Multiple sequence alignment - TraesCS4A01G142100

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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 TraesCS4A01G142100 chr4A 100.000 2329 0 0 1 2329 225578841 225581169 0.000000e+00 4301.0
1 TraesCS4A01G142100 chr4A 100.000 2153 0 0 2944 5096 225581784 225583936 0.000000e+00 3976.0
2 TraesCS4A01G142100 chr4A 97.002 1301 25 1 1 1301 195314532 195313246 0.000000e+00 2174.0
3 TraesCS4A01G142100 chr4A 95.077 1300 34 6 3620 4893 195313169 195311874 0.000000e+00 2019.0
4 TraesCS4A01G142100 chr4A 98.837 86 1 0 1347 1432 195313245 195313160 2.460000e-33 154.0
5 TraesCS4A01G142100 chr5D 94.948 1445 52 8 1 1432 437573144 437571708 0.000000e+00 2244.0
6 TraesCS4A01G142100 chr5D 93.893 1310 43 12 3620 4908 437571717 437570424 0.000000e+00 1941.0
7 TraesCS4A01G142100 chr5D 95.484 155 4 3 4886 5040 453465726 453465575 1.420000e-60 244.0
8 TraesCS4A01G142100 chr5D 95.946 148 5 1 4886 5033 232820267 232820413 6.590000e-59 239.0
9 TraesCS4A01G142100 chr5B 94.444 1440 72 4 1 1432 261376452 261375013 0.000000e+00 2209.0
10 TraesCS4A01G142100 chr5B 89.534 1309 71 21 3620 4893 261375022 261373745 0.000000e+00 1598.0
11 TraesCS4A01G142100 chr5B 88.139 919 86 9 1431 2329 576162692 576163607 0.000000e+00 1072.0
12 TraesCS4A01G142100 chr3B 88.262 1312 86 28 159 1432 527299605 527298324 0.000000e+00 1507.0
13 TraesCS4A01G142100 chr3B 87.559 1053 79 20 3671 4708 527298132 527297117 0.000000e+00 1171.0
14 TraesCS4A01G142100 chr3B 87.856 914 91 8 1433 2329 106721017 106721927 0.000000e+00 1055.0
15 TraesCS4A01G142100 chr3B 96.970 33 1 0 3619 3651 545194344 545194376 7.130000e-04 56.5
16 TraesCS4A01G142100 chr5A 91.247 914 60 9 1433 2329 683628342 683629252 0.000000e+00 1227.0
17 TraesCS4A01G142100 chr5A 91.009 912 62 7 1434 2329 681902181 681901274 0.000000e+00 1212.0
18 TraesCS4A01G142100 chr5A 88.792 687 64 7 2944 3619 681901083 681900399 0.000000e+00 830.0
19 TraesCS4A01G142100 chr5A 88.792 687 63 8 2944 3619 683629444 683630127 0.000000e+00 830.0
20 TraesCS4A01G142100 chr5A 95.833 120 5 0 1 120 45451701 45451820 1.450000e-45 195.0
21 TraesCS4A01G142100 chr5A 94.167 120 7 0 1 120 702768144 702768263 3.130000e-42 183.0
22 TraesCS4A01G142100 chr5A 79.000 200 35 7 3424 3620 355118631 355118826 4.140000e-26 130.0
23 TraesCS4A01G142100 chr3D 92.115 837 39 16 588 1408 401876260 401875435 0.000000e+00 1155.0
24 TraesCS4A01G142100 chr3D 85.294 986 89 30 3715 4665 401875217 401874253 0.000000e+00 966.0
25 TraesCS4A01G142100 chr3D 88.529 401 33 9 119 509 401876657 401876260 1.660000e-129 473.0
26 TraesCS4A01G142100 chr3D 95.946 148 5 1 4886 5033 138849673 138849819 6.590000e-59 239.0
27 TraesCS4A01G142100 chr3D 91.071 112 6 1 1 112 404855375 404855268 1.140000e-31 148.0
28 TraesCS4A01G142100 chr4B 89.376 913 77 10 1433 2329 575388070 575387162 0.000000e+00 1131.0
29 TraesCS4A01G142100 chr4B 88.492 756 66 9 1552 2290 379614525 379613774 0.000000e+00 894.0
30 TraesCS4A01G142100 chr4B 87.805 287 25 5 3344 3620 575388108 575388394 1.370000e-85 327.0
31 TraesCS4A01G142100 chr7B 89.290 915 77 7 1432 2329 41307008 41307918 0.000000e+00 1127.0
32 TraesCS4A01G142100 chr3A 86.804 1023 86 26 3671 4662 522178154 522177150 0.000000e+00 1096.0
33 TraesCS4A01G142100 chr3A 93.487 522 34 0 911 1432 522179061 522178540 0.000000e+00 776.0
34 TraesCS4A01G142100 chr3A 85.504 476 32 15 464 925 522179556 522179104 3.590000e-126 462.0
35 TraesCS4A01G142100 chr3A 90.476 231 16 3 119 344 522179795 522179566 2.980000e-77 300.0
36 TraesCS4A01G142100 chr2B 88.403 914 78 10 1433 2329 490788814 490787912 0.000000e+00 1075.0
37 TraesCS4A01G142100 chr2B 87.064 688 73 7 2944 3620 490787449 490786767 0.000000e+00 763.0
38 TraesCS4A01G142100 chr6D 87.978 915 78 10 1432 2329 134715829 134716728 0.000000e+00 1051.0
39 TraesCS4A01G142100 chr6D 87.445 916 81 12 1432 2329 134310591 134311490 0.000000e+00 1024.0
40 TraesCS4A01G142100 chr6D 88.728 692 63 6 2944 3623 134311720 134312408 0.000000e+00 832.0
41 TraesCS4A01G142100 chr6D 88.456 693 64 7 2944 3623 134717060 134717749 0.000000e+00 822.0
42 TraesCS4A01G142100 chr6D 86.162 542 59 4 3090 3620 134716366 134715830 5.720000e-159 571.0
43 TraesCS4A01G142100 chr6D 85.556 540 62 3 1433 1957 134312404 134311866 7.460000e-153 551.0
44 TraesCS4A01G142100 chr6D 85.424 542 62 5 3090 3620 134311127 134310592 9.650000e-152 547.0
45 TraesCS4A01G142100 chr6D 85.397 541 62 5 1433 1957 134717745 134717206 3.470000e-151 545.0
46 TraesCS4A01G142100 chr6D 96.622 148 4 1 4886 5033 75207761 75207907 1.420000e-60 244.0
47 TraesCS4A01G142100 chr6D 96.622 148 4 1 4886 5033 84894113 84894259 1.420000e-60 244.0
48 TraesCS4A01G142100 chr6D 95.946 148 5 1 4886 5033 307581176 307581322 6.590000e-59 239.0
49 TraesCS4A01G142100 chr7D 87.285 755 74 6 1592 2329 156838593 156839342 0.000000e+00 843.0
50 TraesCS4A01G142100 chr7D 88.295 692 62 11 2944 3621 156839553 156840239 0.000000e+00 811.0
51 TraesCS4A01G142100 chr7D 90.037 271 26 1 1433 1703 156838317 156838586 2.920000e-92 350.0
52 TraesCS4A01G142100 chr7D 95.946 148 5 1 4886 5033 530814819 530814965 6.590000e-59 239.0
