Multiple sequence alignment - TraesCS3D01G371900

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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 TraesCS3D01G371900 chr3D 100.000 4805 0 0 1 4805 485073294 485068490 0.000000e+00 8874.0
1 TraesCS3D01G371900 chr3D 93.023 731 49 2 1 730 49451005 49450276 0.000000e+00 1066.0
2 TraesCS3D01G371900 chr3D 80.769 416 61 11 4111 4514 488277051 488276643 1.680000e-79 307.0
3 TraesCS3D01G371900 chr3D 94.737 38 1 1 4106 4142 165958554 165958517 1.870000e-04 58.4
4 TraesCS3D01G371900 chr3A 88.915 1678 101 25 733 2358 627969010 627967366 0.000000e+00 1989.0
5 TraesCS3D01G371900 chr3A 92.632 570 40 2 161 729 33448851 33448283 0.000000e+00 819.0
6 TraesCS3D01G371900 chr3A 91.009 545 45 2 154 694 194079491 194078947 0.000000e+00 732.0
7 TraesCS3D01G371900 chr3A 85.965 684 70 19 2442 3111 627967286 627966615 0.000000e+00 708.0
8 TraesCS3D01G371900 chr3A 85.908 589 54 21 3317 3892 627966602 627966030 6.880000e-168 601.0
9 TraesCS3D01G371900 chr3B 90.730 1370 74 25 732 2067 647823389 647822039 0.000000e+00 1777.0
10 TraesCS3D01G371900 chr3B 93.007 572 29 7 162 730 41314298 41313735 0.000000e+00 824.0
11 TraesCS3D01G371900 chr3B 91.701 482 35 4 3504 3980 647820219 647819738 0.000000e+00 664.0
12 TraesCS3D01G371900 chr3B 93.968 315 11 4 2809 3119 647820950 647820640 2.020000e-128 470.0
13 TraesCS3D01G371900 chr3B 89.498 219 21 2 2588 2806 647821367 647821151 4.740000e-70 276.0
14 TraesCS3D01G371900 chr3B 86.425 221 27 3 4543 4762 445309312 445309530 6.220000e-59 239.0
15 TraesCS3D01G371900 chr3B 86.010 193 24 2 2125 2314 647821954 647821762 2.270000e-48 204.0
16 TraesCS3D01G371900 chr3B 85.621 153 21 1 3116 3267 798557678 798557830 4.980000e-35 159.0
17 TraesCS3D01G371900 chr3B 79.909 219 31 5 2370 2576 647821736 647821519 1.080000e-31 148.0
18 TraesCS3D01G371900 chr4D 92.750 731 52 1 1 730 234449000 234449730 0.000000e+00 1055.0
19 TraesCS3D01G371900 chr4D 93.482 583 34 4 150 730 505306236 505305656 0.000000e+00 863.0
20 TraesCS3D01G371900 chr6B 91.940 732 56 3 1 730 9150069 9150799 0.000000e+00 1022.0
21 TraesCS3D01G371900 chr6B 100.000 28 0 0 3991 4018 488916520 488916493 9.000000e-03 52.8
22 TraesCS3D01G371900 chr2D 95.088 509 22 3 1 507 633759421 633759928 0.000000e+00 798.0
23 TraesCS3D01G371900 chr2D 84.187 449 51 15 4082 4514 543177320 543176876 7.440000e-113 418.0
24 TraesCS3D01G371900 chr2D 90.347 259 24 1 1 259 368480271 368480014 5.960000e-89 339.0
25 TraesCS3D01G371900 chr2D 84.112 214 31 3 4546 4758 543176734 543176523 2.270000e-48 204.0
26 TraesCS3D01G371900 chr2D 84.967 153 21 2 3116 3267 426426284 426426435 2.320000e-33 154.0
27 TraesCS3D01G371900 chr2D 90.625 64 6 0 1805 1868 50989535 50989472 8.570000e-13 86.1
28 TraesCS3D01G371900 chrUn 92.500 560 28 2 1 559 395437280 395437826 0.000000e+00 789.0
29 TraesCS3D01G371900 chrUn 85.256 156 22 1 3113 3267 127140187 127140032 4.980000e-35 159.0
30 TraesCS3D01G371900 chr2A 94.068 472 25 3 261 730 776499909 776499439 0.000000e+00 713.0
31 TraesCS3D01G371900 chr2A 86.957 207 21 5 4562 4764 208563935 208563731 1.350000e-55 228.0
32 TraesCS3D01G371900 chr2A 90.625 64 6 0 1805 1868 52392945 52392882 8.570000e-13 86.1
33 TraesCS3D01G371900 chr7D 79.172 797 98 44 4018 4758 83409759 83408975 1.550000e-134 490.0
34 TraesCS3D01G371900 chr7D 83.376 391 50 11 4134 4515 233865659 233865275 9.900000e-92 348.0
35 TraesCS3D01G371900 chr7B 83.268 508 77 8 4019 4518 484740162 484740669 1.220000e-125 460.0
36 TraesCS3D01G371900 chr7B 81.221 213 38 2 4546 4758 467224623 467224833 2.300000e-38 171.0
37 TraesCS3D01G371900 chr1D 83.784 518 51 20 4022 4513 192366360 192365850 1.220000e-125 460.0
38 TraesCS3D01G371900 chr1D 81.553 206 33 5 4546 4749 433781420 433781218 1.070000e-36 165.0
39 TraesCS3D01G371900 chr5B 81.076 539 82 16 3993 4518 604845435 604844904 3.460000e-111 412.0
40 TraesCS3D01G371900 chr5B 88.688 221 23 2 4546 4766 604293563 604293345 7.930000e-68 268.0
41 TraesCS3D01G371900 chr5B 84.967 153 22 1 3116 3267 712462366 712462214 2.320000e-33 154.0
42 TraesCS3D01G371900 chr1B 84.456 386 50 10 4133 4513 17587681 17587301 5.870000e-99 372.0
43 TraesCS3D01G371900 chr1B 83.333 216 32 4 4550 4764 17587160 17586948 3.790000e-46 196.0
44 TraesCS3D01G371900 chr5A 79.961 519 78 14 4019 4518 591949309 591949820 4.570000e-95 359.0
45 TraesCS3D01G371900 chr5A 85.621 153 20 2 3116 3267 640351203 640351052 4.980000e-35 159.0
46 TraesCS3D01G371900 chr4B 82.629 213 28 7 4546 4755 119258794 119259000 3.820000e-41 180.0
