Multiple sequence alignment - TraesCS5A01G556000

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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 TraesCS5A01G556000 chr5A 100.000 2465 0 0 1 2465 707267105 707269569 0.000000e+00 4553
1 TraesCS5A01G556000 chr5A 98.077 208 4 0 2258 2465 551249742 551249949 1.800000e-96 363
2 TraesCS5A01G556000 chr5A 97.183 213 6 0 2253 2465 550248436 550248224 6.480000e-96 361
3 TraesCS5A01G556000 chrUn 96.412 864 24 5 27 885 99396910 99397771 0.000000e+00 1417
4 TraesCS5A01G556000 chrUn 97.015 670 10 4 880 1545 99397797 99398460 0.000000e+00 1118
5 TraesCS5A01G556000 chrUn 97.490 239 6 0 1560 1798 99398597 99398835 2.280000e-110 409
6 TraesCS5A01G556000 chrUn 85.567 388 20 9 1857 2238 99399138 99399495 8.320000e-100 374
7 TraesCS5A01G556000 chr4B 94.235 902 33 10 1 885 672938259 672937360 0.000000e+00 1360
8 TraesCS5A01G556000 chr4B 97.024 672 14 2 880 1545 672937334 672936663 0.000000e+00 1125
9 TraesCS5A01G556000 chr4B 96.241 133 4 1 1560 1692 672936542 672936411 1.480000e-52 217
10 TraesCS5A01G556000 chr6A 98.558 208 3 0 2258 2465 613137705 613137498 3.870000e-98 368
11 TraesCS5A01G556000 chr6A 96.774 217 5 2 2251 2465 574024361 574024145 6.480000e-96 361
12 TraesCS5A01G556000 chr6A 97.608 209 5 0 2257 2465 584126284 584126492 2.330000e-95 359
13 TraesCS5A01G556000 chr3A 98.086 209 4 0 2257 2465 739036549 739036341 5.010000e-97 364
14 TraesCS5A01G556000 chr4A 98.077 208 4 0 2258 2465 307267705 307267498 1.800000e-96 363
15 TraesCS5A01G556000 chr7A 96.759 216 7 0 2250 2465 631112314 631112099 6.480000e-96 361
16 TraesCS5A01G556000 chr1A 97.608 209 5 0 2257 2465 41908052 41908260 2.330000e-95 359


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 TraesCS5A01G556000 chr5A 707267105 707269569 2464 False 4553.000000 4553 100.000000 1 2465 1 chr5A.!!$F2 2464
1 TraesCS5A01G556000 chrUn 99396910 99399495 2585 False 829.500000 1417 94.121000 27 2238 4 chrUn.!!$F1 2211
2 TraesCS5A01G556000 chr4B 672936411 672938259 1848 True 900.666667 1360 95.833333 1 1692 3 chr4B.!!$R1 1691

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
608 631 2.662156 GTCCGTGAGAAGATGTTCGAAC 59.338 50.0 21.42 21.42 37.79 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2778 0.028902 GCACGAACCGGGATAAATGC 59.971 55.0 6.32 4.0 28.17 3.56 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
60 61 6.351033 CCTGCTCAAAACCTAGATGTGTAGTA 60.351 42.308 0.00 0.00 0.00 1.82
127 129 3.648339 TGGTCGACCAGTAGTTTGTAC 57.352 47.619 33.23 2.79 42.01 2.90
205 213 3.384789 AGCGCTATGAGACTATCCAAACA 59.615 43.478 8.99 0.00 0.00 2.83
206 214 3.491267 GCGCTATGAGACTATCCAAACAC 59.509 47.826 0.00 0.00 0.00 3.32
244 256 6.676990 ATATAGATGAGAACATGCTGGTCA 57.323 37.500 0.00 0.00 36.30 4.02
288 300 5.141182 TCCTTAGCAGGTAACCTCTAGATG 58.859 45.833 0.00 0.00 41.69 2.90
309 321 3.111484 GGCCTCCCCCAAATTCATAAAA 58.889 45.455 0.00 0.00 0.00 1.52
344 362 7.546250 TGAAAAATTTATCTAGTTTGGGGCA 57.454 32.000 0.00 0.00 0.00 5.36
348 366 7.732222 AAATTTATCTAGTTTGGGGCATGAA 57.268 32.000 0.00 0.00 0.00 2.57
417 435 7.174080 GCACAATAGGAAGAAGAGAAGACTTTT 59.826 37.037 0.00 0.00 0.00 2.27
608 631 2.662156 GTCCGTGAGAAGATGTTCGAAC 59.338 50.000 21.42 21.42 37.79 3.95
793 816 4.134379 AGTTGAGGATGATGTGCTACAG 57.866 45.455 0.00 0.00 0.00 2.74
1149 1203 0.602060 GGCATACCGTAGCTACCTCC 59.398 60.000 18.16 6.63 0.00 4.30
1469 1525 6.518208 ACTTCTTGTCAGTACCTAGCTAAG 57.482 41.667 0.00 0.00 0.00 2.18
1481 1537 4.720046 ACCTAGCTAAGTGATGAGATCGA 58.280 43.478 0.00 0.00 0.00 3.59
1494 1550 3.541632 TGAGATCGAAATTAAGGGTGGC 58.458 45.455 0.00 0.00 0.00 5.01
1507 1563 9.536510 AAATTAAGGGTGGCTGTAATAAGTTTA 57.463 29.630 0.00 0.00 0.00 2.01
1545 1609 6.127423 TGTCTACTTATGTAAGCAGTCCCTTC 60.127 42.308 0.00 0.00 36.79 3.46
1546 1610 5.955959 TCTACTTATGTAAGCAGTCCCTTCA 59.044 40.000 0.00 0.00 36.79 3.02
1548 1612 2.409948 ATGTAAGCAGTCCCTTCAGC 57.590 50.000 0.00 0.00 0.00 4.26
1549 1613 1.352083 TGTAAGCAGTCCCTTCAGCT 58.648 50.000 0.00 0.00 39.37 4.24
1550 1614 2.536066 TGTAAGCAGTCCCTTCAGCTA 58.464 47.619 0.00 0.00 36.07 3.32
1552 1616 3.519510 TGTAAGCAGTCCCTTCAGCTATT 59.480 43.478 0.00 0.00 36.07 1.73
1553 1617 3.728385 AAGCAGTCCCTTCAGCTATTT 57.272 42.857 0.00 0.00 36.07 1.40
1554 1618 3.728385 AGCAGTCCCTTCAGCTATTTT 57.272 42.857 0.00 0.00 35.19 1.82
1555 1619 4.039603 AGCAGTCCCTTCAGCTATTTTT 57.960 40.909 0.00 0.00 35.19 1.94
1556 1620 4.013050 AGCAGTCCCTTCAGCTATTTTTC 58.987 43.478 0.00 0.00 35.19 2.29
1557 1621 4.013050 GCAGTCCCTTCAGCTATTTTTCT 58.987 43.478 0.00 0.00 0.00 2.52
1558 1622 4.142513 GCAGTCCCTTCAGCTATTTTTCTG 60.143 45.833 0.00 0.00 0.00 3.02
1695 1886 4.536065 TGTCACGATTGATGCTTTGAAAC 58.464 39.130 0.00 0.00 33.11 2.78
1871 2306 2.512896 ACTTGGAGATAGGGTCGGAGTA 59.487 50.000 0.00 0.00 0.00 2.59
1872 2307 3.140519 ACTTGGAGATAGGGTCGGAGTAT 59.859 47.826 0.00 0.00 0.00 2.12
1873 2308 4.353191 ACTTGGAGATAGGGTCGGAGTATA 59.647 45.833 0.00 0.00 0.00 1.47
1874 2309 5.163012 ACTTGGAGATAGGGTCGGAGTATAA 60.163 44.000 0.00 0.00 0.00 0.98
1875 2310 4.919793 TGGAGATAGGGTCGGAGTATAAG 58.080 47.826 0.00 0.00 0.00 1.73
