Multiple sequence alignment - TraesCS6D01G212800

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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 TraesCS6D01G212800 chr6D 100.000 2522 0 0 1 2522 301806197 301803676 0.000000e+00 4658.0
1 TraesCS6D01G212800 chr6D 95.257 253 12 0 2245 2497 301789134 301788882 3.910000e-108 401.0
2 TraesCS6D01G212800 chr6D 87.259 259 25 7 2245 2497 227462252 227461996 3.170000e-74 289.0
3 TraesCS6D01G212800 chr6B 92.834 1856 83 11 362 2199 466966526 466968349 0.000000e+00 2645.0
4 TraesCS6D01G212800 chr6B 90.078 383 18 14 1 373 466966085 466966457 1.750000e-131 479.0
5 TraesCS6D01G212800 chr6A 93.746 1647 60 14 1 1618 415097265 415098897 0.000000e+00 2431.0
6 TraesCS6D01G212800 chr6A 93.289 596 26 6 1616 2199 415098939 415099532 0.000000e+00 867.0
7 TraesCS6D01G212800 chr6A 82.639 144 10 2 1955 2096 607391733 607391863 2.050000e-21 113.0
8 TraesCS6D01G212800 chr5D 89.575 259 24 2 2242 2497 80652828 80653086 2.420000e-85 326.0
9 TraesCS6D01G212800 chr5D 89.453 256 24 2 2245 2497 80665886 80666141 1.130000e-83 320.0
10 TraesCS6D01G212800 chr5D 100.000 30 0 0 2493 2522 297886554 297886525 3.500000e-04 56.5
11 TraesCS6D01G212800 chr4D 93.519 216 10 2 1885 2096 307813148 307813363 4.050000e-83 318.0
12 TraesCS6D01G212800 chr4D 100.000 28 0 0 2495 2522 112289730 112289703 5.000000e-03 52.8
13 TraesCS6D01G212800 chr7D 89.286 252 24 2 2245 2494 458420935 458420685 1.880000e-81 313.0
14 TraesCS6D01G212800 chr7D 88.492 252 27 1 2245 2494 458495985 458495734 1.130000e-78 303.0
15 TraesCS6D01G212800 chr7D 86.111 252 31 2 2245 2493 627523017 627523267 4.140000e-68 268.0
16 TraesCS6D01G212800 chr3D 86.822 258 27 4 2245 2497 313947659 313947404 5.310000e-72 281.0
17 TraesCS6D01G212800 chr2D 85.938 256 28 6 2245 2494 283172727 283172980 1.490000e-67 267.0
18 TraesCS6D01G212800 chr2A 90.303 165 12 2 1936 2096 12176265 12176429 1.970000e-51 213.0
19 TraesCS6D01G212800 chr3B 87.273 165 15 3 1936 2096 450356863 450356701 1.540000e-42 183.0


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 TraesCS6D01G212800 chr6D 301803676 301806197 2521 True 4658 4658 100.0000 1 2522 1 chr6D.!!$R3 2521
1 TraesCS6D01G212800 chr6B 466966085 466968349 2264 False 1562 2645 91.4560 1 2199 2 chr6B.!!$F1 2198
2 TraesCS6D01G212800 chr6A 415097265 415099532 2267 False 1649 2431 93.5175 1 2199 2 chr6A.!!$F2 2198

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
146 168 0.670239 TGCGCGGCATCGATTGATAT 60.670 50.0 8.83 0.0 39.00 1.63 F
303 333 0.741326 ACGTCTATGTGCATCTCGCT 59.259 50.0 0.00 0.0 43.06 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1230 0.179220 CTGACTCGTCGAACTCGTCC 60.179 60.0 9.17 0.0 40.8 4.79 R
2260 2476 0.034477 CTGGGCGGGTTAACTCCAAT 60.034 55.0 5.42 0.0 0.0 3.16 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
144 166 2.588596 TGCGCGGCATCGATTGAT 60.589 55.556 8.83 0.00 39.00 2.57
145 167 1.300542 TGCGCGGCATCGATTGATA 60.301 52.632 8.83 0.00 39.00 2.15
146 168 0.670239 TGCGCGGCATCGATTGATAT 60.670 50.000 8.83 0.00 39.00 1.63
147 169 1.277326 GCGCGGCATCGATTGATATA 58.723 50.000 8.83 0.00 39.00 0.86
148 170 1.860950 GCGCGGCATCGATTGATATAT 59.139 47.619 8.83 0.00 39.00 0.86
149 171 2.347939 GCGCGGCATCGATTGATATATG 60.348 50.000 8.83 0.00 39.00 1.78
152 174 3.492383 GCGGCATCGATTGATATATGGAG 59.508 47.826 0.00 0.00 39.00 3.86
195 225 1.471119 CTGGAGCATCAATTGTGGCT 58.529 50.000 20.95 20.95 39.75 4.75
213 243 4.034048 GTGGCTGACATTCATTACTAACGG 59.966 45.833 0.00 0.00 0.00 4.44
303 333 0.741326 ACGTCTATGTGCATCTCGCT 59.259 50.000 0.00 0.00 43.06 4.93
364 395 5.051907 CGGATGTTACTAACACGTATGCTTC 60.052 44.000 3.67 0.00 45.50 3.86
385 497 4.894784 TCTGTAAAGATGTCAACCAGGAC 58.105 43.478 0.00 0.00 38.29 3.85
450 562 6.583806 GGAGATTGAACAAACACTTGCTATTG 59.416 38.462 0.00 0.00 35.84 1.90
478 590 2.892852 CCCTGAGAGCCAGATTAGAGAG 59.107 54.545 0.00 0.00 45.78 3.20
482 594 3.384146 TGAGAGCCAGATTAGAGAGCAAG 59.616 47.826 0.00 0.00 0.00 4.01
741 858 3.129462 CGGAGATATCATCCACGTAGCAT 59.871 47.826 16.59 0.00 36.57 3.79
813 930 1.518133 CTCCGCTTTCTGCTCTCGG 60.518 63.158 0.00 0.00 41.30 4.63
947 1064 4.324991 ACGTTTCCCCTCACCGCC 62.325 66.667 0.00 0.00 0.00 6.13
1143 1260 1.972223 CGAGTCAGACGTCTGGGGT 60.972 63.158 37.82 25.21 43.91 4.95
1249 1366 2.291043 GGGAGGAAGACCAAGCCGA 61.291 63.158 0.00 0.00 38.94 5.54
1661 1830 0.462225 CGGCGTAGAGAGAGGAGTGA 60.462 60.000 0.00 0.00 0.00 3.41
1698 1867 5.264060 TCATTGTTCTTCGATTGTTCGTC 57.736 39.130 0.00 0.00 45.65 4.20
1735 1924 1.878522 CCGGAGAGAACGCGGAATG 60.879 63.158 12.47 0.00 0.00 2.67
1739 1928 1.804748 GGAGAGAACGCGGAATGTTTT 59.195 47.619 12.47 0.00 0.00 2.43
1740 1929 2.159693 GGAGAGAACGCGGAATGTTTTC 60.160 50.000 12.47 2.78 32.32 2.29
1741 1930 2.737252 GAGAGAACGCGGAATGTTTTCT 59.263 45.455 12.47 8.46 41.74 2.52
