Multiple sequence alignment - TraesCS3D01G359700

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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 TraesCS3D01G359700 chr3D 100.000 4211 0 0 1 4211 473481160 473485370 0.000000e+00 7777.0
1 TraesCS3D01G359700 chr3D 96.970 33 1 0 4143 4175 473485519 473485487 5.880000e-04 56.5
2 TraesCS3D01G359700 chr3B 93.304 2733 103 29 755 3451 629195547 629192859 0.000000e+00 3960.0
3 TraesCS3D01G359700 chr3B 83.558 742 60 31 3 717 629196245 629195539 4.590000e-179 638.0
4 TraesCS3D01G359700 chr3B 83.421 380 25 10 3477 3826 629192861 629192490 6.790000e-83 318.0
5 TraesCS3D01G359700 chr3B 95.455 44 0 2 709 752 729441551 729441592 7.550000e-08 69.4
6 TraesCS3D01G359700 chr3A 90.749 2951 125 56 755 3652 615938220 615941075 0.000000e+00 3801.0
7 TraesCS3D01G359700 chr3A 86.265 415 31 14 3711 4118 615941700 615942095 1.080000e-115 427.0
8 TraesCS3D01G359700 chr3A 83.529 425 29 16 18 432 615934440 615934833 4.000000e-95 359.0
9 TraesCS3D01G359700 chr3A 82.895 304 11 11 425 717 615937955 615938228 7.040000e-58 235.0
10 TraesCS3D01G359700 chr3A 92.308 52 2 2 697 748 606666476 606666525 5.840000e-09 73.1
11 TraesCS3D01G359700 chr3A 87.500 64 1 4 3647 3703 615941610 615941673 2.720000e-07 67.6
12 TraesCS3D01G359700 chr1D 76.066 2064 329 105 1145 3160 375989727 375991673 0.000000e+00 922.0
13 TraesCS3D01G359700 chr1D 94.118 51 2 1 698 748 53262058 53262009 4.510000e-10 76.8
14 TraesCS3D01G359700 chr1B 75.469 2079 348 109 1145 3160 502218002 502219981 0.000000e+00 865.0
15 TraesCS3D01G359700 chr5D 74.469 1696 308 73 1508 3160 42725390 42727003 5.980000e-173 617.0
16 TraesCS3D01G359700 chr5D 74.190 1697 296 83 1508 3160 249912099 249913697 1.020000e-160 577.0
17 TraesCS3D01G359700 chr1A 76.093 1029 186 43 2165 3160 474792586 474793587 2.280000e-132 483.0
18 TraesCS3D01G359700 chr1A 73.840 1422 257 72 1511 2890 59211675 59210327 3.840000e-125 459.0
19 TraesCS3D01G359700 chr2D 74.636 1029 201 40 2165 3160 185366410 185367411 2.360000e-107 399.0
20 TraesCS3D01G359700 chr2D 75.824 637 99 29 1508 2127 185365809 185366407 5.360000e-69 272.0
21 TraesCS3D01G359700 chr2D 88.136 59 5 2 691 748 593274224 593274281 7.550000e-08 69.4
22 TraesCS3D01G359700 chr7A 91.071 56 1 4 701 755 114027174 114027122 5.840000e-09 73.1
23 TraesCS3D01G359700 chr4D 89.831 59 3 3 697 753 136498933 136498876 5.840000e-09 73.1
24 TraesCS3D01G359700 chr4D 89.474 57 3 3 694 749 37941629 37941683 7.550000e-08 69.4
25 TraesCS3D01G359700 chr2A 92.308 52 2 2 697 747 738120034 738119984 5.840000e-09 73.1
26 TraesCS3D01G359700 chr4A 92.000 50 3 1 699 748 631219797 631219845 7.550000e-08 69.4


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 TraesCS3D01G359700 chr3D 473481160 473485370 4210 False 7777.000000 7777 100.0000 1 4211 1 chr3D.!!$F1 4210
1 TraesCS3D01G359700 chr3B 629192490 629196245 3755 True 1638.666667 3960 86.7610 3 3826 3 chr3B.!!$R1 3823
2 TraesCS3D01G359700 chr3A 615934440 615942095 7655 False 977.920000 3801 86.1876 18 4118 5 chr3A.!!$F2 4100
3 TraesCS3D01G359700 chr1D 375989727 375991673 1946 False 922.000000 922 76.0660 1145 3160 1 chr1D.!!$F1 2015
4 TraesCS3D01G359700 chr1B 502218002 502219981 1979 False 865.000000 865 75.4690 1145 3160 1 chr1B.!!$F1 2015
5 TraesCS3D01G359700 chr5D 42725390 42727003 1613 False 617.000000 617 74.4690 1508 3160 1 chr5D.!!$F1 1652
6 TraesCS3D01G359700 chr5D 249912099 249913697 1598 False 577.000000 577 74.1900 1508 3160 1 chr5D.!!$F2 1652
7 TraesCS3D01G359700 chr1A 474792586 474793587 1001 False 483.000000 483 76.0930 2165 3160 1 chr1A.!!$F1 995
8 TraesCS3D01G359700 chr1A 59210327 59211675 1348 True 459.000000 459 73.8400 1511 2890 1 chr1A.!!$R1 1379
9 TraesCS3D01G359700 chr2D 185365809 185367411 1602 False 335.500000 399 75.2300 1508 3160 2 chr2D.!!$F2 1652

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
721 3910 0.107848 CGCAAATACTCCCCTCCGTT 60.108 55.0 0.0 0.0 0.0 4.44 F
1062 4266 0.489567 ACTCCTCCCAGAACCAGAGT 59.510 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2370 5618 1.079405 TTCAAGGTCGCCATCGTCC 60.079 57.895 0.0 0.0 42.81 4.79 R
3313 6669 9.691362 GACACTAAAATGCAAGAGGAAATTAAA 57.309 29.630 0.0 0.0 0.00 1.52 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
100 101 3.206964 GAGGATAGAAAGGGAAAAGCCG 58.793 50.000 0.00 0.00 37.63 5.52
188 189 1.668419 CTTTGACCGGGCAGGATTAG 58.332 55.000 11.51 0.11 45.00 1.73
223 224 2.479656 CACAAAAACCCCATGCAAATCG 59.520 45.455 0.00 0.00 0.00 3.34
243 244 2.005451 GTGCATCATCCTGTGACTGTC 58.995 52.381 0.00 0.00 40.28 3.51
