Multiple sequence alignment - TraesCS3D01G421500

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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 TraesCS3D01G421500 chr3D 100.000 6595 0 0 1 6595 533866993 533873587 0.000000e+00 12179
1 TraesCS3D01G421500 chr3B 92.697 4149 233 33 644 4736 705698801 705702935 0.000000e+00 5919
2 TraesCS3D01G421500 chr3B 92.965 1862 67 25 4786 6595 705702935 705704784 0.000000e+00 2654
3 TraesCS3D01G421500 chr3B 85.185 513 53 8 128 619 705698183 705698693 7.630000e-139 505
4 TraesCS3D01G421500 chr3B 91.453 117 10 0 1 117 705594120 705594236 1.900000e-35 161
5 TraesCS3D01G421500 chr3A 93.622 3559 168 24 749 4256 669616110 669619660 0.000000e+00 5260
6 TraesCS3D01G421500 chr3A 91.624 1743 81 23 4900 6595 669620319 669622043 0.000000e+00 2350
7 TraesCS3D01G421500 chr3A 95.563 631 27 1 4248 4878 669619701 669620330 0.000000e+00 1009


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 TraesCS3D01G421500 chr3D 533866993 533873587 6594 False 12179 12179 100.000000 1 6595 1 chr3D.!!$F1 6594
1 TraesCS3D01G421500 chr3B 705698183 705704784 6601 False 3026 5919 90.282333 128 6595 3 chr3B.!!$F2 6467
2 TraesCS3D01G421500 chr3A 669616110 669622043 5933 False 2873 5260 93.603000 749 6595 3 chr3A.!!$F1 5846

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
106 107 0.108138 ACACCAGCTCGTCCTAATGC 60.108 55.000 0.00 0.00 0.00 3.56 F
520 542 0.110486 CCTGTTGGGTTGTGGCTAGT 59.890 55.000 0.00 0.00 0.00 2.57 F
729 844 0.340208 GGGGAGGAGGAGAAAGAGGA 59.660 60.000 0.00 0.00 0.00 3.71 F
1251 1375 0.391263 GTTCAGCGGGGGTGAGTTAG 60.391 60.000 0.00 0.00 41.12 2.34 F
1686 1828 1.269309 TGTGCCATTGTTGCCGTAAAC 60.269 47.619 0.00 0.00 0.00 2.01 F
2055 2203 1.990160 TTTGTGTGGAAGCGGGGAGT 61.990 55.000 0.00 0.00 0.00 3.85 F
3502 3674 1.795286 GTACGCTCATCTATTGCCTGC 59.205 52.381 0.00 0.00 0.00 4.85 F
4710 4935 0.250081 GTCAGGCTATAGGCACAGGC 60.250 60.000 26.41 14.26 44.01 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1465 0.546122 TTCCGCATACTTCCCTGCAT 59.454 50.0 0.00 0.0 38.30 3.96 R
2114 2262 0.521291 TGCGAAGAAATTGGAAGCCG 59.479 50.0 0.00 0.0 0.00 5.52 R
2555 2720 0.250727 GGGGACTAAGCAGCAACACA 60.251 55.0 0.00 0.0 0.00 3.72 R
2914 3081 1.286248 ATTGGAGCGAAGTACCCCTT 58.714 50.0 0.00 0.0 35.59 3.95 R
3485 3657 0.250209 AGGCAGGCAATAGATGAGCG 60.250 55.0 0.00 0.0 0.00 5.03 R
3753 3925 1.412079 AACAAACCATTGGCAGCTGA 58.588 45.0 20.43 0.0 41.01 4.26 R
5202 5434 0.467290 GCACTTCCAAGTCCAACCCA 60.467 55.0 0.00 0.0 37.08 4.51 R
5701 5956 0.607217 GTTGAAACCGGTCGGGGATT 60.607 55.0 8.04 0.0 41.60 3.01 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
19 20 2.827642 GCATCAGTGGAGCCAGCC 60.828 66.667 0.00 0.00 0.00 4.85
20 21 2.672908 CATCAGTGGAGCCAGCCA 59.327 61.111 0.00 0.00 35.02 4.75
21 22 1.001764 CATCAGTGGAGCCAGCCAA 60.002 57.895 0.00 0.00 40.20 4.52
22 23 1.030488 CATCAGTGGAGCCAGCCAAG 61.030 60.000 0.00 0.00 40.20 3.61
23 24 2.207501 ATCAGTGGAGCCAGCCAAGG 62.208 60.000 0.00 0.00 40.20 3.61
24 25 2.856000 AGTGGAGCCAGCCAAGGT 60.856 61.111 0.00 0.00 40.20 3.50
25 26 2.674380 GTGGAGCCAGCCAAGGTG 60.674 66.667 0.00 0.00 40.20 4.00
31 32 2.276740 CCAGCCAAGGTGGGATCC 59.723 66.667 1.92 1.92 46.19 3.36
32 33 2.276740 CAGCCAAGGTGGGATCCC 59.723 66.667 25.22 25.22 38.19 3.85
33 34 3.023735 AGCCAAGGTGGGATCCCC 61.024 66.667 28.58 18.49 45.71 4.81
45 46 0.778083 GGATCCCCCACCTATTTCCC 59.222 60.000 0.00 0.00 34.14 3.97
46 47 1.702567 GGATCCCCCACCTATTTCCCT 60.703 57.143 0.00 0.00 34.14 4.20
47 48 2.144450 GATCCCCCACCTATTTCCCTT 58.856 52.381 0.00 0.00 0.00 3.95
48 49 1.603634 TCCCCCACCTATTTCCCTTC 58.396 55.000 0.00 0.00 0.00 3.46
49 50 1.083912 TCCCCCACCTATTTCCCTTCT 59.916 52.381 0.00 0.00 0.00 2.85
50 51 1.930204 CCCCCACCTATTTCCCTTCTT 59.070 52.381 0.00 0.00 0.00 2.52
51 52 2.091830 CCCCCACCTATTTCCCTTCTTC 60.092 54.545 0.00 0.00 0.00 2.87
52 53 2.091830 CCCCACCTATTTCCCTTCTTCC 60.092 54.545 0.00 0.00 0.00 3.46
53 54 2.580783 CCCACCTATTTCCCTTCTTCCA 59.419 50.000 0.00 0.00 0.00 3.53
54 55 3.205282 CCCACCTATTTCCCTTCTTCCAT 59.795 47.826 0.00 0.00 0.00 3.41
55 56 4.326132 CCCACCTATTTCCCTTCTTCCATT 60.326 45.833 0.00 0.00 0.00 3.16
56 57 4.646492 CCACCTATTTCCCTTCTTCCATTG 59.354 45.833 0.00 0.00 0.00 2.82
57 58 4.098501 CACCTATTTCCCTTCTTCCATTGC 59.901 45.833 0.00 0.00 0.00 3.56
58 59 3.316308 CCTATTTCCCTTCTTCCATTGCG 59.684 47.826 0.00 0.00 0.00 4.85
59 60 2.577606 TTTCCCTTCTTCCATTGCGA 57.422 45.000 0.00 0.00 0.00 5.10
60 61 1.821216 TTCCCTTCTTCCATTGCGAC 58.179 50.000 0.00 0.00 0.00 5.19
61 62 0.690192 TCCCTTCTTCCATTGCGACA 59.310 50.000 0.00 0.00 0.00 4.35
62 63 1.073125 TCCCTTCTTCCATTGCGACAA 59.927 47.619 0.00 0.00 0.00 3.18
63 64 2.094675 CCCTTCTTCCATTGCGACAAT 58.905 47.619 0.00 0.00 0.00 2.71
64 65 3.054728 TCCCTTCTTCCATTGCGACAATA 60.055 43.478 5.03 0.00 0.00 1.90
65 66 3.694072 CCCTTCTTCCATTGCGACAATAA 59.306 43.478 5.03 0.00 0.00 1.40
66 67 4.201950 CCCTTCTTCCATTGCGACAATAAG 60.202 45.833 5.03 6.71 0.00 1.73
67 68 4.201950 CCTTCTTCCATTGCGACAATAAGG 60.202 45.833 12.47 12.47 0.00 2.69
68 69 4.214986 TCTTCCATTGCGACAATAAGGA 57.785 40.909 5.03 6.27 0.00 3.36
69 70 4.191544 TCTTCCATTGCGACAATAAGGAG 58.808 43.478 5.03 4.92 0.00 3.69
70 71 3.904800 TCCATTGCGACAATAAGGAGA 57.095 42.857 5.03 0.00 0.00 3.71
