Multiple sequence alignment - TraesCS5A01G172500

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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 TraesCS5A01G172500 chr5A 100.000 2643 0 0 1 2643 365664704 365667346 0.000000e+00 4881
1 TraesCS5A01G172500 chr3D 92.987 1868 98 18 181 2025 124068843 124066986 0.000000e+00 2693
2 TraesCS5A01G172500 chr3A 90.129 1864 156 20 190 2028 600090475 600088615 0.000000e+00 2398
3 TraesCS5A01G172500 chr3A 98.333 180 3 0 1 180 374471807 374471986 1.530000e-82 316
4 TraesCS5A01G172500 chr1A 89.347 1868 147 23 190 2019 520768079 520769932 0.000000e+00 2300
5 TraesCS5A01G172500 chr1A 97.802 182 4 0 1 182 229383405 229383586 5.490000e-82 315
6 TraesCS5A01G172500 chr1A 97.790 181 4 0 1 181 244050194 244050014 1.980000e-81 313
7 TraesCS5A01G172500 chr1A 96.757 185 6 0 1 185 347525223 347525039 2.560000e-80 309
8 TraesCS5A01G172500 chr5D 93.671 1501 81 3 181 1680 39089686 39091173 0.000000e+00 2233
9 TraesCS5A01G172500 chr5D 94.429 359 20 0 1671 2029 353958685 353959043 1.070000e-153 553
10 TraesCS5A01G172500 chr5D 92.837 363 25 1 1671 2033 347373113 347372752 2.330000e-145 525
11 TraesCS5A01G172500 chr5D 92.479 359 26 1 1671 2029 39091198 39091555 1.810000e-141 512
12 TraesCS5A01G172500 chr5D 91.429 350 25 1 2026 2370 276934993 276935342 2.380000e-130 475
13 TraesCS5A01G172500 chr5D 92.262 168 13 0 2476 2643 276935368 276935535 3.400000e-59 239
14 TraesCS5A01G172500 chr5D 95.699 93 3 1 2388 2479 276935324 276935416 5.890000e-32 148
15 TraesCS5A01G172500 chr7D 92.639 1508 95 7 181 1684 561525366 561523871 0.000000e+00 2156
16 TraesCS5A01G172500 chr7D 92.364 1506 108 3 181 1680 131323944 131325448 0.000000e+00 2137
17 TraesCS5A01G172500 chr7D 92.303 1507 106 7 181 1684 174131829 174133328 0.000000e+00 2132
18 TraesCS5A01G172500 chr7D 92.642 1196 75 5 181 1375 626150162 626151345 0.000000e+00 1709
19 TraesCS5A01G172500 chr7D 88.378 1282 103 20 181 1437 113010782 113012042 0.000000e+00 1500
20 TraesCS5A01G172500 chr7D 93.056 360 25 0 1671 2030 626191891 626192250 6.480000e-146 527
21 TraesCS5A01G172500 chr7D 85.465 344 28 16 181 514 235569493 235569162 3.260000e-89 339
22 TraesCS5A01G172500 chr1D 92.426 1492 102 2 190 1680 481925426 481926907 0.000000e+00 2119
23 TraesCS5A01G172500 chr1D 93.983 349 21 0 1671 2019 481926932 481927280 1.800000e-146 529
24 TraesCS5A01G172500 chrUn 90.837 1506 126 6 181 1680 32170780 32169281 0.000000e+00 2006
25 TraesCS5A01G172500 chr2D 93.503 354 23 0 1671 2024 646798747 646798394 6.480000e-146 527
26 TraesCS5A01G172500 chr6D 92.603 365 26 1 1671 2035 11694935 11694572 8.380000e-145 523
27 TraesCS5A01G172500 chr4D 93.220 354 24 0 1671 2024 460660217 460659864 3.010000e-144 521
28 TraesCS5A01G172500 chr4D 93.220 354 24 0 1671 2024 460661482 460661129 3.010000e-144 521
29 TraesCS5A01G172500 chr4A 98.333 180 3 0 1 180 196719845 196720024 1.530000e-82 316
30 TraesCS5A01G172500 chr4A 97.268 183 5 0 1 183 248770593 248770411 7.100000e-81 311
31 TraesCS5A01G172500 chr2A 98.333 180 3 0 1 180 235721503 235721682 1.530000e-82 316
32 TraesCS5A01G172500 chr2A 98.333 180 3 0 1 180 419229468 419229289 1.530000e-82 316
33 TraesCS5A01G172500 chr2A 94.845 194 9 1 1 194 73214662 73214470 4.280000e-78 302
34 TraesCS5A01G172500 chr5B 91.057 123 5 3 2095 2216 314298350 314298233 7.570000e-36 161
35 TraesCS5A01G172500 chr5B 94.382 89 5 0 2215 2303 314297906 314297818 1.280000e-28 137


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 TraesCS5A01G172500 chr5A 365664704 365667346 2642 False 4881.000000 4881 100.0000 1 2643 1 chr5A.!!$F1 2642
1 TraesCS5A01G172500 chr3D 124066986 124068843 1857 True 2693.000000 2693 92.9870 181 2025 1 chr3D.!!$R1 1844
2 TraesCS5A01G172500 chr3A 600088615 600090475 1860 True 2398.000000 2398 90.1290 190 2028 1 chr3A.!!$R1 1838
3 TraesCS5A01G172500 chr1A 520768079 520769932 1853 False 2300.000000 2300 89.3470 190 2019 1 chr1A.!!$F2 1829
4 TraesCS5A01G172500 chr5D 39089686 39091555 1869 False 1372.500000 2233 93.0750 181 2029 2 chr5D.!!$F2 1848
5 TraesCS5A01G172500 chr5D 276934993 276935535 542 False 287.333333 475 93.1300 2026 2643 3 chr5D.!!$F3 617
6 TraesCS5A01G172500 chr7D 561523871 561525366 1495 True 2156.000000 2156 92.6390 181 1684 1 chr7D.!!$R2 1503
7 TraesCS5A01G172500 chr7D 131323944 131325448 1504 False 2137.000000 2137 92.3640 181 1680 1 chr7D.!!$F2 1499
