Multiple sequence alignment - TraesCS5A01G162900

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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 TraesCS5A01G162900 chr5A 100.000 9275 0 0 1 9275 348709084 348718358 0.000000e+00 17128.0
1 TraesCS5A01G162900 chr5A 88.721 1587 165 7 3645 5219 74010309 74008725 0.000000e+00 1927.0
2 TraesCS5A01G162900 chr5A 83.189 1386 146 34 5800 7099 73955226 73953842 0.000000e+00 1188.0
3 TraesCS5A01G162900 chr5A 81.148 488 61 16 7497 7977 350526447 350525984 6.850000e-96 363.0
4 TraesCS5A01G162900 chr5A 87.692 325 11 14 7193 7495 348712629 348712946 1.480000e-92 351.0
5 TraesCS5A01G162900 chr5A 88.745 231 23 3 7266 7495 74010335 74010563 7.090000e-71 279.0
6 TraesCS5A01G162900 chr5A 82.482 274 44 2 3273 3545 608877248 608876978 4.330000e-58 237.0
7 TraesCS5A01G162900 chr5A 78.125 96 19 2 7885 7979 537248214 537248308 1.010000e-04 60.2
8 TraesCS5A01G162900 chr5B 96.716 2588 72 4 962 3545 295376841 295379419 0.000000e+00 4296.0
9 TraesCS5A01G162900 chr5B 95.179 1784 59 5 7496 9275 295379415 295381175 0.000000e+00 2793.0
10 TraesCS5A01G162900 chr5B 88.889 54 3 3 7929 7981 611866237 611866288 7.780000e-06 63.9
11 TraesCS5A01G162900 chr5D 95.880 2597 75 13 963 3545 262835115 262837693 0.000000e+00 4174.0
12 TraesCS5A01G162900 chr5D 88.631 2287 229 17 3544 5803 193519132 193516850 0.000000e+00 2754.0
13 TraesCS5A01G162900 chr5D 96.119 876 29 3 8400 9275 262838790 262839660 0.000000e+00 1424.0
14 TraesCS5A01G162900 chr5D 97.765 671 13 1 7733 8401 262838026 262838696 0.000000e+00 1155.0
15 TraesCS5A01G162900 chr5D 81.621 1431 158 43 6145 7495 193514794 193513389 0.000000e+00 1088.0
16 TraesCS5A01G162900 chr5D 84.649 912 118 12 5874 6764 213531866 213530956 0.000000e+00 889.0
17 TraesCS5A01G162900 chr5D 88.631 431 27 7 486 895 6985214 6984785 1.070000e-138 505.0
18 TraesCS5A01G162900 chr5D 95.565 248 11 0 7496 7743 262837689 262837936 1.880000e-106 398.0
19 TraesCS5A01G162900 chr5D 85.470 351 45 5 3191 3537 264376116 264375768 2.460000e-95 361.0
20 TraesCS5A01G162900 chr3D 91.327 2283 169 15 3546 5801 96357592 96355312 0.000000e+00 3092.0
21 TraesCS5A01G162900 chr3D 87.780 1162 93 19 5877 6996 96256054 96254900 0.000000e+00 1314.0
22 TraesCS5A01G162900 chr3D 92.316 911 51 5 1 893 25157260 25156351 0.000000e+00 1277.0
23 TraesCS5A01G162900 chr3D 92.223 913 50 6 1 893 173704438 173703527 0.000000e+00 1273.0
24 TraesCS5A01G162900 chr3D 93.867 799 43 1 1 793 614100719 614099921 0.000000e+00 1199.0
25 TraesCS5A01G162900 chr3D 86.924 543 32 17 6991 7495 96212054 96211513 2.910000e-159 573.0
26 TraesCS5A01G162900 chr3D 86.667 330 17 9 7193 7495 96357592 96357263 3.210000e-89 340.0
27 TraesCS5A01G162900 chr3D 80.622 418 72 8 7496 7908 73456500 73456087 1.940000e-81 315.0
28 TraesCS5A01G162900 chr4D 88.421 2280 232 23 3546 5803 105255324 105253055 0.000000e+00 2719.0
29 TraesCS5A01G162900 chr4D 85.304 1463 132 27 5870 7283 105251182 105249754 0.000000e+00 1434.0
30 TraesCS5A01G162900 chr4D 90.143 558 33 7 356 893 22021212 22021767 0.000000e+00 706.0
31 TraesCS5A01G162900 chr7A 88.253 2290 228 25 3546 5803 492246812 492249092 0.000000e+00 2700.0
32 TraesCS5A01G162900 chr7A 85.958 1759 156 47 5808 7496 374547254 374548991 0.000000e+00 1796.0
33 TraesCS5A01G162900 chr7A 78.328 323 60 7 7499 7816 512258279 512257962 5.680000e-47 200.0
34 TraesCS5A01G162900 chr7B 88.222 2284 236 17 3546 5801 724466410 724464132 0.000000e+00 2697.0
35 TraesCS5A01G162900 chr7B 84.405 622 51 21 6910 7495 724405838 724405227 3.760000e-158 569.0
36 TraesCS5A01G162900 chr7B 86.970 330 15 7 7193 7495 724466410 724466082 6.890000e-91 346.0
37 TraesCS5A01G162900 chr4B 87.730 2282 243 20 3546 5798 322525734 322528007 0.000000e+00 2628.0
38 TraesCS5A01G162900 chr4B 89.833 1918 178 12 3898 5801 322639346 322641260 0.000000e+00 2446.0
39 TraesCS5A01G162900 chr4B 86.167 1453 101 42 6127 7497 322643097 322644531 0.000000e+00 1478.0
40 TraesCS5A01G162900 chr4B 86.383 705 78 13 4 704 547548105 547547415 0.000000e+00 754.0
41 TraesCS5A01G162900 chr4B 79.480 731 91 25 5798 6505 61529750 61530444 1.820000e-126 464.0
42 TraesCS5A01G162900 chr4B 84.989 473 44 9 7051 7497 322585139 322585610 1.100000e-123 455.0
43 TraesCS5A01G162900 chr2D 87.167 2291 239 23 3546 5804 327939293 327941560 0.000000e+00 2551.0
44 TraesCS5A01G162900 chr2D 84.182 1473 153 34 6093 7495 296387023 296388485 0.000000e+00 1356.0
45 TraesCS5A01G162900 chr2D 92.004 913 54 5 1 895 33027352 33028263 0.000000e+00 1264.0
46 TraesCS5A01G162900 chr2D 87.477 1070 122 7 4746 5803 187456037 187454968 0.000000e+00 1223.0
47 TraesCS5A01G162900 chr2D 82.279 1360 168 39 6193 7495 327956557 327957900 0.000000e+00 1109.0
48 TraesCS5A01G162900 chr2D 86.657 667 60 16 2 647 405398369 405397711 0.000000e+00 712.0
49 TraesCS5A01G162900 chr2D 88.559 236 21 5 7263 7495 327939392 327939624 1.970000e-71 281.0
50 TraesCS5A01G162900 chr3B 87.500 1720 176 21 3593 5290 67396676 67398378 0.000000e+00 1949.0
51 TraesCS5A01G162900 chr3B 82.517 1716 197 47 5870 7495 67400014 67401716 0.000000e+00 1411.0
52 TraesCS5A01G162900 chr3B 83.186 904 99 19 6432 7283 338598259 338597357 0.000000e+00 778.0
53 TraesCS5A01G162900 chr3B 79.612 927 106 44 6623 7496 705034865 705033969 1.040000e-163 588.0
54 TraesCS5A01G162900 chr3B 78.972 428 83 4 7496 7917 118806035 118805609 1.520000e-72 285.0
