Multiple sequence alignment - TraesCS7D01G433500

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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 TraesCS7D01G433500 chr7D 100.000 5416 0 0 1 5416 553422536 553417121 0.000000e+00 10002
1 TraesCS7D01G433500 chr7A 94.332 4305 177 22 1 4271 639277157 639272886 0.000000e+00 6536
2 TraesCS7D01G433500 chr7A 89.749 517 41 6 4540 5046 639272552 639272038 0.000000e+00 651
3 TraesCS7D01G433500 chr7A 89.971 349 22 8 5071 5412 639272062 639271720 6.440000e-119 438
4 TraesCS7D01G433500 chr7A 89.412 85 7 2 4823 4906 249584013 249584096 7.420000e-19 106
5 TraesCS7D01G433500 chr7B 93.410 2868 143 18 1427 4285 599805742 599802912 0.000000e+00 4207
6 TraesCS7D01G433500 chr7B 88.228 756 55 17 700 1435 599806657 599805916 0.000000e+00 872
7 TraesCS7D01G433500 chr7B 88.054 519 46 12 4540 5046 599802572 599802058 7.760000e-168 601
8 TraesCS7D01G433500 chr7B 87.912 364 41 3 315 676 599807011 599806649 5.010000e-115 425
9 TraesCS7D01G433500 chr7B 89.080 348 25 7 5071 5412 599802082 599801742 2.330000e-113 420
10 TraesCS7D01G433500 chr2B 85.345 348 36 9 5078 5412 510590637 510590982 4.020000e-91 346


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 TraesCS7D01G433500 chr7D 553417121 553422536 5415 True 10002.000000 10002 100.000000 1 5416 1 chr7D.!!$R1 5415
1 TraesCS7D01G433500 chr7A 639271720 639277157 5437 True 2541.666667 6536 91.350667 1 5412 3 chr7A.!!$R1 5411
2 TraesCS7D01G433500 chr7B 599801742 599807011 5269 True 1305.000000 4207 89.336800 315 5412 5 chr7B.!!$R1 5097

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
614 623 1.304381 TTTGGGAGCCATCAGTGCC 60.304 57.895 0.00 0.0 31.53 5.01 F
1606 1850 0.320697 AACAACCTGTACTCGCCCTC 59.679 55.000 0.00 0.0 0.00 4.30 F
2157 2401 0.386352 CACGTTCCGCGACTACTTCA 60.386 55.000 8.23 0.0 44.77 3.02 F
2846 3090 0.179127 CCACGTCGAGTCTGCATGAT 60.179 55.000 0.00 0.0 0.00 2.45 F
4339 4669 0.185901 ACTGCCCACTTGGTTGATGT 59.814 50.000 0.00 0.0 36.04 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1932 0.107945 GGTCCATCCTGTGCTCTGAC 60.108 60.000 0.00 0.0 0.00 3.51 R
2433 2677 0.242017 AAGCAGTGCTCATTTTCGCC 59.758 50.000 20.03 0.0 38.25 5.54 R
3548 3820 1.741028 TCCCACATCAACTCCTCCAA 58.259 50.000 0.00 0.0 0.00 3.53 R
4344 4674 0.515564 CGTCAAAATCCGGACACACC 59.484 55.000 6.12 0.0 33.66 4.16 R
5224 5602 3.266772 TCTGATGGTTGGCAGGAAATAGT 59.733 43.478 0.00 0.0 33.05 2.12 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
107 110 3.910627 ACTTAGATATGGCCCACCCTAAG 59.089 47.826 20.93 20.93 39.08 2.18
141 144 8.109634 ACAATCAAGAGTATGGTCCAAAATACT 58.890 33.333 3.68 3.68 41.27 2.12
250 255 2.542595 GCCTACATTCGAATTACCACCG 59.457 50.000 8.21 0.00 0.00 4.94
310 316 3.264477 CCCCCTAGGATGTCACCAT 57.736 57.895 11.48 0.00 38.24 3.55
548 557 9.170734 CTTGATTTCTTTTCATAGGTCAGATGA 57.829 33.333 0.00 0.00 0.00 2.92
614 623 1.304381 TTTGGGAGCCATCAGTGCC 60.304 57.895 0.00 0.00 31.53 5.01
681 691 2.351706 AAGCCGGTGGTTTTTCTACA 57.648 45.000 1.90 0.00 0.00 2.74
712 722 1.520600 AATCGTGGTCGTTTTGCCCC 61.521 55.000 0.00 0.00 38.33 5.80
719 729 2.494073 TGGTCGTTTTGCCCCAAATATC 59.506 45.455 0.00 0.00 33.19 1.63
730 740 3.403038 CCCCAAATATCCGTCTGATGTC 58.597 50.000 0.00 0.00 34.76 3.06
745 755 7.095229 CCGTCTGATGTCTCTTAAAAATTGACA 60.095 37.037 0.00 0.00 41.07 3.58
790 800 6.169557 AGTAAAATATATGGAGGTGCGTCA 57.830 37.500 0.00 0.00 0.00 4.35
991 1005 1.865865 ACCAGCTTACACAAGACACG 58.134 50.000 0.00 0.00 33.20 4.49
995 1009 2.097396 CAGCTTACACAAGACACGTTCG 60.097 50.000 0.00 0.00 33.20 3.95
1091 1114 1.712977 GCCAGGACGACTACGACGAT 61.713 60.000 0.00 0.00 42.66 3.73
1097 1120 1.005137 GACGACTACGACGATGAGGAC 60.005 57.143 0.00 0.00 42.66 3.85
1101 1124 1.288350 CTACGACGATGAGGACGACT 58.712 55.000 0.00 0.00 34.70 4.18
1106 1129 2.096664 CGACGATGAGGACGACTATGAG 60.097 54.545 0.00 0.00 34.70 2.90
1109 1132 2.224549 CGATGAGGACGACTATGAGGAC 59.775 54.545 0.00 0.00 0.00 3.85
1258 1310 5.297776 CACCAACTTTGATCTCTTGAACACT 59.702 40.000 0.00 0.00 0.00 3.55
1262 1314 6.369059 ACTTTGATCTCTTGAACACTTGTG 57.631 37.500 0.00 0.00 0.00 3.33