244 245 1.624813 TGCATCATCCTGTGACTGTCA 59.375 47.619 6.36 6.36 40.28 3.58
291 292 1.755179 CATTGTCATGACAGGGGTCC 58.245 55.000 26.48 0.00 43.65 4.46
295 296 1.780309 TGTCATGACAGGGGTCCTTTT 59.220 47.619 24.56 0.00 43.65 2.27
300 301 1.064825 GACAGGGGTCCTTTTCTCCA 58.935 55.000 0.00 0.00 38.12 3.86
309 310 3.554960 GGTCCTTTTCTCCACAAAATGCC 60.555 47.826 0.00 0.00 0.00 4.40
310 311 3.069443 GTCCTTTTCTCCACAAAATGCCA 59.931 43.478 0.00 0.00 0.00 4.92
311 312 3.903090 TCCTTTTCTCCACAAAATGCCAT 59.097 39.130 0.00 0.00 0.00 4.40
312 313 4.347583 TCCTTTTCTCCACAAAATGCCATT 59.652 37.500 0.00 0.00 0.00 3.16
313 314 4.453136 CCTTTTCTCCACAAAATGCCATTG 59.547 41.667 0.00 0.00 0.00 2.82
314 315 4.952071 TTTCTCCACAAAATGCCATTGA 57.048 36.364 0.00 0.00 0.00 2.57
315 316 5.486735 TTTCTCCACAAAATGCCATTGAT 57.513 34.783 0.00 0.00 0.00 2.57
316 317 5.486735 TTCTCCACAAAATGCCATTGATT 57.513 34.783 0.00 0.00 0.00 2.57
317 318 5.486735 TCTCCACAAAATGCCATTGATTT 57.513 34.783 0.00 0.00 0.00 2.17
318 319 5.867330 TCTCCACAAAATGCCATTGATTTT 58.133 33.333 0.00 0.00 34.10 1.82
319 320 5.933463 TCTCCACAAAATGCCATTGATTTTC 59.067 36.000 0.00 0.00 31.96 2.29
320 321 5.867330 TCCACAAAATGCCATTGATTTTCT 58.133 33.333 0.00 0.00 31.96 2.52
321 322 6.297582 TCCACAAAATGCCATTGATTTTCTT 58.702 32.000 0.00 0.00 31.96 2.52
322 323 6.771749 TCCACAAAATGCCATTGATTTTCTTT 59.228 30.769 0.00 0.00 31.96 2.52
323 324 7.284944 TCCACAAAATGCCATTGATTTTCTTTT 59.715 29.630 0.00 0.00 31.96 2.27
324 325 7.592164 CCACAAAATGCCATTGATTTTCTTTTC 59.408 33.333 0.00 0.00 31.96 2.29
352 353 4.503714 TGAGGATGATACCTTTGGTTCC 57.496 45.455 0.00 0.00 40.73 3.62
469 3642 2.222819 GCATTTCTCGGAACTACAAGCG 60.223 50.000 0.00 0.00 0.00 4.68
474 3647 2.027073 CGGAACTACAAGCGCTGCA 61.027 57.895 12.58 0.00 0.00 4.41
476 3649 0.375106 GGAACTACAAGCGCTGCATC 59.625 55.000 12.58 3.93 0.00 3.91
708 3897 2.862512 CGTGCAAGGTTATTCGCAAAT 58.137 42.857 0.00 0.00 35.87 2.32
709 3898 3.729462 GCGTGCAAGGTTATTCGCAAATA 60.729 43.478 8.91 0.00 42.54 1.40
710 3899 3.783943 CGTGCAAGGTTATTCGCAAATAC 59.216 43.478 0.00 0.00 35.87 1.89
711 3900 4.436852 CGTGCAAGGTTATTCGCAAATACT 60.437 41.667 0.00 0.00 35.87 2.12
712 3901 5.028375 GTGCAAGGTTATTCGCAAATACTC 58.972 41.667 0.00 0.00 35.87 2.59
713 3902 4.095782 TGCAAGGTTATTCGCAAATACTCC 59.904 41.667 0.00 0.00 0.00 3.85
714 3903 4.497507 GCAAGGTTATTCGCAAATACTCCC 60.498 45.833 0.00 0.00 0.00 4.30
715 3904 3.816994 AGGTTATTCGCAAATACTCCCC 58.183 45.455 0.00 0.00 0.00 4.81
716 3905 3.458487 AGGTTATTCGCAAATACTCCCCT 59.542 43.478 0.00 0.00 0.00 4.79
717 3906 3.813724 GGTTATTCGCAAATACTCCCCTC 59.186 47.826 0.00 0.00 0.00 4.30
718 3907 2.640316 ATTCGCAAATACTCCCCTCC 57.360 50.000 0.00 0.00 0.00 4.30
719 3908 0.177141 TTCGCAAATACTCCCCTCCG 59.823 55.000 0.00 0.00 0.00 4.63
720 3909 0.974010 TCGCAAATACTCCCCTCCGT 60.974 55.000 0.00 0.00 0.00 4.69
721 3910 0.107848 CGCAAATACTCCCCTCCGTT 60.108 55.000 0.00 0.00 0.00 4.44
722 3911 1.664873 GCAAATACTCCCCTCCGTTC 58.335 55.000 0.00 0.00 0.00 3.95
723 3912 1.746171 GCAAATACTCCCCTCCGTTCC 60.746 57.143 0.00 0.00 0.00 3.62
724 3913 1.557832 CAAATACTCCCCTCCGTTCCA 59.442 52.381 0.00 0.00 0.00 3.53
725 3914 1.961133 AATACTCCCCTCCGTTCCAA 58.039 50.000 0.00 0.00 0.00 3.53
726 3915 1.961133 ATACTCCCCTCCGTTCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
727 3916 1.732117 TACTCCCCTCCGTTCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
728 3917 1.073098 ACTCCCCTCCGTTCCAAAAT 58.927 50.000 0.00 0.00 0.00 1.82
729 3918 2.271777 ACTCCCCTCCGTTCCAAAATA 58.728 47.619 0.00 0.00 0.00 1.40
730 3919 2.238898 ACTCCCCTCCGTTCCAAAATAG 59.761 50.000 0.00 0.00 0.00 1.73
731 3920 2.504175 CTCCCCTCCGTTCCAAAATAGA 59.496 50.000 0.00 0.00 0.00 1.98
732 3921 3.120108 TCCCCTCCGTTCCAAAATAGAT 58.880 45.455 0.00 0.00 0.00 1.98
733 3922 3.118038 TCCCCTCCGTTCCAAAATAGATG 60.118 47.826 0.00 0.00 0.00 2.90
734 3923 3.118038 CCCCTCCGTTCCAAAATAGATGA 60.118 47.826 0.00 0.00 0.00 2.92
735 3924 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
736 3925 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
737 3926 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
738 3927 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
739 3928 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
740 3929 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
741 3930 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
742 3931 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
743 3932 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
