Multiple sequence alignment - TraesCS4A01G318200

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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 TraesCS4A01G318200 chr4A 100.000 2346 0 0 1 2346 607269018 607271363 0.000000e+00 4333
1 TraesCS4A01G318200 chr5D 86.588 1603 102 24 795 2346 565709653 565711193 0.000000e+00 1664
2 TraesCS4A01G318200 chr5D 84.353 556 66 8 76 612 565708905 565709458 2.070000e-145 525
3 TraesCS4A01G318200 chr5D 86.735 98 7 5 1653 1746 565716022 565716117 1.150000e-18 104
4 TraesCS4A01G318200 chr5D 88.750 80 9 0 1815 1894 565717172 565717251 5.340000e-17 99
5 TraesCS4A01G318200 chr5B 84.138 870 72 36 795 1637 707432960 707432130 0.000000e+00 782
6 TraesCS4A01G318200 chr5B 86.458 576 33 19 1326 1894 707430403 707429866 7.220000e-165 590
7 TraesCS4A01G318200 chr5B 91.371 394 12 4 1955 2346 707423330 707422957 9.610000e-144 520
8 TraesCS4A01G318200 chr5B 76.655 287 37 20 1108 1387 707388536 707388273 5.260000e-27 132
9 TraesCS4A01G318200 chr5B 90.789 76 5 2 1683 1757 707418200 707418126 1.480000e-17 100
10 TraesCS4A01G318200 chr7B 100.000 79 0 0 1 79 1143717 1143639 1.880000e-31 147
11 TraesCS4A01G318200 chr7B 98.734 79 1 0 1 79 78317767 78317689 8.740000e-30 141
12 TraesCS4A01G318200 chr5A 100.000 79 0 0 1 79 380624868 380624790 1.880000e-31 147
13 TraesCS4A01G318200 chr5A 98.734 79 1 0 1 79 708624265 708624343 8.740000e-30 141
14 TraesCS4A01G318200 chr3A 100.000 79 0 0 1 79 9075195 9075273 1.880000e-31 147
15 TraesCS4A01G318200 chr3A 100.000 78 0 0 1 78 569578964 569578887 6.760000e-31 145
16 TraesCS4A01G318200 chr7A 98.734 79 1 0 1 79 488496956 488497034 8.740000e-30 141
17 TraesCS4A01G318200 chr7A 98.734 79 1 0 1 79 621350486 621350408 8.740000e-30 141
18 TraesCS4A01G318200 chr1A 98.734 79 1 0 1 79 569143089 569143011 8.740000e-30 141


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 TraesCS4A01G318200 chr4A 607269018 607271363 2345 False 4333.0 4333 100.0000 1 2346 1 chr4A.!!$F1 2345
1 TraesCS4A01G318200 chr5D 565708905 565711193 2288 False 1094.5 1664 85.4705 76 2346 2 chr5D.!!$F1 2270
2 TraesCS4A01G318200 chr5B 707429866 707432960 3094 True 686.0 782 85.2980 795 1894 2 chr5B.!!$R4 1099

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
528 531 0.032912 AGGGCATGCAACATGGATCA 60.033 50.0 21.36 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1537 0.403271 AGGGTGTTTGCTCTGCTGAT 59.597 50.0 0.0 0.0 0.0 2.9 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
23 24 6.573664 CTCCATCAGTCTCCTAACTAGATG 57.426 45.833 0.00 0.00 36.11 2.90
24 25 6.267492 TCCATCAGTCTCCTAACTAGATGA 57.733 41.667 0.00 0.00 37.18 2.92
25 26 6.673583 TCCATCAGTCTCCTAACTAGATGAA 58.326 40.000 0.00 0.00 37.18 2.57
26 27 7.301420 TCCATCAGTCTCCTAACTAGATGAAT 58.699 38.462 0.00 0.00 37.18 2.57
27 28 7.450014 TCCATCAGTCTCCTAACTAGATGAATC 59.550 40.741 0.00 0.00 37.18 2.52
28 29 7.309744 CCATCAGTCTCCTAACTAGATGAATCC 60.310 44.444 0.00 0.00 37.18 3.01
29 30 6.673583 TCAGTCTCCTAACTAGATGAATCCA 58.326 40.000 0.00 0.00 0.00 3.41
30 31 7.301420 TCAGTCTCCTAACTAGATGAATCCAT 58.699 38.462 0.00 0.00 35.29 3.41
31 32 7.786943 TCAGTCTCCTAACTAGATGAATCCATT 59.213 37.037 0.00 0.00 32.09 3.16
32 33 8.087750 CAGTCTCCTAACTAGATGAATCCATTC 58.912 40.741 0.00 0.00 37.31 2.67
33 34 8.010105 AGTCTCCTAACTAGATGAATCCATTCT 58.990 37.037 0.00 0.00 37.67 2.40
34 35 8.646900 GTCTCCTAACTAGATGAATCCATTCTT 58.353 37.037 0.00 0.00 37.67 2.52
35 36 8.865090 TCTCCTAACTAGATGAATCCATTCTTC 58.135 37.037 0.00 6.97 39.74 2.87
36 37 7.967908 TCCTAACTAGATGAATCCATTCTTCC 58.032 38.462 0.00 0.00 40.08 3.46
37 38 7.016661 TCCTAACTAGATGAATCCATTCTTCCC 59.983 40.741 0.00 0.00 40.08 3.97
38 39 6.581388 AACTAGATGAATCCATTCTTCCCA 57.419 37.500 0.00 1.47 40.08 4.37
39 40 6.581388 ACTAGATGAATCCATTCTTCCCAA 57.419 37.500 0.00 0.00 40.08 4.12
40 41 6.360618 ACTAGATGAATCCATTCTTCCCAAC 58.639 40.000 0.00 0.00 40.08 3.77
41 42 4.202441 AGATGAATCCATTCTTCCCAACG 58.798 43.478 10.21 0.00 40.08 4.10
42 43 3.712016 TGAATCCATTCTTCCCAACGA 57.288 42.857 0.00 0.00 37.67 3.85
43 44 4.235079 TGAATCCATTCTTCCCAACGAT 57.765 40.909 0.00 0.00 37.67 3.73
44 45 4.599041 TGAATCCATTCTTCCCAACGATT 58.401 39.130 0.00 0.00 37.67 3.34
45 46 4.398988 TGAATCCATTCTTCCCAACGATTG 59.601 41.667 0.00 0.00 37.67 2.67
