Multiple sequence alignment - TraesCS6D01G164300

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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 TraesCS6D01G164300 chr6D 100.000 4742 0 0 1 4742 143404723 143399982 0.000000e+00 8757
1 TraesCS6D01G164300 chr6A 91.822 3497 178 40 182 3628 205101174 205104612 0.000000e+00 4774
2 TraesCS6D01G164300 chr6A 89.540 631 41 13 4126 4742 205105235 205105854 0.000000e+00 776
3 TraesCS6D01G164300 chr6A 82.778 180 8 9 3623 3796 205104639 205104801 6.400000e-29 139
4 TraesCS6D01G164300 chr6B 93.371 2836 135 23 818 3628 255271582 255268775 0.000000e+00 4146
5 TraesCS6D01G164300 chr6B 91.315 852 41 16 6 841 255272782 255271948 0.000000e+00 1133
6 TraesCS6D01G164300 chr6B 89.246 623 45 11 4126 4742 255268197 255267591 0.000000e+00 760
7 TraesCS6D01G164300 chr6B 89.249 586 55 5 1 579 255468867 255468283 0.000000e+00 726
8 TraesCS6D01G164300 chr6B 85.401 137 6 6 3623 3753 255268745 255268617 3.850000e-26 130
9 TraesCS6D01G164300 chr6B 93.750 80 4 1 373 452 109102226 109102148 8.340000e-23 119
10 TraesCS6D01G164300 chr5D 81.273 550 65 21 373 888 504576233 504576778 1.230000e-110 411
11 TraesCS6D01G164300 chr7A 78.938 565 79 25 364 894 642891638 642891080 9.770000e-92 348
12 TraesCS6D01G164300 chr4B 79.070 559 71 26 373 894 349151829 349151280 4.540000e-90 342
13 TraesCS6D01G164300 chr1A 79.767 430 50 22 373 771 137799202 137799625 1.300000e-70 278
14 TraesCS6D01G164300 chr3A 78.344 471 65 21 364 813 156130423 156130877 2.170000e-68 270


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 TraesCS6D01G164300 chr6D 143399982 143404723 4741 True 8757.000000 8757 100.000000 1 4742 1 chr6D.!!$R1 4741
1 TraesCS6D01G164300 chr6A 205101174 205105854 4680 False 1896.333333 4774 88.046667 182 4742 3 chr6A.!!$F1 4560
2 TraesCS6D01G164300 chr6B 255267591 255272782 5191 True 1542.250000 4146 89.833250 6 4742 4 chr6B.!!$R3 4736
3 TraesCS6D01G164300 chr6B 255468283 255468867 584 True 726.000000 726 89.249000 1 579 1 chr6B.!!$R2 578
4 TraesCS6D01G164300 chr5D 504576233 504576778 545 False 411.000000 411 81.273000 373 888 1 chr5D.!!$F1 515
5 TraesCS6D01G164300 chr7A 642891080 642891638 558 True 348.000000 348 78.938000 364 894 1 chr7A.!!$R1 530
6 TraesCS6D01G164300 chr4B 349151280 349151829 549 True 342.000000 342 79.070000 373 894 1 chr4B.!!$R1 521

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
876 1324 0.036765 TCCGAATCCACTTCCAACCG 60.037 55.0 0.00 0.00 0.0 4.44 F
889 1337 0.105964 CCAACCGGATCGCATTAGGA 59.894 55.0 9.46 0.00 0.0 2.94 F
1122 1577 0.543174 AAACAGAGAGGAGCTCCCGT 60.543 55.0 29.54 16.94 45.1 5.28 F
2996 3478 0.471617 ATGCTATGCCTGGGACACTC 59.528 55.0 0.00 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2609 3082 0.390472 CGAGGGTCCAAGAAGAGCAC 60.390 60.000 0.0 0.0 35.95 4.40 R
2721 3201 3.631250 TCCCAAAAAGACAGAAGCAACT 58.369 40.909 0.0 0.0 0.00 3.16 R
3119 3602 3.120060 CGATGAGAAGGTTTGCCTGAAAG 60.120 47.826 0.0 0.0 46.33 2.62 R
4516 5281 0.041238 TGCCCTCAGCTAGGTAGTGT 59.959 55.000 0.0 0.0 44.90 3.55 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
82 85 1.338579 GGACCAGCTCTATGCCTATGC 60.339 57.143 0.00 0.00 44.23 3.14
102 105 2.291043 AAAGGAGATGGCGGACCGT 61.291 57.895 16.73 0.00 39.70 4.83
114 117 4.370917 TGGCGGACCGTTTAATAGATTAC 58.629 43.478 16.73 0.00 39.70 1.89
359 364 3.859414 GGCCCTGATCTCGCTGCT 61.859 66.667 0.00 0.00 0.00 4.24
390 398 1.109920 TCCTCTGGTCCGCTATGAGC 61.110 60.000 0.00 0.00 38.02 4.26
466 477 5.284079 CAACACCCTGATGAGAAACAAAAG 58.716 41.667 0.00 0.00 0.00 2.27
478 492 7.938140 TGAGAAACAAAAGGAAGAGAAGAAA 57.062 32.000 0.00 0.00 0.00 2.52
654 693 3.006728 CAGACCGGGCTGGGGTTA 61.007 66.667 31.05 0.00 44.64 2.85
708 747 3.064987 GAGCTCTTCGGCGGTGCTA 62.065 63.158 7.21 0.00 34.35 3.49
783 825 2.266055 CGTCCCTCTGTTCTGGCC 59.734 66.667 0.00 0.00 0.00 5.36
784 826 2.286523 CGTCCCTCTGTTCTGGCCT 61.287 63.158 3.32 0.00 0.00 5.19
828 1273 5.518847 CGTTTCCTTTTCCTTTTTGAGTTCC 59.481 40.000 0.00 0.00 0.00 3.62
876 1324 0.036765 TCCGAATCCACTTCCAACCG 60.037 55.000 0.00 0.00 0.00 4.44
889 1337 0.105964 CCAACCGGATCGCATTAGGA 59.894 55.000 9.46 0.00 0.00 2.94
890 1338 1.270839 CCAACCGGATCGCATTAGGAT 60.271 52.381 9.46 0.00 0.00 3.24
900 1348 5.455326 GGATCGCATTAGGATATAAGCCCAT 60.455 44.000 0.00 0.00 0.00 4.00
981 1432 2.963599 TTAAAGGAGAAAAGCCCGGT 57.036 45.000 0.00 0.00 0.00 5.28
994 1445 1.376812 CCCGGTTTTCCTTCCTCCG 60.377 63.158 0.00 0.00 40.72 4.63
1048 1499 0.958876 CAAACCCTCGCAAGTACCCC 60.959 60.000 0.00 0.00 39.48 4.95
1055 1506 2.675371 GCAAGTACCCCCTCCCAC 59.325 66.667 0.00 0.00 0.00 4.61
1056 1507 2.987125 CAAGTACCCCCTCCCACG 59.013 66.667 0.00 0.00 0.00 4.94
