Multiple sequence alignment - TraesCS5B01G385300

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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 TraesCS5B01G385300 chr5B 100.000 6058 0 0 1657 7714 564993354 564987297 0.000000e+00 11188.0
1 TraesCS5B01G385300 chr5B 100.000 1416 0 0 1 1416 564995010 564993595 0.000000e+00 2615.0
2 TraesCS5B01G385300 chr5B 92.418 765 53 4 6954 7714 37503446 37504209 0.000000e+00 1086.0
3 TraesCS5B01G385300 chr5B 84.140 744 76 22 5352 6090 564526496 564525790 0.000000e+00 682.0
4 TraesCS5B01G385300 chr5B 83.536 741 82 20 5354 6090 564464584 564463880 0.000000e+00 656.0
5 TraesCS5B01G385300 chr5B 84.934 677 67 17 3812 4469 564439624 564438964 0.000000e+00 652.0
6 TraesCS5B01G385300 chr5B 84.885 655 86 7 4289 4941 563695472 563694829 0.000000e+00 649.0
7 TraesCS5B01G385300 chr5B 84.638 677 69 17 3812 4469 564377471 564376811 6.530000e-180 641.0
8 TraesCS5B01G385300 chr5B 83.152 736 80 21 5360 6090 564193997 564193301 3.930000e-177 632.0
9 TraesCS5B01G385300 chr5B 84.389 679 64 19 3812 4469 564026893 564026236 5.080000e-176 628.0
10 TraesCS5B01G385300 chr5B 78.304 1097 142 46 4988 6051 563662954 563661921 3.060000e-173 619.0
11 TraesCS5B01G385300 chr5B 83.947 679 73 18 3810 4469 564479702 564479041 1.100000e-172 617.0
12 TraesCS5B01G385300 chr5B 86.402 478 42 11 3812 4282 564316754 564316293 1.160000e-137 501.0
13 TraesCS5B01G385300 chr5B 84.241 514 55 10 3973 4469 564446226 564445722 1.950000e-130 477.0
14 TraesCS5B01G385300 chr5B 81.261 571 71 15 4991 5539 563694863 563694307 5.530000e-116 429.0
15 TraesCS5B01G385300 chr5B 88.215 297 33 2 3320 3615 564486237 564485942 3.420000e-93 353.0
16 TraesCS5B01G385300 chr5B 86.186 333 38 3 4143 4473 564529285 564528959 3.420000e-93 353.0
17 TraesCS5B01G385300 chr5B 87.900 281 32 2 3320 3599 564486553 564486274 5.770000e-86 329.0
18 TraesCS5B01G385300 chr5B 83.243 370 48 9 4994 5351 564526923 564526556 2.080000e-85 327.0
19 TraesCS5B01G385300 chr5B 80.624 449 54 17 6230 6677 564477723 564477307 4.490000e-82 316.0
20 TraesCS5B01G385300 chr5B 77.715 534 79 36 6193 6702 563661839 563661322 2.720000e-74 291.0
21 TraesCS5B01G385300 chr5B 81.572 369 50 8 4994 5351 564465009 564464648 9.790000e-74 289.0
22 TraesCS5B01G385300 chr5B 77.316 529 84 32 6193 6702 563693680 563693169 5.890000e-71 279.0
23 TraesCS5B01G385300 chr5B 78.714 451 64 19 6228 6677 564509405 564508986 9.860000e-69 272.0
24 TraesCS5B01G385300 chr5B 89.524 210 21 1 3035 3244 564452868 564452660 1.650000e-66 265.0
25 TraesCS5B01G385300 chr5B 78.972 428 57 15 6228 6652 564218379 564217982 2.140000e-65 261.0
26 TraesCS5B01G385300 chr5B 89.048 210 21 2 3035 3244 564532055 564531848 7.680000e-65 259.0
27 TraesCS5B01G385300 chr5B 77.148 512 69 27 5551 6051 563694236 563693762 3.570000e-63 254.0
28 TraesCS5B01G385300 chr5B 88.571 210 22 2 3035 3244 564473339 564473132 3.570000e-63 254.0
29 TraesCS5B01G385300 chr5B 83.577 274 35 2 2972 3245 564181285 564181022 1.660000e-61 248.0
30 TraesCS5B01G385300 chr5B 96.970 66 2 0 4904 4969 564990023 564989958 2.280000e-20 111.0
31 TraesCS5B01G385300 chr5B 96.970 66 2 0 4988 5053 564990107 564990042 2.280000e-20 111.0
32 TraesCS5B01G385300 chr5B 100.000 42 0 0 2607 2648 564992363 564992404 2.310000e-10 78.7
33 TraesCS5B01G385300 chr5D 96.434 1991 37 10 4988 6965 459864265 459862296 0.000000e+00 3253.0
34 TraesCS5B01G385300 chr5D 93.816 1326 46 14 2518 3809 459866750 459865427 0.000000e+00 1962.0
35 TraesCS5B01G385300 chr5D 96.499 1171 22 3 3805 4969 459865357 459864200 0.000000e+00 1917.0
36 TraesCS5B01G385300 chr5D 86.231 1300 123 29 134 1416 459869028 459867768 0.000000e+00 1358.0
37 TraesCS5B01G385300 chr5D 92.005 888 42 13 1657 2522 459867652 459866772 0.000000e+00 1219.0
38 TraesCS5B01G385300 chr5D 85.854 714 68 18 5049 5755 459735819 459735132 0.000000e+00 728.0
39 TraesCS5B01G385300 chr5D 85.355 676 62 17 3814 4469 459752346 459751688 0.000000e+00 665.0
40 TraesCS5B01G385300 chr5D 83.914 603 85 7 4374 4970 459731851 459731255 4.040000e-157 566.0
41 TraesCS5B01G385300 chr5D 87.427 342 39 3 4560 4900 459736806 459736468 2.610000e-104 390.0
42 TraesCS5B01G385300 chr5D 88.552 297 32 2 3320 3615 459765544 459765249 7.360000e-95 359.0
43 TraesCS5B01G385300 chr5D 89.324 281 28 2 3320 3599 459765861 459765582 1.230000e-92 351.0
44 TraesCS5B01G385300 chr5D 82.842 373 44 14 4994 5351 459750257 459749890 4.490000e-82 316.0
45 TraesCS5B01G385300 chr5D 81.761 318 43 6 5049 5356 459574214 459573902 1.290000e-62 252.0
46 TraesCS5B01G385300 chr5D 79.396 364 50 15 2905 3250 459575152 459574796 4.650000e-57 233.0
47 TraesCS5B01G385300 chr5D 84.921 126 16 3 4852 4975 459750315 459750191 2.920000e-24 124.0
48 TraesCS5B01G385300 chr5D 85.217 115 11 3 4457 4571 459574579 459574471 6.330000e-21 113.0
49 TraesCS5B01G385300 chr5D 90.164 61 5 1 4514 4574 459580692 459580633 2.310000e-10 78.7
50 TraesCS5B01G385300 chr5D 100.000 28 0 0 2603 2630 421173810 421173837 1.400000e-02 52.8
51 TraesCS5B01G385300 chr5A 95.486 1994 47 12 4988 6965 579439404 579441370 0.000000e+00 3144.0
