Multiple sequence alignment - TraesCS5B01G431500

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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 TraesCS5B01G431500 chr5B 100.000 6170 0 0 1 6170 606031293 606025124 0.000000e+00 11394
1 TraesCS5B01G431500 chr5B 98.441 834 13 0 4 837 372565913 372565080 0.000000e+00 1469
2 TraesCS5B01G431500 chr5D 92.283 3369 158 34 2126 5427 491446847 491443514 0.000000e+00 4687
3 TraesCS5B01G431500 chr5D 93.707 1319 39 21 845 2149 491448193 491446905 0.000000e+00 1936
4 TraesCS5B01G431500 chr5D 93.780 418 20 2 5754 6170 491443048 491442636 1.890000e-174 623
5 TraesCS5B01G431500 chr5D 94.675 169 9 0 5426 5594 274578012 274578180 4.740000e-66 263
6 TraesCS5B01G431500 chr5D 86.957 92 6 2 5661 5752 491443376 491443291 1.420000e-16 99
7 TraesCS5B01G431500 chr5A 93.686 2344 98 15 2215 4520 613596523 613594192 0.000000e+00 3463
8 TraesCS5B01G431500 chr5A 88.803 1429 97 23 845 2220 613598016 613596598 0.000000e+00 1694
9 TraesCS5B01G431500 chr5A 91.638 873 48 11 4561 5415 613594198 613593333 0.000000e+00 1184
10 TraesCS5B01G431500 chr5A 91.770 486 35 4 5661 6144 613593214 613592732 0.000000e+00 671
11 TraesCS5B01G431500 chr5A 94.706 170 9 0 5423 5592 290391864 290391695 1.320000e-66 265
12 TraesCS5B01G431500 chr6B 98.206 836 15 0 4 839 64731488 64730653 0.000000e+00 1461
13 TraesCS5B01G431500 chr3A 97.849 837 18 0 1 837 125493615 125494451 0.000000e+00 1447
14 TraesCS5B01G431500 chr4A 97.733 838 18 1 1 837 215029043 215029880 0.000000e+00 1441
15 TraesCS5B01G431500 chr2B 97.246 835 22 1 4 837 150532735 150531901 0.000000e+00 1413
16 TraesCS5B01G431500 chr2B 94.994 839 40 1 5 841 194994367 194993529 0.000000e+00 1315
17 TraesCS5B01G431500 chr2B 91.489 188 12 3 5410 5594 594834057 594833871 7.940000e-64 255
18 TraesCS5B01G431500 chr3B 96.420 838 29 1 1 837 583991158 583991995 0.000000e+00 1380
19 TraesCS5B01G431500 chr4B 95.689 835 35 1 4 837 543360630 543359796 0.000000e+00 1341
20 TraesCS5B01G431500 chr4D 92.298 831 58 6 10 837 105925612 105926439 0.000000e+00 1175
21 TraesCS5B01G431500 chr4D 94.186 172 10 0 5426 5597 93338206 93338035 4.740000e-66 263
22 TraesCS5B01G431500 chr1D 94.828 174 9 0 5426 5599 238940216 238940389 7.880000e-69 272
23 TraesCS5B01G431500 chr2D 94.675 169 9 0 5424 5592 560959483 560959651 4.740000e-66 263
24 TraesCS5B01G431500 chr1B 94.706 170 8 1 5426 5595 266805933 266806101 4.740000e-66 263
25 TraesCS5B01G431500 chr1A 94.186 172 10 0 5423 5594 233421509 233421338 4.740000e-66 263
26 TraesCS5B01G431500 chr7B 92.308 182 13 1 5408 5588 588861663 588861844 2.210000e-64 257


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 TraesCS5B01G431500 chr5B 606025124 606031293 6169 True 11394.00 11394 100.00000 1 6170 1 chr5B.!!$R2 6169
1 TraesCS5B01G431500 chr5B 372565080 372565913 833 True 1469.00 1469 98.44100 4 837 1 chr5B.!!$R1 833
2 TraesCS5B01G431500 chr5D 491442636 491448193 5557 True 1836.25 4687 91.68175 845 6170 4 chr5D.!!$R1 5325
3 TraesCS5B01G431500 chr5A 613592732 613598016 5284 True 1753.00 3463 91.47425 845 6144 4 chr5A.!!$R2 5299
4 TraesCS5B01G431500 chr6B 64730653 64731488 835 True 1461.00 1461 98.20600 4 839 1 chr6B.!!$R1 835
5 TraesCS5B01G431500 chr3A 125493615 125494451 836 False 1447.00 1447 97.84900 1 837 1 chr3A.!!$F1 836
6 TraesCS5B01G431500 chr4A 215029043 215029880 837 False 1441.00 1441 97.73300 1 837 1 chr4A.!!$F1 836
7 TraesCS5B01G431500 chr2B 150531901 150532735 834 True 1413.00 1413 97.24600 4 837 1 chr2B.!!$R1 833
8 TraesCS5B01G431500 chr2B 194993529 194994367 838 True 1315.00 1315 94.99400 5 841 1 chr2B.!!$R2 836
9 TraesCS5B01G431500 chr3B 583991158 583991995 837 False 1380.00 1380 96.42000 1 837 1 chr3B.!!$F1 836
10 TraesCS5B01G431500 chr4B 543359796 543360630 834 True 1341.00 1341 95.68900 4 837 1 chr4B.!!$R1 833
11 TraesCS5B01G431500 chr4D 105925612 105926439 827 False 1175.00 1175 92.29800 10 837 1 chr4D.!!$F1 827

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
681 682 0.106318 GGCAGGAGCATTTGGAGGAT 60.106 55.0 0.0 0.0 44.61 3.24 F
903 911 0.108138 ATGCTAGGGTTGAGCGACAC 60.108 55.0 0.0 0.0 43.19 3.67 F
2419 2584 0.609131 AAGCACAACATTCCCTCCGG 60.609 55.0 0.0 0.0 0.00 5.14 F
