Multiple sequence alignment - TraesCS2A01G091100

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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 TraesCS2A01G091100 chr2A 100.000 8369 0 0 1 8369 43490466 43482098 0.000000e+00 15455.0
1 TraesCS2A01G091100 chr2A 90.899 901 46 16 6441 7309 43458742 43459638 0.000000e+00 1177.0
2 TraesCS2A01G091100 chr2A 90.888 845 55 14 6441 7266 43429988 43430829 0.000000e+00 1114.0
3 TraesCS2A01G091100 chr2A 92.462 650 37 5 727 1365 43458101 43458749 0.000000e+00 918.0
4 TraesCS2A01G091100 chr2A 88.403 526 47 10 847 1365 43429477 43429995 9.230000e-174 621.0
5 TraesCS2A01G091100 chr2A 83.019 106 5 6 7256 7349 43431095 43431199 5.380000e-12 84.2
6 TraesCS2A01G091100 chr4B 99.685 5075 11 1 1366 6440 20895111 20890042 0.000000e+00 9278.0
7 TraesCS2A01G091100 chr4B 87.455 1403 140 18 5046 6441 242677178 242675805 0.000000e+00 1583.0
8 TraesCS2A01G091100 chr4B 92.809 737 44 5 1366 2097 9995479 9996211 0.000000e+00 1059.0
9 TraesCS2A01G091100 chr4B 88.333 60 7 0 423 482 594536925 594536866 1.170000e-08 73.1
10 TraesCS2A01G091100 chr4B 88.136 59 3 3 418 472 652405188 652405246 5.420000e-07 67.6
11 TraesCS2A01G091100 chr6B 99.547 5076 17 2 1366 6440 578221348 578216278 0.000000e+00 9241.0
12 TraesCS2A01G091100 chr6B 91.228 57 5 0 423 479 358634661 358634605 2.500000e-10 78.7
13 TraesCS2A01G091100 chr6B 91.228 57 5 0 423 479 696787519 696787463 2.500000e-10 78.7
14 TraesCS2A01G091100 chr7B 99.488 5077 21 1 1364 6440 93335365 93330294 0.000000e+00 9226.0
15 TraesCS2A01G091100 chr7B 97.341 5077 125 5 1366 6440 243955206 243950138 0.000000e+00 8619.0
16 TraesCS2A01G091100 chr7B 92.857 56 4 0 428 483 114499661 114499606 1.940000e-11 82.4
17 TraesCS2A01G091100 chr7B 89.394 66 2 4 418 479 615810805 615810869 2.500000e-10 78.7
18 TraesCS2A01G091100 chr4D 92.910 5106 289 34 1365 6440 145689580 145694642 0.000000e+00 7356.0
19 TraesCS2A01G091100 chr4D 80.805 646 71 29 1366 1982 218260228 218260849 2.750000e-124 457.0
20 TraesCS2A01G091100 chr4D 80.800 625 69 29 1366 1961 218120485 218119883 7.710000e-120 442.0
21 TraesCS2A01G091100 chr4D 83.645 214 20 8 1389 1598 59449541 59449743 3.990000e-43 187.0
22 TraesCS2A01G091100 chr4D 91.228 57 5 0 423 479 364374202 364374258 2.500000e-10 78.7
23 TraesCS2A01G091100 chr7D 92.318 5103 281 43 1366 6440 178935100 178930081 0.000000e+00 7149.0
24 TraesCS2A01G091100 chr7D 87.431 907 91 12 7468 8369 156211796 156212684 0.000000e+00 1022.0
25 TraesCS2A01G091100 chr7D 93.617 47 3 0 428 474 530046058 530046012 4.190000e-08 71.3
26 TraesCS2A01G091100 chr7D 86.364 66 5 3 418 479 7730838 7730903 1.510000e-07 69.4
27 TraesCS2A01G091100 chr2B 92.023 5152 309 49 1354 6443 546330265 546335376 0.000000e+00 7143.0
28 TraesCS2A01G091100 chr2B 90.913 5117 372 47 1363 6441 228000950 228006011 0.000000e+00 6787.0
29 TraesCS2A01G091100 chr2B 97.512 804 20 0 1388 2191 214467856 214467053 0.000000e+00 1375.0
30 TraesCS2A01G091100 chr2B 92.711 878 53 6 6441 7308 67658590 67657714 0.000000e+00 1256.0
31 TraesCS2A01G091100 chr2B 90.970 897 64 10 6441 7327 67464878 67465767 0.000000e+00 1192.0
32 TraesCS2A01G091100 chr2B 89.936 934 60 17 6441 7344 67541479 67540550 0.000000e+00 1173.0
33 TraesCS2A01G091100 chr2B 97.970 542 11 0 5899 6440 214467056 214466515 0.000000e+00 941.0
34 TraesCS2A01G091100 chr2B 89.607 712 46 14 656 1365 67464200 67464885 0.000000e+00 880.0
35 TraesCS2A01G091100 chr2B 86.639 726 55 19 673 1365 67659299 67658583 0.000000e+00 765.0
36 TraesCS2A01G091100 chr2B 86.865 571 39 15 813 1365 67424074 67424626 2.580000e-169 606.0
37 TraesCS2A01G091100 chr2B 83.540 644 64 24 748 1365 67542099 67541472 1.580000e-156 564.0
38 TraesCS2A01G091100 chr2B 93.061 245 17 0 6441 6685 67424619 67424863 7.990000e-95 359.0
39 TraesCS2A01G091100 chr2B 83.232 328 40 10 7070 7388 67424874 67425195 3.820000e-73 287.0
40 TraesCS2A01G091100 chr2B 85.401 274 33 6 148 421 67661835 67661569 2.300000e-70 278.0
41 TraesCS2A01G091100 chr1D 91.646 5147 302 63 1366 6440 317792568 317787478 0.000000e+00 7005.0
42 TraesCS2A01G091100 chr1D 90.346 953 66 6 1359 2309 302286287 302287215 0.000000e+00 1227.0
43 TraesCS2A01G091100 chr1D 88.036 1003 97 13 7381 8366 475108392 475109388 0.000000e+00 1166.0
44 TraesCS2A01G091100 chr1D 85.998 957 110 17 7415 8354 419715010 419715959 0.000000e+00 1003.0
45 TraesCS2A01G091100 chr1D 83.750 320 40 6 1365 1673 209805860 209805542 8.220000e-75 292.0
46 TraesCS2A01G091100 chr5B 91.105 5160 316 70 1360 6441 588670557 588675651 0.000000e+00 6854.0
47 TraesCS2A01G091100 chr5B 90.897 5141 343 60 1364 6440 396636574 396641653 0.000000e+00 6785.0
48 TraesCS2A01G091100 chr5B 79.768 1295 177 57 5182 6440 166417407 166416162 0.000000e+00 861.0
49 TraesCS2A01G091100 chr5B 91.228 57 5 0 423 479 422292713 422292769 2.500000e-10 78.7
50 TraesCS2A01G091100 chr5B 91.228 57 5 0 423 479 620123680 620123736 2.500000e-10 78.7
51 TraesCS2A01G091100 chr2D 90.481 977 58 17 6441 7388 38637656 38638626 0.000000e+00 1256.0
52 TraesCS2A01G091100 chr2D 91.759 898 56 12 6441 7327 40902720 40901830 0.000000e+00 1232.0
53 TraesCS2A01G091100 chr2D 91.559 853 42 11 6441 7263 38782117 38781265 0.000000e+00 1149.0
54 TraesCS2A01G091100 chr2D 92.941 765 41 3 6441 7192 38678915 38679679 0.000000e+00 1101.0
55 TraesCS2A01G091100 chr2D 90.584 754 46 14 6441 7172 40850081 40850831 0.000000e+00 976.0
56 TraesCS2A01G091100 chr2D 90.909 627 42 8 6668 7283 38685834 38685212 0.000000e+00 828.0
