Multiple sequence alignment - TraesCS3A01G442100

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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 TraesCS3A01G442100 chr3A 100.000 6189 0 0 1 6189 684053579 684047391 0.000000e+00 11430.0
1 TraesCS3A01G442100 chr3D 94.165 4610 172 45 877 5453 547309948 547305403 0.000000e+00 6933.0
2 TraesCS3A01G442100 chr3D 80.104 578 52 24 5503 6056 547305324 547304786 7.580000e-99 372.0
3 TraesCS3A01G442100 chr3D 94.521 73 3 1 3575 3646 46481650 46481722 1.820000e-20 111.0
4 TraesCS3A01G442100 chr3D 100.000 36 0 0 5450 5485 547305357 547305322 4.000000e-07 67.6
5 TraesCS3A01G442100 chr3B 95.716 3268 103 18 1586 4836 724754427 724751180 0.000000e+00 5225.0
6 TraesCS3A01G442100 chr3B 95.346 709 27 5 885 1589 724755255 724754549 0.000000e+00 1122.0
7 TraesCS3A01G442100 chr3B 80.663 905 50 52 5369 6189 724745045 724744182 2.490000e-163 586.0
8 TraesCS3A01G442100 chr3B 84.725 563 35 30 4821 5371 724751163 724750640 3.310000e-142 516.0
9 TraesCS3A01G442100 chr3B 94.521 73 4 0 3575 3647 72711662 72711734 5.070000e-21 113.0
10 TraesCS3A01G442100 chr5A 94.790 883 41 4 1 878 456102632 456103514 0.000000e+00 1371.0
11 TraesCS3A01G442100 chr4B 93.326 884 50 5 1 880 147351809 147350931 0.000000e+00 1297.0
12 TraesCS3A01G442100 chr4B 100.000 29 0 0 1021 1049 148504756 148504728 3.000000e-03 54.7
13 TraesCS3A01G442100 chr4A 91.883 887 53 14 1 880 485135263 485134389 0.000000e+00 1221.0
14 TraesCS3A01G442100 chr4A 91.270 882 48 13 1 878 542232699 542231843 0.000000e+00 1175.0
15 TraesCS3A01G442100 chr4A 86.025 322 37 6 401 716 674996754 674997073 7.680000e-89 339.0
16 TraesCS3A01G442100 chr4A 75.516 339 67 13 2647 2975 620191256 620190924 1.070000e-32 152.0
17 TraesCS3A01G442100 chr4A 93.056 72 5 0 3575 3646 75435230 75435301 8.480000e-19 106.0
18 TraesCS3A01G442100 chr1B 87.983 699 58 8 151 847 636680924 636680250 0.000000e+00 802.0
19 TraesCS3A01G442100 chr1B 90.102 586 46 4 137 720 636665397 636664822 0.000000e+00 750.0
20 TraesCS3A01G442100 chr1B 93.571 140 9 0 1 140 636681248 636681109 6.290000e-50 209.0
21 TraesCS3A01G442100 chr1B 92.143 140 11 0 1 140 636665724 636665585 1.360000e-46 198.0
22 TraesCS3A01G442100 chr2B 86.626 329 35 7 401 723 359273055 359273380 7.630000e-94 355.0
23 TraesCS3A01G442100 chr2B 88.800 125 12 1 19 141 142998106 142998230 1.070000e-32 152.0
24 TraesCS3A01G442100 chr1A 89.643 280 26 2 137 415 553907387 553907110 2.740000e-93 353.0
25 TraesCS3A01G442100 chr1A 90.714 140 13 0 1 140 553933584 553933445 2.950000e-43 187.0
26 TraesCS3A01G442100 chr6A 86.068 323 36 7 401 716 35126684 35126364 7.680000e-89 339.0
27 TraesCS3A01G442100 chr7B 84.375 320 41 6 402 716 533374991 533374676 7.790000e-79 305.0
28 TraesCS3A01G442100 chr7B 94.444 72 4 0 3575 3646 566838806 566838877 1.820000e-20 111.0
29 TraesCS3A01G442100 chr7A 86.380 279 30 4 374 650 669494295 669494023 1.300000e-76 298.0
30 TraesCS3A01G442100 chr7A 88.000 125 13 1 19 141 669494760 669494636 5.000000e-31 147.0
31 TraesCS3A01G442100 chr5D 85.235 149 16 6 1255 1400 522032709 522032854 1.390000e-31 148.0
32 TraesCS3A01G442100 chr5D 84.564 149 17 6 1255 1400 522010278 522010423 6.470000e-30 143.0
33 TraesCS3A01G442100 chr5D 74.631 339 70 14 2647 2975 548881504 548881172 1.080000e-27 135.0
34 TraesCS3A01G442100 chr5D 74.556 338 70 13 2648 2975 522034908 522035239 3.890000e-27 134.0
35 TraesCS3A01G442100 chr5D 93.243 74 4 1 3573 3646 92152105 92152177 2.360000e-19 108.0
36 TraesCS3A01G442100 chr5B 84.564 149 17 6 1255 1400 700335688 700335543 6.470000e-30 143.0
37 TraesCS3A01G442100 chr5B 74.852 338 70 12 2647 2975 700332824 700332493 8.370000e-29 139.0
38 TraesCS3A01G442100 chr5B 94.444 72 4 0 3575 3646 487599641 487599570 1.820000e-20 111.0
39 TraesCS3A01G442100 chr4D 95.833 72 3 0 3575 3646 409444423 409444352 3.920000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G442100 chr3A 684047391 684053579 6188 True 11430.000000 11430 100.0000 1 6189 1 chr3A.!!$R1 6188
1 TraesCS3A01G442100 chr3D 547304786 547309948 5162 True 2457.533333 6933 91.4230 877 6056 3 chr3D.!!$R1 5179