8 TraesCS5A01G172500 chr7D 174131829 174133328 1499 False 2132.000000 2132 92.3030 181 1684 1 chr7D.!!$F3 1503
9 TraesCS5A01G172500 chr7D 626150162 626151345 1183 False 1709.000000 1709 92.6420 181 1375 1 chr7D.!!$F4 1194
10 TraesCS5A01G172500 chr7D 113010782 113012042 1260 False 1500.000000 1500 88.3780 181 1437 1 chr7D.!!$F1 1256
11 TraesCS5A01G172500 chr1D 481925426 481927280 1854 False 1324.000000 2119 93.2045 190 2019 2 chr1D.!!$F1 1829
12 TraesCS5A01G172500 chrUn 32169281 32170780 1499 True 2006.000000 2006 90.8370 181 1680 1 chrUn.!!$R1 1499
13 TraesCS5A01G172500 chr4D 460659864 460661482 1618 True 521.000000 521 93.2200 1671 2024 2 chr4D.!!$R1 353

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
122 123 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.0 0.0 0.0 0.0 2.90 F
126 127 0.176680 CCCGTGAGTCCCTGATCTTG 59.823 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1570 1629 0.620556 ACGACCTCAATGCCATCCTT 59.379 50.000 0.0 0.0 0.00 3.36 R
1910 2027 1.209019 TGCATGTTGTTTGGTTGCCTT 59.791 42.857 0.0 0.0 32.39 4.35 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
24 25 3.809234 CTCGTCTATGATCGAGCTCTTG 58.191 50.000 12.85 0.00 44.82 3.02
28 29 5.470437 TCGTCTATGATCGAGCTCTTGTATT 59.530 40.000 12.85 0.00 0.00 1.89
29 30 5.792962 CGTCTATGATCGAGCTCTTGTATTC 59.207 44.000 12.85 0.36 0.00 1.75
32 33 4.216366 TGATCGAGCTCTTGTATTCGAG 57.784 45.455 12.85 0.00 44.14 4.04
37 38 1.859383 GCTCTTGTATTCGAGCCCTC 58.141 55.000 0.00 0.00 45.21 4.30
60 61 2.656947 GCCCCTGGCTTGTAATATGA 57.343 50.000 0.00 0.00 46.69 2.15
61 62 3.160679 GCCCCTGGCTTGTAATATGAT 57.839 47.619 0.00 0.00 46.69 2.45
62 63 2.821969 GCCCCTGGCTTGTAATATGATG 59.178 50.000 0.00 0.00 46.69 3.07
63 64 2.821969 CCCCTGGCTTGTAATATGATGC 59.178 50.000 0.00 0.00 0.00 3.91
68 69 5.764686 CCTGGCTTGTAATATGATGCTTGTA 59.235 40.000 0.00 0.00 0.00 2.41
69 70 6.432162 CCTGGCTTGTAATATGATGCTTGTAT 59.568 38.462 0.00 0.00 0.00 2.29
70 71 7.205737 TGGCTTGTAATATGATGCTTGTATG 57.794 36.000 0.00 0.00 0.00 2.39
71 72 6.997476 TGGCTTGTAATATGATGCTTGTATGA 59.003 34.615 0.00 0.00 0.00 2.15
72 73 7.041167 TGGCTTGTAATATGATGCTTGTATGAC 60.041 37.037 0.00 0.00 0.00 3.06
74 75 8.562892 GCTTGTAATATGATGCTTGTATGACTT 58.437 33.333 0.00 0.00 0.00 3.01
109 110 8.682936 ATAGATTTGTGTTGTGATATCTTCCC 57.317 34.615 3.98 0.00 0.00 3.97
110 111 5.586243 AGATTTGTGTTGTGATATCTTCCCG 59.414 40.000 3.98 0.00 0.00 5.14
111 112 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
112 113 3.595173 TGTGTTGTGATATCTTCCCGTG 58.405 45.455 3.98 0.00 0.00 4.94
115 116 3.513912 TGTTGTGATATCTTCCCGTGAGT 59.486 43.478 3.98 0.00 0.00 3.41
117 118 2.693591 TGTGATATCTTCCCGTGAGTCC 59.306 50.000 3.98 0.00 0.00 3.85
118 119 2.036089 GTGATATCTTCCCGTGAGTCCC 59.964 54.545 3.98 0.00 0.00 4.46
119 120 2.091278 TGATATCTTCCCGTGAGTCCCT 60.091 50.000 3.98 0.00 0.00 4.20
122 123 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
123 124 0.461961 CTTCCCGTGAGTCCCTGATC 59.538 60.000 0.00 0.00 0.00 2.92
126 127 0.176680 CCCGTGAGTCCCTGATCTTG 59.823 60.000 0.00 0.00 0.00 3.02
127 128 1.186200 CCGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
128 129 1.759445 CCGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
129 130 2.223923 CCGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
130 131 2.542618 CGTGAGTCCCTGATCTTGATCG 60.543 54.545 6.19 2.03 0.00 3.69
131 132 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
132 133 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
133 134 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
134 135 3.632333 AGTCCCTGATCTTGATCGTACA 58.368 45.455 6.19 0.00 0.00 2.90
136 137 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
137 138 2.099263 CCCTGATCTTGATCGTACACGT 59.901 50.000 1.19 0.00 40.80 4.49
138 139 3.428999 CCCTGATCTTGATCGTACACGTT 60.429 47.826 1.19 0.00 40.80 3.99
139 140 4.174009 CCTGATCTTGATCGTACACGTTT 58.826 43.478 1.19 0.00 40.80 3.60
141 142 3.366724 TGATCTTGATCGTACACGTTTGC 59.633 43.478 1.19 0.00 40.80 3.68
142 143 1.717113 TCTTGATCGTACACGTTTGCG 59.283 47.619 5.81 5.81 44.93 4.85
156 157 4.577687 CGTTTGCGTGTATGATTAGTGT 57.422 40.909 0.00 0.00 0.00 3.55
159 160 5.478001 GTTTGCGTGTATGATTAGTGTACG 58.522 41.667 0.00 0.00 0.00 3.67
160 161 3.697982 TGCGTGTATGATTAGTGTACGG 58.302 45.455 0.00 0.00 0.00 4.02