57 TraesCS2A01G091100 chr2D 86.736 671 70 16 5774 6440 435227038 435226383 0.000000e+00 728.0
58 TraesCS2A01G091100 chr2D 88.036 560 35 16 813 1365 38678388 38678922 1.190000e-177 634.0
59 TraesCS2A01G091100 chr2D 89.498 438 36 7 938 1365 38637226 38637663 5.710000e-151 545.0
60 TraesCS2A01G091100 chr2D 87.007 431 43 7 939 1365 38782531 38782110 2.730000e-129 473.0
61 TraesCS2A01G091100 chr2D 86.897 435 39 11 939 1365 40903137 40902713 9.830000e-129 472.0
62 TraesCS2A01G091100 chr2D 88.511 235 27 0 6441 6675 38688466 38688232 1.370000e-72 285.0
63 TraesCS2A01G091100 chr2D 83.509 285 31 10 88 368 38741237 38740965 1.390000e-62 252.0
64 TraesCS2A01G091100 chr2D 91.279 172 15 0 1194 1365 40849917 40850088 1.400000e-57 235.0
65 TraesCS2A01G091100 chr2D 83.197 244 26 10 92 327 38783861 38783625 8.510000e-50 209.0
66 TraesCS2A01G091100 chr2D 83.197 244 26 10 92 327 40904466 40904230 8.510000e-50 209.0
67 TraesCS2A01G091100 chr2D 88.971 136 13 2 510 643 40903623 40903488 5.200000e-37 167.0
68 TraesCS2A01G091100 chr2D 88.235 136 14 2 510 643 38783017 38782882 2.420000e-35 161.0
69 TraesCS2A01G091100 chr2D 85.065 154 19 3 7237 7388 40851991 40852142 4.050000e-33 154.0
70 TraesCS2A01G091100 chr2D 81.208 149 14 8 7247 7388 38679678 38679819 3.190000e-19 108.0
71 TraesCS2A01G091100 chr2D 89.394 66 3 3 418 479 430440576 430440641 6.960000e-11 80.5
72 TraesCS2A01G091100 chr2D 94.231 52 2 1 428 479 144581674 144581624 2.500000e-10 78.7
73 TraesCS2A01G091100 chr3D 88.372 989 85 16 7387 8369 474653940 474652976 0.000000e+00 1162.0
74 TraesCS2A01G091100 chr3D 81.613 620 78 18 1365 1958 504565919 504566528 1.630000e-131 481.0
75 TraesCS2A01G091100 chr3D 89.474 57 6 0 423 479 7310312 7310256 1.170000e-08 73.1
76 TraesCS2A01G091100 chr3D 90.385 52 5 0 428 479 569549762 569549711 1.510000e-07 69.4
77 TraesCS2A01G091100 chr3D 91.304 46 3 1 437 482 30623304 30623260 2.520000e-05 62.1
78 TraesCS2A01G091100 chr3A 87.600 1000 94 13 7387 8369 175639168 175638182 0.000000e+00 1133.0
79 TraesCS2A01G091100 chr3A 85.513 994 125 15 7385 8369 98955946 98954963 0.000000e+00 1020.0
80 TraesCS2A01G091100 chr3A 85.300 1000 110 26 7385 8369 23311924 23310947 0.000000e+00 998.0
81 TraesCS2A01G091100 chr3A 91.228 57 5 0 423 479 151034536 151034592 2.500000e-10 78.7
82 TraesCS2A01G091100 chr5D 87.313 1001 102 15 7382 8369 549990445 549989457 0.000000e+00 1122.0
83 TraesCS2A01G091100 chr5D 85.030 1002 120 19 7385 8369 38746856 38745868 0.000000e+00 992.0
84 TraesCS2A01G091100 chr4A 93.378 740 44 2 1366 2100 284641423 284640684 0.000000e+00 1090.0
85 TraesCS2A01G091100 chr4A 92.857 56 3 1 428 482 604596052 604595997 6.960000e-11 80.5
86 TraesCS2A01G091100 chr6A 85.657 990 126 15 7387 8369 1548301 1549281 0.000000e+00 1027.0
87 TraesCS2A01G091100 chr6A 91.228 57 5 0 423 479 474503403 474503459 2.500000e-10 78.7
88 TraesCS2A01G091100 chr5A 80.515 1360 156 60 5137 6440 598760551 598761857 0.000000e+00 942.0
89 TraesCS2A01G091100 chr5A 91.228 57 5 0 423 479 96921569 96921625 2.500000e-10 78.7
90 TraesCS2A01G091100 chr6D 82.222 225 26 7 1378 1598 2367545 2367759 1.860000e-41 182.0
91 TraesCS2A01G091100 chr6D 80.889 225 30 8 6233 6456 446136444 446136232 1.870000e-36 165.0
92 TraesCS2A01G091100 chr6D 81.347 193 23 5 1352 1544 446137007 446136828 2.430000e-30 145.0
93 TraesCS2A01G091100 chr6D 88.158 76 3 1 6371 6440 303756318 303756393 1.500000e-12 86.1
94 TraesCS2A01G091100 chr6D 91.837 49 2 2 428 475 20792576 20792623 5.420000e-07 67.6
95 TraesCS2A01G091100 chr6D 100.000 34 0 0 1364 1397 2367521 2367554 7.010000e-06 63.9
96 TraesCS2A01G091100 chrUn 92.308 52 4 0 428 479 94844011 94843960 3.240000e-09 75.0
97 TraesCS2A01G091100 chr1A 92.308 52 4 0 428 479 288510313 288510262 3.240000e-09 75.0
98 TraesCS2A01G091100 chr1A 89.091 55 6 0 428 482 52053906 52053852 1.510000e-07 69.4


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 TraesCS2A01G091100 chr2A 43482098 43490466 8368 True 15455.000000 15455 100.000000 1 8369 1 chr2A.!!$R1 8368
1 TraesCS2A01G091100 chr2A 43458101 43459638 1537 False 1047.500000 1177 91.680500 727 7309 2 chr2A.!!$F2 6582
2 TraesCS2A01G091100 chr2A 43429477 43431199 1722 False 606.400000 1114 87.436667 847 7349 3 chr2A.!!$F1 6502
3 TraesCS2A01G091100 chr4B 20890042 20895111 5069 True 9278.000000 9278 99.685000 1366 6440 1 chr4B.!!$R1 5074
4 TraesCS2A01G091100 chr4B 242675805 242677178 1373 True 1583.000000 1583 87.455000 5046 6441 1 chr4B.!!$R2 1395
5 TraesCS2A01G091100 chr4B 9995479 9996211 732 False 1059.000000 1059 92.809000 1366 2097 1 chr4B.!!$F1 731
6 TraesCS2A01G091100 chr6B 578216278 578221348 5070 True 9241.000000 9241 99.547000 1366 6440 1 chr6B.!!$R2 5074
7 TraesCS2A01G091100 chr7B 93330294 93335365 5071 True 9226.000000 9226 99.488000 1364 6440 1 chr7B.!!$R1 5076
8 TraesCS2A01G091100 chr7B 243950138 243955206 5068 True 8619.000000 8619 97.341000 1366 6440 1 chr7B.!!$R3 5074
9 TraesCS2A01G091100 chr4D 145689580 145694642 5062 False 7356.000000 7356 92.910000 1365 6440 1 chr4D.!!$F2 5075
10 TraesCS2A01G091100 chr4D 218260228 218260849 621 False 457.000000 457 80.805000 1366 1982 1 chr4D.!!$F3 616
11 TraesCS2A01G091100 chr4D 218119883 218120485 602 True 442.000000 442 80.800000 1366 1961 1 chr4D.!!$R1 595
12 TraesCS2A01G091100 chr7D 178930081 178935100 5019 True 7149.000000 7149 92.318000 1366 6440 1 chr7D.!!$R1 5074