2 TraesCS3A01G442100 chr3B 724750640 724755255 4615 True 2287.666667 5225 91.9290 885 5371 3 chr3B.!!$R2 4486
3 TraesCS3A01G442100 chr3B 724744182 724745045 863 True 586.000000 586 80.6630 5369 6189 1 chr3B.!!$R1 820
4 TraesCS3A01G442100 chr5A 456102632 456103514 882 False 1371.000000 1371 94.7900 1 878 1 chr5A.!!$F1 877
5 TraesCS3A01G442100 chr4B 147350931 147351809 878 True 1297.000000 1297 93.3260 1 880 1 chr4B.!!$R1 879
6 TraesCS3A01G442100 chr4A 485134389 485135263 874 True 1221.000000 1221 91.8830 1 880 1 chr4A.!!$R1 879
7 TraesCS3A01G442100 chr4A 542231843 542232699 856 True 1175.000000 1175 91.2700 1 878 1 chr4A.!!$R2 877
8 TraesCS3A01G442100 chr1B 636680250 636681248 998 True 505.500000 802 90.7770 1 847 2 chr1B.!!$R2 846
9 TraesCS3A01G442100 chr1B 636664822 636665724 902 True 474.000000 750 91.1225 1 720 2 chr1B.!!$R1 719
10 TraesCS3A01G442100 chr7A 669494023 669494760 737 True 222.500000 298 87.1900 19 650 2 chr7A.!!$R1 631

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
274 470 0.771127 TGTTTCCCCCTCACTCTTGG 59.229 55.0 0.00 0.0 0.00 3.61 F
862 1087 1.433534 TATCGAACATGCGTTGCACA 58.566 45.0 0.00 0.0 43.04 4.57 F
2130 2491 0.033920 TGACACTTCGCAGCACTGAT 59.966 50.0 0.81 0.0 0.00 2.90 F
3606 3969 1.899437 TTCAGCTCTTGCCTACCCCG 61.899 60.0 0.00 0.0 40.80 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1458 0.914644 CAGCTGATCTTCCCCTTCCA 59.085 55.0 8.42 0.0 0.0 3.53 R
2341 2702 1.117150 TGGCGGAGGGACACTTATAC 58.883 55.0 0.00 0.0 0.0 1.47 R
4093 4460 1.053424 TGTAGCGGGGAGACAAAGTT 58.947 50.0 0.00 0.0 0.0 2.66 R
5579 6071 0.242825 TGTTTACACGAGCTCCCGAG 59.757 55.0 8.47 0.0 0.0 4.63 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
84 87 8.430431 AGTAGGACTTCCTTAGTTATATTTGCC 58.570 37.037 2.32 0.00 46.09 4.52
116 119 3.612479 GCATTTGCTACCAAGGTTCAGTG 60.612 47.826 0.00 1.79 38.21 3.66
119 122 1.765904 TGCTACCAAGGTTCAGTGTGA 59.234 47.619 0.00 0.00 0.00 3.58
155 351 6.726379 TGTGATATGGTTAATGTTTCTCCCA 58.274 36.000 0.00 0.00 0.00 4.37
274 470 0.771127 TGTTTCCCCCTCACTCTTGG 59.229 55.000 0.00 0.00 0.00 3.61
328 527 9.946165 GATATTGTTAGTTTAAAATCCTTCCGG 57.054 33.333 0.00 0.00 0.00 5.14
442 659 8.413229 TGTAGAATGGAAGACTTTTCTTTTTGG 58.587 33.333 6.05 0.00 42.53 3.28
742 965 9.715121 ATTTTTGAGAAAGCACATATGACATTT 57.285 25.926 10.38 6.61 0.00 2.32
744 967 6.441093 TGAGAAAGCACATATGACATTTCC 57.559 37.500 10.38 9.91 0.00 3.13
862 1087 1.433534 TATCGAACATGCGTTGCACA 58.566 45.000 0.00 0.00 43.04 4.57
880 1105 5.997732 GCACATGCACACTTATTAGTTTG 57.002 39.130 0.00 0.00 41.59 2.93
888 1113 8.615878 TGCACACTTATTAGTTTGAATACTGT 57.384 30.769 2.30 0.00 34.65 3.55
921 1146 5.752892 TTACGCCTGAAGTGTCTCTATAG 57.247 43.478 0.00 0.00 40.51 1.31
962 1187 2.152699 CGCTCGCCGTACAGTGAAG 61.153 63.158 0.00 0.00 0.00 3.02
1166 1392 2.184322 GGATTCCGCTCGCTGTCA 59.816 61.111 0.00 0.00 0.00 3.58
1232 1458 1.155390 TCCACGGAGGAACCAGAGT 59.845 57.895 0.00 0.00 45.65 3.24
1407 1633 0.743701 TCCTCCTCGTACGACTGCTC 60.744 60.000 15.28 0.00 0.00 4.26
1425 1658 5.424895 ACTGCTCTCTGGTCATTCTTTAGAT 59.575 40.000 0.00 0.00 0.00 1.98
1434 1667 6.480763 TGGTCATTCTTTAGATTTACAGCCA 58.519 36.000 0.00 0.00 0.00 4.75
1484 1720 6.223852 TCAGTACAAAGAATCTTCAGTCACC 58.776 40.000 0.00 0.00 0.00 4.02
1495 1731 0.601558 TCAGTCACCGGAGTGTTAGC 59.398 55.000 9.46 0.00 44.83 3.09
1532 1768 6.927416 TGCATCTTTTGTCATAATTCAGCTT 58.073 32.000 0.00 0.00 0.00 3.74
1553 1789 5.954349 GCTTAAAATCGTCAAGAATCTGTCG 59.046 40.000 0.00 0.00 0.00 4.35
1852 2213 6.016693 CAGAGATCTCCATATCAAGTACGTGT 60.017 42.308 19.30 0.00 0.00 4.49
1893 2254 1.808343 GGGGAACGCGTTTCATACTTT 59.192 47.619 30.17 2.88 35.70 2.66
1909 2270 5.924254 TCATACTTTCGGTTTACAGTGACTG 59.076 40.000 11.70 11.70 37.52 3.51
1961 2322 2.479566 TGGACTGCCAAGATCTGTTC 57.520 50.000 0.00 0.00 42.49 3.18
2016 2377 5.363580 TGGATCTGCTTTCCAGTTTTCTTTT 59.636 36.000 0.00 0.00 42.38 2.27
2076 2437 4.681781 GCAGCTAAGCTAGATGAACTGGAA 60.682 45.833 11.14 0.00 44.59 3.53
2130 2491 0.033920 TGACACTTCGCAGCACTGAT 59.966 50.000 0.81 0.00 0.00 2.90
2234 2595 6.483307 CAGGTACTTCTTGATGTTGTTCTTGA 59.517 38.462 0.00 0.00 34.60 3.02
