Multiple sequence alignment - TraesCS5D01G021300

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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 TraesCS5D01G021300 chr5D 100.000 5276 0 0 1 5276 13921726 13927001 0.000000e+00 9744.0
1 TraesCS5D01G021300 chr5D 95.833 288 10 2 2343 2629 309192976 309192690 1.030000e-126 464.0
2 TraesCS5D01G021300 chr5D 95.486 288 10 2 2343 2629 429179931 429179646 1.730000e-124 457.0
3 TraesCS5D01G021300 chr5D 89.617 183 19 0 1777 1959 446158456 446158274 3.180000e-57 233.0
4 TraesCS5D01G021300 chr5D 96.000 50 2 0 2293 2342 309193050 309193001 1.220000e-11 82.4
5 TraesCS5D01G021300 chr5D 89.062 64 6 1 1954 2017 7947673 7947735 1.580000e-10 78.7
6 TraesCS5D01G021300 chr5B 91.453 1720 83 26 2636 4331 13355210 13356889 0.000000e+00 2303.0
7 TraesCS5D01G021300 chr5B 93.435 1249 45 19 1183 2424 13353694 13354912 0.000000e+00 1818.0
8 TraesCS5D01G021300 chr5B 94.146 837 32 7 3210 4045 42434749 42435569 0.000000e+00 1258.0
9 TraesCS5D01G021300 chr5B 87.750 751 91 1 1 751 46742450 46743199 0.000000e+00 876.0
10 TraesCS5D01G021300 chr5B 89.827 462 22 14 754 1206 13353230 13353675 2.130000e-158 569.0
11 TraesCS5D01G021300 chr5B 82.939 592 36 23 4746 5276 76544177 76543590 1.720000e-129 473.0
12 TraesCS5D01G021300 chr5B 95.833 288 11 1 2343 2629 18175486 18175773 1.030000e-126 464.0
13 TraesCS5D01G021300 chr5B 77.864 646 37 32 4370 4969 13357081 13357666 2.390000e-78 303.0
14 TraesCS5D01G021300 chr5B 94.118 187 11 0 2084 2270 311209019 311208833 8.650000e-73 285.0
15 TraesCS5D01G021300 chr5B 82.573 241 31 7 4050 4290 33130812 33130583 8.960000e-48 202.0
16 TraesCS5D01G021300 chr5B 76.453 344 60 9 3462 3803 55521766 55522090 3.270000e-37 167.0
17 TraesCS5D01G021300 chr5B 85.849 106 8 7 1225 1324 13353664 13353768 7.230000e-19 106.0
18 TraesCS5D01G021300 chr5B 92.958 71 4 1 4558 4627 675730926 675730996 9.350000e-18 102.0
19 TraesCS5D01G021300 chr6A 94.067 1382 57 9 2667 4045 221072663 221071304 0.000000e+00 2074.0
20 TraesCS5D01G021300 chr6A 89.880 751 74 2 1 751 532541544 532542292 0.000000e+00 965.0
21 TraesCS5D01G021300 chr6A 93.704 270 17 0 3060 3329 30496064 30496333 6.360000e-109 405.0
22 TraesCS5D01G021300 chr6A 92.254 142 5 3 2750 2891 30495934 30496069 4.170000e-46 196.0
23 TraesCS5D01G021300 chr6A 95.370 108 5 0 3011 3118 47915117 47915224 7.020000e-39 172.0
24 TraesCS5D01G021300 chr6A 90.323 93 8 1 1462 1553 43398310 43398218 2.580000e-23 121.0
25 TraesCS5D01G021300 chr5A 92.105 1368 51 23 1214 2574 11022261 11023578 0.000000e+00 1875.0
26 TraesCS5D01G021300 chr5A 88.079 302 20 1 2638 2939 11023601 11023886 1.410000e-90 344.0
27 TraesCS5D01G021300 chr5A 90.310 258 13 4 951 1205 11022037 11022285 1.420000e-85 327.0
28 TraesCS5D01G021300 chr5A 84.709 327 25 16 4148 4449 11025375 11025701 2.390000e-78 303.0
29 TraesCS5D01G021300 chr5A 92.632 95 2 4 4566 4657 11025689 11025781 1.190000e-26 132.0
30 TraesCS5D01G021300 chr5A 92.958 71 4 1 4558 4627 14538552 14538622 9.350000e-18 102.0
31 TraesCS5D01G021300 chr5A 90.625 64 5 1 1954 2017 6148162 6148224 3.390000e-12 84.2
32 TraesCS5D01G021300 chr7B 94.726 967 31 6 1441 2397 96800790 96801746 0.000000e+00 1485.0
33 TraesCS5D01G021300 chr7B 90.814 381 19 7 2648 3013 96802031 96802410 3.670000e-136 496.0
34 TraesCS5D01G021300 chr7B 95.439 285 12 1 2346 2629 717672440 717672156 2.240000e-123 453.0
35 TraesCS5D01G021300 chr7B 89.848 197 18 1 2569 2763 43862445 43862641 8.770000e-63 252.0
36 TraesCS5D01G021300 chr7B 88.018 217 16 6 2584 2798 749143833 749144041 1.130000e-61 248.0
37 TraesCS5D01G021300 chr7B 88.398 181 15 2 1777 1957 125076891 125077065 4.140000e-51 213.0
38 TraesCS5D01G021300 chr3B 94.726 967 31 6 1441 2397 568295102 568296058 0.000000e+00 1485.0
39 TraesCS5D01G021300 chr3B 94.026 837 33 7 3210 4045 20904821 20905641 0.000000e+00 1253.0
40 TraesCS5D01G021300 chr3B 84.668 587 25 22 4751 5276 522249024 522248442 4.680000e-145 525.0
41 TraesCS5D01G021300 chr3B 94.118 187 11 0 2084 2270 705446121 705445935 8.650000e-73 285.0
42 TraesCS5D01G021300 chr3B 93.158 190 13 0 2084 2273 519493733 519493544 4.020000e-71 279.0
43 TraesCS5D01G021300 chr3B 90.640 203 17 1 2569 2769 705445732 705445530 8.710000e-68 268.0
44 TraesCS5D01G021300 chr3B 90.148 203 18 1 2569 2769 519493344 519493142 4.050000e-66 263.0
45 TraesCS5D01G021300 chr6B 93.899 967 38 8 1441 2397 99870947 99869992 0.000000e+00 1439.0
46 TraesCS5D01G021300 chr6B 93.309 837 39 10 3210 4045 34761889 34762709 0.000000e+00 1219.0
47 TraesCS5D01G021300 chr6B 94.345 725 24 7 3322 4045 128307206 128306498 0.000000e+00 1096.0
48 TraesCS5D01G021300 chr6B 90.000 380 22 7 2649 3013 99869706 99869328 1.330000e-130 477.0
49 TraesCS5D01G021300 chr7D 98.531 749 9 2 1 749 529067859 529068605 0.000000e+00 1321.0
50 TraesCS5D01G021300 chr7D 96.181 288 10 1 2343 2629 176462909 176462622 2.220000e-128 470.0
