Multiple sequence alignment - TraesCS5A01G442800

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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 TraesCS5A01G442800 chr5A 100.000 6513 0 0 1 6513 623027577 623021065 0.000000e+00 12028.0
1 TraesCS5A01G442800 chr5A 86.395 147 11 6 368 505 414775823 414775677 1.130000e-32 152.0
2 TraesCS5A01G442800 chr5A 83.784 111 16 2 3 112 11077767 11077876 3.210000e-18 104.0
3 TraesCS5A01G442800 chr5D 92.217 3983 153 55 934 4836 498734393 498730488 0.000000e+00 5493.0
4 TraesCS5A01G442800 chr5D 97.143 805 19 2 4833 5633 498730457 498729653 0.000000e+00 1356.0
5 TraesCS5A01G442800 chr5D 89.425 643 59 7 5631 6272 498728234 498727600 0.000000e+00 802.0
6 TraesCS5A01G442800 chr5D 83.333 150 24 1 508 656 103636819 103636670 3.170000e-28 137.0
7 TraesCS5A01G442800 chr5B 94.224 3428 133 32 1445 4836 618286398 618283000 0.000000e+00 5173.0
8 TraesCS5A01G442800 chr5B 91.297 1735 84 31 4833 6513 618282969 618281248 0.000000e+00 2305.0
9 TraesCS5A01G442800 chr5B 90.315 444 5 7 929 1346 618287139 618286708 1.230000e-151 547.0
10 TraesCS5A01G442800 chr5B 90.537 391 31 4 1 389 618289691 618289305 4.500000e-141 512.0
11 TraesCS5A01G442800 chr5B 86.052 466 49 11 388 842 618288897 618288437 2.730000e-133 486.0
12 TraesCS5A01G442800 chr5B 86.364 132 18 0 525 656 417444066 417443935 1.890000e-30 145.0
13 TraesCS5A01G442800 chr5B 86.290 124 10 6 2 123 188018854 188018736 1.910000e-25 128.0
14 TraesCS5A01G442800 chr5B 86.842 76 5 4 768 841 266367277 266367205 5.410000e-11 80.5
15 TraesCS5A01G442800 chr5B 97.778 45 0 1 865 909 618287314 618287271 7.000000e-10 76.8
16 TraesCS5A01G442800 chr5B 84.286 70 11 0 773 842 464353904 464353973 1.170000e-07 69.4
17 TraesCS5A01G442800 chr3A 84.583 1414 156 41 3126 4514 734840488 734841864 0.000000e+00 1347.0
18 TraesCS5A01G442800 chr3A 84.158 1414 162 41 3126 4514 734885872 734887248 0.000000e+00 1314.0
19 TraesCS5A01G442800 chr3A 86.947 475 61 1 4836 5310 734842653 734843126 3.460000e-147 532.0
20 TraesCS5A01G442800 chr3A 86.526 475 63 1 4836 5310 734888037 734888510 7.480000e-144 521.0
21 TraesCS5A01G442800 chr3A 84.919 431 56 7 1834 2262 734839286 734839709 1.680000e-115 427.0
22 TraesCS5A01G442800 chr3A 84.455 431 58 7 1834 2262 734884666 734885089 3.630000e-112 416.0
23 TraesCS5A01G442800 chr3A 95.045 222 10 1 1139 1360 734838545 734838765 1.340000e-91 348.0
24 TraesCS5A01G442800 chr3A 85.621 153 13 6 362 505 585297974 585298126 1.130000e-32 152.0
25 TraesCS5A01G442800 chr3A 86.111 144 11 7 369 503 627964922 627965065 5.260000e-31 147.0
26 TraesCS5A01G442800 chr3A 85.333 150 13 7 365 505 648037282 648037431 5.260000e-31 147.0
27 TraesCS5A01G442800 chr3A 79.592 98 19 1 6217 6314 47496827 47496923 1.170000e-07 69.4
28 TraesCS5A01G442800 chr3D 84.914 1339 151 38 3126 4445 604686049 604687355 0.000000e+00 1306.0
29 TraesCS5A01G442800 chr3D 85.565 478 63 5 4836 5310 604687702 604688176 4.540000e-136 496.0
30 TraesCS5A01G442800 chr3D 86.506 415 49 5 1850 2263 604684853 604685261 3.580000e-122 449.0
31 TraesCS5A01G442800 chr3D 82.789 459 44 15 2537 2967 604685611 604686062 1.710000e-100 377.0
32 TraesCS5A01G442800 chr3D 89.000 300 23 8 1139 1432 604684139 604684434 4.800000e-96 363.0
33 TraesCS5A01G442800 chr3D 87.755 98 10 2 2 98 401895912 401895816 5.340000e-21 113.0
34 TraesCS5A01G442800 chr3B 83.849 1294 147 36 3170 4445 812459866 812461115 0.000000e+00 1175.0
35 TraesCS5A01G442800 chr3B 88.421 475 54 1 4836 5310 812461753 812462226 7.330000e-159 571.0
36 TraesCS5A01G442800 chr3B 79.630 648 100 25 1834 2475 812458676 812459297 2.790000e-118 436.0
37 TraesCS5A01G442800 chr3B 88.424 311 25 8 1134 1433 812458053 812458363 1.330000e-96 364.0
38 TraesCS5A01G442800 chr3B 87.500 64 5 3 755 817 97725616 97725555 3.260000e-08 71.3
39 TraesCS5A01G442800 chr3B 85.965 57 6 2 841 895 668549713 668549769 7.050000e-05 60.2
40 TraesCS5A01G442800 chr2B 84.562 1153 91 38 3165 4304 30335310 30334232 0.000000e+00 1062.0
41 TraesCS5A01G442800 chr2B 83.444 151 23 2 508 656 258157725 258157875 8.810000e-29 139.0
42 TraesCS5A01G442800 chr2B 82.895 76 12 1 767 842 775431553 775431627 4.210000e-07 67.6