2574 2935 4.033709 AGCTAGTCTCTAAATTCCCAGCA 58.966 43.478 0.00 0.00 0.00 4.41
2581 2942 7.278875 AGTCTCTAAATTCCCAGCAGATTAAG 58.721 38.462 0.00 0.00 0.00 1.85
2611 2972 6.812656 TGCTGCATTTTGTTTCATTATTCGAT 59.187 30.769 0.00 0.00 0.00 3.59
2844 3205 2.459934 CTTTTCGTTTGTGGAGCAACC 58.540 47.619 0.00 0.00 36.72 3.77
3088 3449 7.973388 TGTTATCATGCCAATTTGTTTAGTAGC 59.027 33.333 0.00 0.00 0.00 3.58
3137 3498 5.057149 GTCTCAAAGTTTACCTCTGCTTCA 58.943 41.667 0.00 0.00 0.00 3.02
3206 3567 3.737559 ATCTACCCAAATGCAAGGACA 57.262 42.857 4.90 0.00 0.00 4.02
3375 3738 4.455533 TGTGTGCCATTTGTATCAAGAGAC 59.544 41.667 0.00 0.00 0.00 3.36
3384 3747 2.094700 TGTATCAAGAGACAGCGTCCAC 60.095 50.000 5.29 1.72 32.18 4.02
3606 3969 1.899437 TTCAGCTCTTGCCTACCCCG 61.899 60.000 0.00 0.00 40.80 5.73
3639 4002 5.999600 GGGACTAAAGGCTTAGTTGTTGTTA 59.000 40.000 0.00 0.00 46.31 2.41
3642 4005 8.021396 GGACTAAAGGCTTAGTTGTTGTTATTG 58.979 37.037 0.00 0.00 46.31 1.90
3646 4009 6.952773 AGGCTTAGTTGTTGTTATTGTTGA 57.047 33.333 0.00 0.00 0.00 3.18
3880 4247 6.739112 AGTTGTTTTTCTTTGGCTCATAGTC 58.261 36.000 0.00 0.00 0.00 2.59
3899 4266 5.117355 AGTCATTCATTGTTGTGCTTCTG 57.883 39.130 0.00 0.00 0.00 3.02
3977 4344 9.408648 CCAGTTAGGGTTAAGAATTCATACAAT 57.591 33.333 8.44 0.00 0.00 2.71
4093 4460 1.571955 TACCTCTCAAGCAGCCATCA 58.428 50.000 0.00 0.00 0.00 3.07
4332 4699 5.106475 CGAAGACCTAGGCATATCTGTAGAC 60.106 48.000 9.30 0.00 0.00 2.59
4424 4791 2.507484 TCAACAGGCAAGTTCATCCAG 58.493 47.619 0.00 0.00 0.00 3.86
4446 4813 5.700832 CAGGTTCATGCTAAGTGTCAAGTAA 59.299 40.000 0.00 0.00 0.00 2.24
4469 4836 4.141711 ACTGTACCTGTGATTGAACTGTGT 60.142 41.667 0.00 0.00 0.00 3.72
4473 4840 3.117888 ACCTGTGATTGAACTGTGTTCCT 60.118 43.478 7.81 0.00 0.00 3.36
4474 4841 4.102524 ACCTGTGATTGAACTGTGTTCCTA 59.897 41.667 7.81 0.00 0.00 2.94
4475 4842 5.063204 CCTGTGATTGAACTGTGTTCCTAA 58.937 41.667 7.81 0.00 0.00 2.69
4481 4848 8.299570 GTGATTGAACTGTGTTCCTAATTCATT 58.700 33.333 7.81 0.00 0.00 2.57
4559 4926 6.472163 CCATTGTTTCGGAAAATGTAGTATGC 59.528 38.462 4.46 0.00 30.84 3.14
4560 4927 6.811253 TTGTTTCGGAAAATGTAGTATGCT 57.189 33.333 4.46 0.00 0.00 3.79
4561 4928 7.908827 TTGTTTCGGAAAATGTAGTATGCTA 57.091 32.000 4.46 0.00 0.00 3.49
4562 4929 7.534085 TGTTTCGGAAAATGTAGTATGCTAG 57.466 36.000 4.46 0.00 0.00 3.42
4563 4930 6.036735 TGTTTCGGAAAATGTAGTATGCTAGC 59.963 38.462 8.10 8.10 0.00 3.42
4564 4931 5.531122 TCGGAAAATGTAGTATGCTAGCT 57.469 39.130 17.23 4.07 0.00 3.32
4565 4932 5.914033 TCGGAAAATGTAGTATGCTAGCTT 58.086 37.500 17.23 12.56 0.00 3.74
4566 4933 6.346096 TCGGAAAATGTAGTATGCTAGCTTT 58.654 36.000 17.23 4.37 0.00 3.51
4567 4934 6.479001 TCGGAAAATGTAGTATGCTAGCTTTC 59.521 38.462 17.23 13.02 0.00 2.62
4568 4935 6.480320 CGGAAAATGTAGTATGCTAGCTTTCT 59.520 38.462 17.23 14.84 0.00 2.52
4569 4936 7.652105 CGGAAAATGTAGTATGCTAGCTTTCTA 59.348 37.037 17.23 13.82 0.00 2.10
4570 4937 9.326413 GGAAAATGTAGTATGCTAGCTTTCTAA 57.674 33.333 17.23 8.42 0.00 2.10
4610 4978 5.278061 AGTAAGCTTCCTCCCTTACATACA 58.722 41.667 0.00 0.00 43.55 2.29
4638 5006 4.502962 GATCTCCTCTTCACTGTCCTTTG 58.497 47.826 0.00 0.00 0.00 2.77
4646 5014 7.228706 TCCTCTTCACTGTCCTTTGTAAATTTC 59.771 37.037 0.00 0.00 0.00 2.17
4653 5021 6.993902 ACTGTCCTTTGTAAATTTCGTAGGAA 59.006 34.615 10.89 0.00 32.54 3.36
4704 5072 1.926561 TCGCATTCGTCCATCTTCTG 58.073 50.000 0.00 0.00 36.96 3.02
4749 5117 1.091537 TCGGGAATGTGCGAAAATCC 58.908 50.000 0.00 0.00 0.00 3.01
4800 5181 6.805713 ACCAACTTTACAGAAACATTTCCTG 58.194 36.000 0.68 0.00 37.92 3.86
4828 5209 3.291585 GACAGTCGCAAACAAACATCAG 58.708 45.455 0.00 0.00 0.00 2.90
4836 5217 4.546570 GCAAACAAACATCAGACTAACCC 58.453 43.478 0.00 0.00 0.00 4.11
4849 5263 7.921041 TCAGACTAACCCATATTCTCATCTT 57.079 36.000 0.00 0.00 0.00 2.40
4861 5275 5.659849 ATTCTCATCTTAAGGCCTTCCAT 57.340 39.130 24.49 9.65 33.74 3.41
4876 5290 3.618351 CTTCCATGTGCTGAGGAGAATT 58.382 45.455 0.00 0.00 32.11 2.17
4951 5368 2.478370 CCCATTGCATCAAACTACTGCG 60.478 50.000 0.00 0.00 38.75 5.18
4999 5420 3.623960 CCACGGTGTCTGTTGAGTTAAAA 59.376 43.478 7.45 0.00 0.00 1.52
5006 5427 7.044314 CGGTGTCTGTTGAGTTAAAACATTTTC 60.044 37.037 0.00 0.00 36.95 2.29
