Multiple sequence alignment - TraesCS3A01G221200

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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 TraesCS3A01G221200 chr3A 100.000 2811 0 0 1 2811 410233192 410236002 0.000000e+00 5192.0
1 TraesCS3A01G221200 chr3A 90.765 1646 141 6 55 1700 410246639 410248273 0.000000e+00 2187.0
2 TraesCS3A01G221200 chr3A 92.915 1115 69 6 1700 2811 410248238 410249345 0.000000e+00 1613.0
3 TraesCS3A01G221200 chr3A 81.295 278 43 8 2007 2281 496004360 496004631 1.700000e-52 217.0
4 TraesCS3A01G221200 chr3A 89.706 136 13 1 1121 1256 258704893 258704759 3.720000e-39 172.0
5 TraesCS3A01G221200 chr3A 77.352 287 57 7 1850 2134 160704692 160704972 2.240000e-36 163.0
6 TraesCS3A01G221200 chr3A 86.861 137 18 0 877 1013 207407360 207407496 1.350000e-33 154.0
7 TraesCS3A01G221200 chr3A 79.651 172 28 5 1988 2158 583810457 583810292 1.770000e-22 117.0
8 TraesCS3A01G221200 chr3A 90.244 82 8 0 2726 2807 292484134 292484215 1.060000e-19 108.0
9 TraesCS3A01G221200 chr3A 82.203 118 12 9 1350 1463 328425836 328425724 2.980000e-15 93.5
10 TraesCS3A01G221200 chr3A 79.310 116 15 9 1352 1463 272028918 272029028 3.880000e-09 73.1
11 TraesCS3A01G221200 chr3A 95.455 44 2 0 1 44 363783986 363784029 1.400000e-08 71.3
12 TraesCS3A01G221200 chr3A 100.000 36 0 0 1700 1735 410234856 410234891 1.810000e-07 67.6
13 TraesCS3A01G221200 chr3A 100.000 36 0 0 1665 1700 410234891 410234926 1.810000e-07 67.6
14 TraesCS3A01G221200 chr4D 82.595 948 123 30 1886 2811 191323145 191322218 0.000000e+00 798.0
15 TraesCS3A01G221200 chr4D 82.840 810 114 16 2007 2811 191304153 191303364 0.000000e+00 702.0
16 TraesCS3A01G221200 chr4D 82.441 598 91 14 45 633 186726247 186725655 6.950000e-141 510.0
17 TraesCS3A01G221200 chr4D 78.003 691 114 29 45 714 365612605 365611932 1.570000e-107 399.0
18 TraesCS3A01G221200 chr4D 77.826 690 118 28 45 714 365620732 365620058 7.300000e-106 394.0
19 TraesCS3A01G221200 chr4D 75.656 419 64 22 1741 2134 143607708 143608113 1.040000e-39 174.0
20 TraesCS3A01G221200 chr4D 85.093 161 11 3 1121 1279 239119486 239119635 4.850000e-33 152.0
21 TraesCS3A01G221200 chr4D 75.786 318 58 12 1851 2154 245016410 245016098 2.920000e-30 143.0
22 TraesCS3A01G221200 chr4D 74.309 362 65 19 1781 2132 167053724 167053381 8.170000e-26 128.0
23 TraesCS3A01G221200 chr4D 73.780 328 67 11 1853 2168 174102657 174102337 8.230000e-21 111.0
24 TraesCS3A01G221200 chr4D 72.911 395 74 23 1778 2158 368794013 368794388 3.830000e-19 106.0
25 TraesCS3A01G221200 chr4D 83.495 103 14 3 1851 1951 174110162 174110061 2.980000e-15 93.5
26 TraesCS3A01G221200 chr4D 71.611 391 80 21 1781 2158 229940640 229941012 8.350000e-11 78.7
27 TraesCS3A01G221200 chr4D 76.471 153 31 4 2007 2158 229949183 229949331 8.350000e-11 78.7
28 TraesCS3A01G221200 chr4D 76.316 152 25 7 2007 2157 105226067 105225926 1.400000e-08 71.3
29 TraesCS3A01G221200 chr4D 95.455 44 2 0 1 44 439544596 439544553 1.400000e-08 71.3
30 TraesCS3A01G221200 chr4D 71.320 394 72 26 1778 2154 148802789 148803158 2.340000e-06 63.9
31 TraesCS3A01G221200 chr4D 74.317 183 29 13 1776 1953 148794726 148794895 8.410000e-06 62.1
32 TraesCS3A01G221200 chr4D 96.875 32 0 1 1781 1812 150249453 150249483 5.000000e-03 52.8
33 TraesCS3A01G221200 chr4D 96.875 32 0 1 1781 1812 150257382 150257412 5.000000e-03 52.8
34 TraesCS3A01G221200 chr4A 89.122 524 51 5 2290 2811 410032461 410031942 0.000000e+00 647.0
35 TraesCS3A01G221200 chr4A 83.866 626 87 14 2144 2765 292233519 292234134 4.030000e-163 584.0
36 TraesCS3A01G221200 chr4A 79.344 610 89 29 57 652 94088710 94088124 7.300000e-106 394.0
37 TraesCS3A01G221200 chr4A 88.172 186 19 3 1459 1642 166507273 166507089 4.710000e-53 219.0
38 TraesCS3A01G221200 chr4A 91.525 59 1 3 702 759 298567967 298567912 8.350000e-11 78.7
39 TraesCS3A01G221200 chr4A 86.441 59 7 1 1774 1832 393423454 393423511 2.340000e-06 63.9
40 TraesCS3A01G221200 chr4A 85.484 62 5 3 1754 1812 42206671 42206731 8.410000e-06 62.1
41 TraesCS3A01G221200 chrUn 84.337 664 88 15 2148 2806 92433502 92432850 1.100000e-178 636.0
42 TraesCS3A01G221200 chrUn 93.966 116 7 0 1585 1700 92433944 92433829 2.880000e-40 176.0
43 TraesCS3A01G221200 chrUn 92.079 101 8 0 1700 1800 92433864 92433764 2.920000e-30 143.0
44 TraesCS3A01G221200 chrUn 100.000 40 0 0 5 44 180589491 180589452 1.080000e-09 75.0
45 TraesCS3A01G221200 chr1A 84.211 646 87 14 2144 2784 179773877 179774512 5.150000e-172 614.0
46 TraesCS3A01G221200 chr1A 79.115 565 86 23 2007 2554 195169657 195169108 7.400000e-96 361.0
47 TraesCS3A01G221200 chr1A 86.310 168 21 2 1120 1285 302862579 302862412 6.190000e-42 182.0
