Multiple sequence alignment - TraesCS4A01G090000

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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 TraesCS4A01G090000 chr4A 100.000 3449 0 0 1 3449 96280550 96277102 0.000000e+00 6370
1 TraesCS4A01G090000 chr4A 91.220 410 32 2 2897 3306 677896880 677897285 3.890000e-154 555
2 TraesCS4A01G090000 chr4B 94.659 2902 109 17 1 2896 453770348 453773209 0.000000e+00 4458
3 TraesCS4A01G090000 chr4B 90.930 430 23 7 2894 3312 27124910 27124486 6.460000e-157 564
4 TraesCS4A01G090000 chr4B 92.308 143 4 2 3307 3449 453773201 453773336 2.720000e-46 196
5 TraesCS4A01G090000 chr4D 97.439 1718 44 0 892 2609 368496589 368498306 0.000000e+00 2929
6 TraesCS4A01G090000 chr4D 85.264 794 65 24 1 771 368494329 368495093 0.000000e+00 771
7 TraesCS4A01G090000 chr4D 94.186 258 8 4 2646 2896 368498308 368498565 1.500000e-103 387
8 TraesCS4A01G090000 chr4D 90.210 143 6 3 3307 3449 368498557 368498691 2.730000e-41 180
9 TraesCS4A01G090000 chr5D 94.146 410 22 2 2897 3306 22789715 22789308 1.050000e-174 623
10 TraesCS4A01G090000 chr3B 92.701 411 26 4 2897 3306 614905923 614906330 1.070000e-164 590
11 TraesCS4A01G090000 chr3B 92.457 411 28 3 2897 3306 3783386 3782978 4.960000e-163 584
12 TraesCS4A01G090000 chr3B 92.233 412 30 2 2896 3307 147876806 147877215 1.780000e-162 582
13 TraesCS4A01G090000 chr3B 92.214 411 29 3 2897 3306 4683263 4682855 2.310000e-161 579
14 TraesCS4A01G090000 chr3B 87.603 121 14 1 1 120 615966767 615966887 4.640000e-29 139
15 TraesCS4A01G090000 chr2D 92.402 408 30 1 2899 3306 640367314 640367720 6.420000e-162 580
16 TraesCS4A01G090000 chr7D 91.262 412 33 2 2899 3309 589510794 589511203 3.010000e-155 558
17 TraesCS4A01G090000 chr7D 89.320 103 10 1 19 120 560755497 560755599 1.000000e-25 128
18 TraesCS4A01G090000 chr3D 88.333 120 14 0 1 120 565652083 565651964 9.980000e-31 145
19 TraesCS4A01G090000 chr6D 90.476 105 9 1 19 122 80096898 80096794 1.670000e-28 137
20 TraesCS4A01G090000 chr2B 88.034 117 13 1 5 120 331026765 331026881 1.670000e-28 137
21 TraesCS4A01G090000 chr2A 88.034 117 13 1 5 120 286414958 286415074 1.670000e-28 137
22 TraesCS4A01G090000 chr5B 85.470 117 16 1 5 120 680338303 680338419 1.680000e-23 121
23 TraesCS4A01G090000 chr1B 84.746 118 17 1 1 117 120659710 120659827 2.170000e-22 117


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 TraesCS4A01G090000 chr4A 96277102 96280550 3448 True 6370.00 6370 100.00000 1 3449 1 chr4A.!!$R1 3448
1 TraesCS4A01G090000 chr4B 453770348 453773336 2988 False 2327.00 4458 93.48350 1 3449 2 chr4B.!!$F1 3448
2 TraesCS4A01G090000 chr4D 368494329 368498691 4362 False 1066.75 2929 91.77475 1 3449 4 chr4D.!!$F1 3448

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
135 152 2.333926 TGCTCGACGTGTTTCTAATGG 58.666 47.619 0.0 0.0 0.0 3.16 F
1077 2495 0.669318 CGAAGCAGCTAAACGTGGGA 60.669 55.000 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 3215 0.041135 CTAGTCGATCCGGCGAAGAC 60.041 60.0 9.30 11.91 42.55 3.01 R
2904 4330 0.390472 GGAGCTCAGTCTCCGTTTGG 60.390 60.0 17.19 0.00 42.74 3.28 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
122 138 6.270815 TGGTAGTAAACTAATCATGCTCGAC 58.729 40.000 0.00 0.00 0.00 4.20
129 146 3.612860 ACTAATCATGCTCGACGTGTTTC 59.387 43.478 0.00 0.00 36.60 2.78
130 147 2.370281 ATCATGCTCGACGTGTTTCT 57.630 45.000 0.00 0.00 36.60 2.52
135 152 2.333926 TGCTCGACGTGTTTCTAATGG 58.666 47.619 0.00 0.00 0.00 3.16
145 162 8.154038 CGACGTGTTTCTAATGGAAATATATCG 58.846 37.037 0.00 8.96 44.46 2.92
146 163 8.882415 ACGTGTTTCTAATGGAAATATATCGT 57.118 30.769 0.00 0.00 44.46 3.73
208 232 3.769189 TCTTAGAGGACACCCACCATA 57.231 47.619 0.00 0.00 33.88 2.74
287 311 5.608449 TCATAGATTTCTCAGAGTGCATGG 58.392 41.667 0.00 0.00 0.00 3.66
322 346 2.354821 ACGTGGAGCTTGAACAACTTTC 59.645 45.455 0.00 0.00 0.00 2.62
351 375 4.019174 CCTTGTTGAGCATTTATGGGAGT 58.981 43.478 0.00 0.00 0.00 3.85
406 430 6.869913 AGTTTGACACATTTTGATTGCTATGG 59.130 34.615 0.00 0.00 0.00 2.74
463 487 6.890979 TGATGTTGAATTATGTGTGGTTGA 57.109 33.333 0.00 0.00 0.00 3.18
537 562 6.750148 TGAGTCTCCTCAGAAAAGTTACTTC 58.250 40.000 0.00 0.00 42.80 3.01
538 563 6.551601 TGAGTCTCCTCAGAAAAGTTACTTCT 59.448 38.462 0.00 0.00 42.80 2.85
539 564 7.070074 TGAGTCTCCTCAGAAAAGTTACTTCTT 59.930 37.037 0.00 0.00 42.80 2.52
541 566 7.929245 AGTCTCCTCAGAAAAGTTACTTCTTTC 59.071 37.037 0.00 0.00 36.75 2.62
542 567 6.924060 TCTCCTCAGAAAAGTTACTTCTTTCG 59.076 38.462 0.00 0.00 36.75 3.46
543 568 6.579865 TCCTCAGAAAAGTTACTTCTTTCGT 58.420 36.000 0.00 0.00 36.75 3.85
