGTTGCGTG 59.741 52.381 0.00 0.00 0.00 5.34
488 492 2.239201 GCCTAGCGCGTTAACAAAAAG 58.761 47.619 8.43 0.00 0.00 2.27
502 506 4.836688 GCGCTTTTGCCGCCTAGC 62.837 66.667 0.00 0.00 43.93 3.42
509 513 3.879351 CTCGTGGTGCGCTTTTGCC 62.879 63.158 9.73 3.75 43.93 4.52
510 514 2.427410 CTCGTGGTGCGCTTTTGC 60.427 61.111 9.73 0.00 41.07 3.68
540 545 0.756294 TATCCCGCCATGTTCGACAT 59.244 50.000 6.23 0.00 39.91 3.06
542 547 1.329599 GTTTATCCCGCCATGTTCGAC 59.670 52.381 6.23 0.00 0.00 4.20
544 549 1.374560 TGTTTATCCCGCCATGTTCG 58.625 50.000 0.00 0.00 0.00 3.95
546 551 3.678529 GCAATTGTTTATCCCGCCATGTT 60.679 43.478 7.40 0.00 0.00 2.71
547 552 2.159114 GCAATTGTTTATCCCGCCATGT 60.159 45.455 7.40 0.00 0.00 3.21
548 553 2.472816 GCAATTGTTTATCCCGCCATG 58.527 47.619 7.40 0.00 0.00 3.66
587 592 6.780706 ACGGAAATGATGTATCGATAAACC 57.219 37.500 6.72 0.00 0.00 3.27
598 603 4.744631 GTGCAAAAGAAACGGAAATGATGT 59.255 37.500 0.00 0.00 0.00 3.06
618 627 2.472909 GCCGGGCTTAGTGATGTGC 61.473 63.158 12.87 0.00 0.00 4.57
623 632 2.639065 CTTTAATGCCGGGCTTAGTGA 58.361 47.619 21.46 0.00 0.00 3.41
638 647 3.860536 GTGCGTCCAAAAACAAGCTTTAA 59.139 39.130 0.00 0.00 0.00 1.52
673 682 2.778899 CCCCCTCTGAAACAGACCT 58.221 57.895 0.00 0.00 35.39 3.85
692 701 1.810197 AATCATTACGCGCGCTTTTC 58.190 45.000 32.58 0.00 0.00 2.29
745 755 5.758296 TGTTACAAAGATCGCCTTATGATCC 59.242 40.000 0.00 0.00 42.57 3.36
779 812 6.976088 TCTTCTGTCACTGAGAAACTTCTAG 58.024 40.000 0.00 0.00 37.73 2.43
869 932 4.698304 CCAGCGTCCTCTTAATTTTAACCA 59.302 41.667 0.00 0.00 0.00 3.67
952 1024 1.603802 CGTCTGGCTTCTTGCTTTGAA 59.396 47.619 0.00 0.00 42.39 2.69
954 1026 1.229428 TCGTCTGGCTTCTTGCTTTG 58.771 50.000 0.00 0.00 42.39 2.77
1172 1252 1.227999 CGTGTGTGTCGCCAGGATTT 61.228 55.000 0.00 0.00 0.00 2.17
1173 1253 1.667830 CGTGTGTGTCGCCAGGATT 60.668 57.895 0.00 0.00 0.00 3.01
1174 1254 2.048222 CGTGTGTGTCGCCAGGAT 60.048 61.111 0.00 0.00 0.00 3.24
1190 1283 1.491127 CCGTATGTGTGTGTGTGCG 59.509 57.895 0.00 0.00 0.00 5.34
1192 1285 2.073117 TAGCCGTATGTGTGTGTGTG 57.927 50.000 0.00 0.00 0.00 3.82
1193 1286 2.823924 TTAGCCGTATGTGTGTGTGT 57.176 45.000 0.00 0.00 0.00 3.72
1194 1287 2.351418 CCATTAGCCGTATGTGTGTGTG 59.649 50.000 0.00 0.00 0.00 3.82
1195 1288 2.235155 TCCATTAGCCGTATGTGTGTGT 59.765 45.455 0.00 0.00 0.00 3.72
1198 1291 3.742882 CAGATCCATTAGCCGTATGTGTG 59.257 47.826 0.00 0.00 0.00 3.82
1199 1292 3.388024 ACAGATCCATTAGCCGTATGTGT 59.612 43.478 0.00 0.00 0.00 3.72
1201 1294 4.345257 AGAACAGATCCATTAGCCGTATGT 59.655 41.667 0.00 0.00 0.00 2.29
