Multiple sequence alignment - TraesCS5B01G502300

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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 TraesCS5B01G502300 chr5B 100.000 3564 0 0 1 3564 669480745 669484308 0.000000e+00 6582
1 TraesCS5B01G502300 chr5B 85.507 138 19 1 3427 3564 669439053 669438917 3.710000e-30 143
2 TraesCS5B01G502300 chr5B 84.783 138 21 0 3427 3564 669443249 669443112 4.800000e-29 139
3 TraesCS5B01G502300 chr5B 84.848 132 20 0 3433 3564 669434850 669434719 2.230000e-27 134
4 TraesCS5B01G502300 chr5D 93.907 2429 103 26 901 3318 530404717 530407111 0.000000e+00 3624
5 TraesCS5B01G502300 chr5D 89.356 761 56 14 22 769 530403967 530404715 0.000000e+00 933
6 TraesCS5B01G502300 chr5D 99.301 143 1 0 3422 3564 530407110 530407252 3.530000e-65 259
7 TraesCS5B01G502300 chr5D 86.364 132 18 0 3433 3564 530221024 530220893 1.030000e-30 145
8 TraesCS5B01G502300 chr5D 86.364 132 18 0 3433 3564 530302818 530302687 1.030000e-30 145
9 TraesCS5B01G502300 chr5D 86.607 112 7 5 3162 3271 530360921 530360816 2.250000e-22 117
10 TraesCS5B01G502300 chr5A 90.384 2475 156 35 556 3009 658597086 658599499 0.000000e+00 3177
11 TraesCS5B01G502300 chr5A 90.264 493 40 6 23 514 658596604 658597089 3.880000e-179 638
12 TraesCS5B01G502300 chr5A 95.798 119 4 1 3307 3424 245653770 245653652 1.310000e-44 191
13 TraesCS5B01G502300 chr5A 91.852 135 11 0 3427 3561 658599736 658599870 4.700000e-44 189
14 TraesCS5B01G502300 chr5A 86.719 128 16 1 3431 3557 658507840 658507713 1.330000e-29 141
15 TraesCS5B01G502300 chr5A 82.576 132 23 0 3433 3564 658490590 658490459 2.250000e-22 117
16 TraesCS5B01G502300 chr3B 100.000 108 0 0 3317 3424 593563583 593563690 2.170000e-47 200
17 TraesCS5B01G502300 chr3B 99.091 110 1 0 3314 3423 577429315 577429206 7.800000e-47 198
18 TraesCS5B01G502300 chr3B 99.091 110 1 0 3314 3423 776360336 776360227 7.800000e-47 198
19 TraesCS5B01G502300 chr3A 98.214 112 2 0 3313 3424 707385971 707385860 2.810000e-46 196
20 TraesCS5B01G502300 chr7B 97.368 114 3 0 3315 3428 622241333 622241446 1.010000e-45 195
21 TraesCS5B01G502300 chr7B 93.600 125 6 2 3316 3438 29592151 29592275 6.080000e-43 185
22 TraesCS5B01G502300 chr1B 97.368 114 3 0 3314 3427 491705798 491705685 1.010000e-45 195
23 TraesCS5B01G502300 chr6B 97.345 113 3 0 3312 3424 120355392 120355504 3.630000e-45 193


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 TraesCS5B01G502300 chr5B 669480745 669484308 3563 False 6582.000000 6582 100.000000 1 3564 1 chr5B.!!$F1 3563
1 TraesCS5B01G502300 chr5D 530403967 530407252 3285 False 1605.333333 3624 94.188000 22 3564 3 chr5D.!!$F1 3542
2 TraesCS5B01G502300 chr5A 658596604 658599870 3266 False 1334.666667 3177 90.833333 23 3561 3 chr5A.!!$F1 3538

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
468 477 0.248565 TGTCACTCAGCTGATCTGGC 59.751 55.0 18.63 16.95 43.06 4.85 F
472 481 0.249676 ACTCAGCTGATCTGGCAGTG 59.750 55.0 18.63 4.48 43.06 3.66 F
854 867 0.383590 GTGAGCTAGCGCAGATCTCA 59.616 55.0 22.18 17.53 40.51 3.27 F
2018 2046 0.723414 CTACATCAGCACTTGTGGCG 59.277 55.0 2.81 0.00 36.08 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 1917 0.950116 GATGCTGCTGATGGCCTAAC 59.050 55.0 3.32 0.00 40.92 2.34 R
1897 1924 1.015109 GACACTGGATGCTGCTGATG 58.985 55.0 0.00 0.00 0.00 3.07 R
2274 2304 1.698874 AATCCTCCCTGGGATGGTTT 58.301 50.0 17.51 16.45 44.50 3.27 R
3410 3468 0.251519 ACGTTCCTACTCCCTCCGTT 60.252 55.0 0.00 0.00 0.00 4.44 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
112 113 2.406616 CCCTGTTGCCATACGCCAC 61.407 63.158 0.00 0.00 36.24 5.01
119 120 0.391927 TGCCATACGCCACCAAGTAC 60.392 55.000 0.00 0.00 36.24 2.73
122 123 2.277084 CCATACGCCACCAAGTACTTC 58.723 52.381 4.77 0.00 0.00 3.01
139 140 3.449227 CTGTGCCCATGCCTGCAG 61.449 66.667 6.78 6.78 38.34 4.41
144 145 2.996395 CCCATGCCTGCAGACTCT 59.004 61.111 17.39 0.00 0.00 3.24
146 147 1.600638 CCATGCCTGCAGACTCTGA 59.399 57.895 17.39 0.00 32.44 3.27
