Multiple sequence alignment - TraesCS1A01G248500

Loading Multiple Alignment...

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 TraesCS1A01G248500 chr1A 100.000 9911 0 0 1 9911 440781455 440771545 0.000000e+00 18303.0
1 TraesCS1A01G248500 chr1A 92.683 1025 69 6 8892 9911 305080369 305079346 0.000000e+00 1472.0
2 TraesCS1A01G248500 chr2A 95.341 4422 196 6 1920 6338 702078388 702082802 0.000000e+00 7016.0
3 TraesCS1A01G248500 chr2A 94.879 1699 76 6 6336 8025 702082838 702084534 0.000000e+00 2645.0
4 TraesCS1A01G248500 chr2A 93.307 1031 64 5 8886 9911 501877379 501878409 0.000000e+00 1517.0
5 TraesCS1A01G248500 chr5B 95.268 4417 205 4 1924 6338 677830889 677826475 0.000000e+00 6996.0
6 TraesCS1A01G248500 chr5B 95.173 4413 203 7 1932 6338 558410122 558414530 0.000000e+00 6961.0
7 TraesCS1A01G248500 chr5B 94.932 1697 76 7 6336 8025 558414566 558416259 0.000000e+00 2649.0
8 TraesCS1A01G248500 chr5B 92.318 742 57 0 5597 6338 281361919 281362660 0.000000e+00 1055.0
9 TraesCS1A01G248500 chr5B 88.500 400 46 0 5635 6034 603398216 603397817 1.500000e-132 484.0
10 TraesCS1A01G248500 chr4A 95.268 4417 204 5 1924 6338 665652665 665657078 0.000000e+00 6994.0
11 TraesCS1A01G248500 chr4A 94.030 1005 57 3 8891 9893 471563055 471562052 0.000000e+00 1520.0
12 TraesCS1A01G248500 chr4A 93.463 1025 62 5 8890 9911 118730718 118729696 0.000000e+00 1517.0
13 TraesCS1A01G248500 chr4A 92.864 1023 69 3 8891 9911 499212786 499211766 0.000000e+00 1482.0
14 TraesCS1A01G248500 chr2B 95.181 4420 204 9 1922 6338 790869567 790873980 0.000000e+00 6974.0
15 TraesCS1A01G248500 chr2B 94.947 1702 72 7 6336 8026 798688698 798687000 0.000000e+00 2654.0
16 TraesCS1A01G248500 chr1D 95.162 4423 200 10 1920 6338 470511064 470506652 0.000000e+00 6970.0
17 TraesCS1A01G248500 chr1D 94.245 1390 45 8 543 1921 341030322 341028957 0.000000e+00 2091.0
18 TraesCS1A01G248500 chr1D 96.083 868 34 0 8025 8892 341028962 341028095 0.000000e+00 1415.0
19 TraesCS1A01G248500 chr1D 91.590 868 73 0 8025 8892 465902130 465901263 0.000000e+00 1199.0
20 TraesCS1A01G248500 chr1D 85.824 1037 113 19 911 1921 430123609 430124637 0.000000e+00 1070.0
21 TraesCS1A01G248500 chr1D 94.721 341 16 2 1 340 341030801 341030462 6.820000e-146 529.0
22 TraesCS1A01G248500 chr1D 97.590 83 2 0 463 545 341030464 341030382 1.040000e-29 143.0
23 TraesCS1A01G248500 chr7A 94.960 4425 208 10 1924 6338 721578086 721582505 0.000000e+00 6922.0
24 TraesCS1A01G248500 chr7B 94.876 4430 212 12 1916 6338 24271571 24275992 0.000000e+00 6909.0
25 TraesCS1A01G248500 chr3A 94.885 4418 218 7 1924 6338 26500268 26495856 0.000000e+00 6900.0
26 TraesCS1A01G248500 chr3A 93.073 1025 66 4 8891 9911 703165887 703164864 0.000000e+00 1495.0
27 TraesCS1A01G248500 chr3A 92.390 1025 73 5 8891 9911 170458749 170459772 0.000000e+00 1456.0
28 TraesCS1A01G248500 chr3A 92.980 869 61 0 8025 8893 127857921 127857053 0.000000e+00 1267.0
29 TraesCS1A01G248500 chr3A 91.830 869 69 1 8025 8893 127821677 127820811 0.000000e+00 1210.0
30 TraesCS1A01G248500 chr3A 82.164 342 26 16 838 1156 127066250 127066579 2.750000e-65 261.0
31 TraesCS1A01G248500 chr3A 89.474 95 6 1 744 838 127834905 127834815 6.290000e-22 117.0
32 TraesCS1A01G248500 chr5A 95.465 1698 65 9 6336 8025 601251832 601253525 0.000000e+00 2699.0
33 TraesCS1A01G248500 chr5A 92.962 1023 70 2 8891 9911 132380906 132381928 0.000000e+00 1489.0
34 TraesCS1A01G248500 chr2D 95.068 1703 72 8 6336 8030 35275614 35277312 0.000000e+00 2669.0
35 TraesCS1A01G248500 chr2D 95.165 1696 72 6 6336 8023 35306808 35308501 0.000000e+00 2669.0
36 TraesCS1A01G248500 chr2D 94.572 1695 86 3 6336 8026 638747571 638749263 0.000000e+00 2615.0
37 TraesCS1A01G248500 chr2D 92.491 1638 103 4 4701 6338 20303201 20304818 0.000000e+00 2326.0
38 TraesCS1A01G248500 chr2D 96.154 858 33 0 5481 6338 643112917 643112060 0.000000e+00 1402.0
39 TraesCS1A01G248500 chr6B 94.808 1695 79 6 6336 8025 30301907 30300217 0.000000e+00 2634.0
40 TraesCS1A01G248500 chr6B 85.821 402 49 5 1953 2350 1371334 1370937 4.280000e-113 420.0
41 TraesCS1A01G248500 chr6A 94.749 1695 80 6 6336 8025 24184839 24186529 0.000000e+00 2628.0
42 TraesCS1A01G248500 chr6A 92.871 1024 69 4 8891 9911 28860464 28859442 0.000000e+00 1483.0
43 TraesCS1A01G248500 chr1B 93.739 1134 40 8 799 1921 456714357 456713244 0.000000e+00 1672.0
44 TraesCS1A01G248500 chr1B 94.585 868 47 0 8025 8892 456713249 456712382 0.000000e+00 1343.0
45 TraesCS1A01G248500 chr1B 94.273 227 10 1 543 769 456714580 456714357 2.650000e-90 344.0
46 TraesCS1A01G248500 chr1B 87.273 220 19 4 226 439 456715394 456715178 9.950000e-60 243.0
47 TraesCS1A01G248500 chr1B 95.614 114 5 0 432 545 456714778 456714665 6.110000e-42 183.0
48 TraesCS1A01G248500 chr3B 90.752 1157 79 11 771 1921 172981949 172980815 0.000000e+00 1519.0
49 TraesCS1A01G248500 chr3B 88.844 1228 97 20 706 1921 172092163 172093362 0.000000e+00 1472.0
50 TraesCS1A01G248500 chr3B 88.020 1227 106 20 706 1921 172211621 172212817 0.000000e+00 1413.0
51 TraesCS1A01G248500 chr3B 89.727 1100 77 18 838 1921 146982530 146981451 0.000000e+00 1373.0
