Multiple sequence alignment - TraesCS7B01G194900

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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 TraesCS7B01G194900 chr7B 100.000 2357 0 0 1 2357 334797360 334799716 0.000000e+00 4353
1 TraesCS7B01G194900 chr7D 88.917 1570 98 37 588 2127 190128793 190130316 0.000000e+00 1866
2 TraesCS7B01G194900 chr7D 90.126 557 45 7 34 581 190128182 190128737 0.000000e+00 715
3 TraesCS7B01G194900 chr7A 83.127 1292 104 41 628 1851 199004239 199005484 0.000000e+00 1074
4 TraesCS7B01G194900 chr7A 87.687 268 21 7 294 549 199003927 199004194 3.810000e-78 302
5 TraesCS7B01G194900 chr7A 85.890 163 14 2 157 310 199003748 199003910 5.210000e-37 165
6 TraesCS7B01G194900 chr2D 94.915 177 9 0 2179 2355 503580778 503580954 6.420000e-71 278
7 TraesCS7B01G194900 chr2D 91.620 179 15 0 2179 2357 505824014 505823836 5.030000e-62 248
8 TraesCS7B01G194900 chr4D 94.350 177 9 1 2179 2355 459256096 459256271 1.070000e-68 270
9 TraesCS7B01G194900 chr4D 91.061 179 16 0 2179 2357 105125966 105125788 2.340000e-60 243
10 TraesCS7B01G194900 chr6B 93.333 180 11 1 2179 2357 481266686 481266507 4.990000e-67 265
11 TraesCS7B01G194900 chr6B 90.659 182 17 0 2176 2357 481264980 481265161 2.340000e-60 243
12 TraesCS7B01G194900 chr3D 93.750 176 11 0 2180 2355 260972733 260972558 4.990000e-67 265
13 TraesCS7B01G194900 chr1B 92.179 179 14 0 2179 2357 29917823 29917645 1.080000e-63 254
14 TraesCS7B01G194900 chr4A 90.710 183 17 0 2175 2357 650308819 650309001 6.510000e-61 244


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 TraesCS7B01G194900 chr7B 334797360 334799716 2356 False 4353.000000 4353 100.0000 1 2357 1 chr7B.!!$F1 2356
1 TraesCS7B01G194900 chr7D 190128182 190130316 2134 False 1290.500000 1866 89.5215 34 2127 2 chr7D.!!$F1 2093
2 TraesCS7B01G194900 chr7A 199003748 199005484 1736 False 513.666667 1074 85.5680 157 1851 3 chr7A.!!$F1 1694

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
142 143 0.036952 AACATCACCTCTGACGGCTG 60.037 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2315 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.0 0.0 0.0 0.0 3.72 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
19 20 3.039988 CAGCAGCAGCAGCAGTTT 58.960 55.556 12.92 0.00 45.49 2.66
20 21 1.081376 CAGCAGCAGCAGCAGTTTC 60.081 57.895 12.92 0.00 45.49 2.78
21 22 2.257676 GCAGCAGCAGCAGTTTCC 59.742 61.111 4.63 0.00 45.49 3.13
22 23 2.266627 GCAGCAGCAGCAGTTTCCT 61.267 57.895 4.63 0.00 45.49 3.36
23 24 1.579932 CAGCAGCAGCAGTTTCCTG 59.420 57.895 3.17 0.00 45.49 3.86
24 25 0.887836 CAGCAGCAGCAGTTTCCTGA 60.888 55.000 3.17 0.00 45.49 3.86
25 26 0.037877 AGCAGCAGCAGTTTCCTGAT 59.962 50.000 3.17 0.00 45.49 2.90
32 33 4.978083 CAGCAGTTTCCTGATGCTAAAT 57.022 40.909 0.00 0.00 46.92 1.40
33 34 5.320549 CAGCAGTTTCCTGATGCTAAATT 57.679 39.130 0.00 0.00 46.92 1.82
34 35 5.100259 CAGCAGTTTCCTGATGCTAAATTG 58.900 41.667 0.00 0.00 46.92 2.32
35 36 3.861689 GCAGTTTCCTGATGCTAAATTGC 59.138 43.478 0.00 0.00 41.50 3.56
36 37 4.381292 GCAGTTTCCTGATGCTAAATTGCT 60.381 41.667 0.00 0.00 40.55 3.91
37 38 5.163622 GCAGTTTCCTGATGCTAAATTGCTA 60.164 40.000 0.00 0.00 40.55 3.49
78 79 2.435422 GAGGAGCCGTAGTATCCTACC 58.565 57.143 0.00 0.00 43.57 3.18
83 84 1.355720 GCCGTAGTATCCTACCCCCTA 59.644 57.143 0.00 0.00 40.46 3.53
118 119 1.266718 GACAATTTGCGTGCTCAGGAA 59.733 47.619 0.00 0.00 0.00 3.36
134 135 5.310409 TCAGGAAAAAGAACATCACCTCT 57.690 39.130 0.00 0.00 0.00 3.69
140 141 0.247736 AGAACATCACCTCTGACGGC 59.752 55.000 0.00 0.00 0.00 5.68
142 143 0.036952 AACATCACCTCTGACGGCTG 60.037 55.000 0.00 0.00 0.00 4.85
143 144 0.900182 ACATCACCTCTGACGGCTGA 60.900 55.000 0.00 0.00 0.00 4.26
145 146 0.749649 ATCACCTCTGACGGCTGATC 59.250 55.000 0.00 0.00 0.00 2.92
153 154 0.465705 TGACGGCTGATCCTGGATTC 59.534 55.000 11.17 3.81 0.00 2.52
158 159 2.357009 CGGCTGATCCTGGATTCTTTTG 59.643 50.000 11.17 0.00 0.00 2.44
187 188 1.322338 GCAATTTGCAATGCTACGCTG 59.678 47.619 16.35 0.00 44.26 5.18
190 191 2.830772 TTTGCAATGCTACGCTGATC 57.169 45.000 6.82 0.00 0.00 2.92
193 194 0.230769 GCAATGCTACGCTGATCGAC 59.769 55.000 0.00 0.00 41.67 4.20
200 201 4.257376 CGCTGATCGACTTGCGCG 62.257 66.667 13.24 0.00 41.85 6.86
229 230 2.032030 CGGCTCACACAAAATCGAAAGT 60.032 45.455 0.00 0.00 0.00 2.66
273 274 2.460757 GTGAAAGGGCACGTAGGTTA 57.539 50.000 0.00 0.00 0.00 2.85
275 276 3.140623 GTGAAAGGGCACGTAGGTTAAA 58.859 45.455 0.00 0.00 0.00 1.52
279 280 5.412286 TGAAAGGGCACGTAGGTTAAATTAC 59.588 40.000 0.00 0.00 0.00 1.89
