Multiple sequence alignment - TraesCS1B01G194900

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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 TraesCS1B01G194900 chr1B 100.000 2844 0 0 1 2844 349829497 349832340 0.000000e+00 5252.0
1 TraesCS1B01G194900 chr1B 91.346 208 12 1 2199 2400 349831487 349831694 2.160000e-71 279.0
2 TraesCS1B01G194900 chr1B 91.346 208 12 1 1991 2198 349831695 349831896 2.160000e-71 279.0
3 TraesCS1B01G194900 chr1B 88.793 116 12 1 2036 2150 433422918 433422803 1.060000e-29 141.0
4 TraesCS1B01G194900 chr1B 81.690 142 22 4 2455 2593 669165575 669165435 6.440000e-22 115.0
5 TraesCS1B01G194900 chr1D 92.919 1158 59 7 741 1882 261893397 261892247 0.000000e+00 1663.0
6 TraesCS1B01G194900 chr1D 90.041 723 68 4 18 738 3844004 3843284 0.000000e+00 933.0
7 TraesCS1B01G194900 chr1D 88.581 289 23 5 2557 2844 261892033 261891754 2.710000e-90 342.0
8 TraesCS1B01G194900 chr1D 88.406 69 7 1 2036 2103 296692615 296692683 6.530000e-12 82.4
9 TraesCS1B01G194900 chr1D 94.737 38 2 0 2254 2291 478706620 478706657 3.060000e-05 60.2
10 TraesCS1B01G194900 chr3D 91.286 723 59 3 18 738 578895458 578896178 0.000000e+00 983.0
11 TraesCS1B01G194900 chr3D 81.208 149 20 7 2448 2593 277134919 277135062 2.320000e-21 113.0
12 TraesCS1B01G194900 chr3D 90.244 82 7 1 2039 2120 541296339 541296259 3.880000e-19 106.0
13 TraesCS1B01G194900 chr3D 82.857 70 11 1 2244 2313 554769091 554769023 8.510000e-06 62.1
14 TraesCS1B01G194900 chr7D 90.884 724 62 3 18 738 549798619 549799341 0.000000e+00 968.0
15 TraesCS1B01G194900 chr7D 85.600 125 17 1 2469 2593 75346788 75346911 2.300000e-26 130.0
16 TraesCS1B01G194900 chr7D 86.607 112 13 2 2244 2353 578789747 578789636 3.850000e-24 122.0
17 TraesCS1B01G194900 chr7B 90.947 718 62 2 23 738 544619664 544618948 0.000000e+00 963.0
18 TraesCS1B01G194900 chr5B 91.168 702 59 3 18 716 16413954 16413253 0.000000e+00 950.0
19 TraesCS1B01G194900 chr5B 90.483 725 62 6 18 738 478545211 478545932 0.000000e+00 950.0
20 TraesCS1B01G194900 chr5B 85.039 127 14 4 2469 2593 273302887 273303010 1.070000e-24 124.0
21 TraesCS1B01G194900 chr5D 91.051 704 57 5 23 720 558875460 558874757 0.000000e+00 946.0
22 TraesCS1B01G194900 chr5D 89.903 723 71 1 18 738 44087999 44087277 0.000000e+00 929.0
23 TraesCS1B01G194900 chr5D 84.884 86 11 2 1952 2035 408543882 408543797 5.050000e-13 86.1
24 TraesCS1B01G194900 chr3B 90.180 723 64 4 18 738 162515449 162514732 0.000000e+00 935.0
25 TraesCS1B01G194900 chr3B 86.408 103 13 1 2036 2137 716301604 716301502 8.330000e-21 111.0
26 TraesCS1B01G194900 chr1A 91.796 646 24 9 799 1416 337947660 337948304 0.000000e+00 872.0
27 TraesCS1B01G194900 chr1A 89.344 610 43 9 1434 2039 337948759 337949350 0.000000e+00 747.0
28 TraesCS1B01G194900 chr1A 85.000 620 69 12 2245 2842 337949391 337950008 2.420000e-170 608.0
29 TraesCS1B01G194900 chrUn 85.039 127 15 3 2469 2593 112557430 112557306 2.970000e-25 126.0
30 TraesCS1B01G194900 chrUn 89.474 76 4 4 1949 2021 38450032 38450106 3.020000e-15 93.5
31 TraesCS1B01G194900 chrUn 82.857 70 11 1 2244 2313 45262121 45262189 8.510000e-06 62.1
32 TraesCS1B01G194900 chr4D 76.210 248 53 4 1092 1336 465357969 465358213 2.970000e-25 126.0
33 TraesCS1B01G194900 chr4D 87.368 95 9 3 1948 2039 51076341 51076247 3.880000e-19 106.0
34 TraesCS1B01G194900 chr4D 86.022 93 11 2 1949 2039 500823258 500823350 6.480000e-17 99.0
35 TraesCS1B01G194900 chr7A 84.375 128 19 1 2468 2595 443969583 443969457 1.070000e-24 124.0
36 TraesCS1B01G194900 chr7A 83.673 98 14 2 1944 2039 47049071 47048974 1.090000e-14 91.6
37 TraesCS1B01G194900 chr4A 82.394 142 25 0 1107 1248 5115167 5115026 1.070000e-24 124.0
38 TraesCS1B01G194900 chr2D 84.921 126 15 3 2469 2593 6865066 6864944 1.070000e-24 124.0
39 TraesCS1B01G194900 chr2D 83.333 108 13 4 2036 2140 641623604 641623499 8.390000e-16 95.3
40 TraesCS1B01G194900 chr2B 83.582 134 14 7 2465 2593 530249143 530249273 4.980000e-23 119.0
41 TraesCS1B01G194900 chr3A 83.898 118 15 4 2036 2150 15562110 15561994 3.000000e-20 110.0
42 TraesCS1B01G194900 chr5A 85.556 90 11 2 1952 2039 493864108 493864197 3.020000e-15 93.5
43 TraesCS1B01G194900 chr6D 83.158 95 12 4 1948 2039 319259231 319259138 1.820000e-12 84.2
44 TraesCS1B01G194900 chr4B 82.979 94 14 2 1948 2039 99014927 99015020 1.820000e-12 84.2


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 TraesCS1B01G194900 chr1B 349829497 349832340 2843 False 1936.666667 5252 94.230667 1 2844 3 chr1B.!!$F1 2843
1 TraesCS1B01G194900 chr1D 261891754 261893397 1643 True 1002.500000 1663 90.750000 741 2844 2 chr1D.!!$R2 2103
2 TraesCS1B01G194900 chr1D 3843284 3844004 720 True 933.000000 933 90.041000 18 738 1 chr1D.!!$R1 720
3 TraesCS1B01G194900 chr3D 578895458 578896178 720 False 983.000000 983 91.286000 18 738 1 chr3D.!!$F2 720
4 TraesCS1B01G194900 chr7D 549798619 549799341 722 False 968.000000 968 90.884000 18 738 1 chr7D.!!$F2 720
5 TraesCS1B01G194900 chr7B 544618948 544619664 716 True 963.000000 963 90.947000 23 738 1 chr7B.!!$R1 715
