Multiple sequence alignment - TraesCS3A01G337700

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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 TraesCS3A01G337700 chr3A 100.000 3662 0 0 1 3662 584476668 584473007 0.000000e+00 6763.0
1 TraesCS3A01G337700 chr3A 87.825 1306 103 30 1668 2921 584377813 584376512 0.000000e+00 1480.0
2 TraesCS3A01G337700 chr3A 89.216 408 35 3 2527 2925 584355007 584354600 5.460000e-138 501.0
3 TraesCS3A01G337700 chr3A 83.432 338 22 14 1001 1332 584373160 584372851 2.150000e-72 283.0
4 TraesCS3A01G337700 chr3A 82.038 373 30 19 966 1332 584378190 584377849 2.150000e-72 283.0
5 TraesCS3A01G337700 chr3A 85.366 82 8 1 1541 1618 584377913 584377832 8.430000e-12 82.4
6 TraesCS3A01G337700 chr3D 96.700 1394 24 4 1541 2925 443443494 443442114 0.000000e+00 2300.0
7 TraesCS3A01G337700 chr3D 86.874 1318 108 27 1666 2921 443430741 443429427 0.000000e+00 1415.0
8 TraesCS3A01G337700 chr3D 83.265 1458 151 52 1541 2925 443364045 443362608 0.000000e+00 1254.0
9 TraesCS3A01G337700 chr3D 84.567 1121 107 27 1865 2925 443421014 443419900 0.000000e+00 1051.0
10 TraesCS3A01G337700 chr3D 89.660 793 73 6 1 786 12216974 12216184 0.000000e+00 1002.0
11 TraesCS3A01G337700 chr3D 87.438 804 95 3 1 798 602097444 602096641 0.000000e+00 920.0
12 TraesCS3A01G337700 chr3D 87.848 790 86 6 1 783 315790 315004 0.000000e+00 918.0
13 TraesCS3A01G337700 chr3D 82.613 1110 125 41 1862 2917 443319263 443318168 0.000000e+00 918.0
14 TraesCS3A01G337700 chr3D 89.118 533 21 12 800 1313 443443963 443443449 2.400000e-176 628.0
15 TraesCS3A01G337700 chr3D 80.926 367 31 16 958 1317 443431278 443430944 1.690000e-63 254.0
16 TraesCS3A01G337700 chr3D 82.524 309 21 15 1011 1314 443319763 443319483 1.310000e-59 241.0
17 TraesCS3A01G337700 chr3D 85.311 177 14 4 966 1142 443421685 443421521 4.860000e-39 172.0
18 TraesCS3A01G337700 chr3D 85.256 156 18 5 1668 1821 443438376 443438224 4.900000e-34 156.0
19 TraesCS3A01G337700 chr3D 92.208 77 5 1 1541 1617 443319530 443319455 1.390000e-19 108.0
20 TraesCS3A01G337700 chr3D 95.745 47 2 0 1541 1587 443430994 443430948 3.920000e-10 76.8
21 TraesCS3A01G337700 chr3D 90.566 53 5 0 1541 1593 443421340 443421288 1.820000e-08 71.3
22 TraesCS3A01G337700 chr3B 87.844 1308 104 25 1666 2921 581134451 581133147 0.000000e+00 1483.0
23 TraesCS3A01G337700 chr3B 93.842 747 40 3 2922 3662 828757865 828758611 0.000000e+00 1120.0
24 TraesCS3A01G337700 chr3B 82.799 1122 124 31 1862 2918 581091592 581090475 0.000000e+00 939.0
25 TraesCS3A01G337700 chr3B 80.414 1353 153 52 1668 2925 710388595 710389930 0.000000e+00 928.0
26 TraesCS3A01G337700 chr3B 80.114 699 80 29 1862 2512 581127477 581126790 1.990000e-127 466.0
27 TraesCS3A01G337700 chr3B 84.419 353 32 9 967 1314 581128205 581127871 3.530000e-85 326.0
28 TraesCS3A01G337700 chr3B 80.392 357 36 18 967 1313 581267906 581267574 1.310000e-59 241.0
29 TraesCS3A01G337700 chr3B 79.331 329 28 21 1001 1314 710388245 710388548 1.040000e-45 195.0
30 TraesCS3A01G337700 chr3B 93.671 79 5 0 1540 1618 581091855 581091777 6.420000e-23 119.0
31 TraesCS3A01G337700 chr3B 92.308 78 6 0 1541 1618 581267620 581267543 1.070000e-20 111.0
32 TraesCS3A01G337700 chr5B 87.155 1269 92 24 1726 2925 577365784 577364518 0.000000e+00 1375.0
33 TraesCS3A01G337700 chr5B 83.193 357 30 16 1014 1364 577366473 577366141 2.140000e-77 300.0
34 TraesCS3A01G337700 chr5B 92.537 67 4 1 1660 1726 577366129 577366064 1.080000e-15 95.3
35 TraesCS3A01G337700 chr5A 96.356 741 25 1 2924 3662 6261253 6260513 0.000000e+00 1218.0
36 TraesCS3A01G337700 chr5A 87.073 936 72 12 2005 2904 590678592 590677670 0.000000e+00 1013.0
37 TraesCS3A01G337700 chr5A 84.416 308 28 14 1014 1314 590679370 590679076 5.990000e-73 285.0
38 TraesCS3A01G337700 chr5A 85.350 157 15 3 1729 1877 590678972 590678816 4.900000e-34 156.0
39 TraesCS3A01G337700 chr5D 87.088 1092 80 23 1865 2904 469729662 469728580 0.000000e+00 1179.0
40 TraesCS3A01G337700 chr5D 94.213 743 36 6 2925 3662 6871771 6872511 0.000000e+00 1127.0
41 TraesCS3A01G337700 chr5D 87.531 802 89 8 3 798 17120357 17119561 0.000000e+00 917.0
42 TraesCS3A01G337700 chr5D 87.189 804 95 4 1 798 434300765 434301566 0.000000e+00 907.0
43 TraesCS3A01G337700 chr5D 82.831 332 27 19 1014 1332 469730256 469729942 1.680000e-68 270.0
44 TraesCS3A01G337700 chr5D 84.279 229 25 4 1660 1877 469729904 469729676 2.860000e-51 213.0
45 TraesCS3A01G337700 chr6D 94.118 748 38 6 2920 3662 158846506 158845760 0.000000e+00 1133.0
46 TraesCS3A01G337700 chr7D 93.968 746 38 5 2923 3662 25136609 25137353 0.000000e+00 1122.0
47 TraesCS3A01G337700 chr7D 88.820 805 83 4 1 798 50084850 50084046 0.000000e+00 981.0
48 TraesCS3A01G337700 chr7B 93.952 744 39 4 2925 3662 537160954 537160211 0.000000e+00 1120.0
49 TraesCS3A01G337700 chr2D 93.834 746 38 5 2925 3662 31780028 31780773 0.000000e+00 1116.0
50 TraesCS3A01G337700 chr1D 93.801 742 41 5 2924 3662 43000760 43000021 0.000000e+00 1110.0
