Multiple sequence alignment - TraesCS1A01G092700

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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 TraesCS1A01G092700 chr1A 100.000 3332 0 0 979 4310 85032415 85035746 0.000000e+00 6154.0
1 TraesCS1A01G092700 chr1A 100.000 661 0 0 1 661 85031437 85032097 0.000000e+00 1221.0
2 TraesCS1A01G092700 chr1D 96.209 2954 88 10 981 3919 89123794 89126738 0.000000e+00 4813.0
3 TraesCS1A01G092700 chr1D 84.554 628 72 14 4 618 89122861 89123476 2.220000e-167 599.0
4 TraesCS1A01G092700 chr1D 91.096 146 10 2 4168 4310 89126731 89126876 1.220000e-45 195.0
5 TraesCS1A01G092700 chr1B 95.272 2771 92 12 981 3734 142296515 142299263 0.000000e+00 4355.0
6 TraesCS1A01G092700 chr1B 85.761 611 59 14 4 596 142294569 142295169 4.730000e-174 621.0
7 TraesCS1A01G092700 chr1B 96.237 186 7 0 3730 3915 142317439 142317624 5.410000e-79 305.0
8 TraesCS1A01G092700 chr1B 86.473 207 28 0 986 1192 142295184 142295390 1.210000e-55 228.0
9 TraesCS1A01G092700 chr1B 91.096 146 10 2 4168 4310 142317620 142317765 1.220000e-45 195.0
10 TraesCS1A01G092700 chr1B 80.488 164 22 2 3913 4067 44062683 44062845 2.720000e-22 117.0
11 TraesCS1A01G092700 chr1B 90.110 91 8 1 523 613 142296359 142296448 2.720000e-22 117.0
12 TraesCS1A01G092700 chr4A 81.325 166 21 5 3911 4067 111053523 111053359 4.520000e-25 126.0
13 TraesCS1A01G092700 chr4A 79.042 167 23 4 3911 4067 626955369 626955533 2.120000e-18 104.0
14 TraesCS1A01G092700 chr7D 81.098 164 19 4 3914 4067 65776450 65776611 2.110000e-23 121.0
15 TraesCS1A01G092700 chr2B 85.345 116 8 3 3961 4067 791445538 791445423 1.270000e-20 111.0
16 TraesCS1A01G092700 chr6B 81.651 109 18 1 3911 4017 663721881 663721773 5.940000e-14 89.8
17 TraesCS1A01G092700 chr5A 93.220 59 4 0 3959 4017 431916711 431916769 2.140000e-13 87.9


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 TraesCS1A01G092700 chr1A 85031437 85035746 4309 False 3687.50 6154 100.000000 1 4310 2 chr1A.!!$F1 4309
1 TraesCS1A01G092700 chr1D 89122861 89126876 4015 False 1869.00 4813 90.619667 4 4310 3 chr1D.!!$F1 4306
2 TraesCS1A01G092700 chr1B 142294569 142299263 4694 False 1330.25 4355 89.404000 4 3734 4 chr1B.!!$F2 3730

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
374 377 0.111253 AACTTCAACCCAGAGGCCAG 59.889 55.0 5.01 0.0 36.11 4.85 F
379 382 0.111253 CAACCCAGAGGCCAGAAGTT 59.889 55.0 5.01 0.0 36.11 2.66 F
1567 3095 0.101399 CTAGTTGCGCTCGAGATGGT 59.899 55.0 18.75 0.0 0.00 3.55 F
1568 3096 0.179137 TAGTTGCGCTCGAGATGGTG 60.179 55.0 18.75 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 3094 0.108585 TCACCTCCACAAAGGCTCAC 59.891 55.000 0.00 0.0 40.34 3.51 R
1569 3097 0.610232 GCATCACCTCCACAAAGGCT 60.610 55.000 0.00 0.0 40.34 4.58 R
2904 4441 0.171679 AATGCACGATCGACACGGTA 59.828 50.000 24.34 5.5 34.93 4.02 R
3487 5033 1.436336 GCGACTGCGTATGTAGGGT 59.564 57.895 4.98 0.0 40.36 4.34 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
21 22 2.343758 GCACCGGCTCACTGAAGA 59.656 61.111 0.00 0.00 36.96 2.87
35 36 1.884926 GAAGAGGATGGCGCTTCGG 60.885 63.158 7.64 0.00 0.00 4.30
51 52 1.125093 TCGGGGAGAAAGAGGCAACA 61.125 55.000 0.00 0.00 41.41 3.33
57 58 1.072331 GAGAAAGAGGCAACACTCCCA 59.928 52.381 0.00 0.00 36.02 4.37
60 61 1.366319 AAGAGGCAACACTCCCAGAT 58.634 50.000 0.00 0.00 36.02 2.90
84 85 3.717294 GGCCGCTTGGGGAGAGAA 61.717 66.667 7.95 0.00 35.78 2.87
86 87 2.660064 GCCGCTTGGGGAGAGAAGA 61.660 63.158 7.95 0.00 35.78 2.87
114 115 1.134788 GGATCGAAAGGAAAGAGGCGA 60.135 52.381 0.00 0.00 0.00 5.54
115 116 2.618053 GATCGAAAGGAAAGAGGCGAA 58.382 47.619 0.00 0.00 0.00 4.70
189 190 1.486310 TCCCACATAGACACATGGAGC 59.514 52.381 0.00 0.00 33.80 4.70
253 254 9.967346 GTCTAAAAGAAAGCATTTTCCTAAAGT 57.033 29.630 0.00 0.00 42.99 2.66
296 299 4.574674 ATGGGATGTATATGCGTTGGAT 57.425 40.909 0.00 0.00 0.00 3.41
301 304 2.403259 TGTATATGCGTTGGATGCTCG 58.597 47.619 0.00 0.00 0.00 5.03
363 366 9.974750 GAAGTATAGCATTCTGTTAACTTCAAC 57.025 33.333 7.22 0.00 32.63 3.18
369 372 5.335191 GCATTCTGTTAACTTCAACCCAGAG 60.335 44.000 7.22 0.00 0.00 3.35
371 374 2.814336 CTGTTAACTTCAACCCAGAGGC 59.186 50.000 7.22 0.00 36.11 4.70
372 375 2.160205 GTTAACTTCAACCCAGAGGCC 58.840 52.381 0.00 0.00 36.11 5.19
373 376 1.440618 TAACTTCAACCCAGAGGCCA 58.559 50.000 5.01 0.00 36.11 5.36
374 377 0.111253 AACTTCAACCCAGAGGCCAG 59.889 55.000 5.01 0.00 36.11 4.85
375 378 0.768221 ACTTCAACCCAGAGGCCAGA 60.768 55.000 5.01 0.00 36.11 3.86
376 379 0.401738 CTTCAACCCAGAGGCCAGAA 59.598 55.000 5.01 0.00 36.11 3.02
377 380 0.401738 TTCAACCCAGAGGCCAGAAG 59.598 55.000 5.01 0.00 36.11 2.85
379 382 0.111253 CAACCCAGAGGCCAGAAGTT 59.889 55.000 5.01 0.00 36.11 2.66
380 383 1.351017 CAACCCAGAGGCCAGAAGTTA 59.649 52.381 5.01 0.00 36.11 2.24
382 385 2.279173 ACCCAGAGGCCAGAAGTTATT 58.721 47.619 5.01 0.00 36.11 1.40
383 386 2.025887 ACCCAGAGGCCAGAAGTTATTG 60.026 50.000 5.01 0.00 36.11 1.90
384 387 2.025887 CCCAGAGGCCAGAAGTTATTGT 60.026 50.000 5.01 0.00 0.00 2.71
385 388 3.274288 CCAGAGGCCAGAAGTTATTGTC 58.726 50.000 5.01 0.00 0.00 3.18
393 396 8.682936 AGGCCAGAAGTTATTGTCTTTATATG 57.317 34.615 5.01 0.00 0.00 1.78
427 430 7.218228 TCTGTCACATGCTTCATATGTTTTT 57.782 32.000 1.90 0.00 36.67 1.94
540 558 1.897137 GCCCAGGGCCTATTTACGC 60.897 63.158 21.62 0.00 44.06 4.42
601 1881 4.816925 GCTCAGAATTATCTAACCCACACC 59.183 45.833 0.00 0.00 33.50 4.16
