Multiple sequence alignment - TraesCS1B01G141000

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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 TraesCS1B01G141000 chr1B 100.000 3638 0 0 1 3638 188263227 188259590 0.000000e+00 6719
1 TraesCS1B01G141000 chr1D 95.933 3147 82 12 1 3123 123701425 123698301 0.000000e+00 5060
2 TraesCS1B01G141000 chr1A 95.667 3139 93 11 1 3123 135969561 135966450 0.000000e+00 5003
3 TraesCS1B01G141000 chr2D 85.064 1011 129 5 1170 2171 43285094 43284097 0.000000e+00 1011
4 TraesCS1B01G141000 chr2B 80.750 987 147 28 1161 2133 68150738 68149781 0.000000e+00 730
5 TraesCS1B01G141000 chr2B 95.192 416 17 3 3122 3534 36838631 36839046 0.000000e+00 654
6 TraesCS1B01G141000 chr3B 96.347 438 13 2 3124 3559 141865620 141865184 0.000000e+00 717
7 TraesCS1B01G141000 chr7B 95.900 439 15 2 3124 3560 351929384 351929821 0.000000e+00 708
8 TraesCS1B01G141000 chr7B 95.238 441 18 3 3122 3560 246018449 246018888 0.000000e+00 695
9 TraesCS1B01G141000 chr4A 95.672 439 16 2 3124 3560 637413879 637414316 0.000000e+00 702
10 TraesCS1B01G141000 chr6B 94.318 440 24 1 3122 3560 569048109 569047670 0.000000e+00 673
11 TraesCS1B01G141000 chr6B 92.308 442 28 2 3121 3561 107879411 107879847 1.110000e-174 623
12 TraesCS1B01G141000 chr5B 94.331 441 22 2 3124 3562 384739962 384739523 0.000000e+00 673
13 TraesCS1B01G141000 chr5B 93.363 452 21 4 3124 3568 679824502 679824053 0.000000e+00 660
14 TraesCS1B01G141000 chr3A 74.058 902 189 34 1230 2104 77410178 77411061 9.740000e-86 327
15 TraesCS1B01G141000 chr2A 82.770 296 41 6 1661 1947 44850030 44849736 4.660000e-64 255
16 TraesCS1B01G141000 chr3D 72.512 844 189 32 1230 2047 66311222 66310396 2.180000e-57 233


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 TraesCS1B01G141000 chr1B 188259590 188263227 3637 True 6719 6719 100.000 1 3638 1 chr1B.!!$R1 3637
1 TraesCS1B01G141000 chr1D 123698301 123701425 3124 True 5060 5060 95.933 1 3123 1 chr1D.!!$R1 3122
2 TraesCS1B01G141000 chr1A 135966450 135969561 3111 True 5003 5003 95.667 1 3123 1 chr1A.!!$R1 3122
3 TraesCS1B01G141000 chr2D 43284097 43285094 997 True 1011 1011 85.064 1170 2171 1 chr2D.!!$R1 1001
4 TraesCS1B01G141000 chr2B 68149781 68150738 957 True 730 730 80.750 1161 2133 1 chr2B.!!$R1 972
5 TraesCS1B01G141000 chr3A 77410178 77411061 883 False 327 327 74.058 1230 2104 1 chr3A.!!$F1 874
6 TraesCS1B01G141000 chr3D 66310396 66311222 826 True 233 233 72.512 1230 2047 1 chr3D.!!$R1 817

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
513 514 1.363744 GCTACACGCTCAGCAAATCT 58.636 50.0 0.00 0.0 37.73 2.4 F
1065 1067 0.316689 GTTTTGACACGGCGAACAGG 60.317 55.0 16.62 0.0 0.00 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 2538 0.606944 AGCCAAGACTCGACGAGACT 60.607 55.0 30.56 25.76 36.37 3.24 R
2951 2999 0.874390 CCAAATCAGTCCACCACACG 59.126 55.0 0.00 0.00 0.00 4.49 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
61 62 6.070424 TGAGGGTAAAGTTATAGGTGTCTTGG 60.070 42.308 0.00 0.00 0.00 3.61
218 219 8.954350 AGACTGGTCAATTGATTTCTAAGAATG 58.046 33.333 12.12 0.00 0.00 2.67
247 248 7.217200 AGCATATTACGTCCACATGACTTTAT 58.783 34.615 0.00 0.00 42.13 1.40
268 269 2.239654 TCACCCACATTCCCATCTCTTC 59.760 50.000 0.00 0.00 0.00 2.87
281 282 4.442612 CCCATCTCTTCGACATGAGAACAT 60.443 45.833 13.59 0.00 41.82 2.71
361 362 5.279384 CGCGTCACCTACTATGACTTTATT 58.721 41.667 0.00 0.00 43.60 1.40
385 386 9.740239 ATTAATGTTAATTAGACTGCATTGCAG 57.260 29.630 31.84 31.84 44.56 4.41
413 414 7.210718 TGCAATTCATTATGCTGGATTCTAG 57.789 36.000 0.00 0.00 42.97 2.43
513 514 1.363744 GCTACACGCTCAGCAAATCT 58.636 50.000 0.00 0.00 37.73 2.40
534 535 2.697425 CGACCAGCGATCTTTGCG 59.303 61.111 0.00 0.00 44.57 4.85
573 574 5.950758 ATGCGTTGGAATTTACACAAGTA 57.049 34.783 0.00 0.00 0.00 2.24
607 608 7.038729 TGAGAGTCAGATTTCCAACTAGAACAT 60.039 37.037 0.00 0.00 0.00 2.71
790 791 8.428852 ACTTAAAATGTTAGCCAATTTGGTCTT 58.571 29.630 16.62 5.99 40.46 3.01
836 837 3.630168 TGACATGGGTATGGACAAATGG 58.370 45.455 0.00 0.00 38.66 3.16
844 845 5.832595 TGGGTATGGACAAATGGATATTGTG 59.167 40.000 0.00 0.00 40.90 3.33
872 873 8.958119 TTCCTTCCACATTATGATACTTACAC 57.042 34.615 0.00 0.00 0.00 2.90
1055 1057 1.370051 GAAGCCCGCGTTTTGACAC 60.370 57.895 4.92 0.00 0.00 3.67
1058 1060 4.676586 CCCGCGTTTTGACACGGC 62.677 66.667 4.92 0.00 44.29 5.68
1065 1067 0.316689 GTTTTGACACGGCGAACAGG 60.317 55.000 16.62 0.00 0.00 4.00