51 TraesCS3A01G337700 chr1D 93.342 751 45 5 2916 3662 207045120 207044371 0.000000e+00 1105.0
52 TraesCS3A01G337700 chr1D 87.920 803 87 7 1 798 442043847 442044644 0.000000e+00 937.0
53 TraesCS3A01G337700 chr6B 87.965 806 87 7 1 798 674361166 674361969 0.000000e+00 942.0
54 TraesCS3A01G337700 chr4D 87.329 805 91 7 1 798 297101615 297102415 0.000000e+00 911.0


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 TraesCS3A01G337700 chr3A 584473007 584476668 3661 True 6763.000000 6763 100.000000 1 3662 1 chr3A.!!$R2 3661
1 TraesCS3A01G337700 chr3A 584372851 584378190 5339 True 532.100000 1480 84.665250 966 2921 4 chr3A.!!$R3 1955
2 TraesCS3A01G337700 chr3D 443362608 443364045 1437 True 1254.000000 1254 83.265000 1541 2925 1 chr3D.!!$R3 1384
3 TraesCS3A01G337700 chr3D 443438224 443443963 5739 True 1028.000000 2300 90.358000 800 2925 3 chr3D.!!$R8 2125
4 TraesCS3A01G337700 chr3D 12216184 12216974 790 True 1002.000000 1002 89.660000 1 786 1 chr3D.!!$R2 785
5 TraesCS3A01G337700 chr3D 602096641 602097444 803 True 920.000000 920 87.438000 1 798 1 chr3D.!!$R4 797
6 TraesCS3A01G337700 chr3D 315004 315790 786 True 918.000000 918 87.848000 1 783 1 chr3D.!!$R1 782
7 TraesCS3A01G337700 chr3D 443429427 443431278 1851 True 581.933333 1415 87.848333 958 2921 3 chr3D.!!$R7 1963
8 TraesCS3A01G337700 chr3D 443419900 443421685 1785 True 431.433333 1051 86.814667 966 2925 3 chr3D.!!$R6 1959
9 TraesCS3A01G337700 chr3D 443318168 443319763 1595 True 422.333333 918 85.781667 1011 2917 3 chr3D.!!$R5 1906
10 TraesCS3A01G337700 chr3B 581133147 581134451 1304 True 1483.000000 1483 87.844000 1666 2921 1 chr3B.!!$R1 1255
11 TraesCS3A01G337700 chr3B 828757865 828758611 746 False 1120.000000 1120 93.842000 2922 3662 1 chr3B.!!$F1 740
12 TraesCS3A01G337700 chr3B 710388245 710389930 1685 False 561.500000 928 79.872500 1001 2925 2 chr3B.!!$F2 1924
13 TraesCS3A01G337700 chr3B 581090475 581091855 1380 True 529.000000 939 88.235000 1540 2918 2 chr3B.!!$R2 1378
14 TraesCS3A01G337700 chr3B 581126790 581128205 1415 True 396.000000 466 82.266500 967 2512 2 chr3B.!!$R3 1545
15 TraesCS3A01G337700 chr5B 577364518 577366473 1955 True 590.100000 1375 87.628333 1014 2925 3 chr5B.!!$R1 1911
16 TraesCS3A01G337700 chr5A 6260513 6261253 740 True 1218.000000 1218 96.356000 2924 3662 1 chr5A.!!$R1 738
17 TraesCS3A01G337700 chr5A 590677670 590679370 1700 True 484.666667 1013 85.613000 1014 2904 3 chr5A.!!$R2 1890
18 TraesCS3A01G337700 chr5D 6871771 6872511 740 False 1127.000000 1127 94.213000 2925 3662 1 chr5D.!!$F1 737
19 TraesCS3A01G337700 chr5D 17119561 17120357 796 True 917.000000 917 87.531000 3 798 1 chr5D.!!$R1 795
20 TraesCS3A01G337700 chr5D 434300765 434301566 801 False 907.000000 907 87.189000 1 798 1 chr5D.!!$F2 797
21 TraesCS3A01G337700 chr5D 469728580 469730256 1676 True 554.000000 1179 84.732667 1014 2904 3 chr5D.!!$R2 1890
22 TraesCS3A01G337700 chr6D 158845760 158846506 746 True 1133.000000 1133 94.118000 2920 3662 1 chr6D.!!$R1 742
23 TraesCS3A01G337700 chr7D 25136609 25137353 744 False 1122.000000 1122 93.968000 2923 3662 1 chr7D.!!$F1 739
24 TraesCS3A01G337700 chr7D 50084046 50084850 804 True 981.000000 981 88.820000 1 798 1 chr7D.!!$R1 797
25 TraesCS3A01G337700 chr7B 537160211 537160954 743 True 1120.000000 1120 93.952000 2925 3662 1 chr7B.!!$R1 737
26 TraesCS3A01G337700 chr2D 31780028 31780773 745 False 1116.000000 1116 93.834000 2925 3662 1 chr2D.!!$F1 737
27 TraesCS3A01G337700 chr1D 43000021 43000760 739 True 1110.000000 1110 93.801000 2924 3662 1 chr1D.!!$R1 738
28 TraesCS3A01G337700 chr1D 207044371 207045120 749 True 1105.000000 1105 93.342000 2916 3662 1 chr1D.!!$R2 746
29 TraesCS3A01G337700 chr1D 442043847 442044644 797 False 937.000000 937 87.920000 1 798 1 chr1D.!!$F1 797
30 TraesCS3A01G337700 chr6B 674361166 674361969 803 False 942.000000 942 87.965000 1 798 1 chr6B.!!$F1 797
31 TraesCS3A01G337700 chr4D 297101615 297102415 800 False 911.000000 911 87.329000 1 798 1 chr4D.!!$F1 797

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
931 947 0.617413 CCCATGAGAGAGGTTGCTGT 59.383 55.0 0.00 0.0 0.0 4.40 F
1370 1522 0.036164 TTCCGGTGCTGCAACTACAT 59.964 50.0 16.61 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2610 3498 3.940852 TGCATATGCTGTGAAATCTTCGT 59.059 39.13 27.13 0.0 42.66 3.85 R
2938 3842 0.404040 CAGAGGCTGGGGTAAAACCA 59.596 55.00 0.00 0.0 41.02 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.752358 CCTGAGTTGAGGCTGCCA 59.248 61.111 22.65 0.00 0.00 4.92
73 74 3.692406 GCCAAGGACGAGACCGGT 61.692 66.667 6.92 6.92 40.78 5.28
128 129 2.589540 GGCGGGTGATGTGGATCA 59.410 61.111 0.00 0.00 36.16 2.92
135 136 1.685803 GGTGATGTGGATCAATGGGCA 60.686 52.381 0.00 0.00 40.39 5.36
333 335 2.282958 CGGAGGATAGGCCGGCTA 60.283 66.667 28.56 16.88 43.67 3.93
372 375 2.994995 ACATGCTCGGGGTCGACA 60.995 61.111 18.91 0.00 40.88 4.35
