Multiple sequence alignment - TraesCS5A01G073800

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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 TraesCS5A01G073800 chr5A 100.000 1256 0 0 1 1256 86184272 86183017 0.000000e+00 2320
1 TraesCS5A01G073800 chr5A 100.000 1047 0 0 2423 3469 86181850 86180804 0.000000e+00 1934
2 TraesCS5A01G073800 chr5D 89.577 1276 51 30 1 1256 92466587 92465374 0.000000e+00 1544
3 TraesCS5A01G073800 chr5D 94.654 636 32 2 2442 3077 92464607 92463974 0.000000e+00 985
4 TraesCS5A01G073800 chr5D 85.938 128 8 5 3184 3301 92463913 92463786 1.010000e-25 128
5 TraesCS5A01G073800 chr5B 91.170 940 46 21 344 1256 98521173 98520244 0.000000e+00 1242
6 TraesCS5A01G073800 chr5B 89.432 511 32 13 2423 2917 98519240 98518736 2.940000e-175 625
7 TraesCS5A01G073800 chr5B 91.126 462 23 7 1 456 98521636 98521187 8.230000e-171 610
8 TraesCS5A01G073800 chr7A 91.234 308 27 0 2423 2730 647934092 647933785 1.490000e-113 420
9 TraesCS5A01G073800 chr7A 93.962 265 16 0 992 1256 647307622 647307358 5.390000e-108 401
10 TraesCS5A01G073800 chr7A 85.242 393 47 10 2423 2808 647315410 647315022 9.020000e-106 394
11 TraesCS5A01G073800 chr7D 94.677 263 14 0 992 1254 562149195 562148933 3.220000e-110 409
12 TraesCS5A01G073800 chr7D 90.789 304 28 0 2427 2730 562425698 562426001 1.160000e-109 407
13 TraesCS5A01G073800 chr7D 82.305 486 69 17 2423 2904 562148533 562148061 4.170000e-109 405
14 TraesCS5A01G073800 chr7D 89.841 315 31 1 2424 2737 562389873 562390187 1.500000e-108 403
15 TraesCS5A01G073800 chr7D 90.236 297 25 4 962 1256 562389248 562389542 5.430000e-103 385
16 TraesCS5A01G073800 chrUn 94.297 263 15 0 994 1256 20430135 20430397 1.500000e-108 403
17 TraesCS5A01G073800 chr6B 93.680 269 17 0 986 1254 92532742 92532474 1.500000e-108 403
18 TraesCS5A01G073800 chr6A 93.985 266 16 0 986 1251 55709393 55709658 1.500000e-108 403
19 TraesCS5A01G073800 chr7B 90.698 301 25 2 2423 2720 612006461 612006161 6.980000e-107 398
20 TraesCS5A01G073800 chr7B 87.952 332 33 5 2423 2749 612255566 612255237 5.430000e-103 385
21 TraesCS5A01G073800 chr7B 87.059 340 36 7 919 1254 611742441 611742106 9.090000e-101 377


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 TraesCS5A01G073800 chr5A 86180804 86184272 3468 True 2127.000000 2320 100.000000 1 3469 2 chr5A.!!$R1 3468
1 TraesCS5A01G073800 chr5D 92463786 92466587 2801 True 885.666667 1544 90.056333 1 3301 3 chr5D.!!$R1 3300
2 TraesCS5A01G073800 chr5B 98518736 98521636 2900 True 825.666667 1242 90.576000 1 2917 3 chr5B.!!$R1 2916
3 TraesCS5A01G073800 chr7D 562148061 562149195 1134 True 407.000000 409 88.491000 992 2904 2 chr7D.!!$R1 1912
4 TraesCS5A01G073800 chr7D 562389248 562390187 939 False 394.000000 403 90.038500 962 2737 2 chr7D.!!$F2 1775

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
517 653 0.179124 CTAGGTTCCTGCTGAGTCGC 60.179 60.0 1.12 0.77 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2900 3.06638 CACATTGTCGATGGTGTCTGAA 58.934 45.455 5.04 0.0 40.21 3.02 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
40 41 0.683504 TAGCCTCACGGGACTCTTCC 60.684 60.000 0.00 0.00 41.95 3.46
55 56 1.934480 TCTTCCCCCTTTAAATCCCCC 59.066 52.381 0.00 0.00 0.00 5.40
104 105 2.543067 AATCCTCCCTGCCAAGCGAC 62.543 60.000 0.00 0.00 0.00 5.19
140 141 0.815615 ATCGAATCGAAGCCAAGGCC 60.816 55.000 10.12 0.00 39.99 5.19
147 148 2.360475 AAGCCAAGGCCTTCTCGC 60.360 61.111 17.29 17.32 43.17 5.03
181 185 1.134694 GTGAATTTCAGACCGCGCC 59.865 57.895 0.00 0.00 0.00 6.53
182 186 2.038269 TGAATTTCAGACCGCGCCC 61.038 57.895 0.00 0.00 0.00 6.13
183 187 2.750237 AATTTCAGACCGCGCCCC 60.750 61.111 0.00 0.00 0.00 5.80
184 188 3.561120 AATTTCAGACCGCGCCCCA 62.561 57.895 0.00 0.00 0.00 4.96
212 216 4.619863 GCCCCTCGCTATTATCGTTGATTA 60.620 45.833 0.00 0.00 0.00 1.75
213 217 5.661458 CCCCTCGCTATTATCGTTGATTAT 58.339 41.667 0.00 0.00 0.00 1.28
214 218 5.520288 CCCCTCGCTATTATCGTTGATTATG 59.480 44.000 0.00 0.00 0.00 1.90
273 282 4.891992 TCCCTCTCGATTTGGATTATCC 57.108 45.455 3.91 3.91 36.96 2.59
298 307 3.034635 AGATCTGCCGATTAGAGGTGTT 58.965 45.455 0.00 0.00 0.00 3.32
299 308 2.961526 TCTGCCGATTAGAGGTGTTC 57.038 50.000 0.00 0.00 0.00 3.18
300 309 2.457598 TCTGCCGATTAGAGGTGTTCT 58.542 47.619 0.00 0.00 40.06 3.01
301 310 3.628008 TCTGCCGATTAGAGGTGTTCTA 58.372 45.455 0.00 0.00 37.36 2.10
302 311 3.632604 TCTGCCGATTAGAGGTGTTCTAG 59.367 47.826 0.00 0.00 39.50 2.43
304 313 3.767673 TGCCGATTAGAGGTGTTCTAGTT 59.232 43.478 0.00 0.00 39.50 2.24
305 314 4.113354 GCCGATTAGAGGTGTTCTAGTTG 58.887 47.826 0.00 0.00 39.50 3.16
306 315 4.142227 GCCGATTAGAGGTGTTCTAGTTGA 60.142 45.833 0.00 0.00 39.50 3.18
