Multiple sequence alignment - TraesCS3A01G314900

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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 TraesCS3A01G314900 chr3A 100.000 2415 0 0 1 2415 556341632 556339218 0.000000e+00 4460.0
1 TraesCS3A01G314900 chr3A 88.255 1175 84 23 522 1686 556354423 556353293 0.000000e+00 1356.0
2 TraesCS3A01G314900 chr3A 95.931 639 20 2 1775 2413 575761326 575760694 0.000000e+00 1031.0
3 TraesCS3A01G314900 chr3A 78.725 1067 121 70 687 1712 556261163 556260162 1.230000e-172 616.0
4 TraesCS3A01G314900 chr3A 82.463 479 49 19 955 1415 556678398 556678859 1.050000e-103 387.0
5 TraesCS3A01G314900 chr3B 90.188 1437 97 17 297 1721 561840114 561841518 0.000000e+00 1832.0
6 TraesCS3A01G314900 chr3B 87.948 1145 70 26 501 1626 561592119 561593214 0.000000e+00 1288.0
7 TraesCS3A01G314900 chr3B 79.812 1065 118 63 684 1714 561888890 561889891 0.000000e+00 686.0
8 TraesCS3A01G314900 chr3B 89.634 492 37 6 1936 2415 510793559 510794048 4.410000e-172 614.0
9 TraesCS3A01G314900 chr3B 82.166 471 54 16 958 1415 561044777 561044324 6.300000e-101 377.0
10 TraesCS3A01G314900 chr3B 80.353 453 54 18 968 1418 561039116 561038697 6.480000e-81 311.0
11 TraesCS3A01G314900 chr3B 94.845 97 5 0 1779 1875 614899378 614899474 4.160000e-33 152.0
12 TraesCS3A01G314900 chr3B 95.000 40 2 0 1720 1759 809343493 809343454 2.000000e-06 63.9
13 TraesCS3A01G314900 chr3D 88.567 1172 73 24 546 1698 429636845 429637974 0.000000e+00 1365.0
14 TraesCS3A01G314900 chr3D 79.363 911 88 66 586 1463 429647108 429647951 1.260000e-152 549.0
15 TraesCS3A01G314900 chr3D 80.786 458 66 12 969 1415 429044263 429043817 2.970000e-89 339.0
16 TraesCS3A01G314900 chr3D 80.044 451 53 20 968 1418 428994406 428993993 1.400000e-77 300.0
17 TraesCS3A01G314900 chr3D 85.380 171 13 6 976 1137 429085743 429085576 1.490000e-37 167.0
18 TraesCS3A01G314900 chr3D 100.000 31 0 0 1335 1365 602716288 602716318 9.330000e-05 58.4
19 TraesCS3A01G314900 chr2A 95.532 649 21 2 1767 2415 746818599 746819239 0.000000e+00 1031.0
20 TraesCS3A01G314900 chr2A 94.976 637 26 1 1779 2415 676165902 676166532 0.000000e+00 994.0
21 TraesCS3A01G314900 chr2A 82.283 587 81 14 1779 2354 384552704 384552130 1.000000e-133 486.0
22 TraesCS3A01G314900 chr6B 89.765 469 38 5 1955 2415 560661709 560661243 2.070000e-165 592.0
23 TraesCS3A01G314900 chr6B 88.913 469 40 5 1955 2415 560640788 560640324 3.480000e-158 568.0
24 TraesCS3A01G314900 chr6B 93.069 101 7 0 1775 1875 560641033 560640933 5.380000e-32 148.0
25 TraesCS3A01G314900 chr5D 84.677 496 59 13 1779 2261 375753666 375754157 1.680000e-131 479.0
26 TraesCS3A01G314900 chr5D 81.893 486 82 5 1772 2257 357380793 357380314 2.890000e-109 405.0
27 TraesCS3A01G314900 chr1B 81.913 481 75 9 1770 2249 645297781 645298250 1.740000e-106 396.0
28 TraesCS3A01G314900 chr1A 83.019 159 25 1 1719 1875 197138055 197137897 2.500000e-30 143.0
29 TraesCS3A01G314900 chr1D 96.721 61 2 0 1719 1779 367145861 367145801 4.250000e-18 102.0
30 TraesCS3A01G314900 chr4D 92.857 70 4 1 1711 1779 389003401 389003470 1.530000e-17 100.0
31 TraesCS3A01G314900 chr4D 88.679 53 5 1 1716 1768 296678040 296678091 2.000000e-06 63.9


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 TraesCS3A01G314900 chr3A 556339218 556341632 2414 True 4460 4460 100.000 1 2415 1 chr3A.!!$R2 2414
1 TraesCS3A01G314900 chr3A 556353293 556354423 1130 True 1356 1356 88.255 522 1686 1 chr3A.!!$R3 1164
2 TraesCS3A01G314900 chr3A 575760694 575761326 632 True 1031 1031 95.931 1775 2413 1 chr3A.!!$R4 638
3 TraesCS3A01G314900 chr3A 556260162 556261163 1001 True 616 616 78.725 687 1712 1 chr3A.!!$R1 1025
4 TraesCS3A01G314900 chr3B 561840114 561841518 1404 False 1832 1832 90.188 297 1721 1 chr3B.!!$F3 1424
5 TraesCS3A01G314900 chr3B 561592119 561593214 1095 False 1288 1288 87.948 501 1626 1 chr3B.!!$F2 1125
6 TraesCS3A01G314900 chr3B 561888890 561889891 1001 False 686 686 79.812 684 1714 1 chr3B.!!$F4 1030
7 TraesCS3A01G314900 chr3D 429636845 429637974 1129 False 1365 1365 88.567 546 1698 1 chr3D.!!$F1 1152
8 TraesCS3A01G314900 chr3D 429647108 429647951 843 False 549 549 79.363 586 1463 1 chr3D.!!$F2 877
9 TraesCS3A01G314900 chr2A 746818599 746819239 640 False 1031 1031 95.532 1767 2415 1 chr2A.!!$F2 648
10 TraesCS3A01G314900 chr2A 676165902 676166532 630 False 994 994 94.976 1779 2415 1 chr2A.!!$F1 636
11 TraesCS3A01G314900 chr2A 384552130 384552704 574 True 486 486 82.283 1779 2354 1 chr2A.!!$R1 575
12 TraesCS3A01G314900 chr6B 560640324 560641033 709 True 358 568 90.991 1775 2415 2 chr6B.!!$R2 640

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
948 989 0.031449 GAGCCTGACGAGCACCTATC 59.969 60.0 0.0 0.0 0.0 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2035 0.736053 TTTTCGTTGTGTGAGTGCCC 59.264 50.0 0.0 0.0 0.0 5.36 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
23 24 3.356529 AGGTGGTGGATCATCTTCAAC 57.643 47.619 0.00 0.00 0.00 3.18
24 25 2.644299 AGGTGGTGGATCATCTTCAACA 59.356 45.455 0.00 0.00 0.00 3.33
25 26 3.012518 GGTGGTGGATCATCTTCAACAG 58.987 50.000 0.00 0.00 0.00 3.16
26 27 3.012518 GTGGTGGATCATCTTCAACAGG 58.987 50.000 0.00 0.00 0.00 4.00
27 28 2.912295 TGGTGGATCATCTTCAACAGGA 59.088 45.455 0.00 0.00 0.00 3.86
28 29 3.054875 TGGTGGATCATCTTCAACAGGAG 60.055 47.826 0.00 0.00 0.00 3.69