13 TraesCS2A01G091100 chr7D 156211796 156212684 888 False 1022.000000 1022 87.431000 7468 8369 1 chr7D.!!$F2 901
14 TraesCS2A01G091100 chr2B 546330265 546335376 5111 False 7143.000000 7143 92.023000 1354 6443 1 chr2B.!!$F2 5089
15 TraesCS2A01G091100 chr2B 228000950 228006011 5061 False 6787.000000 6787 90.913000 1363 6441 1 chr2B.!!$F1 5078
16 TraesCS2A01G091100 chr2B 214466515 214467856 1341 True 1158.000000 1375 97.741000 1388 6440 2 chr2B.!!$R3 5052
17 TraesCS2A01G091100 chr2B 67464200 67465767 1567 False 1036.000000 1192 90.288500 656 7327 2 chr2B.!!$F4 6671
18 TraesCS2A01G091100 chr2B 67540550 67542099 1549 True 868.500000 1173 86.738000 748 7344 2 chr2B.!!$R1 6596
19 TraesCS2A01G091100 chr2B 67657714 67661835 4121 True 766.333333 1256 88.250333 148 7308 3 chr2B.!!$R2 7160
20 TraesCS2A01G091100 chr2B 67424074 67425195 1121 False 417.333333 606 87.719333 813 7388 3 chr2B.!!$F3 6575
21 TraesCS2A01G091100 chr1D 317787478 317792568 5090 True 7005.000000 7005 91.646000 1366 6440 1 chr1D.!!$R2 5074
22 TraesCS2A01G091100 chr1D 302286287 302287215 928 False 1227.000000 1227 90.346000 1359 2309 1 chr1D.!!$F1 950
23 TraesCS2A01G091100 chr1D 475108392 475109388 996 False 1166.000000 1166 88.036000 7381 8366 1 chr1D.!!$F3 985
24 TraesCS2A01G091100 chr1D 419715010 419715959 949 False 1003.000000 1003 85.998000 7415 8354 1 chr1D.!!$F2 939
25 TraesCS2A01G091100 chr5B 588670557 588675651 5094 False 6854.000000 6854 91.105000 1360 6441 1 chr5B.!!$F3 5081
26 TraesCS2A01G091100 chr5B 396636574 396641653 5079 False 6785.000000 6785 90.897000 1364 6440 1 chr5B.!!$F1 5076
27 TraesCS2A01G091100 chr5B 166416162 166417407 1245 True 861.000000 861 79.768000 5182 6440 1 chr5B.!!$R1 1258
28 TraesCS2A01G091100 chr2D 38637226 38638626 1400 False 900.500000 1256 89.989500 938 7388 2 chr2D.!!$F2 6450
29 TraesCS2A01G091100 chr2D 435226383 435227038 655 True 728.000000 728 86.736000 5774 6440 1 chr2D.!!$R3 666
30 TraesCS2A01G091100 chr2D 38678388 38679819 1431 False 614.333333 1101 87.395000 813 7388 3 chr2D.!!$F3 6575
31 TraesCS2A01G091100 chr2D 38685212 38688466 3254 True 556.500000 828 89.710000 6441 7283 2 chr2D.!!$R4 842
32 TraesCS2A01G091100 chr2D 40901830 40904466 2636 True 520.000000 1232 87.706000 92 7327 4 chr2D.!!$R6 7235
33 TraesCS2A01G091100 chr2D 38781265 38783861 2596 True 498.000000 1149 87.499500 92 7263 4 chr2D.!!$R5 7171
34 TraesCS2A01G091100 chr2D 40849917 40852142 2225 False 455.000000 976 88.976000 1194 7388 3 chr2D.!!$F4 6194
35 TraesCS2A01G091100 chr3D 474652976 474653940 964 True 1162.000000 1162 88.372000 7387 8369 1 chr3D.!!$R3 982
36 TraesCS2A01G091100 chr3D 504565919 504566528 609 False 481.000000 481 81.613000 1365 1958 1 chr3D.!!$F1 593
37 TraesCS2A01G091100 chr3A 175638182 175639168 986 True 1133.000000 1133 87.600000 7387 8369 1 chr3A.!!$R3 982
38 TraesCS2A01G091100 chr3A 98954963 98955946 983 True 1020.000000 1020 85.513000 7385 8369 1 chr3A.!!$R2 984
39 TraesCS2A01G091100 chr3A 23310947 23311924 977 True 998.000000 998 85.300000 7385 8369 1 chr3A.!!$R1 984
40 TraesCS2A01G091100 chr5D 549989457 549990445 988 True 1122.000000 1122 87.313000 7382 8369 1 chr5D.!!$R2 987
41 TraesCS2A01G091100 chr5D 38745868 38746856 988 True 992.000000 992 85.030000 7385 8369 1 chr5D.!!$R1 984
42 TraesCS2A01G091100 chr4A 284640684 284641423 739 True 1090.000000 1090 93.378000 1366 2100 1 chr4A.!!$R1 734
43 TraesCS2A01G091100 chr6A 1548301 1549281 980 False 1027.000000 1027 85.657000 7387 8369 1 chr6A.!!$F1 982
44 TraesCS2A01G091100 chr5A 598760551 598761857 1306 False 942.000000 942 80.515000 5137 6440 1 chr5A.!!$F2 1303

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
97 98 0.108138 CCGGGTGAATGAGTGAGACC 60.108 60.000 0.00 0.00 0.00 3.85 F
573 2894 0.171903 TAGACGCGGCTCTGTAAACC 59.828 55.000 23.11 0.00 0.00 3.27 F
643 2964 0.460109 TTGACCTGATGATCGCACGG 60.460 55.000 0.00 0.00 0.00 4.94 F
1083 3722 0.863538 CATGACCGCTCTCGACTTCG 60.864 60.000 0.00 0.00 38.10 3.79 F
1496 4163 2.025898 TGCGGATTATGTCGGACTACA 58.974 47.619 9.88 0.00 0.00 2.74 F
5065 7887 3.267759 GCAACACTGCTTTTGCTCCGA 62.268 52.381 0.00 0.00 45.74 4.55 F
5324 8166 2.193536 GCAAGTGTTGGCCGGAACT 61.194 57.895 5.05 3.11 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 4016 1.257750 ATCCCTAGTCGCAGTGCACA 61.258 55.000 21.04 0.00 0.00 4.57 R
1496 4163 3.288290 CGCCTCCGCTCCGTATCT 61.288 66.667 0.00 0.00 0.00 1.98 R
2605 5413 8.051535 CCTTCATGATGATTAATGCCCTATACT 58.948 37.037 10.07 0.00 0.00 2.12 R
5065 7887 5.407407 ACTATTCAGTTCAGATCACCGTT 57.593 39.130 0.00 0.00 0.00 4.44 R
5324 8166 9.298250 AGAGACAGACAGAAACAGTAGTATTTA 57.702 33.333 0.00 0.00 0.00 1.40 R
7160 12662 0.040692 GTGACACTCGAGCACGTACA 60.041 55.000 13.61 5.51 40.69 2.90 R
7784 14782 0.242825 GGTCCTCGACAATGACGACA 59.757 55.000 3.42 0.00 35.88 4.35 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
28 29 3.010624 CGATAGTGCACATCAGGAGAG 57.989 52.381 21.04 3.05 0.00 3.20
29 30 2.753296 GATAGTGCACATCAGGAGAGC 58.247 52.381 21.04 0.00 0.00 4.09
30 31 1.857965 TAGTGCACATCAGGAGAGCT 58.142 50.000 21.04 0.00 0.00 4.09
31 32 1.857965 AGTGCACATCAGGAGAGCTA 58.142 50.000 21.04 0.00 0.00 3.32
32 33 1.480137 AGTGCACATCAGGAGAGCTAC 59.520 52.381 21.04 0.00 0.00 3.58
33 34 1.205655 GTGCACATCAGGAGAGCTACA 59.794 52.381 13.17 0.00 0.00 2.74
34 35 2.113807 TGCACATCAGGAGAGCTACAT 58.886 47.619 0.00 0.00 0.00 2.29
35 36 2.159000 TGCACATCAGGAGAGCTACATG 60.159 50.000 0.00 0.00 0.00 3.21