333 342 3.073678 TCGTTCCGTGTTAGCAGTACTA 58.926 45.455 0.00 0.00 0.00 1.82
348 483 4.084433 GCAGTACTAGTTCGAGACGATAGG 60.084 50.000 0.00 0.00 43.77 2.57
394 529 0.442699 GCTCCGTTGTCGTGAAATCC 59.557 55.000 0.00 0.00 35.01 3.01
418 553 3.646162 TCACGGTTATGCCTGGATTATCT 59.354 43.478 0.00 0.00 34.25 1.98
440 576 3.181475 TGGTAGATCTGCCGATTTGAGAC 60.181 47.826 22.95 0.60 38.25 3.36
483 619 2.078849 TGTTCATCTAGGCGTGTGTG 57.921 50.000 0.00 0.00 0.00 3.82
500 636 3.006940 GTGTGGTTGATTGATTCCGCTA 58.993 45.455 0.00 0.00 0.00 4.26
517 653 0.179124 CTAGGTTCCTGCTGAGTCGC 60.179 60.000 1.12 0.77 0.00 5.19
531 667 3.290776 GTCGCTCAGACTTTGTGGT 57.709 52.632 0.00 0.00 46.13 4.16
588 724 5.241728 TGATCTGTGAACGGATATACCTGAG 59.758 44.000 4.75 0.00 41.75 3.35
591 727 5.006153 TGTGAACGGATATACCTGAGTTG 57.994 43.478 0.00 0.00 36.31 3.16
595 731 5.303333 TGAACGGATATACCTGAGTTGCATA 59.697 40.000 0.00 0.00 36.31 3.14
606 743 1.200020 GAGTTGCATACTTGGGCACAC 59.800 52.381 0.00 0.00 40.23 3.82
613 750 3.071023 GCATACTTGGGCACACCTAGATA 59.929 47.826 0.00 0.00 43.79 1.98
698 835 1.598130 GTGCACCGGTTCTGCTCTT 60.598 57.895 2.97 0.00 35.53 2.85
723 860 6.064846 AGAGTCAATTGTGTTTGCTTACAG 57.935 37.500 5.13 0.00 0.00 2.74
774 912 7.967854 TGTATCTTGTTGTGTCAAAACTTGAAG 59.032 33.333 7.41 3.34 42.15 3.02
796 940 3.557595 GGTATCTGTACTTGTGCATCAGC 59.442 47.826 0.00 0.00 42.57 4.26
911 1074 5.152623 ACAATTTCGTCTCTCTTGGATCA 57.847 39.130 0.00 0.00 0.00 2.92
921 1084 2.172082 TCTCTTGGATCATGGCCTTCTG 59.828 50.000 3.32 0.00 0.00 3.02
970 1133 6.258727 CAGTTTCATGATTACGAGTGCCTTAT 59.741 38.462 0.00 0.00 0.00 1.73
1167 1330 3.692406 GAGGACGGTCGCACCCTT 61.692 66.667 1.43 0.00 33.75 3.95
2557 2948 0.419459 AGATCCAGGACAAGGAGGGT 59.581 55.000 0.00 0.00 38.83 4.34
2725 3116 1.804372 GCTTATGTCTCTGGGCTCACG 60.804 57.143 0.00 0.00 0.00 4.35
2740 3131 2.470821 CTCACGAGTCGGTTGTCTTTT 58.529 47.619 18.30 0.00 0.00 2.27
2746 3137 3.552699 CGAGTCGGTTGTCTTTTTGTGTA 59.447 43.478 4.10 0.00 0.00 2.90
2752 3143 3.624410 GGTTGTCTTTTTGTGTACTCCGT 59.376 43.478 0.00 0.00 0.00 4.69
2755 3146 4.255301 TGTCTTTTTGTGTACTCCGTTGT 58.745 39.130 0.00 0.00 0.00 3.32
2783 3175 1.957562 CGTGTCCTCGTCTGGTCTT 59.042 57.895 0.00 0.00 0.00 3.01
2803 3195 2.634600 TGTTCTTTGTTGCTACCGTGT 58.365 42.857 0.00 0.00 0.00 4.49
2820 3212 3.427909 CCGTGTTGTGGTCTAGCGTTATA 60.428 47.826 0.00 0.00 0.00 0.98
2826 3226 3.005472 TGTGGTCTAGCGTTATATCTGGC 59.995 47.826 0.00 0.00 0.00 4.85
2829 3229 3.246619 GTCTAGCGTTATATCTGGCTGC 58.753 50.000 0.00 0.00 36.97 5.25
2841 3242 1.343142 TCTGGCTGCGTCTGAACTTTA 59.657 47.619 0.00 0.00 0.00 1.85
2848 3249 2.480037 TGCGTCTGAACTTTATGCTGTG 59.520 45.455 0.00 0.00 0.00 3.66
2849 3250 2.726066 GCGTCTGAACTTTATGCTGTGC 60.726 50.000 0.00 0.00 0.00 4.57
2945 3352 1.202710 TGCAGTTCCTAAACCTTCGCA 60.203 47.619 0.00 0.00 35.92 5.10
2960 3367 3.550275 CCTTCGCAATTGCATTTGATCTG 59.450 43.478 28.77 10.19 42.21 2.90
2967 3374 4.707030 ATTGCATTTGATCTGCTTTCGA 57.293 36.364 6.93 0.00 40.34 3.71
2983 3390 9.289303 TCTGCTTTCGATGCTTTATTTTAAATC 57.711 29.630 11.32 0.00 0.00 2.17
3077 3484 0.037326 CTCAGCTTCAACGGGTGCTA 60.037 55.000 0.00 0.00 34.10 3.49
3079 3486 1.202710 TCAGCTTCAACGGGTGCTAAA 60.203 47.619 0.00 0.00 34.10 1.85
3080 3487 1.606668 CAGCTTCAACGGGTGCTAAAA 59.393 47.619 0.00 0.00 34.10 1.52
3081 3488 1.880027 AGCTTCAACGGGTGCTAAAAG 59.120 47.619 0.00 0.00 33.64 2.27
3082 3489 1.068541 GCTTCAACGGGTGCTAAAAGG 60.069 52.381 0.00 0.00 0.00 3.11
3083 3490 2.500229 CTTCAACGGGTGCTAAAAGGA 58.500 47.619 0.00 0.00 0.00 3.36
3084 3491 2.178912 TCAACGGGTGCTAAAAGGAG 57.821 50.000 0.00 0.00 0.00 3.69
3085 3492 1.695242 TCAACGGGTGCTAAAAGGAGA 59.305 47.619 0.00 0.00 0.00 3.71
3086 3493 1.804748 CAACGGGTGCTAAAAGGAGAC 59.195 52.381 0.00 0.00 0.00 3.36
3087 3494 1.053424 ACGGGTGCTAAAAGGAGACA 58.947 50.000 0.00 0.00 0.00 3.41
3088 3495 1.418637 ACGGGTGCTAAAAGGAGACAA 59.581 47.619 0.00 0.00 0.00 3.18
3089 3496 1.804748 CGGGTGCTAAAAGGAGACAAC 59.195 52.381 0.00 0.00 0.00 3.32
3091 3498 2.488347 GGGTGCTAAAAGGAGACAACCA 60.488 50.000 0.00 0.00 38.04 3.67
3092 3499 3.421844 GGTGCTAAAAGGAGACAACCAT 58.578 45.455 0.00 0.00 0.00 3.55
3093 3500 3.191371 GGTGCTAAAAGGAGACAACCATG 59.809 47.826 0.00 0.00 0.00 3.66
3094 3501 3.821033 GTGCTAAAAGGAGACAACCATGT 59.179 43.478 0.00 0.00 44.25 3.21
3107 3514 5.756195 ACAACCATGTCCGATATCATTTG 57.244 39.130 3.12 0.00 33.41 2.32
3108 3515 4.036734 ACAACCATGTCCGATATCATTTGC 59.963 41.667 3.12 0.00 33.41 3.68
3109 3516 3.819368 ACCATGTCCGATATCATTTGCA 58.181 40.909 3.12 0.00 0.00 4.08
