Multiple sequence alignment - TraesCS5D01G040400

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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 TraesCS5D01G040400 chr5D 100.000 3284 0 0 1 3284 41295808 41299091 0.000000e+00 6065.0
1 TraesCS5D01G040400 chr5D 98.361 61 1 0 3061 3121 41298807 41298867 1.250000e-19 108.0
2 TraesCS5D01G040400 chr5D 98.361 61 1 0 3000 3060 41298868 41298928 1.250000e-19 108.0
3 TraesCS5D01G040400 chr5A 89.649 1739 109 43 911 2595 29626472 29628193 0.000000e+00 2148.0
4 TraesCS5D01G040400 chr5A 86.129 620 75 10 1 614 29625678 29626292 0.000000e+00 658.0
5 TraesCS5D01G040400 chr5A 90.226 133 13 0 2143 2275 23823663 23823531 1.210000e-39 174.0
6 TraesCS5D01G040400 chr5B 88.420 1468 77 38 1177 2594 35288772 35290196 0.000000e+00 1683.0
7 TraesCS5D01G040400 chr5B 84.530 362 39 11 2249 2600 35508465 35508819 3.140000e-90 342.0
8 TraesCS5D01G040400 chr5B 98.193 166 2 1 968 1132 35288602 35288767 4.150000e-74 289.0
9 TraesCS5D01G040400 chr5B 84.064 251 22 7 381 614 35287806 35288055 3.300000e-55 226.0
10 TraesCS5D01G040400 chr5B 81.119 286 37 10 1998 2275 26445640 26445364 2.570000e-51 213.0
11 TraesCS5D01G040400 chr5B 89.908 109 8 3 786 892 35288154 35288261 1.590000e-28 137.0
12 TraesCS5D01G040400 chr5B 78.218 202 33 7 370 567 381060355 381060549 5.760000e-23 119.0
13 TraesCS5D01G040400 chr5B 89.412 85 9 0 2826 2910 118561425 118561509 1.250000e-19 108.0
14 TraesCS5D01G040400 chr5B 96.774 62 2 0 3223 3284 35290192 35290253 1.610000e-18 104.0
15 TraesCS5D01G040400 chr5B 81.053 95 11 6 3138 3228 35520131 35520222 5.880000e-08 69.4
16 TraesCS5D01G040400 chrUn 88.076 889 66 16 2184 3059 331823850 331822989 0.000000e+00 1018.0
17 TraesCS5D01G040400 chrUn 91.472 598 46 4 1585 2182 290597887 290597295 0.000000e+00 817.0
18 TraesCS5D01G040400 chrUn 83.217 429 47 10 1188 1612 11987980 11987573 1.440000e-98 370.0
19 TraesCS5D01G040400 chrUn 91.703 229 13 4 3061 3284 331823051 331822824 2.460000e-81 313.0
20 TraesCS5D01G040400 chrUn 75.369 203 36 10 281 478 101053594 101053401 5.840000e-13 86.1
21 TraesCS5D01G040400 chr3B 87.605 597 55 13 1023 1612 545652016 545651432 0.000000e+00 675.0
22 TraesCS5D01G040400 chr3B 87.374 594 58 8 1025 1612 545532313 545531731 0.000000e+00 665.0
23 TraesCS5D01G040400 chr3B 83.491 424 45 13 1186 1605 356351942 356352344 4.000000e-99 372.0
24 TraesCS5D01G040400 chr3B 89.831 236 17 4 1023 1255 335361217 335360986 2.480000e-76 296.0
25 TraesCS5D01G040400 chr3B 99.065 107 1 0 1023 1129 356349493 356349599 3.340000e-45 193.0
26 TraesCS5D01G040400 chr3A 83.991 431 44 7 1186 1612 734395467 734395876 1.100000e-104 390.0
27 TraesCS5D01G040400 chr3A 83.759 431 45 12 1186 1612 403130929 403130520 5.140000e-103 385.0
28 TraesCS5D01G040400 chr2A 90.688 247 12 3 1165 1410 92831112 92831348 5.290000e-83 318.0
29 TraesCS5D01G040400 chr2A 88.664 247 17 3 1165 1410 31373084 31372848 1.150000e-74 291.0
30 TraesCS5D01G040400 chr2A 80.149 403 39 26 2140 2518 720384515 720384900 2.510000e-66 263.0
31 TraesCS5D01G040400 chr2A 81.405 242 31 9 900 1129 720383053 720383292 5.600000e-43 185.0
32 TraesCS5D01G040400 chr2A 80.952 189 32 2 2875 3059 684914417 684914229 2.640000e-31 147.0
33 TraesCS5D01G040400 chr2A 90.000 90 8 1 1971 2060 21091147 21091235 7.450000e-22 115.0
34 TraesCS5D01G040400 chr2A 89.247 93 9 1 1971 2063 774247842 774247751 7.450000e-22 115.0
35 TraesCS5D01G040400 chr2A 85.000 100 14 1 1964 2063 720384304 720384402 2.090000e-17 100.0
36 TraesCS5D01G040400 chr2A 82.927 82 10 2 3062 3139 684914290 684914209 1.630000e-08 71.3
37 TraesCS5D01G040400 chr3D 81.039 385 37 18 2140 2500 25523435 25523807 1.160000e-69 274.0
38 TraesCS5D01G040400 chr7D 80.296 406 40 20 2140 2518 37663100 37662708 1.500000e-68 270.0
39 TraesCS5D01G040400 chr7D 83.333 240 27 11 900 1129 37664526 37664290 3.320000e-50 209.0
40 TraesCS5D01G040400 chr4A 82.927 287 23 12 2140 2406 687317207 687317487 5.480000e-58 235.0
41 TraesCS5D01G040400 chr4A 88.750 160 17 1 971 1129 687315788 687315947 9.300000e-46 195.0
42 TraesCS5D01G040400 chr4A 81.333 225 31 5 267 480 605734512 605734736 4.360000e-39 172.0
43 TraesCS5D01G040400 chr4A 75.000 392 70 19 1683 2063 687316705 687317079 4.390000e-34 156.0
44 TraesCS5D01G040400 chr2B 91.411 163 11 2 1023 1183 109347421 109347260 1.530000e-53 220.0
45 TraesCS5D01G040400 chr1B 84.545 220 30 2 2844 3059 341934649 341934868 7.140000e-52 215.0
