Multiple sequence alignment - TraesCS1D01G042700

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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 TraesCS1D01G042700 chr1D 100.000 5222 0 0 2587 7808 21457819 21452598 0.000000e+00 9644.0
1 TraesCS1D01G042700 chr1D 100.000 2119 0 0 1 2119 21460405 21458287 0.000000e+00 3914.0
2 TraesCS1D01G042700 chr1D 100.000 470 0 0 8107 8576 21452299 21451830 0.000000e+00 869.0
3 TraesCS1D01G042700 chr1A 97.418 5228 90 9 2590 7797 23008189 23002987 0.000000e+00 8865.0
4 TraesCS1D01G042700 chr1A 89.294 878 30 5 1265 2117 23009442 23008604 0.000000e+00 1042.0
5 TraesCS1D01G042700 chr1A 93.633 534 15 5 703 1220 23009957 23009427 0.000000e+00 780.0
6 TraesCS1D01G042700 chr1A 96.211 475 12 3 8107 8576 23002582 23002109 0.000000e+00 773.0
7 TraesCS1D01G042700 chr1A 90.476 168 16 0 536 703 23010287 23010120 1.120000e-53 222.0
8 TraesCS1D01G042700 chr1B 97.106 3939 68 10 2587 6514 35702401 35698498 0.000000e+00 6601.0
9 TraesCS1D01G042700 chr1B 94.803 4233 166 17 2587 6802 35128680 35132875 0.000000e+00 6549.0
10 TraesCS1D01G042700 chr1B 89.598 1442 75 26 703 2117 35127230 35128623 0.000000e+00 1762.0
11 TraesCS1D01G042700 chr1B 93.425 1019 48 4 6805 7805 35132939 35133956 0.000000e+00 1493.0
12 TraesCS1D01G042700 chr1B 97.727 572 12 1 6661 7232 35698499 35697929 0.000000e+00 983.0
13 TraesCS1D01G042700 chr1B 89.822 786 39 11 703 1477 35705569 35704814 0.000000e+00 970.0
14 TraesCS1D01G042700 chr1B 96.987 531 15 1 7275 7805 35689327 35688798 0.000000e+00 891.0
15 TraesCS1D01G042700 chr1B 96.186 472 16 2 8107 8576 35688771 35688300 0.000000e+00 771.0
16 TraesCS1D01G042700 chr1B 89.621 607 35 6 1468 2052 35703176 35702576 0.000000e+00 747.0
17 TraesCS1D01G042700 chr1B 90.339 383 33 3 325 703 35126682 35127064 4.620000e-137 499.0
18 TraesCS1D01G042700 chr1B 94.475 181 10 0 8107 8287 35133983 35134163 6.560000e-71 279.0
19 TraesCS1D01G042700 chr1B 91.892 185 12 2 328 509 35705876 35705692 1.100000e-63 255.0
20 TraesCS1D01G042700 chr1B 91.892 185 12 2 328 509 35797171 35796987 1.100000e-63 255.0
21 TraesCS1D01G042700 chr1B 94.194 155 7 1 173 325 35706183 35706029 1.440000e-57 235.0
22 TraesCS1D01G042700 chr1B 94.194 155 6 2 173 325 35797477 35797324 5.180000e-57 233.0
23 TraesCS1D01G042700 chr1B 96.104 77 3 0 8500 8576 35134284 35134360 9.040000e-25 126.0
24 TraesCS1D01G042700 chr1B 100.000 68 0 0 2050 2117 35702530 35702463 9.040000e-25 126.0
25 TraesCS1D01G042700 chr1B 97.727 44 1 0 7228 7271 35689392 35689349 9.230000e-10 76.8
26 TraesCS1D01G042700 chr4A 94.096 4099 137 33 2725 6802 591847065 591851079 0.000000e+00 6131.0
27 TraesCS1D01G042700 chr4A 93.057 893 35 5 6803 7668 591851141 591852033 0.000000e+00 1280.0
28 TraesCS1D01G042700 chr4A 83.980 1211 84 54 954 2114 591845789 591846939 0.000000e+00 1061.0
29 TraesCS1D01G042700 chr4A 89.071 366 33 3 342 703 591845061 591845423 1.700000e-121 448.0
30 TraesCS1D01G042700 chr4A 82.314 458 40 17 4713 5155 109426939 109427370 8.190000e-95 359.0
31 TraesCS1D01G042700 chr4A 91.500 200 13 3 700 898 591845593 591845789 1.100000e-68 272.0
32 TraesCS1D01G042700 chr4A 91.200 125 9 2 7664 7786 591852508 591852632 1.480000e-37 169.0
33 TraesCS1D01G042700 chr4A 95.000 80 4 0 2587 2666 591846999 591847078 9.040000e-25 126.0
34 TraesCS1D01G042700 chr4D 95.287 2716 101 12 2587 5283 10968825 10971532 0.000000e+00 4281.0
35 TraesCS1D01G042700 chr4D 93.542 1022 45 3 6803 7805 10973274 10974293 0.000000e+00 1502.0
36 TraesCS1D01G042700 chr4D 94.772 899 42 5 5907 6802 10972316 10973212 0.000000e+00 1395.0
37 TraesCS1D01G042700 chr4D 86.003 1286 71 43 880 2117 10967544 10968768 0.000000e+00 1277.0
38 TraesCS1D01G042700 chr4D 95.621 708 26 3 5282 5984 10971614 10972321 0.000000e+00 1131.0
39 TraesCS1D01G042700 chr4D 88.220 382 36 5 325 703 10965368 10965743 1.700000e-121 448.0
40 TraesCS1D01G042700 chr4D 94.853 136 4 3 173 307 10963731 10963864 8.720000e-50 209.0
41 TraesCS1D01G042700 chr4D 88.525 122 13 1 8456 8576 10975798 10975919 6.940000e-31 147.0
42 TraesCS1D01G042700 chr4D 89.130 92 10 0 4613 4704 355855892 355855801 1.960000e-21 115.0
43 TraesCS1D01G042700 chrUn 96.660 2335 43 8 4182 6514 328886668 328888969 0.000000e+00 3847.0
44 TraesCS1D01G042700 chrUn 98.533 1091 16 0 2593 3683 440910307 440909217 0.000000e+00 1927.0
45 TraesCS1D01G042700 chrUn 97.806 547 11 1 6661 7207 328888968 328889513 0.000000e+00 942.0
46 TraesCS1D01G042700 chrUn 89.621 607 35 6 1468 2052 465907243 465906643 0.000000e+00 747.0
47 TraesCS1D01G042700 chrUn 89.293 467 30 5 1011 1477 356845362 356844916 1.250000e-157 568.0
48 TraesCS1D01G042700 chrUn 89.293 467 30 5 1011 1477 356896950 356896504 1.250000e-157 568.0
49 TraesCS1D01G042700 chrUn 89.293 467 30 5 1011 1477 474797292 474796846 1.250000e-157 568.0
50 TraesCS1D01G042700 chrUn 91.525 354 9 6 703 1045 379145482 379145139 1.300000e-127 468.0
51 TraesCS1D01G042700 chrUn 91.525 354 9 6 703 1045 379147270 379146927 1.300000e-127 468.0
52 TraesCS1D01G042700 chrUn 92.432 185 11 2 328 509 379145789 379145605 2.370000e-65 261.0
