Multiple sequence alignment - TraesCS5A01G444700

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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 TraesCS5A01G444700 chr5A 100.000 5595 0 0 1 5595 624726853 624721259 0.000000e+00 10333.0
1 TraesCS5A01G444700 chr5A 87.698 1390 161 6 3055 4440 624712212 624710829 0.000000e+00 1611.0
2 TraesCS5A01G444700 chr5A 80.822 1898 268 50 682 2527 624714245 624712392 0.000000e+00 1400.0
3 TraesCS5A01G444700 chr5A 86.957 115 13 2 615 728 624714358 624714245 1.640000e-25 128.0
4 TraesCS5A01G444700 chr5B 91.832 2571 141 29 1 2531 621481028 621478487 0.000000e+00 3520.0
5 TraesCS5A01G444700 chr5B 96.415 1813 64 1 2844 4656 621478253 621476442 0.000000e+00 2987.0
6 TraesCS5A01G444700 chr5B 84.313 1753 246 20 2728 4466 621469608 621467871 0.000000e+00 1687.0
7 TraesCS5A01G444700 chr5B 80.865 1897 269 53 681 2524 621471553 621469698 0.000000e+00 1406.0
8 TraesCS5A01G444700 chr5B 96.296 216 7 1 2645 2859 621478488 621478273 2.480000e-93 353.0
9 TraesCS5A01G444700 chr5B 95.238 63 3 0 4702 4764 621476430 621476368 3.570000e-17 100.0
10 TraesCS5A01G444700 chr5D 91.724 2489 157 20 1 2464 500141172 500138708 0.000000e+00 3410.0
11 TraesCS5A01G444700 chr5D 88.861 1966 181 24 2700 4652 500138605 500136665 0.000000e+00 2383.0
12 TraesCS5A01G444700 chr5D 85.028 1810 226 30 2747 4533 500133408 500131621 0.000000e+00 1799.0
13 TraesCS5A01G444700 chr5D 80.675 1718 262 34 835 2524 500135331 500133656 0.000000e+00 1269.0
14 TraesCS5A01G444700 chr5D 92.087 872 33 6 4759 5595 241425083 241424213 0.000000e+00 1195.0
15 TraesCS5A01G444700 chr5D 85.981 107 10 3 682 783 500135456 500135350 5.930000e-20 110.0
16 TraesCS5A01G444700 chr5D 94.231 52 3 0 682 733 500135599 500135548 4.650000e-11 80.5
17 TraesCS5A01G444700 chr3D 83.407 1808 255 24 2819 4624 605973103 605974867 0.000000e+00 1635.0
18 TraesCS5A01G444700 chr3D 85.148 1589 202 23 3089 4655 606773666 606772090 0.000000e+00 1596.0
19 TraesCS5A01G444700 chr3D 78.867 1713 253 63 827 2520 605971317 605972939 0.000000e+00 1057.0
20 TraesCS5A01G444700 chr3D 79.459 1368 207 45 827 2167 605953132 605954452 0.000000e+00 902.0
21 TraesCS5A01G444700 chr3D 77.578 892 155 31 825 1704 606000204 606001062 1.080000e-136 497.0
22 TraesCS5A01G444700 chr3D 88.214 280 24 5 5319 5595 45585360 45585087 5.410000e-85 326.0
23 TraesCS5A01G444700 chr3D 82.006 339 51 6 900 1231 605590315 605590650 4.270000e-71 279.0
24 TraesCS5A01G444700 chr3D 93.011 186 12 1 4763 4948 45585576 45585392 2.570000e-68 270.0
25 TraesCS5A01G444700 chr3D 85.768 267 25 11 2283 2541 605954643 605954904 2.570000e-68 270.0
26 TraesCS5A01G444700 chr3D 76.145 524 82 28 1981 2474 605705757 605706267 9.370000e-58 235.0
27 TraesCS5A01G444700 chr3D 79.808 312 50 10 1837 2140 606775098 606774792 1.220000e-51 215.0
28 TraesCS5A01G444700 chr3D 90.977 133 4 4 2515 2646 394956529 394956404 7.450000e-39 172.0
29 TraesCS5A01G444700 chr3D 97.674 43 1 0 825 867 605952927 605952969 2.160000e-09 75.0
30 TraesCS5A01G444700 chr3B 85.560 1579 206 17 3089 4655 816172331 816170763 0.000000e+00 1633.0
31 TraesCS5A01G444700 chrUn 85.370 1579 209 17 3089 4655 42327097 42325529 0.000000e+00 1616.0
32 TraesCS5A01G444700 chrUn 97.396 576 12 3 5023 5595 326203 325628 0.000000e+00 977.0
33 TraesCS5A01G444700 chrUn 97.183 284 6 2 4764 5046 326489 326207 3.920000e-131 479.0
34 TraesCS5A01G444700 chrUn 75.906 635 113 25 1856 2465 344270992 344270373 7.090000e-74 289.0
35 TraesCS5A01G444700 chr3A 97.156 844 15 5 4761 5595 437857085 437857928 0.000000e+00 1417.0
36 TraesCS5A01G444700 chr3A 74.804 1532 312 54 887 2379 738250947 738249451 1.710000e-174 623.0
37 TraesCS5A01G444700 chr3A 78.865 828 150 20 887 1704 738307629 738306817 2.290000e-148 536.0
38 TraesCS5A01G444700 chr3A 83.969 524 68 7 1963 2472 738693036 738692515 6.510000e-134 488.0
39 TraesCS5A01G444700 chr3A 76.542 827 153 26 887 1704 738694129 738693335 1.120000e-111 414.0
40 TraesCS5A01G444700 chr3A 81.496 508 81 6 1952 2448 738306531 738306026 6.750000e-109 405.0
41 TraesCS5A01G444700 chr3A 77.827 672 108 23 1835 2474 738865879 738865217 1.470000e-100 377.0
42 TraesCS5A01G444700 chr3A 77.185 675 105 27 1835 2474 738920567 738919907 1.150000e-91 348.0
43 TraesCS5A01G444700 chr3A 79.584 529 72 17 1971 2474 738320134 738319617 4.150000e-91 346.0
44 TraesCS5A01G444700 chr3A 76.532 669 107 33 1812 2466 738224565 738223933 2.510000e-83 320.0
45 TraesCS5A01G444700 chr3A 75.906 635 113 25 1856 2465 738599983 738599364 7.090000e-74 289.0
46 TraesCS5A01G444700 chr3A 75.906 635 113 25 1856 2465 738678950 738678331 7.090000e-74 289.0