1057 1508 2.285144 AAGTACCCCCTCCCACGG 60.285 66.667 0.00 0.00 0.00 4.94
1103 1558 3.379445 GGAGACGGAGGCGACCAA 61.379 66.667 0.00 0.00 0.00 3.67
1120 1575 1.339535 CCAAAACAGAGAGGAGCTCCC 60.340 57.143 29.54 19.90 45.10 4.30
1122 1577 0.543174 AAACAGAGAGGAGCTCCCGT 60.543 55.000 29.54 16.94 45.10 5.28
1215 1670 2.483188 CCAGGTACGTTCCTTGGCTATC 60.483 54.545 11.54 0.00 35.37 2.08
1219 1674 1.148498 CGTTCCTTGGCTATCCCCC 59.852 63.158 0.00 0.00 0.00 5.40
1282 1737 1.136984 CGTAGGAGTGTGCGAGGAC 59.863 63.158 0.00 0.00 0.00 3.85
1356 1811 2.966516 GCCTAGTTAGGAGCACCTGTAT 59.033 50.000 13.60 0.67 46.63 2.29
1366 1827 1.004745 AGCACCTGTATTTCCCACCAG 59.995 52.381 0.00 0.00 0.00 4.00
1455 1916 5.007626 TCGAAATGAGCCTGGATTTAAATCG 59.992 40.000 19.41 9.10 36.27 3.34
1472 1933 9.813080 ATTTAAATCGATAAAAGCTCTAATCGC 57.187 29.630 15.75 0.00 40.68 4.58
1478 1939 2.789409 AAAGCTCTAATCGCCCAAGT 57.211 45.000 0.00 0.00 0.00 3.16
1508 1969 5.777850 ACACATACTTAAAACCCAACACC 57.222 39.130 0.00 0.00 0.00 4.16
1545 2006 8.816144 CAAGCTTTACATAAAGAAGCACAAAAA 58.184 29.630 14.27 0.00 46.17 1.94
1604 2065 2.625737 CTCATTGTCAGGATCAAGCGT 58.374 47.619 0.00 0.00 0.00 5.07
1625 2086 2.595238 ACTTCTGTAGTCTCGGTGGTT 58.405 47.619 0.00 0.00 28.23 3.67
1637 2098 1.666700 TCGGTGGTTGTTTTTCGTCTG 59.333 47.619 0.00 0.00 0.00 3.51
1883 2344 0.741574 TCGCGCCATGTAATTTCCGT 60.742 50.000 0.00 0.00 0.00 4.69
1893 2354 5.692654 CCATGTAATTTCCGTTTTTCCGTTT 59.307 36.000 0.00 0.00 0.00 3.60
1911 2372 3.723835 CGTTTTAGATTTTGCGGGTCTCG 60.724 47.826 0.00 0.00 42.76 4.04
2028 2491 1.134521 GGCCACAGGTCATTCGTCATA 60.135 52.381 0.00 0.00 0.00 2.15
2036 2499 3.071602 AGGTCATTCGTCATAAGGGATGG 59.928 47.826 0.00 0.00 36.08 3.51
2449 2922 5.848921 ACTTCTCATGCCCTTCCTCTATAAT 59.151 40.000 0.00 0.00 0.00 1.28
2450 2923 5.752036 TCTCATGCCCTTCCTCTATAATG 57.248 43.478 0.00 0.00 0.00 1.90
2462 2935 7.018650 CCTTCCTCTATAATGGGGTAATTCCTT 59.981 40.741 0.00 0.00 36.25 3.36
2528 3001 5.726980 TTCACCCTAAACGTAGAGCTTTA 57.273 39.130 0.00 0.00 0.00 1.85
2538 3011 4.369182 ACGTAGAGCTTTATGTGCATACC 58.631 43.478 8.27 0.00 0.00 2.73
2551 3024 5.132897 TGTGCATACCACCTCAAAATTTC 57.867 39.130 0.00 0.00 44.01 2.17
2563 3036 8.150296 CCACCTCAAAATTTCCAATTTCTAGTT 58.850 33.333 0.00 0.00 0.00 2.24
2609 3082 6.873076 ACTATTGCATTTTGGGTTTACACATG 59.127 34.615 0.00 0.00 0.00 3.21
2690 3170 6.049955 TCTGTAGTTGCAAATAGGCTTACT 57.950 37.500 6.89 0.00 35.00 2.24
2702 3182 5.975988 ATAGGCTTACTCCCATTTCTTGA 57.024 39.130 0.00 0.00 0.00 3.02
2718 3198 4.998671 TCTTGAAATCTGTTGGCAAACA 57.001 36.364 6.47 6.47 44.06 2.83
2720 3200 4.402155 TCTTGAAATCTGTTGGCAAACACT 59.598 37.500 1.39 0.00 41.41 3.55
2721 3201 5.592282 TCTTGAAATCTGTTGGCAAACACTA 59.408 36.000 1.39 0.00 41.41 2.74
2726 3206 2.357637 TCTGTTGGCAAACACTAGTTGC 59.642 45.455 1.39 9.16 41.41 4.17
2751 3231 5.147032 TCTGTCTTTTTGGGAACATCCATT 58.853 37.500 0.00 0.00 42.32 3.16
2996 3478 0.471617 ATGCTATGCCTGGGACACTC 59.528 55.000 0.00 0.00 0.00 3.51
3061 3543 0.605319 TACCGCCTTCAAACTGCCAG 60.605 55.000 0.00 0.00 0.00 4.85
3074 3556 5.047377 TCAAACTGCCAGACATTTAAATCCC 60.047 40.000 0.00 0.00 0.00 3.85
3081 3563 7.610865 TGCCAGACATTTAAATCCCTTTTAAG 58.389 34.615 0.00 0.00 40.08 1.85
3119 3602 5.705609 TGCTTACCCTGTCTTCATTTTTC 57.294 39.130 0.00 0.00 0.00 2.29
3202 3685 9.942850 AAAAGAAGAAGAAAAGATTGAAAACCA 57.057 25.926 0.00 0.00 0.00 3.67
3223 3706 6.130569 ACCACAACTACTGGGTAATTTTCAA 58.869 36.000 0.00 0.00 32.45 2.69
3224 3707 6.780522 ACCACAACTACTGGGTAATTTTCAAT 59.219 34.615 0.00 0.00 32.45 2.57
3229 3712 5.949952 ACTACTGGGTAATTTTCAATGTCCC 59.050 40.000 0.00 0.00 0.00 4.46
3233 3716 3.759618 GGGTAATTTTCAATGTCCCGTCA 59.240 43.478 0.00 0.00 0.00 4.35
3254 3737 8.765219 CCGTCATCTCGTATGATTTTCTTTTAT 58.235 33.333 6.51 0.00 0.00 1.40
3420 3903 5.984695 AGAATCCTAATGCTATGCGTCTA 57.015 39.130 0.00 0.00 0.00 2.59
3460 3943 0.394565 GAGTTGAGTGTGGCAGACCT 59.605 55.000 11.60 0.79 36.63 3.85
3483 3966 3.817647 AGGCAGTTTCTGAATTCTGTGTC 59.182 43.478 17.75 2.43 32.44 3.67
3490 3973 2.300152 TCTGAATTCTGTGTCGAGGCTT 59.700 45.455 7.05 0.00 0.00 4.35
3534 4017 7.414540 GGTTGACAGGTTGAGATATCAATTGTC 60.415 40.741 26.90 26.90 41.72 3.18
3541 4024 8.844244 AGGTTGAGATATCAATTGTCTTTATGC 58.156 33.333 5.98 0.00 31.79 3.14
3665 4189 4.039245 ACGGATAATGTATCACCTGTGAGG 59.961 45.833 6.13 0.00 43.61 3.86
3702 4232 3.004106 GCATAATGTTCACCTCTCCATGC 59.996 47.826 0.00 0.00 0.00 4.06
3706 4236 0.460987 GTTCACCTCTCCATGCTCCG 60.461 60.000 0.00 0.00 0.00 4.63
3743 4273 3.808466 TGTGCTTTATGTGTTTGCCAA 57.192 38.095 0.00 0.00 0.00 4.52
3777 4307 8.879227 TCCTTTGGGAATGAGATTTTATGTTTT 58.121 29.630 0.00 0.00 38.93 2.43