160 161 3.387374 AGACTCTGATAGCTTCCATGGTG 59.613 47.826 12.58 7.38 0.00 4.17
174 179 0.751277 ATGGTGTGGTGTGGTGTGTG 60.751 55.000 0.00 0.00 0.00 3.82
182 187 1.001378 GGTGTGGTGTGTGCAGATTTC 60.001 52.381 0.00 0.00 0.00 2.17
210 215 8.420374 TTCATTTCTCTTACCGATGTCATTAC 57.580 34.615 0.00 0.00 0.00 1.89
223 228 2.092429 TGTCATTACAGGGGATGGAAGC 60.092 50.000 0.00 0.00 34.35 3.86
226 231 1.681229 TTACAGGGGATGGAAGCCTT 58.319 50.000 0.00 0.00 46.10 4.35
228 233 0.786435 ACAGGGGATGGAAGCCTTTT 59.214 50.000 0.00 0.00 46.10 2.27
269 277 4.837896 TCTAGACTGGATGATAACTGCG 57.162 45.455 0.00 0.00 0.00 5.18
283 291 6.869695 TGATAACTGCGAATTAGACAACCTA 58.130 36.000 0.00 0.00 0.00 3.08
349 358 2.698274 TGGTGACTGACTGACTGCTAAA 59.302 45.455 0.00 0.00 0.00 1.85
361 370 3.753272 TGACTGCTAAAGAACAATCAGGC 59.247 43.478 0.00 0.00 0.00 4.85
369 378 7.286087 TGCTAAAGAACAATCAGGCAATATCAT 59.714 33.333 0.00 0.00 0.00 2.45
373 382 7.976135 AGAACAATCAGGCAATATCATCTAC 57.024 36.000 0.00 0.00 0.00 2.59
385 394 7.332926 GGCAATATCATCTACACAACCTGATAG 59.667 40.741 0.00 0.00 33.62 2.08
386 395 7.875041 GCAATATCATCTACACAACCTGATAGT 59.125 37.037 0.00 0.00 33.62 2.12
387 396 9.770097 CAATATCATCTACACAACCTGATAGTT 57.230 33.333 0.00 0.00 33.62 2.24
439 448 8.621286 CAACAATATGGTAAATCCTAACAGACC 58.379 37.037 0.00 0.00 37.07 3.85
461 470 2.625737 CCTGGTAATGTCACTCAGCTG 58.374 52.381 7.63 7.63 0.00 4.24
468 477 0.248565 TGTCACTCAGCTGATCTGGC 59.751 55.000 18.63 16.95 43.06 4.85
472 481 0.249676 ACTCAGCTGATCTGGCAGTG 59.750 55.000 18.63 4.48 43.06 3.66
477 486 2.113807 AGCTGATCTGGCAGTGACATA 58.886 47.619 15.27 0.00 38.17 2.29
479 488 3.054875 AGCTGATCTGGCAGTGACATAAA 60.055 43.478 15.27 0.00 38.17 1.40
498 507 7.771183 ACATAAACAACATATGGTGGTCATTC 58.229 34.615 24.24 0.00 36.97 2.67
536 546 1.402787 AGTGGGCACAAGACCTTTTG 58.597 50.000 0.00 0.00 46.30 2.44
555 565 1.843206 TGGTATTGGCACCTGATAGCA 59.157 47.619 5.04 5.04 39.50 3.49
588 598 5.452078 AATCTGAGAGCTGACATACTAGC 57.548 43.478 0.00 0.00 40.18 3.42
607 617 7.136822 ACTAGCACAGGATAACCATAATTCA 57.863 36.000 0.00 0.00 38.94 2.57
820 833 8.846211 TGGTCGAAACAAAAGAGAGAATTTTAT 58.154 29.630 0.00 0.00 0.00 1.40
844 857 5.255710 TGAAGTGAAGATAGTGAGCTAGC 57.744 43.478 6.62 6.62 34.04 3.42
845 858 3.980646 AGTGAAGATAGTGAGCTAGCG 57.019 47.619 9.55 0.00 38.53 4.26
846 859 2.034053 AGTGAAGATAGTGAGCTAGCGC 59.966 50.000 12.00 12.00 38.53 5.92
847 860 2.024414 TGAAGATAGTGAGCTAGCGCA 58.976 47.619 17.82 17.82 38.53 6.09
848 861 2.033927 TGAAGATAGTGAGCTAGCGCAG 59.966 50.000 22.18 6.31 38.53 5.18
849 862 1.974265 AGATAGTGAGCTAGCGCAGA 58.026 50.000 22.18 13.09 38.53 4.26
850 863 2.513753 AGATAGTGAGCTAGCGCAGAT 58.486 47.619 22.18 17.21 38.53 2.90
851 864 2.487762 AGATAGTGAGCTAGCGCAGATC 59.512 50.000 22.18 23.57 40.26 2.75
852 865 1.974265 TAGTGAGCTAGCGCAGATCT 58.026 50.000 22.18 16.97 40.51 2.75
853 866 0.667993 AGTGAGCTAGCGCAGATCTC 59.332 55.000 22.18 17.48 40.51 2.75
854 867 0.383590 GTGAGCTAGCGCAGATCTCA 59.616 55.000 22.18 17.53 40.51 3.27
855 868 1.106285 TGAGCTAGCGCAGATCTCAA 58.894 50.000 17.82 0.00 40.51 3.02
856 869 1.202348 TGAGCTAGCGCAGATCTCAAC 60.202 52.381 17.82 1.81 40.51 3.18
857 870 0.820226 AGCTAGCGCAGATCTCAACA 59.180 50.000 11.47 0.00 39.10 3.33
858 871 1.411977 AGCTAGCGCAGATCTCAACAT 59.588 47.619 11.47 0.00 39.10 2.71
859 872 2.625314 AGCTAGCGCAGATCTCAACATA 59.375 45.455 11.47 0.00 39.10 2.29
860 873 2.985809 GCTAGCGCAGATCTCAACATAG 59.014 50.000 11.47 0.00 35.78 2.23
861 874 3.304996 GCTAGCGCAGATCTCAACATAGA 60.305 47.826 11.47 0.00 35.78 1.98
862 875 3.808466 AGCGCAGATCTCAACATAGAA 57.192 42.857 11.47 0.00 0.00 2.10
863 876 3.452474 AGCGCAGATCTCAACATAGAAC 58.548 45.455 11.47 0.00 0.00 3.01
864 877 3.131933 AGCGCAGATCTCAACATAGAACT 59.868 43.478 11.47 0.00 0.00 3.01
865 878 4.339530 AGCGCAGATCTCAACATAGAACTA 59.660 41.667 11.47 0.00 28.51 2.24
866 879 4.442733 GCGCAGATCTCAACATAGAACTAC 59.557 45.833 0.30 0.00 28.51 2.73
867 880 4.672862 CGCAGATCTCAACATAGAACTACG 59.327 45.833 0.00 0.00 31.56 3.51