1202 1295 4.687948 CAGAACAGATCCATTAGCCGTATG 59.312 45.833 0.00 0.00 0.00 2.39
1203 1296 4.345257 ACAGAACAGATCCATTAGCCGTAT 59.655 41.667 0.00 0.00 0.00 3.06
1204 1297 3.704566 ACAGAACAGATCCATTAGCCGTA 59.295 43.478 0.00 0.00 0.00 4.02
1205 1298 2.501723 ACAGAACAGATCCATTAGCCGT 59.498 45.455 0.00 0.00 0.00 5.68
1206 1299 2.868583 CACAGAACAGATCCATTAGCCG 59.131 50.000 0.00 0.00 0.00 5.52
1214 1307 2.871022 CTGCATAGCACAGAACAGATCC 59.129 50.000 0.00 0.00 37.32 3.36
1499 1592 0.733150 GTGAGCTATTTTCACCGGCC 59.267 55.000 0.00 0.00 39.17 6.13
1522 1618 0.179134 GAGATGGTTGGACCGACGAG 60.179 60.000 5.75 0.00 42.58 4.18
1557 1653 5.808366 AGACAAGACAGAGGTGATTAACA 57.192 39.130 0.00 0.00 0.00 2.41
1571 1667 9.436957 TCAATCCAAACTAAAGATAGACAAGAC 57.563 33.333 0.00 0.00 33.15 3.01
1593 1690 6.594788 ACTTGCCATACACTTCATTTCAAT 57.405 33.333 0.00 0.00 0.00 2.57
1604 1701 1.470098 CTCCTGCAACTTGCCATACAC 59.530 52.381 11.29 0.00 44.23 2.90
1641 1739 4.370364 AGCCAACTTACAACAACACTTG 57.630 40.909 0.00 0.00 0.00 3.16
1667 1768 2.289072 CGATTATCCATCCGGTTGCTCT 60.289 50.000 7.02 0.00 0.00 4.09
1675 1776 3.897325 TCGAGAAACGATTATCCATCCG 58.103 45.455 0.00 0.00 46.45 4.18
1702 1803 5.346011 AGAATATATGATACGCACGCTTGTG 59.654 40.000 1.67 1.67 46.67 3.33
1705 1806 4.864806 CCAGAATATATGATACGCACGCTT 59.135 41.667 0.00 0.00 0.00 4.68
1708 1809 4.266265 CAGCCAGAATATATGATACGCACG 59.734 45.833 0.00 0.00 0.00 5.34
1713 1814 9.416794 CGATTATCCAGCCAGAATATATGATAC 57.583 37.037 0.00 0.00 0.00 2.24
1714 1815 9.147732 ACGATTATCCAGCCAGAATATATGATA 57.852 33.333 0.00 0.00 0.00 2.15
1715 1816 8.027524 ACGATTATCCAGCCAGAATATATGAT 57.972 34.615 0.00 0.00 0.00 2.45
1716 1817 7.423844 ACGATTATCCAGCCAGAATATATGA 57.576 36.000 0.00 0.00 0.00 2.15
1717 1818 9.770097 AATACGATTATCCAGCCAGAATATATG 57.230 33.333 0.00 0.00 0.00 1.78
1719 1820 9.817809 GAAATACGATTATCCAGCCAGAATATA 57.182 33.333 0.00 0.00 0.00 0.86
1755 2176 5.177511 TGATCTTCACTGAAACTTTAGCACG 59.822 40.000 0.00 0.00 0.00 5.34
1767 2188 4.633126 GCTTGCTTACATGATCTTCACTGA 59.367 41.667 0.00 0.00 0.00 3.41
1768 2189 4.201891 GGCTTGCTTACATGATCTTCACTG 60.202 45.833 0.00 0.00 0.00 3.66
1781 2202 1.669265 GGTCAATACCGGCTTGCTTAC 59.331 52.381 0.00 0.28 35.62 2.34
1783 2204 2.868253 GGTCAATACCGGCTTGCTT 58.132 52.632 0.00 0.00 35.62 3.91
1794 4410 4.345547 TCATGTAGCAATACCGGGTCAATA 59.654 41.667 6.32 0.00 0.00 1.90
1801 4417 1.726791 GCGATCATGTAGCAATACCGG 59.273 52.381 0.00 0.00 0.00 5.28
1803 4419 3.130633 TGTGCGATCATGTAGCAATACC 58.869 45.455 12.41 3.72 40.23 2.73
1805 4421 4.815846 ACATTGTGCGATCATGTAGCAATA 59.184 37.500 12.41 6.05 40.23 1.90