29 30 3.539604 GTGGATCATCTTCAACAGGAGG 58.460 50.000 0.00 0.00 0.00 4.30
30 31 2.092753 TGGATCATCTTCAACAGGAGGC 60.093 50.000 0.00 0.00 0.00 4.70
31 32 2.092753 GGATCATCTTCAACAGGAGGCA 60.093 50.000 0.00 0.00 0.00 4.75
32 33 2.479566 TCATCTTCAACAGGAGGCAC 57.520 50.000 0.00 0.00 0.00 5.01
45 46 2.277858 AGGCACTCGTTCTAGGTGG 58.722 57.895 0.00 0.00 0.00 4.61
46 47 1.448013 GGCACTCGTTCTAGGTGGC 60.448 63.158 6.83 6.83 46.00 5.01
47 48 1.805945 GCACTCGTTCTAGGTGGCG 60.806 63.158 0.00 0.00 0.00 5.69
48 49 1.880894 CACTCGTTCTAGGTGGCGA 59.119 57.895 0.00 0.00 0.00 5.54
50 51 1.433879 CTCGTTCTAGGTGGCGAGG 59.566 63.158 14.01 2.28 44.68 4.63
51 52 1.303888 TCGTTCTAGGTGGCGAGGT 60.304 57.895 0.00 0.00 0.00 3.85
52 53 0.896940 TCGTTCTAGGTGGCGAGGTT 60.897 55.000 0.00 0.00 0.00 3.50
53 54 0.736325 CGTTCTAGGTGGCGAGGTTG 60.736 60.000 0.00 0.00 0.00 3.77
54 55 1.019805 GTTCTAGGTGGCGAGGTTGC 61.020 60.000 0.00 0.00 0.00 4.17
55 56 2.501223 TTCTAGGTGGCGAGGTTGCG 62.501 60.000 0.00 0.00 35.06 4.85
56 57 3.296709 CTAGGTGGCGAGGTTGCGT 62.297 63.158 0.00 0.00 35.06 5.24
57 58 1.940883 CTAGGTGGCGAGGTTGCGTA 61.941 60.000 0.00 0.00 35.06 4.42
58 59 2.216750 TAGGTGGCGAGGTTGCGTAC 62.217 60.000 0.00 0.00 35.06 3.67
59 60 2.356553 GTGGCGAGGTTGCGTACA 60.357 61.111 0.00 0.00 35.06 2.90
60 61 2.356553 TGGCGAGGTTGCGTACAC 60.357 61.111 0.00 0.00 35.06 2.90
61 62 3.116531 GGCGAGGTTGCGTACACC 61.117 66.667 0.00 0.00 35.06 4.16
62 63 3.475774 GCGAGGTTGCGTACACCG 61.476 66.667 0.00 0.00 40.40 4.94
63 64 2.256158 CGAGGTTGCGTACACCGA 59.744 61.111 0.00 0.00 39.56 4.69
64 65 2.084681 CGAGGTTGCGTACACCGAC 61.085 63.158 0.00 0.00 39.56 4.79
65 66 1.007038 GAGGTTGCGTACACCGACA 60.007 57.895 0.00 0.00 39.56 4.35
66 67 1.280206 GAGGTTGCGTACACCGACAC 61.280 60.000 0.00 0.00 39.56 3.67
67 68 2.312436 GGTTGCGTACACCGACACC 61.312 63.158 0.00 0.00 39.56 4.16
68 69 1.592131 GTTGCGTACACCGACACCA 60.592 57.895 0.00 0.00 39.56 4.17
69 70 1.592131 TTGCGTACACCGACACCAC 60.592 57.895 0.00 0.00 39.56 4.16
70 71 2.735857 GCGTACACCGACACCACC 60.736 66.667 0.00 0.00 39.56 4.61
71 72 2.048877 CGTACACCGACACCACCC 60.049 66.667 0.00 0.00 39.56 4.61
72 73 2.567497 CGTACACCGACACCACCCT 61.567 63.158 0.00 0.00 39.56 4.34
73 74 1.291272 GTACACCGACACCACCCTC 59.709 63.158 0.00 0.00 0.00 4.30
74 75 1.909781 TACACCGACACCACCCTCC 60.910 63.158 0.00 0.00 0.00 4.30
75 76 4.373116 CACCGACACCACCCTCCG 62.373 72.222 0.00 0.00 0.00 4.63
76 77 4.608774 ACCGACACCACCCTCCGA 62.609 66.667 0.00 0.00 0.00 4.55
77 78 4.065281 CCGACACCACCCTCCGAC 62.065 72.222 0.00 0.00 0.00 4.79
78 79 2.989824 CGACACCACCCTCCGACT 60.990 66.667 0.00 0.00 0.00 4.18
79 80 2.571216 CGACACCACCCTCCGACTT 61.571 63.158 0.00 0.00 0.00 3.01
80 81 1.004918 GACACCACCCTCCGACTTG 60.005 63.158 0.00 0.00 0.00 3.16
81 82 2.347490 CACCACCCTCCGACTTGG 59.653 66.667 0.00 0.00 40.09 3.61
82 83 3.637273 ACCACCCTCCGACTTGGC 61.637 66.667 0.00 0.00 37.80 4.52
83 84 3.636231 CCACCCTCCGACTTGGCA 61.636 66.667 0.00 0.00 37.80 4.92
84 85 2.358737 CACCCTCCGACTTGGCAC 60.359 66.667 0.00 0.00 37.80 5.01
85 86 4.003788 ACCCTCCGACTTGGCACG 62.004 66.667 0.00 0.00 37.80 5.34
86 87 3.691342 CCCTCCGACTTGGCACGA 61.691 66.667 0.00 0.00 37.80 4.35
87 88 2.432628 CCTCCGACTTGGCACGAC 60.433 66.667 0.00 0.00 37.80 4.34
88 89 2.338620 CTCCGACTTGGCACGACA 59.661 61.111 0.00 0.00 37.80 4.35
89 90 2.022129 CTCCGACTTGGCACGACAC 61.022 63.158 0.00 0.00 37.80 3.67
90 91 2.279851 CCGACTTGGCACGACACA 60.280 61.111 0.00 0.00 0.00 3.72
91 92 1.667830 CCGACTTGGCACGACACAT 60.668 57.895 0.00 0.00 0.00 3.21
92 93 1.626654 CCGACTTGGCACGACACATC 61.627 60.000 0.00 0.00 0.00 3.06
93 94 1.626654 CGACTTGGCACGACACATCC 61.627 60.000 0.00 0.00 0.00 3.51
94 95 1.626654 GACTTGGCACGACACATCCG 61.627 60.000 0.00 0.00 0.00 4.18
95 96 3.027170 CTTGGCACGACACATCCGC 62.027 63.158 0.00 0.00 0.00 5.54
96 97 3.529341 TTGGCACGACACATCCGCT 62.529 57.895 0.00 0.00 0.00 5.52
97 98 3.188786 GGCACGACACATCCGCTC 61.189 66.667 0.00 0.00 0.00 5.03
98 99 3.188786 GCACGACACATCCGCTCC 61.189 66.667 0.00 0.00 0.00 4.70
99 100 2.509336 CACGACACATCCGCTCCC 60.509 66.667 0.00 0.00 0.00 4.30
100 101 2.994995 ACGACACATCCGCTCCCA 60.995 61.111 0.00 0.00 0.00 4.37
101 102 2.509336 CGACACATCCGCTCCCAC 60.509 66.667 0.00 0.00 0.00 4.61
102 103 2.662596 GACACATCCGCTCCCACA 59.337 61.111 0.00 0.00 0.00 4.17
103 104 1.741770 GACACATCCGCTCCCACAC 60.742 63.158 0.00 0.00 0.00 3.82
104 105 2.436646 CACATCCGCTCCCACACC 60.437 66.667 0.00 0.00 0.00 4.16
105 106 2.927856 ACATCCGCTCCCACACCA 60.928 61.111 0.00 0.00 0.00 4.17
106 107 2.436646 CATCCGCTCCCACACCAC 60.437 66.667 0.00 0.00 0.00 4.16
107 108 4.082523 ATCCGCTCCCACACCACG 62.083 66.667 0.00 0.00 0.00 4.94
109 110 4.742201 CCGCTCCCACACCACGAG 62.742 72.222 0.00 0.00 0.00 4.18
110 111 4.742201 CGCTCCCACACCACGAGG 62.742 72.222 0.00 0.00 42.21 4.63
112 113 3.625897 CTCCCACACCACGAGGCA 61.626 66.667 0.00 0.00 39.06 4.75
113 114 2.927856 TCCCACACCACGAGGCAT 60.928 61.111 0.00 0.00 39.06 4.40
114 115 2.034066 CCCACACCACGAGGCATT 59.966 61.111 0.00 0.00 39.06 3.56
115 116 2.334946 CCCACACCACGAGGCATTG 61.335 63.158 0.00 0.00 39.06 2.82
116 117 2.334946 CCACACCACGAGGCATTGG 61.335 63.158 0.00 0.00 39.06 3.16
117 118 2.034066 ACACCACGAGGCATTGGG 59.966 61.111 0.00 0.00 39.06 4.12
118 119 3.443045 CACCACGAGGCATTGGGC 61.443 66.667 0.00 0.00 43.74 5.36