51 TraesCS5D01G021300 chr7D 95.139 288 13 1 2343 2629 172775081 172774794 2.240000e-123 453.0
52 TraesCS5D01G021300 chr7D 95.492 244 11 0 2359 2602 110227329 110227572 1.780000e-104 390.0
53 TraesCS5D01G021300 chr7D 89.071 183 20 0 1777 1959 486202731 486202549 1.480000e-55 228.0
54 TraesCS5D01G021300 chr1B 94.424 825 29 10 3222 4045 31928822 31928014 0.000000e+00 1253.0
55 TraesCS5D01G021300 chr1B 94.014 735 25 9 3312 4045 545753641 545754357 0.000000e+00 1096.0
56 TraesCS5D01G021300 chr1B 83.529 595 30 23 4746 5276 303880808 303880218 1.320000e-135 494.0
57 TraesCS5D01G021300 chr1B 87.156 218 18 6 2583 2798 182653850 182654059 6.830000e-59 239.0
58 TraesCS5D01G021300 chr7A 94.303 825 30 10 3222 4045 58716895 58716087 0.000000e+00 1247.0
59 TraesCS5D01G021300 chr7A 89.880 751 74 2 1 750 497616508 497617257 0.000000e+00 965.0
60 TraesCS5D01G021300 chr7A 83.067 750 124 3 2 750 670832503 670831756 0.000000e+00 678.0
61 TraesCS5D01G021300 chr4B 93.429 837 38 10 3210 4045 90366294 90367114 0.000000e+00 1225.0
62 TraesCS5D01G021300 chr4B 90.909 583 53 0 166 748 88221071 88221653 0.000000e+00 784.0
63 TraesCS5D01G021300 chr4B 85.156 128 17 2 3074 3201 43592651 43592526 4.290000e-26 130.0
64 TraesCS5D01G021300 chr4B 90.541 74 6 1 4558 4630 34974578 34974505 4.350000e-16 97.1
65 TraesCS5D01G021300 chr2B 94.483 725 23 7 3322 4045 413957945 413957237 0.000000e+00 1101.0
66 TraesCS5D01G021300 chr2B 95.833 288 11 1 2343 2629 673104901 673105188 1.030000e-126 464.0
67 TraesCS5D01G021300 chr2B 91.379 174 15 0 1556 1729 603800094 603799921 6.830000e-59 239.0
68 TraesCS5D01G021300 chr3A 94.014 735 25 9 3312 4045 52899954 52900670 0.000000e+00 1096.0
69 TraesCS5D01G021300 chr3A 94.215 726 24 8 3322 4045 109527825 109527116 0.000000e+00 1092.0
70 TraesCS5D01G021300 chrUn 93.740 607 21 7 3440 4045 401535372 401535962 0.000000e+00 894.0
71 TraesCS5D01G021300 chrUn 92.274 453 19 9 3210 3662 437565393 437565829 3.470000e-176 628.0
72 TraesCS5D01G021300 chrUn 95.833 288 11 1 2343 2629 77137666 77137953 1.030000e-126 464.0
73 TraesCS5D01G021300 chrUn 96.000 50 2 0 2293 2342 77137592 77137641 1.220000e-11 82.4
74 TraesCS5D01G021300 chr1D 86.835 752 96 3 1 751 21545485 21546234 0.000000e+00 837.0
75 TraesCS5D01G021300 chr1D 94.465 271 15 0 2359 2629 318519331 318519601 8.170000e-113 418.0
76 TraesCS5D01G021300 chr1D 89.247 93 9 1 1462 1553 412907859 412907767 1.200000e-21 115.0
77 TraesCS5D01G021300 chr6D 88.689 610 69 0 1 610 467046755 467047364 0.000000e+00 745.0
78 TraesCS5D01G021300 chr6D 84.615 416 53 4 3107 3514 458993364 458993776 2.290000e-108 403.0
79 TraesCS5D01G021300 chr6D 75.683 366 56 16 3820 4159 463225658 463225300 9.150000e-33 152.0
80 TraesCS5D01G021300 chr2D 82.713 752 127 2 1 751 66149891 66149142 0.000000e+00 665.0
81 TraesCS5D01G021300 chr1A 94.763 401 13 4 2667 3065 10764157 10763763 7.510000e-173 617.0
82 TraesCS5D01G021300 chr1A 95.187 187 9 0 2084 2270 379187848 379187662 4.000000e-76 296.0
83 TraesCS5D01G021300 chr1A 91.626 203 15 1 2569 2769 379187459 379187257 4.020000e-71 279.0
84 TraesCS5D01G021300 chr1A 91.813 171 14 0 1559 1729 584980699 584980529 6.830000e-59 239.0
85 TraesCS5D01G021300 chr1A 90.805 174 16 0 1556 1729 522947791 522947964 3.180000e-57 233.0
86 TraesCS5D01G021300 chr1A 82.286 175 20 7 1832 2005 515153151 515152987 1.980000e-29 141.0
87 TraesCS5D01G021300 chr1A 81.714 175 21 7 1832 2005 514896924 514896760 9.220000e-28 135.0
88 TraesCS5D01G021300 chr3D 96.181 288 10 1 2343 2629 119680664 119680951 2.220000e-128 470.0
89 TraesCS5D01G021300 chr3D 96.000 50 2 0 2293 2342 119680590 119680639 1.220000e-11 82.4
90 TraesCS5D01G021300 chr2A 90.148 203 18 1 2569 2769 549135125 549134923 4.050000e-66 263.0
91 TraesCS5D01G021300 chr2A 91.954 174 14 0 1556 1729 762670456 762670629 1.470000e-60 244.0
92 TraesCS5D01G021300 chr2A 90.541 74 6 1 4558 4630 160293359 160293286 4.350000e-16 97.1
93 TraesCS5D01G021300 chr4D 89.655 203 19 1 2569 2769 258681422 258681220 1.890000e-64 257.0
94 TraesCS5D01G021300 chr4A 86.339 183 24 1 1777 1959 26834701 26834882 1.160000e-46 198.0
95 TraesCS5D01G021300 chr4A 93.976 83 5 0 1462 1544 633088396 633088478 5.550000e-25 126.0
96 TraesCS5D01G021300 chr4A 92.593 81 6 0 1462 1542 633151987 633152067 3.340000e-22 117.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G021300 chr5D 13921726 13927001 5275 False 9744.0 9744 100.0000 1 5276 1 chr5D.!!$F2 5275
1 TraesCS5D01G021300 chr5B 42434749 42435569 820 False 1258.0 1258 94.1460 3210 4045 1 chr5B.!!$F2 835
2 TraesCS5D01G021300 chr5B 13353230 13357666 4436 False 1019.8 2303 87.6856 754 4969 5 chr5B.!!$F6 4215
3 TraesCS5D01G021300 chr5B 46742450 46743199 749 False 876.0 876 87.7500 1 751 1 chr5B.!!$F3 750
4 TraesCS5D01G021300 chr5B 76543590 76544177 587 True 473.0 473 82.9390 4746 5276 1 chr5B.!!$R2 530
5 TraesCS5D01G021300 chr6A 221071304 221072663 1359 True 2074.0 2074 94.0670 2667 4045 1 chr6A.!!$R2 1378