1876 2311 4.353191 TGGAGATAGGGTCGGAGTATAAGT 59.647 45.833 0.00 0.00 0.00 2.24
1877 2312 4.943093 GGAGATAGGGTCGGAGTATAAGTC 59.057 50.000 0.00 0.00 0.00 3.01
1878 2313 5.514484 GGAGATAGGGTCGGAGTATAAGTCA 60.514 48.000 0.00 0.00 0.00 3.41
1904 2343 5.250982 TGATTCTGATCTGATTGCACAAGT 58.749 37.500 2.84 0.00 33.28 3.16
1906 2345 7.052248 TGATTCTGATCTGATTGCACAAGTAT 58.948 34.615 2.84 0.00 33.28 2.12
1909 2348 8.429493 TTCTGATCTGATTGCACAAGTATAAG 57.571 34.615 2.84 0.00 0.00 1.73
1912 2351 6.763135 TGATCTGATTGCACAAGTATAAGACC 59.237 38.462 0.00 0.00 0.00 3.85
1913 2352 6.048732 TCTGATTGCACAAGTATAAGACCA 57.951 37.500 0.00 0.00 0.00 4.02
1941 2380 4.175962 AGATAACTTTGGAGTGGAAGGGA 58.824 43.478 0.00 0.00 35.91 4.20
1957 2396 1.838077 AGGGACTCCGGATTTTGGTAG 59.162 52.381 3.57 0.00 38.33 3.18
1958 2397 1.558294 GGGACTCCGGATTTTGGTAGT 59.442 52.381 3.57 0.00 0.00 2.73
1959 2398 2.629051 GGACTCCGGATTTTGGTAGTG 58.371 52.381 3.57 0.00 0.00 2.74
1960 2399 2.007608 GACTCCGGATTTTGGTAGTGC 58.992 52.381 3.57 0.00 0.00 4.40
1961 2400 1.349688 ACTCCGGATTTTGGTAGTGCA 59.650 47.619 3.57 0.00 0.00 4.57
1962 2401 2.009774 CTCCGGATTTTGGTAGTGCAG 58.990 52.381 3.57 0.00 0.00 4.41
1963 2402 1.626321 TCCGGATTTTGGTAGTGCAGA 59.374 47.619 0.00 0.00 0.00 4.26
1964 2403 2.238646 TCCGGATTTTGGTAGTGCAGAT 59.761 45.455 0.00 0.00 0.00 2.90
1965 2404 3.452990 TCCGGATTTTGGTAGTGCAGATA 59.547 43.478 0.00 0.00 0.00 1.98
1966 2405 4.080807 TCCGGATTTTGGTAGTGCAGATAA 60.081 41.667 0.00 0.00 0.00 1.75
1967 2406 4.273480 CCGGATTTTGGTAGTGCAGATAAG 59.727 45.833 0.00 0.00 0.00 1.73
1968 2407 4.273480 CGGATTTTGGTAGTGCAGATAAGG 59.727 45.833 0.00 0.00 0.00 2.69
1969 2408 5.193679 GGATTTTGGTAGTGCAGATAAGGT 58.806 41.667 0.00 0.00 0.00 3.50
1970 2409 5.297029 GGATTTTGGTAGTGCAGATAAGGTC 59.703 44.000 0.00 0.00 0.00 3.85
1971 2410 4.901197 TTTGGTAGTGCAGATAAGGTCA 57.099 40.909 0.00 0.00 0.00 4.02
1972 2411 4.471904 TTGGTAGTGCAGATAAGGTCAG 57.528 45.455 0.00 0.00 0.00 3.51
2027 2466 5.353123 CCATGTAATAGCGTGTGTAAACCTT 59.647 40.000 0.00 0.00 0.00 3.50
2049 2488 3.362040 CCATTTGGCTGGACAGGAA 57.638 52.632 1.01 0.00 38.69 3.36
2050 2489 1.631405 CCATTTGGCTGGACAGGAAA 58.369 50.000 1.01 0.00 38.69 3.13
2051 2490 2.181975 CCATTTGGCTGGACAGGAAAT 58.818 47.619 1.01 0.00 38.69 2.17
2052 2491 2.568509 CCATTTGGCTGGACAGGAAATT 59.431 45.455 1.01 0.00 38.69 1.82
2053 2492 3.368739 CCATTTGGCTGGACAGGAAATTC 60.369 47.826 1.01 0.00 38.69 2.17
2054 2493 2.673775 TTGGCTGGACAGGAAATTCA 57.326 45.000 1.01 0.00 0.00 2.57
2055 2494 2.673775 TGGCTGGACAGGAAATTCAA 57.326 45.000 1.01 0.00 0.00 2.69
2056 2495 2.956132 TGGCTGGACAGGAAATTCAAA 58.044 42.857 1.01 0.00 0.00 2.69
2057 2496 2.627699 TGGCTGGACAGGAAATTCAAAC 59.372 45.455 1.01 0.00 0.00 2.93
2071 2510 6.481976 GGAAATTCAAACCACCAAAACTAAGG 59.518 38.462 0.00 0.00 0.00 2.69
2072 2511 6.800072 AATTCAAACCACCAAAACTAAGGA 57.200 33.333 0.00 0.00 0.00 3.36
2092 2531 3.796717 GGAAGAAAGAAAACAAGGCAACG 59.203 43.478 0.00 0.00 46.39 4.10
2114 2553 5.163561 ACGGAAATGAAAGAAAGAGCACAAA 60.164 36.000 0.00 0.00 0.00 2.83
2187 2628 1.330521 GCAAACGTCAAGAGCACAGAA 59.669 47.619 0.00 0.00 0.00 3.02
2199 2640 4.764172 AGAGCACAGAATACACATTCTCC 58.236 43.478 0.00 0.00 46.50 3.71
2218 2659 2.234661 TCCTCAGTTCTGCAATCGACAT 59.765 45.455 0.00 0.00 0.00 3.06
2221 2662 1.089920 AGTTCTGCAATCGACATGCC 58.910 50.000 19.09 6.71 43.16 4.40
2240 2681 6.757897 ATGCCGAGACATGATTAAAAAGAA 57.242 33.333 0.00 0.00 0.00 2.52
2241 2682 6.182039 TGCCGAGACATGATTAAAAAGAAG 57.818 37.500 0.00 0.00 0.00 2.85
2242 2683 5.937540 TGCCGAGACATGATTAAAAAGAAGA 59.062 36.000 0.00 0.00 0.00 2.87
2243 2684 6.599244 TGCCGAGACATGATTAAAAAGAAGAT 59.401 34.615 0.00 0.00 0.00 2.40
2244 2685 7.121168 TGCCGAGACATGATTAAAAAGAAGATT 59.879 33.333 0.00 0.00 0.00 2.40
2245 2686 7.970614 GCCGAGACATGATTAAAAAGAAGATTT 59.029 33.333 0.00 0.00 0.00 2.17
2259 2700 9.481340 AAAAAGAAGATTTAAAGCCAGATTCAC 57.519 29.630 0.00 0.00 0.00 3.18
2260 2701 8.414629 AAAGAAGATTTAAAGCCAGATTCACT 57.585 30.769 0.00 0.00 0.00 3.41
2261 2702 9.520515 AAAGAAGATTTAAAGCCAGATTCACTA 57.479 29.630 0.00 0.00 0.00 2.74
2262 2703 8.729805 AGAAGATTTAAAGCCAGATTCACTAG 57.270 34.615 0.00 0.00 0.00 2.57
2263 2704 8.325046 AGAAGATTTAAAGCCAGATTCACTAGT 58.675 33.333 0.00 0.00 0.00 2.57
2264 2705 9.601217 GAAGATTTAAAGCCAGATTCACTAGTA 57.399 33.333 0.00 0.00 0.00 1.82
2265 2706 9.606631 AAGATTTAAAGCCAGATTCACTAGTAG 57.393 33.333 0.00 0.00 0.00 2.57
2266 2707 8.982723 AGATTTAAAGCCAGATTCACTAGTAGA 58.017 33.333 3.59 0.00 0.00 2.59
2267 2708 9.601217 GATTTAAAGCCAGATTCACTAGTAGAA 57.399 33.333 3.59 2.62 0.00 2.10
2268 2709 9.959721 ATTTAAAGCCAGATTCACTAGTAGAAA 57.040 29.630 3.59 0.00 0.00 2.52
2269 2710 9.787435 TTTAAAGCCAGATTCACTAGTAGAAAA 57.213 29.630 3.59 0.00 0.00 2.29
2270 2711 7.913674 AAAGCCAGATTCACTAGTAGAAAAG 57.086 36.000 3.59 5.44 0.00 2.27
2271 2712 5.983540 AGCCAGATTCACTAGTAGAAAAGG 58.016 41.667 3.59 12.12 0.00 3.11
2272 2713 5.721960 AGCCAGATTCACTAGTAGAAAAGGA 59.278 40.000 3.59 2.11 0.00 3.36
2273 2714 6.045955 GCCAGATTCACTAGTAGAAAAGGAG 58.954 44.000 3.59 8.20 0.00 3.69