1742 1931 2.480419 AGAGAACGCGGAATGTTTTCTG 59.520 45.455 12.47 0.00 38.78 3.02
1743 1932 2.478894 GAGAACGCGGAATGTTTTCTGA 59.521 45.455 12.47 0.00 40.14 3.27
1744 1933 3.074412 AGAACGCGGAATGTTTTCTGAT 58.926 40.909 12.47 0.00 40.14 2.90
1745 1934 3.125316 AGAACGCGGAATGTTTTCTGATC 59.875 43.478 12.47 0.00 40.14 2.92
1746 1935 1.737793 ACGCGGAATGTTTTCTGATCC 59.262 47.619 12.47 0.00 40.14 3.36
1747 1936 2.009774 CGCGGAATGTTTTCTGATCCT 58.990 47.619 0.00 0.00 40.14 3.24
1748 1937 2.223112 CGCGGAATGTTTTCTGATCCTG 60.223 50.000 0.00 0.00 40.14 3.86
1749 1938 2.478539 GCGGAATGTTTTCTGATCCTGC 60.479 50.000 0.00 0.00 40.14 4.85
1750 1939 2.223112 CGGAATGTTTTCTGATCCTGCG 60.223 50.000 0.00 0.00 40.14 5.18
1751 1940 2.478539 GGAATGTTTTCTGATCCTGCGC 60.479 50.000 0.00 0.00 32.16 6.09
1752 1941 1.825090 ATGTTTTCTGATCCTGCGCA 58.175 45.000 10.98 10.98 0.00 6.09
1753 1942 1.603456 TGTTTTCTGATCCTGCGCAA 58.397 45.000 13.05 0.00 0.00 4.85
1754 1943 2.161855 TGTTTTCTGATCCTGCGCAAT 58.838 42.857 13.05 1.92 0.00 3.56
1755 1944 2.557924 TGTTTTCTGATCCTGCGCAATT 59.442 40.909 13.05 0.00 0.00 2.32
1756 1945 3.005684 TGTTTTCTGATCCTGCGCAATTT 59.994 39.130 13.05 0.00 0.00 1.82
1757 1946 3.940209 TTTCTGATCCTGCGCAATTTT 57.060 38.095 13.05 0.00 0.00 1.82
1758 1947 3.940209 TTCTGATCCTGCGCAATTTTT 57.060 38.095 13.05 0.00 0.00 1.94
1881 2084 4.079970 TCGAGAGTGTTGTCCTTATCTGT 58.920 43.478 0.00 0.00 0.00 3.41
2026 2237 1.681538 TACGCTGGCCAAAAAGTCAA 58.318 45.000 7.01 0.00 0.00 3.18
2177 2390 1.167781 CGGGGCCACGTACAAAACTT 61.168 55.000 22.33 0.00 0.00 2.66
2208 2424 5.756195 AAAACCAAAGTAAGTAACGGTCC 57.244 39.130 0.00 0.00 0.00 4.46
2209 2425 4.694760 AACCAAAGTAAGTAACGGTCCT 57.305 40.909 0.00 0.00 0.00 3.85
2210 2426 3.999046 ACCAAAGTAAGTAACGGTCCTG 58.001 45.455 0.00 0.00 0.00 3.86
2211 2427 3.642848 ACCAAAGTAAGTAACGGTCCTGA 59.357 43.478 0.00 0.00 0.00 3.86
2212 2428 4.243270 CCAAAGTAAGTAACGGTCCTGAG 58.757 47.826 0.00 0.00 0.00 3.35
2213 2429 4.021719 CCAAAGTAAGTAACGGTCCTGAGA 60.022 45.833 0.00 0.00 0.00 3.27
2214 2430 5.162075 CAAAGTAAGTAACGGTCCTGAGAG 58.838 45.833 0.00 0.00 0.00 3.20
2215 2431 2.754002 AGTAAGTAACGGTCCTGAGAGC 59.246 50.000 0.00 0.00 37.15 4.09
2216 2432 1.629043 AAGTAACGGTCCTGAGAGCA 58.371 50.000 0.00 0.00 40.69 4.26
2217 2433 1.629043 AGTAACGGTCCTGAGAGCAA 58.371 50.000 0.00 0.00 40.69 3.91
2218 2434 1.272769 AGTAACGGTCCTGAGAGCAAC 59.727 52.381 0.00 0.00 40.69 4.17
2219 2435 1.272769 GTAACGGTCCTGAGAGCAACT 59.727 52.381 0.00 0.00 40.69 3.16
2220 2436 0.318762 AACGGTCCTGAGAGCAACTC 59.681 55.000 4.35 4.35 45.11 3.01
2221 2437 1.216710 CGGTCCTGAGAGCAACTCC 59.783 63.158 8.13 0.00 44.34 3.85
2222 2438 1.536073 CGGTCCTGAGAGCAACTCCA 61.536 60.000 8.13 0.00 44.34 3.86
2223 2439 0.687354 GGTCCTGAGAGCAACTCCAA 59.313 55.000 8.13 0.00 44.34 3.53
2224 2440 1.609320 GGTCCTGAGAGCAACTCCAAC 60.609 57.143 8.13 4.52 44.34 3.77
2225 2441 0.318441 TCCTGAGAGCAACTCCAACG 59.682 55.000 8.13 0.00 44.34 4.10
2226 2442 0.671781 CCTGAGAGCAACTCCAACGG 60.672 60.000 8.13 1.69 44.34 4.44
2227 2443 0.671781 CTGAGAGCAACTCCAACGGG 60.672 60.000 8.13 0.00 44.34 5.28
2228 2444 1.376037 GAGAGCAACTCCAACGGGG 60.376 63.158 0.33 0.00 39.53 5.73
2229 2445 3.056328 GAGCAACTCCAACGGGGC 61.056 66.667 0.00 0.00 36.21 5.80
2232 2448 2.046314 CAACTCCAACGGGGCGAT 60.046 61.111 0.00 0.00 36.21 4.58
2233 2449 2.106683 CAACTCCAACGGGGCGATC 61.107 63.158 0.00 0.00 36.21 3.69
2234 2450 2.291043 AACTCCAACGGGGCGATCT 61.291 57.895 0.00 0.00 36.21 2.75
2235 2451 0.974010 AACTCCAACGGGGCGATCTA 60.974 55.000 0.00 0.00 36.21 1.98
2236 2452 0.759436 ACTCCAACGGGGCGATCTAT 60.759 55.000 0.00 0.00 36.21 1.98
2237 2453 0.393077 CTCCAACGGGGCGATCTATT 59.607 55.000 0.00 0.00 36.21 1.73
2238 2454 0.391597 TCCAACGGGGCGATCTATTC 59.608 55.000 0.00 0.00 36.21 1.75
2239 2455 0.602905 CCAACGGGGCGATCTATTCC 60.603 60.000 0.00 0.00 0.00 3.01
2240 2456 0.944311 CAACGGGGCGATCTATTCCG 60.944 60.000 10.59 10.59 45.42 4.30
2241 2457 3.048602 CGGGGCGATCTATTCCGT 58.951 61.111 0.00 0.00 36.38 4.69
2242 2458 1.080705 CGGGGCGATCTATTCCGTC 60.081 63.158 0.00 0.00 36.38 4.79
2243 2459 4.990288 GGGCGATCTATTCCGTCC 57.010 61.111 0.00 0.00 43.55 4.79
2244 2460 2.352817 GGGCGATCTATTCCGTCCT 58.647 57.895 0.00 0.00 46.10 3.85
2245 2461 0.038159 GGGCGATCTATTCCGTCCTG 60.038 60.000 0.00 0.00 46.10 3.86
2246 2462 0.674534 GGCGATCTATTCCGTCCTGT 59.325 55.000 0.00 0.00 0.00 4.00
2247 2463 1.068741 GGCGATCTATTCCGTCCTGTT 59.931 52.381 0.00 0.00 0.00 3.16
2248 2464 2.295349 GGCGATCTATTCCGTCCTGTTA 59.705 50.000 0.00 0.00 0.00 2.41
2249 2465 3.566523 GCGATCTATTCCGTCCTGTTAG 58.433 50.000 0.00 0.00 0.00 2.34
2250 2466 3.612004 GCGATCTATTCCGTCCTGTTAGG 60.612 52.174 0.00 0.00 36.46 2.69
2251 2467 3.057456 CGATCTATTCCGTCCTGTTAGGG 60.057 52.174 0.00 0.00 35.59 3.53
2252 2468 3.675348 TCTATTCCGTCCTGTTAGGGA 57.325 47.619 0.00 0.00 35.59 4.20