48 TraesCS3A01G221200 chr1A 85.714 168 22 2 1120 1285 302870642 302870475 2.880000e-40 176.0
49 TraesCS3A01G221200 chr1A 100.000 41 0 0 1783 1823 177533716 177533756 3.000000e-10 76.8
50 TraesCS3A01G221200 chr1A 95.556 45 2 0 1418 1462 55433716 55433760 3.880000e-09 73.1
51 TraesCS3A01G221200 chr1A 95.455 44 2 0 1419 1462 55425181 55425224 1.400000e-08 71.3
52 TraesCS3A01G221200 chr2A 83.061 673 90 21 2144 2808 310297857 310297201 8.670000e-165 590.0
53 TraesCS3A01G221200 chr2A 80.130 307 48 10 1980 2286 273918934 273918641 1.700000e-52 217.0
54 TraesCS3A01G221200 chr2A 87.027 185 23 1 1459 1642 216320969 216320785 1.020000e-49 207.0
55 TraesCS3A01G221200 chr2A 86.301 146 18 2 1121 1265 233616389 233616533 1.040000e-34 158.0
56 TraesCS3A01G221200 chr2A 86.861 137 18 0 877 1013 470691465 470691601 1.350000e-33 154.0
57 TraesCS3A01G221200 chr2A 86.331 139 16 3 1502 1638 224395513 224395376 6.270000e-32 148.0
58 TraesCS3A01G221200 chr2A 82.099 162 15 7 877 1038 296078051 296078198 2.940000e-25 126.0
59 TraesCS3A01G221200 chr2A 90.000 60 3 3 702 761 297146321 297146265 1.080000e-09 75.0
60 TraesCS3A01G221200 chr2A 86.885 61 6 2 702 761 297154113 297154054 1.810000e-07 67.6
61 TraesCS3A01G221200 chr7A 83.010 671 87 24 2146 2806 280407950 280407297 1.450000e-162 582.0
62 TraesCS3A01G221200 chr7A 81.915 282 43 7 2007 2286 252474241 252474516 6.060000e-57 231.0
63 TraesCS3A01G221200 chr7A 84.530 181 23 4 1459 1638 325548478 325548302 1.040000e-39 174.0
64 TraesCS3A01G221200 chr7A 85.075 67 8 2 1747 1812 248120459 248120394 1.810000e-07 67.6
65 TraesCS3A01G221200 chr5D 82.661 669 102 14 2144 2806 47678425 47677765 5.220000e-162 580.0
66 TraesCS3A01G221200 chr5D 78.003 691 116 29 45 714 159856603 159857278 4.360000e-108 401.0
67 TraesCS3A01G221200 chr5D 72.519 393 70 24 1781 2158 86028436 86028067 2.980000e-15 93.5
68 TraesCS3A01G221200 chr5D 92.308 39 1 2 1781 1819 153777922 153777886 1.000000e-03 54.7
69 TraesCS3A01G221200 chr2B 81.135 599 84 23 45 632 463742810 463743390 1.190000e-123 453.0
70 TraesCS3A01G221200 chr7B 80.690 580 87 24 53 621 169593344 169592779 7.200000e-116 427.0
71 TraesCS3A01G221200 chr7B 97.500 40 1 0 5 44 388529124 388529085 5.020000e-08 69.4
72 TraesCS3A01G221200 chr7B 95.122 41 1 1 5 44 419287815 419287855 2.340000e-06 63.9
73 TraesCS3A01G221200 chr2D 80.065 617 89 26 45 649 205102892 205103486 7.200000e-116 427.0
74 TraesCS3A01G221200 chr2D 77.762 688 109 37 45 714 356037832 356038493 1.580000e-102 383.0
75 TraesCS3A01G221200 chr2D 75.758 297 51 13 1851 2133 576070990 576071279 2.270000e-26 130.0
76 TraesCS3A01G221200 chr6D 79.741 617 89 26 45 649 45261411 45260819 5.600000e-112 414.0
77 TraesCS3A01G221200 chr6D 74.879 414 75 18 1740 2133 165144518 165144114 8.060000e-36 161.0
78 TraesCS3A01G221200 chr6D 73.671 414 80 20 1740 2133 165125051 165124647 1.760000e-27 134.0
79 TraesCS3A01G221200 chr6D 72.774 393 74 21 1781 2158 279344206 279343832 4.950000e-18 102.0
80 TraesCS3A01G221200 chr6D 72.475 396 72 26 1781 2158 279335887 279335511 2.980000e-15 93.5
81 TraesCS3A01G221200 chr6D 75.000 148 34 2 2007 2154 186272313 186272457 6.500000e-07 65.8
82 TraesCS3A01G221200 chr3D 78.343 688 109 34 45 714 219499816 219500481 2.610000e-110 409.0
83 TraesCS3A01G221200 chr3D 79.204 452 69 16 1848 2286 164922954 164923393 9.850000e-75 291.0
84 TraesCS3A01G221200 chr3D 80.145 413 57 16 1848 2246 164918757 164919158 4.580000e-73 285.0
85 TraesCS3A01G221200 chr3D 75.875 543 88 28 45 571 47446172 47446687 1.300000e-58 237.0
86 TraesCS3A01G221200 chr3D 76.136 352 69 12 1796 2137 254210362 254210708 1.340000e-38 171.0
87 TraesCS3A01G221200 chr3D 75.359 418 67 23 1741 2134 203645930 203646335 4.820000e-38 169.0
88 TraesCS3A01G221200 chr3D 73.710 407 83 17 1766 2159 461835576 461835181 1.360000e-28 137.0
89 TraesCS3A01G221200 chr3D 72.902 417 87 18 1766 2169 461807447 461807044 1.370000e-23 121.0
90 TraesCS3A01G221200 chr3D 76.471 170 26 12 1995 2158 368530311 368530150 2.320000e-11 80.5
91 TraesCS3A01G221200 chr3D 95.455 44 2 0 1 44 75794898 75794855 1.400000e-08 71.3
92 TraesCS3A01G221200 chr3D 79.339 121 8 11 689 794 47439165 47439283 5.020000e-08 69.4
93 TraesCS3A01G221200 chr6B 77.467 750 119 39 31 745 100400384 100401118 1.210000e-108 403.0
94 TraesCS3A01G221200 chr6B 94.231 52 3 0 1781 1832 650264543 650264594 2.320000e-11 80.5
95 TraesCS3A01G221200 chr6B 94.231 52 3 0 1781 1832 662640484 662640433 2.320000e-11 80.5
96 TraesCS3A01G221200 chr6B 85.714 56 6 2 1757 1812 153176738 153176791 1.090000e-04 58.4