47 TraesCS3D01G371900 chr2B 86.364 154 20 1 3115 3267 503982002 503981849 2.970000e-37 167.0
48 TraesCS3D01G371900 chr2B 89.552 67 7 0 1802 1868 79247606 79247672 8.570000e-13 86.1
49 TraesCS3D01G371900 chr5D 81.643 207 31 6 4562 4764 109579448 109579245 1.070000e-36 165.0
50 TraesCS3D01G371900 chr5D 75.562 356 48 31 4034 4367 426452557 426452895 6.480000e-29 139.0
51 TraesCS3D01G371900 chr7A 84.967 153 22 1 3116 3267 336801648 336801496 2.320000e-33 154.0
52 TraesCS3D01G371900 chr6D 84.967 153 22 1 3116 3267 351246503 351246351 2.320000e-33 154.0
53 TraesCS3D01G371900 chr6D 85.161 155 18 4 3116 3267 470893999 470893847 2.320000e-33 154.0


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 TraesCS3D01G371900 chr3D 485068490 485073294 4804 True 8874.000000 8874 100.000000 1 4805 1 chr3D.!!$R3 4804
1 TraesCS3D01G371900 chr3D 49450276 49451005 729 True 1066.000000 1066 93.023000 1 730 1 chr3D.!!$R1 729
2 TraesCS3D01G371900 chr3A 627966030 627969010 2980 True 1099.333333 1989 86.929333 733 3892 3 chr3A.!!$R3 3159
3 TraesCS3D01G371900 chr3A 33448283 33448851 568 True 819.000000 819 92.632000 161 729 1 chr3A.!!$R1 568
4 TraesCS3D01G371900 chr3A 194078947 194079491 544 True 732.000000 732 91.009000 154 694 1 chr3A.!!$R2 540
5 TraesCS3D01G371900 chr3B 41313735 41314298 563 True 824.000000 824 93.007000 162 730 1 chr3B.!!$R1 568
6 TraesCS3D01G371900 chr3B 647819738 647823389 3651 True 589.833333 1777 88.636000 732 3980 6 chr3B.!!$R2 3248
7 TraesCS3D01G371900 chr4D 234449000 234449730 730 False 1055.000000 1055 92.750000 1 730 1 chr4D.!!$F1 729
8 TraesCS3D01G371900 chr4D 505305656 505306236 580 True 863.000000 863 93.482000 150 730 1 chr4D.!!$R1 580
9 TraesCS3D01G371900 chr6B 9150069 9150799 730 False 1022.000000 1022 91.940000 1 730 1 chr6B.!!$F1 729
10 TraesCS3D01G371900 chr2D 633759421 633759928 507 False 798.000000 798 95.088000 1 507 1 chr2D.!!$F2 506
11 TraesCS3D01G371900 chr2D 543176523 543177320 797 True 311.000000 418 84.149500 4082 4758 2 chr2D.!!$R3 676
12 TraesCS3D01G371900 chrUn 395437280 395437826 546 False 789.000000 789 92.500000 1 559 1 chrUn.!!$F1 558
13 TraesCS3D01G371900 chr7D 83408975 83409759 784 True 490.000000 490 79.172000 4018 4758 1 chr7D.!!$R1 740
14 TraesCS3D01G371900 chr7B 484740162 484740669 507 False 460.000000 460 83.268000 4019 4518 1 chr7B.!!$F2 499
15 TraesCS3D01G371900 chr1D 192365850 192366360 510 True 460.000000 460 83.784000 4022 4513 1 chr1D.!!$R1 491
16 TraesCS3D01G371900 chr5B 604844904 604845435 531 True 412.000000 412 81.076000 3993 4518 1 chr5B.!!$R2 525
17 TraesCS3D01G371900 chr1B 17586948 17587681 733 True 284.000000 372 83.894500 4133 4764 2 chr1B.!!$R1 631
18 TraesCS3D01G371900 chr5A 591949309 591949820 511 False 359.000000 359 79.961000 4019 4518 1 chr5A.!!$F1 499

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
752 759 0.038892 CACAAATGAGCCACAGCACC 60.039 55.0 0.00 0.0 43.56 5.01 F
1576 1627 0.415429 AGGTGTGGAGGGAGATCACT 59.585 55.0 0.00 0.0 33.04 3.41 F
1952 2027 0.523968 CTGGCCATGCGAATTTGACG 60.524 55.0 5.51 0.0 0.00 4.35 F
2624 2904 0.533032 ACTCAGCCTTCCGTCTTAGC 59.467 55.0 0.00 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 2893 0.321298 GTTGGCAGGCTAAGACGGAA 60.321 55.000 0.0 0.0 0.00 4.30 R
3266 3757 0.668535 GACCACTTTGCCTGGAACAC 59.331 55.000 0.0 0.0 32.55 3.32 R
3271 3762 1.271543 TGATCAGACCACTTTGCCTGG 60.272 52.381 0.0 0.0 34.62 4.45 R
4350 5076 0.394352 CATGGTGGCTAGGGTTGTCC 60.394 60.000 0.0 0.0 0.00 4.02 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
55 56 5.364446 TGAAATACCGGCTCCAGAGTTTATA 59.636 40.000 0.00 0.00 0.00 0.98
62 63 4.935808 CGGCTCCAGAGTTTATACTTGTTT 59.064 41.667 0.00 0.00 33.84 2.83
90 91 2.972713 GGTATATCTGGTGGCAGAGGAA 59.027 50.000 0.00 0.00 34.35 3.36
290 292 1.220477 GAGACCTTGGCAGGAGCTC 59.780 63.158 4.71 4.71 44.19 4.09
396 398 3.743396 GCAGAGATAAAGGCTATTCGGTG 59.257 47.826 0.00 0.00 0.00 4.94
435 438 5.003160 TCAAATATCGGGTGCTCCAATATG 58.997 41.667 7.20 1.53 34.36 1.78
526 530 1.293924 GCCAATCATCACCGAGACTG 58.706 55.000 0.00 0.00 0.00 3.51
751 758 0.670162 ACACAAATGAGCCACAGCAC 59.330 50.000 0.00 0.00 43.56 4.40
752 759 0.038892 CACAAATGAGCCACAGCACC 60.039 55.000 0.00 0.00 43.56 5.01
920 927 2.351726 CGACGGGAGATCAAATCAAACC 59.648 50.000 0.00 0.00 0.00 3.27
999 1006 2.511452 CCATCTTCCCCGCCGATCT 61.511 63.158 0.00 0.00 0.00 2.75
1045 1053 2.277692 TCACTCGCGCCGTAATCG 60.278 61.111 0.00 0.00 0.00 3.34
1281 1320 2.958739 AGGTGGGCCTAGGAGGGA 60.959 66.667 14.75 0.00 44.90 4.20