1295 1353 5.247110 TCAGGATCACTTTCTTACTGCTTCT 59.753 40.000 0.00 0.00 0.00 2.85
1296 1354 5.580297 CAGGATCACTTTCTTACTGCTTCTC 59.420 44.000 0.00 0.00 0.00 2.87
1297 1355 5.483583 AGGATCACTTTCTTACTGCTTCTCT 59.516 40.000 0.00 0.00 0.00 3.10
1298 1356 6.665680 AGGATCACTTTCTTACTGCTTCTCTA 59.334 38.462 0.00 0.00 0.00 2.43
1299 1357 6.978080 GGATCACTTTCTTACTGCTTCTCTAG 59.022 42.308 0.00 0.00 0.00 2.43
1300 1358 7.147983 GGATCACTTTCTTACTGCTTCTCTAGA 60.148 40.741 0.00 0.00 0.00 2.43
1406 1464 4.470304 AGGAATGTTCACCTAACCTACCTC 59.530 45.833 0.00 0.00 37.27 3.85
1424 1482 1.691434 CTCTCCTTCCTCAGGTATGCC 59.309 57.143 0.00 0.00 44.37 4.40
1489 1733 5.718146 CTCCTGATCGACAGTAATATGCAT 58.282 41.667 3.79 3.79 44.40 3.96
1532 1776 2.159043 TGGCGATCTGGAGAAAGATGTC 60.159 50.000 0.00 0.00 37.03 3.06
1601 1845 3.713288 TCTCACAAACAACCTGTACTCG 58.287 45.455 0.00 0.00 0.00 4.18
1602 1846 2.206750 TCACAAACAACCTGTACTCGC 58.793 47.619 0.00 0.00 0.00 5.03
1604 1848 0.872388 CAAACAACCTGTACTCGCCC 59.128 55.000 0.00 0.00 0.00 6.13
1605 1849 0.763035 AAACAACCTGTACTCGCCCT 59.237 50.000 0.00 0.00 0.00 5.19
1606 1850 0.320697 AACAACCTGTACTCGCCCTC 59.679 55.000 0.00 0.00 0.00 4.30
1607 1851 1.153823 CAACCTGTACTCGCCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
1688 1932 1.993370 GATCCGTTGGACGTTCTTCTG 59.007 52.381 0.00 0.00 40.58 3.02
1691 1935 1.537348 CCGTTGGACGTTCTTCTGTCA 60.537 52.381 0.00 0.00 40.58 3.58
1736 1980 1.746991 GCTCCTTGAAGCGGAAGGG 60.747 63.158 10.45 4.46 40.52 3.95
1782 2026 1.592669 GACGCCCAGATGATCACGG 60.593 63.158 0.00 0.00 0.00 4.94
1784 2028 2.190313 GCCCAGATGATCACGGCA 59.810 61.111 15.40 0.00 39.50 5.69
1951 2195 2.231478 TCCTCTTCAAGTTCTACAGCCG 59.769 50.000 0.00 0.00 0.00 5.52
1952 2196 2.611518 CTCTTCAAGTTCTACAGCCGG 58.388 52.381 0.00 0.00 0.00 6.13
2046 2290 1.686428 CGGTCTTCTCCTCCATCCTCA 60.686 57.143 0.00 0.00 0.00 3.86
2157 2401 0.386352 CACGTTCCGCGACTACTTCA 60.386 55.000 8.23 0.00 44.77 3.02
2176 2420 1.067582 GGTCCGTATCAGAAGCCGG 59.932 63.158 0.00 0.00 41.75 6.13
2282 2526 3.949754 TGGAAGATGTCAAGGCATTGATC 59.050 43.478 17.80 11.60 46.75 2.92
2363 2607 2.203084 TTGGTTTGCTCCGACGCA 60.203 55.556 0.00 0.00 38.31 5.24
2400 2644 2.000803 TCCTCAGGTCAGGAGTCCTAA 58.999 52.381 12.53 0.00 37.68 2.69
2409 2653 2.091775 TCAGGAGTCCTAAGGCTACCTC 60.092 54.545 12.53 0.00 30.89 3.85
2415 2659 1.465200 CCTAAGGCTACCTCCCGCTC 61.465 65.000 0.00 0.00 30.89 5.03
2705 2949 1.216977 CGCCCACGGTGTCTTCATA 59.783 57.895 7.45 0.00 34.97 2.15
2728 2972 2.051345 CAACAACCAAGCGTCGCC 60.051 61.111 14.86 0.00 0.00 5.54
2756 3000 1.671379 GGAACCAGAACTCCACGGC 60.671 63.158 0.00 0.00 0.00 5.68
2846 3090 0.179127 CCACGTCGAGTCTGCATGAT 60.179 55.000 0.00 0.00 0.00 2.45
2934 3190 0.601558 GCGGGTGAGACAGTTGAGTA 59.398 55.000 0.00 0.00 0.00 2.59
2960 3216 4.740822 GGCACCATCTTGGCCGGT 62.741 66.667 1.90 0.00 42.67 5.28
3090 3346 3.499918 GGACACACTTCTTCATCAGGTTG 59.500 47.826 0.00 0.00 0.00 3.77
3111 3367 3.223157 GGTTGAACAAATCTTGTACGCG 58.777 45.455 3.53 3.53 44.59 6.01
3175 3445 5.355630 TCTCATCTTACAGAGACTGTACTGC 59.644 44.000 10.53 0.00 45.13 4.40
3177 3447 4.768130 TCTTACAGAGACTGTACTGCAC 57.232 45.455 10.53 0.00 45.13 4.57
3307 3577 7.888250 AGAGAAAATATCATCTTTGGAACCC 57.112 36.000 0.00 0.00 0.00 4.11
3487 3759 1.617947 GCTGGTGGGAGGTGGAGTAG 61.618 65.000 0.00 0.00 0.00 2.57
3530 3802 4.376340 AAGAAGCAACTGTTCAAAGTGG 57.624 40.909 0.00 0.00 0.00 4.00
3531 3803 3.356290 AGAAGCAACTGTTCAAAGTGGT 58.644 40.909 0.00 0.00 0.00 4.16
3548 3820 2.612212 GTGGTGAAGATGTGTTCAACGT 59.388 45.455 3.87 0.00 45.63 3.99
3606 3878 5.579047 AGAGATGAGGAGACCGATGATAAT 58.421 41.667 0.00 0.00 0.00 1.28
3866 4138 1.823899 GTGATGGAATGGGCGGGAC 60.824 63.158 0.00 0.00 0.00 4.46
3885 4157 2.125753 GGAGGCTCAGACGCTGTG 60.126 66.667 17.69 5.85 32.61 3.66
3959 4231 1.780503 ACCTTGCCAGAACTTTTGCT 58.219 45.000 0.00 0.00 0.00 3.91
4196 4468 2.726821 GAGATGGCAATGAAGGAACCA 58.273 47.619 0.00 0.00 34.28 3.67
4263 4535 5.874810 TGTTCAAGACATGTATACAGAAGCC 59.125 40.000 11.91 0.00 32.00 4.35
