Multiple sequence alignment - TraesCS3A01G527300

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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 TraesCS3A01G527300 chr3A 100.000 4952 0 0 1 4952 741752955 741757906 0.000000e+00 9145.0
1 TraesCS3A01G527300 chr3D 91.597 2392 116 32 881 3233 608667637 608669982 0.000000e+00 3225.0
2 TraesCS3A01G527300 chr3D 90.920 1630 87 28 3229 4842 608670008 608671592 0.000000e+00 2134.0
3 TraesCS3A01G527300 chr3D 88.412 466 27 9 441 879 608667131 608667596 2.030000e-148 536.0
4 TraesCS3A01G527300 chr3D 88.636 396 24 12 1 377 608666743 608667136 3.490000e-126 462.0
5 TraesCS3A01G527300 chr3D 84.746 118 12 3 4841 4952 608671748 608671865 4.050000e-21 113.0
6 TraesCS3A01G527300 chr3D 92.857 56 3 1 4841 4896 279912054 279912000 4.110000e-11 80.5
7 TraesCS3A01G527300 chr3B 90.112 1426 100 20 1834 3233 818849144 818847734 0.000000e+00 1814.0
8 TraesCS3A01G527300 chr3B 91.967 971 56 10 881 1836 818850210 818849247 0.000000e+00 1341.0
9 TraesCS3A01G527300 chr3B 95.213 376 14 2 1 376 818851089 818850718 4.270000e-165 592.0
10 TraesCS3A01G527300 chr3B 86.765 476 29 14 441 882 818850720 818850245 2.660000e-137 499.0
11 TraesCS3A01G527300 chr3B 87.248 298 23 7 3229 3516 818847708 818847416 4.780000e-85 326.0
12 TraesCS3A01G527300 chr3B 90.385 52 4 1 3620 3671 43486364 43486414 3.200000e-07 67.6
13 TraesCS3A01G527300 chr6D 92.424 66 5 0 377 442 407837296 407837231 1.470000e-15 95.3
14 TraesCS3A01G527300 chr2B 92.424 66 5 0 377 442 490719108 490719173 1.470000e-15 95.3
15 TraesCS3A01G527300 chr2B 98.039 51 1 0 4841 4891 165067317 165067267 6.830000e-14 89.8
16 TraesCS3A01G527300 chr2B 97.143 35 0 1 4494 4527 26860003 26860037 1.930000e-04 58.4
17 TraesCS3A01G527300 chr7B 92.308 65 5 0 377 441 578859446 578859510 5.280000e-15 93.5
18 TraesCS3A01G527300 chr6A 91.176 68 2 4 377 442 37661151 37661216 6.830000e-14 89.8
19 TraesCS3A01G527300 chr6A 94.231 52 2 1 4842 4893 574915745 574915795 1.480000e-10 78.7
20 TraesCS3A01G527300 chr5D 91.045 67 4 2 377 442 471506019 471506084 6.830000e-14 89.8
21 TraesCS3A01G527300 chr5D 95.833 48 2 0 4795 4842 264022626 264022579 1.480000e-10 78.7
22 TraesCS3A01G527300 chr4B 90.909 66 6 0 377 442 632831308 632831373 6.830000e-14 89.8
23 TraesCS3A01G527300 chr4B 97.959 49 1 0 4842 4890 106740352 106740304 8.830000e-13 86.1
24 TraesCS3A01G527300 chr4B 94.231 52 2 1 4842 4893 113753446 113753496 1.480000e-10 78.7
25 TraesCS3A01G527300 chr2D 90.909 66 6 0 377 442 112593414 112593479 6.830000e-14 89.8
26 TraesCS3A01G527300 chr1D 91.045 67 4 2 377 442 369525433 369525498 6.830000e-14 89.8
27 TraesCS3A01G527300 chr1D 97.959 49 1 0 4841 4889 463979185 463979233 8.830000e-13 86.1
28 TraesCS3A01G527300 chr1B 91.045 67 4 2 377 442 471364913 471364848 6.830000e-14 89.8
29 TraesCS3A01G527300 chr6B 97.959 49 1 0 4841 4889 691036852 691036900 8.830000e-13 86.1
30 TraesCS3A01G527300 chr7A 94.340 53 2 1 4841 4893 503433199 503433250 4.110000e-11 80.5
31 TraesCS3A01G527300 chrUn 94.231 52 2 1 4841 4892 407142325 407142275 1.480000e-10 78.7


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 TraesCS3A01G527300 chr3A 741752955 741757906 4951 False 9145.0 9145 100.0000 1 4952 1 chr3A.!!$F1 4951
1 TraesCS3A01G527300 chr3D 608666743 608671865 5122 False 1294.0 3225 88.8622 1 4952 5 chr3D.!!$F1 4951
2 TraesCS3A01G527300 chr3B 818847416 818851089 3673 True 914.4 1814 90.2610 1 3516 5 chr3B.!!$R1 3515

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
970 1078 0.035439 CAACACCCGAGGGCATACTT 60.035 55.000 8.33 0.00 39.32 2.24 F
1058 1166 0.598065 ATCAAAAGTCGCCAGCAACC 59.402 50.000 0.00 0.00 0.00 3.77 F
1219 1330 0.613572 TCCATGGCAGGACTACGACA 60.614 55.000 6.96 0.00 31.23 4.35 F
2970 3231 0.534877 TTGTTCAGTGATGCAGGCGT 60.535 50.000 0.00 0.00 0.00 5.68 F
3704 4011 1.203237 TGGCCCATGGTACCATTTTGT 60.203 47.619 25.25 1.15 33.90 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 2972 0.112995 TTGGAGCTTGAGGCAATGGT 59.887 50.000 0.00 0.00 44.79 3.55 R
2719 2977 0.607489 GCTTCTTGGAGCTTGAGGCA 60.607 55.000 0.00 0.00 44.79 4.75 R
3034 3295 1.080093 CGAGTTGCAAGACGGCCTA 60.080 57.895 14.72 0.00 0.00 3.93 R
3893 4202 0.605589 ACTGGTCCTCAGAAGCTTCG 59.394 55.000 20.43 15.04 46.18 3.79 R
4833 5150 2.303175 GACCAACTTAGGTGTGGCAAA 58.697 47.619 0.00 0.00 43.38 3.68 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
147 148 1.133637 TGTTAGGCAGGGCAGTTCAAA 60.134 47.619 0.00 0.00 0.00 2.69
183 184 6.377146 CCTGCACCACAACCTTTTATAGTTAT 59.623 38.462 0.00 0.00 0.00 1.89
184 185 7.554835 CCTGCACCACAACCTTTTATAGTTATA 59.445 37.037 0.00 0.00 0.00 0.98
185 186 8.500753 TGCACCACAACCTTTTATAGTTATAG 57.499 34.615 0.00 0.00 0.00 1.31
186 187 8.104566 TGCACCACAACCTTTTATAGTTATAGT 58.895 33.333 0.00 0.00 0.00 2.12
