Multiple sequence alignment - TraesCS2D01G186400

Loading Multiple Alignment...

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 TraesCS2D01G186400 chr2D 100.000 2678 0 0 1 2678 131074424 131077101 0.000000e+00 4946.0
1 TraesCS2D01G186400 chr2D 83.333 888 113 23 648 1514 130991692 130992565 0.000000e+00 787.0
2 TraesCS2D01G186400 chr2D 86.784 681 74 14 830 1504 131120168 131120838 0.000000e+00 745.0
3 TraesCS2D01G186400 chr2D 89.560 546 46 8 2142 2678 332553995 332553452 0.000000e+00 682.0
4 TraesCS2D01G186400 chr2D 89.091 550 48 9 2138 2678 81840341 81840887 0.000000e+00 673.0
5 TraesCS2D01G186400 chr2D 87.203 547 60 7 952 1489 131136255 131136800 4.900000e-172 614.0
6 TraesCS2D01G186400 chr2D 88.452 407 37 5 1680 2082 131050075 131050475 1.440000e-132 483.0
7 TraesCS2D01G186400 chr2D 84.545 440 39 20 341 766 131119703 131120127 2.480000e-110 409.0
8 TraesCS2D01G186400 chr2D 86.667 105 10 2 25 129 131116854 131116954 2.180000e-21 113.0
9 TraesCS2D01G186400 chr2A 86.888 1533 153 34 628 2136 137130702 137132210 0.000000e+00 1674.0
10 TraesCS2D01G186400 chr2A 85.219 548 71 6 952 1489 137229307 137229854 3.010000e-154 555.0
11 TraesCS2D01G186400 chr2A 93.478 92 4 1 341 432 137143624 137143713 4.650000e-28 135.0
12 TraesCS2D01G186400 chr2B 85.239 1111 102 27 1047 2136 184496620 184497689 0.000000e+00 1086.0
13 TraesCS2D01G186400 chr2B 87.006 785 80 13 830 1602 184577344 184578118 0.000000e+00 865.0
14 TraesCS2D01G186400 chr2B 88.566 551 50 10 2138 2678 412272474 412273021 0.000000e+00 656.0
15 TraesCS2D01G186400 chr2B 85.610 549 67 8 953 1489 184595920 184596468 1.390000e-157 566.0
16 TraesCS2D01G186400 chr2B 85.092 436 37 20 341 766 184576883 184577300 1.150000e-113 420.0
17 TraesCS2D01G186400 chr2B 86.454 251 20 8 44 287 184514911 184515154 2.040000e-66 263.0
18 TraesCS2D01G186400 chr2B 84.305 223 28 5 1920 2136 215498276 215498055 7.510000e-51 211.0
19 TraesCS2D01G186400 chr2B 82.266 203 19 8 44 236 184576640 184576835 2.760000e-35 159.0
20 TraesCS2D01G186400 chrUn 84.935 770 92 18 835 1599 326757707 326756957 0.000000e+00 758.0
21 TraesCS2D01G186400 chrUn 80.546 293 42 11 341 621 13409240 13409529 7.510000e-51 211.0
22 TraesCS2D01G186400 chrUn 80.546 293 42 11 341 621 360045469 360045758 7.510000e-51 211.0
23 TraesCS2D01G186400 chr7D 91.682 553 37 6 2133 2677 528783817 528784368 0.000000e+00 758.0
24 TraesCS2D01G186400 chr3A 91.257 549 37 6 2138 2678 539360490 539361035 0.000000e+00 737.0
25 TraesCS2D01G186400 chr3D 87.523 553 53 9 2138 2678 267264618 267264070 2.260000e-175 625.0
26 TraesCS2D01G186400 chr7A 87.455 550 57 9 2138 2678 153402020 153401474 8.140000e-175 623.0
27 TraesCS2D01G186400 chr4D 87.500 552 51 11 2138 2678 438162362 438162906 2.930000e-174 621.0
28 TraesCS2D01G186400 chr3B 87.432 549 54 9 2138 2678 654486641 654487182 3.790000e-173 617.0
29 TraesCS2D01G186400 chr4A 100.000 31 0 0 287 317 477033209 477033179 1.040000e-04 58.4


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 TraesCS2D01G186400 chr2D 131074424 131077101 2677 False 4946.000000 4946 100.000000 1 2678 1 chr2D.!!$F4 2677
1 TraesCS2D01G186400 chr2D 130991692 130992565 873 False 787.000000 787 83.333000 648 1514 1 chr2D.!!$F2 866
2 TraesCS2D01G186400 chr2D 332553452 332553995 543 True 682.000000 682 89.560000 2142 2678 1 chr2D.!!$R1 536
3 TraesCS2D01G186400 chr2D 81840341 81840887 546 False 673.000000 673 89.091000 2138 2678 1 chr2D.!!$F1 540
4 TraesCS2D01G186400 chr2D 131136255 131136800 545 False 614.000000 614 87.203000 952 1489 1 chr2D.!!$F5 537
5 TraesCS2D01G186400 chr2D 131116854 131120838 3984 False 422.333333 745 85.998667 25 1504 3 chr2D.!!$F6 1479
6 TraesCS2D01G186400 chr2A 137130702 137132210 1508 False 1674.000000 1674 86.888000 628 2136 1 chr2A.!!$F1 1508
7 TraesCS2D01G186400 chr2A 137229307 137229854 547 False 555.000000 555 85.219000 952 1489 1 chr2A.!!$F3 537
8 TraesCS2D01G186400 chr2B 184496620 184497689 1069 False 1086.000000 1086 85.239000 1047 2136 1 chr2B.!!$F1 1089
9 TraesCS2D01G186400 chr2B 412272474 412273021 547 False 656.000000 656 88.566000 2138 2678 1 chr2B.!!$F4 540
