Multiple sequence alignment - TraesCS3A01G146900

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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 TraesCS3A01G146900 chr3A 100.000 5726 0 0 1 5726 128544689 128538964 0.000000e+00 10575.0
1 TraesCS3A01G146900 chr3A 95.364 302 12 1 4725 5026 12175399 12175698 4.010000e-131 479.0
2 TraesCS3A01G146900 chr1A 96.102 4746 112 36 1 4711 389828949 389833656 0.000000e+00 7672.0
3 TraesCS3A01G146900 chr1A 91.130 699 47 11 5027 5723 389833648 389834333 0.000000e+00 933.0
4 TraesCS3A01G146900 chr1D 94.174 2180 91 19 2552 4711 309987260 309989423 0.000000e+00 3290.0
5 TraesCS3A01G146900 chr1D 91.732 2056 122 14 505 2521 309985214 309987260 0.000000e+00 2811.0
6 TraesCS3A01G146900 chr1D 86.750 400 43 3 5328 5726 310131455 310131845 2.450000e-118 436.0
7 TraesCS3A01G146900 chr1D 91.429 315 13 7 1 301 309982247 309982561 2.470000e-113 420.0
8 TraesCS3A01G146900 chr1D 79.861 144 11 9 369 508 309982587 309982716 7.900000e-14 89.8
9 TraesCS3A01G146900 chr1B 89.470 2583 164 38 10 2521 419973494 419970949 0.000000e+00 3164.0
10 TraesCS3A01G146900 chr1B 91.186 1543 95 20 2552 4061 419970949 419969415 0.000000e+00 2058.0
11 TraesCS3A01G146900 chr1B 96.206 659 22 1 4056 4711 419969378 419968720 0.000000e+00 1075.0
12 TraesCS3A01G146900 chr1B 91.429 70 6 0 5120 5189 419968119 419968050 4.720000e-16 97.1
13 TraesCS3A01G146900 chr1B 97.561 41 1 0 5283 5323 419967913 419967873 2.860000e-08 71.3
14 TraesCS3A01G146900 chrUn 96.118 644 22 1 4071 4711 440332670 440332027 0.000000e+00 1048.0
15 TraesCS3A01G146900 chr2A 96.118 644 22 1 4071 4711 35795384 35794741 0.000000e+00 1048.0
16 TraesCS3A01G146900 chr2A 95.380 303 12 1 4725 5027 693233664 693233364 1.120000e-131 481.0
17 TraesCS3A01G146900 chr2A 95.050 303 13 1 4725 5027 1504275 1503975 5.190000e-130 475.0
18 TraesCS3A01G146900 chr2A 94.389 303 15 1 4725 5027 230805641 230805941 1.120000e-126 464.0
19 TraesCS3A01G146900 chr2A 94.371 302 15 1 4726 5027 744619578 744619877 4.040000e-126 462.0
20 TraesCS3A01G146900 chr2A 93.485 307 18 1 4725 5031 200415603 200415907 6.760000e-124 455.0
21 TraesCS3A01G146900 chr2A 89.500 200 17 3 5529 5726 743375193 743375390 3.430000e-62 250.0
22 TraesCS3A01G146900 chr2A 88.832 197 21 1 5529 5725 539305309 539305114 2.060000e-59 241.0
23 TraesCS3A01G146900 chr5A 93.750 336 11 7 4705 5034 368127382 368127713 3.980000e-136 496.0
24 TraesCS3A01G146900 chr5A 95.050 303 12 2 4725 5026 680837557 680837257 1.870000e-129 473.0
25 TraesCS3A01G146900 chr6A 94.586 314 14 2 4713 5026 29150071 29149761 3.100000e-132 483.0
26 TraesCS3A01G146900 chr2B 89.394 198 19 2 5529 5726 381292070 381292265 1.230000e-61 248.0
27 TraesCS3A01G146900 chr7B 88.500 200 20 3 5529 5726 663837633 663837831 7.410000e-59 239.0
28 TraesCS3A01G146900 chr2D 88.442 199 21 2 5528 5726 12302163 12301967 7.410000e-59 239.0
29 TraesCS3A01G146900 chr3B 87.805 205 21 4 5523 5726 623667587 623667386 2.670000e-58 237.0
30 TraesCS3A01G146900 chr3B 87.745 204 22 3 5524 5726 32447515 32447716 9.590000e-58 235.0
31 TraesCS3A01G146900 chr4A 87.379 206 23 3 5522 5726 572708410 572708613 3.450000e-57 233.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G146900 chr3A 128538964 128544689 5725 True 10575.00 10575 100.0000 1 5726 1 chr3A.!!$R1 5725
1 TraesCS3A01G146900 chr1A 389828949 389834333 5384 False 4302.50 7672 93.6160 1 5723 2 chr1A.!!$F1 5722
2 TraesCS3A01G146900 chr1D 309982247 309989423 7176 False 1652.70 3290 89.2990 1 4711 4 chr1D.!!$F2 4710
3 TraesCS3A01G146900 chr1B 419967873 419973494 5621 True 1293.08 3164 93.1704 10 5323 5 chr1B.!!$R1 5313
4 TraesCS3A01G146900 chrUn 440332027 440332670 643 True 1048.00 1048 96.1180 4071 4711 1 chrUn.!!$R1 640
5 TraesCS3A01G146900 chr2A 35794741 35795384 643 True 1048.00 1048 96.1180 4071 4711 1 chr2A.!!$R2 640

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
547 3084 0.388649 ACTTACTGCGACTTCGGCAG 60.389 55.000 11.85 11.85 43.66 4.85 F
681 3224 1.071542 TCACCAACTCATTCGCTTCCA 59.928 47.619 0.00 0.00 0.00 3.53 F
1488 4077 1.945354 GAGGGATCAACGGACGAGCA 61.945 60.000 0.00 0.00 0.00 4.26 F
1920 4524 1.112315 AGTGCAATTGCCGGGTGAAA 61.112 50.000 26.94 3.21 41.18 2.69 F
3068 5684 0.098905 TCGAAGAGAATCAGACGCCG 59.901 55.000 0.00 0.00 37.82 6.46 F
3828 6455 0.184933 AGGGCTGCCAACTTGTGTAA 59.815 50.000 22.05 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 4025 1.076332 GAACCGAAGAACCATCCGTG 58.924 55.000 0.00 0.00 0.00 4.94 R
1558 4150 1.565305 CATAGCGTCAGGAGAACAGC 58.435 55.000 0.00 0.00 0.00 4.40 R
3054 5670 0.103208 ACATCCGGCGTCTGATTCTC 59.897 55.000 6.01 0.00 0.00 2.87 R