266 276 7.090173 GCTTTGCTTCTACAATGTTCCAAATA 58.910 34.615 0.00 0.00 0.00 1.40
397 419 9.525826 AAAAATGGGTTAATTGAATAAATGCCA 57.474 25.926 0.00 0.00 0.00 4.92
398 420 8.504812 AAATGGGTTAATTGAATAAATGCCAC 57.495 30.769 0.00 0.00 0.00 5.01
399 421 6.865834 TGGGTTAATTGAATAAATGCCACT 57.134 33.333 0.00 0.00 0.00 4.00
400 422 6.872920 TGGGTTAATTGAATAAATGCCACTC 58.127 36.000 0.00 0.00 0.00 3.51
401 423 5.977129 GGGTTAATTGAATAAATGCCACTCG 59.023 40.000 0.00 0.00 0.00 4.18
402 424 6.183360 GGGTTAATTGAATAAATGCCACTCGA 60.183 38.462 0.00 0.00 0.00 4.04
403 425 7.254852 GGTTAATTGAATAAATGCCACTCGAA 58.745 34.615 0.00 0.00 0.00 3.71
404 426 7.920682 GGTTAATTGAATAAATGCCACTCGAAT 59.079 33.333 0.00 0.00 0.00 3.34
405 427 9.301153 GTTAATTGAATAAATGCCACTCGAATT 57.699 29.630 0.00 0.00 0.00 2.17
406 428 7.992180 AATTGAATAAATGCCACTCGAATTC 57.008 32.000 0.00 0.00 0.00 2.17
407 429 6.757897 TTGAATAAATGCCACTCGAATTCT 57.242 33.333 3.52 0.00 0.00 2.40
408 430 6.122850 TGAATAAATGCCACTCGAATTCTG 57.877 37.500 3.52 0.00 0.00 3.02
409 431 5.066375 TGAATAAATGCCACTCGAATTCTGG 59.934 40.000 7.66 7.66 0.00 3.86
410 432 2.496899 AATGCCACTCGAATTCTGGT 57.503 45.000 12.41 4.64 0.00 4.00
411 433 2.496899 ATGCCACTCGAATTCTGGTT 57.503 45.000 12.41 0.74 0.00 3.67
412 434 3.627395 ATGCCACTCGAATTCTGGTTA 57.373 42.857 12.41 4.60 0.00 2.85
413 435 3.627395 TGCCACTCGAATTCTGGTTAT 57.373 42.857 12.41 0.00 0.00 1.89
414 436 3.950397 TGCCACTCGAATTCTGGTTATT 58.050 40.909 12.41 0.00 0.00 1.40
415 437 3.938963 TGCCACTCGAATTCTGGTTATTC 59.061 43.478 12.41 0.00 0.00 1.75
416 438 3.312697 GCCACTCGAATTCTGGTTATTCC 59.687 47.826 12.41 0.00 0.00 3.01
417 439 3.555956 CCACTCGAATTCTGGTTATTCCG 59.444 47.826 3.52 0.00 39.52 4.30
418 440 4.430007 CACTCGAATTCTGGTTATTCCGA 58.570 43.478 3.52 0.00 39.52 4.55
419 441 4.504461 CACTCGAATTCTGGTTATTCCGAG 59.496 45.833 3.52 0.00 37.91 4.63
420 442 4.401519 ACTCGAATTCTGGTTATTCCGAGA 59.598 41.667 14.13 0.00 36.83 4.04
421 443 5.105473 ACTCGAATTCTGGTTATTCCGAGAA 60.105 40.000 14.13 0.00 36.83 2.87
422 444 5.726397 TCGAATTCTGGTTATTCCGAGAAA 58.274 37.500 3.52 0.00 37.12 2.52
423 445 6.346096 TCGAATTCTGGTTATTCCGAGAAAT 58.654 36.000 3.52 0.00 37.12 2.17
424 446 6.257849 TCGAATTCTGGTTATTCCGAGAAATG 59.742 38.462 3.52 0.00 37.12 2.32
425 447 5.757850 ATTCTGGTTATTCCGAGAAATGC 57.242 39.130 0.00 0.00 37.12 3.56
426 448 3.541632 TCTGGTTATTCCGAGAAATGCC 58.458 45.455 0.00 0.00 39.52 4.40
427 449 3.054728 TCTGGTTATTCCGAGAAATGCCA 60.055 43.478 0.00 0.00 39.52 4.92
428 450 3.013921 TGGTTATTCCGAGAAATGCCAC 58.986 45.455 0.00 0.00 39.52 5.01
429 451 3.279434 GGTTATTCCGAGAAATGCCACT 58.721 45.455 0.00 0.00 0.00 4.00
430 452 3.065371 GGTTATTCCGAGAAATGCCACTG 59.935 47.826 0.00 0.00 0.00 3.66
431 453 1.098050 ATTCCGAGAAATGCCACTGC 58.902 50.000 0.00 0.00 38.26 4.40
440 462 4.490696 TGCCACTGCAATTTCCGA 57.509 50.000 0.00 0.00 46.66 4.55
441 463 2.725811 TGCCACTGCAATTTCCGAA 58.274 47.368 0.00 0.00 46.66 4.30
442 464 1.035923 TGCCACTGCAATTTCCGAAA 58.964 45.000 0.00 0.00 46.66 3.46
443 465 1.410517 TGCCACTGCAATTTCCGAAAA 59.589 42.857 0.00 0.00 46.66 2.29
471 494 2.238521 GATGGGGCAGTTTTCAGTTGA 58.761 47.619 0.00 0.00 0.00 3.18
480 503 5.448089 GGCAGTTTTCAGTTGAAACGAACTA 60.448 40.000 6.79 0.00 43.01 2.24
494 517 4.850347 ACGAACTATAGATGGGCAGTAC 57.150 45.455 6.78 0.00 0.00 2.73
507 530 6.767902 AGATGGGCAGTACATTAAACATACTG 59.232 38.462 15.01 15.01 45.67 2.74
509 532 6.948589 TGGGCAGTACATTAAACATACTGTA 58.051 36.000 18.17 3.98 45.02 2.74
512 535 7.224167 GGGCAGTACATTAAACATACTGTAGTC 59.776 40.741 18.17 7.74 45.02 2.59
707 731 7.201522 CGATCCTCGATTGTTCTTTGTCAATAA 60.202 37.037 0.00 0.00 43.74 1.40
735 787 1.762957 ACTTAGTGTCAGTGTGTGCCT 59.237 47.619 0.00 0.00 0.00 4.75
748 804 8.458843 GTCAGTGTGTGCCTTAATATAAACATT 58.541 33.333 0.00 0.00 0.00 2.71
757 813 7.782168 TGCCTTAATATAAACATTCATGGTGGA 59.218 33.333 0.00 0.00 0.00 4.02
766 822 5.901413 ACATTCATGGTGGACATATCTCT 57.099 39.130 0.00 0.00 37.84 3.10
781 837 3.627395 ATCTCTTGCACCGTCCAATTA 57.373 42.857 0.00 0.00 0.00 1.40
824 880 2.231716 AGGTTGATTGGTAAAGGGGC 57.768 50.000 0.00 0.00 0.00 5.80
827 883 3.021695 GGTTGATTGGTAAAGGGGCTAC 58.978 50.000 0.00 0.00 0.00 3.58
879 939 6.245890 ACTATTTGATCCTTCAGCTAGCTT 57.754 37.500 16.46 0.00 32.27 3.74
899 998 4.626172 GCTTGCAGAAGTAAGTAGTACCAC 59.374 45.833 0.00 0.00 39.36 4.16
900 999 5.567025 GCTTGCAGAAGTAAGTAGTACCACT 60.567 44.000 0.00 0.00 39.36 4.00
906 1011 7.335422 GCAGAAGTAAGTAGTACCACTGTAGTA 59.665 40.741 0.00 0.00 38.02 1.82
909 1014 9.225436 GAAGTAAGTAGTACCACTGTAGTAACT 57.775 37.037 0.00 0.00 35.23 2.24
955 1063 8.818622 ATCTATGGTGTAGTAAGTAGTCAACA 57.181 34.615 0.00 0.00 0.00 3.33
960 1068 4.216257 GTGTAGTAAGTAGTCAACACCCGA 59.784 45.833 0.00 0.00 32.94 5.14
