Multiple sequence alignment - TraesCS3B01G314700

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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 TraesCS3B01G314700 chr3B 100.000 4143 0 0 708 4850 506197264 506193122 0.000000e+00 7651
1 TraesCS3B01G314700 chr3B 100.000 405 0 0 1 405 506197971 506197567 0.000000e+00 749
2 TraesCS3B01G314700 chr3B 86.111 144 11 5 1847 1989 106421326 106421191 3.910000e-31 147
3 TraesCS3B01G314700 chr3A 95.880 2500 72 9 708 3185 509866548 509864058 0.000000e+00 4017
4 TraesCS3B01G314700 chr3A 88.504 1183 97 21 3309 4473 509864027 509862866 0.000000e+00 1395
5 TraesCS3B01G314700 chr3A 98.715 389 5 0 1 389 509867430 509867042 0.000000e+00 691
6 TraesCS3B01G314700 chr3A 98.830 171 2 0 235 405 509866797 509866627 6.100000e-79 305
7 TraesCS3B01G314700 chr3A 81.234 389 26 19 4472 4849 509862751 509862399 2.220000e-68 270
8 TraesCS3B01G314700 chr3D 94.597 1388 32 9 708 2061 388795016 388793638 0.000000e+00 2108
9 TraesCS3B01G314700 chr3D 96.237 1063 33 5 2126 3185 388793611 388792553 0.000000e+00 1735
10 TraesCS3B01G314700 chr3D 91.259 572 44 4 3312 3879 388792519 388791950 0.000000e+00 774
11 TraesCS3B01G314700 chr3D 98.519 405 6 0 1 405 388795493 388795089 0.000000e+00 715
12 TraesCS3B01G314700 chr3D 86.458 480 41 10 3823 4291 388791949 388791483 5.600000e-139 505
13 TraesCS3B01G314700 chr3D 85.442 419 28 21 4444 4850 388791253 388790856 5.850000e-109 405
14 TraesCS3B01G314700 chr3D 90.678 118 8 2 3192 3309 47619817 47619931 2.340000e-33 154
15 TraesCS3B01G314700 chr1A 84.677 248 32 5 4188 4431 498534238 498534483 4.850000e-60 243
16 TraesCS3B01G314700 chr1A 95.495 111 4 1 3194 3304 439332871 439332980 4.990000e-40 176
17 TraesCS3B01G314700 chr2D 82.041 245 40 3 4188 4429 14087318 14087561 6.360000e-49 206
18 TraesCS3B01G314700 chr2D 80.534 262 46 4 4177 4435 180881763 180881504 3.830000e-46 196
19 TraesCS3B01G314700 chr2D 85.915 142 15 4 1847 1986 544673139 544673001 3.910000e-31 147
20 TraesCS3B01G314700 chr7B 81.102 254 44 3 4185 4435 598296410 598296158 2.960000e-47 200
21 TraesCS3B01G314700 chr7A 81.349 252 39 7 4187 4434 584381831 584381584 1.060000e-46 198
22 TraesCS3B01G314700 chr7A 86.957 138 15 3 1853 1989 422830959 422830824 8.410000e-33 152
23 TraesCS3B01G314700 chr2A 81.200 250 43 2 4184 4431 665831606 665831359 1.060000e-46 198
24 TraesCS3B01G314700 chr2A 90.076 131 11 2 1857 1986 628670170 628670041 8.350000e-38 169
25 TraesCS3B01G314700 chr2A 89.565 115 11 1 3194 3308 7300238 7300351 1.410000e-30 145
26 TraesCS3B01G314700 chr6D 80.934 257 41 7 4183 4435 426200977 426200725 3.830000e-46 196
27 TraesCS3B01G314700 chr6D 94.231 104 3 3 3192 3294 87464748 87464647 6.500000e-34 156
28 TraesCS3B01G314700 chr6D 86.726 113 11 4 3189 3300 411927052 411926943 6.590000e-24 122
29 TraesCS3B01G314700 chr5A 80.952 252 44 4 4187 4435 352869868 352869618 3.830000e-46 196
30 TraesCS3B01G314700 chr5A 94.215 121 7 0 3187 3307 174573869 174573749 8.290000e-43 185
31 TraesCS3B01G314700 chr6B 80.952 252 42 5 4188 4435 715838669 715838420 1.380000e-45 195
32 TraesCS3B01G314700 chr6B 92.920 113 7 1 3192 3304 198970151 198970262 3.880000e-36 163
33 TraesCS3B01G314700 chr5B 95.495 111 2 2 3194 3304 647985712 647985819 1.790000e-39 174
34 TraesCS3B01G314700 chr5B 87.324 142 14 4 1847 1985 675874920 675875060 5.020000e-35 159
35 TraesCS3B01G314700 chr1B 94.643 112 5 1 3193 3304 296479051 296479161 6.450000e-39 172
36 TraesCS3B01G314700 chr6A 88.636 132 12 3 1857 1986 235489252 235489122 1.810000e-34 158
37 TraesCS3B01G314700 chr6A 87.879 132 13 3 1857 1986 243958420 243958290 8.410000e-33 152
38 TraesCS3B01G314700 chr5D 86.014 143 15 5 1847 1986 265961978 265961838 1.090000e-31 148


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 TraesCS3B01G314700 chr3B 506193122 506197971 4849 True 4200.000000 7651 100.000000 1 4850 2 chr3B.!!$R2 4849
1 TraesCS3B01G314700 chr3A 509862399 509867430 5031 True 1335.600000 4017 92.632600 1 4849 5 chr3A.!!$R1 4848
2 TraesCS3B01G314700 chr3D 388790856 388795493 4637 True 1040.333333 2108 92.085333 1 4850 6 chr3D.!!$R1 4849

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
31 32 1.378882 GCATTCGCTCATTGCTGGGA 61.379 55.000 0.0 0.0 40.11 4.37 F
941 1341 3.194329 TGACAGAGTTGAGATCGAAGCAT 59.806 43.478 0.0 0.0 0.00 3.79 F
1134 1534 0.247460 ATGCTGCTGTTACTCGCTCA 59.753 50.000 0.0 0.0 0.00 4.26 F
2076 2516 0.250467 TTGAAGAGGTGCCAGACTGC 60.250 55.000 0.0 0.0 0.00 4.40 F
3258 3701 0.323629 CAGGTAGAAGGCGGGAAACA 59.676 55.000 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 1420 0.179089 CATGGACTCTCTTGCCCTCG 60.179 60.0 0.00 0.00 0.00 4.63 R
