Multiple sequence alignment - TraesCS6A01G227700

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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 TraesCS6A01G227700 chr6A 100.000 3038 0 0 1 3038 428425012 428428049 0.000000e+00 5611.0
1 TraesCS6A01G227700 chr6B 91.326 1199 55 18 40 1205 457218274 457217092 0.000000e+00 1592.0
2 TraesCS6A01G227700 chr6B 91.077 919 54 14 1219 2121 457217038 457216132 0.000000e+00 1218.0
3 TraesCS6A01G227700 chr6B 85.417 240 32 2 2642 2880 457180480 457180243 2.340000e-61 246.0
4 TraesCS6A01G227700 chr6D 91.774 1167 42 22 81 1210 292739200 292738051 0.000000e+00 1574.0
5 TraesCS6A01G227700 chr6D 92.567 1009 45 7 1219 2208 292738008 292737011 0.000000e+00 1421.0
6 TraesCS6A01G227700 chr6D 83.705 583 71 14 2307 2880 292737007 292736440 2.070000e-146 529.0
7 TraesCS6A01G227700 chr6D 85.227 88 10 3 1473 1558 309719543 309719629 1.500000e-13 87.9
8 TraesCS6A01G227700 chr2D 78.973 409 63 19 1232 1629 466724234 466723838 1.080000e-64 257.0
9 TraesCS6A01G227700 chr2D 93.023 129 9 0 2910 3038 617317727 617317855 4.000000e-44 189.0
10 TraesCS6A01G227700 chr2D 83.529 85 12 2 2211 2293 538943507 538943423 9.030000e-11 78.7
11 TraesCS6A01G227700 chr1A 91.489 141 7 2 2900 3035 73112538 73112678 4.000000e-44 189.0
12 TraesCS6A01G227700 chr2B 87.654 162 14 5 1469 1629 545366063 545365907 1.860000e-42 183.0
13 TraesCS6A01G227700 chr2A 87.037 162 15 4 1469 1629 607841877 607841721 8.660000e-41 178.0
14 TraesCS6A01G227700 chr5A 87.234 94 10 2 1477 1569 676887309 676887401 4.140000e-19 106.0
15 TraesCS6A01G227700 chr4D 87.234 94 10 2 1477 1569 497126484 497126576 4.140000e-19 106.0
16 TraesCS6A01G227700 chr4B 87.234 94 10 2 1477 1569 637622199 637622291 4.140000e-19 106.0
17 TraesCS6A01G227700 chr5D 85.227 88 11 2 2209 2294 446767256 446767169 4.170000e-14 89.8
18 TraesCS6A01G227700 chr5B 84.783 92 11 2 2205 2293 47504115 47504206 4.170000e-14 89.8
19 TraesCS6A01G227700 chr5B 82.979 94 14 2 2202 2293 505573925 505573832 1.940000e-12 84.2
20 TraesCS6A01G227700 chr5B 83.908 87 10 3 2210 2293 42698222 42698137 2.510000e-11 80.5
21 TraesCS6A01G227700 chr7B 85.057 87 11 1 2209 2293 747594374 747594288 1.500000e-13 87.9
22 TraesCS6A01G227700 chr7A 82.609 92 13 2 2208 2296 197997848 197997939 9.030000e-11 78.7
23 TraesCS6A01G227700 chr1D 82.418 91 14 2 2206 2294 58438782 58438872 9.030000e-11 78.7
24 TraesCS6A01G227700 chr1B 80.556 108 14 7 2194 2297 510917848 510917952 3.250000e-10 76.8


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 TraesCS6A01G227700 chr6A 428425012 428428049 3037 False 5611.000000 5611 100.000000 1 3038 1 chr6A.!!$F1 3037
1 TraesCS6A01G227700 chr6B 457216132 457218274 2142 True 1405.000000 1592 91.201500 40 2121 2 chr6B.!!$R2 2081
2 TraesCS6A01G227700 chr6D 292736440 292739200 2760 True 1174.666667 1574 89.348667 81 2880 3 chr6D.!!$R1 2799

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
470 471 0.389391 CTCCATCGCACGAAGGGTAT 59.611 55.0 13.71 0.00 34.12 2.73 F
1806 1914 0.033504 ATATGGCGGACATGGACGAC 59.966 55.0 6.59 12.15 40.82 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 1929 0.179148 CCGACGTCGACATTGGATCA 60.179 55.0 37.65 0.0 43.02 2.92 R
2892 3017 0.865111 CGCGTGACACATGAGGAAAA 59.135 50.0 6.37 0.0 0.00 2.29 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
27 28 9.950496 ATCTATTGCAAGTTTATGGGTCTATAG 57.050 33.333 4.94 0.00 0.00 1.31
28 29 8.934697 TCTATTGCAAGTTTATGGGTCTATAGT 58.065 33.333 4.94 0.00 0.00 2.12
29 30 9.209175 CTATTGCAAGTTTATGGGTCTATAGTC 57.791 37.037 4.94 0.00 0.00 2.59
30 31 5.925509 TGCAAGTTTATGGGTCTATAGTCC 58.074 41.667 7.44 7.44 0.00 3.85
31 32 5.665812 TGCAAGTTTATGGGTCTATAGTCCT 59.334 40.000 14.56 0.35 0.00 3.85
32 33 6.183360 TGCAAGTTTATGGGTCTATAGTCCTC 60.183 42.308 14.56 6.73 0.00 3.71
33 34 6.042208 GCAAGTTTATGGGTCTATAGTCCTCT 59.958 42.308 14.56 6.17 0.00 3.69
34 35 7.419172 GCAAGTTTATGGGTCTATAGTCCTCTT 60.419 40.741 14.56 6.93 0.00 2.85
35 36 7.604657 AGTTTATGGGTCTATAGTCCTCTTG 57.395 40.000 14.56 0.00 0.00 3.02
36 37 6.042208 AGTTTATGGGTCTATAGTCCTCTTGC 59.958 42.308 14.56 0.24 0.00 4.01
37 38 2.679082 TGGGTCTATAGTCCTCTTGCC 58.321 52.381 14.56 0.00 0.00 4.52
38 39 2.247635 TGGGTCTATAGTCCTCTTGCCT 59.752 50.000 14.56 0.00 0.00 4.75
52 53 7.051000 GTCCTCTTGCCTCTTCAGTTTATAAT 58.949 38.462 0.00 0.00 0.00 1.28
53 54 8.204836 GTCCTCTTGCCTCTTCAGTTTATAATA 58.795 37.037 0.00 0.00 0.00 0.98
54 55 8.204836 TCCTCTTGCCTCTTCAGTTTATAATAC 58.795 37.037 0.00 0.00 0.00 1.89
55 56 7.169982 CCTCTTGCCTCTTCAGTTTATAATACG 59.830 40.741 0.00 0.00 0.00 3.06
56 57 7.553334 TCTTGCCTCTTCAGTTTATAATACGT 58.447 34.615 0.00 0.00 0.00 3.57
57 58 8.689061 TCTTGCCTCTTCAGTTTATAATACGTA 58.311 33.333 0.00 0.00 0.00 3.57
58 59 8.638685 TTGCCTCTTCAGTTTATAATACGTAC 57.361 34.615 0.00 0.00 0.00 3.67
59 60 7.205297 TGCCTCTTCAGTTTATAATACGTACC 58.795 38.462 0.00 0.00 0.00 3.34
60 61 7.147863 TGCCTCTTCAGTTTATAATACGTACCA 60.148 37.037 0.00 0.00 0.00 3.25
156 157 3.252701 ACAGTACTACACGTCCTCTTGTG 59.747 47.826 0.00 0.00 41.81 3.33