52 TraesCS1A01G248500 chr3B 88.718 1108 94 16 833 1921 172052070 172053165 0.000000e+00 1325.0
53 TraesCS1A01G248500 chr3B 90.101 990 76 9 947 1921 172170543 172171525 0.000000e+00 1266.0
54 TraesCS1A01G248500 chr3B 92.635 869 64 0 8025 8893 172980820 172979952 0.000000e+00 1251.0
55 TraesCS1A01G248500 chr3B 89.697 990 80 9 947 1921 173007801 173006819 0.000000e+00 1243.0
56 TraesCS1A01G248500 chr3B 92.405 869 66 0 8025 8893 146981456 146980588 0.000000e+00 1240.0
57 TraesCS1A01G248500 chr3B 85.603 514 49 12 1 503 146983438 146982939 5.310000e-142 516.0
58 TraesCS1A01G248500 chr3B 86.479 355 31 9 187 530 172091579 172091927 3.380000e-99 374.0
59 TraesCS1A01G248500 chr3B 86.197 355 31 10 187 530 172211093 172211440 1.570000e-97 368.0
60 TraesCS1A01G248500 chr3B 89.879 247 22 3 1 245 173000402 173000157 2.080000e-81 315.0
61 TraesCS1A01G248500 chr3B 78.767 292 37 18 557 838 146982859 146982583 1.320000e-38 172.0
62 TraesCS1A01G248500 chr3B 89.091 110 5 2 545 647 172092037 172092146 8.080000e-26 130.0
63 TraesCS1A01G248500 chr3B 86.076 79 7 2 1 78 172091497 172091572 2.290000e-11 82.4
64 TraesCS1A01G248500 chr3D 89.192 1101 82 16 841 1921 121268889 121267806 0.000000e+00 1339.0
65 TraesCS1A01G248500 chr3D 88.949 1104 85 14 838 1921 121334847 121333761 0.000000e+00 1328.0
66 TraesCS1A01G248500 chr3D 89.898 980 86 7 947 1921 120142523 120143494 0.000000e+00 1249.0
67 TraesCS1A01G248500 chr3D 91.830 869 71 0 8025 8893 121267811 121266943 0.000000e+00 1212.0
68 TraesCS1A01G248500 chr3D 88.288 555 38 12 1 534 121269864 121269316 3.020000e-179 640.0
69 TraesCS1A01G248500 chr3D 87.188 320 23 8 80 385 116075217 116074902 2.050000e-91 348.0
70 TraesCS1A01G248500 chr3D 85.938 192 14 4 656 838 121335085 121334898 1.020000e-44 193.0
71 TraesCS1A01G248500 chr3D 80.198 303 21 12 545 838 121269212 121268940 3.650000e-44 191.0
72 TraesCS1A01G248500 chr3D 93.103 58 3 1 833 889 120124777 120124834 6.380000e-12 84.2
73 TraesCS1A01G248500 chr6D 91.426 933 68 6 994 1921 452127913 452126988 0.000000e+00 1269.0
74 TraesCS1A01G248500 chr6D 91.945 869 70 0 8025 8893 452126993 452126125 0.000000e+00 1218.0


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 TraesCS1A01G248500 chr1A 440771545 440781455 9910 True 18303.00 18303 100.00000 1 9911 1 chr1A.!!$R2 9910
1 TraesCS1A01G248500 chr1A 305079346 305080369 1023 True 1472.00 1472 92.68300 8892 9911 1 chr1A.!!$R1 1019
2 TraesCS1A01G248500 chr2A 702078388 702084534 6146 False 4830.50 7016 95.11000 1920 8025 2 chr2A.!!$F2 6105
3 TraesCS1A01G248500 chr2A 501877379 501878409 1030 False 1517.00 1517 93.30700 8886 9911 1 chr2A.!!$F1 1025
4 TraesCS1A01G248500 chr5B 677826475 677830889 4414 True 6996.00 6996 95.26800 1924 6338 1 chr5B.!!$R2 4414
5 TraesCS1A01G248500 chr5B 558410122 558416259 6137 False 4805.00 6961 95.05250 1932 8025 2 chr5B.!!$F2 6093
6 TraesCS1A01G248500 chr5B 281361919 281362660 741 False 1055.00 1055 92.31800 5597 6338 1 chr5B.!!$F1 741
7 TraesCS1A01G248500 chr4A 665652665 665657078 4413 False 6994.00 6994 95.26800 1924 6338 1 chr4A.!!$F1 4414
8 TraesCS1A01G248500 chr4A 471562052 471563055 1003 True 1520.00 1520 94.03000 8891 9893 1 chr4A.!!$R2 1002
9 TraesCS1A01G248500 chr4A 118729696 118730718 1022 True 1517.00 1517 93.46300 8890 9911 1 chr4A.!!$R1 1021
10 TraesCS1A01G248500 chr4A 499211766 499212786 1020 True 1482.00 1482 92.86400 8891 9911 1 chr4A.!!$R3 1020
11 TraesCS1A01G248500 chr2B 790869567 790873980 4413 False 6974.00 6974 95.18100 1922 6338 1 chr2B.!!$F1 4416
12 TraesCS1A01G248500 chr2B 798687000 798688698 1698 True 2654.00 2654 94.94700 6336 8026 1 chr2B.!!$R1 1690
13 TraesCS1A01G248500 chr1D 470506652 470511064 4412 True 6970.00 6970 95.16200 1920 6338 1 chr1D.!!$R2 4418
14 TraesCS1A01G248500 chr1D 465901263 465902130 867 True 1199.00 1199 91.59000 8025 8892 1 chr1D.!!$R1 867
15 TraesCS1A01G248500 chr1D 430123609 430124637 1028 False 1070.00 1070 85.82400 911 1921 1 chr1D.!!$F1 1010
16 TraesCS1A01G248500 chr1D 341028095 341030801 2706 True 1044.50 2091 95.65975 1 8892 4 chr1D.!!$R3 8891
17 TraesCS1A01G248500 chr7A 721578086 721582505 4419 False 6922.00 6922 94.96000 1924 6338 1 chr7A.!!$F1 4414
18 TraesCS1A01G248500 chr7B 24271571 24275992 4421 False 6909.00 6909 94.87600 1916 6338 1 chr7B.!!$F1 4422
19 TraesCS1A01G248500 chr3A 26495856 26500268 4412 True 6900.00 6900 94.88500 1924 6338 1 chr3A.!!$R1 4414
20 TraesCS1A01G248500 chr3A 703164864 703165887 1023 True 1495.00 1495 93.07300 8891 9911 1 chr3A.!!$R5 1020
21 TraesCS1A01G248500 chr3A 170458749 170459772 1023 False 1456.00 1456 92.39000 8891 9911 1 chr3A.!!$F2 1020
22 TraesCS1A01G248500 chr3A 127857053 127857921 868 True 1267.00 1267 92.98000 8025 8893 1 chr3A.!!$R4 868
23 TraesCS1A01G248500 chr3A 127820811 127821677 866 True 1210.00 1210 91.83000 8025 8893 1 chr3A.!!$R2 868
24 TraesCS1A01G248500 chr5A 601251832 601253525 1693 False 2699.00 2699 95.46500 6336 8025 1 chr5A.!!$F2 1689
25 TraesCS1A01G248500 chr5A 132380906 132381928 1022 False 1489.00 1489 92.96200 8891 9911 1 chr5A.!!$F1 1020
