Multiple sequence alignment - TraesCS5D01G508300

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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 TraesCS5D01G508300 chr5D 100.000 6849 0 0 830 7678 533247377 533254225 0.000000e+00 12648
1 TraesCS5D01G508300 chr5D 96.810 5957 172 10 1032 6981 311467713 311473658 0.000000e+00 9932
2 TraesCS5D01G508300 chr5D 100.000 428 0 0 1 428 533246548 533246975 0.000000e+00 791
3 TraesCS5D01G508300 chr5D 97.664 428 10 0 1 428 311466678 311467105 0.000000e+00 736
4 TraesCS5D01G508300 chrUn 97.324 6165 155 6 830 6986 81312115 81318277 0.000000e+00 10462
5 TraesCS5D01G508300 chrUn 96.963 428 12 1 1 428 81311586 81312012 0.000000e+00 717
6 TraesCS5D01G508300 chr6D 96.758 5860 172 11 830 6687 380503653 380497810 0.000000e+00 9753
7 TraesCS5D01G508300 chr6D 96.729 428 14 0 1 428 380504183 380503756 0.000000e+00 713
8 TraesCS5D01G508300 chr6D 94.186 172 9 1 6733 6903 380497809 380497638 2.130000e-65 261
9 TraesCS5D01G508300 chr7D 93.793 4801 293 5 830 5629 614796313 614801109 0.000000e+00 7210
10 TraesCS5D01G508300 chr7D 93.434 4752 299 13 2233 6980 614818240 614822982 0.000000e+00 7035
11 TraesCS5D01G508300 chr7D 93.164 1302 89 0 907 2208 614816943 614818244 0.000000e+00 1912
12 TraesCS5D01G508300 chr7D 88.204 1492 170 5 830 2321 14413435 14411950 0.000000e+00 1775
13 TraesCS5D01G508300 chr7D 94.326 423 24 0 6 428 614795788 614796210 0.000000e+00 649
14 TraesCS5D01G508300 chr7D 92.523 428 30 2 1 428 614816358 614816783 5.090000e-171 612
15 TraesCS5D01G508300 chr7D 94.672 244 12 1 186 428 614740505 614740748 2.020000e-100 377
16 TraesCS5D01G508300 chr7D 94.652 187 10 0 6 192 614729495 614729681 2.710000e-74 291
17 TraesCS5D01G508300 chr2D 91.170 4870 387 30 2130 6981 563764874 563760030 0.000000e+00 6571
18 TraesCS5D01G508300 chr2D 86.576 3166 375 32 3821 6981 13143406 13146526 0.000000e+00 3446
19 TraesCS5D01G508300 chr2D 92.477 771 35 4 6213 6981 349225407 349226156 0.000000e+00 1081
20 TraesCS5D01G508300 chr2D 88.785 428 48 0 1 428 563782612 563782185 6.830000e-145 525
21 TraesCS5D01G508300 chr2D 88.514 148 17 0 831 978 36063568 36063715 6.120000e-41 180
22 TraesCS5D01G508300 chr4B 90.026 4983 456 30 2016 6981 5582042 5577084 0.000000e+00 6410
23 TraesCS5D01G508300 chr4A 87.962 5358 615 11 1328 6680 731638258 731643590 0.000000e+00 6294
24 TraesCS5D01G508300 chr4A 88.390 2093 200 27 4903 6981 688506567 688508630 0.000000e+00 2479
25 TraesCS5D01G508300 chr4A 85.176 425 63 0 1 425 688501729 688502153 3.290000e-118 436
26 TraesCS5D01G508300 chr3A 88.507 4507 482 31 2189 6677 746379875 746384363 0.000000e+00 5421
27 TraesCS5D01G508300 chr7A 87.612 2115 254 6 830 2944 641424035 641421929 0.000000e+00 2447
28 TraesCS5D01G508300 chr5B 82.948 563 69 17 6982 7532 673285561 673286108 4.170000e-132 483
29 TraesCS5D01G508300 chr6A 84.198 424 66 1 1 424 91337741 91337319 1.990000e-110 411
30 TraesCS5D01G508300 chr5A 88.000 150 17 1 6799 6947 410796229 410796080 7.920000e-40 176


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 TraesCS5D01G508300 chr5D 533246548 533254225 7677 False 6719.500000 12648 100.000000 1 7678 2 chr5D.!!$F2 7677
1 TraesCS5D01G508300 chr5D 311466678 311473658 6980 False 5334.000000 9932 97.237000 1 6981 2 chr5D.!!$F1 6980
2 TraesCS5D01G508300 chrUn 81311586 81318277 6691 False 5589.500000 10462 97.143500 1 6986 2 chrUn.!!$F1 6985
3 TraesCS5D01G508300 chr6D 380497638 380504183 6545 True 3575.666667 9753 95.891000 1 6903 3 chr6D.!!$R1 6902
4 TraesCS5D01G508300 chr7D 614795788 614801109 5321 False 3929.500000 7210 94.059500 6 5629 2 chr7D.!!$F3 5623
5 TraesCS5D01G508300 chr7D 614816358 614822982 6624 False 3186.333333 7035 93.040333 1 6980 3 chr7D.!!$F4 6979
6 TraesCS5D01G508300 chr7D 14411950 14413435 1485 True 1775.000000 1775 88.204000 830 2321 1 chr7D.!!$R1 1491
7 TraesCS5D01G508300 chr2D 563760030 563764874 4844 True 6571.000000 6571 91.170000 2130 6981 1 chr2D.!!$R1 4851
8 TraesCS5D01G508300 chr2D 13143406 13146526 3120 False 3446.000000 3446 86.576000 3821 6981 1 chr2D.!!$F1 3160
9 TraesCS5D01G508300 chr2D 349225407 349226156 749 False 1081.000000 1081 92.477000 6213 6981 1 chr2D.!!$F3 768
10 TraesCS5D01G508300 chr4B 5577084 5582042 4958 True 6410.000000 6410 90.026000 2016 6981 1 chr4B.!!$R1 4965
11 TraesCS5D01G508300 chr4A 731638258 731643590 5332 False 6294.000000 6294 87.962000 1328 6680 1 chr4A.!!$F3 5352
12 TraesCS5D01G508300 chr4A 688506567 688508630 2063 False 2479.000000 2479 88.390000 4903 6981 1 chr4A.!!$F2 2078
13 TraesCS5D01G508300 chr3A 746379875 746384363 4488 False 5421.000000 5421 88.507000 2189 6677 1 chr3A.!!$F1 4488
