Multiple sequence alignment - TraesCS6A01G234100

Loading Multiple Alignment...

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 TraesCS6A01G234100 chr6A 100.000 5140 0 0 1 5140 441524303 441519164 0.000000e+00 9492.0
1 TraesCS6A01G234100 chr6A 97.572 659 16 0 1706 2364 604836012 604836670 0.000000e+00 1129.0
2 TraesCS6A01G234100 chr6A 97.269 659 17 1 1706 2363 158913941 158914599 0.000000e+00 1116.0
3 TraesCS6A01G234100 chr6A 97.170 106 3 0 5035 5140 29887376 29887481 4.090000e-41 180.0
4 TraesCS6A01G234100 chr6D 95.034 2517 80 19 2558 5037 306145335 306142827 0.000000e+00 3914.0
5 TraesCS6A01G234100 chr6D 94.945 811 26 8 900 1708 306146134 306145337 0.000000e+00 1256.0
6 TraesCS6A01G234100 chr6D 86.422 928 86 21 1 892 306147095 306146172 0.000000e+00 979.0
7 TraesCS6A01G234100 chr6D 97.073 205 6 0 2356 2560 79863991 79864195 3.810000e-91 346.0
8 TraesCS6A01G234100 chr6D 93.220 118 7 1 5023 5140 395474659 395474775 6.840000e-39 172.0
9 TraesCS6A01G234100 chr6D 94.595 111 5 1 5030 5140 91173728 91173619 2.460000e-38 171.0
10 TraesCS6A01G234100 chr6D 95.283 106 5 0 5035 5140 62899246 62899351 8.850000e-38 169.0
11 TraesCS6A01G234100 chr6D 95.455 44 2 0 4285 4328 282079159 282079202 2.570000e-08 71.3
12 TraesCS6A01G234100 chr6D 93.617 47 3 0 4284 4330 344172557 344172511 2.570000e-08 71.3
13 TraesCS6A01G234100 chr6B 92.852 2546 100 33 2558 5037 473088275 473085746 0.000000e+00 3618.0
14 TraesCS6A01G234100 chr6B 93.342 796 31 8 911 1705 473089054 473088280 0.000000e+00 1157.0
15 TraesCS6A01G234100 chr6B 79.434 778 113 23 61 821 473089854 473089107 1.650000e-139 507.0
16 TraesCS6A01G234100 chr3D 93.772 835 38 9 1740 2560 487413330 487414164 0.000000e+00 1242.0
17 TraesCS6A01G234100 chr2D 98.328 658 11 0 1706 2363 20651269 20651926 0.000000e+00 1155.0
18 TraesCS6A01G234100 chr2D 97.576 660 14 2 1705 2363 205593318 205592660 0.000000e+00 1129.0
19 TraesCS6A01G234100 chr2D 97.115 208 6 0 2356 2563 435769681 435769474 8.190000e-93 351.0
20 TraesCS6A01G234100 chr2D 94.783 115 6 0 5026 5140 622425345 622425231 4.090000e-41 180.0
21 TraesCS6A01G234100 chr2D 93.805 113 7 0 5025 5137 191199077 191199189 2.460000e-38 171.0
22 TraesCS6A01G234100 chr2D 97.826 46 1 0 4283 4328 83962520 83962475 4.270000e-11 80.5
23 TraesCS6A01G234100 chr2D 93.750 48 1 2 4284 4330 367239376 367239330 2.570000e-08 71.3
24 TraesCS6A01G234100 chr1D 98.024 658 13 0 1706 2363 460551614 460550957 0.000000e+00 1144.0
25 TraesCS6A01G234100 chr1D 97.549 204 4 1 2360 2563 468556753 468556551 1.060000e-91 348.0
26 TraesCS6A01G234100 chr1D 96.635 208 7 0 2356 2563 149533104 149532897 3.810000e-91 346.0
27 TraesCS6A01G234100 chr1D 97.087 206 5 1 2356 2560 486710343 486710548 3.810000e-91 346.0
28 TraesCS6A01G234100 chr1D 97.170 106 3 0 5035 5140 419176951 419177056 4.090000e-41 180.0
29 TraesCS6A01G234100 chr1D 95.495 111 4 1 5031 5140 107485905 107485795 5.290000e-40 176.0
30 TraesCS6A01G234100 chr1D 96.190 105 4 0 5036 5140 196003268 196003372 6.840000e-39 172.0
31 TraesCS6A01G234100 chr1D 95.238 105 5 0 5036 5140 488605919 488605815 3.180000e-37 167.0
32 TraesCS6A01G234100 chr1D 90.000 50 3 2 4279 4327 468248425 468248473 4.300000e-06 63.9
33 TraesCS6A01G234100 chr1D 90.698 43 4 0 4286 4328 335584676 335584718 2.000000e-04 58.4
34 TraesCS6A01G234100 chr7A 97.872 658 14 0 1706 2363 497684728 497684071 0.000000e+00 1138.0
35 TraesCS6A01G234100 chr7A 92.157 51 4 0 4277 4327 83530387 83530437 7.140000e-09 73.1
36 TraesCS6A01G234100 chr7D 97.720 658 15 0 1706 2363 556706286 556705629 0.000000e+00 1133.0
37 TraesCS6A01G234100 chr7D 97.565 657 15 1 1706 2362 374567552 374568207 0.000000e+00 1123.0
38 TraesCS6A01G234100 chr7D 96.364 110 4 0 5031 5140 52450119 52450010 1.140000e-41 182.0
39 TraesCS6A01G234100 chr7D 97.143 105 3 0 5036 5140 622031859 622031755 1.470000e-40 178.0
40 TraesCS6A01G234100 chr5D 97.568 658 15 1 1706 2363 310266256 310266912 0.000000e+00 1125.0
41 TraesCS6A01G234100 chr5D 96.226 106 4 0 5035 5140 44933856 44933961 1.900000e-39 174.0
42 TraesCS6A01G234100 chr5D 95.238 42 2 0 4285 4326 482889470 482889429 3.320000e-07 67.6
43 TraesCS6A01G234100 chr5D 91.304 46 4 0 4284 4329 558893877 558893832 4.300000e-06 63.9
44 TraesCS6A01G234100 chr5D 97.143 35 1 0 4283 4317 563599628 563599662 5.560000e-05 60.2
45 TraesCS6A01G234100 chr3A 97.561 205 5 0 2356 2560 738074818 738075022 8.190000e-93 351.0
46 TraesCS6A01G234100 chr3A 96.226 106 4 0 5035 5140 11173396 11173291 1.900000e-39 174.0
47 TraesCS6A01G234100 chr3A 91.803 122 10 0 5019 5140 743321417 743321296 2.460000e-38 171.0
48 TraesCS6A01G234100 chr4D 96.635 208 7 0 2356 2563 22936890 22936683 3.810000e-91 346.0
49 TraesCS6A01G234100 chr4D 96.635 208 7 0 2356 2563 431414554 431414347 3.810000e-91 346.0