3782 4312 7.454380 TGGGAATGAGATTTTATGTTTTCCTGT 59.546 33.333 0.00 0.00 33.51 4.00
3789 4319 9.774742 GAGATTTTATGTTTTCCTGTATGTGTC 57.225 33.333 0.00 0.00 0.00 3.67
3796 4326 7.124347 TGTTTTCCTGTATGTGTCGTTATTC 57.876 36.000 0.00 0.00 0.00 1.75
3798 4328 7.442969 TGTTTTCCTGTATGTGTCGTTATTCTT 59.557 33.333 0.00 0.00 0.00 2.52
3799 4329 7.591006 TTTCCTGTATGTGTCGTTATTCTTC 57.409 36.000 0.00 0.00 0.00 2.87
3813 4343 9.474249 GTCGTTATTCTTCTTAATACAAACAGC 57.526 33.333 0.00 0.00 0.00 4.40
3814 4344 9.210329 TCGTTATTCTTCTTAATACAAACAGCA 57.790 29.630 0.00 0.00 0.00 4.41
3815 4345 9.478019 CGTTATTCTTCTTAATACAAACAGCAG 57.522 33.333 0.00 0.00 0.00 4.24
3819 4349 9.899226 ATTCTTCTTAATACAAACAGCAGAAAC 57.101 29.630 0.00 0.00 0.00 2.78
3820 4350 8.445275 TCTTCTTAATACAAACAGCAGAAACA 57.555 30.769 0.00 0.00 0.00 2.83
3821 4351 9.066892 TCTTCTTAATACAAACAGCAGAAACAT 57.933 29.630 0.00 0.00 0.00 2.71
3822 4352 9.683069 CTTCTTAATACAAACAGCAGAAACATT 57.317 29.630 0.00 0.00 0.00 2.71
3824 4354 9.462174 TCTTAATACAAACAGCAGAAACATTTG 57.538 29.630 0.00 0.00 36.54 2.32
3825 4355 9.462174 CTTAATACAAACAGCAGAAACATTTGA 57.538 29.630 2.27 0.00 34.93 2.69
3826 4356 9.809096 TTAATACAAACAGCAGAAACATTTGAA 57.191 25.926 2.27 0.00 34.93 2.69
3827 4357 7.935338 ATACAAACAGCAGAAACATTTGAAG 57.065 32.000 2.27 0.00 34.93 3.02
3828 4358 4.567959 ACAAACAGCAGAAACATTTGAAGC 59.432 37.500 2.27 0.00 34.93 3.86
3829 4359 4.389890 AACAGCAGAAACATTTGAAGCA 57.610 36.364 0.00 0.00 0.00 3.91
3830 4360 3.709987 ACAGCAGAAACATTTGAAGCAC 58.290 40.909 0.00 0.00 0.00 4.40
3832 4362 4.580167 ACAGCAGAAACATTTGAAGCACTA 59.420 37.500 0.00 0.00 0.00 2.74
3833 4363 5.152097 CAGCAGAAACATTTGAAGCACTAG 58.848 41.667 0.00 0.00 0.00 2.57
3835 4365 4.913924 GCAGAAACATTTGAAGCACTAGTG 59.086 41.667 18.93 18.93 0.00 2.74
3854 4384 9.901724 CACTAGTGCAAAATTAATTAGTCGTAG 57.098 33.333 10.54 2.35 0.00 3.51
3855 4385 8.601476 ACTAGTGCAAAATTAATTAGTCGTAGC 58.399 33.333 0.01 0.00 0.00 3.58
3858 4388 6.957077 GTGCAAAATTAATTAGTCGTAGCGAA 59.043 34.615 0.01 0.00 37.72 4.70
3859 4389 7.638683 GTGCAAAATTAATTAGTCGTAGCGAAT 59.361 33.333 0.01 0.00 37.72 3.34
3860 4390 8.819015 TGCAAAATTAATTAGTCGTAGCGAATA 58.181 29.630 0.01 0.00 37.72 1.75
3888 4418 6.197364 ACTATATATGCTGAACCTCTACGC 57.803 41.667 0.00 0.00 0.00 4.42
3892 4422 9.274206 CTATATATGCTGAACCTCTACGCTATA 57.726 37.037 0.00 0.00 0.00 1.31
3894 4424 5.730296 ATGCTGAACCTCTACGCTATATT 57.270 39.130 0.00 0.00 0.00 1.28
3895 4425 6.835819 ATGCTGAACCTCTACGCTATATTA 57.164 37.500 0.00 0.00 0.00 0.98
3896 4426 6.835819 TGCTGAACCTCTACGCTATATTAT 57.164 37.500 0.00 0.00 0.00 1.28
3897 4427 7.228314 TGCTGAACCTCTACGCTATATTATT 57.772 36.000 0.00 0.00 0.00 1.40
3902 4631 9.074576 TGAACCTCTACGCTATATTATTCTTGA 57.925 33.333 0.00 0.00 0.00 3.02
3919 4648 9.627123 TTATTCTTGATAAATACAAGGGTCTGG 57.373 33.333 0.00 0.00 43.11 3.86
3920 4649 5.437060 TCTTGATAAATACAAGGGTCTGGC 58.563 41.667 0.00 0.00 43.11 4.85
3921 4650 4.853468 TGATAAATACAAGGGTCTGGCA 57.147 40.909 0.00 0.00 0.00 4.92
3922 4651 5.186256 TGATAAATACAAGGGTCTGGCAA 57.814 39.130 0.00 0.00 0.00 4.52
3923 4652 5.192927 TGATAAATACAAGGGTCTGGCAAG 58.807 41.667 0.00 0.00 0.00 4.01
3924 4653 1.839424 AATACAAGGGTCTGGCAAGC 58.161 50.000 0.00 0.00 0.00 4.01
3925 4654 0.995024 ATACAAGGGTCTGGCAAGCT 59.005 50.000 0.00 0.00 0.00 3.74
3926 4655 0.324943 TACAAGGGTCTGGCAAGCTC 59.675 55.000 0.00 0.00 0.00 4.09
3927 4656 1.377994 CAAGGGTCTGGCAAGCTCT 59.622 57.895 0.00 0.00 0.00 4.09
3928 4657 0.959372 CAAGGGTCTGGCAAGCTCTG 60.959 60.000 0.00 0.00 0.00 3.35
3929 4658 2.045536 GGGTCTGGCAAGCTCTGG 60.046 66.667 0.00 0.00 0.00 3.86
3930 4659 2.596851 GGGTCTGGCAAGCTCTGGA 61.597 63.158 0.00 0.00 0.00 3.86
3931 4660 1.376553 GGTCTGGCAAGCTCTGGAC 60.377 63.158 0.00 0.00 0.00 4.02
3932 4661 1.372683 GTCTGGCAAGCTCTGGACA 59.627 57.895 0.00 0.00 0.00 4.02
3933 4662 0.250467 GTCTGGCAAGCTCTGGACAA 60.250 55.000 0.00 0.00 0.00 3.18
3934 4663 0.473755 TCTGGCAAGCTCTGGACAAA 59.526 50.000 0.00 0.00 0.00 2.83
3935 4664 1.133823 TCTGGCAAGCTCTGGACAAAA 60.134 47.619 0.00 0.00 0.00 2.44
3936 4665 1.891150 CTGGCAAGCTCTGGACAAAAT 59.109 47.619 0.00 0.00 0.00 1.82
3937 4666 1.888512 TGGCAAGCTCTGGACAAAATC 59.111 47.619 0.00 0.00 0.00 2.17
3938 4667 2.165998 GGCAAGCTCTGGACAAAATCT 58.834 47.619 0.00 0.00 0.00 2.40
3939 4668 2.560105 GGCAAGCTCTGGACAAAATCTT 59.440 45.455 0.00 0.00 0.00 2.40
3940 4669 3.006217 GGCAAGCTCTGGACAAAATCTTT 59.994 43.478 0.00 0.00 0.00 2.52
3941 4670 3.985925 GCAAGCTCTGGACAAAATCTTTG 59.014 43.478 0.00 0.00 0.00 2.77
3942 4671 4.261741 GCAAGCTCTGGACAAAATCTTTGA 60.262 41.667 6.15 0.00 0.00 2.69
3943 4672 5.737063 GCAAGCTCTGGACAAAATCTTTGAA 60.737 40.000 6.15 0.00 0.00 2.69