10 TraesCS2D01G186400 chr2B 184595920 184596468 548 False 566.000000 566 85.610000 953 1489 1 chr2B.!!$F3 536
11 TraesCS2D01G186400 chr2B 184576640 184578118 1478 False 481.333333 865 84.788000 44 1602 3 chr2B.!!$F5 1558
12 TraesCS2D01G186400 chrUn 326756957 326757707 750 True 758.000000 758 84.935000 835 1599 1 chrUn.!!$R1 764
13 TraesCS2D01G186400 chr7D 528783817 528784368 551 False 758.000000 758 91.682000 2133 2677 1 chr7D.!!$F1 544
14 TraesCS2D01G186400 chr3A 539360490 539361035 545 False 737.000000 737 91.257000 2138 2678 1 chr3A.!!$F1 540
15 TraesCS2D01G186400 chr3D 267264070 267264618 548 True 625.000000 625 87.523000 2138 2678 1 chr3D.!!$R1 540
16 TraesCS2D01G186400 chr7A 153401474 153402020 546 True 623.000000 623 87.455000 2138 2678 1 chr7A.!!$R1 540
17 TraesCS2D01G186400 chr4D 438162362 438162906 544 False 621.000000 621 87.500000 2138 2678 1 chr4D.!!$F1 540
18 TraesCS2D01G186400 chr3B 654486641 654487182 541 False 617.000000 617 87.432000 2138 2678 1 chr3B.!!$F1 540

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
21 22 0.103208 CCGAACGCTCCTAGCATCTT 59.897 55.0 0.0 0.0 42.58 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 4521 0.10852 GTTAGGATTCCGTGCGGTGA 60.109 55.0 10.6 1.53 36.47 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.107141 GCCGAACGCTCCTAGCAT 59.893 61.111 0.00 0.00 42.58 3.79
19 20 1.951631 GCCGAACGCTCCTAGCATC 60.952 63.158 0.00 0.00 42.58 3.91
20 21 1.736586 CCGAACGCTCCTAGCATCT 59.263 57.895 0.00 0.00 42.58 2.90
21 22 0.103208 CCGAACGCTCCTAGCATCTT 59.897 55.000 0.00 0.00 42.58 2.40
22 23 1.482278 CGAACGCTCCTAGCATCTTC 58.518 55.000 0.00 0.00 42.58 2.87
23 24 1.482278 GAACGCTCCTAGCATCTTCG 58.518 55.000 0.00 0.00 42.58 3.79
26 27 1.204941 ACGCTCCTAGCATCTTCGTTT 59.795 47.619 0.00 0.00 42.58 3.60
37 38 7.534239 CCTAGCATCTTCGTTTAAAAGACAAAC 59.466 37.037 3.14 0.00 35.68 2.93
40 41 7.220108 AGCATCTTCGTTTAAAAGACAAACAAC 59.780 33.333 3.14 0.00 35.68 3.32
80 81 1.999048 TACCAACATTACCGAGTGCG 58.001 50.000 0.00 0.00 37.24 5.34
82 83 1.019278 CCAACATTACCGAGTGCGCT 61.019 55.000 9.73 0.00 35.83 5.92
83 84 1.635844 CAACATTACCGAGTGCGCTA 58.364 50.000 9.73 0.00 35.83 4.26
84 85 1.323534 CAACATTACCGAGTGCGCTAC 59.676 52.381 9.73 5.32 35.83 3.58
85 86 0.524816 ACATTACCGAGTGCGCTACG 60.525 55.000 9.73 11.57 35.83 3.51
86 87 0.524816 CATTACCGAGTGCGCTACGT 60.525 55.000 9.73 1.40 35.83 3.57
101 102 4.713806 CGCTACGTACTCTCCTGAATATG 58.286 47.826 0.00 0.00 0.00 1.78
104 105 5.335035 GCTACGTACTCTCCTGAATATGGAC 60.335 48.000 0.00 0.00 0.00 4.02
186 1762 9.740710 ATTAAGTAGGTTTGAAGCTGAAGTAAT 57.259 29.630 5.75 2.81 37.33 1.89
217 1793 2.641439 TACACGTTTTGGCCGGTCGT 62.641 55.000 0.00 3.59 35.12 4.34
220 1796 2.248835 CGTTTTGGCCGGTCGTTCT 61.249 57.895 0.00 0.00 0.00 3.01
224 1800 2.035237 TTTGGCCGGTCGTTCTCACT 62.035 55.000 0.00 0.00 0.00 3.41
227 1803 1.300697 GCCGGTCGTTCTCACTGTT 60.301 57.895 1.90 0.00 0.00 3.16
228 1804 1.282930 GCCGGTCGTTCTCACTGTTC 61.283 60.000 1.90 0.00 0.00 3.18
229 1805 0.314302 CCGGTCGTTCTCACTGTTCT 59.686 55.000 0.00 0.00 0.00 3.01
230 1806 1.538512 CCGGTCGTTCTCACTGTTCTA 59.461 52.381 0.00 0.00 0.00 2.10
231 1807 2.582687 CGGTCGTTCTCACTGTTCTAC 58.417 52.381 0.00 0.00 0.00 2.59
232 1808 2.225963 CGGTCGTTCTCACTGTTCTACT 59.774 50.000 0.00 0.00 0.00 2.57
233 1809 3.667430 CGGTCGTTCTCACTGTTCTACTC 60.667 52.174 0.00 0.00 0.00 2.59
234 1810 3.502979 GGTCGTTCTCACTGTTCTACTCT 59.497 47.826 0.00 0.00 0.00 3.24
235 1811 4.378666 GGTCGTTCTCACTGTTCTACTCTC 60.379 50.000 0.00 0.00 0.00 3.20
236 1812 4.213694 GTCGTTCTCACTGTTCTACTCTCA 59.786 45.833 0.00 0.00 0.00 3.27
237 1813 4.213694 TCGTTCTCACTGTTCTACTCTCAC 59.786 45.833 0.00 0.00 0.00 3.51
238 1814 4.614078 CGTTCTCACTGTTCTACTCTCACC 60.614 50.000 0.00 0.00 0.00 4.02
239 1815 4.374689 TCTCACTGTTCTACTCTCACCT 57.625 45.455 0.00 0.00 0.00 4.00
240 1816 4.075682 TCTCACTGTTCTACTCTCACCTG 58.924 47.826 0.00 0.00 0.00 4.00
252 2851 4.076394 ACTCTCACCTGTGTACTCTCTTC 58.924 47.826 0.00 0.00 0.00 2.87
257 2856 1.827969 CCTGTGTACTCTCTTCCCCTG 59.172 57.143 0.00 0.00 0.00 4.45