3527 3712 0.962356 GGCTCCCAACCATCAGTGTG 60.962 60.0 0.0 0.0 0.00 3.82 F
4147 4334 2.430704 TTTTCCCAGCTCCCAGCCAG 62.431 60.0 0.0 0.0 43.77 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1849 0.390735 ACTTGGATAACGCCACGGAC 60.391 55.000 0.00 0.0 37.75 4.79 R
2761 2926 1.480545 GCAGTTCAAACAACCCTGGTT 59.519 47.619 0.00 0.0 39.13 3.67 R
4074 4261 0.588252 CAGCCCAGTGACAAACTTCG 59.412 55.000 0.00 0.0 36.83 3.79 R
4861 5074 2.353406 GCTTTTGAGTACCGACTAGGCA 60.353 50.000 0.00 0.0 46.52 4.75 R
5783 6317 1.055849 ACATGTGTACAGACAGGCCA 58.944 50.000 5.01 0.0 35.82 5.36 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
570 571 1.490490 TCTGCTGGACACTTTGGAAGT 59.510 47.619 0.00 0.00 44.06 3.01
620 621 3.056891 GCCAAATCAAGAACGAATGGGAA 60.057 43.478 0.00 0.00 0.00 3.97
681 682 0.106318 GGCAGGAGCATTTGGAGGAT 60.106 55.000 0.00 0.00 44.61 3.24
870 872 6.879400 ACACAAACAAAATAGGGCACTAAAA 58.121 32.000 0.00 0.00 31.86 1.52
903 911 0.108138 ATGCTAGGGTTGAGCGACAC 60.108 55.000 0.00 0.00 43.19 3.67
945 954 2.852281 GCCCCAAAACCCTCCTCCA 61.852 63.158 0.00 0.00 0.00 3.86
1220 1239 2.685380 CCGCCCCTCTTCCAGACT 60.685 66.667 0.00 0.00 0.00 3.24
1314 1333 4.767255 CAGGACTGCCCGCACCTC 62.767 72.222 0.00 0.00 40.87 3.85
1419 1438 3.510753 AGGTAGTTTCTTCTCTTCCGGAC 59.489 47.826 1.83 0.00 0.00 4.79
1426 1445 4.457834 TCTTCTCTTCCGGACAAATCTC 57.542 45.455 1.83 0.00 0.00 2.75
1427 1446 3.195825 TCTTCTCTTCCGGACAAATCTCC 59.804 47.826 1.83 0.00 0.00 3.71
1508 1532 2.151172 GCTGACATTTTCGTGCGTTTTC 59.849 45.455 0.00 0.00 0.00 2.29
1581 1605 4.134563 GAGTTGTAACCCTTCTTTCAGCA 58.865 43.478 0.00 0.00 0.00 4.41
1663 1702 9.355215 CGAATTAACAGAAAGTAGTAGTGATGT 57.645 33.333 0.00 0.00 0.00 3.06
1799 1849 6.573434 TGTGTATGTTGATAGCTTAGACTGG 58.427 40.000 0.00 0.00 0.00 4.00
1832 1882 1.055040 CCAAGTTGCCAATTTGGGGA 58.945 50.000 20.65 0.00 42.63 4.81
1882 1942 2.359981 TATACAGACTGGGACGAGGG 57.640 55.000 7.51 0.00 0.00 4.30
2063 2126 6.918022 GGTTGGTACTTCTGATTTTGTTCTTG 59.082 38.462 0.00 0.00 0.00 3.02
2151 2214 4.201657 CACCATTGTCTATTGCATCCTGA 58.798 43.478 0.00 0.00 0.00 3.86
2157 2220 7.417003 CCATTGTCTATTGCATCCTGAAATGAA 60.417 37.037 9.79 0.00 26.69 2.57
2161 2224 7.148188 TGTCTATTGCATCCTGAAATGAAGAAC 60.148 37.037 0.00 0.00 26.69 3.01
2163 2226 2.749076 TGCATCCTGAAATGAAGAACCG 59.251 45.455 0.00 0.00 0.00 4.44
2172 2235 6.256757 CCTGAAATGAAGAACCGTCTCTATTC 59.743 42.308 0.00 0.00 30.70 1.75
2207 2270 7.087409 TGTCTTATACAATGCTGGTTGATTG 57.913 36.000 4.48 0.00 34.29 2.67
2208 2271 6.095300 TGTCTTATACAATGCTGGTTGATTGG 59.905 38.462 0.00 0.00 34.29 3.16
2316 2481 8.882736 GGCTGTATGCTTGCTTTATTTAAAAAT 58.117 29.630 0.00 0.00 42.39 1.82
2419 2584 0.609131 AAGCACAACATTCCCTCCGG 60.609 55.000 0.00 0.00 0.00 5.14
2542 2707 2.000447 GTGAATGCACCTACCGAAGAC 59.000 52.381 0.00 0.00 39.14 3.01
2553 2718 4.213513 CCTACCGAAGACCAGGTTAGTAT 58.786 47.826 0.00 0.00 41.63 2.12
2556 2721 4.091549 ACCGAAGACCAGGTTAGTATTGA 58.908 43.478 0.00 0.00 37.49 2.57
2564 2729 8.980481 AGACCAGGTTAGTATTGAATATTTGG 57.020 34.615 0.00 0.00 0.00 3.28
2566 2731 8.747538 ACCAGGTTAGTATTGAATATTTGGTC 57.252 34.615 0.00 0.00 28.49 4.02
2591 2756 6.142817 CCATTTTTACTGCAACTAGTGTCAC 58.857 40.000 0.00 0.00 32.19 3.67
2620 2785 5.337813 GGATCTTTGGCTTGATTTCATGGTT 60.338 40.000 0.00 0.00 0.00 3.67
2754 2919 6.262944 TGTTGTGAATTGCATCTGTAAAGTCT 59.737 34.615 0.00 0.00 0.00 3.24
2755 2920 7.443879 TGTTGTGAATTGCATCTGTAAAGTCTA 59.556 33.333 0.00 0.00 0.00 2.59
2909 3074 9.982651 TCTATGTATAGTTGAAGAAGTTATGCC 57.017 33.333 0.00 0.00 0.00 4.40
2926 3091 1.751437 GCCTACTGCACCCCTAAAAG 58.249 55.000 0.00 0.00 40.77 2.27
2976 3141 6.077322 ACTGGAATTCATTGGGAAGAAAGAA 58.923 36.000 7.93 0.00 39.30 2.52
3054 3219 5.931441 ACTTGAGGCGAGCAATATTATTC 57.069 39.130 0.00 0.00 0.00 1.75
3129 3295 7.145932 ACTGCAGTTCTGTTAATATTGGTTC 57.854 36.000 15.25 0.00 0.00 3.62
3361 3528 4.927049 AGGTCTGTCATGTTTCATTCCAT 58.073 39.130 0.00 0.00 0.00 3.41
3379 3546 2.424557 CATCTTCTGTTGAGCTGCAGT 58.575 47.619 16.64 1.59 34.57 4.40
3387 3554 1.807142 GTTGAGCTGCAGTTCCCTAAC 59.193 52.381 25.45 19.05 35.72 2.34
3392 3559 2.038033 AGCTGCAGTTCCCTAACGTTTA 59.962 45.455 16.64 0.00 40.73 2.01
3401 3568 3.663025 TCCCTAACGTTTACCTTTTCCG 58.337 45.455 5.91 0.00 0.00 4.30