14 TraesCS5D01G508300 chr7A 641421929 641424035 2106 True 2447.000000 2447 87.612000 830 2944 1 chr7A.!!$R1 2114
15 TraesCS5D01G508300 chr5B 673285561 673286108 547 False 483.000000 483 82.948000 6982 7532 1 chr5B.!!$F1 550

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
942 943 1.254975 TTGATCCTCCTCCGACGCAA 61.255 55.0 0.0 0.0 0.00 4.85 F
1209 1513 0.239082 TCTTCGACGAGCGCTACAAA 59.761 50.0 11.5 0.0 40.61 2.83 F
1628 1932 0.700564 TTCCCTGCCTTTGATCTGCT 59.299 50.0 0.0 0.0 0.00 4.24 F
2633 2939 1.256812 CAAAACCTGGAAATCGCCCT 58.743 50.0 0.0 0.0 0.00 5.19 F
3959 4275 0.032813 CCAATGCTGGGGATGTCCTT 60.033 55.0 0.0 0.0 39.30 3.36 F
5564 5886 0.114364 GGATTTTGGTGGTCTGGGGT 59.886 55.0 0.0 0.0 0.00 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1933 2237 1.427809 TCATCAGCCCCTATCTGGTG 58.572 55.000 0.00 0.0 42.48 4.17 R
3177 3489 1.645402 CCCACAAGGATACCCCCAGG 61.645 65.000 0.00 0.0 38.24 4.45 R
3548 3862 4.889409 TCAATAGTGGCAAAGATGGGATTC 59.111 41.667 0.00 0.0 0.00 2.52 R
4419 4740 6.333416 CCATTCTCAAAATCTCTCACGAGTA 58.667 40.000 0.00 0.0 38.45 2.59 R
5690 6013 1.533753 CACCCTGTTTGGCCCACAT 60.534 57.895 0.00 0.0 0.00 3.21 R
7493 7849 0.034337 AGACGCGGTGTGGTACAATT 59.966 50.000 12.47 0.0 44.16 2.32 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
58 59 2.123854 ACCGAGCGCCTGAGGATA 60.124 61.111 0.65 0.00 0.00 2.59
124 125 2.424302 CCGTGGTTTGGAGACCGT 59.576 61.111 0.00 0.00 42.83 4.83
218 219 5.961843 CAGCTGTTTTCACAATCGATGATAC 59.038 40.000 5.25 0.00 30.36 2.24
278 279 3.176708 GAGAATCGAAAATCACCGTCGA 58.823 45.455 0.00 0.00 46.74 4.20
942 943 1.254975 TTGATCCTCCTCCGACGCAA 61.255 55.000 0.00 0.00 0.00 4.85
1154 1458 0.944311 CAAACTACCGTCGCTGTGCT 60.944 55.000 0.00 0.00 0.00 4.40
1209 1513 0.239082 TCTTCGACGAGCGCTACAAA 59.761 50.000 11.50 0.00 40.61 2.83
1228 1532 6.280855 ACAAAGATATGGTTTGCTTTACCC 57.719 37.500 6.94 0.00 38.27 3.69
1308 1612 2.109834 TGGATTGGAGGGTCACAATGTT 59.890 45.455 0.00 0.00 37.43 2.71
1360 1664 1.069049 CAGTTGCCACTTTCTTTGGGG 59.931 52.381 0.00 0.00 34.35 4.96
1437 1741 3.515602 AGTTGGCTGAACTTCAGGAAT 57.484 42.857 18.53 0.00 42.70 3.01
1628 1932 0.700564 TTCCCTGCCTTTGATCTGCT 59.299 50.000 0.00 0.00 0.00 4.24
1728 2032 2.705658 AGTTGTTGAGGGTCTGTCATCA 59.294 45.455 0.00 0.00 0.00 3.07
1933 2237 7.664318 TCTTATCCTTTACTGTGGAAGGTTTTC 59.336 37.037 18.36 0.00 42.43 2.29
1996 2300 6.327626 ACCTACTAACATAGCTGTGGATGATT 59.672 38.462 15.46 2.16 35.22 2.57
2057 2361 2.121948 CCTGGATGATGGAGAGGAACA 58.878 52.381 0.00 0.00 0.00 3.18
2383 2689 6.552445 ACTGTTCTGGTATGCTAGAAGAAT 57.448 37.500 9.82 0.00 41.77 2.40
2629 2935 5.772521 AGATGAAACAAAACCTGGAAATCG 58.227 37.500 0.00 0.00 0.00 3.34
2633 2939 1.256812 CAAAACCTGGAAATCGCCCT 58.743 50.000 0.00 0.00 0.00 5.19
2819 3128 1.694150 TCCTGAAATATCTCCGCCTGG 59.306 52.381 0.00 0.00 0.00 4.45
2894 3203 2.031120 CATTCCCAACACCAACACACT 58.969 47.619 0.00 0.00 0.00 3.55
2944 3253 1.833630 CTGGGAATGCTGTGAGAGGTA 59.166 52.381 0.00 0.00 0.00 3.08
3208 3520 7.237055 GGGTATCCTTGTGGGTACTAAATCTAT 59.763 40.741 5.61 0.00 46.55 1.98
3959 4275 0.032813 CCAATGCTGGGGATGTCCTT 60.033 55.000 0.00 0.00 39.30 3.36
4419 4740 8.695456 GGAGGTTATCAAACATGATTTTATGGT 58.305 33.333 0.00 0.00 37.34 3.55
4542 4863 7.460910 AGGAAATTTAGGCCAATTTGTTTGAT 58.539 30.769 16.29 0.00 36.64 2.57
4642 4963 3.758554 GCCAATCTGCTTTTGTAAGAGGA 59.241 43.478 0.00 0.00 32.92 3.71
4789 5110 7.956328 TTTCCTAGTAGAGATGCTAACTTCA 57.044 36.000 0.00 0.00 0.00 3.02
4882 5203 9.853177 AAAATTAATGATGTCCTAGGACCTTAG 57.147 33.333 34.05 0.00 43.97 2.18
4968 5290 1.135489 TGACGTGTTCTCTCGTATGCC 60.135 52.381 0.00 0.00 42.45 4.40
5224 5546 5.812127 GCTACTTTCCCAAATATTTTGCTGG 59.188 40.000 0.00 0.00 0.00 4.85
5239 5561 1.132881 TGCTGGAAGTTGGGGGATTTT 60.133 47.619 0.00 0.00 35.30 1.82
5439 5761 6.252233 TGTCTGTCATCAAATTCCCCAAATA 58.748 36.000 0.00 0.00 0.00 1.40
5564 5886 0.114364 GGATTTTGGTGGTCTGGGGT 59.886 55.000 0.00 0.00 0.00 4.95
5690 6013 9.747898 AATATAGAACTGACAAACCCAATGTAA 57.252 29.630 0.00 0.00 0.00 2.41
5847 6170 6.222038 GGATTCTTCCCTAAAAACCCAATC 57.778 41.667 0.00 0.00 35.84 2.67
6183 6506 8.283291 GTGGTTAGCTTTCCATAATAAGATTCG 58.717 37.037 11.72 0.00 36.09 3.34
6436 6762 4.403432 CCATTTGGAGCATTTGGACTATGT 59.597 41.667 0.00 0.00 37.39 2.29
6503 6829 2.758979 CAATCTTGGCAAGGATCAGCTT 59.241 45.455 25.92 6.87 0.00 3.74
6523 6849 4.377841 GCTTATCGCTACATCAATGGAAGC 60.378 45.833 8.68 8.68 37.48 3.86
6602 6928 1.079543 GAAGAGGCGAGCTGCTCAA 60.080 57.895 27.46 0.00 45.43 3.02
7010 7355 2.037381 GAGGACGACAGAAAAAGGAGGT 59.963 50.000 0.00 0.00 0.00 3.85
7020 7365 2.881111 AAAAGGAGGTAGCCTGTTCC 57.119 50.000 0.00 0.00 38.58 3.62
7023 7368 0.325765 AGGAGGTAGCCTGTTCCCTC 60.326 60.000 0.00 0.00 42.28 4.30