345 390 0.858583 TTAATGCCGCGTGATCATCG 59.141 50.000 4.92 6.01 0.00 3.84
398 444 0.802607 GAGCCGTAAACTGGAGCTCG 60.803 60.000 7.83 0.00 40.43 5.03
399 445 1.810030 GCCGTAAACTGGAGCTCGG 60.810 63.158 7.83 4.64 40.72 4.63
402 452 0.736325 CGTAAACTGGAGCTCGGGTG 60.736 60.000 7.83 0.03 0.00 4.61
420 471 3.050120 CGTACGTGAACGCAGACG 58.950 61.111 7.22 6.92 44.43 4.18
449 501 8.300286 TCAGGTGAAATGAATTATTGCGTTTTA 58.700 29.630 0.00 0.00 0.00 1.52
465 518 3.435671 CGTTTTATGTTCTCCCTGTCCAC 59.564 47.826 0.00 0.00 0.00 4.02
524 578 2.537560 GCCGCCATCTTCATCACCG 61.538 63.158 0.00 0.00 0.00 4.94
585 666 9.751542 AGTCAGACATTACATAATTAGTAGTGC 57.248 33.333 2.66 8.81 33.89 4.40
586 667 9.529325 GTCAGACATTACATAATTAGTAGTGCA 57.471 33.333 12.89 0.00 33.89 4.57
623 753 5.231568 GCGTAGAATATTGCATCGGGTATAC 59.768 44.000 0.00 0.00 0.00 1.47
683 813 7.013655 CGGAAACTCCATGGAAGAATATCAATT 59.986 37.037 17.00 0.00 35.91 2.32
684 814 8.699130 GGAAACTCCATGGAAGAATATCAATTT 58.301 33.333 17.00 4.35 36.28 1.82
689 819 9.790344 CTCCATGGAAGAATATCAATTTAGACT 57.210 33.333 17.00 0.00 0.00 3.24
692 822 9.790344 CATGGAAGAATATCAATTTAGACTCCT 57.210 33.333 0.00 0.00 0.00 3.69
698 828 8.381636 AGAATATCAATTTAGACTCCTGGGATG 58.618 37.037 0.00 0.00 0.00 3.51
703 833 1.866015 TAGACTCCTGGGATGTGGTG 58.134 55.000 0.00 0.00 0.00 4.17
719 849 0.460987 GGTGGTGAATCTGGAGCTCG 60.461 60.000 7.83 0.00 0.00 5.03
728 858 0.529833 TCTGGAGCTCGAGCAGAAAG 59.470 55.000 36.87 26.23 45.16 2.62
733 863 2.408050 GAGCTCGAGCAGAAAGTTTCA 58.592 47.619 36.87 0.00 45.16 2.69
734 864 2.802816 GAGCTCGAGCAGAAAGTTTCAA 59.197 45.455 36.87 0.00 45.16 2.69
744 874 5.981915 AGCAGAAAGTTTCAATTTCTCTTGC 59.018 36.000 17.65 13.81 43.42 4.01
760 892 2.680312 TTGCGAGAGGAAGGAAGATG 57.320 50.000 0.00 0.00 36.14 2.90
761 893 0.826715 TGCGAGAGGAAGGAAGATGG 59.173 55.000 0.00 0.00 0.00 3.51
762 894 1.115467 GCGAGAGGAAGGAAGATGGA 58.885 55.000 0.00 0.00 0.00 3.41
763 895 1.691434 GCGAGAGGAAGGAAGATGGAT 59.309 52.381 0.00 0.00 0.00 3.41
764 896 2.894126 GCGAGAGGAAGGAAGATGGATA 59.106 50.000 0.00 0.00 0.00 2.59
765 897 3.056891 GCGAGAGGAAGGAAGATGGATAG 60.057 52.174 0.00 0.00 0.00 2.08
796 928 2.924290 GGATTAGATCACGCCGATTAGC 59.076 50.000 0.00 0.00 33.17 3.09
841 981 3.020984 TCCAACCCACTTGTTTGACTTC 58.979 45.455 0.00 0.00 0.00 3.01
872 1012 3.706373 CACCACCCAGACCCGAGG 61.706 72.222 0.00 0.00 0.00 4.63
966 1106 1.942657 CACAAACCAGAGACCACACAG 59.057 52.381 0.00 0.00 0.00 3.66
968 1108 0.179018 AAACCAGAGACCACACAGGC 60.179 55.000 0.00 0.00 43.14 4.85
978 1118 1.529010 CACACAGGCAGCCAAGGAA 60.529 57.895 15.80 0.00 0.00 3.36
994 1162 3.060020 GAACGTGAGATCGGCCGGA 62.060 63.158 27.83 12.89 34.94 5.14
1215 1386 2.301583 GAGGAAGGAGATACTCATGGGC 59.698 54.545 0.00 0.00 31.08 5.36
1335 1506 1.448013 GGCGTCCTTTAAGCTCGCT 60.448 57.895 22.34 0.00 45.01 4.93
1404 1578 1.617947 CCTCCTCGTCCTTCCTTGGG 61.618 65.000 0.00 0.00 0.00 4.12
1405 1579 2.245438 CTCCTCGTCCTTCCTTGGGC 62.245 65.000 0.00 0.00 0.00 5.36
1406 1580 2.269241 CTCGTCCTTCCTTGGGCC 59.731 66.667 0.00 0.00 0.00 5.80
1407 1581 3.665675 CTCGTCCTTCCTTGGGCCG 62.666 68.421 0.00 0.00 0.00 6.13
1517 1691 4.612486 GCTTCTTCTTAGTGCTCTGTTTGC 60.612 45.833 0.00 0.00 0.00 3.68
1523 1697 5.126067 TCTTAGTGCTCTGTTTGCTTTTCT 58.874 37.500 0.00 0.00 0.00 2.52
1593 1773 3.556775 CCTGCAAAATTTGGTGTTGTCTG 59.443 43.478 7.89 0.00 0.00 3.51
1776 2021 0.036732 GCCAGGTCACATGAGTCCAA 59.963 55.000 0.00 0.00 0.00 3.53
1779 2024 1.800586 CAGGTCACATGAGTCCAAACG 59.199 52.381 0.00 0.00 0.00 3.60
1785 2030 3.009723 CACATGAGTCCAAACGCCTATT 58.990 45.455 0.00 0.00 0.00 1.73
1801 2046 3.805823 CCTATTTGTTCAACGAACCGTG 58.194 45.455 4.51 0.00 41.35 4.94
1863 2108 3.576118 TCTGCCTGTTATATGCCTCTCTC 59.424 47.826 0.00 0.00 0.00 3.20
1867 2112 5.104360 TGCCTGTTATATGCCTCTCTCTTTT 60.104 40.000 0.00 0.00 0.00 2.27
1868 2113 5.825151 GCCTGTTATATGCCTCTCTCTTTTT 59.175 40.000 0.00 0.00 0.00 1.94
1870 2115 6.238593 CCTGTTATATGCCTCTCTCTTTTTGC 60.239 42.308 0.00 0.00 0.00 3.68
1872 2117 1.457346 ATGCCTCTCTCTTTTTGCGG 58.543 50.000 0.00 0.00 0.00 5.69
1873 2118 0.606401 TGCCTCTCTCTTTTTGCGGG 60.606 55.000 0.00 0.00 0.00 6.13
1874 2119 0.321653 GCCTCTCTCTTTTTGCGGGA 60.322 55.000 0.00 0.00 0.00 5.14
1875 2120 1.680249 GCCTCTCTCTTTTTGCGGGAT 60.680 52.381 0.00 0.00 0.00 3.85
1876 2121 2.420129 GCCTCTCTCTTTTTGCGGGATA 60.420 50.000 0.00 0.00 0.00 2.59
1916 2161 7.758528 GTCTTACTCAAGTATCACGGTTACAAT 59.241 37.037 0.00 0.00 33.20 2.71
1930 2175 5.048991 ACGGTTACAATCATTTTGGTGTCTC 60.049 40.000 0.00 0.00 0.00 3.36