52 TraesCS5B01G385300 chr5A 96.357 1153 40 1 3819 4969 579438317 579439469 0.000000e+00 1895.0
53 TraesCS5B01G385300 chr5A 94.525 1169 41 12 2658 3811 579437094 579438254 0.000000e+00 1783.0
54 TraesCS5B01G385300 chr5A 85.920 1321 111 32 134 1413 579434713 579435999 0.000000e+00 1339.0
55 TraesCS5B01G385300 chr5A 89.279 998 36 29 1657 2608 579436117 579437089 0.000000e+00 1184.0
56 TraesCS5B01G385300 chr5A 83.176 743 84 21 5352 6090 579902564 579901859 6.530000e-180 641.0
57 TraesCS5B01G385300 chr5A 83.824 680 69 19 3812 4469 579848795 579849455 6.620000e-170 608.0
58 TraesCS5B01G385300 chr5A 83.694 509 51 17 5586 6090 579861279 579860799 1.180000e-122 451.0
59 TraesCS5B01G385300 chr5A 83.369 463 69 3 4289 4751 579153044 579152590 9.260000e-114 422.0
60 TraesCS5B01G385300 chr5A 82.549 510 56 19 5586 6090 580192330 580191849 1.200000e-112 418.0
61 TraesCS5B01G385300 chr5A 87.202 336 34 8 4143 4473 579868151 579867820 2.630000e-99 374.0
62 TraesCS5B01G385300 chr5A 88.552 297 28 5 3320 3615 579841730 579842021 9.520000e-94 355.0
63 TraesCS5B01G385300 chr5A 85.498 331 44 3 4143 4471 579917442 579917114 7.410000e-90 342.0
64 TraesCS5B01G385300 chr5A 80.837 454 51 19 6228 6677 579845273 579845694 2.680000e-84 324.0
65 TraesCS5B01G385300 chr5A 83.235 340 39 8 3812 4149 579854972 579854649 5.850000e-76 296.0
66 TraesCS5B01G385300 chr5A 81.301 369 55 9 4995 5351 579902991 579902625 3.520000e-73 287.0
67 TraesCS5B01G385300 chr5A 87.500 248 29 1 6203 6450 579151410 579151165 1.270000e-72 285.0
68 TraesCS5B01G385300 chr5A 90.476 210 19 1 3035 3244 579846733 579846941 7.630000e-70 276.0
69 TraesCS5B01G385300 chr5A 88.517 209 23 1 4734 4941 579152576 579152368 1.290000e-62 252.0
70 TraesCS5B01G385300 chr5A 83.755 277 34 6 2968 3244 579857022 579856757 1.290000e-62 252.0
71 TraesCS5B01G385300 chr5A 87.619 210 24 2 3035 3244 579870879 579870672 7.730000e-60 243.0
72 TraesCS5B01G385300 chr5A 84.722 144 14 3 3179 3321 579841542 579841678 3.750000e-28 137.0
73 TraesCS5B01G385300 chr5A 100.000 46 0 0 2602 2647 326659581 326659536 1.380000e-12 86.1
74 TraesCS5B01G385300 chr5A 97.727 44 1 0 2605 2648 326659533 326659576 8.300000e-10 76.8
75 TraesCS5B01G385300 chr3B 94.702 755 36 3 6964 7714 20466284 20465530 0.000000e+00 1170.0
76 TraesCS5B01G385300 chr3B 92.500 40 2 1 2626 2665 214029465 214029503 1.000000e-03 56.5
77 TraesCS5B01G385300 chr2B 94.071 759 38 6 6961 7714 731339612 731338856 0.000000e+00 1146.0
78 TraesCS5B01G385300 chr2B 93.395 757 42 7 6964 7714 607059462 607060216 0.000000e+00 1114.0
79 TraesCS5B01G385300 chr2B 93.254 756 45 5 6964 7714 184789185 184788431 0.000000e+00 1109.0
80 TraesCS5B01G385300 chr1B 94.780 728 32 5 6992 7714 667674976 667674250 0.000000e+00 1129.0
81 TraesCS5B01G385300 chr6B 93.395 757 45 4 6962 7714 613592570 613593325 0.000000e+00 1116.0
82 TraesCS5B01G385300 chr7B 93.094 753 47 4 6960 7708 638059438 638060189 0.000000e+00 1098.0
83 TraesCS5B01G385300 chr7B 92.980 755 47 5 6964 7714 424534781 424535533 0.000000e+00 1096.0
84 TraesCS5B01G385300 chrUn 85.494 648 85 4 4289 4935 68137656 68138295 0.000000e+00 667.0
85 TraesCS5B01G385300 chrUn 85.321 654 87 4 4289 4941 315403856 315403211 0.000000e+00 667.0
86 TraesCS5B01G385300 chrUn 91.018 167 14 1 3078 3244 459191108 459190943 2.800000e-54 224.0
87 TraesCS5B01G385300 chrUn 100.000 29 0 0 2626 2654 319631092 319631064 4.000000e-03 54.7
88 TraesCS5B01G385300 chrUn 100.000 28 0 0 2627 2654 163390502 163390475 1.400000e-02 52.8
89 TraesCS5B01G385300 chrUn 100.000 28 0 0 2627 2654 189191472 189191499 1.400000e-02 52.8
90 TraesCS5B01G385300 chrUn 100.000 28 0 0 2627 2654 189226984 189227011 1.400000e-02 52.8
91 TraesCS5B01G385300 chrUn 100.000 28 0 0 2602 2629 307259687 307259660 1.400000e-02 52.8
92 TraesCS5B01G385300 chrUn 100.000 28 0 0 2627 2654 363114022 363114049 1.400000e-02 52.8
93 TraesCS5B01G385300 chrUn 100.000 28 0 0 2627 2654 367073139 367073166 1.400000e-02 52.8
94 TraesCS5B01G385300 chrUn 100.000 28 0 0 2602 2629 405825501 405825474 1.400000e-02 52.8
95 TraesCS5B01G385300 chrUn 100.000 28 0 0 2602 2629 473080457 473080430 1.400000e-02 52.8
96 TraesCS5B01G385300 chr3A 92.000 50 2 2 2605 2653 655540456 655540408 1.390000e-07 69.4
97 TraesCS5B01G385300 chr3A 95.000 40 1 1 2609 2648 655540416 655540454 2.320000e-05 62.1
98 TraesCS5B01G385300 chr1D 100.000 31 0 0 2626 2656 464799749 464799719 3.010000e-04 58.4
99 TraesCS5B01G385300 chr1D 100.000 30 0 0 2626 2655 331283856 331283827 1.000000e-03 56.5
100 TraesCS5B01G385300 chr1D 100.000 29 0 0 2626 2654 246070256 246070228 4.000000e-03 54.7
101 TraesCS5B01G385300 chr7D 100.000 30 0 0 2626 2655 22964319 22964348 1.000000e-03 56.5
102 TraesCS5B01G385300 chr3D 100.000 30 0 0 2626 2655 300256227 300256198 1.000000e-03 56.5
103 TraesCS5B01G385300 chr3D 100.000 29 0 0 2626 2654 54370435 54370407 4.000000e-03 54.7
104 TraesCS5B01G385300 chr3D 100.000 29 0 0 2626 2654 464111786 464111758 4.000000e-03 54.7
105 TraesCS5B01G385300 chr3D 100.000 28 0 0 2602 2629 427225836 427225809 1.400000e-02 52.8
