Multiple sequence alignment - TraesCS5A01G519500

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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 TraesCS5A01G519500 chr5A 100.000 2378 0 0 1 2378 680919325 680916948 0.000000e+00 4392
1 TraesCS5A01G519500 chr5A 82.993 1029 102 36 709 1701 680910769 680909778 0.000000e+00 863
2 TraesCS5A01G519500 chr1B 86.186 666 77 11 1718 2377 678412445 678411789 0.000000e+00 706
3 TraesCS5A01G519500 chr1B 83.942 137 20 1 557 691 381609946 381609810 1.920000e-26 130
4 TraesCS5A01G519500 chr4D 86.015 665 82 8 1718 2377 196881588 196882246 0.000000e+00 702
5 TraesCS5A01G519500 chr4D 85.714 665 84 7 1718 2377 342537555 342538213 0.000000e+00 691
6 TraesCS5A01G519500 chr6B 85.865 665 83 9 1718 2377 11729539 11730197 0.000000e+00 697
7 TraesCS5A01G519500 chr5B 85.886 666 81 10 1718 2377 490539239 490539897 0.000000e+00 697
8 TraesCS5A01G519500 chr3D 85.822 663 86 7 1718 2377 120120620 120119963 0.000000e+00 697
9 TraesCS5A01G519500 chr3B 85.822 663 87 5 1718 2377 51123885 51124543 0.000000e+00 697
10 TraesCS5A01G519500 chr3B 85.886 666 81 10 1718 2377 449309689 449310347 0.000000e+00 697
11 TraesCS5A01G519500 chr3B 87.013 154 11 3 224 375 765723628 765723774 5.260000e-37 165
12 TraesCS5A01G519500 chr3B 73.921 579 62 37 1131 1660 765725725 765726263 1.470000e-32 150
13 TraesCS5A01G519500 chr1D 85.843 664 78 11 1718 2377 111496180 111496831 0.000000e+00 691
14 TraesCS5A01G519500 chrUn 87.636 550 52 7 1133 1670 60451704 60452249 2.010000e-175 625
15 TraesCS5A01G519500 chrUn 86.754 536 34 8 448 964 60420844 60421361 1.600000e-156 562
16 TraesCS5A01G519500 chrUn 90.000 410 27 6 1 409 60419178 60419574 3.500000e-143 518
17 TraesCS5A01G519500 chrUn 80.130 463 49 17 692 1135 16762622 16763060 2.970000e-79 305
18 TraesCS5A01G519500 chrUn 80.313 447 35 20 713 1131 60451247 60451668 2.990000e-74 289
19 TraesCS5A01G519500 chrUn 87.013 154 11 3 224 375 277591093 277591239 5.260000e-37 165
20 TraesCS5A01G519500 chrUn 73.921 579 62 37 1131 1660 277593190 277593728 1.470000e-32 150
21 TraesCS5A01G519500 chr4B 84.787 539 38 8 448 967 643524515 643524002 3.530000e-138 501
22 TraesCS5A01G519500 chr4B 84.146 410 25 12 1 409 643526207 643525837 6.250000e-96 361
23 TraesCS5A01G519500 chr7A 84.211 133 19 1 557 687 596735703 596735571 6.900000e-26 128
24 TraesCS5A01G519500 chr2A 85.047 107 14 1 561 665 161944771 161944665 8.990000e-20 108


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 TraesCS5A01G519500 chr5A 680916948 680919325 2377 True 4392 4392 100.0000 1 2378 1 chr5A.!!$R2 2377
1 TraesCS5A01G519500 chr5A 680909778 680910769 991 True 863 863 82.9930 709 1701 1 chr5A.!!$R1 992
2 TraesCS5A01G519500 chr1B 678411789 678412445 656 True 706 706 86.1860 1718 2377 1 chr1B.!!$R2 659
3 TraesCS5A01G519500 chr4D 196881588 196882246 658 False 702 702 86.0150 1718 2377 1 chr4D.!!$F1 659
4 TraesCS5A01G519500 chr4D 342537555 342538213 658 False 691 691 85.7140 1718 2377 1 chr4D.!!$F2 659
5 TraesCS5A01G519500 chr6B 11729539 11730197 658 False 697 697 85.8650 1718 2377 1 chr6B.!!$F1 659
6 TraesCS5A01G519500 chr5B 490539239 490539897 658 False 697 697 85.8860 1718 2377 1 chr5B.!!$F1 659
7 TraesCS5A01G519500 chr3D 120119963 120120620 657 True 697 697 85.8220 1718 2377 1 chr3D.!!$R1 659
8 TraesCS5A01G519500 chr3B 51123885 51124543 658 False 697 697 85.8220 1718 2377 1 chr3B.!!$F1 659
9 TraesCS5A01G519500 chr3B 449309689 449310347 658 False 697 697 85.8860 1718 2377 1 chr3B.!!$F2 659
10 TraesCS5A01G519500 chr1D 111496180 111496831 651 False 691 691 85.8430 1718 2377 1 chr1D.!!$F1 659
11 TraesCS5A01G519500 chrUn 60419178 60421361 2183 False 540 562 88.3770 1 964 2 chrUn.!!$F2 963
12 TraesCS5A01G519500 chrUn 60451247 60452249 1002 False 457 625 83.9745 713 1670 2 chrUn.!!$F3 957
13 TraesCS5A01G519500 chr4B 643524002 643526207 2205 True 431 501 84.4665 1 967 2 chr4B.!!$R1 966

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
864 2205 0.03101 CTGGGGGAAGGTAGCTAGGT 60.031 60.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 3467 0.322322 TTTCAACAGGCGACGGGTAT 59.678 50.0 0.0 0.0 0.0 2.73 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
18 19 3.261441 CTGCTTGCTGTGTGTTTGG 57.739 52.632 0.00 0.00 0.00 3.28