154 155 3.846360 GCTCTTTTAGCCACGTTCTAGA 58.154 45.455 0.00 0.00 46.25 2.43
155 156 3.860536 GCTCTTTTAGCCACGTTCTAGAG 59.139 47.826 0.00 0.00 46.25 2.43
156 157 4.425520 CTCTTTTAGCCACGTTCTAGAGG 58.574 47.826 0.00 0.00 0.00 3.69
157 158 4.084287 TCTTTTAGCCACGTTCTAGAGGA 58.916 43.478 0.00 0.00 0.00 3.71
158 159 4.525487 TCTTTTAGCCACGTTCTAGAGGAA 59.475 41.667 0.00 0.00 0.00 3.36
159 160 4.451629 TTTAGCCACGTTCTAGAGGAAG 57.548 45.455 0.00 0.00 34.23 3.46
160 161 1.187087 AGCCACGTTCTAGAGGAAGG 58.813 55.000 0.00 0.26 43.17 3.46
161 162 0.460459 GCCACGTTCTAGAGGAAGGC 60.460 60.000 11.09 11.09 41.80 4.35
162 163 0.895530 CCACGTTCTAGAGGAAGGCA 59.104 55.000 0.00 0.00 41.80 4.75
163 164 1.404315 CCACGTTCTAGAGGAAGGCAC 60.404 57.143 0.00 0.00 41.80 5.01
164 165 0.526662 ACGTTCTAGAGGAAGGCACG 59.473 55.000 8.85 8.85 41.80 5.34
165 166 0.809385 CGTTCTAGAGGAAGGCACGA 59.191 55.000 5.18 0.00 34.23 4.35
166 167 1.467713 CGTTCTAGAGGAAGGCACGAC 60.468 57.143 5.18 0.00 34.23 4.34
167 168 0.809385 TTCTAGAGGAAGGCACGACG 59.191 55.000 0.00 0.00 0.00 5.12
168 169 0.322277 TCTAGAGGAAGGCACGACGT 60.322 55.000 0.00 0.00 0.00 4.34
169 170 1.065926 TCTAGAGGAAGGCACGACGTA 60.066 52.381 0.00 0.00 0.00 3.57
170 171 1.331138 CTAGAGGAAGGCACGACGTAG 59.669 57.143 0.00 0.00 0.00 3.51
171 172 1.139095 GAGGAAGGCACGACGTAGG 59.861 63.158 0.00 0.00 0.00 3.18
172 173 2.183555 GGAAGGCACGACGTAGGG 59.816 66.667 0.00 0.00 0.00 3.53
173 174 2.508663 GAAGGCACGACGTAGGGC 60.509 66.667 15.17 15.17 40.45 5.19
174 175 4.430765 AAGGCACGACGTAGGGCG 62.431 66.667 16.89 9.56 42.53 6.13
189 190 3.112709 GCGTCCAGCTCACGGAAC 61.113 66.667 14.91 0.00 44.04 3.62
190 191 2.338620 CGTCCAGCTCACGGAACA 59.661 61.111 6.81 0.00 33.29 3.18
191 192 1.734477 CGTCCAGCTCACGGAACAG 60.734 63.158 6.81 0.00 33.29 3.16
192 193 1.666011 GTCCAGCTCACGGAACAGA 59.334 57.895 0.00 0.00 33.29 3.41
193 194 0.389166 GTCCAGCTCACGGAACAGAG 60.389 60.000 0.00 0.00 33.29 3.35
211 212 4.504916 CCGACGGCAGGAGCAGAG 62.505 72.222 0.00 0.00 44.61 3.35
213 214 4.828925 GACGGCAGGAGCAGAGCC 62.829 72.222 0.00 0.00 44.61 4.70
218 219 4.172512 CAGGAGCAGAGCCGCCAT 62.173 66.667 0.00 0.00 0.00 4.40
219 220 4.172512 AGGAGCAGAGCCGCCATG 62.173 66.667 0.00 0.00 0.00 3.66
231 232 3.792736 GCCATGGCGTAGGTGGGA 61.793 66.667 23.48 0.00 33.58 4.37
232 233 2.994699 CCATGGCGTAGGTGGGAA 59.005 61.111 0.00 0.00 0.00 3.97
233 234 1.153168 CCATGGCGTAGGTGGGAAG 60.153 63.158 0.00 0.00 0.00 3.46
234 235 1.153168 CATGGCGTAGGTGGGAAGG 60.153 63.158 0.00 0.00 0.00 3.46
235 236 2.375345 ATGGCGTAGGTGGGAAGGG 61.375 63.158 0.00 0.00 0.00 3.95
236 237 4.484872 GGCGTAGGTGGGAAGGGC 62.485 72.222 0.00 0.00 0.00 5.19
237 238 4.832608 GCGTAGGTGGGAAGGGCG 62.833 72.222 0.00 0.00 0.00 6.13
238 239 3.387947 CGTAGGTGGGAAGGGCGT 61.388 66.667 0.00 0.00 0.00 5.68
239 240 2.582978 GTAGGTGGGAAGGGCGTC 59.417 66.667 0.00 0.00 0.00 5.19
240 241 3.072468 TAGGTGGGAAGGGCGTCG 61.072 66.667 0.00 0.00 0.00 5.12
241 242 3.588817 TAGGTGGGAAGGGCGTCGA 62.589 63.158 0.00 0.00 0.00 4.20
242 243 4.452733 GGTGGGAAGGGCGTCGAG 62.453 72.222 0.00 0.00 0.00 4.04
243 244 4.452733 GTGGGAAGGGCGTCGAGG 62.453 72.222 0.00 0.00 0.00 4.63
244 245 4.689549 TGGGAAGGGCGTCGAGGA 62.690 66.667 9.75 0.00 0.00 3.71
245 246 4.144703 GGGAAGGGCGTCGAGGAC 62.145 72.222 9.75 5.69 0.00 3.85
267 268 2.666989 CTTAAGAAGGACGAGGCGC 58.333 57.895 0.00 0.00 0.00 6.53
268 269 0.806492 CTTAAGAAGGACGAGGCGCC 60.806 60.000 21.89 21.89 0.00 6.53
269 270 2.234913 TTAAGAAGGACGAGGCGCCC 62.235 60.000 26.15 14.23 0.00 6.13
311 312 0.322975 GCCCATCCTGCGATACTGAT 59.677 55.000 0.00 0.00 0.00 2.90
321 322 4.217334 CCTGCGATACTGATCTACACTGAT 59.783 45.833 0.00 0.00 0.00 2.90
326 327 6.729187 CGATACTGATCTACACTGATCACAA 58.271 40.000 3.42 0.00 45.29 3.33
327 328 7.366513 CGATACTGATCTACACTGATCACAAT 58.633 38.462 3.42 1.29 45.29 2.71
344 345 6.066054 TCACAATGATCGAGAGTGATAGAC 57.934 41.667 2.06 0.00 34.59 2.59
361 362 5.411053 TGATAGACAACAATCGCATTTCACA 59.589 36.000 0.00 0.00 0.00 3.58
374 375 5.043248 CGCATTTCACACCTTCTTTTTCTT 58.957 37.500 0.00 0.00 0.00 2.52
418 420 1.343142 TGATCTGTGTACAGGTTGCGT 59.657 47.619 11.76 0.00 43.91 5.24
437 439 2.793585 CGTAGTCGTGTCATGCCGTAAT 60.794 50.000 0.00 0.00 0.00 1.89
443 445 3.805422 TCGTGTCATGCCGTAATATTTCC 59.195 43.478 0.00 0.00 0.00 3.13
444 446 3.362596 CGTGTCATGCCGTAATATTTCCG 60.363 47.826 0.00 0.00 0.00 4.30
446 448 2.806244 GTCATGCCGTAATATTTCCGCT 59.194 45.455 0.00 0.00 0.00 5.52
454 456 4.916249 CCGTAATATTTCCGCTACTCAGAC 59.084 45.833 0.00 0.00 0.00 3.51
455 457 5.506815 CCGTAATATTTCCGCTACTCAGACA 60.507 44.000 0.00 0.00 0.00 3.41
456 458 5.398711 CGTAATATTTCCGCTACTCAGACAC 59.601 44.000 0.00 0.00 0.00 3.67
457 459 2.674796 ATTTCCGCTACTCAGACACC 57.325 50.000 0.00 0.00 0.00 4.16
485 487 5.232202 GTCCTCTTTTCTTTTCCTTTTTGCG 59.768 40.000 0.00 0.00 0.00 4.85
521 523 3.117701 CCTCTCTGATCCTACTGTCCTCA 60.118 52.174 0.00 0.00 0.00 3.86
529 531 4.163441 TCCTACTGTCCTCATCTCTCTG 57.837 50.000 0.00 0.00 0.00 3.35
569 571 3.809832 CGTTCTTGTTTCTCCACTGTCAT 59.190 43.478 0.00 0.00 0.00 3.06
577 579 1.482182 TCTCCACTGTCATTGCGCTAT 59.518 47.619 9.73 2.86 0.00 2.97
607 621 5.105392 ACATGGAGCAAGACAGTTTTTCAAA 60.105 36.000 0.00 0.00 0.00 2.69
608 622 4.743493 TGGAGCAAGACAGTTTTTCAAAC 58.257 39.130 0.00 0.00 0.00 2.93
