Multiple sequence alignment - TraesCS4A01G074100

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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 TraesCS4A01G074100 chr4A 100.000 4194 0 0 1 4194 73247140 73251333 0.000000e+00 7745.0
1 TraesCS4A01G074100 chr4A 96.739 92 1 2 1 92 97966751 97966662 7.260000e-33 152.0
2 TraesCS4A01G074100 chr4B 91.202 2978 176 41 979 3903 481521389 481524333 0.000000e+00 3969.0
3 TraesCS4A01G074100 chr4B 87.234 376 35 4 528 895 481506507 481506877 2.330000e-112 416.0
4 TraesCS4A01G074100 chr4B 78.462 455 42 14 84 519 481506111 481506528 3.240000e-61 246.0
5 TraesCS4A01G074100 chr4B 81.849 292 29 4 3899 4187 481527046 481527316 1.520000e-54 224.0
6 TraesCS4A01G074100 chr4B 80.829 193 23 9 3877 4067 481523972 481524152 5.650000e-29 139.0
7 TraesCS4A01G074100 chr4B 88.333 60 7 0 4113 4172 481524227 481524286 5.820000e-09 73.1
8 TraesCS4A01G074100 chr4D 89.253 2438 132 55 535 2883 391490434 391492830 0.000000e+00 2931.0
9 TraesCS4A01G074100 chr4D 89.865 1332 82 15 2899 4187 391492816 391494137 0.000000e+00 1663.0
10 TraesCS4A01G074100 chr4D 94.845 97 3 2 1 95 409514055 409514151 2.610000e-32 150.0
11 TraesCS4A01G074100 chr4D 79.793 193 25 9 3877 4067 391493491 391493671 1.220000e-25 128.0
12 TraesCS4A01G074100 chr7A 100.000 84 0 0 1 84 418570539 418570622 5.610000e-34 156.0
13 TraesCS4A01G074100 chr5A 100.000 84 0 0 1 84 133884350 133884433 5.610000e-34 156.0
14 TraesCS4A01G074100 chr3A 100.000 84 0 0 1 84 664129456 664129539 5.610000e-34 156.0
15 TraesCS4A01G074100 chr6A 91.667 108 7 2 1 106 424306952 424307059 9.390000e-32 148.0
16 TraesCS4A01G074100 chr6D 93.814 97 6 0 1 97 397615988 397615892 3.380000e-31 147.0
17 TraesCS4A01G074100 chr7B 95.604 91 2 2 1 91 424603855 424603943 1.220000e-30 145.0
18 TraesCS4A01G074100 chr5D 88.034 117 9 4 1 117 534652881 534652770 2.630000e-27 134.0


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 TraesCS4A01G074100 chr4A 73247140 73251333 4193 False 7745.000 7745 100.000000 1 4194 1 chr4A.!!$F1 4193
1 TraesCS4A01G074100 chr4B 481521389 481527316 5927 False 1101.275 3969 85.553250 979 4187 4 chr4B.!!$F2 3208
2 TraesCS4A01G074100 chr4B 481506111 481506877 766 False 331.000 416 82.848000 84 895 2 chr4B.!!$F1 811
3 TraesCS4A01G074100 chr4D 391490434 391494137 3703 False 1574.000 2931 86.303667 535 4187 3 chr4D.!!$F2 3652

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
515 535 0.039618 CCAAGTGGGCCACCTACATT 59.960 55.0 32.3 17.22 37.76 2.71 F
1232 1302 0.168348 CGCTCTCTTTCTTCGACGGA 59.832 55.0 0.0 0.00 0.00 4.69 F
2139 2256 0.179234 CCACAGTACCACACACCACA 59.821 55.0 0.0 0.00 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1400 0.107643 TCCTGCCACGAACATGTCAA 59.892 50.0 0.00 0.0 0.00 3.18 R
2778 2898 0.391927 CGGTTCTTTGCCGGACCATA 60.392 55.0 5.05 0.0 44.98 2.74 R
3434 3575 0.461516 AGCATCACGGCATGAGTCAG 60.462 55.0 0.00 0.0 41.91 3.51 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
22 23 5.559148 GTGATATCTTCCCATGAGTCCTT 57.441 43.478 3.98 0.00 0.00 3.36
23 24 5.303971 GTGATATCTTCCCATGAGTCCTTG 58.696 45.833 3.98 0.00 0.00 3.61
24 25 5.070981 GTGATATCTTCCCATGAGTCCTTGA 59.929 44.000 3.98 0.00 0.00 3.02
25 26 5.848369 TGATATCTTCCCATGAGTCCTTGAT 59.152 40.000 3.98 0.00 0.00 2.57
26 27 4.703379 ATCTTCCCATGAGTCCTTGATC 57.297 45.455 0.00 0.00 0.00 2.92
27 28 3.729108 TCTTCCCATGAGTCCTTGATCT 58.271 45.455 0.00 0.00 0.00 2.75
28 29 4.107072 TCTTCCCATGAGTCCTTGATCTT 58.893 43.478 0.00 0.00 0.00 2.40
29 30 3.920231 TCCCATGAGTCCTTGATCTTG 57.080 47.619 0.00 0.00 0.00 3.02
30 31 3.453868 TCCCATGAGTCCTTGATCTTGA 58.546 45.455 0.00 0.00 0.00 3.02
31 32 4.042884 TCCCATGAGTCCTTGATCTTGAT 58.957 43.478 0.00 0.00 0.00 2.57
32 33 4.102210 TCCCATGAGTCCTTGATCTTGATC 59.898 45.833 0.00 3.82 0.00 2.92
33 34 4.056740 CCATGAGTCCTTGATCTTGATCG 58.943 47.826 0.00 0.00 0.00 3.69
34 35 4.442612 CCATGAGTCCTTGATCTTGATCGT 60.443 45.833 0.00 0.00 0.00 3.73
35 36 5.221322 CCATGAGTCCTTGATCTTGATCGTA 60.221 44.000 0.00 0.00 0.00 3.43
36 37 5.250235 TGAGTCCTTGATCTTGATCGTAC 57.750 43.478 6.19 2.53 0.00 3.67
37 38 4.705023 TGAGTCCTTGATCTTGATCGTACA 59.295 41.667 6.19 0.00 0.00 2.90
38 39 5.000012 AGTCCTTGATCTTGATCGTACAC 58.000 43.478 6.19 1.73 0.00 2.90
39 40 4.462834 AGTCCTTGATCTTGATCGTACACA 59.537 41.667 6.19 0.00 0.00 3.72
40 41 5.127845 AGTCCTTGATCTTGATCGTACACAT 59.872 40.000 6.19 0.00 0.00 3.21
41 42 5.812642 GTCCTTGATCTTGATCGTACACATT 59.187 40.000 6.19 0.00 0.00 2.71
42 43 6.313905 GTCCTTGATCTTGATCGTACACATTT 59.686 38.462 6.19 0.00 0.00 2.32
43 44 6.313658 TCCTTGATCTTGATCGTACACATTTG 59.686 38.462 6.19 0.00 0.00 2.32
44 45 5.469373 TGATCTTGATCGTACACATTTGC 57.531 39.130 6.19 0.00 0.00 3.68
45 46 3.989705 TCTTGATCGTACACATTTGCG 57.010 42.857 0.00 0.00 0.00 4.85
46 47 3.322369 TCTTGATCGTACACATTTGCGT 58.678 40.909 0.00 0.00 0.00 5.24
47 48 3.122780 TCTTGATCGTACACATTTGCGTG 59.877 43.478 0.00 0.00 42.81 5.34
59 60 5.868257 CACATTTGCGTGTATGATTAGTGT 58.132 37.500 0.00 0.00 32.00 3.55
60 61 6.999456 CACATTTGCGTGTATGATTAGTGTA 58.001 36.000 0.00 0.00 32.00 2.90
61 62 6.899771 CACATTTGCGTGTATGATTAGTGTAC 59.100 38.462 0.00 0.00 32.00 2.90
62 63 5.689927 TTTGCGTGTATGATTAGTGTACG 57.310 39.130 0.00 0.00 0.00 3.67
63 64 3.697982 TGCGTGTATGATTAGTGTACGG 58.302 45.455 0.00 0.00 0.00 4.02
64 65 3.129113 TGCGTGTATGATTAGTGTACGGT 59.871 43.478 0.00 0.00 0.00 4.83