25 26 1.067916 CTGTGTGTTTGGGGCTTGC 59.932 57.895 0.00 0.00 0.00 4.01
58 59 6.272318 TGAACACTTGAACTTGCTTATTTGG 58.728 36.000 0.00 0.00 0.00 3.28
59 60 5.852282 ACACTTGAACTTGCTTATTTGGT 57.148 34.783 0.00 0.00 0.00 3.67
60 61 6.952773 ACACTTGAACTTGCTTATTTGGTA 57.047 33.333 0.00 0.00 0.00 3.25
61 62 7.524717 ACACTTGAACTTGCTTATTTGGTAT 57.475 32.000 0.00 0.00 0.00 2.73
62 63 7.951591 ACACTTGAACTTGCTTATTTGGTATT 58.048 30.769 0.00 0.00 0.00 1.89
63 64 8.421002 ACACTTGAACTTGCTTATTTGGTATTT 58.579 29.630 0.00 0.00 0.00 1.40
64 65 9.260002 CACTTGAACTTGCTTATTTGGTATTTT 57.740 29.630 0.00 0.00 0.00 1.82
65 66 9.260002 ACTTGAACTTGCTTATTTGGTATTTTG 57.740 29.630 0.00 0.00 0.00 2.44
66 67 8.600449 TTGAACTTGCTTATTTGGTATTTTGG 57.400 30.769 0.00 0.00 0.00 3.28
77 78 2.500098 TGGTATTTTGGTCCCTCGAGAG 59.500 50.000 15.71 0.00 0.00 3.20
88 89 3.004315 GTCCCTCGAGAGCTTAAGAGATG 59.996 52.174 15.71 0.00 32.84 2.90
90 91 3.253188 CCCTCGAGAGCTTAAGAGATGAG 59.747 52.174 15.71 6.00 32.84 2.90
91 92 3.253188 CCTCGAGAGCTTAAGAGATGAGG 59.747 52.174 15.71 11.04 35.05 3.86
92 93 3.882888 CTCGAGAGCTTAAGAGATGAGGT 59.117 47.826 6.58 0.00 32.84 3.85
94 95 3.716601 GAGAGCTTAAGAGATGAGGTGC 58.283 50.000 6.67 0.00 0.00 5.01
95 96 3.102972 AGAGCTTAAGAGATGAGGTGCA 58.897 45.455 6.67 0.00 0.00 4.57
96 97 3.710677 AGAGCTTAAGAGATGAGGTGCAT 59.289 43.478 6.67 0.00 40.77 3.96
97 98 3.806380 AGCTTAAGAGATGAGGTGCATG 58.194 45.455 6.67 0.00 37.34 4.06
98 99 3.199508 AGCTTAAGAGATGAGGTGCATGT 59.800 43.478 6.67 0.00 37.34 3.21
99 100 3.559242 GCTTAAGAGATGAGGTGCATGTC 59.441 47.826 6.67 0.00 45.14 3.06
100 101 4.763073 CTTAAGAGATGAGGTGCATGTCA 58.237 43.478 0.00 3.66 46.69 3.58
112 113 3.394800 CATGTCAGCATGTGTGTGC 57.605 52.632 0.00 0.00 45.48 4.57
118 119 2.872557 GCATGTGTGTGCGATGCT 59.127 55.556 0.00 0.00 39.54 3.79
127 128 3.787634 GTGTGTGCGATGCTATGATTTTG 59.212 43.478 0.00 0.00 0.00 2.44
128 129 3.439825 TGTGTGCGATGCTATGATTTTGT 59.560 39.130 0.00 0.00 0.00 2.83
136 137 4.970662 TGCTATGATTTTGTGAGGAAGC 57.029 40.909 0.00 0.00 0.00 3.86
137 138 4.334552 TGCTATGATTTTGTGAGGAAGCA 58.665 39.130 0.00 0.00 35.26 3.91
148 149 3.118038 TGTGAGGAAGCACAGTAGGTTTT 60.118 43.478 0.00 0.00 43.35 2.43
151 152 1.804748 GGAAGCACAGTAGGTTTTCCG 59.195 52.381 0.00 0.00 46.35 4.30
173 174 8.902540 TCCGACTGCATGTATTTATATTTTCT 57.097 30.769 0.00 0.00 0.00 2.52
197 198 8.098912 TCTAAAGTATGTACAAGAAGGTTTCCC 58.901 37.037 0.00 0.00 0.00 3.97
213 214 4.202050 GGTTTCCCTACTGCATGCATTTAG 60.202 45.833 22.97 22.14 0.00 1.85
236 237 5.047377 AGACTTCTCAGAGCAGAAAAGGTAG 60.047 44.000 3.83 0.00 31.86 3.18
278 280 4.115398 AGGCTCCCTACTGTATAATCGT 57.885 45.455 0.00 0.00 28.47 3.73
292 294 9.826574 ACTGTATAATCGTATAAAGGCTTGAAA 57.173 29.630 0.00 0.00 33.32 2.69
302 304 6.855763 ATAAAGGCTTGAAACCATGATTGA 57.144 33.333 0.00 0.00 0.00 2.57
338 340 3.378427 ACTTTGTCTTTGCTCTGTGAACC 59.622 43.478 0.00 0.00 0.00 3.62
384 386 1.755395 GCCCTGCATGCATTCCTGA 60.755 57.895 22.97 0.00 0.00 3.86
403 405 7.181569 TCCTGATTATCCAAATTGAAAACCC 57.818 36.000 0.00 0.00 0.00 4.11
427 1741 1.032014 TTTGTTCAGGCAGCAAGTCC 58.968 50.000 0.00 0.00 0.00 3.85
429 1743 0.183492 TGTTCAGGCAGCAAGTCCTT 59.817 50.000 0.00 0.00 0.00 3.36
430 1744 0.877743 GTTCAGGCAGCAAGTCCTTC 59.122 55.000 0.00 0.00 0.00 3.46
431 1745 0.250901 TTCAGGCAGCAAGTCCTTCC 60.251 55.000 0.00 0.00 0.00 3.46
432 1746 1.073722 CAGGCAGCAAGTCCTTCCA 59.926 57.895 0.00 0.00 0.00 3.53
433 1747 0.538057 CAGGCAGCAAGTCCTTCCAA 60.538 55.000 0.00 0.00 0.00 3.53
434 1748 0.185901 AGGCAGCAAGTCCTTCCAAA 59.814 50.000 0.00 0.00 0.00 3.28
435 1749 0.600057 GGCAGCAAGTCCTTCCAAAG 59.400 55.000 0.00 0.00 0.00 2.77
436 1750 0.038801 GCAGCAAGTCCTTCCAAAGC 60.039 55.000 0.00 0.00 0.00 3.51
437 1751 0.600057 CAGCAAGTCCTTCCAAAGCC 59.400 55.000 0.00 0.00 0.00 4.35
438 1752 0.185901 AGCAAGTCCTTCCAAAGCCA 59.814 50.000 0.00 0.00 0.00 4.75
439 1753 0.315251 GCAAGTCCTTCCAAAGCCAC 59.685 55.000 0.00 0.00 0.00 5.01
440 1754 0.961753 CAAGTCCTTCCAAAGCCACC 59.038 55.000 0.00 0.00 0.00 4.61
441 1755 0.853530 AAGTCCTTCCAAAGCCACCT 59.146 50.000 0.00 0.00 0.00 4.00
442 1756 1.742308 AGTCCTTCCAAAGCCACCTA 58.258 50.000 0.00 0.00 0.00 3.08