614 1894 0.532573 CCACACCAGCACTCGAGTAT 59.467 55.000 19.57 7.24 0.00 2.12
618 1898 4.433615 CACACCAGCACTCGAGTATTATT 58.566 43.478 19.57 0.00 0.00 1.40
619 1899 5.451381 CCACACCAGCACTCGAGTATTATTA 60.451 44.000 19.57 0.00 0.00 0.98
620 1900 6.216569 CACACCAGCACTCGAGTATTATTAT 58.783 40.000 19.57 0.00 0.00 1.28
621 1901 6.701841 CACACCAGCACTCGAGTATTATTATT 59.298 38.462 19.57 0.00 0.00 1.40
622 1902 7.865889 CACACCAGCACTCGAGTATTATTATTA 59.134 37.037 19.57 0.00 0.00 0.98
623 1903 8.082852 ACACCAGCACTCGAGTATTATTATTAG 58.917 37.037 19.57 2.62 0.00 1.73
631 2159 9.857957 ACTCGAGTATTATTATTAGCCTAAAGC 57.142 33.333 18.46 0.00 44.25 3.51
1088 2616 4.803426 GCTCTCGTCCGCCCACAG 62.803 72.222 0.00 0.00 0.00 3.66
1106 2634 0.470833 AGCATCGTGAGCCCCTATCT 60.471 55.000 0.00 0.00 0.00 1.98
1108 2636 0.242286 CATCGTGAGCCCCTATCTCG 59.758 60.000 0.00 0.00 35.58 4.04
1220 2748 2.949909 CGGTGGTGATCGTGGGGAA 61.950 63.158 0.00 0.00 0.00 3.97
1407 2935 5.325494 GCAGTCGAATCGGATATACAGTAG 58.675 45.833 1.76 0.00 0.00 2.57
1437 2965 1.548719 CGTGGTACTGGGAGAACATGA 59.451 52.381 0.00 0.00 0.00 3.07
1462 2990 1.668419 GTGTTTGGCACTGTGAGTCT 58.332 50.000 12.86 0.00 44.41 3.24
1475 3003 2.158608 TGTGAGTCTCTCCTGTGTCAGA 60.159 50.000 0.65 0.00 32.44 3.27
1506 3034 3.643763 CCGTAGATGCAGTCATTCCTAC 58.356 50.000 0.00 0.00 31.66 3.18
1513 3041 2.027192 TGCAGTCATTCCTACCTGGTTC 60.027 50.000 3.84 0.00 37.07 3.62
1533 3061 5.390991 GGTTCGTTCAGATGAATTTGGAGAC 60.391 44.000 0.00 0.00 36.33 3.36
1550 3078 3.131046 GGAGACGGTTAAATTCGGTCCTA 59.869 47.826 0.00 0.00 36.34 2.94
1556 3084 3.063045 GGTTAAATTCGGTCCTAGTTGCG 59.937 47.826 0.00 0.00 0.00 4.85
1565 3093 0.382158 TCCTAGTTGCGCTCGAGATG 59.618 55.000 18.75 8.80 0.00 2.90
1566 3094 0.596083 CCTAGTTGCGCTCGAGATGG 60.596 60.000 18.75 5.35 0.00 3.51
1567 3095 0.101399 CTAGTTGCGCTCGAGATGGT 59.899 55.000 18.75 0.00 0.00 3.55
1568 3096 0.179137 TAGTTGCGCTCGAGATGGTG 60.179 55.000 18.75 0.00 0.00 4.17
1569 3097 1.446099 GTTGCGCTCGAGATGGTGA 60.446 57.895 18.75 0.00 0.00 4.02
1580 3108 1.003580 GAGATGGTGAGCCTTTGTGGA 59.996 52.381 0.00 0.00 38.35 4.02
1581 3109 1.004044 AGATGGTGAGCCTTTGTGGAG 59.996 52.381 0.00 0.00 38.35 3.86
1583 3111 1.352622 TGGTGAGCCTTTGTGGAGGT 61.353 55.000 0.00 0.00 39.11 3.85
1617 3145 1.755783 CTGCTTGGGATTCCCTGGC 60.756 63.158 22.38 22.96 45.70 4.85
1631 3159 1.526887 CTGGCCCGGATTTGCTCTA 59.473 57.895 0.73 0.00 0.00 2.43
1639 3167 2.932614 CCGGATTTGCTCTACAGTTGAG 59.067 50.000 7.59 7.59 34.87 3.02
1644 3172 6.166982 GGATTTGCTCTACAGTTGAGTTAGT 58.833 40.000 12.82 0.03 34.30 2.24
1652 3180 7.342769 TCTACAGTTGAGTTAGTGTGAAAGA 57.657 36.000 0.00 0.00 33.82 2.52
1653 3181 7.426410 TCTACAGTTGAGTTAGTGTGAAAGAG 58.574 38.462 0.00 0.00 33.82 2.85
1679 3207 7.487822 AGAGAAGTCTGATCCTGTTTATTCA 57.512 36.000 0.00 0.00 0.00 2.57
1684 3212 8.723942 AAGTCTGATCCTGTTTATTCATGTAC 57.276 34.615 0.00 0.00 0.00 2.90
1699 3227 5.627499 TCATGTACAGTTCAATCCTTTGC 57.373 39.130 0.33 0.00 32.61 3.68
1701 3229 4.829064 TGTACAGTTCAATCCTTTGCAC 57.171 40.909 0.00 0.00 32.61 4.57
1778 3306 4.664062 CCCGGAATGGCATCAGTT 57.336 55.556 0.73 0.00 35.87 3.16
1779 3307 2.886382 CCCGGAATGGCATCAGTTT 58.114 52.632 0.73 0.00 35.87 2.66
1963 3491 7.176690 TCAGTACTCATCATCTTGTGTGTTCTA 59.823 37.037 0.00 0.00 0.00 2.10
1986 3514 3.537337 TCCCCAGTTTCTGAGGGATTAA 58.463 45.455 16.36 2.25 45.80 1.40
2156 3684 1.698506 TGGAATTTTCTGTTGGGCGT 58.301 45.000 0.00 0.00 0.00 5.68
2326 3854 2.888212 AGGGCACAAAATGGAGCTTTA 58.112 42.857 0.00 0.00 0.00 1.85
2339 3867 3.119101 TGGAGCTTTAGTCGATCAGGTTC 60.119 47.826 0.00 0.00 0.00 3.62
2370 3907 9.883142 TTTGAAATGTGGTCTTAAATTTTCAGT 57.117 25.926 0.00 0.00 0.00 3.41
2450 3987 2.223386 GCTCTACGCTTCTACAGTCTGG 60.223 54.545 4.53 0.00 35.14 3.86
2466 4003 7.923414 ACAGTCTGGTATTTGGAATTCTTAC 57.077 36.000 5.23 3.23 0.00 2.34
2636 4173 2.699846 TCCTTTGAACATTGGCAAGCTT 59.300 40.909 5.96 0.00 0.00 3.74
2694 4231 1.003545 CGCCAAAGGTATCGATTGCAG 60.004 52.381 1.71 0.00 0.00 4.41
2765 4302 3.880490 TGTAACATCTTTGCCTTCGTGTT 59.120 39.130 0.00 0.00 34.54 3.32
3038 4575 2.381752 AGCCCACCCTATTTTATGGC 57.618 50.000 0.00 0.00 37.68 4.40
3108 4649 2.433888 TGGATCAAACCAGGCGCA 59.566 55.556 10.83 0.00 34.77 6.09
3198 4739 0.911769 ATGTGGATTTCTCGGAGGCA 59.088 50.000 4.96 0.00 0.00 4.75
3357 4898 2.647683 TGATGTTGTAACTGGGTGCA 57.352 45.000 0.00 0.00 0.00 4.57
3423 4964 3.064958 TCGAGATCAATAAACGACGCTCT 59.935 43.478 0.00 0.00 0.00 4.09
3487 5033 2.436646 GCTTTGGCTGGCGCTCTA 60.437 61.111 7.64 0.00 36.09 2.43
3537 5083 0.035056 AGGGACGAAGCAAATCCAGG 60.035 55.000 0.00 0.00 33.87 4.45
3542 5088 1.577328 CGAAGCAAATCCAGGTGCGT 61.577 55.000 0.00 0.00 45.62 5.24
3723 5269 0.251165 TCGGCTGGGGAAAAAGAAGG 60.251 55.000 0.00 0.00 0.00 3.46
3724 5270 0.539669 CGGCTGGGGAAAAAGAAGGT 60.540 55.000 0.00 0.00 0.00 3.50
3727 5273 1.632589 CTGGGGAAAAAGAAGGTGGG 58.367 55.000 0.00 0.00 0.00 4.61
3729 5275 0.190069 GGGGAAAAAGAAGGTGGGGT 59.810 55.000 0.00 0.00 0.00 4.95
3730 5276 1.338107 GGGAAAAAGAAGGTGGGGTG 58.662 55.000 0.00 0.00 0.00 4.61
3731 5277 1.412505 GGGAAAAAGAAGGTGGGGTGT 60.413 52.381 0.00 0.00 0.00 4.16
3732 5278 2.158430 GGGAAAAAGAAGGTGGGGTGTA 60.158 50.000 0.00 0.00 0.00 2.90
3763 5309 1.078848 GCTGCTGACCGTTGGATCT 60.079 57.895 0.00 0.00 0.00 2.75