106 TraesCS5B01G385300 chr3D 100.000 28 0 0 2602 2629 445028257 445028284 1.400000e-02 52.8
107 TraesCS5B01G385300 chr7A 96.875 32 1 0 2621 2652 58845029 58845060 4.000000e-03 54.7
108 TraesCS5B01G385300 chr7A 96.875 32 1 0 2598 2629 611490943 611490912 4.000000e-03 54.7
109 TraesCS5B01G385300 chr4D 94.286 35 2 0 2600 2634 60134659 60134693 4.000000e-03 54.7
110 TraesCS5B01G385300 chr4B 94.286 35 2 0 2600 2634 89304600 89304634 4.000000e-03 54.7
111 TraesCS5B01G385300 chr4A 100.000 29 0 0 2626 2654 653207590 653207562 4.000000e-03 54.7
112 TraesCS5B01G385300 chr4A 100.000 28 0 0 2602 2629 584543178 584543205 1.400000e-02 52.8
113 TraesCS5B01G385300 chr1A 100.000 29 0 0 2626 2654 307037036 307037008 4.000000e-03 54.7
114 TraesCS5B01G385300 chr6D 100.000 28 0 0 2603 2630 342467204 342467231 1.400000e-02 52.8


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 TraesCS5B01G385300 chr5B 564987297 564995010 7713 True 3506.250000 11188 98.485000 1 7714 4 chr5B.!!$R17 7713
1 TraesCS5B01G385300 chr5B 37503446 37504209 763 False 1086.000000 1086 92.418000 6954 7714 1 chr5B.!!$F1 760
2 TraesCS5B01G385300 chr5B 564438964 564439624 660 True 652.000000 652 84.934000 3812 4469 1 chr5B.!!$R7 657
3 TraesCS5B01G385300 chr5B 564376811 564377471 660 True 641.000000 641 84.638000 3812 4469 1 chr5B.!!$R6 657
4 TraesCS5B01G385300 chr5B 564193301 564193997 696 True 632.000000 632 83.152000 5360 6090 1 chr5B.!!$R3 730
5 TraesCS5B01G385300 chr5B 564026236 564026893 657 True 628.000000 628 84.389000 3812 4469 1 chr5B.!!$R1 657
6 TraesCS5B01G385300 chr5B 564445722 564446226 504 True 477.000000 477 84.241000 3973 4469 1 chr5B.!!$R8 496
7 TraesCS5B01G385300 chr5B 564463880 564465009 1129 True 472.500000 656 82.554000 4994 6090 2 chr5B.!!$R13 1096
8 TraesCS5B01G385300 chr5B 563661322 563662954 1632 True 455.000000 619 78.009500 4988 6702 2 chr5B.!!$R11 1714
9 TraesCS5B01G385300 chr5B 564525790 564532055 6265 True 405.250000 682 85.654250 3035 6090 4 chr5B.!!$R16 3055
10 TraesCS5B01G385300 chr5B 563693169 563695472 2303 True 402.750000 649 80.152500 4289 6702 4 chr5B.!!$R12 2413
11 TraesCS5B01G385300 chr5B 564473132 564479702 6570 True 395.666667 617 84.380667 3035 6677 3 chr5B.!!$R14 3642
12 TraesCS5B01G385300 chr5B 564485942 564486553 611 True 341.000000 353 88.057500 3320 3615 2 chr5B.!!$R15 295
13 TraesCS5B01G385300 chr5D 459862296 459869028 6732 True 1941.800000 3253 92.997000 134 6965 5 chr5D.!!$R6 6831
14 TraesCS5B01G385300 chr5D 459731255 459736806 5551 True 561.333333 728 85.731667 4374 5755 3 chr5D.!!$R3 1381
15 TraesCS5B01G385300 chr5D 459749890 459752346 2456 True 368.333333 665 84.372667 3814 5351 3 chr5D.!!$R4 1537
16 TraesCS5B01G385300 chr5D 459765249 459765861 612 True 355.000000 359 88.938000 3320 3615 2 chr5D.!!$R5 295
17 TraesCS5B01G385300 chr5A 579434713 579441370 6657 False 1869.000000 3144 92.313400 134 6965 5 chr5A.!!$F2 6831
18 TraesCS5B01G385300 chr5A 579901859 579902991 1132 True 464.000000 641 82.238500 4995 6090 2 chr5A.!!$R7 1095
19 TraesCS5B01G385300 chr5A 579841542 579849455 7913 False 340.000000 608 85.682200 3035 6677 5 chr5A.!!$F3 3642
20 TraesCS5B01G385300 chr5A 579854649 579861279 6630 True 333.000000 451 83.561333 2968 6090 3 chr5A.!!$R5 3122
21 TraesCS5B01G385300 chr5A 579151165 579153044 1879 True 319.666667 422 86.462000 4289 6450 3 chr5A.!!$R4 2161
22 TraesCS5B01G385300 chr5A 579867820 579870879 3059 True 308.500000 374 87.410500 3035 4473 2 chr5A.!!$R6 1438
23 TraesCS5B01G385300 chr3B 20465530 20466284 754 True 1170.000000 1170 94.702000 6964 7714 1 chr3B.!!$R1 750
24 TraesCS5B01G385300 chr2B 731338856 731339612 756 True 1146.000000 1146 94.071000 6961 7714 1 chr2B.!!$R2 753
25 TraesCS5B01G385300 chr2B 607059462 607060216 754 False 1114.000000 1114 93.395000 6964 7714 1 chr2B.!!$F1 750
26 TraesCS5B01G385300 chr2B 184788431 184789185 754 True 1109.000000 1109 93.254000 6964 7714 1 chr2B.!!$R1 750
27 TraesCS5B01G385300 chr1B 667674250 667674976 726 True 1129.000000 1129 94.780000 6992 7714 1 chr1B.!!$R1 722
28 TraesCS5B01G385300 chr6B 613592570 613593325 755 False 1116.000000 1116 93.395000 6962 7714 1 chr6B.!!$F1 752
29 TraesCS5B01G385300 chr7B 638059438 638060189 751 False 1098.000000 1098 93.094000 6960 7708 1 chr7B.!!$F2 748
30 TraesCS5B01G385300 chr7B 424534781 424535533 752 False 1096.000000 1096 92.980000 6964 7714 1 chr7B.!!$F1 750
31 TraesCS5B01G385300 chrUn 68137656 68138295 639 False 667.000000 667 85.494000 4289 4935 1 chrUn.!!$F1 646
32 TraesCS5B01G385300 chrUn 315403211 315403856 645 True 667.000000 667 85.321000 4289 4941 1 chrUn.!!$R3 652

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
70 71 0.105039 GATAGGGCTCCCGTCACTTG 59.895 60.000 0.00 0.00 41.95 3.16 F
74 75 0.322546 GGGCTCCCGTCACTTGAAAT 60.323 55.000 0.00 0.00 0.00 2.17 F
1393 1443 0.920438 TTCTCTCTCTCTACCCCGCT 59.080 55.000 0.00 0.00 0.00 5.52 F
1957 2008 1.153686 GGCGTTTCCTCTCGGGTAC 60.154 63.158 0.00 0.00 36.25 3.34 F
2794 2940 0.473501 AGAGGCCTGGAGGATGATCC 60.474 60.000 12.00 2.46 40.03 3.36 F
3549 6429 0.179073 CTCCCTCCTATTGCACGTGG 60.179 60.000 18.88 0.00 0.00 4.94 F