65 66 3.727723 GCGTGTATGATTAGTGTACGGTC 59.272 47.826 0.00 0.00 0.00 4.79
66 67 4.731483 GCGTGTATGATTAGTGTACGGTCA 60.731 45.833 0.00 0.00 0.00 4.02
67 68 5.334319 CGTGTATGATTAGTGTACGGTCAA 58.666 41.667 0.00 0.00 0.00 3.18
68 69 5.801444 CGTGTATGATTAGTGTACGGTCAAA 59.199 40.000 0.00 0.00 0.00 2.69
69 70 6.474427 CGTGTATGATTAGTGTACGGTCAAAT 59.526 38.462 0.00 0.00 0.00 2.32
70 71 7.305820 CGTGTATGATTAGTGTACGGTCAAATC 60.306 40.741 0.00 0.00 0.00 2.17
71 72 6.693978 TGTATGATTAGTGTACGGTCAAATCG 59.306 38.462 0.00 0.00 0.00 3.34
72 73 4.426416 TGATTAGTGTACGGTCAAATCGG 58.574 43.478 0.00 0.00 0.00 4.18
73 74 2.945447 TAGTGTACGGTCAAATCGGG 57.055 50.000 0.00 0.00 0.00 5.14
74 75 0.248289 AGTGTACGGTCAAATCGGGG 59.752 55.000 0.00 0.00 0.00 5.73
75 76 0.741927 GTGTACGGTCAAATCGGGGG 60.742 60.000 0.00 0.00 0.00 5.40
76 77 1.816679 GTACGGTCAAATCGGGGGC 60.817 63.158 0.00 0.00 0.00 5.80
77 78 3.374012 TACGGTCAAATCGGGGGCG 62.374 63.158 0.00 0.00 0.00 6.13
78 79 4.770874 CGGTCAAATCGGGGGCGT 62.771 66.667 0.00 0.00 0.00 5.68
79 80 2.822701 GGTCAAATCGGGGGCGTC 60.823 66.667 0.00 0.00 0.00 5.19
80 81 2.046700 GTCAAATCGGGGGCGTCA 60.047 61.111 0.00 0.00 0.00 4.35
81 82 2.046700 TCAAATCGGGGGCGTCAC 60.047 61.111 0.00 0.00 0.00 3.67
82 83 2.359354 CAAATCGGGGGCGTCACA 60.359 61.111 0.00 0.00 0.00 3.58
83 84 2.046314 AAATCGGGGGCGTCACAG 60.046 61.111 0.00 0.00 0.00 3.66
84 85 4.778143 AATCGGGGGCGTCACAGC 62.778 66.667 0.00 0.00 0.00 4.40
89 90 4.314440 GGGGCGTCACAGCACTCA 62.314 66.667 0.00 0.00 41.08 3.41
98 99 3.120752 CGTCACAGCACTCAAGATGAAAG 60.121 47.826 0.00 0.00 0.00 2.62
127 128 5.271598 TGCCTTATTCATTGGAGGTGATTT 58.728 37.500 0.00 0.00 0.00 2.17
133 134 4.789012 TCATTGGAGGTGATTTTCAAGC 57.211 40.909 0.00 0.00 0.00 4.01
144 145 6.042143 GGTGATTTTCAAGCAACTCAAGAAA 58.958 36.000 0.00 0.00 30.31 2.52
148 149 4.637483 TTCAAGCAACTCAAGAAACCTG 57.363 40.909 0.00 0.00 0.00 4.00
150 151 2.951642 CAAGCAACTCAAGAAACCTGGA 59.048 45.455 0.00 0.00 0.00 3.86
156 157 5.563671 GCAACTCAAGAAACCTGGAAGAATC 60.564 44.000 0.00 0.00 34.07 2.52
168 169 7.747809 ACCTGGAAGAATCTAGAAGATCTTT 57.252 36.000 9.87 2.63 36.31 2.52
171 172 8.431222 CCTGGAAGAATCTAGAAGATCTTTGAT 58.569 37.037 9.87 10.82 36.31 2.57
179 180 9.829507 AATCTAGAAGATCTTTGATGTCGATTT 57.170 29.630 9.87 0.00 32.89 2.17
206 207 5.416271 TGACAATACCTTAGGGACAAGAC 57.584 43.478 2.32 0.00 36.25 3.01
207 208 4.841813 TGACAATACCTTAGGGACAAGACA 59.158 41.667 2.32 0.00 36.25 3.41
211 212 3.555117 ACCTTAGGGACAAGACACCTA 57.445 47.619 2.32 0.00 35.84 3.08
220 239 3.368531 GGACAAGACACCTATGACCAGTC 60.369 52.174 0.00 0.00 0.00 3.51
226 245 2.563179 ACACCTATGACCAGTCTCACAC 59.437 50.000 0.00 0.00 0.00 3.82
229 248 2.231478 CCTATGACCAGTCTCACACGTT 59.769 50.000 0.00 0.00 0.00 3.99
237 256 0.161658 GTCTCACACGTTGATGCACG 59.838 55.000 0.00 0.00 46.04 5.34
245 264 3.181486 ACACGTTGATGCACGATAGAGAT 60.181 43.478 1.06 0.00 43.15 2.75
254 273 5.440234 TGCACGATAGAGATAAGGAAGAC 57.560 43.478 0.00 0.00 41.38 3.01
261 280 4.429854 AGAGATAAGGAAGACAATGGGC 57.570 45.455 0.00 0.00 0.00 5.36
262 281 4.043596 AGAGATAAGGAAGACAATGGGCT 58.956 43.478 0.00 0.00 0.00 5.19
318 338 4.410400 GGCGTTGTCCCCTCCCAG 62.410 72.222 0.00 0.00 0.00 4.45
320 340 4.410400 CGTTGTCCCCTCCCAGCC 62.410 72.222 0.00 0.00 0.00 4.85
321 341 4.048470 GTTGTCCCCTCCCAGCCC 62.048 72.222 0.00 0.00 0.00 5.19
333 353 4.431524 CAGCCCCCTCCCACCCTA 62.432 72.222 0.00 0.00 0.00 3.53
334 354 3.633145 AGCCCCCTCCCACCCTAA 61.633 66.667 0.00 0.00 0.00 2.69
348 368 8.004801 CCTCCCACCCTAAATATTTAGTGAAAT 58.995 37.037 26.18 9.92 38.73 2.17
384 404 2.507484 TGAAGAGTGCAGTCATTTGGG 58.493 47.619 23.21 0.00 0.00 4.12
403 423 1.972795 GGCCCACCAATGATGCATATT 59.027 47.619 0.00 0.00 35.26 1.28
404 424 2.369532 GGCCCACCAATGATGCATATTT 59.630 45.455 0.00 0.00 35.26 1.40
405 425 3.181452 GGCCCACCAATGATGCATATTTT 60.181 43.478 0.00 0.00 35.26 1.82
407 427 4.202284 GCCCACCAATGATGCATATTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
411 431 7.270047 CCACCAATGATGCATATTTTCTCTTT 58.730 34.615 0.00 0.00 0.00 2.52
412 432 7.223971 CCACCAATGATGCATATTTTCTCTTTG 59.776 37.037 0.00 1.12 0.00 2.77
413 433 6.759827 ACCAATGATGCATATTTTCTCTTTGC 59.240 34.615 0.00 0.00 0.00 3.68
414 434 6.202188 CCAATGATGCATATTTTCTCTTTGCC 59.798 38.462 0.00 0.00 32.39 4.52
415 435 5.266733 TGATGCATATTTTCTCTTTGCCC 57.733 39.130 0.00 0.00 32.39 5.36
416 436 4.710865 TGATGCATATTTTCTCTTTGCCCA 59.289 37.500 0.00 0.00 32.39 5.36
417 437 4.454728 TGCATATTTTCTCTTTGCCCAC 57.545 40.909 0.00 0.00 32.39 4.61
418 438 3.195396 TGCATATTTTCTCTTTGCCCACC 59.805 43.478 0.00 0.00 32.39 4.61
419 439 3.448660 GCATATTTTCTCTTTGCCCACCT 59.551 43.478 0.00 0.00 0.00 4.00
420 440 4.440663 GCATATTTTCTCTTTGCCCACCTC 60.441 45.833 0.00 0.00 0.00 3.85
421 441 1.995376 TTTTCTCTTTGCCCACCTCC 58.005 50.000 0.00 0.00 0.00 4.30
422 442 0.112412 TTTCTCTTTGCCCACCTCCC 59.888 55.000 0.00 0.00 0.00 4.30
423 443 1.789576 TTCTCTTTGCCCACCTCCCC 61.790 60.000 0.00 0.00 0.00 4.81
424 444 2.121506 TCTTTGCCCACCTCCCCT 60.122 61.111 0.00 0.00 0.00 4.79
425 445 1.778383 TCTTTGCCCACCTCCCCTT 60.778 57.895 0.00 0.00 0.00 3.95
426 446 1.607467 CTTTGCCCACCTCCCCTTG 60.607 63.158 0.00 0.00 0.00 3.61
427 447 3.826265 TTTGCCCACCTCCCCTTGC 62.826 63.158 0.00 0.00 0.00 4.01
443 463 2.499289 CCTTGCTTCTCTCTTAGCTCCA 59.501 50.000 0.00 0.00 38.22 3.86