1931 2176 5.049060 CGGTTACAATCATTTTGGTGTCTCA 60.049 40.000 0.00 0.00 0.00 3.27
1980 2225 4.602340 ACGGTATGTAGCCATTAGAAGG 57.398 45.455 0.00 0.00 32.29 3.46
2000 2245 6.940867 AGAAGGGATTTTAAGAACCTGTGTAC 59.059 38.462 0.00 0.00 0.00 2.90
2005 2250 6.183360 GGATTTTAAGAACCTGTGTACATCGG 60.183 42.308 0.00 5.30 0.00 4.18
2040 2285 7.598493 TCATAAAACTTAGCCAAAAAGACATGC 59.402 33.333 0.00 0.00 0.00 4.06
2070 2315 6.017523 TCTGCAAAATACGACAAAAGATCACA 60.018 34.615 0.00 0.00 0.00 3.58
2078 2323 3.063316 CGACAAAAGATCACACACACACA 59.937 43.478 0.00 0.00 0.00 3.72
2080 2325 3.755905 ACAAAAGATCACACACACACACA 59.244 39.130 0.00 0.00 0.00 3.72
2081 2326 4.097714 CAAAAGATCACACACACACACAC 58.902 43.478 0.00 0.00 0.00 3.82
2082 2327 2.689553 AGATCACACACACACACACA 57.310 45.000 0.00 0.00 0.00 3.72
2083 2328 2.279741 AGATCACACACACACACACAC 58.720 47.619 0.00 0.00 0.00 3.82
2084 2329 2.006169 GATCACACACACACACACACA 58.994 47.619 0.00 0.00 0.00 3.72
2085 2330 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
2086 2331 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2087 2332 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2088 2333 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2089 2334 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2090 2335 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2164 2409 2.814805 CCATCCAGGTCAGAAATGGT 57.185 50.000 2.73 0.00 35.51 3.55
2165 2410 2.648059 CCATCCAGGTCAGAAATGGTC 58.352 52.381 2.73 0.00 35.51 4.02
2166 2411 2.025981 CCATCCAGGTCAGAAATGGTCA 60.026 50.000 2.73 0.00 35.51 4.02
2167 2412 3.372349 CCATCCAGGTCAGAAATGGTCAT 60.372 47.826 2.73 0.00 35.51 3.06
2168 2413 4.141413 CCATCCAGGTCAGAAATGGTCATA 60.141 45.833 2.73 0.00 35.51 2.15
2169 2414 5.457197 CCATCCAGGTCAGAAATGGTCATAT 60.457 44.000 2.73 0.00 35.51 1.78
2170 2415 5.715439 TCCAGGTCAGAAATGGTCATATT 57.285 39.130 2.73 0.00 35.51 1.28
2171 2416 6.823286 TCCAGGTCAGAAATGGTCATATTA 57.177 37.500 2.73 0.00 35.51 0.98
2172 2417 6.591935 TCCAGGTCAGAAATGGTCATATTAC 58.408 40.000 2.73 0.00 35.51 1.89
2173 2418 6.386927 TCCAGGTCAGAAATGGTCATATTACT 59.613 38.462 2.73 0.00 35.51 2.24
2174 2419 7.056635 CCAGGTCAGAAATGGTCATATTACTT 58.943 38.462 0.00 0.00 0.00 2.24
2175 2420 8.210946 CCAGGTCAGAAATGGTCATATTACTTA 58.789 37.037 0.00 0.00 0.00 2.24
2176 2421 9.613428 CAGGTCAGAAATGGTCATATTACTTAA 57.387 33.333 0.00 0.00 0.00 1.85
2177 2422 9.614792 AGGTCAGAAATGGTCATATTACTTAAC 57.385 33.333 0.00 0.00 0.00 2.01
2178 2423 8.548721 GGTCAGAAATGGTCATATTACTTAACG 58.451 37.037 0.00 0.00 0.00 3.18
2179 2424 9.309516 GTCAGAAATGGTCATATTACTTAACGA 57.690 33.333 0.00 0.00 0.00 3.85
2180 2425 9.529325 TCAGAAATGGTCATATTACTTAACGAG 57.471 33.333 0.00 0.00 0.00 4.18
2181 2426 9.314321 CAGAAATGGTCATATTACTTAACGAGT 57.686 33.333 0.00 0.00 42.55 4.18
2182 2427 9.886132 AGAAATGGTCATATTACTTAACGAGTT 57.114 29.630 0.00 0.00 39.86 3.01
2196 2441 8.976986 ACTTAACGAGTTAAATACACTACAGG 57.023 34.615 9.36 0.00 33.92 4.00
2197 2442 8.579863 ACTTAACGAGTTAAATACACTACAGGT 58.420 33.333 9.36 0.00 33.92 4.00
2198 2443 8.746922 TTAACGAGTTAAATACACTACAGGTG 57.253 34.615 6.01 0.00 40.33 4.00
2199 2444 7.329226 TTAACGAGTTAAATACACTACAGGTGC 59.671 37.037 6.01 0.00 39.32 5.01
2208 2453 2.699954 CACTACAGGTGCCCTAACTTG 58.300 52.381 0.00 0.00 39.22 3.16
2209 2454 2.038557 CACTACAGGTGCCCTAACTTGT 59.961 50.000 0.00 0.00 42.39 3.16
2210 2455 2.302157 ACTACAGGTGCCCTAACTTGTC 59.698 50.000 0.00 0.00 39.37 3.18
2211 2456 0.400594 ACAGGTGCCCTAACTTGTCC 59.599 55.000 0.00 0.00 35.67 4.02
2212 2457 0.673644 CAGGTGCCCTAACTTGTCCG 60.674 60.000 0.00 0.00 29.64 4.79
2213 2458 1.376812 GGTGCCCTAACTTGTCCGG 60.377 63.158 0.00 0.00 0.00 5.14
2214 2459 2.038837 GTGCCCTAACTTGTCCGGC 61.039 63.158 0.00 0.00 40.16 6.13
2215 2460 2.818274 GCCCTAACTTGTCCGGCG 60.818 66.667 0.00 0.00 0.00 6.46
2216 2461 2.818274 CCCTAACTTGTCCGGCGC 60.818 66.667 0.00 0.00 0.00 6.53
2217 2462 3.186047 CCTAACTTGTCCGGCGCG 61.186 66.667 0.00 0.00 0.00 6.86
2218 2463 2.126228 CTAACTTGTCCGGCGCGA 60.126 61.111 12.10 0.00 0.00 5.87
2219 2464 1.518572 CTAACTTGTCCGGCGCGAT 60.519 57.895 12.10 0.00 0.00 4.58
2220 2465 1.480219 CTAACTTGTCCGGCGCGATC 61.480 60.000 12.10 0.00 0.00 3.69
2221 2466 2.215465 TAACTTGTCCGGCGCGATCA 62.215 55.000 12.10 0.00 0.00 2.92
2222 2467 3.257561 CTTGTCCGGCGCGATCAG 61.258 66.667 12.10 0.00 0.00 2.90
2223 2468 3.989698 CTTGTCCGGCGCGATCAGT 62.990 63.158 12.10 0.00 0.00 3.41
2224 2469 3.583276 TTGTCCGGCGCGATCAGTT 62.583 57.895 12.10 0.00 0.00 3.16
2225 2470 2.813908 GTCCGGCGCGATCAGTTT 60.814 61.111 12.10 0.00 0.00 2.66
