Multiple sequence alignment - TraesCS7B01G461100

Loading Multiple Alignment...

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 TraesCS7B01G461100 chr7B 100.000 6434 0 0 1 6434 718465919 718472352 0.000000e+00 11882.0
1 TraesCS7B01G461100 chr7B 94.340 53 3 0 3116 3168 159137579 159137631 1.490000e-11 82.4
2 TraesCS7B01G461100 chr7D 94.452 3803 134 26 2021 5804 621486375 621482631 0.000000e+00 5782.0
3 TraesCS7B01G461100 chr7D 96.741 1258 32 3 766 2017 621487597 621486343 0.000000e+00 2087.0
4 TraesCS7B01G461100 chr7D 88.138 784 60 12 1 765 621488445 621487676 0.000000e+00 902.0
5 TraesCS7B01G461100 chr7D 93.462 260 11 2 5822 6081 621482503 621482250 1.310000e-101 381.0
6 TraesCS7B01G461100 chr7D 98.171 164 3 0 6271 6434 621482048 621481885 2.940000e-73 287.0
7 TraesCS7B01G461100 chr7D 96.226 53 2 0 3116 3168 195308272 195308324 3.200000e-13 87.9
8 TraesCS7B01G461100 chr7D 83.871 93 5 3 3115 3206 56418861 56418944 5.350000e-11 80.5
9 TraesCS7B01G461100 chr7A 91.542 3937 213 47 483 4406 717041676 717037847 0.000000e+00 5315.0
10 TraesCS7B01G461100 chr7A 89.219 1382 89 30 4390 5751 717037826 717036485 0.000000e+00 1672.0
11 TraesCS7B01G461100 chr7A 91.906 383 22 5 5819 6200 717036364 717035990 1.590000e-145 527.0
12 TraesCS7B01G461100 chr4B 83.969 131 21 0 5950 6080 457799139 457799009 6.770000e-25 126.0
13 TraesCS7B01G461100 chr2B 81.560 141 26 0 5949 6089 17143918 17143778 4.080000e-22 117.0
14 TraesCS7B01G461100 chr2D 86.813 91 3 4 3114 3204 36689353 36689434 6.870000e-15 93.5
15 TraesCS7B01G461100 chr6B 83.696 92 15 0 5998 6089 574630145 574630054 3.200000e-13 87.9
16 TraesCS7B01G461100 chr5B 77.931 145 28 3 5949 6091 340598470 340598612 3.200000e-13 87.9
17 TraesCS7B01G461100 chr4D 94.643 56 3 0 3113 3168 482160748 482160693 3.200000e-13 87.9
18 TraesCS7B01G461100 chr3B 96.000 50 2 0 3119 3168 48803333 48803284 1.490000e-11 82.4
19 TraesCS7B01G461100 chr3D 92.593 54 4 0 3114 3167 550194748 550194695 1.920000e-10 78.7
20 TraesCS7B01G461100 chr4A 77.236 123 26 2 5970 6091 317421459 317421580 3.220000e-08 71.3


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 TraesCS7B01G461100 chr7B 718465919 718472352 6433 False 11882.000000 11882 100.0000 1 6434 1 chr7B.!!$F2 6433
1 TraesCS7B01G461100 chr7D 621481885 621488445 6560 True 1887.800000 5782 94.1928 1 6434 5 chr7D.!!$R1 6433
2 TraesCS7B01G461100 chr7A 717035990 717041676 5686 True 2504.666667 5315 90.8890 483 6200 3 chr7A.!!$R1 5717

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
49 51 0.182775 GGGATTGGATAACAGGGCGT 59.817 55.0 0.0 0.0 0.00 5.68 F
1080 1179 0.037326 CCACGCAAGCCTGTAAGAGA 60.037 55.0 0.0 0.0 45.62 3.10 F
2368 2473 0.747255 TTCTATCAGCGTGCCCTCTC 59.253 55.0 0.0 0.0 0.00 3.20 F
3178 3285 0.535780 TGAACTGCCTGAACTGCCAG 60.536 55.0 0.0 0.0 0.00 4.85 F
5022 5183 0.459237 GTGACCATCCAGCGAGTCTG 60.459 60.0 0.0 0.0 42.49 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2096 0.387239 GAAACCTTGGTGCATGCGAC 60.387 55.0 14.09 12.05 0.00 5.19 R
2710 2815 0.399454 AGCACATCAGCCAGAACTGT 59.601 50.0 1.18 0.00 38.84 3.55 R
3583 3691 1.382522 ACCATTTCCATAGCACGCAG 58.617 50.0 0.00 0.00 0.00 5.18 R
5145 5306 0.328258 TTAGCTTGGCAGGAGGGTTC 59.672 55.0 0.00 0.00 0.00 3.62 R
5955 6258 0.883370 ACTCCGTTCGGGAAGCAAAC 60.883 55.0 11.37 0.00 46.61 2.93 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
27 29 1.550130 TTTCGGGTGGCTCCTTCGAT 61.550 55.000 5.46 0.00 31.94 3.59
41 43 3.719479 TCCTTCGATTGGGGATTGGATAA 59.281 43.478 5.33 0.00 0.00 1.75
43 45 4.460263 CTTCGATTGGGGATTGGATAACA 58.540 43.478 0.00 0.00 0.00 2.41
49 51 0.182775 GGGATTGGATAACAGGGCGT 59.817 55.000 0.00 0.00 0.00 5.68
63 66 0.461516 GGGCGTCTACCTGGCTTAAC 60.462 60.000 0.00 0.00 0.00 2.01
66 69 2.419667 GCGTCTACCTGGCTTAACAAA 58.580 47.619 0.00 0.00 0.00 2.83
68 71 3.000727 CGTCTACCTGGCTTAACAAAGG 58.999 50.000 0.00 0.00 35.82 3.11
79 82 4.874396 GGCTTAACAAAGGCTCGTAGTATT 59.126 41.667 4.59 0.00 41.57 1.89
80 83 6.044682 GGCTTAACAAAGGCTCGTAGTATTA 58.955 40.000 4.59 0.00 41.57 0.98
85 88 6.466885 ACAAAGGCTCGTAGTATTATGTCT 57.533 37.500 0.00 0.00 0.00 3.41
87 90 6.096423 ACAAAGGCTCGTAGTATTATGTCTGA 59.904 38.462 0.00 0.00 0.00 3.27
89 92 4.762765 AGGCTCGTAGTATTATGTCTGAGG 59.237 45.833 0.00 0.00 0.00 3.86
105 112 2.707791 CTGAGGAATCTCCAATAGGCCA 59.292 50.000 5.01 0.00 39.61 5.36
120 127 3.771577 AGGCCATTAACCCTAGAATCG 57.228 47.619 5.01 0.00 0.00 3.34
121 128 3.046374 AGGCCATTAACCCTAGAATCGT 58.954 45.455 5.01 0.00 0.00 3.73