4279 4551 6.116126 ACAGAAGCCCTAATGAGACAAATAC 58.884 40.000 0.00 0.00 0.00 1.89
4287 4612 7.336931 GCCCTAATGAGACAAATACTTGAAGAA 59.663 37.037 0.00 0.00 36.33 2.52
4289 4614 9.442047 CCTAATGAGACAAATACTTGAAGAACT 57.558 33.333 0.00 0.00 36.33 3.01
4294 4619 5.177696 AGACAAATACTTGAAGAACTCGTGC 59.822 40.000 0.00 0.00 36.33 5.34
4295 4620 4.814234 ACAAATACTTGAAGAACTCGTGCA 59.186 37.500 0.00 0.00 36.33 4.57
4309 4635 1.129624 TCGTGCATTGCAACGGATAAC 59.870 47.619 23.51 7.41 41.47 1.89
4321 4647 6.833839 TGCAACGGATAACAAAACTATGTAC 58.166 36.000 0.00 0.00 32.02 2.90
4324 4650 6.657836 ACGGATAACAAAACTATGTACTGC 57.342 37.500 0.00 0.00 32.02 4.40
4335 4665 1.909700 ATGTACTGCCCACTTGGTTG 58.090 50.000 0.00 0.00 36.04 3.77
4336 4666 0.840617 TGTACTGCCCACTTGGTTGA 59.159 50.000 0.00 0.00 36.04 3.18
4337 4667 1.423541 TGTACTGCCCACTTGGTTGAT 59.576 47.619 0.00 0.00 36.04 2.57
4338 4668 1.812571 GTACTGCCCACTTGGTTGATG 59.187 52.381 0.00 0.00 36.04 3.07
4339 4669 0.185901 ACTGCCCACTTGGTTGATGT 59.814 50.000 0.00 0.00 36.04 3.06
4340 4670 1.423541 ACTGCCCACTTGGTTGATGTA 59.576 47.619 0.00 0.00 36.04 2.29
4341 4671 2.158534 ACTGCCCACTTGGTTGATGTAA 60.159 45.455 0.00 0.00 36.04 2.41
4344 4674 2.166254 GCCCACTTGGTTGATGTAATGG 59.834 50.000 0.00 0.00 36.04 3.16
4351 4681 3.417101 TGGTTGATGTAATGGGTGTGTC 58.583 45.455 0.00 0.00 0.00 3.67
4359 4689 2.302587 AATGGGTGTGTCCGGATTTT 57.697 45.000 7.81 0.00 37.00 1.82
4369 4699 0.599558 TCCGGATTTTGACGTCTCGT 59.400 50.000 17.92 0.00 45.10 4.18
4397 4727 9.607988 ATTGGTTGATGTACGATTGTTAGATAA 57.392 29.630 0.00 0.00 0.00 1.75
4430 4761 8.200792 AGCACTTTATGAGGTAATTCTAGACTG 58.799 37.037 0.00 0.00 0.00 3.51
4450 4781 7.692088 AGACTGATAATTGAAATTCTTCTGCG 58.308 34.615 0.00 0.00 32.33 5.18
4455 4786 9.288576 TGATAATTGAAATTCTTCTGCGGATAT 57.711 29.630 0.00 0.00 32.33 1.63
4464 4795 7.588143 ATTCTTCTGCGGATATTAATTCTCG 57.412 36.000 0.00 0.00 0.00 4.04
4472 4803 5.523916 GCGGATATTAATTCTCGCATGGTAT 59.476 40.000 17.78 0.00 42.27 2.73
4490 4821 5.642686 TGGTATAAATGTTAAAGCCGCAAC 58.357 37.500 0.00 0.00 0.00 4.17
4506 4837 4.549458 CCGCAACAAAATTCTGAGTTGAT 58.451 39.130 9.96 0.00 42.87 2.57
4538 4903 9.877137 AATTTTGAACAAAAACAAAAGTCTCAC 57.123 25.926 15.00 0.00 44.94 3.51
4545 4910 7.547227 ACAAAAACAAAAGTCTCACTAGCAAT 58.453 30.769 0.00 0.00 0.00 3.56
4546 4911 7.489113 ACAAAAACAAAAGTCTCACTAGCAATG 59.511 33.333 0.00 0.00 0.00 2.82
4554 4919 4.223700 AGTCTCACTAGCAATGATTGTGGA 59.776 41.667 12.47 6.68 0.00 4.02
4555 4920 4.937620 GTCTCACTAGCAATGATTGTGGAA 59.062 41.667 12.47 0.00 0.00 3.53
4558 4923 3.379372 CACTAGCAATGATTGTGGAAGGG 59.621 47.826 7.05 0.00 0.00 3.95
4560 4925 3.393426 AGCAATGATTGTGGAAGGGAT 57.607 42.857 7.05 0.00 0.00 3.85
4561 4926 4.524802 AGCAATGATTGTGGAAGGGATA 57.475 40.909 7.05 0.00 0.00 2.59
4562 4927 4.467769 AGCAATGATTGTGGAAGGGATAG 58.532 43.478 7.05 0.00 0.00 2.08
4563 4928 3.571401 GCAATGATTGTGGAAGGGATAGG 59.429 47.826 7.05 0.00 0.00 2.57
4564 4929 4.796606 CAATGATTGTGGAAGGGATAGGT 58.203 43.478 0.00 0.00 0.00 3.08
4565 4930 5.690097 GCAATGATTGTGGAAGGGATAGGTA 60.690 44.000 7.05 0.00 0.00 3.08
4584 4949 3.381590 GGTAGCAGGCTAAAGGAAAATGG 59.618 47.826 1.98 0.00 0.00 3.16
4602 4967 0.322456 GGCTGATGTGGTGTAAGGCA 60.322 55.000 0.00 0.00 33.88 4.75
4603 4968 1.533625 GCTGATGTGGTGTAAGGCAA 58.466 50.000 0.00 0.00 0.00 4.52
4624 4989 5.234972 GCAAATCCTTTTCTGTGGTTTTGAG 59.765 40.000 15.48 0.00 41.72 3.02
4630 4995 4.963276 TTTCTGTGGTTTTGAGTGAGTG 57.037 40.909 0.00 0.00 0.00 3.51
4646 5011 1.072331 GAGTGGACCATGGAGTTGTGT 59.928 52.381 21.47 0.00 0.00 3.72
4660 5025 5.308497 TGGAGTTGTGTATTCCTGGTTTCTA 59.692 40.000 0.00 0.00 32.12 2.10
4666 5031 6.833041 TGTGTATTCCTGGTTTCTACTTTGA 58.167 36.000 0.00 0.00 0.00 2.69
4698 5063 9.762381 TTCATAACTAAAATTGGTAATCCCAGT 57.238 29.630 0.00 0.00 46.31 4.00
4703 5068 9.636789 AACTAAAATTGGTAATCCCAGTATACC 57.363 33.333 0.00 0.00 46.31 2.73
4718 5083 8.384718 TCCCAGTATACCTCTCTATAAGTCTTC 58.615 40.741 0.00 0.00 0.00 2.87
4736 5101 8.466617 AAGTCTTCTAGTCTGAACTCTTACAA 57.533 34.615 0.00 0.00 36.92 2.41