53 TraesCS1D01G042700 chrUn 91.892 185 12 2 328 509 379147577 379147393 1.100000e-63 255.0
54 TraesCS1D01G042700 chrUn 94.340 159 6 2 328 483 480481545 480481387 3.090000e-59 241.0
55 TraesCS1D01G042700 chrUn 94.194 155 7 2 173 325 379146096 379145942 1.440000e-57 235.0
56 TraesCS1D01G042700 chrUn 94.194 155 7 1 173 325 379147884 379147730 1.440000e-57 235.0
57 TraesCS1D01G042700 chrUn 100.000 68 0 0 2050 2117 465906597 465906530 9.040000e-25 126.0
58 TraesCS1D01G042700 chrUn 94.872 78 4 0 173 250 465442856 465442779 1.170000e-23 122.0
59 TraesCS1D01G042700 chrUn 97.222 72 2 0 254 325 480481769 480481698 1.170000e-23 122.0
60 TraesCS1D01G042700 chr5A 93.855 2376 98 14 2590 4939 622206349 622203996 0.000000e+00 3535.0
61 TraesCS1D01G042700 chr5A 94.283 1819 67 15 4980 6787 622203853 622202061 0.000000e+00 2748.0
62 TraesCS1D01G042700 chr5A 89.932 1023 49 9 6803 7805 622201994 622201006 0.000000e+00 1269.0
63 TraesCS1D01G042700 chr5A 83.424 1472 83 45 703 2117 622207776 622206409 0.000000e+00 1218.0
64 TraesCS1D01G042700 chr5A 87.766 188 19 1 521 704 622208116 622207929 5.210000e-52 217.0
65 TraesCS1D01G042700 chr5A 81.250 224 31 6 8360 8576 622200176 622199957 4.120000e-38 171.0
66 TraesCS1D01G042700 chr4B 95.874 2133 79 6 4673 6800 20720019 20722147 0.000000e+00 3443.0
67 TraesCS1D01G042700 chr4B 92.878 1025 45 6 6803 7805 20722212 20723230 0.000000e+00 1463.0
68 TraesCS1D01G042700 chr4B 95.412 850 27 8 3234 4080 20718418 20719258 0.000000e+00 1343.0
69 TraesCS1D01G042700 chr4B 83.851 1480 68 42 703 2117 20716410 20717783 0.000000e+00 1251.0
70 TraesCS1D01G042700 chr4B 93.869 685 21 5 4078 4750 20719381 20720056 0.000000e+00 1013.0
71 TraesCS1D01G042700 chr4B 95.517 580 26 0 2587 3166 20717839 20718418 0.000000e+00 928.0
72 TraesCS1D01G042700 chr4B 88.312 462 47 6 5324 5781 439317101 439316643 1.630000e-151 547.0
73 TraesCS1D01G042700 chr4B 87.563 394 40 7 325 715 20715872 20716259 1.700000e-121 448.0
74 TraesCS1D01G042700 chr4B 82.299 435 38 17 4713 5134 439318897 439318489 2.960000e-89 340.0
75 TraesCS1D01G042700 chr4B 94.000 150 7 2 173 322 20715572 20715719 8.660000e-55 226.0
76 TraesCS1D01G042700 chr4B 88.701 177 9 3 4334 4510 439319196 439319031 1.130000e-48 206.0
77 TraesCS1D01G042700 chr4B 81.223 229 30 6 8360 8576 20723580 20723807 1.140000e-38 172.0
78 TraesCS1D01G042700 chr3A 94.355 124 3 1 54 173 25400141 25400264 4.090000e-43 187.0


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 TraesCS1D01G042700 chr1D 21451830 21460405 8575 True 4809.000000 9644 100.000000 1 8576 3 chr1D.!!$R1 8575
1 TraesCS1D01G042700 chr1A 23002109 23010287 8178 True 2336.400000 8865 93.406400 536 8576 5 chr1A.!!$R1 8040
2 TraesCS1D01G042700 chr1B 35126682 35134360 7678 False 1784.666667 6549 93.124000 325 8576 6 chr1B.!!$F1 8251
3 TraesCS1D01G042700 chr1B 35697929 35706183 8254 True 1416.714286 6601 94.337429 173 7232 7 chr1B.!!$R2 7059
4 TraesCS1D01G042700 chr1B 35688300 35689392 1092 True 579.600000 891 96.966667 7228 8576 3 chr1B.!!$R1 1348
5 TraesCS1D01G042700 chr4A 591845061 591852632 7571 False 1355.285714 6131 91.129143 342 7786 7 chr4A.!!$F2 7444
6 TraesCS1D01G042700 chr4D 10963731 10975919 12188 False 1298.750000 4281 92.102875 173 8576 8 chr4D.!!$F1 8403
7 TraesCS1D01G042700 chrUn 328886668 328889513 2845 False 2394.500000 3847 97.233000 4182 7207 2 chrUn.!!$F1 3025
8 TraesCS1D01G042700 chrUn 440909217 440910307 1090 True 1927.000000 1927 98.533000 2593 3683 1 chrUn.!!$R3 1090
9 TraesCS1D01G042700 chrUn 465906530 465907243 713 True 436.500000 747 94.810500 1468 2117 2 chrUn.!!$R7 649
10 TraesCS1D01G042700 chrUn 379145139 379147884 2745 True 320.333333 468 92.627000 173 1045 6 chrUn.!!$R6 872
11 TraesCS1D01G042700 chr5A 622199957 622208116 8159 True 1526.333333 3535 88.418333 521 8576 6 chr5A.!!$R1 8055
12 TraesCS1D01G042700 chr4B 20715572 20723807 8235 False 1143.000000 3443 91.131889 173 8576 9 chr4B.!!$F1 8403
13 TraesCS1D01G042700 chr4B 439316643 439319196 2553 True 364.333333 547 86.437333 4334 5781 3 chr4B.!!$R1 1447

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
157 158 0.107017 CATCGCCTCCCACCAGATTT 60.107 55.000 0.00 0.0 0.00 2.17 F
158 159 0.181350 ATCGCCTCCCACCAGATTTC 59.819 55.000 0.00 0.0 0.00 2.17 F
162 163 0.745845 CCTCCCACCAGATTTCGCAG 60.746 60.000 0.00 0.0 0.00 5.18 F
326 1816 1.153168 CCCCTAAGCGTCCACCATG 60.153 63.158 0.00 0.0 0.00 3.66 F
1230 6165 1.525077 CGAGGACGAGGAGGAGGAG 60.525 68.421 0.00 0.0 42.66 3.69 F
1750 8351 2.871453 ACTGGGGTTTAATTGAAGCGT 58.129 42.857 6.13 0.0 0.00 5.07 F
2787 9480 2.103941 CCTAAGGATCAGTGGGAAGAGC 59.896 54.545 0.00 0.0 0.00 4.09 F
3624 10327 4.335037 CCTCCTCTCTTTTTGCTAAGCATC 59.665 45.833 0.00 0.0 38.76 3.91 F
4770 11681 0.815734 ATCCGTAGAGTTGGTCCACG 59.184 55.000 0.00 0.0 0.00 4.94 F
6312 14686 3.244422 TGTCACTGCGATAACCCTTCTTT 60.244 43.478 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 6192 1.448189 CTCGTCCTCGTCCTCGTCT 60.448 63.158 0.00 0.00 38.33 4.18 R
1891 8530 2.065899 AAACAGGGCAACTAAGCACA 57.934 45.000 0.00 0.00 41.46 4.57 R