43 TraesCS5A01G442800 chr7D 82.447 1316 119 54 3145 4445 499627168 499625950 0.000000e+00 1048.0
44 TraesCS5A01G442800 chr7D 83.660 153 22 2 507 656 582130436 582130284 2.450000e-29 141.0
45 TraesCS5A01G442800 chr7D 84.211 76 11 1 767 842 591456896 591456822 9.060000e-09 73.1
46 TraesCS5A01G442800 chr7D 81.579 76 13 1 767 842 577704363 577704289 1.960000e-05 62.1
47 TraesCS5A01G442800 chr7A 83.656 1187 101 46 3145 4317 61493609 61492502 0.000000e+00 1031.0
48 TraesCS5A01G442800 chr7A 82.088 1312 132 52 3145 4445 109230668 109229449 0.000000e+00 1026.0
49 TraesCS5A01G442800 chr7A 85.333 150 20 2 508 656 674076622 674076474 3.140000e-33 154.0
50 TraesCS5A01G442800 chr7A 88.393 112 12 1 2 112 194793645 194793756 4.100000e-27 134.0
51 TraesCS5A01G442800 chr7A 90.566 53 1 3 839 888 308336117 308336066 4.210000e-07 67.6
52 TraesCS5A01G442800 chr7A 87.719 57 5 1 841 895 679357737 679357681 1.520000e-06 65.8
53 TraesCS5A01G442800 chr7A 87.719 57 5 1 841 895 679372385 679372329 1.520000e-06 65.8
54 TraesCS5A01G442800 chr7A 87.273 55 4 3 841 892 37186543 37186597 7.050000e-05 60.2
55 TraesCS5A01G442800 chr4B 81.202 1314 139 54 3143 4445 642737280 642738496 0.000000e+00 959.0
56 TraesCS5A01G442800 chr4B 83.444 151 23 1 508 656 90721808 90721658 8.810000e-29 139.0
57 TraesCS5A01G442800 chr6B 79.070 301 43 9 369 656 82007390 82007683 8.620000e-44 189.0
58 TraesCS5A01G442800 chr6B 89.583 48 5 0 841 888 176527727 176527774 1.960000e-05 62.1
59 TraesCS5A01G442800 chr2A 78.261 299 39 15 2584 2858 434076438 434076734 1.120000e-37 169.0
60 TraesCS5A01G442800 chr2A 87.273 55 4 3 841 892 70446009 70446063 7.050000e-05 60.2
61 TraesCS5A01G442800 chr1B 90.984 122 10 1 3 123 390427077 390427198 5.230000e-36 163.0
62 TraesCS5A01G442800 chr1B 85.616 146 12 5 369 505 414091029 414090884 1.890000e-30 145.0
63 TraesCS5A01G442800 chr1B 100.000 29 0 0 841 869 662324906 662324878 3.000000e-03 54.7
64 TraesCS5A01G442800 chr4D 86.842 152 11 6 363 505 36603041 36603192 1.880000e-35 161.0
65 TraesCS5A01G442800 chr6D 76.506 332 44 22 2590 2890 7276565 7276237 4.070000e-32 150.0
66 TraesCS5A01G442800 chr6D 83.333 78 11 2 767 844 437151264 437151189 3.260000e-08 71.3
67 TraesCS5A01G442800 chr1D 85.915 142 15 2 369 505 452344728 452344587 5.260000e-31 147.0
68 TraesCS5A01G442800 chr7B 83.553 152 22 2 508 656 627977213 627977364 8.810000e-29 139.0
69 TraesCS5A01G442800 chr2D 88.288 111 11 2 3 112 325808569 325808460 1.470000e-26 132.0
70 TraesCS5A01G442800 chr2D 94.000 50 3 0 841 890 638855023 638854974 7.000000e-10 76.8
71 TraesCS5A01G442800 chr2D 80.000 105 13 7 759 856 138293850 138293747 3.260000e-08 71.3
72 TraesCS5A01G442800 chr1A 76.531 294 38 17 2592 2858 79271031 79271320 1.470000e-26 132.0
73 TraesCS5A01G442800 chr1A 87.273 55 4 3 841 892 60670869 60670815 7.050000e-05 60.2
74 TraesCS5A01G442800 chr6A 85.455 110 15 1 4 112 297628541 297628650 5.340000e-21 113.0
75 TraesCS5A01G442800 chr6A 84.685 111 15 2 3 112 398185039 398184930 6.900000e-20 110.0
76 TraesCS5A01G442800 chrUn 87.719 57 5 1 841 895 420574331 420574275 1.520000e-06 65.8


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 TraesCS5A01G442800 chr5A 623021065 623027577 6512 True 12028.000000 12028 100.000000 1 6513 1 chr5A.!!$R2 6512
1 TraesCS5A01G442800 chr5D 498727600 498734393 6793 True 2550.333333 5493 92.928333 934 6272 3 chr5D.!!$R2 5338
2 TraesCS5A01G442800 chr5B 618281248 618289691 8443 True 1516.633333 5173 91.700500 1 6513 6 chr5B.!!$R4 6512
3 TraesCS5A01G442800 chr3A 734884666 734888510 3844 False 750.333333 1314 85.046333 1834 5310 3 chr3A.!!$F6 3476
4 TraesCS5A01G442800 chr3A 734838545 734843126 4581 False 663.500000 1347 87.873500 1139 5310 4 chr3A.!!$F5 4171
5 TraesCS5A01G442800 chr3D 604684139 604688176 4037 False 598.200000 1306 85.754800 1139 5310 5 chr3D.!!$F1 4171
6 TraesCS5A01G442800 chr3B 812458053 812462226 4173 False 636.500000 1175 85.081000 1134 5310 4 chr3B.!!$F2 4176
7 TraesCS5A01G442800 chr2B 30334232 30335310 1078 True 1062.000000 1062 84.562000 3165 4304 1 chr2B.!!$R1 1139
8 TraesCS5A01G442800 chr7D 499625950 499627168 1218 True 1048.000000 1048 82.447000 3145 4445 1 chr7D.!!$R1 1300