609 623 4.219507 TGGAGCAAGACAGTTTTTCAAACA 59.780 37.500 2.38 0.00 0.00 2.83
610 624 5.167845 GGAGCAAGACAGTTTTTCAAACAA 58.832 37.500 2.38 0.00 0.00 2.83
611 625 5.637387 GGAGCAAGACAGTTTTTCAAACAAA 59.363 36.000 2.38 0.00 0.00 2.83
612 626 6.147000 GGAGCAAGACAGTTTTTCAAACAAAA 59.853 34.615 2.38 0.00 0.00 2.44
613 627 7.307692 GGAGCAAGACAGTTTTTCAAACAAAAA 60.308 33.333 2.38 0.00 0.00 1.94
637 651 3.722147 AGTGAGCAGTGTGAGTGTAAAG 58.278 45.455 0.00 0.00 0.00 1.85
661 676 0.039618 AGGCCCGGTCAAAATCACAT 59.960 50.000 0.00 0.00 0.00 3.21
733 749 2.770904 GGATTACCCCGAGGCCCA 60.771 66.667 0.00 0.00 36.11 5.36
734 750 2.509422 GATTACCCCGAGGCCCAC 59.491 66.667 0.00 0.00 36.11 4.61
744 764 1.910580 CGAGGCCCACCCTGTGTTAT 61.911 60.000 0.00 0.00 46.60 1.89
756 776 3.370978 CCCTGTGTTATGAACGACATGTC 59.629 47.826 16.21 16.21 39.77 3.06
757 777 3.370978 CCTGTGTTATGAACGACATGTCC 59.629 47.826 20.03 6.94 39.77 4.02
758 778 3.993736 CTGTGTTATGAACGACATGTCCA 59.006 43.478 20.03 12.52 39.77 4.02
759 779 4.574892 TGTGTTATGAACGACATGTCCAT 58.425 39.130 20.03 18.19 39.77 3.41
784 804 0.654683 CCGTTCTCAGCATAAGCAGC 59.345 55.000 0.00 0.00 45.49 5.25
906 939 2.258748 AAAGGGCGAGGGCTAAGCTC 62.259 60.000 0.00 0.00 39.81 4.09
920 961 1.649321 AAGCTCTCTCATCACCACCA 58.351 50.000 0.00 0.00 0.00 4.17
921 962 0.901124 AGCTCTCTCATCACCACCAC 59.099 55.000 0.00 0.00 0.00 4.16
922 963 0.107945 GCTCTCTCATCACCACCACC 60.108 60.000 0.00 0.00 0.00 4.61
947 988 0.396417 AGAGCCTGACGAGCACCTAT 60.396 55.000 0.00 0.00 0.00 2.57
948 989 0.031449 GAGCCTGACGAGCACCTATC 59.969 60.000 0.00 0.00 0.00 2.08
963 1006 5.656859 AGCACCTATCATCCGCTTATACATA 59.343 40.000 0.00 0.00 0.00 2.29
965 1008 7.505923 AGCACCTATCATCCGCTTATACATATA 59.494 37.037 0.00 0.00 0.00 0.86
966 1009 8.307483 GCACCTATCATCCGCTTATACATATAT 58.693 37.037 0.00 0.00 0.00 0.86
1008 1058 4.704007 GCATCTGCAATGGCGAAG 57.296 55.556 9.81 0.00 45.35 3.79
1023 1073 3.591254 GAAGAACCACGGAGCCGCT 62.591 63.158 9.14 0.00 44.19 5.52
1143 1193 0.882927 CCACGTCAACCGGTCAACAT 60.883 55.000 8.04 0.00 42.24 2.71
1144 1194 0.511221 CACGTCAACCGGTCAACATC 59.489 55.000 8.04 0.00 42.24 3.06
1145 1195 0.942410 ACGTCAACCGGTCAACATCG 60.942 55.000 8.04 10.09 42.24 3.84
1175 1249 0.895100 TCTGGCCAAATGTGCTGGAC 60.895 55.000 7.01 0.00 42.98 4.02
1201 1282 2.639286 CTTTGGACGTGTGCCTGC 59.361 61.111 0.00 0.00 0.00 4.85
1415 1499 1.437986 GACGCGTCCTCTGCCTAAT 59.562 57.895 28.61 0.00 0.00 1.73
1459 1559 1.659098 GCGTCGTTAAGTTGCTGCTAT 59.341 47.619 0.00 0.00 0.00 2.97
1503 1603 1.971695 TCGCTCTGACGCTCCTCAA 60.972 57.895 0.00 0.00 0.00 3.02
1532 1635 2.285220 CCGCCATTATTCGAGTTGAGTG 59.715 50.000 0.00 0.00 0.00 3.51
1541 1644 7.972832 TTATTCGAGTTGAGTGTGGTATTTT 57.027 32.000 0.00 0.00 0.00 1.82
1552 1655 6.183361 TGAGTGTGGTATTTTTACTTCCCTCA 60.183 38.462 0.00 0.00 0.00 3.86
1631 1748 3.405831 ACCGGTTCAGTTAGTTTAAGCC 58.594 45.455 0.00 0.00 0.00 4.35
1668 1788 4.986659 GCGTTTACCTTGTGTCTCTCTTTA 59.013 41.667 0.00 0.00 0.00 1.85
1714 1834 2.796031 CGTTACTTGGTGTGTCGCTTTA 59.204 45.455 0.00 0.00 0.00 1.85
1715 1835 3.245754 CGTTACTTGGTGTGTCGCTTTAA 59.754 43.478 0.00 0.00 0.00 1.52
1721 1841 4.799419 TGGTGTGTCGCTTTAAGTAAAC 57.201 40.909 0.00 0.00 0.00 2.01
1722 1842 4.444536 TGGTGTGTCGCTTTAAGTAAACT 58.555 39.130 0.00 0.00 0.00 2.66
1723 1843 5.599732 TGGTGTGTCGCTTTAAGTAAACTA 58.400 37.500 0.00 0.00 0.00 2.24
1724 1844 5.693104 TGGTGTGTCGCTTTAAGTAAACTAG 59.307 40.000 0.00 0.00 0.00 2.57
1725 1845 5.922544 GGTGTGTCGCTTTAAGTAAACTAGA 59.077 40.000 0.00 0.00 0.00 2.43
1726 1846 6.128982 GGTGTGTCGCTTTAAGTAAACTAGAC 60.129 42.308 0.00 0.00 0.00 2.59
1727 1847 5.626543 TGTGTCGCTTTAAGTAAACTAGACG 59.373 40.000 0.00 0.00 0.00 4.18
1728 1848 5.853282 GTGTCGCTTTAAGTAAACTAGACGA 59.147 40.000 0.00 0.00 0.00 4.20
1729 1849 6.525976 GTGTCGCTTTAAGTAAACTAGACGAT 59.474 38.462 0.00 0.00 0.00 3.73
1730 1850 7.693951 GTGTCGCTTTAAGTAAACTAGACGATA 59.306 37.037 0.00 0.00 0.00 2.92
1731 1851 7.693951 TGTCGCTTTAAGTAAACTAGACGATAC 59.306 37.037 0.00 0.00 0.00 2.24
1732 1852 7.164990 GTCGCTTTAAGTAAACTAGACGATACC 59.835 40.741 0.00 0.00 0.00 2.73
1733 1853 6.416161 CGCTTTAAGTAAACTAGACGATACCC 59.584 42.308 0.00 0.00 0.00 3.69
1734 1854 6.699204 GCTTTAAGTAAACTAGACGATACCCC 59.301 42.308 0.00 0.00 0.00 4.95
1735 1855 4.907879 AAGTAAACTAGACGATACCCCG 57.092 45.455 0.00 0.00 0.00 5.73
1736 1856 2.620585 AGTAAACTAGACGATACCCCGC 59.379 50.000 0.00 0.00 0.00 6.13
1737 1857 0.383231 AAACTAGACGATACCCCGCG 59.617 55.000 0.00 0.00 0.00 6.46
1738 1858 2.068277 AACTAGACGATACCCCGCGC 62.068 60.000 0.00 0.00 0.00 6.86
1739 1859 2.516695 TAGACGATACCCCGCGCA 60.517 61.111 8.75 0.00 0.00 6.09
1740 1860 1.863662 CTAGACGATACCCCGCGCAT 61.864 60.000 8.75 0.00 0.00 4.73
1741 1861 1.457823 TAGACGATACCCCGCGCATT 61.458 55.000 8.75 0.00 0.00 3.56
1742 1862 2.587753 ACGATACCCCGCGCATTG 60.588 61.111 8.75 0.00 0.00 2.82
1743 1863 4.012895 CGATACCCCGCGCATTGC 62.013 66.667 8.75 0.00 41.47 3.56
1744 1864 2.591715 GATACCCCGCGCATTGCT 60.592 61.111 8.75 0.00 43.27 3.91
1745 1865 2.896801 GATACCCCGCGCATTGCTG 61.897 63.158 8.75 1.74 43.27 4.41
1755 1875 1.711500 GCATTGCTGCGGAAATTGC 59.289 52.632 0.00 0.55 38.92 3.56
1756 1876 0.738412 GCATTGCTGCGGAAATTGCT 60.738 50.000 0.00 0.00 38.92 3.91
1757 1877 1.717194 CATTGCTGCGGAAATTGCTT 58.283 45.000 0.00 0.00 0.00 3.91