7027 7372 1.217183 AGGTAGCCTGTTCCCTCGATA 59.783 52.381 0.00 0.00 29.57 2.92
7034 7379 2.496070 CCTGTTCCCTCGATAGTTCACA 59.504 50.000 0.00 0.00 37.40 3.58
7041 7386 3.190874 CCTCGATAGTTCACAAGAAGCC 58.809 50.000 0.00 0.00 33.63 4.35
7044 7389 3.006430 TCGATAGTTCACAAGAAGCCACA 59.994 43.478 0.00 0.00 33.63 4.17
7048 7393 0.179234 TTCACAAGAAGCCACACCGA 59.821 50.000 0.00 0.00 0.00 4.69
7052 7397 1.081892 CAAGAAGCCACACCGATGAG 58.918 55.000 0.00 0.00 0.00 2.90
7062 7407 1.270826 ACACCGATGAGCATATCTCCG 59.729 52.381 0.00 0.00 41.18 4.63
7065 7410 2.288457 ACCGATGAGCATATCTCCGTTG 60.288 50.000 0.00 0.00 41.18 4.10
7067 7412 3.384668 CGATGAGCATATCTCCGTTGTT 58.615 45.455 0.00 0.00 41.18 2.83
7069 7414 3.610040 TGAGCATATCTCCGTTGTTGT 57.390 42.857 0.00 0.00 41.18 3.32
7070 7415 3.937814 TGAGCATATCTCCGTTGTTGTT 58.062 40.909 0.00 0.00 41.18 2.83
7072 7417 3.270877 AGCATATCTCCGTTGTTGTTCC 58.729 45.455 0.00 0.00 0.00 3.62
7074 7419 3.438781 GCATATCTCCGTTGTTGTTCCAA 59.561 43.478 0.00 0.00 0.00 3.53
7075 7420 4.671766 GCATATCTCCGTTGTTGTTCCAAC 60.672 45.833 0.22 0.22 41.01 3.77
7082 7427 0.727970 TTGTTGTTCCAACGTGGTCG 59.272 50.000 0.00 0.00 39.03 4.79
7083 7428 1.090625 TGTTGTTCCAACGTGGTCGG 61.091 55.000 0.00 0.00 39.03 4.79
7116 7461 4.487714 AACTCTGGTTTGAAGTCACAGA 57.512 40.909 0.00 0.00 36.78 3.41
7124 7469 4.157840 GGTTTGAAGTCACAGAAAAGTGGT 59.842 41.667 0.00 0.00 39.93 4.16
7148 7493 2.050144 AGGAAACTGCTGAGGTCTTCA 58.950 47.619 0.00 0.00 41.13 3.02
7164 7509 4.503991 GGTCTTCAGTTGTGTGGATCTCTT 60.504 45.833 0.00 0.00 0.00 2.85
7165 7510 5.059833 GTCTTCAGTTGTGTGGATCTCTTT 58.940 41.667 0.00 0.00 0.00 2.52
7168 7513 6.260936 TCTTCAGTTGTGTGGATCTCTTTTTC 59.739 38.462 0.00 0.00 0.00 2.29
7169 7514 5.684704 TCAGTTGTGTGGATCTCTTTTTCT 58.315 37.500 0.00 0.00 0.00 2.52
7170 7515 5.528690 TCAGTTGTGTGGATCTCTTTTTCTG 59.471 40.000 0.00 0.00 0.00 3.02
7185 7530 2.222007 TTCTGGTGCAAATGTTGTGC 57.778 45.000 0.00 0.00 42.55 4.57
7190 7535 1.994779 GGTGCAAATGTTGTGCTATGC 59.005 47.619 0.00 0.00 42.69 3.14
7191 7536 1.650153 GTGCAAATGTTGTGCTATGCG 59.350 47.619 0.00 0.00 42.69 4.73
7198 7543 2.276201 TGTTGTGCTATGCGATGTACC 58.724 47.619 0.00 0.00 0.00 3.34
7242 7590 3.049674 ACAAGTCGCATGCACCCG 61.050 61.111 19.57 10.81 0.00 5.28
7254 7602 2.409870 GCACCCGCAATCCCTTCTG 61.410 63.158 0.00 0.00 38.36 3.02
7260 7608 1.135689 CCGCAATCCCTTCTGTTTTCG 60.136 52.381 0.00 0.00 0.00 3.46
7265 7613 0.320421 TCCCTTCTGTTTTCGGCTCG 60.320 55.000 0.00 0.00 0.00 5.03
7268 7616 2.076863 CCTTCTGTTTTCGGCTCGAAT 58.923 47.619 10.19 0.00 45.28 3.34
7288 7636 2.541466 TCCTTCTTCCTCCTCCAGAAC 58.459 52.381 0.00 0.00 0.00 3.01
7307 7655 0.618680 CATCCCCACTCCCTCTCACA 60.619 60.000 0.00 0.00 0.00 3.58
7312 7660 1.599606 CCACTCCCTCTCACACCTCG 61.600 65.000 0.00 0.00 0.00 4.63
7315 7663 0.743688 CTCCCTCTCACACCTCGATG 59.256 60.000 0.00 0.00 0.00 3.84
7320 7668 2.416566 CCTCTCACACCTCGATGTCTTG 60.417 54.545 0.00 0.00 0.00 3.02
7327 7675 1.450312 CTCGATGTCTTGCCCACCC 60.450 63.158 0.00 0.00 0.00 4.61
7331 7679 3.224007 ATGTCTTGCCCACCCCCAC 62.224 63.158 0.00 0.00 0.00 4.61
7340 7688 3.252284 CACCCCCACTGCACTCCT 61.252 66.667 0.00 0.00 0.00 3.69
7341 7689 2.930562 ACCCCCACTGCACTCCTC 60.931 66.667 0.00 0.00 0.00 3.71
7342 7690 4.087892 CCCCCACTGCACTCCTCG 62.088 72.222 0.00 0.00 0.00 4.63
7344 7692 2.362369 CCCCACTGCACTCCTCGAT 61.362 63.158 0.00 0.00 0.00 3.59
7373 7721 6.035542 CGGCAACAAGTTACAACAAAGAAAAT 59.964 34.615 0.00 0.00 0.00 1.82
7382 7730 8.841300 AGTTACAACAAAGAAAATTCTCTCCTC 58.159 33.333 0.00 0.00 36.28 3.71
7385 7733 7.880105 ACAACAAAGAAAATTCTCTCCTCATC 58.120 34.615 0.00 0.00 36.28 2.92
7388 7736 6.370166 ACAAAGAAAATTCTCTCCTCATCGTC 59.630 38.462 0.00 0.00 36.28 4.20
7391 7739 4.664150 AAATTCTCTCCTCATCGTCCTC 57.336 45.455 0.00 0.00 0.00 3.71
7405 7756 1.130749 CGTCCTCCTACTCTTCACACG 59.869 57.143 0.00 0.00 0.00 4.49
7409 7760 1.269723 CTCCTACTCTTCACACGCACA 59.730 52.381 0.00 0.00 0.00 4.57
7423 7774 0.725784 CGCACAAACGGCTTGATCAC 60.726 55.000 0.00 0.00 38.50 3.06
7424 7775 0.593128 GCACAAACGGCTTGATCACT 59.407 50.000 0.00 0.00 38.50 3.41
7425 7776 1.400242 GCACAAACGGCTTGATCACTC 60.400 52.381 0.00 0.00 38.50 3.51
7427 7778 1.148310 CAAACGGCTTGATCACTCGT 58.852 50.000 10.24 10.24 37.17 4.18
7428 7779 2.288579 ACAAACGGCTTGATCACTCGTA 60.289 45.455 14.71 0.00 38.50 3.43
7430 7781 0.885879 ACGGCTTGATCACTCGTACA 59.114 50.000 13.30 0.00 32.03 2.90
7431 7782 1.476891 ACGGCTTGATCACTCGTACAT 59.523 47.619 13.30 0.00 32.03 2.29
7451 7807 5.907207 ACATACGAGATACATGTTTGCTCT 58.093 37.500 2.30 1.50 28.56 4.09
7452 7808 5.750547 ACATACGAGATACATGTTTGCTCTG 59.249 40.000 2.30 6.16 28.56 3.35
7453 7809 2.932614 ACGAGATACATGTTTGCTCTGC 59.067 45.455 2.30 0.00 0.00 4.26