970 1078 0.035439 CAACACCCGAGGGCATACTT 60.035 55.000 8.33 0.00 39.32 2.24
1058 1166 0.598065 ATCAAAAGTCGCCAGCAACC 59.402 50.000 0.00 0.00 0.00 3.77
1111 1219 2.936498 GCTAGCCATTACGACAACACAT 59.064 45.455 2.29 0.00 0.00 3.21
1124 1232 5.221263 ACGACAACACATCCCAGATATAGTC 60.221 44.000 0.00 0.00 0.00 2.59
1134 1242 9.113797 ACATCCCAGATATAGTCAGTAGTACTA 57.886 37.037 1.57 0.00 34.11 1.82
1219 1330 0.613572 TCCATGGCAGGACTACGACA 60.614 55.000 6.96 0.00 31.23 4.35
1221 1332 1.539065 CCATGGCAGGACTACGACATC 60.539 57.143 0.00 0.00 0.00 3.06
1280 1391 4.194720 GACGACGGCGCCATCTCT 62.195 66.667 28.98 8.44 42.48 3.10
1282 1393 2.050895 CGACGGCGCCATCTCTAG 60.051 66.667 28.98 10.77 0.00 2.43
1284 1395 3.138930 GACGGCGCCATCTCTAGCA 62.139 63.158 28.98 0.00 0.00 3.49
1300 1411 4.980903 CAGCAACACCAACGGCGC 62.981 66.667 6.90 0.00 0.00 6.53
1344 1455 6.070194 ACAATTCTTCTTCTTCCGATAAGGGA 60.070 38.462 0.00 0.00 41.52 4.20
1440 1551 2.731571 GCCCACCCTCAGCGACATA 61.732 63.158 0.00 0.00 0.00 2.29
1467 1578 3.764466 CTCTCCTTCACCGGCGCT 61.764 66.667 7.64 0.00 0.00 5.92
1561 1672 6.712095 TCATATCTATGCCAAGAACAACCATC 59.288 38.462 0.00 0.00 33.76 3.51
1564 1675 6.252599 TCTATGCCAAGAACAACCATCTAT 57.747 37.500 0.00 0.00 0.00 1.98
1583 1694 8.307483 CCATCTATGTACAATTCTCCGTAGATT 58.693 37.037 0.00 0.00 35.16 2.40
1592 1703 4.377839 TTCTCCGTAGATTCAAGCTCAG 57.622 45.455 0.00 0.00 0.00 3.35
1606 1717 4.040339 TCAAGCTCAGTTTGGACATCTGTA 59.960 41.667 0.87 0.00 0.00 2.74
1660 1771 2.517959 CTGGGCAAGATGGAGAACAAA 58.482 47.619 0.00 0.00 0.00 2.83
1781 1899 7.166167 CCCAAGGTACTATTTACAGTTTCACT 58.834 38.462 0.00 0.00 38.49 3.41
1782 1900 7.664318 CCCAAGGTACTATTTACAGTTTCACTT 59.336 37.037 0.00 0.00 38.49 3.16
1783 1901 9.063615 CCAAGGTACTATTTACAGTTTCACTTT 57.936 33.333 0.00 0.00 38.49 2.66
1785 1903 9.841295 AAGGTACTATTTACAGTTTCACTTTCA 57.159 29.630 0.00 0.00 38.49 2.69
1786 1904 9.269453 AGGTACTATTTACAGTTTCACTTTCAC 57.731 33.333 0.00 0.00 36.02 3.18
1889 2112 7.462109 TTTGCAAGCAATTTTACTTACAGTG 57.538 32.000 8.46 0.00 35.70 3.66
1911 2134 2.166050 GCATAATCACCATGGTGCAACA 59.834 45.455 35.73 21.59 45.04 3.33
1959 2186 9.627395 AGCGTGTATATATTTATCTGTTCACTC 57.373 33.333 0.00 0.00 0.00 3.51
1974 2201 3.576078 TCACTCTTCAAACATGGGTGT 57.424 42.857 0.00 0.00 41.28 4.16
1983 2210 1.039856 AACATGGGTGTGTGAAAGGC 58.960 50.000 0.00 0.00 38.92 4.35
2060 2287 6.705825 GGAGCAATTACTTTTGTGAACCAAAT 59.294 34.615 0.00 0.00 42.45 2.32
2061 2288 7.307337 GGAGCAATTACTTTTGTGAACCAAATG 60.307 37.037 0.00 0.00 42.45 2.32
2092 2319 1.489481 AGCTAGCTATGCACTGTCCA 58.511 50.000 17.69 0.00 0.00 4.02
2093 2320 2.045524 AGCTAGCTATGCACTGTCCAT 58.954 47.619 17.69 0.00 0.00 3.41
2109 2336 6.429692 CACTGTCCATACTTAATTCCACAACA 59.570 38.462 0.00 0.00 0.00 3.33
2158 2386 1.364536 CACAGCTTGCATGCCACAA 59.635 52.632 19.99 1.52 0.00 3.33
2167 2395 3.138884 TGCATGCCACAATCCGTATAT 57.861 42.857 16.68 0.00 0.00 0.86
2168 2396 4.278975 TGCATGCCACAATCCGTATATA 57.721 40.909 16.68 0.00 0.00 0.86
2169 2397 4.252878 TGCATGCCACAATCCGTATATAG 58.747 43.478 16.68 0.00 0.00 1.31
2170 2398 3.063997 GCATGCCACAATCCGTATATAGC 59.936 47.826 6.36 0.00 0.00 2.97
2174 2402 4.770531 TGCCACAATCCGTATATAGCTAGT 59.229 41.667 0.00 0.00 0.00 2.57
2180 2408 6.096987 ACAATCCGTATATAGCTAGTCATGGG 59.903 42.308 0.00 0.00 0.00 4.00
2193 2421 2.423538 AGTCATGGGCAAAGTTAATCGC 59.576 45.455 0.00 0.00 0.00 4.58
2235 2470 2.175202 CAGAGGTGGAGTAGCTGAGTT 58.825 52.381 0.00 0.00 37.23 3.01
2378 2613 3.673338 GGCTAATTTGGCAAGAAAACGAC 59.327 43.478 8.53 0.00 0.00 4.34
2385 2620 1.673920 GGCAAGAAAACGACAGTGGAA 59.326 47.619 0.00 0.00 0.00 3.53
2386 2621 2.293399 GGCAAGAAAACGACAGTGGAAT 59.707 45.455 0.00 0.00 0.00 3.01
2389 2627 4.282068 CAAGAAAACGACAGTGGAATGTG 58.718 43.478 0.00 0.00 32.25 3.21
2392 2630 4.750098 AGAAAACGACAGTGGAATGTGTAG 59.250 41.667 0.00 0.00 32.25 2.74
2396 2634 4.448210 ACGACAGTGGAATGTGTAGTTTT 58.552 39.130 0.00 0.00 29.35 2.43
2449 2687 4.481930 TTTCAGTCACCTAAATTGCACG 57.518 40.909 0.00 0.00 0.00 5.34
2452 2690 3.000041 CAGTCACCTAAATTGCACGCTA 59.000 45.455 0.00 0.00 0.00 4.26
2453 2691 3.000727 AGTCACCTAAATTGCACGCTAC 58.999 45.455 0.00 0.00 0.00 3.58
2454 2692 3.000727 GTCACCTAAATTGCACGCTACT 58.999 45.455 0.00 0.00 0.00 2.57
2456 2694 4.809426 GTCACCTAAATTGCACGCTACTAT 59.191 41.667 0.00 0.00 0.00 2.12
2457 2695 5.293569 GTCACCTAAATTGCACGCTACTATT 59.706 40.000 0.00 0.00 0.00 1.73
2458 2696 5.293324 TCACCTAAATTGCACGCTACTATTG 59.707 40.000 0.00 0.00 0.00 1.90
2516 2766 9.658475 GTAACTTTTCATTTGGTTAATTTTGGC 57.342 29.630 0.00 0.00 0.00 4.52
2694 2952 1.834856 TTCCTCCAGCAGCAGACCAG 61.835 60.000 0.00 0.00 0.00 4.00
2773 3034 3.573491 GCCGGCGCCATTACAGTC 61.573 66.667 28.98 0.00 0.00 3.51
2790 3051 1.152631 TCACAGACTCCCACCACGA 60.153 57.895 0.00 0.00 0.00 4.35