3944 4673 6.453092 CAAGCTCTGGACAAAATCTTTGAAT 58.547 36.000 6.15 0.00 0.00 2.57
3945 4674 6.661304 AGCTCTGGACAAAATCTTTGAATT 57.339 33.333 6.15 0.00 0.00 2.17
3946 4675 6.453092 AGCTCTGGACAAAATCTTTGAATTG 58.547 36.000 6.15 0.00 0.00 2.32
3971 4700 9.462174 TGACAAATTTGATAGTACAAAAAGCAG 57.538 29.630 24.64 0.00 41.88 4.24
3984 4713 8.817100 AGTACAAAAAGCAGAAAAATGTAAAGC 58.183 29.630 0.00 0.00 0.00 3.51
3985 4714 7.608308 ACAAAAAGCAGAAAAATGTAAAGCA 57.392 28.000 0.00 0.00 0.00 3.91
3987 4716 7.334171 ACAAAAAGCAGAAAAATGTAAAGCAGT 59.666 29.630 0.00 0.00 0.00 4.40
3988 4717 8.816144 CAAAAAGCAGAAAAATGTAAAGCAGTA 58.184 29.630 0.00 0.00 0.00 2.74
3990 4719 6.884280 AGCAGAAAAATGTAAAGCAGTAGT 57.116 33.333 0.00 0.00 0.00 2.73
3991 4720 6.672147 AGCAGAAAAATGTAAAGCAGTAGTG 58.328 36.000 0.00 0.00 0.00 2.74
4026 4755 8.437360 TGATATATGGTAAAGTGTTTCTGCTG 57.563 34.615 0.00 0.00 0.00 4.41
4027 4756 8.046708 TGATATATGGTAAAGTGTTTCTGCTGT 58.953 33.333 0.00 0.00 0.00 4.40
4029 4758 5.852282 ATGGTAAAGTGTTTCTGCTGTTT 57.148 34.783 0.00 0.00 0.00 2.83
4030 4759 4.992688 TGGTAAAGTGTTTCTGCTGTTTG 58.007 39.130 0.00 0.00 0.00 2.93
4039 4791 7.767261 AGTGTTTCTGCTGTTTGTATTAAACA 58.233 30.769 5.27 5.27 37.76 2.83
4042 4794 7.168972 TGTTTCTGCTGTTTGTATTAAACATGC 59.831 33.333 5.77 10.98 39.16 4.06
4048 4800 8.961634 TGCTGTTTGTATTAAACATGCCTATTA 58.038 29.630 16.54 0.00 39.16 0.98
4061 4813 9.732130 AAACATGCCTATTAAGAGATTCTATCC 57.268 33.333 0.00 0.00 0.00 2.59
4069 4821 6.576662 TTAAGAGATTCTATCCGTAGCCTG 57.423 41.667 0.00 0.00 0.00 4.85
4072 4824 3.821600 GAGATTCTATCCGTAGCCTGTGA 59.178 47.826 0.00 0.00 0.00 3.58
4074 4826 1.306148 TCTATCCGTAGCCTGTGACG 58.694 55.000 0.00 0.00 38.79 4.35
4081 4833 1.068472 CGTAGCCTGTGACGAACTCTT 60.068 52.381 0.00 0.00 41.60 2.85
4082 4834 2.161012 CGTAGCCTGTGACGAACTCTTA 59.839 50.000 0.00 0.00 41.60 2.10
4083 4835 3.181499 CGTAGCCTGTGACGAACTCTTAT 60.181 47.826 0.00 0.00 41.60 1.73
4084 4836 4.034858 CGTAGCCTGTGACGAACTCTTATA 59.965 45.833 0.00 0.00 41.60 0.98
4085 4837 5.277876 CGTAGCCTGTGACGAACTCTTATAT 60.278 44.000 0.00 0.00 41.60 0.86
4086 4838 5.599999 AGCCTGTGACGAACTCTTATATT 57.400 39.130 0.00 0.00 0.00 1.28
4087 4839 5.978814 AGCCTGTGACGAACTCTTATATTT 58.021 37.500 0.00 0.00 0.00 1.40
4088 4840 5.812642 AGCCTGTGACGAACTCTTATATTTG 59.187 40.000 0.00 0.00 0.00 2.32
4089 4841 5.581085 GCCTGTGACGAACTCTTATATTTGT 59.419 40.000 0.00 0.00 0.00 2.83
4090 4842 6.237861 GCCTGTGACGAACTCTTATATTTGTC 60.238 42.308 0.00 0.00 38.98 3.18
4091 4843 6.811665 CCTGTGACGAACTCTTATATTTGTCA 59.188 38.462 3.46 3.46 43.72 3.58
4092 4844 7.330946 CCTGTGACGAACTCTTATATTTGTCAA 59.669 37.037 8.29 0.00 46.08 3.18
4093 4845 8.239681 TGTGACGAACTCTTATATTTGTCAAG 57.760 34.615 8.29 0.00 46.08 3.02
4094 4846 8.085909 TGTGACGAACTCTTATATTTGTCAAGA 58.914 33.333 8.29 0.00 46.08 3.02
4095 4847 8.922676 GTGACGAACTCTTATATTTGTCAAGAA 58.077 33.333 8.29 0.00 46.08 2.52
4096 4848 9.653287 TGACGAACTCTTATATTTGTCAAGAAT 57.347 29.630 4.87 0.00 43.23 2.40
4115 4867 9.330063 TCAAGAATATGACATAAAGATGGTGAC 57.670 33.333 0.00 0.00 37.39 3.67
4116 4868 7.953158 AGAATATGACATAAAGATGGTGACG 57.047 36.000 0.00 0.00 37.39 4.35
4117 4869 7.500992 AGAATATGACATAAAGATGGTGACGT 58.499 34.615 0.00 0.00 37.39 4.34
4118 4870 7.987458 AGAATATGACATAAAGATGGTGACGTT 59.013 33.333 0.00 0.00 37.39 3.99
4119 4871 8.506168 AATATGACATAAAGATGGTGACGTTT 57.494 30.769 0.00 0.00 37.39 3.60
4120 4872 6.817765 ATGACATAAAGATGGTGACGTTTT 57.182 33.333 0.00 0.00 37.39 2.43
4121 4873 6.627395 TGACATAAAGATGGTGACGTTTTT 57.373 33.333 0.00 0.00 37.42 1.94
4122 4874 7.731882 TGACATAAAGATGGTGACGTTTTTA 57.268 32.000 0.00 0.00 39.40 1.52
4123 4875 8.155821 TGACATAAAGATGGTGACGTTTTTAA 57.844 30.769 0.00 0.00 38.79 1.52
4124 4876 8.071368 TGACATAAAGATGGTGACGTTTTTAAC 58.929 33.333 0.00 0.00 38.79 2.01
4147 4899 7.005062 ACGAAATTATGTTCTCTATGTGTGC 57.995 36.000 0.00 0.00 0.00 4.57
4171 4923 6.484977 GCTTGGACAATTTTTGTTTCCCATTA 59.515 34.615 0.00 0.00 45.52 1.90
4174 4926 7.569240 TGGACAATTTTTGTTTCCCATTAACT 58.431 30.769 0.00 0.00 45.52 2.24
4175 4927 7.497249 TGGACAATTTTTGTTTCCCATTAACTG 59.503 33.333 0.00 0.00 45.52 3.16
4176 4928 7.713073 GGACAATTTTTGTTTCCCATTAACTGA 59.287 33.333 0.00 0.00 45.52 3.41
4177 4929 8.432110 ACAATTTTTGTTTCCCATTAACTGAC 57.568 30.769 0.00 0.00 42.22 3.51
4187 4950 7.773489 TTCCCATTAACTGACAAAATCATGA 57.227 32.000 0.00 0.00 36.48 3.07
4199 4962 9.956720 CTGACAAAATCATGATAAAATCTACCC 57.043 33.333 9.04 0.00 36.48 3.69
4236 4999 2.727777 TGCGCAAGTATAAGTCGCTAG 58.272 47.619 8.16 0.00 45.24 3.42
4241 5004 3.043586 CAAGTATAAGTCGCTAGCCGTG 58.956 50.000 9.66 0.00 38.35 4.94
4291 5054 8.375506 TGAGTTAAATTGAGTGAGTACAGGAAT 58.624 33.333 0.00 0.00 0.00 3.01