444 464 3.520569 CTTGCTTCTCTCTTAGCTCCAC 58.479 50.000 0.00 0.00 38.22 4.02
453 473 0.461548 CTTAGCTCCACCATCGCTGA 59.538 55.000 0.00 0.00 35.33 4.26
454 474 0.901827 TTAGCTCCACCATCGCTGAA 59.098 50.000 0.00 0.00 35.33 3.02
455 475 0.461548 TAGCTCCACCATCGCTGAAG 59.538 55.000 0.00 0.00 35.33 3.02
456 476 1.817099 GCTCCACCATCGCTGAAGG 60.817 63.158 0.00 0.00 0.00 3.46
457 477 1.817099 CTCCACCATCGCTGAAGGC 60.817 63.158 0.00 0.00 37.64 4.35
458 478 2.825836 CCACCATCGCTGAAGGCC 60.826 66.667 0.00 0.00 37.74 5.19
459 479 2.046023 CACCATCGCTGAAGGCCA 60.046 61.111 5.01 0.00 37.74 5.36
468 488 1.004560 CTGAAGGCCAACTCGAGCA 60.005 57.895 13.61 0.00 0.00 4.26
473 493 0.603975 AGGCCAACTCGAGCAAAGAC 60.604 55.000 13.61 0.66 0.00 3.01
475 495 1.493311 CCAACTCGAGCAAAGACGC 59.507 57.895 13.61 0.00 0.00 5.19
476 496 1.493311 CAACTCGAGCAAAGACGCC 59.507 57.895 13.61 0.00 0.00 5.68
513 533 3.166434 CCAAGTGGGCCACCTACA 58.834 61.111 32.30 0.00 37.76 2.74
514 534 1.691219 CCAAGTGGGCCACCTACAT 59.309 57.895 32.30 11.57 37.76 2.29
515 535 0.039618 CCAAGTGGGCCACCTACATT 59.960 55.000 32.30 17.22 37.76 2.71
516 536 1.549950 CCAAGTGGGCCACCTACATTT 60.550 52.381 32.30 16.47 37.76 2.32
517 537 2.247358 CAAGTGGGCCACCTACATTTT 58.753 47.619 32.30 15.72 37.76 1.82
518 538 2.632512 CAAGTGGGCCACCTACATTTTT 59.367 45.455 32.30 14.96 37.76 1.94
579 599 2.469274 AGAGAGCCACACAACATCAG 57.531 50.000 0.00 0.00 0.00 2.90
582 602 0.607489 GAGCCACACAACATCAGCCT 60.607 55.000 0.00 0.00 0.00 4.58
583 603 0.178981 AGCCACACAACATCAGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
592 612 5.040635 CACAACATCAGCCTTTTAAAACGT 58.959 37.500 0.00 0.00 0.00 3.99
598 618 5.759506 TCAGCCTTTTAAAACGTCAATGA 57.240 34.783 0.00 0.00 0.00 2.57
685 708 3.040099 CGACACGTCGCATATGTGATAA 58.960 45.455 21.21 0.00 46.40 1.75
696 719 5.807520 CGCATATGTGATAACTACCTGGATC 59.192 44.000 10.90 0.00 0.00 3.36
719 742 3.126001 ACCATGTGAACTTGTGATCGT 57.874 42.857 0.00 0.00 0.00 3.73
749 777 4.832608 GTTCCTAGCGCCACGGGG 62.833 72.222 2.29 0.00 37.18 5.73
755 783 2.510064 CTAGCGCCACGGGGTGTAAA 62.510 60.000 20.42 3.56 46.76 2.01
767 795 5.986135 CACGGGGTGTAAATGAAATGAAAAA 59.014 36.000 0.00 0.00 0.00 1.94
928 958 9.855021 TTTTTCTCCTAAAACAAAGAAGTGAAG 57.145 29.630 0.00 0.00 0.00 3.02
929 959 8.801882 TTTCTCCTAAAACAAAGAAGTGAAGA 57.198 30.769 0.00 0.00 0.00 2.87
931 961 8.801882 TCTCCTAAAACAAAGAAGTGAAGAAA 57.198 30.769 0.00 0.00 0.00 2.52
933 963 8.801882 TCCTAAAACAAAGAAGTGAAGAAAGA 57.198 30.769 0.00 0.00 0.00 2.52
964 1008 4.590222 AGTGGGAATGAACAGAAAGCAAAT 59.410 37.500 0.00 0.00 0.00 2.32
972 1016 6.130298 TGAACAGAAAGCAAATCGAAAAGA 57.870 33.333 0.00 0.00 0.00 2.52
975 1019 7.220683 TGAACAGAAAGCAAATCGAAAAGAAAG 59.779 33.333 0.00 0.00 0.00 2.62
976 1020 5.979517 ACAGAAAGCAAATCGAAAAGAAAGG 59.020 36.000 0.00 0.00 0.00 3.11
977 1021 5.403466 CAGAAAGCAAATCGAAAAGAAAGGG 59.597 40.000 0.00 0.00 0.00 3.95
1016 1083 2.508361 CCATGGAAATGGTGGAGGC 58.492 57.895 5.56 0.00 36.95 4.70
1123 1193 1.407437 GCATTCATCTCCCTCCGTTGT 60.407 52.381 0.00 0.00 0.00 3.32
1156 1226 1.867919 CGAACTCAGTCTCACCCGCT 61.868 60.000 0.00 0.00 0.00 5.52
1220 1290 0.677098 TCAAGTACTCCGCGCTCTCT 60.677 55.000 5.56 0.00 0.00 3.10
1229 1299 1.406970 CCGCGCTCTCTTTCTTCGAC 61.407 60.000 5.56 0.00 0.00 4.20
1232 1302 0.168348 CGCTCTCTTTCTTCGACGGA 59.832 55.000 0.00 0.00 0.00 4.69
1261 1331 4.116328 CGCGCTTCCGAGGTGAGA 62.116 66.667 5.56 0.00 36.29 3.27
1262 1332 2.202676 GCGCTTCCGAGGTGAGAG 60.203 66.667 0.00 0.00 36.29 3.20
1263 1333 2.492090 CGCTTCCGAGGTGAGAGG 59.508 66.667 0.00 0.00 36.29 3.69
1264 1334 2.344203 CGCTTCCGAGGTGAGAGGT 61.344 63.158 0.00 0.00 36.29 3.85
1265 1335 1.216710 GCTTCCGAGGTGAGAGGTG 59.783 63.158 0.00 0.00 0.00 4.00
1266 1336 1.251527 GCTTCCGAGGTGAGAGGTGA 61.252 60.000 0.00 0.00 0.00 4.02
1288 1358 1.454111 CGGTCGATCTCCCACTCCT 60.454 63.158 0.00 0.00 0.00 3.69
1320 1390 0.891904 TAGTTTTGGTTGGGGCGAGC 60.892 55.000 0.00 0.00 0.00 5.03
1325 1395 1.460273 TTGGTTGGGGCGAGCTTTTC 61.460 55.000 0.00 0.00 0.00 2.29
1330 1400 1.002011 GGGGCGAGCTTTTCCTTCT 60.002 57.895 0.00 0.00 0.00 2.85
1362 1435 1.213296 GGCAGGAAGATGGGGTTCTA 58.787 55.000 0.00 0.00 0.00 2.10
1437 1510 1.004440 GCAACCTGGAGCTCTTCGT 60.004 57.895 14.64 3.99 0.00 3.85
1495 1568 2.672381 GTGAGCATCTCAGCAAACTCTC 59.328 50.000 0.00 0.00 41.46 3.20
1505 1578 0.594602 GCAAACTCTCTGTGCATGCA 59.405 50.000 18.46 18.46 38.19 3.96
1506 1579 1.201647 GCAAACTCTCTGTGCATGCAT 59.798 47.619 25.64 2.10 38.19 3.96
1507 1580 2.863739 CAAACTCTCTGTGCATGCATG 58.136 47.619 25.64 22.70 0.00 4.06
1541 1616 4.394920 GCATCATTACCTTCCTTTTCGTGA 59.605 41.667 0.00 0.00 0.00 4.35
1552 1627 5.828299 TCCTTTTCGTGATGTTTTCTGTT 57.172 34.783 0.00 0.00 0.00 3.16
1664 1739 2.792290 CGCGGATGCTGTGAGTTCG 61.792 63.158 0.00 0.00 39.65 3.95
1688 1763 5.754890 GTGGTGCATTGTTCTCTTTCATTTT 59.245 36.000 0.00 0.00 0.00 1.82
1709 1784 2.213499 GGTTCCTGATTATGCGGACTG 58.787 52.381 0.00 0.00 0.00 3.51
1725 1800 3.001939 CGGACTGAAGGTGTTTGTTGTAC 59.998 47.826 0.00 0.00 0.00 2.90
1819 1894 4.755411 TCGTCTTCCCACACTATGAAATC 58.245 43.478 0.00 0.00 0.00 2.17
1827 1902 5.049060 TCCCACACTATGAAATCGTTGTTTG 60.049 40.000 0.00 0.00 0.00 2.93
1894 1969 4.823989 ACATTGCTTTCATATACCTGGAGC 59.176 41.667 0.00 0.00 0.00 4.70
1954 2047 3.785486 TCATTCGCTAATCACTGACCAG 58.215 45.455 0.00 0.00 0.00 4.00