1582 1593 3.882326 CCAGGGAGGCCGATGCAT 61.882 66.667 0.00 0.00 40.13 3.96
2503 2538 1.417288 AGGTGCTCATGATCCGATCA 58.583 50.000 13.46 13.46 44.55 2.92
2607 2642 2.835431 ACGCGGGATGAGGAGGAG 60.835 66.667 12.47 0.00 0.00 3.69
2611 2646 1.540435 GCGGGATGAGGAGGAGGATC 61.540 65.000 0.00 0.00 0.00 3.36
2614 2659 1.253100 GGATGAGGAGGAGGATCGAC 58.747 60.000 0.00 0.00 34.37 4.20
2710 2757 3.841758 GGGGACGGACGCGGTATT 61.842 66.667 12.47 0.00 0.00 1.89
2816 2864 4.078516 CGGGTGGGGAGAACGGAC 62.079 72.222 0.00 0.00 0.00 4.79
2818 2866 4.078516 GGTGGGGAGAACGGACGG 62.079 72.222 0.00 0.00 0.00 4.79
2819 2867 4.078516 GTGGGGAGAACGGACGGG 62.079 72.222 0.00 0.00 0.00 5.28
2820 2868 4.626402 TGGGGAGAACGGACGGGT 62.626 66.667 0.00 0.00 0.00 5.28
2821 2869 4.078516 GGGGAGAACGGACGGGTG 62.079 72.222 0.00 0.00 0.00 4.61
2822 2870 2.993264 GGGAGAACGGACGGGTGA 60.993 66.667 0.00 0.00 0.00 4.02
2916 2964 3.934068 CCGCAACGGGGTTCTATTATAT 58.066 45.455 0.00 0.00 44.15 0.86
2917 2965 4.320870 CCGCAACGGGGTTCTATTATATT 58.679 43.478 0.00 0.00 44.15 1.28
2951 2999 6.737254 TGGAAAAGGAAAATATCGTCTGTC 57.263 37.500 0.00 0.00 0.00 3.51
3014 3062 1.906824 GGAGTGGTGGACTGACCGA 60.907 63.158 0.00 0.00 42.61 4.69
3088 3136 1.134521 TGTATGGCCGGCTAGTCTTTG 60.135 52.381 28.56 0.00 0.00 2.77
3123 3171 2.264794 GTCAACCGGATCGCCACT 59.735 61.111 9.46 0.00 0.00 4.00
3124 3172 1.514087 GTCAACCGGATCGCCACTA 59.486 57.895 9.46 0.00 0.00 2.74
3125 3173 0.104304 GTCAACCGGATCGCCACTAT 59.896 55.000 9.46 0.00 0.00 2.12
3126 3174 1.338973 GTCAACCGGATCGCCACTATA 59.661 52.381 9.46 0.00 0.00 1.31
3127 3175 1.611977 TCAACCGGATCGCCACTATAG 59.388 52.381 9.46 0.00 0.00 1.31
3128 3176 0.317479 AACCGGATCGCCACTATAGC 59.683 55.000 9.46 0.00 0.00 2.97
3129 3177 0.539901 ACCGGATCGCCACTATAGCT 60.540 55.000 9.46 0.00 0.00 3.32
3130 3178 0.109086 CCGGATCGCCACTATAGCTG 60.109 60.000 0.00 0.00 0.00 4.24
3131 3179 0.109086 CGGATCGCCACTATAGCTGG 60.109 60.000 13.86 13.86 0.00 4.85
3138 3186 1.299541 CCACTATAGCTGGCCAAACG 58.700 55.000 7.01 0.00 0.00 3.60
3139 3187 1.299541 CACTATAGCTGGCCAAACGG 58.700 55.000 7.01 0.00 0.00 4.44
3140 3188 0.180406 ACTATAGCTGGCCAAACGGG 59.820 55.000 7.01 0.00 40.85 5.28
3149 3197 2.203153 CCAAACGGGCCGGGATAG 60.203 66.667 31.78 14.48 0.00 2.08
3150 3198 2.587889 CAAACGGGCCGGGATAGT 59.412 61.111 31.78 4.41 0.00 2.12
3151 3199 1.078001 CAAACGGGCCGGGATAGTT 60.078 57.895 31.78 11.46 0.00 2.24
3152 3200 1.078001 AAACGGGCCGGGATAGTTG 60.078 57.895 31.78 0.00 0.00 3.16
3153 3201 2.546114 AAACGGGCCGGGATAGTTGG 62.546 60.000 31.78 0.00 0.00 3.77
3154 3202 4.250305 CGGGCCGGGATAGTTGGG 62.250 72.222 20.56 0.00 0.00 4.12
3155 3203 4.581093 GGGCCGGGATAGTTGGGC 62.581 72.222 2.18 0.00 46.84 5.36
3157 3205 4.929707 GCCGGGATAGTTGGGCCG 62.930 72.222 2.18 0.00 39.67 6.13
3158 3206 4.250305 CCGGGATAGTTGGGCCGG 62.250 72.222 0.00 0.00 34.60 6.13
3159 3207 4.929707 CGGGATAGTTGGGCCGGC 62.930 72.222 21.18 21.18 0.00 6.13
3160 3208 4.581093 GGGATAGTTGGGCCGGCC 62.581 72.222 38.57 38.57 0.00 6.13
3246 3294 2.187946 CCGTGCCTAGGCCTGAAG 59.812 66.667 30.81 14.39 41.09 3.02
3247 3295 2.187946 CGTGCCTAGGCCTGAAGG 59.812 66.667 30.81 17.05 41.09 3.46
3248 3296 2.592308 GTGCCTAGGCCTGAAGGG 59.408 66.667 30.81 15.41 41.09 3.95
3285 3333 2.124860 GGCACGGCCCGATTAACT 60.125 61.111 11.71 0.00 44.06 2.24
3286 3334 1.747745 GGCACGGCCCGATTAACTT 60.748 57.895 11.71 0.00 44.06 2.66
3287 3335 1.310216 GGCACGGCCCGATTAACTTT 61.310 55.000 11.71 0.00 44.06 2.66
3288 3336 0.524414 GCACGGCCCGATTAACTTTT 59.476 50.000 11.71 0.00 0.00 2.27
3289 3337 1.068125 GCACGGCCCGATTAACTTTTT 60.068 47.619 11.71 0.00 0.00 1.94
3320 3368 8.644374 TTTTATGTATCCTAATATGGGCCAAC 57.356 34.615 11.89 0.35 0.00 3.77
3321 3369 5.858876 ATGTATCCTAATATGGGCCAACA 57.141 39.130 11.89 7.42 0.00 3.33
3322 3370 5.241403 TGTATCCTAATATGGGCCAACAG 57.759 43.478 11.89 5.14 0.00 3.16
3323 3371 4.910913 TGTATCCTAATATGGGCCAACAGA 59.089 41.667 11.89 2.12 0.00 3.41
3324 3372 5.551583 TGTATCCTAATATGGGCCAACAGAT 59.448 40.000 11.89 9.94 0.00 2.90
3325 3373 6.733334 TGTATCCTAATATGGGCCAACAGATA 59.267 38.462 11.89 8.94 0.00 1.98
3326 3374 6.718593 ATCCTAATATGGGCCAACAGATAA 57.281 37.500 11.89 0.00 0.00 1.75
3327 3375 6.523035 TCCTAATATGGGCCAACAGATAAA 57.477 37.500 11.89 0.00 0.00 1.40
3328 3376 6.916909 TCCTAATATGGGCCAACAGATAAAA 58.083 36.000 11.89 0.00 0.00 1.52