383 386 2.126228 GTCGACAACGGCGATGGA 60.126 61.111 21.20 7.04 40.19 3.41
395 398 1.225376 GCGATGGACGACACAAACCA 61.225 55.000 0.00 0.00 45.77 3.67
409 412 7.822334 ACGACACAAACCAATCAAGAATAGATA 59.178 33.333 0.00 0.00 0.00 1.98
435 438 1.473278 ACCAAAAAGAAACCACGCGAA 59.527 42.857 15.93 0.00 0.00 4.70
444 447 1.808411 AACCACGCGAACAAGATGAT 58.192 45.000 15.93 0.00 0.00 2.45
632 641 1.906574 AGGGTTTAGGATCGACTTGCA 59.093 47.619 0.00 0.00 0.00 4.08
640 649 4.679373 AGGATCGACTTGCAACAGATAT 57.321 40.909 0.00 0.00 0.00 1.63
651 660 8.565896 ACTTGCAACAGATATCATGTTAGAAA 57.434 30.769 15.61 11.62 38.80 2.52
719 734 7.903145 TCGTGGGCATTTACATATAGAAGTAT 58.097 34.615 0.00 0.00 0.00 2.12
827 843 5.898606 GCGTTCAGATAAAAATGTCTCGATG 59.101 40.000 0.00 0.00 0.00 3.84
881 897 1.305297 AGGATCGCCAGGTCTGACA 60.305 57.895 10.38 0.00 36.29 3.58
904 920 8.261492 ACAGCAGAGAAACATTATTAAGTCTG 57.739 34.615 0.00 0.00 34.55 3.51
919 935 1.021390 GTCTGGTTGCGTCCCATGAG 61.021 60.000 0.00 0.00 0.00 2.90
931 947 0.617413 CCCATGAGAGAGGTTGCTGT 59.383 55.000 0.00 0.00 0.00 4.40
996 1024 3.828451 ACACAAAGGCACAAGCATAGATT 59.172 39.130 0.00 0.00 44.61 2.40
1042 1079 3.005539 TCCTGCTGTCCCTCTGGC 61.006 66.667 0.00 0.00 0.00 4.85
1043 1080 3.007920 CCTGCTGTCCCTCTGGCT 61.008 66.667 0.00 0.00 0.00 4.75
1044 1081 2.583520 CTGCTGTCCCTCTGGCTC 59.416 66.667 0.00 0.00 0.00 4.70
1045 1082 1.988956 CTGCTGTCCCTCTGGCTCT 60.989 63.158 0.00 0.00 0.00 4.09
1046 1083 2.241479 CTGCTGTCCCTCTGGCTCTG 62.241 65.000 0.00 0.00 0.00 3.35
1047 1084 3.028921 GCTGTCCCTCTGGCTCTGG 62.029 68.421 0.00 0.00 0.00 3.86
1142 1194 3.433173 GGAACCTCGGCATACCAAGTAAT 60.433 47.826 0.00 0.00 34.57 1.89
1144 1196 3.039011 ACCTCGGCATACCAAGTAATCT 58.961 45.455 0.00 0.00 34.57 2.40
1163 1223 3.283751 TCTTTTTCTCGTTTGGGCTGAA 58.716 40.909 0.00 0.00 0.00 3.02
1166 1226 2.341846 TTCTCGTTTGGGCTGAAGTT 57.658 45.000 0.00 0.00 0.00 2.66
1167 1227 1.878953 TCTCGTTTGGGCTGAAGTTC 58.121 50.000 0.00 0.00 0.00 3.01
1168 1228 1.416401 TCTCGTTTGGGCTGAAGTTCT 59.584 47.619 4.17 0.00 0.00 3.01
1169 1229 1.532868 CTCGTTTGGGCTGAAGTTCTG 59.467 52.381 4.17 4.85 0.00 3.02
1170 1230 0.593128 CGTTTGGGCTGAAGTTCTGG 59.407 55.000 11.26 2.59 0.00 3.86
1171 1231 0.315251 GTTTGGGCTGAAGTTCTGGC 59.685 55.000 23.05 23.05 39.56 4.85
1172 1232 1.172180 TTTGGGCTGAAGTTCTGGCG 61.172 55.000 23.78 4.50 40.84 5.69
1174 1234 2.328099 GGGCTGAAGTTCTGGCGTG 61.328 63.158 23.78 2.46 40.84 5.34
1175 1235 2.558313 GCTGAAGTTCTGGCGTGC 59.442 61.111 11.26 0.28 0.00 5.34
1249 1401 3.007940 TGCATGTATAGTATGAGGGTGCC 59.992 47.826 0.00 0.00 0.00 5.01
1309 1461 1.648720 CACTCACGCAGGTTGGTTG 59.351 57.895 0.00 0.00 0.00 3.77
1310 1462 2.186826 ACTCACGCAGGTTGGTTGC 61.187 57.895 0.00 0.00 38.18 4.17
1311 1463 1.893808 CTCACGCAGGTTGGTTGCT 60.894 57.895 0.00 0.00 39.38 3.91
1312 1464 0.602638 CTCACGCAGGTTGGTTGCTA 60.603 55.000 0.00 0.00 39.38 3.49
1313 1465 0.882927 TCACGCAGGTTGGTTGCTAC 60.883 55.000 0.00 0.00 39.38 3.58
1314 1466 0.884704 CACGCAGGTTGGTTGCTACT 60.885 55.000 0.00 0.00 39.38 2.57
1315 1467 0.602905 ACGCAGGTTGGTTGCTACTC 60.603 55.000 0.00 0.00 39.38 2.59
1316 1468 1.298859 CGCAGGTTGGTTGCTACTCC 61.299 60.000 0.00 0.00 39.38 3.85
1317 1469 0.036875 GCAGGTTGGTTGCTACTCCT 59.963 55.000 0.00 1.89 38.51 3.69
1318 1470 1.278127 GCAGGTTGGTTGCTACTCCTA 59.722 52.381 0.00 0.00 38.51 2.94
1319 1471 2.935676 GCAGGTTGGTTGCTACTCCTAC 60.936 54.545 0.00 0.00 38.51 3.18
1320 1472 2.567615 CAGGTTGGTTGCTACTCCTACT 59.432 50.000 0.00 0.00 31.99 2.57
1321 1473 3.008049 CAGGTTGGTTGCTACTCCTACTT 59.992 47.826 0.00 0.00 31.99 2.24
1322 1474 3.008049 AGGTTGGTTGCTACTCCTACTTG 59.992 47.826 0.00 0.00 31.99 3.16
1323 1475 3.244457 GGTTGGTTGCTACTCCTACTTGT 60.244 47.826 0.00 0.00 31.99 3.16
1324 1476 4.386711 GTTGGTTGCTACTCCTACTTGTT 58.613 43.478 0.00 0.00 0.00 2.83
1325 1477 4.699925 TGGTTGCTACTCCTACTTGTTT 57.300 40.909 0.00 0.00 0.00 2.83
1326 1478 4.385825 TGGTTGCTACTCCTACTTGTTTG 58.614 43.478 0.00 0.00 0.00 2.93
1327 1479 4.141574 TGGTTGCTACTCCTACTTGTTTGT 60.142 41.667 0.00 0.00 0.00 2.83
1328 1480 4.213482 GGTTGCTACTCCTACTTGTTTGTG 59.787 45.833 0.00 0.00 0.00 3.33
1329 1481 4.948341 TGCTACTCCTACTTGTTTGTGA 57.052 40.909 0.00 0.00 0.00 3.58
1330 1482 5.284861 TGCTACTCCTACTTGTTTGTGAA 57.715 39.130 0.00 0.00 0.00 3.18
1331 1483 5.676552 TGCTACTCCTACTTGTTTGTGAAA 58.323 37.500 0.00 0.00 0.00 2.69
1332 1484 5.526111 TGCTACTCCTACTTGTTTGTGAAAC 59.474 40.000 0.00 0.00 41.73 2.78
1349 1501 6.969828 GTGAAACAAGCATAACTAGCTAGT 57.030 37.500 20.95 20.95 42.53 2.57
1350 1502 7.365840 GTGAAACAAGCATAACTAGCTAGTT 57.634 36.000 34.85 34.85 42.53 2.24
1351 1503 7.807680 GTGAAACAAGCATAACTAGCTAGTTT 58.192 34.615 36.91 23.79 42.53 2.66
1352 1504 8.290325 GTGAAACAAGCATAACTAGCTAGTTTT 58.710 33.333 36.91 28.38 42.53 2.43
1353 1505 8.504005 TGAAACAAGCATAACTAGCTAGTTTTC 58.496 33.333 36.91 29.37 43.57 2.29
1354 1506 6.986904 ACAAGCATAACTAGCTAGTTTTCC 57.013 37.500 36.91 23.32 43.57 3.13