2804 3065 2.203640 ACGAGAGCACCCCTGTGA 60.204 61.111 0.00 0.00 45.76 3.58
2820 3081 2.665185 GACAACAACCTCGCCGCT 60.665 61.111 0.00 0.00 0.00 5.52
2965 3226 1.855213 GCGGCTTGTTCAGTGATGCA 61.855 55.000 0.00 0.00 0.00 3.96
2970 3231 0.534877 TTGTTCAGTGATGCAGGCGT 60.535 50.000 0.00 0.00 0.00 5.68
3034 3295 4.760047 GTGCCGCTGATGGTCCGT 62.760 66.667 0.00 0.00 0.00 4.69
3035 3296 3.071837 TGCCGCTGATGGTCCGTA 61.072 61.111 0.00 0.00 0.00 4.02
3118 3379 2.774951 GATTGTGTCGTCGCCGTCG 61.775 63.158 0.00 0.00 35.01 5.12
3195 3456 3.987745 TCCTCTCCAACATCTTCTAGCT 58.012 45.455 0.00 0.00 0.00 3.32
3454 3760 7.331440 GGATGTTGAATGAATAATTGTGTGCAA 59.669 33.333 0.00 0.00 39.16 4.08
3487 3793 8.482943 AGTAATACTCATACTTATGGTGTGCAA 58.517 33.333 0.00 0.00 37.05 4.08
3502 3808 2.336945 TGCAAGGATGGCAGATGTAG 57.663 50.000 0.00 0.00 42.69 2.74
3503 3809 1.561076 TGCAAGGATGGCAGATGTAGT 59.439 47.619 0.00 0.00 42.69 2.73
3504 3810 2.771372 TGCAAGGATGGCAGATGTAGTA 59.229 45.455 0.00 0.00 42.69 1.82
3511 3817 5.782331 AGGATGGCAGATGTAGTATATGTGT 59.218 40.000 6.02 0.00 0.00 3.72
3532 3838 8.785329 TGTGTGTAGCAAATATAATTGTGAGA 57.215 30.769 2.60 0.00 32.80 3.27
3537 3843 8.830580 TGTAGCAAATATAATTGTGAGAGAAGC 58.169 33.333 2.60 0.00 32.80 3.86
3539 3845 8.517062 AGCAAATATAATTGTGAGAGAAGCTT 57.483 30.769 0.00 0.00 32.80 3.74
3543 3849 7.798596 ATATAATTGTGAGAGAAGCTTGTGG 57.201 36.000 2.10 0.00 0.00 4.17
3554 3860 5.069781 AGAGAAGCTTGTGGGATATGTAGTC 59.930 44.000 2.10 0.00 0.00 2.59
3572 3878 6.522054 TGTAGTCTGTTAACTTTTCTCTGGG 58.478 40.000 7.22 0.00 0.00 4.45
3616 3922 4.104776 GGCACAATTGACCATGTTATTCG 58.895 43.478 13.59 0.00 0.00 3.34
3704 4011 1.203237 TGGCCCATGGTACCATTTTGT 60.203 47.619 25.25 1.15 33.90 2.83
3775 4082 6.551385 AGCAACTATATAGTGCAAATGCTC 57.449 37.500 24.00 3.06 39.74 4.26
3782 4089 1.284657 AGTGCAAATGCTCGATCTCG 58.715 50.000 6.97 0.00 42.66 4.04
3795 4102 1.849219 CGATCTCGCTTACTGCAAGAC 59.151 52.381 0.00 0.00 37.57 3.01
3864 4173 1.673009 GACCGACAAAATGGCCCGA 60.673 57.895 0.00 0.00 0.00 5.14
3893 4202 0.793861 TGTGATACGAGCGGTTTTGC 59.206 50.000 0.00 0.00 0.00 3.68
3947 4256 6.012658 TCCATCATGTCACTTAAAAAGCAC 57.987 37.500 0.00 0.00 0.00 4.40
3970 4279 7.500141 CACCTTATTAAATGGGGAAGGAATTG 58.500 38.462 5.99 0.00 39.26 2.32
4004 4313 3.317430 GGCTCTGATGACCCATTCATTTC 59.683 47.826 0.00 0.00 45.67 2.17
4058 4367 5.667172 TGGATCTTTCCTCCATATCTGTTGA 59.333 40.000 0.00 0.00 43.07 3.18
4065 4374 4.403752 TCCTCCATATCTGTTGAGTGTGAG 59.596 45.833 0.00 0.00 0.00 3.51
4066 4375 4.118410 CTCCATATCTGTTGAGTGTGAGC 58.882 47.826 0.00 0.00 0.00 4.26
4080 4389 3.319405 AGTGTGAGCCTAGGTTGATATCG 59.681 47.826 11.31 0.00 0.00 2.92
4116 4425 4.466255 TCCTACCTGGATTAGTCCTACC 57.534 50.000 0.00 0.00 45.32 3.18
4117 4426 4.060192 TCCTACCTGGATTAGTCCTACCT 58.940 47.826 0.00 0.00 45.32 3.08
4118 4427 4.485021 TCCTACCTGGATTAGTCCTACCTT 59.515 45.833 0.00 0.00 45.32 3.50
4119 4428 5.678206 TCCTACCTGGATTAGTCCTACCTTA 59.322 44.000 0.00 0.00 45.32 2.69
4120 4429 6.162779 TCCTACCTGGATTAGTCCTACCTTAA 59.837 42.308 0.00 0.00 45.32 1.85
4121 4430 7.017531 CCTACCTGGATTAGTCCTACCTTAAT 58.982 42.308 0.00 0.00 45.32 1.40
4122 4431 6.997942 ACCTGGATTAGTCCTACCTTAATC 57.002 41.667 0.00 0.00 45.32 1.75
4162 4471 5.759273 CCACTCCAATCTCAATCTTCTGATC 59.241 44.000 0.00 0.00 31.51 2.92
4190 4499 0.591659 GAAGGTTCCACGCTGGTTTC 59.408 55.000 4.33 2.61 39.03 2.78
4203 4512 4.640647 ACGCTGGTTTCTTCTTCTTTCTTT 59.359 37.500 0.00 0.00 0.00 2.52
4204 4513 5.125578 ACGCTGGTTTCTTCTTCTTTCTTTT 59.874 36.000 0.00 0.00 0.00 2.27
4205 4514 6.317893 ACGCTGGTTTCTTCTTCTTTCTTTTA 59.682 34.615 0.00 0.00 0.00 1.52
4206 4515 7.013369 ACGCTGGTTTCTTCTTCTTTCTTTTAT 59.987 33.333 0.00 0.00 0.00 1.40
4207 4516 7.324616 CGCTGGTTTCTTCTTCTTTCTTTTATG 59.675 37.037 0.00 0.00 0.00 1.90
4208 4517 8.138074 GCTGGTTTCTTCTTCTTTCTTTTATGT 58.862 33.333 0.00 0.00 0.00 2.29
4209 4518 9.455847 CTGGTTTCTTCTTCTTTCTTTTATGTG 57.544 33.333 0.00 0.00 0.00 3.21
4210 4519 8.966868 TGGTTTCTTCTTCTTTCTTTTATGTGT 58.033 29.630 0.00 0.00 0.00 3.72
4211 4520 9.803315 GGTTTCTTCTTCTTTCTTTTATGTGTT 57.197 29.630 0.00 0.00 0.00 3.32
4256 4566 7.736447 TGTTTGCCTTTTCTTTTCTTTTTCA 57.264 28.000 0.00 0.00 0.00 2.69
4262 4572 9.230122 TGCCTTTTCTTTTCTTTTTCATCTTTT 57.770 25.926 0.00 0.00 0.00 2.27
4295 4605 7.447374 TGTTGACCTTTCTAATACACATTGG 57.553 36.000 0.00 0.00 0.00 3.16
4435 4745 9.921637 TTCTAAACACAAGTTGAACATTTCTTT 57.078 25.926 10.54 0.00 38.17 2.52
4470 4780 7.914871 TGAACACATTTTTACACTGTCATGAAG 59.085 33.333 0.00 0.00 0.00 3.02
4475 4785 9.651913 ACATTTTTACACTGTCATGAAGTTTTT 57.348 25.926 0.00 0.00 0.00 1.94
4482 4792 8.687824 ACACTGTCATGAAGTTTTTACAAAAG 57.312 30.769 0.00 0.00 0.00 2.27
4558 4870 8.811378 CAAACATATGTACAGACTACATGACAG 58.189 37.037 9.21 0.00 38.47 3.51