1957 8596 4.457603 AGCATGTTTGGCAACTATTTACGA 59.542 37.500 0.00 0.00 33.58 3.43 R
2009 8648 7.823745 ACAACCAGAAGATTGAACATTAAGT 57.176 32.000 0.00 0.00 0.00 2.24 R
2787 9480 4.766375 AGTTCCCACAGAATATAACCACG 58.234 43.478 0.00 0.00 36.69 4.94 R
3534 10237 1.196127 GCCGTACGAAGGTTTTCCAAG 59.804 52.381 18.76 0.00 43.73 3.61 R
4457 11327 6.113411 ACTATCTCGGGGTGTAAGAATTTTG 58.887 40.000 0.00 0.00 0.00 2.44 R
5108 12155 1.575419 ACCAAGCAATTGCCATGGAT 58.425 45.000 39.10 27.16 45.85 3.41 R
6610 14985 1.822990 TCGGTACTAAGGAGGCAACAG 59.177 52.381 0.00 0.00 41.41 3.16 R
7578 16199 0.765510 GTCAGTGGAGTGGGGTTTCT 59.234 55.000 0.00 0.00 0.00 2.52 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
20 21 2.996249 TTGCAGAAAATTTGCCACCA 57.004 40.000 0.00 0.00 40.81 4.17
21 22 2.996249 TGCAGAAAATTTGCCACCAA 57.004 40.000 0.00 0.00 40.81 3.67
22 23 2.836262 TGCAGAAAATTTGCCACCAAG 58.164 42.857 0.00 0.00 40.81 3.61
23 24 2.433604 TGCAGAAAATTTGCCACCAAGA 59.566 40.909 0.00 0.00 40.81 3.02
24 25 2.802247 GCAGAAAATTTGCCACCAAGAC 59.198 45.455 0.00 0.00 35.54 3.01
25 26 3.392882 CAGAAAATTTGCCACCAAGACC 58.607 45.455 0.00 0.00 31.52 3.85
26 27 3.070015 CAGAAAATTTGCCACCAAGACCT 59.930 43.478 0.00 0.00 31.52 3.85
27 28 3.070015 AGAAAATTTGCCACCAAGACCTG 59.930 43.478 0.00 0.00 31.52 4.00
28 29 2.380064 AATTTGCCACCAAGACCTGA 57.620 45.000 0.00 0.00 31.52 3.86
29 30 2.380064 ATTTGCCACCAAGACCTGAA 57.620 45.000 0.00 0.00 31.52 3.02
30 31 1.691196 TTTGCCACCAAGACCTGAAG 58.309 50.000 0.00 0.00 31.52 3.02
31 32 0.550914 TTGCCACCAAGACCTGAAGT 59.449 50.000 0.00 0.00 0.00 3.01
32 33 0.179020 TGCCACCAAGACCTGAAGTG 60.179 55.000 0.00 0.00 0.00 3.16
33 34 3.329300 CCACCAAGACCTGAAGTGG 57.671 57.895 0.00 0.00 41.84 4.00
34 35 0.890996 CCACCAAGACCTGAAGTGGC 60.891 60.000 0.00 0.00 41.38 5.01
35 36 0.179020 CACCAAGACCTGAAGTGGCA 60.179 55.000 0.00 0.00 34.27 4.92
36 37 0.550914 ACCAAGACCTGAAGTGGCAA 59.449 50.000 0.00 0.00 34.27 4.52
37 38 0.954452 CCAAGACCTGAAGTGGCAAC 59.046 55.000 0.00 0.00 0.00 4.17
38 39 0.954452 CAAGACCTGAAGTGGCAACC 59.046 55.000 0.00 0.00 0.00 3.77
39 40 0.178990 AAGACCTGAAGTGGCAACCC 60.179 55.000 0.00 0.00 0.00 4.11
40 41 1.603739 GACCTGAAGTGGCAACCCC 60.604 63.158 0.00 0.00 0.00 4.95
41 42 2.672996 CCTGAAGTGGCAACCCCG 60.673 66.667 0.00 0.00 35.87 5.73
42 43 3.365265 CTGAAGTGGCAACCCCGC 61.365 66.667 0.00 0.00 44.77 6.13
57 58 3.458163 CGCGCCCCACCTCTAGAA 61.458 66.667 0.00 0.00 0.00 2.10
58 59 2.187163 GCGCCCCACCTCTAGAAC 59.813 66.667 0.00 0.00 0.00 3.01
59 60 2.901042 CGCCCCACCTCTAGAACC 59.099 66.667 0.00 0.00 0.00 3.62
60 61 2.732619 CGCCCCACCTCTAGAACCC 61.733 68.421 0.00 0.00 0.00 4.11
61 62 1.307084 GCCCCACCTCTAGAACCCT 60.307 63.158 0.00 0.00 0.00 4.34
62 63 0.914902 GCCCCACCTCTAGAACCCTT 60.915 60.000 0.00 0.00 0.00 3.95
63 64 0.912486 CCCCACCTCTAGAACCCTTG 59.088 60.000 0.00 0.00 0.00 3.61
64 65 1.657804 CCCACCTCTAGAACCCTTGT 58.342 55.000 0.00 0.00 0.00 3.16
65 66 1.279271 CCCACCTCTAGAACCCTTGTG 59.721 57.143 0.00 0.00 0.00 3.33
66 67 1.978580 CCACCTCTAGAACCCTTGTGT 59.021 52.381 0.00 0.00 0.00 3.72
67 68 2.372172 CCACCTCTAGAACCCTTGTGTT 59.628 50.000 0.00 0.00 0.00 3.32
68 69 3.581332 CCACCTCTAGAACCCTTGTGTTA 59.419 47.826 0.00 0.00 0.00 2.41
69 70 4.041198 CCACCTCTAGAACCCTTGTGTTAA 59.959 45.833 0.00 0.00 0.00 2.01
70 71 5.280521 CCACCTCTAGAACCCTTGTGTTAAT 60.281 44.000 0.00 0.00 0.00 1.40
71 72 6.238648 CACCTCTAGAACCCTTGTGTTAATT 58.761 40.000 0.00 0.00 0.00 1.40
72 73 6.371825 CACCTCTAGAACCCTTGTGTTAATTC 59.628 42.308 0.00 0.00 0.00 2.17
73 74 5.880887 CCTCTAGAACCCTTGTGTTAATTCC 59.119 44.000 0.00 0.00 0.00 3.01
74 75 5.484715 TCTAGAACCCTTGTGTTAATTCCG 58.515 41.667 0.00 0.00 0.00 4.30
75 76 4.360951 AGAACCCTTGTGTTAATTCCGA 57.639 40.909 0.00 0.00 0.00 4.55
76 77 4.918588 AGAACCCTTGTGTTAATTCCGAT 58.081 39.130 0.00 0.00 0.00 4.18
77 78 6.057321 AGAACCCTTGTGTTAATTCCGATA 57.943 37.500 0.00 0.00 0.00 2.92
78 79 6.478129 AGAACCCTTGTGTTAATTCCGATAA 58.522 36.000 0.00 0.00 0.00 1.75
79 80 6.598064 AGAACCCTTGTGTTAATTCCGATAAG 59.402 38.462 0.00 0.00 0.00 1.73
80 81 5.190677 ACCCTTGTGTTAATTCCGATAAGG 58.809 41.667 0.00 0.00 42.97 2.69
81 82 4.036380 CCCTTGTGTTAATTCCGATAAGGC 59.964 45.833 0.00 0.00 40.77 4.35
82 83 4.638421 CCTTGTGTTAATTCCGATAAGGCA 59.362 41.667 0.00 0.00 40.77 4.75
83 84 5.124776 CCTTGTGTTAATTCCGATAAGGCAA 59.875 40.000 0.00 0.00 40.77 4.52
84 85 5.811399 TGTGTTAATTCCGATAAGGCAAG 57.189 39.130 0.00 0.00 40.77 4.01
85 86 5.250200 TGTGTTAATTCCGATAAGGCAAGT 58.750 37.500 0.00 0.00 40.77 3.16
86 87 5.708230 TGTGTTAATTCCGATAAGGCAAGTT 59.292 36.000 0.00 0.00 40.77 2.66
87 88 6.207810 TGTGTTAATTCCGATAAGGCAAGTTT 59.792 34.615 0.00 0.00 40.77 2.66
88 89 6.745907 GTGTTAATTCCGATAAGGCAAGTTTC 59.254 38.462 0.00 0.00 40.77 2.78
89 90 6.657541 TGTTAATTCCGATAAGGCAAGTTTCT 59.342 34.615 0.00 0.00 40.77 2.52
90 91 5.819825 AATTCCGATAAGGCAAGTTTCTC 57.180 39.130 0.00 0.00 40.77 2.87
91 92 3.261981 TCCGATAAGGCAAGTTTCTCC 57.738 47.619 0.00 0.00 40.77 3.71
92 93 2.838202 TCCGATAAGGCAAGTTTCTCCT 59.162 45.455 0.00 0.00 40.77 3.69
93 94 4.028131 TCCGATAAGGCAAGTTTCTCCTA 58.972 43.478 0.00 0.00 40.77 2.94