36 37 2.158986 GCACATCAGGAGAGCTACATGT 60.159 50.000 2.69 2.69 0.00 3.21
37 38 3.455327 CACATCAGGAGAGCTACATGTG 58.545 50.000 9.11 0.00 36.28 3.21
38 39 3.131755 CACATCAGGAGAGCTACATGTGA 59.868 47.826 9.11 0.00 42.41 3.58
39 40 3.966006 ACATCAGGAGAGCTACATGTGAT 59.034 43.478 9.11 0.00 0.00 3.06
40 41 4.408270 ACATCAGGAGAGCTACATGTGATT 59.592 41.667 9.11 0.00 0.00 2.57
41 42 4.397481 TCAGGAGAGCTACATGTGATTG 57.603 45.455 9.11 0.00 0.00 2.67
42 43 2.871022 CAGGAGAGCTACATGTGATTGC 59.129 50.000 9.11 7.66 0.00 3.56
43 44 2.502947 AGGAGAGCTACATGTGATTGCA 59.497 45.455 9.11 0.00 0.00 4.08
44 45 2.871022 GGAGAGCTACATGTGATTGCAG 59.129 50.000 9.11 0.00 0.00 4.41
45 46 2.286872 AGAGCTACATGTGATTGCAGC 58.713 47.619 9.11 8.33 0.00 5.25
46 47 2.011947 GAGCTACATGTGATTGCAGCA 58.988 47.619 16.25 0.00 0.00 4.41
47 48 2.014857 AGCTACATGTGATTGCAGCAG 58.985 47.619 16.25 1.09 0.00 4.24
48 49 2.011947 GCTACATGTGATTGCAGCAGA 58.988 47.619 9.11 0.00 0.00 4.26
49 50 2.617308 GCTACATGTGATTGCAGCAGAT 59.383 45.455 9.11 0.00 0.00 2.90
50 51 3.303857 GCTACATGTGATTGCAGCAGATC 60.304 47.826 9.11 3.08 0.00 2.75
51 52 2.718563 ACATGTGATTGCAGCAGATCA 58.281 42.857 13.24 13.24 0.00 2.92
52 53 3.288092 ACATGTGATTGCAGCAGATCAT 58.712 40.909 17.74 9.74 35.01 2.45
53 54 4.457466 ACATGTGATTGCAGCAGATCATA 58.543 39.130 17.74 16.17 35.01 2.15
54 55 5.070685 ACATGTGATTGCAGCAGATCATAT 58.929 37.500 17.74 17.23 35.37 1.78
55 56 5.393962 CATGTGATTGCAGCAGATCATATG 58.606 41.667 25.07 25.07 41.87 1.78
56 57 3.252458 TGTGATTGCAGCAGATCATATGC 59.748 43.478 17.74 0.00 44.18 3.14
57 58 2.817844 TGATTGCAGCAGATCATATGCC 59.182 45.455 0.00 0.00 44.97 4.40
58 59 2.651382 TTGCAGCAGATCATATGCCT 57.349 45.000 0.00 0.00 44.97 4.75
59 60 3.775261 TTGCAGCAGATCATATGCCTA 57.225 42.857 0.00 0.00 44.97 3.93
60 61 3.329929 TGCAGCAGATCATATGCCTAG 57.670 47.619 0.00 0.00 44.97 3.02
61 62 2.008329 GCAGCAGATCATATGCCTAGC 58.992 52.381 0.00 0.00 44.97 3.42
62 63 2.614734 GCAGCAGATCATATGCCTAGCA 60.615 50.000 0.00 0.00 44.97 3.49
63 64 3.263261 CAGCAGATCATATGCCTAGCAG 58.737 50.000 0.00 0.00 43.65 4.24
64 65 3.056035 CAGCAGATCATATGCCTAGCAGA 60.056 47.826 0.00 0.00 43.65 4.26
65 66 3.196039 AGCAGATCATATGCCTAGCAGAG 59.804 47.826 0.00 0.00 43.65 3.35
67 68 3.106054 AGATCATATGCCTAGCAGAGGG 58.894 50.000 6.80 0.00 46.81 4.30
68 69 0.979665 TCATATGCCTAGCAGAGGGC 59.020 55.000 6.80 4.80 46.81 5.19
72 73 2.820973 GCCTAGCAGAGGGCAGAG 59.179 66.667 6.80 0.00 46.81 3.35
73 74 1.760086 GCCTAGCAGAGGGCAGAGA 60.760 63.158 6.80 0.00 46.81 3.10
74 75 1.120795 GCCTAGCAGAGGGCAGAGAT 61.121 60.000 6.80 0.00 46.81 2.75
75 76 1.825242 GCCTAGCAGAGGGCAGAGATA 60.825 57.143 6.80 0.00 46.81 1.98
76 77 3.152373 GCCTAGCAGAGGGCAGAGATAT 61.152 54.545 6.80 0.00 46.81 1.63
77 78 4.995434 GCCTAGCAGAGGGCAGAGATATC 61.995 56.522 6.80 0.00 46.81 1.63
79 80 0.612744 GCAGAGGGCAGAGATATCCC 59.387 60.000 0.00 0.00 43.97 3.85
80 81 0.894141 CAGAGGGCAGAGATATCCCG 59.106 60.000 0.00 0.00 44.70 5.14
81 82 0.252012 AGAGGGCAGAGATATCCCGG 60.252 60.000 0.00 0.00 44.70 5.73
82 83 1.229336 AGGGCAGAGATATCCCGGG 60.229 63.158 16.85 16.85 44.70 5.73
83 84 1.536662 GGGCAGAGATATCCCGGGT 60.537 63.158 22.86 10.79 0.00 5.28
84 85 1.674057 GGCAGAGATATCCCGGGTG 59.326 63.158 22.86 10.81 0.00 4.61
85 86 0.832135 GGCAGAGATATCCCGGGTGA 60.832 60.000 22.86 10.30 0.00 4.02
86 87 1.048601 GCAGAGATATCCCGGGTGAA 58.951 55.000 22.86 7.58 0.00 3.18
87 88 1.625818 GCAGAGATATCCCGGGTGAAT 59.374 52.381 22.86 12.59 0.00 2.57
88 89 2.613977 GCAGAGATATCCCGGGTGAATG 60.614 54.545 22.86 12.31 0.00 2.67
89 90 2.899900 CAGAGATATCCCGGGTGAATGA 59.100 50.000 22.86 0.00 0.00 2.57
90 91 3.056250 CAGAGATATCCCGGGTGAATGAG 60.056 52.174 22.86 1.86 0.00 2.90
97 98 0.108138 CCGGGTGAATGAGTGAGACC 60.108 60.000 0.00 0.00 0.00 3.85
101 102 3.486383 GGGTGAATGAGTGAGACCAAAA 58.514 45.455 0.00 0.00 0.00 2.44
105 106 5.455392 GTGAATGAGTGAGACCAAAATGTG 58.545 41.667 0.00 0.00 0.00 3.21
106 107 4.022935 TGAATGAGTGAGACCAAAATGTGC 60.023 41.667 0.00 0.00 0.00 4.57
117 118 1.042229 AAAATGTGCAGGCAAGCAGA 58.958 45.000 4.83 4.60 46.69 4.26
121 123 1.288127 GTGCAGGCAAGCAGAAAGG 59.712 57.895 4.83 0.00 46.69 3.11
129 131 1.152368 AAGCAGAAAGGGTGCAGCT 59.848 52.632 16.65 0.83 43.82 4.24
182 191 1.209261 TCAGGCTACCAATCAATGCGA 59.791 47.619 0.00 0.00 0.00 5.10
192 201 3.251487 CCAATCAATGCGATCATGTGCTA 59.749 43.478 8.37 0.00 31.11 3.49
202 211 7.903995 TGCGATCATGTGCTATCAAATATAA 57.096 32.000 8.37 0.00 0.00 0.98
223 232 3.907221 AGTGGGCATGATTAGCTCAAAT 58.093 40.909 0.00 0.00 45.39 2.32
224 233 3.887716 AGTGGGCATGATTAGCTCAAATC 59.112 43.478 0.00 0.00 45.39 2.17
227 236 3.633525 GGGCATGATTAGCTCAAATCACA 59.366 43.478 12.96 0.00 45.90 3.58
233 242 2.010145 TAGCTCAAATCACAGACGCC 57.990 50.000 0.00 0.00 0.00 5.68
240 249 3.758023 TCAAATCACAGACGCCAAATGAT 59.242 39.130 0.00 0.00 0.00 2.45
245 254 5.697473 TCACAGACGCCAAATGATAAAAA 57.303 34.783 0.00 0.00 0.00 1.94
246 255 5.698832 TCACAGACGCCAAATGATAAAAAG 58.301 37.500 0.00 0.00 0.00 2.27
249 258 6.640499 CACAGACGCCAAATGATAAAAAGAAA 59.360 34.615 0.00 0.00 0.00 2.52
250 259 6.640907 ACAGACGCCAAATGATAAAAAGAAAC 59.359 34.615 0.00 0.00 0.00 2.78
251 260 6.640499 CAGACGCCAAATGATAAAAAGAAACA 59.360 34.615 0.00 0.00 0.00 2.83
252 261 7.168972 CAGACGCCAAATGATAAAAAGAAACAA 59.831 33.333 0.00 0.00 0.00 2.83
265 274 0.593128 GAAACAAGGTCGTGCTGCAT 59.407 50.000 5.27 0.00 0.00 3.96
306 315 0.758734 TCAACCGGCTGCAGCTATAT 59.241 50.000 35.82 18.56 41.70 0.86
310 319 1.001406 ACCGGCTGCAGCTATATCTTC 59.999 52.381 35.82 16.98 41.70 2.87