268 2867 7.130681 ACTCTCTTCCCCTGTTATCTTAATG 57.869 40.000 0.00 0.00 0.00 1.90
276 2875 7.506114 TCCCCTGTTATCTTAATGTATGACAC 58.494 38.462 0.00 0.00 0.00 3.67
277 2876 7.126573 TCCCCTGTTATCTTAATGTATGACACA 59.873 37.037 0.00 0.00 42.69 3.72
278 2877 7.226720 CCCCTGTTATCTTAATGTATGACACAC 59.773 40.741 0.00 0.00 40.86 3.82
308 2907 8.791355 AATAATTTGAACTAAAACCACGACAC 57.209 30.769 0.00 0.00 0.00 3.67
309 2908 6.445357 AATTTGAACTAAAACCACGACACT 57.555 33.333 0.00 0.00 0.00 3.55
310 2909 7.556733 AATTTGAACTAAAACCACGACACTA 57.443 32.000 0.00 0.00 0.00 2.74
311 2910 6.981762 TTTGAACTAAAACCACGACACTAA 57.018 33.333 0.00 0.00 0.00 2.24
312 2911 7.556733 TTTGAACTAAAACCACGACACTAAT 57.443 32.000 0.00 0.00 0.00 1.73
313 2912 7.556733 TTGAACTAAAACCACGACACTAATT 57.443 32.000 0.00 0.00 0.00 1.40
314 2913 7.556733 TGAACTAAAACCACGACACTAATTT 57.443 32.000 0.00 0.00 0.00 1.82
315 2914 7.987649 TGAACTAAAACCACGACACTAATTTT 58.012 30.769 0.00 0.00 0.00 1.82
316 2915 7.911205 TGAACTAAAACCACGACACTAATTTTG 59.089 33.333 0.00 0.00 0.00 2.44
317 2916 7.556733 ACTAAAACCACGACACTAATTTTGA 57.443 32.000 0.00 0.00 0.00 2.69
318 2917 7.987649 ACTAAAACCACGACACTAATTTTGAA 58.012 30.769 0.00 0.00 0.00 2.69
319 2918 8.626526 ACTAAAACCACGACACTAATTTTGAAT 58.373 29.630 0.00 0.00 0.00 2.57
320 2919 7.924103 AAAACCACGACACTAATTTTGAATC 57.076 32.000 0.00 0.00 0.00 2.52
321 2920 5.622770 ACCACGACACTAATTTTGAATCC 57.377 39.130 0.00 0.00 0.00 3.01
322 2921 4.153475 ACCACGACACTAATTTTGAATCCG 59.847 41.667 0.00 0.00 0.00 4.18
323 2922 4.390603 CCACGACACTAATTTTGAATCCGA 59.609 41.667 0.00 0.00 0.00 4.55
324 2923 5.445939 CCACGACACTAATTTTGAATCCGAG 60.446 44.000 0.00 0.00 0.00 4.63
325 2924 4.630069 ACGACACTAATTTTGAATCCGAGG 59.370 41.667 0.00 0.00 0.00 4.63
326 2925 4.034048 CGACACTAATTTTGAATCCGAGGG 59.966 45.833 0.00 0.00 0.00 4.30
327 2926 5.174037 ACACTAATTTTGAATCCGAGGGA 57.826 39.130 0.00 0.00 35.55 4.20
328 2927 5.186198 ACACTAATTTTGAATCCGAGGGAG 58.814 41.667 0.00 0.00 34.05 4.30
329 2928 5.186198 CACTAATTTTGAATCCGAGGGAGT 58.814 41.667 0.00 0.00 34.05 3.85
330 2929 6.070424 ACACTAATTTTGAATCCGAGGGAGTA 60.070 38.462 0.00 0.00 34.05 2.59
331 2930 6.480320 CACTAATTTTGAATCCGAGGGAGTAG 59.520 42.308 0.00 0.00 34.05 2.57
332 2931 5.437191 AATTTTGAATCCGAGGGAGTAGT 57.563 39.130 0.00 0.00 34.05 2.73
333 2932 6.555463 AATTTTGAATCCGAGGGAGTAGTA 57.445 37.500 0.00 0.00 34.05 1.82
334 2933 6.749036 ATTTTGAATCCGAGGGAGTAGTAT 57.251 37.500 0.00 0.00 34.05 2.12
335 2934 6.555463 TTTTGAATCCGAGGGAGTAGTATT 57.445 37.500 0.00 0.00 34.05 1.89
336 2935 6.555463 TTTGAATCCGAGGGAGTAGTATTT 57.445 37.500 0.00 0.00 34.05 1.40
337 2936 7.664552 TTTGAATCCGAGGGAGTAGTATTTA 57.335 36.000 0.00 0.00 34.05 1.40
338 2937 6.896021 TGAATCCGAGGGAGTAGTATTTAG 57.104 41.667 0.00 0.00 34.05 1.85
339 2938 5.243283 TGAATCCGAGGGAGTAGTATTTAGC 59.757 44.000 0.00 0.00 34.05 3.09
382 2981 1.074167 AGGGCCTAGGTGATCAGGG 60.074 63.158 2.82 0.00 32.15 4.45
429 3055 4.970662 ATGTATTTCACTGTGTGCATCC 57.029 40.909 7.79 0.00 32.98 3.51
443 3069 3.244665 TGTGCATCCTTCATGTCTTCAGT 60.245 43.478 0.00 0.00 34.56 3.41
444 3070 4.020307 TGTGCATCCTTCATGTCTTCAGTA 60.020 41.667 0.00 0.00 34.56 2.74
445 3071 4.937620 GTGCATCCTTCATGTCTTCAGTAA 59.062 41.667 0.00 0.00 34.56 2.24
446 3072 4.937620 TGCATCCTTCATGTCTTCAGTAAC 59.062 41.667 0.00 0.00 34.56 2.50
447 3073 5.181748 GCATCCTTCATGTCTTCAGTAACT 58.818 41.667 0.00 0.00 34.56 2.24
448 3074 5.293079 GCATCCTTCATGTCTTCAGTAACTC 59.707 44.000 0.00 0.00 34.56 3.01
449 3075 6.638610 CATCCTTCATGTCTTCAGTAACTCT 58.361 40.000 0.00 0.00 0.00 3.24
450 3076 6.672266 TCCTTCATGTCTTCAGTAACTCTT 57.328 37.500 0.00 0.00 0.00 2.85
451 3077 7.776618 TCCTTCATGTCTTCAGTAACTCTTA 57.223 36.000 0.00 0.00 0.00 2.10
452 3078 8.190326 TCCTTCATGTCTTCAGTAACTCTTAA 57.810 34.615 0.00 0.00 0.00 1.85
453 3079 8.307483 TCCTTCATGTCTTCAGTAACTCTTAAG 58.693 37.037 0.00 0.00 0.00 1.85
454 3080 8.091449 CCTTCATGTCTTCAGTAACTCTTAAGT 58.909 37.037 1.63 0.00 37.32 2.24
455 3081 9.134734 CTTCATGTCTTCAGTAACTCTTAAGTC 57.865 37.037 1.63 0.00 33.48 3.01