2274 2715 6.578023 CCAGATTCACTAGTAGAAAAGGAGG 58.422 44.000 3.59 6.49 0.00 4.30
2275 2716 6.045955 CAGATTCACTAGTAGAAAAGGAGGC 58.954 44.000 3.59 0.00 0.00 4.70
2276 2717 5.961421 AGATTCACTAGTAGAAAAGGAGGCT 59.039 40.000 3.59 0.00 0.00 4.58
2277 2718 6.442244 AGATTCACTAGTAGAAAAGGAGGCTT 59.558 38.462 3.59 0.00 0.00 4.35
2278 2719 6.435292 TTCACTAGTAGAAAAGGAGGCTTT 57.565 37.500 3.59 0.00 0.00 3.51
2279 2720 5.794894 TCACTAGTAGAAAAGGAGGCTTTG 58.205 41.667 3.59 0.00 0.00 2.77
2280 2721 4.938226 CACTAGTAGAAAAGGAGGCTTTGG 59.062 45.833 3.59 0.00 0.00 3.28
2281 2722 4.597940 ACTAGTAGAAAAGGAGGCTTTGGT 59.402 41.667 3.59 0.00 0.00 3.67
2282 2723 4.022413 AGTAGAAAAGGAGGCTTTGGTC 57.978 45.455 0.00 0.00 0.00 4.02
2283 2724 2.294449 AGAAAAGGAGGCTTTGGTCC 57.706 50.000 0.00 0.00 0.00 4.46
2284 2725 1.499007 AGAAAAGGAGGCTTTGGTCCA 59.501 47.619 0.00 0.00 35.02 4.02
2285 2726 1.889170 GAAAAGGAGGCTTTGGTCCAG 59.111 52.381 0.00 0.00 35.02 3.86
2286 2727 0.113190 AAAGGAGGCTTTGGTCCAGG 59.887 55.000 0.00 0.00 35.02 4.45
2287 2728 2.361737 GGAGGCTTTGGTCCAGGC 60.362 66.667 9.58 9.58 37.08 4.85
2288 2729 2.361737 GAGGCTTTGGTCCAGGCC 60.362 66.667 22.87 22.87 44.38 5.19
2292 2733 3.966543 CTTTGGTCCAGGCCGGGT 61.967 66.667 22.25 0.00 34.36 5.28
2293 2734 2.529643 TTTGGTCCAGGCCGGGTA 60.530 61.111 22.25 5.89 34.36 3.69
2294 2735 2.132089 CTTTGGTCCAGGCCGGGTAA 62.132 60.000 22.25 12.58 34.36 2.85
2295 2736 2.132089 TTTGGTCCAGGCCGGGTAAG 62.132 60.000 22.25 0.00 34.36 2.34
2296 2737 4.484872 GGTCCAGGCCGGGTAAGC 62.485 72.222 22.25 9.46 34.36 3.09
2308 2749 3.700198 GGTAAGCCCATTAGTCCCG 57.300 57.895 0.00 0.00 0.00 5.14
2309 2750 0.108019 GGTAAGCCCATTAGTCCCGG 59.892 60.000 0.00 0.00 0.00 5.73
2310 2751 0.835276 GTAAGCCCATTAGTCCCGGT 59.165 55.000 0.00 0.00 0.00 5.28
2311 2752 1.211212 GTAAGCCCATTAGTCCCGGTT 59.789 52.381 0.00 0.00 0.00 4.44
2312 2753 0.255033 AAGCCCATTAGTCCCGGTTC 59.745 55.000 0.00 0.00 0.00 3.62
2313 2754 0.912487 AGCCCATTAGTCCCGGTTCA 60.912 55.000 0.00 0.00 0.00 3.18
2314 2755 0.463833 GCCCATTAGTCCCGGTTCAG 60.464 60.000 0.00 0.00 0.00 3.02
2315 2756 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
2316 2757 1.134491 CCCATTAGTCCCGGTTCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
2317 2758 1.134491 CCATTAGTCCCGGTTCAGTCC 60.134 57.143 0.00 0.00 0.00 3.85
2318 2759 1.553248 CATTAGTCCCGGTTCAGTCCA 59.447 52.381 0.00 0.00 0.00 4.02
2319 2760 1.263356 TTAGTCCCGGTTCAGTCCAG 58.737 55.000 0.00 0.00 0.00 3.86
2320 2761 0.406750 TAGTCCCGGTTCAGTCCAGA 59.593 55.000 0.00 0.00 0.00 3.86
2321 2762 0.471211 AGTCCCGGTTCAGTCCAGAA 60.471 55.000 0.00 0.00 0.00 3.02
2322 2763 0.320508 GTCCCGGTTCAGTCCAGAAC 60.321 60.000 0.00 0.00 45.50 3.01
2326 2767 4.695560 GTTCAGTCCAGAACCGGG 57.304 61.111 6.32 0.00 41.52 5.73
2327 2768 2.055299 GTTCAGTCCAGAACCGGGA 58.945 57.895 6.32 0.00 41.52 5.14
2332 2773 4.243550 TCCAGAACCGGGACCAAT 57.756 55.556 6.32 0.00 0.00 3.16
2333 2774 1.682849 TCCAGAACCGGGACCAATG 59.317 57.895 6.32 0.00 0.00 2.82
2334 2775 1.378514 CCAGAACCGGGACCAATGG 60.379 63.158 6.32 0.00 0.00 3.16
2335 2776 1.378514 CAGAACCGGGACCAATGGG 60.379 63.158 6.32 0.00 41.29 4.00
2348 2789 1.340889 CCAATGGGTGCATTTATCCCG 59.659 52.381 4.96 0.00 43.75 5.14
2349 2790 1.340889 CAATGGGTGCATTTATCCCGG 59.659 52.381 4.96 0.00 43.75 5.73
2350 2791 0.555769 ATGGGTGCATTTATCCCGGT 59.444 50.000 0.00 0.00 43.75 5.28
2351 2792 0.333312 TGGGTGCATTTATCCCGGTT 59.667 50.000 0.00 0.00 43.75 4.44
2352 2793 1.029681 GGGTGCATTTATCCCGGTTC 58.970 55.000 0.00 0.00 0.00 3.62
2353 2794 0.661020 GGTGCATTTATCCCGGTTCG 59.339 55.000 0.00 0.00 0.00 3.95
2354 2795 1.375551 GTGCATTTATCCCGGTTCGT 58.624 50.000 0.00 0.00 0.00 3.85
2355 2796 1.063469 GTGCATTTATCCCGGTTCGTG 59.937 52.381 0.00 0.00 0.00 4.35
2356 2797 0.028902 GCATTTATCCCGGTTCGTGC 59.971 55.000 0.00 0.00 0.00 5.34
2357 2798 0.303493 CATTTATCCCGGTTCGTGCG 59.697 55.000 0.00 0.00 0.00 5.34
2358 2799 0.812412 ATTTATCCCGGTTCGTGCGG 60.812 55.000 0.00 0.00 0.00 5.69
2359 2800 4.517815 TATCCCGGTTCGTGCGGC 62.518 66.667 0.00 0.00 0.00 6.53
2362 2803 4.745751 CCCGGTTCGTGCGGCTAA 62.746 66.667 0.00 0.00 0.00 3.09
2363 2804 3.186047 CCGGTTCGTGCGGCTAAG 61.186 66.667 0.00 0.00 0.00 2.18
2364 2805 3.186047 CGGTTCGTGCGGCTAAGG 61.186 66.667 0.00 0.00 0.00 2.69
2365 2806 3.497031 GGTTCGTGCGGCTAAGGC 61.497 66.667 0.00 0.00 37.82 4.35
2366 2807 2.740826 GTTCGTGCGGCTAAGGCA 60.741 61.111 0.00 0.00 40.87 4.75
2367 2808 2.106683 GTTCGTGCGGCTAAGGCAT 61.107 57.895 0.00 0.00 43.19 4.40
2368 2809 1.376683 TTCGTGCGGCTAAGGCATT 60.377 52.632 0.00 0.00 43.19 3.56
2369 2810 0.108089 TTCGTGCGGCTAAGGCATTA 60.108 50.000 0.00 0.00 43.19 1.90
2370 2811 0.529773 TCGTGCGGCTAAGGCATTAG 60.530 55.000 13.70 13.70 43.19 1.73
2371 2812 0.810031 CGTGCGGCTAAGGCATTAGT 60.810 55.000 18.55 0.00 43.19 2.24
2372 2813 0.938008 GTGCGGCTAAGGCATTAGTC 59.062 55.000 18.55 15.72 43.19 2.59
2373 2814 0.179056 TGCGGCTAAGGCATTAGTCC 60.179 55.000 16.40 16.54 39.96 3.85
2374 2815 0.885150 GCGGCTAAGGCATTAGTCCC 60.885 60.000 16.40 10.33 39.96 4.46
2375 2816 0.600255 CGGCTAAGGCATTAGTCCCG 60.600 60.000 16.40 17.46 39.96 5.14