4743 5108 9.862371 TCTAGTCTGAACTCTTACAAATCAATC 57.138 33.333 0.00 0.00 36.92 2.67
4764 5129 3.074412 CAAATAAAGCAGGGTCACGAGT 58.926 45.455 0.00 0.00 0.00 4.18
4775 5140 3.326880 AGGGTCACGAGTGGTTTTTCTAT 59.673 43.478 3.19 0.00 0.00 1.98
4800 5166 5.385509 AAAAATGAGGTCCAACGGTATTG 57.614 39.130 0.00 0.00 0.00 1.90
4805 5171 3.516300 TGAGGTCCAACGGTATTGTACAT 59.484 43.478 0.00 0.00 0.00 2.29
4825 5191 7.982919 TGTACATGTACCCACTATTTGTGATAC 59.017 37.037 28.67 4.85 40.79 2.24
4890 5257 8.668510 TCTATTCTAATTTAGAGGCTTGCTTG 57.331 34.615 6.26 0.00 35.96 4.01
4925 5299 3.433306 TTACTGTGGACCATGGAAAGG 57.567 47.619 21.47 5.74 0.00 3.11
4930 5304 0.482446 TGGACCATGGAAAGGCTTGT 59.518 50.000 21.47 0.00 0.00 3.16
4949 5326 5.755375 GCTTGTGCAGCTTGTATCTCTATAA 59.245 40.000 0.00 0.00 46.27 0.98
5001 5378 4.243007 GCAGGTGCAAGTATCAAAACTT 57.757 40.909 0.00 0.00 40.33 2.66
5043 5420 4.713792 AGTCAAACCTTCAGATCAACCT 57.286 40.909 0.00 0.00 0.00 3.50
5044 5421 4.392940 AGTCAAACCTTCAGATCAACCTG 58.607 43.478 0.00 0.00 35.55 4.00
5045 5422 3.057946 GTCAAACCTTCAGATCAACCTGC 60.058 47.826 0.00 0.00 34.28 4.85
5046 5423 1.813513 AACCTTCAGATCAACCTGCG 58.186 50.000 0.00 0.00 34.28 5.18
5047 5424 0.687354 ACCTTCAGATCAACCTGCGT 59.313 50.000 0.00 0.00 34.28 5.24
5048 5425 1.899814 ACCTTCAGATCAACCTGCGTA 59.100 47.619 0.00 0.00 34.28 4.42
5049 5426 2.093973 ACCTTCAGATCAACCTGCGTAG 60.094 50.000 0.00 0.00 34.28 3.51
5050 5427 2.093973 CCTTCAGATCAACCTGCGTAGT 60.094 50.000 0.00 0.00 34.28 2.73
5051 5428 3.130516 CCTTCAGATCAACCTGCGTAGTA 59.869 47.826 0.00 0.00 34.28 1.82
5052 5429 3.777465 TCAGATCAACCTGCGTAGTAC 57.223 47.619 0.00 0.00 34.28 2.73
5053 5430 3.086282 TCAGATCAACCTGCGTAGTACA 58.914 45.455 0.00 0.00 34.28 2.90
5054 5431 3.119602 TCAGATCAACCTGCGTAGTACAC 60.120 47.826 0.00 0.00 34.28 2.90
5055 5432 2.823747 AGATCAACCTGCGTAGTACACA 59.176 45.455 0.00 0.00 0.00 3.72
5056 5433 3.447586 AGATCAACCTGCGTAGTACACAT 59.552 43.478 0.00 0.00 0.00 3.21
5057 5434 3.671008 TCAACCTGCGTAGTACACATT 57.329 42.857 0.00 0.00 0.00 2.71
5058 5435 3.322369 TCAACCTGCGTAGTACACATTG 58.678 45.455 0.00 0.28 0.00 2.82
5059 5436 2.380084 ACCTGCGTAGTACACATTGG 57.620 50.000 0.00 0.00 0.00 3.16
5060 5437 1.621814 ACCTGCGTAGTACACATTGGT 59.378 47.619 0.00 0.00 0.00 3.67
5066 5443 2.991190 CGTAGTACACATTGGTGGTGTC 59.009 50.000 0.94 0.00 45.89 3.67
5067 5444 3.553302 CGTAGTACACATTGGTGGTGTCA 60.553 47.826 0.94 0.00 45.89 3.58
5068 5445 3.569194 AGTACACATTGGTGGTGTCAA 57.431 42.857 0.94 0.00 45.89 3.18
5069 5446 3.211045 AGTACACATTGGTGGTGTCAAC 58.789 45.455 0.94 0.00 45.89 3.18
5070 5447 2.136298 ACACATTGGTGGTGTCAACA 57.864 45.000 0.00 0.00 45.89 3.33
5075 5452 2.498644 TTGGTGGTGTCAACAAGTCA 57.501 45.000 0.00 0.00 44.78 3.41
5076 5453 2.498644 TGGTGGTGTCAACAAGTCAA 57.501 45.000 0.00 0.00 37.71 3.18
5077 5454 3.011566 TGGTGGTGTCAACAAGTCAAT 57.988 42.857 0.00 0.00 37.71 2.57
5078 5455 2.948979 TGGTGGTGTCAACAAGTCAATC 59.051 45.455 0.00 0.00 37.71 2.67
5079 5456 2.293399 GGTGGTGTCAACAAGTCAATCC 59.707 50.000 0.00 0.00 0.00 3.01
5080 5457 3.214328 GTGGTGTCAACAAGTCAATCCT 58.786 45.455 0.00 0.00 0.00 3.24
5081 5458 3.632145 GTGGTGTCAACAAGTCAATCCTT 59.368 43.478 0.00 0.00 0.00 3.36
5082 5459 3.882888 TGGTGTCAACAAGTCAATCCTTC 59.117 43.478 0.00 0.00 0.00 3.46
5083 5460 3.882888 GGTGTCAACAAGTCAATCCTTCA 59.117 43.478 0.00 0.00 0.00 3.02
5084 5461 4.023707 GGTGTCAACAAGTCAATCCTTCAG 60.024 45.833 0.00 0.00 0.00 3.02
5085 5462 4.816385 GTGTCAACAAGTCAATCCTTCAGA 59.184 41.667 0.00 0.00 0.00 3.27
5086 5463 5.471456 GTGTCAACAAGTCAATCCTTCAGAT 59.529 40.000 0.00 0.00 36.48 2.90
5087 5464 5.702670 TGTCAACAAGTCAATCCTTCAGATC 59.297 40.000 0.00 0.00 32.47 2.75
5088 5465 5.702670 GTCAACAAGTCAATCCTTCAGATCA 59.297 40.000 0.00 0.00 32.47 2.92
5089 5466 6.205464 GTCAACAAGTCAATCCTTCAGATCAA 59.795 38.462 0.00 0.00 32.47 2.57
5090 5467 6.205464 TCAACAAGTCAATCCTTCAGATCAAC 59.795 38.462 0.00 0.00 32.47 3.18
5091 5468 4.692625 ACAAGTCAATCCTTCAGATCAACG 59.307 41.667 0.00 0.00 32.47 4.10
5095 5472 0.911769 ATCCTTCAGATCAACGGCCA 59.088 50.000 2.24 0.00 0.00 5.36
