Multiple sequence alignment - TraesCS2D01G407100

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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 TraesCS2D01G407100 chr2D 100.000 3856 0 0 1 3856 522547311 522551166 0.000000e+00 7121.0
1 TraesCS2D01G407100 chr2D 86.705 173 20 3 3340 3509 450951351 450951179 5.090000e-44 189.0
2 TraesCS2D01G407100 chr2D 84.302 172 19 7 3340 3508 450951437 450951603 1.110000e-35 161.0
3 TraesCS2D01G407100 chr2A 87.419 1995 183 41 1895 3848 667932052 667934019 0.000000e+00 2231.0
4 TraesCS2D01G407100 chr2A 90.555 1154 68 15 731 1867 667930937 667932066 0.000000e+00 1489.0
5 TraesCS2D01G407100 chr2A 86.239 654 70 9 98 736 667930236 667930884 0.000000e+00 691.0
6 TraesCS2D01G407100 chr2A 94.737 38 2 0 3528 3565 768629776 768629739 4.160000e-05 60.2
7 TraesCS2D01G407100 chr2B 87.918 1465 132 24 1895 3343 615438459 615439894 0.000000e+00 1683.0
8 TraesCS2D01G407100 chr2B 92.150 1121 67 16 760 1867 615437361 615438473 0.000000e+00 1563.0
9 TraesCS2D01G407100 chr2B 89.086 394 40 3 3369 3760 615440306 615440698 1.610000e-133 486.0
10 TraesCS2D01G407100 chr2B 93.243 74 5 0 97 170 615373785 615373858 4.070000e-20 110.0
11 TraesCS2D01G407100 chr5D 82.759 377 56 7 2242 2616 484017846 484017477 1.030000e-85 327.0
12 TraesCS2D01G407100 chr7D 88.095 168 19 1 3343 3509 511167274 511167441 8.450000e-47 198.0
13 TraesCS2D01G407100 chr7D 85.549 173 21 3 3340 3510 37237175 37237345 1.100000e-40 178.0
14 TraesCS2D01G407100 chr7B 86.391 169 21 1 3343 3509 539986269 539986437 2.370000e-42 183.0
15 TraesCS2D01G407100 chr6B 85.057 174 21 5 3340 3511 175215816 175215646 5.120000e-39 172.0
16 TraesCS2D01G407100 chr4B 83.908 174 21 6 3340 3509 44658433 44658603 3.990000e-35 159.0
17 TraesCS2D01G407100 chr1A 97.826 46 1 0 2787 2832 185845288 185845333 3.190000e-11 80.5
18 TraesCS2D01G407100 chr1A 95.652 46 2 0 2787 2832 162721376 162721331 1.490000e-09 75.0
19 TraesCS2D01G407100 chr1A 92.308 52 4 0 2781 2832 166660911 166660962 1.490000e-09 75.0
20 TraesCS2D01G407100 chr1A 93.478 46 3 0 2787 2832 162651072 162651027 6.910000e-08 69.4
21 TraesCS2D01G407100 chr6A 95.556 45 2 0 2788 2832 167190188 167190232 5.340000e-09 73.1
22 TraesCS2D01G407100 chr5A 95.556 45 2 0 2788 2832 651017696 651017652 5.340000e-09 73.1
23 TraesCS2D01G407100 chr5A 92.105 38 3 0 3528 3565 422999197 422999160 2.000000e-03 54.7
24 TraesCS2D01G407100 chr4A 92.105 38 3 0 3528 3565 492372476 492372513 2.000000e-03 54.7


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 TraesCS2D01G407100 chr2D 522547311 522551166 3855 False 7121.000000 7121 100.000 1 3856 1 chr2D.!!$F2 3855
1 TraesCS2D01G407100 chr2A 667930236 667934019 3783 False 1470.333333 2231 88.071 98 3848 3 chr2A.!!$F1 3750
2 TraesCS2D01G407100 chr2B 615437361 615440698 3337 False 1244.000000 1683 89.718 760 3760 3 chr2B.!!$F2 3000

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
178 181 0.033366 AAACCCAATGGCGCAAGTTC 59.967 50.0 10.83 0.0 41.68 3.01 F
207 210 0.321653 GACACCCACCGAAGCAATCT 60.322 55.0 0.00 0.0 0.00 2.40 F
434 437 0.331616 GTGGGGCTATGGTCAACCTT 59.668 55.0 0.10 0.0 36.82 3.50 F
2147 2259 0.039035 ATGCCGGGCTTGAAACCTAA 59.961 50.0 21.46 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2236 0.039035 TTAGGTTTCAAGCCCGGCAT 59.961 50.000 13.15 0.00 0.0 4.40 R
2131 2239 2.289565 GATCTTAGGTTTCAAGCCCGG 58.710 52.381 0.00 0.00 0.0 5.73 R
2274 2387 2.325583 AACCAAAACAGAGAGCACGA 57.674 45.000 0.00 0.00 0.0 4.35 R
3627 4155 0.250252 TTTGGTGCAGCACTCATCGA 60.250 50.000 24.75 5.45 34.4 3.59 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 2.959275 CTTGTTCTAGCGGCGGTAG 58.041 57.895 33.53 33.53 35.26 3.18
19 20 0.454600 CTTGTTCTAGCGGCGGTAGA 59.545 55.000 36.50 36.50 40.26 2.59
20 21 0.454600 TTGTTCTAGCGGCGGTAGAG 59.545 55.000 37.04 22.51 42.36 2.43
21 22 1.359475 GTTCTAGCGGCGGTAGAGG 59.641 63.158 37.04 20.05 42.36 3.69
22 23 1.077212 TTCTAGCGGCGGTAGAGGT 60.077 57.895 37.04 6.82 42.36 3.85
23 24 1.099879 TTCTAGCGGCGGTAGAGGTC 61.100 60.000 37.04 8.70 42.36 3.85
24 25 2.894565 CTAGCGGCGGTAGAGGTCG 61.895 68.421 35.32 12.81 35.90 4.79
25 26 3.687321 TAGCGGCGGTAGAGGTCGT 62.687 63.158 15.64 0.00 0.00 4.34
26 27 4.549516 GCGGCGGTAGAGGTCGTC 62.550 72.222 9.78 0.00 0.00 4.20
27 28 3.885521 CGGCGGTAGAGGTCGTCC 61.886 72.222 0.00 0.00 0.00 4.79
28 29 2.753043 GGCGGTAGAGGTCGTCCA 60.753 66.667 0.51 0.00 35.89 4.02
29 30 2.125961 GGCGGTAGAGGTCGTCCAT 61.126 63.158 0.51 0.00 35.89 3.41
30 31 1.673808 GGCGGTAGAGGTCGTCCATT 61.674 60.000 0.51 0.00 35.89 3.16
31 32 0.527817 GCGGTAGAGGTCGTCCATTG 60.528 60.000 0.51 0.00 35.89 2.82
32 33 0.102481 CGGTAGAGGTCGTCCATTGG 59.898 60.000 0.51 0.00 35.89 3.16
33 34 1.192428 GGTAGAGGTCGTCCATTGGT 58.808 55.000 1.86 0.00 35.89 3.67
34 35 2.381911 GGTAGAGGTCGTCCATTGGTA 58.618 52.381 1.86 0.00 35.89 3.25
35 36 2.963782 GGTAGAGGTCGTCCATTGGTAT 59.036 50.000 1.86 0.00 35.89 2.73
36 37 4.147321 GGTAGAGGTCGTCCATTGGTATA 58.853 47.826 1.86 0.00 35.89 1.47
37 38 4.217983 GGTAGAGGTCGTCCATTGGTATAG 59.782 50.000 1.86 0.00 35.89 1.31
38 39 3.231818 AGAGGTCGTCCATTGGTATAGG 58.768 50.000 1.86 0.00 35.89 2.57
39 40 2.299297 GAGGTCGTCCATTGGTATAGGG 59.701 54.545 1.86 0.00 35.89 3.53