122 129 4.228824 AGGCCATTAACCCTAGAATCGTA 58.771 43.478 5.01 0.00 0.00 3.43
123 130 4.040095 AGGCCATTAACCCTAGAATCGTAC 59.960 45.833 5.01 0.00 0.00 3.67
124 131 4.040095 GGCCATTAACCCTAGAATCGTACT 59.960 45.833 0.00 0.00 0.00 2.73
125 132 5.228665 GCCATTAACCCTAGAATCGTACTC 58.771 45.833 0.00 0.00 0.00 2.59
131 138 8.618702 TTAACCCTAGAATCGTACTCTAGATG 57.381 38.462 15.72 10.40 43.45 2.90
136 143 7.446013 CCCTAGAATCGTACTCTAGATGTCTTT 59.554 40.741 15.72 0.00 43.45 2.52
141 148 4.034163 TCGTACTCTAGATGTCTTTCGCTG 59.966 45.833 0.00 0.00 0.00 5.18
149 156 0.960364 TGTCTTTCGCTGATTGGGCC 60.960 55.000 0.00 0.00 0.00 5.80
151 158 2.033448 TTTCGCTGATTGGGCCGT 59.967 55.556 0.00 0.00 0.00 5.68
163 170 2.184579 GGCCGTCCACTCTAGCAC 59.815 66.667 0.00 0.00 0.00 4.40
177 184 4.829492 ACTCTAGCACAATTGAGGCTTTTT 59.171 37.500 25.97 11.20 39.01 1.94
184 191 4.931002 CACAATTGAGGCTTTTTGGGTATG 59.069 41.667 13.59 0.00 0.00 2.39
204 211 3.197983 TGTTGGGGAATCTCCAATAGGT 58.802 45.455 18.69 0.00 44.87 3.08
210 217 4.102054 GGGGAATCTCCAATAGGTCGTTTA 59.898 45.833 0.00 0.00 38.64 2.01
213 220 6.204882 GGGAATCTCCAATAGGTCGTTTATTG 59.795 42.308 0.00 8.39 38.64 1.90
218 225 4.920376 CCAATAGGTCGTTTATTGGCTTG 58.080 43.478 16.47 0.00 46.14 4.01
232 239 4.553330 TTGGCTTGTTACTAGGAGAAGG 57.447 45.455 0.00 0.00 0.00 3.46
280 287 2.145865 GGCCATTCAGCTAGCCCTA 58.854 57.895 12.13 0.00 39.60 3.53
288 295 6.421485 CCATTCAGCTAGCCCTATTGATTAT 58.579 40.000 12.13 0.00 0.00 1.28
293 300 6.936900 TCAGCTAGCCCTATTGATTATCAAAC 59.063 38.462 12.13 0.38 40.12 2.93
294 301 6.712095 CAGCTAGCCCTATTGATTATCAAACA 59.288 38.462 12.13 2.49 40.12 2.83
317 337 2.656947 TGGATAATACCCTGCTTGGC 57.343 50.000 0.00 0.00 0.00 4.52
335 355 3.319135 CAGTATGCTGCCTCCATCC 57.681 57.895 0.00 0.00 35.77 3.51
355 375 3.449377 TCCTGGTGACATAATCGCAGTAA 59.551 43.478 0.00 0.00 41.51 2.24
410 430 1.120530 ATGCTTGGTAGTAGGGGTCG 58.879 55.000 0.00 0.00 0.00 4.79
418 438 1.678101 GTAGTAGGGGTCGTAACGCAT 59.322 52.381 0.00 0.00 39.99 4.73
486 506 3.933332 CCGAACACAGGATAAGGAAAGTC 59.067 47.826 0.00 0.00 0.00 3.01
510 530 5.234116 CGTCCCTTTTTGGAAAAATTGTCTG 59.766 40.000 0.00 0.00 37.27 3.51
523 543 7.396540 AAAAATTGTCTGTGAACTCTGACTT 57.603 32.000 12.37 1.53 37.25 3.01
573 593 5.390885 CCTGTGTGTTCTATGCATGTTACAC 60.391 44.000 22.60 22.60 38.06 2.90
581 601 8.308207 TGTTCTATGCATGTTACACTTACTGTA 58.692 33.333 10.16 0.00 33.91 2.74
586 606 8.737168 ATGCATGTTACACTTACTGTATTCAT 57.263 30.769 0.00 0.00 35.18 2.57
611 631 3.064207 TCTGTTTTGTTACTAGCTGCCG 58.936 45.455 0.00 0.00 0.00 5.69
622 642 1.001293 CTAGCTGCCGCAGATTATGGA 59.999 52.381 24.80 0.89 39.10 3.41
623 643 0.250209 AGCTGCCGCAGATTATGGAG 60.250 55.000 24.80 0.00 39.10 3.86
624 644 1.233285 GCTGCCGCAGATTATGGAGG 61.233 60.000 24.80 0.00 32.44 4.30
625 645 3.660621 GCCGCAGATTATGGAGGC 58.339 61.111 0.00 0.00 42.61 4.70
627 647 3.639099 CCGCAGATTATGGAGGCAT 57.361 52.632 0.00 0.00 0.00 4.40
628 648 2.768253 CCGCAGATTATGGAGGCATA 57.232 50.000 0.00 0.00 0.00 3.14
629 649 3.057969 CCGCAGATTATGGAGGCATAA 57.942 47.619 0.00 0.00 0.00 1.90
748 768 4.482386 TCGTTGTCTGTATGAGCTGTTAC 58.518 43.478 0.00 0.00 0.00 2.50
841 939 8.415950 ACTGTTCATCCTAGAATGGATAGTAG 57.584 38.462 0.00 0.00 44.38 2.57
842 940 8.007742 ACTGTTCATCCTAGAATGGATAGTAGT 58.992 37.037 0.00 0.00 44.38 2.73
843 941 9.521841 CTGTTCATCCTAGAATGGATAGTAGTA 57.478 37.037 0.00 0.00 44.38 1.82
846 944 8.865420 TCATCCTAGAATGGATAGTAGTACAC 57.135 38.462 2.52 0.00 44.38 2.90
850 948 6.709397 CCTAGAATGGATAGTAGTACACGACA 59.291 42.308 2.52 0.00 0.00 4.35
1080 1179 0.037326 CCACGCAAGCCTGTAAGAGA 60.037 55.000 0.00 0.00 45.62 3.10
1369 1468 2.270352 TATCCGCAATCCAATGGACC 57.730 50.000 3.09 0.00 32.98 4.46
1556 1655 8.771521 TGGACATCATATGAAAGAAAATGGAT 57.228 30.769 9.99 0.00 0.00 3.41
1977 2081 1.750780 GCTGGTAGCAAAGAGGGCC 60.751 63.158 0.00 0.00 41.89 5.80
1989 2093 3.584733 AAGAGGGCCCTTTACATCATC 57.415 47.619 29.39 10.09 0.00 2.92
1992 2096 1.496429 AGGGCCCTTTACATCATCCTG 59.504 52.381 22.28 0.00 0.00 3.86
2135 2240 2.519013 AGCAAATTCTCAGTTGTCCCC 58.481 47.619 0.00 0.00 30.31 4.81
2343 2448 2.467880 TCGCCTCTTTCTTCCTATGGT 58.532 47.619 0.00 0.00 0.00 3.55
2359 2464 2.672961 TGGTCAAGGTTCTATCAGCG 57.327 50.000 0.00 0.00 0.00 5.18
2368 2473 0.747255 TTCTATCAGCGTGCCCTCTC 59.253 55.000 0.00 0.00 0.00 3.20
2641 2746 8.279970 TCTGGACCATGTAATTTTCTGTAATG 57.720 34.615 0.00 0.00 0.00 1.90