5103 5480 1.364626 GATCAACGGCCACTCTGCAG 61.365 60.000 7.63 7.63 0.00 4.41
5133 5510 6.147492 GGCAATGTTACAATGAAAATCAAGCA 59.853 34.615 4.40 0.00 0.00 3.91
5135 5512 6.932901 ATGTTACAATGAAAATCAAGCACG 57.067 33.333 0.00 0.00 0.00 5.34
5147 5525 3.617540 TCAAGCACGGTACACATTTTG 57.382 42.857 0.00 0.00 0.00 2.44
5181 5559 5.269459 GCAAAGGCTGATATACATACACG 57.731 43.478 0.00 0.00 36.96 4.49
5182 5560 4.988540 GCAAAGGCTGATATACATACACGA 59.011 41.667 0.00 0.00 36.96 4.35
5210 5588 4.096681 TCAAGGAGAGCTTCATCCACTTA 58.903 43.478 14.02 0.00 38.12 2.24
5217 5595 5.869579 AGAGCTTCATCCACTTACTTGAAA 58.130 37.500 0.00 0.00 0.00 2.69
5222 5600 7.066766 AGCTTCATCCACTTACTTGAAATCATC 59.933 37.037 0.00 0.00 0.00 2.92
5224 5602 8.634335 TTCATCCACTTACTTGAAATCATCAA 57.366 30.769 0.00 0.00 45.71 2.57
5340 5723 9.533831 ACAACTATCAAATGAAGGAGGTTTATT 57.466 29.630 0.00 0.00 0.00 1.40
5384 5767 8.691661 AGGATGCGGTAAATTACATAAAGAAT 57.308 30.769 5.45 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 110 2.206576 ACTCTTGATTGTCTTGGGCC 57.793 50.000 0.00 0.00 0.00 5.80
226 231 3.000925 GTGGTAATTCGAATGTAGGCACG 59.999 47.826 12.25 0.00 0.00 5.34
250 255 0.596600 TTGAGTTCTGTCCGTCACGC 60.597 55.000 0.00 0.00 0.00 5.34
262 267 2.989840 CAGATGACCGACTGTTGAGTTC 59.010 50.000 0.00 0.00 30.16 3.01
664 674 3.117794 GTTTTGTAGAAAAACCACCGGC 58.882 45.455 0.00 0.00 34.88 6.13
704 714 2.757868 CAGACGGATATTTGGGGCAAAA 59.242 45.455 0.00 0.00 36.90 2.44
712 722 8.648557 TTTAAGAGACATCAGACGGATATTTG 57.351 34.615 0.00 0.00 33.95 2.32
719 729 7.095229 TGTCAATTTTTAAGAGACATCAGACGG 60.095 37.037 0.00 0.00 34.59 4.79
772 782 6.166279 CAGTAATGACGCACCTCCATATATT 58.834 40.000 0.00 0.00 0.00 1.28
777 787 1.134401 CCAGTAATGACGCACCTCCAT 60.134 52.381 0.00 0.00 0.00 3.41
778 788 0.249120 CCAGTAATGACGCACCTCCA 59.751 55.000 0.00 0.00 0.00 3.86
790 800 7.287696 ACATTCTTGACTTTTTCACCCAGTAAT 59.712 33.333 0.00 0.00 32.26 1.89
890 903 2.475466 CCGGCCATCAGCATCACAC 61.475 63.158 2.24 0.00 46.50 3.82
954 967 1.009829 GTAGCTGTTGCGGATCTTGG 58.990 55.000 0.00 0.00 45.42 3.61
991 1005 4.718940 ATGGAATTGGAATGGAACGAAC 57.281 40.909 0.00 0.00 0.00 3.95
995 1009 4.423732 CGTGAATGGAATTGGAATGGAAC 58.576 43.478 0.00 0.00 36.07 3.62
1071 1094 2.099831 GTCGTAGTCGTCCTGGCG 59.900 66.667 4.48 4.48 38.33 5.69
1091 1114 1.208776 TCGTCCTCATAGTCGTCCTCA 59.791 52.381 0.00 0.00 0.00 3.86
1097 1120 1.202663 TCCTCCTCGTCCTCATAGTCG 60.203 57.143 0.00 0.00 0.00 4.18
1101 1124 0.835276 TCGTCCTCCTCGTCCTCATA 59.165 55.000 0.00 0.00 0.00 2.15
1106 1129 2.435586 TCGTCGTCCTCCTCGTCC 60.436 66.667 0.00 0.00 0.00 4.79
1109 1132 0.582482 CATAGTCGTCGTCCTCCTCG 59.418 60.000 0.00 0.00 0.00 4.63
1258 1310 0.538584 ATCCTGATCGAGCTGCACAA 59.461 50.000 0.90 0.00 0.00 3.33
1262 1314 0.388659 AGTGATCCTGATCGAGCTGC 59.611 55.000 0.90 0.00 40.63 5.25
1406 1464 8.473352 GATGTATGGCATACCTGAGGAAGGAG 62.473 50.000 29.44 0.00 42.86 3.69
1424 1482 3.303495 GGTTGACTGACGAACGATGTATG 59.697 47.826 0.14 0.00 0.00 2.39
1532 1776 1.361668 CCTGGCGTTTGAGATGGTCG 61.362 60.000 0.00 0.00 0.00 4.79
1601 1845 1.542492 TCTCCGGTATTATCGAGGGC 58.458 55.000 0.00 0.00 0.00 5.19
1602 1846 4.219944 TGAATTCTCCGGTATTATCGAGGG 59.780 45.833 7.05 0.00 0.00 4.30
1604 1848 6.213677 TGTTGAATTCTCCGGTATTATCGAG 58.786 40.000 7.05 0.00 0.00 4.04
1605 1849 6.151663 TGTTGAATTCTCCGGTATTATCGA 57.848 37.500 7.05 0.00 0.00 3.59
1606 1850 6.838198 TTGTTGAATTCTCCGGTATTATCG 57.162 37.500 7.05 0.00 0.00 2.92
1607 1851 8.836413 TCAATTGTTGAATTCTCCGGTATTATC 58.164 33.333 7.05 0.00 36.59 1.75
1673 1917 3.053455 CTCTGACAGAAGAACGTCCAAC 58.947 50.000 6.61 0.00 0.00 3.77
1688 1932 0.107945 GGTCCATCCTGTGCTCTGAC 60.108 60.000 0.00 0.00 0.00 3.51
1691 1935 0.617413 CTTGGTCCATCCTGTGCTCT 59.383 55.000 0.00 0.00 37.07 4.09
1736 1980 2.359230 AGTTTCTCCAGCGCCTGC 60.359 61.111 2.29 0.00 43.24 4.85
1782 2026 4.824166 CAGCGCGGACATGCTTGC 62.824 66.667 8.83 0.00 40.03 4.01
1784 2028 3.121030 GACAGCGCGGACATGCTT 61.121 61.111 16.26 0.00 40.03 3.91
1913 2157 3.524648 GAGGTGGTTCGCCCGTTGA 62.525 63.158 0.00 0.00 33.99 3.18