71 72 3.797039 TCCATTGCGACAATAAGGAGAG 58.203 45.455 5.03 0.00 0.00 3.20
72 73 3.450817 TCCATTGCGACAATAAGGAGAGA 59.549 43.478 5.03 0.00 0.00 3.10
73 74 4.081142 TCCATTGCGACAATAAGGAGAGAA 60.081 41.667 5.03 0.00 0.00 2.87
74 75 4.818546 CCATTGCGACAATAAGGAGAGAAT 59.181 41.667 5.03 0.00 0.00 2.40
75 76 5.297776 CCATTGCGACAATAAGGAGAGAATT 59.702 40.000 5.03 0.00 0.00 2.17
76 77 5.801350 TTGCGACAATAAGGAGAGAATTG 57.199 39.130 0.00 0.00 36.80 2.32
77 78 5.084818 TGCGACAATAAGGAGAGAATTGA 57.915 39.130 1.59 0.00 35.18 2.57
78 79 5.487433 TGCGACAATAAGGAGAGAATTGAA 58.513 37.500 1.59 0.00 35.18 2.69
79 80 5.582269 TGCGACAATAAGGAGAGAATTGAAG 59.418 40.000 1.59 0.00 35.18 3.02
80 81 5.007136 GCGACAATAAGGAGAGAATTGAAGG 59.993 44.000 1.59 0.00 35.18 3.46
81 82 5.525378 CGACAATAAGGAGAGAATTGAAGGG 59.475 44.000 1.59 0.00 35.18 3.95
82 83 6.394345 ACAATAAGGAGAGAATTGAAGGGT 57.606 37.500 1.59 0.00 35.18 4.34
83 84 6.183347 ACAATAAGGAGAGAATTGAAGGGTG 58.817 40.000 1.59 0.00 35.18 4.61
84 85 2.797177 AGGAGAGAATTGAAGGGTGC 57.203 50.000 0.00 0.00 0.00 5.01
85 86 1.283321 AGGAGAGAATTGAAGGGTGCC 59.717 52.381 0.00 0.00 0.00 5.01
86 87 1.683319 GGAGAGAATTGAAGGGTGCCC 60.683 57.143 0.00 0.00 0.00 5.36
87 88 1.004745 GAGAGAATTGAAGGGTGCCCA 59.995 52.381 10.26 0.00 38.92 5.36
88 89 1.177401 GAGAATTGAAGGGTGCCCAC 58.823 55.000 10.26 3.98 38.92 4.61
89 90 0.482446 AGAATTGAAGGGTGCCCACA 59.518 50.000 10.26 6.55 38.92 4.17
90 91 0.603065 GAATTGAAGGGTGCCCACAC 59.397 55.000 10.26 0.00 46.66 3.82
98 99 4.626081 GTGCCCACACCAGCTCGT 62.626 66.667 0.00 0.00 41.21 4.18
99 100 4.314440 TGCCCACACCAGCTCGTC 62.314 66.667 0.00 0.00 0.00 4.20
101 102 3.314331 CCCACACCAGCTCGTCCT 61.314 66.667 0.00 0.00 0.00 3.85
102 103 1.982395 CCCACACCAGCTCGTCCTA 60.982 63.158 0.00 0.00 0.00 2.94
103 104 1.541310 CCCACACCAGCTCGTCCTAA 61.541 60.000 0.00 0.00 0.00 2.69
104 105 0.537188 CCACACCAGCTCGTCCTAAT 59.463 55.000 0.00 0.00 0.00 1.73
105 106 1.645034 CACACCAGCTCGTCCTAATG 58.355 55.000 0.00 0.00 0.00 1.90
106 107 0.108138 ACACCAGCTCGTCCTAATGC 60.108 55.000 0.00 0.00 0.00 3.56
107 108 0.811616 CACCAGCTCGTCCTAATGCC 60.812 60.000 0.00 0.00 0.00 4.40
108 109 1.227674 CCAGCTCGTCCTAATGCCC 60.228 63.158 0.00 0.00 0.00 5.36
109 110 1.592669 CAGCTCGTCCTAATGCCCG 60.593 63.158 0.00 0.00 0.00 6.13
110 111 2.280186 GCTCGTCCTAATGCCCGG 60.280 66.667 0.00 0.00 0.00 5.73
111 112 3.090219 GCTCGTCCTAATGCCCGGT 62.090 63.158 0.00 0.00 0.00 5.28
112 113 1.520666 CTCGTCCTAATGCCCGGTT 59.479 57.895 0.00 0.00 0.00 4.44
113 114 0.810031 CTCGTCCTAATGCCCGGTTG 60.810 60.000 0.00 0.00 0.00 3.77
114 115 1.219664 CGTCCTAATGCCCGGTTGA 59.780 57.895 0.00 0.00 0.00 3.18
115 116 0.391927 CGTCCTAATGCCCGGTTGAA 60.392 55.000 0.00 0.00 0.00 2.69
116 117 1.092348 GTCCTAATGCCCGGTTGAAC 58.908 55.000 0.00 0.00 0.00 3.18
117 118 0.988832 TCCTAATGCCCGGTTGAACT 59.011 50.000 0.00 0.00 0.00 3.01
118 119 1.353022 TCCTAATGCCCGGTTGAACTT 59.647 47.619 0.00 0.00 0.00 2.66
119 120 2.572556 TCCTAATGCCCGGTTGAACTTA 59.427 45.455 0.00 0.00 0.00 2.24
120 121 3.201266 TCCTAATGCCCGGTTGAACTTAT 59.799 43.478 0.00 0.00 0.00 1.73
121 122 3.951680 CCTAATGCCCGGTTGAACTTATT 59.048 43.478 0.00 0.00 0.00 1.40
122 123 4.401202 CCTAATGCCCGGTTGAACTTATTT 59.599 41.667 0.00 0.00 0.00 1.40
123 124 3.866883 ATGCCCGGTTGAACTTATTTG 57.133 42.857 0.00 0.00 0.00 2.32
124 125 1.889829 TGCCCGGTTGAACTTATTTGG 59.110 47.619 0.00 0.00 0.00 3.28
125 126 1.203758 GCCCGGTTGAACTTATTTGGG 59.796 52.381 0.00 0.00 38.47 4.12
126 127 1.822371 CCCGGTTGAACTTATTTGGGG 59.178 52.381 0.00 0.00 0.00 4.96
146 147 1.986882 GGGGGTATCTGCCAAATCTG 58.013 55.000 0.00 0.00 0.00 2.90
147 148 1.479389 GGGGGTATCTGCCAAATCTGG 60.479 57.143 0.00 0.00 46.65 3.86
159 160 2.029623 CAAATCTGGCTCCTTCCCATG 58.970 52.381 0.00 0.00 0.00 3.66
200 201 4.181578 GGTGCAGTAAACGATGACATAGT 58.818 43.478 0.00 0.00 0.00 2.12
240 245 2.035832 CCAAACACAAGACAATGACCCC 59.964 50.000 0.00 0.00 0.00 4.95
245 250 2.162208 CACAAGACAATGACCCCAATCG 59.838 50.000 0.00 0.00 0.00 3.34
255 260 2.703536 TGACCCCAATCGTGCTATACAT 59.296 45.455 0.00 0.00 0.00 2.29
260 265 4.578516 CCCCAATCGTGCTATACATTGAAA 59.421 41.667 0.00 0.00 33.46 2.69
280 295 2.539081 AACCCAAGCTCCCCACTCC 61.539 63.158 0.00 0.00 0.00 3.85
314 329 4.677584 CTGACGTAGAAAAGAGATGGGAG 58.322 47.826 0.00 0.00 0.00 4.30
317 332 2.799917 CGTAGAAAAGAGATGGGAGCCG 60.800 54.545 0.00 0.00 0.00 5.52
322 337 1.201429 AAGAGATGGGAGCCGGTGTT 61.201 55.000 1.90 0.00 0.00 3.32
335 350 0.179081 CGGTGTTAGGCCTAGGCTTC 60.179 60.000 32.18 17.43 39.70 3.86
358 373 1.819288 TCGACATCAGTTGGTCTCTCC 59.181 52.381 0.00 0.00 31.88 3.71
359 374 1.134965 CGACATCAGTTGGTCTCTCCC 60.135 57.143 0.00 0.00 34.77 4.30
382 397 4.281688 CCAGTTCACATGTCCATTTCCTTT 59.718 41.667 0.00 0.00 0.00 3.11
386 401 7.121759 CAGTTCACATGTCCATTTCCTTTAGAT 59.878 37.037 0.00 0.00 0.00 1.98
393 408 8.499162 CATGTCCATTTCCTTTAGATAACGATC 58.501 37.037 0.00 0.00 0.00 3.69
420 435 2.890808 TCCTACAGCCGTGATTCATC 57.109 50.000 0.00 0.00 0.00 2.92
427 442 1.143838 CCGTGATTCATCCGGAGCA 59.856 57.895 11.34 0.00 40.63 4.26
431 446 2.141517 GTGATTCATCCGGAGCATGAG 58.858 52.381 11.34 0.00 0.00 2.90
432 447 1.764723 TGATTCATCCGGAGCATGAGT 59.235 47.619 11.34 5.70 0.00 3.41