40 41 2.090943 AGGTCGTCCATTGGTATAGGGA 60.091 50.000 1.86 0.00 35.89 4.20
41 42 2.036862 GGTCGTCCATTGGTATAGGGAC 59.963 54.545 1.86 0.00 44.97 4.46
42 43 2.036862 GTCGTCCATTGGTATAGGGACC 59.963 54.545 1.86 0.00 45.51 4.46
77 78 9.899661 TTAATTATATCTGGTGTGCTTTGTACT 57.100 29.630 0.00 0.00 0.00 2.73
78 79 8.807948 AATTATATCTGGTGTGCTTTGTACTT 57.192 30.769 0.00 0.00 0.00 2.24
79 80 8.807948 ATTATATCTGGTGTGCTTTGTACTTT 57.192 30.769 0.00 0.00 0.00 2.66
80 81 8.630054 TTATATCTGGTGTGCTTTGTACTTTT 57.370 30.769 0.00 0.00 0.00 2.27
81 82 4.630894 TCTGGTGTGCTTTGTACTTTTG 57.369 40.909 0.00 0.00 0.00 2.44
82 83 3.380004 TCTGGTGTGCTTTGTACTTTTGG 59.620 43.478 0.00 0.00 0.00 3.28
83 84 3.093057 TGGTGTGCTTTGTACTTTTGGT 58.907 40.909 0.00 0.00 0.00 3.67
84 85 3.119316 TGGTGTGCTTTGTACTTTTGGTG 60.119 43.478 0.00 0.00 0.00 4.17
85 86 3.129638 GGTGTGCTTTGTACTTTTGGTGA 59.870 43.478 0.00 0.00 0.00 4.02
86 87 4.381079 GGTGTGCTTTGTACTTTTGGTGAA 60.381 41.667 0.00 0.00 0.00 3.18
87 88 4.561213 GTGTGCTTTGTACTTTTGGTGAAC 59.439 41.667 0.00 0.00 0.00 3.18
88 89 4.461081 TGTGCTTTGTACTTTTGGTGAACT 59.539 37.500 0.00 0.00 0.00 3.01
89 90 5.047660 TGTGCTTTGTACTTTTGGTGAACTT 60.048 36.000 0.00 0.00 0.00 2.66
90 91 5.867174 GTGCTTTGTACTTTTGGTGAACTTT 59.133 36.000 0.00 0.00 0.00 2.66
91 92 7.030768 GTGCTTTGTACTTTTGGTGAACTTTA 58.969 34.615 0.00 0.00 0.00 1.85
92 93 7.704899 GTGCTTTGTACTTTTGGTGAACTTTAT 59.295 33.333 0.00 0.00 0.00 1.40
93 94 7.704472 TGCTTTGTACTTTTGGTGAACTTTATG 59.296 33.333 0.00 0.00 0.00 1.90
94 95 7.918562 GCTTTGTACTTTTGGTGAACTTTATGA 59.081 33.333 0.00 0.00 0.00 2.15
95 96 9.965824 CTTTGTACTTTTGGTGAACTTTATGAT 57.034 29.630 0.00 0.00 0.00 2.45
107 108 7.364762 GGTGAACTTTATGATAGAGGTGGAAGA 60.365 40.741 0.00 0.00 0.00 2.87
108 109 7.708752 GTGAACTTTATGATAGAGGTGGAAGAG 59.291 40.741 0.00 0.00 0.00 2.85
121 122 3.308046 GGTGGAAGAGGAAAGATCAAGCT 60.308 47.826 0.00 0.00 0.00 3.74
126 127 2.828520 AGAGGAAAGATCAAGCTGTCGA 59.171 45.455 0.00 0.00 0.00 4.20
127 128 3.450457 AGAGGAAAGATCAAGCTGTCGAT 59.550 43.478 0.00 0.00 0.00 3.59
133 136 3.519579 AGATCAAGCTGTCGATGACTTG 58.480 45.455 14.57 14.57 40.66 3.16
153 156 3.808728 TGTGAGTTCAGTTCTTCCTTGG 58.191 45.455 0.00 0.00 0.00 3.61
161 164 3.136443 TCAGTTCTTCCTTGGAGCTCAAA 59.864 43.478 17.19 10.13 34.56 2.69
173 176 2.929903 GCTCAAACCCAATGGCGCA 61.930 57.895 10.83 0.00 33.59 6.09
176 179 1.112315 TCAAACCCAATGGCGCAAGT 61.112 50.000 10.83 0.00 41.68 3.16
178 181 0.033366 AAACCCAATGGCGCAAGTTC 59.967 50.000 10.83 0.00 41.68 3.01
195 198 5.163405 GCAAGTTCTAGAGATATGACACCCA 60.163 44.000 0.00 0.00 0.00 4.51
196 199 6.276847 CAAGTTCTAGAGATATGACACCCAC 58.723 44.000 0.00 0.00 0.00 4.61
207 210 0.321653 GACACCCACCGAAGCAATCT 60.322 55.000 0.00 0.00 0.00 2.40
210 213 1.452108 CCCACCGAAGCAATCTCCC 60.452 63.158 0.00 0.00 0.00 4.30
212 215 1.815421 CACCGAAGCAATCTCCCCG 60.815 63.158 0.00 0.00 0.00 5.73
213 216 2.291043 ACCGAAGCAATCTCCCCGT 61.291 57.895 0.00 0.00 0.00 5.28
234 237 2.220653 TTGGGAGGATCTTGCTTTGG 57.779 50.000 0.00 0.00 33.73 3.28
240 243 2.154462 AGGATCTTGCTTTGGTGTTCG 58.846 47.619 0.00 0.00 0.00 3.95
241 244 1.880027 GGATCTTGCTTTGGTGTTCGT 59.120 47.619 0.00 0.00 0.00 3.85
253 256 3.122971 GTTCGTTGGGCGGCCTAC 61.123 66.667 28.36 28.36 41.72 3.18
292 295 2.570442 TTTTGGTCAAAAGGCGACAC 57.430 45.000 4.92 0.00 35.57 3.67
306 309 1.826024 GACACCATGGAGCTCCGAT 59.174 57.895 27.43 18.30 39.43 4.18
307 310 0.531532 GACACCATGGAGCTCCGATG 60.532 60.000 27.43 26.59 39.43 3.84
314 317 1.758514 GGAGCTCCGATGTCCCTCA 60.759 63.158 19.06 0.00 0.00 3.86
322 325 1.154205 CGATGTCCCTCAACGATGCC 61.154 60.000 0.00 0.00 43.34 4.40
338 341 1.208165 TGCCTCCTTTCCTTCCTCCC 61.208 60.000 0.00 0.00 0.00 4.30
339 342 1.908483 CCTCCTTTCCTTCCTCCCG 59.092 63.158 0.00 0.00 0.00 5.14
340 343 0.617820 CCTCCTTTCCTTCCTCCCGA 60.618 60.000 0.00 0.00 0.00 5.14
350 353 0.836400 TTCCTCCCGACCTTTGAGCT 60.836 55.000 0.00 0.00 0.00 4.09
366 369 5.743636 TTGAGCTAAAAGGGATGCAATTT 57.256 34.783 0.00 0.00 0.00 1.82
382 385 1.256812 ATTTGGCCTTAGCTTTGCGT 58.743 45.000 3.32 0.00 39.73 5.24
399 402 1.467713 GCGTCTACAACTCCTTCCTCG 60.468 57.143 0.00 0.00 0.00 4.63
423 426 2.238319 ATCCTCTCACGGTGGGGCTA 62.238 60.000 8.39 0.00 0.00 3.93
434 437 0.331616 GTGGGGCTATGGTCAACCTT 59.668 55.000 0.10 0.00 36.82 3.50
466 469 1.352687 TGGTTTCGTCCCCAATGATGA 59.647 47.619 0.00 0.00 0.00 2.92
475 478 4.263025 CGTCCCCAATGATGATGGATTCTA 60.263 45.833 0.00 0.00 40.56 2.10
482 485 6.542735 CCAATGATGATGGATTCTAGGCTATG 59.457 42.308 0.00 0.00 40.56 2.23
484 487 6.291648 TGATGATGGATTCTAGGCTATGTC 57.708 41.667 0.00 0.00 0.00 3.06
524 529 8.455682 AGGATTAAATTGCGATTTAGTTTTCGA 58.544 29.630 16.77 3.80 38.56 3.71
534 539 5.106673 CGATTTAGTTTTCGAGGCCTCTTTT 60.107 40.000 29.73 11.86 37.55 2.27
543 548 3.190535 TCGAGGCCTCTTTTGTAAAATGC 59.809 43.478 29.73 0.00 0.00 3.56
546 551 2.986479 GGCCTCTTTTGTAAAATGCACG 59.014 45.455 0.00 0.00 0.00 5.34
548 553 3.574614 CCTCTTTTGTAAAATGCACGGG 58.425 45.455 0.00 0.00 0.00 5.28
553 558 4.792521 TTTGTAAAATGCACGGGCTAAT 57.207 36.364 12.74 0.00 41.91 1.73
559 564 7.997482 TGTAAAATGCACGGGCTAATTTATAA 58.003 30.769 12.74 4.31 41.91 0.98
600 615 6.901300 AGGTCCTTGTACCATCTCAAATACTA 59.099 38.462 0.00 0.00 42.40 1.82