3329 3377 7.358263 TCCTAATATGGGCCAACAGATAAAAA 58.642 34.615 11.89 0.00 0.00 1.94
3330 3378 8.010105 TCCTAATATGGGCCAACAGATAAAAAT 58.990 33.333 11.89 0.00 0.00 1.82
3331 3379 9.308000 CCTAATATGGGCCAACAGATAAAAATA 57.692 33.333 11.89 0.00 0.00 1.40
3333 3381 7.781324 ATATGGGCCAACAGATAAAAATAGG 57.219 36.000 11.89 0.00 0.00 2.57
3334 3382 3.704061 TGGGCCAACAGATAAAAATAGGC 59.296 43.478 2.13 0.00 40.08 3.93
3335 3383 3.960755 GGGCCAACAGATAAAAATAGGCT 59.039 43.478 4.39 0.00 40.61 4.58
3336 3384 5.137551 GGGCCAACAGATAAAAATAGGCTA 58.862 41.667 4.39 0.00 40.61 3.93
3337 3385 5.009710 GGGCCAACAGATAAAAATAGGCTAC 59.990 44.000 4.39 0.00 40.61 3.58
3338 3386 5.592688 GGCCAACAGATAAAAATAGGCTACA 59.407 40.000 0.00 0.00 40.61 2.74
3339 3387 6.096282 GGCCAACAGATAAAAATAGGCTACAA 59.904 38.462 0.00 0.00 40.61 2.41
3340 3388 7.363443 GGCCAACAGATAAAAATAGGCTACAAA 60.363 37.037 0.00 0.00 40.61 2.83
3341 3389 8.032451 GCCAACAGATAAAAATAGGCTACAAAA 58.968 33.333 0.00 0.00 37.89 2.44
3342 3390 9.353999 CCAACAGATAAAAATAGGCTACAAAAC 57.646 33.333 0.00 0.00 0.00 2.43
3343 3391 9.061610 CAACAGATAAAAATAGGCTACAAAACG 57.938 33.333 0.00 0.00 0.00 3.60
3344 3392 7.248437 ACAGATAAAAATAGGCTACAAAACGC 58.752 34.615 0.00 0.00 0.00 4.84
3345 3393 7.120726 ACAGATAAAAATAGGCTACAAAACGCT 59.879 33.333 0.00 0.00 0.00 5.07
3346 3394 8.609176 CAGATAAAAATAGGCTACAAAACGCTA 58.391 33.333 0.00 0.00 0.00 4.26
3347 3395 9.169592 AGATAAAAATAGGCTACAAAACGCTAA 57.830 29.630 0.00 0.00 0.00 3.09
3348 3396 9.777575 GATAAAAATAGGCTACAAAACGCTAAA 57.222 29.630 0.00 0.00 0.00 1.85
3350 3398 8.460831 AAAAATAGGCTACAAAACGCTAAATG 57.539 30.769 0.00 0.00 0.00 2.32
3351 3399 3.487563 AGGCTACAAAACGCTAAATGC 57.512 42.857 0.00 0.00 38.57 3.56
3363 3411 3.174799 GCTAAATGCGCGAAATAGGAG 57.825 47.619 12.10 2.23 0.00 3.69
3364 3412 2.096218 GCTAAATGCGCGAAATAGGAGG 60.096 50.000 12.10 0.00 0.00 4.30
3365 3413 2.038387 AAATGCGCGAAATAGGAGGT 57.962 45.000 12.10 0.00 0.00 3.85
3366 3414 2.902705 AATGCGCGAAATAGGAGGTA 57.097 45.000 12.10 0.00 0.00 3.08
3367 3415 2.440539 ATGCGCGAAATAGGAGGTAG 57.559 50.000 12.10 0.00 0.00 3.18
3368 3416 1.395635 TGCGCGAAATAGGAGGTAGA 58.604 50.000 12.10 0.00 0.00 2.59
3369 3417 1.961394 TGCGCGAAATAGGAGGTAGAT 59.039 47.619 12.10 0.00 0.00 1.98
3370 3418 2.364324 TGCGCGAAATAGGAGGTAGATT 59.636 45.455 12.10 0.00 0.00 2.40
3371 3419 3.570975 TGCGCGAAATAGGAGGTAGATTA 59.429 43.478 12.10 0.00 0.00 1.75
3372 3420 4.167268 GCGCGAAATAGGAGGTAGATTAG 58.833 47.826 12.10 0.00 0.00 1.73
3373 3421 4.321082 GCGCGAAATAGGAGGTAGATTAGT 60.321 45.833 12.10 0.00 0.00 2.24
3374 3422 5.154932 CGCGAAATAGGAGGTAGATTAGTG 58.845 45.833 0.00 0.00 0.00 2.74
3375 3423 5.471257 GCGAAATAGGAGGTAGATTAGTGG 58.529 45.833 0.00 0.00 0.00 4.00
3376 3424 5.567025 GCGAAATAGGAGGTAGATTAGTGGG 60.567 48.000 0.00 0.00 0.00 4.61
3377 3425 5.567025 CGAAATAGGAGGTAGATTAGTGGGC 60.567 48.000 0.00 0.00 0.00 5.36
3378 3426 4.768807 ATAGGAGGTAGATTAGTGGGCT 57.231 45.455 0.00 0.00 0.00 5.19
3379 3427 3.423058 AGGAGGTAGATTAGTGGGCTT 57.577 47.619 0.00 0.00 0.00 4.35
3380 3428 3.041946 AGGAGGTAGATTAGTGGGCTTG 58.958 50.000 0.00 0.00 0.00 4.01
3381 3429 3.039011 GGAGGTAGATTAGTGGGCTTGA 58.961 50.000 0.00 0.00 0.00 3.02
3382 3430 3.181464 GGAGGTAGATTAGTGGGCTTGAC 60.181 52.174 0.00 0.00 0.00 3.18
3383 3431 2.431057 AGGTAGATTAGTGGGCTTGACG 59.569 50.000 0.00 0.00 0.00 4.35
3384 3432 2.167900 GGTAGATTAGTGGGCTTGACGT 59.832 50.000 0.00 0.00 0.00 4.34
3385 3433 2.386661 AGATTAGTGGGCTTGACGTG 57.613 50.000 0.00 0.00 0.00 4.49
3386 3434 0.727398 GATTAGTGGGCTTGACGTGC 59.273 55.000 0.00 0.00 0.00 5.34
3409 3457 4.643387 GGCCGGCCCGATTAGCAT 62.643 66.667 36.64 0.00 0.00 3.79
3410 3458 2.345991 GCCGGCCCGATTAGCATA 59.654 61.111 18.11 0.00 0.00 3.14
3411 3459 2.033194 GCCGGCCCGATTAGCATAC 61.033 63.158 18.11 0.00 0.00 2.39
3412 3460 1.736645 CCGGCCCGATTAGCATACG 60.737 63.158 3.71 0.00 0.00 3.06
3413 3461 1.736645 CGGCCCGATTAGCATACGG 60.737 63.158 0.00 0.00 45.24 4.02
3416 3464 4.278956 CCGATTAGCATACGGGCC 57.721 61.111 0.00 0.00 42.48 5.80
3417 3465 1.736645 CCGATTAGCATACGGGCCG 60.737 63.158 27.06 27.06 42.48 6.13
3418 3466 1.006571 CGATTAGCATACGGGCCGT 60.007 57.895 35.91 35.91 44.35 5.68
3419 3467 1.282248 CGATTAGCATACGGGCCGTG 61.282 60.000 39.80 25.77 41.39 4.94
3420 3468 1.566018 GATTAGCATACGGGCCGTGC 61.566 60.000 39.80 33.49 41.39 5.34
3472 3520 3.610637 GGCACGGCCCGTATAATAA 57.389 52.632 9.25 0.00 44.06 1.40