247 248 1.838112 ACCCACGTTCAATGATGCAT 58.162 45.000 0.00 0.00 0.00 3.96
259 260 4.624015 CAATGATGCATTGGTGGTAATCC 58.376 43.478 0.00 0.00 45.03 3.01
356 357 3.991367 TCGTCGACTAGATCTAGATGCA 58.009 45.455 31.91 12.60 36.97 3.96
444 445 5.808042 ACATGCGATATTATTGCTGATCC 57.192 39.130 15.34 0.00 40.43 3.36
467 468 0.598680 GATCTCCATCGCACGAAGGG 60.599 60.000 13.71 10.47 34.12 3.95
470 471 0.389391 CTCCATCGCACGAAGGGTAT 59.611 55.000 13.71 0.00 34.12 2.73
707 711 3.264947 TCATCATGCCTGTCGAGAAAAG 58.735 45.455 0.00 0.00 0.00 2.27
722 726 3.891977 GAGAAAAGGAGGAGCAAAAGGTT 59.108 43.478 0.00 0.00 0.00 3.50
726 730 3.532641 AGGAGGAGCAAAAGGTTGATT 57.467 42.857 0.00 0.00 36.83 2.57
730 734 5.044550 AGGAGGAGCAAAAGGTTGATTAGAT 60.045 40.000 0.00 0.00 36.83 1.98
734 738 8.650143 AGGAGCAAAAGGTTGATTAGATTTAA 57.350 30.769 0.00 0.00 36.83 1.52
735 739 8.743714 AGGAGCAAAAGGTTGATTAGATTTAAG 58.256 33.333 0.00 0.00 36.83 1.85
736 740 8.739972 GGAGCAAAAGGTTGATTAGATTTAAGA 58.260 33.333 0.00 0.00 36.83 2.10
925 934 0.960861 TCGTTTGTTGCACACCACCA 60.961 50.000 0.00 0.00 0.00 4.17
927 936 0.459411 GTTTGTTGCACACCACCACC 60.459 55.000 0.00 0.00 0.00 4.61
928 937 0.613292 TTTGTTGCACACCACCACCT 60.613 50.000 0.00 0.00 0.00 4.00
929 938 1.034838 TTGTTGCACACCACCACCTC 61.035 55.000 0.00 0.00 0.00 3.85
930 939 1.453015 GTTGCACACCACCACCTCA 60.453 57.895 0.00 0.00 0.00 3.86
931 940 1.453015 TTGCACACCACCACCTCAC 60.453 57.895 0.00 0.00 0.00 3.51
932 941 2.594592 GCACACCACCACCTCACC 60.595 66.667 0.00 0.00 0.00 4.02
933 942 3.120086 GCACACCACCACCTCACCT 62.120 63.158 0.00 0.00 0.00 4.00
934 943 1.071471 CACACCACCACCTCACCTC 59.929 63.158 0.00 0.00 0.00 3.85
935 944 1.383943 ACACCACCACCTCACCTCA 60.384 57.895 0.00 0.00 0.00 3.86
936 945 1.071471 CACCACCACCTCACCTCAC 59.929 63.158 0.00 0.00 0.00 3.51
937 946 1.074471 ACCACCACCTCACCTCACT 60.074 57.895 0.00 0.00 0.00 3.41
941 950 0.896019 ACCACCTCACCTCACTCTCG 60.896 60.000 0.00 0.00 0.00 4.04
959 978 1.453015 GCTCGCTCTCTCTCCCTGA 60.453 63.158 0.00 0.00 0.00 3.86
1010 1050 5.815581 AGTTATTGTTGGAATGGAGCAGTA 58.184 37.500 0.00 0.00 0.00 2.74
1101 1141 1.524621 CTATGTTCGGCAGCAGGGG 60.525 63.158 0.00 0.00 0.00 4.79
1156 1210 0.179227 TGCGCAATCATTCGTGTTCG 60.179 50.000 8.16 0.00 38.55 3.95
1161 1215 4.145276 CGCAATCATTCGTGTTCGTTAAA 58.855 39.130 0.00 0.00 38.33 1.52
1164 1218 6.183359 CGCAATCATTCGTGTTCGTTAAATTT 60.183 34.615 0.00 0.00 38.33 1.82
1207 1261 1.189989 GCGCATGCAAATTCGTCGAG 61.190 55.000 19.57 0.00 42.15 4.04
1210 1264 1.466360 GCATGCAAATTCGTCGAGCTT 60.466 47.619 14.21 0.00 0.00 3.74
1211 1265 2.171567 CATGCAAATTCGTCGAGCTTG 58.828 47.619 11.89 11.89 0.00 4.01
1212 1266 0.110238 TGCAAATTCGTCGAGCTTGC 60.110 50.000 25.08 25.08 42.12 4.01
1215 1269 2.171567 CAAATTCGTCGAGCTTGCATG 58.828 47.619 0.00 0.00 0.00 4.06
1216 1270 1.442769 AATTCGTCGAGCTTGCATGT 58.557 45.000 0.00 0.00 0.00 3.21
1414 1522 2.280753 ATGCATGCCATGAGCCCA 59.719 55.556 16.68 0.00 42.71 5.36
1415 1523 1.152333 ATGCATGCCATGAGCCCAT 60.152 52.632 16.68 0.00 42.71 4.00
1445 1553 2.096218 GGATCGAGCTCACAAAACACAC 60.096 50.000 15.40 0.00 0.00 3.82
1540 1648 3.512033 ACGAGATCAAGAACTACTGGC 57.488 47.619 0.00 0.00 0.00 4.85
1691 1799 2.027073 CTGCTAGCGCGGACAACAA 61.027 57.895 8.83 0.00 45.62 2.83
1731 1839 1.812235 ATCACGCAGATGAAGCAACA 58.188 45.000 0.00 0.00 35.06 3.33
1735 1843 1.881973 ACGCAGATGAAGCAACAACAT 59.118 42.857 0.00 0.00 0.00 2.71
1743 1851 1.401318 AAGCAACAACATGGCCAGCA 61.401 50.000 13.05 0.00 0.00 4.41
1788 1896 2.031616 CTGGCGATGATGCGGGAT 59.968 61.111 0.00 0.00 35.06 3.85
1806 1914 0.033504 ATATGGCGGACATGGACGAC 59.966 55.000 6.59 12.15 40.82 4.34
1819 1927 0.108756 GGACGACTTCCTGCAGTACC 60.109 60.000 13.81 0.48 41.95 3.34
1821 1929 1.204941 GACGACTTCCTGCAGTACCAT 59.795 52.381 13.81 0.00 0.00 3.55
1822 1930 1.066858 ACGACTTCCTGCAGTACCATG 60.067 52.381 13.81 0.76 0.00 3.66
1824 1932 2.159043 CGACTTCCTGCAGTACCATGAT 60.159 50.000 13.81 0.00 0.00 2.45
1827 1938 1.878211 TCCTGCAGTACCATGATCCA 58.122 50.000 13.81 0.00 0.00 3.41
1835 1946 3.804325 CAGTACCATGATCCAATGTCGAC 59.196 47.826 9.11 9.11 0.00 4.20
1855 1966 0.683504 GTCGGCCTACTTCCTCCTCA 60.684 60.000 0.00 0.00 0.00 3.86
1906 2017 4.271816 CCAGCGGGGAGATCGACG 62.272 72.222 0.00 0.00 40.01 5.12
1948 2059 0.666577 CTTGTGGAACCTCGACGACC 60.667 60.000 0.00 0.00 34.36 4.79
2132 2246 0.178068 AAGGATGCGTCGCCAACTAT 59.822 50.000 15.88 0.00 0.00 2.12
2133 2247 1.037493 AGGATGCGTCGCCAACTATA 58.963 50.000 15.88 0.00 0.00 1.31
2160 2278 2.214181 CTTCGACTAGCCTGCCACGT 62.214 60.000 0.00 0.00 0.00 4.49
2184 2302 4.141846 TGGCATGTCTAGCTCCTTTTAGAG 60.142 45.833 0.00 0.00 36.92 2.43
2218 2337 8.865420 AGGAAAAGAAAATAAACTACTCCCTC 57.135 34.615 0.00 0.00 0.00 4.30
2219 2338 7.889073 AGGAAAAGAAAATAAACTACTCCCTCC 59.111 37.037 0.00 0.00 0.00 4.30
2220 2339 7.148289 GGAAAAGAAAATAAACTACTCCCTCCG 60.148 40.741 0.00 0.00 0.00 4.63
2221 2340 6.370186 AAGAAAATAAACTACTCCCTCCGT 57.630 37.500 0.00 0.00 0.00 4.69