2073 2513 0.171455 GGTACAGACGAGACTGGCAG 59.829 60.0 14.16 14.16 41.59 4.85 R
2302 2745 0.394080 AGCAGCAATGGAGAAGCCTC 60.394 55.0 0.00 0.00 38.70 4.70 R
3570 4013 0.033504 ACAGCTACAGTCAACCCACG 59.966 55.0 0.00 0.00 0.00 4.94 R
4720 5477 0.393077 CCCAGTAGGTAGCCGGATTG 59.607 60.0 5.05 0.00 0.00 2.67 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
31 32 1.378882 GCATTCGCTCATTGCTGGGA 61.379 55.000 0.00 0.00 40.11 4.37
831 1231 8.193438 CCAATTCTCTCAAATAACAAGGATTCC 58.807 37.037 0.00 0.00 0.00 3.01
941 1341 3.194329 TGACAGAGTTGAGATCGAAGCAT 59.806 43.478 0.00 0.00 0.00 3.79
992 1392 5.717119 AGGAAACACCATTAGAAGCCTAT 57.283 39.130 0.00 0.00 42.04 2.57
1134 1534 0.247460 ATGCTGCTGTTACTCGCTCA 59.753 50.000 0.00 0.00 0.00 4.26
1222 1622 2.501723 GCATGTCTCAAGGAGAAGGGTA 59.498 50.000 0.00 0.00 40.59 3.69
1461 1861 2.418746 GGTGGTTCGTGCAGAGTATGAT 60.419 50.000 0.00 0.00 0.00 2.45
1821 2228 5.734855 ATGTTATTCAGTCATTGTACCGC 57.265 39.130 0.00 0.00 0.00 5.68
1840 2247 6.161911 ACCGCGAACTCTTTTTATTACTTC 57.838 37.500 8.23 0.00 0.00 3.01
2027 2465 2.312140 AGACTAGTGGCAGGAGAAGGTA 59.688 50.000 0.00 0.00 0.00 3.08
2069 2509 4.395231 GGTTATACTTGTTGAAGAGGTGCC 59.605 45.833 0.00 0.00 32.98 5.01
2070 2510 3.788227 ATACTTGTTGAAGAGGTGCCA 57.212 42.857 0.00 0.00 32.98 4.92
2071 2511 1.972872 ACTTGTTGAAGAGGTGCCAG 58.027 50.000 0.00 0.00 32.98 4.85
2072 2512 1.490490 ACTTGTTGAAGAGGTGCCAGA 59.510 47.619 0.00 0.00 32.98 3.86
2073 2513 1.876156 CTTGTTGAAGAGGTGCCAGAC 59.124 52.381 0.00 0.00 0.00 3.51
2074 2514 1.131638 TGTTGAAGAGGTGCCAGACT 58.868 50.000 0.00 0.00 0.00 3.24
2075 2515 1.202687 TGTTGAAGAGGTGCCAGACTG 60.203 52.381 0.00 0.00 0.00 3.51
2076 2516 0.250467 TTGAAGAGGTGCCAGACTGC 60.250 55.000 0.00 0.00 0.00 4.40
2077 2517 1.376553 GAAGAGGTGCCAGACTGCC 60.377 63.158 0.00 0.00 0.00 4.85
2143 2583 6.408206 GGCTCTAGCTTATCAACTTAAGGGAA 60.408 42.308 7.53 0.00 41.70 3.97
2216 2656 4.769345 TTTCAAGGCCAAATTGGTTCTT 57.231 36.364 14.17 13.99 40.46 2.52
2292 2735 4.019321 CCACTTGAGGAAAGGTGGAGATTA 60.019 45.833 5.16 0.00 40.51 1.75
2321 2764 0.394080 GAGGCTTCTCCATTGCTGCT 60.394 55.000 0.00 0.00 37.29 4.24
2325 2768 2.292845 GGCTTCTCCATTGCTGCTTATC 59.707 50.000 0.00 0.00 34.01 1.75
2332 2775 5.129320 TCTCCATTGCTGCTTATCAGTCTTA 59.871 40.000 0.00 0.00 44.66 2.10
2413 2856 0.723981 GCTGCGTCTTTCATCTCCAC 59.276 55.000 0.00 0.00 0.00 4.02
2451 2894 4.946784 AGTTGCCTGCTAATAGTTTTCG 57.053 40.909 0.00 0.00 0.00 3.46
2483 2926 0.871057 AGTGCAAAGAGCTTTCTCGC 59.129 50.000 0.00 0.00 45.94 5.03
2544 2987 2.316586 GGGTCCCCATCACCACCAT 61.317 63.158 0.00 0.00 35.35 3.55
2588 3031 9.869844 CTGTCACTTAGAAAGAAACATTAACAG 57.130 33.333 0.00 0.00 32.96 3.16
2644 3087 3.126686 GCATTCCTTTCTCACAGCTCTTC 59.873 47.826 0.00 0.00 0.00 2.87
2752 3195 8.753497 ATGTTGGAGATAAGGGAATAAGTTTC 57.247 34.615 0.00 0.00 0.00 2.78
2827 3270 7.067981 AGACTTCAGAAAAGAGAAATTTGTGCT 59.932 33.333 0.00 0.00 32.73 4.40
2870 3313 9.368674 CAATCATTAAGTCCAAATGTTGCATTA 57.631 29.630 0.00 0.00 36.07 1.90
2957 3400 1.946283 GCTGGGTCAGTCTACCTTTGC 60.946 57.143 0.00 0.00 39.65 3.68
3165 3608 5.614324 TTAGGTCTGGTGATATCAAGGTG 57.386 43.478 7.07 0.00 0.00 4.00
3182 3625 4.207891 AGGTGTGTTCCATATCACTGAC 57.792 45.455 0.00 0.00 35.82 3.51
3185 3628 3.367932 GTGTGTTCCATATCACTGACGTG 59.632 47.826 0.00 0.00 42.59 4.49
3215 3658 4.379339 TTTTTCTTGAAAGAACCGGTGG 57.621 40.909 8.52 0.00 44.18 4.61
3216 3659 1.975660 TTCTTGAAAGAACCGGTGGG 58.024 50.000 8.52 0.00 39.95 4.61
3217 3660 0.536460 TCTTGAAAGAACCGGTGGGC 60.536 55.000 8.52 0.00 36.48 5.36
3218 3661 1.524008 CTTGAAAGAACCGGTGGGCC 61.524 60.000 8.52 0.00 36.48 5.80
3219 3662 2.114411 GAAAGAACCGGTGGGCCA 59.886 61.111 8.52 0.00 36.48 5.36
3220 3663 2.203437 AAAGAACCGGTGGGCCAC 60.203 61.111 28.69 28.69 36.48 5.01
3239 3682 5.235305 CCACCGGCATTCATATATTAAGC 57.765 43.478 0.00 0.00 0.00 3.09
3240 3683 4.699735 CCACCGGCATTCATATATTAAGCA 59.300 41.667 0.00 0.00 0.00 3.91
3241 3684 5.163723 CCACCGGCATTCATATATTAAGCAG 60.164 44.000 0.00 0.00 0.00 4.24
3242 3685 4.943705 ACCGGCATTCATATATTAAGCAGG 59.056 41.667 0.00 13.41 40.80 4.85
3243 3686 4.943705 CCGGCATTCATATATTAAGCAGGT 59.056 41.667 0.00 0.00 32.44 4.00
3244 3687 6.112734 CCGGCATTCATATATTAAGCAGGTA 58.887 40.000 0.00 0.00 32.44 3.08
3245 3688 6.258727 CCGGCATTCATATATTAAGCAGGTAG 59.741 42.308 0.00 0.00 32.44 3.18
3246 3689 7.041721 CGGCATTCATATATTAAGCAGGTAGA 58.958 38.462 0.00 0.00 0.00 2.59
3247 3690 7.549134 CGGCATTCATATATTAAGCAGGTAGAA 59.451 37.037 0.00 0.00 0.00 2.10
3248 3691 8.887717 GGCATTCATATATTAAGCAGGTAGAAG 58.112 37.037 0.00 0.00 0.00 2.85