1758 1878 1.392168 CATTGCTGCGGAAATTGCTTG 59.608 47.619 0.00 0.00 0.00 4.01
1759 1879 0.945265 TTGCTGCGGAAATTGCTTGC 60.945 50.000 0.00 0.00 34.72 4.01
1760 1880 1.373246 GCTGCGGAAATTGCTTGCA 60.373 52.632 0.00 4.22 34.45 4.08
1761 1881 1.620413 GCTGCGGAAATTGCTTGCAC 61.620 55.000 0.00 0.00 34.45 4.57
1762 1882 0.038892 CTGCGGAAATTGCTTGCACT 60.039 50.000 0.00 0.00 0.00 4.40
1763 1883 1.199789 CTGCGGAAATTGCTTGCACTA 59.800 47.619 0.00 0.00 0.00 2.74
1764 1884 1.818060 TGCGGAAATTGCTTGCACTAT 59.182 42.857 0.00 0.00 0.00 2.12
1765 1885 3.013219 TGCGGAAATTGCTTGCACTATA 58.987 40.909 0.00 0.00 0.00 1.31
1766 1886 3.631686 TGCGGAAATTGCTTGCACTATAT 59.368 39.130 0.00 0.00 0.00 0.86
1767 1887 4.097741 TGCGGAAATTGCTTGCACTATATT 59.902 37.500 0.00 0.00 0.00 1.28
1768 1888 5.043248 GCGGAAATTGCTTGCACTATATTT 58.957 37.500 0.00 0.00 0.00 1.40
1769 1889 5.519927 GCGGAAATTGCTTGCACTATATTTT 59.480 36.000 0.00 0.00 0.00 1.82
1770 1890 6.695278 GCGGAAATTGCTTGCACTATATTTTA 59.305 34.615 0.00 0.00 0.00 1.52
1771 1891 7.096477 GCGGAAATTGCTTGCACTATATTTTAG 60.096 37.037 0.00 0.00 0.00 1.85
1772 1892 7.915397 CGGAAATTGCTTGCACTATATTTTAGT 59.085 33.333 0.00 0.00 0.00 2.24
1884 2035 4.296265 GTCCTTTACGGTGGCCTG 57.704 61.111 3.32 0.00 0.00 4.85
1962 2154 8.548025 TCTCTCTCTCTCTCTCTCAAAAAGATA 58.452 37.037 0.00 0.00 32.19 1.98
2234 2426 9.895138 ATATAACATGTTAAAACCGGAGTTACT 57.105 29.630 21.57 3.45 34.19 2.24
2288 2488 6.016693 TGCTGATTGATTAACCGAAAAGTCAA 60.017 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.634397 TGAAGATGATCCACCACCTTC 57.366 47.619 0.00 0.00 0.00 3.46
3 4 2.644299 TGTTGAAGATGATCCACCACCT 59.356 45.455 0.00 0.00 0.00 4.00
7 8 3.539604 CTCCTGTTGAAGATGATCCACC 58.460 50.000 0.00 0.00 0.00 4.61
10 11 2.092753 TGCCTCCTGTTGAAGATGATCC 60.093 50.000 0.00 0.00 0.00 3.36
11 12 2.941720 GTGCCTCCTGTTGAAGATGATC 59.058 50.000 0.00 0.00 0.00 2.92
12 13 2.575279 AGTGCCTCCTGTTGAAGATGAT 59.425 45.455 0.00 0.00 0.00 2.45
13 14 1.980765 AGTGCCTCCTGTTGAAGATGA 59.019 47.619 0.00 0.00 0.00 2.92
14 15 2.354259 GAGTGCCTCCTGTTGAAGATG 58.646 52.381 0.00 0.00 0.00 2.90
15 16 1.066573 CGAGTGCCTCCTGTTGAAGAT 60.067 52.381 0.00 0.00 0.00 2.40
16 17 0.318441 CGAGTGCCTCCTGTTGAAGA 59.682 55.000 0.00 0.00 0.00 2.87
17 18 0.034059 ACGAGTGCCTCCTGTTGAAG 59.966 55.000 0.00 0.00 0.00 3.02
18 19 0.468226 AACGAGTGCCTCCTGTTGAA 59.532 50.000 0.00 0.00 0.00 2.69
19 20 0.033504 GAACGAGTGCCTCCTGTTGA 59.966 55.000 0.00 0.00 0.00 3.18
20 21 0.034059 AGAACGAGTGCCTCCTGTTG 59.966 55.000 0.00 0.00 0.00 3.33
21 22 1.546476 CTAGAACGAGTGCCTCCTGTT 59.454 52.381 0.00 0.00 0.00 3.16
22 23 1.178276 CTAGAACGAGTGCCTCCTGT 58.822 55.000 0.00 0.00 0.00 4.00
23 24 0.457851 CCTAGAACGAGTGCCTCCTG 59.542 60.000 0.00 0.00 0.00 3.86
24 25 0.039911 ACCTAGAACGAGTGCCTCCT 59.960 55.000 0.00 0.00 0.00 3.69
25 26 0.173708 CACCTAGAACGAGTGCCTCC 59.826 60.000 0.00 0.00 0.00 4.30
26 27 0.173708 CCACCTAGAACGAGTGCCTC 59.826 60.000 0.00 0.00 0.00 4.70
27 28 1.889530 GCCACCTAGAACGAGTGCCT 61.890 60.000 0.00 0.00 0.00 4.75
28 29 1.448013 GCCACCTAGAACGAGTGCC 60.448 63.158 0.00 0.00 0.00 5.01
29 30 1.805945 CGCCACCTAGAACGAGTGC 60.806 63.158 0.00 0.00 0.00 4.40
30 31 0.179161 CTCGCCACCTAGAACGAGTG 60.179 60.000 12.55 3.23 45.21 3.51
31 32 2.181584 CTCGCCACCTAGAACGAGT 58.818 57.895 12.55 0.00 45.21 4.18
33 34 0.896940 AACCTCGCCACCTAGAACGA 60.897 55.000 0.00 0.00 0.00 3.85
34 35 0.736325 CAACCTCGCCACCTAGAACG 60.736 60.000 0.00 0.00 0.00 3.95
35 36 1.019805 GCAACCTCGCCACCTAGAAC 61.020 60.000 0.00 0.00 0.00 3.01
36 37 1.295423 GCAACCTCGCCACCTAGAA 59.705 57.895 0.00 0.00 0.00 2.10
37 38 2.978824 GCAACCTCGCCACCTAGA 59.021 61.111 0.00 0.00 0.00 2.43
38 39 1.940883 TACGCAACCTCGCCACCTAG 61.941 60.000 0.00 0.00 0.00 3.02
39 40 1.978080 TACGCAACCTCGCCACCTA 60.978 57.895 0.00 0.00 0.00 3.08
40 41 3.307906 TACGCAACCTCGCCACCT 61.308 61.111 0.00 0.00 0.00 4.00
41 42 3.116531 GTACGCAACCTCGCCACC 61.117 66.667 0.00 0.00 0.00 4.61
42 43 2.356553 TGTACGCAACCTCGCCAC 60.357 61.111 0.00 0.00 0.00 5.01
43 44 2.356553 GTGTACGCAACCTCGCCA 60.357 61.111 0.39 0.00 0.00 5.69
44 45 3.116531 GGTGTACGCAACCTCGCC 61.117 66.667 8.97 0.00 0.00 5.54
45 46 3.475774 CGGTGTACGCAACCTCGC 61.476 66.667 8.97 0.00 34.82 5.03
46 47 2.084681 GTCGGTGTACGCAACCTCG 61.085 63.158 8.97 2.23 43.86 4.63
47 48 1.007038 TGTCGGTGTACGCAACCTC 60.007 57.895 8.97 0.00 43.86 3.85
48 49 1.300388 GTGTCGGTGTACGCAACCT 60.300 57.895 8.97 0.00 43.86 3.50
49 50 2.312436 GGTGTCGGTGTACGCAACC 61.312 63.158 8.97 6.43 43.86 3.77
50 51 1.592131 TGGTGTCGGTGTACGCAAC 60.592 57.895 8.97 6.50 43.86 4.17
51 52 1.592131 GTGGTGTCGGTGTACGCAA 60.592 57.895 8.97 0.00 43.86 4.85
52 53 2.027897 GTGGTGTCGGTGTACGCA 59.972 61.111 8.97 0.00 43.86 5.24
53 54 2.735857 GGTGGTGTCGGTGTACGC 60.736 66.667 0.00 0.00 43.86 4.42
54 55 2.048877 GGGTGGTGTCGGTGTACG 60.049 66.667 0.00 0.00 46.11 3.67
55 56 1.291272 GAGGGTGGTGTCGGTGTAC 59.709 63.158 0.00 0.00 0.00 2.90
56 57 1.909781 GGAGGGTGGTGTCGGTGTA 60.910 63.158 0.00 0.00 0.00 2.90
57 58 3.239253 GGAGGGTGGTGTCGGTGT 61.239 66.667 0.00 0.00 0.00 4.16
58 59 4.373116 CGGAGGGTGGTGTCGGTG 62.373 72.222 0.00 0.00 0.00 4.94
59 60 4.608774 TCGGAGGGTGGTGTCGGT 62.609 66.667 0.00 0.00 0.00 4.69
60 61 4.065281 GTCGGAGGGTGGTGTCGG 62.065 72.222 0.00 0.00 0.00 4.79
61 62 2.571216 AAGTCGGAGGGTGGTGTCG 61.571 63.158 0.00 0.00 0.00 4.35