1355 1507 5.581085 ACAAGCATAACTAGCTAGTTTTCCG 59.419 40.000 36.91 24.48 43.57 4.30
1356 1508 4.694339 AGCATAACTAGCTAGTTTTCCGG 58.306 43.478 36.91 23.66 43.57 5.14
1357 1509 4.161754 AGCATAACTAGCTAGTTTTCCGGT 59.838 41.667 36.91 25.34 43.57 5.28
1358 1510 4.270325 GCATAACTAGCTAGTTTTCCGGTG 59.730 45.833 36.91 25.42 43.57 4.94
1359 1511 2.381725 ACTAGCTAGTTTTCCGGTGC 57.618 50.000 20.95 0.00 31.13 5.01
1360 1512 1.900486 ACTAGCTAGTTTTCCGGTGCT 59.100 47.619 20.95 4.01 31.13 4.40
1361 1513 2.271800 CTAGCTAGTTTTCCGGTGCTG 58.728 52.381 12.92 0.00 32.72 4.41
1362 1514 0.955919 AGCTAGTTTTCCGGTGCTGC 60.956 55.000 0.00 0.00 0.00 5.25
1363 1515 1.234615 GCTAGTTTTCCGGTGCTGCA 61.235 55.000 0.00 0.00 0.00 4.41
1364 1516 1.234821 CTAGTTTTCCGGTGCTGCAA 58.765 50.000 2.77 0.00 0.00 4.08
1365 1517 0.948678 TAGTTTTCCGGTGCTGCAAC 59.051 50.000 7.83 7.83 0.00 4.17
1366 1518 0.751643 AGTTTTCCGGTGCTGCAACT 60.752 50.000 16.61 5.58 0.00 3.16
1367 1519 0.948678 GTTTTCCGGTGCTGCAACTA 59.051 50.000 16.61 0.37 0.00 2.24
1368 1520 0.948678 TTTTCCGGTGCTGCAACTAC 59.051 50.000 16.61 0.00 0.00 2.73
1369 1521 0.179043 TTTCCGGTGCTGCAACTACA 60.179 50.000 16.61 0.00 0.00 2.74
1370 1522 0.036164 TTCCGGTGCTGCAACTACAT 59.964 50.000 16.61 0.00 0.00 2.29
1371 1523 0.036164 TCCGGTGCTGCAACTACATT 59.964 50.000 16.61 0.00 0.00 2.71
1372 1524 0.881118 CCGGTGCTGCAACTACATTT 59.119 50.000 16.61 0.00 0.00 2.32
1373 1525 1.269448 CCGGTGCTGCAACTACATTTT 59.731 47.619 16.61 0.00 0.00 1.82
1374 1526 2.318578 CGGTGCTGCAACTACATTTTG 58.681 47.619 16.61 0.00 0.00 2.44
1375 1527 2.287547 CGGTGCTGCAACTACATTTTGT 60.288 45.455 16.61 0.00 0.00 2.83
1376 1528 3.716601 GGTGCTGCAACTACATTTTGTT 58.283 40.909 11.11 0.00 0.00 2.83
1377 1529 4.119136 GGTGCTGCAACTACATTTTGTTT 58.881 39.130 11.11 0.00 0.00 2.83
1378 1530 4.570369 GGTGCTGCAACTACATTTTGTTTT 59.430 37.500 11.11 0.00 0.00 2.43
1379 1531 5.751028 GGTGCTGCAACTACATTTTGTTTTA 59.249 36.000 11.11 0.00 0.00 1.52
1380 1532 6.074356 GGTGCTGCAACTACATTTTGTTTTAG 60.074 38.462 11.11 0.00 0.00 1.85
1381 1533 5.461737 TGCTGCAACTACATTTTGTTTTAGC 59.538 36.000 0.00 0.00 35.22 3.09
1382 1534 5.461737 GCTGCAACTACATTTTGTTTTAGCA 59.538 36.000 0.00 0.00 34.99 3.49
1383 1535 6.146021 GCTGCAACTACATTTTGTTTTAGCAT 59.854 34.615 0.00 0.00 34.99 3.79
1384 1536 7.405469 TGCAACTACATTTTGTTTTAGCATG 57.595 32.000 0.00 0.00 0.00 4.06
1385 1537 6.423302 TGCAACTACATTTTGTTTTAGCATGG 59.577 34.615 0.00 0.00 0.00 3.66
1386 1538 6.128580 GCAACTACATTTTGTTTTAGCATGGG 60.129 38.462 0.00 0.00 0.00 4.00
1387 1539 6.664428 ACTACATTTTGTTTTAGCATGGGT 57.336 33.333 0.00 0.00 0.00 4.51
1388 1540 6.454795 ACTACATTTTGTTTTAGCATGGGTG 58.545 36.000 0.00 0.00 0.00 4.61
1403 1555 4.885413 CATGGGTGCATATTATTTGTGGG 58.115 43.478 0.00 0.00 0.00 4.61
1404 1556 2.697751 TGGGTGCATATTATTTGTGGGC 59.302 45.455 0.00 0.00 0.00 5.36
1405 1557 2.697751 GGGTGCATATTATTTGTGGGCA 59.302 45.455 0.00 0.00 0.00 5.36
1406 1558 3.324556 GGGTGCATATTATTTGTGGGCAT 59.675 43.478 0.00 0.00 31.92 4.40
1407 1559 4.202346 GGGTGCATATTATTTGTGGGCATT 60.202 41.667 0.00 0.00 31.92 3.56
1408 1560 5.367302 GGTGCATATTATTTGTGGGCATTT 58.633 37.500 0.00 0.00 31.92 2.32
1409 1561 5.821995 GGTGCATATTATTTGTGGGCATTTT 59.178 36.000 0.00 0.00 31.92 1.82
1410 1562 6.989169 GGTGCATATTATTTGTGGGCATTTTA 59.011 34.615 0.00 0.00 31.92 1.52
1411 1563 7.661027 GGTGCATATTATTTGTGGGCATTTTAT 59.339 33.333 0.00 0.00 31.92 1.40
1412 1564 9.703892 GTGCATATTATTTGTGGGCATTTTATA 57.296 29.630 0.00 0.00 31.92 0.98
1447 1599 7.448748 TTTCAAGTGCCTAAGAAATAGAACC 57.551 36.000 0.00 0.00 33.04 3.62
1448 1600 6.374417 TCAAGTGCCTAAGAAATAGAACCT 57.626 37.500 0.00 0.00 33.04 3.50
1449 1601 6.779860 TCAAGTGCCTAAGAAATAGAACCTT 58.220 36.000 0.00 0.00 33.04 3.50
1450 1602 6.655003 TCAAGTGCCTAAGAAATAGAACCTTG 59.345 38.462 0.00 0.00 33.04 3.61
1451 1603 4.944317 AGTGCCTAAGAAATAGAACCTTGC 59.056 41.667 0.00 0.00 33.04 4.01
1452 1604 3.938963 TGCCTAAGAAATAGAACCTTGCG 59.061 43.478 0.00 0.00 33.04 4.85
1453 1605 3.242772 GCCTAAGAAATAGAACCTTGCGC 60.243 47.826 0.00 0.00 33.04 6.09
1454 1606 3.938963 CCTAAGAAATAGAACCTTGCGCA 59.061 43.478 5.66 5.66 33.04 6.09
1455 1607 3.831715 AAGAAATAGAACCTTGCGCAC 57.168 42.857 11.12 0.00 0.00 5.34
1456 1608 3.059352 AGAAATAGAACCTTGCGCACT 57.941 42.857 11.12 6.07 0.00 4.40
1457 1609 2.744202 AGAAATAGAACCTTGCGCACTG 59.256 45.455 11.12 6.71 0.00 3.66
1458 1610 2.185004 AATAGAACCTTGCGCACTGT 57.815 45.000 11.12 7.52 0.00 3.55
1459 1611 3.328382 AATAGAACCTTGCGCACTGTA 57.672 42.857 11.12 0.00 0.00 2.74
1460 1612 2.363788 TAGAACCTTGCGCACTGTAG 57.636 50.000 11.12 4.29 0.00 2.74
1461 1613 0.393077 AGAACCTTGCGCACTGTAGT 59.607 50.000 11.12 0.00 0.00 2.73
1462 1614 1.616865 AGAACCTTGCGCACTGTAGTA 59.383 47.619 11.12 0.00 0.00 1.82
1463 1615 2.233922 AGAACCTTGCGCACTGTAGTAT 59.766 45.455 11.12 0.00 0.00 2.12
1464 1616 3.446161 AGAACCTTGCGCACTGTAGTATA 59.554 43.478 11.12 0.00 0.00 1.47