3805 6432 1.228367 CAAGTTGGCAGCCCTCAGT 60.228 57.895 9.64 0.00 0.00 3.41 R
4716 7418 0.175760 ACGGTGACATTCAGGATCCG 59.824 55.000 5.98 1.36 41.77 4.18 R
5541 8853 0.031585 TGAACGCTTGCGTCTGTACT 59.968 50.000 20.87 4.26 0.00 2.73 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
178 190 0.825010 ACGCATACCGGTAGGGGTAG 60.825 60.000 37.61 19.71 45.29 3.18
181 193 1.157039 ATACCGGTAGGGGTAGGCC 59.843 63.158 20.91 0.00 45.29 5.19
182 194 1.667935 ATACCGGTAGGGGTAGGCCA 61.668 60.000 20.91 0.00 45.29 5.36
268 291 0.530744 TAGAACTGTAGCACCGGCAG 59.469 55.000 0.00 2.29 44.61 4.85
351 374 2.511600 GCCCTGTTGATCGTCGGG 60.512 66.667 7.57 7.57 37.97 5.14
547 3084 0.388649 ACTTACTGCGACTTCGGCAG 60.389 55.000 11.85 11.85 43.66 4.85
681 3224 1.071542 TCACCAACTCATTCGCTTCCA 59.928 47.619 0.00 0.00 0.00 3.53
951 3531 3.667360 TGCTCATATAATGCTCATGCGT 58.333 40.909 0.00 0.00 43.34 5.24
953 3533 3.241900 GCTCATATAATGCTCATGCGTCG 60.242 47.826 0.00 0.00 43.34 5.12
1488 4077 1.945354 GAGGGATCAACGGACGAGCA 61.945 60.000 0.00 0.00 0.00 4.26
1558 4150 6.577427 GTGAGTACAAAAAGAACAATTAGCCG 59.423 38.462 0.00 0.00 0.00 5.52
1882 4483 5.107133 TCGTCAGGCTAGTGTAATTTTAGC 58.893 41.667 0.00 0.00 39.19 3.09
1888 4492 8.243426 TCAGGCTAGTGTAATTTTAGCATTTTG 58.757 33.333 5.26 0.00 41.15 2.44
1889 4493 8.028938 CAGGCTAGTGTAATTTTAGCATTTTGT 58.971 33.333 5.26 0.00 41.15 2.83
1920 4524 1.112315 AGTGCAATTGCCGGGTGAAA 61.112 50.000 26.94 3.21 41.18 2.69
2401 5010 6.459848 CCAAGATCAAGCATGAATCTTTCTCC 60.460 42.308 11.42 0.00 39.49 3.71
2578 5192 9.710900 TGCTAATATTTACAGTCAGATGTATGG 57.289 33.333 0.00 0.00 35.65 2.74
2633 5247 2.113860 TGTACTTTCAGGAGCATGCC 57.886 50.000 15.66 5.80 0.00 4.40
2697 5311 5.363562 TCAGGAGATGCTGTGATTAATGT 57.636 39.130 0.00 0.00 0.00 2.71
3054 5670 6.453003 CGAAGTATGTTCAATCACAGTCGAAG 60.453 42.308 0.00 0.00 0.00 3.79
3068 5684 0.098905 TCGAAGAGAATCAGACGCCG 59.901 55.000 0.00 0.00 37.82 6.46
3238 5856 6.156949 AGCTTGAAAGGGTTGATCTGAGTATA 59.843 38.462 0.00 0.00 0.00 1.47
3490 6110 8.047310 AGGATATTTTAGTTACAGTTGTCCCTG 58.953 37.037 0.00 0.00 38.45 4.45
3512 6132 3.873952 GGAGTGCTGGAGTTCATAATGAC 59.126 47.826 0.00 0.00 0.00 3.06
3631 6251 3.186047 CCGCGGATTGGTCGTGTC 61.186 66.667 24.07 0.00 36.53 3.67
3766 6386 7.448588 TTCATCAAATTCACTGAAACAAACG 57.551 32.000 0.00 0.00 0.00 3.60
3770 6390 5.802956 TCAAATTCACTGAAACAAACGGAAC 59.197 36.000 0.00 0.00 0.00 3.62
3805 6432 8.615878 AACACACTAGTAATCAAATTAGCACA 57.384 30.769 0.00 0.00 0.00 4.57
3818 6445 4.648626 GCACACTGAGGGCTGCCA 62.649 66.667 22.05 0.00 45.63 4.92
3819 6446 2.113774 CACACTGAGGGCTGCCAA 59.886 61.111 22.05 4.32 0.00 4.52
3820 6447 2.113986 ACACTGAGGGCTGCCAAC 59.886 61.111 22.05 13.75 0.00 3.77
3821 6448 2.433446 CACTGAGGGCTGCCAACT 59.567 61.111 22.05 9.28 0.00 3.16
3822 6449 1.228367 CACTGAGGGCTGCCAACTT 60.228 57.895 22.05 2.22 0.00 2.66
3823 6450 1.228367 ACTGAGGGCTGCCAACTTG 60.228 57.895 22.05 8.55 0.00 3.16
3824 6451 1.228367 CTGAGGGCTGCCAACTTGT 60.228 57.895 22.05 0.00 0.00 3.16
3827 6454 0.250727 GAGGGCTGCCAACTTGTGTA 60.251 55.000 22.05 0.00 0.00 2.90
3828 6455 0.184933 AGGGCTGCCAACTTGTGTAA 59.815 50.000 22.05 0.00 0.00 2.41
3832 6459 2.225727 GGCTGCCAACTTGTGTAAGTAC 59.774 50.000 15.17 0.00 46.14 2.73
3862 6489 6.963322 ACCTTCTATCTCATGCCTAAGTTTT 58.037 36.000 0.00 0.00 0.00 2.43
3865 6492 7.226325 CCTTCTATCTCATGCCTAAGTTTTGAG 59.774 40.741 0.00 0.00 36.09 3.02
3963 6609 3.388345 GGATACTTTCTAGGAAGCGGG 57.612 52.381 10.95 0.00 0.00 6.13
3992 6638 7.658179 TTATGCTTGAAGAACTCAGTACTTG 57.342 36.000 0.00 0.00 34.81 3.16
4015 6665 1.852633 ACCAAGGCCCTAAATTCAGC 58.147 50.000 0.00 0.00 0.00 4.26
4316 7013 2.125269 GCCGCCACCGTACTTGAT 60.125 61.111 0.00 0.00 0.00 2.57
4317 7014 2.171725 GCCGCCACCGTACTTGATC 61.172 63.158 0.00 0.00 0.00 2.92
4335 7037 4.268720 GATCTCCTCGAGGCCTGT 57.731 61.111 27.39 12.12 34.44 4.00
4724 7426 2.278857 CGCGAGAACCGGATCCTG 60.279 66.667 9.46 5.80 39.04 3.86
4725 7427 2.771639 CGCGAGAACCGGATCCTGA 61.772 63.158 9.46 0.00 39.04 3.86
4726 7428 1.515954 GCGAGAACCGGATCCTGAA 59.484 57.895 9.46 0.00 39.04 3.02
4727 7429 0.105039 GCGAGAACCGGATCCTGAAT 59.895 55.000 9.46 0.00 39.04 2.57
4728 7430 1.858091 CGAGAACCGGATCCTGAATG 58.142 55.000 9.46 0.00 33.91 2.67
4729 7431 1.137086 CGAGAACCGGATCCTGAATGT 59.863 52.381 9.46 0.00 33.91 2.71
4730 7432 2.799917 CGAGAACCGGATCCTGAATGTC 60.800 54.545 9.46 5.66 33.91 3.06
4731 7433 2.168521 GAGAACCGGATCCTGAATGTCA 59.831 50.000 9.46 0.00 0.00 3.58
4732 7434 2.093447 AGAACCGGATCCTGAATGTCAC 60.093 50.000 9.46 0.00 0.00 3.67
4733 7435 0.541863 ACCGGATCCTGAATGTCACC 59.458 55.000 9.46 0.00 0.00 4.02
4734 7436 0.530650 CCGGATCCTGAATGTCACCG 60.531 60.000 10.75 0.00 38.83 4.94