94 95 4.099573 TCCGATAAGGCAAGTTTCTCCTAG 59.900 45.833 0.00 0.00 40.77 3.02
95 96 4.099573 CCGATAAGGCAAGTTTCTCCTAGA 59.900 45.833 0.00 0.00 0.00 2.43
96 97 5.044558 CGATAAGGCAAGTTTCTCCTAGAC 58.955 45.833 0.00 0.00 0.00 2.59
97 98 3.320673 AAGGCAAGTTTCTCCTAGACG 57.679 47.619 0.00 0.00 0.00 4.18
98 99 1.066787 AGGCAAGTTTCTCCTAGACGC 60.067 52.381 0.00 0.00 0.00 5.19
99 100 0.992802 GCAAGTTTCTCCTAGACGCG 59.007 55.000 3.53 3.53 0.00 6.01
100 101 1.402456 GCAAGTTTCTCCTAGACGCGA 60.402 52.381 15.93 0.00 0.00 5.87
101 102 2.735762 GCAAGTTTCTCCTAGACGCGAT 60.736 50.000 15.93 2.85 0.00 4.58
102 103 3.109619 CAAGTTTCTCCTAGACGCGATC 58.890 50.000 15.93 6.88 0.00 3.69
103 104 2.645802 AGTTTCTCCTAGACGCGATCT 58.354 47.619 15.93 14.74 41.95 2.75
104 105 2.356382 AGTTTCTCCTAGACGCGATCTG 59.644 50.000 15.93 7.07 38.49 2.90
105 106 2.327200 TTCTCCTAGACGCGATCTGA 57.673 50.000 15.93 5.90 38.49 3.27
106 107 2.552599 TCTCCTAGACGCGATCTGAT 57.447 50.000 15.93 0.00 38.49 2.90
107 108 2.852449 TCTCCTAGACGCGATCTGATT 58.148 47.619 15.93 0.00 38.49 2.57
108 109 3.215151 TCTCCTAGACGCGATCTGATTT 58.785 45.455 15.93 0.00 38.49 2.17
109 110 3.003793 TCTCCTAGACGCGATCTGATTTG 59.996 47.826 15.93 4.12 38.49 2.32
110 111 2.949644 TCCTAGACGCGATCTGATTTGA 59.050 45.455 15.93 3.74 38.49 2.69
111 112 3.570125 TCCTAGACGCGATCTGATTTGAT 59.430 43.478 15.93 0.00 38.49 2.57
112 113 4.038042 TCCTAGACGCGATCTGATTTGATT 59.962 41.667 15.93 0.00 38.49 2.57
113 114 4.149571 CCTAGACGCGATCTGATTTGATTG 59.850 45.833 15.93 0.00 38.49 2.67
114 115 2.286294 AGACGCGATCTGATTTGATTGC 59.714 45.455 15.93 6.64 45.60 3.56
119 120 3.305964 CGATCTGATTTGATTGCATGCC 58.694 45.455 16.68 0.00 0.00 4.40
120 121 3.004419 CGATCTGATTTGATTGCATGCCT 59.996 43.478 16.68 1.69 0.00 4.75
121 122 4.499188 CGATCTGATTTGATTGCATGCCTT 60.499 41.667 16.68 1.48 0.00 4.35
122 123 4.811969 TCTGATTTGATTGCATGCCTTT 57.188 36.364 16.68 0.00 0.00 3.11
123 124 5.918426 TCTGATTTGATTGCATGCCTTTA 57.082 34.783 16.68 0.00 0.00 1.85
124 125 5.653507 TCTGATTTGATTGCATGCCTTTAC 58.346 37.500 16.68 2.98 0.00 2.01
125 126 5.419788 TCTGATTTGATTGCATGCCTTTACT 59.580 36.000 16.68 0.00 0.00 2.24
126 127 5.412640 TGATTTGATTGCATGCCTTTACTG 58.587 37.500 16.68 0.00 0.00 2.74
127 128 3.872511 TTGATTGCATGCCTTTACTGG 57.127 42.857 16.68 0.00 0.00 4.00
128 129 2.101783 TGATTGCATGCCTTTACTGGG 58.898 47.619 16.68 0.00 0.00 4.45
129 130 2.102578 GATTGCATGCCTTTACTGGGT 58.897 47.619 16.68 0.00 0.00 4.51
130 131 2.889170 TTGCATGCCTTTACTGGGTA 57.111 45.000 16.68 0.00 0.00 3.69
131 132 2.889170 TGCATGCCTTTACTGGGTAA 57.111 45.000 16.68 0.00 0.00 2.85
132 133 3.162147 TGCATGCCTTTACTGGGTAAA 57.838 42.857 16.68 3.40 35.92 2.01
133 134 3.707316 TGCATGCCTTTACTGGGTAAAT 58.293 40.909 16.68 0.00 37.37 1.40
134 135 3.699038 TGCATGCCTTTACTGGGTAAATC 59.301 43.478 16.68 1.36 37.37 2.17
135 136 3.243068 GCATGCCTTTACTGGGTAAATCG 60.243 47.826 6.36 0.24 37.37 3.34
136 137 3.985019 TGCCTTTACTGGGTAAATCGA 57.015 42.857 3.78 0.00 37.37 3.59
137 138 3.869065 TGCCTTTACTGGGTAAATCGAG 58.131 45.455 3.78 0.00 37.37 4.04
138 139 2.612672 GCCTTTACTGGGTAAATCGAGC 59.387 50.000 3.78 2.65 37.37 5.03
139 140 3.869065 CCTTTACTGGGTAAATCGAGCA 58.131 45.455 3.78 0.00 37.37 4.26
140 141 4.451900 CCTTTACTGGGTAAATCGAGCAT 58.548 43.478 3.78 0.00 37.37 3.79
141 142 4.511826 CCTTTACTGGGTAAATCGAGCATC 59.488 45.833 3.78 0.00 37.37 3.91
142 143 4.116961 TTTACTGGGTAAATCGAGCATCG 58.883 43.478 0.00 0.00 45.18 3.84
143 144 5.501712 TTTACTGGGTAAATCGAGCATCGC 61.502 45.833 0.00 0.00 44.33 4.58
152 153 3.785859 GAGCATCGCCTCCCACCA 61.786 66.667 0.00 0.00 0.00 4.17
153 154 3.746949 GAGCATCGCCTCCCACCAG 62.747 68.421 0.00 0.00 0.00 4.00
154 155 3.785859 GCATCGCCTCCCACCAGA 61.786 66.667 0.00 0.00 0.00 3.86
155 156 3.112205 GCATCGCCTCCCACCAGAT 62.112 63.158 0.00 0.00 0.00 2.90
156 157 1.528824 CATCGCCTCCCACCAGATT 59.471 57.895 0.00 0.00 0.00 2.40
157 158 0.107017 CATCGCCTCCCACCAGATTT 60.107 55.000 0.00 0.00 0.00 2.17
158 159 0.181350 ATCGCCTCCCACCAGATTTC 59.819 55.000 0.00 0.00 0.00 2.17
159 160 1.815421 CGCCTCCCACCAGATTTCG 60.815 63.158 0.00 0.00 0.00 3.46
160 161 2.115291 GCCTCCCACCAGATTTCGC 61.115 63.158 0.00 0.00 0.00 4.70
161 162 1.299648 CCTCCCACCAGATTTCGCA 59.700 57.895 0.00 0.00 0.00 5.10
162 163 0.745845 CCTCCCACCAGATTTCGCAG 60.746 60.000 0.00 0.00 0.00 5.18
163 164 1.372087 CTCCCACCAGATTTCGCAGC 61.372 60.000 0.00 0.00 0.00 5.25
164 165 2.753966 CCCACCAGATTTCGCAGCG 61.754 63.158 9.06 9.06 0.00 5.18
165 166 2.099062 CACCAGATTTCGCAGCGC 59.901 61.111 10.87 0.00 0.00 5.92
166 167 3.127533 ACCAGATTTCGCAGCGCC 61.128 61.111 10.87 0.00 0.00 6.53
167 168 3.880846 CCAGATTTCGCAGCGCCC 61.881 66.667 10.87 0.00 0.00 6.13
168 169 3.880846 CAGATTTCGCAGCGCCCC 61.881 66.667 10.87 0.00 0.00 5.80
181 182 4.301027 GCCCCCTCCGCATCTACG 62.301 72.222 0.00 0.00 0.00 3.51
197 198 7.758076 CCGCATCTACGTTCATAAATATAGGAA 59.242 37.037 0.00 0.00 29.89 3.36
306 1644 4.829872 ATTGGTAGTATGAACCACCGAA 57.170 40.909 0.00 0.00 46.56 4.30
326 1816 1.153168 CCCCTAAGCGTCCACCATG 60.153 63.158 0.00 0.00 0.00 3.66
