Multiple sequence alignment - TraesCS3A01G070400

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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 TraesCS3A01G070400 chr3A 100.000 7624 0 0 1 7624 42372268 42364645 0.000000e+00 14079.0
1 TraesCS3A01G070400 chr3A 92.469 3346 185 37 3610 6935 42798870 42795572 0.000000e+00 4721.0
2 TraesCS3A01G070400 chr3A 82.843 2378 304 52 4357 6678 42381281 42383610 0.000000e+00 2036.0
3 TraesCS3A01G070400 chr3A 92.356 1112 43 21 3982 5087 43291009 43289934 0.000000e+00 1544.0
4 TraesCS3A01G070400 chr3A 92.176 1112 45 21 3982 5087 43874378 43873303 0.000000e+00 1533.0
5 TraesCS3A01G070400 chr3A 92.771 996 59 5 978 1963 42800991 42799999 0.000000e+00 1428.0
6 TraesCS3A01G070400 chr3A 91.609 1013 52 16 978 1963 43293362 43292356 0.000000e+00 1369.0
7 TraesCS3A01G070400 chr3A 90.634 1025 69 7 1971 2968 42799908 42798884 0.000000e+00 1336.0
8 TraesCS3A01G070400 chr3A 92.369 878 40 14 1113 1963 43876602 43875725 0.000000e+00 1225.0
9 TraesCS3A01G070400 chr3A 88.202 873 63 23 6033 6896 43871673 43870832 0.000000e+00 1005.0
10 TraesCS3A01G070400 chr3A 88.087 873 64 23 6033 6896 43288806 43287965 0.000000e+00 1000.0
11 TraesCS3A01G070400 chr3A 92.824 641 36 8 1965 2601 43292271 43291637 0.000000e+00 920.0
12 TraesCS3A01G070400 chr3A 92.824 641 36 8 1965 2601 43875640 43875006 0.000000e+00 920.0
13 TraesCS3A01G070400 chr3A 85.217 805 109 6 1157 1955 42378330 42379130 0.000000e+00 819.0
14 TraesCS3A01G070400 chr3A 91.952 584 44 3 2998 3579 740092163 740092745 0.000000e+00 815.0
15 TraesCS3A01G070400 chr3A 73.815 1646 351 56 4261 5869 51770901 51769299 5.130000e-161 579.0
16 TraesCS3A01G070400 chr3A 92.515 334 21 2 3580 3913 43874704 43874375 6.920000e-130 475.0
17 TraesCS3A01G070400 chr3A 92.216 334 22 2 3580 3913 43291335 43291006 3.220000e-128 470.0
18 TraesCS3A01G070400 chr3A 90.462 325 21 2 2673 2997 43291642 43291328 3.290000e-113 420.0
19 TraesCS3A01G070400 chr3A 90.462 325 21 2 2673 2997 43875011 43874697 3.290000e-113 420.0
20 TraesCS3A01G070400 chr3A 83.421 380 49 10 2216 2583 42379541 42379918 2.630000e-89 340.0
21 TraesCS3A01G070400 chr3A 91.284 218 18 1 1965 2182 42379249 42379465 5.780000e-76 296.0
22 TraesCS3A01G070400 chr3D 94.044 3207 122 29 3580 6779 30413128 30409984 0.000000e+00 4800.0
23 TraesCS3A01G070400 chr3D 83.537 2369 276 58 4357 6675 30676464 30674160 0.000000e+00 2109.0
24 TraesCS3A01G070400 chr3D 82.203 2388 299 66 4357 6691 30427933 30430247 0.000000e+00 1940.0
25 TraesCS3A01G070400 chr3D 95.141 885 38 3 1082 1963 30418542 30417660 0.000000e+00 1391.0
26 TraesCS3A01G070400 chr3D 97.270 806 15 1 6826 7624 30409971 30409166 0.000000e+00 1360.0
27 TraesCS3A01G070400 chr3D 90.523 1013 63 16 978 1963 30415164 30414158 0.000000e+00 1308.0
28 TraesCS3A01G070400 chr3D 92.980 641 35 8 1965 2601 30414073 30413439 0.000000e+00 926.0
29 TraesCS3A01G070400 chr3D 83.828 977 134 12 986 1955 30679364 30678405 0.000000e+00 907.0
30 TraesCS3A01G070400 chr3D 88.868 521 52 3 82 596 586930657 586931177 3.000000e-178 636.0
31 TraesCS3A01G070400 chr3D 73.876 1646 350 57 4261 5869 31435054 31436656 1.100000e-162 584.0
32 TraesCS3A01G070400 chr3D 92.923 325 22 1 2673 2997 30413444 30413121 8.950000e-129 472.0
33 TraesCS3A01G070400 chr3D 83.592 451 59 11 2216 2654 30425399 30425846 7.120000e-110 409.0
34 TraesCS3A01G070400 chr3D 92.920 226 15 1 865 1089 30419046 30418821 2.050000e-85 327.0
35 TraesCS3A01G070400 chr3D 90.367 218 20 1 1965 2182 30678286 30678070 1.250000e-72 285.0
36 TraesCS3A01G070400 chr3D 84.932 219 7 3 595 812 30419245 30419052 1.680000e-46 198.0
37 TraesCS3A01G070400 chr3D 75.347 288 40 23 603 882 30423557 30423821 8.090000e-20 110.0
38 TraesCS3A01G070400 chr3D 86.111 72 5 2 681 752 26279261 26279195 1.060000e-08 73.1
39 TraesCS3A01G070400 chr3B 91.996 3261 147 44 3580 6792 53219833 53216639 0.000000e+00 4471.0
40 TraesCS3A01G070400 chr3B 87.347 1557 172 16 4357 5897 53356229 53354682 0.000000e+00 1760.0
41 TraesCS3A01G070400 chr3B 92.308 1014 47 16 980 1963 53223197 53222185 0.000000e+00 1411.0
42 TraesCS3A01G070400 chr3B 91.049 1039 76 11 1965 2997 53220853 53219826 0.000000e+00 1387.0
43 TraesCS3A01G070400 chr3B 89.133 773 44 9 6811 7544 53216593 53215822 0.000000e+00 926.0
44 TraesCS3A01G070400 chr3B 86.296 810 102 7 1160 1963 53358964 53358158 0.000000e+00 872.0
45 TraesCS3A01G070400 chr3B 91.252 583 49 1 2998 3580 730402323 730401743 0.000000e+00 793.0
46 TraesCS3A01G070400 chr3B 90.566 583 53 1 2998 3580 730384411 730383831 0.000000e+00 771.0
47 TraesCS3A01G070400 chr3B 89.908 218 21 1 1965 2182 53358048 53357832 5.830000e-71 279.0