26 TraesCS1A01G248500 chr2D 35275614 35277312 1698 False 2669.00 2669 95.06800 6336 8030 1 chr2D.!!$F2 1694
27 TraesCS1A01G248500 chr2D 35306808 35308501 1693 False 2669.00 2669 95.16500 6336 8023 1 chr2D.!!$F3 1687
28 TraesCS1A01G248500 chr2D 638747571 638749263 1692 False 2615.00 2615 94.57200 6336 8026 1 chr2D.!!$F4 1690
29 TraesCS1A01G248500 chr2D 20303201 20304818 1617 False 2326.00 2326 92.49100 4701 6338 1 chr2D.!!$F1 1637
30 TraesCS1A01G248500 chr2D 643112060 643112917 857 True 1402.00 1402 96.15400 5481 6338 1 chr2D.!!$R1 857
31 TraesCS1A01G248500 chr6B 30300217 30301907 1690 True 2634.00 2634 94.80800 6336 8025 1 chr6B.!!$R2 1689
32 TraesCS1A01G248500 chr6A 24184839 24186529 1690 False 2628.00 2628 94.74900 6336 8025 1 chr6A.!!$F1 1689
33 TraesCS1A01G248500 chr6A 28859442 28860464 1022 True 1483.00 1483 92.87100 8891 9911 1 chr6A.!!$R1 1020
34 TraesCS1A01G248500 chr1B 456712382 456715394 3012 True 757.00 1672 93.09680 226 8892 5 chr1B.!!$R1 8666
35 TraesCS1A01G248500 chr3B 172979952 172981949 1997 True 1385.00 1519 91.69350 771 8893 2 chr3B.!!$R4 8122
36 TraesCS1A01G248500 chr3B 172052070 172053165 1095 False 1325.00 1325 88.71800 833 1921 1 chr3B.!!$F1 1088
37 TraesCS1A01G248500 chr3B 172170543 172171525 982 False 1266.00 1266 90.10100 947 1921 1 chr3B.!!$F2 974
38 TraesCS1A01G248500 chr3B 173006819 173007801 982 True 1243.00 1243 89.69700 947 1921 1 chr3B.!!$R2 974
39 TraesCS1A01G248500 chr3B 172211093 172212817 1724 False 890.50 1413 87.10850 187 1921 2 chr3B.!!$F4 1734
40 TraesCS1A01G248500 chr3B 146980588 146983438 2850 True 825.25 1373 86.62550 1 8893 4 chr3B.!!$R3 8892
41 TraesCS1A01G248500 chr3B 172091497 172093362 1865 False 514.60 1472 87.62250 1 1921 4 chr3B.!!$F3 1920
42 TraesCS1A01G248500 chr3D 120142523 120143494 971 False 1249.00 1249 89.89800 947 1921 1 chr3D.!!$F2 974
43 TraesCS1A01G248500 chr3D 121266943 121269864 2921 True 845.50 1339 87.37700 1 8893 4 chr3D.!!$R2 8892
44 TraesCS1A01G248500 chr3D 121333761 121335085 1324 True 760.50 1328 87.44350 656 1921 2 chr3D.!!$R3 1265
45 TraesCS1A01G248500 chr6D 452126125 452127913 1788 True 1243.50 1269 91.68550 994 8893 2 chr6D.!!$R1 7899

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
587 1130 0.680061 AAAGAAGAAGCTCCGGTCGT 59.320 50.000 0.00 0.00 0.00 4.34 F
1221 1876 0.749454 GGCACAAGCTCGGGATCATT 60.749 55.000 0.00 0.00 41.70 2.57 F
1634 2291 0.950836 CTGATCAGGAGCTCGTCGAT 59.049 55.000 15.38 12.50 0.00 3.59 F
1817 2482 1.006043 TCCAAGATGGACGGAGAGAGT 59.994 52.381 0.00 0.00 42.67 3.24 F
2722 3400 1.067915 GTGTGCTCTCACTCTCACTCC 60.068 57.143 0.00 0.00 43.49 3.85 F
2912 3604 1.152333 GCCCAACAAACTCCCCCTT 60.152 57.895 0.00 0.00 0.00 3.95 F
4388 5080 1.155859 TGCCCTTGGGCAACTTCAT 59.844 52.632 29.06 0.00 42.27 2.57 F
5049 5742 1.349026 CATCCTTGTCACACCAGACCT 59.651 52.381 0.00 0.00 37.73 3.85 F
6332 7027 1.211212 CCCTTCTGATGGCAGTGATGA 59.789 52.381 4.12 0.00 42.84 2.92 F
6832 7567 1.033746 CCCACAAGCTTGGCGATGAT 61.034 55.000 29.18 4.47 35.00 2.45 F
7495 8237 0.449388 GCAGGCAAGTAGACACATGC 59.551 55.000 0.00 0.00 46.22 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 2204 0.682855 CGAGCCTCTCCTTGTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69 R
2912 3604 0.032117 AGACCCTCCATGATGTCGGA 60.032 55.000 0.00 0.00 33.04 4.55 R
2961 3653 0.321298 AACTTGAAGTATGCCGCCGT 60.321 50.000 0.00 0.00 0.00 5.68 R
3441 4133 0.542938 TGAGATATCTCCGGGGCAGG 60.543 60.000 26.33 0.00 42.20 4.85 R
4288 4980 0.042731 AGGTACAAGGCCAGGCTAGA 59.957 55.000 12.43 0.00 0.00 2.43 R
4715 5408 0.599558 TGCAAGTTGAAGCAGATGCC 59.400 50.000 7.16 0.00 43.38 4.40 R
6046 6741 0.676782 GGACAGCGGTGCTACCATTT 60.677 55.000 15.82 0.00 38.47 2.32 R
6524 7259 1.338136 ATTACCGGACAGCTGGGAGG 61.338 60.000 19.93 18.88 45.41 4.30 R
7256 7998 0.178533 AAGTTTTGTGGACCGGTCGA 59.821 50.000 27.68 22.29 0.00 4.20 R
7718 8460 0.482446 TGGTGGTTGGAGGCTCAAAT 59.518 50.000 17.69 0.00 0.00 2.32 R
9049 9806 1.153667 CTCTTCTGCCTGTCGAGCC 60.154 63.158 0.00 0.00 0.00 4.70 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
48 50 4.298626 TGGCAGAAGTGTAGATATCCCTT 58.701 43.478 0.00 0.00 0.00 3.95
49 51 4.101585 TGGCAGAAGTGTAGATATCCCTTG 59.898 45.833 0.00 0.00 0.00 3.61
74 76 8.405531 TGTCAAATCTTCCTTCTTACAAACAAG 58.594 33.333 0.00 0.00 0.00 3.16
172 184 7.697291 GCAAAATCAACATTGACAAACAAACAT 59.303 29.630 0.00 0.00 42.03 2.71
175 187 5.728471 TCAACATTGACAAACAAACATGGT 58.272 33.333 0.00 0.00 42.03 3.55
199 211 9.476202 GGTATCAAAGCAACAAACTAATTTCTT 57.524 29.630 0.00 0.00 0.00 2.52
204 216 9.476761 CAAAGCAACAAACTAATTTCTTTCAAC 57.523 29.630 0.00 0.00 0.00 3.18
278 295 8.214721 ACACACTCCTTTAGAAGAAGAAAAAG 57.785 34.615 0.00 0.00 0.00 2.27
284 302 7.931275 TCCTTTAGAAGAAGAAAAAGAACAGC 58.069 34.615 0.00 0.00 31.96 4.40
404 432 2.262774 CTCGGCCAGGCTCCATCTTT 62.263 60.000 12.43 0.00 0.00 2.52
439 874 8.175069 ACAACACGTAAATGTAGATAGCATTTG 58.825 33.333 11.94 1.25 43.70 2.32
461 896 4.522789 TGGGCAGAAAAATAAAGACAGACC 59.477 41.667 0.00 0.00 0.00 3.85