435 450 2.890808 TCATCCGGAGCATGAGTAAC 57.109 50.000 11.34 0.00 0.00 2.50
436 451 2.388735 TCATCCGGAGCATGAGTAACT 58.611 47.619 11.34 0.00 0.00 2.24
448 463 1.001633 TGAGTAACTCCTTCAACGGCC 59.998 52.381 0.00 0.00 0.00 6.13
454 469 2.513897 CCTTCAACGGCCCGGATC 60.514 66.667 8.57 0.00 0.00 3.36
475 496 6.750039 GGATCACCGTTAATTACCATTGTTTG 59.250 38.462 0.00 0.00 0.00 2.93
478 499 5.923684 CACCGTTAATTACCATTGTTTGCTT 59.076 36.000 0.00 0.00 0.00 3.91
479 500 6.422400 CACCGTTAATTACCATTGTTTGCTTT 59.578 34.615 0.00 0.00 0.00 3.51
482 503 7.062488 CCGTTAATTACCATTGTTTGCTTTACC 59.938 37.037 0.00 0.00 0.00 2.85
495 516 1.314730 CTTTACCGTGCAACCACCTT 58.685 50.000 0.00 0.00 38.79 3.50
496 517 2.496111 CTTTACCGTGCAACCACCTTA 58.504 47.619 0.00 0.00 38.79 2.69
499 520 1.989706 ACCGTGCAACCACCTTAAAT 58.010 45.000 0.00 0.00 38.79 1.40
503 524 2.525368 GTGCAACCACCTTAAATCCCT 58.475 47.619 0.00 0.00 35.92 4.20
504 525 2.231235 GTGCAACCACCTTAAATCCCTG 59.769 50.000 0.00 0.00 35.92 4.45
505 526 2.158385 TGCAACCACCTTAAATCCCTGT 60.158 45.455 0.00 0.00 0.00 4.00
506 527 2.897326 GCAACCACCTTAAATCCCTGTT 59.103 45.455 0.00 0.00 0.00 3.16
520 542 0.110486 CCTGTTGGGTTGTGGCTAGT 59.890 55.000 0.00 0.00 0.00 2.57
540 562 7.185453 GCTAGTGTTCTTATGCTTGATTTGAG 58.815 38.462 0.00 0.00 0.00 3.02
547 569 7.926674 TCTTATGCTTGATTTGAGTCATTCA 57.073 32.000 0.00 0.00 0.00 2.57
555 577 5.646606 TGATTTGAGTCATTCATGCATGTG 58.353 37.500 25.43 17.49 35.27 3.21
556 578 5.416326 TGATTTGAGTCATTCATGCATGTGA 59.584 36.000 25.43 19.45 35.27 3.58
564 586 6.600427 AGTCATTCATGCATGTGACAATAGAA 59.400 34.615 34.08 18.74 42.51 2.10
573 595 8.907222 TGCATGTGACAATAGAACATATACAT 57.093 30.769 0.00 0.00 33.31 2.29
619 641 3.244561 TGTCCCTCTTTGCTTGACCTTAG 60.245 47.826 0.00 0.00 0.00 2.18
631 698 6.582636 TGCTTGACCTTAGACTAATACATGG 58.417 40.000 0.00 0.00 0.00 3.66
639 706 6.497259 CCTTAGACTAATACATGGCCCTCTTA 59.503 42.308 0.00 0.00 0.00 2.10
640 707 5.810080 AGACTAATACATGGCCCTCTTAC 57.190 43.478 0.00 0.00 0.00 2.34
642 709 2.930826 AATACATGGCCCTCTTACCG 57.069 50.000 0.00 0.00 0.00 4.02
658 763 6.583050 CCTCTTACCGATCTTCGATACAATTC 59.417 42.308 0.00 0.00 43.74 2.17
659 764 7.273320 TCTTACCGATCTTCGATACAATTCT 57.727 36.000 0.00 0.00 43.74 2.40
666 771 7.216522 CGATCTTCGATACAATTCTTTGATCG 58.783 38.462 0.00 0.00 43.74 3.69
674 779 1.667236 ATTCTTTGATCGCCATCGCA 58.333 45.000 0.00 0.00 35.26 5.10
675 780 1.447945 TTCTTTGATCGCCATCGCAA 58.552 45.000 0.00 0.00 35.26 4.85
678 783 3.202097 TCTTTGATCGCCATCGCAAATA 58.798 40.909 0.00 0.00 31.06 1.40
691 796 1.181098 GCAAATATGGCAGCCGGGAT 61.181 55.000 7.03 0.00 0.00 3.85
693 798 1.812571 CAAATATGGCAGCCGGGATAC 59.187 52.381 7.03 0.00 0.00 2.24
694 799 1.064003 AATATGGCAGCCGGGATACA 58.936 50.000 7.03 0.00 39.74 2.29
709 814 3.003480 GGATACAAGGCACACTCTCAAC 58.997 50.000 0.00 0.00 0.00 3.18
711 816 0.532862 ACAAGGCACACTCTCAACGG 60.533 55.000 0.00 0.00 0.00 4.44
723 838 0.614979 CTCAACGGGGAGGAGGAGAA 60.615 60.000 0.00 0.00 0.00 2.87
729 844 0.340208 GGGGAGGAGGAGAAAGAGGA 59.660 60.000 0.00 0.00 0.00 3.71
731 846 1.289530 GGGAGGAGGAGAAAGAGGAGA 59.710 57.143 0.00 0.00 0.00 3.71
733 848 2.666317 GAGGAGGAGAAAGAGGAGAGG 58.334 57.143 0.00 0.00 0.00 3.69
734 849 2.007636 AGGAGGAGAAAGAGGAGAGGT 58.992 52.381 0.00 0.00 0.00 3.85
773 890 1.082756 CAACCGCGTTGAGAAGTGC 60.083 57.895 4.92 0.00 45.28 4.40
774 891 2.251642 AACCGCGTTGAGAAGTGCC 61.252 57.895 4.92 0.00 0.00 5.01
986 1106 3.807839 CGATCCCCCATGGCACCA 61.808 66.667 6.09 0.00 0.00 4.17
1162 1286 0.943673 GCATTTGGTGGTTTGTTGCC 59.056 50.000 0.00 0.00 0.00 4.52
1249 1373 2.430367 GTTCAGCGGGGGTGAGTT 59.570 61.111 0.00 0.00 41.12 3.01
1251 1375 0.391263 GTTCAGCGGGGGTGAGTTAG 60.391 60.000 0.00 0.00 41.12 2.34
1254 1378 3.793888 GCGGGGGTGAGTTAGGGG 61.794 72.222 0.00 0.00 0.00 4.79
1323 1455 2.027837 TCTGCTCTGATGCTTGCTAACA 60.028 45.455 0.00 0.00 0.00 2.41
1331 1463 2.057137 TGCTTGCTAACATGGGGATC 57.943 50.000 0.00 0.00 0.00 3.36
1333 1465 1.475034 GCTTGCTAACATGGGGATCGA 60.475 52.381 0.00 0.00 0.00 3.59
1466 1598 2.874701 GCGCTGATGGATACTCACAATT 59.125 45.455 0.00 0.00 37.61 2.32
1500 1634 4.118023 CAAATGTTTGGATGTTTGCACG 57.882 40.909 0.00 0.00 34.59 5.34
1513 1647 3.042887 GTTTGCACGTTTTTCCTGCTAG 58.957 45.455 0.00 0.00 0.00 3.42
1539 1673 1.336440 TGCCGTGTCATGAACTTTTGG 59.664 47.619 0.00 0.00 0.00 3.28
1550 1684 8.801299 TGTCATGAACTTTTGGCTTATCAATTA 58.199 29.630 0.00 0.00 0.00 1.40
1559 1693 7.673641 TTTGGCTTATCAATTATTGGACCAT 57.326 32.000 5.02 0.00 0.00 3.55
1584 1718 5.463392 TGTAATTTGAGCTAGCGATGCTAAG 59.537 40.000 9.55 0.00 40.82 2.18
1590 1724 1.777101 CTAGCGATGCTAAGGAGTGC 58.223 55.000 0.00 0.00 40.82 4.40
1641 1783 9.771915 CTTTATTTTGTTTGAGCAAATGTTTGT 57.228 25.926 7.26 0.00 40.24 2.83
1649 1791 3.118847 TGAGCAAATGTTTGTGCCTTTCA 60.119 39.130 7.26 0.00 41.88 2.69
1665 1807 3.372206 CCTTTCATCTGCTAACTTCGTGG 59.628 47.826 0.00 0.00 0.00 4.94
1686 1828 1.269309 TGTGCCATTGTTGCCGTAAAC 60.269 47.619 0.00 0.00 0.00 2.01
1690 1832 3.318275 TGCCATTGTTGCCGTAAACTTTA 59.682 39.130 0.00 0.00 0.00 1.85
1746 1888 5.476945 TGAGTGTACACTTCTGCTGATAAGA 59.523 40.000 28.49 0.00 42.66 2.10
1798 1941 4.706476 AGTTGCATTGTATATGCTGGTTGT 59.294 37.500 10.67 0.00 44.79 3.32
1875 2018 3.005791 ACAAAGAAAAGGCAAAGGATCCG 59.994 43.478 5.98 0.00 0.00 4.18