3790 5336 3.181487 CCGATGTCCCAAATGAATTGACC 60.181 47.826 0.00 0.00 41.85 4.02
3792 5338 2.166829 TGTCCCAAATGAATTGACCGG 58.833 47.619 0.00 0.00 41.85 5.28
3832 5378 7.224297 TCAATCAATTTACCTGTAGCCTATCC 58.776 38.462 0.00 0.00 0.00 2.59
3852 5398 8.221944 CCTATCCCCACTGTACCAAAATATAAA 58.778 37.037 0.00 0.00 0.00 1.40
3885 5431 9.766277 TTTCAGTTCAATTTTAAATGCAAACAC 57.234 25.926 0.00 0.00 0.00 3.32
3915 5461 7.275920 ACTGCCTCTGTACCAAAATATAAGAG 58.724 38.462 0.00 0.00 0.00 2.85
3916 5462 6.055588 TGCCTCTGTACCAAAATATAAGAGC 58.944 40.000 0.00 0.00 0.00 4.09
3917 5463 6.055588 GCCTCTGTACCAAAATATAAGAGCA 58.944 40.000 0.00 0.00 0.00 4.26
3919 5465 7.095017 GCCTCTGTACCAAAATATAAGAGCATC 60.095 40.741 0.00 0.00 0.00 3.91
3932 5478 1.085091 GAGCATCTCCAACAGCTGTG 58.915 55.000 22.49 14.24 37.48 3.66
3933 5479 0.959372 AGCATCTCCAACAGCTGTGC 60.959 55.000 22.49 17.30 35.72 4.57
3934 5480 1.792301 CATCTCCAACAGCTGTGCG 59.208 57.895 22.49 14.77 0.00 5.34
3935 5481 1.376424 ATCTCCAACAGCTGTGCGG 60.376 57.895 22.49 23.20 0.00 5.69
3936 5482 3.730761 CTCCAACAGCTGTGCGGC 61.731 66.667 22.49 0.00 0.00 6.53
3937 5483 4.560743 TCCAACAGCTGTGCGGCA 62.561 61.111 22.49 11.12 34.17 5.69
3977 5523 3.641437 TTTTTGCAGCGCTGAAATAGT 57.359 38.095 40.21 0.00 0.00 2.12
3978 5524 2.617250 TTTGCAGCGCTGAAATAGTG 57.383 45.000 40.21 13.39 39.95 2.74
3979 5525 1.522668 TTGCAGCGCTGAAATAGTGT 58.477 45.000 40.21 0.00 39.16 3.55
3980 5526 1.522668 TGCAGCGCTGAAATAGTGTT 58.477 45.000 40.21 0.00 39.16 3.32
3981 5527 1.879380 TGCAGCGCTGAAATAGTGTTT 59.121 42.857 40.21 0.00 39.16 2.83
3982 5528 2.293122 TGCAGCGCTGAAATAGTGTTTT 59.707 40.909 40.21 0.00 39.16 2.43
3983 5529 3.243367 TGCAGCGCTGAAATAGTGTTTTT 60.243 39.130 40.21 0.00 39.16 1.94
3984 5530 3.120121 GCAGCGCTGAAATAGTGTTTTTG 59.880 43.478 40.21 9.77 39.16 2.44
3985 5531 3.120121 CAGCGCTGAAATAGTGTTTTTGC 59.880 43.478 33.66 0.00 39.16 3.68
3986 5532 2.088969 GCGCTGAAATAGTGTTTTTGCG 59.911 45.455 20.03 20.03 40.91 4.85
3987 5533 2.088969 CGCTGAAATAGTGTTTTTGCGC 59.911 45.455 15.42 0.00 36.17 6.09
3988 5534 2.088969 GCTGAAATAGTGTTTTTGCGCG 59.911 45.455 0.00 0.00 0.00 6.86
3989 5535 2.047769 TGAAATAGTGTTTTTGCGCGC 58.952 42.857 27.26 27.26 0.00 6.86
3990 5536 1.049251 AAATAGTGTTTTTGCGCGCG 58.951 45.000 28.44 28.44 0.00 6.86
3991 5537 0.727793 AATAGTGTTTTTGCGCGCGG 60.728 50.000 33.06 13.66 0.00 6.46
3992 5538 2.521733 ATAGTGTTTTTGCGCGCGGG 62.522 55.000 33.06 20.05 0.00 6.13
3993 5539 4.615834 GTGTTTTTGCGCGCGGGA 62.616 61.111 33.06 12.38 0.00 5.14
3994 5540 4.320928 TGTTTTTGCGCGCGGGAG 62.321 61.111 33.06 3.25 0.00 4.30
3999 5545 4.683721 TTGCGCGCGGGAGGTTTA 62.684 61.111 33.06 1.38 0.00 2.01
4002 5548 4.745751 CGCGCGGGAGGTTTACCA 62.746 66.667 24.84 0.00 38.89 3.25
4003 5549 2.124860 GCGCGGGAGGTTTACCAT 60.125 61.111 8.83 0.00 38.89 3.55
4004 5550 1.144496 GCGCGGGAGGTTTACCATA 59.856 57.895 8.83 0.00 38.89 2.74
4005 5551 0.250166 GCGCGGGAGGTTTACCATAT 60.250 55.000 8.83 0.00 38.89 1.78
4006 5552 1.508632 CGCGGGAGGTTTACCATATG 58.491 55.000 0.00 0.00 38.89 1.78
4007 5553 1.235724 GCGGGAGGTTTACCATATGC 58.764 55.000 1.13 0.00 38.89 3.14
4008 5554 1.476110 GCGGGAGGTTTACCATATGCA 60.476 52.381 1.13 0.00 38.89 3.96
4009 5555 2.218603 CGGGAGGTTTACCATATGCAC 58.781 52.381 1.13 0.00 38.89 4.57
4010 5556 2.420827 CGGGAGGTTTACCATATGCACA 60.421 50.000 1.13 0.00 38.89 4.57
4011 5557 3.626930 GGGAGGTTTACCATATGCACAA 58.373 45.455 1.13 0.00 38.89 3.33
4012 5558 4.020543 GGGAGGTTTACCATATGCACAAA 58.979 43.478 1.13 0.00 38.89 2.83
4013 5559 4.464597 GGGAGGTTTACCATATGCACAAAA 59.535 41.667 1.13 0.00 38.89 2.44
4014 5560 5.046950 GGGAGGTTTACCATATGCACAAAAA 60.047 40.000 1.13 0.00 38.89 1.94
4015 5561 5.867174 GGAGGTTTACCATATGCACAAAAAC 59.133 40.000 1.13 3.26 38.89 2.43
4016 5562 6.412362 AGGTTTACCATATGCACAAAAACA 57.588 33.333 1.13 0.00 38.89 2.83
4017 5563 6.821388 AGGTTTACCATATGCACAAAAACAA 58.179 32.000 1.13 0.00 38.89 2.83
4018 5564 6.704050 AGGTTTACCATATGCACAAAAACAAC 59.296 34.615 1.13 0.00 38.89 3.32
4019 5565 6.704050 GGTTTACCATATGCACAAAAACAACT 59.296 34.615 0.00 0.00 35.64 3.16
4020 5566 7.095816 GGTTTACCATATGCACAAAAACAACTC 60.096 37.037 0.00 0.00 35.64 3.01
4021 5567 4.545610 ACCATATGCACAAAAACAACTCG 58.454 39.130 0.00 0.00 0.00 4.18
4022 5568 4.277174 ACCATATGCACAAAAACAACTCGA 59.723 37.500 0.00 0.00 0.00 4.04
4023 5569 4.616802 CCATATGCACAAAAACAACTCGAC 59.383 41.667 0.00 0.00 0.00 4.20
4024 5570 2.166741 TGCACAAAAACAACTCGACG 57.833 45.000 0.00 0.00 0.00 5.12
4025 5571 1.202087 TGCACAAAAACAACTCGACGG 60.202 47.619 0.00 0.00 0.00 4.79
4026 5572 1.462791 CACAAAAACAACTCGACGGC 58.537 50.000 0.00 0.00 0.00 5.68
4027 5573 0.379316 ACAAAAACAACTCGACGGCC 59.621 50.000 0.00 0.00 0.00 6.13
4028 5574 0.317519 CAAAAACAACTCGACGGCCC 60.318 55.000 0.00 0.00 0.00 5.80
4029 5575 1.449726 AAAAACAACTCGACGGCCCC 61.450 55.000 0.00 0.00 0.00 5.80
4030 5576 2.612095 AAAACAACTCGACGGCCCCA 62.612 55.000 0.00 0.00 0.00 4.96
4031 5577 3.819877 AACAACTCGACGGCCCCAC 62.820 63.158 0.00 0.00 0.00 4.61
4032 5578 4.308458 CAACTCGACGGCCCCACA 62.308 66.667 0.00 0.00 0.00 4.17
4033 5579 3.319198 AACTCGACGGCCCCACAT 61.319 61.111 0.00 0.00 0.00 3.21
4034 5580 3.605749 AACTCGACGGCCCCACATG 62.606 63.158 0.00 0.00 0.00 3.21
4041 5587 4.073200 GGCCCCACATGCAGCAAC 62.073 66.667 0.00 0.00 0.00 4.17