2710 2815 2.951642 AGCAAGTTTTCTGCTGCACTTA 59.048 40.909 0.00 0.00 36.46 2.24
2830 2935 6.015940 GCAGCAAGAAGGTAATAATTAGCCAT 60.016 38.462 6.37 0.00 34.26 4.40
2881 2986 4.032960 TGGATACATTTTGCTGTCCACT 57.967 40.909 0.00 0.00 46.17 4.00
3009 3116 9.727859 AAACCCAAAATAAACTACACTTGTTTT 57.272 25.926 0.00 0.00 38.41 2.43
3178 3285 0.535780 TGAACTGCCTGAACTGCCAG 60.536 55.000 0.00 0.00 0.00 4.85
3267 3374 1.452651 CGATGCTGGGATTGCTGGT 60.453 57.895 0.00 0.00 0.00 4.00
3274 3381 1.819632 GGGATTGCTGGTAGTGGCG 60.820 63.158 0.00 0.00 0.00 5.69
3276 3383 0.811616 GGATTGCTGGTAGTGGCGAG 60.812 60.000 0.00 0.00 0.00 5.03
3450 3558 5.799681 ACAAAAAGAATGCCAAAAGTGTG 57.200 34.783 0.00 0.00 0.00 3.82
3509 3617 6.777091 TGTGTATTTCATGCCTTGGCTTATAT 59.223 34.615 13.18 3.32 0.00 0.86
3513 3621 5.772825 TTCATGCCTTGGCTTATATTGAC 57.227 39.130 13.18 0.00 0.00 3.18
3520 3628 5.221048 GCCTTGGCTTATATTGACGTTTCAT 60.221 40.000 4.11 0.00 0.00 2.57
3527 3635 8.276325 GGCTTATATTGACGTTTCATCTAGTTG 58.724 37.037 0.00 0.00 0.00 3.16
3583 3691 5.855740 ACTGGCTAGGAACTGATAGTTAC 57.144 43.478 0.85 0.00 38.80 2.50
3593 3701 4.920640 ACTGATAGTTACTGCGTGCTAT 57.079 40.909 0.00 0.00 0.00 2.97
3619 3727 6.239487 GGAAATGGTTTATATGCCTTAACCCC 60.239 42.308 0.00 0.00 39.39 4.95
3737 3846 2.297033 GCCAGCCAATTTGAAGAGTTCA 59.703 45.455 0.00 0.00 38.04 3.18
3759 3869 9.646427 GTTCAAGTTTGTCTCTAGTCATTCTAT 57.354 33.333 0.00 0.00 0.00 1.98
3792 3902 5.060506 CGCCATATGTTTCCATTACCAGTA 58.939 41.667 1.24 0.00 32.29 2.74
3833 3943 7.870445 TGGAACATTGTATTTTTCTACTTTGCC 59.130 33.333 0.00 0.00 0.00 4.52
4093 4203 6.346919 GCTGGTAGATACGCATCAGTTAATTG 60.347 42.308 0.00 0.00 33.21 2.32
4117 4227 2.687700 CAGTTGCCTGTCAGCTAGAT 57.312 50.000 0.00 0.00 34.29 1.98
4124 4234 3.244009 TGCCTGTCAGCTAGATAATCAGC 60.244 47.826 0.00 0.00 38.09 4.26
4580 4732 8.657387 TGTTGGATTTATTTTGGGTAGAATCA 57.343 30.769 0.00 0.00 0.00 2.57
4606 4758 7.118680 AGCAGTTCAATGGAAATAAAGCAAATG 59.881 33.333 0.00 0.00 34.13 2.32
4709 4870 2.363306 TGGGCAACAACATGAACTCT 57.637 45.000 0.00 0.00 39.74 3.24
4785 4946 1.154469 GTACTCTTTTGTGCCGCGC 60.154 57.895 0.00 0.00 0.00 6.86
4830 4991 5.182380 GCCGTTAAATGCTGGCCTTATTATA 59.818 40.000 3.32 0.00 41.70 0.98
4831 4992 6.294286 GCCGTTAAATGCTGGCCTTATTATAA 60.294 38.462 3.32 0.00 41.70 0.98
4986 5147 1.369625 GCTGGCACTACACATGGTAC 58.630 55.000 0.00 0.00 0.00 3.34
5000 5161 1.938585 TGGTACTAGCTGCTTGTCCT 58.061 50.000 19.47 0.00 0.00 3.85
5001 5162 1.550524 TGGTACTAGCTGCTTGTCCTG 59.449 52.381 19.47 1.24 0.00 3.86
5022 5183 0.459237 GTGACCATCCAGCGAGTCTG 60.459 60.000 0.00 0.00 42.49 3.51
5040 5201 2.637382 TCTGTAAGCTTGATGTCCCACA 59.363 45.455 9.86 1.49 0.00 4.17
5064 5225 5.243954 AGTGGCTATTCAACCTTTTTCCTTC 59.756 40.000 0.00 0.00 0.00 3.46
5085 5246 4.564041 TCTTGCAGATGAAGAAGACTGTC 58.436 43.478 0.00 0.00 33.57 3.51
5142 5303 4.326504 AAACATCAGCAAAAAGTGGGAG 57.673 40.909 0.00 0.00 0.00 4.30
5145 5306 3.879912 CAGCAAAAAGTGGGAGCTG 57.120 52.632 0.00 0.00 45.44 4.24
5166 5327 0.548510 ACCCTCCTGCCAAGCTAATC 59.451 55.000 0.00 0.00 0.00 1.75
5287 5454 3.588842 AGATGAAATGGAGGACTCACCAA 59.411 43.478 1.32 0.00 42.04 3.67
5337 5504 2.994995 TCCGTGGATGCCGACAGT 60.995 61.111 0.00 0.00 0.00 3.55
5338 5505 2.815211 CCGTGGATGCCGACAGTG 60.815 66.667 0.00 0.00 0.00 3.66
5343 5510 0.102300 TGGATGCCGACAGTGTATCG 59.898 55.000 0.00 0.00 39.33 2.92
5352 5519 0.614979 ACAGTGTATCGCCACCCTCT 60.615 55.000 0.00 0.00 35.93 3.69
5355 5522 0.249398 GTGTATCGCCACCCTCTGTT 59.751 55.000 0.00 0.00 0.00 3.16
5358 5525 0.535335 TATCGCCACCCTCTGTTGAC 59.465 55.000 0.00 0.00 0.00 3.18
5382 5549 2.045340 AGCATGTTACCACCCGCC 60.045 61.111 0.00 0.00 0.00 6.13
5385 5552 2.104253 CATGTTACCACCCGCCGTC 61.104 63.158 0.00 0.00 0.00 4.79
5394 5561 2.129146 ACCCGCCGTCGATATGGAA 61.129 57.895 5.59 0.00 38.10 3.53
5412 5579 1.623542 AAATCGACGGGGAGGAAGGG 61.624 60.000 0.00 0.00 0.00 3.95
5418 5585 1.384643 CGGGGAGGAAGGGGAGATT 60.385 63.158 0.00 0.00 0.00 2.40
5451 5618 4.023536 GGGTAGCATTCGTTTTTCTTGTGA 60.024 41.667 0.00 0.00 0.00 3.58
5479 5646 4.922103 TGTTTCGCATACGTATTGTGTACA 59.078 37.500 5.03 12.63 41.18 2.90
5480 5647 5.164070 TGTTTCGCATACGTATTGTGTACAC 60.164 40.000 19.36 19.36 41.18 2.90
5531 5698 1.153369 CGATGTGATTCTGCCCCGT 60.153 57.895 0.00 0.00 0.00 5.28
5532 5699 1.431488 CGATGTGATTCTGCCCCGTG 61.431 60.000 0.00 0.00 0.00 4.94
5536 5703 2.268920 GATTCTGCCCCGTGAGCA 59.731 61.111 0.00 0.00 38.82 4.26
5545 5712 1.221840 CCCGTGAGCAGGCTATGTT 59.778 57.895 0.00 0.00 0.00 2.71