9 TraesCS5A01G442800 chr7A 61492502 61493609 1107 True 1031.000000 1031 83.656000 3145 4317 1 chr7A.!!$R1 1172
10 TraesCS5A01G442800 chr7A 109229449 109230668 1219 True 1026.000000 1026 82.088000 3145 4445 1 chr7A.!!$R2 1300
11 TraesCS5A01G442800 chr4B 642737280 642738496 1216 False 959.000000 959 81.202000 3143 4445 1 chr4B.!!$F1 1302

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
752 1173 0.901124 ATCCTCTGTGCAGTCCAGAC 59.099 55.000 1.56 0.00 35.23 3.51 F
1448 3149 0.039978 CCGCTACGGCTGTCTAGATG 60.040 60.000 0.00 0.00 41.17 2.90 F
1470 3338 0.251916 TTGTTCTAGGGTGGATGCGG 59.748 55.000 0.00 0.00 0.00 5.69 F
1578 3447 0.751643 GGTTTGGGCAGTGTGAGTGT 60.752 55.000 0.00 0.00 0.00 3.55 F
2800 4857 0.758685 TTGCAGTTTTCACCCTGGGG 60.759 55.000 18.88 7.87 42.03 4.96 F
3022 5086 1.561542 CCTCCTTATGGGTGTTGAGCT 59.438 52.381 0.00 0.00 36.25 4.09 F
3394 5464 2.083774 GCATGGCAGTACAGCTTGTTA 58.916 47.619 10.30 0.00 34.17 2.41 F
3405 5475 2.864343 ACAGCTTGTTAACGAGTCACAC 59.136 45.455 21.42 6.95 0.00 3.82 F
3917 6015 3.688272 CACTTCACTGTTTCTTGCACTG 58.312 45.455 0.00 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 4284 0.824759 GGAGCACCGTCCACTTCTAT 59.175 55.000 0.00 0.00 36.51 1.98 R
3102 5166 1.298953 TAGATGAAAGGCCTTGGCCT 58.701 50.000 26.23 26.23 42.86 5.19 R
3394 5464 1.338107 TCATCCCAGTGTGACTCGTT 58.662 50.000 0.00 0.00 0.00 3.85 R
3504 5575 5.380900 TGGTGTAAATGAAACCATGACTCA 58.619 37.500 0.00 0.00 39.05 3.41 R
3901 5999 2.679837 ACAGTCAGTGCAAGAAACAGTG 59.320 45.455 0.00 0.00 39.38 3.66 R
4372 6488 3.211045 TGGTCCAGTGCAGTAAAAACTC 58.789 45.455 0.00 0.00 0.00 3.01 R
5248 7854 1.758280 TGAATCAATCAAGGCATGGCC 59.242 47.619 16.82 6.86 40.45 5.36 R
5510 8116 7.280876 TGCATTGGACTATACAGAAAATGAGAC 59.719 37.037 0.00 0.00 0.00 3.36 R
5766 9798 1.534729 AAGATTGGCTCCCAACGAAC 58.465 50.000 0.00 0.00 46.95 3.95 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
23 24 1.468914 TGCGTTGCAATGCGGTATAAA 59.531 42.857 32.28 14.98 43.79 1.40
34 35 9.884636 TGCAATGCGGTATAAATATTCTAGTAT 57.115 29.630 0.00 0.00 0.00 2.12
56 57 6.699575 ATGTTAGTTCATGATTTACCTGCC 57.300 37.500 0.00 0.00 0.00 4.85
159 160 6.968263 TTTGATGGTCAATTGTTTGGTAGA 57.032 33.333 5.13 0.00 36.11 2.59
161 162 6.573664 TGATGGTCAATTGTTTGGTAGAAG 57.426 37.500 5.13 0.00 33.44 2.85
224 227 3.942130 AAAAGGCATGACAACTAAGGC 57.058 42.857 0.00 0.00 0.00 4.35
245 248 7.355332 AGGCAAATTTCAAGAAAAATCGATG 57.645 32.000 0.00 0.00 33.56 3.84
246 249 6.017325 GGCAAATTTCAAGAAAAATCGATGC 58.983 36.000 0.00 0.00 34.85 3.91
254 257 7.990541 TCAAGAAAAATCGATGCAAATATGG 57.009 32.000 0.00 0.00 0.00 2.74
259 262 5.695851 AAATCGATGCAAATATGGGAGAC 57.304 39.130 0.00 0.00 0.00 3.36
265 268 3.114606 TGCAAATATGGGAGACAGGAGA 58.885 45.455 0.00 0.00 0.00 3.71
266 269 3.718434 TGCAAATATGGGAGACAGGAGAT 59.282 43.478 0.00 0.00 0.00 2.75
275 278 7.878621 ATGGGAGACAGGAGATAAAATATCA 57.121 36.000 0.67 0.00 0.00 2.15
310 313 8.708378 AGATGAACATGAGAATGTACATAAGGA 58.292 33.333 9.21 0.00 33.81 3.36
326 329 7.682787 ACATAAGGATAGACAAAGGATGAGT 57.317 36.000 0.00 0.00 0.00 3.41
332 335 5.292101 GGATAGACAAAGGATGAGTTGAACG 59.708 44.000 0.00 0.00 0.00 3.95
349 352 7.556844 AGTTGAACGACATATCCTTACATTCT 58.443 34.615 0.00 0.00 0.00 2.40
350 353 8.041323 AGTTGAACGACATATCCTTACATTCTT 58.959 33.333 0.00 0.00 0.00 2.52
397 809 9.425248 TCCCTTCGTTCCTAAATATAAGTCTTA 57.575 33.333 0.00 0.00 0.00 2.10
464 878 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
465 879 3.942829 AGATTCACTCATTTTGCTCCGA 58.057 40.909 0.00 0.00 0.00 4.55
470 884 3.189080 TCACTCATTTTGCTCCGAATGTG 59.811 43.478 0.00 0.00 35.35 3.21
498 912 9.396022 TCCATATTGGAATGTCTAAAAAGACTC 57.604 33.333 7.04 0.00 45.00 3.36
506 920 9.508567 GGAATGTCTAAAAAGACTCATATTTGC 57.491 33.333 7.04 0.00 39.41 3.68
510 924 8.721478 TGTCTAAAAAGACTCATATTTGCACTC 58.279 33.333 7.04 0.00 39.41 3.51
512 926 6.899393 AAAAAGACTCATATTTGCACTCCA 57.101 33.333 0.00 0.00 0.00 3.86
514 928 6.690194 AAAGACTCATATTTGCACTCCATC 57.310 37.500 0.00 0.00 0.00 3.51
515 929 4.712476 AGACTCATATTTGCACTCCATCC 58.288 43.478 0.00 0.00 0.00 3.51
531 947 6.816640 CACTCCATCCGTTTCTAAATAAGACA 59.183 38.462 0.00 0.00 32.51 3.41
562 978 6.785191 AGATTTCAATACAAACTACATGCGG 58.215 36.000 0.00 0.00 0.00 5.69