340 349 1.485895 GCTTCTCTTCCTCTGCATCCT 59.514 52.381 0.00 0.00 0.00 3.24
358 367 5.911752 CATCCTTCACTAGATGCAACTACT 58.088 41.667 0.00 0.00 33.99 2.57
359 368 6.344500 CATCCTTCACTAGATGCAACTACTT 58.656 40.000 0.00 0.00 33.99 2.24
360 369 7.492524 CATCCTTCACTAGATGCAACTACTTA 58.507 38.462 0.00 0.00 33.99 2.24
395 869 9.326413 CCAACAAGATTTACTCCGTATATTCTT 57.674 33.333 0.00 0.00 0.00 2.52
421 895 5.893255 TGCTGGATCTTGCTAAAATGGTATT 59.107 36.000 10.71 0.00 0.00 1.89
422 896 6.380846 TGCTGGATCTTGCTAAAATGGTATTT 59.619 34.615 10.71 0.00 0.00 1.40
423 897 7.093377 TGCTGGATCTTGCTAAAATGGTATTTT 60.093 33.333 10.71 5.07 0.00 1.82
424 898 7.765819 GCTGGATCTTGCTAAAATGGTATTTTT 59.234 33.333 5.02 0.00 33.56 1.94
469 943 9.402320 TCCATTTTGATGATAAGTATTTTCGGA 57.598 29.630 0.00 0.00 0.00 4.55
470 944 9.450807 CCATTTTGATGATAAGTATTTTCGGAC 57.549 33.333 0.00 0.00 0.00 4.79
471 945 9.158364 CATTTTGATGATAAGTATTTTCGGACG 57.842 33.333 0.00 0.00 0.00 4.79
472 946 8.481974 TTTTGATGATAAGTATTTTCGGACGA 57.518 30.769 0.00 0.00 0.00 4.20
473 947 8.481974 TTTGATGATAAGTATTTTCGGACGAA 57.518 30.769 2.62 2.62 0.00 3.85
474 948 7.694388 TGATGATAAGTATTTTCGGACGAAG 57.306 36.000 7.25 0.00 35.38 3.79
475 949 6.700081 TGATGATAAGTATTTTCGGACGAAGG 59.300 38.462 7.25 0.00 35.38 3.46
476 950 5.353938 TGATAAGTATTTTCGGACGAAGGG 58.646 41.667 7.25 0.00 35.38 3.95
477 951 3.967332 AAGTATTTTCGGACGAAGGGA 57.033 42.857 7.25 0.00 35.38 4.20
478 952 3.521947 AGTATTTTCGGACGAAGGGAG 57.478 47.619 7.25 0.00 35.38 4.30
479 953 3.094572 AGTATTTTCGGACGAAGGGAGA 58.905 45.455 7.25 0.00 35.38 3.71
480 954 3.512724 AGTATTTTCGGACGAAGGGAGAA 59.487 43.478 7.25 0.00 35.38 2.87
481 955 3.629142 ATTTTCGGACGAAGGGAGAAT 57.371 42.857 7.25 1.95 35.38 2.40
482 956 2.667473 TTTCGGACGAAGGGAGAATC 57.333 50.000 7.25 0.00 35.38 2.52
518 992 3.467226 CGCCCACGGGTCCAGTAT 61.467 66.667 3.54 0.00 37.65 2.12
521 1043 2.367202 CCCACGGGTCCAGTATGCT 61.367 63.158 0.00 0.00 31.97 3.79
533 1055 3.452264 TCCAGTATGCTGTGCAAGACTAT 59.548 43.478 10.09 0.00 43.62 2.12
534 1056 4.649218 TCCAGTATGCTGTGCAAGACTATA 59.351 41.667 10.09 1.18 43.62 1.31
535 1057 4.747108 CCAGTATGCTGTGCAAGACTATAC 59.253 45.833 10.09 0.00 43.62 1.47
536 1058 5.452496 CCAGTATGCTGTGCAAGACTATACT 60.452 44.000 10.09 0.00 43.62 2.12
537 1059 6.239036 CCAGTATGCTGTGCAAGACTATACTA 60.239 42.308 10.09 0.00 43.62 1.82
538 1060 7.203218 CAGTATGCTGTGCAAGACTATACTAA 58.797 38.462 2.12 0.00 43.62 2.24
539 1061 7.168302 CAGTATGCTGTGCAAGACTATACTAAC 59.832 40.741 2.12 0.00 43.62 2.34
573 2894 0.171903 TAGACGCGGCTCTGTAAACC 59.828 55.000 23.11 0.00 0.00 3.27
589 2910 9.469807 CTCTGTAAACCATGATTACTCTCATAC 57.530 37.037 17.01 0.00 34.11 2.39
621 2942 2.427095 ACTTGGAGCACAAAAAGGTGAC 59.573 45.455 0.00 0.00 41.32 3.67
639 2960 2.159184 TGACTCTTGACCTGATGATCGC 60.159 50.000 0.00 0.00 0.00 4.58
643 2964 0.460109 TTGACCTGATGATCGCACGG 60.460 55.000 0.00 0.00 0.00 4.94
644 2965 1.592669 GACCTGATGATCGCACGGG 60.593 63.158 9.08 9.08 36.28 5.28
645 2966 2.298158 GACCTGATGATCGCACGGGT 62.298 60.000 14.18 14.18 44.64 5.28
668 3208 1.543802 GAACGGCCATCATTTGACCAA 59.456 47.619 2.24 0.00 0.00 3.67
671 3211 1.560505 GGCCATCATTTGACCAACCT 58.439 50.000 0.00 0.00 0.00 3.50
710 3268 3.188011 CAGATGGCACTGCTGCTG 58.812 61.111 4.89 4.89 43.66 4.41
711 3269 2.750637 AGATGGCACTGCTGCTGC 60.751 61.111 8.89 8.89 43.66 5.25
712 3270 2.750637 GATGGCACTGCTGCTGCT 60.751 61.111 17.00 0.00 43.66 4.24
713 3271 1.450848 GATGGCACTGCTGCTGCTA 60.451 57.895 17.00 7.95 43.66 3.49
714 3272 1.437772 GATGGCACTGCTGCTGCTAG 61.438 60.000 17.00 13.80 43.66 3.42
715 3273 3.507009 GGCACTGCTGCTGCTAGC 61.507 66.667 17.00 8.10 43.66 3.42
716 3274 2.436292 GCACTGCTGCTGCTAGCT 60.436 61.111 17.23 0.00 42.97 3.32
717 3275 2.751913 GCACTGCTGCTGCTAGCTG 61.752 63.158 17.23 16.92 42.97 4.24
780 3344 1.226101 CGCCATGAACGCACACATC 60.226 57.895 0.00 0.00 0.00 3.06
1043 3668 2.674852 CTGAAAGTCCCACACATCATCG 59.325 50.000 0.00 0.00 0.00 3.84
1083 3722 0.863538 CATGACCGCTCTCGACTTCG 60.864 60.000 0.00 0.00 38.10 3.79
1262 3926 3.904233 GATTGTGCGCGCGTTCGTT 62.904 57.895 32.35 14.02 38.14 3.85
1496 4163 2.025898 TGCGGATTATGTCGGACTACA 58.974 47.619 9.88 0.00 0.00 2.74
5065 7887 3.267759 GCAACACTGCTTTTGCTCCGA 62.268 52.381 0.00 0.00 45.74 4.55
5324 8166 2.193536 GCAAGTGTTGGCCGGAACT 61.194 57.895 5.05 3.11 0.00 3.01
6462 9497 3.681835 GACGTGTCGGTGGAGGCT 61.682 66.667 0.00 0.00 0.00 4.58
7080 12562 2.280592 GGGCACAACCTCGTCGTT 60.281 61.111 0.00 0.00 39.10 3.85
7137 12626 2.618241 GCTGTGATGGTGAAGTCAAACA 59.382 45.455 0.00 0.00 0.00 2.83
7159 12661 1.361204 TTGAGATGCAGTTGGAGGGA 58.639 50.000 0.00 0.00 0.00 4.20
7160 12662 1.588239 TGAGATGCAGTTGGAGGGAT 58.412 50.000 0.00 0.00 0.00 3.85
7197 12704 2.760650 TCACCATCAAGTACAGCTCGAT 59.239 45.455 0.00 0.00 0.00 3.59
7198 12705 3.951680 TCACCATCAAGTACAGCTCGATA 59.048 43.478 0.00 0.00 0.00 2.92
7226 12737 0.028505 CAAGCCGCATGCATGTACTC 59.971 55.000 26.79 13.88 44.83 2.59
7302 14229 5.621197 TGGTGTTTATTCGATCTGTTTGG 57.379 39.130 0.00 0.00 0.00 3.28
7349 14291 4.583073 GCCTGGTTTTTCTTCTTCTTACCA 59.417 41.667 0.00 0.00 33.50 3.25
7360 14302 7.083875 TCTTCTTCTTACCAAAACTGTTGTG 57.916 36.000 3.64 3.64 0.00 3.33
7364 14306 4.337145 TCTTACCAAAACTGTTGTGGTGT 58.663 39.130 35.00 18.58 45.30 4.16
7377 14319 0.179134 GTGGTGTCCGGATCGAGAAG 60.179 60.000 7.81 0.00 0.00 2.85
7436 14379 1.953311 GCGCTAAAAATCACCCCCTGA 60.953 52.381 0.00 0.00 0.00 3.86