4559 4871 7.881775 ACATATGTACAGACTACATGACAGA 57.118 36.000 6.56 0.00 38.47 3.41
4620 4933 9.868277 ATCAACAAATCTTTAAACTTGTGAACA 57.132 25.926 6.41 0.00 32.50 3.18
4621 4934 9.868277 TCAACAAATCTTTAAACTTGTGAACAT 57.132 25.926 6.41 0.00 32.50 2.71
4681 4994 9.573133 CAAACTGTTTACAAAGAGATCAAAAGT 57.427 29.630 5.31 0.00 33.83 2.66
4692 5005 7.511959 AAGAGATCAAAAGTTTTACACTCCC 57.488 36.000 16.77 0.94 32.94 4.30
4695 5008 5.770162 AGATCAAAAGTTTTACACTCCCTGG 59.230 40.000 0.00 0.00 32.94 4.45
4815 5132 3.844640 ACTAAAGGGCTGTTTGGATTGT 58.155 40.909 3.90 0.00 0.00 2.71
4818 5135 2.610438 AGGGCTGTTTGGATTGTGAT 57.390 45.000 0.00 0.00 0.00 3.06
4827 5144 7.092716 GCTGTTTGGATTGTGATTATCTTTGT 58.907 34.615 0.00 0.00 0.00 2.83
4847 5321 5.895636 TGTCATATTTTGCCACACCTAAG 57.104 39.130 0.00 0.00 0.00 2.18
4878 5352 0.766674 TGCCTAAGGTGAGGTGTGGT 60.767 55.000 0.00 0.00 39.02 4.16
4883 5357 3.326880 CCTAAGGTGAGGTGTGGTAAAGT 59.673 47.826 0.00 0.00 0.00 2.66
4891 5365 2.440253 AGGTGTGGTAAAGTGTGGCTAA 59.560 45.455 0.00 0.00 0.00 3.09
4893 5367 3.473625 GTGTGGTAAAGTGTGGCTAAGT 58.526 45.455 0.00 0.00 0.00 2.24
4894 5368 3.881089 GTGTGGTAAAGTGTGGCTAAGTT 59.119 43.478 0.00 0.00 0.00 2.66
4895 5369 3.880490 TGTGGTAAAGTGTGGCTAAGTTG 59.120 43.478 0.00 0.00 0.00 3.16
4896 5370 3.252458 GTGGTAAAGTGTGGCTAAGTTGG 59.748 47.826 0.00 0.00 0.00 3.77
4897 5371 3.117813 TGGTAAAGTGTGGCTAAGTTGGT 60.118 43.478 0.00 0.00 0.00 3.67
4898 5372 3.501062 GGTAAAGTGTGGCTAAGTTGGTC 59.499 47.826 0.00 0.00 0.00 4.02
4900 5374 3.290948 AAGTGTGGCTAAGTTGGTCAA 57.709 42.857 0.00 0.00 0.00 3.18
4902 5376 2.949644 AGTGTGGCTAAGTTGGTCAAAC 59.050 45.455 6.04 6.04 39.24 2.93
4941 5421 3.563808 CAGACGTCCTTCTCTCTATGAGG 59.436 52.174 13.01 0.00 42.86 3.86
4948 5428 5.476945 GTCCTTCTCTCTATGAGGAAGATCC 59.523 48.000 18.44 0.00 42.86 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 1.618343 GCAGTGCCCATAAAACAAGGT 59.382 47.619 2.85 0.00 0.00 3.50
147 148 0.253160 TGGTGCAGGGAGGGTTCTAT 60.253 55.000 0.00 0.00 0.00 1.98
291 301 9.777297 ACTTAATTATGTTTCAGTGGCAAATTT 57.223 25.926 0.00 0.00 0.00 1.82
377 399 5.977129 CGAGTGGCATTTATTCAATTAACCC 59.023 40.000 0.00 0.00 0.00 4.11
378 400 6.791303 TCGAGTGGCATTTATTCAATTAACC 58.209 36.000 0.00 0.00 0.00 2.85
379 401 8.856490 ATTCGAGTGGCATTTATTCAATTAAC 57.144 30.769 0.00 0.00 0.00 2.01
380 402 9.515020 GAATTCGAGTGGCATTTATTCAATTAA 57.485 29.630 0.00 0.00 0.00 1.40
381 403 8.902806 AGAATTCGAGTGGCATTTATTCAATTA 58.097 29.630 0.00 0.00 0.00 1.40
382 404 7.703621 CAGAATTCGAGTGGCATTTATTCAATT 59.296 33.333 0.00 3.68 0.00 2.32
383 405 7.198390 CAGAATTCGAGTGGCATTTATTCAAT 58.802 34.615 0.00 0.00 0.00 2.57
384 406 6.404623 CCAGAATTCGAGTGGCATTTATTCAA 60.405 38.462 0.00 0.00 0.00 2.69
385 407 5.066375 CCAGAATTCGAGTGGCATTTATTCA 59.934 40.000 0.00 0.00 0.00 2.57
386 408 5.066505 ACCAGAATTCGAGTGGCATTTATTC 59.933 40.000 11.19 0.00 34.40 1.75
387 409 4.949856 ACCAGAATTCGAGTGGCATTTATT 59.050 37.500 11.19 0.00 34.40 1.40
388 410 4.526970 ACCAGAATTCGAGTGGCATTTAT 58.473 39.130 11.19 0.00 34.40 1.40
389 411 3.950397 ACCAGAATTCGAGTGGCATTTA 58.050 40.909 11.19 0.00 34.40 1.40
390 412 2.795329 ACCAGAATTCGAGTGGCATTT 58.205 42.857 11.19 0.00 34.40 2.32
391 413 2.496899 ACCAGAATTCGAGTGGCATT 57.503 45.000 11.19 0.00 34.40 3.56
392 414 2.496899 AACCAGAATTCGAGTGGCAT 57.503 45.000 11.19 0.11 34.40 4.40
393 415 3.627395 ATAACCAGAATTCGAGTGGCA 57.373 42.857 11.19 1.96 34.40 4.92
394 416 3.312697 GGAATAACCAGAATTCGAGTGGC 59.687 47.826 11.19 0.00 38.79 5.01
395 417 3.555956 CGGAATAACCAGAATTCGAGTGG 59.444 47.826 9.98 9.98 38.90 4.00
396 418 4.430007 TCGGAATAACCAGAATTCGAGTG 58.570 43.478 0.00 0.00 38.90 3.51
397 419 4.401519 TCTCGGAATAACCAGAATTCGAGT 59.598 41.667 0.00 0.00 36.50 4.18
398 420 4.933330 TCTCGGAATAACCAGAATTCGAG 58.067 43.478 0.00 0.00 38.90 4.04
399 421 4.994907 TCTCGGAATAACCAGAATTCGA 57.005 40.909 0.00 0.00 38.90 3.71
400 422 6.422223 CATTTCTCGGAATAACCAGAATTCG 58.578 40.000 0.00 0.00 36.49 3.34
401 423 6.202226 GCATTTCTCGGAATAACCAGAATTC 58.798 40.000 0.00 0.00 36.49 2.17
402 424 5.067805 GGCATTTCTCGGAATAACCAGAATT 59.932 40.000 0.00 0.00 36.49 2.17
403 425 4.580580 GGCATTTCTCGGAATAACCAGAAT 59.419 41.667 0.00 0.00 36.49 2.40
404 426 3.945285 GGCATTTCTCGGAATAACCAGAA 59.055 43.478 0.00 0.00 38.90 3.02
405 427 3.054728 TGGCATTTCTCGGAATAACCAGA 60.055 43.478 0.00 0.00 38.90 3.86
406 428 3.065371 GTGGCATTTCTCGGAATAACCAG 59.935 47.826 0.00 0.00 38.90 4.00
407 429 3.013921 GTGGCATTTCTCGGAATAACCA 58.986 45.455 0.00 0.00 38.90 3.67
408 430 3.065371 CAGTGGCATTTCTCGGAATAACC 59.935 47.826 0.00 0.00 0.00 2.85
409 431 3.487544 GCAGTGGCATTTCTCGGAATAAC 60.488 47.826 0.00 0.00 40.72 1.89
410 432 2.682856 GCAGTGGCATTTCTCGGAATAA 59.317 45.455 0.00 0.00 40.72 1.40
411 433 2.288666 GCAGTGGCATTTCTCGGAATA 58.711 47.619 0.00 0.00 40.72 1.75