3418 3585 6.238925 CCTTTTCCGTTCATTTCCTGTTTACT 60.239 38.462 0.00 0.00 0.00 2.24
3419 3586 5.682943 TTCCGTTCATTTCCTGTTTACTG 57.317 39.130 0.00 0.00 0.00 2.74
3420 3587 4.710324 TCCGTTCATTTCCTGTTTACTGT 58.290 39.130 0.00 0.00 0.00 3.55
3426 3611 7.647715 CGTTCATTTCCTGTTTACTGTTTTCAT 59.352 33.333 0.00 0.00 0.00 2.57
3428 3613 7.359595 TCATTTCCTGTTTACTGTTTTCATCG 58.640 34.615 0.00 0.00 0.00 3.84
3515 3700 2.108601 TCATGCATCATAATGGCTCCCA 59.891 45.455 0.00 0.00 38.19 4.37
3516 3701 2.752075 TGCATCATAATGGCTCCCAA 57.248 45.000 0.00 0.00 36.95 4.12
3527 3712 0.962356 GGCTCCCAACCATCAGTGTG 60.962 60.000 0.00 0.00 0.00 3.82
3625 3810 5.061179 CCAGCATTGATGTCATGAGATGTA 58.939 41.667 10.56 0.00 0.00 2.29
3678 3863 3.647590 TGGTAATGGATCTGCATCTGCTA 59.352 43.478 3.53 0.00 42.66 3.49
3915 4100 9.846248 AAATTCTATGAGTTACTTGTGAATTGC 57.154 29.630 12.96 0.00 34.47 3.56
4074 4261 6.648725 AGAAGTTAGACTCTGATTTGAAGCAC 59.351 38.462 0.00 0.00 0.00 4.40
4147 4334 2.430704 TTTTCCCAGCTCCCAGCCAG 62.431 60.000 0.00 0.00 43.77 4.85
4381 4584 6.373005 TTTTCATCTGGAAGGTACATCTCA 57.627 37.500 0.00 0.00 36.72 3.27
4441 4644 4.163458 TGTCAGGTTTCTTGTTGGTCTAGT 59.837 41.667 0.00 0.00 0.00 2.57
4447 4650 4.481368 TTCTTGTTGGTCTAGTGTGTGT 57.519 40.909 0.00 0.00 0.00 3.72
4487 4690 7.711339 ACCGATAATTTGACTTCTCTGGTTATC 59.289 37.037 0.00 0.00 0.00 1.75
4488 4691 7.710907 CCGATAATTTGACTTCTCTGGTTATCA 59.289 37.037 0.00 0.00 31.19 2.15
4489 4692 9.265901 CGATAATTTGACTTCTCTGGTTATCAT 57.734 33.333 0.00 0.00 31.19 2.45
4571 4774 6.610830 AGGATTAGAGTGTCATGTCTTCTCAT 59.389 38.462 13.87 5.54 0.00 2.90
4573 4776 8.584157 GGATTAGAGTGTCATGTCTTCTCATAT 58.416 37.037 13.87 8.80 0.00 1.78
4589 4792 7.879677 TCTTCTCATATTACGATTTGATGGCAT 59.120 33.333 0.00 0.00 0.00 4.40
4600 4803 6.035217 CGATTTGATGGCATCATGTAACAAA 58.965 36.000 29.22 18.84 39.39 2.83
4694 4898 4.522022 ACTTTCCTCAAAATGGAGCTTCAG 59.478 41.667 0.00 0.00 34.76 3.02
4755 4959 6.369629 TGAAAAACTCCTTACAATCCTCCAA 58.630 36.000 0.00 0.00 0.00 3.53
4756 4960 6.490040 TGAAAAACTCCTTACAATCCTCCAAG 59.510 38.462 0.00 0.00 0.00 3.61
4785 4989 3.895998 AGGAAATCCTTTGGATCAGAGC 58.104 45.455 0.00 0.00 46.09 4.09
4826 5039 8.758829 ACCTCAAGATCTGTGTACATTGTATTA 58.241 33.333 0.00 0.00 0.00 0.98
4846 5059 5.821516 TTACAATATTTTGGGTGGCTACG 57.178 39.130 0.89 0.00 37.15 3.51
4861 5074 1.922570 CTACGATTGTAGCGGCACTT 58.077 50.000 7.20 0.00 41.51 3.16
4902 5115 1.064946 GATCCCTGACTCGTCTGCG 59.935 63.158 0.00 0.00 39.92 5.18
5085 5298 2.046988 TCTGATGTGTGGGCGCTG 60.047 61.111 7.64 0.00 0.00 5.18
5090 5303 1.709147 GATGTGTGGGCGCTGACATC 61.709 60.000 21.32 21.32 38.34 3.06
5149 5362 9.282247 GAATTCATGTGAGCAAGTACTTATTTG 57.718 33.333 8.04 0.00 0.00 2.32
5232 5445 1.238439 CCTTGTGCTTGGACGTCAAT 58.762 50.000 18.91 0.00 34.45 2.57
5284 5497 3.093717 ACAGGGTGCTAAACGATATCG 57.906 47.619 23.18 23.18 46.33 2.92
5305 5518 5.145564 TCGCTACCTCCTTTCTGGTTATAT 58.854 41.667 0.00 0.00 37.74 0.86
5310 5523 7.016366 GCTACCTCCTTTCTGGTTATATAAGGT 59.984 40.741 0.00 0.00 37.06 3.50
5317 5533 9.117183 CCTTTCTGGTTATATAAGGTTTACACC 57.883 37.037 0.00 0.00 44.67 4.16
5406 5630 4.332819 GGTACAAGTGTTCTGATATGTGCC 59.667 45.833 0.00 0.00 36.62 5.01
5420 5644 2.320745 TGTGCCAGAGATACATGCAG 57.679 50.000 0.00 0.00 31.69 4.41
5423 5647 2.052468 TGCCAGAGATACATGCAGGAT 58.948 47.619 4.84 0.00 0.00 3.24
5427 5651 4.620332 GCCAGAGATACATGCAGGATCTAC 60.620 50.000 4.84 3.21 30.01 2.59
5428 5652 4.771577 CCAGAGATACATGCAGGATCTACT 59.228 45.833 4.84 5.24 30.01 2.57
5429 5653 5.105797 CCAGAGATACATGCAGGATCTACTC 60.106 48.000 4.84 6.54 30.01 2.59
5430 5654 5.016173 AGAGATACATGCAGGATCTACTCC 58.984 45.833 4.84 0.00 45.33 3.85
5431 5655 4.093011 AGATACATGCAGGATCTACTCCC 58.907 47.826 4.84 0.00 46.27 4.30
5432 5656 2.485966 ACATGCAGGATCTACTCCCT 57.514 50.000 4.84 0.00 46.27 4.20
5433 5657 2.324541 ACATGCAGGATCTACTCCCTC 58.675 52.381 4.84 0.00 46.27 4.30
5434 5658 1.622811 CATGCAGGATCTACTCCCTCC 59.377 57.143 0.00 0.00 46.27 4.30
5435 5659 0.468214 TGCAGGATCTACTCCCTCCG 60.468 60.000 0.00 0.00 46.27 4.63
5436 5660 0.468400 GCAGGATCTACTCCCTCCGT 60.468 60.000 0.00 0.00 46.27 4.69
5437 5661 2.030045 GCAGGATCTACTCCCTCCGTT 61.030 57.143 0.00 0.00 46.27 4.44
5438 5662 1.957877 CAGGATCTACTCCCTCCGTTC 59.042 57.143 0.00 0.00 46.27 3.95