53 TraesCS4A01G142100 chr7D 80.660 212 28 8 3424 3624 160540384 160540175 8.840000e-33 152.0
54 TraesCS4A01G142100 chr7D 80.676 207 29 6 3424 3620 126583854 126584059 3.180000e-32 150.0
55 TraesCS4A01G142100 chr4D 87.936 688 67 6 2944 3620 501051243 501051925 0.000000e+00 797.0
56 TraesCS4A01G142100 chr4D 84.559 544 65 5 1429 1957 501051928 501051389 5.850000e-144 521.0
57 TraesCS4A01G142100 chr6B 85.652 690 82 8 2944 3620 435055856 435055171 0.000000e+00 710.0
58 TraesCS4A01G142100 chr1B 82.743 678 109 8 2944 3619 683096710 683096039 9.440000e-167 597.0
59 TraesCS4A01G142100 chr2D 96.026 151 5 1 4883 5033 501922999 501923148 1.420000e-60 244.0
60 TraesCS4A01G142100 chr1D 94.839 155 5 3 4886 5040 341882952 341882801 6.590000e-59 239.0
61 TraesCS4A01G142100 chr1A 96.667 120 4 0 1 120 563805423 563805304 3.110000e-47 200.0
62 TraesCS4A01G142100 chr1A 90.090 111 11 0 4786 4896 563801651 563801541 1.480000e-30 145.0
63 TraesCS4A01G142100 chr1A 88.889 108 12 0 4786 4893 559359104 559358997 3.200000e-27 134.0
64 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 4271836 4271772 2.490000e-23 121.0
65 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 156438931 156438867 2.490000e-23 121.0
66 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 222495528 222495592 2.490000e-23 121.0
67 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 227167484 227167548 2.490000e-23 121.0
68 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 324005574 324005638 2.490000e-23 121.0
69 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 507429178 507429242 2.490000e-23 121.0
70 TraesCS4A01G142100 chr1A 100.000 65 0 0 5032 5096 507471227 507471291 2.490000e-23 121.0
71 TraesCS4A01G142100 chrUn 100.000 65 0 0 5032 5096 342738140 342738076 2.490000e-23 121.0
72 TraesCS4A01G142100 chrUn 100.000 65 0 0 5032 5096 448806579 448806643 2.490000e-23 121.0


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 TraesCS4A01G142100 chr4A 225578841 225583936 5095 False 4138.500000 4301 100.00000 1 5096 2 chr4A.!!$F1 5095
1 TraesCS4A01G142100 chr4A 195311874 195314532 2658 True 1449.000000 2174 96.97200 1 4893 3 chr4A.!!$R1 4892
2 TraesCS4A01G142100 chr5D 437570424 437573144 2720 True 2092.500000 2244 94.42050 1 4908 2 chr5D.!!$R2 4907
3 TraesCS4A01G142100 chr5B 261373745 261376452 2707 True 1903.500000 2209 91.98900 1 4893 2 chr5B.!!$R1 4892
4 TraesCS4A01G142100 chr5B 576162692 576163607 915 False 1072.000000 1072 88.13900 1431 2329 1 chr5B.!!$F1 898
5 TraesCS4A01G142100 chr3B 527297117 527299605 2488 True 1339.000000 1507 87.91050 159 4708 2 chr3B.!!$R1 4549
6 TraesCS4A01G142100 chr3B 106721017 106721927 910 False 1055.000000 1055 87.85600 1433 2329 1 chr3B.!!$F1 896
7 TraesCS4A01G142100 chr5A 683628342 683630127 1785 False 1028.500000 1227 90.01950 1433 3619 2 chr5A.!!$F4 2186
8 TraesCS4A01G142100 chr5A 681900399 681902181 1782 True 1021.000000 1212 89.90050 1434 3619 2 chr5A.!!$R1 2185
9 TraesCS4A01G142100 chr3D 401874253 401876657 2404 True 864.666667 1155 88.64600 119 4665 3 chr3D.!!$R2 4546
10 TraesCS4A01G142100 chr4B 575387162 575388070 908 True 1131.000000 1131 89.37600 1433 2329 1 chr4B.!!$R2 896
11 TraesCS4A01G142100 chr4B 379613774 379614525 751 True 894.000000 894 88.49200 1552 2290 1 chr4B.!!$R1 738
12 TraesCS4A01G142100 chr7B 41307008 41307918 910 False 1127.000000 1127 89.29000 1432 2329 1 chr7B.!!$F1 897
13 TraesCS4A01G142100 chr3A 522177150 522179795 2645 True 658.500000 1096 89.06775 119 4662 4 chr3A.!!$R1 4543
14 TraesCS4A01G142100 chr2B 490786767 490788814 2047 True 919.000000 1075 87.73350 1433 3620 2 chr2B.!!$R1 2187
15 TraesCS4A01G142100 chr6D 134715829 134717749 1920 False 936.500000 1051 88.21700 1432 3623 2 chr6D.!!$F5 2191
16 TraesCS4A01G142100 chr6D 134310591 134312408 1817 False 928.000000 1024 88.08650 1432 3623 2 chr6D.!!$F4 2191
17 TraesCS4A01G142100 chr6D 134715830 134717745 1915 True 558.000000 571 85.77950 1433 3620 2 chr6D.!!$R2 2187
18 TraesCS4A01G142100 chr6D 134310592 134312404 1812 True 549.000000 551 85.49000 1433 3620 2 chr6D.!!$R1 2187
19 TraesCS4A01G142100 chr7D 156838317 156840239 1922 False 668.000000 843 88.53900 1433 3621 3 chr7D.!!$F3 2188
20 TraesCS4A01G142100 chr4D 501051243 501051925 682 False 797.000000 797 87.93600 2944 3620 1 chr4D.!!$F1 676
21 TraesCS4A01G142100 chr4D 501051389 501051928 539 True 521.000000 521 84.55900 1429 1957 1 chr4D.!!$R1 528
22 TraesCS4A01G142100 chr6B 435055171 435055856 685 True 710.000000 710 85.65200 2944 3620 1 chr6B.!!$R1 676
23 TraesCS4A01G142100 chr1B 683096039 683096710 671 True 597.000000 597 82.74300 2944 3619 1 chr1B.!!$R1 675

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
244 258 3.908103 AGGACCTGCCTCTGTTTTTACTA 59.092 43.478 0.00 0.00 46.97 1.82 F
1428 1572 0.107897 TTGGTTCATGGTCCGATCGG 60.108 55.000 28.62 28.62 0.00 4.18 F
1726 2006 0.801067 GATTCGAACCCACGACGGAG 60.801 60.000 0.00 0.00 41.97 4.63 F
1908 2194 1.371183 CACGTCCTGGCCTTCTTCA 59.629 57.895 3.32 0.00 0.00 3.02 F