4735 7437 0.175760 CGGATCCTGAATGTCACCGT 59.824 55.000 10.75 0.00 35.21 4.83
4736 7438 1.656652 GGATCCTGAATGTCACCGTG 58.343 55.000 3.84 0.00 0.00 4.94
4737 7439 1.009829 GATCCTGAATGTCACCGTGC 58.990 55.000 0.00 0.00 0.00 5.34
4738 7440 0.615331 ATCCTGAATGTCACCGTGCT 59.385 50.000 0.00 0.00 0.00 4.40
4739 7441 1.262417 TCCTGAATGTCACCGTGCTA 58.738 50.000 0.00 0.00 0.00 3.49
4740 7442 1.831106 TCCTGAATGTCACCGTGCTAT 59.169 47.619 0.00 0.00 0.00 2.97
4741 7443 3.028130 TCCTGAATGTCACCGTGCTATA 58.972 45.455 0.00 0.00 0.00 1.31
4742 7444 3.123804 CCTGAATGTCACCGTGCTATAC 58.876 50.000 0.00 0.00 0.00 1.47
4743 7445 3.430236 CCTGAATGTCACCGTGCTATACA 60.430 47.826 0.00 0.00 0.00 2.29
4744 7446 3.780902 TGAATGTCACCGTGCTATACAG 58.219 45.455 0.00 0.00 0.00 2.74
4745 7447 3.194755 TGAATGTCACCGTGCTATACAGT 59.805 43.478 0.00 0.00 0.00 3.55
4746 7448 2.647529 TGTCACCGTGCTATACAGTG 57.352 50.000 0.00 0.00 38.72 3.66
4747 7449 1.890489 TGTCACCGTGCTATACAGTGT 59.110 47.619 0.00 0.00 38.54 3.55
4748 7450 2.297880 TGTCACCGTGCTATACAGTGTT 59.702 45.455 0.00 0.00 38.54 3.32
4749 7451 3.506844 TGTCACCGTGCTATACAGTGTTA 59.493 43.478 0.00 0.00 38.54 2.41
4750 7452 4.103357 GTCACCGTGCTATACAGTGTTAG 58.897 47.826 0.00 4.72 38.54 2.34
4751 7453 3.129813 TCACCGTGCTATACAGTGTTAGG 59.870 47.826 0.00 0.00 38.54 2.69
4752 7454 2.159142 ACCGTGCTATACAGTGTTAGGC 60.159 50.000 0.00 4.11 0.00 3.93
4753 7455 2.100916 CCGTGCTATACAGTGTTAGGCT 59.899 50.000 0.00 0.00 0.00 4.58
4754 7456 3.317149 CCGTGCTATACAGTGTTAGGCTA 59.683 47.826 0.00 0.00 0.00 3.93
4755 7457 4.537965 CGTGCTATACAGTGTTAGGCTAG 58.462 47.826 0.00 0.00 0.00 3.42
4756 7458 4.036498 CGTGCTATACAGTGTTAGGCTAGT 59.964 45.833 0.00 0.00 0.00 2.57
4757 7459 5.282510 GTGCTATACAGTGTTAGGCTAGTG 58.717 45.833 0.00 0.00 0.00 2.74
4758 7460 4.954202 TGCTATACAGTGTTAGGCTAGTGT 59.046 41.667 0.00 2.11 34.94 3.55
4759 7461 6.039047 GTGCTATACAGTGTTAGGCTAGTGTA 59.961 42.308 0.00 6.04 37.19 2.90
4760 7462 6.604396 TGCTATACAGTGTTAGGCTAGTGTAA 59.396 38.462 0.00 0.00 36.59 2.41
4761 7463 7.123098 TGCTATACAGTGTTAGGCTAGTGTAAA 59.877 37.037 0.00 0.00 36.59 2.01
4762 7464 7.977853 GCTATACAGTGTTAGGCTAGTGTAAAA 59.022 37.037 0.00 0.48 36.59 1.52
4764 7466 8.718102 ATACAGTGTTAGGCTAGTGTAAAATG 57.282 34.615 0.00 0.00 36.59 2.32
4765 7467 6.765403 ACAGTGTTAGGCTAGTGTAAAATGA 58.235 36.000 0.00 0.00 0.00 2.57
4766 7468 7.221450 ACAGTGTTAGGCTAGTGTAAAATGAA 58.779 34.615 0.00 0.00 0.00 2.57
4767 7469 7.387948 ACAGTGTTAGGCTAGTGTAAAATGAAG 59.612 37.037 0.00 0.00 0.00 3.02
4768 7470 7.602644 CAGTGTTAGGCTAGTGTAAAATGAAGA 59.397 37.037 0.00 0.00 0.00 2.87
4769 7471 8.154856 AGTGTTAGGCTAGTGTAAAATGAAGAA 58.845 33.333 0.00 0.00 0.00 2.52
4770 7472 8.443937 GTGTTAGGCTAGTGTAAAATGAAGAAG 58.556 37.037 0.00 0.00 0.00 2.85
4771 7473 7.606456 TGTTAGGCTAGTGTAAAATGAAGAAGG 59.394 37.037 0.00 0.00 0.00 3.46
4772 7474 6.374417 AGGCTAGTGTAAAATGAAGAAGGA 57.626 37.500 0.00 0.00 0.00 3.36
4773 7475 6.779860 AGGCTAGTGTAAAATGAAGAAGGAA 58.220 36.000 0.00 0.00 0.00 3.36
4774 7476 7.231467 AGGCTAGTGTAAAATGAAGAAGGAAA 58.769 34.615 0.00 0.00 0.00 3.13
4775 7477 7.391833 AGGCTAGTGTAAAATGAAGAAGGAAAG 59.608 37.037 0.00 0.00 0.00 2.62
4776 7478 7.175119 GGCTAGTGTAAAATGAAGAAGGAAAGT 59.825 37.037 0.00 0.00 0.00 2.66
4777 7479 8.568794 GCTAGTGTAAAATGAAGAAGGAAAGTT 58.431 33.333 0.00 0.00 0.00 2.66
4780 7482 9.067986 AGTGTAAAATGAAGAAGGAAAGTTAGG 57.932 33.333 0.00 0.00 0.00 2.69
4781 7483 9.063615 GTGTAAAATGAAGAAGGAAAGTTAGGA 57.936 33.333 0.00 0.00 0.00 2.94
4782 7484 9.635404 TGTAAAATGAAGAAGGAAAGTTAGGAA 57.365 29.630 0.00 0.00 0.00 3.36
4785 7487 9.987272 AAAATGAAGAAGGAAAGTTAGGAATTG 57.013 29.630 0.00 0.00 0.00 2.32
4786 7488 8.712228 AATGAAGAAGGAAAGTTAGGAATTGT 57.288 30.769 0.00 0.00 0.00 2.71
4787 7489 8.712228 ATGAAGAAGGAAAGTTAGGAATTGTT 57.288 30.769 0.00 0.00 0.00 2.83
4788 7490 9.807921 ATGAAGAAGGAAAGTTAGGAATTGTTA 57.192 29.630 0.00 0.00 0.00 2.41
4789 7491 9.284968 TGAAGAAGGAAAGTTAGGAATTGTTAG 57.715 33.333 0.00 0.00 0.00 2.34
4790 7492 9.286170 GAAGAAGGAAAGTTAGGAATTGTTAGT 57.714 33.333 0.00 0.00 0.00 2.24
4792 7494 9.945904 AGAAGGAAAGTTAGGAATTGTTAGTAG 57.054 33.333 0.00 0.00 0.00 2.57
4793 7495 9.939802 GAAGGAAAGTTAGGAATTGTTAGTAGA 57.060 33.333 0.00 0.00 0.00 2.59
4795 7497 9.892130 AGGAAAGTTAGGAATTGTTAGTAGATG 57.108 33.333 0.00 0.00 0.00 2.90
4796 7498 9.886132 GGAAAGTTAGGAATTGTTAGTAGATGA 57.114 33.333 0.00 0.00 0.00 2.92
4828 7530 9.569122 AGATTGTTTAGTGTTGGTATTTACTGT 57.431 29.630 0.00 0.00 0.00 3.55
4877 7579 9.896263 ATTTTATTTCACCATCAATTTGTTTGC 57.104 25.926 0.00 0.00 35.16 3.68
4878 7580 8.442632 TTTATTTCACCATCAATTTGTTTGCA 57.557 26.923 0.00 0.00 35.16 4.08