47 TraesCS5A01G444700 chr3A 86.239 218 29 1 2263 2479 738759277 738759060 9.370000e-58 235.0
48 TraesCS5A01G444700 chr3A 77.410 363 53 18 944 1294 738225458 738225113 7.400000e-44 189.0
49 TraesCS5A01G444700 chr1A 95.099 857 17 6 4764 5595 25304550 25305406 0.000000e+00 1327.0
50 TraesCS5A01G444700 chr1A 97.183 284 6 2 4764 5046 25303933 25304215 3.920000e-131 479.0
51 TraesCS5A01G444700 chr1A 92.366 131 6 3 2519 2646 17975197 17975326 3.440000e-42 183.0
52 TraesCS5A01G444700 chr4A 88.036 560 50 10 5043 5595 673160573 673161122 0.000000e+00 647.0
53 TraesCS5A01G444700 chr4A 87.640 267 17 11 4764 5029 673160276 673160527 4.240000e-76 296.0
54 TraesCS5A01G444700 chr2B 96.825 126 1 3 2523 2646 777494901 777495025 2.040000e-49 207.0
55 TraesCS5A01G444700 chr2B 96.639 119 2 1 2530 2646 534232622 534232740 4.420000e-46 196.0
56 TraesCS5A01G444700 chr1D 96.610 118 3 1 2529 2645 212424938 212424821 1.590000e-45 195.0
57 TraesCS5A01G444700 chr1D 94.915 118 6 0 2529 2646 3824267 3824150 9.570000e-43 185.0
58 TraesCS5A01G444700 chr6D 96.491 114 4 0 2533 2646 77237160 77237047 7.400000e-44 189.0
59 TraesCS5A01G444700 chr6D 95.763 118 4 1 2529 2645 97868708 97868825 7.400000e-44 189.0
60 TraesCS5A01G444700 chr4B 91.729 133 3 4 2517 2649 424274518 424274394 1.600000e-40 178.0


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 TraesCS5A01G444700 chr5A 624721259 624726853 5594 True 10333.000000 10333 100.000000 1 5595 1 chr5A.!!$R1 5594
1 TraesCS5A01G444700 chr5A 624710829 624714358 3529 True 1046.333333 1611 85.159000 615 4440 3 chr5A.!!$R2 3825
2 TraesCS5A01G444700 chr5B 621476368 621481028 4660 True 1740.000000 3520 94.945250 1 4764 4 chr5B.!!$R2 4763
3 TraesCS5A01G444700 chr5B 621467871 621471553 3682 True 1546.500000 1687 82.589000 681 4466 2 chr5B.!!$R1 3785
4 TraesCS5A01G444700 chr5D 500131621 500141172 9551 True 1508.583333 3410 87.750000 1 4652 6 chr5D.!!$R2 4651
5 TraesCS5A01G444700 chr5D 241424213 241425083 870 True 1195.000000 1195 92.087000 4759 5595 1 chr5D.!!$R1 836
6 TraesCS5A01G444700 chr3D 605971317 605974867 3550 False 1346.000000 1635 81.137000 827 4624 2 chr3D.!!$F5 3797
7 TraesCS5A01G444700 chr3D 606772090 606775098 3008 True 905.500000 1596 82.478000 1837 4655 2 chr3D.!!$R3 2818
8 TraesCS5A01G444700 chr3D 606000204 606001062 858 False 497.000000 497 77.578000 825 1704 1 chr3D.!!$F3 879
9 TraesCS5A01G444700 chr3D 605952927 605954904 1977 False 415.666667 902 87.633667 825 2541 3 chr3D.!!$F4 1716
10 TraesCS5A01G444700 chr3D 605705757 605706267 510 False 235.000000 235 76.145000 1981 2474 1 chr3D.!!$F2 493
11 TraesCS5A01G444700 chr3B 816170763 816172331 1568 True 1633.000000 1633 85.560000 3089 4655 1 chr3B.!!$R1 1566
12 TraesCS5A01G444700 chrUn 42325529 42327097 1568 True 1616.000000 1616 85.370000 3089 4655 1 chrUn.!!$R1 1566
13 TraesCS5A01G444700 chrUn 325628 326489 861 True 728.000000 977 97.289500 4764 5595 2 chrUn.!!$R3 831
14 TraesCS5A01G444700 chrUn 344270373 344270992 619 True 289.000000 289 75.906000 1856 2465 1 chrUn.!!$R2 609
15 TraesCS5A01G444700 chr3A 437857085 437857928 843 False 1417.000000 1417 97.156000 4761 5595 1 chr3A.!!$F1 834
16 TraesCS5A01G444700 chr3A 738249451 738250947 1496 True 623.000000 623 74.804000 887 2379 1 chr3A.!!$R1 1492
17 TraesCS5A01G444700 chr3A 738306026 738307629 1603 True 470.500000 536 80.180500 887 2448 2 chr3A.!!$R9 1561
18 TraesCS5A01G444700 chr3A 738692515 738694129 1614 True 451.000000 488 80.255500 887 2472 2 chr3A.!!$R10 1585
19 TraesCS5A01G444700 chr3A 738865217 738865879 662 True 377.000000 377 77.827000 1835 2474 1 chr3A.!!$R6 639
20 TraesCS5A01G444700 chr3A 738919907 738920567 660 True 348.000000 348 77.185000 1835 2474 1 chr3A.!!$R7 639
21 TraesCS5A01G444700 chr3A 738319617 738320134 517 True 346.000000 346 79.584000 1971 2474 1 chr3A.!!$R2 503
22 TraesCS5A01G444700 chr3A 738599364 738599983 619 True 289.000000 289 75.906000 1856 2465 1 chr3A.!!$R3 609
23 TraesCS5A01G444700 chr3A 738678331 738678950 619 True 289.000000 289 75.906000 1856 2465 1 chr3A.!!$R4 609
24 TraesCS5A01G444700 chr3A 738223933 738225458 1525 True 254.500000 320 76.971000 944 2466 2 chr3A.!!$R8 1522
25 TraesCS5A01G444700 chr1A 25303933 25305406 1473 False 903.000000 1327 96.141000 4764 5595 2 chr1A.!!$F2 831
26 TraesCS5A01G444700 chr4A 673160276 673161122 846 False 471.500000 647 87.838000 4764 5595 2 chr4A.!!$F1 831

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
610 619 1.305213 AGGATGGCACCCGCAAAAT 60.305 52.632 0.00 0.0 41.24 1.82 F
1780 2170 1.078848 AGCGACCATTCTGAGTGCC 60.079 57.895 0.00 0.0 0.00 5.01 F