48 TraesCS3A01G070400 chr3B 97.500 40 1 0 7585 7624 53215821 53215782 1.370000e-07 69.4
49 TraesCS3A01G070400 chrUn 96.429 1372 33 3 4371 5737 406952165 406950805 0.000000e+00 2248.0
50 TraesCS3A01G070400 chrUn 96.429 1372 33 3 4371 5737 406953633 406952273 0.000000e+00 2248.0
51 TraesCS3A01G070400 chrUn 91.609 1013 53 15 978 1963 332581877 332582884 0.000000e+00 1371.0
52 TraesCS3A01G070400 chrUn 96.849 603 14 1 5140 5737 472518170 472518772 0.000000e+00 1003.0
53 TraesCS3A01G070400 chrUn 92.947 638 35 8 1965 2598 332582969 332583600 0.000000e+00 920.0
54 TraesCS3A01G070400 chrUn 90.462 325 21 2 2673 2997 332583598 332583912 3.290000e-113 420.0
55 TraesCS3A01G070400 chrUn 95.161 124 6 0 3580 3703 332583905 332584028 6.040000e-46 196.0
56 TraesCS3A01G070400 chr2B 98.797 582 7 0 2998 3579 757275533 757274952 0.000000e+00 1037.0
57 TraesCS3A01G070400 chr2B 94.391 517 23 1 80 596 682234379 682233869 0.000000e+00 789.0
58 TraesCS3A01G070400 chr6A 92.845 587 40 2 2997 3582 48087840 48087255 0.000000e+00 850.0
59 TraesCS3A01G070400 chr6A 85.333 75 6 5 3797 3867 85574233 85574306 1.060000e-08 73.1
60 TraesCS3A01G070400 chr1B 92.967 583 41 0 2998 3580 30737759 30737177 0.000000e+00 850.0
61 TraesCS3A01G070400 chr5A 92.612 582 41 1 2998 3579 475516005 475516584 0.000000e+00 835.0
62 TraesCS3A01G070400 chr5A 87.472 447 46 7 158 596 580397085 580396641 2.450000e-139 507.0
63 TraesCS3A01G070400 chr7B 92.440 582 41 3 2998 3579 494490254 494490832 0.000000e+00 828.0
64 TraesCS3A01G070400 chr7B 84.000 75 12 0 7515 7589 728288598 728288672 1.060000e-08 73.1
65 TraesCS3A01G070400 chr5B 91.695 590 45 2 2998 3583 127537318 127536729 0.000000e+00 815.0
66 TraesCS3A01G070400 chr5B 84.783 138 18 3 5713 5849 26851524 26851389 1.330000e-27 135.0
67 TraesCS3A01G070400 chr7D 89.504 524 49 4 79 596 180752819 180753342 0.000000e+00 658.0
68 TraesCS3A01G070400 chr7D 89.313 524 50 3 79 596 113888868 113888345 0.000000e+00 652.0
69 TraesCS3A01G070400 chr7D 87.546 538 48 11 78 596 561690422 561690959 8.460000e-169 604.0
70 TraesCS3A01G070400 chr7D 84.000 75 12 0 7515 7589 627315502 627315576 1.060000e-08 73.1
71 TraesCS3A01G070400 chr2D 87.896 537 46 13 79 596 37224396 37223860 1.410000e-171 614.0
72 TraesCS3A01G070400 chr2D 86.454 502 50 11 83 566 612890399 612889898 1.130000e-147 534.0
73 TraesCS3A01G070400 chr5D 87.664 535 48 13 80 596 100858981 100858447 2.350000e-169 606.0
74 TraesCS3A01G070400 chr5D 87.290 535 50 10 80 596 205591804 205592338 5.090000e-166 595.0
75 TraesCS3A01G070400 chr2A 87.452 526 57 6 79 596 176559616 176560140 1.420000e-166 597.0
76 TraesCS3A01G070400 chr2A 86.957 69 8 1 3786 3853 27627320 27627388 8.200000e-10 76.8
77 TraesCS3A01G070400 chr7A 84.000 75 12 0 7515 7589 723256124 723256198 1.060000e-08 73.1
78 TraesCS3A01G070400 chr4D 84.932 73 8 3 3797 3867 97759389 97759318 3.820000e-08 71.3
79 TraesCS3A01G070400 chr4B 84.932 73 8 3 3797 3867 139534593 139534664 3.820000e-08 71.3


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 TraesCS3A01G070400 chr3A 42364645 42372268 7623 True 14079.000000 14079 100.000000 1 7624 1 chr3A.!!$R1 7623
1 TraesCS3A01G070400 chr3A 42795572 42800991 5419 True 2495.000000 4721 91.958000 978 6935 3 chr3A.!!$R3 5957
2 TraesCS3A01G070400 chr3A 43287965 43293362 5397 True 953.833333 1544 91.259000 978 6896 6 chr3A.!!$R4 5918
3 TraesCS3A01G070400 chr3A 43870832 43876602 5770 True 929.666667 1533 91.424667 1113 6896 6 chr3A.!!$R5 5783
4 TraesCS3A01G070400 chr3A 42378330 42383610 5280 False 872.750000 2036 85.691250 1157 6678 4 chr3A.!!$F2 5521
5 TraesCS3A01G070400 chr3A 740092163 740092745 582 False 815.000000 815 91.952000 2998 3579 1 chr3A.!!$F1 581
6 TraesCS3A01G070400 chr3A 51769299 51770901 1602 True 579.000000 579 73.815000 4261 5869 1 chr3A.!!$R2 1608
7 TraesCS3A01G070400 chr3D 30409166 30419245 10079 True 1347.750000 4800 92.591625 595 7624 8 chr3D.!!$R2 7029
8 TraesCS3A01G070400 chr3D 30674160 30679364 5204 True 1100.333333 2109 85.910667 986 6675 3 chr3D.!!$R3 5689
9 TraesCS3A01G070400 chr3D 30423557 30430247 6690 False 819.666667 1940 80.380667 603 6691 3 chr3D.!!$F3 6088
10 TraesCS3A01G070400 chr3D 586930657 586931177 520 False 636.000000 636 88.868000 82 596 1 chr3D.!!$F2 514
11 TraesCS3A01G070400 chr3D 31435054 31436656 1602 False 584.000000 584 73.876000 4261 5869 1 chr3D.!!$F1 1608
12 TraesCS3A01G070400 chr3B 53215782 53223197 7415 True 1652.880000 4471 92.397200 980 7624 5 chr3B.!!$R3 6644
13 TraesCS3A01G070400 chr3B 53354682 53358964 4282 True 970.333333 1760 87.850333 1160 5897 3 chr3B.!!$R4 4737
14 TraesCS3A01G070400 chr3B 730401743 730402323 580 True 793.000000 793 91.252000 2998 3580 1 chr3B.!!$R2 582