46 47 2.091541 TCCATTCTTCCCAACGATTGC 58.908 47.619 0.00 0.00 0.00 3.56
47 48 1.134946 CCATTCTTCCCAACGATTGCC 59.865 52.381 0.00 0.00 0.00 4.52
48 49 1.134946 CATTCTTCCCAACGATTGCCC 59.865 52.381 0.00 0.00 0.00 5.36
49 50 0.958382 TTCTTCCCAACGATTGCCCG 60.958 55.000 0.00 0.00 0.00 6.13
50 51 3.051392 CTTCCCAACGATTGCCCGC 62.051 63.158 0.00 0.00 0.00 6.13
51 52 3.561120 TTCCCAACGATTGCCCGCT 62.561 57.895 0.00 0.00 0.00 5.52
52 53 2.124901 CCCAACGATTGCCCGCTA 60.125 61.111 0.00 0.00 0.00 4.26
53 54 2.180204 CCCAACGATTGCCCGCTAG 61.180 63.158 0.00 0.00 0.00 3.42
54 55 2.709475 CAACGATTGCCCGCTAGC 59.291 61.111 4.06 4.06 0.00 3.42
55 56 2.890474 AACGATTGCCCGCTAGCG 60.890 61.111 29.93 29.93 36.73 4.26
56 57 3.365291 AACGATTGCCCGCTAGCGA 62.365 57.895 37.39 18.79 42.83 4.93
57 58 3.330853 CGATTGCCCGCTAGCGAC 61.331 66.667 37.39 27.40 42.83 5.19
58 59 2.967615 GATTGCCCGCTAGCGACC 60.968 66.667 37.39 25.79 42.83 4.79
59 60 4.891727 ATTGCCCGCTAGCGACCG 62.892 66.667 37.39 23.64 42.83 4.79
64 65 4.170062 CCGCTAGCGACCGTCGAA 62.170 66.667 37.39 10.33 43.74 3.71
65 66 2.202388 CGCTAGCGACCGTCGAAA 60.202 61.111 32.98 9.98 43.74 3.46
66 67 2.494591 CGCTAGCGACCGTCGAAAC 61.495 63.158 32.98 7.01 43.74 2.78
67 68 1.154073 GCTAGCGACCGTCGAAACT 60.154 57.895 24.78 13.96 43.74 2.66
68 69 1.403972 GCTAGCGACCGTCGAAACTG 61.404 60.000 24.78 9.69 43.74 3.16
69 70 0.167470 CTAGCGACCGTCGAAACTGA 59.833 55.000 24.78 1.51 43.74 3.41
70 71 0.592637 TAGCGACCGTCGAAACTGAA 59.407 50.000 24.78 0.00 43.74 3.02
71 72 0.038526 AGCGACCGTCGAAACTGAAT 60.039 50.000 24.78 0.00 43.74 2.57
72 73 1.200716 AGCGACCGTCGAAACTGAATA 59.799 47.619 24.78 0.00 43.74 1.75
73 74 2.159282 AGCGACCGTCGAAACTGAATAT 60.159 45.455 24.78 0.00 43.74 1.28
74 75 2.601763 GCGACCGTCGAAACTGAATATT 59.398 45.455 24.78 0.00 43.74 1.28
87 88 7.064134 CGAAACTGAATATTAAGGTGCACACTA 59.936 37.037 20.43 6.09 0.00 2.74
88 89 7.849804 AACTGAATATTAAGGTGCACACTAG 57.150 36.000 20.43 7.41 0.00 2.57
93 94 7.663905 TGAATATTAAGGTGCACACTAGTTTGT 59.336 33.333 20.43 0.00 0.00 2.83
102 103 2.548057 CACACTAGTTTGTGGCGTGATT 59.452 45.455 5.73 0.00 42.79 2.57
128 129 2.327081 TCTCACTTTCTACGTGACGC 57.673 50.000 4.25 0.00 36.54 5.19
138 139 0.579630 TACGTGACGCTGCAAAACTG 59.420 50.000 4.25 0.00 0.00 3.16
147 148 1.467374 GCTGCAAAACTGTTGTGACGT 60.467 47.619 14.77 0.00 0.00 4.34
148 149 2.862512 CTGCAAAACTGTTGTGACGTT 58.137 42.857 14.77 0.00 0.00 3.99
159 160 9.607285 AAACTGTTGTGACGTTATGAAATTATC 57.393 29.630 0.00 0.00 0.00 1.75
162 163 7.747888 TGTTGTGACGTTATGAAATTATCCTG 58.252 34.615 0.00 0.00 0.00 3.86
164 165 6.411376 TGTGACGTTATGAAATTATCCTGGT 58.589 36.000 0.00 0.00 0.00 4.00
186 187 0.626382 GGAGCCTCCCCTAAAAGCTT 59.374 55.000 0.00 0.00 32.97 3.74
193 194 3.255888 CCTCCCCTAAAAGCTTGAAACAC 59.744 47.826 0.00 0.00 0.00 3.32
195 196 2.030274 CCCCTAAAAGCTTGAAACACCG 60.030 50.000 0.00 0.00 0.00 4.94
202 203 2.919228 AGCTTGAAACACCGAGAAGTT 58.081 42.857 0.00 0.00 0.00 2.66
223 224 9.511144 GAAGTTTTGTCGGAGAAAATTCTTTAA 57.489 29.630 14.98 0.00 39.69 1.52
246 247 0.655208 TGTGTGCGTGATGTGTTGTC 59.345 50.000 0.00 0.00 0.00 3.18
247 248 0.041312 GTGTGCGTGATGTGTTGTCC 60.041 55.000 0.00 0.00 0.00 4.02
249 250 0.874390 GTGCGTGATGTGTTGTCCAT 59.126 50.000 0.00 0.00 0.00 3.41
260 261 3.282021 GTGTTGTCCATCATATGTGCCT 58.718 45.455 1.90 0.00 0.00 4.75
262 263 3.947196 TGTTGTCCATCATATGTGCCTTC 59.053 43.478 1.90 0.00 0.00 3.46
272 273 7.597369 CCATCATATGTGCCTTCAATTGTAATG 59.403 37.037 5.13 0.00 0.00 1.90
278 279 6.389091 TGTGCCTTCAATTGTAATGAATGAC 58.611 36.000 5.13 0.00 36.30 3.06
293 294 2.892784 ATGACCTAGTTAAGCTCGGC 57.107 50.000 0.00 0.00 33.65 5.54
294 295 0.822164 TGACCTAGTTAAGCTCGGCC 59.178 55.000 0.00 0.00 33.65 6.13
295 296 0.822164 GACCTAGTTAAGCTCGGCCA 59.178 55.000 2.24 0.00 33.65 5.36
299 300 0.822164 TAGTTAAGCTCGGCCAGGTC 59.178 55.000 2.24 0.00 30.18 3.85
300 301 0.905337 AGTTAAGCTCGGCCAGGTCT 60.905 55.000 2.24 0.00 30.18 3.85
313 316 1.407437 CCAGGTCTCAAGGCACCATAC 60.407 57.143 0.00 0.00 34.80 2.39
323 326 3.004752 AGGCACCATACCTTGATGAAC 57.995 47.619 0.00 0.00 31.87 3.18
328 331 4.035675 GCACCATACCTTGATGAACTAAGC 59.964 45.833 0.00 0.00 0.00 3.09
329 332 5.185454 CACCATACCTTGATGAACTAAGCA 58.815 41.667 0.00 0.00 0.00 3.91