162 163 3.727723 GCGTGTATGATTAGTGTACGGTC 59.272 47.826 0.00 0.00 0.00 4.79
163 164 4.731483 GCGTGTATGATTAGTGTACGGTCA 60.731 45.833 0.00 0.00 0.00 4.02
164 165 5.334319 CGTGTATGATTAGTGTACGGTCAA 58.666 41.667 0.00 0.00 0.00 3.18
165 166 5.801444 CGTGTATGATTAGTGTACGGTCAAA 59.199 40.000 0.00 0.00 0.00 2.69
166 167 6.237384 CGTGTATGATTAGTGTACGGTCAAAC 60.237 42.308 0.00 0.00 0.00 2.93
167 168 6.035327 GTGTATGATTAGTGTACGGTCAAACC 59.965 42.308 0.00 0.00 34.05 3.27
179 180 2.193517 CAAACCGGGGGTGTCACA 59.806 61.111 6.32 0.00 35.34 3.58
446 490 0.671251 GAGGTCGATCTGCCAGGTAG 59.329 60.000 0.91 0.00 0.00 3.18
452 496 1.001760 ATCTGCCAGGTAGGACGGT 59.998 57.895 4.47 0.00 41.22 4.83
621 669 4.743955 GCACCACTTCTTCCTCTGTTTAGT 60.744 45.833 0.00 0.00 0.00 2.24
859 907 2.203209 GCCCTCCAGCCAATACCG 60.203 66.667 0.00 0.00 0.00 4.02
876 924 2.851045 GCAAGGGAAGGGGTTGGA 59.149 61.111 0.00 0.00 0.00 3.53
878 926 1.304464 CAAGGGAAGGGGTTGGAGC 60.304 63.158 0.00 0.00 0.00 4.70
933 982 2.569404 GGAGGAAGGTTGACAGTGAGAT 59.431 50.000 0.00 0.00 0.00 2.75
938 987 5.046950 AGGAAGGTTGACAGTGAGATAAGAC 60.047 44.000 0.00 0.00 0.00 3.01
999 1053 1.694169 GGGGGATGCAGAGGAGGAA 60.694 63.158 0.00 0.00 0.00 3.36
1008 1062 2.909006 TGCAGAGGAGGAAAAGAGTGAT 59.091 45.455 0.00 0.00 0.00 3.06
1021 1075 6.183360 GGAAAAGAGTGATAGTCATGCTGTTC 60.183 42.308 0.00 0.00 31.50 3.18
1034 1088 5.352569 GTCATGCTGTTCTAACTACATGCTT 59.647 40.000 16.91 0.00 40.01 3.91
1085 1139 1.805943 TGACTCCATGAATTGTGTGCG 59.194 47.619 0.00 0.00 0.00 5.34
1109 1163 5.541868 GGATCAAGGAGAGTAATGAGATGGA 59.458 44.000 0.00 0.00 0.00 3.41
1140 1194 1.830408 CCCGGCCCTTGACAACAAA 60.830 57.895 0.00 0.00 35.49 2.83
1160 1214 2.115910 CAAGCAGCCCCTTCACCA 59.884 61.111 0.00 0.00 0.00 4.17
1170 1224 0.684153 CCCTTCACCAAATGCCCGAT 60.684 55.000 0.00 0.00 0.00 4.18
1244 1298 3.461773 CGACGAGGGCATGGAGGT 61.462 66.667 0.00 0.00 0.00 3.85
1295 1354 5.715921 TGACCACTATCATTAGGAGGATGA 58.284 41.667 0.00 0.00 37.86 2.92
1311 1370 2.039084 GGATGACCCAACTCACTTCTGT 59.961 50.000 0.00 0.00 34.14 3.41
1375 1434 1.211703 TGGACTTCACCAAGCACTTCA 59.788 47.619 0.00 0.00 36.96 3.02
1503 1562 2.387309 CGCAGCCGTTCATCAGATT 58.613 52.632 0.00 0.00 0.00 2.40
1570 1629 3.118992 CCTCAAGGTCATCATCTTCGACA 60.119 47.826 0.00 0.00 0.00 4.35
1655 1720 3.646715 CCGGGCCACCTCTTTCCA 61.647 66.667 4.39 0.00 33.28 3.53
1656 1721 2.045926 CGGGCCACCTCTTTCCAG 60.046 66.667 4.39 0.00 33.28 3.86
1657 1722 2.361737 GGGCCACCTCTTTCCAGC 60.362 66.667 4.39 0.00 0.00 4.85
1658 1723 2.747855 GGCCACCTCTTTCCAGCG 60.748 66.667 0.00 0.00 0.00 5.18
1659 1724 2.032681 GCCACCTCTTTCCAGCGT 59.967 61.111 0.00 0.00 0.00 5.07
1661 1726 1.019805 GCCACCTCTTTCCAGCGTAC 61.020 60.000 0.00 0.00 0.00 3.67
1665 1730 3.491104 CCACCTCTTTCCAGCGTACTATC 60.491 52.174 0.00 0.00 0.00 2.08
1666 1731 3.130516 CACCTCTTTCCAGCGTACTATCA 59.869 47.826 0.00 0.00 0.00 2.15
1667 1732 3.767673 ACCTCTTTCCAGCGTACTATCAA 59.232 43.478 0.00 0.00 0.00 2.57
1668 1733 4.142138 ACCTCTTTCCAGCGTACTATCAAG 60.142 45.833 0.00 0.00 0.00 3.02
1671 1736 4.705507 TCTTTCCAGCGTACTATCAAGTCT 59.294 41.667 0.00 0.00 37.15 3.24
1672 1737 4.371855 TTCCAGCGTACTATCAAGTCTG 57.628 45.455 0.00 0.00 37.15 3.51
1673 1738 2.099263 TCCAGCGTACTATCAAGTCTGC 59.901 50.000 0.00 0.00 37.15 4.26
1700 1804 7.891498 TGAAGTGTGGTACTGCTTATATCTA 57.109 36.000 0.00 0.00 40.26 1.98
1703 1807 9.250624 GAAGTGTGGTACTGCTTATATCTAAAG 57.749 37.037 0.00 0.00 40.26 1.85
1723 1838 5.350504 AAGTATGCTAGTTGATGCTCTGT 57.649 39.130 0.00 0.00 0.00 3.41
1724 1839 5.350504 AGTATGCTAGTTGATGCTCTGTT 57.649 39.130 0.00 0.00 0.00 3.16
1725 1840 5.738909 AGTATGCTAGTTGATGCTCTGTTT 58.261 37.500 0.00 0.00 0.00 2.83
1726 1841 6.878317 AGTATGCTAGTTGATGCTCTGTTTA 58.122 36.000 0.00 0.00 0.00 2.01
1727 1842 7.504403 AGTATGCTAGTTGATGCTCTGTTTAT 58.496 34.615 0.00 0.00 0.00 1.40
1728 1843 8.642432 AGTATGCTAGTTGATGCTCTGTTTATA 58.358 33.333 0.00 0.00 0.00 0.98
1729 1844 7.721286 ATGCTAGTTGATGCTCTGTTTATAC 57.279 36.000 0.00 0.00 0.00 1.47
1730 1845 6.878317 TGCTAGTTGATGCTCTGTTTATACT 58.122 36.000 0.00 0.00 0.00 2.12
1731 1846 6.980978 TGCTAGTTGATGCTCTGTTTATACTC 59.019 38.462 0.00 0.00 0.00 2.59
1732 1847 7.147828 TGCTAGTTGATGCTCTGTTTATACTCT 60.148 37.037 0.00 0.00 0.00 3.24
1733 1848 8.353684 GCTAGTTGATGCTCTGTTTATACTCTA 58.646 37.037 0.00 0.00 0.00 2.43