601 616 7.402071 AGGTCCTTGTACCATCTCAAATACTAA 59.598 37.037 0.00 0.00 42.40 2.24
686 701 9.950680 ATACGCCATTTAACTTCAGAATTATTG 57.049 29.630 0.00 0.00 0.00 1.90
756 829 5.497474 TGTAATGCCTTCTTTCTTAGGGTC 58.503 41.667 0.00 0.00 31.95 4.46
757 830 4.657814 AATGCCTTCTTTCTTAGGGTCA 57.342 40.909 0.00 0.00 31.95 4.02
765 838 7.417456 GCCTTCTTTCTTAGGGTCAAAGAAAAA 60.417 37.037 11.02 8.20 46.68 1.94
791 864 1.516110 ATCTATTGCAGCCTGGGTCT 58.484 50.000 0.00 0.00 0.00 3.85
823 897 3.181474 CGAGACCCTTTCCCTAGCTAAAG 60.181 52.174 0.00 0.00 33.41 1.85
836 910 8.102484 TCCCTAGCTAAAGGTAAATGATTTCT 57.898 34.615 8.88 0.00 34.56 2.52
837 911 9.220906 TCCCTAGCTAAAGGTAAATGATTTCTA 57.779 33.333 8.88 0.00 34.56 2.10
959 1034 3.309682 CGATTGCTTATCTCGCCTTCAAA 59.690 43.478 0.00 0.00 0.00 2.69
1199 1285 2.290122 ATCAGAGAAGCCGTCGCCAG 62.290 60.000 0.00 0.00 34.57 4.85
1224 1310 2.034221 GGCCGCTTCCTTCAGGTT 59.966 61.111 0.00 0.00 36.34 3.50
1250 1336 3.270877 CACCAAACCCTTAATCTCTCCG 58.729 50.000 0.00 0.00 0.00 4.63
1251 1337 2.289565 CCAAACCCTTAATCTCTCCGC 58.710 52.381 0.00 0.00 0.00 5.54
1417 1505 2.620251 TGGATTAGCGACTGAATGGG 57.380 50.000 0.00 0.00 0.00 4.00
1437 1530 3.653344 GGAAATTTCCAAGGTTCAGTGC 58.347 45.455 28.76 0.00 46.76 4.40
1477 1570 7.757941 TTCAGTTGAAATGTATGATGTTGGA 57.242 32.000 0.00 0.00 0.00 3.53
1480 1573 5.948162 AGTTGAAATGTATGATGTTGGAGCT 59.052 36.000 0.00 0.00 0.00 4.09
1481 1574 6.094603 AGTTGAAATGTATGATGTTGGAGCTC 59.905 38.462 4.71 4.71 0.00 4.09
1482 1575 5.499313 TGAAATGTATGATGTTGGAGCTCA 58.501 37.500 17.19 0.00 0.00 4.26
1483 1576 5.587443 TGAAATGTATGATGTTGGAGCTCAG 59.413 40.000 17.19 0.00 0.00 3.35
1484 1577 5.363562 AATGTATGATGTTGGAGCTCAGA 57.636 39.130 17.19 0.00 0.00 3.27
1485 1578 4.824479 TGTATGATGTTGGAGCTCAGAA 57.176 40.909 17.19 4.58 0.00 3.02
1486 1579 5.164620 TGTATGATGTTGGAGCTCAGAAA 57.835 39.130 17.19 3.76 0.00 2.52
1529 1622 4.202441 TCTGCAAAATAGAGATTGGAGCC 58.798 43.478 2.63 0.00 42.58 4.70
1598 1691 3.870723 TTGTTCTGTGCAATCGTGTAC 57.129 42.857 0.00 0.00 40.49 2.90
1629 1723 8.442632 TTGCTGATATTGGATTAGAACTTCTG 57.557 34.615 1.17 0.00 0.00 3.02
1639 1733 8.268850 TGGATTAGAACTTCTGCTAATTTGAC 57.731 34.615 1.17 0.00 37.42 3.18
1650 1744 2.548480 GCTAATTTGACATACCCTCGCC 59.452 50.000 0.00 0.00 0.00 5.54
1766 1860 4.780021 AGCTACTGATTCCCAGAAGAAAGA 59.220 41.667 0.00 0.00 45.78 2.52
1776 1870 3.345414 CCAGAAGAAAGATGCTGCTCTT 58.655 45.455 0.00 4.95 37.06 2.85
1808 1902 8.567285 CTGAAAGGTAAATGTTCAGTTCCTAT 57.433 34.615 4.79 0.00 42.09 2.57
1819 1913 5.991606 TGTTCAGTTCCTATTGTTGTCAGAG 59.008 40.000 0.00 0.00 0.00 3.35
1834 1928 3.829026 TGTCAGAGCTTACAGAGATGTGT 59.171 43.478 0.00 0.00 36.51 3.72
1836 1930 4.862018 GTCAGAGCTTACAGAGATGTGTTC 59.138 45.833 0.00 0.00 36.51 3.18
1843 1937 5.106908 GCTTACAGAGATGTGTTCAACTTCC 60.107 44.000 0.00 0.00 34.26 3.46
1850 1944 3.576078 TGTGTTCAACTTCCCTGATGT 57.424 42.857 0.00 0.00 0.00 3.06
1851 1945 4.698201 TGTGTTCAACTTCCCTGATGTA 57.302 40.909 0.00 0.00 0.00 2.29
1852 1946 4.385825 TGTGTTCAACTTCCCTGATGTAC 58.614 43.478 0.00 0.00 0.00 2.90
1853 1947 4.102524 TGTGTTCAACTTCCCTGATGTACT 59.897 41.667 0.00 0.00 0.00 2.73
1854 1948 4.452455 GTGTTCAACTTCCCTGATGTACTG 59.548 45.833 0.00 0.00 0.00 2.74
1855 1949 4.102524 TGTTCAACTTCCCTGATGTACTGT 59.897 41.667 0.00 0.00 0.00 3.55
1856 1950 4.271696 TCAACTTCCCTGATGTACTGTG 57.728 45.455 0.00 0.00 0.00 3.66
1857 1951 3.646162 TCAACTTCCCTGATGTACTGTGT 59.354 43.478 0.00 0.00 0.00 3.72
1858 1952 4.836175 TCAACTTCCCTGATGTACTGTGTA 59.164 41.667 0.00 0.00 0.00 2.90
1859 1953 5.483937 TCAACTTCCCTGATGTACTGTGTAT 59.516 40.000 0.00 0.00 0.00 2.29
1860 1954 5.344743 ACTTCCCTGATGTACTGTGTATG 57.655 43.478 0.00 0.00 0.00 2.39
1861 1955 4.777896 ACTTCCCTGATGTACTGTGTATGT 59.222 41.667 0.00 0.00 0.00 2.29
1862 1956 5.248477 ACTTCCCTGATGTACTGTGTATGTT 59.752 40.000 0.00 0.00 0.00 2.71
1863 1957 5.755409 TCCCTGATGTACTGTGTATGTTT 57.245 39.130 0.00 0.00 0.00 2.83
1864 1958 6.121776 TCCCTGATGTACTGTGTATGTTTT 57.878 37.500 0.00 0.00 0.00 2.43
1865 1959 5.937540 TCCCTGATGTACTGTGTATGTTTTG 59.062 40.000 0.00 0.00 0.00 2.44
1866 1960 5.123820 CCCTGATGTACTGTGTATGTTTTGG 59.876 44.000 0.00 0.00 0.00 3.28
1867 1961 5.123820 CCTGATGTACTGTGTATGTTTTGGG 59.876 44.000 0.00 0.00 0.00 4.12
1868 1962 5.626142 TGATGTACTGTGTATGTTTTGGGT 58.374 37.500 0.00 0.00 0.00 4.51
1869 1963 5.703592 TGATGTACTGTGTATGTTTTGGGTC 59.296 40.000 0.00 0.00 0.00 4.46
1870 1964 4.391155 TGTACTGTGTATGTTTTGGGTCC 58.609 43.478 0.00 0.00 0.00 4.46
1871 1965 2.500229 ACTGTGTATGTTTTGGGTCCG 58.500 47.619 0.00 0.00 0.00 4.79
1872 1966 2.105134 ACTGTGTATGTTTTGGGTCCGA 59.895 45.455 0.00 0.00 0.00 4.55
1873 1967 2.742053 CTGTGTATGTTTTGGGTCCGAG 59.258 50.000 0.00 0.00 0.00 4.63
1874 1968 2.105134 TGTGTATGTTTTGGGTCCGAGT 59.895 45.455 0.00 0.00 0.00 4.18
1875 1969 3.324268 TGTGTATGTTTTGGGTCCGAGTA 59.676 43.478 0.00 0.00 0.00 2.59
1876 1970 4.020039 TGTGTATGTTTTGGGTCCGAGTAT 60.020 41.667 0.00 0.00 0.00 2.12
1877 1971 4.331717 GTGTATGTTTTGGGTCCGAGTATG 59.668 45.833 0.00 0.00 0.00 2.39
1878 1972 3.713826 ATGTTTTGGGTCCGAGTATGT 57.286 42.857 0.00 0.00 0.00 2.29
1879 1973 3.495434 TGTTTTGGGTCCGAGTATGTT 57.505 42.857 0.00 0.00 0.00 2.71
1880 1974 3.822940 TGTTTTGGGTCCGAGTATGTTT 58.177 40.909 0.00 0.00 0.00 2.83