97 TraesCS3A01G221200 chr1B 76.869 709 123 33 45 729 508185831 508185140 2.060000e-96 363.0
98 TraesCS3A01G221200 chr1B 84.932 73 5 4 1738 1808 520549871 520549939 5.020000e-08 69.4
99 TraesCS3A01G221200 chr1B 89.362 47 3 1 773 819 123172563 123172607 1.090000e-04 58.4
100 TraesCS3A01G221200 chr4B 77.796 617 95 31 138 729 458813745 458814344 2.680000e-90 342.0
101 TraesCS3A01G221200 chr4B 73.420 459 81 30 1741 2178 392777998 392777560 1.760000e-27 134.0
102 TraesCS3A01G221200 chr4B 71.394 409 72 35 1767 2154 136608797 136608413 6.500000e-07 65.8
103 TraesCS3A01G221200 chr7D 90.204 245 20 4 1459 1700 360474179 360473936 1.630000e-82 316.0
104 TraesCS3A01G221200 chr7D 76.053 451 72 24 1852 2286 302162418 302161988 4.750000e-48 202.0
105 TraesCS3A01G221200 chr7D 90.099 101 10 0 1700 1800 360473971 360473871 6.320000e-27 132.0
106 TraesCS3A01G221200 chr7D 72.289 415 77 26 1760 2158 377697987 377698379 8.290000e-16 95.3
107 TraesCS3A01G221200 chr7D 91.176 68 6 0 1459 1526 360446857 360446790 2.980000e-15 93.5
108 TraesCS3A01G221200 chr7D 95.455 44 2 0 1 44 257971891 257971934 1.400000e-08 71.3
109 TraesCS3A01G221200 chr6A 82.738 168 25 4 1121 1285 240638544 240638378 2.260000e-31 147.0
110 TraesCS3A01G221200 chr6A 85.981 107 10 4 1392 1496 110128402 110128505 2.960000e-20 110.0
111 TraesCS3A01G221200 chr6A 85.088 114 10 5 1392 1503 398693260 398693152 2.960000e-20 110.0
112 TraesCS3A01G221200 chr6A 85.088 114 10 5 1392 1503 408351450 408351342 2.960000e-20 110.0
113 TraesCS3A01G221200 chr6A 90.385 52 4 1 1209 1260 200787337 200787287 1.810000e-07 67.6
114 TraesCS3A01G221200 chr6A 90.385 52 4 1 1209 1260 200795333 200795283 1.810000e-07 67.6
115 TraesCS3A01G221200 chr5B 73.522 389 75 21 1776 2158 204479056 204478690 3.800000e-24 122.0
116 TraesCS3A01G221200 chr5B 73.247 385 74 20 1776 2154 204471288 204470927 2.290000e-21 113.0
117 TraesCS3A01G221200 chr5B 97.500 40 1 0 5 44 328434104 328434143 5.020000e-08 69.4
118 TraesCS3A01G221200 chr1D 77.714 175 34 4 1995 2169 82110253 82110422 4.950000e-18 102.0
119 TraesCS3A01G221200 chr1D 76.136 176 26 12 1781 1953 123139952 123140114 8.350000e-11 78.7
120 TraesCS3A01G221200 chr1D 93.182 44 2 1 1 44 339220624 339220666 2.340000e-06 63.9
121 TraesCS3A01G221200 chr1D 100.000 32 0 0 1776 1807 438009500 438009469 3.020000e-05 60.2
122 TraesCS3A01G221200 chr3B 88.889 72 7 1 1392 1463 537119008 537119078 1.390000e-13 87.9
123 TraesCS3A01G221200 chr5A 81.034 116 13 9 1352 1463 342219029 342219139 1.790000e-12 84.2
124 TraesCS3A01G221200 chr5A 80.172 116 14 9 1352 1463 342211107 342211217 8.350000e-11 78.7


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 TraesCS3A01G221200 chr3A 410233192 410236002 2810 False 1775.733333 5192 100.000000 1 2811 3 chr3A.!!$F7 2810
1 TraesCS3A01G221200 chr3A 410246639 410249345 2706 False 1900.000000 2187 91.840000 55 2811 2 chr3A.!!$F8 2756
2 TraesCS3A01G221200 chr4D 191322218 191323145 927 True 798.000000 798 82.595000 1886 2811 1 chr4D.!!$R7 925
3 TraesCS3A01G221200 chr4D 191303364 191304153 789 True 702.000000 702 82.840000 2007 2811 1 chr4D.!!$R6 804
4 TraesCS3A01G221200 chr4D 186725655 186726247 592 True 510.000000 510 82.441000 45 633 1 chr4D.!!$R5 588
5 TraesCS3A01G221200 chr4D 365611932 365612605 673 True 399.000000 399 78.003000 45 714 1 chr4D.!!$R9 669
6 TraesCS3A01G221200 chr4D 365620058 365620732 674 True 394.000000 394 77.826000 45 714 1 chr4D.!!$R10 669
7 TraesCS3A01G221200 chr4A 410031942 410032461 519 True 647.000000 647 89.122000 2290 2811 1 chr4A.!!$R4 521
8 TraesCS3A01G221200 chr4A 292233519 292234134 615 False 584.000000 584 83.866000 2144 2765 1 chr4A.!!$F2 621
9 TraesCS3A01G221200 chr4A 94088124 94088710 586 True 394.000000 394 79.344000 57 652 1 chr4A.!!$R1 595
10 TraesCS3A01G221200 chrUn 92432850 92433944 1094 True 318.333333 636 90.127333 1585 2806 3 chrUn.!!$R2 1221
11 TraesCS3A01G221200 chr1A 179773877 179774512 635 False 614.000000 614 84.211000 2144 2784 1 chr1A.!!$F4 640
12 TraesCS3A01G221200 chr1A 195169108 195169657 549 True 361.000000 361 79.115000 2007 2554 1 chr1A.!!$R1 547
13 TraesCS3A01G221200 chr2A 310297201 310297857 656 True 590.000000 590 83.061000 2144 2808 1 chr2A.!!$R6 664
14 TraesCS3A01G221200 chr7A 280407297 280407950 653 True 582.000000 582 83.010000 2146 2806 1 chr7A.!!$R2 660
15 TraesCS3A01G221200 chr5D 47677765 47678425 660 True 580.000000 580 82.661000 2144 2806 1 chr5D.!!$R1 662
16 TraesCS3A01G221200 chr5D 159856603 159857278 675 False 401.000000 401 78.003000 45 714 1 chr5D.!!$F1 669
17 TraesCS3A01G221200 chr2B 463742810 463743390 580 False 453.000000 453 81.135000 45 632 1 chr2B.!!$F1 587