2545 8900 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.0 0.00 3.53 F
4301 10859 0.110486 GGTTCTTGAGGAGGCAACCA 59.890 55.000 3.78 0.0 37.13 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2395 0.460987 ATGGCTCGCAGAAGCTGTAC 60.461 55.000 0.0 0.0 39.1 2.90 R
3049 9592 0.537188 AGTAGTTCAGGACATGGGCG 59.463 55.000 0.0 0.0 0.0 6.13 R
4424 10982 1.205655 TCTCGGATCTGCTTGACTTGG 59.794 52.381 0.0 0.0 0.0 3.61 R
5519 12766 1.569479 GCTTCAGTGTCCGACTTGGC 61.569 60.000 0.0 0.0 37.8 4.52 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
85 86 2.907179 CGCCCCCTTCCTCCAGTTT 61.907 63.158 0.00 0.00 0.00 2.66
387 394 3.368013 CGTGTACAGGTGCTCATTTCCTA 60.368 47.826 7.41 0.00 0.00 2.94
454 463 7.148474 GCGGTCAGAATTTCTTACTTTGTGATA 60.148 37.037 9.87 0.00 0.00 2.15
458 467 7.610305 TCAGAATTTCTTACTTTGTGATACCCC 59.390 37.037 0.00 0.00 0.00 4.95
461 470 3.175594 TCTTACTTTGTGATACCCCCGT 58.824 45.455 0.00 0.00 0.00 5.28
520 529 8.258708 GGATGGAGTTCAGTTACTGTTACTTAT 58.741 37.037 18.21 15.89 31.67 1.73
583 592 2.448582 GCCATCCGGGTATGGTGGA 61.449 63.158 20.26 0.00 46.93 4.02
610 619 1.305213 AGGATGGCACCCGCAAAAT 60.305 52.632 0.00 0.00 41.24 1.82
729 799 1.739466 CGCATCAAATACACCAGTGCT 59.261 47.619 0.00 0.00 0.00 4.40
737 807 3.719268 ATACACCAGTGCTCCATTCAA 57.281 42.857 0.00 0.00 0.00 2.69
812 882 2.019984 GTCTCCTTTCACATGGCCATC 58.980 52.381 17.61 0.00 0.00 3.51
1085 1403 1.234821 GCATCCGGAGTTGTGACAAA 58.765 50.000 11.34 0.00 0.00 2.83
1145 1463 1.445410 CCGGTTTCACGCTCGATGA 60.445 57.895 0.00 0.00 0.00 2.92
1637 1988 7.707624 AATTTGTCTATGACCATGACACAAT 57.292 32.000 0.00 11.53 39.95 2.71
1669 2020 3.090037 GCACACTCTAACCAGACCTCTA 58.910 50.000 0.00 0.00 0.00 2.43
1780 2170 1.078848 AGCGACCATTCTGAGTGCC 60.079 57.895 0.00 0.00 0.00 5.01
1783 2173 2.434884 ACCATTCTGAGTGCCGCG 60.435 61.111 0.00 0.00 0.00 6.46
1784 2174 3.197790 CCATTCTGAGTGCCGCGG 61.198 66.667 24.05 24.05 0.00 6.46
1785 2175 2.434884 CATTCTGAGTGCCGCGGT 60.435 61.111 28.70 6.76 0.00 5.68
1801 2194 3.170505 CGCGGTTACAACTACGATACAA 58.829 45.455 0.00 0.00 31.92 2.41
1802 2195 3.001758 CGCGGTTACAACTACGATACAAC 60.002 47.826 0.00 0.00 31.92 3.32
1833 2280 2.715046 TCAAGAAATGGCTACAGCTGG 58.285 47.619 19.93 1.57 41.70 4.85
1941 2403 3.927142 GCTAATCAAGTGACGTACAGCTT 59.073 43.478 0.00 0.00 0.00 3.74
1946 2408 0.387367 AGTGACGTACAGCTTCTGCG 60.387 55.000 0.00 0.00 45.42 5.18
1949 2413 1.406970 GACGTACAGCTTCTGCGAGC 61.407 60.000 5.75 0.00 45.42 5.03
1976 2449 5.459536 TTTGGCATTTGTACATGCTAACA 57.540 34.783 16.87 7.12 46.69 2.41
2203 7705 7.451731 TGATGAAGGGACCTTTAATATCACT 57.548 36.000 4.89 0.00 36.26 3.41
2204 7706 7.872138 TGATGAAGGGACCTTTAATATCACTT 58.128 34.615 4.89 0.00 38.81 3.16
2225 7741 1.358759 GCTGACCAACAACGTTGGG 59.641 57.895 30.34 24.07 43.71 4.12
2254 7818 2.486918 TCAGAACGTCACAGTCTCGTA 58.513 47.619 0.00 0.00 36.80 3.43
2256 7820 4.248058 TCAGAACGTCACAGTCTCGTATA 58.752 43.478 0.00 0.00 36.80 1.47
2452 8792 6.012745 AGGAAATCCATATATCCAAAGTGGC 58.987 40.000 1.67 0.00 36.45 5.01
2541 8896 4.181799 ACTATTAGCTACTCCCTCCGTT 57.818 45.455 0.00 0.00 0.00 4.44
2542 8897 4.143543 ACTATTAGCTACTCCCTCCGTTC 58.856 47.826 0.00 0.00 0.00 3.95
2543 8898 1.772836 TTAGCTACTCCCTCCGTTCC 58.227 55.000 0.00 0.00 0.00 3.62
2544 8899 0.627451 TAGCTACTCCCTCCGTTCCA 59.373 55.000 0.00 0.00 0.00 3.53
2545 8900 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2546 8901 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2547 8902 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
2548 8903 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
2549 8904 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
2550 8905 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2551 8906 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2552 8907 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2553 8908 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2554 8909 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2555 8910 3.332034 CCTCCGTTCCAAATTACTCGTT 58.668 45.455 0.00 0.00 0.00 3.85
2556 8911 3.124636 CCTCCGTTCCAAATTACTCGTTG 59.875 47.826 0.00 0.00 0.00 4.10
2557 8912 3.731089 TCCGTTCCAAATTACTCGTTGT 58.269 40.909 0.00 0.00 0.00 3.32
2558 8913 3.495377 TCCGTTCCAAATTACTCGTTGTG 59.505 43.478 0.00 0.00 0.00 3.33
2559 8914 3.364565 CCGTTCCAAATTACTCGTTGTGG 60.365 47.826 0.00 0.00 0.00 4.17
2560 8915 3.249080 CGTTCCAAATTACTCGTTGTGGT 59.751 43.478 0.00 0.00 0.00 4.16
2561 8916 4.260866 CGTTCCAAATTACTCGTTGTGGTT 60.261 41.667 0.00 0.00 0.00 3.67
2562 8917 5.584442 GTTCCAAATTACTCGTTGTGGTTT 58.416 37.500 0.00 0.00 0.00 3.27