1465 1617 3.880047 ACCTTGCGCACTGTAGTATAA 57.120 42.857 11.12 0.00 0.00 0.98
1466 1618 4.196626 ACCTTGCGCACTGTAGTATAAA 57.803 40.909 11.12 0.00 0.00 1.40
1467 1619 4.766375 ACCTTGCGCACTGTAGTATAAAT 58.234 39.130 11.12 0.00 0.00 1.40
1468 1620 5.909477 ACCTTGCGCACTGTAGTATAAATA 58.091 37.500 11.12 0.00 0.00 1.40
1469 1621 6.522054 ACCTTGCGCACTGTAGTATAAATAT 58.478 36.000 11.12 0.00 0.00 1.28
1470 1622 6.990349 ACCTTGCGCACTGTAGTATAAATATT 59.010 34.615 11.12 0.00 0.00 1.28
1471 1623 7.497909 ACCTTGCGCACTGTAGTATAAATATTT 59.502 33.333 11.12 5.89 0.00 1.40
1472 1624 8.984764 CCTTGCGCACTGTAGTATAAATATTTA 58.015 33.333 11.12 10.27 0.00 1.40
1491 1643 9.489084 AATATTTAAAACCAGTTCTTTCTTGGC 57.511 29.630 0.00 0.00 0.00 4.52
1492 1644 5.923733 TTAAAACCAGTTCTTTCTTGGCA 57.076 34.783 0.00 0.00 0.00 4.92
1493 1645 3.801114 AAACCAGTTCTTTCTTGGCAC 57.199 42.857 0.00 0.00 0.00 5.01
1494 1646 2.435372 ACCAGTTCTTTCTTGGCACA 57.565 45.000 0.00 0.00 0.00 4.57
1507 1659 2.039818 TGGCACAACAGTTTTACGGA 57.960 45.000 0.00 0.00 31.92 4.69
1508 1660 1.944024 TGGCACAACAGTTTTACGGAG 59.056 47.619 0.00 0.00 31.92 4.63
1509 1661 1.334689 GGCACAACAGTTTTACGGAGC 60.335 52.381 0.00 0.00 0.00 4.70
1510 1662 1.332375 GCACAACAGTTTTACGGAGCA 59.668 47.619 0.00 0.00 0.00 4.26
1511 1663 2.031157 GCACAACAGTTTTACGGAGCAT 60.031 45.455 0.00 0.00 0.00 3.79
1512 1664 3.810373 CACAACAGTTTTACGGAGCATC 58.190 45.455 0.00 0.00 0.00 3.91
1513 1665 3.498397 CACAACAGTTTTACGGAGCATCT 59.502 43.478 0.00 0.00 33.73 2.90
1514 1666 3.746492 ACAACAGTTTTACGGAGCATCTC 59.254 43.478 0.00 0.00 33.73 2.75
1515 1667 3.963428 ACAGTTTTACGGAGCATCTCT 57.037 42.857 0.00 0.00 33.73 3.10
1516 1668 3.589988 ACAGTTTTACGGAGCATCTCTG 58.410 45.455 1.37 1.37 42.15 3.35
1518 1670 3.997021 CAGTTTTACGGAGCATCTCTGTT 59.003 43.478 12.85 0.00 46.59 3.16
1519 1671 3.997021 AGTTTTACGGAGCATCTCTGTTG 59.003 43.478 12.85 0.00 46.59 3.33
1520 1672 2.010145 TTACGGAGCATCTCTGTTGC 57.990 50.000 12.85 0.00 46.59 4.17
1531 1683 6.576551 GCATCTCTGTTGCTAGTTACTAAC 57.423 41.667 0.00 0.00 37.14 2.34
1532 1684 6.100004 GCATCTCTGTTGCTAGTTACTAACA 58.900 40.000 1.79 0.00 37.14 2.41
1533 1685 6.758886 GCATCTCTGTTGCTAGTTACTAACAT 59.241 38.462 0.00 0.00 37.14 2.71
1534 1686 7.254252 GCATCTCTGTTGCTAGTTACTAACATG 60.254 40.741 0.00 0.00 37.14 3.21
1535 1687 7.228314 TCTCTGTTGCTAGTTACTAACATGT 57.772 36.000 0.00 0.00 33.15 3.21
1536 1688 7.667557 TCTCTGTTGCTAGTTACTAACATGTT 58.332 34.615 16.68 16.68 33.15 2.71
1537 1689 8.148351 TCTCTGTTGCTAGTTACTAACATGTTT 58.852 33.333 17.78 1.74 33.15 2.83
1538 1690 9.419297 CTCTGTTGCTAGTTACTAACATGTTTA 57.581 33.333 17.78 0.63 33.15 2.01
1648 1975 6.072008 TGCAGCTACATTTTCTTTTAGCATGA 60.072 34.615 0.00 0.00 39.59 3.07
1986 2701 1.203237 AATATGGGCCCCTGCAAAAC 58.797 50.000 22.27 0.00 40.13 2.43
2008 2802 6.992063 ACATTGAGCGTTTCTCTTATGAAT 57.008 33.333 11.57 0.00 42.38 2.57
2239 3054 2.169978 CCCAAAGGGCTACAGTACTACC 59.830 54.545 0.00 0.00 35.35 3.18
2415 3270 3.305720 TGGTCTCCGTGCTATTTATCCT 58.694 45.455 0.00 0.00 0.00 3.24
2436 3291 5.104776 TCCTAGGAATTCAAGTCCACATCAG 60.105 44.000 9.71 0.00 37.65 2.90
2513 3368 5.450818 AAGCCCCAGAATTATGTAAGTGA 57.549 39.130 0.00 0.00 0.00 3.41
2800 3688 0.816373 GGGACTCTAGTGTCGAACCC 59.184 60.000 16.53 10.37 37.81 4.11
2815 3710 2.767505 GAACCCCAGCTCATAATACCG 58.232 52.381 0.00 0.00 0.00 4.02
3017 4644 2.291741 CCAGCAACAAGTCTTCAAGTCC 59.708 50.000 0.00 0.00 0.00 3.85
3120 5404 6.216251 ACATGCCTATCCTATTACATGACCAT 59.784 38.462 0.00 0.00 38.55 3.55
3165 5449 1.621992 GAGCTACCATCTCCCATCGA 58.378 55.000 0.00 0.00 0.00 3.59
3243 6560 1.810030 GATCAACGTCGTGGCCCTC 60.810 63.158 0.00 0.00 0.00 4.30
3271 6588 4.734398 ACCTGCAAAAAGTGAATGTTCA 57.266 36.364 0.00 0.00 34.20 3.18
3465 6785 0.179000 ACAGAATCTTAGCCAGCGGG 59.821 55.000 0.00 0.00 37.18 6.13
3643 8066 0.941542 CCAAACGTGCTTCGAGGAAA 59.058 50.000 0.00 0.00 42.86 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 4.127744 CACATCACCCGCCCCCAT 62.128 66.667 0.00 0.00 0.00 4.00
110 111 2.203209 GATCCACATCACCCGCCC 60.203 66.667 0.00 0.00 0.00 6.13
144 145 2.349969 AATCATAGCCGTCGCTCGCA 62.350 55.000 0.00 0.00 43.95 5.10
197 198 2.819595 CCGGAACACCTGCATCGG 60.820 66.667 0.00 0.00 0.00 4.18
356 358 2.100631 GTTGTCGACCCCGAGCATG 61.101 63.158 14.12 0.00 46.52 4.06
357 359 2.264794 GTTGTCGACCCCGAGCAT 59.735 61.111 14.12 0.00 46.52 3.79
372 375 2.431942 GTGTCGTCCATCGCCGTT 60.432 61.111 0.00 0.00 39.67 4.44
379 382 2.857483 TGATTGGTTTGTGTCGTCCAT 58.143 42.857 0.00 0.00 0.00 3.41
383 386 5.995282 TCTATTCTTGATTGGTTTGTGTCGT 59.005 36.000 0.00 0.00 0.00 4.34
409 412 4.390603 GCGTGGTTTCTTTTTGGTTTTTCT 59.609 37.500 0.00 0.00 0.00 2.52
435 438 1.043116 TCTCCCGCCGATCATCTTGT 61.043 55.000 0.00 0.00 0.00 3.16
444 447 1.590147 GTTTTCTCTCTCCCGCCGA 59.410 57.895 0.00 0.00 0.00 5.54
551 557 4.873129 CCTCCATGACCGCCGTCG 62.873 72.222 0.00 0.00 42.37 5.12
640 649 8.746052 TCAAACCTCTTTTCTTTCTAACATGA 57.254 30.769 0.00 0.00 0.00 3.07
