Multiple sequence alignment - TraesCS3B01G474600

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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 TraesCS3B01G474600 chr3B 100.000 2902 0 0 1 2902 723470983 723468082 0.000000e+00 5360.0
1 TraesCS3B01G474600 chr3B 92.537 67 5 0 2626 2692 229295932 229295998 2.380000e-16 97.1
2 TraesCS3B01G474600 chr3B 98.000 50 1 0 263 312 723470673 723470624 1.430000e-13 87.9
3 TraesCS3B01G474600 chr3B 98.000 50 1 0 311 360 723470721 723470672 1.430000e-13 87.9
4 TraesCS3B01G474600 chr3D 91.795 1560 64 13 995 2528 546391861 546390340 0.000000e+00 2113.0
5 TraesCS3B01G474600 chr3D 86.876 701 52 13 311 996 546392567 546391892 0.000000e+00 749.0
6 TraesCS3B01G474600 chr3D 89.103 312 31 3 1 311 546392829 546392520 4.540000e-103 385.0
7 TraesCS3B01G474600 chr3D 92.417 211 12 3 2693 2902 546390043 546389836 6.080000e-77 298.0
8 TraesCS3B01G474600 chr3D 100.000 66 0 0 2574 2639 546390093 546390028 3.930000e-24 122.0
9 TraesCS3B01G474600 chr3A 84.800 125 14 5 61 181 50742524 50742647 1.410000e-23 121.0
10 TraesCS3B01G474600 chr2B 79.365 189 26 7 478 661 768559878 768559698 1.410000e-23 121.0
11 TraesCS3B01G474600 chr6B 100.000 56 0 0 2637 2692 314575905 314575960 1.420000e-18 104.0
12 TraesCS3B01G474600 chr4A 96.825 63 1 1 2633 2695 479322994 479322933 1.420000e-18 104.0
13 TraesCS3B01G474600 chr4A 96.667 60 2 0 2633 2692 111286913 111286972 1.840000e-17 100.0
14 TraesCS3B01G474600 chr5B 95.385 65 1 2 2630 2692 253163008 253163072 5.120000e-18 102.0
15 TraesCS3B01G474600 chr5B 100.000 28 0 0 61 88 477962372 477962345 5.000000e-03 52.8
16 TraesCS3B01G474600 chr4B 98.305 59 0 1 2635 2692 461272287 461272345 5.120000e-18 102.0
17 TraesCS3B01G474600 chr4B 96.667 60 2 0 2633 2692 126079212 126079271 1.840000e-17 100.0
18 TraesCS3B01G474600 chr4B 100.000 29 0 0 62 90 638454764 638454736 1.000000e-03 54.7
19 TraesCS3B01G474600 chr4B 100.000 28 0 0 64 91 317152087 317152060 5.000000e-03 52.8
20 TraesCS3B01G474600 chr1A 92.958 71 1 4 2624 2692 276573267 276573335 1.840000e-17 100.0
21 TraesCS3B01G474600 chr2D 76.963 191 33 7 64 247 627643001 627643187 6.620000e-17 99.0
22 TraesCS3B01G474600 chr2D 88.136 59 6 1 51 108 192069444 192069386 5.190000e-08 69.4
23 TraesCS3B01G474600 chr2D 90.385 52 4 1 61 111 248741712 248741763 1.870000e-07 67.6
24 TraesCS3B01G474600 chr7B 87.952 83 5 5 2615 2695 620659551 620659472 3.080000e-15 93.5
25 TraesCS3B01G474600 chr2A 90.000 70 7 0 242 311 379832858 379832789 1.110000e-14 91.6
26 TraesCS3B01G474600 chr1B 94.286 35 2 0 60 94 391998406 391998440 1.000000e-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 TraesCS3B01G474600 chr3B 723468082 723470983 2901 True 1845.266667 5360 98.666667 1 2902 3 chr3B.!!$R1 2901
1 TraesCS3B01G474600 chr3D 546389836 546392829 2993 True 733.400000 2113 92.038200 1 2902 5 chr3D.!!$R1 2901

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
298 300 0.036388 GAGTCCAACTGCCATCGGAA 60.036 55.0 0.0 0.0 0.00 4.30 F
896 912 0.106469 TGATCTCCCTGTCCCTCTCG 60.106 60.0 0.0 0.0 0.00 4.04 F
1680 1754 0.906775 TGCTGATGATGACTCTGCCA 59.093 50.0 0.0 0.0 36.93 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 1210 0.033781 TCTACCAACGGAAACCACGG 59.966 55.0 0.0 0.0 35.23 4.94 R
1729 1803 0.108585 TTCCTTCTTCAGCGGCTTGT 59.891 50.0 0.0 0.0 0.00 3.16 R
2663 2944 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.0 0.0 0.0 41.52 2.85 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
21 22 1.568504 TTTCGGCCTGTATCTGAGGT 58.431 50.000 0.00 0.00 32.60 3.85
25 26 2.891580 TCGGCCTGTATCTGAGGTATTC 59.108 50.000 0.00 0.00 32.60 1.75
26 27 2.028930 CGGCCTGTATCTGAGGTATTCC 60.029 54.545 0.00 0.00 32.60 3.01
34 35 6.124340 TGTATCTGAGGTATTCCGTGAACTA 58.876 40.000 0.00 0.00 39.05 2.24
83 84 0.176910 GAGCAACTCTAGCAGACCCC 59.823 60.000 0.00 0.00 0.00 4.95
116 118 1.578583 ACCGCATAATAACCACTCGC 58.421 50.000 0.00 0.00 0.00 5.03
120 122 3.994392 CCGCATAATAACCACTCGCTTAT 59.006 43.478 0.00 0.00 0.00 1.73
165 167 1.597663 GATCAGAAAACGTATGGCCCG 59.402 52.381 0.00 0.00 0.00 6.13
166 168 0.391927 TCAGAAAACGTATGGCCCGG 60.392 55.000 0.00 0.00 0.00 5.73
167 169 1.747745 AGAAAACGTATGGCCCGGC 60.748 57.895 0.00 0.00 0.00 6.13
173 175 2.816718 GTATGGCCCGGCGAACTA 59.183 61.111 9.30 0.00 0.00 2.24
180 182 1.951602 GGCCCGGCGAACTATAAAAAT 59.048 47.619 9.30 0.00 0.00 1.82
183 185 4.216902 GGCCCGGCGAACTATAAAAATAAT 59.783 41.667 9.30 0.00 0.00 1.28
185 187 6.072563 GGCCCGGCGAACTATAAAAATAATTA 60.073 38.462 9.30 0.00 0.00 1.40
186 188 6.798476 GCCCGGCGAACTATAAAAATAATTAC 59.202 38.462 9.30 0.00 0.00 1.89
190 192 7.300320 GGCGAACTATAAAAATAATTACGGGG 58.700 38.462 0.00 0.00 0.00 5.73
192 194 7.520292 GCGAACTATAAAAATAATTACGGGGCA 60.520 37.037 0.00 0.00 0.00 5.36
193 195 7.799914 CGAACTATAAAAATAATTACGGGGCAC 59.200 37.037 0.00 0.00 0.00 5.01
205 207 1.663739 GGGGCACGGAAAAACTTCC 59.336 57.895 0.00 0.00 37.75 3.46
208 210 0.826256 GGCACGGAAAAACTTCCCCT 60.826 55.000 0.00 0.00 37.84 4.79
211 213 2.303175 CACGGAAAAACTTCCCCTTCA 58.697 47.619 0.00 0.00 37.84 3.02