3304 4365 0.798776 CGTAACGTAGTGGTCTCCGT 59.201 55.000 0.00 0.00 45.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1710 1.337817 CGCTGTCAGTTTCTCCGTCG 61.338 60.0 0.93 0.00 0.00 5.12 R
3202 4263 0.459489 TTGCTGGGCAACTGTTTCAC 59.541 50.0 0.51 0.00 43.99 3.18 R
3281 4342 0.961019 AGACCACTACGTTACGCCAA 59.039 50.0 4.09 0.00 0.00 4.52 R
3622 4695 1.008329 GAAAACACGACCACAACCGA 58.992 50.0 0.00 0.00 0.00 4.69 R
5068 6650 0.041833 TCTCTCTAGGCTTGCCTGGT 59.958 55.0 23.03 0.73 0.00 4.00 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
95 103 5.313506 TCCCTATTGGCTACAGAGAGAGATA 59.686 44.000 0.00 0.00 0.00 1.98
244 258 3.908103 AGGACCTGCCTCTGTTTTTACTA 59.092 43.478 0.00 0.00 46.97 1.82
497 525 7.514721 AGGTAGTACTTTGAGGTTTTGAATGA 58.485 34.615 0.00 0.00 0.00 2.57
729 778 5.168569 GTCGTGAAGGACATAGATGTGAAA 58.831 41.667 0.00 0.00 41.95 2.69
1010 1137 7.954705 GTTTAGCAACAAACATGCAGAGGCA 62.955 44.000 0.00 0.00 46.22 4.75
1273 1400 5.999205 ACTTGATGGTTTTATGATGGCAA 57.001 34.783 0.00 0.00 0.00 4.52
1298 1442 4.929211 TGATTACAACTGACATTGACTCCG 59.071 41.667 0.00 0.00 33.57 4.63
1308 1452 4.992319 TGACATTGACTCCGACGTAATTTT 59.008 37.500 0.00 0.00 0.00 1.82
1338 1482 4.039004 TGCTTGTGGTGCAATAATCTTTGT 59.961 37.500 0.00 0.00 37.51 2.83
1427 1571 1.867233 GATTGGTTCATGGTCCGATCG 59.133 52.381 8.51 8.51 35.66 3.69
1428 1572 0.107897 TTGGTTCATGGTCCGATCGG 60.108 55.000 28.62 28.62 0.00 4.18
1429 1573 1.261938 TGGTTCATGGTCCGATCGGT 61.262 55.000 32.15 11.81 36.47 4.69
1490 1634 9.994432 CATTAGAAACAGATTGGTATCAAGTTC 57.006 33.333 0.00 0.00 36.19 3.01
1631 1892 6.608610 ACGTGGCATCTTATTTTACAGAAAC 58.391 36.000 0.00 0.00 0.00 2.78
1633 1894 7.081349 CGTGGCATCTTATTTTACAGAAACAA 58.919 34.615 0.00 0.00 0.00 2.83
1726 2006 0.801067 GATTCGAACCCACGACGGAG 60.801 60.000 0.00 0.00 41.97 4.63
1753 2033 1.912043 AGGGAAAGTCCAGATGACCAG 59.088 52.381 0.00 0.00 45.68 4.00
1780 2060 3.552604 ACGCCACAACATTCAATACAC 57.447 42.857 0.00 0.00 0.00 2.90
1860 2146 8.932963 CAACTGTTTCATTTTTAATGCGTTTTC 58.067 29.630 0.00 0.00 0.00 2.29
1908 2194 1.371183 CACGTCCTGGCCTTCTTCA 59.629 57.895 3.32 0.00 0.00 3.02
2060 2349 1.439353 CCACCCATCGATTTCAGCGG 61.439 60.000 0.00 0.00 0.00 5.52
2244 2535 4.988540 CGGTGAACATTTTCTCAGTACTCA 59.011 41.667 0.00 0.00 32.36 3.41
3214 4275 5.005299 ACGCATTAAAAAGTGAAACAGTTGC 59.995 36.000 0.00 0.00 41.43 4.17
3234 4295 2.687425 GCCCAGCAACAAAAATGGTTTT 59.313 40.909 0.00 0.00 37.43 2.43
3268 4329 3.791973 AAAAACGTTCAAGCATCCACA 57.208 38.095 0.00 0.00 0.00 4.17
3281 4342 3.149196 GCATCCACATTATCCAACGGAT 58.851 45.455 0.43 0.43 45.40 4.18
3300 4361 0.961019 TTGGCGTAACGTAGTGGTCT 59.039 50.000 0.00 0.00 45.00 3.85
3304 4365 0.798776 CGTAACGTAGTGGTCTCCGT 59.201 55.000 0.00 0.00 45.00 4.69
3362 4424 2.350760 CGGGCGCGCGAAATTTAG 60.351 61.111 39.50 12.61 0.00 1.85
3411 4474 1.963515 ACAAGGCCCTTTGTGTGATTC 59.036 47.619 9.45 0.00 39.68 2.52
3609 4682 3.560453 GCCCCAATTGTGGTACTTCTGTA 60.560 47.826 8.84 0.00 44.30 2.74
3661 4734 9.883142 TGTTTTCTTTTTATTTCCACATCACTT 57.117 25.926 0.00 0.00 0.00 3.16
3769 5249 8.798748 ATTCAGATTTATCTCGGTTACTAACG 57.201 34.615 0.00 0.00 34.22 3.18
3850 5330 4.654915 TGGATCATGCCCTACATACAATG 58.345 43.478 0.00 0.00 36.64 2.82
3989 5481 1.229082 AGGTGGAGCAGGTAACCGA 60.229 57.895 0.00 0.00 37.78 4.69
4199 5712 1.403647 CGCGAGTTGTGAATAGTCCCA 60.404 52.381 0.00 0.00 0.00 4.37
4306 5836 4.156455 CCTGGTAGTAACGAGGTACCTA 57.844 50.000 16.29 0.00 44.36 3.08
4473 6008 6.072673 GGAACATTGAAAAAGTACGTCAGGAT 60.073 38.462 0.00 0.00 0.00 3.24
4743 6322 3.865929 CTTGCGTGGCTGTCGGACT 62.866 63.158 9.88 0.00 0.00 3.85
4759 6341 1.602327 GACTAAACCTCGTCCCCGCT 61.602 60.000 0.00 0.00 0.00 5.52
4774 6356 3.721706 GCTGCCACCTACTGCCCT 61.722 66.667 0.00 0.00 0.00 5.19
4816 6398 6.594788 ACCATATTCTCAATTTGCACAGTT 57.405 33.333 0.00 0.00 0.00 3.16
4865 6447 3.392947 TGTGTGAGGTTATGTTTCTCCCA 59.607 43.478 0.00 0.00 0.00 4.37
4893 6475 3.221964 GCACAGGCAATTTTCCTAGTG 57.778 47.619 14.72 14.72 40.72 2.74
4894 6476 2.819608 GCACAGGCAATTTTCCTAGTGA 59.180 45.455 19.09 0.00 40.72 3.41
4895 6477 3.255642 GCACAGGCAATTTTCCTAGTGAA 59.744 43.478 19.09 0.00 40.72 3.18
4896 6478 4.798574 CACAGGCAATTTTCCTAGTGAAC 58.201 43.478 14.28 0.00 36.11 3.18
4900 6482 6.775629 ACAGGCAATTTTCCTAGTGAACTTAA 59.224 34.615 0.00 0.00 31.05 1.85
4901 6483 7.451566 ACAGGCAATTTTCCTAGTGAACTTAAT 59.548 33.333 0.00 0.00 31.05 1.40
4902 6484 8.956426 CAGGCAATTTTCCTAGTGAACTTAATA 58.044 33.333 0.00 0.00 31.05 0.98
4903 6485 8.957466 AGGCAATTTTCCTAGTGAACTTAATAC 58.043 33.333 0.00 0.00 31.05 1.89
4904 6486 8.957466 GGCAATTTTCCTAGTGAACTTAATACT 58.043 33.333 0.00 0.00 31.05 2.12
4905 6487 9.989869 GCAATTTTCCTAGTGAACTTAATACTC 57.010 33.333 0.00 0.00 31.05 2.59
4912 6494 9.069082 TCCTAGTGAACTTAATACTCTAGATGC 57.931 37.037 0.00 0.00 32.81 3.91
4913 6495 8.851145 CCTAGTGAACTTAATACTCTAGATGCA 58.149 37.037 0.00 0.00 32.81 3.96
4916 6498 7.655328 AGTGAACTTAATACTCTAGATGCATGC 59.345 37.037 11.82 11.82 0.00 4.06
4917 6499 7.655328 GTGAACTTAATACTCTAGATGCATGCT 59.345 37.037 20.33 4.11 0.00 3.79
4918 6500 7.654923 TGAACTTAATACTCTAGATGCATGCTG 59.345 37.037 20.33 4.23 0.00 4.41