2002 2095 8.854117 CATTAGGAGCAATTCTTATAGCCTTTT 58.146 33.333 0.00 0.00 0.00 2.27
2010 2103 7.201705 GCAATTCTTATAGCCTTTTAGAACCGT 60.202 37.037 0.00 0.00 0.00 4.83
2138 2255 0.179468 ACCACAGTACCACACACCAC 59.821 55.000 0.00 0.00 0.00 4.16
2139 2256 0.179234 CCACAGTACCACACACCACA 59.821 55.000 0.00 0.00 0.00 4.17
2140 2257 1.202758 CCACAGTACCACACACCACAT 60.203 52.381 0.00 0.00 0.00 3.21
2147 2264 1.108727 CCACACACCACATGCAGGTT 61.109 55.000 0.00 0.00 37.23 3.50
2196 2313 4.883585 TCTGTTGCATTCAGTTTCTCACTT 59.116 37.500 15.67 0.00 30.92 3.16
2210 2327 1.002868 CACTTCCCCCTGAGCAGTG 60.003 63.158 0.00 0.00 0.00 3.66
2235 2352 8.181573 TGCACTTGACTCTTTGTAAGTTTTTAG 58.818 33.333 0.00 0.00 31.47 1.85
2266 2384 2.438021 AGACACAGTACACACCACCATT 59.562 45.455 0.00 0.00 0.00 3.16
2464 2584 5.011090 TCTTCACTGACAGGGAAATATCG 57.989 43.478 20.35 9.13 37.15 2.92
2548 2668 3.947834 CCGAAGATACCTCATGGCTTTTT 59.052 43.478 0.00 0.00 36.63 1.94
2593 2713 5.012664 TGCTTCAACTCTTGTATGTTCCCTA 59.987 40.000 0.00 0.00 0.00 3.53
2598 2718 6.374333 TCAACTCTTGTATGTTCCCTAAATGC 59.626 38.462 0.00 0.00 0.00 3.56
2626 2746 4.984295 TCCCACTGACATTGAAAAGATGA 58.016 39.130 0.00 0.00 0.00 2.92
2636 2756 9.486497 TGACATTGAAAAGATGATAGATAGAGC 57.514 33.333 0.00 0.00 0.00 4.09
2639 2759 7.959689 TTGAAAAGATGATAGATAGAGCTGC 57.040 36.000 0.00 0.00 0.00 5.25
2649 2769 4.655762 AGATAGAGCTGCGACAATGTTA 57.344 40.909 0.00 0.00 0.00 2.41
2652 2772 1.667724 AGAGCTGCGACAATGTTATGC 59.332 47.619 0.00 0.00 0.00 3.14
2657 2777 3.788797 GCTGCGACAATGTTATGCCTAAC 60.789 47.826 5.05 5.05 38.17 2.34
2658 2778 2.350192 TGCGACAATGTTATGCCTAACG 59.650 45.455 7.29 0.00 40.15 3.18
2659 2779 2.849502 GCGACAATGTTATGCCTAACGC 60.850 50.000 7.29 0.00 40.15 4.84
2671 2791 1.067495 GCCTAACGCTGTCTGTCTCTT 60.067 52.381 0.00 0.00 0.00 2.85
2775 2895 4.078363 GCTGCGTGCTTCACTTTATTTA 57.922 40.909 0.00 0.00 38.95 1.40
2778 2898 5.621197 TGCGTGCTTCACTTTATTTATGT 57.379 34.783 0.00 0.00 31.34 2.29
2786 2906 7.011950 TGCTTCACTTTATTTATGTATGGTCCG 59.988 37.037 0.00 0.00 0.00 4.79
2787 2907 7.519970 GCTTCACTTTATTTATGTATGGTCCGG 60.520 40.741 0.00 0.00 0.00 5.14
2796 2916 1.092348 GTATGGTCCGGCAAAGAACC 58.908 55.000 0.00 0.00 0.00 3.62
2996 3122 4.339247 GGCCTGCATATGTAAGAATTGTGT 59.661 41.667 4.29 0.00 0.00 3.72
3002 3131 8.785329 TGCATATGTAAGAATTGTGTGTCTAA 57.215 30.769 4.29 0.00 0.00 2.10
3038 3167 5.645497 GCTGAATCAGTAAGGTTCTGACATT 59.355 40.000 12.29 0.00 43.32 2.71
3039 3168 6.183360 GCTGAATCAGTAAGGTTCTGACATTC 60.183 42.308 12.29 0.00 43.32 2.67
3049 3181 3.189287 GGTTCTGACATTCATCACACACC 59.811 47.826 0.00 0.00 0.00 4.16
3088 3220 2.552599 TTGCAGTCCGATTTACCACA 57.447 45.000 0.00 0.00 0.00 4.17
3198 3330 4.207165 AGAGAGTTCAGTATCTGAGGCTC 58.793 47.826 7.79 7.79 41.75 4.70
3212 3344 2.694628 TGAGGCTCATTGCAAACTGTTT 59.305 40.909 14.43 0.00 45.15 2.83
3222 3354 7.584108 TCATTGCAAACTGTTTATGTGTAGAG 58.416 34.615 1.71 0.00 0.00 2.43
3281 3413 1.002900 CTAACACCGTGCAACCAAGTG 60.003 52.381 0.00 0.00 35.00 3.16
3351 3492 1.731709 GATTTCCAAAATTGCCGTGGC 59.268 47.619 3.30 3.30 42.35 5.01
3361 3502 1.092921 TTGCCGTGGCCGCTAATTAG 61.093 55.000 15.69 8.20 41.09 1.73
3363 3504 1.496403 GCCGTGGCCGCTAATTAGAC 61.496 60.000 16.85 6.74 34.56 2.59
3402 3543 3.244976 GCTGAATGTATTGTTGCCACAC 58.755 45.455 0.00 0.00 30.32 3.82
3432 3573 4.251268 TGACAATTCAGCTCAGATGACTG 58.749 43.478 0.00 0.00 44.66 3.51
3434 3575 4.252073 ACAATTCAGCTCAGATGACTGAC 58.748 43.478 7.96 0.00 46.55 3.51
3440 3581 2.754552 AGCTCAGATGACTGACTGACTC 59.245 50.000 0.00 0.00 46.55 3.36
3445 3586 2.168106 AGATGACTGACTGACTCATGCC 59.832 50.000 0.00 0.00 0.00 4.40
3468 3609 4.218200 CGTGATGCTAGATCTCTCCTTGAT 59.782 45.833 0.00 0.00 0.00 2.57
3474 3636 3.593442 AGATCTCTCCTTGATCCTCGT 57.407 47.619 0.00 0.00 40.69 4.18
3484 3646 0.108186 TGATCCTCGTGTCCATGTGC 60.108 55.000 0.00 0.00 0.00 4.57
3503 3665 4.051237 GTGCCACTCACCAATTTTCTTTC 58.949 43.478 0.00 0.00 39.79 2.62
3527 3689 7.279750 CCATTTGATGGTTATGATGACATCA 57.720 36.000 20.09 20.09 45.53 3.07
3582 3744 8.302438 TGCAATTGTATAACATGACATGAAACA 58.698 29.630 22.19 15.17 0.00 2.83
3605 3767 7.984391 ACAATTTTATTCAGCGTATCATGACA 58.016 30.769 0.00 0.00 0.00 3.58
3680 3842 7.775093 TGAAGATACTCCTTGTTCCATAATTGG 59.225 37.037 0.00 0.00 45.15 3.16
3743 3906 7.885297 TGAAAGTCACTTTCCCATAATTGAAG 58.115 34.615 24.57 0.00 46.36 3.02
3790 3953 8.940397 AGAATGAAAAACAGTATATATGGGGG 57.060 34.615 0.00 0.00 0.00 5.40
3791 3954 8.511126 AGAATGAAAAACAGTATATATGGGGGT 58.489 33.333 0.00 0.00 0.00 4.95
3794 3957 5.594199 AAAACAGTATATATGGGGGTCCC 57.406 43.478 0.00 0.00 45.71 4.46
3867 4036 3.698040 CACAGGCCATCAGCTTTCTTTAT 59.302 43.478 5.01 0.00 43.05 1.40
3958 6844 2.501723 GGGCATGACCTCTCAACTCTTA 59.498 50.000 11.56 0.00 39.10 2.10
3961 6847 5.189180 GGCATGACCTCTCAACTCTTAATT 58.811 41.667 0.00 0.00 34.51 1.40
3963 6849 5.065731 GCATGACCTCTCAACTCTTAATTGG 59.934 44.000 0.00 0.00 0.00 3.16
3964 6850 6.409704 CATGACCTCTCAACTCTTAATTGGA 58.590 40.000 0.00 0.00 0.00 3.53
3966 6852 6.231211 TGACCTCTCAACTCTTAATTGGAAC 58.769 40.000 0.00 0.00 0.00 3.62
4026 6913 9.753674 AGATACTCCTTGTTCCATAATTGAAAA 57.246 29.630 0.00 0.00 0.00 2.29
4108 7001 6.944862 AGACTGAAAGATCATATTTATGGGGC 59.055 38.462 0.00 0.00 37.43 5.80
4111 7004 5.076318 TGAAAGATCATATTTATGGGGCCCT 59.924 40.000 25.93 12.02 34.50 5.19