563 979 5.950758 TTTCAATACAAACTACATGCGGT 57.049 34.783 0.00 0.00 0.00 5.68
574 990 7.982919 ACAAACTACATGCGGTTGTATATAGAA 59.017 33.333 15.11 0.00 34.29 2.10
616 1032 5.459768 TCACTCATTTTGCTACGTACGTAA 58.540 37.500 26.68 15.33 0.00 3.18
618 1034 6.252015 TCACTCATTTTGCTACGTACGTAATC 59.748 38.462 26.68 20.78 0.00 1.75
619 1035 6.252869 CACTCATTTTGCTACGTACGTAATCT 59.747 38.462 26.68 5.07 0.00 2.40
620 1036 7.430211 CACTCATTTTGCTACGTACGTAATCTA 59.570 37.037 26.68 15.85 0.00 1.98
658 1074 9.930158 TTAATGGGGCTTATATTTAGAAACAGT 57.070 29.630 0.00 0.00 0.00 3.55
659 1075 8.838649 AATGGGGCTTATATTTAGAAACAGTT 57.161 30.769 0.00 0.00 0.00 3.16
661 1077 9.930158 ATGGGGCTTATATTTAGAAACAGTTAA 57.070 29.630 0.00 0.00 0.00 2.01
695 1116 7.286316 CCATGCCTTTTGGTCTCTTTTCTATAT 59.714 37.037 0.00 0.00 42.99 0.86
730 1151 7.389053 GCAAATAAATGAAACAACCCCAATACA 59.611 33.333 0.00 0.00 0.00 2.29
740 1161 5.694995 ACAACCCCAATACAATATCCTCTG 58.305 41.667 0.00 0.00 0.00 3.35
752 1173 0.901124 ATCCTCTGTGCAGTCCAGAC 59.099 55.000 1.56 0.00 35.23 3.51
836 1257 9.448294 AAATAAATAACGTACAAAGCAAAACGA 57.552 25.926 0.23 0.00 38.64 3.85
847 1281 6.503524 ACAAAGCAAAACGAGTGAAATATGT 58.496 32.000 0.00 0.00 0.00 2.29
848 1282 6.636850 ACAAAGCAAAACGAGTGAAATATGTC 59.363 34.615 0.00 0.00 0.00 3.06
851 1285 7.061752 AGCAAAACGAGTGAAATATGTCTAC 57.938 36.000 0.00 0.00 0.00 2.59
859 1293 9.817809 ACGAGTGAAATATGTCTACATACATTT 57.182 29.630 4.98 4.61 41.15 2.32
900 2421 7.051000 TGAAATTTCTAAAAACACTTTGGGGG 58.949 34.615 18.64 0.00 0.00 5.40
901 2422 6.816616 AATTTCTAAAAACACTTTGGGGGA 57.183 33.333 0.00 0.00 0.00 4.81
904 2425 1.801242 AAAAACACTTTGGGGGAGGG 58.199 50.000 0.00 0.00 0.00 4.30
910 2435 0.908180 ACTTTGGGGGAGGGAGTACG 60.908 60.000 0.00 0.00 0.00 3.67
918 2443 2.424812 GGGGAGGGAGTACGGTAATACA 60.425 54.545 0.00 0.00 0.00 2.29
919 2444 2.889678 GGGAGGGAGTACGGTAATACAG 59.110 54.545 0.00 0.00 0.00 2.74
920 2445 3.560105 GGAGGGAGTACGGTAATACAGT 58.440 50.000 0.00 1.38 0.00 3.55
921 2446 4.446311 GGGAGGGAGTACGGTAATACAGTA 60.446 50.000 0.00 0.00 0.00 2.74
922 2447 4.517075 GGAGGGAGTACGGTAATACAGTAC 59.483 50.000 20.82 20.82 45.75 2.73
1080 2738 3.854669 CCCCCTACCTGCAGCGAG 61.855 72.222 8.66 7.17 0.00 5.03
1374 3032 3.260100 CCCCCACTGCCTGGACTT 61.260 66.667 0.00 0.00 43.95 3.01
1376 3034 1.153756 CCCCACTGCCTGGACTTTT 59.846 57.895 0.00 0.00 43.95 2.27
1446 3147 3.823402 CCGCTACGGCTGTCTAGA 58.177 61.111 0.00 0.00 41.17 2.43
1447 3148 2.332277 CCGCTACGGCTGTCTAGAT 58.668 57.895 0.00 0.00 41.17 1.98
1448 3149 0.039978 CCGCTACGGCTGTCTAGATG 60.040 60.000 0.00 0.00 41.17 2.90
1449 3150 0.663688 CGCTACGGCTGTCTAGATGT 59.336 55.000 0.00 0.00 36.09 3.06
1469 3337 2.107950 TTTGTTCTAGGGTGGATGCG 57.892 50.000 0.00 0.00 0.00 4.73
1470 3338 0.251916 TTGTTCTAGGGTGGATGCGG 59.748 55.000 0.00 0.00 0.00 5.69
1475 3343 2.351336 CTAGGGTGGATGCGGTCGAC 62.351 65.000 7.13 7.13 35.08 4.20
1481 3349 2.024871 GATGCGGTCGACTCCTCG 59.975 66.667 16.46 11.46 41.65 4.63
1491 3359 1.509004 GACTCCTCGGCTGAGTGTC 59.491 63.158 21.06 21.61 42.94 3.67
1507 3376 3.399181 TCCCTGTGGTGATCCGCC 61.399 66.667 0.00 0.00 43.03 6.13
1514 3383 1.271871 TGTGGTGATCCGCCAGATTTT 60.272 47.619 6.38 0.00 45.19 1.82
1551 3420 2.146342 CTGTCTCGTGTTTCTGGCATT 58.854 47.619 0.00 0.00 0.00 3.56
1567 3436 1.469079 GCATTACACGATGGTTTGGGC 60.469 52.381 0.00 0.00 0.00 5.36
1578 3447 0.751643 GGTTTGGGCAGTGTGAGTGT 60.752 55.000 0.00 0.00 0.00 3.55
1630 3531 1.003718 CTGGACCGGGACCTGTTTC 60.004 63.158 16.37 0.00 0.00 2.78
1732 3636 1.783284 TTCTGTTGTCTGCACTAGCG 58.217 50.000 0.00 0.00 46.23 4.26
1753 3676 4.560716 GCGTCAGTACTATATTGATGCCCA 60.561 45.833 12.84 0.00 45.90 5.36
1790 3714 2.615986 TGACTCTAGGTAAGTGGCCA 57.384 50.000 0.00 0.00 0.00 5.36
1811 3735 3.492383 CAGTGCAAGGTGATTCTATAGCG 59.508 47.826 0.00 0.00 0.00 4.26
1845 3797 3.938963 GGAATAACGGAATTGCTGTCTGA 59.061 43.478 0.00 0.00 34.15 3.27
1906 3858 1.600058 TGGAATTGGGCAGGAGATCT 58.400 50.000 0.00 0.00 0.00 2.75
1908 3860 1.492176 GGAATTGGGCAGGAGATCTCA 59.508 52.381 23.85 2.00 0.00 3.27
1971 3923 2.579787 CGGGCTCGTGATGTCGAC 60.580 66.667 9.11 9.11 35.91 4.20
2247 4200 4.001652 GTGTTTAGTAGCAGAGGGGTTTC 58.998 47.826 0.00 0.00 0.00 2.78