55 TraesCS5A01G162900 chr3B 83.448 145 12 9 3546 3684 360108582 360108444 3.520000e-24 124.0
56 TraesCS5A01G162900 chr4A 84.113 1731 175 35 5798 7433 688976697 688974972 0.000000e+00 1581.0
57 TraesCS5A01G162900 chr4A 90.667 900 63 12 1 895 163909210 163910093 0.000000e+00 1177.0
58 TraesCS5A01G162900 chr4A 88.718 780 70 10 1 769 603418671 603417899 0.000000e+00 937.0
59 TraesCS5A01G162900 chr4A 89.681 659 53 7 5156 5803 688978863 688978209 0.000000e+00 826.0
60 TraesCS5A01G162900 chr2B 83.531 1688 204 38 5870 7495 365992627 365990952 0.000000e+00 1509.0
61 TraesCS5A01G162900 chr2B 82.845 1673 205 37 5870 7495 137794637 137796274 0.000000e+00 1424.0
62 TraesCS5A01G162900 chr2B 80.000 395 55 17 7589 7976 717496516 717496139 4.270000e-68 270.0
63 TraesCS5A01G162900 chr2B 75.225 222 38 14 7190 7398 63169479 63169262 1.280000e-13 89.8
64 TraesCS5A01G162900 chr7D 92.325 912 49 5 1 893 597914446 597915355 0.000000e+00 1277.0
65 TraesCS5A01G162900 chr7D 88.167 693 66 11 4 692 576655356 576654676 0.000000e+00 811.0
66 TraesCS5A01G162900 chr1D 91.575 914 53 11 1 893 74344421 74345331 0.000000e+00 1240.0
67 TraesCS5A01G162900 chr1D 92.556 806 40 5 33 831 391337734 391338526 0.000000e+00 1138.0
68 TraesCS5A01G162900 chr1D 88.189 635 74 1 5874 6508 143172538 143173171 0.000000e+00 756.0
69 TraesCS5A01G162900 chr6B 84.932 1095 126 24 5798 6856 197671149 197672240 0.000000e+00 1072.0
70 TraesCS5A01G162900 chr6B 84.124 485 70 6 7497 7977 341764217 341764698 6.560000e-126 462.0
71 TraesCS5A01G162900 chr6B 83.019 212 25 7 6922 7123 197687354 197687564 2.060000e-41 182.0
72 TraesCS5A01G162900 chr6B 89.583 48 4 1 7932 7979 211810896 211810942 1.010000e-04 60.2
73 TraesCS5A01G162900 chr2A 89.080 696 62 8 1 688 391877696 391878385 0.000000e+00 852.0
74 TraesCS5A01G162900 chr2A 88.679 53 3 3 7929 7980 725890599 725890649 2.800000e-05 62.1
75 TraesCS5A01G162900 chr6A 79.799 698 101 22 6615 7278 617256261 617255570 1.090000e-128 472.0
76 TraesCS5A01G162900 chr6D 85.060 415 56 5 7497 7908 261010675 261010264 1.440000e-112 418.0
77 TraesCS5A01G162900 chr6D 83.607 427 51 10 3121 3545 261011081 261010672 5.250000e-102 383.0
78 TraesCS5A01G162900 chr3A 82.675 329 48 8 7496 7819 86474075 86473751 5.480000e-72 283.0
79 TraesCS5A01G162900 chr1B 88.235 51 5 1 7929 7979 553454072 553454121 1.010000e-04 60.2


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 TraesCS5A01G162900 chr5A 348709084 348718358 9274 False 17128.00 17128 100.00000 1 9275 1 chr5A.!!$F2 9274
1 TraesCS5A01G162900 chr5A 74008725 74010309 1584 True 1927.00 1927 88.72100 3645 5219 1 chr5A.!!$R2 1574
2 TraesCS5A01G162900 chr5A 73953842 73955226 1384 True 1188.00 1188 83.18900 5800 7099 1 chr5A.!!$R1 1299
3 TraesCS5A01G162900 chr5B 295376841 295381175 4334 False 3544.50 4296 95.94750 962 9275 2 chr5B.!!$F2 8313
4 TraesCS5A01G162900 chr5D 193513389 193519132 5743 True 1921.00 2754 85.12600 3544 7495 2 chr5D.!!$R4 3951
5 TraesCS5A01G162900 chr5D 262835115 262839660 4545 False 1787.75 4174 96.33225 963 9275 4 chr5D.!!$F1 8312
6 TraesCS5A01G162900 chr5D 213530956 213531866 910 True 889.00 889 84.64900 5874 6764 1 chr5D.!!$R2 890
7 TraesCS5A01G162900 chr3D 96355312 96357592 2280 True 1716.00 3092 88.99700 3546 7495 2 chr3D.!!$R7 3949
8 TraesCS5A01G162900 chr3D 96254900 96256054 1154 True 1314.00 1314 87.78000 5877 6996 1 chr3D.!!$R4 1119
9 TraesCS5A01G162900 chr3D 25156351 25157260 909 True 1277.00 1277 92.31600 1 893 1 chr3D.!!$R1 892
10 TraesCS5A01G162900 chr3D 173703527 173704438 911 True 1273.00 1273 92.22300 1 893 1 chr3D.!!$R5 892
11 TraesCS5A01G162900 chr3D 614099921 614100719 798 True 1199.00 1199 93.86700 1 793 1 chr3D.!!$R6 792
12 TraesCS5A01G162900 chr3D 96211513 96212054 541 True 573.00 573 86.92400 6991 7495 1 chr3D.!!$R3 504
13 TraesCS5A01G162900 chr4D 105249754 105255324 5570 True 2076.50 2719 86.86250 3546 7283 2 chr4D.!!$R1 3737
14 TraesCS5A01G162900 chr4D 22021212 22021767 555 False 706.00 706 90.14300 356 893 1 chr4D.!!$F1 537
15 TraesCS5A01G162900 chr7A 492246812 492249092 2280 False 2700.00 2700 88.25300 3546 5803 1 chr7A.!!$F2 2257
16 TraesCS5A01G162900 chr7A 374547254 374548991 1737 False 1796.00 1796 85.95800 5808 7496 1 chr7A.!!$F1 1688
17 TraesCS5A01G162900 chr7B 724464132 724466410 2278 True 1521.50 2697 87.59600 3546 7495 2 chr7B.!!$R2 3949
18 TraesCS5A01G162900 chr7B 724405227 724405838 611 True 569.00 569 84.40500 6910 7495 1 chr7B.!!$R1 585
19 TraesCS5A01G162900 chr4B 322525734 322528007 2273 False 2628.00 2628 87.73000 3546 5798 1 chr4B.!!$F2 2252
20 TraesCS5A01G162900 chr4B 322639346 322644531 5185 False 1962.00 2446 88.00000 3898 7497 2 chr4B.!!$F4 3599
21 TraesCS5A01G162900 chr4B 547547415 547548105 690 True 754.00 754 86.38300 4 704 1 chr4B.!!$R1 700
22 TraesCS5A01G162900 chr4B 61529750 61530444 694 False 464.00 464 79.48000 5798 6505 1 chr4B.!!$F1 707
23 TraesCS5A01G162900 chr2D 327939293 327941560 2267 False 1416.00 2551 87.86300 3546 7495 2 chr2D.!!$F4 3949
24 TraesCS5A01G162900 chr2D 296387023 296388485 1462 False 1356.00 1356 84.18200 6093 7495 1 chr2D.!!$F2 1402
25 TraesCS5A01G162900 chr2D 33027352 33028263 911 False 1264.00 1264 92.00400 1 895 1 chr2D.!!$F1 894
26 TraesCS5A01G162900 chr2D 187454968 187456037 1069 True 1223.00 1223 87.47700 4746 5803 1 chr2D.!!$R1 1057
27 TraesCS5A01G162900 chr2D 327956557 327957900 1343 False 1109.00 1109 82.27900 6193 7495 1 chr2D.!!$F3 1302