2226 2471 2.813474 TCCGGCGCGATCAGTTTG 60.813 61.111 12.10 0.00 0.00 2.93
2227 2472 3.864686 CCGGCGCGATCAGTTTGG 61.865 66.667 12.10 0.00 0.00 3.28
2228 2473 3.118454 CGGCGCGATCAGTTTGGT 61.118 61.111 12.10 0.00 0.00 3.67
2229 2474 2.480555 GGCGCGATCAGTTTGGTG 59.519 61.111 12.10 0.00 0.00 4.17
2230 2475 2.202349 GCGCGATCAGTTTGGTGC 60.202 61.111 12.10 0.00 0.00 5.01
2231 2476 2.480555 CGCGATCAGTTTGGTGCC 59.519 61.111 0.00 0.00 0.00 5.01
2232 2477 2.034879 CGCGATCAGTTTGGTGCCT 61.035 57.895 0.00 0.00 0.00 4.75
2233 2478 0.739462 CGCGATCAGTTTGGTGCCTA 60.739 55.000 0.00 0.00 0.00 3.93
2234 2479 1.448985 GCGATCAGTTTGGTGCCTAA 58.551 50.000 0.00 0.00 0.00 2.69
2235 2480 1.810151 GCGATCAGTTTGGTGCCTAAA 59.190 47.619 0.00 0.00 0.00 1.85
2236 2481 2.414161 GCGATCAGTTTGGTGCCTAAAC 60.414 50.000 6.19 6.19 38.09 2.01
2237 2482 3.074412 CGATCAGTTTGGTGCCTAAACT 58.926 45.455 9.73 9.73 46.23 2.66
2238 2483 3.502211 CGATCAGTTTGGTGCCTAAACTT 59.498 43.478 11.95 2.49 43.71 2.66
2239 2484 4.613622 CGATCAGTTTGGTGCCTAAACTTG 60.614 45.833 11.95 9.11 43.71 3.16
2240 2485 3.892284 TCAGTTTGGTGCCTAAACTTGA 58.108 40.909 11.95 10.61 43.71 3.02
2241 2486 4.274147 TCAGTTTGGTGCCTAAACTTGAA 58.726 39.130 11.95 2.27 43.71 2.69
2242 2487 4.707448 TCAGTTTGGTGCCTAAACTTGAAA 59.293 37.500 11.95 0.48 43.71 2.69
2243 2488 5.186021 TCAGTTTGGTGCCTAAACTTGAAAA 59.814 36.000 11.95 0.00 43.71 2.29
2244 2489 5.872070 CAGTTTGGTGCCTAAACTTGAAAAA 59.128 36.000 11.95 0.00 43.71 1.94
2245 2490 6.538381 CAGTTTGGTGCCTAAACTTGAAAAAT 59.462 34.615 11.95 0.00 43.71 1.82
2246 2491 7.708752 CAGTTTGGTGCCTAAACTTGAAAAATA 59.291 33.333 11.95 0.00 43.71 1.40
2247 2492 7.709182 AGTTTGGTGCCTAAACTTGAAAAATAC 59.291 33.333 9.73 0.00 43.71 1.89
2248 2493 6.716934 TGGTGCCTAAACTTGAAAAATACA 57.283 33.333 0.00 0.00 0.00 2.29
2249 2494 6.508777 TGGTGCCTAAACTTGAAAAATACAC 58.491 36.000 0.00 0.00 0.00 2.90
2250 2495 6.096987 TGGTGCCTAAACTTGAAAAATACACA 59.903 34.615 0.00 0.00 0.00 3.72
2251 2496 6.981559 GGTGCCTAAACTTGAAAAATACACAA 59.018 34.615 0.00 0.00 0.00 3.33
2252 2497 7.492994 GGTGCCTAAACTTGAAAAATACACAAA 59.507 33.333 0.00 0.00 0.00 2.83
2253 2498 8.874816 GTGCCTAAACTTGAAAAATACACAAAA 58.125 29.630 0.00 0.00 0.00 2.44
2254 2499 9.092876 TGCCTAAACTTGAAAAATACACAAAAG 57.907 29.630 0.00 0.00 0.00 2.27
2255 2500 9.093970 GCCTAAACTTGAAAAATACACAAAAGT 57.906 29.630 0.00 0.00 0.00 2.66
2258 2503 8.840833 AAACTTGAAAAATACACAAAAGTGGT 57.159 26.923 0.38 0.00 0.00 4.16
2259 2504 7.826260 ACTTGAAAAATACACAAAAGTGGTG 57.174 32.000 0.38 0.00 41.95 4.17
2260 2505 6.816140 ACTTGAAAAATACACAAAAGTGGTGG 59.184 34.615 0.38 0.00 40.54 4.61
2261 2506 6.531503 TGAAAAATACACAAAAGTGGTGGA 57.468 33.333 0.38 0.00 40.54 4.02
2262 2507 6.568869 TGAAAAATACACAAAAGTGGTGGAG 58.431 36.000 0.38 0.00 40.54 3.86
2263 2508 6.153680 TGAAAAATACACAAAAGTGGTGGAGT 59.846 34.615 0.38 0.00 40.54 3.85
2264 2509 7.339721 TGAAAAATACACAAAAGTGGTGGAGTA 59.660 33.333 0.38 0.00 40.54 2.59
2265 2510 7.648039 AAAATACACAAAAGTGGTGGAGTAA 57.352 32.000 0.38 0.00 40.54 2.24
2266 2511 6.628919 AATACACAAAAGTGGTGGAGTAAC 57.371 37.500 0.38 0.00 40.54 2.50
2267 2512 4.230745 ACACAAAAGTGGTGGAGTAACT 57.769 40.909 0.38 0.00 40.54 2.24
2268 2513 4.595986 ACACAAAAGTGGTGGAGTAACTT 58.404 39.130 0.38 0.00 40.54 2.66
2269 2514 4.398044 ACACAAAAGTGGTGGAGTAACTTG 59.602 41.667 0.38 0.00 40.54 3.16
2270 2515 4.398044 CACAAAAGTGGTGGAGTAACTTGT 59.602 41.667 0.00 0.00 34.46 3.16
2271 2516 4.638865 ACAAAAGTGGTGGAGTAACTTGTC 59.361 41.667 0.00 0.00 34.46 3.18
2272 2517 4.772886 AAAGTGGTGGAGTAACTTGTCT 57.227 40.909 0.00 0.00 34.46 3.41
2273 2518 5.881923 AAAGTGGTGGAGTAACTTGTCTA 57.118 39.130 0.00 0.00 34.46 2.59
2274 2519 5.470047 AAGTGGTGGAGTAACTTGTCTAG 57.530 43.478 0.00 0.00 33.01 2.43
2275 2520 3.833070 AGTGGTGGAGTAACTTGTCTAGG 59.167 47.826 0.00 0.00 0.00 3.02
2276 2521 2.565834 TGGTGGAGTAACTTGTCTAGGC 59.434 50.000 0.00 0.00 0.00 3.93
2277 2522 2.565834 GGTGGAGTAACTTGTCTAGGCA 59.434 50.000 0.00 0.00 0.00 4.75
2278 2523 3.197983 GGTGGAGTAACTTGTCTAGGCAT 59.802 47.826 0.00 0.00 0.00 4.40
2279 2524 4.323562 GGTGGAGTAACTTGTCTAGGCATT 60.324 45.833 0.00 0.00 0.00 3.56
2280 2525 4.870991 GTGGAGTAACTTGTCTAGGCATTC 59.129 45.833 0.00 0.00 0.00 2.67
2281 2526 4.530553 TGGAGTAACTTGTCTAGGCATTCA 59.469 41.667 0.00 0.00 0.00 2.57
2282 2527 5.012664 TGGAGTAACTTGTCTAGGCATTCAA 59.987 40.000 0.00 0.00 0.00 2.69
2283 2528 5.938125 GGAGTAACTTGTCTAGGCATTCAAA 59.062 40.000 0.00 0.00 0.00 2.69