876 889 5.826208 TCAACATAGAACTACGCCTAGATGA 59.174 40.000 0.00 0.00 0.00 2.92
893 906 2.198827 TGAAAGGGTGTAGGTGCATG 57.801 50.000 0.00 0.00 0.00 4.06
894 907 1.271871 TGAAAGGGTGTAGGTGCATGG 60.272 52.381 0.00 0.00 0.00 3.66
911 924 3.261643 GCATGGGGTTTCAGAAAATTCCT 59.738 43.478 0.00 0.00 0.00 3.36
920 933 8.638873 GGGTTTCAGAAAATTCCTTCTCTAAAA 58.361 33.333 0.00 0.00 33.25 1.52
985 998 6.110033 TGTTCTGCTTAGTTGAACAAGTACA 58.890 36.000 15.39 2.00 44.44 2.90
986 999 6.765989 TGTTCTGCTTAGTTGAACAAGTACAT 59.234 34.615 15.39 0.00 44.44 2.29
991 1008 3.120321 AGTTGAACAAGTACATGCCGA 57.880 42.857 0.00 0.00 0.00 5.54
1059 1076 1.625818 GATGGCCTCTATGGGGTACAG 59.374 57.143 3.32 0.00 36.00 2.74
1185 1202 3.684788 TGAAGATCAAGTAAGCTTTCGGC 59.315 43.478 3.20 0.00 42.19 5.54
1205 1223 4.464008 GGCTTTCAGTCCCATCATTATGA 58.536 43.478 0.00 0.00 34.84 2.15
1670 1696 5.153950 ACTCACTAATTGGAGTTGGAGTC 57.846 43.478 0.00 0.00 41.40 3.36
1791 1817 9.854303 AGATATGTTTATAGGGTAATGGGTAGT 57.146 33.333 0.00 0.00 0.00 2.73
1890 1917 7.642978 GATGTGTTCATTCTGCTTAATAAGCTG 59.357 37.037 23.43 22.21 43.63 4.24
1966 1994 8.693120 TCCTACTTGAATATTACGAGATCTGT 57.307 34.615 0.00 1.20 0.00 3.41
1967 1995 8.568794 TCCTACTTGAATATTACGAGATCTGTG 58.431 37.037 0.00 0.00 0.00 3.66
1989 2017 7.276658 TGTGTGTGATAACCTTCTTTCTGTTA 58.723 34.615 0.00 0.00 0.00 2.41
2018 2046 0.723414 CTACATCAGCACTTGTGGCG 59.277 55.000 2.81 0.00 36.08 5.69
2270 2300 7.615365 TCCTGCCATGTTACTTTCAGAATAATT 59.385 33.333 0.00 0.00 0.00 1.40
2271 2301 8.902806 CCTGCCATGTTACTTTCAGAATAATTA 58.097 33.333 0.00 0.00 0.00 1.40
2360 2390 4.507756 CGAAATGACACACAAGAGTTCTCA 59.492 41.667 2.64 0.00 0.00 3.27
2368 2398 3.072184 ACACAAGAGTTCTCATTCTGCCT 59.928 43.478 2.64 0.00 0.00 4.75
2571 2601 4.696479 AGCTTCTTGAATGACGGGATAT 57.304 40.909 0.00 0.00 0.00 1.63
2618 2648 4.466828 CCGCTGTTCAGTTATCAACAAAG 58.533 43.478 1.78 0.00 32.16 2.77
2656 2686 2.159379 TCGACCTGTCAGACATTGATCG 60.159 50.000 2.97 10.88 38.29 3.69
2727 2757 6.952358 TGGAGGATTAGTACACAGGGTATATC 59.048 42.308 0.00 0.00 33.76 1.63
2728 2758 6.952358 GGAGGATTAGTACACAGGGTATATCA 59.048 42.308 0.00 0.00 33.76 2.15
2759 2790 1.901591 TGAGACGAACTAGGAACCGT 58.098 50.000 0.00 0.00 38.01 4.83
2766 2797 2.867975 CGAACTAGGAACCGTTTTGTGT 59.132 45.455 0.00 0.00 0.00 3.72
2767 2798 3.302870 CGAACTAGGAACCGTTTTGTGTG 60.303 47.826 0.00 0.00 0.00 3.82
2923 2956 7.595819 TGGTTATTGACATTTTCCTTTCTGT 57.404 32.000 0.00 0.00 0.00 3.41
3009 3045 4.608948 AAGAACATCTCGTTGAAGACCT 57.391 40.909 0.00 0.00 38.19 3.85
3031 3069 4.326826 TCCTTCTGTCATTTAGCAACCAG 58.673 43.478 0.00 0.00 0.00 4.00
3064 3102 6.054941 CCAAGACCAAATTAAGGTTTGCTTT 58.945 36.000 4.19 0.00 40.09 3.51
3067 3105 9.271828 CAAGACCAAATTAAGGTTTGCTTTATT 57.728 29.630 4.19 0.00 40.09 1.40
3070 3108 8.831715 ACCAAATTAAGGTTTGCTTTATTCTG 57.168 30.769 0.00 0.00 37.67 3.02
3074 3112 9.830975 AAATTAAGGTTTGCTTTATTCTGTGTT 57.169 25.926 0.00 0.00 0.00 3.32
3075 3113 9.476202 AATTAAGGTTTGCTTTATTCTGTGTTC 57.524 29.630 0.00 0.00 0.00 3.18
3076 3114 6.715347 AAGGTTTGCTTTATTCTGTGTTCT 57.285 33.333 0.00 0.00 0.00 3.01
3077 3115 6.715347 AGGTTTGCTTTATTCTGTGTTCTT 57.285 33.333 0.00 0.00 0.00 2.52
3078 3116 7.112452 AGGTTTGCTTTATTCTGTGTTCTTT 57.888 32.000 0.00 0.00 0.00 2.52
3079 3117 7.555965 AGGTTTGCTTTATTCTGTGTTCTTTT 58.444 30.769 0.00 0.00 0.00 2.27
3080 3118 7.706607 AGGTTTGCTTTATTCTGTGTTCTTTTC 59.293 33.333 0.00 0.00 0.00 2.29
3083 3121 8.633075 TTGCTTTATTCTGTGTTCTTTTCTTG 57.367 30.769 0.00 0.00 0.00 3.02
3084 3122 7.995289 TGCTTTATTCTGTGTTCTTTTCTTGA 58.005 30.769 0.00 0.00 0.00 3.02
3085 3123 7.915397 TGCTTTATTCTGTGTTCTTTTCTTGAC 59.085 33.333 0.00 0.00 0.00 3.18
3086 3124 7.915397 GCTTTATTCTGTGTTCTTTTCTTGACA 59.085 33.333 0.00 0.00 0.00 3.58
3087 3125 9.787532 CTTTATTCTGTGTTCTTTTCTTGACAA 57.212 29.630 0.00 0.00 0.00 3.18
3089 3127 9.950680 TTATTCTGTGTTCTTTTCTTGACAATC 57.049 29.630 0.00 0.00 0.00 2.67
3091 3129 7.019774 TCTGTGTTCTTTTCTTGACAATCTG 57.980 36.000 0.00 0.00 0.00 2.90