334 337 5.904362 ACCTTGATGAACTAAGCAATTCC 57.096 39.130 0.00 0.00 0.00 3.01
376 379 3.684305 TGCTGGTGTCTTTGATGATTACG 59.316 43.478 0.00 0.00 0.00 3.18
382 385 5.360591 GTGTCTTTGATGATTACGGGATCT 58.639 41.667 0.00 0.00 0.00 2.75
387 390 5.862678 TTGATGATTACGGGATCTGTACA 57.137 39.130 0.00 0.00 0.00 2.90
392 395 1.688772 TACGGGATCTGTACAGCTCC 58.311 55.000 29.79 29.79 41.70 4.70
405 408 5.216622 TGTACAGCTCCTAGTGGGATTAAT 58.783 41.667 0.00 0.00 44.15 1.40
411 414 4.802248 GCTCCTAGTGGGATTAATCAGCTG 60.802 50.000 17.07 7.63 44.15 4.24
422 425 7.233962 TGGGATTAATCAGCTGAATAATGCAAT 59.766 33.333 36.44 21.06 38.90 3.56
423 426 8.742777 GGGATTAATCAGCTGAATAATGCAATA 58.257 33.333 36.44 15.58 38.90 1.90
468 471 1.542492 AAGGCAATCCAAGCACTCAG 58.458 50.000 0.00 0.00 33.74 3.35
479 482 3.220110 CAAGCACTCAGATAATGGCCAT 58.780 45.455 14.09 14.09 0.00 4.40
484 487 3.059097 ACTCAGATAATGGCCATCCCTT 58.941 45.455 21.08 6.62 0.00 3.95
487 490 4.473444 TCAGATAATGGCCATCCCTTTTC 58.527 43.478 21.08 8.87 33.41 2.29
488 491 3.575687 CAGATAATGGCCATCCCTTTTCC 59.424 47.826 21.08 2.91 33.41 3.13
492 495 1.643310 TGGCCATCCCTTTTCCTTTG 58.357 50.000 0.00 0.00 0.00 2.77
506 509 6.096282 CCTTTTCCTTTGTTGGACAGTTAGAA 59.904 38.462 0.00 0.00 35.58 2.10
511 514 5.239525 CCTTTGTTGGACAGTTAGAAAGAGG 59.760 44.000 0.00 0.00 0.00 3.69
525 528 0.040058 AAGAGGGCATGCAACATGGA 59.960 50.000 21.36 0.00 0.00 3.41
527 530 0.672342 GAGGGCATGCAACATGGATC 59.328 55.000 21.36 1.30 0.00 3.36
528 531 0.032912 AGGGCATGCAACATGGATCA 60.033 50.000 21.36 0.00 0.00 2.92
530 533 1.202486 GGGCATGCAACATGGATCAAG 60.202 52.381 21.36 0.00 0.00 3.02
559 574 2.925706 TAGCACAAGGGGCGGACA 60.926 61.111 0.00 0.00 36.08 4.02
564 579 2.676471 CAAGGGGCGGACAAAGGG 60.676 66.667 0.00 0.00 0.00 3.95
574 589 0.323451 GGACAAAGGGGGAGCGAAAT 60.323 55.000 0.00 0.00 0.00 2.17
575 590 0.811281 GACAAAGGGGGAGCGAAATG 59.189 55.000 0.00 0.00 0.00 2.32
624 648 2.918934 TCCATGAAAGGGAGATGGAACA 59.081 45.455 0.00 0.00 45.19 3.18
627 651 4.713321 CCATGAAAGGGAGATGGAACAAAT 59.287 41.667 0.00 0.00 43.46 2.32
628 652 5.893255 CCATGAAAGGGAGATGGAACAAATA 59.107 40.000 0.00 0.00 43.46 1.40
657 715 8.669243 GTGAAGGAACAAATAATGTAAGGAGAG 58.331 37.037 0.00 0.00 42.99 3.20
669 727 6.969993 ATGTAAGGAGAGATAGTGAAGGTC 57.030 41.667 0.00 0.00 0.00 3.85
670 728 5.202004 TGTAAGGAGAGATAGTGAAGGTCC 58.798 45.833 0.00 0.00 0.00 4.46
675 735 5.788014 AGGAGAGATAGTGAAGGTCCTTTTT 59.212 40.000 5.36 0.00 28.07 1.94
680 740 8.261522 AGAGATAGTGAAGGTCCTTTTTACATC 58.738 37.037 5.36 10.53 0.00 3.06
682 742 8.043710 AGATAGTGAAGGTCCTTTTTACATCAG 58.956 37.037 5.36 0.00 0.00 2.90
683 743 4.762251 AGTGAAGGTCCTTTTTACATCAGC 59.238 41.667 5.36 0.00 0.00 4.26
708 768 7.908601 GCGACCTTAATAAGTTTGTAAGAATGG 59.091 37.037 0.00 0.00 0.00 3.16
719 779 6.206829 AGTTTGTAAGAATGGACTTAGTTGCC 59.793 38.462 0.00 0.00 33.79 4.52
721 781 5.876357 TGTAAGAATGGACTTAGTTGCCTT 58.124 37.500 0.00 0.00 33.79 4.35
722 782 7.011499 TGTAAGAATGGACTTAGTTGCCTTA 57.989 36.000 0.00 0.00 33.79 2.69
761 823 3.087370 GGGACCTCAGTGGCTAATTTT 57.913 47.619 0.00 0.00 40.22 1.82
762 824 2.755103 GGGACCTCAGTGGCTAATTTTG 59.245 50.000 0.00 0.00 40.22 2.44
763 825 3.421844 GGACCTCAGTGGCTAATTTTGT 58.578 45.455 0.00 0.00 40.22 2.83
764 826 3.826729 GGACCTCAGTGGCTAATTTTGTT 59.173 43.478 0.00 0.00 40.22 2.83
765 827 4.280929 GGACCTCAGTGGCTAATTTTGTTT 59.719 41.667 0.00 0.00 40.22 2.83
766 828 5.221441 GGACCTCAGTGGCTAATTTTGTTTT 60.221 40.000 0.00 0.00 40.22 2.43
767 829 5.842907 ACCTCAGTGGCTAATTTTGTTTTC 58.157 37.500 0.00 0.00 40.22 2.29
768 830 5.362430 ACCTCAGTGGCTAATTTTGTTTTCA 59.638 36.000 0.00 0.00 40.22 2.69
769 831 5.922544 CCTCAGTGGCTAATTTTGTTTTCAG 59.077 40.000 0.00 0.00 0.00 3.02
770 832 5.841810 TCAGTGGCTAATTTTGTTTTCAGG 58.158 37.500 0.00 0.00 0.00 3.86
771 833 5.596361 TCAGTGGCTAATTTTGTTTTCAGGA 59.404 36.000 0.00 0.00 0.00 3.86
772 834 6.097554 TCAGTGGCTAATTTTGTTTTCAGGAA 59.902 34.615 0.00 0.00 0.00 3.36
773 835 6.760770 CAGTGGCTAATTTTGTTTTCAGGAAA 59.239 34.615 0.00 0.00 0.00 3.13
774 836 7.279758 CAGTGGCTAATTTTGTTTTCAGGAAAA 59.720 33.333 3.19 3.19 37.90 2.29
775 837 7.826744 AGTGGCTAATTTTGTTTTCAGGAAAAA 59.173 29.630 8.64 0.00 41.37 1.94
807 869 9.912634 GAGTGAAATATTGTTTTCAGGAATGAA 57.087 29.630 0.15 0.00 44.06 2.57