4297 5060 5.598416 TGAGTGAGTACAGGAATACATGG 57.402 43.478 0.00 0.00 31.68 3.66
4299 5062 5.719563 TGAGTGAGTACAGGAATACATGGAA 59.280 40.000 0.00 0.00 31.68 3.53
4300 5063 5.978814 AGTGAGTACAGGAATACATGGAAC 58.021 41.667 0.00 0.00 31.68 3.62
4345 5108 6.038714 CAGTCCAATAAGAATCTTACAAGCCC 59.961 42.308 4.66 0.00 0.00 5.19
4346 5109 5.885912 GTCCAATAAGAATCTTACAAGCCCA 59.114 40.000 4.66 0.00 0.00 5.36
4347 5110 5.885912 TCCAATAAGAATCTTACAAGCCCAC 59.114 40.000 4.66 0.00 0.00 4.61
4348 5111 5.220854 CCAATAAGAATCTTACAAGCCCACG 60.221 44.000 4.66 0.00 0.00 4.94
4349 5112 3.418684 AAGAATCTTACAAGCCCACGT 57.581 42.857 0.00 0.00 0.00 4.49
4350 5113 3.418684 AGAATCTTACAAGCCCACGTT 57.581 42.857 0.00 0.00 0.00 3.99
4351 5114 3.074412 AGAATCTTACAAGCCCACGTTG 58.926 45.455 0.00 0.00 0.00 4.10
4376 5139 4.388485 ACCATTGCCAAAAGAAATCAACC 58.612 39.130 0.00 0.00 0.00 3.77
4378 5141 4.213906 CCATTGCCAAAAGAAATCAACCAC 59.786 41.667 0.00 0.00 0.00 4.16
4389 5152 0.536460 ATCAACCACACACGGAACCC 60.536 55.000 0.00 0.00 0.00 4.11
4390 5153 1.452289 CAACCACACACGGAACCCA 60.452 57.895 0.00 0.00 0.00 4.51
4391 5154 1.153046 AACCACACACGGAACCCAG 60.153 57.895 0.00 0.00 0.00 4.45
4404 5167 3.600388 GGAACCCAGACAAGTACATCTG 58.400 50.000 12.52 12.52 41.75 2.90
4421 5184 0.400213 CTGTGGACTGGTAAAGGGCA 59.600 55.000 0.00 0.00 0.00 5.36
4465 5228 1.795768 ACAACCATACGCACAGACAG 58.204 50.000 0.00 0.00 0.00 3.51
4478 5243 3.251729 GCACAGACAGACACAAATCACAT 59.748 43.478 0.00 0.00 0.00 3.21
4606 5371 0.965866 TCTCTTCGGTGATGGCGTCT 60.966 55.000 8.40 0.00 0.00 4.18
4645 5413 2.667418 CCCTGGACAGAGCTGGTG 59.333 66.667 0.00 0.00 34.19 4.17
4681 5449 6.096846 TGAACAGATCGTCATTCTCCAAGATA 59.903 38.462 0.00 0.00 0.00 1.98
4682 5450 6.471233 ACAGATCGTCATTCTCCAAGATAA 57.529 37.500 0.00 0.00 0.00 1.75
4723 5491 1.004044 CCCTTGAGCATCTCCACAACT 59.996 52.381 0.00 0.00 34.92 3.16
4726 5494 3.405831 CTTGAGCATCTCCACAACTTCA 58.594 45.455 0.00 0.00 34.92 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 85 1.452108 GGTCCGCCATCTCCTTTGG 60.452 63.158 0.00 0.00 37.31 3.28
95 98 4.147653 CAGCGTAATCTATTAAACGGTCCG 59.852 45.833 10.48 10.48 0.00 4.79
114 117 8.909708 TTATAAACTTTCCATCAATTTCAGCG 57.090 30.769 0.00 0.00 0.00 5.18
143 146 3.651562 ACACGACGTTTTTGTCTTCTG 57.348 42.857 0.00 0.00 36.71 3.02
358 363 0.894141 CAGAGGACTGGACTGGACAG 59.106 60.000 0.00 0.00 40.14 3.51
359 364 3.057749 CAGAGGACTGGACTGGACA 57.942 57.895 0.00 0.00 40.14 4.02
390 398 1.579698 CCGGATGCAGAGTGAAGATG 58.420 55.000 0.00 0.00 0.00 2.90
466 477 5.046231 ACACATACTCCCTTTCTTCTCTTCC 60.046 44.000 0.00 0.00 0.00 3.46
478 492 3.748645 AGACTGAGACACATACTCCCT 57.251 47.619 0.00 0.00 33.95 4.20
556 595 8.045507 TGATAATTCTCTGAATCTCAACTTGCT 58.954 33.333 0.00 0.00 0.00 3.91
783 825 2.202623 GGCGCACGACTACTGGAG 60.203 66.667 10.83 0.00 0.00 3.86
784 826 3.755628 GGGCGCACGACTACTGGA 61.756 66.667 10.83 0.00 0.00 3.86
828 1273 0.447801 CCTCCACAAATTCGAAGGCG 59.552 55.000 3.35 0.00 39.35 5.52
876 1324 4.141711 TGGGCTTATATCCTAATGCGATCC 60.142 45.833 0.00 0.00 0.00 3.36
994 1445 1.449778 GAAGGGAACAGCCGTAGCC 60.450 63.158 0.00 0.00 41.25 3.93
1103 1558 0.543174 ACGGGAGCTCCTCTCTGTTT 60.543 55.000 31.36 5.08 41.60 2.83
1122 1577 3.800863 GAGCTGAGACGTCGCCGA 61.801 66.667 16.94 0.00 37.88 5.54
1219 1674 0.612174 TCTCTTCTCACAGGACCGGG 60.612 60.000 6.32 0.00 0.00 5.73
1366 1827 1.006454 GGAGCGTAGTAATCGGCCC 60.006 63.158 0.00 0.00 0.00 5.80
1455 1916 4.816925 ACTTGGGCGATTAGAGCTTTTATC 59.183 41.667 0.00 0.00 34.52 1.75
1497 1958 2.520741 CCCAGCGGTGTTGGGTTT 60.521 61.111 14.40 0.00 46.83 3.27
1508 1969 1.031571 TAAAGCTTGCATCCCCAGCG 61.032 55.000 0.00 0.00 33.85 5.18
1545 2006 0.469070 GTCTCCCTGCTGCTCATGAT 59.531 55.000 0.00 0.00 0.00 2.45
1604 2065 3.430042 ACCACCGAGACTACAGAAGTA 57.570 47.619 0.00 0.00 39.07 2.24
1625 2086 2.218603 GAGGAAGCCAGACGAAAAACA 58.781 47.619 0.00 0.00 0.00 2.83
1637 2098 6.596621 ACTAGATTAAAGAATGGAGGAAGCC 58.403 40.000 0.00 0.00 0.00 4.35
1782 2243 5.280945 TCAAACAGTATCAAAAGTGCAAGC 58.719 37.500 0.00 0.00 0.00 4.01
1883 2344 4.745620 CCCGCAAAATCTAAAACGGAAAAA 59.254 37.500 0.00 0.00 43.19 1.94
1893 2354 2.754946 ACGAGACCCGCAAAATCTAA 57.245 45.000 0.00 0.00 43.32 2.10
1935 2396 4.283363 AGACTAATCTAGCATGCCATGG 57.717 45.455 15.66 7.63 31.46 3.66
2036 2499 3.631686 TGTGCATATGAATGGTAGGCAAC 59.368 43.478 6.97 0.00 40.06 4.17
2243 2708 6.374333 ACAAATTTCTGCATGACCTTATACGT 59.626 34.615 0.00 0.00 0.00 3.57
2244 2709 6.785191 ACAAATTTCTGCATGACCTTATACG 58.215 36.000 0.00 0.00 0.00 3.06
2254 2719 6.599244 TCTCTACCCTTACAAATTTCTGCATG 59.401 38.462 0.00 0.00 0.00 4.06
2339 2804 1.181098 ACAATCACCTGCCCACAAGC 61.181 55.000 0.00 0.00 0.00 4.01