544 569 7.719483 TCCTCAGAAAAGTTACTTCTTTCGTA 58.281 34.615 0.00 0.00 36.75 3.43
545 570 8.365647 TCCTCAGAAAAGTTACTTCTTTCGTAT 58.634 33.333 0.00 0.00 36.75 3.06
546 571 8.648968 CCTCAGAAAAGTTACTTCTTTCGTATC 58.351 37.037 0.00 0.00 36.75 2.24
563 588 8.585189 TTTCGTATCATCATGAGAGATTTCTG 57.415 34.615 15.99 1.19 32.53 3.02
683 709 9.783256 ATTTATTTTACATTCTTCGGTGCTAAC 57.217 29.630 0.00 0.00 0.00 2.34
696 722 5.413499 TCGGTGCTAACCTTTTAGTGATAC 58.587 41.667 0.00 0.00 45.17 2.24
734 760 6.949352 ATGTGAGATGTCTGTGAAAACTTT 57.051 33.333 0.00 0.00 0.00 2.66
737 763 6.150976 TGTGAGATGTCTGTGAAAACTTTGTT 59.849 34.615 0.00 0.00 0.00 2.83
784 818 8.602328 CAGCTCTTAAAGATGTTTGTAGAGATG 58.398 37.037 21.63 21.63 41.06 2.90
792 826 8.779354 AAGATGTTTGTAGAGATGGAAAGTAC 57.221 34.615 0.00 0.00 0.00 2.73
793 827 8.140112 AGATGTTTGTAGAGATGGAAAGTACT 57.860 34.615 0.00 0.00 0.00 2.73
794 828 8.254508 AGATGTTTGTAGAGATGGAAAGTACTC 58.745 37.037 0.00 0.00 0.00 2.59
796 830 7.152645 TGTTTGTAGAGATGGAAAGTACTCAC 58.847 38.462 0.00 0.00 32.59 3.51
798 832 6.761099 TGTAGAGATGGAAAGTACTCACTC 57.239 41.667 0.00 1.02 32.29 3.51
800 834 3.697045 AGAGATGGAAAGTACTCACTCCG 59.303 47.826 0.00 0.00 32.29 4.63
802 836 3.833070 AGATGGAAAGTACTCACTCCGTT 59.167 43.478 12.32 4.91 32.29 4.44
803 837 4.283722 AGATGGAAAGTACTCACTCCGTTT 59.716 41.667 12.32 6.47 32.29 3.60
804 838 3.986277 TGGAAAGTACTCACTCCGTTTC 58.014 45.455 0.00 0.00 32.29 2.78
805 839 2.985139 GGAAAGTACTCACTCCGTTTCG 59.015 50.000 0.00 0.00 32.29 3.46
1077 2495 0.669318 CGAAGCAGCTAAACGTGGGA 60.669 55.000 0.00 0.00 0.00 4.37
1134 2552 1.075970 CTCCCTGTCCCTCGATCCA 60.076 63.158 0.00 0.00 0.00 3.41
1797 3215 2.202756 GGGAGTGCGGCTAAGTCG 60.203 66.667 0.00 0.00 0.00 4.18
2049 3467 5.135383 TGCTCAAAATCAGGAGATATTGGG 58.865 41.667 0.00 0.00 33.08 4.12
2136 3554 2.044946 GGGGGTCATGGCAGTGTC 60.045 66.667 0.00 0.00 0.00 3.67
2233 3651 2.481568 CGAGATGACACATGCAACTTGT 59.518 45.455 0.00 0.00 0.00 3.16
2390 3808 5.106908 GCTTATTTGTGACCAGAGAAGACAC 60.107 44.000 0.00 0.00 28.25 3.67
2427 3845 2.058595 GGAGAGTTCCCGCCTAGCA 61.059 63.158 0.00 0.00 37.53 3.49
2476 3894 6.381498 TTTTCCCTTGTATACAGGATGACA 57.619 37.500 16.07 3.49 39.69 3.58
2685 4104 3.258971 AGCCTTAGCACTAAGAGCTTG 57.741 47.619 17.14 3.33 43.90 4.01
2762 4184 6.092670 GCAATGTTGTTATTCAGCTCACTCTA 59.907 38.462 0.00 0.00 0.00 2.43
2896 4322 8.684973 AGTTCGTAGATAATGACTTACAACAC 57.315 34.615 0.00 0.00 35.04 3.32
2897 4323 8.301720 AGTTCGTAGATAATGACTTACAACACA 58.698 33.333 0.00 0.00 35.04 3.72
2898 4324 8.918658 GTTCGTAGATAATGACTTACAACACAA 58.081 33.333 0.00 0.00 35.04 3.33
2899 4325 9.478768 TTCGTAGATAATGACTTACAACACAAA 57.521 29.630 0.00 0.00 35.04 2.83
2900 4326 9.478768 TCGTAGATAATGACTTACAACACAAAA 57.521 29.630 0.00 0.00 0.00 2.44
2904 4330 9.410556 AGATAATGACTTACAACACAAAAATGC 57.589 29.630 0.00 0.00 0.00 3.56
2905 4331 6.843069 AATGACTTACAACACAAAAATGCC 57.157 33.333 0.00 0.00 0.00 4.40
2906 4332 5.330455 TGACTTACAACACAAAAATGCCA 57.670 34.783 0.00 0.00 0.00 4.92
2907 4333 5.724328 TGACTTACAACACAAAAATGCCAA 58.276 33.333 0.00 0.00 0.00 4.52
2908 4334 6.166279 TGACTTACAACACAAAAATGCCAAA 58.834 32.000 0.00 0.00 0.00 3.28
2909 4335 6.091441 TGACTTACAACACAAAAATGCCAAAC 59.909 34.615 0.00 0.00 0.00 2.93
2910 4336 5.062809 ACTTACAACACAAAAATGCCAAACG 59.937 36.000 0.00 0.00 0.00 3.60
2911 4337 2.675348 ACAACACAAAAATGCCAAACGG 59.325 40.909 0.00 0.00 0.00 4.44
2912 4338 2.932614 CAACACAAAAATGCCAAACGGA 59.067 40.909 0.00 0.00 0.00 4.69
2913 4339 2.820330 ACACAAAAATGCCAAACGGAG 58.180 42.857 0.00 0.00 0.00 4.63
2914 4340 2.428890 ACACAAAAATGCCAAACGGAGA 59.571 40.909 0.00 0.00 0.00 3.71
2915 4341 2.794350 CACAAAAATGCCAAACGGAGAC 59.206 45.455 0.00 0.00 0.00 3.36
2916 4342 2.693074 ACAAAAATGCCAAACGGAGACT 59.307 40.909 0.00 0.00 0.00 3.24
2917 4343 3.052036 CAAAAATGCCAAACGGAGACTG 58.948 45.455 0.00 0.00 0.00 3.51
2918 4344 2.270352 AAATGCCAAACGGAGACTGA 57.730 45.000 0.00 0.00 0.00 3.41
2919 4345 1.813513 AATGCCAAACGGAGACTGAG 58.186 50.000 0.00 0.00 0.00 3.35
2920 4346 0.674895 ATGCCAAACGGAGACTGAGC 60.675 55.000 0.00 0.00 0.00 4.26
2921 4347 1.004440 GCCAAACGGAGACTGAGCT 60.004 57.895 0.00 0.00 0.00 4.09
2922 4348 1.016653 GCCAAACGGAGACTGAGCTC 61.017 60.000 6.82 6.82 0.00 4.09
2930 4356 0.752054 GAGACTGAGCTCCATGGAGG 59.248 60.000 36.92 24.67 42.19 4.30
2931 4357 1.145819 GACTGAGCTCCATGGAGGC 59.854 63.158 36.92 28.76 42.19 4.70
2932 4358 2.322638 GACTGAGCTCCATGGAGGCC 62.323 65.000 36.92 23.97 42.19 5.19
2933 4359 2.041762 TGAGCTCCATGGAGGCCT 59.958 61.111 36.92 27.78 42.19 5.19