15 TraesCS3A01G070400 chr3B 730383831 730384411 580 True 771.000000 771 90.566000 2998 3580 1 chr3B.!!$R1 582
16 TraesCS3A01G070400 chrUn 406950805 406953633 2828 True 2248.000000 2248 96.429000 4371 5737 2 chrUn.!!$R1 1366
17 TraesCS3A01G070400 chrUn 472518170 472518772 602 False 1003.000000 1003 96.849000 5140 5737 1 chrUn.!!$F1 597
18 TraesCS3A01G070400 chrUn 332581877 332584028 2151 False 726.750000 1371 92.544750 978 3703 4 chrUn.!!$F2 2725
19 TraesCS3A01G070400 chr2B 757274952 757275533 581 True 1037.000000 1037 98.797000 2998 3579 1 chr2B.!!$R2 581
20 TraesCS3A01G070400 chr2B 682233869 682234379 510 True 789.000000 789 94.391000 80 596 1 chr2B.!!$R1 516
21 TraesCS3A01G070400 chr6A 48087255 48087840 585 True 850.000000 850 92.845000 2997 3582 1 chr6A.!!$R1 585
22 TraesCS3A01G070400 chr1B 30737177 30737759 582 True 850.000000 850 92.967000 2998 3580 1 chr1B.!!$R1 582
23 TraesCS3A01G070400 chr5A 475516005 475516584 579 False 835.000000 835 92.612000 2998 3579 1 chr5A.!!$F1 581
24 TraesCS3A01G070400 chr7B 494490254 494490832 578 False 828.000000 828 92.440000 2998 3579 1 chr7B.!!$F1 581
25 TraesCS3A01G070400 chr5B 127536729 127537318 589 True 815.000000 815 91.695000 2998 3583 1 chr5B.!!$R2 585
26 TraesCS3A01G070400 chr7D 180752819 180753342 523 False 658.000000 658 89.504000 79 596 1 chr7D.!!$F1 517
27 TraesCS3A01G070400 chr7D 113888345 113888868 523 True 652.000000 652 89.313000 79 596 1 chr7D.!!$R1 517
28 TraesCS3A01G070400 chr7D 561690422 561690959 537 False 604.000000 604 87.546000 78 596 1 chr7D.!!$F2 518
29 TraesCS3A01G070400 chr2D 37223860 37224396 536 True 614.000000 614 87.896000 79 596 1 chr2D.!!$R1 517
30 TraesCS3A01G070400 chr2D 612889898 612890399 501 True 534.000000 534 86.454000 83 566 1 chr2D.!!$R2 483
31 TraesCS3A01G070400 chr5D 100858447 100858981 534 True 606.000000 606 87.664000 80 596 1 chr5D.!!$R1 516
32 TraesCS3A01G070400 chr5D 205591804 205592338 534 False 595.000000 595 87.290000 80 596 1 chr5D.!!$F1 516
33 TraesCS3A01G070400 chr2A 176559616 176560140 524 False 597.000000 597 87.452000 79 596 1 chr2A.!!$F2 517

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
380 402 0.036010 ATCAGGTCGGCCACTTCAAG 60.036 55.000 9.71 0.00 37.19 3.02 F
881 912 0.321653 CACCCTCCCCTCTTTTGTCG 60.322 60.000 0.00 0.00 0.00 4.35 F
2716 8334 0.694771 AGGCCATCTGTTCTGCTTCA 59.305 50.000 5.01 0.00 0.00 3.02 F
2840 8495 0.252197 AGCCGAGGTTTGATGGTACC 59.748 55.000 4.43 4.43 34.54 3.34 F
3639 9362 0.472044 TCTTGCAGTTGCCCTGTACA 59.528 50.000 1.06 0.00 43.55 2.90 F
3784 10374 0.031994 ACAACACGCATGGGAAAAGC 59.968 50.000 17.76 0.00 0.00 3.51 F
4052 10645 1.022735 GCATTCTGCTGCAGTGCTAT 58.977 50.000 27.93 16.38 40.96 2.97 F
5509 13647 0.106708 GGGCGCATCTACCAATCAGA 59.893 55.000 10.83 0.00 0.00 3.27 F
5952 14118 3.442977 TGAGGAAGTTTAGTAGCCTCGAC 59.557 47.826 0.00 0.00 46.29 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2229 7615 0.960286 CATGTGTGACCCATGTGCAA 59.040 50.000 0.00 0.0 35.94 4.08 R
2751 8369 1.550524 TCTACTGATGTGTGGTCAGCC 59.449 52.381 3.23 0.0 45.42 4.85 R
3639 9362 0.036306 GACACCCGAGTCCCAATTGT 59.964 55.000 4.43 0.0 32.36 2.71 R
3771 10361 0.602562 TGGAAAGCTTTTCCCATGCG 59.397 50.000 15.05 0.0 37.79 4.73 R
4759 12878 1.856920 GGGAGGGGATAACCATTGGAA 59.143 52.381 10.37 0.0 42.91 3.53 R
5509 13647 3.007831 CCCACTTGTGGCCATTAATTTGT 59.992 43.478 9.72 0.0 0.00 2.83 R
6031 14853 5.293324 TCGCACCAGTGTCATATGTTATTTC 59.707 40.000 1.90 0.0 0.00 2.17 R
6602 15484 0.387239 AGAATTGTTTTCGCTGCCGC 60.387 50.000 0.00 0.0 0.00 6.53 R
6803 15690 0.690762 TCTCTTAACGGCCCTGCTTT 59.309 50.000 0.00 0.0 0.00 3.51 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
21 22 4.220533 GCCACACGAATCGTATAGTAGT 57.779 45.455 8.35 0.00 38.32 2.73
22 23 3.973135 GCCACACGAATCGTATAGTAGTG 59.027 47.826 8.35 11.08 38.32 2.74
23 24 4.497006 GCCACACGAATCGTATAGTAGTGT 60.497 45.833 8.35 0.00 38.32 3.55
24 25 5.277490 GCCACACGAATCGTATAGTAGTGTA 60.277 44.000 8.35 0.00 38.32 2.90
25 26 6.132056 CCACACGAATCGTATAGTAGTGTAC 58.868 44.000 8.35 0.00 38.32 2.90
26 27 6.238184 CCACACGAATCGTATAGTAGTGTACA 60.238 42.308 8.35 0.00 38.32 2.90
27 28 7.182089 CACACGAATCGTATAGTAGTGTACAA 58.818 38.462 8.35 0.00 38.32 2.41
28 29 7.693536 CACACGAATCGTATAGTAGTGTACAAA 59.306 37.037 8.35 0.00 38.32 2.83
29 30 8.236586 ACACGAATCGTATAGTAGTGTACAAAA 58.763 33.333 8.35 0.00 38.32 2.44
30 31 9.064804 CACGAATCGTATAGTAGTGTACAAAAA 57.935 33.333 8.35 0.00 38.32 1.94
31 32 9.793252 ACGAATCGTATAGTAGTGTACAAAAAT 57.207 29.630 6.47 0.00 38.73 1.82
56 57 8.712285 TCTGTAAATCTAACAAAGGTAATCCG 57.288 34.615 0.00 0.00 39.05 4.18