6 TraesCS1B01G194900 chr5B 16413253 16413954 701 True 950.000000 950 91.168000 18 716 1 chr5B.!!$R1 698
7 TraesCS1B01G194900 chr5B 478545211 478545932 721 False 950.000000 950 90.483000 18 738 1 chr5B.!!$F2 720
8 TraesCS1B01G194900 chr5D 558874757 558875460 703 True 946.000000 946 91.051000 23 720 1 chr5D.!!$R3 697
9 TraesCS1B01G194900 chr5D 44087277 44087999 722 True 929.000000 929 89.903000 18 738 1 chr5D.!!$R1 720
10 TraesCS1B01G194900 chr3B 162514732 162515449 717 True 935.000000 935 90.180000 18 738 1 chr3B.!!$R1 720
11 TraesCS1B01G194900 chr1A 337947660 337950008 2348 False 742.333333 872 88.713333 799 2842 3 chr1A.!!$F1 2043

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
861 883 0.039798 TGGTACACAAGTCGAGCGAC 60.04 55.0 14.65 14.65 44.86 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2385 0.035439 GCCAGCAGGTTACTTAGCCA 60.035 55.0 0.0 0.0 37.19 4.75 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
20 21 1.273327 CCCTTTTTCCACCAGTGATGC 59.727 52.381 0.00 0.00 0.00 3.91
75 76 6.446318 AGTGTTTATGTGGTTTGTGCATAAG 58.554 36.000 0.00 0.00 36.72 1.73
129 131 2.866156 ACGCAATTGGACATGATCTACG 59.134 45.455 7.72 0.00 0.00 3.51
157 159 1.462791 CTTTTGCGACCAACACGAAC 58.537 50.000 0.00 0.00 0.00 3.95
175 177 4.401202 ACGAACCAATCAAACACCTCTTTT 59.599 37.500 0.00 0.00 0.00 2.27
239 243 5.941647 ACATAGCTTTTAACATTACCACCGT 59.058 36.000 0.00 0.00 0.00 4.83
263 267 4.174009 CTCTATCAACGCGTTATATGGGG 58.826 47.826 26.11 18.22 0.00 4.96
293 297 7.164122 GCTTGATGGGATAGATTCAGATACAA 58.836 38.462 0.00 0.00 0.00 2.41
294 298 7.828223 GCTTGATGGGATAGATTCAGATACAAT 59.172 37.037 0.00 0.00 0.00 2.71
313 317 9.909644 GATACAATAAGACATATTCGTGTAGGT 57.090 33.333 0.00 0.00 31.69 3.08
421 425 3.040965 CAGGGCCACTGTGTTGATT 57.959 52.632 6.18 0.00 42.42 2.57
427 431 3.527533 GGCCACTGTGTTGATTCGTATA 58.472 45.455 7.08 0.00 0.00 1.47
449 455 0.520404 GTCGCTACTCACTCCAACGA 59.480 55.000 0.00 0.00 0.00 3.85
466 472 1.298667 GAAGGCCAGGGAGCGTTTA 59.701 57.895 5.01 0.00 40.69 2.01
483 489 3.366273 CGTTTAGTTACTGCGTCTACCCA 60.366 47.826 0.00 0.00 0.00 4.51
522 528 3.440872 CGGGATATTTTCAACCGGTTTGA 59.559 43.478 19.55 15.72 42.83 2.69
531 541 1.110518 AACCGGTTTGAATGGCGGTT 61.111 50.000 15.86 0.00 35.27 4.44
543 553 5.302360 TGAATGGCGGTTATGTAATAGGAC 58.698 41.667 0.00 0.00 0.00 3.85
600 610 4.638304 GGTTGTGGCTTTTCTACTACTGA 58.362 43.478 0.00 0.00 33.75 3.41
655 669 3.784701 TCGAGACTTGGAGACTTATGC 57.215 47.619 0.00 0.00 0.00 3.14
720 734 4.496336 GCAGAGGCTGGGGCGAAT 62.496 66.667 0.00 0.00 39.81 3.34
758 772 1.135460 CGTGGTCTCGAGAAGGTTACC 60.135 57.143 18.55 14.06 0.00 2.85
783 797 2.030457 CCACAGAAAATCCGATACACGC 59.970 50.000 0.00 0.00 41.07 5.34
790 804 2.131294 ATCCGATACACGCTCGCTCC 62.131 60.000 0.00 0.00 41.07 4.70
834 848 1.792949 GTCATCAAGAAACGTGCGTCT 59.207 47.619 0.00 0.00 0.00 4.18
861 883 0.039798 TGGTACACAAGTCGAGCGAC 60.040 55.000 14.65 14.65 44.86 5.19
923 958 2.017049 GTAGTGGCCGATGCTTCAATT 58.983 47.619 0.00 0.00 37.74 2.32
1027 1071 1.289380 GAGAAACAGGAGACGGCGT 59.711 57.895 14.65 14.65 0.00 5.68
1228 1272 0.965439 CTCCGAGTCCCTCATCATCC 59.035 60.000 0.00 0.00 0.00 3.51
1236 1280 3.143741 AGTCCCTCATCATCCTCCAGTAT 59.856 47.826 0.00 0.00 0.00 2.12
1430 1476 5.772393 TGAGATTACAAAGCTTTCCCCTA 57.228 39.130 9.23 0.00 0.00 3.53
1446 1929 1.265905 CCCTAAACAAACGTGTGCTCC 59.734 52.381 5.39 0.00 38.27 4.70
1450 1933 0.393808 AACAAACGTGTGCTCCCTGT 60.394 50.000 5.39 0.00 38.27 4.00
1468 1951 3.063997 CCTGTTCAATGGATGCGTAGTTC 59.936 47.826 0.00 0.00 0.00 3.01
1569 2052 4.785453 CCTGGAGGTGGCCTTCGC 62.785 72.222 3.32 0.00 29.90 4.70
1652 2135 3.458163 GGTCGCACCTCGGATGGA 61.458 66.667 0.00 0.00 39.05 3.41
1717 2200 0.681243 CCAAGGTTCCTAAGCTGGCC 60.681 60.000 0.00 0.00 39.57 5.36
1720 2203 2.824489 GTTCCTAAGCTGGCCGCC 60.824 66.667 14.64 1.04 40.39 6.13
1806 2289 1.734465 GGAGTTCAGCGTCAAGAATGG 59.266 52.381 0.00 0.00 0.00 3.16
1814 2297 3.126879 TCAAGAATGGCGGCGCTG 61.127 61.111 32.30 20.49 0.00 5.18
1836 2319 2.432874 TGAAGGCGGCTAGTGCTAATTA 59.567 45.455 13.71 0.00 39.59 1.40
1853 2336 6.071463 GCTAATTACAAGTGAACGAACTGTG 58.929 40.000 0.00 0.00 0.00 3.66
1894 2377 4.960938 TCGATGGCATAGCAAGAATAAGT 58.039 39.130 0.00 0.00 0.00 2.24
1895 2378 6.096673 TCGATGGCATAGCAAGAATAAGTA 57.903 37.500 0.00 0.00 0.00 2.24
1896 2379 6.521162 TCGATGGCATAGCAAGAATAAGTAA 58.479 36.000 0.00 0.00 0.00 2.24
1897 2380 6.423905 TCGATGGCATAGCAAGAATAAGTAAC 59.576 38.462 0.00 0.00 0.00 2.50
1900 2383 5.822519 TGGCATAGCAAGAATAAGTAACCTG 59.177 40.000 0.00 0.00 0.00 4.00
1901 2384 5.278022 GGCATAGCAAGAATAAGTAACCTGC 60.278 44.000 0.00 0.00 0.00 4.85
1902 2385 5.529060 GCATAGCAAGAATAAGTAACCTGCT 59.471 40.000 0.00 0.00 0.00 4.24
1903 2386 6.512415 GCATAGCAAGAATAAGTAACCTGCTG 60.512 42.308 4.01 0.00 0.00 4.41
1904 2387 4.265073 AGCAAGAATAAGTAACCTGCTGG 58.735 43.478 8.29 8.29 39.83 4.85
1905 2388 3.181496 GCAAGAATAAGTAACCTGCTGGC 60.181 47.826 9.95 0.00 36.63 4.85