2934 4360 1.617536 TGAGCTCCATGGAGGCCTT 60.618 57.895 36.92 17.72 42.19 4.35
2935 4361 1.210204 TGAGCTCCATGGAGGCCTTT 61.210 55.000 36.92 17.10 42.19 3.11
2936 4362 0.839946 GAGCTCCATGGAGGCCTTTA 59.160 55.000 36.92 4.58 42.19 1.85
2937 4363 1.423161 GAGCTCCATGGAGGCCTTTAT 59.577 52.381 36.92 16.48 42.19 1.40
2938 4364 1.855599 AGCTCCATGGAGGCCTTTATT 59.144 47.619 36.92 13.75 42.19 1.40
2939 4365 2.245806 AGCTCCATGGAGGCCTTTATTT 59.754 45.455 36.92 13.14 42.19 1.40
2940 4366 3.463329 AGCTCCATGGAGGCCTTTATTTA 59.537 43.478 36.92 2.30 42.19 1.40
2941 4367 4.079212 AGCTCCATGGAGGCCTTTATTTAA 60.079 41.667 36.92 1.84 42.19 1.52
2942 4368 4.649218 GCTCCATGGAGGCCTTTATTTAAA 59.351 41.667 36.92 1.17 42.19 1.52
2943 4369 5.128663 GCTCCATGGAGGCCTTTATTTAAAA 59.871 40.000 36.92 0.77 42.19 1.52
2944 4370 6.351796 GCTCCATGGAGGCCTTTATTTAAAAA 60.352 38.462 36.92 0.41 42.19 1.94
2945 4371 6.941857 TCCATGGAGGCCTTTATTTAAAAAC 58.058 36.000 11.44 0.00 37.29 2.43
2946 4372 6.728632 TCCATGGAGGCCTTTATTTAAAAACT 59.271 34.615 11.44 0.00 37.29 2.66
2947 4373 7.236640 TCCATGGAGGCCTTTATTTAAAAACTT 59.763 33.333 11.44 0.00 37.29 2.66
2948 4374 7.549134 CCATGGAGGCCTTTATTTAAAAACTTC 59.451 37.037 6.77 0.00 0.00 3.01
2949 4375 7.604657 TGGAGGCCTTTATTTAAAAACTTCA 57.395 32.000 6.77 0.00 0.00 3.02
2950 4376 8.024145 TGGAGGCCTTTATTTAAAAACTTCAA 57.976 30.769 6.77 0.00 0.00 2.69
2951 4377 8.487028 TGGAGGCCTTTATTTAAAAACTTCAAA 58.513 29.630 6.77 0.00 0.00 2.69
2952 4378 9.332502 GGAGGCCTTTATTTAAAAACTTCAAAA 57.667 29.630 6.77 0.00 0.00 2.44
3024 4450 9.965824 TGTCTAGATACATAATGTACATGTGTG 57.034 33.333 25.77 19.10 35.42 3.82
3025 4451 8.916654 GTCTAGATACATAATGTACATGTGTGC 58.083 37.037 25.77 19.80 35.42 4.57
3026 4452 8.637986 TCTAGATACATAATGTACATGTGTGCA 58.362 33.333 25.77 14.40 44.32 4.57
3027 4453 9.260002 CTAGATACATAATGTACATGTGTGCAA 57.740 33.333 25.77 13.89 43.49 4.08
3028 4454 8.504812 AGATACATAATGTACATGTGTGCAAA 57.495 30.769 25.77 13.64 43.49 3.68
3029 4455 9.123902 AGATACATAATGTACATGTGTGCAAAT 57.876 29.630 25.77 16.51 43.49 2.32
3030 4456 9.734620 GATACATAATGTACATGTGTGCAAATT 57.265 29.630 25.77 6.78 43.49 1.82
3032 4458 8.830201 ACATAATGTACATGTGTGCAAATTTT 57.170 26.923 20.33 1.42 43.49 1.82
3033 4459 8.924691 ACATAATGTACATGTGTGCAAATTTTC 58.075 29.630 20.33 0.00 43.49 2.29
3034 4460 8.923683 CATAATGTACATGTGTGCAAATTTTCA 58.076 29.630 9.63 0.00 43.49 2.69
3035 4461 7.410800 AATGTACATGTGTGCAAATTTTCAG 57.589 32.000 9.63 0.00 43.49 3.02
3036 4462 5.288015 TGTACATGTGTGCAAATTTTCAGG 58.712 37.500 9.11 0.00 37.70 3.86
3037 4463 4.405116 ACATGTGTGCAAATTTTCAGGT 57.595 36.364 0.00 0.00 0.00 4.00
3038 4464 4.370917 ACATGTGTGCAAATTTTCAGGTC 58.629 39.130 0.00 0.00 0.00 3.85
3039 4465 3.077229 TGTGTGCAAATTTTCAGGTCG 57.923 42.857 0.00 0.00 0.00 4.79
3040 4466 2.685388 TGTGTGCAAATTTTCAGGTCGA 59.315 40.909 0.00 0.00 0.00 4.20
3041 4467 3.129462 TGTGTGCAAATTTTCAGGTCGAA 59.871 39.130 0.00 0.00 0.00 3.71
3042 4468 4.109050 GTGTGCAAATTTTCAGGTCGAAA 58.891 39.130 0.00 0.00 41.95 3.46
3043 4469 4.744631 GTGTGCAAATTTTCAGGTCGAAAT 59.255 37.500 0.00 0.00 43.12 2.17
3044 4470 5.918011 GTGTGCAAATTTTCAGGTCGAAATA 59.082 36.000 0.00 0.00 43.12 1.40
3045 4471 5.918011 TGTGCAAATTTTCAGGTCGAAATAC 59.082 36.000 0.00 0.00 43.12 1.89
3046 4472 5.918011 GTGCAAATTTTCAGGTCGAAATACA 59.082 36.000 0.00 0.00 43.12 2.29
3047 4473 6.586082 GTGCAAATTTTCAGGTCGAAATACAT 59.414 34.615 0.00 0.00 43.12 2.29
3048 4474 7.116233 GTGCAAATTTTCAGGTCGAAATACATT 59.884 33.333 0.00 0.00 43.12 2.71
3049 4475 8.300286 TGCAAATTTTCAGGTCGAAATACATTA 58.700 29.630 0.00 0.00 43.12 1.90
3050 4476 9.134734 GCAAATTTTCAGGTCGAAATACATTAA 57.865 29.630 0.00 0.00 43.12 1.40
3056 4482 9.834628 TTTCAGGTCGAAATACATTAAAATGTC 57.165 29.630 11.45 0.00 42.25 3.06
3057 4483 8.554835 TCAGGTCGAAATACATTAAAATGTCA 57.445 30.769 11.45 0.67 46.10 3.58
3058 4484 8.664798 TCAGGTCGAAATACATTAAAATGTCAG 58.335 33.333 11.45 1.83 46.10 3.51
3059 4485 7.429340 CAGGTCGAAATACATTAAAATGTCAGC 59.571 37.037 11.45 1.03 46.10 4.26
3060 4486 7.336931 AGGTCGAAATACATTAAAATGTCAGCT 59.663 33.333 11.45 3.64 46.10 4.24
3061 4487 8.609176 GGTCGAAATACATTAAAATGTCAGCTA 58.391 33.333 11.45 0.00 46.10 3.32
3062 4488 9.422196 GTCGAAATACATTAAAATGTCAGCTAC 57.578 33.333 11.45 2.57 46.10 3.58
3063 4489 9.157104 TCGAAATACATTAAAATGTCAGCTACA 57.843 29.630 11.45 0.00 46.10 2.74
3064 4490 9.210426 CGAAATACATTAAAATGTCAGCTACAC 57.790 33.333 11.45 0.00 46.10 2.90
3089 4515 6.721704 AAAAAGACAAATCTGAGGCTTTCT 57.278 33.333 0.00 0.00 34.48 2.52