2281 4265 6.660521 TCTCTTGCCAACATTAATCTTGATGT 59.339 34.615 5.14 0.00 38.81 3.06
2300 4284 5.366477 TGATGTGGGTAGATGCATTTCTAGA 59.634 40.000 0.00 0.00 0.00 2.43
2312 4296 5.592054 TGCATTTCTAGATAGAAGTGGACG 58.408 41.667 20.22 2.94 44.98 4.79
2357 4346 3.650942 ACCTTCCAGATACACCTTTGTGA 59.349 43.478 0.00 0.00 45.76 3.58
2424 4416 2.044650 TGCCCTGAATCCTGCTGC 60.045 61.111 0.00 0.00 0.00 5.25
2534 4545 5.488341 GTTCTGGTCTGCTGGTTAATCTTA 58.512 41.667 0.00 0.00 0.00 2.10
2536 4547 5.023452 TCTGGTCTGCTGGTTAATCTTAGA 58.977 41.667 0.00 0.00 0.00 2.10
2540 4551 6.599244 TGGTCTGCTGGTTAATCTTAGAAATG 59.401 38.462 0.00 0.00 0.00 2.32
2542 4553 5.590259 TCTGCTGGTTAATCTTAGAAATGGC 59.410 40.000 0.00 0.00 0.00 4.40
2544 4555 5.357878 TGCTGGTTAATCTTAGAAATGGCTG 59.642 40.000 0.00 0.00 0.00 4.85
2545 4556 5.221126 GCTGGTTAATCTTAGAAATGGCTGG 60.221 44.000 0.00 0.00 0.00 4.85
2546 4557 5.826643 TGGTTAATCTTAGAAATGGCTGGT 58.173 37.500 0.00 0.00 0.00 4.00
2550 4585 5.975988 AATCTTAGAAATGGCTGGTCCTA 57.024 39.130 0.00 0.00 35.26 2.94
2553 4588 4.534500 TCTTAGAAATGGCTGGTCCTAACA 59.466 41.667 0.00 0.00 35.26 2.41
2604 4640 1.072648 CCCGGGTCTTGTTTTGTCCTA 59.927 52.381 14.18 0.00 0.00 2.94
2800 4857 0.758685 TTGCAGTTTTCACCCTGGGG 60.759 55.000 18.88 7.87 42.03 4.96
2853 4910 6.879458 GGAGAACTTTCTTCAATAGCAAGGTA 59.121 38.462 0.00 0.00 37.73 3.08
2858 4915 9.686683 AACTTTCTTCAATAGCAAGGTATGTAT 57.313 29.630 0.00 0.00 32.18 2.29
2859 4916 9.113838 ACTTTCTTCAATAGCAAGGTATGTATG 57.886 33.333 0.00 0.00 32.18 2.39
2862 4926 7.801104 TCTTCAATAGCAAGGTATGTATGGAA 58.199 34.615 0.00 0.00 0.00 3.53
3002 5066 6.850752 TTTTGGGGGAAATCTAGTTGATTC 57.149 37.500 0.14 0.00 43.99 2.52
3022 5086 1.561542 CCTCCTTATGGGTGTTGAGCT 59.438 52.381 0.00 0.00 36.25 4.09
3180 5249 6.747414 TTCCTTATATGCTTCTCTTGGCTA 57.253 37.500 0.00 0.00 0.00 3.93
3352 5422 7.519002 ACGATTGAGTTTGACTTTATACTTGC 58.481 34.615 0.00 0.00 0.00 4.01
3394 5464 2.083774 GCATGGCAGTACAGCTTGTTA 58.916 47.619 10.30 0.00 34.17 2.41
3405 5475 2.864343 ACAGCTTGTTAACGAGTCACAC 59.136 45.455 21.42 6.95 0.00 3.82
3732 5806 9.833894 CATCTTTAACTTGAAATGTTTTGAACG 57.166 29.630 0.00 0.00 35.64 3.95
3901 5999 5.583854 TGATCAATCTCTTTAGCTGCACTTC 59.416 40.000 1.02 0.00 0.00 3.01
3917 6015 3.688272 CACTTCACTGTTTCTTGCACTG 58.312 45.455 0.00 0.00 0.00 3.66
4372 6488 7.283127 ACTTAATTATGACATGGCAGTACAAGG 59.717 37.037 7.63 0.00 0.00 3.61
4585 6914 9.696572 TTCCTGAGTACATGAACTATTACTAGT 57.303 33.333 0.00 0.00 39.97 2.57
4761 7313 7.707464 TCATTGCAATCTTGGCAGTATTATTTG 59.293 33.333 9.53 0.00 43.05 2.32
4773 7336 6.030228 GCAGTATTATTTGTCTTTGTCTGGC 58.970 40.000 0.00 0.00 0.00 4.85
5049 7655 5.183228 AGGTATACTACAAACATGTGCACC 58.817 41.667 15.69 0.00 0.00 5.01
5157 7763 4.082523 CTTCCAGCGCCTCCGGAA 62.083 66.667 5.23 10.87 37.28 4.30
5567 8173 4.742438 TCGTTCTTGTTACTTTGGCATC 57.258 40.909 0.00 0.00 0.00 3.91
5569 8175 3.252215 CGTTCTTGTTACTTTGGCATCCA 59.748 43.478 0.00 0.00 0.00 3.41
5725 9757 2.363306 TTGCAACACCTTGTGAGGAT 57.637 45.000 0.00 0.00 46.74 3.24
5726 9758 2.363306 TGCAACACCTTGTGAGGATT 57.637 45.000 0.49 0.00 46.74 3.01
5727 9759 2.665165 TGCAACACCTTGTGAGGATTT 58.335 42.857 0.49 0.00 46.74 2.17
5728 9760 3.030291 TGCAACACCTTGTGAGGATTTT 58.970 40.909 0.49 0.00 46.74 1.82
5729 9761 3.450457 TGCAACACCTTGTGAGGATTTTT 59.550 39.130 0.49 0.00 46.74 1.94
5766 9798 4.227538 ACGGAAATGATATCTAGCGAACG 58.772 43.478 3.98 3.29 0.00 3.95
5793 9825 0.931005 GGAGCCAATCTTAGCGAACG 59.069 55.000 0.00 0.00 0.00 3.95
5860 9892 7.308891 CCACGTAGATAAGCTAGAGTCATTCAT 60.309 40.741 0.00 0.00 0.00 2.57
5883 9915 0.684805 AACCCGTTTCCAGGCAAACA 60.685 50.000 12.35 0.00 36.23 2.83
5885 9917 1.362355 CCGTTTCCAGGCAAACACC 59.638 57.895 12.35 0.00 36.23 4.16
5899 9931 5.430089 AGGCAAACACCCTCTTTCTATCTAT 59.570 40.000 0.00 0.00 0.00 1.98
5900 9932 5.760743 GGCAAACACCCTCTTTCTATCTATC 59.239 44.000 0.00 0.00 0.00 2.08
5901 9933 6.408662 GGCAAACACCCTCTTTCTATCTATCT 60.409 42.308 0.00 0.00 0.00 1.98
5902 9934 7.202011 GGCAAACACCCTCTTTCTATCTATCTA 60.202 40.741 0.00 0.00 0.00 1.98
5966 9998 4.262036 GGGGGTTTGTGAAATCTTGAGTTC 60.262 45.833 4.15 4.15 0.00 3.01
6055 10087 7.070571 TGACCAAATAAAATCCAGAAAACCTGT 59.929 33.333 0.00 0.00 41.33 4.00