3473 3521 2.103537 GGCACGGCCCGTATAATAAT 57.896 50.000 9.25 0.00 44.06 1.28
3474 3522 2.004733 GGCACGGCCCGTATAATAATC 58.995 52.381 9.25 0.00 44.06 1.75
3475 3523 1.657094 GCACGGCCCGTATAATAATCG 59.343 52.381 9.25 0.00 38.32 3.34
3476 3524 2.927871 GCACGGCCCGTATAATAATCGT 60.928 50.000 9.25 0.00 38.32 3.73
3477 3525 2.664568 CACGGCCCGTATAATAATCGTG 59.335 50.000 9.25 0.00 38.32 4.35
3478 3526 1.657094 CGGCCCGTATAATAATCGTGC 59.343 52.381 0.00 0.00 0.00 5.34
3479 3527 2.004733 GGCCCGTATAATAATCGTGCC 58.995 52.381 0.00 0.00 40.23 5.01
3480 3528 2.354403 GGCCCGTATAATAATCGTGCCT 60.354 50.000 0.00 0.00 42.74 4.75
3481 3529 3.119029 GGCCCGTATAATAATCGTGCCTA 60.119 47.826 0.00 0.00 42.74 3.93
3482 3530 4.110482 GCCCGTATAATAATCGTGCCTAG 58.890 47.826 0.00 0.00 0.00 3.02
3483 3531 4.679662 CCCGTATAATAATCGTGCCTAGG 58.320 47.826 3.67 3.67 0.00 3.02
3484 3532 4.110482 CCGTATAATAATCGTGCCTAGGC 58.890 47.826 27.71 27.71 42.35 3.93
3485 3533 3.789756 CGTATAATAATCGTGCCTAGGCG 59.210 47.826 28.28 15.51 45.51 5.52
3486 3534 2.736144 TAATAATCGTGCCTAGGCGG 57.264 50.000 28.28 21.97 45.51 6.13
3487 3535 0.034896 AATAATCGTGCCTAGGCGGG 59.965 55.000 28.28 21.60 45.51 6.13
3513 3561 3.720494 TGCCAGGCACGATTAGGA 58.280 55.556 11.22 0.00 31.71 2.94
3514 3562 2.220953 TGCCAGGCACGATTAGGAT 58.779 52.632 11.22 0.00 31.71 3.24
3515 3563 0.179048 TGCCAGGCACGATTAGGATG 60.179 55.000 11.22 0.00 31.71 3.51
3516 3564 0.886490 GCCAGGCACGATTAGGATGG 60.886 60.000 6.55 0.00 0.00 3.51
3517 3565 0.250467 CCAGGCACGATTAGGATGGG 60.250 60.000 0.00 0.00 0.00 4.00
3518 3566 0.886490 CAGGCACGATTAGGATGGGC 60.886 60.000 0.00 0.00 0.00 5.36
3519 3567 1.600916 GGCACGATTAGGATGGGCC 60.601 63.158 0.00 0.00 0.00 5.80
3520 3568 1.961277 GCACGATTAGGATGGGCCG 60.961 63.158 0.00 0.00 43.43 6.13
3521 3569 1.445942 CACGATTAGGATGGGCCGT 59.554 57.895 0.00 0.00 43.43 5.68
3522 3570 0.880278 CACGATTAGGATGGGCCGTG 60.880 60.000 1.02 0.00 43.43 4.94
3523 3571 1.961277 CGATTAGGATGGGCCGTGC 60.961 63.158 9.57 9.57 43.43 5.34
3560 3608 3.487576 CCCGTTTGGCCAGCTATAA 57.512 52.632 5.11 0.00 0.00 0.98
3561 3609 1.981256 CCCGTTTGGCCAGCTATAAT 58.019 50.000 5.11 0.00 0.00 1.28
3562 3610 1.880027 CCCGTTTGGCCAGCTATAATC 59.120 52.381 5.11 0.00 0.00 1.75
3563 3611 1.531149 CCGTTTGGCCAGCTATAATCG 59.469 52.381 5.11 0.53 0.00 3.34
3564 3612 1.069906 CGTTTGGCCAGCTATAATCGC 60.070 52.381 5.11 0.00 0.00 4.58
3565 3613 1.266989 GTTTGGCCAGCTATAATCGCC 59.733 52.381 5.11 0.00 40.16 5.54
3567 3615 0.472044 TGGCCAGCTATAATCGCCAA 59.528 50.000 0.00 0.00 46.28 4.52
3568 3616 1.133945 TGGCCAGCTATAATCGCCAAA 60.134 47.619 0.00 0.00 46.28 3.28
3569 3617 1.953686 GGCCAGCTATAATCGCCAAAA 59.046 47.619 0.00 0.00 39.50 2.44
3570 3618 2.287608 GGCCAGCTATAATCGCCAAAAC 60.288 50.000 0.00 0.00 39.50 2.43
3571 3619 2.618709 GCCAGCTATAATCGCCAAAACT 59.381 45.455 0.00 0.00 0.00 2.66
3572 3620 3.813166 GCCAGCTATAATCGCCAAAACTA 59.187 43.478 0.00 0.00 0.00 2.24
3573 3621 4.083802 GCCAGCTATAATCGCCAAAACTAG 60.084 45.833 0.00 0.00 0.00 2.57
3574 3622 5.057149 CCAGCTATAATCGCCAAAACTAGT 58.943 41.667 0.00 0.00 0.00 2.57
3575 3623 5.050091 CCAGCTATAATCGCCAAAACTAGTG 60.050 44.000 0.00 0.00 0.00 2.74
3576 3624 4.511826 AGCTATAATCGCCAAAACTAGTGC 59.488 41.667 0.00 0.00 0.00 4.40
3577 3625 4.319549 GCTATAATCGCCAAAACTAGTGCC 60.320 45.833 0.00 0.00 0.00 5.01
3578 3626 2.200373 AATCGCCAAAACTAGTGCCT 57.800 45.000 0.00 0.00 0.00 4.75
3579 3627 1.739067 ATCGCCAAAACTAGTGCCTC 58.261 50.000 0.00 0.00 0.00 4.70
3580 3628 0.321298 TCGCCAAAACTAGTGCCTCC 60.321 55.000 0.00 0.00 0.00 4.30
3581 3629 1.635663 CGCCAAAACTAGTGCCTCCG 61.636 60.000 0.00 0.00 0.00 4.63
3582 3630 0.605589 GCCAAAACTAGTGCCTCCGT 60.606 55.000 0.00 0.00 0.00 4.69
3583 3631 1.439679 CCAAAACTAGTGCCTCCGTC 58.560 55.000 0.00 0.00 0.00 4.79
3584 3632 1.439679 CAAAACTAGTGCCTCCGTCC 58.560 55.000 0.00 0.00 0.00 4.79
3585 3633 0.323957 AAAACTAGTGCCTCCGTCCC 59.676 55.000 0.00 0.00 0.00 4.46
3586 3634 0.834687 AAACTAGTGCCTCCGTCCCA 60.835 55.000 0.00 0.00 0.00 4.37
3587 3635 0.617820 AACTAGTGCCTCCGTCCCAT 60.618 55.000 0.00 0.00 0.00 4.00
3588 3636 0.260816 ACTAGTGCCTCCGTCCCATA 59.739 55.000 0.00 0.00 0.00 2.74
3589 3637 1.342674 ACTAGTGCCTCCGTCCCATAA 60.343 52.381 0.00 0.00 0.00 1.90
3590 3638 1.971357 CTAGTGCCTCCGTCCCATAAT 59.029 52.381 0.00 0.00 0.00 1.28
3591 3639 2.097110 AGTGCCTCCGTCCCATAATA 57.903 50.000 0.00 0.00 0.00 0.98