456 3082 8.178313 TCATGTCTTCAGTAACTCTTAAGTCA 57.822 34.615 1.63 0.00 33.48 3.41
479 3105 9.875691 GTCATATTGATGCAGATATTAGGTACA 57.124 33.333 0.00 0.00 32.62 2.90
484 3110 9.935241 ATTGATGCAGATATTAGGTACAACTAG 57.065 33.333 0.00 0.00 0.00 2.57
485 3111 8.478775 TGATGCAGATATTAGGTACAACTAGT 57.521 34.615 0.00 0.00 0.00 2.57
486 3112 9.582648 TGATGCAGATATTAGGTACAACTAGTA 57.417 33.333 0.00 0.00 0.00 1.82
544 3171 8.670521 AAATTGAACCCCATCTAGAAAAATCT 57.329 30.769 0.00 0.00 0.00 2.40
572 3199 4.188462 CCAAATGGTCACGCATTAGACTA 58.812 43.478 0.00 0.00 35.18 2.59
604 3231 3.835790 TTGGGCGCTGCTAACCGTT 62.836 57.895 7.64 0.00 0.00 4.44
620 3247 0.389817 CGTTGAGCTCGGATGTTGGA 60.390 55.000 9.64 0.00 0.00 3.53
621 3248 1.363744 GTTGAGCTCGGATGTTGGAG 58.636 55.000 9.64 0.00 0.00 3.86
622 3249 1.066858 GTTGAGCTCGGATGTTGGAGA 60.067 52.381 9.64 0.00 31.90 3.71
633 3260 3.539604 GATGTTGGAGAAGGATGGAGTG 58.460 50.000 0.00 0.00 0.00 3.51
699 3330 1.881973 TGCTGATGTCCAAACTTGCTC 59.118 47.619 0.00 0.00 0.00 4.26
720 3351 5.323371 TCGTGTTCATGTGTGATCTGATA 57.677 39.130 0.00 0.00 33.56 2.15
721 3352 5.719173 TCGTGTTCATGTGTGATCTGATAA 58.281 37.500 0.00 0.00 33.56 1.75
722 3353 6.162777 TCGTGTTCATGTGTGATCTGATAAA 58.837 36.000 0.00 0.00 33.56 1.40
732 3363 3.879892 GTGATCTGATAAAGGTCCCTTGC 59.120 47.826 0.00 0.00 34.83 4.01
762 3393 1.520342 CGTCTTAGCAGCTGGCCTC 60.520 63.158 17.12 0.00 46.50 4.70
770 3401 1.376424 CAGCTGGCCTCACAATCGT 60.376 57.895 5.57 0.00 0.00 3.73
785 3416 2.878406 CAATCGTGTGTTTTCTCCAGGT 59.122 45.455 0.00 0.00 0.00 4.00
786 3417 2.234300 TCGTGTGTTTTCTCCAGGTC 57.766 50.000 0.00 0.00 0.00 3.85
789 3420 2.480419 CGTGTGTTTTCTCCAGGTCATC 59.520 50.000 0.00 0.00 0.00 2.92
798 3429 3.036819 TCTCCAGGTCATCATCCTCAAG 58.963 50.000 0.00 0.00 32.37 3.02
800 3431 3.036819 TCCAGGTCATCATCCTCAAGAG 58.963 50.000 0.00 0.00 32.37 2.85
807 3438 1.220206 CATCCTCAAGAGCAGCCGT 59.780 57.895 0.00 0.00 0.00 5.68
826 3473 2.546789 CGTAAAAGCCGAAAGAACACCT 59.453 45.455 0.00 0.00 0.00 4.00
870 3522 8.361139 CCAGACTTAGACTCTGAAACTAAAGAA 58.639 37.037 1.97 0.00 37.90 2.52
876 3528 5.749109 AGACTCTGAAACTAAAGAACACACG 59.251 40.000 0.00 0.00 0.00 4.49
881 3533 8.428186 TCTGAAACTAAAGAACACACGTAAAT 57.572 30.769 0.00 0.00 0.00 1.40
917 3574 2.565834 GAGTAGGTGACCAGCCTTGTTA 59.434 50.000 3.63 0.00 37.54 2.41
918 3575 3.182152 AGTAGGTGACCAGCCTTGTTAT 58.818 45.455 3.63 0.00 37.54 1.89
927 3584 5.480073 TGACCAGCCTTGTTATAAAGCATTT 59.520 36.000 0.00 0.00 43.42 2.32
934 3591 8.534496 AGCCTTGTTATAAAGCATTTGATTCTT 58.466 29.630 0.00 0.00 39.63 2.52
942 3599 6.721571 AAAGCATTTGATTCTTGCAAGATG 57.278 33.333 28.89 22.37 36.60 2.90
944 3601 7.238564 AAAGCATTTGATTCTTGCAAGATGCA 61.239 34.615 34.50 28.32 45.06 3.96
964 3624 9.236006 AGATGCAAGTGTTTTGAACTCTATAAT 57.764 29.630 0.00 0.00 34.41 1.28
978 3638 9.952188 TGAACTCTATAATTAGAATGTGAGACG 57.048 33.333 0.00 0.00 34.06 4.18
980 3640 9.953697 AACTCTATAATTAGAATGTGAGACGTC 57.046 33.333 7.70 7.70 34.06 4.34
988 3648 3.886505 AGAATGTGAGACGTCCTATCTCC 59.113 47.826 13.01 0.00 41.72 3.71
999 3659 2.982488 GTCCTATCTCCCCCACATCAAT 59.018 50.000 0.00 0.00 0.00 2.57
1108 3781 4.794439 TCGTGCGTCGCCATGAGG 62.794 66.667 15.88 1.50 39.67 3.86
1162 3839 3.826282 TCCAAAGGGGAGGAGCAG 58.174 61.111 0.00 0.00 42.15 4.24
1198 3875 1.002134 GCTGCCCAAGGTTGAGCTA 60.002 57.895 0.00 0.00 32.64 3.32
1199 3876 0.394899 GCTGCCCAAGGTTGAGCTAT 60.395 55.000 0.00 0.00 32.64 2.97
1204 3881 0.179000 CCAAGGTTGAGCTATCGCCT 59.821 55.000 0.00 0.00 35.65 5.52
1337 4014 3.249189 TTCCAGGCAAGCCGGAGT 61.249 61.111 18.91 0.00 38.96 3.85
1400 4077 2.434359 CGGAGTTCCACTTCCCGC 60.434 66.667 0.00 0.00 30.55 6.13
1402 4079 1.072505 GGAGTTCCACTTCCCGCAA 59.927 57.895 0.00 0.00 35.64 4.85
1516 4195 6.325028 TGGGATTGTTTAGTGTGGATTTTTCA 59.675 34.615 0.00 0.00 0.00 2.69
1527 4206 8.408043 AGTGTGGATTTTTCATGAGTCATTTA 57.592 30.769 1.86 0.00 0.00 1.40
1577 4260 6.183360 GCGCCTATTTAGATGGAATGTACATC 60.183 42.308 9.23 2.93 43.87 3.06
1641 4326 7.230849 TGAGTTCCACAATTAATTGAGCAAT 57.769 32.000 30.18 13.40 40.14 3.56