3090 4516 7.823745 AAAAAGACAAATCTGAGGCTTTCTA 57.176 32.000 0.00 0.00 34.48 2.10
3091 4517 7.823745 AAAAGACAAATCTGAGGCTTTCTAA 57.176 32.000 0.00 0.00 34.48 2.10
3092 4518 6.809630 AAGACAAATCTGAGGCTTTCTAAC 57.190 37.500 0.00 0.00 34.48 2.34
3093 4519 5.869579 AGACAAATCTGAGGCTTTCTAACA 58.130 37.500 0.00 0.00 32.29 2.41
3094 4520 6.479884 AGACAAATCTGAGGCTTTCTAACAT 58.520 36.000 0.00 0.00 32.29 2.71
3095 4521 6.597280 AGACAAATCTGAGGCTTTCTAACATC 59.403 38.462 0.00 0.00 32.29 3.06
3096 4522 6.479884 ACAAATCTGAGGCTTTCTAACATCT 58.520 36.000 0.00 0.00 0.00 2.90
3097 4523 6.373774 ACAAATCTGAGGCTTTCTAACATCTG 59.626 38.462 0.00 0.00 0.00 2.90
3098 4524 5.690464 ATCTGAGGCTTTCTAACATCTGT 57.310 39.130 0.00 0.00 0.00 3.41
3099 4525 6.798427 ATCTGAGGCTTTCTAACATCTGTA 57.202 37.500 0.00 0.00 0.00 2.74
3100 4526 5.967088 TCTGAGGCTTTCTAACATCTGTAC 58.033 41.667 0.00 0.00 0.00 2.90
3101 4527 5.717178 TCTGAGGCTTTCTAACATCTGTACT 59.283 40.000 0.00 0.00 0.00 2.73
3102 4528 5.724328 TGAGGCTTTCTAACATCTGTACTG 58.276 41.667 0.00 0.00 0.00 2.74
3103 4529 5.246203 TGAGGCTTTCTAACATCTGTACTGT 59.754 40.000 0.00 0.00 0.00 3.55
3104 4530 6.115448 AGGCTTTCTAACATCTGTACTGTT 57.885 37.500 4.60 4.60 39.93 3.16
3105 4531 6.166982 AGGCTTTCTAACATCTGTACTGTTC 58.833 40.000 2.53 0.00 37.89 3.18
3106 4532 5.932303 GGCTTTCTAACATCTGTACTGTTCA 59.068 40.000 2.53 0.00 37.89 3.18
3107 4533 6.595716 GGCTTTCTAACATCTGTACTGTTCAT 59.404 38.462 2.53 0.00 37.89 2.57
3108 4534 7.119846 GGCTTTCTAACATCTGTACTGTTCATT 59.880 37.037 2.53 0.00 37.89 2.57
3109 4535 8.507249 GCTTTCTAACATCTGTACTGTTCATTT 58.493 33.333 2.53 0.00 37.89 2.32
3118 4544 9.612620 CATCTGTACTGTTCATTTTTAAAGTCC 57.387 33.333 0.00 0.00 0.00 3.85
3119 4545 8.740123 TCTGTACTGTTCATTTTTAAAGTCCA 57.260 30.769 0.00 0.00 0.00 4.02
3120 4546 9.349713 TCTGTACTGTTCATTTTTAAAGTCCAT 57.650 29.630 0.00 0.00 0.00 3.41
3121 4547 9.398170 CTGTACTGTTCATTTTTAAAGTCCATG 57.602 33.333 0.00 0.00 0.00 3.66
3122 4548 9.126151 TGTACTGTTCATTTTTAAAGTCCATGA 57.874 29.630 0.00 0.00 0.00 3.07
3155 4581 2.342910 GTGCAGCTCACAATTCAAGG 57.657 50.000 10.30 0.00 44.98 3.61
3156 4582 0.599558 TGCAGCTCACAATTCAAGGC 59.400 50.000 0.00 0.00 0.00 4.35
3157 4583 0.599558 GCAGCTCACAATTCAAGGCA 59.400 50.000 0.00 0.00 0.00 4.75
3158 4584 1.203994 GCAGCTCACAATTCAAGGCAT 59.796 47.619 0.00 0.00 0.00 4.40
3159 4585 2.353406 GCAGCTCACAATTCAAGGCATT 60.353 45.455 0.00 0.00 0.00 3.56
3160 4586 3.863400 GCAGCTCACAATTCAAGGCATTT 60.863 43.478 0.00 0.00 0.00 2.32
3161 4587 3.924686 CAGCTCACAATTCAAGGCATTTC 59.075 43.478 0.00 0.00 0.00 2.17
3162 4588 3.575256 AGCTCACAATTCAAGGCATTTCA 59.425 39.130 0.00 0.00 0.00 2.69
3163 4589 4.222145 AGCTCACAATTCAAGGCATTTCAT 59.778 37.500 0.00 0.00 0.00 2.57
3164 4590 4.565564 GCTCACAATTCAAGGCATTTCATC 59.434 41.667 0.00 0.00 0.00 2.92
3165 4591 5.075858 TCACAATTCAAGGCATTTCATCC 57.924 39.130 0.00 0.00 0.00 3.51
3166 4592 4.773674 TCACAATTCAAGGCATTTCATCCT 59.226 37.500 0.00 0.00 0.00 3.24
3167 4593 4.868171 CACAATTCAAGGCATTTCATCCTG 59.132 41.667 0.00 0.00 32.00 3.86
3168 4594 4.773674 ACAATTCAAGGCATTTCATCCTGA 59.226 37.500 0.00 0.00 32.00 3.86
3169 4595 5.246656 ACAATTCAAGGCATTTCATCCTGAA 59.753 36.000 0.00 0.00 34.03 3.02
3170 4596 6.070424 ACAATTCAAGGCATTTCATCCTGAAT 60.070 34.615 0.00 0.00 36.11 2.57
3171 4597 6.555463 ATTCAAGGCATTTCATCCTGAATT 57.445 33.333 0.00 0.00 36.11 2.17
3172 4598 6.363167 TTCAAGGCATTTCATCCTGAATTT 57.637 33.333 0.00 0.00 36.11 1.82
3173 4599 6.363167 TCAAGGCATTTCATCCTGAATTTT 57.637 33.333 0.00 0.00 36.11 1.82
3174 4600 6.771573 TCAAGGCATTTCATCCTGAATTTTT 58.228 32.000 0.00 0.00 36.11 1.94
3197 4623 9.944663 TTTTTCACACATACACTTTACATCTTC 57.055 29.630 0.00 0.00 0.00 2.87
3198 4624 6.944557 TCACACATACACTTTACATCTTCG 57.055 37.500 0.00 0.00 0.00 3.79
3199 4625 5.347635 TCACACATACACTTTACATCTTCGC 59.652 40.000 0.00 0.00 0.00 4.70
3200 4626 5.120053 CACACATACACTTTACATCTTCGCA 59.880 40.000 0.00 0.00 0.00 5.10
3201 4627 5.874810 ACACATACACTTTACATCTTCGCAT 59.125 36.000 0.00 0.00 0.00 4.73
3202 4628 7.010091 CACACATACACTTTACATCTTCGCATA 59.990 37.037 0.00 0.00 0.00 3.14
3203 4629 7.010183 ACACATACACTTTACATCTTCGCATAC 59.990 37.037 0.00 0.00 0.00 2.39
3204 4630 7.010091 CACATACACTTTACATCTTCGCATACA 59.990 37.037 0.00 0.00 0.00 2.29
3205 4631 7.710907 ACATACACTTTACATCTTCGCATACAT 59.289 33.333 0.00 0.00 0.00 2.29
3206 4632 6.349973 ACACTTTACATCTTCGCATACATG 57.650 37.500 0.00 0.00 0.00 3.21
3207 4633 5.874810 ACACTTTACATCTTCGCATACATGT 59.125 36.000 2.69 2.69 33.95 3.21
3208 4634 6.183360 ACACTTTACATCTTCGCATACATGTG 60.183 38.462 9.11 0.00 39.55 3.21