62 63 1.004918 CAAGTCGGAGGGTGGTGTC 60.005 63.158 0.00 0.00 0.00 3.67
63 64 2.516888 CCAAGTCGGAGGGTGGTGT 61.517 63.158 0.00 0.00 36.56 4.16
64 65 2.347490 CCAAGTCGGAGGGTGGTG 59.653 66.667 0.00 0.00 36.56 4.17
65 66 3.637273 GCCAAGTCGGAGGGTGGT 61.637 66.667 4.11 0.00 36.56 4.16
66 67 3.636231 TGCCAAGTCGGAGGGTGG 61.636 66.667 0.00 0.00 36.56 4.61
67 68 2.358737 GTGCCAAGTCGGAGGGTG 60.359 66.667 0.00 0.00 36.56 4.61
68 69 4.003788 CGTGCCAAGTCGGAGGGT 62.004 66.667 0.00 0.00 36.56 4.34
69 70 3.691342 TCGTGCCAAGTCGGAGGG 61.691 66.667 0.00 0.00 36.56 4.30
70 71 2.432628 GTCGTGCCAAGTCGGAGG 60.433 66.667 0.00 0.00 36.56 4.30
71 72 2.022129 GTGTCGTGCCAAGTCGGAG 61.022 63.158 0.00 0.00 36.56 4.63
72 73 2.028484 GTGTCGTGCCAAGTCGGA 59.972 61.111 0.00 0.00 36.56 4.55
73 74 1.626654 GATGTGTCGTGCCAAGTCGG 61.627 60.000 0.00 0.00 38.11 4.79
74 75 1.626654 GGATGTGTCGTGCCAAGTCG 61.627 60.000 0.00 0.00 0.00 4.18
75 76 1.626654 CGGATGTGTCGTGCCAAGTC 61.627 60.000 0.00 0.00 0.00 3.01
76 77 1.667830 CGGATGTGTCGTGCCAAGT 60.668 57.895 0.00 0.00 0.00 3.16
77 78 3.027170 GCGGATGTGTCGTGCCAAG 62.027 63.158 0.00 0.00 0.00 3.61
78 79 3.047280 GCGGATGTGTCGTGCCAA 61.047 61.111 0.00 0.00 0.00 4.52
79 80 3.932580 GAGCGGATGTGTCGTGCCA 62.933 63.158 0.00 0.00 0.00 4.92
80 81 3.188786 GAGCGGATGTGTCGTGCC 61.189 66.667 0.00 0.00 0.00 5.01
81 82 3.188786 GGAGCGGATGTGTCGTGC 61.189 66.667 0.00 0.00 0.00 5.34
82 83 2.509336 GGGAGCGGATGTGTCGTG 60.509 66.667 0.00 0.00 0.00 4.35
83 84 2.994995 TGGGAGCGGATGTGTCGT 60.995 61.111 0.00 0.00 0.00 4.34
84 85 2.509336 GTGGGAGCGGATGTGTCG 60.509 66.667 0.00 0.00 0.00 4.35
85 86 1.741770 GTGTGGGAGCGGATGTGTC 60.742 63.158 0.00 0.00 0.00 3.67
86 87 2.347490 GTGTGGGAGCGGATGTGT 59.653 61.111 0.00 0.00 0.00 3.72
87 88 2.436646 GGTGTGGGAGCGGATGTG 60.437 66.667 0.00 0.00 0.00 3.21
88 89 2.927856 TGGTGTGGGAGCGGATGT 60.928 61.111 0.00 0.00 0.00 3.06
89 90 2.436646 GTGGTGTGGGAGCGGATG 60.437 66.667 0.00 0.00 0.00 3.51
90 91 4.082523 CGTGGTGTGGGAGCGGAT 62.083 66.667 0.00 0.00 0.00 4.18
92 93 4.742201 CTCGTGGTGTGGGAGCGG 62.742 72.222 0.00 0.00 0.00 5.52
93 94 4.742201 CCTCGTGGTGTGGGAGCG 62.742 72.222 0.00 0.00 0.00 5.03
95 96 2.469465 AATGCCTCGTGGTGTGGGAG 62.469 60.000 5.26 0.00 34.89 4.30
96 97 2.525124 AATGCCTCGTGGTGTGGGA 61.525 57.895 5.26 0.00 35.94 4.37
97 98 2.034066 AATGCCTCGTGGTGTGGG 59.966 61.111 5.26 0.00 35.27 4.61
98 99 2.334946 CCAATGCCTCGTGGTGTGG 61.335 63.158 5.26 6.62 35.27 4.17
99 100 2.334946 CCCAATGCCTCGTGGTGTG 61.335 63.158 5.26 1.32 32.60 3.82
100 101 2.034066 CCCAATGCCTCGTGGTGT 59.966 61.111 5.26 0.00 32.60 4.16
101 102 3.443045 GCCCAATGCCTCGTGGTG 61.443 66.667 5.26 0.00 32.60 4.17
126 127 4.542075 GCTAAAAGAGCCTCGGGG 57.458 61.111 0.00 0.00 46.41 5.73
134 135 4.158025 TCCTCTAGAACGTGGCTAAAAGAG 59.842 45.833 0.00 0.00 0.00 2.85
135 136 4.084287 TCCTCTAGAACGTGGCTAAAAGA 58.916 43.478 0.00 0.00 0.00 2.52
136 137 4.451629 TCCTCTAGAACGTGGCTAAAAG 57.548 45.455 0.00 0.00 0.00 2.27
137 138 4.322499 CCTTCCTCTAGAACGTGGCTAAAA 60.322 45.833 0.00 0.00 0.00 1.52
138 139 3.194968 CCTTCCTCTAGAACGTGGCTAAA 59.805 47.826 0.00 0.00 0.00 1.85
139 140 2.758979 CCTTCCTCTAGAACGTGGCTAA 59.241 50.000 0.00 0.00 0.00 3.09
140 141 2.376109 CCTTCCTCTAGAACGTGGCTA 58.624 52.381 0.00 0.00 0.00 3.93
141 142 1.187087 CCTTCCTCTAGAACGTGGCT 58.813 55.000 0.00 0.00 0.00 4.75
142 143 0.460459 GCCTTCCTCTAGAACGTGGC 60.460 60.000 9.67 9.67 36.50 5.01
143 144 0.895530 TGCCTTCCTCTAGAACGTGG 59.104 55.000 0.00 0.00 0.00 4.94
144 145 1.732732 CGTGCCTTCCTCTAGAACGTG 60.733 57.143 0.00 0.00 0.00 4.49
145 146 0.526662 CGTGCCTTCCTCTAGAACGT 59.473 55.000 0.00 0.00 0.00 3.99
146 147 0.809385 TCGTGCCTTCCTCTAGAACG 59.191 55.000 4.83 4.83 0.00 3.95
147 148 1.467713 CGTCGTGCCTTCCTCTAGAAC 60.468 57.143 0.00 0.00 0.00 3.01
148 149 0.809385 CGTCGTGCCTTCCTCTAGAA 59.191 55.000 0.00 0.00 0.00 2.10
149 150 0.322277 ACGTCGTGCCTTCCTCTAGA 60.322 55.000 0.00 0.00 0.00 2.43
150 151 1.331138 CTACGTCGTGCCTTCCTCTAG 59.669 57.143 8.47 0.00 0.00 2.43
151 152 1.376543 CTACGTCGTGCCTTCCTCTA 58.623 55.000 8.47 0.00 0.00 2.43
152 153 1.313812 CCTACGTCGTGCCTTCCTCT 61.314 60.000 8.47 0.00 0.00 3.69
153 154 1.139095 CCTACGTCGTGCCTTCCTC 59.861 63.158 8.47 0.00 0.00 3.71
154 155 2.348888 CCCTACGTCGTGCCTTCCT 61.349 63.158 8.47 0.00 0.00 3.36
155 156 2.183555 CCCTACGTCGTGCCTTCC 59.816 66.667 8.47 0.00 0.00 3.46
156 157 2.508663 GCCCTACGTCGTGCCTTC 60.509 66.667 8.47 0.00 0.00 3.46
157 158 4.430765 CGCCCTACGTCGTGCCTT 62.431 66.667 8.47 0.00 36.87 4.35
167 168 2.184579 GTGAGCTGGACGCCCTAC 59.815 66.667 0.00 0.00 40.39 3.18
168 169 3.449227 CGTGAGCTGGACGCCCTA 61.449 66.667 0.00 0.00 40.39 3.53
171 172 4.373116 TTCCGTGAGCTGGACGCC 62.373 66.667 8.99 0.00 40.39 5.68
172 173 3.112709 GTTCCGTGAGCTGGACGC 61.113 66.667 8.99 0.00 34.56 5.19
173 174 1.734477 CTGTTCCGTGAGCTGGACG 60.734 63.158 7.72 7.72 34.56 4.79
174 175 0.389166 CTCTGTTCCGTGAGCTGGAC 60.389 60.000 0.00 0.00 34.56 4.02
175 176 1.967535 CTCTGTTCCGTGAGCTGGA 59.032 57.895 0.00 0.00 0.00 3.86
176 177 4.586618 CTCTGTTCCGTGAGCTGG 57.413 61.111 0.00 0.00 0.00 4.85
180 181 1.444553 GTCGGCTCTGTTCCGTGAG 60.445 63.158 9.35 0.00 46.49 3.51
181 182 2.649034 GTCGGCTCTGTTCCGTGA 59.351 61.111 9.35 0.00 46.49 4.35
182 183 2.805353 CGTCGGCTCTGTTCCGTG 60.805 66.667 9.35 2.32 46.49 4.94
