Multiple sequence alignment - TraesCS4B01G073900

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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 TraesCS4B01G073900 chr4B 100.000 5431 0 0 1001 6431 69312036 69306606 0.000000e+00 10030.0
1 TraesCS4B01G073900 chr4B 100.000 2852 0 0 6882 9733 69306155 69303304 0.000000e+00 5267.0
2 TraesCS4B01G073900 chr4B 86.359 1041 103 21 2795 3826 115400100 115401110 0.000000e+00 1099.0
3 TraesCS4B01G073900 chr4B 100.000 487 0 0 1 487 69313036 69312550 0.000000e+00 900.0
4 TraesCS4B01G073900 chr4B 89.286 140 14 1 2800 2938 12891364 12891225 3.610000e-39 174.0
5 TraesCS4B01G073900 chr4A 95.424 5463 173 33 1001 6431 550500838 550506255 0.000000e+00 8632.0
6 TraesCS4B01G073900 chr4A 93.237 2410 87 34 6897 9266 550507146 550509519 0.000000e+00 3478.0
7 TraesCS4B01G073900 chr4A 88.873 1393 80 28 7899 9262 550291662 550293008 0.000000e+00 1644.0
8 TraesCS4B01G073900 chr4A 94.676 432 22 1 3 434 550500163 550500593 0.000000e+00 669.0
9 TraesCS4B01G073900 chr4A 92.806 278 20 0 9376 9653 550293009 550293286 4.230000e-108 403.0
10 TraesCS4B01G073900 chr4A 94.052 269 11 2 9377 9645 550509517 550509780 4.230000e-108 403.0
11 TraesCS4B01G073900 chr4D 97.222 4680 110 12 1702 6372 47492594 47487926 0.000000e+00 7904.0
12 TraesCS4B01G073900 chr4D 94.014 2205 77 23 6901 9069 47486835 47484650 0.000000e+00 3290.0
13 TraesCS4B01G073900 chr4D 90.141 710 46 14 1001 1694 47493586 47492885 0.000000e+00 902.0
14 TraesCS4B01G073900 chr4D 94.274 489 12 3 1 487 47494264 47493790 0.000000e+00 734.0
15 TraesCS4B01G073900 chr4D 92.905 296 21 0 9382 9677 47484184 47483889 1.940000e-116 431.0
16 TraesCS4B01G073900 chr4D 93.985 133 5 3 9128 9258 47484318 47484187 2.140000e-46 198.0
17 TraesCS4B01G073900 chr5D 86.556 900 91 17 2869 3759 432447408 432448286 0.000000e+00 965.0
18 TraesCS4B01G073900 chr1A 89.083 458 43 5 2861 3311 137737815 137738272 6.600000e-156 562.0
19 TraesCS4B01G073900 chr1A 84.879 496 57 10 3344 3826 137738273 137738763 1.470000e-132 484.0
20 TraesCS4B01G073900 chr3A 81.900 558 75 16 4085 4630 712625687 712626230 1.930000e-121 448.0
21 TraesCS4B01G073900 chr3A 88.889 117 12 1 3964 4080 712625501 712625616 1.020000e-29 143.0
22 TraesCS4B01G073900 chr3A 81.529 157 24 4 8871 9025 104424104 104423951 3.690000e-24 124.0
23 TraesCS4B01G073900 chr7A 81.688 557 76 15 4085 4629 134554109 134554651 3.230000e-119 440.0
24 TraesCS4B01G073900 chr7A 89.744 117 11 1 3964 4080 134553923 134554038 2.190000e-31 148.0
25 TraesCS4B01G073900 chrUn 87.701 187 22 1 1964 2149 136403740 136403926 5.920000e-52 217.0
26 TraesCS4B01G073900 chrUn 82.283 254 35 7 1668 1920 136395341 136395585 2.750000e-50 211.0
27 TraesCS4B01G073900 chr3D 79.621 211 29 11 8805 9012 87938354 87938155 1.320000e-28 139.0
28 TraesCS4B01G073900 chr6B 79.512 205 33 8 8834 9034 481851385 481851584 4.740000e-28 137.0
29 TraesCS4B01G073900 chr6B 84.058 138 16 5 8879 9014 146135484 146135617 2.850000e-25 128.0
30 TraesCS4B01G073900 chr3B 83.333 144 20 3 8871 9012 137330097 137329956 7.930000e-26 130.0
31 TraesCS4B01G073900 chr3B 78.689 183 32 5 8840 9019 71815694 71815516 2.220000e-21 115.0
32 TraesCS4B01G073900 chr5A 91.525 59 0 3 9264 9321 3435906 3435852 1.050000e-09 76.8
33 TraesCS4B01G073900 chr2B 86.111 72 5 4 9253 9321 13019770 13019839 1.360000e-08 73.1
34 TraesCS4B01G073900 chr2B 95.652 46 1 1 9256 9301 386286324 386286368 1.360000e-08 73.1
35 TraesCS4B01G073900 chr2A 87.879 66 2 5 9257 9321 608930259 608930319 1.360000e-08 73.1
36 TraesCS4B01G073900 chr2A 85.484 62 8 1 9238 9298 39602353 39602292 8.160000e-06 63.9
37 TraesCS4B01G073900 chr7B 87.097 62 6 1 9250 9309 566635057 566634996 1.750000e-07 69.4
38 TraesCS4B01G073900 chr6D 87.097 62 5 2 9263 9321 95288745 95288684 6.310000e-07 67.6
39 TraesCS4B01G073900 chr1D 85.294 68 5 3 9258 9321 467003867 467003933 2.270000e-06 65.8
40 TraesCS4B01G073900 chr7D 84.375 64 6 3 9258 9321 76953577 76953636 1.060000e-04 60.2


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 TraesCS4B01G073900 chr4B 69303304 69313036 9732 True 5399.000000 10030 100.000000 1 9733 3 chr4B.!!$R2 9732