3249 3692 8.887717 GCATTCATATATTAAGCAGGTAGAAGG 58.112 37.037 0.00 0.00 0.00 3.46
3250 3693 8.887717 CATTCATATATTAAGCAGGTAGAAGGC 58.112 37.037 0.00 0.00 0.00 4.35
3251 3694 6.631016 TCATATATTAAGCAGGTAGAAGGCG 58.369 40.000 0.00 0.00 0.00 5.52
3252 3695 2.622064 ATTAAGCAGGTAGAAGGCGG 57.378 50.000 0.00 0.00 0.00 6.13
3253 3696 0.539986 TTAAGCAGGTAGAAGGCGGG 59.460 55.000 0.00 0.00 0.00 6.13
3254 3697 0.324923 TAAGCAGGTAGAAGGCGGGA 60.325 55.000 0.00 0.00 0.00 5.14
3255 3698 1.198759 AAGCAGGTAGAAGGCGGGAA 61.199 55.000 0.00 0.00 0.00 3.97
3256 3699 1.198759 AGCAGGTAGAAGGCGGGAAA 61.199 55.000 0.00 0.00 0.00 3.13
3257 3700 1.025113 GCAGGTAGAAGGCGGGAAAC 61.025 60.000 0.00 0.00 0.00 2.78
3258 3701 0.323629 CAGGTAGAAGGCGGGAAACA 59.676 55.000 0.00 0.00 0.00 2.83
3259 3702 1.065418 CAGGTAGAAGGCGGGAAACAT 60.065 52.381 0.00 0.00 0.00 2.71
3260 3703 1.065418 AGGTAGAAGGCGGGAAACATG 60.065 52.381 0.00 0.00 0.00 3.21
3261 3704 1.339727 GGTAGAAGGCGGGAAACATGT 60.340 52.381 0.00 0.00 0.00 3.21
3262 3705 2.433436 GTAGAAGGCGGGAAACATGTT 58.567 47.619 4.92 4.92 0.00 2.71
3263 3706 1.534729 AGAAGGCGGGAAACATGTTC 58.465 50.000 12.39 5.57 0.00 3.18
3264 3707 1.202879 AGAAGGCGGGAAACATGTTCA 60.203 47.619 12.39 0.00 0.00 3.18
3265 3708 1.818674 GAAGGCGGGAAACATGTTCAT 59.181 47.619 12.39 0.00 0.00 2.57
3266 3709 1.176527 AGGCGGGAAACATGTTCATG 58.823 50.000 12.39 10.72 0.00 3.07
3267 3710 1.173043 GGCGGGAAACATGTTCATGA 58.827 50.000 12.39 0.00 0.00 3.07
3268 3711 1.750778 GGCGGGAAACATGTTCATGAT 59.249 47.619 12.39 4.90 0.00 2.45
3269 3712 2.223572 GGCGGGAAACATGTTCATGATC 60.224 50.000 12.39 5.09 0.00 2.92
3270 3713 2.423185 GCGGGAAACATGTTCATGATCA 59.577 45.455 12.39 8.86 0.00 2.92
3271 3714 3.119531 GCGGGAAACATGTTCATGATCAA 60.120 43.478 12.39 0.00 0.00 2.57
3272 3715 4.665212 CGGGAAACATGTTCATGATCAAG 58.335 43.478 12.39 8.75 0.00 3.02
3273 3716 4.156556 CGGGAAACATGTTCATGATCAAGT 59.843 41.667 12.39 9.38 0.00 3.16
3274 3717 5.404946 GGGAAACATGTTCATGATCAAGTG 58.595 41.667 12.39 9.73 0.00 3.16
3275 3718 5.183713 GGGAAACATGTTCATGATCAAGTGA 59.816 40.000 12.39 0.00 0.00 3.41
3276 3719 6.127535 GGGAAACATGTTCATGATCAAGTGAT 60.128 38.462 12.39 7.59 37.51 3.06
3290 3733 5.482163 TCAAGTGATCATGAGTGGTTACA 57.518 39.130 0.00 0.00 27.89 2.41
3291 3734 5.863965 TCAAGTGATCATGAGTGGTTACAA 58.136 37.500 0.00 0.00 27.89 2.41
3292 3735 5.934043 TCAAGTGATCATGAGTGGTTACAAG 59.066 40.000 0.00 0.00 27.89 3.16
3293 3736 5.745312 AGTGATCATGAGTGGTTACAAGA 57.255 39.130 0.00 0.00 27.89 3.02
3294 3737 5.728471 AGTGATCATGAGTGGTTACAAGAG 58.272 41.667 0.00 0.00 27.89 2.85
3295 3738 5.481824 AGTGATCATGAGTGGTTACAAGAGA 59.518 40.000 0.00 0.00 27.89 3.10
3296 3739 6.155910 AGTGATCATGAGTGGTTACAAGAGAT 59.844 38.462 0.00 0.00 27.89 2.75
3297 3740 6.820656 GTGATCATGAGTGGTTACAAGAGATT 59.179 38.462 0.00 0.00 0.00 2.40
3298 3741 6.820152 TGATCATGAGTGGTTACAAGAGATTG 59.180 38.462 0.09 0.00 0.00 2.67
3299 3742 5.491070 TCATGAGTGGTTACAAGAGATTGG 58.509 41.667 0.00 0.00 0.00 3.16
3300 3743 4.974645 TGAGTGGTTACAAGAGATTGGT 57.025 40.909 0.00 0.00 0.00 3.67
3303 3746 5.763204 TGAGTGGTTACAAGAGATTGGTTTC 59.237 40.000 0.00 0.00 0.00 2.78
3305 3748 6.126409 AGTGGTTACAAGAGATTGGTTTCAA 58.874 36.000 0.00 0.00 37.28 2.69
3307 3750 7.123547 AGTGGTTACAAGAGATTGGTTTCAAAA 59.876 33.333 0.00 0.00 36.36 2.44
3316 3759 8.034058 AGAGATTGGTTTCAAAAAGTCTATCG 57.966 34.615 0.00 0.00 36.36 2.92
3318 3761 8.567285 AGATTGGTTTCAAAAAGTCTATCGAT 57.433 30.769 2.16 2.16 36.36 3.59
3357 3800 5.880054 TTAAGTACTGAGCTGCAATTTCC 57.120 39.130 1.02 0.00 0.00 3.13
3369 3812 2.911636 TGCAATTTCCCCATTGGTTGAT 59.088 40.909 1.20 0.00 35.07 2.57
3370 3813 3.272581 GCAATTTCCCCATTGGTTGATG 58.727 45.455 1.20 0.00 35.07 3.07
3428 3871 3.725490 ACGACAGGTAGAGTTTTTGGAC 58.275 45.455 0.00 0.00 0.00 4.02
3512 3955 3.758023 TCTGGTTGAAGGTGCATTACATG 59.242 43.478 0.00 0.00 0.00 3.21
3515 3958 4.343526 TGGTTGAAGGTGCATTACATGTTT 59.656 37.500 2.30 0.00 0.00 2.83
3528 3971 6.368516 GCATTACATGTTTACAGTGGCAAAAT 59.631 34.615 2.30 0.00 0.00 1.82
3581 4024 2.100879 GAGACCTGCGTGGGTTGACT 62.101 60.000 3.20 0.00 40.06 3.41
3596 4039 3.053455 GTTGACTGTAGCTGTCTGTCAC 58.947 50.000 22.54 16.82 41.11 3.67
3627 4071 5.417754 TTTATTCTGAATGGGCATTTGCA 57.582 34.783 13.01 0.00 44.36 4.08
3628 4072 2.747396 TTCTGAATGGGCATTTGCAC 57.253 45.000 4.74 0.57 46.69 4.57
3629 4073 0.896923 TCTGAATGGGCATTTGCACC 59.103 50.000 1.71 2.98 45.73 5.01
3632 4076 0.108041 GAATGGGCATTTGCACCCTG 60.108 55.000 11.17 0.00 45.73 4.45
3633 4077 0.544833 AATGGGCATTTGCACCCTGA 60.545 50.000 11.17 0.00 45.73 3.86