46 TraesCS5D01G040400 chr1B 89.247 93 9 1 1971 2063 685034709 685034800 7.450000e-22 115.0
47 TraesCS5D01G040400 chr6D 82.266 203 26 4 281 479 221003287 221003091 2.030000e-37 167.0
48 TraesCS5D01G040400 chr6D 80.603 232 28 5 2829 3057 466924426 466924643 2.620000e-36 163.0
49 TraesCS5D01G040400 chr6D 86.076 79 8 1 3061 3136 466924583 466924661 7.550000e-12 82.4
50 TraesCS5D01G040400 chr6A 87.402 127 14 2 2917 3042 617839684 617839559 9.500000e-31 145.0
51 TraesCS5D01G040400 chr1A 77.593 241 37 10 2801 3041 494069080 494068857 2.660000e-26 130.0
52 TraesCS5D01G040400 chr2D 80.982 163 24 5 345 503 114530974 114530815 4.450000e-24 122.0
53 TraesCS5D01G040400 chr6B 77.674 215 26 11 282 480 15221944 15222152 9.630000e-21 111.0
54 TraesCS5D01G040400 chr6B 79.688 128 22 4 1288 1412 630549414 630549540 4.510000e-14 89.8
55 TraesCS5D01G040400 chr4D 88.889 90 9 1 1971 2060 12067694 12067782 3.460000e-20 110.0
56 TraesCS5D01G040400 chr4D 84.783 92 13 1 383 473 470796453 470796544 1.250000e-14 91.6
57 TraesCS5D01G040400 chr4B 77.957 186 32 8 383 567 592984066 592984243 1.250000e-19 108.0
58 TraesCS5D01G040400 chr1D 87.671 73 9 0 408 480 218323296 218323368 5.840000e-13 86.1


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 TraesCS5D01G040400 chr5D 41295808 41299091 3283 False 2093.666667 6065 98.907333 1 3284 3 chr5D.!!$F1 3283
1 TraesCS5D01G040400 chr5A 29625678 29628193 2515 False 1403.000000 2148 87.889000 1 2595 2 chr5A.!!$F1 2594
2 TraesCS5D01G040400 chr5B 35287806 35290253 2447 False 487.800000 1683 91.471800 381 3284 5 chr5B.!!$F5 2903
3 TraesCS5D01G040400 chrUn 290597295 290597887 592 True 817.000000 817 91.472000 1585 2182 1 chrUn.!!$R3 597
4 TraesCS5D01G040400 chrUn 331822824 331823850 1026 True 665.500000 1018 89.889500 2184 3284 2 chrUn.!!$R4 1100
5 TraesCS5D01G040400 chr3B 545651432 545652016 584 True 675.000000 675 87.605000 1023 1612 1 chr3B.!!$R3 589
6 TraesCS5D01G040400 chr3B 545531731 545532313 582 True 665.000000 665 87.374000 1025 1612 1 chr3B.!!$R2 587
7 TraesCS5D01G040400 chr3B 356349493 356352344 2851 False 282.500000 372 91.278000 1023 1605 2 chr3B.!!$F1 582
8 TraesCS5D01G040400 chr7D 37662708 37664526 1818 True 239.500000 270 81.814500 900 2518 2 chr7D.!!$R1 1618

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
747 778 0.037232 ACAGGAAGTAAGCTCGTGGC 60.037 55.0 0.0 0.0 42.19 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 5775 0.534203 TTTGACGGGTCTGTTCTGCC 60.534 55.0 0.0 0.0 0.0 4.85 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 1.305623 CCTTCATTGGCTGGGCTCT 59.694 57.895 0.00 0.00 0.00 4.09
22 23 1.078214 TTCATTGGCTGGGCTCTCG 60.078 57.895 0.00 0.00 0.00 4.04
44 45 3.108144 CAAAAAGTTCTTGGTGCAGTCG 58.892 45.455 0.00 0.00 0.00 4.18
55 56 1.540267 GGTGCAGTCGTCTAGAAGACA 59.460 52.381 31.62 15.14 45.30 3.41
94 95 8.733857 AGTTGCTAAAAGAAAATCGAATCTTG 57.266 30.769 10.94 2.80 36.09 3.02
95 96 7.809806 AGTTGCTAAAAGAAAATCGAATCTTGG 59.190 33.333 10.94 7.11 36.09 3.61
97 98 7.083858 TGCTAAAAGAAAATCGAATCTTGGTG 58.916 34.615 10.94 6.62 36.09 4.17
111 112 6.291585 CGAATCTTGGTGCAGTTGTTAAAAAC 60.292 38.462 0.00 0.00 0.00 2.43
113 114 6.761099 TCTTGGTGCAGTTGTTAAAAACTA 57.239 33.333 10.75 0.00 38.34 2.24
114 115 6.791303 TCTTGGTGCAGTTGTTAAAAACTAG 58.209 36.000 10.75 4.34 38.34 2.57
122 123 8.691797 TGCAGTTGTTAAAAACTAGAGGAAAAT 58.308 29.630 10.75 0.00 38.34 1.82
180 181 3.689649 ACCTTGAAATGCAGGTCGTTATC 59.310 43.478 0.00 0.00 0.00 1.75
181 182 3.065371 CCTTGAAATGCAGGTCGTTATCC 59.935 47.826 0.00 0.00 0.00 2.59
201 203 2.551071 CCGAAAGTCCTCTTTTGCTCCT 60.551 50.000 0.00 0.00 42.99 3.69
223 225 1.303309 GCTCAAATGAGGTCCGGATG 58.697 55.000 7.81 0.00 42.29 3.51
227 229 1.665679 CAAATGAGGTCCGGATGAACG 59.334 52.381 7.81 0.00 35.10 3.95
292 294 9.877178 TGACAAACTTTGGTAAATGTTTTGTAT 57.123 25.926 6.47 0.00 40.02 2.29
334 336 3.350833 AGATGGCATTCTTGGAAGTCAC 58.649 45.455 0.00 0.00 0.00 3.67
343 345 2.098443 TCTTGGAAGTCACGGCAAAAAC 59.902 45.455 0.00 0.00 0.00 2.43
347 349 3.254892 GGAAGTCACGGCAAAAACAAAA 58.745 40.909 0.00 0.00 0.00 2.44
349 351 4.434989 GGAAGTCACGGCAAAAACAAAAAC 60.435 41.667 0.00 0.00 0.00 2.43
352 354 2.413453 TCACGGCAAAAACAAAAACAGC 59.587 40.909 0.00 0.00 0.00 4.40
364 366 4.190772 ACAAAAACAGCACTCCAAAATGG 58.809 39.130 0.00 0.00 39.43 3.16
368 370 3.733443 ACAGCACTCCAAAATGGTTTC 57.267 42.857 0.00 0.00 39.03 2.78
403 410 3.220507 TGGAGCATTGATCTTTTTGCG 57.779 42.857 1.44 0.00 40.00 4.85