5439 5663 1.133419 AGGATCTACTCCCTCCGTTCC 60.133 57.143 0.00 0.00 46.27 3.62
5440 5664 1.133419 GGATCTACTCCCTCCGTTCCT 60.133 57.143 0.00 0.00 38.19 3.36
5441 5665 2.107901 GGATCTACTCCCTCCGTTCCTA 59.892 54.545 0.00 0.00 38.19 2.94
5442 5666 3.436180 GGATCTACTCCCTCCGTTCCTAA 60.436 52.174 0.00 0.00 38.19 2.69
5443 5667 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
5444 5668 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
5445 5669 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
5446 5670 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
5447 5671 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
5448 5672 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
5449 5673 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
5450 5674 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
5451 5675 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
5452 5676 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
5453 5677 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
5454 5678 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
5455 5679 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
5456 5680 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
5474 5698 9.793259 TGTCTTTTTAGAGTATTCAAATGGACT 57.207 29.630 0.00 0.00 0.00 3.85
5483 5707 9.988815 AGAGTATTCAAATGGACTATCACATAC 57.011 33.333 0.00 0.00 0.00 2.39
5484 5708 8.818141 AGTATTCAAATGGACTATCACATACG 57.182 34.615 0.00 0.00 0.00 3.06
5485 5709 7.872993 AGTATTCAAATGGACTATCACATACGG 59.127 37.037 0.00 0.00 0.00 4.02
5486 5710 5.862678 TCAAATGGACTATCACATACGGA 57.137 39.130 0.00 0.00 0.00 4.69
5487 5711 6.419484 TCAAATGGACTATCACATACGGAT 57.581 37.500 0.00 0.00 0.00 4.18
5488 5712 6.223120 TCAAATGGACTATCACATACGGATG 58.777 40.000 5.94 5.94 39.16 3.51
5490 5714 6.911250 AATGGACTATCACATACGGATGTA 57.089 37.500 14.23 2.61 44.82 2.29
5491 5715 7.482169 AATGGACTATCACATACGGATGTAT 57.518 36.000 14.23 10.02 44.82 2.29
5492 5716 8.589701 AATGGACTATCACATACGGATGTATA 57.410 34.615 14.23 10.59 44.82 1.47
5493 5717 8.768501 ATGGACTATCACATACGGATGTATAT 57.231 34.615 14.23 12.50 44.82 0.86
5494 5718 9.862149 ATGGACTATCACATACGGATGTATATA 57.138 33.333 14.23 12.96 44.82 0.86
5495 5719 9.338622 TGGACTATCACATACGGATGTATATAG 57.661 37.037 26.27 26.27 44.82 1.31
5496 5720 9.557061 GGACTATCACATACGGATGTATATAGA 57.443 37.037 30.73 19.35 44.82 1.98
5498 5722 9.901172 ACTATCACATACGGATGTATATAGACA 57.099 33.333 30.73 11.02 44.82 3.41
5531 5755 5.633830 TGAAGATTCACTCATTTTGCTCC 57.366 39.130 0.00 0.00 31.01 4.70
5532 5756 4.154737 TGAAGATTCACTCATTTTGCTCCG 59.845 41.667 0.00 0.00 31.01 4.63
5533 5757 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
5534 5758 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
5535 5759 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
5536 5760 6.582636 AGATTCACTCATTTTGCTCCGTATA 58.417 36.000 0.00 0.00 0.00 1.47
5537 5761 7.220030 AGATTCACTCATTTTGCTCCGTATAT 58.780 34.615 0.00 0.00 0.00 0.86
5538 5762 8.367911 AGATTCACTCATTTTGCTCCGTATATA 58.632 33.333 0.00 0.00 0.00 0.86
5539 5763 7.946655 TTCACTCATTTTGCTCCGTATATAG 57.053 36.000 0.00 0.00 0.00 1.31
5540 5764 7.050970 TCACTCATTTTGCTCCGTATATAGT 57.949 36.000 0.00 0.00 0.00 2.12
5541 5765 7.145985 TCACTCATTTTGCTCCGTATATAGTC 58.854 38.462 0.00 0.00 0.00 2.59
5542 5766 6.923508 CACTCATTTTGCTCCGTATATAGTCA 59.076 38.462 0.00 0.00 0.00 3.41
5543 5767 6.924060 ACTCATTTTGCTCCGTATATAGTCAC 59.076 38.462 0.00 0.00 0.00 3.67
5544 5768 7.050970 TCATTTTGCTCCGTATATAGTCACT 57.949 36.000 0.00 0.00 0.00 3.41
5545 5769 7.497595 TCATTTTGCTCCGTATATAGTCACTT 58.502 34.615 0.00 0.00 0.00 3.16
5546 5770 7.438160 TCATTTTGCTCCGTATATAGTCACTTG 59.562 37.037 0.00 0.00 0.00 3.16
5547 5771 5.847111 TTGCTCCGTATATAGTCACTTGT 57.153 39.130 0.00 0.00 0.00 3.16
5548 5772 5.847111 TGCTCCGTATATAGTCACTTGTT 57.153 39.130 0.00 0.00 0.00 2.83
5549 5773 5.588240 TGCTCCGTATATAGTCACTTGTTG 58.412 41.667 0.00 0.00 0.00 3.33
5550 5774 5.358725 TGCTCCGTATATAGTCACTTGTTGA 59.641 40.000 0.00 0.00 0.00 3.18
5551 5775 6.127563 TGCTCCGTATATAGTCACTTGTTGAA 60.128 38.462 0.00 0.00 35.39 2.69
5552 5776 6.755141 GCTCCGTATATAGTCACTTGTTGAAA 59.245 38.462 0.00 0.00 35.39 2.69