4117 7010 1.076438 ATTTATGGGGCCCTAGGAGC 58.924 55.000 25.93 12.06 0.00 4.70
4187 7080 6.402766 CGCAAGCCATTGAATTGAATTGAATT 60.403 34.615 2.26 2.26 38.83 2.17
4188 7081 6.745450 GCAAGCCATTGAATTGAATTGAATTG 59.255 34.615 7.65 0.00 38.83 2.32
4189 7082 7.361371 GCAAGCCATTGAATTGAATTGAATTGA 60.361 33.333 7.65 0.00 38.83 2.57
4190 7083 8.508062 CAAGCCATTGAATTGAATTGAATTGAA 58.492 29.630 7.65 6.18 38.83 2.69
4191 7084 8.801882 AGCCATTGAATTGAATTGAATTGAAT 57.198 26.923 7.65 8.27 31.67 2.57
4192 7085 8.673711 AGCCATTGAATTGAATTGAATTGAATG 58.326 29.630 24.79 24.79 42.16 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.218959 TCAAGGACTCATGGGAAGATATCA 58.781 41.667 0.00 0.00 0.00 2.15
2 3 5.815233 TCAAGGACTCATGGGAAGATATC 57.185 43.478 0.00 0.00 0.00 1.63
3 4 6.090186 AGATCAAGGACTCATGGGAAGATAT 58.910 40.000 0.00 0.00 0.00 1.63
5 6 4.305524 AGATCAAGGACTCATGGGAAGAT 58.694 43.478 0.00 0.00 0.00 2.40
6 7 3.729108 AGATCAAGGACTCATGGGAAGA 58.271 45.455 0.00 0.00 0.00 2.87
7 8 4.080695 TCAAGATCAAGGACTCATGGGAAG 60.081 45.833 0.00 0.00 0.00 3.46
8 9 3.845992 TCAAGATCAAGGACTCATGGGAA 59.154 43.478 0.00 0.00 0.00 3.97
9 10 3.453868 TCAAGATCAAGGACTCATGGGA 58.546 45.455 0.00 0.00 0.00 4.37
10 11 3.920231 TCAAGATCAAGGACTCATGGG 57.080 47.619 0.00 0.00 0.00 4.00
11 12 4.056740 CGATCAAGATCAAGGACTCATGG 58.943 47.826 10.39 0.00 37.69 3.66
12 13 4.691175 ACGATCAAGATCAAGGACTCATG 58.309 43.478 10.39 0.00 37.69 3.07
13 14 5.360999 TGTACGATCAAGATCAAGGACTCAT 59.639 40.000 10.39 0.00 37.69 2.90
14 15 4.705023 TGTACGATCAAGATCAAGGACTCA 59.295 41.667 10.39 0.00 37.69 3.41
15 16 5.038033 GTGTACGATCAAGATCAAGGACTC 58.962 45.833 10.39 0.26 37.69 3.36
16 17 4.462834 TGTGTACGATCAAGATCAAGGACT 59.537 41.667 10.39 0.00 37.69 3.85
17 18 4.744570 TGTGTACGATCAAGATCAAGGAC 58.255 43.478 10.39 2.84 37.69 3.85
18 19 5.598416 ATGTGTACGATCAAGATCAAGGA 57.402 39.130 10.39 0.00 37.69 3.36
19 20 6.481134 CAAATGTGTACGATCAAGATCAAGG 58.519 40.000 10.39 0.00 37.69 3.61
20 21 5.961843 GCAAATGTGTACGATCAAGATCAAG 59.038 40.000 10.39 0.00 37.69 3.02
21 22 5.445806 CGCAAATGTGTACGATCAAGATCAA 60.446 40.000 10.39 0.00 37.69 2.57
22 23 4.032786 CGCAAATGTGTACGATCAAGATCA 59.967 41.667 10.39 0.00 37.69 2.92
23 24 4.032900 ACGCAAATGTGTACGATCAAGATC 59.967 41.667 0.00 0.00 36.94 2.75
24 25 3.932710 ACGCAAATGTGTACGATCAAGAT 59.067 39.130 0.00 0.00 36.94 2.40
25 26 3.122780 CACGCAAATGTGTACGATCAAGA 59.877 43.478 0.00 0.00 36.94 3.02
26 27 3.407252 CACGCAAATGTGTACGATCAAG 58.593 45.455 0.00 0.00 36.94 3.02
27 28 3.447752 CACGCAAATGTGTACGATCAA 57.552 42.857 0.00 0.00 36.94 2.57
36 37 5.868257 ACACTAATCATACACGCAAATGTG 58.132 37.500 0.00 0.00 45.41 3.21
37 38 6.237728 CGTACACTAATCATACACGCAAATGT 60.238 38.462 0.00 0.00 36.56 2.71
38 39 6.120157 CGTACACTAATCATACACGCAAATG 58.880 40.000 0.00 0.00 0.00 2.32
39 40 5.233476 CCGTACACTAATCATACACGCAAAT 59.767 40.000 0.00 0.00 0.00 2.32
40 41 4.563580 CCGTACACTAATCATACACGCAAA 59.436 41.667 0.00 0.00 0.00 3.68
41 42 4.106909 CCGTACACTAATCATACACGCAA 58.893 43.478 0.00 0.00 0.00 4.85
42 43 3.129113 ACCGTACACTAATCATACACGCA 59.871 43.478 0.00 0.00 0.00 5.24
43 44 3.699067 ACCGTACACTAATCATACACGC 58.301 45.455 0.00 0.00 0.00 5.34
44 45 4.912214 TGACCGTACACTAATCATACACG 58.088 43.478 0.00 0.00 0.00 4.49
45 46 7.305820 CGATTTGACCGTACACTAATCATACAC 60.306 40.741 13.93 0.00 32.03 2.90
46 47 6.693978 CGATTTGACCGTACACTAATCATACA 59.306 38.462 13.93 0.00 32.03 2.29
47 48 6.143438 CCGATTTGACCGTACACTAATCATAC 59.857 42.308 13.93 0.00 32.03 2.39
48 49 6.210796 CCGATTTGACCGTACACTAATCATA 58.789 40.000 13.93 0.23 32.03 2.15
49 50 5.047847 CCGATTTGACCGTACACTAATCAT 58.952 41.667 13.93 0.00 32.03 2.45
50 51 4.426416 CCGATTTGACCGTACACTAATCA 58.574 43.478 13.93 0.90 32.03 2.57
51 52 3.800506 CCCGATTTGACCGTACACTAATC 59.199 47.826 0.00 2.04 0.00 1.75
52 53 3.431207 CCCCGATTTGACCGTACACTAAT 60.431 47.826 0.00 0.00 0.00 1.73
53 54 2.094078 CCCCGATTTGACCGTACACTAA 60.094 50.000 0.00 0.00 0.00 2.24
54 55 1.477700 CCCCGATTTGACCGTACACTA 59.522 52.381 0.00 0.00 0.00 2.74
55 56 0.248289 CCCCGATTTGACCGTACACT 59.752 55.000 0.00 0.00 0.00 3.55
56 57 0.741927 CCCCCGATTTGACCGTACAC 60.742 60.000 0.00 0.00 0.00 2.90
57 58 1.597989 CCCCCGATTTGACCGTACA 59.402 57.895 0.00 0.00 0.00 2.90
58 59 1.816679 GCCCCCGATTTGACCGTAC 60.817 63.158 0.00 0.00 0.00 3.67
59 60 2.585698 GCCCCCGATTTGACCGTA 59.414 61.111 0.00 0.00 0.00 4.02
60 61 4.770874 CGCCCCCGATTTGACCGT 62.771 66.667 0.00 0.00 36.29 4.83
61 62 4.770874 ACGCCCCCGATTTGACCG 62.771 66.667 0.00 0.00 38.29 4.79
62 63 2.822701 GACGCCCCCGATTTGACC 60.823 66.667 0.00 0.00 38.29 4.02
63 64 2.046700 TGACGCCCCCGATTTGAC 60.047 61.111 0.00 0.00 38.29 3.18
64 65 2.046700 GTGACGCCCCCGATTTGA 60.047 61.111 0.00 0.00 38.29 2.69
65 66 2.359354 TGTGACGCCCCCGATTTG 60.359 61.111 0.00 0.00 38.29 2.32
66 67 2.046314 CTGTGACGCCCCCGATTT 60.046 61.111 0.00 0.00 38.29 2.17
67 68 4.778143 GCTGTGACGCCCCCGATT 62.778 66.667 0.00 0.00 38.29 3.34
72 73 3.825160 TTGAGTGCTGTGACGCCCC 62.825 63.158 0.00 0.00 0.00 5.80
73 74 2.280797 TTGAGTGCTGTGACGCCC 60.281 61.111 0.00 0.00 0.00 6.13
74 75 0.671781 ATCTTGAGTGCTGTGACGCC 60.672 55.000 0.00 0.00 0.00 5.68
75 76 0.441533 CATCTTGAGTGCTGTGACGC 59.558 55.000 0.00 0.00 0.00 5.19
76 77 2.070262 TCATCTTGAGTGCTGTGACG 57.930 50.000 0.00 0.00 0.00 4.35
77 78 4.060900 TCTTTCATCTTGAGTGCTGTGAC 58.939 43.478 0.00 0.00 0.00 3.67