412 434 1.098050 GCAGTGGCATTTCTCGGAAT 58.902 50.000 0.00 0.00 40.72 3.01
413 435 2.555123 GCAGTGGCATTTCTCGGAA 58.445 52.632 0.00 0.00 40.72 4.30
414 436 4.301505 GCAGTGGCATTTCTCGGA 57.698 55.556 0.00 0.00 40.72 4.55
424 446 2.147436 TTTTCGGAAATTGCAGTGGC 57.853 45.000 3.67 0.00 41.68 5.01
425 447 2.470999 CGTTTTTCGGAAATTGCAGTGG 59.529 45.455 3.67 0.00 35.71 4.00
426 448 3.179599 GTCGTTTTTCGGAAATTGCAGTG 59.820 43.478 3.67 0.00 40.32 3.66
427 449 3.181495 TGTCGTTTTTCGGAAATTGCAGT 60.181 39.130 3.67 0.00 40.32 4.40
428 450 3.179599 GTGTCGTTTTTCGGAAATTGCAG 59.820 43.478 3.67 0.00 40.32 4.41
429 451 3.109619 GTGTCGTTTTTCGGAAATTGCA 58.890 40.909 3.67 0.00 40.32 4.08
430 452 2.150424 CGTGTCGTTTTTCGGAAATTGC 59.850 45.455 3.67 0.00 40.32 3.56
431 453 3.609475 TCGTGTCGTTTTTCGGAAATTG 58.391 40.909 3.67 0.00 40.32 2.32
432 454 3.948196 TCGTGTCGTTTTTCGGAAATT 57.052 38.095 3.67 0.00 40.32 1.82
433 455 3.364565 CCATCGTGTCGTTTTTCGGAAAT 60.365 43.478 3.67 0.00 40.32 2.17
434 456 2.032722 CCATCGTGTCGTTTTTCGGAAA 60.033 45.455 0.00 0.00 40.32 3.13
435 457 1.527736 CCATCGTGTCGTTTTTCGGAA 59.472 47.619 0.00 0.00 40.32 4.30
436 458 1.141645 CCATCGTGTCGTTTTTCGGA 58.858 50.000 0.00 0.00 40.32 4.55
437 459 0.165079 CCCATCGTGTCGTTTTTCGG 59.835 55.000 0.00 0.00 40.32 4.30
438 460 0.165079 CCCCATCGTGTCGTTTTTCG 59.835 55.000 0.00 0.00 41.41 3.46
439 461 0.109919 GCCCCATCGTGTCGTTTTTC 60.110 55.000 0.00 0.00 0.00 2.29
440 462 0.820074 TGCCCCATCGTGTCGTTTTT 60.820 50.000 0.00 0.00 0.00 1.94
441 463 1.228003 TGCCCCATCGTGTCGTTTT 60.228 52.632 0.00 0.00 0.00 2.43
442 464 1.671054 CTGCCCCATCGTGTCGTTT 60.671 57.895 0.00 0.00 0.00 3.60
443 465 2.047274 CTGCCCCATCGTGTCGTT 60.047 61.111 0.00 0.00 0.00 3.85
471 494 4.755266 ACTGCCCATCTATAGTTCGTTT 57.245 40.909 0.00 0.00 0.00 3.60
480 503 8.660435 AGTATGTTTAATGTACTGCCCATCTAT 58.340 33.333 0.00 0.00 0.00 1.98
507 530 5.202004 TCATCAGAGAACTAAGGGGACTAC 58.798 45.833 0.00 0.00 42.68 2.73
512 535 5.128919 CCAAATCATCAGAGAACTAAGGGG 58.871 45.833 0.00 0.00 0.00 4.79
552 575 6.157211 CCAAGTCGAGTCAACATTAGTTAGT 58.843 40.000 0.00 0.00 35.85 2.24
553 576 5.577164 CCCAAGTCGAGTCAACATTAGTTAG 59.423 44.000 0.00 0.00 35.85 2.34
604 628 5.971202 GCTTTTTGTACATATGATTGGACCG 59.029 40.000 10.38 0.00 28.61 4.79
608 632 4.437495 CGCGCTTTTTGTACATATGATTGG 59.563 41.667 10.38 0.00 0.00 3.16
707 731 7.921214 GCACACACTGACACTAAGTACATATAT 59.079 37.037 0.00 0.00 0.00 0.86
713 737 3.057734 GGCACACACTGACACTAAGTAC 58.942 50.000 0.00 0.00 0.00 2.73
714 738 2.963101 AGGCACACACTGACACTAAGTA 59.037 45.455 0.00 0.00 0.00 2.24
720 744 6.978343 TTATATTAAGGCACACACTGACAC 57.022 37.500 0.00 0.00 0.00 3.67
725 749 8.574251 TGAATGTTTATATTAAGGCACACACT 57.426 30.769 0.00 0.00 0.00 3.55
748 804 3.455543 TGCAAGAGATATGTCCACCATGA 59.544 43.478 0.00 0.00 34.86 3.07
757 813 1.831106 TGGACGGTGCAAGAGATATGT 59.169 47.619 0.00 0.00 0.00 2.29
766 822 2.577700 ACTTGTAATTGGACGGTGCAA 58.422 42.857 17.41 17.41 30.73 4.08
781 837 2.245287 TGAGGGGGTTGGTTTAACTTGT 59.755 45.455 0.00 0.00 39.31 3.16
824 880 4.700213 CAGGTACACCCTTTGATTTGGTAG 59.300 45.833 0.00 0.00 42.73 3.18
827 883 2.231235 GCAGGTACACCCTTTGATTTGG 59.769 50.000 0.00 0.00 42.73 3.28
879 939 4.831155 ACAGTGGTACTACTTACTTCTGCA 59.169 41.667 9.48 0.00 36.13 4.41
899 998 8.638629 ATTCACCCTAGCTATAGTTACTACAG 57.361 38.462 0.84 0.00 0.00 2.74
941 1049 2.824341 CCTCGGGTGTTGACTACTTACT 59.176 50.000 0.00 0.00 0.00 2.24
946 1054 1.079336 GCCCTCGGGTGTTGACTAC 60.079 63.158 3.54 0.00 37.65 2.73
955 1063 0.907704 TGACAAGTATGCCCTCGGGT 60.908 55.000 3.54 0.00 37.65 5.28
960 1068 3.266772 TGGAGAAATGACAAGTATGCCCT 59.733 43.478 0.00 0.00 0.00 5.19
970 1078 2.512692 CACCCCATGGAGAAATGACA 57.487 50.000 15.22 0.00 34.81 3.58
1029 1137 2.543653 GCGACTTTTGATTGCACCAACT 60.544 45.455 0.58 0.00 0.00 3.16
1058 1166 3.937706 ACCGAATGAAGCAAGAAGAGATG 59.062 43.478 0.00 0.00 0.00 2.90
1111 1219 7.458488 AGCTAGTACTACTGACTATATCTGGGA 59.542 40.741 0.00 0.00 0.00 4.37
1124 1232 5.066634 TCTTGCTTGCTAGCTAGTACTACTG 59.933 44.000 24.76 8.01 46.24 2.74
1148 1256 2.546899 TGGACAACACCTGGCTAGTAT 58.453 47.619 0.00 0.00 31.36 2.12
1219 1330 2.840102 CTCCTCCCCGAAGCCGAT 60.840 66.667 0.00 0.00 38.22 4.18
1254 1365 4.081030 GCCGTCGTCGTCTCGTCA 62.081 66.667 0.71 0.00 35.01 4.35
1276 1387 1.605457 CGTTGGTGTTGCTGCTAGAGA 60.605 52.381 0.00 0.00 0.00 3.10
1278 1389 0.602638 CCGTTGGTGTTGCTGCTAGA 60.603 55.000 0.00 0.00 0.00 2.43
1280 1391 2.258013 GCCGTTGGTGTTGCTGCTA 61.258 57.895 0.00 0.00 0.00 3.49
1282 1393 4.980903 CGCCGTTGGTGTTGCTGC 62.981 66.667 0.00 0.00 0.00 5.25
1310 1421 2.462456 AGAAGAATTGTCAGCGCTCA 57.538 45.000 7.13 0.00 0.00 4.26
1320 1431 7.500559 ATTCCCTTATCGGAAGAAGAAGAATTG 59.499 37.037 4.97 0.00 45.03 2.32
1344 1455 1.279271 CCTTCCTCCTCGTCACCAATT 59.721 52.381 0.00 0.00 0.00 2.32