2284 2529 6.599638 GGAGTAACTTGTCTAGGCATTCAAAT 59.400 38.462 0.00 0.00 0.00 2.32
2285 2530 7.769044 GGAGTAACTTGTCTAGGCATTCAAATA 59.231 37.037 0.00 0.00 0.00 1.40
2286 2531 8.494016 AGTAACTTGTCTAGGCATTCAAATAC 57.506 34.615 0.00 0.00 0.00 1.89
2287 2532 6.422776 AACTTGTCTAGGCATTCAAATACG 57.577 37.500 0.00 0.00 0.00 3.06
2288 2533 4.876107 ACTTGTCTAGGCATTCAAATACGG 59.124 41.667 0.00 0.00 0.00 4.02
2289 2534 4.481368 TGTCTAGGCATTCAAATACGGT 57.519 40.909 0.00 0.00 0.00 4.83
2290 2535 4.188462 TGTCTAGGCATTCAAATACGGTG 58.812 43.478 0.00 0.00 0.00 4.94
2291 2536 3.002348 GTCTAGGCATTCAAATACGGTGC 59.998 47.826 0.00 0.00 35.17 5.01
2294 2539 2.475200 GCATTCAAATACGGTGCCTC 57.525 50.000 0.00 0.00 0.00 4.70
2295 2540 2.017049 GCATTCAAATACGGTGCCTCT 58.983 47.619 0.00 0.00 0.00 3.69
2296 2541 3.202906 GCATTCAAATACGGTGCCTCTA 58.797 45.455 0.00 0.00 0.00 2.43
2297 2542 3.248602 GCATTCAAATACGGTGCCTCTAG 59.751 47.826 0.00 0.00 0.00 2.43
2298 2543 4.693283 CATTCAAATACGGTGCCTCTAGA 58.307 43.478 0.00 0.00 0.00 2.43
2299 2544 4.386867 TTCAAATACGGTGCCTCTAGAG 57.613 45.455 13.18 13.18 0.00 2.43
2309 2554 1.968310 CCTCTAGAGGTATGCCGCC 59.032 63.158 28.12 0.00 43.61 6.13
2310 2555 1.581954 CTCTAGAGGTATGCCGCCG 59.418 63.158 12.27 0.00 40.50 6.46
2311 2556 1.152819 TCTAGAGGTATGCCGCCGT 60.153 57.895 0.00 0.00 40.50 5.68
2312 2557 0.109153 TCTAGAGGTATGCCGCCGTA 59.891 55.000 0.00 0.00 40.50 4.02
2313 2558 1.174783 CTAGAGGTATGCCGCCGTAT 58.825 55.000 0.00 0.00 40.50 3.06
2314 2559 1.132643 CTAGAGGTATGCCGCCGTATC 59.867 57.143 0.00 0.00 40.50 2.24
2315 2560 0.826256 AGAGGTATGCCGCCGTATCA 60.826 55.000 0.00 0.00 40.50 2.15
2316 2561 0.032952 GAGGTATGCCGCCGTATCAA 59.967 55.000 0.00 0.00 40.50 2.57
2317 2562 0.033504 AGGTATGCCGCCGTATCAAG 59.966 55.000 0.00 0.00 40.50 3.02
2318 2563 0.249741 GGTATGCCGCCGTATCAAGT 60.250 55.000 0.00 0.00 0.00 3.16
2319 2564 0.859232 GTATGCCGCCGTATCAAGTG 59.141 55.000 0.00 0.00 0.00 3.16
2320 2565 0.878523 TATGCCGCCGTATCAAGTGC 60.879 55.000 0.00 0.00 0.00 4.40
2321 2566 3.573491 GCCGCCGTATCAAGTGCC 61.573 66.667 0.00 0.00 0.00 5.01
2322 2567 2.895372 CCGCCGTATCAAGTGCCC 60.895 66.667 0.00 0.00 0.00 5.36
2323 2568 3.261951 CGCCGTATCAAGTGCCCG 61.262 66.667 0.00 0.00 0.00 6.13
2324 2569 2.125269 GCCGTATCAAGTGCCCGT 60.125 61.111 0.00 0.00 0.00 5.28
2325 2570 2.461110 GCCGTATCAAGTGCCCGTG 61.461 63.158 0.00 0.00 0.00 4.94
2326 2571 1.813753 CCGTATCAAGTGCCCGTGG 60.814 63.158 0.00 0.00 0.00 4.94
2327 2572 1.813753 CGTATCAAGTGCCCGTGGG 60.814 63.158 0.00 0.00 38.57 4.61
2340 2585 3.434319 GTGGGGCATGTCAGCGTG 61.434 66.667 0.00 0.00 34.64 5.34
2341 2586 3.952508 TGGGGCATGTCAGCGTGT 61.953 61.111 0.00 0.00 34.24 4.49
2342 2587 3.127533 GGGGCATGTCAGCGTGTC 61.128 66.667 0.00 0.00 35.60 3.67
2343 2588 3.490759 GGGCATGTCAGCGTGTCG 61.491 66.667 0.00 0.00 37.12 4.35
2354 2599 3.049674 CGTGTCGCTTGGCCACAT 61.050 61.111 3.88 0.00 0.00 3.21
2355 2600 2.562912 GTGTCGCTTGGCCACATG 59.437 61.111 3.88 0.00 0.00 3.21
2356 2601 2.112928 TGTCGCTTGGCCACATGT 59.887 55.556 3.88 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.266627 GGAAACTGCTGCTGCTGCT 61.267 57.895 27.67 11.28 41.07 4.24
5 6 4.076244 AGGAAACTGCTGCTGCTG 57.924 55.556 18.66 18.66 41.13 4.41
15 16 7.651027 ATTAGCAATTTAGCATCAGGAAACT 57.349 32.000 0.00 0.00 38.08 2.66
16 17 9.403110 CATATTAGCAATTTAGCATCAGGAAAC 57.597 33.333 0.00 0.00 36.85 2.78
17 18 9.353431 TCATATTAGCAATTTAGCATCAGGAAA 57.647 29.630 0.00 0.00 36.85 3.13
18 19 8.922931 TCATATTAGCAATTTAGCATCAGGAA 57.077 30.769 0.00 0.00 36.85 3.36
19 20 9.170734 GATCATATTAGCAATTTAGCATCAGGA 57.829 33.333 0.00 0.00 36.85 3.86
20 21 8.953313 TGATCATATTAGCAATTTAGCATCAGG 58.047 33.333 0.00 0.00 36.85 3.86
33 34 9.889128 TCGGAAATTGATATGATCATATTAGCA 57.111 29.630 25.41 17.36 39.39 3.49
37 38 9.610705 CTCCTCGGAAATTGATATGATCATATT 57.389 33.333 25.41 12.78 39.39 1.28
96 97 1.400629 CCTGAGCACGCAAATTGTCTG 60.401 52.381 0.00 0.00 0.00 3.51
98 99 0.874390 TCCTGAGCACGCAAATTGTC 59.126 50.000 0.00 0.00 0.00 3.18
104 105 1.674359 TCTTTTTCCTGAGCACGCAA 58.326 45.000 0.00 0.00 0.00 4.85
107 108 3.250762 TGATGTTCTTTTTCCTGAGCACG 59.749 43.478 0.00 0.00 0.00 5.34
118 119 3.403038 CCGTCAGAGGTGATGTTCTTTT 58.597 45.455 0.00 0.00 37.94 2.27
134 135 0.465705 GAATCCAGGATCAGCCGTCA 59.534 55.000 1.11 0.00 43.43 4.35
140 141 3.129988 GCACCAAAAGAATCCAGGATCAG 59.870 47.826 1.11 0.00 0.00 2.90
142 143 2.428530 GGCACCAAAAGAATCCAGGATC 59.571 50.000 1.11 0.00 0.00 3.36
143 144 2.460669 GGCACCAAAAGAATCCAGGAT 58.539 47.619 0.00 0.00 0.00 3.24