3592 3640 2.621070 AGTGCCTCCGTCCCATAATAT 58.379 47.619 0.00 0.00 0.00 1.28
3593 3641 3.786553 AGTGCCTCCGTCCCATAATATA 58.213 45.455 0.00 0.00 0.00 0.86
3594 3642 3.514309 AGTGCCTCCGTCCCATAATATAC 59.486 47.826 0.00 0.00 0.00 1.47
3595 3643 3.514309 GTGCCTCCGTCCCATAATATACT 59.486 47.826 0.00 0.00 0.00 2.12
3596 3644 4.020485 GTGCCTCCGTCCCATAATATACTT 60.020 45.833 0.00 0.00 0.00 2.24
3597 3645 5.186409 GTGCCTCCGTCCCATAATATACTTA 59.814 44.000 0.00 0.00 0.00 2.24
3598 3646 5.781306 TGCCTCCGTCCCATAATATACTTAA 59.219 40.000 0.00 0.00 0.00 1.85
3599 3647 6.442564 TGCCTCCGTCCCATAATATACTTAAT 59.557 38.462 0.00 0.00 0.00 1.40
3600 3648 7.620491 TGCCTCCGTCCCATAATATACTTAATA 59.380 37.037 0.00 0.00 0.00 0.98
3601 3649 8.648693 GCCTCCGTCCCATAATATACTTAATAT 58.351 37.037 0.00 0.00 31.75 1.28
3627 3675 8.980481 AACAGCATTTTTAGTACTATATGGCT 57.020 30.769 2.79 7.04 0.00 4.75
3628 3676 8.608844 ACAGCATTTTTAGTACTATATGGCTC 57.391 34.615 2.79 0.00 0.00 4.70
3629 3677 7.661847 ACAGCATTTTTAGTACTATATGGCTCC 59.338 37.037 2.79 0.00 0.00 4.70
3630 3678 7.119846 CAGCATTTTTAGTACTATATGGCTCCC 59.880 40.741 2.79 0.00 0.00 4.30
3631 3679 7.017651 AGCATTTTTAGTACTATATGGCTCCCT 59.982 37.037 2.79 0.00 0.00 4.20
3632 3680 7.119846 GCATTTTTAGTACTATATGGCTCCCTG 59.880 40.741 2.79 0.00 0.00 4.45
3633 3681 7.685849 TTTTTAGTACTATATGGCTCCCTGT 57.314 36.000 2.79 0.00 0.00 4.00
3634 3682 8.786710 TTTTTAGTACTATATGGCTCCCTGTA 57.213 34.615 2.79 0.00 0.00 2.74
3635 3683 8.418597 TTTTAGTACTATATGGCTCCCTGTAG 57.581 38.462 2.79 0.00 0.00 2.74
3636 3684 5.602291 AGTACTATATGGCTCCCTGTAGT 57.398 43.478 0.00 6.06 0.00 2.73
3637 3685 5.966684 AGTACTATATGGCTCCCTGTAGTT 58.033 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.882623 CAGGACAGGTTTTTCCAGAGC 59.117 52.381 0.00 0.00 39.02 4.09
171 172 9.985318 CAGTCTTTTAAAAGCTTATCTGATCAG 57.015 33.333 20.93 17.07 35.99 2.90
183 184 8.593492 AATCAATTGACCAGTCTTTTAAAAGC 57.407 30.769 20.93 15.92 35.99 3.51
218 219 3.074504 TGTGGACGTAATATGCTCGAC 57.925 47.619 0.00 0.00 0.00 4.20
247 248 1.971149 AGAGATGGGAATGTGGGTGA 58.029 50.000 0.00 0.00 0.00 4.02
268 269 6.034363 CAGTGAGTCTTTATGTTCTCATGTCG 59.966 42.308 0.00 0.00 38.80 4.35
385 386 6.913873 ATCCAGCATAATGAATTGCAAAAC 57.086 33.333 1.71 0.80 41.35 2.43
413 414 7.064728 ACGATAGAGAAATTTTGTGAGGCTAAC 59.935 37.037 0.00 0.00 41.38 2.34
513 514 2.954684 AAAGATCGCTGGTCGCCCA 61.955 57.895 0.00 0.00 38.87 5.36
534 535 1.146263 ATTTCCATCCGGGTCTCGC 59.854 57.895 0.00 0.00 38.11 5.03
573 574 5.188555 TGGAAATCTGACTCTCACTTGCTAT 59.811 40.000 0.00 0.00 0.00 2.97
607 608 2.371841 ACAAGCACCATTCTGTGAGGTA 59.628 45.455 0.00 0.00 38.55 3.08
836 837 9.903682 CATAATGTGGAAGGAATTCACAATATC 57.096 33.333 7.93 0.00 43.38 1.63
872 873 1.665679 ACGTAGCGCATTCAAATCTGG 59.334 47.619 11.47 0.00 0.00 3.86
965 967 4.686091 CAGTTCAGAACATACAGCTTTCGA 59.314 41.667 15.85 0.00 0.00 3.71
1058 1060 0.976073 TTCCTCTAGGGGCCTGTTCG 60.976 60.000 2.72 0.00 35.41 3.95
1065 1067 1.540580 GCGTTACATTCCTCTAGGGGC 60.541 57.143 2.72 0.00 35.41 5.80
1582 1593 4.424566 GGCGCCTTCACGGACGTA 62.425 66.667 22.15 0.00 35.59 3.57
1747 1758 2.597340 CAGGCCATGTCCGGGATT 59.403 61.111 5.01 0.00 0.00 3.01
1758 1769 2.935481 CCTCCAGGTTCCAGGCCA 60.935 66.667 5.01 0.00 0.00 5.36
2266 2289 4.453480 AATGACTGGTCAAGGAAGGAAA 57.547 40.909 7.53 0.00 43.58 3.13
2351 2386 1.227176 CCTTCCCTTACTACGGCGC 60.227 63.158 6.90 0.00 0.00 6.53
2503 2538 0.606944 AGCCAAGACTCGACGAGACT 60.607 55.000 30.56 25.76 36.37 3.24
2551 2586 1.542915 TGCCAGTACTGTACTTCCGAC 59.457 52.381 21.18 6.62 36.76 4.79
2554 2589 2.415625 CGACTGCCAGTACTGTACTTCC 60.416 54.545 21.18 11.65 36.76 3.46
2607 2642 1.500512 CTCCTCCTCGTCGTCGATCC 61.501 65.000 5.00 0.00 45.21 3.36
2611 2646 2.125229 TCCTCCTCCTCGTCGTCG 60.125 66.667 0.00 0.00 38.55 5.12
2614 2659 1.169661 CCATCTCCTCCTCCTCGTCG 61.170 65.000 0.00 0.00 0.00 5.12
2696 2743 2.100991 ACGAATACCGCGTCCGTC 59.899 61.111 4.92 0.00 43.32 4.79
2697 2744 2.202518 CACGAATACCGCGTCCGT 60.203 61.111 4.92 3.97 40.44 4.69
2698 2745 2.100797 TCACGAATACCGCGTCCG 59.899 61.111 4.92 3.29 40.44 4.79
2699 2746 2.219562 CGTCACGAATACCGCGTCC 61.220 63.158 4.92 0.00 40.44 4.79
2710 2757 3.947910 AATTTTAGTCTCCCGTCACGA 57.052 42.857 0.00 0.00 0.00 4.35
2816 2864 2.990479 CTTTCCTCCCCTCACCCG 59.010 66.667 0.00 0.00 0.00 5.28
2818 2866 2.245438 CTCGCTTTCCTCCCCTCACC 62.245 65.000 0.00 0.00 0.00 4.02