1328 1367 3.424859 TGATGGCGTCGTCGTCGA 61.425 61.111 15.85 0.00 45.30 4.20
1454 1505 3.430565 CTGCTCCGCGGCATCTACA 62.431 63.158 23.51 10.65 41.63 2.74
1462 1513 3.323136 GGCATCTACAGCGACGCG 61.323 66.667 15.18 3.53 0.00 6.01
1576 1627 0.415429 AGGTGTGGAGGGAGATCACT 59.585 55.000 0.00 0.00 33.04 3.41
1875 1944 2.436115 GAAGCAGGTGGGCGGTAC 60.436 66.667 0.00 0.00 39.27 3.34
1897 1966 3.477899 AACTCGTTACGTAGTACTGCC 57.522 47.619 5.39 0.00 45.76 4.85
1902 1971 4.969816 TCGTTACGTAGTACTGCCTTTAC 58.030 43.478 5.39 0.00 45.76 2.01
1932 2007 3.744660 ACACAAAGATCGAAAGCTCCTT 58.255 40.909 0.00 0.00 0.00 3.36
1937 2012 1.134551 AGATCGAAAGCTCCTTCTGGC 60.135 52.381 0.00 0.00 0.00 4.85
1952 2027 0.523968 CTGGCCATGCGAATTTGACG 60.524 55.000 5.51 0.00 0.00 4.35
1985 2061 3.544637 GCGGTAATATTTTGGTTCGTCCG 60.545 47.826 0.00 0.00 39.52 4.79
2076 2152 5.425217 TCCAAAGAGCAGGTATAGAATGTGA 59.575 40.000 0.00 0.00 0.00 3.58
2092 2168 1.211703 TGTGACTGTGCCCTTTCTTCA 59.788 47.619 0.00 0.00 0.00 3.02
2094 2170 0.877743 GACTGTGCCCTTTCTTCAGC 59.122 55.000 0.00 0.00 0.00 4.26
2095 2171 0.538287 ACTGTGCCCTTTCTTCAGCC 60.538 55.000 0.00 0.00 0.00 4.85
2096 2172 1.580845 CTGTGCCCTTTCTTCAGCCG 61.581 60.000 0.00 0.00 0.00 5.52
2097 2173 1.302511 GTGCCCTTTCTTCAGCCGA 60.303 57.895 0.00 0.00 0.00 5.54
2098 2174 1.003355 TGCCCTTTCTTCAGCCGAG 60.003 57.895 0.00 0.00 0.00 4.63
2099 2175 1.003233 GCCCTTTCTTCAGCCGAGT 60.003 57.895 0.00 0.00 0.00 4.18
2101 2177 1.897560 CCCTTTCTTCAGCCGAGTTT 58.102 50.000 0.00 0.00 0.00 2.66
2102 2178 2.230660 CCCTTTCTTCAGCCGAGTTTT 58.769 47.619 0.00 0.00 0.00 2.43
2103 2179 2.226674 CCCTTTCTTCAGCCGAGTTTTC 59.773 50.000 0.00 0.00 0.00 2.29
2104 2180 3.142174 CCTTTCTTCAGCCGAGTTTTCT 58.858 45.455 0.00 0.00 0.00 2.52
2105 2181 3.565902 CCTTTCTTCAGCCGAGTTTTCTT 59.434 43.478 0.00 0.00 0.00 2.52
2106 2182 4.319839 CCTTTCTTCAGCCGAGTTTTCTTC 60.320 45.833 0.00 0.00 0.00 2.87
2109 2217 1.512926 TCAGCCGAGTTTTCTTCAGC 58.487 50.000 0.00 0.00 0.00 4.26
2112 2220 0.949105 GCCGAGTTTTCTTCAGCCGA 60.949 55.000 0.00 0.00 0.00 5.54
2122 2230 1.623311 TCTTCAGCCGAGTTTCCATGA 59.377 47.619 0.00 0.00 0.00 3.07
2123 2231 1.734465 CTTCAGCCGAGTTTCCATGAC 59.266 52.381 0.00 0.00 0.00 3.06
2145 2253 5.647589 ACTAGATCTTGCATTGCATGTTTG 58.352 37.500 20.16 12.28 38.76 2.93
2195 2306 4.315803 ACGGTTTTAGAACTCTCATGGTG 58.684 43.478 0.00 0.00 36.03 4.17
2270 2381 7.281774 AGAGGTATGTTTATGAGATGTTGCTTG 59.718 37.037 0.00 0.00 0.00 4.01
2277 2388 7.538334 TGTTTATGAGATGTTGCTTGAAATTCG 59.462 33.333 0.00 0.00 0.00 3.34
2287 2400 6.748658 TGTTGCTTGAAATTCGATCATGATTC 59.251 34.615 10.14 3.60 0.00 2.52
2336 2449 4.377021 ACCACATAATAGTATGCCACACG 58.623 43.478 10.02 0.00 40.83 4.49
2341 2454 5.932303 ACATAATAGTATGCCACACGATTCC 59.068 40.000 10.02 0.00 40.83 3.01
2347 2460 1.686355 TGCCACACGATTCCAAAGTT 58.314 45.000 0.00 0.00 0.00 2.66
2358 2471 8.458843 ACACGATTCCAAAGTTATTAGGATTTG 58.541 33.333 0.00 0.00 33.45 2.32
2360 2473 9.238368 ACGATTCCAAAGTTATTAGGATTTGAA 57.762 29.630 0.00 0.00 35.19 2.69
2374 2492 6.313519 AGGATTTGAATGGCTAACTAGTGA 57.686 37.500 0.00 0.00 0.00 3.41
2378 2496 9.289782 GGATTTGAATGGCTAACTAGTGATTAT 57.710 33.333 0.00 0.00 0.00 1.28
2387 2505 5.872070 GCTAACTAGTGATTATGATCAGCCC 59.128 44.000 0.09 0.00 42.73 5.19
2389 2507 2.175878 AGTGATTATGATCAGCCCGC 57.824 50.000 0.09 0.00 42.73 6.13
2390 2508 1.696336 AGTGATTATGATCAGCCCGCT 59.304 47.619 0.09 0.00 42.73 5.52
2395 2513 2.820059 TATGATCAGCCCGCTAACAG 57.180 50.000 0.09 0.00 0.00 3.16
2402 2520 1.069227 CAGCCCGCTAACAGAAAACAC 60.069 52.381 0.00 0.00 0.00 3.32
2412 2530 7.394872 CGCTAACAGAAAACACAATCTATCTC 58.605 38.462 0.00 0.00 0.00 2.75
2413 2531 7.063426 CGCTAACAGAAAACACAATCTATCTCA 59.937 37.037 0.00 0.00 0.00 3.27
2434 2556 5.431765 TCATTGAAGTAGATTGCCCTTCTC 58.568 41.667 0.00 0.00 36.43 2.87
2436 2558 3.454858 TGAAGTAGATTGCCCTTCTCCT 58.545 45.455 0.00 0.00 36.43 3.69
2439 2561 4.544564 AGTAGATTGCCCTTCTCCTCTA 57.455 45.455 0.00 0.00 0.00 2.43
2440 2562 4.219919 AGTAGATTGCCCTTCTCCTCTAC 58.780 47.826 0.00 0.00 36.78 2.59
2453 2592 1.819288 TCCTCTACTTTGAGCGGACTG 59.181 52.381 0.00 0.00 33.02 3.51
2524 2664 7.174946 TCCTTTACTCTAGAAATTGCAACCTTG 59.825 37.037 0.00 0.92 0.00 3.61
2531 2671 4.432712 AGAAATTGCAACCTTGTGAACAC 58.567 39.130 0.00 0.00 0.00 3.32
2533 2673 5.359576 AGAAATTGCAACCTTGTGAACACTA 59.640 36.000 0.00 0.00 0.00 2.74
2540 2680 5.239525 GCAACCTTGTGAACACTAGAAGATT 59.760 40.000 15.43 0.00 36.50 2.40
2576 2716 1.263217 GGTCAGTGTTTCGCGATGTTT 59.737 47.619 10.88 0.00 0.00 2.83