1 TraesCS4B01G073900 chr4B 115400100 115401110 1010 False 1099.000000 1099 86.359000 2795 3826 1 chr4B.!!$F1 1031
2 TraesCS4B01G073900 chr4A 550500163 550509780 9617 False 3295.500000 8632 94.347250 3 9645 4 chr4A.!!$F2 9642
3 TraesCS4B01G073900 chr4A 550291662 550293286 1624 False 1023.500000 1644 90.839500 7899 9653 2 chr4A.!!$F1 1754
4 TraesCS4B01G073900 chr4D 47483889 47494264 10375 True 2243.166667 7904 93.756833 1 9677 6 chr4D.!!$R1 9676
5 TraesCS4B01G073900 chr5D 432447408 432448286 878 False 965.000000 965 86.556000 2869 3759 1 chr5D.!!$F1 890
6 TraesCS4B01G073900 chr1A 137737815 137738763 948 False 523.000000 562 86.981000 2861 3826 2 chr1A.!!$F1 965
7 TraesCS4B01G073900 chr3A 712625501 712626230 729 False 295.500000 448 85.394500 3964 4630 2 chr3A.!!$F1 666
8 TraesCS4B01G073900 chr7A 134553923 134554651 728 False 294.000000 440 85.716000 3964 4629 2 chr7A.!!$F1 665

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
448 451 0.876342 GGGCCGCGAACTAATCTCAG 60.876 60.000 8.23 0.00 0.00 3.35 F
1024 1027 0.537600 TCAGGATCCGGATCGACCTC 60.538 60.000 32.72 20.87 38.69 3.85 F
1576 1592 1.069227 AGCGATTTTGGCTCGTGTTTC 60.069 47.619 0.00 0.00 35.37 2.78 F
3255 3569 3.303229 GTCTTGCCAACACAAAAACGAAG 59.697 43.478 0.00 0.00 0.00 3.79 F
3689 4017 2.949644 ACAGTTTGGACCAGTGCTTAAC 59.050 45.455 0.00 0.00 0.00 2.01 F
4126 4520 0.320946 GTAGTAGGTTTGTGCGGGCA 60.321 55.000 0.00 0.00 0.00 5.36 F
5341 5746 0.463474 CTCCAAGCCAGCTTCTAGCC 60.463 60.000 0.90 0.00 43.77 3.93 F
7058 8110 0.104409 AAGGCGAAGGGATAGGGGAT 60.104 55.000 0.00 0.00 0.00 3.85 F
7133 8185 0.536006 GGGTATGCAGGTGGATGAGC 60.536 60.000 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1278 0.676782 CAACCGGGGCTTACCAAGAG 60.677 60.000 6.32 0.00 42.91 2.85 R
2783 3090 1.495878 CATCGCACATGAGGACTAGC 58.504 55.000 0.00 0.00 0.00 3.42 R
3263 3577 0.978146 AGGACTCTGGGATGGGAACG 60.978 60.000 0.00 0.00 0.00 3.95 R
4117 4511 0.893270 AGTTTGCTATTGCCCGCACA 60.893 50.000 0.00 0.00 38.71 4.57 R
4943 5348 1.129811 GAATTAGCAAACCCACGGACG 59.870 52.381 0.00 0.00 0.00 4.79 R
5732 6137 0.532115 GCCCTCGTCCATGCAAAAAT 59.468 50.000 0.00 0.00 0.00 1.82 R
7133 8185 1.301716 CTCCAACGGTCCACACCAG 60.302 63.158 0.00 0.00 44.02 4.00 R
8623 9715 0.391927 TAGGGTTGCACGTGCCATAC 60.392 55.000 35.72 27.87 41.18 2.39 R
8930 10024 3.102204 TCTCAGTCTCATCCTTCATGCA 58.898 45.455 0.00 0.00 31.70 3.96 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
390 393 4.409218 TGTGGCTCGTACGCGGTC 62.409 66.667 12.47 8.04 38.89 4.79
421 424 5.232414 GTCAACGACAGTGAATAATAGCTCC 59.768 44.000 0.00 0.00 32.09 4.70
422 425 3.966154 ACGACAGTGAATAATAGCTCCG 58.034 45.455 0.00 0.00 0.00 4.63
444 447 2.965462 CCGGGCCGCGAACTAATC 60.965 66.667 23.20 0.00 0.00 1.75
445 448 2.106332 CGGGCCGCGAACTAATCT 59.894 61.111 15.42 0.00 0.00 2.40
446 449 1.949631 CGGGCCGCGAACTAATCTC 60.950 63.158 15.42 0.00 0.00 2.75
447 450 1.143183 GGGCCGCGAACTAATCTCA 59.857 57.895 8.23 0.00 0.00 3.27
448 451 0.876342 GGGCCGCGAACTAATCTCAG 60.876 60.000 8.23 0.00 0.00 3.35
1020 1023 1.257743 GGATTCAGGATCCGGATCGA 58.742 55.000 32.72 24.04 44.73 3.59
1024 1027 0.537600 TCAGGATCCGGATCGACCTC 60.538 60.000 32.72 20.87 38.69 3.85
1064 1067 3.260100 CAGCACCCACTCCCCCTT 61.260 66.667 0.00 0.00 0.00 3.95
1085 1088 3.338249 TGCTGAATTCTTGACCAGTAGC 58.662 45.455 7.05 4.48 0.00 3.58
1116 1119 2.125673 TTCTTGGCGGTAGAGCGC 60.126 61.111 17.24 17.24 38.18 5.92
1128 1131 1.529152 TAGAGCGCAGTTCCGTTCCA 61.529 55.000 11.47 0.00 39.04 3.53
1129 1132 1.959226 GAGCGCAGTTCCGTTCCAA 60.959 57.895 11.47 0.00 33.19 3.53
1136 1139 2.268298 CAGTTCCGTTCCAATAGTCGG 58.732 52.381 0.00 0.00 43.65 4.79
1187 1190 5.513376 TGACATGCGATTCTGATAAATTGC 58.487 37.500 0.00 2.55 43.51 3.56
1371 1383 1.808945 CTCTGTGCTTTGCCTCGATTT 59.191 47.619 0.00 0.00 0.00 2.17
1372 1384 3.002791 CTCTGTGCTTTGCCTCGATTTA 58.997 45.455 0.00 0.00 0.00 1.40
1373 1385 3.002791 TCTGTGCTTTGCCTCGATTTAG 58.997 45.455 0.00 0.00 0.00 1.85
1374 1386 3.002791 CTGTGCTTTGCCTCGATTTAGA 58.997 45.455 0.00 0.00 0.00 2.10
1376 1388 4.009675 TGTGCTTTGCCTCGATTTAGATT 58.990 39.130 0.00 0.00 0.00 2.40
1377 1389 5.182487 TGTGCTTTGCCTCGATTTAGATTA 58.818 37.500 0.00 0.00 0.00 1.75