7454 7810 3.193263 CGAGATACATGTTTGCTCTGCT 58.807 45.455 2.30 0.00 0.00 4.24
7455 7811 3.244814 CGAGATACATGTTTGCTCTGCTC 59.755 47.826 2.30 0.00 0.00 4.26
7456 7812 3.193263 AGATACATGTTTGCTCTGCTCG 58.807 45.455 2.30 0.00 0.00 5.03
7457 7813 2.741759 TACATGTTTGCTCTGCTCGA 57.258 45.000 2.30 0.00 0.00 4.04
7458 7814 1.151668 ACATGTTTGCTCTGCTCGAC 58.848 50.000 0.00 0.00 0.00 4.20
7459 7815 1.270518 ACATGTTTGCTCTGCTCGACT 60.271 47.619 0.00 0.00 0.00 4.18
7460 7816 1.128136 CATGTTTGCTCTGCTCGACTG 59.872 52.381 0.00 0.00 0.00 3.51
7461 7817 1.224069 TGTTTGCTCTGCTCGACTGC 61.224 55.000 0.00 0.00 0.00 4.40
7462 7818 0.948141 GTTTGCTCTGCTCGACTGCT 60.948 55.000 0.00 0.00 0.00 4.24
7463 7819 0.947660 TTTGCTCTGCTCGACTGCTG 60.948 55.000 0.00 0.00 0.00 4.41
7464 7820 3.187414 GCTCTGCTCGACTGCTGC 61.187 66.667 0.00 0.00 32.95 5.25
7465 7821 2.260743 CTCTGCTCGACTGCTGCA 59.739 61.111 0.88 0.88 35.30 4.41
7467 7823 3.476646 CTGCTCGACTGCTGCACG 61.477 66.667 0.00 1.64 32.91 5.34
7486 7842 1.002379 AGTCCTCGTGCTACTCGGT 60.002 57.895 0.00 0.00 0.00 4.69
7493 7849 0.240145 CGTGCTACTCGGTTGAGACA 59.760 55.000 0.00 0.00 45.57 3.41
7509 7865 0.165079 GACAATTGTACCACACCGCG 59.835 55.000 11.95 0.00 0.00 6.46
7532 7888 3.876914 TCTACAACCATCAATCAATCGGC 59.123 43.478 0.00 0.00 0.00 5.54
7533 7889 2.445427 ACAACCATCAATCAATCGGCA 58.555 42.857 0.00 0.00 0.00 5.69
7534 7890 2.164219 ACAACCATCAATCAATCGGCAC 59.836 45.455 0.00 0.00 0.00 5.01
7559 7915 2.259511 ACGGGGCGAGACGTTAAC 59.740 61.111 0.00 0.00 40.99 2.01
7560 7916 2.877582 CGGGGCGAGACGTTAACG 60.878 66.667 25.68 25.68 46.33 3.18
7561 7917 2.507769 GGGGCGAGACGTTAACGG 60.508 66.667 29.81 14.35 44.95 4.44
7562 7918 2.568090 GGGCGAGACGTTAACGGA 59.432 61.111 29.81 0.00 44.95 4.69
7563 7919 1.515736 GGGCGAGACGTTAACGGAG 60.516 63.158 29.81 18.37 44.95 4.63
7564 7920 1.515736 GGCGAGACGTTAACGGAGG 60.516 63.158 29.81 17.14 44.95 4.30
7565 7921 1.503542 GCGAGACGTTAACGGAGGA 59.496 57.895 29.81 0.00 44.95 3.71
7566 7922 0.796113 GCGAGACGTTAACGGAGGAC 60.796 60.000 29.81 13.73 44.95 3.85
7567 7923 0.518636 CGAGACGTTAACGGAGGACA 59.481 55.000 29.81 0.00 44.95 4.02
7568 7924 1.727213 CGAGACGTTAACGGAGGACAC 60.727 57.143 29.81 13.27 44.95 3.67
7569 7925 1.267806 GAGACGTTAACGGAGGACACA 59.732 52.381 29.81 0.00 44.95 3.72
7570 7926 1.268899 AGACGTTAACGGAGGACACAG 59.731 52.381 29.81 0.79 44.95 3.66
7571 7927 1.267806 GACGTTAACGGAGGACACAGA 59.732 52.381 29.81 0.00 44.95 3.41
7572 7928 1.000938 ACGTTAACGGAGGACACAGAC 60.001 52.381 29.81 0.00 44.95 3.51
7573 7929 1.694639 GTTAACGGAGGACACAGACG 58.305 55.000 0.00 0.00 0.00 4.18
7574 7930 0.599558 TTAACGGAGGACACAGACGG 59.400 55.000 0.00 0.00 0.00 4.79
7575 7931 1.870055 TAACGGAGGACACAGACGGC 61.870 60.000 0.00 0.00 0.00 5.68
7576 7932 4.778415 CGGAGGACACAGACGGCG 62.778 72.222 4.80 4.80 0.00 6.46
7577 7933 3.371063 GGAGGACACAGACGGCGA 61.371 66.667 16.62 0.00 0.00 5.54
7578 7934 2.649034 GAGGACACAGACGGCGAA 59.351 61.111 16.62 0.00 0.00 4.70
7579 7935 1.444553 GAGGACACAGACGGCGAAG 60.445 63.158 16.62 5.04 0.00 3.79
7580 7936 2.143594 GAGGACACAGACGGCGAAGT 62.144 60.000 16.62 5.78 0.00 3.01
7581 7937 1.733399 GGACACAGACGGCGAAGTC 60.733 63.158 16.62 13.02 41.23 3.01
7587 7943 3.470567 GACGGCGAAGTCTGCGTG 61.471 66.667 16.62 0.00 38.09 5.34
7590 7946 3.782244 GGCGAAGTCTGCGTGCTG 61.782 66.667 1.31 0.00 0.00 4.41
7591 7947 3.038417 GCGAAGTCTGCGTGCTGT 61.038 61.111 1.31 0.00 0.00 4.40
7592 7948 3.004734 GCGAAGTCTGCGTGCTGTC 62.005 63.158 1.31 0.00 0.00 3.51
7593 7949 2.710971 CGAAGTCTGCGTGCTGTCG 61.711 63.158 0.00 0.00 0.00 4.35
7594 7950 2.356313 AAGTCTGCGTGCTGTCGG 60.356 61.111 0.00 0.00 0.00 4.79
7605 7961 4.680237 CTGTCGGCGGCCTTCACA 62.680 66.667 18.34 15.08 0.00 3.58
7606 7962 3.958147 CTGTCGGCGGCCTTCACAT 62.958 63.158 18.34 0.00 0.00 3.21
7607 7963 3.195698 GTCGGCGGCCTTCACATC 61.196 66.667 18.34 0.00 0.00 3.06
7608 7964 4.467084 TCGGCGGCCTTCACATCC 62.467 66.667 18.34 0.00 0.00 3.51
7609 7965 4.473520 CGGCGGCCTTCACATCCT 62.474 66.667 18.34 0.00 0.00 3.24
7610 7966 2.825836 GGCGGCCTTCACATCCTG 60.826 66.667 12.87 0.00 0.00 3.86
7611 7967 3.512516 GCGGCCTTCACATCCTGC 61.513 66.667 0.00 0.00 0.00 4.85
7612 7968 2.825836 CGGCCTTCACATCCTGCC 60.826 66.667 0.00 0.00 38.74 4.85
7613 7969 2.440980 GGCCTTCACATCCTGCCC 60.441 66.667 0.00 0.00 36.07 5.36
7614 7970 2.356278 GCCTTCACATCCTGCCCA 59.644 61.111 0.00 0.00 0.00 5.36
7615 7971 2.048603 GCCTTCACATCCTGCCCAC 61.049 63.158 0.00 0.00 0.00 4.61
7616 7972 1.379916 CCTTCACATCCTGCCCACA 59.620 57.895 0.00 0.00 0.00 4.17
7617 7973 0.962356 CCTTCACATCCTGCCCACAC 60.962 60.000 0.00 0.00 0.00 3.82
7618 7974 0.037303 CTTCACATCCTGCCCACACT 59.963 55.000 0.00 0.00 0.00 3.55