50 TraesCS6A01G234100 chr4D 96.154 104 4 0 5037 5140 418827437 418827540 2.460000e-38 171.0
51 TraesCS6A01G234100 chr4D 96.154 104 4 0 5037 5140 460958329 460958432 2.460000e-38 171.0
52 TraesCS6A01G234100 chr4D 97.619 42 1 0 4287 4328 87721795 87721754 7.140000e-09 73.1
53 TraesCS6A01G234100 chr5B 94.783 115 5 1 5026 5140 689171657 689171544 1.470000e-40 178.0
54 TraesCS6A01G234100 chr5B 97.115 104 3 0 5037 5140 16209172 16209275 5.290000e-40 176.0
55 TraesCS6A01G234100 chr5B 97.727 44 1 0 4283 4326 696337380 696337337 5.520000e-10 76.8
56 TraesCS6A01G234100 chr5B 97.368 38 1 0 4284 4321 685672422 685672459 1.190000e-06 65.8
57 TraesCS6A01G234100 chr5A 94.068 118 6 1 5023 5140 11889552 11889668 1.470000e-40 178.0
58 TraesCS6A01G234100 chrUn 95.413 109 4 1 5033 5140 346142770 346142662 6.840000e-39 172.0
59 TraesCS6A01G234100 chrUn 95.192 104 5 0 5037 5140 27673882 27673779 1.140000e-36 165.0
60 TraesCS6A01G234100 chrUn 95.192 104 5 0 5037 5140 71600459 71600562 1.140000e-36 165.0
61 TraesCS6A01G234100 chrUn 94.444 108 5 1 5034 5140 194117167 194117060 1.140000e-36 165.0
62 TraesCS6A01G234100 chrUn 96.040 101 4 0 5040 5140 253745292 253745192 1.140000e-36 165.0
63 TraesCS6A01G234100 chrUn 95.192 104 5 0 5037 5140 442673316 442673419 1.140000e-36 165.0
64 TraesCS6A01G234100 chrUn 93.578 109 6 1 5033 5140 283989923 283989815 1.480000e-35 161.0
65 TraesCS6A01G234100 chrUn 93.578 109 6 1 5033 5140 283996512 283996404 1.480000e-35 161.0
66 TraesCS6A01G234100 chrUn 93.578 109 6 1 5033 5140 296028796 296028904 1.480000e-35 161.0
67 TraesCS6A01G234100 chr4A 95.745 47 0 2 4284 4329 75357034 75357079 1.980000e-09 75.0
68 TraesCS6A01G234100 chr2A 95.556 45 2 0 4283 4327 235675399 235675443 7.140000e-09 73.1
69 TraesCS6A01G234100 chr1B 92.308 52 2 2 4284 4334 879230 879180 7.140000e-09 73.1
70 TraesCS6A01G234100 chr1B 95.455 44 2 0 4285 4328 524393944 524393987 2.570000e-08 71.3
71 TraesCS6A01G234100 chr1B 93.478 46 3 0 4283 4328 535908063 535908108 9.230000e-08 69.4
72 TraesCS6A01G234100 chr1B 93.478 46 3 0 4284 4329 569443040 569442995 9.230000e-08 69.4
73 TraesCS6A01G234100 chr1B 86.207 58 6 2 4279 4336 287710917 287710862 1.550000e-05 62.1
74 TraesCS6A01G234100 chr7B 91.837 49 4 0 4283 4331 138653828 138653876 9.230000e-08 69.4
75 TraesCS6A01G234100 chr4B 91.667 48 4 0 4281 4328 613711514 613711467 3.320000e-07 67.6


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 TraesCS6A01G234100 chr6A 441519164 441524303 5139 True 9492.000000 9492 100.000000 1 5140 1 chr6A.!!$R1 5139
1 TraesCS6A01G234100 chr6A 604836012 604836670 658 False 1129.000000 1129 97.572000 1706 2364 1 chr6A.!!$F3 658
2 TraesCS6A01G234100 chr6A 158913941 158914599 658 False 1116.000000 1116 97.269000 1706 2363 1 chr6A.!!$F2 657
3 TraesCS6A01G234100 chr6D 306142827 306147095 4268 True 2049.666667 3914 92.133667 1 5037 3 chr6D.!!$R3 5036
4 TraesCS6A01G234100 chr6B 473085746 473089854 4108 True 1760.666667 3618 88.542667 61 5037 3 chr6B.!!$R1 4976
5 TraesCS6A01G234100 chr3D 487413330 487414164 834 False 1242.000000 1242 93.772000 1740 2560 1 chr3D.!!$F1 820
6 TraesCS6A01G234100 chr2D 20651269 20651926 657 False 1155.000000 1155 98.328000 1706 2363 1 chr2D.!!$F1 657
7 TraesCS6A01G234100 chr2D 205592660 205593318 658 True 1129.000000 1129 97.576000 1705 2363 1 chr2D.!!$R2 658
8 TraesCS6A01G234100 chr1D 460550957 460551614 657 True 1144.000000 1144 98.024000 1706 2363 1 chr1D.!!$R3 657
9 TraesCS6A01G234100 chr7A 497684071 497684728 657 True 1138.000000 1138 97.872000 1706 2363 1 chr7A.!!$R1 657
10 TraesCS6A01G234100 chr7D 556705629 556706286 657 True 1133.000000 1133 97.720000 1706 2363 1 chr7D.!!$R2 657
11 TraesCS6A01G234100 chr7D 374567552 374568207 655 False 1123.000000 1123 97.565000 1706 2362 1 chr7D.!!$F1 656
12 TraesCS6A01G234100 chr5D 310266256 310266912 656 False 1125.000000 1125 97.568000 1706 2363 1 chr5D.!!$F2 657

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
73 74 0.390866 CTCTCGGTGTTCAGCATGCT 60.391 55.0 16.3 16.3 34.76 3.79 F
636 667 0.437295 GCGTGATGTCCGTACACAAC 59.563 55.0 0.0 0.0 38.78 3.32 F
2201 2286 1.002366 CGATGCAACAGTACAGCTCC 58.998 55.0 0.0 0.0 0.00 4.70 F
2352 2524 0.107654 GGTTTGGCTGCGAGGTCTAT 60.108 55.0 0.0 0.0 0.00 1.98 F
2357 2529 0.107654 GGCTGCGAGGTCTATTTGGT 60.108 55.0 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 1453 0.248215 CAAACAGCGCGAATGGATCC 60.248 55.000 12.1 4.2 0.00 3.36 R
2333 2505 0.107654 ATAGACCTCGCAGCCAAACC 60.108 55.000 0.0 0.0 0.00 3.27 R
3908 4110 1.204941 AGAACTCTCAATTCCGACCGG 59.795 52.381 0.0 0.0 0.00 5.28 R
3910 4112 3.594603 TCAGAACTCTCAATTCCGACC 57.405 47.619 0.0 0.0 0.00 4.79 R
4321 4540 4.946157 CCCAGAAAGCATTGAGATGTACTT 59.054 41.667 0.0 0.0 35.63 2.24 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