744 3933 8.717821 CGTTCCAAAATAGATGACTCAACTTTA 58.282 33.333 0.00 0.00 0.00 1.85
904 4104 5.767665 TGCAAAGCAAAAGGAACTATAGACA 59.232 36.000 6.78 0.00 33.27 3.41
922 4122 2.939103 GACACAGAGAGAGAGAGAGAGC 59.061 54.545 0.00 0.00 0.00 4.09
926 4126 1.414181 AGAGAGAGAGAGAGAGCGAGG 59.586 57.143 0.00 0.00 0.00 4.63
927 4127 1.139058 GAGAGAGAGAGAGAGCGAGGT 59.861 57.143 0.00 0.00 0.00 3.85
929 4129 0.908910 AGAGAGAGAGAGCGAGGTGA 59.091 55.000 0.00 0.00 0.00 4.02
1062 4266 0.489567 ACTCCTCCCAGAACCAGAGT 59.510 55.000 0.00 0.00 0.00 3.24
1082 4286 1.574428 GCACGAGCAAACGTTGGAT 59.426 52.632 6.92 0.00 44.76 3.41
2046 5294 1.304282 GGAGAAGCCATCCAAGCCA 59.696 57.895 0.00 0.00 36.79 4.75
2139 5387 2.125633 GACCCGCGTTTCTCCCTC 60.126 66.667 4.92 0.00 0.00 4.30
2141 5389 3.755628 CCCGCGTTTCTCCCTCGA 61.756 66.667 4.92 0.00 0.00 4.04
2142 5390 2.506438 CCGCGTTTCTCCCTCGAC 60.506 66.667 4.92 0.00 0.00 4.20
2143 5391 2.874780 CGCGTTTCTCCCTCGACG 60.875 66.667 0.00 0.00 38.45 5.12
2145 5393 2.506438 CGTTTCTCCCTCGACGCC 60.506 66.667 0.00 0.00 0.00 5.68
2146 5394 2.506438 GTTTCTCCCTCGACGCCG 60.506 66.667 0.00 0.00 37.07 6.46
2147 5395 3.755628 TTTCTCCCTCGACGCCGG 61.756 66.667 0.00 0.00 36.24 6.13
2162 5410 4.889856 CGGCCGCATGTCCATCGA 62.890 66.667 14.67 0.00 0.00 3.59
2244 5492 1.667722 GGACGGGTACTTGTTCGGT 59.332 57.895 0.00 0.00 0.00 4.69
2370 5618 2.440247 GGCCAAATCCCCGTGGAG 60.440 66.667 0.00 0.00 46.08 3.86
2664 5936 2.825836 CTGGAGGCGGCAATGTCC 60.826 66.667 13.08 10.10 0.00 4.02
2730 6035 4.090588 GGGTTCATCCACCGGCGA 62.091 66.667 9.30 0.00 37.76 5.54
3312 6668 2.753055 TAACACGCAGGCAGTTCATA 57.247 45.000 2.88 0.00 0.00 2.15
3313 6669 2.113860 AACACGCAGGCAGTTCATAT 57.886 45.000 0.00 0.00 0.00 1.78
3347 6704 2.288579 TGCATTTTAGTGTCCTCGTCGT 60.289 45.455 0.00 0.00 0.00 4.34
3355 6712 1.674441 GTGTCCTCGTCGTATGATCCA 59.326 52.381 0.00 0.00 0.00 3.41
3356 6713 1.947456 TGTCCTCGTCGTATGATCCAG 59.053 52.381 0.00 0.00 0.00 3.86
3357 6714 0.952280 TCCTCGTCGTATGATCCAGC 59.048 55.000 0.00 0.00 0.00 4.85
3358 6715 0.386100 CCTCGTCGTATGATCCAGCG 60.386 60.000 0.00 0.00 0.00 5.18
3359 6716 0.386100 CTCGTCGTATGATCCAGCGG 60.386 60.000 0.00 0.00 0.00 5.52
3360 6717 1.099295 TCGTCGTATGATCCAGCGGT 61.099 55.000 0.00 0.00 0.00 5.68
3363 6720 1.067212 GTCGTATGATCCAGCGGTTCT 59.933 52.381 0.00 0.00 0.00 3.01
3367 6724 2.029838 ATGATCCAGCGGTTCTTGTC 57.970 50.000 0.00 0.00 0.00 3.18
3371 6728 0.675083 TCCAGCGGTTCTTGTCGTTA 59.325 50.000 0.00 0.00 0.00 3.18
3372 6729 1.068895 TCCAGCGGTTCTTGTCGTTAA 59.931 47.619 0.00 0.00 0.00 2.01
3373 6730 1.868498 CCAGCGGTTCTTGTCGTTAAA 59.132 47.619 0.00 0.00 0.00 1.52
3375 6732 3.424433 CCAGCGGTTCTTGTCGTTAAATC 60.424 47.826 0.00 0.00 0.00 2.17
3376 6733 3.185594 CAGCGGTTCTTGTCGTTAAATCA 59.814 43.478 0.00 0.00 0.00 2.57
3377 6734 4.000988 AGCGGTTCTTGTCGTTAAATCAT 58.999 39.130 0.00 0.00 0.00 2.45
3378 6735 5.062934 CAGCGGTTCTTGTCGTTAAATCATA 59.937 40.000 0.00 0.00 0.00 2.15
3379 6736 5.291128 AGCGGTTCTTGTCGTTAAATCATAG 59.709 40.000 0.00 0.00 0.00 2.23
3381 6738 6.254157 GCGGTTCTTGTCGTTAAATCATAGTA 59.746 38.462 0.00 0.00 0.00 1.82
3382 6739 7.607005 CGGTTCTTGTCGTTAAATCATAGTAC 58.393 38.462 0.00 0.00 0.00 2.73
3385 6753 9.095065 GTTCTTGTCGTTAAATCATAGTACCAT 57.905 33.333 0.00 0.00 0.00 3.55
3393 6761 9.261180 CGTTAAATCATAGTACCATCAGTTGAT 57.739 33.333 0.00 0.00 34.56 2.57
3412 6800 0.602638 TGTTCTGGACGTGTCATGCC 60.603 55.000 0.00 0.00 0.00 4.40
3415 6803 0.817654 TCTGGACGTGTCATGCCTAG 59.182 55.000 0.00 0.00 0.00 3.02
3418 6806 0.535335 GGACGTGTCATGCCTAGGAA 59.465 55.000 14.75 0.50 0.00 3.36
3451 6839 1.733912 TGCGATCTTGTGTCAATCTGC 59.266 47.619 0.00 0.00 0.00 4.26
3452 6840 1.267235 GCGATCTTGTGTCAATCTGCG 60.267 52.381 0.00 0.00 0.00 5.18
3453 6841 1.267235 CGATCTTGTGTCAATCTGCGC 60.267 52.381 0.00 0.00 0.00 6.09
3454 6842 1.063174 GATCTTGTGTCAATCTGCGCC 59.937 52.381 4.18 0.00 0.00 6.53
3455 6843 0.035317 TCTTGTGTCAATCTGCGCCT 59.965 50.000 4.18 0.00 0.00 5.52
3456 6844 0.167470 CTTGTGTCAATCTGCGCCTG 59.833 55.000 4.18 0.00 0.00 4.85
3457 6845 1.855213 TTGTGTCAATCTGCGCCTGC 61.855 55.000 4.18 0.00 43.20 4.85
3458 6846 2.037136 GTGTCAATCTGCGCCTGCT 61.037 57.895 4.18 0.00 43.34 4.24
3459 6847 0.740868 GTGTCAATCTGCGCCTGCTA 60.741 55.000 4.18 0.00 43.34 3.49
3460 6848 0.036483 TGTCAATCTGCGCCTGCTAA 60.036 50.000 4.18 0.00 43.34 3.09
3461 6849 1.303309 GTCAATCTGCGCCTGCTAAT 58.697 50.000 4.18 0.00 43.34 1.73
3462 6850 1.672881 GTCAATCTGCGCCTGCTAATT 59.327 47.619 4.18 0.00 43.34 1.40
3463 6851 1.942657 TCAATCTGCGCCTGCTAATTC 59.057 47.619 4.18 0.00 43.34 2.17