5556 5723 2.545526 CAGGCTATGTTGACATAAGCGG 59.454 50.000 5.45 4.44 38.26 5.52
5557 5724 1.264288 GGCTATGTTGACATAAGCGGC 59.736 52.381 5.45 0.00 38.26 6.53
5558 5725 2.213499 GCTATGTTGACATAAGCGGCT 58.787 47.619 0.00 0.00 38.26 5.52
5600 5767 4.859798 GTGGTATTCAGAGTGAGTTTCTCG 59.140 45.833 0.00 0.00 37.07 4.04
5601 5768 4.523173 TGGTATTCAGAGTGAGTTTCTCGT 59.477 41.667 0.00 0.00 37.07 4.18
5602 5769 5.708697 TGGTATTCAGAGTGAGTTTCTCGTA 59.291 40.000 0.00 0.00 37.07 3.43
5603 5770 6.028987 GGTATTCAGAGTGAGTTTCTCGTAC 58.971 44.000 0.00 0.00 37.07 3.67
5627 5798 7.138736 ACGAATGTTCTGTAAAACAATTGGAG 58.861 34.615 10.83 0.00 42.10 3.86
5631 5802 9.883142 AATGTTCTGTAAAACAATTGGAGAAAA 57.117 25.926 10.83 3.30 42.10 2.29
5632 5803 9.883142 ATGTTCTGTAAAACAATTGGAGAAAAA 57.117 25.926 10.83 1.20 42.10 1.94
5636 5807 8.413229 TCTGTAAAACAATTGGAGAAAAAGAGG 58.587 33.333 10.83 0.00 0.00 3.69
5680 5855 5.116180 AGTGCTTGTGTATATACATTGCGT 58.884 37.500 18.27 11.01 38.63 5.24
5681 5856 5.006649 AGTGCTTGTGTATATACATTGCGTG 59.993 40.000 18.27 7.59 38.63 5.34
5726 5905 4.073200 GCATTTTGCCTGCGCCCT 62.073 61.111 4.18 0.00 37.42 5.19
5727 5906 2.125832 CATTTTGCCTGCGCCCTG 60.126 61.111 4.18 0.00 0.00 4.45
5728 5907 4.073200 ATTTTGCCTGCGCCCTGC 62.073 61.111 4.18 5.30 46.70 4.85
5737 5916 3.503363 GCGCCCTGCAGTCATGAC 61.503 66.667 18.47 18.47 45.45 3.06
5738 5917 2.046988 CGCCCTGCAGTCATGACA 60.047 61.111 27.02 6.47 0.00 3.58
5739 5918 1.672030 CGCCCTGCAGTCATGACAA 60.672 57.895 27.02 11.57 0.00 3.18
5740 5919 1.642037 CGCCCTGCAGTCATGACAAG 61.642 60.000 27.02 19.19 0.00 3.16
5741 5920 1.930908 GCCCTGCAGTCATGACAAGC 61.931 60.000 27.02 26.95 35.90 4.01
5742 5921 0.607217 CCCTGCAGTCATGACAAGCA 60.607 55.000 31.14 31.14 40.52 3.91
5743 5922 0.520404 CCTGCAGTCATGACAAGCAC 59.480 55.000 30.32 15.77 38.85 4.40
5744 5923 1.232119 CTGCAGTCATGACAAGCACA 58.768 50.000 30.32 18.61 38.85 4.57
5745 5924 1.810755 CTGCAGTCATGACAAGCACAT 59.189 47.619 30.32 8.48 38.85 3.21
5746 5925 1.808343 TGCAGTCATGACAAGCACATC 59.192 47.619 30.32 11.76 38.85 3.06
5747 5926 1.131883 GCAGTCATGACAAGCACATCC 59.868 52.381 27.98 6.91 35.58 3.51
5748 5927 2.708051 CAGTCATGACAAGCACATCCT 58.292 47.619 27.02 0.00 0.00 3.24
5749 5928 2.418976 CAGTCATGACAAGCACATCCTG 59.581 50.000 27.02 9.08 0.00 3.86
5775 5966 0.543277 TCCTGATGGTGATGGACAGC 59.457 55.000 0.00 0.00 45.87 4.40
5779 5970 2.169144 CTGATGGTGATGGACAGCTACA 59.831 50.000 0.00 0.00 45.86 2.74
5804 5995 3.022406 AGGGTAACTACGCTAGGACTTG 58.978 50.000 4.75 0.00 46.01 3.16
5809 6112 4.868314 AACTACGCTAGGACTTGAAGTT 57.132 40.909 0.00 0.00 0.00 2.66
5835 6138 1.003355 CCTCGGTGCAATGGTCACT 60.003 57.895 0.00 0.00 34.97 3.41
5916 6219 0.251634 TGGAATGCGCAGGTATGTCA 59.748 50.000 18.32 4.28 0.00 3.58
5917 6220 1.134128 TGGAATGCGCAGGTATGTCAT 60.134 47.619 18.32 0.00 0.00 3.06
5918 6221 1.265095 GGAATGCGCAGGTATGTCATG 59.735 52.381 18.32 0.00 0.00 3.07
5919 6222 1.942657 GAATGCGCAGGTATGTCATGT 59.057 47.619 18.32 0.00 0.00 3.21
5920 6223 1.586422 ATGCGCAGGTATGTCATGTC 58.414 50.000 18.32 0.00 0.00 3.06
5960 6263 0.878416 TACATGAAGGGCGTGTTTGC 59.122 50.000 0.00 0.00 44.17 3.68
5981 6284 1.548081 TCCCGAACGGAGTGTAATGA 58.452 50.000 15.07 0.00 45.00 2.57
6011 6314 3.181453 TGGTTCCGTTTCACTGTAATGGA 60.181 43.478 5.46 5.46 38.57 3.41
6018 6321 5.278758 CCGTTTCACTGTAATGGATTGGTTT 60.279 40.000 1.24 0.00 34.25 3.27
6023 6326 4.695455 CACTGTAATGGATTGGTTTCGTCT 59.305 41.667 0.00 0.00 0.00 4.18
6095 6398 2.205022 TGGTTTGAGAGATGGCTTGG 57.795 50.000 0.00 0.00 0.00 3.61
6102 6405 2.817423 GAGATGGCTTGGCGCTTCG 61.817 63.158 7.64 0.00 39.13 3.79
6103 6406 3.127533 GATGGCTTGGCGCTTCGT 61.128 61.111 7.64 0.00 39.13 3.85
6190 6493 3.196685 AGAAGGGAGCTGATGTTGTAGAC 59.803 47.826 0.00 0.00 0.00 2.59
6191 6494 1.478510 AGGGAGCTGATGTTGTAGACG 59.521 52.381 0.00 0.00 0.00 4.18
6194 6497 3.182967 GGAGCTGATGTTGTAGACGAAG 58.817 50.000 0.00 0.00 0.00 3.79
6196 6499 2.826128 AGCTGATGTTGTAGACGAAGGA 59.174 45.455 0.00 0.00 0.00 3.36
6199 6502 4.618460 GCTGATGTTGTAGACGAAGGAAGA 60.618 45.833 0.00 0.00 0.00 2.87
6200 6503 4.806330 TGATGTTGTAGACGAAGGAAGAC 58.194 43.478 0.00 0.00 0.00 3.01
6201 6504 4.279922 TGATGTTGTAGACGAAGGAAGACA 59.720 41.667 0.00 0.00 0.00 3.41
6202 6505 4.238761 TGTTGTAGACGAAGGAAGACAG 57.761 45.455 0.00 0.00 0.00 3.51
6203 6506 2.987821 GTTGTAGACGAAGGAAGACAGC 59.012 50.000 0.00 0.00 0.00 4.40
6204 6507 1.544691 TGTAGACGAAGGAAGACAGCC 59.455 52.381 0.00 0.00 0.00 4.85
