Multiple sequence alignment - TraesCS1B01G234900

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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 TraesCS1B01G234900 chr1B 100.000 3184 0 0 1 3184 420993227 420996410 0.000000e+00 5880
1 TraesCS1B01G234900 chr1D 88.830 3017 132 70 89 3025 311256259 311259150 0.000000e+00 3515
2 TraesCS1B01G234900 chr1D 84.028 144 9 9 3016 3146 311342261 311342403 3.330000e-25 126
3 TraesCS1B01G234900 chr1A 89.773 1144 43 26 612 1724 391235215 391236315 0.000000e+00 1397
4 TraesCS1B01G234900 chr1A 86.326 724 58 23 1767 2462 391236325 391237035 0.000000e+00 750
5 TraesCS1B01G234900 chr1A 85.658 509 33 19 2666 3147 391239737 391240232 1.710000e-137 499
6 TraesCS1B01G234900 chr1A 85.856 403 29 18 89 465 391234822 391235222 1.380000e-108 403
7 TraesCS1B01G234900 chr2A 92.885 253 17 1 1023 1275 104770702 104770451 1.800000e-97 366
8 TraesCS1B01G234900 chr4D 74.642 698 118 41 1063 1721 497915949 497915272 1.470000e-63 254
9 TraesCS1B01G234900 chr6A 95.082 122 6 0 1085 1206 20336243 20336122 3.240000e-45 193
10 TraesCS1B01G234900 chr3A 93.443 122 8 0 1085 1206 101958811 101958690 7.020000e-42 182
11 TraesCS1B01G234900 chr4A 95.238 105 5 0 1446 1550 36622875 36622771 1.960000e-37 167
12 TraesCS1B01G234900 chr4A 82.803 157 17 8 2309 2462 145036288 145036139 7.170000e-27 132
13 TraesCS1B01G234900 chr6B 92.381 105 3 3 1079 1182 25967268 25967168 9.210000e-31 145


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 TraesCS1B01G234900 chr1B 420993227 420996410 3183 False 5880.00 5880 100.00000 1 3184 1 chr1B.!!$F1 3183
1 TraesCS1B01G234900 chr1D 311256259 311259150 2891 False 3515.00 3515 88.83000 89 3025 1 chr1D.!!$F1 2936
2 TraesCS1B01G234900 chr1A 391234822 391240232 5410 False 762.25 1397 86.90325 89 3147 4 chr1A.!!$F1 3058
3 TraesCS1B01G234900 chr4D 497915272 497915949 677 True 254.00 254 74.64200 1063 1721 1 chr4D.!!$R1 658

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
836 890 0.036022 GCTGCCTCCATCTATCCACC 59.964 60.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2811 5554 0.321653 ATCTGCACTTCCACGGGTTC 60.322 55.0 0.0 0.0 0.0 3.62 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
18 19 3.733709 AACTGGGAAGGAACTGCTG 57.266 52.632 0.00 0.00 40.86 4.41
19 20 0.111253 AACTGGGAAGGAACTGCTGG 59.889 55.000 0.00 0.00 40.86 4.85
20 21 1.676967 CTGGGAAGGAACTGCTGGC 60.677 63.158 0.00 0.00 40.86 4.85
21 22 2.747855 GGGAAGGAACTGCTGGCG 60.748 66.667 0.00 0.00 40.86 5.69
22 23 2.747855 GGAAGGAACTGCTGGCGG 60.748 66.667 0.00 0.00 40.86 6.13
23 24 2.032681 GAAGGAACTGCTGGCGGT 59.967 61.111 0.69 0.69 40.86 5.68
24 25 1.600916 GAAGGAACTGCTGGCGGTT 60.601 57.895 18.14 18.14 46.94 4.44
25 26 0.321298 GAAGGAACTGCTGGCGGTTA 60.321 55.000 18.12 0.00 44.62 2.85
26 27 0.328258 AAGGAACTGCTGGCGGTTAT 59.672 50.000 18.12 8.74 44.62 1.89
27 28 0.107654 AGGAACTGCTGGCGGTTATC 60.108 55.000 18.12 13.57 44.62 1.75
28 29 1.429148 GGAACTGCTGGCGGTTATCG 61.429 60.000 18.12 0.00 44.62 2.92
29 30 1.429148 GAACTGCTGGCGGTTATCGG 61.429 60.000 18.12 0.00 44.62 4.18
30 31 2.588877 CTGCTGGCGGTTATCGGG 60.589 66.667 0.00 0.00 39.69 5.14
31 32 4.169696 TGCTGGCGGTTATCGGGG 62.170 66.667 0.00 0.00 39.69 5.73
37 38 4.963428 CGGTTATCGGGGCGCCTC 62.963 72.222 28.56 24.23 34.75 4.70
38 39 4.620937 GGTTATCGGGGCGCCTCC 62.621 72.222 28.56 23.91 0.00 4.30
39 40 3.857038 GTTATCGGGGCGCCTCCA 61.857 66.667 28.56 12.77 36.21 3.86
40 41 3.857038 TTATCGGGGCGCCTCCAC 61.857 66.667 28.56 9.46 36.21 4.02
51 52 4.100084 CCTCCACATGGGCGCTGA 62.100 66.667 7.64 0.00 36.21 4.26
52 53 2.821366 CTCCACATGGGCGCTGAC 60.821 66.667 7.64 0.00 36.21 3.51
53 54 4.758251 TCCACATGGGCGCTGACG 62.758 66.667 7.64 0.00 44.07 4.35
54 55 4.758251 CCACATGGGCGCTGACGA 62.758 66.667 7.64 0.00 43.93 4.20
76 77 4.125695 GCGTACCGGCGGACTCTT 62.126 66.667 35.78 12.77 0.00 2.85
77 78 2.101770 CGTACCGGCGGACTCTTC 59.898 66.667 35.78 13.85 0.00 2.87