2819 2867 1.219393 CTCGCTTTCCTCCCCTCAC 59.781 63.158 0.00 0.00 0.00 3.51
2820 2868 1.229209 ACTCGCTTTCCTCCCCTCA 60.229 57.895 0.00 0.00 0.00 3.86
2821 2869 1.219393 CACTCGCTTTCCTCCCCTC 59.781 63.158 0.00 0.00 0.00 4.30
2822 2870 2.294078 CCACTCGCTTTCCTCCCCT 61.294 63.158 0.00 0.00 0.00 4.79
2916 2964 4.206244 TCCTTTTCCATTTTCCCCTCAA 57.794 40.909 0.00 0.00 0.00 3.02
2917 2965 3.913370 TCCTTTTCCATTTTCCCCTCA 57.087 42.857 0.00 0.00 0.00 3.86
2951 2999 0.874390 CCAAATCAGTCCACCACACG 59.126 55.000 0.00 0.00 0.00 4.49
3088 3136 1.299926 CGCGTAGGCACCCATAGAC 60.300 63.158 8.32 0.00 39.92 2.59
3132 3180 2.203153 CTATCCCGGCCCGTTTGG 60.203 66.667 0.85 0.00 37.09 3.28
3133 3181 1.078001 AACTATCCCGGCCCGTTTG 60.078 57.895 0.85 0.00 0.00 2.93
3134 3182 1.078001 CAACTATCCCGGCCCGTTT 60.078 57.895 0.85 0.00 0.00 3.60
3135 3183 2.587889 CAACTATCCCGGCCCGTT 59.412 61.111 0.85 0.00 0.00 4.44
3136 3184 3.476419 CCAACTATCCCGGCCCGT 61.476 66.667 0.85 0.00 0.00 5.28
3137 3185 4.250305 CCCAACTATCCCGGCCCG 62.250 72.222 0.00 0.00 0.00 6.13
3138 3186 4.581093 GCCCAACTATCCCGGCCC 62.581 72.222 0.00 0.00 35.23 5.80
3140 3188 4.929707 CGGCCCAACTATCCCGGC 62.930 72.222 0.00 0.00 40.85 6.13
3142 3190 4.929707 GCCGGCCCAACTATCCCG 62.930 72.222 18.11 0.00 40.39 5.14
3143 3191 4.581093 GGCCGGCCCAACTATCCC 62.581 72.222 36.64 5.01 0.00 3.85
3184 3232 4.097863 GCCCGTTTAGCACGTGCC 62.098 66.667 35.51 19.74 45.60 5.01
3228 3276 4.096003 TTCAGGCCTAGGCACGGC 62.096 66.667 34.09 17.37 46.83 5.68
3229 3277 2.187946 CTTCAGGCCTAGGCACGG 59.812 66.667 34.09 22.65 44.11 4.94
3230 3278 2.187946 CCTTCAGGCCTAGGCACG 59.812 66.667 34.09 23.65 44.11 5.34
3231 3279 2.592308 CCCTTCAGGCCTAGGCAC 59.408 66.667 34.09 22.83 44.11 5.01
3269 3317 0.524414 AAAAGTTAATCGGGCCGTGC 59.476 50.000 27.32 12.25 0.00 5.34
3294 3342 9.084533 GTTGGCCCATATTAGGATACATAAAAA 57.915 33.333 0.00 0.00 41.41 1.94
3295 3343 8.228206 TGTTGGCCCATATTAGGATACATAAAA 58.772 33.333 0.00 0.00 41.41 1.52
3296 3344 7.760607 TGTTGGCCCATATTAGGATACATAAA 58.239 34.615 0.00 0.00 41.41 1.40
3297 3345 7.238723 TCTGTTGGCCCATATTAGGATACATAA 59.761 37.037 0.00 0.00 41.41 1.90
3298 3346 6.733334 TCTGTTGGCCCATATTAGGATACATA 59.267 38.462 0.00 0.00 41.41 2.29
3299 3347 5.551583 TCTGTTGGCCCATATTAGGATACAT 59.448 40.000 0.00 0.00 41.41 2.29
3300 3348 4.910913 TCTGTTGGCCCATATTAGGATACA 59.089 41.667 0.00 0.00 41.41 2.29
3301 3349 5.499004 TCTGTTGGCCCATATTAGGATAC 57.501 43.478 0.00 0.00 0.00 2.24
3302 3350 7.822749 TTATCTGTTGGCCCATATTAGGATA 57.177 36.000 0.00 0.00 0.00 2.59
3303 3351 6.718593 TTATCTGTTGGCCCATATTAGGAT 57.281 37.500 0.00 0.00 0.00 3.24
3304 3352 6.523035 TTTATCTGTTGGCCCATATTAGGA 57.477 37.500 0.00 0.00 0.00 2.94
3305 3353 7.595819 TTTTTATCTGTTGGCCCATATTAGG 57.404 36.000 0.00 0.00 0.00 2.69
3307 3355 9.308000 CCTATTTTTATCTGTTGGCCCATATTA 57.692 33.333 0.00 0.00 0.00 0.98
3308 3356 7.256296 GCCTATTTTTATCTGTTGGCCCATATT 60.256 37.037 0.00 0.00 33.66 1.28
3309 3357 6.211384 GCCTATTTTTATCTGTTGGCCCATAT 59.789 38.462 0.00 0.00 33.66 1.78
3310 3358 5.538433 GCCTATTTTTATCTGTTGGCCCATA 59.462 40.000 0.00 0.00 33.66 2.74
3311 3359 4.344968 GCCTATTTTTATCTGTTGGCCCAT 59.655 41.667 0.00 0.00 33.66 4.00
3312 3360 3.704061 GCCTATTTTTATCTGTTGGCCCA 59.296 43.478 0.00 0.00 33.66 5.36
3313 3361 3.960755 AGCCTATTTTTATCTGTTGGCCC 59.039 43.478 0.00 0.00 39.90 5.80
3314 3362 5.592688 TGTAGCCTATTTTTATCTGTTGGCC 59.407 40.000 0.00 0.00 39.90 5.36
3315 3363 6.693315 TGTAGCCTATTTTTATCTGTTGGC 57.307 37.500 0.00 0.00 39.40 4.52
3316 3364 9.353999 GTTTTGTAGCCTATTTTTATCTGTTGG 57.646 33.333 0.00 0.00 0.00 3.77
3317 3365 9.061610 CGTTTTGTAGCCTATTTTTATCTGTTG 57.938 33.333 0.00 0.00 0.00 3.33
3318 3366 7.753580 GCGTTTTGTAGCCTATTTTTATCTGTT 59.246 33.333 0.00 0.00 0.00 3.16
3319 3367 7.120726 AGCGTTTTGTAGCCTATTTTTATCTGT 59.879 33.333 0.00 0.00 0.00 3.41
3320 3368 7.472543 AGCGTTTTGTAGCCTATTTTTATCTG 58.527 34.615 0.00 0.00 0.00 2.90
3321 3369 7.625828 AGCGTTTTGTAGCCTATTTTTATCT 57.374 32.000 0.00 0.00 0.00 1.98
3322 3370 9.777575 TTTAGCGTTTTGTAGCCTATTTTTATC 57.222 29.630 0.00 0.00 0.00 1.75
3324 3372 9.562583 CATTTAGCGTTTTGTAGCCTATTTTTA 57.437 29.630 0.00 0.00 0.00 1.52
3325 3373 7.062956 GCATTTAGCGTTTTGTAGCCTATTTTT 59.937 33.333 0.00 0.00 0.00 1.94
3326 3374 6.530181 GCATTTAGCGTTTTGTAGCCTATTTT 59.470 34.615 0.00 0.00 0.00 1.82
3327 3375 6.033966 GCATTTAGCGTTTTGTAGCCTATTT 58.966 36.000 0.00 0.00 0.00 1.40