3209 4635 5.874810 ACTTTACATCTTCGCATACATGTGT 59.125 36.000 9.11 0.00 39.25 3.72
3210 4636 7.010091 CACTTTACATCTTCGCATACATGTGTA 59.990 37.037 9.11 0.00 39.25 2.90
3211 4637 7.710907 ACTTTACATCTTCGCATACATGTGTAT 59.289 33.333 9.11 0.00 41.58 2.29
3212 4638 8.432110 TTTACATCTTCGCATACATGTGTATT 57.568 30.769 9.11 0.00 39.06 1.89
3213 4639 6.925610 ACATCTTCGCATACATGTGTATTT 57.074 33.333 9.11 0.00 39.06 1.40
3214 4640 7.320443 ACATCTTCGCATACATGTGTATTTT 57.680 32.000 9.11 0.00 39.06 1.82
3215 4641 7.761409 ACATCTTCGCATACATGTGTATTTTT 58.239 30.769 9.11 0.00 39.06 1.94
3275 4701 7.977789 TGAATTTTTCAAAATAAAGGGCTCC 57.022 32.000 0.00 0.00 37.62 4.70
3276 4702 7.512992 TGAATTTTTCAAAATAAAGGGCTCCA 58.487 30.769 0.00 0.00 37.62 3.86
3277 4703 8.162746 TGAATTTTTCAAAATAAAGGGCTCCAT 58.837 29.630 0.00 0.00 37.62 3.41
3278 4704 7.926674 ATTTTTCAAAATAAAGGGCTCCATG 57.073 32.000 0.00 0.00 36.88 3.66
3279 4705 5.419239 TTTCAAAATAAAGGGCTCCATGG 57.581 39.130 4.97 4.97 0.00 3.66
3280 4706 4.329638 TCAAAATAAAGGGCTCCATGGA 57.670 40.909 15.27 15.27 0.00 3.41
3281 4707 4.280819 TCAAAATAAAGGGCTCCATGGAG 58.719 43.478 33.73 33.73 44.56 3.86
3289 4715 3.947173 CTCCATGGAGCTCGGTCT 58.053 61.111 28.45 0.00 35.31 3.85
3290 4716 1.739049 CTCCATGGAGCTCGGTCTC 59.261 63.158 28.45 0.00 35.31 3.36
3298 4724 0.729690 GAGCTCGGTCTCCAAAATGC 59.270 55.000 0.00 0.00 0.00 3.56
3299 4725 0.678048 AGCTCGGTCTCCAAAATGCC 60.678 55.000 0.00 0.00 0.00 4.40
3300 4726 1.657751 GCTCGGTCTCCAAAATGCCC 61.658 60.000 0.00 0.00 0.00 5.36
3301 4727 0.035056 CTCGGTCTCCAAAATGCCCT 60.035 55.000 0.00 0.00 0.00 5.19
3302 4728 1.209504 CTCGGTCTCCAAAATGCCCTA 59.790 52.381 0.00 0.00 0.00 3.53
3303 4729 1.065709 TCGGTCTCCAAAATGCCCTAC 60.066 52.381 0.00 0.00 0.00 3.18
3304 4730 1.065418 CGGTCTCCAAAATGCCCTACT 60.065 52.381 0.00 0.00 0.00 2.57
3305 4731 2.644676 GGTCTCCAAAATGCCCTACTC 58.355 52.381 0.00 0.00 0.00 2.59
3306 4732 2.644676 GTCTCCAAAATGCCCTACTCC 58.355 52.381 0.00 0.00 0.00 3.85
3307 4733 2.239907 GTCTCCAAAATGCCCTACTCCT 59.760 50.000 0.00 0.00 0.00 3.69
3308 4734 2.919602 TCTCCAAAATGCCCTACTCCTT 59.080 45.455 0.00 0.00 0.00 3.36
3309 4735 4.080526 GTCTCCAAAATGCCCTACTCCTTA 60.081 45.833 0.00 0.00 0.00 2.69
3310 4736 4.080526 TCTCCAAAATGCCCTACTCCTTAC 60.081 45.833 0.00 0.00 0.00 2.34
3311 4737 3.589735 TCCAAAATGCCCTACTCCTTACA 59.410 43.478 0.00 0.00 0.00 2.41
3312 4738 4.043561 TCCAAAATGCCCTACTCCTTACAA 59.956 41.667 0.00 0.00 0.00 2.41
3313 4739 4.157840 CCAAAATGCCCTACTCCTTACAAC 59.842 45.833 0.00 0.00 0.00 3.32
3314 4740 4.650972 AAATGCCCTACTCCTTACAACA 57.349 40.909 0.00 0.00 0.00 3.33
3320 4746 7.440505 TGCCCTACTCCTTACAACATTATAA 57.559 36.000 0.00 0.00 0.00 0.98
3417 4843 7.514127 TGCTCTTCCAATATACTTCCTCCTATT 59.486 37.037 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.141597 TGTGAGATGGGTGTGACAACTTTA 60.142 41.667 0.00 0.00 0.00 1.85
96 112 6.755141 TCGAGCATGATTAGTTTACTACCAAC 59.245 38.462 0.00 0.00 0.00 3.77
104 120 4.740268 ACACGTCGAGCATGATTAGTTTA 58.260 39.130 0.00 0.00 0.00 2.01
109 125 3.845178 AGAAACACGTCGAGCATGATTA 58.155 40.909 0.00 0.00 0.00 1.75
135 152 9.667107 TTGGATTTCTATGGGACGATATATTTC 57.333 33.333 0.00 0.00 0.00 2.17
145 162 3.181439 CCCTCCTTGGATTTCTATGGGAC 60.181 52.174 2.71 0.00 38.35 4.46
146 163 3.056080 CCCTCCTTGGATTTCTATGGGA 58.944 50.000 2.71 0.00 38.35 4.37
239 263 8.822652 AAATCATTGTTCATTCTTTTGAGGTC 57.177 30.769 0.00 0.00 0.00 3.85
287 311 3.975035 GCTCCACGTGTCTTCAATTTTTC 59.025 43.478 15.65 0.00 0.00 2.29
322 346 1.542492 ATGCTCAACAAGGCCTTCAG 58.458 50.000 17.29 8.33 0.00 3.02
351 375 6.121776 TGAAGAAGTTTAGCCACCATAGAA 57.878 37.500 0.00 0.00 0.00 2.10
406 430 6.074888 CCACAACTTTGAAATTCACATTCGAC 60.075 38.462 0.00 0.00 0.00 4.20
537 562 8.701540 CAGAAATCTCTCATGATGATACGAAAG 58.298 37.037 10.52 0.00 0.00 2.62
538 563 8.200120 ACAGAAATCTCTCATGATGATACGAAA 58.800 33.333 10.52 0.00 0.00 3.46
539 564 7.720442 ACAGAAATCTCTCATGATGATACGAA 58.280 34.615 10.52 0.00 0.00 3.85
541 566 8.296000 AGTACAGAAATCTCTCATGATGATACG 58.704 37.037 10.52 0.00 0.00 3.06
545 570 8.140628 GCTTAGTACAGAAATCTCTCATGATGA 58.859 37.037 0.00 0.00 0.00 2.92
546 571 7.924947 TGCTTAGTACAGAAATCTCTCATGATG 59.075 37.037 0.00 0.00 0.00 3.07
705 731 7.800155 TTTCACAGACATCTCACATTAACAA 57.200 32.000 0.00 0.00 0.00 2.83
752 778 6.321181 ACAAACATCTTTAAGAGCTGAACCAA 59.679 34.615 0.03 0.00 0.00 3.67
756 782 8.367911 TCTCTACAAACATCTTTAAGAGCTGAA 58.632 33.333 0.03 0.00 33.01 3.02
784 818 2.985139 CGAAACGGAGTGAGTACTTTCC 59.015 50.000 0.00 4.47 45.00 3.13