28 TraesCS5A01G162900 chr2D 405397711 405398369 658 True 712.00 712 86.65700 2 647 1 chr2D.!!$R2 645
29 TraesCS5A01G162900 chr3B 67396676 67401716 5040 False 1680.00 1949 85.00850 3593 7495 2 chr3B.!!$F1 3902
30 TraesCS5A01G162900 chr3B 338597357 338598259 902 True 778.00 778 83.18600 6432 7283 1 chr3B.!!$R2 851
31 TraesCS5A01G162900 chr3B 705033969 705034865 896 True 588.00 588 79.61200 6623 7496 1 chr3B.!!$R4 873
32 TraesCS5A01G162900 chr4A 688974972 688978863 3891 True 1203.50 1581 86.89700 5156 7433 2 chr4A.!!$R2 2277
33 TraesCS5A01G162900 chr4A 163909210 163910093 883 False 1177.00 1177 90.66700 1 895 1 chr4A.!!$F1 894
34 TraesCS5A01G162900 chr4A 603417899 603418671 772 True 937.00 937 88.71800 1 769 1 chr4A.!!$R1 768
35 TraesCS5A01G162900 chr2B 365990952 365992627 1675 True 1509.00 1509 83.53100 5870 7495 1 chr2B.!!$R2 1625
36 TraesCS5A01G162900 chr2B 137794637 137796274 1637 False 1424.00 1424 82.84500 5870 7495 1 chr2B.!!$F1 1625
37 TraesCS5A01G162900 chr7D 597914446 597915355 909 False 1277.00 1277 92.32500 1 893 1 chr7D.!!$F1 892
38 TraesCS5A01G162900 chr7D 576654676 576655356 680 True 811.00 811 88.16700 4 692 1 chr7D.!!$R1 688
39 TraesCS5A01G162900 chr1D 74344421 74345331 910 False 1240.00 1240 91.57500 1 893 1 chr1D.!!$F1 892
40 TraesCS5A01G162900 chr1D 391337734 391338526 792 False 1138.00 1138 92.55600 33 831 1 chr1D.!!$F3 798
41 TraesCS5A01G162900 chr1D 143172538 143173171 633 False 756.00 756 88.18900 5874 6508 1 chr1D.!!$F2 634
42 TraesCS5A01G162900 chr6B 197671149 197672240 1091 False 1072.00 1072 84.93200 5798 6856 1 chr6B.!!$F1 1058
43 TraesCS5A01G162900 chr2A 391877696 391878385 689 False 852.00 852 89.08000 1 688 1 chr2A.!!$F1 687
44 TraesCS5A01G162900 chr6A 617255570 617256261 691 True 472.00 472 79.79900 6615 7278 1 chr6A.!!$R1 663
45 TraesCS5A01G162900 chr6D 261010264 261011081 817 True 400.50 418 84.33350 3121 7908 2 chr6D.!!$R1 4787

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
831 882 0.818445 TTTTAAACGCGTCTGGGGCA 60.818 50.0 14.44 0.00 0.00 5.36 F
1255 1310 0.239347 CTCCCTTTGCTGCTCGTTTG 59.761 55.0 0.00 0.00 0.00 2.93 F
2112 2178 0.457851 CAGAGACATGGAGACCGGAC 59.542 60.0 9.46 0.10 0.00 4.79 F
2262 2328 0.679002 GGCTGAGACACATGGCATGT 60.679 55.0 26.78 26.78 46.22 3.21 F
3542 3611 0.878523 TGCGGAAAGAGTTGGTCGTG 60.879 55.0 0.00 0.00 0.00 4.35 F
4190 4283 0.608856 TTGCTGATGCGTTCCACCAT 60.609 50.0 0.00 0.00 43.34 3.55 F
4620 4714 0.105964 TCACCTTGTTGACCACCTCG 59.894 55.0 0.00 0.00 0.00 4.63 F
5424 5544 0.234884 CGGTGAAGTCGAAGCCAAAC 59.765 55.0 0.00 0.00 0.00 2.93 F
6715 8929 0.250770 GGAAACTGGACCTGGTGGAC 60.251 60.0 2.82 0.00 37.04 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1713 1.002257 ATGCTTGCGTGTGGGATGA 60.002 52.632 0.00 0.0 0.00 2.92 R
2233 2299 1.059098 TGTCTCAGCCTGTCATGGTT 58.941 50.000 0.00 0.0 0.00 3.67 R
4086 4178 0.603707 TCAAGCCTTTCCGCAGTGAG 60.604 55.000 0.00 0.0 0.00 3.51 R
4145 4238 1.076332 CTACCGCCTTCAACTTTCGG 58.924 55.000 0.00 0.0 45.04 4.30 R
4446 4540 0.691078 GCCCTCCACCACTCATCCTA 60.691 60.000 0.00 0.0 0.00 2.94 R
5774 5895 0.033503 TCTCGTGGGATACTGAGGCA 60.034 55.000 0.00 0.0 33.61 4.75 R
5789 5910 1.059369 CAATTGCGACGCCTTCTCG 59.941 57.895 18.69 0.0 0.00 4.04 R
7326 9738 0.328258 ACTATTGCCCGGCTCACTTT 59.672 50.000 11.61 0.0 0.00 2.66 R
8682 11298 1.153168 AAACTGACCGTGCTGTGCT 60.153 52.632 0.00 0.0 0.00 4.40 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
24 25 3.681835 GGTCGCACACTCGAGGGT 61.682 66.667 16.38 16.38 39.34 4.34
304 317 4.500116 GTGCCTCCTCGTCGGCTC 62.500 72.222 0.00 0.00 46.42 4.70
625 670 2.282958 AGGAGAAGGCCGACGACA 60.283 61.111 0.00 0.00 0.00 4.35
737 787 6.560711 GGCGAACTTTGTCCAAATATATGTT 58.439 36.000 0.00 0.00 0.00 2.71
769 819 2.981400 AATTTGTCGTGTTTAGCCGG 57.019 45.000 0.00 0.00 0.00 6.13
786 837 1.300697 GGACTTCGCCGAACTGTGT 60.301 57.895 0.00 0.00 0.00 3.72
831 882 0.818445 TTTTAAACGCGTCTGGGGCA 60.818 50.000 14.44 0.00 0.00 5.36
832 883 0.818445 TTTAAACGCGTCTGGGGCAA 60.818 50.000 14.44 0.00 0.00 4.52
834 885 2.386064 TAAACGCGTCTGGGGCAACT 62.386 55.000 14.44 0.00 0.00 3.16
838 889 3.059982 CGTCTGGGGCAACTCTGA 58.940 61.111 0.00 0.00 43.59 3.27
842 893 2.853542 TGGGGCAACTCTGAGGCA 60.854 61.111 9.85 0.00 38.64 4.75
900 955 4.154347 GGCTCACCCCAGCTCGAG 62.154 72.222 8.45 8.45 39.58 4.04
901 956 3.071206 GCTCACCCCAGCTCGAGA 61.071 66.667 18.75 0.00 36.38 4.04
902 957 2.430610 GCTCACCCCAGCTCGAGAT 61.431 63.158 18.75 7.13 36.38 2.75
903 958 1.440893 CTCACCCCAGCTCGAGATG 59.559 63.158 23.51 23.51 0.00 2.90
913 968 4.887748 CCAGCTCGAGATGGTATAATTGT 58.112 43.478 35.98 0.00 45.94 2.71
914 969 5.300752 CCAGCTCGAGATGGTATAATTGTT 58.699 41.667 35.98 0.00 45.94 2.83
915 970 5.760253 CCAGCTCGAGATGGTATAATTGTTT 59.240 40.000 35.98 0.00 45.94 2.83
916 971 6.293081 CCAGCTCGAGATGGTATAATTGTTTG 60.293 42.308 35.98 10.51 45.94 2.93
917 972 5.760253 AGCTCGAGATGGTATAATTGTTTGG 59.240 40.000 18.75 0.00 0.00 3.28
918 973 5.560953 GCTCGAGATGGTATAATTGTTTGGC 60.561 44.000 18.75 0.00 0.00 4.52
919 974 5.680619 TCGAGATGGTATAATTGTTTGGCT 58.319 37.500 0.00 0.00 0.00 4.75
920 975 6.119536 TCGAGATGGTATAATTGTTTGGCTT 58.880 36.000 0.00 0.00 0.00 4.35
921 976 6.601613 TCGAGATGGTATAATTGTTTGGCTTT 59.398 34.615 0.00 0.00 0.00 3.51
922 977 6.692681 CGAGATGGTATAATTGTTTGGCTTTG 59.307 38.462 0.00 0.00 0.00 2.77
923 978 7.415095 CGAGATGGTATAATTGTTTGGCTTTGA 60.415 37.037 0.00 0.00 0.00 2.69