2055 2203 1.990160 TTTGTGTGGAAGCGGGGAGT 61.990 55.000 0.00 0.00 0.00 3.85
2082 2230 7.447853 TCTTCTAATCCTACGGTCCTTCTAATC 59.552 40.741 0.00 0.00 0.00 1.75
2114 2262 5.794894 TCCATCTCAGGTCAGTTTTTAGAC 58.205 41.667 0.00 0.00 0.00 2.59
2327 2475 9.212641 GCAGAGAAAAGCTATGTCATTCATATA 57.787 33.333 0.00 0.00 38.11 0.86
2350 2498 6.667007 ATTGGCAAAACACTTTCTGAAAAG 57.333 33.333 3.01 2.91 46.11 2.27
2403 2551 5.696724 CGGACCAATATAGAAAGTCATCACC 59.303 44.000 0.00 0.00 0.00 4.02
2411 2559 3.660865 AGAAAGTCATCACCGGTACAAC 58.339 45.455 6.87 3.38 0.00 3.32
2425 2573 3.119101 CGGTACAACTTATCAGCCTCTGT 60.119 47.826 0.00 0.00 32.61 3.41
2445 2593 5.869344 TCTGTCGTCAGAAATCAATAACAGG 59.131 40.000 10.00 0.00 46.17 4.00
2498 2662 3.199071 ACCCACAAAACTTTTTCCCCTTC 59.801 43.478 0.00 0.00 0.00 3.46
2555 2720 3.586100 AACTGGTTGCGTTTCTGTTTT 57.414 38.095 0.00 0.00 0.00 2.43
2567 2732 3.591196 TTCTGTTTTGTGTTGCTGCTT 57.409 38.095 0.00 0.00 0.00 3.91
2590 2755 3.579151 AGTCCCCAGAAGTTAGAACAGTC 59.421 47.826 0.00 0.00 0.00 3.51
2593 2758 3.307059 CCCCAGAAGTTAGAACAGTCAGG 60.307 52.174 0.00 0.00 0.00 3.86
2749 2914 4.668576 ACAATCGTGTTGAACTGCATAG 57.331 40.909 9.62 0.00 32.58 2.23
2762 2927 8.883731 GTTGAACTGCATAGTAATGTGAACTAT 58.116 33.333 0.00 0.00 40.07 2.12
2854 3019 3.554934 TGTTGTTCAGGTGCTTCTCATT 58.445 40.909 0.00 0.00 0.00 2.57
2867 3032 4.580167 TGCTTCTCATTATATGGGTGTTGC 59.420 41.667 0.00 0.00 31.00 4.17
2880 3045 5.833406 TGGGTGTTGCTTAATGTATCATG 57.167 39.130 0.00 0.00 0.00 3.07
2905 3072 6.074356 GGTGTGTGTTTTAATGCAAGAATGTC 60.074 38.462 0.00 0.00 0.00 3.06
2952 3119 7.857885 GCTCCAATTGTAGTCAAATATGCTAAC 59.142 37.037 4.43 0.00 37.11 2.34
2985 3152 5.411669 GGACAAGTTGAACCACCTTATACTG 59.588 44.000 10.54 0.00 0.00 2.74
3045 3212 4.142093 GCACAGGCATTTTGGTGAGATAAT 60.142 41.667 0.00 0.00 40.72 1.28
3046 3213 5.625197 GCACAGGCATTTTGGTGAGATAATT 60.625 40.000 0.00 0.00 40.72 1.40
3088 3255 8.906867 AGCTTCATTATACATTAAGTGTTGCAT 58.093 29.630 0.00 0.00 42.29 3.96
3165 3332 6.920758 GCTGATCACGGGATATCTCATATTAC 59.079 42.308 0.00 0.00 32.67 1.89
3242 3409 3.504520 TCTTGTTGGGCGAAGTATTTTCC 59.495 43.478 0.00 0.00 0.00 3.13
3282 3449 5.183228 GTGCCAACTTTGCCTAGACTTATA 58.817 41.667 0.00 0.00 0.00 0.98
3284 3451 5.822519 TGCCAACTTTGCCTAGACTTATATG 59.177 40.000 0.00 0.00 0.00 1.78
3293 3465 9.474313 TTTGCCTAGACTTATATGACCATTTTT 57.526 29.630 0.00 0.00 0.00 1.94
3485 3657 6.803366 TGGGAAAGGATCTTAAGGTAGTAC 57.197 41.667 1.85 0.00 0.00 2.73
3502 3674 1.795286 GTACGCTCATCTATTGCCTGC 59.205 52.381 0.00 0.00 0.00 4.85
3690 3862 2.738743 ACAATATGTTGGGGCTTGAGG 58.261 47.619 7.15 0.00 39.70 3.86
3753 3925 2.492484 TGGCCTAAAACACAACGTTGTT 59.508 40.909 30.49 18.71 41.62 2.83
3779 3951 4.561326 GCTGCCAATGGTTTGTTTCTGTAT 60.561 41.667 0.00 0.00 0.00 2.29
3883 4055 7.229506 CAGGTCTAGATTATTTTCATGGTTCCC 59.770 40.741 0.00 0.00 0.00 3.97
3932 4104 5.095691 TCTTCTTTTTCTTGCGCAACTAG 57.904 39.130 21.02 10.37 0.00 2.57
3960 4132 5.163814 GGATGTCTGGATCTTGTTTTCTTCG 60.164 44.000 0.00 0.00 0.00 3.79
3961 4133 4.065088 TGTCTGGATCTTGTTTTCTTCGG 58.935 43.478 0.00 0.00 0.00 4.30
3965 4137 3.496884 TGGATCTTGTTTTCTTCGGTTCG 59.503 43.478 0.00 0.00 0.00 3.95
4098 4270 9.181805 GCTGTTGAAACTTTATTTACTTCCTTC 57.818 33.333 0.00 0.00 0.00 3.46
4145 4317 3.797256 CCGCCACAAATGTCGTTTTTAAA 59.203 39.130 0.00 0.00 0.00 1.52
4157 4329 8.928270 ATGTCGTTTTTAAATGTTTACACCAA 57.072 26.923 0.00 0.00 0.00 3.67
4174 4350 2.624838 ACCAATGCAAAACTGACTCAGG 59.375 45.455 10.86 0.00 35.51 3.86
4272 4497 7.657336 ACAAGGTGTGTTAAAAGTATTCCATG 58.343 34.615 0.00 0.00 37.01 3.66
4547 4772 2.875317 TGTTGTCTGCATAAGCGTTTGA 59.125 40.909 0.00 0.00 46.23 2.69
4567 4792 9.318041 CGTTTGACTTCATCTAATTGTAGTTTG 57.682 33.333 0.00 0.00 28.73 2.93
4710 4935 0.250081 GTCAGGCTATAGGCACAGGC 60.250 60.000 26.41 14.26 44.01 4.85
4755 4980 7.450124 TGCATTACCTCCGTTGTTTTTAATA 57.550 32.000 0.00 0.00 0.00 0.98
4759 4984 9.120422 CATTACCTCCGTTGTTTTTAATAACAC 57.880 33.333 10.52 6.26 37.72 3.32
4888 5113 8.726870 TTTTAGTAAGGTTGATCTATTTCCGG 57.273 34.615 0.00 0.00 0.00 5.14
5059 5284 3.251484 AGGAGACCAGGATTGACTTCAA 58.749 45.455 0.00 0.00 40.51 2.69
5247 5484 3.969466 TGGGGCATTATGAAAGGATGA 57.031 42.857 0.00 0.00 0.00 2.92
5252 5489 4.828939 GGGCATTATGAAAGGATGACATGA 59.171 41.667 0.00 0.00 30.25 3.07
5384 5622 5.958321 TGACATGATGAGGAGTAGGACTAT 58.042 41.667 0.00 0.00 0.00 2.12
5385 5623 7.091533 TGACATGATGAGGAGTAGGACTATA 57.908 40.000 0.00 0.00 0.00 1.31
5407 5656 3.930336 TCTAAGTGCTGACTCCACAATG 58.070 45.455 0.00 0.00 35.69 2.82
5459 5708 4.358851 TGATTTTGTTGCTGAACTTTCCG 58.641 39.130 0.00 0.00 32.79 4.30
5509 5758 6.182507 ACCAACAGTTTAGTCTGGTTCATA 57.817 37.500 0.00 0.00 37.05 2.15
5516 5765 6.986817 CAGTTTAGTCTGGTTCATACCTATGG 59.013 42.308 0.00 0.00 45.27 2.74
5664 5913 1.247567 GCCCTTGCTTGCACTTTCTA 58.752 50.000 0.00 0.00 33.53 2.10
5701 5956 9.877178 TTTTCCTTTAATTTAAGCACAGTTTCA 57.123 25.926 0.00 0.00 0.00 2.69
5713 5970 1.024579 CAGTTTCAATCCCCGACCGG 61.025 60.000 0.00 0.00 0.00 5.28
5945 6202 8.898792 GTTATTGGATACGTTTTTCAGTGTTTC 58.101 33.333 0.00 0.00 42.51 2.78
6000 6257 1.399440 CAAGATCAACACAGATGGCCG 59.601 52.381 0.00 0.00 0.00 6.13
6073 6330 0.742990 CGTGTCCCATGCCACGTAAT 60.743 55.000 17.42 0.00 46.87 1.89