7619 7975 1.278985 CTTCACATCCTGCCCACACTA 59.721 52.381 0.00 0.00 0.00 2.74
7620 7976 1.583556 TCACATCCTGCCCACACTAT 58.416 50.000 0.00 0.00 0.00 2.12
7621 7977 1.486310 TCACATCCTGCCCACACTATC 59.514 52.381 0.00 0.00 0.00 2.08
7622 7978 1.210234 CACATCCTGCCCACACTATCA 59.790 52.381 0.00 0.00 0.00 2.15
7623 7979 1.210478 ACATCCTGCCCACACTATCAC 59.790 52.381 0.00 0.00 0.00 3.06
7624 7980 0.839946 ATCCTGCCCACACTATCACC 59.160 55.000 0.00 0.00 0.00 4.02
7625 7981 0.546507 TCCTGCCCACACTATCACCA 60.547 55.000 0.00 0.00 0.00 4.17
7626 7982 0.107508 CCTGCCCACACTATCACCAG 60.108 60.000 0.00 0.00 0.00 4.00
7627 7983 0.615331 CTGCCCACACTATCACCAGT 59.385 55.000 0.00 0.00 0.00 4.00
7628 7984 0.613260 TGCCCACACTATCACCAGTC 59.387 55.000 0.00 0.00 0.00 3.51
7629 7985 0.613260 GCCCACACTATCACCAGTCA 59.387 55.000 0.00 0.00 0.00 3.41
7630 7986 1.003118 GCCCACACTATCACCAGTCAA 59.997 52.381 0.00 0.00 0.00 3.18
7631 7987 2.699954 CCCACACTATCACCAGTCAAC 58.300 52.381 0.00 0.00 0.00 3.18
7632 7988 2.337583 CCACACTATCACCAGTCAACG 58.662 52.381 0.00 0.00 0.00 4.10
7633 7989 1.726791 CACACTATCACCAGTCAACGC 59.273 52.381 0.00 0.00 0.00 4.84
7634 7990 1.343142 ACACTATCACCAGTCAACGCA 59.657 47.619 0.00 0.00 0.00 5.24
7635 7991 2.028112 ACACTATCACCAGTCAACGCAT 60.028 45.455 0.00 0.00 0.00 4.73
7636 7992 3.002791 CACTATCACCAGTCAACGCATT 58.997 45.455 0.00 0.00 0.00 3.56
7637 7993 3.002791 ACTATCACCAGTCAACGCATTG 58.997 45.455 0.00 0.00 37.14 2.82
7638 7994 0.523072 ATCACCAGTCAACGCATTGC 59.477 50.000 0.00 0.00 35.63 3.56
7649 8005 4.741781 GCATTGCGCGCACTTCGT 62.742 61.111 36.72 14.75 41.07 3.85
7650 8006 2.571611 CATTGCGCGCACTTCGTC 60.572 61.111 36.72 0.01 41.07 4.20
7651 8007 4.134187 ATTGCGCGCACTTCGTCG 62.134 61.111 36.72 0.00 41.07 5.12
7654 8010 4.253273 GCGCGCACTTCGTCGATC 62.253 66.667 29.10 0.00 39.02 3.69
7655 8011 2.874315 CGCGCACTTCGTCGATCA 60.874 61.111 8.75 0.00 39.02 2.92
7656 8012 2.839438 CGCGCACTTCGTCGATCAG 61.839 63.158 8.75 0.00 39.02 2.90
7657 8013 1.801913 GCGCACTTCGTCGATCAGT 60.802 57.895 0.30 0.00 41.07 3.41
7658 8014 0.522705 GCGCACTTCGTCGATCAGTA 60.523 55.000 0.30 0.00 41.07 2.74
7659 8015 1.181001 CGCACTTCGTCGATCAGTAC 58.819 55.000 0.00 0.00 0.00 2.73
7660 8016 1.546834 GCACTTCGTCGATCAGTACC 58.453 55.000 0.00 0.00 0.00 3.34
7661 8017 1.132643 GCACTTCGTCGATCAGTACCT 59.867 52.381 0.00 0.00 0.00 3.08
7662 8018 2.791849 GCACTTCGTCGATCAGTACCTC 60.792 54.545 0.00 0.00 0.00 3.85
7663 8019 2.418976 CACTTCGTCGATCAGTACCTCA 59.581 50.000 0.00 0.00 0.00 3.86
7664 8020 3.065510 CACTTCGTCGATCAGTACCTCAT 59.934 47.826 0.00 0.00 0.00 2.90
7665 8021 3.312973 ACTTCGTCGATCAGTACCTCATC 59.687 47.826 0.00 0.00 0.00 2.92
7666 8022 2.219458 TCGTCGATCAGTACCTCATCC 58.781 52.381 0.00 0.00 0.00 3.51
7667 8023 2.158798 TCGTCGATCAGTACCTCATCCT 60.159 50.000 0.00 0.00 0.00 3.24
7668 8024 2.224549 CGTCGATCAGTACCTCATCCTC 59.775 54.545 0.00 0.00 0.00 3.71
7669 8025 2.224549 GTCGATCAGTACCTCATCCTCG 59.775 54.545 0.00 0.00 0.00 4.63
7670 8026 1.068885 CGATCAGTACCTCATCCTCGC 60.069 57.143 0.00 0.00 0.00 5.03
7671 8027 1.271102 GATCAGTACCTCATCCTCGCC 59.729 57.143 0.00 0.00 0.00 5.54
7672 8028 0.755698 TCAGTACCTCATCCTCGCCC 60.756 60.000 0.00 0.00 0.00 6.13
7673 8029 0.757188 CAGTACCTCATCCTCGCCCT 60.757 60.000 0.00 0.00 0.00 5.19
7674 8030 0.851469 AGTACCTCATCCTCGCCCTA 59.149 55.000 0.00 0.00 0.00 3.53
7675 8031 1.429687 AGTACCTCATCCTCGCCCTAT 59.570 52.381 0.00 0.00 0.00 2.57
7676 8032 1.546476 GTACCTCATCCTCGCCCTATG 59.454 57.143 0.00 0.00 0.00 2.23
7677 8033 0.105453 ACCTCATCCTCGCCCTATGT 60.105 55.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.229723 ATCCACCCCACCCGTAACT 60.230 57.895 0.00 0.00 0.00 2.24
218 219 5.715070 CTCAACCTCTACTGGTTCTAACAG 58.285 45.833 0.00 0.00 46.37 3.16
278 279 0.893727 GGCAATTTGGACCTCACCGT 60.894 55.000 0.00 0.00 0.00 4.83
942 943 2.406559 CCCTCCCTGATGATCTTGAGT 58.593 52.381 0.00 0.00 0.00 3.41
1154 1458 2.836360 GAGGGATCGGTGGCGGTA 60.836 66.667 0.00 0.00 0.00 4.02
1209 1513 2.949644 GCGGGTAAAGCAAACCATATCT 59.050 45.455 4.75 0.00 38.87 1.98
1308 1612 2.031120 GCCCAGGCTGCACAATTATTA 58.969 47.619 9.56 0.00 38.26 0.98
1360 1664 1.298014 CCAGTCCCAGAGCAGAACC 59.702 63.158 0.00 0.00 0.00 3.62
1437 1741 2.559698 TGATCCAAACTTCTCCGCAA 57.440 45.000 0.00 0.00 0.00 4.85
1628 1932 2.164422 GACACAGACACTCCATCGATGA 59.836 50.000 26.86 11.61 0.00 2.92
1728 2032 3.244181 GGACTTTCCATGTGCACCATTTT 60.244 43.478 15.69 0.00 36.28 1.82
1933 2237 1.427809 TCATCAGCCCCTATCTGGTG 58.572 55.000 0.00 0.00 42.48 4.17
1996 2300 6.214615 TCCTCCTCATCAATTACCTTGTTGTA 59.785 38.462 0.00 0.00 36.40 2.41
2057 2361 3.643792 GGCAAGGTCTAGGTCATCTATGT 59.356 47.826 0.00 0.00 0.00 2.29