3464 6852 1.945394 CAATCTGCGCCTGCTAATTCT 59.055 47.619 4.18 0.00 43.34 2.40
3465 6853 2.338577 ATCTGCGCCTGCTAATTCTT 57.661 45.000 4.18 0.00 43.34 2.52
3466 6854 1.372582 TCTGCGCCTGCTAATTCTTG 58.627 50.000 4.18 0.00 43.34 3.02
3467 6855 0.379669 CTGCGCCTGCTAATTCTTGG 59.620 55.000 4.18 0.00 43.34 3.61
3468 6856 0.035534 TGCGCCTGCTAATTCTTGGA 60.036 50.000 4.18 0.00 43.34 3.53
3469 6857 0.659957 GCGCCTGCTAATTCTTGGAG 59.340 55.000 0.00 0.00 38.39 3.86
3470 6858 1.303309 CGCCTGCTAATTCTTGGAGG 58.697 55.000 8.52 8.52 43.41 4.30
3472 6860 2.425143 CCTGCTAATTCTTGGAGGCA 57.575 50.000 1.82 0.00 35.14 4.75
3473 6861 2.726821 CCTGCTAATTCTTGGAGGCAA 58.273 47.619 1.82 0.00 35.14 4.52
3474 6862 2.424956 CCTGCTAATTCTTGGAGGCAAC 59.575 50.000 1.82 0.00 35.14 4.17
3475 6863 2.424956 CTGCTAATTCTTGGAGGCAACC 59.575 50.000 0.00 0.00 37.17 3.77
3476 6864 1.751351 GCTAATTCTTGGAGGCAACCC 59.249 52.381 0.00 0.00 37.17 4.11
3477 6865 2.621668 GCTAATTCTTGGAGGCAACCCT 60.622 50.000 0.00 0.00 46.74 4.34
3478 6866 1.928868 AATTCTTGGAGGCAACCCTG 58.071 50.000 0.00 0.00 43.12 4.45
3479 6867 0.040204 ATTCTTGGAGGCAACCCTGG 59.960 55.000 0.00 0.00 43.12 4.45
3486 6874 2.069165 GAGGCAACCCTGGTTCTGGT 62.069 60.000 0.00 0.00 43.12 4.00
3589 6985 3.561241 TGCCCGTGCAGGTACCAA 61.561 61.111 15.94 0.00 44.23 3.67
3623 7019 2.911819 TTCAATCGTGCGGAAATTCC 57.088 45.000 0.99 0.99 0.00 3.01
3624 7020 2.107950 TCAATCGTGCGGAAATTCCT 57.892 45.000 10.64 0.00 33.30 3.36
3625 7021 2.006888 TCAATCGTGCGGAAATTCCTC 58.993 47.619 10.64 2.36 33.30 3.71
3626 7022 2.009774 CAATCGTGCGGAAATTCCTCT 58.990 47.619 10.64 0.00 33.30 3.69
3627 7023 2.403252 ATCGTGCGGAAATTCCTCTT 57.597 45.000 10.64 0.00 33.30 2.85
3628 7024 1.722011 TCGTGCGGAAATTCCTCTTC 58.278 50.000 10.64 0.00 33.30 2.87
3645 7045 1.255667 TTCCTTCCTTCCGAGTCCCG 61.256 60.000 0.00 0.00 38.18 5.14
3714 7680 1.200020 GGCACGTACGTACTACTGGTT 59.800 52.381 22.34 0.00 0.00 3.67
3736 7702 2.509651 AACGTTGGCGGTACAGGGA 61.510 57.895 0.00 0.00 43.45 4.20
3766 7736 0.603707 CCACTGCACGTGATTGGTCT 60.604 55.000 22.23 0.00 46.81 3.85
3775 7745 3.818773 CACGTGATTGGTCTTTAAAGGGT 59.181 43.478 10.90 0.00 0.00 4.34
3838 7816 4.501915 CGTTAAAGGCGTCCCATATTCCTA 60.502 45.833 0.00 0.00 0.00 2.94
3839 7817 5.557866 GTTAAAGGCGTCCCATATTCCTAT 58.442 41.667 0.00 0.00 0.00 2.57
3840 7818 3.983044 AAGGCGTCCCATATTCCTATC 57.017 47.619 0.00 0.00 0.00 2.08
3842 7820 2.188817 GGCGTCCCATATTCCTATCCT 58.811 52.381 0.00 0.00 0.00 3.24
3843 7821 2.168728 GGCGTCCCATATTCCTATCCTC 59.831 54.545 0.00 0.00 0.00 3.71
3844 7822 2.168728 GCGTCCCATATTCCTATCCTCC 59.831 54.545 0.00 0.00 0.00 4.30
3845 7823 2.427453 CGTCCCATATTCCTATCCTCCG 59.573 54.545 0.00 0.00 0.00 4.63
3846 7824 2.168728 GTCCCATATTCCTATCCTCCGC 59.831 54.545 0.00 0.00 0.00 5.54
3847 7825 2.044492 TCCCATATTCCTATCCTCCGCT 59.956 50.000 0.00 0.00 0.00 5.52
3848 7826 2.169352 CCCATATTCCTATCCTCCGCTG 59.831 54.545 0.00 0.00 0.00 5.18
3850 7828 1.267121 TATTCCTATCCTCCGCTGGC 58.733 55.000 0.00 0.00 0.00 4.85
3851 7829 0.472734 ATTCCTATCCTCCGCTGGCT 60.473 55.000 0.00 0.00 0.00 4.75
3852 7830 1.402896 TTCCTATCCTCCGCTGGCTG 61.403 60.000 0.00 0.00 0.00 4.85
3853 7831 2.739784 CTATCCTCCGCTGGCTGG 59.260 66.667 0.00 0.00 0.00 4.85
3854 7832 3.527775 CTATCCTCCGCTGGCTGGC 62.528 68.421 0.00 0.00 0.00 4.85
3882 7862 0.456142 CGCTTGTTCTCGTCGGATCA 60.456 55.000 0.00 0.00 0.00 2.92
3888 7868 2.097629 TGTTCTCGTCGGATCAGACATC 59.902 50.000 23.07 10.11 40.98 3.06
3889 7869 2.038387 TCTCGTCGGATCAGACATCA 57.962 50.000 23.07 7.71 40.98 3.07
3898 7878 2.419297 GGATCAGACATCAGTGTGGGTC 60.419 54.545 0.00 0.00 39.36 4.46
3930 7910 4.020617 CCACCGGCAGAGCAAGGA 62.021 66.667 0.00 0.00 33.41 3.36
3986 7966 0.308684 CGCTCTGCTGCTTTTGTTCA 59.691 50.000 0.00 0.00 0.00 3.18
3987 7967 1.763634 GCTCTGCTGCTTTTGTTCAC 58.236 50.000 0.00 0.00 0.00 3.18
3988 7968 1.336125 GCTCTGCTGCTTTTGTTCACT 59.664 47.619 0.00 0.00 0.00 3.41
3989 7969 2.857489 GCTCTGCTGCTTTTGTTCACTG 60.857 50.000 0.00 0.00 0.00 3.66
3992 7972 2.291465 CTGCTGCTTTTGTTCACTGCTA 59.709 45.455 0.00 0.00 0.00 3.49
4003 7983 1.227089 CACTGCTACTAGCTGCCCG 60.227 63.158 13.38 1.40 42.95 6.13
4007 7987 0.104855 TGCTACTAGCTGCCCGATTG 59.895 55.000 9.49 0.00 42.97 2.67
4056 8036 1.367471 CTGCCGGTTCAGACACAGA 59.633 57.895 1.90 0.00 36.19 3.41
4065 8045 1.079266 CAGACACAGAGCTCCTGCC 60.079 63.158 10.93 0.00 46.81 4.85
4072 8052 0.532573 CAGAGCTCCTGCCGTTTCTA 59.467 55.000 10.93 0.00 40.80 2.10
4073 8053 0.533032 AGAGCTCCTGCCGTTTCTAC 59.467 55.000 10.93 0.00 40.80 2.59
4109 8089 2.419436 CCATGTTCCCATGCACGTACTA 60.419 50.000 0.00 0.00 45.90 1.82