2222 2341 5.975282 AGAAAATAAACTACTCCCTCCGTC 58.025 41.667 0.00 0.00 0.00 4.79
2223 2342 5.720520 AGAAAATAAACTACTCCCTCCGTCT 59.279 40.000 0.00 0.00 0.00 4.18
2224 2343 5.595257 AAATAAACTACTCCCTCCGTCTC 57.405 43.478 0.00 0.00 0.00 3.36
2225 2344 2.599408 AAACTACTCCCTCCGTCTCA 57.401 50.000 0.00 0.00 0.00 3.27
2226 2345 2.830651 AACTACTCCCTCCGTCTCAT 57.169 50.000 0.00 0.00 0.00 2.90
2227 2346 3.947612 AACTACTCCCTCCGTCTCATA 57.052 47.619 0.00 0.00 0.00 2.15
2228 2347 3.947612 ACTACTCCCTCCGTCTCATAA 57.052 47.619 0.00 0.00 0.00 1.90
2229 2348 4.456662 ACTACTCCCTCCGTCTCATAAT 57.543 45.455 0.00 0.00 0.00 1.28
2230 2349 4.145807 ACTACTCCCTCCGTCTCATAATG 58.854 47.826 0.00 0.00 0.00 1.90
2231 2350 3.033659 ACTCCCTCCGTCTCATAATGT 57.966 47.619 0.00 0.00 0.00 2.71
2232 2351 4.180377 ACTCCCTCCGTCTCATAATGTA 57.820 45.455 0.00 0.00 0.00 2.29
2233 2352 4.543689 ACTCCCTCCGTCTCATAATGTAA 58.456 43.478 0.00 0.00 0.00 2.41
2234 2353 4.585162 ACTCCCTCCGTCTCATAATGTAAG 59.415 45.833 0.00 0.00 0.00 2.34
2235 2354 4.800023 TCCCTCCGTCTCATAATGTAAGA 58.200 43.478 0.00 0.00 0.00 2.10
2236 2355 5.394738 TCCCTCCGTCTCATAATGTAAGAT 58.605 41.667 0.00 0.00 0.00 2.40
2237 2356 5.243954 TCCCTCCGTCTCATAATGTAAGATG 59.756 44.000 0.00 0.00 0.00 2.90
2238 2357 4.926238 CCTCCGTCTCATAATGTAAGATGC 59.074 45.833 0.00 0.00 0.00 3.91
2239 2358 5.279206 CCTCCGTCTCATAATGTAAGATGCT 60.279 44.000 0.00 0.00 0.00 3.79
2240 2359 6.161855 TCCGTCTCATAATGTAAGATGCTT 57.838 37.500 0.00 0.00 0.00 3.91
2241 2360 6.582636 TCCGTCTCATAATGTAAGATGCTTT 58.417 36.000 0.00 0.00 0.00 3.51
2242 2361 7.047891 TCCGTCTCATAATGTAAGATGCTTTT 58.952 34.615 0.00 0.00 0.00 2.27
2243 2362 7.552687 TCCGTCTCATAATGTAAGATGCTTTTT 59.447 33.333 0.00 0.00 0.00 1.94
2244 2363 8.826710 CCGTCTCATAATGTAAGATGCTTTTTA 58.173 33.333 0.00 0.00 0.00 1.52
2289 2408 9.661563 AATGTCTTACATTATGTAACGAAGGAA 57.338 29.630 13.14 0.23 46.11 3.36
2290 2409 8.697846 TGTCTTACATTATGTAACGAAGGAAG 57.302 34.615 13.14 4.18 37.86 3.46
2291 2410 8.308931 TGTCTTACATTATGTAACGAAGGAAGT 58.691 33.333 13.14 0.00 37.86 3.01
2292 2411 9.793252 GTCTTACATTATGTAACGAAGGAAGTA 57.207 33.333 13.14 0.00 37.86 2.24
2302 2421 8.297470 TGTAACGAAGGAAGTATTATACTGGT 57.703 34.615 5.58 0.00 39.39 4.00
2303 2422 9.407380 TGTAACGAAGGAAGTATTATACTGGTA 57.593 33.333 5.58 0.00 39.39 3.25
2304 2423 9.890352 GTAACGAAGGAAGTATTATACTGGTAG 57.110 37.037 5.58 0.00 39.39 3.18
2305 2424 7.521871 ACGAAGGAAGTATTATACTGGTAGG 57.478 40.000 5.58 0.00 39.39 3.18
2339 2461 5.867903 TGAAAAGGCAATGAAAGAAAGGA 57.132 34.783 0.00 0.00 0.00 3.36
2359 2481 1.340991 ACAGGTGTTCAAAGGTGCACT 60.341 47.619 17.98 0.00 32.90 4.40
2360 2482 1.750778 CAGGTGTTCAAAGGTGCACTT 59.249 47.619 17.98 6.12 42.52 3.16
2361 2483 2.948979 CAGGTGTTCAAAGGTGCACTTA 59.051 45.455 17.98 0.00 38.85 2.24
2367 2489 1.953686 TCAAAGGTGCACTTAAGCCAC 59.046 47.619 17.98 15.07 38.85 5.01
2380 2502 1.486211 AAGCCACCTAGCTCACGTAT 58.514 50.000 0.00 0.00 44.11 3.06
2385 2507 2.952978 CCACCTAGCTCACGTATTCTCT 59.047 50.000 0.00 0.00 0.00 3.10
2387 2509 2.873472 ACCTAGCTCACGTATTCTCTCG 59.127 50.000 0.00 0.00 0.00 4.04
2394 2516 4.497674 GCTCACGTATTCTCTCGGTTACAT 60.498 45.833 0.00 0.00 0.00 2.29
2397 2519 7.087409 TCACGTATTCTCTCGGTTACATTTA 57.913 36.000 0.00 0.00 0.00 1.40
2398 2520 6.968904 TCACGTATTCTCTCGGTTACATTTAC 59.031 38.462 0.00 0.00 0.00 2.01
2399 2521 6.971184 CACGTATTCTCTCGGTTACATTTACT 59.029 38.462 0.00 0.00 0.00 2.24
2400 2522 7.165483 CACGTATTCTCTCGGTTACATTTACTC 59.835 40.741 0.00 0.00 0.00 2.59
2402 2524 4.627611 TCTCTCGGTTACATTTACTCCG 57.372 45.455 0.00 0.00 42.12 4.63
2403 2525 3.114065 CTCTCGGTTACATTTACTCCGC 58.886 50.000 0.00 0.00 40.81 5.54
2412 2537 4.184079 ACATTTACTCCGCGTCTAACTT 57.816 40.909 4.92 0.00 0.00 2.66
2420 2545 2.939103 TCCGCGTCTAACTTCTACTACC 59.061 50.000 4.92 0.00 0.00 3.18
2422 2547 3.376546 CCGCGTCTAACTTCTACTACCTT 59.623 47.826 4.92 0.00 0.00 3.50
2424 2549 4.495514 CGCGTCTAACTTCTACTACCTTCC 60.496 50.000 0.00 0.00 0.00 3.46
2427 2552 6.350027 GCGTCTAACTTCTACTACCTTCCTTT 60.350 42.308 0.00 0.00 0.00 3.11
2428 2553 7.249858 CGTCTAACTTCTACTACCTTCCTTTC 58.750 42.308 0.00 0.00 0.00 2.62
2471 2596 9.453325 TGTCAATTTAAATTTAACCGACAAGAC 57.547 29.630 22.06 15.69 29.62 3.01
2472 2597 8.624028 GTCAATTTAAATTTAACCGACAAGACG 58.376 33.333 10.77 0.00 0.00 4.18
2545 2670 9.167311 ACCTTTTTATCTAAGCTCATGTACTTG 57.833 33.333 11.60 2.36 0.00 3.16
2551 2676 7.721286 ATCTAAGCTCATGTACTTGTTATGC 57.279 36.000 8.46 8.83 0.00 3.14
2552 2677 6.049149 TCTAAGCTCATGTACTTGTTATGCC 58.951 40.000 8.46 0.00 0.00 4.40
2553 2678 3.198068 AGCTCATGTACTTGTTATGCCG 58.802 45.455 8.46 0.00 0.00 5.69
2554 2679 2.286418 GCTCATGTACTTGTTATGCCGC 60.286 50.000 8.46 0.16 0.00 6.53
2561 2686 5.849510 TGTACTTGTTATGCCGCTATGTAT 58.150 37.500 0.00 0.00 0.00 2.29
2571 2696 6.668541 ATGCCGCTATGTATTTGATGTATC 57.331 37.500 0.00 0.00 0.00 2.24
2573 2698 5.408299 TGCCGCTATGTATTTGATGTATCAC 59.592 40.000 0.00 0.00 36.36 3.06
2577 2702 8.595533 CCGCTATGTATTTGATGTATCACATAC 58.404 37.037 17.87 17.87 44.62 2.39