233 235 2.236395 ACCTTTAGATTCACGAGGTGGG 59.764 50.000 0.00 0.00 39.18 4.61
238 240 1.613630 ATTCACGAGGTGGGAGGCT 60.614 57.895 0.00 0.00 33.87 4.58
240 242 4.087892 CACGAGGTGGGAGGCTGG 62.088 72.222 0.00 0.00 0.00 4.85
250 252 2.524394 GAGGCTGGCCCGAGGATA 60.524 66.667 8.11 0.00 39.21 2.59
288 290 3.692406 GTCGGCGGGAGTCCAACT 61.692 66.667 12.30 0.00 0.00 3.16
289 291 3.691342 TCGGCGGGAGTCCAACTG 61.691 66.667 12.30 7.33 0.00 3.16
295 297 4.208632 GGAGTCCAACTGCCATCG 57.791 61.111 3.60 0.00 29.54 3.84
296 298 1.450312 GGAGTCCAACTGCCATCGG 60.450 63.158 3.60 0.00 29.54 4.18
297 299 1.596934 GAGTCCAACTGCCATCGGA 59.403 57.895 0.00 0.00 0.00 4.55
298 300 0.036388 GAGTCCAACTGCCATCGGAA 60.036 55.000 0.00 0.00 0.00 4.30
299 301 0.400213 AGTCCAACTGCCATCGGAAA 59.600 50.000 0.00 0.00 0.00 3.13
300 302 0.521735 GTCCAACTGCCATCGGAAAC 59.478 55.000 0.00 0.00 0.00 2.78
301 303 0.400213 TCCAACTGCCATCGGAAACT 59.600 50.000 0.00 0.00 0.00 2.66
302 304 1.202879 TCCAACTGCCATCGGAAACTT 60.203 47.619 0.00 0.00 0.00 2.66
303 305 1.200020 CCAACTGCCATCGGAAACTTC 59.800 52.381 0.00 0.00 0.00 3.01
304 306 1.879380 CAACTGCCATCGGAAACTTCA 59.121 47.619 0.00 0.00 0.00 3.02
305 307 2.489329 CAACTGCCATCGGAAACTTCAT 59.511 45.455 0.00 0.00 0.00 2.57
306 308 3.627395 ACTGCCATCGGAAACTTCATA 57.373 42.857 0.00 0.00 0.00 2.15
307 309 3.535561 ACTGCCATCGGAAACTTCATAG 58.464 45.455 0.00 0.00 0.00 2.23
308 310 2.288666 TGCCATCGGAAACTTCATAGC 58.711 47.619 0.00 0.00 0.00 2.97
309 311 2.092968 TGCCATCGGAAACTTCATAGCT 60.093 45.455 0.00 0.00 0.00 3.32
310 312 2.545946 GCCATCGGAAACTTCATAGCTC 59.454 50.000 0.00 0.00 0.00 4.09
311 313 2.797156 CCATCGGAAACTTCATAGCTCG 59.203 50.000 0.00 0.00 0.00 5.03
312 314 3.490933 CCATCGGAAACTTCATAGCTCGA 60.491 47.826 0.00 0.00 0.00 4.04
313 315 3.861276 TCGGAAACTTCATAGCTCGAA 57.139 42.857 0.00 0.00 0.00 3.71
314 316 4.182693 TCGGAAACTTCATAGCTCGAAA 57.817 40.909 0.00 0.00 0.00 3.46
315 317 4.174009 TCGGAAACTTCATAGCTCGAAAG 58.826 43.478 0.00 0.00 0.00 2.62
316 318 4.082408 TCGGAAACTTCATAGCTCGAAAGA 60.082 41.667 8.42 0.00 39.12 2.52
317 319 4.031878 CGGAAACTTCATAGCTCGAAAGAC 59.968 45.833 8.42 1.72 35.39 3.01
318 320 4.330347 GGAAACTTCATAGCTCGAAAGACC 59.670 45.833 8.42 5.77 35.39 3.85
319 321 3.152261 ACTTCATAGCTCGAAAGACCG 57.848 47.619 8.42 0.00 35.39 4.79
320 322 2.492484 ACTTCATAGCTCGAAAGACCGT 59.508 45.455 8.42 0.00 35.39 4.83
321 323 2.846039 TCATAGCTCGAAAGACCGTC 57.154 50.000 0.00 0.00 35.39 4.79
322 324 1.063616 TCATAGCTCGAAAGACCGTCG 59.936 52.381 0.00 0.00 39.88 5.12
323 325 0.381089 ATAGCTCGAAAGACCGTCGG 59.619 55.000 10.48 10.48 39.01 4.79
324 326 2.262471 TAGCTCGAAAGACCGTCGGC 62.262 60.000 12.28 4.24 39.01 5.54
325 327 2.874780 CTCGAAAGACCGTCGGCG 60.875 66.667 12.28 0.29 39.01 6.46
354 356 3.627395 ACTGCCATCGGAAACTTCATA 57.373 42.857 0.00 0.00 0.00 2.15
359 361 2.797156 CCATCGGAAACTTCATAGCTCG 59.203 50.000 0.00 0.00 0.00 5.03
389 391 3.885521 CGCCCGTCCGTCCTAGTC 61.886 72.222 0.00 0.00 0.00 2.59
390 392 3.885521 GCCCGTCCGTCCTAGTCG 61.886 72.222 0.00 0.00 0.00 4.18
391 393 3.885521 CCCGTCCGTCCTAGTCGC 61.886 72.222 0.00 0.00 0.00 5.19
392 394 3.885521 CCGTCCGTCCTAGTCGCC 61.886 72.222 0.00 0.00 0.00 5.54
393 395 4.233635 CGTCCGTCCTAGTCGCCG 62.234 72.222 0.00 0.00 0.00 6.46
474 476 3.752796 GGATCAATCCGGACACGAA 57.247 52.632 6.12 0.00 44.60 3.85
475 477 2.240493 GGATCAATCCGGACACGAAT 57.760 50.000 6.12 0.00 44.60 3.34
514 517 4.880537 CCGGCCACAGCGAGCTAG 62.881 72.222 2.24 0.00 41.24 3.42
541 544 3.533720 GGATCCATCCGACCACGA 58.466 61.111 6.95 0.00 42.66 4.35
553 556 0.878961 GACCACGAACGAGTTGCCTT 60.879 55.000 0.14 0.00 0.00 4.35
560 563 2.427506 GAACGAGTTGCCTTCTGGATT 58.572 47.619 0.00 0.00 34.57 3.01
565 568 3.441572 CGAGTTGCCTTCTGGATTGATTT 59.558 43.478 0.00 0.00 34.57 2.17
576 579 2.093921 TGGATTGATTTGGCGACTACGA 60.094 45.455 0.00 0.00 42.66 3.43
577 580 2.933906 GGATTGATTTGGCGACTACGAA 59.066 45.455 0.00 0.00 42.66 3.85
583 586 1.236616 TTGGCGACTACGAAGACGGA 61.237 55.000 0.00 0.00 44.46 4.69
588 591 1.790838 CGACTACGAAGACGGAAGCTG 60.791 57.143 0.00 0.00 44.46 4.24
594 597 2.159366 ACGAAGACGGAAGCTGACTATG 60.159 50.000 0.00 0.00 44.46 2.23
601 604 2.271800 GGAAGCTGACTATGAACACGG 58.728 52.381 0.00 0.00 0.00 4.94
603 606 3.585862 GAAGCTGACTATGAACACGGAA 58.414 45.455 0.00 0.00 0.00 4.30
606 609 3.064207 GCTGACTATGAACACGGAAACA 58.936 45.455 0.00 0.00 0.00 2.83
610 613 4.876679 TGACTATGAACACGGAAACAAACA 59.123 37.500 0.00 0.00 0.00 2.83
631 634 4.127171 CAAGAGGAAGAAAAAGACGTGGA 58.873 43.478 0.00 0.00 0.00 4.02
632 635 3.996480 AGAGGAAGAAAAAGACGTGGAG 58.004 45.455 0.00 0.00 0.00 3.86
687 691 1.611977 GTTTAAAGGTTTGCTCGGCCT 59.388 47.619 0.00 0.00 0.00 5.19
689 693 0.672401 TAAAGGTTTGCTCGGCCTCG 60.672 55.000 0.00 0.00 37.82 4.63
691 695 4.699522 GGTTTGCTCGGCCTCGGT 62.700 66.667 0.00 0.00 36.95 4.69
693 697 1.375013 GTTTGCTCGGCCTCGGTTA 60.375 57.895 0.00 0.00 36.95 2.85
736 740 4.561735 TTTCAGTTTCGCAGTTTAAGGG 57.438 40.909 0.00 0.00 0.00 3.95
738 742 3.135994 TCAGTTTCGCAGTTTAAGGGTC 58.864 45.455 0.00 0.00 0.00 4.46