65 66 3.662247 TTCTCTTTCCTCTCGGTGTTC 57.338 47.619 0.00 0.00 0.00 3.18
72 73 1.364626 CCTCTCGGTGTTCAGCATGC 61.365 60.000 10.51 10.51 34.76 4.06
73 74 0.390866 CTCTCGGTGTTCAGCATGCT 60.391 55.000 16.30 16.30 34.76 3.79
78 79 1.154338 GTGTTCAGCATGCTCGTGC 60.154 57.895 19.68 9.09 45.38 5.34
80 81 3.120385 TTCAGCATGCTCGTGCCG 61.120 61.111 19.68 5.58 46.19 5.69
165 166 2.820197 CCAAACCTTCTAGACAAAGGCC 59.180 50.000 8.62 0.00 46.03 5.19
180 181 0.623723 AGGCCGAGGCTTCCAAAATA 59.376 50.000 14.33 0.00 41.60 1.40
196 197 4.098654 CCAAAATATGGTGCGGGAAATGTA 59.901 41.667 0.00 0.00 44.85 2.29
206 207 2.032178 GCGGGAAATGTAGAATGAGCAC 59.968 50.000 0.00 0.00 0.00 4.40
253 254 4.947420 CGTCTAGCAGCTGAGTTAAAAAC 58.053 43.478 20.43 2.88 0.00 2.43
317 320 6.743110 TGGAACGTCAAATTTCAAATCATGA 58.257 32.000 0.00 0.00 35.85 3.07
363 366 1.207089 GGACATCACCATGGAGTCGAA 59.793 52.381 21.47 0.00 33.82 3.71
402 405 2.871263 CGAGAGCTGCTCAAGTTTTC 57.129 50.000 29.49 16.52 44.15 2.29
403 406 1.125748 CGAGAGCTGCTCAAGTTTTCG 59.874 52.381 29.49 23.20 44.15 3.46
404 407 1.462670 GAGAGCTGCTCAAGTTTTCGG 59.537 52.381 29.49 0.00 43.38 4.30
405 408 1.202698 AGAGCTGCTCAAGTTTTCGGT 60.203 47.619 29.49 3.72 32.06 4.69
475 488 2.100916 CGAGACGACCAGACCCAATTAT 59.899 50.000 0.00 0.00 0.00 1.28
477 490 2.838202 AGACGACCAGACCCAATTATGT 59.162 45.455 0.00 0.00 0.00 2.29
495 508 2.226330 TGTTGCAGCGGATGTAAAAGT 58.774 42.857 0.00 0.00 35.11 2.66
500 513 2.032178 GCAGCGGATGTAAAAGTCCATC 59.968 50.000 0.00 0.00 37.36 3.51
510 523 5.964758 TGTAAAAGTCCATCCATCAAATGC 58.035 37.500 0.00 0.00 0.00 3.56
519 548 1.514087 CATCAAATGCTGGCGGCTT 59.486 52.632 20.66 10.76 42.39 4.35
524 553 1.002033 CAAATGCTGGCGGCTTAGATC 60.002 52.381 20.66 0.00 42.39 2.75
607 638 1.422531 TTGTGGGCAAAATGCTCCTT 58.577 45.000 0.00 0.00 45.08 3.36
609 640 1.767681 TGTGGGCAAAATGCTCCTTTT 59.232 42.857 0.00 0.00 45.08 2.27
610 641 2.172293 TGTGGGCAAAATGCTCCTTTTT 59.828 40.909 0.00 0.00 45.08 1.94
619 650 2.420628 TGCTCCTTTTTGTGATTGCG 57.579 45.000 0.00 0.00 0.00 4.85
625 656 3.317711 TCCTTTTTGTGATTGCGTGATGT 59.682 39.130 0.00 0.00 0.00 3.06
633 664 1.323534 GATTGCGTGATGTCCGTACAC 59.676 52.381 0.00 0.00 38.78 2.90
636 667 0.437295 GCGTGATGTCCGTACACAAC 59.563 55.000 0.00 0.00 38.78 3.32
660 691 3.830178 TGGTAAAGTCTGGACATTCGAGA 59.170 43.478 3.51 0.00 0.00 4.04
756 788 5.297547 TGTCTTATTTGTCACGAGCTTCTT 58.702 37.500 0.00 0.00 0.00 2.52
856 910 1.604604 CTGTTCACCGGGTGTTGATT 58.395 50.000 25.53 0.00 34.79 2.57
860 914 2.282887 ACCGGGTGTTGATTGGCC 60.283 61.111 6.32 0.00 0.00 5.36
879 933 1.292061 CGGGGCGTCGAATTGAATTA 58.708 50.000 0.00 0.00 0.00 1.40
881 935 2.289547 CGGGGCGTCGAATTGAATTATT 59.710 45.455 0.00 0.00 0.00 1.40
892 946 5.622448 CGAATTGAATTATTGCAGTCCATCG 59.378 40.000 0.00 0.00 0.00 3.84
893 947 6.455360 AATTGAATTATTGCAGTCCATCGT 57.545 33.333 0.00 0.00 0.00 3.73
894 948 5.484173 TTGAATTATTGCAGTCCATCGTC 57.516 39.130 0.00 0.00 0.00 4.20
896 950 3.558931 ATTATTGCAGTCCATCGTCCA 57.441 42.857 0.00 0.00 0.00 4.02
897 951 3.558931 TTATTGCAGTCCATCGTCCAT 57.441 42.857 0.00 0.00 0.00 3.41
902 986 1.600663 GCAGTCCATCGTCCATCTACG 60.601 57.143 0.00 0.00 44.19 3.51
917 1001 1.072489 TCTACGTTGCAAATGTCCCCA 59.928 47.619 0.00 0.00 44.07 4.96
960 1044 8.810652 TTGCAAATGGACTGAAAACTAATAAC 57.189 30.769 0.00 0.00 0.00 1.89
1254 1339 2.559922 ATCTCTCCCAGTCGCCGTCT 62.560 60.000 0.00 0.00 0.00 4.18
1368 1453 2.184579 GAGACCTCCTTTCGGCCG 59.815 66.667 22.12 22.12 0.00 6.13
1398 1483 1.193665 CGCTGTTTGTGTGCGTGAAC 61.194 55.000 0.00 0.00 44.00 3.18
1434 1519 9.780413 CAGAAAGCTTTCCTTCTTATCAAATAC 57.220 33.333 30.83 5.18 37.92 1.89
1435 1520 8.669243 AGAAAGCTTTCCTTCTTATCAAATACG 58.331 33.333 30.83 0.00 37.92 3.06
1436 1521 6.927294 AGCTTTCCTTCTTATCAAATACGG 57.073 37.500 0.00 0.00 0.00 4.02
1466 1551 8.581578 AGTACGATTTGTGATTTATTGGGTTTT 58.418 29.630 0.00 0.00 0.00 2.43
1467 1552 9.198837 GTACGATTTGTGATTTATTGGGTTTTT 57.801 29.630 0.00 0.00 0.00 1.94
1485 1570 7.754851 GGTTTTTCTTACCCTACAAAGATGA 57.245 36.000 0.00 0.00 32.05 2.92
1569 1654 8.963130 TGTCAAATTTTAATCGTTCAATCACAC 58.037 29.630 0.00 0.00 0.00 3.82
1650 1735 2.230660 GATGCCTACCAAATAGCCCAC 58.769 52.381 0.00 0.00 0.00 4.61
2201 2286 1.002366 CGATGCAACAGTACAGCTCC 58.998 55.000 0.00 0.00 0.00 4.70
2217 2302 3.006217 CAGCTCCGAAGATGGATATGTGA 59.994 47.826 0.00 0.00 37.41 3.58
2244 2329 3.792736 GTGGCGGCCTCATACCCA 61.793 66.667 21.46 0.00 0.00 4.51
2335 2507 4.949121 ACCTCAGGTCTTAGATGTTAGGT 58.051 43.478 0.00 4.26 0.00 3.08
2336 2508 5.342866 ACCTCAGGTCTTAGATGTTAGGTT 58.657 41.667 0.00 0.00 30.79 3.50
2337 2509 5.785940 ACCTCAGGTCTTAGATGTTAGGTTT 59.214 40.000 0.00 0.00 30.79 3.27