4118 8098 3.322369 CATGCACGTACTACCTCACAAA 58.678 45.455 0.00 0.00 0.00 2.83
4119 8099 2.746269 TGCACGTACTACCTCACAAAC 58.254 47.619 0.00 0.00 0.00 2.93
4120 8100 1.717645 GCACGTACTACCTCACAAACG 59.282 52.381 0.00 0.00 36.48 3.60
4121 8101 2.605338 GCACGTACTACCTCACAAACGA 60.605 50.000 0.00 0.00 34.62 3.85
4122 8102 2.975851 CACGTACTACCTCACAAACGAC 59.024 50.000 0.00 0.00 34.62 4.34
4123 8103 2.030805 ACGTACTACCTCACAAACGACC 60.031 50.000 0.00 0.00 34.62 4.79
4124 8104 2.669391 CGTACTACCTCACAAACGACCC 60.669 54.545 0.00 0.00 32.35 4.46
4125 8105 1.713297 ACTACCTCACAAACGACCCT 58.287 50.000 0.00 0.00 0.00 4.34
4126 8106 2.880443 ACTACCTCACAAACGACCCTA 58.120 47.619 0.00 0.00 0.00 3.53
4127 8107 2.560105 ACTACCTCACAAACGACCCTAC 59.440 50.000 0.00 0.00 0.00 3.18
4128 8108 1.713297 ACCTCACAAACGACCCTACT 58.287 50.000 0.00 0.00 0.00 2.57
4129 8109 2.880443 ACCTCACAAACGACCCTACTA 58.120 47.619 0.00 0.00 0.00 1.82
4130 8110 3.438183 ACCTCACAAACGACCCTACTAT 58.562 45.455 0.00 0.00 0.00 2.12
4131 8111 3.446516 ACCTCACAAACGACCCTACTATC 59.553 47.826 0.00 0.00 0.00 2.08
4132 8112 3.700038 CCTCACAAACGACCCTACTATCT 59.300 47.826 0.00 0.00 0.00 1.98
4133 8113 4.202030 CCTCACAAACGACCCTACTATCTC 60.202 50.000 0.00 0.00 0.00 2.75
4134 8114 3.698040 TCACAAACGACCCTACTATCTCC 59.302 47.826 0.00 0.00 0.00 3.71
4135 8115 3.446161 CACAAACGACCCTACTATCTCCA 59.554 47.826 0.00 0.00 0.00 3.86
4136 8116 3.446516 ACAAACGACCCTACTATCTCCAC 59.553 47.826 0.00 0.00 0.00 4.02
4137 8117 1.964552 ACGACCCTACTATCTCCACG 58.035 55.000 0.00 0.00 0.00 4.94
4138 8118 0.592148 CGACCCTACTATCTCCACGC 59.408 60.000 0.00 0.00 0.00 5.34
4139 8119 1.688772 GACCCTACTATCTCCACGCA 58.311 55.000 0.00 0.00 0.00 5.24
4140 8120 1.337387 GACCCTACTATCTCCACGCAC 59.663 57.143 0.00 0.00 0.00 5.34
4141 8121 1.341679 ACCCTACTATCTCCACGCACA 60.342 52.381 0.00 0.00 0.00 4.57
4142 8122 1.964223 CCCTACTATCTCCACGCACAT 59.036 52.381 0.00 0.00 0.00 3.21
4143 8123 3.154710 CCCTACTATCTCCACGCACATA 58.845 50.000 0.00 0.00 0.00 2.29
4144 8124 3.191581 CCCTACTATCTCCACGCACATAG 59.808 52.174 0.00 0.00 0.00 2.23
4145 8125 4.072839 CCTACTATCTCCACGCACATAGA 58.927 47.826 0.00 0.00 0.00 1.98
4146 8126 4.702612 CCTACTATCTCCACGCACATAGAT 59.297 45.833 0.00 0.00 33.42 1.98
4147 8127 5.184096 CCTACTATCTCCACGCACATAGATT 59.816 44.000 0.00 0.00 31.38 2.40
4148 8128 5.537300 ACTATCTCCACGCACATAGATTT 57.463 39.130 0.00 0.00 31.38 2.17
4149 8129 5.292765 ACTATCTCCACGCACATAGATTTG 58.707 41.667 0.00 0.00 31.38 2.32
4150 8130 3.610040 TCTCCACGCACATAGATTTGT 57.390 42.857 0.00 0.00 0.00 2.83
4151 8131 4.729227 TCTCCACGCACATAGATTTGTA 57.271 40.909 0.00 0.00 0.00 2.41
4152 8132 5.079689 TCTCCACGCACATAGATTTGTAA 57.920 39.130 0.00 0.00 0.00 2.41
4153 8133 4.868171 TCTCCACGCACATAGATTTGTAAC 59.132 41.667 0.00 0.00 0.00 2.50
4154 8134 4.570930 TCCACGCACATAGATTTGTAACA 58.429 39.130 0.00 0.00 0.00 2.41
4155 8135 4.629634 TCCACGCACATAGATTTGTAACAG 59.370 41.667 0.00 0.00 0.00 3.16
4156 8136 4.629634 CCACGCACATAGATTTGTAACAGA 59.370 41.667 0.00 0.00 0.00 3.41
4157 8137 5.121611 CCACGCACATAGATTTGTAACAGAA 59.878 40.000 0.00 0.00 0.00 3.02
4158 8138 6.243551 CACGCACATAGATTTGTAACAGAAG 58.756 40.000 0.00 0.00 0.00 2.85
4159 8139 5.932303 ACGCACATAGATTTGTAACAGAAGT 59.068 36.000 0.00 0.00 0.00 3.01
4160 8140 7.062956 CACGCACATAGATTTGTAACAGAAGTA 59.937 37.037 0.00 0.00 0.00 2.24
4161 8141 7.764443 ACGCACATAGATTTGTAACAGAAGTAT 59.236 33.333 0.00 0.00 0.00 2.12
4162 8142 8.058328 CGCACATAGATTTGTAACAGAAGTATG 58.942 37.037 0.00 0.00 0.00 2.39
4163 8143 8.883731 GCACATAGATTTGTAACAGAAGTATGT 58.116 33.333 0.00 0.00 33.96 2.29
4169 8149 9.778741 AGATTTGTAACAGAAGTATGTCAGAAA 57.221 29.630 0.00 0.00 31.50 2.52
4187 8167 9.710979 TGTCAGAAATTTTAAACTAAACAGACG 57.289 29.630 0.00 0.00 0.00 4.18
4188 8168 9.925268 GTCAGAAATTTTAAACTAAACAGACGA 57.075 29.630 0.00 0.00 0.00 4.20
4198 8178 7.667043 AAACTAAACAGACGAGATTTATGCA 57.333 32.000 0.00 0.00 0.00 3.96
4199 8179 7.667043 AACTAAACAGACGAGATTTATGCAA 57.333 32.000 0.00 0.00 0.00 4.08
4200 8180 7.667043 ACTAAACAGACGAGATTTATGCAAA 57.333 32.000 0.00 0.00 0.00 3.68
4201 8181 7.519002 ACTAAACAGACGAGATTTATGCAAAC 58.481 34.615 0.00 0.00 0.00 2.93
4202 8182 4.946784 ACAGACGAGATTTATGCAAACC 57.053 40.909 0.00 0.00 0.00 3.27
4203 8183 3.370978 ACAGACGAGATTTATGCAAACCG 59.629 43.478 0.00 0.00 0.00 4.44
4204 8184 2.936498 AGACGAGATTTATGCAAACCGG 59.064 45.455 0.00 0.00 0.00 5.28
4205 8185 2.933906 GACGAGATTTATGCAAACCGGA 59.066 45.455 9.46 0.00 0.00 5.14
4206 8186 2.676342 ACGAGATTTATGCAAACCGGAC 59.324 45.455 9.46 0.00 0.00 4.79