78 79 2.493501 GTACCGGCGGACTCTTCC 59.506 66.667 35.78 7.66 38.77 3.46
79 80 2.050934 GTACCGGCGGACTCTTCCT 61.051 63.158 35.78 10.16 40.23 3.36
80 81 2.050350 TACCGGCGGACTCTTCCTG 61.050 63.158 35.78 1.17 40.23 3.86
81 82 2.776370 TACCGGCGGACTCTTCCTGT 62.776 60.000 35.78 8.45 40.23 4.00
82 83 2.657237 CGGCGGACTCTTCCTGTT 59.343 61.111 0.00 0.00 40.23 3.16
83 84 1.446272 CGGCGGACTCTTCCTGTTC 60.446 63.158 0.00 0.00 40.23 3.18
84 85 1.079057 GGCGGACTCTTCCTGTTCC 60.079 63.158 0.00 0.00 40.23 3.62
85 86 1.671742 GCGGACTCTTCCTGTTCCA 59.328 57.895 0.00 0.00 40.23 3.53
86 87 0.390472 GCGGACTCTTCCTGTTCCAG 60.390 60.000 0.00 0.00 40.23 3.86
87 88 1.257743 CGGACTCTTCCTGTTCCAGA 58.742 55.000 0.00 0.00 40.23 3.86
94 95 2.301296 TCTTCCTGTTCCAGAAGAGCTG 59.699 50.000 0.00 0.00 44.49 4.24
158 161 1.629013 GCCGTGCCAATTTAAGCTTC 58.371 50.000 0.00 0.00 0.00 3.86
238 246 0.668401 GGTAACAGACGTGTTCCGGG 60.668 60.000 0.00 0.00 43.88 5.73
303 324 0.869730 AACGTACGCCATGTGTTTCC 59.130 50.000 16.72 0.00 0.00 3.13
335 356 1.401905 CCGGCCTGCTTTAATCACTTC 59.598 52.381 0.00 0.00 0.00 3.01
348 369 7.737311 GCTTTAATCACTTCGCAATTCTTTTTG 59.263 33.333 0.00 0.00 0.00 2.44
349 370 8.641499 TTTAATCACTTCGCAATTCTTTTTGT 57.359 26.923 0.00 0.00 0.00 2.83
371 395 7.297936 TGTAATATAATGCCCGAAGAAGAGA 57.702 36.000 0.00 0.00 0.00 3.10
411 435 3.245518 TCCCACATTGAGACATACGTG 57.754 47.619 0.00 0.00 0.00 4.49
428 463 1.439679 GTGCAAGAAAGGGTCGTAGG 58.560 55.000 0.00 0.00 0.00 3.18
429 464 0.321298 TGCAAGAAAGGGTCGTAGGC 60.321 55.000 0.00 0.00 0.00 3.93
430 465 0.036294 GCAAGAAAGGGTCGTAGGCT 60.036 55.000 0.00 0.00 0.00 4.58
431 466 2.007547 GCAAGAAAGGGTCGTAGGCTC 61.008 57.143 0.00 0.00 0.00 4.70
432 467 0.531200 AAGAAAGGGTCGTAGGCTCG 59.469 55.000 0.00 0.00 38.32 5.03
433 468 0.611340 AGAAAGGGTCGTAGGCTCGT 60.611 55.000 0.00 0.00 38.32 4.18
434 469 1.098050 GAAAGGGTCGTAGGCTCGTA 58.902 55.000 0.00 0.00 38.32 3.43
435 470 1.065251 GAAAGGGTCGTAGGCTCGTAG 59.935 57.143 0.00 0.00 38.32 3.51
436 471 1.382692 AAGGGTCGTAGGCTCGTAGC 61.383 60.000 0.00 0.00 38.32 3.58
467 503 1.204704 TCTTCACCTACACGATGCTGG 59.795 52.381 0.00 0.00 0.00 4.85
468 504 0.973632 TTCACCTACACGATGCTGGT 59.026 50.000 0.00 0.00 0.00 4.00
469 505 0.246360 TCACCTACACGATGCTGGTG 59.754 55.000 16.27 16.27 41.91 4.17
471 507 1.134699 CACCTACACGATGCTGGTGAT 60.135 52.381 16.90 0.00 42.62 3.06
472 508 1.555075 ACCTACACGATGCTGGTGATT 59.445 47.619 8.90 0.00 38.73 2.57
475 511 0.740868 ACACGATGCTGGTGATTCGG 60.741 55.000 8.90 0.00 38.73 4.30
477 513 0.740868 ACGATGCTGGTGATTCGGTG 60.741 55.000 0.00 0.00 35.98 4.94
478 514 1.431488 CGATGCTGGTGATTCGGTGG 61.431 60.000 0.00 0.00 0.00 4.61
479 515 1.077501 ATGCTGGTGATTCGGTGGG 60.078 57.895 0.00 0.00 0.00 4.61
480 516 3.134127 GCTGGTGATTCGGTGGGC 61.134 66.667 0.00 0.00 0.00 5.36
481 517 2.350895 CTGGTGATTCGGTGGGCA 59.649 61.111 0.00 0.00 0.00 5.36
482 518 1.303236 CTGGTGATTCGGTGGGCAA 60.303 57.895 0.00 0.00 0.00 4.52
483 519 0.680921 CTGGTGATTCGGTGGGCAAT 60.681 55.000 0.00 0.00 0.00 3.56
484 520 0.251564 TGGTGATTCGGTGGGCAATT 60.252 50.000 0.00 0.00 0.00 2.32
485 521 0.173255 GGTGATTCGGTGGGCAATTG 59.827 55.000 0.00 0.00 0.00 2.32
486 522 0.173255 GTGATTCGGTGGGCAATTGG 59.827 55.000 7.72 0.00 0.00 3.16
487 523 0.969917 TGATTCGGTGGGCAATTGGG 60.970 55.000 7.72 0.00 0.00 4.12
488 524 1.675720 GATTCGGTGGGCAATTGGGG 61.676 60.000 7.72 0.00 0.00 4.96
489 525 2.161713 ATTCGGTGGGCAATTGGGGA 62.162 55.000 7.72 0.00 0.00 4.81
490 526 2.755469 CGGTGGGCAATTGGGGAG 60.755 66.667 7.72 0.00 0.00 4.30
491 527 2.445155 GGTGGGCAATTGGGGAGT 59.555 61.111 7.72 0.00 0.00 3.85
492 528 1.682344 GGTGGGCAATTGGGGAGTC 60.682 63.158 7.72 0.00 0.00 3.36
493 529 1.384191 GTGGGCAATTGGGGAGTCT 59.616 57.895 7.72 0.00 0.00 3.24
494 530 0.681243 GTGGGCAATTGGGGAGTCTC 60.681 60.000 7.72 0.00 0.00 3.36
495 531 0.846427 TGGGCAATTGGGGAGTCTCT 60.846 55.000 7.72 0.00 0.00 3.10
496 532 0.106967 GGGCAATTGGGGAGTCTCTC 60.107 60.000 7.72 0.00 0.00 3.20