3110 3517 4.206375 ACCATGTCCGATATCATTTGCAA 58.794 39.130 3.12 0.00 0.00 4.08
3111 3518 4.036734 ACCATGTCCGATATCATTTGCAAC 59.963 41.667 0.00 0.00 0.00 4.17
3112 3519 4.276678 CCATGTCCGATATCATTTGCAACT 59.723 41.667 0.00 0.00 0.00 3.16
3113 3520 5.469760 CCATGTCCGATATCATTTGCAACTA 59.530 40.000 0.00 0.00 0.00 2.24
3114 3521 6.017192 CCATGTCCGATATCATTTGCAACTAA 60.017 38.462 0.00 0.00 0.00 2.24
3115 3522 6.993786 TGTCCGATATCATTTGCAACTAAA 57.006 33.333 0.00 0.00 0.00 1.85
3116 3523 7.015226 TGTCCGATATCATTTGCAACTAAAG 57.985 36.000 0.00 0.00 0.00 1.85
3117 3524 5.909610 GTCCGATATCATTTGCAACTAAAGC 59.090 40.000 0.00 0.00 0.00 3.51
3118 3525 5.008613 TCCGATATCATTTGCAACTAAAGCC 59.991 40.000 0.00 0.00 0.00 4.35
3119 3526 5.221028 CCGATATCATTTGCAACTAAAGCCA 60.221 40.000 0.00 0.00 0.00 4.75
3120 3527 6.264832 CGATATCATTTGCAACTAAAGCCAA 58.735 36.000 0.00 0.00 0.00 4.52
3121 3528 6.197096 CGATATCATTTGCAACTAAAGCCAAC 59.803 38.462 0.00 0.00 0.00 3.77
3122 3529 4.662468 TCATTTGCAACTAAAGCCAACA 57.338 36.364 0.00 0.00 0.00 3.33
3123 3530 5.016051 TCATTTGCAACTAAAGCCAACAA 57.984 34.783 0.00 0.00 0.00 2.83
3124 3531 5.423015 TCATTTGCAACTAAAGCCAACAAA 58.577 33.333 0.00 0.00 0.00 2.83
3125 3532 6.054295 TCATTTGCAACTAAAGCCAACAAAT 58.946 32.000 0.00 0.00 36.87 2.32
3126 3533 5.982465 TTTGCAACTAAAGCCAACAAATC 57.018 34.783 0.00 0.00 0.00 2.17
3127 3534 3.637432 TGCAACTAAAGCCAACAAATCG 58.363 40.909 0.00 0.00 0.00 3.34
3128 3535 2.986479 GCAACTAAAGCCAACAAATCGG 59.014 45.455 0.00 0.00 0.00 4.18
3129 3536 3.305064 GCAACTAAAGCCAACAAATCGGA 60.305 43.478 0.00 0.00 0.00 4.55
3130 3537 4.475944 CAACTAAAGCCAACAAATCGGAG 58.524 43.478 0.00 0.00 0.00 4.63
3131 3538 2.488153 ACTAAAGCCAACAAATCGGAGC 59.512 45.455 0.00 0.00 0.00 4.70
3132 3539 1.620822 AAAGCCAACAAATCGGAGCT 58.379 45.000 0.00 0.00 0.00 4.09
3133 3540 1.168714 AAGCCAACAAATCGGAGCTC 58.831 50.000 4.71 4.71 0.00 4.09
3134 3541 0.036732 AGCCAACAAATCGGAGCTCA 59.963 50.000 17.19 0.00 0.00 4.26
3135 3542 0.449388 GCCAACAAATCGGAGCTCAG 59.551 55.000 17.19 12.42 0.00 3.35
3136 3543 1.945819 GCCAACAAATCGGAGCTCAGA 60.946 52.381 19.05 19.05 0.00 3.27
3137 3544 2.005451 CCAACAAATCGGAGCTCAGAG 58.995 52.381 21.13 10.80 0.00 3.35
3138 3545 1.396301 CAACAAATCGGAGCTCAGAGC 59.604 52.381 21.13 15.25 42.84 4.09
3148 3555 2.157421 GCTCAGAGCTTGTGAACCG 58.843 57.895 15.78 0.00 38.45 4.44
3149 3556 0.319900 GCTCAGAGCTTGTGAACCGA 60.320 55.000 15.78 0.00 38.45 4.69
3150 3557 1.707632 CTCAGAGCTTGTGAACCGAG 58.292 55.000 0.00 0.00 0.00 4.63
3151 3558 0.318441 TCAGAGCTTGTGAACCGAGG 59.682 55.000 0.00 0.00 0.00 4.63
3152 3559 0.318441 CAGAGCTTGTGAACCGAGGA 59.682 55.000 0.00 0.00 0.00 3.71
3165 3572 3.339713 ACCGAGGAATCTACCCCATTA 57.660 47.619 0.00 0.00 0.00 1.90
3166 3573 3.240302 ACCGAGGAATCTACCCCATTAG 58.760 50.000 0.00 0.00 0.00 1.73
3168 3575 3.646637 CCGAGGAATCTACCCCATTAGTT 59.353 47.826 0.00 0.00 0.00 2.24
3170 3577 5.397559 CCGAGGAATCTACCCCATTAGTTTT 60.398 44.000 0.00 0.00 0.00 2.43
3171 3578 5.527582 CGAGGAATCTACCCCATTAGTTTTG 59.472 44.000 0.00 0.00 0.00 2.44
3173 3580 6.800890 AGGAATCTACCCCATTAGTTTTGTT 58.199 36.000 0.00 0.00 0.00 2.83
3174 3581 7.935405 AGGAATCTACCCCATTAGTTTTGTTA 58.065 34.615 0.00 0.00 0.00 2.41
3175 3582 8.566109 AGGAATCTACCCCATTAGTTTTGTTAT 58.434 33.333 0.00 0.00 0.00 1.89
3176 3583 9.197306 GGAATCTACCCCATTAGTTTTGTTATT 57.803 33.333 0.00 0.00 0.00 1.40
3301 3734 7.969690 AATATGTTCATGGATTTAACACCCA 57.030 32.000 0.00 0.00 36.06 4.51
3302 3735 5.659440 ATGTTCATGGATTTAACACCCAC 57.341 39.130 0.00 0.00 36.06 4.61
3303 3736 3.829601 TGTTCATGGATTTAACACCCACC 59.170 43.478 0.00 0.00 32.07 4.61
3304 3737 3.816398 TCATGGATTTAACACCCACCA 57.184 42.857 0.00 0.00 32.07 4.17
3305 3738 3.696045 TCATGGATTTAACACCCACCAG 58.304 45.455 0.00 0.00 32.07 4.00
3306 3739 3.075283 TCATGGATTTAACACCCACCAGT 59.925 43.478 0.00 0.00 32.07 4.00
3307 3740 2.870175 TGGATTTAACACCCACCAGTG 58.130 47.619 0.00 0.00 43.65 3.66
3314 3747 3.494850 CACCCACCAGTGTTTCTGT 57.505 52.632 0.00 0.00 42.19 3.41
3315 3748 2.631160 CACCCACCAGTGTTTCTGTA 57.369 50.000 0.00 0.00 42.19 2.74
3316 3749 2.925724 CACCCACCAGTGTTTCTGTAA 58.074 47.619 0.00 0.00 42.19 2.41
3317 3750 2.878406 CACCCACCAGTGTTTCTGTAAG 59.122 50.000 0.00 0.00 42.19 2.34
3318 3751 1.880027 CCCACCAGTGTTTCTGTAAGC 59.120 52.381 0.00 0.00 42.19 3.09
3319 3752 2.571212 CCACCAGTGTTTCTGTAAGCA 58.429 47.619 0.00 0.00 42.19 3.91
3320 3753 2.290641 CCACCAGTGTTTCTGTAAGCAC 59.709 50.000 0.00 0.00 44.55 4.40
3328 3761 5.744490 GTGTTTCTGTAAGCACGTATTTGT 58.256 37.500 0.00 0.00 37.13 2.83
3329 3762 6.196571 GTGTTTCTGTAAGCACGTATTTGTT 58.803 36.000 0.00 0.00 37.13 2.83