18 TraesCS3A01G221200 chr7B 169592779 169593344 565 True 427.000000 427 80.690000 53 621 1 chr7B.!!$R1 568
19 TraesCS3A01G221200 chr2D 205102892 205103486 594 False 427.000000 427 80.065000 45 649 1 chr2D.!!$F1 604
20 TraesCS3A01G221200 chr2D 356037832 356038493 661 False 383.000000 383 77.762000 45 714 1 chr2D.!!$F2 669
21 TraesCS3A01G221200 chr6D 45260819 45261411 592 True 414.000000 414 79.741000 45 649 1 chr6D.!!$R1 604
22 TraesCS3A01G221200 chr3D 219499816 219500481 665 False 409.000000 409 78.343000 45 714 1 chr3D.!!$F4 669
23 TraesCS3A01G221200 chr3D 164918757 164923393 4636 False 288.000000 291 79.674500 1848 2286 2 chr3D.!!$F6 438
24 TraesCS3A01G221200 chr3D 47446172 47446687 515 False 237.000000 237 75.875000 45 571 1 chr3D.!!$F2 526
25 TraesCS3A01G221200 chr6B 100400384 100401118 734 False 403.000000 403 77.467000 31 745 1 chr6B.!!$F1 714
26 TraesCS3A01G221200 chr1B 508185140 508185831 691 True 363.000000 363 76.869000 45 729 1 chr1B.!!$R1 684
27 TraesCS3A01G221200 chr4B 458813745 458814344 599 False 342.000000 342 77.796000 138 729 1 chr4B.!!$F1 591

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
830 892 0.040499 AGCTCCTCCTCTCGAACCTT 59.960 55.0 0.0 0.0 0.00 3.50 F
1065 1127 0.036448 TCAGTCTTCCTCGTCCTCGT 59.964 55.0 0.0 0.0 38.33 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1772 0.165944 GCTTGTCAAATCCCACGACG 59.834 55.000 0.0 0.0 32.17 5.12 R
2089 2166 1.000843 CGATGATCCGGTGGCTCATTA 59.999 52.381 0.0 0.0 38.47 1.90 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
17 18 4.716025 GAGAGGGCATGGGAGAGA 57.284 61.111 0.00 0.00 0.00 3.10
18 19 3.162394 GAGAGGGCATGGGAGAGAT 57.838 57.895 0.00 0.00 0.00 2.75
19 20 2.317371 GAGAGGGCATGGGAGAGATA 57.683 55.000 0.00 0.00 0.00 1.98
20 21 2.831565 GAGAGGGCATGGGAGAGATAT 58.168 52.381 0.00 0.00 0.00 1.63
21 22 2.765699 GAGAGGGCATGGGAGAGATATC 59.234 54.545 0.00 0.00 0.00 1.63
22 23 2.113233 AGAGGGCATGGGAGAGATATCA 59.887 50.000 5.32 0.00 0.00 2.15
23 24 2.235898 GAGGGCATGGGAGAGATATCAC 59.764 54.545 5.32 0.00 0.00 3.06
24 25 1.066573 GGGCATGGGAGAGATATCACG 60.067 57.143 5.32 0.00 0.00 4.35
25 26 1.895798 GGCATGGGAGAGATATCACGA 59.104 52.381 5.32 0.00 0.00 4.35
26 27 2.094286 GGCATGGGAGAGATATCACGAG 60.094 54.545 5.32 0.00 0.00 4.18
27 28 2.822561 GCATGGGAGAGATATCACGAGA 59.177 50.000 5.32 0.00 0.00 4.04
28 29 3.256879 GCATGGGAGAGATATCACGAGAA 59.743 47.826 5.32 0.00 0.00 2.87
29 30 4.262207 GCATGGGAGAGATATCACGAGAAA 60.262 45.833 5.32 0.00 0.00 2.52
30 31 5.568423 GCATGGGAGAGATATCACGAGAAAT 60.568 44.000 5.32 0.00 0.00 2.17
31 32 5.459536 TGGGAGAGATATCACGAGAAATG 57.540 43.478 5.32 0.00 0.00 2.32
32 33 5.140454 TGGGAGAGATATCACGAGAAATGA 58.860 41.667 5.32 0.00 0.00 2.57
33 34 5.242615 TGGGAGAGATATCACGAGAAATGAG 59.757 44.000 5.32 0.00 0.00 2.90
34 35 5.475220 GGGAGAGATATCACGAGAAATGAGA 59.525 44.000 5.32 0.00 0.00 3.27
35 36 6.349280 GGGAGAGATATCACGAGAAATGAGAG 60.349 46.154 5.32 0.00 0.00 3.20
36 37 6.429692 GGAGAGATATCACGAGAAATGAGAGA 59.570 42.308 5.32 0.00 0.00 3.10
37 38 7.361201 GGAGAGATATCACGAGAAATGAGAGAG 60.361 44.444 5.32 0.00 0.00 3.20
38 39 6.430925 AGAGATATCACGAGAAATGAGAGAGG 59.569 42.308 5.32 0.00 0.00 3.69
39 40 6.068010 AGATATCACGAGAAATGAGAGAGGT 58.932 40.000 5.32 0.00 0.00 3.85
40 41 4.647424 ATCACGAGAAATGAGAGAGGTC 57.353 45.455 0.00 0.00 0.00 3.85
41 42 3.691575 TCACGAGAAATGAGAGAGGTCT 58.308 45.455 0.00 0.00 34.86 3.85
42 43 4.844884 TCACGAGAAATGAGAGAGGTCTA 58.155 43.478 0.00 0.00 30.97 2.59
43 44 4.878971 TCACGAGAAATGAGAGAGGTCTAG 59.121 45.833 0.00 0.00 30.97 2.43
51 52 4.283363 TGAGAGAGGTCTAGTGTAACGT 57.717 45.455 0.00 0.00 35.51 3.99
73 74 1.158484 CGAGACCGACGCTCCAGATA 61.158 60.000 0.00 0.00 38.22 1.98
74 75 1.240256 GAGACCGACGCTCCAGATAT 58.760 55.000 0.00 0.00 0.00 1.63
104 106 4.454161 TGTTTTGCGTGTCAGCTATGTTAT 59.546 37.500 0.00 0.00 38.13 1.89
167 184 4.476862 GCATCATCTCATCATGCAATCAC 58.523 43.478 0.00 0.00 42.18 3.06
452 486 0.846693 ACCTTCCAAACCAGCACTCT 59.153 50.000 0.00 0.00 0.00 3.24
548 591 5.592282 TCATGGACCGTGCATATTTTTATGT 59.408 36.000 9.00 0.00 0.00 2.29
658 708 2.776913 GGAGAGAGAGAACCGGCGG 61.777 68.421 27.06 27.06 0.00 6.13
745 807 1.228769 CCCGACCGATCCCCATCTA 60.229 63.158 0.00 0.00 0.00 1.98
750 812 1.550976 GACCGATCCCCATCTATCCAC 59.449 57.143 0.00 0.00 0.00 4.02
760 822 3.430453 CCATCTATCCACTCTCTCCCTC 58.570 54.545 0.00 0.00 0.00 4.30
763 825 2.370519 TCTATCCACTCTCTCCCTCTCG 59.629 54.545 0.00 0.00 0.00 4.04
830 892 0.040499 AGCTCCTCCTCTCGAACCTT 59.960 55.000 0.00 0.00 0.00 3.50
833 895 0.408309 TCCTCCTCTCGAACCTTCCA 59.592 55.000 0.00 0.00 0.00 3.53