503 515 5.810074 ACCCGAAAGTTCTTGATTTGTTTTG 59.190 36.000 0.00 0.00 0.00 2.44
521 533 8.458212 TTGTTTTGCAAAATTTTGGATTTGAC 57.542 26.923 26.24 20.20 38.31 3.18
537 558 0.389817 TGACCGTTCATCAAGGAGCG 60.390 55.000 0.00 0.00 40.57 5.03
567 588 0.457851 GCAGCAGATACTCCACGTCT 59.542 55.000 0.00 0.00 0.00 4.18
572 593 2.092323 CAGATACTCCACGTCTGTCCA 58.908 52.381 0.00 0.00 35.72 4.02
606 629 0.521291 TTTTGCGATGAAAGGAGGCG 59.479 50.000 0.00 0.00 0.00 5.52
614 637 2.859165 TGAAAGGAGGCGTTCATTCT 57.141 45.000 4.48 0.00 0.00 2.40
615 638 2.699954 TGAAAGGAGGCGTTCATTCTC 58.300 47.619 4.48 0.00 0.00 2.87
616 639 1.661112 GAAAGGAGGCGTTCATTCTCG 59.339 52.381 0.00 0.00 0.00 4.04
626 649 4.133856 CGTTCATTCTCGCAAAAACTCT 57.866 40.909 0.00 0.00 0.00 3.24
627 650 4.527564 CGTTCATTCTCGCAAAAACTCTT 58.472 39.130 0.00 0.00 0.00 2.85
628 651 4.970003 CGTTCATTCTCGCAAAAACTCTTT 59.030 37.500 0.00 0.00 0.00 2.52
629 652 5.114124 CGTTCATTCTCGCAAAAACTCTTTC 59.886 40.000 0.00 0.00 0.00 2.62
630 653 5.749596 TCATTCTCGCAAAAACTCTTTCA 57.250 34.783 0.00 0.00 0.00 2.69
631 654 6.130298 TCATTCTCGCAAAAACTCTTTCAA 57.870 33.333 0.00 0.00 0.00 2.69
632 655 6.559810 TCATTCTCGCAAAAACTCTTTCAAA 58.440 32.000 0.00 0.00 0.00 2.69
633 656 7.032580 TCATTCTCGCAAAAACTCTTTCAAAA 58.967 30.769 0.00 0.00 0.00 2.44
634 657 7.543868 TCATTCTCGCAAAAACTCTTTCAAAAA 59.456 29.630 0.00 0.00 0.00 1.94
677 701 1.473677 TGAATGATGCGCCCTTCAAAG 59.526 47.619 4.18 0.00 0.00 2.77
708 732 3.569277 TGAATGATGCAATAATCCACCGG 59.431 43.478 0.00 0.00 0.00 5.28
711 735 3.831323 TGATGCAATAATCCACCGGAAT 58.169 40.909 9.46 0.00 34.34 3.01
713 737 2.582052 TGCAATAATCCACCGGAATCC 58.418 47.619 9.46 0.00 34.34 3.01
740 771 5.607119 TTTTCGATCAACAGGAAGTAAGC 57.393 39.130 0.00 0.00 0.00 3.09
741 772 4.537135 TTCGATCAACAGGAAGTAAGCT 57.463 40.909 0.00 0.00 0.00 3.74
743 774 2.854777 CGATCAACAGGAAGTAAGCTCG 59.145 50.000 0.00 0.00 0.00 5.03
745 776 3.026630 TCAACAGGAAGTAAGCTCGTG 57.973 47.619 0.00 0.00 0.00 4.35
746 777 2.069273 CAACAGGAAGTAAGCTCGTGG 58.931 52.381 0.00 0.00 0.00 4.94
747 778 0.037232 ACAGGAAGTAAGCTCGTGGC 60.037 55.000 0.00 0.00 42.19 5.01
756 787 2.900273 GCTCGTGGCTCCATACCA 59.100 61.111 0.00 0.00 38.06 3.25
757 788 1.227380 GCTCGTGGCTCCATACCAG 60.227 63.158 0.00 0.00 38.04 4.00
758 789 1.227380 CTCGTGGCTCCATACCAGC 60.227 63.158 0.00 0.00 38.04 4.85
759 790 2.586079 CGTGGCTCCATACCAGCG 60.586 66.667 0.00 0.00 38.04 5.18
760 791 2.897350 GTGGCTCCATACCAGCGC 60.897 66.667 0.00 0.00 38.04 5.92
761 792 3.083349 TGGCTCCATACCAGCGCT 61.083 61.111 2.64 2.64 37.81 5.92
777 808 1.795286 GCGCTCCAATTTCCTATCGAG 59.205 52.381 0.00 0.00 0.00 4.04
892 926 2.284515 AAACCCTCATCCCGCATCCC 62.285 60.000 0.00 0.00 0.00 3.85
893 927 4.320456 CCCTCATCCCGCATCCCG 62.320 72.222 0.00 0.00 0.00 5.14
894 928 4.996434 CCTCATCCCGCATCCCGC 62.996 72.222 0.00 0.00 35.03 6.13
895 929 4.240103 CTCATCCCGCATCCCGCA 62.240 66.667 0.00 0.00 42.60 5.69
896 930 4.240103 TCATCCCGCATCCCGCAG 62.240 66.667 0.00 0.00 42.60 5.18
897 931 4.240103 CATCCCGCATCCCGCAGA 62.240 66.667 0.00 0.00 42.60 4.26
898 932 3.933722 ATCCCGCATCCCGCAGAG 61.934 66.667 0.00 0.00 42.60 3.35
906 940 1.074775 ATCCCGCAGAGGCAAAACA 59.925 52.632 0.00 0.00 41.24 2.83
907 941 0.962356 ATCCCGCAGAGGCAAAACAG 60.962 55.000 0.00 0.00 41.24 3.16
911 945 1.509644 CGCAGAGGCAAAACAGAGCA 61.510 55.000 0.00 0.00 41.24 4.26
913 947 1.601412 GCAGAGGCAAAACAGAGCAAC 60.601 52.381 0.00 0.00 40.72 4.17
1157 1457 2.065799 TCCTCCTTGCTTCCTTCCTTT 58.934 47.619 0.00 0.00 0.00 3.11
1387 4062 1.112916 TGCGGAGAAGGTGACTGACA 61.113 55.000 0.00 0.00 42.68 3.58
1443 4311 2.897350 GTGCCCTGTATGCTCGCC 60.897 66.667 0.00 0.00 0.00 5.54
1493 4460 3.118811 GCTTCTCTGTAGAATCAGGCTGT 60.119 47.826 15.27 0.00 40.92 4.40
1507 4478 3.199946 TCAGGCTGTTTAGGGTTAGATGG 59.800 47.826 15.27 0.00 0.00 3.51
1510 4481 2.683362 GCTGTTTAGGGTTAGATGGCAC 59.317 50.000 0.00 0.00 0.00 5.01
1512 4483 2.303600 TGTTTAGGGTTAGATGGCACGT 59.696 45.455 0.00 0.00 0.00 4.49
1546 4517 4.829064 TGTATGGACAGTTCTTTGTTGC 57.171 40.909 0.00 0.00 0.00 4.17
1605 4582 8.278639 TGAAGTTCATAGCCCATAGGATTTTAA 58.721 33.333 0.08 0.00 30.98 1.52
1819 4813 3.875134 TCCGAAGAAAACACTTGTCCTTC 59.125 43.478 0.00 0.00 0.00 3.46
1838 4832 2.999331 TCCTACTTGGTAATGCAAGCC 58.001 47.619 0.00 0.00 37.07 4.35
1943 4956 6.126409 CCACTTGGGCTACAAATAGGATTAA 58.874 40.000 0.00 0.00 38.91 1.40