1806 4422 3.628942 ACATTGTGCGATCATGTAGCAAT 59.371 39.130 12.41 5.05 40.23 3.56
1808 4424 2.609002 GACATTGTGCGATCATGTAGCA 59.391 45.455 0.00 8.05 36.01 3.49
1809 4425 2.609002 TGACATTGTGCGATCATGTAGC 59.391 45.455 0.00 0.00 0.00 3.58
1811 4427 3.618150 CACTGACATTGTGCGATCATGTA 59.382 43.478 0.00 0.00 0.00 2.29
1858 4492 6.856426 TCATCATTAGACGTGCTTTATACTCG 59.144 38.462 0.00 0.00 0.00 4.18
1896 4530 2.762327 AGGATTGTTATGCAAGCAAGGG 59.238 45.455 0.00 0.00 44.63 3.95
1929 4563 6.645415 ACACCACTAACGAAAGAATCTGTAAG 59.355 38.462 0.00 0.00 0.00 2.34
1933 4567 8.697846 TTATACACCACTAACGAAAGAATCTG 57.302 34.615 0.00 0.00 0.00 2.90
1934 4568 9.148104 GTTTATACACCACTAACGAAAGAATCT 57.852 33.333 0.00 0.00 0.00 2.40
1935 4569 8.928733 TGTTTATACACCACTAACGAAAGAATC 58.071 33.333 0.00 0.00 0.00 2.52
1936 4570 8.836268 TGTTTATACACCACTAACGAAAGAAT 57.164 30.769 0.00 0.00 0.00 2.40
1937 4571 8.550376 GTTGTTTATACACCACTAACGAAAGAA 58.450 33.333 0.00 0.00 32.98 2.52
1938 4572 7.710044 TGTTGTTTATACACCACTAACGAAAGA 59.290 33.333 0.00 0.00 32.98 2.52
1939 4573 7.853524 TGTTGTTTATACACCACTAACGAAAG 58.146 34.615 0.00 0.00 32.98 2.62
1940 4574 7.783090 TGTTGTTTATACACCACTAACGAAA 57.217 32.000 0.00 0.00 32.98 3.46
1967 4608 8.421784 GTCACAGGTCTTATGAAGGTCATTATA 58.578 37.037 0.00 0.00 38.26 0.98
1968 4609 7.092891 TGTCACAGGTCTTATGAAGGTCATTAT 60.093 37.037 0.00 0.00 38.26 1.28
1969 4610 6.212589 TGTCACAGGTCTTATGAAGGTCATTA 59.787 38.462 0.00 0.00 38.26 1.90
1970 4611 5.013079 TGTCACAGGTCTTATGAAGGTCATT 59.987 40.000 0.00 0.00 38.26 2.57
2004 4648 3.725895 CGCACCTTCAAATCTCATTCACG 60.726 47.826 0.00 0.00 0.00 4.35
2005 4649 3.751621 CGCACCTTCAAATCTCATTCAC 58.248 45.455 0.00 0.00 0.00 3.18
2007 4651 2.162208 TGCGCACCTTCAAATCTCATTC 59.838 45.455 5.66 0.00 0.00 2.67
2008 4652 2.161855 TGCGCACCTTCAAATCTCATT 58.838 42.857 5.66 0.00 0.00 2.57
2011 4666 1.537202 ACTTGCGCACCTTCAAATCTC 59.463 47.619 11.12 0.00 0.00 2.75
2037 4692 2.446435 TGGCCTTTATCCTGCACTTTC 58.554 47.619 3.32 0.00 0.00 2.62
2096 4754 5.755409 TCAGAACTAAAGTTAGGCATGGA 57.245 39.130 0.00 0.00 38.56 3.41
2118 4776 6.062749 CCAGTGGAGATGAGATGATGAAAAT 58.937 40.000 1.68 0.00 0.00 1.82
2161 4819 0.240945 CCATTTTGCCGCGGATATCC 59.759 55.000 33.48 12.14 0.00 2.59
2247 4907 2.268076 GGCCAAACATGTCCGCACT 61.268 57.895 0.00 0.00 0.00 4.40
2270 4930 2.030274 CGGTCTGAACAAATTTGGGGAC 60.030 50.000 21.74 19.53 0.00 4.46
2271 4931 2.235016 CGGTCTGAACAAATTTGGGGA 58.765 47.619 21.74 10.84 0.00 4.81
2273 4933 1.960689 ACCGGTCTGAACAAATTTGGG 59.039 47.619 21.74 12.59 0.00 4.12