4042 5588 4.073200 GCCCCACATGCAGCAACC 62.073 66.667 0.00 0.00 0.00 3.77
4043 5589 3.384532 CCCCACATGCAGCAACCC 61.385 66.667 0.00 0.00 0.00 4.11
4044 5590 3.751246 CCCACATGCAGCAACCCG 61.751 66.667 0.00 0.00 0.00 5.28
4045 5591 2.985282 CCACATGCAGCAACCCGT 60.985 61.111 0.00 0.00 0.00 5.28
4046 5592 2.256158 CACATGCAGCAACCCGTG 59.744 61.111 0.00 0.97 0.00 4.94
4054 5600 4.980903 GCAACCCGTGCGCACAAG 62.981 66.667 37.03 28.92 45.10 3.16
4055 5601 4.980903 CAACCCGTGCGCACAAGC 62.981 66.667 37.03 13.56 37.71 4.01
4067 5613 4.974721 ACAAGCCGGCACCCCAAG 62.975 66.667 31.54 11.95 0.00 3.61
4075 5621 4.347453 GCACCCCAAGCGCACAAG 62.347 66.667 11.47 0.00 0.00 3.16
4076 5622 4.347453 CACCCCAAGCGCACAAGC 62.347 66.667 11.47 0.00 37.42 4.01
4086 5632 4.715523 GCACAAGCCGGCACCCTA 62.716 66.667 31.54 0.00 33.58 3.53
4087 5633 2.033448 CACAAGCCGGCACCCTAA 59.967 61.111 31.54 0.00 0.00 2.69
4088 5634 1.602323 CACAAGCCGGCACCCTAAA 60.602 57.895 31.54 0.00 0.00 1.85
4089 5635 0.965363 CACAAGCCGGCACCCTAAAT 60.965 55.000 31.54 0.76 0.00 1.40
4090 5636 0.251608 ACAAGCCGGCACCCTAAATT 60.252 50.000 31.54 8.56 0.00 1.82
4091 5637 0.894835 CAAGCCGGCACCCTAAATTT 59.105 50.000 31.54 7.70 0.00 1.82
4092 5638 0.894835 AAGCCGGCACCCTAAATTTG 59.105 50.000 31.54 0.00 0.00 2.32
4093 5639 1.153647 GCCGGCACCCTAAATTTGC 60.154 57.895 24.80 0.00 35.40 3.68
4094 5640 1.882989 GCCGGCACCCTAAATTTGCA 61.883 55.000 24.80 0.00 38.04 4.08
4095 5641 0.605589 CCGGCACCCTAAATTTGCAA 59.394 50.000 0.00 0.00 38.04 4.08
4096 5642 1.671556 CCGGCACCCTAAATTTGCAAC 60.672 52.381 0.00 0.00 38.04 4.17
4097 5643 1.671556 CGGCACCCTAAATTTGCAACC 60.672 52.381 0.00 0.00 38.04 3.77
4098 5644 1.338674 GGCACCCTAAATTTGCAACCC 60.339 52.381 0.00 0.00 38.04 4.11
4099 5645 1.338674 GCACCCTAAATTTGCAACCCC 60.339 52.381 0.00 0.00 36.22 4.95
4100 5646 1.067213 CACCCTAAATTTGCAACCCCG 60.067 52.381 0.00 0.00 0.00 5.73
4101 5647 0.108377 CCCTAAATTTGCAACCCCGC 60.108 55.000 0.00 0.00 0.00 6.13
4102 5648 0.605589 CCTAAATTTGCAACCCCGCA 59.394 50.000 0.00 0.00 41.03 5.69
4103 5649 1.404047 CCTAAATTTGCAACCCCGCAG 60.404 52.381 0.00 0.00 44.14 5.18
4104 5650 0.037790 TAAATTTGCAACCCCGCAGC 60.038 50.000 0.00 0.00 44.14 5.25
4105 5651 2.730066 AAATTTGCAACCCCGCAGCC 62.730 55.000 0.00 0.00 44.14 4.85
4122 5668 4.093952 CCGCGTGCTTTGCTGGAG 62.094 66.667 4.92 0.00 0.00 3.86
4123 5669 4.748679 CGCGTGCTTTGCTGGAGC 62.749 66.667 0.00 0.00 40.53 4.70
4124 5670 4.748679 GCGTGCTTTGCTGGAGCG 62.749 66.667 0.00 0.00 45.83 5.03
4125 5671 3.349006 CGTGCTTTGCTGGAGCGT 61.349 61.111 0.00 0.00 45.83 5.07
4126 5672 2.896801 CGTGCTTTGCTGGAGCGTT 61.897 57.895 0.00 0.00 45.83 4.84
4127 5673 1.360192 GTGCTTTGCTGGAGCGTTT 59.640 52.632 0.00 0.00 45.83 3.60
4128 5674 0.249031 GTGCTTTGCTGGAGCGTTTT 60.249 50.000 0.00 0.00 45.83 2.43
4129 5675 0.459489 TGCTTTGCTGGAGCGTTTTT 59.541 45.000 0.00 0.00 45.83 1.94
4130 5676 1.131771 GCTTTGCTGGAGCGTTTTTC 58.868 50.000 0.00 0.00 45.83 2.29
4131 5677 1.269257 GCTTTGCTGGAGCGTTTTTCT 60.269 47.619 0.00 0.00 45.83 2.52
4132 5678 2.799562 GCTTTGCTGGAGCGTTTTTCTT 60.800 45.455 0.00 0.00 45.83 2.52
4133 5679 2.490328 TTGCTGGAGCGTTTTTCTTG 57.510 45.000 0.00 0.00 45.83 3.02
4134 5680 0.667993 TGCTGGAGCGTTTTTCTTGG 59.332 50.000 0.00 0.00 45.83 3.61
4135 5681 0.668535 GCTGGAGCGTTTTTCTTGGT 59.331 50.000 0.00 0.00 0.00 3.67
4136 5682 1.335051 GCTGGAGCGTTTTTCTTGGTC 60.335 52.381 0.00 0.00 0.00 4.02
4137 5683 1.946768 CTGGAGCGTTTTTCTTGGTCA 59.053 47.619 0.00 0.00 31.98 4.02
4138 5684 2.554032 CTGGAGCGTTTTTCTTGGTCAT 59.446 45.455 0.00 0.00 31.98 3.06
4139 5685 2.955660 TGGAGCGTTTTTCTTGGTCATT 59.044 40.909 0.00 0.00 31.98 2.57
4140 5686 3.383185 TGGAGCGTTTTTCTTGGTCATTT 59.617 39.130 0.00 0.00 31.98 2.32
4141 5687 4.580995 TGGAGCGTTTTTCTTGGTCATTTA 59.419 37.500 0.00 0.00 31.98 1.40
4142 5688 5.242838 TGGAGCGTTTTTCTTGGTCATTTAT 59.757 36.000 0.00 0.00 31.98 1.40
4143 5689 6.431543 TGGAGCGTTTTTCTTGGTCATTTATA 59.568 34.615 0.00 0.00 31.98 0.98
4144 5690 7.122055 TGGAGCGTTTTTCTTGGTCATTTATAT 59.878 33.333 0.00 0.00 31.98 0.86
4145 5691 8.617809 GGAGCGTTTTTCTTGGTCATTTATATA 58.382 33.333 0.00 0.00 31.98 0.86
4146 5692 9.651718 GAGCGTTTTTCTTGGTCATTTATATAG 57.348 33.333 0.00 0.00 0.00 1.31
4147 5693 8.129211 AGCGTTTTTCTTGGTCATTTATATAGC 58.871 33.333 0.00 0.00 0.00 2.97
4148 5694 7.913297 GCGTTTTTCTTGGTCATTTATATAGCA 59.087 33.333 0.00 0.00 0.00 3.49
4149 5695 9.221775 CGTTTTTCTTGGTCATTTATATAGCAC 57.778 33.333 0.00 0.00 0.00 4.40
4150 5696 9.516314 GTTTTTCTTGGTCATTTATATAGCACC 57.484 33.333 0.00 0.00 0.00 5.01
4151 5697 9.474313 TTTTTCTTGGTCATTTATATAGCACCT 57.526 29.630 0.00 0.00 0.00 4.00
4152 5698 8.677148 TTTCTTGGTCATTTATATAGCACCTC 57.323 34.615 0.00 0.00 0.00 3.85
4153 5699 7.618019 TCTTGGTCATTTATATAGCACCTCT 57.382 36.000 0.00 0.00 0.00 3.69
4154 5700 7.445121 TCTTGGTCATTTATATAGCACCTCTG 58.555 38.462 0.00 0.00 0.00 3.35
4155 5701 6.747414 TGGTCATTTATATAGCACCTCTGT 57.253 37.500 0.00 0.00 0.00 3.41
4156 5702 7.136822 TGGTCATTTATATAGCACCTCTGTT 57.863 36.000 0.00 0.00 0.00 3.16
4157 5703 6.992123 TGGTCATTTATATAGCACCTCTGTTG 59.008 38.462 0.00 0.00 0.00 3.33
4158 5704 6.428159 GGTCATTTATATAGCACCTCTGTTGG 59.572 42.308 0.00 0.00 0.00 3.77
4159 5705 7.217200 GTCATTTATATAGCACCTCTGTTGGA 58.783 38.462 0.00 0.00 0.00 3.53
4160 5706 7.386299 GTCATTTATATAGCACCTCTGTTGGAG 59.614 40.741 0.00 0.00 41.51 3.86