4207 8187 2.675844 CGAGATTTATGCAAACCGGACA 59.324 45.455 9.46 0.14 0.00 4.02
4208 8188 3.242413 CGAGATTTATGCAAACCGGACAG 60.242 47.826 9.46 0.00 0.00 3.51
4209 8189 3.938963 GAGATTTATGCAAACCGGACAGA 59.061 43.478 9.46 0.00 0.00 3.41
4210 8190 4.526970 AGATTTATGCAAACCGGACAGAT 58.473 39.130 9.46 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.542702 CCCTCCACCACAAAGCCAAT 60.543 55.000 0.00 0.00 0.00 3.16
1 2 1.152567 CCCTCCACCACAAAGCCAA 60.153 57.895 0.00 0.00 0.00 4.52
179 180 4.934602 GCATCCAGATAGTTCTAATCCTGC 59.065 45.833 0.00 0.00 0.00 4.85
188 189 5.402398 GGTTTTTGTGCATCCAGATAGTTC 58.598 41.667 0.00 0.00 0.00 3.01
223 224 2.005451 GACAGTCACAGGATGATGCAC 58.995 52.381 0.00 0.00 40.28 4.57
243 244 2.224137 TGAAGGCTTGACTCACAGAGTG 60.224 50.000 3.46 0.00 43.53 3.51
244 245 2.042464 TGAAGGCTTGACTCACAGAGT 58.958 47.619 3.46 0.00 46.42 3.24
247 248 2.141517 CAGTGAAGGCTTGACTCACAG 58.858 52.381 16.71 5.77 34.12 3.66
248 249 1.762370 TCAGTGAAGGCTTGACTCACA 59.238 47.619 16.71 1.16 34.12 3.58
249 250 2.533266 TCAGTGAAGGCTTGACTCAC 57.467 50.000 16.71 12.34 0.00 3.51
291 292 5.299148 TCAATGGCATTTTGTGGAGAAAAG 58.701 37.500 10.65 0.00 0.00 2.27
295 296 5.486735 AAATCAATGGCATTTTGTGGAGA 57.513 34.783 10.65 3.25 0.00 3.71
300 301 7.503230 AGGAAAAGAAAATCAATGGCATTTTGT 59.497 29.630 10.65 0.00 34.30 2.83
348 349 0.322546 CCTGGTACTGGGCAAGGAAC 60.323 60.000 0.00 0.00 44.20 3.62
394 432 9.950496 TCTGAATACTCTGCTAAAAAGAGATTT 57.050 29.630 7.42 1.02 43.27 2.17
434 472 2.302445 AGAAATGCTCTGCTCACTCACT 59.698 45.455 0.00 0.00 31.12 3.41
436 474 2.673326 CGAGAAATGCTCTGCTCACTCA 60.673 50.000 0.00 0.00 41.66 3.41
439 477 1.005340 CCGAGAAATGCTCTGCTCAC 58.995 55.000 0.00 0.00 41.66 3.51
474 3647 1.386525 ATCAATGGGCTTTGCGCGAT 61.387 50.000 12.10 0.00 44.57 4.58
476 3649 1.874915 CATCAATGGGCTTTGCGCG 60.875 57.895 0.00 0.00 44.57 6.86
685 3870 1.580132 CGAATAACCTTGCACGCGC 60.580 57.895 5.73 0.00 39.24 6.86
708 3897 1.732117 TTTTGGAACGGAGGGGAGTA 58.268 50.000 0.00 0.00 0.00 2.59
709 3898 1.073098 ATTTTGGAACGGAGGGGAGT 58.927 50.000 0.00 0.00 0.00 3.85
710 3899 2.504175 TCTATTTTGGAACGGAGGGGAG 59.496 50.000 0.00 0.00 0.00 4.30
711 3900 2.553464 TCTATTTTGGAACGGAGGGGA 58.447 47.619 0.00 0.00 0.00 4.81
712 3901 3.118038 TCATCTATTTTGGAACGGAGGGG 60.118 47.826 0.00 0.00 0.00 4.79
713 3902 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
714 3903 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
715 3904 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
716 3905 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
717 3906 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
718 3907 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
745 3934 9.559732 CTGATCCAAAGGTGATTACAATATGTA 57.440 33.333 0.00 0.00 0.00 2.29
746 3935 7.013655 GCTGATCCAAAGGTGATTACAATATGT 59.986 37.037 0.00 0.00 0.00 2.29
747 3936 7.365741 GCTGATCCAAAGGTGATTACAATATG 58.634 38.462 0.00 0.00 0.00 1.78
748 3937 6.491403 GGCTGATCCAAAGGTGATTACAATAT 59.509 38.462 0.00 0.00 34.01 1.28
749 3938 5.827797 GGCTGATCCAAAGGTGATTACAATA 59.172 40.000 0.00 0.00 34.01 1.90
750 3939 4.646492 GGCTGATCCAAAGGTGATTACAAT 59.354 41.667 0.00 0.00 34.01 2.71
751 3940 4.016444 GGCTGATCCAAAGGTGATTACAA 58.984 43.478 0.00 0.00 34.01 2.41
752 3941 3.010027 TGGCTGATCCAAAGGTGATTACA 59.990 43.478 0.00 0.00 43.21 2.41
753 3942 3.620488 TGGCTGATCCAAAGGTGATTAC 58.380 45.455 0.00 0.00 43.21 1.89
904 4104 1.831106 TCGCTCTCTCTCTCTCTCTGT 59.169 52.381 0.00 0.00 0.00 3.41
922 4122 3.522731 CCCCGCTCTCTCACCTCG 61.523 72.222 0.00 0.00 0.00 4.63
926 4126 3.844090 GCTCCCCCGCTCTCTCAC 61.844 72.222 0.00 0.00 0.00 3.51
1034 4238 3.003763 GGGAGGAGTGAGCGGGTT 61.004 66.667 0.00 0.00 0.00 4.11
1062 4266 2.712539 CAACGTTTGCTCGTGCCA 59.287 55.556 7.05 0.00 43.38 4.92
1082 4286 2.643272 GACGTCACCTCACAGCGA 59.357 61.111 11.55 0.00 0.00 4.93
1134 4338 3.499737 GACATTGCCGTGCCCTCG 61.500 66.667 0.00 0.00 0.00 4.63
1135 4339 3.499737 CGACATTGCCGTGCCCTC 61.500 66.667 0.00 0.00 0.00 4.30
1593 4828 2.059190 GGAGGAGACCGGGAAGGAC 61.059 68.421 6.32 0.00 45.00 3.85
2145 5393 4.889856 TCGATGGACATGCGGCCG 62.890 66.667 24.05 24.05 0.00 6.13
2146 5394 3.272334 GTCGATGGACATGCGGCC 61.272 66.667 2.59 0.00 42.91 6.13
2147 5395 3.630148 CGTCGATGGACATGCGGC 61.630 66.667 8.67 0.00 43.61 6.53
2149 5397 2.568031 CGTCGTCGATGGACATGCG 61.568 63.158 16.59 5.21 43.61 4.73
2150 5398 2.860628 GCGTCGTCGATGGACATGC 61.861 63.158 15.93 8.32 43.61 4.06
2151 5399 2.230940 GGCGTCGTCGATGGACATG 61.231 63.158 15.93 0.00 43.61 3.21