5553 5777 7.277098 GCTCCGTATATAGTCACTTGTTGAAAA 59.723 37.037 0.00 0.00 35.39 2.29
5584 5808 9.780186 AGAAAGATAAATATTTAGGAACGGAGG 57.220 33.333 13.15 0.00 0.00 4.30
5585 5809 8.919777 AAAGATAAATATTTAGGAACGGAGGG 57.080 34.615 13.15 0.00 0.00 4.30
5586 5810 7.867160 AGATAAATATTTAGGAACGGAGGGA 57.133 36.000 13.15 0.00 0.00 4.20
5587 5811 7.908453 AGATAAATATTTAGGAACGGAGGGAG 58.092 38.462 13.15 0.00 0.00 4.30
5588 5812 4.353383 AATATTTAGGAACGGAGGGAGC 57.647 45.455 0.00 0.00 0.00 4.70
5609 5833 6.039382 GGAGCATAAATTAGAAACGGGATTGT 59.961 38.462 0.00 0.00 0.00 2.71
5618 5842 8.905103 ATTAGAAACGGGATTGTTAAATTTCG 57.095 30.769 0.00 0.00 0.00 3.46
5622 5846 5.456548 ACGGGATTGTTAAATTTCGGTTT 57.543 34.783 0.00 0.00 0.00 3.27
5627 5851 6.809689 GGGATTGTTAAATTTCGGTTTACTGG 59.190 38.462 0.00 0.00 0.00 4.00
5655 5879 8.947115 ACTTAACCAAGTCTCAATTAATGCTAC 58.053 33.333 0.00 0.00 41.25 3.58
5659 5952 5.882557 CCAAGTCTCAATTAATGCTACACCT 59.117 40.000 0.00 0.00 0.00 4.00
5725 6018 4.728058 GCCAAGCGCTTTTGAACA 57.272 50.000 22.51 0.00 0.00 3.18
5726 6019 2.970576 GCCAAGCGCTTTTGAACAA 58.029 47.368 22.51 0.00 0.00 2.83
5729 6022 3.253230 GCCAAGCGCTTTTGAACAATAT 58.747 40.909 22.51 0.00 0.00 1.28
5733 6026 5.577945 CCAAGCGCTTTTGAACAATATCAAT 59.422 36.000 22.51 0.00 38.98 2.57
5793 6327 1.331756 GCAAATACGATGGCCTGTCTG 59.668 52.381 3.32 2.04 0.00 3.51
5841 6376 6.521162 TCACAAAAGAGTTGTGCTAGTATGA 58.479 36.000 13.13 0.00 46.78 2.15
5922 6457 5.944007 AGGATAATGACAAGCCTTTACGTTT 59.056 36.000 0.00 0.00 0.00 3.60
6023 6558 7.660208 GGAATTCTAACACAGAAAAGTACTCCA 59.340 37.037 5.23 0.00 46.29 3.86
6062 6597 1.614051 GGCAACACCATCCATCTGACA 60.614 52.381 0.00 0.00 38.86 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.842052 TCATCCAAGCATGCATGTGT 58.158 45.000 26.79 12.77 0.00 3.72
440 441 1.648116 ATGTTGGGCAAAGCTCCATT 58.352 45.000 0.00 0.00 31.26 3.16
570 571 2.543012 CGAATACTCTCGCGTTCCTCTA 59.457 50.000 5.77 0.00 31.04 2.43
620 621 1.616865 TCGAAGATCAAGTCCACGGTT 59.383 47.619 0.00 0.00 0.00 4.44
681 682 6.422344 ACTCTACTACTCAGGTATCGATCA 57.578 41.667 0.00 0.00 0.00 2.92
797 799 6.544564 GCCAAAGGTGTACCATAGCTTTATAA 59.455 38.462 8.12 0.00 42.14 0.98
814 816 0.475044 TTTGAGGGTACGCCAAAGGT 59.525 50.000 16.88 0.00 36.17 3.50
839 841 8.921670 GTGCCCTATTTTGTTTGTGTAATAAAG 58.078 33.333 0.00 0.00 30.02 1.85
840 842 8.643324 AGTGCCCTATTTTGTTTGTGTAATAAA 58.357 29.630 0.00 0.00 0.00 1.40
841 843 8.184304 AGTGCCCTATTTTGTTTGTGTAATAA 57.816 30.769 0.00 0.00 0.00 1.40
843 845 6.664428 AGTGCCCTATTTTGTTTGTGTAAT 57.336 33.333 0.00 0.00 0.00 1.89
857 859 3.706086 CTGCCCAAATTTTAGTGCCCTAT 59.294 43.478 0.00 0.00 0.00 2.57
870 872 3.073062 CCCTAGCATACTACTGCCCAAAT 59.927 47.826 0.00 0.00 43.33 2.32
1089 1098 1.524849 GCATCTTCGCCCTCCTTCC 60.525 63.158 0.00 0.00 0.00 3.46
1091 1100 1.222936 CAGCATCTTCGCCCTCCTT 59.777 57.895 0.00 0.00 0.00 3.36
1093 1102 1.817099 CACAGCATCTTCGCCCTCC 60.817 63.158 0.00 0.00 0.00 4.30
1094 1103 1.817099 CCACAGCATCTTCGCCCTC 60.817 63.158 0.00 0.00 0.00 4.30
1095 1104 2.270205 CCACAGCATCTTCGCCCT 59.730 61.111 0.00 0.00 0.00 5.19
1212 1231 1.007238 CCCTGGGAGAGTAGTCTGGAA 59.993 57.143 7.01 0.00 30.97 3.53
1314 1333 2.427753 GGCGGGCCATAGAAGAGG 59.572 66.667 4.39 0.00 35.81 3.69
1419 1438 6.690194 AAAATCCAGATCTTCGGAGATTTG 57.310 37.500 15.78 15.78 42.66 2.32
1477 1501 5.743398 CACGAAAATGTCAGCAGAAGAAAAA 59.257 36.000 0.00 0.00 0.00 1.94
1478 1502 5.273170 CACGAAAATGTCAGCAGAAGAAAA 58.727 37.500 0.00 0.00 0.00 2.29
1482 1506 2.578495 GCACGAAAATGTCAGCAGAAG 58.422 47.619 0.00 0.00 0.00 2.85
1508 1532 0.888736 TCACCTGCAACGGAACCATG 60.889 55.000 0.00 0.00 0.00 3.66
1581 1605 5.648092 CCATAAGAAGGAAAAACGGAGATGT 59.352 40.000 0.00 0.00 0.00 3.06
1663 1702 0.890542 GCCACATGAGCTGACAACCA 60.891 55.000 0.00 0.00 0.00 3.67
1745 1784 6.154192 TGGCAAATGCTATGTTTTCCTATCAA 59.846 34.615 5.25 0.00 41.70 2.57
1799 1849 0.390735 ACTTGGATAACGCCACGGAC 60.391 55.000 0.00 0.00 37.75 4.79
1832 1882 5.102953 TGCACCTCAATTTCATAGCTACT 57.897 39.130 0.00 0.00 0.00 2.57
1859 1919 3.952323 CCTCGTCCCAGTCTGTATAAAGA 59.048 47.826 0.00 0.00 0.00 2.52
1882 1942 1.533338 CGCCAGCTCAAGATCAAATGC 60.533 52.381 0.00 0.00 0.00 3.56
2090 2153 6.150140 AGCTAGTGGCAATTTCTTTGTAAGAG 59.850 38.462 0.00 0.00 44.79 2.85