4879 7581 8.618702 TTATTTCACCATCAATTTGTTTGCAT 57.381 26.923 0.00 0.00 35.16 3.96
4880 7582 9.716531 TTATTTCACCATCAATTTGTTTGCATA 57.283 25.926 0.00 0.00 35.16 3.14
4881 7583 8.795842 ATTTCACCATCAATTTGTTTGCATAT 57.204 26.923 0.00 0.00 35.16 1.78
4882 7584 9.887629 ATTTCACCATCAATTTGTTTGCATATA 57.112 25.926 0.00 0.00 35.16 0.86
4883 7585 9.716531 TTTCACCATCAATTTGTTTGCATATAA 57.283 25.926 0.00 0.00 35.16 0.98
4884 7586 9.887629 TTCACCATCAATTTGTTTGCATATAAT 57.112 25.926 0.00 0.00 35.16 1.28
4885 7587 9.887629 TCACCATCAATTTGTTTGCATATAATT 57.112 25.926 0.00 0.00 35.16 1.40
4918 7620 7.652300 TGTATACGGTAGATCATCAAATTGC 57.348 36.000 0.00 0.00 0.00 3.56
4919 7621 7.213678 TGTATACGGTAGATCATCAAATTGCA 58.786 34.615 0.00 0.00 0.00 4.08
4920 7622 7.713073 TGTATACGGTAGATCATCAAATTGCAA 59.287 33.333 0.00 0.00 0.00 4.08
4921 7623 5.895636 ACGGTAGATCATCAAATTGCAAA 57.104 34.783 1.71 0.00 0.00 3.68
4922 7624 6.455360 ACGGTAGATCATCAAATTGCAAAT 57.545 33.333 1.71 0.00 0.00 2.32
4923 7625 6.866480 ACGGTAGATCATCAAATTGCAAATT 58.134 32.000 1.71 0.00 0.00 1.82
4924 7626 7.995289 ACGGTAGATCATCAAATTGCAAATTA 58.005 30.769 1.71 0.00 0.00 1.40
4925 7627 8.465999 ACGGTAGATCATCAAATTGCAAATTAA 58.534 29.630 1.71 0.00 0.00 1.40
4926 7628 9.467258 CGGTAGATCATCAAATTGCAAATTAAT 57.533 29.630 1.71 0.00 0.00 1.40
4990 7692 9.863845 AGAAAAGTTAGAGTATTGTAGCTTCTC 57.136 33.333 0.00 0.00 0.00 2.87
4991 7693 9.863845 GAAAAGTTAGAGTATTGTAGCTTCTCT 57.136 33.333 0.00 0.00 38.69 3.10
4999 7701 8.417884 AGAGTATTGTAGCTTCTCTAACATTCC 58.582 37.037 0.00 0.00 34.34 3.01
5000 7702 8.312669 AGTATTGTAGCTTCTCTAACATTCCT 57.687 34.615 0.00 0.00 0.00 3.36
5001 7703 8.763601 AGTATTGTAGCTTCTCTAACATTCCTT 58.236 33.333 0.00 0.00 0.00 3.36
5002 7704 9.036671 GTATTGTAGCTTCTCTAACATTCCTTC 57.963 37.037 0.00 0.00 0.00 3.46
5003 7705 6.859112 TGTAGCTTCTCTAACATTCCTTCT 57.141 37.500 0.00 0.00 0.00 2.85
5004 7706 7.246171 TGTAGCTTCTCTAACATTCCTTCTT 57.754 36.000 0.00 0.00 0.00 2.52
5005 7707 8.362464 TGTAGCTTCTCTAACATTCCTTCTTA 57.638 34.615 0.00 0.00 0.00 2.10
5006 7708 8.812972 TGTAGCTTCTCTAACATTCCTTCTTAA 58.187 33.333 0.00 0.00 0.00 1.85
5007 7709 9.825109 GTAGCTTCTCTAACATTCCTTCTTAAT 57.175 33.333 0.00 0.00 0.00 1.40
5008 7710 8.729805 AGCTTCTCTAACATTCCTTCTTAATG 57.270 34.615 0.00 0.00 39.68 1.90
5009 7711 8.325046 AGCTTCTCTAACATTCCTTCTTAATGT 58.675 33.333 0.00 0.00 46.77 2.71
5018 7720 8.649973 ACATTCCTTCTTAATGTTAGACGATC 57.350 34.615 0.00 0.00 43.31 3.69
5019 7721 7.711339 ACATTCCTTCTTAATGTTAGACGATCC 59.289 37.037 0.00 0.00 43.31 3.36
5020 7722 5.828747 TCCTTCTTAATGTTAGACGATCCG 58.171 41.667 0.00 0.00 0.00 4.18
5021 7723 4.982916 CCTTCTTAATGTTAGACGATCCGG 59.017 45.833 0.00 0.00 0.00 5.14
5022 7724 5.451520 CCTTCTTAATGTTAGACGATCCGGT 60.452 44.000 0.00 0.00 0.00 5.28
5023 7725 5.587388 TCTTAATGTTAGACGATCCGGTT 57.413 39.130 0.00 0.00 0.00 4.44
5024 7726 5.585390 TCTTAATGTTAGACGATCCGGTTC 58.415 41.667 0.00 0.74 0.00 3.62
5025 7727 2.884894 ATGTTAGACGATCCGGTTCC 57.115 50.000 0.00 0.00 0.00 3.62
5026 7728 0.452987 TGTTAGACGATCCGGTTCCG 59.547 55.000 0.00 6.34 0.00 4.30
5027 7729 0.869028 GTTAGACGATCCGGTTCCGC 60.869 60.000 0.00 0.00 0.00 5.54
5028 7730 2.008268 TTAGACGATCCGGTTCCGCC 62.008 60.000 0.00 0.00 0.00 6.13
5052 7754 0.811616 CGGTGCTGGCCTAGATTGTC 60.812 60.000 3.32 0.00 0.00 3.18
5073 7775 2.512515 GCCTTCGTAGCTGCTGGG 60.513 66.667 13.43 3.83 0.00 4.45
5091 7802 1.511305 GTGCAGCTGCCGAGTACTA 59.489 57.895 34.64 11.80 41.18 1.82
5092 7803 0.108804 GTGCAGCTGCCGAGTACTAA 60.109 55.000 34.64 11.00 41.18 2.24
5093 7804 0.173481 TGCAGCTGCCGAGTACTAAG 59.827 55.000 34.64 0.00 41.18 2.18
5094 7805 0.173708 GCAGCTGCCGAGTACTAAGT 59.826 55.000 28.76 0.00 34.31 2.24
5095 7806 1.404391 GCAGCTGCCGAGTACTAAGTA 59.596 52.381 28.76 0.00 34.31 2.24
5096 7807 2.795331 GCAGCTGCCGAGTACTAAGTAC 60.795 54.545 28.76 0.00 35.78 2.73
5097 7808 2.422479 CAGCTGCCGAGTACTAAGTACA 59.578 50.000 0.00 0.00 41.03 2.90
5135 8353 6.460676 GGTTTTGGGATTGAGATGATGATGTC 60.461 42.308 0.00 0.00 0.00 3.06
5220 8531 1.459592 AGATTTTGTGCTGCGTACGTC 59.540 47.619 17.90 9.82 0.00 4.34
5323 8634 1.079819 CCCACGATCGAGCTTGTGT 60.080 57.895 24.34 0.00 0.00 3.72
5439 8750 2.617274 GCCACCGTGCCTTTCTCAC 61.617 63.158 0.00 0.00 0.00 3.51
5441 8752 1.227823 CACCGTGCCTTTCTCACCA 60.228 57.895 0.00 0.00 0.00 4.17
5445 8756 1.845809 CGTGCCTTTCTCACCACAGC 61.846 60.000 0.00 0.00 0.00 4.40
5472 8783 1.785041 GAAGTGGCAGCGCTTGTTGA 61.785 55.000 7.50 0.00 0.00 3.18
5479 8790 1.865248 GCAGCGCTTGTTGATGTGTTT 60.865 47.619 7.50 0.00 0.00 2.83
5481 8792 0.503961 GCGCTTGTTGATGTGTTTGC 59.496 50.000 0.00 0.00 0.00 3.68