1881 1975 4.208746 TGTTTTGGGTCCGAGTATGTTTT 58.791 39.130 0.00 0.00 0.00 2.43
1882 1976 4.645588 TGTTTTGGGTCCGAGTATGTTTTT 59.354 37.500 0.00 0.00 0.00 1.94
1902 1996 5.836024 TTTTTAGGTGAGTCTGGGTATGT 57.164 39.130 0.00 0.00 0.00 2.29
1915 2009 3.895041 CTGGGTATGTTTTTGGTCAGGTT 59.105 43.478 0.00 0.00 0.00 3.50
1949 2048 8.666129 TTAGGATATCGAACCATTTCCTCTAT 57.334 34.615 8.84 0.00 36.14 1.98
1950 2049 9.763837 TTAGGATATCGAACCATTTCCTCTATA 57.236 33.333 8.84 0.00 36.14 1.31
1952 2051 9.273137 AGGATATCGAACCATTTCCTCTATAAT 57.727 33.333 8.84 0.00 30.61 1.28
1989 2088 8.840833 TTTATAGAAGCACAATGTTCTGTGTA 57.159 30.769 5.69 0.00 46.93 2.90
1997 2099 5.123820 GCACAATGTTCTGTGTACATACCAT 59.876 40.000 0.00 0.00 46.93 3.55
1999 2101 7.148323 GCACAATGTTCTGTGTACATACCATTA 60.148 37.037 0.00 0.00 46.93 1.90
2004 2106 9.851686 ATGTTCTGTGTACATACCATTATGATT 57.148 29.630 0.00 0.00 37.86 2.57
2005 2107 9.108284 TGTTCTGTGTACATACCATTATGATTG 57.892 33.333 0.00 0.00 37.86 2.67
2006 2108 7.728847 TCTGTGTACATACCATTATGATTGC 57.271 36.000 0.00 0.00 37.86 3.56
2007 2109 7.278875 TCTGTGTACATACCATTATGATTGCA 58.721 34.615 0.00 0.00 37.86 4.08
2009 2111 8.462589 TGTGTACATACCATTATGATTGCAAT 57.537 30.769 12.83 12.83 37.86 3.56
2010 2112 8.567104 TGTGTACATACCATTATGATTGCAATC 58.433 33.333 28.83 28.83 37.86 2.67
2011 2113 8.786898 GTGTACATACCATTATGATTGCAATCT 58.213 33.333 33.23 22.80 37.86 2.40
2081 2189 9.017509 CATTGATATGTTACATTTCATAGCCCT 57.982 33.333 16.67 0.00 33.67 5.19
2090 2198 3.370840 TTTCATAGCCCTGCACTTGAT 57.629 42.857 0.00 0.00 0.00 2.57
2094 2202 4.199310 TCATAGCCCTGCACTTGATAAAC 58.801 43.478 0.00 0.00 0.00 2.01
2095 2203 1.453155 AGCCCTGCACTTGATAAACG 58.547 50.000 0.00 0.00 0.00 3.60
2096 2204 1.165270 GCCCTGCACTTGATAAACGT 58.835 50.000 0.00 0.00 0.00 3.99
2100 2208 4.442706 CCCTGCACTTGATAAACGTCTAT 58.557 43.478 0.00 0.00 0.00 1.98
2101 2209 4.876107 CCCTGCACTTGATAAACGTCTATT 59.124 41.667 0.00 0.00 0.00 1.73
2103 2211 5.351465 CCTGCACTTGATAAACGTCTATTGT 59.649 40.000 0.00 0.00 0.00 2.71
2139 2247 1.321474 AATGTATCATGCCGGGCTTG 58.679 50.000 24.64 24.64 35.46 4.01
2147 2259 0.039035 ATGCCGGGCTTGAAACCTAA 59.961 50.000 21.46 0.00 0.00 2.69
2149 2261 0.322187 GCCGGGCTTGAAACCTAAGA 60.322 55.000 12.87 0.00 0.00 2.10
2181 2294 8.974060 TGTATTTGTCAGGATTCTTATTACCC 57.026 34.615 0.00 0.00 0.00 3.69
2184 2297 8.697507 ATTTGTCAGGATTCTTATTACCCATC 57.302 34.615 0.00 0.00 0.00 3.51
2185 2298 6.823286 TGTCAGGATTCTTATTACCCATCA 57.177 37.500 0.00 0.00 0.00 3.07
2186 2299 6.830912 TGTCAGGATTCTTATTACCCATCAG 58.169 40.000 0.00 0.00 0.00 2.90
2187 2300 6.615316 TGTCAGGATTCTTATTACCCATCAGA 59.385 38.462 0.00 0.00 0.00 3.27
2188 2301 7.127186 TGTCAGGATTCTTATTACCCATCAGAA 59.873 37.037 0.00 0.00 31.06 3.02
2189 2302 7.659390 GTCAGGATTCTTATTACCCATCAGAAG 59.341 40.741 0.00 0.00 30.19 2.85
2190 2303 7.348274 TCAGGATTCTTATTACCCATCAGAAGT 59.652 37.037 0.00 0.00 30.19 3.01
2191 2304 7.995488 CAGGATTCTTATTACCCATCAGAAGTT 59.005 37.037 0.00 0.00 30.19 2.66
2192 2305 9.225682 AGGATTCTTATTACCCATCAGAAGTTA 57.774 33.333 0.00 0.00 30.19 2.24
2229 2342 7.492669 ACATATACACACTATTCACAGAAGCAC 59.507 37.037 0.00 0.00 0.00 4.40
2239 2352 6.922247 ATTCACAGAAGCACTATGAATCTG 57.078 37.500 10.26 8.77 45.91 2.90
2243 2356 7.785033 TCACAGAAGCACTATGAATCTGAATA 58.215 34.615 14.46 2.09 39.85 1.75
2266 2379 5.767816 TGTTTACTTCTTTCTGGAAAGCC 57.232 39.130 15.76 0.00 45.48 4.35
2274 2387 6.551227 ACTTCTTTCTGGAAAGCCACTTAAAT 59.449 34.615 15.76 0.00 45.48 1.40
2275 2388 6.575162 TCTTTCTGGAAAGCCACTTAAATC 57.425 37.500 15.76 0.00 45.48 2.17
2276 2389 5.181245 TCTTTCTGGAAAGCCACTTAAATCG 59.819 40.000 15.76 0.00 45.48 3.34
2277 2390 4.015872 TCTGGAAAGCCACTTAAATCGT 57.984 40.909 0.00 0.00 39.92 3.73
2278 2391 3.751175 TCTGGAAAGCCACTTAAATCGTG 59.249 43.478 0.00 0.00 39.92 4.35
2279 2392 2.227865 TGGAAAGCCACTTAAATCGTGC 59.772 45.455 0.00 0.00 39.92 5.34
2280 2393 2.488153 GGAAAGCCACTTAAATCGTGCT 59.512 45.455 0.00 0.00 0.00 4.40
2297 2410 3.807622 CGTGCTCTCTGTTTTGGTTTAGA 59.192 43.478 0.00 0.00 0.00 2.10
2344 2458 7.386848 GGCTTAATGCTTATACCTGACGATTTA 59.613 37.037 0.00 0.00 42.39 1.40
2360 2474 4.689345 ACGATTTAAAGGGTCTTCTGAACG 59.311 41.667 0.00 0.00 0.00 3.95
2367 2481 1.653151 GGTCTTCTGAACGTATGGGC 58.347 55.000 0.00 0.00 0.00 5.36
2372 2486 3.260884 TCTTCTGAACGTATGGGCTCTTT 59.739 43.478 0.00 0.00 0.00 2.52
2376 2490 4.404394 TCTGAACGTATGGGCTCTTTATCA 59.596 41.667 0.00 0.00 0.00 2.15
2379 2493 4.008074 ACGTATGGGCTCTTTATCATGG 57.992 45.455 0.00 0.00 0.00 3.66
2429 2543 3.268023 GGCTAATTAGTCTGCCACTGT 57.732 47.619 13.91 0.00 44.34 3.55
2430 2544 4.402056 GGCTAATTAGTCTGCCACTGTA 57.598 45.455 13.91 0.00 44.34 2.74
2438 2552 3.820557 AGTCTGCCACTGTACATTTTGT 58.179 40.909 0.00 0.00 32.26 2.83
2512 2626 3.903616 CTGCTGCTGCTGAGCCTGT 62.904 63.158 17.00 0.00 45.57 4.00
2522 2636 1.398390 GCTGAGCCTGTTAAACCATCG 59.602 52.381 0.00 0.00 0.00 3.84
2551 2665 4.469227 ACCTGCAGTTAGAGATGTCAAGAT 59.531 41.667 13.81 0.00 0.00 2.40
2555 2669 6.104665 TGCAGTTAGAGATGTCAAGATCAAG 58.895 40.000 0.00 0.00 0.00 3.02
2558 2672 3.557228 AGAGATGTCAAGATCAAGCCC 57.443 47.619 0.00 0.00 0.00 5.19
2614 2728 1.280457 CCCCAGATAGGCCAGGATAC 58.720 60.000 5.01 0.00 35.39 2.24