4919 6501 6.462500 ACTTAATACTCTAGATGCATGCTGG 58.538 40.000 20.33 3.51 0.00 4.85
4920 6502 6.268617 ACTTAATACTCTAGATGCATGCTGGA 59.731 38.462 20.33 7.90 0.00 3.86
4921 6503 5.758790 AATACTCTAGATGCATGCTGGAT 57.241 39.130 20.33 3.62 0.00 3.41
4922 6504 6.864151 AATACTCTAGATGCATGCTGGATA 57.136 37.500 20.33 5.84 0.00 2.59
4923 6505 4.804868 ACTCTAGATGCATGCTGGATAG 57.195 45.455 20.33 14.76 0.00 2.08
4932 6514 4.251760 GCTGGATAGCGGTCGATG 57.748 61.111 0.00 0.00 40.67 3.84
4933 6515 1.364171 GCTGGATAGCGGTCGATGT 59.636 57.895 0.00 0.00 40.67 3.06
4934 6516 0.941463 GCTGGATAGCGGTCGATGTG 60.941 60.000 0.00 0.00 40.67 3.21
4935 6517 0.385751 CTGGATAGCGGTCGATGTGT 59.614 55.000 0.00 0.00 0.00 3.72
4936 6518 0.102300 TGGATAGCGGTCGATGTGTG 59.898 55.000 0.00 0.00 0.00 3.82
4937 6519 0.597637 GGATAGCGGTCGATGTGTGG 60.598 60.000 0.00 0.00 0.00 4.17
4938 6520 0.384309 GATAGCGGTCGATGTGTGGA 59.616 55.000 0.00 0.00 0.00 4.02
4939 6521 0.385751 ATAGCGGTCGATGTGTGGAG 59.614 55.000 0.00 0.00 0.00 3.86
4940 6522 0.963856 TAGCGGTCGATGTGTGGAGT 60.964 55.000 0.00 0.00 0.00 3.85
4941 6523 0.963856 AGCGGTCGATGTGTGGAGTA 60.964 55.000 0.00 0.00 0.00 2.59
4942 6524 0.108992 GCGGTCGATGTGTGGAGTAA 60.109 55.000 0.00 0.00 0.00 2.24
4943 6525 1.470979 GCGGTCGATGTGTGGAGTAAT 60.471 52.381 0.00 0.00 0.00 1.89
4944 6526 2.223641 GCGGTCGATGTGTGGAGTAATA 60.224 50.000 0.00 0.00 0.00 0.98
4945 6527 3.629058 CGGTCGATGTGTGGAGTAATAG 58.371 50.000 0.00 0.00 0.00 1.73
4946 6528 3.066342 CGGTCGATGTGTGGAGTAATAGT 59.934 47.826 0.00 0.00 0.00 2.12
4947 6529 4.274214 CGGTCGATGTGTGGAGTAATAGTA 59.726 45.833 0.00 0.00 0.00 1.82
4948 6530 5.560375 CGGTCGATGTGTGGAGTAATAGTAG 60.560 48.000 0.00 0.00 0.00 2.57
4949 6531 5.298777 GGTCGATGTGTGGAGTAATAGTAGT 59.701 44.000 0.00 0.00 0.00 2.73
4950 6532 6.484643 GGTCGATGTGTGGAGTAATAGTAGTA 59.515 42.308 0.00 0.00 0.00 1.82
4951 6533 7.307870 GGTCGATGTGTGGAGTAATAGTAGTAG 60.308 44.444 0.00 0.00 0.00 2.57
4952 6534 7.440556 GTCGATGTGTGGAGTAATAGTAGTAGA 59.559 40.741 0.00 0.00 0.00 2.59
4953 6535 8.155510 TCGATGTGTGGAGTAATAGTAGTAGAT 58.844 37.037 0.00 0.00 0.00 1.98
4954 6536 8.231161 CGATGTGTGGAGTAATAGTAGTAGATG 58.769 40.741 0.00 0.00 0.00 2.90
4955 6537 7.273320 TGTGTGGAGTAATAGTAGTAGATGC 57.727 40.000 0.00 0.00 0.00 3.91
4956 6538 6.831868 TGTGTGGAGTAATAGTAGTAGATGCA 59.168 38.462 0.00 0.00 0.00 3.96
4957 6539 7.013369 TGTGTGGAGTAATAGTAGTAGATGCAG 59.987 40.741 0.00 0.00 0.00 4.41
4958 6540 6.490381 TGTGGAGTAATAGTAGTAGATGCAGG 59.510 42.308 0.00 0.00 0.00 4.85
4959 6541 5.477291 TGGAGTAATAGTAGTAGATGCAGGC 59.523 44.000 0.00 0.00 0.00 4.85
4960 6542 5.477291 GGAGTAATAGTAGTAGATGCAGGCA 59.523 44.000 0.00 0.00 0.00 4.75
4961 6543 6.349777 GGAGTAATAGTAGTAGATGCAGGCAG 60.350 46.154 0.00 0.00 0.00 4.85
4962 6544 4.881019 AATAGTAGTAGATGCAGGCAGG 57.119 45.455 0.00 0.00 0.00 4.85
4963 6545 2.461300 AGTAGTAGATGCAGGCAGGA 57.539 50.000 0.00 0.00 0.00 3.86
4964 6546 2.315176 AGTAGTAGATGCAGGCAGGAG 58.685 52.381 0.00 0.00 0.00 3.69
4965 6547 2.035632 GTAGTAGATGCAGGCAGGAGT 58.964 52.381 0.00 0.00 0.00 3.85
4966 6548 1.118838 AGTAGATGCAGGCAGGAGTC 58.881 55.000 0.00 0.00 0.00 3.36
4967 6549 0.826715 GTAGATGCAGGCAGGAGTCA 59.173 55.000 0.00 0.00 0.00 3.41
4968 6550 1.117994 TAGATGCAGGCAGGAGTCAG 58.882 55.000 0.00 0.00 0.00 3.51
4969 6551 0.908656 AGATGCAGGCAGGAGTCAGT 60.909 55.000 0.00 0.00 0.00 3.41
4970 6552 0.461693 GATGCAGGCAGGAGTCAGTC 60.462 60.000 0.00 0.00 0.00 3.51
4971 6553 0.908656 ATGCAGGCAGGAGTCAGTCT 60.909 55.000 0.00 0.00 0.00 3.24
4972 6554 0.251787 TGCAGGCAGGAGTCAGTCTA 60.252 55.000 0.00 0.00 0.00 2.59
4973 6555 0.174617 GCAGGCAGGAGTCAGTCTAC 59.825 60.000 0.00 0.00 0.00 2.59
4974 6556 1.846007 CAGGCAGGAGTCAGTCTACT 58.154 55.000 0.00 0.00 37.96 2.57
4975 6557 2.175202 CAGGCAGGAGTCAGTCTACTT 58.825 52.381 0.00 0.00 34.61 2.24
4976 6558 2.094286 CAGGCAGGAGTCAGTCTACTTG 60.094 54.545 0.00 0.00 34.61 3.16
4977 6559 1.896465 GGCAGGAGTCAGTCTACTTGT 59.104 52.381 0.00 0.00 34.61 3.16
4978 6560 2.094442 GGCAGGAGTCAGTCTACTTGTC 60.094 54.545 0.00 0.00 34.61 3.18
4979 6561 2.558795 GCAGGAGTCAGTCTACTTGTCA 59.441 50.000 0.00 0.00 34.61 3.58
4980 6562 3.612955 GCAGGAGTCAGTCTACTTGTCAC 60.613 52.174 0.00 0.00 34.61 3.67
4981 6563 2.814919 AGGAGTCAGTCTACTTGTCACG 59.185 50.000 0.00 0.00 32.50 4.35
4982 6564 2.095161 GGAGTCAGTCTACTTGTCACGG 60.095 54.545 0.00 0.00 0.00 4.94
4983 6565 2.812591 GAGTCAGTCTACTTGTCACGGA 59.187 50.000 0.00 0.00 0.00 4.69
4984 6566 2.553172 AGTCAGTCTACTTGTCACGGAC 59.447 50.000 7.48 7.48 36.02 4.79
4985 6567 2.292569 GTCAGTCTACTTGTCACGGACA 59.707 50.000 3.02 3.02 41.09 4.02
4986 6568 3.057456 GTCAGTCTACTTGTCACGGACAT 60.057 47.826 7.43 0.00 42.40 3.06
4987 6569 3.057526 TCAGTCTACTTGTCACGGACATG 60.058 47.826 14.24 14.24 42.40 3.21
4988 6570 3.057526 CAGTCTACTTGTCACGGACATGA 60.058 47.826 19.51 9.46 42.40 3.07
4989 6571 3.764434 AGTCTACTTGTCACGGACATGAT 59.236 43.478 19.51 10.73 42.40 2.45
4990 6572 3.859961 GTCTACTTGTCACGGACATGATG 59.140 47.826 19.51 13.55 42.40 3.07
4991 6573 1.442769 ACTTGTCACGGACATGATGC 58.557 50.000 19.51 0.00 42.40 3.91