339 1829 2.109834 TCCACCATGATCACAAAAGGGT 59.890 45.455 0.00 0.00 0.00 4.34
389 1882 9.531942 TTTGCAAACCATTTCAATGCTATATAG 57.468 29.630 8.05 5.30 37.86 1.31
451 1944 6.984474 TGTCTCTTTGACTAATATTTAGCCCG 59.016 38.462 0.00 0.00 45.54 6.13
496 1990 7.484975 TCTTTTATTTGACGTGAAACACCATT 58.515 30.769 1.24 0.00 35.74 3.16
502 1996 3.059257 TGACGTGAAACACCATTCATTCG 60.059 43.478 0.00 0.00 41.09 3.34
528 2022 4.402056 ACTAGTGGGTCCGTCAATATTG 57.598 45.455 9.29 9.29 0.00 1.90
558 2052 1.684734 ACCGCTTACATCTCGGGGT 60.685 57.895 4.89 0.00 46.78 4.95
595 2089 7.522073 GCCAAATATGTTGGTTGTCGATCATAT 60.522 37.037 14.31 0.00 41.53 1.78
626 2120 5.459505 ACCATAACCAGCTAGTAGATGAGT 58.540 41.667 16.97 9.89 32.38 3.41
628 2122 7.242359 ACCATAACCAGCTAGTAGATGAGTAT 58.758 38.462 16.97 10.22 32.38 2.12
629 2123 7.730784 ACCATAACCAGCTAGTAGATGAGTATT 59.269 37.037 16.97 7.91 32.38 1.89
630 2124 8.589338 CCATAACCAGCTAGTAGATGAGTATTT 58.411 37.037 16.97 4.65 32.38 1.40
669 2167 8.768019 CGAGAACAAGCATCAATCTTATAATCA 58.232 33.333 0.00 0.00 0.00 2.57
867 4016 2.265904 GCGTCTGGGTGGGGTTTTC 61.266 63.158 0.00 0.00 0.00 2.29
1194 6114 2.683933 GACCAGGAAGAGGGCGGA 60.684 66.667 0.00 0.00 0.00 5.54
1230 6165 1.525077 CGAGGACGAGGAGGAGGAG 60.525 68.421 0.00 0.00 42.66 3.69
1234 6169 2.947785 ACGAGGAGGAGGAGGGGT 60.948 66.667 0.00 0.00 0.00 4.95
1254 6192 3.036959 GGGGAGGAGGAGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
1708 8309 4.331168 GCTGAGAACTGCCACTATGTTTAG 59.669 45.833 0.00 0.00 35.44 1.85
1745 8346 8.707796 TGTTATTACAACTGGGGTTTAATTGA 57.292 30.769 0.00 0.00 32.73 2.57
1750 8351 2.871453 ACTGGGGTTTAATTGAAGCGT 58.129 42.857 6.13 0.00 0.00 5.07
1753 8354 4.100344 ACTGGGGTTTAATTGAAGCGTTTT 59.900 37.500 6.13 0.00 0.00 2.43
1804 8406 7.148255 CCAATTTGCATTTACAGCTGACTACTA 60.148 37.037 23.35 0.00 0.00 1.82
1957 8596 4.640771 TTTAGATGCCTTGTCAGGAAGT 57.359 40.909 0.00 0.00 44.19 3.01
2787 9480 2.103941 CCTAAGGATCAGTGGGAAGAGC 59.896 54.545 0.00 0.00 0.00 4.09
3117 9814 9.590088 CAAAAAGTTAAGGTCGATAACTGTAAC 57.410 33.333 9.97 9.53 41.49 2.50
3396 10094 7.995289 TCTAAGAGCAAATCAAGTGTTCAAAA 58.005 30.769 0.00 0.00 0.00 2.44
3534 10237 5.886960 ATAACCTTGTGATTGAAGTGCTC 57.113 39.130 0.00 0.00 0.00 4.26
3624 10327 4.335037 CCTCCTCTCTTTTTGCTAAGCATC 59.665 45.833 0.00 0.00 38.76 3.91
3782 10485 7.599998 GTGGAGCAATTGTTTCTAAATCATGTT 59.400 33.333 7.40 0.00 0.00 2.71
3784 10487 9.294030 GGAGCAATTGTTTCTAAATCATGTTAG 57.706 33.333 7.40 0.00 33.16 2.34
3828 10531 5.195756 AGGTTGGGTATCTTTGGGATTATGT 59.804 40.000 0.00 0.00 35.98 2.29
3829 10532 5.897250 GGTTGGGTATCTTTGGGATTATGTT 59.103 40.000 0.00 0.00 35.98 2.71
3832 10538 7.654022 TGGGTATCTTTGGGATTATGTTTTC 57.346 36.000 0.00 0.00 35.98 2.29
4457 11327 6.897259 TGACTTGTGTTACTGTCTGTAAAC 57.103 37.500 4.09 6.13 42.12 2.01
4770 11681 0.815734 ATCCGTAGAGTTGGTCCACG 59.184 55.000 0.00 0.00 0.00 4.94
4992 12036 7.215719 TCGTCATCGAATAGTTTCTATGGAT 57.784 36.000 0.00 0.00 43.34 3.41
5329 13607 6.819146 ACTTCTATAGCAGTGAAAGCCTTTAC 59.181 38.462 4.10 0.00 0.00 2.01
6217 14587 8.955388 GGCCATTTGTTGTTTTCCAATAATATT 58.045 29.630 0.00 0.00 34.61 1.28
6312 14686 3.244422 TGTCACTGCGATAACCCTTCTTT 60.244 43.478 0.00 0.00 0.00 2.52
6369 14743 9.238368 CAGTAATGGATTCACCTTACCTTTTTA 57.762 33.333 0.00 0.00 39.86 1.52
6610 14985 7.311364 ACATTTTGGAAGAAATGCATTATGC 57.689 32.000 13.39 10.65 46.14 3.14
6623 14998 2.951642 GCATTATGCTGTTGCCTCCTTA 59.048 45.455 10.27 0.00 40.96 2.69
6643 15018 6.071221 TCCTTAGTACCGAATTGTTAGCTTGA 60.071 38.462 0.00 0.00 0.00 3.02
7054 15650 1.672881 GTGCCATTACAGTGATCCAGC 59.327 52.381 0.00 0.00 0.00 4.85
7501 16122 1.959985 TGAGATGGATCGAGGAGAAGC 59.040 52.381 0.00 0.00 0.00 3.86
7578 16199 1.736645 GAACGCGCTCTGCTAACCA 60.737 57.895 5.73 0.00 43.27 3.67
7647 16269 0.174389 TGACCTGAGAGAGAATGCGC 59.826 55.000 0.00 0.00 0.00 6.09
7794 16991 0.258484 TTGGGCATGGGTGGTGATAG 59.742 55.000 0.00 0.00 0.00 2.08
7797 16994 0.536006 GGCATGGGTGGTGATAGAGC 60.536 60.000 0.00 0.00 0.00 4.09
8172 17464 8.762426 GGTAAAAACTATATCTGTCATCCGAAC 58.238 37.037 0.00 0.00 0.00 3.95
8247 17543 6.560253 TGAATGCCAGTTTTCTCTTACTTC 57.440 37.500 0.00 0.00 0.00 3.01
8557 19281 1.003851 CATTGTAACCCGTAGTGGCG 58.996 55.000 0.00 0.00 35.87 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.272574 TGGTGGCAAATTTTCTGCAAA 57.727 38.095 3.19 0.00 41.78 3.68
1 2 2.996249 TGGTGGCAAATTTTCTGCAA 57.004 40.000 3.19 0.00 41.78 4.08
2 3 2.433604 TCTTGGTGGCAAATTTTCTGCA 59.566 40.909 3.19 0.00 41.78 4.41
3 4 2.802247 GTCTTGGTGGCAAATTTTCTGC 59.198 45.455 0.00 0.00 39.16 4.26
4 5 3.070015 AGGTCTTGGTGGCAAATTTTCTG 59.930 43.478 0.00 0.00 0.00 3.02
5 6 3.070015 CAGGTCTTGGTGGCAAATTTTCT 59.930 43.478 0.00 0.00 0.00 2.52
6 7 3.069443 TCAGGTCTTGGTGGCAAATTTTC 59.931 43.478 0.00 0.00 0.00 2.29
7 8 3.037549 TCAGGTCTTGGTGGCAAATTTT 58.962 40.909 0.00 0.00 0.00 1.82
8 9 2.676748 TCAGGTCTTGGTGGCAAATTT 58.323 42.857 0.00 0.00 0.00 1.82
9 10 2.380064 TCAGGTCTTGGTGGCAAATT 57.620 45.000 0.00 0.00 0.00 1.82
10 11 2.242043 CTTCAGGTCTTGGTGGCAAAT 58.758 47.619 0.00 0.00 0.00 2.32
11 12 1.064017 ACTTCAGGTCTTGGTGGCAAA 60.064 47.619 0.00 0.00 0.00 3.68