1378 1390 5.064707 TGTGCTTTGCCTCGATTTAGATTAC 59.935 40.000 0.00 0.00 0.00 1.89
1379 1391 5.294552 GTGCTTTGCCTCGATTTAGATTACT 59.705 40.000 0.00 0.00 0.00 2.24
1380 1392 5.294306 TGCTTTGCCTCGATTTAGATTACTG 59.706 40.000 0.00 0.00 0.00 2.74
1433 1445 9.585099 TTTTTAGTCAAGTTTAACGAGTCTGTA 57.415 29.630 0.00 0.00 0.00 2.74
1464 1476 3.129638 TGCCACCTCTGTTTTGTTTGTAC 59.870 43.478 0.00 0.00 0.00 2.90
1465 1477 3.490249 GCCACCTCTGTTTTGTTTGTACC 60.490 47.826 0.00 0.00 0.00 3.34
1493 1509 8.292444 TCATTTAATAGGGTGGAAATGAACAG 57.708 34.615 6.45 0.00 42.41 3.16
1509 1525 4.353777 TGAACAGTTAGGAGGCATAGACT 58.646 43.478 0.00 0.00 0.00 3.24
1510 1526 5.516044 TGAACAGTTAGGAGGCATAGACTA 58.484 41.667 0.00 0.00 0.00 2.59
1566 1582 8.076178 CCCTTGTAATAAATCTAGCGATTTTGG 58.924 37.037 5.11 0.00 45.18 3.28
1576 1592 1.069227 AGCGATTTTGGCTCGTGTTTC 60.069 47.619 0.00 0.00 35.37 2.78
1594 1610 6.461698 CGTGTTTCGTTACTAGAATGAAATGC 59.538 38.462 17.59 14.04 37.45 3.56
1925 2229 5.907207 TCTAGCTGTAGATGGAAATCACAC 58.093 41.667 0.00 0.00 29.69 3.82
2051 2355 6.038603 TGAATTCAACATCTTGTAGCTATGCC 59.961 38.462 5.45 0.00 0.00 4.40
2074 2378 6.321181 GCCATCTATGTCATCCTTTTTGGTAA 59.679 38.462 0.00 0.00 37.07 2.85
2133 2437 9.388506 CTGCATAAGGAAAATATACTATCCAGG 57.611 37.037 0.00 0.00 34.30 4.45
2469 2775 6.811253 TCCTTCCACACACATATTTGTTAC 57.189 37.500 0.00 0.00 32.34 2.50
2728 3034 3.996150 ACAGAGAAATGGTTTGCTGTG 57.004 42.857 0.00 0.00 35.11 3.66
2783 3090 4.085312 CCACAAACAAAATTCGCGTAAAGG 60.085 41.667 5.77 0.00 0.00 3.11
3255 3569 3.303229 GTCTTGCCAACACAAAAACGAAG 59.697 43.478 0.00 0.00 0.00 3.79
3263 3577 5.173131 CCAACACAAAAACGAAGCATCTAAC 59.827 40.000 0.00 0.00 0.00 2.34
3337 3652 8.040727 TGCTATAGTTATAATGTGGGTGCTATG 58.959 37.037 0.84 0.00 0.00 2.23
3387 3702 8.056571 GTCATAGTTTCAGTATATTTCACGCAC 58.943 37.037 0.00 0.00 0.00 5.34
3689 4017 2.949644 ACAGTTTGGACCAGTGCTTAAC 59.050 45.455 0.00 0.00 0.00 2.01
3986 4314 9.480053 AATTGCAATTATATGATGTTAACCAGC 57.520 29.630 22.95 0.00 0.00 4.85
4045 4374 5.705609 ATTTGTATTGTCCCTGTGTCAAC 57.294 39.130 0.00 0.00 0.00 3.18
4117 4511 5.723355 TGATATAGGGGCTGTAGTAGGTTT 58.277 41.667 0.00 0.00 0.00 3.27
4126 4520 0.320946 GTAGTAGGTTTGTGCGGGCA 60.321 55.000 0.00 0.00 0.00 5.36
4239 4635 5.421056 ACAAATAGAACTATGTCGGTGAGGA 59.579 40.000 0.00 0.00 0.00 3.71
4294 4690 9.658799 TCTTTTGTTTTGGTCAATTAATTGTCA 57.341 25.926 23.95 19.96 38.84 3.58
4299 4695 9.442047 TGTTTTGGTCAATTAATTGTCAAGTTT 57.558 25.926 23.95 0.00 38.84 2.66
4334 4730 0.609151 TTCTGCCACATGCCAAATGG 59.391 50.000 0.00 0.00 40.16 3.16
4521 4918 6.344500 TCCTTAGATTCTGCTTGAGATGTTC 58.656 40.000 0.00 0.00 0.00 3.18
4602 5006 5.411361 TGTGTACTGTTACATCAAATCTGGC 59.589 40.000 0.00 0.00 40.40 4.85
4671 5076 2.530701 GAGTGGTCTTCCTCTCCAGAA 58.469 52.381 5.38 0.00 44.16 3.02
5060 5465 7.761249 CCTTTCAGTTGAATGAAGTTTTGTTCT 59.239 33.333 8.76 0.00 40.16 3.01
5070 5475 6.223138 TGAAGTTTTGTTCTGTATAGTGCG 57.777 37.500 0.00 0.00 0.00 5.34
5076 5481 4.983671 TGTTCTGTATAGTGCGTGAGAT 57.016 40.909 0.00 0.00 0.00 2.75
5084 5489 2.861462 AGTGCGTGAGATAGAGAAGC 57.139 50.000 0.00 0.00 0.00 3.86
5341 5746 0.463474 CTCCAAGCCAGCTTCTAGCC 60.463 60.000 0.90 0.00 43.77 3.93
5646 6051 6.428159 CCTGCACCTATGGACATATTTAGAAC 59.572 42.308 0.00 0.00 0.00 3.01
5732 6137 4.654262 AGGGACTTAACTCACAGTCTTCAA 59.346 41.667 0.00 0.00 39.61 2.69
5820 6225 7.200434 ACTTGCCTCCTAGATTGAAATCTAA 57.800 36.000 12.58 0.74 44.82 2.10
5974 6380 9.283768 CATTGATAGCTGTGTATAAATACCCAA 57.716 33.333 0.00 0.00 32.33 4.12
5993 6399 7.520451 ACCCAACAAAGAGAGTAAATAAACC 57.480 36.000 0.00 0.00 0.00 3.27
6003 6409 3.621558 AGTAAATAAACCAGGGCAGAGC 58.378 45.455 0.00 0.00 0.00 4.09
6065 6471 5.922544 AGGAAGAAAAATTGAAATGCTCACG 59.077 36.000 0.00 0.00 32.21 4.35
6314 6724 2.872842 GCATTTTTGCTGTGGCTTGGAT 60.873 45.455 0.00 0.00 39.59 3.41
7058 8110 0.104409 AAGGCGAAGGGATAGGGGAT 60.104 55.000 0.00 0.00 0.00 3.85
7133 8185 0.536006 GGGTATGCAGGTGGATGAGC 60.536 60.000 0.00 0.00 0.00 4.26
7324 8380 6.460781 TGTGTACCATTTTGAAGATCTACGT 58.539 36.000 0.00 0.00 0.00 3.57
7328 8384 4.631813 ACCATTTTGAAGATCTACGTGAGC 59.368 41.667 0.00 0.00 0.00 4.26