183 184 4.052229 CCGTCGGCTCTGTTCCGT 62.052 66.667 0.00 0.00 46.49 4.69
194 195 4.504916 CTCTGCTCCTGCCGTCGG 62.505 72.222 6.99 6.99 38.71 4.79
196 197 4.828925 GGCTCTGCTCCTGCCGTC 62.829 72.222 0.00 0.00 37.11 4.79
201 202 4.172512 ATGGCGGCTCTGCTCCTG 62.173 66.667 11.43 0.00 34.52 3.86
202 203 4.172512 CATGGCGGCTCTGCTCCT 62.173 66.667 11.43 0.00 34.52 3.69
214 215 3.338275 TTCCCACCTACGCCATGGC 62.338 63.158 27.67 27.67 37.85 4.40
215 216 1.153168 CTTCCCACCTACGCCATGG 60.153 63.158 7.63 7.63 0.00 3.66
216 217 1.153168 CCTTCCCACCTACGCCATG 60.153 63.158 0.00 0.00 0.00 3.66
217 218 2.375345 CCCTTCCCACCTACGCCAT 61.375 63.158 0.00 0.00 0.00 4.40
218 219 3.006728 CCCTTCCCACCTACGCCA 61.007 66.667 0.00 0.00 0.00 5.69
219 220 4.484872 GCCCTTCCCACCTACGCC 62.485 72.222 0.00 0.00 0.00 5.68
220 221 4.832608 CGCCCTTCCCACCTACGC 62.833 72.222 0.00 0.00 0.00 4.42
221 222 3.366739 GACGCCCTTCCCACCTACG 62.367 68.421 0.00 0.00 0.00 3.51
222 223 2.582978 GACGCCCTTCCCACCTAC 59.417 66.667 0.00 0.00 0.00 3.18
223 224 3.072468 CGACGCCCTTCCCACCTA 61.072 66.667 0.00 0.00 0.00 3.08
225 226 4.452733 CTCGACGCCCTTCCCACC 62.453 72.222 0.00 0.00 0.00 4.61
226 227 4.452733 CCTCGACGCCCTTCCCAC 62.453 72.222 0.00 0.00 0.00 4.61
227 228 4.689549 TCCTCGACGCCCTTCCCA 62.690 66.667 0.00 0.00 0.00 4.37
228 229 4.144703 GTCCTCGACGCCCTTCCC 62.145 72.222 0.00 0.00 0.00 3.97
237 238 0.529378 TTCTTAAGGCCGTCCTCGAC 59.471 55.000 1.85 0.00 43.40 4.20
238 239 0.815734 CTTCTTAAGGCCGTCCTCGA 59.184 55.000 1.85 0.00 43.40 4.04
239 240 0.179108 CCTTCTTAAGGCCGTCCTCG 60.179 60.000 1.85 0.00 43.40 4.63
240 241 3.762674 CCTTCTTAAGGCCGTCCTC 57.237 57.895 1.85 0.00 43.40 3.71
241 242 2.835696 CGTCCTTCTTAAGGCCGTCCT 61.836 57.143 1.85 0.00 44.46 3.85
242 243 0.459759 CGTCCTTCTTAAGGCCGTCC 60.460 60.000 1.85 0.00 44.46 4.79
243 244 3.046280 CGTCCTTCTTAAGGCCGTC 57.954 57.895 1.85 0.00 44.46 4.79
249 250 0.806492 GGCGCCTCGTCCTTCTTAAG 60.806 60.000 22.15 0.00 0.00 1.85
250 251 1.217244 GGCGCCTCGTCCTTCTTAA 59.783 57.895 22.15 0.00 0.00 1.85
251 252 2.890371 GGCGCCTCGTCCTTCTTA 59.110 61.111 22.15 0.00 0.00 2.10
294 295 3.507622 TGTAGATCAGTATCGCAGGATGG 59.492 47.826 0.00 0.00 37.19 3.51
295 296 4.217334 AGTGTAGATCAGTATCGCAGGATG 59.783 45.833 0.00 0.00 37.19 3.51
296 297 4.217334 CAGTGTAGATCAGTATCGCAGGAT 59.783 45.833 0.00 0.00 37.19 3.24
297 298 3.565902 CAGTGTAGATCAGTATCGCAGGA 59.434 47.826 0.00 0.00 37.19 3.86
298 299 3.565902 TCAGTGTAGATCAGTATCGCAGG 59.434 47.826 0.00 0.00 37.19 4.85
299 300 4.820284 TCAGTGTAGATCAGTATCGCAG 57.180 45.455 0.00 0.00 37.19 5.18
300 301 4.821805 TGATCAGTGTAGATCAGTATCGCA 59.178 41.667 2.73 0.00 46.92 5.10
301 302 5.363979 TGATCAGTGTAGATCAGTATCGC 57.636 43.478 2.73 0.00 46.92 4.58
321 322 5.590259 TGTCTATCACTCTCGATCATTGTGA 59.410 40.000 9.26 9.26 41.07 3.58
326 327 6.456795 TTGTTGTCTATCACTCTCGATCAT 57.543 37.500 0.00 0.00 0.00 2.45
327 328 5.897377 TTGTTGTCTATCACTCTCGATCA 57.103 39.130 0.00 0.00 0.00 2.92
344 345 3.287312 AGGTGTGAAATGCGATTGTTG 57.713 42.857 0.00 0.00 0.00 3.33
386 387 7.277539 CCTGTACACAGATCAGAGAGATTTTTC 59.722 40.741 10.96 0.00 46.59 2.29
392 394 4.308526 ACCTGTACACAGATCAGAGAGA 57.691 45.455 10.96 0.00 46.59 3.10
393 395 4.742417 CAACCTGTACACAGATCAGAGAG 58.258 47.826 10.96 0.00 46.59 3.20
397 399 1.995484 CGCAACCTGTACACAGATCAG 59.005 52.381 10.96 0.00 46.59 2.90
399 401 2.080286 ACGCAACCTGTACACAGATC 57.920 50.000 10.96 0.00 46.59 2.75
406 408 1.334054 CACGACTACGCAACCTGTAC 58.666 55.000 0.00 0.00 43.96 2.90
418 420 4.841443 ATATTACGGCATGACACGACTA 57.159 40.909 0.00 0.00 0.00 2.59
437 439 2.098607 CGGTGTCTGAGTAGCGGAAATA 59.901 50.000 5.77 0.00 32.59 1.40
443 445 1.515088 CTGCGGTGTCTGAGTAGCG 60.515 63.158 8.52 8.52 40.42 4.26
444 446 0.456995 GACTGCGGTGTCTGAGTAGC 60.457 60.000 0.80 0.00 34.39 3.58
446 448 0.251209 AGGACTGCGGTGTCTGAGTA 60.251 55.000 0.80 0.00 37.16 2.59
454 456 1.884235 AAGAAAAGAGGACTGCGGTG 58.116 50.000 0.80 0.00 0.00 4.94
455 457 2.640316 AAAGAAAAGAGGACTGCGGT 57.360 45.000 0.00 0.00 0.00 5.68
456 458 2.226674 GGAAAAGAAAAGAGGACTGCGG 59.773 50.000 0.00 0.00 0.00 5.69
457 459 3.142174 AGGAAAAGAAAAGAGGACTGCG 58.858 45.455 0.00 0.00 0.00 5.18
485 487 0.036858 GAGAGGACTGCAGTCAACCC 60.037 60.000 39.71 27.17 46.47 4.11
521 523 0.248565 TCGCAGCAAAGCAGAGAGAT 59.751 50.000 0.00 0.00 0.00 2.75
529 531 0.652751 CGAATCGATCGCAGCAAAGC 60.653 55.000 11.09 0.00 45.89 3.51
569 571 1.093972 CCATGTTGGTGATAGCGCAA 58.906 50.000 11.47 0.00 31.35 4.85
577 579 1.142667 TGTCTTGCTCCATGTTGGTGA 59.857 47.619 0.00 0.00 39.03 4.02
612 626 3.347216 ACACTCACACTGCTCACTTTTT 58.653 40.909 0.00 0.00 0.00 1.94
613 627 2.991250 ACACTCACACTGCTCACTTTT 58.009 42.857 0.00 0.00 0.00 2.27
614 628 2.698855 ACACTCACACTGCTCACTTT 57.301 45.000 0.00 0.00 0.00 2.66
615 629 3.819564 TTACACTCACACTGCTCACTT 57.180 42.857 0.00 0.00 0.00 3.16
616 630 3.133003 ACTTTACACTCACACTGCTCACT 59.867 43.478 0.00 0.00 0.00 3.41
624 638 4.874396 GGGCCTAATACTTTACACTCACAC 59.126 45.833 0.84 0.00 0.00 3.82
625 639 4.382254 CGGGCCTAATACTTTACACTCACA 60.382 45.833 0.84 0.00 0.00 3.58
637 651 3.314357 GTGATTTTGACCGGGCCTAATAC 59.686 47.826 3.83 0.69 0.00 1.89
661 676 3.131577 ACTGTAATATTCTTCGACCGCCA 59.868 43.478 0.00 0.00 0.00 5.69
729 745 1.173913 GTTCATAACACAGGGTGGGC 58.826 55.000 1.07 0.00 37.94 5.36