1647 4332 8.070034 TCCACAATTAATTGAGCAATCATCTT 57.930 30.769 30.18 4.69 40.14 2.40
1648 4333 8.192774 TCCACAATTAATTGAGCAATCATCTTC 58.807 33.333 30.18 0.00 40.14 2.87
1649 4334 8.195436 CCACAATTAATTGAGCAATCATCTTCT 58.805 33.333 30.18 4.10 40.14 2.85
1729 4423 8.504812 ACATATATTAGTGTTGATTGCACACA 57.495 30.769 7.10 0.00 39.17 3.72
1820 4521 9.513906 CCAATTGGAAGTTTTTACCCAATAAAT 57.486 29.630 20.50 0.00 45.60 1.40
1823 4524 9.719355 ATTGGAAGTTTTTACCCAATAAATCAC 57.281 29.630 0.00 0.00 44.81 3.06
1858 4561 1.475280 ACTCTGGCACGCTATTTACGA 59.525 47.619 0.00 0.00 0.00 3.43
1885 4588 2.036346 GCATTGTCCTTTGAGTTTGGCT 59.964 45.455 0.00 0.00 0.00 4.75
1935 4638 2.705127 AGTAGGGTTTGGTTACCGTTCA 59.295 45.455 0.00 0.00 39.18 3.18
1940 4643 3.004002 GGGTTTGGTTACCGTTCAGAAAG 59.996 47.826 0.00 0.00 39.18 2.62
1985 4688 6.495181 TCCTAGGAGTGATATGAACAATCTCC 59.505 42.308 7.62 0.00 39.88 3.71
2002 4705 2.107031 TCTCCATGGGCATGAAGGTATG 59.893 50.000 13.02 0.00 41.20 2.39
2030 4737 2.524306 TGGGTGGTAGCAAATTCTTGG 58.476 47.619 0.00 0.00 32.76 3.61
2038 4745 4.949856 GGTAGCAAATTCTTGGAATCCTGA 59.050 41.667 0.00 0.00 32.76 3.86
2054 4761 0.250234 CTGATGGTTCGAGGGCTCAA 59.750 55.000 0.00 0.00 0.00 3.02
2055 4762 0.250234 TGATGGTTCGAGGGCTCAAG 59.750 55.000 0.00 0.00 0.00 3.02
2136 4845 0.306228 TGTGGAATTGCAACGACGTG 59.694 50.000 0.00 0.00 0.00 4.49
2173 4882 4.453751 TCGCCCCGCTTTATAAATAAAGT 58.546 39.130 18.85 0.00 46.78 2.66
2323 5041 2.045926 AGAACATGTCCAGCGCCC 60.046 61.111 2.29 0.00 0.00 6.13
2328 5046 2.124151 ATGTCCAGCGCCCAATCC 60.124 61.111 2.29 0.00 0.00 3.01
2333 5051 2.753043 CAGCGCCCAATCCAGCTT 60.753 61.111 2.29 0.00 37.94 3.74
2394 5117 1.218316 GAAGGTCGGCGATGAAGGT 59.782 57.895 14.79 0.00 0.00 3.50
2403 5126 0.179000 GCGATGAAGGTGGAGATGGT 59.821 55.000 0.00 0.00 0.00 3.55
2411 5134 1.987855 GTGGAGATGGTGTCCCGGA 60.988 63.158 0.73 0.00 32.49 5.14
2450 5174 0.313672 CCGCCAAAGCTGCAAGTAAA 59.686 50.000 1.02 0.00 36.60 2.01
2484 5210 0.679002 AGAGCGTTAGTAGCCCGTCA 60.679 55.000 0.00 0.00 34.64 4.35
2535 5263 0.902531 GATCGTCCAGAGGGTCCAAA 59.097 55.000 0.00 0.00 34.93 3.28
2548 5276 2.989253 CCAAACGAGGGCCCCAAC 60.989 66.667 21.43 9.86 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.951631 GATGCTAGGAGCGTTCGGC 60.952 63.158 0.00 0.00 46.26 5.54
2 3 0.103208 AAGATGCTAGGAGCGTTCGG 59.897 55.000 0.00 0.00 46.26 4.30
3 4 1.482278 GAAGATGCTAGGAGCGTTCG 58.518 55.000 0.00 0.00 46.26 3.95
4 5 1.202313 ACGAAGATGCTAGGAGCGTTC 60.202 52.381 0.00 0.00 46.26 3.95
5 6 0.818296 ACGAAGATGCTAGGAGCGTT 59.182 50.000 0.00 0.00 46.26 4.84
6 7 0.818296 AACGAAGATGCTAGGAGCGT 59.182 50.000 0.00 0.00 46.26 5.07
7 8 1.927895 AAACGAAGATGCTAGGAGCG 58.072 50.000 0.00 0.00 46.26 5.03
8 9 5.581085 TCTTTTAAACGAAGATGCTAGGAGC 59.419 40.000 0.00 0.00 42.82 4.70
9 10 6.590292 TGTCTTTTAAACGAAGATGCTAGGAG 59.410 38.462 0.00 0.00 35.74 3.69
10 11 6.460781 TGTCTTTTAAACGAAGATGCTAGGA 58.539 36.000 0.00 0.00 35.74 2.94
11 12 6.721571 TGTCTTTTAAACGAAGATGCTAGG 57.278 37.500 0.00 0.00 35.74 3.02
12 13 8.067784 TGTTTGTCTTTTAAACGAAGATGCTAG 58.932 33.333 0.00 0.00 40.10 3.42
13 14 7.921787 TGTTTGTCTTTTAAACGAAGATGCTA 58.078 30.769 0.00 0.00 40.10 3.49
14 15 6.791303 TGTTTGTCTTTTAAACGAAGATGCT 58.209 32.000 0.00 0.00 40.10 3.79
15 16 7.008810 TGTTGTTTGTCTTTTAAACGAAGATGC 59.991 33.333 0.00 0.00 40.10 3.91
16 17 8.388319 TGTTGTTTGTCTTTTAAACGAAGATG 57.612 30.769 0.00 0.00 40.10 2.90
17 18 8.973835 TTGTTGTTTGTCTTTTAAACGAAGAT 57.026 26.923 0.00 0.00 40.10 2.40
18 19 8.973835 ATTGTTGTTTGTCTTTTAAACGAAGA 57.026 26.923 0.00 0.00 40.10 2.87
20 21 9.843334 ACTATTGTTGTTTGTCTTTTAAACGAA 57.157 25.926 0.00 0.00 40.10 3.85
80 81 4.760715 TCCATATTCAGGAGAGTACGTAGC 59.239 45.833 0.00 0.00 0.00 3.58
82 83 5.763698 CAGTCCATATTCAGGAGAGTACGTA 59.236 44.000 0.00 0.00 35.42 3.57
83 84 4.580995 CAGTCCATATTCAGGAGAGTACGT 59.419 45.833 0.00 0.00 35.42 3.57
84 85 4.822350 TCAGTCCATATTCAGGAGAGTACG 59.178 45.833 0.00 0.00 35.42 3.67
85 86 6.016610 GTCTCAGTCCATATTCAGGAGAGTAC 60.017 46.154 0.00 0.00 35.42 2.73
86 87 6.065374 GTCTCAGTCCATATTCAGGAGAGTA 58.935 44.000 0.00 0.00 35.42 2.59