2563 8918 5.838531 TCCAAATTACTCGTTGTGGTTTT 57.161 34.783 0.00 0.00 0.00 2.43
2564 8919 6.939132 TCCAAATTACTCGTTGTGGTTTTA 57.061 33.333 0.00 0.00 0.00 1.52
2565 8920 6.961576 TCCAAATTACTCGTTGTGGTTTTAG 58.038 36.000 0.00 0.00 0.00 1.85
2566 8921 6.543100 TCCAAATTACTCGTTGTGGTTTTAGT 59.457 34.615 0.00 0.00 0.00 2.24
2567 8922 7.067251 TCCAAATTACTCGTTGTGGTTTTAGTT 59.933 33.333 0.00 0.00 0.00 2.24
2568 8923 7.377662 CCAAATTACTCGTTGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 0.00 3.01
2569 8924 7.556733 AATTACTCGTTGTGGTTTTAGTTCA 57.443 32.000 0.00 0.00 0.00 3.18
2570 8925 6.981762 TTACTCGTTGTGGTTTTAGTTCAA 57.018 33.333 0.00 0.00 0.00 2.69
2571 8926 5.883503 ACTCGTTGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
2572 8927 6.445357 ACTCGTTGTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
2573 8928 6.859017 ACTCGTTGTGGTTTTAGTTCAAATT 58.141 32.000 0.00 0.00 0.00 1.82
2574 8929 7.317390 ACTCGTTGTGGTTTTAGTTCAAATTT 58.683 30.769 0.00 0.00 0.00 1.82
2575 8930 7.274686 ACTCGTTGTGGTTTTAGTTCAAATTTG 59.725 33.333 12.15 12.15 0.00 2.32
2576 8931 7.313646 TCGTTGTGGTTTTAGTTCAAATTTGA 58.686 30.769 16.91 16.91 34.92 2.69
2577 8932 7.813148 TCGTTGTGGTTTTAGTTCAAATTTGAA 59.187 29.630 26.01 26.01 44.31 2.69
2590 8945 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
2591 8946 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
2592 8947 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
2593 8948 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
2594 8949 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2595 8950 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2596 8951 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2597 8952 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2598 8953 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2599 8954 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2600 8955 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2601 8956 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2602 8957 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2603 8958 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2604 8959 3.934068 ACCACGACGAGTAATTTGGAAT 58.066 40.909 0.00 0.00 0.00 3.01
2605 8960 4.320870 ACCACGACGAGTAATTTGGAATT 58.679 39.130 0.00 0.00 0.00 2.17
2606 8961 4.153475 ACCACGACGAGTAATTTGGAATTG 59.847 41.667 0.00 0.00 0.00 2.32
2607 8962 4.390603 CCACGACGAGTAATTTGGAATTGA 59.609 41.667 0.00 0.00 0.00 2.57
2608 8963 5.106869 CCACGACGAGTAATTTGGAATTGAA 60.107 40.000 0.00 0.00 0.00 2.69
2609 8964 5.788531 CACGACGAGTAATTTGGAATTGAAC 59.211 40.000 0.00 0.00 0.00 3.18
2610 8965 5.699458 ACGACGAGTAATTTGGAATTGAACT 59.301 36.000 0.00 0.00 0.00 3.01
2611 8966 6.869913 ACGACGAGTAATTTGGAATTGAACTA 59.130 34.615 0.00 0.00 0.00 2.24
2612 8967 7.385752 ACGACGAGTAATTTGGAATTGAACTAA 59.614 33.333 0.00 0.00 0.00 2.24
2613 8968 8.225107 CGACGAGTAATTTGGAATTGAACTAAA 58.775 33.333 0.00 0.00 0.00 1.85
2614 8969 9.887406 GACGAGTAATTTGGAATTGAACTAAAA 57.113 29.630 0.00 0.00 0.00 1.52
2615 8970 9.673454 ACGAGTAATTTGGAATTGAACTAAAAC 57.327 29.630 0.00 0.00 0.00 2.43
2616 8971 9.124807 CGAGTAATTTGGAATTGAACTAAAACC 57.875 33.333 0.00 0.00 0.00 3.27
2617 8972 9.974980 GAGTAATTTGGAATTGAACTAAAACCA 57.025 29.630 0.00 0.00 0.00 3.67
2618 8973 9.758651 AGTAATTTGGAATTGAACTAAAACCAC 57.241 29.630 0.00 0.00 30.91 4.16
2619 8974 7.707774 AATTTGGAATTGAACTAAAACCACG 57.292 32.000 0.00 0.00 30.91 4.94
2620 8975 6.452494 TTTGGAATTGAACTAAAACCACGA 57.548 33.333 0.00 0.00 30.91 4.35
2621 8976 5.427036 TGGAATTGAACTAAAACCACGAC 57.573 39.130 0.00 0.00 0.00 4.34
2622 8977 4.024725 TGGAATTGAACTAAAACCACGACG 60.025 41.667 0.00 0.00 0.00 5.12
2623 8978 4.211794 GGAATTGAACTAAAACCACGACGA 59.788 41.667 0.00 0.00 0.00 4.20
2624 8979 4.985044 ATTGAACTAAAACCACGACGAG 57.015 40.909 0.00 0.00 0.00 4.18
2625 8980 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
2626 8981 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
2627 8982 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
2628 8983 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
2629 8984 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
2630 8985 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
2631 8986 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
2632 8987 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
2633 8988 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
2634 8989 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
2635 8990 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
2636 8991 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
2637 8992 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