1906 2389 4.265073 CAAGAATAAGTAACCTGCTGGCT 58.735 43.478 9.95 0.00 36.63 4.75
1907 2390 5.428253 CAAGAATAAGTAACCTGCTGGCTA 58.572 41.667 9.95 0.00 36.63 3.93
1908 2391 5.693769 AGAATAAGTAACCTGCTGGCTAA 57.306 39.130 9.95 0.00 36.63 3.09
1909 2392 5.675538 AGAATAAGTAACCTGCTGGCTAAG 58.324 41.667 9.95 0.00 36.63 2.18
1925 2408 2.622436 CTAAGTAACCTGCTGGCTGTC 58.378 52.381 9.95 0.00 36.63 3.51
1949 2432 4.792528 TGTAAACCGTCCTTTTTACACG 57.207 40.909 3.40 0.00 41.21 4.49
1950 2433 4.437239 TGTAAACCGTCCTTTTTACACGA 58.563 39.130 3.40 0.00 41.21 4.35
1951 2434 4.872691 TGTAAACCGTCCTTTTTACACGAA 59.127 37.500 3.40 0.00 41.21 3.85
1952 2435 4.961435 AAACCGTCCTTTTTACACGAAA 57.039 36.364 0.00 0.00 35.49 3.46
1963 2448 9.849166 TCCTTTTTACACGAAAATGATAAATCC 57.151 29.630 0.00 0.00 36.89 3.01
1968 2453 5.875930 ACACGAAAATGATAAATCCCGAAC 58.124 37.500 0.00 0.00 0.00 3.95
1972 2457 5.675444 CGAAAATGATAAATCCCGAACGTTC 59.325 40.000 18.47 18.47 0.00 3.95
1992 2477 3.554934 TCGGATTTAAGCATGGCAATCT 58.445 40.909 0.00 0.00 0.00 2.40
1996 2481 6.265196 TCGGATTTAAGCATGGCAATCTAAAT 59.735 34.615 0.00 0.00 0.00 1.40
1997 2482 6.364165 CGGATTTAAGCATGGCAATCTAAATG 59.636 38.462 10.20 0.00 0.00 2.32
1998 2483 7.212274 GGATTTAAGCATGGCAATCTAAATGT 58.788 34.615 10.20 0.00 0.00 2.71
1999 2484 7.712205 GGATTTAAGCATGGCAATCTAAATGTT 59.288 33.333 10.20 0.00 0.00 2.71
2000 2485 9.101655 GATTTAAGCATGGCAATCTAAATGTTT 57.898 29.630 10.20 2.01 0.00 2.83
2001 2486 8.845413 TTTAAGCATGGCAATCTAAATGTTTT 57.155 26.923 0.00 0.00 0.00 2.43
2002 2487 8.845413 TTAAGCATGGCAATCTAAATGTTTTT 57.155 26.923 0.00 0.00 0.00 1.94
2003 2488 9.935241 TTAAGCATGGCAATCTAAATGTTTTTA 57.065 25.926 0.00 0.00 0.00 1.52
2005 2490 8.428186 AGCATGGCAATCTAAATGTTTTTATG 57.572 30.769 0.00 0.00 0.00 1.90
2006 2491 8.259411 AGCATGGCAATCTAAATGTTTTTATGA 58.741 29.630 0.00 0.00 0.00 2.15
2007 2492 8.330302 GCATGGCAATCTAAATGTTTTTATGAC 58.670 33.333 0.00 0.00 0.00 3.06
2008 2493 9.368674 CATGGCAATCTAAATGTTTTTATGACA 57.631 29.630 0.00 0.00 31.01 3.58
2009 2494 9.941325 ATGGCAATCTAAATGTTTTTATGACAA 57.059 25.926 0.00 0.00 30.52 3.18
2010 2495 9.202273 TGGCAATCTAAATGTTTTTATGACAAC 57.798 29.630 0.00 0.00 25.87 3.32
2011 2496 9.202273 GGCAATCTAAATGTTTTTATGACAACA 57.798 29.630 0.00 0.00 37.31 3.33
2022 2507 9.737427 TGTTTTTATGACAACATTAATTCACGT 57.263 25.926 0.00 0.00 37.87 4.49
2023 2508 9.987901 GTTTTTATGACAACATTAATTCACGTG 57.012 29.630 9.94 9.94 37.87 4.49
2024 2509 9.952188 TTTTTATGACAACATTAATTCACGTGA 57.048 25.926 15.76 15.76 37.87 4.35
2025 2510 9.605955 TTTTATGACAACATTAATTCACGTGAG 57.394 29.630 19.11 8.51 37.87 3.51
2026 2511 5.605564 TGACAACATTAATTCACGTGAGG 57.394 39.130 19.11 7.92 0.00 3.86
2027 2512 5.060506 TGACAACATTAATTCACGTGAGGT 58.939 37.500 19.11 12.86 0.00 3.85
2028 2513 5.529430 TGACAACATTAATTCACGTGAGGTT 59.471 36.000 19.11 18.63 0.00 3.50
2029 2514 5.757886 ACAACATTAATTCACGTGAGGTTG 58.242 37.500 25.73 25.73 39.07 3.77
2030 2515 5.529430 ACAACATTAATTCACGTGAGGTTGA 59.471 36.000 29.74 21.94 37.22 3.18
2031 2516 5.607119 ACATTAATTCACGTGAGGTTGAC 57.393 39.130 19.11 0.00 0.00 3.18
2032 2517 5.060506 ACATTAATTCACGTGAGGTTGACA 58.939 37.500 19.11 1.90 0.00 3.58
2033 2518 5.529430 ACATTAATTCACGTGAGGTTGACAA 59.471 36.000 19.11 9.49 0.00 3.18
2034 2519 6.038825 ACATTAATTCACGTGAGGTTGACAAA 59.961 34.615 19.11 9.18 0.00 2.83
2035 2520 3.963383 ATTCACGTGAGGTTGACAAAC 57.037 42.857 19.11 0.00 35.40 2.93
2036 2521 2.388310 TCACGTGAGGTTGACAAACA 57.612 45.000 15.76 0.00 38.10 2.83
2037 2522 2.912771 TCACGTGAGGTTGACAAACAT 58.087 42.857 15.76 0.00 38.10 2.71
2038 2523 2.611751 TCACGTGAGGTTGACAAACATG 59.388 45.455 15.76 7.33 38.10 3.21
2039 2524 2.354510 CACGTGAGGTTGACAAACATGT 59.645 45.455 10.90 7.90 38.10 3.21
2040 2525 3.013921 ACGTGAGGTTGACAAACATGTT 58.986 40.909 4.92 4.92 38.10 2.71
2041 2526 3.442273 ACGTGAGGTTGACAAACATGTTT 59.558 39.130 18.13 18.13 38.10 2.83
2042 2527 4.082463 ACGTGAGGTTGACAAACATGTTTT 60.082 37.500 21.10 12.50 38.10 2.43
2043 2528 5.124138 ACGTGAGGTTGACAAACATGTTTTA 59.876 36.000 21.10 8.17 38.10 1.52
2044 2529 6.030849 CGTGAGGTTGACAAACATGTTTTAA 58.969 36.000 21.10 13.35 38.10 1.52
2045 2530 6.020995 CGTGAGGTTGACAAACATGTTTTAAC 60.021 38.462 21.10 21.96 38.10 2.01
2046 2531 6.809196 GTGAGGTTGACAAACATGTTTTAACA 59.191 34.615 27.04 21.24 38.10 2.41
2047 2532 7.329717 GTGAGGTTGACAAACATGTTTTAACAA 59.670 33.333 27.04 23.99 38.10 2.83
2048 2533 7.329717 TGAGGTTGACAAACATGTTTTAACAAC 59.670 33.333 30.92 30.92 38.10 3.32
2049 2534 7.382898 AGGTTGACAAACATGTTTTAACAACT 58.617 30.769 33.41 25.58 38.10 3.16
2050 2535 8.524487 AGGTTGACAAACATGTTTTAACAACTA 58.476 29.630 33.41 17.44 38.10 2.24
2051 2536 9.141400 GGTTGACAAACATGTTTTAACAACTAA 57.859 29.630 33.41 18.18 38.10 2.24
2054 2539 9.915629 TGACAAACATGTTTTAACAACTAAAGT 57.084 25.926 21.10 11.06 43.03 2.66
2066 2551 2.902705 ACTAAAGTTGTCACCTCGCA 57.097 45.000 0.00 0.00 0.00 5.10
2067 2552 3.402628 ACTAAAGTTGTCACCTCGCAT 57.597 42.857 0.00 0.00 0.00 4.73