6205 6508 0.809385 TAGACGAAGGAAGACAGCCG 59.191 55.000 0.00 0.00 0.00 5.52
6207 6510 3.181967 CGAAGGAAGACAGCCGCG 61.182 66.667 0.00 0.00 0.00 6.46
6208 6511 2.815647 GAAGGAAGACAGCCGCGG 60.816 66.667 24.05 24.05 0.00 6.46
6235 6538 4.543590 TTTGGTGCCAAAAGTTGAAGAA 57.456 36.364 13.40 0.00 42.16 2.52
6236 6539 4.751767 TTGGTGCCAAAAGTTGAAGAAT 57.248 36.364 0.47 0.00 32.44 2.40
6237 6540 4.057406 TGGTGCCAAAAGTTGAAGAATG 57.943 40.909 0.00 0.00 0.00 2.67
6238 6541 2.802247 GGTGCCAAAAGTTGAAGAATGC 59.198 45.455 0.00 0.00 0.00 3.56
6239 6542 2.472488 GTGCCAAAAGTTGAAGAATGCG 59.528 45.455 0.00 0.00 0.00 4.73
6240 6543 2.061028 GCCAAAAGTTGAAGAATGCGG 58.939 47.619 0.00 0.00 0.00 5.69
6241 6544 2.288152 GCCAAAAGTTGAAGAATGCGGA 60.288 45.455 0.00 0.00 0.00 5.54
6242 6545 3.798548 GCCAAAAGTTGAAGAATGCGGAA 60.799 43.478 0.00 0.00 0.00 4.30
6243 6546 4.367450 CCAAAAGTTGAAGAATGCGGAAA 58.633 39.130 0.00 0.00 0.00 3.13
6244 6547 4.808364 CCAAAAGTTGAAGAATGCGGAAAA 59.192 37.500 0.00 0.00 0.00 2.29
6246 6549 6.018016 CCAAAAGTTGAAGAATGCGGAAAATT 60.018 34.615 0.00 0.00 0.00 1.82
6247 6550 6.529463 AAAGTTGAAGAATGCGGAAAATTG 57.471 33.333 0.00 0.00 0.00 2.32
6248 6551 5.200368 AGTTGAAGAATGCGGAAAATTGT 57.800 34.783 0.00 0.00 0.00 2.71
6250 6553 6.924111 AGTTGAAGAATGCGGAAAATTGTAT 58.076 32.000 0.00 0.00 0.00 2.29
6251 6554 8.050778 AGTTGAAGAATGCGGAAAATTGTATA 57.949 30.769 0.00 0.00 0.00 1.47
6252 6555 8.686334 AGTTGAAGAATGCGGAAAATTGTATAT 58.314 29.630 0.00 0.00 0.00 0.86
6254 6557 9.868277 TTGAAGAATGCGGAAAATTGTATATTT 57.132 25.926 0.00 0.00 0.00 1.40
6255 6558 9.299963 TGAAGAATGCGGAAAATTGTATATTTG 57.700 29.630 0.00 0.00 0.00 2.32
6256 6559 9.301153 GAAGAATGCGGAAAATTGTATATTTGT 57.699 29.630 0.00 0.00 0.00 2.83
6257 6560 8.633075 AGAATGCGGAAAATTGTATATTTGTG 57.367 30.769 0.00 0.00 0.00 3.33
6258 6561 6.826893 ATGCGGAAAATTGTATATTTGTGC 57.173 33.333 0.00 0.00 0.00 4.57
6259 6562 5.714047 TGCGGAAAATTGTATATTTGTGCA 58.286 33.333 0.00 0.00 0.00 4.57
6261 6564 6.815641 TGCGGAAAATTGTATATTTGTGCATT 59.184 30.769 0.00 0.00 0.00 3.56
6262 6565 7.976175 TGCGGAAAATTGTATATTTGTGCATTA 59.024 29.630 0.00 0.00 0.00 1.90
6263 6566 8.977505 GCGGAAAATTGTATATTTGTGCATTAT 58.022 29.630 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 13 1.815421 CAATCGAAGGAGCCACCCG 60.815 63.158 0.00 0.00 40.05 5.28
27 29 1.063266 GCCCTGTTATCCAATCCCCAA 60.063 52.381 0.00 0.00 0.00 4.12
41 43 3.391382 GCCAGGTAGACGCCCTGT 61.391 66.667 11.16 0.00 46.68 4.00
43 45 0.616679 TTAAGCCAGGTAGACGCCCT 60.617 55.000 0.00 0.00 0.00 5.19
49 51 2.642807 AGCCTTTGTTAAGCCAGGTAGA 59.357 45.455 0.00 0.00 0.00 2.59
56 59 2.696506 ACTACGAGCCTTTGTTAAGCC 58.303 47.619 0.00 0.00 0.00 4.35
59 62 8.472413 AGACATAATACTACGAGCCTTTGTTAA 58.528 33.333 0.00 0.00 0.00 2.01
63 66 6.504398 TCAGACATAATACTACGAGCCTTTG 58.496 40.000 0.00 0.00 0.00 2.77
66 69 4.762765 CCTCAGACATAATACTACGAGCCT 59.237 45.833 0.00 0.00 0.00 4.58
68 71 5.943706 TCCTCAGACATAATACTACGAGC 57.056 43.478 0.00 0.00 0.00 5.03
79 82 5.247110 GCCTATTGGAGATTCCTCAGACATA 59.753 44.000 0.00 0.00 41.20 2.29
80 83 4.041444 GCCTATTGGAGATTCCTCAGACAT 59.959 45.833 0.00 0.00 41.20 3.06
85 88 2.775418 TGGCCTATTGGAGATTCCTCA 58.225 47.619 3.32 0.00 41.20 3.86
87 90 5.458215 GGTTAATGGCCTATTGGAGATTCCT 60.458 44.000 3.32 0.00 37.46 3.36
89 92 4.767409 GGGTTAATGGCCTATTGGAGATTC 59.233 45.833 3.32 0.00 34.57 2.52
105 112 9.233649 CATCTAGAGTACGATTCTAGGGTTAAT 57.766 37.037 14.43 2.21 42.76 1.40
120 127 5.487153 TCAGCGAAAGACATCTAGAGTAC 57.513 43.478 0.00 0.00 0.00 2.73
121 128 6.460261 CCAATCAGCGAAAGACATCTAGAGTA 60.460 42.308 0.00 0.00 0.00 2.59
122 129 5.347342 CAATCAGCGAAAGACATCTAGAGT 58.653 41.667 0.00 0.00 0.00 3.24
123 130 4.744137 CCAATCAGCGAAAGACATCTAGAG 59.256 45.833 0.00 0.00 0.00 2.43
124 131 4.442052 CCCAATCAGCGAAAGACATCTAGA 60.442 45.833 0.00 0.00 0.00 2.43
125 132 3.806521 CCCAATCAGCGAAAGACATCTAG 59.193 47.826 0.00 0.00 0.00 2.43
131 138 1.803289 GGCCCAATCAGCGAAAGAC 59.197 57.895 0.00 0.00 0.00 3.01
136 143 4.467084 GGACGGCCCAATCAGCGA 62.467 66.667 0.00 0.00 34.14 4.93
149 156 2.926200 CTCAATTGTGCTAGAGTGGACG 59.074 50.000 5.13 0.00 0.00 4.79
151 158 2.355108 GCCTCAATTGTGCTAGAGTGGA 60.355 50.000 5.13 0.00 0.00 4.02
159 166 2.224354 CCCAAAAAGCCTCAATTGTGCT 60.224 45.455 16.13 16.13 36.79 4.40
163 170 5.151297 ACATACCCAAAAAGCCTCAATTG 57.849 39.130 0.00 0.00 0.00 2.32
177 184 1.850345 GGAGATTCCCCAACATACCCA 59.150 52.381 0.00 0.00 0.00 4.51