7461 14405 1.005867 ACCGGCGTAAATCGTGTGT 60.006 52.632 6.01 0.00 42.13 3.72
7541 14493 1.791785 CAAACACGGCGCAAATTCAAT 59.208 42.857 10.83 0.00 0.00 2.57
7743 14735 3.655211 CAGCTGCACCCCTTCCCT 61.655 66.667 0.00 0.00 0.00 4.20
7773 14771 3.628982 GGGTTGAACGGTCCGGGA 61.629 66.667 17.28 0.00 0.00 5.14
7791 14789 2.050714 GCGTCCTCGTTGTCGTCA 60.051 61.111 0.00 0.00 39.49 4.35
7792 14790 1.443872 GCGTCCTCGTTGTCGTCAT 60.444 57.895 0.00 0.00 39.49 3.06
7802 14800 1.719780 GTTGTCGTCATTGTCGAGGAC 59.280 52.381 6.25 6.78 46.22 3.85
7853 14851 2.989824 GCGGGCGGCTATCTCCTA 60.990 66.667 9.56 0.00 39.11 2.94
7881 14879 4.147449 CGCTGCCGGACCATCTCA 62.147 66.667 5.05 0.00 0.00 3.27
7993 14992 1.198094 TCCACCTTCGGCCTGATGAA 61.198 55.000 0.00 0.00 0.00 2.57
8179 15181 2.197605 TCCACGAGCTTCCACGTCA 61.198 57.895 0.00 0.00 40.76 4.35
8200 15202 2.606826 GGAGAAGGACGGGGGTGT 60.607 66.667 0.00 0.00 0.00 4.16
8210 15212 2.124312 GGGGGTGTGGGGTACTCT 59.876 66.667 0.00 0.00 0.00 3.24
8216 15218 1.569653 GTGTGGGGTACTCTAGCCTT 58.430 55.000 0.00 0.00 45.49 4.35
8220 15222 0.981277 GGGGTACTCTAGCCTTGGCA 60.981 60.000 14.54 0.00 45.49 4.92
8237 15239 1.227527 CATGTTGCCGCCCTCGATA 60.228 57.895 0.00 0.00 38.10 2.92
8348 15351 4.074526 GTGGCCTCGAGCTGCTCA 62.075 66.667 27.46 14.45 43.05 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.760650 TCTCCTGATGTGCACTATCGTT 59.239 45.455 19.41 0.00 0.00 3.85
7 8 2.360483 CTCTCCTGATGTGCACTATCGT 59.640 50.000 19.41 0.00 0.00 3.73
8 9 2.861750 GCTCTCCTGATGTGCACTATCG 60.862 54.545 19.41 13.69 0.00 2.92
9 10 2.364970 AGCTCTCCTGATGTGCACTATC 59.635 50.000 19.41 18.10 0.00 2.08
10 11 2.396608 AGCTCTCCTGATGTGCACTAT 58.603 47.619 19.41 9.88 0.00 2.12
11 12 1.857965 AGCTCTCCTGATGTGCACTA 58.142 50.000 19.41 4.84 0.00 2.74
12 13 1.480137 GTAGCTCTCCTGATGTGCACT 59.520 52.381 19.41 3.19 0.00 4.40
13 14 1.205655 TGTAGCTCTCCTGATGTGCAC 59.794 52.381 10.75 10.75 0.00 4.57
14 15 1.560505 TGTAGCTCTCCTGATGTGCA 58.439 50.000 0.00 0.00 0.00 4.57
15 16 2.158986 ACATGTAGCTCTCCTGATGTGC 60.159 50.000 0.00 0.00 30.83 4.57
16 17 3.131755 TCACATGTAGCTCTCCTGATGTG 59.868 47.826 0.00 0.00 41.96 3.21
17 18 3.369175 TCACATGTAGCTCTCCTGATGT 58.631 45.455 0.00 0.00 31.63 3.06
18 19 4.603989 ATCACATGTAGCTCTCCTGATG 57.396 45.455 0.00 0.00 0.00 3.07
19 20 4.743045 GCAATCACATGTAGCTCTCCTGAT 60.743 45.833 0.00 0.00 0.00 2.90
20 21 3.431346 GCAATCACATGTAGCTCTCCTGA 60.431 47.826 0.00 0.00 0.00 3.86
21 22 2.871022 GCAATCACATGTAGCTCTCCTG 59.129 50.000 0.00 0.00 0.00 3.86
22 23 2.502947 TGCAATCACATGTAGCTCTCCT 59.497 45.455 0.00 0.00 0.00 3.69
23 24 2.871022 CTGCAATCACATGTAGCTCTCC 59.129 50.000 0.00 0.00 0.00 3.71
29 30 3.875134 TGATCTGCTGCAATCACATGTAG 59.125 43.478 17.52 0.00 36.28 2.74
30 31 3.876341 TGATCTGCTGCAATCACATGTA 58.124 40.909 17.52 0.00 0.00 2.29
31 32 2.718563 TGATCTGCTGCAATCACATGT 58.281 42.857 17.52 0.00 0.00 3.21
32 33 3.990318 ATGATCTGCTGCAATCACATG 57.010 42.857 21.27 0.00 34.88 3.21
33 34 4.082733 GCATATGATCTGCTGCAATCACAT 60.083 41.667 21.27 16.01 34.88 3.21
34 35 3.252458 GCATATGATCTGCTGCAATCACA 59.748 43.478 21.27 14.86 34.88 3.58
35 36 3.366070 GGCATATGATCTGCTGCAATCAC 60.366 47.826 21.27 12.99 39.60 3.06
36 37 2.817844 GGCATATGATCTGCTGCAATCA 59.182 45.455 21.17 21.17 39.60 2.57
37 38 3.082548 AGGCATATGATCTGCTGCAATC 58.917 45.455 6.97 10.27 39.60 2.67
38 39 3.156288 AGGCATATGATCTGCTGCAAT 57.844 42.857 6.97 0.24 39.60 3.56
39 40 2.651382 AGGCATATGATCTGCTGCAA 57.349 45.000 6.97 0.00 39.60 4.08
40 41 2.614734 GCTAGGCATATGATCTGCTGCA 60.615 50.000 6.97 0.88 39.60 4.41
41 42 2.008329 GCTAGGCATATGATCTGCTGC 58.992 52.381 6.97 5.60 39.60 5.25
42 43 3.056035 TCTGCTAGGCATATGATCTGCTG 60.056 47.826 6.97 8.87 38.13 4.41
43 44 3.171528 TCTGCTAGGCATATGATCTGCT 58.828 45.455 6.97 0.00 38.13 4.24
44 45 3.523547 CTCTGCTAGGCATATGATCTGC 58.476 50.000 6.97 5.64 38.13 4.26
45 46 3.118702 CCCTCTGCTAGGCATATGATCTG 60.119 52.174 6.97 0.00 45.03 2.90
46 47 3.106054 CCCTCTGCTAGGCATATGATCT 58.894 50.000 6.97 5.61 45.03 2.75
47 48 3.540314 CCCTCTGCTAGGCATATGATC 57.460 52.381 6.97 0.00 45.03 2.92
56 57 2.300956 TATCTCTGCCCTCTGCTAGG 57.699 55.000 0.00 0.00 46.09 3.02
57 58 2.760092 GGATATCTCTGCCCTCTGCTAG 59.240 54.545 2.05 0.00 42.00 3.42
58 59 2.558575 GGGATATCTCTGCCCTCTGCTA 60.559 54.545 2.05 0.00 42.00 3.49
59 60 1.643310 GGATATCTCTGCCCTCTGCT 58.357 55.000 2.05 0.00 42.00 4.24
60 61 0.612744 GGGATATCTCTGCCCTCTGC 59.387 60.000 2.05 0.00 38.85 4.26
61 62 0.894141 CGGGATATCTCTGCCCTCTG 59.106 60.000 0.09 0.00 39.79 3.35
62 63 0.252012 CCGGGATATCTCTGCCCTCT 60.252 60.000 0.09 0.00 39.79 3.69
63 64 1.261238 CCCGGGATATCTCTGCCCTC 61.261 65.000 18.48 0.00 39.79 4.30
64 65 1.229336 CCCGGGATATCTCTGCCCT 60.229 63.158 18.48 0.00 39.79 5.19
65 66 1.536662 ACCCGGGATATCTCTGCCC 60.537 63.158 32.02 0.00 38.53 5.36
66 67 0.832135 TCACCCGGGATATCTCTGCC 60.832 60.000 32.02 0.00 0.00 4.85
67 68 1.048601 TTCACCCGGGATATCTCTGC 58.951 55.000 32.02 0.00 0.00 4.26
68 69 2.899900 TCATTCACCCGGGATATCTCTG 59.100 50.000 32.02 13.78 0.00 3.35
69 70 3.169099 CTCATTCACCCGGGATATCTCT 58.831 50.000 32.02 0.00 0.00 3.10
70 71 2.900546 ACTCATTCACCCGGGATATCTC 59.099 50.000 32.02 0.00 0.00 2.75
71 72 2.634940 CACTCATTCACCCGGGATATCT 59.365 50.000 32.02 0.00 0.00 1.98
72 73 2.632996 TCACTCATTCACCCGGGATATC 59.367 50.000 32.02 0.00 0.00 1.63
73 74 2.634940 CTCACTCATTCACCCGGGATAT 59.365 50.000 32.02 14.31 0.00 1.63
74 75 2.039418 CTCACTCATTCACCCGGGATA 58.961 52.381 32.02 12.14 0.00 2.59