7424 8481 4.310769 CAGGACTTGCACTATATAGGCAC 58.689 47.826 19.41 11.74 37.26 5.01
7709 8767 9.126151 TGATGTAAACTTGAATAAGGTGTTTCA 57.874 29.630 0.00 0.00 38.26 2.69
7908 8967 5.241403 TCTGGAAACCACATTGTATGAGT 57.759 39.130 0.00 0.00 0.00 3.41
8227 9286 4.811024 GGATTGATCGTGATTGCAGAGTAA 59.189 41.667 0.00 0.00 0.00 2.24
8375 9435 4.033776 CTTGAGAAGGCGGCCCCA 62.034 66.667 17.02 6.15 35.39 4.96
8604 9696 6.735130 ACAAACTGAGGTGTTAAATTACAGC 58.265 36.000 2.91 2.91 44.66 4.40
8728 9820 1.404843 AGTATCTCGTCCTTGGGAGC 58.595 55.000 0.00 0.00 29.39 4.70
8830 9922 3.181520 CGGTTCAAAAGAATAGTGGAGCG 60.182 47.826 0.00 0.00 35.65 5.03
8873 9965 6.038161 GGAGATTTTTCCTTGGTTTTGGTTTG 59.962 38.462 0.00 0.00 34.27 2.93
8927 10021 7.751646 TCACTTGGACCTCTTTTAATTTCCTA 58.248 34.615 0.00 0.00 0.00 2.94
8928 10022 8.390921 TCACTTGGACCTCTTTTAATTTCCTAT 58.609 33.333 0.00 0.00 0.00 2.57
8946 10040 6.291648 TCCTATATGCATGAAGGATGAGAC 57.708 41.667 21.72 0.00 33.18 3.36
9065 10159 6.122277 TCCTATGTTTCTCCATCCATTGTTC 58.878 40.000 0.00 0.00 0.00 3.18
9095 10189 4.020039 TGCATTCCAATCCAATTTCTGCTT 60.020 37.500 0.00 0.00 0.00 3.91
9101 10199 6.009589 TCCAATCCAATTTCTGCTTCTTGTA 58.990 36.000 0.00 0.00 0.00 2.41
9229 10596 8.936787 TGGGATATTAATTCTACCGTAAAAGGA 58.063 33.333 0.00 0.00 34.73 3.36
9270 10639 9.790297 ATTATAGACAATATGATGGTACTCCCT 57.210 33.333 0.00 0.00 0.00 4.20
9271 10640 7.726033 ATAGACAATATGATGGTACTCCCTC 57.274 40.000 0.00 0.00 0.00 4.30
9272 10641 5.721225 AGACAATATGATGGTACTCCCTCT 58.279 41.667 0.00 0.00 31.14 3.69
9273 10642 5.541868 AGACAATATGATGGTACTCCCTCTG 59.458 44.000 0.00 0.00 31.14 3.35
9274 10643 5.219739 ACAATATGATGGTACTCCCTCTGT 58.780 41.667 0.00 0.00 31.14 3.41
9275 10644 6.382087 ACAATATGATGGTACTCCCTCTGTA 58.618 40.000 0.00 0.00 31.14 2.74
9276 10645 6.844388 ACAATATGATGGTACTCCCTCTGTAA 59.156 38.462 0.00 0.00 31.14 2.41
9277 10646 7.347222 ACAATATGATGGTACTCCCTCTGTAAA 59.653 37.037 0.00 0.00 31.14 2.01
9278 10647 5.878406 ATGATGGTACTCCCTCTGTAAAG 57.122 43.478 0.00 0.00 31.14 1.85
9279 10648 4.942944 TGATGGTACTCCCTCTGTAAAGA 58.057 43.478 0.00 0.00 31.14 2.52
9280 10649 5.338632 TGATGGTACTCCCTCTGTAAAGAA 58.661 41.667 0.00 0.00 31.14 2.52
9281 10650 5.783360 TGATGGTACTCCCTCTGTAAAGAAA 59.217 40.000 0.00 0.00 31.14 2.52
9282 10651 6.443849 TGATGGTACTCCCTCTGTAAAGAAAT 59.556 38.462 0.00 0.00 31.14 2.17
9283 10652 7.622081 TGATGGTACTCCCTCTGTAAAGAAATA 59.378 37.037 0.00 0.00 31.14 1.40
9284 10653 7.989947 TGGTACTCCCTCTGTAAAGAAATAT 57.010 36.000 0.00 0.00 0.00 1.28
9285 10654 9.670442 ATGGTACTCCCTCTGTAAAGAAATATA 57.330 33.333 0.00 0.00 0.00 0.86
9286 10655 9.496710 TGGTACTCCCTCTGTAAAGAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
9290 10659 9.397280 ACTCCCTCTGTAAAGAAATATAAAAGC 57.603 33.333 0.00 0.00 0.00 3.51
9291 10660 8.433421 TCCCTCTGTAAAGAAATATAAAAGCG 57.567 34.615 0.00 0.00 0.00 4.68
9292 10661 8.044908 TCCCTCTGTAAAGAAATATAAAAGCGT 58.955 33.333 0.00 0.00 0.00 5.07
9293 10662 8.122952 CCCTCTGTAAAGAAATATAAAAGCGTG 58.877 37.037 0.00 0.00 0.00 5.34
9294 10663 8.665685 CCTCTGTAAAGAAATATAAAAGCGTGT 58.334 33.333 0.00 0.00 0.00 4.49
9305 10674 9.450807 AAATATAAAAGCGTGTAGATCAAATGC 57.549 29.630 0.00 0.00 0.00 3.56
9306 10675 6.683974 ATAAAAGCGTGTAGATCAAATGCT 57.316 33.333 0.00 0.00 34.36 3.79
9307 10676 4.606457 AAAGCGTGTAGATCAAATGCTC 57.394 40.909 8.83 0.00 32.66 4.26
9308 10677 3.533606 AGCGTGTAGATCAAATGCTCT 57.466 42.857 0.00 0.00 29.44 4.09
9309 10678 3.866651 AGCGTGTAGATCAAATGCTCTT 58.133 40.909 0.00 0.00 29.44 2.85
9310 10679 5.011090 AGCGTGTAGATCAAATGCTCTTA 57.989 39.130 0.00 0.00 29.44 2.10
9311 10680 5.605534 AGCGTGTAGATCAAATGCTCTTAT 58.394 37.500 0.00 0.00 29.44 1.73
9312 10681 6.749139 AGCGTGTAGATCAAATGCTCTTATA 58.251 36.000 0.00 0.00 29.44 0.98
9313 10682 7.382110 AGCGTGTAGATCAAATGCTCTTATAT 58.618 34.615 0.00 0.00 29.44 0.86
9314 10683 7.875041 AGCGTGTAGATCAAATGCTCTTATATT 59.125 33.333 0.00 0.00 29.44 1.28
9315 10684 8.499162 GCGTGTAGATCAAATGCTCTTATATTT 58.501 33.333 0.00 0.00 0.00 1.40
9374 10743 8.934973 ATATAAGAGCGTTTGATTTAAATCGC 57.065 30.769 20.45 19.63 43.04 4.58
9375 10744 4.678509 AGAGCGTTTGATTTAAATCGCA 57.321 36.364 24.84 13.02 44.05 5.10