2253 2469 4.194678 TCTATTCCGTCCTGTTAGGGAT 57.805 45.455 0.00 0.00 37.73 3.85
2254 2470 5.329191 TCTATTCCGTCCTGTTAGGGATA 57.671 43.478 0.00 0.00 37.73 2.59
2255 2471 5.900437 TCTATTCCGTCCTGTTAGGGATAT 58.100 41.667 0.00 0.00 37.73 1.63
2256 2472 7.036154 TCTATTCCGTCCTGTTAGGGATATA 57.964 40.000 0.00 0.00 37.73 0.86
2257 2473 7.472741 TCTATTCCGTCCTGTTAGGGATATAA 58.527 38.462 0.00 0.00 37.73 0.98
2258 2474 5.796424 TTCCGTCCTGTTAGGGATATAAC 57.204 43.478 0.00 0.00 37.73 1.89
2259 2475 5.070823 TCCGTCCTGTTAGGGATATAACT 57.929 43.478 0.00 0.00 37.73 2.24
2260 2476 6.204852 TCCGTCCTGTTAGGGATATAACTA 57.795 41.667 0.00 0.00 37.73 2.24
2261 2477 6.797707 TCCGTCCTGTTAGGGATATAACTAT 58.202 40.000 0.00 0.00 37.73 2.12
2262 2478 7.243824 TCCGTCCTGTTAGGGATATAACTATT 58.756 38.462 0.00 0.00 37.73 1.73
2263 2479 7.177921 TCCGTCCTGTTAGGGATATAACTATTG 59.822 40.741 0.00 0.00 37.73 1.90
2264 2480 7.321153 CGTCCTGTTAGGGATATAACTATTGG 58.679 42.308 0.00 0.00 37.73 3.16
2265 2481 7.177921 CGTCCTGTTAGGGATATAACTATTGGA 59.822 40.741 0.00 0.00 37.73 3.53
2266 2482 8.532819 GTCCTGTTAGGGATATAACTATTGGAG 58.467 40.741 0.00 0.00 37.73 3.86
2267 2483 8.239478 TCCTGTTAGGGATATAACTATTGGAGT 58.761 37.037 0.00 0.00 36.42 3.85
2276 2492 2.704464 ACTATTGGAGTTAACCCGCC 57.296 50.000 0.88 2.44 33.13 6.13
2277 2493 1.211212 ACTATTGGAGTTAACCCGCCC 59.789 52.381 0.88 0.00 33.13 6.13
2278 2494 1.210967 CTATTGGAGTTAACCCGCCCA 59.789 52.381 0.88 2.44 0.00 5.36
2279 2495 0.034477 ATTGGAGTTAACCCGCCCAG 60.034 55.000 0.88 0.00 0.00 4.45
2280 2496 1.128809 TTGGAGTTAACCCGCCCAGA 61.129 55.000 0.88 0.00 0.00 3.86
2281 2497 1.128809 TGGAGTTAACCCGCCCAGAA 61.129 55.000 0.88 0.00 0.00 3.02
2282 2498 0.392595 GGAGTTAACCCGCCCAGAAG 60.393 60.000 0.88 0.00 0.00 2.85
2283 2499 0.392595 GAGTTAACCCGCCCAGAAGG 60.393 60.000 0.88 0.00 39.47 3.46
2293 2509 2.933834 CCAGAAGGGGGTCGGGTT 60.934 66.667 0.00 0.00 0.00 4.11
2294 2510 1.614226 CCAGAAGGGGGTCGGGTTA 60.614 63.158 0.00 0.00 0.00 2.85
2295 2511 1.202769 CCAGAAGGGGGTCGGGTTAA 61.203 60.000 0.00 0.00 0.00 2.01
2296 2512 0.252197 CAGAAGGGGGTCGGGTTAAG 59.748 60.000 0.00 0.00 0.00 1.85
2297 2513 1.077930 GAAGGGGGTCGGGTTAAGC 60.078 63.158 0.00 0.00 0.00 3.09
2298 2514 2.547640 GAAGGGGGTCGGGTTAAGCC 62.548 65.000 13.92 13.92 0.00 4.35
2313 2529 3.688086 GCCCATGGCGGTTTAACA 58.312 55.556 6.09 0.00 39.62 2.41
2314 2530 1.968310 GCCCATGGCGGTTTAACAA 59.032 52.632 6.09 0.00 39.62 2.83
2315 2531 0.108851 GCCCATGGCGGTTTAACAAG 60.109 55.000 6.09 0.00 39.62 3.16
2316 2532 0.530288 CCCATGGCGGTTTAACAAGG 59.470 55.000 6.09 0.00 0.00 3.61
2317 2533 0.108851 CCATGGCGGTTTAACAAGGC 60.109 55.000 0.00 8.79 0.00 4.35
2318 2534 0.600557 CATGGCGGTTTAACAAGGCA 59.399 50.000 17.47 17.47 43.15 4.75
2319 2535 1.000283 CATGGCGGTTTAACAAGGCAA 60.000 47.619 18.57 4.34 42.30 4.52
2320 2536 1.112113 TGGCGGTTTAACAAGGCAAA 58.888 45.000 14.18 0.00 36.23 3.68
2321 2537 1.480954 TGGCGGTTTAACAAGGCAAAA 59.519 42.857 14.18 0.00 36.23 2.44
2322 2538 1.862201 GGCGGTTTAACAAGGCAAAAC 59.138 47.619 10.34 0.00 33.37 2.43
2323 2539 2.482316 GGCGGTTTAACAAGGCAAAACT 60.482 45.455 10.34 0.00 34.34 2.66
2324 2540 2.792674 GCGGTTTAACAAGGCAAAACTC 59.207 45.455 0.00 0.00 34.34 3.01
2325 2541 3.735514 GCGGTTTAACAAGGCAAAACTCA 60.736 43.478 0.00 0.00 34.34 3.41
2326 2542 4.041723 CGGTTTAACAAGGCAAAACTCAG 58.958 43.478 0.00 0.00 34.34 3.35
2327 2543 4.368315 GGTTTAACAAGGCAAAACTCAGG 58.632 43.478 0.00 0.00 34.34 3.86
2328 2544 4.098807 GGTTTAACAAGGCAAAACTCAGGA 59.901 41.667 0.00 0.00 34.34 3.86
2329 2545 5.281727 GTTTAACAAGGCAAAACTCAGGAG 58.718 41.667 0.00 0.00 31.83 3.69
2330 2546 1.986882 ACAAGGCAAAACTCAGGAGG 58.013 50.000 0.83 0.00 0.00 4.30
2331 2547 1.494721 ACAAGGCAAAACTCAGGAGGA 59.505 47.619 0.83 0.00 0.00 3.71
2332 2548 2.108952 ACAAGGCAAAACTCAGGAGGAT 59.891 45.455 0.83 0.00 0.00 3.24
2333 2549 2.490903 CAAGGCAAAACTCAGGAGGATG 59.509 50.000 0.83 0.00 0.00 3.51
2334 2550 0.813821 GGCAAAACTCAGGAGGATGC 59.186 55.000 12.07 12.07 35.83 3.91
2335 2551 1.615384 GGCAAAACTCAGGAGGATGCT 60.615 52.381 16.94 0.00 37.06 3.79
2346 2562 3.883669 AGGAGGATGCTGAAGACAATTC 58.116 45.455 0.00 0.00 32.93 2.17
2347 2563 3.265221 AGGAGGATGCTGAAGACAATTCA 59.735 43.478 0.00 0.00 32.93 2.57
2348 2564 3.376546 GGAGGATGCTGAAGACAATTCAC 59.623 47.826 0.00 0.00 0.00 3.18
2349 2565 4.260170 GAGGATGCTGAAGACAATTCACT 58.740 43.478 0.00 0.00 0.00 3.41
2350 2566 4.008330 AGGATGCTGAAGACAATTCACTG 58.992 43.478 0.00 0.00 0.00 3.66
2351 2567 3.427233 GGATGCTGAAGACAATTCACTGC 60.427 47.826 0.00 0.00 0.00 4.40
2352 2568 2.574450 TGCTGAAGACAATTCACTGCA 58.426 42.857 0.00 0.00 35.05 4.41
2353 2569 2.291465 TGCTGAAGACAATTCACTGCAC 59.709 45.455 0.00 0.00 33.73 4.57
2354 2570 2.291465 GCTGAAGACAATTCACTGCACA 59.709 45.455 0.00 0.00 0.00 4.57