4598 16020 1.070289 GACAGGACGGAGAACCAAAGT 59.930 52.381 0.00 0.00 35.59 2.66 F
4923 17470 0.036105 TACGGAGTCTAGTCGTGGCA 60.036 55.000 11.23 0.00 43.93 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1946 1.599047 CAGACCCAGCTCCAACGAT 59.401 57.895 0.00 0.00 0.00 3.73 R
2020 2071 3.733960 GGCGAAGAAACCACGGCC 61.734 66.667 0.00 0.00 44.46 6.13 R
2582 2691 0.952497 AGACAGCACGCCACTGAATG 60.952 55.000 6.90 0.00 38.55 2.67 R
3549 6429 3.186001 CGACTTATCCAATGATGCTCTGC 59.814 47.826 0.00 0.00 32.18 4.26 R
4598 16020 4.517285 GGATGTGATAGTCCTTCTTGCAA 58.483 43.478 0.00 0.00 0.00 4.08 R
4904 17451 0.036105 TGCCACGACTAGACTCCGTA 60.036 55.000 0.00 0.00 34.91 4.02 R
5984 18708 1.527433 GCAGCAGGGTGGTTCCTTTC 61.527 60.000 0.24 0.00 34.31 2.62 R
6906 19683 1.002544 GTGGAGGTAGCTGTTCAGCTT 59.997 52.381 28.13 13.75 43.52 3.74 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
27 28 2.666272 TGCCCTATGTGAACAAACCA 57.334 45.000 0.00 0.00 0.00 3.67
28 29 2.950781 TGCCCTATGTGAACAAACCAA 58.049 42.857 0.00 0.00 0.00 3.67
29 30 3.505386 TGCCCTATGTGAACAAACCAAT 58.495 40.909 0.00 0.00 0.00 3.16
30 31 4.667573 TGCCCTATGTGAACAAACCAATA 58.332 39.130 0.00 0.00 0.00 1.90
31 32 4.461081 TGCCCTATGTGAACAAACCAATAC 59.539 41.667 0.00 0.00 0.00 1.89
33 34 5.013547 CCCTATGTGAACAAACCAATACCA 58.986 41.667 0.00 0.00 0.00 3.25
34 35 5.125417 CCCTATGTGAACAAACCAATACCAG 59.875 44.000 0.00 0.00 0.00 4.00
35 36 5.125417 CCTATGTGAACAAACCAATACCAGG 59.875 44.000 0.00 0.00 0.00 4.45
38 39 2.625790 TGAACAAACCAATACCAGGCAC 59.374 45.455 0.00 0.00 0.00 5.01
40 41 1.202830 ACAAACCAATACCAGGCACGA 60.203 47.619 0.00 0.00 0.00 4.35
41 42 1.199097 CAAACCAATACCAGGCACGAC 59.801 52.381 0.00 0.00 0.00 4.34
42 43 0.690762 AACCAATACCAGGCACGACT 59.309 50.000 0.00 0.00 0.00 4.18
44 45 1.206371 ACCAATACCAGGCACGACTAC 59.794 52.381 0.00 0.00 0.00 2.73
45 46 1.472728 CCAATACCAGGCACGACTACC 60.473 57.143 0.00 0.00 0.00 3.18
49 50 0.249398 ACCAGGCACGACTACCATTC 59.751 55.000 0.00 0.00 0.00 2.67
51 52 1.645034 CAGGCACGACTACCATTCAG 58.355 55.000 0.00 0.00 0.00 3.02
52 53 1.204704 CAGGCACGACTACCATTCAGA 59.795 52.381 0.00 0.00 0.00 3.27
53 54 2.111384 AGGCACGACTACCATTCAGAT 58.889 47.619 0.00 0.00 0.00 2.90
54 55 3.068165 CAGGCACGACTACCATTCAGATA 59.932 47.826 0.00 0.00 0.00 1.98
56 57 3.553096 GGCACGACTACCATTCAGATAGG 60.553 52.174 0.00 0.00 0.00 2.57
57 58 3.553096 GCACGACTACCATTCAGATAGGG 60.553 52.174 0.00 0.00 0.00 3.53
58 59 2.628657 ACGACTACCATTCAGATAGGGC 59.371 50.000 0.00 0.00 0.00 5.19
63 64 0.322975 CCATTCAGATAGGGCTCCCG 59.677 60.000 0.00 0.00 41.95 5.14
67 68 0.755698 TCAGATAGGGCTCCCGTCAC 60.756 60.000 13.32 2.59 41.95 3.67
70 71 0.105039 GATAGGGCTCCCGTCACTTG 59.895 60.000 0.00 0.00 41.95 3.16
72 73 0.543410 TAGGGCTCCCGTCACTTGAA 60.543 55.000 0.00 0.00 41.95 2.69
73 74 1.072505 GGGCTCCCGTCACTTGAAA 59.927 57.895 0.00 0.00 0.00 2.69
74 75 0.322546 GGGCTCCCGTCACTTGAAAT 60.323 55.000 0.00 0.00 0.00 2.17
75 76 1.065709 GGGCTCCCGTCACTTGAAATA 60.066 52.381 0.00 0.00 0.00 1.40
76 77 2.421529 GGGCTCCCGTCACTTGAAATAT 60.422 50.000 0.00 0.00 0.00 1.28
78 79 3.312697 GGCTCCCGTCACTTGAAATATTC 59.687 47.826 0.00 0.00 0.00 1.75
178 179 7.967854 TGTTGATAGCATTAAGAAAAATGTCCG 59.032 33.333 0.00 0.00 38.78 4.79
180 181 7.471721 TGATAGCATTAAGAAAAATGTCCGTG 58.528 34.615 0.00 0.00 38.78 4.94
336 371 8.751302 GGTTTCATACCATTGAAAAATACGTT 57.249 30.769 0.00 0.00 44.71 3.99
337 372 8.856247 GGTTTCATACCATTGAAAAATACGTTC 58.144 33.333 0.00 0.00 44.71 3.95
338 373 8.572151 GTTTCATACCATTGAAAAATACGTTCG 58.428 33.333 0.00 0.00 44.71 3.95
340 375 7.237871 TCATACCATTGAAAAATACGTTCGTG 58.762 34.615 8.14 0.00 0.00 4.35
342 377 5.445845 ACCATTGAAAAATACGTTCGTGAC 58.554 37.500 8.14 0.00 0.00 3.67
529 564 3.134127 GGCTGGCCCACTAAAGCG 61.134 66.667 0.00 0.00 36.50 4.68
616 652 3.602483 TCCGGTGTAGAAAATAAGCACC 58.398 45.455 0.00 0.00 44.31 5.01
638 674 2.299993 TGAGATGCGAGCTACCAAAG 57.700 50.000 0.00 0.00 0.00 2.77
659 695 1.164041 AACCGCAGAACTTTGTCCCG 61.164 55.000 0.00 0.00 0.00 5.14
739 775 1.734388 AAGCCGAGCAACCAAACACC 61.734 55.000 0.00 0.00 0.00 4.16
770 806 7.680588 GCAATTTTACCCTCTTTAGCATCTCTG 60.681 40.741 0.00 0.00 0.00 3.35
771 807 6.620877 TTTTACCCTCTTTAGCATCTCTGA 57.379 37.500 0.00 0.00 0.00 3.27
774 810 4.293494 ACCCTCTTTAGCATCTCTGATGA 58.707 43.478 11.25 0.00 0.00 2.92
862 902 1.571955 AATTGGAATGGCCTGGTTCC 58.428 50.000 21.19 21.19 43.33 3.62
939 979 3.686016 ACAAATCGCACATAGGTCCTTT 58.314 40.909 0.00 0.00 0.00 3.11
940 980 4.839121 ACAAATCGCACATAGGTCCTTTA 58.161 39.130 0.00 0.00 0.00 1.85
944 984 4.866508 TCGCACATAGGTCCTTTATAGG 57.133 45.455 0.00 0.00 43.46 2.57
945 985 3.006537 TCGCACATAGGTCCTTTATAGGC 59.993 47.826 0.00 0.00 41.69 3.93
946 986 3.006967 CGCACATAGGTCCTTTATAGGCT 59.993 47.826 0.00 0.00 41.69 4.58
947 987 4.319177 GCACATAGGTCCTTTATAGGCTG 58.681 47.826 0.00 0.00 41.69 4.85
990 1030 1.220206 CAATCGCCTCTGCCACTCT 59.780 57.895 0.00 0.00 0.00 3.24
993 1033 1.418334 ATCGCCTCTGCCACTCTAAT 58.582 50.000 0.00 0.00 0.00 1.73
1387 1437 4.394920 CACCTGTGAGTTCTCTCTCTCTAC 59.605 50.000 1.53 0.00 40.98 2.59