750 754 3.611766 TTAAGGGTCTGCTAGAGTTGC 57.388 47.619 0.00 0.00 0.00 4.17
757 761 3.697045 GGTCTGCTAGAGTTGCTCTAAGA 59.303 47.826 7.22 5.68 41.74 2.10
767 774 5.656416 AGAGTTGCTCTAAGACTGCTCTAAT 59.344 40.000 0.00 0.00 39.28 1.73
771 778 7.978975 AGTTGCTCTAAGACTGCTCTAATTTAG 59.021 37.037 0.00 0.00 0.00 1.85
881 897 2.746359 CGCCCCCTCCATCTGATC 59.254 66.667 0.00 0.00 0.00 2.92
882 898 1.840650 CGCCCCCTCCATCTGATCT 60.841 63.158 0.00 0.00 0.00 2.75
883 899 1.825281 CGCCCCCTCCATCTGATCTC 61.825 65.000 0.00 0.00 0.00 2.75
884 900 1.487850 GCCCCCTCCATCTGATCTCC 61.488 65.000 0.00 0.00 0.00 3.71
896 912 0.106469 TGATCTCCCTGTCCCTCTCG 60.106 60.000 0.00 0.00 0.00 4.04
916 932 2.895372 CGCCCGCATTACACCTCC 60.895 66.667 0.00 0.00 0.00 4.30
948 964 1.065345 AGCAGCAGATTCATCAGCAGT 60.065 47.619 6.91 0.00 41.18 4.40
1158 1221 1.732259 CTGAGAAATCCGTGGTTTCCG 59.268 52.381 6.15 0.00 36.48 4.30
1169 1232 2.546373 CGTGGTTTCCGTTGGTAGAGAA 60.546 50.000 0.00 0.00 0.00 2.87
1170 1233 3.671716 GTGGTTTCCGTTGGTAGAGAAT 58.328 45.455 0.00 0.00 0.00 2.40
1171 1234 4.618927 CGTGGTTTCCGTTGGTAGAGAATA 60.619 45.833 0.00 0.00 0.00 1.75
1172 1235 4.868734 GTGGTTTCCGTTGGTAGAGAATAG 59.131 45.833 0.00 0.00 0.00 1.73
1173 1236 3.869832 GGTTTCCGTTGGTAGAGAATAGC 59.130 47.826 0.00 0.00 0.00 2.97
1174 1237 4.501071 GTTTCCGTTGGTAGAGAATAGCA 58.499 43.478 0.00 0.00 0.00 3.49
1198 1261 2.677902 GCATAGCATAGCGGGCAGAATA 60.678 50.000 0.00 0.00 0.00 1.75
1227 1290 1.758514 GCTCGGGATCTCTGACCCA 60.759 63.158 0.00 0.00 45.83 4.51
1246 1309 3.261897 CCCATTTCACTAGTCTGGTCTGT 59.738 47.826 0.00 0.00 0.00 3.41
1349 1412 4.497291 TGGTAGTTTCTGTTGGTGTTCT 57.503 40.909 0.00 0.00 0.00 3.01
1387 1451 4.511454 TGATTCGTCTTGTTTCTGGTTCAG 59.489 41.667 0.00 0.00 0.00 3.02
1474 1544 4.842531 TCTTGCTTACAGGGATCATGAA 57.157 40.909 0.00 0.00 0.00 2.57
1475 1545 5.378230 TCTTGCTTACAGGGATCATGAAT 57.622 39.130 0.00 0.00 0.00 2.57
1476 1546 5.759059 TCTTGCTTACAGGGATCATGAATT 58.241 37.500 0.00 0.00 0.00 2.17
1477 1547 5.824624 TCTTGCTTACAGGGATCATGAATTC 59.175 40.000 0.00 0.00 0.00 2.17
1478 1548 5.114764 TGCTTACAGGGATCATGAATTCA 57.885 39.130 11.26 11.26 0.00 2.57
1479 1549 5.698104 TGCTTACAGGGATCATGAATTCAT 58.302 37.500 15.36 15.36 36.96 2.57
1504 1574 3.501349 TCATGCCATCTAGTCTAGGGTC 58.499 50.000 7.05 0.00 0.00 4.46
1525 1595 1.009829 GATCTGCACCTTGCTTACCG 58.990 55.000 0.00 0.00 45.31 4.02
1541 1615 5.184479 TGCTTACCGGTCATAGTATCATACC 59.816 44.000 12.40 0.00 0.00 2.73
1542 1616 5.184479 GCTTACCGGTCATAGTATCATACCA 59.816 44.000 12.40 0.00 0.00 3.25
1543 1617 6.579666 TTACCGGTCATAGTATCATACCAC 57.420 41.667 12.40 0.00 0.00 4.16
1574 1648 7.634671 TTCAATCAAAGTGCTATGTGATCAT 57.365 32.000 0.00 0.00 38.00 2.45
1610 1684 7.283354 CCTCAAACTTGGTATATTCTTTCCTCC 59.717 40.741 0.00 0.00 0.00 4.30
1628 1702 3.323403 CCTCCACATTTGGGCAAAACTAA 59.677 43.478 0.00 0.00 44.11 2.24
1631 1705 6.279513 TCCACATTTGGGCAAAACTAATAG 57.720 37.500 0.00 0.00 44.11 1.73
1639 1713 5.437060 TGGGCAAAACTAATAGATGTCCTC 58.563 41.667 13.75 0.00 36.72 3.71
1680 1754 0.906775 TGCTGATGATGACTCTGCCA 59.093 50.000 0.00 0.00 36.93 4.92
1729 1803 7.265599 TCTATGGTCTCCCTGAAAAATACAA 57.734 36.000 0.00 0.00 0.00 2.41
1751 1825 1.003233 GCCGCTGAAGAAGGAACCT 60.003 57.895 0.00 0.00 0.00 3.50
1754 1828 1.134670 CCGCTGAAGAAGGAACCTAGG 60.135 57.143 7.41 7.41 0.00 3.02
1852 1926 3.381272 CCGAGGATGCAATTTGGTTGTAT 59.619 43.478 0.00 0.00 44.44 2.29
1856 1930 6.238731 CGAGGATGCAATTTGGTTGTATACAT 60.239 38.462 6.36 0.00 43.84 2.29
1910 1984 2.955614 ACGACGAAATGACCTTACTGG 58.044 47.619 0.00 0.00 42.93 4.00
1927 2001 3.321950 ACTGGAATAGATCAAGGGAGGG 58.678 50.000 0.00 0.00 32.84 4.30
1947 2021 3.826157 GGGGATCATTTCTTTGTCACACA 59.174 43.478 0.00 0.00 0.00 3.72
1948 2022 4.321230 GGGGATCATTTCTTTGTCACACAC 60.321 45.833 0.00 0.00 0.00 3.82
1949 2023 4.278170 GGGATCATTTCTTTGTCACACACA 59.722 41.667 0.00 0.00 0.00 3.72
1986 2061 3.119245 GCTTCCGTTATGAGGTACAGACA 60.119 47.826 0.00 0.00 0.00 3.41
2003 2078 3.809832 CAGACACGAGTTCAAATCCTTGT 59.190 43.478 0.00 0.00 33.94 3.16
2009 2084 5.411361 CACGAGTTCAAATCCTTGTTATGGA 59.589 40.000 0.00 0.00 38.06 3.41
2015 2090 5.200483 TCAAATCCTTGTTATGGACCCATC 58.800 41.667 4.57 0.00 36.30 3.51
2029 2106 9.852784 TTATGGACCCATCCTCTTATAATAAGA 57.147 33.333 4.57 0.00 46.43 2.10
2091 2169 1.836802 TATCCAATTGCAGCACAGCA 58.163 45.000 0.00 0.00 43.99 4.41
2113 2191 1.384191 GGGGCAATGGACCTTCTGT 59.616 57.895 0.00 0.00 44.19 3.41
2129 2207 7.255660 GGACCTTCTGTATACTCTACTGAATGG 60.256 44.444 4.17 9.92 35.74 3.16
2142 2220 1.004044 CTGAATGGGCCAGTCTGACTT 59.996 52.381 31.36 10.78 31.07 3.01
2159 2237 6.868864 GTCTGACTTAATTACTTCTGTCTGCA 59.131 38.462 0.00 0.00 0.00 4.41
2233 2311 4.157656 AGACTGTCAGACTGCTCTTCATAC 59.842 45.833 10.88 0.00 0.00 2.39
2263 2341 5.705905 ACCAGCTGTCTAGTTGAAAATAACC 59.294 40.000 13.81 0.00 37.32 2.85
2339 2419 8.050778 TGGCTATATAAAGTTTCAAACACCAG 57.949 34.615 2.41 0.00 0.00 4.00
2404 2484 4.822026 AGAGAAACCAATTGTACGAGGAG 58.178 43.478 4.43 0.00 0.00 3.69