1877 1994 0.820871 GGCAACCAAACACCAGACAA 59.179 50.000 0.00 0.00 0.00 3.18
1910 2027 0.323999 ATGCAAGCAAGAGGCCATGA 60.324 50.000 5.01 0.00 46.50 3.07
1949 2066 2.646930 CAGATGGTGCATTTGAGGCTA 58.353 47.619 0.00 0.00 28.98 3.93
1950 2067 3.220110 CAGATGGTGCATTTGAGGCTAT 58.780 45.455 0.00 0.00 28.98 2.97
1978 2095 1.152830 GCCAGGTTGGGTGGAGAAA 59.847 57.895 0.00 0.00 38.19 2.52
2052 2169 1.536766 CCGGCATGCATATAGGTTGTG 59.463 52.381 21.36 0.00 0.00 3.33
2065 2182 7.628366 GCATATAGGTTGTGCTTGTGTTTGTAT 60.628 37.037 0.00 0.00 36.02 2.29
2078 2195 7.307989 GCTTGTGTTTGTATGAGAAAAGAGCTA 60.308 37.037 0.00 0.00 0.00 3.32
2081 2198 8.364894 TGTGTTTGTATGAGAAAAGAGCTAGTA 58.635 33.333 0.00 0.00 0.00 1.82
2082 2199 9.204570 GTGTTTGTATGAGAAAAGAGCTAGTAA 57.795 33.333 0.00 0.00 0.00 2.24
2156 2278 1.830587 ATGTCTGACGGCAAGCCTCA 61.831 55.000 9.73 10.55 0.00 3.86
2189 2311 9.528489 TCTGATAAAAGCCTACCAAAATTAACT 57.472 29.630 0.00 0.00 0.00 2.24
2198 2320 3.727726 ACCAAAATTAACTGTGCAAGGC 58.272 40.909 0.00 0.00 0.00 4.35
2210 2332 3.900446 GCAAGGCTTTGTTGCTCAT 57.100 47.368 10.54 0.00 45.67 2.90
2221 2343 6.749118 GGCTTTGTTGCTCATATTTTGACTAG 59.251 38.462 0.00 0.00 0.00 2.57
2224 2346 6.061022 TGTTGCTCATATTTTGACTAGGGA 57.939 37.500 0.00 0.00 0.00 4.20
2273 2395 0.829333 TGGCACAACAGTTTGGCAAT 59.171 45.000 16.85 0.00 44.57 3.56
2274 2396 1.209019 TGGCACAACAGTTTGGCAATT 59.791 42.857 16.85 0.00 44.57 2.32
2286 2408 5.262714 GTTTGGCAATTATTCAAACACGG 57.737 39.130 17.85 0.00 45.41 4.94
2303 2425 0.033228 CGGGCCAAATTCTTGTGCAA 59.967 50.000 4.39 0.00 33.10 4.08
2304 2426 1.511850 GGGCCAAATTCTTGTGCAAC 58.488 50.000 4.39 0.00 33.10 4.17
2355 2477 9.503399 TGGAGAAGAACTAAATAGGAAAAAGAC 57.497 33.333 0.00 0.00 0.00 3.01
2356 2478 8.657729 GGAGAAGAACTAAATAGGAAAAAGACG 58.342 37.037 0.00 0.00 0.00 4.18
2357 2479 8.030744 AGAAGAACTAAATAGGAAAAAGACGC 57.969 34.615 0.00 0.00 0.00 5.19
2358 2480 7.660208 AGAAGAACTAAATAGGAAAAAGACGCA 59.340 33.333 0.00 0.00 0.00 5.24
2359 2481 7.923414 AGAACTAAATAGGAAAAAGACGCAT 57.077 32.000 0.00 0.00 0.00 4.73
2360 2482 7.975750 AGAACTAAATAGGAAAAAGACGCATC 58.024 34.615 0.00 0.00 0.00 3.91
2361 2483 6.679327 ACTAAATAGGAAAAAGACGCATCC 57.321 37.500 0.00 0.00 0.00 3.51
2362 2484 6.177610 ACTAAATAGGAAAAAGACGCATCCA 58.822 36.000 0.00 0.00 34.30 3.41
2363 2485 5.975693 AAATAGGAAAAAGACGCATCCAA 57.024 34.783 0.00 0.00 34.30 3.53
2364 2486 5.975693 AATAGGAAAAAGACGCATCCAAA 57.024 34.783 0.00 0.00 34.30 3.28
2365 2487 3.643159 AGGAAAAAGACGCATCCAAAC 57.357 42.857 0.00 0.00 34.30 2.93
2366 2488 2.031157 AGGAAAAAGACGCATCCAAACG 60.031 45.455 0.00 0.00 34.30 3.60
2367 2489 1.713932 GAAAAAGACGCATCCAAACGC 59.286 47.619 0.00 0.00 0.00 4.84
2368 2490 0.039527 AAAAGACGCATCCAAACGCC 60.040 50.000 0.00 0.00 0.00 5.68
2369 2491 2.182614 AAAGACGCATCCAAACGCCG 62.183 55.000 0.00 0.00 0.00 6.46
2370 2492 3.115892 GACGCATCCAAACGCCGA 61.116 61.111 0.00 0.00 0.00 5.54
2371 2493 3.083600 GACGCATCCAAACGCCGAG 62.084 63.158 0.00 0.00 0.00 4.63
2372 2494 4.520846 CGCATCCAAACGCCGAGC 62.521 66.667 0.00 0.00 0.00 5.03
2373 2495 4.179579 GCATCCAAACGCCGAGCC 62.180 66.667 0.00 0.00 0.00 4.70
2374 2496 2.745884 CATCCAAACGCCGAGCCA 60.746 61.111 0.00 0.00 0.00 4.75
2375 2497 2.114670 CATCCAAACGCCGAGCCAT 61.115 57.895 0.00 0.00 0.00 4.40
2376 2498 1.819632 ATCCAAACGCCGAGCCATC 60.820 57.895 0.00 0.00 0.00 3.51
2386 2508 4.357699 GAGCCATCGATGCTGGAG 57.642 61.111 20.25 7.05 39.69 3.86
2387 2509 1.744639 GAGCCATCGATGCTGGAGA 59.255 57.895 20.25 0.00 39.69 3.71
2388 2510 0.105593 GAGCCATCGATGCTGGAGAA 59.894 55.000 20.25 0.00 39.69 2.87
2412 2534 1.167851 CATCCAAACACCGTGATGCT 58.832 50.000 5.28 0.00 0.00 3.79
2419 2541 0.669318 ACACCGTGATGCTACAACCG 60.669 55.000 5.28 0.00 0.00 4.44
2429 2551 1.736645 CTACAACCGGCACCTGTCG 60.737 63.158 0.00 0.00 43.72 4.35
2475 2598 3.883997 GCAACCGGCAATCAAAAGA 57.116 47.368 0.00 0.00 43.97 2.52
2476 2599 2.368655 GCAACCGGCAATCAAAAGAT 57.631 45.000 0.00 0.00 43.97 2.40
2477 2600 1.994779 GCAACCGGCAATCAAAAGATG 59.005 47.619 0.00 0.00 43.97 2.90
2478 2601 1.994779 CAACCGGCAATCAAAAGATGC 59.005 47.619 0.00 0.00 39.33 3.91
2479 2602 1.549203 ACCGGCAATCAAAAGATGCT 58.451 45.000 0.00 0.00 39.94 3.79
2480 2603 1.203052 ACCGGCAATCAAAAGATGCTG 59.797 47.619 0.00 0.00 44.23 4.41
2481 2604 1.917273 CGGCAATCAAAAGATGCTGG 58.083 50.000 0.00 0.00 41.62 4.85