1968 2212 1.228583 ACCTCAGCTCCTCGACACA 60.229 57.895 0.00 0.00 0.00 3.72
1970 2214 0.323816 ATGACCTCAGCTCCTCGACA 60.324 55.000 0.00 0.00 0.00 4.35
2046 2290 2.574399 GAAGCTCCTCGACGCCTT 59.426 61.111 0.00 0.00 0.00 4.35
2110 2354 4.402616 AAGTCATCAATTTCCCCCTTCA 57.597 40.909 0.00 0.00 0.00 3.02
2113 2357 4.089361 GACAAAGTCATCAATTTCCCCCT 58.911 43.478 0.00 0.00 32.09 4.79
2157 2401 2.116383 CGGCTTCTGATACGGACCT 58.884 57.895 0.00 0.00 0.00 3.85
2188 2432 4.694233 CAGTCGCCAGTGCCAGCT 62.694 66.667 0.00 0.00 0.00 4.24
2282 2526 4.113815 TCCTCCATGCAAGGCCGG 62.114 66.667 2.20 6.45 33.65 6.13
2363 2607 2.535317 AACCTCCCCAGCACCCAT 60.535 61.111 0.00 0.00 0.00 4.00
2400 2644 4.862823 GGGAGCGGGAGGTAGCCT 62.863 72.222 0.00 0.00 43.00 4.58
2426 2670 3.381169 CTCATTTTCGCCACCGCCG 62.381 63.158 0.00 0.00 0.00 6.46
2431 2675 0.730494 GCAGTGCTCATTTTCGCCAC 60.730 55.000 8.18 0.00 0.00 5.01
2432 2676 0.890542 AGCAGTGCTCATTTTCGCCA 60.891 50.000 13.14 0.00 30.62 5.69
2433 2677 0.242017 AAGCAGTGCTCATTTTCGCC 59.758 50.000 20.03 0.00 38.25 5.54
2434 2678 1.334054 CAAGCAGTGCTCATTTTCGC 58.666 50.000 20.03 0.00 38.25 4.70
2705 2949 1.065551 GACGCTTGGTTGTTGCTCTTT 59.934 47.619 0.00 0.00 0.00 2.52
2728 2972 0.389817 TTCTGGTTCCATCTGCGACG 60.390 55.000 0.00 0.00 0.00 5.12
2735 2979 1.676014 CCGTGGAGTTCTGGTTCCATC 60.676 57.143 0.00 0.00 44.74 3.51
2737 2981 1.752198 CCGTGGAGTTCTGGTTCCA 59.248 57.895 0.00 0.00 41.06 3.53
2756 3000 2.766313 TCCTTGATGAACACGGTCAAG 58.234 47.619 7.23 7.23 45.18 3.02
2786 3030 3.557054 GGCAGAAGTGTGTCCATACTTGA 60.557 47.826 13.22 0.00 41.77 3.02
2836 3080 4.332543 TCGATGTTGGTTTATCATGCAGAC 59.667 41.667 0.00 0.00 0.00 3.51
2846 3090 2.442212 TCGCTGTCGATGTTGGTTTA 57.558 45.000 0.00 0.00 40.21 2.01
2934 3190 3.559069 CCAAGATGGTGCCATACAGATT 58.441 45.455 3.37 0.00 36.70 2.40
2960 3216 4.041198 AGTTTTCTCATGGTCCCGTCTTTA 59.959 41.667 0.00 0.00 0.00 1.85
3090 3346 3.223157 CGCGTACAAGATTTGTTCAACC 58.777 45.455 0.00 0.00 42.22 3.77
3175 3445 3.170791 ACATCTAACTGGATCTGCGTG 57.829 47.619 0.00 0.00 0.00 5.34
3177 3447 3.785486 TGAACATCTAACTGGATCTGCG 58.215 45.455 0.00 0.00 0.00 5.18
3307 3577 7.226720 ACTGTTAATTGTTACCTCTTCACACTG 59.773 37.037 0.00 0.00 0.00 3.66
3407 3679 4.102210 CCTCTTCATGGATGGTATCACTGT 59.898 45.833 0.00 0.00 0.00 3.55
3487 3759 6.428159 TCTTTTTCTTGTGAACTGGAGCTATC 59.572 38.462 0.00 0.00 31.02 2.08
3530 3802 3.311322 TCCAACGTTGAACACATCTTCAC 59.689 43.478 29.35 0.00 29.62 3.18
3531 3803 3.536570 TCCAACGTTGAACACATCTTCA 58.463 40.909 29.35 0.00 0.00 3.02
3548 3820 1.741028 TCCCACATCAACTCCTCCAA 58.259 50.000 0.00 0.00 0.00 3.53
3606 3878 4.279922 TCGTTCTGATCTAAACTGGTGACA 59.720 41.667 0.00 0.00 39.59 3.58
3866 4138 2.183811 CAGCGTCTGAGCCTCCTG 59.816 66.667 1.18 0.00 38.01 3.86
3904 4176 5.743872 CGTCATCTTCATCTTCGTGTGAATA 59.256 40.000 0.00 0.00 34.18 1.75
3959 4231 3.459828 TGGATAGGGTTCATCTTGTCCA 58.540 45.455 0.00 0.00 32.48 4.02
4082 4354 4.148825 GCCTCCTGATGTCGGCGT 62.149 66.667 6.85 0.00 32.22 5.68
4196 4468 3.647590 AGGTTTCCTGAATGCAATTTGGT 59.352 39.130 0.00 0.00 36.07 3.67
4263 4535 9.442047 AGTTCTTCAAGTATTTGTCTCATTAGG 57.558 33.333 0.00 0.00 35.73 2.69
4279 4551 2.031769 TGCAATGCACGAGTTCTTCAAG 60.032 45.455 2.72 0.00 31.71 3.02
4287 4612 0.955428 ATCCGTTGCAATGCACGAGT 60.955 50.000 23.91 13.26 38.71 4.18
4289 4614 1.129624 GTTATCCGTTGCAATGCACGA 59.870 47.619 23.91 14.23 38.71 4.35
4294 4619 6.806249 ACATAGTTTTGTTATCCGTTGCAATG 59.194 34.615 11.90 11.90 0.00 2.82
4295 4620 6.919721 ACATAGTTTTGTTATCCGTTGCAAT 58.080 32.000 0.59 0.00 0.00 3.56
4309 4635 4.082787 CCAAGTGGGCAGTACATAGTTTTG 60.083 45.833 0.00 0.00 0.00 2.44
4321 4647 2.198827 TACATCAACCAAGTGGGCAG 57.801 50.000 1.69 0.00 42.05 4.85
4324 4650 2.760092 CCCATTACATCAACCAAGTGGG 59.240 50.000 1.69 0.00 44.81 4.61
4335 4665 1.208535 TCCGGACACACCCATTACATC 59.791 52.381 0.00 0.00 34.64 3.06
4336 4666 1.281419 TCCGGACACACCCATTACAT 58.719 50.000 0.00 0.00 34.64 2.29
4337 4667 1.281419 ATCCGGACACACCCATTACA 58.719 50.000 6.12 0.00 34.64 2.41