78 79 4.341366 TCTTTCATCTTGAGTGCTGTGA 57.659 40.909 0.00 0.00 0.00 3.58
79 80 4.274214 TGTTCTTTCATCTTGAGTGCTGTG 59.726 41.667 0.00 0.00 0.00 3.66
80 81 4.454678 TGTTCTTTCATCTTGAGTGCTGT 58.545 39.130 0.00 0.00 0.00 4.40
81 82 5.428496 TTGTTCTTTCATCTTGAGTGCTG 57.572 39.130 0.00 0.00 0.00 4.41
82 83 5.564259 GCATTGTTCTTTCATCTTGAGTGCT 60.564 40.000 0.00 0.00 0.00 4.40
83 84 4.620184 GCATTGTTCTTTCATCTTGAGTGC 59.380 41.667 0.00 0.00 0.00 4.40
84 85 5.048224 AGGCATTGTTCTTTCATCTTGAGTG 60.048 40.000 0.00 0.00 0.00 3.51
85 86 5.075493 AGGCATTGTTCTTTCATCTTGAGT 58.925 37.500 0.00 0.00 0.00 3.41
86 87 5.640189 AGGCATTGTTCTTTCATCTTGAG 57.360 39.130 0.00 0.00 0.00 3.02
87 88 7.707624 ATAAGGCATTGTTCTTTCATCTTGA 57.292 32.000 0.00 0.00 0.00 3.02
88 89 8.030692 TGAATAAGGCATTGTTCTTTCATCTTG 58.969 33.333 19.10 0.00 37.41 3.02
89 90 8.125978 TGAATAAGGCATTGTTCTTTCATCTT 57.874 30.769 19.10 0.00 37.41 2.40
98 99 5.127682 ACCTCCAATGAATAAGGCATTGTTC 59.872 40.000 12.91 12.91 46.91 3.18
127 128 3.381272 CCAGGTTTCTTGAGTTGCTTGAA 59.619 43.478 0.00 0.00 0.00 2.69
133 134 5.767168 AGATTCTTCCAGGTTTCTTGAGTTG 59.233 40.000 0.00 0.00 0.00 3.16
139 140 7.560796 TCTTCTAGATTCTTCCAGGTTTCTT 57.439 36.000 0.00 0.00 0.00 2.52
144 145 7.401493 TCAAAGATCTTCTAGATTCTTCCAGGT 59.599 37.037 8.78 0.00 34.53 4.00
148 149 9.260002 GACATCAAAGATCTTCTAGATTCTTCC 57.740 37.037 8.78 0.00 34.53 3.46
150 151 8.690884 TCGACATCAAAGATCTTCTAGATTCTT 58.309 33.333 8.78 0.39 34.53 2.52
156 157 7.096271 CGGAAATCGACATCAAAGATCTTCTAG 60.096 40.741 8.78 2.39 42.43 2.43
179 180 3.640029 GTCCCTAAGGTATTGTCATCGGA 59.360 47.826 0.00 0.00 0.00 4.55
190 191 3.555117 AGGTGTCTTGTCCCTAAGGTA 57.445 47.619 0.00 0.00 0.00 3.08
206 207 2.416027 CGTGTGAGACTGGTCATAGGTG 60.416 54.545 3.51 0.00 0.00 4.00
207 208 1.819288 CGTGTGAGACTGGTCATAGGT 59.181 52.381 3.51 0.00 0.00 3.08
211 212 1.686587 TCAACGTGTGAGACTGGTCAT 59.313 47.619 3.51 0.00 0.00 3.06
220 239 1.070821 ATCGTGCATCAACGTGTGAG 58.929 50.000 0.00 0.00 43.96 3.51
226 245 4.618912 CCTTATCTCTATCGTGCATCAACG 59.381 45.833 0.00 0.00 44.92 4.10
229 248 5.770162 TCTTCCTTATCTCTATCGTGCATCA 59.230 40.000 0.00 0.00 0.00 3.07
237 256 6.013812 AGCCCATTGTCTTCCTTATCTCTATC 60.014 42.308 0.00 0.00 0.00 2.08
245 264 4.380843 TTGAAGCCCATTGTCTTCCTTA 57.619 40.909 11.16 0.00 38.26 2.69
273 292 0.394216 AATGCATGTAGCTCCGCCAA 60.394 50.000 0.00 0.00 45.94 4.52
304 324 4.048470 GGGCTGGGAGGGGACAAC 62.048 72.222 0.00 0.00 0.00 3.32
316 336 3.962530 TTAGGGTGGGAGGGGGCTG 62.963 68.421 0.00 0.00 0.00 4.85
317 337 2.524045 ATTTAGGGTGGGAGGGGGCT 62.524 60.000 0.00 0.00 0.00 5.19
318 338 0.699922 TATTTAGGGTGGGAGGGGGC 60.700 60.000 0.00 0.00 0.00 5.80
319 339 2.149521 ATATTTAGGGTGGGAGGGGG 57.850 55.000 0.00 0.00 0.00 5.40
320 340 4.668335 ACTAAATATTTAGGGTGGGAGGGG 59.332 45.833 29.82 9.63 43.38 4.79
321 341 5.371472 TCACTAAATATTTAGGGTGGGAGGG 59.629 44.000 28.46 10.75 43.13 4.30
322 342 6.509523 TCACTAAATATTTAGGGTGGGAGG 57.490 41.667 28.46 13.17 43.13 4.30
323 343 8.996651 ATTTCACTAAATATTTAGGGTGGGAG 57.003 34.615 28.46 11.65 43.13 4.30
360 380 1.436600 ATGACTGCACTCTTCAAGCG 58.563 50.000 0.00 0.00 0.00 4.68
365 385 1.200948 GCCCAAATGACTGCACTCTTC 59.799 52.381 0.00 0.00 0.00 2.87
384 404 3.756933 AAATATGCATCATTGGTGGGC 57.243 42.857 0.19 0.00 0.00 5.36
403 423 0.112412 GGGAGGTGGGCAAAGAGAAA 59.888 55.000 0.00 0.00 0.00 2.52
404 424 1.767692 GGGAGGTGGGCAAAGAGAA 59.232 57.895 0.00 0.00 0.00 2.87
405 425 2.231380 GGGGAGGTGGGCAAAGAGA 61.231 63.158 0.00 0.00 0.00 3.10
407 427 1.778383 AAGGGGAGGTGGGCAAAGA 60.778 57.895 0.00 0.00 0.00 2.52
412 432 3.946126 GAAGCAAGGGGAGGTGGGC 62.946 68.421 0.00 0.00 0.00 5.36
413 433 2.203549 GAGAAGCAAGGGGAGGTGGG 62.204 65.000 0.00 0.00 0.00 4.61
414 434 1.204113 AGAGAAGCAAGGGGAGGTGG 61.204 60.000 0.00 0.00 0.00 4.61
415 435 0.251634 GAGAGAAGCAAGGGGAGGTG 59.748 60.000 0.00 0.00 0.00 4.00
416 436 0.118144 AGAGAGAAGCAAGGGGAGGT 59.882 55.000 0.00 0.00 0.00 3.85
417 437 1.284313 AAGAGAGAAGCAAGGGGAGG 58.716 55.000 0.00 0.00 0.00 4.30
418 438 2.158971 GCTAAGAGAGAAGCAAGGGGAG 60.159 54.545 0.00 0.00 38.63 4.30
419 439 1.834263 GCTAAGAGAGAAGCAAGGGGA 59.166 52.381 0.00 0.00 38.63 4.81
420 440 1.836802 AGCTAAGAGAGAAGCAAGGGG 59.163 52.381 0.00 0.00 41.32 4.79
421 441 2.158971 GGAGCTAAGAGAGAAGCAAGGG 60.159 54.545 0.00 0.00 41.32 3.95
422 442 2.499289 TGGAGCTAAGAGAGAAGCAAGG 59.501 50.000 0.00 0.00 41.32 3.61
423 443 3.520569 GTGGAGCTAAGAGAGAAGCAAG 58.479 50.000 0.00 0.00 41.32 4.01
424 444 2.234908 GGTGGAGCTAAGAGAGAAGCAA 59.765 50.000 0.00 0.00 41.32 3.91
425 445 1.827969 GGTGGAGCTAAGAGAGAAGCA 59.172 52.381 0.00 0.00 41.32 3.91
426 446 1.827969 TGGTGGAGCTAAGAGAGAAGC 59.172 52.381 0.00 0.00 39.08 3.86
427 447 3.243367 CGATGGTGGAGCTAAGAGAGAAG 60.243 52.174 0.00 0.00 0.00 2.85
443 463 1.675641 GTTGGCCTTCAGCGATGGT 60.676 57.895 3.32 0.00 45.17 3.55
444 464 1.372087 GAGTTGGCCTTCAGCGATGG 61.372 60.000 3.32 6.24 45.17 3.51
453 473 0.108585 TCTTTGCTCGAGTTGGCCTT 59.891 50.000 15.13 0.00 0.00 4.35
454 474 0.603975 GTCTTTGCTCGAGTTGGCCT 60.604 55.000 15.13 0.00 0.00 5.19
455 475 1.869690 GTCTTTGCTCGAGTTGGCC 59.130 57.895 15.13 0.00 0.00 5.36
456 476 1.493311 CGTCTTTGCTCGAGTTGGC 59.507 57.895 15.13 0.06 0.00 4.52
457 477 1.493311 GCGTCTTTGCTCGAGTTGG 59.507 57.895 15.13 2.60 0.00 3.77
458 478 0.946221 AGGCGTCTTTGCTCGAGTTG 60.946 55.000 15.13 2.23 34.52 3.16