2482 2605 1.470285 CGGCAATCAAAAGATGCTGGG 60.470 52.381 0.00 0.00 41.62 4.45
2483 2606 1.826720 GGCAATCAAAAGATGCTGGGA 59.173 47.619 0.00 0.00 39.94 4.37
2484 2607 2.417787 GGCAATCAAAAGATGCTGGGAC 60.418 50.000 0.00 0.00 39.94 4.46
2485 2608 2.733227 GCAATCAAAAGATGCTGGGACG 60.733 50.000 0.00 0.00 37.12 4.79
2486 2609 2.749076 CAATCAAAAGATGCTGGGACGA 59.251 45.455 0.00 0.00 0.00 4.20
2487 2610 1.808411 TCAAAAGATGCTGGGACGAC 58.192 50.000 0.00 0.00 0.00 4.34
2488 2611 0.443869 CAAAAGATGCTGGGACGACG 59.556 55.000 0.00 0.00 0.00 5.12
2489 2612 0.673644 AAAAGATGCTGGGACGACGG 60.674 55.000 0.00 0.00 0.00 4.79
2490 2613 3.665675 AAGATGCTGGGACGACGGC 62.666 63.158 0.00 0.00 43.06 5.68
2495 2618 4.308458 CTGGGACGACGGCCACAA 62.308 66.667 23.92 5.36 0.00 3.33
2496 2619 4.308458 TGGGACGACGGCCACAAG 62.308 66.667 23.92 0.00 0.00 3.16
2498 2621 4.681978 GGACGACGGCCACAAGCT 62.682 66.667 16.92 0.00 43.05 3.74
2505 2628 3.608662 GGCCACAAGCTGCTGCAA 61.609 61.111 18.42 0.00 43.05 4.08
2506 2629 2.654877 GCCACAAGCTGCTGCAAT 59.345 55.556 18.42 3.15 42.74 3.56
2507 2630 1.445582 GCCACAAGCTGCTGCAATC 60.446 57.895 18.42 0.00 42.74 2.67
2508 2631 1.154093 CCACAAGCTGCTGCAATCG 60.154 57.895 18.42 5.30 42.74 3.34
2509 2632 1.154093 CACAAGCTGCTGCAATCGG 60.154 57.895 18.42 4.62 42.74 4.18
2510 2633 2.202570 CAAGCTGCTGCAATCGGC 60.203 61.111 18.42 10.54 44.80 5.54
2524 2647 3.513662 CAATCGGCAATCAAAAGATGCA 58.486 40.909 0.00 0.00 41.80 3.96
2538 2661 2.238521 AGATGCAACCGTGGTTTCAAT 58.761 42.857 8.14 0.00 35.21 2.57
2541 2664 1.751351 TGCAACCGTGGTTTCAATGAA 59.249 42.857 0.44 0.00 36.00 2.57
2542 2665 2.124122 GCAACCGTGGTTTCAATGAAC 58.876 47.619 0.44 0.00 36.00 3.18
2556 2679 2.684374 CAATGAACTGGAATCGGCATCA 59.316 45.455 0.00 0.00 0.00 3.07
2576 2699 1.302033 CCACCAGAAAGCTGCGACT 60.302 57.895 0.00 0.00 40.91 4.18
2636 2759 4.899239 GAGCGATGAGGCGTGGGG 62.899 72.222 0.00 0.00 38.18 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.617540 ACAAGAGCTCGATCATAGACG 57.382 47.619 8.37 0.00 0.00 4.18
6 7 5.792962 CGAATACAAGAGCTCGATCATAGAC 59.207 44.000 8.37 0.00 33.13 2.59
7 8 5.701290 TCGAATACAAGAGCTCGATCATAGA 59.299 40.000 8.37 0.82 35.52 1.98
8 9 5.932661 TCGAATACAAGAGCTCGATCATAG 58.067 41.667 8.37 0.00 35.52 2.23
9 10 5.932661 CTCGAATACAAGAGCTCGATCATA 58.067 41.667 8.37 0.00 39.39 2.15
10 11 4.793071 CTCGAATACAAGAGCTCGATCAT 58.207 43.478 8.37 0.00 39.39 2.45
42 43 2.821969 GCATCATATTACAAGCCAGGGG 59.178 50.000 0.00 0.00 0.00 4.79
43 44 3.759581 AGCATCATATTACAAGCCAGGG 58.240 45.455 0.00 0.00 0.00 4.45
44 45 4.581824 ACAAGCATCATATTACAAGCCAGG 59.418 41.667 0.00 0.00 0.00 4.45
45 46 5.762825 ACAAGCATCATATTACAAGCCAG 57.237 39.130 0.00 0.00 0.00 4.85
48 49 8.092521 AGTCATACAAGCATCATATTACAAGC 57.907 34.615 0.00 0.00 0.00 4.01
84 85 7.442364 CGGGAAGATATCACAACACAAATCTAT 59.558 37.037 5.32 0.00 0.00 1.98
85 86 6.761242 CGGGAAGATATCACAACACAAATCTA 59.239 38.462 5.32 0.00 0.00 1.98
86 87 5.586243 CGGGAAGATATCACAACACAAATCT 59.414 40.000 5.32 0.00 0.00 2.40
89 90 4.454161 CACGGGAAGATATCACAACACAAA 59.546 41.667 5.32 0.00 0.00 2.83
90 91 4.000325 CACGGGAAGATATCACAACACAA 59.000 43.478 5.32 0.00 0.00 3.33
95 96 3.132289 GGACTCACGGGAAGATATCACAA 59.868 47.826 5.32 0.00 0.00 3.33
98 99 2.091278 AGGGACTCACGGGAAGATATCA 60.091 50.000 5.32 0.00 0.00 2.15
99 100 2.297597 CAGGGACTCACGGGAAGATATC 59.702 54.545 0.00 0.00 34.60 1.63
101 102 1.286849 TCAGGGACTCACGGGAAGATA 59.713 52.381 0.00 0.00 34.60 1.98
102 103 0.041238 TCAGGGACTCACGGGAAGAT 59.959 55.000 0.00 0.00 34.60 2.40
103 104 0.041238 ATCAGGGACTCACGGGAAGA 59.959 55.000 0.00 0.00 34.60 2.87
104 105 0.461961 GATCAGGGACTCACGGGAAG 59.538 60.000 0.00 0.00 34.60 3.46
105 106 0.041238 AGATCAGGGACTCACGGGAA 59.959 55.000 0.00 0.00 34.60 3.97
106 107 0.041238 AAGATCAGGGACTCACGGGA 59.959 55.000 0.00 0.00 34.60 5.14
109 110 2.542618 CGATCAAGATCAGGGACTCACG 60.543 54.545 10.39 0.00 34.60 4.35
110 111 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
111 112 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
112 113 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
115 116 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
117 118 3.422417 ACGTGTACGATCAAGATCAGG 57.578 47.619 11.79 0.51 43.02 3.86
118 119 4.490959 GCAAACGTGTACGATCAAGATCAG 60.491 45.833 11.79 5.82 43.02 2.90