587 1130 0.680061 AAAGAAGAAGCTCCGGTCGT 59.320 50.000 0.00 0.00 0.00 4.34
675 1218 1.907222 CTCCCCGTACCACCCTTTCC 61.907 65.000 0.00 0.00 0.00 3.13
703 1246 1.005037 TGCCGTTGTAGGACAGCAG 60.005 57.895 0.00 0.00 29.20 4.24
790 1351 1.151668 CTCAGCGTTACTTTGCAGCT 58.848 50.000 0.00 0.00 38.90 4.24
791 1352 2.029380 TCTCAGCGTTACTTTGCAGCTA 60.029 45.455 0.00 0.00 36.28 3.32
792 1353 2.066262 TCAGCGTTACTTTGCAGCTAC 58.934 47.619 0.00 0.00 36.28 3.58
793 1354 1.068474 AGCGTTACTTTGCAGCTACG 58.932 50.000 0.00 0.00 36.28 3.51
977 1613 4.992319 CGAGAGTAGTAATCCACGAGAGAT 59.008 45.833 8.42 0.00 0.00 2.75
992 1632 1.543941 GAGATGCAGCGAATCGACCG 61.544 60.000 6.91 4.85 0.00 4.79
1068 1722 2.351276 GAGGCCACCACCAACGAT 59.649 61.111 5.01 0.00 0.00 3.73
1132 1787 2.797156 CTCTCCATATTCAAAGGCGACG 59.203 50.000 0.00 0.00 0.00 5.12
1217 1872 4.115199 GGGGCACAAGCTCGGGAT 62.115 66.667 0.00 0.00 44.30 3.85
1218 1873 2.514824 GGGCACAAGCTCGGGATC 60.515 66.667 0.00 0.00 41.70 3.36
1219 1874 2.268920 GGCACAAGCTCGGGATCA 59.731 61.111 0.00 0.00 41.70 2.92
1220 1875 1.153086 GGCACAAGCTCGGGATCAT 60.153 57.895 0.00 0.00 41.70 2.45
1221 1876 0.749454 GGCACAAGCTCGGGATCATT 60.749 55.000 0.00 0.00 41.70 2.57
1222 1877 1.475034 GGCACAAGCTCGGGATCATTA 60.475 52.381 0.00 0.00 41.70 1.90
1242 1897 2.713531 ATCAACAAGGTGGCCCGCTT 62.714 55.000 0.00 0.00 35.12 4.68
1389 2045 1.560146 GCCTACCTCAAGCCCTACTTT 59.440 52.381 0.00 0.00 36.04 2.66
1466 2122 1.446272 GGAGCGTCGAGTTCAAGGG 60.446 63.158 0.00 0.00 0.00 3.95
1536 2192 2.162008 GGAGATATTCTACGAGGGCGAC 59.838 54.545 0.00 0.00 41.64 5.19
1634 2291 0.950836 CTGATCAGGAGCTCGTCGAT 59.049 55.000 15.38 12.50 0.00 3.59
1705 2370 2.333069 CAAGGGCATCCTCCTCTATGA 58.667 52.381 0.00 0.00 44.07 2.15
1737 2402 2.815211 GCAAGACGCTGATCGCCA 60.815 61.111 4.37 0.00 43.23 5.69
1807 2472 3.324846 CCGGAGATAATGTCCAAGATGGA 59.675 47.826 0.00 0.00 45.98 3.41
1817 2482 1.006043 TCCAAGATGGACGGAGAGAGT 59.994 52.381 0.00 0.00 42.67 3.24
1919 2584 3.768008 TCCGAACAGGGAGAAGACT 57.232 52.632 0.00 0.00 41.52 3.24
1920 2585 1.546961 TCCGAACAGGGAGAAGACTC 58.453 55.000 0.00 0.00 41.52 3.36
1921 2586 1.075698 TCCGAACAGGGAGAAGACTCT 59.924 52.381 0.00 0.00 42.28 3.24
1922 2587 2.307980 TCCGAACAGGGAGAAGACTCTA 59.692 50.000 0.00 0.00 42.28 2.43
1923 2588 3.053544 TCCGAACAGGGAGAAGACTCTAT 60.054 47.826 0.00 0.00 42.28 1.98
1924 2589 3.702045 CCGAACAGGGAGAAGACTCTATT 59.298 47.826 0.00 0.00 42.28 1.73
1925 2590 4.440802 CCGAACAGGGAGAAGACTCTATTG 60.441 50.000 0.00 0.00 42.28 1.90
1926 2591 4.440802 CGAACAGGGAGAAGACTCTATTGG 60.441 50.000 0.00 0.00 42.28 3.16
1927 2592 3.379452 ACAGGGAGAAGACTCTATTGGG 58.621 50.000 0.00 0.00 42.28 4.12
1928 2593 3.246167 ACAGGGAGAAGACTCTATTGGGT 60.246 47.826 0.00 0.00 42.28 4.51
2022 2689 4.687901 TGTGATGAACTTTGAGGACAGA 57.312 40.909 0.00 0.00 0.00 3.41
2040 2707 5.531287 GGACAGATTCAACCAACAAGTAAGT 59.469 40.000 0.00 0.00 0.00 2.24
2085 2752 4.766373 TGCACATGTGACACAGGATTTAAT 59.234 37.500 29.80 0.00 33.56 1.40
2327 2995 5.576774 GTGTTTTGCAAACTGCTCTTAAACT 59.423 36.000 12.39 0.00 45.31 2.66
2328 2996 6.750039 GTGTTTTGCAAACTGCTCTTAAACTA 59.250 34.615 12.39 0.00 45.31 2.24
2465 3133 7.282450 CCCAAAACTACTCTGTTCTAAAACTGT 59.718 37.037 0.00 0.00 36.17 3.55
2511 3179 4.713814 ACTCTCAAATCTGATGCTCCACTA 59.286 41.667 0.00 0.00 0.00 2.74
2555 3223 7.817962 GCTAACCAGATCAAAGTACTCAAAGTA 59.182 37.037 0.00 0.00 0.00 2.24
2625 3293 1.102154 CAACCACCAGCTTGAACACA 58.898 50.000 0.00 0.00 0.00 3.72
2722 3400 1.067915 GTGTGCTCTCACTCTCACTCC 60.068 57.143 0.00 0.00 43.49 3.85
2790 3477 3.134623 TCTCCTTGCTTCACTTCACTTGA 59.865 43.478 0.00 0.00 0.00 3.02
2860 3552 3.737559 TGGACTTATGGGCTGATGTTT 57.262 42.857 0.00 0.00 0.00 2.83
2912 3604 1.152333 GCCCAACAAACTCCCCCTT 60.152 57.895 0.00 0.00 0.00 3.95
2986 3678 3.188460 GCGGCATACTTCAAGTTTCTTCA 59.812 43.478 0.00 0.00 0.00 3.02
2996 3688 5.756195 TCAAGTTTCTTCATTGTCACCAG 57.244 39.130 0.00 0.00 0.00 4.00
3125 3817 7.950512 TGCTTAAACCTTGAATGAAAGATTGA 58.049 30.769 0.00 0.00 0.00 2.57
3178 3870 6.580963 TGTCACAAAACAACACATATTTGC 57.419 33.333 0.00 0.00 36.48 3.68
3182 3874 7.436673 GTCACAAAACAACACATATTTGCCTTA 59.563 33.333 0.00 0.00 36.48 2.69
3285 3977 4.766373 TCAGTTGTATTCAATGCCACACAT 59.234 37.500 0.00 0.00 42.30 3.21
3302 3994 3.181467 ACACATTTTTGCAGCCTGCTTTA 60.181 39.130 18.96 0.19 45.31 1.85
3434 4126 3.432046 CCACCACCAAAGCAAAGTTTCAT 60.432 43.478 0.00 0.00 0.00 2.57
3441 4133 7.307337 CCACCAAAGCAAAGTTTCATATTTGTC 60.307 37.037 0.00 0.00 38.41 3.18
3494 4186 1.283321 GGCTTCCCAATGAGGTCTTCT 59.717 52.381 0.00 0.00 34.66 2.85
3516 4208 5.591472 TCTTGGATTGGACATAAATCTGCTG 59.409 40.000 0.00 0.00 34.95 4.41
3649 4341 2.749621 GTGGTAGGACATTGCTTTCTGG 59.250 50.000 0.00 0.00 0.00 3.86
3698 4390 6.756542 GGACAACTCACAACTTTAGCATTTTT 59.243 34.615 0.00 0.00 0.00 1.94
3772 4464 5.723295 ACAACTTGTTGCAATTTCTGTCTT 58.277 33.333 12.76 0.00 0.00 3.01
3788 4480 3.264947 TGTCTTGCTCAATTCTCATCCG 58.735 45.455 0.00 0.00 0.00 4.18
3849 4541 7.413328 GCAAAACATTTGCTCAACTTCTTCTTT 60.413 33.333 17.94 0.00 41.87 2.52