845 907 2.669133 CCTTCCAGCCCCGTCATCA 61.669 63.158 0.00 0.00 0.00 3.07
856 918 1.811266 CGTCATCACCGCCCTTCTG 60.811 63.158 0.00 0.00 0.00 3.02
908 970 1.617839 CTTCCTCCCCCAGCCTTCT 60.618 63.158 0.00 0.00 0.00 2.85
915 977 1.078848 CCCCAGCCTTCTTCGTCTG 60.079 63.158 0.00 0.00 0.00 3.51
919 981 1.075425 CAGCCTTCTTCGTCTGCTCG 61.075 60.000 0.00 0.00 0.00 5.03
1048 1110 3.080641 CTGCCCCACACCATCTCA 58.919 61.111 0.00 0.00 0.00 3.27
1059 1121 1.821753 CACCATCTCAGTCTTCCTCGT 59.178 52.381 0.00 0.00 0.00 4.18
1061 1123 1.407258 CCATCTCAGTCTTCCTCGTCC 59.593 57.143 0.00 0.00 0.00 4.79
1063 1125 2.116827 TCTCAGTCTTCCTCGTCCTC 57.883 55.000 0.00 0.00 0.00 3.71
1064 1126 0.730265 CTCAGTCTTCCTCGTCCTCG 59.270 60.000 0.00 0.00 38.55 4.63
1065 1127 0.036448 TCAGTCTTCCTCGTCCTCGT 59.964 55.000 0.00 0.00 38.33 4.18
1066 1128 0.169230 CAGTCTTCCTCGTCCTCGTG 59.831 60.000 0.00 0.00 38.33 4.35
1067 1129 1.153997 GTCTTCCTCGTCCTCGTGC 60.154 63.158 0.00 0.00 38.33 5.34
1068 1130 2.182030 CTTCCTCGTCCTCGTGCC 59.818 66.667 0.00 0.00 38.33 5.01
1123 1185 1.270305 TGGAAGTCGCAAGGAACTCAG 60.270 52.381 0.00 0.00 38.49 3.35
1149 1211 2.696125 TGGCCCTCATCCCCTTCC 60.696 66.667 0.00 0.00 0.00 3.46
1153 1215 2.507944 CCTCATCCCCTTCCGCTG 59.492 66.667 0.00 0.00 0.00 5.18
1174 1236 2.359975 CCGTTCTGCCCAAGGTCC 60.360 66.667 0.00 0.00 0.00 4.46
1185 1247 1.443407 CAAGGTCCGGCGAGATCAT 59.557 57.895 9.30 0.00 0.00 2.45
1186 1248 0.877649 CAAGGTCCGGCGAGATCATG 60.878 60.000 9.30 3.87 0.00 3.07
1196 1258 1.346062 CGAGATCATGGGTGGATCCT 58.654 55.000 14.23 0.00 41.64 3.24
1249 1311 1.002134 CCACCACCTCGCCTTCATT 60.002 57.895 0.00 0.00 0.00 2.57
1256 1318 2.202743 TCGCCTTCATTCGCCTCG 60.203 61.111 0.00 0.00 0.00 4.63
1260 1322 2.897350 CTTCATTCGCCTCGCCCC 60.897 66.667 0.00 0.00 0.00 5.80
1261 1323 3.391665 CTTCATTCGCCTCGCCCCT 62.392 63.158 0.00 0.00 0.00 4.79
1289 1351 2.046023 TGCCGCCTCACCTTCATG 60.046 61.111 0.00 0.00 0.00 3.07
1290 1352 3.512516 GCCGCCTCACCTTCATGC 61.513 66.667 0.00 0.00 0.00 4.06
1299 1361 2.293318 ACCTTCATGCCTCGAGCCA 61.293 57.895 6.99 1.48 42.71 4.75
1308 1370 2.581354 CTCGAGCCACCCCTCTTG 59.419 66.667 0.00 0.00 0.00 3.02
1316 1378 2.116125 ACCCCTCTTGCCAGTTGC 59.884 61.111 0.00 0.00 41.77 4.17
1318 1380 1.228675 CCCCTCTTGCCAGTTGCTT 60.229 57.895 0.00 0.00 42.00 3.91
1326 1388 0.473755 TGCCAGTTGCTTCTTCTCCA 59.526 50.000 0.00 0.00 42.00 3.86
1328 1390 1.815408 GCCAGTTGCTTCTTCTCCACA 60.815 52.381 0.00 0.00 36.87 4.17
1361 1423 2.028484 TCGTTGTCACCACGAGCC 59.972 61.111 0.00 0.00 0.00 4.70
1363 1425 2.668550 GTTGTCACCACGAGCCCC 60.669 66.667 0.00 0.00 0.00 5.80
1381 1443 2.181021 GTGCATGCTTCCTGCTGC 59.819 61.111 20.33 0.00 42.19 5.25
1382 1444 2.035155 TGCATGCTTCCTGCTGCT 59.965 55.556 20.33 0.00 42.28 4.24
1383 1445 1.028330 GTGCATGCTTCCTGCTGCTA 61.028 55.000 20.33 0.00 42.28 3.49
1405 1467 2.825836 CCACCATCGCCTCCTTGC 60.826 66.667 0.00 0.00 0.00 4.01
1406 1468 2.046023 CACCATCGCCTCCTTGCA 60.046 61.111 0.00 0.00 0.00 4.08
1416 1478 3.564345 CTCCTTGCAGCTGCCCACT 62.564 63.158 34.64 0.00 41.18 4.00
1417 1479 3.060615 CCTTGCAGCTGCCCACTC 61.061 66.667 34.64 8.07 41.18 3.51
1437 1499 3.365265 GGCCCTGGTGTTGCTTCG 61.365 66.667 0.00 0.00 0.00 3.79
1442 1504 0.041312 CCTGGTGTTGCTTCGTTTCG 60.041 55.000 0.00 0.00 0.00 3.46
1455 1517 1.076332 CGTTTCGGACCATCAAGACC 58.924 55.000 0.00 0.00 0.00 3.85
1465 1527 0.443869 CATCAAGACCGGCAAGAACG 59.556 55.000 0.00 0.00 0.00 3.95
1487 1549 3.114065 CCTTCGTAGATTCGCCAAGTAC 58.886 50.000 0.00 0.00 35.04 2.73
1507 1569 0.949105 CCACACCGGCAAGACTACAC 60.949 60.000 0.00 0.00 0.00 2.90
1526 1588 3.119708 ACACGGACGTTCAATCTACTACC 60.120 47.826 0.00 0.00 0.00 3.18
1528 1590 3.128242 ACGGACGTTCAATCTACTACCAG 59.872 47.826 0.00 0.00 0.00 4.00
1559 1621 1.779569 AGGTCGACTACGTTTTGCTG 58.220 50.000 16.46 0.00 40.69 4.41
1567 1629 1.787057 TACGTTTTGCTGCCCCGTTG 61.787 55.000 0.00 0.00 33.32 4.10
1608 1670 4.640771 AGACCACATTGACACCAAGTAT 57.359 40.909 0.00 0.00 35.48 2.12
1611 1673 5.241506 AGACCACATTGACACCAAGTATTTG 59.758 40.000 0.00 0.00 35.48 2.32
1687 1749 1.829222 ACTACCATCGTCGTGGGATTT 59.171 47.619 15.29 1.27 43.77 2.17
1688 1750 2.201732 CTACCATCGTCGTGGGATTTG 58.798 52.381 15.29 0.00 43.77 2.32
1689 1751 0.611200 ACCATCGTCGTGGGATTTGA 59.389 50.000 15.29 0.00 43.77 2.69
1690 1752 1.006832 CCATCGTCGTGGGATTTGAC 58.993 55.000 6.09 0.00 35.55 3.18
1691 1753 1.674519 CCATCGTCGTGGGATTTGACA 60.675 52.381 6.09 0.00 35.55 3.58
1692 1754 2.073056 CATCGTCGTGGGATTTGACAA 58.927 47.619 0.00 0.00 32.91 3.18
1693 1755 1.790755 TCGTCGTGGGATTTGACAAG 58.209 50.000 0.00 0.00 32.91 3.16
1694 1756 0.165944 CGTCGTGGGATTTGACAAGC 59.834 55.000 0.00 0.00 32.91 4.01