6 TraesCS5D01G021300 chr6A 532541544 532542292 748 False 965.0 965 89.8800 1 751 1 chr6A.!!$F2 750
7 TraesCS5D01G021300 chr5A 11022037 11025781 3744 False 596.2 1875 89.5670 951 4657 5 chr5A.!!$F3 3706
8 TraesCS5D01G021300 chr7B 96800790 96802410 1620 False 990.5 1485 92.7700 1441 3013 2 chr7B.!!$F4 1572
9 TraesCS5D01G021300 chr3B 568295102 568296058 956 False 1485.0 1485 94.7260 1441 2397 1 chr3B.!!$F2 956
10 TraesCS5D01G021300 chr3B 20904821 20905641 820 False 1253.0 1253 94.0260 3210 4045 1 chr3B.!!$F1 835
11 TraesCS5D01G021300 chr3B 522248442 522249024 582 True 525.0 525 84.6680 4751 5276 1 chr3B.!!$R1 525
12 TraesCS5D01G021300 chr3B 705445530 705446121 591 True 276.5 285 92.3790 2084 2769 2 chr3B.!!$R3 685
13 TraesCS5D01G021300 chr3B 519493142 519493733 591 True 271.0 279 91.6530 2084 2769 2 chr3B.!!$R2 685
14 TraesCS5D01G021300 chr6B 34761889 34762709 820 False 1219.0 1219 93.3090 3210 4045 1 chr6B.!!$F1 835
15 TraesCS5D01G021300 chr6B 128306498 128307206 708 True 1096.0 1096 94.3450 3322 4045 1 chr6B.!!$R1 723
16 TraesCS5D01G021300 chr6B 99869328 99870947 1619 True 958.0 1439 91.9495 1441 3013 2 chr6B.!!$R2 1572
17 TraesCS5D01G021300 chr7D 529067859 529068605 746 False 1321.0 1321 98.5310 1 749 1 chr7D.!!$F2 748
18 TraesCS5D01G021300 chr1B 31928014 31928822 808 True 1253.0 1253 94.4240 3222 4045 1 chr1B.!!$R1 823
19 TraesCS5D01G021300 chr1B 545753641 545754357 716 False 1096.0 1096 94.0140 3312 4045 1 chr1B.!!$F2 733
20 TraesCS5D01G021300 chr1B 303880218 303880808 590 True 494.0 494 83.5290 4746 5276 1 chr1B.!!$R2 530
21 TraesCS5D01G021300 chr7A 58716087 58716895 808 True 1247.0 1247 94.3030 3222 4045 1 chr7A.!!$R1 823
22 TraesCS5D01G021300 chr7A 497616508 497617257 749 False 965.0 965 89.8800 1 750 1 chr7A.!!$F1 749
23 TraesCS5D01G021300 chr7A 670831756 670832503 747 True 678.0 678 83.0670 2 750 1 chr7A.!!$R2 748
24 TraesCS5D01G021300 chr4B 90366294 90367114 820 False 1225.0 1225 93.4290 3210 4045 1 chr4B.!!$F2 835
25 TraesCS5D01G021300 chr4B 88221071 88221653 582 False 784.0 784 90.9090 166 748 1 chr4B.!!$F1 582
26 TraesCS5D01G021300 chr2B 413957237 413957945 708 True 1101.0 1101 94.4830 3322 4045 1 chr2B.!!$R1 723
27 TraesCS5D01G021300 chr3A 52899954 52900670 716 False 1096.0 1096 94.0140 3312 4045 1 chr3A.!!$F1 733
28 TraesCS5D01G021300 chr3A 109527116 109527825 709 True 1092.0 1092 94.2150 3322 4045 1 chr3A.!!$R1 723
29 TraesCS5D01G021300 chrUn 401535372 401535962 590 False 894.0 894 93.7400 3440 4045 1 chrUn.!!$F1 605
30 TraesCS5D01G021300 chr1D 21545485 21546234 749 False 837.0 837 86.8350 1 751 1 chr1D.!!$F1 750
31 TraesCS5D01G021300 chr6D 467046755 467047364 609 False 745.0 745 88.6890 1 610 1 chr6D.!!$F2 609
32 TraesCS5D01G021300 chr2D 66149142 66149891 749 True 665.0 665 82.7130 1 751 1 chr2D.!!$R1 750
33 TraesCS5D01G021300 chr1A 379187257 379187848 591 True 287.5 296 93.4065 2084 2769 2 chr1A.!!$R5 685

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
934 948 1.158944 GTATCCCCTCCCCTCCCTC 59.841 68.421 0.0 0.0 0.0 4.30 F
1181 1198 2.520741 CGCCCTCTCCTCCTCCTC 60.521 72.222 0.0 0.0 0.0 3.71 F
2299 2384 1.004394 TCCTCTACTCTGTTCTGCCGA 59.996 52.381 0.0 0.0 0.0 5.54 F
2895 3257 1.301423 TTCGTACTGTTTGGTGGTGC 58.699 50.000 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1877 2.032681 GTGGTGCGGAAGAAGGCT 59.967 61.111 0.0 0.0 0.00 4.58 R
3096 4078 1.068333 CATGCAAAGTTCCAAGGGTCG 60.068 52.381 0.0 0.0 0.00 4.79 R
3790 4793 1.276622 TGCTAGGAGGAAGACCAACC 58.723 55.000 0.0 0.0 38.94 3.77 R
4677 5899 0.173481 ACACGGACACCAGATGATCG 59.827 55.000 0.0 0.0 34.90 3.69 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
74 75 1.464734 TCTCTGTCATCACGGTCTCC 58.535 55.000 0.00 0.00 0.00 3.71
353 354 2.615493 GGATCATTCCGGACTGTGTGTT 60.615 50.000 20.06 3.10 30.72 3.32
742 751 3.329929 AATAAAGGCCGACGTTCTCTT 57.670 42.857 0.00 0.00 0.00 2.85
766 775 1.555477 AAAATCGGGTGGGAGGCGTA 61.555 55.000 0.00 0.00 0.00 4.42
796 809 4.481112 CGCAAATCCGGCAGCACC 62.481 66.667 0.00 0.00 0.00 5.01
894 907 2.858476 TGCCCCTCAAGGAAGCCA 60.858 61.111 0.00 0.00 38.24 4.75
897 910 2.045926 CCCTCAAGGAAGCCACCG 60.046 66.667 0.00 0.00 38.24 4.94
933 947 2.791406 CGTATCCCCTCCCCTCCCT 61.791 68.421 0.00 0.00 0.00 4.20
934 948 1.158944 GTATCCCCTCCCCTCCCTC 59.841 68.421 0.00 0.00 0.00 4.30
943 957 4.806339 CCCTCCCTCCGCTCCCTT 62.806 72.222 0.00 0.00 0.00 3.95
944 958 3.157949 CCTCCCTCCGCTCCCTTC 61.158 72.222 0.00 0.00 0.00 3.46
945 959 3.532155 CTCCCTCCGCTCCCTTCG 61.532 72.222 0.00 0.00 0.00 3.79
1180 1197 3.024356 TCGCCCTCTCCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
1181 1198 2.520741 CGCCCTCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1214 1273 2.812609 CGACGACGAGGACGAGGA 60.813 66.667 0.00 0.00 42.66 3.71
2274 2349 7.041916 AGGTACTACTCAGATTAAACTCGATCG 60.042 40.741 9.36 9.36 36.02 3.69
2299 2384 1.004394 TCCTCTACTCTGTTCTGCCGA 59.996 52.381 0.00 0.00 0.00 5.54