2383 2689 4.774726 AGTATCAGAAGCAGAGTCTTCCAA 59.225 41.667 0.00 0.00 42.52 3.53
2629 2935 7.698506 AGGACTTACTTTTAAATGTAAGGGC 57.301 36.000 34.34 28.63 44.48 5.19
2764 3071 7.416817 GCAAATACAAGGCATTTTTCAGTTTT 58.583 30.769 0.00 0.00 0.00 2.43
2813 3122 2.814919 CCAGTATCTAGACTACCAGGCG 59.185 54.545 0.00 0.00 0.00 5.52
2894 3203 3.329889 CACCAGCAGTGCCCCCTA 61.330 66.667 12.58 0.00 40.28 3.53
3074 3386 7.389053 GTCTCTCTCTTAATTTCTTGAAAGCCA 59.611 37.037 2.25 0.00 0.00 4.75
3177 3489 1.645402 CCCACAAGGATACCCCCAGG 61.645 65.000 0.00 0.00 38.24 4.45
3208 3520 6.826741 ACTAACACTAAGCACCTCAAAAAGAA 59.173 34.615 0.00 0.00 0.00 2.52
3548 3862 4.889409 TCAATAGTGGCAAAGATGGGATTC 59.111 41.667 0.00 0.00 0.00 2.52
3700 4014 6.492087 CCACCACTTCTCAAATTTAAAGGGTA 59.508 38.462 13.63 0.00 0.00 3.69
3959 4275 6.387192 TCTCCCCTGATTTGTTTCATTCTA 57.613 37.500 0.00 0.00 0.00 2.10
4419 4740 6.333416 CCATTCTCAAAATCTCTCACGAGTA 58.667 40.000 0.00 0.00 38.45 2.59
4655 4976 2.445682 TGGGCAGTAACCACACTTTT 57.554 45.000 0.00 0.00 31.83 2.27
4789 5110 2.490902 CCACTTAGCTCCAAAACCCCTT 60.491 50.000 0.00 0.00 0.00 3.95
4968 5290 2.723124 ATTGTTAACAGCTTTGGCCG 57.277 45.000 8.56 0.00 39.73 6.13
5111 5433 5.495640 AGAAAGGTTTTCAAAACATGCCAA 58.504 33.333 14.92 0.00 0.00 4.52
5224 5546 3.092301 CAGAGGAAAATCCCCCAACTTC 58.908 50.000 0.00 0.00 37.19 3.01
5239 5561 5.209659 GGAACTCCTAGGTATTTCAGAGGA 58.790 45.833 9.08 0.00 35.06 3.71
5564 5886 8.808092 CATGTTAAATTCCCTTAAGTTGGGTAA 58.192 33.333 0.97 0.00 44.84 2.85
5690 6013 1.533753 CACCCTGTTTGGCCCACAT 60.534 57.895 0.00 0.00 0.00 3.21
5847 6170 5.127519 TGGCAGATTTCATAAACATCCCAAG 59.872 40.000 0.00 0.00 0.00 3.61
5857 6180 4.280425 TGCTGTTGTTGGCAGATTTCATAA 59.720 37.500 0.00 0.00 36.12 1.90
6120 6443 0.681175 GTGGGGCACAGCAATTTTCT 59.319 50.000 0.00 0.00 34.08 2.52
6207 6530 3.955524 TTAAGTTTTCCACCACCCTCA 57.044 42.857 0.00 0.00 0.00 3.86
6436 6762 3.758023 CCCTGAAAGCACATGTCATTACA 59.242 43.478 0.00 0.00 40.69 2.41
6503 6829 4.607293 AGCTTCCATTGATGTAGCGATA 57.393 40.909 0.00 0.00 38.09 2.92
6523 6849 1.374758 GGTCGCCCACACAGAGAAG 60.375 63.158 0.00 0.00 0.00 2.85
6991 7336 2.545537 ACCTCCTTTTTCTGTCGTCC 57.454 50.000 0.00 0.00 0.00 4.79
6997 7342 3.425162 ACAGGCTACCTCCTTTTTCTG 57.575 47.619 0.00 0.00 33.25 3.02
7010 7355 2.750141 ACTATCGAGGGAACAGGCTA 57.250 50.000 0.00 0.00 0.00 3.93
7020 7365 3.190874 GGCTTCTTGTGAACTATCGAGG 58.809 50.000 0.00 0.00 0.00 4.63
7023 7368 3.123621 GTGTGGCTTCTTGTGAACTATCG 59.876 47.826 0.00 0.00 0.00 2.92
7027 7372 1.680338 GGTGTGGCTTCTTGTGAACT 58.320 50.000 0.00 0.00 0.00 3.01
7034 7379 0.674895 GCTCATCGGTGTGGCTTCTT 60.675 55.000 0.00 0.00 0.00 2.52
7041 7386 2.681706 GGAGATATGCTCATCGGTGTG 58.318 52.381 0.00 0.00 45.81 3.82
7044 7389 1.621992 ACGGAGATATGCTCATCGGT 58.378 50.000 0.00 0.00 45.81 4.69
7048 7393 4.142609 ACAACAACGGAGATATGCTCAT 57.857 40.909 0.00 0.00 45.81 2.90
7052 7397 3.006940 TGGAACAACAACGGAGATATGC 58.993 45.455 0.00 0.00 31.92 3.14
7062 7407 4.683901 CCGACCACGTTGGAACAACAAC 62.684 54.545 12.04 0.00 45.49 3.32
7065 7410 0.810823 TCCGACCACGTTGGAACAAC 60.811 55.000 10.46 2.17 42.55 3.32
7067 7412 1.068417 CTCCGACCACGTTGGAACA 59.932 57.895 10.46 0.00 44.54 3.18
7069 7414 2.738480 CCTCCGACCACGTTGGAA 59.262 61.111 10.46 0.00 44.54 3.53
7070 7415 3.307906 CCCTCCGACCACGTTGGA 61.308 66.667 10.46 0.86 43.20 3.53
7072 7417 4.308458 TGCCCTCCGACCACGTTG 62.308 66.667 0.00 0.00 37.88 4.10
7074 7419 4.988716 TCTGCCCTCCGACCACGT 62.989 66.667 0.00 0.00 37.88 4.49
7075 7420 4.135153 CTCTGCCCTCCGACCACG 62.135 72.222 0.00 0.00 39.43 4.94
7076 7421 3.775654 CCTCTGCCCTCCGACCAC 61.776 72.222 0.00 0.00 0.00 4.16
7077 7422 3.539593 TTCCTCTGCCCTCCGACCA 62.540 63.158 0.00 0.00 0.00 4.02
7079 7424 1.079057 GTTTCCTCTGCCCTCCGAC 60.079 63.158 0.00 0.00 0.00 4.79
7080 7425 1.229209 AGTTTCCTCTGCCCTCCGA 60.229 57.895 0.00 0.00 0.00 4.55
7082 7427 2.690367 AGAGTTTCCTCTGCCCTCC 58.310 57.895 0.00 0.00 46.45 4.30
7116 7461 2.952310 GCAGTTTCCTGAGACCACTTTT 59.048 45.455 0.00 0.00 41.50 2.27
7148 7493 4.823989 CCAGAAAAAGAGATCCACACAACT 59.176 41.667 0.00 0.00 0.00 3.16
7151 7496 4.136796 CACCAGAAAAAGAGATCCACACA 58.863 43.478 0.00 0.00 0.00 3.72
7164 7509 2.935201 GCACAACATTTGCACCAGAAAA 59.065 40.909 0.00 0.00 39.93 2.29
7165 7510 2.168106 AGCACAACATTTGCACCAGAAA 59.832 40.909 0.00 0.00 42.83 2.52
7168 7513 3.247442 CATAGCACAACATTTGCACCAG 58.753 45.455 0.00 0.00 42.83 4.00
7169 7514 2.609984 GCATAGCACAACATTTGCACCA 60.610 45.455 0.00 0.00 42.83 4.17
7170 7515 1.994779 GCATAGCACAACATTTGCACC 59.005 47.619 0.00 0.00 42.83 5.01
7215 7563 2.031258 TGCGACTTGTGAGGTTTTCA 57.969 45.000 0.00 0.00 0.00 2.69
7218 7566 0.593128 GCATGCGACTTGTGAGGTTT 59.407 50.000 0.00 0.00 0.00 3.27