2103 2166 3.092301 GGGAAGAAAAGCTAGTGGCAAT 58.908 45.455 0.00 0.00 44.79 3.56
2151 2214 5.582665 GCTGAATAGAGACGGTTCTTCATTT 59.417 40.000 0.00 0.00 29.47 2.32
2157 2220 3.701542 TCATGCTGAATAGAGACGGTTCT 59.298 43.478 0.00 0.00 33.37 3.01
2161 2224 4.052159 ACTTCATGCTGAATAGAGACGG 57.948 45.455 0.00 0.00 35.59 4.79
2163 2226 6.105333 AGACAACTTCATGCTGAATAGAGAC 58.895 40.000 0.00 0.00 35.59 3.36
2201 2264 7.284489 ACTGAAAAGTACTAACAAGCCAATCAA 59.716 33.333 0.00 0.00 0.00 2.57
2207 2270 5.061179 TCCACTGAAAAGTACTAACAAGCC 58.939 41.667 0.00 0.00 0.00 4.35
2208 2271 6.426937 TCATCCACTGAAAAGTACTAACAAGC 59.573 38.462 0.00 0.00 0.00 4.01
2419 2584 4.333926 GCACTGTATTTCTCCATTGTCCTC 59.666 45.833 0.00 0.00 0.00 3.71
2542 2707 7.230712 GGGACCAAATATTCAATACTAACCTGG 59.769 40.741 0.00 0.00 0.00 4.45
2553 2718 7.821846 GCAGTAAAAATGGGACCAAATATTCAA 59.178 33.333 0.00 0.00 0.00 2.69
2556 2721 7.251321 TGCAGTAAAAATGGGACCAAATATT 57.749 32.000 0.00 0.00 0.00 1.28
2564 2729 5.240844 ACACTAGTTGCAGTAAAAATGGGAC 59.759 40.000 0.00 0.00 0.00 4.46
2566 2731 5.240623 TGACACTAGTTGCAGTAAAAATGGG 59.759 40.000 0.00 0.00 0.00 4.00
2591 2756 4.796038 AATCAAGCCAAAGATCCACAAG 57.204 40.909 0.00 0.00 0.00 3.16
2620 2785 5.538813 CACCCTATTAGACATAGTAGCACCA 59.461 44.000 0.00 0.00 0.00 4.17
2724 2889 5.762045 ACAGATGCAATTCACAACACTTAC 58.238 37.500 0.00 0.00 0.00 2.34
2754 2919 5.633655 TCAAACAACCCTGGTTAAGTCTA 57.366 39.130 0.32 0.00 36.46 2.59
2755 2920 4.513406 TCAAACAACCCTGGTTAAGTCT 57.487 40.909 0.32 0.00 36.46 3.24
2761 2926 1.480545 GCAGTTCAAACAACCCTGGTT 59.519 47.619 0.00 0.00 39.13 3.67
2865 3030 6.845908 ACATAGAATAATGAGGTTGGAGCAT 58.154 36.000 0.00 0.00 0.00 3.79
2909 3074 2.618053 CGACTTTTAGGGGTGCAGTAG 58.382 52.381 0.00 0.00 0.00 2.57
2926 3091 2.907910 ACAATCTGCAAATGAGCGAC 57.092 45.000 0.00 0.00 37.31 5.19
3129 3295 6.258727 CACATATAAAACTAGGGACACAGCAG 59.741 42.308 0.00 0.00 0.00 4.24
3167 3333 4.922471 AAACTAAAGGGCGTAAAAAGCA 57.078 36.364 0.00 0.00 36.08 3.91
3361 3528 2.487934 GAACTGCAGCTCAACAGAAGA 58.512 47.619 15.27 0.00 37.35 2.87
3379 3546 4.064388 CGGAAAAGGTAAACGTTAGGGAA 58.936 43.478 0.00 0.00 0.00 3.97
3387 3554 4.913345 GGAAATGAACGGAAAAGGTAAACG 59.087 41.667 0.00 0.00 0.00 3.60
3392 3559 3.562182 ACAGGAAATGAACGGAAAAGGT 58.438 40.909 0.00 0.00 0.00 3.50
3401 3568 8.871686 ATGAAAACAGTAAACAGGAAATGAAC 57.128 30.769 0.00 0.00 0.00 3.18
3418 3585 7.151308 AGGAAAACAAATATGCGATGAAAACA 58.849 30.769 0.00 0.00 0.00 2.83
3419 3586 7.581011 AGGAAAACAAATATGCGATGAAAAC 57.419 32.000 0.00 0.00 0.00 2.43
3420 3587 8.600449 AAAGGAAAACAAATATGCGATGAAAA 57.400 26.923 0.00 0.00 0.00 2.29
3515 3700 2.354704 CGATGGGTACACACTGATGGTT 60.355 50.000 0.00 0.00 0.00 3.67
3516 3701 1.207089 CGATGGGTACACACTGATGGT 59.793 52.381 0.00 0.00 0.00 3.55
3570 3755 8.413229 GGCCACATGTAGTTATGTTATGAAATT 58.587 33.333 0.00 0.00 39.17 1.82
3581 3766 2.923121 CTGCTGGCCACATGTAGTTAT 58.077 47.619 0.00 0.00 0.00 1.89
3642 3827 6.425210 TCCATTACCACTCCTATCAGATTG 57.575 41.667 0.00 0.00 0.00 2.67
3678 3863 8.561738 ACACAAGACGAAAATATAACATTCCT 57.438 30.769 0.00 0.00 0.00 3.36
3915 4100 2.426024 CAAGATGCTTTCAGGTGGGATG 59.574 50.000 0.00 0.00 0.00 3.51
3987 4172 1.541588 GTTTAGCTTGCACCCTCAAGG 59.458 52.381 0.00 0.00 42.68 3.61
3988 4173 2.508526 AGTTTAGCTTGCACCCTCAAG 58.491 47.619 0.00 0.00 44.63 3.02
4002 4189 8.578308 TCTGCAATTGTCAAAATCAAGTTTAG 57.422 30.769 7.40 0.00 0.00 1.85
4011 4198 8.603181 GTTAACAACTTCTGCAATTGTCAAAAT 58.397 29.630 7.40 0.00 35.54 1.82
4074 4261 0.588252 CAGCCCAGTGACAAACTTCG 59.412 55.000 0.00 0.00 36.83 3.79
4130 4317 3.333219 CTGGCTGGGAGCTGGGAA 61.333 66.667 0.00 0.00 41.99 3.97
4131 4318 4.664267 ACTGGCTGGGAGCTGGGA 62.664 66.667 0.00 0.00 41.99 4.37
4234 4421 6.067217 ACAAAAGGCCATAGACATAAGAGT 57.933 37.500 5.01 0.00 0.00 3.24
4241 4428 7.093945 GGAAGAAAATACAAAAGGCCATAGACA 60.094 37.037 5.01 0.00 0.00 3.41
4381 4584 3.704061 ACACCAGTTTGTAAAAGGTGCAT 59.296 39.130 20.88 8.03 44.09 3.96
4441 4644 6.221659 TCGGTACAATACAAATACACACACA 58.778 36.000 0.00 0.00 0.00 3.72
4487 4690 5.065218 GCTAGGTCCATTAATGCCGATAATG 59.935 44.000 10.11 6.36 39.41 1.90
4488 4691 5.045578 AGCTAGGTCCATTAATGCCGATAAT 60.046 40.000 10.11 0.00 0.00 1.28
4489 4692 4.286032 AGCTAGGTCCATTAATGCCGATAA 59.714 41.667 10.11 0.00 0.00 1.75