2445 2525 3.920231 TTGGTCATCTCTTCTCCCATG 57.080 47.619 0.00 0.00 0.00 3.66
2467 2547 2.859165 TTCCCTTGTGCTCTGGTTAG 57.141 50.000 0.00 0.00 0.00 2.34
2528 2608 6.640499 CGTAGGCAAAAGTGAATGAAAATTCA 59.360 34.615 0.00 0.00 42.14 2.57
2529 2609 7.148918 CGTAGGCAAAAGTGAATGAAAATTCAG 60.149 37.037 1.48 0.00 40.77 3.02
2530 2610 5.993441 AGGCAAAAGTGAATGAAAATTCAGG 59.007 36.000 1.48 0.00 40.77 3.86
2531 2611 5.759763 GGCAAAAGTGAATGAAAATTCAGGT 59.240 36.000 1.48 0.00 40.77 4.00
2532 2612 6.293027 GGCAAAAGTGAATGAAAATTCAGGTG 60.293 38.462 1.48 0.59 40.77 4.00
2533 2613 6.652245 CAAAAGTGAATGAAAATTCAGGTGC 58.348 36.000 1.48 0.00 40.77 5.01
2534 2614 5.534207 AAGTGAATGAAAATTCAGGTGCA 57.466 34.783 1.48 0.00 40.77 4.57
2535 2615 4.874970 AGTGAATGAAAATTCAGGTGCAC 58.125 39.130 8.80 8.80 40.77 4.57
2536 2616 4.341806 AGTGAATGAAAATTCAGGTGCACA 59.658 37.500 20.43 0.00 40.77 4.57
2537 2617 4.445385 GTGAATGAAAATTCAGGTGCACAC 59.555 41.667 20.43 8.23 40.77 3.82
2560 2640 3.015145 CCCCCTCCGGTGACCATT 61.015 66.667 4.76 0.00 0.00 3.16
2561 2641 1.691337 CCCCCTCCGGTGACCATTA 60.691 63.158 4.76 0.00 0.00 1.90
2562 2642 1.276140 CCCCCTCCGGTGACCATTAA 61.276 60.000 4.76 0.00 0.00 1.40
2563 2643 0.621609 CCCCTCCGGTGACCATTAAA 59.378 55.000 4.76 0.00 0.00 1.52
2564 2644 1.680860 CCCCTCCGGTGACCATTAAAC 60.681 57.143 4.76 0.00 0.00 2.01
2565 2645 1.365699 CCTCCGGTGACCATTAAACG 58.634 55.000 4.76 0.00 0.00 3.60
2566 2646 1.066716 CCTCCGGTGACCATTAAACGA 60.067 52.381 4.76 0.00 0.00 3.85
2567 2647 2.613474 CCTCCGGTGACCATTAAACGAA 60.613 50.000 4.76 0.00 0.00 3.85
2568 2648 2.671396 CTCCGGTGACCATTAAACGAAG 59.329 50.000 1.11 0.00 0.00 3.79
2569 2649 1.735571 CCGGTGACCATTAAACGAAGG 59.264 52.381 1.11 0.00 0.00 3.46
2570 2650 2.419667 CGGTGACCATTAAACGAAGGT 58.580 47.619 1.11 0.00 37.00 3.50
2571 2651 2.809696 CGGTGACCATTAAACGAAGGTT 59.190 45.455 1.11 0.00 38.22 3.50
2660 2941 1.692411 AAAAAGGACAGACCCAGTGC 58.308 50.000 0.00 0.00 40.05 4.40
2661 2942 0.550914 AAAAGGACAGACCCAGTGCA 59.449 50.000 0.00 0.00 40.05 4.57
2662 2943 0.773644 AAAGGACAGACCCAGTGCAT 59.226 50.000 0.00 0.00 40.05 3.96
2663 2944 1.656587 AAGGACAGACCCAGTGCATA 58.343 50.000 0.00 0.00 40.05 3.14
2664 2945 1.198713 AGGACAGACCCAGTGCATAG 58.801 55.000 0.00 0.00 40.05 2.23
2665 2946 1.195115 GGACAGACCCAGTGCATAGA 58.805 55.000 0.00 0.00 0.00 1.98
2666 2947 1.555075 GGACAGACCCAGTGCATAGAA 59.445 52.381 0.00 0.00 0.00 2.10
2667 2948 2.419297 GGACAGACCCAGTGCATAGAAG 60.419 54.545 0.00 0.00 0.00 2.85
2668 2949 1.065854 ACAGACCCAGTGCATAGAAGC 60.066 52.381 0.00 0.00 0.00 3.86
2669 2950 1.209019 CAGACCCAGTGCATAGAAGCT 59.791 52.381 0.00 0.00 34.99 3.74
2670 2951 1.484240 AGACCCAGTGCATAGAAGCTC 59.516 52.381 0.00 0.00 34.99 4.09
2671 2952 0.543749 ACCCAGTGCATAGAAGCTCC 59.456 55.000 0.00 0.00 34.99 4.70
2672 2953 0.179034 CCCAGTGCATAGAAGCTCCC 60.179 60.000 0.00 0.00 34.99 4.30
2673 2954 0.543277 CCAGTGCATAGAAGCTCCCA 59.457 55.000 0.00 0.00 34.99 4.37
2674 2955 1.661341 CAGTGCATAGAAGCTCCCAC 58.339 55.000 0.00 0.00 34.99 4.61
2675 2956 1.065926 CAGTGCATAGAAGCTCCCACA 60.066 52.381 0.00 0.00 34.99 4.17
2676 2957 1.065854 AGTGCATAGAAGCTCCCACAC 60.066 52.381 0.00 0.00 34.99 3.82
2677 2958 0.983467 TGCATAGAAGCTCCCACACA 59.017 50.000 0.00 0.00 34.99 3.72
2678 2959 1.350684 TGCATAGAAGCTCCCACACAA 59.649 47.619 0.00 0.00 34.99 3.33
2679 2960 2.012673 GCATAGAAGCTCCCACACAAG 58.987 52.381 0.00 0.00 0.00 3.16
2680 2961 2.636830 CATAGAAGCTCCCACACAAGG 58.363 52.381 0.00 0.00 0.00 3.61
2681 2962 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
2689 2970 4.481195 CACACAAGGTGGGGTCTG 57.519 61.111 1.07 0.00 44.04 3.51
2690 2971 1.228245 CACACAAGGTGGGGTCTGG 60.228 63.158 1.07 0.00 44.04 3.86
2691 2972 2.436109 CACAAGGTGGGGTCTGGG 59.564 66.667 0.00 0.00 0.00 4.45
2692 2973 2.038762 ACAAGGTGGGGTCTGGGT 60.039 61.111 0.00 0.00 0.00 4.51
2693 2974 1.131303 CACAAGGTGGGGTCTGGGTA 61.131 60.000 0.00 0.00 0.00 3.69
2694 2975 0.840722 ACAAGGTGGGGTCTGGGTAG 60.841 60.000 0.00 0.00 0.00 3.18
2695 2976 0.546747 CAAGGTGGGGTCTGGGTAGA 60.547 60.000 0.00 0.00 0.00 2.59
2696 2977 0.252742 AAGGTGGGGTCTGGGTAGAG 60.253 60.000 0.00 0.00 32.48 2.43
2708 2989 6.610741 GTCTGGGTAGAGCAAGAAATATTG 57.389 41.667 0.00 0.00 32.48 1.90
2709 2990 6.116126 GTCTGGGTAGAGCAAGAAATATTGT 58.884 40.000 0.00 0.00 32.48 2.71
2710 2991 6.037610 GTCTGGGTAGAGCAAGAAATATTGTG 59.962 42.308 0.00 0.00 32.48 3.33
2711 2992 6.061022 TGGGTAGAGCAAGAAATATTGTGA 57.939 37.500 0.00 0.00 32.56 3.58
2712 2993 6.115446 TGGGTAGAGCAAGAAATATTGTGAG 58.885 40.000 0.00 0.00 32.56 3.51
2713 2994 5.529060 GGGTAGAGCAAGAAATATTGTGAGG 59.471 44.000 0.00 0.00 32.56 3.86
2714 2995 6.349300 GGTAGAGCAAGAAATATTGTGAGGA 58.651 40.000 0.00 0.00 32.56 3.71
2715 2996 6.823689 GGTAGAGCAAGAAATATTGTGAGGAA 59.176 38.462 0.00 0.00 32.56 3.36
2716 2997 7.336931 GGTAGAGCAAGAAATATTGTGAGGAAA 59.663 37.037 0.00 0.00 32.56 3.13
2717 2998 7.951347 AGAGCAAGAAATATTGTGAGGAAAT 57.049 32.000 0.00 0.00 32.56 2.17
2767 3049 6.016693 TCTCAAAATTTTCTCATTGCACGGTA 60.017 34.615 0.00 0.00 0.00 4.02