2585 2710 6.790232 TTGATGTATCACATACTCTGGACA 57.210 37.500 0.00 0.00 39.27 4.02
2661 2786 0.941542 TTACACTGCCTTGTTCGTGC 59.058 50.000 0.00 0.00 0.00 5.34
2662 2787 0.179070 TACACTGCCTTGTTCGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
2715 2840 0.389025 CCTTGTTGGGCCTTTGTGTC 59.611 55.000 4.53 0.00 0.00 3.67
2721 2846 1.527380 GGGCCTTTGTGTCCGTTCA 60.527 57.895 0.84 0.00 0.00 3.18
2730 2855 2.557317 TGTGTCCGTTCAGTCCTTTTC 58.443 47.619 0.00 0.00 0.00 2.29
2731 2856 1.871676 GTGTCCGTTCAGTCCTTTTCC 59.128 52.381 0.00 0.00 0.00 3.13
2732 2857 1.202722 TGTCCGTTCAGTCCTTTTCCC 60.203 52.381 0.00 0.00 0.00 3.97
2733 2858 1.071857 GTCCGTTCAGTCCTTTTCCCT 59.928 52.381 0.00 0.00 0.00 4.20
2736 2861 3.391955 TCCGTTCAGTCCTTTTCCCTTTA 59.608 43.478 0.00 0.00 0.00 1.85
2737 2862 4.042435 TCCGTTCAGTCCTTTTCCCTTTAT 59.958 41.667 0.00 0.00 0.00 1.40
2740 2865 6.379386 CGTTCAGTCCTTTTCCCTTTATTTC 58.621 40.000 0.00 0.00 0.00 2.17
2741 2866 6.379386 GTTCAGTCCTTTTCCCTTTATTTCG 58.621 40.000 0.00 0.00 0.00 3.46
2742 2867 4.457949 TCAGTCCTTTTCCCTTTATTTCGC 59.542 41.667 0.00 0.00 0.00 4.70
2746 2871 5.633601 GTCCTTTTCCCTTTATTTCGCTTTG 59.366 40.000 0.00 0.00 0.00 2.77
2752 2877 4.097286 TCCCTTTATTTCGCTTTGTATGGC 59.903 41.667 0.00 0.00 0.00 4.40
2754 2879 5.273944 CCTTTATTTCGCTTTGTATGGCTC 58.726 41.667 0.00 0.00 0.00 4.70
2767 2892 9.528018 GCTTTGTATGGCTCTATCTATATTCTC 57.472 37.037 0.00 0.00 0.00 2.87
2785 2910 5.640158 TTCTCACACCCTAAAGAAAGGAA 57.360 39.130 0.00 0.00 39.15 3.36
2786 2911 5.228945 TCTCACACCCTAAAGAAAGGAAG 57.771 43.478 0.00 0.00 39.15 3.46
2787 2912 3.751518 TCACACCCTAAAGAAAGGAAGC 58.248 45.455 0.00 0.00 39.15 3.86
2789 2914 2.084546 CACCCTAAAGAAAGGAAGCGG 58.915 52.381 0.00 0.00 39.15 5.52
2791 2916 2.107726 ACCCTAAAGAAAGGAAGCGGTT 59.892 45.455 0.00 0.00 39.15 4.44
2792 2917 3.328637 ACCCTAAAGAAAGGAAGCGGTTA 59.671 43.478 0.00 0.00 39.15 2.85
2793 2918 4.018688 ACCCTAAAGAAAGGAAGCGGTTAT 60.019 41.667 0.00 0.00 39.15 1.89
2794 2919 4.335594 CCCTAAAGAAAGGAAGCGGTTATG 59.664 45.833 0.00 0.00 39.15 1.90
2795 2920 4.941873 CCTAAAGAAAGGAAGCGGTTATGT 59.058 41.667 0.00 0.00 39.15 2.29
2796 2921 6.110707 CCTAAAGAAAGGAAGCGGTTATGTA 58.889 40.000 0.00 0.00 39.15 2.29
2797 2922 6.766467 CCTAAAGAAAGGAAGCGGTTATGTAT 59.234 38.462 0.00 0.00 39.15 2.29
2798 2923 6.679327 AAAGAAAGGAAGCGGTTATGTATC 57.321 37.500 0.00 0.00 0.00 2.24
2799 2924 4.704965 AGAAAGGAAGCGGTTATGTATCC 58.295 43.478 0.00 0.00 0.00 2.59
2800 2925 3.487120 AAGGAAGCGGTTATGTATCCC 57.513 47.619 0.00 0.00 0.00 3.85
2805 2930 3.857157 AGCGGTTATGTATCCCATGTT 57.143 42.857 0.00 0.00 34.86 2.71
2806 2931 3.476552 AGCGGTTATGTATCCCATGTTG 58.523 45.455 0.00 0.00 34.86 3.33
2808 2933 4.101898 AGCGGTTATGTATCCCATGTTGTA 59.898 41.667 0.00 0.00 34.86 2.41
2814 2939 8.157476 GGTTATGTATCCCATGTTGTAAGATCT 58.843 37.037 0.00 0.00 34.86 2.75
2820 2945 6.235231 TCCCATGTTGTAAGATCTAAGGAC 57.765 41.667 0.00 0.00 0.00 3.85
2824 2949 6.405953 CCATGTTGTAAGATCTAAGGACGTCT 60.406 42.308 16.46 0.00 0.00 4.18
2827 2952 4.763073 TGTAAGATCTAAGGACGTCTCGA 58.237 43.478 16.46 7.25 0.00 4.04
2833 2958 2.740981 TCTAAGGACGTCTCGACTCAAC 59.259 50.000 16.46 0.00 0.00 3.18
2842 2967 2.432628 CGACTCAACGGTGCCCTC 60.433 66.667 0.00 0.00 0.00 4.30
2861 2986 1.153289 CCAGCGCTGCTATTGGACT 60.153 57.895 31.96 0.00 36.40 3.85
2863 2988 0.460811 CAGCGCTGCTATTGGACTGA 60.461 55.000 26.68 0.00 36.40 3.41
2880 3005 3.702045 GACTGACACAAGTAGCTCCCTAT 59.298 47.826 0.00 0.00 0.00 2.57
2881 3006 3.449018 ACTGACACAAGTAGCTCCCTATG 59.551 47.826 0.00 0.00 0.00 2.23
2882 3007 3.701542 CTGACACAAGTAGCTCCCTATGA 59.298 47.826 0.00 0.00 0.00 2.15
2883 3008 4.290093 TGACACAAGTAGCTCCCTATGAT 58.710 43.478 0.00 0.00 0.00 2.45
2884 3009 4.716784 TGACACAAGTAGCTCCCTATGATT 59.283 41.667 0.00 0.00 0.00 2.57
2885 3010 5.897250 TGACACAAGTAGCTCCCTATGATTA 59.103 40.000 0.00 0.00 0.00 1.75
2886 3011 6.382859 TGACACAAGTAGCTCCCTATGATTAA 59.617 38.462 0.00 0.00 0.00 1.40
2887 3012 7.093068 TGACACAAGTAGCTCCCTATGATTAAA 60.093 37.037 0.00 0.00 0.00 1.52
2888 3013 7.275920 ACACAAGTAGCTCCCTATGATTAAAG 58.724 38.462 0.00 0.00 0.00 1.85
2889 3014 6.708054 CACAAGTAGCTCCCTATGATTAAAGG 59.292 42.308 0.00 0.00 0.00 3.11
2890 3015 6.615726 ACAAGTAGCTCCCTATGATTAAAGGA 59.384 38.462 0.00 0.00 34.58 3.36
2891 3016 6.926630 AGTAGCTCCCTATGATTAAAGGAG 57.073 41.667 0.00 0.00 45.74 3.69
2892 3017 6.386284 AGTAGCTCCCTATGATTAAAGGAGT 58.614 40.000 6.26 0.00 44.94 3.85
2893 3018 6.847036 AGTAGCTCCCTATGATTAAAGGAGTT 59.153 38.462 6.26 2.91 44.94 3.01
2894 3019 6.582929 AGCTCCCTATGATTAAAGGAGTTT 57.417 37.500 6.26 0.00 44.94 2.66
2895 3020 6.974795 AGCTCCCTATGATTAAAGGAGTTTT 58.025 36.000 6.26 0.00 44.94 2.43
2896 3021 7.057264 AGCTCCCTATGATTAAAGGAGTTTTC 58.943 38.462 6.26 0.00 44.94 2.29
2897 3022 6.263392 GCTCCCTATGATTAAAGGAGTTTTCC 59.737 42.308 6.26 0.00 44.94 3.13
2909 3034 2.480419 GGAGTTTTCCTCATGTGTCACG 59.520 50.000 0.00 0.00 42.40 4.35
2910 3035 1.873591 AGTTTTCCTCATGTGTCACGC 59.126 47.619 0.00 0.00 0.00 5.34
2911 3036 0.865111 TTTTCCTCATGTGTCACGCG 59.135 50.000 3.53 3.53 0.00 6.01