4161 5707 7.290014 TCATTTATATAGCACCTCTGTTGGAGA 59.710 37.037 0.00 0.00 44.45 3.71
4162 5708 7.618019 TTTATATAGCACCTCTGTTGGAGAT 57.382 36.000 0.00 0.00 44.45 2.75
4163 5709 3.834489 ATAGCACCTCTGTTGGAGATG 57.166 47.619 0.00 0.00 44.45 2.90
4164 5710 1.356124 AGCACCTCTGTTGGAGATGT 58.644 50.000 0.00 0.00 44.45 3.06
4165 5711 1.701847 AGCACCTCTGTTGGAGATGTT 59.298 47.619 0.00 0.00 44.45 2.71
4166 5712 2.079925 GCACCTCTGTTGGAGATGTTC 58.920 52.381 0.00 0.00 44.45 3.18
4167 5713 2.289945 GCACCTCTGTTGGAGATGTTCT 60.290 50.000 0.00 0.00 44.45 3.01
4168 5714 3.055819 GCACCTCTGTTGGAGATGTTCTA 60.056 47.826 0.00 0.00 44.45 2.10
4169 5715 4.563580 GCACCTCTGTTGGAGATGTTCTAA 60.564 45.833 0.00 0.00 44.45 2.10
4170 5716 5.174395 CACCTCTGTTGGAGATGTTCTAAG 58.826 45.833 0.00 0.00 44.45 2.18
4171 5717 5.047021 CACCTCTGTTGGAGATGTTCTAAGA 60.047 44.000 0.00 0.00 44.45 2.10
4172 5718 5.046950 ACCTCTGTTGGAGATGTTCTAAGAC 60.047 44.000 0.00 0.00 44.45 3.01
4173 5719 5.060662 TCTGTTGGAGATGTTCTAAGACG 57.939 43.478 0.00 0.00 0.00 4.18
4174 5720 4.523173 TCTGTTGGAGATGTTCTAAGACGT 59.477 41.667 0.00 0.00 0.00 4.34
4175 5721 5.010719 TCTGTTGGAGATGTTCTAAGACGTT 59.989 40.000 0.00 0.00 0.00 3.99
4176 5722 5.607477 TGTTGGAGATGTTCTAAGACGTTT 58.393 37.500 0.00 0.00 0.00 3.60
4177 5723 6.053005 TGTTGGAGATGTTCTAAGACGTTTT 58.947 36.000 0.00 0.00 0.00 2.43
4178 5724 6.540914 TGTTGGAGATGTTCTAAGACGTTTTT 59.459 34.615 0.00 0.00 0.00 1.94
4179 5725 6.539649 TGGAGATGTTCTAAGACGTTTTTG 57.460 37.500 0.00 0.00 0.00 2.44
4180 5726 5.049680 TGGAGATGTTCTAAGACGTTTTTGC 60.050 40.000 0.00 0.00 0.00 3.68
4181 5727 5.049680 GGAGATGTTCTAAGACGTTTTTGCA 60.050 40.000 0.00 0.00 0.00 4.08
4182 5728 5.990408 AGATGTTCTAAGACGTTTTTGCAG 58.010 37.500 0.00 0.00 0.00 4.41
4183 5729 3.947626 TGTTCTAAGACGTTTTTGCAGC 58.052 40.909 0.00 0.00 0.00 5.25
4184 5730 3.625764 TGTTCTAAGACGTTTTTGCAGCT 59.374 39.130 0.00 0.00 0.00 4.24
4185 5731 4.095782 TGTTCTAAGACGTTTTTGCAGCTT 59.904 37.500 0.00 0.00 0.00 3.74
4186 5732 4.893424 TCTAAGACGTTTTTGCAGCTTT 57.107 36.364 0.00 0.00 0.00 3.51
4187 5733 5.243426 TCTAAGACGTTTTTGCAGCTTTT 57.757 34.783 0.00 0.00 0.00 2.27
4188 5734 5.034152 TCTAAGACGTTTTTGCAGCTTTTG 58.966 37.500 0.00 0.00 0.00 2.44
4283 5830 6.687604 CGTAAGTTTGGAATTCAGGGATTTT 58.312 36.000 7.93 0.00 0.00 1.82
4306 5853 3.719268 TCCACCAAGCACTCAACATAT 57.281 42.857 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.463474 GCCATCCTCTTCAGTGAGCC 60.463 60.000 0.00 0.00 33.02 4.70
11 12 0.809241 GCGCCATCCTCTTCAGTGAG 60.809 60.000 0.00 0.00 0.00 3.51
16 17 1.153568 CGAAGCGCCATCCTCTTCA 60.154 57.895 2.29 0.00 36.83 3.02
35 36 1.611936 GGAGTGTTGCCTCTTTCTCCC 60.612 57.143 0.00 0.00 36.46 4.30
57 58 3.017581 AAGCGGCCCTTCCCATCT 61.018 61.111 0.00 0.00 0.00 2.90
84 85 1.381327 TTTCGATCCCCTCCGCTCT 60.381 57.895 0.00 0.00 0.00 4.09
86 87 2.435693 CCTTTCGATCCCCTCCGCT 61.436 63.158 0.00 0.00 0.00 5.52
121 122 4.166246 TCTTATCTCCTCGGCTCAACTA 57.834 45.455 0.00 0.00 0.00 2.24
127 128 4.770010 CCTTTCTATCTTATCTCCTCGGCT 59.230 45.833 0.00 0.00 0.00 5.52
134 135 6.533367 CGCTTATGCCCTTTCTATCTTATCTC 59.467 42.308 0.00 0.00 35.36 2.75
176 177 0.911769 CCCCTTGCTCCATGTGTCTA 59.088 55.000 0.00 0.00 0.00 2.59
177 178 0.842030 TCCCCTTGCTCCATGTGTCT 60.842 55.000 0.00 0.00 0.00 3.41
189 190 0.745845 CATCTGTCGCCTTCCCCTTG 60.746 60.000 0.00 0.00 0.00 3.61
273 276 5.491323 TCCAACGCATATACATCCCATAA 57.509 39.130 0.00 0.00 0.00 1.90
274 277 5.427378 CATCCAACGCATATACATCCCATA 58.573 41.667 0.00 0.00 0.00 2.74
280 283 2.995939 CGAGCATCCAACGCATATACAT 59.004 45.455 0.00 0.00 0.00 2.29
337 340 9.974750 GTTGAAGTTAACAGAATGCTATACTTC 57.025 33.333 8.61 0.00 42.53 3.01
341 344 7.398829 TGGGTTGAAGTTAACAGAATGCTATA 58.601 34.615 8.61 0.00 42.53 1.31
363 366 2.025887 ACAATAACTTCTGGCCTCTGGG 60.026 50.000 3.32 0.00 0.00 4.45
369 372 7.502561 ACCATATAAAGACAATAACTTCTGGCC 59.497 37.037 0.00 0.00 0.00 5.36
393 396 6.316140 TGAAGCATGTGACAGAATATTGTACC 59.684 38.462 0.00 0.00 0.00 3.34
540 558 3.613432 GCTGTTTCTGATTGGGCTTTCTG 60.613 47.826 0.00 0.00 0.00 3.02
601 1881 7.316640 AGGCTAATAATAATACTCGAGTGCTG 58.683 38.462 28.12 0.00 0.00 4.41
614 1894 9.469097 TTTCTGTTGGCTTTAGGCTAATAATAA 57.531 29.630 7.96 0.00 43.04 1.40
618 1898 6.717540 TGTTTTCTGTTGGCTTTAGGCTAATA 59.282 34.615 7.96 0.00 43.04 0.98
619 1899 5.538433 TGTTTTCTGTTGGCTTTAGGCTAAT 59.462 36.000 7.96 0.00 43.04 1.73
620 1900 4.890581 TGTTTTCTGTTGGCTTTAGGCTAA 59.109 37.500 2.04 2.04 41.69 3.09
621 1901 4.465886 TGTTTTCTGTTGGCTTTAGGCTA 58.534 39.130 4.87 0.00 41.69 3.93
622 1902 3.295973 TGTTTTCTGTTGGCTTTAGGCT 58.704 40.909 4.87 0.00 41.69 4.58
623 1903 3.642705 CTGTTTTCTGTTGGCTTTAGGC 58.357 45.455 0.00 0.00 41.50 3.93
630 2158 1.597937 CGAGTGCTGTTTTCTGTTGGC 60.598 52.381 0.00 0.00 0.00 4.52
631 2159 1.939934 TCGAGTGCTGTTTTCTGTTGG 59.060 47.619 0.00 0.00 0.00 3.77
992 2520 0.102300 GATTTGCGCCATTGGGGTAC 59.898 55.000 19.74 6.09 39.65 3.34
1088 2616 0.037790 GAGATAGGGGCTCACGATGC 60.038 60.000 0.00 0.00 32.67 3.91
1220 2748 1.867919 CGTCTGCGAGTCCTTCCTGT 61.868 60.000 0.00 0.00 41.33 4.00
1378 2906 2.278857 CGATTCGACTGCGGAGGG 60.279 66.667 9.36 0.00 38.28 4.30
1407 2935 2.612221 CCCAGTACCACGAAAGGAAGAC 60.612 54.545 0.00 0.00 0.00 3.01
1457 2985 2.487762 CAGTCTGACACAGGAGAGACTC 59.512 54.545 10.88 0.00 42.61 3.36