1440 1551 1.756561 GAAGGAGAGGGCGCTCTCT 60.757 63.158 42.07 39.21 46.61 3.10
1561 1672 9.186323 CTTGAATCTACGGAGAATTGTACATAG 57.814 37.037 0.00 0.00 34.61 2.23
1564 1675 5.810587 GCTTGAATCTACGGAGAATTGTACA 59.189 40.000 0.00 0.00 34.61 2.90
1583 1694 3.181451 ACAGATGTCCAAACTGAGCTTGA 60.181 43.478 0.00 0.00 35.85 3.02
1592 1703 5.705441 TGAGTTTCCATACAGATGTCCAAAC 59.295 40.000 0.00 0.00 31.47 2.93
1660 1771 5.288015 CAGCTCTTGATCTTCATCGTGTAT 58.712 41.667 0.00 0.00 0.00 2.29
1708 1819 3.433173 GGCCGTATTTCCTCCACTTGTAT 60.433 47.826 0.00 0.00 0.00 2.29
1781 1899 8.010697 TGAGAGATAGGTTGATATAGGGTGAAA 58.989 37.037 0.00 0.00 0.00 2.69
1782 1900 7.535738 TGAGAGATAGGTTGATATAGGGTGAA 58.464 38.462 0.00 0.00 0.00 3.18
1783 1901 7.103745 TGAGAGATAGGTTGATATAGGGTGA 57.896 40.000 0.00 0.00 0.00 4.02
1784 1902 7.147759 CCATGAGAGATAGGTTGATATAGGGTG 60.148 44.444 0.00 0.00 0.00 4.61
1785 1903 6.900186 CCATGAGAGATAGGTTGATATAGGGT 59.100 42.308 0.00 0.00 0.00 4.34
1786 1904 6.183360 GCCATGAGAGATAGGTTGATATAGGG 60.183 46.154 0.00 0.00 0.00 3.53
1911 2134 5.453057 GCTGTCTCTCATATGTCAACTGGAT 60.453 44.000 1.90 0.00 0.00 3.41
1983 2210 0.580578 GCTAGCTGCGATGTCATGTG 59.419 55.000 7.70 0.00 0.00 3.21
2060 2287 0.539051 GCTAGCTTGCTCTTCCTCCA 59.461 55.000 13.17 0.00 0.00 3.86
2061 2288 0.829990 AGCTAGCTTGCTCTTCCTCC 59.170 55.000 17.30 0.00 39.34 4.30
2158 2386 4.585162 GCCCATGACTAGCTATATACGGAT 59.415 45.833 0.00 0.00 0.00 4.18
2167 2395 5.429681 TTAACTTTGCCCATGACTAGCTA 57.570 39.130 0.00 0.00 0.00 3.32
2168 2396 2.887151 AACTTTGCCCATGACTAGCT 57.113 45.000 0.00 0.00 0.00 3.32
2169 2397 4.260784 CGATTAACTTTGCCCATGACTAGC 60.261 45.833 0.00 0.00 0.00 3.42
2170 2398 4.260784 GCGATTAACTTTGCCCATGACTAG 60.261 45.833 0.00 0.00 0.00 2.57
2174 2402 2.423185 CAGCGATTAACTTTGCCCATGA 59.577 45.455 0.00 0.00 0.00 3.07
2180 2408 1.585214 GCATGCAGCGATTAACTTTGC 59.415 47.619 14.21 0.00 35.42 3.68
2193 2421 1.549203 AACCCCTTACTTGCATGCAG 58.451 50.000 21.50 16.80 0.00 4.41
2235 2470 0.817634 GCAAGCACACACACCTACCA 60.818 55.000 0.00 0.00 0.00 3.25
2378 2613 9.528018 AATTTACAAAAACTACACATTCCACTG 57.472 29.630 0.00 0.00 0.00 3.66
2420 2658 8.825745 GCAATTTAGGTGACTGAAATTTTCAAA 58.174 29.630 12.62 2.86 43.88 2.69
2421 2659 7.984050 TGCAATTTAGGTGACTGAAATTTTCAA 59.016 29.630 12.62 0.00 43.88 2.69
2424 2662 6.420604 CGTGCAATTTAGGTGACTGAAATTTT 59.579 34.615 0.00 0.00 43.88 1.82
2430 2668 1.804151 GCGTGCAATTTAGGTGACTGA 59.196 47.619 0.00 0.00 43.88 3.41
2496 2739 5.237344 CACCGCCAAAATTAACCAAATGAAA 59.763 36.000 0.00 0.00 0.00 2.69
2499 2746 3.434984 CCACCGCCAAAATTAACCAAATG 59.565 43.478 0.00 0.00 0.00 2.32
2503 2753 1.705873 ACCACCGCCAAAATTAACCA 58.294 45.000 0.00 0.00 0.00 3.67
2505 2755 6.623486 AGTTATTACCACCGCCAAAATTAAC 58.377 36.000 0.00 0.00 0.00 2.01
2507 2757 7.934855 TTAGTTATTACCACCGCCAAAATTA 57.065 32.000 0.00 0.00 0.00 1.40
2516 2766 6.455913 CCACGTCAATTTAGTTATTACCACCG 60.456 42.308 0.00 0.00 0.00 4.94
2714 2972 0.112995 TTGGAGCTTGAGGCAATGGT 59.887 50.000 0.00 0.00 44.79 3.55
2717 2975 2.444421 CTTCTTGGAGCTTGAGGCAAT 58.556 47.619 0.00 0.00 44.79 3.56
2718 2976 1.901591 CTTCTTGGAGCTTGAGGCAA 58.098 50.000 0.00 0.00 44.79 4.52
2719 2977 0.607489 GCTTCTTGGAGCTTGAGGCA 60.607 55.000 0.00 0.00 44.79 4.75
2773 3034 1.179174 TCTCGTGGTGGGAGTCTGTG 61.179 60.000 0.00 0.00 33.26 3.66
2790 3051 1.344953 TGTTGTCACAGGGGTGCTCT 61.345 55.000 0.00 0.00 44.87 4.09
2804 3065 2.665185 GAGCGGCGAGGTTGTTGT 60.665 61.111 12.98 0.00 0.00 3.32
2851 3112 4.731612 CTGTCGCCGCTGCTGTCT 62.732 66.667 0.00 0.00 34.43 3.41
2930 3191 2.565394 CGCCGTCGAACAGATACGC 61.565 63.158 0.00 0.00 38.10 4.42
2998 3259 1.692042 CATGTCCTCCAGGAGCCCT 60.692 63.158 11.57 0.00 46.49 5.19
3034 3295 1.080093 CGAGTTGCAAGACGGCCTA 60.080 57.895 14.72 0.00 0.00 3.93
3035 3296 2.357517 CGAGTTGCAAGACGGCCT 60.358 61.111 14.72 1.45 0.00 5.19
3115 3376 2.202756 GACGATGTGGAGGGCGAC 60.203 66.667 0.00 0.00 0.00 5.19
3118 3379 3.771160 ACGGACGATGTGGAGGGC 61.771 66.667 0.00 0.00 0.00 5.19
3127 3388 3.285371 GTCCAGGACACGGACGAT 58.715 61.111 15.43 0.00 43.36 3.73
3195 3456 5.047872 TGGACAAATTGACACTACGCTACTA 60.048 40.000 0.00 0.00 0.00 1.82
3214 3475 3.733443 ATTCGATCATCGTGATGGACA 57.267 42.857 7.00 5.46 40.49 4.02
3348 3645 4.399303 CCTTATTTTGGGAGTAAGCCACAG 59.601 45.833 0.00 0.00 0.00 3.66
3377 3674 9.020813 CATACTATACTCACACAACACATACAC 57.979 37.037 0.00 0.00 0.00 2.90
3487 3793 5.782331 ACACATATACTACATCTGCCATCCT 59.218 40.000 0.00 0.00 0.00 3.24
3511 3817 8.830580 GCTTCTCTCACAATTATATTTGCTACA 58.169 33.333 7.17 0.00 0.00 2.74
3529 3835 4.414337 ACATATCCCACAAGCTTCTCTC 57.586 45.455 0.00 0.00 0.00 3.20
3532 3838 4.965532 AGACTACATATCCCACAAGCTTCT 59.034 41.667 0.00 0.00 0.00 2.85