12 13 0.550914 ACTTCAGGTCTTGGTGGCAA 59.449 50.000 0.00 0.00 0.00 4.52
13 14 0.179020 CACTTCAGGTCTTGGTGGCA 60.179 55.000 0.00 0.00 0.00 4.92
14 15 0.890996 CCACTTCAGGTCTTGGTGGC 60.891 60.000 0.00 0.00 40.44 5.01
15 16 3.329300 CCACTTCAGGTCTTGGTGG 57.671 57.895 0.00 0.00 40.84 4.61
16 17 0.179020 TGCCACTTCAGGTCTTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
17 18 0.550914 TTGCCACTTCAGGTCTTGGT 59.449 50.000 0.00 0.00 0.00 3.67
18 19 0.954452 GTTGCCACTTCAGGTCTTGG 59.046 55.000 0.00 0.00 0.00 3.61
19 20 0.954452 GGTTGCCACTTCAGGTCTTG 59.046 55.000 0.00 0.00 0.00 3.02
20 21 0.178990 GGGTTGCCACTTCAGGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
21 22 1.456287 GGGTTGCCACTTCAGGTCT 59.544 57.895 0.00 0.00 0.00 3.85
22 23 1.603739 GGGGTTGCCACTTCAGGTC 60.604 63.158 0.00 0.00 0.00 3.85
23 24 2.520968 GGGGTTGCCACTTCAGGT 59.479 61.111 0.00 0.00 0.00 4.00
24 25 2.672996 CGGGGTTGCCACTTCAGG 60.673 66.667 0.00 0.00 0.00 3.86
25 26 3.365265 GCGGGGTTGCCACTTCAG 61.365 66.667 0.00 0.00 0.00 3.02
40 41 3.458163 TTCTAGAGGTGGGGCGCG 61.458 66.667 0.00 0.00 0.00 6.86
41 42 2.187163 GTTCTAGAGGTGGGGCGC 59.813 66.667 0.00 0.00 0.00 6.53
42 43 2.732619 GGGTTCTAGAGGTGGGGCG 61.733 68.421 0.00 0.00 0.00 6.13
43 44 0.914902 AAGGGTTCTAGAGGTGGGGC 60.915 60.000 0.00 0.00 0.00 5.80
44 45 0.912486 CAAGGGTTCTAGAGGTGGGG 59.088 60.000 0.00 0.00 0.00 4.96
45 46 1.279271 CACAAGGGTTCTAGAGGTGGG 59.721 57.143 0.00 0.00 0.00 4.61
46 47 1.978580 ACACAAGGGTTCTAGAGGTGG 59.021 52.381 0.00 0.00 0.00 4.61
47 48 3.771577 AACACAAGGGTTCTAGAGGTG 57.228 47.619 0.00 0.00 0.00 4.00
48 49 6.449830 AATTAACACAAGGGTTCTAGAGGT 57.550 37.500 0.00 0.00 32.29 3.85
49 50 5.880887 GGAATTAACACAAGGGTTCTAGAGG 59.119 44.000 0.00 0.00 32.29 3.69
50 51 5.581085 CGGAATTAACACAAGGGTTCTAGAG 59.419 44.000 0.00 0.00 32.29 2.43
51 52 5.246656 TCGGAATTAACACAAGGGTTCTAGA 59.753 40.000 0.00 0.00 32.29 2.43
52 53 5.484715 TCGGAATTAACACAAGGGTTCTAG 58.515 41.667 0.00 0.00 32.29 2.43
53 54 5.486735 TCGGAATTAACACAAGGGTTCTA 57.513 39.130 0.00 0.00 32.29 2.10
54 55 4.360951 TCGGAATTAACACAAGGGTTCT 57.639 40.909 0.00 0.00 32.29 3.01
55 56 6.183360 CCTTATCGGAATTAACACAAGGGTTC 60.183 42.308 0.00 0.00 33.16 3.62
56 57 5.650703 CCTTATCGGAATTAACACAAGGGTT 59.349 40.000 0.00 0.00 33.16 4.11
57 58 5.190677 CCTTATCGGAATTAACACAAGGGT 58.809 41.667 0.00 0.00 33.16 4.34
58 59 4.036380 GCCTTATCGGAATTAACACAAGGG 59.964 45.833 8.77 0.00 33.44 3.95
59 60 4.638421 TGCCTTATCGGAATTAACACAAGG 59.362 41.667 0.00 0.00 35.47 3.61
60 61 5.811399 TGCCTTATCGGAATTAACACAAG 57.189 39.130 0.00 0.00 33.16 3.16
61 62 5.708230 ACTTGCCTTATCGGAATTAACACAA 59.292 36.000 0.00 0.00 33.16 3.33
62 63 5.250200 ACTTGCCTTATCGGAATTAACACA 58.750 37.500 0.00 0.00 33.16 3.72
63 64 5.813080 ACTTGCCTTATCGGAATTAACAC 57.187 39.130 0.00 0.00 33.16 3.32
64 65 6.657541 AGAAACTTGCCTTATCGGAATTAACA 59.342 34.615 0.00 0.00 33.16 2.41
65 66 7.085052 AGAAACTTGCCTTATCGGAATTAAC 57.915 36.000 0.00 0.00 33.16 2.01
66 67 6.317893 GGAGAAACTTGCCTTATCGGAATTAA 59.682 38.462 0.00 0.00 33.16 1.40
67 68 5.820947 GGAGAAACTTGCCTTATCGGAATTA 59.179 40.000 0.00 0.00 33.16 1.40
68 69 4.640647 GGAGAAACTTGCCTTATCGGAATT 59.359 41.667 0.00 0.00 33.16 2.17
69 70 4.080299 AGGAGAAACTTGCCTTATCGGAAT 60.080 41.667 0.00 0.00 33.16 3.01
70 71 3.263425 AGGAGAAACTTGCCTTATCGGAA 59.737 43.478 0.00 0.00 33.16 4.30
71 72 2.838202 AGGAGAAACTTGCCTTATCGGA 59.162 45.455 0.00 0.00 33.16 4.55
72 73 3.268023 AGGAGAAACTTGCCTTATCGG 57.732 47.619 0.00 0.00 0.00 4.18
73 74 5.044558 GTCTAGGAGAAACTTGCCTTATCG 58.955 45.833 0.00 0.00 33.28 2.92
74 75 5.044558 CGTCTAGGAGAAACTTGCCTTATC 58.955 45.833 0.00 0.00 33.28 1.75
75 76 4.680975 GCGTCTAGGAGAAACTTGCCTTAT 60.681 45.833 0.00 0.00 33.28 1.73
76 77 3.368116 GCGTCTAGGAGAAACTTGCCTTA 60.368 47.826 0.00 0.00 33.28 2.69
77 78 2.613223 GCGTCTAGGAGAAACTTGCCTT 60.613 50.000 0.00 0.00 33.28 4.35
78 79 1.066787 GCGTCTAGGAGAAACTTGCCT 60.067 52.381 0.00 0.00 35.82 4.75
79 80 1.360820 GCGTCTAGGAGAAACTTGCC 58.639 55.000 0.00 0.00 0.00 4.52
80 81 0.992802 CGCGTCTAGGAGAAACTTGC 59.007 55.000 0.00 0.00 0.00 4.01
81 82 2.631418 TCGCGTCTAGGAGAAACTTG 57.369 50.000 5.77 0.00 0.00 3.16
82 83 3.018149 AGATCGCGTCTAGGAGAAACTT 58.982 45.455 5.77 0.00 34.69 2.66
83 84 2.356382 CAGATCGCGTCTAGGAGAAACT 59.644 50.000 5.77 0.00 34.69 2.66
84 85 2.355132 TCAGATCGCGTCTAGGAGAAAC 59.645 50.000 5.77 0.00 34.69 2.78
85 86 2.640184 TCAGATCGCGTCTAGGAGAAA 58.360 47.619 5.77 0.00 34.69 2.52
86 87 2.327200 TCAGATCGCGTCTAGGAGAA 57.673 50.000 5.77 0.00 34.69 2.87
87 88 2.552599 ATCAGATCGCGTCTAGGAGA 57.447 50.000 5.77 2.77 34.69 3.71
88 89 3.003793 TCAAATCAGATCGCGTCTAGGAG 59.996 47.826 5.77 0.00 34.69 3.69
89 90 2.949644 TCAAATCAGATCGCGTCTAGGA 59.050 45.455 5.77 3.81 34.69 2.94
90 91 3.355626 TCAAATCAGATCGCGTCTAGG 57.644 47.619 5.77 0.00 34.69 3.02
91 92 4.375807 GCAATCAAATCAGATCGCGTCTAG 60.376 45.833 5.77 4.28 34.69 2.43
92 93 3.490896 GCAATCAAATCAGATCGCGTCTA 59.509 43.478 5.77 0.00 34.69 2.59
93 94 2.286294 GCAATCAAATCAGATCGCGTCT 59.714 45.455 5.77 5.63 37.80 4.18