6162 6419 0.675083 CCATGTTTGTGGCTCTGCAA 59.325 50.000 0.00 0.00 31.43 4.08
6222 6479 2.438021 TGGTGCTGACAAACTAGGACTT 59.562 45.455 0.00 0.00 35.82 3.01
6403 6681 7.771183 AGATGACTTTGTGAAAGCTTTTGTTA 58.229 30.769 14.05 3.80 42.27 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.996395 CTGGCTCCACTGATGCCT 59.004 61.111 11.72 0.00 46.23 4.75
1 2 2.827642 GCTGGCTCCACTGATGCC 60.828 66.667 0.00 0.00 46.26 4.40
2 3 2.827642 GGCTGGCTCCACTGATGC 60.828 66.667 0.00 0.00 0.00 3.91
3 4 1.001764 TTGGCTGGCTCCACTGATG 60.002 57.895 2.00 0.00 35.50 3.07
4 5 1.302285 CTTGGCTGGCTCCACTGAT 59.698 57.895 2.00 0.00 35.50 2.90
5 6 2.752358 CTTGGCTGGCTCCACTGA 59.248 61.111 2.00 0.00 35.50 3.41
6 7 2.360852 CCTTGGCTGGCTCCACTG 60.361 66.667 2.00 0.00 35.50 3.66
7 8 2.856000 ACCTTGGCTGGCTCCACT 60.856 61.111 2.00 0.00 35.50 4.00
8 9 2.674380 CACCTTGGCTGGCTCCAC 60.674 66.667 2.00 0.00 35.50 4.02
9 10 3.970410 CCACCTTGGCTGGCTCCA 61.970 66.667 2.00 0.00 0.00 3.86
10 11 4.748144 CCCACCTTGGCTGGCTCC 62.748 72.222 2.00 0.00 35.79 4.70
11 12 2.900671 GATCCCACCTTGGCTGGCTC 62.901 65.000 2.00 0.00 35.79 4.70
12 13 2.943265 ATCCCACCTTGGCTGGCT 60.943 61.111 2.00 0.00 35.79 4.75
13 14 2.440980 GATCCCACCTTGGCTGGC 60.441 66.667 0.00 0.00 35.79 4.85
14 15 2.276740 GGATCCCACCTTGGCTGG 59.723 66.667 0.00 0.00 35.79 4.85
15 16 2.276740 GGGATCCCACCTTGGCTG 59.723 66.667 26.95 0.00 35.79 4.85
16 17 3.023735 GGGGATCCCACCTTGGCT 61.024 66.667 32.07 0.00 44.65 4.75
26 27 0.778083 GGGAAATAGGTGGGGGATCC 59.222 60.000 1.92 1.92 0.00 3.36
27 28 1.834540 AGGGAAATAGGTGGGGGATC 58.165 55.000 0.00 0.00 0.00 3.36
28 29 2.144450 GAAGGGAAATAGGTGGGGGAT 58.856 52.381 0.00 0.00 0.00 3.85
29 30 1.083912 AGAAGGGAAATAGGTGGGGGA 59.916 52.381 0.00 0.00 0.00 4.81
30 31 1.608425 AGAAGGGAAATAGGTGGGGG 58.392 55.000 0.00 0.00 0.00 5.40
31 32 2.091830 GGAAGAAGGGAAATAGGTGGGG 60.092 54.545 0.00 0.00 0.00 4.96
32 33 2.580783 TGGAAGAAGGGAAATAGGTGGG 59.419 50.000 0.00 0.00 0.00 4.61
33 34 4.526438 ATGGAAGAAGGGAAATAGGTGG 57.474 45.455 0.00 0.00 0.00 4.61
34 35 4.098501 GCAATGGAAGAAGGGAAATAGGTG 59.901 45.833 0.00 0.00 0.00 4.00
35 36 4.281657 GCAATGGAAGAAGGGAAATAGGT 58.718 43.478 0.00 0.00 0.00 3.08
36 37 3.316308 CGCAATGGAAGAAGGGAAATAGG 59.684 47.826 0.00 0.00 0.00 2.57
37 38 4.035675 GTCGCAATGGAAGAAGGGAAATAG 59.964 45.833 0.00 0.00 0.00 1.73
38 39 3.945285 GTCGCAATGGAAGAAGGGAAATA 59.055 43.478 0.00 0.00 0.00 1.40
39 40 2.755103 GTCGCAATGGAAGAAGGGAAAT 59.245 45.455 0.00 0.00 0.00 2.17
40 41 2.159382 GTCGCAATGGAAGAAGGGAAA 58.841 47.619 0.00 0.00 0.00 3.13
41 42 1.073125 TGTCGCAATGGAAGAAGGGAA 59.927 47.619 0.00 0.00 0.00 3.97
42 43 0.690192 TGTCGCAATGGAAGAAGGGA 59.310 50.000 0.00 0.00 0.00 4.20
43 44 1.533625 TTGTCGCAATGGAAGAAGGG 58.466 50.000 0.00 0.00 0.00 3.95
44 45 4.201950 CCTTATTGTCGCAATGGAAGAAGG 60.202 45.833 13.17 12.77 0.00 3.46
45 46 4.635765 TCCTTATTGTCGCAATGGAAGAAG 59.364 41.667 13.17 9.01 0.00 2.85
46 47 4.584874 TCCTTATTGTCGCAATGGAAGAA 58.415 39.130 13.17 1.74 0.00 2.52
47 48 4.081142 TCTCCTTATTGTCGCAATGGAAGA 60.081 41.667 13.17 8.78 0.00 2.87
48 49 4.191544 TCTCCTTATTGTCGCAATGGAAG 58.808 43.478 13.17 10.05 0.00 3.46
49 50 4.081142 TCTCTCCTTATTGTCGCAATGGAA 60.081 41.667 13.17 2.84 0.00 3.53
50 51 3.450817 TCTCTCCTTATTGTCGCAATGGA 59.549 43.478 13.17 11.19 0.00 3.41
51 52 3.797039 TCTCTCCTTATTGTCGCAATGG 58.203 45.455 13.17 8.29 0.00 3.16
52 53 5.998454 ATTCTCTCCTTATTGTCGCAATG 57.002 39.130 13.17 0.96 0.00 2.82
53 54 6.115446 TCAATTCTCTCCTTATTGTCGCAAT 58.885 36.000 9.46 9.46 32.49 3.56
54 55 5.487433 TCAATTCTCTCCTTATTGTCGCAA 58.513 37.500 0.00 0.00 32.49 4.85
55 56 5.084818 TCAATTCTCTCCTTATTGTCGCA 57.915 39.130 0.00 0.00 32.49 5.10
56 57 5.007136 CCTTCAATTCTCTCCTTATTGTCGC 59.993 44.000 0.00 0.00 32.49 5.19
57 58 5.525378 CCCTTCAATTCTCTCCTTATTGTCG 59.475 44.000 0.00 0.00 32.49 4.35
58 59 6.317391 CACCCTTCAATTCTCTCCTTATTGTC 59.683 42.308 0.00 0.00 32.49 3.18
59 60 6.183347 CACCCTTCAATTCTCTCCTTATTGT 58.817 40.000 0.00 0.00 32.49 2.71
60 61 5.067023 GCACCCTTCAATTCTCTCCTTATTG 59.933 44.000 0.00 0.00 0.00 1.90
61 62 5.196695 GCACCCTTCAATTCTCTCCTTATT 58.803 41.667 0.00 0.00 0.00 1.40
62 63 4.385754 GGCACCCTTCAATTCTCTCCTTAT 60.386 45.833 0.00 0.00 0.00 1.73
63 64 3.054361 GGCACCCTTCAATTCTCTCCTTA 60.054 47.826 0.00 0.00 0.00 2.69
64 65 2.291217 GGCACCCTTCAATTCTCTCCTT 60.291 50.000 0.00 0.00 0.00 3.36
65 66 1.283321 GGCACCCTTCAATTCTCTCCT 59.717 52.381 0.00 0.00 0.00 3.69
66 67 1.756430 GGCACCCTTCAATTCTCTCC 58.244 55.000 0.00 0.00 0.00 3.71
81 82 4.626081 ACGAGCTGGTGTGGGCAC 62.626 66.667 0.00 0.00 44.53 5.01
82 83 4.314440 GACGAGCTGGTGTGGGCA 62.314 66.667 5.94 0.00 0.00 5.36
84 85 1.541310 TTAGGACGAGCTGGTGTGGG 61.541 60.000 5.94 0.00 0.00 4.61
85 86 0.537188 ATTAGGACGAGCTGGTGTGG 59.463 55.000 5.94 0.00 0.00 4.17
86 87 1.645034 CATTAGGACGAGCTGGTGTG 58.355 55.000 5.94 0.00 0.00 3.82
87 88 0.108138 GCATTAGGACGAGCTGGTGT 60.108 55.000 5.94 0.00 0.00 4.16
88 89 0.811616 GGCATTAGGACGAGCTGGTG 60.812 60.000 5.94 0.00 0.00 4.17
89 90 1.522569 GGCATTAGGACGAGCTGGT 59.477 57.895 0.00 0.00 0.00 4.00
90 91 1.227674 GGGCATTAGGACGAGCTGG 60.228 63.158 0.00 0.00 0.00 4.85
91 92 1.592669 CGGGCATTAGGACGAGCTG 60.593 63.158 0.00 0.00 0.00 4.24