2338 2510 6.109359 CCTCAGGTCTTAGATGTTAGGTTTG 58.891 44.000 0.00 0.00 0.00 2.93
2339 2511 6.049955 TCAGGTCTTAGATGTTAGGTTTGG 57.950 41.667 0.00 0.00 0.00 3.28
2340 2512 4.636206 CAGGTCTTAGATGTTAGGTTTGGC 59.364 45.833 0.00 0.00 0.00 4.52
2341 2513 4.536489 AGGTCTTAGATGTTAGGTTTGGCT 59.464 41.667 0.00 0.00 0.00 4.75
2342 2514 4.636206 GGTCTTAGATGTTAGGTTTGGCTG 59.364 45.833 0.00 0.00 0.00 4.85
2343 2515 4.095036 GTCTTAGATGTTAGGTTTGGCTGC 59.905 45.833 0.00 0.00 0.00 5.25
2344 2516 1.453155 AGATGTTAGGTTTGGCTGCG 58.547 50.000 0.00 0.00 0.00 5.18
2345 2517 1.003118 AGATGTTAGGTTTGGCTGCGA 59.997 47.619 0.00 0.00 0.00 5.10
2346 2518 1.398390 GATGTTAGGTTTGGCTGCGAG 59.602 52.381 0.00 0.00 0.00 5.03
2347 2519 0.605319 TGTTAGGTTTGGCTGCGAGG 60.605 55.000 0.00 0.00 0.00 4.63
2348 2520 0.605589 GTTAGGTTTGGCTGCGAGGT 60.606 55.000 0.00 0.00 0.00 3.85
2349 2521 0.321298 TTAGGTTTGGCTGCGAGGTC 60.321 55.000 0.00 0.00 0.00 3.85
2350 2522 1.192146 TAGGTTTGGCTGCGAGGTCT 61.192 55.000 0.00 0.00 0.00 3.85
2351 2523 1.192146 AGGTTTGGCTGCGAGGTCTA 61.192 55.000 0.00 0.00 0.00 2.59
2352 2524 0.107654 GGTTTGGCTGCGAGGTCTAT 60.108 55.000 0.00 0.00 0.00 1.98
2353 2525 1.679032 GGTTTGGCTGCGAGGTCTATT 60.679 52.381 0.00 0.00 0.00 1.73
2354 2526 2.084546 GTTTGGCTGCGAGGTCTATTT 58.915 47.619 0.00 0.00 0.00 1.40
2355 2527 1.737838 TTGGCTGCGAGGTCTATTTG 58.262 50.000 0.00 0.00 0.00 2.32
2356 2528 0.107703 TGGCTGCGAGGTCTATTTGG 60.108 55.000 0.00 0.00 0.00 3.28
2357 2529 0.107654 GGCTGCGAGGTCTATTTGGT 60.108 55.000 0.00 0.00 0.00 3.67
2358 2530 1.138266 GGCTGCGAGGTCTATTTGGTA 59.862 52.381 0.00 0.00 0.00 3.25
2359 2531 2.224305 GGCTGCGAGGTCTATTTGGTAT 60.224 50.000 0.00 0.00 0.00 2.73
2360 2532 3.467803 GCTGCGAGGTCTATTTGGTATT 58.532 45.455 0.00 0.00 0.00 1.89
2361 2533 4.502604 GGCTGCGAGGTCTATTTGGTATTA 60.503 45.833 0.00 0.00 0.00 0.98
2362 2534 4.686554 GCTGCGAGGTCTATTTGGTATTAG 59.313 45.833 0.00 0.00 0.00 1.73
2363 2535 5.509163 GCTGCGAGGTCTATTTGGTATTAGA 60.509 44.000 0.00 0.00 0.00 2.10
2364 2536 6.665992 TGCGAGGTCTATTTGGTATTAGAT 57.334 37.500 0.00 0.00 0.00 1.98
2365 2537 6.455647 TGCGAGGTCTATTTGGTATTAGATG 58.544 40.000 0.00 0.00 0.00 2.90
2366 2538 6.041637 TGCGAGGTCTATTTGGTATTAGATGT 59.958 38.462 0.00 0.00 0.00 3.06
2367 2539 6.929606 GCGAGGTCTATTTGGTATTAGATGTT 59.070 38.462 0.00 0.00 0.00 2.71
2435 2607 3.306364 CGCCCCTTCATCAGTTAGATAGG 60.306 52.174 0.00 0.00 34.43 2.57
2444 2616 6.477253 TCATCAGTTAGATAGGAGTAGCGAT 58.523 40.000 0.00 0.00 34.43 4.58
2536 2708 1.388547 AATTGGCCGTATGCATCGTT 58.611 45.000 0.19 0.00 43.89 3.85
2731 2903 7.761409 TGTGTTTATAGAACATGCTGATTTCC 58.239 34.615 0.00 0.00 32.23 3.13
2774 2946 4.810191 ACTTCTTTTACAGCTCCGAGAT 57.190 40.909 0.00 0.00 0.00 2.75
2846 3021 6.777213 TGGGTAGTCTGACTAGAGAATTTC 57.223 41.667 17.43 3.87 30.12 2.17
3070 3272 1.442017 GCGCAGTTTTTAGCACGGG 60.442 57.895 0.30 0.00 0.00 5.28
3169 3371 2.099756 GGCACCAGTTATCTGATTTGGC 59.900 50.000 12.60 5.41 43.76 4.52
3339 3541 9.856162 AACTTAGTGATAAAGGTTTAAAGGTGA 57.144 29.630 0.00 0.00 0.00 4.02
3359 3561 2.281484 GCGTCAGGGTGCCAGAAA 60.281 61.111 0.00 0.00 0.00 2.52
3452 3654 3.297134 TTGAACTTGGAAGAGCTTGGT 57.703 42.857 0.00 0.00 0.00 3.67
3599 3801 2.167900 TGAGGTCTCGTCGTCATCTCTA 59.832 50.000 7.62 0.00 0.00 2.43
3600 3802 3.181464 TGAGGTCTCGTCGTCATCTCTAT 60.181 47.826 7.62 0.00 0.00 1.98
3638 3840 1.143620 TTGCAGCAAAGTGGGCAAC 59.856 52.632 4.99 0.00 40.94 4.17
3644 3846 0.746659 GCAAAGTGGGCAACAAGTCT 59.253 50.000 0.00 0.00 39.74 3.24
3719 3921 3.570926 TGTCGGGATATTAGCGATGAC 57.429 47.619 0.00 0.00 0.00 3.06
3746 3948 3.495543 GCACTAGCTCTTGCCTGC 58.504 61.111 8.04 0.00 40.80 4.85
3908 4110 1.401539 GGCATGGAAGCGAACTTGTTC 60.402 52.381 3.60 3.60 35.82 3.18
3910 4112 1.135972 CATGGAAGCGAACTTGTTCCG 60.136 52.381 7.78 4.91 42.42 4.30
4167 4369 4.586841 AGCTATGAACTCCGATTAGAGCTT 59.413 41.667 0.00 0.00 37.39 3.74
4285 4504 9.189156 TCAATTGGAATAATTCTTCGATCCTTT 57.811 29.630 5.42 0.00 0.00 3.11
4358 4577 2.631160 TCTGGGTATAATGGCGTTGG 57.369 50.000 1.27 0.00 0.00 3.77
4360 4579 2.240160 TCTGGGTATAATGGCGTTGGTT 59.760 45.455 1.27 0.00 0.00 3.67
4389 4608 5.345741 GCTAAATGTTGTAAATGTGGCACAG 59.654 40.000 26.04 7.85 41.80 3.66
4788 5028 8.758633 TTTTAACGTTTGACAAAATTTCCTCA 57.241 26.923 5.91 0.00 0.00 3.86
4793 5033 3.624326 TGACAAAATTTCCTCACTGCG 57.376 42.857 0.00 0.00 0.00 5.18
4839 5080 2.614057 CACCAGAGAGAACGTGCTTTTT 59.386 45.455 0.00 0.00 0.00 1.94
4948 5190 2.223340 ACACTTGCTCAAACTTCAAGCG 60.223 45.455 0.00 0.00 40.45 4.68
5014 5256 5.221581 GGCATTTCCTAGGCATTGATGATTT 60.222 40.000 2.96 0.00 0.00 2.17
5057 5299 6.894339 AATACAAGTTTTAGAGTGGTTGGG 57.106 37.500 0.00 0.00 0.00 4.12
5058 5300 2.956333 ACAAGTTTTAGAGTGGTTGGGC 59.044 45.455 0.00 0.00 0.00 5.36
5059 5301 3.222603 CAAGTTTTAGAGTGGTTGGGCT 58.777 45.455 0.00 0.00 0.00 5.19