2068 2553 3.326747 ACTAAAGTTGTCACCTCGCATC 58.673 45.455 0.00 0.00 0.00 3.91
2069 2554 2.254546 AAAGTTGTCACCTCGCATCA 57.745 45.000 0.00 0.00 0.00 3.07
2070 2555 2.254546 AAGTTGTCACCTCGCATCAA 57.745 45.000 0.00 0.00 0.00 2.57
2071 2556 1.512926 AGTTGTCACCTCGCATCAAC 58.487 50.000 0.00 0.00 38.69 3.18
2072 2557 1.070758 AGTTGTCACCTCGCATCAACT 59.929 47.619 0.00 0.00 42.15 3.16
2073 2558 2.299013 AGTTGTCACCTCGCATCAACTA 59.701 45.455 7.01 0.00 44.11 2.24
2074 2559 3.064207 GTTGTCACCTCGCATCAACTAA 58.936 45.455 0.00 0.00 36.49 2.24
2075 2560 3.394674 TGTCACCTCGCATCAACTAAA 57.605 42.857 0.00 0.00 0.00 1.85
2076 2561 3.064207 TGTCACCTCGCATCAACTAAAC 58.936 45.455 0.00 0.00 0.00 2.01
2077 2562 3.244078 TGTCACCTCGCATCAACTAAACT 60.244 43.478 0.00 0.00 0.00 2.66
2078 2563 3.746492 GTCACCTCGCATCAACTAAACTT 59.254 43.478 0.00 0.00 0.00 2.66
2079 2564 3.745975 TCACCTCGCATCAACTAAACTTG 59.254 43.478 0.00 0.00 0.00 3.16
2080 2565 3.498397 CACCTCGCATCAACTAAACTTGT 59.502 43.478 0.00 0.00 0.00 3.16
2081 2566 3.746492 ACCTCGCATCAACTAAACTTGTC 59.254 43.478 0.00 0.00 0.00 3.18
2082 2567 3.745975 CCTCGCATCAACTAAACTTGTCA 59.254 43.478 0.00 0.00 0.00 3.58
2083 2568 4.393062 CCTCGCATCAACTAAACTTGTCAT 59.607 41.667 0.00 0.00 0.00 3.06
2084 2569 5.281693 TCGCATCAACTAAACTTGTCATG 57.718 39.130 0.00 0.00 0.00 3.07
2085 2570 4.994217 TCGCATCAACTAAACTTGTCATGA 59.006 37.500 0.00 0.00 0.00 3.07
2086 2571 5.468409 TCGCATCAACTAAACTTGTCATGAA 59.532 36.000 0.00 0.00 0.00 2.57
2087 2572 6.017523 TCGCATCAACTAAACTTGTCATGAAA 60.018 34.615 0.00 0.00 0.00 2.69
2088 2573 6.636447 CGCATCAACTAAACTTGTCATGAAAA 59.364 34.615 0.00 0.00 0.00 2.29
2089 2574 7.167302 CGCATCAACTAAACTTGTCATGAAAAA 59.833 33.333 0.00 0.00 0.00 1.94
2116 2601 9.581099 ACATTCGGAATTACATGTTTAAAATCC 57.419 29.630 2.30 3.70 0.00 3.01
2117 2602 8.742188 CATTCGGAATTACATGTTTAAAATCCG 58.258 33.333 22.20 22.20 41.40 4.18
2118 2603 7.612668 TCGGAATTACATGTTTAAAATCCGA 57.387 32.000 24.96 24.96 43.74 4.55
2119 2604 8.041829 TCGGAATTACATGTTTAAAATCCGAA 57.958 30.769 25.90 15.26 43.40 4.30
2120 2605 8.512956 TCGGAATTACATGTTTAAAATCCGAAA 58.487 29.630 25.90 12.41 43.40 3.46
2121 2606 9.130312 CGGAATTACATGTTTAAAATCCGAAAA 57.870 29.630 23.18 1.67 41.97 2.29
2137 2622 4.237349 CGAAAATCGGGATTTATTGGGG 57.763 45.455 7.05 0.00 39.88 4.96
2138 2623 3.634910 CGAAAATCGGGATTTATTGGGGT 59.365 43.478 7.05 0.00 39.88 4.95
2139 2624 4.261447 CGAAAATCGGGATTTATTGGGGTC 60.261 45.833 7.05 0.00 39.88 4.46
2140 2625 4.536295 AAATCGGGATTTATTGGGGTCT 57.464 40.909 4.89 0.00 39.08 3.85
2141 2626 4.536295 AATCGGGATTTATTGGGGTCTT 57.464 40.909 0.00 0.00 0.00 3.01
2142 2627 4.536295 ATCGGGATTTATTGGGGTCTTT 57.464 40.909 0.00 0.00 0.00 2.52
2143 2628 4.325084 TCGGGATTTATTGGGGTCTTTT 57.675 40.909 0.00 0.00 0.00 2.27
2170 2655 5.702349 AATGAAGAAAAGAGCTCTTGGTG 57.298 39.130 29.09 0.00 36.12 4.17
2172 2657 4.780815 TGAAGAAAAGAGCTCTTGGTGAA 58.219 39.130 29.09 11.23 36.12 3.18
2176 2661 3.930634 AAAGAGCTCTTGGTGAAATGC 57.069 42.857 29.09 0.00 36.12 3.56
2177 2662 1.446907 AGAGCTCTTGGTGAAATGCG 58.553 50.000 11.45 0.00 0.00 4.73
2178 2663 0.449388 GAGCTCTTGGTGAAATGCGG 59.551 55.000 6.43 0.00 0.00 5.69
2180 2665 1.589716 GCTCTTGGTGAAATGCGGCT 61.590 55.000 0.00 0.00 0.00 5.52
2181 2666 0.449388 CTCTTGGTGAAATGCGGCTC 59.551 55.000 0.00 0.00 0.00 4.70
2182 2667 0.250684 TCTTGGTGAAATGCGGCTCA 60.251 50.000 0.00 0.00 0.00 4.26
2184 2669 1.203052 CTTGGTGAAATGCGGCTCAAT 59.797 47.619 0.00 0.00 0.00 2.57
2185 2670 2.121291 TGGTGAAATGCGGCTCAATA 57.879 45.000 0.00 0.00 0.00 1.90
2186 2671 1.742831 TGGTGAAATGCGGCTCAATAC 59.257 47.619 0.00 0.00 0.00 1.89
2187 2672 2.017049 GGTGAAATGCGGCTCAATACT 58.983 47.619 0.00 0.00 0.00 2.12
2188 2673 2.223340 GGTGAAATGCGGCTCAATACTG 60.223 50.000 0.00 0.00 0.00 2.74
2189 2674 2.420022 GTGAAATGCGGCTCAATACTGT 59.580 45.455 0.00 0.00 0.00 3.55
2190 2675 3.081061 TGAAATGCGGCTCAATACTGTT 58.919 40.909 0.00 0.00 0.00 3.16
2191 2676 3.505680 TGAAATGCGGCTCAATACTGTTT 59.494 39.130 0.00 0.00 0.00 2.83
2192 2677 4.697828 TGAAATGCGGCTCAATACTGTTTA 59.302 37.500 0.00 0.00 0.00 2.01
2193 2678 4.882671 AATGCGGCTCAATACTGTTTAG 57.117 40.909 0.00 0.00 0.00 1.85
2194 2679 3.603158 TGCGGCTCAATACTGTTTAGA 57.397 42.857 0.00 0.00 0.00 2.10
2195 2680 3.932822 TGCGGCTCAATACTGTTTAGAA 58.067 40.909 0.00 0.00 0.00 2.10
2196 2681 4.320023 TGCGGCTCAATACTGTTTAGAAA 58.680 39.130 0.00 0.00 0.00 2.52
2197 2682 4.941263 TGCGGCTCAATACTGTTTAGAAAT 59.059 37.500 0.00 0.00 0.00 2.17
2198 2683 5.414454 TGCGGCTCAATACTGTTTAGAAATT 59.586 36.000 0.00 0.00 0.00 1.82
2199 2684 5.965918 GCGGCTCAATACTGTTTAGAAATTC 59.034 40.000 0.00 0.00 0.00 2.17
2200 2685 6.183360 GCGGCTCAATACTGTTTAGAAATTCT 60.183 38.462 0.00 0.00 0.00 2.40
2201 2686 7.011109 GCGGCTCAATACTGTTTAGAAATTCTA 59.989 37.037 0.00 0.00 0.00 2.10
2202 2687 8.879759 CGGCTCAATACTGTTTAGAAATTCTAA 58.120 33.333 11.10 11.10 37.20 2.10
2233 2718 2.805671 TGGCAACATTAGTTCACGTGAG 59.194 45.455 19.11 8.51 46.17 3.51