9380 10749 5.737290 AGCGTTTGATTTAAATCGCATACAC 59.263 36.000 24.84 13.98 44.05 2.90
9395 10764 9.555727 AATCGCATACACCTTATATACTTTTGT 57.444 29.630 0.00 0.00 0.00 2.83
9396 10765 8.583810 TCGCATACACCTTATATACTTTTGTC 57.416 34.615 0.00 0.00 0.00 3.18
9419 10788 5.939883 TCCTGAACAATTGATGGTTGTAGAG 59.060 40.000 13.59 0.00 38.76 2.43
9430 10799 6.366340 TGATGGTTGTAGAGGTTTTTGGTTA 58.634 36.000 0.00 0.00 0.00 2.85
9475 10844 2.851195 GGGACCAGACGATGCAAATAT 58.149 47.619 0.00 0.00 0.00 1.28
9518 10887 6.369065 CGTGGTTATCTAAGCAAAGTTCTCTT 59.631 38.462 3.59 0.00 44.15 2.85
9581 10950 1.067565 GCCTAACTGCTTTGGCTTTCC 60.068 52.381 4.30 0.00 42.99 3.13
9657 11026 0.819259 ACATGGTTGCAGTTGCGTCT 60.819 50.000 0.00 0.00 45.83 4.18
9667 11036 3.259064 GCAGTTGCGTCTAGGTTATTGA 58.741 45.455 0.00 0.00 0.00 2.57
9677 11046 0.108329 AGGTTATTGACGGTGGAGCG 60.108 55.000 0.00 0.00 0.00 5.03
9678 11047 0.390735 GGTTATTGACGGTGGAGCGT 60.391 55.000 3.09 3.09 0.00 5.07
9679 11048 1.135024 GGTTATTGACGGTGGAGCGTA 60.135 52.381 3.51 0.00 0.00 4.42
9680 11049 2.482490 GGTTATTGACGGTGGAGCGTAT 60.482 50.000 3.51 0.00 0.00 3.06
9681 11050 3.243501 GGTTATTGACGGTGGAGCGTATA 60.244 47.826 3.51 0.00 0.00 1.47
9682 11051 4.362279 GTTATTGACGGTGGAGCGTATAA 58.638 43.478 3.51 3.57 0.00 0.98
9683 11052 3.746045 ATTGACGGTGGAGCGTATAAT 57.254 42.857 3.51 5.82 0.00 1.28
9684 11053 2.502213 TGACGGTGGAGCGTATAATG 57.498 50.000 3.51 0.00 0.00 1.90
9685 11054 2.025898 TGACGGTGGAGCGTATAATGA 58.974 47.619 3.51 0.00 0.00 2.57
9686 11055 2.034179 TGACGGTGGAGCGTATAATGAG 59.966 50.000 3.51 0.00 0.00 2.90
9687 11056 2.292569 GACGGTGGAGCGTATAATGAGA 59.707 50.000 3.51 0.00 0.00 3.27
9688 11057 2.691526 ACGGTGGAGCGTATAATGAGAA 59.308 45.455 1.31 0.00 0.00 2.87
9689 11058 3.321111 ACGGTGGAGCGTATAATGAGAAT 59.679 43.478 1.31 0.00 0.00 2.40
9690 11059 3.675225 CGGTGGAGCGTATAATGAGAATG 59.325 47.826 0.00 0.00 0.00 2.67
9691 11060 3.433615 GGTGGAGCGTATAATGAGAATGC 59.566 47.826 0.00 0.00 0.00 3.56
9692 11061 4.058124 GTGGAGCGTATAATGAGAATGCA 58.942 43.478 0.00 0.00 0.00 3.96
9693 11062 4.511454 GTGGAGCGTATAATGAGAATGCAA 59.489 41.667 0.00 0.00 0.00 4.08
9694 11063 4.511454 TGGAGCGTATAATGAGAATGCAAC 59.489 41.667 0.00 0.00 0.00 4.17
9695 11064 4.511454 GGAGCGTATAATGAGAATGCAACA 59.489 41.667 0.00 0.00 0.00 3.33
9696 11065 5.180117 GGAGCGTATAATGAGAATGCAACAT 59.820 40.000 0.00 0.00 0.00 2.71
9697 11066 6.368791 GGAGCGTATAATGAGAATGCAACATA 59.631 38.462 0.00 0.00 0.00 2.29
9698 11067 7.356641 AGCGTATAATGAGAATGCAACATAG 57.643 36.000 0.00 0.00 0.00 2.23
9699 11068 7.154656 AGCGTATAATGAGAATGCAACATAGA 58.845 34.615 0.00 0.00 0.00 1.98
9700 11069 7.821359 AGCGTATAATGAGAATGCAACATAGAT 59.179 33.333 0.00 0.00 0.00 1.98
9701 11070 9.087424 GCGTATAATGAGAATGCAACATAGATA 57.913 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 222 2.561467 TATCCACCTCTCCGTGCGGA 62.561 60.000 13.01 13.01 42.90 5.54
233 236 2.639065 GGCAGAAAACGGTGATATCCA 58.361 47.619 0.00 0.00 0.00 3.41
234 237 1.947456 GGGCAGAAAACGGTGATATCC 59.053 52.381 0.00 0.00 0.00 2.59
297 300 4.154347 CTCTGCTCCCACCTCCGC 62.154 72.222 0.00 0.00 0.00 5.54
390 393 2.738521 CTGTCGTTGACCCGCTGG 60.739 66.667 0.00 0.00 37.80 4.85
392 395 2.023414 TTCACTGTCGTTGACCCGCT 62.023 55.000 0.00 0.00 0.00 5.52
434 437 2.259618 TGAACGCTGAGATTAGTTCGC 58.740 47.619 3.29 0.00 44.07 4.70
435 438 3.759418 TCTGAACGCTGAGATTAGTTCG 58.241 45.455 3.29 0.00 44.07 3.95
436 439 5.344066 TCATCTGAACGCTGAGATTAGTTC 58.656 41.667 0.77 0.77 42.19 3.01
437 440 5.330455 TCATCTGAACGCTGAGATTAGTT 57.670 39.130 0.00 0.00 0.00 2.24
438 441 4.991153 TCATCTGAACGCTGAGATTAGT 57.009 40.909 0.00 0.00 0.00 2.24
439 442 5.981915 TGATTCATCTGAACGCTGAGATTAG 59.018 40.000 0.00 0.00 36.80 1.73
440 443 5.906073 TGATTCATCTGAACGCTGAGATTA 58.094 37.500 0.00 0.00 36.80 1.75
441 444 4.763073 TGATTCATCTGAACGCTGAGATT 58.237 39.130 0.00 0.00 36.80 2.40
442 445 4.370049 CTGATTCATCTGAACGCTGAGAT 58.630 43.478 0.00 0.00 36.80 2.75
443 446 3.429960 CCTGATTCATCTGAACGCTGAGA 60.430 47.826 0.00 0.00 36.80 3.27
444 447 2.864946 CCTGATTCATCTGAACGCTGAG 59.135 50.000 0.00 0.00 36.80 3.35
445 448 2.419159 CCCTGATTCATCTGAACGCTGA 60.419 50.000 0.00 0.00 36.80 4.26