2798 3080 2.656560 AACAGCGCCTTACAGACTAG 57.343 50.000 2.29 0.00 0.00 2.57
2806 3088 3.002862 CGCCTTACAGACTAGCTCTAGTG 59.997 52.174 13.74 4.08 45.63 2.74
2823 3105 6.404074 GCTCTAGTGGTCTTCAATGGAAATTG 60.404 42.308 0.00 0.00 30.93 2.32
2838 3120 4.834496 TGGAAATTGTTCTCCTCTGCATTT 59.166 37.500 0.00 0.00 33.92 2.32
2839 3121 5.166398 GGAAATTGTTCTCCTCTGCATTTG 58.834 41.667 0.00 0.00 33.92 2.32
2880 3162 2.729028 TAGGTCCAGCTAAATTGCCC 57.271 50.000 0.00 0.00 0.00 5.36
2895 3177 1.962306 GCCCGGTACAAGTTGCGAA 60.962 57.895 1.81 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.028930 CGGAATACCTCAGATACAGGCC 60.029 54.545 0.00 0.00 33.84 5.19
16 17 7.123098 TGAGTTTATAGTTCACGGAATACCTCA 59.877 37.037 0.00 0.00 0.00 3.86
25 26 7.063074 CCTGTAAAGTGAGTTTATAGTTCACGG 59.937 40.741 13.25 0.33 44.45 4.94
26 27 7.597743 ACCTGTAAAGTGAGTTTATAGTTCACG 59.402 37.037 13.25 3.29 44.45 4.35
34 35 4.251268 GCGGACCTGTAAAGTGAGTTTAT 58.749 43.478 0.00 0.00 33.11 1.40
83 84 2.078341 GCGGTTGGCGCGTTTTAAG 61.078 57.895 8.43 0.00 0.00 1.85
154 156 4.825252 GTTCGCCGGGCCATACGT 62.825 66.667 14.55 0.00 0.00 3.57
165 167 7.300320 CCCCGTAATTATTTTTATAGTTCGCC 58.700 38.462 0.00 0.00 0.00 5.54
166 168 6.798476 GCCCCGTAATTATTTTTATAGTTCGC 59.202 38.462 0.00 0.00 0.00 4.70
167 169 7.799914 GTGCCCCGTAATTATTTTTATAGTTCG 59.200 37.037 0.00 0.00 0.00 3.95
173 175 5.131784 TCCGTGCCCCGTAATTATTTTTAT 58.868 37.500 0.00 0.00 33.66 1.40
180 182 2.486472 TTTTCCGTGCCCCGTAATTA 57.514 45.000 0.00 0.00 33.66 1.40
183 185 0.179023 AGTTTTTCCGTGCCCCGTAA 60.179 50.000 0.00 0.00 33.66 3.18
185 187 1.449726 GAAGTTTTTCCGTGCCCCGT 61.450 55.000 0.00 0.00 33.66 5.28
186 188 1.284715 GAAGTTTTTCCGTGCCCCG 59.715 57.895 0.00 0.00 0.00 5.73
205 207 4.575885 TCGTGAATCTAAAGGTTGAAGGG 58.424 43.478 0.00 0.00 0.00 3.95
208 210 4.994852 CACCTCGTGAATCTAAAGGTTGAA 59.005 41.667 0.00 0.00 38.27 2.69
211 213 3.307480 CCCACCTCGTGAATCTAAAGGTT 60.307 47.826 0.00 0.00 38.27 3.50
233 235 2.524394 TATCCTCGGGCCAGCCTC 60.524 66.667 4.39 0.00 36.10 4.70
238 240 1.951923 TACAGGGTATCCTCGGGCCA 61.952 60.000 4.39 0.00 42.67 5.36
240 242 2.226962 TATACAGGGTATCCTCGGGC 57.773 55.000 0.00 0.00 42.67 6.13
250 252 2.223971 CGGTCTTTCGCATATACAGGGT 60.224 50.000 0.00 0.00 0.00 4.34
277 279 1.450312 CGATGGCAGTTGGACTCCC 60.450 63.158 0.00 0.00 0.00 4.30
278 280 1.450312 CCGATGGCAGTTGGACTCC 60.450 63.158 0.00 0.00 0.00 3.85
279 281 0.036388 TTCCGATGGCAGTTGGACTC 60.036 55.000 4.79 0.00 31.25 3.36
280 282 0.400213 TTTCCGATGGCAGTTGGACT 59.600 50.000 4.79 0.00 31.25 3.85
281 283 0.521735 GTTTCCGATGGCAGTTGGAC 59.478 55.000 4.79 0.00 31.25 4.02
282 284 0.400213 AGTTTCCGATGGCAGTTGGA 59.600 50.000 0.00 0.00 0.00 3.53
283 285 1.200020 GAAGTTTCCGATGGCAGTTGG 59.800 52.381 0.00 0.00 0.00 3.77
284 286 1.879380 TGAAGTTTCCGATGGCAGTTG 59.121 47.619 0.00 0.00 0.00 3.16
285 287 2.270352 TGAAGTTTCCGATGGCAGTT 57.730 45.000 0.00 0.00 0.00 3.16
286 288 2.496899 ATGAAGTTTCCGATGGCAGT 57.503 45.000 0.00 0.00 0.00 4.40
287 289 2.289002 GCTATGAAGTTTCCGATGGCAG 59.711 50.000 0.00 0.00 0.00 4.85
288 290 2.092968 AGCTATGAAGTTTCCGATGGCA 60.093 45.455 0.00 0.00 0.00 4.92
289 291 2.545946 GAGCTATGAAGTTTCCGATGGC 59.454 50.000 0.00 0.00 0.00 4.40
290 292 2.797156 CGAGCTATGAAGTTTCCGATGG 59.203 50.000 0.00 0.00 0.00 3.51
291 293 3.706698 TCGAGCTATGAAGTTTCCGATG 58.293 45.455 0.00 0.00 0.00 3.84
292 294 4.386867 TTCGAGCTATGAAGTTTCCGAT 57.613 40.909 0.00 0.00 0.00 4.18
293 295 3.861276 TTCGAGCTATGAAGTTTCCGA 57.139 42.857 0.00 0.00 0.00 4.55
294 296 4.031878 GTCTTTCGAGCTATGAAGTTTCCG 59.968 45.833 0.00 0.00 0.00 4.30
295 297 4.330347 GGTCTTTCGAGCTATGAAGTTTCC 59.670 45.833 0.00 0.00 34.86 3.13
296 298 4.031878 CGGTCTTTCGAGCTATGAAGTTTC 59.968 45.833 0.00 0.00 35.54 2.78
297 299 3.927142 CGGTCTTTCGAGCTATGAAGTTT 59.073 43.478 0.00 0.00 35.54 2.66
298 300 3.056749 ACGGTCTTTCGAGCTATGAAGTT 60.057 43.478 0.00 0.00 35.54 2.66
299 301 2.492484 ACGGTCTTTCGAGCTATGAAGT 59.508 45.455 0.00 0.00 35.54 3.01
300 302 3.109619 GACGGTCTTTCGAGCTATGAAG 58.890 50.000 0.00 0.00 35.54 3.02
301 303 2.477357 CGACGGTCTTTCGAGCTATGAA 60.477 50.000 6.57 0.00 38.85 2.57
302 304 1.063616 CGACGGTCTTTCGAGCTATGA 59.936 52.381 6.57 0.00 38.85 2.15
303 305 1.467875 CGACGGTCTTTCGAGCTATG 58.532 55.000 6.57 0.00 38.85 2.23
304 306 0.381089 CCGACGGTCTTTCGAGCTAT 59.619 55.000 5.48 0.00 38.85 2.97
305 307 1.798735 CCGACGGTCTTTCGAGCTA 59.201 57.895 5.48 0.00 38.85 3.32
306 308 2.567049 CCGACGGTCTTTCGAGCT 59.433 61.111 5.48 0.00 38.85 4.09
307 309 3.179939 GCCGACGGTCTTTCGAGC 61.180 66.667 16.73 0.00 38.85 5.03
308 310 2.874780 CGCCGACGGTCTTTCGAG 60.875 66.667 16.73 0.00 38.85 4.04
309 311 3.318539 CTCGCCGACGGTCTTTCGA 62.319 63.158 16.73 13.99 38.85 3.71
310 312 2.874780 CTCGCCGACGGTCTTTCG 60.875 66.667 16.73 10.13 40.63 3.46
311 313 1.514443 CTCTCGCCGACGGTCTTTC 60.514 63.158 16.73 0.00 40.63 2.62
312 314 2.197643 GACTCTCGCCGACGGTCTTT 62.198 60.000 16.73 0.00 40.63 2.52
313 315 2.672307 ACTCTCGCCGACGGTCTT 60.672 61.111 16.73 0.00 40.63 3.01