7242 7590 1.402852 GCCGAAAACAGAAGGGATTGC 60.403 52.381 0.00 0.00 0.00 3.56
7244 7592 2.437413 GAGCCGAAAACAGAAGGGATT 58.563 47.619 0.00 0.00 0.00 3.01
7268 7616 2.158158 TGTTCTGGAGGAGGAAGAAGGA 60.158 50.000 0.00 0.00 30.84 3.36
7288 7636 0.618680 TGTGAGAGGGAGTGGGGATG 60.619 60.000 0.00 0.00 0.00 3.51
7307 7655 1.296715 GTGGGCAAGACATCGAGGT 59.703 57.895 0.50 0.50 0.00 3.85
7312 7660 2.043953 GGGGGTGGGCAAGACATC 60.044 66.667 0.00 0.00 0.00 3.06
7315 7663 3.580319 AGTGGGGGTGGGCAAGAC 61.580 66.667 0.00 0.00 0.00 3.01
7327 7675 1.142748 GATCGAGGAGTGCAGTGGG 59.857 63.158 0.00 0.00 0.00 4.61
7331 7679 2.279120 GCCGATCGAGGAGTGCAG 60.279 66.667 18.66 0.00 0.00 4.41
7334 7682 4.933064 GCCGCCGATCGAGGAGTG 62.933 72.222 26.41 13.16 41.67 3.51
7340 7688 2.813474 CTTGTTGCCGCCGATCGA 60.813 61.111 18.66 0.00 41.67 3.59
7341 7689 1.355796 TAACTTGTTGCCGCCGATCG 61.356 55.000 8.51 8.51 38.08 3.69
7342 7690 0.096454 GTAACTTGTTGCCGCCGATC 59.904 55.000 0.00 0.00 0.00 3.69
7344 7692 0.814410 TTGTAACTTGTTGCCGCCGA 60.814 50.000 0.00 0.00 0.00 5.54
7373 7721 1.566703 AGGAGGACGATGAGGAGAGAA 59.433 52.381 0.00 0.00 0.00 2.87
7382 7730 3.017442 TGTGAAGAGTAGGAGGACGATG 58.983 50.000 0.00 0.00 0.00 3.84
7385 7733 1.130749 CGTGTGAAGAGTAGGAGGACG 59.869 57.143 0.00 0.00 0.00 4.79
7388 7736 0.888619 TGCGTGTGAAGAGTAGGAGG 59.111 55.000 0.00 0.00 0.00 4.30
7391 7739 2.148916 TTGTGCGTGTGAAGAGTAGG 57.851 50.000 0.00 0.00 0.00 3.18
7405 7756 0.593128 AGTGATCAAGCCGTTTGTGC 59.407 50.000 0.00 0.00 38.01 4.57
7409 7760 2.288579 TGTACGAGTGATCAAGCCGTTT 60.289 45.455 18.84 3.42 35.05 3.60
7427 7778 6.918022 CAGAGCAAACATGTATCTCGTATGTA 59.082 38.462 0.00 0.00 34.18 2.29
7428 7779 5.750547 CAGAGCAAACATGTATCTCGTATGT 59.249 40.000 0.00 0.00 36.66 2.29
7430 7781 4.747108 GCAGAGCAAACATGTATCTCGTAT 59.253 41.667 0.00 0.00 0.00 3.06
7431 7782 4.112634 GCAGAGCAAACATGTATCTCGTA 58.887 43.478 0.00 0.00 0.00 3.43
7443 7799 0.948141 AGCAGTCGAGCAGAGCAAAC 60.948 55.000 0.00 0.00 36.85 2.93
7447 7803 3.187414 GCAGCAGTCGAGCAGAGC 61.187 66.667 0.00 0.00 36.85 4.09
7451 7807 3.903932 CTCGTGCAGCAGTCGAGCA 62.904 63.158 19.14 0.00 42.94 4.26
7452 7808 3.177920 CTCGTGCAGCAGTCGAGC 61.178 66.667 19.14 0.00 42.94 5.03
7454 7810 2.255554 GACTCGTGCAGCAGTCGA 59.744 61.111 7.78 7.78 30.15 4.20
7455 7811 2.807045 GGACTCGTGCAGCAGTCG 60.807 66.667 15.59 0.00 40.11 4.18
7456 7812 1.445238 GAGGACTCGTGCAGCAGTC 60.445 63.158 14.28 14.28 38.71 3.51
7457 7813 2.653702 GAGGACTCGTGCAGCAGT 59.346 61.111 0.00 0.00 0.00 4.40
7458 7814 2.505777 CGAGGACTCGTGCAGCAG 60.506 66.667 13.23 0.00 46.99 4.24
7467 7823 1.025647 ACCGAGTAGCACGAGGACTC 61.026 60.000 0.00 0.00 36.95 3.36
7476 7832 3.244078 ACAATTGTCTCAACCGAGTAGCA 60.244 43.478 4.92 0.00 40.44 3.49
7478 7834 4.863131 GGTACAATTGTCTCAACCGAGTAG 59.137 45.833 15.85 0.00 40.44 2.57
7480 7836 3.070446 TGGTACAATTGTCTCAACCGAGT 59.930 43.478 15.85 0.00 36.40 4.18
7481 7837 3.432252 GTGGTACAATTGTCTCAACCGAG 59.568 47.826 15.85 0.00 44.16 4.63
7486 7842 3.135225 CGGTGTGGTACAATTGTCTCAA 58.865 45.455 15.85 0.30 44.16 3.02
7493 7849 0.034337 AGACGCGGTGTGGTACAATT 59.966 50.000 12.47 0.00 44.16 2.32
7509 7865 4.260784 GCCGATTGATTGATGGTTGTAGAC 60.261 45.833 0.00 0.00 0.00 2.59
7539 7895 2.768503 TTAACGTCTCGCCCCGTTGG 62.769 60.000 13.53 0.00 45.86 3.77
7540 7896 1.373246 TTAACGTCTCGCCCCGTTG 60.373 57.895 13.53 0.00 45.86 4.10
7542 7898 2.259511 GTTAACGTCTCGCCCCGT 59.740 61.111 0.00 0.00 39.32 5.28
7543 7899 2.877582 CGTTAACGTCTCGCCCCG 60.878 66.667 19.75 0.00 34.11 5.73
7544 7900 2.507769 CCGTTAACGTCTCGCCCC 60.508 66.667 25.15 0.00 37.74 5.80
7545 7901 1.515736 CTCCGTTAACGTCTCGCCC 60.516 63.158 25.15 0.00 37.74 6.13
7546 7902 1.515736 CCTCCGTTAACGTCTCGCC 60.516 63.158 25.15 0.00 37.74 5.54
7547 7903 0.796113 GTCCTCCGTTAACGTCTCGC 60.796 60.000 25.15 9.76 37.74 5.03
7548 7904 0.518636 TGTCCTCCGTTAACGTCTCG 59.481 55.000 25.15 11.02 37.74 4.04
7549 7905 1.267806 TGTGTCCTCCGTTAACGTCTC 59.732 52.381 25.15 11.76 37.74 3.36
7550 7906 1.268899 CTGTGTCCTCCGTTAACGTCT 59.731 52.381 25.15 0.00 37.74 4.18
7551 7907 1.267806 TCTGTGTCCTCCGTTAACGTC 59.732 52.381 25.15 11.14 37.74 4.34
7552 7908 1.000938 GTCTGTGTCCTCCGTTAACGT 60.001 52.381 25.15 0.00 37.74 3.99
7553 7909 1.694639 GTCTGTGTCCTCCGTTAACG 58.305 55.000 20.99 20.99 39.44 3.18
7554 7910 1.668047 CCGTCTGTGTCCTCCGTTAAC 60.668 57.143 0.00 0.00 0.00 2.01
7555 7911 0.599558 CCGTCTGTGTCCTCCGTTAA 59.400 55.000 0.00 0.00 0.00 2.01
7556 7912 1.870055 GCCGTCTGTGTCCTCCGTTA 61.870 60.000 0.00 0.00 0.00 3.18
7557 7913 3.048602 CCGTCTGTGTCCTCCGTT 58.951 61.111 0.00 0.00 0.00 4.44
7558 7914 3.681835 GCCGTCTGTGTCCTCCGT 61.682 66.667 0.00 0.00 0.00 4.69