3328 3376 5.578776 GCATTTAGCGTTTTGTAGCCTATT 58.421 37.500 0.00 0.00 0.00 1.73
3329 3377 5.169836 GCATTTAGCGTTTTGTAGCCTAT 57.830 39.130 0.00 0.00 0.00 2.57
3330 3378 4.609691 GCATTTAGCGTTTTGTAGCCTA 57.390 40.909 0.00 0.00 0.00 3.93
3331 3379 3.487563 GCATTTAGCGTTTTGTAGCCT 57.512 42.857 0.00 0.00 0.00 4.58
3343 3391 2.096218 CCTCCTATTTCGCGCATTTAGC 60.096 50.000 8.75 0.00 40.87 3.09
3344 3392 3.131396 ACCTCCTATTTCGCGCATTTAG 58.869 45.455 8.75 2.40 0.00 1.85
3345 3393 3.188159 ACCTCCTATTTCGCGCATTTA 57.812 42.857 8.75 0.00 0.00 1.40
3346 3394 2.038387 ACCTCCTATTTCGCGCATTT 57.962 45.000 8.75 0.00 0.00 2.32
3347 3395 2.364324 TCTACCTCCTATTTCGCGCATT 59.636 45.455 8.75 0.00 0.00 3.56
3348 3396 1.961394 TCTACCTCCTATTTCGCGCAT 59.039 47.619 8.75 0.00 0.00 4.73
3349 3397 1.395635 TCTACCTCCTATTTCGCGCA 58.604 50.000 8.75 0.00 0.00 6.09
3350 3398 2.726832 ATCTACCTCCTATTTCGCGC 57.273 50.000 0.00 0.00 0.00 6.86
3351 3399 5.154932 CACTAATCTACCTCCTATTTCGCG 58.845 45.833 0.00 0.00 0.00 5.87
3352 3400 5.471257 CCACTAATCTACCTCCTATTTCGC 58.529 45.833 0.00 0.00 0.00 4.70
3353 3401 5.567025 GCCCACTAATCTACCTCCTATTTCG 60.567 48.000 0.00 0.00 0.00 3.46
3354 3402 5.544562 AGCCCACTAATCTACCTCCTATTTC 59.455 44.000 0.00 0.00 0.00 2.17
3355 3403 5.477913 AGCCCACTAATCTACCTCCTATTT 58.522 41.667 0.00 0.00 0.00 1.40
3356 3404 5.094569 AGCCCACTAATCTACCTCCTATT 57.905 43.478 0.00 0.00 0.00 1.73
3357 3405 4.768807 AGCCCACTAATCTACCTCCTAT 57.231 45.455 0.00 0.00 0.00 2.57
3358 3406 4.078805 TCAAGCCCACTAATCTACCTCCTA 60.079 45.833 0.00 0.00 0.00 2.94
3359 3407 3.041946 CAAGCCCACTAATCTACCTCCT 58.958 50.000 0.00 0.00 0.00 3.69
3360 3408 3.039011 TCAAGCCCACTAATCTACCTCC 58.961 50.000 0.00 0.00 0.00 4.30
3361 3409 3.491104 CGTCAAGCCCACTAATCTACCTC 60.491 52.174 0.00 0.00 0.00 3.85
3362 3410 2.431057 CGTCAAGCCCACTAATCTACCT 59.569 50.000 0.00 0.00 0.00 3.08
3363 3411 2.167900 ACGTCAAGCCCACTAATCTACC 59.832 50.000 0.00 0.00 0.00 3.18
3364 3412 3.187700 CACGTCAAGCCCACTAATCTAC 58.812 50.000 0.00 0.00 0.00 2.59
3365 3413 2.418197 GCACGTCAAGCCCACTAATCTA 60.418 50.000 0.00 0.00 0.00 1.98
3366 3414 1.676014 GCACGTCAAGCCCACTAATCT 60.676 52.381 0.00 0.00 0.00 2.40
3367 3415 0.727398 GCACGTCAAGCCCACTAATC 59.273 55.000 0.00 0.00 0.00 1.75
3368 3416 0.676782 GGCACGTCAAGCCCACTAAT 60.677 55.000 4.06 0.00 46.50 1.73
3369 3417 1.302192 GGCACGTCAAGCCCACTAA 60.302 57.895 4.06 0.00 46.50 2.24
3370 3418 2.345991 GGCACGTCAAGCCCACTA 59.654 61.111 4.06 0.00 46.50 2.74
3392 3440 3.248446 TATGCTAATCGGGCCGGCC 62.248 63.158 38.57 38.57 0.00 6.13
3393 3441 2.033194 GTATGCTAATCGGGCCGGC 61.033 63.158 27.98 21.18 0.00 6.13
3394 3442 1.736645 CGTATGCTAATCGGGCCGG 60.737 63.158 27.98 11.17 0.00 6.13
3395 3443 1.736645 CCGTATGCTAATCGGGCCG 60.737 63.158 22.51 22.51 40.49 6.13
3396 3444 4.278956 CCGTATGCTAATCGGGCC 57.721 61.111 0.00 0.00 40.49 5.80
3399 3447 1.736645 CGGCCCGTATGCTAATCGG 60.737 63.158 0.00 0.00 43.30 4.18
3400 3448 1.006571 ACGGCCCGTATGCTAATCG 60.007 57.895 7.20 0.00 38.73 3.34
3401 3449 1.566018 GCACGGCCCGTATGCTAATC 61.566 60.000 9.25 0.00 38.32 1.75
3402 3450 1.597027 GCACGGCCCGTATGCTAAT 60.597 57.895 9.25 0.00 38.32 1.73
3403 3451 2.202960 GCACGGCCCGTATGCTAA 60.203 61.111 9.25 0.00 38.32 3.09
3404 3452 4.230002 GGCACGGCCCGTATGCTA 62.230 66.667 9.25 0.00 44.06 3.49
3455 3503 1.657094 CGATTATTATACGGGCCGTGC 59.343 52.381 39.80 16.99 41.39 5.34
3456 3504 2.664568 CACGATTATTATACGGGCCGTG 59.335 50.000 39.80 22.32 41.39 4.94
3457 3505 2.950433 CACGATTATTATACGGGCCGT 58.050 47.619 35.91 35.91 44.35 5.68
3461 3509 4.679662 CCTAGGCACGATTATTATACGGG 58.320 47.826 0.00 0.00 0.00 5.28
3462 3510 4.110482 GCCTAGGCACGATTATTATACGG 58.890 47.826 29.33 0.00 41.49 4.02
3463 3511 3.789756 CGCCTAGGCACGATTATTATACG 59.210 47.826 32.47 7.82 42.06 3.06
3464 3512 4.110482 CCGCCTAGGCACGATTATTATAC 58.890 47.826 32.47 0.00 42.06 1.47
3465 3513 3.131577 CCCGCCTAGGCACGATTATTATA 59.868 47.826 32.47 0.00 42.06 0.98
3466 3514 2.093658 CCCGCCTAGGCACGATTATTAT 60.094 50.000 32.47 0.00 42.06 1.28
3467 3515 1.274167 CCCGCCTAGGCACGATTATTA 59.726 52.381 32.47 0.00 42.06 0.98
3468 3516 0.034896 CCCGCCTAGGCACGATTATT 59.965 55.000 32.47 0.00 42.06 1.40
3469 3517 1.671742 CCCGCCTAGGCACGATTAT 59.328 57.895 32.47 0.00 42.06 1.28
3470 3518 3.134879 CCCGCCTAGGCACGATTA 58.865 61.111 32.47 0.00 42.06 1.75
3496 3544 0.179048 CATCCTAATCGTGCCTGGCA 60.179 55.000 19.30 19.30 35.60 4.92