2638 8993 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
2639 8994 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2640 8995 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2641 8996 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2642 8997 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2643 8998 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2708 9189 9.596677 TTTGTATTTAAATGCACGTGTTACTAC 57.403 29.630 17.25 11.66 30.62 2.73
2726 9211 9.496873 TGTTACTACAATAACTGCATGTTACTT 57.503 29.630 9.85 5.19 43.08 2.24
2815 9317 7.028962 TGTACTGTTTCATGCTAATTCAATGC 58.971 34.615 0.00 0.00 0.00 3.56
2970 9513 7.705325 TGACTAGATTAGCCGTGAAATAGTTTC 59.295 37.037 0.00 0.00 40.08 2.78
3047 9590 7.446931 TGTTTGTCCAAAGTTGCTATGAAGATA 59.553 33.333 0.00 0.00 0.00 1.98
3104 9649 8.988060 TCAGAGGGAGTATATATTTTGTCAACA 58.012 33.333 0.00 0.00 0.00 3.33
3227 9772 3.421844 TGAATGTCCTCTCGAGACTGAA 58.578 45.455 12.08 0.00 0.00 3.02
3251 9796 8.597662 AATATGATCCATTAAAAATGCAGTGC 57.402 30.769 8.58 8.58 0.00 4.40
3385 9943 0.754957 TTGGGCTGTCCTGTGGTTTG 60.755 55.000 0.00 0.00 36.20 2.93
3417 9975 3.650070 TCTGAGCTTCAGTGTAGTGTG 57.350 47.619 11.37 0.00 44.58 3.82
3494 10052 2.300437 CGGAAGAACCAAGGTCTTCTCT 59.700 50.000 18.97 3.16 39.63 3.10
3575 10133 3.195396 AGAAGAGCTAGAGAAGGCAACAG 59.805 47.826 0.00 0.00 41.41 3.16
3964 10522 8.367156 TCAATATCAATCTTCCATCGTGATGTA 58.633 33.333 8.89 0.00 37.11 2.29
4132 10690 6.426646 ACCAGACAGTTAAATGAGAAGAGT 57.573 37.500 10.35 0.00 0.00 3.24
4301 10859 0.110486 GGTTCTTGAGGAGGCAACCA 59.890 55.000 3.78 0.00 37.13 3.67
4384 10942 6.126409 AGAAAGACCCACAATGAAACAAGTA 58.874 36.000 0.00 0.00 0.00 2.24
4424 10982 0.593008 GCGAACAAAACGGGTGAACC 60.593 55.000 0.00 0.00 0.00 3.62
4561 11128 4.083749 CGACGATGCTATAGCTTAGAGTGT 60.084 45.833 24.61 13.09 42.66 3.55
4652 11220 9.157104 TGATTATGCTCGTTTTGTAAACTGATA 57.843 29.630 0.00 0.00 0.00 2.15
4656 11224 6.598525 TGCTCGTTTTGTAAACTGATACATG 58.401 36.000 0.00 0.00 35.80 3.21
4657 11225 6.021596 GCTCGTTTTGTAAACTGATACATGG 58.978 40.000 0.00 0.00 35.80 3.66
4658 11226 6.489127 TCGTTTTGTAAACTGATACATGGG 57.511 37.500 0.00 0.00 35.80 4.00
4659 11227 5.998981 TCGTTTTGTAAACTGATACATGGGT 59.001 36.000 0.00 0.00 35.80 4.51
4660 11228 6.487331 TCGTTTTGTAAACTGATACATGGGTT 59.513 34.615 0.00 0.00 35.80 4.11
4661 11229 7.013464 TCGTTTTGTAAACTGATACATGGGTTT 59.987 33.333 0.00 3.40 35.80 3.27
4662 11230 8.291032 CGTTTTGTAAACTGATACATGGGTTTA 58.709 33.333 0.00 2.50 35.80 2.01
4665 11233 8.871629 TTGTAAACTGATACATGGGTTTATGT 57.128 30.769 0.00 0.00 43.34 2.29
4666 11234 8.871629 TGTAAACTGATACATGGGTTTATGTT 57.128 30.769 0.00 0.00 41.31 2.71
4667 11235 9.303116 TGTAAACTGATACATGGGTTTATGTTT 57.697 29.630 0.00 2.72 41.31 2.83
4671 11239 9.747898 AACTGATACATGGGTTTATGTTTTAGA 57.252 29.630 0.00 0.00 41.31 2.10
4672 11240 9.174166 ACTGATACATGGGTTTATGTTTTAGAC 57.826 33.333 0.00 0.00 41.31 2.59
4673 11241 9.173021 CTGATACATGGGTTTATGTTTTAGACA 57.827 33.333 0.00 0.00 41.31 3.41
4674 11242 9.173021 TGATACATGGGTTTATGTTTTAGACAG 57.827 33.333 0.00 0.00 42.62 3.51
4675 11243 9.391006 GATACATGGGTTTATGTTTTAGACAGA 57.609 33.333 0.00 0.00 42.62 3.41
4676 11244 7.448748 ACATGGGTTTATGTTTTAGACAGAC 57.551 36.000 0.00 0.00 42.62 3.51
4677 11245 7.001674 ACATGGGTTTATGTTTTAGACAGACA 58.998 34.615 0.00 0.00 42.62 3.41
4678 11246 7.504238 ACATGGGTTTATGTTTTAGACAGACAA 59.496 33.333 0.00 0.00 42.62 3.18
4679 11247 7.883391 TGGGTTTATGTTTTAGACAGACAAA 57.117 32.000 0.00 0.00 42.62 2.83
4680 11248 8.294954 TGGGTTTATGTTTTAGACAGACAAAA 57.705 30.769 0.00 0.00 42.62 2.44
4681 11249 8.192110 TGGGTTTATGTTTTAGACAGACAAAAC 58.808 33.333 3.59 3.59 42.62 2.43
4682 11250 8.410912 GGGTTTATGTTTTAGACAGACAAAACT 58.589 33.333 10.28 0.00 42.46 2.66
4693 11261 7.633193 AGACAGACAAAACTATAGAGATCGT 57.367 36.000 6.78 0.00 0.00 3.73
4694 11262 8.734218 AGACAGACAAAACTATAGAGATCGTA 57.266 34.615 6.78 0.00 0.00 3.43
4695 11263 8.614346 AGACAGACAAAACTATAGAGATCGTAC 58.386 37.037 6.78 0.00 0.00 3.67
4696 11264 7.408123 ACAGACAAAACTATAGAGATCGTACG 58.592 38.462 9.53 9.53 0.00 3.67
4697 11265 7.279536 ACAGACAAAACTATAGAGATCGTACGA 59.720 37.037 21.93 21.93 0.00 3.43
4698 11266 7.794810 CAGACAAAACTATAGAGATCGTACGAG 59.205 40.741 23.89 9.57 0.00 4.18
4699 11267 7.495279 AGACAAAACTATAGAGATCGTACGAGT 59.505 37.037 23.89 13.26 0.00 4.18
4700 11268 7.983307 ACAAAACTATAGAGATCGTACGAGTT 58.017 34.615 23.89 15.48 0.00 3.01
4844 11412 5.156355 GGCATCTTTGTTGTACACATTGAG 58.844 41.667 0.00 0.00 34.43 3.02
5077 12313 6.173339 CACATGTTTTACATACTGGGTCTCT 58.827 40.000 0.00 0.00 36.53 3.10