443 1757 2.062636 AGTCCTTCCAAAGCCACCTAA 58.937 47.619 0.00 0.00 0.00 2.69
444 1758 2.649816 AGTCCTTCCAAAGCCACCTAAT 59.350 45.455 0.00 0.00 0.00 1.73
445 1759 3.076032 AGTCCTTCCAAAGCCACCTAATT 59.924 43.478 0.00 0.00 0.00 1.40
446 1760 3.193479 GTCCTTCCAAAGCCACCTAATTG 59.807 47.826 0.00 0.00 0.00 2.32
447 1761 2.497273 CCTTCCAAAGCCACCTAATTGG 59.503 50.000 0.00 0.00 42.92 3.16
454 1768 3.551259 CCACCTAATTGGCACGTCT 57.449 52.632 0.00 0.00 40.22 4.18
455 1769 1.369625 CCACCTAATTGGCACGTCTC 58.630 55.000 0.00 0.00 40.22 3.36
514 1828 4.869861 GGCCCAAAAGTAATTTGTATGCAG 59.130 41.667 0.00 0.00 45.72 4.41
594 1909 1.447838 CCATGAGGTCACGGGTTCG 60.448 63.158 0.00 0.00 43.02 3.95
596 1911 0.736325 CATGAGGTCACGGGTTCGAC 60.736 60.000 0.00 0.00 40.11 4.20
599 1914 1.228490 AGGTCACGGGTTCGACTCT 60.228 57.895 0.00 0.00 40.11 3.24
601 1916 1.080705 GTCACGGGTTCGACTCTGG 60.081 63.158 0.00 0.00 40.11 3.86
622 1937 3.334691 GGAAATAGCCCCTTGCAAAAAC 58.665 45.455 0.00 0.00 44.83 2.43
623 1938 2.741759 AATAGCCCCTTGCAAAAACG 57.258 45.000 0.00 0.00 44.83 3.60
628 1943 0.601057 CCCCTTGCAAAAACGTAGGG 59.399 55.000 10.03 10.03 44.27 3.53
654 1969 5.510671 ACTGCGTACAAAAGATTCAAAGTG 58.489 37.500 0.00 0.00 0.00 3.16
667 1982 0.396811 CAAAGTGGTCGGACCCTTCT 59.603 55.000 23.81 15.83 37.50 2.85
671 1986 1.155390 TGGTCGGACCCTTCTCTGT 59.845 57.895 23.81 0.00 37.50 3.41
673 1988 1.104630 GGTCGGACCCTTCTCTGTAG 58.895 60.000 16.55 0.00 30.04 2.74
678 1993 0.827368 GACCCTTCTCTGTAGCCTGG 59.173 60.000 0.00 0.00 0.00 4.45
704 2036 1.400494 CGGGTGCCCTTTTATTCTTCG 59.600 52.381 5.64 0.00 0.00 3.79
705 2037 1.134367 GGGTGCCCTTTTATTCTTCGC 59.866 52.381 0.00 0.00 0.00 4.70
707 2039 3.275999 GGTGCCCTTTTATTCTTCGCTA 58.724 45.455 0.00 0.00 0.00 4.26
711 2043 4.574828 TGCCCTTTTATTCTTCGCTATGTC 59.425 41.667 0.00 0.00 0.00 3.06
776 2108 2.515996 GAATGGACGCGTTCCCCTCA 62.516 60.000 16.49 6.92 45.17 3.86
784 2116 2.289819 ACGCGTTCCCCTCATTTTTCTA 60.290 45.455 5.58 0.00 0.00 2.10
808 2148 7.073342 ACCTTCAAACTGATTACTTATTCGC 57.927 36.000 0.00 0.00 0.00 4.70
829 2170 2.286713 CCATTTTGACTCGTTGAACGCA 60.287 45.455 13.62 2.41 42.21 5.24
830 2171 2.445453 TTTTGACTCGTTGAACGCAC 57.555 45.000 13.62 7.20 42.21 5.34
831 2172 1.647346 TTTGACTCGTTGAACGCACT 58.353 45.000 13.62 0.00 42.21 4.40
859 2200 2.666098 TTCGCTGGGGGAAGGTAGC 61.666 63.158 0.00 0.00 31.13 3.58
863 2204 1.411651 GCTGGGGGAAGGTAGCTAGG 61.412 65.000 0.00 0.00 33.53 3.02
864 2205 0.031010 CTGGGGGAAGGTAGCTAGGT 60.031 60.000 0.00 0.00 0.00 3.08
865 2206 1.219724 CTGGGGGAAGGTAGCTAGGTA 59.780 57.143 0.00 0.00 0.00 3.08
866 2207 1.219724 TGGGGGAAGGTAGCTAGGTAG 59.780 57.143 0.86 0.00 0.00 3.18
908 2249 7.224753 CGGTGAGATTAACTTGCATGTATAAGT 59.775 37.037 5.56 0.50 38.70 2.24
909 2250 9.542462 GGTGAGATTAACTTGCATGTATAAGTA 57.458 33.333 5.56 0.00 36.19 2.24
928 2269 1.270907 ACTACTCACTCAAGGGGCTG 58.729 55.000 0.00 0.00 0.00 4.85
953 2306 3.446873 GGTCATCAGTGAGACAGTCATCT 59.553 47.826 18.39 0.00 37.56 2.90
964 2317 5.888161 TGAGACAGTCATCTATCAGCTAACA 59.112 40.000 2.66 0.00 0.00 2.41
968 2325 6.344500 ACAGTCATCTATCAGCTAACAAAGG 58.656 40.000 0.00 0.00 0.00 3.11
990 2347 2.421619 GCCCTTTGCATAGCTAGCTAG 58.578 52.381 27.42 16.84 40.77 3.42
1010 2381 2.636647 TGAGAATCAATGGCGGCATA 57.363 45.000 26.05 11.21 45.97 3.14
1012 2383 3.489355 TGAGAATCAATGGCGGCATATT 58.511 40.909 26.05 20.98 45.97 1.28
1041 2412 1.153745 GCTGGTGCTACTCAGGTCG 60.154 63.158 0.00 0.00 36.03 4.79
1043 2414 2.184579 GGTGCTACTCAGGTCGCC 59.815 66.667 0.00 0.00 33.87 5.54
1048 2419 3.075005 TACTCAGGTCGCCAGGGC 61.075 66.667 0.00 0.00 37.85 5.19
1060 2431 2.267006 CAGGGCAGCGACATCTGT 59.733 61.111 0.00 0.00 36.49 3.41
1092 2463 2.426406 ATCGTCATCCTCCGCTGCA 61.426 57.895 0.00 0.00 0.00 4.41
1098 2469 3.984193 ATCCTCCGCTGCACCAAGC 62.984 63.158 0.00 0.00 45.96 4.01
1116 2487 0.464452 GCACTATTACGCCTCCACCT 59.536 55.000 0.00 0.00 0.00 4.00
1117 2488 1.806623 GCACTATTACGCCTCCACCTG 60.807 57.143 0.00 0.00 0.00 4.00
1150 2555 5.762218 GGTATGCACATCTTCTTCTTGCTAT 59.238 40.000 0.00 0.00 34.18 2.97
1216 2626 2.612221 GGAGGACGTACCAGTTCCAAAG 60.612 54.545 0.00 0.00 42.04 2.77
1247 2657 7.168905 CCTAAATACTGGATTTATGGACCTCC 58.831 42.308 5.56 0.00 38.92 4.30
1260 2670 2.029666 CCTCCCGGCTTAGCATCG 59.970 66.667 6.53 0.74 0.00 3.84