2376 2817 0.250338 GGCTAAGGCATTAGTCCCGG 60.250 60.000 18.55 0.00 40.55 5.73
2377 2818 0.468648 GCTAAGGCATTAGTCCCGGT 59.531 55.000 18.55 0.00 40.55 5.28
2378 2819 1.134189 GCTAAGGCATTAGTCCCGGTT 60.134 52.381 18.55 0.00 40.55 4.44
2379 2820 2.835027 CTAAGGCATTAGTCCCGGTTC 58.165 52.381 9.96 0.00 34.77 3.62
2380 2821 0.988832 AAGGCATTAGTCCCGGTTCA 59.011 50.000 0.00 0.00 0.00 3.18
2381 2822 0.252197 AGGCATTAGTCCCGGTTCAC 59.748 55.000 0.00 0.00 0.00 3.18
2382 2823 0.746923 GGCATTAGTCCCGGTTCACC 60.747 60.000 0.00 0.00 0.00 4.02
2383 2824 0.252197 GCATTAGTCCCGGTTCACCT 59.748 55.000 0.00 0.00 0.00 4.00
2384 2825 1.339727 GCATTAGTCCCGGTTCACCTT 60.340 52.381 0.00 0.00 0.00 3.50
2385 2826 2.356135 CATTAGTCCCGGTTCACCTTG 58.644 52.381 0.00 0.00 0.00 3.61
2386 2827 0.688487 TTAGTCCCGGTTCACCTTGG 59.312 55.000 0.00 0.00 0.00 3.61
2387 2828 1.833787 TAGTCCCGGTTCACCTTGGC 61.834 60.000 0.00 0.00 0.00 4.52
2388 2829 3.961414 TCCCGGTTCACCTTGGCC 61.961 66.667 0.00 0.00 0.00 5.36
2390 2831 3.966543 CCGGTTCACCTTGGCCCT 61.967 66.667 0.00 0.00 0.00 5.19
2391 2832 2.115266 CGGTTCACCTTGGCCCTT 59.885 61.111 0.00 0.00 0.00 3.95
2392 2833 1.530655 CGGTTCACCTTGGCCCTTT 60.531 57.895 0.00 0.00 0.00 3.11
2393 2834 0.250989 CGGTTCACCTTGGCCCTTTA 60.251 55.000 0.00 0.00 0.00 1.85
2394 2835 1.545841 GGTTCACCTTGGCCCTTTAG 58.454 55.000 0.00 0.00 0.00 1.85
2395 2836 1.203013 GGTTCACCTTGGCCCTTTAGT 60.203 52.381 0.00 0.00 0.00 2.24
2396 2837 2.160205 GTTCACCTTGGCCCTTTAGTC 58.840 52.381 0.00 0.00 0.00 2.59
2397 2838 0.696501 TCACCTTGGCCCTTTAGTCC 59.303 55.000 0.00 0.00 0.00 3.85
2398 2839 0.323451 CACCTTGGCCCTTTAGTCCC 60.323 60.000 0.00 0.00 0.00 4.46
2399 2840 1.077716 CCTTGGCCCTTTAGTCCCG 60.078 63.158 0.00 0.00 0.00 5.14
2400 2841 1.077716 CTTGGCCCTTTAGTCCCGG 60.078 63.158 0.00 0.00 0.00 5.73
2401 2842 1.848886 CTTGGCCCTTTAGTCCCGGT 61.849 60.000 0.00 0.00 0.00 5.28
2402 2843 1.428718 TTGGCCCTTTAGTCCCGGTT 61.429 55.000 0.00 0.00 0.00 4.44
2403 2844 1.077930 GGCCCTTTAGTCCCGGTTC 60.078 63.158 0.00 0.00 0.00 3.62
2404 2845 1.449070 GCCCTTTAGTCCCGGTTCG 60.449 63.158 0.00 0.00 0.00 3.95
2405 2846 1.977685 CCCTTTAGTCCCGGTTCGT 59.022 57.895 0.00 0.00 0.00 3.85
2406 2847 0.390735 CCCTTTAGTCCCGGTTCGTG 60.391 60.000 0.00 0.00 0.00 4.35
2407 2848 1.017701 CCTTTAGTCCCGGTTCGTGC 61.018 60.000 0.00 0.00 0.00 5.34
2408 2849 1.004679 TTTAGTCCCGGTTCGTGCC 60.005 57.895 0.00 0.00 0.00 5.01
2409 2850 1.756408 TTTAGTCCCGGTTCGTGCCA 61.756 55.000 0.00 0.00 0.00 4.92
2410 2851 2.438951 TTAGTCCCGGTTCGTGCCAC 62.439 60.000 0.00 0.00 0.00 5.01
2420 2861 3.041940 CGTGCCACGAACCAGGAC 61.042 66.667 12.85 0.00 46.05 3.85
2421 2862 2.426023 GTGCCACGAACCAGGACT 59.574 61.111 0.00 0.00 0.00 3.85
2422 2863 1.669440 GTGCCACGAACCAGGACTA 59.331 57.895 0.00 0.00 0.00 2.59
2423 2864 0.034337 GTGCCACGAACCAGGACTAA 59.966 55.000 0.00 0.00 0.00 2.24
2424 2865 0.759959 TGCCACGAACCAGGACTAAA 59.240 50.000 0.00 0.00 0.00 1.85
2425 2866 1.270625 TGCCACGAACCAGGACTAAAG 60.271 52.381 0.00 0.00 0.00 1.85
2426 2867 1.944430 GCCACGAACCAGGACTAAAGG 60.944 57.143 0.00 0.00 0.00 3.11
2427 2868 1.338769 CCACGAACCAGGACTAAAGGG 60.339 57.143 0.00 0.00 0.00 3.95
2428 2869 1.346722 CACGAACCAGGACTAAAGGGT 59.653 52.381 0.00 0.00 34.43 4.34
2429 2870 1.346722 ACGAACCAGGACTAAAGGGTG 59.653 52.381 0.00 0.00 33.00 4.61
2430 2871 1.822506 GAACCAGGACTAAAGGGTGC 58.177 55.000 0.00 0.00 33.00 5.01
2431 2872 0.036306 AACCAGGACTAAAGGGTGCG 59.964 55.000 0.00 0.00 33.00 5.34
2432 2873 0.834687 ACCAGGACTAAAGGGTGCGA 60.835 55.000 0.00 0.00 32.80 5.10
2433 2874 0.541863 CCAGGACTAAAGGGTGCGAT 59.458 55.000 0.00 0.00 32.80 4.58
2434 2875 1.656652 CAGGACTAAAGGGTGCGATG 58.343 55.000 0.00 0.00 32.80 3.84
2435 2876 0.107654 AGGACTAAAGGGTGCGATGC 60.108 55.000 0.00 0.00 32.80 3.91
2436 2877 1.095807 GGACTAAAGGGTGCGATGCC 61.096 60.000 0.00 0.00 0.00 4.40
2437 2878 1.077716 ACTAAAGGGTGCGATGCCC 60.078 57.895 1.67 1.67 46.43 5.36
2442 2883 3.530260 GGGTGCGATGCCCATTGG 61.530 66.667 0.00 0.00 45.40 3.16
2443 2884 2.755469 GGTGCGATGCCCATTGGT 60.755 61.111 1.20 0.00 0.00 3.67
2444 2885 2.774799 GGTGCGATGCCCATTGGTC 61.775 63.158 1.20 0.00 0.00 4.02
2445 2886 2.440065 TGCGATGCCCATTGGTCC 60.440 61.111 1.20 0.00 0.00 4.46
2446 2887 3.219198 GCGATGCCCATTGGTCCC 61.219 66.667 1.20 0.00 0.00 4.46
2447 2888 2.275089 CGATGCCCATTGGTCCCA 59.725 61.111 1.20 0.00 0.00 4.37
2448 2889 1.825191 CGATGCCCATTGGTCCCAG 60.825 63.158 1.20 0.00 0.00 4.45
2449 2890 1.307647 GATGCCCATTGGTCCCAGT 59.692 57.895 1.20 0.00 0.00 4.00
2450 2891 0.324645 GATGCCCATTGGTCCCAGTT 60.325 55.000 1.20 0.00 0.00 3.16
2451 2892 0.615544 ATGCCCATTGGTCCCAGTTG 60.616 55.000 1.20 0.00 0.00 3.16
2452 2893 1.984026 GCCCATTGGTCCCAGTTGG 60.984 63.158 1.20 9.36 33.52 3.77
2453 2894 1.464722 CCCATTGGTCCCAGTTGGT 59.535 57.895 13.35 0.00 32.53 3.67
2454 2895 0.899717 CCCATTGGTCCCAGTTGGTG 60.900 60.000 13.35 4.93 32.53 4.17
2456 2897 1.228862 ATTGGTCCCAGTTGGTGGC 60.229 57.895 0.00 0.00 46.45 5.01
2457 2898 2.017668 ATTGGTCCCAGTTGGTGGCA 62.018 55.000 0.00 0.00 46.45 4.92
2458 2899 2.597510 GGTCCCAGTTGGTGGCAC 60.598 66.667 9.70 9.70 46.45 5.01