2578 2718 2.964768 GTCAGTGTTTCGCGATGTTTTC 59.035 45.455 10.88 0.00 0.00 2.29
2580 2720 4.052608 TCAGTGTTTCGCGATGTTTTCTA 58.947 39.130 10.88 0.00 0.00 2.10
2581 2721 4.688879 TCAGTGTTTCGCGATGTTTTCTAT 59.311 37.500 10.88 0.00 0.00 1.98
2583 2723 4.688879 AGTGTTTCGCGATGTTTTCTATCA 59.311 37.500 10.88 0.00 0.00 2.15
2584 2724 5.178623 AGTGTTTCGCGATGTTTTCTATCAA 59.821 36.000 10.88 0.00 0.00 2.57
2585 2725 5.849081 GTGTTTCGCGATGTTTTCTATCAAA 59.151 36.000 10.88 0.00 0.00 2.69
2586 2726 6.523201 GTGTTTCGCGATGTTTTCTATCAAAT 59.477 34.615 10.88 0.00 0.00 2.32
2613 2893 3.988976 TCAGAAAGCATAACTCAGCCT 57.011 42.857 0.00 0.00 0.00 4.58
2619 2899 1.134670 AGCATAACTCAGCCTTCCGTC 60.135 52.381 0.00 0.00 0.00 4.79
2624 2904 0.533032 ACTCAGCCTTCCGTCTTAGC 59.467 55.000 0.00 0.00 0.00 3.09
2640 2920 1.737838 TAGCCTGCCAACATTCTTCG 58.262 50.000 0.00 0.00 0.00 3.79
2642 2929 1.508088 CCTGCCAACATTCTTCGGC 59.492 57.895 0.00 0.00 45.11 5.54
2644 2931 4.868195 GCCAACATTCTTCGGCAC 57.132 55.556 0.00 0.00 44.25 5.01
2649 2936 2.811431 CCAACATTCTTCGGCACACTTA 59.189 45.455 0.00 0.00 0.00 2.24
2662 2949 4.562394 CGGCACACTTAAAAATATTGCCTG 59.438 41.667 8.00 0.00 44.86 4.85
2706 2993 6.148150 GTGGGAATACACGTTTCAGAACATAA 59.852 38.462 1.25 0.00 35.44 1.90
2714 3001 6.206634 ACACGTTTCAGAACATAATCATGGTT 59.793 34.615 0.00 0.00 36.39 3.67
2766 3053 4.749099 GCATGCTCTATGGTTTCTCTACTG 59.251 45.833 11.37 0.00 37.26 2.74
2787 3074 2.932614 GTGGACTGTATGATGTGCTGTC 59.067 50.000 0.00 0.00 39.51 3.51
2793 3080 1.594862 GTATGATGTGCTGTCCTTCGC 59.405 52.381 0.00 0.00 0.00 4.70
2907 3395 3.800685 TTCGGCCACGTCCACACAG 62.801 63.158 2.24 0.00 41.85 3.66
2941 3429 2.389059 CCAAGCGTGAGATCGTCTATG 58.611 52.381 0.00 0.00 0.00 2.23
2942 3430 2.223595 CCAAGCGTGAGATCGTCTATGT 60.224 50.000 0.00 0.00 0.00 2.29
2944 3432 3.341857 AGCGTGAGATCGTCTATGTTC 57.658 47.619 0.00 0.00 0.00 3.18
2945 3433 2.946329 AGCGTGAGATCGTCTATGTTCT 59.054 45.455 0.00 0.00 0.00 3.01
2994 3482 1.235724 GGACCCTTTCCAACTCAACG 58.764 55.000 0.00 0.00 45.10 4.10
3017 3505 4.278419 GTGGGTACATTTCATAGGCCATTC 59.722 45.833 5.01 0.00 0.00 2.67
3183 3674 8.668510 ATGGACTACATACAGAGCAAAATAAG 57.331 34.615 0.00 0.00 38.26 1.73
3184 3675 7.620880 TGGACTACATACAGAGCAAAATAAGT 58.379 34.615 0.00 0.00 0.00 2.24
3185 3676 7.549134 TGGACTACATACAGAGCAAAATAAGTG 59.451 37.037 0.00 0.00 0.00 3.16
3186 3677 7.764443 GGACTACATACAGAGCAAAATAAGTGA 59.236 37.037 0.00 0.00 0.00 3.41
3187 3678 9.151471 GACTACATACAGAGCAAAATAAGTGAA 57.849 33.333 0.00 0.00 0.00 3.18
3188 3679 9.672673 ACTACATACAGAGCAAAATAAGTGAAT 57.327 29.630 0.00 0.00 0.00 2.57
3190 3681 8.798859 ACATACAGAGCAAAATAAGTGAATCT 57.201 30.769 0.00 0.00 0.00 2.40
3191 3682 9.890629 ACATACAGAGCAAAATAAGTGAATCTA 57.109 29.630 0.00 0.00 0.00 1.98
3272 3763 8.754230 AAGACTTATAGTTAGAAACGTGTTCC 57.246 34.615 0.00 0.00 36.23 3.62
3276 3767 2.490991 AGTTAGAAACGTGTTCCAGGC 58.509 47.619 0.00 0.00 36.23 4.85
3284 3775 1.101049 CGTGTTCCAGGCAAAGTGGT 61.101 55.000 0.00 0.00 36.37 4.16
3290 3781 1.003580 TCCAGGCAAAGTGGTCTGATC 59.996 52.381 0.00 0.00 43.12 2.92
3306 3797 5.220796 GGTCTGATCACACATCATGTTCATG 60.221 44.000 3.41 6.46 40.64 3.07
3331 3822 0.467384 AGGGAATGGTCTGCATCTCG 59.533 55.000 0.00 0.00 0.00 4.04
3342 3833 3.247173 GTCTGCATCTCGGCTTAGAAATG 59.753 47.826 0.00 0.00 34.04 2.32
3343 3834 2.547211 CTGCATCTCGGCTTAGAAATGG 59.453 50.000 0.00 0.00 34.04 3.16
3344 3835 2.170397 TGCATCTCGGCTTAGAAATGGA 59.830 45.455 0.00 0.00 34.04 3.41
3345 3836 2.805099 GCATCTCGGCTTAGAAATGGAG 59.195 50.000 0.00 0.00 0.00 3.86
3346 3837 3.742640 GCATCTCGGCTTAGAAATGGAGT 60.743 47.826 0.00 0.00 0.00 3.85
3387 3878 8.373981 TGATTTTCCAGATTAATTGCCTTCAAA 58.626 29.630 0.00 0.00 35.56 2.69
3434 3925 8.796475 GCCATCATTGCCTAAAAGAATTCTATA 58.204 33.333 8.75 4.68 0.00 1.31
3473 3970 2.292845 GACTCCCCTTACTCGTATTCCG 59.707 54.545 0.00 0.00 38.13 4.30
3478 3975 3.118665 CCCCTTACTCGTATTCCGGAAAA 60.119 47.826 23.08 8.04 37.11 2.29
3479 3976 4.117685 CCCTTACTCGTATTCCGGAAAAG 58.882 47.826 23.08 17.19 37.11 2.27
3510 4186 4.153673 TCCCTGTCTTCGTGGTTTTTAA 57.846 40.909 0.00 0.00 0.00 1.52
3534 4210 8.976986 AATTCATTTTAGATGCTTGTCTGAAC 57.023 30.769 0.00 0.00 0.00 3.18
3567 4243 3.255149 ACTTCATGCAGCTCAAGGAAAAG 59.745 43.478 0.00 0.00 0.00 2.27
3643 4319 5.089970 CTCAATGGAGTGGTAGACATGAA 57.910 43.478 0.00 0.00 36.36 2.57
3738 4414 5.818857 TGGAGTTAACTCAGTTGTTGTAACC 59.181 40.000 31.30 14.26 44.60 2.85
3847 4523 6.238566 GCAGCTTATATTCTGTCTGATTTGCA 60.239 38.462 0.00 0.00 33.09 4.08