2021 5039 4.098807 TGAGCAAATGATGATTCCACATGG 59.901 41.667 0.00 0.00 0.00 3.66
2031 5049 3.820467 TGATTCCACATGGTGTTTCTGAC 59.180 43.478 0.00 0.00 36.34 3.51
2412 5492 3.510388 TCGCCTTGTGATTCAGAGTAG 57.490 47.619 0.00 0.00 0.00 2.57
2472 5552 1.999071 TTTGGTGTGTTGCGCTGGAC 61.999 55.000 9.73 5.53 0.00 4.02
2507 5589 2.009051 TGGCTCGCTATTGATGTGTTG 58.991 47.619 0.00 0.00 0.00 3.33
2523 5605 4.979335 TGTGTTGGAGATTTGGTGTCATA 58.021 39.130 0.00 0.00 0.00 2.15
2600 5682 8.494016 ACTATCAGGTGCAGTATTTAAGAAAC 57.506 34.615 0.00 0.00 0.00 2.78
2605 5687 8.035394 TCAGGTGCAGTATTTAAGAAACTAGAG 58.965 37.037 0.00 0.00 0.00 2.43
2633 5724 2.096248 AGCAAACCACGGAACTGAAAA 58.904 42.857 0.00 0.00 0.00 2.29
2636 5727 2.793278 AACCACGGAACTGAAAATGC 57.207 45.000 0.00 0.00 0.00 3.56
2651 5742 4.856115 AAAATGCGGTTTTCAGTTTGTG 57.144 36.364 0.00 0.00 35.06 3.33
2660 5751 4.633565 GGTTTTCAGTTTGTGGAAAATGCA 59.366 37.500 0.00 0.00 42.80 3.96
2661 5752 5.296531 GGTTTTCAGTTTGTGGAAAATGCAT 59.703 36.000 0.00 0.00 42.80 3.96
2669 5760 8.610896 CAGTTTGTGGAAAATGCATTTTAAGAA 58.389 29.630 31.79 24.09 39.86 2.52
2684 5775 0.798776 AAGAATCGGTTTGAGCTGCG 59.201 50.000 0.00 0.00 0.00 5.18
2693 5784 1.509644 TTTGAGCTGCGGCAGAACAG 61.510 55.000 32.72 8.04 41.70 3.16
2698 5789 4.680237 TGCGGCAGAACAGACCCG 62.680 66.667 0.00 0.00 43.38 5.28
2707 5798 2.544267 CAGAACAGACCCGTCAAACTTC 59.456 50.000 0.00 0.00 0.00 3.01
2726 5817 9.458374 CAAACTTCAACTGTAAAACCGAATATT 57.542 29.630 0.00 0.00 0.00 1.28
2760 5851 0.533032 CCCACGTCTTCTTCCTCTCC 59.467 60.000 0.00 0.00 0.00 3.71
2767 5859 0.533032 CTTCTTCCTCTCCCCGTGTC 59.467 60.000 0.00 0.00 0.00 3.67
2781 5873 0.179100 CGTGTCCATGGTCAGCTAGG 60.179 60.000 12.24 0.00 0.00 3.02
2783 5875 1.279271 GTGTCCATGGTCAGCTAGGTT 59.721 52.381 12.24 0.00 0.00 3.50
2805 5897 2.879462 CTACGAAGCGGCCGTGTC 60.879 66.667 28.70 22.10 40.76 3.67
2865 5957 3.177884 TGTGGCAGTTGGGCTCCT 61.178 61.111 0.00 0.00 43.83 3.69
2882 5974 2.569404 CTCCTGCCAACTACTTTCTCCT 59.431 50.000 0.00 0.00 0.00 3.69
2919 6011 2.230508 AGAAGCGGACACGAAGATTGTA 59.769 45.455 0.00 0.00 44.60 2.41
2934 6026 4.925068 AGATTGTATTTTTGCAGATCGGC 58.075 39.130 11.23 11.23 0.00 5.54
2937 6029 2.423185 TGTATTTTTGCAGATCGGCAGG 59.577 45.455 19.78 0.00 45.88 4.85
2939 6031 1.614996 TTTTTGCAGATCGGCAGGAA 58.385 45.000 19.78 15.55 45.88 3.36
2940 6032 0.881118 TTTTGCAGATCGGCAGGAAC 59.119 50.000 19.78 0.00 45.88 3.62
2948 6040 4.003648 CAGATCGGCAGGAACTTTTTACT 58.996 43.478 0.00 0.00 34.60 2.24
2950 6042 3.202829 TCGGCAGGAACTTTTTACTGT 57.797 42.857 0.00 0.00 44.74 3.55
2962 6054 8.694540 GGAACTTTTTACTGTACCCCTTAAAAA 58.305 33.333 0.00 1.41 34.10 1.94
2990 6082 3.438183 AGGTCGAAGGTGTATAAGGTGT 58.562 45.455 0.00 0.00 0.00 4.16
3030 6122 5.488645 TCCGTCCAAAACTAAAAACTGAC 57.511 39.130 0.00 0.00 0.00 3.51
3063 6158 9.455144 TTTATTCAGTGGGATATAAGGGAACTA 57.545 33.333 0.00 0.00 42.68 2.24
3064 6159 6.742559 TTCAGTGGGATATAAGGGAACTAC 57.257 41.667 0.00 0.00 42.68 2.73
3065 6160 6.039415 TCAGTGGGATATAAGGGAACTACT 57.961 41.667 0.00 0.00 42.68 2.57
3066 6161 6.449956 TCAGTGGGATATAAGGGAACTACTT 58.550 40.000 0.00 0.00 42.68 2.24
3067 6162 6.906901 TCAGTGGGATATAAGGGAACTACTTT 59.093 38.462 0.00 0.00 42.68 2.66
3068 6163 7.404980 TCAGTGGGATATAAGGGAACTACTTTT 59.595 37.037 0.00 0.00 42.68 2.27
3069 6164 8.053355 CAGTGGGATATAAGGGAACTACTTTTT 58.947 37.037 0.00 0.00 42.68 1.94
3070 6165 8.272889 AGTGGGATATAAGGGAACTACTTTTTC 58.727 37.037 0.00 0.00 42.68 2.29
3071 6166 7.501559 GTGGGATATAAGGGAACTACTTTTTCC 59.498 40.741 0.00 0.00 42.68 3.13
3072 6167 6.709397 GGGATATAAGGGAACTACTTTTTCCG 59.291 42.308 0.00 0.00 43.20 4.30
3073 6168 7.278135 GGATATAAGGGAACTACTTTTTCCGT 58.722 38.462 0.00 0.00 43.20 4.69
3074 6169 7.440556 GGATATAAGGGAACTACTTTTTCCGTC 59.559 40.741 0.00 0.00 43.20 4.79
3075 6170 3.413846 AGGGAACTACTTTTTCCGTCC 57.586 47.619 0.00 0.00 43.20 4.79
3076 6171 2.707257 AGGGAACTACTTTTTCCGTCCA 59.293 45.455 0.00 0.00 43.20 4.02
3077 6172 3.136992 AGGGAACTACTTTTTCCGTCCAA 59.863 43.478 0.00 0.00 43.20 3.53
3078 6173 3.884693 GGGAACTACTTTTTCCGTCCAAA 59.115 43.478 0.00 0.00 43.20 3.28
3079 6174 4.338964 GGGAACTACTTTTTCCGTCCAAAA 59.661 41.667 0.00 0.00 43.20 2.44
3080 6175 5.276270 GGAACTACTTTTTCCGTCCAAAAC 58.724 41.667 0.00 0.00 33.46 2.43
3081 6176 5.066893 GGAACTACTTTTTCCGTCCAAAACT 59.933 40.000 0.00 0.00 33.46 2.66
3082 6177 6.260714 GGAACTACTTTTTCCGTCCAAAACTA 59.739 38.462 0.00 0.00 33.46 2.24
