Multiple sequence alignment - TraesCS3B01G596400

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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 TraesCS3B01G596400 chr3B 100.000 5053 0 0 1 5053 819297156 819302208 0.000000e+00 9332.0
1 TraesCS3B01G596400 chr3B 95.702 1489 57 4 2796 4279 819522985 819524471 0.000000e+00 2388.0
2 TraesCS3B01G596400 chr3B 92.210 1489 107 5 2794 4279 819651078 819652560 0.000000e+00 2098.0
3 TraesCS3B01G596400 chr3B 91.863 1487 110 8 2794 4279 819382180 819383656 0.000000e+00 2065.0
4 TraesCS3B01G596400 chr3B 83.809 1507 201 20 2794 4279 819740879 819742363 0.000000e+00 1391.0
5 TraesCS3B01G596400 chr3B 97.690 736 6 2 4287 5012 17406298 17407032 0.000000e+00 1254.0
6 TraesCS3B01G596400 chr3B 97.059 578 16 1 920 1497 819649966 819650542 0.000000e+00 972.0
7 TraesCS3B01G596400 chr3B 96.021 578 19 2 920 1497 819522317 819522890 0.000000e+00 937.0
8 TraesCS3B01G596400 chr3B 93.015 587 37 3 920 1505 819381274 819381857 0.000000e+00 854.0
9 TraesCS3B01G596400 chr3B 86.304 533 68 4 959 1488 819740033 819740563 4.390000e-160 575.0
10 TraesCS3B01G596400 chr3B 84.586 532 70 9 959 1484 753164610 753164085 7.500000e-143 518.0
11 TraesCS3B01G596400 chr3B 83.607 305 18 14 2435 2712 819381882 819382181 1.810000e-64 257.0
12 TraesCS3B01G596400 chr3B 96.226 106 4 0 2607 2712 819650974 819651079 1.870000e-39 174.0
13 TraesCS3B01G596400 chr3D 92.335 1396 103 4 2794 4186 608951893 608953287 0.000000e+00 1982.0
14 TraesCS3B01G596400 chr3D 84.487 1502 190 19 2794 4279 609005422 609006896 0.000000e+00 1443.0
15 TraesCS3B01G596400 chr3D 94.365 834 38 5 1 826 584687790 584686958 0.000000e+00 1271.0
16 TraesCS3B01G596400 chr3D 85.188 1249 174 8 2905 4150 609286678 609285438 0.000000e+00 1271.0
17 TraesCS3B01G596400 chr3D 94.075 827 40 5 1 820 74319073 74319897 0.000000e+00 1247.0
18 TraesCS3B01G596400 chr3D 88.301 889 82 16 1508 2387 328345477 328344602 0.000000e+00 1046.0
19 TraesCS3B01G596400 chr3D 95.205 584 27 1 920 1503 608950814 608951396 0.000000e+00 922.0
20 TraesCS3B01G596400 chr3D 89.897 485 47 2 3796 4279 608991546 608992029 1.540000e-174 623.0
21 TraesCS3B01G596400 chr3D 87.453 534 61 5 959 1488 609004575 609005106 1.200000e-170 610.0
22 TraesCS3B01G596400 chr3D 88.152 211 11 4 2386 2596 608951389 608951585 6.540000e-59 239.0
23 TraesCS3B01G596400 chr3D 92.553 94 6 1 2707 2799 15450672 15450765 3.170000e-27 134.0
24 TraesCS3B01G596400 chr3D 89.130 92 8 2 829 918 482762061 482762152 4.130000e-21 113.0
25 TraesCS3B01G596400 chr3D 93.243 74 4 1 2523 2596 608981851 608981923 1.920000e-19 108.0
26 TraesCS3B01G596400 chr3D 87.912 91 9 2 829 918 8873139 8873050 6.920000e-19 106.0
27 TraesCS3B01G596400 chr3D 87.234 94 11 1 826 918 173712921 173713014 6.920000e-19 106.0
28 TraesCS3B01G596400 chr3A 90.778 1182 105 3 3100 4279 742313762 742314941 0.000000e+00 1576.0
29 TraesCS3B01G596400 chr3A 83.023 1502 216 19 2793 4279 742356228 742357705 0.000000e+00 1325.0
30 TraesCS3B01G596400 chr3A 95.122 574 26 2 920 1492 742332177 742332749 0.000000e+00 904.0
31 TraesCS3B01G596400 chr3A 87.194 531 62 4 959 1488 742355389 742355914 2.600000e-167 599.0
32 TraesCS3B01G596400 chr3A 87.778 90 10 1 830 918 569644493 569644582 2.490000e-18 104.0
33 TraesCS3B01G596400 chr4D 94.478 833 38 4 1 826 297381324 297380493 0.000000e+00 1277.0
34 TraesCS3B01G596400 chr4D 80.597 201 28 7 1510 1709 432585930 432585740 1.470000e-30 145.0
35 TraesCS3B01G596400 chr4D 87.500 80 10 0 1510 1589 469640917 469640838 5.390000e-15 93.5
36 TraesCS3B01G596400 chr7A 98.098 736 4 1 4287 5012 491485639 491484904 0.000000e+00 1273.0
37 TraesCS3B01G596400 chr7A 97.826 736 6 1 4287 5012 653536865 653536130 0.000000e+00 1262.0
38 TraesCS3B01G596400 chr7A 90.000 110 6 5 2692 2798 129876920 129877027 2.450000e-28 137.0
39 TraesCS3B01G596400 chr6A 98.098 736 4 1 4287 5012 169212821 169213556 0.000000e+00 1273.0
40 TraesCS3B01G596400 chr2A 97.962 736 5 1 4287 5012 79522400 79523135 0.000000e+00 1267.0
41 TraesCS3B01G596400 chr2A 90.271 884 68 10 1508 2385 47856488 47857359 0.000000e+00 1140.0
42 TraesCS3B01G596400 chr1A 97.962 736 5 1 4287 5012 490509078 490508343 0.000000e+00 1267.0
43 TraesCS3B01G596400 chr1A 97.418 736 9 1 4287 5012 569898062 569898797 0.000000e+00 1245.0
44 TraesCS3B01G596400 chr1A 93.277 833 47 5 1 826 27313891 27314721 0.000000e+00 1219.0
45 TraesCS3B01G596400 chr1A 87.191 445 30 17 1861 2288 24456170 24455736 9.840000e-132 481.0
46 TraesCS3B01G596400 chr1A 90.000 100 9 1 2711 2810 48977165 48977263 1.480000e-25 128.0
47 TraesCS3B01G596400 chr1A 88.776 98 9 2 2296 2391 24453139 24453042 8.890000e-23 119.0
48 TraesCS3B01G596400 chr1A 88.608 79 7 2 1508 1585 16029943 16030020 1.500000e-15 95.3
49 TraesCS3B01G596400 chr1A 83.333 102 13 3 1510 1608 73292859 73292759 1.940000e-14 91.6
50 TraesCS3B01G596400 chr5B 97.706 741 6 2 4287 5017 325155240 325154501 0.000000e+00 1264.0
51 TraesCS3B01G596400 chr5B 97.826 736 6 1 4287 5012 576289250 576289985 0.000000e+00 1262.0
52 TraesCS3B01G596400 chr5B 91.667 96 7 1 2707 2801 206473018 206473113 1.140000e-26 132.0