497 533 0.462759 GGCAATTGGGGAGTCTCTCG 60.463 60.000 7.72 0.00 0.00 4.04
524 560 2.029020 GGGGCAGAACATTTTTCCTCAC 60.029 50.000 0.00 0.00 0.00 3.51
526 562 2.029020 GGCAGAACATTTTTCCTCACCC 60.029 50.000 0.00 0.00 0.00 4.61
559 595 1.346479 TTTCCCAAGACCCACGACCA 61.346 55.000 0.00 0.00 0.00 4.02
580 616 2.116827 TGTCGGGTTCAACACAAGTT 57.883 45.000 0.00 0.00 38.88 2.66
803 850 2.622903 TAAACCATCTCGCCGGCTCG 62.623 60.000 26.68 15.32 0.00 5.03
836 890 0.036022 GCTGCCTCCATCTATCCACC 59.964 60.000 0.00 0.00 0.00 4.61
921 984 1.051556 TCACCACCACACCACAGCTA 61.052 55.000 0.00 0.00 0.00 3.32
971 1034 2.819667 CGGACTGCTGTCTGTCTTG 58.180 57.895 21.08 4.06 42.90 3.02
975 1038 1.301244 CTGCTGTCTGTCTTGGCGT 60.301 57.895 0.00 0.00 0.00 5.68
981 1044 2.281070 CTGTCTTGGCGTGCAGGT 60.281 61.111 8.40 0.00 0.00 4.00
1011 1074 0.322456 CGTGGGGCATGGAGAAGAAA 60.322 55.000 0.00 0.00 0.00 2.52
1359 1428 5.542635 TGAGTAGAGTACCCAGATTGTGTTT 59.457 40.000 0.00 0.00 0.00 2.83
1364 1433 5.998363 AGAGTACCCAGATTGTGTTTTTCTC 59.002 40.000 0.00 0.00 0.00 2.87
1735 1843 2.577059 CTCGCCACCTCGCCTTTA 59.423 61.111 0.00 0.00 0.00 1.85
1754 1862 5.411669 CCTTTACTTCTCCGTAAATTGCACT 59.588 40.000 0.00 0.00 38.33 4.40
1756 1864 2.484264 ACTTCTCCGTAAATTGCACTGC 59.516 45.455 0.00 0.00 0.00 4.40
1764 1872 2.684001 AAATTGCACTGCCATCCATG 57.316 45.000 0.00 0.00 0.00 3.66
1804 1912 6.841286 CGTTTGCGTGATGAAAGATAATACTC 59.159 38.462 0.00 0.00 0.00 2.59
1806 1914 9.031360 GTTTGCGTGATGAAAGATAATACTCTA 57.969 33.333 0.00 0.00 0.00 2.43
1809 1917 9.063615 TGCGTGATGAAAGATAATACTCTACTA 57.936 33.333 0.00 0.00 0.00 1.82
1827 1935 0.533531 TACTATCTCGCCGAGCCGAA 60.534 55.000 9.77 0.00 36.72 4.30
1934 2048 3.541632 GATTCCCTCGCCAAGTCATTAA 58.458 45.455 0.00 0.00 0.00 1.40
1960 2074 2.162681 AGCTGCCGAAATGTTTAAGCT 58.837 42.857 0.00 0.00 34.80 3.74
1972 2086 7.686938 CGAAATGTTTAAGCTAAAAGGAGTACG 59.313 37.037 0.00 0.00 0.00 3.67
1973 2087 5.851047 TGTTTAAGCTAAAAGGAGTACGC 57.149 39.130 0.00 0.00 0.00 4.42
1974 2088 5.299148 TGTTTAAGCTAAAAGGAGTACGCA 58.701 37.500 0.00 0.00 0.00 5.24
1975 2089 5.178067 TGTTTAAGCTAAAAGGAGTACGCAC 59.822 40.000 0.00 0.00 0.00 5.34
1976 2090 3.679824 AAGCTAAAAGGAGTACGCACT 57.320 42.857 0.00 0.00 37.87 4.40
1977 2091 4.796038 AAGCTAAAAGGAGTACGCACTA 57.204 40.909 0.00 0.00 34.21 2.74
1979 2093 5.340439 AGCTAAAAGGAGTACGCACTATT 57.660 39.130 0.00 0.00 34.21 1.73
1980 2094 5.349809 AGCTAAAAGGAGTACGCACTATTC 58.650 41.667 0.00 0.00 34.21 1.75
1990 2104 6.911511 GGAGTACGCACTATTCTACTAACAAG 59.088 42.308 0.00 0.00 34.21 3.16
1992 2106 5.909621 ACGCACTATTCTACTAACAAGGA 57.090 39.130 0.00 0.00 0.00 3.36
1993 2107 6.276832 ACGCACTATTCTACTAACAAGGAA 57.723 37.500 0.00 0.00 0.00 3.36
1994 2108 6.694447 ACGCACTATTCTACTAACAAGGAAA 58.306 36.000 0.00 0.00 0.00 3.13
1995 2109 6.812160 ACGCACTATTCTACTAACAAGGAAAG 59.188 38.462 0.00 0.00 0.00 2.62
1996 2110 6.812160 CGCACTATTCTACTAACAAGGAAAGT 59.188 38.462 0.00 0.00 0.00 2.66
2053 2167 2.224523 ACTCTGCACCGGATGAGAAAAA 60.225 45.455 9.46 0.00 0.00 1.94
2073 2187 9.741647 AGAAAAACAGAGAGCTTTTATTTTCTG 57.258 29.630 17.47 11.51 41.61 3.02
2074 2188 9.736023 GAAAAACAGAGAGCTTTTATTTTCTGA 57.264 29.630 6.33 0.00 36.46 3.27
2203 2319 4.380531 TGACATGGTGTTCTCAACTTCTC 58.619 43.478 0.00 0.00 31.63 2.87
2307 2437 1.202879 TGAGGTCCATCGGTGCTTTTT 60.203 47.619 0.00 0.00 0.00 1.94
2337 2475 8.554490 AGTGGAGATACTGTAAATATGGAACT 57.446 34.615 0.00 0.00 0.00 3.01
2351 2489 1.070134 TGGAACTGTCGTGCTTAGCTT 59.930 47.619 5.60 0.00 0.00 3.74
2364 2502 0.828677 TTAGCTTAGTTCGGCCTCCC 59.171 55.000 0.00 0.00 0.00 4.30
2375 2513 2.414594 GCCTCCCGCAATGCAATC 59.585 61.111 5.91 0.00 37.47 2.67
2428 2569 2.529151 CACCTTGTTTTGTGTGCTCAC 58.471 47.619 11.94 11.94 44.08 3.51
2433 2574 2.288666 TGTTTTGTGTGCTCACTCTCC 58.711 47.619 18.85 6.41 44.14 3.71
2478 5172 7.256368 GCCTTGCTTATAGTAGAGGTCCTATTT 60.256 40.741 0.00 0.00 0.00 1.40
2542 5237 3.379688 GGAGGAGGAAAATTCAGTGATGC 59.620 47.826 0.00 0.00 0.00 3.91