2152 5400 2.104331 GGCGTCGTCGATGGACAT 59.896 61.111 15.93 0.00 43.61 3.06
2153 5401 4.470170 CGGCGTCGTCGATGGACA 62.470 66.667 15.33 0.00 43.61 4.02
2370 5618 1.079405 TTCAAGGTCGCCATCGTCC 60.079 57.895 0.00 0.00 42.81 4.79
3313 6669 9.691362 GACACTAAAATGCAAGAGGAAATTAAA 57.309 29.630 0.00 0.00 0.00 1.52
3347 6704 2.481276 CGACAAGAACCGCTGGATCATA 60.481 50.000 0.00 0.00 0.00 2.15
3355 6712 3.395639 TGATTTAACGACAAGAACCGCT 58.604 40.909 0.00 0.00 0.00 5.52
3356 6713 3.799137 TGATTTAACGACAAGAACCGC 57.201 42.857 0.00 0.00 0.00 5.68
3357 6714 6.642683 ACTATGATTTAACGACAAGAACCG 57.357 37.500 0.00 0.00 0.00 4.44
3358 6715 7.546667 TGGTACTATGATTTAACGACAAGAACC 59.453 37.037 0.00 0.00 0.00 3.62
3359 6716 8.470040 TGGTACTATGATTTAACGACAAGAAC 57.530 34.615 0.00 0.00 0.00 3.01
3360 6717 9.309516 GATGGTACTATGATTTAACGACAAGAA 57.690 33.333 0.00 0.00 0.00 2.52
3363 6720 8.255206 ACTGATGGTACTATGATTTAACGACAA 58.745 33.333 0.00 0.00 0.00 3.18
3367 6724 8.642908 TCAACTGATGGTACTATGATTTAACG 57.357 34.615 0.00 0.00 0.00 3.18
3385 6753 2.102420 ACACGTCCAGAACATCAACTGA 59.898 45.455 0.00 0.00 36.38 3.41
3393 6761 0.602638 GGCATGACACGTCCAGAACA 60.603 55.000 0.00 0.00 0.00 3.18
3434 6822 1.063174 GGCGCAGATTGACACAAGATC 59.937 52.381 10.83 0.00 0.00 2.75
3442 6830 1.303309 ATTAGCAGGCGCAGATTGAC 58.697 50.000 10.83 0.00 42.27 3.18
3451 6839 1.303309 CCTCCAAGAATTAGCAGGCG 58.697 55.000 0.00 0.00 0.00 5.52
3452 6840 1.028130 GCCTCCAAGAATTAGCAGGC 58.972 55.000 0.00 0.00 39.75 4.85
3453 6841 2.424956 GTTGCCTCCAAGAATTAGCAGG 59.575 50.000 0.00 0.00 0.00 4.85
3454 6842 2.424956 GGTTGCCTCCAAGAATTAGCAG 59.575 50.000 0.00 0.00 0.00 4.24
3455 6843 2.446435 GGTTGCCTCCAAGAATTAGCA 58.554 47.619 0.00 0.00 0.00 3.49
3456 6844 1.751351 GGGTTGCCTCCAAGAATTAGC 59.249 52.381 0.00 0.00 0.00 3.09
3457 6845 3.019564 CAGGGTTGCCTCCAAGAATTAG 58.980 50.000 0.00 0.00 0.00 1.73
3458 6846 2.291540 CCAGGGTTGCCTCCAAGAATTA 60.292 50.000 0.00 0.00 0.00 1.40
3459 6847 1.550869 CCAGGGTTGCCTCCAAGAATT 60.551 52.381 0.00 0.00 0.00 2.17
3460 6848 0.040204 CCAGGGTTGCCTCCAAGAAT 59.960 55.000 0.00 0.00 0.00 2.40
3461 6849 1.360393 ACCAGGGTTGCCTCCAAGAA 61.360 55.000 0.00 0.00 0.00 2.52
3462 6850 1.360393 AACCAGGGTTGCCTCCAAGA 61.360 55.000 2.23 0.00 36.91 3.02
3463 6851 0.895559 GAACCAGGGTTGCCTCCAAG 60.896 60.000 8.73 0.00 38.60 3.61
3464 6852 1.152830 GAACCAGGGTTGCCTCCAA 59.847 57.895 8.73 0.00 38.60 3.53
3465 6853 1.774217 AGAACCAGGGTTGCCTCCA 60.774 57.895 8.73 0.00 38.60 3.86
3466 6854 1.303643 CAGAACCAGGGTTGCCTCC 60.304 63.158 8.73 0.00 38.60 4.30
3467 6855 1.303643 CCAGAACCAGGGTTGCCTC 60.304 63.158 8.73 0.00 38.60 4.70
3468 6856 1.655114 AACCAGAACCAGGGTTGCCT 61.655 55.000 8.73 0.00 45.35 4.75
3469 6857 1.152546 AACCAGAACCAGGGTTGCC 60.153 57.895 8.73 0.00 45.35 4.52
3470 6858 4.599036 AACCAGAACCAGGGTTGC 57.401 55.556 8.73 0.84 45.35 4.17
3473 6861 1.536676 CCACAACCAGAACCAGGGT 59.463 57.895 0.00 0.00 39.65 4.34
3474 6862 1.903404 GCCACAACCAGAACCAGGG 60.903 63.158 0.00 0.00 0.00 4.45
3475 6863 0.890996 GAGCCACAACCAGAACCAGG 60.891 60.000 0.00 0.00 0.00 4.45
3476 6864 0.890996 GGAGCCACAACCAGAACCAG 60.891 60.000 0.00 0.00 0.00 4.00
3477 6865 1.150536 GGAGCCACAACCAGAACCA 59.849 57.895 0.00 0.00 0.00 3.67
3478 6866 1.603739 GGGAGCCACAACCAGAACC 60.604 63.158 0.00 0.00 0.00 3.62
3479 6867 1.603739 GGGGAGCCACAACCAGAAC 60.604 63.158 0.00 0.00 0.00 3.01
3486 6874 0.185416 TTTAAACCGGGGAGCCACAA 59.815 50.000 6.32 0.00 0.00 3.33
3524 6920 1.091771 CAAAGCGATGATGCCGGTCT 61.092 55.000 1.90 0.00 36.70 3.85
3579 6975 2.288213 GCCAAAAAGACTTGGTACCTGC 60.288 50.000 14.36 0.00 46.53 4.85
3585 6981 3.517500 TGAAAAGGCCAAAAAGACTTGGT 59.482 39.130 5.01 0.00 46.53 3.67
3587 6983 5.050837 CGATTGAAAAGGCCAAAAAGACTTG 60.051 40.000 5.01 0.00 0.00 3.16
3589 6985 4.099419 ACGATTGAAAAGGCCAAAAAGACT 59.901 37.500 5.01 0.00 0.00 3.24
3599 6995 0.239879 TTCCGCACGATTGAAAAGGC 59.760 50.000 0.00 0.00 0.00 4.35
3623 7019 1.478916 GGACTCGGAAGGAAGGAAGAG 59.521 57.143 0.00 0.00 0.00 2.85
3624 7020 1.558233 GGACTCGGAAGGAAGGAAGA 58.442 55.000 0.00 0.00 0.00 2.87
3625 7021 0.537653 GGGACTCGGAAGGAAGGAAG 59.462 60.000 0.00 0.00 0.00 3.46
3626 7022 1.255667 CGGGACTCGGAAGGAAGGAA 61.256 60.000 0.00 0.00 34.75 3.36
3627 7023 1.681327 CGGGACTCGGAAGGAAGGA 60.681 63.158 0.00 0.00 34.75 3.36
3628 7024 1.681327 TCGGGACTCGGAAGGAAGG 60.681 63.158 0.00 0.00 39.77 3.46
3645 7045 0.533032 CCTCTCGGGACTCAAAGGTC 59.467 60.000 0.00 0.00 37.23 3.85
3702 7648 3.017265 ACGTTGGAAACCAGTAGTACG 57.983 47.619 9.41 9.41 46.28 3.67