5187 12425 9.269453 AGAAGTACTACAAAACATACAAAGTCC 57.731 33.333 0.00 0.00 0.00 3.85
5270 12509 9.563748 TTAATCTGCATCACATGATTGATAGAA 57.436 29.630 0.00 0.00 34.29 2.10
5369 12611 5.125900 TGAAACAGATTGCATAGATGGTTGG 59.874 40.000 0.00 0.00 0.00 3.77
5519 12766 1.202371 TGATAACTCGGCCAGCTTACG 60.202 52.381 2.24 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.603946 GATGGGGTAGGACGGCGC 62.604 72.222 6.90 0.00 0.00 6.53
77 78 1.283793 CCAAGCGCACAAACTGGAG 59.716 57.895 11.47 0.00 0.00 3.86
83 84 0.383949 GGAGAAACCAAGCGCACAAA 59.616 50.000 11.47 0.00 38.79 2.83
85 86 0.884704 GAGGAGAAACCAAGCGCACA 60.885 55.000 11.47 0.00 42.04 4.57
396 405 6.877611 AATTACAGACACGGAATCAAGTTT 57.122 33.333 0.00 0.00 0.00 2.66
397 406 6.877611 AAATTACAGACACGGAATCAAGTT 57.122 33.333 0.00 0.00 0.00 2.66
454 463 1.303317 CTAAGCTGCAAACGGGGGT 60.303 57.895 1.02 0.00 0.00 4.95
458 467 1.573829 TTCGCCTAAGCTGCAAACGG 61.574 55.000 1.02 0.00 36.60 4.44
461 470 0.874390 CTGTTCGCCTAAGCTGCAAA 59.126 50.000 1.02 0.00 36.60 3.68
520 529 7.616150 ACTTAGTGGAAGATAAGCTAACTGAGA 59.384 37.037 0.00 0.00 38.65 3.27
583 592 0.178998 GGTGCCATCCTGCTCATCAT 60.179 55.000 0.00 0.00 0.00 2.45
610 619 7.499292 CAAATAATTCAAGCCCACCATAATCA 58.501 34.615 0.00 0.00 0.00 2.57
729 799 4.081406 CTGTGGATTTGGACTTGAATGGA 58.919 43.478 0.00 0.00 0.00 3.41
737 807 1.444933 TGGTCCTGTGGATTTGGACT 58.555 50.000 10.60 0.00 46.76 3.85
812 882 2.168496 TCGTGTGGAACTTCCTAGGAG 58.832 52.381 12.26 8.97 37.46 3.69
1085 1403 3.710722 CTTCGGGGCTCTGCTGGT 61.711 66.667 0.00 0.00 0.00 4.00
1669 2020 7.363793 GGTTATGCTGATTTTATCCCACAACTT 60.364 37.037 0.00 0.00 0.00 2.66
1707 2067 6.735229 TCCCTATATCCCATGAGAGCATTAAA 59.265 38.462 0.00 0.00 30.68 1.52
1780 2170 2.784505 TGTATCGTAGTTGTAACCGCG 58.215 47.619 0.00 0.00 0.00 6.46
1783 2173 4.328169 GCCAGTTGTATCGTAGTTGTAACC 59.672 45.833 0.00 0.00 0.00 2.85
1784 2174 4.925054 TGCCAGTTGTATCGTAGTTGTAAC 59.075 41.667 0.00 0.00 0.00 2.50
1785 2175 5.136816 TGCCAGTTGTATCGTAGTTGTAA 57.863 39.130 0.00 0.00 0.00 2.41
1801 2194 3.446161 CCATTTCTTGATGTCATGCCAGT 59.554 43.478 0.00 0.00 0.00 4.00
1802 2195 3.737047 GCCATTTCTTGATGTCATGCCAG 60.737 47.826 0.00 0.00 0.00 4.85
1851 2298 1.150764 GGGGTTGCCTGTATAGCCC 59.849 63.158 0.00 0.00 41.88 5.19
1917 2372 4.398358 AGCTGTACGTCACTTGATTAGCTA 59.602 41.667 0.00 0.00 0.00 3.32
1918 2373 3.193691 AGCTGTACGTCACTTGATTAGCT 59.806 43.478 0.00 0.00 0.00 3.32
1919 2374 3.512680 AGCTGTACGTCACTTGATTAGC 58.487 45.455 0.00 0.00 0.00 3.09
1933 2395 0.460987 ATGGCTCGCAGAAGCTGTAC 60.461 55.000 0.00 0.00 39.10 2.90
1949 2413 4.972201 GCATGTACAAATGCCAAAAATGG 58.028 39.130 9.84 0.00 45.93 3.16
2203 7705 2.600731 CAACGTTGTTGGTCAGCAAAA 58.399 42.857 20.21 0.00 33.43 2.44
2204 7706 1.135257 CCAACGTTGTTGGTCAGCAAA 60.135 47.619 25.63 0.00 33.43 3.68
2225 7741 2.167693 TGTGACGTTCTGATATGGGGTC 59.832 50.000 0.00 0.00 0.00 4.46
2256 7820 8.717717 TGACAGAGAGAAATAACCCATATTCAT 58.282 33.333 0.00 0.00 32.96 2.57
2541 8896 5.838531 AAAACCACAACGAGTAATTTGGA 57.161 34.783 0.00 0.00 0.00 3.53
2542 8897 6.731164 ACTAAAACCACAACGAGTAATTTGG 58.269 36.000 0.00 0.00 0.00 3.28
2543 8898 7.911205 TGAACTAAAACCACAACGAGTAATTTG 59.089 33.333 0.00 0.00 0.00 2.32
2544 8899 7.987649 TGAACTAAAACCACAACGAGTAATTT 58.012 30.769 0.00 0.00 0.00 1.82
2545 8900 7.556733 TGAACTAAAACCACAACGAGTAATT 57.443 32.000 0.00 0.00 0.00 1.40
2546 8901 7.556733 TTGAACTAAAACCACAACGAGTAAT 57.443 32.000 0.00 0.00 0.00 1.89
2547 8902 6.981762 TTGAACTAAAACCACAACGAGTAA 57.018 33.333 0.00 0.00 0.00 2.24
2548 8903 6.981762 TTTGAACTAAAACCACAACGAGTA 57.018 33.333 0.00 0.00 0.00 2.59
2549 8904 5.883503 TTTGAACTAAAACCACAACGAGT 57.116 34.783 0.00 0.00 0.00 4.18
2550 8905 7.486551 TCAAATTTGAACTAAAACCACAACGAG 59.513 33.333 18.45 0.00 33.55 4.18
2551 8906 7.313646 TCAAATTTGAACTAAAACCACAACGA 58.686 30.769 18.45 0.00 33.55 3.85
2552 8907 7.513190 TCAAATTTGAACTAAAACCACAACG 57.487 32.000 18.45 0.00 33.55 4.10
2566 8921 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
2567 8922 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
2568 8923 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
2569 8924 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
2570 8925 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
2571 8926 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
2572 8927 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