3154 3192 7.390996 TGGCATAAAAATGAAGCAAATGTGATT 59.609 29.630 0.00 0.00 35.64 2.57
3175 3233 9.277783 GTGATTATATTCACATAACCTGCTTCT 57.722 33.333 18.50 0.00 44.38 2.85
3181 3239 5.086104 TCACATAACCTGCTTCTAGAACC 57.914 43.478 0.00 0.00 0.00 3.62
3182 3240 4.530553 TCACATAACCTGCTTCTAGAACCA 59.469 41.667 0.00 0.18 0.00 3.67
3185 3243 2.481289 ACCTGCTTCTAGAACCAAGC 57.519 50.000 0.00 4.04 44.55 4.01
3204 3262 1.511613 CCATGAAGGCTTCCCCTAGA 58.488 55.000 23.68 4.97 45.62 2.43
3207 3265 3.309121 CCATGAAGGCTTCCCCTAGAAAA 60.309 47.826 23.68 2.72 45.62 2.29
3216 3274 2.898662 TCCCCTAGAAAAGAGAACGGT 58.101 47.619 0.00 0.00 0.00 4.83
3295 3353 6.995511 TGGTAATGCAACTAGGAATGTTAC 57.004 37.500 0.00 0.00 0.00 2.50
3316 3374 1.460504 TCGAGTTCGACCATGCTACT 58.539 50.000 0.00 0.00 44.22 2.57
3317 3375 2.635714 TCGAGTTCGACCATGCTACTA 58.364 47.619 0.00 0.00 44.22 1.82
3318 3376 2.353889 TCGAGTTCGACCATGCTACTAC 59.646 50.000 0.00 0.00 44.22 2.73
3319 3377 2.355132 CGAGTTCGACCATGCTACTACT 59.645 50.000 0.00 0.00 43.02 2.57
3323 3381 1.214673 TCGACCATGCTACTACTCCCT 59.785 52.381 0.00 0.00 0.00 4.20
3324 3382 1.609555 CGACCATGCTACTACTCCCTC 59.390 57.143 0.00 0.00 0.00 4.30
3325 3383 1.964933 GACCATGCTACTACTCCCTCC 59.035 57.143 0.00 0.00 0.00 4.30
3327 3385 1.693627 CATGCTACTACTCCCTCCGT 58.306 55.000 0.00 0.00 0.00 4.69
3328 3386 2.032620 CATGCTACTACTCCCTCCGTT 58.967 52.381 0.00 0.00 0.00 4.44
3329 3387 1.760192 TGCTACTACTCCCTCCGTTC 58.240 55.000 0.00 0.00 0.00 3.95
3332 3390 0.911769 TACTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
3333 3391 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
3335 3393 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3336 3394 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3337 3395 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3339 3397 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3340 3398 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3342 3400 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3344 3402 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
3345 3403 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3346 3404 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
3347 3405 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
3348 3406 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
3349 3407 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
3350 3408 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
3352 3410 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
3353 3411 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
3355 3413 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
3356 3414 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
3358 3416 4.504858 ACTTGTCTCGGAAATGGATGTAC 58.495 43.478 0.00 0.00 0.00 2.90
3359 3417 3.536956 TGTCTCGGAAATGGATGTACC 57.463 47.619 0.00 0.00 39.54 3.34
3360 3418 3.104512 TGTCTCGGAAATGGATGTACCT 58.895 45.455 0.00 0.00 39.86 3.08
3363 3421 4.583489 GTCTCGGAAATGGATGTACCTAGA 59.417 45.833 0.00 0.00 39.86 2.43
3364 3422 5.068723 GTCTCGGAAATGGATGTACCTAGAA 59.931 44.000 0.00 0.00 39.86 2.10
3366 3424 4.960469 TCGGAAATGGATGTACCTAGAACT 59.040 41.667 0.00 0.00 39.86 3.01
3367 3425 6.131264 TCGGAAATGGATGTACCTAGAACTA 58.869 40.000 0.00 0.00 39.86 2.24
3368 3426 6.608405 TCGGAAATGGATGTACCTAGAACTAA 59.392 38.462 0.00 0.00 39.86 2.24
3370 3428 7.767198 CGGAAATGGATGTACCTAGAACTAAAA 59.233 37.037 0.00 0.00 39.86 1.52
3371 3429 9.628500 GGAAATGGATGTACCTAGAACTAAAAT 57.372 33.333 0.00 0.00 39.86 1.82
3397 3455 8.637196 ACATCTAGATACATCCATTTCTACGA 57.363 34.615 4.54 0.00 0.00 3.43
3398 3456 8.516234 ACATCTAGATACATCCATTTCTACGAC 58.484 37.037 4.54 0.00 0.00 4.34
3399 3457 8.515414 CATCTAGATACATCCATTTCTACGACA 58.485 37.037 4.54 0.00 0.00 4.35
3400 3458 8.459911 TCTAGATACATCCATTTCTACGACAA 57.540 34.615 0.00 0.00 0.00 3.18
3401 3459 8.568794 TCTAGATACATCCATTTCTACGACAAG 58.431 37.037 0.00 0.00 0.00 3.16
3402 3460 7.113658 AGATACATCCATTTCTACGACAAGT 57.886 36.000 0.00 0.00 0.00 3.16