3639 4083 2.421952 GGCATTTGCACCCTGATCTCTA 60.422 50.000 4.74 0.00 44.36 2.43
3641 4085 3.314635 GCATTTGCACCCTGATCTCTAAG 59.685 47.826 0.00 0.00 41.59 2.18
3645 4089 2.025155 GCACCCTGATCTCTAAGTCGA 58.975 52.381 0.00 0.00 0.00 4.20
3646 4090 2.223618 GCACCCTGATCTCTAAGTCGAC 60.224 54.545 7.70 7.70 0.00 4.20
3662 4108 6.436843 AAGTCGACTTTTGTTCTGAAATGT 57.563 33.333 24.93 0.00 30.82 2.71
3678 4124 0.907704 ATGTGCAGGACCGGGAGTTA 60.908 55.000 6.32 0.00 0.00 2.24
3750 4196 0.033011 GTGAGAGGGGGCTCTACTCA 60.033 60.000 10.68 9.24 35.91 3.41
3829 4275 1.690283 CGACATCGAGCAGCAGTTGG 61.690 60.000 0.00 0.00 43.02 3.77
3872 4377 1.008538 GGTCGCTGTTGTTTGCCAG 60.009 57.895 0.00 0.00 0.00 4.85
3875 4380 2.029518 GCTGTTGTTTGCCAGGGC 59.970 61.111 2.62 2.62 42.35 5.19
3881 4386 4.043200 GTTTGCCAGGGCGACAGC 62.043 66.667 5.74 0.00 45.51 4.40
3954 4460 3.627577 GGCGAGAATGATACCATGTTTGT 59.372 43.478 0.00 0.00 32.36 2.83
3960 4466 6.873997 AGAATGATACCATGTTTGTCGACTA 58.126 36.000 17.92 6.32 32.36 2.59
3966 4472 1.390123 CATGTTTGTCGACTACAGCCG 59.610 52.381 22.20 13.27 39.87 5.52
3969 4475 0.942410 TTTGTCGACTACAGCCGTGC 60.942 55.000 17.92 0.00 39.87 5.34
3970 4476 2.874780 GTCGACTACAGCCGTGCG 60.875 66.667 8.70 0.00 0.00 5.34
3971 4477 4.771356 TCGACTACAGCCGTGCGC 62.771 66.667 0.00 0.00 37.98 6.09
4021 4536 8.033626 GGTAGTGCTTGTATAGGGTATTGTATC 58.966 40.741 0.00 0.00 0.00 2.24
4031 4546 9.355215 GTATAGGGTATTGTATCTGTCGATTTG 57.645 37.037 0.00 0.00 0.00 2.32
4033 4548 6.281405 AGGGTATTGTATCTGTCGATTTGTC 58.719 40.000 0.00 0.00 0.00 3.18
4034 4549 5.175126 GGGTATTGTATCTGTCGATTTGTCG 59.825 44.000 0.00 0.00 0.00 4.35
4127 4642 2.890311 TCATGTTTTGACAATCGGGCTT 59.110 40.909 0.00 0.00 0.00 4.35
4155 4670 2.805099 GCCTCGACTGATCAATGAATCC 59.195 50.000 0.00 0.00 0.00 3.01
4177 4692 6.601332 TCCAGATTGGTTTTCCCTATATCAC 58.399 40.000 0.00 0.00 39.03 3.06
4178 4693 6.159575 TCCAGATTGGTTTTCCCTATATCACA 59.840 38.462 0.00 0.00 39.03 3.58
4180 4695 7.040201 CCAGATTGGTTTTCCCTATATCACATG 60.040 40.741 0.00 0.00 39.73 3.21
4181 4696 7.503566 CAGATTGGTTTTCCCTATATCACATGT 59.496 37.037 0.00 0.00 39.73 3.21
4182 4697 8.723365 AGATTGGTTTTCCCTATATCACATGTA 58.277 33.333 0.00 0.00 39.73 2.29
4183 4698 9.520515 GATTGGTTTTCCCTATATCACATGTAT 57.479 33.333 0.00 0.00 39.73 2.29
4202 4717 7.672660 ACATGTATATATACTCCCTCGGTTTCA 59.327 37.037 20.80 0.02 34.41 2.69
4218 4733 6.345298 TCGGTTTCATTTCACTCTGCATATA 58.655 36.000 0.00 0.00 0.00 0.86
4220 4735 7.335673 TCGGTTTCATTTCACTCTGCATATAAA 59.664 33.333 0.00 0.00 0.00 1.40
4412 5047 9.950680 TTTATGAAGTTTGACTTGAGACAAATC 57.049 29.630 10.77 7.07 38.80 2.17
4413 5048 6.048073 TGAAGTTTGACTTGAGACAAATCG 57.952 37.500 10.77 0.00 38.80 3.34
4420 5055 5.946298 TGACTTGAGACAAATCGTATACGT 58.054 37.500 23.67 9.53 40.80 3.57
4426 5061 8.424274 TTGAGACAAATCGTATACGTAGAGTA 57.576 34.615 23.67 4.88 40.80 2.59
4463 5098 7.145985 TGACTGAGTAATGTATATTTCCTCGC 58.854 38.462 0.00 0.00 31.14 5.03
4469 5104 2.324860 TGTATATTTCCTCGCGCATCG 58.675 47.619 8.75 0.00 40.15 3.84
4483 5233 1.009829 GCATCGAACCTACCAGCAAG 58.990 55.000 0.00 0.00 0.00 4.01
4484 5234 1.009829 CATCGAACCTACCAGCAAGC 58.990 55.000 0.00 0.00 0.00 4.01
4485 5235 0.613260 ATCGAACCTACCAGCAAGCA 59.387 50.000 0.00 0.00 0.00 3.91
4487 5237 0.517316 CGAACCTACCAGCAAGCAAC 59.483 55.000 0.00 0.00 0.00 4.17
4488 5238 1.878102 CGAACCTACCAGCAAGCAACT 60.878 52.381 0.00 0.00 0.00 3.16
4489 5239 1.537202 GAACCTACCAGCAAGCAACTG 59.463 52.381 0.00 0.00 34.82 3.16
4490 5240 0.764890 ACCTACCAGCAAGCAACTGA 59.235 50.000 2.54 0.00 37.32 3.41
4491 5241 1.160137 CCTACCAGCAAGCAACTGAC 58.840 55.000 2.54 0.00 37.32 3.51
4492 5242 1.271054 CCTACCAGCAAGCAACTGACT 60.271 52.381 2.54 0.00 37.32 3.41
4503 5253 1.534595 GCAACTGACTGGAAGCTTCAG 59.465 52.381 27.02 22.11 41.41 3.02
4528 5278 6.727824 AGTTGGTATTCAGAACAAGATTCG 57.272 37.500 0.00 0.00 0.00 3.34
4529 5279 5.122396 AGTTGGTATTCAGAACAAGATTCGC 59.878 40.000 0.00 0.00 0.00 4.70
4530 5280 4.832248 TGGTATTCAGAACAAGATTCGCT 58.168 39.130 0.00 0.00 0.00 4.93
4533 5283 6.024049 GGTATTCAGAACAAGATTCGCTTTG 58.976 40.000 0.00 0.00 33.60 2.77
4535 5285 3.476552 TCAGAACAAGATTCGCTTTGGT 58.523 40.909 0.00 0.00 33.60 3.67
4536 5286 3.250762 TCAGAACAAGATTCGCTTTGGTG 59.749 43.478 0.00 0.00 33.60 4.17
4537 5287 3.003689 CAGAACAAGATTCGCTTTGGTGT 59.996 43.478 0.00 0.00 33.60 4.16
4538 5288 3.632145 AGAACAAGATTCGCTTTGGTGTT 59.368 39.130 0.00 0.00 33.60 3.32
4539 5289 3.626028 ACAAGATTCGCTTTGGTGTTC 57.374 42.857 0.00 0.00 33.60 3.18
4540 5290 2.032030 ACAAGATTCGCTTTGGTGTTCG 60.032 45.455 0.00 0.00 33.60 3.95
4541 5291 2.163818 AGATTCGCTTTGGTGTTCGA 57.836 45.000 0.00 0.00 0.00 3.71