800 834 0.890683 TACTCCCTCCGTTCCGAAAC 59.109 55.000 0.00 0.00 0.00 2.78
802 836 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
803 837 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
804 838 1.020437 GTACTACTCCCTCCGTTCCG 58.980 60.000 0.00 0.00 0.00 4.30
805 839 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
807 841 1.271597 ACACGTACTACTCCCTCCGTT 60.272 52.381 0.00 0.00 0.00 4.44
808 842 0.326264 ACACGTACTACTCCCTCCGT 59.674 55.000 0.00 0.00 0.00 4.69
809 843 0.731417 CACACGTACTACTCCCTCCG 59.269 60.000 0.00 0.00 0.00 4.63
810 844 1.831580 ACACACGTACTACTCCCTCC 58.168 55.000 0.00 0.00 0.00 4.30
811 845 4.194640 TGATACACACGTACTACTCCCTC 58.805 47.826 0.00 0.00 0.00 4.30
813 847 4.820716 AGATGATACACACGTACTACTCCC 59.179 45.833 0.00 0.00 0.00 4.30
815 849 7.249147 ACAAAGATGATACACACGTACTACTC 58.751 38.462 0.00 0.00 0.00 2.59
816 850 7.154435 ACAAAGATGATACACACGTACTACT 57.846 36.000 0.00 0.00 0.00 2.57
817 851 7.807687 AACAAAGATGATACACACGTACTAC 57.192 36.000 0.00 0.00 0.00 2.73
818 852 8.821147 AAAACAAAGATGATACACACGTACTA 57.179 30.769 0.00 0.00 0.00 1.82
819 853 7.724305 AAAACAAAGATGATACACACGTACT 57.276 32.000 0.00 0.00 0.00 2.73
863 2281 5.509840 CCATTCTGGTACTCGATAAGAAGGG 60.510 48.000 10.12 10.12 40.97 3.95
864 2282 5.302059 TCCATTCTGGTACTCGATAAGAAGG 59.698 44.000 0.00 0.00 39.03 3.46
1134 2552 0.251608 CGAAAGTTGGGGTTGGGGAT 60.252 55.000 0.00 0.00 0.00 3.85
1181 2599 2.936912 CGGATGGCGGAGAGGATCC 61.937 68.421 2.48 2.48 45.64 3.36
1539 2957 1.153429 GTCGTACACATGGAGCCCC 60.153 63.158 0.00 0.00 0.00 5.80
1587 3005 4.496670 GTCGGGTCTGACCATTCG 57.503 61.111 26.94 20.57 41.02 3.34
1656 3074 3.857854 GTGTCAGCGGCATCAGCG 61.858 66.667 1.45 0.00 43.41 5.18
1797 3215 0.041135 CTAGTCGATCCGGCGAAGAC 60.041 60.000 9.30 11.91 42.55 3.01
1830 3248 0.687427 AAGCAAACACCAGCCCAAGT 60.687 50.000 0.00 0.00 0.00 3.16
2025 3443 5.773680 CCCAATATCTCCTGATTTTGAGCAT 59.226 40.000 9.58 0.00 41.18 3.79
2136 3554 1.098050 GGGACTTGTAGCAATGCAGG 58.902 55.000 8.35 0.00 0.00 4.85
2390 3808 1.648720 CACACTTCCACAACTGGCG 59.351 57.895 0.00 0.00 37.49 5.69
2427 3845 2.100128 ATGCCAGAGAGATAGCACCT 57.900 50.000 0.00 0.00 38.21 4.00
2514 3932 6.373774 ACACAAGAAGAGCCATATTTTCAGAG 59.626 38.462 0.00 0.00 0.00 3.35
2577 3996 6.544928 TTGAATACATCTGTAGAGGCAAGA 57.455 37.500 0.00 0.00 33.52 3.02
2896 4322 3.052036 CAGTCTCCGTTTGGCATTTTTG 58.948 45.455 0.00 0.00 34.14 2.44
2897 4323 2.955660 TCAGTCTCCGTTTGGCATTTTT 59.044 40.909 0.00 0.00 34.14 1.94
2898 4324 2.554032 CTCAGTCTCCGTTTGGCATTTT 59.446 45.455 0.00 0.00 34.14 1.82
2899 4325 2.154462 CTCAGTCTCCGTTTGGCATTT 58.846 47.619 0.00 0.00 34.14 2.32
2900 4326 1.813513 CTCAGTCTCCGTTTGGCATT 58.186 50.000 0.00 0.00 34.14 3.56
2901 4327 0.674895 GCTCAGTCTCCGTTTGGCAT 60.675 55.000 0.00 0.00 34.14 4.40
2902 4328 1.301716 GCTCAGTCTCCGTTTGGCA 60.302 57.895 0.00 0.00 34.14 4.92
2903 4329 1.004440 AGCTCAGTCTCCGTTTGGC 60.004 57.895 0.00 0.00 34.14 4.52
2904 4330 0.390472 GGAGCTCAGTCTCCGTTTGG 60.390 60.000 17.19 0.00 42.74 3.28
2905 4331 3.129792 GGAGCTCAGTCTCCGTTTG 57.870 57.895 17.19 0.00 42.74 2.93
2911 4337 0.752054 CCTCCATGGAGCTCAGTCTC 59.248 60.000 32.97 0.00 40.69 3.36
2912 4338 1.336632 GCCTCCATGGAGCTCAGTCT 61.337 60.000 32.97 0.00 40.69 3.24
2913 4339 1.145819 GCCTCCATGGAGCTCAGTC 59.854 63.158 32.97 14.41 40.69 3.51
2914 4340 2.373707 GGCCTCCATGGAGCTCAGT 61.374 63.158 32.97 0.00 40.69 3.41
2915 4341 1.633915 AAGGCCTCCATGGAGCTCAG 61.634 60.000 32.97 21.23 40.69 3.35
2916 4342 1.210204 AAAGGCCTCCATGGAGCTCA 61.210 55.000 32.97 2.79 40.69 4.26
2917 4343 0.839946 TAAAGGCCTCCATGGAGCTC 59.160 55.000 32.97 25.21 40.69 4.09
2918 4344 1.527457 ATAAAGGCCTCCATGGAGCT 58.473 50.000 32.97 23.24 40.69 4.09
2919 4345 2.371658 AATAAAGGCCTCCATGGAGC 57.628 50.000 32.97 26.44 40.69 4.70
2920 4346 6.790232 TTTTAAATAAAGGCCTCCATGGAG 57.210 37.500 31.69 31.69 41.63 3.86
2921 4347 6.728632 AGTTTTTAAATAAAGGCCTCCATGGA 59.271 34.615 15.27 15.27 38.35 3.41
2922 4348 6.946340 AGTTTTTAAATAAAGGCCTCCATGG 58.054 36.000 5.23 4.97 39.35 3.66
2923 4349 8.093927 TGAAGTTTTTAAATAAAGGCCTCCATG 58.906 33.333 5.23 0.00 0.00 3.66
2924 4350 8.201242 TGAAGTTTTTAAATAAAGGCCTCCAT 57.799 30.769 5.23 0.00 0.00 3.41
2925 4351 7.604657 TGAAGTTTTTAAATAAAGGCCTCCA 57.395 32.000 5.23 0.00 0.00 3.86
2926 4352 8.896320 TTTGAAGTTTTTAAATAAAGGCCTCC 57.104 30.769 5.23 0.00 0.00 4.30
2998 4424 9.965824 CACACATGTACATTATGTATCTAGACA 57.034 33.333 17.98 3.76 36.67 3.41
2999 4425 8.916654 GCACACATGTACATTATGTATCTAGAC 58.083 37.037 17.98 0.00 36.67 2.59