2549 5244 5.591877 AGGAAAATTCAGTGATGCACCTATC 59.408 40.000 0.00 0.00 34.49 2.08
2594 5289 2.349532 CGCTGGAGAAGTTTTCGGAAAC 60.350 50.000 11.58 11.58 44.35 2.78
2613 5308 1.202313 ACGCCGTAGAAGATTCTGCTC 60.202 52.381 0.00 0.00 37.71 4.26
2620 5315 3.172229 AGAAGATTCTGCTCCTAACGC 57.828 47.619 0.00 0.00 35.89 4.84
2632 5327 3.437049 GCTCCTAACGCTTCAGACAAAAT 59.563 43.478 0.00 0.00 0.00 1.82
2655 5371 1.762419 TCGACGACGAAAACTGAAGG 58.238 50.000 7.68 0.00 45.74 3.46
2742 5485 0.793250 GAGTTCAGAAACGAGCCAGC 59.207 55.000 0.00 0.00 40.48 4.85
2758 5501 0.869454 CAGCGTTTTCAAAGCGGCAA 60.869 50.000 8.55 0.00 35.78 4.52
2796 5539 2.586357 GTCGGGCGAGCCTCATTC 60.586 66.667 14.33 0.00 36.10 2.67
2808 5551 2.125147 TCATTCGCCGAGGCCAAG 60.125 61.111 5.01 0.00 37.98 3.61
2809 5552 2.436646 CATTCGCCGAGGCCAAGT 60.437 61.111 5.01 0.00 37.98 3.16
2810 5553 2.436646 ATTCGCCGAGGCCAAGTG 60.437 61.111 5.01 0.00 37.98 3.16
2811 5554 3.976701 ATTCGCCGAGGCCAAGTGG 62.977 63.158 5.01 1.16 37.98 4.00
2813 5556 4.697756 CGCCGAGGCCAAGTGGAA 62.698 66.667 5.01 0.00 37.98 3.53
2814 5557 3.056328 GCCGAGGCCAAGTGGAAC 61.056 66.667 5.01 0.00 37.39 3.62
2815 5558 2.359975 CCGAGGCCAAGTGGAACC 60.360 66.667 5.01 0.00 37.80 3.62
2816 5559 2.359975 CGAGGCCAAGTGGAACCC 60.360 66.667 5.01 0.00 37.80 4.11
2903 5646 3.450115 GGGGACGTGCGAGCTACT 61.450 66.667 0.00 0.00 0.00 2.57
2999 5760 3.743396 ACTTGCACGCTTTTCTAGAAGAG 59.257 43.478 16.76 16.76 33.38 2.85
3012 5773 3.880490 TCTAGAAGAGAACTCGCAGATCC 59.120 47.826 0.00 0.00 33.89 3.36
3018 5779 5.235850 AGAGAACTCGCAGATCCTATCTA 57.764 43.478 0.00 0.00 34.40 1.98
3029 5790 4.462483 CAGATCCTATCTACCTCTTCCTGC 59.538 50.000 0.00 0.00 37.58 4.85
3052 5813 8.537049 TGCAGGAAAATGATAAGAATTTGTTG 57.463 30.769 0.00 0.00 0.00 3.33
3053 5814 7.603404 TGCAGGAAAATGATAAGAATTTGTTGG 59.397 33.333 0.00 0.00 0.00 3.77
3054 5815 7.413328 GCAGGAAAATGATAAGAATTTGTTGGC 60.413 37.037 0.00 0.00 0.00 4.52
3055 5816 6.813152 AGGAAAATGATAAGAATTTGTTGGCG 59.187 34.615 0.00 0.00 0.00 5.69
3056 5817 6.035975 GGAAAATGATAAGAATTTGTTGGCGG 59.964 38.462 0.00 0.00 0.00 6.13
3057 5818 4.654091 ATGATAAGAATTTGTTGGCGGG 57.346 40.909 0.00 0.00 0.00 6.13
3060 5821 5.010933 TGATAAGAATTTGTTGGCGGGTTA 58.989 37.500 0.00 0.00 0.00 2.85
3062 5823 3.866883 AGAATTTGTTGGCGGGTTATG 57.133 42.857 0.00 0.00 0.00 1.90
3064 5825 3.829601 AGAATTTGTTGGCGGGTTATGAA 59.170 39.130 0.00 0.00 0.00 2.57
3065 5826 4.466015 AGAATTTGTTGGCGGGTTATGAAT 59.534 37.500 0.00 0.00 0.00 2.57
3066 5827 3.859411 TTTGTTGGCGGGTTATGAATC 57.141 42.857 0.00 0.00 0.00 2.52
3084 5853 1.580059 TCTACCATCCTCGCCCTTTT 58.420 50.000 0.00 0.00 0.00 2.27
3094 5863 3.133003 TCCTCGCCCTTTTCTAGAAGATG 59.867 47.826 5.12 0.00 0.00 2.90
3100 5869 5.220681 CGCCCTTTTCTAGAAGATGCTTTAC 60.221 44.000 5.12 0.00 0.00 2.01
3101 5870 5.648092 GCCCTTTTCTAGAAGATGCTTTACA 59.352 40.000 5.12 0.00 0.00 2.41
3121 5891 3.828451 ACAAAGGCTGTCATGTTGCTTAT 59.172 39.130 0.00 0.00 29.87 1.73
3147 5917 2.227194 GATGGACGGTTTTGTTGGACT 58.773 47.619 0.00 0.00 0.00 3.85
3148 5918 3.404899 GATGGACGGTTTTGTTGGACTA 58.595 45.455 0.00 0.00 0.00 2.59
3149 5919 3.495434 TGGACGGTTTTGTTGGACTAT 57.505 42.857 0.00 0.00 0.00 2.12
3150 5920 3.404899 TGGACGGTTTTGTTGGACTATC 58.595 45.455 0.00 0.00 0.00 2.08
3151 5921 3.071892 TGGACGGTTTTGTTGGACTATCT 59.928 43.478 0.00 0.00 0.00 1.98
3152 5922 4.070009 GGACGGTTTTGTTGGACTATCTT 58.930 43.478 0.00 0.00 0.00 2.40
3153 5923 4.517832 GGACGGTTTTGTTGGACTATCTTT 59.482 41.667 0.00 0.00 0.00 2.52
3154 5924 5.702209 GGACGGTTTTGTTGGACTATCTTTA 59.298 40.000 0.00 0.00 0.00 1.85
3155 5925 6.373495 GGACGGTTTTGTTGGACTATCTTTAT 59.627 38.462 0.00 0.00 0.00 1.40
3156 5926 7.141100 ACGGTTTTGTTGGACTATCTTTATG 57.859 36.000 0.00 0.00 0.00 1.90
3157 5927 6.713450 ACGGTTTTGTTGGACTATCTTTATGT 59.287 34.615 0.00 0.00 0.00 2.29
3158 5928 7.094933 ACGGTTTTGTTGGACTATCTTTATGTC 60.095 37.037 0.00 0.00 0.00 3.06