3083 6178 7.201723 GGAACTACTTTTTCCGTCCAAAACTAA 60.202 37.037 0.00 0.00 33.46 2.24
3084 6179 7.628769 ACTACTTTTTCCGTCCAAAACTAAA 57.371 32.000 0.00 0.00 0.00 1.85
3085 6180 8.054152 ACTACTTTTTCCGTCCAAAACTAAAA 57.946 30.769 0.00 0.00 0.00 1.52
3086 6181 8.522003 ACTACTTTTTCCGTCCAAAACTAAAAA 58.478 29.630 0.00 0.00 33.26 1.94
3087 6182 7.585286 ACTTTTTCCGTCCAAAACTAAAAAC 57.415 32.000 0.00 0.00 32.04 2.43
3088 6183 7.380536 ACTTTTTCCGTCCAAAACTAAAAACT 58.619 30.769 0.00 0.00 32.04 2.66
3089 6184 7.329962 ACTTTTTCCGTCCAAAACTAAAAACTG 59.670 33.333 0.00 0.00 32.04 3.16
3090 6185 6.512342 TTTCCGTCCAAAACTAAAAACTGA 57.488 33.333 0.00 0.00 0.00 3.41
3091 6186 5.488645 TCCGTCCAAAACTAAAAACTGAC 57.511 39.130 0.00 0.00 0.00 3.51
3092 6187 4.034279 TCCGTCCAAAACTAAAAACTGACG 59.966 41.667 0.00 0.00 42.72 4.35
3093 6188 4.276460 CGTCCAAAACTAAAAACTGACGG 58.724 43.478 0.00 0.00 40.27 4.79
3094 6189 4.201841 CGTCCAAAACTAAAAACTGACGGT 60.202 41.667 0.00 0.00 40.27 4.83
3095 6190 5.643664 GTCCAAAACTAAAAACTGACGGTT 58.356 37.500 0.00 0.00 40.28 4.44
3096 6191 6.456718 CGTCCAAAACTAAAAACTGACGGTTA 60.457 38.462 0.00 0.00 40.27 2.85
3097 6192 7.420002 GTCCAAAACTAAAAACTGACGGTTAT 58.580 34.615 0.00 0.00 37.12 1.89
3098 6193 7.916977 GTCCAAAACTAAAAACTGACGGTTATT 59.083 33.333 0.00 0.00 37.12 1.40
3099 6194 8.468399 TCCAAAACTAAAAACTGACGGTTATTT 58.532 29.630 0.00 6.37 37.12 1.40
3100 6195 9.089601 CCAAAACTAAAAACTGACGGTTATTTT 57.910 29.630 0.00 1.36 37.12 1.82
3108 6203 9.458374 AAAAACTGACGGTTATTTTATTCAGTG 57.542 29.630 0.00 0.00 42.17 3.66
3109 6204 6.737254 ACTGACGGTTATTTTATTCAGTGG 57.263 37.500 1.36 0.00 41.59 4.00
3110 6205 5.646360 ACTGACGGTTATTTTATTCAGTGGG 59.354 40.000 1.36 0.00 41.59 4.61
3111 6206 5.806818 TGACGGTTATTTTATTCAGTGGGA 58.193 37.500 0.00 0.00 0.00 4.37
3112 6207 6.419791 TGACGGTTATTTTATTCAGTGGGAT 58.580 36.000 0.00 0.00 0.00 3.85
3113 6208 6.540914 TGACGGTTATTTTATTCAGTGGGATC 59.459 38.462 0.00 0.00 0.00 3.36
3114 6209 6.659824 ACGGTTATTTTATTCAGTGGGATCT 58.340 36.000 0.00 0.00 0.00 2.75
3115 6210 7.798071 ACGGTTATTTTATTCAGTGGGATCTA 58.202 34.615 0.00 0.00 0.00 1.98
3116 6211 8.269317 ACGGTTATTTTATTCAGTGGGATCTAA 58.731 33.333 0.00 0.00 0.00 2.10
3117 6212 8.774586 CGGTTATTTTATTCAGTGGGATCTAAG 58.225 37.037 0.00 0.00 0.00 2.18
3118 6213 9.067986 GGTTATTTTATTCAGTGGGATCTAAGG 57.932 37.037 0.00 0.00 0.00 2.69
3119 6214 9.067986 GTTATTTTATTCAGTGGGATCTAAGGG 57.932 37.037 0.00 0.00 0.00 3.95
3120 6215 6.901615 TTTTATTCAGTGGGATCTAAGGGA 57.098 37.500 0.00 0.00 0.00 4.20
3121 6216 7.465900 TTTTATTCAGTGGGATCTAAGGGAT 57.534 36.000 0.00 0.00 37.37 3.85
3122 6217 7.465900 TTTATTCAGTGGGATCTAAGGGATT 57.534 36.000 0.00 0.00 34.33 3.01
3130 6225 4.594920 TGGGATCTAAGGGATTTGCTAGAG 59.405 45.833 0.00 0.00 34.33 2.43
3152 6247 4.406972 AGATGCTCTTATAACCTGCACAGA 59.593 41.667 0.00 0.00 36.44 3.41
3167 6263 3.932089 TGCACAGAAAAAGCAGGAAAAAC 59.068 39.130 0.00 0.00 33.75 2.43
3190 6286 3.636153 ACAAAAGCTATCTGAGGGACC 57.364 47.619 0.00 0.00 0.00 4.46
3191 6287 3.185455 ACAAAAGCTATCTGAGGGACCT 58.815 45.455 0.00 0.00 0.00 3.85
3213 6309 5.591877 CCTGAGTAGCTAATGCCTTCAAAAT 59.408 40.000 0.00 0.00 40.80 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.474478 TGCACCAAGAACTTTTTGCGA 59.526 42.857 10.53 0.00 32.93 5.10
22 23 2.860136 GACTGCACCAAGAACTTTTTGC 59.140 45.455 9.08 9.08 0.00 3.68
65 66 9.346725 GATTCGATTTTCTTTTAGCAACTTCAT 57.653 29.630 0.00 0.00 0.00 2.57
87 88 6.756542 AGTTTTTAACAACTGCACCAAGATTC 59.243 34.615 6.21 0.00 35.57 2.52
94 95 5.529800 TCCTCTAGTTTTTAACAACTGCACC 59.470 40.000 15.67 0.00 37.57 5.01
95 96 6.613755 TCCTCTAGTTTTTAACAACTGCAC 57.386 37.500 15.67 0.00 37.57 4.57
97 98 9.529325 AATTTTCCTCTAGTTTTTAACAACTGC 57.471 29.630 15.67 0.00 37.57 4.40
132 133 4.283467 ACAAGAAGTGGTAGTATGTGCTGA 59.717 41.667 0.00 0.00 0.00 4.26
180 181 1.807142 GGAGCAAAAGAGGACTTTCGG 59.193 52.381 0.00 0.00 44.32 4.30
181 182 2.481952 CAGGAGCAAAAGAGGACTTTCG 59.518 50.000 0.00 0.00 44.32 3.46
201 203 0.250234 CCGGACCTCATTTGAGCTCA 59.750 55.000 13.74 13.74 40.75 4.26
259 261 9.442047 ACATTTACCAAAGTTTGTCATTTTCAA 57.558 25.926 14.36 0.00 0.00 2.69
269 271 8.825745 AGCATACAAAACATTTACCAAAGTTTG 58.174 29.630 8.73 8.73 34.70 2.93
270 272 8.956533 AGCATACAAAACATTTACCAAAGTTT 57.043 26.923 0.00 0.00 35.87 2.66
271 273 8.825745 CAAGCATACAAAACATTTACCAAAGTT 58.174 29.630 0.00 0.00 0.00 2.66
272 274 8.200792 TCAAGCATACAAAACATTTACCAAAGT 58.799 29.630 0.00 0.00 0.00 2.66