3850 4526 8.910944 AGCTTATATTCTGTCTGATTTGCATTT 58.089 29.630 0.00 0.00 0.00 2.32
3858 4534 8.721019 TCTGTCTGATTTGCATTTTTCTTTTT 57.279 26.923 0.00 0.00 0.00 1.94
3859 4535 9.814899 TCTGTCTGATTTGCATTTTTCTTTTTA 57.185 25.926 0.00 0.00 0.00 1.52
3876 4558 8.972458 TTCTTTTTATGCTGCCAGTATGTATA 57.028 30.769 5.47 0.00 0.00 1.47
3878 4560 8.210946 TCTTTTTATGCTGCCAGTATGTATAGT 58.789 33.333 5.47 0.00 0.00 2.12
3897 4579 8.691797 TGTATAGTGATGTAGAGCACAATACAA 58.308 33.333 11.14 0.00 41.19 2.41
3909 4591 6.262944 AGAGCACAATACAAACAGAACATCAA 59.737 34.615 0.00 0.00 0.00 2.57
3913 4595 9.190858 GCACAATACAAACAGAACATCAAAATA 57.809 29.630 0.00 0.00 0.00 1.40
3940 4622 8.565896 TGTTCAAACATAATGCTAGAGACATT 57.434 30.769 0.00 0.00 36.50 2.71
3954 4636 6.074569 GCTAGAGACATTTAGCGAACAGAATC 60.075 42.308 0.00 0.00 33.68 2.52
3956 4638 5.578727 AGAGACATTTAGCGAACAGAATCAC 59.421 40.000 0.00 0.00 0.00 3.06
3957 4639 5.237815 AGACATTTAGCGAACAGAATCACA 58.762 37.500 0.00 0.00 0.00 3.58
3958 4640 5.877012 AGACATTTAGCGAACAGAATCACAT 59.123 36.000 0.00 0.00 0.00 3.21
3964 4646 2.160219 GCGAACAGAATCACATGCAAGA 59.840 45.455 0.00 0.00 0.00 3.02
3983 4665 9.979578 ATGCAAGACATGAAACAAAATAACTAA 57.020 25.926 0.00 0.00 37.70 2.24
3984 4666 9.243637 TGCAAGACATGAAACAAAATAACTAAC 57.756 29.630 0.00 0.00 0.00 2.34
3985 4667 8.699749 GCAAGACATGAAACAAAATAACTAACC 58.300 33.333 0.00 0.00 0.00 2.85
3986 4668 8.901748 CAAGACATGAAACAAAATAACTAACCG 58.098 33.333 0.00 0.00 0.00 4.44
3987 4669 8.385898 AGACATGAAACAAAATAACTAACCGA 57.614 30.769 0.00 0.00 0.00 4.69
3988 4670 8.842280 AGACATGAAACAAAATAACTAACCGAA 58.158 29.630 0.00 0.00 0.00 4.30
3989 4671 8.791355 ACATGAAACAAAATAACTAACCGAAC 57.209 30.769 0.00 0.00 0.00 3.95
3990 4672 8.407064 ACATGAAACAAAATAACTAACCGAACA 58.593 29.630 0.00 0.00 0.00 3.18
3991 4673 9.239002 CATGAAACAAAATAACTAACCGAACAA 57.761 29.630 0.00 0.00 0.00 2.83
4008 4690 4.666655 CGAACAATAAGAGCAACTCCAACG 60.667 45.833 0.00 0.00 0.00 4.10
4009 4691 2.484264 ACAATAAGAGCAACTCCAACGC 59.516 45.455 0.00 0.00 0.00 4.84
4065 4748 1.974343 GTAATGGCCCAACGCACCA 60.974 57.895 0.00 0.00 40.31 4.17
4127 4830 2.552591 CCAAATTTGGGCCTGAAATGCA 60.553 45.455 26.87 0.00 44.70 3.96
4349 5075 3.775654 CACCCTCTGCTCCCCGTC 61.776 72.222 0.00 0.00 0.00 4.79
4383 5113 1.452108 CCATGGGGTTCTTCTCCGC 60.452 63.158 2.85 0.00 40.23 5.54
4515 5245 2.050985 GCACTTGAAGCACCGCAC 60.051 61.111 0.00 0.00 0.00 5.34
4518 5248 3.726517 CTTGAAGCACCGCACCCG 61.727 66.667 0.00 0.00 0.00 5.28
4604 5443 1.449601 CGATTGGGAGGTCCGGTTG 60.450 63.158 0.00 0.00 38.76 3.77
4610 5449 3.047877 GAGGTCCGGTTGGCGTTG 61.048 66.667 0.00 0.00 34.14 4.10
4624 5463 2.659610 GTTGGAGCACGAGGAGCT 59.340 61.111 0.00 0.00 46.82 4.09
4628 5467 4.121669 GAGCACGAGGAGCTGCGA 62.122 66.667 0.00 0.00 43.58 5.10
4758 5598 0.179124 CGAAAGCGAGGAAGAGGAGG 60.179 60.000 0.00 0.00 40.82 4.30
4759 5599 0.461163 GAAAGCGAGGAAGAGGAGGC 60.461 60.000 0.00 0.00 0.00 4.70
4761 5601 4.214327 GCGAGGAAGAGGAGGCGG 62.214 72.222 0.00 0.00 0.00 6.13
4762 5602 4.214327 CGAGGAAGAGGAGGCGGC 62.214 72.222 0.00 0.00 0.00 6.53
4763 5603 4.214327 GAGGAAGAGGAGGCGGCG 62.214 72.222 0.51 0.51 0.00 6.46
4765 5605 3.145551 GGAAGAGGAGGCGGCGTA 61.146 66.667 9.37 0.00 0.00 4.42
4766 5606 2.104530 GAAGAGGAGGCGGCGTAC 59.895 66.667 9.37 1.56 0.00 3.67
4767 5607 3.427598 GAAGAGGAGGCGGCGTACC 62.428 68.421 9.37 9.84 0.00 3.34
4768 5608 4.753662 AGAGGAGGCGGCGTACCA 62.754 66.667 20.13 0.00 34.57 3.25
4769 5609 4.208686 GAGGAGGCGGCGTACCAG 62.209 72.222 20.13 0.00 34.57 4.00
4772 5612 4.509737 GAGGCGGCGTACCAGGAC 62.510 72.222 9.37 0.00 34.57 3.85
4778 5618 4.814294 GCGTACCAGGACCGGCTG 62.814 72.222 0.00 0.73 0.00 4.85
4779 5619 3.379445 CGTACCAGGACCGGCTGT 61.379 66.667 0.00 0.00 0.00 4.40
4780 5620 2.577593 GTACCAGGACCGGCTGTC 59.422 66.667 0.00 0.00 43.67 3.51
4781 5621 3.066190 TACCAGGACCGGCTGTCG 61.066 66.667 0.00 0.00 45.46 4.35
4791 5631 4.864334 GGCTGTCGGAGGCCATGG 62.864 72.222 7.63 7.63 46.84 3.66
4798 5638 4.925861 GGAGGCCATGGCGCTCTC 62.926 72.222 34.66 30.44 43.06 3.20
4799 5639 4.925861 GAGGCCATGGCGCTCTCC 62.926 72.222 31.84 19.71 43.06 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 2.371841 GCCACCAGATATACCACATGGA 59.628 50.000 4.53 0.00 38.94 3.41
90 91 0.886490 CACTCCTTTCACCGCTTGCT 60.886 55.000 0.00 0.00 0.00 3.91
290 292 3.978723 CTCTCGCCACAGCTCCACG 62.979 68.421 0.00 0.00 36.60 4.94
396 398 6.073548 CGATATTTGAAGCCAGATAAGACCAC 60.074 42.308 0.00 0.00 0.00 4.16
526 530 0.321653 AAGTCCATCGCCAACAGACC 60.322 55.000 0.00 0.00 0.00 3.85