53 TraesCS3B01G596400 chr6B 94.118 833 42 3 1 826 705855593 705856425 0.000000e+00 1260.0
54 TraesCS3B01G596400 chr6B 91.270 882 63 8 1508 2385 717895919 717896790 0.000000e+00 1190.0
55 TraesCS3B01G596400 chr6B 87.657 559 52 11 1739 2288 647705324 647705874 7.140000e-178 634.0
56 TraesCS3B01G596400 chr6B 91.770 243 17 2 1508 1747 647703854 647704096 8.110000e-88 335.0
57 TraesCS3B01G596400 chr6B 93.069 101 7 0 2286 2386 647707498 647707598 1.130000e-31 148.0
58 TraesCS3B01G596400 chr6B 94.186 86 5 0 2710 2795 607208131 607208216 1.140000e-26 132.0
59 TraesCS3B01G596400 chr4B 97.690 736 7 1 4287 5012 661283432 661284167 0.000000e+00 1256.0
60 TraesCS3B01G596400 chr4B 91.053 883 64 9 1508 2385 667350555 667349683 0.000000e+00 1179.0
61 TraesCS3B01G596400 chr4B 90.919 881 64 9 1508 2385 667570649 667571516 0.000000e+00 1170.0
62 TraesCS3B01G596400 chr4B 90.211 899 71 11 1508 2401 530200415 530201301 0.000000e+00 1157.0
63 TraesCS3B01G596400 chr4B 90.147 883 71 10 1508 2385 530013747 530014618 0.000000e+00 1134.0
64 TraesCS3B01G596400 chr4B 89.391 886 75 9 1508 2385 530198795 530197921 0.000000e+00 1098.0
65 TraesCS3B01G596400 chr4B 91.914 371 27 2 1508 1875 30854528 30854158 2.700000e-142 516.0
66 TraesCS3B01G596400 chr4B 89.423 104 7 4 2294 2395 30851096 30850995 1.480000e-25 128.0
67 TraesCS3B01G596400 chr6D 93.758 833 45 3 1 826 83435801 83434969 0.000000e+00 1243.0
68 TraesCS3B01G596400 chr6D 91.667 96 4 3 2704 2798 15347937 15348029 4.110000e-26 130.0
69 TraesCS3B01G596400 chr6D 88.764 89 9 1 831 918 84259116 84259204 1.920000e-19 108.0
70 TraesCS3B01G596400 chr6D 87.912 91 10 1 829 918 140015145 140015235 6.920000e-19 106.0
71 TraesCS3B01G596400 chr6D 87.234 94 10 2 827 918 352826631 352826724 6.920000e-19 106.0
72 TraesCS3B01G596400 chr6D 87.912 91 10 1 829 918 436683968 436684058 6.920000e-19 106.0
73 TraesCS3B01G596400 chr7D 93.637 833 43 5 1 826 16200651 16201480 0.000000e+00 1236.0
74 TraesCS3B01G596400 chr1B 93.517 833 46 4 1 826 194780248 194779417 0.000000e+00 1232.0
75 TraesCS3B01G596400 chr1B 87.875 866 80 18 1527 2385 555793748 555792901 0.000000e+00 994.0
76 TraesCS3B01G596400 chr1B 93.407 91 6 0 2705 2795 485476073 485476163 8.820000e-28 135.0
77 TraesCS3B01G596400 chrUn 93.277 833 48 4 1 826 349628610 349629441 0.000000e+00 1221.0
78 TraesCS3B01G596400 chrUn 90.260 883 72 11 1508 2385 10139058 10139931 0.000000e+00 1142.0
79 TraesCS3B01G596400 chrUn 89.594 788 64 13 1508 2288 50894310 50895086 0.000000e+00 985.0
80 TraesCS3B01G596400 chrUn 88.873 701 60 13 1595 2288 50876237 50876926 0.000000e+00 846.0
81 TraesCS3B01G596400 chrUn 92.391 92 7 0 2704 2795 135090711 135090802 1.140000e-26 132.0
82 TraesCS3B01G596400 chrUn 90.426 94 8 1 2294 2386 50896653 50896746 6.870000e-24 122.0
83 TraesCS3B01G596400 chr7B 91.076 874 63 8 1508 2376 230215935 230216798 0.000000e+00 1168.0
84 TraesCS3B01G596400 chr7B 95.380 736 23 2 4294 5019 506620266 506621000 0.000000e+00 1160.0
85 TraesCS3B01G596400 chr7B 92.553 94 6 1 2711 2804 289427288 289427196 3.170000e-27 134.0
86 TraesCS3B01G596400 chr5D 80.882 204 32 7 1508 1706 124357829 124357628 2.440000e-33 154.0
87 TraesCS3B01G596400 chr4A 81.667 180 30 3 1508 1685 405573468 405573646 4.080000e-31 147.0
88 TraesCS3B01G596400 chr4A 81.868 182 26 4 1508 1685 429439996 429440174 4.080000e-31 147.0
89 TraesCS3B01G596400 chr4A 79.147 211 37 7 1508 1714 596719889 596719682 6.820000e-29 139.0
90 TraesCS3B01G596400 chr4A 95.238 42 2 0 1510 1551 19831166 19831207 3.260000e-07 67.6
91 TraesCS3B01G596400 chr5A 86.957 92 10 2 829 918 366139019 366139110 8.950000e-18 102.0


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 TraesCS3B01G596400 chr3B 819297156 819302208 5052 False 9332.000000 9332 100.000000 1 5053 1 chr3B.!!$F2 5052
1 TraesCS3B01G596400 chr3B 819522317 819524471 2154 False 1662.500000 2388 95.861500 920 4279 2 chr3B.!!$F4 3359
2 TraesCS3B01G596400 chr3B 17406298 17407032 734 False 1254.000000 1254 97.690000 4287 5012 1 chr3B.!!$F1 725
3 TraesCS3B01G596400 chr3B 819649966 819652560 2594 False 1081.333333 2098 95.165000 920 4279 3 chr3B.!!$F5 3359
4 TraesCS3B01G596400 chr3B 819381274 819383656 2382 False 1058.666667 2065 89.495000 920 4279 3 chr3B.!!$F3 3359
5 TraesCS3B01G596400 chr3B 819740033 819742363 2330 False 983.000000 1391 85.056500 959 4279 2 chr3B.!!$F6 3320
6 TraesCS3B01G596400 chr3B 753164085 753164610 525 True 518.000000 518 84.586000 959 1484 1 chr3B.!!$R1 525
7 TraesCS3B01G596400 chr3D 584686958 584687790 832 True 1271.000000 1271 94.365000 1 826 1 chr3D.!!$R3 825
8 TraesCS3B01G596400 chr3D 609285438 609286678 1240 True 1271.000000 1271 85.188000 2905 4150 1 chr3D.!!$R4 1245
9 TraesCS3B01G596400 chr3D 74319073 74319897 824 False 1247.000000 1247 94.075000 1 820 1 chr3D.!!$F2 819
10 TraesCS3B01G596400 chr3D 608950814 608953287 2473 False 1047.666667 1982 91.897333 920 4186 3 chr3D.!!$F7 3266
11 TraesCS3B01G596400 chr3D 328344602 328345477 875 True 1046.000000 1046 88.301000 1508 2387 1 chr3D.!!$R2 879