5486 8797 1.020437 TGTTGATGTGTTTGCTGCGA 58.980 45.000 0.00 0.00 0.00 5.10
5507 8819 3.616956 TCATGGAGCACTAGTTCTTGG 57.383 47.619 0.00 0.00 0.00 3.61
5517 8829 3.380004 CACTAGTTCTTGGAGAGCGAGAT 59.620 47.826 8.42 0.00 33.29 2.75
5521 8833 2.427453 GTTCTTGGAGAGCGAGATGGTA 59.573 50.000 0.00 0.00 0.00 3.25
5522 8834 2.735151 TCTTGGAGAGCGAGATGGTAA 58.265 47.619 0.00 0.00 0.00 2.85
5524 8836 2.961526 TGGAGAGCGAGATGGTAAAC 57.038 50.000 0.00 0.00 0.00 2.01
5533 8845 5.758924 AGCGAGATGGTAAACTTGTTTTTC 58.241 37.500 4.00 0.00 0.00 2.29
5534 8846 5.531287 AGCGAGATGGTAAACTTGTTTTTCT 59.469 36.000 4.00 3.15 0.00 2.52
5535 8847 6.039382 AGCGAGATGGTAAACTTGTTTTTCTT 59.961 34.615 4.00 0.00 0.00 2.52
5537 8849 7.858879 GCGAGATGGTAAACTTGTTTTTCTTAA 59.141 33.333 4.00 0.00 0.00 1.85
5538 8850 9.166126 CGAGATGGTAAACTTGTTTTTCTTAAC 57.834 33.333 4.00 0.00 0.00 2.01
5540 8852 9.797556 AGATGGTAAACTTGTTTTTCTTAACAC 57.202 29.630 4.00 0.00 37.72 3.32
5541 8853 9.575783 GATGGTAAACTTGTTTTTCTTAACACA 57.424 29.630 4.00 0.00 37.72 3.72
5542 8854 8.973835 TGGTAAACTTGTTTTTCTTAACACAG 57.026 30.769 4.00 0.00 37.72 3.66
5549 8861 8.448615 ACTTGTTTTTCTTAACACAGTACAGAC 58.551 33.333 0.00 0.00 37.72 3.51
5551 8863 5.646467 TTTTCTTAACACAGTACAGACGC 57.354 39.130 0.00 0.00 0.00 5.19
5568 8880 2.308347 CGCAAGCGTTCACATAAACA 57.692 45.000 6.25 0.00 34.35 2.83
5569 8881 1.969256 CGCAAGCGTTCACATAAACAC 59.031 47.619 6.25 0.00 34.35 3.32
5570 8882 1.969256 GCAAGCGTTCACATAAACACG 59.031 47.619 0.00 0.00 35.71 4.49
5581 8893 5.175127 TCACATAAACACGCATACACTCAT 58.825 37.500 0.00 0.00 0.00 2.90
5591 8903 3.990469 CGCATACACTCATCCCTATGAAC 59.010 47.826 0.00 0.00 41.57 3.18
5599 8911 1.665679 CATCCCTATGAACGCACACAC 59.334 52.381 0.00 0.00 34.84 3.82
5603 8915 0.721154 CTATGAACGCACACACGCAT 59.279 50.000 0.00 0.00 36.19 4.73
5605 8917 1.368641 ATGAACGCACACACGCATAT 58.631 45.000 0.00 0.00 36.19 1.78
5607 8919 0.026285 GAACGCACACACGCATATCC 59.974 55.000 0.00 0.00 36.19 2.59
5608 8920 0.391130 AACGCACACACGCATATCCT 60.391 50.000 0.00 0.00 36.19 3.24
5609 8921 0.458260 ACGCACACACGCATATCCTA 59.542 50.000 0.00 0.00 36.19 2.94
5610 8922 0.852777 CGCACACACGCATATCCTAC 59.147 55.000 0.00 0.00 0.00 3.18
5612 8924 1.865865 CACACACGCATATCCTACCC 58.134 55.000 0.00 0.00 0.00 3.69
5613 8925 1.412710 CACACACGCATATCCTACCCT 59.587 52.381 0.00 0.00 0.00 4.34
5625 8937 3.130734 TCCTACCCTTATGAGCACCTT 57.869 47.619 0.00 0.00 0.00 3.50
5645 8957 0.179111 CGAGAAACTGAGCCGGCATA 60.179 55.000 31.54 16.21 0.00 3.14
5650 8962 2.645838 AACTGAGCCGGCATATCATT 57.354 45.000 31.54 15.16 0.00 2.57
5652 8964 2.936202 ACTGAGCCGGCATATCATTTT 58.064 42.857 31.54 3.33 0.00 1.82
5711 9023 1.305549 GGAACGTCCCCTCCCACTA 60.306 63.158 0.00 0.00 0.00 2.74
5716 9028 1.538687 CGTCCCCTCCCACTAAACGT 61.539 60.000 0.00 0.00 0.00 3.99
5723 9035 1.017177 TCCCACTAAACGTGCATCGC 61.017 55.000 8.31 0.00 42.42 4.58
5724 9036 1.423845 CCACTAAACGTGCATCGCC 59.576 57.895 8.31 0.00 42.42 5.54
5725 9037 1.058748 CACTAAACGTGCATCGCCG 59.941 57.895 8.31 0.93 44.19 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 190 2.918300 GATTCCTTCCCTGGCTGGCC 62.918 65.000 4.64 4.43 0.00 5.36
181 193 0.329261 TGTGATTCCTTCCCTGGCTG 59.671 55.000 0.00 0.00 0.00 4.85
182 194 1.302907 ATGTGATTCCTTCCCTGGCT 58.697 50.000 0.00 0.00 0.00 4.75
268 291 1.009389 CGACCCGTCAGAGAAACTGC 61.009 60.000 0.00 0.00 45.38 4.40
337 360 0.246635 AAGTCCCCGACGATCAACAG 59.753 55.000 0.00 0.00 37.67 3.16
351 374 1.139095 CCGCGACTACTCCAAGTCC 59.861 63.158 8.23 0.00 42.46 3.85
681 3224 0.542232 AGTGGGAGGAGTAACTGCGT 60.542 55.000 0.00 0.00 0.00 5.24
951 3531 1.371183 CAACAGTCCAGAAGGGCGA 59.629 57.895 0.00 0.00 46.92 5.54
953 3533 1.973812 GGCAACAGTCCAGAAGGGC 60.974 63.158 0.00 0.00 40.92 5.19
1436 4025 1.076332 GAACCGAAGAACCATCCGTG 58.924 55.000 0.00 0.00 0.00 4.94
1558 4150 1.565305 CATAGCGTCAGGAGAACAGC 58.435 55.000 0.00 0.00 0.00 4.40
1882 4483 5.921976 TGCACTGCTTCTATTCAACAAAATG 59.078 36.000 1.98 0.00 0.00 2.32
1888 4492 4.325472 GCAATTGCACTGCTTCTATTCAAC 59.675 41.667 25.36 0.00 41.59 3.18
1889 4493 4.487948 GCAATTGCACTGCTTCTATTCAA 58.512 39.130 25.36 0.00 41.59 2.69
1920 4524 2.108250 ACACTTTCCCCTGTGTGCTATT 59.892 45.455 0.00 0.00 44.52 1.73
2401 5010 1.721489 CGAACATCCAACGTTTCGCTG 60.721 52.381 0.00 0.00 0.00 5.18
2419 5028 3.706373 GCAAGGGAGGCAGGACGA 61.706 66.667 0.00 0.00 0.00 4.20
2566 5176 7.095607 CGAGTATAAAAAGGCCATACATCTGAC 60.096 40.741 5.01 0.00 0.00 3.51
2578 5192 7.702348 AGAATTTGCATTCGAGTATAAAAAGGC 59.298 33.333 0.00 0.00 43.38 4.35
2771 5387 7.333528 TGAATAAGGCAGCTATTTGTAAAGG 57.666 36.000 0.00 0.00 0.00 3.11
3054 5670 0.103208 ACATCCGGCGTCTGATTCTC 59.897 55.000 6.01 0.00 0.00 2.87