6111 10143 4.609098 TTTTTGGCCATGTCCCGT 57.391 50.000 6.09 0.00 0.00 5.28
6139 10171 9.566432 TTTTTACAAGTCCATGGCAATATTTTT 57.434 25.926 6.96 0.00 0.00 1.94
6141 10173 5.490159 ACAAGTCCATGGCAATATTTTTGG 58.510 37.500 6.96 0.00 0.00 3.28
6142 10174 4.758773 AGTCCATGGCAATATTTTTGGG 57.241 40.909 6.96 0.00 0.00 4.12
6151 10183 7.446001 TGGCAATATTTTTGGGATTGTTTTC 57.554 32.000 0.00 0.00 0.00 2.29
6184 10216 8.730970 TCACGTGGCAGTTTATTATTTAAAAC 57.269 30.769 17.00 0.00 36.13 2.43
6321 10430 9.343539 AGAGGATGGCATTTTTATTAGTAAGAC 57.656 33.333 0.00 0.00 0.00 3.01
6387 10496 1.880819 GCCAAGGCAATCCCTGTGTG 61.881 60.000 6.14 0.00 45.62 3.82
6442 10552 7.939588 ACAATAGAATCTAACTTGGGGCTTATC 59.060 37.037 8.09 0.00 0.00 1.75
6445 10555 5.373854 AGAATCTAACTTGGGGCTTATCCAT 59.626 40.000 0.00 0.00 36.21 3.41
6450 10560 8.282801 TCTAACTTGGGGCTTATCCATATAAA 57.717 34.615 0.00 0.00 36.21 1.40
6498 10608 6.447162 AGTTTTCTAAAGTTTAGCATGGCAC 58.553 36.000 16.46 7.96 0.00 5.01
6506 10616 9.423061 CTAAAGTTTAGCATGGCACTTTTATTT 57.577 29.630 9.65 0.00 39.58 1.40
6508 10618 7.656707 AGTTTAGCATGGCACTTTTATTTTG 57.343 32.000 0.00 0.00 0.00 2.44
6509 10619 7.216494 AGTTTAGCATGGCACTTTTATTTTGT 58.784 30.769 0.00 0.00 0.00 2.83
6511 10621 8.647226 GTTTAGCATGGCACTTTTATTTTGTAG 58.353 33.333 0.00 0.00 0.00 2.74
6512 10622 6.588719 AGCATGGCACTTTTATTTTGTAGA 57.411 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.504005 ACTAGAATATTTATACCGCATTGCAAC 58.496 33.333 0.00 0.00 0.00 4.17
34 35 4.947388 GGGCAGGTAAATCATGAACTAACA 59.053 41.667 0.00 0.00 0.00 2.41
40 41 8.805175 CATTAATATGGGCAGGTAAATCATGAA 58.195 33.333 0.00 0.00 0.00 2.57
88 89 7.719633 GGTAGGTAAATCATAGGCAAGATTTGA 59.280 37.037 16.79 0.00 42.58 2.69
143 144 7.029563 CCAATAGCTTCTACCAAACAATTGAC 58.970 38.462 13.59 0.00 38.94 3.18
161 162 7.969536 TCTATGTCTTTCATAAGCCAATAGC 57.030 36.000 0.00 0.00 38.38 2.97
198 201 7.488150 GCCTTAGTTGTCATGCCTTTTATTAAC 59.512 37.037 0.00 0.00 0.00 2.01
204 207 3.230134 TGCCTTAGTTGTCATGCCTTTT 58.770 40.909 0.00 0.00 0.00 2.27
205 208 2.875296 TGCCTTAGTTGTCATGCCTTT 58.125 42.857 0.00 0.00 0.00 3.11
214 217 8.785329 TTTTTCTTGAAATTTGCCTTAGTTGT 57.215 26.923 0.00 0.00 0.00 3.32
224 227 8.990722 TTTGCATCGATTTTTCTTGAAATTTG 57.009 26.923 0.00 0.00 29.75 2.32
245 248 3.845781 TCTCCTGTCTCCCATATTTGC 57.154 47.619 0.00 0.00 0.00 3.68
246 249 8.930846 ATTTTATCTCCTGTCTCCCATATTTG 57.069 34.615 0.00 0.00 0.00 2.32
275 278 9.021807 ACATTCTCATGTTCATCTCTTCATTTT 57.978 29.630 0.00 0.00 41.16 1.82
310 313 5.869888 GTCGTTCAACTCATCCTTTGTCTAT 59.130 40.000 0.00 0.00 0.00 1.98
326 329 8.786826 AAAGAATGTAAGGATATGTCGTTCAA 57.213 30.769 0.33 0.00 34.54 2.69
453 867 2.415893 GGACCACATTCGGAGCAAAATG 60.416 50.000 0.00 0.00 38.54 2.32
458 872 1.199615 TATGGACCACATTCGGAGCA 58.800 50.000 0.00 0.00 41.03 4.26
459 873 2.549754 CAATATGGACCACATTCGGAGC 59.450 50.000 0.00 0.00 41.03 4.70
470 884 8.406297 GTCTTTTTAGACATTCCAATATGGACC 58.594 37.037 0.00 0.00 41.28 4.46
498 912 4.336433 AGAAACGGATGGAGTGCAAATATG 59.664 41.667 0.00 0.00 0.00 1.78
501 915 2.795329 AGAAACGGATGGAGTGCAAAT 58.205 42.857 0.00 0.00 0.00 2.32
506 920 6.816640 TGTCTTATTTAGAAACGGATGGAGTG 59.183 38.462 0.00 0.00 33.81 3.51
548 964 7.494211 TCTATATACAACCGCATGTAGTTTGT 58.506 34.615 10.03 10.03 39.04 2.83
589 1005 6.073440 ACGTACGTAGCAAAATGAGTGAATTT 60.073 34.615 21.41 0.00 0.00 1.82
590 1006 5.407387 ACGTACGTAGCAAAATGAGTGAATT 59.593 36.000 21.41 0.00 0.00 2.17
632 1048 9.930158 ACTGTTTCTAAATATAAGCCCCATTAA 57.070 29.630 0.00 0.00 0.00 1.40
636 1052 9.930158 ATTAACTGTTTCTAAATATAAGCCCCA 57.070 29.630 0.00 0.00 0.00 4.96
654 1070 5.179452 AGGCATGGTAGACAATTAACTGT 57.821 39.130 0.00 0.00 0.00 3.55
658 1074 6.279513 CCAAAAGGCATGGTAGACAATTAA 57.720 37.500 0.00 0.00 33.08 1.40
659 1075 5.913137 CCAAAAGGCATGGTAGACAATTA 57.087 39.130 0.00 0.00 33.08 1.40
700 1121 7.628234 TGGGGTTGTTTCATTTATTTGCATAT 58.372 30.769 0.00 0.00 0.00 1.78
701 1122 7.009179 TGGGGTTGTTTCATTTATTTGCATA 57.991 32.000 0.00 0.00 0.00 3.14
714 1135 6.833933 AGAGGATATTGTATTGGGGTTGTTTC 59.166 38.462 0.00 0.00 0.00 2.78
730 1151 3.133721 GTCTGGACTGCACAGAGGATATT 59.866 47.826 5.79 0.00 44.90 1.28
740 1161 5.449177 GCTTATTATTTGGTCTGGACTGCAC 60.449 44.000 0.67 0.00 0.00 4.57