2573 8928 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2574 8929 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2575 8930 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2576 8931 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2577 8932 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2578 8933 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2579 8934 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2580 8935 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2581 8936 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2582 8937 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2583 8938 3.389925 TTCCAAATTACTCGTCGTGGT 57.610 42.857 0.00 0.00 0.00 4.16
2584 8939 4.390603 TCAATTCCAAATTACTCGTCGTGG 59.609 41.667 0.00 0.00 0.00 4.94
2585 8940 5.524511 TCAATTCCAAATTACTCGTCGTG 57.475 39.130 0.00 0.00 0.00 4.35
2586 8941 5.699458 AGTTCAATTCCAAATTACTCGTCGT 59.301 36.000 0.00 0.00 0.00 4.34
2587 8942 6.165659 AGTTCAATTCCAAATTACTCGTCG 57.834 37.500 0.00 0.00 0.00 5.12
2588 8943 9.887406 TTTTAGTTCAATTCCAAATTACTCGTC 57.113 29.630 0.00 0.00 0.00 4.20
2589 8944 9.673454 GTTTTAGTTCAATTCCAAATTACTCGT 57.327 29.630 0.00 0.00 0.00 4.18
2590 8945 9.124807 GGTTTTAGTTCAATTCCAAATTACTCG 57.875 33.333 0.00 0.00 0.00 4.18
2591 8946 9.974980 TGGTTTTAGTTCAATTCCAAATTACTC 57.025 29.630 0.00 0.00 0.00 2.59
2592 8947 9.758651 GTGGTTTTAGTTCAATTCCAAATTACT 57.241 29.630 0.00 0.00 0.00 2.24
2593 8948 8.696175 CGTGGTTTTAGTTCAATTCCAAATTAC 58.304 33.333 0.00 0.00 0.00 1.89
2594 8949 8.630917 TCGTGGTTTTAGTTCAATTCCAAATTA 58.369 29.630 0.00 0.00 0.00 1.40
2595 8950 7.436970 GTCGTGGTTTTAGTTCAATTCCAAATT 59.563 33.333 0.00 0.00 0.00 1.82
2596 8951 6.921307 GTCGTGGTTTTAGTTCAATTCCAAAT 59.079 34.615 0.00 0.00 0.00 2.32
2597 8952 6.267070 GTCGTGGTTTTAGTTCAATTCCAAA 58.733 36.000 0.00 0.00 0.00 3.28
2598 8953 5.504337 CGTCGTGGTTTTAGTTCAATTCCAA 60.504 40.000 0.00 0.00 0.00 3.53
2599 8954 4.024725 CGTCGTGGTTTTAGTTCAATTCCA 60.025 41.667 0.00 0.00 0.00 3.53
2600 8955 4.211794 TCGTCGTGGTTTTAGTTCAATTCC 59.788 41.667 0.00 0.00 0.00 3.01
2601 8956 5.050567 ACTCGTCGTGGTTTTAGTTCAATTC 60.051 40.000 0.00 0.00 0.00 2.17
2602 8957 4.812626 ACTCGTCGTGGTTTTAGTTCAATT 59.187 37.500 0.00 0.00 0.00 2.32
2603 8958 4.374399 ACTCGTCGTGGTTTTAGTTCAAT 58.626 39.130 0.00 0.00 0.00 2.57
2604 8959 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
2605 8960 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
2606 8961 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
2607 8962 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
2608 8963 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
2609 8964 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
2610 8965 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
2611 8966 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
2612 8967 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
2613 8968 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
2614 8969 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
2615 8970 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
2616 8971 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
2617 8972 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
2618 8973 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2619 8974 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2620 8975 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2621 8976 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2622 8977 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2623 8978 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2624 8979 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2625 8980 5.703730 AATACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
2626 8981 4.586306 AATACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
2627 8982 4.227527 AGAAATACTCCCTCCGTTCCAAAT 59.772 41.667 0.00 0.00 0.00 2.32
2628 8983 3.585732 AGAAATACTCCCTCCGTTCCAAA 59.414 43.478 0.00 0.00 0.00 3.28
2629 8984 3.178865 AGAAATACTCCCTCCGTTCCAA 58.821 45.455 0.00 0.00 0.00 3.53
2630 8985 2.829023 AGAAATACTCCCTCCGTTCCA 58.171 47.619 0.00 0.00 0.00 3.53
2631 8986 3.908643 AAGAAATACTCCCTCCGTTCC 57.091 47.619 0.00 0.00 0.00 3.62
2632 8987 5.975282 AGTTAAGAAATACTCCCTCCGTTC 58.025 41.667 0.00 0.00 0.00 3.95
2633 8988 5.720520 AGAGTTAAGAAATACTCCCTCCGTT 59.279 40.000 0.00 0.00 41.31 4.44
2634 8989 5.270794 AGAGTTAAGAAATACTCCCTCCGT 58.729 41.667 0.00 0.00 41.31 4.69
2635 8990 5.595133 AGAGAGTTAAGAAATACTCCCTCCG 59.405 44.000 0.00 0.00 41.31 4.63
2636 8991 8.715190 ATAGAGAGTTAAGAAATACTCCCTCC 57.285 38.462 0.00 0.00 41.31 4.30
2708 9189 7.312154 TGGCTAAAAGTAACATGCAGTTATTG 58.688 34.615 10.56 0.00 44.06 1.90
3047 9590 1.264749 TAGTTCAGGACATGGGCGCT 61.265 55.000 7.64 0.00 0.00 5.92
3049 9592 0.537188 AGTAGTTCAGGACATGGGCG 59.463 55.000 0.00 0.00 0.00 6.13