3403 3461 8.234136 AGATACATCCATTTCTACGACAAGTA 57.766 34.615 0.00 0.00 0.00 2.24
3404 3462 8.692710 AGATACATCCATTTCTACGACAAGTAA 58.307 33.333 0.00 0.00 34.45 2.24
3405 3463 9.477484 GATACATCCATTTCTACGACAAGTAAT 57.523 33.333 0.00 0.00 34.45 1.89
3406 3464 9.832445 ATACATCCATTTCTACGACAAGTAATT 57.168 29.630 0.00 0.00 34.45 1.40
3407 3465 8.197988 ACATCCATTTCTACGACAAGTAATTC 57.802 34.615 0.00 0.00 34.45 2.17
3408 3466 7.280205 ACATCCATTTCTACGACAAGTAATTCC 59.720 37.037 0.00 0.00 34.45 3.01
3409 3467 5.808540 TCCATTTCTACGACAAGTAATTCCG 59.191 40.000 0.00 0.00 34.45 4.30
3410 3468 5.808540 CCATTTCTACGACAAGTAATTCCGA 59.191 40.000 0.00 0.00 34.45 4.55
3411 3469 6.311935 CCATTTCTACGACAAGTAATTCCGAA 59.688 38.462 0.00 0.00 34.45 4.30
3412 3470 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
3413 3471 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
3414 3472 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
3415 3473 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
3416 3474 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3417 3475 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3418 3476 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3419 3477 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3420 3478 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.043852 GTCGAGCTCCTCCCAGGA 60.044 66.667 8.47 0.00 43.43 3.86
112 113 2.086869 CATGGGCACAGAAGTACTTGG 58.913 52.381 14.14 7.58 0.00 3.61
119 120 2.707849 GCAGGCATGGGCACAGAAG 61.708 63.158 0.00 0.00 43.71 2.85
122 123 3.449227 CTGCAGGCATGGGCACAG 61.449 66.667 5.57 0.00 43.71 3.66
139 140 3.133721 ACACCATGGAAGCTATCAGAGTC 59.866 47.826 21.47 0.00 0.00 3.36
160 161 0.819259 ATCTGCACACACCACACCAC 60.819 55.000 0.00 0.00 0.00 4.16
168 169 6.643770 AGAAATGAAATGAAATCTGCACACAC 59.356 34.615 0.00 0.00 0.00 3.82
174 179 7.430502 CGGTAAGAGAAATGAAATGAAATCTGC 59.569 37.037 0.00 0.00 0.00 4.26
182 187 7.307493 TGACATCGGTAAGAGAAATGAAATG 57.693 36.000 0.00 0.00 0.00 2.32
210 215 1.942776 AAAAAGGCTTCCATCCCCTG 58.057 50.000 0.00 0.00 0.00 4.45
228 233 9.973450 GTCTAGATATCTAAGCACATGAAGAAA 57.027 33.333 13.41 0.00 0.00 2.52
231 239 8.028354 CCAGTCTAGATATCTAAGCACATGAAG 58.972 40.741 13.41 0.27 0.00 3.02
283 291 8.435931 TGCCAGATTATGTAGGTGATATTACT 57.564 34.615 0.00 0.00 0.00 2.24
349 358 7.443575 GTGTAGATGATATTGCCTGATTGTTCT 59.556 37.037 0.00 0.00 0.00 3.01
361 370 9.770097 AACTATCAGGTTGTGTAGATGATATTG 57.230 33.333 0.00 0.00 33.62 1.90
439 448 1.645034 CTGAGTGACATTACCAGGCG 58.355 55.000 0.00 0.00 0.00 5.52
461 470 4.455533 TGTTGTTTATGTCACTGCCAGATC 59.544 41.667 0.00 0.00 0.00 2.75
468 477 6.150976 ACCACCATATGTTGTTTATGTCACTG 59.849 38.462 1.24 0.00 0.00 3.66
472 481 6.751514 TGACCACCATATGTTGTTTATGTC 57.248 37.500 1.24 1.34 0.00 3.06
477 486 6.916360 AAGAATGACCACCATATGTTGTTT 57.084 33.333 1.24 0.00 34.45 2.83
479 488 5.336690 GCAAAGAATGACCACCATATGTTGT 60.337 40.000 1.24 0.00 34.45 3.32
536 546 2.158755 AGTGCTATCAGGTGCCAATACC 60.159 50.000 0.00 0.00 41.17 2.73
555 565 8.481314 TGTCAGCTCTCAGATTATTATCAAAGT 58.519 33.333 0.00 0.00 32.95 2.66
573 583 2.690497 TCCTGTGCTAGTATGTCAGCTC 59.310 50.000 0.00 0.00 38.63 4.09
607 617 3.447229 CCCCTTTCGGCATGAAAAATACT 59.553 43.478 0.00 0.00 45.59 2.12
728 738 5.801531 TGAGTACTACAGTGTGTGGAAAT 57.198 39.130 5.88 0.00 32.79 2.17
729 739 5.069914 ACATGAGTACTACAGTGTGTGGAAA 59.930 40.000 5.88 0.00 32.79 3.13
739 749 8.757164 TTCACAACAATACATGAGTACTACAG 57.243 34.615 0.00 0.00 31.96 2.74
778 791 9.967346 TGTTTCGACCAAATAAATCAAACATAA 57.033 25.926 0.00 0.00 29.75 1.90
820 833 6.293680 CGCTAGCTCACTATCTTCACTTCATA 60.294 42.308 13.93 0.00 0.00 2.15
841 854 4.339530 AGTTCTATGTTGAGATCTGCGCTA 59.660 41.667 9.73 0.00 0.00 4.26
843 856 3.452474 AGTTCTATGTTGAGATCTGCGC 58.548 45.455 0.00 0.00 0.00 6.09
844 857 4.672862 CGTAGTTCTATGTTGAGATCTGCG 59.327 45.833 0.00 7.33 41.59 5.18
845 858 4.442733 GCGTAGTTCTATGTTGAGATCTGC 59.557 45.833 0.00 0.00 30.06 4.26