1695 1757 1.523758 GTCGTGGGATTTGACAAGCT 58.476 50.000 0.00 0.00 32.91 3.74
1696 1758 1.464997 GTCGTGGGATTTGACAAGCTC 59.535 52.381 0.00 0.00 32.91 4.09
1697 1759 1.071542 TCGTGGGATTTGACAAGCTCA 59.928 47.619 0.00 0.00 0.00 4.26
1698 1760 1.879380 CGTGGGATTTGACAAGCTCAA 59.121 47.619 0.00 0.00 37.08 3.02
1699 1761 2.489329 CGTGGGATTTGACAAGCTCAAT 59.511 45.455 0.00 0.00 38.74 2.57
1700 1762 3.426695 CGTGGGATTTGACAAGCTCAATC 60.427 47.826 0.00 0.00 38.74 2.67
1701 1763 3.091545 TGGGATTTGACAAGCTCAATCC 58.908 45.455 7.15 7.15 38.74 3.01
1702 1764 3.091545 GGGATTTGACAAGCTCAATCCA 58.908 45.455 14.80 0.00 38.74 3.41
1703 1765 3.119352 GGGATTTGACAAGCTCAATCCAC 60.119 47.826 14.80 4.36 38.74 4.02
1704 1766 3.760684 GGATTTGACAAGCTCAATCCACT 59.239 43.478 9.91 0.00 38.74 4.00
1705 1767 4.943705 GGATTTGACAAGCTCAATCCACTA 59.056 41.667 9.91 0.00 38.74 2.74
1706 1768 5.163713 GGATTTGACAAGCTCAATCCACTAC 60.164 44.000 9.91 0.00 38.74 2.73
1707 1769 3.334583 TGACAAGCTCAATCCACTACC 57.665 47.619 0.00 0.00 0.00 3.18
1708 1770 2.637382 TGACAAGCTCAATCCACTACCA 59.363 45.455 0.00 0.00 0.00 3.25
1709 1771 3.264193 TGACAAGCTCAATCCACTACCAT 59.736 43.478 0.00 0.00 0.00 3.55
1710 1772 3.873952 GACAAGCTCAATCCACTACCATC 59.126 47.826 0.00 0.00 0.00 3.51
1711 1773 2.868583 CAAGCTCAATCCACTACCATCG 59.131 50.000 0.00 0.00 0.00 3.84
1712 1774 2.111384 AGCTCAATCCACTACCATCGT 58.889 47.619 0.00 0.00 0.00 3.73
1713 1775 2.101582 AGCTCAATCCACTACCATCGTC 59.898 50.000 0.00 0.00 0.00 4.20
1714 1776 2.732366 CTCAATCCACTACCATCGTCG 58.268 52.381 0.00 0.00 0.00 5.12
1715 1777 2.097036 TCAATCCACTACCATCGTCGT 58.903 47.619 0.00 0.00 0.00 4.34
1716 1778 2.159296 TCAATCCACTACCATCGTCGTG 60.159 50.000 0.00 0.00 35.87 4.35
1717 1779 4.806571 CCACTACCATCGTCGTGG 57.193 61.111 0.00 0.00 46.05 4.94
1718 1780 1.141019 CCACTACCATCGTCGTGGG 59.859 63.158 6.30 10.09 46.96 4.61
1719 1781 1.317431 CCACTACCATCGTCGTGGGA 61.317 60.000 6.30 8.22 46.96 4.37
1720 1782 0.744874 CACTACCATCGTCGTGGGAT 59.255 55.000 15.29 2.10 43.77 3.85
1721 1783 1.136305 CACTACCATCGTCGTGGGATT 59.864 52.381 15.29 2.16 43.77 3.01
1722 1784 1.829222 ACTACCATCGTCGTGGGATTT 59.171 47.619 15.29 1.27 43.77 2.17
1774 1836 1.555533 GGATTCGTCAAGTTCCCCTCT 59.444 52.381 0.00 0.00 0.00 3.69
1781 1843 1.841556 AAGTTCCCCTCTGTCGCCA 60.842 57.895 0.00 0.00 0.00 5.69
1808 1870 1.093159 CTACTTCCACTACCGTCGCT 58.907 55.000 0.00 0.00 0.00 4.93
1832 1894 6.363065 TGAGGACCGATAGTATCACTACTTT 58.637 40.000 10.71 0.00 39.04 2.66
1833 1895 6.262496 TGAGGACCGATAGTATCACTACTTTG 59.738 42.308 10.71 0.00 39.04 2.77
1837 1899 7.028926 ACCGATAGTATCACTACTTTGACTG 57.971 40.000 10.71 0.00 39.04 3.51
1839 1901 6.459710 CCGATAGTATCACTACTTTGACTGCA 60.460 42.308 10.71 0.00 39.04 4.41
1841 1903 4.822026 AGTATCACTACTTTGACTGCACC 58.178 43.478 0.00 0.00 34.42 5.01
1842 1904 3.769739 ATCACTACTTTGACTGCACCA 57.230 42.857 0.00 0.00 0.00 4.17
1904 1968 5.143376 ACACACGCTACAAAGGTATAACT 57.857 39.130 0.00 0.00 0.00 2.24
1911 1975 4.335594 GCTACAAAGGTATAACTGCCAAGG 59.664 45.833 0.00 0.00 0.00 3.61
2089 2166 1.470805 GCTTTGTTGCACCGGTTTCTT 60.471 47.619 2.97 0.00 0.00 2.52
2140 2244 2.288702 CGTGGCACCATTTCCATTTTCA 60.289 45.455 12.86 0.00 34.47 2.69
2282 2401 2.423538 GTCACCCTCATGCATGTTAACC 59.576 50.000 25.43 6.24 0.00 2.85
2319 2439 9.495754 TGTTGTTTGCATTAAAAATTGCTAAAC 57.504 25.926 13.75 13.75 39.60 2.01
2422 2542 8.196771 GGAAAAATGCATAGATTAACATGGTGA 58.803 33.333 0.00 0.00 0.00 4.02
2453 2573 9.646427 ACTTTGCATGTTTAACAACTCTAAAAA 57.354 25.926 0.66 0.00 33.58 1.94
2538 2661 2.554893 GTTTGTTGTTTCCGGCCTCATA 59.445 45.455 0.00 0.00 0.00 2.15
2581 2706 7.066645 GGTAGTTTTATTATGTTCGCCCTCTTT 59.933 37.037 0.00 0.00 0.00 2.52
2704 2830 9.515226 TTGAGCTCCACTTAATTTGTAGTATTT 57.485 29.630 12.15 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.317371 TATCTCTCCCATGCCCTCTC 57.683 55.000 0.00 0.00 0.00 3.20
1 2 2.113233 TGATATCTCTCCCATGCCCTCT 59.887 50.000 3.98 0.00 0.00 3.69
2 3 2.235898 GTGATATCTCTCCCATGCCCTC 59.764 54.545 3.98 0.00 0.00 4.30
3 4 2.264455 GTGATATCTCTCCCATGCCCT 58.736 52.381 3.98 0.00 0.00 5.19
4 5 1.066573 CGTGATATCTCTCCCATGCCC 60.067 57.143 3.98 0.00 0.00 5.36
5 6 1.895798 TCGTGATATCTCTCCCATGCC 59.104 52.381 3.98 0.00 0.00 4.40
6 7 2.822561 TCTCGTGATATCTCTCCCATGC 59.177 50.000 3.98 0.00 0.00 4.06
7 8 5.459536 TTTCTCGTGATATCTCTCCCATG 57.540 43.478 3.98 0.00 0.00 3.66
8 9 5.777223 TCATTTCTCGTGATATCTCTCCCAT 59.223 40.000 3.98 0.00 0.00 4.00
9 10 5.140454 TCATTTCTCGTGATATCTCTCCCA 58.860 41.667 3.98 0.00 0.00 4.37
10 11 5.475220 TCTCATTTCTCGTGATATCTCTCCC 59.525 44.000 3.98 0.00 0.00 4.30