5010 5431 5.651530 TGTTGAGTTAAAACATTTTCGGCA 58.348 33.333 0.00 0.00 32.71 5.69
5011 5432 6.276847 TGTTGAGTTAAAACATTTTCGGCAT 58.723 32.000 0.00 0.00 32.71 4.40
5014 5435 5.010112 TGAGTTAAAACATTTTCGGCATGGA 59.990 36.000 0.00 0.00 0.00 3.41
5015 5436 5.848406 AGTTAAAACATTTTCGGCATGGAA 58.152 33.333 0.00 0.00 0.00 3.53
5053 5474 2.002586 GTGAACATGTCCCTGATCGTG 58.997 52.381 0.00 0.00 0.00 4.35
5105 5526 1.078848 CTCCACCAGGCCTTCTTCG 60.079 63.158 0.00 0.00 33.74 3.79
5106 5527 1.535444 TCCACCAGGCCTTCTTCGA 60.535 57.895 0.00 0.00 33.74 3.71
5107 5528 1.078848 CCACCAGGCCTTCTTCGAG 60.079 63.158 0.00 0.00 0.00 4.04
5108 5529 1.078848 CACCAGGCCTTCTTCGAGG 60.079 63.158 0.00 0.86 39.93 4.63
5109 5530 2.294078 ACCAGGCCTTCTTCGAGGG 61.294 63.158 0.00 0.00 37.29 4.30
5110 5531 1.990060 CCAGGCCTTCTTCGAGGGA 60.990 63.158 0.00 0.00 37.29 4.20
5207 5628 7.993758 AGCTGTGATGAGTATTCAGTAGTAGTA 59.006 37.037 0.00 0.00 36.61 1.82
5208 5629 8.286800 GCTGTGATGAGTATTCAGTAGTAGTAG 58.713 40.741 0.00 0.00 36.61 2.57
5209 5630 9.332502 CTGTGATGAGTATTCAGTAGTAGTAGT 57.667 37.037 0.00 0.00 36.61 2.73
5242 5663 6.578944 TGTAGTAGTGTGTGTTTTCAGTCAT 58.421 36.000 0.00 0.00 0.00 3.06
5244 5665 5.670485 AGTAGTGTGTGTTTTCAGTCATGA 58.330 37.500 0.00 0.00 0.00 3.07
5284 5707 1.006086 GCAAAAGCAAAACAACGGCT 58.994 45.000 0.00 0.00 40.14 5.52
5312 5735 5.480422 TGTGGACTTGTAGACTGTGATGTAT 59.520 40.000 0.00 0.00 0.00 2.29
5313 5736 6.037098 GTGGACTTGTAGACTGTGATGTATC 58.963 44.000 0.00 0.00 0.00 2.24
5446 5871 0.376152 CGCCTCGTACATGTAGACGT 59.624 55.000 18.04 0.00 40.00 4.34
5490 5971 3.275617 TGAATAACCGAAGTCCCATGG 57.724 47.619 4.14 4.14 0.00 3.66
5492 5973 0.182775 ATAACCGAAGTCCCATGGCC 59.817 55.000 6.09 0.00 0.00 5.36
5578 6070 4.759693 ACAATGTGTCAACGATAACATGGT 59.240 37.500 0.00 0.00 33.32 3.55
5579 6071 5.106712 ACAATGTGTCAACGATAACATGGTC 60.107 40.000 0.00 0.00 32.88 4.02
5580 6072 4.265904 TGTGTCAACGATAACATGGTCT 57.734 40.909 0.00 0.00 0.00 3.85
5581 6073 4.242475 TGTGTCAACGATAACATGGTCTC 58.758 43.478 0.00 0.00 0.00 3.36
5582 6074 3.303495 GTGTCAACGATAACATGGTCTCG 59.697 47.826 16.14 16.14 37.17 4.04
5583 6075 2.858344 GTCAACGATAACATGGTCTCGG 59.142 50.000 20.86 6.06 35.52 4.63
5585 6077 1.771565 ACGATAACATGGTCTCGGGA 58.228 50.000 20.86 0.00 35.52 5.14
5586 6078 1.681793 ACGATAACATGGTCTCGGGAG 59.318 52.381 20.86 0.00 35.52 4.30
5587 6079 1.603172 CGATAACATGGTCTCGGGAGC 60.603 57.143 7.76 7.76 40.08 4.70
5588 6080 1.689273 GATAACATGGTCTCGGGAGCT 59.311 52.381 16.66 0.00 40.29 4.09
5609 6106 2.159531 TCGTGTAAACATACGGACGAGG 60.160 50.000 0.00 0.00 40.48 4.63
5622 6119 2.286772 CGGACGAGGTTTGTCAAAAAGG 60.287 50.000 0.00 0.00 38.10 3.11
5623 6120 2.946990 GGACGAGGTTTGTCAAAAAGGA 59.053 45.455 0.00 0.00 38.10 3.36
5624 6121 3.242969 GGACGAGGTTTGTCAAAAAGGAC 60.243 47.826 0.00 0.00 38.10 3.85
5631 6137 0.662619 TGTCAAAAAGGACGCTGCTG 59.337 50.000 0.00 0.00 40.72 4.41
5636 6142 0.603975 AAAAGGACGCTGCTGGTCTC 60.604 55.000 7.45 0.00 34.82 3.36
5667 6173 1.224075 CAGAACTGCAGACCACTGTG 58.776 55.000 23.35 0.00 45.04 3.66
5668 6174 0.533755 AGAACTGCAGACCACTGTGC 60.534 55.000 23.35 0.00 45.04 4.57
5671 6177 4.068280 TGCAGACCACTGTGCATG 57.932 55.556 1.29 1.76 44.70 4.06
5672 6178 2.263021 TGCAGACCACTGTGCATGC 61.263 57.895 11.82 11.82 44.70 4.06
5691 6197 1.138464 GCTGCCATGATCAGTCTCTCA 59.862 52.381 0.09 0.00 34.21 3.27
5692 6198 2.823984 CTGCCATGATCAGTCTCTCAC 58.176 52.381 0.09 0.00 0.00 3.51
5705 6217 3.151022 CTCACGAGCCTCCCTCCC 61.151 72.222 0.00 0.00 37.27 4.30
5710 6222 4.467107 GAGCCTCCCTCCCTCCGT 62.467 72.222 0.00 0.00 34.35 4.69
5747 6259 1.684450 TGATGGTTGATGGATGCATGC 59.316 47.619 11.82 11.82 0.00 4.06
5748 6260 1.684450 GATGGTTGATGGATGCATGCA 59.316 47.619 25.04 25.04 0.00 3.96
5749 6261 0.818938 TGGTTGATGGATGCATGCAC 59.181 50.000 25.37 16.53 0.00 4.57
5750 6262 0.103572 GGTTGATGGATGCATGCACC 59.896 55.000 25.37 24.57 0.00 5.01
5751 6263 0.818938 GTTGATGGATGCATGCACCA 59.181 50.000 30.91 30.91 38.09 4.17
5755 6267 0.323999 ATGGATGCATGCACCACACT 60.324 50.000 31.21 19.64 36.49 3.55
5756 6268 1.245376 TGGATGCATGCACCACACTG 61.245 55.000 27.56 0.00 0.00 3.66