2912 3037 0.948623 TTTCCTCATGTGTCACGCGG 60.949 55.000 12.47 0.00 0.00 6.46
2913 3038 2.048222 CCTCATGTGTCACGCGGT 60.048 61.111 12.47 0.00 0.00 5.68
2914 3039 2.382746 CCTCATGTGTCACGCGGTG 61.383 63.158 12.47 6.71 34.45 4.94
2915 3040 3.015293 CTCATGTGTCACGCGGTGC 62.015 63.158 12.47 0.00 32.98 5.01
2958 3083 4.977126 CGACCTACGCGGCGGATC 62.977 72.222 27.37 12.76 35.61 3.36
2959 3084 3.593794 GACCTACGCGGCGGATCT 61.594 66.667 27.37 7.96 35.61 2.75
2960 3085 3.539560 GACCTACGCGGCGGATCTC 62.540 68.421 27.37 11.42 35.61 2.75
2961 3086 4.344474 CCTACGCGGCGGATCTCC 62.344 72.222 27.37 0.00 0.00 3.71
2962 3087 3.288290 CTACGCGGCGGATCTCCT 61.288 66.667 27.37 5.96 0.00 3.69
2963 3088 3.256716 CTACGCGGCGGATCTCCTC 62.257 68.421 27.37 0.00 0.00 3.71
2984 3109 3.255379 GCCCGCTCGATCACGTTC 61.255 66.667 0.00 0.00 40.69 3.95
2985 3110 2.949678 CCCGCTCGATCACGTTCG 60.950 66.667 3.24 3.24 40.69 3.95
2986 3111 2.099638 CCGCTCGATCACGTTCGA 59.900 61.111 11.51 11.51 45.27 3.71
2987 3112 2.215604 CCGCTCGATCACGTTCGAC 61.216 63.158 8.21 5.49 42.81 4.20
3020 3145 2.430921 CTTCGACACGAGGCGCTT 60.431 61.111 7.64 0.00 37.14 4.68
3021 3146 2.430244 TTCGACACGAGGCGCTTC 60.430 61.111 9.88 9.88 37.14 3.86
3022 3147 4.753877 TCGACACGAGGCGCTTCG 62.754 66.667 36.01 36.01 45.70 3.79
3033 3158 2.815647 CGCTTCGGCTGGTCCTTC 60.816 66.667 0.00 0.00 39.13 3.46
3034 3159 2.665603 GCTTCGGCTGGTCCTTCT 59.334 61.111 0.00 0.00 38.08 2.85
3035 3160 1.448717 GCTTCGGCTGGTCCTTCTC 60.449 63.158 0.00 0.00 38.08 2.87
3036 3161 1.153745 CTTCGGCTGGTCCTTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
3037 3162 1.595993 CTTCGGCTGGTCCTTCTCGA 61.596 60.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.950496 CTATAGACCCATAAACTTGCAATAGAT 57.050 33.333 0.00 0.00 0.00 1.98
2 3 8.934697 ACTATAGACCCATAAACTTGCAATAGA 58.065 33.333 6.78 0.00 0.00 1.98
3 4 9.209175 GACTATAGACCCATAAACTTGCAATAG 57.791 37.037 6.78 0.00 0.00 1.73
4 5 8.154856 GGACTATAGACCCATAAACTTGCAATA 58.845 37.037 6.78 0.00 0.00 1.90
5 6 6.998673 GGACTATAGACCCATAAACTTGCAAT 59.001 38.462 6.78 0.00 0.00 3.56
6 7 6.157994 AGGACTATAGACCCATAAACTTGCAA 59.842 38.462 16.36 0.00 0.00 4.08
7 8 5.665812 AGGACTATAGACCCATAAACTTGCA 59.334 40.000 16.36 0.00 0.00 4.08
8 9 6.042208 AGAGGACTATAGACCCATAAACTTGC 59.958 42.308 16.36 0.00 0.00 4.01
9 10 7.604657 AGAGGACTATAGACCCATAAACTTG 57.395 40.000 16.36 0.00 0.00 3.16
10 11 7.419172 GCAAGAGGACTATAGACCCATAAACTT 60.419 40.741 16.36 10.12 0.00 2.66
11 12 6.042208 GCAAGAGGACTATAGACCCATAAACT 59.958 42.308 16.36 5.58 0.00 2.66
12 13 6.224584 GCAAGAGGACTATAGACCCATAAAC 58.775 44.000 16.36 0.89 0.00 2.01
13 14 5.307196 GGCAAGAGGACTATAGACCCATAAA 59.693 44.000 16.36 0.00 0.00 1.40
14 15 4.838986 GGCAAGAGGACTATAGACCCATAA 59.161 45.833 16.36 0.00 0.00 1.90
15 16 4.108124 AGGCAAGAGGACTATAGACCCATA 59.892 45.833 16.36 0.00 27.39 2.74
16 17 3.116551 AGGCAAGAGGACTATAGACCCAT 60.117 47.826 16.36 4.13 27.39 4.00
17 18 2.247635 AGGCAAGAGGACTATAGACCCA 59.752 50.000 16.36 0.00 27.39 4.51
18 19 2.894765 GAGGCAAGAGGACTATAGACCC 59.105 54.545 16.36 11.64 31.94 4.46
19 20 3.839778 AGAGGCAAGAGGACTATAGACC 58.160 50.000 12.73 12.73 31.94 3.85
20 21 4.890581 TGAAGAGGCAAGAGGACTATAGAC 59.109 45.833 6.78 0.00 31.94 2.59
21 22 5.130705 TGAAGAGGCAAGAGGACTATAGA 57.869 43.478 6.78 0.00 31.94 1.98
22 23 4.892934 ACTGAAGAGGCAAGAGGACTATAG 59.107 45.833 0.00 0.00 31.94 1.31
23 24 4.873010 ACTGAAGAGGCAAGAGGACTATA 58.127 43.478 0.00 0.00 31.94 1.31
24 25 3.718723 ACTGAAGAGGCAAGAGGACTAT 58.281 45.455 0.00 0.00 31.94 2.12
25 26 3.176924 ACTGAAGAGGCAAGAGGACTA 57.823 47.619 0.00 0.00 31.94 2.59
26 27 2.022718 ACTGAAGAGGCAAGAGGACT 57.977 50.000 0.00 0.00 37.85 3.85
27 28 2.849294 AACTGAAGAGGCAAGAGGAC 57.151 50.000 0.00 0.00 0.00 3.85
28 29 6.620877 TTATAAACTGAAGAGGCAAGAGGA 57.379 37.500 0.00 0.00 0.00 3.71
29 30 7.169982 CGTATTATAAACTGAAGAGGCAAGAGG 59.830 40.741 0.00 0.00 0.00 3.69
30 31 7.707035 ACGTATTATAAACTGAAGAGGCAAGAG 59.293 37.037 0.00 0.00 0.00 2.85
31 32 7.553334 ACGTATTATAAACTGAAGAGGCAAGA 58.447 34.615 0.00 0.00 0.00 3.02
32 33 7.772332 ACGTATTATAAACTGAAGAGGCAAG 57.228 36.000 0.00 0.00 0.00 4.01
33 34 7.707893 GGTACGTATTATAAACTGAAGAGGCAA 59.292 37.037 0.00 0.00 0.00 4.52
34 35 7.147863 TGGTACGTATTATAAACTGAAGAGGCA 60.148 37.037 0.00 0.00 0.00 4.75
35 36 7.205297 TGGTACGTATTATAAACTGAAGAGGC 58.795 38.462 0.00 0.00 0.00 4.70
36 37 9.760077 ATTGGTACGTATTATAAACTGAAGAGG 57.240 33.333 0.00 0.00 0.00 3.69
52 53 4.957954 AGTCCCTACATTCATTGGTACGTA 59.042 41.667 0.00 0.00 0.00 3.57
53 54 3.773119 AGTCCCTACATTCATTGGTACGT 59.227 43.478 0.00 0.00 0.00 3.57
54 55 4.402056 AGTCCCTACATTCATTGGTACG 57.598 45.455 0.00 0.00 0.00 3.67
55 56 5.944007 ACAAAGTCCCTACATTCATTGGTAC 59.056 40.000 0.00 0.00 0.00 3.34
56 57 6.134535 ACAAAGTCCCTACATTCATTGGTA 57.865 37.500 0.00 0.00 0.00 3.25
57 58 4.998051 ACAAAGTCCCTACATTCATTGGT 58.002 39.130 0.00 0.00 0.00 3.67
58 59 7.461182 TTTACAAAGTCCCTACATTCATTGG 57.539 36.000 0.00 0.00 0.00 3.16