846 859 4.979197 GGCGTAGTTCTATGTTGAGATCTG 59.021 45.833 0.00 0.00 30.06 2.90
847 860 4.890581 AGGCGTAGTTCTATGTTGAGATCT 59.109 41.667 0.00 0.00 31.79 2.75
848 861 5.189659 AGGCGTAGTTCTATGTTGAGATC 57.810 43.478 1.80 0.00 0.00 2.75
849 862 6.062749 TCTAGGCGTAGTTCTATGTTGAGAT 58.937 40.000 12.88 0.00 0.00 2.75
850 863 5.434408 TCTAGGCGTAGTTCTATGTTGAGA 58.566 41.667 12.88 0.00 0.00 3.27
851 864 5.752892 TCTAGGCGTAGTTCTATGTTGAG 57.247 43.478 12.88 0.00 0.00 3.02
852 865 5.826208 TCATCTAGGCGTAGTTCTATGTTGA 59.174 40.000 12.88 3.32 0.00 3.18
853 866 6.073327 TCATCTAGGCGTAGTTCTATGTTG 57.927 41.667 12.88 1.42 0.00 3.33
854 867 6.710597 TTCATCTAGGCGTAGTTCTATGTT 57.289 37.500 12.88 0.00 0.00 2.71
855 868 6.239064 CCTTTCATCTAGGCGTAGTTCTATGT 60.239 42.308 12.88 0.00 0.00 2.29
856 869 6.153067 CCTTTCATCTAGGCGTAGTTCTATG 58.847 44.000 12.88 9.32 0.00 2.23
857 870 5.244178 CCCTTTCATCTAGGCGTAGTTCTAT 59.756 44.000 12.88 0.00 0.00 1.98
858 871 4.583489 CCCTTTCATCTAGGCGTAGTTCTA 59.417 45.833 12.88 0.00 0.00 2.10
859 872 3.385111 CCCTTTCATCTAGGCGTAGTTCT 59.615 47.826 12.88 0.00 0.00 3.01
860 873 3.132467 ACCCTTTCATCTAGGCGTAGTTC 59.868 47.826 12.88 0.00 0.00 3.01
861 874 3.105283 ACCCTTTCATCTAGGCGTAGTT 58.895 45.455 12.88 2.37 0.00 2.24
862 875 2.431057 CACCCTTTCATCTAGGCGTAGT 59.569 50.000 12.88 0.00 0.00 2.73
863 876 2.431057 ACACCCTTTCATCTAGGCGTAG 59.569 50.000 7.12 7.12 0.00 3.51
864 877 2.463752 ACACCCTTTCATCTAGGCGTA 58.536 47.619 0.00 0.00 0.00 4.42
865 878 1.276622 ACACCCTTTCATCTAGGCGT 58.723 50.000 0.00 0.00 0.00 5.68
866 879 2.224066 CCTACACCCTTTCATCTAGGCG 60.224 54.545 0.00 0.00 0.00 5.52
867 880 2.772515 ACCTACACCCTTTCATCTAGGC 59.227 50.000 0.00 0.00 0.00 3.93
876 889 0.039618 CCCATGCACCTACACCCTTT 59.960 55.000 0.00 0.00 0.00 3.11
893 906 5.080337 AGAGAAGGAATTTTCTGAAACCCC 58.920 41.667 1.58 4.68 37.53 4.95
894 907 7.761038 TTAGAGAAGGAATTTTCTGAAACCC 57.239 36.000 1.58 5.02 37.53 4.11
920 933 6.238759 GGGAAAATAGTTGCGCTGAGATATTT 60.239 38.462 9.73 9.47 0.00 1.40
985 998 3.016736 CTCCCATTTACTTGTTCGGCAT 58.983 45.455 0.00 0.00 0.00 4.40
986 999 2.224670 ACTCCCATTTACTTGTTCGGCA 60.225 45.455 0.00 0.00 0.00 5.69
991 1008 3.826729 GCCTGAACTCCCATTTACTTGTT 59.173 43.478 0.00 0.00 0.00 2.83
1077 1094 8.834465 GTTTTGATAGCTTCATCATCACTGTAT 58.166 33.333 0.00 0.00 34.95 2.29
1146 1163 2.542020 TCAAACTTCGAGTCATGCCA 57.458 45.000 0.00 0.00 0.00 4.92
1185 1202 6.183360 GGTGTTCATAATGATGGGACTGAAAG 60.183 42.308 0.00 0.00 34.91 2.62
1190 1208 4.860802 TGGTGTTCATAATGATGGGACT 57.139 40.909 0.00 0.00 33.49 3.85
1205 1223 5.630121 TCTAACAATTGTCTGGATGGTGTT 58.370 37.500 12.39 0.00 0.00 3.32
1296 1322 1.997874 GGCATGGGGGTCTCTGTCT 60.998 63.158 0.00 0.00 0.00 3.41
1890 1917 0.950116 GATGCTGCTGATGGCCTAAC 59.050 55.000 3.32 0.00 40.92 2.34
1892 1919 1.347243 TGGATGCTGCTGATGGCCTA 61.347 55.000 3.32 0.00 40.92 3.93
1897 1924 1.015109 GACACTGGATGCTGCTGATG 58.985 55.000 0.00 0.00 0.00 3.07
1942 1970 8.353684 ACACAGATCTCGTAATATTCAAGTAGG 58.646 37.037 0.00 0.00 0.00 3.18
1966 1994 7.506114 ACTAACAGAAAGAAGGTTATCACACA 58.494 34.615 0.00 0.00 0.00 3.72
1967 1995 7.964604 ACTAACAGAAAGAAGGTTATCACAC 57.035 36.000 0.00 0.00 0.00 3.82
2018 2046 4.974399 AGGTACAAGCTATAAATCAGGCC 58.026 43.478 0.00 0.00 0.00 5.19
2053 2081 9.347240 AGAAGTTGCAGTCATAATATAATGCTT 57.653 29.630 0.00 0.00 34.80 3.91
2054 2082 8.915057 AGAAGTTGCAGTCATAATATAATGCT 57.085 30.769 0.00 0.00 34.80 3.79
2270 2300 4.029142 TCCTCCCTGGGATGGTTTATTA 57.971 45.455 17.51 0.41 36.20 0.98
2271 2301 2.871796 TCCTCCCTGGGATGGTTTATT 58.128 47.619 17.51 0.00 36.20 1.40
2272 2302 2.605825 TCCTCCCTGGGATGGTTTAT 57.394 50.000 17.51 0.00 36.20 1.40
2273 2303 2.605825 ATCCTCCCTGGGATGGTTTA 57.394 50.000 17.51 4.91 43.70 2.01
2274 2304 1.698874 AATCCTCCCTGGGATGGTTT 58.301 50.000 17.51 16.45 44.50 3.27
2275 2305 1.698874 AAATCCTCCCTGGGATGGTT 58.301 50.000 17.51 13.55 44.50 3.67
2283 2313 6.665248 AGAACCAAAGAAATAAATCCTCCCTG 59.335 38.462 0.00 0.00 0.00 4.45