2355 2571 3.057736 GCTGAAGACAATTCACTGCACAT 60.058 43.478 0.00 0.00 0.00 3.21
2356 2572 4.558095 GCTGAAGACAATTCACTGCACATT 60.558 41.667 0.00 0.00 0.00 2.71
2357 2573 4.862350 TGAAGACAATTCACTGCACATTG 58.138 39.130 0.00 0.00 34.60 2.82
2358 2574 3.293311 AGACAATTCACTGCACATTGC 57.707 42.857 0.00 0.00 45.29 3.56
2359 2575 2.889045 AGACAATTCACTGCACATTGCT 59.111 40.909 0.00 0.00 45.31 3.91
2360 2576 3.319972 AGACAATTCACTGCACATTGCTT 59.680 39.130 0.00 0.00 45.31 3.91
2361 2577 3.386486 ACAATTCACTGCACATTGCTTG 58.614 40.909 0.00 0.00 45.31 4.01
2362 2578 3.068448 ACAATTCACTGCACATTGCTTGA 59.932 39.130 0.00 0.00 45.31 3.02
2363 2579 4.052608 CAATTCACTGCACATTGCTTGAA 58.947 39.130 14.28 14.28 45.31 2.69
2364 2580 3.358707 TTCACTGCACATTGCTTGAAG 57.641 42.857 10.10 0.00 45.31 3.02
2365 2581 1.610038 TCACTGCACATTGCTTGAAGG 59.390 47.619 0.00 0.00 45.31 3.46
2366 2582 0.316204 ACTGCACATTGCTTGAAGGC 59.684 50.000 0.00 0.00 45.31 4.35
2367 2583 0.389426 CTGCACATTGCTTGAAGGCC 60.389 55.000 0.00 0.00 45.31 5.19
2368 2584 0.828762 TGCACATTGCTTGAAGGCCT 60.829 50.000 0.00 0.00 45.31 5.19
2369 2585 0.389426 GCACATTGCTTGAAGGCCTG 60.389 55.000 5.69 0.00 40.96 4.85
2370 2586 1.250328 CACATTGCTTGAAGGCCTGA 58.750 50.000 5.69 0.00 0.00 3.86
2371 2587 1.614903 CACATTGCTTGAAGGCCTGAA 59.385 47.619 5.69 0.76 0.00 3.02
2372 2588 1.891150 ACATTGCTTGAAGGCCTGAAG 59.109 47.619 5.69 13.42 0.00 3.02
2373 2589 0.893447 ATTGCTTGAAGGCCTGAAGC 59.107 50.000 30.41 30.41 42.07 3.86
2396 2612 4.657952 GGCGACTTAAGGCCCAAT 57.342 55.556 10.74 0.00 43.64 3.16
2397 2613 2.882170 GGCGACTTAAGGCCCAATT 58.118 52.632 10.74 0.00 43.64 2.32
2398 2614 2.047002 GGCGACTTAAGGCCCAATTA 57.953 50.000 10.74 0.00 43.64 1.40
2399 2615 1.947456 GGCGACTTAAGGCCCAATTAG 59.053 52.381 10.74 0.00 43.64 1.73
2400 2616 2.640184 GCGACTTAAGGCCCAATTAGT 58.360 47.619 7.53 0.00 0.00 2.24
2401 2617 2.354821 GCGACTTAAGGCCCAATTAGTG 59.645 50.000 7.53 0.00 0.00 2.74
2402 2618 3.606687 CGACTTAAGGCCCAATTAGTGT 58.393 45.455 7.53 0.00 0.00 3.55
2403 2619 4.761975 CGACTTAAGGCCCAATTAGTGTA 58.238 43.478 7.53 0.00 0.00 2.90
2404 2620 5.180271 CGACTTAAGGCCCAATTAGTGTAA 58.820 41.667 7.53 0.00 0.00 2.41
2405 2621 5.644636 CGACTTAAGGCCCAATTAGTGTAAA 59.355 40.000 7.53 0.00 0.00 2.01
2406 2622 6.402875 CGACTTAAGGCCCAATTAGTGTAAAC 60.403 42.308 7.53 0.00 0.00 2.01
2407 2623 5.713389 ACTTAAGGCCCAATTAGTGTAAACC 59.287 40.000 7.53 0.00 0.00 3.27
2408 2624 2.718563 AGGCCCAATTAGTGTAAACCG 58.281 47.619 0.00 0.00 0.00 4.44
2409 2625 1.133598 GGCCCAATTAGTGTAAACCGC 59.866 52.381 0.00 0.00 0.00 5.68
2410 2626 1.133598 GCCCAATTAGTGTAAACCGCC 59.866 52.381 0.00 0.00 0.00 6.13
2411 2627 2.438411 CCCAATTAGTGTAAACCGCCA 58.562 47.619 0.00 0.00 0.00 5.69
2412 2628 3.020984 CCCAATTAGTGTAAACCGCCAT 58.979 45.455 0.00 0.00 0.00 4.40
2413 2629 4.200874 CCCAATTAGTGTAAACCGCCATA 58.799 43.478 0.00 0.00 0.00 2.74
2414 2630 4.825085 CCCAATTAGTGTAAACCGCCATAT 59.175 41.667 0.00 0.00 0.00 1.78
2415 2631 5.278266 CCCAATTAGTGTAAACCGCCATATG 60.278 44.000 0.00 0.00 0.00 1.78
2416 2632 5.298276 CCAATTAGTGTAAACCGCCATATGT 59.702 40.000 1.24 0.00 0.00 2.29
2417 2633 6.198687 CAATTAGTGTAAACCGCCATATGTG 58.801 40.000 1.24 0.00 0.00 3.21
2418 2634 3.343941 AGTGTAAACCGCCATATGTGT 57.656 42.857 1.24 0.00 0.00 3.72
2419 2635 4.475051 AGTGTAAACCGCCATATGTGTA 57.525 40.909 1.24 0.00 0.00 2.90
2420 2636 5.031066 AGTGTAAACCGCCATATGTGTAT 57.969 39.130 1.24 0.00 0.00 2.29
2421 2637 4.814234 AGTGTAAACCGCCATATGTGTATG 59.186 41.667 1.24 0.00 37.93 2.39
2422 2638 4.812091 GTGTAAACCGCCATATGTGTATGA 59.188 41.667 1.24 0.00 40.12 2.15
2423 2639 4.812091 TGTAAACCGCCATATGTGTATGAC 59.188 41.667 1.24 0.00 40.12 3.06
2424 2640 3.838244 AACCGCCATATGTGTATGACT 57.162 42.857 1.24 0.00 40.12 3.41
2425 2641 3.838244 ACCGCCATATGTGTATGACTT 57.162 42.857 1.24 0.00 40.12 3.01
2426 2642 3.466836 ACCGCCATATGTGTATGACTTG 58.533 45.455 1.24 0.00 40.12 3.16
2427 2643 3.118408 ACCGCCATATGTGTATGACTTGT 60.118 43.478 1.24 0.00 40.12 3.16
2428 2644 4.100344 ACCGCCATATGTGTATGACTTGTA 59.900 41.667 1.24 0.00 40.12 2.41
2429 2645 5.221641 ACCGCCATATGTGTATGACTTGTAT 60.222 40.000 1.24 0.00 40.12 2.29
2430 2646 5.700832 CCGCCATATGTGTATGACTTGTATT 59.299 40.000 1.24 0.00 40.12 1.89
2431 2647 6.871492 CCGCCATATGTGTATGACTTGTATTA 59.129 38.462 1.24 0.00 40.12 0.98
2432 2648 7.549134 CCGCCATATGTGTATGACTTGTATTAT 59.451 37.037 1.24 0.00 40.12 1.28
2433 2649 9.581099 CGCCATATGTGTATGACTTGTATTATA 57.419 33.333 1.24 0.00 40.12 0.98
2446 2662 9.845740 TGACTTGTATTATAAGGCATGTACAAT 57.154 29.630 4.72 0.00 38.22 2.71
2454 2670 8.671384 TTATAAGGCATGTACAATTAGTCACC 57.329 34.615 0.00 0.00 0.00 4.02
2455 2671 3.531538 AGGCATGTACAATTAGTCACCG 58.468 45.455 0.00 0.00 0.00 4.94
2456 2672 3.196901 AGGCATGTACAATTAGTCACCGA 59.803 43.478 0.00 0.00 0.00 4.69
2457 2673 3.555956 GGCATGTACAATTAGTCACCGAG 59.444 47.826 0.00 0.00 0.00 4.63