2459 2900 2.597510 GTCCCAGTTGGTGGCACC 60.598 66.667 29.75 29.75 46.45 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.809806 GCATCCTTACAAACATTATATGCCTTC 59.190 37.037 0.00 0.00 32.95 3.46
75 76 3.244181 TGAGCTTTCAGTGCACATACTCA 60.244 43.478 21.04 17.94 0.00 3.41
76 77 3.329386 TGAGCTTTCAGTGCACATACTC 58.671 45.455 21.04 15.73 0.00 2.59
127 129 0.855349 GCCTATGTGATCTGTTCGCG 59.145 55.000 0.00 0.00 37.69 5.87
237 249 0.601311 AGTCACGCTTTCTGACCAGC 60.601 55.000 0.00 0.00 39.15 4.85
244 256 1.532868 GAATGTGCAGTCACGCTTTCT 59.467 47.619 0.00 0.00 46.01 2.52
288 300 2.470057 TTATGAATTTGGGGGAGGCC 57.530 50.000 0.00 0.00 0.00 5.19
348 366 9.503399 CCAACTAGTTCCTCTATGTTTTAGTTT 57.497 33.333 4.77 0.00 30.19 2.66
426 444 7.491696 AGCCACTCGTTAGTTCATATAAGAAAC 59.508 37.037 0.00 0.00 31.97 2.78
461 484 6.599244 TCCTACAAAATGGAGATGAACATCAC 59.401 38.462 15.63 9.93 40.22 3.06
608 631 4.251268 TCATTGATGAGCACAGAGACTTG 58.749 43.478 0.00 0.00 32.11 3.16
713 736 5.513094 GGAATATATGTCCCAGCTTAGCACA 60.513 44.000 7.07 1.89 0.00 4.57
793 816 7.224753 TCCATGCATTTCGAGTCTATAAGTTTC 59.775 37.037 0.00 0.00 0.00 2.78
1469 1525 5.237344 CCACCCTTAATTTCGATCTCATCAC 59.763 44.000 0.00 0.00 0.00 3.06
1481 1537 8.430573 AAACTTATTACAGCCACCCTTAATTT 57.569 30.769 0.00 0.00 0.00 1.82
1545 1609 3.670627 GCCGAACCACAGAAAAATAGCTG 60.671 47.826 0.00 0.00 38.10 4.24
1546 1610 2.488153 GCCGAACCACAGAAAAATAGCT 59.512 45.455 0.00 0.00 0.00 3.32
1548 1612 4.003648 AGAGCCGAACCACAGAAAAATAG 58.996 43.478 0.00 0.00 0.00 1.73
1549 1613 4.015872 AGAGCCGAACCACAGAAAAATA 57.984 40.909 0.00 0.00 0.00 1.40
1550 1614 2.863809 AGAGCCGAACCACAGAAAAAT 58.136 42.857 0.00 0.00 0.00 1.82
1552 1616 3.244422 ACATAGAGCCGAACCACAGAAAA 60.244 43.478 0.00 0.00 0.00 2.29
1553 1617 2.301870 ACATAGAGCCGAACCACAGAAA 59.698 45.455 0.00 0.00 0.00 2.52
1554 1618 1.899814 ACATAGAGCCGAACCACAGAA 59.100 47.619 0.00 0.00 0.00 3.02
1555 1619 1.557099 ACATAGAGCCGAACCACAGA 58.443 50.000 0.00 0.00 0.00 3.41
1556 1620 2.386661 AACATAGAGCCGAACCACAG 57.613 50.000 0.00 0.00 0.00 3.66
1557 1621 2.851263 AAACATAGAGCCGAACCACA 57.149 45.000 0.00 0.00 0.00 4.17
1558 1622 3.751698 AGAAAAACATAGAGCCGAACCAC 59.248 43.478 0.00 0.00 0.00 4.16
1648 1839 7.537596 TGGGAAATGTCAAAACATATGAAGT 57.462 32.000 10.38 0.00 45.48 3.01
1716 1907 9.710900 ATAAAAGCACCCTTTATTGAGAAAAAG 57.289 29.630 0.00 0.00 40.30 2.27
1830 2021 8.842764 TCCAAGTTAAGAATACCTATTCCCTTT 58.157 33.333 2.04 0.00 42.29 3.11
1831 2022 8.401955 TCCAAGTTAAGAATACCTATTCCCTT 57.598 34.615 2.04 0.00 42.29 3.95
1833 2024 8.030913 TCTCCAAGTTAAGAATACCTATTCCC 57.969 38.462 2.04 0.00 42.29 3.97
1837 2028 9.327731 CCCTATCTCCAAGTTAAGAATACCTAT 57.672 37.037 0.00 0.00 0.00 2.57
1838 2029 8.294690 ACCCTATCTCCAAGTTAAGAATACCTA 58.705 37.037 0.00 0.00 0.00 3.08
1839 2030 7.140304 ACCCTATCTCCAAGTTAAGAATACCT 58.860 38.462 0.00 0.00 0.00 3.08
1840 2031 7.376335 ACCCTATCTCCAAGTTAAGAATACC 57.624 40.000 0.00 0.00 0.00 2.73
1841 2032 7.146648 CGACCCTATCTCCAAGTTAAGAATAC 58.853 42.308 0.00 0.00 0.00 1.89
1843 2034 5.070580 CCGACCCTATCTCCAAGTTAAGAAT 59.929 44.000 0.00 0.00 0.00 2.40
1844 2035 4.404715 CCGACCCTATCTCCAAGTTAAGAA 59.595 45.833 0.00 0.00 0.00 2.52
1846 2037 3.958798 TCCGACCCTATCTCCAAGTTAAG 59.041 47.826 0.00 0.00 0.00 1.85
1847 2038 3.958798 CTCCGACCCTATCTCCAAGTTAA 59.041 47.826 0.00 0.00 0.00 2.01
1848 2039 3.053095 ACTCCGACCCTATCTCCAAGTTA 60.053 47.826 0.00 0.00 0.00 2.24
1850 2041 1.288335 ACTCCGACCCTATCTCCAAGT 59.712 52.381 0.00 0.00 0.00 3.16
1851 2042 2.074729 ACTCCGACCCTATCTCCAAG 57.925 55.000 0.00 0.00 0.00 3.61
1852 2043 3.897657 ATACTCCGACCCTATCTCCAA 57.102 47.619 0.00 0.00 0.00 3.53
1853 2044 4.353191 ACTTATACTCCGACCCTATCTCCA 59.647 45.833 0.00 0.00 0.00 3.86
1854 2045 4.920999 ACTTATACTCCGACCCTATCTCC 58.079 47.826 0.00 0.00 0.00 3.71
1855 2046 5.558818 TGACTTATACTCCGACCCTATCTC 58.441 45.833 0.00 0.00 0.00 2.75
1871 2306 9.713713 CAATCAGATCAGAATCAGATGACTTAT 57.286 33.333 0.00 0.00 37.96 1.73
1872 2307 7.656542 GCAATCAGATCAGAATCAGATGACTTA 59.343 37.037 0.00 0.00 37.96 2.24
1873 2308 6.483974 GCAATCAGATCAGAATCAGATGACTT 59.516 38.462 0.00 0.00 37.96 3.01
1874 2309 5.992829 GCAATCAGATCAGAATCAGATGACT 59.007 40.000 0.00 0.00 37.96 3.41
1875 2310 5.758784 TGCAATCAGATCAGAATCAGATGAC 59.241 40.000 0.00 0.00 37.96 3.06
1876 2311 5.758784 GTGCAATCAGATCAGAATCAGATGA 59.241 40.000 0.00 0.00 37.96 2.92
1877 2312 5.527582 TGTGCAATCAGATCAGAATCAGATG 59.472 40.000 0.00 0.00 37.96 2.90
1878 2313 5.681639 TGTGCAATCAGATCAGAATCAGAT 58.318 37.500 0.00 0.00 39.16 2.90
1904 2343 7.419057 CCAAAGTTATCTCAGCCTGGTCTTATA 60.419 40.741 0.00 0.00 0.00 0.98
1906 2345 5.338381 CCAAAGTTATCTCAGCCTGGTCTTA 60.338 44.000 0.00 0.00 0.00 2.10
1909 2348 3.055094 TCCAAAGTTATCTCAGCCTGGTC 60.055 47.826 0.00 0.00 0.00 4.02
1912 2351 3.937706 CACTCCAAAGTTATCTCAGCCTG 59.062 47.826 0.00 0.00 31.71 4.85
1913 2352 3.054802 CCACTCCAAAGTTATCTCAGCCT 60.055 47.826 0.00 0.00 31.71 4.58
1941 2380 1.349688 TGCACTACCAAAATCCGGAGT 59.650 47.619 11.34 3.58 0.00 3.85
1957 2396 3.334583 TGAACCTGACCTTATCTGCAC 57.665 47.619 0.00 0.00 0.00 4.57