865 929 1.153168 CGTGGGCTCATAAGGTGGG 60.153 63.158 0.00 0.00 0.00 4.61
873 937 0.550914 TCATAAGGTGGGCCATGACC 59.449 55.000 10.70 6.51 37.19 4.02
874 938 0.258484 CATAAGGTGGGCCATGACCA 59.742 55.000 10.70 2.45 39.14 4.02
875 939 1.133388 CATAAGGTGGGCCATGACCAT 60.133 52.381 10.70 1.38 45.49 3.55
876 940 1.900254 TAAGGTGGGCCATGACCATA 58.100 50.000 10.70 0.22 45.49 2.74
877 941 0.258774 AAGGTGGGCCATGACCATAC 59.741 55.000 10.70 4.55 45.49 2.39
878 942 1.152756 GGTGGGCCATGACCATACC 60.153 63.158 10.70 9.61 45.49 2.73
879 943 1.612513 GTGGGCCATGACCATACCA 59.387 57.895 10.70 0.20 45.49 3.25
880 944 0.185901 GTGGGCCATGACCATACCAT 59.814 55.000 10.70 0.00 45.49 3.55
881 945 0.185658 TGGGCCATGACCATACCATG 59.814 55.000 0.00 0.00 34.69 3.66
891 955 1.305959 CATACCATGGTGGCCCACA 59.694 57.895 28.17 5.58 45.65 4.17
899 963 3.685435 GTGGCCCACACCAAGATG 58.315 61.111 9.55 0.00 44.49 2.90
925 989 4.382320 CGGCCCGGAAACCTCGAA 62.382 66.667 0.73 0.00 0.00 3.71
949 1013 1.687368 GCAGGCTTCCCATCATTTCCT 60.687 52.381 0.00 0.00 0.00 3.36
953 1017 2.092212 GGCTTCCCATCATTTCCTCTCA 60.092 50.000 0.00 0.00 0.00 3.27
954 1018 3.624777 GCTTCCCATCATTTCCTCTCAA 58.375 45.455 0.00 0.00 0.00 3.02
1104 1200 2.449518 TGCAGGTTCCACCCCTCA 60.450 61.111 0.00 0.00 39.75 3.86
1106 1202 0.548926 TGCAGGTTCCACCCCTCATA 60.549 55.000 0.00 0.00 39.75 2.15
1170 1266 1.202580 CGATCCCCACTCTTCCATCAC 60.203 57.143 0.00 0.00 0.00 3.06
1185 1281 2.332104 CATCACCAATCCGCTAGATCG 58.668 52.381 0.00 0.00 32.47 3.69
1192 1288 4.671569 CCGCTAGATCGGCCTGGC 62.672 72.222 11.05 11.05 43.18 4.85
1194 1290 3.606662 GCTAGATCGGCCTGGCGA 61.607 66.667 18.19 18.19 31.19 5.54
1195 1291 2.936912 GCTAGATCGGCCTGGCGAT 61.937 63.158 25.74 25.74 31.19 4.58
1237 1347 2.356382 CAGGTACTACGAGCTCAAGGAG 59.644 54.545 15.40 6.93 36.02 3.69
1344 1454 2.758089 CCTACGACGACCCCGAGTG 61.758 68.421 0.00 0.00 39.50 3.51
1346 1456 1.078214 TACGACGACCCCGAGTGAT 60.078 57.895 0.00 0.00 39.50 3.06
1347 1457 0.677731 TACGACGACCCCGAGTGATT 60.678 55.000 0.00 0.00 39.50 2.57
1359 1473 2.615493 CCGAGTGATTAGCCAACCAACT 60.615 50.000 0.00 0.00 0.00 3.16
1380 1496 3.380479 ACTAGTACGCTTGCTTGTTCA 57.620 42.857 0.00 0.00 0.00 3.18
1421 1537 5.220510 CGCAGTGTTCTGTTACTTTGTACAA 60.221 40.000 3.59 3.59 43.05 2.41
1426 1542 6.851330 GTGTTCTGTTACTTTGTACAATCAGC 59.149 38.462 9.56 0.78 0.00 4.26
1439 1555 1.068055 CAATCAGCAGAGCAAACACCC 60.068 52.381 0.00 0.00 0.00 4.61
1440 1556 0.403271 ATCAGCAGAGCAAACACCCT 59.597 50.000 0.00 0.00 0.00 4.34
1441 1557 0.535780 TCAGCAGAGCAAACACCCTG 60.536 55.000 0.00 0.00 0.00 4.45
1442 1558 0.820891 CAGCAGAGCAAACACCCTGT 60.821 55.000 0.00 0.00 0.00 4.00
1443 1559 0.106519 AGCAGAGCAAACACCCTGTT 60.107 50.000 0.00 0.00 43.41 3.16
1444 1560 1.142870 AGCAGAGCAAACACCCTGTTA 59.857 47.619 0.00 0.00 40.14 2.41
1445 1561 1.537202 GCAGAGCAAACACCCTGTTAG 59.463 52.381 0.00 0.00 40.14 2.34
1446 1562 2.851195 CAGAGCAAACACCCTGTTAGT 58.149 47.619 0.00 0.00 40.14 2.24
1453 1569 3.703001 AACACCCTGTTAGTCATCTGG 57.297 47.619 0.00 0.00 39.09 3.86
1483 1599 9.561069 GTGTGTATAAATCAGGGTTCAGAATAT 57.439 33.333 0.00 0.00 0.00 1.28
1489 1606 7.986085 AAATCAGGGTTCAGAATATAATCCG 57.014 36.000 0.00 0.00 30.75 4.18
1491 1608 6.097915 TCAGGGTTCAGAATATAATCCGAC 57.902 41.667 0.00 0.00 30.75 4.79
1498 1615 6.835819 TCAGAATATAATCCGACCCTGTAG 57.164 41.667 0.00 0.00 0.00 2.74
1557 1674 2.551459 GGCTGCGAGCAATAATTCAGAT 59.449 45.455 9.78 0.00 44.75 2.90
1564 1681 5.390356 GCGAGCAATAATTCAGATAAGGAGC 60.390 44.000 0.00 0.00 0.00 4.70
1565 1682 5.164012 CGAGCAATAATTCAGATAAGGAGCG 60.164 44.000 0.00 0.00 0.00 5.03
1619 3744 5.047021 TCTCCAGATGTCTGAAACCTGTAAG 60.047 44.000 11.47 0.00 46.59 2.34
1621 3746 5.306937 TCCAGATGTCTGAAACCTGTAAGAA 59.693 40.000 11.47 0.00 46.59 2.52
1637 3765 8.097662 ACCTGTAAGAAAATTCTCTAGTGAAGG 58.902 37.037 12.41 6.80 36.28 3.46
1651 3779 0.310543 TGAAGGAATTGCGTGTGTGC 59.689 50.000 0.00 0.00 0.00 4.57
1671 3799 2.549926 CGCAGTATAGTGTGCCATGAA 58.450 47.619 8.14 0.00 36.24 2.57
1818 3951 3.249559 GTGGCAAGAGAGTTTGTCTGAAG 59.750 47.826 0.00 0.00 34.71 3.02
1819 3952 3.134623 TGGCAAGAGAGTTTGTCTGAAGA 59.865 43.478 0.00 0.00 34.71 2.87
1820 3953 4.130118 GGCAAGAGAGTTTGTCTGAAGAA 58.870 43.478 0.00 0.00 34.71 2.52
1868 4001 5.012664 TGCAGTGAAAAGTCTGAACCCTATA 59.987 40.000 0.00 0.00 34.02 1.31