2367 2489 9.017509 ACTTTGATGTTTATGAATCTGATGTGT 57.982 29.630 0.00 0.00 0.00 3.72
2388 2510 3.988976 AAGCATGTCCACATCTGTAGT 57.011 42.857 0.00 0.00 33.61 2.73
2424 2547 4.294232 CATGACTAGTGATCGATGGTGAC 58.706 47.826 0.54 0.00 0.00 3.67
2427 2550 3.357203 ACTAGTGATCGATGGTGACTGT 58.643 45.455 0.54 0.00 0.00 3.55
2428 2551 3.764434 ACTAGTGATCGATGGTGACTGTT 59.236 43.478 0.54 0.00 0.00 3.16
2429 2552 3.238108 AGTGATCGATGGTGACTGTTC 57.762 47.619 0.54 0.00 0.00 3.18
2430 2553 2.093973 AGTGATCGATGGTGACTGTTCC 60.094 50.000 0.54 0.00 0.00 3.62
2431 2554 2.093973 GTGATCGATGGTGACTGTTCCT 60.094 50.000 0.54 0.00 0.00 3.36
2432 2555 2.094026 TGATCGATGGTGACTGTTCCTG 60.094 50.000 0.54 0.00 0.00 3.86
2433 2556 1.338107 TCGATGGTGACTGTTCCTGT 58.662 50.000 5.00 0.00 0.00 4.00
2434 2557 2.521126 TCGATGGTGACTGTTCCTGTA 58.479 47.619 5.00 0.00 0.00 2.74
2435 2558 2.492088 TCGATGGTGACTGTTCCTGTAG 59.508 50.000 5.00 0.00 0.00 2.74
2436 2559 2.231478 CGATGGTGACTGTTCCTGTAGT 59.769 50.000 5.00 0.00 0.00 2.73
2437 2560 3.306088 CGATGGTGACTGTTCCTGTAGTT 60.306 47.826 5.00 0.00 0.00 2.24
2438 2561 3.469008 TGGTGACTGTTCCTGTAGTTG 57.531 47.619 5.00 0.00 0.00 3.16
2439 2562 3.035363 TGGTGACTGTTCCTGTAGTTGA 58.965 45.455 5.00 0.00 0.00 3.18
2440 2563 3.646162 TGGTGACTGTTCCTGTAGTTGAT 59.354 43.478 5.00 0.00 0.00 2.57
2441 2564 4.836175 TGGTGACTGTTCCTGTAGTTGATA 59.164 41.667 5.00 0.00 0.00 2.15
2442 2565 5.169295 GGTGACTGTTCCTGTAGTTGATAC 58.831 45.833 0.00 0.00 34.72 2.24
2443 2566 5.279306 GGTGACTGTTCCTGTAGTTGATACA 60.279 44.000 0.00 0.00 42.21 2.29
2444 2567 6.398918 GTGACTGTTCCTGTAGTTGATACAT 58.601 40.000 0.00 0.00 43.44 2.29
2445 2568 6.531948 GTGACTGTTCCTGTAGTTGATACATC 59.468 42.308 0.00 0.00 43.44 3.06
2446 2569 6.437477 TGACTGTTCCTGTAGTTGATACATCT 59.563 38.462 0.00 0.00 43.44 2.90
2447 2570 6.634805 ACTGTTCCTGTAGTTGATACATCTG 58.365 40.000 0.00 0.00 43.44 2.90
2448 2571 6.211584 ACTGTTCCTGTAGTTGATACATCTGT 59.788 38.462 0.00 0.00 43.44 3.41
2449 2572 6.398095 TGTTCCTGTAGTTGATACATCTGTG 58.602 40.000 0.00 0.00 43.44 3.66
2450 2573 5.598416 TCCTGTAGTTGATACATCTGTGG 57.402 43.478 0.00 0.00 43.44 4.17
2451 2574 5.269189 TCCTGTAGTTGATACATCTGTGGA 58.731 41.667 0.00 0.00 43.44 4.02
2452 2575 5.719563 TCCTGTAGTTGATACATCTGTGGAA 59.280 40.000 0.00 0.00 43.44 3.53
2453 2576 5.812642 CCTGTAGTTGATACATCTGTGGAAC 59.187 44.000 0.00 0.00 43.44 3.62
2548 2671 2.158871 ACTGGACCTTTGCACGACTAAA 60.159 45.455 0.00 0.00 0.00 1.85
2549 2672 2.875933 CTGGACCTTTGCACGACTAAAA 59.124 45.455 0.00 0.00 0.00 1.52
2565 2688 7.744715 CACGACTAAAATTTCAAGTGTGGATAC 59.255 37.037 10.07 0.00 0.00 2.24
2610 2733 4.692625 CACTTCTGTAGGTTTCTGATGTGG 59.307 45.833 0.00 0.00 36.40 4.17
2628 2751 2.172679 TGGAACACCTACGCATGACTA 58.827 47.619 0.00 0.00 0.00 2.59
2630 2753 3.196901 TGGAACACCTACGCATGACTAAT 59.803 43.478 0.00 0.00 0.00 1.73
2631 2754 4.189231 GGAACACCTACGCATGACTAATT 58.811 43.478 0.00 0.00 0.00 1.40
2632 2755 4.034048 GGAACACCTACGCATGACTAATTG 59.966 45.833 0.00 0.00 0.00 2.32
2633 2756 4.202245 ACACCTACGCATGACTAATTGT 57.798 40.909 0.00 0.00 0.00 2.71
2635 2758 4.630069 ACACCTACGCATGACTAATTGTTC 59.370 41.667 0.00 0.00 0.00 3.18
2646 2991 7.907045 GCATGACTAATTGTTCAGTTGATACAG 59.093 37.037 0.00 0.00 0.00 2.74
2850 3212 6.714810 AGATTAGTAGGACTCTGCATGACTAG 59.285 42.308 0.00 0.00 0.00 2.57
2895 3257 1.301423 TTCGTACTGTTTGGTGGTGC 58.699 50.000 0.00 0.00 0.00 5.01
3096 4078 7.695618 GTGTTTCTGAATGTGAAAGCATATCTC 59.304 37.037 0.00 0.00 34.58 2.75
3220 4210 5.373812 TTCTTTGGATCCATAGAACCTCC 57.626 43.478 31.99 0.00 38.45 4.30
3346 4336 2.601240 TGGATCCATTGCACCTTTGA 57.399 45.000 11.44 0.00 0.00 2.69
3550 4543 5.066893 GCTGTCAATTGGATCATGCTTCTTA 59.933 40.000 5.42 0.00 0.00 2.10
3728 4730 3.250762 TGTTCAACCTCAGAATGCTTTCG 59.749 43.478 6.68 3.01 36.93 3.46
4056 5084 9.899661 TGATGTATAATTTGTAAGCTGTTACCT 57.100 29.630 0.00 0.00 38.24 3.08
4058 5086 8.500753 TGTATAATTTGTAAGCTGTTACCTGG 57.499 34.615 0.00 0.00 38.24 4.45
4059 5087 7.554835 TGTATAATTTGTAAGCTGTTACCTGGG 59.445 37.037 0.00 0.00 38.24 4.45
4060 5088 3.868619 TTTGTAAGCTGTTACCTGGGT 57.131 42.857 0.00 0.00 38.24 4.51
4061 5089 4.978438 TTTGTAAGCTGTTACCTGGGTA 57.022 40.909 0.00 0.00 38.24 3.69
4062 5090 3.967332 TGTAAGCTGTTACCTGGGTAC 57.033 47.619 0.00 0.00 38.24 3.34
4063 5091 2.568509 TGTAAGCTGTTACCTGGGTACC 59.431 50.000 2.17 2.17 43.33 3.34
4064 5092 2.836372 GTAAGCTGTTACCTGGGTACCT 59.164 50.000 12.72 0.00 40.42 3.08
4065 5093 5.840910 TGTAAGCTGTTACCTGGGTACCTG 61.841 50.000 12.72 5.17 43.39 4.00
4083 5111 6.704937 GGTACCTGCTAATGTTAACAGATACC 59.295 42.308 14.65 9.76 38.28 2.73
4084 5112 6.561519 ACCTGCTAATGTTAACAGATACCT 57.438 37.500 14.65 0.00 30.38 3.08
4085 5113 7.670605 ACCTGCTAATGTTAACAGATACCTA 57.329 36.000 14.65 0.00 30.38 3.08
4086 5114 7.727181 ACCTGCTAATGTTAACAGATACCTAG 58.273 38.462 14.65 8.35 30.38 3.02
4087 5115 7.563924 ACCTGCTAATGTTAACAGATACCTAGA 59.436 37.037 14.65 0.00 30.38 2.43