5758 6270 1.592400 GATGCATGCACCACACTGCT 61.592 55.000 25.37 2.84 38.07 4.24
5866 6409 0.670546 ATGCTACTGCGACCACACAC 60.671 55.000 0.00 0.00 43.34 3.82
5868 6411 1.007734 CTACTGCGACCACACACGT 60.008 57.895 0.00 0.00 0.00 4.49
5869 6412 0.239082 CTACTGCGACCACACACGTA 59.761 55.000 0.00 0.00 0.00 3.57
5870 6413 0.883153 TACTGCGACCACACACGTAT 59.117 50.000 0.00 0.00 0.00 3.06
5871 6414 0.883153 ACTGCGACCACACACGTATA 59.117 50.000 0.00 0.00 0.00 1.47
5873 6416 0.454789 TGCGACCACACACGTATACG 60.455 55.000 23.24 23.24 46.33 3.06
5888 6431 5.896922 CGTATACGTGCTACTACAGTACT 57.103 43.478 17.16 0.00 37.70 2.73
5889 6432 5.899318 CGTATACGTGCTACTACAGTACTC 58.101 45.833 17.16 0.00 37.70 2.59
5907 6450 1.442769 TCAGCATGAGGAAAACGAGC 58.557 50.000 0.00 0.00 42.56 5.03
5928 6471 1.012086 CATGATGAGTGCCGACCAAG 58.988 55.000 0.00 0.00 0.00 3.61
6152 6696 2.649257 GGCTCGGATTCGATTCGCG 61.649 63.158 0.00 0.00 45.04 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.578576 ACATGATATGCTTTTGTACCAATCTAT 57.421 29.630 0.00 0.00 0.00 1.98
84 87 2.031682 GGTAGCAAATGCAAGGCTATCG 60.032 50.000 16.94 0.00 45.16 2.92
116 119 5.464722 CCATATCACAGTTGAGCTACATCAC 59.535 44.000 0.00 0.00 34.35 3.06
119 122 5.620738 ACCATATCACAGTTGAGCTACAT 57.379 39.130 0.00 0.00 34.35 2.29
155 351 4.103153 ACCGATCCACACCAGAATAATCAT 59.897 41.667 0.00 0.00 0.00 2.45
274 470 1.138069 GCTTCAGAAGGGCCTCTAGAC 59.862 57.143 6.46 0.00 0.00 2.59
328 527 7.925483 ACTCTTATGCATATCACAAAGTCTCTC 59.075 37.037 7.36 0.00 0.00 3.20
422 633 5.660864 TCCACCAAAAAGAAAAGTCTTCCAT 59.339 36.000 0.00 0.00 43.59 3.41
442 659 6.017400 TGCTTCTTTTGATTCAGATTCCAC 57.983 37.500 0.00 0.00 0.00 4.02
527 745 8.797350 TCAAATATCATCTAATCCATCGCATT 57.203 30.769 0.00 0.00 0.00 3.56
783 1007 6.902224 AGTTTTATTTCTGTGGTTGTTTGC 57.098 33.333 0.00 0.00 0.00 3.68
862 1087 9.231297 ACAGTATTCAAACTAATAAGTGTGCAT 57.769 29.630 0.00 0.00 40.33 3.96
880 1105 8.876790 AGGCGTAATTGTAGTTTTACAGTATTC 58.123 33.333 0.00 0.00 40.68 1.75
888 1113 6.707161 ACACTTCAGGCGTAATTGTAGTTTTA 59.293 34.615 0.00 0.00 0.00 1.52
893 1118 4.495422 AGACACTTCAGGCGTAATTGTAG 58.505 43.478 0.00 0.00 0.00 2.74
897 1122 3.963428 AGAGACACTTCAGGCGTAATT 57.037 42.857 0.00 0.00 0.00 1.40
921 1146 1.730612 GGCGGCTTTCCTATATTACGC 59.269 52.381 0.00 0.00 44.41 4.42
962 1187 1.594310 GACTGGACTGCTGACTCCC 59.406 63.158 0.00 0.00 0.00 4.30
1166 1392 3.080121 CGCCCTCTCTCTTGGCCT 61.080 66.667 3.32 0.00 42.29 5.19
1228 1454 2.476199 CTGATCTTCCCCTTCCACTCT 58.524 52.381 0.00 0.00 0.00 3.24
1232 1458 0.914644 CAGCTGATCTTCCCCTTCCA 59.085 55.000 8.42 0.00 0.00 3.53
1407 1633 7.011857 GGCTGTAAATCTAAAGAATGACCAGAG 59.988 40.741 0.00 0.00 0.00 3.35
1484 1720 4.557205 ACTTCACTTTAGCTAACACTCCG 58.443 43.478 5.45 0.00 0.00 4.63
1495 1731 7.701924 TGACAAAAGATGCAAACTTCACTTTAG 59.298 33.333 9.38 0.00 0.00 1.85
1532 1768 6.617879 TCTCGACAGATTCTTGACGATTTTA 58.382 36.000 0.00 0.00 42.40 1.52
1852 2213 5.305585 CCCTAGTAAACTGACTGAAAAGCA 58.694 41.667 0.00 0.00 0.00 3.91
1888 2249 4.053295 GCAGTCACTGTAAACCGAAAGTA 58.947 43.478 6.68 0.00 33.43 2.24
1893 2254 2.902705 AAGCAGTCACTGTAAACCGA 57.097 45.000 6.68 0.00 33.43 4.69
1909 2270 3.674997 TGTCCTGGATTGACAGTAAAGC 58.325 45.455 0.00 0.00 37.80 3.51
1961 2322 2.433239 AGTTAGCGGGGTTACCATGTAG 59.567 50.000 2.98 0.00 40.22 2.74
2076 2437 1.678101 GCAACACCTTTCAAGAGCTGT 59.322 47.619 0.00 0.00 0.00 4.40
2130 2491 5.048083 GCATTCTCCAAATGACACAAGGTAA 60.048 40.000 2.07 0.00 0.00 2.85
2234 2595 5.072741 AGCATAGTGGTTCACAGTGAAAAT 58.927 37.500 17.83 5.42 38.22 1.82
2341 2702 1.117150 TGGCGGAGGGACACTTATAC 58.883 55.000 0.00 0.00 0.00 1.47
2410 2771 4.756642 GTGTTGAGAACATGGAGTGAATCA 59.243 41.667 0.00 0.00 44.35 2.57
2574 2935 6.752168 ACAAAATGCAGCAGAAACTTAATCT 58.248 32.000 0.00 0.00 0.00 2.40
2581 2942 5.662211 ATGAAACAAAATGCAGCAGAAAC 57.338 34.783 0.00 0.00 0.00 2.78
2611 2972 9.567776 TGAAGACAATTTAGAACCAACAAGATA 57.432 29.630 0.00 0.00 0.00 1.98
2771 3132 5.968167 AGGAACCCAGTAACAATAGGTATCA 59.032 40.000 0.00 0.00 0.00 2.15
2772 3133 6.496144 AGGAACCCAGTAACAATAGGTATC 57.504 41.667 0.00 0.00 0.00 2.24
2844 3205 2.986479 GGCAACCGCAATGAACTAAAAG 59.014 45.455 0.00 0.00 41.24 2.27