273 275 8.586570 TCAAGCATACAAAACATTTACCAAAG 57.413 30.769 0.00 0.00 0.00 2.77
334 336 2.414825 AGTGCTGTTTTTGTTTTTGCCG 59.585 40.909 0.00 0.00 0.00 5.69
343 345 4.190772 ACCATTTTGGAGTGCTGTTTTTG 58.809 39.130 0.00 0.00 40.96 2.44
347 349 3.450457 TGAAACCATTTTGGAGTGCTGTT 59.550 39.130 0.00 0.00 40.96 3.16
349 351 3.731652 TGAAACCATTTTGGAGTGCTG 57.268 42.857 0.00 0.00 40.96 4.41
352 354 7.226325 TGCTATTTTTGAAACCATTTTGGAGTG 59.774 33.333 0.00 0.00 40.96 3.51
364 366 7.638134 TGCTCCAAAATTGCTATTTTTGAAAC 58.362 30.769 14.90 12.18 43.50 2.78
368 370 7.808672 TCAATGCTCCAAAATTGCTATTTTTG 58.191 30.769 14.90 12.27 40.97 2.44
403 410 1.002087 AGGACATTCGTGGAAGTGGTC 59.998 52.381 0.00 0.00 0.00 4.02
503 515 5.007136 TGAACGGTCAAATCCAAAATTTTGC 59.993 36.000 22.90 9.14 36.86 3.68
519 531 1.696832 GCGCTCCTTGATGAACGGTC 61.697 60.000 0.00 0.00 0.00 4.79
521 533 1.021390 AAGCGCTCCTTGATGAACGG 61.021 55.000 12.06 0.00 30.99 4.44
537 558 3.497932 CTGCTGCCGAGCTCAAGC 61.498 66.667 20.60 20.60 46.39 4.01
592 613 1.656652 ATGAACGCCTCCTTTCATCG 58.343 50.000 0.00 0.00 35.71 3.84
595 616 2.699954 GAGAATGAACGCCTCCTTTCA 58.300 47.619 0.00 0.00 34.30 2.69
606 629 5.971202 TGAAAGAGTTTTTGCGAGAATGAAC 59.029 36.000 0.00 0.00 0.00 3.18
650 673 2.762327 AGGGCGCATCATTCATCTTTTT 59.238 40.909 10.83 0.00 0.00 1.94
651 674 2.381911 AGGGCGCATCATTCATCTTTT 58.618 42.857 10.83 0.00 0.00 2.27
726 757 2.069273 CCACGAGCTTACTTCCTGTTG 58.931 52.381 0.00 0.00 0.00 3.33
739 770 1.227380 CTGGTATGGAGCCACGAGC 60.227 63.158 0.00 0.00 44.25 5.03
740 771 1.227380 GCTGGTATGGAGCCACGAG 60.227 63.158 0.00 0.00 31.85 4.18
741 772 2.900273 GCTGGTATGGAGCCACGA 59.100 61.111 0.00 0.00 31.85 4.35
743 774 2.897350 GCGCTGGTATGGAGCCAC 60.897 66.667 0.00 0.00 32.41 5.01
745 776 2.280457 GAGCGCTGGTATGGAGCC 60.280 66.667 18.48 0.00 32.41 4.70
746 777 2.280457 GGAGCGCTGGTATGGAGC 60.280 66.667 18.48 0.00 0.00 4.70
747 778 0.107456 ATTGGAGCGCTGGTATGGAG 59.893 55.000 18.48 0.00 0.00 3.86
748 779 0.546122 AATTGGAGCGCTGGTATGGA 59.454 50.000 18.48 0.00 0.00 3.41
749 780 1.334869 GAAATTGGAGCGCTGGTATGG 59.665 52.381 18.48 0.00 0.00 2.74
750 781 1.334869 GGAAATTGGAGCGCTGGTATG 59.665 52.381 18.48 0.00 0.00 2.39
751 782 1.212935 AGGAAATTGGAGCGCTGGTAT 59.787 47.619 18.48 0.97 0.00 2.73
752 783 0.618458 AGGAAATTGGAGCGCTGGTA 59.382 50.000 18.48 0.00 0.00 3.25
753 784 0.618458 TAGGAAATTGGAGCGCTGGT 59.382 50.000 18.48 0.00 0.00 4.00
754 785 1.876156 GATAGGAAATTGGAGCGCTGG 59.124 52.381 18.48 0.00 0.00 4.85
755 786 1.528586 CGATAGGAAATTGGAGCGCTG 59.471 52.381 18.48 0.00 0.00 5.18
756 787 1.412710 TCGATAGGAAATTGGAGCGCT 59.587 47.619 11.27 11.27 0.00 5.92
757 788 1.795286 CTCGATAGGAAATTGGAGCGC 59.205 52.381 0.00 0.00 0.00 5.92
758 789 1.795286 GCTCGATAGGAAATTGGAGCG 59.205 52.381 0.00 0.00 37.72 5.03
759 790 1.795286 CGCTCGATAGGAAATTGGAGC 59.205 52.381 0.97 0.97 42.49 4.70
760 791 3.053455 GTCGCTCGATAGGAAATTGGAG 58.947 50.000 0.00 0.00 0.00 3.86
761 792 2.543031 CGTCGCTCGATAGGAAATTGGA 60.543 50.000 0.00 0.00 42.86 3.53
777 808 1.515304 GACTTGGAGAGAGCGTCGC 60.515 63.158 9.80 9.80 0.00 5.19
786 817 4.631493 TCCGTTGGGACTTGGAGA 57.369 55.556 0.00 0.00 37.43 3.71
892 926 1.208614 GCTCTGTTTTGCCTCTGCG 59.791 57.895 0.00 0.00 41.78 5.18
893 927 0.670162 TTGCTCTGTTTTGCCTCTGC 59.330 50.000 0.00 0.00 38.26 4.26
894 928 1.000938 GGTTGCTCTGTTTTGCCTCTG 60.001 52.381 0.00 0.00 0.00 3.35
895 929 1.133668 AGGTTGCTCTGTTTTGCCTCT 60.134 47.619 0.00 0.00 0.00 3.69
896 930 1.268079 GAGGTTGCTCTGTTTTGCCTC 59.732 52.381 0.00 0.00 35.00 4.70
897 931 1.322442 GAGGTTGCTCTGTTTTGCCT 58.678 50.000 0.00 0.00 0.00 4.75
898 932 0.315251 GGAGGTTGCTCTGTTTTGCC 59.685 55.000 0.00 0.00 0.00 4.52
906 940 2.936032 GGGGGTGGAGGTTGCTCT 60.936 66.667 0.00 0.00 0.00 4.09
907 941 3.256960 TGGGGGTGGAGGTTGCTC 61.257 66.667 0.00 0.00 0.00 4.26
1157 1457 1.059098 CCCCATCATCATCGGAAGGA 58.941 55.000 0.00 0.00 0.00 3.36
1443 4311 2.009625 GACGCCGTAGTTGCATGACG 62.010 60.000 0.00 8.20 36.36 4.35
1472 4439 4.734398 ACAGCCTGATTCTACAGAGAAG 57.266 45.455 0.00 0.00 44.90 2.85
1493 4460 2.568062 TGACGTGCCATCTAACCCTAAA 59.432 45.455 0.00 0.00 0.00 1.85
1507 4478 5.965334 CCATACAATCAATTTACTGACGTGC 59.035 40.000 0.00 0.00 0.00 5.34
1510 4481 7.064609 ACTGTCCATACAATCAATTTACTGACG 59.935 37.037 0.00 0.00 34.49 4.35
1512 4483 8.862325 AACTGTCCATACAATCAATTTACTGA 57.138 30.769 0.00 0.00 34.49 3.41
1546 4517 6.312426 CAGTTGATCTCTTGGCTAACAACTAG 59.688 42.308 13.07 6.77 42.47 2.57