1261 2671 2.797278 CCTCCCGGCTTAGCATCGT 61.797 63.158 6.53 0.00 0.00 3.73
1262 2672 1.300233 CTCCCGGCTTAGCATCGTC 60.300 63.158 6.53 0.00 0.00 4.20
1279 2689 4.790765 TCGTCTATGCTATCCTTGATGG 57.209 45.455 0.00 0.00 37.10 3.51
1307 2717 1.460305 CCCCCTCATCCTCCGATGT 60.460 63.158 0.38 0.00 45.32 3.06
1309 2719 1.070445 CCCTCATCCTCCGATGTGC 59.930 63.158 0.38 0.00 45.32 4.57
1315 2725 2.321263 ATCCTCCGATGTGCCAGCAG 62.321 60.000 0.00 0.00 0.00 4.24
1344 2754 1.078709 CTGTTATCACTGGGCACGTG 58.921 55.000 12.28 12.28 0.00 4.49
1361 2771 1.615919 CGTGCCTTATGAACCCCCTTT 60.616 52.381 0.00 0.00 0.00 3.11
1362 2772 1.824852 GTGCCTTATGAACCCCCTTTG 59.175 52.381 0.00 0.00 0.00 2.77
1369 2779 2.926778 TGAACCCCCTTTGCAAAATG 57.073 45.000 13.84 7.32 0.00 2.32
1385 2795 4.171005 CAAAATGCAACATAGCTGTGAGG 58.829 43.478 18.24 9.36 35.22 3.86
1411 2821 8.367911 GTCATGATACAGTGACCTATAATGGAA 58.632 37.037 0.00 0.00 38.98 3.53
1420 2830 6.746120 GTGACCTATAATGGAAGTCACGTAT 58.254 40.000 5.90 0.00 45.36 3.06
1453 2871 9.179552 TGTCATATTGATTTTTCTTTTGACACG 57.820 29.630 0.00 0.00 36.85 4.49
1454 2872 8.638565 GTCATATTGATTTTTCTTTTGACACGG 58.361 33.333 0.00 0.00 33.08 4.94
1531 2949 2.463752 TCCTTGTTATGTAGAGGCCGT 58.536 47.619 0.00 0.00 0.00 5.68
1542 2960 1.688772 AGAGGCCGTACGATGTATGT 58.311 50.000 18.76 0.00 0.00 2.29
1544 2962 2.034305 AGAGGCCGTACGATGTATGTTC 59.966 50.000 18.76 2.96 0.00 3.18
1545 2963 1.126079 GGCCGTACGATGTATGTTCG 58.874 55.000 18.76 0.00 42.20 3.95
1584 3004 7.603515 GCTTGATGCGACATTTTAAGTTAATG 58.396 34.615 0.00 0.00 38.61 1.90
1624 3045 9.109393 TCATAAAAGTATACTGCTCCAATCAAC 57.891 33.333 6.06 0.00 0.00 3.18
1643 3064 4.823442 TCAACTTGATCAAGAACTGTGCAT 59.177 37.500 36.15 12.32 40.79 3.96
1671 3092 8.810652 TCAAATTTTTATTTTGAACGGGAGAG 57.189 30.769 0.00 0.00 39.46 3.20
1672 3093 7.870445 TCAAATTTTTATTTTGAACGGGAGAGG 59.130 33.333 0.00 0.00 39.46 3.69
1691 3112 1.335872 GGCCACGTGATTGAACTTTGG 60.336 52.381 19.30 0.00 0.00 3.28
1697 3118 5.280945 CACGTGATTGAACTTTGGTGATTT 58.719 37.500 10.90 0.00 0.00 2.17
1701 3122 5.176223 GTGATTGAACTTTGGTGATTTGCAG 59.824 40.000 0.00 0.00 0.00 4.41
1702 3123 4.734398 TTGAACTTTGGTGATTTGCAGT 57.266 36.364 0.00 0.00 0.00 4.40
1703 3124 4.734398 TGAACTTTGGTGATTTGCAGTT 57.266 36.364 0.00 0.00 0.00 3.16
1704 3125 5.843673 TGAACTTTGGTGATTTGCAGTTA 57.156 34.783 0.00 0.00 0.00 2.24
1705 3126 6.403866 TGAACTTTGGTGATTTGCAGTTAT 57.596 33.333 0.00 0.00 0.00 1.89
1706 3127 7.517614 TGAACTTTGGTGATTTGCAGTTATA 57.482 32.000 0.00 0.00 0.00 0.98
1707 3128 7.592938 TGAACTTTGGTGATTTGCAGTTATAG 58.407 34.615 0.00 0.00 0.00 1.31
1708 3129 6.515272 ACTTTGGTGATTTGCAGTTATAGG 57.485 37.500 0.00 0.00 0.00 2.57
1709 3130 6.010219 ACTTTGGTGATTTGCAGTTATAGGT 58.990 36.000 0.00 0.00 0.00 3.08
1710 3131 6.151144 ACTTTGGTGATTTGCAGTTATAGGTC 59.849 38.462 0.00 0.00 0.00 3.85
1711 3132 5.172687 TGGTGATTTGCAGTTATAGGTCA 57.827 39.130 0.00 0.00 0.00 4.02
1712 3133 5.754782 TGGTGATTTGCAGTTATAGGTCAT 58.245 37.500 0.00 0.00 0.00 3.06
1713 3134 6.894682 TGGTGATTTGCAGTTATAGGTCATA 58.105 36.000 0.00 0.00 0.00 2.15
1714 3135 7.517320 TGGTGATTTGCAGTTATAGGTCATAT 58.483 34.615 0.00 0.00 0.00 1.78
1715 3136 7.661437 TGGTGATTTGCAGTTATAGGTCATATC 59.339 37.037 0.00 0.00 0.00 1.63
1716 3137 7.661437 GGTGATTTGCAGTTATAGGTCATATCA 59.339 37.037 0.00 0.00 0.00 2.15
1755 3176 8.177119 TGCTTATTGGAGGCGATTTTAATATT 57.823 30.769 0.00 0.00 0.00 1.28
1765 3186 9.708092 GAGGCGATTTTAATATTCTTAGGTACT 57.292 33.333 0.00 0.00 46.37 2.73
1803 3224 7.830940 AATATTACCGTTTCGACACACATTA 57.169 32.000 2.18 0.00 0.00 1.90
1838 3259 5.042593 TCAATGTTGTGATTGACAGTTTGC 58.957 37.500 0.00 0.00 37.41 3.68
1847 3268 2.542020 TGACAGTTTGCATCTTCGGA 57.458 45.000 0.00 0.00 0.00 4.55
1861 3282 3.596214 TCTTCGGAAGGCTTGTATGTTC 58.404 45.455 17.19 0.00 0.00 3.18
1867 3288 2.403586 GCTTGTATGTTCGGGCGC 59.596 61.111 0.00 0.00 0.00 6.53
1886 3307 2.171003 GCCAGTTCACTTGGGCTAATT 58.829 47.619 0.00 0.00 43.09 1.40
1887 3308 3.352648 GCCAGTTCACTTGGGCTAATTA 58.647 45.455 0.00 0.00 43.09 1.40
1888 3309 3.954258 GCCAGTTCACTTGGGCTAATTAT 59.046 43.478 0.00 0.00 43.09 1.28
1898 3319 6.317893 CACTTGGGCTAATTATAACCGTTCTT 59.682 38.462 0.00 0.00 0.00 2.52