4992 6574 0.729116 CTTGTCACGGACATGATGCC 59.271 55.000 0.00 0.00 42.40 4.40
4993 6575 0.324614 TTGTCACGGACATGATGCCT 59.675 50.000 0.00 0.00 42.40 4.75
4994 6576 1.190643 TGTCACGGACATGATGCCTA 58.809 50.000 0.00 0.00 37.67 3.93
4995 6577 1.762370 TGTCACGGACATGATGCCTAT 59.238 47.619 0.00 0.00 37.67 2.57
4996 6578 2.962421 TGTCACGGACATGATGCCTATA 59.038 45.455 0.00 0.00 37.67 1.31
4997 6579 3.578282 TGTCACGGACATGATGCCTATAT 59.422 43.478 0.00 0.00 37.67 0.86
4998 6580 4.770010 TGTCACGGACATGATGCCTATATA 59.230 41.667 0.00 0.00 37.67 0.86
4999 6581 5.103000 GTCACGGACATGATGCCTATATAC 58.897 45.833 0.00 0.00 32.09 1.47
5000 6582 4.770010 TCACGGACATGATGCCTATATACA 59.230 41.667 0.00 0.00 0.00 2.29
5001 6583 5.422012 TCACGGACATGATGCCTATATACAT 59.578 40.000 0.00 0.00 0.00 2.29
5002 6584 5.521372 CACGGACATGATGCCTATATACATG 59.479 44.000 0.00 0.00 42.37 3.21
5003 6585 5.422012 ACGGACATGATGCCTATATACATGA 59.578 40.000 14.10 0.00 40.13 3.07
5004 6586 6.098838 ACGGACATGATGCCTATATACATGAT 59.901 38.462 14.10 0.09 40.13 2.45
5005 6587 6.644181 CGGACATGATGCCTATATACATGATC 59.356 42.308 14.10 9.18 40.13 2.92
5006 6588 7.503549 GGACATGATGCCTATATACATGATCA 58.496 38.462 14.10 0.00 40.13 2.92
5007 6589 8.155510 GGACATGATGCCTATATACATGATCAT 58.844 37.037 14.10 1.18 40.13 2.45
5034 6616 9.814899 ATCTACATATTCTCATAACTATGCTGC 57.185 33.333 0.00 0.00 33.76 5.25
5035 6617 6.957984 ACATATTCTCATAACTATGCTGCG 57.042 37.500 0.00 0.00 33.76 5.18
5036 6618 5.871524 ACATATTCTCATAACTATGCTGCGG 59.128 40.000 0.00 0.00 33.76 5.69
5037 6619 4.607293 ATTCTCATAACTATGCTGCGGA 57.393 40.909 0.00 0.00 33.76 5.54
5038 6620 4.607293 TTCTCATAACTATGCTGCGGAT 57.393 40.909 0.00 0.00 33.76 4.18
5039 6621 4.607293 TCTCATAACTATGCTGCGGATT 57.393 40.909 0.00 0.00 33.76 3.01
5040 6622 4.309933 TCTCATAACTATGCTGCGGATTG 58.690 43.478 0.00 0.00 33.76 2.67
5041 6623 4.039124 TCTCATAACTATGCTGCGGATTGA 59.961 41.667 0.00 0.00 33.76 2.57
5042 6624 4.309933 TCATAACTATGCTGCGGATTGAG 58.690 43.478 0.00 0.00 33.76 3.02
5043 6625 2.988010 AACTATGCTGCGGATTGAGA 57.012 45.000 0.00 0.00 0.00 3.27
5044 6626 2.988010 ACTATGCTGCGGATTGAGAA 57.012 45.000 0.00 0.00 0.00 2.87
5045 6627 3.266510 ACTATGCTGCGGATTGAGAAA 57.733 42.857 0.00 0.00 0.00 2.52
5046 6628 3.201290 ACTATGCTGCGGATTGAGAAAG 58.799 45.455 0.00 0.00 0.00 2.62
5047 6629 1.386533 ATGCTGCGGATTGAGAAAGG 58.613 50.000 0.00 0.00 0.00 3.11
5048 6630 0.324614 TGCTGCGGATTGAGAAAGGA 59.675 50.000 0.00 0.00 0.00 3.36
5049 6631 0.729690 GCTGCGGATTGAGAAAGGAC 59.270 55.000 0.00 0.00 0.00 3.85
5050 6632 1.677217 GCTGCGGATTGAGAAAGGACT 60.677 52.381 0.00 0.00 0.00 3.85
5051 6633 2.418746 GCTGCGGATTGAGAAAGGACTA 60.419 50.000 0.00 0.00 0.00 2.59
5052 6634 3.452474 CTGCGGATTGAGAAAGGACTAG 58.548 50.000 0.00 0.00 0.00 2.57
5053 6635 2.205911 GCGGATTGAGAAAGGACTAGC 58.794 52.381 0.00 0.00 0.00 3.42
5054 6636 2.827652 CGGATTGAGAAAGGACTAGCC 58.172 52.381 0.00 0.00 0.00 3.93
5055 6637 2.168521 CGGATTGAGAAAGGACTAGCCA 59.831 50.000 6.07 0.00 40.02 4.75
5056 6638 3.536570 GGATTGAGAAAGGACTAGCCAC 58.463 50.000 6.07 0.00 40.02 5.01
5057 6639 3.536570 GATTGAGAAAGGACTAGCCACC 58.463 50.000 6.07 0.35 40.02 4.61
5058 6640 1.276622 TGAGAAAGGACTAGCCACCC 58.723 55.000 6.07 0.00 40.02 4.61
5059 6641 1.203313 TGAGAAAGGACTAGCCACCCT 60.203 52.381 6.07 0.00 40.02 4.34
5060 6642 2.043939 TGAGAAAGGACTAGCCACCCTA 59.956 50.000 6.07 0.00 40.02 3.53
5061 6643 3.105283 GAGAAAGGACTAGCCACCCTAA 58.895 50.000 6.07 0.00 40.02 2.69
5062 6644 2.838813 AGAAAGGACTAGCCACCCTAAC 59.161 50.000 6.07 0.05 40.02 2.34
5063 6645 2.644060 AAGGACTAGCCACCCTAACT 57.356 50.000 6.07 0.00 40.02 2.24
5064 6646 2.162264 AGGACTAGCCACCCTAACTC 57.838 55.000 6.07 0.00 40.02 3.01
5065 6647 1.361543 AGGACTAGCCACCCTAACTCA 59.638 52.381 6.07 0.00 40.02 3.41
5066 6648 2.185387 GGACTAGCCACCCTAACTCAA 58.815 52.381 0.00 0.00 36.34 3.02
5067 6649 2.570302 GGACTAGCCACCCTAACTCAAA 59.430 50.000 0.00 0.00 36.34 2.69
5068 6650 3.008704 GGACTAGCCACCCTAACTCAAAA 59.991 47.826 0.00 0.00 36.34 2.44
5069 6651 4.001652 GACTAGCCACCCTAACTCAAAAC 58.998 47.826 0.00 0.00 0.00 2.43
5070 6652 2.287977 AGCCACCCTAACTCAAAACC 57.712 50.000 0.00 0.00 0.00 3.27
5071 6653 1.497286 AGCCACCCTAACTCAAAACCA 59.503 47.619 0.00 0.00 0.00 3.67
5072 6654 1.886542 GCCACCCTAACTCAAAACCAG 59.113 52.381 0.00 0.00 0.00 4.00
5073 6655 2.514803 CCACCCTAACTCAAAACCAGG 58.485 52.381 0.00 0.00 0.00 4.45
5074 6656 1.886542 CACCCTAACTCAAAACCAGGC 59.113 52.381 0.00 0.00 0.00 4.85
5075 6657 1.497286 ACCCTAACTCAAAACCAGGCA 59.503 47.619 0.00 0.00 0.00 4.75
5076 6658 2.091555 ACCCTAACTCAAAACCAGGCAA 60.092 45.455 0.00 0.00 0.00 4.52
5077 6659 2.558359 CCCTAACTCAAAACCAGGCAAG 59.442 50.000 0.00 0.00 0.00 4.01
5078 6660 2.029918 CCTAACTCAAAACCAGGCAAGC 60.030 50.000 0.00 0.00 0.00 4.01
5079 6661 0.752658 AACTCAAAACCAGGCAAGCC 59.247 50.000 2.02 2.02 0.00 4.35
5081 6663 1.144913 ACTCAAAACCAGGCAAGCCTA 59.855 47.619 14.18 0.00 46.28 3.93
5082 6664 1.815003 CTCAAAACCAGGCAAGCCTAG 59.185 52.381 14.18 9.33 46.28 3.02
5083 6665 1.423541 TCAAAACCAGGCAAGCCTAGA 59.576 47.619 14.18 2.78 46.28 2.43
5084 6666 1.815003 CAAAACCAGGCAAGCCTAGAG 59.185 52.381 14.18 8.24 46.28 2.43