3348 5967 6.820656 TGACACACTGGCAAAATTACAAAATT 59.179 30.769 0.00 0.00 28.38 1.82
3349 5968 6.344500 TGACACACTGGCAAAATTACAAAAT 58.656 32.000 0.00 0.00 28.38 1.82
3490 6110 3.873952 GTCATTATGAACTCCAGCACTCC 59.126 47.826 0.00 0.00 0.00 3.85
3512 6132 5.545658 ATGTGAGTTATTTGTTAGCCACG 57.454 39.130 0.00 0.00 0.00 4.94
3631 6251 4.083643 GGCATGAGATCACAAATCATACGG 60.084 45.833 0.00 0.00 32.51 4.02
3766 6386 7.435068 ACTAGTGTGTTATTCATGTTGTTCC 57.565 36.000 0.00 0.00 0.00 3.62
3805 6432 1.228367 CAAGTTGGCAGCCCTCAGT 60.228 57.895 9.64 0.00 0.00 3.41
3818 6445 4.275936 AGGTCGTACGTACTTACACAAGTT 59.724 41.667 22.55 2.71 42.51 2.66
3819 6446 3.815401 AGGTCGTACGTACTTACACAAGT 59.185 43.478 22.55 0.00 46.77 3.16
3820 6447 4.410492 AGGTCGTACGTACTTACACAAG 57.590 45.455 22.55 5.50 37.81 3.16
3821 6448 4.515191 AGAAGGTCGTACGTACTTACACAA 59.485 41.667 22.55 0.00 0.00 3.33
3822 6449 4.065088 AGAAGGTCGTACGTACTTACACA 58.935 43.478 22.55 0.00 0.00 3.72
3823 6450 4.670227 AGAAGGTCGTACGTACTTACAC 57.330 45.455 22.55 13.15 0.00 2.90
3824 6451 6.341316 AGATAGAAGGTCGTACGTACTTACA 58.659 40.000 22.55 14.40 0.00 2.41
3827 6454 5.423015 TGAGATAGAAGGTCGTACGTACTT 58.577 41.667 22.55 20.96 0.00 2.24
3828 6455 5.016051 TGAGATAGAAGGTCGTACGTACT 57.984 43.478 22.55 11.62 0.00 2.73
3832 6459 3.556513 GCATGAGATAGAAGGTCGTACG 58.443 50.000 9.53 9.53 0.00 3.67
3890 6517 3.616821 TGTTTTATCTGAAGCCGTCGATG 59.383 43.478 0.00 0.00 0.00 3.84
3891 6518 3.857052 TGTTTTATCTGAAGCCGTCGAT 58.143 40.909 0.00 0.00 0.00 3.59
3947 6593 0.250513 CAGCCCGCTTCCTAGAAAGT 59.749 55.000 0.00 0.00 0.00 2.66
3961 6607 3.507622 AGTTCTTCAAGCATAAACAGCCC 59.492 43.478 0.00 0.00 0.00 5.19
3962 6608 4.216257 TGAGTTCTTCAAGCATAAACAGCC 59.784 41.667 0.00 0.00 31.34 4.85
3963 6609 5.049129 ACTGAGTTCTTCAAGCATAAACAGC 60.049 40.000 0.00 0.00 34.81 4.40
3992 6638 3.161866 TGAATTTAGGGCCTTGGTTCAC 58.838 45.455 13.45 0.00 0.00 3.18
4015 6665 6.016860 TCTGAATTCATGAACAGTTGACCAAG 60.017 38.462 19.83 5.36 0.00 3.61
4537 7239 3.335534 GTCCAAGTTGTCGCGCGT 61.336 61.111 30.98 6.92 0.00 6.01
4711 7413 2.093447 GTGACATTCAGGATCCGGTTCT 60.093 50.000 11.92 0.56 0.00 3.01
4712 7414 2.280628 GTGACATTCAGGATCCGGTTC 58.719 52.381 11.92 1.67 0.00 3.62
4713 7415 1.065418 GGTGACATTCAGGATCCGGTT 60.065 52.381 11.92 0.00 0.00 4.44
4714 7416 0.541863 GGTGACATTCAGGATCCGGT 59.458 55.000 11.92 3.95 0.00 5.28
4715 7417 0.530650 CGGTGACATTCAGGATCCGG 60.531 60.000 5.98 5.68 34.05 5.14
4716 7418 0.175760 ACGGTGACATTCAGGATCCG 59.824 55.000 5.98 1.36 41.77 4.18
4717 7419 1.656652 CACGGTGACATTCAGGATCC 58.343 55.000 2.48 2.48 0.00 3.36
4718 7420 1.009829 GCACGGTGACATTCAGGATC 58.990 55.000 13.29 0.00 0.00 3.36
4719 7421 0.615331 AGCACGGTGACATTCAGGAT 59.385 50.000 13.29 0.00 0.00 3.24
4720 7422 1.262417 TAGCACGGTGACATTCAGGA 58.738 50.000 13.29 0.00 0.00 3.86
4721 7423 2.315925 ATAGCACGGTGACATTCAGG 57.684 50.000 13.29 0.00 0.00 3.86
4722 7424 3.780902 TGTATAGCACGGTGACATTCAG 58.219 45.455 13.29 0.00 0.00 3.02
4723 7425 3.194755 ACTGTATAGCACGGTGACATTCA 59.805 43.478 13.29 6.88 45.40 2.57
4724 7426 3.782046 ACTGTATAGCACGGTGACATTC 58.218 45.455 13.29 2.58 45.40 2.67
4725 7427 3.887621 ACTGTATAGCACGGTGACATT 57.112 42.857 13.29 0.00 45.40 2.71
4732 7434 2.100916 AGCCTAACACTGTATAGCACGG 59.899 50.000 0.00 0.00 39.65 4.94
4733 7435 3.438297 AGCCTAACACTGTATAGCACG 57.562 47.619 0.00 0.00 0.00 5.34
4734 7436 5.163540 ACACTAGCCTAACACTGTATAGCAC 60.164 44.000 0.00 0.00 0.00 4.40
4735 7437 4.954202 ACACTAGCCTAACACTGTATAGCA 59.046 41.667 0.00 0.00 0.00 3.49
4736 7438 5.517322 ACACTAGCCTAACACTGTATAGC 57.483 43.478 0.00 0.00 0.00 2.97
4738 7440 9.811995 CATTTTACACTAGCCTAACACTGTATA 57.188 33.333 0.00 0.00 0.00 1.47
4739 7441 8.537016 TCATTTTACACTAGCCTAACACTGTAT 58.463 33.333 0.00 0.00 0.00 2.29
4740 7442 7.898918 TCATTTTACACTAGCCTAACACTGTA 58.101 34.615 0.00 0.00 0.00 2.74
4741 7443 6.765403 TCATTTTACACTAGCCTAACACTGT 58.235 36.000 0.00 0.00 0.00 3.55
4742 7444 7.602644 TCTTCATTTTACACTAGCCTAACACTG 59.397 37.037 0.00 0.00 0.00 3.66
4743 7445 7.676947 TCTTCATTTTACACTAGCCTAACACT 58.323 34.615 0.00 0.00 0.00 3.55
4744 7446 7.900782 TCTTCATTTTACACTAGCCTAACAC 57.099 36.000 0.00 0.00 0.00 3.32
4745 7447 7.606456 CCTTCTTCATTTTACACTAGCCTAACA 59.394 37.037 0.00 0.00 0.00 2.41
4746 7448 7.822822 TCCTTCTTCATTTTACACTAGCCTAAC 59.177 37.037 0.00 0.00 0.00 2.34
4747 7449 7.913789 TCCTTCTTCATTTTACACTAGCCTAA 58.086 34.615 0.00 0.00 0.00 2.69
4748 7450 7.490657 TCCTTCTTCATTTTACACTAGCCTA 57.509 36.000 0.00 0.00 0.00 3.93
4749 7451 6.374417 TCCTTCTTCATTTTACACTAGCCT 57.626 37.500 0.00 0.00 0.00 4.58