3952 4644 5.997746 CCTGAGAACCTCTGAATAAACACAA 59.002 40.000 0.00 0.00 32.36 3.33
3966 4658 3.996150 AACACAAAATGGTCTGAGCTG 57.004 42.857 8.47 0.58 0.00 4.24
4014 4706 7.309377 CCCATGACAGTTTCAAACTTCATGTAT 60.309 37.037 29.54 12.85 44.44 2.29
4062 4754 6.109359 GCCATAGAGACTTTTCTTCAGCTTA 58.891 40.000 0.00 0.00 29.47 3.09
4084 4776 5.483685 ACACACATAGTCTTCTTTGCCTA 57.516 39.130 0.00 0.00 0.00 3.93
4102 4794 3.372025 GCCTATCACAAGAAACCCCTCAT 60.372 47.826 0.00 0.00 0.00 2.90
4220 4912 4.457257 GCCAAGGATTACTCTTATGGATGC 59.543 45.833 0.00 0.00 0.00 3.91
4233 4925 5.716228 TCTTATGGATGCCATTTTCACAACT 59.284 36.000 4.03 0.00 42.23 3.16
4236 4928 2.354003 GGATGCCATTTTCACAACTGGG 60.354 50.000 0.00 0.00 34.03 4.45
4245 4937 6.014669 CCATTTTCACAACTGGGGAAAAGATA 60.015 38.462 9.91 0.00 41.96 1.98
4288 4980 3.199946 TCTCTGGCCGAATCCTTTTACAT 59.800 43.478 0.00 0.00 0.00 2.29
4388 5080 1.155859 TGCCCTTGGGCAACTTCAT 59.844 52.632 29.06 0.00 42.27 2.57
4451 5144 4.592942 TCTTGCATAGCATTTTCCACTCT 58.407 39.130 0.00 0.00 38.76 3.24
4454 5147 5.726980 TGCATAGCATTTTCCACTCTTTT 57.273 34.783 0.00 0.00 31.71 2.27
4623 5316 1.833630 CTGGTGCTTCCTACTGATCCA 59.166 52.381 0.00 0.00 37.07 3.41
4781 5474 4.946157 GGGTCAGAATCAATCATGTCTTGT 59.054 41.667 9.52 0.00 0.00 3.16
4829 5522 7.201767 CCCTTTGTCTTCACAATATCCTCAATC 60.202 40.741 0.00 0.00 42.28 2.67
4879 5572 2.952310 GGCTTCTCACAACTTTCCTTGT 59.048 45.455 0.00 0.00 34.56 3.16
4892 5585 7.728532 ACAACTTTCCTTGTTATAGGGTCAAAT 59.271 33.333 0.00 0.00 35.90 2.32
4917 5610 3.719268 TGTAGCCAAACTCATCACCAT 57.281 42.857 0.00 0.00 0.00 3.55
5049 5742 1.349026 CATCCTTGTCACACCAGACCT 59.651 52.381 0.00 0.00 37.73 3.85
5149 5842 5.167845 CCAAAAGTGTTTGTGTAGCTTTGT 58.832 37.500 0.00 0.00 42.26 2.83
5475 6168 2.027192 GCACCACCAAGAGATCTTACCA 60.027 50.000 0.00 0.00 34.28 3.25
5699 6392 4.070009 GCCATAGAGCACATTGATCATCA 58.930 43.478 0.00 0.00 34.77 3.07
5779 6474 5.324409 TGAGACCATTTTACCTCTTGCAAT 58.676 37.500 0.00 0.00 0.00 3.56
5831 6526 3.457234 CCCTTTTCCAAAACTGCTCAAC 58.543 45.455 0.00 0.00 0.00 3.18
5898 6593 1.375908 GCCTCGACATGCCTCACAA 60.376 57.895 0.00 0.00 0.00 3.33
5927 6622 4.076394 GGACTAACCTTGTACCATTTGCA 58.924 43.478 0.00 0.00 35.41 4.08
5947 6642 3.340928 CAGTCTCCAAATGCACATCTCA 58.659 45.455 0.00 0.00 0.00 3.27
6046 6741 2.227626 GCTCTCTGCGAGATGTAGCATA 59.772 50.000 0.00 0.00 42.62 3.14
6193 6888 4.018490 TGCATAACAAGCATGATGTCCTT 58.982 39.130 0.00 0.00 37.02 3.36
6224 6919 3.635373 CAGTAACTCGGTTGCCCTCTATA 59.365 47.826 0.23 0.00 0.00 1.31
6263 6958 5.555017 ACTTGCTTCTGATCTTGCTTCTTA 58.445 37.500 0.00 0.00 0.00 2.10
6332 7027 1.211212 CCCTTCTGATGGCAGTGATGA 59.789 52.381 4.12 0.00 42.84 2.92
6524 7259 1.335597 GCAAACCGTGACCTTAAAGGC 60.336 52.381 0.00 0.00 39.63 4.35
6555 7290 3.220940 GTCCGGTAATGAGCCTAGTAGT 58.779 50.000 0.00 0.00 0.00 2.73
6589 7324 9.770503 CTCTCACTTCATCTTCAAATGTTATTG 57.229 33.333 0.00 0.00 0.00 1.90
6597 7332 7.977293 TCATCTTCAAATGTTATTGCCATTGAG 59.023 33.333 0.00 0.00 33.01 3.02
6649 7384 8.735692 TGTATTCACATGATCTGCAATTAGAA 57.264 30.769 0.00 0.00 0.00 2.10
6778 7513 5.619309 GCATGTGTCTCATCAATGATATGGC 60.619 44.000 0.00 0.00 36.02 4.40
6832 7567 1.033746 CCCACAAGCTTGGCGATGAT 61.034 55.000 29.18 4.47 35.00 2.45
6837 7572 2.283298 CAAGCTTGGCGATGATGTACT 58.717 47.619 19.14 0.00 0.00 2.73
6927 7662 7.861629 TCACATATAACAAGTCCTCCATCTTT 58.138 34.615 0.00 0.00 0.00 2.52
7055 7790 3.810743 GCTCTGATACCACTTTGTTGGGT 60.811 47.826 0.00 0.00 41.49 4.51
7059 7794 2.445682 TACCACTTTGTTGGGTGCTT 57.554 45.000 0.00 0.00 41.49 3.91
7121 7856 1.492133 ATGCACACTACACAGCCCCT 61.492 55.000 0.00 0.00 0.00 4.79
7148 7883 5.240183 CACTTGTGATGAACTTTGAGGACAT 59.760 40.000 0.00 0.00 0.00 3.06
7149 7884 6.427853 CACTTGTGATGAACTTTGAGGACATA 59.572 38.462 0.00 0.00 0.00 2.29
7270 8012 1.909287 TGGATCGACCGGTCCACAA 60.909 57.895 28.52 12.19 39.51 3.33
7314 8056 9.699703 GATGAGTACAAAGTTTTCTCTAGAACT 57.300 33.333 0.00 0.00 37.69 3.01
7374 8116 1.473080 GGCAACAGCAACAACAACCAT 60.473 47.619 0.00 0.00 0.00 3.55
7419 8161 4.932200 GCAGAGTTTACACAGCTTCTGTAT 59.068 41.667 9.01 0.00 43.43 2.29
7451 8193 4.727507 TTTGCAAACTGCTCTTAAACCA 57.272 36.364 8.05 0.00 45.31 3.67
7495 8237 0.449388 GCAGGCAAGTAGACACATGC 59.551 55.000 0.00 0.00 46.22 4.06
7516 8258 3.257393 CGTTCTTGACATCTCCTCCAAG 58.743 50.000 0.00 0.00 37.82 3.61
7572 8314 4.618920 ACTGTTCGTCTCCCAAAACTAT 57.381 40.909 0.00 0.00 0.00 2.12
7585 8327 7.944554 TCTCCCAAAACTATTCTGTTCTGAAAT 59.055 33.333 0.00 0.00 0.00 2.17
7680 8422 6.989659 ACCAGATCGAAGTACTCAAAGTAAA 58.010 36.000 0.00 0.00 31.62 2.01
7718 8460 0.687920 TTGGGGTCGATACAAGCACA 59.312 50.000 0.00 0.00 0.00 4.57
7845 8596 1.067915 GTGTGCTCTCACTCTCACTCC 60.068 57.143 0.00 0.00 43.49 3.85
7859 8614 2.270205 CTCCCACGAATGGCAGCT 59.730 61.111 0.00 0.00 45.76 4.24
7860 8615 2.046023 TCCCACGAATGGCAGCTG 60.046 61.111 10.11 10.11 45.76 4.24
7888 8644 3.090532 GGGTGGAGTGGCTAGGGG 61.091 72.222 0.00 0.00 0.00 4.79
8115 8871 0.540923 TGCATGTCATCGTCATGGGA 59.459 50.000 7.78 0.00 41.77 4.37