4088 5116 8.085296 CCTGCTAATGTTAACAGATACCTAGAG 58.915 40.741 14.65 0.72 30.38 2.43
4089 5117 7.434492 TGCTAATGTTAACAGATACCTAGAGC 58.566 38.462 14.65 10.01 0.00 4.09
4090 5118 6.583050 GCTAATGTTAACAGATACCTAGAGCG 59.417 42.308 14.65 0.00 0.00 5.03
4091 5119 6.710597 AATGTTAACAGATACCTAGAGCGA 57.289 37.500 14.65 0.00 0.00 4.93
4092 5120 6.710597 ATGTTAACAGATACCTAGAGCGAA 57.289 37.500 14.65 0.00 0.00 4.70
4093 5121 6.710597 TGTTAACAGATACCTAGAGCGAAT 57.289 37.500 3.59 0.00 0.00 3.34
4094 5122 6.504398 TGTTAACAGATACCTAGAGCGAATG 58.496 40.000 3.59 0.00 0.00 2.67
4118 5146 6.643770 TGCTGATTCTTCTTTTGCTGAATTTC 59.356 34.615 0.00 0.00 30.41 2.17
4128 5156 8.856490 TCTTTTGCTGAATTTCTACAAGTTTC 57.144 30.769 0.00 0.00 0.00 2.78
4139 5167 9.793259 AATTTCTACAAGTTTCTCAATGTAGGA 57.207 29.630 10.79 1.06 43.35 2.94
4144 5172 9.219603 CTACAAGTTTCTCAATGTAGGAATTCA 57.780 33.333 7.93 0.00 40.83 2.57
4162 5190 8.352942 AGGAATTCAGAAAGTTGACAATGTTAC 58.647 33.333 7.93 0.00 0.00 2.50
4209 5237 2.427506 GTGGGATCTGTGTTCAAGACC 58.572 52.381 0.00 0.00 0.00 3.85
4344 5398 0.616964 TCCTCTGCTCCATGCTGACT 60.617 55.000 0.00 0.00 43.20 3.41
4480 5682 3.749665 TCTTTGGATGGCAGTTTTTGG 57.250 42.857 0.00 0.00 0.00 3.28
4491 5693 1.595794 CAGTTTTTGGCTGCTTTGCTG 59.404 47.619 0.00 0.00 0.00 4.41
4533 5741 8.669243 GCAGTTTCTCTAGTAATGCAAAACTAT 58.331 33.333 10.86 0.00 34.65 2.12
4536 5744 8.669243 GTTTCTCTAGTAATGCAAAACTATGCT 58.331 33.333 10.86 0.00 46.54 3.79
4537 5745 9.884636 TTTCTCTAGTAATGCAAAACTATGCTA 57.115 29.630 10.86 0.00 46.54 3.49
4538 5746 8.873215 TCTCTAGTAATGCAAAACTATGCTAC 57.127 34.615 10.86 0.00 46.54 3.58
4539 5747 7.648112 TCTCTAGTAATGCAAAACTATGCTACG 59.352 37.037 10.86 1.34 46.54 3.51
4540 5748 7.485810 TCTAGTAATGCAAAACTATGCTACGA 58.514 34.615 10.86 3.24 46.54 3.43
4541 5749 8.141909 TCTAGTAATGCAAAACTATGCTACGAT 58.858 33.333 10.86 0.00 46.54 3.73
4542 5750 7.178712 AGTAATGCAAAACTATGCTACGATC 57.821 36.000 2.65 0.00 46.54 3.69
4543 5751 6.986817 AGTAATGCAAAACTATGCTACGATCT 59.013 34.615 2.65 0.00 46.54 2.75
4544 5752 6.683974 AATGCAAAACTATGCTACGATCTT 57.316 33.333 0.00 0.00 46.54 2.40
4545 5753 5.469373 TGCAAAACTATGCTACGATCTTG 57.531 39.130 0.00 0.00 46.54 3.02
4546 5754 4.935205 TGCAAAACTATGCTACGATCTTGT 59.065 37.500 0.00 0.00 46.54 3.16
4547 5755 5.411361 TGCAAAACTATGCTACGATCTTGTT 59.589 36.000 0.00 0.00 46.54 2.83
4548 5756 6.072728 TGCAAAACTATGCTACGATCTTGTTT 60.073 34.615 0.00 0.00 46.54 2.83
4549 5757 6.466097 GCAAAACTATGCTACGATCTTGTTTC 59.534 38.462 0.00 0.00 43.06 2.78
4550 5758 7.624344 GCAAAACTATGCTACGATCTTGTTTCT 60.624 37.037 0.00 0.00 43.06 2.52
4551 5759 7.907214 AAACTATGCTACGATCTTGTTTCTT 57.093 32.000 0.00 0.00 0.00 2.52
4552 5760 7.907214 AACTATGCTACGATCTTGTTTCTTT 57.093 32.000 0.00 0.00 0.00 2.52
4580 5788 5.699097 TTTTTCCAAGGGACGAAACTATG 57.301 39.130 0.00 0.00 0.00 2.23
4581 5789 4.360951 TTTCCAAGGGACGAAACTATGT 57.639 40.909 0.00 0.00 0.00 2.29
4584 5792 3.581332 TCCAAGGGACGAAACTATGTTCT 59.419 43.478 0.00 0.00 0.00 3.01
4627 5836 4.937696 TTTTGTCTGCCATGTACATACG 57.062 40.909 8.32 2.87 0.00 3.06
4659 5870 4.135153 CAGACTGCCCCCGTCGAG 62.135 72.222 0.00 0.00 36.53 4.04
4660 5871 4.680537 AGACTGCCCCCGTCGAGT 62.681 66.667 0.00 0.00 36.53 4.18
4672 5894 2.348666 CCCGTCGAGTTCTTAATTGCTG 59.651 50.000 0.00 0.00 0.00 4.41
4676 5898 5.163854 CCGTCGAGTTCTTAATTGCTGAATT 60.164 40.000 0.00 0.00 35.83 2.17
4677 5899 5.954349 CGTCGAGTTCTTAATTGCTGAATTC 59.046 40.000 0.00 0.00 33.63 2.17
4693 5920 2.515926 ATTCGATCATCTGGTGTCCG 57.484 50.000 0.00 0.00 0.00 4.79
4695 5922 0.455815 TCGATCATCTGGTGTCCGTG 59.544 55.000 0.00 0.00 0.00 4.94
4699 5926 1.266178 TCATCTGGTGTCCGTGTGAT 58.734 50.000 0.00 0.00 0.00 3.06
4742 5969 5.047377 TGGATGCTTTCTTGAATGTTTACCC 60.047 40.000 0.00 0.00 0.00 3.69
4749 5976 5.223449 TCTTGAATGTTTACCCTCGTTCT 57.777 39.130 0.00 0.00 32.70 3.01
4757 5984 0.392461 TACCCTCGTTCTTGCATGGC 60.392 55.000 0.00 0.00 0.00 4.40
4804 6036 1.002900 CGTGCGTGTTGTTTGGATTCT 60.003 47.619 0.00 0.00 0.00 2.40
4833 6065 2.162681 GCTTGTACTCCCTGTTTGCAT 58.837 47.619 0.00 0.00 0.00 3.96
4834 6066 2.162408 GCTTGTACTCCCTGTTTGCATC 59.838 50.000 0.00 0.00 0.00 3.91
4835 6067 3.679389 CTTGTACTCCCTGTTTGCATCT 58.321 45.455 0.00 0.00 0.00 2.90
4836 6068 3.788227 TGTACTCCCTGTTTGCATCTT 57.212 42.857 0.00 0.00 0.00 2.40
4837 6069 4.901197 TGTACTCCCTGTTTGCATCTTA 57.099 40.909 0.00 0.00 0.00 2.10
4838 6070 5.435686 TGTACTCCCTGTTTGCATCTTAT 57.564 39.130 0.00 0.00 0.00 1.73
4839 6071 6.553953 TGTACTCCCTGTTTGCATCTTATA 57.446 37.500 0.00 0.00 0.00 0.98
4840 6072 7.136822 TGTACTCCCTGTTTGCATCTTATAT 57.863 36.000 0.00 0.00 0.00 0.86
4841 6073 6.992123 TGTACTCCCTGTTTGCATCTTATATG 59.008 38.462 0.00 0.00 0.00 1.78
4842 6074 6.006275 ACTCCCTGTTTGCATCTTATATGT 57.994 37.500 0.00 0.00 0.00 2.29
4843 6075 6.426587 ACTCCCTGTTTGCATCTTATATGTT 58.573 36.000 0.00 0.00 0.00 2.71
4844 6076 6.319658 ACTCCCTGTTTGCATCTTATATGTTG 59.680 38.462 0.00 0.00 0.00 3.33