4556 5306 4.446234 GTGTTCGATCGCTTATGTTATGC 58.554 43.478 11.09 0.00 0.00 3.14
4565 5318 5.656480 TCGCTTATGTTATGCTACACTTGA 58.344 37.500 0.00 0.00 0.00 3.02
4627 5380 3.130516 TCATCGAGTTCACTTTCGGCTAT 59.869 43.478 0.00 0.00 37.42 2.97
4630 5383 3.057104 TCGAGTTCACTTTCGGCTATGAA 60.057 43.478 0.00 0.00 37.42 2.57
4636 5389 6.894828 GTTCACTTTCGGCTATGAACTTTTA 58.105 36.000 13.03 0.00 44.83 1.52
4638 5391 7.499321 TCACTTTCGGCTATGAACTTTTAAA 57.501 32.000 0.00 0.00 0.00 1.52
4644 5397 9.921637 TTTCGGCTATGAACTTTTAAATTTGAT 57.078 25.926 0.00 0.00 0.00 2.57
4648 5401 9.154847 GGCTATGAACTTTTAAATTTGATGCTT 57.845 29.630 0.00 0.00 0.00 3.91
4675 5428 1.501604 AGGTCCCTCTTCCTAGCTAGG 59.498 57.143 30.94 30.94 45.02 3.02
4716 5473 4.589374 GCCCTAGCTAGGACTGAATAAAGA 59.411 45.833 36.80 0.00 46.63 2.52
4717 5474 5.279256 GCCCTAGCTAGGACTGAATAAAGAG 60.279 48.000 36.80 18.07 46.63 2.85
4718 5475 5.245075 CCCTAGCTAGGACTGAATAAAGAGG 59.755 48.000 36.80 13.87 46.63 3.69
4720 5477 5.862678 AGCTAGGACTGAATAAAGAGGAC 57.137 43.478 0.00 0.00 0.00 3.85
4782 5541 0.534873 AAGCCGTGCACCAAAAGTTT 59.465 45.000 12.15 0.00 0.00 2.66
4793 5552 1.294857 CAAAAGTTTTGGTTGCCGGG 58.705 50.000 18.80 0.00 0.00 5.73
4823 5582 0.809636 CTGTGCGTATCATGGGCGAA 60.810 55.000 8.26 0.00 0.00 4.70
4837 5596 1.573829 GGCGAAATGACAGCAACGGA 61.574 55.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.839063 TGATTTATTCTCCCCTATCGAGTGT 59.161 40.000 0.00 0.00 0.00 3.55
133 134 8.978539 GCTACTTAAATTGCAAAAGCTAAGTTT 58.021 29.630 21.06 11.34 33.45 2.66
160 161 8.267620 TGACATGAGGAATTAAGTACATTGTG 57.732 34.615 0.00 0.00 0.00 3.33
202 203 1.783711 GAGCACGTCGATCATGATGAC 59.216 52.381 14.30 17.98 0.00 3.06
831 1231 1.688772 CAGATGGGAATGGAAGGCAG 58.311 55.000 0.00 0.00 0.00 4.85
941 1341 2.292569 GCTAGTAGTATGCGGCTGTGTA 59.707 50.000 0.00 0.00 0.00 2.90
992 1392 1.552792 TCCAGTGATCCATGCACGTAA 59.447 47.619 0.00 0.00 41.04 3.18
1020 1420 0.179089 CATGGACTCTCTTGCCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
1134 1534 0.824759 GAACCCAGGTACATCGCTCT 59.175 55.000 0.00 0.00 0.00 4.09
1222 1622 1.489481 TCAAGGATGAGGCTGTCGAT 58.511 50.000 0.00 0.00 0.00 3.59
1461 1861 2.621338 CGCCATAACAGAAGCTTCTCA 58.379 47.619 26.18 14.36 34.74 3.27
1908 2316 7.551262 ACATACAGACTGAAACACACTAAAACA 59.449 33.333 10.08 0.00 0.00 2.83
2071 2511 1.135632 GTACAGACGAGACTGGCAGTC 60.136 57.143 34.76 34.76 45.38 3.51
2072 2512 0.882474 GTACAGACGAGACTGGCAGT 59.118 55.000 22.26 22.26 41.59 4.40
2073 2513 0.171455 GGTACAGACGAGACTGGCAG 59.829 60.000 14.16 14.16 41.59 4.85
2074 2514 0.538746 TGGTACAGACGAGACTGGCA 60.539 55.000 7.40 0.00 41.59 4.92
2075 2515 0.601558 TTGGTACAGACGAGACTGGC 59.398 55.000 7.40 0.66 42.39 4.85
2076 2516 1.401148 CGTTGGTACAGACGAGACTGG 60.401 57.143 13.12 0.00 42.26 4.00
2077 2517 1.534163 TCGTTGGTACAGACGAGACTG 59.466 52.381 16.02 1.34 42.95 3.51
2197 2637 2.224257 GCAAGAACCAATTTGGCCTTGA 60.224 45.455 33.06 0.00 45.91 3.02
2292 2735 2.376518 TGGAGAAGCCTCTTGTTCCAAT 59.623 45.455 6.83 0.00 39.38 3.16
2302 2745 0.394080 AGCAGCAATGGAGAAGCCTC 60.394 55.000 0.00 0.00 38.70 4.70
2349 2792 1.016627 CACGCGTGGGAATGAATCAT 58.983 50.000 31.15 0.00 0.00 2.45
2413 2856 5.154222 GGCAACTAATCAAGGAAAAGAACG 58.846 41.667 0.00 0.00 0.00 3.95
2451 2894 3.699038 TCTTTGCACTATAATTGGGGCAC 59.301 43.478 4.69 0.00 0.00 5.01
2483 2926 7.615582 TCATAGTTTTCCTGTGAAGCATAAG 57.384 36.000 0.00 0.00 38.24 1.73
2544 2987 4.646492 TGACAGACTTATGCTATGCTCTCA 59.354 41.667 0.00 0.00 0.00 3.27
2588 3031 8.669243 CATAAAAGGTAGGTTCTCAAGTCATTC 58.331 37.037 0.00 0.00 0.00 2.67
2661 3104 6.639632 TGCTTGCTTTTCTTAATCTCACTT 57.360 33.333 0.00 0.00 0.00 3.16
2752 3195 2.566824 CCAATTTGGTCCCTGGACG 58.433 57.895 10.10 0.00 45.41 4.79
2838 3281 7.775120 ACATTTGGACTTAATGATTGGATCAC 58.225 34.615 0.00 0.00 43.01 3.06
2870 3313 1.425448 AGCTAGCCCTCACAAAAAGGT 59.575 47.619 12.13 0.00 31.51 3.50
2957 3400 2.177531 GCAGCCACATTGACAGCG 59.822 61.111 0.00 0.00 0.00 5.18
3194 3637 3.131400 CCCACCGGTTCTTTCAAGAAAAA 59.869 43.478 2.97 0.00 45.77 1.94
3195 3638 2.691011 CCCACCGGTTCTTTCAAGAAAA 59.309 45.455 2.97 0.00 45.77 2.29
3196 3639 2.303175 CCCACCGGTTCTTTCAAGAAA 58.697 47.619 2.97 0.00 45.77 2.52
3198 3641 0.536460 GCCCACCGGTTCTTTCAAGA 60.536 55.000 2.97 0.00 0.00 3.02
3199 3642 1.524008 GGCCCACCGGTTCTTTCAAG 61.524 60.000 2.97 0.00 0.00 3.02
3200 3643 1.529713 GGCCCACCGGTTCTTTCAA 60.530 57.895 2.97 0.00 0.00 2.69
3201 3644 2.114411 GGCCCACCGGTTCTTTCA 59.886 61.111 2.97 0.00 0.00 2.69
3202 3645 2.114411 TGGCCCACCGGTTCTTTC 59.886 61.111 2.97 0.00 39.70 2.62