119 120 3.366724 GCAAACGTGTACGATCAAGATCA 59.633 43.478 11.79 0.00 43.02 2.92
122 123 1.717113 CGCAAACGTGTACGATCAAGA 59.283 47.619 11.79 0.00 43.02 3.02
123 124 2.125168 CGCAAACGTGTACGATCAAG 57.875 50.000 11.79 0.00 43.02 3.02
136 137 5.478001 CGTACACTAATCATACACGCAAAC 58.522 41.667 0.00 0.00 0.00 2.93
137 138 4.563580 CCGTACACTAATCATACACGCAAA 59.436 41.667 0.00 0.00 0.00 3.68
138 139 4.106909 CCGTACACTAATCATACACGCAA 58.893 43.478 0.00 0.00 0.00 4.85
139 140 3.129113 ACCGTACACTAATCATACACGCA 59.871 43.478 0.00 0.00 0.00 5.24
141 142 4.912214 TGACCGTACACTAATCATACACG 58.088 43.478 0.00 0.00 0.00 4.49
142 143 6.035327 GGTTTGACCGTACACTAATCATACAC 59.965 42.308 0.00 0.00 0.00 2.90
143 144 6.101332 GGTTTGACCGTACACTAATCATACA 58.899 40.000 0.00 0.00 0.00 2.29
144 145 6.579491 GGTTTGACCGTACACTAATCATAC 57.421 41.667 0.00 0.00 0.00 2.39
159 160 2.281970 GACACCCCCGGTTTGACC 60.282 66.667 0.00 0.00 31.02 4.02
160 161 1.895231 GTGACACCCCCGGTTTGAC 60.895 63.158 0.00 0.00 31.02 3.18
162 163 1.896660 CTGTGACACCCCCGGTTTG 60.897 63.158 0.00 0.00 31.02 2.93
163 164 2.513895 CTGTGACACCCCCGGTTT 59.486 61.111 0.00 0.00 31.02 3.27
164 165 3.566210 CCTGTGACACCCCCGGTT 61.566 66.667 0.00 0.00 31.02 4.44
165 166 3.940806 TATTCCTGTGACACCCCCGGT 62.941 57.143 0.00 0.00 35.62 5.28
166 167 1.268992 TATTCCTGTGACACCCCCGG 61.269 60.000 2.45 0.00 0.00 5.73
167 168 0.178068 CTATTCCTGTGACACCCCCG 59.822 60.000 2.45 0.00 0.00 5.73
170 171 2.188817 ACCTCTATTCCTGTGACACCC 58.811 52.381 2.45 0.00 0.00 4.61
171 172 4.279145 TCTACCTCTATTCCTGTGACACC 58.721 47.826 2.45 0.00 0.00 4.16
172 173 7.584122 TTATCTACCTCTATTCCTGTGACAC 57.416 40.000 0.00 0.00 0.00 3.67
173 174 6.265649 GCTTATCTACCTCTATTCCTGTGACA 59.734 42.308 0.00 0.00 0.00 3.58
174 175 6.265649 TGCTTATCTACCTCTATTCCTGTGAC 59.734 42.308 0.00 0.00 0.00 3.67
175 176 6.373759 TGCTTATCTACCTCTATTCCTGTGA 58.626 40.000 0.00 0.00 0.00 3.58
179 180 7.129425 CCCTATGCTTATCTACCTCTATTCCT 58.871 42.308 0.00 0.00 0.00 3.36
546 593 1.504900 CGTGCCGCAGTGTACTAGA 59.495 57.895 0.00 0.00 0.00 2.43
621 669 1.215382 CAGGCCGTCTTCGATGACA 59.785 57.895 25.61 0.00 39.71 3.58
692 740 1.824230 AGAGCTGAAGACGCTGATTCT 59.176 47.619 0.00 0.00 37.96 2.40
859 907 1.304464 CTCCAACCCCTTCCCTTGC 60.304 63.158 0.00 0.00 0.00 4.01
933 982 1.152701 ACTTACCCACCCCCTGTCTTA 59.847 52.381 0.00 0.00 0.00 2.10
938 987 0.909623 CACTACTTACCCACCCCCTG 59.090 60.000 0.00 0.00 0.00 4.45
999 1053 6.047511 AGAACAGCATGACTATCACTCTTT 57.952 37.500 0.00 0.00 39.69 2.52
1008 1062 6.042777 GCATGTAGTTAGAACAGCATGACTA 58.957 40.000 22.22 0.00 41.46 2.59
1021 1075 7.761409 TGGCTAATTGAAAAGCATGTAGTTAG 58.239 34.615 5.45 0.00 40.61 2.34
1034 1088 5.769662 ACACAGAGTTCATGGCTAATTGAAA 59.230 36.000 0.00 0.00 33.90 2.69
1085 1139 5.541868 TCCATCTCATTACTCTCCTTGATCC 59.458 44.000 0.00 0.00 0.00 3.36
1109 1163 3.314331 CCGGGAGCACCTCTGTGT 61.314 66.667 0.00 0.00 44.65 3.72
1160 1214 1.176527 CACAACCTCATCGGGCATTT 58.823 50.000 0.00 0.00 36.97 2.32
1170 1224 2.904866 GGCGGCAACACAACCTCA 60.905 61.111 3.07 0.00 0.00 3.86
1295 1354 3.046374 ACCTTACAGAAGTGAGTTGGGT 58.954 45.455 0.00 0.00 29.85 4.51
1464 1523 2.616458 GGTGGCCCAACCCTGATCT 61.616 63.158 0.00 0.00 37.83 2.75
1503 1562 2.034179 CGTCACCATGTAGCCGATCTTA 59.966 50.000 0.00 0.00 0.00 2.10
1570 1629 0.620556 ACGACCTCAATGCCATCCTT 59.379 50.000 0.00 0.00 0.00 3.36
1652 1717 2.099263 GCAGACTTGATAGTACGCTGGA 59.901 50.000 0.00 0.00 33.84 3.86
1653 1718 2.099921 AGCAGACTTGATAGTACGCTGG 59.900 50.000 0.00 0.00 39.33 4.85
1655 1720 4.822350 TCATAGCAGACTTGATAGTACGCT 59.178 41.667 0.00 0.00 41.94 5.07
1656 1721 5.109662 TCATAGCAGACTTGATAGTACGC 57.890 43.478 0.00 0.00 33.84 4.42
1657 1722 6.634837 CACTTCATAGCAGACTTGATAGTACG 59.365 42.308 0.00 0.00 33.84 3.67
1658 1723 7.433719 CACACTTCATAGCAGACTTGATAGTAC 59.566 40.741 0.00 0.00 33.84 2.73
1659 1724 7.416777 CCACACTTCATAGCAGACTTGATAGTA 60.417 40.741 0.00 0.00 33.84 1.82
1661 1726 5.752472 CCACACTTCATAGCAGACTTGATAG 59.248 44.000 0.00 0.00 0.00 2.08
1665 1730 3.668447 ACCACACTTCATAGCAGACTTG 58.332 45.455 0.00 0.00 0.00 3.16
1666 1731 4.528596 AGTACCACACTTCATAGCAGACTT 59.471 41.667 0.00 0.00 31.59 3.01
1667 1732 4.081972 CAGTACCACACTTCATAGCAGACT 60.082 45.833 0.00 0.00 34.26 3.24
1668 1733 4.177026 CAGTACCACACTTCATAGCAGAC 58.823 47.826 0.00 0.00 34.26 3.51
1671 1736 2.567169 AGCAGTACCACACTTCATAGCA 59.433 45.455 0.00 0.00 34.26 3.49