3536 3842 4.408182 ACAGACTACATATCCCACAAGC 57.592 45.455 0.00 0.00 0.00 4.01
3537 3843 7.556844 AGTTAACAGACTACATATCCCACAAG 58.443 38.462 8.61 0.00 0.00 3.16
3539 3845 7.490657 AAGTTAACAGACTACATATCCCACA 57.509 36.000 8.61 0.00 0.00 4.17
3554 3860 4.761739 TCATGCCCAGAGAAAAGTTAACAG 59.238 41.667 8.61 0.00 0.00 3.16
3572 3878 3.269178 CCTGAAGAGGAGAAACTCATGC 58.731 50.000 0.00 0.00 42.93 4.06
3723 4030 4.320935 CGCTAACTTAATGCCCAAACAAGT 60.321 41.667 0.00 0.00 0.00 3.16
3782 4089 1.000145 GCTACGGTCTTGCAGTAAGC 59.000 55.000 0.00 0.00 45.96 3.09
3824 4133 3.315470 CGCTTGAGGTGACACTAGCTATA 59.685 47.826 5.39 0.00 44.67 1.31
3893 4202 0.605589 ACTGGTCCTCAGAAGCTTCG 59.394 55.000 20.43 15.04 46.18 3.79
3947 4256 7.784550 TCTCAATTCCTTCCCCATTTAATAAGG 59.215 37.037 0.00 0.00 38.44 2.69
3970 4279 4.332268 GTCATCAGAGCCTTCACATTTCTC 59.668 45.833 0.00 0.00 0.00 2.87
4058 4367 3.319405 CGATATCAACCTAGGCTCACACT 59.681 47.826 9.30 0.00 0.00 3.55
4065 4374 4.323553 ACTCAACGATATCAACCTAGGC 57.676 45.455 9.30 0.00 0.00 3.93
4066 4375 5.050490 CCAACTCAACGATATCAACCTAGG 58.950 45.833 7.41 7.41 0.00 3.02
4106 4415 9.310449 GGACATGATAGATTAAGGTAGGACTAA 57.690 37.037 0.00 0.00 0.00 2.24
4108 4417 7.453126 CAGGACATGATAGATTAAGGTAGGACT 59.547 40.741 0.00 0.00 0.00 3.85
4109 4418 7.607250 CAGGACATGATAGATTAAGGTAGGAC 58.393 42.308 0.00 0.00 0.00 3.85
4110 4419 6.211584 GCAGGACATGATAGATTAAGGTAGGA 59.788 42.308 0.00 0.00 0.00 2.94
4111 4420 6.014242 TGCAGGACATGATAGATTAAGGTAGG 60.014 42.308 0.00 0.00 0.00 3.18
4112 4421 6.997655 TGCAGGACATGATAGATTAAGGTAG 58.002 40.000 0.00 0.00 0.00 3.18
4113 4422 6.994421 TGCAGGACATGATAGATTAAGGTA 57.006 37.500 0.00 0.00 0.00 3.08
4114 4423 5.894298 TGCAGGACATGATAGATTAAGGT 57.106 39.130 0.00 0.00 0.00 3.50
4115 4424 5.471456 GGTTGCAGGACATGATAGATTAAGG 59.529 44.000 0.00 0.00 0.00 2.69
4116 4425 6.017605 GTGGTTGCAGGACATGATAGATTAAG 60.018 42.308 0.00 0.00 0.00 1.85
4117 4426 5.822519 GTGGTTGCAGGACATGATAGATTAA 59.177 40.000 0.00 0.00 0.00 1.40
4118 4427 5.130975 AGTGGTTGCAGGACATGATAGATTA 59.869 40.000 0.00 0.00 0.00 1.75
4119 4428 4.080129 AGTGGTTGCAGGACATGATAGATT 60.080 41.667 0.00 0.00 0.00 2.40
4120 4429 3.457380 AGTGGTTGCAGGACATGATAGAT 59.543 43.478 0.00 0.00 0.00 1.98
4121 4430 2.840038 AGTGGTTGCAGGACATGATAGA 59.160 45.455 0.00 0.00 0.00 1.98
4122 4431 3.201290 GAGTGGTTGCAGGACATGATAG 58.799 50.000 0.00 0.00 0.00 2.08
4185 4494 9.803315 AACACATAAAAGAAAGAAGAAGAAACC 57.197 29.630 0.00 0.00 0.00 3.27
4233 4542 8.668353 AGATGAAAAAGAAAAGAAAAGGCAAAC 58.332 29.630 0.00 0.00 0.00 2.93
4234 4543 8.791327 AGATGAAAAAGAAAAGAAAAGGCAAA 57.209 26.923 0.00 0.00 0.00 3.68
4282 4592 8.450964 AGACGAAAAATGTCCAATGTGTATTAG 58.549 33.333 0.00 0.00 37.04 1.73
4295 4605 8.783999 TCTTCGATCTATAGACGAAAAATGTC 57.216 34.615 25.85 10.87 43.48 3.06
4435 4745 9.539825 AGTGTAAAAATGTGTTCATGCAATTTA 57.460 25.926 0.00 0.00 34.19 1.40
4589 4902 9.744468 ACAAGTTTAAAGATTTGTTGATGGTAC 57.256 29.630 6.78 0.00 30.05 3.34
4592 4905 8.870160 TCACAAGTTTAAAGATTTGTTGATGG 57.130 30.769 8.97 1.54 31.84 3.51
4631 4944 4.668289 ACCAATCAAAAGTTGTTCGTGAC 58.332 39.130 0.00 0.00 0.00 3.67
4666 4979 7.862873 GGGAGTGTAAAACTTTTGATCTCTTTG 59.137 37.037 0.00 0.00 40.07 2.77
4672 4985 5.768164 TCCAGGGAGTGTAAAACTTTTGATC 59.232 40.000 0.00 0.00 40.07 2.92
4711 5024 9.921637 AACTTAAGTTTCAAAACAGTTCATCAA 57.078 25.926 15.22 0.00 41.30 2.57
4788 5105 3.641436 CCAAACAGCCCTTTAGTTCCTTT 59.359 43.478 0.00 0.00 0.00 3.11
4794 5111 3.573967 CACAATCCAAACAGCCCTTTAGT 59.426 43.478 0.00 0.00 0.00 2.24
4795 5112 3.826157 TCACAATCCAAACAGCCCTTTAG 59.174 43.478 0.00 0.00 0.00 1.85
4799 5116 2.610438 ATCACAATCCAAACAGCCCT 57.390 45.000 0.00 0.00 0.00 5.19
4827 5144 5.184864 CCAACTTAGGTGTGGCAAAATATGA 59.815 40.000 0.00 0.00 0.00 2.15
4833 5150 2.303175 GACCAACTTAGGTGTGGCAAA 58.697 47.619 0.00 0.00 43.38 3.68
4847 5321 2.956333 ACCTTAGGCAAGTTTGACCAAC 59.044 45.455 0.00 0.00 36.67 3.77
4878 5352 4.425180 TGACCAACTTAGCCACACTTTA 57.575 40.909 0.00 0.00 0.00 1.85
4883 5357 2.685897 GTGTTTGACCAACTTAGCCACA 59.314 45.455 0.00 0.00 36.21 4.17
4891 5365 5.106317 CGCCAATAATAGTGTTTGACCAACT 60.106 40.000 0.00 0.00 36.21 3.16
4893 5367 5.004448 TCGCCAATAATAGTGTTTGACCAA 58.996 37.500 0.00 0.00 0.00 3.67
4894 5368 4.580868 TCGCCAATAATAGTGTTTGACCA 58.419 39.130 0.00 0.00 0.00 4.02
4895 5369 4.035208 CCTCGCCAATAATAGTGTTTGACC 59.965 45.833 0.00 0.00 0.00 4.02
4896 5370 4.495844 GCCTCGCCAATAATAGTGTTTGAC 60.496 45.833 0.00 0.00 0.00 3.18
4897 5371 3.625764 GCCTCGCCAATAATAGTGTTTGA 59.374 43.478 0.00 0.00 0.00 2.69
4898 5372 3.376859 TGCCTCGCCAATAATAGTGTTTG 59.623 43.478 0.00 0.00 0.00 2.93
4900 5374 3.118408 TCTGCCTCGCCAATAATAGTGTT 60.118 43.478 0.00 0.00 0.00 3.32
4902 5376 2.802816 GTCTGCCTCGCCAATAATAGTG 59.197 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.