2655 2769 1.080995 GCCTGTAAGCTCGCAGACTG 61.081 60.000 16.27 0.00 34.87 3.51
2658 2772 0.318441 TGTAAGCTCGCAGACTGCTT 59.682 50.000 24.36 14.30 46.87 3.91
2689 2803 3.348647 TCATCGAGAAGCCAATCCAAA 57.651 42.857 0.00 0.00 0.00 3.28
2744 2858 1.134189 GGGCGCTTACAAGGGTCTTAT 60.134 52.381 7.64 0.00 42.50 1.73
2892 3006 5.243954 ACTCTGCAGTCTAACATGTAGTTCA 59.756 40.000 14.67 0.00 41.64 3.18
2894 3008 4.234574 TGCAGTCTAACATGTAGTTCACG 58.765 43.478 0.00 0.00 41.64 4.35
3023 3146 2.961741 ACATGGCGAGAGTATCATCAGT 59.038 45.455 0.00 0.00 37.82 3.41
3047 3170 5.467399 TGAGCATCATTTTGGAAAGCTTTTG 59.533 36.000 14.05 6.56 42.56 2.44
3188 3312 3.378427 GGAAGTAGCTTAAGCACATTGGG 59.622 47.826 28.39 0.00 45.16 4.12
3238 3362 2.930040 AGTCCAAAAGCATATGACGTCG 59.070 45.455 11.62 0.00 0.00 5.12
3510 4034 1.308998 GTGCACCAGATATTTCCCCG 58.691 55.000 5.22 0.00 0.00 5.73
3513 4037 1.409661 GCACCAGATATTTCCCCGGTT 60.410 52.381 0.00 0.00 0.00 4.44
3516 4040 2.306847 CCAGATATTTCCCCGGTTTGG 58.693 52.381 0.00 0.00 37.55 3.28
3519 4043 2.578940 AGATATTTCCCCGGTTTGGTGA 59.421 45.455 0.00 0.00 35.15 4.02
3524 4048 0.767446 TCCCCGGTTTGGTGAAGGTA 60.767 55.000 0.00 0.00 35.15 3.08
3525 4049 0.330267 CCCCGGTTTGGTGAAGGTAT 59.670 55.000 0.00 0.00 35.15 2.73
3594 4118 1.680338 GTGCAGGTCCTGTGAAGTTT 58.320 50.000 20.24 0.00 33.43 2.66
3627 4155 2.607750 ACAGATCCGGCCAGGTGT 60.608 61.111 2.24 3.12 41.99 4.16
3653 4181 1.962807 AGTGCTGCACCAAATTAGCAA 59.037 42.857 27.74 0.00 46.46 3.91
3667 4195 6.017275 CCAAATTAGCAATGGAACTTTGCAAA 60.017 34.615 12.14 12.14 36.27 3.68
3692 4221 1.474077 AGATGAAGTGCAATTTCGCCC 59.526 47.619 0.00 0.00 34.99 6.13
3703 4232 0.254747 ATTTCGCCCGATGGAGGAAA 59.745 50.000 0.00 4.52 38.86 3.13
3705 4234 0.037017 TTCGCCCGATGGAGGAAAAA 59.963 50.000 0.00 0.00 31.33 1.94
3717 4246 2.347731 GAGGAAAAAGCGAAGGACGAT 58.652 47.619 0.00 0.00 45.77 3.73
3746 4275 5.578727 GGATGATAGGCGATAACAACTGATC 59.421 44.000 0.00 0.00 0.00 2.92
3747 4276 5.791336 TGATAGGCGATAACAACTGATCT 57.209 39.130 0.00 0.00 0.00 2.75
3750 4279 6.490381 TGATAGGCGATAACAACTGATCTAGT 59.510 38.462 0.00 0.00 42.89 2.57
3751 4280 5.189659 AGGCGATAACAACTGATCTAGTC 57.810 43.478 0.00 0.00 39.18 2.59
3802 4336 4.328169 GGATAAAACTGTTCGTAAGGGTCG 59.672 45.833 0.00 0.00 38.47 4.79
3803 4337 1.505425 AAACTGTTCGTAAGGGTCGC 58.495 50.000 0.00 0.00 38.47 5.19
3804 4338 0.665369 AACTGTTCGTAAGGGTCGCG 60.665 55.000 0.00 0.00 38.47 5.87
3806 4340 0.797249 CTGTTCGTAAGGGTCGCGAG 60.797 60.000 10.24 0.00 36.00 5.03
3848 4383 8.129161 TCGTAGATTTTAAAAAGTGTTGACGA 57.871 30.769 4.44 10.12 0.00 4.20
3849 4384 8.602328 TCGTAGATTTTAAAAAGTGTTGACGAA 58.398 29.630 4.44 0.00 30.96 3.85
3850 4385 9.377383 CGTAGATTTTAAAAAGTGTTGACGAAT 57.623 29.630 4.44 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.454600 TCTACCGCCGCTAGAACAAG 59.545 55.000 0.00 0.00 0.00 3.16
1 2 0.454600 CTCTACCGCCGCTAGAACAA 59.545 55.000 0.00 0.00 0.00 2.83
2 3 1.381928 CCTCTACCGCCGCTAGAACA 61.382 60.000 0.00 0.00 0.00 3.18
3 4 1.359475 CCTCTACCGCCGCTAGAAC 59.641 63.158 0.00 0.00 0.00 3.01
4 5 1.077212 ACCTCTACCGCCGCTAGAA 60.077 57.895 0.00 0.00 0.00 2.10
5 6 1.525535 GACCTCTACCGCCGCTAGA 60.526 63.158 0.00 0.00 0.00 2.43
6 7 2.894565 CGACCTCTACCGCCGCTAG 61.895 68.421 0.00 0.00 0.00 3.42
7 8 2.898840 CGACCTCTACCGCCGCTA 60.899 66.667 0.00 0.00 0.00 4.26
9 10 4.549516 GACGACCTCTACCGCCGC 62.550 72.222 0.00 0.00 0.00 6.53
10 11 3.885521 GGACGACCTCTACCGCCG 61.886 72.222 0.00 0.00 0.00 6.46
11 12 1.673808 AATGGACGACCTCTACCGCC 61.674 60.000 5.33 0.00 37.04 6.13
12 13 0.527817 CAATGGACGACCTCTACCGC 60.528 60.000 5.33 0.00 37.04 5.68
13 14 0.102481 CCAATGGACGACCTCTACCG 59.898 60.000 5.33 0.00 37.04 4.02
14 15 1.192428 ACCAATGGACGACCTCTACC 58.808 55.000 6.16 0.00 37.04 3.18
15 16 4.217983 CCTATACCAATGGACGACCTCTAC 59.782 50.000 6.16 0.00 37.04 2.59
16 17 4.404640 CCTATACCAATGGACGACCTCTA 58.595 47.826 6.16 0.00 37.04 2.43
17 18 3.231818 CCTATACCAATGGACGACCTCT 58.768 50.000 6.16 0.00 37.04 3.69
18 19 2.299297 CCCTATACCAATGGACGACCTC 59.701 54.545 6.16 0.00 37.04 3.85
19 20 2.090943 TCCCTATACCAATGGACGACCT 60.091 50.000 6.16 0.00 37.04 3.85
20 21 2.036862 GTCCCTATACCAATGGACGACC 59.963 54.545 6.16 0.00 38.07 4.79
21 22 2.036862 GGTCCCTATACCAATGGACGAC 59.963 54.545 6.16 1.78 46.60 4.34
22 23 2.322658 GGTCCCTATACCAATGGACGA 58.677 52.381 6.16 0.00 46.60 4.20
23 24 2.043992 TGGTCCCTATACCAATGGACG 58.956 52.381 6.16 0.00 46.55 4.79
51 52 9.899661 AGTACAAAGCACACCAGATATAATTAA 57.100 29.630 0.00 0.00 0.00 1.40
52 53 9.899661 AAGTACAAAGCACACCAGATATAATTA 57.100 29.630 0.00 0.00 0.00 1.40
53 54 8.807948 AAGTACAAAGCACACCAGATATAATT 57.192 30.769 0.00 0.00 0.00 1.40
54 55 8.807948 AAAGTACAAAGCACACCAGATATAAT 57.192 30.769 0.00 0.00 0.00 1.28
55 56 8.511321 CAAAAGTACAAAGCACACCAGATATAA 58.489 33.333 0.00 0.00 0.00 0.98
56 57 7.120579 CCAAAAGTACAAAGCACACCAGATATA 59.879 37.037 0.00 0.00 0.00 0.86
57 58 6.071952 CCAAAAGTACAAAGCACACCAGATAT 60.072 38.462 0.00 0.00 0.00 1.63
58 59 5.240623 CCAAAAGTACAAAGCACACCAGATA 59.759 40.000 0.00 0.00 0.00 1.98
59 60 4.037923 CCAAAAGTACAAAGCACACCAGAT 59.962 41.667 0.00 0.00 0.00 2.90
60 61 3.380004 CCAAAAGTACAAAGCACACCAGA 59.620 43.478 0.00 0.00 0.00 3.86
61 62 3.130340 ACCAAAAGTACAAAGCACACCAG 59.870 43.478 0.00 0.00 0.00 4.00