5085 6667 1.362224 AAACCAGGCAAGCCTAGAGA 58.638 50.000 14.18 0.00 46.28 3.10
5086 6668 0.908198 AACCAGGCAAGCCTAGAGAG 59.092 55.000 14.18 0.59 46.28 3.20
5087 6669 0.041833 ACCAGGCAAGCCTAGAGAGA 59.958 55.000 14.18 0.00 46.28 3.10
5088 6670 1.198713 CCAGGCAAGCCTAGAGAGAA 58.801 55.000 14.18 0.00 46.28 2.87
5089 6671 1.767681 CCAGGCAAGCCTAGAGAGAAT 59.232 52.381 14.18 0.00 46.28 2.40
5090 6672 2.224257 CCAGGCAAGCCTAGAGAGAATC 60.224 54.545 14.18 0.00 46.28 2.52
5091 6673 2.433604 CAGGCAAGCCTAGAGAGAATCA 59.566 50.000 14.18 0.00 46.28 2.57
5092 6674 3.071312 CAGGCAAGCCTAGAGAGAATCAT 59.929 47.826 14.18 0.00 46.28 2.45
5093 6675 3.071312 AGGCAAGCCTAGAGAGAATCATG 59.929 47.826 12.82 0.00 46.14 3.07
5094 6676 3.401182 GCAAGCCTAGAGAGAATCATGG 58.599 50.000 0.00 0.00 37.82 3.66
5095 6677 3.070734 GCAAGCCTAGAGAGAATCATGGA 59.929 47.826 0.00 0.00 37.82 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.936203 GTCCACAGACGCCACCCA 61.936 66.667 0.00 0.00 32.18 4.51
95 103 7.362056 CGACAAACAAATCAAATCTGACCCTAT 60.362 37.037 0.00 0.00 33.30 2.57
471 490 8.653191 TCATTCAAAACCTCAAAGTACTACCTA 58.347 33.333 0.00 0.00 0.00 3.08
696 737 4.637276 TGTCCTTCACGACACATACAATT 58.363 39.130 0.00 0.00 37.85 2.32
729 778 9.363401 AGGATTGAACATCATCATCAACAATAT 57.637 29.630 0.00 0.00 36.03 1.28
1010 1137 1.806542 CAGTTGCACGTCCAATAAGCT 59.193 47.619 0.00 0.00 0.00 3.74
1273 1400 6.092670 CGGAGTCAATGTCAGTTGTAATCATT 59.907 38.462 0.00 0.00 0.00 2.57
1308 1452 1.769026 TGCACCACAAGCAACCTAAA 58.231 45.000 0.00 0.00 39.39 1.85
1310 1454 3.503998 TTGCACCACAAGCAACCTA 57.496 47.368 0.00 0.00 46.13 3.08
1338 1482 3.072330 TGAGTTGCCACTTCTATGAACCA 59.928 43.478 0.00 0.00 31.22 3.67
1427 1571 4.278419 ACTTCTGTGCAATTAACTCCAACC 59.722 41.667 0.00 0.00 0.00 3.77
1428 1572 5.438761 ACTTCTGTGCAATTAACTCCAAC 57.561 39.130 0.00 0.00 0.00 3.77
1429 1573 5.472137 GGTACTTCTGTGCAATTAACTCCAA 59.528 40.000 0.00 0.00 0.00 3.53
1490 1634 5.404968 TGGTACTGACACGTAAAAATTACCG 59.595 40.000 0.00 0.00 30.93 4.02
1566 1710 1.337817 CGCTGTCAGTTTCTCCGTCG 61.338 60.000 0.93 0.00 0.00 5.12
1631 1892 8.126700 GTGTGATTAAATATAAACCGAGGGTTG 58.873 37.037 2.08 0.00 46.20 3.77
1633 1894 7.340256 TGTGTGATTAAATATAAACCGAGGGT 58.660 34.615 0.00 0.00 37.65 4.34
1726 2006 2.046217 GGACTTTCCCTCGGGCAC 60.046 66.667 0.00 0.00 34.68 5.01
1803 2083 9.884465 GCAAGAAATATGGTTTCTGATGTATAC 57.116 33.333 8.22 0.00 38.62 1.47
1881 2167 2.039879 AGGCCAGGACGTGTCTAAAAAT 59.960 45.455 5.01 0.00 0.00 1.82
1908 2194 7.523219 CGCAAAAGTTTTAAAAAGGAAAACCT 58.477 30.769 1.31 0.00 44.36 3.50
2051 2340 7.452880 AATATACATGTATTGCCGCTGAAAT 57.547 32.000 22.90 4.37 0.00 2.17
2060 2349 9.296400 ACCGTTTTTGAAATATACATGTATTGC 57.704 29.630 22.90 7.95 0.00 3.56
3202 4263 0.459489 TTGCTGGGCAACTGTTTCAC 59.541 50.000 0.51 0.00 43.99 3.18
3214 4275 4.979943 AAAAACCATTTTTGTTGCTGGG 57.020 36.364 0.00 0.00 41.04 4.45
3281 4342 0.961019 AGACCACTACGTTACGCCAA 59.039 50.000 4.09 0.00 0.00 4.52
3300 4361 2.682494 CCGAGGGAAGGGAACGGA 60.682 66.667 0.00 0.00 45.31 4.69
3393 4456 2.380064 TGAATCACACAAAGGGCCTT 57.620 45.000 14.48 14.48 0.00 4.35
3411 4474 6.378280 ACAGAAAAACCCCTCAGCTTATATTG 59.622 38.462 0.00 0.00 0.00 1.90
3576 4649 3.133362 CACAATTGGGGCATTAGAAGCAT 59.867 43.478 10.83 0.00 0.00 3.79
3609 4682 3.682858 CCACAACCGATCGAGTTAATTGT 59.317 43.478 18.66 13.10 0.00 2.71
3621 4694 1.600485 GAAAACACGACCACAACCGAT 59.400 47.619 0.00 0.00 0.00 4.18
3622 4695 1.008329 GAAAACACGACCACAACCGA 58.992 50.000 0.00 0.00 0.00 4.69
3623 4696 1.011333 AGAAAACACGACCACAACCG 58.989 50.000 0.00 0.00 0.00 4.44
3803 5283 8.963130 CAAATTAACTGTCAGCGATTTGTTTTA 58.037 29.630 18.66 1.03 32.62 1.52
3850 5330 3.198068 TCTCTGCACAACTCTTGACAAC 58.802 45.455 0.00 0.00 0.00 3.32
3902 5394 5.044919 TCCATCTTCTCCTTTATTTCCTGCA 60.045 40.000 0.00 0.00 0.00 4.41
3980 5472 2.687566 CCCCTGCCTCGGTTACCT 60.688 66.667 0.00 0.00 0.00 3.08
4199 5712 3.519510 TCCAATTCGGACCAAATCTCTCT 59.480 43.478 0.00 0.00 39.64 3.10
4306 5836 7.431249 TCTGAACACGAAGTAACTACAATTCT 58.569 34.615 0.00 0.00 41.61 2.40
4473 6008 4.194640 ACGTAGAGTCCTTAATACGAGCA 58.805 43.478 13.82 0.00 42.66 4.26
4774 6356 2.034999 CTTTGGTTAGGCGGGGCA 59.965 61.111 0.00 0.00 0.00 5.36
4854 6436 2.568062 TGCATTGCAATGGGAGAAACAT 59.432 40.909 34.23 0.00 34.76 2.71
4893 6475 7.117523 CCAGCATGCATCTAGAGTATTAAGTTC 59.882 40.741 21.98 0.00 31.97 3.01
4894 6476 6.933521 CCAGCATGCATCTAGAGTATTAAGTT 59.066 38.462 21.98 0.00 31.97 2.66
4895 6477 6.268617 TCCAGCATGCATCTAGAGTATTAAGT 59.731 38.462 21.98 0.00 31.97 2.24
4896 6478 6.695429 TCCAGCATGCATCTAGAGTATTAAG 58.305 40.000 21.98 0.00 31.97 1.85
4900 6482 6.468333 CTATCCAGCATGCATCTAGAGTAT 57.532 41.667 21.98 2.66 31.97 2.12
4901 6483 5.911378 CTATCCAGCATGCATCTAGAGTA 57.089 43.478 21.98 0.94 31.97 2.59
4902 6484 4.804868 CTATCCAGCATGCATCTAGAGT 57.195 45.455 21.98 0.00 31.97 3.24
4915 6497 0.941463 CACATCGACCGCTATCCAGC 60.941 60.000 0.00 0.00 44.90 4.85
4916 6498 0.385751 ACACATCGACCGCTATCCAG 59.614 55.000 0.00 0.00 0.00 3.86
4917 6499 0.102300 CACACATCGACCGCTATCCA 59.898 55.000 0.00 0.00 0.00 3.41