57 58 7.767198 TCTGTAAATCTAACAAAGGTAATCCGG 59.233 37.037 0.00 0.00 39.05 5.14
58 59 5.830000 AAATCTAACAAAGGTAATCCGGC 57.170 39.130 0.00 0.00 39.05 6.13
59 60 4.772886 ATCTAACAAAGGTAATCCGGCT 57.227 40.909 0.00 0.00 39.05 5.52
60 61 4.133013 TCTAACAAAGGTAATCCGGCTC 57.867 45.455 0.00 0.00 39.05 4.70
61 62 3.773119 TCTAACAAAGGTAATCCGGCTCT 59.227 43.478 0.00 0.00 39.05 4.09
62 63 2.693267 ACAAAGGTAATCCGGCTCTC 57.307 50.000 0.00 0.00 39.05 3.20
63 64 1.209747 ACAAAGGTAATCCGGCTCTCC 59.790 52.381 0.00 0.00 39.05 3.71
64 65 0.837940 AAAGGTAATCCGGCTCTCCC 59.162 55.000 0.00 0.00 39.05 4.30
65 66 1.054978 AAGGTAATCCGGCTCTCCCC 61.055 60.000 0.00 0.00 39.05 4.81
66 67 2.517798 GGTAATCCGGCTCTCCCCC 61.518 68.421 0.00 0.00 0.00 5.40
67 68 1.459730 GTAATCCGGCTCTCCCCCT 60.460 63.158 0.00 0.00 0.00 4.79
68 69 1.152312 TAATCCGGCTCTCCCCCTC 60.152 63.158 0.00 0.00 0.00 4.30
69 70 2.674672 TAATCCGGCTCTCCCCCTCC 62.675 65.000 0.00 0.00 0.00 4.30
75 76 3.077556 CTCTCCCCCTCCACGGTG 61.078 72.222 0.00 0.00 0.00 4.94
76 77 3.596799 TCTCCCCCTCCACGGTGA 61.597 66.667 10.28 0.00 0.00 4.02
77 78 2.606519 CTCCCCCTCCACGGTGAA 60.607 66.667 10.28 0.00 0.00 3.18
113 114 9.658799 TGAAAGAAAAGGTAGATCATGTTCTAG 57.341 33.333 12.79 0.00 0.00 2.43
234 237 3.254411 GCCTGAGAAGAAAAACAAGGGAG 59.746 47.826 0.00 0.00 0.00 4.30
250 254 0.694783 GGAGGGTAGGAAGGAAGGGG 60.695 65.000 0.00 0.00 0.00 4.79
257 261 3.054287 GGTAGGAAGGAAGGGGAGAAAAG 60.054 52.174 0.00 0.00 0.00 2.27
258 262 1.996291 AGGAAGGAAGGGGAGAAAAGG 59.004 52.381 0.00 0.00 0.00 3.11
260 264 2.378886 GGAAGGAAGGGGAGAAAAGGAA 59.621 50.000 0.00 0.00 0.00 3.36
261 265 3.181422 GGAAGGAAGGGGAGAAAAGGAAA 60.181 47.826 0.00 0.00 0.00 3.13
310 332 3.956199 CACCATTACATCAGCCCAAGAAT 59.044 43.478 0.00 0.00 0.00 2.40
336 358 1.001393 TTCCCTGACATTTCCCGCC 60.001 57.895 0.00 0.00 0.00 6.13
375 397 1.194781 ACTTGATCAGGTCGGCCACT 61.195 55.000 9.71 0.00 37.19 4.00
380 402 0.036010 ATCAGGTCGGCCACTTCAAG 60.036 55.000 9.71 0.00 37.19 3.02
384 406 0.955919 GGTCGGCCACTTCAAGAAGG 60.956 60.000 13.83 0.00 42.53 3.46
391 413 2.508526 CCACTTCAAGAAGGACCCTTG 58.491 52.381 13.83 5.30 42.53 3.61
441 463 2.125552 TCGTTCCGAGCATGCCAG 60.126 61.111 15.66 8.66 0.00 4.85
495 517 0.917533 AGAGATTGCCATGTGCCTCT 59.082 50.000 4.07 5.91 40.16 3.69
497 519 1.404391 GAGATTGCCATGTGCCTCTTG 59.596 52.381 4.07 0.00 40.16 3.02
546 568 4.564041 CTGTAGACTCACATGAAACTGCT 58.436 43.478 0.00 0.00 0.00 4.24
614 636 2.080693 TCCACGGTGAAAATTGATCGG 58.919 47.619 10.28 0.00 0.00 4.18
619 641 1.202143 GGTGAAAATTGATCGGCGTCC 60.202 52.381 6.85 0.00 0.00 4.79
654 677 0.811281 CCGTTCCATCTTTTCCTGCC 59.189 55.000 0.00 0.00 0.00 4.85
814 845 0.890683 CTGCGATTTCTGGGGCTTTT 59.109 50.000 0.00 0.00 0.00 2.27
815 846 0.602562 TGCGATTTCTGGGGCTTTTG 59.397 50.000 0.00 0.00 0.00 2.44
816 847 0.887933 GCGATTTCTGGGGCTTTTGA 59.112 50.000 0.00 0.00 0.00 2.69
818 849 2.480244 GCGATTTCTGGGGCTTTTGATC 60.480 50.000 0.00 0.00 0.00 2.92
821 852 4.082026 CGATTTCTGGGGCTTTTGATCTTT 60.082 41.667 0.00 0.00 0.00 2.52
822 853 4.605640 TTTCTGGGGCTTTTGATCTTTG 57.394 40.909 0.00 0.00 0.00 2.77
863 894 1.281867 CAGTGATTAGCTGAACCCCCA 59.718 52.381 0.00 0.00 36.12 4.96
881 912 0.321653 CACCCTCCCCTCTTTTGTCG 60.322 60.000 0.00 0.00 0.00 4.35
887 918 1.003118 TCCCCTCTTTTGTCGTGATGG 59.997 52.381 0.00 0.00 0.00 3.51
910 942 1.379044 ATTTCCTCCCTTGCGGCTG 60.379 57.895 0.00 0.00 0.00 4.85
922 954 1.512734 GCGGCTGAACGATTTGCTG 60.513 57.895 0.00 0.00 35.47 4.41
947 979 1.132262 CCAATGGCGTTCGCAGTTTAT 59.868 47.619 18.46 2.69 0.00 1.40
952 984 3.462982 TGGCGTTCGCAGTTTATCATAT 58.537 40.909 18.46 0.00 0.00 1.78
995 1102 1.839994 CCTATTTCCACTCCAGGCTGA 59.160 52.381 17.94 0.95 0.00 4.26
996 1103 2.420687 CCTATTTCCACTCCAGGCTGAC 60.421 54.545 17.94 0.00 0.00 3.51
1050 1157 5.876357 AGCCAGACCAAGATACAAAAAGTA 58.124 37.500 0.00 0.00 37.06 2.24
1184 1593 3.447918 TCCCTAACTAGGAAATTCGCG 57.552 47.619 0.00 0.00 46.63 5.87
1247 1656 2.030027 TCTGGTCAAGGTGTCTGGAT 57.970 50.000 0.00 0.00 0.00 3.41
1264 1673 4.347876 TCTGGATGGAACTCAGTGAAGAAA 59.652 41.667 0.00 0.00 0.00 2.52
1498 1923 9.219603 TGACTTCATTAAGTTTGGTTAGATCTG 57.780 33.333 5.18 0.00 46.09 2.90
1979 7321 3.515602 AAAACTGTCTCAGCATCCCTT 57.484 42.857 0.00 0.00 34.37 3.95
2093 7435 7.094205 GGGATGAACTTTTATGCTGAGAAAGAA 60.094 37.037 2.45 0.00 35.09 2.52
2224 7610 6.406692 TGTCCTCCATACTGTCTTATTAGC 57.593 41.667 0.00 0.00 0.00 3.09
2229 7615 8.548877 TCCTCCATACTGTCTTATTAGCTTTTT 58.451 33.333 0.00 0.00 0.00 1.94
2257 7643 2.290260 TGGGTCACACATGCTTAGGAAG 60.290 50.000 0.00 0.00 0.00 3.46
2289 7675 6.121776 TGGTGGAAAGCTTAATCAAGAGTA 57.878 37.500 0.00 0.00 33.20 2.59