145 146 0.527565 CGGCACCAAAAGAATCCAGG 59.472 55.000 0.00 0.00 0.00 4.45
187 188 1.389106 ACTAAAACGCGCAAGTCGATC 59.611 47.619 5.73 0.00 41.67 3.69
190 191 3.253827 GACTAAAACGCGCAAGTCG 57.746 52.632 5.73 0.00 41.43 4.18
193 194 1.509162 GCCGACTAAAACGCGCAAG 60.509 57.895 5.73 0.31 43.44 4.01
200 201 3.955771 TTTGTGTGAGCCGACTAAAAC 57.044 42.857 0.00 0.00 0.00 2.43
229 230 2.412870 CATATCGCTAAACGCCCATCA 58.587 47.619 0.00 0.00 43.23 3.07
254 255 2.460757 TAACCTACGTGCCCTTTCAC 57.539 50.000 0.00 0.00 0.00 3.18
267 268 6.172630 GTTGACCCCGAAGTAATTTAACCTA 58.827 40.000 0.00 0.00 0.00 3.08
273 274 3.418047 CTGGTTGACCCCGAAGTAATTT 58.582 45.455 0.00 0.00 34.29 1.82
275 276 1.280998 CCTGGTTGACCCCGAAGTAAT 59.719 52.381 0.00 0.00 34.29 1.89
279 280 0.321653 CTTCCTGGTTGACCCCGAAG 60.322 60.000 10.24 10.24 35.33 3.79
345 390 1.073768 GAGCGAGAAGGCGTCAAGAC 61.074 60.000 2.69 0.00 38.18 3.01
420 471 6.974622 ACGCAATAATTCATTTCACCTGATTC 59.025 34.615 0.00 0.00 0.00 2.52
449 501 1.561542 GGATGTGGACAGGGAGAACAT 59.438 52.381 0.00 0.00 34.28 2.71
465 518 1.517257 GCTCGTCCGTCAGTGGATG 60.517 63.158 0.00 0.00 44.87 3.51
581 662 6.338146 TCTACGCTTGAAATACTTATGCACT 58.662 36.000 0.00 0.00 0.00 4.40
582 663 6.583912 TCTACGCTTGAAATACTTATGCAC 57.416 37.500 0.00 0.00 0.00 4.57
583 664 7.786178 ATTCTACGCTTGAAATACTTATGCA 57.214 32.000 0.00 0.00 0.00 3.96
587 668 9.320352 TGCAATATTCTACGCTTGAAATACTTA 57.680 29.630 0.00 0.00 0.00 2.24
588 669 8.208718 TGCAATATTCTACGCTTGAAATACTT 57.791 30.769 0.00 0.00 0.00 2.24
589 670 7.786178 TGCAATATTCTACGCTTGAAATACT 57.214 32.000 0.00 0.00 0.00 2.12
591 672 7.360017 CCGATGCAATATTCTACGCTTGAAATA 60.360 37.037 0.00 0.00 0.00 1.40
592 673 6.365839 CGATGCAATATTCTACGCTTGAAAT 58.634 36.000 0.00 0.00 0.00 2.17
594 675 4.211164 CCGATGCAATATTCTACGCTTGAA 59.789 41.667 0.00 0.00 0.00 2.69
595 676 3.740832 CCGATGCAATATTCTACGCTTGA 59.259 43.478 0.00 0.00 0.00 3.02
596 677 3.120546 CCCGATGCAATATTCTACGCTTG 60.121 47.826 0.00 0.00 0.00 4.01
597 678 3.067106 CCCGATGCAATATTCTACGCTT 58.933 45.455 0.00 0.00 0.00 4.68
599 680 2.413837 ACCCGATGCAATATTCTACGC 58.586 47.619 0.00 0.00 0.00 4.42
683 813 2.187958 CACCACATCCCAGGAGTCTAA 58.812 52.381 0.00 0.00 0.00 2.10
684 814 1.622449 CCACCACATCCCAGGAGTCTA 60.622 57.143 0.00 0.00 0.00 2.59
685 815 0.911525 CCACCACATCCCAGGAGTCT 60.912 60.000 0.00 0.00 0.00 3.24
689 819 0.770166 TTCACCACCACATCCCAGGA 60.770 55.000 0.00 0.00 0.00 3.86
692 822 1.004628 CAGATTCACCACCACATCCCA 59.995 52.381 0.00 0.00 0.00 4.37
698 828 0.326264 AGCTCCAGATTCACCACCAC 59.674 55.000 0.00 0.00 0.00 4.16
703 833 0.529555 GCTCGAGCTCCAGATTCACC 60.530 60.000 29.88 0.00 38.21 4.02
719 849 6.143598 GCAAGAGAAATTGAAACTTTCTGCTC 59.856 38.462 3.22 0.00 41.73 4.26
744 874 3.056891 GCTATCCATCTTCCTTCCTCTCG 60.057 52.174 0.00 0.00 0.00 4.04
771 903 0.852777 CGGCGTGATCTAATCCAACG 59.147 55.000 0.00 0.00 0.00 4.10
772 904 2.218953 TCGGCGTGATCTAATCCAAC 57.781 50.000 6.85 0.00 0.00 3.77
796 928 8.394121 GGAAAGAGATTTGTCTACTTATTGCTG 58.606 37.037 0.00 0.00 0.00 4.41
853 993 4.567597 TCGGGTCTGGGTGGTGGT 62.568 66.667 0.00 0.00 0.00 4.16
854 994 3.706373 CTCGGGTCTGGGTGGTGG 61.706 72.222 0.00 0.00 0.00 4.61
875 1015 1.445942 CATATATAGGCGGCGGGGG 59.554 63.158 9.78 0.00 0.00 5.40
966 1106 2.281484 TCACGTTCCTTGGCTGCC 60.281 61.111 12.87 12.87 0.00 4.85
968 1108 1.363744 GATCTCACGTTCCTTGGCTG 58.636 55.000 0.00 0.00 0.00 4.85
978 1118 3.823330 GTCCGGCCGATCTCACGT 61.823 66.667 30.73 0.00 0.00 4.49
1087 1255 4.999939 CTTGCCGTTGCCGTTGCC 63.000 66.667 0.00 0.00 36.33 4.52
1089 1257 4.999939 GGCTTGCCGTTGCCGTTG 63.000 66.667 0.00 0.00 39.71 4.10
1326 1497 3.118454 GCGTTGGCAGCGAGCTTA 61.118 61.111 27.88 0.00 44.79 3.09
1376 1547 1.610873 GACGAGGAGGAGGAGGAGT 59.389 63.158 0.00 0.00 0.00 3.85
1410 1584 3.194308 GCTCTGCTCGGCTCAAGC 61.194 66.667 0.00 0.00 40.26 4.01
1411 1585 2.884685 CGCTCTGCTCGGCTCAAG 60.885 66.667 0.00 0.00 0.00 3.02
1412 1586 4.441695 CCGCTCTGCTCGGCTCAA 62.442 66.667 0.00 0.00 40.46 3.02
1414 1588 3.649277 TTTCCGCTCTGCTCGGCTC 62.649 63.158 0.00 0.00 46.05 4.70
1415 1589 3.655810 CTTTCCGCTCTGCTCGGCT 62.656 63.158 0.00 0.00 46.05 5.52
1453 1627 1.797025 CCTCTCTCACCGGACAAAAC 58.203 55.000 9.46 0.00 0.00 2.43
1776 2021 3.304190 GGTTCGTTGAACAAATAGGCGTT 60.304 43.478 11.39 0.00 43.54 4.84
1779 2024 2.224784 ACGGTTCGTTGAACAAATAGGC 59.775 45.455 11.39 0.00 43.54 3.93
1785 2030 1.722677 GGCACGGTTCGTTGAACAA 59.277 52.632 11.39 0.00 43.54 2.83
1801 2046 2.836479 AACGGTGCAATATTTACGGC 57.164 45.000 0.00 0.00 0.00 5.68