2258 2786 7.330700 AGGTTGACAAACATGTTTTAACAACTG 59.669 33.333 33.41 22.29 38.10 3.16
2272 2800 3.006672 AACTGAAGTTGCCACCTCG 57.993 52.632 0.00 0.00 36.80 4.63
2273 2801 1.166531 AACTGAAGTTGCCACCTCGC 61.167 55.000 0.00 0.00 36.80 5.03
2274 2802 1.597854 CTGAAGTTGCCACCTCGCA 60.598 57.895 0.00 0.00 36.85 5.10
2282 2810 0.108186 TGCCACCTCGCATCAACTAG 60.108 55.000 0.00 0.00 32.62 2.57
2327 2856 6.071672 TCGGAATGACATGCTTAAAATCCAAA 60.072 34.615 0.00 0.00 0.00 3.28
2329 2858 7.117523 CGGAATGACATGCTTAAAATCCAAAAA 59.882 33.333 0.00 0.00 0.00 1.94
2332 2861 7.579589 TGACATGCTTAAAATCCAAAAATCG 57.420 32.000 0.00 0.00 0.00 3.34
2333 2862 6.589523 TGACATGCTTAAAATCCAAAAATCGG 59.410 34.615 0.00 0.00 0.00 4.18
2368 2905 6.601217 GGGTCATAATGAAGAAAAGAGCTCTT 59.399 38.462 23.49 23.49 37.91 2.85
2373 2910 4.422073 TGAAGAAAAGAGCTCTTGGTGA 57.578 40.909 29.09 9.11 36.12 4.02
2379 2916 1.446907 AGAGCTCTTGGTGAAATGCG 58.553 50.000 11.45 0.00 0.00 4.73
2388 2925 1.202639 TGGTGAAATGCGGCTCGATAT 60.203 47.619 0.00 0.00 0.00 1.63
2393 2930 3.376859 TGAAATGCGGCTCGATATTGTTT 59.623 39.130 0.00 0.00 0.00 2.83
2497 3139 8.679288 TCTTAATACAGTACAAACTTAGACGC 57.321 34.615 0.00 0.00 31.97 5.19
2502 3144 4.923871 ACAGTACAAACTTAGACGCTCATG 59.076 41.667 0.00 0.00 31.97 3.07
2508 3150 3.099267 ACTTAGACGCTCATGCATACC 57.901 47.619 0.00 0.00 39.64 2.73
2515 3157 1.800586 CGCTCATGCATACCCACATAC 59.199 52.381 0.00 0.00 39.64 2.39
2517 3159 2.549754 GCTCATGCATACCCACATACAC 59.450 50.000 0.00 0.00 39.41 2.90
2522 3164 5.130311 TCATGCATACCCACATACACTTACT 59.870 40.000 0.00 0.00 0.00 2.24
2524 3166 4.141801 TGCATACCCACATACACTTACTCC 60.142 45.833 0.00 0.00 0.00 3.85
2536 3178 3.257375 ACACTTACTCCTATGAACGCACA 59.743 43.478 0.00 0.00 0.00 4.57
2545 3187 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
2553 3195 1.374252 CACACGCACACCCTACCTC 60.374 63.158 0.00 0.00 0.00 3.85
2584 3226 0.315886 TCGCAAGACTAAGCCGACAA 59.684 50.000 0.00 0.00 45.01 3.18
2599 3241 1.135717 CGACAAATCATCTTTGCCGCA 60.136 47.619 0.00 0.00 29.57 5.69
2636 3278 1.519408 TCGTTTGGCCTCTACTTTGC 58.481 50.000 3.32 0.00 0.00 3.68
2641 3283 1.275666 TGGCCTCTACTTTGCAGCTA 58.724 50.000 3.32 0.00 0.00 3.32
2642 3284 1.839994 TGGCCTCTACTTTGCAGCTAT 59.160 47.619 3.32 0.00 0.00 2.97
2661 3303 8.146479 CAGCTATGCTATCATTTGTCTAACAA 57.854 34.615 0.00 0.00 36.40 2.83
2667 3309 7.112122 TGCTATCATTTGTCTAACAATCTGGT 58.888 34.615 0.00 0.00 38.00 4.00
2721 3371 6.289834 TGTTTCCTTTTTGCATCATCATTGT 58.710 32.000 0.00 0.00 0.00 2.71
2748 3398 6.994496 CCAAGCTCATCTCATAAACCTATTCA 59.006 38.462 0.00 0.00 0.00 2.57
2751 3401 6.989169 AGCTCATCTCATAAACCTATTCACAC 59.011 38.462 0.00 0.00 0.00 3.82
2753 3403 7.042187 GCTCATCTCATAAACCTATTCACACAG 60.042 40.741 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.273327 GCATCACTGGTGGAAAAAGGG 59.727 52.381 0.70 0.00 0.00 3.95
1 2 2.242043 AGCATCACTGGTGGAAAAAGG 58.758 47.619 0.70 0.00 0.00 3.11
2 3 3.553508 CCAAGCATCACTGGTGGAAAAAG 60.554 47.826 0.70 0.00 32.27 2.27
3 4 2.364970 CCAAGCATCACTGGTGGAAAAA 59.635 45.455 0.70 0.00 32.27 1.94
4 5 1.962807 CCAAGCATCACTGGTGGAAAA 59.037 47.619 0.70 0.00 32.27 2.29
5 6 1.144708 TCCAAGCATCACTGGTGGAAA 59.855 47.619 0.70 0.00 31.54 3.13
6 7 0.770499 TCCAAGCATCACTGGTGGAA 59.230 50.000 0.70 0.00 31.54 3.53
7 8 0.770499 TTCCAAGCATCACTGGTGGA 59.230 50.000 0.70 0.00 32.27 4.02
8 9 1.542915 CTTTCCAAGCATCACTGGTGG 59.457 52.381 0.70 0.00 32.27 4.61
9 10 2.233271 ACTTTCCAAGCATCACTGGTG 58.767 47.619 0.00 0.00 32.27 4.17
10 11 2.664402 ACTTTCCAAGCATCACTGGT 57.336 45.000 0.00 0.00 33.62 4.00
11 12 5.010012 ACTTTAACTTTCCAAGCATCACTGG 59.990 40.000 0.00 0.00 0.00 4.00
12 13 6.076981 ACTTTAACTTTCCAAGCATCACTG 57.923 37.500 0.00 0.00 0.00 3.66
13 14 7.502561 AGTTACTTTAACTTTCCAAGCATCACT 59.497 33.333 0.00 0.00 46.27 3.41
14 15 7.649057 AGTTACTTTAACTTTCCAAGCATCAC 58.351 34.615 0.00 0.00 46.27 3.06
15 16 7.817418 AGTTACTTTAACTTTCCAAGCATCA 57.183 32.000 0.00 0.00 46.27 3.07
129 131 2.346803 TGGTCGCAAAAGCTACATCTC 58.653 47.619 0.00 0.00 0.00 2.75
175 177 1.035923 TTTGCCAGCGGACAATCAAA 58.964 45.000 0.00 0.00 0.00 2.69
239 243 5.106038 CCCCATATAACGCGTTGATAGAGTA 60.106 44.000 33.40 12.12 0.00 2.59
263 267 0.106708 TCTATCCCATCAAGCCACGC 59.893 55.000 0.00 0.00 0.00 5.34
293 297 8.857098 ACATACACCTACACGAATATGTCTTAT 58.143 33.333 0.00 0.00 33.85 1.73
294 298 8.132995 CACATACACCTACACGAATATGTCTTA 58.867 37.037 0.00 0.00 32.35 2.10
295 299 6.978659 CACATACACCTACACGAATATGTCTT 59.021 38.462 0.00 0.00 32.35 3.01
313 317 5.445069 ACTGCCCATAATAAAGCACATACA 58.555 37.500 0.00 0.00 0.00 2.29
421 425 3.736720 AGTGAGTAGCGACCATATACGA 58.263 45.455 0.00 0.00 0.00 3.43
427 431 1.204941 GTTGGAGTGAGTAGCGACCAT 59.795 52.381 0.00 0.00 0.00 3.55
449 455 1.299976 CTAAACGCTCCCTGGCCTT 59.700 57.895 3.32 0.00 0.00 4.35
466 472 5.253015 CCCATTGGGTAGACGCAGTAACT 62.253 52.174 14.10 0.00 38.75 2.24
483 489 0.469917 CCGTGCTACCATCTCCCATT 59.530 55.000 0.00 0.00 0.00 3.16
522 528 5.298989 TGTCCTATTACATAACCGCCATT 57.701 39.130 0.00 0.00 0.00 3.16