924 979 7.775120 AGATGGTATAATTGTTTGGCTTTGAG 58.225 34.615 0.00 0.00 0.00 3.02
925 980 7.615365 AGATGGTATAATTGTTTGGCTTTGAGA 59.385 33.333 0.00 0.00 0.00 3.27
926 981 7.156876 TGGTATAATTGTTTGGCTTTGAGAG 57.843 36.000 0.00 0.00 0.00 3.20
927 982 6.719370 TGGTATAATTGTTTGGCTTTGAGAGT 59.281 34.615 0.00 0.00 0.00 3.24
928 983 7.885922 TGGTATAATTGTTTGGCTTTGAGAGTA 59.114 33.333 0.00 0.00 0.00 2.59
929 984 8.398665 GGTATAATTGTTTGGCTTTGAGAGTAG 58.601 37.037 0.00 0.00 0.00 2.57
930 985 8.947115 GTATAATTGTTTGGCTTTGAGAGTAGT 58.053 33.333 0.00 0.00 0.00 2.73
932 987 7.440523 AATTGTTTGGCTTTGAGAGTAGTAG 57.559 36.000 0.00 0.00 0.00 2.57
933 988 5.801531 TGTTTGGCTTTGAGAGTAGTAGA 57.198 39.130 0.00 0.00 0.00 2.59
934 989 5.539048 TGTTTGGCTTTGAGAGTAGTAGAC 58.461 41.667 0.00 0.00 0.00 2.59
935 990 4.436242 TTGGCTTTGAGAGTAGTAGACG 57.564 45.455 0.00 0.00 0.00 4.18
936 991 2.753452 TGGCTTTGAGAGTAGTAGACGG 59.247 50.000 0.00 0.00 0.00 4.79
937 992 2.479901 GGCTTTGAGAGTAGTAGACGGC 60.480 54.545 0.00 0.00 0.00 5.68
938 993 2.791849 GCTTTGAGAGTAGTAGACGGCG 60.792 54.545 4.80 4.80 0.00 6.46
939 994 2.391616 TTGAGAGTAGTAGACGGCGA 57.608 50.000 16.62 0.00 0.00 5.54
940 995 1.937278 TGAGAGTAGTAGACGGCGAG 58.063 55.000 16.62 0.00 0.00 5.03
941 996 1.206610 TGAGAGTAGTAGACGGCGAGT 59.793 52.381 16.62 1.72 0.00 4.18
954 1009 3.562635 CGAGTCGCCAGTTTTCCC 58.437 61.111 0.00 0.00 0.00 3.97
955 1010 2.033194 CGAGTCGCCAGTTTTCCCC 61.033 63.158 0.00 0.00 0.00 4.81
956 1011 1.674651 GAGTCGCCAGTTTTCCCCC 60.675 63.158 0.00 0.00 0.00 5.40
957 1012 2.114411 GTCGCCAGTTTTCCCCCA 59.886 61.111 0.00 0.00 0.00 4.96
958 1013 2.114411 TCGCCAGTTTTCCCCCAC 59.886 61.111 0.00 0.00 0.00 4.61
959 1014 2.989253 CGCCAGTTTTCCCCCACC 60.989 66.667 0.00 0.00 0.00 4.61
960 1015 2.526110 GCCAGTTTTCCCCCACCT 59.474 61.111 0.00 0.00 0.00 4.00
1222 1277 2.951101 CGGCCGAACCAGGGTAAGT 61.951 63.158 24.07 0.00 39.03 2.24
1235 1290 1.192428 GGTAAGTGGTCGTCCCTCAT 58.808 55.000 0.00 0.00 0.00 2.90
1249 1304 0.255318 CCTCATCTCCCTTTGCTGCT 59.745 55.000 0.00 0.00 0.00 4.24
1255 1310 0.239347 CTCCCTTTGCTGCTCGTTTG 59.761 55.000 0.00 0.00 0.00 2.93
1460 1515 0.594028 CGTGCGCGTGTAGGATATGT 60.594 55.000 12.43 0.00 0.00 2.29
1613 1673 7.868415 GGTTGTGTTTTGCATAAGTATTTGGTA 59.132 33.333 0.00 0.00 0.00 3.25
1649 1710 5.767816 TCTTTTAGGGAAACAAGCAACTC 57.232 39.130 0.00 0.00 0.00 3.01
1652 1713 3.439440 GGGAAACAAGCAACTCCCT 57.561 52.632 0.00 0.00 43.74 4.20
1862 1927 3.074390 TGGACTTTCTCCCATGTGTCATT 59.926 43.478 0.00 0.00 38.49 2.57
1924 1990 3.728718 GTCAAACGTTTAACCTGCACATG 59.271 43.478 14.20 0.00 0.00 3.21
1929 1995 3.568007 ACGTTTAACCTGCACATGATTGT 59.432 39.130 0.00 0.00 36.15 2.71
2025 2091 5.278169 GGTTATCCACAATGCATCTGTCATC 60.278 44.000 0.00 0.00 0.00 2.92
2112 2178 0.457851 CAGAGACATGGAGACCGGAC 59.542 60.000 9.46 0.10 0.00 4.79
2233 2299 5.957771 AGCACTTGGTATTCCTGAGATTA 57.042 39.130 0.00 0.00 34.23 1.75
2251 2317 3.334583 TTAACCATGACAGGCTGAGAC 57.665 47.619 23.66 12.30 0.00 3.36
2262 2328 0.679002 GGCTGAGACACATGGCATGT 60.679 55.000 26.78 26.78 46.22 3.21
2396 2462 7.761249 TGATGACTGTGTGACATTATTAGACAG 59.239 37.037 0.00 0.00 40.38 3.51
2630 2696 6.577427 CGGCAAATTTGTTTTCAGTACTAGTC 59.423 38.462 19.03 0.00 0.00 2.59
2780 2848 7.732996 AGTCCTTATGCAGGTAATTTACGTAT 58.267 34.615 0.00 0.00 44.37 3.06
2852 2920 8.673711 ACGAGAATTAGATATGCACTAGAGATC 58.326 37.037 0.00 0.00 0.00 2.75
3142 3210 2.627221 GAGCATCTCTAGCAGATCCACA 59.373 50.000 0.00 0.00 40.20 4.17
3181 3249 5.400066 AAAATCATTTTAGGGTTCCCACG 57.600 39.130 10.73 0.00 0.00 4.94
3182 3250 4.310022 AATCATTTTAGGGTTCCCACGA 57.690 40.909 10.73 0.00 0.00 4.35
3183 3251 3.791953 TCATTTTAGGGTTCCCACGAA 57.208 42.857 10.73 2.02 0.00 3.85
3184 3252 4.101645 TCATTTTAGGGTTCCCACGAAA 57.898 40.909 10.73 7.94 0.00 3.46
3185 3253 4.471548 TCATTTTAGGGTTCCCACGAAAA 58.528 39.130 10.73 12.53 0.00 2.29
3186 3254 4.521256 TCATTTTAGGGTTCCCACGAAAAG 59.479 41.667 10.73 5.41 0.00 2.27
3187 3255 3.581265 TTTAGGGTTCCCACGAAAAGT 57.419 42.857 10.73 0.00 0.00 2.66
3188 3256 2.845363 TAGGGTTCCCACGAAAAGTC 57.155 50.000 10.73 0.00 0.00 3.01
3203 3271 5.613964 GAAAAGTCGAAAACGATTTTGCA 57.386 34.783 12.15 0.00 31.94 4.08
3257 3325 7.174253 TCCTGTAAATCTCGTACTGCAAATTTT 59.826 33.333 0.00 0.00 0.00 1.82
3461 3530 2.665603 GGCGGCACCTTCTTCTCT 59.334 61.111 3.07 0.00 34.51 3.10
3542 3611 0.878523 TGCGGAAAGAGTTGGTCGTG 60.879 55.000 0.00 0.00 0.00 4.35
3576 3645 1.972075 GGGATCCTACCAGTTCTAGCC 59.028 57.143 12.58 0.00 0.00 3.93
3603 3672 1.023719 TGTAGGGATGGAAGGGAGGA 58.976 55.000 0.00 0.00 0.00 3.71
3612 3681 2.770048 AAGGGAGGATGGCGAGGG 60.770 66.667 0.00 0.00 0.00 4.30
3613 3682 3.332393 AAGGGAGGATGGCGAGGGA 62.332 63.158 0.00 0.00 0.00 4.20
3666 3743 2.438614 CGACGAGAGGAGGAGGCA 60.439 66.667 0.00 0.00 0.00 4.75
3670 3748 2.366570 GAGAGGAGGAGGCAGGGT 59.633 66.667 0.00 0.00 0.00 4.34
3818 3910 1.693062 GGCTAAGCCCCTAACTAGACC 59.307 57.143 0.00 0.00 44.06 3.85
3868 3960 1.480954 ACGCCGGTCATAACATCTCTT 59.519 47.619 1.90 0.00 0.00 2.85
3878 3970 1.841302 AACATCTCTTCCCGCCTGCA 61.841 55.000 0.00 0.00 0.00 4.41
3935 4027 4.475135 GGCGGAACTCCTGGAGCC 62.475 72.222 23.43 15.37 37.61 4.70
4021 4113 1.839424 GCTATTGGGCCTTCAACACT 58.161 50.000 4.53 0.00 0.00 3.55
4031 4123 1.308998 CTTCAACACTTTCGCTGGGT 58.691 50.000 0.00 0.00 0.00 4.51
4045 4137 2.125633 GGGTCCGGAAGAAGACGC 60.126 66.667 5.23 0.00 0.00 5.19