730 737 0.038892 GCTGTGGCTCATTTGTGTGG 60.039 55.000 0.00 0.00 35.22 4.17
751 758 4.778415 CTCGTCTCACCCGTGCGG 62.778 72.222 3.25 3.25 37.81 5.69
752 759 4.778415 CCTCGTCTCACCCGTGCG 62.778 72.222 0.00 0.00 0.00 5.34
999 1006 1.519234 GCGCGATGTGATGTGAGGA 60.519 57.895 12.10 0.00 0.00 3.71
1045 1053 1.957186 TGTTACGGAAGGTGCGTGC 60.957 57.895 4.99 0.00 45.89 5.34
1081 1089 3.491652 GCTTCTCGTGGCTTCCGC 61.492 66.667 0.00 0.00 0.00 5.54
1082 1090 2.815647 GGCTTCTCGTGGCTTCCG 60.816 66.667 0.00 0.00 0.00 4.30
1083 1091 2.815647 CGGCTTCTCGTGGCTTCC 60.816 66.667 0.00 0.00 0.00 3.46
1084 1092 1.807573 CTCGGCTTCTCGTGGCTTC 60.808 63.158 0.00 0.00 0.00 3.86
1138 1146 2.221299 CCTGGAAACGTGGGGGAGA 61.221 63.158 0.00 0.00 0.00 3.71
1267 1306 3.028683 CTCTCCCTCCTAGGCCCA 58.971 66.667 2.96 0.00 32.73 5.36
1551 1602 2.603473 CCCTCCACACCTCGTCCA 60.603 66.667 0.00 0.00 0.00 4.02
1629 1680 2.121538 TCCTCCAGCGTCATCTCCG 61.122 63.158 0.00 0.00 0.00 4.63
1685 1736 4.577246 CGCTACCTGCTCCTCCGC 62.577 72.222 0.00 0.00 40.11 5.54
1840 1909 2.041115 CCTCTCTCGTGACCTCGCA 61.041 63.158 0.00 0.00 0.00 5.10
1875 1944 3.605486 GGCAGTACTACGTAACGAGTTTG 59.395 47.826 0.00 0.00 0.00 2.93
1902 1971 8.283291 AGCTTTCGATCTTTGTGTAAAAGTAAG 58.717 33.333 0.00 0.00 0.00 2.34
1932 2007 0.810648 GTCAAATTCGCATGGCCAGA 59.189 50.000 13.05 0.00 0.00 3.86
1937 2012 1.086696 ACTCCGTCAAATTCGCATGG 58.913 50.000 0.00 0.00 0.00 3.66
1952 2027 2.406596 TATTACCGCCAAACCACTCC 57.593 50.000 0.00 0.00 0.00 3.85
1985 2061 1.373059 GGCTATGTAGGCCTGGAGC 59.627 63.158 17.99 17.50 45.57 4.70
2076 2152 0.538287 GGCTGAAGAAAGGGCACAGT 60.538 55.000 0.00 0.00 0.00 3.55
2092 2168 0.951040 CGGCTGAAGAAAACTCGGCT 60.951 55.000 3.83 0.00 43.48 5.52
2094 2170 1.071605 CTCGGCTGAAGAAAACTCGG 58.928 55.000 0.00 0.00 0.00 4.63
2095 2171 1.784525 ACTCGGCTGAAGAAAACTCG 58.215 50.000 0.00 0.00 0.00 4.18
2096 2172 3.058846 GGAAACTCGGCTGAAGAAAACTC 60.059 47.826 0.00 0.00 0.00 3.01
2097 2173 2.879026 GGAAACTCGGCTGAAGAAAACT 59.121 45.455 0.00 0.00 0.00 2.66
2098 2174 2.616842 TGGAAACTCGGCTGAAGAAAAC 59.383 45.455 0.00 0.00 0.00 2.43
2099 2175 2.925724 TGGAAACTCGGCTGAAGAAAA 58.074 42.857 0.00 0.00 0.00 2.29
2101 2177 2.038426 TCATGGAAACTCGGCTGAAGAA 59.962 45.455 0.00 0.00 0.00 2.52
2102 2178 1.623311 TCATGGAAACTCGGCTGAAGA 59.377 47.619 0.00 0.00 0.00 2.87
2103 2179 1.734465 GTCATGGAAACTCGGCTGAAG 59.266 52.381 0.00 0.00 0.00 3.02
2104 2180 1.347707 AGTCATGGAAACTCGGCTGAA 59.652 47.619 0.00 0.00 0.00 3.02
2105 2181 0.976641 AGTCATGGAAACTCGGCTGA 59.023 50.000 0.00 0.00 0.00 4.26
2106 2182 2.166459 TCTAGTCATGGAAACTCGGCTG 59.834 50.000 0.00 0.00 0.00 4.85
2109 2217 4.927978 AGATCTAGTCATGGAAACTCGG 57.072 45.455 0.00 0.00 0.00 4.63
2112 2220 5.426689 TGCAAGATCTAGTCATGGAAACT 57.573 39.130 0.00 0.00 0.00 2.66
2195 2306 4.396166 CCTGGAACACACCAAAGACATATC 59.604 45.833 0.00 0.00 39.59 1.63
2314 2427 4.100344 TCGTGTGGCATACTATTATGTGGT 59.900 41.667 12.66 0.00 37.92 4.16
2325 2438 2.747446 ACTTTGGAATCGTGTGGCATAC 59.253 45.455 4.05 4.05 0.00 2.39
2326 2439 3.066291 ACTTTGGAATCGTGTGGCATA 57.934 42.857 0.00 0.00 0.00 3.14
2347 2460 9.778741 CACTAGTTAGCCATTCAAATCCTAATA 57.221 33.333 0.00 0.00 0.00 0.98
2358 2471 9.149225 CTGATCATAATCACTAGTTAGCCATTC 57.851 37.037 0.00 0.00 36.98 2.67
2360 2473 7.102346 GCTGATCATAATCACTAGTTAGCCAT 58.898 38.462 0.00 0.00 36.98 4.40
2362 2475 5.872070 GGCTGATCATAATCACTAGTTAGCC 59.128 44.000 0.00 0.00 36.98 3.93
2374 2492 3.324846 TCTGTTAGCGGGCTGATCATAAT 59.675 43.478 2.86 0.00 0.00 1.28
2378 2496 0.901827 TTCTGTTAGCGGGCTGATCA 59.098 50.000 2.86 0.00 0.00 2.92
2387 2505 7.063426 TGAGATAGATTGTGTTTTCTGTTAGCG 59.937 37.037 0.00 0.00 0.00 4.26
2412 2530 4.578105 GGAGAAGGGCAATCTACTTCAATG 59.422 45.833 0.00 0.00 42.24 2.82
2413 2531 4.476479 AGGAGAAGGGCAATCTACTTCAAT 59.524 41.667 0.00 0.00 42.24 2.57
2434 2556 1.819288 TCAGTCCGCTCAAAGTAGAGG 59.181 52.381 0.00 0.00 37.76 3.69
2436 2558 2.097629 CGATCAGTCCGCTCAAAGTAGA 59.902 50.000 0.00 0.00 0.00 2.59
2439 2561 3.425578 CGATCAGTCCGCTCAAAGT 57.574 52.632 0.00 0.00 0.00 2.66
2481 2621 5.487861 AAAGGAGGTAATGGGATCCAAAT 57.512 39.130 15.23 3.49 36.95 2.32
2494 2634 7.490657 TGCAATTTCTAGAGTAAAGGAGGTA 57.509 36.000 0.00 0.00 0.00 3.08
2524 2664 7.873505 AGTGGTAGAAAATCTTCTAGTGTTCAC 59.126 37.037 0.00 0.00 43.35 3.18
2564 2704 9.858247 GTATATTTGATAGAAAACATCGCGAAA 57.142 29.630 15.24 0.00 0.00 3.46
2585 2725 9.050601 GCTGAGTTATGCTTTCTGAAAGTATAT 57.949 33.333 29.09 20.56 42.80 0.86