59 60 8.028938 CCTTTTACAAAGTCCCTACATTCATTG 58.971 37.037 0.00 0.00 0.00 2.82
60 61 7.947890 TCCTTTTACAAAGTCCCTACATTCATT 59.052 33.333 0.00 0.00 0.00 2.57
247 248 5.034200 TCCTAGCTAAAGGATTACCACCAA 58.966 41.667 0.72 0.00 40.86 3.67
356 357 2.037144 AGTTACCTTGTCTCGTGTGGT 58.963 47.619 0.00 0.00 35.05 4.16
467 468 4.010349 ACAGTTTTTGCTAGCCCTCATAC 58.990 43.478 13.29 3.14 0.00 2.39
470 471 2.622942 CAACAGTTTTTGCTAGCCCTCA 59.377 45.455 13.29 0.00 0.00 3.86
500 501 1.662309 CGGCACATCGATCGTACTACC 60.662 57.143 15.94 11.48 0.00 3.18
542 543 2.203437 TAGCTAGCCGGCCATCGA 60.203 61.111 26.15 5.39 42.43 3.59
707 711 4.589908 TCTAATCAACCTTTTGCTCCTCC 58.410 43.478 0.00 0.00 32.17 4.30
722 726 8.454293 GATCGCTCGATTCTTAAATCTAATCA 57.546 34.615 6.22 0.00 39.36 2.57
880 889 4.439123 CGTGCTATCGCTGCATATATACTG 59.561 45.833 0.00 0.00 42.69 2.74
925 934 0.963355 GAGCGAGAGTGAGGTGAGGT 60.963 60.000 0.00 0.00 0.00 3.85
927 936 1.427419 CGAGCGAGAGTGAGGTGAG 59.573 63.158 0.00 0.00 0.00 3.51
928 937 2.691771 GCGAGCGAGAGTGAGGTGA 61.692 63.158 0.00 0.00 0.00 4.02
929 938 2.202544 GCGAGCGAGAGTGAGGTG 60.203 66.667 0.00 0.00 0.00 4.00
930 939 2.360600 AGCGAGCGAGAGTGAGGT 60.361 61.111 0.00 0.00 0.00 3.85
931 940 2.047151 GAGAGCGAGCGAGAGTGAGG 62.047 65.000 0.00 0.00 0.00 3.86
932 941 1.089481 AGAGAGCGAGCGAGAGTGAG 61.089 60.000 0.00 0.00 0.00 3.51
933 942 1.078778 AGAGAGCGAGCGAGAGTGA 60.079 57.895 0.00 0.00 0.00 3.41
934 943 1.089481 AGAGAGAGCGAGCGAGAGTG 61.089 60.000 0.00 0.00 0.00 3.51
935 944 0.810031 GAGAGAGAGCGAGCGAGAGT 60.810 60.000 0.00 0.00 0.00 3.24
936 945 1.498865 GGAGAGAGAGCGAGCGAGAG 61.499 65.000 0.00 0.00 0.00 3.20
937 946 1.522806 GGAGAGAGAGCGAGCGAGA 60.523 63.158 0.00 0.00 0.00 4.04
941 950 1.453015 TCAGGGAGAGAGAGCGAGC 60.453 63.158 0.00 0.00 0.00 5.03
959 978 1.749638 CGAGCTGTAGACTCCCCGT 60.750 63.158 0.00 0.00 0.00 5.28
990 1017 5.132502 CCATACTGCTCCATTCCAACAATA 58.867 41.667 0.00 0.00 0.00 1.90
1010 1050 2.697644 CCTCCCTTCCCCAGCCAT 60.698 66.667 0.00 0.00 0.00 4.40
1101 1141 1.566231 ACAGAATTCCACCTCCCATCC 59.434 52.381 0.65 0.00 0.00 3.51
1156 1210 1.660104 CGCATGCAGCCCAAATTTAAC 59.340 47.619 19.57 0.00 41.38 2.01
1161 1215 1.809207 GTACGCATGCAGCCCAAAT 59.191 52.632 19.57 0.00 41.38 2.32
1198 1252 1.002366 GACATGCAAGCTCGACGAAT 58.998 50.000 0.00 0.00 0.00 3.34
1211 1265 0.721718 AAACGAGCTTAGCGACATGC 59.278 50.000 0.00 0.00 46.98 4.06
1212 1266 2.762472 CAAAACGAGCTTAGCGACATG 58.238 47.619 0.00 0.00 0.00 3.21
1215 1269 0.790814 AGCAAAACGAGCTTAGCGAC 59.209 50.000 0.00 0.00 39.87 5.19
1216 1270 0.790207 CAGCAAAACGAGCTTAGCGA 59.210 50.000 0.00 0.00 41.14 4.93
1321 1415 0.386113 GTATGACGGTCTCCTCCTGC 59.614 60.000 9.88 0.00 0.00 4.85
1332 1426 0.955178 ATGGAGCTCGAGTATGACGG 59.045 55.000 15.13 0.00 0.00 4.79
1445 1553 5.142635 TCGATCATCACAAATTAAGTGCG 57.857 39.130 6.17 4.58 36.93 5.34
1540 1648 1.291877 CCCTTCTTGAAGTGCGTCCG 61.292 60.000 9.21 0.00 0.00 4.79
1728 1836 2.563798 CGGTGCTGGCCATGTTGTT 61.564 57.895 5.51 0.00 0.00 2.83
1788 1896 1.040893 AGTCGTCCATGTCCGCCATA 61.041 55.000 0.00 0.00 30.71 2.74
1806 1914 2.171237 TGGATCATGGTACTGCAGGAAG 59.829 50.000 19.93 0.33 0.00 3.46
1819 1927 1.518515 CGACGTCGACATTGGATCATG 59.481 52.381 33.35 0.00 43.02 3.07
1821 1929 0.179148 CCGACGTCGACATTGGATCA 60.179 55.000 37.65 0.00 43.02 2.92
1822 1930 1.480219 GCCGACGTCGACATTGGATC 61.480 60.000 37.65 11.45 43.02 3.36
1824 1932 2.126228 GCCGACGTCGACATTGGA 60.126 61.111 37.65 0.00 43.02 3.53
1827 1938 1.138247 GTAGGCCGACGTCGACATT 59.862 57.895 37.65 20.76 43.02 2.71
1835 1946 1.726533 GAGGAGGAAGTAGGCCGACG 61.727 65.000 10.60 0.00 0.00 5.12
1887 1998 2.043349 TCGATCTCCCCGCTGGAA 60.043 61.111 0.00 0.00 44.57 3.53
1930 2041 1.111116 AGGTCGTCGAGGTTCCACAA 61.111 55.000 18.28 0.00 0.00 3.33
2132 2246 1.041447 GCTAGTCGAAGTGGGGGCTA 61.041 60.000 0.00 0.00 0.00 3.93
2133 2247 2.359967 GCTAGTCGAAGTGGGGGCT 61.360 63.158 0.00 0.00 0.00 5.19
2160 2278 3.439857 AAAAGGAGCTAGACATGCCAA 57.560 42.857 0.00 0.00 0.00 4.52
2196 2315 7.229308 ACGGAGGGAGTAGTTTATTTTCTTTT 58.771 34.615 0.00 0.00 0.00 2.27
2197 2316 6.776744 ACGGAGGGAGTAGTTTATTTTCTTT 58.223 36.000 0.00 0.00 0.00 2.52
2208 2327 3.947612 TTATGAGACGGAGGGAGTAGT 57.052 47.619 0.00 0.00 0.00 2.73
2209 2328 4.145807 ACATTATGAGACGGAGGGAGTAG 58.854 47.826 0.00 0.00 0.00 2.57
2211 2330 3.033659 ACATTATGAGACGGAGGGAGT 57.966 47.619 0.00 0.00 0.00 3.85
2212 2331 4.827835 TCTTACATTATGAGACGGAGGGAG 59.172 45.833 0.00 0.00 0.00 4.30
2213 2332 4.800023 TCTTACATTATGAGACGGAGGGA 58.200 43.478 0.00 0.00 0.00 4.20
2214 2333 5.473931 CATCTTACATTATGAGACGGAGGG 58.526 45.833 0.00 0.00 0.00 4.30
2215 2334 4.926238 GCATCTTACATTATGAGACGGAGG 59.074 45.833 0.00 0.00 0.00 4.30
2216 2335 5.777802 AGCATCTTACATTATGAGACGGAG 58.222 41.667 0.00 0.00 0.00 4.63
2217 2336 5.791336 AGCATCTTACATTATGAGACGGA 57.209 39.130 0.00 0.00 0.00 4.69
2218 2337 6.851222 AAAGCATCTTACATTATGAGACGG 57.149 37.500 0.00 0.00 0.00 4.79
2262 2381 9.661563 TCCTTCGTTACATAATGTAAGACATTT 57.338 29.630 9.92 0.00 45.80 2.32