1605 4582 3.838565 AGATGGTAGGATCGATCACTGT 58.161 45.455 25.93 10.33 0.00 3.55
1772 4765 5.127682 AGAAAACATAGCATTAAAGGGGCTG 59.872 40.000 0.00 0.00 38.55 4.85
1819 4813 2.722094 TGGCTTGCATTACCAAGTAGG 58.278 47.619 0.65 0.00 43.17 3.18
1838 4832 3.141398 AGGACTGCACTTGTAACACATG 58.859 45.455 0.00 0.00 0.00 3.21
1890 4903 7.950512 CCATATGGTGCTGGTTAATAAAATCA 58.049 34.615 14.09 0.00 0.00 2.57
1943 4956 9.739276 TCTTAGTGAAACCATAAGTTGAATGAT 57.261 29.630 0.00 0.00 39.19 2.45
1962 4975 4.470462 GTGCAACTGCTTCATTCTTAGTG 58.530 43.478 2.95 0.00 42.66 2.74
2031 5049 6.364165 AGCTCGATTTTGAAACATCAAATGTG 59.636 34.615 4.97 2.27 44.07 3.21
2116 5174 2.165030 CACACCAAAGGAAGATGGCATC 59.835 50.000 19.78 19.78 40.51 3.91
2250 5309 1.208706 TGGTCACCTCAACCTCAACA 58.791 50.000 0.00 0.00 37.69 3.33
2412 5492 4.560136 TGATATCTCAGACGACAAGAGC 57.440 45.455 3.98 0.00 0.00 4.09
2472 5552 5.423015 AGCGAGCCATGTATAAATATCCAG 58.577 41.667 0.00 0.00 0.00 3.86
2507 5589 5.705441 TGACAACTTATGACACCAAATCTCC 59.295 40.000 0.00 0.00 0.00 3.71
2523 5605 9.665719 AACAACTAATGGAAATTTTGACAACTT 57.334 25.926 0.00 0.00 0.00 2.66
2548 5630 1.421268 AGCAATGTCCTCACAGTGGAA 59.579 47.619 0.00 0.00 46.60 3.53
2605 5687 1.009829 CCGTGGTTTGCTAGAGATGC 58.990 55.000 0.00 0.00 0.00 3.91
2612 5694 2.623878 TTCAGTTCCGTGGTTTGCTA 57.376 45.000 0.00 0.00 0.00 3.49
2614 5696 2.570442 TTTTCAGTTCCGTGGTTTGC 57.430 45.000 0.00 0.00 0.00 3.68
2633 5724 2.028130 TCCACAAACTGAAAACCGCAT 58.972 42.857 0.00 0.00 0.00 4.73
2636 5727 4.260172 GCATTTTCCACAAACTGAAAACCG 60.260 41.667 0.00 0.00 41.67 4.44
2650 5741 6.696411 ACCGATTCTTAAAATGCATTTTCCA 58.304 32.000 34.40 23.00 40.24 3.53
2651 5742 7.595311 AACCGATTCTTAAAATGCATTTTCC 57.405 32.000 34.40 18.54 40.24 3.13
2660 5751 5.402398 GCAGCTCAAACCGATTCTTAAAAT 58.598 37.500 0.00 0.00 0.00 1.82
2661 5752 4.612712 CGCAGCTCAAACCGATTCTTAAAA 60.613 41.667 0.00 0.00 0.00 1.52
2669 5760 3.127533 GCCGCAGCTCAAACCGAT 61.128 61.111 0.00 0.00 35.50 4.18
2684 5775 0.534203 TTTGACGGGTCTGTTCTGCC 60.534 55.000 0.00 0.00 0.00 4.85
2693 5784 2.285977 ACAGTTGAAGTTTGACGGGTC 58.714 47.619 0.00 0.00 0.00 4.46
2698 5789 5.871539 TCGGTTTTACAGTTGAAGTTTGAC 58.128 37.500 0.00 0.00 0.00 3.18
2760 5851 1.613317 TAGCTGACCATGGACACGGG 61.613 60.000 21.47 8.18 0.00 5.28
2767 5859 0.254178 AGCAACCTAGCTGACCATGG 59.746 55.000 11.19 11.19 44.66 3.66
2781 5873 2.453638 GCCGCTTCGTAGGAGCAAC 61.454 63.158 0.96 0.00 0.00 4.17
2783 5875 4.143333 GGCCGCTTCGTAGGAGCA 62.143 66.667 0.96 0.00 0.00 4.26
2789 5881 4.424566 GGACACGGCCGCTTCGTA 62.425 66.667 28.58 0.00 38.94 3.43
2824 5916 2.134287 ATCTCCATGACCCGTCCGG 61.134 63.158 0.00 0.00 37.81 5.14
2830 5922 3.012518 CACAGAAACATCTCCATGACCC 58.987 50.000 0.00 0.00 33.72 4.46
2865 5957 4.530553 TGTATCAGGAGAAAGTAGTTGGCA 59.469 41.667 0.00 0.00 0.00 4.92
2882 5974 1.754803 CTTCTACGGTGCCCTGTATCA 59.245 52.381 0.00 0.00 0.00 2.15
2903 5995 4.553429 GCAAAAATACAATCTTCGTGTCCG 59.447 41.667 0.00 0.00 0.00 4.79
2908 6000 6.250819 CGATCTGCAAAAATACAATCTTCGT 58.749 36.000 0.00 0.00 0.00 3.85
2919 6011 1.838112 TCCTGCCGATCTGCAAAAAT 58.162 45.000 13.09 0.00 41.51 1.82
2934 6026 4.981812 AGGGGTACAGTAAAAAGTTCCTG 58.018 43.478 0.00 0.00 0.00 3.86
2962 6054 6.598064 CCTTATACACCTTCGACCTTCAATTT 59.402 38.462 0.00 0.00 0.00 1.82
2963 6055 6.113411 CCTTATACACCTTCGACCTTCAATT 58.887 40.000 0.00 0.00 0.00 2.32
2964 6056 5.189145 ACCTTATACACCTTCGACCTTCAAT 59.811 40.000 0.00 0.00 0.00 2.57
2965 6057 4.529377 ACCTTATACACCTTCGACCTTCAA 59.471 41.667 0.00 0.00 0.00 2.69
2966 6058 4.081862 CACCTTATACACCTTCGACCTTCA 60.082 45.833 0.00 0.00 0.00 3.02
2967 6059 4.081807 ACACCTTATACACCTTCGACCTTC 60.082 45.833 0.00 0.00 0.00 3.46
2968 6060 3.836562 ACACCTTATACACCTTCGACCTT 59.163 43.478 0.00 0.00 0.00 3.50
2969 6061 3.438183 ACACCTTATACACCTTCGACCT 58.562 45.455 0.00 0.00 0.00 3.85
2970 6062 3.881937 ACACCTTATACACCTTCGACC 57.118 47.619 0.00 0.00 0.00 4.79
2971 6063 4.992951 ACAAACACCTTATACACCTTCGAC 59.007 41.667 0.00 0.00 0.00 4.20
3013 6105 8.637281 AAATAACCGTCAGTTTTTAGTTTTGG 57.363 30.769 0.00 0.00 40.05 3.28
3044 6139 7.766736 AAAAGTAGTTCCCTTATATCCCACT 57.233 36.000 0.00 0.00 0.00 4.00
3059 6154 7.628769 TTAGTTTTGGACGGAAAAAGTAGTT 57.371 32.000 0.00 0.00 35.14 2.24
3060 6155 7.628769 TTTAGTTTTGGACGGAAAAAGTAGT 57.371 32.000 0.00 0.00 35.14 2.73
3062 6157 8.522003 AGTTTTTAGTTTTGGACGGAAAAAGTA 58.478 29.630 0.00 0.00 38.46 2.24