459 479 0.601558 TAGGCGTCTTTGCTCGAGTT 59.398 50.000 15.13 0.00 34.52 3.01
468 488 2.717639 ATTGATGGCTAGGCGTCTTT 57.282 45.000 31.57 19.59 0.00 2.52
473 493 3.681897 GTCTATGAATTGATGGCTAGGCG 59.318 47.826 12.19 0.00 0.00 5.52
475 495 4.042062 TGGGTCTATGAATTGATGGCTAGG 59.958 45.833 0.00 0.00 0.00 3.02
476 496 5.233083 TGGGTCTATGAATTGATGGCTAG 57.767 43.478 0.00 0.00 0.00 3.42
516 536 3.572255 GTGGCATACTTGTCCCTCAAAAA 59.428 43.478 0.00 0.00 35.48 1.94
517 537 3.153919 GTGGCATACTTGTCCCTCAAAA 58.846 45.455 0.00 0.00 35.48 2.44
518 538 2.554344 GGTGGCATACTTGTCCCTCAAA 60.554 50.000 0.00 0.00 35.48 2.69
519 539 1.004277 GGTGGCATACTTGTCCCTCAA 59.996 52.381 0.00 0.00 34.61 3.02
520 540 0.618458 GGTGGCATACTTGTCCCTCA 59.382 55.000 0.00 0.00 0.00 3.86
521 541 0.912486 AGGTGGCATACTTGTCCCTC 59.088 55.000 0.00 0.00 0.00 4.30
522 542 1.838077 GTAGGTGGCATACTTGTCCCT 59.162 52.381 0.00 0.00 34.06 4.20
523 543 1.557832 TGTAGGTGGCATACTTGTCCC 59.442 52.381 0.00 0.00 0.00 4.46
524 544 3.206150 CATGTAGGTGGCATACTTGTCC 58.794 50.000 0.00 0.00 0.00 4.02
525 545 3.873910 ACATGTAGGTGGCATACTTGTC 58.126 45.455 11.76 1.59 37.07 3.18
526 546 4.301072 AACATGTAGGTGGCATACTTGT 57.699 40.909 11.76 11.76 40.95 3.16
527 547 4.699735 TGAAACATGTAGGTGGCATACTTG 59.300 41.667 0.00 10.78 35.51 3.16
528 548 4.917385 TGAAACATGTAGGTGGCATACTT 58.083 39.130 0.00 0.00 0.00 2.24
529 549 4.568072 TGAAACATGTAGGTGGCATACT 57.432 40.909 0.00 0.00 0.00 2.12
530 550 4.700213 AGTTGAAACATGTAGGTGGCATAC 59.300 41.667 0.00 0.00 0.00 2.39
531 551 4.917385 AGTTGAAACATGTAGGTGGCATA 58.083 39.130 0.00 0.00 0.00 3.14
532 552 3.758554 GAGTTGAAACATGTAGGTGGCAT 59.241 43.478 0.00 0.00 0.00 4.40
533 553 3.146066 GAGTTGAAACATGTAGGTGGCA 58.854 45.455 0.00 0.00 0.00 4.92
579 599 4.295051 TGCTCATTGACGTTTTAAAAGGC 58.705 39.130 18.10 12.29 0.00 4.35
582 602 7.202016 AGAGATGCTCATTGACGTTTTAAAA 57.798 32.000 0.00 0.00 32.06 1.52
583 603 6.801539 AGAGATGCTCATTGACGTTTTAAA 57.198 33.333 0.00 0.00 32.06 1.52
616 639 2.369532 ACATGAAGCCATTGTTGCCTTT 59.630 40.909 0.00 0.00 0.00 3.11
634 657 8.552296 AGGAAGAATAAAGAGGAACATACACAT 58.448 33.333 0.00 0.00 0.00 3.21
696 719 4.221342 CGATCACAAGTTCACATGGTTTG 58.779 43.478 0.00 0.00 0.00 2.93
737 765 1.901654 ATTTACACCCCGTGGCGCTA 61.902 55.000 7.64 0.00 37.94 4.26
739 767 2.748647 ATTTACACCCCGTGGCGC 60.749 61.111 0.00 0.00 37.94 6.53
741 769 1.249407 TTTCATTTACACCCCGTGGC 58.751 50.000 0.00 0.00 37.94 5.01
743 771 4.775058 TTCATTTCATTTACACCCCGTG 57.225 40.909 0.00 0.00 39.75 4.94
767 795 6.803807 GCGCATCTTTTTGAGTTCTTCTATTT 59.196 34.615 0.30 0.00 0.00 1.40
815 843 8.752254 CACATGGTTACATTAACTATCTACACG 58.248 37.037 0.00 0.00 37.71 4.49
912 942 9.981114 TCTTTTCTTTCTTCACTTCTTTGTTTT 57.019 25.926 0.00 0.00 0.00 2.43
918 948 9.631452 CACTTTTCTTTTCTTTCTTCACTTCTT 57.369 29.630 0.00 0.00 0.00 2.52
926 956 8.078060 TCATTCCCACTTTTCTTTTCTTTCTT 57.922 30.769 0.00 0.00 0.00 2.52
928 958 7.763985 TGTTCATTCCCACTTTTCTTTTCTTTC 59.236 33.333 0.00 0.00 0.00 2.62
929 959 7.619965 TGTTCATTCCCACTTTTCTTTTCTTT 58.380 30.769 0.00 0.00 0.00 2.52
931 961 6.607198 TCTGTTCATTCCCACTTTTCTTTTCT 59.393 34.615 0.00 0.00 0.00 2.52
933 963 6.790232 TCTGTTCATTCCCACTTTTCTTTT 57.210 33.333 0.00 0.00 0.00 2.27
964 1008 0.604511 GACGGCCCCTTTCTTTTCGA 60.605 55.000 0.00 0.00 0.00 3.71
991 1058 2.349672 CCATTTCCATGGTGGCGCA 61.350 57.895 12.58 0.00 44.81 6.09
1156 1226 3.599285 AAGGAAATCGCGGACGGCA 62.599 57.895 6.13 0.00 43.84 5.69
1165 1235 0.931005 GAGCCGCTACAAGGAAATCG 59.069 55.000 0.00 0.00 0.00 3.34
1220 1290 0.665369 GGAAGCGTCCGTCGAAGAAA 60.665 55.000 1.94 0.00 42.86 2.52
1260 1330 3.753070 GATCGACCGCCGTCACCTC 62.753 68.421 6.03 0.00 39.11 3.85
1261 1331 3.823330 GATCGACCGCCGTCACCT 61.823 66.667 6.03 0.00 39.11 4.00
1262 1332 3.753070 GAGATCGACCGCCGTCACC 62.753 68.421 6.03 0.00 39.11 4.02
1263 1333 2.278013 GAGATCGACCGCCGTCAC 60.278 66.667 6.03 0.00 39.11 3.67
1264 1334 3.515286 GGAGATCGACCGCCGTCA 61.515 66.667 6.03 0.00 39.11 4.35
1265 1335 4.267503 GGGAGATCGACCGCCGTC 62.268 72.222 0.00 0.00 39.75 4.79
1288 1358 7.013846 CCCAACCAAAACTAGAAATTGTGTCTA 59.986 37.037 0.00 0.00 0.00 2.59
1320 1390 5.207768 CACGAACATGTCAAGAAGGAAAAG 58.792 41.667 0.00 0.00 0.00 2.27
1325 1395 1.197721 GCCACGAACATGTCAAGAAGG 59.802 52.381 0.00 0.00 0.00 3.46
1330 1400 0.107643 TCCTGCCACGAACATGTCAA 59.892 50.000 0.00 0.00 0.00 3.18
1506 1579 1.951923 AATGATGCTCCCCCATGGCA 61.952 55.000 6.09 0.25 40.32 4.92
1507 1580 0.112995 TAATGATGCTCCCCCATGGC 59.887 55.000 6.09 0.00 0.00 4.40
1508 1581 1.548582 GGTAATGATGCTCCCCCATGG 60.549 57.143 4.14 4.14 0.00 3.66
1509 1582 1.426598 AGGTAATGATGCTCCCCCATG 59.573 52.381 0.00 0.00 0.00 3.66
1510 1583 1.838611 AGGTAATGATGCTCCCCCAT 58.161 50.000 0.00 0.00 0.00 4.00
1511 1584 1.494721 GAAGGTAATGATGCTCCCCCA 59.505 52.381 0.00 0.00 0.00 4.96
1541 1616 6.944290 TCTCATGGATCTGAAACAGAAAACAT 59.056 34.615 5.57 7.64 44.04 2.71
1552 1627 2.371179 GGCCTCATCTCATGGATCTGAA 59.629 50.000 0.00 0.00 31.27 3.02
1664 1739 3.988379 TGAAAGAGAACAATGCACCAC 57.012 42.857 0.00 0.00 0.00 4.16
1688 1763 1.837439 AGTCCGCATAATCAGGAACCA 59.163 47.619 0.00 0.00 35.60 3.67
1709 1784 2.286772 CGGCAGTACAACAAACACCTTC 60.287 50.000 0.00 0.00 0.00 3.46
1819 1894 2.418628 ACAGACCACTCAACAAACAACG 59.581 45.455 0.00 0.00 0.00 4.10