94 95 2.030823 TGCAATCAAATCAGATCGCGTC 59.969 45.455 5.77 2.98 30.60 5.19
95 96 2.009051 TGCAATCAAATCAGATCGCGT 58.991 42.857 5.77 0.00 30.60 6.01
96 97 2.742954 TGCAATCAAATCAGATCGCG 57.257 45.000 0.00 0.00 30.60 5.87
97 98 2.724690 GCATGCAATCAAATCAGATCGC 59.275 45.455 14.21 0.00 0.00 4.58
98 99 3.004419 AGGCATGCAATCAAATCAGATCG 59.996 43.478 21.36 0.00 0.00 3.69
99 100 4.585955 AGGCATGCAATCAAATCAGATC 57.414 40.909 21.36 0.00 0.00 2.75
100 101 5.353394 AAAGGCATGCAATCAAATCAGAT 57.647 34.783 21.36 0.00 0.00 2.90
101 102 4.811969 AAAGGCATGCAATCAAATCAGA 57.188 36.364 21.36 0.00 0.00 3.27
102 103 5.518847 CAGTAAAGGCATGCAATCAAATCAG 59.481 40.000 21.36 0.00 0.00 2.90
103 104 5.412640 CAGTAAAGGCATGCAATCAAATCA 58.587 37.500 21.36 0.00 0.00 2.57
104 105 4.807304 CCAGTAAAGGCATGCAATCAAATC 59.193 41.667 21.36 0.00 0.00 2.17
105 106 4.383335 CCCAGTAAAGGCATGCAATCAAAT 60.383 41.667 21.36 0.36 0.00 2.32
106 107 3.055963 CCCAGTAAAGGCATGCAATCAAA 60.056 43.478 21.36 0.00 0.00 2.69
107 108 2.496871 CCCAGTAAAGGCATGCAATCAA 59.503 45.455 21.36 0.00 0.00 2.57
108 109 2.101783 CCCAGTAAAGGCATGCAATCA 58.898 47.619 21.36 0.00 0.00 2.57
109 110 2.102578 ACCCAGTAAAGGCATGCAATC 58.897 47.619 21.36 1.57 0.00 2.67
110 111 2.236489 ACCCAGTAAAGGCATGCAAT 57.764 45.000 21.36 4.13 0.00 3.56
111 112 2.889170 TACCCAGTAAAGGCATGCAA 57.111 45.000 21.36 0.00 0.00 4.08
112 113 2.889170 TTACCCAGTAAAGGCATGCA 57.111 45.000 21.36 0.00 0.00 3.96
113 114 3.243068 CGATTTACCCAGTAAAGGCATGC 60.243 47.826 9.90 9.90 40.58 4.06
114 115 4.196193 TCGATTTACCCAGTAAAGGCATG 58.804 43.478 6.15 0.00 40.58 4.06
115 116 4.451900 CTCGATTTACCCAGTAAAGGCAT 58.548 43.478 6.15 0.00 40.58 4.40
116 117 3.869065 CTCGATTTACCCAGTAAAGGCA 58.131 45.455 6.15 0.00 40.58 4.75
117 118 2.612672 GCTCGATTTACCCAGTAAAGGC 59.387 50.000 6.15 4.60 40.58 4.35
118 119 3.869065 TGCTCGATTTACCCAGTAAAGG 58.131 45.455 6.15 1.76 40.58 3.11
119 120 4.209288 CGATGCTCGATTTACCCAGTAAAG 59.791 45.833 6.15 0.00 43.74 1.85
120 121 4.116961 CGATGCTCGATTTACCCAGTAAA 58.883 43.478 2.65 2.65 43.74 2.01
121 122 3.713288 CGATGCTCGATTTACCCAGTAA 58.287 45.455 0.00 0.00 43.74 2.24
122 123 2.545113 GCGATGCTCGATTTACCCAGTA 60.545 50.000 9.32 0.00 43.74 2.74
123 124 1.806623 GCGATGCTCGATTTACCCAGT 60.807 52.381 9.32 0.00 43.74 4.00
124 125 0.861837 GCGATGCTCGATTTACCCAG 59.138 55.000 9.32 0.00 43.74 4.45
125 126 0.531974 GGCGATGCTCGATTTACCCA 60.532 55.000 9.32 0.00 43.74 4.51
126 127 0.249911 AGGCGATGCTCGATTTACCC 60.250 55.000 9.32 1.09 43.74 3.69
127 128 1.140816 GAGGCGATGCTCGATTTACC 58.859 55.000 9.32 1.68 43.74 2.85
128 129 1.140816 GGAGGCGATGCTCGATTTAC 58.859 55.000 9.32 0.00 43.74 2.01
129 130 0.033504 GGGAGGCGATGCTCGATTTA 59.966 55.000 9.32 0.00 43.74 1.40
130 131 1.227674 GGGAGGCGATGCTCGATTT 60.228 57.895 9.32 0.00 43.74 2.17
131 132 2.423446 GGGAGGCGATGCTCGATT 59.577 61.111 9.32 0.00 43.74 3.34
132 133 2.839632 TGGGAGGCGATGCTCGAT 60.840 61.111 9.32 0.00 43.74 3.59
133 134 3.838271 GTGGGAGGCGATGCTCGA 61.838 66.667 9.32 0.00 43.74 4.04
134 135 4.899239 GGTGGGAGGCGATGCTCG 62.899 72.222 0.00 1.80 43.89 5.03
135 136 3.746949 CTGGTGGGAGGCGATGCTC 62.747 68.421 0.00 0.00 0.00 4.26
136 137 3.790437 CTGGTGGGAGGCGATGCT 61.790 66.667 0.00 0.00 0.00 3.79
137 138 2.615227 AATCTGGTGGGAGGCGATGC 62.615 60.000 0.00 0.00 0.00 3.91
138 139 0.107017 AAATCTGGTGGGAGGCGATG 60.107 55.000 0.00 0.00 0.00 3.84
139 140 0.181350 GAAATCTGGTGGGAGGCGAT 59.819 55.000 0.00 0.00 0.00 4.58
140 141 1.602237 GAAATCTGGTGGGAGGCGA 59.398 57.895 0.00 0.00 0.00 5.54
141 142 1.815421 CGAAATCTGGTGGGAGGCG 60.815 63.158 0.00 0.00 0.00 5.52
142 143 2.115291 GCGAAATCTGGTGGGAGGC 61.115 63.158 0.00 0.00 0.00 4.70
143 144 0.745845 CTGCGAAATCTGGTGGGAGG 60.746 60.000 0.00 0.00 0.00 4.30
144 145 1.372087 GCTGCGAAATCTGGTGGGAG 61.372 60.000 0.00 0.00 0.00 4.30
145 146 1.377202 GCTGCGAAATCTGGTGGGA 60.377 57.895 0.00 0.00 0.00 4.37
146 147 2.753966 CGCTGCGAAATCTGGTGGG 61.754 63.158 18.66 0.00 0.00 4.61
147 148 2.787249 CGCTGCGAAATCTGGTGG 59.213 61.111 18.66 0.00 0.00 4.61
148 149 2.099062 GCGCTGCGAAATCTGGTG 59.901 61.111 28.07 0.00 0.00 4.17
149 150 3.127533 GGCGCTGCGAAATCTGGT 61.128 61.111 28.07 0.00 0.00 4.00
150 151 3.880846 GGGCGCTGCGAAATCTGG 61.881 66.667 28.07 0.00 0.00 3.86
151 152 3.880846 GGGGCGCTGCGAAATCTG 61.881 66.667 28.07 0.00 0.00 2.90
163 164 4.301027 GTAGATGCGGAGGGGGCG 62.301 72.222 0.00 0.00 0.00 6.13
164 165 4.301027 CGTAGATGCGGAGGGGGC 62.301 72.222 0.00 0.00 0.00 5.80
165 166 2.365095 GAACGTAGATGCGGAGGGGG 62.365 65.000 0.00 0.00 35.98 5.40
166 167 1.067582 GAACGTAGATGCGGAGGGG 59.932 63.158 0.00 0.00 35.98 4.79
167 168 0.389391 ATGAACGTAGATGCGGAGGG 59.611 55.000 0.00 0.00 35.98 4.30
168 169 3.364889 TTATGAACGTAGATGCGGAGG 57.635 47.619 0.00 0.00 35.98 4.30
169 170 7.432545 CCTATATTTATGAACGTAGATGCGGAG 59.567 40.741 0.00 0.00 35.98 4.63
170 171 7.121611 TCCTATATTTATGAACGTAGATGCGGA 59.878 37.037 0.00 0.00 35.98 5.54
171 172 7.255569 TCCTATATTTATGAACGTAGATGCGG 58.744 38.462 0.00 0.00 35.98 5.69
306 1644 3.007323 GGTGGACGCTTAGGGGGT 61.007 66.667 0.55 0.00 43.96 4.95