1905 3326 6.293244 GCTAATTATAACCGTTCTTTGCCGAT 60.293 38.462 0.00 0.00 0.00 4.18
1958 3379 4.513406 ACCGAATGGGAGCCTAAATTTA 57.487 40.909 0.00 0.00 40.75 1.40
1964 3385 6.710744 CGAATGGGAGCCTAAATTTACTATGT 59.289 38.462 0.00 0.00 0.00 2.29
1995 3416 1.457009 GCCCTAGAGCGAATCGAGGT 61.457 60.000 6.91 0.00 46.53 3.85
2019 3440 0.740149 TTGGATCATGCGCCAATCAC 59.260 50.000 4.18 0.76 39.14 3.06
2046 3467 8.204160 TCTTGATTCTTATTCTTCGAGCCATTA 58.796 33.333 0.00 0.00 0.00 1.90
2058 3479 1.119574 AGCCATTATACCCGTCGCCT 61.120 55.000 0.00 0.00 0.00 5.52
2059 3480 0.949105 GCCATTATACCCGTCGCCTG 60.949 60.000 0.00 0.00 0.00 4.85
2062 3483 1.864711 CATTATACCCGTCGCCTGTTG 59.135 52.381 0.00 0.00 0.00 3.33
2097 3518 0.899717 TGGCTGCATTGGGAAGGTTC 60.900 55.000 0.50 0.00 0.00 3.62
2123 3544 6.932400 TGTAGACATAATCAAGAACGTTTGGT 59.068 34.615 0.46 0.00 0.00 3.67
2132 3553 0.035739 GAACGTTTGGTAGAGGCCCA 59.964 55.000 0.46 0.00 0.00 5.36
2137 3558 0.623723 TTTGGTAGAGGCCCACCATC 59.376 55.000 19.23 1.61 44.14 3.51
2145 3566 4.856801 GCCCACCATCGGTCGCAT 62.857 66.667 0.00 0.00 31.02 4.73
2147 3568 1.371183 CCCACCATCGGTCGCATAT 59.629 57.895 0.00 0.00 31.02 1.78
2211 3632 0.462759 CTCTCTGGATGGGCGAAACC 60.463 60.000 0.00 0.00 37.93 3.27
2212 3633 1.198094 TCTCTGGATGGGCGAAACCA 61.198 55.000 0.00 0.00 46.24 3.67
2213 3634 1.002624 TCTGGATGGGCGAAACCAC 60.003 57.895 0.00 0.00 44.72 4.16
2215 3636 3.131478 GGATGGGCGAAACCACCG 61.131 66.667 0.00 0.00 44.72 4.94
2219 3642 2.903350 GGGCGAAACCACCGTGTT 60.903 61.111 0.00 0.00 42.05 3.32
2220 3643 1.597578 GGGCGAAACCACCGTGTTA 60.598 57.895 0.00 0.00 42.05 2.41
2223 3646 2.075338 GGCGAAACCACCGTGTTATAA 58.925 47.619 0.00 0.00 38.86 0.98
2229 3652 6.968335 GCGAAACCACCGTGTTATAAATAAAT 59.032 34.615 0.00 0.00 0.00 1.40
2267 3690 6.521427 GCCTCTATACCATCATTGATGACCTT 60.521 42.308 24.93 10.99 42.09 3.50
2278 3701 6.457355 TCATTGATGACCTTGACAAAATTGG 58.543 36.000 0.00 0.00 0.00 3.16
2285 3708 5.053978 ACCTTGACAAAATTGGAGAGACT 57.946 39.130 0.00 0.00 0.00 3.24
2287 3710 5.065914 CCTTGACAAAATTGGAGAGACTCA 58.934 41.667 5.02 0.00 31.08 3.41
2341 3765 7.707624 AAATCAATCTAATGAGAAGGTTGCA 57.292 32.000 0.00 0.00 34.61 4.08
2342 3766 7.707624 AATCAATCTAATGAGAAGGTTGCAA 57.292 32.000 0.00 0.00 34.61 4.08
2361 3785 3.134458 CAAGTCTTTTGCGAGAGAAGGT 58.866 45.455 0.00 0.00 0.00 3.50
2368 3792 2.662006 TGCGAGAGAAGGTGATCAAG 57.338 50.000 0.00 0.00 0.00 3.02
2377 3801 6.017192 AGAGAAGGTGATCAAGTACTACCAA 58.983 40.000 13.09 0.00 33.88 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.679734 AGTTCAAGTGTTCAATACAGCAG 57.320 39.130 0.00 0.00 37.45 4.24
58 59 2.168728 AGCTCTCGAGGGACCAAAATAC 59.831 50.000 18.81 0.00 0.00 1.89
59 60 2.467880 AGCTCTCGAGGGACCAAAATA 58.532 47.619 18.81 0.00 0.00 1.40
60 61 1.280457 AGCTCTCGAGGGACCAAAAT 58.720 50.000 18.81 0.00 0.00 1.82
61 62 1.056660 AAGCTCTCGAGGGACCAAAA 58.943 50.000 18.81 0.00 0.00 2.44
62 63 1.933021 TAAGCTCTCGAGGGACCAAA 58.067 50.000 18.81 0.00 0.00 3.28
63 64 1.825474 CTTAAGCTCTCGAGGGACCAA 59.175 52.381 18.81 4.59 0.00 3.67
64 65 1.005569 TCTTAAGCTCTCGAGGGACCA 59.994 52.381 18.81 0.00 0.00 4.02
65 66 1.679153 CTCTTAAGCTCTCGAGGGACC 59.321 57.143 18.81 0.00 0.00 4.46
66 67 2.645802 TCTCTTAAGCTCTCGAGGGAC 58.354 52.381 18.81 7.62 0.00 4.46
77 78 3.539604 ACATGCACCTCATCTCTTAAGC 58.460 45.455 0.00 0.00 31.79 3.09
95 96 0.603439 TCGCACACACATGCTGACAT 60.603 50.000 0.00 0.00 43.80 3.06
96 97 0.603439 ATCGCACACACATGCTGACA 60.603 50.000 0.00 0.00 43.80 3.58
97 98 0.179207 CATCGCACACACATGCTGAC 60.179 55.000 0.00 0.00 43.80 3.51
98 99 1.914531 GCATCGCACACACATGCTGA 61.915 55.000 0.00 0.00 43.80 4.26
99 100 1.513373 GCATCGCACACACATGCTG 60.513 57.895 0.00 0.00 43.80 4.41
100 101 1.673337 AGCATCGCACACACATGCT 60.673 52.632 0.00 0.00 46.78 3.79
112 113 5.739752 TTCCTCACAAAATCATAGCATCG 57.260 39.130 0.00 0.00 0.00 3.84
116 117 4.156556 TGTGCTTCCTCACAAAATCATAGC 59.843 41.667 0.00 0.00 43.27 2.97
118 119 5.316167 ACTGTGCTTCCTCACAAAATCATA 58.684 37.500 0.00 0.00 45.22 2.15
127 128 2.841442 AACCTACTGTGCTTCCTCAC 57.159 50.000 0.00 0.00 37.48 3.51
128 129 3.496160 GGAAAACCTACTGTGCTTCCTCA 60.496 47.826 0.00 0.00 37.05 3.86
136 137 1.798813 GCAGTCGGAAAACCTACTGTG 59.201 52.381 17.63 1.13 41.11 3.66