651 660 7.119846 CGAACTATTCCATCAAACCTCTTTTCT 59.880 37.037 0.00 0.00 0.00 2.52
798 814 7.464045 CGAGACATTTTTATCTGAACGCACATA 60.464 37.037 0.00 0.00 0.00 2.29
827 843 1.305219 TACAATGCCTGCACGCTTCC 61.305 55.000 9.13 0.00 0.00 3.46
881 897 7.398024 ACCAGACTTAATAATGTTTCTCTGCT 58.602 34.615 0.00 0.00 0.00 4.24
904 920 0.460987 CTCTCTCATGGGACGCAACC 60.461 60.000 0.00 0.00 0.00 3.77
919 935 6.456181 CGAATTAATCTCAACAGCAACCTCTC 60.456 42.308 0.00 0.00 0.00 3.20
931 947 6.208599 GGGATTTATGCCCGAATTAATCTCAA 59.791 38.462 0.00 0.00 35.50 3.02
996 1024 0.620410 AGGCAGTAGCACCCATACCA 60.620 55.000 0.00 0.00 44.61 3.25
1042 1079 1.004044 AGTTGCATCCTGAACCCAGAG 59.996 52.381 0.00 0.00 43.02 3.35
1043 1080 1.067295 AGTTGCATCCTGAACCCAGA 58.933 50.000 0.00 0.00 43.02 3.86
1044 1081 1.171308 CAGTTGCATCCTGAACCCAG 58.829 55.000 7.90 0.00 40.09 4.45
1045 1082 0.895100 GCAGTTGCATCCTGAACCCA 60.895 55.000 15.88 0.00 41.59 4.51
1046 1083 1.885871 GCAGTTGCATCCTGAACCC 59.114 57.895 15.88 0.00 41.59 4.11
1065 1111 2.039480 TCTTGTGAAGCCAAGATCAGCT 59.961 45.455 0.00 0.00 44.39 4.24
1142 1194 2.925724 TCAGCCCAAACGAGAAAAAGA 58.074 42.857 0.00 0.00 0.00 2.52
1144 1196 3.020984 ACTTCAGCCCAAACGAGAAAAA 58.979 40.909 0.00 0.00 0.00 1.94
1163 1223 1.070134 TGAACTAAGCACGCCAGAACT 59.930 47.619 0.00 0.00 0.00 3.01
1166 1226 0.320421 GGTGAACTAAGCACGCCAGA 60.320 55.000 0.00 0.00 37.13 3.86
1167 1227 1.626654 CGGTGAACTAAGCACGCCAG 61.627 60.000 0.00 0.00 37.13 4.85
1168 1228 1.666553 CGGTGAACTAAGCACGCCA 60.667 57.895 0.00 0.00 37.13 5.69
1169 1229 2.388232 CCGGTGAACTAAGCACGCC 61.388 63.158 0.00 0.00 37.13 5.68
1170 1230 2.388232 CCCGGTGAACTAAGCACGC 61.388 63.158 0.00 0.00 37.13 5.34
1171 1231 1.005394 ACCCGGTGAACTAAGCACG 60.005 57.895 0.00 0.00 37.13 5.34
1172 1232 1.574702 GCACCCGGTGAACTAAGCAC 61.575 60.000 22.37 0.00 35.23 4.40
1174 1234 2.038837 GGCACCCGGTGAACTAAGC 61.039 63.158 22.37 3.37 35.23 3.09
1175 1235 1.740296 CGGCACCCGGTGAACTAAG 60.740 63.158 22.37 1.29 44.15 2.18
1249 1401 2.110967 CCTGCCATCCTCAGCAACG 61.111 63.158 0.00 0.00 38.82 4.10
1290 1442 1.525995 AACCAACCTGCGTGAGTGG 60.526 57.895 0.00 0.00 0.00 4.00
1309 1461 5.986936 GTTTCACAAACAAGTAGGAGTAGC 58.013 41.667 0.00 0.00 41.04 3.58
1322 1474 6.438763 AGCTAGTTATGCTTGTTTCACAAAC 58.561 36.000 0.00 0.00 37.69 2.93
1323 1475 6.633500 AGCTAGTTATGCTTGTTTCACAAA 57.367 33.333 0.00 0.00 37.69 2.83
1324 1476 6.934645 ACTAGCTAGTTATGCTTGTTTCACAA 59.065 34.615 20.95 0.00 42.01 3.33
1325 1477 6.464222 ACTAGCTAGTTATGCTTGTTTCACA 58.536 36.000 20.95 0.00 42.01 3.58
1326 1478 6.969828 ACTAGCTAGTTATGCTTGTTTCAC 57.030 37.500 20.95 0.00 42.01 3.18
1331 1483 5.581085 CGGAAAACTAGCTAGTTATGCTTGT 59.419 40.000 33.60 17.23 45.17 3.16
1332 1484 5.006746 CCGGAAAACTAGCTAGTTATGCTTG 59.993 44.000 33.60 21.71 45.17 4.01
1333 1485 5.116882 CCGGAAAACTAGCTAGTTATGCTT 58.883 41.667 33.60 25.01 45.17 3.91
1334 1486 4.161754 ACCGGAAAACTAGCTAGTTATGCT 59.838 41.667 33.60 18.90 45.17 3.79
1335 1487 4.270325 CACCGGAAAACTAGCTAGTTATGC 59.730 45.833 33.60 24.79 45.17 3.14
1336 1488 4.270325 GCACCGGAAAACTAGCTAGTTATG 59.730 45.833 33.60 24.12 45.17 1.90
1337 1489 4.161754 AGCACCGGAAAACTAGCTAGTTAT 59.838 41.667 33.60 22.15 45.17 1.89
1338 1490 3.512724 AGCACCGGAAAACTAGCTAGTTA 59.487 43.478 33.60 0.00 45.17 2.24
1340 1492 1.900486 AGCACCGGAAAACTAGCTAGT 59.100 47.619 20.95 20.95 38.39 2.57
1341 1493 2.271800 CAGCACCGGAAAACTAGCTAG 58.728 52.381 19.44 19.44 0.00 3.42
1342 1494 1.674817 GCAGCACCGGAAAACTAGCTA 60.675 52.381 9.46 0.00 0.00 3.32
1343 1495 0.955919 GCAGCACCGGAAAACTAGCT 60.956 55.000 9.46 2.39 0.00 3.32
1344 1496 1.234615 TGCAGCACCGGAAAACTAGC 61.235 55.000 9.46 3.05 0.00 3.42
1345 1497 1.069227 GTTGCAGCACCGGAAAACTAG 60.069 52.381 9.46 0.00 0.00 2.57
1346 1498 0.948678 GTTGCAGCACCGGAAAACTA 59.051 50.000 9.46 0.00 0.00 2.24
1347 1499 0.751643 AGTTGCAGCACCGGAAAACT 60.752 50.000 9.46 5.43 0.00 2.66
1348 1500 0.948678 TAGTTGCAGCACCGGAAAAC 59.051 50.000 9.46 3.01 0.00 2.43
1349 1501 0.948678 GTAGTTGCAGCACCGGAAAA 59.051 50.000 9.46 0.00 0.00 2.29
1350 1502 0.179043 TGTAGTTGCAGCACCGGAAA 60.179 50.000 9.46 0.00 0.00 3.13
1351 1503 0.036164 ATGTAGTTGCAGCACCGGAA 59.964 50.000 9.46 0.00 0.00 4.30
1352 1504 0.036164 AATGTAGTTGCAGCACCGGA 59.964 50.000 9.46 0.00 0.00 5.14
1353 1505 0.881118 AAATGTAGTTGCAGCACCGG 59.119 50.000 0.00 0.00 0.00 5.28
1354 1506 2.287547 ACAAAATGTAGTTGCAGCACCG 60.288 45.455 2.55 0.00 0.00 4.94
1355 1507 3.369546 ACAAAATGTAGTTGCAGCACC 57.630 42.857 2.55 0.00 0.00 5.01
1356 1508 5.717038 AAAACAAAATGTAGTTGCAGCAC 57.283 34.783 2.55 0.00 0.00 4.40
1357 1509 5.461737 GCTAAAACAAAATGTAGTTGCAGCA 59.538 36.000 2.55 0.00 36.32 4.41
1358 1510 5.461737 TGCTAAAACAAAATGTAGTTGCAGC 59.538 36.000 0.00 0.00 36.59 5.25
1359 1511 7.359431 CCATGCTAAAACAAAATGTAGTTGCAG 60.359 37.037 0.00 0.00 0.00 4.41
1360 1512 6.423302 CCATGCTAAAACAAAATGTAGTTGCA 59.577 34.615 0.00 0.00 0.00 4.08