1908 4041 2.126228 CTGCATTTGCGCCCAGTG 60.126 61.111 4.18 0.00 45.83 3.66
1913 4046 0.447801 CATTTGCGCCCAGTGTAGTC 59.552 55.000 4.18 0.00 0.00 2.59
1914 4047 0.324943 ATTTGCGCCCAGTGTAGTCT 59.675 50.000 4.18 0.00 0.00 3.24
1925 4058 5.681437 GCCCAGTGTAGTCTATCGAATGAAA 60.681 44.000 0.00 0.00 0.00 2.69
1948 4081 0.463654 TCGAGCCTTGCTTTGTGTGT 60.464 50.000 0.00 0.00 39.88 3.72
1953 4086 0.457035 CCTTGCTTTGTGTGTGCACT 59.543 50.000 19.41 0.00 45.44 4.40
1986 4146 2.618241 TCATTGACAAACACACTCCTGC 59.382 45.455 0.00 0.00 0.00 4.85
2086 4246 8.941977 TCTACAACACAATCCACAAATATGTAC 58.058 33.333 0.00 0.00 37.82 2.90
2087 4247 7.759489 ACAACACAATCCACAAATATGTACT 57.241 32.000 0.00 0.00 37.82 2.73
2088 4248 7.592938 ACAACACAATCCACAAATATGTACTG 58.407 34.615 0.00 0.00 37.82 2.74
2089 4249 7.230510 ACAACACAATCCACAAATATGTACTGT 59.769 33.333 0.00 0.00 37.82 3.55
2090 4250 8.726068 CAACACAATCCACAAATATGTACTGTA 58.274 33.333 0.00 0.00 37.82 2.74
2190 4350 3.406764 AGAACCAAAGCAAGCTAGTGAG 58.593 45.455 0.00 0.00 0.00 3.51
2306 4466 6.150474 CCGAGTACCAATAAACTGTCCATTTT 59.850 38.462 0.00 0.00 0.00 1.82
2334 4494 0.671781 CAGGAAGGTGCAGAAGACCG 60.672 60.000 0.00 0.00 38.64 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.303054 TCATCTAGTTAGGAGACTGATGGAG 58.697 44.000 0.00 0.00 43.88 3.86
1 2 6.267492 TCATCTAGTTAGGAGACTGATGGA 57.733 41.667 0.00 0.00 43.88 3.41
2 3 6.968263 TTCATCTAGTTAGGAGACTGATGG 57.032 41.667 0.00 0.00 43.88 3.51
3 4 7.232330 TGGATTCATCTAGTTAGGAGACTGATG 59.768 40.741 0.00 0.00 43.88 3.07
4 5 7.301420 TGGATTCATCTAGTTAGGAGACTGAT 58.699 38.462 0.00 0.00 43.88 2.90
5 6 6.673583 TGGATTCATCTAGTTAGGAGACTGA 58.326 40.000 0.00 0.00 43.88 3.41
6 7 6.968263 TGGATTCATCTAGTTAGGAGACTG 57.032 41.667 0.00 0.00 43.88 3.51
7 8 8.010105 AGAATGGATTCATCTAGTTAGGAGACT 58.990 37.037 2.32 0.00 41.07 3.24
8 9 8.189119 AGAATGGATTCATCTAGTTAGGAGAC 57.811 38.462 2.32 0.00 39.23 3.36
9 10 8.789767 AAGAATGGATTCATCTAGTTAGGAGA 57.210 34.615 2.32 0.00 39.23 3.71
10 11 8.093927 GGAAGAATGGATTCATCTAGTTAGGAG 58.906 40.741 2.32 0.00 39.23 3.69
11 12 7.016661 GGGAAGAATGGATTCATCTAGTTAGGA 59.983 40.741 2.32 0.00 39.23 2.94
12 13 7.164803 GGGAAGAATGGATTCATCTAGTTAGG 58.835 42.308 2.32 0.00 39.23 2.69
13 14 7.739825 TGGGAAGAATGGATTCATCTAGTTAG 58.260 38.462 2.32 0.00 39.23 2.34
14 15 7.690454 TGGGAAGAATGGATTCATCTAGTTA 57.310 36.000 2.32 0.00 39.23 2.24
15 16 6.581388 TGGGAAGAATGGATTCATCTAGTT 57.419 37.500 2.32 0.00 39.23 2.24
16 17 6.360618 GTTGGGAAGAATGGATTCATCTAGT 58.639 40.000 2.32 0.00 39.23 2.57
17 18 5.468072 CGTTGGGAAGAATGGATTCATCTAG 59.532 44.000 2.32 0.00 39.23 2.43
18 19 5.130311 TCGTTGGGAAGAATGGATTCATCTA 59.870 40.000 2.32 0.00 39.23 1.98
19 20 4.080356 TCGTTGGGAAGAATGGATTCATCT 60.080 41.667 2.32 0.00 39.23 2.90
20 21 4.199310 TCGTTGGGAAGAATGGATTCATC 58.801 43.478 2.32 0.00 39.23 2.92
21 22 4.235079 TCGTTGGGAAGAATGGATTCAT 57.765 40.909 2.32 0.00 39.23 2.57
22 23 3.712016 TCGTTGGGAAGAATGGATTCA 57.288 42.857 2.32 0.00 39.23 2.57
23 24 4.734695 GCAATCGTTGGGAAGAATGGATTC 60.735 45.833 0.00 0.00 37.06 2.52
24 25 3.131046 GCAATCGTTGGGAAGAATGGATT 59.869 43.478 1.01 0.00 0.00 3.01
25 26 2.689983 GCAATCGTTGGGAAGAATGGAT 59.310 45.455 1.01 0.00 0.00 3.41
26 27 2.091541 GCAATCGTTGGGAAGAATGGA 58.908 47.619 1.01 0.00 0.00 3.41
27 28 1.134946 GGCAATCGTTGGGAAGAATGG 59.865 52.381 0.00 0.00 0.00 3.16
28 29 1.134946 GGGCAATCGTTGGGAAGAATG 59.865 52.381 0.00 0.00 0.00 2.67
29 30 1.474330 GGGCAATCGTTGGGAAGAAT 58.526 50.000 0.00 0.00 0.00 2.40
30 31 0.958382 CGGGCAATCGTTGGGAAGAA 60.958 55.000 0.00 0.00 0.00 2.52
31 32 1.376683 CGGGCAATCGTTGGGAAGA 60.377 57.895 0.00 0.00 0.00 2.87
32 33 3.051392 GCGGGCAATCGTTGGGAAG 62.051 63.158 0.00 0.00 0.00 3.46
33 34 2.186602 TAGCGGGCAATCGTTGGGAA 62.187 55.000 0.00 0.00 0.00 3.97
34 35 2.587322 CTAGCGGGCAATCGTTGGGA 62.587 60.000 0.00 0.00 0.00 4.37
35 36 2.124901 TAGCGGGCAATCGTTGGG 60.125 61.111 0.00 0.00 0.00 4.12
36 37 2.823829 GCTAGCGGGCAATCGTTGG 61.824 63.158 0.00 0.00 0.00 3.77
37 38 2.709475 GCTAGCGGGCAATCGTTG 59.291 61.111 0.00 0.00 0.00 4.10
38 39 2.890474 CGCTAGCGGGCAATCGTT 60.890 61.111 29.29 0.00 35.56 3.85
39 40 3.833645 TCGCTAGCGGGCAATCGT 61.834 61.111 34.76 0.00 40.25 3.73
40 41 3.330853 GTCGCTAGCGGGCAATCG 61.331 66.667 34.76 6.46 40.25 3.34