1459 2987 1.067915 GCAGTCTGACACAGGAGAGAC 60.068 57.143 10.88 0.00 35.97 3.36
1462 2990 1.342496 CAAGCAGTCTGACACAGGAGA 59.658 52.381 10.88 0.00 31.51 3.71
1506 3034 4.379813 CCAAATTCATCTGAACGAACCAGG 60.380 45.833 0.00 0.00 36.80 4.45
1513 3041 3.062639 CCGTCTCCAAATTCATCTGAACG 59.937 47.826 0.00 0.00 36.80 3.95
1533 3061 3.063045 GCAACTAGGACCGAATTTAACCG 59.937 47.826 0.00 0.00 0.00 4.44
1550 3078 1.446792 CACCATCTCGAGCGCAACT 60.447 57.895 11.47 0.00 0.00 3.16
1565 3093 0.890996 CACCTCCACAAAGGCTCACC 60.891 60.000 0.00 0.00 40.34 4.02
1566 3094 0.108585 TCACCTCCACAAAGGCTCAC 59.891 55.000 0.00 0.00 40.34 3.51
1567 3095 1.067295 ATCACCTCCACAAAGGCTCA 58.933 50.000 0.00 0.00 40.34 4.26
1568 3096 1.457346 CATCACCTCCACAAAGGCTC 58.543 55.000 0.00 0.00 40.34 4.70
1569 3097 0.610232 GCATCACCTCCACAAAGGCT 60.610 55.000 0.00 0.00 40.34 4.58
1580 3108 3.009723 CAGTAAACGAATGGCATCACCT 58.990 45.455 0.00 0.00 40.22 4.00
1581 3109 2.477863 GCAGTAAACGAATGGCATCACC 60.478 50.000 0.00 0.00 39.84 4.02
1583 3111 2.710377 AGCAGTAAACGAATGGCATCA 58.290 42.857 0.00 0.00 0.00 3.07
1617 3145 2.009774 CAACTGTAGAGCAAATCCGGG 58.990 52.381 0.00 0.00 0.00 5.73
1631 3159 5.978814 ACTCTTTCACACTAACTCAACTGT 58.021 37.500 0.00 0.00 0.00 3.55
1639 3167 7.806014 CAGACTTCTCTACTCTTTCACACTAAC 59.194 40.741 0.00 0.00 0.00 2.34
1644 3172 6.151985 GGATCAGACTTCTCTACTCTTTCACA 59.848 42.308 0.00 0.00 0.00 3.58
1652 3180 8.602472 AATAAACAGGATCAGACTTCTCTACT 57.398 34.615 0.00 0.00 0.00 2.57
1653 3181 8.470805 TGAATAAACAGGATCAGACTTCTCTAC 58.529 37.037 0.00 0.00 0.00 2.59
1679 3207 5.376854 GTGCAAAGGATTGAACTGTACAT 57.623 39.130 0.00 0.00 41.26 2.29
1699 3227 2.289547 CCCAGTAAACAACGTTCCAGTG 59.710 50.000 0.00 0.00 0.00 3.66
1701 3229 1.265905 GCCCAGTAAACAACGTTCCAG 59.734 52.381 0.00 0.00 0.00 3.86
1778 3306 6.137794 ACGAAAACACACATAATGGTGAAA 57.862 33.333 7.36 0.00 41.32 2.69
1779 3307 5.759506 ACGAAAACACACATAATGGTGAA 57.240 34.783 7.36 0.00 41.32 3.18
2326 3854 5.215252 TCAAAAAGAGAACCTGATCGACT 57.785 39.130 0.00 0.00 0.00 4.18
2450 3987 9.614792 ACATGTAGGAGTAAGAATTCCAAATAC 57.385 33.333 0.00 1.47 33.96 1.89
2466 4003 4.256920 ACAAGCTTTGCTACATGTAGGAG 58.743 43.478 29.45 18.90 38.25 3.69
2636 4173 2.291089 TGGATCTCTGCCTTTCATTGCA 60.291 45.455 0.00 0.00 35.86 4.08
2694 4231 1.200020 AGAAATGCCGTGCTTAAGTGC 59.800 47.619 4.02 3.24 0.00 4.40
2765 4302 7.395772 TGCATCCCTTCATATAAGTGAACAAAA 59.604 33.333 0.00 0.00 34.58 2.44
2904 4441 0.171679 AATGCACGATCGACACGGTA 59.828 50.000 24.34 5.50 34.93 4.02
3038 4575 2.744202 AGCAGTCAGAATTAAGGCAACG 59.256 45.455 0.00 0.00 46.39 4.10
3108 4649 4.175489 CCGACGTCGATGACCGCT 62.175 66.667 37.65 0.00 43.02 5.52
3198 4739 3.936203 TGACCCGCGACCTTGCTT 61.936 61.111 8.23 0.00 0.00 3.91
3423 4964 2.425592 CCCAACTGGTGAGCGACA 59.574 61.111 0.00 0.00 0.00 4.35
3487 5033 1.436336 GCGACTGCGTATGTAGGGT 59.564 57.895 4.98 0.00 40.36 4.34
3537 5083 4.024725 ACATCTACTCTATCTCGAACGCAC 60.025 45.833 0.00 0.00 0.00 5.34
3542 5088 3.821600 GGCCACATCTACTCTATCTCGAA 59.178 47.826 0.00 0.00 0.00 3.71
3701 5247 2.074729 TCTTTTTCCCCAGCCGAAAA 57.925 45.000 0.00 0.00 37.42 2.29
3702 5248 1.960689 CTTCTTTTTCCCCAGCCGAAA 59.039 47.619 0.00 0.00 0.00 3.46
3723 5269 2.552373 CCTTCTTCAACCTACACCCCAC 60.552 54.545 0.00 0.00 0.00 4.61
3724 5270 1.702957 CCTTCTTCAACCTACACCCCA 59.297 52.381 0.00 0.00 0.00 4.96
3727 5273 1.351350 AGCCCTTCTTCAACCTACACC 59.649 52.381 0.00 0.00 0.00 4.16
3729 5275 1.271379 GCAGCCCTTCTTCAACCTACA 60.271 52.381 0.00 0.00 0.00 2.74
3730 5276 1.003696 AGCAGCCCTTCTTCAACCTAC 59.996 52.381 0.00 0.00 0.00 3.18
3731 5277 1.003580 CAGCAGCCCTTCTTCAACCTA 59.996 52.381 0.00 0.00 0.00 3.08
3732 5278 0.251077 CAGCAGCCCTTCTTCAACCT 60.251 55.000 0.00 0.00 0.00 3.50
3763 5309 4.495690 TTCATTTGGGACATCGGATACA 57.504 40.909 0.00 0.00 39.30 2.29
3790 5336 5.233988 TGATTGAAAATTGTTTTAGGGCCG 58.766 37.500 0.00 0.00 31.94 6.13
3832 5378 6.031471 GCGTTTTATATTTTGGTACAGTGGG 58.969 40.000 0.00 0.00 42.39 4.61
3852 5398 9.701355 CATTTAAAATTGAACTGAAAAAGCGTT 57.299 25.926 0.00 0.00 0.00 4.84
3873 5419 5.556915 AGGCAGTAGTAGTGTTTGCATTTA 58.443 37.500 6.84 0.00 36.53 1.40
3876 5422 3.261897 AGAGGCAGTAGTAGTGTTTGCAT 59.738 43.478 6.84 0.00 36.53 3.96
3885 5431 5.401531 TTTTGGTACAGAGGCAGTAGTAG 57.598 43.478 0.00 0.00 42.39 2.57
3915 5461 1.505353 GCACAGCTGTTGGAGATGC 59.495 57.895 18.94 12.22 42.24 3.91
3916 5462 1.642037 CCGCACAGCTGTTGGAGATG 61.642 60.000 24.48 10.85 44.22 2.90
3917 5463 1.376424 CCGCACAGCTGTTGGAGAT 60.376 57.895 24.48 0.00 0.00 2.75
3919 5465 3.730761 GCCGCACAGCTGTTGGAG 61.731 66.667 30.24 17.36 0.00 3.86
3921 5467 4.034258 CTGCCGCACAGCTGTTGG 62.034 66.667 24.44 24.44 40.19 3.77
3957 5503 3.243367 ACACTATTTCAGCGCTGCAAAAA 60.243 39.130 32.44 25.82 0.00 1.94
3958 5504 2.293122 ACACTATTTCAGCGCTGCAAAA 59.707 40.909 32.44 26.52 0.00 2.44
3959 5505 1.879380 ACACTATTTCAGCGCTGCAAA 59.121 42.857 32.44 28.54 0.00 3.68
3960 5506 1.522668 ACACTATTTCAGCGCTGCAA 58.477 45.000 32.44 28.23 0.00 4.08
3961 5507 1.522668 AACACTATTTCAGCGCTGCA 58.477 45.000 32.44 20.57 0.00 4.41
3962 5508 2.619013 AAACACTATTTCAGCGCTGC 57.381 45.000 32.44 0.00 0.00 5.25
3963 5509 3.120121 GCAAAAACACTATTTCAGCGCTG 59.880 43.478 31.53 31.53 0.00 5.18
3964 5510 3.308530 GCAAAAACACTATTTCAGCGCT 58.691 40.909 2.64 2.64 0.00 5.92