446 449 1.938577 CCCTGATTCATCTGAACGCTG 59.061 52.381 0.00 0.00 36.80 5.18
447 450 1.745141 GCCCTGATTCATCTGAACGCT 60.745 52.381 0.00 0.00 36.80 5.07
448 451 0.659957 GCCCTGATTCATCTGAACGC 59.340 55.000 0.00 0.00 36.80 4.84
1011 1014 4.534824 GGGGGAGGTCGATCCGGA 62.535 72.222 6.61 6.61 40.56 5.14
1020 1023 1.151413 TGAAGACTTACAGGGGGAGGT 59.849 52.381 0.00 0.00 0.00 3.85
1024 1027 2.290323 CCAGTTGAAGACTTACAGGGGG 60.290 54.545 0.00 0.00 36.10 5.40
1064 1067 3.008375 AGCTACTGGTCAAGAATTCAGCA 59.992 43.478 8.44 2.18 0.00 4.41
1106 1109 2.579787 CGGAACTGCGCTCTACCG 60.580 66.667 9.73 15.02 34.77 4.02
1116 1119 2.268298 CCGACTATTGGAACGGAACTG 58.732 52.381 0.00 0.00 46.94 3.16
1136 1139 4.654015 TGCAAATTCGCGGTTATTCTAAC 58.346 39.130 6.13 0.00 33.35 2.34
1206 1209 0.038159 ACTCTGTACACGCAGAAGGC 60.038 55.000 0.00 0.00 43.92 4.35
1245 1257 8.470805 CAAGAGATATAGGCAGACGGTATTATT 58.529 37.037 0.00 0.00 0.00 1.40
1246 1258 7.068839 CCAAGAGATATAGGCAGACGGTATTAT 59.931 40.741 0.00 0.00 0.00 1.28
1266 1278 0.676782 CAACCGGGGCTTACCAAGAG 60.677 60.000 6.32 0.00 42.91 2.85
1371 1383 7.071196 AGGCAGGTCAAATATGTCAGTAATCTA 59.929 37.037 0.00 0.00 0.00 1.98
1372 1384 6.058183 GGCAGGTCAAATATGTCAGTAATCT 58.942 40.000 0.00 0.00 0.00 2.40
1373 1385 6.017605 CAGGCAGGTCAAATATGTCAGTAATC 60.018 42.308 0.00 0.00 0.00 1.75
1374 1386 5.824624 CAGGCAGGTCAAATATGTCAGTAAT 59.175 40.000 0.00 0.00 0.00 1.89
1376 1388 4.384098 CCAGGCAGGTCAAATATGTCAGTA 60.384 45.833 0.00 0.00 0.00 2.74
1377 1389 3.614092 CAGGCAGGTCAAATATGTCAGT 58.386 45.455 0.00 0.00 0.00 3.41
1378 1390 2.947652 CCAGGCAGGTCAAATATGTCAG 59.052 50.000 0.00 0.00 0.00 3.51
1379 1391 3.003394 CCAGGCAGGTCAAATATGTCA 57.997 47.619 0.00 0.00 0.00 3.58
1400 1412 7.495279 TCGTTAAACTTGACTAAAAAGTAGGCA 59.505 33.333 0.00 0.00 36.87 4.75
1401 1413 7.854534 TCGTTAAACTTGACTAAAAAGTAGGC 58.145 34.615 0.00 0.00 36.87 3.93
1404 1416 9.807649 AGACTCGTTAAACTTGACTAAAAAGTA 57.192 29.630 0.00 0.00 36.87 2.24
1433 1445 2.949447 ACAGAGGTGGCAAAGAACATT 58.051 42.857 0.00 0.00 0.00 2.71
1464 1476 9.586732 TTCATTTCCACCCTATTAAATGATAGG 57.413 33.333 9.41 4.64 43.84 2.57
1493 1509 4.417437 TCCCATAGTCTATGCCTCCTAAC 58.583 47.826 13.60 0.00 34.85 2.34
1509 1525 3.045634 AGGGTCGAATCATGTTCCCATA 58.954 45.455 6.28 0.00 37.56 2.74
1510 1526 1.846439 AGGGTCGAATCATGTTCCCAT 59.154 47.619 6.28 0.00 37.56 4.00
1566 1582 4.855388 TCATTCTAGTAACGAAACACGAGC 59.145 41.667 0.00 0.00 45.77 5.03
1634 1655 6.701400 GCAATTCACTAGTTGGTCAACAAAAT 59.299 34.615 15.12 5.42 43.47 1.82
1719 2022 2.518407 ACAACCTTTCTTCCCCCTTTCT 59.482 45.455 0.00 0.00 0.00 2.52
1727 2030 6.691508 AGATATTTTGCACAACCTTTCTTCC 58.308 36.000 0.00 0.00 0.00 3.46
1812 2116 6.713762 TGAAAATGAGAGTTGGACACATTT 57.286 33.333 0.00 0.00 41.03 2.32
1925 2229 6.796705 ACCTTTGTACGTCAAGGAATTAAG 57.203 37.500 21.91 7.04 37.35 1.85
2051 2355 7.557719 AGGTTACCAAAAAGGATGACATAGATG 59.442 37.037 3.51 0.00 41.22 2.90
2074 2378 5.073554 TGGATATTGCCTATCATTGTCAGGT 59.926 40.000 5.93 0.00 38.41 4.00
2224 2528 5.353394 AGACTGTTCCAAACTACTTGACA 57.647 39.130 0.00 0.00 37.17 3.58
2225 2529 6.278363 TGTAGACTGTTCCAAACTACTTGAC 58.722 40.000 0.00 0.00 37.17 3.18
2346 2652 1.531748 CCACCTGCGAATACCCCAT 59.468 57.895 0.00 0.00 0.00 4.00
2469 2775 3.461061 AGCAATCATCACCACAGTATCG 58.539 45.455 0.00 0.00 0.00 2.92
2783 3090 1.495878 CATCGCACATGAGGACTAGC 58.504 55.000 0.00 0.00 0.00 3.42
3255 3569 1.134220 TGGGATGGGAACGTTAGATGC 60.134 52.381 0.00 0.00 0.00 3.91
3263 3577 0.978146 AGGACTCTGGGATGGGAACG 60.978 60.000 0.00 0.00 0.00 3.95
3337 3652 1.286260 CGAGGGCAGGTATAGACGC 59.714 63.158 0.00 0.00 0.00 5.19
3387 3702 8.082242 ACAAGTACCAAAATAGCTGCTAAAAAG 58.918 33.333 14.13 4.72 0.00 2.27
3423 3742 5.183713 CCAGTTTCATGGTTGCTAAGATGAA 59.816 40.000 0.00 0.00 35.47 2.57
3510 3830 2.880890 GTCAAGGATGAAACTGCACAGT 59.119 45.455 0.00 0.00 44.94 3.55
3511 3831 3.144506 AGTCAAGGATGAAACTGCACAG 58.855 45.455 0.00 0.00 37.30 3.66
3659 3987 4.196193 CTGGTCCAAACTGTCACTTAACA 58.804 43.478 0.00 0.00 0.00 2.41
3689 4017 0.536260 CCCTCTGCCAGAAGACTCAG 59.464 60.000 0.00 0.00 0.00 3.35
3986 4314 9.994432 CAAGTAAGTAATTTGCTTAGAGATTGG 57.006 33.333 7.14 0.00 39.34 3.16