2458 2674 3.001330 GCATGTACAATTAGTCACCGAGC 59.999 47.826 0.00 0.00 0.00 5.03
2459 2675 3.241067 TGTACAATTAGTCACCGAGCC 57.759 47.619 0.00 0.00 0.00 4.70
2460 2676 2.190981 GTACAATTAGTCACCGAGCCG 58.809 52.381 0.00 0.00 0.00 5.52
2471 2687 3.103911 CGAGCCGGACACGTTGTC 61.104 66.667 5.05 8.94 46.23 3.18
2472 2688 2.338984 GAGCCGGACACGTTGTCT 59.661 61.111 5.05 0.00 46.19 3.41
2473 2689 1.582968 GAGCCGGACACGTTGTCTA 59.417 57.895 5.05 0.00 46.19 2.59
2474 2690 0.731855 GAGCCGGACACGTTGTCTAC 60.732 60.000 5.05 7.39 46.19 2.59
2483 2699 2.508663 GTTGTCTACGAGCCGGCC 60.509 66.667 26.15 14.23 0.00 6.13
2484 2700 4.124351 TTGTCTACGAGCCGGCCG 62.124 66.667 28.27 28.27 0.00 6.13
2501 2717 3.773370 GGGACTCCGTGAGTGTGA 58.227 61.111 10.72 0.00 43.53 3.58
2502 2718 1.289380 GGGACTCCGTGAGTGTGAC 59.711 63.158 10.72 0.00 43.53 3.67
2503 2719 1.461091 GGGACTCCGTGAGTGTGACA 61.461 60.000 10.72 0.00 43.53 3.58
2504 2720 0.318784 GGACTCCGTGAGTGTGACAC 60.319 60.000 7.83 7.83 43.53 3.67
2505 2721 0.318784 GACTCCGTGAGTGTGACACC 60.319 60.000 12.81 4.70 43.53 4.16
2506 2722 1.006102 CTCCGTGAGTGTGACACCC 60.006 63.158 12.81 0.00 34.49 4.61
2507 2723 2.030562 CCGTGAGTGTGACACCCC 59.969 66.667 12.81 5.44 34.49 4.95
2508 2724 2.030562 CGTGAGTGTGACACCCCC 59.969 66.667 12.81 2.82 34.49 5.40
2509 2725 2.030562 GTGAGTGTGACACCCCCG 59.969 66.667 12.81 0.00 34.49 5.73
2510 2726 2.123208 TGAGTGTGACACCCCCGA 60.123 61.111 12.81 0.00 34.49 5.14
2511 2727 1.535444 TGAGTGTGACACCCCCGAT 60.535 57.895 12.81 0.00 34.49 4.18
2512 2728 1.125093 TGAGTGTGACACCCCCGATT 61.125 55.000 12.81 0.00 34.49 3.34
2513 2729 0.036306 GAGTGTGACACCCCCGATTT 59.964 55.000 12.81 0.00 34.49 2.17
2514 2730 0.250727 AGTGTGACACCCCCGATTTG 60.251 55.000 12.81 0.00 34.49 2.32
2515 2731 0.250553 GTGTGACACCCCCGATTTGA 60.251 55.000 3.92 0.00 0.00 2.69
2516 2732 0.250553 TGTGACACCCCCGATTTGAC 60.251 55.000 2.45 0.00 0.00 3.18
2517 2733 0.958876 GTGACACCCCCGATTTGACC 60.959 60.000 0.00 0.00 0.00 4.02
2518 2734 1.743995 GACACCCCCGATTTGACCG 60.744 63.158 0.00 0.00 0.00 4.79
2519 2735 2.349755 CACCCCCGATTTGACCGT 59.650 61.111 0.00 0.00 0.00 4.83
2520 2736 1.193462 ACACCCCCGATTTGACCGTA 61.193 55.000 0.00 0.00 0.00 4.02
2521 2737 0.741927 CACCCCCGATTTGACCGTAC 60.742 60.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.874231 TGATGATCGACTAGAGCGGAC 59.126 52.381 0.00 0.00 38.28 4.79
144 166 3.520696 CATGGGTCCCAGACTCCATATA 58.479 50.000 17.70 0.00 39.64 0.86
145 167 2.342659 CATGGGTCCCAGACTCCATAT 58.657 52.381 17.70 0.00 39.64 1.78
146 168 1.806496 CATGGGTCCCAGACTCCATA 58.194 55.000 17.70 0.00 39.64 2.74
147 169 1.639635 GCATGGGTCCCAGACTCCAT 61.640 60.000 17.70 10.26 41.08 3.41
148 170 2.300967 GCATGGGTCCCAGACTCCA 61.301 63.158 17.70 7.20 36.75 3.86
149 171 1.639635 ATGCATGGGTCCCAGACTCC 61.640 60.000 17.70 3.14 36.75 3.85
152 174 1.454479 CCATGCATGGGTCCCAGAC 60.454 63.158 34.31 11.28 44.31 3.51
190 220 4.034048 CCGTTAGTAATGAATGTCAGCCAC 59.966 45.833 3.54 0.00 0.00 5.01
195 225 3.199071 AGGCCCGTTAGTAATGAATGTCA 59.801 43.478 0.00 0.00 0.00 3.58
213 243 0.806241 TCCGCGACAAATTTAAGGCC 59.194 50.000 8.23 0.00 0.00 5.19
303 333 1.619827 CTGGAATTGCTTTTGGCTGGA 59.380 47.619 0.00 0.00 42.39 3.86
364 395 3.679980 CGTCCTGGTTGACATCTTTACAG 59.320 47.826 0.00 0.00 34.88 2.74
385 497 5.111989 AGTCACACATGTTGGATTATCTCG 58.888 41.667 0.00 0.00 0.00 4.04
478 590 3.067320 AGAAGAGTTTCTTGGCAACTTGC 59.933 43.478 5.08 5.08 40.79 4.01
482 594 7.674471 AACTATAGAAGAGTTTCTTGGCAAC 57.326 36.000 6.78 0.00 40.79 4.17
741 858 2.421751 TCACCCTTGACGTTTTGGAA 57.578 45.000 0.00 0.00 0.00 3.53
885 1002 1.433534 GAAGTTGAAGACCTGCGGAG 58.566 55.000 0.00 0.00 0.00 4.63
1113 1230 0.179220 CTGACTCGTCGAACTCGTCC 60.179 60.000 9.17 0.00 40.80 4.79
1143 1260 1.301401 CTCTGCCGGGTTGAACGAA 60.301 57.895 2.18 0.00 0.00 3.85
1604 1732 6.982852 TGTCAAAACAACCAACTTGTAGAAA 58.017 32.000 0.00 0.00 42.70 2.52
1610 1738 3.859386 GCTCTGTCAAAACAACCAACTTG 59.141 43.478 0.00 0.00 34.24 3.16
1645 1814 4.456222 TCAGTTTTCACTCCTCTCTCTACG 59.544 45.833 0.00 0.00 0.00 3.51
1661 1830 7.756395 AGAACAATGATCACTCATCAGTTTT 57.244 32.000 0.00 0.00 45.11 2.43
1735 1924 2.927553 ATTGCGCAGGATCAGAAAAC 57.072 45.000 11.31 0.00 0.00 2.43
1758 1947 1.095600 TGCGTGGTGCTACACAAAAA 58.904 45.000 11.01 0.00 46.63 1.94
1759 1948 1.064803 CTTGCGTGGTGCTACACAAAA 59.935 47.619 11.01 4.58 46.63 2.44
1760 1949 0.660488 CTTGCGTGGTGCTACACAAA 59.340 50.000 11.01 4.86 46.63 2.83
1817 2012 5.366482 TCATCCCCTCGACAAATCATTTA 57.634 39.130 0.00 0.00 0.00 1.40
2026 2237 0.541392 TGGTACGAGCATCATTGGCT 59.459 50.000 0.00 0.00 46.07 4.75
2191 2407 5.130292 TCTCAGGACCGTTACTTACTTTG 57.870 43.478 0.00 0.00 0.00 2.77
2199 2415 1.272769 AGTTGCTCTCAGGACCGTTAC 59.727 52.381 0.00 0.00 0.00 2.50
2200 2416 1.544691 GAGTTGCTCTCAGGACCGTTA 59.455 52.381 4.98 0.00 42.34 3.18