3330 3763 6.356190 GTGTTTCTGTAAGCACGTATTTGTTC 59.644 38.462 0.00 0.00 37.13 3.18
3331 3764 6.259167 TGTTTCTGTAAGCACGTATTTGTTCT 59.741 34.615 0.00 0.00 0.00 3.01
3332 3765 6.854496 TTCTGTAAGCACGTATTTGTTCTT 57.146 33.333 0.00 0.00 0.00 2.52
3333 3766 6.223138 TCTGTAAGCACGTATTTGTTCTTG 57.777 37.500 0.00 0.00 0.00 3.02
3334 3767 5.756347 TCTGTAAGCACGTATTTGTTCTTGT 59.244 36.000 0.00 0.00 0.00 3.16
3335 3768 6.259167 TCTGTAAGCACGTATTTGTTCTTGTT 59.741 34.615 0.00 0.00 0.00 2.83
3336 3769 6.787225 TGTAAGCACGTATTTGTTCTTGTTT 58.213 32.000 0.00 0.00 0.00 2.83
3337 3770 6.689241 TGTAAGCACGTATTTGTTCTTGTTTG 59.311 34.615 0.00 0.00 0.00 2.93
3338 3771 5.243426 AGCACGTATTTGTTCTTGTTTGT 57.757 34.783 0.00 0.00 0.00 2.83
3339 3772 5.646606 AGCACGTATTTGTTCTTGTTTGTT 58.353 33.333 0.00 0.00 0.00 2.83
3340 3773 5.514914 AGCACGTATTTGTTCTTGTTTGTTG 59.485 36.000 0.00 0.00 0.00 3.33
3341 3774 5.287513 GCACGTATTTGTTCTTGTTTGTTGT 59.712 36.000 0.00 0.00 0.00 3.32
3342 3775 6.469595 GCACGTATTTGTTCTTGTTTGTTGTA 59.530 34.615 0.00 0.00 0.00 2.41
3343 3776 7.008447 GCACGTATTTGTTCTTGTTTGTTGTAA 59.992 33.333 0.00 0.00 0.00 2.41
3344 3777 8.520258 CACGTATTTGTTCTTGTTTGTTGTAAG 58.480 33.333 0.00 0.00 0.00 2.34
3345 3778 8.452534 ACGTATTTGTTCTTGTTTGTTGTAAGA 58.547 29.630 0.00 0.00 0.00 2.10
3346 3779 9.445786 CGTATTTGTTCTTGTTTGTTGTAAGAT 57.554 29.630 0.00 0.00 31.21 2.40
3349 3782 9.651913 ATTTGTTCTTGTTTGTTGTAAGATGTT 57.348 25.926 0.00 0.00 31.21 2.71
3350 3783 8.459521 TTGTTCTTGTTTGTTGTAAGATGTTG 57.540 30.769 0.00 0.00 31.21 3.33
3351 3784 7.821652 TGTTCTTGTTTGTTGTAAGATGTTGA 58.178 30.769 0.00 0.00 31.21 3.18
3352 3785 8.465999 TGTTCTTGTTTGTTGTAAGATGTTGAT 58.534 29.630 0.00 0.00 31.21 2.57
3353 3786 8.958043 GTTCTTGTTTGTTGTAAGATGTTGATC 58.042 33.333 0.00 0.00 31.21 2.92
3354 3787 7.351981 TCTTGTTTGTTGTAAGATGTTGATCG 58.648 34.615 0.00 0.00 33.34 3.69
3355 3788 6.852858 TGTTTGTTGTAAGATGTTGATCGA 57.147 33.333 0.00 0.00 33.34 3.59
3356 3789 7.433708 TGTTTGTTGTAAGATGTTGATCGAT 57.566 32.000 0.00 0.00 33.34 3.59
3357 3790 7.297391 TGTTTGTTGTAAGATGTTGATCGATG 58.703 34.615 0.54 0.00 33.34 3.84
3358 3791 7.041440 TGTTTGTTGTAAGATGTTGATCGATGT 60.041 33.333 0.54 0.00 33.34 3.06
3359 3792 8.440059 GTTTGTTGTAAGATGTTGATCGATGTA 58.560 33.333 0.54 0.00 33.34 2.29
3360 3793 8.541133 TTGTTGTAAGATGTTGATCGATGTAA 57.459 30.769 0.54 0.00 33.34 2.41
3361 3794 8.716646 TGTTGTAAGATGTTGATCGATGTAAT 57.283 30.769 0.54 0.00 33.34 1.89
3362 3795 9.161629 TGTTGTAAGATGTTGATCGATGTAATT 57.838 29.630 0.54 0.00 33.34 1.40
3363 3796 9.988350 GTTGTAAGATGTTGATCGATGTAATTT 57.012 29.630 0.54 0.00 33.34 1.82
3365 3798 9.377312 TGTAAGATGTTGATCGATGTAATTTCA 57.623 29.630 0.54 0.00 33.34 2.69
3368 3801 9.778993 AAGATGTTGATCGATGTAATTTCAAAG 57.221 29.630 0.54 0.00 33.34 2.77
3369 3802 7.912250 AGATGTTGATCGATGTAATTTCAAAGC 59.088 33.333 0.54 0.00 33.34 3.51
3370 3803 6.907741 TGTTGATCGATGTAATTTCAAAGCA 58.092 32.000 0.54 0.00 0.00 3.91
3371 3804 7.022979 TGTTGATCGATGTAATTTCAAAGCAG 58.977 34.615 0.54 0.00 0.00 4.24
3372 3805 6.122850 TGATCGATGTAATTTCAAAGCAGG 57.877 37.500 0.54 0.00 0.00 4.85
3373 3806 4.963276 TCGATGTAATTTCAAAGCAGGG 57.037 40.909 0.00 0.00 0.00 4.45
3374 3807 3.128589 TCGATGTAATTTCAAAGCAGGGC 59.871 43.478 0.00 0.00 0.00 5.19
3375 3808 3.129287 CGATGTAATTTCAAAGCAGGGCT 59.871 43.478 0.00 0.00 42.56 5.19
3376 3809 4.676546 GATGTAATTTCAAAGCAGGGCTC 58.323 43.478 0.00 0.00 38.25 4.70
3377 3810 3.766545 TGTAATTTCAAAGCAGGGCTCT 58.233 40.909 0.00 0.00 38.25 4.09
3378 3811 4.151883 TGTAATTTCAAAGCAGGGCTCTT 58.848 39.130 0.00 0.00 38.25 2.85
3379 3812 4.588528 TGTAATTTCAAAGCAGGGCTCTTT 59.411 37.500 0.00 0.00 38.25 2.52
3380 3813 4.694760 AATTTCAAAGCAGGGCTCTTTT 57.305 36.364 0.00 0.00 38.25 2.27
3381 3814 4.694760 ATTTCAAAGCAGGGCTCTTTTT 57.305 36.364 0.00 0.00 38.25 1.94
3382 3815 3.457610 TTCAAAGCAGGGCTCTTTTTG 57.542 42.857 12.22 12.22 38.25 2.44
3383 3816 2.665165 TCAAAGCAGGGCTCTTTTTGA 58.335 42.857 15.68 15.68 38.25 2.69
3384 3817 2.624838 TCAAAGCAGGGCTCTTTTTGAG 59.375 45.455 15.68 0.00 45.33 3.02
3397 3830 5.816919 CTCTTTTTGAGCCTTCGTTTTACA 58.183 37.500 0.00 0.00 35.84 2.41
3398 3831 6.197364 TCTTTTTGAGCCTTCGTTTTACAA 57.803 33.333 0.00 0.00 0.00 2.41
3399 3832 6.622549 TCTTTTTGAGCCTTCGTTTTACAAA 58.377 32.000 0.00 0.00 0.00 2.83
3400 3833 7.091443 TCTTTTTGAGCCTTCGTTTTACAAAA 58.909 30.769 0.00 0.00 35.17 2.44
3401 3834 7.599245 TCTTTTTGAGCCTTCGTTTTACAAAAA 59.401 29.630 0.00 0.00 40.67 1.94
3402 3835 6.635166 TTTGAGCCTTCGTTTTACAAAAAC 57.365 33.333 5.40 5.40 0.00 2.43
3403 3836 5.570234 TGAGCCTTCGTTTTACAAAAACT 57.430 34.783 12.07 0.00 0.00 2.66