4571 4774 8.503196 GTTACATGATGCCATCAAATCGTAATA 58.497 33.333 12.08 0.00 43.50 0.98
4573 4776 6.317391 TGTTACATGATGCCATCAAATCGTAA 59.683 34.615 12.08 13.13 43.50 3.18
4600 4803 6.430000 AGTGCAGTCAAATCTACGGTTTTTAT 59.570 34.615 0.00 0.00 0.00 1.40
4694 4898 7.639113 TCAATTTGTAGGATTGTATTCCACC 57.361 36.000 0.00 0.00 38.32 4.61
4785 4989 9.420118 AGATCTTGAGGTATATATAAGCCAGAG 57.580 37.037 0.00 4.10 0.00 3.35
4826 5039 3.958018 TCGTAGCCACCCAAAATATTGT 58.042 40.909 0.00 0.00 34.60 2.71
4861 5074 2.353406 GCTTTTGAGTACCGACTAGGCA 60.353 50.000 0.00 0.00 46.52 4.75
5085 5298 7.274468 CACTGACTGAGTAACATACAAGATGTC 59.726 40.741 0.00 0.00 31.73 3.06
5090 5303 7.594714 ACTACACTGACTGAGTAACATACAAG 58.405 38.462 0.00 0.00 31.73 3.16
5149 5362 7.332678 ACCTTTCAATAGCAAATGATTCAAAGC 59.667 33.333 0.00 0.00 0.00 3.51
5232 5445 4.412796 AGGATGAGATGCTGAAATTCGA 57.587 40.909 0.00 0.00 0.00 3.71
5284 5497 7.016366 ACCTTATATAACCAGAAAGGAGGTAGC 59.984 40.741 6.43 0.00 39.26 3.58
5387 5611 4.256110 TCTGGCACATATCAGAACACTTG 58.744 43.478 0.00 0.00 38.20 3.16
5390 5614 4.128925 TCTCTGGCACATATCAGAACAC 57.871 45.455 0.00 0.00 39.23 3.32
5406 5630 5.105797 GGAGTAGATCCTGCATGTATCTCTG 60.106 48.000 8.41 0.00 45.64 3.35
5423 5647 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
5427 5651 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5428 5652 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5429 5653 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5430 5654 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
5448 5672 9.793259 AGTCCATTTGAATACTCTAAAAAGACA 57.207 29.630 0.00 0.00 0.00 3.41
5457 5681 9.988815 GTATGTGATAGTCCATTTGAATACTCT 57.011 33.333 0.00 0.00 0.00 3.24
5458 5682 8.916654 CGTATGTGATAGTCCATTTGAATACTC 58.083 37.037 0.00 0.00 0.00 2.59
5459 5683 7.872993 CCGTATGTGATAGTCCATTTGAATACT 59.127 37.037 0.00 0.00 0.00 2.12
5460 5684 7.870954 TCCGTATGTGATAGTCCATTTGAATAC 59.129 37.037 0.00 0.00 0.00 1.89
5461 5685 7.958088 TCCGTATGTGATAGTCCATTTGAATA 58.042 34.615 0.00 0.00 0.00 1.75
5462 5686 6.826668 TCCGTATGTGATAGTCCATTTGAAT 58.173 36.000 0.00 0.00 0.00 2.57
5463 5687 6.228616 TCCGTATGTGATAGTCCATTTGAA 57.771 37.500 0.00 0.00 0.00 2.69
5464 5688 5.862678 TCCGTATGTGATAGTCCATTTGA 57.137 39.130 0.00 0.00 0.00 2.69
5465 5689 5.991606 ACATCCGTATGTGATAGTCCATTTG 59.008 40.000 0.00 0.00 44.79 2.32
5466 5690 6.174720 ACATCCGTATGTGATAGTCCATTT 57.825 37.500 0.00 0.00 44.79 2.32
5467 5691 5.808366 ACATCCGTATGTGATAGTCCATT 57.192 39.130 0.00 0.00 44.79 3.16
5468 5692 8.768501 ATATACATCCGTATGTGATAGTCCAT 57.231 34.615 3.56 0.00 45.99 3.41
5469 5693 9.338622 CTATATACATCCGTATGTGATAGTCCA 57.661 37.037 3.56 0.00 45.99 4.02
5470 5694 9.557061 TCTATATACATCCGTATGTGATAGTCC 57.443 37.037 17.08 0.00 45.99 3.85
5472 5696 9.901172 TGTCTATATACATCCGTATGTGATAGT 57.099 33.333 17.08 3.55 45.99 2.12
5509 5733 4.154737 CGGAGCAAAATGAGTGAATCTTCA 59.845 41.667 0.00 0.00 34.20 3.02
5510 5734 4.154918 ACGGAGCAAAATGAGTGAATCTTC 59.845 41.667 0.00 0.00 0.00 2.87
5511 5735 4.074970 ACGGAGCAAAATGAGTGAATCTT 58.925 39.130 0.00 0.00 0.00 2.40
5512 5736 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
5513 5737 5.741388 ATACGGAGCAAAATGAGTGAATC 57.259 39.130 0.00 0.00 0.00 2.52
5514 5738 8.150945 ACTATATACGGAGCAAAATGAGTGAAT 58.849 33.333 0.00 0.00 0.00 2.57
5515 5739 7.497595 ACTATATACGGAGCAAAATGAGTGAA 58.502 34.615 0.00 0.00 0.00 3.18
5516 5740 7.050970 ACTATATACGGAGCAAAATGAGTGA 57.949 36.000 0.00 0.00 0.00 3.41
5517 5741 6.923508 TGACTATATACGGAGCAAAATGAGTG 59.076 38.462 0.00 0.00 0.00 3.51
5518 5742 6.924060 GTGACTATATACGGAGCAAAATGAGT 59.076 38.462 0.00 0.00 0.00 3.41
5519 5743 7.148641 AGTGACTATATACGGAGCAAAATGAG 58.851 38.462 0.00 0.00 0.00 2.90
5520 5744 7.050970 AGTGACTATATACGGAGCAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
5521 5745 7.224753 ACAAGTGACTATATACGGAGCAAAATG 59.775 37.037 0.00 0.00 0.00 2.32
5522 5746 7.272978 ACAAGTGACTATATACGGAGCAAAAT 58.727 34.615 0.00 0.00 0.00 1.82
5523 5747 6.636705 ACAAGTGACTATATACGGAGCAAAA 58.363 36.000 0.00 0.00 0.00 2.44
5524 5748 6.216801 ACAAGTGACTATATACGGAGCAAA 57.783 37.500 0.00 0.00 0.00 3.68
5525 5749 5.847111 ACAAGTGACTATATACGGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