3203 3646 2.203437 GTGGCCCACCGGTTCTTT 60.203 61.111 2.97 0.00 39.70 2.52
3217 3660 4.699735 TGCTTAATATATGAATGCCGGTGG 59.300 41.667 1.90 0.00 0.00 4.61
3218 3661 5.163723 CCTGCTTAATATATGAATGCCGGTG 60.164 44.000 1.90 0.00 0.00 4.94
3219 3662 4.943705 CCTGCTTAATATATGAATGCCGGT 59.056 41.667 1.90 0.00 0.00 5.28
3220 3663 4.943705 ACCTGCTTAATATATGAATGCCGG 59.056 41.667 0.00 0.00 0.00 6.13
3221 3664 7.041721 TCTACCTGCTTAATATATGAATGCCG 58.958 38.462 0.00 0.00 0.00 5.69
3222 3665 8.792830 TTCTACCTGCTTAATATATGAATGCC 57.207 34.615 0.00 0.00 0.00 4.40
3223 3666 8.887717 CCTTCTACCTGCTTAATATATGAATGC 58.112 37.037 0.00 0.00 0.00 3.56
3224 3667 8.887717 GCCTTCTACCTGCTTAATATATGAATG 58.112 37.037 0.00 0.00 0.00 2.67
3225 3668 7.766278 CGCCTTCTACCTGCTTAATATATGAAT 59.234 37.037 0.00 0.00 0.00 2.57
3226 3669 7.097192 CGCCTTCTACCTGCTTAATATATGAA 58.903 38.462 0.00 0.00 0.00 2.57
3227 3670 6.351033 CCGCCTTCTACCTGCTTAATATATGA 60.351 42.308 0.00 0.00 0.00 2.15
3228 3671 5.812642 CCGCCTTCTACCTGCTTAATATATG 59.187 44.000 0.00 0.00 0.00 1.78
3229 3672 5.104900 CCCGCCTTCTACCTGCTTAATATAT 60.105 44.000 0.00 0.00 0.00 0.86
3230 3673 4.222145 CCCGCCTTCTACCTGCTTAATATA 59.778 45.833 0.00 0.00 0.00 0.86
3231 3674 3.008049 CCCGCCTTCTACCTGCTTAATAT 59.992 47.826 0.00 0.00 0.00 1.28
3232 3675 2.367567 CCCGCCTTCTACCTGCTTAATA 59.632 50.000 0.00 0.00 0.00 0.98
3233 3676 1.141053 CCCGCCTTCTACCTGCTTAAT 59.859 52.381 0.00 0.00 0.00 1.40
3234 3677 0.539986 CCCGCCTTCTACCTGCTTAA 59.460 55.000 0.00 0.00 0.00 1.85
3235 3678 0.324923 TCCCGCCTTCTACCTGCTTA 60.325 55.000 0.00 0.00 0.00 3.09
3236 3679 1.198759 TTCCCGCCTTCTACCTGCTT 61.199 55.000 0.00 0.00 0.00 3.91
3237 3680 1.198759 TTTCCCGCCTTCTACCTGCT 61.199 55.000 0.00 0.00 0.00 4.24
3238 3681 1.025113 GTTTCCCGCCTTCTACCTGC 61.025 60.000 0.00 0.00 0.00 4.85
3239 3682 0.323629 TGTTTCCCGCCTTCTACCTG 59.676 55.000 0.00 0.00 0.00 4.00
3240 3683 1.065418 CATGTTTCCCGCCTTCTACCT 60.065 52.381 0.00 0.00 0.00 3.08
3241 3684 1.339727 ACATGTTTCCCGCCTTCTACC 60.340 52.381 0.00 0.00 0.00 3.18
3242 3685 2.109425 ACATGTTTCCCGCCTTCTAC 57.891 50.000 0.00 0.00 0.00 2.59
3243 3686 2.039216 TGAACATGTTTCCCGCCTTCTA 59.961 45.455 13.36 0.00 0.00 2.10
3244 3687 1.202879 TGAACATGTTTCCCGCCTTCT 60.203 47.619 13.36 0.00 0.00 2.85
3245 3688 1.243902 TGAACATGTTTCCCGCCTTC 58.756 50.000 13.36 0.00 0.00 3.46
3246 3689 1.545582 CATGAACATGTTTCCCGCCTT 59.454 47.619 13.36 0.00 34.23 4.35
3247 3690 1.176527 CATGAACATGTTTCCCGCCT 58.823 50.000 13.36 0.00 34.23 5.52
3248 3691 1.173043 TCATGAACATGTTTCCCGCC 58.827 50.000 13.36 0.00 39.72 6.13
3249 3692 2.423185 TGATCATGAACATGTTTCCCGC 59.577 45.455 13.36 0.00 39.72 6.13
3250 3693 4.156556 ACTTGATCATGAACATGTTTCCCG 59.843 41.667 13.36 2.42 39.72 5.14
3251 3694 5.183713 TCACTTGATCATGAACATGTTTCCC 59.816 40.000 18.19 0.30 39.72 3.97
3252 3695 6.258230 TCACTTGATCATGAACATGTTTCC 57.742 37.500 18.19 1.09 39.72 3.13
3267 3710 6.053632 TGTAACCACTCATGATCACTTGAT 57.946 37.500 0.00 0.00 37.51 2.57
3268 3711 5.482163 TGTAACCACTCATGATCACTTGA 57.518 39.130 0.00 0.00 0.00 3.02
3269 3712 5.934043 TCTTGTAACCACTCATGATCACTTG 59.066 40.000 0.00 0.00 0.00 3.16
3270 3713 6.014242 TCTCTTGTAACCACTCATGATCACTT 60.014 38.462 0.00 0.00 0.00 3.16
3271 3714 5.481824 TCTCTTGTAACCACTCATGATCACT 59.518 40.000 0.00 0.00 0.00 3.41
3272 3715 5.724328 TCTCTTGTAACCACTCATGATCAC 58.276 41.667 0.00 0.00 0.00 3.06
3273 3716 6.550938 ATCTCTTGTAACCACTCATGATCA 57.449 37.500 0.00 0.00 0.00 2.92
3274 3717 6.259608 CCAATCTCTTGTAACCACTCATGATC 59.740 42.308 0.00 0.00 0.00 2.92
3275 3718 6.118170 CCAATCTCTTGTAACCACTCATGAT 58.882 40.000 0.00 0.00 0.00 2.45
3276 3719 5.013079 ACCAATCTCTTGTAACCACTCATGA 59.987 40.000 0.00 0.00 0.00 3.07
3277 3720 5.248640 ACCAATCTCTTGTAACCACTCATG 58.751 41.667 0.00 0.00 0.00 3.07
3278 3721 5.505181 ACCAATCTCTTGTAACCACTCAT 57.495 39.130 0.00 0.00 0.00 2.90
3279 3722 4.974645 ACCAATCTCTTGTAACCACTCA 57.025 40.909 0.00 0.00 0.00 3.41
3280 3723 5.763204 TGAAACCAATCTCTTGTAACCACTC 59.237 40.000 0.00 0.00 0.00 3.51
3281 3724 5.690865 TGAAACCAATCTCTTGTAACCACT 58.309 37.500 0.00 0.00 0.00 4.00
3282 3725 6.385649 TTGAAACCAATCTCTTGTAACCAC 57.614 37.500 0.00 0.00 0.00 4.16
3283 3726 7.411486 TTTTGAAACCAATCTCTTGTAACCA 57.589 32.000 0.00 0.00 0.00 3.67
3284 3727 7.979537 ACTTTTTGAAACCAATCTCTTGTAACC 59.020 33.333 0.00 0.00 0.00 2.85
3285 3728 8.926715 ACTTTTTGAAACCAATCTCTTGTAAC 57.073 30.769 0.00 0.00 0.00 2.50
3286 3729 8.966868 AGACTTTTTGAAACCAATCTCTTGTAA 58.033 29.630 0.00 0.00 0.00 2.41
3287 3730 8.519799 AGACTTTTTGAAACCAATCTCTTGTA 57.480 30.769 0.00 0.00 0.00 2.41
3288 3731 7.410120 AGACTTTTTGAAACCAATCTCTTGT 57.590 32.000 0.00 0.00 0.00 3.16