2462 2935 2.111460 ACAAAGCCGCAACCCGTA 59.889 55.556 0.00 0.00 34.38 4.02
2528 3001 5.337491 GGAAATTTTGAGGTGGTATGCACAT 60.337 40.000 0.00 0.00 0.00 3.21
2538 3011 9.196552 GAACTAGAAATTGGAAATTTTGAGGTG 57.803 33.333 0.00 0.00 0.00 4.00
2551 3024 5.734720 TCAGTAGGCAGAACTAGAAATTGG 58.265 41.667 0.00 0.00 0.00 3.16
2563 3036 2.632512 TGACATGTGTTCAGTAGGCAGA 59.367 45.455 1.15 0.00 0.00 4.26
2609 3082 0.390472 CGAGGGTCCAAGAAGAGCAC 60.390 60.000 0.00 0.00 35.95 4.40
2690 3170 4.021192 GCCAACAGATTTCAAGAAATGGGA 60.021 41.667 12.39 0.00 40.77 4.37
2702 3182 5.591099 CAACTAGTGTTTGCCAACAGATTT 58.409 37.500 3.15 0.00 43.83 2.17
2718 3198 4.580580 CCCAAAAAGACAGAAGCAACTAGT 59.419 41.667 0.00 0.00 0.00 2.57
2720 3200 4.787551 TCCCAAAAAGACAGAAGCAACTA 58.212 39.130 0.00 0.00 0.00 2.24
2721 3201 3.631250 TCCCAAAAAGACAGAAGCAACT 58.369 40.909 0.00 0.00 0.00 3.16
2726 3206 4.584325 TGGATGTTCCCAAAAAGACAGAAG 59.416 41.667 0.00 0.00 35.03 2.85
2996 3478 3.734902 GCATTTCAATTACGCTCTTGGGG 60.735 47.826 0.00 0.00 0.00 4.96
3074 3556 8.992073 AGCAATAATGTCCAAAAAGCTTAAAAG 58.008 29.630 0.00 0.00 0.00 2.27
3081 3563 5.580691 GGGTAAGCAATAATGTCCAAAAAGC 59.419 40.000 0.00 0.00 0.00 3.51
3119 3602 3.120060 CGATGAGAAGGTTTGCCTGAAAG 60.120 47.826 0.00 0.00 46.33 2.62
3141 3624 7.176690 TGGTTTACATTTTCTTCCTCAGAATCC 59.823 37.037 0.00 0.00 41.42 3.01
3201 3684 7.657336 ACATTGAAAATTACCCAGTAGTTGTG 58.343 34.615 0.00 0.00 0.00 3.33
3202 3685 7.039993 GGACATTGAAAATTACCCAGTAGTTGT 60.040 37.037 0.00 0.00 0.00 3.32
3223 3706 2.583143 TCATACGAGATGACGGGACAT 58.417 47.619 0.00 0.00 37.61 3.06
3224 3707 2.047002 TCATACGAGATGACGGGACA 57.953 50.000 0.00 0.00 37.61 4.02
3254 3737 9.220906 ACATTAGGAACCATTAGGATAACAGTA 57.779 33.333 0.00 0.00 38.69 2.74
3263 3746 9.057089 GTCTGATAAACATTAGGAACCATTAGG 57.943 37.037 0.00 0.00 42.21 2.69
3273 3756 7.921786 TGTTTCAGGTCTGATAAACATTAGG 57.078 36.000 11.85 0.00 39.64 2.69
3339 3822 0.827368 GACTCAGGAATTCGAGGGCT 59.173 55.000 13.02 0.00 33.36 5.19
3460 3943 4.973168 ACACAGAATTCAGAAACTGCCTA 58.027 39.130 8.44 0.00 34.25 3.93
3483 3966 3.129792 GTCTTCCAGACAAGCCTCG 57.870 57.895 0.00 0.00 44.45 4.63
3541 4024 7.585210 CACAAGCATATATGTTCTCATCAAACG 59.415 37.037 14.14 0.00 35.70 3.60
3665 4189 1.009078 TATGCGCATTCAGCTCACAC 58.991 50.000 30.42 0.00 41.38 3.82
3666 4190 1.736612 TTATGCGCATTCAGCTCACA 58.263 45.000 30.42 3.49 41.38 3.58
3667 4191 2.032550 ACATTATGCGCATTCAGCTCAC 59.967 45.455 30.42 0.00 41.38 3.51
3668 4192 2.291365 ACATTATGCGCATTCAGCTCA 58.709 42.857 30.42 5.25 42.99 4.26
3669 4193 3.242837 TGAACATTATGCGCATTCAGCTC 60.243 43.478 30.42 19.16 42.61 4.09
3670 4194 2.684374 TGAACATTATGCGCATTCAGCT 59.316 40.909 30.42 10.95 42.61 4.24
3671 4195 2.785477 GTGAACATTATGCGCATTCAGC 59.215 45.455 30.42 15.67 40.87 4.26
3685 4209 1.211457 GGAGCATGGAGAGGTGAACAT 59.789 52.381 0.00 0.00 0.00 2.71
3687 4211 0.460987 CGGAGCATGGAGAGGTGAAC 60.461 60.000 0.00 0.00 0.00 3.18
3702 4232 1.009829 GCTTCACAGTAATGCCGGAG 58.990 55.000 5.05 0.00 0.00 4.63
3706 4236 2.733227 GCACATGCTTCACAGTAATGCC 60.733 50.000 0.00 0.00 38.21 4.40
3777 4307 6.525578 AGAAGAATAACGACACATACAGGA 57.474 37.500 0.00 0.00 0.00 3.86
3789 4319 9.478019 CTGCTGTTTGTATTAAGAAGAATAACG 57.522 33.333 0.00 0.00 0.00 3.18
3796 4326 9.683069 AATGTTTCTGCTGTTTGTATTAAGAAG 57.317 29.630 0.00 0.00 0.00 2.85
3798 4328 9.462174 CAAATGTTTCTGCTGTTTGTATTAAGA 57.538 29.630 0.00 0.00 0.00 2.10
3799 4329 9.462174 TCAAATGTTTCTGCTGTTTGTATTAAG 57.538 29.630 0.00 0.00 32.97 1.85
3805 4335 4.567959 GCTTCAAATGTTTCTGCTGTTTGT 59.432 37.500 0.00 0.00 32.97 2.83
3806 4336 4.567558 TGCTTCAAATGTTTCTGCTGTTTG 59.432 37.500 0.00 0.00 0.00 2.93
3807 4337 4.567959 GTGCTTCAAATGTTTCTGCTGTTT 59.432 37.500 0.00 0.00 0.00 2.83
3808 4338 4.114794 GTGCTTCAAATGTTTCTGCTGTT 58.885 39.130 0.00 0.00 0.00 3.16
3809 4339 3.382546 AGTGCTTCAAATGTTTCTGCTGT 59.617 39.130 0.00 0.00 0.00 4.40
3810 4340 3.973657 AGTGCTTCAAATGTTTCTGCTG 58.026 40.909 0.00 0.00 0.00 4.41
3811 4341 4.823989 ACTAGTGCTTCAAATGTTTCTGCT 59.176 37.500 0.00 0.00 0.00 4.24
3812 4342 4.913924 CACTAGTGCTTCAAATGTTTCTGC 59.086 41.667 10.54 0.00 0.00 4.26
3828 4358 9.901724 CTACGACTAATTAATTTTGCACTAGTG 57.098 33.333 18.93 18.93 0.00 2.74
3829 4359 8.601476 GCTACGACTAATTAATTTTGCACTAGT 58.399 33.333 5.91 1.67 0.00 2.57
3830 4360 7.787935 CGCTACGACTAATTAATTTTGCACTAG 59.212 37.037 5.91 0.00 0.00 2.57
3832 4362 6.311935 TCGCTACGACTAATTAATTTTGCACT 59.688 34.615 5.91 0.00 0.00 4.40
3833 4363 6.471839 TCGCTACGACTAATTAATTTTGCAC 58.528 36.000 5.91 0.00 0.00 4.57
3835 4365 9.807386 ATATTCGCTACGACTAATTAATTTTGC 57.193 29.630 5.91 0.05 34.89 3.68
3862 4392 8.407064 GCGTAGAGGTTCAGCATATATAGTATT 58.593 37.037 0.00 0.00 0.00 1.89