1958 2397 4.365514 TTTGAACCTGACCTTATCTGCA 57.634 40.909 0.00 0.00 0.00 4.41
1959 2398 5.189180 AGATTTGAACCTGACCTTATCTGC 58.811 41.667 0.00 0.00 0.00 4.26
1960 2399 6.881065 TGAAGATTTGAACCTGACCTTATCTG 59.119 38.462 0.00 0.00 0.00 2.90
1961 2400 6.881602 GTGAAGATTTGAACCTGACCTTATCT 59.118 38.462 0.00 0.00 0.00 1.98
1962 2401 6.881602 AGTGAAGATTTGAACCTGACCTTATC 59.118 38.462 0.00 0.00 0.00 1.75
1963 2402 6.784031 AGTGAAGATTTGAACCTGACCTTAT 58.216 36.000 0.00 0.00 0.00 1.73
1964 2403 6.043243 AGAGTGAAGATTTGAACCTGACCTTA 59.957 38.462 0.00 0.00 0.00 2.69
1965 2404 5.053978 AGTGAAGATTTGAACCTGACCTT 57.946 39.130 0.00 0.00 0.00 3.50
1966 2405 4.349342 AGAGTGAAGATTTGAACCTGACCT 59.651 41.667 0.00 0.00 0.00 3.85
1967 2406 4.646572 AGAGTGAAGATTTGAACCTGACC 58.353 43.478 0.00 0.00 0.00 4.02
1968 2407 5.350091 GCTAGAGTGAAGATTTGAACCTGAC 59.650 44.000 0.00 0.00 0.00 3.51
1969 2408 5.247110 AGCTAGAGTGAAGATTTGAACCTGA 59.753 40.000 0.00 0.00 0.00 3.86
1970 2409 5.486526 AGCTAGAGTGAAGATTTGAACCTG 58.513 41.667 0.00 0.00 0.00 4.00
1971 2410 5.753721 AGCTAGAGTGAAGATTTGAACCT 57.246 39.130 0.00 0.00 0.00 3.50
1972 2411 6.635755 ACTAGCTAGAGTGAAGATTTGAACC 58.364 40.000 27.45 0.00 0.00 3.62
2039 2478 3.005791 GGTGGTTTGAATTTCCTGTCCAG 59.994 47.826 0.00 0.00 0.00 3.86
2044 2483 5.427378 AGTTTTGGTGGTTTGAATTTCCTG 58.573 37.500 0.00 0.00 0.00 3.86
2045 2484 5.692115 AGTTTTGGTGGTTTGAATTTCCT 57.308 34.783 0.00 0.00 0.00 3.36
2046 2485 6.481976 CCTTAGTTTTGGTGGTTTGAATTTCC 59.518 38.462 0.00 0.00 0.00 3.13
2047 2486 7.269316 TCCTTAGTTTTGGTGGTTTGAATTTC 58.731 34.615 0.00 0.00 0.00 2.17
2048 2487 7.189079 TCCTTAGTTTTGGTGGTTTGAATTT 57.811 32.000 0.00 0.00 0.00 1.82
2049 2488 6.800072 TCCTTAGTTTTGGTGGTTTGAATT 57.200 33.333 0.00 0.00 0.00 2.17
2050 2489 6.609616 TCTTCCTTAGTTTTGGTGGTTTGAAT 59.390 34.615 0.00 0.00 0.00 2.57
2051 2490 5.952947 TCTTCCTTAGTTTTGGTGGTTTGAA 59.047 36.000 0.00 0.00 0.00 2.69
2052 2491 5.511363 TCTTCCTTAGTTTTGGTGGTTTGA 58.489 37.500 0.00 0.00 0.00 2.69
2053 2492 5.845391 TCTTCCTTAGTTTTGGTGGTTTG 57.155 39.130 0.00 0.00 0.00 2.93
2054 2493 6.666113 TCTTTCTTCCTTAGTTTTGGTGGTTT 59.334 34.615 0.00 0.00 0.00 3.27
2055 2494 6.192044 TCTTTCTTCCTTAGTTTTGGTGGTT 58.808 36.000 0.00 0.00 0.00 3.67
2056 2495 5.762279 TCTTTCTTCCTTAGTTTTGGTGGT 58.238 37.500 0.00 0.00 0.00 4.16
2057 2496 6.709018 TTCTTTCTTCCTTAGTTTTGGTGG 57.291 37.500 0.00 0.00 0.00 4.61
2071 2510 3.796717 CCGTTGCCTTGTTTTCTTTCTTC 59.203 43.478 0.00 0.00 0.00 2.87
2072 2511 3.445805 TCCGTTGCCTTGTTTTCTTTCTT 59.554 39.130 0.00 0.00 0.00 2.52
2092 2531 6.042143 TGTTTGTGCTCTTTCTTTCATTTCC 58.958 36.000 0.00 0.00 0.00 3.13
2114 2553 4.993029 TTCTGAAACGTTTTGGGAATGT 57.007 36.364 15.89 0.00 0.00 2.71
2187 2628 4.223700 TGCAGAACTGAGGAGAATGTGTAT 59.776 41.667 5.97 0.00 0.00 2.29
2199 2640 2.222976 GCATGTCGATTGCAGAACTGAG 60.223 50.000 15.88 0.00 39.90 3.35
2218 2659 5.937540 TCTTCTTTTTAATCATGTCTCGGCA 59.062 36.000 0.00 0.00 0.00 5.69
2238 2679 8.499403 ACTAGTGAATCTGGCTTTAAATCTTC 57.501 34.615 0.00 0.00 0.00 2.87
2239 2680 9.606631 CTACTAGTGAATCTGGCTTTAAATCTT 57.393 33.333 5.39 0.00 0.00 2.40
2240 2681 8.982723 TCTACTAGTGAATCTGGCTTTAAATCT 58.017 33.333 5.39 0.00 0.00 2.40
2241 2682 9.601217 TTCTACTAGTGAATCTGGCTTTAAATC 57.399 33.333 5.39 0.00 0.00 2.17
2242 2683 9.959721 TTTCTACTAGTGAATCTGGCTTTAAAT 57.040 29.630 5.39 0.00 0.00 1.40
2243 2684 9.787435 TTTTCTACTAGTGAATCTGGCTTTAAA 57.213 29.630 5.39 0.00 0.00 1.52
2244 2685 9.436957 CTTTTCTACTAGTGAATCTGGCTTTAA 57.563 33.333 5.39 0.00 0.00 1.52
2245 2686 8.041323 CCTTTTCTACTAGTGAATCTGGCTTTA 58.959 37.037 5.39 0.00 0.00 1.85
2246 2687 6.881602 CCTTTTCTACTAGTGAATCTGGCTTT 59.118 38.462 5.39 0.00 0.00 3.51
2247 2688 6.213600 TCCTTTTCTACTAGTGAATCTGGCTT 59.786 38.462 5.39 0.00 0.00 4.35
2248 2689 5.721960 TCCTTTTCTACTAGTGAATCTGGCT 59.278 40.000 5.39 0.00 0.00 4.75
2249 2690 5.978814 TCCTTTTCTACTAGTGAATCTGGC 58.021 41.667 5.39 0.00 0.00 4.85
2250 2691 6.578023 CCTCCTTTTCTACTAGTGAATCTGG 58.422 44.000 5.39 9.39 0.00 3.86
2251 2692 6.045955 GCCTCCTTTTCTACTAGTGAATCTG 58.954 44.000 5.39 1.89 0.00 2.90
2252 2693 5.961421 AGCCTCCTTTTCTACTAGTGAATCT 59.039 40.000 5.39 0.00 0.00 2.40
2253 2694 6.228616 AGCCTCCTTTTCTACTAGTGAATC 57.771 41.667 5.39 0.00 0.00 2.52
2254 2695 6.628644 AAGCCTCCTTTTCTACTAGTGAAT 57.371 37.500 5.39 0.00 0.00 2.57
2255 2696 6.231211 CAAAGCCTCCTTTTCTACTAGTGAA 58.769 40.000 5.39 4.72 39.20 3.18
2256 2697 5.280011 CCAAAGCCTCCTTTTCTACTAGTGA 60.280 44.000 5.39 0.00 39.20 3.41
2257 2698 4.938226 CCAAAGCCTCCTTTTCTACTAGTG 59.062 45.833 5.39 0.00 39.20 2.74
2258 2699 4.597940 ACCAAAGCCTCCTTTTCTACTAGT 59.402 41.667 0.00 0.00 39.20 2.57
2259 2700 5.167303 ACCAAAGCCTCCTTTTCTACTAG 57.833 43.478 0.00 0.00 39.20 2.57
2260 2701 4.019591 GGACCAAAGCCTCCTTTTCTACTA 60.020 45.833 0.00 0.00 39.20 1.82
2261 2702 3.244946 GGACCAAAGCCTCCTTTTCTACT 60.245 47.826 0.00 0.00 39.20 2.57
2262 2703 3.082548 GGACCAAAGCCTCCTTTTCTAC 58.917 50.000 0.00 0.00 39.20 2.59
2263 2704 2.714250 TGGACCAAAGCCTCCTTTTCTA 59.286 45.455 0.00 0.00 39.20 2.10
2264 2705 1.499007 TGGACCAAAGCCTCCTTTTCT 59.501 47.619 0.00 0.00 39.20 2.52