8155 8911 1.613630 ATCGACCCTGCCTTGAGGT 60.614 57.895 0.00 0.00 37.57 3.85
8254 9010 3.030291 ACCAAAAACATGAAGCTGGACA 58.970 40.909 0.00 0.00 0.00 4.02
8324 9080 4.492160 CGACTTGGCCGCGCTCTA 62.492 66.667 5.56 0.00 0.00 2.43
8365 9121 1.487976 GCATCAGGGAGAAGATGGACA 59.512 52.381 0.00 0.00 41.43 4.02
8444 9200 2.356135 CAATGACCACCTTAAGACGGG 58.644 52.381 3.36 4.83 0.00 5.28
8445 9201 0.252197 ATGACCACCTTAAGACGGGC 59.748 55.000 3.36 6.54 0.00 6.13
8689 9445 1.275010 TGATCGCTAACAAGTGCCAGA 59.725 47.619 0.00 0.00 0.00 3.86
8711 9467 3.087031 CCAACTTCATCAGCATCAAGGT 58.913 45.455 0.00 0.00 0.00 3.50
8758 9514 1.078848 GAGAGCGAGGCCAATGTGT 60.079 57.895 5.01 0.00 0.00 3.72
8815 9571 1.933853 GTGTGCTGTTCTTTGACGAGT 59.066 47.619 0.00 0.00 0.00 4.18
8883 9639 2.599578 GCGGCGGATAGGGTCCTA 60.600 66.667 9.78 0.00 45.46 2.94
9015 9772 1.887854 TCGACCATAACGTTCCACTCA 59.112 47.619 2.82 0.00 0.00 3.41
9031 9788 6.058553 TCCACTCAGAAGAATCAATGTCAT 57.941 37.500 0.00 0.00 0.00 3.06
9049 9806 0.511221 ATTCGACCGTCGCAAAAGTG 59.489 50.000 16.24 0.00 40.21 3.16
9050 9807 1.492319 TTCGACCGTCGCAAAAGTGG 61.492 55.000 16.24 0.00 40.21 4.00
9057 9814 1.227409 TCGCAAAAGTGGCTCGACA 60.227 52.632 0.00 0.00 0.00 4.35
9115 9872 4.095036 GGTTGAGCATTTACTTGTAGGCTC 59.905 45.833 16.76 16.76 45.89 4.70
9320 10081 0.465824 GGCTCTGAGACGTAGGGCTA 60.466 60.000 9.28 0.00 41.43 3.93
9341 10102 2.623418 TACTTCCTCTGAGAAGGGCA 57.377 50.000 6.17 0.00 46.24 5.36
9555 10319 2.423446 GGCCGCGAGATCCATCTT 59.577 61.111 8.23 0.00 37.25 2.40
9605 10369 3.049674 TTGGCTCCAAGAAGCGCG 61.050 61.111 0.00 0.00 43.45 6.86
9699 10463 1.132453 CAGCCGTCGACTCAGTATCAA 59.868 52.381 14.70 0.00 0.00 2.57
9703 10467 2.287103 CCGTCGACTCAGTATCAATCGA 59.713 50.000 14.70 0.00 39.35 3.59
9842 10608 0.959553 TCGAGCCTGACGAAACTCTT 59.040 50.000 0.00 0.00 36.84 2.85
9880 10646 1.753649 GCTCTGTAGAGACTGCATCCA 59.246 52.381 12.89 0.00 44.74 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 3.068732 CACTTCTGCCATAGATCGGAAGA 59.931 47.826 15.28 0.00 44.44 2.87
48 50 7.873719 TGTTTGTAAGAAGGAAGATTTGACA 57.126 32.000 0.00 0.00 0.00 3.58
49 51 7.379797 GCTTGTTTGTAAGAAGGAAGATTTGAC 59.620 37.037 0.00 0.00 32.78 3.18
74 76 6.036470 GTCTATTTACCCTTCATTTGCTTGC 58.964 40.000 0.00 0.00 0.00 4.01
172 184 8.637986 AGAAATTAGTTTGTTGCTTTGATACCA 58.362 29.630 0.00 0.00 0.00 3.25
278 295 5.276348 GCAGTTTGTGTTTGTTATGCTGTTC 60.276 40.000 0.00 0.00 0.00 3.18
284 302 2.150985 CGCGCAGTTTGTGTTTGTTATG 59.849 45.455 8.75 0.00 0.00 1.90
404 432 0.178301 TTACGTGTTGTGGCAGTGGA 59.822 50.000 0.00 0.00 0.00 4.02
439 874 4.379499 CGGTCTGTCTTTATTTTTCTGCCC 60.379 45.833 0.00 0.00 0.00 5.36
461 896 3.201290 CCTTCATGTTCTCTCCCAATCG 58.799 50.000 0.00 0.00 0.00 3.34
497 932 0.461961 CCTCTCCCTCCGTCAACATC 59.538 60.000 0.00 0.00 0.00 3.06
675 1218 0.974010 TACAACGGCAGGAGGTAGGG 60.974 60.000 0.00 0.00 0.00 3.53
703 1246 3.160748 GCTGAGAGGAGGGAGGCC 61.161 72.222 0.00 0.00 0.00 5.19
792 1353 3.033873 CTCATATTCGTCCACGTGTACG 58.966 50.000 25.48 25.48 46.33 3.67
793 1354 3.369385 CCTCATATTCGTCCACGTGTAC 58.631 50.000 15.65 8.18 40.80 2.90
897 1518 3.408853 GGTACCTGGGGGTGAGGC 61.409 72.222 4.06 0.00 46.75 4.70
934 1557 1.666189 GTTTGATGTCGAGGGCTTAGC 59.334 52.381 0.00 0.00 0.00 3.09
935 1558 1.927174 CGTTTGATGTCGAGGGCTTAG 59.073 52.381 0.00 0.00 0.00 2.18
936 1559 1.546923 TCGTTTGATGTCGAGGGCTTA 59.453 47.619 0.00 0.00 0.00 3.09
977 1613 1.373622 TTTCGGTCGATTCGCTGCA 60.374 52.632 0.00 0.00 0.00 4.41
1068 1722 0.463654 GGGTGCACACAGAGTTGTCA 60.464 55.000 20.43 0.00 34.62 3.58
1132 1787 3.426568 GCCCTTGAGCAGCACGAC 61.427 66.667 0.00 0.00 0.00 4.34
1216 1871 3.706086 GGGCCACCTTGTTGATTAATGAT 59.294 43.478 4.39 0.00 0.00 2.45
1217 1872 3.096092 GGGCCACCTTGTTGATTAATGA 58.904 45.455 4.39 0.00 0.00 2.57
1218 1873 2.159254 CGGGCCACCTTGTTGATTAATG 60.159 50.000 4.39 0.00 33.28 1.90
1219 1874 2.099405 CGGGCCACCTTGTTGATTAAT 58.901 47.619 4.39 0.00 33.28 1.40
1220 1875 1.540267 CGGGCCACCTTGTTGATTAA 58.460 50.000 4.39 0.00 33.28 1.40
1221 1876 0.963355 GCGGGCCACCTTGTTGATTA 60.963 55.000 4.39 0.00 33.28 1.75
1222 1877 2.275380 GCGGGCCACCTTGTTGATT 61.275 57.895 4.39 0.00 33.28 2.57
1242 1897 3.925362 ATGCGCACGCGTAGGTTGA 62.925 57.895 14.90 0.00 45.51 3.18
1466 2122 2.029666 CGGGGTCGATCTCCATGC 59.970 66.667 0.00 0.00 36.19 4.06
1536 2192 3.068691 TCCTCTCGCTTGACCGGG 61.069 66.667 6.32 0.00 0.00 5.73
1548 2204 0.682855 CGAGCCTCTCCTTGTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69
1583 2239 3.384532 CCATGCCACCCACCTTGC 61.385 66.667 0.00 0.00 0.00 4.01
1585 2241 2.029892 TTTCCCATGCCACCCACCTT 62.030 55.000 0.00 0.00 0.00 3.50
1587 2243 1.535202 TTTTCCCATGCCACCCACC 60.535 57.895 0.00 0.00 0.00 4.61
1751 2416 2.203938 AAGAAGGCCCCGGTCTCA 60.204 61.111 0.00 0.00 0.00 3.27
1807 2472 0.885196 GTTGCTCTCACTCTCTCCGT 59.115 55.000 0.00 0.00 0.00 4.69
1817 2482 0.979665 CCTTCCTCAGGTTGCTCTCA 59.020 55.000 0.00 0.00 37.99 3.27
1915 2580 1.834263 GTCCAGCACCCAATAGAGTCT 59.166 52.381 0.00 0.00 0.00 3.24
1916 2581 1.555075 TGTCCAGCACCCAATAGAGTC 59.445 52.381 0.00 0.00 0.00 3.36