3289 3732 9.617975 GATAGACTTTTTGAAACCAATCTCTTG 57.382 33.333 0.00 0.00 0.00 3.02
3290 3733 8.507249 CGATAGACTTTTTGAAACCAATCTCTT 58.493 33.333 0.00 0.00 39.76 2.85
3291 3734 7.878127 TCGATAGACTTTTTGAAACCAATCTCT 59.122 33.333 0.00 0.00 42.67 3.10
3292 3735 8.029642 TCGATAGACTTTTTGAAACCAATCTC 57.970 34.615 0.00 0.00 42.67 2.75
3293 3736 7.979444 TCGATAGACTTTTTGAAACCAATCT 57.021 32.000 0.00 0.00 42.67 2.40
3303 3746 6.019961 GCAGAGACTGATCGATAGACTTTTTG 60.020 42.308 0.00 4.71 39.13 2.44
3305 3748 5.451242 GGCAGAGACTGATCGATAGACTTTT 60.451 44.000 0.00 0.00 39.13 2.27
3307 3750 3.568007 GGCAGAGACTGATCGATAGACTT 59.432 47.826 0.00 0.00 39.13 3.01
3316 3759 9.036671 GTACTTAAATTAAGGCAGAGACTGATC 57.963 37.037 16.15 0.00 40.08 2.92
3318 3761 8.035394 CAGTACTTAAATTAAGGCAGAGACTGA 58.965 37.037 16.15 0.00 40.08 3.41
3357 3800 2.363038 CCTGCATACATCAACCAATGGG 59.637 50.000 3.55 0.00 41.29 4.00
3369 3812 0.756294 CCCGGATACACCTGCATACA 59.244 55.000 0.73 0.00 36.31 2.29
3370 3813 0.602905 GCCCGGATACACCTGCATAC 60.603 60.000 0.73 0.00 35.24 2.39
3428 3871 0.944311 CAAAGTCCTCCGACCGTGTG 60.944 60.000 0.00 0.00 40.12 3.82
3515 3958 9.202273 GTCATTTTAATTCATTTTGCCACTGTA 57.798 29.630 0.00 0.00 0.00 2.74
3564 4007 1.961277 CAGTCAACCCACGCAGGTC 60.961 63.158 0.00 0.00 40.05 3.85
3570 4013 0.033504 ACAGCTACAGTCAACCCACG 59.966 55.000 0.00 0.00 0.00 4.94
3574 4017 2.035961 TGACAGACAGCTACAGTCAACC 59.964 50.000 13.10 0.78 38.46 3.77
3581 4024 2.627699 TGACATGTGACAGACAGCTACA 59.372 45.455 1.15 0.00 38.23 2.74
3596 4039 6.038356 GCCCATTCAGAATAAAACTGACATG 58.962 40.000 0.00 0.00 42.84 3.21
3627 4071 3.655615 AGTCGACTTAGAGATCAGGGT 57.344 47.619 13.58 0.00 0.00 4.34
3628 4072 4.993029 AAAGTCGACTTAGAGATCAGGG 57.007 45.455 29.91 0.00 34.61 4.45
3629 4073 5.715070 ACAAAAGTCGACTTAGAGATCAGG 58.285 41.667 29.91 13.73 34.61 3.86
3632 4076 7.085116 TCAGAACAAAAGTCGACTTAGAGATC 58.915 38.462 29.91 22.94 34.61 2.75
3633 4077 6.982852 TCAGAACAAAAGTCGACTTAGAGAT 58.017 36.000 29.91 16.98 34.61 2.75
3639 4083 6.258160 CACATTTCAGAACAAAAGTCGACTT 58.742 36.000 24.93 24.93 37.91 3.01
3641 4085 4.437820 GCACATTTCAGAACAAAAGTCGAC 59.562 41.667 7.70 7.70 0.00 4.20
3645 4089 4.402155 TCCTGCACATTTCAGAACAAAAGT 59.598 37.500 0.00 0.00 33.54 2.66
3646 4090 4.741676 GTCCTGCACATTTCAGAACAAAAG 59.258 41.667 0.00 0.00 33.54 2.27
3662 4108 0.988832 AAATAACTCCCGGTCCTGCA 59.011 50.000 0.00 0.00 0.00 4.41
3678 4124 4.381932 GGCAATCCATCTTTGTCCGAAAAT 60.382 41.667 0.00 0.00 0.00 1.82
3765 4211 2.351276 GTTCCCATCAGGCCACGT 59.649 61.111 5.01 0.00 34.51 4.49
3829 4275 0.905357 TAGAGCTTCCCTTCAGCACC 59.095 55.000 0.00 0.00 39.99 5.01
3853 4299 1.723608 CTGGCAAACAACAGCGACCA 61.724 55.000 0.00 0.00 0.00 4.02
3881 4386 4.570663 GTCGATGGACGCCTCCCG 62.571 72.222 0.00 0.00 42.26 5.14
3895 4401 4.708868 TTCACAAACTCGAGATTTGTCG 57.291 40.909 27.97 23.84 44.97 4.35
3899 4405 9.383519 ACACATATATTCACAAACTCGAGATTT 57.616 29.630 21.68 12.81 0.00 2.17
3900 4406 8.948631 ACACATATATTCACAAACTCGAGATT 57.051 30.769 21.68 11.42 0.00 2.40
3905 4411 8.420374 AACCTACACATATATTCACAAACTCG 57.580 34.615 0.00 0.00 0.00 4.18
3970 4476 2.709475 CATAGCCGCTTCAACCGC 59.291 61.111 0.00 0.00 0.00 5.68
3971 4477 1.815421 AGCATAGCCGCTTCAACCG 60.815 57.895 0.00 0.00 39.99 4.44
4031 4546 6.143278 GTCATCAAAACCAAAATAACACCGAC 59.857 38.462 0.00 0.00 0.00 4.79
4033 4548 6.212955 AGTCATCAAAACCAAAATAACACCG 58.787 36.000 0.00 0.00 0.00 4.94
4034 4549 8.974408 GTTAGTCATCAAAACCAAAATAACACC 58.026 33.333 0.00 0.00 0.00 4.16
4127 4642 1.071542 TGATCAGTCGAGGCCAAACAA 59.928 47.619 5.01 0.00 0.00 2.83
4155 4670 7.503566 ACATGTGATATAGGGAAAACCAATCTG 59.496 37.037 0.00 0.00 43.89 2.90
4177 4692 8.063200 TGAAACCGAGGGAGTATATATACATG 57.937 38.462 22.00 0.00 35.74 3.21
4178 4693 8.840200 ATGAAACCGAGGGAGTATATATACAT 57.160 34.615 22.00 9.41 35.74 2.29
4180 4695 9.583765 GAAATGAAACCGAGGGAGTATATATAC 57.416 37.037 14.05 14.05 0.00 1.47
4181 4696 9.316594 TGAAATGAAACCGAGGGAGTATATATA 57.683 33.333 0.00 0.00 0.00 0.86
4182 4697 8.095169 GTGAAATGAAACCGAGGGAGTATATAT 58.905 37.037 0.00 0.00 0.00 0.86
4183 4698 7.289317 AGTGAAATGAAACCGAGGGAGTATATA 59.711 37.037 0.00 0.00 0.00 0.86
4184 4699 6.099845 AGTGAAATGAAACCGAGGGAGTATAT 59.900 38.462 0.00 0.00 0.00 0.86
4185 4700 5.424252 AGTGAAATGAAACCGAGGGAGTATA 59.576 40.000 0.00 0.00 0.00 1.47
4186 4701 4.225267 AGTGAAATGAAACCGAGGGAGTAT 59.775 41.667 0.00 0.00 0.00 2.12
4187 4702 3.581332 AGTGAAATGAAACCGAGGGAGTA 59.419 43.478 0.00 0.00 0.00 2.59
4188 4703 2.372172 AGTGAAATGAAACCGAGGGAGT 59.628 45.455 0.00 0.00 0.00 3.85