3159 5929 7.241376 GGTTTTGTTGGACTATCTTTATGTCG 58.759 38.462 0.00 0.00 0.00 4.35
3160 5930 7.094933 GGTTTTGTTGGACTATCTTTATGTCGT 60.095 37.037 0.00 0.00 0.00 4.34
3161 5931 6.961359 TTGTTGGACTATCTTTATGTCGTG 57.039 37.500 0.00 0.00 0.00 4.35
3162 5932 6.275494 TGTTGGACTATCTTTATGTCGTGA 57.725 37.500 0.00 0.00 0.00 4.35
3163 5933 6.873997 TGTTGGACTATCTTTATGTCGTGAT 58.126 36.000 0.00 0.00 0.00 3.06
3164 5934 7.327975 TGTTGGACTATCTTTATGTCGTGATT 58.672 34.615 0.00 0.00 0.00 2.57
3165 5935 7.491372 TGTTGGACTATCTTTATGTCGTGATTC 59.509 37.037 0.00 0.00 0.00 2.52
3166 5936 7.107639 TGGACTATCTTTATGTCGTGATTCA 57.892 36.000 0.00 0.00 0.00 2.57
3167 5937 7.552459 TGGACTATCTTTATGTCGTGATTCAA 58.448 34.615 0.00 0.00 0.00 2.69
3168 5938 7.706607 TGGACTATCTTTATGTCGTGATTCAAG 59.293 37.037 0.00 0.00 0.00 3.02
3169 5939 7.707035 GGACTATCTTTATGTCGTGATTCAAGT 59.293 37.037 0.00 0.00 0.00 3.16
3170 5940 9.088512 GACTATCTTTATGTCGTGATTCAAGTT 57.911 33.333 0.00 0.00 0.00 2.66
3171 5941 9.088512 ACTATCTTTATGTCGTGATTCAAGTTC 57.911 33.333 0.00 0.00 0.00 3.01
3172 5942 7.905604 ATCTTTATGTCGTGATTCAAGTTCA 57.094 32.000 0.00 2.14 0.00 3.18
3173 5943 7.722795 TCTTTATGTCGTGATTCAAGTTCAA 57.277 32.000 0.00 0.00 0.00 2.69
3174 5944 7.796838 TCTTTATGTCGTGATTCAAGTTCAAG 58.203 34.615 0.00 0.00 0.00 3.02
3175 5945 7.441157 TCTTTATGTCGTGATTCAAGTTCAAGT 59.559 33.333 0.00 0.00 0.00 3.16
3176 5946 8.596271 TTTATGTCGTGATTCAAGTTCAAGTA 57.404 30.769 0.00 0.00 0.00 2.24
3177 5947 8.771920 TTATGTCGTGATTCAAGTTCAAGTAT 57.228 30.769 0.00 0.00 0.00 2.12
3178 5948 9.863845 TTATGTCGTGATTCAAGTTCAAGTATA 57.136 29.630 0.00 0.00 0.00 1.47
3179 5949 8.771920 ATGTCGTGATTCAAGTTCAAGTATAA 57.228 30.769 0.00 0.00 0.00 0.98
3180 5950 8.596271 TGTCGTGATTCAAGTTCAAGTATAAA 57.404 30.769 0.00 0.00 0.00 1.40
3181 5951 8.708742 TGTCGTGATTCAAGTTCAAGTATAAAG 58.291 33.333 0.00 0.00 0.00 1.85
3182 5952 8.922676 GTCGTGATTCAAGTTCAAGTATAAAGA 58.077 33.333 0.00 0.00 0.00 2.52
3183 5953 9.140286 TCGTGATTCAAGTTCAAGTATAAAGAG 57.860 33.333 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.111253 CCAGCAGTTCCTTCCCAGTT 59.889 55.000 0.00 0.00 0.00 3.16
1 2 1.763770 CCAGCAGTTCCTTCCCAGT 59.236 57.895 0.00 0.00 0.00 4.00
2 3 1.676967 GCCAGCAGTTCCTTCCCAG 60.677 63.158 0.00 0.00 0.00 4.45
3 4 2.436109 GCCAGCAGTTCCTTCCCA 59.564 61.111 0.00 0.00 0.00 4.37
4 5 2.747855 CGCCAGCAGTTCCTTCCC 60.748 66.667 0.00 0.00 0.00 3.97
5 6 2.747855 CCGCCAGCAGTTCCTTCC 60.748 66.667 0.00 0.00 0.00 3.46
6 7 0.321298 TAACCGCCAGCAGTTCCTTC 60.321 55.000 0.00 0.00 0.00 3.46
7 8 0.328258 ATAACCGCCAGCAGTTCCTT 59.672 50.000 0.00 0.00 0.00 3.36
8 9 0.107654 GATAACCGCCAGCAGTTCCT 60.108 55.000 0.00 0.00 0.00 3.36
9 10 1.429148 CGATAACCGCCAGCAGTTCC 61.429 60.000 0.00 0.00 0.00 3.62
10 11 1.429148 CCGATAACCGCCAGCAGTTC 61.429 60.000 0.00 0.00 36.84 3.01
11 12 1.449601 CCGATAACCGCCAGCAGTT 60.450 57.895 0.00 0.00 36.84 3.16
12 13 2.186903 CCGATAACCGCCAGCAGT 59.813 61.111 0.00 0.00 36.84 4.40
13 14 2.588877 CCCGATAACCGCCAGCAG 60.589 66.667 0.00 0.00 36.84 4.24
14 15 4.169696 CCCCGATAACCGCCAGCA 62.170 66.667 0.00 0.00 36.84 4.41
20 21 4.963428 GAGGCGCCCCGATAACCG 62.963 72.222 26.15 0.00 35.76 4.44
21 22 4.620937 GGAGGCGCCCCGATAACC 62.621 72.222 26.15 11.54 35.76 2.85
22 23 3.857038 TGGAGGCGCCCCGATAAC 61.857 66.667 26.15 6.21 35.76 1.89
23 24 3.857038 GTGGAGGCGCCCCGATAA 61.857 66.667 26.15 5.18 35.76 1.75
34 35 4.100084 TCAGCGCCCATGTGGAGG 62.100 66.667 2.29 0.00 37.39 4.30
35 36 2.821366 GTCAGCGCCCATGTGGAG 60.821 66.667 2.29 2.50 37.39 3.86
36 37 4.758251 CGTCAGCGCCCATGTGGA 62.758 66.667 2.29 0.00 37.39 4.02
37 38 4.758251 TCGTCAGCGCCCATGTGG 62.758 66.667 2.29 0.00 38.14 4.17
38 39 3.490759 GTCGTCAGCGCCCATGTG 61.491 66.667 2.29 0.00 38.14 3.21
60 61 3.407046 GGAAGAGTCCGCCGGTACG 62.407 68.421 1.63 0.00 43.47 3.67
61 62 2.493501 GGAAGAGTCCGCCGGTAC 59.506 66.667 1.63 0.00 33.05 3.34
113 116 1.289380 GTCCAGGTCCAGTCACGAC 59.711 63.158 0.00 0.00 0.00 4.34