5060 5302 3.595190 AGTTTTAGAGTGGTTGGGCTT 57.405 42.857 0.00 0.00 0.00 4.35
5061 5303 3.910989 AGTTTTAGAGTGGTTGGGCTTT 58.089 40.909 0.00 0.00 0.00 3.51
5062 5304 4.286707 AGTTTTAGAGTGGTTGGGCTTTT 58.713 39.130 0.00 0.00 0.00 2.27
5063 5305 4.714802 AGTTTTAGAGTGGTTGGGCTTTTT 59.285 37.500 0.00 0.00 0.00 1.94
5084 5326 7.839438 TTTTTACAACCGTTTATTGATGTCG 57.161 32.000 0.00 0.00 0.00 4.35
5085 5327 6.782298 TTTACAACCGTTTATTGATGTCGA 57.218 33.333 0.00 0.00 0.00 4.20
5086 5328 6.971527 TTACAACCGTTTATTGATGTCGAT 57.028 33.333 0.00 0.00 0.00 3.59
5087 5329 5.464965 ACAACCGTTTATTGATGTCGATC 57.535 39.130 0.00 0.00 0.00 3.69
5088 5330 5.175859 ACAACCGTTTATTGATGTCGATCT 58.824 37.500 0.00 0.00 0.00 2.75
5089 5331 6.334989 ACAACCGTTTATTGATGTCGATCTA 58.665 36.000 0.00 0.00 0.00 1.98
5090 5332 6.814644 ACAACCGTTTATTGATGTCGATCTAA 59.185 34.615 0.00 0.00 0.00 2.10
5091 5333 6.823678 ACCGTTTATTGATGTCGATCTAAC 57.176 37.500 0.00 0.00 0.00 2.34
5092 5334 5.457799 ACCGTTTATTGATGTCGATCTAACG 59.542 40.000 16.07 16.07 37.49 3.18
5093 5335 5.107989 CCGTTTATTGATGTCGATCTAACGG 60.108 44.000 21.98 21.98 43.51 4.44
5094 5336 5.609696 CGTTTATTGATGTCGATCTAACGGC 60.610 44.000 15.62 0.00 35.96 5.68
5099 5341 1.170442 TGTCGATCTAACGGCAGACA 58.830 50.000 0.00 0.00 42.82 3.41
5100 5342 1.542472 TGTCGATCTAACGGCAGACAA 59.458 47.619 0.00 0.00 42.82 3.18
5101 5343 2.029739 TGTCGATCTAACGGCAGACAAA 60.030 45.455 0.00 0.00 42.82 2.83
5102 5344 3.187700 GTCGATCTAACGGCAGACAAAT 58.812 45.455 0.00 0.00 37.83 2.32
5103 5345 4.142337 TGTCGATCTAACGGCAGACAAATA 60.142 41.667 0.00 0.00 42.82 1.40
5104 5346 4.982916 GTCGATCTAACGGCAGACAAATAT 59.017 41.667 0.00 0.00 37.83 1.28
5105 5347 4.982295 TCGATCTAACGGCAGACAAATATG 59.018 41.667 0.00 0.00 0.00 1.78
5106 5348 4.982295 CGATCTAACGGCAGACAAATATGA 59.018 41.667 0.00 0.00 0.00 2.15
5107 5349 5.462068 CGATCTAACGGCAGACAAATATGAA 59.538 40.000 0.00 0.00 0.00 2.57
5108 5350 6.346120 CGATCTAACGGCAGACAAATATGAAG 60.346 42.308 0.00 0.00 0.00 3.02
5109 5351 5.730550 TCTAACGGCAGACAAATATGAAGT 58.269 37.500 0.00 0.00 0.00 3.01
5110 5352 6.869695 TCTAACGGCAGACAAATATGAAGTA 58.130 36.000 0.00 0.00 0.00 2.24
5111 5353 5.796350 AACGGCAGACAAATATGAAGTAC 57.204 39.130 0.00 0.00 0.00 2.73
5112 5354 5.086104 ACGGCAGACAAATATGAAGTACT 57.914 39.130 0.00 0.00 0.00 2.73
5113 5355 4.870426 ACGGCAGACAAATATGAAGTACTG 59.130 41.667 0.00 0.00 0.00 2.74
5114 5356 4.271049 CGGCAGACAAATATGAAGTACTGG 59.729 45.833 0.00 0.00 0.00 4.00
5115 5357 4.576463 GGCAGACAAATATGAAGTACTGGG 59.424 45.833 0.00 0.00 0.00 4.45
5116 5358 5.186198 GCAGACAAATATGAAGTACTGGGT 58.814 41.667 0.00 0.00 0.00 4.51
5117 5359 6.346096 GCAGACAAATATGAAGTACTGGGTA 58.654 40.000 0.00 0.00 0.00 3.69
5118 5360 6.480320 GCAGACAAATATGAAGTACTGGGTAG 59.520 42.308 0.00 0.00 0.00 3.18
5119 5361 7.556844 CAGACAAATATGAAGTACTGGGTAGT 58.443 38.462 0.00 0.00 40.99 2.73
5120 5362 8.692710 CAGACAAATATGAAGTACTGGGTAGTA 58.307 37.037 0.00 0.00 38.36 1.82
5130 5372 3.377253 ACTGGGTAGTACTCCGATGAA 57.623 47.619 0.00 0.00 34.74 2.57
5131 5373 3.705051 ACTGGGTAGTACTCCGATGAAA 58.295 45.455 0.00 0.00 34.74 2.69
5132 5374 3.700038 ACTGGGTAGTACTCCGATGAAAG 59.300 47.826 0.00 0.00 34.74 2.62
5133 5375 3.700038 CTGGGTAGTACTCCGATGAAAGT 59.300 47.826 0.00 0.00 0.00 2.66
5134 5376 4.858850 TGGGTAGTACTCCGATGAAAGTA 58.141 43.478 0.00 0.00 0.00 2.24
5135 5377 4.641989 TGGGTAGTACTCCGATGAAAGTAC 59.358 45.833 0.00 4.85 45.30 2.73
5138 5380 2.107178 GTACTCCGATGAAAGTACGCG 58.893 52.381 3.53 3.53 38.72 6.01
5139 5381 0.806868 ACTCCGATGAAAGTACGCGA 59.193 50.000 15.93 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.447683 CCAATCAACTATTGTGACGACATGG 60.448 44.000 0.00 0.00 43.03 3.66
7 8 4.635765 CCCAATCAACTATTGTGACGACAT 59.364 41.667 0.00 0.00 43.03 3.06
78 79 5.156355 CAAAAGAAGTGGACAATGATTCGG 58.844 41.667 0.00 0.00 0.00 4.30
80 81 6.089249 ACCAAAAGAAGTGGACAATGATTC 57.911 37.500 0.00 0.00 39.62 2.52
115 116 2.480555 GTTTCCTCACCGCATGCG 59.519 61.111 32.60 32.60 39.44 4.73
139 140 6.531021 CCTTTGTCTAGAAGGTTTGGAAGTA 58.469 40.000 0.00 0.00 39.05 2.24
176 177 4.787551 TCTACATTTCCCGCACCATATTT 58.212 39.130 0.00 0.00 0.00 1.40
180 181 2.799126 TTCTACATTTCCCGCACCAT 57.201 45.000 0.00 0.00 0.00 3.55
187 188 3.620488 TGGTGCTCATTCTACATTTCCC 58.380 45.455 0.00 0.00 0.00 3.97
196 197 1.822990 CAATTGGCTGGTGCTCATTCT 59.177 47.619 0.00 0.00 39.59 2.40
206 207 0.979187 AGGGATTGGCAATTGGCTGG 60.979 55.000 29.53 0.00 44.01 4.85
253 254 3.853330 CAATCGTGCGAGCGGTGG 61.853 66.667 0.00 0.00 0.00 4.61
307 310 5.985530 CACCTCGTTAGCTATCATGATTTGA 59.014 40.000 14.65 0.00 39.12 2.69
317 320 4.338682 ACGAAGAATCACCTCGTTAGCTAT 59.661 41.667 0.00 0.00 32.90 2.97
363 366 1.226542 TCGCCATCCGAGAGTACCT 59.773 57.895 0.00 0.00 41.89 3.08