3002 3363 7.333528 TCCAGAAATCAATAGTATGGTTTGC 57.666 36.000 0.00 0.00 33.88 3.68
3088 3449 8.818057 CAAAACTTCTAATAACGAGGGATACAG 58.182 37.037 0.00 0.00 39.74 2.74
3137 3498 2.467880 ACATCCTTCCACACCTATCGT 58.532 47.619 0.00 0.00 0.00 3.73
3206 3567 6.045072 TCATCAAATGTTAAGTACGGGACT 57.955 37.500 0.00 0.00 41.56 3.85
3375 3738 1.719709 CAGCATCATGTGGACGCTG 59.280 57.895 0.00 0.00 43.55 5.18
3384 3747 2.991190 GTGCAGTTTTTCCAGCATCATG 59.009 45.455 0.00 0.00 39.43 3.07
3540 3903 2.664402 AGCACACCAAATGTTCTCCT 57.336 45.000 0.00 0.00 40.64 3.69
3606 3969 3.487372 AGCCTTTAGTCCCAAACAAGTC 58.513 45.455 0.00 0.00 0.00 3.01
3639 4002 8.632906 ATCTTCTGATCTTTGACTTCAACAAT 57.367 30.769 0.00 0.00 35.28 2.71
3866 4233 6.446781 ACAATGAATGACTATGAGCCAAAG 57.553 37.500 0.00 0.00 0.00 2.77
3899 4266 4.314740 TTGTGGATGTAAAACCTGTTGC 57.685 40.909 0.00 0.00 0.00 4.17
3977 4344 1.562672 GGGTGCCTGGAGCTTTAGGA 61.563 60.000 18.41 4.08 44.23 2.94
4093 4460 1.053424 TGTAGCGGGGAGACAAAGTT 58.947 50.000 0.00 0.00 0.00 2.66
4215 4582 2.778299 ACTGAATGTTTCGGCAGCTTA 58.222 42.857 0.00 0.00 39.72 3.09
4281 4648 2.392613 AAAACACCTGCTCAAGCGCG 62.393 55.000 0.00 0.00 45.83 6.86
4282 4649 0.661483 GAAAACACCTGCTCAAGCGC 60.661 55.000 0.00 0.00 45.83 5.92
4332 4699 0.109086 CCTCACTAGTCGCCACACAG 60.109 60.000 0.00 0.00 0.00 3.66
4424 4791 5.701290 AGTTACTTGACACTTAGCATGAACC 59.299 40.000 0.00 0.00 0.00 3.62
4446 4813 4.141711 ACACAGTTCAATCACAGGTACAGT 60.142 41.667 0.00 0.00 0.00 3.55
4469 4836 8.303876 GTGCTAGTTTTCCAAATGAATTAGGAA 58.696 33.333 0.00 0.00 38.31 3.36
4473 4840 7.531857 TGGTGCTAGTTTTCCAAATGAATTA 57.468 32.000 0.00 0.00 31.67 1.40
4474 4841 6.418057 TGGTGCTAGTTTTCCAAATGAATT 57.582 33.333 0.00 0.00 31.67 2.17
4475 4842 6.400568 CATGGTGCTAGTTTTCCAAATGAAT 58.599 36.000 0.00 0.00 33.55 2.57
4481 4848 1.892474 GCCATGGTGCTAGTTTTCCAA 59.108 47.619 14.67 0.00 33.55 3.53
4493 4860 4.627611 CTCATTTTACAGAGCCATGGTG 57.372 45.455 14.67 6.44 0.00 4.17
4515 4882 4.916983 TGGTCAAGAAACAAACCATCAG 57.083 40.909 0.00 0.00 36.88 2.90
4520 4887 5.005299 CGAAACAATGGTCAAGAAACAAACC 59.995 40.000 0.00 0.00 0.00 3.27
4540 4907 6.346096 AGCTAGCATACTACATTTTCCGAAA 58.654 36.000 18.83 0.00 0.00 3.46
4559 4926 4.513318 GCTACCAAGCCATTAGAAAGCTAG 59.487 45.833 0.00 0.00 43.40 3.42
4560 4927 4.451900 GCTACCAAGCCATTAGAAAGCTA 58.548 43.478 0.00 0.00 43.40 3.32
4561 4928 3.282885 GCTACCAAGCCATTAGAAAGCT 58.717 45.455 0.00 0.00 43.40 3.74
4562 4929 3.699779 GCTACCAAGCCATTAGAAAGC 57.300 47.619 0.00 0.00 43.40 3.51
4586 4953 5.724854 TGTATGTAAGGGAGGAAGCTTACTT 59.275 40.000 13.78 8.57 39.43 2.24
4587 4954 5.128991 GTGTATGTAAGGGAGGAAGCTTACT 59.871 44.000 12.17 12.17 34.47 2.24
4588 4955 5.358090 GTGTATGTAAGGGAGGAAGCTTAC 58.642 45.833 0.00 0.00 34.10 2.34
4589 4956 4.407945 GGTGTATGTAAGGGAGGAAGCTTA 59.592 45.833 0.00 0.00 0.00 3.09
4590 4957 3.200165 GGTGTATGTAAGGGAGGAAGCTT 59.800 47.826 0.00 0.00 0.00 3.74
4604 4972 2.175931 AGAGGAGATCGAGGGTGTATGT 59.824 50.000 0.00 0.00 0.00 2.29
4605 4973 2.870175 AGAGGAGATCGAGGGTGTATG 58.130 52.381 0.00 0.00 0.00 2.39
4610 4978 1.286553 AGTGAAGAGGAGATCGAGGGT 59.713 52.381 0.00 0.00 0.00 4.34
4638 5006 6.790285 TGGTCAAGTTCCTACGAAATTTAC 57.210 37.500 0.00 0.00 34.19 2.01
4646 5014 2.346803 CCACATGGTCAAGTTCCTACG 58.653 52.381 0.00 0.00 0.00 3.51
4704 5072 1.857837 GAGACTATCGCTCTTTGCTGC 59.142 52.381 0.00 0.00 40.11 5.25
4800 5181 3.524648 TTTGCGACTGTCGTCCCCC 62.525 63.158 28.38 13.79 42.81 5.40
4817 5198 8.109634 AGAATATGGGTTAGTCTGATGTTTGTT 58.890 33.333 0.00 0.00 34.08 2.83
4828 5209 7.604545 GCCTTAAGATGAGAATATGGGTTAGTC 59.395 40.741 3.36 0.00 0.00 2.59
4836 5217 6.537355 TGGAAGGCCTTAAGATGAGAATATG 58.463 40.000 20.54 0.00 34.31 1.78
4849 5263 0.991146 TCAGCACATGGAAGGCCTTA 59.009 50.000 20.54 3.65 34.31 2.69
4861 5275 0.329261 CCCCAATTCTCCTCAGCACA 59.671 55.000 0.00 0.00 0.00 4.57
4876 5290 1.667595 TCATCTGGACATTGACCCCA 58.332 50.000 2.69 0.79 0.00 4.96
4929 5346 2.493278 GCAGTAGTTTGATGCAATGGGT 59.507 45.455 0.00 0.00 39.75 4.51
4999 5420 3.002102 GCAAATTCCATGCCGAAAATGT 58.998 40.909 0.00 0.00 37.85 2.71