2201 2417 0.318762 GAGTTGCTCTCAGGACCGTT 59.681 55.000 4.98 0.00 42.34 4.44
2202 2418 1.536943 GGAGTTGCTCTCAGGACCGT 61.537 60.000 10.56 0.00 44.40 4.83
2203 2419 1.216710 GGAGTTGCTCTCAGGACCG 59.783 63.158 10.56 0.00 44.40 4.79
2204 2420 0.687354 TTGGAGTTGCTCTCAGGACC 59.313 55.000 10.56 0.00 44.40 4.46
2205 2421 1.802069 GTTGGAGTTGCTCTCAGGAC 58.198 55.000 10.56 3.82 44.40 3.85
2206 2422 0.318441 CGTTGGAGTTGCTCTCAGGA 59.682 55.000 10.56 0.00 44.40 3.86
2207 2423 0.671781 CCGTTGGAGTTGCTCTCAGG 60.672 60.000 10.56 5.50 44.40 3.86
2208 2424 0.671781 CCCGTTGGAGTTGCTCTCAG 60.672 60.000 10.56 1.41 44.40 3.35
2209 2425 1.371183 CCCGTTGGAGTTGCTCTCA 59.629 57.895 10.56 0.00 44.40 3.27
2210 2426 1.376037 CCCCGTTGGAGTTGCTCTC 60.376 63.158 1.79 1.79 42.07 3.20
2211 2427 2.750350 CCCCGTTGGAGTTGCTCT 59.250 61.111 0.00 0.00 35.39 4.09
2212 2428 3.056328 GCCCCGTTGGAGTTGCTC 61.056 66.667 0.00 0.00 35.39 4.26
2215 2431 2.046314 ATCGCCCCGTTGGAGTTG 60.046 61.111 0.00 0.00 35.07 3.16
2216 2432 0.974010 TAGATCGCCCCGTTGGAGTT 60.974 55.000 0.00 0.00 35.07 3.01
2217 2433 0.759436 ATAGATCGCCCCGTTGGAGT 60.759 55.000 0.00 0.00 35.07 3.85
2218 2434 0.393077 AATAGATCGCCCCGTTGGAG 59.607 55.000 0.00 0.00 35.39 3.86
2219 2435 0.391597 GAATAGATCGCCCCGTTGGA 59.608 55.000 0.00 0.00 35.39 3.53
2220 2436 0.602905 GGAATAGATCGCCCCGTTGG 60.603 60.000 0.00 0.00 37.09 3.77
2221 2437 0.944311 CGGAATAGATCGCCCCGTTG 60.944 60.000 9.61 0.00 35.83 4.10
2222 2438 1.366366 CGGAATAGATCGCCCCGTT 59.634 57.895 9.61 0.00 35.83 4.44
2223 2439 3.048602 CGGAATAGATCGCCCCGT 58.951 61.111 9.61 0.00 35.83 5.28
2224 2440 1.080705 GACGGAATAGATCGCCCCG 60.081 63.158 14.25 14.25 45.09 5.73
2225 2441 1.186267 AGGACGGAATAGATCGCCCC 61.186 60.000 0.00 0.00 0.00 5.80
2226 2442 0.038159 CAGGACGGAATAGATCGCCC 60.038 60.000 0.00 0.00 0.00 6.13
2227 2443 0.674534 ACAGGACGGAATAGATCGCC 59.325 55.000 0.00 0.00 0.00 5.54
2228 2444 2.510768 AACAGGACGGAATAGATCGC 57.489 50.000 0.00 0.00 0.00 4.58
2229 2445 3.057456 CCCTAACAGGACGGAATAGATCG 60.057 52.174 0.00 0.00 37.67 3.69
2230 2446 4.150359 TCCCTAACAGGACGGAATAGATC 58.850 47.826 0.00 0.00 37.67 2.75
2231 2447 4.194678 TCCCTAACAGGACGGAATAGAT 57.805 45.455 0.00 0.00 37.67 1.98
2232 2448 3.675348 TCCCTAACAGGACGGAATAGA 57.325 47.619 0.00 0.00 37.67 1.98
2233 2449 7.396623 AGTTATATCCCTAACAGGACGGAATAG 59.603 40.741 0.00 0.00 39.24 1.73
2234 2450 7.243824 AGTTATATCCCTAACAGGACGGAATA 58.756 38.462 0.00 0.00 39.24 1.75
2235 2451 6.082707 AGTTATATCCCTAACAGGACGGAAT 58.917 40.000 0.00 0.00 39.24 3.01
2236 2452 5.461327 AGTTATATCCCTAACAGGACGGAA 58.539 41.667 0.00 0.00 39.24 4.30
2237 2453 5.070823 AGTTATATCCCTAACAGGACGGA 57.929 43.478 0.00 0.00 39.24 4.69
2238 2454 7.321153 CAATAGTTATATCCCTAACAGGACGG 58.679 42.308 0.00 0.00 39.24 4.79
2239 2455 7.177921 TCCAATAGTTATATCCCTAACAGGACG 59.822 40.741 0.00 0.00 39.24 4.79
2240 2456 8.431910 TCCAATAGTTATATCCCTAACAGGAC 57.568 38.462 0.00 0.00 39.24 3.85
2241 2457 8.239478 ACTCCAATAGTTATATCCCTAACAGGA 58.761 37.037 0.00 0.00 33.50 3.86
2242 2458 8.437274 ACTCCAATAGTTATATCCCTAACAGG 57.563 38.462 0.00 0.00 33.35 4.00
2255 2471 3.118298 GGGCGGGTTAACTCCAATAGTTA 60.118 47.826 5.42 0.00 46.85 2.24
2257 2473 1.211212 GGGCGGGTTAACTCCAATAGT 59.789 52.381 5.42 0.00 41.49 2.12
2258 2474 1.210967 TGGGCGGGTTAACTCCAATAG 59.789 52.381 5.42 0.00 0.00 1.73
2259 2475 1.210967 CTGGGCGGGTTAACTCCAATA 59.789 52.381 5.42 0.00 0.00 1.90
2260 2476 0.034477 CTGGGCGGGTTAACTCCAAT 60.034 55.000 5.42 0.00 0.00 3.16
2261 2477 1.128809 TCTGGGCGGGTTAACTCCAA 61.129 55.000 5.42 0.00 0.00 3.53
2262 2478 1.128809 TTCTGGGCGGGTTAACTCCA 61.129 55.000 5.42 7.73 0.00 3.86
2263 2479 0.392595 CTTCTGGGCGGGTTAACTCC 60.393 60.000 5.42 4.41 0.00 3.85
2264 2480 0.392595 CCTTCTGGGCGGGTTAACTC 60.393 60.000 5.42 0.00 0.00 3.01
2265 2481 1.683441 CCTTCTGGGCGGGTTAACT 59.317 57.895 5.42 0.00 0.00 2.24
2266 2482 4.313819 CCTTCTGGGCGGGTTAAC 57.686 61.111 0.00 0.00 0.00 2.01
2276 2492 1.202769 TTAACCCGACCCCCTTCTGG 61.203 60.000 0.00 0.00 0.00 3.86
2277 2493 0.252197 CTTAACCCGACCCCCTTCTG 59.748 60.000 0.00 0.00 0.00 3.02
2278 2494 1.559965 GCTTAACCCGACCCCCTTCT 61.560 60.000 0.00 0.00 0.00 2.85
2279 2495 1.077930 GCTTAACCCGACCCCCTTC 60.078 63.158 0.00 0.00 0.00 3.46
2280 2496 2.609534 GGCTTAACCCGACCCCCTT 61.610 63.158 0.00 0.00 0.00 3.95
2281 2497 3.013327 GGCTTAACCCGACCCCCT 61.013 66.667 0.00 0.00 0.00 4.79
2296 2512 0.108851 CTTGTTAAACCGCCATGGGC 60.109 55.000 15.13 4.92 46.75 5.36
2297 2513 0.530288 CCTTGTTAAACCGCCATGGG 59.470 55.000 15.13 3.37 44.64 4.00
2298 2514 0.108851 GCCTTGTTAAACCGCCATGG 60.109 55.000 7.63 7.63 46.41 3.66
2299 2515 0.600557 TGCCTTGTTAAACCGCCATG 59.399 50.000 0.00 0.00 0.00 3.66
2300 2516 1.333177 TTGCCTTGTTAAACCGCCAT 58.667 45.000 0.00 0.00 0.00 4.40