531 541 6.993079 CACTACATGCCTGTCCTATTACATA 58.007 40.000 0.00 0.00 36.79 2.29
568 578 3.266964 CCACAACCGACTGGCATG 58.733 61.111 0.00 0.00 39.70 4.06
621 635 6.094881 TCCAAGTCTCGAACAAAGAACAAAAT 59.905 34.615 0.00 0.00 0.00 1.82
738 752 1.135460 GGTAACCTTCTCGAGACCACG 60.135 57.143 16.36 5.18 0.00 4.94
739 753 2.094649 CAGGTAACCTTCTCGAGACCAC 60.095 54.545 16.36 8.39 37.17 4.16
752 766 3.756963 GGATTTTCTGTGGTCAGGTAACC 59.243 47.826 0.00 0.00 41.59 2.85
758 772 4.330074 GTGTATCGGATTTTCTGTGGTCAG 59.670 45.833 0.00 0.00 42.54 3.51
783 797 0.734253 CCTTTCGTCACAGGAGCGAG 60.734 60.000 0.00 0.00 36.00 5.03
790 804 2.383527 GCGAGCCCTTTCGTCACAG 61.384 63.158 0.00 0.00 42.38 3.66
834 848 2.228103 CGACTTGTGTACCAGTGAGCTA 59.772 50.000 0.00 0.00 0.00 3.32
861 883 1.442520 CATGGTTTGAAGCCGTGCG 60.443 57.895 7.35 0.00 36.38 5.34
923 958 5.077564 AGGCGGTATGTCTATATGAAGTGA 58.922 41.667 0.00 0.00 0.00 3.41
941 976 3.073735 AGGACTGAGCTGAGGCGG 61.074 66.667 4.85 0.00 44.37 6.13
996 1040 2.800544 CTGTTTCTCCGACGACATGTTT 59.199 45.455 0.00 0.00 0.00 2.83
1228 1272 0.029567 GCCTCGTCGACATACTGGAG 59.970 60.000 17.16 12.10 0.00 3.86
1416 1462 4.048504 CGTTTGTTTAGGGGAAAGCTTTG 58.951 43.478 18.30 0.00 0.00 2.77
1417 1463 3.702548 ACGTTTGTTTAGGGGAAAGCTTT 59.297 39.130 12.53 12.53 0.00 3.51
1418 1464 3.067601 CACGTTTGTTTAGGGGAAAGCTT 59.932 43.478 0.00 0.00 0.00 3.74
1419 1465 2.621526 CACGTTTGTTTAGGGGAAAGCT 59.378 45.455 0.00 0.00 0.00 3.74
1420 1466 2.359848 ACACGTTTGTTTAGGGGAAAGC 59.640 45.455 0.00 0.00 28.43 3.51
1421 1467 3.794138 GCACACGTTTGTTTAGGGGAAAG 60.794 47.826 3.29 0.00 31.66 2.62
1430 1476 0.738389 CAGGGAGCACACGTTTGTTT 59.262 50.000 3.29 0.00 31.66 2.83
1446 1929 2.632377 ACTACGCATCCATTGAACAGG 58.368 47.619 0.00 0.00 0.00 4.00
1450 1933 2.238646 AGGGAACTACGCATCCATTGAA 59.761 45.455 0.00 0.00 40.61 2.69
1569 2052 3.551496 TTCCCTTGGCTGCAGTCGG 62.551 63.158 14.71 9.63 0.00 4.79
1573 2056 0.324091 AATCCTTCCCTTGGCTGCAG 60.324 55.000 10.11 10.11 0.00 4.41
1577 2060 2.092914 CGAAGTAATCCTTCCCTTGGCT 60.093 50.000 0.00 0.00 45.75 4.75
1612 2095 1.282157 AGAGCAATGTCCAGGTAACCC 59.718 52.381 0.00 0.00 37.17 4.11
1652 2135 0.485099 ATCCTCTCTACCGCCCTGAT 59.515 55.000 0.00 0.00 0.00 2.90
1720 2203 2.202932 CAGAACCGATCCGCCCAG 60.203 66.667 0.00 0.00 0.00 4.45
1771 2254 1.004918 CTCCACGAACCTGTCCACC 60.005 63.158 0.00 0.00 0.00 4.61
1814 2297 0.108329 TTAGCACTAGCCGCCTTCAC 60.108 55.000 1.26 0.00 43.56 3.18
1836 2319 2.006888 CACCACAGTTCGTTCACTTGT 58.993 47.619 0.00 0.00 0.00 3.16
1894 2377 3.055385 CAGGTTACTTAGCCAGCAGGTTA 60.055 47.826 0.00 0.00 37.19 2.85
1895 2378 1.985895 AGGTTACTTAGCCAGCAGGTT 59.014 47.619 0.00 0.00 37.19 3.50
1896 2379 1.279271 CAGGTTACTTAGCCAGCAGGT 59.721 52.381 0.00 0.00 37.19 4.00
1897 2380 2.014068 GCAGGTTACTTAGCCAGCAGG 61.014 57.143 2.24 0.00 38.60 4.85
1900 2383 1.373570 CAGCAGGTTACTTAGCCAGC 58.626 55.000 0.00 0.00 38.93 4.85
1901 2384 2.014068 GCCAGCAGGTTACTTAGCCAG 61.014 57.143 0.00 0.00 37.19 4.85
1902 2385 0.035439 GCCAGCAGGTTACTTAGCCA 60.035 55.000 0.00 0.00 37.19 4.75
1903 2386 0.253327 AGCCAGCAGGTTACTTAGCC 59.747 55.000 0.00 0.00 37.19 3.93
1904 2387 1.339151 ACAGCCAGCAGGTTACTTAGC 60.339 52.381 0.00 0.00 37.19 3.09
1905 2388 2.622436 GACAGCCAGCAGGTTACTTAG 58.378 52.381 0.00 0.00 37.19 2.18
1906 2389 1.067142 CGACAGCCAGCAGGTTACTTA 60.067 52.381 0.00 0.00 37.19 2.24
1907 2390 0.320771 CGACAGCCAGCAGGTTACTT 60.321 55.000 0.00 0.00 37.19 2.24
1908 2391 1.293498 CGACAGCCAGCAGGTTACT 59.707 57.895 0.00 0.00 37.19 2.24
1909 2392 1.741770 CCGACAGCCAGCAGGTTAC 60.742 63.158 0.00 0.00 37.19 2.50
1939 2422 8.794406 CGGGATTTATCATTTTCGTGTAAAAAG 58.206 33.333 0.00 0.00 40.37 2.27
1943 2426 7.465989 GTTCGGGATTTATCATTTTCGTGTAA 58.534 34.615 0.00 0.00 0.00 2.41
1945 2428 5.446741 CGTTCGGGATTTATCATTTTCGTGT 60.447 40.000 0.00 0.00 0.00 4.49
1946 2429 4.961551 CGTTCGGGATTTATCATTTTCGTG 59.038 41.667 0.00 0.00 0.00 4.35
1947 2430 4.632688 ACGTTCGGGATTTATCATTTTCGT 59.367 37.500 0.00 0.00 0.00 3.85
1948 2431 5.151632 ACGTTCGGGATTTATCATTTTCG 57.848 39.130 0.00 0.00 0.00 3.46
1949 2432 5.675444 CGAACGTTCGGGATTTATCATTTTC 59.325 40.000 36.53 2.01 46.30 2.29
1950 2433 5.565695 CGAACGTTCGGGATTTATCATTTT 58.434 37.500 36.53 0.00 46.30 1.82
1951 2434 5.151632 CGAACGTTCGGGATTTATCATTT 57.848 39.130 36.53 0.00 46.30 2.32
1952 2435 4.789095 CGAACGTTCGGGATTTATCATT 57.211 40.909 36.53 0.00 46.30 2.57
1968 2453 1.400142 TGCCATGCTTAAATCCGAACG 59.600 47.619 0.00 0.00 0.00 3.95
1972 2457 3.996150 AGATTGCCATGCTTAAATCCG 57.004 42.857 0.00 0.00 30.83 4.18
1979 2464 8.885722 CATAAAAACATTTAGATTGCCATGCTT 58.114 29.630 0.00 0.00 0.00 3.91
1981 2466 8.330302 GTCATAAAAACATTTAGATTGCCATGC 58.670 33.333 0.00 0.00 0.00 4.06
1982 2467 9.368674 TGTCATAAAAACATTTAGATTGCCATG 57.631 29.630 0.00 0.00 0.00 3.66
1983 2468 9.941325 TTGTCATAAAAACATTTAGATTGCCAT 57.059 25.926 0.00 0.00 0.00 4.40
1996 2481 9.737427 ACGTGAATTAATGTTGTCATAAAAACA 57.263 25.926 0.00 0.00 40.36 2.83