1672 1737 3.252974 AGCAGTACCACACTTCATAGC 57.747 47.619 0.00 0.00 34.26 2.97
1673 1738 8.580720 AGATATAAGCAGTACCACACTTCATAG 58.419 37.037 0.00 0.00 34.26 2.23
1700 1804 5.738909 ACAGAGCATCAACTAGCATACTTT 58.261 37.500 0.00 0.00 37.82 2.66
1703 1807 7.721286 ATAAACAGAGCATCAACTAGCATAC 57.279 36.000 0.00 0.00 37.82 2.39
1725 1840 9.696917 CACACATCATAAGCACAATAGAGTATA 57.303 33.333 0.00 0.00 0.00 1.47
1726 1841 7.172190 GCACACATCATAAGCACAATAGAGTAT 59.828 37.037 0.00 0.00 0.00 2.12
1727 1842 6.479990 GCACACATCATAAGCACAATAGAGTA 59.520 38.462 0.00 0.00 0.00 2.59
1728 1843 5.295292 GCACACATCATAAGCACAATAGAGT 59.705 40.000 0.00 0.00 0.00 3.24
1729 1844 5.526479 AGCACACATCATAAGCACAATAGAG 59.474 40.000 0.00 0.00 0.00 2.43
1730 1845 5.295045 CAGCACACATCATAAGCACAATAGA 59.705 40.000 0.00 0.00 0.00 1.98
1731 1846 5.507974 CAGCACACATCATAAGCACAATAG 58.492 41.667 0.00 0.00 0.00 1.73
1732 1847 4.201940 GCAGCACACATCATAAGCACAATA 60.202 41.667 0.00 0.00 0.00 1.90
1733 1848 3.428452 GCAGCACACATCATAAGCACAAT 60.428 43.478 0.00 0.00 0.00 2.71
1828 1943 1.412343 GTGGACAAACCCAAAGCATGT 59.588 47.619 0.00 0.00 38.06 3.21
1877 1994 4.023137 GCATGGGCAGAACCACAT 57.977 55.556 0.00 0.00 44.72 3.21
1910 2027 1.209019 TGCATGTTGTTTGGTTGCCTT 59.791 42.857 0.00 0.00 32.39 4.35
1949 2066 3.233507 CCCAACCTGGCTATGCAAATAT 58.766 45.455 0.00 0.00 35.79 1.28
1950 2067 2.024464 ACCCAACCTGGCTATGCAAATA 60.024 45.455 0.00 0.00 35.79 1.40
1978 2095 2.221169 CAGTACCCGCATTGCATACAT 58.779 47.619 9.69 0.00 0.00 2.29
2019 2136 2.983791 GCCGGTACACTAAGGGCA 59.016 61.111 1.90 0.00 43.23 5.36
2052 2169 5.626955 GCTCTTTTCTCATACAAACACAAGC 59.373 40.000 0.00 0.00 0.00 4.01
2065 2182 6.328641 ACGACTTTACTAGCTCTTTTCTCA 57.671 37.500 0.00 0.00 0.00 3.27
2078 2195 3.119424 GGAAGCTCTGCTACGACTTTACT 60.119 47.826 0.00 0.00 38.25 2.24
2081 2198 1.618837 TGGAAGCTCTGCTACGACTTT 59.381 47.619 0.00 0.00 38.25 2.66
2082 2199 1.257743 TGGAAGCTCTGCTACGACTT 58.742 50.000 0.00 0.00 38.25 3.01
2156 2278 8.650143 TTGGTAGGCTTTTATCAGATTTTCTT 57.350 30.769 0.00 0.00 0.00 2.52
2189 2311 0.102844 GAGCAACAAAGCCTTGCACA 59.897 50.000 5.96 0.00 45.48 4.57
2198 2320 7.121168 TCCCTAGTCAAAATATGAGCAACAAAG 59.879 37.037 0.00 0.00 39.19 2.77
2210 2332 5.525484 TCTGGCTACTCCCTAGTCAAAATA 58.475 41.667 0.00 0.00 36.61 1.40
2221 2343 1.139256 GCCTACTTTCTGGCTACTCCC 59.861 57.143 0.00 0.00 45.26 4.30
2246 2368 1.484038 ACTGTTGTGCCATTGTGGTT 58.516 45.000 0.00 0.00 40.46 3.67
2247 2369 1.484038 AACTGTTGTGCCATTGTGGT 58.516 45.000 0.00 0.00 40.46 4.16
2262 2384 5.107530 CCGTGTTTGAATAATTGCCAAACTG 60.108 40.000 21.55 16.71 45.71 3.16
2266 2388 3.862642 GCCCGTGTTTGAATAATTGCCAA 60.863 43.478 0.00 0.00 0.00 4.52
2273 2395 4.282195 AGAATTTGGCCCGTGTTTGAATAA 59.718 37.500 0.00 0.00 0.00 1.40
2274 2396 3.829601 AGAATTTGGCCCGTGTTTGAATA 59.170 39.130 0.00 0.00 0.00 1.75
2286 2408 1.866601 GTGTTGCACAAGAATTTGGCC 59.133 47.619 0.00 0.00 38.66 5.36
2303 2425 1.259609 TCGTACCGATCTTTGGGTGT 58.740 50.000 0.66 0.00 35.33 4.16
2304 2426 2.596904 ATCGTACCGATCTTTGGGTG 57.403 50.000 0.66 0.00 43.45 4.61
2305 2427 4.161001 AGTTAATCGTACCGATCTTTGGGT 59.839 41.667 0.00 0.00 46.30 4.51
2312 2434 5.179045 TCTCCAAGTTAATCGTACCGATC 57.821 43.478 0.00 0.00 46.30 3.69
2326 2448 9.862149 TTTTTCCTATTTAGTTCTTCTCCAAGT 57.138 29.630 0.00 0.00 0.00 3.16
2353 2475 3.083600 CTCGGCGTTTGGATGCGTC 62.084 63.158 6.85 0.00 38.73 5.19
2354 2476 3.118454 CTCGGCGTTTGGATGCGT 61.118 61.111 6.85 0.00 38.73 5.24
2355 2477 4.520846 GCTCGGCGTTTGGATGCG 62.521 66.667 6.85 0.00 38.73 4.73
2356 2478 4.179579 GGCTCGGCGTTTGGATGC 62.180 66.667 6.85 1.40 37.06 3.91
2357 2479 2.051804 GATGGCTCGGCGTTTGGATG 62.052 60.000 6.85 0.00 0.00 3.51
2358 2480 1.819632 GATGGCTCGGCGTTTGGAT 60.820 57.895 6.85 0.00 0.00 3.41
2359 2481 2.435938 GATGGCTCGGCGTTTGGA 60.436 61.111 6.85 0.00 0.00 3.53
2360 2482 3.864686 CGATGGCTCGGCGTTTGG 61.865 66.667 6.85 0.00 41.27 3.28
2361 2483 2.173669 ATCGATGGCTCGGCGTTTG 61.174 57.895 6.85 0.00 45.10 2.93
2362 2484 2.173669 CATCGATGGCTCGGCGTTT 61.174 57.895 17.96 0.00 45.10 3.60
2363 2485 2.586079 CATCGATGGCTCGGCGTT 60.586 61.111 17.96 0.00 45.10 4.84
2365 2487 4.957684 AGCATCGATGGCTCGGCG 62.958 66.667 26.00 0.00 45.10 6.46
2366 2488 3.344215 CAGCATCGATGGCTCGGC 61.344 66.667 26.00 11.09 45.10 5.54