2301 2517 1.112113 TTTGCCTTGTTAAACCGCCA 58.888 45.000 0.00 0.00 0.00 5.69
2302 2518 1.862201 GTTTTGCCTTGTTAAACCGCC 59.138 47.619 0.00 0.00 0.00 6.13
2303 2519 2.792674 GAGTTTTGCCTTGTTAAACCGC 59.207 45.455 0.00 0.00 33.38 5.68
2304 2520 4.035278 TGAGTTTTGCCTTGTTAAACCG 57.965 40.909 0.00 0.00 33.38 4.44
2305 2521 4.098807 TCCTGAGTTTTGCCTTGTTAAACC 59.901 41.667 0.00 0.00 33.38 3.27
2306 2522 5.257082 TCCTGAGTTTTGCCTTGTTAAAC 57.743 39.130 0.00 0.00 33.16 2.01
2307 2523 4.340950 CCTCCTGAGTTTTGCCTTGTTAAA 59.659 41.667 0.00 0.00 0.00 1.52
2308 2524 3.888930 CCTCCTGAGTTTTGCCTTGTTAA 59.111 43.478 0.00 0.00 0.00 2.01
2309 2525 3.137544 TCCTCCTGAGTTTTGCCTTGTTA 59.862 43.478 0.00 0.00 0.00 2.41
2310 2526 2.091885 TCCTCCTGAGTTTTGCCTTGTT 60.092 45.455 0.00 0.00 0.00 2.83
2311 2527 1.494721 TCCTCCTGAGTTTTGCCTTGT 59.505 47.619 0.00 0.00 0.00 3.16
2312 2528 2.276732 TCCTCCTGAGTTTTGCCTTG 57.723 50.000 0.00 0.00 0.00 3.61
2313 2529 2.800250 CATCCTCCTGAGTTTTGCCTT 58.200 47.619 0.00 0.00 0.00 4.35
2314 2530 1.615384 GCATCCTCCTGAGTTTTGCCT 60.615 52.381 0.00 0.00 0.00 4.75
2315 2531 0.813821 GCATCCTCCTGAGTTTTGCC 59.186 55.000 0.00 0.00 0.00 4.52
2316 2532 1.471684 CAGCATCCTCCTGAGTTTTGC 59.528 52.381 0.00 5.54 32.03 3.68
2317 2533 3.063510 TCAGCATCCTCCTGAGTTTTG 57.936 47.619 0.00 0.00 34.59 2.44
2318 2534 3.328931 TCTTCAGCATCCTCCTGAGTTTT 59.671 43.478 0.00 0.00 40.16 2.43
2319 2535 2.909006 TCTTCAGCATCCTCCTGAGTTT 59.091 45.455 0.00 0.00 40.16 2.66
2320 2536 2.235898 GTCTTCAGCATCCTCCTGAGTT 59.764 50.000 0.00 0.00 40.16 3.01
2321 2537 1.830477 GTCTTCAGCATCCTCCTGAGT 59.170 52.381 0.00 0.00 40.16 3.41
2322 2538 1.829849 TGTCTTCAGCATCCTCCTGAG 59.170 52.381 0.00 0.00 40.16 3.35
2323 2539 1.942776 TGTCTTCAGCATCCTCCTGA 58.057 50.000 0.00 0.00 37.54 3.86
2324 2540 2.775911 TTGTCTTCAGCATCCTCCTG 57.224 50.000 0.00 0.00 0.00 3.86
2325 2541 3.265221 TGAATTGTCTTCAGCATCCTCCT 59.735 43.478 0.00 0.00 0.00 3.69
2326 2542 3.376546 GTGAATTGTCTTCAGCATCCTCC 59.623 47.826 0.00 0.00 0.00 4.30
2327 2543 4.094590 CAGTGAATTGTCTTCAGCATCCTC 59.905 45.833 0.00 0.00 0.00 3.71
2328 2544 4.008330 CAGTGAATTGTCTTCAGCATCCT 58.992 43.478 0.00 0.00 0.00 3.24
2329 2545 3.427233 GCAGTGAATTGTCTTCAGCATCC 60.427 47.826 0.00 0.00 0.00 3.51
2330 2546 3.189910 TGCAGTGAATTGTCTTCAGCATC 59.810 43.478 0.00 0.00 0.00 3.91
2331 2547 3.057736 GTGCAGTGAATTGTCTTCAGCAT 60.058 43.478 0.00 0.00 0.00 3.79
2332 2548 2.291465 GTGCAGTGAATTGTCTTCAGCA 59.709 45.455 0.00 0.00 0.00 4.41
2333 2549 2.291465 TGTGCAGTGAATTGTCTTCAGC 59.709 45.455 0.00 0.00 0.00 4.26
2334 2550 4.761235 ATGTGCAGTGAATTGTCTTCAG 57.239 40.909 0.00 0.00 0.00 3.02
2335 2551 4.793678 GCAATGTGCAGTGAATTGTCTTCA 60.794 41.667 3.69 0.00 44.26 3.02
2336 2552 3.671928 GCAATGTGCAGTGAATTGTCTTC 59.328 43.478 3.69 0.00 44.26 2.87
2337 2553 3.645884 GCAATGTGCAGTGAATTGTCTT 58.354 40.909 3.69 0.00 44.26 3.01
2338 2554 3.293311 GCAATGTGCAGTGAATTGTCT 57.707 42.857 3.69 0.00 44.26 3.41
2350 2566 0.389426 CAGGCCTTCAAGCAATGTGC 60.389 55.000 0.00 0.00 45.46 4.57
2351 2567 1.250328 TCAGGCCTTCAAGCAATGTG 58.750 50.000 0.00 0.00 0.00 3.21
2352 2568 1.891150 CTTCAGGCCTTCAAGCAATGT 59.109 47.619 0.00 0.00 0.00 2.71
2353 2569 1.403780 GCTTCAGGCCTTCAAGCAATG 60.404 52.381 29.85 8.61 41.87 2.82
2354 2570 0.893447 GCTTCAGGCCTTCAAGCAAT 59.107 50.000 29.85 0.00 41.87 3.56
2355 2571 2.344535 GCTTCAGGCCTTCAAGCAA 58.655 52.632 29.85 7.36 41.87 3.91
2356 2572 4.085876 GCTTCAGGCCTTCAAGCA 57.914 55.556 29.85 1.13 41.87 3.91
2373 2589 1.313091 GGCCTTAAGTCGCCTTTGGG 61.313 60.000 13.74 0.00 42.21 4.12
2374 2590 1.313091 GGGCCTTAAGTCGCCTTTGG 61.313 60.000 18.64 0.00 45.01 3.28
2375 2591 0.608035 TGGGCCTTAAGTCGCCTTTG 60.608 55.000 18.64 0.00 45.01 2.77
2376 2592 0.111639 TTGGGCCTTAAGTCGCCTTT 59.888 50.000 18.64 0.00 45.01 3.11
2377 2593 0.331616 ATTGGGCCTTAAGTCGCCTT 59.668 50.000 18.64 5.54 45.01 4.35
2378 2594 0.331616 AATTGGGCCTTAAGTCGCCT 59.668 50.000 18.64 1.12 45.01 5.52
2379 2595 1.947456 CTAATTGGGCCTTAAGTCGCC 59.053 52.381 12.88 12.88 44.92 5.54
2380 2596 2.354821 CACTAATTGGGCCTTAAGTCGC 59.645 50.000 4.53 0.00 0.00 5.19
2381 2597 3.606687 ACACTAATTGGGCCTTAAGTCG 58.393 45.455 4.53 0.00 0.00 4.18
2382 2598 6.127814 GGTTTACACTAATTGGGCCTTAAGTC 60.128 42.308 4.53 0.00 0.00 3.01
2383 2599 5.713389 GGTTTACACTAATTGGGCCTTAAGT 59.287 40.000 4.53 0.04 0.00 2.24
2384 2600 5.163693 CGGTTTACACTAATTGGGCCTTAAG 60.164 44.000 4.53 0.00 0.00 1.85
2385 2601 4.701171 CGGTTTACACTAATTGGGCCTTAA 59.299 41.667 4.53 0.00 0.00 1.85
2386 2602 4.263435 CGGTTTACACTAATTGGGCCTTA 58.737 43.478 4.53 0.00 0.00 2.69
2387 2603 3.086282 CGGTTTACACTAATTGGGCCTT 58.914 45.455 4.53 0.00 0.00 4.35
2388 2604 2.718563 CGGTTTACACTAATTGGGCCT 58.281 47.619 4.53 0.00 0.00 5.19
2389 2605 1.133598 GCGGTTTACACTAATTGGGCC 59.866 52.381 0.00 0.00 0.00 5.80