4918 6500 0.597637 CCACACATCGACCGCTATCC 60.598 60.000 0.00 0.00 0.00 2.59
4919 6501 0.384309 TCCACACATCGACCGCTATC 59.616 55.000 0.00 0.00 0.00 2.08
4920 6502 0.385751 CTCCACACATCGACCGCTAT 59.614 55.000 0.00 0.00 0.00 2.97
4921 6503 0.963856 ACTCCACACATCGACCGCTA 60.964 55.000 0.00 0.00 0.00 4.26
4922 6504 0.963856 TACTCCACACATCGACCGCT 60.964 55.000 0.00 0.00 0.00 5.52
4923 6505 0.108992 TTACTCCACACATCGACCGC 60.109 55.000 0.00 0.00 0.00 5.68
4924 6506 2.579207 ATTACTCCACACATCGACCG 57.421 50.000 0.00 0.00 0.00 4.79
4925 6507 4.650754 ACTATTACTCCACACATCGACC 57.349 45.455 0.00 0.00 0.00 4.79
4926 6508 6.374565 ACTACTATTACTCCACACATCGAC 57.625 41.667 0.00 0.00 0.00 4.20
4927 6509 7.503549 TCTACTACTATTACTCCACACATCGA 58.496 38.462 0.00 0.00 0.00 3.59
4928 6510 7.725818 TCTACTACTATTACTCCACACATCG 57.274 40.000 0.00 0.00 0.00 3.84
4929 6511 8.024285 GCATCTACTACTATTACTCCACACATC 58.976 40.741 0.00 0.00 0.00 3.06
4930 6512 7.505923 TGCATCTACTACTATTACTCCACACAT 59.494 37.037 0.00 0.00 0.00 3.21
4931 6513 6.831868 TGCATCTACTACTATTACTCCACACA 59.168 38.462 0.00 0.00 0.00 3.72
4932 6514 7.273320 TGCATCTACTACTATTACTCCACAC 57.727 40.000 0.00 0.00 0.00 3.82
4933 6515 6.490381 CCTGCATCTACTACTATTACTCCACA 59.510 42.308 0.00 0.00 0.00 4.17
4934 6516 6.570764 GCCTGCATCTACTACTATTACTCCAC 60.571 46.154 0.00 0.00 0.00 4.02
4935 6517 5.477291 GCCTGCATCTACTACTATTACTCCA 59.523 44.000 0.00 0.00 0.00 3.86
4936 6518 5.477291 TGCCTGCATCTACTACTATTACTCC 59.523 44.000 0.00 0.00 0.00 3.85
4937 6519 6.349777 CCTGCCTGCATCTACTACTATTACTC 60.350 46.154 0.00 0.00 0.00 2.59
4938 6520 5.478679 CCTGCCTGCATCTACTACTATTACT 59.521 44.000 0.00 0.00 0.00 2.24
4939 6521 5.477291 TCCTGCCTGCATCTACTACTATTAC 59.523 44.000 0.00 0.00 0.00 1.89
4940 6522 5.641155 TCCTGCCTGCATCTACTACTATTA 58.359 41.667 0.00 0.00 0.00 0.98
4941 6523 4.483950 TCCTGCCTGCATCTACTACTATT 58.516 43.478 0.00 0.00 0.00 1.73
4942 6524 4.085733 CTCCTGCCTGCATCTACTACTAT 58.914 47.826 0.00 0.00 0.00 2.12
4943 6525 3.117474 ACTCCTGCCTGCATCTACTACTA 60.117 47.826 0.00 0.00 0.00 1.82
4944 6526 2.315176 CTCCTGCCTGCATCTACTACT 58.685 52.381 0.00 0.00 0.00 2.57
4945 6527 2.035321 GACTCCTGCCTGCATCTACTAC 59.965 54.545 0.00 0.00 0.00 2.73
4946 6528 2.311463 GACTCCTGCCTGCATCTACTA 58.689 52.381 0.00 0.00 0.00 1.82
4947 6529 1.118838 GACTCCTGCCTGCATCTACT 58.881 55.000 0.00 0.00 0.00 2.57
4948 6530 0.826715 TGACTCCTGCCTGCATCTAC 59.173 55.000 0.00 0.00 0.00 2.59
4949 6531 1.117994 CTGACTCCTGCCTGCATCTA 58.882 55.000 0.00 0.00 0.00 1.98
4950 6532 0.908656 ACTGACTCCTGCCTGCATCT 60.909 55.000 0.00 0.00 0.00 2.90
4951 6533 0.461693 GACTGACTCCTGCCTGCATC 60.462 60.000 0.00 0.00 0.00 3.91
4952 6534 0.908656 AGACTGACTCCTGCCTGCAT 60.909 55.000 0.00 0.00 0.00 3.96
4953 6535 0.251787 TAGACTGACTCCTGCCTGCA 60.252 55.000 0.00 0.00 0.00 4.41
4954 6536 0.174617 GTAGACTGACTCCTGCCTGC 59.825 60.000 0.00 0.00 0.00 4.85
4955 6537 1.846007 AGTAGACTGACTCCTGCCTG 58.154 55.000 0.00 0.00 0.00 4.85
4956 6538 2.175202 CAAGTAGACTGACTCCTGCCT 58.825 52.381 0.00 0.00 0.00 4.75
4957 6539 1.896465 ACAAGTAGACTGACTCCTGCC 59.104 52.381 0.00 0.00 0.00 4.85
4958 6540 2.558795 TGACAAGTAGACTGACTCCTGC 59.441 50.000 0.00 0.00 0.00 4.85
4959 6541 3.365465 CGTGACAAGTAGACTGACTCCTG 60.365 52.174 0.00 0.00 0.00 3.86
4960 6542 2.814919 CGTGACAAGTAGACTGACTCCT 59.185 50.000 0.00 0.00 0.00 3.69
4961 6543 2.095161 CCGTGACAAGTAGACTGACTCC 60.095 54.545 0.00 0.00 0.00 3.85
4962 6544 2.812591 TCCGTGACAAGTAGACTGACTC 59.187 50.000 0.00 0.00 0.00 3.36
4963 6545 2.553172 GTCCGTGACAAGTAGACTGACT 59.447 50.000 0.00 0.00 32.09 3.41
4964 6546 2.292569 TGTCCGTGACAAGTAGACTGAC 59.707 50.000 4.51 0.00 39.78 3.51
4965 6547 2.578786 TGTCCGTGACAAGTAGACTGA 58.421 47.619 4.51 0.00 39.78 3.41
4966 6548 3.057526 TCATGTCCGTGACAAGTAGACTG 60.058 47.826 10.17 3.87 45.96 3.51
4967 6549 3.154710 TCATGTCCGTGACAAGTAGACT 58.845 45.455 10.17 0.00 45.96 3.24
4968 6550 3.570926 TCATGTCCGTGACAAGTAGAC 57.429 47.619 10.17 0.00 45.96 2.59
4969 6551 3.676049 GCATCATGTCCGTGACAAGTAGA 60.676 47.826 10.17 7.28 45.96 2.59
4970 6552 2.604914 GCATCATGTCCGTGACAAGTAG 59.395 50.000 10.17 5.54 45.96 2.57
4971 6553 2.616960 GCATCATGTCCGTGACAAGTA 58.383 47.619 10.17 1.37 45.96 2.24
4972 6554 1.442769 GCATCATGTCCGTGACAAGT 58.557 50.000 10.17 0.00 45.96 3.16
4973 6555 0.729116 GGCATCATGTCCGTGACAAG 59.271 55.000 10.17 6.82 45.96 3.16
4974 6556 0.324614 AGGCATCATGTCCGTGACAA 59.675 50.000 10.17 0.00 45.96 3.18
4975 6557 1.190643 TAGGCATCATGTCCGTGACA 58.809 50.000 8.81 8.81 46.90 3.58
4976 6558 2.533266 ATAGGCATCATGTCCGTGAC 57.467 50.000 0.00 0.00 0.00 3.67
4977 6559 4.770010 TGTATATAGGCATCATGTCCGTGA 59.230 41.667 0.00 0.00 0.00 4.35
4978 6560 5.072040 TGTATATAGGCATCATGTCCGTG 57.928 43.478 0.00 0.00 0.00 4.94
4979 6561 5.422012 TCATGTATATAGGCATCATGTCCGT 59.578 40.000 9.06 0.00 37.64 4.69
4980 6562 5.906073 TCATGTATATAGGCATCATGTCCG 58.094 41.667 9.06 0.00 37.64 4.79
4981 6563 7.503549 TGATCATGTATATAGGCATCATGTCC 58.496 38.462 9.06 0.00 37.64 4.02
5008 6590 9.814899 GCAGCATAGTTATGAGAATATGTAGAT 57.185 33.333 3.38 0.00 35.75 1.98
5009 6591 7.970614 CGCAGCATAGTTATGAGAATATGTAGA 59.029 37.037 3.38 0.00 35.75 2.59