2345 7757 4.749245 ACTGCAGCTAACAACACATTAC 57.251 40.909 15.27 0.00 0.00 1.89
2377 7797 6.100004 TCTTGCGTTGTTGGAAAATTTGTTA 58.900 32.000 0.00 0.00 0.00 2.41
2431 7852 7.725251 TCTAAAAGAATGTGCAGGATTTTTGT 58.275 30.769 0.00 0.00 0.00 2.83
2508 7929 6.906659 AGAACAGTTAAAGCATGATCACAAG 58.093 36.000 0.00 0.00 0.00 3.16
2539 7960 2.425312 AGTGAGGAGTCTAACATGCTCG 59.575 50.000 0.00 0.00 36.75 5.03
2552 7973 9.627395 GTCTAACATGCTCGATTACTGTAATAT 57.373 33.333 12.73 0.63 0.00 1.28
2565 7986 9.197694 GATTACTGTAATATTGAGCGAATGAGT 57.802 33.333 12.73 0.00 0.00 3.41
2577 7998 5.977725 TGAGCGAATGAGTACTATTTAGCAC 59.022 40.000 18.26 14.36 0.00 4.40
2630 8051 5.876460 GGCCTGATTTGCAAATAAACTTGAT 59.124 36.000 24.15 0.00 0.00 2.57
2643 8066 8.644619 CAAATAAACTTGATTGAGCACATTCTG 58.355 33.333 7.40 3.86 0.00 3.02
2648 8071 5.180868 ACTTGATTGAGCACATTCTGTTCTC 59.819 40.000 7.40 0.77 40.31 2.87
2659 8277 3.520290 TTCTGTTCTCGATAACGGCAT 57.480 42.857 15.66 0.00 40.21 4.40
2675 8293 6.764308 AACGGCATACAACTAGTCTAACTA 57.236 37.500 0.00 0.00 0.00 2.24
2694 8312 8.383175 TCTAACTAAAACATTTCCTGGATGACT 58.617 33.333 4.36 0.00 0.00 3.41
2710 8328 4.530161 GGATGACTATAGGCCATCTGTTCT 59.470 45.833 24.27 2.47 37.44 3.01
2716 8334 0.694771 AGGCCATCTGTTCTGCTTCA 59.305 50.000 5.01 0.00 0.00 3.02
2726 8344 3.567530 TGTTCTGCTTCATGCGAATTTG 58.432 40.909 0.00 0.00 46.63 2.32
2840 8495 0.252197 AGCCGAGGTTTGATGGTACC 59.748 55.000 4.43 4.43 34.54 3.34
2889 8565 6.534793 AGTTTCTGAAATGCGTTGTTTTGATT 59.465 30.769 6.06 0.00 0.00 2.57
2915 8624 8.856153 TTTTTGTAATACTTGCATCTGGTAGA 57.144 30.769 0.00 0.00 0.00 2.59
3117 8830 8.949177 GTAAGTATCCCTTGGTTTTTCGATTTA 58.051 33.333 0.00 0.00 34.46 1.40
3323 9038 3.489047 GCAAGAGAGAATCGATGCACTAC 59.511 47.826 6.08 0.00 42.08 2.73
3639 9362 0.472044 TCTTGCAGTTGCCCTGTACA 59.528 50.000 1.06 0.00 43.55 2.90
3652 9375 2.346803 CCTGTACACAATTGGGACTCG 58.653 52.381 16.31 0.00 0.00 4.18
3784 10374 0.031994 ACAACACGCATGGGAAAAGC 59.968 50.000 17.76 0.00 0.00 3.51
3792 10382 1.338105 GCATGGGAAAAGCTTTCCACC 60.338 52.381 18.96 17.30 43.45 4.61
3795 10385 2.247358 TGGGAAAAGCTTTCCACCATC 58.753 47.619 19.56 10.46 35.01 3.51
3799 10389 4.711846 GGGAAAAGCTTTCCACCATCTTAT 59.288 41.667 22.39 2.71 40.32 1.73
3804 10394 5.316158 AGCTTTCCACCATCTTATGCTAT 57.684 39.130 0.00 0.00 0.00 2.97
3990 10580 8.377799 GGTATCCATGCATACATATCATCCATA 58.622 37.037 9.00 0.00 33.67 2.74
4024 10615 6.982852 TGTGGATTTCTCTATTACTCCGATC 58.017 40.000 0.00 0.00 0.00 3.69
4027 10618 6.096695 GGATTTCTCTATTACTCCGATCAGC 58.903 44.000 0.00 0.00 0.00 4.26
4047 10640 1.938577 CTTATCGCATTCTGCTGCAGT 59.061 47.619 27.24 8.26 42.25 4.40
4052 10645 1.022735 GCATTCTGCTGCAGTGCTAT 58.977 50.000 27.93 16.38 40.96 2.97
4078 10671 8.859236 AAATAAGAAAGGACCTGGTAGTAAAC 57.141 34.615 0.00 0.00 0.00 2.01
4145 10745 7.394359 TGAGAAAAGCACCTTAAGATTGCTAAT 59.606 33.333 23.88 17.81 45.93 1.73
4146 10746 7.766283 AGAAAAGCACCTTAAGATTGCTAATC 58.234 34.615 23.88 22.47 45.93 1.75
4234 10834 7.865706 ACAATCATTTGTAGAATCTGGGTAC 57.134 36.000 0.00 0.00 44.22 3.34
4235 10835 7.402054 ACAATCATTTGTAGAATCTGGGTACA 58.598 34.615 0.00 0.00 44.22 2.90
4236 10836 8.055181 ACAATCATTTGTAGAATCTGGGTACAT 58.945 33.333 0.00 0.00 44.22 2.29
4237 10837 9.559732 CAATCATTTGTAGAATCTGGGTACATA 57.440 33.333 0.00 0.00 0.00 2.29
4238 10838 9.561069 AATCATTTGTAGAATCTGGGTACATAC 57.439 33.333 0.00 0.00 0.00 2.39
4239 10839 8.319057 TCATTTGTAGAATCTGGGTACATACT 57.681 34.615 0.00 0.00 0.00 2.12
4240 10840 8.768397 TCATTTGTAGAATCTGGGTACATACTT 58.232 33.333 0.00 0.00 0.00 2.24
4243 10843 8.834004 TTGTAGAATCTGGGTACATACTTAGT 57.166 34.615 0.00 0.00 0.00 2.24
4244 10844 8.234136 TGTAGAATCTGGGTACATACTTAGTG 57.766 38.462 0.00 0.00 0.00 2.74
4245 10845 7.837689 TGTAGAATCTGGGTACATACTTAGTGT 59.162 37.037 0.00 0.00 0.00 3.55
4246 10846 7.113658 AGAATCTGGGTACATACTTAGTGTG 57.886 40.000 7.56 7.56 0.00 3.82
4247 10847 6.668283 AGAATCTGGGTACATACTTAGTGTGT 59.332 38.462 18.08 18.08 40.68 3.72
4248 10848 6.869206 ATCTGGGTACATACTTAGTGTGTT 57.131 37.500 19.09 5.03 38.68 3.32
4249 10849 6.675413 TCTGGGTACATACTTAGTGTGTTT 57.325 37.500 19.09 0.00 38.68 2.83
4250 10850 7.069877 TCTGGGTACATACTTAGTGTGTTTT 57.930 36.000 19.09 0.00 38.68 2.43
4251 10851 7.511268 TCTGGGTACATACTTAGTGTGTTTTT 58.489 34.615 19.09 0.00 38.68 1.94
4520 12634 2.488891 CCAGAATGTCAACCAGGTTGGA 60.489 50.000 28.83 17.70 42.99 3.53
4535 12654 6.158598 CCAGGTTGGATCACTTTTAATGTTG 58.841 40.000 0.00 0.00 40.96 3.33
4640 12759 3.690685 TTATGTTCTGGGCGGCCGG 62.691 63.158 30.31 30.31 0.00 6.13
4720 12839 6.591935 TGGGGTCATCAATCACTTAACTATC 58.408 40.000 0.00 0.00 0.00 2.08