4750 7452 7.175119 ACTTTCCTTCTTCATTTTACACTAGCC 59.825 37.037 0.00 0.00 0.00 3.93
4751 7453 8.100508 ACTTTCCTTCTTCATTTTACACTAGC 57.899 34.615 0.00 0.00 0.00 3.42
4754 7456 9.067986 CCTAACTTTCCTTCTTCATTTTACACT 57.932 33.333 0.00 0.00 0.00 3.55
4755 7457 9.063615 TCCTAACTTTCCTTCTTCATTTTACAC 57.936 33.333 0.00 0.00 0.00 2.90
4756 7458 9.635404 TTCCTAACTTTCCTTCTTCATTTTACA 57.365 29.630 0.00 0.00 0.00 2.41
4759 7461 9.987272 CAATTCCTAACTTTCCTTCTTCATTTT 57.013 29.630 0.00 0.00 0.00 1.82
4760 7462 9.147732 ACAATTCCTAACTTTCCTTCTTCATTT 57.852 29.630 0.00 0.00 0.00 2.32
4761 7463 8.712228 ACAATTCCTAACTTTCCTTCTTCATT 57.288 30.769 0.00 0.00 0.00 2.57
4762 7464 8.712228 AACAATTCCTAACTTTCCTTCTTCAT 57.288 30.769 0.00 0.00 0.00 2.57
4763 7465 9.284968 CTAACAATTCCTAACTTTCCTTCTTCA 57.715 33.333 0.00 0.00 0.00 3.02
4764 7466 9.286170 ACTAACAATTCCTAACTTTCCTTCTTC 57.714 33.333 0.00 0.00 0.00 2.87
4766 7468 9.945904 CTACTAACAATTCCTAACTTTCCTTCT 57.054 33.333 0.00 0.00 0.00 2.85
4767 7469 9.939802 TCTACTAACAATTCCTAACTTTCCTTC 57.060 33.333 0.00 0.00 0.00 3.46
4769 7471 9.892130 CATCTACTAACAATTCCTAACTTTCCT 57.108 33.333 0.00 0.00 0.00 3.36
4770 7472 9.886132 TCATCTACTAACAATTCCTAACTTTCC 57.114 33.333 0.00 0.00 0.00 3.13
4802 7504 9.569122 ACAGTAAATACCAACACTAAACAATCT 57.431 29.630 0.00 0.00 0.00 2.40
4851 7553 9.896263 GCAAACAAATTGATGGTGAAATAAAAT 57.104 25.926 0.00 0.00 41.85 1.82
4852 7554 8.896744 TGCAAACAAATTGATGGTGAAATAAAA 58.103 25.926 0.00 0.00 41.85 1.52
4853 7555 8.442632 TGCAAACAAATTGATGGTGAAATAAA 57.557 26.923 0.00 0.00 41.85 1.40
4854 7556 8.618702 ATGCAAACAAATTGATGGTGAAATAA 57.381 26.923 0.00 0.00 41.85 1.40
4855 7557 9.887629 ATATGCAAACAAATTGATGGTGAAATA 57.112 25.926 0.00 0.00 41.85 1.40
4856 7558 8.795842 ATATGCAAACAAATTGATGGTGAAAT 57.204 26.923 0.00 0.00 41.85 2.17
4857 7559 9.716531 TTATATGCAAACAAATTGATGGTGAAA 57.283 25.926 0.00 0.00 41.85 2.69
4858 7560 9.887629 ATTATATGCAAACAAATTGATGGTGAA 57.112 25.926 0.00 0.00 41.85 3.18
4859 7561 9.887629 AATTATATGCAAACAAATTGATGGTGA 57.112 25.926 0.00 0.00 41.85 4.02
4892 7594 8.721478 GCAATTTGATGATCTACCGTATACATT 58.279 33.333 3.32 0.00 0.00 2.71
4893 7595 7.877612 TGCAATTTGATGATCTACCGTATACAT 59.122 33.333 3.32 0.00 0.00 2.29
4894 7596 7.213678 TGCAATTTGATGATCTACCGTATACA 58.786 34.615 3.32 0.00 0.00 2.29
4895 7597 7.652300 TGCAATTTGATGATCTACCGTATAC 57.348 36.000 0.00 0.00 0.00 1.47
4896 7598 8.669946 TTTGCAATTTGATGATCTACCGTATA 57.330 30.769 0.00 0.00 0.00 1.47
4897 7599 7.566760 TTTGCAATTTGATGATCTACCGTAT 57.433 32.000 0.00 0.00 0.00 3.06
4898 7600 6.993786 TTTGCAATTTGATGATCTACCGTA 57.006 33.333 0.00 0.00 0.00 4.02
4899 7601 5.895636 TTTGCAATTTGATGATCTACCGT 57.104 34.783 0.00 0.00 0.00 4.83
4900 7602 8.854979 TTAATTTGCAATTTGATGATCTACCG 57.145 30.769 15.14 0.00 0.00 4.02
4964 7666 9.863845 GAGAAGCTACAATACTCTAACTTTTCT 57.136 33.333 0.00 0.00 0.00 2.52
4965 7667 9.863845 AGAGAAGCTACAATACTCTAACTTTTC 57.136 33.333 0.00 0.00 36.39 2.29
4973 7675 8.417884 GGAATGTTAGAGAAGCTACAATACTCT 58.582 37.037 0.00 0.00 40.37 3.24
4974 7676 8.417884 AGGAATGTTAGAGAAGCTACAATACTC 58.582 37.037 0.00 0.00 0.00 2.59
4975 7677 8.312669 AGGAATGTTAGAGAAGCTACAATACT 57.687 34.615 0.00 0.00 0.00 2.12
4976 7678 8.950208 AAGGAATGTTAGAGAAGCTACAATAC 57.050 34.615 0.00 0.00 0.00 1.89
4977 7679 8.982723 AGAAGGAATGTTAGAGAAGCTACAATA 58.017 33.333 0.00 0.00 0.00 1.90
4978 7680 7.856415 AGAAGGAATGTTAGAGAAGCTACAAT 58.144 34.615 0.00 0.00 0.00 2.71
4979 7681 7.246171 AGAAGGAATGTTAGAGAAGCTACAA 57.754 36.000 0.00 0.00 0.00 2.41
4980 7682 6.859112 AGAAGGAATGTTAGAGAAGCTACA 57.141 37.500 0.00 0.00 0.00 2.74
4981 7683 9.825109 ATTAAGAAGGAATGTTAGAGAAGCTAC 57.175 33.333 0.00 0.00 0.00 3.58
4982 7684 9.823647 CATTAAGAAGGAATGTTAGAGAAGCTA 57.176 33.333 0.00 0.00 31.00 3.32
4983 7685 8.325046 ACATTAAGAAGGAATGTTAGAGAAGCT 58.675 33.333 0.00 0.00 43.38 3.74
4984 7686 8.499403 ACATTAAGAAGGAATGTTAGAGAAGC 57.501 34.615 0.00 0.00 43.38 3.86
4993 7695 7.711339 GGATCGTCTAACATTAAGAAGGAATGT 59.289 37.037 0.00 0.00 46.89 2.71
4994 7696 7.096023 CGGATCGTCTAACATTAAGAAGGAATG 60.096 40.741 0.00 0.00 39.68 2.67
4995 7697 6.924060 CGGATCGTCTAACATTAAGAAGGAAT 59.076 38.462 0.00 0.00 0.00 3.01
4996 7698 6.270815 CGGATCGTCTAACATTAAGAAGGAA 58.729 40.000 0.00 0.00 0.00 3.36
4997 7699 5.221185 CCGGATCGTCTAACATTAAGAAGGA 60.221 44.000 0.00 0.00 0.00 3.36
4998 7700 4.982916 CCGGATCGTCTAACATTAAGAAGG 59.017 45.833 0.00 0.00 0.00 3.46
4999 7701 5.589192 ACCGGATCGTCTAACATTAAGAAG 58.411 41.667 9.46 0.00 0.00 2.85
5000 7702 5.587388 ACCGGATCGTCTAACATTAAGAA 57.413 39.130 9.46 0.00 0.00 2.52
5001 7703 5.450965 GGAACCGGATCGTCTAACATTAAGA 60.451 44.000 9.46 0.00 0.00 2.10