314 316 3.126225 GACTCTCGCCGACGGTCT 61.126 66.667 16.73 0.00 40.63 3.85
315 317 4.176851 GGACTCTCGCCGACGGTC 62.177 72.222 16.73 7.00 40.63 4.79
317 319 3.744719 TTGGACTCTCGCCGACGG 61.745 66.667 10.29 10.29 40.63 4.79
318 320 2.504244 GTTGGACTCTCGCCGACG 60.504 66.667 0.00 0.00 42.01 5.12
319 321 1.444553 CAGTTGGACTCTCGCCGAC 60.445 63.158 0.00 0.00 39.64 4.79
320 322 2.962569 CAGTTGGACTCTCGCCGA 59.037 61.111 0.00 0.00 0.00 5.54
321 323 2.811317 GCAGTTGGACTCTCGCCG 60.811 66.667 0.00 0.00 0.00 6.46
322 324 2.435059 GGCAGTTGGACTCTCGCC 60.435 66.667 0.00 0.00 0.00 5.54
323 325 1.078848 ATGGCAGTTGGACTCTCGC 60.079 57.895 0.00 0.00 0.00 5.03
324 326 0.803768 CGATGGCAGTTGGACTCTCG 60.804 60.000 0.00 0.00 0.00 4.04
325 327 0.460987 CCGATGGCAGTTGGACTCTC 60.461 60.000 0.00 0.00 0.00 3.20
375 377 3.885521 GGCGACTAGGACGGACGG 61.886 72.222 12.12 0.00 0.00 4.79
376 378 4.233635 CGGCGACTAGGACGGACG 62.234 72.222 0.00 0.47 0.00 4.79
377 379 4.549516 GCGGCGACTAGGACGGAC 62.550 72.222 12.98 0.00 0.00 4.79
384 386 4.554363 CAGACGGGCGGCGACTAG 62.554 72.222 14.66 10.27 0.00 2.57
461 463 0.537188 AGCTCATTCGTGTCCGGATT 59.463 50.000 7.81 0.00 26.60 3.01
466 468 2.860582 GCTAGCTAGCTCATTCGTGTCC 60.861 54.545 33.71 4.59 45.62 4.02
468 470 2.500509 GCTAGCTAGCTCATTCGTGT 57.499 50.000 33.71 0.00 45.62 4.49
514 517 1.594310 GATGGATCCGGGAGCTAGC 59.406 63.158 12.67 6.62 0.00 3.42
553 556 2.787473 AGTCGCCAAATCAATCCAGA 57.213 45.000 0.00 0.00 0.00 3.86
560 563 2.602878 GTCTTCGTAGTCGCCAAATCA 58.397 47.619 0.00 0.00 36.96 2.57
565 568 1.236616 TTCCGTCTTCGTAGTCGCCA 61.237 55.000 3.37 0.00 36.96 5.69
576 579 3.258372 TGTTCATAGTCAGCTTCCGTCTT 59.742 43.478 0.00 0.00 0.00 3.01
577 580 2.826128 TGTTCATAGTCAGCTTCCGTCT 59.174 45.455 0.00 0.00 0.00 4.18
583 586 3.678056 TTCCGTGTTCATAGTCAGCTT 57.322 42.857 0.00 0.00 0.00 3.74
588 591 5.412526 TGTTTGTTTCCGTGTTCATAGTC 57.587 39.130 0.00 0.00 0.00 2.59
594 597 3.375922 TCCTCTTGTTTGTTTCCGTGTTC 59.624 43.478 0.00 0.00 0.00 3.18
601 604 7.008357 CGTCTTTTTCTTCCTCTTGTTTGTTTC 59.992 37.037 0.00 0.00 0.00 2.78
603 606 6.072119 ACGTCTTTTTCTTCCTCTTGTTTGTT 60.072 34.615 0.00 0.00 0.00 2.83
606 609 5.163652 CCACGTCTTTTTCTTCCTCTTGTTT 60.164 40.000 0.00 0.00 0.00 2.83
610 613 4.101119 TCTCCACGTCTTTTTCTTCCTCTT 59.899 41.667 0.00 0.00 0.00 2.85
658 661 8.294577 CCGAGCAAACCTTTAAACTAAAACTAT 58.705 33.333 0.00 0.00 0.00 2.12
659 662 7.641760 CCGAGCAAACCTTTAAACTAAAACTA 58.358 34.615 0.00 0.00 0.00 2.24
660 663 6.500910 CCGAGCAAACCTTTAAACTAAAACT 58.499 36.000 0.00 0.00 0.00 2.66
671 675 1.966451 CGAGGCCGAGCAAACCTTT 60.966 57.895 0.00 0.00 38.22 3.11
677 681 0.250381 TTTTAACCGAGGCCGAGCAA 60.250 50.000 0.00 0.00 38.22 3.91
680 684 2.463592 GGTTTTAACCGAGGCCGAG 58.536 57.895 0.00 0.00 39.66 4.63
691 695 9.516546 AAAACACATTTTAAGGGTTGGTTTTAA 57.483 25.926 0.00 0.00 36.22 1.52
693 697 7.665974 TGAAAACACATTTTAAGGGTTGGTTTT 59.334 29.630 0.00 0.00 38.17 2.43
701 705 6.292114 GCGAAACTGAAAACACATTTTAAGGG 60.292 38.462 2.68 0.00 39.73 3.95
707 711 4.743493 ACTGCGAAACTGAAAACACATTT 58.257 34.783 0.00 0.00 0.00 2.32
708 712 4.370364 ACTGCGAAACTGAAAACACATT 57.630 36.364 0.00 0.00 0.00 2.71
711 715 5.229260 CCTTAAACTGCGAAACTGAAAACAC 59.771 40.000 0.00 0.00 0.00 3.32
736 740 4.398044 AGTCTTAGAGCAACTCTAGCAGAC 59.602 45.833 19.61 19.61 43.79 3.51
738 742 4.671377 CAGTCTTAGAGCAACTCTAGCAG 58.329 47.826 4.64 1.69 42.92 4.24
767 774 0.739462 CGCGTCATGGTGGCTCTAAA 60.739 55.000 0.00 0.00 0.00 1.85
771 778 2.434185 TTCGCGTCATGGTGGCTC 60.434 61.111 5.77 0.00 0.00 4.70
881 897 3.151022 GGCGAGAGGGACAGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
882 898 4.779733 GGGCGAGAGGGACAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
948 964 3.509388 GGAACGGAGAGAAAGCGAA 57.491 52.632 0.00 0.00 0.00 4.70
977 993 3.175240 CTTGCGGAGTCGTCAGCG 61.175 66.667 0.00 0.00 46.01 5.18
1040 1103 4.845580 AGAGGAGCAATGCCGCCG 62.846 66.667 0.00 0.00 0.00 6.46
1042 1105 2.883267 AAGGAGAGGAGCAATGCCGC 62.883 60.000 0.00 0.00 0.00 6.53
1089 1152 4.241555 CCTTGGATCCTCCCGGCG 62.242 72.222 14.23 0.00 35.03 6.46
1147 1210 0.033781 TCTACCAACGGAAACCACGG 59.966 55.000 0.00 0.00 35.23 4.94
1158 1221 6.533367 GCTATGCTATGCTATTCTCTACCAAC 59.467 42.308 0.00 0.00 0.00 3.77
1169 1232 3.244009 CCCGCTATGCTATGCTATGCTAT 60.244 47.826 0.00 0.00 0.00 2.97
1170 1233 2.101415 CCCGCTATGCTATGCTATGCTA 59.899 50.000 0.00 0.00 0.00 3.49
1171 1234 1.134580 CCCGCTATGCTATGCTATGCT 60.135 52.381 0.00 0.00 0.00 3.79
1172 1235 1.293924 CCCGCTATGCTATGCTATGC 58.706 55.000 0.00 0.00 0.00 3.14
1173 1236 1.293924 GCCCGCTATGCTATGCTATG 58.706 55.000 0.00 0.00 0.00 2.23
1174 1237 0.904649 TGCCCGCTATGCTATGCTAT 59.095 50.000 0.00 0.00 0.00 2.97
1227 1290 5.552870 ACAACAGACCAGACTAGTGAAAT 57.447 39.130 0.00 0.00 0.00 2.17
1246 1309 7.391554 GCATCTGATATGAAATAGGCCTTACAA 59.608 37.037 12.58 0.00 28.50 2.41
1299 1362 8.651389 CCACCTATCTATAATCTCACCTCAAAA 58.349 37.037 0.00 0.00 0.00 2.44
1300 1363 8.010697 TCCACCTATCTATAATCTCACCTCAAA 58.989 37.037 0.00 0.00 0.00 2.69
1301 1364 7.535738 TCCACCTATCTATAATCTCACCTCAA 58.464 38.462 0.00 0.00 0.00 3.02