752 1173 8.926710 CGGAGAGTAGTATTGCTTATTATTTGG 58.073 37.037 0.00 0.00 0.00 3.28
811 1232 9.109533 CTCGTTTTGCTTTGTACGTTATTTATT 57.890 29.630 0.00 0.00 35.63 1.40
814 1235 6.412653 CACTCGTTTTGCTTTGTACGTTATTT 59.587 34.615 0.00 0.00 35.63 1.40
818 1239 3.371591 TCACTCGTTTTGCTTTGTACGTT 59.628 39.130 0.00 0.00 35.63 3.99
820 1241 3.579147 TCACTCGTTTTGCTTTGTACG 57.421 42.857 0.00 0.00 35.46 3.67
824 1245 6.857964 AGACATATTTCACTCGTTTTGCTTTG 59.142 34.615 0.00 0.00 0.00 2.77
825 1246 6.970484 AGACATATTTCACTCGTTTTGCTTT 58.030 32.000 0.00 0.00 0.00 3.51
900 2421 5.126067 TGTACTGTATTACCGTACTCCCTC 58.874 45.833 21.57 3.59 38.87 4.30
901 2422 5.116084 TGTACTGTATTACCGTACTCCCT 57.884 43.478 21.57 0.00 38.87 4.20
904 2425 7.778470 ACTACTGTACTGTATTACCGTACTC 57.222 40.000 21.57 5.19 38.87 2.59
927 2452 9.798994 CCCTCCGTATCATAATTAATACTGTAC 57.201 37.037 5.99 0.00 0.00 2.90
990 2641 0.533032 GGAGTGAAGTCGGGAGGAAG 59.467 60.000 0.00 0.00 0.00 3.46
1379 3037 0.386113 CGTGGGGCGAAAAGGAAAAA 59.614 50.000 0.00 0.00 44.77 1.94
1433 3134 4.530710 ACAAAACATCTAGACAGCCGTA 57.469 40.909 0.00 0.00 0.00 4.02
1434 3135 3.402628 ACAAAACATCTAGACAGCCGT 57.597 42.857 0.00 0.00 0.00 5.68
1435 3136 3.997021 AGAACAAAACATCTAGACAGCCG 59.003 43.478 0.00 0.00 0.00 5.52
1436 3137 5.582665 CCTAGAACAAAACATCTAGACAGCC 59.417 44.000 10.56 0.00 45.17 4.85
1437 3138 5.582665 CCCTAGAACAAAACATCTAGACAGC 59.417 44.000 10.56 0.00 45.17 4.40
1439 3140 6.464222 CACCCTAGAACAAAACATCTAGACA 58.536 40.000 10.56 0.00 45.17 3.41
1440 3141 5.875359 CCACCCTAGAACAAAACATCTAGAC 59.125 44.000 10.56 0.00 45.17 2.59
1441 3142 5.783360 TCCACCCTAGAACAAAACATCTAGA 59.217 40.000 10.56 0.00 45.17 2.43
1442 3143 6.049955 TCCACCCTAGAACAAAACATCTAG 57.950 41.667 0.00 3.40 43.05 2.43
1443 3144 6.414732 CATCCACCCTAGAACAAAACATCTA 58.585 40.000 0.00 0.00 0.00 1.98
1444 3145 4.993705 TCCACCCTAGAACAAAACATCT 57.006 40.909 0.00 0.00 0.00 2.90
1445 3146 4.142381 GCATCCACCCTAGAACAAAACATC 60.142 45.833 0.00 0.00 0.00 3.06
1446 3147 3.763897 GCATCCACCCTAGAACAAAACAT 59.236 43.478 0.00 0.00 0.00 2.71
1447 3148 3.153919 GCATCCACCCTAGAACAAAACA 58.846 45.455 0.00 0.00 0.00 2.83
1448 3149 2.161609 CGCATCCACCCTAGAACAAAAC 59.838 50.000 0.00 0.00 0.00 2.43
1449 3150 2.432444 CGCATCCACCCTAGAACAAAA 58.568 47.619 0.00 0.00 0.00 2.44
1475 3343 2.716017 GGGACACTCAGCCGAGGAG 61.716 68.421 1.26 0.00 44.17 3.69
1481 3349 2.348998 CCACAGGGACACTCAGCC 59.651 66.667 0.00 0.00 35.59 4.85
1491 3359 3.687321 CTGGCGGATCACCACAGGG 62.687 68.421 2.67 0.00 37.25 4.45
1514 3383 6.706270 ACGAGACAGAAATTCTTTCAAGCTTA 59.294 34.615 11.22 0.00 42.10 3.09
1544 3413 2.159393 CCAAACCATCGTGTAATGCCAG 60.159 50.000 0.00 0.00 0.00 4.85
1551 3420 0.398696 ACTGCCCAAACCATCGTGTA 59.601 50.000 0.00 0.00 0.00 2.90
1567 3436 3.003378 TGACTAGACGAACACTCACACTG 59.997 47.826 0.00 0.00 0.00 3.66
1578 3447 2.742053 GCAGCCAATTTGACTAGACGAA 59.258 45.455 0.00 0.00 0.00 3.85
1630 3531 2.067616 GCAAATGCAGCGAGCTTTG 58.932 52.632 16.60 16.60 45.94 2.77
1659 3562 2.485814 GACAAATTTTCAGAGCTCCGCT 59.514 45.455 10.93 0.00 43.88 5.52
1732 3636 4.932200 GCTGGGCATCAATATAGTACTGAC 59.068 45.833 5.39 0.00 0.00 3.51
1790 3714 3.384789 TCGCTATAGAATCACCTTGCACT 59.615 43.478 3.21 0.00 0.00 4.40
1811 3735 2.223377 CCGTTATTCCGGCTAAAGCATC 59.777 50.000 0.00 0.00 41.78 3.91
1845 3797 6.744175 ATCAGAATCACACTACCATCTGAT 57.256 37.500 9.60 9.60 44.85 2.90
1906 3858 1.622607 AATCTCCCGCCCGACAATGA 61.623 55.000 0.00 0.00 0.00 2.57
1908 3860 1.146263 GAATCTCCCGCCCGACAAT 59.854 57.895 0.00 0.00 0.00 2.71
1971 3923 2.380084 TGATCCCCTTTTTCTCGTCG 57.620 50.000 0.00 0.00 0.00 5.12
2274 4257 4.885907 AGAAATGCATCTACCCACATCAAG 59.114 41.667 0.00 0.00 0.00 3.02
2281 4265 7.510685 ACTTCTATCTAGAAATGCATCTACCCA 59.489 37.037 0.00 0.00 41.37 4.51
2300 4284 0.824759 GGAGCACCGTCCACTTCTAT 59.175 55.000 0.00 0.00 36.51 1.98
2312 4296 1.404843 AACCTCTCGATAGGAGCACC 58.595 55.000 22.62 0.00 42.82 5.01
2380 4369 7.765695 ATTAGGCAGTTGGATAACCATAATG 57.234 36.000 0.00 0.00 46.34 1.90
2424 4416 5.858381 TGCAGATAAATAGGACAGCCTTAG 58.142 41.667 0.00 0.00 43.90 2.18
2534 4545 3.806949 TTGTTAGGACCAGCCATTTCT 57.193 42.857 0.00 0.00 40.02 2.52
2536 4547 3.844640 ACTTTGTTAGGACCAGCCATTT 58.155 40.909 0.00 0.00 40.02 2.32