4069 4161 2.665603 GAGGTTGGAGGAAGCGCT 59.334 61.111 2.64 2.64 37.13 5.92
4125 4218 0.895100 GCAAGCCCACATGGAAGACA 60.895 55.000 0.00 0.00 37.39 3.41
4128 4221 0.994247 AGCCCACATGGAAGACATCA 59.006 50.000 0.00 0.00 37.84 3.07
4136 4229 3.219281 CATGGAAGACATCATGGATGCA 58.781 45.455 6.15 0.00 43.15 3.96
4190 4283 0.608856 TTGCTGATGCGTTCCACCAT 60.609 50.000 0.00 0.00 43.34 3.55
4271 4364 1.304962 TAGAGCGGTGAAGGAGCCA 60.305 57.895 0.00 0.00 0.00 4.75
4453 4547 0.979187 GGGGTCAACCGGTAGGATGA 60.979 60.000 8.00 4.72 45.49 2.92
4541 4635 0.541392 TAGTAGTACTCCGCCCACGA 59.459 55.000 5.96 0.00 43.93 4.35
4560 4654 2.856000 AGCCAGTCCACCCAAGCT 60.856 61.111 0.00 0.00 0.00 3.74
4620 4714 0.105964 TCACCTTGTTGACCACCTCG 59.894 55.000 0.00 0.00 0.00 4.63
4654 4748 1.994885 CTGGGGGTGGAATGCCGTAT 61.995 60.000 0.00 0.00 36.79 3.06
4656 4750 1.106944 GGGGGTGGAATGCCGTATTG 61.107 60.000 0.00 0.00 36.79 1.90
4786 4881 2.733593 GTCGAAGAAGGCACGCGT 60.734 61.111 5.58 5.58 39.69 6.01
4845 4940 4.202357 TGAAGTGTGCATACTTGGAGAAGT 60.202 41.667 30.47 6.72 44.90 3.01
4877 4972 0.976641 TGAGGATGACGGACTTGCTT 59.023 50.000 0.00 0.00 0.00 3.91
4934 5029 2.060980 GTCGGCCCAGACCTGAGAT 61.061 63.158 0.00 0.00 35.22 2.75
4964 5060 2.393630 GGTCTATAGTAGGCCCACCA 57.606 55.000 0.00 0.00 44.88 4.17
5040 5137 2.046892 CACCAGCGCCTAGTTGCT 60.047 61.111 2.29 0.37 43.58 3.91
5059 5156 2.856222 CTGGGGATGTAGAAATCTGCC 58.144 52.381 0.00 0.00 0.00 4.85
5110 5207 4.988716 TGACCGACCGAGTGGGCT 62.989 66.667 5.26 0.00 43.41 5.19
5115 5212 2.184579 GACCGAGTGGGCTAGCAC 59.815 66.667 18.24 14.86 41.70 4.40
5185 5282 2.611800 TGCAGGACCAGGCCATCT 60.612 61.111 5.01 0.00 0.00 2.90
5248 5357 3.499737 CGAAGGAGCCGCGCATTT 61.500 61.111 8.75 0.00 0.00 2.32
5249 5358 2.171079 CGAAGGAGCCGCGCATTTA 61.171 57.895 8.75 0.00 0.00 1.40
5261 5370 1.715585 GCATTTAGAGCGCTCGCAA 59.284 52.632 30.39 25.59 44.88 4.85
5264 5373 0.305922 ATTTAGAGCGCTCGCAATGC 59.694 50.000 30.39 6.85 44.88 3.56
5424 5544 0.234884 CGGTGAAGTCGAAGCCAAAC 59.765 55.000 0.00 0.00 0.00 2.93
5426 5546 1.673920 GGTGAAGTCGAAGCCAAACAA 59.326 47.619 0.00 0.00 0.00 2.83
5513 5634 2.124903 GTGATCGTGCGAATACGGAAT 58.875 47.619 0.00 0.00 43.85 3.01
5564 5685 3.819652 ACCACCTGCACCAAGCCA 61.820 61.111 0.00 0.00 44.83 4.75
5716 5837 0.959553 AAGAGCTTGTCGAAGTCCGA 59.040 50.000 0.00 0.00 46.35 4.55
5774 5895 2.355481 GACGTGAACGCCTCGGTT 60.355 61.111 2.11 0.00 44.43 4.44
5789 5910 0.462047 CGGTTGCCTCAGTATCCCAC 60.462 60.000 0.00 0.00 0.00 4.61
5804 7758 2.733218 CACGAGAAGGCGTCGCAA 60.733 61.111 20.50 0.00 43.59 4.85
5865 7819 4.796495 GGGTGAGCCGGCGGAAAT 62.796 66.667 33.44 15.04 34.97 2.17
5866 7820 3.508840 GGTGAGCCGGCGGAAATG 61.509 66.667 33.44 2.12 0.00 2.32
5867 7821 2.435938 GTGAGCCGGCGGAAATGA 60.436 61.111 33.44 5.57 0.00 2.57
5868 7822 1.819632 GTGAGCCGGCGGAAATGAT 60.820 57.895 33.44 7.04 0.00 2.45
6025 8008 1.606601 CCGTCTGGAGGTCCTGTGA 60.607 63.158 0.00 0.00 37.49 3.58
6103 8087 4.827087 CTGCTGGCGAGCCGTGAT 62.827 66.667 18.69 0.00 45.57 3.06
6157 8141 4.373116 GGCGAAGTCCTGCACCGA 62.373 66.667 0.00 0.00 0.00 4.69
6239 8223 0.444260 GTAAGAGGCAAAGCTCGTGC 59.556 55.000 12.76 12.76 41.45 5.34
6715 8929 0.250770 GGAAACTGGACCTGGTGGAC 60.251 60.000 2.82 0.00 37.04 4.02
6959 9268 3.449227 CCGTAGTGGCTGGCGAGA 61.449 66.667 0.00 0.00 0.00 4.04
6962 9271 0.669318 CGTAGTGGCTGGCGAGAAAA 60.669 55.000 0.00 0.00 0.00 2.29
7002 9312 2.359404 GGGTGAGGTCTCGGAGGA 59.641 66.667 4.96 0.00 0.00 3.71
7034 9344 1.246056 CCTTCGGGGTGTAGACGACA 61.246 60.000 0.00 0.00 36.24 4.35
7039 9350 2.356780 GGGTGTAGACGACAGGGGG 61.357 68.421 0.00 0.00 39.29 5.40
7040 9351 1.304713 GGTGTAGACGACAGGGGGA 60.305 63.158 0.00 0.00 39.29 4.81
7042 9353 1.000019 TGTAGACGACAGGGGGAGG 60.000 63.158 0.00 0.00 32.86 4.30
7234 9557 2.093447 CAGGTCTAGCCCTTAGGTTGTG 60.093 54.545 0.00 0.00 38.26 3.33
7326 9738 2.026915 GGTTTTAGGGTTTCGGCTCCTA 60.027 50.000 0.00 0.00 32.46 2.94
7330 9742 1.359168 AGGGTTTCGGCTCCTAAAGT 58.641 50.000 0.00 0.00 0.00 2.66
7389 9801 2.271944 AGGTGGCCTTACAAGTGTTC 57.728 50.000 3.32 0.00 0.00 3.18
7461 9873 2.180159 AACTAGACGCGCCATTGGGT 62.180 55.000 5.73 0.00 37.78 4.51
7486 9898 0.959553 CCGGCTATATGAGACACCGT 59.040 55.000 0.00 0.00 38.99 4.83
7731 10150 4.174129 GCGGAATTTGTCGCCGGG 62.174 66.667 2.18 0.00 45.42 5.73
7750 10269 1.988406 GTTGGGGAGGTCTAGCGGT 60.988 63.158 0.00 0.00 0.00 5.68
7754 10273 3.075005 GGAGGTCTAGCGGTGGCA 61.075 66.667 0.00 0.00 43.41 4.92
7826 10345 2.631062 CAACCCCGTACATATAGCTCCA 59.369 50.000 0.00 0.00 0.00 3.86
7841 10360 0.995024 CTCCAGAGGGGTGGATTTGT 59.005 55.000 0.00 0.00 45.87 2.83
7899 10418 1.204146 TAGTGGATCTGTTCAGGCCC 58.796 55.000 0.00 2.97 0.00 5.80
7927 10446 1.743772 CGGAGATCCTGCAAAACGGAT 60.744 52.381 4.95 4.95 42.55 4.18
8312 10833 2.635427 GAGTTTCACTCCTTCCCTCACT 59.365 50.000 0.00 0.00 39.28 3.41
8427 11043 5.105716 TGAGGAACTTGTAGTCTAGATGCAC 60.106 44.000 0.00 0.00 41.55 4.57
8435 11051 1.001120 TCTAGATGCACGGTCCCCA 59.999 57.895 0.00 0.00 0.00 4.96
8440 11056 0.606401 GATGCACGGTCCCCATATGG 60.606 60.000 15.41 15.41 0.00 2.74
8514 11130 0.694771 AGGAGTTTGCTGCTGGATCA 59.305 50.000 0.00 0.00 42.01 2.92
8527 11143 1.889170 CTGGATCAGCGGCTACTCATA 59.111 52.381 0.26 0.00 0.00 2.15
8528 11144 2.495270 CTGGATCAGCGGCTACTCATAT 59.505 50.000 0.26 0.00 0.00 1.78
8542 11158 6.038492 GGCTACTCATATACCGAATAGACCTC 59.962 46.154 0.00 0.00 0.00 3.85