75 76 0.833287 CTCACTCATTCACCCGGGAT 59.167 55.000 32.02 7.61 0.00 3.85
76 77 0.252057 TCTCACTCATTCACCCGGGA 60.252 55.000 32.02 4.68 0.00 5.14
77 78 0.108138 GTCTCACTCATTCACCCGGG 60.108 60.000 22.25 22.25 0.00 5.73
78 79 0.108138 GGTCTCACTCATTCACCCGG 60.108 60.000 0.00 0.00 0.00 5.73
79 80 0.608130 TGGTCTCACTCATTCACCCG 59.392 55.000 0.00 0.00 0.00 5.28
80 81 2.859165 TTGGTCTCACTCATTCACCC 57.141 50.000 0.00 0.00 0.00 4.61
81 82 4.520492 ACATTTTGGTCTCACTCATTCACC 59.480 41.667 0.00 0.00 0.00 4.02
82 83 5.455392 CACATTTTGGTCTCACTCATTCAC 58.545 41.667 0.00 0.00 0.00 3.18
83 84 4.022935 GCACATTTTGGTCTCACTCATTCA 60.023 41.667 0.00 0.00 0.00 2.57
84 85 4.022935 TGCACATTTTGGTCTCACTCATTC 60.023 41.667 0.00 0.00 0.00 2.67
85 86 3.890756 TGCACATTTTGGTCTCACTCATT 59.109 39.130 0.00 0.00 0.00 2.57
86 87 3.489355 TGCACATTTTGGTCTCACTCAT 58.511 40.909 0.00 0.00 0.00 2.90
87 88 2.880268 CTGCACATTTTGGTCTCACTCA 59.120 45.455 0.00 0.00 0.00 3.41
88 89 2.227388 CCTGCACATTTTGGTCTCACTC 59.773 50.000 0.00 0.00 0.00 3.51
89 90 2.233271 CCTGCACATTTTGGTCTCACT 58.767 47.619 0.00 0.00 0.00 3.41
90 91 1.336240 GCCTGCACATTTTGGTCTCAC 60.336 52.381 0.00 0.00 0.00 3.51
97 98 1.144969 CTGCTTGCCTGCACATTTTG 58.855 50.000 0.00 0.00 38.12 2.44
101 102 0.601558 CTTTCTGCTTGCCTGCACAT 59.398 50.000 0.00 0.00 38.12 3.21
105 106 1.905354 ACCCTTTCTGCTTGCCTGC 60.905 57.895 0.00 0.00 0.00 4.85
106 107 1.962144 CACCCTTTCTGCTTGCCTG 59.038 57.895 0.00 0.00 0.00 4.85
160 169 2.031420 CGCATTGATTGGTAGCCTGATG 60.031 50.000 0.00 0.00 0.00 3.07
164 173 2.158769 TGATCGCATTGATTGGTAGCCT 60.159 45.455 0.00 0.00 37.47 4.58
182 191 7.121759 GCCCACTTATATTTGATAGCACATGAT 59.878 37.037 0.00 0.00 0.00 2.45
192 201 7.892241 AGCTAATCATGCCCACTTATATTTGAT 59.108 33.333 0.00 0.00 0.00 2.57
202 211 3.370840 TTTGAGCTAATCATGCCCACT 57.629 42.857 0.00 0.00 37.89 4.00
223 232 5.471797 TCTTTTTATCATTTGGCGTCTGTGA 59.528 36.000 0.00 0.00 0.00 3.58
224 233 5.698832 TCTTTTTATCATTTGGCGTCTGTG 58.301 37.500 0.00 0.00 0.00 3.66
227 236 6.744112 TGTTTCTTTTTATCATTTGGCGTCT 58.256 32.000 0.00 0.00 0.00 4.18
233 242 8.479280 CACGACCTTGTTTCTTTTTATCATTTG 58.521 33.333 0.00 0.00 0.00 2.32
240 249 4.732355 GCAGCACGACCTTGTTTCTTTTTA 60.732 41.667 0.00 0.00 0.00 1.52
245 254 0.463654 TGCAGCACGACCTTGTTTCT 60.464 50.000 0.00 0.00 0.00 2.52
246 255 0.593128 ATGCAGCACGACCTTGTTTC 59.407 50.000 0.00 0.00 0.00 2.78
249 258 2.620112 GCATGCAGCACGACCTTGT 61.620 57.895 14.21 0.00 44.79 3.16
250 259 2.177531 GCATGCAGCACGACCTTG 59.822 61.111 14.21 0.00 44.79 3.61
265 274 2.237643 TGCAATAAGAAACTGCAGGCA 58.762 42.857 19.93 11.44 41.01 4.75
323 332 2.499289 GTGAAGGATGCAGAGGAAGAGA 59.501 50.000 0.00 0.00 0.00 3.10
324 333 2.500910 AGTGAAGGATGCAGAGGAAGAG 59.499 50.000 0.00 0.00 0.00 2.85
395 869 5.448654 ACCATTTTAGCAAGATCCAGCATA 58.551 37.500 9.36 0.00 0.00 3.14
443 917 9.402320 TCCGAAAATACTTATCATCAAAATGGA 57.598 29.630 0.00 0.00 33.42 3.41
444 918 9.450807 GTCCGAAAATACTTATCATCAAAATGG 57.549 33.333 0.00 0.00 33.42 3.16
445 919 9.158364 CGTCCGAAAATACTTATCATCAAAATG 57.842 33.333 0.00 0.00 0.00 2.32
446 920 9.104965 TCGTCCGAAAATACTTATCATCAAAAT 57.895 29.630 0.00 0.00 0.00 1.82
447 921 8.481974 TCGTCCGAAAATACTTATCATCAAAA 57.518 30.769 0.00 0.00 0.00 2.44
448 922 8.481974 TTCGTCCGAAAATACTTATCATCAAA 57.518 30.769 0.00 0.00 0.00 2.69
449 923 7.223971 CCTTCGTCCGAAAATACTTATCATCAA 59.776 37.037 3.52 0.00 33.34 2.57
450 924 6.700081 CCTTCGTCCGAAAATACTTATCATCA 59.300 38.462 3.52 0.00 33.34 3.07
451 925 6.145696 CCCTTCGTCCGAAAATACTTATCATC 59.854 42.308 3.52 0.00 33.34 2.92
452 926 5.989777 CCCTTCGTCCGAAAATACTTATCAT 59.010 40.000 3.52 0.00 33.34 2.45
453 927 5.127519 TCCCTTCGTCCGAAAATACTTATCA 59.872 40.000 3.52 0.00 33.34 2.15
454 928 5.594926 TCCCTTCGTCCGAAAATACTTATC 58.405 41.667 3.52 0.00 33.34 1.75
455 929 5.361857 TCTCCCTTCGTCCGAAAATACTTAT 59.638 40.000 3.52 0.00 33.34 1.73
456 930 4.706476 TCTCCCTTCGTCCGAAAATACTTA 59.294 41.667 3.52 0.00 33.34 2.24
457 931 3.512724 TCTCCCTTCGTCCGAAAATACTT 59.487 43.478 3.52 0.00 33.34 2.24
458 932 3.094572 TCTCCCTTCGTCCGAAAATACT 58.905 45.455 3.52 0.00 33.34 2.12
459 933 3.515330 TCTCCCTTCGTCCGAAAATAC 57.485 47.619 3.52 0.00 33.34 1.89
460 934 4.442472 GGATTCTCCCTTCGTCCGAAAATA 60.442 45.833 3.52 0.00 33.34 1.40
461 935 3.532542 GATTCTCCCTTCGTCCGAAAAT 58.467 45.455 3.52 0.42 33.34 1.82
462 936 2.354403 GGATTCTCCCTTCGTCCGAAAA 60.354 50.000 3.52 0.00 33.34 2.29
463 937 1.206371 GGATTCTCCCTTCGTCCGAAA 59.794 52.381 3.52 0.00 33.34 3.46
464 938 0.822164 GGATTCTCCCTTCGTCCGAA 59.178 55.000 1.81 1.81 0.00 4.30
465 939 0.323999 TGGATTCTCCCTTCGTCCGA 60.324 55.000 0.00 0.00 35.03 4.55
466 940 0.535335 TTGGATTCTCCCTTCGTCCG 59.465 55.000 0.00 0.00 35.03 4.79
467 941 1.407025 GGTTGGATTCTCCCTTCGTCC 60.407 57.143 0.00 0.00 35.03 4.79
468 942 1.555533 AGGTTGGATTCTCCCTTCGTC 59.444 52.381 0.00 0.00 35.03 4.20
469 943 1.279271 CAGGTTGGATTCTCCCTTCGT 59.721 52.381 0.00 0.00 35.03 3.85
470 944 2.014068 GCAGGTTGGATTCTCCCTTCG 61.014 57.143 0.00 0.00 35.03 3.79
471 945 1.283321 AGCAGGTTGGATTCTCCCTTC 59.717 52.381 0.00 0.00 35.03 3.46
472 946 1.005215 CAGCAGGTTGGATTCTCCCTT 59.995 52.381 0.00 0.00 35.03 3.95
473 947 0.622665 CAGCAGGTTGGATTCTCCCT 59.377 55.000 0.00 0.00 35.03 4.20
474 948 0.394899 CCAGCAGGTTGGATTCTCCC 60.395 60.000 0.00 0.00 40.87 4.30
475 949 0.620556 TCCAGCAGGTTGGATTCTCC 59.379 55.000 0.26 0.00 42.24 3.71
476 950 2.087646 GTTCCAGCAGGTTGGATTCTC 58.912 52.381 5.67 0.00 46.22 2.87