184 191 3.744530 CGACCTATTGGAGATTCCCCAAC 60.745 52.174 1.23 0.00 45.40 3.77
204 211 6.040209 TCCTAGTAACAAGCCAATAAACGA 57.960 37.500 0.00 0.00 0.00 3.85
210 217 4.080299 CCCTTCTCCTAGTAACAAGCCAAT 60.080 45.833 0.00 0.00 0.00 3.16
213 220 3.105283 TCCCTTCTCCTAGTAACAAGCC 58.895 50.000 0.00 0.00 0.00 4.35
258 265 0.107017 GGCTAGCTGAATGGCCTTCA 60.107 55.000 15.72 10.70 43.15 3.02
259 266 0.821301 GGGCTAGCTGAATGGCCTTC 60.821 60.000 15.72 6.14 45.61 3.46
270 277 6.712547 GTGTTTGATAATCAATAGGGCTAGCT 59.287 38.462 15.72 0.00 36.11 3.32
288 295 5.445069 CAGGGTATTATCCATGGTGTTTGA 58.555 41.667 12.58 0.00 35.89 2.69
293 300 3.795688 AGCAGGGTATTATCCATGGTG 57.204 47.619 12.58 0.00 45.86 4.17
335 355 4.449068 GGATTACTGCGATTATGTCACCAG 59.551 45.833 0.00 0.00 34.05 4.00
410 430 1.724429 TGGGAAACGGTATGCGTTAC 58.276 50.000 0.00 0.00 0.00 2.50
418 438 1.478837 TGCCAACAATGGGAAACGGTA 60.479 47.619 0.00 0.00 45.07 4.02
486 506 5.234116 CAGACAATTTTTCCAAAAAGGGACG 59.766 40.000 3.74 0.00 40.78 4.79
510 530 6.920569 TTCCAAGTAAAAGTCAGAGTTCAC 57.079 37.500 0.00 0.00 0.00 3.18
523 543 9.474920 GACAATCATCAAATGTTTCCAAGTAAA 57.525 29.630 0.00 0.00 0.00 2.01
573 593 9.003658 ACAAAACAGAAGGATGAATACAGTAAG 57.996 33.333 0.00 0.00 0.00 2.34
581 601 7.885399 AGCTAGTAACAAAACAGAAGGATGAAT 59.115 33.333 0.00 0.00 0.00 2.57
586 606 4.755123 GCAGCTAGTAACAAAACAGAAGGA 59.245 41.667 0.00 0.00 0.00 3.36
611 631 2.751806 GCCTTATGCCTCCATAATCTGC 59.248 50.000 0.00 0.00 41.66 4.26
622 642 3.951563 TGGAGTTAATGCCTTATGCCT 57.048 42.857 0.00 0.00 40.16 4.75
623 643 3.305608 GCATGGAGTTAATGCCTTATGCC 60.306 47.826 0.00 0.00 43.78 4.40
624 644 3.905784 GCATGGAGTTAATGCCTTATGC 58.094 45.455 0.00 0.00 43.78 3.14
659 679 6.931840 AGTAAGAACTCTGAATCTGGAACAAC 59.068 38.462 0.00 0.00 38.70 3.32
841 939 5.251999 GACAATGAGACTTTGTCGTGTAC 57.748 43.478 12.26 0.00 42.35 2.90
850 948 2.900546 AGACGGAGGACAATGAGACTTT 59.099 45.455 0.00 0.00 0.00 2.66
1080 1179 5.363005 ACTGCTTATATAAACTGACCTCCGT 59.637 40.000 9.08 0.00 0.00 4.69
1369 1468 2.260844 TTCTTCTTGACAGTGCCCAG 57.739 50.000 0.00 0.00 0.00 4.45
1556 1655 2.300152 ACTGGCTTCAGATTTCTGTCGA 59.700 45.455 7.42 0.00 44.12 4.20
1760 1859 7.661040 AGCAGTACATTAAAATCATATTGCCC 58.339 34.615 0.00 0.00 0.00 5.36
1977 2081 2.905075 TGCGACAGGATGATGTAAAGG 58.095 47.619 0.00 0.00 39.69 3.11
1989 2093 2.693762 CCTTGGTGCATGCGACAGG 61.694 63.158 14.09 14.11 0.00 4.00
1992 2096 0.387239 GAAACCTTGGTGCATGCGAC 60.387 55.000 14.09 12.05 0.00 5.19
2135 2240 7.934120 CCTAAAGATGGAATACAAGTCTTAGGG 59.066 40.741 0.00 0.00 0.00 3.53
2343 2448 1.405526 GGCACGCTGATAGAACCTTGA 60.406 52.381 0.00 0.00 0.00 3.02
2359 2464 6.529220 ACAAAGATATGATAAGAGAGGGCAC 58.471 40.000 0.00 0.00 0.00 5.01
2492 2597 1.095600 TCCGTCTCCTGAGATTCACG 58.904 55.000 0.00 0.09 39.97 4.35
2710 2815 0.399454 AGCACATCAGCCAGAACTGT 59.601 50.000 1.18 0.00 38.84 3.55
2830 2935 8.687292 ATATAAAATTGCTGATCAGAAGCTCA 57.313 30.769 27.04 11.23 41.42 4.26
2881 2986 5.353394 ACTTGACCAAACTCACAGAACTA 57.647 39.130 0.00 0.00 0.00 2.24
2952 3059 9.887406 GAAAAAGTATCACATTTAAAGAACGGA 57.113 29.630 0.00 0.00 0.00 4.69
3019 3126 8.194104 TCAAACAAGTTTAGCTTATTTTCTGCA 58.806 29.630 0.00 0.00 32.03 4.41
3178 3285 7.229506 CCCTCTGTTCCCAAATATAAGATGTTC 59.770 40.741 0.00 0.00 0.00 3.18
3267 3374 4.778579 ACTATAGTGAAGACTCGCCACTA 58.221 43.478 4.10 12.77 44.43 2.74
3274 3381 6.039270 AGCATGTGAGACTATAGTGAAGACTC 59.961 42.308 10.90 10.50 36.64 3.36
3276 3383 5.976534 CAGCATGTGAGACTATAGTGAAGAC 59.023 44.000 10.90 2.36 0.00 3.01
3331 3438 9.429359 ACTATCAAGATAAAATATCAAGCCTCG 57.571 33.333 0.67 0.00 0.00 4.63
3450 3558 4.953579 TGTACAAATAAATCTGGGGAAGGC 59.046 41.667 0.00 0.00 0.00 4.35
3509 3617 4.883083 AGCTCAACTAGATGAAACGTCAA 58.117 39.130 4.11 0.00 37.30 3.18
3513 3621 7.693951 CCAAAATTAGCTCAACTAGATGAAACG 59.306 37.037 4.11 0.00 30.79 3.60
3520 3628 6.434028 ACAATGCCAAAATTAGCTCAACTAGA 59.566 34.615 0.00 0.00 30.79 2.43
3527 3635 5.956171 GCTAACAATGCCAAAATTAGCTC 57.044 39.130 6.97 0.00 42.80 4.09
3583 3691 1.382522 ACCATTTCCATAGCACGCAG 58.617 50.000 0.00 0.00 0.00 5.18
3593 3701 6.325286 GGGTTAAGGCATATAAACCATTTCCA 59.675 38.462 10.99 0.00 42.61 3.53
3619 3727 5.880054 ACAACCATTTTAAGAGTGGATCG 57.120 39.130 9.12 0.00 36.82 3.69
3737 3846 8.254508 GGACATAGAATGACTAGAGACAAACTT 58.745 37.037 0.00 0.00 34.35 2.66
3739 3848 7.777095 AGGACATAGAATGACTAGAGACAAAC 58.223 38.462 0.00 0.00 34.35 2.93