12 TraesCS3B01G596400 chr3D 609004575 609006896 2321 False 1026.500000 1443 85.970000 959 4279 2 chr3D.!!$F8 3320
13 TraesCS3B01G596400 chr3A 742313762 742314941 1179 False 1576.000000 1576 90.778000 3100 4279 1 chr3A.!!$F2 1179
14 TraesCS3B01G596400 chr3A 742355389 742357705 2316 False 962.000000 1325 85.108500 959 4279 2 chr3A.!!$F4 3320
15 TraesCS3B01G596400 chr3A 742332177 742332749 572 False 904.000000 904 95.122000 920 1492 1 chr3A.!!$F3 572
16 TraesCS3B01G596400 chr4D 297380493 297381324 831 True 1277.000000 1277 94.478000 1 826 1 chr4D.!!$R1 825
17 TraesCS3B01G596400 chr7A 491484904 491485639 735 True 1273.000000 1273 98.098000 4287 5012 1 chr7A.!!$R1 725
18 TraesCS3B01G596400 chr7A 653536130 653536865 735 True 1262.000000 1262 97.826000 4287 5012 1 chr7A.!!$R2 725
19 TraesCS3B01G596400 chr6A 169212821 169213556 735 False 1273.000000 1273 98.098000 4287 5012 1 chr6A.!!$F1 725
20 TraesCS3B01G596400 chr2A 79522400 79523135 735 False 1267.000000 1267 97.962000 4287 5012 1 chr2A.!!$F2 725
21 TraesCS3B01G596400 chr2A 47856488 47857359 871 False 1140.000000 1140 90.271000 1508 2385 1 chr2A.!!$F1 877
22 TraesCS3B01G596400 chr1A 490508343 490509078 735 True 1267.000000 1267 97.962000 4287 5012 1 chr1A.!!$R2 725
23 TraesCS3B01G596400 chr1A 569898062 569898797 735 False 1245.000000 1245 97.418000 4287 5012 1 chr1A.!!$F4 725
24 TraesCS3B01G596400 chr1A 27313891 27314721 830 False 1219.000000 1219 93.277000 1 826 1 chr1A.!!$F2 825
25 TraesCS3B01G596400 chr1A 24453042 24456170 3128 True 300.000000 481 87.983500 1861 2391 2 chr1A.!!$R3 530
26 TraesCS3B01G596400 chr5B 325154501 325155240 739 True 1264.000000 1264 97.706000 4287 5017 1 chr5B.!!$R1 730
27 TraesCS3B01G596400 chr5B 576289250 576289985 735 False 1262.000000 1262 97.826000 4287 5012 1 chr5B.!!$F2 725
28 TraesCS3B01G596400 chr6B 705855593 705856425 832 False 1260.000000 1260 94.118000 1 826 1 chr6B.!!$F2 825
29 TraesCS3B01G596400 chr6B 717895919 717896790 871 False 1190.000000 1190 91.270000 1508 2385 1 chr6B.!!$F3 877
30 TraesCS3B01G596400 chr6B 647703854 647707598 3744 False 372.333333 634 90.832000 1508 2386 3 chr6B.!!$F4 878
31 TraesCS3B01G596400 chr4B 661283432 661284167 735 False 1256.000000 1256 97.690000 4287 5012 1 chr4B.!!$F3 725
32 TraesCS3B01G596400 chr4B 667349683 667350555 872 True 1179.000000 1179 91.053000 1508 2385 1 chr4B.!!$R2 877
33 TraesCS3B01G596400 chr4B 667570649 667571516 867 False 1170.000000 1170 90.919000 1508 2385 1 chr4B.!!$F4 877
34 TraesCS3B01G596400 chr4B 530200415 530201301 886 False 1157.000000 1157 90.211000 1508 2401 1 chr4B.!!$F2 893
35 TraesCS3B01G596400 chr4B 530013747 530014618 871 False 1134.000000 1134 90.147000 1508 2385 1 chr4B.!!$F1 877
36 TraesCS3B01G596400 chr4B 530197921 530198795 874 True 1098.000000 1098 89.391000 1508 2385 1 chr4B.!!$R1 877
37 TraesCS3B01G596400 chr4B 30850995 30854528 3533 True 322.000000 516 90.668500 1508 2395 2 chr4B.!!$R3 887
38 TraesCS3B01G596400 chr6D 83434969 83435801 832 True 1243.000000 1243 93.758000 1 826 1 chr6D.!!$R1 825
39 TraesCS3B01G596400 chr7D 16200651 16201480 829 False 1236.000000 1236 93.637000 1 826 1 chr7D.!!$F1 825
40 TraesCS3B01G596400 chr1B 194779417 194780248 831 True 1232.000000 1232 93.517000 1 826 1 chr1B.!!$R1 825
41 TraesCS3B01G596400 chr1B 555792901 555793748 847 True 994.000000 994 87.875000 1527 2385 1 chr1B.!!$R2 858
42 TraesCS3B01G596400 chrUn 349628610 349629441 831 False 1221.000000 1221 93.277000 1 826 1 chrUn.!!$F4 825
43 TraesCS3B01G596400 chrUn 10139058 10139931 873 False 1142.000000 1142 90.260000 1508 2385 1 chrUn.!!$F1 877
44 TraesCS3B01G596400 chrUn 50876237 50876926 689 False 846.000000 846 88.873000 1595 2288 1 chrUn.!!$F2 693
45 TraesCS3B01G596400 chrUn 50894310 50896746 2436 False 553.500000 985 90.010000 1508 2386 2 chrUn.!!$F5 878
46 TraesCS3B01G596400 chr7B 230215935 230216798 863 False 1168.000000 1168 91.076000 1508 2376 1 chr7B.!!$F1 868
47 TraesCS3B01G596400 chr7B 506620266 506621000 734 False 1160.000000 1160 95.380000 4294 5019 1 chr7B.!!$F2 725

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
399 406 0.036010 AATGGAACCTCTGAGTGCGG 60.036 55.0 3.66 0.0 0.00 5.69 F
1422 1443 0.179215 CCATGCGCAAGTTCTTCGTC 60.179 55.0 17.11 0.0 41.68 4.20 F
2149 3490 0.249953 TGGTTTGCATTGGCTTGCTG 60.250 50.0 12.87 0.0 43.18 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1487 0.179076 CGTACCTGATGCTGGCATGA 60.179 55.0 13.04 3.57 36.70 3.07 R
2378 6324 0.321919 CTACACATGCTGCCAGTGGT 60.322 55.0 20.61 11.64 37.58 4.16 R
4067 8461 0.177836 TCTATGGGGTGTGTCATGCG 59.822 55.0 0.00 0.00 0.00 4.73 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
83 85 2.283388 AGACGCTCCCACCCGTAA 60.283 61.111 0.00 0.00 37.87 3.18
132 134 1.078709 CAAGCCAGTGACCGTATGTG 58.921 55.000 0.00 0.00 0.00 3.21
179 186 3.521560 GACGCTATTTGGATCACTGACA 58.478 45.455 0.00 0.00 0.00 3.58
196 203 4.570772 ACTGACAATATAGAACGCGCAAAT 59.429 37.500 5.73 0.00 0.00 2.32
276 283 1.153066 TTCCTTGCCAGTTGCGTCA 60.153 52.632 0.00 0.00 45.60 4.35
312 319 4.901197 TTGTTAGCACAACTCCTATCCA 57.099 40.909 3.29 0.00 38.03 3.41
399 406 0.036010 AATGGAACCTCTGAGTGCGG 60.036 55.000 3.66 0.00 0.00 5.69