1867 2112 9.787435 AGACTACAAATTATTATTATCCCGCAA 57.213 29.630 0.00 0.00 0.00 4.85
1868 2113 9.787435 AAGACTACAAATTATTATTATCCCGCA 57.213 29.630 0.00 0.00 0.00 5.69
1892 2137 7.758076 TGATTGTAACCGTGATACTTGAGTAAG 59.242 37.037 0.00 0.00 39.86 2.34
1901 2146 6.745450 CACCAAAATGATTGTAACCGTGATAC 59.255 38.462 0.00 0.00 0.00 2.24
1980 2225 6.183360 CCGATGTACACAGGTTCTTAAAATCC 60.183 42.308 0.00 0.00 0.00 3.01
2000 2245 7.611213 AAGTTTTATGAAGTAGGTTCCGATG 57.389 36.000 0.00 0.00 33.75 3.84
2005 2250 7.916914 TGGCTAAGTTTTATGAAGTAGGTTC 57.083 36.000 0.00 0.00 35.48 3.62
2040 2285 6.690957 TCTTTTGTCGTATTTTGCAGAACTTG 59.309 34.615 0.00 0.00 0.00 3.16
2056 2301 3.063316 TGTGTGTGTGTGATCTTTTGTCG 59.937 43.478 0.00 0.00 0.00 4.35
2070 2315 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2078 2323 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
2080 2325 5.574891 AATTATTGTGTGTGTGTGTGTGT 57.425 34.783 0.00 0.00 0.00 3.72
2081 2326 9.670719 TTATTAATTATTGTGTGTGTGTGTGTG 57.329 29.630 0.00 0.00 0.00 3.82
2145 2390 2.025981 TGACCATTTCTGACCTGGATGG 60.026 50.000 0.00 4.38 42.28 3.51
2146 2391 3.354948 TGACCATTTCTGACCTGGATG 57.645 47.619 0.00 0.00 34.08 3.51
2147 2392 5.919348 ATATGACCATTTCTGACCTGGAT 57.081 39.130 0.00 0.00 34.08 3.41
2148 2393 5.715439 AATATGACCATTTCTGACCTGGA 57.285 39.130 0.00 0.00 34.08 3.86
2149 2394 6.595682 AGTAATATGACCATTTCTGACCTGG 58.404 40.000 0.00 0.00 36.09 4.45
2150 2395 9.613428 TTAAGTAATATGACCATTTCTGACCTG 57.387 33.333 0.00 0.00 0.00 4.00
2151 2396 9.614792 GTTAAGTAATATGACCATTTCTGACCT 57.385 33.333 0.00 0.00 0.00 3.85
2152 2397 8.548721 CGTTAAGTAATATGACCATTTCTGACC 58.451 37.037 0.00 0.00 0.00 4.02
2153 2398 9.309516 TCGTTAAGTAATATGACCATTTCTGAC 57.690 33.333 0.00 0.00 0.00 3.51
2154 2399 9.529325 CTCGTTAAGTAATATGACCATTTCTGA 57.471 33.333 0.00 0.00 0.00 3.27
2155 2400 9.314321 ACTCGTTAAGTAATATGACCATTTCTG 57.686 33.333 0.00 0.00 36.07 3.02
2156 2401 9.886132 AACTCGTTAAGTAATATGACCATTTCT 57.114 29.630 0.00 0.00 37.17 2.52
2171 2416 8.579863 ACCTGTAGTGTATTTAACTCGTTAAGT 58.420 33.333 2.89 3.26 41.10 2.24
2172 2417 8.857216 CACCTGTAGTGTATTTAACTCGTTAAG 58.143 37.037 2.89 0.00 41.93 1.85
2173 2418 8.746922 CACCTGTAGTGTATTTAACTCGTTAA 57.253 34.615 0.00 0.00 41.93 2.01
2196 2441 2.038837 GCCGGACAAGTTAGGGCAC 61.039 63.158 5.05 0.00 43.23 5.01
2197 2442 2.349755 GCCGGACAAGTTAGGGCA 59.650 61.111 5.05 0.00 43.23 5.36
2198 2443 2.818274 CGCCGGACAAGTTAGGGC 60.818 66.667 5.05 0.00 40.36 5.19
2199 2444 2.818274 GCGCCGGACAAGTTAGGG 60.818 66.667 5.05 0.00 0.00 3.53
2200 2445 2.901051 ATCGCGCCGGACAAGTTAGG 62.901 60.000 5.05 0.00 0.00 2.69
2201 2446 1.480219 GATCGCGCCGGACAAGTTAG 61.480 60.000 5.05 0.00 0.00 2.34
2202 2447 1.517694 GATCGCGCCGGACAAGTTA 60.518 57.895 5.05 0.00 0.00 2.24
2203 2448 2.813908 GATCGCGCCGGACAAGTT 60.814 61.111 5.05 0.00 0.00 2.66
2204 2449 3.989698 CTGATCGCGCCGGACAAGT 62.990 63.158 5.05 0.00 0.00 3.16
2205 2450 3.257561 CTGATCGCGCCGGACAAG 61.258 66.667 5.05 0.00 0.00 3.16
2206 2451 3.583276 AACTGATCGCGCCGGACAA 62.583 57.895 5.05 0.00 0.00 3.18
2207 2452 3.583276 AAACTGATCGCGCCGGACA 62.583 57.895 5.05 0.00 0.00 4.02
2208 2453 2.813908 AAACTGATCGCGCCGGAC 60.814 61.111 5.05 0.00 0.00 4.79
2209 2454 2.813474 CAAACTGATCGCGCCGGA 60.813 61.111 5.05 0.00 0.00 5.14
2210 2455 3.864686 CCAAACTGATCGCGCCGG 61.865 66.667 0.00 0.00 0.00 6.13
2211 2456 3.118454 ACCAAACTGATCGCGCCG 61.118 61.111 0.00 0.00 0.00 6.46
2212 2457 2.480555 CACCAAACTGATCGCGCC 59.519 61.111 0.00 0.00 0.00 6.53
2213 2458 2.202349 GCACCAAACTGATCGCGC 60.202 61.111 0.00 0.00 0.00 6.86
2214 2459 0.739462 TAGGCACCAAACTGATCGCG 60.739 55.000 0.00 0.00 0.00 5.87
2215 2460 1.448985 TTAGGCACCAAACTGATCGC 58.551 50.000 0.00 0.00 0.00 4.58
2216 2461 3.074412 AGTTTAGGCACCAAACTGATCG 58.926 45.455 13.13 0.00 42.98 3.69
2217 2462 4.518970 TCAAGTTTAGGCACCAAACTGATC 59.481 41.667 14.07 0.00 43.62 2.92
2218 2463 4.469657 TCAAGTTTAGGCACCAAACTGAT 58.530 39.130 14.07 2.55 43.62 2.90
2219 2464 3.892284 TCAAGTTTAGGCACCAAACTGA 58.108 40.909 14.07 11.62 43.62 3.41
2220 2465 4.647424 TTCAAGTTTAGGCACCAAACTG 57.353 40.909 14.07 10.26 43.62 3.16
2221 2466 5.669164 TTTTCAAGTTTAGGCACCAAACT 57.331 34.783 9.87 9.87 45.73 2.66
2222 2467 6.918892 ATTTTTCAAGTTTAGGCACCAAAC 57.081 33.333 6.62 6.62 36.37 2.93
2223 2468 7.492994 GTGTATTTTTCAAGTTTAGGCACCAAA 59.507 33.333 0.00 0.00 0.00 3.28
2224 2469 6.981559 GTGTATTTTTCAAGTTTAGGCACCAA 59.018 34.615 0.00 0.00 0.00 3.67
2225 2470 6.096987 TGTGTATTTTTCAAGTTTAGGCACCA 59.903 34.615 0.00 0.00 0.00 4.17