137 138 1.414919 TGCAGTCGGAAAACCTACTGT 59.585 47.619 17.63 0.00 41.11 3.55
148 149 8.902540 AGAAAATATAAATACATGCAGTCGGA 57.097 30.769 0.00 0.00 0.00 4.55
197 198 5.814188 TGAGAAGTCTAAATGCATGCAGTAG 59.186 40.000 26.69 25.74 0.00 2.57
213 214 4.001618 ACCTTTTCTGCTCTGAGAAGTC 57.998 45.455 12.38 0.00 33.50 3.01
236 237 1.001633 TCGGCCTTGTACCAGTCTTTC 59.998 52.381 0.00 0.00 0.00 2.62
278 280 7.953005 TCAATCATGGTTTCAAGCCTTTATA 57.047 32.000 0.00 0.00 0.00 0.98
292 294 4.870636 TCATTTAGGCCTTCAATCATGGT 58.129 39.130 12.58 0.00 0.00 3.55
302 304 5.248380 AGACAAAGTCTCATTTAGGCCTT 57.752 39.130 12.58 0.00 38.71 4.35
338 340 3.001414 CAAGCAGGAGATGTCTCTGTTG 58.999 50.000 9.68 7.41 42.48 3.33
403 405 3.254166 ACTTGCTGCCTGAACAAATACAG 59.746 43.478 0.00 0.00 0.00 2.74
409 411 0.183492 AGGACTTGCTGCCTGAACAA 59.817 50.000 0.00 0.00 32.06 2.83
427 1741 3.874392 CCAATTAGGTGGCTTTGGAAG 57.126 47.619 0.00 0.00 40.89 3.46
436 1750 1.369625 GAGACGTGCCAATTAGGTGG 58.630 55.000 0.00 0.00 42.05 4.61
437 1751 1.369625 GGAGACGTGCCAATTAGGTG 58.630 55.000 0.00 0.00 40.61 4.00
438 1752 0.252197 GGGAGACGTGCCAATTAGGT 59.748 55.000 0.00 0.00 40.61 3.08
439 1753 0.251916 TGGGAGACGTGCCAATTAGG 59.748 55.000 0.00 0.00 42.18 2.69
440 1754 3.853104 TGGGAGACGTGCCAATTAG 57.147 52.632 0.00 0.00 42.18 1.73
445 1759 2.281484 GCTTTGGGAGACGTGCCA 60.281 61.111 0.00 0.00 43.75 4.92
446 1760 3.056328 GGCTTTGGGAGACGTGCC 61.056 66.667 0.00 0.00 33.79 5.01
447 1761 2.281484 TGGCTTTGGGAGACGTGC 60.281 61.111 0.00 0.00 35.50 5.34
448 1762 1.966451 GGTGGCTTTGGGAGACGTG 60.966 63.158 0.00 0.00 35.50 4.49
449 1763 0.834687 TAGGTGGCTTTGGGAGACGT 60.835 55.000 0.00 0.00 35.50 4.34
450 1764 0.323629 TTAGGTGGCTTTGGGAGACG 59.676 55.000 0.00 0.00 35.50 4.18
451 1765 2.755103 CAATTAGGTGGCTTTGGGAGAC 59.245 50.000 0.00 0.00 0.00 3.36
452 1766 2.883888 GCAATTAGGTGGCTTTGGGAGA 60.884 50.000 0.00 0.00 0.00 3.71
453 1767 1.478105 GCAATTAGGTGGCTTTGGGAG 59.522 52.381 0.00 0.00 0.00 4.30
454 1768 1.077005 AGCAATTAGGTGGCTTTGGGA 59.923 47.619 0.00 0.00 33.21 4.37
455 1769 1.205417 CAGCAATTAGGTGGCTTTGGG 59.795 52.381 0.00 0.00 41.98 4.12
514 1828 7.050970 AGGATAAAAAGTTTCAGGTTTCCAC 57.949 36.000 0.00 0.00 0.00 4.02
552 1867 1.915141 AAGGCAGCAGCTTTACACAT 58.085 45.000 0.00 0.00 38.40 3.21
601 1916 3.334691 GTTTTTGCAAGGGGCTATTTCC 58.665 45.455 0.00 0.00 45.15 3.13
611 1926 3.067601 AGTTTCCCTACGTTTTTGCAAGG 59.932 43.478 0.00 0.00 0.00 3.61
614 1929 2.223618 GCAGTTTCCCTACGTTTTTGCA 60.224 45.455 0.00 0.00 0.00 4.08
622 1937 2.068837 TTGTACGCAGTTTCCCTACG 57.931 50.000 0.00 0.00 37.78 3.51
623 1938 4.060205 TCTTTTGTACGCAGTTTCCCTAC 58.940 43.478 0.00 0.00 37.78 3.18
628 1943 6.691388 ACTTTGAATCTTTTGTACGCAGTTTC 59.309 34.615 0.00 0.00 37.78 2.78
638 1953 4.036380 GTCCGACCACTTTGAATCTTTTGT 59.964 41.667 0.00 0.00 0.00 2.83
654 1969 1.104630 CTACAGAGAAGGGTCCGACC 58.895 60.000 9.30 9.30 37.60 4.79
667 1982 2.671070 GCTTGCCCAGGCTACAGA 59.329 61.111 10.58 0.00 42.51 3.41
704 2036 3.891977 TCAGAGTCCATACCAGACATAGC 59.108 47.826 0.00 0.00 36.68 2.97
705 2037 5.596361 ACTTCAGAGTCCATACCAGACATAG 59.404 44.000 0.00 0.00 36.68 2.23
707 2039 4.357325 ACTTCAGAGTCCATACCAGACAT 58.643 43.478 0.00 0.00 36.68 3.06
711 2043 4.707448 ACTGTACTTCAGAGTCCATACCAG 59.293 45.833 1.79 0.00 46.27 4.00
784 2116 6.093633 GGCGAATAAGTAATCAGTTTGAAGGT 59.906 38.462 0.00 0.00 0.00 3.50
800 2135 4.600012 ACGAGTCAAAATGGCGAATAAG 57.400 40.909 0.00 0.00 0.00 1.73
808 2148 2.286713 TGCGTTCAACGAGTCAAAATGG 60.287 45.455 15.79 0.00 46.05 3.16
829 2170 3.022406 CCCCAGCGAACTACTACTAAGT 58.978 50.000 0.00 0.00 39.91 2.24
830 2171 2.361438 CCCCCAGCGAACTACTACTAAG 59.639 54.545 0.00 0.00 0.00 2.18
831 2172 2.025037 TCCCCCAGCGAACTACTACTAA 60.025 50.000 0.00 0.00 0.00 2.24
859 2200 1.069358 GCACCCAGCTTAGCTACCTAG 59.931 57.143 6.35 0.00 36.40 3.02
863 2204 0.179070 GAGGCACCCAGCTTAGCTAC 60.179 60.000 6.35 0.00 44.79 3.58
864 2205 1.676678 CGAGGCACCCAGCTTAGCTA 61.677 60.000 6.35 0.00 44.79 3.32
865 2206 2.993853 GAGGCACCCAGCTTAGCT 59.006 61.111 0.00 0.00 44.79 3.32
866 2207 2.512515 CGAGGCACCCAGCTTAGC 60.513 66.667 0.00 0.00 44.79 3.09
908 2249 2.457598 CAGCCCCTTGAGTGAGTAGTA 58.542 52.381 0.00 0.00 0.00 1.82