90 91 3.551863 GCGTCTCAGTCCATATTCAGGAG 60.552 52.174 0.00 0.00 35.42 3.69
101 102 1.373497 CCAGTGTGCGTCTCAGTCC 60.373 63.158 0.00 0.00 0.00 3.85
104 105 2.029518 TGCCAGTGTGCGTCTCAG 59.970 61.111 0.00 0.00 0.00 3.35
186 1762 7.251994 GGCCAAAACGTGTATTATGATTGTTA 58.748 34.615 0.00 0.00 0.00 2.41
187 1763 6.096695 GGCCAAAACGTGTATTATGATTGTT 58.903 36.000 0.00 0.00 0.00 2.83
188 1764 5.646606 GGCCAAAACGTGTATTATGATTGT 58.353 37.500 0.00 0.00 0.00 2.71
200 1776 2.704973 GAACGACCGGCCAAAACGTG 62.705 60.000 0.00 0.00 37.28 4.49
201 1777 2.514360 AACGACCGGCCAAAACGT 60.514 55.556 0.00 5.97 38.81 3.99
217 1793 4.520874 CAGGTGAGAGTAGAACAGTGAGAA 59.479 45.833 0.00 0.00 0.00 2.87
220 1796 3.570125 CACAGGTGAGAGTAGAACAGTGA 59.430 47.826 0.00 0.00 0.00 3.41
224 1800 4.726583 AGTACACAGGTGAGAGTAGAACA 58.273 43.478 6.40 0.00 0.00 3.18
227 1803 4.532916 AGAGAGTACACAGGTGAGAGTAGA 59.467 45.833 6.40 0.00 0.00 2.59
228 1804 4.839121 AGAGAGTACACAGGTGAGAGTAG 58.161 47.826 6.40 0.00 0.00 2.57
229 1805 4.912317 AGAGAGTACACAGGTGAGAGTA 57.088 45.455 6.40 0.00 0.00 2.59
230 1806 3.799432 AGAGAGTACACAGGTGAGAGT 57.201 47.619 6.40 0.00 0.00 3.24
231 1807 3.442273 GGAAGAGAGTACACAGGTGAGAG 59.558 52.174 6.40 0.00 0.00 3.20
232 1808 3.422796 GGAAGAGAGTACACAGGTGAGA 58.577 50.000 6.40 0.00 0.00 3.27
233 1809 2.494073 GGGAAGAGAGTACACAGGTGAG 59.506 54.545 6.40 0.00 0.00 3.51
234 1810 2.526432 GGGAAGAGAGTACACAGGTGA 58.474 52.381 6.40 0.00 0.00 4.02
235 1811 1.550976 GGGGAAGAGAGTACACAGGTG 59.449 57.143 0.00 0.00 0.00 4.00
236 1812 1.433592 AGGGGAAGAGAGTACACAGGT 59.566 52.381 0.00 0.00 0.00 4.00
237 1813 1.827969 CAGGGGAAGAGAGTACACAGG 59.172 57.143 0.00 0.00 0.00 4.00
238 1814 2.530701 ACAGGGGAAGAGAGTACACAG 58.469 52.381 0.00 0.00 0.00 3.66
239 1815 2.696526 ACAGGGGAAGAGAGTACACA 57.303 50.000 0.00 0.00 0.00 3.72
240 1816 4.957327 AGATAACAGGGGAAGAGAGTACAC 59.043 45.833 0.00 0.00 0.00 2.90
252 2851 7.226720 GTGTGTCATACATTAAGATAACAGGGG 59.773 40.741 0.00 0.00 42.24 4.79
287 2886 7.556733 TTAGTGTCGTGGTTTTAGTTCAAAT 57.443 32.000 0.00 0.00 0.00 2.32
289 2888 7.556733 AATTAGTGTCGTGGTTTTAGTTCAA 57.443 32.000 0.00 0.00 0.00 2.69
290 2889 7.556733 AAATTAGTGTCGTGGTTTTAGTTCA 57.443 32.000 0.00 0.00 0.00 3.18
291 2890 8.124199 TCAAAATTAGTGTCGTGGTTTTAGTTC 58.876 33.333 0.00 0.00 0.00 3.01
292 2891 7.987649 TCAAAATTAGTGTCGTGGTTTTAGTT 58.012 30.769 0.00 0.00 0.00 2.24
293 2892 7.556733 TCAAAATTAGTGTCGTGGTTTTAGT 57.443 32.000 0.00 0.00 0.00 2.24
295 2894 8.077386 GGATTCAAAATTAGTGTCGTGGTTTTA 58.923 33.333 0.00 0.00 0.00 1.52
297 2896 6.443792 GGATTCAAAATTAGTGTCGTGGTTT 58.556 36.000 0.00 0.00 0.00 3.27
298 2897 5.334569 CGGATTCAAAATTAGTGTCGTGGTT 60.335 40.000 0.00 0.00 0.00 3.67
299 2898 4.153475 CGGATTCAAAATTAGTGTCGTGGT 59.847 41.667 0.00 0.00 0.00 4.16
300 2899 4.390603 TCGGATTCAAAATTAGTGTCGTGG 59.609 41.667 0.00 0.00 0.00 4.94
301 2900 5.445939 CCTCGGATTCAAAATTAGTGTCGTG 60.446 44.000 0.00 0.00 0.00 4.35
302 2901 4.630069 CCTCGGATTCAAAATTAGTGTCGT 59.370 41.667 0.00 0.00 0.00 4.34
303 2902 4.034048 CCCTCGGATTCAAAATTAGTGTCG 59.966 45.833 0.00 0.00 0.00 4.35
304 2903 5.183228 TCCCTCGGATTCAAAATTAGTGTC 58.817 41.667 0.00 0.00 0.00 3.67
305 2904 5.174037 TCCCTCGGATTCAAAATTAGTGT 57.826 39.130 0.00 0.00 0.00 3.55
306 2905 5.186198 ACTCCCTCGGATTCAAAATTAGTG 58.814 41.667 0.00 0.00 0.00 2.74
307 2906 5.437191 ACTCCCTCGGATTCAAAATTAGT 57.563 39.130 0.00 0.00 0.00 2.24
308 2907 6.583562 ACTACTCCCTCGGATTCAAAATTAG 58.416 40.000 0.00 0.00 0.00 1.73
309 2908 6.555463 ACTACTCCCTCGGATTCAAAATTA 57.445 37.500 0.00 0.00 0.00 1.40
310 2909 5.437191 ACTACTCCCTCGGATTCAAAATT 57.563 39.130 0.00 0.00 0.00 1.82
311 2910 6.749036 ATACTACTCCCTCGGATTCAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
312 2911 6.555463 AATACTACTCCCTCGGATTCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
313 2912 6.555463 AAATACTACTCCCTCGGATTCAAA 57.445 37.500 0.00 0.00 0.00 2.69
314 2913 6.239232 GCTAAATACTACTCCCTCGGATTCAA 60.239 42.308 0.00 0.00 0.00 2.69
315 2914 5.243283 GCTAAATACTACTCCCTCGGATTCA 59.757 44.000 0.00 0.00 0.00 2.57