3965 5511 2.088969 CGCAAAAACACTATTTCAGCGC 59.911 45.455 0.00 0.00 38.73 5.92
3966 5512 2.088969 GCGCAAAAACACTATTTCAGCG 59.911 45.455 0.30 12.25 43.49 5.18
3967 5513 2.088969 CGCGCAAAAACACTATTTCAGC 59.911 45.455 8.75 0.00 0.00 4.26
3968 5514 2.088969 GCGCGCAAAAACACTATTTCAG 59.911 45.455 29.10 0.00 0.00 3.02
3969 5515 2.047769 GCGCGCAAAAACACTATTTCA 58.952 42.857 29.10 0.00 0.00 2.69
3970 5516 1.055753 CGCGCGCAAAAACACTATTTC 59.944 47.619 32.61 0.00 0.00 2.17
3971 5517 1.049251 CGCGCGCAAAAACACTATTT 58.951 45.000 32.61 0.00 0.00 1.40
3972 5518 0.727793 CCGCGCGCAAAAACACTATT 60.728 50.000 32.61 0.00 0.00 1.73
3973 5519 1.154301 CCGCGCGCAAAAACACTAT 60.154 52.632 32.61 0.00 0.00 2.12
3974 5520 2.249896 CCGCGCGCAAAAACACTA 59.750 55.556 32.61 0.00 0.00 2.74
3975 5521 4.622456 CCCGCGCGCAAAAACACT 62.622 61.111 32.61 0.00 0.00 3.55
3976 5522 4.615834 TCCCGCGCGCAAAAACAC 62.616 61.111 32.61 0.00 0.00 3.32
3977 5523 4.320928 CTCCCGCGCGCAAAAACA 62.321 61.111 32.61 6.95 0.00 2.83
3982 5528 4.683721 TAAACCTCCCGCGCGCAA 62.684 61.111 32.61 14.83 0.00 4.85
3985 5531 2.632136 TATGGTAAACCTCCCGCGCG 62.632 60.000 25.67 25.67 36.82 6.86
3986 5532 0.250166 ATATGGTAAACCTCCCGCGC 60.250 55.000 0.00 0.00 36.82 6.86
3987 5533 1.508632 CATATGGTAAACCTCCCGCG 58.491 55.000 0.00 0.00 36.82 6.46
3988 5534 1.235724 GCATATGGTAAACCTCCCGC 58.764 55.000 4.56 0.00 36.82 6.13
3989 5535 2.218603 GTGCATATGGTAAACCTCCCG 58.781 52.381 4.56 0.00 36.82 5.14
3990 5536 3.290948 TGTGCATATGGTAAACCTCCC 57.709 47.619 4.56 0.00 36.82 4.30
3991 5537 5.652994 TTTTGTGCATATGGTAAACCTCC 57.347 39.130 4.56 0.00 36.82 4.30
3992 5538 6.451393 TGTTTTTGTGCATATGGTAAACCTC 58.549 36.000 4.56 0.00 36.82 3.85
3993 5539 6.412362 TGTTTTTGTGCATATGGTAAACCT 57.588 33.333 4.56 0.00 36.82 3.50
3994 5540 6.704050 AGTTGTTTTTGTGCATATGGTAAACC 59.296 34.615 4.56 0.00 0.00 3.27
3995 5541 7.358023 CGAGTTGTTTTTGTGCATATGGTAAAC 60.358 37.037 4.56 0.00 0.00 2.01
3996 5542 6.638873 CGAGTTGTTTTTGTGCATATGGTAAA 59.361 34.615 4.56 0.00 0.00 2.01
3997 5543 6.017026 TCGAGTTGTTTTTGTGCATATGGTAA 60.017 34.615 4.56 0.00 0.00 2.85
3998 5544 5.470437 TCGAGTTGTTTTTGTGCATATGGTA 59.530 36.000 4.56 0.00 0.00 3.25
3999 5545 4.277174 TCGAGTTGTTTTTGTGCATATGGT 59.723 37.500 4.56 0.00 0.00 3.55
4000 5546 4.616802 GTCGAGTTGTTTTTGTGCATATGG 59.383 41.667 4.56 0.00 0.00 2.74
4001 5547 4.318071 CGTCGAGTTGTTTTTGTGCATATG 59.682 41.667 0.00 0.00 0.00 1.78
4002 5548 4.463209 CGTCGAGTTGTTTTTGTGCATAT 58.537 39.130 0.00 0.00 0.00 1.78
4003 5549 3.303461 CCGTCGAGTTGTTTTTGTGCATA 60.303 43.478 0.00 0.00 0.00 3.14
4004 5550 2.540769 CCGTCGAGTTGTTTTTGTGCAT 60.541 45.455 0.00 0.00 0.00 3.96
4005 5551 1.202087 CCGTCGAGTTGTTTTTGTGCA 60.202 47.619 0.00 0.00 0.00 4.57
4006 5552 1.462791 CCGTCGAGTTGTTTTTGTGC 58.537 50.000 0.00 0.00 0.00 4.57
4007 5553 1.462791 GCCGTCGAGTTGTTTTTGTG 58.537 50.000 0.00 0.00 0.00 3.33
4008 5554 0.379316 GGCCGTCGAGTTGTTTTTGT 59.621 50.000 0.00 0.00 0.00 2.83
4009 5555 0.317519 GGGCCGTCGAGTTGTTTTTG 60.318 55.000 0.00 0.00 0.00 2.44
4010 5556 1.449726 GGGGCCGTCGAGTTGTTTTT 61.450 55.000 0.00 0.00 0.00 1.94
4011 5557 1.895231 GGGGCCGTCGAGTTGTTTT 60.895 57.895 0.00 0.00 0.00 2.43
4012 5558 2.281276 GGGGCCGTCGAGTTGTTT 60.281 61.111 0.00 0.00 0.00 2.83
4013 5559 3.552384 TGGGGCCGTCGAGTTGTT 61.552 61.111 0.00 0.00 0.00 2.83
4014 5560 4.309950 GTGGGGCCGTCGAGTTGT 62.310 66.667 0.00 0.00 0.00 3.32
4015 5561 3.605749 ATGTGGGGCCGTCGAGTTG 62.606 63.158 0.00 0.00 0.00 3.16
4016 5562 3.319198 ATGTGGGGCCGTCGAGTT 61.319 61.111 0.00 0.00 0.00 3.01
4017 5563 4.082523 CATGTGGGGCCGTCGAGT 62.083 66.667 0.00 0.00 0.00 4.18
4024 5570 4.073200 GTTGCTGCATGTGGGGCC 62.073 66.667 1.84 0.00 0.00 5.80
4025 5571 4.073200 GGTTGCTGCATGTGGGGC 62.073 66.667 1.84 0.00 0.00 5.80
4026 5572 3.384532 GGGTTGCTGCATGTGGGG 61.385 66.667 1.84 0.00 0.00 4.96
4027 5573 3.751246 CGGGTTGCTGCATGTGGG 61.751 66.667 1.84 0.00 0.00 4.61
4028 5574 2.985282 ACGGGTTGCTGCATGTGG 60.985 61.111 1.84 0.00 0.00 4.17
4029 5575 2.256158 CACGGGTTGCTGCATGTG 59.744 61.111 1.84 6.79 0.00 3.21
4038 5584 4.980903 GCTTGTGCGCACGGGTTG 62.981 66.667 33.22 21.21 0.00 3.77
4050 5596 4.974721 CTTGGGGTGCCGGCTTGT 62.975 66.667 29.70 0.00 0.00 3.16
4059 5605 4.347453 GCTTGTGCGCTTGGGGTG 62.347 66.667 9.73 0.00 0.00 4.61
4069 5615 4.715523 TAGGGTGCCGGCTTGTGC 62.716 66.667 29.70 12.11 38.76 4.57
4070 5616 0.965363 ATTTAGGGTGCCGGCTTGTG 60.965 55.000 29.70 0.00 0.00 3.33
4071 5617 0.251608 AATTTAGGGTGCCGGCTTGT 60.252 50.000 29.70 12.14 0.00 3.16
4072 5618 0.894835 AAATTTAGGGTGCCGGCTTG 59.105 50.000 29.70 0.00 0.00 4.01
4073 5619 0.894835 CAAATTTAGGGTGCCGGCTT 59.105 50.000 29.70 13.03 0.00 4.35
4074 5620 1.604147 GCAAATTTAGGGTGCCGGCT 61.604 55.000 29.70 9.99 31.94 5.52
4075 5621 1.153647 GCAAATTTAGGGTGCCGGC 60.154 57.895 22.73 22.73 31.94 6.13
4076 5622 0.605589 TTGCAAATTTAGGGTGCCGG 59.394 50.000 0.00 0.00 37.48 6.13
4077 5623 1.671556 GGTTGCAAATTTAGGGTGCCG 60.672 52.381 0.00 0.00 37.48 5.69
4078 5624 1.338674 GGGTTGCAAATTTAGGGTGCC 60.339 52.381 0.00 0.00 37.48 5.01
4079 5625 1.338674 GGGGTTGCAAATTTAGGGTGC 60.339 52.381 0.00 0.00 38.78 5.01
4080 5626 1.067213 CGGGGTTGCAAATTTAGGGTG 60.067 52.381 0.00 0.00 0.00 4.61
4081 5627 1.262417 CGGGGTTGCAAATTTAGGGT 58.738 50.000 0.00 0.00 0.00 4.34