1388 1438 3.945285 CCTGTGAGTTCTCTCTCTCTACC 59.055 52.174 1.53 0.00 40.98 3.18
1393 1443 0.920438 TTCTCTCTCTCTACCCCGCT 59.080 55.000 0.00 0.00 0.00 5.52
1895 1946 1.227883 TTGGCCGGCGTTCTTGTTA 60.228 52.632 22.54 0.00 0.00 2.41
1957 2008 1.153686 GGCGTTTCCTCTCGGGTAC 60.154 63.158 0.00 0.00 36.25 3.34
2187 2238 4.323417 CTGTTGCATTAAGTACAGGGTCA 58.677 43.478 6.13 0.00 35.51 4.02
2189 2260 4.517453 TGTTGCATTAAGTACAGGGTCAAC 59.483 41.667 0.00 3.17 33.86 3.18
2207 2278 7.979537 AGGGTCAACAACAGAAATAAGAAAAAC 59.020 33.333 0.00 0.00 0.00 2.43
2301 2382 2.003301 GCTAAAGCCTGCACTCACTAC 58.997 52.381 0.00 0.00 34.31 2.73
2366 2449 5.308825 TCCTCTTGTTTCTCTCATTCCAAC 58.691 41.667 0.00 0.00 0.00 3.77
2582 2691 4.660789 TCTGGTTATTAGTAGAACGGGC 57.339 45.455 0.00 0.00 0.00 6.13
2621 2730 3.659195 TCTTATATACTCCCTCCGTCCCA 59.341 47.826 0.00 0.00 0.00 4.37
2622 2731 4.294168 TCTTATATACTCCCTCCGTCCCAT 59.706 45.833 0.00 0.00 0.00 4.00
2673 2807 8.364894 AGTTATTTGTTTTGTATTGGGGAAGTC 58.635 33.333 0.00 0.00 0.00 3.01
2715 2849 4.323868 GGTATAGTCGCGCTTCACATTATC 59.676 45.833 5.56 0.00 0.00 1.75
2782 2916 1.885049 ACCACATGATGTAGAGGCCT 58.115 50.000 3.86 3.86 0.00 5.19
2794 2940 0.473501 AGAGGCCTGGAGGATGATCC 60.474 60.000 12.00 2.46 40.03 3.36
3075 4365 5.833131 AGTTTGCCGGGAATGTATTATGAAT 59.167 36.000 10.01 0.00 0.00 2.57
3549 6429 0.179073 CTCCCTCCTATTGCACGTGG 60.179 60.000 18.88 0.00 0.00 4.94
4041 13546 4.142600 CCTTATACAGCAGAAAAGTGCACC 60.143 45.833 14.63 0.00 46.60 5.01
4044 13549 3.146104 ACAGCAGAAAAGTGCACCTAT 57.854 42.857 14.63 0.00 46.60 2.57
4129 13634 9.547279 AAAAATGGTTCCTTCTGGATATTAGTT 57.453 29.630 0.00 0.00 42.81 2.24
4462 14777 9.205513 AGGCTATCAGAAATTATTTGTTTCCAT 57.794 29.630 0.00 0.00 36.48 3.41
4598 16020 1.070289 GACAGGACGGAGAACCAAAGT 59.930 52.381 0.00 0.00 35.59 2.66
4910 17457 2.301577 CTTGAGAAGCCCTTACGGAG 57.698 55.000 0.00 0.00 0.00 4.63
4912 17459 1.183549 TGAGAAGCCCTTACGGAGTC 58.816 55.000 0.00 0.00 43.93 3.36
4913 17460 1.272536 TGAGAAGCCCTTACGGAGTCT 60.273 52.381 0.00 0.00 43.93 3.24
4914 17461 2.025605 TGAGAAGCCCTTACGGAGTCTA 60.026 50.000 0.00 0.00 43.93 2.59
4915 17462 2.619646 GAGAAGCCCTTACGGAGTCTAG 59.380 54.545 0.00 0.00 43.93 2.43
4916 17463 2.025131 AGAAGCCCTTACGGAGTCTAGT 60.025 50.000 0.00 0.00 43.93 2.57
4917 17464 2.055684 AGCCCTTACGGAGTCTAGTC 57.944 55.000 0.00 0.00 43.93 2.59
4918 17465 0.662085 GCCCTTACGGAGTCTAGTCG 59.338 60.000 0.00 0.00 43.93 4.18
4919 17466 2.016096 GCCCTTACGGAGTCTAGTCGT 61.016 57.143 0.00 0.00 43.93 4.34
4920 17467 1.669779 CCCTTACGGAGTCTAGTCGTG 59.330 57.143 11.23 0.00 43.93 4.35
4921 17468 1.669779 CCTTACGGAGTCTAGTCGTGG 59.330 57.143 11.23 4.26 43.93 4.94
4922 17469 1.063764 CTTACGGAGTCTAGTCGTGGC 59.936 57.143 11.23 0.00 43.93 5.01
4923 17470 0.036105 TACGGAGTCTAGTCGTGGCA 60.036 55.000 11.23 0.00 43.93 4.92
4924 17471 0.892358 ACGGAGTCTAGTCGTGGCAA 60.892 55.000 0.00 0.00 29.74 4.52
4925 17472 0.179161 CGGAGTCTAGTCGTGGCAAG 60.179 60.000 0.00 0.00 0.00 4.01
4926 17473 0.458716 GGAGTCTAGTCGTGGCAAGC 60.459 60.000 0.00 0.00 0.00 4.01
4927 17474 0.798771 GAGTCTAGTCGTGGCAAGCG 60.799 60.000 0.00 0.00 0.00 4.68
4928 17475 2.126071 TCTAGTCGTGGCAAGCGC 60.126 61.111 0.00 0.00 37.44 5.92
4929 17476 3.545481 CTAGTCGTGGCAAGCGCG 61.545 66.667 0.00 0.00 39.92 6.86
4930 17477 3.964221 CTAGTCGTGGCAAGCGCGA 62.964 63.158 12.10 6.32 39.92 5.87
4931 17478 3.561217 TAGTCGTGGCAAGCGCGAA 62.561 57.895 12.10 0.00 39.92 4.70
4932 17479 4.430423 GTCGTGGCAAGCGCGAAG 62.430 66.667 12.10 0.00 39.92 3.79
4933 17480 4.656117 TCGTGGCAAGCGCGAAGA 62.656 61.111 12.10 0.00 39.92 2.87
4934 17481 3.711842 CGTGGCAAGCGCGAAGAA 61.712 61.111 12.10 0.00 39.92 2.52
4935 17482 2.637025 GTGGCAAGCGCGAAGAAA 59.363 55.556 12.10 0.00 39.92 2.52
4936 17483 1.210155 GTGGCAAGCGCGAAGAAAT 59.790 52.632 12.10 0.00 39.92 2.17
4937 17484 0.794605 GTGGCAAGCGCGAAGAAATC 60.795 55.000 12.10 0.00 39.92 2.17
4949 17496 3.933031 CGAAGAAATCGCAGAATCCAAG 58.067 45.455 0.00 0.00 45.89 3.61
4950 17497 3.372206 CGAAGAAATCGCAGAATCCAAGT 59.628 43.478 0.00 0.00 45.89 3.16
4951 17498 4.142816 CGAAGAAATCGCAGAATCCAAGTT 60.143 41.667 0.00 0.00 45.89 2.66
4952 17499 4.954092 AGAAATCGCAGAATCCAAGTTC 57.046 40.909 0.00 0.00 43.58 3.01
4953 17500 4.583871 AGAAATCGCAGAATCCAAGTTCT 58.416 39.130 0.00 0.00 43.58 3.01
4954 17501 5.006386 AGAAATCGCAGAATCCAAGTTCTT 58.994 37.500 0.00 0.00 43.58 2.52
4955 17502 4.691860 AATCGCAGAATCCAAGTTCTTG 57.308 40.909 5.66 5.66 43.58 3.02
4956 17503 3.126001 TCGCAGAATCCAAGTTCTTGT 57.874 42.857 10.93 0.00 36.33 3.16
4957 17504 3.476552 TCGCAGAATCCAAGTTCTTGTT 58.523 40.909 10.93 0.98 36.33 2.83
4958 17505 3.498397 TCGCAGAATCCAAGTTCTTGTTC 59.502 43.478 10.93 8.99 36.33 3.18
4959 17506 3.365364 CGCAGAATCCAAGTTCTTGTTCC 60.365 47.826 10.93 0.00 36.33 3.62
4960 17507 3.569701 GCAGAATCCAAGTTCTTGTTCCA 59.430 43.478 10.93 0.00 36.33 3.53
4961 17508 4.037923 GCAGAATCCAAGTTCTTGTTCCAA 59.962 41.667 10.93 0.00 36.33 3.53
4962 17509 5.766222 CAGAATCCAAGTTCTTGTTCCAAG 58.234 41.667 10.93 0.00 36.33 3.61
4963 17510 4.829492 AGAATCCAAGTTCTTGTTCCAAGG 59.171 41.667 10.93 0.00 34.92 3.61