8552 11168 5.562635 ACCGAATAGACCTCGAGAGATATT 58.437 41.667 15.71 13.80 40.84 1.28
8645 11261 1.605500 CATGTTGTATGTGCACACGC 58.394 50.000 24.37 17.96 39.24 5.34
8663 11279 3.674753 CACGCCCATCATTTTGAAAGTTC 59.325 43.478 0.00 0.00 0.00 3.01
8682 11298 5.308014 AGTTCGCAGATCCATATTGCATTA 58.692 37.500 4.94 0.00 37.69 1.90
8733 11349 1.076438 TGGTCAGACCCAGAGAGAGA 58.924 55.000 17.59 0.00 37.50 3.10
8734 11350 1.005332 TGGTCAGACCCAGAGAGAGAG 59.995 57.143 17.59 0.00 37.50 3.20
8735 11351 1.102978 GTCAGACCCAGAGAGAGAGC 58.897 60.000 0.00 0.00 0.00 4.09
8736 11352 0.701147 TCAGACCCAGAGAGAGAGCA 59.299 55.000 0.00 0.00 0.00 4.26
8737 11353 1.076187 TCAGACCCAGAGAGAGAGCAA 59.924 52.381 0.00 0.00 0.00 3.91
8738 11354 1.477700 CAGACCCAGAGAGAGAGCAAG 59.522 57.143 0.00 0.00 0.00 4.01
8739 11355 0.823460 GACCCAGAGAGAGAGCAAGG 59.177 60.000 0.00 0.00 0.00 3.61
8780 11396 6.430451 CACTGGTCACATTACAAAGAAGTTC 58.570 40.000 0.00 0.00 0.00 3.01
8819 11435 0.179000 GGGTGTAGTGCTCCATCTGG 59.821 60.000 1.67 0.00 32.58 3.86
8900 11516 4.175489 CTCGACGGCGTCATCGGT 62.175 66.667 35.62 1.56 38.86 4.69
9140 11836 2.204029 TACCCCGGGAAAGCCACT 60.204 61.111 26.32 0.00 35.15 4.00
9172 12881 2.107750 CTGCAGCCCATCGTCGAT 59.892 61.111 0.00 0.75 0.00 3.59
9258 13034 3.017314 CGTAGCCGTCGTCATCGC 61.017 66.667 0.00 0.00 36.96 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.299850 CTCGAGGTGCGTCAACACA 60.300 57.895 3.91 0.00 42.55 3.72
28 29 4.373116 GCCCTCGAGGTGCGTCAA 62.373 66.667 29.25 0.00 41.80 3.18
304 317 4.856607 GACGAAGCGCGGAGGAGG 62.857 72.222 8.83 0.00 46.49 4.30
599 644 1.545706 GGCCTTCTCCTCCTTGACGT 61.546 60.000 0.00 0.00 0.00 4.34
625 670 4.814294 GTCGTCGCCGCCATCCTT 62.814 66.667 0.00 0.00 0.00 3.36
737 787 2.287308 CGACAAATTTCGGCCAACTTGA 60.287 45.455 2.24 0.00 35.26 3.02
769 819 1.606350 CGACACAGTTCGGCGAAGTC 61.606 60.000 25.90 23.86 35.26 3.01
810 861 1.068125 GCCCCAGACGCGTTTAAAAAT 60.068 47.619 15.53 0.00 0.00 1.82
815 866 1.962306 GTTGCCCCAGACGCGTTTA 60.962 57.895 15.53 0.00 0.00 2.01
818 869 4.681978 GAGTTGCCCCAGACGCGT 62.682 66.667 13.85 13.85 0.00 6.01
819 870 4.379243 AGAGTTGCCCCAGACGCG 62.379 66.667 3.53 3.53 0.00 6.01
820 871 2.743928 CAGAGTTGCCCCAGACGC 60.744 66.667 0.00 0.00 0.00 5.19
821 872 1.079543 CTCAGAGTTGCCCCAGACG 60.080 63.158 0.00 0.00 0.00 4.18
822 873 1.298014 CCTCAGAGTTGCCCCAGAC 59.702 63.158 0.00 0.00 0.00 3.51
824 875 2.045536 GCCTCAGAGTTGCCCCAG 60.046 66.667 0.00 0.00 0.00 4.45
825 876 2.853542 TGCCTCAGAGTTGCCCCA 60.854 61.111 0.00 0.00 0.00 4.96
831 882 4.400961 GCCGCCTGCCTCAGAGTT 62.401 66.667 0.00 0.00 32.44 3.01
853 905 2.514824 GGATCTGGGCGAGTTGGC 60.515 66.667 0.00 0.00 43.88 4.52
893 948 5.760253 CCAAACAATTATACCATCTCGAGCT 59.240 40.000 7.81 0.00 0.00 4.09
894 949 5.560953 GCCAAACAATTATACCATCTCGAGC 60.561 44.000 7.81 0.00 0.00 5.03
895 950 5.760253 AGCCAAACAATTATACCATCTCGAG 59.240 40.000 5.93 5.93 0.00 4.04
896 951 5.680619 AGCCAAACAATTATACCATCTCGA 58.319 37.500 0.00 0.00 0.00 4.04
897 952 6.377327 AAGCCAAACAATTATACCATCTCG 57.623 37.500 0.00 0.00 0.00 4.04
898 953 7.771183 TCAAAGCCAAACAATTATACCATCTC 58.229 34.615 0.00 0.00 0.00 2.75
899 954 7.615365 TCTCAAAGCCAAACAATTATACCATCT 59.385 33.333 0.00 0.00 0.00 2.90
900 955 7.771183 TCTCAAAGCCAAACAATTATACCATC 58.229 34.615 0.00 0.00 0.00 3.51
901 956 7.397192 ACTCTCAAAGCCAAACAATTATACCAT 59.603 33.333 0.00 0.00 0.00 3.55
902 957 6.719370 ACTCTCAAAGCCAAACAATTATACCA 59.281 34.615 0.00 0.00 0.00 3.25
903 958 7.158099 ACTCTCAAAGCCAAACAATTATACC 57.842 36.000 0.00 0.00 0.00 2.73
904 959 8.947115 ACTACTCTCAAAGCCAAACAATTATAC 58.053 33.333 0.00 0.00 0.00 1.47
906 961 9.167311 CTACTACTCTCAAAGCCAAACAATTAT 57.833 33.333 0.00 0.00 0.00 1.28
907 962 8.372459 TCTACTACTCTCAAAGCCAAACAATTA 58.628 33.333 0.00 0.00 0.00 1.40
908 963 7.173390 GTCTACTACTCTCAAAGCCAAACAATT 59.827 37.037 0.00 0.00 0.00 2.32
909 964 6.651225 GTCTACTACTCTCAAAGCCAAACAAT 59.349 38.462 0.00 0.00 0.00 2.71
910 965 5.989777 GTCTACTACTCTCAAAGCCAAACAA 59.010 40.000 0.00 0.00 0.00 2.83
911 966 5.539048 GTCTACTACTCTCAAAGCCAAACA 58.461 41.667 0.00 0.00 0.00 2.83
912 967 4.621886 CGTCTACTACTCTCAAAGCCAAAC 59.378 45.833 0.00 0.00 0.00 2.93
913 968 4.321750 CCGTCTACTACTCTCAAAGCCAAA 60.322 45.833 0.00 0.00 0.00 3.28
914 969 3.192844 CCGTCTACTACTCTCAAAGCCAA 59.807 47.826 0.00 0.00 0.00 4.52
915 970 2.753452 CCGTCTACTACTCTCAAAGCCA 59.247 50.000 0.00 0.00 0.00 4.75
916 971 2.479901 GCCGTCTACTACTCTCAAAGCC 60.480 54.545 0.00 0.00 0.00 4.35
917 972 2.791849 CGCCGTCTACTACTCTCAAAGC 60.792 54.545 0.00 0.00 0.00 3.51
918 973 2.676839 TCGCCGTCTACTACTCTCAAAG 59.323 50.000 0.00 0.00 0.00 2.77
919 974 2.676839 CTCGCCGTCTACTACTCTCAAA 59.323 50.000 0.00 0.00 0.00 2.69
920 975 2.277969 CTCGCCGTCTACTACTCTCAA 58.722 52.381 0.00 0.00 0.00 3.02
921 976 1.206610 ACTCGCCGTCTACTACTCTCA 59.793 52.381 0.00 0.00 0.00 3.27
922 977 1.860326 GACTCGCCGTCTACTACTCTC 59.140 57.143 0.00 0.00 39.61 3.20
923 978 1.802136 CGACTCGCCGTCTACTACTCT 60.802 57.143 3.74 0.00 40.59 3.24
924 979 0.576328 CGACTCGCCGTCTACTACTC 59.424 60.000 3.74 0.00 40.59 2.59
925 980 2.675519 CGACTCGCCGTCTACTACT 58.324 57.895 3.74 0.00 40.59 2.57
937 992 2.033194 GGGGAAAACTGGCGACTCG 61.033 63.158 0.00 0.00 0.00 4.18
938 993 1.674651 GGGGGAAAACTGGCGACTC 60.675 63.158 0.00 0.00 0.00 3.36
939 994 2.434774 GGGGGAAAACTGGCGACT 59.565 61.111 0.00 0.00 0.00 4.18
940 995 2.114411 TGGGGGAAAACTGGCGAC 59.886 61.111 0.00 0.00 0.00 5.19