5010 5431 2.406596 GCAATGGTGGCAAATTCCAT 57.593 45.000 1.72 1.72 42.82 3.41
5011 5432 3.931768 GCAATGGTGGCAAATTCCA 57.068 47.368 0.00 0.00 35.64 3.53
5053 5474 2.126071 TTAGCCTCGCTGTCGTGC 60.126 61.111 0.00 0.00 40.10 5.34
5068 5489 1.671054 GGCTTCCACGCACAGCTTA 60.671 57.895 0.00 0.00 33.76 3.09
5105 5526 3.934962 GCCATCGCCCTCTCCCTC 61.935 72.222 0.00 0.00 0.00 4.30
5108 5529 3.620785 ATCGCCATCGCCCTCTCC 61.621 66.667 0.00 0.00 35.26 3.71
5109 5530 2.356793 CATCGCCATCGCCCTCTC 60.357 66.667 0.00 0.00 35.26 3.20
5110 5531 3.933722 CCATCGCCATCGCCCTCT 61.934 66.667 0.00 0.00 35.26 3.69
5207 5628 7.675062 ACACACACTACTACAGTACTACTACT 58.325 38.462 0.00 0.00 34.98 2.57
5208 5629 7.897575 ACACACACTACTACAGTACTACTAC 57.102 40.000 0.00 0.00 34.98 2.73
5209 5630 8.908786 AAACACACACTACTACAGTACTACTA 57.091 34.615 0.00 0.00 34.98 1.82
5210 5631 7.814264 AAACACACACTACTACAGTACTACT 57.186 36.000 0.00 0.00 34.98 2.57
5211 5632 8.131100 TGAAAACACACACTACTACAGTACTAC 58.869 37.037 0.00 0.00 34.98 2.73
5212 5633 8.224389 TGAAAACACACACTACTACAGTACTA 57.776 34.615 0.00 0.00 34.98 1.82
5213 5634 7.104043 TGAAAACACACACTACTACAGTACT 57.896 36.000 0.00 0.00 34.98 2.73
5214 5635 6.976925 ACTGAAAACACACACTACTACAGTAC 59.023 38.462 0.00 0.00 34.98 2.73
5215 5636 7.104043 ACTGAAAACACACACTACTACAGTA 57.896 36.000 0.00 0.00 34.98 2.74
5216 5637 5.974108 ACTGAAAACACACACTACTACAGT 58.026 37.500 0.00 0.00 38.32 3.55
5217 5638 6.040247 TGACTGAAAACACACACTACTACAG 58.960 40.000 0.00 0.00 0.00 2.74
5218 5639 5.968254 TGACTGAAAACACACACTACTACA 58.032 37.500 0.00 0.00 0.00 2.74
5219 5640 6.700081 TCATGACTGAAAACACACACTACTAC 59.300 38.462 0.00 0.00 0.00 2.73
5220 5641 6.700081 GTCATGACTGAAAACACACACTACTA 59.300 38.462 18.83 0.00 31.85 1.82
5221 5642 5.523916 GTCATGACTGAAAACACACACTACT 59.476 40.000 18.83 0.00 31.85 2.57
5242 5663 2.548295 GCGGTTTTTCCAGGCGTCA 61.548 57.895 0.00 0.00 35.57 4.35
5244 5665 2.203294 AGCGGTTTTTCCAGGCGT 60.203 55.556 0.00 0.00 35.57 5.68
5284 5707 3.572682 CACAGTCTACAAGTCCACACCTA 59.427 47.826 0.00 0.00 0.00 3.08
5312 5735 1.632948 CGCGACTCCACGTGTAGAGA 61.633 60.000 23.33 9.86 38.67 3.10
5313 5736 1.226046 CGCGACTCCACGTGTAGAG 60.226 63.158 15.73 16.56 38.67 2.43
5335 5758 3.039002 TGCACGCACGTACGCATT 61.039 55.556 16.72 0.00 36.19 3.56
5364 5787 6.908870 TTCAGTATTCATCACATGTACAGC 57.091 37.500 0.00 0.00 0.00 4.40
5429 5854 2.182825 GCAACGTCTACATGTACGAGG 58.817 52.381 24.02 19.72 41.55 4.63
5432 5857 2.321263 TGTGCAACGTCTACATGTACG 58.679 47.619 17.40 17.40 42.39 3.67
5544 6028 2.358247 ACATTGTCACCGGCGACC 60.358 61.111 19.57 2.88 34.88 4.79
5545 6029 1.897398 GACACATTGTCACCGGCGAC 61.897 60.000 15.83 15.83 46.22 5.19
5546 6030 1.666553 GACACATTGTCACCGGCGA 60.667 57.895 9.30 0.00 46.22 5.54
5547 6031 2.860293 GACACATTGTCACCGGCG 59.140 61.111 0.00 0.00 46.22 6.46
5571 6063 1.901085 GAGCTCCCGAGACCATGTT 59.099 57.895 0.87 0.00 0.00 2.71
5575 6067 2.473891 TACACGAGCTCCCGAGACCA 62.474 60.000 8.47 0.00 0.00 4.02
5576 6068 1.310933 TTACACGAGCTCCCGAGACC 61.311 60.000 8.47 0.00 0.00 3.85
5578 6070 0.524862 GTTTACACGAGCTCCCGAGA 59.475 55.000 8.47 0.00 0.00 4.04
5579 6071 0.242825 TGTTTACACGAGCTCCCGAG 59.757 55.000 8.47 0.00 0.00 4.63
5580 6072 0.892755 ATGTTTACACGAGCTCCCGA 59.107 50.000 8.47 0.00 0.00 5.14
5581 6073 2.190981 GTATGTTTACACGAGCTCCCG 58.809 52.381 8.47 0.00 0.00 5.14
5582 6074 2.190981 CGTATGTTTACACGAGCTCCC 58.809 52.381 8.47 0.00 40.56 4.30
5583 6075 2.159338 TCCGTATGTTTACACGAGCTCC 60.159 50.000 8.47 0.00 40.56 4.70
5585 6077 2.730090 CGTCCGTATGTTTACACGAGCT 60.730 50.000 0.00 0.00 40.56 4.09
5586 6078 1.580704 CGTCCGTATGTTTACACGAGC 59.419 52.381 0.00 0.00 40.56 5.03
5587 6079 3.096461 CTCGTCCGTATGTTTACACGAG 58.904 50.000 5.03 5.03 42.92 4.18
5588 6080 2.159531 CCTCGTCCGTATGTTTACACGA 60.160 50.000 0.00 0.00 40.56 4.35
5609 6106 1.852280 GCAGCGTCCTTTTTGACAAAC 59.148 47.619 0.00 0.00 34.88 2.93
5622 6119 2.945398 GATCGGAGACCAGCAGCGTC 62.945 65.000 0.00 0.00 42.51 5.19
5623 6120 3.069980 GATCGGAGACCAGCAGCGT 62.070 63.158 0.00 0.00 42.51 5.07
5624 6121 2.279120 GATCGGAGACCAGCAGCG 60.279 66.667 0.00 0.00 42.51 5.18
5668 6174 1.874231 GAGACTGATCATGGCAGCATG 59.126 52.381 14.02 0.00 36.86 4.06