5016 13136 1.130955 GTGTTGTTGCATTGGCTTCG 58.869 50.000 0.00 0.00 41.91 3.79
5203 13341 3.949113 TCGGCAAGTTTGGTTAGAACTTT 59.051 39.130 0.00 0.00 42.90 2.66
5254 13392 6.723131 CCTTAAGGTTGTTACTCTGCTAAC 57.277 41.667 13.83 0.00 0.00 2.34
5387 13525 6.241207 ACATTGCAACATTACAGTCTACAC 57.759 37.500 0.00 0.00 0.00 2.90
5496 13634 1.075050 AGGTAGTAGCTATAGGGCGCA 59.925 52.381 10.83 0.00 37.29 6.09
5509 13647 0.106708 GGGCGCATCTACCAATCAGA 59.893 55.000 10.83 0.00 0.00 3.27
5952 14118 3.442977 TGAGGAAGTTTAGTAGCCTCGAC 59.557 47.826 0.00 0.00 46.29 4.20
6031 14853 7.543947 TGAATAGAACTGTTGTGCATATGAG 57.456 36.000 6.97 0.00 0.00 2.90
6052 14874 7.848223 TGAGAAATAACATATGACACTGGTG 57.152 36.000 10.38 0.00 0.00 4.17
6086 14909 3.660111 GTGGTTGTGGCCGACAGC 61.660 66.667 11.79 11.79 42.60 4.40
6095 14918 3.873883 GCCGACAGCTGAGCATGC 61.874 66.667 23.35 10.51 38.99 4.06
6147 14979 9.078990 TGGAAGTATTGTATCGTATCTCTCATT 57.921 33.333 0.00 0.00 0.00 2.57
6202 15035 6.943899 ATATGGGTTGGTTTTGGTTGTTAT 57.056 33.333 0.00 0.00 0.00 1.89
6604 15486 9.208022 TGTGGAAGAAGAAATTATATATCAGCG 57.792 33.333 0.00 0.00 0.00 5.18
6605 15487 8.660373 GTGGAAGAAGAAATTATATATCAGCGG 58.340 37.037 0.00 0.00 0.00 5.52
6606 15488 7.334421 TGGAAGAAGAAATTATATATCAGCGGC 59.666 37.037 0.00 0.00 0.00 6.53
6607 15489 7.334421 GGAAGAAGAAATTATATATCAGCGGCA 59.666 37.037 1.45 0.00 0.00 5.69
6751 15637 4.294970 ACCCCTAATCTGAACCCTGAAATT 59.705 41.667 0.00 0.00 0.00 1.82
6752 15638 4.889995 CCCCTAATCTGAACCCTGAAATTC 59.110 45.833 0.00 0.00 0.00 2.17
6753 15639 5.340360 CCCCTAATCTGAACCCTGAAATTCT 60.340 44.000 0.00 0.00 0.00 2.40
6773 15659 7.636150 ATTCTACTAGCTTAAGAACGTACCA 57.364 36.000 6.67 0.00 32.38 3.25
6803 15690 3.958798 GTGATGGACCTGTACTAAGGCTA 59.041 47.826 0.00 0.00 41.46 3.93
6807 15694 3.197116 TGGACCTGTACTAAGGCTAAAGC 59.803 47.826 0.00 0.00 41.46 3.51
6836 15751 0.252742 AAGAGACGGGTTGGGGAGAT 60.253 55.000 0.00 0.00 0.00 2.75
6880 15796 3.207778 AGTTTGTTTGCAGCTACGGTTA 58.792 40.909 0.00 0.00 0.00 2.85
6882 15798 4.083484 AGTTTGTTTGCAGCTACGGTTATC 60.083 41.667 0.00 0.00 0.00 1.75
7105 16029 7.452880 TCAGGATGAACAGTAAATCCAAAAG 57.547 36.000 14.23 4.53 45.97 2.27
7191 16115 5.028549 AGCAGAAATGATATTCGTGGAGT 57.971 39.130 0.00 0.00 34.46 3.85
7397 16348 1.033746 CCAAGCACGCCATCTCCAAT 61.034 55.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.793252 ATTTTTGTACACTACTATACGATTCGT 57.207 29.630 16.86 16.86 44.35 3.85
30 31 9.326413 CGGATTACCTTTGTTAGATTTACAGAT 57.674 33.333 0.00 0.00 0.00 2.90
31 32 7.767198 CCGGATTACCTTTGTTAGATTTACAGA 59.233 37.037 0.00 0.00 0.00 3.41
32 33 7.466860 GCCGGATTACCTTTGTTAGATTTACAG 60.467 40.741 5.05 0.00 0.00 2.74
33 34 6.316890 GCCGGATTACCTTTGTTAGATTTACA 59.683 38.462 5.05 0.00 0.00 2.41
34 35 6.541278 AGCCGGATTACCTTTGTTAGATTTAC 59.459 38.462 5.05 0.00 0.00 2.01
35 36 6.655930 AGCCGGATTACCTTTGTTAGATTTA 58.344 36.000 5.05 0.00 0.00 1.40
36 37 5.506708 AGCCGGATTACCTTTGTTAGATTT 58.493 37.500 5.05 0.00 0.00 2.17
37 38 5.104485 AGAGCCGGATTACCTTTGTTAGATT 60.104 40.000 5.05 0.00 0.00 2.40
38 39 4.409247 AGAGCCGGATTACCTTTGTTAGAT 59.591 41.667 5.05 0.00 0.00 1.98
39 40 3.773119 AGAGCCGGATTACCTTTGTTAGA 59.227 43.478 5.05 0.00 0.00 2.10
40 41 4.120589 GAGAGCCGGATTACCTTTGTTAG 58.879 47.826 5.05 0.00 0.00 2.34
41 42 3.118519 GGAGAGCCGGATTACCTTTGTTA 60.119 47.826 5.05 0.00 0.00 2.41
42 43 2.355818 GGAGAGCCGGATTACCTTTGTT 60.356 50.000 5.05 0.00 0.00 2.83
43 44 1.209747 GGAGAGCCGGATTACCTTTGT 59.790 52.381 5.05 0.00 0.00 2.83
44 45 1.475213 GGGAGAGCCGGATTACCTTTG 60.475 57.143 5.05 0.00 33.83 2.77
45 46 0.837940 GGGAGAGCCGGATTACCTTT 59.162 55.000 5.05 0.00 33.83 3.11
46 47 1.054978 GGGGAGAGCCGGATTACCTT 61.055 60.000 5.05 0.00 33.83 3.50
47 48 1.459730 GGGGAGAGCCGGATTACCT 60.460 63.158 5.05 0.00 33.83 3.08
48 49 2.517798 GGGGGAGAGCCGGATTACC 61.518 68.421 5.05 6.60 33.83 2.85
49 50 1.459730 AGGGGGAGAGCCGGATTAC 60.460 63.158 5.05 0.00 33.83 1.89
50 51 1.152312 GAGGGGGAGAGCCGGATTA 60.152 63.158 5.05 0.00 33.83 1.75
51 52 2.446802 GAGGGGGAGAGCCGGATT 60.447 66.667 5.05 0.00 33.83 3.01
52 53 4.565850 GGAGGGGGAGAGCCGGAT 62.566 72.222 5.05 0.00 33.83 4.18
58 59 3.077556 CACCGTGGAGGGGGAGAG 61.078 72.222 0.00 0.00 46.96 3.20
59 60 2.471084 ATTCACCGTGGAGGGGGAGA 62.471 60.000 0.00 0.00 45.91 3.71
60 61 1.562672 AATTCACCGTGGAGGGGGAG 61.563 60.000 0.00 0.00 45.91 4.30
61 62 1.137594 AAATTCACCGTGGAGGGGGA 61.138 55.000 0.00 0.00 45.91 4.81
62 63 0.251608 AAAATTCACCGTGGAGGGGG 60.252 55.000 0.00 0.00 45.91 5.40
113 114 2.931969 GGCCTGTTTTGAATGCATAAGC 59.068 45.455 0.00 0.00 42.57 3.09
234 237 0.342313 TCTCCCCTTCCTTCCTACCC 59.658 60.000 0.00 0.00 0.00 3.69
250 254 7.674937 GCAAAGCTTTTTCTGTTTCCTTTTCTC 60.675 37.037 9.53 0.00 0.00 2.87