2540 4551 2.160205 GGAACTTTGTTAGGACCAGCC 58.840 52.381 0.00 0.00 0.00 4.85
2542 4553 4.651778 TCATGGAACTTTGTTAGGACCAG 58.348 43.478 0.00 0.00 36.90 4.00
2544 4555 8.211629 AGTATATCATGGAACTTTGTTAGGACC 58.788 37.037 0.00 0.00 0.00 4.46
2545 4556 9.046296 CAGTATATCATGGAACTTTGTTAGGAC 57.954 37.037 0.00 0.00 0.00 3.85
2546 4557 7.715249 GCAGTATATCATGGAACTTTGTTAGGA 59.285 37.037 0.00 0.00 0.00 2.94
2550 4585 9.632638 ATTAGCAGTATATCATGGAACTTTGTT 57.367 29.630 0.00 0.00 0.00 2.83
2604 4640 5.106396 GCATGCAGAGAAGTGTTAGTCAATT 60.106 40.000 14.21 0.00 37.04 2.32
2800 4857 6.408858 TCTTCATTCACGTTCATTAGCTTC 57.591 37.500 0.00 0.00 0.00 3.86
2853 4910 8.405531 GTGTTGCTACATAATGTTTCCATACAT 58.594 33.333 3.85 0.00 37.18 2.29
2858 4915 4.461081 GGGTGTTGCTACATAATGTTTCCA 59.539 41.667 3.85 0.00 36.50 3.53
2859 4916 4.705023 AGGGTGTTGCTACATAATGTTTCC 59.295 41.667 3.85 0.00 36.50 3.13
2862 4926 4.662278 ACAGGGTGTTGCTACATAATGTT 58.338 39.130 3.85 0.00 36.50 2.71
2983 5047 4.446455 GGAGGAATCAACTAGATTTCCCCC 60.446 50.000 0.00 0.00 46.76 5.40
2984 5048 4.413851 AGGAGGAATCAACTAGATTTCCCC 59.586 45.833 0.00 6.88 46.76 4.81
3002 5066 1.561542 AGCTCAACACCCATAAGGAGG 59.438 52.381 0.00 0.00 39.89 4.30
3022 5086 2.489437 GGGGTGCCTGGTTTACAAAGTA 60.489 50.000 0.00 0.00 0.00 2.24
3070 5134 6.657541 TCCATTCAAAGCTTAAAGTTCGGTAT 59.342 34.615 0.00 0.00 0.00 2.73
3102 5166 1.298953 TAGATGAAAGGCCTTGGCCT 58.701 50.000 26.23 26.23 42.86 5.19
3137 5201 4.201920 GGAAAGCGAAGACATAAATCCACC 60.202 45.833 0.00 0.00 0.00 4.61
3180 5249 2.224113 CCTGCCTGCACTGAAATTTGTT 60.224 45.455 0.00 0.00 0.00 2.83
3319 5389 5.821204 AGTCAAACTCAATCGTTTTCCAAG 58.179 37.500 0.00 0.00 35.06 3.61
3352 5422 1.986378 GTCACTTCCGTCGTCATTCTG 59.014 52.381 0.00 0.00 0.00 3.02
3394 5464 1.338107 TCATCCCAGTGTGACTCGTT 58.662 50.000 0.00 0.00 0.00 3.85
3405 5475 9.107177 GCTATGATTATAACAAGATCATCCCAG 57.893 37.037 0.00 0.00 40.14 4.45
3504 5575 5.380900 TGGTGTAAATGAAACCATGACTCA 58.619 37.500 0.00 0.00 39.05 3.41
3901 5999 2.679837 ACAGTCAGTGCAAGAAACAGTG 59.320 45.455 0.00 0.00 39.38 3.66
4372 6488 3.211045 TGGTCCAGTGCAGTAAAAACTC 58.789 45.455 0.00 0.00 0.00 3.01
4585 6914 8.794553 GCAGCTCCAGAACTATTACTATTACTA 58.205 37.037 0.00 0.00 0.00 1.82
4586 6915 7.287927 TGCAGCTCCAGAACTATTACTATTACT 59.712 37.037 0.00 0.00 0.00 2.24
4587 6916 7.434492 TGCAGCTCCAGAACTATTACTATTAC 58.566 38.462 0.00 0.00 0.00 1.89
4589 6918 6.325028 TCTGCAGCTCCAGAACTATTACTATT 59.675 38.462 4.41 0.00 38.81 1.73
4590 6919 5.835819 TCTGCAGCTCCAGAACTATTACTAT 59.164 40.000 4.41 0.00 38.81 2.12
4761 7313 3.248266 GAAATGCATGCCAGACAAAGAC 58.752 45.455 16.68 0.00 0.00 3.01
4773 7336 4.177165 TGCAGTTTAGGTGAAATGCATG 57.823 40.909 0.00 0.00 37.00 4.06
5049 7655 3.692593 TGCCATGATCATGTTTGTCAGAG 59.307 43.478 29.23 14.60 37.11 3.35
5157 7763 6.827762 TGAATTTTTGGTTTGGAGCTTTCATT 59.172 30.769 0.00 0.00 0.00 2.57
5248 7854 1.758280 TGAATCAATCAAGGCATGGCC 59.242 47.619 16.82 6.86 40.45 5.36
5510 8116 7.280876 TGCATTGGACTATACAGAAAATGAGAC 59.719 37.037 0.00 0.00 0.00 3.36
5547 8153 3.252215 TGGATGCCAAAGTAACAAGAACG 59.748 43.478 0.00 0.00 0.00 3.95
5583 8193 4.763073 TGAAGTCCTCATGCTCTTATGTG 58.237 43.478 0.00 0.00 0.00 3.21
5682 9714 8.792633 CAATCAAATACTTACACTGGAAAAGGA 58.207 33.333 0.00 0.00 0.00 3.36
5766 9798 1.534729 AAGATTGGCTCCCAACGAAC 58.465 50.000 0.00 0.00 46.95 3.95
5793 9825 1.675641 ATGCAACGTCAGGGAAGGC 60.676 57.895 0.00 0.00 0.00 4.35
5966 9998 7.823310 AGCTTCAAGGATACATATAGCATCTTG 59.177 37.037 0.00 0.00 41.41 3.02
6139 10171 5.048364 CGTGATAAAGTGGAAAACAATCCCA 60.048 40.000 0.00 0.00 38.82 4.37
6141 10173 5.856455 CACGTGATAAAGTGGAAAACAATCC 59.144 40.000 10.90 0.00 40.10 3.01
6142 10174 6.911484 CACGTGATAAAGTGGAAAACAATC 57.089 37.500 10.90 0.00 34.93 2.67
6357 10466 4.323409 GGATTGCCTTGGCCAATAAAAGAA 60.323 41.667 20.85 6.78 33.34 2.52
6358 10467 3.197549 GGATTGCCTTGGCCAATAAAAGA 59.802 43.478 20.85 3.74 33.34 2.52
6413 10523 6.603599 AGCCCCAAGTTAGATTCTATTGTTTC 59.396 38.462 0.00 0.00 0.00 2.78
6480 10590 8.986477 AATAAAAGTGCCATGCTAAACTTTAG 57.014 30.769 11.32 4.39 40.91 1.85


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

AutoCloner maintained by Alex Coulton.