92 93 2.797278 CCGGGCATTAGGACGAGCT 61.797 63.158 0.00 0.00 0.00 4.09
93 94 2.280186 CCGGGCATTAGGACGAGC 60.280 66.667 0.00 0.00 0.00 5.03
94 95 0.810031 CAACCGGGCATTAGGACGAG 60.810 60.000 6.32 0.00 0.00 4.18
95 96 1.219664 CAACCGGGCATTAGGACGA 59.780 57.895 6.32 0.00 0.00 4.20
96 97 0.391927 TTCAACCGGGCATTAGGACG 60.392 55.000 6.32 0.00 0.00 4.79
97 98 1.092348 GTTCAACCGGGCATTAGGAC 58.908 55.000 6.32 0.00 0.00 3.85
98 99 0.988832 AGTTCAACCGGGCATTAGGA 59.011 50.000 6.32 0.00 0.00 2.94
99 100 1.834188 AAGTTCAACCGGGCATTAGG 58.166 50.000 6.32 0.00 0.00 2.69
100 101 5.339990 CAAATAAGTTCAACCGGGCATTAG 58.660 41.667 6.32 0.00 0.00 1.73
101 102 4.158764 CCAAATAAGTTCAACCGGGCATTA 59.841 41.667 6.32 0.00 0.00 1.90
102 103 3.056179 CCAAATAAGTTCAACCGGGCATT 60.056 43.478 6.32 0.00 0.00 3.56
103 104 2.495669 CCAAATAAGTTCAACCGGGCAT 59.504 45.455 6.32 0.00 0.00 4.40
104 105 1.889829 CCAAATAAGTTCAACCGGGCA 59.110 47.619 6.32 0.00 0.00 5.36
105 106 1.203758 CCCAAATAAGTTCAACCGGGC 59.796 52.381 6.32 0.00 0.00 6.13
106 107 1.822371 CCCCAAATAAGTTCAACCGGG 59.178 52.381 6.32 0.00 0.00 5.73
107 108 1.822371 CCCCCAAATAAGTTCAACCGG 59.178 52.381 0.00 0.00 0.00 5.28
146 147 1.529309 GAGGACATGGGAAGGAGCC 59.471 63.158 0.00 0.00 0.00 4.70
147 148 1.274703 TGGAGGACATGGGAAGGAGC 61.275 60.000 0.00 0.00 0.00 4.70
169 170 1.764571 TTTACTGCACCGCCTCCACT 61.765 55.000 0.00 0.00 0.00 4.00
200 201 0.890542 GCCTTGTGTCATGACTGGCA 60.891 55.000 29.45 21.89 35.75 4.92
240 245 6.468956 GGTTGTTTCAATGTATAGCACGATTG 59.531 38.462 0.00 0.00 31.95 2.67
245 250 5.637006 TGGGTTGTTTCAATGTATAGCAC 57.363 39.130 0.00 0.00 0.00 4.40
255 260 1.408969 GGGAGCTTGGGTTGTTTCAA 58.591 50.000 0.00 0.00 0.00 2.69
260 265 2.069165 GAGTGGGGAGCTTGGGTTGT 62.069 60.000 0.00 0.00 0.00 3.32
280 295 3.179265 CGTCAGCGTTGCTACCCG 61.179 66.667 0.00 0.00 36.40 5.28
303 318 1.201429 AACACCGGCTCCCATCTCTT 61.201 55.000 0.00 0.00 0.00 2.85
314 329 2.504519 CCTAGGCCTAACACCGGC 59.495 66.667 14.85 0.00 46.83 6.13
317 332 0.909623 TGAAGCCTAGGCCTAACACC 59.090 55.000 30.42 11.65 43.17 4.16
322 337 0.257905 TCGACTGAAGCCTAGGCCTA 59.742 55.000 30.42 13.09 43.17 3.93
327 342 2.425312 ACTGATGTCGACTGAAGCCTAG 59.575 50.000 17.92 6.39 0.00 3.02
335 350 2.230025 AGAGACCAACTGATGTCGACTG 59.770 50.000 17.92 5.15 36.61 3.51
358 373 2.493278 GGAAATGGACATGTGAACTGGG 59.507 50.000 1.15 0.00 0.00 4.45
359 374 3.424703 AGGAAATGGACATGTGAACTGG 58.575 45.455 1.15 0.00 0.00 4.00
393 408 2.728817 GGCTGTAGGATCCGACGG 59.271 66.667 25.15 25.15 0.00 4.79
407 422 1.443407 CTCCGGATGAATCACGGCT 59.557 57.895 3.57 0.00 46.78 5.52
408 423 2.247437 GCTCCGGATGAATCACGGC 61.247 63.158 3.57 0.00 46.78 5.68
420 435 3.669354 GGAGTTACTCATGCTCCGG 57.331 57.895 14.72 0.00 39.29 5.14
427 442 2.354805 GGCCGTTGAAGGAGTTACTCAT 60.355 50.000 14.72 3.86 31.08 2.90
431 446 1.017701 CGGGCCGTTGAAGGAGTTAC 61.018 60.000 19.97 0.00 0.00 2.50
432 447 1.294138 CGGGCCGTTGAAGGAGTTA 59.706 57.895 19.97 0.00 0.00 2.24
435 450 2.925162 GATCCGGGCCGTTGAAGGAG 62.925 65.000 26.32 6.71 34.14 3.69
436 451 3.006728 ATCCGGGCCGTTGAAGGA 61.007 61.111 26.32 14.10 35.24 3.36
454 469 5.465935 AGCAAACAATGGTAATTAACGGTG 58.534 37.500 0.00 0.00 38.18 4.94
460 481 7.085116 CACGGTAAAGCAAACAATGGTAATTA 58.915 34.615 0.00 0.00 39.29 1.40
466 487 2.058057 GCACGGTAAAGCAAACAATGG 58.942 47.619 0.00 0.00 0.00 3.16
475 496 1.170290 AGGTGGTTGCACGGTAAAGC 61.170 55.000 0.00 0.00 0.00 3.51
478 499 2.634815 TTAAGGTGGTTGCACGGTAA 57.365 45.000 0.00 0.00 0.00 2.85
479 500 2.634815 TTTAAGGTGGTTGCACGGTA 57.365 45.000 0.00 0.00 0.00 4.02
482 503 1.201414 GGGATTTAAGGTGGTTGCACG 59.799 52.381 0.00 0.00 0.00 5.34
495 516 2.883026 CCACAACCCAACAGGGATTTA 58.117 47.619 7.71 0.00 46.20 1.40
496 517 1.715785 CCACAACCCAACAGGGATTT 58.284 50.000 7.71 0.00 46.20 2.17
499 520 1.063070 TAGCCACAACCCAACAGGGA 61.063 55.000 7.71 0.00 46.20 4.20
503 524 0.548989 ACACTAGCCACAACCCAACA 59.451 50.000 0.00 0.00 0.00 3.33
504 525 1.607148 GAACACTAGCCACAACCCAAC 59.393 52.381 0.00 0.00 0.00 3.77
505 526 1.493022 AGAACACTAGCCACAACCCAA 59.507 47.619 0.00 0.00 0.00 4.12
506 527 1.136828 AGAACACTAGCCACAACCCA 58.863 50.000 0.00 0.00 0.00 4.51
516 538 8.261492 ACTCAAATCAAGCATAAGAACACTAG 57.739 34.615 0.00 0.00 0.00 2.57
520 542 7.692460 ATGACTCAAATCAAGCATAAGAACA 57.308 32.000 0.00 0.00 30.82 3.18
540 562 6.367686 TCTATTGTCACATGCATGAATGAC 57.632 37.500 29.83 29.83 41.51 3.06
547 569 8.907222 TGTATATGTTCTATTGTCACATGCAT 57.093 30.769 0.00 0.00 33.19 3.96
582 604 9.559732 CAAAGAGGGACATGTATTGATACAATA 57.440 33.333 0.00 0.00 45.40 1.90
584 606 6.318648 GCAAAGAGGGACATGTATTGATACAA 59.681 38.462 0.00 0.00 45.40 2.41
586 608 6.058183 AGCAAAGAGGGACATGTATTGATAC 58.942 40.000 0.00 0.00 0.00 2.24
589 611 4.574674 AGCAAAGAGGGACATGTATTGA 57.425 40.909 0.00 0.00 0.00 2.57
590 612 4.701651 TCAAGCAAAGAGGGACATGTATTG 59.298 41.667 0.00 0.00 0.00 1.90
599 621 3.008049 GTCTAAGGTCAAGCAAAGAGGGA 59.992 47.826 0.00 0.00 0.00 4.20
619 641 4.560919 CGGTAAGAGGGCCATGTATTAGTC 60.561 50.000 6.18 0.00 0.00 2.59
631 698 1.030457 TCGAAGATCGGTAAGAGGGC 58.970 55.000 0.00 0.00 40.88 5.19
639 706 6.338146 TCAAAGAATTGTATCGAAGATCGGT 58.662 36.000 0.00 0.00 38.51 4.69
640 707 6.828502 TCAAAGAATTGTATCGAAGATCGG 57.171 37.500 0.00 0.00 38.51 4.18