4964 17511 3.943671 TCCAAGTTCTTGTTCCAAGGA 57.056 42.857 10.93 0.00 0.00 3.36
4965 17512 4.243793 TCCAAGTTCTTGTTCCAAGGAA 57.756 40.909 10.93 0.00 0.00 3.36
4966 17513 4.605183 TCCAAGTTCTTGTTCCAAGGAAA 58.395 39.130 2.55 0.00 35.75 3.13
4967 17514 4.644685 TCCAAGTTCTTGTTCCAAGGAAAG 59.355 41.667 2.55 0.00 35.75 2.62
4968 17515 4.402474 CCAAGTTCTTGTTCCAAGGAAAGT 59.598 41.667 2.55 0.00 35.75 2.66
4969 17516 5.105351 CCAAGTTCTTGTTCCAAGGAAAGTT 60.105 40.000 2.55 0.00 35.75 2.66
4970 17517 5.836821 AGTTCTTGTTCCAAGGAAAGTTC 57.163 39.130 2.55 0.00 35.75 3.01
4971 17518 5.261216 AGTTCTTGTTCCAAGGAAAGTTCA 58.739 37.500 2.55 0.00 35.75 3.18
4972 17519 5.358160 AGTTCTTGTTCCAAGGAAAGTTCAG 59.642 40.000 2.55 0.00 35.75 3.02
4973 17520 5.110814 TCTTGTTCCAAGGAAAGTTCAGA 57.889 39.130 2.55 0.00 35.75 3.27
4974 17521 5.505780 TCTTGTTCCAAGGAAAGTTCAGAA 58.494 37.500 2.55 0.00 35.75 3.02
4975 17522 5.590259 TCTTGTTCCAAGGAAAGTTCAGAAG 59.410 40.000 2.55 0.00 35.75 2.85
4976 17523 3.632145 TGTTCCAAGGAAAGTTCAGAAGC 59.368 43.478 2.55 0.00 35.75 3.86
4977 17524 2.863809 TCCAAGGAAAGTTCAGAAGCC 58.136 47.619 0.00 0.00 0.00 4.35
4978 17525 1.889170 CCAAGGAAAGTTCAGAAGCCC 59.111 52.381 0.00 0.00 0.00 5.19
4979 17526 2.489802 CCAAGGAAAGTTCAGAAGCCCT 60.490 50.000 0.00 0.00 0.00 5.19
4980 17527 3.225940 CAAGGAAAGTTCAGAAGCCCTT 58.774 45.455 0.00 0.00 33.25 3.95
4981 17528 4.398319 CAAGGAAAGTTCAGAAGCCCTTA 58.602 43.478 0.00 0.00 31.94 2.69
4982 17529 4.022413 AGGAAAGTTCAGAAGCCCTTAC 57.978 45.455 0.00 0.00 0.00 2.34
4983 17530 2.742589 GGAAAGTTCAGAAGCCCTTACG 59.257 50.000 0.00 0.00 0.00 3.18
4984 17531 2.474410 AAGTTCAGAAGCCCTTACGG 57.526 50.000 0.00 0.00 0.00 4.02
4985 17532 1.640917 AGTTCAGAAGCCCTTACGGA 58.359 50.000 0.00 0.00 0.00 4.69
4986 17533 1.550976 AGTTCAGAAGCCCTTACGGAG 59.449 52.381 0.00 0.00 0.00 4.63
5042 17592 2.160417 CGCAGAATCCAAGTTCTTGTCC 59.840 50.000 10.93 0.00 36.33 4.02
5051 17611 3.319122 CCAAGTTCTTGTCCCAAGGAAAG 59.681 47.826 10.93 0.00 31.38 2.62
5115 17675 4.122046 CAGACTCGCATGATGGAATAACA 58.878 43.478 0.00 0.00 0.00 2.41
5444 18092 3.366052 TGCCCCTTTTCCTGTTATCTC 57.634 47.619 0.00 0.00 0.00 2.75
5600 18307 1.838112 TCCGAAAATCCTGCATGCTT 58.162 45.000 20.33 2.89 0.00 3.91
5837 18547 4.873817 TCCATTTTTGATTGCTGTCACTG 58.126 39.130 0.00 0.00 0.00 3.66
5863 18573 1.270907 CCCTACTCAAGTCTGTGCCT 58.729 55.000 0.00 0.00 0.00 4.75
5914 18638 9.924650 GTACTACATTTACCGATAAATCTGGAT 57.075 33.333 0.00 0.00 38.67 3.41
5973 18697 2.445155 GGGCCACTGTCCCCATTT 59.555 61.111 4.39 0.00 41.13 2.32
5984 18708 4.223477 ACTGTCCCCATTTGATTTCCATTG 59.777 41.667 0.00 0.00 0.00 2.82
6054 18787 6.966435 AGGATTTAATTGCACCATTTTTCG 57.034 33.333 0.00 0.00 0.00 3.46
6150 18886 0.031314 AGTGAGTGTGCGTGAGTCTG 59.969 55.000 0.00 0.00 0.00 3.51
6209 18945 3.666274 TGTTTGACCCCTTGTGTATACG 58.334 45.455 0.00 0.00 0.00 3.06
6410 19146 4.043200 GCCCCTTTGCTGCACGAC 62.043 66.667 0.00 0.00 0.00 4.34
6653 19424 8.784043 AGACAAAGAATACGAAAAGTTTATGCT 58.216 29.630 0.00 0.00 0.00 3.79
6679 19450 8.301002 TGGCTACATTTTTGGTTTACAGTTATC 58.699 33.333 0.00 0.00 0.00 1.75
6720 19491 2.704190 TCCTCAGTTGTTCCTCTCCT 57.296 50.000 0.00 0.00 0.00 3.69
6722 19493 2.110899 TCCTCAGTTGTTCCTCTCCTCT 59.889 50.000 0.00 0.00 0.00 3.69
6723 19494 2.495669 CCTCAGTTGTTCCTCTCCTCTC 59.504 54.545 0.00 0.00 0.00 3.20
6724 19495 2.495669 CTCAGTTGTTCCTCTCCTCTCC 59.504 54.545 0.00 0.00 0.00 3.71
6769 19541 3.222173 TGTTTCTTACCCACTGTGCAT 57.778 42.857 1.29 0.00 0.00 3.96
6847 19624 2.158726 GGTTTGTCCTGTGGTGGTCTAA 60.159 50.000 0.00 0.00 0.00 2.10
6906 19683 2.203195 AAAGCTGCACACCGAGCA 60.203 55.556 1.02 0.00 40.19 4.26
6966 19750 5.701750 GCTCGTCTATGTCTATGTCTAAGGA 59.298 44.000 0.00 0.00 0.00 3.36
6977 19761 1.751351 TGTCTAAGGACATCTCCAGCG 59.249 52.381 0.00 0.00 46.19 5.18
7073 21450 2.395360 CGATTTTCGCCGGCTTGGA 61.395 57.895 26.68 12.15 42.00 3.53
7231 21610 2.125673 CATCGCCTCGTTTCCCGT 60.126 61.111 0.00 0.00 37.94 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.142469 GGTTTGTTCACATAGGGCATGTAC 60.142 45.833 0.00 0.00 46.47 2.90
8 9 2.666272 TGGTTTGTTCACATAGGGCA 57.334 45.000 0.00 0.00 0.00 5.36
9 10 4.142249 GGTATTGGTTTGTTCACATAGGGC 60.142 45.833 0.00 0.00 0.00 5.19
10 11 5.013547 TGGTATTGGTTTGTTCACATAGGG 58.986 41.667 0.00 0.00 0.00 3.53
11 12 5.125417 CCTGGTATTGGTTTGTTCACATAGG 59.875 44.000 0.00 0.00 0.00 2.57
12 13 5.393027 GCCTGGTATTGGTTTGTTCACATAG 60.393 44.000 0.00 0.00 0.00 2.23
16 17 2.625790 TGCCTGGTATTGGTTTGTTCAC 59.374 45.455 0.00 0.00 0.00 3.18
18 19 2.351350 CGTGCCTGGTATTGGTTTGTTC 60.351 50.000 0.00 0.00 0.00 3.18
19 20 1.611491 CGTGCCTGGTATTGGTTTGTT 59.389 47.619 0.00 0.00 0.00 2.83
24 25 1.206371 GTAGTCGTGCCTGGTATTGGT 59.794 52.381 0.00 0.00 0.00 3.67
25 26 1.472728 GGTAGTCGTGCCTGGTATTGG 60.473 57.143 0.00 0.00 0.00 3.16
27 28 1.563924 TGGTAGTCGTGCCTGGTATT 58.436 50.000 0.00 0.00 0.00 1.89
28 29 1.789523 ATGGTAGTCGTGCCTGGTAT 58.210 50.000 0.00 0.00 0.00 2.73
29 30 1.479323 GAATGGTAGTCGTGCCTGGTA 59.521 52.381 0.00 0.00 0.00 3.25
30 31 0.249398 GAATGGTAGTCGTGCCTGGT 59.751 55.000 0.00 0.00 0.00 4.00