1302 1365 7.103745 TCCACCTATCTATAATCTCACCTCA 57.896 40.000 0.00 0.00 0.00 3.86
1303 1366 8.474025 CATTCCACCTATCTATAATCTCACCTC 58.526 40.741 0.00 0.00 0.00 3.85
1304 1367 7.401493 CCATTCCACCTATCTATAATCTCACCT 59.599 40.741 0.00 0.00 0.00 4.00
1305 1368 7.181125 ACCATTCCACCTATCTATAATCTCACC 59.819 40.741 0.00 0.00 0.00 4.02
1306 1369 8.140112 ACCATTCCACCTATCTATAATCTCAC 57.860 38.462 0.00 0.00 0.00 3.51
1307 1370 9.480861 CTACCATTCCACCTATCTATAATCTCA 57.519 37.037 0.00 0.00 0.00 3.27
1308 1371 9.482175 ACTACCATTCCACCTATCTATAATCTC 57.518 37.037 0.00 0.00 0.00 2.75
1309 1372 9.845214 AACTACCATTCCACCTATCTATAATCT 57.155 33.333 0.00 0.00 0.00 2.40
1312 1375 9.670442 AGAAACTACCATTCCACCTATCTATAA 57.330 33.333 0.00 0.00 0.00 0.98
1313 1376 9.090103 CAGAAACTACCATTCCACCTATCTATA 57.910 37.037 0.00 0.00 0.00 1.31
1314 1377 7.569111 ACAGAAACTACCATTCCACCTATCTAT 59.431 37.037 0.00 0.00 0.00 1.98
1315 1378 6.901300 ACAGAAACTACCATTCCACCTATCTA 59.099 38.462 0.00 0.00 0.00 1.98
1316 1379 5.726793 ACAGAAACTACCATTCCACCTATCT 59.273 40.000 0.00 0.00 0.00 1.98
1317 1380 5.990668 ACAGAAACTACCATTCCACCTATC 58.009 41.667 0.00 0.00 0.00 2.08
1318 1381 6.180472 CAACAGAAACTACCATTCCACCTAT 58.820 40.000 0.00 0.00 0.00 2.57
1319 1382 5.514136 CCAACAGAAACTACCATTCCACCTA 60.514 44.000 0.00 0.00 0.00 3.08
1320 1383 4.398319 CAACAGAAACTACCATTCCACCT 58.602 43.478 0.00 0.00 0.00 4.00
1349 1412 5.421056 AGACGAATCACTTGGGTGTAGATTA 59.579 40.000 0.00 0.00 43.41 1.75
1387 1451 8.957466 AGGTGCTTAATAAAAGATGGTTAGAAC 58.043 33.333 0.00 0.00 0.00 3.01
1474 1544 6.780901 AGACTAGATGGCATGAATCATGAAT 58.219 36.000 25.77 17.35 43.81 2.57
1475 1545 6.183810 AGACTAGATGGCATGAATCATGAA 57.816 37.500 25.77 13.53 43.81 2.57
1476 1546 5.820404 AGACTAGATGGCATGAATCATGA 57.180 39.130 25.77 7.23 43.81 3.07
1477 1547 6.107343 CCTAGACTAGATGGCATGAATCATG 58.893 44.000 18.25 18.25 43.91 3.07
1478 1548 5.189342 CCCTAGACTAGATGGCATGAATCAT 59.811 44.000 3.81 0.00 0.00 2.45
1479 1549 4.529769 CCCTAGACTAGATGGCATGAATCA 59.470 45.833 3.81 0.00 0.00 2.57
1480 1550 4.530161 ACCCTAGACTAGATGGCATGAATC 59.470 45.833 3.81 0.00 0.00 2.52
1481 1551 4.497516 ACCCTAGACTAGATGGCATGAAT 58.502 43.478 3.81 0.00 0.00 2.57
1487 1557 3.231207 TCTGACCCTAGACTAGATGGC 57.769 52.381 11.27 4.64 0.00 4.40
1490 1560 4.105537 TGCAGATCTGACCCTAGACTAGAT 59.894 45.833 27.04 0.00 0.00 1.98
1525 1595 5.046304 AGCATGGTGGTATGATACTATGACC 60.046 44.000 0.00 4.98 37.81 4.02
1541 1615 3.430895 GCACTTTGATTGAAAGCATGGTG 59.569 43.478 0.00 8.68 44.48 4.17
1542 1616 3.322828 AGCACTTTGATTGAAAGCATGGT 59.677 39.130 0.00 0.00 44.48 3.55
1543 1617 3.921677 AGCACTTTGATTGAAAGCATGG 58.078 40.909 0.00 0.00 44.48 3.66
1574 1648 2.562298 CCAAGTTTGAGGGCATTGCTTA 59.438 45.455 8.82 0.00 0.00 3.09
1610 1684 7.322664 ACATCTATTAGTTTTGCCCAAATGTG 58.677 34.615 0.00 0.00 0.00 3.21
1628 1702 2.437281 CTGTTGGCCAGAGGACATCTAT 59.563 50.000 5.11 0.00 42.18 1.98
1631 1705 0.615331 TCTGTTGGCCAGAGGACATC 59.385 55.000 5.11 0.00 42.18 3.06
1639 1713 3.452627 ACTTCCTATACTCTGTTGGCCAG 59.547 47.826 5.11 0.00 42.97 4.85
1651 1725 6.015519 AGAGTCATCATCAGCACTTCCTATAC 60.016 42.308 0.00 0.00 0.00 1.47
1680 1754 2.057922 CATATACACCTTGAGCCCCCT 58.942 52.381 0.00 0.00 0.00 4.79
1729 1803 0.108585 TTCCTTCTTCAGCGGCTTGT 59.891 50.000 0.00 0.00 0.00 3.16
1776 1850 5.447778 AACTGTTCCATGAAGATCTCCAT 57.552 39.130 0.00 0.00 0.00 3.41
1795 1869 1.134521 TCACACTCGGCAACAGAAACT 60.135 47.619 0.00 0.00 0.00 2.66
1808 1882 5.237344 CGGGATTAAAATCTGGATCACACTC 59.763 44.000 0.00 0.00 35.73 3.51
1852 1926 3.811497 GCTGCACATCTGAATAGCATGTA 59.189 43.478 0.00 0.00 34.35 2.29
1856 1930 1.292992 CGCTGCACATCTGAATAGCA 58.707 50.000 0.00 0.00 0.00 3.49
1910 1984 4.171234 TGATCCCCTCCCTTGATCTATTC 58.829 47.826 0.00 0.00 36.65 1.75
1927 2001 5.437289 TGTGTGTGACAAAGAAATGATCC 57.563 39.130 0.00 0.00 0.00 3.36
1947 2021 1.696063 AGCAAGCACCAAAGTCATGT 58.304 45.000 0.00 0.00 0.00 3.21
1948 2022 2.608752 GGAAGCAAGCACCAAAGTCATG 60.609 50.000 0.00 0.00 0.00 3.07
1949 2023 1.615392 GGAAGCAAGCACCAAAGTCAT 59.385 47.619 0.00 0.00 0.00 3.06
1986 2061 5.411669 GTCCATAACAAGGATTTGAACTCGT 59.588 40.000 0.00 0.00 37.52 4.18
2029 2106 7.040478 ACACATGTACTCAGCATTACACAATTT 60.040 33.333 0.00 0.00 31.09 1.82
2038 2115 4.314961 TCGAAACACATGTACTCAGCATT 58.685 39.130 0.00 0.00 0.00 3.56
2040 2117 3.317150 CTCGAAACACATGTACTCAGCA 58.683 45.455 0.00 0.00 0.00 4.41
2091 2169 0.324645 GAAGGTCCATTGCCCCATGT 60.325 55.000 0.00 0.00 0.00 3.21
2113 2191 4.816126 ACTGGCCCATTCAGTAGAGTATA 58.184 43.478 0.00 0.00 42.91 1.47
2129 2207 5.582665 CAGAAGTAATTAAGTCAGACTGGCC 59.417 44.000 3.05 0.00 0.00 5.36
2142 2220 6.726258 CACATGTGCAGACAGAAGTAATTA 57.274 37.500 13.94 0.00 34.87 1.40
2233 2311 5.330455 TCAACTAGACAGCTGGTTATGAG 57.670 43.478 19.93 8.53 43.02 2.90
2263 2341 6.207417 GGAAATATGGTATGGAATGACAGGTG 59.793 42.308 0.00 0.00 0.00 4.00
2330 2410 9.665264 GTTAAAGAAAGATAGAACTGGTGTTTG 57.335 33.333 0.00 0.00 36.39 2.93
2372 2452 7.365497 ACAATTGGTTTCTCTTCCTGAAATT 57.635 32.000 10.83 0.00 36.10 1.82