1361 1513 6.128580 CCCATGCTAAAACAAAATGTAGTTGC 60.129 38.462 0.00 0.00 0.00 4.17
1362 1514 6.928492 ACCCATGCTAAAACAAAATGTAGTTG 59.072 34.615 0.00 0.00 0.00 3.16
1363 1515 6.928492 CACCCATGCTAAAACAAAATGTAGTT 59.072 34.615 0.00 0.00 0.00 2.24
1364 1516 6.454795 CACCCATGCTAAAACAAAATGTAGT 58.545 36.000 0.00 0.00 0.00 2.73
1365 1517 6.949578 CACCCATGCTAAAACAAAATGTAG 57.050 37.500 0.00 0.00 0.00 2.74
1381 1533 4.800249 GCCCACAAATAATATGCACCCATG 60.800 45.833 0.00 0.00 32.85 3.66
1382 1534 3.324556 GCCCACAAATAATATGCACCCAT 59.675 43.478 0.00 0.00 35.44 4.00
1383 1535 2.697751 GCCCACAAATAATATGCACCCA 59.302 45.455 0.00 0.00 0.00 4.51
1384 1536 2.697751 TGCCCACAAATAATATGCACCC 59.302 45.455 0.00 0.00 0.00 4.61
1385 1537 4.605640 ATGCCCACAAATAATATGCACC 57.394 40.909 0.00 0.00 0.00 5.01
1386 1538 6.923928 AAAATGCCCACAAATAATATGCAC 57.076 33.333 0.00 0.00 0.00 4.57
1421 1573 9.174166 GGTTCTATTTCTTAGGCACTTGAAATA 57.826 33.333 0.00 0.00 43.22 1.40
1422 1574 7.890655 AGGTTCTATTTCTTAGGCACTTGAAAT 59.109 33.333 0.00 0.00 45.16 2.17
1423 1575 7.231467 AGGTTCTATTTCTTAGGCACTTGAAA 58.769 34.615 0.00 0.00 41.23 2.69
1424 1576 6.779860 AGGTTCTATTTCTTAGGCACTTGAA 58.220 36.000 0.00 0.00 41.75 2.69
1425 1577 6.374417 AGGTTCTATTTCTTAGGCACTTGA 57.626 37.500 0.00 0.00 41.75 3.02
1426 1578 6.623767 GCAAGGTTCTATTTCTTAGGCACTTG 60.624 42.308 0.00 0.00 41.75 3.16
1427 1579 5.416013 GCAAGGTTCTATTTCTTAGGCACTT 59.584 40.000 0.00 0.00 41.75 3.16
1428 1580 4.944317 GCAAGGTTCTATTTCTTAGGCACT 59.056 41.667 0.00 0.00 46.37 4.40
1429 1581 4.201822 CGCAAGGTTCTATTTCTTAGGCAC 60.202 45.833 0.00 0.00 0.00 5.01
1430 1582 3.938963 CGCAAGGTTCTATTTCTTAGGCA 59.061 43.478 0.00 0.00 0.00 4.75
1431 1583 3.242772 GCGCAAGGTTCTATTTCTTAGGC 60.243 47.826 0.30 0.00 38.28 3.93
1432 1584 3.938963 TGCGCAAGGTTCTATTTCTTAGG 59.061 43.478 8.16 0.00 38.28 2.69
1433 1585 4.631813 AGTGCGCAAGGTTCTATTTCTTAG 59.368 41.667 14.00 0.00 38.28 2.18
1434 1586 4.391830 CAGTGCGCAAGGTTCTATTTCTTA 59.608 41.667 14.00 0.00 38.28 2.10
1435 1587 3.189287 CAGTGCGCAAGGTTCTATTTCTT 59.811 43.478 14.00 0.00 38.28 2.52
1436 1588 2.744202 CAGTGCGCAAGGTTCTATTTCT 59.256 45.455 14.00 0.00 38.28 2.52
1437 1589 2.484264 ACAGTGCGCAAGGTTCTATTTC 59.516 45.455 14.00 0.00 38.28 2.17
1438 1590 2.504367 ACAGTGCGCAAGGTTCTATTT 58.496 42.857 14.00 0.00 38.28 1.40
1439 1591 2.185004 ACAGTGCGCAAGGTTCTATT 57.815 45.000 14.00 0.00 38.28 1.73
1440 1592 2.233922 ACTACAGTGCGCAAGGTTCTAT 59.766 45.455 14.00 0.00 38.28 1.98
1441 1593 1.616865 ACTACAGTGCGCAAGGTTCTA 59.383 47.619 14.00 0.00 38.28 2.10
1442 1594 0.393077 ACTACAGTGCGCAAGGTTCT 59.607 50.000 14.00 0.23 38.28 3.01
1443 1595 2.074547 TACTACAGTGCGCAAGGTTC 57.925 50.000 14.00 0.00 38.28 3.62
1444 1596 2.762535 ATACTACAGTGCGCAAGGTT 57.237 45.000 14.00 1.61 38.28 3.50
1445 1597 3.880047 TTATACTACAGTGCGCAAGGT 57.120 42.857 14.00 16.45 38.28 3.50
1446 1598 7.421530 AATATTTATACTACAGTGCGCAAGG 57.578 36.000 14.00 10.28 38.28 3.61
1465 1617 9.489084 GCCAAGAAAGAACTGGTTTTAAATATT 57.511 29.630 0.00 0.00 0.00 1.28
1466 1618 8.646900 TGCCAAGAAAGAACTGGTTTTAAATAT 58.353 29.630 0.00 0.00 0.00 1.28
1467 1619 7.923878 GTGCCAAGAAAGAACTGGTTTTAAATA 59.076 33.333 0.00 0.00 0.00 1.40
1468 1620 6.761242 GTGCCAAGAAAGAACTGGTTTTAAAT 59.239 34.615 0.00 0.00 0.00 1.40
1469 1621 6.103330 GTGCCAAGAAAGAACTGGTTTTAAA 58.897 36.000 0.00 0.00 0.00 1.52
1470 1622 5.186021 TGTGCCAAGAAAGAACTGGTTTTAA 59.814 36.000 0.00 0.00 0.00 1.52
1471 1623 4.707448 TGTGCCAAGAAAGAACTGGTTTTA 59.293 37.500 0.00 0.00 0.00 1.52
1472 1624 3.513515 TGTGCCAAGAAAGAACTGGTTTT 59.486 39.130 0.00 0.00 0.00 2.43
1473 1625 3.096092 TGTGCCAAGAAAGAACTGGTTT 58.904 40.909 0.00 0.00 0.00 3.27
1474 1626 2.733956 TGTGCCAAGAAAGAACTGGTT 58.266 42.857 0.00 0.00 0.00 3.67
1475 1627 2.427095 GTTGTGCCAAGAAAGAACTGGT 59.573 45.455 0.00 0.00 0.00 4.00
1476 1628 2.426738 TGTTGTGCCAAGAAAGAACTGG 59.573 45.455 0.00 0.00 0.00 4.00
1477 1629 3.129287 ACTGTTGTGCCAAGAAAGAACTG 59.871 43.478 0.00 0.00 0.00 3.16
1478 1630 3.356290 ACTGTTGTGCCAAGAAAGAACT 58.644 40.909 0.00 0.00 0.00 3.01
1479 1631 3.782889 ACTGTTGTGCCAAGAAAGAAC 57.217 42.857 0.00 0.00 0.00 3.01
1480 1632 4.799564 AAACTGTTGTGCCAAGAAAGAA 57.200 36.364 0.00 0.00 0.00 2.52
1481 1633 4.799564 AAAACTGTTGTGCCAAGAAAGA 57.200 36.364 0.00 0.00 0.00 2.52
1482 1634 4.499040 CGTAAAACTGTTGTGCCAAGAAAG 59.501 41.667 0.00 0.00 0.00 2.62
1483 1635 4.416620 CGTAAAACTGTTGTGCCAAGAAA 58.583 39.130 0.00 0.00 0.00 2.52
1484 1636 3.181495 CCGTAAAACTGTTGTGCCAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
1485 1637 2.356382 CCGTAAAACTGTTGTGCCAAGA 59.644 45.455 0.00 0.00 0.00 3.02
1486 1638 2.356382 TCCGTAAAACTGTTGTGCCAAG 59.644 45.455 0.00 0.00 0.00 3.61
1487 1639 2.356382 CTCCGTAAAACTGTTGTGCCAA 59.644 45.455 0.00 0.00 0.00 4.52
1488 1640 1.944024 CTCCGTAAAACTGTTGTGCCA 59.056 47.619 0.00 0.00 0.00 4.92
1489 1641 1.334689 GCTCCGTAAAACTGTTGTGCC 60.335 52.381 0.00 0.00 0.00 5.01