3000 4426 8.637986 TGCACACATGTACATTATGTATCTAGA 58.362 33.333 17.98 0.00 36.67 2.43
3001 4427 8.816640 TGCACACATGTACATTATGTATCTAG 57.183 34.615 17.98 9.67 36.67 2.43
3002 4428 9.606631 TTTGCACACATGTACATTATGTATCTA 57.393 29.630 17.98 9.97 36.67 1.98
3003 4429 8.504812 TTTGCACACATGTACATTATGTATCT 57.495 30.769 17.98 0.00 36.67 1.98
3004 4430 9.734620 AATTTGCACACATGTACATTATGTATC 57.265 29.630 17.98 14.10 36.67 2.24
3006 4432 9.920133 AAAATTTGCACACATGTACATTATGTA 57.080 25.926 17.98 0.29 36.67 2.29
3007 4433 8.830201 AAAATTTGCACACATGTACATTATGT 57.170 26.923 14.24 14.24 39.23 2.29
3008 4434 8.923683 TGAAAATTTGCACACATGTACATTATG 58.076 29.630 5.37 10.25 0.00 1.90
3009 4435 9.142515 CTGAAAATTTGCACACATGTACATTAT 57.857 29.630 5.37 0.00 0.00 1.28
3010 4436 7.598118 CCTGAAAATTTGCACACATGTACATTA 59.402 33.333 5.37 0.00 0.00 1.90
3011 4437 6.424509 CCTGAAAATTTGCACACATGTACATT 59.575 34.615 5.37 0.00 0.00 2.71
3012 4438 5.927689 CCTGAAAATTTGCACACATGTACAT 59.072 36.000 1.41 1.41 0.00 2.29
3013 4439 5.163468 ACCTGAAAATTTGCACACATGTACA 60.163 36.000 0.00 0.00 0.00 2.90
3014 4440 5.288804 ACCTGAAAATTTGCACACATGTAC 58.711 37.500 0.00 0.00 0.00 2.90
3015 4441 5.527951 GACCTGAAAATTTGCACACATGTA 58.472 37.500 0.00 0.00 0.00 2.29
3016 4442 4.370917 GACCTGAAAATTTGCACACATGT 58.629 39.130 0.00 0.00 0.00 3.21
3017 4443 3.426191 CGACCTGAAAATTTGCACACATG 59.574 43.478 0.00 0.00 0.00 3.21
3018 4444 3.317711 TCGACCTGAAAATTTGCACACAT 59.682 39.130 0.00 0.00 0.00 3.21
3019 4445 2.685388 TCGACCTGAAAATTTGCACACA 59.315 40.909 0.00 0.00 0.00 3.72
3020 4446 3.347958 TCGACCTGAAAATTTGCACAC 57.652 42.857 0.00 0.00 0.00 3.82
3021 4447 4.377839 TTTCGACCTGAAAATTTGCACA 57.622 36.364 0.00 0.00 43.46 4.57
3066 4492 6.721704 AGAAAGCCTCAGATTTGTCTTTTT 57.278 33.333 0.00 0.00 30.04 1.94
3067 4493 7.285401 TGTTAGAAAGCCTCAGATTTGTCTTTT 59.715 33.333 0.00 0.00 30.04 2.27
3068 4494 6.772716 TGTTAGAAAGCCTCAGATTTGTCTTT 59.227 34.615 0.00 0.00 30.04 2.52
3069 4495 6.299141 TGTTAGAAAGCCTCAGATTTGTCTT 58.701 36.000 0.00 0.00 30.04 3.01
3070 4496 5.869579 TGTTAGAAAGCCTCAGATTTGTCT 58.130 37.500 0.00 0.00 30.04 3.41
3071 4497 6.597280 AGATGTTAGAAAGCCTCAGATTTGTC 59.403 38.462 0.00 0.00 30.04 3.18
3072 4498 6.373774 CAGATGTTAGAAAGCCTCAGATTTGT 59.626 38.462 0.00 0.00 30.04 2.83
3073 4499 6.373774 ACAGATGTTAGAAAGCCTCAGATTTG 59.626 38.462 0.00 0.00 30.04 2.32
3074 4500 6.479884 ACAGATGTTAGAAAGCCTCAGATTT 58.520 36.000 0.00 0.00 33.35 2.17
3075 4501 6.059787 ACAGATGTTAGAAAGCCTCAGATT 57.940 37.500 0.00 0.00 0.00 2.40
3076 4502 5.690464 ACAGATGTTAGAAAGCCTCAGAT 57.310 39.130 0.00 0.00 0.00 2.90
3077 4503 5.717178 AGTACAGATGTTAGAAAGCCTCAGA 59.283 40.000 0.00 0.00 0.00 3.27
3078 4504 5.809562 CAGTACAGATGTTAGAAAGCCTCAG 59.190 44.000 0.00 0.00 0.00 3.35
3079 4505 5.246203 ACAGTACAGATGTTAGAAAGCCTCA 59.754 40.000 0.00 0.00 0.00 3.86
3080 4506 5.725362 ACAGTACAGATGTTAGAAAGCCTC 58.275 41.667 0.00 0.00 0.00 4.70
3081 4507 5.746990 ACAGTACAGATGTTAGAAAGCCT 57.253 39.130 0.00 0.00 0.00 4.58
3082 4508 5.932303 TGAACAGTACAGATGTTAGAAAGCC 59.068 40.000 0.00 0.00 40.86 4.35
3083 4509 7.602517 ATGAACAGTACAGATGTTAGAAAGC 57.397 36.000 0.00 0.00 40.86 3.51
3092 4518 9.612620 GGACTTTAAAAATGAACAGTACAGATG 57.387 33.333 0.00 0.00 0.00 2.90
3093 4519 9.349713 TGGACTTTAAAAATGAACAGTACAGAT 57.650 29.630 0.00 0.00 0.00 2.90
3094 4520 8.740123 TGGACTTTAAAAATGAACAGTACAGA 57.260 30.769 0.00 0.00 0.00 3.41
3095 4521 9.398170 CATGGACTTTAAAAATGAACAGTACAG 57.602 33.333 0.00 0.00 28.64 2.74
3096 4522 9.126151 TCATGGACTTTAAAAATGAACAGTACA 57.874 29.630 0.00 0.00 29.71 2.90
3137 4563 0.599558 GCCTTGAATTGTGAGCTGCA 59.400 50.000 1.02 0.00 0.00 4.41
3138 4564 0.599558 TGCCTTGAATTGTGAGCTGC 59.400 50.000 0.00 0.00 0.00 5.25
3139 4565 3.587797 AATGCCTTGAATTGTGAGCTG 57.412 42.857 0.00 0.00 0.00 4.24
3140 4566 3.575256 TGAAATGCCTTGAATTGTGAGCT 59.425 39.130 0.00 0.00 0.00 4.09
3141 4567 3.916761 TGAAATGCCTTGAATTGTGAGC 58.083 40.909 0.00 0.00 0.00 4.26
3142 4568 5.105473 AGGATGAAATGCCTTGAATTGTGAG 60.105 40.000 0.00 0.00 33.77 3.51
3143 4569 4.773674 AGGATGAAATGCCTTGAATTGTGA 59.226 37.500 0.00 0.00 33.77 3.58
3144 4570 4.868171 CAGGATGAAATGCCTTGAATTGTG 59.132 41.667 0.00 0.00 39.69 3.33
3145 4571 4.773674 TCAGGATGAAATGCCTTGAATTGT 59.226 37.500 0.00 0.00 45.97 2.71
3146 4572 5.333299 TCAGGATGAAATGCCTTGAATTG 57.667 39.130 0.00 0.00 45.97 2.32
3171 4597 9.944663 GAAGATGTAAAGTGTATGTGTGAAAAA 57.055 29.630 0.00 0.00 0.00 1.94
3172 4598 8.279800 CGAAGATGTAAAGTGTATGTGTGAAAA 58.720 33.333 0.00 0.00 0.00 2.29