2264 2383 9.314321 CTTCCTTCGTTACATAATGTAAGACAT 57.686 33.333 0.00 0.00 42.78 3.06
2265 2384 8.308931 ACTTCCTTCGTTACATAATGTAAGACA 58.691 33.333 0.00 0.00 42.78 3.41
2266 2385 8.699283 ACTTCCTTCGTTACATAATGTAAGAC 57.301 34.615 0.00 0.00 42.78 3.01
2276 2395 8.921205 ACCAGTATAATACTTCCTTCGTTACAT 58.079 33.333 0.00 0.00 36.76 2.29
2277 2396 8.297470 ACCAGTATAATACTTCCTTCGTTACA 57.703 34.615 0.00 0.00 36.76 2.41
2278 2397 9.890352 CTACCAGTATAATACTTCCTTCGTTAC 57.110 37.037 0.00 0.00 36.76 2.50
2279 2398 9.071276 CCTACCAGTATAATACTTCCTTCGTTA 57.929 37.037 0.00 0.00 36.76 3.18
2280 2399 7.562821 ACCTACCAGTATAATACTTCCTTCGTT 59.437 37.037 0.00 0.00 36.76 3.85
2281 2400 7.065504 ACCTACCAGTATAATACTTCCTTCGT 58.934 38.462 0.00 0.00 36.76 3.85
2282 2401 7.521871 ACCTACCAGTATAATACTTCCTTCG 57.478 40.000 0.00 0.00 36.76 3.79
2316 2435 6.048509 GTCCTTTCTTTCATTGCCTTTTCAA 58.951 36.000 0.00 0.00 0.00 2.69
2319 2438 5.453762 CCTGTCCTTTCTTTCATTGCCTTTT 60.454 40.000 0.00 0.00 0.00 2.27
2324 2443 3.319122 ACACCTGTCCTTTCTTTCATTGC 59.681 43.478 0.00 0.00 0.00 3.56
2325 2444 5.067674 TGAACACCTGTCCTTTCTTTCATTG 59.932 40.000 0.00 0.00 0.00 2.82
2330 2452 4.402474 CCTTTGAACACCTGTCCTTTCTTT 59.598 41.667 0.00 0.00 0.00 2.52
2337 2459 0.668535 GCACCTTTGAACACCTGTCC 59.331 55.000 0.00 0.00 0.00 4.02
2339 2461 1.102978 GTGCACCTTTGAACACCTGT 58.897 50.000 5.22 0.00 30.37 4.00
2359 2481 1.263356 ACGTGAGCTAGGTGGCTTAA 58.737 50.000 0.00 0.00 43.20 1.85
2360 2482 2.133281 TACGTGAGCTAGGTGGCTTA 57.867 50.000 0.00 0.00 43.20 3.09
2361 2483 1.486211 ATACGTGAGCTAGGTGGCTT 58.514 50.000 0.00 0.00 43.20 4.35
2367 2489 2.224549 CCGAGAGAATACGTGAGCTAGG 59.775 54.545 0.00 0.00 0.00 3.02
2380 2502 4.676196 GCGGAGTAAATGTAACCGAGAGAA 60.676 45.833 12.25 0.00 45.31 2.87
2385 2507 1.202114 ACGCGGAGTAAATGTAACCGA 59.798 47.619 12.47 0.00 45.31 4.69
2387 2509 2.884827 AGACGCGGAGTAAATGTAACC 58.115 47.619 12.47 0.00 0.00 2.85
2394 2516 4.697352 AGTAGAAGTTAGACGCGGAGTAAA 59.303 41.667 12.47 0.00 0.00 2.01
2397 2519 2.709213 AGTAGAAGTTAGACGCGGAGT 58.291 47.619 12.47 0.00 0.00 3.85
2398 2520 3.002144 GGTAGTAGAAGTTAGACGCGGAG 59.998 52.174 12.47 0.00 0.00 4.63
2399 2521 2.939103 GGTAGTAGAAGTTAGACGCGGA 59.061 50.000 12.47 0.00 0.00 5.54
2400 2522 2.941720 AGGTAGTAGAAGTTAGACGCGG 59.058 50.000 12.47 0.00 0.00 6.46
2402 2524 4.639755 AGGAAGGTAGTAGAAGTTAGACGC 59.360 45.833 0.00 0.00 0.00 5.19
2403 2525 6.756299 AAGGAAGGTAGTAGAAGTTAGACG 57.244 41.667 0.00 0.00 0.00 4.18
2446 2571 8.624028 CGTCTTGTCGGTTAAATTTAAATTGAC 58.376 33.333 14.04 20.63 0.00 3.18
2450 2575 9.518906 AAAACGTCTTGTCGGTTAAATTTAAAT 57.481 25.926 12.14 0.00 39.90 1.40
2529 2654 5.050769 CGGCATAACAAGTACATGAGCTTAG 60.051 44.000 4.87 1.71 0.00 2.18
2532 2657 3.198068 CGGCATAACAAGTACATGAGCT 58.802 45.455 4.87 0.00 0.00 4.09
2534 2659 3.198068 AGCGGCATAACAAGTACATGAG 58.802 45.455 4.87 0.00 0.00 2.90
2545 2670 6.241207 ACATCAAATACATAGCGGCATAAC 57.759 37.500 1.45 0.00 0.00 1.89
2547 2672 7.277760 GTGATACATCAAATACATAGCGGCATA 59.722 37.037 1.45 0.00 38.75 3.14
2548 2673 6.092670 GTGATACATCAAATACATAGCGGCAT 59.907 38.462 1.45 0.00 38.75 4.40
2549 2674 5.408299 GTGATACATCAAATACATAGCGGCA 59.592 40.000 1.45 0.00 38.75 5.69
2550 2675 5.408299 TGTGATACATCAAATACATAGCGGC 59.592 40.000 0.00 0.00 38.75 6.53
2551 2676 7.601073 ATGTGATACATCAAATACATAGCGG 57.399 36.000 0.00 0.00 32.38 5.52
2561 2686 7.181569 TGTCCAGAGTATGTGATACATCAAA 57.818 36.000 0.00 0.00 39.88 2.69
2597 2722 8.836413 AGAACAAAGTCGATTATGACAAAGAAA 58.164 29.630 0.00 0.00 41.41 2.52
2598 2723 8.378172 AGAACAAAGTCGATTATGACAAAGAA 57.622 30.769 0.00 0.00 41.41 2.52
2602 2727 9.653287 AGAATAGAACAAAGTCGATTATGACAA 57.347 29.630 0.00 0.00 41.41 3.18
2629 2754 5.560724 AGGCAGTGTAAAGTATGATGTGTT 58.439 37.500 0.00 0.00 0.00 3.32
2633 2758 6.500684 AACAAGGCAGTGTAAAGTATGATG 57.499 37.500 0.00 0.00 0.00 3.07
2639 2764 2.612212 CACGAACAAGGCAGTGTAAAGT 59.388 45.455 0.00 0.00 0.00 2.66
2640 2765 2.602217 GCACGAACAAGGCAGTGTAAAG 60.602 50.000 0.00 0.00 36.99 1.85
2661 2786 8.394877 TGGCACGAATAACAAAAATAGATACTG 58.605 33.333 0.00 0.00 0.00 2.74
2662 2787 8.500753 TGGCACGAATAACAAAAATAGATACT 57.499 30.769 0.00 0.00 0.00 2.12
2663 2788 9.169468 CATGGCACGAATAACAAAAATAGATAC 57.831 33.333 0.00 0.00 0.00 2.24
2707 2832 2.240493 AGGACTGAACGGACACAAAG 57.760 50.000 0.00 0.00 0.00 2.77
2710 2835 2.557317 GAAAAGGACTGAACGGACACA 58.443 47.619 0.00 0.00 0.00 3.72
2715 2840 2.271944 AAGGGAAAAGGACTGAACGG 57.728 50.000 0.00 0.00 0.00 4.44
2721 2846 4.663334 AGCGAAATAAAGGGAAAAGGACT 58.337 39.130 0.00 0.00 0.00 3.85
2730 2855 4.097892 AGCCATACAAAGCGAAATAAAGGG 59.902 41.667 0.00 0.00 0.00 3.95
2731 2856 5.066505 AGAGCCATACAAAGCGAAATAAAGG 59.933 40.000 0.00 0.00 0.00 3.11
2732 2857 6.124088 AGAGCCATACAAAGCGAAATAAAG 57.876 37.500 0.00 0.00 0.00 1.85
2733 2858 7.715249 AGATAGAGCCATACAAAGCGAAATAAA 59.285 33.333 0.00 0.00 0.00 1.40
2736 2861 5.615289 AGATAGAGCCATACAAAGCGAAAT 58.385 37.500 0.00 0.00 0.00 2.17
2737 2862 5.023533 AGATAGAGCCATACAAAGCGAAA 57.976 39.130 0.00 0.00 0.00 3.46