5669 6175 1.769465 AGAGACTGATCATGGCAGCAT 59.231 47.619 14.02 5.46 36.86 3.79
5670 6176 1.138464 GAGAGACTGATCATGGCAGCA 59.862 52.381 14.02 0.00 36.86 4.41
5671 6177 1.138464 TGAGAGACTGATCATGGCAGC 59.862 52.381 14.02 8.68 36.86 5.25
5672 6178 2.798853 CGTGAGAGACTGATCATGGCAG 60.799 54.545 12.92 12.92 39.26 4.85
5691 6197 4.467107 GGAGGGAGGGAGGCTCGT 62.467 72.222 8.69 0.00 0.00 4.18
5709 6221 1.817941 ATCCATGCCGTGCCGTAAC 60.818 57.895 0.00 0.00 0.00 2.50
5710 6222 1.817520 CATCCATGCCGTGCCGTAA 60.818 57.895 0.00 0.00 0.00 3.18
5747 6259 0.317160 TCTCCGTTAGCAGTGTGGTG 59.683 55.000 0.00 0.00 0.00 4.17
5748 6260 0.317479 GTCTCCGTTAGCAGTGTGGT 59.683 55.000 0.00 0.00 0.00 4.16
5749 6261 0.732880 CGTCTCCGTTAGCAGTGTGG 60.733 60.000 0.00 0.00 0.00 4.17
5750 6262 0.240145 TCGTCTCCGTTAGCAGTGTG 59.760 55.000 0.00 0.00 35.01 3.82
5751 6263 0.240411 GTCGTCTCCGTTAGCAGTGT 59.760 55.000 0.00 0.00 35.01 3.55
5755 6267 0.038892 GTTGGTCGTCTCCGTTAGCA 60.039 55.000 0.00 0.00 35.01 3.49
5756 6268 0.735287 GGTTGGTCGTCTCCGTTAGC 60.735 60.000 0.00 0.00 35.01 3.09
5758 6270 0.827089 TGGGTTGGTCGTCTCCGTTA 60.827 55.000 0.00 0.00 35.01 3.18
5866 6409 5.460091 TGAGTACTGTAGTAGCACGTATACG 59.540 44.000 23.24 23.24 46.33 3.06
5868 6411 5.464722 GCTGAGTACTGTAGTAGCACGTATA 59.535 44.000 0.00 0.00 0.00 1.47
5869 6412 4.272991 GCTGAGTACTGTAGTAGCACGTAT 59.727 45.833 0.00 0.00 0.00 3.06
5870 6413 3.620374 GCTGAGTACTGTAGTAGCACGTA 59.380 47.826 0.00 0.00 0.00 3.57
5871 6414 2.419324 GCTGAGTACTGTAGTAGCACGT 59.581 50.000 0.00 0.00 0.00 4.49
5873 6416 4.096532 TCATGCTGAGTACTGTAGTAGCAC 59.903 45.833 19.56 0.11 33.04 4.40
5874 6417 4.270008 TCATGCTGAGTACTGTAGTAGCA 58.730 43.478 19.50 19.50 34.17 3.49
5876 6419 5.126779 TCCTCATGCTGAGTACTGTAGTAG 58.873 45.833 0.00 0.00 42.80 2.57
5877 6420 5.112129 TCCTCATGCTGAGTACTGTAGTA 57.888 43.478 0.00 0.00 42.80 1.82
5878 6421 3.969553 TCCTCATGCTGAGTACTGTAGT 58.030 45.455 0.00 0.00 42.80 2.73
5879 6422 4.991153 TTCCTCATGCTGAGTACTGTAG 57.009 45.455 0.00 0.00 42.80 2.74
5880 6423 5.479306 GTTTTCCTCATGCTGAGTACTGTA 58.521 41.667 0.00 0.00 42.80 2.74
5881 6424 4.319177 GTTTTCCTCATGCTGAGTACTGT 58.681 43.478 0.00 0.00 42.80 3.55
5882 6425 3.369147 CGTTTTCCTCATGCTGAGTACTG 59.631 47.826 0.00 0.00 42.80 2.74
5883 6426 3.258372 TCGTTTTCCTCATGCTGAGTACT 59.742 43.478 0.00 0.00 42.80 2.73
5884 6427 3.585862 TCGTTTTCCTCATGCTGAGTAC 58.414 45.455 10.86 0.00 42.80 2.73
5885 6428 3.849911 CTCGTTTTCCTCATGCTGAGTA 58.150 45.455 10.86 0.00 42.80 2.59
5886 6429 2.693069 CTCGTTTTCCTCATGCTGAGT 58.307 47.619 10.86 0.00 42.80 3.41
5887 6430 1.396301 GCTCGTTTTCCTCATGCTGAG 59.604 52.381 6.28 6.28 43.91 3.35
5888 6431 1.002430 AGCTCGTTTTCCTCATGCTGA 59.998 47.619 0.00 0.00 0.00 4.26
5889 6432 1.396301 GAGCTCGTTTTCCTCATGCTG 59.604 52.381 0.00 0.00 0.00 4.41
5952 6496 4.700365 GCAGTTTGGTTCGCCGGC 62.700 66.667 19.07 19.07 41.18 6.13
6056 6600 2.040606 TACCCCTCACTCCCTGCC 59.959 66.667 0.00 0.00 0.00 4.85
6061 6605 0.106819 TAGTCGCTACCCCTCACTCC 60.107 60.000 0.00 0.00 0.00 3.85
6062 6606 1.310904 CTAGTCGCTACCCCTCACTC 58.689 60.000 0.00 0.00 0.00 3.51
6063 6607 0.752376 GCTAGTCGCTACCCCTCACT 60.752 60.000 0.00 0.00 35.14 3.41
6064 6608 1.734748 GCTAGTCGCTACCCCTCAC 59.265 63.158 0.00 0.00 35.14 3.51
6065 6609 1.822613 CGCTAGTCGCTACCCCTCA 60.823 63.158 0.00 0.00 36.13 3.86
6066 6610 0.533755 TACGCTAGTCGCTACCCCTC 60.534 60.000 6.50 0.00 43.23 4.30
6084 6628 4.260538 GCTTTTACTACTACTCGCTCGCTA 60.261 45.833 0.00 0.00 0.00 4.26
6085 6629 3.487209 GCTTTTACTACTACTCGCTCGCT 60.487 47.826 0.00 0.00 0.00 4.93
6086 6630 2.782738 GCTTTTACTACTACTCGCTCGC 59.217 50.000 0.00 0.00 0.00 5.03
6087 6631 3.027710 CGCTTTTACTACTACTCGCTCG 58.972 50.000 0.00 0.00 0.00 5.03
6088 6632 4.270178 TCGCTTTTACTACTACTCGCTC 57.730 45.455 0.00 0.00 0.00 5.03
6089 6633 3.065095 CCTCGCTTTTACTACTACTCGCT 59.935 47.826 0.00 0.00 0.00 4.93
6090 6634 3.361414 CCTCGCTTTTACTACTACTCGC 58.639 50.000 0.00 0.00 0.00 5.03
6091 6635 3.065095 AGCCTCGCTTTTACTACTACTCG 59.935 47.826 0.00 0.00 33.89 4.18


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

AutoCloner maintained by Alex Coulton.