909 2250 1.270907 CAGCCCCTTGAGTGAGTAGT 58.729 55.000 0.00 0.00 0.00 2.73
910 2251 0.539051 CCAGCCCCTTGAGTGAGTAG 59.461 60.000 0.00 0.00 0.00 2.57
914 2255 4.020617 CGCCAGCCCCTTGAGTGA 62.021 66.667 0.00 0.00 0.00 3.41
928 2269 0.459237 CTGTCTCACTGATGACCGCC 60.459 60.000 0.00 0.00 32.67 6.13
935 2288 5.009911 GCTGATAGATGACTGTCTCACTGAT 59.990 44.000 9.51 0.00 35.70 2.90
978 2335 6.812656 CCATTGATTCTCACTAGCTAGCTATG 59.187 42.308 24.36 21.56 0.00 2.23
979 2336 6.574073 GCCATTGATTCTCACTAGCTAGCTAT 60.574 42.308 24.36 9.26 0.00 2.97
980 2337 5.279206 GCCATTGATTCTCACTAGCTAGCTA 60.279 44.000 22.85 22.85 0.00 3.32
981 2338 4.502950 GCCATTGATTCTCACTAGCTAGCT 60.503 45.833 23.12 23.12 0.00 3.32
982 2339 3.745458 GCCATTGATTCTCACTAGCTAGC 59.255 47.826 20.91 6.62 0.00 3.42
983 2340 3.986572 CGCCATTGATTCTCACTAGCTAG 59.013 47.826 19.44 19.44 0.00 3.42
984 2341 3.243873 CCGCCATTGATTCTCACTAGCTA 60.244 47.826 0.00 0.00 0.00 3.32
985 2342 2.484417 CCGCCATTGATTCTCACTAGCT 60.484 50.000 0.00 0.00 0.00 3.32
986 2343 1.869767 CCGCCATTGATTCTCACTAGC 59.130 52.381 0.00 0.00 0.00 3.42
987 2344 1.869767 GCCGCCATTGATTCTCACTAG 59.130 52.381 0.00 0.00 0.00 2.57
990 2347 1.027357 ATGCCGCCATTGATTCTCAC 58.973 50.000 0.00 0.00 0.00 3.51
1041 2412 4.479993 AGATGTCGCTGCCCTGGC 62.480 66.667 0.00 0.00 42.35 4.85
1043 2414 1.376424 AACAGATGTCGCTGCCCTG 60.376 57.895 0.00 0.00 39.51 4.45
1048 2419 2.284263 TAGCTCAACAGATGTCGCTG 57.716 50.000 12.03 0.00 41.63 5.18
1092 2463 1.134491 GGAGGCGTAATAGTGCTTGGT 60.134 52.381 0.00 0.00 0.00 3.67
1098 2469 1.806623 GCAGGTGGAGGCGTAATAGTG 60.807 57.143 0.00 0.00 0.00 2.74
1099 2470 0.464452 GCAGGTGGAGGCGTAATAGT 59.536 55.000 0.00 0.00 0.00 2.12
1102 2473 1.522569 GAGCAGGTGGAGGCGTAAT 59.477 57.895 0.00 0.00 34.54 1.89
1173 2579 1.009829 GGTCACGGATGAAGCATGTC 58.990 55.000 0.00 0.00 36.31 3.06
1216 2626 2.841442 ATCCAGTATTTAGGCGAGCC 57.159 50.000 5.89 5.89 0.00 4.70
1224 2634 6.239772 CGGGAGGTCCATAAATCCAGTATTTA 60.240 42.308 0.00 0.00 42.73 1.40
1227 2637 3.583086 CGGGAGGTCCATAAATCCAGTAT 59.417 47.826 0.00 0.00 37.91 2.12
1247 2657 1.702886 CATAGACGATGCTAAGCCGG 58.297 55.000 0.00 0.00 0.00 6.13
1260 2670 3.999663 GCACCATCAAGGATAGCATAGAC 59.000 47.826 0.00 0.00 41.22 2.59
1261 2671 3.906218 AGCACCATCAAGGATAGCATAGA 59.094 43.478 0.00 0.00 41.22 1.98
1262 2672 4.283363 AGCACCATCAAGGATAGCATAG 57.717 45.455 0.00 0.00 41.22 2.23
1279 2689 0.466124 GATGAGGGGGTGAGTAGCAC 59.534 60.000 0.00 0.00 46.98 4.40
1307 2717 2.360726 CACCATCAGCTGCTGGCA 60.361 61.111 31.62 11.57 44.79 4.92
1309 2719 2.045242 AGCACCATCAGCTGCTGG 60.045 61.111 30.41 30.41 42.29 4.85
1315 2725 2.353889 CAGTGATAACAGCACCATCAGC 59.646 50.000 0.00 0.00 36.95 4.26
1344 2754 0.824109 GCAAAGGGGGTTCATAAGGC 59.176 55.000 0.00 0.00 0.00 4.35
1362 2772 3.577667 TCACAGCTATGTTGCATTTTGC 58.422 40.909 0.00 0.00 40.12 3.68
1369 2779 2.099141 TGACCTCACAGCTATGTTGC 57.901 50.000 0.00 0.00 37.65 4.17
1372 2782 4.651045 TGTATCATGACCTCACAGCTATGT 59.349 41.667 0.00 0.00 41.57 2.29
1385 2795 7.896811 TCCATTATAGGTCACTGTATCATGAC 58.103 38.462 0.00 0.00 43.75 3.06
1404 2814 9.740239 GACAATAGTAATACGTGACTTCCATTA 57.260 33.333 0.00 0.00 0.00 1.90
1453 2871 7.275779 CACGTAGAATTACCTATATGACATGCC 59.724 40.741 0.00 0.00 0.00 4.40
1454 2872 7.813148 ACACGTAGAATTACCTATATGACATGC 59.187 37.037 0.00 0.00 0.00 4.06
1495 2913 6.543430 AACAAGGATGCATATAGCCAAAAA 57.457 33.333 0.00 0.00 44.83 1.94
1515 2933 2.642427 TCGTACGGCCTCTACATAACA 58.358 47.619 16.52 0.00 0.00 2.41
1542 2960 7.287950 GCATCAAGCGATACAATTATAACGAA 58.712 34.615 0.00 0.00 0.00 3.85
1624 3045 4.761235 ACATGCACAGTTCTTGATCAAG 57.239 40.909 26.56 26.56 39.71 3.02
1660 3081 3.691342 CGTGGCCTCTCCCGTTCA 61.691 66.667 3.32 0.00 0.00 3.18
1664 3085 3.019003 AATCACGTGGCCTCTCCCG 62.019 63.158 17.00 0.78 35.52 5.14
1670 3091 1.608590 CAAAGTTCAATCACGTGGCCT 59.391 47.619 17.00 0.00 0.00 5.19
1671 3092 1.335872 CCAAAGTTCAATCACGTGGCC 60.336 52.381 17.00 0.00 0.00 5.36
1672 3093 1.336755 ACCAAAGTTCAATCACGTGGC 59.663 47.619 17.00 0.00 32.61 5.01
1691 3112 8.607441 TGATATGACCTATAACTGCAAATCAC 57.393 34.615 0.00 0.00 0.00 3.06
1697 3118 6.992123 CAGGTTTGATATGACCTATAACTGCA 59.008 38.462 2.59 0.00 44.28 4.41
1701 3122 7.876582 GGGTACAGGTTTGATATGACCTATAAC 59.123 40.741 0.00 0.00 44.28 1.89