436 443 2.755655 AGAGTCAACTGTGTAGGATCCG 59.244 50.000 5.98 0.00 0.00 4.18
514 521 4.019681 TCCAAACGGGATAGAAGATGTTGT 60.020 41.667 0.00 0.00 42.15 3.32
526 534 0.523072 GATGTTGTCATGCGCAAGGT 59.477 50.000 17.11 0.00 34.06 3.50
679 688 0.995024 CCACCTGTCCTCCCAGAAAT 59.005 55.000 0.00 0.00 34.23 2.17
693 702 2.103094 CCAGAAATGTATCTCGGAGCCA 59.897 50.000 0.00 0.00 0.00 4.75
774 783 3.828451 ACCAAAAATGTGAGTCATCAGGG 59.172 43.478 0.00 0.00 35.66 4.45
777 786 5.221501 CCAAAAATGTGAGTCATCAGGGTTT 60.222 40.000 0.00 0.00 35.66 3.27
826 835 4.058817 GCCTAGATACTTATTGCGCAACT 58.941 43.478 27.64 18.03 0.00 3.16
827 836 5.227908 GCCTAGATACTTATTGCGCAACTA 58.772 41.667 27.64 18.19 0.00 2.24
828 837 5.694910 GCCTAGATACTTATTGCGCAACTAA 59.305 40.000 27.64 21.30 0.00 2.24
829 838 6.202188 GCCTAGATACTTATTGCGCAACTAAA 59.798 38.462 27.64 18.29 0.00 1.85
830 839 7.254658 GCCTAGATACTTATTGCGCAACTAAAA 60.255 37.037 27.64 15.81 0.00 1.52
831 840 8.609176 CCTAGATACTTATTGCGCAACTAAAAA 58.391 33.333 27.64 13.36 0.00 1.94
856 865 1.095600 GAAGAATTCACTTCCCCGGC 58.904 55.000 8.44 0.00 46.62 6.13
857 866 0.323451 AAGAATTCACTTCCCCGGCC 60.323 55.000 8.44 0.00 34.11 6.13
858 867 1.208165 AGAATTCACTTCCCCGGCCT 61.208 55.000 8.44 0.00 34.11 5.19
859 868 0.748367 GAATTCACTTCCCCGGCCTC 60.748 60.000 0.00 0.00 0.00 4.70
860 869 1.208165 AATTCACTTCCCCGGCCTCT 61.208 55.000 0.00 0.00 0.00 3.69
861 870 1.915078 ATTCACTTCCCCGGCCTCTG 61.915 60.000 0.00 0.00 0.00 3.35
862 871 4.785453 CACTTCCCCGGCCTCTGC 62.785 72.222 0.00 0.00 0.00 4.26
864 873 4.785453 CTTCCCCGGCCTCTGCAC 62.785 72.222 0.00 0.00 40.13 4.57
869 878 4.335647 CCGGCCTCTGCACCAACT 62.336 66.667 0.00 0.00 40.13 3.16
870 879 2.662596 CGGCCTCTGCACCAACTA 59.337 61.111 0.00 0.00 40.13 2.24
871 880 1.448540 CGGCCTCTGCACCAACTAG 60.449 63.158 0.00 0.00 40.13 2.57
872 881 1.078143 GGCCTCTGCACCAACTAGG 60.078 63.158 0.00 0.00 45.67 3.02
873 882 1.553690 GGCCTCTGCACCAACTAGGA 61.554 60.000 0.00 0.00 42.07 2.94
874 883 0.324943 GCCTCTGCACCAACTAGGAA 59.675 55.000 0.00 0.00 42.07 3.36
875 884 1.065126 GCCTCTGCACCAACTAGGAAT 60.065 52.381 0.00 0.00 42.07 3.01
876 885 2.170607 GCCTCTGCACCAACTAGGAATA 59.829 50.000 0.00 0.00 42.07 1.75
877 886 3.798202 CCTCTGCACCAACTAGGAATAC 58.202 50.000 0.00 0.00 41.22 1.89
878 887 3.197766 CCTCTGCACCAACTAGGAATACA 59.802 47.826 0.00 0.00 41.22 2.29
879 888 4.141620 CCTCTGCACCAACTAGGAATACAT 60.142 45.833 0.00 0.00 41.22 2.29
880 889 5.070446 CCTCTGCACCAACTAGGAATACATA 59.930 44.000 0.00 0.00 41.22 2.29
881 890 5.914033 TCTGCACCAACTAGGAATACATAC 58.086 41.667 0.00 0.00 41.22 2.39
882 891 4.689071 TGCACCAACTAGGAATACATACG 58.311 43.478 0.00 0.00 41.22 3.06
883 892 4.056050 GCACCAACTAGGAATACATACGG 58.944 47.826 0.00 0.00 41.22 4.02
884 893 4.056050 CACCAACTAGGAATACATACGGC 58.944 47.826 0.00 0.00 41.22 5.68
885 894 3.965347 ACCAACTAGGAATACATACGGCT 59.035 43.478 0.00 0.00 41.22 5.52
886 895 4.407945 ACCAACTAGGAATACATACGGCTT 59.592 41.667 0.00 0.00 41.22 4.35
887 896 5.104652 ACCAACTAGGAATACATACGGCTTT 60.105 40.000 0.00 0.00 41.22 3.51
888 897 5.820947 CCAACTAGGAATACATACGGCTTTT 59.179 40.000 0.00 0.00 41.22 2.27
889 898 6.317893 CCAACTAGGAATACATACGGCTTTTT 59.682 38.462 0.00 0.00 41.22 1.94
890 899 7.496591 CCAACTAGGAATACATACGGCTTTTTA 59.503 37.037 0.00 0.00 41.22 1.52
891 900 8.885722 CAACTAGGAATACATACGGCTTTTTAA 58.114 33.333 0.00 0.00 0.00 1.52
892 901 9.452287 AACTAGGAATACATACGGCTTTTTAAA 57.548 29.630 0.00 0.00 0.00 1.52
893 902 9.623000 ACTAGGAATACATACGGCTTTTTAAAT 57.377 29.630 0.00 0.00 0.00 1.40
1156 1177 3.489513 GGGTTCCGATCCTGGGGG 61.490 72.222 0.00 0.00 0.00 5.40
1298 1319 1.589993 CGCGCGAGGTGATGAAGAT 60.590 57.895 28.94 0.00 0.00 2.40
1372 1393 0.526662 CTACGGCCTCAAGAACGTCT 59.473 55.000 0.00 0.00 40.38 4.18
1422 1443 0.179215 CCATGCGCAAGTTCTTCGTC 60.179 55.000 17.11 0.00 41.68 4.20
1545 1566 4.757594 TGCAATGCATACCCAATCTTTTC 58.242 39.130 2.72 0.00 31.71 2.29
1754 3014 0.600255 ACAAAGCCGAGGAGACAACG 60.600 55.000 0.00 0.00 0.00 4.10
1795 3055 0.996462 GATCGTTCGATTCAACCGCA 59.004 50.000 9.05 0.00 0.00 5.69
1801 3061 2.679934 CGATTCAACCGCAGCTGCA 61.680 57.895 36.03 17.81 42.21 4.41
1811 3071 4.039357 CAGCTGCACTGCACTGCC 62.039 66.667 14.65 1.87 40.19 4.85
1921 3229 3.862744 ATCGATCTCCCCGCGCCTA 62.863 63.158 0.00 0.00 0.00 3.93
1987 3312 0.806102 ACCGACGCACACATATCAGC 60.806 55.000 0.00 0.00 0.00 4.26
2032 3371 7.408132 TTTTTCGAGTCAGTGAGTATTCAAG 57.592 36.000 0.00 0.00 34.49 3.02
2048 3387 7.914465 AGTATTCAAGCTTGATTTCTTCGATC 58.086 34.615 28.89 10.96 37.00 3.69
2084 3423 9.972106 AGAAGAGATGATTATTTTTCACTTCCT 57.028 29.630 0.00 0.00 36.85 3.36
2149 3490 0.249953 TGGTTTGCATTGGCTTGCTG 60.250 50.000 12.87 0.00 43.18 4.41
2190 3531 6.931840 AGTACAGAGAAAACAAGGTGAATCTC 59.068 38.462 0.00 0.00 0.00 2.75
2191 3532 4.752101 ACAGAGAAAACAAGGTGAATCTCG 59.248 41.667 0.00 0.00 0.00 4.04
2192 3533 4.991056 CAGAGAAAACAAGGTGAATCTCGA 59.009 41.667 0.00 0.00 0.00 4.04
2193 3534 5.641209 CAGAGAAAACAAGGTGAATCTCGAT 59.359 40.000 0.00 0.00 0.00 3.59
2194 3535 6.148480 CAGAGAAAACAAGGTGAATCTCGATT 59.852 38.462 0.00 0.00 0.00 3.34