2297 4964 0.739813 CTTGTGGGATTCCGGACGTC 60.740 60.000 1.83 7.13 35.24 4.34
2305 4972 3.536956 TGGTATCGACTTGTGGGATTC 57.463 47.619 0.00 0.00 0.00 2.52
2366 5033 5.854866 GGGTTTCGCTTGTAAACAATAAGTC 59.145 40.000 0.00 0.00 38.34 3.01
2427 5095 3.878667 GGCCGGAATGAGAGGGGG 61.879 72.222 5.05 0.00 0.00 5.40
2428 5096 3.878667 GGGCCGGAATGAGAGGGG 61.879 72.222 5.05 0.00 0.00 4.79
2429 5097 2.403132 GATGGGCCGGAATGAGAGGG 62.403 65.000 5.05 0.00 0.00 4.30
2430 5098 1.072159 GATGGGCCGGAATGAGAGG 59.928 63.158 5.05 0.00 0.00 3.69
2431 5099 1.301244 CGATGGGCCGGAATGAGAG 60.301 63.158 5.05 0.00 0.00 3.20
2432 5100 2.028125 GACGATGGGCCGGAATGAGA 62.028 60.000 5.05 0.00 0.00 3.27
2433 5101 1.595382 GACGATGGGCCGGAATGAG 60.595 63.158 5.05 0.00 0.00 2.90
2434 5102 2.504032 GACGATGGGCCGGAATGA 59.496 61.111 5.05 0.00 0.00 2.57
2435 5103 2.967076 CGACGATGGGCCGGAATG 60.967 66.667 5.05 0.00 0.00 2.67
2436 5104 3.441011 GACGACGATGGGCCGGAAT 62.441 63.158 5.05 0.00 0.00 3.01
2437 5105 4.137872 GACGACGATGGGCCGGAA 62.138 66.667 5.05 0.00 0.00 4.30
2441 5109 4.832608 GGTGGACGACGATGGGCC 62.833 72.222 0.00 0.00 0.00 5.80
2459 5127 4.077184 TCCATCACGGCGGTGGTC 62.077 66.667 22.51 0.00 44.50 4.02
2460 5128 4.082523 CTCCATCACGGCGGTGGT 62.083 66.667 22.51 14.46 44.50 4.16
2467 5135 4.873129 CCGACGGCTCCATCACGG 62.873 72.222 0.00 0.00 34.77 4.94
2468 5136 3.758088 CTCCGACGGCTCCATCACG 62.758 68.421 9.66 0.00 0.00 4.35
2469 5137 2.105128 CTCCGACGGCTCCATCAC 59.895 66.667 9.66 0.00 0.00 3.06
2470 5138 3.147595 CCTCCGACGGCTCCATCA 61.148 66.667 9.66 0.00 0.00 3.07
2471 5139 2.833582 TCCTCCGACGGCTCCATC 60.834 66.667 9.66 0.00 0.00 3.51
2472 5140 2.835431 CTCCTCCGACGGCTCCAT 60.835 66.667 9.66 0.00 0.00 3.41
2473 5141 4.361971 ACTCCTCCGACGGCTCCA 62.362 66.667 9.66 0.00 0.00 3.86
2474 5142 3.519930 GACTCCTCCGACGGCTCC 61.520 72.222 9.66 0.00 0.00 4.70
2475 5143 3.878519 CGACTCCTCCGACGGCTC 61.879 72.222 9.66 0.00 0.00 4.70
2476 5144 2.321263 TATCGACTCCTCCGACGGCT 62.321 60.000 9.66 0.00 38.97 5.52
2477 5145 1.442526 TTATCGACTCCTCCGACGGC 61.443 60.000 9.66 0.00 38.97 5.68
2478 5146 0.307146 GTTATCGACTCCTCCGACGG 59.693 60.000 7.84 7.84 38.97 4.79
2479 5147 1.012086 TGTTATCGACTCCTCCGACG 58.988 55.000 0.00 0.00 38.97 5.12
2480 5148 3.712091 ATTGTTATCGACTCCTCCGAC 57.288 47.619 0.00 0.00 38.97 4.79
2481 5149 5.533528 TGAATATTGTTATCGACTCCTCCGA 59.466 40.000 0.00 0.00 40.53 4.55
2482 5150 5.769367 TGAATATTGTTATCGACTCCTCCG 58.231 41.667 0.00 0.00 0.00 4.63
2483 5151 7.820044 GATGAATATTGTTATCGACTCCTCC 57.180 40.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.