3759 3869 4.819630 GGAAACATATGGCGAAATAGGACA 59.180 41.667 7.80 0.00 0.00 4.02
3833 3943 6.822170 AGTAATATCTGTATCATGCCATGCTG 59.178 38.462 0.00 0.00 0.00 4.41
3886 3996 5.420104 CCTCAATTTTGTAGGGATGCTCTTT 59.580 40.000 0.00 0.00 0.00 2.52
4064 4174 3.487372 TGATGCGTATCTACCAGCTACT 58.513 45.455 14.76 0.00 34.31 2.57
4072 4182 8.903723 GTCTACAATTAACTGATGCGTATCTAC 58.096 37.037 14.76 0.00 34.31 2.59
4280 4390 6.151648 ACTTACATACCAGACGCTACAGTAAA 59.848 38.462 0.00 0.00 0.00 2.01
4518 4670 2.380941 AGCCATGCTTCATGTATGCAA 58.619 42.857 12.23 0.00 41.16 4.08
4580 4732 5.726980 TGCTTTATTTCCATTGAACTGCT 57.273 34.783 0.00 0.00 0.00 4.24
4606 4758 6.691508 AGAGAAATTCCAATTTGTTAGGTGC 58.308 36.000 1.94 0.00 38.64 5.01
4709 4870 7.645058 AGAGTTTCTGTTCTCCATTTTCAAA 57.355 32.000 0.00 0.00 0.00 2.69
4785 4946 4.379813 GGCAATGGTGTAACTCAATGTCAG 60.380 45.833 0.00 0.00 36.74 3.51
4830 4991 5.277828 GCACAGAACGAATTTGGAGTAAGTT 60.278 40.000 0.00 0.00 0.00 2.66
4831 4992 4.213482 GCACAGAACGAATTTGGAGTAAGT 59.787 41.667 0.00 0.00 0.00 2.24
4835 4996 1.880027 GGCACAGAACGAATTTGGAGT 59.120 47.619 0.00 0.00 0.00 3.85
4892 5053 2.203238 TGTGCAGCAGCTTCAGCA 60.203 55.556 0.00 0.00 45.16 4.41
4986 5147 1.001293 TCACACAGGACAAGCAGCTAG 59.999 52.381 0.00 0.00 0.00 3.42
5000 5161 1.293179 CTCGCTGGATGGTCACACA 59.707 57.895 0.00 0.00 0.00 3.72
5001 5162 0.737715 GACTCGCTGGATGGTCACAC 60.738 60.000 0.00 0.00 0.00 3.82
5022 5183 2.744202 CACTGTGGGACATCAAGCTTAC 59.256 50.000 0.00 0.00 44.52 2.34
5040 5201 4.740902 AGGAAAAAGGTTGAATAGCCACT 58.259 39.130 0.00 0.00 0.00 4.00
5064 5225 3.367327 CGACAGTCTTCTTCATCTGCAAG 59.633 47.826 0.00 0.00 0.00 4.01
5082 5243 0.858583 CGCTGTTGTCAATGTCGACA 59.141 50.000 22.48 22.48 44.05 4.35
5085 5246 1.139989 AGTCGCTGTTGTCAATGTCG 58.860 50.000 0.00 0.00 0.00 4.35
5142 5303 1.676967 CTTGGCAGGAGGGTTCAGC 60.677 63.158 0.00 0.00 0.00 4.26
5145 5306 0.328258 TTAGCTTGGCAGGAGGGTTC 59.672 55.000 0.00 0.00 0.00 3.62
5166 5327 2.156446 CCCGTCGACGAAATCCACG 61.156 63.158 37.65 18.39 43.02 4.94
5232 5393 5.975282 TCTTCCATGTCTCTCTTCATGAAG 58.025 41.667 26.56 26.56 42.52 3.02
5250 5411 4.457834 TTCATCTTCGACCTCTTCTTCC 57.542 45.455 0.00 0.00 0.00 3.46
5287 5454 1.595993 CTGTCGACATCCACGGAGGT 61.596 60.000 20.40 2.43 42.11 3.85
5337 5504 0.249120 CAACAGAGGGTGGCGATACA 59.751 55.000 0.00 0.00 0.00 2.29
5338 5505 0.535335 TCAACAGAGGGTGGCGATAC 59.465 55.000 0.00 0.00 0.00 2.24
5343 5510 1.668151 GACGTCAACAGAGGGTGGC 60.668 63.158 11.55 0.00 0.00 5.01
5355 5522 2.139917 GGTAACATGCTGTTGACGTCA 58.860 47.619 15.76 15.76 41.30 4.35
5370 5537 2.003658 TATCGACGGCGGGTGGTAAC 62.004 60.000 12.58 0.00 38.28 2.50
5385 5552 1.271379 TCCCCGTCGATTTCCATATCG 59.729 52.381 0.00 0.00 46.63 2.92
5394 5561 2.064581 CCCTTCCTCCCCGTCGATT 61.065 63.158 0.00 0.00 0.00 3.34
5412 5579 1.751927 CCCACAGCAGCCAATCTCC 60.752 63.158 0.00 0.00 0.00 3.71
5418 5585 3.248418 TGCTACCCACAGCAGCCA 61.248 61.111 0.00 0.00 46.41 4.75
5439 5606 6.007079 GCGAAACAAAGTTCACAAGAAAAAC 58.993 36.000 0.00 0.00 35.08 2.43
5451 5618 5.849081 CACAATACGTATGCGAAACAAAGTT 59.151 36.000 11.07 0.00 42.00 2.66
5479 5646 1.904144 CGATGTACGATCGTGTTGGT 58.096 50.000 30.23 11.58 45.77 3.67
5531 5698 4.445453 CTTATGTCAACATAGCCTGCTCA 58.555 43.478 0.00 0.00 39.69 4.26
5532 5699 3.249559 GCTTATGTCAACATAGCCTGCTC 59.750 47.826 0.00 0.00 39.69 4.26
5536 5703 2.838736 CCGCTTATGTCAACATAGCCT 58.161 47.619 13.84 0.00 39.69 4.58
5545 5712 0.740868 GCACTCAGCCGCTTATGTCA 60.741 55.000 0.00 0.00 37.23 3.58
5556 5723 1.871080 ACAGTTACAGTGCACTCAGC 58.129 50.000 18.64 10.01 45.96 4.26
5557 5724 3.001634 CACAACAGTTACAGTGCACTCAG 59.998 47.826 18.64 9.76 0.00 3.35
5558 5725 2.935849 CACAACAGTTACAGTGCACTCA 59.064 45.455 18.64 4.78 0.00 3.41
5600 5767 8.071368 TCCAATTGTTTTACAGAACATTCGTAC 58.929 33.333 4.43 0.00 39.12 3.67
5601 5768 8.155821 TCCAATTGTTTTACAGAACATTCGTA 57.844 30.769 4.43 0.00 39.12 3.43
5602 5769 7.012894 TCTCCAATTGTTTTACAGAACATTCGT 59.987 33.333 4.43 0.00 39.12 3.85
5603 5770 7.359595 TCTCCAATTGTTTTACAGAACATTCG 58.640 34.615 4.43 0.00 39.12 3.34
5673 5848 1.512522 CACCATCGCACACGCAATG 60.513 57.895 0.00 0.00 39.84 2.82
5680 5855 0.107897 GGATACACCACCATCGCACA 60.108 55.000 0.00 0.00 38.79 4.57
5681 5856 0.107897 TGGATACACCACCATCGCAC 60.108 55.000 0.00 0.00 46.17 5.34
5722 5901 1.930908 GCTTGTCATGACTGCAGGGC 61.931 60.000 27.27 18.05 33.92 5.19
5723 5902 0.607217 TGCTTGTCATGACTGCAGGG 60.607 55.000 29.45 15.07 36.90 4.45