2269 3612 1.153188 CCAGTATGCCGCCATCACA 60.153 57.895 0.00 0.00 32.85 3.58
2339 6284 6.125327 TCTTACAATGTCGTGAAGCAAAAA 57.875 33.333 0.00 0.00 0.00 1.94
2376 6322 2.224867 CCCATATCGGAAATCCTGGCTT 60.225 50.000 0.00 0.00 36.56 4.35
2378 6324 3.496692 CCATATCGGAAATCCTGGCTTCA 60.497 47.826 9.61 0.00 36.56 3.02
2403 6349 4.034858 CACTGGCAGCATGTGTAGAATTAG 59.965 45.833 15.89 0.00 39.31 1.73
2465 6413 7.175641 GCAGGGCATTATGTGTAGAATTATCTT 59.824 37.037 0.00 0.00 37.10 2.40
2515 6466 2.442212 TCGCGGTTAATGTGTTCTCA 57.558 45.000 6.13 0.00 0.00 3.27
2518 6469 2.415168 CGCGGTTAATGTGTTCTCATGT 59.585 45.455 0.00 0.00 0.00 3.21
2519 6470 3.615056 CGCGGTTAATGTGTTCTCATGTA 59.385 43.478 0.00 0.00 0.00 2.29
2520 6471 4.491924 CGCGGTTAATGTGTTCTCATGTAC 60.492 45.833 0.00 0.00 0.00 2.90
2521 6472 4.630069 GCGGTTAATGTGTTCTCATGTACT 59.370 41.667 0.00 0.00 0.00 2.73
2585 6770 3.485378 CGCAACCACAAAATGTAACACTG 59.515 43.478 0.00 0.00 0.00 3.66
2596 6781 5.530519 AATGTAACACTGTAATGTGCTCG 57.469 39.130 0.00 0.00 41.30 5.03
2597 6782 2.734606 TGTAACACTGTAATGTGCTCGC 59.265 45.455 0.00 0.00 41.30 5.03
2598 6783 2.169832 AACACTGTAATGTGCTCGCT 57.830 45.000 0.00 0.00 41.30 4.93
2599 6784 1.714794 ACACTGTAATGTGCTCGCTC 58.285 50.000 0.00 0.00 41.30 5.03
2600 6785 1.002366 CACTGTAATGTGCTCGCTCC 58.998 55.000 0.00 0.00 0.00 4.70
2601 6786 0.608130 ACTGTAATGTGCTCGCTCCA 59.392 50.000 0.00 0.00 0.00 3.86
2603 6788 2.076100 CTGTAATGTGCTCGCTCCAAA 58.924 47.619 0.00 0.00 0.00 3.28
2604 6789 2.483877 CTGTAATGTGCTCGCTCCAAAA 59.516 45.455 0.00 0.00 0.00 2.44
2605 6790 2.225491 TGTAATGTGCTCGCTCCAAAAC 59.775 45.455 0.00 0.00 0.00 2.43
2716 7096 7.906199 ATAAGAGATGGTATATGCTACTCCC 57.094 40.000 0.00 0.00 0.00 4.30
2717 7097 5.544441 AGAGATGGTATATGCTACTCCCT 57.456 43.478 0.00 0.00 0.00 4.20
2718 7098 5.909760 AGAGATGGTATATGCTACTCCCTT 58.090 41.667 0.00 0.00 0.00 3.95
2719 7099 5.955355 AGAGATGGTATATGCTACTCCCTTC 59.045 44.000 0.00 0.00 0.00 3.46
2720 7100 4.707448 AGATGGTATATGCTACTCCCTTCG 59.293 45.833 0.00 0.00 0.00 3.79
2721 7101 3.840991 TGGTATATGCTACTCCCTTCGT 58.159 45.455 0.00 0.00 0.00 3.85
2722 7102 3.825014 TGGTATATGCTACTCCCTTCGTC 59.175 47.826 0.00 0.00 0.00 4.20
2723 7103 3.193056 GGTATATGCTACTCCCTTCGTCC 59.807 52.174 0.00 0.00 0.00 4.79
2724 7104 1.700955 TATGCTACTCCCTTCGTCCC 58.299 55.000 0.00 0.00 0.00 4.46
2725 7105 0.325296 ATGCTACTCCCTTCGTCCCA 60.325 55.000 0.00 0.00 0.00 4.37
2726 7106 0.325296 TGCTACTCCCTTCGTCCCAT 60.325 55.000 0.00 0.00 0.00 4.00
2727 7107 1.063492 TGCTACTCCCTTCGTCCCATA 60.063 52.381 0.00 0.00 0.00 2.74
2728 7108 2.037144 GCTACTCCCTTCGTCCCATAA 58.963 52.381 0.00 0.00 0.00 1.90
2729 7109 2.633481 GCTACTCCCTTCGTCCCATAAT 59.367 50.000 0.00 0.00 0.00 1.28
2730 7110 3.555168 GCTACTCCCTTCGTCCCATAATG 60.555 52.174 0.00 0.00 0.00 1.90
2731 7111 2.478292 ACTCCCTTCGTCCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
2732 7112 3.649843 ACTCCCTTCGTCCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
2733 7113 4.035112 ACTCCCTTCGTCCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
2734 7114 4.101119 ACTCCCTTCGTCCCATAATGTAAG 59.899 45.833 0.00 0.00 0.00 2.34
2735 7115 4.291792 TCCCTTCGTCCCATAATGTAAGA 58.708 43.478 0.00 0.00 0.00 2.10
2736 7116 4.100498 TCCCTTCGTCCCATAATGTAAGAC 59.900 45.833 0.00 0.00 0.00 3.01
2737 7117 4.141801 CCCTTCGTCCCATAATGTAAGACA 60.142 45.833 0.00 0.00 0.00 3.41
2738 7118 5.454755 CCCTTCGTCCCATAATGTAAGACAT 60.455 44.000 0.00 0.00 41.31 3.06
2740 7120 6.542370 CCTTCGTCCCATAATGTAAGACATTT 59.458 38.462 9.92 0.00 45.80 2.32
2741 7121 7.067008 CCTTCGTCCCATAATGTAAGACATTTT 59.933 37.037 9.92 0.33 45.80 1.82
2742 7122 7.931578 TCGTCCCATAATGTAAGACATTTTT 57.068 32.000 9.92 0.00 45.80 1.94
2768 7148 8.851960 TGACACTATACTAGTATCAAAAAGCG 57.148 34.615 18.68 7.27 39.11 4.68
2769 7149 8.464404 TGACACTATACTAGTATCAAAAAGCGT 58.536 33.333 18.68 10.22 39.11 5.07
2770 7150 8.853469 ACACTATACTAGTATCAAAAAGCGTC 57.147 34.615 18.68 0.00 37.23 5.19
2771 7151 8.684520 ACACTATACTAGTATCAAAAAGCGTCT 58.315 33.333 18.68 0.00 37.23 4.18
2772 7152 9.517609 CACTATACTAGTATCAAAAAGCGTCTT 57.482 33.333 18.68 0.00 37.23 3.01
2777 7157 8.773404 ACTAGTATCAAAAAGCGTCTTACATT 57.227 30.769 0.00 0.00 0.00 2.71
2778 7158 9.865321 ACTAGTATCAAAAAGCGTCTTACATTA 57.135 29.630 0.00 0.00 0.00 1.90
2781 7161 8.612619 AGTATCAAAAAGCGTCTTACATTATGG 58.387 33.333 0.00 0.00 0.00 2.74
2782 7162 6.189677 TCAAAAAGCGTCTTACATTATGGG 57.810 37.500 0.00 0.00 0.00 4.00
2783 7163 5.941058 TCAAAAAGCGTCTTACATTATGGGA 59.059 36.000 0.00 0.00 0.00 4.37
2784 7164 5.813080 AAAAGCGTCTTACATTATGGGAC 57.187 39.130 0.00 1.75 0.00 4.46
2800 7180 1.840635 GGGACAGAGGGAGTATTTGCT 59.159 52.381 0.00 0.00 0.00 3.91
2812 7192 5.067805 GGGAGTATTTGCTTATTTCAGTGGG 59.932 44.000 0.00 0.00 0.00 4.61
2878 7260 6.378582 ACAAATTGTGCATAGTAGAAAACCG 58.621 36.000 0.00 0.00 0.00 4.44
3017 7401 1.686355 TCGACATGCTTGGTTTTGGT 58.314 45.000 4.44 0.00 0.00 3.67
3212 7598 5.923114 GCAGCTTGATACATTCTTCGAGATA 59.077 40.000 0.00 0.00 0.00 1.98
3274 7660 2.129146 ACGGTGACCTCGTTGACCA 61.129 57.895 0.00 0.00 37.61 4.02