398 401 2.158740 TCAAGGGATGTCACACCGAAAA 60.159 45.455 0.00 0.00 0.00 2.29
400 403 1.001974 CTCAAGGGATGTCACACCGAA 59.998 52.381 0.00 0.00 0.00 4.30
401 404 0.608130 CTCAAGGGATGTCACACCGA 59.392 55.000 0.00 0.00 0.00 4.69
402 405 1.021390 GCTCAAGGGATGTCACACCG 61.021 60.000 0.00 0.00 0.00 4.94
403 406 1.021390 CGCTCAAGGGATGTCACACC 61.021 60.000 0.00 0.00 0.00 4.16
404 407 1.021390 CCGCTCAAGGGATGTCACAC 61.021 60.000 0.00 0.00 0.00 3.82
405 408 1.296392 CCGCTCAAGGGATGTCACA 59.704 57.895 0.00 0.00 0.00 3.58
455 467 3.118738 ACATAATTGGGTCTGGTCGTCTC 60.119 47.826 0.00 0.00 0.00 3.36
461 474 3.091545 CTGCAACATAATTGGGTCTGGT 58.908 45.455 0.00 0.00 0.00 4.00
475 488 2.225491 GACTTTTACATCCGCTGCAACA 59.775 45.455 0.00 0.00 0.00 3.33
477 490 1.810151 GGACTTTTACATCCGCTGCAA 59.190 47.619 0.00 0.00 0.00 4.08
508 521 2.930385 GCTGATCTAAGCCGCCAGCA 62.930 60.000 10.93 0.00 46.68 4.41
509 522 2.250237 GCTGATCTAAGCCGCCAGC 61.250 63.158 0.00 0.00 42.52 4.85
510 523 4.040068 GCTGATCTAAGCCGCCAG 57.960 61.111 0.00 0.00 37.20 4.85
519 548 0.616395 TTCACACCCGGGCTGATCTA 60.616 55.000 24.08 3.84 0.00 1.98
524 553 0.828022 TACTATTCACACCCGGGCTG 59.172 55.000 24.08 20.40 0.00 4.85
590 621 2.549064 AAAAGGAGCATTTTGCCCAC 57.451 45.000 8.89 0.00 46.52 4.61
591 622 2.172293 ACAAAAAGGAGCATTTTGCCCA 59.828 40.909 10.66 0.00 46.52 5.36
593 624 3.465871 TCACAAAAAGGAGCATTTTGCC 58.534 40.909 10.66 0.00 46.52 4.52
598 629 3.243839 ACGCAATCACAAAAAGGAGCATT 60.244 39.130 0.00 0.00 0.00 3.56
607 638 2.350293 CGGACATCACGCAATCACAAAA 60.350 45.455 0.00 0.00 0.00 2.44
609 640 0.795698 CGGACATCACGCAATCACAA 59.204 50.000 0.00 0.00 0.00 3.33
610 641 0.320334 ACGGACATCACGCAATCACA 60.320 50.000 0.00 0.00 34.00 3.58
619 650 2.478894 CCAAGTTGTGTACGGACATCAC 59.521 50.000 2.42 3.70 38.04 3.06
625 656 4.099881 AGACTTTACCAAGTTGTGTACGGA 59.900 41.667 1.45 0.00 43.79 4.69
633 664 5.334105 CGAATGTCCAGACTTTACCAAGTTG 60.334 44.000 0.00 0.00 43.79 3.16
636 667 4.566004 TCGAATGTCCAGACTTTACCAAG 58.434 43.478 0.00 0.00 35.92 3.61
686 717 8.058915 TGTTTTCAAAAGTTTTTCAGACGTTTG 58.941 29.630 0.00 0.00 43.26 2.93
688 719 7.701809 TGTTTTCAAAAGTTTTTCAGACGTT 57.298 28.000 0.00 0.00 0.00 3.99
689 720 7.222999 TGTTGTTTTCAAAAGTTTTTCAGACGT 59.777 29.630 0.00 0.00 41.76 4.34
690 721 7.559845 TGTTGTTTTCAAAAGTTTTTCAGACG 58.440 30.769 0.00 0.00 41.76 4.18
724 756 7.925993 TCGTGACAAATAAGACAAAATTGACT 58.074 30.769 0.00 0.00 34.79 3.41
728 760 6.970484 AGCTCGTGACAAATAAGACAAAATT 58.030 32.000 0.00 0.00 0.00 1.82
756 788 4.826274 TTTTGGGTTGTTTGGACATTCA 57.174 36.364 0.00 0.00 35.29 2.57
781 813 2.424601 CAAATGGGTGATCTTCGTGCAT 59.575 45.455 0.00 0.00 0.00 3.96
790 822 3.841643 CAAGTTGCTCAAATGGGTGATC 58.158 45.455 0.00 0.00 0.00 2.92
796 828 6.542574 TTTTTATGCAAGTTGCTCAAATGG 57.457 33.333 27.17 0.00 45.31 3.16
822 854 4.354587 GTGAACAGCAGAAAAGAAACCTG 58.645 43.478 0.00 0.00 0.00 4.00
829 863 0.593128 CCCGGTGAACAGCAGAAAAG 59.407 55.000 0.00 0.00 0.00 2.27
836 890 0.889186 ATCAACACCCGGTGAACAGC 60.889 55.000 24.80 0.00 36.96 4.40
860 914 1.292061 TAATTCAATTCGACGCCCCG 58.708 50.000 0.00 0.00 0.00 5.73
879 933 1.487976 AGATGGACGATGGACTGCAAT 59.512 47.619 0.00 0.00 0.00 3.56
881 935 1.409064 GTAGATGGACGATGGACTGCA 59.591 52.381 0.00 0.00 0.00 4.41
892 946 3.181510 GGACATTTGCAACGTAGATGGAC 60.182 47.826 11.65 6.16 26.40 4.02
893 947 3.006940 GGACATTTGCAACGTAGATGGA 58.993 45.455 11.65 0.00 0.00 3.41
894 948 2.097466 GGGACATTTGCAACGTAGATGG 59.903 50.000 11.65 0.00 0.00 3.51
896 950 2.290641 TGGGGACATTTGCAACGTAGAT 60.291 45.455 0.00 0.00 33.40 1.98
897 951 1.072489 TGGGGACATTTGCAACGTAGA 59.928 47.619 0.00 0.00 33.40 2.59
902 986 3.467374 TTCTTTGGGGACATTTGCAAC 57.533 42.857 0.00 0.00 42.32 4.17
917 1001 6.469782 TTGCAATGGAGACTTCTTTTCTTT 57.530 33.333 0.00 0.00 0.00 2.52
977 1061 3.354467 ACCGGAGTTAAGGAGTCACTAG 58.646 50.000 9.46 0.00 0.00 2.57
982 1066 2.496470 ACATGACCGGAGTTAAGGAGTC 59.504 50.000 9.46 0.00 0.00 3.36
989 1073 1.262417 TGCAGACATGACCGGAGTTA 58.738 50.000 9.46 0.00 0.00 2.24
990 1074 0.615331 ATGCAGACATGACCGGAGTT 59.385 50.000 9.46 0.00 34.35 3.01
992 1076 0.176449 TGATGCAGACATGACCGGAG 59.824 55.000 9.46 0.00 36.35 4.63
993 1077 0.108186 GTGATGCAGACATGACCGGA 60.108 55.000 9.46 0.00 34.66 5.14
994 1078 1.423721 CGTGATGCAGACATGACCGG 61.424 60.000 0.00 0.00 37.12 5.28
1254 1339 3.136123 CCGGGGTAGAACGAGCGA 61.136 66.667 0.00 0.00 0.00 4.93
1359 1444 1.498865 CGAATGGATCCGGCCGAAAG 61.499 60.000 30.73 10.73 0.00 2.62
1368 1453 0.248215 CAAACAGCGCGAATGGATCC 60.248 55.000 12.10 4.20 0.00 3.36
1398 1483 2.342910 AAGCTTTCTGCATTTGCGAG 57.657 45.000 0.00 0.00 45.94 5.03
1434 1519 7.925703 ATAAATCACAAATCGTACTACTCCG 57.074 36.000 0.00 0.00 0.00 4.63
1435 1520 8.548721 CCAATAAATCACAAATCGTACTACTCC 58.451 37.037 0.00 0.00 0.00 3.85