2586 2726 7.495934 GGCTGAGTTATGCTTTCTGAAAGTATA 59.504 37.037 26.64 26.64 41.19 1.47
2613 2893 0.321298 GTTGGCAGGCTAAGACGGAA 60.321 55.000 0.00 0.00 0.00 4.30
2619 2899 2.096496 CGAAGAATGTTGGCAGGCTAAG 59.904 50.000 0.00 0.00 0.00 2.18
2624 2904 1.508088 GCCGAAGAATGTTGGCAGG 59.492 57.895 0.00 0.00 46.76 4.85
2642 2929 7.326789 CACTGTCAGGCAATATTTTTAAGTGTG 59.673 37.037 4.53 0.00 0.00 3.82
2644 2931 6.308766 GCACTGTCAGGCAATATTTTTAAGTG 59.691 38.462 4.53 0.00 34.66 3.16
2649 2936 5.473066 AAGCACTGTCAGGCAATATTTTT 57.527 34.783 13.61 0.00 0.00 1.94
2662 2949 3.304257 CCACACAAGATCAAAGCACTGTC 60.304 47.826 0.00 0.00 0.00 3.51
2706 2993 4.729552 ATGGGCATACAGTAACCATGAT 57.270 40.909 11.89 0.00 40.24 2.45
2757 3044 5.952347 ACATCATACAGTCCACAGTAGAGAA 59.048 40.000 0.00 0.00 0.00 2.87
2766 3053 2.932614 GACAGCACATCATACAGTCCAC 59.067 50.000 0.00 0.00 0.00 4.02
2806 3093 3.063997 CCTTAAGCACGTTAGCTCATTGG 59.936 47.826 0.31 0.00 45.89 3.16
2994 3482 3.290948 TGGCCTATGAAATGTACCCAC 57.709 47.619 3.32 0.00 0.00 4.61
3017 3505 6.798482 TGCAGGCTGTGATCATTTTAATAAG 58.202 36.000 17.16 0.00 0.00 1.73
3026 3514 0.910338 AGACTGCAGGCTGTGATCAT 59.090 50.000 24.77 0.00 0.00 2.45
3157 3648 9.764363 CTTATTTTGCTCTGTATGTAGTCCATA 57.236 33.333 0.00 0.00 34.86 2.74
3158 3649 8.267894 ACTTATTTTGCTCTGTATGTAGTCCAT 58.732 33.333 0.00 0.00 37.58 3.41
3159 3650 7.549134 CACTTATTTTGCTCTGTATGTAGTCCA 59.451 37.037 0.00 0.00 0.00 4.02
3160 3651 7.764443 TCACTTATTTTGCTCTGTATGTAGTCC 59.236 37.037 0.00 0.00 0.00 3.85
3161 3652 8.703604 TCACTTATTTTGCTCTGTATGTAGTC 57.296 34.615 0.00 0.00 0.00 2.59
3162 3653 9.672673 ATTCACTTATTTTGCTCTGTATGTAGT 57.327 29.630 0.00 0.00 0.00 2.73
3164 3655 9.890629 AGATTCACTTATTTTGCTCTGTATGTA 57.109 29.630 0.00 0.00 0.00 2.29
3165 3656 8.798859 AGATTCACTTATTTTGCTCTGTATGT 57.201 30.769 0.00 0.00 0.00 2.29
3243 3734 9.754382 ACACGTTTCTAACTATAAGTCTTTTCA 57.246 29.630 0.00 0.00 0.00 2.69
3246 3737 9.201127 GGAACACGTTTCTAACTATAAGTCTTT 57.799 33.333 9.34 0.00 0.00 2.52
3247 3738 8.362639 TGGAACACGTTTCTAACTATAAGTCTT 58.637 33.333 9.34 0.00 0.00 3.01
3248 3739 7.889469 TGGAACACGTTTCTAACTATAAGTCT 58.111 34.615 9.34 0.00 0.00 3.24
3249 3740 7.275123 CCTGGAACACGTTTCTAACTATAAGTC 59.725 40.741 9.34 0.00 0.00 3.01
3250 3741 7.095270 CCTGGAACACGTTTCTAACTATAAGT 58.905 38.462 9.34 0.00 0.00 2.24
3251 3742 6.035758 GCCTGGAACACGTTTCTAACTATAAG 59.964 42.308 0.00 0.00 0.00 1.73
3252 3743 5.870978 GCCTGGAACACGTTTCTAACTATAA 59.129 40.000 0.00 0.00 0.00 0.98
3253 3744 5.047164 TGCCTGGAACACGTTTCTAACTATA 60.047 40.000 0.00 0.00 0.00 1.31
3254 3745 4.251268 GCCTGGAACACGTTTCTAACTAT 58.749 43.478 0.00 0.00 0.00 2.12
3255 3746 3.069872 TGCCTGGAACACGTTTCTAACTA 59.930 43.478 0.00 0.00 0.00 2.24
3256 3747 2.158871 TGCCTGGAACACGTTTCTAACT 60.159 45.455 0.00 0.00 0.00 2.24
3257 3748 2.215196 TGCCTGGAACACGTTTCTAAC 58.785 47.619 0.00 0.00 0.00 2.34
3258 3749 2.623878 TGCCTGGAACACGTTTCTAA 57.376 45.000 0.00 0.98 0.00 2.10
3259 3750 2.623878 TTGCCTGGAACACGTTTCTA 57.376 45.000 0.00 4.25 0.00 2.10
3260 3751 1.676006 CTTTGCCTGGAACACGTTTCT 59.324 47.619 0.00 0.00 0.00 2.52
3261 3752 1.404035 ACTTTGCCTGGAACACGTTTC 59.596 47.619 0.00 0.00 0.00 2.78
3262 3753 1.134175 CACTTTGCCTGGAACACGTTT 59.866 47.619 0.00 0.00 0.00 3.60
3263 3754 0.738389 CACTTTGCCTGGAACACGTT 59.262 50.000 0.00 0.00 0.00 3.99
3264 3755 1.101049 CCACTTTGCCTGGAACACGT 61.101 55.000 0.00 0.00 0.00 4.49
3265 3756 1.101049 ACCACTTTGCCTGGAACACG 61.101 55.000 0.00 0.00 32.55 4.49
3266 3757 0.668535 GACCACTTTGCCTGGAACAC 59.331 55.000 0.00 0.00 32.55 3.32
3271 3762 1.271543 TGATCAGACCACTTTGCCTGG 60.272 52.381 0.00 0.00 34.62 4.45
3272 3763 1.808945 GTGATCAGACCACTTTGCCTG 59.191 52.381 0.00 0.00 0.00 4.85
3276 3767 4.067192 TGATGTGTGATCAGACCACTTTG 58.933 43.478 19.40 0.00 35.66 2.77
3284 3775 5.353123 CACATGAACATGATGTGTGATCAGA 59.647 40.000 19.56 0.00 43.81 3.27
3290 3781 4.976224 ATCCACATGAACATGATGTGTG 57.024 40.909 19.56 16.53 46.25 3.82
3306 3797 1.490490 TGCAGACCATTCCCTATCCAC 59.510 52.381 0.00 0.00 0.00 4.02
3310 3801 2.301296 CGAGATGCAGACCATTCCCTAT 59.699 50.000 0.00 0.00 33.29 2.57
3331 3822 5.488341 TGTGAACTACTCCATTTCTAAGCC 58.512 41.667 0.00 0.00 0.00 4.35
3342 3833 4.537135 TCAACTGGATGTGAACTACTCC 57.463 45.455 0.00 0.00 0.00 3.85
3343 3834 7.361286 GGAAAATCAACTGGATGTGAACTACTC 60.361 40.741 0.00 0.00 36.02 2.59
3344 3835 6.431234 GGAAAATCAACTGGATGTGAACTACT 59.569 38.462 0.00 0.00 36.02 2.57
3345 3836 6.206634 TGGAAAATCAACTGGATGTGAACTAC 59.793 38.462 0.00 0.00 36.02 2.73