2226 2471 6.508777 TGTGTATTTTTCAAGTTTAGGCACC 58.491 36.000 0.00 0.00 0.00 5.01
2227 2472 7.995463 TTGTGTATTTTTCAAGTTTAGGCAC 57.005 32.000 0.00 0.00 0.00 5.01
2228 2473 9.092876 CTTTTGTGTATTTTTCAAGTTTAGGCA 57.907 29.630 0.00 0.00 0.00 4.75
2229 2474 9.093970 ACTTTTGTGTATTTTTCAAGTTTAGGC 57.906 29.630 0.00 0.00 0.00 3.93
2248 2493 4.595986 ACAAGTTACTCCACCACTTTTGT 58.404 39.130 0.00 0.00 0.00 2.83
2249 2494 4.881850 AGACAAGTTACTCCACCACTTTTG 59.118 41.667 0.00 0.00 0.00 2.44
2250 2495 5.112129 AGACAAGTTACTCCACCACTTTT 57.888 39.130 0.00 0.00 0.00 2.27
2251 2496 4.772886 AGACAAGTTACTCCACCACTTT 57.227 40.909 0.00 0.00 0.00 2.66
2252 2497 4.283722 CCTAGACAAGTTACTCCACCACTT 59.716 45.833 0.00 0.00 0.00 3.16
2253 2498 3.833070 CCTAGACAAGTTACTCCACCACT 59.167 47.826 0.00 0.00 0.00 4.00
2254 2499 3.616802 GCCTAGACAAGTTACTCCACCAC 60.617 52.174 0.00 0.00 0.00 4.16
2255 2500 2.565834 GCCTAGACAAGTTACTCCACCA 59.434 50.000 0.00 0.00 0.00 4.17
2256 2501 2.565834 TGCCTAGACAAGTTACTCCACC 59.434 50.000 0.00 0.00 0.00 4.61
2257 2502 3.955650 TGCCTAGACAAGTTACTCCAC 57.044 47.619 0.00 0.00 0.00 4.02
2258 2503 4.530553 TGAATGCCTAGACAAGTTACTCCA 59.469 41.667 0.00 0.00 0.00 3.86
2259 2504 5.086104 TGAATGCCTAGACAAGTTACTCC 57.914 43.478 0.00 0.00 0.00 3.85
2260 2505 7.617041 ATTTGAATGCCTAGACAAGTTACTC 57.383 36.000 0.00 0.00 0.00 2.59
2261 2506 7.277981 CGTATTTGAATGCCTAGACAAGTTACT 59.722 37.037 0.00 0.00 0.00 2.24
2262 2507 7.399523 CGTATTTGAATGCCTAGACAAGTTAC 58.600 38.462 0.00 0.00 0.00 2.50
2263 2508 6.537301 CCGTATTTGAATGCCTAGACAAGTTA 59.463 38.462 0.00 0.00 0.00 2.24
2264 2509 5.354234 CCGTATTTGAATGCCTAGACAAGTT 59.646 40.000 0.00 0.00 0.00 2.66
2265 2510 4.876107 CCGTATTTGAATGCCTAGACAAGT 59.124 41.667 0.00 0.00 0.00 3.16
2266 2511 4.876107 ACCGTATTTGAATGCCTAGACAAG 59.124 41.667 0.00 0.00 0.00 3.16
2267 2512 4.634004 CACCGTATTTGAATGCCTAGACAA 59.366 41.667 0.00 0.00 0.00 3.18
2268 2513 4.188462 CACCGTATTTGAATGCCTAGACA 58.812 43.478 0.00 0.00 0.00 3.41
2269 2514 3.002348 GCACCGTATTTGAATGCCTAGAC 59.998 47.826 0.00 0.00 0.00 2.59
2270 2515 3.202906 GCACCGTATTTGAATGCCTAGA 58.797 45.455 0.00 0.00 0.00 2.43
2271 2516 3.609103 GCACCGTATTTGAATGCCTAG 57.391 47.619 0.00 0.00 0.00 3.02
2275 2520 2.017049 AGAGGCACCGTATTTGAATGC 58.983 47.619 0.00 0.00 35.51 3.56
2276 2521 4.693283 TCTAGAGGCACCGTATTTGAATG 58.307 43.478 0.00 0.00 0.00 2.67
2277 2522 4.202264 CCTCTAGAGGCACCGTATTTGAAT 60.202 45.833 25.73 0.00 42.44 2.57
2278 2523 3.132289 CCTCTAGAGGCACCGTATTTGAA 59.868 47.826 25.73 0.00 42.44 2.69
2279 2524 2.693591 CCTCTAGAGGCACCGTATTTGA 59.306 50.000 25.73 0.00 42.44 2.69
2280 2525 3.099267 CCTCTAGAGGCACCGTATTTG 57.901 52.381 25.73 0.00 42.44 2.32
2292 2537 1.173444 ACGGCGGCATACCTCTAGAG 61.173 60.000 13.24 13.18 0.00 2.43
2293 2538 0.109153 TACGGCGGCATACCTCTAGA 59.891 55.000 13.24 0.00 0.00 2.43
2294 2539 1.132643 GATACGGCGGCATACCTCTAG 59.867 57.143 13.24 0.00 0.00 2.43
2295 2540 1.171308 GATACGGCGGCATACCTCTA 58.829 55.000 13.24 0.00 0.00 2.43
2296 2541 0.826256 TGATACGGCGGCATACCTCT 60.826 55.000 13.24 0.00 0.00 3.69
2297 2542 0.032952 TTGATACGGCGGCATACCTC 59.967 55.000 13.24 0.00 0.00 3.85
2298 2543 0.033504 CTTGATACGGCGGCATACCT 59.966 55.000 13.24 0.00 0.00 3.08
2299 2544 0.249741 ACTTGATACGGCGGCATACC 60.250 55.000 13.24 0.00 0.00 2.73
2300 2545 0.859232 CACTTGATACGGCGGCATAC 59.141 55.000 13.24 0.00 0.00 2.39
2301 2546 0.878523 GCACTTGATACGGCGGCATA 60.879 55.000 13.24 0.00 0.00 3.14
2302 2547 2.180204 GCACTTGATACGGCGGCAT 61.180 57.895 13.24 3.47 0.00 4.40
2303 2548 2.817834 GCACTTGATACGGCGGCA 60.818 61.111 13.24 3.20 0.00 5.69
2304 2549 3.573491 GGCACTTGATACGGCGGC 61.573 66.667 13.24 0.00 0.00 6.53
2305 2550 2.895372 GGGCACTTGATACGGCGG 60.895 66.667 13.24 0.00 0.00 6.13
2306 2551 3.261951 CGGGCACTTGATACGGCG 61.262 66.667 4.80 4.80 0.00 6.46
2307 2552 2.125269 ACGGGCACTTGATACGGC 60.125 61.111 0.00 0.00 0.00 5.68
2308 2553 1.813753 CCACGGGCACTTGATACGG 60.814 63.158 0.00 0.00 0.00 4.02
2309 2554 1.813753 CCCACGGGCACTTGATACG 60.814 63.158 0.00 0.00 0.00 3.06
2310 2555 1.451387 CCCCACGGGCACTTGATAC 60.451 63.158 0.00 0.00 35.35 2.24
2311 2556 2.994699 CCCCACGGGCACTTGATA 59.005 61.111 0.00 0.00 35.35 2.15
2323 2568 3.434319 CACGCTGACATGCCCCAC 61.434 66.667 0.00 0.00 0.00 4.61
2324 2569 3.899981 GACACGCTGACATGCCCCA 62.900 63.158 0.00 0.00 0.00 4.96
2325 2570 3.127533 GACACGCTGACATGCCCC 61.128 66.667 0.00 0.00 0.00 5.80
2326 2571 3.490759 CGACACGCTGACATGCCC 61.491 66.667 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.