1436 1521 8.548721 CCCAATAAATCACAAATCGTACTACTC 58.451 37.037 0.00 0.00 0.00 2.59
1444 1529 8.532977 AGAAAAACCCAATAAATCACAAATCG 57.467 30.769 0.00 0.00 0.00 3.34
1466 1551 7.182760 TCTCTCTCATCTTTGTAGGGTAAGAA 58.817 38.462 0.00 0.00 34.35 2.52
1467 1552 6.732487 TCTCTCTCATCTTTGTAGGGTAAGA 58.268 40.000 0.00 0.00 35.08 2.10
1485 1570 3.623453 GCCCCAGTTTGCTTATTCTCTCT 60.623 47.826 0.00 0.00 0.00 3.10
1569 1654 8.334016 TCATTAAATTTCTTTGTTCACGTGTG 57.666 30.769 16.51 0.00 0.00 3.82
2201 2286 4.053983 CACCTGTCACATATCCATCTTCG 58.946 47.826 0.00 0.00 0.00 3.79
2332 2504 1.192146 TAGACCTCGCAGCCAAACCT 61.192 55.000 0.00 0.00 0.00 3.50
2333 2505 0.107654 ATAGACCTCGCAGCCAAACC 60.108 55.000 0.00 0.00 0.00 3.27
2334 2506 1.739067 AATAGACCTCGCAGCCAAAC 58.261 50.000 0.00 0.00 0.00 2.93
2335 2507 2.083774 CAAATAGACCTCGCAGCCAAA 58.916 47.619 0.00 0.00 0.00 3.28
2336 2508 1.678728 CCAAATAGACCTCGCAGCCAA 60.679 52.381 0.00 0.00 0.00 4.52
2337 2509 0.107703 CCAAATAGACCTCGCAGCCA 60.108 55.000 0.00 0.00 0.00 4.75
2338 2510 0.107654 ACCAAATAGACCTCGCAGCC 60.108 55.000 0.00 0.00 0.00 4.85
2339 2511 2.596904 TACCAAATAGACCTCGCAGC 57.403 50.000 0.00 0.00 0.00 5.25
2340 2512 6.085555 TCTAATACCAAATAGACCTCGCAG 57.914 41.667 0.00 0.00 0.00 5.18
2341 2513 6.041637 ACATCTAATACCAAATAGACCTCGCA 59.958 38.462 0.00 0.00 31.35 5.10
2342 2514 6.456501 ACATCTAATACCAAATAGACCTCGC 58.543 40.000 0.00 0.00 31.35 5.03
2343 2515 9.627395 CTAACATCTAATACCAAATAGACCTCG 57.373 37.037 0.00 0.00 31.35 4.63
2344 2516 9.930693 CCTAACATCTAATACCAAATAGACCTC 57.069 37.037 0.00 0.00 31.35 3.85
2345 2517 9.448587 ACCTAACATCTAATACCAAATAGACCT 57.551 33.333 0.00 0.00 31.35 3.85
2350 2522 9.127277 GCCAAACCTAACATCTAATACCAAATA 57.873 33.333 0.00 0.00 0.00 1.40
2351 2523 7.839200 AGCCAAACCTAACATCTAATACCAAAT 59.161 33.333 0.00 0.00 0.00 2.32
2352 2524 7.122055 CAGCCAAACCTAACATCTAATACCAAA 59.878 37.037 0.00 0.00 0.00 3.28
2353 2525 6.601613 CAGCCAAACCTAACATCTAATACCAA 59.398 38.462 0.00 0.00 0.00 3.67
2354 2526 6.119536 CAGCCAAACCTAACATCTAATACCA 58.880 40.000 0.00 0.00 0.00 3.25
2355 2527 5.008712 GCAGCCAAACCTAACATCTAATACC 59.991 44.000 0.00 0.00 0.00 2.73
2356 2528 5.277345 CGCAGCCAAACCTAACATCTAATAC 60.277 44.000 0.00 0.00 0.00 1.89
2357 2529 4.814234 CGCAGCCAAACCTAACATCTAATA 59.186 41.667 0.00 0.00 0.00 0.98
2358 2530 3.627577 CGCAGCCAAACCTAACATCTAAT 59.372 43.478 0.00 0.00 0.00 1.73
2359 2531 3.006940 CGCAGCCAAACCTAACATCTAA 58.993 45.455 0.00 0.00 0.00 2.10
2360 2532 2.235155 TCGCAGCCAAACCTAACATCTA 59.765 45.455 0.00 0.00 0.00 1.98
2361 2533 1.003118 TCGCAGCCAAACCTAACATCT 59.997 47.619 0.00 0.00 0.00 2.90
2362 2534 1.398390 CTCGCAGCCAAACCTAACATC 59.602 52.381 0.00 0.00 0.00 3.06
2363 2535 1.453155 CTCGCAGCCAAACCTAACAT 58.547 50.000 0.00 0.00 0.00 2.71
2364 2536 0.605319 CCTCGCAGCCAAACCTAACA 60.605 55.000 0.00 0.00 0.00 2.41
2365 2537 0.605589 ACCTCGCAGCCAAACCTAAC 60.606 55.000 0.00 0.00 0.00 2.34
2366 2538 0.321298 GACCTCGCAGCCAAACCTAA 60.321 55.000 0.00 0.00 0.00 2.69
2367 2539 1.192146 AGACCTCGCAGCCAAACCTA 61.192 55.000 0.00 0.00 0.00 3.08
2435 2607 1.602851 TCGCAACCTCTATCGCTACTC 59.397 52.381 0.00 0.00 0.00 2.59
2444 2616 1.207089 CCACCATCTTCGCAACCTCTA 59.793 52.381 0.00 0.00 0.00 2.43
2536 2708 3.473647 CCCGGCCTCTGCATCTGA 61.474 66.667 0.00 0.00 40.13 3.27
2774 2946 8.024285 CACAACAAAGTACCAAACAGAACTTTA 58.976 33.333 0.00 0.00 39.50 1.85
2846 3021 2.945668 GGAAGTACATTTGCCCAGCTAG 59.054 50.000 0.00 0.00 0.00 3.42
2978 3179 5.065218 GTGAATGCATCAATACCGAAGACTT 59.935 40.000 0.00 0.00 40.50 3.01
2982 3183 3.846023 GCGTGAATGCATCAATACCGAAG 60.846 47.826 0.00 0.00 40.50 3.79
3019 3220 5.106475 CCAAAATGGCAATGAAAGATGTTGG 60.106 40.000 0.00 0.00 0.00 3.77
3169 3371 9.573133 GATTAAGGAAATACCAACAATTCACAG 57.427 33.333 0.00 0.00 42.04 3.66
3226 3428 6.384015 TCCAACATCAGTGATACCTAAGACAT 59.616 38.462 5.03 0.00 0.00 3.06
3339 3541 2.360350 CTGGCACCCTGACGCAAT 60.360 61.111 0.00 0.00 0.00 3.56
3359 3561 1.466167 GCGATGTGCAACTGTCTCAAT 59.534 47.619 0.00 0.00 45.45 2.57
3599 3801 5.697633 GCAATCCAACAGTTTCAATGACAAT 59.302 36.000 0.00 0.00 0.00 2.71
3600 3802 5.049167 GCAATCCAACAGTTTCAATGACAA 58.951 37.500 0.00 0.00 0.00 3.18
3644 3846 8.572185 CAGCAGAACTTAGCTAGTGAATAGATA 58.428 37.037 0.00 0.00 39.50 1.98
3908 4110 1.204941 AGAACTCTCAATTCCGACCGG 59.795 52.381 0.00 0.00 0.00 5.28
3910 4112 3.594603 TCAGAACTCTCAATTCCGACC 57.405 47.619 0.00 0.00 0.00 4.79
4321 4540 4.946157 CCCAGAAAGCATTGAGATGTACTT 59.054 41.667 0.00 0.00 35.63 2.24
4358 4577 8.061268 CCACATTTACAACATTTAGCAACAAAC 58.939 33.333 0.00 0.00 0.00 2.93
4360 4579 6.201806 GCCACATTTACAACATTTAGCAACAA 59.798 34.615 0.00 0.00 0.00 2.83
4389 4608 7.916450 AGCTACGTTCATTTAGTCTAGTCATTC 59.084 37.037 0.00 0.00 0.00 2.67