257 261 3.001634 GCTGCAAAGCTTTTTCTGTTTCC 59.998 43.478 9.53 0.00 0.00 3.13
258 262 3.867493 AGCTGCAAAGCTTTTTCTGTTTC 59.133 39.130 9.53 0.00 43.52 2.78
260 264 3.531934 AGCTGCAAAGCTTTTTCTGTT 57.468 38.095 9.53 4.06 43.52 3.16
261 265 4.861102 ATAGCTGCAAAGCTTTTTCTGT 57.139 36.364 9.53 0.04 43.52 3.41
310 332 5.187687 GGGAAATGTCAGGGAACGTTTATA 58.812 41.667 0.46 0.00 38.23 0.98
336 358 2.004808 TATGGACTCTGCGAGCACCG 62.005 60.000 5.63 0.00 42.21 4.94
375 397 1.774254 TCTGCAAGGGTCCTTCTTGAA 59.226 47.619 11.01 1.12 42.94 2.69
380 402 1.743996 GACATCTGCAAGGGTCCTTC 58.256 55.000 0.00 0.00 34.16 3.46
384 406 1.168714 GTTGGACATCTGCAAGGGTC 58.831 55.000 3.40 3.40 37.75 4.46
441 463 4.755614 GCTGCTGCTGTTGCGCTC 62.756 66.667 9.73 2.14 43.34 5.03
495 517 1.357137 TGGGCTCTGACATACCACAA 58.643 50.000 0.00 0.00 0.00 3.33
497 519 1.555075 TCTTGGGCTCTGACATACCAC 59.445 52.381 0.00 0.00 0.00 4.16
546 568 2.666098 GGCCGGCCTTCTGGAGTTA 61.666 63.158 38.76 0.00 41.45 2.24
654 677 3.068691 TCACGGCTCGGGAGAAGG 61.069 66.667 0.00 0.00 32.99 3.46
708 739 0.694444 TGGAGGATCAACCCTAGGGC 60.694 60.000 28.88 10.91 40.05 5.19
709 740 1.132500 GTGGAGGATCAACCCTAGGG 58.868 60.000 27.36 27.36 40.05 3.53
710 741 2.043227 GAGTGGAGGATCAACCCTAGG 58.957 57.143 0.06 0.06 41.05 3.02
814 845 0.530744 AGCTCGTACCGCAAAGATCA 59.469 50.000 0.00 0.00 0.00 2.92
815 846 1.641577 AAGCTCGTACCGCAAAGATC 58.358 50.000 4.82 0.00 0.00 2.75
816 847 2.094762 AAAGCTCGTACCGCAAAGAT 57.905 45.000 4.82 0.00 0.00 2.40
818 849 2.681152 AAAAAGCTCGTACCGCAAAG 57.319 45.000 4.82 0.00 0.00 2.77
835 866 5.415701 GGTTCAGCTAATCACTGGATGAAAA 59.584 40.000 0.00 0.00 41.93 2.29
841 872 1.559682 GGGGTTCAGCTAATCACTGGA 59.440 52.381 0.00 0.00 35.78 3.86
844 875 1.282157 GTGGGGGTTCAGCTAATCACT 59.718 52.381 0.00 0.00 0.00 3.41
852 883 4.048470 GGAGGGTGGGGGTTCAGC 62.048 72.222 0.00 0.00 34.70 4.26
863 894 0.767060 ACGACAAAAGAGGGGAGGGT 60.767 55.000 0.00 0.00 0.00 4.34
881 912 3.701664 AGGGAGGAAATCAAACCATCAC 58.298 45.455 0.00 0.00 0.00 3.06
887 918 2.636768 CGCAAGGGAGGAAATCAAAC 57.363 50.000 0.00 0.00 0.00 2.93
910 942 1.243902 TGGGGTTCAGCAAATCGTTC 58.756 50.000 0.00 0.00 0.00 3.95
947 979 3.987868 GCAAACGCGGATCTAGAATATGA 59.012 43.478 12.47 0.00 0.00 2.15
952 984 2.686405 TCTAGCAAACGCGGATCTAGAA 59.314 45.455 19.74 9.38 34.54 2.10
995 1102 2.205074 CGCCTTCTCGCTTCATATTGT 58.795 47.619 0.00 0.00 0.00 2.71
996 1103 2.205074 ACGCCTTCTCGCTTCATATTG 58.795 47.619 0.00 0.00 0.00 1.90
1050 1157 2.270205 CCTCGCCAAGCTGTCCAT 59.730 61.111 0.00 0.00 0.00 3.41
1184 1593 2.000447 CTTCGAAAGGATTGTCCGGAC 59.000 52.381 28.17 28.17 42.75 4.79
1247 1656 3.067106 GCGATTTCTTCACTGAGTTCCA 58.933 45.455 0.00 0.00 0.00 3.53
1397 1810 2.297701 ACACGGTCTTTTCTGCACAAT 58.702 42.857 0.00 0.00 0.00 2.71
1498 1923 4.521146 AGGATCTTGGTGTCATCATCAAC 58.479 43.478 0.00 0.00 39.41 3.18
1594 2050 9.273137 AGTATATAGCCTGGTTAGCAGAATTAT 57.727 33.333 13.44 9.51 0.00 1.28
1595 2051 8.666129 AGTATATAGCCTGGTTAGCAGAATTA 57.334 34.615 13.44 2.91 0.00 1.40
1596 2052 7.560796 AGTATATAGCCTGGTTAGCAGAATT 57.439 36.000 13.44 0.71 0.00 2.17
1661 2117 3.392947 TCCCAGTTCAAGTGTGTTATCCA 59.607 43.478 0.00 0.00 0.00 3.41
1960 5918 2.373169 TGAAGGGATGCTGAGACAGTTT 59.627 45.455 0.00 0.00 33.43 2.66
1963 5921 2.435069 AGATGAAGGGATGCTGAGACAG 59.565 50.000 0.00 0.00 34.12 3.51
1965 5923 3.557228 AAGATGAAGGGATGCTGAGAC 57.443 47.619 0.00 0.00 0.00 3.36
1966 5924 3.265221 ACAAAGATGAAGGGATGCTGAGA 59.735 43.478 0.00 0.00 0.00 3.27
1967 5925 3.377485 CACAAAGATGAAGGGATGCTGAG 59.623 47.826 0.00 0.00 0.00 3.35
1979 7321 1.881973 GTGAGCCAAGCACAAAGATGA 59.118 47.619 0.00 0.00 36.31 2.92
2229 7615 0.960286 CATGTGTGACCCATGTGCAA 59.040 50.000 0.00 0.00 35.94 4.08
2345 7757 5.295431 TCCAACAACGCAAGAGATTTATG 57.705 39.130 0.00 0.00 43.62 1.90
2356 7768 5.637810 TGTTAACAAATTTTCCAACAACGCA 59.362 32.000 5.64 0.00 0.00 5.24
2448 7869 7.169645 ACAACACATGCAGTAATTCAAACAATC 59.830 33.333 0.00 0.00 0.00 2.67
2456 7877 6.086222 CCTTGTACAACACATGCAGTAATTC 58.914 40.000 3.59 0.00 36.90 2.17
2508 7929 6.152323 TGTTAGACTCCTCACTACATACCAAC 59.848 42.308 0.00 0.00 0.00 3.77
2539 7960 9.197694 ACTCATTCGCTCAATATTACAGTAATC 57.802 33.333 9.20 0.00 0.00 1.75
2552 7973 6.475727 GTGCTAAATAGTACTCATTCGCTCAA 59.524 38.462 0.00 0.00 36.23 3.02
2643 8066 4.110482 AGTTGTATGCCGTTATCGAGAAC 58.890 43.478 12.86 12.86 39.71 3.01
2648 8071 4.856664 AGACTAGTTGTATGCCGTTATCG 58.143 43.478 0.00 0.00 0.00 2.92
2675 8293 6.547510 GCCTATAGTCATCCAGGAAATGTTTT 59.452 38.462 0.00 0.00 0.00 2.43
2694 8312 3.711190 TGAAGCAGAACAGATGGCCTATA 59.289 43.478 3.32 0.00 0.00 1.31