7559 7915 4.778415 CGCCGTCTGTGTCCTCCG 62.778 72.222 0.00 0.00 0.00 4.63
7560 7916 2.820767 CTTCGCCGTCTGTGTCCTCC 62.821 65.000 0.00 0.00 0.00 4.30
7561 7917 1.444553 CTTCGCCGTCTGTGTCCTC 60.445 63.158 0.00 0.00 0.00 3.71
7562 7918 2.143594 GACTTCGCCGTCTGTGTCCT 62.144 60.000 0.00 0.00 0.00 3.85
7563 7919 1.733399 GACTTCGCCGTCTGTGTCC 60.733 63.158 0.00 0.00 0.00 4.02
7564 7920 1.286260 AGACTTCGCCGTCTGTGTC 59.714 57.895 5.76 0.00 42.39 3.67
7565 7921 3.444737 AGACTTCGCCGTCTGTGT 58.555 55.556 5.76 0.00 42.39 3.72
7569 7925 3.671411 ACGCAGACTTCGCCGTCT 61.671 61.111 0.00 1.25 44.72 4.18
7570 7926 3.470567 CACGCAGACTTCGCCGTC 61.471 66.667 0.00 0.00 0.00 4.79
7573 7929 3.782244 CAGCACGCAGACTTCGCC 61.782 66.667 0.00 0.00 0.00 5.54
7574 7930 3.004734 GACAGCACGCAGACTTCGC 62.005 63.158 0.00 0.00 0.00 4.70
7575 7931 2.710971 CGACAGCACGCAGACTTCG 61.711 63.158 0.00 0.00 0.00 3.79
7576 7932 2.375766 CCGACAGCACGCAGACTTC 61.376 63.158 0.00 0.00 0.00 3.01
7577 7933 2.356313 CCGACAGCACGCAGACTT 60.356 61.111 0.00 0.00 0.00 3.01
7588 7944 3.958147 ATGTGAAGGCCGCCGACAG 62.958 63.158 14.75 0.00 0.00 3.51
7589 7945 3.950794 GATGTGAAGGCCGCCGACA 62.951 63.158 12.61 12.61 0.00 4.35
7590 7946 3.195698 GATGTGAAGGCCGCCGAC 61.196 66.667 3.05 3.07 0.00 4.79
7591 7947 4.467084 GGATGTGAAGGCCGCCGA 62.467 66.667 3.05 0.00 0.00 5.54
7592 7948 4.473520 AGGATGTGAAGGCCGCCG 62.474 66.667 3.05 0.00 0.00 6.46
7593 7949 2.825836 CAGGATGTGAAGGCCGCC 60.826 66.667 0.00 0.00 0.00 6.13
7594 7950 3.512516 GCAGGATGTGAAGGCCGC 61.513 66.667 0.00 0.00 39.31 6.53
7595 7951 2.825836 GGCAGGATGTGAAGGCCG 60.826 66.667 0.00 0.00 39.31 6.13
7596 7952 2.440980 GGGCAGGATGTGAAGGCC 60.441 66.667 0.00 0.00 43.86 5.19
7597 7953 2.048603 GTGGGCAGGATGTGAAGGC 61.049 63.158 0.00 0.00 39.31 4.35
7598 7954 0.962356 GTGTGGGCAGGATGTGAAGG 60.962 60.000 0.00 0.00 39.31 3.46
7599 7955 0.037303 AGTGTGGGCAGGATGTGAAG 59.963 55.000 0.00 0.00 39.31 3.02
7600 7956 1.357137 TAGTGTGGGCAGGATGTGAA 58.643 50.000 0.00 0.00 39.31 3.18
7601 7957 1.486310 GATAGTGTGGGCAGGATGTGA 59.514 52.381 0.00 0.00 39.31 3.58
7602 7958 1.210234 TGATAGTGTGGGCAGGATGTG 59.790 52.381 0.00 0.00 39.31 3.21
7603 7959 1.210478 GTGATAGTGTGGGCAGGATGT 59.790 52.381 0.00 0.00 39.31 3.06
7604 7960 1.475751 GGTGATAGTGTGGGCAGGATG 60.476 57.143 0.00 0.00 40.87 3.51
7605 7961 0.839946 GGTGATAGTGTGGGCAGGAT 59.160 55.000 0.00 0.00 0.00 3.24
7606 7962 0.546507 TGGTGATAGTGTGGGCAGGA 60.547 55.000 0.00 0.00 0.00 3.86
7607 7963 0.107508 CTGGTGATAGTGTGGGCAGG 60.108 60.000 0.00 0.00 0.00 4.85
7608 7964 0.615331 ACTGGTGATAGTGTGGGCAG 59.385 55.000 0.00 0.00 0.00 4.85
7609 7965 0.613260 GACTGGTGATAGTGTGGGCA 59.387 55.000 0.00 0.00 0.00 5.36
7610 7966 0.613260 TGACTGGTGATAGTGTGGGC 59.387 55.000 0.00 0.00 0.00 5.36
7611 7967 2.699954 GTTGACTGGTGATAGTGTGGG 58.300 52.381 0.00 0.00 0.00 4.61
7612 7968 2.337583 CGTTGACTGGTGATAGTGTGG 58.662 52.381 0.00 0.00 0.00 4.17
7613 7969 1.726791 GCGTTGACTGGTGATAGTGTG 59.273 52.381 0.00 0.00 0.00 3.82
7614 7970 1.343142 TGCGTTGACTGGTGATAGTGT 59.657 47.619 0.00 0.00 0.00 3.55
7615 7971 2.078849 TGCGTTGACTGGTGATAGTG 57.921 50.000 0.00 0.00 0.00 2.74
7616 7972 3.002791 CAATGCGTTGACTGGTGATAGT 58.997 45.455 13.63 0.00 37.53 2.12
7617 7973 2.223112 GCAATGCGTTGACTGGTGATAG 60.223 50.000 22.81 0.00 37.53 2.08
7618 7974 1.737236 GCAATGCGTTGACTGGTGATA 59.263 47.619 22.81 0.00 37.53 2.15
7619 7975 0.523072 GCAATGCGTTGACTGGTGAT 59.477 50.000 22.81 0.00 37.53 3.06
7620 7976 1.948508 GCAATGCGTTGACTGGTGA 59.051 52.632 22.81 0.00 37.53 4.02
7621 7977 4.539152 GCAATGCGTTGACTGGTG 57.461 55.556 22.81 0.00 37.53 4.17
7632 7988 4.741781 ACGAAGTGCGCGCAATGC 62.742 61.111 38.24 33.26 46.04 3.56
7640 7996 4.380030 AGGTACTGATCGACGAAGTGCG 62.380 54.545 11.56 0.00 38.52 5.34
7641 7997 1.132643 AGGTACTGATCGACGAAGTGC 59.867 52.381 11.56 10.08 38.52 4.40
7642 7998 2.418976 TGAGGTACTGATCGACGAAGTG 59.581 50.000 11.56 3.23 40.67 3.16
7643 7999 2.708051 TGAGGTACTGATCGACGAAGT 58.292 47.619 0.00 4.38 44.36 3.01
7644 8000 3.879427 GATGAGGTACTGATCGACGAAG 58.121 50.000 0.00 0.00 39.60 3.79
7645 8001 3.965292 GATGAGGTACTGATCGACGAA 57.035 47.619 0.00 0.00 39.60 3.85
7652 8008 1.333177 GGCGAGGATGAGGTACTGAT 58.667 55.000 0.00 0.00 41.55 2.90
7653 8009 0.755698 GGGCGAGGATGAGGTACTGA 60.756 60.000 0.00 0.00 41.55 3.41
7654 8010 0.757188 AGGGCGAGGATGAGGTACTG 60.757 60.000 0.00 0.00 41.55 2.74
7656 8012 1.546476 CATAGGGCGAGGATGAGGTAC 59.454 57.143 0.00 0.00 0.00 3.34
7657 8013 1.147191 ACATAGGGCGAGGATGAGGTA 59.853 52.381 0.00 0.00 0.00 3.08
7658 8014 0.105453 ACATAGGGCGAGGATGAGGT 60.105 55.000 0.00 0.00 0.00 3.85
7659 8015 2.751991 ACATAGGGCGAGGATGAGG 58.248 57.895 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.