2367 2489 2.664185 CCAGCATCGATGGCTCGG 60.664 66.667 26.00 19.65 45.10 4.63
2368 2490 1.664017 CTCCAGCATCGATGGCTCG 60.664 63.158 26.00 15.69 46.41 5.03
2369 2491 0.105593 TTCTCCAGCATCGATGGCTC 59.894 55.000 26.00 10.25 39.19 4.70
2370 2492 0.106335 CTTCTCCAGCATCGATGGCT 59.894 55.000 26.00 19.51 39.19 4.75
2371 2493 0.105593 TCTTCTCCAGCATCGATGGC 59.894 55.000 26.00 17.68 39.19 4.40
2372 2494 1.863267 GTCTTCTCCAGCATCGATGG 58.137 55.000 26.00 12.35 40.92 3.51
2373 2495 1.485397 CGTCTTCTCCAGCATCGATG 58.515 55.000 21.27 21.27 0.00 3.84
2374 2496 0.249238 GCGTCTTCTCCAGCATCGAT 60.249 55.000 0.00 0.00 0.00 3.59
2375 2497 1.139734 GCGTCTTCTCCAGCATCGA 59.860 57.895 0.00 0.00 0.00 3.59
2376 2498 0.529337 ATGCGTCTTCTCCAGCATCG 60.529 55.000 0.00 0.00 45.97 3.84
2377 2499 3.376218 ATGCGTCTTCTCCAGCATC 57.624 52.632 0.00 0.00 45.97 3.91
2379 2501 1.219124 GGATGCGTCTTCTCCAGCA 59.781 57.895 5.77 0.00 44.13 4.41
2380 2502 0.391661 TTGGATGCGTCTTCTCCAGC 60.392 55.000 5.77 0.00 40.06 4.85
2381 2503 1.734465 GTTTGGATGCGTCTTCTCCAG 59.266 52.381 5.77 0.00 40.06 3.86
2382 2504 1.071542 TGTTTGGATGCGTCTTCTCCA 59.928 47.619 5.77 0.00 37.29 3.86
2383 2505 1.464997 GTGTTTGGATGCGTCTTCTCC 59.535 52.381 5.77 0.00 0.00 3.71
2384 2506 1.464997 GGTGTTTGGATGCGTCTTCTC 59.535 52.381 5.77 0.00 0.00 2.87
2385 2507 1.523758 GGTGTTTGGATGCGTCTTCT 58.476 50.000 5.77 0.00 0.00 2.85
2386 2508 0.165944 CGGTGTTTGGATGCGTCTTC 59.834 55.000 5.77 0.00 0.00 2.87
2387 2509 0.534203 ACGGTGTTTGGATGCGTCTT 60.534 50.000 5.77 0.00 0.00 3.01
2388 2510 1.070786 ACGGTGTTTGGATGCGTCT 59.929 52.632 5.77 0.00 0.00 4.18
2412 2534 1.537814 ATCGACAGGTGCCGGTTGTA 61.538 55.000 1.90 0.00 0.00 2.41
2419 2541 2.803155 TTCCAGCATCGACAGGTGCC 62.803 60.000 12.07 0.00 42.20 5.01
2470 2593 0.673644 CCGTCGTCCCAGCATCTTTT 60.674 55.000 0.00 0.00 0.00 2.27
2471 2594 1.079127 CCGTCGTCCCAGCATCTTT 60.079 57.895 0.00 0.00 0.00 2.52
2472 2595 2.579201 CCGTCGTCCCAGCATCTT 59.421 61.111 0.00 0.00 0.00 2.40
2473 2596 4.148825 GCCGTCGTCCCAGCATCT 62.149 66.667 0.00 0.00 0.00 2.90
2478 2601 4.308458 TTGTGGCCGTCGTCCCAG 62.308 66.667 0.00 0.00 0.00 4.45
2479 2602 4.308458 CTTGTGGCCGTCGTCCCA 62.308 66.667 0.00 0.00 0.00 4.37
2481 2604 4.681978 AGCTTGTGGCCGTCGTCC 62.682 66.667 0.00 0.00 43.05 4.79
2482 2605 3.414700 CAGCTTGTGGCCGTCGTC 61.415 66.667 0.00 0.00 43.05 4.20
2485 2608 3.730761 CAGCAGCTTGTGGCCGTC 61.731 66.667 0.00 0.00 43.05 4.79
2488 2611 2.830704 GATTGCAGCAGCTTGTGGCC 62.831 60.000 1.76 0.00 43.05 5.36
2489 2612 1.445582 GATTGCAGCAGCTTGTGGC 60.446 57.895 1.76 0.00 42.74 5.01
2490 2613 1.154093 CGATTGCAGCAGCTTGTGG 60.154 57.895 1.76 0.00 42.74 4.17
2491 2614 1.154093 CCGATTGCAGCAGCTTGTG 60.154 57.895 1.76 0.00 42.74 3.33
2492 2615 2.986306 GCCGATTGCAGCAGCTTGT 61.986 57.895 1.76 0.00 42.74 3.16
2493 2616 2.202570 GCCGATTGCAGCAGCTTG 60.203 61.111 1.76 0.00 42.74 4.01
2502 2625 2.283351 GCATCTTTTGATTGCCGATTGC 59.717 45.455 0.00 0.00 36.97 3.56
2503 2626 3.513662 TGCATCTTTTGATTGCCGATTG 58.486 40.909 0.00 0.00 36.97 2.67
2504 2627 3.872511 TGCATCTTTTGATTGCCGATT 57.127 38.095 0.00 0.00 36.97 3.34
2505 2628 3.514645 GTTGCATCTTTTGATTGCCGAT 58.485 40.909 0.00 0.00 36.97 4.18
2506 2629 2.352617 GGTTGCATCTTTTGATTGCCGA 60.353 45.455 0.00 0.00 36.97 5.54
2507 2630 1.994779 GGTTGCATCTTTTGATTGCCG 59.005 47.619 0.00 0.00 36.97 5.69
2508 2631 1.994779 CGGTTGCATCTTTTGATTGCC 59.005 47.619 0.00 0.00 36.97 4.52
2509 2632 2.409378 CACGGTTGCATCTTTTGATTGC 59.591 45.455 0.00 0.00 36.97 3.56
2510 2633 2.988493 CCACGGTTGCATCTTTTGATTG 59.012 45.455 0.00 0.00 36.97 2.67
2511 2634 2.627699 ACCACGGTTGCATCTTTTGATT 59.372 40.909 0.00 0.00 36.97 2.57
2512 2635 2.238521 ACCACGGTTGCATCTTTTGAT 58.761 42.857 0.00 0.00 40.34 2.57
2513 2636 1.686355 ACCACGGTTGCATCTTTTGA 58.314 45.000 0.00 0.00 0.00 2.69
2514 2637 2.507339 AACCACGGTTGCATCTTTTG 57.493 45.000 0.00 0.00 36.91 2.44
2524 2647 2.360801 CCAGTTCATTGAAACCACGGTT 59.639 45.455 0.00 0.00 40.45 4.44
2538 2661 2.013563 GCTGATGCCGATTCCAGTTCA 61.014 52.381 0.00 0.00 0.00 3.18
2541 2664 4.547859 GCTGATGCCGATTCCAGT 57.452 55.556 0.00 0.00 0.00 4.00
2556 2679 2.670934 CGCAGCTTTCTGGTGGCT 60.671 61.111 0.00 0.00 43.78 4.75
2563 2686 2.348998 CCCCAGTCGCAGCTTTCT 59.651 61.111 0.00 0.00 0.00 2.52
2576 2699 0.251742 CCCAGCAAATCTTCACCCCA 60.252 55.000 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.