4082 5628 0.108377 GCGGGGTTGCAAATTTAGGG 60.108 55.000 0.00 0.00 34.15 3.53
4083 5629 0.605589 TGCGGGGTTGCAAATTTAGG 59.394 50.000 0.00 0.00 43.02 2.69
4084 5630 1.994916 CTGCGGGGTTGCAAATTTAG 58.005 50.000 0.00 0.00 45.74 1.85
4085 5631 0.037790 GCTGCGGGGTTGCAAATTTA 60.038 50.000 0.00 0.00 45.74 1.40
4086 5632 1.301637 GCTGCGGGGTTGCAAATTT 60.302 52.632 0.00 0.00 45.74 1.82
4087 5633 2.343387 GCTGCGGGGTTGCAAATT 59.657 55.556 0.00 0.00 45.74 1.82
4088 5634 3.694538 GGCTGCGGGGTTGCAAAT 61.695 61.111 0.00 0.00 45.74 2.32
4105 5651 4.093952 CTCCAGCAAAGCACGCGG 62.094 66.667 12.47 0.00 0.00 6.46
4106 5652 4.748679 GCTCCAGCAAAGCACGCG 62.749 66.667 3.53 3.53 41.59 6.01
4107 5653 4.748679 CGCTCCAGCAAAGCACGC 62.749 66.667 0.00 0.00 42.21 5.34
4108 5654 2.392613 AAACGCTCCAGCAAAGCACG 62.393 55.000 0.00 0.00 42.21 5.34
4109 5655 0.249031 AAAACGCTCCAGCAAAGCAC 60.249 50.000 0.00 0.00 42.21 4.40
4110 5656 0.459489 AAAAACGCTCCAGCAAAGCA 59.541 45.000 0.00 0.00 42.21 3.91
4111 5657 1.131771 GAAAAACGCTCCAGCAAAGC 58.868 50.000 0.00 0.00 42.21 3.51
4112 5658 2.781945 AGAAAAACGCTCCAGCAAAG 57.218 45.000 0.00 0.00 42.21 2.77
4113 5659 2.481104 CCAAGAAAAACGCTCCAGCAAA 60.481 45.455 0.00 0.00 42.21 3.68
4114 5660 1.066908 CCAAGAAAAACGCTCCAGCAA 59.933 47.619 0.00 0.00 42.21 3.91
4115 5661 0.667993 CCAAGAAAAACGCTCCAGCA 59.332 50.000 0.00 0.00 42.21 4.41
4116 5662 0.668535 ACCAAGAAAAACGCTCCAGC 59.331 50.000 0.00 0.00 37.78 4.85
4117 5663 1.946768 TGACCAAGAAAAACGCTCCAG 59.053 47.619 0.00 0.00 0.00 3.86
4118 5664 2.045561 TGACCAAGAAAAACGCTCCA 57.954 45.000 0.00 0.00 0.00 3.86
4119 5665 3.643159 AATGACCAAGAAAAACGCTCC 57.357 42.857 0.00 0.00 0.00 4.70
4120 5666 9.651718 CTATATAAATGACCAAGAAAAACGCTC 57.348 33.333 0.00 0.00 0.00 5.03
4121 5667 8.129211 GCTATATAAATGACCAAGAAAAACGCT 58.871 33.333 0.00 0.00 0.00 5.07
4122 5668 7.913297 TGCTATATAAATGACCAAGAAAAACGC 59.087 33.333 0.00 0.00 0.00 4.84
4123 5669 9.221775 GTGCTATATAAATGACCAAGAAAAACG 57.778 33.333 0.00 0.00 0.00 3.60
4124 5670 9.516314 GGTGCTATATAAATGACCAAGAAAAAC 57.484 33.333 0.00 0.00 0.00 2.43
4125 5671 9.474313 AGGTGCTATATAAATGACCAAGAAAAA 57.526 29.630 0.00 0.00 0.00 1.94
4126 5672 9.120538 GAGGTGCTATATAAATGACCAAGAAAA 57.879 33.333 0.00 0.00 0.00 2.29
4127 5673 8.494433 AGAGGTGCTATATAAATGACCAAGAAA 58.506 33.333 0.00 0.00 0.00 2.52
4128 5674 7.933577 CAGAGGTGCTATATAAATGACCAAGAA 59.066 37.037 0.00 0.00 0.00 2.52
4129 5675 7.071196 ACAGAGGTGCTATATAAATGACCAAGA 59.929 37.037 0.00 0.00 0.00 3.02
4130 5676 7.220030 ACAGAGGTGCTATATAAATGACCAAG 58.780 38.462 0.00 0.00 0.00 3.61
4131 5677 7.136822 ACAGAGGTGCTATATAAATGACCAA 57.863 36.000 0.00 0.00 0.00 3.67
4132 5678 6.747414 ACAGAGGTGCTATATAAATGACCA 57.253 37.500 0.00 0.00 0.00 4.02
4133 5679 6.428159 CCAACAGAGGTGCTATATAAATGACC 59.572 42.308 0.00 0.00 0.00 4.02
4134 5680 7.217200 TCCAACAGAGGTGCTATATAAATGAC 58.783 38.462 0.00 0.00 0.00 3.06
4135 5681 7.290014 TCTCCAACAGAGGTGCTATATAAATGA 59.710 37.037 0.00 0.00 43.44 2.57
4136 5682 7.445121 TCTCCAACAGAGGTGCTATATAAATG 58.555 38.462 0.00 0.00 43.44 2.32
4137 5683 7.618019 TCTCCAACAGAGGTGCTATATAAAT 57.382 36.000 0.00 0.00 43.44 1.40
4138 5684 7.445121 CATCTCCAACAGAGGTGCTATATAAA 58.555 38.462 0.00 0.00 46.55 1.40
4139 5685 6.997655 CATCTCCAACAGAGGTGCTATATAA 58.002 40.000 0.00 0.00 46.55 0.98
4140 5686 6.596309 CATCTCCAACAGAGGTGCTATATA 57.404 41.667 0.00 0.00 46.55 0.86
4141 5687 5.480642 CATCTCCAACAGAGGTGCTATAT 57.519 43.478 0.00 0.00 46.55 0.86
4142 5688 4.944619 CATCTCCAACAGAGGTGCTATA 57.055 45.455 0.00 0.00 46.55 1.31
4143 5689 3.834489 CATCTCCAACAGAGGTGCTAT 57.166 47.619 0.00 0.00 46.55 2.97
4149 5695 5.415221 GTCTTAGAACATCTCCAACAGAGG 58.585 45.833 0.00 0.00 43.44 3.69
4150 5696 5.098893 CGTCTTAGAACATCTCCAACAGAG 58.901 45.833 0.00 0.00 44.75 3.35
4151 5697 4.523173 ACGTCTTAGAACATCTCCAACAGA 59.477 41.667 0.00 0.00 34.78 3.41
4152 5698 4.810790 ACGTCTTAGAACATCTCCAACAG 58.189 43.478 0.00 0.00 0.00 3.16
4153 5699 4.866508 ACGTCTTAGAACATCTCCAACA 57.133 40.909 0.00 0.00 0.00 3.33
4154 5700 6.541111 AAAACGTCTTAGAACATCTCCAAC 57.459 37.500 0.00 0.00 0.00 3.77
4155 5701 6.512741 GCAAAAACGTCTTAGAACATCTCCAA 60.513 38.462 0.00 0.00 0.00 3.53
4156 5702 5.049680 GCAAAAACGTCTTAGAACATCTCCA 60.050 40.000 0.00 0.00 0.00 3.86
4157 5703 5.049680 TGCAAAAACGTCTTAGAACATCTCC 60.050 40.000 0.00 0.00 0.00 3.71
4158 5704 5.985781 TGCAAAAACGTCTTAGAACATCTC 58.014 37.500 0.00 0.00 0.00 2.75
4159 5705 5.560953 GCTGCAAAAACGTCTTAGAACATCT 60.561 40.000 0.00 0.00 0.00 2.90
4160 5706 4.613031 GCTGCAAAAACGTCTTAGAACATC 59.387 41.667 0.00 0.00 0.00 3.06
4161 5707 4.275936 AGCTGCAAAAACGTCTTAGAACAT 59.724 37.500 1.02 0.00 0.00 2.71
4162 5708 3.625764 AGCTGCAAAAACGTCTTAGAACA 59.374 39.130 1.02 0.00 0.00 3.18
4163 5709 4.210832 AGCTGCAAAAACGTCTTAGAAC 57.789 40.909 1.02 0.00 0.00 3.01
4164 5710 4.893424 AAGCTGCAAAAACGTCTTAGAA 57.107 36.364 1.02 0.00 0.00 2.10
4165 5711 4.893424 AAAGCTGCAAAAACGTCTTAGA 57.107 36.364 1.02 0.00 0.00 2.10
4166 5712 5.301500 CAAAAGCTGCAAAAACGTCTTAG 57.699 39.130 1.02 0.00 0.00 2.18
4188 5734 5.614760 CAAATTAGATGTTTTTGCAGCTGC 58.385 37.500 31.89 31.89 35.72 5.25
4230 5776 1.623163 CTTCGGATCTACTCCCTCCC 58.377 60.000 0.00 0.00 41.49 4.30
4283 5830 3.500448 TGTTGAGTGCTTGGTGGAATA 57.500 42.857 0.00 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.