2710 8328 5.707931 TGAATAACAAATTCGCATGAAGCA 58.292 33.333 0.00 0.00 46.13 3.91
2716 8334 5.184864 TCCAGGTTGAATAACAAATTCGCAT 59.815 36.000 0.00 0.00 40.36 4.73
2749 8367 1.644509 ACTGATGTGTGGTCAGCCTA 58.355 50.000 3.23 0.00 45.42 3.93
2751 8369 1.550524 TCTACTGATGTGTGGTCAGCC 59.449 52.381 3.23 0.00 45.42 4.85
2915 8624 5.067413 GGAGATGTTGTCAAATGCAGATCAT 59.933 40.000 0.00 0.00 36.87 2.45
3323 9038 0.387565 CCCGGGTTTGTTGTTCCAAG 59.612 55.000 14.18 0.00 0.00 3.61
3582 9302 3.308117 GGTGGTATGGATTGTCAAGGTCA 60.308 47.826 0.00 0.00 0.00 4.02
3583 9303 3.054361 AGGTGGTATGGATTGTCAAGGTC 60.054 47.826 0.00 0.00 0.00 3.85
3584 9304 2.919602 AGGTGGTATGGATTGTCAAGGT 59.080 45.455 0.00 0.00 0.00 3.50
3585 9305 3.282021 CAGGTGGTATGGATTGTCAAGG 58.718 50.000 0.00 0.00 0.00 3.61
3639 9362 0.036306 GACACCCGAGTCCCAATTGT 59.964 55.000 4.43 0.00 32.36 2.71
3652 9375 7.582667 ATTAATAGCTTAAACATGGACACCC 57.417 36.000 0.00 0.00 30.88 4.61
3763 10353 1.066908 CTTTTCCCATGCGTGTTGTGT 59.933 47.619 4.96 0.00 0.00 3.72
3771 10361 0.602562 TGGAAAGCTTTTCCCATGCG 59.397 50.000 15.05 0.00 37.79 4.73
4047 10640 7.208064 ACCAGGTCCTTTCTTATTTATAGCA 57.792 36.000 0.00 0.00 0.00 3.49
4052 10645 9.948964 GTTTACTACCAGGTCCTTTCTTATTTA 57.051 33.333 0.00 0.00 0.00 1.40
4078 10671 8.807948 TTATAAGGTCTGGGAAATCTTTCAAG 57.192 34.615 5.14 2.58 38.92 3.02
4185 10785 7.118496 TGAAAATTAACATTGGTGGTGACTT 57.882 32.000 0.00 0.00 0.00 3.01
4255 10855 9.010029 CAACCATAAAACTAAGTATGTGGTTCT 57.990 33.333 10.87 0.00 44.38 3.01
4256 10856 7.753580 GCAACCATAAAACTAAGTATGTGGTTC 59.246 37.037 10.87 5.42 44.38 3.62
4257 10857 7.231722 TGCAACCATAAAACTAAGTATGTGGTT 59.768 33.333 8.87 8.87 46.39 3.67
4258 10858 6.717540 TGCAACCATAAAACTAAGTATGTGGT 59.282 34.615 0.00 0.00 40.21 4.16
4259 10859 7.027161 GTGCAACCATAAAACTAAGTATGTGG 58.973 38.462 0.00 0.00 0.00 4.17
4640 12759 7.881775 ATGACTCACCAAAATAAGGATAACC 57.118 36.000 0.00 0.00 0.00 2.85
4720 12839 3.059166 AGCAACGCCTAAATTTTGCAAG 58.941 40.909 11.67 0.00 45.54 4.01
4759 12878 1.856920 GGGAGGGGATAACCATTGGAA 59.143 52.381 10.37 0.00 42.91 3.53
5092 13230 8.974060 TGTTTTTCCTACAAGAGTAATGACTT 57.026 30.769 0.00 0.00 35.45 3.01
5203 13341 3.380004 AGCAACCTTGTTTTCATCGTCAA 59.620 39.130 0.00 0.00 0.00 3.18
5254 13392 6.935167 AGTAGAAGGGGCAATTAAACAATTG 58.065 36.000 3.24 3.24 41.74 2.32
5387 13525 4.689071 TGTGGACTACGGCAATGTTATAG 58.311 43.478 0.00 0.00 0.00 1.31
5496 13634 7.014615 GGCCATTAATTTGTCTGATTGGTAGAT 59.985 37.037 0.00 0.00 0.00 1.98
5509 13647 3.007831 CCCACTTGTGGCCATTAATTTGT 59.992 43.478 9.72 0.00 0.00 2.83
5919 14085 9.553064 CTACTAAACTTCCTCAAGATTGCATAT 57.447 33.333 0.00 0.00 33.34 1.78
5920 14086 7.495934 GCTACTAAACTTCCTCAAGATTGCATA 59.504 37.037 0.00 0.00 33.34 3.14
5921 14087 6.317391 GCTACTAAACTTCCTCAAGATTGCAT 59.683 38.462 0.00 0.00 33.34 3.96
6031 14853 5.293324 TCGCACCAGTGTCATATGTTATTTC 59.707 40.000 1.90 0.00 0.00 2.17
6052 14874 1.278238 CACAGGACGGTCTTTATCGC 58.722 55.000 8.23 0.00 30.11 4.58
6086 14909 1.596260 CGTACAATCAGGCATGCTCAG 59.404 52.381 18.92 7.92 0.00 3.35
6095 14918 6.662414 ATCACAAATGTACGTACAATCAGG 57.338 37.500 30.46 19.62 39.99 3.86
6147 14979 2.906389 AGTTCCAGGTTAGAGTGATGCA 59.094 45.455 0.00 0.00 0.00 3.96
6602 15484 0.387239 AGAATTGTTTTCGCTGCCGC 60.387 50.000 0.00 0.00 0.00 6.53
6603 15485 2.892373 TAGAATTGTTTTCGCTGCCG 57.108 45.000 0.00 0.00 0.00 5.69
6604 15486 3.057526 AGGTTAGAATTGTTTTCGCTGCC 60.058 43.478 0.00 0.00 0.00 4.85
6605 15487 3.914364 CAGGTTAGAATTGTTTTCGCTGC 59.086 43.478 0.00 0.00 0.00 5.25
6606 15488 5.356882 TCAGGTTAGAATTGTTTTCGCTG 57.643 39.130 0.00 0.00 0.00 5.18
6607 15489 5.705441 TCATCAGGTTAGAATTGTTTTCGCT 59.295 36.000 0.00 0.00 0.00 4.93
6611 15493 7.147976 GCACTTCATCAGGTTAGAATTGTTTT 58.852 34.615 0.00 0.00 0.00 2.43
6612 15494 6.265196 TGCACTTCATCAGGTTAGAATTGTTT 59.735 34.615 0.00 0.00 0.00 2.83
6751 15637 7.052873 AGATGGTACGTTCTTAAGCTAGTAGA 58.947 38.462 0.00 0.00 0.00 2.59
6752 15638 7.261829 AGATGGTACGTTCTTAAGCTAGTAG 57.738 40.000 0.00 0.00 0.00 2.57
6753 15639 7.337689 TCAAGATGGTACGTTCTTAAGCTAGTA 59.662 37.037 0.00 0.00 32.79 1.82
6773 15659 4.718774 AGTACAGGTCCATCACATCAAGAT 59.281 41.667 0.00 0.00 0.00 2.40
6803 15690 0.690762 TCTCTTAACGGCCCTGCTTT 59.309 50.000 0.00 0.00 0.00 3.51
6807 15694 4.496670 CGTCTCTTAACGGCCCTG 57.503 61.111 0.00 0.00 38.96 4.45
6836 15751 2.873472 ACAGTGCCGAAAAATACGACAA 59.127 40.909 0.00 0.00 0.00 3.18
6880 15796 6.209192 TGTTCATCACTGTGCCTTAAAATGAT 59.791 34.615 2.12 0.00 0.00 2.45
6882 15798 5.771469 TGTTCATCACTGTGCCTTAAAATG 58.229 37.500 2.12 0.13 0.00 2.32


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

AutoCloner maintained by Alex Coulton.