5010 6592 7.221645 CCGCAGCATAGTTATGAGAATATGTAG 59.778 40.741 3.38 0.00 35.75 2.74
5011 6593 7.035612 CCGCAGCATAGTTATGAGAATATGTA 58.964 38.462 3.38 0.00 35.75 2.29
5012 6594 5.871524 CCGCAGCATAGTTATGAGAATATGT 59.128 40.000 3.38 0.00 35.75 2.29
5013 6595 6.101997 TCCGCAGCATAGTTATGAGAATATG 58.898 40.000 3.38 0.00 35.75 1.78
5014 6596 6.286240 TCCGCAGCATAGTTATGAGAATAT 57.714 37.500 3.38 0.00 35.75 1.28
5015 6597 5.722021 TCCGCAGCATAGTTATGAGAATA 57.278 39.130 3.38 0.00 35.75 1.75
5016 6598 4.607293 TCCGCAGCATAGTTATGAGAAT 57.393 40.909 3.38 0.00 35.75 2.40
5017 6599 4.607293 ATCCGCAGCATAGTTATGAGAA 57.393 40.909 3.38 0.00 35.75 2.87
5018 6600 4.039124 TCAATCCGCAGCATAGTTATGAGA 59.961 41.667 3.38 0.00 35.75 3.27
5019 6601 4.309933 TCAATCCGCAGCATAGTTATGAG 58.690 43.478 3.38 0.00 35.75 2.90
5020 6602 4.039124 TCTCAATCCGCAGCATAGTTATGA 59.961 41.667 3.38 0.00 35.75 2.15
5021 6603 4.309933 TCTCAATCCGCAGCATAGTTATG 58.690 43.478 0.00 0.00 36.78 1.90
5022 6604 4.607293 TCTCAATCCGCAGCATAGTTAT 57.393 40.909 0.00 0.00 0.00 1.89
5023 6605 4.400529 TTCTCAATCCGCAGCATAGTTA 57.599 40.909 0.00 0.00 0.00 2.24
5024 6606 2.988010 TCTCAATCCGCAGCATAGTT 57.012 45.000 0.00 0.00 0.00 2.24
5025 6607 2.988010 TTCTCAATCCGCAGCATAGT 57.012 45.000 0.00 0.00 0.00 2.12
5026 6608 2.547211 CCTTTCTCAATCCGCAGCATAG 59.453 50.000 0.00 0.00 0.00 2.23
5027 6609 2.170397 TCCTTTCTCAATCCGCAGCATA 59.830 45.455 0.00 0.00 0.00 3.14
5028 6610 1.065199 TCCTTTCTCAATCCGCAGCAT 60.065 47.619 0.00 0.00 0.00 3.79
5029 6611 0.324614 TCCTTTCTCAATCCGCAGCA 59.675 50.000 0.00 0.00 0.00 4.41
5030 6612 0.729690 GTCCTTTCTCAATCCGCAGC 59.270 55.000 0.00 0.00 0.00 5.25
5031 6613 2.393271 AGTCCTTTCTCAATCCGCAG 57.607 50.000 0.00 0.00 0.00 5.18
5032 6614 2.418746 GCTAGTCCTTTCTCAATCCGCA 60.419 50.000 0.00 0.00 0.00 5.69
5033 6615 2.205911 GCTAGTCCTTTCTCAATCCGC 58.794 52.381 0.00 0.00 0.00 5.54
5034 6616 2.168521 TGGCTAGTCCTTTCTCAATCCG 59.831 50.000 0.00 0.00 35.26 4.18
5035 6617 3.536570 GTGGCTAGTCCTTTCTCAATCC 58.463 50.000 0.00 0.00 35.26 3.01
5036 6618 3.536570 GGTGGCTAGTCCTTTCTCAATC 58.463 50.000 0.00 0.00 35.26 2.67
5037 6619 2.239907 GGGTGGCTAGTCCTTTCTCAAT 59.760 50.000 0.00 0.00 35.26 2.57
5038 6620 1.628846 GGGTGGCTAGTCCTTTCTCAA 59.371 52.381 0.00 0.00 35.26 3.02
5039 6621 1.203313 AGGGTGGCTAGTCCTTTCTCA 60.203 52.381 0.00 0.00 35.26 3.27
5040 6622 1.574263 AGGGTGGCTAGTCCTTTCTC 58.426 55.000 0.00 0.00 35.26 2.87
5041 6623 2.838813 GTTAGGGTGGCTAGTCCTTTCT 59.161 50.000 0.00 0.00 35.26 2.52
5042 6624 2.838813 AGTTAGGGTGGCTAGTCCTTTC 59.161 50.000 0.00 0.00 35.26 2.62
5043 6625 2.838813 GAGTTAGGGTGGCTAGTCCTTT 59.161 50.000 0.00 0.00 35.26 3.11
5044 6626 2.225547 TGAGTTAGGGTGGCTAGTCCTT 60.226 50.000 0.00 0.00 35.26 3.36
5045 6627 1.361543 TGAGTTAGGGTGGCTAGTCCT 59.638 52.381 0.00 0.00 35.26 3.85
5046 6628 1.861982 TGAGTTAGGGTGGCTAGTCC 58.138 55.000 0.00 0.00 0.00 3.85
5047 6629 3.975168 TTTGAGTTAGGGTGGCTAGTC 57.025 47.619 0.00 0.00 0.00 2.59
5048 6630 3.244805 GGTTTTGAGTTAGGGTGGCTAGT 60.245 47.826 0.00 0.00 0.00 2.57
5049 6631 3.244770 TGGTTTTGAGTTAGGGTGGCTAG 60.245 47.826 0.00 0.00 0.00 3.42
5050 6632 2.712087 TGGTTTTGAGTTAGGGTGGCTA 59.288 45.455 0.00 0.00 0.00 3.93
5051 6633 1.497286 TGGTTTTGAGTTAGGGTGGCT 59.503 47.619 0.00 0.00 0.00 4.75
5052 6634 1.886542 CTGGTTTTGAGTTAGGGTGGC 59.113 52.381 0.00 0.00 0.00 5.01
5053 6635 2.514803 CCTGGTTTTGAGTTAGGGTGG 58.485 52.381 0.00 0.00 0.00 4.61
5054 6636 1.886542 GCCTGGTTTTGAGTTAGGGTG 59.113 52.381 0.00 0.00 0.00 4.61
5055 6637 1.497286 TGCCTGGTTTTGAGTTAGGGT 59.503 47.619 0.00 0.00 0.00 4.34
5056 6638 2.286365 TGCCTGGTTTTGAGTTAGGG 57.714 50.000 0.00 0.00 0.00 3.53
5057 6639 2.029918 GCTTGCCTGGTTTTGAGTTAGG 60.030 50.000 0.00 0.00 0.00 2.69
5058 6640 2.029918 GGCTTGCCTGGTTTTGAGTTAG 60.030 50.000 4.11 0.00 0.00 2.34
5059 6641 1.960689 GGCTTGCCTGGTTTTGAGTTA 59.039 47.619 4.11 0.00 0.00 2.24
5060 6642 0.752658 GGCTTGCCTGGTTTTGAGTT 59.247 50.000 4.11 0.00 0.00 3.01
5061 6643 0.106015 AGGCTTGCCTGGTTTTGAGT 60.106 50.000 13.99 0.00 0.00 3.41
5062 6644 1.815003 CTAGGCTTGCCTGGTTTTGAG 59.185 52.381 23.03 7.59 0.00 3.02
5063 6645 1.423541 TCTAGGCTTGCCTGGTTTTGA 59.576 47.619 23.03 9.10 0.00 2.69
5064 6646 1.815003 CTCTAGGCTTGCCTGGTTTTG 59.185 52.381 23.03 9.28 0.00 2.44
5065 6647 1.705186 TCTCTAGGCTTGCCTGGTTTT 59.295 47.619 23.03 0.00 0.00 2.43
5066 6648 1.280421 CTCTCTAGGCTTGCCTGGTTT 59.720 52.381 23.03 0.00 0.00 3.27
5067 6649 0.908198 CTCTCTAGGCTTGCCTGGTT 59.092 55.000 23.03 0.35 0.00 3.67
5068 6650 0.041833 TCTCTCTAGGCTTGCCTGGT 59.958 55.000 23.03 0.73 0.00 4.00
5069 6651 1.198713 TTCTCTCTAGGCTTGCCTGG 58.801 55.000 23.03 20.15 0.00 4.45
5070 6652 2.433604 TGATTCTCTCTAGGCTTGCCTG 59.566 50.000 23.03 13.19 0.00 4.85
5071 6653 2.756907 TGATTCTCTCTAGGCTTGCCT 58.243 47.619 18.74 18.74 0.00 4.75
5072 6654 3.401182 CATGATTCTCTCTAGGCTTGCC 58.599 50.000 2.97 2.97 0.00 4.52
5073 6655 3.070734 TCCATGATTCTCTCTAGGCTTGC 59.929 47.826 0.00 0.00 0.00 4.01
5074 6656 4.952071 TCCATGATTCTCTCTAGGCTTG 57.048 45.455 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.