1917 2582 1.556911 CTGTCCAGCACCCAATAGAGT 59.443 52.381 0.00 0.00 0.00 3.24
1918 2583 2.322355 CTGTCCAGCACCCAATAGAG 57.678 55.000 0.00 0.00 0.00 2.43
1950 2615 0.941542 CCGTGTCGGTGAATTTGTGT 59.058 50.000 0.00 0.00 42.73 3.72
2022 2689 5.302360 TCGCTACTTACTTGTTGGTTGAAT 58.698 37.500 0.00 0.00 0.00 2.57
2040 2707 5.627367 GCATGTTGTTTGTGTTATTTCGCTA 59.373 36.000 0.00 0.00 0.00 4.26
2147 2815 9.593134 GTACTCATCATTCTCATAGTGAAGTTT 57.407 33.333 0.00 0.00 0.00 2.66
2327 2995 6.723298 AATTTGGTGATGTTTGGTTCAGTA 57.277 33.333 0.00 0.00 0.00 2.74
2328 2996 5.612725 AATTTGGTGATGTTTGGTTCAGT 57.387 34.783 0.00 0.00 0.00 3.41
2360 3028 4.546570 TGTCAAGAACTCATGTGTCTACG 58.453 43.478 0.03 0.00 0.00 3.51
2511 3179 1.147817 AGCTGGTTTGAGGATTGGGTT 59.852 47.619 0.00 0.00 0.00 4.11
2555 3223 1.141053 ACTTGGTGAGCTCGTTCCTTT 59.859 47.619 18.53 5.19 0.00 3.11
2625 3293 3.969287 TTTGCTGCATCTGACTAGACT 57.031 42.857 1.84 0.00 35.34 3.24
2790 3477 1.134220 TCCAACGGTTGAGAGTGCTTT 60.134 47.619 21.88 0.00 0.00 3.51
2860 3552 2.203337 GAGGTGTGTTGGCAGCCA 60.203 61.111 11.22 11.22 37.57 4.75
2912 3604 0.032117 AGACCCTCCATGATGTCGGA 60.032 55.000 0.00 0.00 33.04 4.55
2954 3646 2.903350 TATGCCGCCGTCTCGCTA 60.903 61.111 0.00 0.00 0.00 4.26
2961 3653 0.321298 AACTTGAAGTATGCCGCCGT 60.321 50.000 0.00 0.00 0.00 5.68
2986 3678 4.085357 TGCTGACTAAACTGGTGACAAT 57.915 40.909 0.00 0.00 42.06 2.71
2996 3688 3.142174 GGGGCTGATATGCTGACTAAAC 58.858 50.000 0.00 0.00 0.00 2.01
3121 3813 9.905713 TGCTATCCACTTAAGTAAGAATTCAAT 57.094 29.630 8.04 0.00 37.08 2.57
3178 3870 6.385649 TTGTGAGCTTGGTTTTAAGTAAGG 57.614 37.500 0.00 0.00 0.00 2.69
3182 3874 4.307443 GCTTGTGAGCTTGGTTTTAAGT 57.693 40.909 0.00 0.00 45.65 2.24
3302 3994 3.717294 GGGGAGCGGTGTCATGGT 61.717 66.667 0.00 0.00 0.00 3.55
3323 4015 6.944096 ACTTCAGGTTACTTGGTTACCTATC 58.056 40.000 2.07 0.00 42.61 2.08
3434 4126 0.619255 TCTCCGGGGCAGGACAAATA 60.619 55.000 0.00 0.00 36.14 1.40
3441 4133 0.542938 TGAGATATCTCCGGGGCAGG 60.543 60.000 26.33 0.00 42.20 4.85
3494 4186 5.357878 GTCAGCAGATTTATGTCCAATCCAA 59.642 40.000 0.00 0.00 31.86 3.53
3516 4208 2.194271 GCTCATGCGGTTAGTACTGTC 58.806 52.381 5.39 0.00 32.95 3.51
3649 4341 1.615392 AGCAGCCCATTTCAAGTTGAC 59.385 47.619 4.68 0.00 0.00 3.18
3698 4390 5.087323 AGGTACTTCAGAAGTTCAGGATGA 58.913 41.667 21.05 0.00 39.26 2.92
3772 4464 2.609427 CTCCGGATGAGAATTGAGCA 57.391 50.000 3.57 0.00 44.42 4.26
3788 4480 4.145052 AGGTCCAACAAAGAACATTCTCC 58.855 43.478 0.00 0.00 36.28 3.71
3842 4534 9.256228 TCTCTAGGATTGCTAAGTTAAAGAAGA 57.744 33.333 0.00 0.00 0.00 2.87
3849 4541 8.540507 AGAATGTCTCTAGGATTGCTAAGTTA 57.459 34.615 0.00 0.00 30.22 2.24
3952 4644 2.157738 GAAGTGCAGCTCAGACCATTT 58.842 47.619 0.00 0.00 0.00 2.32
3966 4658 1.466558 GAGCAAGGCTACAAGAAGTGC 59.533 52.381 0.00 0.00 39.88 4.40
4014 4706 3.698539 TGAAACAAGCACCAAGACAATGA 59.301 39.130 0.00 0.00 0.00 2.57
4062 4754 4.357918 AGGCAAAGAAGACTATGTGTGT 57.642 40.909 0.00 0.00 0.00 3.72
4084 4776 3.814504 ACATGAGGGGTTTCTTGTGAT 57.185 42.857 0.00 0.00 35.07 3.06
4102 4794 6.662755 AGGAAGAAATATACATGGAGCAACA 58.337 36.000 0.00 0.00 0.00 3.33
4220 4912 4.100808 TCTTTTCCCCAGTTGTGAAAATGG 59.899 41.667 0.00 0.00 37.36 3.16
4233 4925 7.631510 TGACTATGATGATATCTTTTCCCCA 57.368 36.000 3.98 0.00 0.00 4.96
4236 4928 8.457261 GGCATTGACTATGATGATATCTTTTCC 58.543 37.037 3.98 0.00 36.26 3.13
4245 4937 7.228906 CAGAGAAAAGGCATTGACTATGATGAT 59.771 37.037 0.00 0.00 36.26 2.45
4288 4980 0.042731 AGGTACAAGGCCAGGCTAGA 59.957 55.000 12.43 0.00 0.00 2.43
4454 5147 2.892215 TGCAATGGAAGATGAGCACAAA 59.108 40.909 0.00 0.00 0.00 2.83
4502 5195 7.311092 TCAATACGGGGTGTTATTATCTGAT 57.689 36.000 0.00 0.00 0.00 2.90
4518 5211 4.090090 AGGTATCCCTCAGATCAATACGG 58.910 47.826 0.00 0.00 35.62 4.02
4541 5234 0.618981 GGGGTCGAATTCCTTCCAGT 59.381 55.000 0.00 0.00 0.00 4.00
4623 5316 6.828788 AGTATGATGCTGAAGTTGATGATCT 58.171 36.000 0.00 0.00 0.00 2.75
4715 5408 0.599558 TGCAAGTTGAAGCAGATGCC 59.400 50.000 7.16 0.00 43.38 4.40
4781 5474 1.130054 AGGTTCCTCCTCAGCAGCAA 61.130 55.000 0.00 0.00 44.42 3.91
4829 5522 3.827625 TGTGTTTGTTGAAGACCAAACG 58.172 40.909 9.79 0.00 39.56 3.60
4879 5572 6.100569 TGGCTACAAGCTATTTGACCCTATAA 59.899 38.462 0.00 0.00 41.99 0.98
4892 5585 4.253685 GTGATGAGTTTGGCTACAAGCTA 58.746 43.478 0.00 0.00 46.34 3.32
4917 5610 5.118990 GCAGTGTATCTTTCTTGGCTATGA 58.881 41.667 0.00 0.00 0.00 2.15
5030 5723 1.734655 AGGTCTGGTGTGACAAGGAT 58.265 50.000 0.00 0.00 38.61 3.24
5049 5742 2.642311 TGCAGGGAGATGTTCCTAACAA 59.358 45.455 0.00 0.00 45.86 2.83
5118 5811 2.107366 CAAACACTTTTGGGGTGAGGT 58.893 47.619 0.00 0.00 38.82 3.85
5475 6168 5.964758 ACATTCCGATGTTTGCAATATGTT 58.035 33.333 0.00 0.00 43.92 2.71
5690 6383 7.226128 GTCAATGCACTAGAGAATGATGATCAA 59.774 37.037 0.00 0.00 0.00 2.57
5699 6392 4.874966 GCTTCTGTCAATGCACTAGAGAAT 59.125 41.667 0.00 0.00 0.00 2.40
5779 6474 3.193267 GCTCACCAAAGGCAACATGATTA 59.807 43.478 0.00 0.00 41.41 1.75
5831 6526 5.591472 TGGTTTGCTTGATGGAGATGATTAG 59.409 40.000 0.00 0.00 0.00 1.73