5724 5903 0.520404 GTGCTTGTCATGACTGCAGG 59.480 55.000 31.90 15.44 40.11 4.85
5726 5905 1.808343 GATGTGCTTGTCATGACTGCA 59.192 47.619 29.45 29.45 38.41 4.41
5727 5906 1.131883 GGATGTGCTTGTCATGACTGC 59.868 52.381 25.55 25.96 34.17 4.40
5728 5907 2.418976 CAGGATGTGCTTGTCATGACTG 59.581 50.000 25.55 18.51 0.00 3.51
5730 5909 2.676839 CTCAGGATGTGCTTGTCATGAC 59.323 50.000 19.27 19.27 37.40 3.06
5731 5910 2.981898 CTCAGGATGTGCTTGTCATGA 58.018 47.619 0.00 0.00 37.40 3.07
5740 5919 4.637609 TCAGGATGTGCTCAGGATGTGC 62.638 54.545 0.00 0.00 45.78 4.57
5741 5920 1.208776 TCAGGATGTGCTCAGGATGTG 59.791 52.381 0.00 0.00 35.30 3.21
5742 5921 1.576577 TCAGGATGTGCTCAGGATGT 58.423 50.000 0.00 0.00 35.30 3.06
5743 5922 2.495084 CATCAGGATGTGCTCAGGATG 58.505 52.381 1.07 2.13 37.40 3.51
5744 5923 1.420514 CCATCAGGATGTGCTCAGGAT 59.579 52.381 8.35 0.00 37.11 3.24
5745 5924 0.835276 CCATCAGGATGTGCTCAGGA 59.165 55.000 8.35 0.00 37.11 3.86
5746 5925 0.545171 ACCATCAGGATGTGCTCAGG 59.455 55.000 8.35 0.00 37.11 3.86
5747 5926 1.208776 TCACCATCAGGATGTGCTCAG 59.791 52.381 8.35 0.00 37.11 3.35
5748 5927 1.278537 TCACCATCAGGATGTGCTCA 58.721 50.000 8.35 0.00 37.11 4.26
5749 5928 2.219458 CATCACCATCAGGATGTGCTC 58.781 52.381 8.35 0.00 36.89 4.26
5775 5966 1.202382 GCGTAGTTACCCTGGCTGTAG 60.202 57.143 0.00 0.00 0.00 2.74
5779 5970 1.400737 CTAGCGTAGTTACCCTGGCT 58.599 55.000 0.00 0.00 37.79 4.75
5804 5995 0.250338 ACCGAGGTGCCTTGAACTTC 60.250 55.000 7.04 0.00 0.00 3.01
5817 6120 0.606401 AAGTGACCATTGCACCGAGG 60.606 55.000 0.00 0.00 36.95 4.63
5835 6138 1.881973 GTGTTCATCAGCTGAGCCAAA 59.118 47.619 22.96 10.26 34.41 3.28
5916 6219 1.827315 CGACGGTTGCAACACGACAT 61.827 55.000 32.66 18.84 33.88 3.06
5917 6220 2.518312 CGACGGTTGCAACACGACA 61.518 57.895 32.66 0.00 33.88 4.35
5918 6221 2.244382 CGACGGTTGCAACACGAC 59.756 61.111 32.66 27.38 0.00 4.34
5919 6222 2.702751 ATCCGACGGTTGCAACACGA 62.703 55.000 32.66 20.31 0.00 4.35
5920 6223 2.314647 ATCCGACGGTTGCAACACG 61.315 57.895 29.55 28.45 0.00 4.49
5952 6255 1.083015 CGTTCGGGAAGCAAACACG 60.083 57.895 0.00 0.00 35.35 4.49
5955 6258 0.883370 ACTCCGTTCGGGAAGCAAAC 60.883 55.000 11.37 0.00 46.61 2.93
5960 6263 2.094390 TCATTACACTCCGTTCGGGAAG 60.094 50.000 11.37 5.05 46.61 3.46
5981 6284 3.888930 AGTGAAACGGAACCATGACATTT 59.111 39.130 0.00 0.00 45.86 2.32
6011 6314 4.081917 ACCAAACACAAAGACGAAACCAAT 60.082 37.500 0.00 0.00 0.00 3.16
6018 6321 1.131504 GCACACCAAACACAAAGACGA 59.868 47.619 0.00 0.00 0.00 4.20
6023 6326 3.784701 ATTACGCACACCAAACACAAA 57.215 38.095 0.00 0.00 0.00 2.83
6129 6432 1.641677 GTGTGTGACGGTCTTGCAC 59.358 57.895 9.88 14.68 0.00 4.57
6130 6433 1.522806 GGTGTGTGACGGTCTTGCA 60.523 57.895 9.88 3.40 0.00 4.08
6190 6493 3.181967 CGCGGCTGTCTTCCTTCG 61.182 66.667 0.00 0.00 0.00 3.79
6191 6494 2.815647 CCGCGGCTGTCTTCCTTC 60.816 66.667 14.67 0.00 0.00 3.46
6213 6516 4.751767 TCTTCAACTTTTGGCACCAAAT 57.248 36.364 15.28 0.00 44.14 2.32
6214 6517 4.543590 TTCTTCAACTTTTGGCACCAAA 57.456 36.364 10.79 10.79 43.23 3.28
6217 6520 2.802247 GCATTCTTCAACTTTTGGCACC 59.198 45.455 0.00 0.00 0.00 5.01
6220 6523 2.061028 CCGCATTCTTCAACTTTTGGC 58.939 47.619 0.00 0.00 0.00 4.52
6221 6524 3.641437 TCCGCATTCTTCAACTTTTGG 57.359 42.857 0.00 0.00 0.00 3.28
6222 6525 5.964887 TTTTCCGCATTCTTCAACTTTTG 57.035 34.783 0.00 0.00 0.00 2.44
6223 6526 6.538381 ACAATTTTCCGCATTCTTCAACTTTT 59.462 30.769 0.00 0.00 0.00 2.27
6224 6527 6.048509 ACAATTTTCCGCATTCTTCAACTTT 58.951 32.000 0.00 0.00 0.00 2.66
6225 6528 5.600696 ACAATTTTCCGCATTCTTCAACTT 58.399 33.333 0.00 0.00 0.00 2.66
6226 6529 5.200368 ACAATTTTCCGCATTCTTCAACT 57.800 34.783 0.00 0.00 0.00 3.16
6227 6530 8.856490 ATATACAATTTTCCGCATTCTTCAAC 57.144 30.769 0.00 0.00 0.00 3.18
6229 6532 9.299963 CAAATATACAATTTTCCGCATTCTTCA 57.700 29.630 0.00 0.00 0.00 3.02
6230 6533 9.301153 ACAAATATACAATTTTCCGCATTCTTC 57.699 29.630 0.00 0.00 0.00 2.87
6231 6534 9.086336 CACAAATATACAATTTTCCGCATTCTT 57.914 29.630 0.00 0.00 0.00 2.52
6232 6535 7.222611 GCACAAATATACAATTTTCCGCATTCT 59.777 33.333 0.00 0.00 0.00 2.40
6233 6536 7.009999 TGCACAAATATACAATTTTCCGCATTC 59.990 33.333 0.00 0.00 0.00 2.67
6234 6537 6.815641 TGCACAAATATACAATTTTCCGCATT 59.184 30.769 0.00 0.00 0.00 3.56
6235 6538 6.336566 TGCACAAATATACAATTTTCCGCAT 58.663 32.000 0.00 0.00 0.00 4.73
6236 6539 5.714047 TGCACAAATATACAATTTTCCGCA 58.286 33.333 0.00 0.00 0.00 5.69
6237 6540 6.826893 ATGCACAAATATACAATTTTCCGC 57.173 33.333 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.