2334 2364 4.060038 ACTCTTGTGTGTCATTTCGAGT 57.940 40.909 0.00 0.00 0.00 4.18
2360 2390 3.056322 GCAAATGAAACCTGAGGCAGAAT 60.056 43.478 0.00 0.00 32.44 2.40
2571 2601 2.446435 GGAAGAACATGGCAGCCTTAA 58.554 47.619 14.15 0.00 0.00 1.85
2748 2778 2.940410 CACACACAAAACGGTTCCTAGT 59.060 45.455 0.00 0.00 0.00 2.57
2845 2876 8.330302 ACAACAACAAAGAACATAAGTACGTAC 58.670 33.333 18.10 18.10 0.00 3.67
2846 2877 8.329583 CACAACAACAAAGAACATAAGTACGTA 58.670 33.333 0.00 0.00 0.00 3.57
2847 2878 7.148373 ACACAACAACAAAGAACATAAGTACGT 60.148 33.333 0.00 0.00 0.00 3.57
2848 2879 7.184106 ACACAACAACAAAGAACATAAGTACG 58.816 34.615 0.00 0.00 0.00 3.67
2990 3026 3.056465 AGGAGGTCTTCAACGAGATGTTC 60.056 47.826 0.00 0.00 39.29 3.18
3009 3045 4.202461 ACTGGTTGCTAAATGACAGAAGGA 60.202 41.667 0.00 0.00 0.00 3.36
3064 3102 9.342308 AGATTGTCAAGAAAAGAACACAGAATA 57.658 29.630 0.00 0.00 0.00 1.75
3067 3105 6.599244 ACAGATTGTCAAGAAAAGAACACAGA 59.401 34.615 0.00 0.00 0.00 3.41
3070 3108 7.970614 AGAAACAGATTGTCAAGAAAAGAACAC 59.029 33.333 0.00 0.00 0.00 3.32
3074 3112 7.121168 ACACAGAAACAGATTGTCAAGAAAAGA 59.879 33.333 0.00 0.00 0.00 2.52
3075 3113 7.253422 ACACAGAAACAGATTGTCAAGAAAAG 58.747 34.615 0.00 0.00 0.00 2.27
3076 3114 7.156876 ACACAGAAACAGATTGTCAAGAAAA 57.843 32.000 0.00 0.00 0.00 2.29
3077 3115 6.757897 ACACAGAAACAGATTGTCAAGAAA 57.242 33.333 0.00 0.00 0.00 2.52
3078 3116 6.599244 AGAACACAGAAACAGATTGTCAAGAA 59.401 34.615 0.00 0.00 0.00 2.52
3079 3117 6.115446 AGAACACAGAAACAGATTGTCAAGA 58.885 36.000 0.00 0.00 0.00 3.02
3080 3118 6.369059 AGAACACAGAAACAGATTGTCAAG 57.631 37.500 0.00 0.00 0.00 3.02
3083 3121 7.475840 AGAAAAGAACACAGAAACAGATTGTC 58.524 34.615 0.00 0.00 0.00 3.18
3084 3122 7.396540 AGAAAAGAACACAGAAACAGATTGT 57.603 32.000 0.00 0.00 0.00 2.71
3085 3123 7.970061 TCAAGAAAAGAACACAGAAACAGATTG 59.030 33.333 0.00 0.00 0.00 2.67
3086 3124 7.970614 GTCAAGAAAAGAACACAGAAACAGATT 59.029 33.333 0.00 0.00 0.00 2.40
3087 3125 7.121168 TGTCAAGAAAAGAACACAGAAACAGAT 59.879 33.333 0.00 0.00 0.00 2.90
3088 3126 6.429692 TGTCAAGAAAAGAACACAGAAACAGA 59.570 34.615 0.00 0.00 0.00 3.41
3089 3127 6.611381 TGTCAAGAAAAGAACACAGAAACAG 58.389 36.000 0.00 0.00 0.00 3.16
3091 3129 7.970614 AGATTGTCAAGAAAAGAACACAGAAAC 59.029 33.333 0.00 0.00 0.00 2.78
3154 3192 9.982651 GTTCTAGAAGCAGGTTATGTGAATATA 57.017 33.333 5.12 0.00 0.00 0.86
3185 3243 1.511613 TCTAGGGGAAGCCTTCATGG 58.488 55.000 6.80 0.00 39.35 3.66
3197 3255 3.697619 AACCGTTCTCTTTTCTAGGGG 57.302 47.619 0.00 0.00 0.00 4.79
3200 3258 8.823818 TGTTTCTTTAACCGTTCTCTTTTCTAG 58.176 33.333 0.00 0.00 35.81 2.43
3203 3261 9.378597 GTATGTTTCTTTAACCGTTCTCTTTTC 57.621 33.333 0.00 0.00 35.81 2.29
3204 3262 8.347771 GGTATGTTTCTTTAACCGTTCTCTTTT 58.652 33.333 0.00 0.00 35.81 2.27
3207 3265 6.527423 TGGTATGTTTCTTTAACCGTTCTCT 58.473 36.000 0.00 0.00 35.81 3.10
3316 3374 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3317 3375 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3318 3376 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3319 3377 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3323 3381 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
3324 3382 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3325 3383 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
3327 3385 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
3328 3386 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
3329 3387 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
3332 3390 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
3333 3391 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
3335 3393 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3336 3394 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3337 3395 3.871594 GGTACATCCATTTCCGAGACAAG 59.128 47.826 0.00 0.00 35.97 3.16
3339 3397 3.104512 AGGTACATCCATTTCCGAGACA 58.895 45.455 0.00 0.00 39.02 3.41
3340 3398 3.821421 AGGTACATCCATTTCCGAGAC 57.179 47.619 0.00 0.00 39.02 3.36
3342 3400 5.069251 AGTTCTAGGTACATCCATTTCCGAG 59.931 44.000 0.00 0.00 39.02 4.63