3173 4599 7.570507 GCGAAGATGTAAAGTGTATGTGTGAAA 60.571 37.037 0.00 0.00 0.00 2.69
3174 4600 6.128661 GCGAAGATGTAAAGTGTATGTGTGAA 60.129 38.462 0.00 0.00 0.00 3.18
3175 4601 5.347635 GCGAAGATGTAAAGTGTATGTGTGA 59.652 40.000 0.00 0.00 0.00 3.58
3176 4602 5.120053 TGCGAAGATGTAAAGTGTATGTGTG 59.880 40.000 0.00 0.00 0.00 3.82
3177 4603 5.234752 TGCGAAGATGTAAAGTGTATGTGT 58.765 37.500 0.00 0.00 0.00 3.72
3178 4604 5.778161 TGCGAAGATGTAAAGTGTATGTG 57.222 39.130 0.00 0.00 0.00 3.21
3179 4605 7.039270 TGTATGCGAAGATGTAAAGTGTATGT 58.961 34.615 0.00 0.00 0.00 2.29
3180 4606 7.463469 TGTATGCGAAGATGTAAAGTGTATG 57.537 36.000 0.00 0.00 0.00 2.39
3181 4607 7.710907 ACATGTATGCGAAGATGTAAAGTGTAT 59.289 33.333 0.00 0.00 32.06 2.29
3182 4608 7.010091 CACATGTATGCGAAGATGTAAAGTGTA 59.990 37.037 0.00 0.00 32.06 2.90
3183 4609 5.874810 ACATGTATGCGAAGATGTAAAGTGT 59.125 36.000 0.00 0.00 32.06 3.55
3184 4610 6.183360 ACACATGTATGCGAAGATGTAAAGTG 60.183 38.462 0.00 0.00 32.06 3.16
3185 4611 5.874810 ACACATGTATGCGAAGATGTAAAGT 59.125 36.000 0.00 0.00 32.06 2.66
3186 4612 6.349973 ACACATGTATGCGAAGATGTAAAG 57.650 37.500 0.00 0.00 32.06 1.85
3187 4613 8.432110 AATACACATGTATGCGAAGATGTAAA 57.568 30.769 0.00 0.00 40.78 2.01
3188 4614 8.432110 AAATACACATGTATGCGAAGATGTAA 57.568 30.769 0.00 0.00 40.78 2.41
3189 4615 8.432110 AAAATACACATGTATGCGAAGATGTA 57.568 30.769 0.00 0.00 40.78 2.29
3190 4616 6.925610 AAATACACATGTATGCGAAGATGT 57.074 33.333 0.00 0.00 40.78 3.06
3251 4677 7.512992 TGGAGCCCTTTATTTTGAAAAATTCA 58.487 30.769 6.34 0.00 39.24 2.57
3252 4678 7.977789 TGGAGCCCTTTATTTTGAAAAATTC 57.022 32.000 6.34 0.00 39.24 2.17
3253 4679 7.394077 CCATGGAGCCCTTTATTTTGAAAAATT 59.606 33.333 5.56 0.00 39.24 1.82
3254 4680 6.885918 CCATGGAGCCCTTTATTTTGAAAAAT 59.114 34.615 5.56 6.29 41.24 1.82
3255 4681 6.043706 TCCATGGAGCCCTTTATTTTGAAAAA 59.956 34.615 11.44 0.00 0.00 1.94
3256 4682 5.545723 TCCATGGAGCCCTTTATTTTGAAAA 59.454 36.000 11.44 0.00 0.00 2.29
3257 4683 5.090139 TCCATGGAGCCCTTTATTTTGAAA 58.910 37.500 11.44 0.00 0.00 2.69
3258 4684 4.682563 TCCATGGAGCCCTTTATTTTGAA 58.317 39.130 11.44 0.00 0.00 2.69
3259 4685 4.280819 CTCCATGGAGCCCTTTATTTTGA 58.719 43.478 28.45 0.00 35.31 2.69
3260 4686 4.660789 CTCCATGGAGCCCTTTATTTTG 57.339 45.455 28.45 1.40 35.31 2.44
3272 4698 1.739049 GAGACCGAGCTCCATGGAG 59.261 63.158 33.73 33.73 44.56 3.86
3273 4699 3.941081 GAGACCGAGCTCCATGGA 58.059 61.111 15.27 15.27 0.00 3.41
3279 4705 0.729690 GCATTTTGGAGACCGAGCTC 59.270 55.000 2.73 2.73 0.00 4.09
3280 4706 0.678048 GGCATTTTGGAGACCGAGCT 60.678 55.000 0.00 0.00 0.00 4.09
3281 4707 1.657751 GGGCATTTTGGAGACCGAGC 61.658 60.000 0.00 0.00 0.00 5.03
3282 4708 0.035056 AGGGCATTTTGGAGACCGAG 60.035 55.000 0.00 0.00 0.00 4.63
3283 4709 1.065709 GTAGGGCATTTTGGAGACCGA 60.066 52.381 0.00 0.00 0.00 4.69
3284 4710 1.065418 AGTAGGGCATTTTGGAGACCG 60.065 52.381 0.00 0.00 0.00 4.79
3285 4711 2.644676 GAGTAGGGCATTTTGGAGACC 58.355 52.381 0.00 0.00 0.00 3.85
3286 4712 2.239907 AGGAGTAGGGCATTTTGGAGAC 59.760 50.000 0.00 0.00 0.00 3.36
3287 4713 2.562296 AGGAGTAGGGCATTTTGGAGA 58.438 47.619 0.00 0.00 0.00 3.71
3288 4714 3.372440 AAGGAGTAGGGCATTTTGGAG 57.628 47.619 0.00 0.00 0.00 3.86
3289 4715 3.589735 TGTAAGGAGTAGGGCATTTTGGA 59.410 43.478 0.00 0.00 0.00 3.53
3290 4716 3.963129 TGTAAGGAGTAGGGCATTTTGG 58.037 45.455 0.00 0.00 0.00 3.28
3291 4717 4.764823 TGTTGTAAGGAGTAGGGCATTTTG 59.235 41.667 0.00 0.00 0.00 2.44
3292 4718 4.993028 TGTTGTAAGGAGTAGGGCATTTT 58.007 39.130 0.00 0.00 0.00 1.82
3293 4719 4.650972 TGTTGTAAGGAGTAGGGCATTT 57.349 40.909 0.00 0.00 0.00 2.32
3294 4720 4.862641 ATGTTGTAAGGAGTAGGGCATT 57.137 40.909 0.00 0.00 0.00 3.56
3295 4721 4.862641 AATGTTGTAAGGAGTAGGGCAT 57.137 40.909 0.00 0.00 0.00 4.40
3296 4722 5.968676 ATAATGTTGTAAGGAGTAGGGCA 57.031 39.130 0.00 0.00 0.00 5.36
3297 4723 8.919777 ATTTATAATGTTGTAAGGAGTAGGGC 57.080 34.615 0.00 0.00 0.00 5.19
3302 4728 9.019656 TGCACAATTTATAATGTTGTAAGGAGT 57.980 29.630 13.33 0.00 34.55 3.85
3303 4729 9.853555 TTGCACAATTTATAATGTTGTAAGGAG 57.146 29.630 13.33 5.76 34.55 3.69
3383 4809 7.408756 AGTATATTGGAAGAGCAAATGCAAA 57.591 32.000 8.28 0.00 45.16 3.68
3384 4810 7.408756 AAGTATATTGGAAGAGCAAATGCAA 57.591 32.000 8.28 0.00 45.16 4.08
3385 4811 6.039717 GGAAGTATATTGGAAGAGCAAATGCA 59.960 38.462 8.28 0.00 45.16 3.96
3386 4812 6.264067 AGGAAGTATATTGGAAGAGCAAATGC 59.736 38.462 0.00 0.00 42.49 3.56
3387 4813 7.040823 GGAGGAAGTATATTGGAAGAGCAAATG 60.041 40.741 0.00 0.00 0.00 2.32
3388 4814 7.001073 GGAGGAAGTATATTGGAAGAGCAAAT 58.999 38.462 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.