2740 2865 8.194104 AGAATATAGATAGAGCCATACAAAGCG 58.806 37.037 0.00 0.00 0.00 4.68
2741 2866 9.528018 GAGAATATAGATAGAGCCATACAAAGC 57.472 37.037 0.00 0.00 0.00 3.51
2746 2871 8.410141 GGTGTGAGAATATAGATAGAGCCATAC 58.590 40.741 0.00 0.00 0.00 2.39
2767 2892 2.484264 CGCTTCCTTTCTTTAGGGTGTG 59.516 50.000 0.00 0.00 35.90 3.82
2768 2893 2.552373 CCGCTTCCTTTCTTTAGGGTGT 60.552 50.000 0.00 0.00 35.90 4.16
2769 2894 2.084546 CCGCTTCCTTTCTTTAGGGTG 58.915 52.381 0.00 0.00 35.90 4.61
2785 2910 3.118038 ACAACATGGGATACATAACCGCT 60.118 43.478 0.00 0.00 37.84 5.52
2786 2911 3.211045 ACAACATGGGATACATAACCGC 58.789 45.455 0.00 0.00 37.84 5.68
2787 2912 6.285224 TCTTACAACATGGGATACATAACCG 58.715 40.000 0.00 0.00 37.84 4.44
2792 2917 8.378565 CCTTAGATCTTACAACATGGGATACAT 58.621 37.037 0.00 0.00 41.57 2.29
2793 2918 7.567250 TCCTTAGATCTTACAACATGGGATACA 59.433 37.037 0.00 0.00 39.74 2.29
2794 2919 7.873505 GTCCTTAGATCTTACAACATGGGATAC 59.126 40.741 0.00 0.00 0.00 2.24
2795 2920 7.255836 CGTCCTTAGATCTTACAACATGGGATA 60.256 40.741 0.00 0.00 0.00 2.59
2796 2921 6.463049 CGTCCTTAGATCTTACAACATGGGAT 60.463 42.308 0.00 0.00 0.00 3.85
2797 2922 5.163447 CGTCCTTAGATCTTACAACATGGGA 60.163 44.000 0.00 0.00 0.00 4.37
2798 2923 5.050490 CGTCCTTAGATCTTACAACATGGG 58.950 45.833 0.00 0.00 0.00 4.00
2799 2924 5.661458 ACGTCCTTAGATCTTACAACATGG 58.339 41.667 0.00 0.00 0.00 3.66
2800 2925 6.565234 AGACGTCCTTAGATCTTACAACATG 58.435 40.000 13.01 0.00 0.00 3.21
2805 2930 4.569966 GTCGAGACGTCCTTAGATCTTACA 59.430 45.833 13.01 0.00 0.00 2.41
2806 2931 4.810491 AGTCGAGACGTCCTTAGATCTTAC 59.190 45.833 13.01 3.63 36.20 2.34
2808 2933 3.872771 GAGTCGAGACGTCCTTAGATCTT 59.127 47.826 13.01 0.00 36.20 2.40
2814 2939 1.462283 CGTTGAGTCGAGACGTCCTTA 59.538 52.381 13.01 0.00 36.20 2.69
2820 2945 2.081212 GCACCGTTGAGTCGAGACG 61.081 63.158 6.55 6.55 36.20 4.18
2842 2967 2.182842 GTCCAATAGCAGCGCTGGG 61.183 63.158 36.47 27.69 40.10 4.45
2861 2986 3.708451 TCATAGGGAGCTACTTGTGTCA 58.292 45.455 4.69 0.00 0.00 3.58
2863 2988 6.808321 TTAATCATAGGGAGCTACTTGTGT 57.192 37.500 4.69 0.00 0.00 3.72
2880 3005 7.004086 ACACATGAGGAAAACTCCTTTAATCA 58.996 34.615 0.00 0.00 46.01 2.57
2881 3006 7.174946 TGACACATGAGGAAAACTCCTTTAATC 59.825 37.037 0.00 0.00 46.01 1.75
2882 3007 7.004086 TGACACATGAGGAAAACTCCTTTAAT 58.996 34.615 0.00 0.00 46.01 1.40
2883 3008 6.262273 GTGACACATGAGGAAAACTCCTTTAA 59.738 38.462 0.00 0.00 46.01 1.52
2884 3009 5.763204 GTGACACATGAGGAAAACTCCTTTA 59.237 40.000 0.00 0.00 46.01 1.85
2885 3010 4.580580 GTGACACATGAGGAAAACTCCTTT 59.419 41.667 0.00 0.00 46.01 3.11
2886 3011 4.137543 GTGACACATGAGGAAAACTCCTT 58.862 43.478 0.00 0.00 46.01 3.36
2887 3012 3.744660 GTGACACATGAGGAAAACTCCT 58.255 45.455 0.00 0.00 46.01 3.69
2888 3013 2.480419 CGTGACACATGAGGAAAACTCC 59.520 50.000 6.37 0.00 46.01 3.85
2889 3014 2.096218 GCGTGACACATGAGGAAAACTC 60.096 50.000 6.37 0.00 46.78 3.01
2890 3015 1.873591 GCGTGACACATGAGGAAAACT 59.126 47.619 6.37 0.00 0.00 2.66
2891 3016 1.398451 CGCGTGACACATGAGGAAAAC 60.398 52.381 6.37 0.00 0.00 2.43
2892 3017 0.865111 CGCGTGACACATGAGGAAAA 59.135 50.000 6.37 0.00 0.00 2.29
2893 3018 0.948623 CCGCGTGACACATGAGGAAA 60.949 55.000 4.92 0.00 41.72 3.13
2894 3019 1.374125 CCGCGTGACACATGAGGAA 60.374 57.895 4.92 0.00 41.72 3.36
2895 3020 2.261361 CCGCGTGACACATGAGGA 59.739 61.111 4.92 0.00 41.72 3.71
2896 3021 2.048222 ACCGCGTGACACATGAGG 60.048 61.111 4.92 11.08 44.08 3.86
2897 3022 3.015293 GCACCGCGTGACACATGAG 62.015 63.158 4.92 0.00 35.23 2.90
2898 3023 3.041351 GCACCGCGTGACACATGA 61.041 61.111 4.92 0.00 35.23 3.07
2941 3066 4.977126 GATCCGCCGCGTAGGTCG 62.977 72.222 12.58 6.09 43.70 4.79
2942 3067 3.539560 GAGATCCGCCGCGTAGGTC 62.540 68.421 12.58 3.01 43.70 3.85
2943 3068 3.593794 GAGATCCGCCGCGTAGGT 61.594 66.667 12.58 0.00 43.70 3.08
2944 3069 4.344474 GGAGATCCGCCGCGTAGG 62.344 72.222 12.58 8.20 44.97 3.18
2945 3070 3.256716 GAGGAGATCCGCCGCGTAG 62.257 68.421 12.58 0.00 42.08 3.51
2946 3071 3.285215 GAGGAGATCCGCCGCGTA 61.285 66.667 12.58 0.00 42.08 4.42
2967 3092 3.255379 GAACGTGATCGAGCGGGC 61.255 66.667 10.67 0.00 40.62 6.13
2968 3093 2.949678 CGAACGTGATCGAGCGGG 60.950 66.667 3.56 1.06 45.48 6.13
2969 3094 2.099638 TCGAACGTGATCGAGCGG 59.900 61.111 8.21 1.40 46.12 5.52
3000 3125 3.470567 CGCCTCGTGTCGAAGCAC 61.471 66.667 12.06 0.00 42.55 4.40
3003 3128 2.430921 AAGCGCCTCGTGTCGAAG 60.431 61.111 2.29 0.00 34.74 3.79
3004 3129 2.430244 GAAGCGCCTCGTGTCGAA 60.430 61.111 2.29 0.00 34.74 3.71
3005 3130 4.753877 CGAAGCGCCTCGTGTCGA 62.754 66.667 19.97 0.00 37.42 4.20
3016 3141 2.815647 GAAGGACCAGCCGAAGCG 60.816 66.667 0.00 0.00 46.67 4.68
3017 3142 1.448717 GAGAAGGACCAGCCGAAGC 60.449 63.158 0.00 0.00 43.43 3.86
3018 3143 1.153745 CGAGAAGGACCAGCCGAAG 60.154 63.158 0.00 0.00 43.43 3.79
3019 3144 1.605451 TCGAGAAGGACCAGCCGAA 60.605 57.895 0.00 0.00 43.43 4.30
3020 3145 2.035155 TCGAGAAGGACCAGCCGA 59.965 61.111 0.00 0.00 43.43 5.54


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

AutoCloner maintained by Alex Coulton.