41 42 2.967615 GGTCGCTAGCGGGCAATC 60.968 66.667 34.76 14.11 40.25 2.67
42 43 4.891727 CGGTCGCTAGCGGGCAAT 62.892 66.667 34.76 0.00 42.79 3.56
49 50 1.154073 AGTTTCGACGGTCGCTAGC 60.154 57.895 24.76 16.22 40.21 3.42
50 51 0.167470 TCAGTTTCGACGGTCGCTAG 59.833 55.000 24.76 12.52 40.21 3.42
51 52 0.592637 TTCAGTTTCGACGGTCGCTA 59.407 50.000 24.76 12.71 40.21 4.26
52 53 0.038526 ATTCAGTTTCGACGGTCGCT 60.039 50.000 24.76 13.78 40.21 4.93
53 54 1.621107 TATTCAGTTTCGACGGTCGC 58.379 50.000 24.76 11.69 40.21 5.19
54 55 5.051907 CCTTAATATTCAGTTTCGACGGTCG 60.052 44.000 23.73 23.73 42.10 4.79
55 56 5.809051 ACCTTAATATTCAGTTTCGACGGTC 59.191 40.000 0.00 0.00 0.00 4.79
56 57 5.579511 CACCTTAATATTCAGTTTCGACGGT 59.420 40.000 0.00 0.00 0.00 4.83
57 58 5.501897 GCACCTTAATATTCAGTTTCGACGG 60.502 44.000 0.00 0.00 0.00 4.79
58 59 5.062934 TGCACCTTAATATTCAGTTTCGACG 59.937 40.000 0.00 0.00 0.00 5.12
59 60 6.128391 TGTGCACCTTAATATTCAGTTTCGAC 60.128 38.462 15.69 0.00 0.00 4.20
60 61 5.935206 TGTGCACCTTAATATTCAGTTTCGA 59.065 36.000 15.69 0.00 0.00 3.71
61 62 6.021596 GTGTGCACCTTAATATTCAGTTTCG 58.978 40.000 15.69 0.00 0.00 3.46
62 63 7.145932 AGTGTGCACCTTAATATTCAGTTTC 57.854 36.000 15.69 0.00 0.00 2.78
63 64 7.883311 ACTAGTGTGCACCTTAATATTCAGTTT 59.117 33.333 15.69 0.00 0.00 2.66
64 65 7.394816 ACTAGTGTGCACCTTAATATTCAGTT 58.605 34.615 15.69 0.00 0.00 3.16
65 66 6.947464 ACTAGTGTGCACCTTAATATTCAGT 58.053 36.000 15.69 5.95 0.00 3.41
66 67 7.849804 AACTAGTGTGCACCTTAATATTCAG 57.150 36.000 15.69 5.36 0.00 3.02
67 68 7.663905 ACAAACTAGTGTGCACCTTAATATTCA 59.336 33.333 15.69 0.00 0.00 2.57
68 69 7.962918 CACAAACTAGTGTGCACCTTAATATTC 59.037 37.037 15.69 0.00 42.26 1.75
69 70 7.094377 CCACAAACTAGTGTGCACCTTAATATT 60.094 37.037 15.69 0.00 46.24 1.28
70 71 6.374333 CCACAAACTAGTGTGCACCTTAATAT 59.626 38.462 15.69 0.00 46.24 1.28
71 72 5.703592 CCACAAACTAGTGTGCACCTTAATA 59.296 40.000 15.69 0.00 46.24 0.98
72 73 4.518970 CCACAAACTAGTGTGCACCTTAAT 59.481 41.667 15.69 0.00 46.24 1.40
73 74 3.880490 CCACAAACTAGTGTGCACCTTAA 59.120 43.478 15.69 0.00 46.24 1.85
74 75 3.472652 CCACAAACTAGTGTGCACCTTA 58.527 45.455 15.69 5.82 46.24 2.69
87 88 4.207891 AGAGATAATCACGCCACAAACT 57.792 40.909 0.00 0.00 0.00 2.66
88 89 4.631813 AGAAGAGATAATCACGCCACAAAC 59.368 41.667 0.00 0.00 0.00 2.93
93 94 3.701542 AGTGAGAAGAGATAATCACGCCA 59.298 43.478 0.00 0.00 45.25 5.69
128 129 2.542766 ACGTCACAACAGTTTTGCAG 57.457 45.000 0.00 0.00 0.00 4.41
138 139 7.148306 ACCAGGATAATTTCATAACGTCACAAC 60.148 37.037 0.00 0.00 0.00 3.32
147 148 5.692781 GCTCCCCACCAGGATAATTTCATAA 60.693 44.000 0.00 0.00 38.24 1.90
148 149 4.202567 GCTCCCCACCAGGATAATTTCATA 60.203 45.833 0.00 0.00 38.24 2.15
180 181 3.279434 ACTTCTCGGTGTTTCAAGCTTT 58.721 40.909 0.00 0.00 0.00 3.51
186 187 3.062909 CGACAAAACTTCTCGGTGTTTCA 59.937 43.478 0.00 0.00 35.63 2.69
193 194 2.433868 TCTCCGACAAAACTTCTCGG 57.566 50.000 0.00 0.00 46.95 4.63
195 196 6.960468 AGAATTTTCTCCGACAAAACTTCTC 58.040 36.000 0.00 0.00 29.94 2.87
202 203 9.243637 CACAATTAAAGAATTTTCTCCGACAAA 57.756 29.630 0.00 0.00 40.09 2.83
214 215 5.826586 TCACGCACACACAATTAAAGAATT 58.173 33.333 0.00 0.00 35.56 2.17
223 224 1.308047 ACACATCACGCACACACAAT 58.692 45.000 0.00 0.00 0.00 2.71
246 247 5.524971 ACAATTGAAGGCACATATGATGG 57.475 39.130 13.59 0.00 33.60 3.51
247 248 8.354426 TCATTACAATTGAAGGCACATATGATG 58.646 33.333 13.59 5.38 0.00 3.07
249 250 7.878547 TCATTACAATTGAAGGCACATATGA 57.121 32.000 13.59 4.70 0.00 2.15
256 257 5.716228 AGGTCATTCATTACAATTGAAGGCA 59.284 36.000 13.59 0.00 0.00 4.75
262 263 9.722056 GCTTAACTAGGTCATTCATTACAATTG 57.278 33.333 3.24 3.24 0.00 2.32
278 279 0.105039 CCTGGCCGAGCTTAACTAGG 59.895 60.000 0.00 0.00 43.72 3.02
293 294 0.911769 TATGGTGCCTTGAGACCTGG 59.088 55.000 0.00 0.00 32.98 4.45
294 295 1.407437 GGTATGGTGCCTTGAGACCTG 60.407 57.143 0.00 0.00 32.98 4.00
295 296 0.912486 GGTATGGTGCCTTGAGACCT 59.088 55.000 0.00 0.00 32.98 3.85
309 310 7.284034 AGGAATTGCTTAGTTCATCAAGGTATG 59.716 37.037 0.00 0.00 0.00 2.39
313 316 5.220739 CGAGGAATTGCTTAGTTCATCAAGG 60.221 44.000 0.00 0.00 35.52 3.61
323 326 3.250744 TCGTTGACGAGGAATTGCTTAG 58.749 45.455 0.00 1.36 44.22 2.18
334 337 7.682885 CAGCATGAATGGAATCGTTGACGAG 62.683 48.000 12.08 0.00 46.71 4.18