11 12 6.429692 TCTCTCATTTCTCGTGATATCTCTCC 59.570 42.308 3.98 0.00 0.00 3.71
12 13 7.361201 CCTCTCTCATTTCTCGTGATATCTCTC 60.361 44.444 3.98 0.00 0.00 3.20
13 14 6.430925 CCTCTCTCATTTCTCGTGATATCTCT 59.569 42.308 3.98 0.00 0.00 3.10
14 15 6.206634 ACCTCTCTCATTTCTCGTGATATCTC 59.793 42.308 3.98 0.00 0.00 2.75
15 16 6.068010 ACCTCTCTCATTTCTCGTGATATCT 58.932 40.000 3.98 0.00 0.00 1.98
16 17 6.206634 AGACCTCTCTCATTTCTCGTGATATC 59.793 42.308 0.00 0.00 0.00 1.63
17 18 6.068010 AGACCTCTCTCATTTCTCGTGATAT 58.932 40.000 0.00 0.00 0.00 1.63
18 19 5.441500 AGACCTCTCTCATTTCTCGTGATA 58.558 41.667 0.00 0.00 0.00 2.15
19 20 4.277476 AGACCTCTCTCATTTCTCGTGAT 58.723 43.478 0.00 0.00 0.00 3.06
20 21 3.691575 AGACCTCTCTCATTTCTCGTGA 58.308 45.455 0.00 0.00 0.00 4.35
21 22 4.638421 ACTAGACCTCTCTCATTTCTCGTG 59.362 45.833 0.00 0.00 0.00 4.35
22 23 4.638421 CACTAGACCTCTCTCATTTCTCGT 59.362 45.833 0.00 0.00 0.00 4.18
23 24 4.638421 ACACTAGACCTCTCTCATTTCTCG 59.362 45.833 0.00 0.00 0.00 4.04
24 25 7.477494 GTTACACTAGACCTCTCTCATTTCTC 58.523 42.308 0.00 0.00 0.00 2.87
25 26 6.094325 CGTTACACTAGACCTCTCTCATTTCT 59.906 42.308 0.00 0.00 0.00 2.52
26 27 6.127952 ACGTTACACTAGACCTCTCTCATTTC 60.128 42.308 0.00 0.00 0.00 2.17
27 28 5.711036 ACGTTACACTAGACCTCTCTCATTT 59.289 40.000 0.00 0.00 0.00 2.32
28 29 5.254901 ACGTTACACTAGACCTCTCTCATT 58.745 41.667 0.00 0.00 0.00 2.57
29 30 4.846040 ACGTTACACTAGACCTCTCTCAT 58.154 43.478 0.00 0.00 0.00 2.90
30 31 4.252073 GACGTTACACTAGACCTCTCTCA 58.748 47.826 0.00 0.00 0.00 3.27
31 32 3.622612 GGACGTTACACTAGACCTCTCTC 59.377 52.174 0.00 0.00 0.00 3.20
32 33 3.608796 GGACGTTACACTAGACCTCTCT 58.391 50.000 0.00 0.00 0.00 3.10
33 34 2.682352 GGGACGTTACACTAGACCTCTC 59.318 54.545 0.00 0.00 0.00 3.20
34 35 2.720915 GGGACGTTACACTAGACCTCT 58.279 52.381 0.00 0.00 0.00 3.69
73 74 2.884012 TGACACGCAAAACATGGAAGAT 59.116 40.909 0.00 0.00 0.00 2.40
74 75 2.290367 CTGACACGCAAAACATGGAAGA 59.710 45.455 0.00 0.00 0.00 2.87
152 156 8.752766 AGTTTTAAAAGTGATTGCATGATGAG 57.247 30.769 7.49 0.00 0.00 2.90
197 219 7.779798 TCCCTTGATTTAAATGGATCGAAGATT 59.220 33.333 5.17 0.00 45.12 2.40
312 342 7.633193 ATTATTTGCAAGTGGGTTACGATTA 57.367 32.000 4.47 0.00 0.00 1.75
314 344 6.405397 GGAATTATTTGCAAGTGGGTTACGAT 60.405 38.462 4.47 0.00 0.00 3.73
315 345 5.106078 GGAATTATTTGCAAGTGGGTTACGA 60.106 40.000 4.47 0.00 0.00 3.43
445 479 4.225942 TCAAATGGGTGAATAGAGAGTGCT 59.774 41.667 0.00 0.00 0.00 4.40
446 480 4.517285 TCAAATGGGTGAATAGAGAGTGC 58.483 43.478 0.00 0.00 0.00 4.40
548 591 1.428139 TGGGGTTAATTTTCCCGGACA 59.572 47.619 0.73 0.00 44.27 4.02
676 727 3.637273 GGCCGGTCTGGTTGGTCT 61.637 66.667 1.90 0.00 41.21 3.85
745 807 0.923358 ACGAGAGGGAGAGAGTGGAT 59.077 55.000 0.00 0.00 0.00 3.41
789 851 4.925861 GCCATGCCTCCGCCTCTC 62.926 72.222 0.00 0.00 0.00 3.20
802 864 2.841988 GGAGGAGCTCGAGGCCAT 60.842 66.667 15.58 0.00 43.05 4.40
812 874 0.458260 GAAGGTTCGAGAGGAGGAGC 59.542 60.000 0.00 0.00 0.00 4.70
814 876 0.408309 TGGAAGGTTCGAGAGGAGGA 59.592 55.000 0.00 0.00 0.00 3.71
830 892 3.399181 GGTGATGACGGGGCTGGA 61.399 66.667 0.00 0.00 0.00 3.86
1048 1110 1.587933 GCACGAGGACGAGGAAGACT 61.588 60.000 0.00 0.00 42.66 3.24
1079 1141 4.610714 GGAAGGAGGCGCCGGATC 62.611 72.222 23.20 17.53 43.43 3.36
1088 1150 3.474570 CCAGGGCGAGGAAGGAGG 61.475 72.222 0.00 0.00 0.00 4.30
1094 1156 3.068691 CGACTTCCAGGGCGAGGA 61.069 66.667 0.00 0.00 0.00 3.71
1153 1215 3.423154 CTTGGGCAGAACGGCGTC 61.423 66.667 15.17 7.22 42.43 5.19
1158 1220 2.742372 CGGACCTTGGGCAGAACG 60.742 66.667 0.00 0.00 0.00 3.95
1174 1236 2.104572 ATCCACCCATGATCTCGCCG 62.105 60.000 0.00 0.00 0.00 6.46
1178 1240 2.038295 GACAGGATCCACCCATGATCTC 59.962 54.545 15.82 0.00 38.89 2.75
1196 1258 2.764128 GGGAGATGCGAGGGGACA 60.764 66.667 0.00 0.00 0.00 4.02
1219 1281 4.590553 TGGTGGAGGCCAGGTCCA 62.591 66.667 8.12 8.12 42.06 4.02
1274 1336 2.825836 GGCATGAAGGTGAGGCGG 60.826 66.667 0.00 0.00 0.00 6.13
1277 1339 0.179089 CTCGAGGCATGAAGGTGAGG 60.179 60.000 3.91 0.00 0.00 3.86
1278 1340 0.809241 GCTCGAGGCATGAAGGTGAG 60.809 60.000 15.58 0.00 41.35 3.51
1279 1341 1.219124 GCTCGAGGCATGAAGGTGA 59.781 57.895 15.58 0.00 41.35 4.02
1290 1352 2.685380 AAGAGGGGTGGCTCGAGG 60.685 66.667 15.58 0.00 0.00 4.63
1299 1361 2.116125 GCAACTGGCAAGAGGGGT 59.884 61.111 0.00 0.00 43.97 4.95
1308 1370 0.877743 GTGGAGAAGAAGCAACTGGC 59.122 55.000 0.00 0.00 45.30 4.85
1316 1378 0.605589 AGAGGCGTGTGGAGAAGAAG 59.394 55.000 0.00 0.00 0.00 2.85
1318 1380 0.827925 ACAGAGGCGTGTGGAGAAGA 60.828 55.000 8.51 0.00 0.00 2.87
1361 1423 3.818787 GCAGGAAGCATGCACGGG 61.819 66.667 21.98 6.25 43.31 5.28