4845 6077 6.422333 TCCCTGTTTGCATCTTATATGTTGA 58.578 36.000 0.00 0.00 0.00 3.18
4846 6078 6.543465 TCCCTGTTTGCATCTTATATGTTGAG 59.457 38.462 0.00 0.00 0.00 3.02
4847 6079 6.543465 CCCTGTTTGCATCTTATATGTTGAGA 59.457 38.462 0.00 0.00 0.00 3.27
4848 6080 7.067372 CCCTGTTTGCATCTTATATGTTGAGAA 59.933 37.037 0.00 0.00 0.00 2.87
4849 6081 8.627403 CCTGTTTGCATCTTATATGTTGAGAAT 58.373 33.333 0.00 0.00 0.00 2.40
4850 6082 9.447040 CTGTTTGCATCTTATATGTTGAGAATG 57.553 33.333 0.00 0.00 0.00 2.67
4851 6083 9.176460 TGTTTGCATCTTATATGTTGAGAATGA 57.824 29.630 0.00 0.00 0.00 2.57
4852 6084 9.661187 GTTTGCATCTTATATGTTGAGAATGAG 57.339 33.333 0.00 0.00 0.00 2.90
4853 6085 7.430992 TGCATCTTATATGTTGAGAATGAGC 57.569 36.000 1.83 0.00 0.00 4.26
4865 6116 4.818642 TGAGAATGAGCTCTTGTCTGAAG 58.181 43.478 16.19 0.00 35.91 3.02
4866 6117 4.525874 TGAGAATGAGCTCTTGTCTGAAGA 59.474 41.667 16.19 0.00 35.91 2.87
4901 6155 8.296713 GCAATGTTTGGATTCAGTTACTAAGAA 58.703 33.333 0.00 0.00 0.00 2.52
4924 6178 5.652744 TGAAAAGTCGTTGAAGCTTCTAC 57.347 39.130 25.30 25.30 0.00 2.59
4931 6185 0.328258 TTGAAGCTTCTACCCCCTGC 59.672 55.000 26.09 0.00 0.00 4.85
4943 6211 1.339727 ACCCCCTGCGTTCTGATAAAC 60.340 52.381 0.00 0.00 0.00 2.01
4961 6229 9.672086 CTGATAAACCAAACGAGTTCAAAATTA 57.328 29.630 0.00 0.00 0.00 1.40
5117 6401 1.547372 GTGGATCAAGGCAATGCAGTT 59.453 47.619 7.79 0.00 0.00 3.16
5151 6435 3.685139 TCTGACAGTTCCTTCACCATC 57.315 47.619 1.59 0.00 0.00 3.51
5152 6436 2.303022 TCTGACAGTTCCTTCACCATCC 59.697 50.000 1.59 0.00 0.00 3.51
5164 6460 2.046314 CCATCCGTCCCGCAAACT 60.046 61.111 0.00 0.00 0.00 2.66
5199 6498 2.368439 TCAGCACCTGCAACCATAATC 58.632 47.619 0.00 0.00 45.16 1.75
5260 6568 0.028505 CTGCGCAATCTGTGTATGCC 59.971 55.000 13.05 0.00 36.75 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.952296 GCTTCCCAGATGTGCCATAAG 59.048 52.381 0.00 0.00 0.00 1.73
759 768 1.523938 GGGCACATTCCTACGCCTC 60.524 63.158 0.00 0.00 44.27 4.70
766 775 2.803593 ATTTGCGGGGGCACATTCCT 62.804 55.000 0.00 0.00 0.00 3.36
832 845 1.374758 GCGGGCGAGAGGATATTGG 60.375 63.158 0.00 0.00 0.00 3.16
834 847 2.932234 CGGCGGGCGAGAGGATATT 61.932 63.158 20.10 0.00 0.00 1.28
835 848 3.374402 CGGCGGGCGAGAGGATAT 61.374 66.667 20.10 0.00 0.00 1.63
836 849 4.574271 TCGGCGGGCGAGAGGATA 62.574 66.667 23.31 0.00 0.00 2.59
894 907 4.404654 GGCGTACGTCGGTTCGGT 62.405 66.667 17.90 0.00 37.41 4.69
913 926 2.923568 GAGGGGAGGGGATACGGC 60.924 72.222 0.00 0.00 37.60 5.68
915 928 2.203803 GGGAGGGGAGGGGATACG 60.204 72.222 0.00 0.00 37.60 3.06
916 929 1.158944 GAGGGAGGGGAGGGGATAC 59.841 68.421 0.00 0.00 0.00 2.24
917 930 2.104921 GGAGGGAGGGGAGGGGATA 61.105 68.421 0.00 0.00 0.00 2.59
918 931 3.462501 GGAGGGAGGGGAGGGGAT 61.463 72.222 0.00 0.00 0.00 3.85
942 956 2.295909 GCAATTTATATGGGCTGCCGAA 59.704 45.455 13.40 3.60 0.00 4.30
943 957 1.885887 GCAATTTATATGGGCTGCCGA 59.114 47.619 13.40 9.69 0.00 5.54
944 958 1.067635 GGCAATTTATATGGGCTGCCG 60.068 52.381 13.40 0.00 39.92 5.69
945 959 1.067635 CGGCAATTTATATGGGCTGCC 60.068 52.381 11.05 11.05 44.73 4.85
946 960 2.352503 CGGCAATTTATATGGGCTGC 57.647 50.000 0.00 0.00 0.00 5.25
947 961 1.067635 GGCGGCAATTTATATGGGCTG 60.068 52.381 3.07 0.00 0.00 4.85
948 962 1.256812 GGCGGCAATTTATATGGGCT 58.743 50.000 3.07 0.00 0.00 5.19
953 967 1.472480 GATGGCGGCGGCAATTTATAT 59.528 47.619 39.04 21.68 42.43 0.86
1031 1045 4.643387 GCTCCGCTGGGTGTTGGT 62.643 66.667 0.00 0.00 33.83 3.67
1180 1197 3.114616 GTCGTCGTCCTCGTCGGA 61.115 66.667 7.27 0.00 45.17 4.55
1181 1198 4.495939 CGTCGTCGTCCTCGTCGG 62.496 72.222 7.27 0.00 45.17 4.79
1193 1210 3.771491 CGTCCTCGTCGTCGTCGT 61.771 66.667 11.41 0.00 38.33 4.34
1206 1223 2.114051 GTCCTCGTCCTCCTCGTCC 61.114 68.421 0.00 0.00 0.00 4.79
1208 1225 2.436292 CGTCCTCGTCCTCCTCGT 60.436 66.667 0.00 0.00 0.00 4.18
1214 1273 3.117171 CGTCGTCGTCCTCGTCCT 61.117 66.667 0.00 0.00 38.33 3.85
1255 1314 2.520741 CTCCTCCTCCTCCGAGCC 60.521 72.222 0.00 0.00 34.49 4.70
1256 1315 2.520741 CCTCCTCCTCCTCCGAGC 60.521 72.222 0.00 0.00 34.49 5.03
1257 1316 1.152839 GTCCTCCTCCTCCTCCGAG 60.153 68.421 0.00 0.00 35.72 4.63
1258 1317 2.691779 GGTCCTCCTCCTCCTCCGA 61.692 68.421 0.00 0.00 0.00 4.55
1259 1318 2.123640 GGTCCTCCTCCTCCTCCG 60.124 72.222 0.00 0.00 0.00 4.63
1260 1319 2.284151 GGGTCCTCCTCCTCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
1261 1320 2.123640 CGGGTCCTCCTCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
1262 1321 2.517582 GAACGGGTCCTCCTCCTCCT 62.518 65.000 0.00 0.00 0.00 3.69
1809 1877 2.032681 GTGGTGCGGAAGAAGGCT 59.967 61.111 0.00 0.00 0.00 4.58
2034 2102 3.884774 TTGGCGTGGAACTGGCCT 61.885 61.111 3.32 0.00 45.14 5.19
2274 2349 2.687935 CAGAACAGAGTAGAGGAGGCTC 59.312 54.545 5.78 5.78 0.00 4.70
2353 2474 5.530171 GGACATGCTTACACATCAGATTCAT 59.470 40.000 0.00 0.00 0.00 2.57
2367 2489 5.656859 AGTACTACAGATGTGGACATGCTTA 59.343 40.000 3.12 0.00 36.57 3.09
2424 2547 6.533012 CACAGATGTATCAACTACAGGAACAG 59.467 42.308 0.00 0.00 43.44 3.16