344 347 3.377253 AGACACCAGCATGAATGGAAT 57.623 42.857 20.72 10.05 40.51 3.01
348 351 4.157105 TCATCAAAGACACCAGCATGAATG 59.843 41.667 0.00 0.00 39.69 2.67
355 358 3.063997 CCGTAATCATCAAAGACACCAGC 59.936 47.826 0.00 0.00 0.00 4.85
392 395 8.944029 CATTATTCAGCTGATTAATCCCACTAG 58.056 37.037 28.61 17.78 31.82 2.57
405 408 5.300034 CCAGGTTATTGCATTATTCAGCTGA 59.700 40.000 13.74 13.74 31.40 4.26
411 414 4.342092 ACTGGCCAGGTTATTGCATTATTC 59.658 41.667 35.42 0.00 0.00 1.75
443 446 1.015607 GCTTGGATTGCCTTTTGCCG 61.016 55.000 0.00 0.00 40.16 5.69
445 448 1.150827 GTGCTTGGATTGCCTTTTGC 58.849 50.000 0.00 0.00 41.77 3.68
468 471 3.849527 AGGAAAAGGGATGGCCATTATC 58.150 45.455 21.84 8.16 37.14 1.75
479 482 3.295973 CTGTCCAACAAAGGAAAAGGGA 58.704 45.455 0.00 0.00 39.92 4.20
484 487 6.887545 TCTTTCTAACTGTCCAACAAAGGAAA 59.112 34.615 0.00 0.00 39.92 3.13
487 490 5.239525 CCTCTTTCTAACTGTCCAACAAAGG 59.760 44.000 0.00 0.00 0.00 3.11
488 491 5.239525 CCCTCTTTCTAACTGTCCAACAAAG 59.760 44.000 0.00 0.00 0.00 2.77
492 495 3.075148 GCCCTCTTTCTAACTGTCCAAC 58.925 50.000 0.00 0.00 0.00 3.77
506 509 0.040058 TCCATGTTGCATGCCCTCTT 59.960 50.000 16.68 1.05 0.00 2.85
511 514 1.202486 CCTTGATCCATGTTGCATGCC 60.202 52.381 16.68 0.28 0.00 4.40
525 528 2.028112 TGCTAGCTCGTTTGACCTTGAT 60.028 45.455 17.23 0.00 0.00 2.57
527 530 1.461127 GTGCTAGCTCGTTTGACCTTG 59.539 52.381 17.23 0.00 0.00 3.61
528 531 1.070134 TGTGCTAGCTCGTTTGACCTT 59.930 47.619 17.23 0.00 0.00 3.50
530 533 1.461127 CTTGTGCTAGCTCGTTTGACC 59.539 52.381 17.23 0.00 0.00 4.02
559 574 1.682344 GGCATTTCGCTCCCCCTTT 60.682 57.895 0.00 0.00 41.91 3.11
564 579 0.532115 ATTTGTGGCATTTCGCTCCC 59.468 50.000 0.00 0.00 41.91 4.30
574 589 3.581770 TCCATCCATCAAAATTTGTGGCA 59.418 39.130 16.88 10.02 34.18 4.92
575 590 4.205065 TCCATCCATCAAAATTTGTGGC 57.795 40.909 16.88 0.00 34.18 5.01
577 592 5.293324 CAGCATCCATCCATCAAAATTTGTG 59.707 40.000 5.56 3.89 0.00 3.33
578 593 5.188163 TCAGCATCCATCCATCAAAATTTGT 59.812 36.000 5.56 0.00 0.00 2.83
579 594 5.666462 TCAGCATCCATCCATCAAAATTTG 58.334 37.500 0.00 0.00 0.00 2.32
580 595 5.943349 TCAGCATCCATCCATCAAAATTT 57.057 34.783 0.00 0.00 0.00 1.82
582 597 5.723672 GATCAGCATCCATCCATCAAAAT 57.276 39.130 0.00 0.00 0.00 1.82
605 624 5.927281 ATTTGTTCCATCTCCCTTTCATG 57.073 39.130 0.00 0.00 0.00 3.07
607 626 6.953520 ACATTATTTGTTCCATCTCCCTTTCA 59.046 34.615 0.00 0.00 33.74 2.69
612 631 6.183360 CCTTCACATTATTTGTTCCATCTCCC 60.183 42.308 0.00 0.00 36.00 4.30
616 640 7.601856 TGTTCCTTCACATTATTTGTTCCATC 58.398 34.615 0.00 0.00 36.00 3.51
628 652 9.308000 TCCTTACATTATTTGTTCCTTCACATT 57.692 29.630 0.00 0.00 39.87 2.71
657 715 7.201652 GCTGATGTAAAAAGGACCTTCACTATC 60.202 40.741 7.34 8.88 0.00 2.08
669 727 5.873179 TTAAGGTCGCTGATGTAAAAAGG 57.127 39.130 0.00 0.00 0.00 3.11
670 728 8.665685 ACTTATTAAGGTCGCTGATGTAAAAAG 58.334 33.333 8.26 0.00 0.00 2.27
675 735 7.101054 ACAAACTTATTAAGGTCGCTGATGTA 58.899 34.615 8.26 0.00 0.00 2.29
680 740 7.591006 TCTTACAAACTTATTAAGGTCGCTG 57.409 36.000 8.26 0.00 0.00 5.18
682 742 7.908601 CCATTCTTACAAACTTATTAAGGTCGC 59.091 37.037 8.26 0.00 0.00 5.19
683 743 9.158233 TCCATTCTTACAAACTTATTAAGGTCG 57.842 33.333 8.26 0.00 0.00 4.79
742 804 3.421844 ACAAAATTAGCCACTGAGGTCC 58.578 45.455 0.00 0.00 40.61 4.46
748 810 5.841810 TCCTGAAAACAAAATTAGCCACTG 58.158 37.500 0.00 0.00 0.00 3.66
779 841 9.695526 CATTCCTGAAAACAATATTTCACTCAA 57.304 29.630 0.00 0.00 42.68 3.02
780 842 9.076781 TCATTCCTGAAAACAATATTTCACTCA 57.923 29.630 0.00 0.00 42.68 3.41
781 843 9.912634 TTCATTCCTGAAAACAATATTTCACTC 57.087 29.630 0.00 0.00 42.68 3.51
801 863 5.220491 GCTCATCCAACGACTACTTTCATTC 60.220 44.000 0.00 0.00 0.00 2.67
807 869 2.826128 TCAGCTCATCCAACGACTACTT 59.174 45.455 0.00 0.00 0.00 2.24
811 875 1.137872 GGATCAGCTCATCCAACGACT 59.862 52.381 12.45 0.00 42.02 4.18
812 876 1.576356 GGATCAGCTCATCCAACGAC 58.424 55.000 12.45 0.00 42.02 4.34
859 923 1.645402 GGTATGGTCATGGCCCACCT 61.645 60.000 23.58 6.53 34.07 4.00
882 946 1.978617 CCATCTTGGTGTGGGCCAC 60.979 63.158 29.75 29.75 43.74 5.01
891 955 4.115199 GGCCTCGCCCATCTTGGT 62.115 66.667 0.00 0.00 44.06 3.67
925 989 0.992431 ATGATGGGAAGCCTGCCTCT 60.992 55.000 0.00 0.00 33.20 3.69
929 993 0.749049 GGAAATGATGGGAAGCCTGC 59.251 55.000 0.00 0.00 0.00 4.85
930 994 2.091994 AGAGGAAATGATGGGAAGCCTG 60.092 50.000 0.00 0.00 0.00 4.85