62 63 3.093057 ACCAAAAGTACAAAGCACACCA 58.907 40.909 0.00 0.00 0.00 4.17
63 64 3.129638 TCACCAAAAGTACAAAGCACACC 59.870 43.478 0.00 0.00 0.00 4.16
64 65 4.364415 TCACCAAAAGTACAAAGCACAC 57.636 40.909 0.00 0.00 0.00 3.82
65 66 4.461081 AGTTCACCAAAAGTACAAAGCACA 59.539 37.500 0.00 0.00 0.00 4.57
66 67 4.993905 AGTTCACCAAAAGTACAAAGCAC 58.006 39.130 0.00 0.00 0.00 4.40
67 68 5.652994 AAGTTCACCAAAAGTACAAAGCA 57.347 34.783 0.00 0.00 0.00 3.91
68 69 7.918562 TCATAAAGTTCACCAAAAGTACAAAGC 59.081 33.333 0.00 0.00 0.00 3.51
69 70 9.965824 ATCATAAAGTTCACCAAAAGTACAAAG 57.034 29.630 0.00 0.00 0.00 2.77
74 75 9.667107 CCTCTATCATAAAGTTCACCAAAAGTA 57.333 33.333 0.00 0.00 0.00 2.24
75 76 8.164070 ACCTCTATCATAAAGTTCACCAAAAGT 58.836 33.333 0.00 0.00 0.00 2.66
76 77 8.454106 CACCTCTATCATAAAGTTCACCAAAAG 58.546 37.037 0.00 0.00 0.00 2.27
77 78 7.393234 CCACCTCTATCATAAAGTTCACCAAAA 59.607 37.037 0.00 0.00 0.00 2.44
78 79 6.884295 CCACCTCTATCATAAAGTTCACCAAA 59.116 38.462 0.00 0.00 0.00 3.28
79 80 6.214615 TCCACCTCTATCATAAAGTTCACCAA 59.785 38.462 0.00 0.00 0.00 3.67
80 81 5.724370 TCCACCTCTATCATAAAGTTCACCA 59.276 40.000 0.00 0.00 0.00 4.17
81 82 6.235231 TCCACCTCTATCATAAAGTTCACC 57.765 41.667 0.00 0.00 0.00 4.02
82 83 7.556844 TCTTCCACCTCTATCATAAAGTTCAC 58.443 38.462 0.00 0.00 0.00 3.18
83 84 7.147655 CCTCTTCCACCTCTATCATAAAGTTCA 60.148 40.741 0.00 0.00 0.00 3.18
84 85 7.070074 TCCTCTTCCACCTCTATCATAAAGTTC 59.930 40.741 0.00 0.00 0.00 3.01
85 86 6.903534 TCCTCTTCCACCTCTATCATAAAGTT 59.096 38.462 0.00 0.00 0.00 2.66
86 87 6.444704 TCCTCTTCCACCTCTATCATAAAGT 58.555 40.000 0.00 0.00 0.00 2.66
87 88 6.985653 TCCTCTTCCACCTCTATCATAAAG 57.014 41.667 0.00 0.00 0.00 1.85
88 89 7.623677 TCTTTCCTCTTCCACCTCTATCATAAA 59.376 37.037 0.00 0.00 0.00 1.40
89 90 7.132805 TCTTTCCTCTTCCACCTCTATCATAA 58.867 38.462 0.00 0.00 0.00 1.90
90 91 6.683537 TCTTTCCTCTTCCACCTCTATCATA 58.316 40.000 0.00 0.00 0.00 2.15
91 92 5.533112 TCTTTCCTCTTCCACCTCTATCAT 58.467 41.667 0.00 0.00 0.00 2.45
92 93 4.947883 TCTTTCCTCTTCCACCTCTATCA 58.052 43.478 0.00 0.00 0.00 2.15
93 94 5.600484 TGATCTTTCCTCTTCCACCTCTATC 59.400 44.000 0.00 0.00 0.00 2.08
94 95 5.533112 TGATCTTTCCTCTTCCACCTCTAT 58.467 41.667 0.00 0.00 0.00 1.98
95 96 4.947883 TGATCTTTCCTCTTCCACCTCTA 58.052 43.478 0.00 0.00 0.00 2.43
96 97 3.796111 TGATCTTTCCTCTTCCACCTCT 58.204 45.455 0.00 0.00 0.00 3.69
107 108 3.196469 TCATCGACAGCTTGATCTTTCCT 59.804 43.478 0.00 0.00 0.00 3.36
108 109 3.308323 GTCATCGACAGCTTGATCTTTCC 59.692 47.826 0.00 0.00 32.09 3.13
121 122 3.068165 ACTGAACTCACAAGTCATCGACA 59.932 43.478 0.00 0.00 33.48 4.35
126 127 5.059833 GGAAGAACTGAACTCACAAGTCAT 58.940 41.667 0.00 0.00 33.48 3.06
127 128 4.162320 AGGAAGAACTGAACTCACAAGTCA 59.838 41.667 0.00 0.00 33.48 3.41
133 136 4.061596 CTCCAAGGAAGAACTGAACTCAC 58.938 47.826 0.00 0.00 0.00 3.51
153 156 1.508088 CGCCATTGGGTTTGAGCTC 59.492 57.895 6.82 6.82 36.17 4.09
161 164 0.037590 TAGAACTTGCGCCATTGGGT 59.962 50.000 4.18 0.00 36.17 4.51
173 176 5.364157 GGTGGGTGTCATATCTCTAGAACTT 59.636 44.000 0.00 0.00 0.00 2.66
176 179 3.889538 CGGTGGGTGTCATATCTCTAGAA 59.110 47.826 0.00 0.00 0.00 2.10
178 181 3.487372 TCGGTGGGTGTCATATCTCTAG 58.513 50.000 0.00 0.00 0.00 2.43
195 198 1.838073 AACGGGGAGATTGCTTCGGT 61.838 55.000 0.00 0.00 0.00 4.69
196 199 0.676782 AAACGGGGAGATTGCTTCGG 60.677 55.000 0.00 0.00 0.00 4.30
210 213 0.811281 GCAAGATCCTCCCAAAACGG 59.189 55.000 0.00 0.00 0.00 4.44
212 215 3.306294 CCAAAGCAAGATCCTCCCAAAAC 60.306 47.826 0.00 0.00 0.00 2.43
213 216 2.899256 CCAAAGCAAGATCCTCCCAAAA 59.101 45.455 0.00 0.00 0.00 2.44
219 222 2.160417 CGAACACCAAAGCAAGATCCTC 59.840 50.000 0.00 0.00 0.00 3.71
228 231 1.299850 GCCCAACGAACACCAAAGC 60.300 57.895 0.00 0.00 0.00 3.51
255 258 4.390909 CCAAAAGATACAACGGTAGGACAC 59.609 45.833 0.00 0.00 31.88 3.67
257 260 4.572909 ACCAAAAGATACAACGGTAGGAC 58.427 43.478 0.00 0.00 31.88 3.85
288 291 0.531532 CATCGGAGCTCCATGGTGTC 60.532 60.000 31.67 9.35 35.14 3.67
292 295 1.070445 GGACATCGGAGCTCCATGG 59.930 63.158 31.36 23.27 35.14 3.66
306 309 1.596934 GAGGCATCGTTGAGGGACA 59.403 57.895 0.00 0.00 0.00 4.02
307 310 1.153349 GGAGGCATCGTTGAGGGAC 60.153 63.158 0.00 0.00 0.00 4.46
314 317 1.340114 GGAAGGAAAGGAGGCATCGTT 60.340 52.381 0.00 0.00 35.09 3.85
322 325 0.537653 GTCGGGAGGAAGGAAAGGAG 59.462 60.000 0.00 0.00 0.00 3.69
350 353 3.180507 AGGCCAAATTGCATCCCTTTTA 58.819 40.909 5.01 0.00 0.00 1.52
366 369 0.611200 TAGACGCAAAGCTAAGGCCA 59.389 50.000 5.01 0.00 39.73 5.36
382 385 1.919240 TGCGAGGAAGGAGTTGTAGA 58.081 50.000 0.00 0.00 0.00 2.59
399 402 0.804989 CCACCGTGAGAGGATTTTGC 59.195 55.000 0.00 0.00 34.73 3.68
423 426 3.039252 TGGGACAAAAAGGTTGACCAT 57.961 42.857 2.56 0.00 36.26 3.55
466 469 4.322349 GCTTCGACATAGCCTAGAATCCAT 60.322 45.833 0.00 0.00 32.45 3.41
475 478 2.283298 CAACATGCTTCGACATAGCCT 58.717 47.619 5.18 0.00 37.85 4.58
482 485 0.874390 TCCTTGCAACATGCTTCGAC 59.126 50.000 0.00 0.00 45.31 4.20
484 487 2.642139 AATCCTTGCAACATGCTTCG 57.358 45.000 0.00 0.00 45.31 3.79
506 509 3.181500 GGCCTCGAAAACTAAATCGCAAT 60.181 43.478 0.00 0.00 38.87 3.56
510 513 3.522553 AGAGGCCTCGAAAACTAAATCG 58.477 45.455 26.95 0.00 40.31 3.34
513 516 4.885325 ACAAAAGAGGCCTCGAAAACTAAA 59.115 37.500 26.95 0.00 34.09 1.85