3527 7920 4.201657 TGATCCGAAATCCACGACTACTA 58.798 43.478 0.00 0.00 0.00 1.82
3542 7935 4.017808 GACTACTAGAGAGGGTGCAAGAA 58.982 47.826 0.00 0.00 0.00 2.52
3551 7944 2.235898 GAGGGTGCAAGAAGAGATCAGT 59.764 50.000 0.00 0.00 0.00 3.41
3683 8076 4.113815 CCAAGGGAGGCCATGCGA 62.114 66.667 5.01 0.00 0.00 5.10
3796 8189 1.605712 CGAGCCGGAAGAGTTCAAACT 60.606 52.381 5.05 0.00 43.16 2.66
3906 8299 1.337384 ATCTATGAGCACGGCCACCA 61.337 55.000 2.24 0.00 0.00 4.17
4017 8410 0.908180 CCCCCTCCTAAAGACACCGT 60.908 60.000 0.00 0.00 0.00 4.83
4019 8412 1.338769 CCCCTCCTAAAGACACCGTTG 60.339 57.143 0.00 0.00 0.00 4.10
4067 8461 2.010145 TCTAAGCACAACGAGGCATC 57.990 50.000 0.00 0.00 0.00 3.91
4083 8479 0.749091 CATCGCATGACACACCCCAT 60.749 55.000 0.00 0.00 0.00 4.00
4084 8480 0.836606 ATCGCATGACACACCCCATA 59.163 50.000 0.00 0.00 0.00 2.74
4111 8512 4.843728 TCCGGTGAAAATTAATCTGCTCT 58.156 39.130 0.00 0.00 0.00 4.09
4122 8523 8.985315 AAATTAATCTGCTCTCATGTATGGAA 57.015 30.769 0.00 0.00 0.00 3.53
4236 8649 3.829948 CTCCTGCATGTTGCTGTAAAAG 58.170 45.455 0.75 0.00 45.31 2.27
4279 8692 8.986929 AGCATTGTTTAGATTATTAAGCCTCT 57.013 30.769 0.00 0.00 0.00 3.69
4280 8693 9.413734 AGCATTGTTTAGATTATTAAGCCTCTT 57.586 29.630 0.00 0.00 0.00 2.85
4281 8694 9.455847 GCATTGTTTAGATTATTAAGCCTCTTG 57.544 33.333 0.00 0.00 0.00 3.02
4506 8919 0.645868 GCCGTTTCGCTTAGCACTAG 59.354 55.000 4.70 0.00 0.00 2.57
4894 9307 2.023791 TGGGTAGGAGTAGTGGCATGTA 60.024 50.000 0.00 0.00 0.00 2.29
5045 9468 6.767524 CCTCTAGGGCAAGTACATATAGAG 57.232 45.833 0.00 3.59 36.25 2.43
5046 9469 5.654650 CCTCTAGGGCAAGTACATATAGAGG 59.345 48.000 15.83 15.83 44.95 3.69
5047 9470 6.215515 TCTAGGGCAAGTACATATAGAGGT 57.784 41.667 0.00 0.00 0.00 3.85
5048 9471 7.339177 TCTAGGGCAAGTACATATAGAGGTA 57.661 40.000 0.00 0.00 0.00 3.08
5049 9472 7.173722 TCTAGGGCAAGTACATATAGAGGTAC 58.826 42.308 4.20 4.20 42.02 3.34
5050 9473 5.712752 AGGGCAAGTACATATAGAGGTACA 58.287 41.667 14.07 0.00 43.71 2.90
5051 9474 6.141083 AGGGCAAGTACATATAGAGGTACAA 58.859 40.000 14.07 0.00 43.71 2.41
5052 9475 6.614087 AGGGCAAGTACATATAGAGGTACAAA 59.386 38.462 14.07 0.00 43.71 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 179 2.857748 TGCGCGTTCTATATTGTCAGTG 59.142 45.455 8.43 0.00 0.00 3.66
196 203 3.620488 ACACCTCTTCTTTCAGTGCAAA 58.380 40.909 0.00 0.00 31.58 3.68
253 260 1.606668 CGCAACTGGCAAGGAAGTAAA 59.393 47.619 0.00 0.00 45.17 2.01
308 315 8.599624 AAGATTTTCATGTGGTATCTTTGGAT 57.400 30.769 0.00 0.00 33.08 3.41
372 379 5.530171 CACTCAGAGGTTCCATTGGATAATG 59.470 44.000 6.15 2.36 42.66 1.90
399 406 1.749634 ACTCTATGTACCGTGCACTCC 59.250 52.381 16.19 0.11 0.00 3.85
436 443 2.362397 TCGCTGGAATCTCACTACATCC 59.638 50.000 0.00 0.00 0.00 3.51
514 521 2.046023 CCTCCACCTTGCGCATGA 60.046 61.111 23.56 2.86 0.00 3.07
526 534 1.009997 AGGGATTTGATTGGCCTCCA 58.990 50.000 3.32 0.00 0.00 3.86
693 702 4.271696 TGGATCATTCGCGATAAAGGAT 57.728 40.909 10.88 8.06 30.42 3.24
774 783 3.427503 CGTTGTCCCAGGCATATTGAAAC 60.428 47.826 0.00 0.00 0.00 2.78
777 786 2.016604 GCGTTGTCCCAGGCATATTGA 61.017 52.381 0.00 0.00 0.00 2.57
837 846 1.095600 GCCGGGGAAGTGAATTCTTC 58.904 55.000 2.18 3.05 41.92 2.87
838 847 0.323451 GGCCGGGGAAGTGAATTCTT 60.323 55.000 2.18 0.00 38.07 2.52
839 848 1.208165 AGGCCGGGGAAGTGAATTCT 61.208 55.000 2.18 0.00 38.07 2.40
840 849 0.748367 GAGGCCGGGGAAGTGAATTC 60.748 60.000 2.18 0.00 37.17 2.17
841 850 1.208165 AGAGGCCGGGGAAGTGAATT 61.208 55.000 2.18 0.00 0.00 2.17
842 851 1.616628 AGAGGCCGGGGAAGTGAAT 60.617 57.895 2.18 0.00 0.00 2.57
843 852 2.203938 AGAGGCCGGGGAAGTGAA 60.204 61.111 2.18 0.00 0.00 3.18
844 853 3.003173 CAGAGGCCGGGGAAGTGA 61.003 66.667 2.18 0.00 0.00 3.41
845 854 4.785453 GCAGAGGCCGGGGAAGTG 62.785 72.222 2.18 0.00 0.00 3.16
847 856 4.785453 GTGCAGAGGCCGGGGAAG 62.785 72.222 2.18 0.00 40.13 3.46
852 861 2.859273 CTAGTTGGTGCAGAGGCCGG 62.859 65.000 0.00 0.00 40.13 6.13
853 862 1.448540 CTAGTTGGTGCAGAGGCCG 60.449 63.158 0.00 0.00 40.13 6.13
854 863 1.078143 CCTAGTTGGTGCAGAGGCC 60.078 63.158 0.00 0.00 40.13 5.19
855 864 0.324943 TTCCTAGTTGGTGCAGAGGC 59.675 55.000 0.00 0.00 37.07 4.70
856 865 3.197766 TGTATTCCTAGTTGGTGCAGAGG 59.802 47.826 0.00 0.00 37.07 3.69
857 866 4.471904 TGTATTCCTAGTTGGTGCAGAG 57.528 45.455 0.00 0.00 37.07 3.35
858 867 5.451381 CGTATGTATTCCTAGTTGGTGCAGA 60.451 44.000 0.00 0.00 37.07 4.26
859 868 4.745125 CGTATGTATTCCTAGTTGGTGCAG 59.255 45.833 0.00 0.00 37.07 4.41
860 869 4.442332 CCGTATGTATTCCTAGTTGGTGCA 60.442 45.833 0.00 0.00 37.07 4.57
861 870 4.056050 CCGTATGTATTCCTAGTTGGTGC 58.944 47.826 0.00 0.00 37.07 5.01
862 871 4.056050 GCCGTATGTATTCCTAGTTGGTG 58.944 47.826 0.00 0.00 37.07 4.17
863 872 3.965347 AGCCGTATGTATTCCTAGTTGGT 59.035 43.478 0.00 0.00 37.07 3.67
864 873 4.602340 AGCCGTATGTATTCCTAGTTGG 57.398 45.455 0.00 0.00 37.10 3.77
865 874 6.920569 AAAAGCCGTATGTATTCCTAGTTG 57.079 37.500 0.00 0.00 0.00 3.16
866 875 9.452287 TTTAAAAAGCCGTATGTATTCCTAGTT 57.548 29.630 0.00 0.00 0.00 2.24
867 876 9.623000 ATTTAAAAAGCCGTATGTATTCCTAGT 57.377 29.630 0.00 0.00 0.00 2.57
899 908 8.745590 GGCCTTTGGAGATTAAAAATTGTAGTA 58.254 33.333 0.00 0.00 0.00 1.82