2431 2511 4.837218 AGGGAATACATGGGAGAAGAGAT 58.163 43.478 0.00 0.00 0.00 2.75
2445 2525 2.789409 ACCAGAGCACAAGGGAATAC 57.211 50.000 0.00 0.00 0.00 1.89
2467 2547 3.306019 CCCCTTGCAACATAGGTTCAAAC 60.306 47.826 0.00 0.00 34.21 2.93
2503 2583 6.640499 TGAATTTTCATTCACTTTTGCCTACG 59.360 34.615 0.00 0.00 43.32 3.51
2547 2627 2.373540 TCGTTTAATGGTCACCGGAG 57.626 50.000 9.46 0.00 0.00 4.63
2548 2628 2.613474 CCTTCGTTTAATGGTCACCGGA 60.613 50.000 9.46 0.00 0.00 5.14
2549 2629 1.735571 CCTTCGTTTAATGGTCACCGG 59.264 52.381 0.00 0.00 0.00 5.28
2550 2630 2.419667 ACCTTCGTTTAATGGTCACCG 58.580 47.619 0.00 0.00 0.00 4.94
2551 2631 4.841443 AAACCTTCGTTTAATGGTCACC 57.159 40.909 0.00 0.00 40.47 4.02
2641 2922 1.064017 TGCACTGGGTCTGTCCTTTTT 60.064 47.619 0.00 0.00 36.25 1.94
2643 2924 0.773644 ATGCACTGGGTCTGTCCTTT 59.226 50.000 0.00 0.00 36.25 3.11
2644 2925 1.556911 CTATGCACTGGGTCTGTCCTT 59.443 52.381 0.00 0.00 36.25 3.36
2646 2927 1.195115 TCTATGCACTGGGTCTGTCC 58.805 55.000 0.00 0.00 0.00 4.02
2647 2928 2.898705 CTTCTATGCACTGGGTCTGTC 58.101 52.381 0.00 0.00 0.00 3.51
2648 2929 1.065854 GCTTCTATGCACTGGGTCTGT 60.066 52.381 0.00 0.00 0.00 3.41
2649 2930 1.209019 AGCTTCTATGCACTGGGTCTG 59.791 52.381 0.00 0.00 34.99 3.51
2650 2931 1.484240 GAGCTTCTATGCACTGGGTCT 59.516 52.381 0.00 0.00 34.99 3.85
2651 2932 1.474143 GGAGCTTCTATGCACTGGGTC 60.474 57.143 0.00 0.00 34.99 4.46
2652 2933 0.543749 GGAGCTTCTATGCACTGGGT 59.456 55.000 0.00 0.00 34.99 4.51
2653 2934 0.179034 GGGAGCTTCTATGCACTGGG 60.179 60.000 0.00 0.00 34.99 4.45
2654 2935 0.543277 TGGGAGCTTCTATGCACTGG 59.457 55.000 0.00 0.00 34.99 4.00
2655 2936 1.065926 TGTGGGAGCTTCTATGCACTG 60.066 52.381 0.00 0.00 34.99 3.66
2656 2937 1.065854 GTGTGGGAGCTTCTATGCACT 60.066 52.381 0.00 0.00 34.99 4.40
2657 2938 1.339055 TGTGTGGGAGCTTCTATGCAC 60.339 52.381 0.00 0.00 34.99 4.57
2658 2939 0.983467 TGTGTGGGAGCTTCTATGCA 59.017 50.000 0.00 0.00 34.99 3.96
2659 2940 2.012673 CTTGTGTGGGAGCTTCTATGC 58.987 52.381 0.00 0.00 0.00 3.14
2660 2941 2.026822 ACCTTGTGTGGGAGCTTCTATG 60.027 50.000 0.00 0.00 0.00 2.23
2661 2942 2.026822 CACCTTGTGTGGGAGCTTCTAT 60.027 50.000 0.00 0.00 41.52 1.98
2662 2943 1.347707 CACCTTGTGTGGGAGCTTCTA 59.652 52.381 0.00 0.00 41.52 2.10
2663 2944 0.109342 CACCTTGTGTGGGAGCTTCT 59.891 55.000 0.00 0.00 41.52 2.85
2664 2945 2.633860 CACCTTGTGTGGGAGCTTC 58.366 57.895 0.00 0.00 41.52 3.86
2665 2946 4.907457 CACCTTGTGTGGGAGCTT 57.093 55.556 0.00 0.00 41.52 3.74
2672 2953 1.228245 CCAGACCCCACCTTGTGTG 60.228 63.158 0.00 0.00 45.01 3.82
2673 2954 2.460853 CCCAGACCCCACCTTGTGT 61.461 63.158 0.00 0.00 0.00 3.72
2674 2955 1.131303 TACCCAGACCCCACCTTGTG 61.131 60.000 0.00 0.00 0.00 3.33
2675 2956 0.840722 CTACCCAGACCCCACCTTGT 60.841 60.000 0.00 0.00 0.00 3.16
2676 2957 0.546747 TCTACCCAGACCCCACCTTG 60.547 60.000 0.00 0.00 0.00 3.61
2677 2958 0.252742 CTCTACCCAGACCCCACCTT 60.253 60.000 0.00 0.00 0.00 3.50
2678 2959 1.392534 CTCTACCCAGACCCCACCT 59.607 63.158 0.00 0.00 0.00 4.00
2679 2960 2.368011 GCTCTACCCAGACCCCACC 61.368 68.421 0.00 0.00 0.00 4.61
2680 2961 1.198759 TTGCTCTACCCAGACCCCAC 61.199 60.000 0.00 0.00 0.00 4.61
2681 2962 0.909610 CTTGCTCTACCCAGACCCCA 60.910 60.000 0.00 0.00 0.00 4.96
2682 2963 0.617820 TCTTGCTCTACCCAGACCCC 60.618 60.000 0.00 0.00 0.00 4.95
2683 2964 1.276622 TTCTTGCTCTACCCAGACCC 58.723 55.000 0.00 0.00 0.00 4.46
2684 2965 3.636153 ATTTCTTGCTCTACCCAGACC 57.364 47.619 0.00 0.00 0.00 3.85
2685 2966 6.037610 CACAATATTTCTTGCTCTACCCAGAC 59.962 42.308 0.00 0.00 0.00 3.51
2686 2967 6.070251 TCACAATATTTCTTGCTCTACCCAGA 60.070 38.462 0.00 0.00 0.00 3.86
2687 2968 6.115446 TCACAATATTTCTTGCTCTACCCAG 58.885 40.000 0.00 0.00 0.00 4.45
2688 2969 6.061022 TCACAATATTTCTTGCTCTACCCA 57.939 37.500 0.00 0.00 0.00 4.51
2689 2970 5.529060 CCTCACAATATTTCTTGCTCTACCC 59.471 44.000 0.00 0.00 0.00 3.69
2690 2971 6.349300 TCCTCACAATATTTCTTGCTCTACC 58.651 40.000 0.00 0.00 0.00 3.18
2691 2972 7.849804 TTCCTCACAATATTTCTTGCTCTAC 57.150 36.000 0.00 0.00 0.00 2.59
2693 2974 7.951347 ATTTCCTCACAATATTTCTTGCTCT 57.049 32.000 0.00 0.00 0.00 4.09
2706 2987 9.528018 GTTGAAGAAACATTTATTTCCTCACAA 57.472 29.630 0.22 0.00 38.27 3.33
2707 2988 8.690884 TGTTGAAGAAACATTTATTTCCTCACA 58.309 29.630 0.22 0.96 43.96 3.58
2749 3030 4.759693 TGTTCTACCGTGCAATGAGAAAAT 59.240 37.500 0.00 0.00 0.00 1.82
2785 3067 3.316868 CCACTAGAGCTAGTCTGTAAGGC 59.683 52.174 7.19 0.00 43.98 4.35
2798 3080 3.895232 TCCATTGAAGACCACTAGAGC 57.105 47.619 0.00 0.00 0.00 4.09
2806 3088 5.478332 AGGAGAACAATTTCCATTGAAGACC 59.522 40.000 1.97 0.00 42.35 3.85
2823 3105 1.734465 CGACCAAATGCAGAGGAGAAC 59.266 52.381 8.66 0.00 0.00 3.01
2838 3120 2.176314 ATCAGCAGAAGCAGCGACCA 62.176 55.000 0.00 0.00 45.49 4.02
2839 3121 1.023513 AATCAGCAGAAGCAGCGACC 61.024 55.000 0.00 0.00 45.49 4.79
2873 3155 0.601057 GCAACTTGTACCGGGCAATT 59.399 50.000 6.32 2.01 0.00 2.32
2875 3157 2.255172 CGCAACTTGTACCGGGCAA 61.255 57.895 6.32 10.05 0.00 4.52


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

AutoCloner maintained by Alex Coulton.