3497 3545 0.886490 CCATCCTAATCGTGCCTGGC 60.886 60.000 12.87 12.87 0.00 4.85
3498 3546 0.250467 CCCATCCTAATCGTGCCTGG 60.250 60.000 0.00 0.00 0.00 4.45
3499 3547 0.886490 GCCCATCCTAATCGTGCCTG 60.886 60.000 0.00 0.00 0.00 4.85
3500 3548 1.451936 GCCCATCCTAATCGTGCCT 59.548 57.895 0.00 0.00 0.00 4.75
3501 3549 1.600916 GGCCCATCCTAATCGTGCC 60.601 63.158 0.00 0.00 0.00 5.01
3502 3550 1.961277 CGGCCCATCCTAATCGTGC 60.961 63.158 0.00 0.00 0.00 5.34
3503 3551 0.880278 CACGGCCCATCCTAATCGTG 60.880 60.000 0.00 0.00 41.09 4.35
3504 3552 1.445942 CACGGCCCATCCTAATCGT 59.554 57.895 0.00 0.00 0.00 3.73
3505 3553 1.961277 GCACGGCCCATCCTAATCG 60.961 63.158 0.00 0.00 0.00 3.34
3506 3554 1.600916 GGCACGGCCCATCCTAATC 60.601 63.158 0.00 0.00 44.06 1.75
3507 3555 2.515901 GGCACGGCCCATCCTAAT 59.484 61.111 0.00 0.00 44.06 1.73
3542 3590 1.880027 GATTATAGCTGGCCAAACGGG 59.120 52.381 7.01 0.00 40.85 5.28
3543 3591 1.531149 CGATTATAGCTGGCCAAACGG 59.469 52.381 7.01 0.00 0.00 4.44
3544 3592 1.069906 GCGATTATAGCTGGCCAAACG 60.070 52.381 7.01 2.03 0.00 3.60
3545 3593 1.266989 GGCGATTATAGCTGGCCAAAC 59.733 52.381 7.01 1.16 43.23 2.93
3546 3594 1.604604 GGCGATTATAGCTGGCCAAA 58.395 50.000 7.01 0.00 43.23 3.28
3547 3595 3.322514 GGCGATTATAGCTGGCCAA 57.677 52.632 7.01 0.00 43.23 4.52
3549 3597 1.604604 TTTGGCGATTATAGCTGGCC 58.395 50.000 0.00 0.00 44.00 5.36
3550 3598 2.618709 AGTTTTGGCGATTATAGCTGGC 59.381 45.455 0.00 0.00 34.52 4.85
3551 3599 5.050091 CACTAGTTTTGGCGATTATAGCTGG 60.050 44.000 0.00 0.00 34.52 4.85
3552 3600 5.559035 GCACTAGTTTTGGCGATTATAGCTG 60.559 44.000 0.00 0.00 34.52 4.24
3553 3601 4.511826 GCACTAGTTTTGGCGATTATAGCT 59.488 41.667 0.00 0.00 34.52 3.32
3554 3602 4.319549 GGCACTAGTTTTGGCGATTATAGC 60.320 45.833 0.00 0.00 0.00 2.97
3555 3603 5.057149 AGGCACTAGTTTTGGCGATTATAG 58.943 41.667 0.00 0.00 44.08 1.31
3556 3604 5.031066 AGGCACTAGTTTTGGCGATTATA 57.969 39.130 0.00 0.00 44.08 0.98
3557 3605 3.877508 GAGGCACTAGTTTTGGCGATTAT 59.122 43.478 0.00 0.00 41.55 1.28
3558 3606 3.267483 GAGGCACTAGTTTTGGCGATTA 58.733 45.455 0.00 0.00 41.55 1.75
3559 3607 2.084546 GAGGCACTAGTTTTGGCGATT 58.915 47.619 0.00 0.00 41.55 3.34
3560 3608 1.679032 GGAGGCACTAGTTTTGGCGAT 60.679 52.381 0.00 0.00 41.55 4.58
3561 3609 0.321298 GGAGGCACTAGTTTTGGCGA 60.321 55.000 0.00 0.00 41.55 5.54
3562 3610 1.635663 CGGAGGCACTAGTTTTGGCG 61.636 60.000 0.00 0.00 41.55 5.69
3563 3611 0.605589 ACGGAGGCACTAGTTTTGGC 60.606 55.000 0.00 0.00 41.55 4.52
3564 3612 1.439679 GACGGAGGCACTAGTTTTGG 58.560 55.000 0.00 0.00 41.55 3.28
3565 3613 1.439679 GGACGGAGGCACTAGTTTTG 58.560 55.000 0.00 0.00 41.55 2.44
3566 3614 0.323957 GGGACGGAGGCACTAGTTTT 59.676 55.000 0.00 0.00 41.55 2.43
3567 3615 0.834687 TGGGACGGAGGCACTAGTTT 60.835 55.000 0.00 0.00 41.55 2.66
3568 3616 0.617820 ATGGGACGGAGGCACTAGTT 60.618 55.000 0.00 0.00 41.55 2.24
3569 3617 0.260816 TATGGGACGGAGGCACTAGT 59.739 55.000 0.00 0.00 41.55 2.57
3570 3618 1.410004 TTATGGGACGGAGGCACTAG 58.590 55.000 0.00 0.00 41.55 2.57
3571 3619 2.097110 ATTATGGGACGGAGGCACTA 57.903 50.000 0.00 0.00 41.55 2.74
3573 3621 3.514309 AGTATATTATGGGACGGAGGCAC 59.486 47.826 0.00 0.00 0.00 5.01
3574 3622 3.786553 AGTATATTATGGGACGGAGGCA 58.213 45.455 0.00 0.00 0.00 4.75
3575 3623 4.820894 AAGTATATTATGGGACGGAGGC 57.179 45.455 0.00 0.00 0.00 4.70
3602 3650 8.980481 AGCCATATAGTACTAAAAATGCTGTT 57.020 30.769 6.70 0.00 0.00 3.16
3603 3651 7.661847 GGAGCCATATAGTACTAAAAATGCTGT 59.338 37.037 16.90 6.21 0.00 4.40
3604 3652 7.119846 GGGAGCCATATAGTACTAAAAATGCTG 59.880 40.741 16.90 7.86 0.00 4.41
3605 3653 7.017651 AGGGAGCCATATAGTACTAAAAATGCT 59.982 37.037 6.70 11.13 0.00 3.79
3606 3654 7.119846 CAGGGAGCCATATAGTACTAAAAATGC 59.880 40.741 6.70 6.67 0.00 3.56
3607 3655 8.157476 ACAGGGAGCCATATAGTACTAAAAATG 58.843 37.037 6.70 10.65 0.00 2.32
3608 3656 8.276453 ACAGGGAGCCATATAGTACTAAAAAT 57.724 34.615 6.70 0.00 0.00 1.82
3609 3657 7.685849 ACAGGGAGCCATATAGTACTAAAAA 57.314 36.000 6.70 0.00 0.00 1.94
3610 3658 8.008922 ACTACAGGGAGCCATATAGTACTAAAA 58.991 37.037 6.70 0.00 0.00 1.52
3611 3659 7.533083 ACTACAGGGAGCCATATAGTACTAAA 58.467 38.462 6.70 0.00 0.00 1.85
3612 3660 7.100068 ACTACAGGGAGCCATATAGTACTAA 57.900 40.000 6.70 0.00 0.00 2.24
3613 3661 6.715350 ACTACAGGGAGCCATATAGTACTA 57.285 41.667 4.77 4.77 0.00 1.82
3614 3662 5.602291 ACTACAGGGAGCCATATAGTACT 57.398 43.478 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.