5526 5750 5.358725 TCAACAAGTGACTATATACGGAGCA 59.641 40.000 0.00 0.00 0.00 4.26
5527 5751 5.828747 TCAACAAGTGACTATATACGGAGC 58.171 41.667 0.00 0.00 0.00 4.70
5528 5752 8.592998 GTTTTCAACAAGTGACTATATACGGAG 58.407 37.037 0.00 0.00 35.39 4.63
5529 5753 8.308931 AGTTTTCAACAAGTGACTATATACGGA 58.691 33.333 0.00 0.00 35.39 4.69
5530 5754 8.475331 AGTTTTCAACAAGTGACTATATACGG 57.525 34.615 0.00 0.00 35.39 4.02
5531 5755 9.355215 AGAGTTTTCAACAAGTGACTATATACG 57.645 33.333 0.00 0.00 35.39 3.06
5536 5760 9.832445 TTTCTAGAGTTTTCAACAAGTGACTAT 57.168 29.630 0.00 0.00 35.39 2.12
5537 5761 9.314321 CTTTCTAGAGTTTTCAACAAGTGACTA 57.686 33.333 0.00 0.00 35.39 2.59
5538 5762 8.041323 TCTTTCTAGAGTTTTCAACAAGTGACT 58.959 33.333 0.00 0.00 35.39 3.41
5539 5763 8.197988 TCTTTCTAGAGTTTTCAACAAGTGAC 57.802 34.615 0.00 0.00 35.39 3.67
5540 5764 8.964476 ATCTTTCTAGAGTTTTCAACAAGTGA 57.036 30.769 0.00 0.00 32.92 3.41
5558 5782 9.780186 CCTCCGTTCCTAAATATTTATCTTTCT 57.220 33.333 8.34 0.00 0.00 2.52
5559 5783 9.000486 CCCTCCGTTCCTAAATATTTATCTTTC 58.000 37.037 8.34 0.00 0.00 2.62
5560 5784 8.720537 TCCCTCCGTTCCTAAATATTTATCTTT 58.279 33.333 8.34 0.00 0.00 2.52
5561 5785 8.271398 TCCCTCCGTTCCTAAATATTTATCTT 57.729 34.615 8.34 0.00 0.00 2.40
5562 5786 7.527363 GCTCCCTCCGTTCCTAAATATTTATCT 60.527 40.741 8.34 0.00 0.00 1.98
5563 5787 6.594547 GCTCCCTCCGTTCCTAAATATTTATC 59.405 42.308 8.34 0.61 0.00 1.75
5564 5788 6.043938 TGCTCCCTCCGTTCCTAAATATTTAT 59.956 38.462 8.34 0.00 0.00 1.40
5565 5789 5.367352 TGCTCCCTCCGTTCCTAAATATTTA 59.633 40.000 7.66 7.66 0.00 1.40
5566 5790 4.165372 TGCTCCCTCCGTTCCTAAATATTT 59.835 41.667 5.89 5.89 0.00 1.40
5567 5791 3.714798 TGCTCCCTCCGTTCCTAAATATT 59.285 43.478 0.00 0.00 0.00 1.28
5568 5792 3.314693 TGCTCCCTCCGTTCCTAAATAT 58.685 45.455 0.00 0.00 0.00 1.28
5569 5793 2.754465 TGCTCCCTCCGTTCCTAAATA 58.246 47.619 0.00 0.00 0.00 1.40
5570 5794 1.580059 TGCTCCCTCCGTTCCTAAAT 58.420 50.000 0.00 0.00 0.00 1.40
5571 5795 1.580059 ATGCTCCCTCCGTTCCTAAA 58.420 50.000 0.00 0.00 0.00 1.85
5572 5796 2.464796 TATGCTCCCTCCGTTCCTAA 57.535 50.000 0.00 0.00 0.00 2.69
5573 5797 2.464796 TTATGCTCCCTCCGTTCCTA 57.535 50.000 0.00 0.00 0.00 2.94
5574 5798 1.580059 TTTATGCTCCCTCCGTTCCT 58.420 50.000 0.00 0.00 0.00 3.36
5575 5799 2.640316 ATTTATGCTCCCTCCGTTCC 57.360 50.000 0.00 0.00 0.00 3.62
5576 5800 4.957296 TCTAATTTATGCTCCCTCCGTTC 58.043 43.478 0.00 0.00 0.00 3.95
5577 5801 5.367945 TTCTAATTTATGCTCCCTCCGTT 57.632 39.130 0.00 0.00 0.00 4.44
5578 5802 5.123936 GTTTCTAATTTATGCTCCCTCCGT 58.876 41.667 0.00 0.00 0.00 4.69
5579 5803 4.211374 CGTTTCTAATTTATGCTCCCTCCG 59.789 45.833 0.00 0.00 0.00 4.63
5580 5804 4.515567 CCGTTTCTAATTTATGCTCCCTCC 59.484 45.833 0.00 0.00 0.00 4.30
5581 5805 4.515567 CCCGTTTCTAATTTATGCTCCCTC 59.484 45.833 0.00 0.00 0.00 4.30
5582 5806 4.165372 TCCCGTTTCTAATTTATGCTCCCT 59.835 41.667 0.00 0.00 0.00 4.20
5583 5807 4.457466 TCCCGTTTCTAATTTATGCTCCC 58.543 43.478 0.00 0.00 0.00 4.30
5584 5808 6.039382 ACAATCCCGTTTCTAATTTATGCTCC 59.961 38.462 0.00 0.00 0.00 4.70
5585 5809 7.027778 ACAATCCCGTTTCTAATTTATGCTC 57.972 36.000 0.00 0.00 0.00 4.26
5586 5810 7.404671 AACAATCCCGTTTCTAATTTATGCT 57.595 32.000 0.00 0.00 0.00 3.79
5587 5811 9.575783 TTTAACAATCCCGTTTCTAATTTATGC 57.424 29.630 0.00 0.00 0.00 3.14
5609 5833 8.567104 GTTAAGTCCCAGTAAACCGAAATTTAA 58.433 33.333 0.00 0.00 0.00 1.52
5618 5842 4.722220 ACTTGGTTAAGTCCCAGTAAACC 58.278 43.478 0.00 0.00 43.53 3.27
5648 5872 7.283329 CCTCCTTTCTAATTAGGTGTAGCATT 58.717 38.462 12.54 0.00 33.15 3.56
5655 5879 5.959583 ACTCCCTCCTTTCTAATTAGGTG 57.040 43.478 12.54 0.27 33.15 4.00
5659 5952 8.315220 ACGATTTACTCCCTCCTTTCTAATTA 57.685 34.615 0.00 0.00 0.00 1.40
5774 6308 2.632377 ACAGACAGGCCATCGTATTTG 58.368 47.619 5.01 0.00 0.00 2.32
5783 6317 1.055849 ACATGTGTACAGACAGGCCA 58.944 50.000 5.01 0.00 35.82 5.36
5841 6376 3.550030 GCACGCCAACATGAACTAAAACT 60.550 43.478 0.00 0.00 0.00 2.66
5908 6443 7.227992 TCAAATTTTCAAACGTAAAGGCTTG 57.772 32.000 0.00 0.00 0.00 4.01
6053 6588 3.849002 CACCCTCTGTGTCAGATGG 57.151 57.895 15.77 15.77 46.74 3.51
6062 6597 8.803235 GGAATTTTTCTAATAAACACCCTCTGT 58.197 33.333 0.00 0.00 32.89 3.41


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

AutoCloner maintained by Alex Coulton.