1702 3123 7.569485 TGGGTACAGGTTTGATATGACCTATAA 59.431 37.037 0.00 0.00 44.28 0.98
1703 3124 7.077095 TGGGTACAGGTTTGATATGACCTATA 58.923 38.462 0.00 0.00 44.28 1.31
1704 3125 5.908831 TGGGTACAGGTTTGATATGACCTAT 59.091 40.000 0.00 0.00 44.28 2.57
1705 3126 5.282129 TGGGTACAGGTTTGATATGACCTA 58.718 41.667 0.00 0.00 44.28 3.08
1706 3127 4.108570 TGGGTACAGGTTTGATATGACCT 58.891 43.478 0.00 0.00 46.99 3.85
1707 3128 4.497291 TGGGTACAGGTTTGATATGACC 57.503 45.455 0.00 0.00 36.15 4.02
1708 3129 5.221048 GCATTGGGTACAGGTTTGATATGAC 60.221 44.000 0.00 0.00 0.00 3.06
1709 3130 4.887071 GCATTGGGTACAGGTTTGATATGA 59.113 41.667 0.00 0.00 0.00 2.15
1710 3131 4.889409 AGCATTGGGTACAGGTTTGATATG 59.111 41.667 0.00 0.00 0.00 1.78
1711 3132 5.129368 AGCATTGGGTACAGGTTTGATAT 57.871 39.130 0.00 0.00 0.00 1.63
1712 3133 4.584638 AGCATTGGGTACAGGTTTGATA 57.415 40.909 0.00 0.00 0.00 2.15
1713 3134 3.456380 AGCATTGGGTACAGGTTTGAT 57.544 42.857 0.00 0.00 0.00 2.57
1714 3135 2.969821 AGCATTGGGTACAGGTTTGA 57.030 45.000 0.00 0.00 0.00 2.69
1715 3136 5.410067 CAATAAGCATTGGGTACAGGTTTG 58.590 41.667 0.00 0.00 38.31 2.93
1716 3137 5.659440 CAATAAGCATTGGGTACAGGTTT 57.341 39.130 0.00 0.00 38.31 3.27
1779 3200 6.730960 AATGTGTGTCGAAACGGTAATATT 57.269 33.333 0.32 0.00 0.00 1.28
1781 3202 5.289193 GCTAATGTGTGTCGAAACGGTAATA 59.711 40.000 0.32 0.00 0.00 0.98
1784 3205 2.988493 GCTAATGTGTGTCGAAACGGTA 59.012 45.455 0.32 0.00 0.00 4.02
1789 3210 3.500680 GGAAAGGCTAATGTGTGTCGAAA 59.499 43.478 0.00 0.00 0.00 3.46
1798 3219 7.397192 ACAACATTGAATAGGAAAGGCTAATGT 59.603 33.333 0.00 0.00 38.66 2.71
1803 3224 5.324409 TCACAACATTGAATAGGAAAGGCT 58.676 37.500 0.00 0.00 0.00 4.58
1838 3259 3.535561 ACATACAAGCCTTCCGAAGATG 58.464 45.455 9.87 6.69 0.00 2.90
1847 3268 1.024579 CGCCCGAACATACAAGCCTT 61.025 55.000 0.00 0.00 0.00 4.35
1861 3282 3.726517 CAAGTGAACTGGCGCCCG 61.727 66.667 26.77 21.78 0.00 6.13
1867 3288 6.039382 GGTTATAATTAGCCCAAGTGAACTGG 59.961 42.308 0.00 0.00 0.00 4.00
1886 3307 3.864243 ACATCGGCAAAGAACGGTTATA 58.136 40.909 0.00 0.00 0.00 0.98
1887 3308 2.706890 ACATCGGCAAAGAACGGTTAT 58.293 42.857 0.00 0.00 0.00 1.89
1888 3309 2.172851 ACATCGGCAAAGAACGGTTA 57.827 45.000 0.00 0.00 0.00 2.85
1898 3319 0.530744 AGCTTCTCGTACATCGGCAA 59.469 50.000 0.00 0.00 40.32 4.52
1930 3351 1.906574 GGCTCCCATTCGGTATCCATA 59.093 52.381 0.00 0.00 0.00 2.74
1950 3371 7.897920 TCGCACGGTTAACATAGTAAATTTAG 58.102 34.615 8.10 0.00 0.00 1.85
1958 3379 1.636988 GCTCGCACGGTTAACATAGT 58.363 50.000 8.10 1.42 0.00 2.12
1964 3385 0.966875 TCTAGGGCTCGCACGGTTAA 60.967 55.000 0.00 0.00 0.00 2.01
2019 3440 6.045318 TGGCTCGAAGAATAAGAATCAAGAG 58.955 40.000 0.00 0.00 34.09 2.85
2030 3451 4.525487 ACGGGTATAATGGCTCGAAGAATA 59.475 41.667 0.00 0.00 34.09 1.75
2036 3457 0.594602 CGACGGGTATAATGGCTCGA 59.405 55.000 0.00 0.00 32.23 4.04
2046 3467 0.322322 TTTCAACAGGCGACGGGTAT 59.678 50.000 0.00 0.00 0.00 2.73
2058 3479 4.215827 GCCATGCCAATTCAAATTTCAACA 59.784 37.500 0.00 0.00 0.00 3.33
2059 3480 4.456566 AGCCATGCCAATTCAAATTTCAAC 59.543 37.500 0.00 0.00 0.00 3.18
2062 3483 4.609691 CAGCCATGCCAATTCAAATTTC 57.390 40.909 0.00 0.00 0.00 2.17
2097 3518 7.117812 ACCAAACGTTCTTGATTATGTCTACAG 59.882 37.037 0.00 0.00 0.00 2.74
2123 3544 1.760875 GACCGATGGTGGGCCTCTA 60.761 63.158 4.53 0.00 35.25 2.43
2132 3553 2.337361 TCGATATGCGACCGATGGT 58.663 52.632 0.00 0.00 45.59 3.55
2171 3592 3.153919 GGTGTTGTCTCATGGCCTTTAA 58.846 45.455 3.32 0.00 0.00 1.52
2185 3606 0.987294 CCCATCCAGAGAGGTGTTGT 59.013 55.000 0.00 0.00 39.02 3.32
2229 3652 7.131907 TGGTATAGAGGCACTGCTTTATTTA 57.868 36.000 0.00 0.00 41.55 1.40
2232 3655 5.307976 TGATGGTATAGAGGCACTGCTTTAT 59.692 40.000 0.00 0.31 41.55 1.40
2233 3656 4.653801 TGATGGTATAGAGGCACTGCTTTA 59.346 41.667 0.00 0.00 41.55 1.85
2248 3671 6.005066 TGTCAAGGTCATCAATGATGGTAT 57.995 37.500 21.58 6.32 40.15 2.73
2267 3690 4.816385 GTGTGAGTCTCTCCAATTTTGTCA 59.184 41.667 0.65 0.00 0.00 3.58
2278 3701 7.551262 TCTTGTAGAGATAAGTGTGAGTCTCTC 59.449 40.741 6.99 0.00 44.53 3.20
2341 3765 3.134458 CACCTTCTCTCGCAAAAGACTT 58.866 45.455 0.00 0.00 0.00 3.01
2342 3766 2.365617 TCACCTTCTCTCGCAAAAGACT 59.634 45.455 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.