233 237 0.909610 AACAAGATCCAGAGCCCGGA 60.910 55.000 0.73 0.00 36.84 5.14
238 246 1.471684 CCAAGCAACAAGATCCAGAGC 59.528 52.381 0.00 0.00 0.00 4.09
308 329 1.312371 TAAAGCAGGCCGGTGCAATC 61.312 55.000 18.35 0.00 46.60 2.67
335 356 8.487176 GGGCATTATATTACAAAAAGAATTGCG 58.513 33.333 0.00 0.00 33.52 4.85
348 369 8.603242 TTTCTCTTCTTCGGGCATTATATTAC 57.397 34.615 0.00 0.00 0.00 1.89
349 370 9.621629 TTTTTCTCTTCTTCGGGCATTATATTA 57.378 29.630 0.00 0.00 0.00 0.98
411 435 0.036294 AGCCTACGACCCTTTCTTGC 60.036 55.000 0.00 0.00 0.00 4.01
428 463 4.822503 CGAGGTATCGCTACGAGC 57.177 61.111 0.00 0.00 42.97 5.03
467 503 0.173255 CCAATTGCCCACCGAATCAC 59.827 55.000 0.00 0.00 0.00 3.06
468 504 0.969917 CCCAATTGCCCACCGAATCA 60.970 55.000 0.00 0.00 0.00 2.57
469 505 1.675720 CCCCAATTGCCCACCGAATC 61.676 60.000 0.00 0.00 0.00 2.52
471 507 2.283532 CCCCAATTGCCCACCGAA 60.284 61.111 0.00 0.00 0.00 4.30
472 508 3.260888 TCCCCAATTGCCCACCGA 61.261 61.111 0.00 0.00 0.00 4.69
475 511 0.681243 GAGACTCCCCAATTGCCCAC 60.681 60.000 0.00 0.00 0.00 4.61
477 513 0.106967 GAGAGACTCCCCAATTGCCC 60.107 60.000 0.00 0.00 0.00 5.36
478 514 0.462759 CGAGAGACTCCCCAATTGCC 60.463 60.000 0.00 0.00 0.00 4.52
479 515 0.250513 ACGAGAGACTCCCCAATTGC 59.749 55.000 0.00 0.00 0.00 3.56
480 516 2.028112 TCAACGAGAGACTCCCCAATTG 60.028 50.000 0.00 0.00 0.00 2.32
481 517 2.028020 GTCAACGAGAGACTCCCCAATT 60.028 50.000 0.00 0.00 33.29 2.32
482 518 1.550976 GTCAACGAGAGACTCCCCAAT 59.449 52.381 0.00 0.00 33.29 3.16
483 519 0.966920 GTCAACGAGAGACTCCCCAA 59.033 55.000 0.00 0.00 33.29 4.12
484 520 1.241990 CGTCAACGAGAGACTCCCCA 61.242 60.000 0.00 0.00 43.02 4.96
485 521 1.507174 CGTCAACGAGAGACTCCCC 59.493 63.158 0.00 0.00 43.02 4.81
486 522 1.507174 CCGTCAACGAGAGACTCCC 59.493 63.158 3.71 0.00 43.02 4.30
487 523 1.507174 CCCGTCAACGAGAGACTCC 59.493 63.158 3.71 0.00 43.02 3.85
488 524 1.507174 CCCCGTCAACGAGAGACTC 59.493 63.158 3.71 0.00 43.02 3.36
489 525 2.637383 GCCCCGTCAACGAGAGACT 61.637 63.158 3.71 0.00 43.02 3.24
490 526 2.126031 GCCCCGTCAACGAGAGAC 60.126 66.667 3.71 0.00 43.02 3.36
491 527 2.599281 TGCCCCGTCAACGAGAGA 60.599 61.111 3.71 0.00 43.02 3.10
492 528 2.125912 CTGCCCCGTCAACGAGAG 60.126 66.667 3.71 0.00 43.02 3.20
493 529 2.204461 TTCTGCCCCGTCAACGAGA 61.204 57.895 3.71 0.00 43.02 4.04
494 530 2.027625 GTTCTGCCCCGTCAACGAG 61.028 63.158 3.71 0.00 43.02 4.18
495 531 2.029964 GTTCTGCCCCGTCAACGA 59.970 61.111 3.71 0.00 43.02 3.85
496 532 1.234615 AATGTTCTGCCCCGTCAACG 61.235 55.000 0.00 0.00 39.44 4.10
497 533 0.958822 AAATGTTCTGCCCCGTCAAC 59.041 50.000 0.00 0.00 0.00 3.18
524 560 0.666577 GAAACCTGACTCGTGACGGG 60.667 60.000 1.98 1.98 39.67 5.28
526 562 2.810486 GGAAACCTGACTCGTGACG 58.190 57.895 0.00 0.00 0.00 4.35
559 595 2.650322 ACTTGTGTTGAACCCGACAAT 58.350 42.857 1.02 0.00 38.35 2.71
573 609 7.413438 GCTCATTTCATCCTACTACAACTTGTG 60.413 40.741 4.57 0.00 0.00 3.33
580 616 4.716784 ACCTGCTCATTTCATCCTACTACA 59.283 41.667 0.00 0.00 0.00 2.74
582 618 5.163301 GGAACCTGCTCATTTCATCCTACTA 60.163 44.000 0.00 0.00 0.00 1.82
583 619 4.384647 GGAACCTGCTCATTTCATCCTACT 60.385 45.833 0.00 0.00 0.00 2.57
584 620 3.879892 GGAACCTGCTCATTTCATCCTAC 59.120 47.826 0.00 0.00 0.00 3.18
585 621 3.432186 CGGAACCTGCTCATTTCATCCTA 60.432 47.826 0.00 0.00 0.00 2.94
586 622 2.681976 CGGAACCTGCTCATTTCATCCT 60.682 50.000 0.00 0.00 0.00 3.24
587 623 1.672881 CGGAACCTGCTCATTTCATCC 59.327 52.381 0.00 0.00 0.00 3.51
588 624 1.672881 CCGGAACCTGCTCATTTCATC 59.327 52.381 0.00 0.00 0.00 2.92
589 625 1.004745 ACCGGAACCTGCTCATTTCAT 59.995 47.619 9.46 0.00 0.00 2.57
590 626 0.400213 ACCGGAACCTGCTCATTTCA 59.600 50.000 9.46 0.00 0.00 2.69
591 627 1.468914 GAACCGGAACCTGCTCATTTC 59.531 52.381 9.46 0.00 0.00 2.17
592 628 1.202879 TGAACCGGAACCTGCTCATTT 60.203 47.619 9.46 0.00 0.00 2.32
593 629 0.400213 TGAACCGGAACCTGCTCATT 59.600 50.000 9.46 0.00 0.00 2.57
594 630 0.321653 GTGAACCGGAACCTGCTCAT 60.322 55.000 9.46 0.00 0.00 2.90