2427 2550 5.719563 TCCACAGATGTATCAACTACAGGAA 59.280 40.000 0.00 0.00 43.44 3.36
2428 2551 5.269189 TCCACAGATGTATCAACTACAGGA 58.731 41.667 0.00 0.00 43.44 3.86
2429 2552 5.598416 TCCACAGATGTATCAACTACAGG 57.402 43.478 0.00 0.00 43.44 4.00
2430 2553 6.634805 AGTTCCACAGATGTATCAACTACAG 58.365 40.000 0.00 0.00 43.44 2.74
2431 2554 6.210584 TGAGTTCCACAGATGTATCAACTACA 59.789 38.462 4.30 0.00 44.29 2.74
2432 2555 6.631016 TGAGTTCCACAGATGTATCAACTAC 58.369 40.000 4.30 0.00 0.00 2.73
2433 2556 6.850752 TGAGTTCCACAGATGTATCAACTA 57.149 37.500 4.30 0.00 0.00 2.24
2434 2557 5.745312 TGAGTTCCACAGATGTATCAACT 57.255 39.130 4.06 4.06 0.00 3.16
2435 2558 5.220739 GCATGAGTTCCACAGATGTATCAAC 60.221 44.000 0.00 0.00 0.00 3.18
2436 2559 4.877823 GCATGAGTTCCACAGATGTATCAA 59.122 41.667 0.00 0.00 0.00 2.57
2437 2560 4.080975 TGCATGAGTTCCACAGATGTATCA 60.081 41.667 0.00 0.00 0.00 2.15
2438 2561 4.445453 TGCATGAGTTCCACAGATGTATC 58.555 43.478 0.00 0.00 0.00 2.24
2439 2562 4.492494 TGCATGAGTTCCACAGATGTAT 57.508 40.909 0.00 0.00 0.00 2.29
2440 2563 3.979101 TGCATGAGTTCCACAGATGTA 57.021 42.857 0.00 0.00 0.00 2.29
2441 2564 2.865119 TGCATGAGTTCCACAGATGT 57.135 45.000 0.00 0.00 0.00 3.06
2442 2565 5.529800 TCAATATGCATGAGTTCCACAGATG 59.470 40.000 10.16 0.00 0.00 2.90
2443 2566 5.530171 GTCAATATGCATGAGTTCCACAGAT 59.470 40.000 10.16 0.00 0.00 2.90
2444 2567 4.877823 GTCAATATGCATGAGTTCCACAGA 59.122 41.667 10.16 0.00 0.00 3.41
2445 2568 4.880120 AGTCAATATGCATGAGTTCCACAG 59.120 41.667 10.16 0.00 0.00 3.66
2446 2569 4.637091 CAGTCAATATGCATGAGTTCCACA 59.363 41.667 10.16 0.00 0.00 4.17
2447 2570 4.036027 CCAGTCAATATGCATGAGTTCCAC 59.964 45.833 10.16 1.51 0.00 4.02
2448 2571 4.080413 TCCAGTCAATATGCATGAGTTCCA 60.080 41.667 10.16 0.00 0.00 3.53
2449 2572 4.454678 TCCAGTCAATATGCATGAGTTCC 58.545 43.478 10.16 0.00 0.00 3.62
2450 2573 7.918536 ATATCCAGTCAATATGCATGAGTTC 57.081 36.000 10.16 0.00 0.00 3.01
2453 2576 9.189723 CGTATATATCCAGTCAATATGCATGAG 57.810 37.037 10.16 0.00 0.00 2.90
2548 2671 9.241919 TGACAATATGTATCCACACTTGAAATT 57.758 29.630 8.20 0.00 37.54 1.82
2549 2672 8.806429 TGACAATATGTATCCACACTTGAAAT 57.194 30.769 8.20 0.00 37.54 2.17
2565 2688 4.041049 GCAGACTCGAGACTGACAATATG 58.959 47.826 37.44 17.42 39.55 1.78
2610 2733 4.630069 ACAATTAGTCATGCGTAGGTGTTC 59.370 41.667 0.00 0.00 0.00 3.18
2619 2742 5.281693 TCAACTGAACAATTAGTCATGCG 57.718 39.130 0.00 0.00 0.00 4.73
2628 2751 9.520204 CAAAGAAACTGTATCAACTGAACAATT 57.480 29.630 0.00 0.00 0.00 2.32
2630 2753 7.122055 ACCAAAGAAACTGTATCAACTGAACAA 59.878 33.333 0.00 0.00 0.00 2.83
2631 2754 6.601613 ACCAAAGAAACTGTATCAACTGAACA 59.398 34.615 0.00 0.00 0.00 3.18
2632 2755 7.027778 ACCAAAGAAACTGTATCAACTGAAC 57.972 36.000 0.00 0.00 0.00 3.18
2633 2756 8.208224 TCTACCAAAGAAACTGTATCAACTGAA 58.792 33.333 0.00 0.00 0.00 3.02
2635 2758 7.441157 TGTCTACCAAAGAAACTGTATCAACTG 59.559 37.037 0.00 0.00 35.47 3.16
2646 2991 4.518970 TCCATGCTTGTCTACCAAAGAAAC 59.481 41.667 0.00 0.00 35.47 2.78
2850 3212 2.309528 TATCACCAACGACCAGCATC 57.690 50.000 0.00 0.00 0.00 3.91
2895 3257 6.507900 TCAGAGAACTACAGAAAACAGTCAG 58.492 40.000 0.00 0.00 0.00 3.51
3039 4018 3.864789 AAGATGGTCCAACTGACAAGT 57.135 42.857 1.80 0.00 46.38 3.16
3096 4078 1.068333 CATGCAAAGTTCCAAGGGTCG 60.068 52.381 0.00 0.00 0.00 4.79
3169 4159 6.939730 TGCATATCAGAAAACTACAGGAACAA 59.060 34.615 0.00 0.00 0.00 2.83
3220 4210 5.630680 AGAAACATGAAAAATTAGCTGTGCG 59.369 36.000 0.00 0.00 0.00 5.34
3523 4516 3.512329 AGCATGATCCAATTGACAGCAAA 59.488 39.130 7.12 0.00 37.59 3.68
3550 4543 2.242043 CAGCCTGACCAATGAAACCTT 58.758 47.619 0.00 0.00 0.00 3.50
3728 4730 2.297701 TCAGCCTGACAAAACAGAACC 58.702 47.619 0.00 0.00 39.94 3.62
3790 4793 1.276622 TGCTAGGAGGAAGACCAACC 58.723 55.000 0.00 0.00 38.94 3.77
4055 5083 4.839121 TGTTAACATTAGCAGGTACCCAG 58.161 43.478 8.74 2.51 0.00 4.45
4056 5084 4.532916 TCTGTTAACATTAGCAGGTACCCA 59.467 41.667 9.13 0.00 40.86 4.51
4057 5085 5.093849 TCTGTTAACATTAGCAGGTACCC 57.906 43.478 9.13 0.00 40.86 3.69
4058 5086 7.710766 GTATCTGTTAACATTAGCAGGTACC 57.289 40.000 20.12 2.73 45.24 3.34
4060 5088 7.670605 AGGTATCTGTTAACATTAGCAGGTA 57.329 36.000 20.78 9.28 40.86 3.08
4061 5089 6.561519 AGGTATCTGTTAACATTAGCAGGT 57.438 37.500 20.78 10.13 40.86 4.00
4062 5090 7.952671 TCTAGGTATCTGTTAACATTAGCAGG 58.047 38.462 20.78 15.25 40.86 4.85
4063 5091 7.596995 GCTCTAGGTATCTGTTAACATTAGCAG 59.403 40.741 20.78 16.86 41.55 4.24
4064 5092 7.434492 GCTCTAGGTATCTGTTAACATTAGCA 58.566 38.462 20.78 11.52 0.00 3.49
4065 5093 6.583050 CGCTCTAGGTATCTGTTAACATTAGC 59.417 42.308 9.13 12.97 0.00 3.09
4074 5102 3.983741 GCATTCGCTCTAGGTATCTGTT 58.016 45.455 0.00 0.00 34.30 3.16
4088 5116 3.302699 GCAAAAGAAGAATCAGCATTCGC 59.697 43.478 0.00 0.00 43.05 4.70
4089 5117 4.557690 CAGCAAAAGAAGAATCAGCATTCG 59.442 41.667 0.00 0.00 43.05 3.34
4090 5118 5.706916 TCAGCAAAAGAAGAATCAGCATTC 58.293 37.500 0.00 0.00 39.10 2.67