31 32 0.249120 TGAATGGTAGTCGTGCCTGG 59.751 55.000 0.00 0.00 0.00 4.45
33 34 1.557099 TCTGAATGGTAGTCGTGCCT 58.443 50.000 0.00 0.00 0.00 4.75
34 35 2.604046 ATCTGAATGGTAGTCGTGCC 57.396 50.000 0.00 0.00 0.00 5.01
35 36 3.553096 CCCTATCTGAATGGTAGTCGTGC 60.553 52.174 0.00 0.00 0.00 5.34
38 39 2.894126 AGCCCTATCTGAATGGTAGTCG 59.106 50.000 0.00 0.00 0.00 4.18
40 41 3.243724 GGAGCCCTATCTGAATGGTAGT 58.756 50.000 0.00 0.00 0.00 2.73
41 42 2.569404 GGGAGCCCTATCTGAATGGTAG 59.431 54.545 0.00 0.00 0.00 3.18
42 43 2.621070 GGGAGCCCTATCTGAATGGTA 58.379 52.381 0.00 0.00 0.00 3.25
44 45 0.322975 CGGGAGCCCTATCTGAATGG 59.677 60.000 3.70 0.00 0.00 3.16
45 46 1.001406 GACGGGAGCCCTATCTGAATG 59.999 57.143 3.70 0.00 0.00 2.67
49 50 0.757188 AGTGACGGGAGCCCTATCTG 60.757 60.000 3.70 0.00 0.00 2.90
51 52 0.105039 CAAGTGACGGGAGCCCTATC 59.895 60.000 3.70 2.10 0.00 2.08
52 53 0.325296 TCAAGTGACGGGAGCCCTAT 60.325 55.000 3.70 0.00 0.00 2.57
53 54 0.543410 TTCAAGTGACGGGAGCCCTA 60.543 55.000 3.70 0.00 0.00 3.53
54 55 1.415672 TTTCAAGTGACGGGAGCCCT 61.416 55.000 3.70 0.00 0.00 5.19
56 57 2.396590 TATTTCAAGTGACGGGAGCC 57.603 50.000 0.00 0.00 0.00 4.70
57 58 4.192317 AGAATATTTCAAGTGACGGGAGC 58.808 43.478 0.00 0.00 0.00 4.70
58 59 7.843490 TTTAGAATATTTCAAGTGACGGGAG 57.157 36.000 0.00 0.00 0.00 4.30
113 114 9.410556 GCATGTATGATGAACACTTTTAAACTT 57.589 29.630 0.00 0.00 0.00 2.66
119 120 8.836268 ATTTTGCATGTATGATGAACACTTTT 57.164 26.923 0.00 0.00 0.00 2.27
122 123 9.926158 TTAAATTTTGCATGTATGATGAACACT 57.074 25.926 0.00 0.00 0.00 3.55
151 152 9.638239 GGACATTTTTCTTAATGCTATCAACAA 57.362 29.630 0.00 0.00 38.74 2.83
178 179 7.908230 ACACATGAATGTTTTTCAAATGTCAC 58.092 30.769 0.00 0.00 39.39 3.67
264 278 9.768662 AACTATTTTGAGAAAATGTGCTGAAAT 57.231 25.926 4.84 0.00 41.01 2.17
320 355 5.338559 GTGTCACGAACGTATTTTTCAATGG 59.661 40.000 0.00 0.00 0.00 3.16
416 451 7.542890 ACATGTTACAAACAACTTGAACATCA 58.457 30.769 0.00 0.00 45.86 3.07
572 608 1.138859 TGTGTCTCCCATATTGCGAGG 59.861 52.381 0.00 0.00 0.00 4.63
616 652 0.312102 TGGTAGCTCGCATCTCATCG 59.688 55.000 0.00 0.00 0.00 3.84
638 674 0.591659 GGACAAAGTTCTGCGGTTCC 59.408 55.000 0.00 0.00 0.00 3.62
659 695 4.223964 GGCTGAAACGCCGCGATC 62.224 66.667 21.79 16.92 40.79 3.69
704 740 0.241213 GCTTGTTTTCGGCCTTCCTC 59.759 55.000 0.00 0.00 0.00 3.71
739 775 2.532250 AGAGGGTAAAATTGCAGGGG 57.468 50.000 0.00 0.00 0.00 4.79
770 806 5.173492 GGTAGCGAATTCTTACGAAGTCATC 59.827 44.000 9.64 1.62 42.66 2.92
771 807 5.041940 GGTAGCGAATTCTTACGAAGTCAT 58.958 41.667 9.64 1.06 42.66 3.06
828 868 7.041107 CCATTCCAATTTTCGTTGTTCCATAT 58.959 34.615 0.00 0.00 0.00 1.78
862 902 1.604604 TCTGCTTTTTCCCCTGTTCG 58.395 50.000 0.00 0.00 0.00 3.95
1895 1946 1.599047 CAGACCCAGCTCCAACGAT 59.401 57.895 0.00 0.00 0.00 3.73
2020 2071 3.733960 GGCGAAGAAACCACGGCC 61.734 66.667 0.00 0.00 44.46 6.13
2187 2238 6.976349 GTCGGGTTTTTCTTATTTCTGTTGTT 59.024 34.615 0.00 0.00 0.00 2.83
2189 2260 6.500041 TGTCGGGTTTTTCTTATTTCTGTTG 58.500 36.000 0.00 0.00 0.00 3.33
2207 2278 3.073086 TGTTGTTGACACTGTCGGG 57.927 52.632 4.71 0.00 34.95 5.14
2250 2329 4.838986 TGGAGGCTTTAAGAGTAGTTCTGT 59.161 41.667 0.00 0.00 35.91 3.41
2291 2372 1.071699 TGTTTGGGAGGTAGTGAGTGC 59.928 52.381 0.00 0.00 0.00 4.40
2301 2382 1.106285 GGCTGCTAATGTTTGGGAGG 58.894 55.000 0.00 0.00 30.33 4.30
2366 2449 2.624364 TGTAGCTGCATGGCATATTTGG 59.376 45.455 0.00 0.00 38.13 3.28
2582 2691 0.952497 AGACAGCACGCCACTGAATG 60.952 55.000 6.90 0.00 38.55 2.67
2621 2730 7.371043 ACTCCCTCCGTCCCATAATATATTAT 58.629 38.462 11.51 11.51 33.44 1.28
2622 2731 6.748969 ACTCCCTCCGTCCCATAATATATTA 58.251 40.000 7.62 7.62 0.00 0.98
2635 2769 4.732672 ACAAATAACTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
2699 2833 4.411993 TTTTTGATAATGTGAAGCGCGA 57.588 36.364 12.10 0.00 0.00 5.87
2851 2997 3.375299 GCTTGAACAAGACTGACAACTGT 59.625 43.478 17.19 0.00 40.79 3.55
3075 4365 7.309499 GCTTCGATCTCCTCCTCATCTATTTTA 60.309 40.741 0.00 0.00 0.00 1.52
3549 6429 3.186001 CGACTTATCCAATGATGCTCTGC 59.814 47.826 0.00 0.00 32.18 4.26
3881 6938 6.806739 GTGAACACCATATTTTACTGAAAGGC 59.193 38.462 0.00 0.00 39.30 4.35
3922 13427 6.241207 TGAACTAATTGTTTCTGCAGCTAC 57.759 37.500 9.47 9.88 39.30 3.58
4462 14777 5.683876 AAAGCATCTACTTCTGCCTTAGA 57.316 39.130 0.00 0.00 39.22 2.10
4598 16020 4.517285 GGATGTGATAGTCCTTCTTGCAA 58.483 43.478 0.00 0.00 0.00 4.08
4903 17450 1.089920 GCCACGACTAGACTCCGTAA 58.910 55.000 0.00 0.00 34.91 3.18
4904 17451 0.036105 TGCCACGACTAGACTCCGTA 60.036 55.000 0.00 0.00 34.91 4.02
4905 17452 0.892358 TTGCCACGACTAGACTCCGT 60.892 55.000 0.00 0.00 36.95 4.69
4906 17453 0.179161 CTTGCCACGACTAGACTCCG 60.179 60.000 0.00 0.00 0.00 4.63
4907 17454 0.458716 GCTTGCCACGACTAGACTCC 60.459 60.000 0.00 0.00 0.00 3.85
4908 17455 0.798771 CGCTTGCCACGACTAGACTC 60.799 60.000 0.00 0.00 0.00 3.36
4909 17456 1.213013 CGCTTGCCACGACTAGACT 59.787 57.895 0.00 0.00 0.00 3.24
4910 17457 2.445438 GCGCTTGCCACGACTAGAC 61.445 63.158 0.00 0.00 0.00 2.59
4911 17458 2.126071 GCGCTTGCCACGACTAGA 60.126 61.111 0.00 0.00 0.00 2.43