4045 4374 4.392138 GTCTTTCAATCGTTACCCCAAGAG 59.608 45.833 0.00 0.00 0.00 2.85
4117 4511 0.893270 AGTTTGCTATTGCCCGCACA 60.893 50.000 0.00 0.00 38.71 4.57
4126 4520 4.010349 AGCGCCTTTAAGAGTTTGCTATT 58.990 39.130 2.29 0.00 0.00 1.73
4521 4918 4.133820 TGTCACTGTTGTTATGGAACCAG 58.866 43.478 0.00 0.00 34.38 4.00
4602 5006 7.996098 TTTCCTGTAGTTCAATAAGGAAAGG 57.004 36.000 10.37 0.00 46.80 3.11
4712 5117 7.552687 TGTGAAGAATAACCCAACATAGATCAC 59.447 37.037 0.00 0.00 33.44 3.06
4943 5348 1.129811 GAATTAGCAAACCCACGGACG 59.870 52.381 0.00 0.00 0.00 4.79
5060 5465 5.049336 GCTTCTCTATCTCACGCACTATACA 60.049 44.000 0.00 0.00 0.00 2.29
5070 5475 6.017440 AGTGAGTTATCGCTTCTCTATCTCAC 60.017 42.308 11.79 11.79 43.89 3.51
5076 5481 3.948473 AGCAGTGAGTTATCGCTTCTCTA 59.052 43.478 0.00 0.00 43.89 2.43
5084 5489 4.610007 GCATATGCAAGCAGTGAGTTATCG 60.610 45.833 22.84 0.00 41.59 2.92
5115 5520 4.083057 GGGATTTCACTTGTCTTGAGAAGC 60.083 45.833 7.33 0.00 0.00 3.86
5387 5792 7.038659 CACTTCAATAGCTCTGCTAGTAGTTT 58.961 38.462 7.77 0.00 44.66 2.66
5646 6051 7.977853 AGATGCAGGATAAAACAAAGCTTTATG 59.022 33.333 12.25 3.72 30.80 1.90
5732 6137 0.532115 GCCCTCGTCCATGCAAAAAT 59.468 50.000 0.00 0.00 0.00 1.82
5874 6280 1.282382 TTTCCCCCACTGGTAGTAGC 58.718 55.000 0.00 0.00 0.00 3.58
5974 6380 5.710567 GCCCTGGTTTATTTACTCTCTTTGT 59.289 40.000 0.00 0.00 0.00 2.83
5993 6399 1.227205 CTAGCTTCGCTCTGCCCTG 60.227 63.158 0.00 0.00 40.44 4.45
6003 6409 5.967674 CCTTGTGAATTTAATGCTAGCTTCG 59.032 40.000 17.23 0.00 0.00 3.79
6063 6469 6.403878 ACTCTGTACCATTTATAAAGCACGT 58.596 36.000 3.94 0.00 0.00 4.49
6065 6471 8.336080 GCTAACTCTGTACCATTTATAAAGCAC 58.664 37.037 3.94 0.30 0.00 4.40
6138 6546 8.638685 TCTATCTACAAAAACTATTACCGCAC 57.361 34.615 0.00 0.00 0.00 5.34
6314 6724 3.756082 ATAACTGGAGGGGCAAAATCA 57.244 42.857 0.00 0.00 0.00 2.57
6384 6794 5.507482 GCATGCACAGATATGAAGCAAAGAT 60.507 40.000 14.21 0.00 38.85 2.40
6918 7970 5.583495 CGTACTGAGTAGTAGGTACGTAGT 58.417 45.833 18.74 7.96 46.64 2.73
7058 8110 3.072330 TCATTCCACAGTAACTCCTTGCA 59.928 43.478 0.00 0.00 0.00 4.08
7133 8185 1.301716 CTCCAACGGTCCACACCAG 60.302 63.158 0.00 0.00 44.02 4.00
7223 8276 7.335422 CACTCTGTTCCTATAAGCAAGAAATGT 59.665 37.037 0.00 0.00 0.00 2.71
7227 8280 6.605471 TCACTCTGTTCCTATAAGCAAGAA 57.395 37.500 0.00 0.00 0.00 2.52
7324 8380 4.846779 ATTTAAGCCAAAAAGACGCTCA 57.153 36.364 0.00 0.00 30.92 4.26
7328 8384 7.483691 GTGGTGTATATTTAAGCCAAAAAGACG 59.516 37.037 0.00 0.00 0.00 4.18
7709 8767 3.825908 AAACACAATGGGACCATACCT 57.174 42.857 3.92 0.00 35.31 3.08
8240 9300 6.928348 TTTCACTAGTCAGAAGTGGGATTA 57.072 37.500 0.00 0.00 43.69 1.75
8296 9356 1.453155 CCACGAAGAGGTTGGGATTG 58.547 55.000 0.00 0.00 32.16 2.67
8375 9435 1.336755 GAATGTTGCCACCGAACTGTT 59.663 47.619 0.00 0.00 0.00 3.16
8516 9600 9.457436 AGTTCGTTACCAACATATTTATTTCCT 57.543 29.630 0.00 0.00 0.00 3.36
8534 9618 6.804677 TGTAGTTTAACACCTCAGTTCGTTA 58.195 36.000 0.00 0.00 33.07 3.18
8604 9696 8.456471 TGCCATACTACTAGTTATGTATAAGCG 58.544 37.037 0.00 0.00 31.85 4.68
8623 9715 0.391927 TAGGGTTGCACGTGCCATAC 60.392 55.000 35.72 27.87 41.18 2.39
8830 9922 7.929941 AATCTCCTCTATTTTTCCTGTGTTC 57.070 36.000 0.00 0.00 0.00 3.18
8883 9975 7.388500 CCAAGTGAATTGTAAAATTCCTGCATT 59.612 33.333 14.54 1.75 38.15 3.56
8927 10021 5.543020 TCTCAGTCTCATCCTTCATGCATAT 59.457 40.000 0.00 0.00 31.70 1.78
8928 10022 4.897670 TCTCAGTCTCATCCTTCATGCATA 59.102 41.667 0.00 0.00 31.70 3.14
8930 10024 3.102204 TCTCAGTCTCATCCTTCATGCA 58.898 45.455 0.00 0.00 31.70 3.96
8939 10033 4.261994 GCCACTAAGGATCTCAGTCTCATC 60.262 50.000 0.00 0.00 41.22 2.92
8946 10040 7.445121 TGTTATTATGCCACTAAGGATCTCAG 58.555 38.462 0.00 0.00 41.22 3.35
9051 10145 4.036027 GCATGTGTAGAACAATGGATGGAG 59.964 45.833 0.00 0.00 43.61 3.86
9059 10153 5.981088 TTGGAATGCATGTGTAGAACAAT 57.019 34.783 0.00 0.00 43.61 2.71
9065 10159 4.987408 TTGGATTGGAATGCATGTGTAG 57.013 40.909 0.00 0.00 36.61 2.74
9180 10547 5.470047 AGTGTTTTACAGACTACAGGAGG 57.530 43.478 0.00 0.00 0.00 4.30
9264 10633 9.397280 GCTTTTATATTTCTTTACAGAGGGAGT 57.603 33.333 0.00 0.00 0.00 3.85
9265 10634 8.552034 CGCTTTTATATTTCTTTACAGAGGGAG 58.448 37.037 0.00 0.00 0.00 4.30