595 631 1.070786 GTGAACCGGAACCTGCTCA 59.929 57.895 9.46 0.00 0.00 4.26
712 754 2.671963 GCGAGTTTGACCCACCCC 60.672 66.667 0.00 0.00 0.00 4.95
902 960 1.051556 TAGCTGTGGTGTGGTGGTGA 61.052 55.000 0.00 0.00 0.00 4.02
921 984 3.632080 TCGGGTTGCGGTGGATGT 61.632 61.111 0.00 0.00 0.00 3.06
969 1032 4.243008 TCGGAACCTGCACGCCAA 62.243 61.111 0.00 0.00 0.00 4.52
994 1057 1.075601 AGTTTCTTCTCCATGCCCCA 58.924 50.000 0.00 0.00 0.00 4.96
1317 1386 1.306825 ACAGAGGATGAGCAGGGCT 60.307 57.895 0.00 0.00 43.88 5.19
1359 1428 0.881118 GAGGTTGCAATGCCGAGAAA 59.119 50.000 0.59 0.00 0.00 2.52
1364 1433 2.141122 AAACCGAGGTTGCAATGCCG 62.141 55.000 8.43 6.38 38.47 5.69
1723 1831 1.736032 CGGAGAAGTAAAGGCGAGGTG 60.736 57.143 0.00 0.00 0.00 4.00
1724 1832 0.531200 CGGAGAAGTAAAGGCGAGGT 59.469 55.000 0.00 0.00 0.00 3.85
1725 1833 0.531200 ACGGAGAAGTAAAGGCGAGG 59.469 55.000 0.00 0.00 0.00 4.63
1726 1834 3.498927 TTACGGAGAAGTAAAGGCGAG 57.501 47.619 0.00 0.00 34.08 5.03
1727 1835 3.940209 TTTACGGAGAAGTAAAGGCGA 57.060 42.857 0.00 0.00 40.43 5.54
1728 1836 4.726876 GCAATTTACGGAGAAGTAAAGGCG 60.727 45.833 8.07 0.00 45.93 5.52
1729 1837 4.155280 TGCAATTTACGGAGAAGTAAAGGC 59.845 41.667 15.65 15.65 45.93 4.35
1730 1838 5.411669 AGTGCAATTTACGGAGAAGTAAAGG 59.588 40.000 8.07 4.78 45.93 3.11
1735 1843 2.484264 GCAGTGCAATTTACGGAGAAGT 59.516 45.455 11.09 0.00 0.00 3.01
1804 1912 1.733360 GGCTCGGCGAGATAGTAGTAG 59.267 57.143 38.56 11.08 0.00 2.57
1806 1914 1.229315 CGGCTCGGCGAGATAGTAGT 61.229 60.000 38.56 0.00 0.00 2.73
1809 1917 1.787057 CTTCGGCTCGGCGAGATAGT 61.787 60.000 38.56 0.00 0.00 2.12
1811 1919 2.552819 CCTTCGGCTCGGCGAGATA 61.553 63.158 38.56 20.15 0.00 1.98
1812 1920 3.905678 CCTTCGGCTCGGCGAGAT 61.906 66.667 38.56 0.00 0.00 2.75
1827 1935 0.976641 TGTTCTCAGGAATCACGCCT 59.023 50.000 0.00 0.00 35.75 5.52
1934 2048 2.125673 ATTTCGGCAGCTACGCGT 60.126 55.556 19.17 19.17 0.00 6.01
1949 2063 6.428771 TGCGTACTCCTTTTAGCTTAAACATT 59.571 34.615 0.00 0.00 0.00 2.71
1960 2074 7.636150 AGTAGAATAGTGCGTACTCCTTTTA 57.364 36.000 10.21 2.55 38.36 1.52
1972 2086 9.649167 TTACTTTCCTTGTTAGTAGAATAGTGC 57.351 33.333 0.00 0.00 0.00 4.40
1979 2093 9.310449 AGATGACTTACTTTCCTTGTTAGTAGA 57.690 33.333 0.00 0.00 29.12 2.59
2045 2159 9.736023 GAAAATAAAAGCTCTCTGTTTTTCTCA 57.264 29.630 0.00 0.00 39.29 3.27
2141 2257 2.776526 TTGGGTGTCTGGTGGCCT 60.777 61.111 3.32 0.00 0.00 5.19
2165 2281 1.957695 TCAGACGCTGCACTGCTTG 60.958 57.895 15.66 0.00 34.57 4.01
2222 2338 9.930693 AAGAAAAACTATCTCCAACTAGTACTG 57.069 33.333 5.39 0.00 0.00 2.74
2227 2344 9.372369 CTACCAAGAAAAACTATCTCCAACTAG 57.628 37.037 0.00 0.00 0.00 2.57
2231 2348 5.944007 GGCTACCAAGAAAAACTATCTCCAA 59.056 40.000 0.00 0.00 0.00 3.53
2337 2475 2.592194 CGAACTAAGCTAAGCACGACA 58.408 47.619 0.00 0.00 0.00 4.35
2351 2489 2.363975 ATTGCGGGAGGCCGAACTA 61.364 57.895 0.00 0.00 42.61 2.24
2375 2513 1.509787 CGTCCTGCATTTCGTTGCG 60.510 57.895 0.00 0.00 45.77 4.85
2409 2547 2.939460 GTGAGCACACAAAACAAGGT 57.061 45.000 9.58 0.00 45.32 3.50
2478 5172 8.990163 AAGGAAGTGGTATGTTTCTAGAAAAA 57.010 30.769 19.30 14.94 31.33 1.94
2542 5237 3.529634 TTCGCACAAAAACGATAGGTG 57.470 42.857 0.00 0.00 38.25 4.00
2574 5269 2.349532 CGTTTCCGAAAACTTCTCCAGC 60.350 50.000 0.00 0.00 42.18 4.85
2594 5289 1.482278 GAGCAGAATCTTCTACGGCG 58.518 55.000 4.80 4.80 35.34 6.46
2595 5290 1.410882 AGGAGCAGAATCTTCTACGGC 59.589 52.381 0.00 0.00 35.34 5.68
2604 5299 2.863137 CTGAAGCGTTAGGAGCAGAATC 59.137 50.000 0.00 0.00 37.01 2.52
2613 5308 6.481954 ACTAATTTTGTCTGAAGCGTTAGG 57.518 37.500 0.00 0.00 0.00 2.69
2620 5315 5.441614 CGTCGTCGACTAATTTTGTCTGAAG 60.442 44.000 22.18 9.48 39.71 3.02
2632 5327 3.607422 TCAGTTTTCGTCGTCGACTAA 57.393 42.857 22.18 15.30 46.03 2.24
2674 5413 5.852738 ACAGATCACAAGTTCAGATTTCG 57.147 39.130 0.00 0.00 0.00 3.46
2675 5414 7.360776 GGAGAACAGATCACAAGTTCAGATTTC 60.361 40.741 17.01 9.03 43.00 2.17
2742 5485 1.648681 GCTATTGCCGCTTTGAAAACG 59.351 47.619 0.00 0.00 0.00 3.60