316 2915 5.619533 CGCTAAATACTACTCCCTCGGATTC 60.620 48.000 0.00 0.00 0.00 2.52
317 2916 4.217983 CGCTAAATACTACTCCCTCGGATT 59.782 45.833 0.00 0.00 0.00 3.01
318 2917 3.757493 CGCTAAATACTACTCCCTCGGAT 59.243 47.826 0.00 0.00 0.00 4.18
319 2918 3.144506 CGCTAAATACTACTCCCTCGGA 58.855 50.000 0.00 0.00 0.00 4.55
320 2919 3.058363 GTCGCTAAATACTACTCCCTCGG 60.058 52.174 0.00 0.00 0.00 4.63
321 2920 3.562973 TGTCGCTAAATACTACTCCCTCG 59.437 47.826 0.00 0.00 0.00 4.63
322 2921 5.511234 TTGTCGCTAAATACTACTCCCTC 57.489 43.478 0.00 0.00 0.00 4.30
323 2922 5.927281 TTTGTCGCTAAATACTACTCCCT 57.073 39.130 0.00 0.00 0.00 4.20
324 2923 5.465724 CCATTTGTCGCTAAATACTACTCCC 59.534 44.000 0.00 0.00 0.00 4.30
325 2924 5.465724 CCCATTTGTCGCTAAATACTACTCC 59.534 44.000 0.00 0.00 0.00 3.85
326 2925 5.050295 GCCCATTTGTCGCTAAATACTACTC 60.050 44.000 0.00 0.00 0.00 2.59
327 2926 4.814771 GCCCATTTGTCGCTAAATACTACT 59.185 41.667 0.00 0.00 0.00 2.57
328 2927 4.573201 TGCCCATTTGTCGCTAAATACTAC 59.427 41.667 0.00 0.00 0.00 2.73
329 2928 4.771903 TGCCCATTTGTCGCTAAATACTA 58.228 39.130 0.00 0.00 0.00 1.82
330 2929 3.616219 TGCCCATTTGTCGCTAAATACT 58.384 40.909 0.00 0.00 0.00 2.12
331 2930 4.102649 GTTGCCCATTTGTCGCTAAATAC 58.897 43.478 0.00 0.00 0.00 1.89
332 2931 4.013728 AGTTGCCCATTTGTCGCTAAATA 58.986 39.130 0.00 0.00 0.00 1.40
333 2932 2.825532 AGTTGCCCATTTGTCGCTAAAT 59.174 40.909 0.00 0.00 0.00 1.40
334 2933 2.235016 AGTTGCCCATTTGTCGCTAAA 58.765 42.857 0.00 0.00 0.00 1.85
335 2934 1.904287 AGTTGCCCATTTGTCGCTAA 58.096 45.000 0.00 0.00 0.00 3.09
336 2935 2.352388 GTAGTTGCCCATTTGTCGCTA 58.648 47.619 0.00 0.00 0.00 4.26
337 2936 1.165270 GTAGTTGCCCATTTGTCGCT 58.835 50.000 0.00 0.00 0.00 4.93
338 2937 0.170339 GGTAGTTGCCCATTTGTCGC 59.830 55.000 0.00 0.00 0.00 5.19
339 2938 1.529226 TGGTAGTTGCCCATTTGTCG 58.471 50.000 0.00 0.00 0.00 4.35
382 2981 2.067013 GGTCTCTAAACTTGTCCACGC 58.933 52.381 0.00 0.00 0.00 5.34
383 2982 2.036733 TGGGTCTCTAAACTTGTCCACG 59.963 50.000 0.00 0.00 0.00 4.94
429 3055 9.134734 GACTTAAGAGTTACTGAAGACATGAAG 57.865 37.037 10.09 0.00 38.95 3.02
453 3079 9.875691 TGTACCTAATATCTGCATCAATATGAC 57.124 33.333 0.00 0.00 34.84 3.06
486 3112 9.862371 AAGCGAAATTACTGATATCGAATAGAT 57.138 29.630 0.00 0.00 43.19 1.98
490 3116 8.799091 CGATAAGCGAAATTACTGATATCGAAT 58.201 33.333 13.35 0.00 41.86 3.34
501 3127 8.934947 GTTCAATTTCTCGATAAGCGAAATTAC 58.065 33.333 17.07 11.66 46.49 1.89
510 3137 6.058183 AGATGGGGTTCAATTTCTCGATAAG 58.942 40.000 0.00 0.00 0.00 1.73
527 3154 6.126478 TGGTCCTTAGATTTTTCTAGATGGGG 60.126 42.308 0.00 0.00 0.00 4.96
569 3196 3.541632 CCCAAACGGTGATGCTATTAGT 58.458 45.455 0.00 0.00 0.00 2.24
572 3199 1.102978 GCCCAAACGGTGATGCTATT 58.897 50.000 0.00 0.00 0.00 1.73
604 3231 1.205655 CTTCTCCAACATCCGAGCTCA 59.794 52.381 15.40 0.00 0.00 4.26
617 3244 0.417437 TCCCACTCCATCCTTCTCCA 59.583 55.000 0.00 0.00 0.00 3.86
620 3247 2.649742 TCTTCCCACTCCATCCTTCT 57.350 50.000 0.00 0.00 0.00 2.85
621 3248 3.615155 CTTTCTTCCCACTCCATCCTTC 58.385 50.000 0.00 0.00 0.00 3.46
622 3249 2.310052 CCTTTCTTCCCACTCCATCCTT 59.690 50.000 0.00 0.00 0.00 3.36
633 3260 0.253207 TCCTCCTCCCCTTTCTTCCC 60.253 60.000 0.00 0.00 0.00 3.97
699 3330 6.407475 TTTATCAGATCACACATGAACACG 57.593 37.500 0.00 0.00 38.69 4.49
720 3351 1.756538 CAACTTGTGCAAGGGACCTTT 59.243 47.619 15.31 0.00 42.53 3.11
721 3352 1.341976 ACAACTTGTGCAAGGGACCTT 60.342 47.619 15.31 0.00 42.53 3.50
722 3353 0.258774 ACAACTTGTGCAAGGGACCT 59.741 50.000 15.31 0.00 42.53 3.85
732 3363 4.518217 CTGCTAAGACGAAACAACTTGTG 58.482 43.478 0.00 0.00 0.00 3.33
770 3401 3.855255 TGATGACCTGGAGAAAACACA 57.145 42.857 0.00 0.00 0.00 3.72
778 3409 3.036819 TCTTGAGGATGATGACCTGGAG 58.963 50.000 0.00 0.00 37.93 3.86
779 3410 3.036819 CTCTTGAGGATGATGACCTGGA 58.963 50.000 0.00 0.00 37.93 3.86
785 3416 1.140452 GGCTGCTCTTGAGGATGATGA 59.860 52.381 0.00 0.00 0.00 2.92
786 3417 1.595466 GGCTGCTCTTGAGGATGATG 58.405 55.000 0.00 0.00 0.00 3.07
789 3420 0.461548 TACGGCTGCTCTTGAGGATG 59.538 55.000 0.00 0.00 0.00 3.51
798 3429 1.296056 TTCGGCTTTTACGGCTGCTC 61.296 55.000 0.00 0.00 36.16 4.26