514 517 4.457466 ACAAAAGAGGCCTCGAAAACTAA 58.543 39.130 26.95 0.00 34.09 2.24
524 529 3.305335 CGTGCATTTTACAAAAGAGGCCT 60.305 43.478 3.86 3.86 0.00 5.19
534 539 4.792521 AAATTAGCCCGTGCATTTTACA 57.207 36.364 0.00 0.00 41.13 2.41
736 751 4.657814 TGACCCTAAGAAAGAAGGCATT 57.342 40.909 0.00 0.00 0.00 3.56
737 752 4.657814 TTGACCCTAAGAAAGAAGGCAT 57.342 40.909 0.00 0.00 0.00 4.40
765 838 4.586001 CCCAGGCTGCAATAGATAACATTT 59.414 41.667 9.56 0.00 0.00 2.32
823 897 7.527457 ACTGCGAAAAGTAGAAATCATTTACC 58.473 34.615 0.00 0.00 36.37 2.85
843 918 7.697710 TCAAGCATTTCTAAATTAATGACTGCG 59.302 33.333 3.36 0.00 34.44 5.18
1150 1236 2.027625 GCGAGTCGTGAAACCCCAG 61.028 63.158 15.08 0.00 0.00 4.45
1224 1310 2.156098 GATTAAGGGTTTGGTGTGCGA 58.844 47.619 0.00 0.00 0.00 5.10
1250 1336 1.664965 AAGACTGAACGGAGTGCGC 60.665 57.895 3.08 0.00 45.00 6.09
1251 1337 1.284982 CCAAGACTGAACGGAGTGCG 61.285 60.000 1.13 1.13 45.00 5.34
1417 1505 4.301628 CAGCACTGAACCTTGGAAATTTC 58.698 43.478 9.83 9.83 0.00 2.17
1437 1530 2.286872 CTGAAACTAGCATGAGCCCAG 58.713 52.381 0.00 0.00 43.56 4.45
1477 1570 3.556004 CCTTTTCTCCGTCTTTCTGAGCT 60.556 47.826 0.00 0.00 0.00 4.09
1480 1573 2.550208 GCCCTTTTCTCCGTCTTTCTGA 60.550 50.000 0.00 0.00 0.00 3.27
1481 1574 1.807142 GCCCTTTTCTCCGTCTTTCTG 59.193 52.381 0.00 0.00 0.00 3.02
1482 1575 1.420138 TGCCCTTTTCTCCGTCTTTCT 59.580 47.619 0.00 0.00 0.00 2.52
1483 1576 1.892209 TGCCCTTTTCTCCGTCTTTC 58.108 50.000 0.00 0.00 0.00 2.62
1484 1577 2.586648 ATGCCCTTTTCTCCGTCTTT 57.413 45.000 0.00 0.00 0.00 2.52
1485 1578 2.304761 TGTATGCCCTTTTCTCCGTCTT 59.695 45.455 0.00 0.00 0.00 3.01
1486 1579 1.906574 TGTATGCCCTTTTCTCCGTCT 59.093 47.619 0.00 0.00 0.00 4.18
1529 1622 2.027625 GTCACCGCCGTCTTTCTGG 61.028 63.158 0.00 0.00 0.00 3.86
1598 1691 4.866508 AATCCAATATCAGCAATGGCAG 57.133 40.909 0.00 0.00 44.61 4.85
1629 1723 2.548480 GGCGAGGGTATGTCAAATTAGC 59.452 50.000 0.00 0.00 0.00 3.09
1639 1733 0.392998 AAACAGCAGGCGAGGGTATG 60.393 55.000 0.00 0.00 0.00 2.39
1650 1744 4.905866 CGACAATTGACAAGTAAACAGCAG 59.094 41.667 13.59 0.00 0.00 4.24
1766 1860 2.117051 TCAGGATCTCAAGAGCAGCAT 58.883 47.619 0.00 0.00 30.87 3.79
1776 1870 6.778821 TGAACATTTACCTTTCAGGATCTCA 58.221 36.000 0.00 0.00 37.67 3.27
1805 1899 6.625362 TCTCTGTAAGCTCTGACAACAATAG 58.375 40.000 0.00 0.00 0.00 1.73
1808 1902 4.937201 TCTCTGTAAGCTCTGACAACAA 57.063 40.909 0.00 0.00 0.00 2.83
1819 1913 5.106908 GGAAGTTGAACACATCTCTGTAAGC 60.107 44.000 0.00 0.00 33.14 3.09
1834 1928 4.102524 ACACAGTACATCAGGGAAGTTGAA 59.897 41.667 0.00 0.00 0.00 2.69
1836 1930 4.008074 ACACAGTACATCAGGGAAGTTG 57.992 45.455 0.00 0.00 0.00 3.16
1843 1937 5.123820 CCCAAAACATACACAGTACATCAGG 59.876 44.000 0.00 0.00 0.00 3.86
1850 1944 3.324268 TCGGACCCAAAACATACACAGTA 59.676 43.478 0.00 0.00 0.00 2.74
1851 1945 2.105134 TCGGACCCAAAACATACACAGT 59.895 45.455 0.00 0.00 0.00 3.55
1852 1946 2.742053 CTCGGACCCAAAACATACACAG 59.258 50.000 0.00 0.00 0.00 3.66
1853 1947 2.105134 ACTCGGACCCAAAACATACACA 59.895 45.455 0.00 0.00 0.00 3.72
1854 1948 2.774687 ACTCGGACCCAAAACATACAC 58.225 47.619 0.00 0.00 0.00 2.90
1855 1949 4.020039 ACATACTCGGACCCAAAACATACA 60.020 41.667 0.00 0.00 0.00 2.29
1856 1950 4.510571 ACATACTCGGACCCAAAACATAC 58.489 43.478 0.00 0.00 0.00 2.39
1857 1951 4.829872 ACATACTCGGACCCAAAACATA 57.170 40.909 0.00 0.00 0.00 2.29
1858 1952 3.713826 ACATACTCGGACCCAAAACAT 57.286 42.857 0.00 0.00 0.00 2.71
1859 1953 3.495434 AACATACTCGGACCCAAAACA 57.505 42.857 0.00 0.00 0.00 2.83
1860 1954 4.841443 AAAACATACTCGGACCCAAAAC 57.159 40.909 0.00 0.00 0.00 2.43
1880 1974 5.836024 ACATACCCAGACTCACCTAAAAA 57.164 39.130 0.00 0.00 0.00 1.94
1881 1975 5.836024 AACATACCCAGACTCACCTAAAA 57.164 39.130 0.00 0.00 0.00 1.52
1882 1976 5.836024 AAACATACCCAGACTCACCTAAA 57.164 39.130 0.00 0.00 0.00 1.85
1883 1977 5.836024 AAAACATACCCAGACTCACCTAA 57.164 39.130 0.00 0.00 0.00 2.69
1884 1978 5.514136 CCAAAAACATACCCAGACTCACCTA 60.514 44.000 0.00 0.00 0.00 3.08
1885 1979 4.398319 CAAAAACATACCCAGACTCACCT 58.602 43.478 0.00 0.00 0.00 4.00
1886 1980 3.506067 CCAAAAACATACCCAGACTCACC 59.494 47.826 0.00 0.00 0.00 4.02
1887 1981 4.142038 ACCAAAAACATACCCAGACTCAC 58.858 43.478 0.00 0.00 0.00 3.51
1888 1982 4.141367 TGACCAAAAACATACCCAGACTCA 60.141 41.667 0.00 0.00 0.00 3.41
1889 1983 4.394729 TGACCAAAAACATACCCAGACTC 58.605 43.478 0.00 0.00 0.00 3.36
1890 1984 4.398319 CTGACCAAAAACATACCCAGACT 58.602 43.478 0.00 0.00 0.00 3.24
1891 1985 3.506067 CCTGACCAAAAACATACCCAGAC 59.494 47.826 0.00 0.00 0.00 3.51
1892 1986 3.139397 ACCTGACCAAAAACATACCCAGA 59.861 43.478 0.00 0.00 0.00 3.86
1893 1987 3.496331 ACCTGACCAAAAACATACCCAG 58.504 45.455 0.00 0.00 0.00 4.45
1896 1990 5.722021 ATGAACCTGACCAAAAACATACC 57.278 39.130 0.00 0.00 0.00 2.73
1902 1996 9.238368 CCTAAACTATATGAACCTGACCAAAAA 57.762 33.333 0.00 0.00 0.00 1.94
1933 2027 8.840321 ACATTGAATTATAGAGGAAATGGTTCG 58.160 33.333 0.00 0.00 34.28 3.95
1974 2073 6.741992 ATGGTATGTACACAGAACATTGTG 57.258 37.500 0.00 4.71 42.21 3.33
1978 2077 9.851686 AATCATAATGGTATGTACACAGAACAT 57.148 29.630 0.00 1.74 46.28 2.71
1979 2078 9.108284 CAATCATAATGGTATGTACACAGAACA 57.892 33.333 0.00 0.00 39.28 3.18
1982 2081 7.278875 TGCAATCATAATGGTATGTACACAGA 58.721 34.615 0.00 0.00 38.63 3.41