642 709 7.006537 GCGATCAAAGAATTGTATCGAAGATC 58.993 38.462 18.48 0.00 42.53 2.75
658 763 2.480224 ATTTGCGATGGCGATCAAAG 57.520 45.000 9.52 0.00 44.10 2.77
659 764 3.304592 CCATATTTGCGATGGCGATCAAA 60.305 43.478 9.52 4.02 44.10 2.69
674 779 1.423541 TGTATCCCGGCTGCCATATTT 59.576 47.619 20.29 1.44 0.00 1.40
675 780 1.064003 TGTATCCCGGCTGCCATATT 58.936 50.000 20.29 2.95 0.00 1.28
678 783 1.149174 CTTGTATCCCGGCTGCCAT 59.851 57.895 20.29 7.37 0.00 4.40
683 788 2.297895 TGTGCCTTGTATCCCGGCT 61.298 57.895 0.00 0.00 44.09 5.52
691 796 1.270094 CCGTTGAGAGTGTGCCTTGTA 60.270 52.381 0.00 0.00 0.00 2.41
693 798 1.230635 CCCGTTGAGAGTGTGCCTTG 61.231 60.000 0.00 0.00 0.00 3.61
694 799 1.071471 CCCGTTGAGAGTGTGCCTT 59.929 57.895 0.00 0.00 0.00 4.35
700 805 1.608717 CCTCCTCCCCGTTGAGAGTG 61.609 65.000 0.32 0.00 34.11 3.51
701 806 1.305381 CCTCCTCCCCGTTGAGAGT 60.305 63.158 0.32 0.00 34.11 3.24
709 814 1.045911 CCTCTTTCTCCTCCTCCCCG 61.046 65.000 0.00 0.00 0.00 5.73
711 816 1.289530 TCTCCTCTTTCTCCTCCTCCC 59.710 57.143 0.00 0.00 0.00 4.30
740 855 1.594331 GGTTGATGTATTCGCTCCCC 58.406 55.000 0.00 0.00 0.00 4.81
741 856 1.217882 CGGTTGATGTATTCGCTCCC 58.782 55.000 0.00 0.00 0.00 4.30
742 857 0.582005 GCGGTTGATGTATTCGCTCC 59.418 55.000 0.00 0.00 42.62 4.70
743 858 0.229753 CGCGGTTGATGTATTCGCTC 59.770 55.000 0.00 0.00 43.57 5.03
783 900 2.287103 GCCTCGTTTCTTTCTTCGTGTT 59.713 45.455 0.00 0.00 0.00 3.32
788 905 0.179248 CGCGCCTCGTTTCTTTCTTC 60.179 55.000 0.00 0.00 0.00 2.87
809 926 1.901833 TCAGTGACTGCTCATGGCTAA 59.098 47.619 7.93 0.00 42.39 3.09
815 932 1.610102 GGCTTGTCAGTGACTGCTCAT 60.610 52.381 27.71 0.00 34.92 2.90
874 994 2.203788 TCCTCCCGCCACAGTTCT 60.204 61.111 0.00 0.00 0.00 3.01
941 1061 0.704076 TGGGGTTTTGGAGGGAGATG 59.296 55.000 0.00 0.00 0.00 2.90
942 1062 1.077169 GTTGGGGTTTTGGAGGGAGAT 59.923 52.381 0.00 0.00 0.00 2.75
1139 1263 1.045911 ACAAACCACCAAATGCGGGT 61.046 50.000 0.00 0.00 39.88 5.28
1162 1286 0.887933 CCAGATCAAACCCAAACCGG 59.112 55.000 0.00 0.00 0.00 5.28
1178 1302 2.030540 CAGATCCTGCAACAAACACCAG 60.031 50.000 0.00 0.00 0.00 4.00
1249 1373 2.236146 CAAGCATACACACAGACCCCTA 59.764 50.000 0.00 0.00 0.00 3.53
1251 1375 1.453155 CAAGCATACACACAGACCCC 58.547 55.000 0.00 0.00 0.00 4.95
1254 1378 3.955429 CGCAAGCATACACACAGAC 57.045 52.632 0.00 0.00 0.00 3.51
1323 1455 1.061905 TTCCCTGCATCGATCCCCAT 61.062 55.000 0.00 0.00 0.00 4.00
1331 1463 1.224069 CCGCATACTTCCCTGCATCG 61.224 60.000 0.00 0.00 38.30 3.84
1333 1465 0.546122 TTCCGCATACTTCCCTGCAT 59.454 50.000 0.00 0.00 38.30 3.96
1355 1487 1.141234 CGACTTACTCGGGCCTTCC 59.859 63.158 0.84 0.00 38.87 3.46
1466 1598 7.206981 TCCAAACATTTGCTCAAAACAAAAA 57.793 28.000 0.00 0.00 40.19 1.94
1470 1602 5.426504 ACATCCAAACATTTGCTCAAAACA 58.573 33.333 0.00 0.00 36.86 2.83
1500 1634 3.304726 GGCACTGAACTAGCAGGAAAAAC 60.305 47.826 0.00 0.00 40.20 2.43
1513 1647 1.069906 GTTCATGACACGGCACTGAAC 60.070 52.381 0.00 10.41 39.00 3.18
1550 1684 6.183360 GCTAGCTCAAATTACAATGGTCCAAT 60.183 38.462 7.70 0.00 0.00 3.16
1552 1686 4.640201 GCTAGCTCAAATTACAATGGTCCA 59.360 41.667 7.70 0.00 0.00 4.02
1553 1687 4.260784 CGCTAGCTCAAATTACAATGGTCC 60.261 45.833 13.93 0.00 0.00 4.46
1559 1693 4.191544 AGCATCGCTAGCTCAAATTACAA 58.808 39.130 13.93 0.00 38.01 2.41
1641 1783 3.002791 CGAAGTTAGCAGATGAAAGGCA 58.997 45.455 0.00 0.00 0.00 4.75
1649 1791 2.688507 CACACCACGAAGTTAGCAGAT 58.311 47.619 0.00 0.00 41.61 2.90
1673 1815 7.441760 TGATAAGTCTAAAGTTTACGGCAACAA 59.558 33.333 2.27 0.00 0.00 2.83
1756 1899 1.519751 TAATTGGCGCCACACCACAC 61.520 55.000 32.95 0.00 36.76 3.82
1767 1910 5.343058 GCATATACAATGCAACTAATTGGCG 59.657 40.000 5.14 0.00 44.00 5.69
1814 1957 5.163468 TGAGCTTTTACCTGCAACAATTTGA 60.163 36.000 2.79 0.00 34.24 2.69
2082 2230 1.285962 ACCTGAGATGGAAACCCATGG 59.714 52.381 4.14 4.14 44.15 3.66
2114 2262 0.521291 TGCGAAGAAATTGGAAGCCG 59.479 50.000 0.00 0.00 0.00 5.52
2327 2475 6.667007 CTTTTCAGAAAGTGTTTTGCCAAT 57.333 33.333 0.00 0.00 37.94 3.16
2350 2498 7.379750 ACTCTTTGAGACTAATGACCAGTAAC 58.620 38.462 1.25 0.00 33.32 2.50
2403 2551 3.119101 ACAGAGGCTGATAAGTTGTACCG 60.119 47.826 0.00 0.00 35.18 4.02
2411 2559 2.685388 TCTGACGACAGAGGCTGATAAG 59.315 50.000 13.61 0.00 46.55 1.73
2425 2573 5.186992 TCTCCCTGTTATTGATTTCTGACGA 59.813 40.000 0.00 0.00 0.00 4.20
2439 2587 4.020218 CCAGTCAAATCTGTCTCCCTGTTA 60.020 45.833 0.00 0.00 34.02 2.41
2445 2593 2.777832 AGCCAGTCAAATCTGTCTCC 57.222 50.000 0.00 0.00 34.02 3.71
2498 2662 1.065418 ACCGCTGAGGGGATTTTACAG 60.065 52.381 23.31 0.00 46.96 2.74
2544 2709 2.027926 GCAGCAACACAAAACAGAAACG 59.972 45.455 0.00 0.00 0.00 3.60
2555 2720 0.250727 GGGGACTAAGCAGCAACACA 60.251 55.000 0.00 0.00 0.00 3.72
2567 2732 4.748701 ACTGTTCTAACTTCTGGGGACTA 58.251 43.478 0.00 0.00 0.00 2.59
2622 2787 5.649782 ATCCAAAACCTGCAGATACAAAG 57.350 39.130 17.39 0.00 0.00 2.77
2724 2889 3.127721 TGCAGTTCAACACGATTGTTTGA 59.872 39.130 0.00 6.61 43.89 2.69
2762 2927 8.585881 GGCTGAAGTATATTCTGGAACATAGTA 58.414 37.037 0.00 0.00 38.20 1.82
2763 2928 7.445945 GGCTGAAGTATATTCTGGAACATAGT 58.554 38.462 0.00 0.00 38.20 2.12
2854 3019 9.230122 CATGATACATTAAGCAACACCCATATA 57.770 33.333 0.00 0.00 0.00 0.86
2880 3045 5.752955 ACATTCTTGCATTAAAACACACACC 59.247 36.000 0.00 0.00 0.00 4.16