2265 2706 1.889170 CTGGACCAAAGCCTCCTTTTC 59.111 52.381 0.00 0.00 39.20 2.29
2266 2707 1.481242 CCTGGACCAAAGCCTCCTTTT 60.481 52.381 0.00 0.00 39.20 2.27
2267 2708 0.113190 CCTGGACCAAAGCCTCCTTT 59.887 55.000 0.00 0.00 41.86 3.11
2268 2709 1.770324 CCTGGACCAAAGCCTCCTT 59.230 57.895 0.00 0.00 0.00 3.36
2269 2710 2.911926 GCCTGGACCAAAGCCTCCT 61.912 63.158 0.00 0.00 0.00 3.69
2270 2711 2.361737 GCCTGGACCAAAGCCTCC 60.362 66.667 0.00 0.00 0.00 4.30
2271 2712 2.361737 GGCCTGGACCAAAGCCTC 60.362 66.667 22.59 3.10 42.34 4.70
2272 2713 4.351054 CGGCCTGGACCAAAGCCT 62.351 66.667 25.43 0.00 43.48 4.58
2275 2716 2.132089 TTACCCGGCCTGGACCAAAG 62.132 60.000 21.63 2.26 42.00 2.77
2276 2717 2.132089 CTTACCCGGCCTGGACCAAA 62.132 60.000 21.63 7.43 42.00 3.28
2277 2718 2.529643 TTACCCGGCCTGGACCAA 60.530 61.111 21.63 7.80 42.00 3.67
2278 2719 3.006728 CTTACCCGGCCTGGACCA 61.007 66.667 21.63 1.34 42.00 4.02
2279 2720 4.484872 GCTTACCCGGCCTGGACC 62.485 72.222 21.63 0.96 42.00 4.46
2280 2721 4.484872 GGCTTACCCGGCCTGGAC 62.485 72.222 21.63 6.01 45.57 4.02
2290 2731 0.108019 CCGGGACTAATGGGCTTACC 59.892 60.000 0.00 0.00 40.81 2.85
2291 2732 0.835276 ACCGGGACTAATGGGCTTAC 59.165 55.000 6.32 0.00 0.00 2.34
2292 2733 1.487558 GAACCGGGACTAATGGGCTTA 59.512 52.381 6.32 0.00 0.00 3.09
2293 2734 0.255033 GAACCGGGACTAATGGGCTT 59.745 55.000 6.32 0.00 0.00 4.35
2294 2735 0.912487 TGAACCGGGACTAATGGGCT 60.912 55.000 6.32 0.00 0.00 5.19
2295 2736 0.463833 CTGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
2296 2737 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
2297 2738 1.134491 GGACTGAACCGGGACTAATGG 60.134 57.143 6.32 0.00 0.00 3.16
2298 2739 1.553248 TGGACTGAACCGGGACTAATG 59.447 52.381 6.32 0.00 0.00 1.90
2299 2740 1.831736 CTGGACTGAACCGGGACTAAT 59.168 52.381 6.32 0.00 33.06 1.73
2300 2741 1.203087 TCTGGACTGAACCGGGACTAA 60.203 52.381 6.32 0.00 36.97 2.24
2301 2742 0.406750 TCTGGACTGAACCGGGACTA 59.593 55.000 6.32 0.00 36.97 2.59
2302 2743 0.471211 TTCTGGACTGAACCGGGACT 60.471 55.000 6.32 0.00 36.97 3.85
2303 2744 0.320508 GTTCTGGACTGAACCGGGAC 60.321 60.000 6.32 0.00 40.10 4.46
2304 2745 2.055299 GTTCTGGACTGAACCGGGA 58.945 57.895 6.32 0.00 40.10 5.14
2305 2746 4.695560 GTTCTGGACTGAACCGGG 57.304 61.111 6.32 0.00 40.10 5.73
2309 2750 2.055299 TCCCGGTTCTGGACTGAAC 58.945 57.895 12.04 12.04 43.88 3.18
2310 2751 4.631493 TCCCGGTTCTGGACTGAA 57.369 55.556 0.00 0.00 36.72 3.02
2315 2756 1.682849 CATTGGTCCCGGTTCTGGA 59.317 57.895 0.00 0.00 0.00 3.86
2316 2757 1.378514 CCATTGGTCCCGGTTCTGG 60.379 63.158 0.00 0.00 0.00 3.86
2317 2758 1.378514 CCCATTGGTCCCGGTTCTG 60.379 63.158 0.00 0.00 0.00 3.02
2318 2759 1.850755 ACCCATTGGTCCCGGTTCT 60.851 57.895 0.00 0.00 43.06 3.01
2319 2760 1.677633 CACCCATTGGTCCCGGTTC 60.678 63.158 0.00 0.00 45.57 3.62
2320 2761 2.438795 CACCCATTGGTCCCGGTT 59.561 61.111 0.00 0.00 45.57 4.44
2321 2762 4.360405 GCACCCATTGGTCCCGGT 62.360 66.667 0.00 0.00 45.57 5.28
2322 2763 3.660422 ATGCACCCATTGGTCCCGG 62.660 63.158 1.20 0.00 45.57 5.73
2323 2764 1.257055 AAATGCACCCATTGGTCCCG 61.257 55.000 1.20 0.00 45.57 5.14
2324 2765 1.859302 TAAATGCACCCATTGGTCCC 58.141 50.000 1.20 0.00 45.57 4.46
2325 2766 2.365293 GGATAAATGCACCCATTGGTCC 59.635 50.000 1.20 0.00 45.57 4.46
2326 2767 2.365293 GGGATAAATGCACCCATTGGTC 59.635 50.000 4.47 0.00 45.57 4.02
2328 2769 1.340889 CGGGATAAATGCACCCATTGG 59.659 52.381 9.80 0.00 40.69 3.16
2329 2770 1.340889 CCGGGATAAATGCACCCATTG 59.659 52.381 9.80 0.00 40.69 2.82
2330 2771 1.063266 ACCGGGATAAATGCACCCATT 60.063 47.619 6.32 0.00 43.32 3.16
2331 2772 0.555769 ACCGGGATAAATGCACCCAT 59.444 50.000 6.32 0.00 43.40 4.00
2332 2773 0.333312 AACCGGGATAAATGCACCCA 59.667 50.000 6.32 0.00 43.40 4.51
2333 2774 1.029681 GAACCGGGATAAATGCACCC 58.970 55.000 6.32 0.00 40.17 4.61
2334 2775 0.661020 CGAACCGGGATAAATGCACC 59.339 55.000 6.32 0.00 0.00 5.01
2335 2776 1.063469 CACGAACCGGGATAAATGCAC 59.937 52.381 6.32 0.00 28.17 4.57
2336 2777 1.374560 CACGAACCGGGATAAATGCA 58.625 50.000 6.32 0.00 28.17 3.96
2337 2778 0.028902 GCACGAACCGGGATAAATGC 59.971 55.000 6.32 4.00 28.17 3.56
2338 2779 0.303493 CGCACGAACCGGGATAAATG 59.697 55.000 6.32 0.00 28.17 2.32
2339 2780 0.812412 CCGCACGAACCGGGATAAAT 60.812 55.000 6.32 0.00 41.99 1.40
2340 2781 1.448189 CCGCACGAACCGGGATAAA 60.448 57.895 6.32 0.00 41.99 1.40
2341 2782 2.184836 CCGCACGAACCGGGATAA 59.815 61.111 6.32 0.00 41.99 1.75
2342 2783 4.517815 GCCGCACGAACCGGGATA 62.518 66.667 6.32 0.00 45.66 2.59
2345 2786 4.745751 TTAGCCGCACGAACCGGG 62.746 66.667 6.32 0.00 45.66 5.73
2347 2788 3.186047 CCTTAGCCGCACGAACCG 61.186 66.667 0.00 0.00 0.00 4.44
2348 2789 3.497031 GCCTTAGCCGCACGAACC 61.497 66.667 0.00 0.00 0.00 3.62
2349 2790 1.644786 AATGCCTTAGCCGCACGAAC 61.645 55.000 0.00 0.00 39.49 3.95
2350 2791 0.108089 TAATGCCTTAGCCGCACGAA 60.108 50.000 0.00 0.00 39.49 3.85
2351 2792 0.529773 CTAATGCCTTAGCCGCACGA 60.530 55.000 0.00 0.00 39.49 4.35
2352 2793 0.810031 ACTAATGCCTTAGCCGCACG 60.810 55.000 8.50 0.00 39.49 5.34
2353 2794 0.938008 GACTAATGCCTTAGCCGCAC 59.062 55.000 8.50 0.00 39.49 5.34
2354 2795 0.179056 GGACTAATGCCTTAGCCGCA 60.179 55.000 8.50 0.00 38.33 5.69