3863 4393 7.776030 AGCGTAGAGGTTCAGCATATATAGTAT 59.224 37.037 0.00 0.00 0.00 2.12
3864 4394 7.110810 AGCGTAGAGGTTCAGCATATATAGTA 58.889 38.462 0.00 0.00 0.00 1.82
3865 4395 5.946972 AGCGTAGAGGTTCAGCATATATAGT 59.053 40.000 0.00 0.00 0.00 2.12
3868 4398 8.698973 ATATAGCGTAGAGGTTCAGCATATAT 57.301 34.615 0.00 0.00 0.00 0.86
3871 4401 6.835819 AATATAGCGTAGAGGTTCAGCATA 57.164 37.500 0.00 0.00 0.00 3.14
3872 4402 5.730296 AATATAGCGTAGAGGTTCAGCAT 57.270 39.130 0.00 0.00 0.00 3.79
3874 4404 7.540299 AGAATAATATAGCGTAGAGGTTCAGC 58.460 38.462 0.00 0.00 0.00 4.26
3875 4405 9.347934 CAAGAATAATATAGCGTAGAGGTTCAG 57.652 37.037 0.00 0.00 0.00 3.02
3894 4424 7.719633 GCCAGACCCTTGTATTTATCAAGAATA 59.280 37.037 7.16 0.00 43.17 1.75
3895 4425 6.547510 GCCAGACCCTTGTATTTATCAAGAAT 59.452 38.462 7.16 0.00 43.17 2.40
3896 4426 5.885912 GCCAGACCCTTGTATTTATCAAGAA 59.114 40.000 7.16 0.00 43.17 2.52
3897 4427 5.045213 TGCCAGACCCTTGTATTTATCAAGA 60.045 40.000 7.16 0.00 43.17 3.02
3902 4631 3.954258 GCTTGCCAGACCCTTGTATTTAT 59.046 43.478 0.00 0.00 0.00 1.40
3907 4636 0.324943 GAGCTTGCCAGACCCTTGTA 59.675 55.000 0.00 0.00 0.00 2.41
3913 4642 1.376553 GTCCAGAGCTTGCCAGACC 60.377 63.158 0.00 0.00 0.00 3.85
3914 4643 0.250467 TTGTCCAGAGCTTGCCAGAC 60.250 55.000 0.00 0.00 0.00 3.51
3915 4644 0.473755 TTTGTCCAGAGCTTGCCAGA 59.526 50.000 0.00 0.00 0.00 3.86
3916 4645 1.321474 TTTTGTCCAGAGCTTGCCAG 58.679 50.000 0.00 0.00 0.00 4.85
3917 4646 1.888512 GATTTTGTCCAGAGCTTGCCA 59.111 47.619 0.00 0.00 0.00 4.92
3918 4647 2.165998 AGATTTTGTCCAGAGCTTGCC 58.834 47.619 0.00 0.00 0.00 4.52
3919 4648 3.930634 AAGATTTTGTCCAGAGCTTGC 57.069 42.857 0.00 0.00 0.00 4.01
3920 4649 5.443185 TCAAAGATTTTGTCCAGAGCTTG 57.557 39.130 0.00 0.00 0.00 4.01
3921 4650 6.661304 ATTCAAAGATTTTGTCCAGAGCTT 57.339 33.333 0.00 0.00 0.00 3.74
3922 4651 6.266103 TCAATTCAAAGATTTTGTCCAGAGCT 59.734 34.615 0.00 0.00 0.00 4.09
3923 4652 6.364435 GTCAATTCAAAGATTTTGTCCAGAGC 59.636 38.462 1.92 0.00 0.00 4.09
3924 4653 7.428020 TGTCAATTCAAAGATTTTGTCCAGAG 58.572 34.615 1.92 0.00 0.00 3.35
3925 4654 7.345422 TGTCAATTCAAAGATTTTGTCCAGA 57.655 32.000 1.92 0.00 0.00 3.86
3926 4655 8.422973 TTTGTCAATTCAAAGATTTTGTCCAG 57.577 30.769 1.92 0.00 34.02 3.86
3927 4656 8.961294 ATTTGTCAATTCAAAGATTTTGTCCA 57.039 26.923 1.92 0.00 40.00 4.02
3944 4673 9.809096 TGCTTTTTGTACTATCAAATTTGTCAA 57.191 25.926 17.47 11.09 37.20 3.18
3945 4674 9.462174 CTGCTTTTTGTACTATCAAATTTGTCA 57.538 29.630 17.47 6.24 37.20 3.58
3946 4675 9.677567 TCTGCTTTTTGTACTATCAAATTTGTC 57.322 29.630 17.47 4.32 37.20 3.18
3958 4687 8.817100 GCTTTACATTTTTCTGCTTTTTGTACT 58.183 29.630 0.00 0.00 0.00 2.73
3959 4688 8.599774 TGCTTTACATTTTTCTGCTTTTTGTAC 58.400 29.630 0.00 0.00 0.00 2.90
3961 4690 7.334171 ACTGCTTTACATTTTTCTGCTTTTTGT 59.666 29.630 0.00 0.00 0.00 2.83
3962 4691 7.687445 ACTGCTTTACATTTTTCTGCTTTTTG 58.313 30.769 0.00 0.00 0.00 2.44
3969 4698 6.437928 TGCACTACTGCTTTACATTTTTCTG 58.562 36.000 0.00 0.00 44.57 3.02
3971 4700 7.692908 TTTGCACTACTGCTTTACATTTTTC 57.307 32.000 0.00 0.00 44.57 2.29
3973 4702 8.661352 AATTTTGCACTACTGCTTTACATTTT 57.339 26.923 0.00 0.00 44.57 1.82
3975 4704 9.927668 ATTAATTTTGCACTACTGCTTTACATT 57.072 25.926 0.00 0.00 44.57 2.71
3977 4706 8.572185 TCATTAATTTTGCACTACTGCTTTACA 58.428 29.630 0.00 0.00 44.57 2.41
3978 4707 8.964420 TCATTAATTTTGCACTACTGCTTTAC 57.036 30.769 0.00 0.00 44.57 2.01
4000 4729 9.060347 CAGCAGAAACACTTTACCATATATCAT 57.940 33.333 0.00 0.00 0.00 2.45
4002 4731 8.438676 ACAGCAGAAACACTTTACCATATATC 57.561 34.615 0.00 0.00 0.00 1.63
4003 4732 8.807948 AACAGCAGAAACACTTTACCATATAT 57.192 30.769 0.00 0.00 0.00 0.86
4004 4733 8.511321 CAAACAGCAGAAACACTTTACCATATA 58.489 33.333 0.00 0.00 0.00 0.86
4006 4735 6.320164 ACAAACAGCAGAAACACTTTACCATA 59.680 34.615 0.00 0.00 0.00 2.74
4009 4738 4.993905 ACAAACAGCAGAAACACTTTACC 58.006 39.130 0.00 0.00 0.00 2.85
4012 4741 9.083080 GTTTAATACAAACAGCAGAAACACTTT 57.917 29.630 0.00 0.00 0.00 2.66
4013 4742 8.247562 TGTTTAATACAAACAGCAGAAACACTT 58.752 29.630 0.00 0.00 35.45 3.16
4014 4743 7.767261 TGTTTAATACAAACAGCAGAAACACT 58.233 30.769 0.00 0.00 35.45 3.55
4015 4744 7.979115 TGTTTAATACAAACAGCAGAAACAC 57.021 32.000 0.00 0.00 35.45 3.32
4016 4745 7.168972 GCATGTTTAATACAAACAGCAGAAACA 59.831 33.333 8.37 0.00 42.57 2.83
4017 4746 7.359181 GGCATGTTTAATACAAACAGCAGAAAC 60.359 37.037 17.64 0.00 42.57 2.78
4018 4747 6.644592 GGCATGTTTAATACAAACAGCAGAAA 59.355 34.615 17.64 0.00 42.57 2.52
4019 4748 6.015519 AGGCATGTTTAATACAAACAGCAGAA 60.016 34.615 17.64 0.00 42.57 3.02
4020 4749 5.476599 AGGCATGTTTAATACAAACAGCAGA 59.523 36.000 17.64 0.00 42.57 4.26
4021 4750 5.713025 AGGCATGTTTAATACAAACAGCAG 58.287 37.500 17.64 9.30 42.57 4.24