1997 2482 9.987901 CACGTGAATTAATGTTGTCATAAAAAC 57.012 29.630 10.90 0.00 33.49 2.43
1998 2483 9.952188 TCACGTGAATTAATGTTGTCATAAAAA 57.048 25.926 17.62 0.00 33.49 1.94
1999 2484 9.605955 CTCACGTGAATTAATGTTGTCATAAAA 57.394 29.630 20.49 0.00 33.49 1.52
2000 2485 8.233868 CCTCACGTGAATTAATGTTGTCATAAA 58.766 33.333 20.49 0.00 33.49 1.40
2001 2486 7.389330 ACCTCACGTGAATTAATGTTGTCATAA 59.611 33.333 20.49 0.00 33.49 1.90
2002 2487 6.876789 ACCTCACGTGAATTAATGTTGTCATA 59.123 34.615 20.49 0.00 33.49 2.15
2003 2488 5.705441 ACCTCACGTGAATTAATGTTGTCAT 59.295 36.000 20.49 0.00 35.59 3.06
2004 2489 5.060506 ACCTCACGTGAATTAATGTTGTCA 58.939 37.500 20.49 0.00 0.00 3.58
2005 2490 5.607119 ACCTCACGTGAATTAATGTTGTC 57.393 39.130 20.49 0.00 0.00 3.18
2006 2491 5.529430 TCAACCTCACGTGAATTAATGTTGT 59.471 36.000 20.49 3.09 33.96 3.32
2007 2492 5.851177 GTCAACCTCACGTGAATTAATGTTG 59.149 40.000 20.49 21.32 33.65 3.33
2008 2493 5.529430 TGTCAACCTCACGTGAATTAATGTT 59.471 36.000 20.49 12.33 0.00 2.71
2009 2494 5.060506 TGTCAACCTCACGTGAATTAATGT 58.939 37.500 20.49 7.13 0.00 2.71
2010 2495 5.605564 TGTCAACCTCACGTGAATTAATG 57.394 39.130 20.49 13.63 0.00 1.90
2011 2496 6.038825 TGTTTGTCAACCTCACGTGAATTAAT 59.961 34.615 20.49 1.49 31.02 1.40
2012 2497 5.354513 TGTTTGTCAACCTCACGTGAATTAA 59.645 36.000 20.49 5.87 31.02 1.40
2013 2498 4.876679 TGTTTGTCAACCTCACGTGAATTA 59.123 37.500 20.49 0.70 31.02 1.40
2014 2499 3.692101 TGTTTGTCAACCTCACGTGAATT 59.308 39.130 20.49 13.84 31.02 2.17
2015 2500 3.275143 TGTTTGTCAACCTCACGTGAAT 58.725 40.909 20.49 7.98 31.02 2.57
2016 2501 2.701107 TGTTTGTCAACCTCACGTGAA 58.299 42.857 20.49 0.47 31.02 3.18
2017 2502 2.388310 TGTTTGTCAACCTCACGTGA 57.612 45.000 18.88 18.88 31.02 4.35
2018 2503 2.354510 ACATGTTTGTCAACCTCACGTG 59.645 45.455 9.94 9.94 31.02 4.49
2019 2504 2.639065 ACATGTTTGTCAACCTCACGT 58.361 42.857 0.00 0.00 31.02 4.49
2020 2505 3.691049 AACATGTTTGTCAACCTCACG 57.309 42.857 4.92 0.00 34.06 4.35
2021 2506 6.809196 TGTTAAAACATGTTTGTCAACCTCAC 59.191 34.615 23.93 8.99 34.06 3.51
2022 2507 6.925211 TGTTAAAACATGTTTGTCAACCTCA 58.075 32.000 23.93 11.71 34.06 3.86
2023 2508 7.544217 AGTTGTTAAAACATGTTTGTCAACCTC 59.456 33.333 32.99 24.78 38.95 3.85
2024 2509 7.382898 AGTTGTTAAAACATGTTTGTCAACCT 58.617 30.769 32.99 25.52 38.95 3.50
2025 2510 7.589574 AGTTGTTAAAACATGTTTGTCAACC 57.410 32.000 32.99 24.58 38.95 3.77
2028 2513 9.915629 ACTTTAGTTGTTAAAACATGTTTGTCA 57.084 25.926 23.93 18.49 38.95 3.58
2046 2531 3.188159 TGCGAGGTGACAACTTTAGTT 57.812 42.857 0.00 0.00 39.12 2.24
2047 2532 2.902705 TGCGAGGTGACAACTTTAGT 57.097 45.000 0.00 0.00 0.00 2.24
2048 2533 3.325870 TGATGCGAGGTGACAACTTTAG 58.674 45.455 0.00 0.00 0.00 1.85
2049 2534 3.394674 TGATGCGAGGTGACAACTTTA 57.605 42.857 0.00 0.00 0.00 1.85
2050 2535 2.254546 TGATGCGAGGTGACAACTTT 57.745 45.000 0.00 0.00 0.00 2.66
2051 2536 1.873591 GTTGATGCGAGGTGACAACTT 59.126 47.619 0.00 0.00 38.10 2.66
2052 2537 1.070758 AGTTGATGCGAGGTGACAACT 59.929 47.619 0.00 0.00 43.72 3.16
2053 2538 1.512926 AGTTGATGCGAGGTGACAAC 58.487 50.000 0.00 0.00 40.37 3.32
2054 2539 3.394674 TTAGTTGATGCGAGGTGACAA 57.605 42.857 0.00 0.00 0.00 3.18
2055 2540 3.064207 GTTTAGTTGATGCGAGGTGACA 58.936 45.455 0.00 0.00 0.00 3.58
2056 2541 3.326747 AGTTTAGTTGATGCGAGGTGAC 58.673 45.455 0.00 0.00 0.00 3.67
2057 2542 3.678056 AGTTTAGTTGATGCGAGGTGA 57.322 42.857 0.00 0.00 0.00 4.02
2058 2543 3.498397 ACAAGTTTAGTTGATGCGAGGTG 59.502 43.478 4.40 0.00 0.00 4.00
2059 2544 3.740115 ACAAGTTTAGTTGATGCGAGGT 58.260 40.909 4.40 0.00 0.00 3.85
2060 2545 3.745975 TGACAAGTTTAGTTGATGCGAGG 59.254 43.478 4.40 0.00 0.00 4.63
2061 2546 4.990543 TGACAAGTTTAGTTGATGCGAG 57.009 40.909 4.40 0.00 0.00 5.03
2062 2547 4.994217 TCATGACAAGTTTAGTTGATGCGA 59.006 37.500 4.40 0.00 0.00 5.10
2063 2548 5.281693 TCATGACAAGTTTAGTTGATGCG 57.718 39.130 4.40 0.00 0.00 4.73
2064 2549 7.928908 TTTTCATGACAAGTTTAGTTGATGC 57.071 32.000 0.00 0.00 0.00 3.91
2090 2575 9.581099 GGATTTTAAACATGTAATTCCGAATGT 57.419 29.630 0.00 0.00 34.79 2.71
2091 2576 8.742188 CGGATTTTAAACATGTAATTCCGAATG 58.258 33.333 25.19 7.60 39.31 2.67
2092 2577 8.679100 TCGGATTTTAAACATGTAATTCCGAAT 58.321 29.630 27.46 12.68 40.94 3.34
2093 2578 8.041829 TCGGATTTTAAACATGTAATTCCGAA 57.958 30.769 27.46 18.01 40.94 4.30
2094 2579 7.612668 TCGGATTTTAAACATGTAATTCCGA 57.387 32.000 26.64 26.64 41.26 4.55
2095 2580 8.676454 TTTCGGATTTTAAACATGTAATTCCG 57.324 30.769 24.26 24.26 38.84 4.30
2116 2601 3.634910 ACCCCAATAAATCCCGATTTTCG 59.365 43.478 7.91 0.00 40.99 3.46
2117 2602 4.893524 AGACCCCAATAAATCCCGATTTTC 59.106 41.667 7.91 0.00 40.99 2.29
2118 2603 4.878968 AGACCCCAATAAATCCCGATTTT 58.121 39.130 7.91 0.00 40.99 1.82
2119 2604 4.536295 AGACCCCAATAAATCCCGATTT 57.464 40.909 7.74 7.74 42.95 2.17
2120 2605 4.536295 AAGACCCCAATAAATCCCGATT 57.464 40.909 0.00 0.00 0.00 3.34
2121 2606 4.536295 AAAGACCCCAATAAATCCCGAT 57.464 40.909 0.00 0.00 0.00 4.18
2122 2607 4.325084 AAAAGACCCCAATAAATCCCGA 57.675 40.909 0.00 0.00 0.00 5.14