800 3431 0.454452 CTTTCGGCTTTTACGGCTGC 60.454 55.000 0.00 0.00 36.16 5.25
807 3438 6.347888 CGATTTAGGTGTTCTTTCGGCTTTTA 60.348 38.462 0.00 0.00 0.00 1.52
826 3473 1.065782 TGGCTGCCTGCTTACGATTTA 60.066 47.619 21.03 0.00 42.39 1.40
870 3522 2.806244 GCAGTTCCAGATTTACGTGTGT 59.194 45.455 0.00 0.00 0.00 3.72
876 3528 1.201921 CGCGTGCAGTTCCAGATTTAC 60.202 52.381 0.00 0.00 0.00 2.01
881 3533 1.520600 TACTCGCGTGCAGTTCCAGA 61.521 55.000 5.77 0.00 0.00 3.86
917 3574 7.011109 GCATCTTGCAAGAATCAAATGCTTTAT 59.989 33.333 31.55 8.36 44.26 1.40
918 3575 6.311935 GCATCTTGCAAGAATCAAATGCTTTA 59.688 34.615 31.55 5.21 44.26 1.85
964 3624 5.531659 GGAGATAGGACGTCTCACATTCTAA 59.468 44.000 16.46 0.00 43.05 2.10
978 3638 2.103153 TGATGTGGGGGAGATAGGAC 57.897 55.000 0.00 0.00 0.00 3.85
980 3640 3.264450 GGTATTGATGTGGGGGAGATAGG 59.736 52.174 0.00 0.00 0.00 2.57
988 3648 1.005332 TGGTGTGGTATTGATGTGGGG 59.995 52.381 0.00 0.00 0.00 4.96
999 3659 1.275291 GCTAGCTCTTGTGGTGTGGTA 59.725 52.381 7.70 0.00 0.00 3.25
1023 3696 1.480545 TGATGGACGACTATGGGTGTG 59.519 52.381 0.00 0.00 0.00 3.82
1027 3700 3.565482 CCATTTTGATGGACGACTATGGG 59.435 47.826 0.00 0.00 44.39 4.00
1108 3781 1.821332 CAGGATTCTTGCCCCGCTC 60.821 63.158 0.00 0.00 0.00 5.03
1142 3819 2.291043 GCTCCTCCCCTTTGGACGA 61.291 63.158 0.00 0.00 38.61 4.20
1198 3875 2.687566 ACCTCCGGGAAAGGCGAT 60.688 61.111 7.59 0.00 37.42 4.58
1199 3876 3.702048 CACCTCCGGGAAAGGCGA 61.702 66.667 7.59 0.00 37.42 5.54
1204 3881 2.852075 AGGTGCACCTCCGGGAAA 60.852 61.111 33.20 0.00 44.77 3.13
1337 4014 1.002134 GCAGCTCCACCTTAGGCAA 60.002 57.895 0.00 0.00 0.00 4.52
1516 4195 8.781196 GTGCTTGATATCACATAAATGACTCAT 58.219 33.333 4.48 0.00 33.63 2.90
1527 4206 7.551974 GCCATAGATAAGTGCTTGATATCACAT 59.448 37.037 4.48 0.00 35.76 3.21
1577 4260 7.962964 ATGTAAACATCCATCCGTATTGTAG 57.037 36.000 0.00 0.00 28.78 2.74
1586 4269 7.257722 CACCTTGTTAATGTAAACATCCATCC 58.742 38.462 0.00 0.00 39.04 3.51
1647 4332 8.472007 TTTGCCTTTTCCATTAGTTAAGAAGA 57.528 30.769 0.00 0.00 0.00 2.87
1648 4333 7.329471 GCTTTGCCTTTTCCATTAGTTAAGAAG 59.671 37.037 0.00 0.00 0.00 2.85
1649 4334 7.015195 AGCTTTGCCTTTTCCATTAGTTAAGAA 59.985 33.333 0.00 0.00 0.00 2.52
1711 4399 5.301551 AGGAAATGTGTGCAATCAACACTAA 59.698 36.000 8.06 0.00 38.86 2.24
1810 4511 1.091537 CGTGCGGTGATTTATTGGGT 58.908 50.000 0.00 0.00 0.00 4.51
1814 4515 2.616842 GGATTCCGTGCGGTGATTTATT 59.383 45.455 10.60 0.00 36.47 1.40
1820 4521 0.108520 GTTAGGATTCCGTGCGGTGA 60.109 55.000 10.60 1.53 36.47 4.02
1823 4524 0.460311 AGAGTTAGGATTCCGTGCGG 59.540 55.000 3.94 3.94 0.00 5.69
1858 4561 3.225104 ACTCAAAGGACAATGCATGTGT 58.775 40.909 0.00 7.10 44.12 3.72
1885 4588 4.396790 CGCAAGGTATTTAGGCCTAACAAA 59.603 41.667 25.13 13.22 34.15 2.83
1956 4659 8.915057 ATTGTTCATATCACTCCTAGGAATTG 57.085 34.615 13.77 12.87 0.00 2.32
1985 4688 1.133388 ACCCATACCTTCATGCCCATG 60.133 52.381 1.86 1.86 40.09 3.66
2002 4705 1.271840 TGCTACCACCCATCTCACCC 61.272 60.000 0.00 0.00 0.00 4.61
2030 4737 1.811941 GCCCTCGAACCATCAGGATTC 60.812 57.143 0.00 0.00 38.69 2.52
2038 4745 1.078143 GCTTGAGCCCTCGAACCAT 60.078 57.895 0.00 0.00 34.31 3.55
2054 4761 8.162878 AGAATTCATCGAATATGAACAATGCT 57.837 30.769 8.44 0.00 40.37 3.79
2055 4762 7.536622 GGAGAATTCATCGAATATGAACAATGC 59.463 37.037 8.44 0.00 40.37 3.56
2173 4882 0.179043 TGTGTGCTCTTGGCGGTTTA 60.179 50.000 0.00 0.00 45.43 2.01
2287 5000 1.074951 CCGGCTCCCCTTGTTTTCT 59.925 57.895 0.00 0.00 0.00 2.52
2323 5041 1.213537 CACCGCCAAAGCTGGATTG 59.786 57.895 0.00 0.00 46.92 2.67
2345 5063 4.003788 CCGTCTGTCGCCACCCTT 62.004 66.667 0.00 0.00 38.35 3.95
2394 5117 1.987855 GTCCGGGACACCATCTCCA 60.988 63.158 22.10 0.00 36.13 3.86
2411 5134 4.410400 GCTTAGCCGCCCACAGGT 62.410 66.667 0.00 0.00 34.57 4.00
2450 5174 4.792521 ACGCTCTCTTCAAACTATCTGT 57.207 40.909 0.00 0.00 0.00 3.41
2484 5210 0.674895 GTGATCCAGCGCACCTCTTT 60.675 55.000 11.47 0.00 0.00 2.52
2548 5276 3.483954 CACATTAGGTGGCCTGAGG 57.516 57.895 3.32 0.00 44.04 3.86
2634 5364 1.135053 GCTTTAGAGAGGTGGTCGGTC 60.135 57.143 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.