4022 4751 5.720371 AGGCATGTTTAATACAAACAGCA 57.280 34.783 17.64 0.00 42.57 4.41
4023 4752 9.796120 TTAATAGGCATGTTTAATACAAACAGC 57.204 29.630 8.37 10.53 42.57 4.40
4039 4791 7.726033 ACGGATAGAATCTCTTAATAGGCAT 57.274 36.000 0.00 0.00 0.00 4.40
4042 4794 7.558444 AGGCTACGGATAGAATCTCTTAATAGG 59.442 40.741 0.00 0.00 0.00 2.57
4048 4800 4.279671 CACAGGCTACGGATAGAATCTCTT 59.720 45.833 0.00 0.00 0.00 2.85
4055 4807 1.134310 TCGTCACAGGCTACGGATAGA 60.134 52.381 8.31 0.00 39.52 1.98
4061 4813 0.522180 AGAGTTCGTCACAGGCTACG 59.478 55.000 1.94 1.94 40.40 3.51
4069 4821 8.462143 TCTTGACAAATATAAGAGTTCGTCAC 57.538 34.615 0.00 0.00 32.27 3.67
4088 4840 9.330063 TCACCATCTTTATGTCATATTCTTGAC 57.670 33.333 0.00 0.00 45.05 3.18
4089 4841 9.330063 GTCACCATCTTTATGTCATATTCTTGA 57.670 33.333 0.00 0.00 0.00 3.02
4090 4842 8.278408 CGTCACCATCTTTATGTCATATTCTTG 58.722 37.037 0.00 0.00 0.00 3.02
4091 4843 7.987458 ACGTCACCATCTTTATGTCATATTCTT 59.013 33.333 0.00 0.00 0.00 2.52
4092 4844 7.500992 ACGTCACCATCTTTATGTCATATTCT 58.499 34.615 0.00 0.00 0.00 2.40
4093 4845 7.715265 ACGTCACCATCTTTATGTCATATTC 57.285 36.000 0.00 0.00 0.00 1.75
4094 4846 8.506168 AAACGTCACCATCTTTATGTCATATT 57.494 30.769 0.00 0.00 0.00 1.28
4095 4847 8.506168 AAAACGTCACCATCTTTATGTCATAT 57.494 30.769 0.00 0.00 0.00 1.78
4096 4848 7.915293 AAAACGTCACCATCTTTATGTCATA 57.085 32.000 0.00 0.00 0.00 2.15
4097 4849 6.817765 AAAACGTCACCATCTTTATGTCAT 57.182 33.333 0.00 0.00 0.00 3.06
4098 4850 6.627395 AAAAACGTCACCATCTTTATGTCA 57.373 33.333 0.00 0.00 0.00 3.58
4099 4851 8.431020 GTTAAAAACGTCACCATCTTTATGTC 57.569 34.615 0.00 0.00 0.00 3.06
4121 4873 8.600625 GCACACATAGAGAACATAATTTCGTTA 58.399 33.333 0.00 0.00 0.00 3.18
4122 4874 7.334421 AGCACACATAGAGAACATAATTTCGTT 59.666 33.333 0.00 0.00 0.00 3.85
4123 4875 6.818644 AGCACACATAGAGAACATAATTTCGT 59.181 34.615 0.00 0.00 0.00 3.85
4124 4876 7.239166 AGCACACATAGAGAACATAATTTCG 57.761 36.000 0.00 0.00 0.00 3.46
4129 4881 5.874810 GTCCAAGCACACATAGAGAACATAA 59.125 40.000 0.00 0.00 0.00 1.90
4139 4891 5.911752 ACAAAAATTGTCCAAGCACACATA 58.088 33.333 0.00 0.00 40.56 2.29
4147 4899 6.940831 AATGGGAAACAAAAATTGTCCAAG 57.059 33.333 6.32 0.00 44.59 3.61
4174 4926 8.620416 CGGGTAGATTTTATCATGATTTTGTCA 58.380 33.333 14.65 0.00 42.06 3.58
4175 4927 8.836413 TCGGGTAGATTTTATCATGATTTTGTC 58.164 33.333 14.65 7.95 0.00 3.18
4176 4928 8.746052 TCGGGTAGATTTTATCATGATTTTGT 57.254 30.769 14.65 0.00 0.00 2.83
4177 4929 8.840321 ACTCGGGTAGATTTTATCATGATTTTG 58.160 33.333 14.65 0.00 0.00 2.44
4196 4959 4.142687 CGCAAAAGATATTTTCACTCGGGT 60.143 41.667 0.00 0.00 0.00 5.28
4198 4961 3.786048 GCGCAAAAGATATTTTCACTCGG 59.214 43.478 0.30 0.00 0.00 4.63
4199 4962 4.402583 TGCGCAAAAGATATTTTCACTCG 58.597 39.130 8.16 0.00 0.00 4.18
4210 4973 4.494199 GCGACTTATACTTGCGCAAAAGAT 60.494 41.667 29.45 21.66 46.19 2.40
4236 4999 2.279186 GTGTGCAAAACCCACGGC 60.279 61.111 0.00 0.00 36.01 5.68
4241 5004 4.021544 TCAATTATCTGGTGTGCAAAACCC 60.022 41.667 15.44 0.00 46.76 4.11
4291 5054 6.072948 CCGACAATAACAAGTTGTTCCATGTA 60.073 38.462 24.06 6.80 40.22 2.29
4297 5060 5.209977 GGTTCCGACAATAACAAGTTGTTC 58.790 41.667 24.06 9.34 40.22 3.18
4299 5062 4.200874 TGGTTCCGACAATAACAAGTTGT 58.799 39.130 1.64 1.64 42.13 3.32
4300 5063 4.274950 ACTGGTTCCGACAATAACAAGTTG 59.725 41.667 0.00 0.00 36.66 3.16
4301 5064 4.457466 ACTGGTTCCGACAATAACAAGTT 58.543 39.130 0.00 0.00 36.66 2.66
4376 5139 0.462937 TTGTCTGGGTTCCGTGTGTG 60.463 55.000 0.00 0.00 0.00 3.82
4378 5141 0.179056 ACTTGTCTGGGTTCCGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
4389 5152 4.240888 CAGTCCACAGATGTACTTGTCTG 58.759 47.826 16.64 16.64 45.65 3.51
4390 5153 3.259374 CCAGTCCACAGATGTACTTGTCT 59.741 47.826 0.00 0.00 0.00 3.41
4391 5154 3.006967 ACCAGTCCACAGATGTACTTGTC 59.993 47.826 0.00 0.00 0.00 3.18
4404 5167 0.109723 TGTGCCCTTTACCAGTCCAC 59.890 55.000 0.00 0.00 0.00 4.02
4414 5177 1.328279 GCAGGTTACTTGTGCCCTTT 58.672 50.000 0.00 0.00 0.00 3.11
4421 5184 2.729194 TGTTGTTGGCAGGTTACTTGT 58.271 42.857 0.00 0.00 0.00 3.16
4465 5228 4.780815 TCCTGGGATATGTGATTTGTGTC 58.219 43.478 0.00 0.00 0.00 3.67
4514 5279 2.291996 TGCCCTCAGCTAGGTAGTGTTA 60.292 50.000 0.00 0.00 44.90 2.41
4515 5280 1.196012 GCCCTCAGCTAGGTAGTGTT 58.804 55.000 0.00 0.00 44.90 3.32
4516 5281 0.041238 TGCCCTCAGCTAGGTAGTGT 59.959 55.000 0.00 0.00 44.90 3.55
4645 5413 2.087646 GATCTGTTCAAGCCTCAACCC 58.912 52.381 0.00 0.00 0.00 4.11
4681 5449 3.339141 GGAATCTGCCGAGAAGTTCTTT 58.661 45.455 6.88 0.00 0.00 2.52
4682 5450 2.355209 GGGAATCTGCCGAGAAGTTCTT 60.355 50.000 6.88 0.00 0.00 2.52
4723 5491 1.596934 GAGGCCGGTGATGTCTGAA 59.403 57.895 1.90 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.