1490 1642 1.332375 TGCTCCGTAAAACTGTTGTGC 59.668 47.619 0.00 0.00 0.00 4.57
1491 1643 3.498397 AGATGCTCCGTAAAACTGTTGTG 59.502 43.478 0.00 0.00 0.00 3.33
1492 1644 3.740115 AGATGCTCCGTAAAACTGTTGT 58.260 40.909 0.00 0.00 0.00 3.32
1493 1645 3.997021 AGAGATGCTCCGTAAAACTGTTG 59.003 43.478 0.00 0.00 0.00 3.33
1494 1646 3.997021 CAGAGATGCTCCGTAAAACTGTT 59.003 43.478 0.00 0.00 0.00 3.16
1495 1647 3.006967 ACAGAGATGCTCCGTAAAACTGT 59.993 43.478 0.00 0.00 0.00 3.55
1496 1648 3.589988 ACAGAGATGCTCCGTAAAACTG 58.410 45.455 0.00 0.00 0.00 3.16
1497 1649 3.963428 ACAGAGATGCTCCGTAAAACT 57.037 42.857 0.00 0.00 0.00 2.66
1498 1650 3.424962 GCAACAGAGATGCTCCGTAAAAC 60.425 47.826 0.00 0.00 40.64 2.43
1499 1651 2.742053 GCAACAGAGATGCTCCGTAAAA 59.258 45.455 0.00 0.00 40.64 1.52
1500 1652 2.346803 GCAACAGAGATGCTCCGTAAA 58.653 47.619 0.00 0.00 40.64 2.01
1501 1653 2.010145 GCAACAGAGATGCTCCGTAA 57.990 50.000 0.00 0.00 40.64 3.18
1502 1654 3.741029 GCAACAGAGATGCTCCGTA 57.259 52.632 0.00 0.00 40.64 4.02
1503 1655 4.606071 GCAACAGAGATGCTCCGT 57.394 55.556 0.00 0.00 40.64 4.69
1508 1660 6.100004 TGTTAGTAACTAGCAACAGAGATGC 58.900 40.000 14.00 0.00 44.15 3.91
1509 1661 7.761704 ACATGTTAGTAACTAGCAACAGAGATG 59.238 37.037 14.00 7.16 34.62 2.90
1510 1662 7.841956 ACATGTTAGTAACTAGCAACAGAGAT 58.158 34.615 14.00 0.00 34.62 2.75
1511 1663 7.228314 ACATGTTAGTAACTAGCAACAGAGA 57.772 36.000 14.00 0.00 34.62 3.10
1512 1664 7.891183 AACATGTTAGTAACTAGCAACAGAG 57.109 36.000 9.97 0.00 34.62 3.35
1513 1665 9.199982 GTAAACATGTTAGTAACTAGCAACAGA 57.800 33.333 12.39 0.00 34.62 3.41
1514 1666 8.160342 CGTAAACATGTTAGTAACTAGCAACAG 58.840 37.037 12.39 0.00 34.62 3.16
1515 1667 7.116662 CCGTAAACATGTTAGTAACTAGCAACA 59.883 37.037 12.39 0.00 31.53 3.33
1516 1668 7.329226 TCCGTAAACATGTTAGTAACTAGCAAC 59.671 37.037 12.39 5.16 31.53 4.17
1517 1669 7.377398 TCCGTAAACATGTTAGTAACTAGCAA 58.623 34.615 12.39 0.00 31.53 3.91
1518 1670 6.923012 TCCGTAAACATGTTAGTAACTAGCA 58.077 36.000 12.39 0.00 32.24 3.49
1519 1671 6.020041 GCTCCGTAAACATGTTAGTAACTAGC 60.020 42.308 12.39 13.81 0.00 3.42
1520 1672 6.474751 GGCTCCGTAAACATGTTAGTAACTAG 59.525 42.308 12.39 8.74 0.00 2.57
1521 1673 6.332630 GGCTCCGTAAACATGTTAGTAACTA 58.667 40.000 12.39 0.00 0.00 2.24
1522 1674 5.173664 GGCTCCGTAAACATGTTAGTAACT 58.826 41.667 12.39 0.00 0.00 2.24
1523 1675 4.330894 GGGCTCCGTAAACATGTTAGTAAC 59.669 45.833 12.39 6.06 0.00 2.50
1524 1676 4.020396 TGGGCTCCGTAAACATGTTAGTAA 60.020 41.667 12.39 0.00 0.00 2.24
1525 1677 3.514706 TGGGCTCCGTAAACATGTTAGTA 59.485 43.478 12.39 0.00 0.00 1.82
1526 1678 2.303600 TGGGCTCCGTAAACATGTTAGT 59.696 45.455 12.39 0.00 0.00 2.24
1527 1679 2.980568 TGGGCTCCGTAAACATGTTAG 58.019 47.619 12.39 6.23 0.00 2.34
1528 1680 3.340034 CTTGGGCTCCGTAAACATGTTA 58.660 45.455 12.39 0.00 0.00 2.41
1529 1681 2.159382 CTTGGGCTCCGTAAACATGTT 58.841 47.619 4.92 4.92 0.00 2.71
1530 1682 1.821216 CTTGGGCTCCGTAAACATGT 58.179 50.000 0.00 0.00 0.00 3.21
1531 1683 0.451783 GCTTGGGCTCCGTAAACATG 59.548 55.000 0.00 0.00 35.22 3.21
1532 1684 0.037590 TGCTTGGGCTCCGTAAACAT 59.962 50.000 0.00 0.00 39.59 2.71
1533 1685 0.605319 CTGCTTGGGCTCCGTAAACA 60.605 55.000 0.00 0.00 39.59 2.83
1534 1686 1.923227 GCTGCTTGGGCTCCGTAAAC 61.923 60.000 0.00 0.00 39.59 2.01
1535 1687 1.674322 GCTGCTTGGGCTCCGTAAA 60.674 57.895 0.00 0.00 39.59 2.01
1536 1688 2.046314 GCTGCTTGGGCTCCGTAA 60.046 61.111 0.00 0.00 39.59 3.18
1537 1689 3.003173 AGCTGCTTGGGCTCCGTA 61.003 61.111 0.00 0.00 39.59 4.02
1538 1690 4.711949 CAGCTGCTTGGGCTCCGT 62.712 66.667 0.00 0.00 38.03 4.69
1648 1975 2.158711 CCATGGTCAGGTCATATGCACT 60.159 50.000 2.57 0.00 0.00 4.40
1986 2701 7.008440 TCATTCATAAGAGAAACGCTCAATG 57.992 36.000 0.00 0.00 46.45 2.82
2008 2802 7.160049 TGCAAAATCAGATAAGCCAAATTTCA 58.840 30.769 0.00 0.00 0.00 2.69
2415 3270 5.485353 AGTCTGATGTGGACTTGAATTCCTA 59.515 40.000 2.27 0.00 40.65 2.94
2436 3291 4.039852 GGGGAAGATCTAGATGGTGAAGTC 59.960 50.000 10.74 0.00 0.00 3.01
2594 3481 9.554724 GAAATCTTCGTTGCATTTTGTAGAATA 57.445 29.630 0.00 0.00 0.00 1.75
2596 3483 7.378461 GTGAAATCTTCGTTGCATTTTGTAGAA 59.622 33.333 0.00 0.00 0.00 2.10
2610 3498 3.940852 TGCATATGCTGTGAAATCTTCGT 59.059 39.130 27.13 0.00 42.66 3.85
2815 3710 4.209452 CAACCGATGCATACACCATAAC 57.791 45.455 0.00 0.00 0.00 1.89
2938 3842 0.404040 CAGAGGCTGGGGTAAAACCA 59.596 55.000 0.00 0.00 41.02 3.67
2992 3925 5.376625 ACTTGAAGACTTGTTGCTGGATTA 58.623 37.500 0.00 0.00 0.00 1.75
3017 4644 5.920273 AGCATTTGTTTATTTCACACTTCGG 59.080 36.000 0.00 0.00 0.00 4.30
3120 5404 5.126384 GGATATTTTCAACCGGTTTGGATGA 59.874 40.000 19.55 9.80 46.81 2.92
3165 5449 3.000727 GCGTTTGGTTACTGCATCTACT 58.999 45.455 0.00 0.00 0.00 2.57
3243 6560 6.925165 ACATTCACTTTTTGCAGGTTATCTTG 59.075 34.615 0.00 0.00 0.00 3.02
3349 6669 2.094182 GGGTTGACTCTGATACAGCGAA 60.094 50.000 0.00 0.00 0.00 4.70
3465 6785 5.186996 TCAAACACCTCTTTCTTGATTGC 57.813 39.130 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.