2143 2628 9.520515 ACCAAGAGCTCTTTTCTTCATTATAAA 57.479 29.630 26.44 0.00 32.75 1.40
2146 2631 7.170965 TCACCAAGAGCTCTTTTCTTCATTAT 58.829 34.615 26.44 0.00 32.75 1.28
2153 2638 4.022503 GCATTTCACCAAGAGCTCTTTTCT 60.023 41.667 26.44 8.74 33.11 2.52
2155 2640 3.304928 CGCATTTCACCAAGAGCTCTTTT 60.305 43.478 26.44 13.55 33.11 2.27
2159 2644 0.449388 CCGCATTTCACCAAGAGCTC 59.551 55.000 5.27 5.27 0.00 4.09
2160 2645 1.589716 GCCGCATTTCACCAAGAGCT 61.590 55.000 0.00 0.00 0.00 4.09
2162 2647 0.449388 GAGCCGCATTTCACCAAGAG 59.551 55.000 0.00 0.00 0.00 2.85
2163 2648 0.250684 TGAGCCGCATTTCACCAAGA 60.251 50.000 0.00 0.00 0.00 3.02
2164 2649 0.597568 TTGAGCCGCATTTCACCAAG 59.402 50.000 0.00 0.00 0.00 3.61
2165 2650 1.255882 ATTGAGCCGCATTTCACCAA 58.744 45.000 0.00 0.00 0.00 3.67
2166 2651 1.742831 GTATTGAGCCGCATTTCACCA 59.257 47.619 0.00 0.00 0.00 4.17
2167 2652 2.017049 AGTATTGAGCCGCATTTCACC 58.983 47.619 0.00 0.00 0.00 4.02
2168 2653 2.420022 ACAGTATTGAGCCGCATTTCAC 59.580 45.455 0.00 0.00 0.00 3.18
2170 2655 3.764885 AACAGTATTGAGCCGCATTTC 57.235 42.857 0.00 0.00 0.00 2.17
2172 2657 4.513442 TCTAAACAGTATTGAGCCGCATT 58.487 39.130 0.00 0.00 0.00 3.56
2176 2661 7.308782 AGAATTTCTAAACAGTATTGAGCCG 57.691 36.000 0.00 0.00 0.00 5.52
2203 2688 7.328249 CGTGAACTAATGTTGCCATAAAAACAT 59.672 33.333 0.00 0.00 46.35 2.71
2204 2689 6.638873 CGTGAACTAATGTTGCCATAAAAACA 59.361 34.615 0.00 0.00 40.36 2.83
2211 2696 3.407698 TCACGTGAACTAATGTTGCCAT 58.592 40.909 17.62 0.00 36.39 4.40
2212 2697 2.805671 CTCACGTGAACTAATGTTGCCA 59.194 45.455 20.49 0.00 36.39 4.92
2213 2698 2.159627 CCTCACGTGAACTAATGTTGCC 59.840 50.000 20.49 0.00 36.39 4.52
2219 2704 4.330944 TGTCAACCTCACGTGAACTAAT 57.669 40.909 20.49 1.49 0.00 1.73
2230 2715 6.925211 TGTTAAAACATGTTTGTCAACCTCA 58.075 32.000 23.93 11.71 34.06 3.86
2231 2716 7.544217 AGTTGTTAAAACATGTTTGTCAACCTC 59.456 33.333 32.99 24.78 38.95 3.85
2233 2718 7.329717 TCAGTTGTTAAAACATGTTTGTCAACC 59.670 33.333 32.99 24.58 38.95 3.77
2264 2792 0.175760 TCTAGTTGATGCGAGGTGGC 59.824 55.000 0.00 0.00 0.00 5.01
2272 2800 3.273434 TCATGGCAAGTCTAGTTGATGC 58.727 45.455 0.00 1.56 36.31 3.91
2273 2801 5.885230 TTTCATGGCAAGTCTAGTTGATG 57.115 39.130 0.00 0.00 0.00 3.07
2274 2802 6.899393 TTTTTCATGGCAAGTCTAGTTGAT 57.101 33.333 0.00 0.00 0.00 2.57
2299 2827 6.418819 GGATTTTAAGCATGTCATTCCGAATG 59.581 38.462 14.05 14.05 40.28 2.67
2300 2828 6.096705 TGGATTTTAAGCATGTCATTCCGAAT 59.903 34.615 0.00 0.00 0.00 3.34
2303 2831 5.247507 TGGATTTTAAGCATGTCATTCCG 57.752 39.130 0.00 0.00 0.00 4.30
2306 2834 8.658609 CGATTTTTGGATTTTAAGCATGTCATT 58.341 29.630 0.00 0.00 0.00 2.57
2327 2856 4.258457 TGACCCCAATAAATCCCGATTT 57.742 40.909 7.74 7.74 42.95 2.17
2329 2858 5.592587 TTATGACCCCAATAAATCCCGAT 57.407 39.130 0.00 0.00 0.00 4.18
2332 2861 7.010160 TCTTCATTATGACCCCAATAAATCCC 58.990 38.462 0.00 0.00 0.00 3.85
2333 2862 8.477419 TTCTTCATTATGACCCCAATAAATCC 57.523 34.615 0.00 0.00 0.00 3.01
2341 2870 4.949856 GCTCTTTTCTTCATTATGACCCCA 59.050 41.667 0.00 0.00 0.00 4.96
2342 2871 5.196695 AGCTCTTTTCTTCATTATGACCCC 58.803 41.667 0.00 0.00 0.00 4.95
2368 2905 0.176910 TATCGAGCCGCATTTCACCA 59.823 50.000 0.00 0.00 0.00 4.17
2373 2910 4.024048 CCTAAACAATATCGAGCCGCATTT 60.024 41.667 0.00 0.00 0.00 2.32
2379 2916 7.964604 AGTTATTCCTAAACAATATCGAGCC 57.035 36.000 0.00 0.00 0.00 4.70
2434 2971 2.997485 AAAAAGCGAGCATGTTCCTC 57.003 45.000 3.76 0.00 0.00 3.71
2471 3113 9.132521 GCGTCTAAGTTTGTACTGTATTAAGAA 57.867 33.333 0.00 0.00 34.01 2.52
2497 3139 4.077300 AGTGTATGTGGGTATGCATGAG 57.923 45.455 10.16 0.00 0.00 2.90
2502 3144 4.101119 AGGAGTAAGTGTATGTGGGTATGC 59.899 45.833 0.00 0.00 0.00 3.14
2508 3150 5.977725 CGTTCATAGGAGTAAGTGTATGTGG 59.022 44.000 0.00 0.00 0.00 4.17
2515 3157 3.612860 GTGTGCGTTCATAGGAGTAAGTG 59.387 47.826 0.00 0.00 0.00 3.16
2517 3159 3.612860 GTGTGTGCGTTCATAGGAGTAAG 59.387 47.826 0.00 0.00 0.00 2.34
2522 3164 1.011968 GCGTGTGTGCGTTCATAGGA 61.012 55.000 0.00 0.00 0.00 2.94
2524 3166 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
2536 3178 0.251474 TAGAGGTAGGGTGTGCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
2545 3187 4.381079 GCGAAGATGCTTATAGAGGTAGGG 60.381 50.000 0.00 0.00 0.00 3.53
2553 3195 6.128956 GCTTAGTCTTGCGAAGATGCTTATAG 60.129 42.308 0.00 0.00 40.18 1.31
2584 3226 1.656818 CGGGTGCGGCAAAGATGATT 61.657 55.000 3.23 0.00 0.00 2.57
2599 3241 2.764572 ACGAAGGAAGTTATGATCGGGT 59.235 45.455 0.00 0.00 34.81 5.28
2636 3278 7.719778 TGTTAGACAAATGATAGCATAGCTG 57.280 36.000 0.00 0.00 40.10 4.24
2641 3283 7.776969 ACCAGATTGTTAGACAAATGATAGCAT 59.223 33.333 9.58 0.00 41.96 3.79
2642 3284 7.112122 ACCAGATTGTTAGACAAATGATAGCA 58.888 34.615 9.58 0.00 41.96 3.49
2698 3348 6.790285 ACAATGATGATGCAAAAAGGAAAC 57.210 33.333 0.00 0.00 0.00 2.78
2702 3352 5.722263 TGGTACAATGATGATGCAAAAAGG 58.278 37.500 0.00 0.00 31.92 3.11
2721 3371 5.957771 AGGTTTATGAGATGAGCTTGGTA 57.042 39.130 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.