2390 2606 1.133598 GGCGGTTTACACTAATTGGGC 59.866 52.381 0.00 0.00 0.00 5.36
2391 2607 2.438411 TGGCGGTTTACACTAATTGGG 58.562 47.619 0.00 0.00 0.00 4.12
2392 2608 5.298276 ACATATGGCGGTTTACACTAATTGG 59.702 40.000 7.80 0.00 0.00 3.16
2393 2609 6.183360 ACACATATGGCGGTTTACACTAATTG 60.183 38.462 7.80 0.00 0.00 2.32
2394 2610 5.883673 ACACATATGGCGGTTTACACTAATT 59.116 36.000 7.80 0.00 0.00 1.40
2395 2611 5.433526 ACACATATGGCGGTTTACACTAAT 58.566 37.500 7.80 0.00 0.00 1.73
2396 2612 4.834534 ACACATATGGCGGTTTACACTAA 58.165 39.130 7.80 0.00 0.00 2.24
2397 2613 4.475051 ACACATATGGCGGTTTACACTA 57.525 40.909 7.80 0.00 0.00 2.74
2398 2614 3.343941 ACACATATGGCGGTTTACACT 57.656 42.857 7.80 0.00 0.00 3.55
2399 2615 4.812091 TCATACACATATGGCGGTTTACAC 59.188 41.667 7.80 0.00 39.04 2.90
2400 2616 4.812091 GTCATACACATATGGCGGTTTACA 59.188 41.667 7.80 0.00 39.04 2.41
2401 2617 5.054477 AGTCATACACATATGGCGGTTTAC 58.946 41.667 7.80 0.00 46.31 2.01
2402 2618 5.284861 AGTCATACACATATGGCGGTTTA 57.715 39.130 7.80 0.00 46.31 2.01
2403 2619 4.150897 AGTCATACACATATGGCGGTTT 57.849 40.909 7.80 0.00 46.31 3.27
2404 2620 3.838244 AGTCATACACATATGGCGGTT 57.162 42.857 7.80 0.00 46.31 4.44
2405 2621 3.118408 ACAAGTCATACACATATGGCGGT 60.118 43.478 7.80 5.03 46.31 5.68
2406 2622 3.466836 ACAAGTCATACACATATGGCGG 58.533 45.455 7.80 0.00 46.31 6.13
2407 2623 6.785488 AATACAAGTCATACACATATGGCG 57.215 37.500 7.80 0.02 46.31 5.69
2414 2630 9.271828 CATGCCTTATAATACAAGTCATACACA 57.728 33.333 0.00 0.00 0.00 3.72
2415 2631 9.273016 ACATGCCTTATAATACAAGTCATACAC 57.727 33.333 0.00 0.00 0.00 2.90
2419 2635 9.845740 TTGTACATGCCTTATAATACAAGTCAT 57.154 29.630 0.00 0.00 31.23 3.06
2420 2636 9.845740 ATTGTACATGCCTTATAATACAAGTCA 57.154 29.630 0.00 3.93 35.07 3.41
2428 2644 9.284968 GGTGACTAATTGTACATGCCTTATAAT 57.715 33.333 0.00 0.00 0.00 1.28
2429 2645 7.439955 CGGTGACTAATTGTACATGCCTTATAA 59.560 37.037 0.00 0.00 0.00 0.98
2430 2646 6.926826 CGGTGACTAATTGTACATGCCTTATA 59.073 38.462 0.00 0.00 0.00 0.98
2431 2647 5.758296 CGGTGACTAATTGTACATGCCTTAT 59.242 40.000 0.00 0.00 0.00 1.73
2432 2648 5.105269 TCGGTGACTAATTGTACATGCCTTA 60.105 40.000 0.00 0.00 0.00 2.69
2433 2649 3.938963 CGGTGACTAATTGTACATGCCTT 59.061 43.478 0.00 0.00 0.00 4.35
2434 2650 3.196901 TCGGTGACTAATTGTACATGCCT 59.803 43.478 0.00 0.00 0.00 4.75
2435 2651 3.527533 TCGGTGACTAATTGTACATGCC 58.472 45.455 0.00 0.00 0.00 4.40
2436 2652 3.001330 GCTCGGTGACTAATTGTACATGC 59.999 47.826 0.00 0.00 0.00 4.06
2437 2653 3.555956 GGCTCGGTGACTAATTGTACATG 59.444 47.826 0.00 0.00 0.00 3.21
2438 2654 3.737047 CGGCTCGGTGACTAATTGTACAT 60.737 47.826 0.00 0.00 0.00 2.29
2439 2655 2.416296 CGGCTCGGTGACTAATTGTACA 60.416 50.000 0.00 0.00 0.00 2.90
2440 2656 2.190981 CGGCTCGGTGACTAATTGTAC 58.809 52.381 0.00 0.00 0.00 2.90
2441 2657 1.135527 CCGGCTCGGTGACTAATTGTA 59.864 52.381 5.56 0.00 42.73 2.41
2442 2658 0.108329 CCGGCTCGGTGACTAATTGT 60.108 55.000 5.56 0.00 42.73 2.71
2443 2659 2.677971 CCGGCTCGGTGACTAATTG 58.322 57.895 5.56 0.00 42.73 2.32
2454 2670 3.103911 GACAACGTGTCCGGCTCG 61.104 66.667 15.42 15.42 41.37 5.03
2466 2682 2.508663 GGCCGGCTCGTAGACAAC 60.509 66.667 28.56 0.41 0.00 3.32
2467 2683 4.124351 CGGCCGGCTCGTAGACAA 62.124 66.667 28.56 0.00 0.00 3.18
2484 2700 1.289380 GTCACACTCACGGAGTCCC 59.711 63.158 2.80 0.00 41.37 4.46
2485 2701 0.318784 GTGTCACACTCACGGAGTCC 60.319 60.000 0.00 0.00 41.37 3.85
2486 2702 0.318784 GGTGTCACACTCACGGAGTC 60.319 60.000 8.12 0.00 41.37 3.36
2487 2703 1.740285 GGTGTCACACTCACGGAGT 59.260 57.895 8.12 1.23 44.44 3.85
2488 2704 1.006102 GGGTGTCACACTCACGGAG 60.006 63.158 8.12 0.03 34.53 4.63
2489 2705 2.504274 GGGGTGTCACACTCACGGA 61.504 63.158 10.77 0.00 36.41 4.69
2490 2706 2.030562 GGGGTGTCACACTCACGG 59.969 66.667 10.77 0.00 36.41 4.94
2491 2707 2.030562 GGGGGTGTCACACTCACG 59.969 66.667 10.77 0.00 36.41 4.35
2492 2708 1.827399 ATCGGGGGTGTCACACTCAC 61.827 60.000 10.77 4.63 36.41 3.51
2493 2709 1.125093 AATCGGGGGTGTCACACTCA 61.125 55.000 10.77 0.00 36.41 3.41
2494 2710 0.036306 AAATCGGGGGTGTCACACTC 59.964 55.000 8.12 2.71 34.40 3.51
2495 2711 0.250727 CAAATCGGGGGTGTCACACT 60.251 55.000 8.12 0.00 34.40 3.55
2496 2712 0.250553 TCAAATCGGGGGTGTCACAC 60.251 55.000 0.00 0.00 0.00 3.82
2497 2713 0.250553 GTCAAATCGGGGGTGTCACA 60.251 55.000 5.12 0.00 0.00 3.58
2498 2714 0.958876 GGTCAAATCGGGGGTGTCAC 60.959 60.000 0.00 0.00 0.00 3.67
2499 2715 1.377229 GGTCAAATCGGGGGTGTCA 59.623 57.895 0.00 0.00 0.00 3.58
2500 2716 1.743995 CGGTCAAATCGGGGGTGTC 60.744 63.158 0.00 0.00 0.00 3.67
2501 2717 1.193462 TACGGTCAAATCGGGGGTGT 61.193 55.000 0.00 0.00 0.00 4.16
2502 2718 0.741927 GTACGGTCAAATCGGGGGTG 60.742 60.000 0.00 0.00 0.00 4.61
2503 2719 1.598517 GTACGGTCAAATCGGGGGT 59.401 57.895 0.00 0.00 0.00 4.95
2504 2720 4.526770 GTACGGTCAAATCGGGGG 57.473 61.111 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.