733 749 3.244422 ACATGTCGTTCATAACACAGGGT 60.244 43.478 0.00 5.26 34.67 4.34
734 750 3.334691 ACATGTCGTTCATAACACAGGG 58.665 45.455 0.00 4.87 34.67 4.45
744 764 2.631267 CATGGATGGACATGTCGTTCA 58.369 47.619 19.33 15.18 42.48 3.18
756 776 1.442526 GCTGAGAACGGCATGGATGG 61.443 60.000 0.00 0.00 46.56 3.51
757 777 2.020131 GCTGAGAACGGCATGGATG 58.980 57.895 0.00 0.00 46.56 3.51
758 778 4.547859 GCTGAGAACGGCATGGAT 57.452 55.556 0.00 0.00 46.56 3.41
827 847 2.293677 GTGGAGAGTGTGACGAAGAGAA 59.706 50.000 0.00 0.00 0.00 2.87
831 851 0.038159 GGGTGGAGAGTGTGACGAAG 60.038 60.000 0.00 0.00 0.00 3.79
879 910 1.749286 GCCCTCGCCCTTTTTATAGCA 60.749 52.381 0.00 0.00 0.00 3.49
906 939 2.430465 CTTTGGTGGTGGTGATGAGAG 58.570 52.381 0.00 0.00 0.00 3.20
920 961 1.302033 CGTCAGGCTCTGCTTTGGT 60.302 57.895 0.00 0.00 0.00 3.67
921 962 1.004560 TCGTCAGGCTCTGCTTTGG 60.005 57.895 0.00 0.00 0.00 3.28
922 963 1.633852 GCTCGTCAGGCTCTGCTTTG 61.634 60.000 0.00 0.00 0.00 2.77
947 988 9.201989 AGAAAGGATATATGTATAAGCGGATGA 57.798 33.333 0.00 0.00 0.00 2.92
948 989 9.823647 AAGAAAGGATATATGTATAAGCGGATG 57.176 33.333 0.00 0.00 0.00 3.51
963 1006 1.868519 GCCGACGCGAAGAAAGGATAT 60.869 52.381 15.93 0.00 0.00 1.63
965 1008 1.810030 GCCGACGCGAAGAAAGGAT 60.810 57.895 15.93 0.00 0.00 3.24
966 1009 2.431942 GCCGACGCGAAGAAAGGA 60.432 61.111 15.93 0.00 0.00 3.36
971 1014 4.435436 ATGCTGCCGACGCGAAGA 62.435 61.111 15.93 0.00 38.08 2.87
1005 1055 3.119096 GCGGCTCCGTGGTTCTTC 61.119 66.667 10.24 0.00 42.09 2.87
1006 1056 3.626924 AGCGGCTCCGTGGTTCTT 61.627 61.111 10.24 0.00 42.09 2.52
1007 1057 4.379243 CAGCGGCTCCGTGGTTCT 62.379 66.667 10.24 0.00 42.09 3.01
1023 1073 2.775856 GGACGCGATCAGGAGAGCA 61.776 63.158 15.93 0.00 0.00 4.26
1078 1128 2.809174 CATCTGCGTCGCGGTGAA 60.809 61.111 24.58 7.17 36.18 3.18
1136 1186 1.990799 TCATGGACGACGATGTTGAC 58.009 50.000 0.00 0.00 34.61 3.18
1175 1249 2.289547 CACACGTCCAAAGGGTTACAAG 59.710 50.000 0.00 0.00 34.93 3.16
1285 1369 1.000993 GAGGGAGGAGCAGGTCTCA 59.999 63.158 0.00 0.00 43.70 3.27
1312 1396 4.631740 TCCTGGGTCAGACCGGCA 62.632 66.667 13.80 5.96 39.83 5.69
1415 1499 0.456482 CACGTACATCCAACGGCGTA 60.456 55.000 15.20 0.00 44.48 4.42
1441 1541 5.677178 GCATAAATAGCAGCAACTTAACGAC 59.323 40.000 0.00 0.00 0.00 4.34
1459 1559 7.779798 ACTTAGCCTCCTTTATTCATGCATAAA 59.220 33.333 9.68 9.68 0.00 1.40
1532 1635 6.887626 TTGTGAGGGAAGTAAAAATACCAC 57.112 37.500 0.00 0.00 0.00 4.16
1541 1644 4.285003 TCGATCCTTTTGTGAGGGAAGTAA 59.715 41.667 0.00 0.00 37.41 2.24
1552 1655 4.562963 GGACTACAACCTCGATCCTTTTGT 60.563 45.833 0.00 0.00 34.79 2.83
1631 1748 3.124636 GGTAAACGCACTGGTGTAATCAG 59.875 47.826 2.64 0.00 36.56 2.90
1668 1788 1.963515 GGCAATCAGGAACAACCAAGT 59.036 47.619 0.00 0.00 42.04 3.16
1714 1834 3.067320 GCGGGGTATCGTCTAGTTTACTT 59.933 47.826 0.00 0.00 0.00 2.24
1715 1835 2.620585 GCGGGGTATCGTCTAGTTTACT 59.379 50.000 0.00 0.00 0.00 2.24
1721 1841 1.863662 ATGCGCGGGGTATCGTCTAG 61.864 60.000 8.83 0.00 0.00 2.43
1722 1842 1.457823 AATGCGCGGGGTATCGTCTA 61.458 55.000 8.83 0.00 0.00 2.59
1723 1843 2.792947 AATGCGCGGGGTATCGTCT 61.793 57.895 8.83 0.00 0.00 4.18
1724 1844 2.279918 AATGCGCGGGGTATCGTC 60.280 61.111 8.83 0.00 0.00 4.20
1725 1845 2.587753 CAATGCGCGGGGTATCGT 60.588 61.111 8.83 0.00 0.00 3.73
1726 1846 4.012895 GCAATGCGCGGGGTATCG 62.013 66.667 8.83 0.00 0.00 2.92
1737 1857 0.738412 AGCAATTTCCGCAGCAATGC 60.738 50.000 0.00 0.00 0.00 3.56
1738 1858 1.392168 CAAGCAATTTCCGCAGCAATG 59.608 47.619 0.00 0.00 0.00 2.82
1739 1859 1.717194 CAAGCAATTTCCGCAGCAAT 58.283 45.000 0.00 0.00 0.00 3.56
1740 1860 0.945265 GCAAGCAATTTCCGCAGCAA 60.945 50.000 0.00 0.00 34.18 3.91
1741 1861 1.373246 GCAAGCAATTTCCGCAGCA 60.373 52.632 0.00 0.00 34.18 4.41
1742 1862 1.373246 TGCAAGCAATTTCCGCAGC 60.373 52.632 0.00 0.00 34.48 5.25
1743 1863 0.038892 AGTGCAAGCAATTTCCGCAG 60.039 50.000 0.00 0.00 32.31 5.18
1744 1864 1.242989 TAGTGCAAGCAATTTCCGCA 58.757 45.000 0.00 0.00 0.00 5.69
1745 1865 2.566952 ATAGTGCAAGCAATTTCCGC 57.433 45.000 0.00 0.00 0.00 5.54
1746 1866 7.915397 ACTAAAATATAGTGCAAGCAATTTCCG 59.085 33.333 0.00 0.11 0.00 4.30
1765 1885 8.687242 GGGCTCTTTTGCTAATCTTACTAAAAT 58.313 33.333 0.00 0.00 0.00 1.82
1766 1886 7.148306 CGGGCTCTTTTGCTAATCTTACTAAAA 60.148 37.037 0.00 0.00 0.00 1.52
1767 1887 6.315393 CGGGCTCTTTTGCTAATCTTACTAAA 59.685 38.462 0.00 0.00 0.00 1.85
1768 1888 5.815740 CGGGCTCTTTTGCTAATCTTACTAA 59.184 40.000 0.00 0.00 0.00 2.24
1769 1889 5.105064 ACGGGCTCTTTTGCTAATCTTACTA 60.105 40.000 0.00 0.00 0.00 1.82
1770 1890 4.192317 CGGGCTCTTTTGCTAATCTTACT 58.808 43.478 0.00 0.00 0.00 2.24
1771 1891 3.939592 ACGGGCTCTTTTGCTAATCTTAC 59.060 43.478 0.00 0.00 0.00 2.34
1772 1892 3.938963 CACGGGCTCTTTTGCTAATCTTA 59.061 43.478 0.00 0.00 0.00 2.10
1773 1893 2.749621 CACGGGCTCTTTTGCTAATCTT 59.250 45.455 0.00 0.00 0.00 2.40
1777 1897 1.573829 CGCACGGGCTCTTTTGCTAA 61.574 55.000 8.62 0.00 38.10 3.09
1884 2035 0.736053 TTTTCGTTGTGTGAGTGCCC 59.264 50.000 0.00 0.00 0.00 5.36
1962 2154 4.322424 GCGGGGGAAAACAACATATTTCTT 60.322 41.667 0.00 0.00 36.15 2.52
2245 2437 6.954616 TCAGCAGCAACAAAATTATTCATG 57.045 33.333 0.00 0.00 0.00 3.07
2379 2580 1.149987 GTTCACCGTCGTGCCATTTA 58.850 50.000 0.00 0.00 40.04 1.40


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

AutoCloner maintained by Alex Coulton.