5002 7704 4.743644 GGAACCGGATCGTCTAACATTAAG 59.256 45.833 9.46 0.00 0.00 1.85
5003 7705 4.685924 GGAACCGGATCGTCTAACATTAA 58.314 43.478 9.46 0.00 0.00 1.40
5004 7706 3.243168 CGGAACCGGATCGTCTAACATTA 60.243 47.826 9.46 0.00 35.56 1.90
5005 7707 2.480759 CGGAACCGGATCGTCTAACATT 60.481 50.000 9.46 0.00 35.56 2.71
5006 7708 1.066605 CGGAACCGGATCGTCTAACAT 59.933 52.381 9.46 0.00 35.56 2.71
5007 7709 0.452987 CGGAACCGGATCGTCTAACA 59.547 55.000 9.46 0.00 35.56 2.41
5008 7710 0.869028 GCGGAACCGGATCGTCTAAC 60.869 60.000 9.46 0.00 40.19 2.34
5009 7711 1.434696 GCGGAACCGGATCGTCTAA 59.565 57.895 9.46 0.00 40.19 2.10
5010 7712 2.484062 GGCGGAACCGGATCGTCTA 61.484 63.158 9.46 0.00 40.19 2.59
5011 7713 3.834799 GGCGGAACCGGATCGTCT 61.835 66.667 9.46 0.00 40.19 4.18
5031 7733 3.740128 AATCTAGGCCAGCACCGCG 62.740 63.158 5.01 0.00 33.69 6.46
5032 7734 2.182842 CAATCTAGGCCAGCACCGC 61.183 63.158 5.01 0.00 33.69 5.68
5033 7735 0.811616 GACAATCTAGGCCAGCACCG 60.812 60.000 5.01 0.00 33.69 4.94
5034 7736 0.464554 GGACAATCTAGGCCAGCACC 60.465 60.000 5.01 0.00 0.00 5.01
5040 7742 1.069935 GGCGAGGACAATCTAGGCC 59.930 63.158 0.00 0.00 32.04 5.19
5052 7754 2.583593 GCAGCTACGAAGGCGAGG 60.584 66.667 0.00 0.00 41.64 4.63
5073 7775 0.108804 TTAGTACTCGGCAGCTGCAC 60.109 55.000 37.63 26.49 44.36 4.57
5135 8353 5.978919 TGCTTTGATTGCTAGTTTGAGTTTG 59.021 36.000 0.00 0.00 0.00 2.93
5220 8531 2.450160 AGAAAGAACAAAAACGCTGCG 58.550 42.857 21.91 21.91 0.00 5.18
5323 8634 3.006940 CACGCAGCCAAATAAAGTCCTA 58.993 45.455 0.00 0.00 0.00 2.94
5441 8752 0.607489 GCCACTTCATCCACAGCTGT 60.607 55.000 15.25 15.25 0.00 4.40
5445 8756 1.642037 CGCTGCCACTTCATCCACAG 61.642 60.000 0.00 0.00 0.00 3.66
5472 8783 1.133598 CCATGATCGCAGCAAACACAT 59.866 47.619 0.00 0.00 0.00 3.21
5479 8790 1.816679 GTGCTCCATGATCGCAGCA 60.817 57.895 0.00 4.15 39.58 4.41
5481 8792 1.068281 ACTAGTGCTCCATGATCGCAG 59.932 52.381 0.00 0.00 33.84 5.18
5486 8797 3.776969 TCCAAGAACTAGTGCTCCATGAT 59.223 43.478 3.08 0.00 0.00 2.45
5507 8819 3.851098 ACAAGTTTACCATCTCGCTCTC 58.149 45.455 0.00 0.00 0.00 3.20
5517 8829 8.578151 ACTGTGTTAAGAAAAACAAGTTTACCA 58.422 29.630 0.00 0.00 40.85 3.25
5521 8833 9.620660 CTGTACTGTGTTAAGAAAAACAAGTTT 57.379 29.630 0.00 0.00 40.85 2.66
5522 8834 9.005777 TCTGTACTGTGTTAAGAAAAACAAGTT 57.994 29.630 0.00 0.00 40.85 2.66
5524 8836 7.634817 CGTCTGTACTGTGTTAAGAAAAACAAG 59.365 37.037 0.00 0.00 40.85 3.16
5533 8845 3.120991 GCTTGCGTCTGTACTGTGTTAAG 60.121 47.826 0.00 0.83 0.00 1.85
5534 8846 2.798283 GCTTGCGTCTGTACTGTGTTAA 59.202 45.455 0.00 0.00 0.00 2.01
5535 8847 2.400399 GCTTGCGTCTGTACTGTGTTA 58.600 47.619 0.00 0.00 0.00 2.41
5537 8849 0.939577 CGCTTGCGTCTGTACTGTGT 60.940 55.000 6.86 0.00 0.00 3.72
5538 8850 0.939577 ACGCTTGCGTCTGTACTGTG 60.940 55.000 15.19 0.00 0.00 3.66
5539 8851 0.249322 AACGCTTGCGTCTGTACTGT 60.249 50.000 20.87 0.00 0.00 3.55
5540 8852 0.435008 GAACGCTTGCGTCTGTACTG 59.565 55.000 20.87 0.00 0.00 2.74
5541 8853 0.031585 TGAACGCTTGCGTCTGTACT 59.968 50.000 20.87 4.26 0.00 2.73
5542 8854 0.161024 GTGAACGCTTGCGTCTGTAC 59.839 55.000 20.87 13.03 0.00 2.90
5549 8861 1.969256 GTGTTTATGTGAACGCTTGCG 59.031 47.619 13.70 13.70 37.14 4.85
5557 8869 4.991687 TGAGTGTATGCGTGTTTATGTGAA 59.008 37.500 0.00 0.00 0.00 3.18
5561 8873 4.024893 GGGATGAGTGTATGCGTGTTTATG 60.025 45.833 0.00 0.00 0.00 1.90
5568 8880 3.230976 TCATAGGGATGAGTGTATGCGT 58.769 45.455 0.00 0.00 37.15 5.24
5569 8881 3.942130 TCATAGGGATGAGTGTATGCG 57.058 47.619 0.00 0.00 37.15 4.73
5570 8882 3.990469 CGTTCATAGGGATGAGTGTATGC 59.010 47.826 0.00 0.00 43.03 3.14
5574 8886 1.831106 TGCGTTCATAGGGATGAGTGT 59.169 47.619 0.00 0.00 43.03 3.55
5581 8893 0.389296 CGTGTGTGCGTTCATAGGGA 60.389 55.000 0.00 0.00 0.00 4.20
5591 8903 0.852777 GTAGGATATGCGTGTGTGCG 59.147 55.000 0.00 0.00 37.81 5.34
5599 8911 3.195610 TGCTCATAAGGGTAGGATATGCG 59.804 47.826 0.00 0.00 0.00 4.73
5603 8915 4.487282 AGGTGCTCATAAGGGTAGGATA 57.513 45.455 0.00 0.00 0.00 2.59
5605 8917 2.868964 AGGTGCTCATAAGGGTAGGA 57.131 50.000 0.00 0.00 0.00 2.94
5607 8919 2.693591 TCGAAGGTGCTCATAAGGGTAG 59.306 50.000 0.00 0.00 0.00 3.18
5608 8920 2.693591 CTCGAAGGTGCTCATAAGGGTA 59.306 50.000 0.00 0.00 0.00 3.69
5609 8921 1.482593 CTCGAAGGTGCTCATAAGGGT 59.517 52.381 0.00 0.00 0.00 4.34
5610 8922 1.757118 TCTCGAAGGTGCTCATAAGGG 59.243 52.381 0.00 0.00 0.00 3.95
5612 8924 4.328440 CAGTTTCTCGAAGGTGCTCATAAG 59.672 45.833 0.00 0.00 0.00 1.73
5613 8925 4.021456 TCAGTTTCTCGAAGGTGCTCATAA 60.021 41.667 0.00 0.00 0.00 1.90
5625 8937 1.888436 ATGCCGGCTCAGTTTCTCGA 61.888 55.000 29.70 1.81 0.00 4.04
5645 8957 9.994432 GATGACTTCGTAAAATCTCAAAATGAT 57.006 29.630 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.