2355 2796 0.885150 GGGACTAATGCCTTAGCCGC 60.885 60.000 8.50 2.93 38.33 6.53
2356 2797 0.600255 CGGGACTAATGCCTTAGCCG 60.600 60.000 8.50 10.12 38.33 5.52
2357 2798 0.250338 CCGGGACTAATGCCTTAGCC 60.250 60.000 8.50 10.09 38.33 3.93
2358 2799 0.468648 ACCGGGACTAATGCCTTAGC 59.531 55.000 6.32 2.56 38.33 3.09
2359 2800 2.169769 TGAACCGGGACTAATGCCTTAG 59.830 50.000 6.32 7.17 40.25 2.18
2360 2801 2.093341 GTGAACCGGGACTAATGCCTTA 60.093 50.000 6.32 0.00 33.05 2.69
2361 2802 0.988832 TGAACCGGGACTAATGCCTT 59.011 50.000 6.32 0.00 33.05 4.35
2362 2803 0.252197 GTGAACCGGGACTAATGCCT 59.748 55.000 6.32 0.00 33.05 4.75
2363 2804 0.746923 GGTGAACCGGGACTAATGCC 60.747 60.000 6.32 0.00 0.00 4.40
2364 2805 0.252197 AGGTGAACCGGGACTAATGC 59.748 55.000 6.32 0.00 42.08 3.56
2365 2806 2.356135 CAAGGTGAACCGGGACTAATG 58.644 52.381 6.32 0.00 42.08 1.90
2366 2807 1.280998 CCAAGGTGAACCGGGACTAAT 59.719 52.381 6.32 0.00 42.08 1.73
2367 2808 0.688487 CCAAGGTGAACCGGGACTAA 59.312 55.000 6.32 0.00 42.08 2.24
2368 2809 1.833787 GCCAAGGTGAACCGGGACTA 61.834 60.000 6.32 0.00 42.08 2.59
2369 2810 3.157680 CCAAGGTGAACCGGGACT 58.842 61.111 6.32 0.00 42.08 3.85
2370 2811 2.671963 GCCAAGGTGAACCGGGAC 60.672 66.667 6.32 0.00 42.08 4.46
2371 2812 3.961414 GGCCAAGGTGAACCGGGA 61.961 66.667 6.32 0.00 42.08 5.14
2373 2814 2.994643 AAAGGGCCAAGGTGAACCGG 62.995 60.000 6.18 0.00 42.08 5.28
2374 2815 0.250989 TAAAGGGCCAAGGTGAACCG 60.251 55.000 6.18 0.00 42.08 4.44
2375 2816 1.203013 ACTAAAGGGCCAAGGTGAACC 60.203 52.381 6.18 0.00 0.00 3.62
2376 2817 2.160205 GACTAAAGGGCCAAGGTGAAC 58.840 52.381 6.18 0.00 0.00 3.18
2377 2818 1.074889 GGACTAAAGGGCCAAGGTGAA 59.925 52.381 6.18 0.00 44.40 3.18
2378 2819 0.696501 GGACTAAAGGGCCAAGGTGA 59.303 55.000 6.18 0.00 44.40 4.02
2379 2820 3.266240 GGACTAAAGGGCCAAGGTG 57.734 57.895 6.18 0.00 44.40 4.00
2385 2826 1.077930 GAACCGGGACTAAAGGGCC 60.078 63.158 6.32 0.00 44.23 5.80
2386 2827 1.449070 CGAACCGGGACTAAAGGGC 60.449 63.158 6.32 0.00 0.00 5.19
2387 2828 0.390735 CACGAACCGGGACTAAAGGG 60.391 60.000 6.32 0.00 28.17 3.95
2388 2829 1.017701 GCACGAACCGGGACTAAAGG 61.018 60.000 6.32 0.00 28.17 3.11
2389 2830 1.017701 GGCACGAACCGGGACTAAAG 61.018 60.000 6.32 0.00 34.24 1.85
2390 2831 1.004679 GGCACGAACCGGGACTAAA 60.005 57.895 6.32 0.00 34.24 1.85
2391 2832 2.208619 TGGCACGAACCGGGACTAA 61.209 57.895 6.32 0.00 40.06 2.24
2392 2833 2.601067 TGGCACGAACCGGGACTA 60.601 61.111 6.32 0.00 40.06 2.59
2393 2834 4.309950 GTGGCACGAACCGGGACT 62.310 66.667 6.32 0.00 40.06 3.85
2403 2844 2.149803 TAGTCCTGGTTCGTGGCACG 62.150 60.000 32.75 32.75 44.19 5.34
2404 2845 0.034337 TTAGTCCTGGTTCGTGGCAC 59.966 55.000 7.79 7.79 0.00 5.01
2405 2846 0.759959 TTTAGTCCTGGTTCGTGGCA 59.240 50.000 0.00 0.00 0.00 4.92
2406 2847 1.439679 CTTTAGTCCTGGTTCGTGGC 58.560 55.000 0.00 0.00 0.00 5.01
2407 2848 1.338769 CCCTTTAGTCCTGGTTCGTGG 60.339 57.143 0.00 0.00 0.00 4.94
2408 2849 1.346722 ACCCTTTAGTCCTGGTTCGTG 59.653 52.381 0.00 0.00 0.00 4.35
2409 2850 1.346722 CACCCTTTAGTCCTGGTTCGT 59.653 52.381 0.00 0.00 0.00 3.85
2410 2851 1.944430 GCACCCTTTAGTCCTGGTTCG 60.944 57.143 0.00 0.00 0.00 3.95
2411 2852 1.822506 GCACCCTTTAGTCCTGGTTC 58.177 55.000 0.00 0.00 0.00 3.62
2412 2853 0.036306 CGCACCCTTTAGTCCTGGTT 59.964 55.000 0.00 0.00 0.00 3.67
2413 2854 0.834687 TCGCACCCTTTAGTCCTGGT 60.835 55.000 0.00 0.00 0.00 4.00
2414 2855 0.541863 ATCGCACCCTTTAGTCCTGG 59.458 55.000 0.00 0.00 0.00 4.45
2415 2856 1.656652 CATCGCACCCTTTAGTCCTG 58.343 55.000 0.00 0.00 0.00 3.86
2416 2857 0.107654 GCATCGCACCCTTTAGTCCT 60.108 55.000 0.00 0.00 0.00 3.85
2417 2858 1.095807 GGCATCGCACCCTTTAGTCC 61.096 60.000 0.00 0.00 0.00 3.85
2418 2859 1.095807 GGGCATCGCACCCTTTAGTC 61.096 60.000 0.40 0.00 44.68 2.59
2419 2860 1.077716 GGGCATCGCACCCTTTAGT 60.078 57.895 0.40 0.00 44.68 2.24
2420 2861 3.827634 GGGCATCGCACCCTTTAG 58.172 61.111 0.40 0.00 44.68 1.85
2426 2867 2.755469 ACCAATGGGCATCGCACC 60.755 61.111 3.55 0.00 37.90 5.01
2427 2868 2.774799 GGACCAATGGGCATCGCAC 61.775 63.158 7.73 0.00 37.90 5.34
2428 2869 2.440065 GGACCAATGGGCATCGCA 60.440 61.111 7.73 0.00 37.90 5.10
2429 2870 3.219198 GGGACCAATGGGCATCGC 61.219 66.667 7.73 0.00 37.90 4.58
2430 2871 1.825191 CTGGGACCAATGGGCATCG 60.825 63.158 7.73 0.00 37.90 3.84
2431 2872 0.324645 AACTGGGACCAATGGGCATC 60.325 55.000 7.73 0.00 37.90 3.91
2432 2873 0.615544 CAACTGGGACCAATGGGCAT 60.616 55.000 7.73 0.00 37.90 4.40
2433 2874 1.228831 CAACTGGGACCAATGGGCA 60.229 57.895 7.73 0.00 37.90 5.36
2434 2875 1.984026 CCAACTGGGACCAATGGGC 60.984 63.158 3.55 0.00 40.01 5.36
2435 2876 0.899717 CACCAACTGGGACCAATGGG 60.900 60.000 20.62 9.28 41.15 4.00
2436 2877 0.899717 CCACCAACTGGGACCAATGG 60.900 60.000 16.97 16.97 41.15 3.16
2437 2878 1.535204 GCCACCAACTGGGACCAATG 61.535 60.000 0.00 0.00 41.02 2.82
2438 2879 1.228862 GCCACCAACTGGGACCAAT 60.229 57.895 0.00 0.00 41.02 3.16
2439 2880 2.197324 GCCACCAACTGGGACCAA 59.803 61.111 0.00 0.00 41.02 3.67
2440 2881 3.099841 TGCCACCAACTGGGACCA 61.100 61.111 0.00 0.00 41.02 4.02


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

AutoCloner maintained by Alex Coulton.