2914 3081 1.286248 ATTGGAGCGAAGTACCCCTT 58.714 50.000 0.00 0.00 35.59 3.95
2952 3119 3.058914 GGTTCAACTTGTCCTGATGTTCG 60.059 47.826 0.00 0.00 0.00 3.95
2985 3152 5.710513 AAAAACTTACCGGTGGATTAACC 57.289 39.130 19.93 0.00 36.82 2.85
3045 3212 8.706322 AATGAAGCTTTAGAGGGAAAACTTAA 57.294 30.769 0.00 0.00 0.00 1.85
3046 3213 9.975218 ATAATGAAGCTTTAGAGGGAAAACTTA 57.025 29.630 0.00 0.00 0.00 2.24
3088 3255 7.201758 CCTTTAACTCATAAATCAGATGCAGCA 60.202 37.037 4.07 0.00 33.15 4.41
3098 3265 9.651718 CGTAATGAAGCCTTTAACTCATAAATC 57.348 33.333 0.00 0.00 33.15 2.17
3123 3290 6.019479 GTGATCAGCCTATAACTCTTGAAACG 60.019 42.308 0.00 0.00 0.00 3.60
3165 3332 4.690184 TTGCATGCTTGTCAGTTATCTG 57.310 40.909 20.33 0.00 42.54 2.90
3179 3346 3.357504 GGATGGAAGCTTTGCATGC 57.642 52.632 11.82 11.82 42.07 4.06
3242 3409 1.672881 GCACAATAGCTGCTAACCTGG 59.327 52.381 14.13 4.18 0.00 4.45
3293 3465 9.921637 AAAGATTTCAGACAGTTGTTTTTAACA 57.078 25.926 0.00 0.00 40.21 2.41
3485 3657 0.250209 AGGCAGGCAATAGATGAGCG 60.250 55.000 0.00 0.00 0.00 5.03
3502 3674 6.537301 GGTTACCCTCTTTTTGAAACAAAAGG 59.463 38.462 11.09 11.09 36.82 3.11
3533 3705 2.203470 TTGGCTGTCTGCATCAATGA 57.797 45.000 3.96 0.00 45.15 2.57
3690 3862 3.179443 TCATAAGTGAGCCAACGATCC 57.821 47.619 0.00 0.00 0.00 3.36
3753 3925 1.412079 AACAAACCATTGGCAGCTGA 58.588 45.000 20.43 0.00 41.01 4.26
3883 4055 5.070446 TGTCAGCCACCTATTCCTAATACAG 59.930 44.000 0.00 0.00 0.00 2.74
3932 4104 5.712152 AAACAAGATCCAGACATCCAAAC 57.288 39.130 0.00 0.00 0.00 2.93
3960 4132 7.329717 TGAAACCAAATTAATAACATGCGAACC 59.670 33.333 0.00 0.00 0.00 3.62
3961 4133 8.233692 TGAAACCAAATTAATAACATGCGAAC 57.766 30.769 0.00 0.00 0.00 3.95
3965 4137 9.369904 AGTCATGAAACCAAATTAATAACATGC 57.630 29.630 0.00 0.00 34.56 4.06
4114 4286 1.811965 CATTTGTGGCGGAGAATGTCA 59.188 47.619 0.00 0.00 0.00 3.58
4121 4293 0.591170 AAACGACATTTGTGGCGGAG 59.409 50.000 8.65 0.00 0.00 4.63
4145 4317 5.752955 GTCAGTTTTGCATTGGTGTAAACAT 59.247 36.000 9.80 0.00 39.22 2.71
4157 4329 2.957402 TCCCTGAGTCAGTTTTGCAT 57.043 45.000 18.74 0.00 0.00 3.96
4174 4350 4.516698 TGCTTGATTTTGAGTCTGACTTCC 59.483 41.667 12.27 0.48 0.00 3.46
4223 4399 5.629079 ACAACAAGGCTTACTTATTCTGC 57.371 39.130 0.00 0.00 37.29 4.26
4272 4497 1.834263 AGTGGGAGTTATCTGAGTGCC 59.166 52.381 0.00 0.00 0.00 5.01
4448 4673 0.991146 TGTCTCCCTGCCATTGCTAA 59.009 50.000 0.00 0.00 38.71 3.09
4567 4792 5.922544 TGCGTAAGTCTTTGGAACTAACTAC 59.077 40.000 0.00 0.00 41.68 2.73
4618 4843 8.181573 ACGTCGTTCATATTTGCAAAAGAATAT 58.818 29.630 17.19 6.58 0.00 1.28
4740 4965 6.939132 TGGAGTGTTATTAAAAACAACGGA 57.061 33.333 0.00 0.00 40.85 4.69
4838 5063 6.151691 TGAGTGTACACGAGGTTTTACATAC 58.848 40.000 19.93 0.00 36.20 2.39
4896 5121 9.575868 CCTCTCTACAGATCAACCTTACTATTA 57.424 37.037 0.00 0.00 0.00 0.98
4898 5123 7.817440 TCCTCTCTACAGATCAACCTTACTAT 58.183 38.462 0.00 0.00 0.00 2.12
4899 5124 7.209340 TCCTCTCTACAGATCAACCTTACTA 57.791 40.000 0.00 0.00 0.00 1.82
4900 5125 6.080969 TCCTCTCTACAGATCAACCTTACT 57.919 41.667 0.00 0.00 0.00 2.24
4901 5126 6.153000 TGTTCCTCTCTACAGATCAACCTTAC 59.847 42.308 0.00 0.00 0.00 2.34
4902 5127 6.253758 TGTTCCTCTCTACAGATCAACCTTA 58.746 40.000 0.00 0.00 0.00 2.69
5059 5284 0.846693 AGCAGTCCTTGGAACAGGTT 59.153 50.000 0.00 0.00 42.39 3.50
5202 5434 0.467290 GCACTTCCAAGTCCAACCCA 60.467 55.000 0.00 0.00 37.08 4.51
5206 5438 3.569194 TGTTAGCACTTCCAAGTCCAA 57.431 42.857 0.00 0.00 37.08 3.53
5207 5439 3.411446 CATGTTAGCACTTCCAAGTCCA 58.589 45.455 0.00 0.00 37.08 4.02
5208 5440 2.749621 CCATGTTAGCACTTCCAAGTCC 59.250 50.000 0.00 0.00 37.08 3.85
5209 5441 2.749621 CCCATGTTAGCACTTCCAAGTC 59.250 50.000 0.00 0.00 37.08 3.01
5210 5442 2.555227 CCCCATGTTAGCACTTCCAAGT 60.555 50.000 0.00 0.00 40.60 3.16
5211 5443 2.094675 CCCCATGTTAGCACTTCCAAG 58.905 52.381 0.00 0.00 0.00 3.61
5247 5484 2.865119 TGCCTGACTGATGTTCATGT 57.135 45.000 0.00 0.00 0.00 3.21
5252 5489 4.025040 TCTTTGATGCCTGACTGATGTT 57.975 40.909 0.00 0.00 0.00 2.71
5298 5535 7.385267 TGAACCAATAAAGATTTTGATGTGGG 58.615 34.615 0.00 0.00 0.00 4.61
5384 5622 5.395657 CCATTGTGGAGTCAGCACTTAGATA 60.396 44.000 0.00 0.00 40.96 1.98
5385 5623 4.511527 CATTGTGGAGTCAGCACTTAGAT 58.488 43.478 0.00 0.00 30.63 1.98
5442 5691 5.761234 AGTAATACGGAAAGTTCAGCAACAA 59.239 36.000 0.00 0.00 34.60 2.83
5509 5758 4.227300 TGCTTGTCATAAAGTCCCATAGGT 59.773 41.667 0.00 0.00 0.00 3.08
5516 5765 7.497249 ACTCATTAGATGCTTGTCATAAAGTCC 59.503 37.037 0.00 0.00 35.05 3.85
5701 5956 0.607217 GTTGAAACCGGTCGGGGATT 60.607 55.000 8.04 0.00 41.60 3.01
5945 6202 8.597227 CATTATAAATCATGCACAACAAAGGTG 58.403 33.333 0.00 0.00 39.25 4.00
6073 6330 9.516314 CAGACTCGTTATAGTTTAATCACATCA 57.484 33.333 0.00 0.00 0.00 3.07
6092 6349 2.926200 CACAGGAGCAATAACAGACTCG 59.074 50.000 0.00 0.00 0.00 4.18
6162 6419 0.947244 CTTTTGAGACCAACGCTGCT 59.053 50.000 0.00 0.00 30.88 4.24
6222 6479 3.949754 GTGCAATCCCAATCTGAGATTCA 59.050 43.478 4.39 0.00 0.00 2.57
6284 6556 6.403855 CGCCCAAAGGTTTTCTTTATTCGATA 60.404 38.462 0.00 0.00 43.32 2.92
6290 6562 2.028476 GCCGCCCAAAGGTTTTCTTTAT 60.028 45.455 0.00 0.00 43.32 1.40
6403 6681 3.482436 TCGGTCCTTACTGTGCATTTTT 58.518 40.909 0.00 0.00 33.38 1.94


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

AutoCloner maintained by Alex Coulton.