3404 3837 5.336744 TGAGCCTTCGTTTTACAAAAACTG 58.663 37.500 12.07 7.05 0.00 3.16
3405 3838 5.124138 TGAGCCTTCGTTTTACAAAAACTGA 59.876 36.000 12.07 8.78 0.00 3.41
3406 3839 6.144078 AGCCTTCGTTTTACAAAAACTGAT 57.856 33.333 12.07 0.00 0.00 2.90
3407 3840 6.569780 AGCCTTCGTTTTACAAAAACTGATT 58.430 32.000 12.07 0.00 0.00 2.57
3408 3841 6.695713 AGCCTTCGTTTTACAAAAACTGATTC 59.304 34.615 12.07 1.62 0.00 2.52
3409 3842 6.344702 GCCTTCGTTTTACAAAAACTGATTCG 60.345 38.462 12.07 0.60 0.00 3.34
3410 3843 6.908284 CCTTCGTTTTACAAAAACTGATTCGA 59.092 34.615 12.07 2.60 0.00 3.71
3411 3844 7.429920 CCTTCGTTTTACAAAAACTGATTCGAA 59.570 33.333 0.00 0.00 0.00 3.71
3412 3845 8.844441 TTCGTTTTACAAAAACTGATTCGAAT 57.156 26.923 11.20 11.20 0.00 3.34
3413 3846 8.844441 TCGTTTTACAAAAACTGATTCGAATT 57.156 26.923 12.81 0.00 0.00 2.17
3414 3847 9.291664 TCGTTTTACAAAAACTGATTCGAATTT 57.708 25.926 12.81 0.00 0.00 1.82
3449 3882 8.558973 AGATTTCAGAGATTCAGTTTAACTGG 57.441 34.615 22.82 7.03 45.94 4.00
3450 3883 8.160106 AGATTTCAGAGATTCAGTTTAACTGGT 58.840 33.333 22.82 13.18 45.94 4.00
3451 3884 9.436957 GATTTCAGAGATTCAGTTTAACTGGTA 57.563 33.333 22.82 12.92 45.94 3.25
3452 3885 9.793259 ATTTCAGAGATTCAGTTTAACTGGTAA 57.207 29.630 22.82 12.48 45.94 2.85
3453 3886 9.621629 TTTCAGAGATTCAGTTTAACTGGTAAA 57.378 29.630 22.82 11.82 45.94 2.01
3454 3887 8.833231 TCAGAGATTCAGTTTAACTGGTAAAG 57.167 34.615 22.82 9.15 45.94 1.85
3455 3888 7.387948 TCAGAGATTCAGTTTAACTGGTAAAGC 59.612 37.037 22.82 13.61 45.94 3.51
3456 3889 7.389053 CAGAGATTCAGTTTAACTGGTAAAGCT 59.611 37.037 22.82 17.57 45.94 3.74
3457 3890 7.389053 AGAGATTCAGTTTAACTGGTAAAGCTG 59.611 37.037 22.82 15.53 45.94 4.24
3458 3891 7.224297 AGATTCAGTTTAACTGGTAAAGCTGA 58.776 34.615 22.82 18.20 45.94 4.26
3459 3892 7.719633 AGATTCAGTTTAACTGGTAAAGCTGAA 59.280 33.333 26.49 26.49 45.94 3.02
3460 3893 6.613755 TCAGTTTAACTGGTAAAGCTGAAC 57.386 37.500 22.82 2.65 45.94 3.18
3461 3894 6.116806 TCAGTTTAACTGGTAAAGCTGAACA 58.883 36.000 22.82 0.00 45.94 3.18
3462 3895 6.770785 TCAGTTTAACTGGTAAAGCTGAACAT 59.229 34.615 22.82 0.00 45.94 2.71
3463 3896 7.934665 TCAGTTTAACTGGTAAAGCTGAACATA 59.065 33.333 22.82 0.00 45.94 2.29
3464 3897 8.564574 CAGTTTAACTGGTAAAGCTGAACATAA 58.435 33.333 16.62 0.00 42.35 1.90
3465 3898 9.297037 AGTTTAACTGGTAAAGCTGAACATAAT 57.703 29.630 0.00 0.00 32.22 1.28
3466 3899 9.556030 GTTTAACTGGTAAAGCTGAACATAATC 57.444 33.333 0.00 0.00 32.22 1.75
3467 3900 6.759497 AACTGGTAAAGCTGAACATAATCC 57.241 37.500 0.00 0.00 0.00 3.01
3468 3901 5.193679 ACTGGTAAAGCTGAACATAATCCC 58.806 41.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.561184 GGGAGGGGGATTTAAAGGGG 59.439 60.000 0.00 0.00 0.00 4.79
55 56 2.123640 GAGGAGACGGGAGGGGAG 60.124 72.222 0.00 0.00 0.00 4.30
104 105 1.737793 CGATCGGAAACTTTCTTGGGG 59.262 52.381 7.38 0.00 0.00 4.96
140 141 1.078848 CTTGGAGGTGGGCGAGAAG 60.079 63.158 0.00 0.00 0.00 2.85
164 168 2.038269 GGGCGCGGTCTGAAATTCA 61.038 57.895 8.83 0.00 0.00 2.57
189 193 1.000506 TCAACGATAATAGCGAGGGGC 59.999 52.381 4.51 0.00 44.05 5.80
190 194 3.594603 ATCAACGATAATAGCGAGGGG 57.405 47.619 4.51 0.00 0.00 4.79
191 195 6.100004 ACATAATCAACGATAATAGCGAGGG 58.900 40.000 4.51 0.00 0.00 4.30
212 216 1.180029 GGGCAGATCAACAGCAACAT 58.820 50.000 0.00 0.00 32.56 2.71
213 217 0.895100 GGGGCAGATCAACAGCAACA 60.895 55.000 0.00 0.00 32.56 3.33
214 218 1.885871 GGGGCAGATCAACAGCAAC 59.114 57.895 0.00 0.00 32.56 4.17
298 307 1.404391 GGAACGAGCGGATCAACTAGA 59.596 52.381 0.00 0.00 0.00 2.43
299 308 1.841450 GGAACGAGCGGATCAACTAG 58.159 55.000 0.00 0.00 0.00 2.57
301 310 4.913126 GGAACGAGCGGATCAACT 57.087 55.556 0.00 0.00 0.00 3.16
333 342 4.022589 TCAACAAACCTATCGTCTCGAACT 60.023 41.667 0.00 0.00 39.99 3.01
348 483 4.536065 TCAACAGCAATCGATCAACAAAC 58.464 39.130 0.00 0.00 0.00 2.93
401 536 6.360370 TCTACCAGATAATCCAGGCATAAC 57.640 41.667 0.00 0.00 0.00 1.89
418 553 3.031013 TCTCAAATCGGCAGATCTACCA 58.969 45.455 12.62 0.11 35.74 3.25
456 592 5.523916 ACACGCCTAGATGAACATAATCAAC 59.476 40.000 0.00 0.00 32.06 3.18
457 593 5.523552 CACACGCCTAGATGAACATAATCAA 59.476 40.000 0.00 0.00 32.06 2.57
458 594 5.049828 CACACGCCTAGATGAACATAATCA 58.950 41.667 0.00 0.00 0.00 2.57
459 595 5.050490 ACACACGCCTAGATGAACATAATC 58.950 41.667 0.00 0.00 0.00 1.75
460 596 4.811024 CACACACGCCTAGATGAACATAAT 59.189 41.667 0.00 0.00 0.00 1.28
461 597 4.180817 CACACACGCCTAGATGAACATAA 58.819 43.478 0.00 0.00 0.00 1.90
483 619 2.919228 ACCTAGCGGAATCAATCAACC 58.081 47.619 0.00 0.00 0.00 3.77
500 636 1.882989 GAGCGACTCAGCAGGAACCT 61.883 60.000 0.00 0.00 40.15 3.50
517 653 2.245159 TGAGCACCACAAAGTCTGAG 57.755 50.000 0.00 0.00 0.00 3.35