3227 9772 7.654520 GTGCACTGCATTTTTAATGGATCATAT 59.345 33.333 10.32 0.00 41.91 1.78
3251 9796 7.819900 AGTAGAGGCTGTTGTTTTATCTTAGTG 59.180 37.037 0.00 0.00 0.00 2.74
3345 9903 5.011329 CCAATAATCATACCTGCAGGCATTT 59.989 40.000 33.06 18.89 39.32 2.32
3385 9943 2.416680 AGCTCAGAAGAAGAATGCCC 57.583 50.000 0.00 0.00 0.00 5.36
3417 9975 3.896648 TTTTCCATCTGCGAGTGAAAC 57.103 42.857 0.00 0.00 0.00 2.78
3494 10052 9.816354 TTCATCAGATGATATCAACGTTTCTAA 57.184 29.630 14.11 0.00 39.39 2.10
3550 10108 5.423610 TGTTGCCTTCTCTAGCTCTTCTAAT 59.576 40.000 0.00 0.00 0.00 1.73
3575 10133 6.097356 TGATACGTGTAGGATCAAAGTTGTC 58.903 40.000 0.00 0.00 46.75 3.18
3625 10183 6.293298 GCTGATCAGATAACATGCCTTTGTAG 60.293 42.308 27.04 0.00 0.00 2.74
3964 10522 7.070074 ACATCCAAGAGTATATTCGAGGACTTT 59.930 37.037 11.85 0.00 31.10 2.66
4132 10690 3.127589 CACACCGAAACTGTACACATCA 58.872 45.455 0.00 0.00 0.00 3.07
4285 10843 1.774254 TCTTTGGTTGCCTCCTCAAGA 59.226 47.619 5.83 5.83 0.00 3.02
4301 10859 3.817647 GCCACACTGTTGATCTCTTCTTT 59.182 43.478 0.00 0.00 0.00 2.52
4384 10942 1.333177 AAGTCTGCAGTTCCGTCTCT 58.667 50.000 14.67 0.00 0.00 3.10
4424 10982 1.205655 TCTCGGATCTGCTTGACTTGG 59.794 52.381 0.00 0.00 0.00 3.61
4427 10985 3.196469 TCATTTCTCGGATCTGCTTGACT 59.804 43.478 0.00 0.00 0.00 3.41
4561 11128 0.894835 TAGCAGACGCCATGAACTCA 59.105 50.000 0.00 0.00 39.83 3.41
4652 11220 7.001674 TGTCTGTCTAAAACATAAACCCATGT 58.998 34.615 0.00 0.00 40.90 3.21
4656 11224 8.410912 AGTTTTGTCTGTCTAAAACATAAACCC 58.589 33.333 13.10 0.00 44.87 4.11
4667 11235 9.175312 ACGATCTCTATAGTTTTGTCTGTCTAA 57.825 33.333 0.00 0.00 0.00 2.10
4668 11236 8.734218 ACGATCTCTATAGTTTTGTCTGTCTA 57.266 34.615 0.00 0.00 0.00 2.59
4669 11237 7.633193 ACGATCTCTATAGTTTTGTCTGTCT 57.367 36.000 0.00 0.00 0.00 3.41
4670 11238 7.583401 CGTACGATCTCTATAGTTTTGTCTGTC 59.417 40.741 10.44 0.00 0.00 3.51
4671 11239 7.279536 TCGTACGATCTCTATAGTTTTGTCTGT 59.720 37.037 15.28 0.00 0.00 3.41
4672 11240 7.628235 TCGTACGATCTCTATAGTTTTGTCTG 58.372 38.462 15.28 0.00 0.00 3.51
4673 11241 7.495279 ACTCGTACGATCTCTATAGTTTTGTCT 59.505 37.037 19.87 0.00 0.00 3.41
4674 11242 7.629130 ACTCGTACGATCTCTATAGTTTTGTC 58.371 38.462 19.87 0.00 0.00 3.18
4675 11243 7.551035 ACTCGTACGATCTCTATAGTTTTGT 57.449 36.000 19.87 4.81 0.00 2.83
4676 11244 8.838452 AAACTCGTACGATCTCTATAGTTTTG 57.162 34.615 19.87 4.14 33.41 2.44
4677 11245 9.852091 AAAAACTCGTACGATCTCTATAGTTTT 57.148 29.630 23.58 23.58 43.80 2.43
4678 11246 9.286946 CAAAAACTCGTACGATCTCTATAGTTT 57.713 33.333 19.87 18.19 37.48 2.66
4679 11247 7.914346 CCAAAAACTCGTACGATCTCTATAGTT 59.086 37.037 19.87 13.36 0.00 2.24
4680 11248 7.281774 TCCAAAAACTCGTACGATCTCTATAGT 59.718 37.037 19.87 7.58 0.00 2.12
4681 11249 7.637229 TCCAAAAACTCGTACGATCTCTATAG 58.363 38.462 19.87 6.88 0.00 1.31
4682 11250 7.558161 TCCAAAAACTCGTACGATCTCTATA 57.442 36.000 19.87 0.00 0.00 1.31
4683 11251 6.446781 TCCAAAAACTCGTACGATCTCTAT 57.553 37.500 19.87 1.10 0.00 1.98
4684 11252 5.885230 TCCAAAAACTCGTACGATCTCTA 57.115 39.130 19.87 0.00 0.00 2.43
4685 11253 4.778534 TCCAAAAACTCGTACGATCTCT 57.221 40.909 19.87 1.21 0.00 3.10
4686 11254 5.220416 CCAATCCAAAAACTCGTACGATCTC 60.220 44.000 19.87 0.00 0.00 2.75
4687 11255 4.630069 CCAATCCAAAAACTCGTACGATCT 59.370 41.667 19.87 5.89 0.00 2.75
4688 11256 4.628333 TCCAATCCAAAAACTCGTACGATC 59.372 41.667 19.87 0.00 0.00 3.69
4689 11257 4.571919 TCCAATCCAAAAACTCGTACGAT 58.428 39.130 19.87 1.16 0.00 3.73
4690 11258 3.992643 TCCAATCCAAAAACTCGTACGA 58.007 40.909 18.41 18.41 0.00 3.43
4691 11259 4.212636 AGTTCCAATCCAAAAACTCGTACG 59.787 41.667 9.53 9.53 0.00 3.67
4692 11260 5.684550 AGTTCCAATCCAAAAACTCGTAC 57.315 39.130 0.00 0.00 0.00 3.67
4693 11261 7.881232 AGAATAGTTCCAATCCAAAAACTCGTA 59.119 33.333 0.00 0.00 34.09 3.43
4694 11262 6.715264 AGAATAGTTCCAATCCAAAAACTCGT 59.285 34.615 0.00 0.00 34.09 4.18
4695 11263 7.145932 AGAATAGTTCCAATCCAAAAACTCG 57.854 36.000 0.00 0.00 34.09 4.18
4696 11264 8.360390 ACAAGAATAGTTCCAATCCAAAAACTC 58.640 33.333 0.00 0.00 34.09 3.01
4697 11265 8.250143 ACAAGAATAGTTCCAATCCAAAAACT 57.750 30.769 0.00 0.00 36.09 2.66
4698 11266 8.887036 AACAAGAATAGTTCCAATCCAAAAAC 57.113 30.769 0.00 0.00 0.00 2.43
4756 11324 2.885894 GCGGGTATAGCTAGTTCACTCT 59.114 50.000 0.00 0.00 0.00 3.24
5187 12425 3.065371 GGAATTAGATGTTCGGTGCCAAG 59.935 47.826 0.00 0.00 0.00 3.61
5425 12667 6.065976 ACATAGTGATCCATGTTTGAGGAA 57.934 37.500 0.00 0.00 37.48 3.36
5519 12766 1.569479 GCTTCAGTGTCCGACTTGGC 61.569 60.000 0.00 0.00 37.80 4.52


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

AutoCloner maintained by Alex Coulton.