932 996 2.092212 TGAGAGGAAATGATGGGAAGCC 60.092 50.000 0.00 0.00 0.00 4.35
933 997 3.287867 TGAGAGGAAATGATGGGAAGC 57.712 47.619 0.00 0.00 0.00 3.86
935 999 4.656100 TGTTGAGAGGAAATGATGGGAA 57.344 40.909 0.00 0.00 0.00 3.97
936 1000 4.656100 TTGTTGAGAGGAAATGATGGGA 57.344 40.909 0.00 0.00 0.00 4.37
974 1040 3.697045 TCACTTCTCCCGATTCTTCTCTC 59.303 47.826 0.00 0.00 0.00 3.20
1185 1281 3.134127 GTGGTCAATCGCCAGGCC 61.134 66.667 5.63 0.00 36.57 5.19
1186 1282 3.499737 CGTGGTCAATCGCCAGGC 61.500 66.667 0.00 0.00 36.57 4.85
1187 1283 2.819595 CCGTGGTCAATCGCCAGG 60.820 66.667 0.00 0.00 40.44 4.45
1188 1284 3.499737 GCCGTGGTCAATCGCCAG 61.500 66.667 0.00 0.00 36.57 4.85
1191 1287 3.849953 GTCGCCGTGGTCAATCGC 61.850 66.667 0.00 0.00 0.00 4.58
1192 1288 3.541831 CGTCGCCGTGGTCAATCG 61.542 66.667 0.00 0.00 0.00 3.34
1193 1289 3.186047 CCGTCGCCGTGGTCAATC 61.186 66.667 0.00 0.00 0.00 2.67
1210 1320 0.802607 GCTCGTAGTACCTGCACAGC 60.803 60.000 7.14 0.00 0.00 4.40
1211 1321 0.811915 AGCTCGTAGTACCTGCACAG 59.188 55.000 12.69 0.00 0.00 3.66
1212 1322 0.809385 GAGCTCGTAGTACCTGCACA 59.191 55.000 0.00 0.00 0.00 4.57
1213 1323 0.809385 TGAGCTCGTAGTACCTGCAC 59.191 55.000 9.64 8.20 0.00 4.57
1344 1454 5.975939 CGTACTAGTAGTTGGTTGGCTAATC 59.024 44.000 8.40 0.00 0.00 1.75
1346 1456 4.380867 GCGTACTAGTAGTTGGTTGGCTAA 60.381 45.833 8.40 0.00 0.00 3.09
1347 1457 3.129287 GCGTACTAGTAGTTGGTTGGCTA 59.871 47.826 8.40 0.00 0.00 3.93
1359 1473 4.508461 TGAACAAGCAAGCGTACTAGTA 57.492 40.909 0.00 0.00 0.00 1.82
1380 1496 1.002430 TGCGTTTGCTTCAGAGGAGAT 59.998 47.619 0.00 0.00 43.34 2.75
1421 1537 0.403271 AGGGTGTTTGCTCTGCTGAT 59.597 50.000 0.00 0.00 0.00 2.90
1426 1542 2.808543 GACTAACAGGGTGTTTGCTCTG 59.191 50.000 0.00 0.00 41.45 3.35
1439 1555 5.240891 ACACACAATCCAGATGACTAACAG 58.759 41.667 0.00 0.00 0.00 3.16
1440 1556 5.227569 ACACACAATCCAGATGACTAACA 57.772 39.130 0.00 0.00 0.00 2.41
1441 1557 8.942338 TTATACACACAATCCAGATGACTAAC 57.058 34.615 0.00 0.00 0.00 2.34
1443 1559 9.764363 GATTTATACACACAATCCAGATGACTA 57.236 33.333 0.00 0.00 0.00 2.59
1444 1560 8.267183 TGATTTATACACACAATCCAGATGACT 58.733 33.333 0.00 0.00 0.00 3.41
1445 1561 8.437360 TGATTTATACACACAATCCAGATGAC 57.563 34.615 0.00 0.00 0.00 3.06
1446 1562 7.716560 CCTGATTTATACACACAATCCAGATGA 59.283 37.037 0.00 0.00 0.00 2.92
1453 1569 7.552687 TCTGAACCCTGATTTATACACACAATC 59.447 37.037 0.00 0.00 0.00 2.67
1483 1599 4.825634 CACTGATACTACAGGGTCGGATTA 59.174 45.833 0.00 0.00 41.59 1.75
1491 1608 5.661056 TTCTGAACACTGATACTACAGGG 57.339 43.478 0.00 0.00 45.62 4.45
1498 1615 8.869897 TGACGATTTTATTCTGAACACTGATAC 58.130 33.333 0.00 0.00 0.00 2.24
1534 1651 1.672363 TGAATTATTGCTCGCAGCCAG 59.328 47.619 5.82 0.00 41.51 4.85
1557 1674 5.888691 TGAATTAATGCAAACGCTCCTTA 57.111 34.783 0.00 0.00 0.00 2.69
1619 3744 6.963805 CGCAATTCCTTCACTAGAGAATTTTC 59.036 38.462 2.92 0.00 34.39 2.29
1621 3746 5.940470 ACGCAATTCCTTCACTAGAGAATTT 59.060 36.000 2.92 0.00 34.39 1.82
1665 3793 6.475596 AGGATTTTAGCCTTTCATTCATGG 57.524 37.500 0.00 0.00 29.44 3.66
1697 3830 3.256879 TCTGTGCAAAGGTTGTCAAACAA 59.743 39.130 3.47 0.00 38.10 2.83
1845 3978 2.576615 AGGGTTCAGACTTTTCACTGC 58.423 47.619 0.00 0.00 34.57 4.40
1913 4046 5.226396 AGGCTCGATTCTTTCATTCGATAG 58.774 41.667 0.00 0.00 40.69 2.08
1914 4047 5.201713 AGGCTCGATTCTTTCATTCGATA 57.798 39.130 0.00 0.00 40.69 2.92
1925 4058 1.808945 CACAAAGCAAGGCTCGATTCT 59.191 47.619 0.00 0.00 38.25 2.40
1948 4081 5.048782 GTCAATGACTGAATTAACCAGTGCA 60.049 40.000 14.80 12.56 44.14 4.57
1953 4086 7.148000 TGTGTTTGTCAATGACTGAATTAACCA 60.148 33.333 14.97 0.00 35.22 3.67
1986 4146 2.198426 ACACCAAGGCCCCTGTTG 59.802 61.111 0.00 0.00 0.00 3.33
1995 4155 4.684134 CCAGGGGCCACACCAAGG 62.684 72.222 8.31 0.25 42.05 3.61
2045 4205 6.442564 TGTGTTGTAGACTAGGGTTTGGATAT 59.557 38.462 0.00 0.00 0.00 1.63
2144 4304 5.404096 CATTTGCTATCATTTGAGTGTGCA 58.596 37.500 0.00 0.00 0.00 4.57
2180 4340 1.548269 GCTGAGACCACTCACTAGCTT 59.452 52.381 0.00 0.00 46.55 3.74
2190 4350 2.386660 GCGCAGAAGCTGAGACCAC 61.387 63.158 0.30 0.00 39.10 4.16
2255 4415 1.479323 GACAGCTTGTATGACCGGGTA 59.521 52.381 6.32 0.00 0.00 3.69
2306 4466 1.768275 TGCACCTTCCTGTTCAAGAGA 59.232 47.619 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.