3344 3402 5.277857 AGTTCTAGGTACATCCATTTCCG 57.722 43.478 0.00 0.00 39.02 4.30
3345 3403 9.628500 ATTTTAGTTCTAGGTACATCCATTTCC 57.372 33.333 0.00 0.00 39.02 3.13
3371 3429 9.734984 TCGTAGAAATGGATGTATCTAGATGTA 57.265 33.333 15.79 4.44 0.00 2.29
3372 3430 8.516234 GTCGTAGAAATGGATGTATCTAGATGT 58.484 37.037 15.79 1.25 39.69 3.06
3373 3431 8.515414 TGTCGTAGAAATGGATGTATCTAGATG 58.485 37.037 15.79 0.00 39.69 2.90
3374 3432 8.637196 TGTCGTAGAAATGGATGTATCTAGAT 57.363 34.615 10.73 10.73 39.69 1.98
3375 3433 8.459911 TTGTCGTAGAAATGGATGTATCTAGA 57.540 34.615 0.00 0.00 39.69 2.43
3376 3434 8.353684 ACTTGTCGTAGAAATGGATGTATCTAG 58.646 37.037 0.00 0.00 39.69 2.43
3377 3435 8.234136 ACTTGTCGTAGAAATGGATGTATCTA 57.766 34.615 0.00 0.00 39.69 1.98
3378 3436 7.113658 ACTTGTCGTAGAAATGGATGTATCT 57.886 36.000 0.00 0.00 39.69 1.98
3379 3437 8.867112 TTACTTGTCGTAGAAATGGATGTATC 57.133 34.615 0.00 0.00 39.69 2.24
3380 3438 9.832445 AATTACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
3381 3439 9.309516 GAATTACTTGTCGTAGAAATGGATGTA 57.690 33.333 0.00 0.00 39.69 2.29
3382 3440 7.280205 GGAATTACTTGTCGTAGAAATGGATGT 59.720 37.037 0.00 0.00 39.69 3.06
3383 3441 7.516785 CGGAATTACTTGTCGTAGAAATGGATG 60.517 40.741 0.00 0.00 39.69 3.51
3384 3442 6.479001 CGGAATTACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
3385 3443 5.808540 CGGAATTACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
3386 3444 5.808540 TCGGAATTACTTGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
3387 3445 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
3388 3446 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
3389 3447 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
3390 3448 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
3391 3449 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
3392 3450 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
3393 3451 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
3394 3452 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
3395 3453 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3396 3454 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3397 3455 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3398 3456 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3399 3457 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3400 3458 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3401 3459 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3402 3460 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3403 3461 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3404 3462 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
3405 3463 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
3406 3464 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
3407 3465 0.682209 TTCCTACTCCCTCCGTTCGG 60.682 60.000 4.74 4.74 0.00 4.30
3408 3466 0.455005 GTTCCTACTCCCTCCGTTCG 59.545 60.000 0.00 0.00 0.00 3.95
3409 3467 0.455005 CGTTCCTACTCCCTCCGTTC 59.545 60.000 0.00 0.00 0.00 3.95
3410 3468 0.251519 ACGTTCCTACTCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
3411 3469 0.620556 TACGTTCCTACTCCCTCCGT 59.379 55.000 0.00 0.00 0.00 4.69
3412 3470 1.020437 GTACGTTCCTACTCCCTCCG 58.980 60.000 0.00 0.00 0.00 4.63
3413 3471 1.020437 CGTACGTTCCTACTCCCTCC 58.980 60.000 7.22 0.00 0.00 4.30
3414 3472 1.399791 CACGTACGTTCCTACTCCCTC 59.600 57.143 20.23 0.00 0.00 4.30
3415 3473 1.003580 TCACGTACGTTCCTACTCCCT 59.996 52.381 20.23 0.00 0.00 4.20
3416 3474 1.453155 TCACGTACGTTCCTACTCCC 58.547 55.000 20.23 0.00 0.00 4.30
3417 3475 2.421424 ACATCACGTACGTTCCTACTCC 59.579 50.000 20.23 0.00 0.00 3.85
3418 3476 3.754188 ACATCACGTACGTTCCTACTC 57.246 47.619 20.23 0.00 0.00 2.59
3419 3477 4.510038 AAACATCACGTACGTTCCTACT 57.490 40.909 20.23 0.00 0.00 2.57
3420 3478 4.681025 TGAAAACATCACGTACGTTCCTAC 59.319 41.667 20.23 6.42 31.50 3.18


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

AutoCloner maintained by Alex Coulton.