5927 6622 3.708403 TGAGATGTGCATTTGGAGACT 57.292 42.857 0.00 0.00 0.00 3.24
5947 6642 3.371965 AGAGCAGCCATCATTGGAAAAT 58.628 40.909 0.00 0.00 46.92 1.82
6046 6741 0.676782 GGACAGCGGTGCTACCATTT 60.677 55.000 15.82 0.00 38.47 2.32
6127 6822 3.519510 TGGTTCCACTATTGAGGAGAAGG 59.480 47.826 0.00 0.00 34.54 3.46
6193 6888 4.304110 CAACCGAGTTACTGCAGTAGAAA 58.696 43.478 24.79 11.39 0.00 2.52
6224 6919 5.157940 AGCAAGTTGACAGTGATAGTGAT 57.842 39.130 7.16 0.00 0.00 3.06
6263 6958 9.725019 AAGTGGAAGAAAGACAAAAAGAAAAAT 57.275 25.926 0.00 0.00 0.00 1.82
6332 7027 2.224793 GGTAAAGGGGCAGAAAGAGTGT 60.225 50.000 0.00 0.00 0.00 3.55
6524 7259 1.338136 ATTACCGGACAGCTGGGAGG 61.338 60.000 19.93 18.88 45.41 4.30
6555 7290 4.815533 AGATGAAGTGAGAGCTTTGCTA 57.184 40.909 0.00 0.00 39.88 3.49
6589 7324 3.881937 AAATCAGCTTTCCTCAATGGC 57.118 42.857 0.00 0.00 35.26 4.40
6597 7332 6.040842 TCCAAGGCATTATAAATCAGCTTTCC 59.959 38.462 0.00 0.00 0.00 3.13
6649 7384 2.619074 GCTTGAGGTACAAAGAGGGCAT 60.619 50.000 0.00 0.00 38.08 4.40
6778 7513 3.501828 TGGGTCGATGACAATGTTTTGAG 59.498 43.478 0.00 0.00 36.64 3.02
6832 7567 3.314693 AGGAAGGTCAGTGGAAAGTACA 58.685 45.455 0.00 0.00 0.00 2.90
6837 7572 3.754965 CATTGAGGAAGGTCAGTGGAAA 58.245 45.455 0.00 0.00 32.09 3.13
6927 7662 5.271598 ACAAATTATCAAGCATGGAAGGGA 58.728 37.500 0.00 0.00 0.00 4.20
7068 7803 3.181515 CGGTGAATTTGTGTAGCGCATTA 60.182 43.478 11.47 0.00 0.00 1.90
7121 7856 4.580167 CCTCAAAGTTCATCACAAGTGGAA 59.420 41.667 0.00 0.00 0.00 3.53
7148 7883 3.932822 TCCGCTGCTTACTTGTTGAATA 58.067 40.909 0.00 0.00 0.00 1.75
7149 7884 2.778299 TCCGCTGCTTACTTGTTGAAT 58.222 42.857 0.00 0.00 0.00 2.57
7256 7998 0.178533 AAGTTTTGTGGACCGGTCGA 59.821 50.000 27.68 22.29 0.00 4.20
7314 8056 8.410673 AGAGTGTGTTGTAAATCTCTCTAGAA 57.589 34.615 0.00 0.00 34.44 2.10
7374 8116 5.009911 TGCTTTGCTGAAATCTTGCTTCTTA 59.990 36.000 0.00 0.00 0.00 2.10
7419 8161 3.675775 GCAGTTTGCAAAACACTGAAGGA 60.676 43.478 26.45 0.00 44.26 3.36
7451 8193 4.817318 ATTTGGTGTTGTTTGGTTCAGT 57.183 36.364 0.00 0.00 0.00 3.41
7495 8237 3.257393 CTTGGAGGAGATGTCAAGAACG 58.743 50.000 0.00 0.00 38.96 3.95
7516 8258 3.002791 TGATGTCCGATTGAGCTGAAAC 58.997 45.455 0.00 0.00 0.00 2.78
7572 8314 3.633525 ACTGCTGCAATTTCAGAACAGAA 59.366 39.130 15.72 0.00 36.19 3.02
7605 8347 4.699257 AGCATCAGATTTGAGAGTGGTTTC 59.301 41.667 0.00 0.00 36.61 2.78
7680 8422 0.759346 AACTTGGTGAGCTCGTTCCT 59.241 50.000 18.53 1.90 0.00 3.36
7710 8452 1.251251 GGAGGCTCAAATGTGCTTGT 58.749 50.000 17.69 0.00 35.15 3.16
7718 8460 0.482446 TGGTGGTTGGAGGCTCAAAT 59.518 50.000 17.69 0.00 0.00 2.32
7888 8644 3.879892 AGTGAAGTGAAGCAAGGAGAAAC 59.120 43.478 0.00 0.00 0.00 2.78
8093 8849 1.944709 CCATGACGATGACATGCATGT 59.055 47.619 31.82 31.82 45.16 3.21
8096 8852 0.540923 TCCCATGACGATGACATGCA 59.459 50.000 0.00 0.00 42.31 3.96
8115 8871 1.978455 TATTGGGGCGATTCGTGGCT 61.978 55.000 8.03 0.00 0.00 4.75
8155 8911 1.515954 GATCGAACCTCCCGAAGCA 59.484 57.895 0.00 0.00 39.62 3.91
8254 9010 2.058675 CCTCCAGGTTGACGTCCTT 58.941 57.895 14.12 0.00 32.37 3.36
8341 9097 2.485124 CCATCTTCTCCCTGATGCACTC 60.485 54.545 0.00 0.00 38.84 3.51
8365 9121 4.279671 GGTGTCATCCTCTAAGTCGATCAT 59.720 45.833 0.00 0.00 0.00 2.45
8396 9152 2.208431 CCATGGAGTTCAAGATCTCGC 58.792 52.381 5.56 0.00 0.00 5.03
8445 9201 3.047877 GGGTTTGTGCCGACGAGG 61.048 66.667 0.00 0.00 44.97 4.63
8529 9285 1.949847 GCAGCTCCCTCTTGACGCTA 61.950 60.000 0.00 0.00 0.00 4.26
8530 9286 2.977178 CAGCTCCCTCTTGACGCT 59.023 61.111 0.00 0.00 0.00 5.07
8669 9425 1.275010 TCTGGCACTTGTTAGCGATCA 59.725 47.619 0.00 0.00 0.00 2.92
8676 9432 3.211045 GAAGTTGGTCTGGCACTTGTTA 58.789 45.455 0.00 0.00 30.71 2.41
8680 9436 2.158623 TGATGAAGTTGGTCTGGCACTT 60.159 45.455 0.00 0.00 33.32 3.16
8689 9445 3.087031 CCTTGATGCTGATGAAGTTGGT 58.913 45.455 0.00 0.00 0.00 3.67
8711 9467 2.599757 ATGGTGAGCAGCTCTGGCA 61.600 57.895 23.15 0.17 41.70 4.92
8736 9492 2.293318 ATTGGCCTCGCTCTCACCA 61.293 57.895 3.32 0.00 0.00 4.17
8951 9707 1.768870 GATCCTGGCTTTAGGGTGCTA 59.231 52.381 0.00 0.00 38.42 3.49
9031 9788 1.492319 CCACTTTTGCGACGGTCGAA 61.492 55.000 32.48 21.56 43.74 3.71
9049 9806 1.153667 CTCTTCTGCCTGTCGAGCC 60.154 63.158 0.00 0.00 0.00 4.70
9050 9807 1.809209 GCTCTTCTGCCTGTCGAGC 60.809 63.158 0.00 0.00 40.07 5.03
9057 9814 2.903135 AGTGACTTTAGCTCTTCTGCCT 59.097 45.455 0.00 0.00 0.00 4.75
9320 10081 3.454858 TGCCCTTCTCAGAGGAAGTAAT 58.545 45.455 0.00 0.00 40.56 1.89
9341 10102 2.407361 CACGCGAGTTTTACGAGTTCAT 59.593 45.455 15.93 0.00 46.40 2.57
9555 10319 4.578898 ACGAACACGAGCGCACCA 62.579 61.111 11.47 0.00 0.00 4.17
9605 10369 1.142778 GAGCGCCTCGACATCAAGTC 61.143 60.000 2.29 0.00 44.02 3.01
9634 10398 3.660111 GCGAAAGTGCGTTGCCCT 61.660 61.111 0.00 0.00 0.00 5.19
9699 10463 1.608717 GGGTCAGCACAGGAGTCGAT 61.609 60.000 0.00 0.00 0.00 3.59
9703 10467 2.930562 GGGGGTCAGCACAGGAGT 60.931 66.667 0.00 0.00 0.00 3.85
9842 10608 1.290955 CCAGTCGAACAGGCCGTAA 59.709 57.895 0.00 0.00 0.00 3.18
9880 10646 2.244651 GGTCGCTGTTGTCGCACTT 61.245 57.895 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.