900 909 7.454694 AGGCCTTTGGAGATTAAAAATTGTAGT 59.545 33.333 0.00 0.00 0.00 2.73
901 910 7.840931 AGGCCTTTGGAGATTAAAAATTGTAG 58.159 34.615 0.00 0.00 0.00 2.74
902 911 7.673926 AGAGGCCTTTGGAGATTAAAAATTGTA 59.326 33.333 6.77 0.00 0.00 2.41
903 912 6.498303 AGAGGCCTTTGGAGATTAAAAATTGT 59.502 34.615 6.77 0.00 0.00 2.71
904 913 6.939622 AGAGGCCTTTGGAGATTAAAAATTG 58.060 36.000 6.77 0.00 0.00 2.32
905 914 8.664669 TTAGAGGCCTTTGGAGATTAAAAATT 57.335 30.769 6.77 0.00 0.00 1.82
906 915 7.343057 CCTTAGAGGCCTTTGGAGATTAAAAAT 59.657 37.037 6.77 0.00 0.00 1.82
907 916 6.663523 CCTTAGAGGCCTTTGGAGATTAAAAA 59.336 38.462 6.77 0.00 0.00 1.94
908 917 6.187682 CCTTAGAGGCCTTTGGAGATTAAAA 58.812 40.000 6.77 0.00 0.00 1.52
909 918 5.755849 CCTTAGAGGCCTTTGGAGATTAAA 58.244 41.667 6.77 0.00 0.00 1.52
910 919 5.373812 CCTTAGAGGCCTTTGGAGATTAA 57.626 43.478 6.77 0.00 0.00 1.40
912 921 3.941704 CCTTAGAGGCCTTTGGAGATT 57.058 47.619 6.77 0.00 0.00 2.40
1298 1319 3.295273 AGCAGTCCTCGTCGTGCA 61.295 61.111 7.42 0.00 38.44 4.57
1464 1485 2.368439 GTACCTGATGCTGGCATGAAA 58.632 47.619 13.04 0.00 36.70 2.69
1466 1487 0.179076 CGTACCTGATGCTGGCATGA 60.179 55.000 13.04 3.57 36.70 3.07
1469 1490 1.987306 TCCGTACCTGATGCTGGCA 60.987 57.895 0.00 0.00 0.00 4.92
1505 1526 1.620822 CATACCCTTGCATTAGCCCC 58.379 55.000 0.00 0.00 41.13 5.80
1506 1527 0.961753 GCATACCCTTGCATTAGCCC 59.038 55.000 0.00 0.00 42.31 5.19
1566 1587 8.043113 TGTGATATAAAGGCATATAGGAGCTTG 58.957 37.037 0.00 0.00 0.00 4.01
1611 1632 6.262496 TCTTCTTCGTTTCTCTTCTCTGTACA 59.738 38.462 0.00 0.00 0.00 2.90
1754 3014 3.474806 CGACACATTCCAGGTCGC 58.525 61.111 0.00 0.00 46.25 5.19
1801 3061 3.325753 GAGGAGGGGCAGTGCAGT 61.326 66.667 18.61 0.00 0.00 4.40
1877 3185 4.022416 GCTAGATCCAAGATGACAGATCGT 60.022 45.833 0.00 0.00 40.06 3.73
1921 3229 0.895100 TTGGAGGCAAAGCAGCGAAT 60.895 50.000 0.00 0.00 34.64 3.34
1932 3240 1.533625 CCGTTTCTCAATTGGAGGCA 58.466 50.000 5.42 0.00 44.19 4.75
1972 3297 0.744414 GGTGGCTGATATGTGTGCGT 60.744 55.000 0.00 0.00 0.00 5.24
1987 3312 2.113860 ACAATCACAGGAATCGGTGG 57.886 50.000 4.31 0.00 39.12 4.61
2026 3365 6.373774 ACAGATCGAAGAAATCAAGCTTGAAT 59.626 34.615 31.55 21.92 43.58 2.57
2032 3371 6.654793 ACTAACAGATCGAAGAAATCAAGC 57.345 37.500 0.00 0.00 43.58 4.01
2149 3490 4.574828 TCTGTACTGCTTCACAAGTTTTCC 59.425 41.667 0.00 0.00 0.00 3.13
2239 3580 0.468585 CATACTGGCATGGTGGGCAT 60.469 55.000 0.00 0.00 42.89 4.40
2339 6284 5.180492 CGATATGGGTATGCGTGGTAAAATT 59.820 40.000 0.00 0.00 0.00 1.82
2340 6285 4.693566 CGATATGGGTATGCGTGGTAAAAT 59.306 41.667 0.00 0.00 0.00 1.82
2376 6322 1.601477 CACATGCTGCCAGTGGTGA 60.601 57.895 11.74 0.00 0.00 4.02
2378 6324 0.321919 CTACACATGCTGCCAGTGGT 60.322 55.000 20.61 11.64 37.58 4.16
2465 6413 3.519107 TGCAGGAGAATATGTTGGAGTGA 59.481 43.478 0.00 0.00 0.00 3.41
2520 6471 9.956797 GCTTACAAAATACACAATGCAAATAAG 57.043 29.630 0.00 0.00 0.00 1.73
2521 6472 9.481340 TGCTTACAAAATACACAATGCAAATAA 57.519 25.926 0.00 0.00 0.00 1.40
2541 6678 2.610374 TGTCGTGTTTCCTTGTGCTTAC 59.390 45.455 0.00 0.00 0.00 2.34
2551 6688 1.010462 GGTTGCGTGTCGTGTTTCC 60.010 57.895 0.00 0.00 0.00 3.13
2585 6770 2.225491 TGTTTTGGAGCGAGCACATTAC 59.775 45.455 0.00 0.00 0.00 1.89
2596 6781 3.502191 TCTGTGTGTTTGTTTTGGAGC 57.498 42.857 0.00 0.00 0.00 4.70
2597 6782 3.859386 GCTTCTGTGTGTTTGTTTTGGAG 59.141 43.478 0.00 0.00 0.00 3.86
2598 6783 3.256879 TGCTTCTGTGTGTTTGTTTTGGA 59.743 39.130 0.00 0.00 0.00 3.53
2599 6784 3.583806 TGCTTCTGTGTGTTTGTTTTGG 58.416 40.909 0.00 0.00 0.00 3.28
2600 6785 5.588568 TTTGCTTCTGTGTGTTTGTTTTG 57.411 34.783 0.00 0.00 0.00 2.44
2601 6786 5.525378 TGTTTTGCTTCTGTGTGTTTGTTTT 59.475 32.000 0.00 0.00 0.00 2.43
2603 6788 4.626042 TGTTTTGCTTCTGTGTGTTTGTT 58.374 34.783 0.00 0.00 0.00 2.83
2604 6789 4.250116 TGTTTTGCTTCTGTGTGTTTGT 57.750 36.364 0.00 0.00 0.00 2.83
2605 6790 5.177327 AGTTTGTTTTGCTTCTGTGTGTTTG 59.823 36.000 0.00 0.00 0.00 2.93
2712 7092 4.344102 TCTTACATTATGGGACGAAGGGAG 59.656 45.833 0.00 0.00 0.00 4.30
2713 7093 4.100498 GTCTTACATTATGGGACGAAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
2714 7094 4.141801 TGTCTTACATTATGGGACGAAGGG 60.142 45.833 0.00 0.00 0.00 3.95
2715 7095 5.018539 TGTCTTACATTATGGGACGAAGG 57.981 43.478 0.00 0.00 0.00 3.46
2751 7131 9.865321 AATGTAAGACGCTTTTTGATACTAGTA 57.135 29.630 4.77 4.77 0.00 1.82
2752 7132 8.773404 AATGTAAGACGCTTTTTGATACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
2755 7135 8.612619 CCATAATGTAAGACGCTTTTTGATACT 58.387 33.333 0.00 0.00 0.00 2.12
2756 7136 7.855904 CCCATAATGTAAGACGCTTTTTGATAC 59.144 37.037 0.00 0.00 0.00 2.24
2757 7137 7.771361 TCCCATAATGTAAGACGCTTTTTGATA 59.229 33.333 0.00 0.00 0.00 2.15
2758 7138 6.601613 TCCCATAATGTAAGACGCTTTTTGAT 59.398 34.615 0.00 0.00 0.00 2.57
2759 7139 5.941058 TCCCATAATGTAAGACGCTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
2760 7140 6.027749 GTCCCATAATGTAAGACGCTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
2761 7141 5.708230 TGTCCCATAATGTAAGACGCTTTTT 59.292 36.000 0.00 0.00 0.00 1.94
2762 7142 5.250200 TGTCCCATAATGTAAGACGCTTTT 58.750 37.500 0.00 0.00 0.00 2.27