1827 1902 3.056749 CCACTACCTACAGACCACTCAAC 60.057 52.174 0.00 0.00 0.00 3.18
1894 1969 3.672808 ACCTGAACTGAATGAGAAGCTG 58.327 45.455 0.00 0.00 0.00 4.24
2018 2111 9.787435 TTCACCACAAACTAGTAATTCAGTATT 57.213 29.630 0.00 0.00 0.00 1.89
2019 2112 9.216117 GTTCACCACAAACTAGTAATTCAGTAT 57.784 33.333 0.00 0.00 0.00 2.12
2036 2131 5.559770 ACAAGATGATACATGTTCACCACA 58.440 37.500 2.30 0.00 40.71 4.17
2138 2255 5.877012 AGTGACTAATTACTGAACCTGCATG 59.123 40.000 0.00 0.00 0.00 4.06
2139 2256 6.054860 AGTGACTAATTACTGAACCTGCAT 57.945 37.500 0.00 0.00 0.00 3.96
2140 2257 5.483685 AGTGACTAATTACTGAACCTGCA 57.516 39.130 0.00 0.00 0.00 4.41
2196 2313 3.640407 GTGCACTGCTCAGGGGGA 61.640 66.667 10.32 0.00 30.94 4.81
2210 2327 8.182227 ACTAAAAACTTACAAAGAGTCAAGTGC 58.818 33.333 0.00 0.00 31.80 4.40
2235 2352 1.597663 GTACTGTGTCTGTGCACCAAC 59.402 52.381 15.69 12.83 38.52 3.77
2266 2384 3.822940 ACTTCGTGGGATTGGTAAACAA 58.177 40.909 0.00 0.00 44.54 2.83
2342 2461 3.623703 TGAGCAGCATATGTTCATGGTT 58.376 40.909 4.29 0.00 43.38 3.67
2464 2584 7.610305 TCCATACTTAAAAGATCACCCAACTTC 59.390 37.037 0.00 0.00 0.00 3.01
2548 2668 1.476833 GCAAGTGGACAGGGAAAGTCA 60.477 52.381 0.00 0.00 37.74 3.41
2593 2713 1.547372 GTCAGTGGGAATGCTGCATTT 59.453 47.619 26.87 12.36 33.90 2.32
2598 2718 2.439409 TCAATGTCAGTGGGAATGCTG 58.561 47.619 0.00 0.00 0.00 4.41
2626 2746 4.862902 ACATTGTCGCAGCTCTATCTAT 57.137 40.909 0.00 0.00 0.00 1.98
2636 2756 3.544048 CGTTAGGCATAACATTGTCGCAG 60.544 47.826 20.13 0.00 41.22 5.18
2639 2759 2.969055 GCGTTAGGCATAACATTGTCG 58.031 47.619 20.13 7.08 41.22 4.35
2652 2772 3.305398 AAAGAGACAGACAGCGTTAGG 57.695 47.619 0.00 0.00 0.00 2.69
2657 2777 3.296322 AGAGAAAAGAGACAGACAGCG 57.704 47.619 0.00 0.00 0.00 5.18
2658 2778 5.637387 CCTTAAGAGAAAAGAGACAGACAGC 59.363 44.000 3.36 0.00 0.00 4.40
2659 2779 6.754193 ACCTTAAGAGAAAAGAGACAGACAG 58.246 40.000 3.36 0.00 0.00 3.51
2756 2876 5.621197 ACATAAATAAAGTGAAGCACGCA 57.379 34.783 0.00 0.00 39.64 5.24
2775 2895 2.365582 GTTCTTTGCCGGACCATACAT 58.634 47.619 5.05 0.00 0.00 2.29
2778 2898 0.391927 CGGTTCTTTGCCGGACCATA 60.392 55.000 5.05 0.00 44.98 2.74
2786 2906 4.632538 ACTATTAATGCGGTTCTTTGCC 57.367 40.909 0.00 0.00 0.00 4.52
2787 2907 6.322491 AGAAACTATTAATGCGGTTCTTTGC 58.678 36.000 11.80 0.00 0.00 3.68
2796 2916 8.760569 ACAAAAACCAAAGAAACTATTAATGCG 58.239 29.630 0.00 0.00 0.00 4.73
2797 2917 9.862585 CACAAAAACCAAAGAAACTATTAATGC 57.137 29.630 0.00 0.00 0.00 3.56
2903 3029 7.016858 ACCACAGGGAACAATAAGTCTTAACTA 59.983 37.037 0.00 0.00 38.05 2.24
2916 3042 5.962031 AGTAGTATATGACCACAGGGAACAA 59.038 40.000 0.00 0.00 38.05 2.83
2996 3122 8.705075 TGATTCAGCAAATCAGTGCATTAGACA 61.705 37.037 9.70 0.00 46.96 3.41
3038 3167 7.765819 CAGATATTGTTAGAAGGTGTGTGATGA 59.234 37.037 0.00 0.00 0.00 2.92
3039 3168 7.466455 GCAGATATTGTTAGAAGGTGTGTGATG 60.466 40.741 0.00 0.00 0.00 3.07
3079 3211 7.994911 TCTTCTTCAGCATATGATGTGGTAAAT 59.005 33.333 19.78 0.00 37.89 1.40
3088 3220 7.908453 TCATGATCTCTTCTTCAGCATATGAT 58.092 34.615 6.97 0.00 37.89 2.45
3198 3330 6.306356 GCTCTACACATAAACAGTTTGCAATG 59.694 38.462 8.93 7.19 0.00 2.82
3212 3344 7.214381 ACACAACTACTTTTGCTCTACACATA 58.786 34.615 0.00 0.00 0.00 2.29
3222 3354 6.902224 AAATTTGGACACAACTACTTTTGC 57.098 33.333 0.00 0.00 36.06 3.68
3281 3413 5.355596 AGCTGCACTATCTTCTACACAATC 58.644 41.667 1.02 0.00 0.00 2.67
3376 3517 4.305769 GGCAACAATACATTCAGCAACAA 58.694 39.130 0.00 0.00 0.00 2.83
3377 3518 3.911868 GGCAACAATACATTCAGCAACA 58.088 40.909 0.00 0.00 0.00 3.33
3402 3543 4.176271 TGAGCTGAATTGTCATGTACTCG 58.824 43.478 0.00 0.00 31.85 4.18
3432 3573 1.284657 CATCACGGCATGAGTCAGTC 58.715 55.000 0.00 0.00 41.91 3.51
3434 3575 0.461516 AGCATCACGGCATGAGTCAG 60.462 55.000 0.00 0.00 41.91 3.51
3440 3581 2.029200 AGAGATCTAGCATCACGGCATG 60.029 50.000 0.00 0.00 35.83 4.06
3445 3586 3.567585 TCAAGGAGAGATCTAGCATCACG 59.432 47.826 0.00 0.00 0.00 4.35
3468 3609 2.213513 TGGCACATGGACACGAGGA 61.214 57.895 0.00 0.00 0.00 3.71
3474 3636 4.798433 GTGAGTGGCACATGGACA 57.202 55.556 21.41 8.67 46.91 4.02
3484 3646 4.935352 TGGAAAGAAAATTGGTGAGTGG 57.065 40.909 0.00 0.00 0.00 4.00
3503 3665 7.279750 TGATGTCATCATAACCATCAAATGG 57.720 36.000 11.62 4.41 44.64 3.16
3527 3689 5.136105 ACAAAAGCAGAATCCAAGAGTCTT 58.864 37.500 0.00 0.00 34.68 3.01
3582 3744 7.645340 GCTTGTCATGATACGCTGAATAAAATT 59.355 33.333 12.79 0.00 0.00 1.82
3605 3767 0.687354 AGAGTTGACGGGTCATGCTT 59.313 50.000 1.83 0.00 39.64 3.91
3680 3842 7.338957 AGGAACATCTTCAAATCATTCTCCTTC 59.661 37.037 0.00 0.00 0.00 3.46
3801 3970 2.579201 CACCCCTGCAGAGTACCG 59.421 66.667 17.39 0.00 0.00 4.02
3867 4036 5.782047 CACCAAGACAAAAGCCATCAAATA 58.218 37.500 0.00 0.00 0.00 1.40
3958 6844 7.123247 CCCATCAACTCTTTATCAGTTCCAATT 59.877 37.037 0.00 0.00 31.40 2.32
3961 6847 5.250543 TCCCATCAACTCTTTATCAGTTCCA 59.749 40.000 0.00 0.00 31.40 3.53
3963 6849 9.566432 AATATCCCATCAACTCTTTATCAGTTC 57.434 33.333 0.00 0.00 31.40 3.01
3964 6850 9.566432 GAATATCCCATCAACTCTTTATCAGTT 57.434 33.333 0.00 0.00 34.24 3.16
3966 6852 9.434420 GAGAATATCCCATCAACTCTTTATCAG 57.566 37.037 0.00 0.00 0.00 2.90
4026 6913 6.069147 AGGGAATATCTTCAGCTCTTTTTCCT 60.069 38.462 0.00 0.00 32.70 3.36
4086 6979 5.420104 GGGCCCCATAAATATGATCTTTCAG 59.580 44.000 12.23 0.00 35.75 3.02
4117 7010 1.380785 TACCCCTACCGAGCACCTG 60.381 63.158 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.