4338 4668 2.413310 AATCCGGACACACCCATTAC 57.587 50.000 6.12 0.00 34.64 1.89
4339 4669 3.085533 CAAAATCCGGACACACCCATTA 58.914 45.455 6.12 0.00 34.64 1.90
4340 4670 1.892474 CAAAATCCGGACACACCCATT 59.108 47.619 6.12 0.00 34.64 3.16
4341 4671 1.074727 TCAAAATCCGGACACACCCAT 59.925 47.619 6.12 0.00 34.64 4.00
4344 4674 0.515564 CGTCAAAATCCGGACACACC 59.484 55.000 6.12 0.00 33.66 4.16
4351 4681 3.117589 ACGAGACGTCAAAATCCGG 57.882 52.632 19.50 0.00 33.69 5.14
4369 4699 7.100409 TCTAACAATCGTACATCAACCAATGA 58.900 34.615 0.00 0.00 43.67 2.57
4397 4727 9.289782 GAATTACCTCATAAAGTGCTGGATTAT 57.710 33.333 0.00 0.00 0.00 1.28
4404 4735 8.200792 CAGTCTAGAATTACCTCATAAAGTGCT 58.799 37.037 0.00 0.00 0.00 4.40
4464 4795 4.679654 GCGGCTTTAACATTTATACCATGC 59.320 41.667 0.00 0.00 0.00 4.06
4472 4803 7.439655 AGAATTTTGTTGCGGCTTTAACATTTA 59.560 29.630 0.00 0.00 36.75 1.40
4533 4864 4.824479 TCCACAATCATTGCTAGTGAGA 57.176 40.909 0.00 0.00 32.14 3.27
4534 4865 4.334759 CCTTCCACAATCATTGCTAGTGAG 59.665 45.833 0.00 0.00 32.14 3.51
4535 4866 4.264253 CCTTCCACAATCATTGCTAGTGA 58.736 43.478 0.00 0.00 32.14 3.41
4538 4903 3.889815 TCCCTTCCACAATCATTGCTAG 58.110 45.455 0.00 0.00 0.00 3.42
4545 4910 3.391296 GCTACCTATCCCTTCCACAATCA 59.609 47.826 0.00 0.00 0.00 2.57
4546 4911 3.391296 TGCTACCTATCCCTTCCACAATC 59.609 47.826 0.00 0.00 0.00 2.67
4554 4919 3.346146 TTAGCCTGCTACCTATCCCTT 57.654 47.619 0.00 0.00 0.00 3.95
4555 4920 3.243724 CTTTAGCCTGCTACCTATCCCT 58.756 50.000 0.00 0.00 0.00 4.20
4558 4923 4.957684 TTCCTTTAGCCTGCTACCTATC 57.042 45.455 0.00 0.00 0.00 2.08
4560 4925 5.437060 CATTTTCCTTTAGCCTGCTACCTA 58.563 41.667 0.00 0.00 0.00 3.08
4561 4926 4.273318 CATTTTCCTTTAGCCTGCTACCT 58.727 43.478 0.00 0.00 0.00 3.08
4562 4927 3.381590 CCATTTTCCTTTAGCCTGCTACC 59.618 47.826 0.00 0.00 0.00 3.18
4563 4928 3.181486 GCCATTTTCCTTTAGCCTGCTAC 60.181 47.826 0.00 0.00 0.00 3.58
4564 4929 3.023832 GCCATTTTCCTTTAGCCTGCTA 58.976 45.455 0.00 0.00 0.00 3.49
4565 4930 1.827344 GCCATTTTCCTTTAGCCTGCT 59.173 47.619 0.00 0.00 0.00 4.24
4584 4949 1.533625 TTGCCTTACACCACATCAGC 58.466 50.000 0.00 0.00 0.00 4.26
4602 4967 6.154363 TCACTCAAAACCACAGAAAAGGATTT 59.846 34.615 0.00 0.00 42.41 2.17
4603 4968 5.656416 TCACTCAAAACCACAGAAAAGGATT 59.344 36.000 0.00 0.00 0.00 3.01
4624 4989 1.072331 ACAACTCCATGGTCCACTCAC 59.928 52.381 12.58 0.00 0.00 3.51
4630 4995 3.054361 AGGAATACACAACTCCATGGTCC 60.054 47.826 12.58 7.12 0.00 4.46
4703 5068 9.832445 AGTTCAGACTAGAAGACTTATAGAGAG 57.168 37.037 20.90 10.81 33.32 3.20
4718 5083 9.645059 TGATTGATTTGTAAGAGTTCAGACTAG 57.355 33.333 0.00 0.00 35.88 2.57
4736 5101 6.625740 CGTGACCCTGCTTTATTTGATTGATT 60.626 38.462 0.00 0.00 0.00 2.57
4743 5108 3.074412 ACTCGTGACCCTGCTTTATTTG 58.926 45.455 0.00 0.00 0.00 2.32
4748 5113 1.071471 CCACTCGTGACCCTGCTTT 59.929 57.895 0.00 0.00 0.00 3.51
4788 5153 4.382901 GGGTACATGTACAATACCGTTGGA 60.383 45.833 31.52 3.05 39.49 3.53
4789 5154 3.872771 GGGTACATGTACAATACCGTTGG 59.127 47.826 31.52 2.15 39.49 3.77
4791 5156 4.223477 AGTGGGTACATGTACAATACCGTT 59.777 41.667 31.52 15.39 39.49 4.44
4793 5158 4.395959 AGTGGGTACATGTACAATACCG 57.604 45.455 31.52 6.03 39.49 4.02
4890 5257 4.010349 CACAGTAATTTCTCCCTGAACCC 58.990 47.826 0.00 0.00 33.88 4.11
4930 5304 6.980978 GTGTCTTTATAGAGATACAAGCTGCA 59.019 38.462 13.30 0.00 37.61 4.41
4949 5326 7.120432 GCTTGAATCCTTCAGAATTAGTGTCTT 59.880 37.037 0.00 0.00 41.38 3.01
5017 5394 7.175641 AGGTTGATCTGAAGGTTTGACTTATTG 59.824 37.037 0.00 0.00 0.00 1.90
5043 5420 1.345089 ACCACCAATGTGTACTACGCA 59.655 47.619 4.93 4.93 43.36 5.24
5044 5421 1.730064 CACCACCAATGTGTACTACGC 59.270 52.381 0.00 0.00 41.09 4.42
5045 5422 2.991190 GACACCACCAATGTGTACTACG 59.009 50.000 0.00 0.00 46.43 3.51
5046 5423 3.997762 TGACACCACCAATGTGTACTAC 58.002 45.455 0.00 0.00 46.43 2.73
5047 5424 4.141688 TGTTGACACCACCAATGTGTACTA 60.142 41.667 0.00 0.00 46.43 1.82
5048 5425 3.211045 GTTGACACCACCAATGTGTACT 58.789 45.455 0.00 0.00 46.43 2.73
5049 5426 2.946329 TGTTGACACCACCAATGTGTAC 59.054 45.455 0.00 0.00 46.43 2.90
5050 5427 3.283259 TGTTGACACCACCAATGTGTA 57.717 42.857 0.00 0.00 46.43 2.90