3346 3837 6.303054 TGGAAAATCAACTGGATGTGAACTA 58.697 36.000 0.00 0.00 36.02 2.24
3444 3941 3.066900 CGAGTAAGGGGAGTCACATACTG 59.933 52.174 13.17 4.57 39.07 2.74
3487 3984 2.474410 AAACCACGAAGACAGGGATC 57.526 50.000 0.00 0.00 0.00 3.36
3488 3985 2.951229 AAAACCACGAAGACAGGGAT 57.049 45.000 0.00 0.00 0.00 3.85
3489 3986 2.721425 AAAAACCACGAAGACAGGGA 57.279 45.000 0.00 0.00 0.00 4.20
3499 3996 9.139174 AGCATCTAAAATGAATTAAAAACCACG 57.861 29.630 0.00 0.00 0.00 4.94
3510 4186 8.114331 TGTTCAGACAAGCATCTAAAATGAAT 57.886 30.769 0.00 0.00 31.49 2.57
3534 4210 7.700505 TGAGCTGCATGAAGTAGATAAATTTG 58.299 34.615 1.73 0.00 30.56 2.32
3543 4219 3.257469 TCCTTGAGCTGCATGAAGTAG 57.743 47.619 1.73 0.00 0.00 2.57
3695 4371 5.774690 ACTCCAATAAACAGAAGAATGGCAA 59.225 36.000 0.00 0.00 0.00 4.52
3769 4445 4.926238 CCTTCCGCTCTACACATTATGATC 59.074 45.833 0.00 0.00 0.00 2.92
3847 4523 8.096414 ACATACTGGCAGCATAAAAAGAAAAAT 58.904 29.630 15.89 0.00 0.00 1.82
3850 4526 6.588719 ACATACTGGCAGCATAAAAAGAAA 57.411 33.333 15.89 0.00 0.00 2.52
3852 4528 8.210946 ACTATACATACTGGCAGCATAAAAAGA 58.789 33.333 15.89 0.00 0.00 2.52
3853 4529 8.285394 CACTATACATACTGGCAGCATAAAAAG 58.715 37.037 15.89 7.82 0.00 2.27
3858 4534 6.211384 ACATCACTATACATACTGGCAGCATA 59.789 38.462 15.89 0.05 0.00 3.14
3859 4535 5.012458 ACATCACTATACATACTGGCAGCAT 59.988 40.000 15.89 3.90 0.00 3.79
3876 4558 6.230472 TGTTTGTATTGTGCTCTACATCACT 58.770 36.000 0.00 0.00 39.48 3.41
3878 4560 6.463360 TCTGTTTGTATTGTGCTCTACATCA 58.537 36.000 0.00 0.00 39.48 3.07
3913 4595 8.565896 TGTCTCTAGCATTATGTTTGAACATT 57.434 30.769 13.94 0.00 46.95 2.71
3918 4600 8.830580 GCTAAATGTCTCTAGCATTATGTTTGA 58.169 33.333 0.00 0.00 40.27 2.69
3940 4622 3.333804 TGCATGTGATTCTGTTCGCTAA 58.666 40.909 0.00 0.00 0.00 3.09
3957 4639 9.979578 TTAGTTATTTTGTTTCATGTCTTGCAT 57.020 25.926 0.00 0.00 38.60 3.96
3958 4640 9.243637 GTTAGTTATTTTGTTTCATGTCTTGCA 57.756 29.630 0.00 0.00 0.00 4.08
3964 4646 8.407064 TGTTCGGTTAGTTATTTTGTTTCATGT 58.593 29.630 0.00 0.00 0.00 3.21
3980 4662 5.063564 GGAGTTGCTCTTATTGTTCGGTTAG 59.936 44.000 0.00 0.00 0.00 2.34
3981 4663 4.933400 GGAGTTGCTCTTATTGTTCGGTTA 59.067 41.667 0.00 0.00 0.00 2.85
3982 4664 3.751698 GGAGTTGCTCTTATTGTTCGGTT 59.248 43.478 0.00 0.00 0.00 4.44
3983 4665 3.244422 TGGAGTTGCTCTTATTGTTCGGT 60.244 43.478 0.00 0.00 0.00 4.69
3984 4666 3.334691 TGGAGTTGCTCTTATTGTTCGG 58.665 45.455 0.00 0.00 0.00 4.30
3985 4667 4.666655 CGTTGGAGTTGCTCTTATTGTTCG 60.667 45.833 0.00 0.00 0.00 3.95
3986 4668 4.712763 CGTTGGAGTTGCTCTTATTGTTC 58.287 43.478 0.00 0.00 0.00 3.18
3987 4669 3.058224 GCGTTGGAGTTGCTCTTATTGTT 60.058 43.478 0.00 0.00 0.00 2.83
3988 4670 2.484264 GCGTTGGAGTTGCTCTTATTGT 59.516 45.455 0.00 0.00 0.00 2.71
3989 4671 2.474526 CGCGTTGGAGTTGCTCTTATTG 60.475 50.000 0.00 0.00 0.00 1.90
3990 4672 1.732259 CGCGTTGGAGTTGCTCTTATT 59.268 47.619 0.00 0.00 0.00 1.40
3991 4673 1.359848 CGCGTTGGAGTTGCTCTTAT 58.640 50.000 0.00 0.00 0.00 1.73
4032 4714 0.725117 ATTACTTTTTCCGCGGCGAG 59.275 50.000 25.92 16.93 0.00 5.03
4065 4748 0.610785 ACGCGATTTGGGAATGGGTT 60.611 50.000 15.93 0.00 0.00 4.11
4093 4795 2.305343 CAAATTTGGGCTGGAAATGGGA 59.695 45.455 10.49 0.00 0.00 4.37
4347 5073 1.079336 GTGGCTAGGGTTGTCCGAC 60.079 63.158 0.00 0.00 41.52 4.79
4348 5074 2.288025 GGTGGCTAGGGTTGTCCGA 61.288 63.158 0.00 0.00 41.52 4.55
4349 5075 1.910580 ATGGTGGCTAGGGTTGTCCG 61.911 60.000 0.00 0.00 41.52 4.79
4350 5076 0.394352 CATGGTGGCTAGGGTTGTCC 60.394 60.000 0.00 0.00 0.00 4.02
4383 5113 1.667722 GCCTTGCCCTTGTTCTTGG 59.332 57.895 0.00 0.00 0.00 3.61
4544 5365 1.671054 GTTAAGGTGCTGCTGCCGA 60.671 57.895 13.47 0.00 38.71 5.54
4559 5398 2.023414 CTGATGCGTAGGCGGGGTTA 62.023 60.000 2.53 0.00 44.10 2.85
4599 5438 4.025401 GTGCTCCAACGCCAACCG 62.025 66.667 0.00 0.00 44.21 4.44
4604 5443 4.373116 TCCTCGTGCTCCAACGCC 62.373 66.667 0.00 0.00 43.26 5.68
4739 5579 0.179124 CCTCCTCTTCCTCGCTTTCG 60.179 60.000 0.00 0.00 0.00 3.46
4751 5591 4.753662 TGGTACGCCGCCTCCTCT 62.754 66.667 0.00 0.00 37.67 3.69
4761 5601 4.814294 CAGCCGGTCCTGGTACGC 62.814 72.222 1.90 4.09 0.00 4.42
4762 5602 3.352338 GACAGCCGGTCCTGGTACG 62.352 68.421 12.92 0.00 40.83 3.67
4763 5603 2.577593 GACAGCCGGTCCTGGTAC 59.422 66.667 12.92 1.94 40.83 3.34
4764 5604 3.066190 CGACAGCCGGTCCTGGTA 61.066 66.667 12.92 0.00 43.95 3.25
4781 5621 4.925861 GAGAGCGCCATGGCCTCC 62.926 72.222 33.72 25.81 38.38 4.30
4782 5622 4.925861 GGAGAGCGCCATGGCCTC 62.926 72.222 31.97 31.97 38.11 4.70


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

AutoCloner maintained by Alex Coulton.