941 996 2.114411 GTGGGGGAAAACTGGCGA 59.886 61.111 0.00 0.00 0.00 5.54
942 997 2.989253 GGTGGGGGAAAACTGGCG 60.989 66.667 0.00 0.00 0.00 5.69
943 998 1.908299 CAGGTGGGGGAAAACTGGC 60.908 63.158 0.00 0.00 0.00 4.85
944 999 1.228862 CCAGGTGGGGGAAAACTGG 60.229 63.158 0.00 0.00 42.28 4.00
945 1000 0.251341 CTCCAGGTGGGGGAAAACTG 60.251 60.000 0.00 0.00 41.01 3.16
946 1001 0.402861 TCTCCAGGTGGGGGAAAACT 60.403 55.000 0.00 0.00 45.71 2.66
947 1002 2.160646 TCTCCAGGTGGGGGAAAAC 58.839 57.895 0.00 0.00 45.71 2.43
948 1003 4.783155 TCTCCAGGTGGGGGAAAA 57.217 55.556 0.00 0.00 45.71 2.29
951 1006 3.596799 TCGTCTCCAGGTGGGGGA 61.597 66.667 0.00 0.00 46.87 4.81
952 1007 3.391382 GTCGTCTCCAGGTGGGGG 61.391 72.222 0.00 0.00 39.19 5.40
953 1008 2.603473 TGTCGTCTCCAGGTGGGG 60.603 66.667 0.00 0.00 37.22 4.96
954 1009 1.599606 CTCTGTCGTCTCCAGGTGGG 61.600 65.000 0.00 0.00 35.41 4.61
955 1010 1.886585 CTCTGTCGTCTCCAGGTGG 59.113 63.158 0.00 0.00 0.00 4.61
956 1011 1.214062 GCTCTGTCGTCTCCAGGTG 59.786 63.158 0.00 0.00 0.00 4.00
957 1012 1.228583 TGCTCTGTCGTCTCCAGGT 60.229 57.895 0.00 0.00 0.00 4.00
958 1013 1.214062 GTGCTCTGTCGTCTCCAGG 59.786 63.158 0.00 0.00 0.00 4.45
959 1014 1.154131 CGTGCTCTGTCGTCTCCAG 60.154 63.158 0.00 0.00 0.00 3.86
960 1015 2.626780 CCGTGCTCTGTCGTCTCCA 61.627 63.158 0.00 0.00 0.00 3.86
1210 1265 0.683412 GACGACCACTTACCCTGGTT 59.317 55.000 0.00 0.00 42.42 3.67
1222 1277 1.381327 GGGAGATGAGGGACGACCA 60.381 63.158 6.20 0.00 43.89 4.02
1235 1290 0.108585 AAACGAGCAGCAAAGGGAGA 59.891 50.000 0.00 0.00 0.00 3.71
1249 1304 2.912771 TCTTCTCCTGCAAACAAACGA 58.087 42.857 0.00 0.00 0.00 3.85
1255 1310 2.673368 CCGTACATCTTCTCCTGCAAAC 59.327 50.000 0.00 0.00 0.00 2.93
1628 1689 4.262036 GGGAGTTGCTTGTTTCCCTAAAAG 60.262 45.833 1.18 0.00 44.82 2.27
1649 1710 1.746615 CTTGCGTGTGGGATGAGGG 60.747 63.158 0.00 0.00 0.00 4.30
1652 1713 1.002257 ATGCTTGCGTGTGGGATGA 60.002 52.632 0.00 0.00 0.00 2.92
1808 1873 5.010516 AGCTTACACAATGGCATGTACAAAA 59.989 36.000 0.00 0.00 31.09 2.44
1905 1970 4.846779 ATCATGTGCAGGTTAAACGTTT 57.153 36.364 18.90 18.90 0.00 3.60
1924 1990 3.619929 GCCCTGCAAATTTCATCACAATC 59.380 43.478 0.00 0.00 0.00 2.67
1929 1995 1.202114 GTCGCCCTGCAAATTTCATCA 59.798 47.619 0.00 0.00 0.00 3.07
2025 2091 2.261345 CCACAAACGCCAATAGCATTG 58.739 47.619 0.00 0.00 44.04 2.82
2112 2178 9.823098 CTGTTCTGAATTTTCTCATAGAAACTG 57.177 33.333 1.67 0.00 43.25 3.16
2233 2299 1.059098 TGTCTCAGCCTGTCATGGTT 58.941 50.000 0.00 0.00 0.00 3.67
2251 2317 1.817357 ACAGTCAGACATGCCATGTG 58.183 50.000 16.43 1.65 45.03 3.21
2359 2425 7.928167 TGTCACACAGTCATCAGAATTATATCC 59.072 37.037 0.00 0.00 0.00 2.59
2396 2462 4.243270 ACAGTGACTAGGAAATACGCAAC 58.757 43.478 0.00 0.00 0.00 4.17
2439 2505 7.977789 TCATAACTTGCAGACAAAGTGATAA 57.022 32.000 0.00 0.00 34.74 1.75
2630 2696 8.719648 CGATAAAGTGGTAGTAGTAGTATGAGG 58.280 40.741 0.00 0.00 0.00 3.86
2852 2920 4.502950 GGGAGGAGAATGCATAGACAAGAG 60.503 50.000 0.00 0.00 0.00 2.85
3142 3210 5.848406 TGATTTTTGCAGTACCGGATTTTT 58.152 33.333 9.46 0.00 0.00 1.94
3188 3256 2.400408 CGTTCCTGCAAAATCGTTTTCG 59.600 45.455 0.00 0.00 45.64 3.46
3203 3271 4.016706 CGGGGCCTTCACGTTCCT 62.017 66.667 0.84 0.00 0.00 3.36
3542 3611 1.836802 GGATCCCAGCTCCTATCATCC 59.163 57.143 0.00 0.00 0.00 3.51
3569 3638 3.381335 CCCTACAACCTAAGGGCTAGAA 58.619 50.000 0.00 0.00 45.91 2.10
3576 3645 3.136626 CCTTCCATCCCTACAACCTAAGG 59.863 52.174 0.00 0.00 0.00 2.69
3591 3660 1.384502 TCGCCATCCTCCCTTCCAT 60.385 57.895 0.00 0.00 0.00 3.41
3651 3723 2.043450 CCTGCCTCCTCCTCTCGT 60.043 66.667 0.00 0.00 0.00 4.18
3670 3748 1.605453 CCTAAAACCCTAGCCGCCA 59.395 57.895 0.00 0.00 0.00 5.69
3834 3926 1.446272 GGCGTCTCATATAGCCGGC 60.446 63.158 21.89 21.89 40.17 6.13
3844 3936 0.821517 ATGTTATGACCGGCGTCTCA 59.178 50.000 6.01 6.56 39.94 3.27
3868 3960 2.594303 CTGTTTGTGCAGGCGGGA 60.594 61.111 0.00 0.00 33.11 5.14
3878 3970 2.376808 CTCGAGGATGAGCTGTTTGT 57.623 50.000 3.91 0.00 0.00 2.83
4005 4097 1.613437 CGAAAGTGTTGAAGGCCCAAT 59.387 47.619 0.00 0.00 0.00 3.16
4006 4098 1.028905 CGAAAGTGTTGAAGGCCCAA 58.971 50.000 0.00 0.00 0.00 4.12
4021 4113 1.760479 TTCTTCCGGACCCAGCGAAA 61.760 55.000 1.83 0.00 0.00 3.46
4031 4123 1.956629 GATGGGCGTCTTCTTCCGGA 61.957 60.000 0.00 0.00 0.00 5.14
4045 4137 1.271840 TTCCTCCAACCTCCGATGGG 61.272 60.000 0.00 0.00 37.31 4.00
4080 4172 3.842925 TTTCCGCAGTGAGCCACCC 62.843 63.158 0.00 0.00 41.38 4.61
4083 4175 2.032528 CCTTTCCGCAGTGAGCCA 59.967 61.111 0.00 0.00 41.38 4.75
4084 4176 3.435186 GCCTTTCCGCAGTGAGCC 61.435 66.667 0.00 0.00 41.38 4.70
4086 4178 0.603707 TCAAGCCTTTCCGCAGTGAG 60.604 55.000 0.00 0.00 0.00 3.51
4091 4184 1.518056 CTTGCTCAAGCCTTTCCGCA 61.518 55.000 0.00 0.00 41.18 5.69
4125 4218 3.282157 GGCGCGTGCATCCATGAT 61.282 61.111 24.18 0.00 45.35 2.45
4145 4238 1.076332 CTACCGCCTTCAACTTTCGG 58.924 55.000 0.00 0.00 45.04 4.30
4190 4283 3.312285 TACGCGGGCCCATTTTCGA 62.312 57.895 24.92 0.00 0.00 3.71
4251 4344 1.605058 GGCTCCTTCACCGCTCTACA 61.605 60.000 0.00 0.00 0.00 2.74
4271 4364 2.203153 GCGACTGGGTGTGGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
4385 4478 0.907486 CCTTCTCTGCATCAGGGACA 59.093 55.000 0.00 0.00 41.07 4.02
4393 4486 1.220206 CTGGCGACCTTCTCTGCAT 59.780 57.895 0.00 0.00 0.00 3.96
4397 4491 3.764466 CGGCTGGCGACCTTCTCT 61.764 66.667 19.64 0.00 0.00 3.10
4446 4540 0.691078 GCCCTCCACCACTCATCCTA 60.691 60.000 0.00 0.00 0.00 2.94