3063 6158 7.329962 CAGTTTTTAGTTTTGGACGGAAAAAGT 59.670 33.333 0.00 0.00 39.51 2.66
3064 6159 7.542824 TCAGTTTTTAGTTTTGGACGGAAAAAG 59.457 33.333 0.00 0.00 37.98 2.27
3065 6160 7.328982 GTCAGTTTTTAGTTTTGGACGGAAAAA 59.671 33.333 0.00 0.00 36.48 1.94
3066 6161 6.807720 GTCAGTTTTTAGTTTTGGACGGAAAA 59.192 34.615 0.00 0.00 0.00 2.29
3067 6162 6.324042 GTCAGTTTTTAGTTTTGGACGGAAA 58.676 36.000 0.00 0.00 0.00 3.13
3068 6163 5.447548 CGTCAGTTTTTAGTTTTGGACGGAA 60.448 40.000 0.00 0.00 42.06 4.30
3069 6164 4.034279 CGTCAGTTTTTAGTTTTGGACGGA 59.966 41.667 0.00 0.00 42.06 4.69
3070 6165 4.276460 CGTCAGTTTTTAGTTTTGGACGG 58.724 43.478 0.00 0.00 42.06 4.79
3071 6166 4.201841 ACCGTCAGTTTTTAGTTTTGGACG 60.202 41.667 0.00 0.00 44.46 4.79
3072 6167 5.239359 ACCGTCAGTTTTTAGTTTTGGAC 57.761 39.130 0.00 0.00 0.00 4.02
3073 6168 5.900865 AACCGTCAGTTTTTAGTTTTGGA 57.099 34.783 0.00 0.00 33.89 3.53
3074 6169 8.637281 AAATAACCGTCAGTTTTTAGTTTTGG 57.363 30.769 0.00 0.00 40.05 3.28
3082 6177 9.458374 CACTGAATAAAATAACCGTCAGTTTTT 57.542 29.630 1.51 0.00 42.19 1.94
3083 6178 8.079809 CCACTGAATAAAATAACCGTCAGTTTT 58.920 33.333 1.51 0.00 42.19 2.43
3084 6179 7.308951 CCCACTGAATAAAATAACCGTCAGTTT 60.309 37.037 1.51 0.00 42.19 2.66
3085 6180 6.150474 CCCACTGAATAAAATAACCGTCAGTT 59.850 38.462 1.51 0.00 42.19 3.16
3086 6181 5.646360 CCCACTGAATAAAATAACCGTCAGT 59.354 40.000 0.00 0.00 44.89 3.41
3087 6182 5.878116 TCCCACTGAATAAAATAACCGTCAG 59.122 40.000 0.00 0.00 38.72 3.51
3088 6183 5.806818 TCCCACTGAATAAAATAACCGTCA 58.193 37.500 0.00 0.00 0.00 4.35
3089 6184 6.766467 AGATCCCACTGAATAAAATAACCGTC 59.234 38.462 0.00 0.00 0.00 4.79
3090 6185 6.659824 AGATCCCACTGAATAAAATAACCGT 58.340 36.000 0.00 0.00 0.00 4.83
3091 6186 8.671384 TTAGATCCCACTGAATAAAATAACCG 57.329 34.615 0.00 0.00 0.00 4.44
3092 6187 9.067986 CCTTAGATCCCACTGAATAAAATAACC 57.932 37.037 0.00 0.00 0.00 2.85
3093 6188 9.067986 CCCTTAGATCCCACTGAATAAAATAAC 57.932 37.037 0.00 0.00 0.00 1.89
3094 6189 9.009675 TCCCTTAGATCCCACTGAATAAAATAA 57.990 33.333 0.00 0.00 0.00 1.40
3095 6190 8.575736 TCCCTTAGATCCCACTGAATAAAATA 57.424 34.615 0.00 0.00 0.00 1.40
3096 6191 7.465900 TCCCTTAGATCCCACTGAATAAAAT 57.534 36.000 0.00 0.00 0.00 1.82
3097 6192 6.901615 TCCCTTAGATCCCACTGAATAAAA 57.098 37.500 0.00 0.00 0.00 1.52
3098 6193 7.465900 AATCCCTTAGATCCCACTGAATAAA 57.534 36.000 0.00 0.00 32.47 1.40
3099 6194 7.290061 CAAATCCCTTAGATCCCACTGAATAA 58.710 38.462 0.00 0.00 32.47 1.40
3100 6195 6.691491 GCAAATCCCTTAGATCCCACTGAATA 60.691 42.308 0.00 0.00 32.47 1.75
3101 6196 5.699143 CAAATCCCTTAGATCCCACTGAAT 58.301 41.667 0.00 0.00 32.47 2.57
3102 6197 4.628715 GCAAATCCCTTAGATCCCACTGAA 60.629 45.833 0.00 0.00 32.47 3.02
3103 6198 3.117888 GCAAATCCCTTAGATCCCACTGA 60.118 47.826 0.00 0.00 32.47 3.41
3104 6199 3.117738 AGCAAATCCCTTAGATCCCACTG 60.118 47.826 0.00 0.00 32.47 3.66
3105 6200 3.126453 AGCAAATCCCTTAGATCCCACT 58.874 45.455 0.00 0.00 32.47 4.00
3106 6201 3.584733 AGCAAATCCCTTAGATCCCAC 57.415 47.619 0.00 0.00 32.47 4.61
3107 6202 4.566837 TCTAGCAAATCCCTTAGATCCCA 58.433 43.478 0.00 0.00 32.47 4.37
3108 6203 4.841246 TCTCTAGCAAATCCCTTAGATCCC 59.159 45.833 0.00 0.00 32.47 3.85
3109 6204 6.405538 CATCTCTAGCAAATCCCTTAGATCC 58.594 44.000 0.00 0.00 32.47 3.36
3110 6205 5.874261 GCATCTCTAGCAAATCCCTTAGATC 59.126 44.000 0.00 0.00 32.47 2.75
3111 6206 5.547276 AGCATCTCTAGCAAATCCCTTAGAT 59.453 40.000 0.00 0.00 36.48 1.98
3112 6207 4.904251 AGCATCTCTAGCAAATCCCTTAGA 59.096 41.667 0.00 0.00 0.00 2.10
3113 6208 5.226194 AGCATCTCTAGCAAATCCCTTAG 57.774 43.478 0.00 0.00 0.00 2.18
3114 6209 5.220710 GAGCATCTCTAGCAAATCCCTTA 57.779 43.478 0.00 0.00 0.00 2.69
3115 6210 4.084011 GAGCATCTCTAGCAAATCCCTT 57.916 45.455 0.00 0.00 0.00 3.95
3116 6211 3.767902 GAGCATCTCTAGCAAATCCCT 57.232 47.619 0.00 0.00 0.00 4.20
3130 6225 4.697514 TCTGTGCAGGTTATAAGAGCATC 58.302 43.478 8.96 5.22 37.56 3.91
3152 6247 6.640499 GCTTTTGTTTGTTTTTCCTGCTTTTT 59.360 30.769 0.00 0.00 0.00 1.94
3167 6263 4.156739 GGTCCCTCAGATAGCTTTTGTTTG 59.843 45.833 0.00 0.00 0.00 2.93
3190 6286 6.690194 ATTTTGAAGGCATTAGCTACTCAG 57.310 37.500 0.00 0.00 41.70 3.35
3191 6287 7.466746 AAATTTTGAAGGCATTAGCTACTCA 57.533 32.000 0.00 0.00 41.70 3.41
3213 6309 7.898636 AGGGGATCATCACAAATAGGTTTAAAA 59.101 33.333 0.00 0.00 0.00 1.52
3237 6333 5.615289 CAGATACTCTTGGGTCCATAAAGG 58.385 45.833 0.00 0.00 39.47 3.11


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

AutoCloner maintained by Alex Coulton.