3766 7736 1.769006 CCCGACCCCACCCTTTAAA 59.231 57.895 0.00 0.00 0.00 1.52
3882 7862 0.318441 CACGACCCACACTGATGTCT 59.682 55.000 0.00 0.00 36.72 3.41
3888 7868 2.734723 CGCTCACGACCCACACTG 60.735 66.667 0.00 0.00 43.93 3.66
3889 7869 3.224324 ACGCTCACGACCCACACT 61.224 61.111 0.00 0.00 43.93 3.55
3923 7903 2.759795 GGCCCAACTCTCCTTGCT 59.240 61.111 0.00 0.00 0.00 3.91
3925 7905 1.301293 GAGGGCCCAACTCTCCTTG 59.699 63.158 27.56 0.00 32.28 3.61
3967 7947 0.308684 TGAACAAAAGCAGCAGAGCG 59.691 50.000 0.00 0.00 40.15 5.03
3969 7949 2.857489 GCAGTGAACAAAAGCAGCAGAG 60.857 50.000 0.00 0.00 0.00 3.35
3975 7955 3.498397 GCTAGTAGCAGTGAACAAAAGCA 59.502 43.478 17.47 0.00 41.89 3.91
3986 7966 0.757188 ATCGGGCAGCTAGTAGCAGT 60.757 55.000 23.77 1.17 45.56 4.40
3987 7967 0.390860 AATCGGGCAGCTAGTAGCAG 59.609 55.000 23.77 17.01 45.56 4.24
3988 7968 0.104855 CAATCGGGCAGCTAGTAGCA 59.895 55.000 23.77 2.41 45.56 3.49
3989 7969 1.224722 GCAATCGGGCAGCTAGTAGC 61.225 60.000 14.62 14.62 42.84 3.58
3992 7972 2.202932 CGCAATCGGGCAGCTAGT 60.203 61.111 0.00 0.00 0.00 2.57
4056 8036 1.597461 GGTAGAAACGGCAGGAGCT 59.403 57.895 0.00 0.00 41.70 4.09
4065 8045 1.141234 GGCGAGGAGGGTAGAAACG 59.859 63.158 0.00 0.00 0.00 3.60
4109 8089 1.713297 AGTAGGGTCGTTTGTGAGGT 58.287 50.000 0.00 0.00 0.00 3.85
4118 8098 1.964552 CGTGGAGATAGTAGGGTCGT 58.035 55.000 0.00 0.00 0.00 4.34
4119 8099 0.592148 GCGTGGAGATAGTAGGGTCG 59.408 60.000 0.00 0.00 0.00 4.79
4120 8100 1.337387 GTGCGTGGAGATAGTAGGGTC 59.663 57.143 0.00 0.00 0.00 4.46
4121 8101 1.341679 TGTGCGTGGAGATAGTAGGGT 60.342 52.381 0.00 0.00 0.00 4.34
4122 8102 1.399714 TGTGCGTGGAGATAGTAGGG 58.600 55.000 0.00 0.00 0.00 3.53
4123 8103 4.072839 TCTATGTGCGTGGAGATAGTAGG 58.927 47.826 5.64 0.00 0.00 3.18
4124 8104 5.888691 ATCTATGTGCGTGGAGATAGTAG 57.111 43.478 5.64 0.00 0.00 2.57
4125 8105 6.040504 ACAAATCTATGTGCGTGGAGATAGTA 59.959 38.462 5.64 0.00 30.82 1.82
4126 8106 5.163405 ACAAATCTATGTGCGTGGAGATAGT 60.163 40.000 5.64 0.00 30.82 2.12
4127 8107 5.292765 ACAAATCTATGTGCGTGGAGATAG 58.707 41.667 0.00 0.00 30.82 2.08
4128 8108 5.276461 ACAAATCTATGTGCGTGGAGATA 57.724 39.130 0.00 0.00 30.82 1.98
4129 8109 4.142609 ACAAATCTATGTGCGTGGAGAT 57.857 40.909 0.00 0.00 30.82 2.75
4130 8110 3.610040 ACAAATCTATGTGCGTGGAGA 57.390 42.857 0.00 0.00 30.82 3.71
4131 8111 4.629634 TGTTACAAATCTATGTGCGTGGAG 59.370 41.667 0.00 0.00 34.75 3.86
4132 8112 4.570930 TGTTACAAATCTATGTGCGTGGA 58.429 39.130 0.00 0.00 34.75 4.02
4133 8113 4.629634 TCTGTTACAAATCTATGTGCGTGG 59.370 41.667 0.00 0.00 34.75 4.94
4134 8114 5.778161 TCTGTTACAAATCTATGTGCGTG 57.222 39.130 0.00 0.00 34.75 5.34
4135 8115 5.932303 ACTTCTGTTACAAATCTATGTGCGT 59.068 36.000 0.00 0.00 34.75 5.24
4136 8116 6.408858 ACTTCTGTTACAAATCTATGTGCG 57.591 37.500 0.00 0.00 34.75 5.34
4137 8117 8.883731 ACATACTTCTGTTACAAATCTATGTGC 58.116 33.333 5.27 0.00 34.75 4.57
4143 8123 9.778741 TTTCTGACATACTTCTGTTACAAATCT 57.221 29.630 0.00 0.00 0.00 2.40
4161 8141 9.710979 CGTCTGTTTAGTTTAAAATTTCTGACA 57.289 29.630 16.00 8.41 0.00 3.58
4162 8142 9.925268 TCGTCTGTTTAGTTTAAAATTTCTGAC 57.075 29.630 0.00 4.52 0.00 3.51
4172 8152 9.210329 TGCATAAATCTCGTCTGTTTAGTTTAA 57.790 29.630 0.00 0.00 0.00 1.52
4173 8153 8.766000 TGCATAAATCTCGTCTGTTTAGTTTA 57.234 30.769 0.00 0.00 0.00 2.01
4174 8154 7.667043 TGCATAAATCTCGTCTGTTTAGTTT 57.333 32.000 0.00 0.00 0.00 2.66
4175 8155 7.667043 TTGCATAAATCTCGTCTGTTTAGTT 57.333 32.000 0.00 0.00 0.00 2.24
4176 8156 7.360946 GGTTTGCATAAATCTCGTCTGTTTAGT 60.361 37.037 0.00 0.00 0.00 2.24
4177 8157 6.961554 GGTTTGCATAAATCTCGTCTGTTTAG 59.038 38.462 0.00 0.00 0.00 1.85
4178 8158 6.401688 CGGTTTGCATAAATCTCGTCTGTTTA 60.402 38.462 0.00 0.00 0.00 2.01
4179 8159 5.616866 CGGTTTGCATAAATCTCGTCTGTTT 60.617 40.000 0.00 0.00 0.00 2.83
4180 8160 4.142902 CGGTTTGCATAAATCTCGTCTGTT 60.143 41.667 0.00 0.00 0.00 3.16
4181 8161 3.370978 CGGTTTGCATAAATCTCGTCTGT 59.629 43.478 0.00 0.00 0.00 3.41
4182 8162 3.242413 CCGGTTTGCATAAATCTCGTCTG 60.242 47.826 0.00 0.00 0.00 3.51
4183 8163 2.936498 CCGGTTTGCATAAATCTCGTCT 59.064 45.455 0.00 0.00 0.00 4.18
4184 8164 2.933906 TCCGGTTTGCATAAATCTCGTC 59.066 45.455 0.00 0.00 0.00 4.20
4185 8165 2.676342 GTCCGGTTTGCATAAATCTCGT 59.324 45.455 0.00 0.00 0.00 4.18
4186 8166 2.675844 TGTCCGGTTTGCATAAATCTCG 59.324 45.455 0.00 0.00 0.00 4.04
4187 8167 3.938963 TCTGTCCGGTTTGCATAAATCTC 59.061 43.478 0.00 0.00 0.00 2.75
4188 8168 3.950397 TCTGTCCGGTTTGCATAAATCT 58.050 40.909 0.00 0.00 0.00 2.40
4189 8169 4.900635 ATCTGTCCGGTTTGCATAAATC 57.099 40.909 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.