4453 4547 2.815684 TATGGTCGCCCTCCACCACT 62.816 60.000 0.00 0.00 45.61 4.00
4476 4570 1.949257 CGCCACACCTTTTGAGGTC 59.051 57.895 0.00 0.00 40.85 3.85
4541 4635 2.900106 GCTTGGGTGGACTGGCTCT 61.900 63.158 0.00 0.00 0.00 4.09
4662 4756 1.448893 GGATGGCGGCGTGAAACTA 60.449 57.895 9.10 0.00 31.75 2.24
4694 4789 1.457303 GTGTTCACTCGTCATGTCTGC 59.543 52.381 0.00 0.00 0.00 4.26
4705 4800 1.663702 CGTGACCCGGTGTTCACTC 60.664 63.158 20.02 2.43 0.00 3.51
4845 4940 3.299977 CCTCACGGTGGTCGACCA 61.300 66.667 33.23 33.23 46.55 4.02
4947 5042 2.011122 GCTGGTGGGCCTACTATAGA 57.989 55.000 19.72 0.00 35.27 1.98
4961 5057 4.008933 GGAGACACTGCGGCTGGT 62.009 66.667 11.64 6.30 0.00 4.00
5033 5130 4.721776 AGATTTCTACATCCCCAGCAACTA 59.278 41.667 0.00 0.00 0.00 2.24
5034 5131 3.525199 AGATTTCTACATCCCCAGCAACT 59.475 43.478 0.00 0.00 0.00 3.16
5037 5134 2.421952 GCAGATTTCTACATCCCCAGCA 60.422 50.000 0.00 0.00 0.00 4.41
5040 5137 1.494721 GGGCAGATTTCTACATCCCCA 59.505 52.381 0.00 0.00 0.00 4.96
5099 5196 3.391382 GGTGCTAGCCCACTCGGT 61.391 66.667 13.29 0.00 36.03 4.69
5149 5246 3.818787 GGGCGTCGGCTCTTCGTA 61.819 66.667 19.00 0.00 36.44 3.43
5231 5340 2.094126 CTAAATGCGCGGCTCCTTCG 62.094 60.000 8.83 0.00 0.00 3.79
5232 5341 0.810031 TCTAAATGCGCGGCTCCTTC 60.810 55.000 8.83 0.00 0.00 3.46
5233 5342 0.811616 CTCTAAATGCGCGGCTCCTT 60.812 55.000 8.83 0.00 0.00 3.36
5234 5343 1.227380 CTCTAAATGCGCGGCTCCT 60.227 57.895 8.83 0.00 0.00 3.69
5235 5344 2.886782 GCTCTAAATGCGCGGCTCC 61.887 63.158 8.83 0.00 0.00 4.70
5236 5345 2.628657 GCTCTAAATGCGCGGCTC 59.371 61.111 8.83 0.00 0.00 4.70
5237 5346 3.264897 CGCTCTAAATGCGCGGCT 61.265 61.111 8.83 0.00 45.00 5.52
5248 5357 2.586079 GGCATTGCGAGCGCTCTA 60.586 61.111 32.88 20.02 42.51 2.43
5261 5370 3.882326 CCCTCATCGCCAGGGCAT 61.882 66.667 11.42 0.46 44.59 4.40
5267 5376 4.161295 CCTTCGCCCTCATCGCCA 62.161 66.667 0.00 0.00 0.00 5.69
5328 5448 2.728383 GACCACGACACCGACACG 60.728 66.667 0.00 0.00 39.50 4.49
5424 5544 3.079578 ACATCAGTGGATCAGCAAGTTG 58.920 45.455 0.00 0.00 0.00 3.16
5426 5546 3.079578 CAACATCAGTGGATCAGCAAGT 58.920 45.455 0.00 0.00 0.00 3.16
5513 5634 3.002620 ATATTTGTGGGGGCGGCCA 62.003 57.895 30.95 7.24 0.00 5.36
5603 5724 3.630013 AGCAGGTCCTTCGCAGCA 61.630 61.111 4.15 0.00 0.00 4.41
5614 5735 1.373497 CTCGCGTTCTTCAGCAGGT 60.373 57.895 5.77 0.00 0.00 4.00
5676 5797 0.902984 ATGGTGGACTGTGACGCCTA 60.903 55.000 11.49 1.68 38.09 3.93
5716 5837 3.083997 GGCCGGTCCTCCAGATGT 61.084 66.667 1.90 0.00 0.00 3.06
5758 5879 2.660552 CAACCGAGGCGTTCACGT 60.661 61.111 0.62 0.00 42.22 4.49
5774 5895 0.033503 TCTCGTGGGATACTGAGGCA 60.034 55.000 0.00 0.00 33.61 4.75
5789 5910 1.059369 CAATTGCGACGCCTTCTCG 59.941 57.895 18.69 0.00 0.00 4.04
5804 7758 1.610624 CGTCAGGGGTTGTGCTACAAT 60.611 52.381 5.26 0.00 40.59 2.71
6025 8008 3.005539 ACGTGGAGATGCAGGGCT 61.006 61.111 0.00 0.00 0.00 5.19
6157 8141 1.900545 GCGCCTACCCTTCACCTCTT 61.901 60.000 0.00 0.00 0.00 2.85
6363 8556 2.360844 TCAGTGCGACCAGTTTTTCAA 58.639 42.857 0.00 0.00 0.00 2.69
6571 8785 2.124570 CCATCCAGTTCGGCAGGG 60.125 66.667 0.00 0.00 33.14 4.45
7002 9312 1.513158 CGAAGGAGATGACGGCTGT 59.487 57.895 0.00 0.00 0.00 4.40
7047 9358 2.956964 GATGTCTTCCGCCGCTCG 60.957 66.667 0.00 0.00 38.08 5.03
7049 9360 4.514577 CCGATGTCTTCCGCCGCT 62.515 66.667 0.00 0.00 0.00 5.52
7234 9557 1.430369 CCATCCTCCCTTCCATCCCC 61.430 65.000 0.00 0.00 0.00 4.81
7326 9738 0.328258 ACTATTGCCCGGCTCACTTT 59.672 50.000 11.61 0.00 0.00 2.66
7330 9742 1.765904 TCATAACTATTGCCCGGCTCA 59.234 47.619 11.61 0.00 0.00 4.26
7461 9873 0.037734 TCTCATATAGCCGGCGGAGA 59.962 55.000 33.44 23.66 0.00 3.71
7486 9898 2.353704 CCACGAGCTCCACTGTTATGAA 60.354 50.000 8.47 0.00 0.00 2.57
7731 10150 2.732619 CCGCTAGACCTCCCCAACC 61.733 68.421 0.00 0.00 0.00 3.77
7826 10345 2.087248 CCCACAAATCCACCCCTCT 58.913 57.895 0.00 0.00 0.00 3.69
7841 10360 1.343069 AAAAATTTACAGGCGGCCCA 58.657 45.000 17.02 0.00 0.00 5.36
7927 10446 1.316706 CGCCGGCCCTTAAAATTCCA 61.317 55.000 23.46 0.00 0.00 3.53
8435 11051 7.192852 TCAAGAGAGCTTCTTTTCTCCATAT 57.807 36.000 8.01 0.00 43.68 1.78
8440 11056 4.143137 CGCTTCAAGAGAGCTTCTTTTCTC 60.143 45.833 8.01 0.23 43.68 2.87
8514 11130 2.195741 TCGGTATATGAGTAGCCGCT 57.804 50.000 0.00 0.00 41.89 5.52
8527 11143 4.620589 TCTCTCGAGGTCTATTCGGTAT 57.379 45.455 13.56 0.00 38.54 2.73
8528 11144 4.620589 ATCTCTCGAGGTCTATTCGGTA 57.379 45.455 13.56 0.00 38.54 4.02
8552 11168 8.144155 TGATCAACGTTTGTGAATAAGTAACA 57.856 30.769 0.00 0.00 0.00 2.41
8599 11215 5.936956 AGAACAAGAGAATTCAGTGATGACC 59.063 40.000 8.44 0.00 0.00 4.02
8645 11261 3.911868 TGCGAACTTTCAAAATGATGGG 58.088 40.909 0.00 0.00 0.00 4.00
8663 11279 4.012319 GCTAATGCAATATGGATCTGCG 57.988 45.455 0.00 0.00 38.97 5.18
8682 11298 1.153168 AAACTGACCGTGCTGTGCT 60.153 52.632 0.00 0.00 0.00 4.40
8733 11349 2.837291 TTGTTTGGCGGCCTTGCT 60.837 55.556 21.46 0.00 34.52 3.91
8734 11350 2.356194 CTTGTTTGGCGGCCTTGC 60.356 61.111 21.46 10.17 0.00 4.01
8735 11351 2.339712 CCTTGTTTGGCGGCCTTG 59.660 61.111 21.46 3.82 0.00 3.61
8736 11352 3.615709 GCCTTGTTTGGCGGCCTT 61.616 61.111 21.46 0.00 43.74 4.35
8758 11374 5.236478 ACGAACTTCTTTGTAATGTGACCAG 59.764 40.000 0.00 0.00 0.00 4.00
8780 11396 2.858344 CCCTATTCGCTAGACACAAACG 59.142 50.000 0.00 0.00 0.00 3.60
9164 12873 2.123251 AGGGGGAGCATCGACGAT 60.123 61.111 4.05 4.05 34.37 3.73


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

AutoCloner maintained by Alex Coulton.