572 708 4.054780 TGCAACTCAGGTATATCCGTTC 57.945 45.455 0.00 0.00 41.99 3.95
588 724 0.243636 GGTGTGCCCAAGTATGCAAC 59.756 55.000 0.00 0.00 39.57 4.17
591 727 1.209504 TCTAGGTGTGCCCAAGTATGC 59.790 52.381 0.00 0.00 34.66 3.14
595 731 2.158755 GCATATCTAGGTGTGCCCAAGT 60.159 50.000 13.43 0.00 34.66 3.16
630 767 3.442625 GGCCCAACAACTAACATAGGAAC 59.557 47.826 0.00 0.00 0.00 3.62
698 835 7.282224 ACTGTAAGCAAACACAATTGACTCTTA 59.718 33.333 13.59 7.62 37.60 2.10
752 890 5.242838 ACCTTCAAGTTTTGACACAACAAGA 59.757 36.000 7.20 1.83 39.87 3.02
774 912 3.557595 GCTGATGCACAAGTACAGATACC 59.442 47.826 0.00 0.00 39.41 2.73
828 973 6.329496 TCAAGTTTGACCACAAGCTAAAAAG 58.671 36.000 0.00 0.00 44.42 2.27
841 986 4.919754 GCAGATTGATGTTCAAGTTTGACC 59.080 41.667 0.00 0.00 40.05 4.02
878 1027 8.524487 AGAGAGACGAAATTGTAACTATGTCTT 58.476 33.333 0.00 0.00 35.73 3.01
879 1028 8.057536 AGAGAGACGAAATTGTAACTATGTCT 57.942 34.615 0.00 0.00 38.09 3.41
880 1029 8.587950 CAAGAGAGACGAAATTGTAACTATGTC 58.412 37.037 0.00 0.00 0.00 3.06
897 1060 1.767681 AGGCCATGATCCAAGAGAGAC 59.232 52.381 5.01 0.00 0.00 3.36
911 1074 4.043812 AGCATATATGAACCAGAAGGCCAT 59.956 41.667 17.10 0.00 39.06 4.40
921 1084 7.874940 TGCAGAACATAAAGCATATATGAACC 58.125 34.615 17.10 0.00 35.28 3.62
970 1133 9.751542 CAAACATAAAGTGTACCAAAACCATAA 57.248 29.630 0.00 0.00 41.14 1.90
1167 1330 3.306989 CCTTCTGGATGTTGTAGTCAGCA 60.307 47.826 0.00 0.00 38.97 4.41
2509 2900 3.066380 CACATTGTCGATGGTGTCTGAA 58.934 45.455 5.04 0.00 40.21 3.02
2512 2903 3.329386 CTTCACATTGTCGATGGTGTCT 58.671 45.455 5.04 0.00 40.21 3.41
2557 2948 2.039787 TGCTGGTCCGGTGGGATA 59.960 61.111 0.00 0.00 46.14 2.59
2725 3116 4.569564 AGTACACAAAAAGACAACCGACTC 59.430 41.667 0.00 0.00 0.00 3.36
2740 3131 3.799366 ACAATCACAACGGAGTACACAA 58.201 40.909 0.00 0.00 45.00 3.33
2752 3143 1.202639 AGGACACGCTGACAATCACAA 60.203 47.619 0.00 0.00 0.00 3.33
2755 3146 0.388520 CGAGGACACGCTGACAATCA 60.389 55.000 0.00 0.00 0.00 2.57
2783 3175 2.634600 ACACGGTAGCAACAAAGAACA 58.365 42.857 0.00 0.00 0.00 3.18
2803 3195 4.500887 GCCAGATATAACGCTAGACCACAA 60.501 45.833 0.00 0.00 0.00 3.33
2820 3212 0.322975 AAGTTCAGACGCAGCCAGAT 59.677 50.000 0.00 0.00 0.00 2.90
2826 3226 2.738846 ACAGCATAAAGTTCAGACGCAG 59.261 45.455 0.00 0.00 0.00 5.18
2829 3229 2.738846 AGCACAGCATAAAGTTCAGACG 59.261 45.455 0.00 0.00 0.00 4.18
2848 3249 1.100510 TCATCCAAATCTGCTGCAGC 58.899 50.000 31.89 31.89 42.50 5.25
2849 3250 2.753452 AGTTCATCCAAATCTGCTGCAG 59.247 45.455 23.31 23.31 0.00 4.41
2882 3289 0.610232 GGCACAAGTTCAGGGCTCAT 60.610 55.000 0.00 0.00 0.00 2.90
2945 3352 5.063180 TCGAAAGCAGATCAAATGCAATT 57.937 34.783 8.02 2.98 46.31 2.32
2999 3406 5.814764 AAATGTTCTCACATCAGCTCATC 57.185 39.130 0.00 0.00 43.34 2.92
3041 3448 4.771054 AGCTGAGCATTCCTTCAGATTTTT 59.229 37.500 7.39 0.00 32.38 1.94
3052 3459 0.449388 CCGTTGAAGCTGAGCATTCC 59.551 55.000 7.39 0.00 0.00 3.01
3085 3492 4.036734 GCAAATGATATCGGACATGGTTGT 59.963 41.667 0.00 0.00 39.32 3.32
3086 3493 4.036616 TGCAAATGATATCGGACATGGTTG 59.963 41.667 0.00 0.00 0.00 3.77
3087 3494 4.206375 TGCAAATGATATCGGACATGGTT 58.794 39.130 0.00 0.00 0.00 3.67
3088 3495 3.819368 TGCAAATGATATCGGACATGGT 58.181 40.909 0.00 0.00 0.00 3.55
3089 3496 4.276678 AGTTGCAAATGATATCGGACATGG 59.723 41.667 0.00 0.00 0.00 3.66
3091 3498 7.566760 TTTAGTTGCAAATGATATCGGACAT 57.433 32.000 10.14 0.00 0.00 3.06
3092 3499 6.458206 GCTTTAGTTGCAAATGATATCGGACA 60.458 38.462 10.14 0.00 0.00 4.02
3093 3500 5.909610 GCTTTAGTTGCAAATGATATCGGAC 59.090 40.000 10.14 0.00 0.00 4.79
3094 3501 5.008613 GGCTTTAGTTGCAAATGATATCGGA 59.991 40.000 10.14 0.00 0.00 4.55
3095 3502 5.215160 GGCTTTAGTTGCAAATGATATCGG 58.785 41.667 10.14 0.00 0.00 4.18
3096 3503 5.820131 TGGCTTTAGTTGCAAATGATATCG 58.180 37.500 10.14 0.00 0.00 2.92
3097 3504 7.035004 TGTTGGCTTTAGTTGCAAATGATATC 58.965 34.615 10.14 0.00 0.00 1.63
3098 3505 6.934056 TGTTGGCTTTAGTTGCAAATGATAT 58.066 32.000 10.14 0.00 0.00 1.63
3099 3506 6.338214 TGTTGGCTTTAGTTGCAAATGATA 57.662 33.333 10.14 0.00 0.00 2.15
3100 3507 5.212532 TGTTGGCTTTAGTTGCAAATGAT 57.787 34.783 10.14 0.00 0.00 2.45
3101 3508 4.662468 TGTTGGCTTTAGTTGCAAATGA 57.338 36.364 10.14 0.00 0.00 2.57
3102 3509 5.731599 TTTGTTGGCTTTAGTTGCAAATG 57.268 34.783 10.14 0.00 0.00 2.32
3103 3510 5.177327 CGATTTGTTGGCTTTAGTTGCAAAT 59.823 36.000 4.23 4.23 37.65 2.32
3104 3511 4.505922 CGATTTGTTGGCTTTAGTTGCAAA 59.494 37.500 0.00 0.00 0.00 3.68
3105 3512 4.047822 CGATTTGTTGGCTTTAGTTGCAA 58.952 39.130 0.00 0.00 0.00 4.08
3106 3513 3.551863 CCGATTTGTTGGCTTTAGTTGCA 60.552 43.478 0.00 0.00 0.00 4.08
3107 3514 2.986479 CCGATTTGTTGGCTTTAGTTGC 59.014 45.455 0.00 0.00 0.00 4.17