9266 10635 8.044908 ACGCTTTTATATTTCTTTACAGAGGGA 58.955 33.333 0.00 0.00 0.00 4.20
9267 10636 8.122952 CACGCTTTTATATTTCTTTACAGAGGG 58.877 37.037 0.00 0.00 0.00 4.30
9268 10637 8.665685 ACACGCTTTTATATTTCTTTACAGAGG 58.334 33.333 0.00 0.00 0.00 3.69
9279 10648 9.450807 GCATTTGATCTACACGCTTTTATATTT 57.549 29.630 0.00 0.00 0.00 1.40
9280 10649 8.840321 AGCATTTGATCTACACGCTTTTATATT 58.160 29.630 0.00 0.00 0.00 1.28
9281 10650 8.383318 AGCATTTGATCTACACGCTTTTATAT 57.617 30.769 0.00 0.00 0.00 0.86
9282 10651 7.710907 AGAGCATTTGATCTACACGCTTTTATA 59.289 33.333 0.00 0.00 39.27 0.98
9283 10652 6.540189 AGAGCATTTGATCTACACGCTTTTAT 59.460 34.615 0.00 0.00 39.27 1.40
9284 10653 5.874810 AGAGCATTTGATCTACACGCTTTTA 59.125 36.000 0.00 0.00 39.27 1.52
9285 10654 4.697352 AGAGCATTTGATCTACACGCTTTT 59.303 37.500 0.00 0.00 39.27 2.27
9286 10655 4.256920 AGAGCATTTGATCTACACGCTTT 58.743 39.130 0.00 0.00 39.27 3.51
9287 10656 3.866651 AGAGCATTTGATCTACACGCTT 58.133 40.909 0.00 0.00 39.27 4.68
9288 10657 3.533606 AGAGCATTTGATCTACACGCT 57.466 42.857 0.00 0.00 39.27 5.07
9289 10658 5.914085 ATAAGAGCATTTGATCTACACGC 57.086 39.130 0.00 0.00 40.30 5.34
9348 10717 9.382244 GCGATTTAAATCAAACGCTCTTATATT 57.618 29.630 24.23 0.00 40.41 1.28
9349 10718 8.556194 TGCGATTTAAATCAAACGCTCTTATAT 58.444 29.630 24.23 0.00 42.22 0.86
9350 10719 7.911343 TGCGATTTAAATCAAACGCTCTTATA 58.089 30.769 24.23 6.27 42.22 0.98
9351 10720 6.781138 TGCGATTTAAATCAAACGCTCTTAT 58.219 32.000 24.23 0.00 42.22 1.73
9352 10721 6.171932 TGCGATTTAAATCAAACGCTCTTA 57.828 33.333 24.23 7.17 42.22 2.10
9353 10722 5.041951 TGCGATTTAAATCAAACGCTCTT 57.958 34.783 24.23 0.00 42.22 2.85
9354 10723 4.678509 TGCGATTTAAATCAAACGCTCT 57.321 36.364 24.23 0.00 42.22 4.09
9355 10724 5.963004 TGTATGCGATTTAAATCAAACGCTC 59.037 36.000 24.23 16.53 42.22 5.03
9356 10725 5.737290 GTGTATGCGATTTAAATCAAACGCT 59.263 36.000 24.23 14.95 42.22 5.07
9357 10726 5.052633 GGTGTATGCGATTTAAATCAAACGC 60.053 40.000 24.23 21.69 42.14 4.84
9358 10727 6.255215 AGGTGTATGCGATTTAAATCAAACG 58.745 36.000 24.23 13.99 35.11 3.60
9359 10728 9.730420 ATAAGGTGTATGCGATTTAAATCAAAC 57.270 29.630 24.23 16.42 35.11 2.93
9369 10738 9.555727 ACAAAAGTATATAAGGTGTATGCGATT 57.444 29.630 0.00 0.00 0.00 3.34
9370 10739 9.204570 GACAAAAGTATATAAGGTGTATGCGAT 57.795 33.333 0.00 0.00 0.00 4.58
9371 10740 7.654520 GGACAAAAGTATATAAGGTGTATGCGA 59.345 37.037 0.00 0.00 0.00 5.10
9372 10741 7.656137 AGGACAAAAGTATATAAGGTGTATGCG 59.344 37.037 0.00 0.00 0.00 4.73
9373 10742 8.774586 CAGGACAAAAGTATATAAGGTGTATGC 58.225 37.037 0.00 0.00 0.00 3.14
9395 10764 5.875224 TCTACAACCATCAATTGTTCAGGA 58.125 37.500 5.13 0.00 40.68 3.86
9396 10765 5.124457 CCTCTACAACCATCAATTGTTCAGG 59.876 44.000 5.13 6.07 40.68 3.86
9419 10788 4.846779 TCACAGCTGATAACCAAAAACC 57.153 40.909 23.35 0.00 0.00 3.27
9430 10799 3.262660 TCCTTTGTCTCATCACAGCTGAT 59.737 43.478 23.35 0.68 37.65 2.90
9475 10844 2.929903 GCCGCCACCTGCAATGAAA 61.930 57.895 0.00 0.00 41.33 2.69
9518 10887 1.004161 TGGCGATCTTTTCCCATGTGA 59.996 47.619 0.00 0.00 0.00 3.58
9549 10918 2.727916 GCAGTTAGGCGTGCACAAATAC 60.728 50.000 18.64 7.74 39.62 1.89
9581 10950 1.484038 CAGAGAAGAGGAGAGGTGGG 58.516 60.000 0.00 0.00 0.00 4.61
9657 11026 1.135527 CGCTCCACCGTCAATAACCTA 59.864 52.381 0.00 0.00 0.00 3.08
9667 11036 2.304092 TCTCATTATACGCTCCACCGT 58.696 47.619 0.00 0.00 44.62 4.83
9673 11042 5.657470 TGTTGCATTCTCATTATACGCTC 57.343 39.130 0.00 0.00 0.00 5.03
9700 11069 9.628500 TCTCTAGTTGCACTGTAATTCTATCTA 57.372 33.333 0.00 0.00 0.00 1.98
9701 11070 8.526667 TCTCTAGTTGCACTGTAATTCTATCT 57.473 34.615 0.00 0.00 0.00 1.98
9702 11071 8.625651 TCTCTCTAGTTGCACTGTAATTCTATC 58.374 37.037 0.00 0.00 0.00 2.08
9703 11072 8.526667 TCTCTCTAGTTGCACTGTAATTCTAT 57.473 34.615 0.00 0.00 0.00 1.98
9704 11073 7.939784 TCTCTCTAGTTGCACTGTAATTCTA 57.060 36.000 0.00 0.00 0.00 2.10
9705 11074 6.842437 TCTCTCTAGTTGCACTGTAATTCT 57.158 37.500 0.00 0.00 0.00 2.40
9706 11075 7.891183 TTTCTCTCTAGTTGCACTGTAATTC 57.109 36.000 0.00 0.00 0.00 2.17
9707 11076 8.677148 TTTTTCTCTCTAGTTGCACTGTAATT 57.323 30.769 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.