326 1816 3.057596 TCGATGCAAACCCTTTTGTGATC 60.058 43.478 0.00 0.00 43.62 2.92
339 1829 8.492673 AAGTATTAAGTCTGAATCGATGCAAA 57.507 30.769 7.67 0.00 0.00 3.68
451 1944 6.541111 AAGAATTTATAATCGGCTCGGTTC 57.459 37.500 0.00 0.00 30.88 3.62
496 1990 4.202080 CGGACCCACTAGTTAATCGAATGA 60.202 45.833 0.00 0.00 0.00 2.57
502 1996 4.460948 TTGACGGACCCACTAGTTAATC 57.539 45.455 0.00 0.00 0.00 1.75
558 2052 7.573710 ACCAACATATTTGGCTTACTGATCTA 58.426 34.615 13.42 0.00 43.23 1.98
595 2089 0.539986 GCTGGTTATGGTTCGAGGGA 59.460 55.000 0.00 0.00 0.00 4.20
628 2122 9.210329 TGCTTGTTCTCGTCTTTGTAATATAAA 57.790 29.630 0.00 0.00 0.00 1.40
629 2123 8.766000 TGCTTGTTCTCGTCTTTGTAATATAA 57.234 30.769 0.00 0.00 0.00 0.98
630 2124 8.942338 ATGCTTGTTCTCGTCTTTGTAATATA 57.058 30.769 0.00 0.00 0.00 0.86
761 3538 0.548510 GGCCCTGATAGTCCTTTGCT 59.451 55.000 0.00 0.00 0.00 3.91
762 3539 0.255890 TGGCCCTGATAGTCCTTTGC 59.744 55.000 0.00 0.00 0.00 3.68
763 3540 1.133976 CCTGGCCCTGATAGTCCTTTG 60.134 57.143 0.00 0.00 0.00 2.77
764 3541 1.216990 CCTGGCCCTGATAGTCCTTT 58.783 55.000 0.00 0.00 0.00 3.11
765 3542 1.348775 GCCTGGCCCTGATAGTCCTT 61.349 60.000 7.66 0.00 0.00 3.36
766 3543 1.768077 GCCTGGCCCTGATAGTCCT 60.768 63.158 7.66 0.00 0.00 3.85
867 4016 5.560966 AGGTCTGGTTTAATAATTGCACG 57.439 39.130 0.00 0.00 0.00 5.34
1185 6105 2.997897 GTGGTGTCTCCGCCCTCT 60.998 66.667 0.00 0.00 40.77 3.69
1194 6114 2.114625 TCGTCCTCCGTGGTGTCT 59.885 61.111 0.00 0.00 37.94 3.41
1230 6165 3.752816 CTCCTCCTCCCCGTACCCC 62.753 73.684 0.00 0.00 0.00 4.95
1234 6169 2.392816 CCTCCTCCTCCTCCCCGTA 61.393 68.421 0.00 0.00 0.00 4.02
1254 6192 1.448189 CTCGTCCTCGTCCTCGTCT 60.448 63.158 0.00 0.00 38.33 4.18
1347 6288 3.866582 GATGGGGTGGGAGGCGAG 61.867 72.222 0.00 0.00 0.00 5.03
1348 6289 4.414956 AGATGGGGTGGGAGGCGA 62.415 66.667 0.00 0.00 0.00 5.54
1349 6290 3.866582 GAGATGGGGTGGGAGGCG 61.867 72.222 0.00 0.00 0.00 5.52
1350 6291 3.493303 GGAGATGGGGTGGGAGGC 61.493 72.222 0.00 0.00 0.00 4.70
1351 6292 2.774351 GGGAGATGGGGTGGGAGG 60.774 72.222 0.00 0.00 0.00 4.30
1352 6293 2.774351 GGGGAGATGGGGTGGGAG 60.774 72.222 0.00 0.00 0.00 4.30
1353 6294 4.815973 CGGGGAGATGGGGTGGGA 62.816 72.222 0.00 0.00 0.00 4.37
1708 8309 5.123344 AGTTGTAATAACAGATTTGGGCGTC 59.877 40.000 0.00 0.00 36.83 5.19
1745 8346 3.177997 ACAATTGCTCCAAAAACGCTT 57.822 38.095 5.05 0.00 0.00 4.68
1750 8351 7.950512 TCATCTAGAAACAATTGCTCCAAAAA 58.049 30.769 5.05 0.00 0.00 1.94
1753 8354 6.405065 GCATCATCTAGAAACAATTGCTCCAA 60.405 38.462 5.05 0.00 0.00 3.53
1804 8406 5.104360 ACTCCAGTTGTAGTGCCATATTCAT 60.104 40.000 0.00 0.00 0.00 2.57
1891 8530 2.065899 AAACAGGGCAACTAAGCACA 57.934 45.000 0.00 0.00 41.46 4.57
1957 8596 4.457603 AGCATGTTTGGCAACTATTTACGA 59.542 37.500 0.00 0.00 33.58 3.43
2009 8648 7.823745 ACAACCAGAAGATTGAACATTAAGT 57.176 32.000 0.00 0.00 0.00 2.24
2787 9480 4.766375 AGTTCCCACAGAATATAACCACG 58.234 43.478 0.00 0.00 36.69 4.94
3085 9782 9.836076 GTTATCGACCTTAACTTTTTGCTTATT 57.164 29.630 0.00 0.00 0.00 1.40
3105 9802 7.596749 AGGAATGAAACAGTTACAGTTATCG 57.403 36.000 0.00 0.00 0.00 2.92
3117 9814 8.352942 AGCTACAAAACTAAAGGAATGAAACAG 58.647 33.333 0.00 0.00 0.00 3.16
3396 10094 7.833285 TGCCTTAATTTCCTTTTGTAGTTCT 57.167 32.000 0.00 0.00 0.00 3.01
3534 10237 1.196127 GCCGTACGAAGGTTTTCCAAG 59.804 52.381 18.76 0.00 43.73 3.61
4457 11327 6.113411 ACTATCTCGGGGTGTAAGAATTTTG 58.887 40.000 0.00 0.00 0.00 2.44
4770 11681 7.812309 AAAGAACAAAAGTCACTAAAGTTGC 57.188 32.000 0.00 0.00 0.00 4.17
4860 11777 9.881529 GAAGAATGAGCTAAGATGATTCAAATC 57.118 33.333 0.00 0.00 35.97 2.17
4861 11778 9.629878 AGAAGAATGAGCTAAGATGATTCAAAT 57.370 29.630 0.00 0.00 0.00 2.32
4891 11808 2.224744 ACACACATGCCTAACCATCACA 60.225 45.455 0.00 0.00 0.00 3.58
4992 12036 5.656416 AGAAGTGTTTGGGAAGATGAAACAA 59.344 36.000 0.00 0.00 40.34 2.83
5064 12109 8.106462 TGACCAAGGATAATTCTACATTGTTCA 58.894 33.333 0.00 0.00 0.00 3.18
5108 12155 1.575419 ACCAAGCAATTGCCATGGAT 58.425 45.000 39.10 27.16 45.85 3.41
5308 13239 7.617041 AAAGTAAAGGCTTTCACTGCTATAG 57.383 36.000 17.13 0.00 33.87 1.31
6152 14522 4.368315 GTTAAGGACCAAAACTTTGCCTG 58.632 43.478 0.00 0.00 36.86 4.85
6369 14743 5.826208 AGAACCCTTTCTGAAACGTGTTAAT 59.174 36.000 0.00 0.00 40.82 1.40
6610 14985 1.822990 TCGGTACTAAGGAGGCAACAG 59.177 52.381 0.00 0.00 41.41 3.16
6623 14998 4.251268 GGTCAAGCTAACAATTCGGTACT 58.749 43.478 0.00 0.00 0.00 2.73
6643 15018 6.296026 TGCTTGTTAAGAGTTATGAGTTGGT 58.704 36.000 0.00 0.00 0.00 3.67
7054 15650 7.145323 ACGGTAAATCTGAAACAATTGAAAGG 58.855 34.615 13.59 0.00 0.00 3.11
7345 15959 7.418483 GCTTAAGATCTAGACTTCCATGAAGGT 60.418 40.741 6.67 0.00 43.25 3.50
7578 16199 0.765510 GTCAGTGGAGTGGGGTTTCT 59.234 55.000 0.00 0.00 0.00 2.52
7647 16269 1.033746 AAATCACAGCGGCCAGATGG 61.034 55.000 15.38 0.00 41.32 3.51
8158 17450 3.574396 ACATATCGGTTCGGATGACAGAT 59.426 43.478 9.05 2.02 36.26 2.90
8172 17464 4.991056 CCATGTCTCAGGTTTACATATCGG 59.009 45.833 0.00 0.00 32.70 4.18
8247 17543 5.805728 AGAGGGTACAGTATTTTCACCAAG 58.194 41.667 0.00 0.00 0.00 3.61
8389 18155 0.860533 TCGCCGAACTTTTAACACCG 59.139 50.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.