1983 2082 7.495135 TGCAATCATAATGGTATGTACACAG 57.505 36.000 0.00 0.00 38.63 3.66
1985 2084 8.786898 AGATTGCAATCATAATGGTATGTACAC 58.213 33.333 34.59 7.90 38.63 2.90
2081 2189 6.795098 AACAATAGACGTTTATCAAGTGCA 57.205 33.333 0.00 0.00 0.00 4.57
2117 2225 0.804989 GCCCGGCATGATACATTAGC 59.195 55.000 3.91 0.00 0.00 3.09
2120 2228 1.133823 TCAAGCCCGGCATGATACATT 60.134 47.619 13.32 0.00 31.25 2.71
2123 2231 1.065551 GTTTCAAGCCCGGCATGATAC 59.934 52.381 17.69 18.06 36.19 2.24
2128 2236 0.039035 TTAGGTTTCAAGCCCGGCAT 59.961 50.000 13.15 0.00 0.00 4.40
2131 2239 2.289565 GATCTTAGGTTTCAAGCCCGG 58.710 52.381 0.00 0.00 0.00 5.73
2206 2319 7.170393 AGTGCTTCTGTGAATAGTGTGTATA 57.830 36.000 0.00 0.00 0.00 1.47
2207 2320 6.042638 AGTGCTTCTGTGAATAGTGTGTAT 57.957 37.500 0.00 0.00 0.00 2.29
2208 2321 5.468540 AGTGCTTCTGTGAATAGTGTGTA 57.531 39.130 0.00 0.00 0.00 2.90
2210 2323 6.101997 TCATAGTGCTTCTGTGAATAGTGTG 58.898 40.000 6.50 0.00 40.42 3.82
2219 2332 6.922247 ATTCAGATTCATAGTGCTTCTGTG 57.078 37.500 0.00 0.00 36.17 3.66
2266 2379 5.597813 AAACAGAGAGCACGATTTAAGTG 57.402 39.130 0.00 0.00 42.15 3.16
2274 2387 2.325583 AACCAAAACAGAGAGCACGA 57.674 45.000 0.00 0.00 0.00 4.35
2275 2388 3.807622 TCTAAACCAAAACAGAGAGCACG 59.192 43.478 0.00 0.00 0.00 5.34
2276 2389 5.751243 TTCTAAACCAAAACAGAGAGCAC 57.249 39.130 0.00 0.00 0.00 4.40
2277 2390 6.959639 ATTTCTAAACCAAAACAGAGAGCA 57.040 33.333 0.00 0.00 0.00 4.26
2278 2391 8.138074 AGAAATTTCTAAACCAAAACAGAGAGC 58.862 33.333 19.17 0.00 35.34 4.09
2279 2392 9.455847 CAGAAATTTCTAAACCAAAACAGAGAG 57.544 33.333 20.07 0.00 35.34 3.20
2280 2393 9.184523 TCAGAAATTTCTAAACCAAAACAGAGA 57.815 29.630 20.07 5.80 35.34 3.10
2344 2458 3.307480 CCCATACGTTCAGAAGACCCTTT 60.307 47.826 0.00 0.00 0.00 3.11
2360 2474 6.261826 GCATATCCATGATAAAGAGCCCATAC 59.738 42.308 0.00 0.00 33.67 2.39
2367 2481 6.753107 TGCATGCATATCCATGATAAAGAG 57.247 37.500 18.46 0.00 44.12 2.85
2372 2486 7.776030 TCAATACATGCATGCATATCCATGATA 59.224 33.333 31.73 14.73 44.12 2.15
2376 2490 6.661805 TCTTCAATACATGCATGCATATCCAT 59.338 34.615 31.73 18.52 34.91 3.41
2420 2534 3.988379 ACACAAAATGTACAGTGGCAG 57.012 42.857 15.11 2.24 40.88 4.85
2425 2539 4.881273 TCTCTGCAACACAAAATGTACAGT 59.119 37.500 0.33 0.00 42.31 3.55
2429 2543 8.629158 ACTTTTATCTCTGCAACACAAAATGTA 58.371 29.630 0.00 0.00 42.31 2.29
2430 2544 7.491682 ACTTTTATCTCTGCAACACAAAATGT 58.508 30.769 0.00 0.00 46.42 2.71
2438 2552 6.294120 CCATGACAACTTTTATCTCTGCAACA 60.294 38.462 0.00 0.00 0.00 3.33
2512 2626 3.055021 TGCAGGTATGTCCGATGGTTTAA 60.055 43.478 0.00 0.00 41.99 1.52
2522 2636 4.100189 ACATCTCTAACTGCAGGTATGTCC 59.900 45.833 19.93 0.00 0.00 4.02
2551 2665 0.467290 AACTTTTCCTGCGGGCTTGA 60.467 50.000 6.73 0.00 0.00 3.02
2555 2669 2.962569 GGAACTTTTCCTGCGGGC 59.037 61.111 6.73 0.00 46.57 6.13
2614 2728 0.173708 GAGTGGTACCTTCTCGCCTG 59.826 60.000 14.36 0.00 0.00 4.85
2655 2769 1.160329 CGATGAATCCCCACGGAAGC 61.160 60.000 0.00 0.00 43.10 3.86
2658 2772 0.396556 TCTCGATGAATCCCCACGGA 60.397 55.000 0.00 0.00 44.33 4.69
2689 2803 1.315257 GCCATGGTTTGCCGTCTCAT 61.315 55.000 14.67 0.00 37.67 2.90
2732 2846 2.370849 ACCAACGACATAAGACCCTTGT 59.629 45.455 0.00 0.00 0.00 3.16
2744 2858 0.834261 TGGGAGATCCACCAACGACA 60.834 55.000 3.61 0.00 41.46 4.35
2795 2909 4.331168 GTCAAGCCATAGTAGACTGCTTTG 59.669 45.833 0.00 1.06 40.08 2.77
3023 3146 4.877378 AAGCTTTCCAAAATGATGCTCA 57.123 36.364 0.00 0.00 0.00 4.26
3188 3312 9.167239 CTTAAAGAAGAAAATGCATCGATCATC 57.833 33.333 0.00 1.73 34.25 2.92
3238 3362 5.009010 AGTCCATCACAATTCACAGAAACAC 59.991 40.000 0.00 0.00 0.00 3.32
3510 4034 4.600692 AAGCAAATACCTTCACCAAACC 57.399 40.909 0.00 0.00 0.00 3.27
3513 4037 5.594725 TGTACAAAGCAAATACCTTCACCAA 59.405 36.000 0.00 0.00 0.00 3.67
3516 4040 9.341899 CTTTATGTACAAAGCAAATACCTTCAC 57.658 33.333 0.00 0.00 0.00 3.18
3594 4118 7.627513 GCCGGATCTGTGTTAAAATTTCATACA 60.628 37.037 5.05 0.00 0.00 2.29
3611 4138 2.187946 GACACCTGGCCGGATCTG 59.812 66.667 15.09 7.74 36.31 2.90
3612 4139 3.461773 CGACACCTGGCCGGATCT 61.462 66.667 15.09 0.00 36.31 2.75
3627 4155 0.250252 TTTGGTGCAGCACTCATCGA 60.250 50.000 24.75 5.45 34.40 3.59
3653 4181 5.302568 TCATCTTCTGTTTGCAAAGTTCCAT 59.697 36.000 13.26 0.00 0.00 3.41
3667 4195 4.614535 GCGAAATTGCACTTCATCTTCTGT 60.615 41.667 8.13 0.00 34.15 3.41
3692 4221 1.398390 CCTTCGCTTTTTCCTCCATCG 59.602 52.381 0.00 0.00 0.00 3.84
3703 4232 0.729116 CATGCATCGTCCTTCGCTTT 59.271 50.000 0.00 0.00 39.67 3.51
3705 4234 1.522355 CCATGCATCGTCCTTCGCT 60.522 57.895 0.00 0.00 39.67 4.93
3717 4246 3.007831 TGTTATCGCCTATCATCCATGCA 59.992 43.478 0.00 0.00 0.00 3.96
3777 4311 4.287845 ACCCTTACGAACAGTTTTATCCCT 59.712 41.667 0.00 0.00 0.00 4.20
3780 4314 4.201656 GCGACCCTTACGAACAGTTTTATC 60.202 45.833 0.00 0.00 0.00 1.75
3781 4315 3.681417 GCGACCCTTACGAACAGTTTTAT 59.319 43.478 0.00 0.00 0.00 1.40
3787 4321 0.797249 CTCGCGACCCTTACGAACAG 60.797 60.000 3.71 0.00 35.07 3.16
3792 4326 2.126228 TTGCTCGCGACCCTTACG 60.126 61.111 3.71 0.00 0.00 3.18
3795 4329 1.227853 AAACTTGCTCGCGACCCTT 60.228 52.632 3.71 0.00 0.00 3.95
3824 4358 8.756376 TTCGTCAACACTTTTTAAAATCTACG 57.244 30.769 0.55 5.96 0.00 3.51


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

AutoCloner maintained by Alex Coulton.