4431 4650 6.049149 TCAATTTTGGATGCGTTTTTGGTTA 58.951 32.000 0.00 0.00 0.00 2.85
4491 4710 9.817809 TCATCTTTACAATCACCTATCTTGTAC 57.182 33.333 0.00 0.00 35.66 2.90
4667 4891 1.171308 GCATTGAAGCTGCCAAGAGA 58.829 50.000 0.00 0.00 33.44 3.10
4891 5133 9.537848 CATGATCATCATAATATTGTGAACACG 57.462 33.333 17.47 8.03 34.28 4.49
4948 5190 4.724279 ATTCACATTACCCCTACCATCC 57.276 45.455 0.00 0.00 0.00 3.51
5033 5275 6.239204 GCCCAACCACTCTAAAACTTGTATTT 60.239 38.462 0.00 0.00 0.00 1.40
5037 5279 2.956333 GCCCAACCACTCTAAAACTTGT 59.044 45.455 0.00 0.00 0.00 3.16
5038 5280 3.222603 AGCCCAACCACTCTAAAACTTG 58.777 45.455 0.00 0.00 0.00 3.16
5039 5281 3.595190 AGCCCAACCACTCTAAAACTT 57.405 42.857 0.00 0.00 0.00 2.66
5040 5282 3.595190 AAGCCCAACCACTCTAAAACT 57.405 42.857 0.00 0.00 0.00 2.66
5041 5283 4.665833 AAAAGCCCAACCACTCTAAAAC 57.334 40.909 0.00 0.00 0.00 2.43
5060 5302 7.637229 TCGACATCAATAAACGGTTGTAAAAA 58.363 30.769 0.00 0.00 0.00 1.94
5061 5303 7.187244 TCGACATCAATAAACGGTTGTAAAA 57.813 32.000 0.00 0.00 0.00 1.52
5062 5304 6.782298 TCGACATCAATAAACGGTTGTAAA 57.218 33.333 0.00 0.00 0.00 2.01
5063 5305 6.814644 AGATCGACATCAATAAACGGTTGTAA 59.185 34.615 0.00 0.00 0.00 2.41
5064 5306 6.334989 AGATCGACATCAATAAACGGTTGTA 58.665 36.000 0.00 0.00 0.00 2.41
5065 5307 5.175859 AGATCGACATCAATAAACGGTTGT 58.824 37.500 0.00 0.00 0.00 3.32
5066 5308 5.718649 AGATCGACATCAATAAACGGTTG 57.281 39.130 0.00 0.00 0.00 3.77
5067 5309 6.020121 CGTTAGATCGACATCAATAAACGGTT 60.020 38.462 0.00 0.00 33.77 4.44
5068 5310 5.457799 CGTTAGATCGACATCAATAAACGGT 59.542 40.000 0.00 0.00 33.77 4.83
5069 5311 5.107989 CCGTTAGATCGACATCAATAAACGG 60.108 44.000 14.69 14.69 41.55 4.44
5070 5312 5.609696 GCCGTTAGATCGACATCAATAAACG 60.610 44.000 0.00 0.00 35.33 3.60
5071 5313 5.233476 TGCCGTTAGATCGACATCAATAAAC 59.767 40.000 0.00 0.00 0.00 2.01
5072 5314 5.353111 TGCCGTTAGATCGACATCAATAAA 58.647 37.500 0.00 0.00 0.00 1.40
5073 5315 4.939271 TGCCGTTAGATCGACATCAATAA 58.061 39.130 0.00 0.00 0.00 1.40
5074 5316 4.277423 TCTGCCGTTAGATCGACATCAATA 59.723 41.667 0.00 0.00 0.00 1.90
5075 5317 3.068165 TCTGCCGTTAGATCGACATCAAT 59.932 43.478 0.00 0.00 0.00 2.57
5076 5318 2.425668 TCTGCCGTTAGATCGACATCAA 59.574 45.455 0.00 0.00 0.00 2.57
5077 5319 2.021457 TCTGCCGTTAGATCGACATCA 58.979 47.619 0.00 0.37 0.00 3.07
5078 5320 2.223502 TGTCTGCCGTTAGATCGACATC 60.224 50.000 0.00 0.00 0.00 3.06
5079 5321 1.749063 TGTCTGCCGTTAGATCGACAT 59.251 47.619 0.00 0.00 0.00 3.06
5080 5322 1.170442 TGTCTGCCGTTAGATCGACA 58.830 50.000 0.00 0.00 0.00 4.35
5081 5323 2.273370 TTGTCTGCCGTTAGATCGAC 57.727 50.000 0.00 0.00 0.00 4.20
5082 5324 3.520290 ATTTGTCTGCCGTTAGATCGA 57.480 42.857 0.00 0.00 0.00 3.59
5083 5325 4.982295 TCATATTTGTCTGCCGTTAGATCG 59.018 41.667 0.00 0.00 0.00 3.69
5084 5326 6.480320 ACTTCATATTTGTCTGCCGTTAGATC 59.520 38.462 0.00 0.00 0.00 2.75
5085 5327 6.349300 ACTTCATATTTGTCTGCCGTTAGAT 58.651 36.000 0.00 0.00 0.00 1.98
5086 5328 5.730550 ACTTCATATTTGTCTGCCGTTAGA 58.269 37.500 0.00 0.00 0.00 2.10
5087 5329 6.757010 AGTACTTCATATTTGTCTGCCGTTAG 59.243 38.462 0.00 0.00 0.00 2.34
5088 5330 6.533723 CAGTACTTCATATTTGTCTGCCGTTA 59.466 38.462 0.00 0.00 0.00 3.18
5089 5331 5.351465 CAGTACTTCATATTTGTCTGCCGTT 59.649 40.000 0.00 0.00 0.00 4.44
5090 5332 4.870426 CAGTACTTCATATTTGTCTGCCGT 59.130 41.667 0.00 0.00 0.00 5.68
5091 5333 4.271049 CCAGTACTTCATATTTGTCTGCCG 59.729 45.833 0.00 0.00 0.00 5.69
5092 5334 4.576463 CCCAGTACTTCATATTTGTCTGCC 59.424 45.833 0.00 0.00 0.00 4.85
5093 5335 5.186198 ACCCAGTACTTCATATTTGTCTGC 58.814 41.667 0.00 0.00 0.00 4.26
5094 5336 7.556844 ACTACCCAGTACTTCATATTTGTCTG 58.443 38.462 0.00 0.00 31.45 3.51
5095 5337 7.735326 ACTACCCAGTACTTCATATTTGTCT 57.265 36.000 0.00 0.00 31.45 3.41
5109 5351 4.508551 TTCATCGGAGTACTACCCAGTA 57.491 45.455 0.00 0.00 36.14 2.74
5110 5352 3.377253 TTCATCGGAGTACTACCCAGT 57.623 47.619 0.00 0.00 38.91 4.00
5111 5353 3.700038 ACTTTCATCGGAGTACTACCCAG 59.300 47.826 0.00 0.00 0.00 4.45
5112 5354 3.705051 ACTTTCATCGGAGTACTACCCA 58.295 45.455 0.00 0.00 0.00 4.51
5113 5355 4.260948 CGTACTTTCATCGGAGTACTACCC 60.261 50.000 0.00 0.00 43.73 3.69
5114 5356 4.787882 GCGTACTTTCATCGGAGTACTACC 60.788 50.000 0.00 0.45 43.73 3.18
5115 5357 4.278058 GCGTACTTTCATCGGAGTACTAC 58.722 47.826 0.00 0.00 43.73 2.73
5116 5358 3.001634 CGCGTACTTTCATCGGAGTACTA 59.998 47.826 0.00 0.00 43.73 1.82
5117 5359 2.223203 CGCGTACTTTCATCGGAGTACT 60.223 50.000 0.00 0.00 43.73 2.73
5118 5360 2.107178 CGCGTACTTTCATCGGAGTAC 58.893 52.381 0.00 4.10 42.92 2.73
5119 5361 2.009051 TCGCGTACTTTCATCGGAGTA 58.991 47.619 5.77 0.00 0.00 2.59
5120 5362 0.806868 TCGCGTACTTTCATCGGAGT 59.193 50.000 5.77 0.00 0.00 3.85
5121 5363 3.616935 TCGCGTACTTTCATCGGAG 57.383 52.632 5.77 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.