477 951 1.611673 CGTTCCAGCAGGTTGGATTCT 60.612 52.381 5.67 0.00 46.22 2.40
478 952 0.804989 CGTTCCAGCAGGTTGGATTC 59.195 55.000 5.67 2.54 46.22 2.52
479 953 1.244019 GCGTTCCAGCAGGTTGGATT 61.244 55.000 5.67 0.00 46.22 3.01
480 954 1.675641 GCGTTCCAGCAGGTTGGAT 60.676 57.895 5.67 0.00 46.22 3.41
481 955 2.281484 GCGTTCCAGCAGGTTGGA 60.281 61.111 0.26 0.26 45.34 3.53
482 956 3.365265 GGCGTTCCAGCAGGTTGG 61.365 66.667 0.00 0.00 39.27 3.77
483 957 2.594303 TGGCGTTCCAGCAGGTTG 60.594 61.111 0.00 0.00 37.47 3.77
484 958 2.594592 GTGGCGTTCCAGCAGGTT 60.595 61.111 0.00 0.00 44.48 3.50
485 959 4.988598 CGTGGCGTTCCAGCAGGT 62.989 66.667 0.00 0.00 44.48 4.00
505 979 4.521075 CAGCATACTGGACCCGTG 57.479 61.111 0.00 0.00 40.48 4.94
514 988 5.860941 AGTATAGTCTTGCACAGCATACT 57.139 39.130 10.87 10.87 38.76 2.12
516 990 7.107639 TGTTAGTATAGTCTTGCACAGCATA 57.892 36.000 0.00 0.00 38.76 3.14
518 992 5.400066 TGTTAGTATAGTCTTGCACAGCA 57.600 39.130 0.00 0.00 36.47 4.41
521 1043 6.072342 TCGTCTTGTTAGTATAGTCTTGCACA 60.072 38.462 0.00 0.00 0.00 4.57
534 1056 8.378421 GCGTCTAATTTTAATCGTCTTGTTAGT 58.622 33.333 0.00 0.00 0.00 2.24
535 1057 7.574481 CGCGTCTAATTTTAATCGTCTTGTTAG 59.426 37.037 0.00 0.00 0.00 2.34
536 1058 7.385650 CGCGTCTAATTTTAATCGTCTTGTTA 58.614 34.615 0.00 0.00 0.00 2.41
537 1059 6.238508 CGCGTCTAATTTTAATCGTCTTGTT 58.761 36.000 0.00 0.00 0.00 2.83
538 1060 5.220340 CCGCGTCTAATTTTAATCGTCTTGT 60.220 40.000 4.92 0.00 0.00 3.16
539 1061 5.188194 CCGCGTCTAATTTTAATCGTCTTG 58.812 41.667 4.92 0.00 0.00 3.02
573 2894 8.697960 CGTGATCAAAGTATGAGAGTAATCATG 58.302 37.037 0.00 0.00 42.53 3.07
589 2910 2.158449 GTGCTCCAAGTCGTGATCAAAG 59.842 50.000 0.00 0.00 0.00 2.77
621 2942 2.200067 GTGCGATCATCAGGTCAAGAG 58.800 52.381 0.00 0.00 0.00 2.85
639 2960 4.920112 TGGCCGTTCACACCCGTG 62.920 66.667 0.00 0.00 45.08 4.94
643 2964 0.887933 AAATGATGGCCGTTCACACC 59.112 50.000 10.15 0.00 0.00 4.16
644 2965 1.539388 TCAAATGATGGCCGTTCACAC 59.461 47.619 10.15 0.00 0.00 3.82
645 2966 1.539388 GTCAAATGATGGCCGTTCACA 59.461 47.619 10.15 0.00 0.00 3.58
654 3194 3.689347 TCTGAGGTTGGTCAAATGATGG 58.311 45.455 0.00 0.00 0.00 3.51
710 3268 2.279784 CTGCCCGCTACAGCTAGC 60.280 66.667 6.62 6.62 41.97 3.42
715 3273 2.816958 CACTGCTGCCCGCTACAG 60.817 66.667 0.00 7.65 40.11 2.74
716 3274 3.310307 TCACTGCTGCCCGCTACA 61.310 61.111 0.00 0.00 40.11 2.74
717 3275 2.815647 GTCACTGCTGCCCGCTAC 60.816 66.667 0.00 0.00 40.11 3.58
780 3344 0.321564 TGCCGTTTGACCCTCATCTG 60.322 55.000 0.00 0.00 0.00 2.90
895 3471 1.804396 TGGCATTTGGCACCGTCTTG 61.804 55.000 2.26 0.00 46.12 3.02
926 3512 4.933064 GATCGGAGCCACGCGGAG 62.933 72.222 12.47 1.22 0.00 4.63
1061 3700 4.193334 TCGAGAGCGGTCATGGCG 62.193 66.667 18.15 14.03 38.28 5.69
1352 4016 1.257750 ATCCCTAGTCGCAGTGCACA 61.258 55.000 21.04 0.00 0.00 4.57
1360 4024 1.406539 TCCGTTTACATCCCTAGTCGC 59.593 52.381 0.00 0.00 0.00 5.19
1496 4163 3.288290 CGCCTCCGCTCCGTATCT 61.288 66.667 0.00 0.00 0.00 1.98
2605 5413 8.051535 CCTTCATGATGATTAATGCCCTATACT 58.948 37.037 10.07 0.00 0.00 2.12
5065 7887 5.407407 ACTATTCAGTTCAGATCACCGTT 57.593 39.130 0.00 0.00 0.00 4.44
5324 8166 9.298250 AGAGACAGACAGAAACAGTAGTATTTA 57.702 33.333 0.00 0.00 0.00 1.40
6505 9540 3.386237 GCAGAGGACGTCCAGCCT 61.386 66.667 35.00 24.35 38.89 4.58
6597 9650 2.081212 GTCGAACTCAGTGGCGTCG 61.081 63.158 0.00 0.00 0.00 5.12
6604 9657 2.050351 CACGCGGTCGAACTCAGT 60.050 61.111 12.47 0.00 39.41 3.41
6606 9659 3.973516 AGCACGCGGTCGAACTCA 61.974 61.111 12.47 0.00 39.41 3.41
6702 12172 3.490759 GCCACCGACACGATGCTG 61.491 66.667 0.00 0.00 0.00 4.41
7091 12573 0.602905 GACGTTCTTGGAGGTGGTGG 60.603 60.000 0.00 0.00 0.00 4.61
7103 12585 1.079819 CACAGCCCGATGACGTTCT 60.080 57.895 0.00 0.00 37.88 3.01
7137 12626 2.092538 CCCTCCAACTGCATCTCAATCT 60.093 50.000 0.00 0.00 0.00 2.40
7159 12661 0.879090 TGACACTCGAGCACGTACAT 59.121 50.000 13.61 0.00 40.69 2.29
7160 12662 0.040692 GTGACACTCGAGCACGTACA 60.041 55.000 13.61 5.51 40.69 2.90
7302 14229 3.827008 TCCATAGTTCATCACTCAGGC 57.173 47.619 0.00 0.00 36.88 4.85
7349 14291 1.099689 CCGGACACCACAACAGTTTT 58.900 50.000 0.00 0.00 0.00 2.43
7360 14302 0.815734 TTCTTCTCGATCCGGACACC 59.184 55.000 6.12 0.00 0.00 4.16
7364 14306 1.835494 ACAGTTCTTCTCGATCCGGA 58.165 50.000 6.61 6.61 0.00 5.14
7377 14319 3.620821 GGCTGAGATGCTCTAAACAGTTC 59.379 47.826 0.00 0.00 0.00 3.01
7454 14398 3.171828 ATCACGCCCCAACACACGA 62.172 57.895 0.00 0.00 0.00 4.35
7541 14493 4.862350 TGTATGAACTCGTCGAAGTTTGA 58.138 39.130 4.09 0.00 39.55 2.69
7591 14548 1.152383 CGGGCCTAGTAGCGCTTTTC 61.152 60.000 18.68 7.06 43.11 2.29
7727 14719 3.655211 CAGGGAAGGGGTGCAGCT 61.655 66.667 16.65 0.00 0.00 4.24
7773 14771 1.863662 ATGACGACAACGAGGACGCT 61.864 55.000 0.00 0.00 43.96 5.07
7784 14782 0.242825 GGTCCTCGACAATGACGACA 59.757 55.000 3.42 0.00 35.88 4.35
7802 14800 4.657824 ACGAGAACGGCGTGGTGG 62.658 66.667 15.70 7.89 44.46 4.61
7881 14879 2.185494 GGACGACTACCTCCGCGAT 61.185 63.158 8.23 0.00 0.00 4.58
8171 15173 2.599281 TTCTCCCGCTGACGTGGA 60.599 61.111 0.00 0.00 43.70 4.02
8198 15200 1.568504 CAAGGCTAGAGTACCCCACA 58.431 55.000 0.00 0.00 0.00 4.17
8200 15202 0.981277 GCCAAGGCTAGAGTACCCCA 60.981 60.000 3.29 0.00 38.26 4.96
8220 15222 0.973632 TATATCGAGGGCGGCAACAT 59.026 50.000 12.47 0.00 38.28 2.71
8325 15328 4.373116 GCTCGAGGCCACCAACGA 62.373 66.667 15.58 7.16 34.76 3.85


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

AutoCloner maintained by Alex Coulton.