4091 5119 5.717078 TCAGCAAAAGAAGAATCAGCATT 57.283 34.783 0.00 0.00 0.00 3.56
4092 5120 5.717078 TTCAGCAAAAGAAGAATCAGCAT 57.283 34.783 0.00 0.00 0.00 3.79
4093 5121 5.717078 ATTCAGCAAAAGAAGAATCAGCA 57.283 34.783 0.00 0.00 0.00 4.41
4094 5122 6.867293 AGAAATTCAGCAAAAGAAGAATCAGC 59.133 34.615 0.00 0.00 30.87 4.26
4118 5146 9.219603 TGAATTCCTACATTGAGAAACTTGTAG 57.780 33.333 2.27 0.00 40.65 2.74
4128 5156 8.233190 GTCAACTTTCTGAATTCCTACATTGAG 58.767 37.037 2.27 0.00 0.00 3.02
4162 5190 5.163814 CCTCCTCGCTGAAAATTACAGAAAG 60.164 44.000 14.18 10.25 37.54 2.62
4209 5237 3.622612 TGTATGTCACGGCTTCATCATTG 59.377 43.478 0.00 0.00 0.00 2.82
4344 5398 3.300388 AGAGACACAAGAGAGGACACAA 58.700 45.455 0.00 0.00 0.00 3.33
4505 5713 7.175641 AGTTTTGCATTACTAGAGAAACTGCAT 59.824 33.333 6.58 0.00 37.90 3.96
4518 5726 6.986817 AGATCGTAGCATAGTTTTGCATTACT 59.013 34.615 6.49 6.49 45.23 2.24
4521 5729 6.094048 ACAAGATCGTAGCATAGTTTTGCATT 59.906 34.615 0.00 0.00 45.23 3.56
4564 5772 4.822026 AGAGAACATAGTTTCGTCCCTTG 58.178 43.478 0.00 0.00 0.00 3.61
4579 5787 7.614583 ACACCTACTAGTAGCAATAAGAGAACA 59.385 37.037 22.39 0.00 31.95 3.18
4580 5788 7.998580 ACACCTACTAGTAGCAATAAGAGAAC 58.001 38.462 22.39 0.00 31.95 3.01
4581 5789 8.591114 AACACCTACTAGTAGCAATAAGAGAA 57.409 34.615 22.39 0.00 31.95 2.87
4584 5792 9.431887 CAAAAACACCTACTAGTAGCAATAAGA 57.568 33.333 22.39 0.00 31.95 2.10
4627 5836 3.619038 GCAGTCTGCATCTAACCAACTAC 59.381 47.826 20.16 0.00 44.26 2.73
4657 5868 7.688372 TGATCGAATTCAGCAATTAAGAACTC 58.312 34.615 6.22 0.00 31.94 3.01
4658 5869 7.615582 TGATCGAATTCAGCAATTAAGAACT 57.384 32.000 6.22 0.00 31.94 3.01
4659 5870 8.341173 AGATGATCGAATTCAGCAATTAAGAAC 58.659 33.333 6.22 0.00 34.50 3.01
4660 5871 8.340443 CAGATGATCGAATTCAGCAATTAAGAA 58.660 33.333 6.22 0.00 34.50 2.52
4672 5894 2.797156 CGGACACCAGATGATCGAATTC 59.203 50.000 0.00 0.00 32.08 2.17
4676 5898 0.455815 CACGGACACCAGATGATCGA 59.544 55.000 0.00 0.00 33.68 3.59
4677 5899 0.173481 ACACGGACACCAGATGATCG 59.827 55.000 0.00 0.00 34.90 3.69
4693 5920 7.485913 CAGAAATTTGCTAACATGGTATCACAC 59.514 37.037 0.00 0.00 0.00 3.82
4695 5922 6.974622 CCAGAAATTTGCTAACATGGTATCAC 59.025 38.462 0.00 0.00 0.00 3.06
4699 5926 6.405731 GCATCCAGAAATTTGCTAACATGGTA 60.406 38.462 0.00 0.00 32.41 3.25
4705 5932 6.393171 AGAAAGCATCCAGAAATTTGCTAAC 58.607 36.000 0.00 0.00 44.26 2.34
4725 5952 6.059484 AGAACGAGGGTAAACATTCAAGAAA 58.941 36.000 0.00 0.00 0.00 2.52
4742 5969 0.674581 TGAGGCCATGCAAGAACGAG 60.675 55.000 5.01 0.00 0.00 4.18
4749 5976 6.097981 TGAAATTATAATGTGAGGCCATGCAA 59.902 34.615 5.01 0.00 0.00 4.08
4785 6013 2.223479 ACAGAATCCAAACAACACGCAC 60.223 45.455 0.00 0.00 0.00 5.34
4804 6036 3.258372 CAGGGAGTACAAGCAGAGTAACA 59.742 47.826 0.00 0.00 0.00 2.41
4833 6065 8.481314 ACAAGAGCTCATTCTCAACATATAAGA 58.519 33.333 17.77 0.00 35.59 2.10
4834 6066 8.659925 ACAAGAGCTCATTCTCAACATATAAG 57.340 34.615 17.77 0.00 35.59 1.73
4835 6067 8.481314 AGACAAGAGCTCATTCTCAACATATAA 58.519 33.333 17.77 0.00 35.59 0.98
4836 6068 7.924947 CAGACAAGAGCTCATTCTCAACATATA 59.075 37.037 17.77 0.00 35.59 0.86
4837 6069 6.762187 CAGACAAGAGCTCATTCTCAACATAT 59.238 38.462 17.77 0.00 35.59 1.78
4838 6070 6.071165 TCAGACAAGAGCTCATTCTCAACATA 60.071 38.462 17.77 0.00 35.59 2.29
4839 6071 4.936411 CAGACAAGAGCTCATTCTCAACAT 59.064 41.667 17.77 0.00 35.59 2.71
4840 6072 4.039609 TCAGACAAGAGCTCATTCTCAACA 59.960 41.667 17.77 0.00 35.59 3.33
4841 6073 4.564041 TCAGACAAGAGCTCATTCTCAAC 58.436 43.478 17.77 0.00 35.59 3.18
4842 6074 4.879197 TCAGACAAGAGCTCATTCTCAA 57.121 40.909 17.77 2.21 35.59 3.02
4843 6075 4.525874 TCTTCAGACAAGAGCTCATTCTCA 59.474 41.667 17.77 0.00 35.59 3.27
4844 6076 5.070770 TCTTCAGACAAGAGCTCATTCTC 57.929 43.478 17.77 4.61 0.00 2.87
4845 6077 5.480642 TTCTTCAGACAAGAGCTCATTCT 57.519 39.130 17.77 11.01 0.00 2.40
4846 6078 5.873712 TGATTCTTCAGACAAGAGCTCATTC 59.126 40.000 17.77 8.76 0.00 2.67
4847 6079 5.802465 TGATTCTTCAGACAAGAGCTCATT 58.198 37.500 17.77 4.52 0.00 2.57
4848 6080 5.417754 TGATTCTTCAGACAAGAGCTCAT 57.582 39.130 17.77 0.00 0.00 2.90
4849 6081 4.879197 TGATTCTTCAGACAAGAGCTCA 57.121 40.909 17.77 0.00 0.00 4.26
4865 6116 7.315142 TGAATCCAAACATTGCTTACTGATTC 58.685 34.615 0.00 0.00 37.28 2.52
4866 6117 7.039504 ACTGAATCCAAACATTGCTTACTGATT 60.040 33.333 0.00 0.00 0.00 2.57
4901 6155 5.179555 GGTAGAAGCTTCAACGACTTTTCAT 59.820 40.000 27.57 5.31 0.00 2.57
4924 6178 1.379527 GTTTATCAGAACGCAGGGGG 58.620 55.000 0.00 0.00 0.00 5.40
4931 6185 4.985044 ACTCGTTTGGTTTATCAGAACG 57.015 40.909 0.00 0.00 43.01 3.95
4980 6257 5.674525 TGTTTTGCATCTAGTATCTCTGGG 58.325 41.667 0.00 0.00 0.00 4.45
5134 6418 1.002087 ACGGATGGTGAAGGAACTGTC 59.998 52.381 0.00 0.00 40.86 3.51
5164 6460 5.357878 CAGGTGCTGATTTATGGAAAGCTAA 59.642 40.000 0.00 0.00 32.02 3.09
5199 6498 3.981071 TGATTAGTCTGGAAGTGTGGG 57.019 47.619 0.00 0.00 33.76 4.61


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

AutoCloner maintained by Alex Coulton.