2763 7143 4.839121 TGTCCCATAATGTAAGACGCTTT 58.161 39.130 0.00 0.00 0.00 3.51
2764 7144 4.161565 TCTGTCCCATAATGTAAGACGCTT 59.838 41.667 0.00 0.00 0.00 4.68
2765 7145 3.704566 TCTGTCCCATAATGTAAGACGCT 59.295 43.478 0.00 0.00 0.00 5.07
2766 7146 4.051922 CTCTGTCCCATAATGTAAGACGC 58.948 47.826 0.00 0.00 0.00 5.19
2767 7147 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
2768 7148 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
2769 7149 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2770 7150 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
2771 7151 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2772 7152 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2773 7153 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2774 7154 5.832539 AATACTCCCTCTGTCCCATAATG 57.167 43.478 0.00 0.00 0.00 1.90
2775 7155 5.456763 GCAAATACTCCCTCTGTCCCATAAT 60.457 44.000 0.00 0.00 0.00 1.28
2776 7156 4.141482 GCAAATACTCCCTCTGTCCCATAA 60.141 45.833 0.00 0.00 0.00 1.90
2777 7157 3.391296 GCAAATACTCCCTCTGTCCCATA 59.609 47.826 0.00 0.00 0.00 2.74
2778 7158 2.173569 GCAAATACTCCCTCTGTCCCAT 59.826 50.000 0.00 0.00 0.00 4.00
2779 7159 1.559682 GCAAATACTCCCTCTGTCCCA 59.440 52.381 0.00 0.00 0.00 4.37
2780 7160 1.840635 AGCAAATACTCCCTCTGTCCC 59.159 52.381 0.00 0.00 0.00 4.46
2781 7161 3.636153 AAGCAAATACTCCCTCTGTCC 57.364 47.619 0.00 0.00 0.00 4.02
2782 7162 6.823689 TGAAATAAGCAAATACTCCCTCTGTC 59.176 38.462 0.00 0.00 0.00 3.51
2783 7163 6.721318 TGAAATAAGCAAATACTCCCTCTGT 58.279 36.000 0.00 0.00 0.00 3.41
2784 7164 6.825721 ACTGAAATAAGCAAATACTCCCTCTG 59.174 38.462 0.00 0.00 0.00 3.35
2785 7165 6.825721 CACTGAAATAAGCAAATACTCCCTCT 59.174 38.462 0.00 0.00 0.00 3.69
2786 7166 6.038714 CCACTGAAATAAGCAAATACTCCCTC 59.961 42.308 0.00 0.00 0.00 4.30
2787 7167 5.888161 CCACTGAAATAAGCAAATACTCCCT 59.112 40.000 0.00 0.00 0.00 4.20
2788 7168 5.067805 CCCACTGAAATAAGCAAATACTCCC 59.932 44.000 0.00 0.00 0.00 4.30
2789 7169 5.652452 ACCCACTGAAATAAGCAAATACTCC 59.348 40.000 0.00 0.00 0.00 3.85
2790 7170 6.759497 ACCCACTGAAATAAGCAAATACTC 57.241 37.500 0.00 0.00 0.00 2.59
2791 7171 8.644374 TTAACCCACTGAAATAAGCAAATACT 57.356 30.769 0.00 0.00 0.00 2.12
2792 7172 9.301153 CATTAACCCACTGAAATAAGCAAATAC 57.699 33.333 0.00 0.00 0.00 1.89
2793 7173 9.030452 ACATTAACCCACTGAAATAAGCAAATA 57.970 29.630 0.00 0.00 0.00 1.40
2794 7174 7.818930 CACATTAACCCACTGAAATAAGCAAAT 59.181 33.333 0.00 0.00 0.00 2.32
2798 7178 5.650543 CCACATTAACCCACTGAAATAAGC 58.349 41.667 0.00 0.00 0.00 3.09
2800 7180 5.047660 GTGCCACATTAACCCACTGAAATAA 60.048 40.000 0.00 0.00 0.00 1.40
2812 7192 1.463444 GAGGACGTGTGCCACATTAAC 59.537 52.381 0.00 0.00 33.40 2.01
2878 7260 0.740737 GGGTGCAATACAGTCCATGC 59.259 55.000 0.00 0.00 39.22 4.06
3001 7385 3.902881 TTTCACCAAAACCAAGCATGT 57.097 38.095 0.00 0.00 0.00 3.21
3017 7401 3.874543 ACTTGTCGCTGTTGTACATTTCA 59.125 39.130 0.00 0.00 0.00 2.69
3125 7511 1.583495 CGACTAGGCGGCCGATGATA 61.583 60.000 33.48 13.87 0.00 2.15
3212 7598 3.380637 GGTCAAGATGCTGCTCAATGATT 59.619 43.478 0.00 0.00 0.00 2.57
3254 7640 0.531311 GGTCAACGAGGTCACCGTTT 60.531 55.000 0.00 0.00 46.52 3.60
3274 7660 5.328565 TGTCCTTCCATAGATCGATGAGAT 58.671 41.667 16.51 0.00 43.51 2.75
3527 7920 2.317371 TCTCTTCTTGCACCCTCTCT 57.683 50.000 0.00 0.00 0.00 3.10
3542 7935 1.593787 CACCACGGCACTGATCTCT 59.406 57.895 0.00 0.00 0.00 3.10
3551 7944 3.164977 TTGTCTCCCACCACGGCA 61.165 61.111 0.00 0.00 0.00 5.69
3683 8076 4.665009 TCATAGCCCCCAATTCTAATGTCT 59.335 41.667 0.00 0.00 0.00 3.41
3796 8189 2.555325 TCGCTCGTTTCAAACCTCTCTA 59.445 45.455 0.00 0.00 0.00 2.43
3906 8299 2.045926 GGCCAGCGTGAACTCCAT 60.046 61.111 0.00 0.00 0.00 3.41
4067 8461 0.177836 TCTATGGGGTGTGTCATGCG 59.822 55.000 0.00 0.00 0.00 4.73
4083 8479 6.706270 GCAGATTAATTTTCACCGGATCTCTA 59.294 38.462 9.46 0.00 0.00 2.43
4084 8480 5.529060 GCAGATTAATTTTCACCGGATCTCT 59.471 40.000 9.46 0.00 0.00 3.10
4122 8523 8.284945 AGTGACAAGATTACATGCATGTTTAT 57.715 30.769 35.45 26.99 41.97 1.40
4202 8614 4.581824 ACATGCAGGAGCCAAGTTATTATG 59.418 41.667 4.84 0.00 41.13 1.90
4236 8649 9.807649 AACAATGCTTTTTGTATATTCATCTCC 57.192 29.630 1.60 0.00 38.85 3.71
4255 8668 9.455847 CAAGAGGCTTAATAATCTAAACAATGC 57.544 33.333 0.00 0.00 0.00 3.56
4283 8696 2.393271 CTTCAAGAAGGATCACGCCT 57.607 50.000 1.86 0.00 40.93 5.52
4506 8919 0.949105 CTCCACCACGGCAAGTACAC 60.949 60.000 0.00 0.00 33.14 2.90
4894 9307 3.028850 CTGAATCCACCATCTTGGCAAT 58.971 45.455 0.00 0.00 42.67 3.56
5022 9445 5.654650 CCTCTATATGTACTTGCCCTAGAGG 59.345 48.000 15.84 15.84 42.45 3.69
5023 9446 6.249951 ACCTCTATATGTACTTGCCCTAGAG 58.750 44.000 0.00 0.00 33.61 2.43
5024 9447 6.215515 ACCTCTATATGTACTTGCCCTAGA 57.784 41.667 0.00 0.00 0.00 2.43
5025 9448 6.946583 TGTACCTCTATATGTACTTGCCCTAG 59.053 42.308 0.00 0.00 38.48 3.02
5026 9449 6.855667 TGTACCTCTATATGTACTTGCCCTA 58.144 40.000 0.00 0.00 38.48 3.53
5027 9450 5.712752 TGTACCTCTATATGTACTTGCCCT 58.287 41.667 0.00 0.00 38.48 5.19
5028 9451 6.415206 TTGTACCTCTATATGTACTTGCCC 57.585 41.667 0.00 0.00 38.48 5.36


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

AutoCloner maintained by Alex Coulton.