4912 17459 3.545481 CGCGCTTGCCACGACTAG 61.545 66.667 5.56 0.00 34.11 2.57
4913 17460 3.561217 TTCGCGCTTGCCACGACTA 62.561 57.895 5.56 0.00 35.20 2.59
4914 17461 4.961511 TTCGCGCTTGCCACGACT 62.962 61.111 5.56 0.00 35.20 4.18
4915 17462 4.430423 CTTCGCGCTTGCCACGAC 62.430 66.667 5.56 0.00 35.20 4.34
4916 17463 4.656117 TCTTCGCGCTTGCCACGA 62.656 61.111 5.56 2.02 34.11 4.35
4917 17464 2.513065 ATTTCTTCGCGCTTGCCACG 62.513 55.000 5.56 0.00 34.11 4.94
4918 17465 0.794605 GATTTCTTCGCGCTTGCCAC 60.795 55.000 5.56 0.00 34.11 5.01
4919 17466 1.501741 GATTTCTTCGCGCTTGCCA 59.498 52.632 5.56 0.00 34.11 4.92
4920 17467 1.581147 CGATTTCTTCGCGCTTGCC 60.581 57.895 5.56 0.00 41.69 4.52
4921 17468 3.953785 CGATTTCTTCGCGCTTGC 58.046 55.556 5.56 0.00 41.69 4.01
4928 17475 8.043723 AGAACTTGGATTCTGCGATTTCTTCG 62.044 42.308 0.00 0.00 39.94 3.79
4929 17476 4.954092 ACTTGGATTCTGCGATTTCTTC 57.046 40.909 0.00 0.00 0.00 2.87
4930 17477 5.006386 AGAACTTGGATTCTGCGATTTCTT 58.994 37.500 0.00 0.00 37.54 2.52
4931 17478 4.583871 AGAACTTGGATTCTGCGATTTCT 58.416 39.130 0.00 0.00 37.54 2.52
4932 17479 4.954092 AGAACTTGGATTCTGCGATTTC 57.046 40.909 0.00 0.00 37.54 2.17
4933 17480 4.520492 ACAAGAACTTGGATTCTGCGATTT 59.480 37.500 17.05 0.00 44.45 2.17
4934 17481 4.074970 ACAAGAACTTGGATTCTGCGATT 58.925 39.130 17.05 0.00 44.45 3.34
4935 17482 3.679389 ACAAGAACTTGGATTCTGCGAT 58.321 40.909 17.05 0.00 44.45 4.58
4936 17483 3.126001 ACAAGAACTTGGATTCTGCGA 57.874 42.857 17.05 0.00 44.45 5.10
4937 17484 3.365364 GGAACAAGAACTTGGATTCTGCG 60.365 47.826 17.05 0.00 44.45 5.18
4938 17485 3.569701 TGGAACAAGAACTTGGATTCTGC 59.430 43.478 17.05 4.33 44.45 4.26
4954 17501 3.632145 GCTTCTGAACTTTCCTTGGAACA 59.368 43.478 0.98 0.00 0.00 3.18
4955 17502 3.004839 GGCTTCTGAACTTTCCTTGGAAC 59.995 47.826 0.98 0.00 0.00 3.62
4956 17503 3.222603 GGCTTCTGAACTTTCCTTGGAA 58.777 45.455 0.00 0.00 0.00 3.53
4957 17504 2.489073 GGGCTTCTGAACTTTCCTTGGA 60.489 50.000 0.00 0.00 0.00 3.53
4958 17505 1.889170 GGGCTTCTGAACTTTCCTTGG 59.111 52.381 0.00 0.00 0.00 3.61
4959 17506 2.868899 AGGGCTTCTGAACTTTCCTTG 58.131 47.619 0.00 0.00 0.00 3.61
4960 17507 3.602205 AAGGGCTTCTGAACTTTCCTT 57.398 42.857 0.00 0.00 0.00 3.36
4961 17508 3.557264 CGTAAGGGCTTCTGAACTTTCCT 60.557 47.826 0.00 0.00 0.00 3.36
4962 17509 2.742589 CGTAAGGGCTTCTGAACTTTCC 59.257 50.000 0.00 0.00 0.00 3.13
4978 17525 5.302357 ACTAAACTCCGTAACTCCGTAAG 57.698 43.478 0.00 0.00 0.00 2.34
4979 17526 4.142902 CGACTAAACTCCGTAACTCCGTAA 60.143 45.833 0.00 0.00 0.00 3.18
4980 17527 3.370978 CGACTAAACTCCGTAACTCCGTA 59.629 47.826 0.00 0.00 0.00 4.02
4981 17528 2.160417 CGACTAAACTCCGTAACTCCGT 59.840 50.000 0.00 0.00 0.00 4.69
4982 17529 2.160417 ACGACTAAACTCCGTAACTCCG 59.840 50.000 0.00 0.00 34.52 4.63
4983 17530 3.496155 CACGACTAAACTCCGTAACTCC 58.504 50.000 0.00 0.00 34.91 3.85
4984 17531 3.496155 CCACGACTAAACTCCGTAACTC 58.504 50.000 0.00 0.00 34.91 3.01
4985 17532 2.352127 GCCACGACTAAACTCCGTAACT 60.352 50.000 0.00 0.00 34.91 2.24
4986 17533 1.988467 GCCACGACTAAACTCCGTAAC 59.012 52.381 0.00 0.00 34.91 2.50
5042 17592 5.126384 TCTGTGGTTGTTTTACTTTCCTTGG 59.874 40.000 0.00 0.00 0.00 3.61
5051 17611 5.106673 GGAGTATGCTCTGTGGTTGTTTTAC 60.107 44.000 10.82 0.00 41.38 2.01
5837 18547 2.808543 CAGACTTGAGTAGGGTTTGTGC 59.191 50.000 0.00 0.00 0.00 4.57
5863 18573 2.205022 AGCAAGCACCTTGATAGCAA 57.795 45.000 9.01 0.00 43.42 3.91
5972 18696 5.221621 GGTGGTTCCTTTCAATGGAAATCAA 60.222 40.000 6.33 0.00 44.14 2.57
5973 18697 4.283212 GGTGGTTCCTTTCAATGGAAATCA 59.717 41.667 6.33 5.94 44.14 2.57
5984 18708 1.527433 GCAGCAGGGTGGTTCCTTTC 61.527 60.000 0.24 0.00 34.31 2.62
6054 18787 3.862264 GCATTCTTTGGGAGCTTTGAACC 60.862 47.826 0.00 0.00 0.00 3.62
6220 18956 2.421952 GGCATAAGATCTCCACCTGCAA 60.422 50.000 0.00 0.00 0.00 4.08
6410 19146 1.660917 GGGAGGGACGCTATCTTCG 59.339 63.158 0.00 0.00 0.00 3.79
6443 19180 4.991024 GGAGACGGAGGAGCTAGT 57.009 61.111 0.00 0.00 0.00 2.57
6653 19424 6.472686 AACTGTAAACCAAAAATGTAGCCA 57.527 33.333 0.00 0.00 0.00 4.75
6679 19450 1.581934 TTTGTCTGCGAGGTCTTGTG 58.418 50.000 0.00 0.00 0.00 3.33
6720 19491 3.576118 CCACAAGAAAGAGACAGAGGAGA 59.424 47.826 0.00 0.00 0.00 3.71
6722 19493 3.309296 ACCACAAGAAAGAGACAGAGGA 58.691 45.455 0.00 0.00 0.00 3.71
6723 19494 3.760580 ACCACAAGAAAGAGACAGAGG 57.239 47.619 0.00 0.00 0.00 3.69
6724 19495 7.736447 AAATTACCACAAGAAAGAGACAGAG 57.264 36.000 0.00 0.00 0.00 3.35
6847 19624 1.253100 CCGTTACCAGCCAAAACCAT 58.747 50.000 0.00 0.00 0.00 3.55
6906 19683 1.002544 GTGGAGGTAGCTGTTCAGCTT 59.997 52.381 28.13 13.75 43.52 3.74
7025 20458 1.203313 CGCGACTGGACCGTTTTTC 59.797 57.895 0.00 0.00 0.00 2.29
7138 21517 3.787146 GCTTTTTCGCGCCAAAACAATTT 60.787 39.130 12.58 0.00 0.00 1.82
7141 21520 0.647925 GCTTTTTCGCGCCAAAACAA 59.352 45.000 12.58 0.00 0.00 2.83
7182 21561 2.701780 GCCGAGAAGAGAGCCGTCA 61.702 63.158 0.00 0.00 0.00 4.35
7183 21562 2.103340 GCCGAGAAGAGAGCCGTC 59.897 66.667 0.00 0.00 0.00 4.79
7235 21836 1.216178 GGCAGCACGGCATTGATTT 59.784 52.632 0.00 0.00 40.76 2.17


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

AutoCloner maintained by Alex Coulton.