5052 5429 2.426738 ACTTGTTGACACCACCAATGTG 59.573 45.455 0.00 0.00 42.39 3.21
5053 5430 2.687935 GACTTGTTGACACCACCAATGT 59.312 45.455 0.00 0.00 0.00 2.71
5054 5431 2.687425 TGACTTGTTGACACCACCAATG 59.313 45.455 0.00 0.00 0.00 2.82
5055 5432 3.011566 TGACTTGTTGACACCACCAAT 57.988 42.857 0.00 0.00 0.00 3.16
5056 5433 2.498644 TGACTTGTTGACACCACCAA 57.501 45.000 0.00 0.00 0.00 3.67
5057 5434 2.498644 TTGACTTGTTGACACCACCA 57.501 45.000 0.00 0.00 0.00 4.17
5058 5435 2.293399 GGATTGACTTGTTGACACCACC 59.707 50.000 0.00 0.00 0.00 4.61
5059 5436 3.214328 AGGATTGACTTGTTGACACCAC 58.786 45.455 0.00 0.00 0.00 4.16
5060 5437 3.576078 AGGATTGACTTGTTGACACCA 57.424 42.857 0.00 0.00 0.00 4.17
5061 5438 3.882888 TGAAGGATTGACTTGTTGACACC 59.117 43.478 0.00 0.00 0.00 4.16
5062 5439 4.816385 TCTGAAGGATTGACTTGTTGACAC 59.184 41.667 0.00 0.00 0.00 3.67
5063 5440 5.034852 TCTGAAGGATTGACTTGTTGACA 57.965 39.130 0.00 0.00 0.00 3.58
5064 5441 5.702670 TGATCTGAAGGATTGACTTGTTGAC 59.297 40.000 0.00 0.00 34.33 3.18
5065 5442 5.868454 TGATCTGAAGGATTGACTTGTTGA 58.132 37.500 0.00 0.00 34.33 3.18
5066 5443 6.376978 GTTGATCTGAAGGATTGACTTGTTG 58.623 40.000 0.00 0.00 34.33 3.33
5067 5444 5.180117 CGTTGATCTGAAGGATTGACTTGTT 59.820 40.000 0.00 0.00 34.33 2.83
5068 5445 4.692625 CGTTGATCTGAAGGATTGACTTGT 59.307 41.667 0.00 0.00 34.33 3.16
5069 5446 4.093998 CCGTTGATCTGAAGGATTGACTTG 59.906 45.833 0.00 0.00 34.33 3.16
5070 5447 4.256920 CCGTTGATCTGAAGGATTGACTT 58.743 43.478 0.00 0.00 34.33 3.01
5071 5448 3.866651 CCGTTGATCTGAAGGATTGACT 58.133 45.455 0.00 0.00 34.33 3.41
5072 5449 2.352960 GCCGTTGATCTGAAGGATTGAC 59.647 50.000 5.98 0.00 34.33 3.18
5073 5450 2.632377 GCCGTTGATCTGAAGGATTGA 58.368 47.619 5.98 0.00 34.33 2.57
5074 5451 1.672881 GGCCGTTGATCTGAAGGATTG 59.327 52.381 0.00 0.00 34.33 2.67
5075 5452 1.281867 TGGCCGTTGATCTGAAGGATT 59.718 47.619 0.00 0.00 34.33 3.01
5076 5453 0.911769 TGGCCGTTGATCTGAAGGAT 59.088 50.000 0.00 0.00 37.37 3.24
5077 5454 0.036388 GTGGCCGTTGATCTGAAGGA 60.036 55.000 0.00 0.00 0.00 3.36
5078 5455 0.036010 AGTGGCCGTTGATCTGAAGG 60.036 55.000 0.00 0.00 0.00 3.46
5079 5456 1.066573 AGAGTGGCCGTTGATCTGAAG 60.067 52.381 0.00 0.00 0.00 3.02
5080 5457 0.976641 AGAGTGGCCGTTGATCTGAA 59.023 50.000 0.00 0.00 0.00 3.02
5081 5458 0.247460 CAGAGTGGCCGTTGATCTGA 59.753 55.000 14.05 0.00 39.80 3.27
5082 5459 1.364626 GCAGAGTGGCCGTTGATCTG 61.365 60.000 14.63 14.63 40.26 2.90
5083 5460 1.078848 GCAGAGTGGCCGTTGATCT 60.079 57.895 0.00 0.00 0.00 2.75
5084 5461 1.364626 CTGCAGAGTGGCCGTTGATC 61.365 60.000 8.42 0.00 0.00 2.92
5085 5462 1.376424 CTGCAGAGTGGCCGTTGAT 60.376 57.895 8.42 0.00 0.00 2.57
5086 5463 2.031012 CTGCAGAGTGGCCGTTGA 59.969 61.111 8.42 0.00 0.00 3.18
5087 5464 2.031012 TCTGCAGAGTGGCCGTTG 59.969 61.111 13.74 0.00 0.00 4.10
5088 5465 2.031163 GTCTGCAGAGTGGCCGTT 59.969 61.111 18.89 0.00 0.00 4.44
5089 5466 4.008933 GGTCTGCAGAGTGGCCGT 62.009 66.667 18.89 0.00 0.00 5.68
5090 5467 3.699894 AGGTCTGCAGAGTGGCCG 61.700 66.667 18.89 0.00 0.00 6.13
5091 5468 2.046507 CAGGTCTGCAGAGTGGCC 60.047 66.667 18.89 14.94 0.00 5.36
5095 5472 0.322277 CATTGCCAGGTCTGCAGAGT 60.322 55.000 18.89 4.41 40.35 3.24
5103 5480 4.782019 TTCATTGTAACATTGCCAGGTC 57.218 40.909 0.00 0.00 0.00 3.85
5181 5559 4.199432 TGAAGCTCTCCTTGAAGTGATC 57.801 45.455 0.00 0.00 32.78 2.92
5182 5560 4.383989 GGATGAAGCTCTCCTTGAAGTGAT 60.384 45.833 0.00 0.00 32.78 3.06
5210 5588 7.363268 GGCAGGAAATAGTTGATGATTTCAAGT 60.363 37.037 8.99 1.72 44.89 3.16
5217 5595 4.646492 GGTTGGCAGGAAATAGTTGATGAT 59.354 41.667 0.00 0.00 0.00 2.45
5222 5600 3.763360 TGATGGTTGGCAGGAAATAGTTG 59.237 43.478 0.00 0.00 0.00 3.16
5224 5602 3.266772 TCTGATGGTTGGCAGGAAATAGT 59.733 43.478 0.00 0.00 33.05 2.12
5340 5723 7.545265 CGCATCCTTCATTTTTATTTTTCCTGA 59.455 33.333 0.00 0.00 0.00 3.86
5384 5767 7.703058 TGAGTTGATCTCTGAGTTACATGTA 57.297 36.000 0.08 0.08 43.13 2.29
5393 5776 5.699438 CGACAATTGAGTTGATCTCTGAG 57.301 43.478 13.59 0.00 43.13 3.35


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

AutoCloner maintained by Alex Coulton.