4192 4707 2.160417 GCAGAGTGAAATGAAACCGAGG 59.840 50.000 0.00 0.00 0.00 4.63
4193 4708 2.807967 TGCAGAGTGAAATGAAACCGAG 59.192 45.455 0.00 0.00 0.00 4.63
4196 4711 9.807649 ATTTTATATGCAGAGTGAAATGAAACC 57.192 29.630 0.00 0.00 0.00 3.27
4385 5020 9.956720 ATTTGTCTCAAGTCAAACTTCATAAAG 57.043 29.630 4.88 0.00 36.03 1.85
4386 5021 9.950680 GATTTGTCTCAAGTCAAACTTCATAAA 57.049 29.630 4.88 0.00 36.03 1.40
4387 5022 8.282592 CGATTTGTCTCAAGTCAAACTTCATAA 58.717 33.333 4.88 0.00 36.03 1.90
4388 5023 7.441157 ACGATTTGTCTCAAGTCAAACTTCATA 59.559 33.333 4.88 0.00 36.03 2.15
4389 5024 6.260936 ACGATTTGTCTCAAGTCAAACTTCAT 59.739 34.615 4.88 0.00 36.03 2.57
4390 5025 5.584649 ACGATTTGTCTCAAGTCAAACTTCA 59.415 36.000 4.88 0.00 36.03 3.02
4403 5038 9.708222 TTTTACTCTACGTATACGATTTGTCTC 57.292 33.333 30.77 0.00 43.02 3.36
4436 5071 7.810282 CGAGGAAATATACATTACTCAGTCAGG 59.190 40.741 11.16 0.00 32.12 3.86
4442 5077 4.921515 GCGCGAGGAAATATACATTACTCA 59.078 41.667 12.10 0.00 32.12 3.41
4447 5082 3.367932 CGATGCGCGAGGAAATATACATT 59.632 43.478 12.10 0.00 44.57 2.71
4450 5085 2.592194 TCGATGCGCGAGGAAATATAC 58.408 47.619 12.10 0.00 45.59 1.47
4463 5098 0.739462 TTGCTGGTAGGTTCGATGCG 60.739 55.000 0.00 0.00 0.00 4.73
4469 5104 1.537202 CAGTTGCTTGCTGGTAGGTTC 59.463 52.381 0.00 0.00 0.00 3.62
4474 5109 1.543208 CCAGTCAGTTGCTTGCTGGTA 60.543 52.381 0.00 0.00 37.48 3.25
4483 5233 1.534595 CTGAAGCTTCCAGTCAGTTGC 59.465 52.381 23.42 0.00 35.17 4.17
4484 5234 3.117491 TCTGAAGCTTCCAGTCAGTTG 57.883 47.619 23.42 3.26 39.82 3.16
4485 5235 3.135530 ACTTCTGAAGCTTCCAGTCAGTT 59.864 43.478 23.42 1.78 39.82 3.16
4487 5237 3.399440 ACTTCTGAAGCTTCCAGTCAG 57.601 47.619 23.42 14.43 40.15 3.51
4488 5238 3.470709 CAACTTCTGAAGCTTCCAGTCA 58.529 45.455 23.42 4.35 33.57 3.41
4489 5239 2.810852 CCAACTTCTGAAGCTTCCAGTC 59.189 50.000 23.42 0.00 33.57 3.51
4490 5240 2.173569 ACCAACTTCTGAAGCTTCCAGT 59.826 45.455 23.42 18.24 33.57 4.00
4491 5241 2.856222 ACCAACTTCTGAAGCTTCCAG 58.144 47.619 23.42 18.89 0.00 3.86
4492 5242 4.640771 ATACCAACTTCTGAAGCTTCCA 57.359 40.909 23.42 10.70 0.00 3.53
4503 5253 7.237173 CGAATCTTGTTCTGAATACCAACTTC 58.763 38.462 0.00 0.00 0.00 3.01
4528 5278 0.517316 AAGCGATCGAACACCAAAGC 59.483 50.000 21.57 0.00 0.00 3.51
4529 5279 3.370978 ACATAAGCGATCGAACACCAAAG 59.629 43.478 21.57 1.18 0.00 2.77
4530 5280 3.331150 ACATAAGCGATCGAACACCAAA 58.669 40.909 21.57 0.00 0.00 3.28
4533 5283 4.608445 GCATAACATAAGCGATCGAACACC 60.608 45.833 21.57 0.00 0.00 4.16
4535 5285 4.368315 AGCATAACATAAGCGATCGAACA 58.632 39.130 21.57 1.94 0.00 3.18
4536 5286 4.974103 AGCATAACATAAGCGATCGAAC 57.026 40.909 21.57 1.19 0.00 3.95
4537 5287 5.401376 GTGTAGCATAACATAAGCGATCGAA 59.599 40.000 21.57 3.19 0.00 3.71
4538 5288 4.915667 GTGTAGCATAACATAAGCGATCGA 59.084 41.667 21.57 0.00 0.00 3.59
4539 5289 4.917998 AGTGTAGCATAACATAAGCGATCG 59.082 41.667 11.69 11.69 0.00 3.69
4540 5290 6.420903 TCAAGTGTAGCATAACATAAGCGATC 59.579 38.462 0.00 0.00 0.00 3.69
4541 5291 6.280643 TCAAGTGTAGCATAACATAAGCGAT 58.719 36.000 0.00 0.00 0.00 4.58
4586 5339 9.208022 CTCGATGATGGAGCAAAGTAATTAATA 57.792 33.333 0.00 0.00 0.00 0.98
4587 5340 7.716998 ACTCGATGATGGAGCAAAGTAATTAAT 59.283 33.333 4.27 0.00 34.87 1.40
4589 5342 6.582636 ACTCGATGATGGAGCAAAGTAATTA 58.417 36.000 4.27 0.00 34.87 1.40
4590 5343 5.431765 ACTCGATGATGGAGCAAAGTAATT 58.568 37.500 4.27 0.00 34.87 1.40
4591 5344 5.028549 ACTCGATGATGGAGCAAAGTAAT 57.971 39.130 4.27 0.00 34.87 1.89
4592 5345 4.471904 ACTCGATGATGGAGCAAAGTAA 57.528 40.909 4.27 0.00 34.87 2.24
4593 5346 4.081697 TGAACTCGATGATGGAGCAAAGTA 60.082 41.667 4.27 0.00 34.87 2.24
4594 5347 3.265791 GAACTCGATGATGGAGCAAAGT 58.734 45.455 4.27 0.00 34.87 2.66
4636 5389 6.153510 GGGACCTCTTCTTAAGCATCAAATTT 59.846 38.462 0.00 0.00 0.00 1.82
4638 5391 5.044550 AGGGACCTCTTCTTAAGCATCAAAT 60.045 40.000 0.00 0.00 0.00 2.32
4658 5411 0.934446 TGCCTAGCTAGGAAGAGGGA 59.066 55.000 38.74 15.92 46.63 4.20
4675 5428 0.876342 GCCGTAGCACTAGGACATGC 60.876 60.000 0.00 0.00 42.39 4.06
4686 5439 1.530891 CCTAGCTAGGGCCGTAGCA 60.531 63.158 42.83 31.31 46.81 3.49
4716 5473 1.063114 AGTAGGTAGCCGGATTGTCCT 60.063 52.381 5.05 10.90 33.30 3.85
4717 5474 1.068741 CAGTAGGTAGCCGGATTGTCC 59.931 57.143 5.05 2.39 0.00 4.02
4718 5475 1.068741 CCAGTAGGTAGCCGGATTGTC 59.931 57.143 5.05 0.00 0.00 3.18
4720 5477 0.393077 CCCAGTAGGTAGCCGGATTG 59.607 60.000 5.05 0.00 0.00 2.67
4773 5532 1.294857 CCGGCAACCAAAACTTTTGG 58.705 50.000 25.71 25.71 44.91 3.28
4817 5576 1.154225 CGTTGCTGTCATTTCGCCC 60.154 57.895 0.00 0.00 0.00 6.13
4823 5582 0.670546 CCGTCTCCGTTGCTGTCATT 60.671 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.