2758 5501 2.481568 CGTGATGCCATCAAATCGCTAT 59.518 45.455 9.36 0.00 41.69 2.97
2796 5539 4.697756 TTCCACTTGGCCTCGGCG 62.698 66.667 3.32 0.00 43.06 6.46
2808 5551 2.258726 GCACTTCCACGGGTTCCAC 61.259 63.158 0.00 0.00 0.00 4.02
2809 5552 2.112297 GCACTTCCACGGGTTCCA 59.888 61.111 0.00 0.00 0.00 3.53
2810 5553 1.966451 CTGCACTTCCACGGGTTCC 60.966 63.158 0.00 0.00 0.00 3.62
2811 5554 0.321653 ATCTGCACTTCCACGGGTTC 60.322 55.000 0.00 0.00 0.00 3.62
2812 5555 0.981183 TATCTGCACTTCCACGGGTT 59.019 50.000 0.00 0.00 0.00 4.11
2813 5556 1.134401 CATATCTGCACTTCCACGGGT 60.134 52.381 0.00 0.00 0.00 5.28
2814 5557 1.134401 ACATATCTGCACTTCCACGGG 60.134 52.381 0.00 0.00 0.00 5.28
2815 5558 2.205074 GACATATCTGCACTTCCACGG 58.795 52.381 0.00 0.00 0.00 4.94
2816 5559 1.854743 CGACATATCTGCACTTCCACG 59.145 52.381 0.00 0.00 0.00 4.94
2856 5599 1.350665 CCGATAAAAACGCCGCCTC 59.649 57.895 0.00 0.00 0.00 4.70
2859 5602 1.226184 CCACCGATAAAAACGCCGC 60.226 57.895 0.00 0.00 0.00 6.53
2898 5641 1.065251 GCACTACCAGGTACGAGTAGC 59.935 57.143 12.82 4.45 40.71 3.58
2903 5646 0.806868 CTTCGCACTACCAGGTACGA 59.193 55.000 6.70 6.70 33.85 3.43
2911 5660 1.877165 GCCGTAGCTTCGCACTACC 60.877 63.158 7.29 0.00 37.33 3.18
2937 5698 0.234884 CAAACGAACGGCACTTCTCC 59.765 55.000 0.00 0.00 0.00 3.71
2999 5760 4.076394 AGGTAGATAGGATCTGCGAGTTC 58.924 47.826 0.00 0.00 42.12 3.01
3012 5773 3.838565 TCCTGCAGGAAGAGGTAGATAG 58.161 50.000 33.41 1.41 42.18 2.08
3029 5790 7.201461 CGCCAACAAATTCTTATCATTTTCCTG 60.201 37.037 0.00 0.00 0.00 3.86
3041 5802 3.829601 TCATAACCCGCCAACAAATTCTT 59.170 39.130 0.00 0.00 0.00 2.52
3043 5804 3.859411 TCATAACCCGCCAACAAATTC 57.141 42.857 0.00 0.00 0.00 2.17
3046 5807 3.426615 AGATTCATAACCCGCCAACAAA 58.573 40.909 0.00 0.00 0.00 2.83
3052 5813 2.922740 TGGTAGATTCATAACCCGCC 57.077 50.000 0.00 0.00 31.97 6.13
3053 5814 3.008049 AGGATGGTAGATTCATAACCCGC 59.992 47.826 0.00 0.00 31.97 6.13
3054 5815 4.618460 CGAGGATGGTAGATTCATAACCCG 60.618 50.000 0.00 0.00 31.97 5.28
3055 5816 4.822026 CGAGGATGGTAGATTCATAACCC 58.178 47.826 0.00 0.00 31.97 4.11
3056 5817 4.246458 GCGAGGATGGTAGATTCATAACC 58.754 47.826 0.00 0.00 0.00 2.85
3057 5818 4.246458 GGCGAGGATGGTAGATTCATAAC 58.754 47.826 0.00 0.00 0.00 1.89
3060 5821 1.625818 GGGCGAGGATGGTAGATTCAT 59.374 52.381 0.00 0.00 0.00 2.57
3062 5823 1.343069 AGGGCGAGGATGGTAGATTC 58.657 55.000 0.00 0.00 0.00 2.52
3064 5825 1.807814 AAAGGGCGAGGATGGTAGAT 58.192 50.000 0.00 0.00 0.00 1.98
3065 5826 1.485066 GAAAAGGGCGAGGATGGTAGA 59.515 52.381 0.00 0.00 0.00 2.59
3066 5827 1.486726 AGAAAAGGGCGAGGATGGTAG 59.513 52.381 0.00 0.00 0.00 3.18
3084 5853 5.877012 CAGCCTTTGTAAAGCATCTTCTAGA 59.123 40.000 0.00 0.00 34.69 2.43
3094 5863 3.923017 ACATGACAGCCTTTGTAAAGC 57.077 42.857 0.00 0.00 41.05 3.51
3100 5869 2.806608 AAGCAACATGACAGCCTTTG 57.193 45.000 0.00 0.00 0.00 2.77
3101 5870 5.221501 ACAAATAAGCAACATGACAGCCTTT 60.222 36.000 0.00 0.00 0.00 3.11
3121 5891 2.379972 ACAAAACCGTCCATCCACAAA 58.620 42.857 0.00 0.00 0.00 2.83
3147 5917 8.996024 TGAACTTGAATCACGACATAAAGATA 57.004 30.769 0.00 0.00 0.00 1.98
3148 5918 7.905604 TGAACTTGAATCACGACATAAAGAT 57.094 32.000 0.00 0.00 0.00 2.40
3149 5919 7.441157 ACTTGAACTTGAATCACGACATAAAGA 59.559 33.333 0.00 0.00 0.00 2.52
3150 5920 7.576236 ACTTGAACTTGAATCACGACATAAAG 58.424 34.615 0.00 0.00 0.00 1.85
3151 5921 7.490962 ACTTGAACTTGAATCACGACATAAA 57.509 32.000 0.00 0.00 0.00 1.40
3152 5922 8.771920 ATACTTGAACTTGAATCACGACATAA 57.228 30.769 0.00 0.00 0.00 1.90
3153 5923 9.863845 TTATACTTGAACTTGAATCACGACATA 57.136 29.630 0.00 0.00 0.00 2.29
3154 5924 8.771920 TTATACTTGAACTTGAATCACGACAT 57.228 30.769 0.00 0.00 0.00 3.06
3155 5925 8.596271 TTTATACTTGAACTTGAATCACGACA 57.404 30.769 0.00 0.00 0.00 4.35
3156 5926 8.922676 TCTTTATACTTGAACTTGAATCACGAC 58.077 33.333 0.00 0.00 0.00 4.34
3157 5927 9.140286 CTCTTTATACTTGAACTTGAATCACGA 57.860 33.333 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.