3108 3515 4.475944 CTCCGATTTGTTGGCTTTAGTTG 58.524 43.478 0.00 0.00 0.00 3.16
3109 3516 3.057526 GCTCCGATTTGTTGGCTTTAGTT 60.058 43.478 0.00 0.00 0.00 2.24
3110 3517 2.488153 GCTCCGATTTGTTGGCTTTAGT 59.512 45.455 0.00 0.00 0.00 2.24
3111 3518 2.749621 AGCTCCGATTTGTTGGCTTTAG 59.250 45.455 0.00 0.00 0.00 1.85
3112 3519 2.747446 GAGCTCCGATTTGTTGGCTTTA 59.253 45.455 0.87 0.00 0.00 1.85
3113 3520 1.541588 GAGCTCCGATTTGTTGGCTTT 59.458 47.619 0.87 0.00 0.00 3.51
3114 3521 1.168714 GAGCTCCGATTTGTTGGCTT 58.831 50.000 0.87 0.00 0.00 4.35
3115 3522 0.036732 TGAGCTCCGATTTGTTGGCT 59.963 50.000 12.15 0.00 0.00 4.75
3116 3523 0.449388 CTGAGCTCCGATTTGTTGGC 59.551 55.000 12.15 0.00 0.00 4.52
3117 3524 2.005451 CTCTGAGCTCCGATTTGTTGG 58.995 52.381 12.15 0.00 0.00 3.77
3118 3525 1.396301 GCTCTGAGCTCCGATTTGTTG 59.604 52.381 21.93 0.00 38.45 3.33
3119 3526 1.731720 GCTCTGAGCTCCGATTTGTT 58.268 50.000 21.93 0.00 38.45 2.83
3120 3527 3.450028 GCTCTGAGCTCCGATTTGT 57.550 52.632 21.93 0.00 38.45 2.83
3130 3537 0.319900 TCGGTTCACAAGCTCTGAGC 60.320 55.000 21.72 21.72 42.84 4.26
3131 3538 1.671261 CCTCGGTTCACAAGCTCTGAG 60.671 57.143 0.00 0.00 34.31 3.35
3132 3539 0.318441 CCTCGGTTCACAAGCTCTGA 59.682 55.000 0.00 0.00 0.00 3.27
3133 3540 0.318441 TCCTCGGTTCACAAGCTCTG 59.682 55.000 0.00 0.00 0.00 3.35
3134 3541 1.048601 TTCCTCGGTTCACAAGCTCT 58.951 50.000 0.00 0.00 0.00 4.09
3135 3542 2.003301 GATTCCTCGGTTCACAAGCTC 58.997 52.381 0.00 0.00 0.00 4.09
3136 3543 1.625818 AGATTCCTCGGTTCACAAGCT 59.374 47.619 0.00 0.00 0.00 3.74
3137 3544 2.100605 AGATTCCTCGGTTCACAAGC 57.899 50.000 0.00 0.00 0.00 4.01
3138 3545 3.522553 GGTAGATTCCTCGGTTCACAAG 58.477 50.000 0.00 0.00 0.00 3.16
3139 3546 2.235402 GGGTAGATTCCTCGGTTCACAA 59.765 50.000 0.00 0.00 0.00 3.33
3140 3547 1.829222 GGGTAGATTCCTCGGTTCACA 59.171 52.381 0.00 0.00 0.00 3.58
3141 3548 1.138464 GGGGTAGATTCCTCGGTTCAC 59.862 57.143 0.00 0.00 0.00 3.18
3142 3549 1.273381 TGGGGTAGATTCCTCGGTTCA 60.273 52.381 0.00 0.00 0.00 3.18
3143 3550 1.492764 TGGGGTAGATTCCTCGGTTC 58.507 55.000 0.00 0.00 0.00 3.62
3144 3551 2.191981 ATGGGGTAGATTCCTCGGTT 57.808 50.000 0.00 0.00 0.00 4.44
3145 3552 2.191981 AATGGGGTAGATTCCTCGGT 57.808 50.000 0.00 0.00 0.00 4.69
3146 3553 3.240302 ACTAATGGGGTAGATTCCTCGG 58.760 50.000 0.00 0.00 0.00 4.63
3147 3554 4.957684 AACTAATGGGGTAGATTCCTCG 57.042 45.455 0.00 0.00 0.00 4.63
3148 3555 6.424032 ACAAAACTAATGGGGTAGATTCCTC 58.576 40.000 0.00 0.00 0.00 3.71
3149 3556 6.402981 ACAAAACTAATGGGGTAGATTCCT 57.597 37.500 0.00 0.00 0.00 3.36
3150 3557 8.762481 ATAACAAAACTAATGGGGTAGATTCC 57.238 34.615 0.00 0.00 0.00 3.01
3279 3712 5.654650 GGTGGGTGTTAAATCCATGAACATA 59.345 40.000 0.00 0.00 35.65 2.29
3282 3715 3.829601 TGGTGGGTGTTAAATCCATGAAC 59.170 43.478 0.00 0.00 32.71 3.18
3304 3737 5.526111 ACAAATACGTGCTTACAGAAACACT 59.474 36.000 0.00 0.00 0.00 3.55
3305 3738 5.744490 ACAAATACGTGCTTACAGAAACAC 58.256 37.500 0.00 0.00 0.00 3.32
3306 3739 5.994887 ACAAATACGTGCTTACAGAAACA 57.005 34.783 0.00 0.00 0.00 2.83
3307 3740 6.656003 AGAACAAATACGTGCTTACAGAAAC 58.344 36.000 0.00 0.00 0.00 2.78
3308 3741 6.854496 AGAACAAATACGTGCTTACAGAAA 57.146 33.333 0.00 0.00 0.00 2.52
3309 3742 6.259167 ACAAGAACAAATACGTGCTTACAGAA 59.741 34.615 0.00 0.00 32.02 3.02
3310 3743 5.756347 ACAAGAACAAATACGTGCTTACAGA 59.244 36.000 0.00 0.00 32.02 3.41
3311 3744 5.985781 ACAAGAACAAATACGTGCTTACAG 58.014 37.500 0.00 0.00 32.02 2.74
3312 3745 5.994887 ACAAGAACAAATACGTGCTTACA 57.005 34.783 0.00 0.00 32.02 2.41
3313 3746 6.689669 ACAAACAAGAACAAATACGTGCTTAC 59.310 34.615 0.00 0.00 32.02 2.34
3314 3747 6.787225 ACAAACAAGAACAAATACGTGCTTA 58.213 32.000 0.00 0.00 32.02 3.09
3315 3748 5.646606 ACAAACAAGAACAAATACGTGCTT 58.353 33.333 0.00 0.00 34.93 3.91
3316 3749 5.243426 ACAAACAAGAACAAATACGTGCT 57.757 34.783 0.00 0.00 0.00 4.40
3317 3750 5.287513 ACAACAAACAAGAACAAATACGTGC 59.712 36.000 0.00 0.00 0.00 5.34
3318 3751 6.862944 ACAACAAACAAGAACAAATACGTG 57.137 33.333 0.00 0.00 0.00 4.49
3319 3752 8.452534 TCTTACAACAAACAAGAACAAATACGT 58.547 29.630 0.00 0.00 0.00 3.57
3320 3753 8.829514 TCTTACAACAAACAAGAACAAATACG 57.170 30.769 0.00 0.00 0.00 3.06
3323 3756 9.651913 AACATCTTACAACAAACAAGAACAAAT 57.348 25.926 0.00 0.00 32.38 2.32
3324 3757 8.920665 CAACATCTTACAACAAACAAGAACAAA 58.079 29.630 0.00 0.00 32.38 2.83
3325 3758 8.300286 TCAACATCTTACAACAAACAAGAACAA 58.700 29.630 0.00 0.00 32.38 2.83
3326 3759 7.821652 TCAACATCTTACAACAAACAAGAACA 58.178 30.769 0.00 0.00 32.38 3.18
3327 3760 8.856490 ATCAACATCTTACAACAAACAAGAAC 57.144 30.769 0.00 0.00 32.38 3.01