1381 1443 0.462047 GAGGCGATGGTGGTGGTTAG 60.462 60.000 0.00 0.00 0.00 2.34
1382 1444 1.600107 GAGGCGATGGTGGTGGTTA 59.400 57.895 0.00 0.00 0.00 2.85
1383 1445 2.351276 GAGGCGATGGTGGTGGTT 59.649 61.111 0.00 0.00 0.00 3.67
1416 1478 4.329545 GCAACACCAGGGCCTCGA 62.330 66.667 0.95 0.00 0.00 4.04
1417 1479 3.850098 AAGCAACACCAGGGCCTCG 62.850 63.158 0.95 0.00 0.00 4.63
1437 1499 1.076332 CGGTCTTGATGGTCCGAAAC 58.924 55.000 0.00 0.00 44.86 2.78
1442 1504 1.002624 TTGCCGGTCTTGATGGTCC 60.003 57.895 1.90 0.00 0.00 4.46
1465 1527 0.931005 CTTGGCGAATCTACGAAGGC 59.069 55.000 0.00 0.00 35.09 4.35
1478 1540 2.740826 CGGTGTGGGTACTTGGCG 60.741 66.667 0.00 0.00 0.00 5.69
1487 1549 1.375523 GTAGTCTTGCCGGTGTGGG 60.376 63.158 1.90 0.00 38.63 4.61
1507 1569 3.376234 TCTGGTAGTAGATTGAACGTCCG 59.624 47.826 0.00 0.00 0.00 4.79
1526 1588 4.235360 AGTCGACCTAACGTTTCAATCTG 58.765 43.478 13.01 0.00 34.70 2.90
1528 1590 4.261581 CGTAGTCGACCTAACGTTTCAATC 59.738 45.833 21.02 0.00 39.71 2.67
1532 1594 3.188895 ACGTAGTCGACCTAACGTTTC 57.811 47.619 26.17 0.00 29.74 2.78
1539 1601 2.923605 GCAGCAAAACGTAGTCGACCTA 60.924 50.000 13.01 1.11 45.00 3.08
1567 1629 0.819582 TCGGGTACTTGACGATTCCC 59.180 55.000 0.00 0.00 0.00 3.97
1574 1636 1.342174 TGTGGTCTTCGGGTACTTGAC 59.658 52.381 0.00 0.00 0.00 3.18
1608 1670 1.940334 CCGAAAACGGCGGTACAAA 59.060 52.632 13.24 0.00 43.66 2.83
1687 1749 2.637382 TGGTAGTGGATTGAGCTTGTCA 59.363 45.455 0.00 0.00 0.00 3.58
1688 1750 3.334583 TGGTAGTGGATTGAGCTTGTC 57.665 47.619 0.00 0.00 0.00 3.18
1689 1751 3.679917 CGATGGTAGTGGATTGAGCTTGT 60.680 47.826 0.00 0.00 0.00 3.16
1690 1752 2.868583 CGATGGTAGTGGATTGAGCTTG 59.131 50.000 0.00 0.00 0.00 4.01
1691 1753 2.501723 ACGATGGTAGTGGATTGAGCTT 59.498 45.455 0.00 0.00 0.00 3.74
1692 1754 2.101582 GACGATGGTAGTGGATTGAGCT 59.898 50.000 0.00 0.00 0.00 4.09
1693 1755 2.474816 GACGATGGTAGTGGATTGAGC 58.525 52.381 0.00 0.00 0.00 4.26
1694 1756 2.099263 ACGACGATGGTAGTGGATTGAG 59.901 50.000 0.00 0.00 30.33 3.02
1695 1757 2.097036 ACGACGATGGTAGTGGATTGA 58.903 47.619 0.00 0.00 30.33 2.57
1696 1758 2.193447 CACGACGATGGTAGTGGATTG 58.807 52.381 12.27 0.00 43.49 2.67
1697 1759 2.579207 CACGACGATGGTAGTGGATT 57.421 50.000 12.27 0.00 43.49 3.01
1701 1763 0.744874 ATCCCACGACGATGGTAGTG 59.255 55.000 12.99 12.99 45.80 2.74
1702 1764 1.481871 AATCCCACGACGATGGTAGT 58.518 50.000 0.00 0.00 38.16 2.73
1703 1765 2.159156 TCAAATCCCACGACGATGGTAG 60.159 50.000 0.00 0.00 38.16 3.18
1704 1766 1.826096 TCAAATCCCACGACGATGGTA 59.174 47.619 0.00 0.00 38.16 3.25
1705 1767 0.611200 TCAAATCCCACGACGATGGT 59.389 50.000 0.00 0.00 38.16 3.55
1706 1768 1.006832 GTCAAATCCCACGACGATGG 58.993 55.000 0.00 5.65 39.71 3.51
1707 1769 1.720805 TGTCAAATCCCACGACGATG 58.279 50.000 0.00 0.00 32.17 3.84
1708 1770 2.346803 CTTGTCAAATCCCACGACGAT 58.653 47.619 0.00 0.00 32.17 3.73
1709 1771 1.790755 CTTGTCAAATCCCACGACGA 58.209 50.000 0.00 0.00 32.17 4.20
1710 1772 0.165944 GCTTGTCAAATCCCACGACG 59.834 55.000 0.00 0.00 32.17 5.12
1711 1773 1.464997 GAGCTTGTCAAATCCCACGAC 59.535 52.381 0.00 0.00 0.00 4.34
1712 1774 1.071542 TGAGCTTGTCAAATCCCACGA 59.928 47.619 0.00 0.00 29.64 4.35
1713 1775 1.522668 TGAGCTTGTCAAATCCCACG 58.477 50.000 0.00 0.00 29.64 4.94
1722 1784 2.614481 GGGGTCGTTATTGAGCTTGTCA 60.614 50.000 0.00 0.00 36.62 3.58
1774 1836 1.552578 AGTAGTGGTACATGGCGACA 58.447 50.000 0.00 0.00 44.52 4.35
1781 1843 3.698040 CGGTAGTGGAAGTAGTGGTACAT 59.302 47.826 0.00 0.00 44.52 2.29
1808 1870 5.563876 AGTAGTGATACTATCGGTCCTCA 57.436 43.478 0.00 0.00 32.65 3.86
1832 1894 3.513515 TGTAGATGTACATGGTGCAGTCA 59.486 43.478 14.43 0.00 34.02 3.41
1833 1895 3.865745 GTGTAGATGTACATGGTGCAGTC 59.134 47.826 14.43 0.00 41.29 3.51
1837 1899 2.201732 CGGTGTAGATGTACATGGTGC 58.798 52.381 14.43 4.57 41.29 5.01
1839 1901 1.828595 TGCGGTGTAGATGTACATGGT 59.171 47.619 14.43 2.66 41.29 3.55
1841 1903 2.726241 CGATGCGGTGTAGATGTACATG 59.274 50.000 14.43 3.71 41.29 3.21
1842 1904 2.621526 TCGATGCGGTGTAGATGTACAT 59.378 45.455 8.43 8.43 41.29 2.29
2035 2112 1.756538 TGCGGAACATGCTAGAGATGA 59.243 47.619 8.71 0.00 0.00 2.92
2089 2166 1.000843 CGATGATCCGGTGGCTCATTA 59.999 52.381 0.00 0.00 38.47 1.90
2140 2244 4.966787 AAATGGTGCCACGGCGGT 62.967 61.111 13.24 0.00 45.51 5.68
2422 2542 8.413229 AGAGTTGTTAAACATGCAAAGTAATGT 58.587 29.630 0.00 0.00 38.88 2.71
2478 2598 4.994217 TCCTCATGCGCATATTTCGAATTA 59.006 37.500 24.84 0.00 0.00 1.40
2573 2698 2.802719 TGGTTAACATGGAAAGAGGGC 58.197 47.619 8.10 0.00 0.00 5.19
2652 2778 4.520743 CAACGAGTTGCATATTGACGAT 57.479 40.909 2.84 0.00 33.45 3.73


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

AutoCloner maintained by Alex Coulton.