3328 3761 7.855409 CGATCAACATCTTACAACAAACAAGAA 59.145 33.333 0.00 0.00 32.38 2.52
3329 3762 7.225734 TCGATCAACATCTTACAACAAACAAGA 59.774 33.333 0.00 0.00 33.12 3.02
3330 3763 7.351981 TCGATCAACATCTTACAACAAACAAG 58.648 34.615 0.00 0.00 0.00 3.16
3331 3764 7.252965 TCGATCAACATCTTACAACAAACAA 57.747 32.000 0.00 0.00 0.00 2.83
3332 3765 6.852858 TCGATCAACATCTTACAACAAACA 57.147 33.333 0.00 0.00 0.00 2.83
3333 3766 7.298122 ACATCGATCAACATCTTACAACAAAC 58.702 34.615 0.00 0.00 0.00 2.93
3334 3767 7.433708 ACATCGATCAACATCTTACAACAAA 57.566 32.000 0.00 0.00 0.00 2.83
3335 3768 8.541133 TTACATCGATCAACATCTTACAACAA 57.459 30.769 0.00 0.00 0.00 2.83
3336 3769 8.716646 ATTACATCGATCAACATCTTACAACA 57.283 30.769 0.00 0.00 0.00 3.33
3337 3770 9.988350 AAATTACATCGATCAACATCTTACAAC 57.012 29.630 0.00 0.00 0.00 3.32
3339 3772 9.377312 TGAAATTACATCGATCAACATCTTACA 57.623 29.630 0.00 0.00 0.00 2.41
3342 3775 9.778993 CTTTGAAATTACATCGATCAACATCTT 57.221 29.630 0.00 0.00 30.34 2.40
3343 3776 7.912250 GCTTTGAAATTACATCGATCAACATCT 59.088 33.333 0.00 0.00 30.34 2.90
3344 3777 7.697710 TGCTTTGAAATTACATCGATCAACATC 59.302 33.333 0.00 0.00 30.34 3.06
3345 3778 7.537715 TGCTTTGAAATTACATCGATCAACAT 58.462 30.769 0.00 0.00 30.34 2.71
3346 3779 6.907741 TGCTTTGAAATTACATCGATCAACA 58.092 32.000 0.00 0.00 30.34 3.33
3347 3780 6.470235 CCTGCTTTGAAATTACATCGATCAAC 59.530 38.462 0.00 0.00 30.34 3.18
3348 3781 6.404623 CCCTGCTTTGAAATTACATCGATCAA 60.405 38.462 0.00 0.00 0.00 2.57
3349 3782 5.066375 CCCTGCTTTGAAATTACATCGATCA 59.934 40.000 0.00 0.00 0.00 2.92
3350 3783 5.514279 CCCTGCTTTGAAATTACATCGATC 58.486 41.667 0.00 0.00 0.00 3.69
3351 3784 4.202050 GCCCTGCTTTGAAATTACATCGAT 60.202 41.667 0.00 0.00 0.00 3.59
3352 3785 3.128589 GCCCTGCTTTGAAATTACATCGA 59.871 43.478 0.00 0.00 0.00 3.59
3353 3786 3.129287 AGCCCTGCTTTGAAATTACATCG 59.871 43.478 0.00 0.00 33.89 3.84
3354 3787 4.400567 AGAGCCCTGCTTTGAAATTACATC 59.599 41.667 0.00 0.00 39.88 3.06
3355 3788 4.347607 AGAGCCCTGCTTTGAAATTACAT 58.652 39.130 0.00 0.00 39.88 2.29
3356 3789 3.766545 AGAGCCCTGCTTTGAAATTACA 58.233 40.909 0.00 0.00 39.88 2.41
3357 3790 4.790765 AAGAGCCCTGCTTTGAAATTAC 57.209 40.909 0.00 0.00 39.88 1.89
3358 3791 5.806654 AAAAGAGCCCTGCTTTGAAATTA 57.193 34.783 0.00 0.00 39.88 1.40
3359 3792 4.694760 AAAAGAGCCCTGCTTTGAAATT 57.305 36.364 0.00 0.00 39.88 1.82
3360 3793 4.101430 TCAAAAAGAGCCCTGCTTTGAAAT 59.899 37.500 4.00 0.00 39.88 2.17
3361 3794 3.450457 TCAAAAAGAGCCCTGCTTTGAAA 59.550 39.130 4.00 0.00 39.88 2.69
3362 3795 3.030291 TCAAAAAGAGCCCTGCTTTGAA 58.970 40.909 4.00 0.00 39.88 2.69
3363 3796 2.624838 CTCAAAAAGAGCCCTGCTTTGA 59.375 45.455 5.86 5.86 39.88 2.69
3364 3797 3.022607 CTCAAAAAGAGCCCTGCTTTG 57.977 47.619 0.00 0.00 39.88 2.77
3375 3808 5.821516 TGTAAAACGAAGGCTCAAAAAGA 57.178 34.783 0.00 0.00 0.00 2.52
3376 3809 6.879188 TTTGTAAAACGAAGGCTCAAAAAG 57.121 33.333 0.00 0.00 0.00 2.27
3377 3810 7.385478 AGTTTTTGTAAAACGAAGGCTCAAAAA 59.615 29.630 12.41 12.41 39.34 1.94
3378 3811 6.869388 AGTTTTTGTAAAACGAAGGCTCAAAA 59.131 30.769 8.80 3.28 35.42 2.44
3379 3812 6.309251 CAGTTTTTGTAAAACGAAGGCTCAAA 59.691 34.615 8.80 0.00 35.42 2.69
3380 3813 5.802956 CAGTTTTTGTAAAACGAAGGCTCAA 59.197 36.000 8.80 0.00 35.42 3.02
3381 3814 5.124138 TCAGTTTTTGTAAAACGAAGGCTCA 59.876 36.000 8.80 0.00 35.42 4.26
3382 3815 5.575019 TCAGTTTTTGTAAAACGAAGGCTC 58.425 37.500 8.80 0.00 35.42 4.70
3383 3816 5.570234 TCAGTTTTTGTAAAACGAAGGCT 57.430 34.783 8.80 0.00 35.42 4.58
3384 3817 6.344702 CGAATCAGTTTTTGTAAAACGAAGGC 60.345 38.462 8.80 1.77 35.42 4.35
3385 3818 6.908284 TCGAATCAGTTTTTGTAAAACGAAGG 59.092 34.615 8.80 2.64 35.42 3.46
3386 3819 7.886191 TCGAATCAGTTTTTGTAAAACGAAG 57.114 32.000 8.80 4.82 35.42 3.79
3387 3820 8.844441 ATTCGAATCAGTTTTTGTAAAACGAA 57.156 26.923 4.39 0.00 38.71 3.85
3388 3821 8.844441 AATTCGAATCAGTTTTTGTAAAACGA 57.156 26.923 11.83 9.43 35.42 3.85
3438 3871 6.371809 TGTTCAGCTTTACCAGTTAAACTG 57.628 37.500 0.00 0.00 45.53 3.16
3439 3872 8.685838 TTATGTTCAGCTTTACCAGTTAAACT 57.314 30.769 0.00 0.00 0.00 2.66
3440 3873 9.556030 GATTATGTTCAGCTTTACCAGTTAAAC 57.444 33.333 0.00 0.00 0.00 2.01
3441 3874 8.736244 GGATTATGTTCAGCTTTACCAGTTAAA 58.264 33.333 0.00 0.00 0.00 1.52
3442 3875 7.338449 GGGATTATGTTCAGCTTTACCAGTTAA 59.662 37.037 0.00 0.00 0.00 2.01
3443 3876 6.826741 GGGATTATGTTCAGCTTTACCAGTTA 59.173 38.462 0.00 0.00 0.00 2.24
3444 3877 5.652452 GGGATTATGTTCAGCTTTACCAGTT 59.348 40.000 0.00 0.00 0.00 3.16
3445 3878 5.193679 GGGATTATGTTCAGCTTTACCAGT 58.806 41.667 0.00 0.00 0.00 4.00
3446 3879 5.757850 GGGATTATGTTCAGCTTTACCAG 57.242 43.478 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.