Multiple sequence alignment - TraesCS1A01G229800

Loading Multiple Alignment...

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 TraesCS1A01G229800 chr1A 100.000 3395 0 0 1 3395 402279773 402276379 0.000000e+00 6270
1 TraesCS1A01G229800 chr1D 93.058 2103 89 31 696 2777 320582050 320584116 0.000000e+00 3022
2 TraesCS1A01G229800 chr1D 90.981 377 18 10 2845 3212 320584174 320584543 8.460000e-136 494
3 TraesCS1A01G229800 chr1B 91.978 2007 85 35 698 2678 433597638 433599594 0.000000e+00 2745
4 TraesCS1A01G229800 chr1B 94.048 168 3 5 2953 3120 433599616 433599776 7.270000e-62 248
5 TraesCS1A01G229800 chr5A 95.882 680 26 2 1 678 640951168 640950489 0.000000e+00 1099
6 TraesCS1A01G229800 chr5A 94.591 684 37 0 1 684 482129615 482130298 0.000000e+00 1059
7 TraesCS1A01G229800 chr5A 90.000 120 10 2 3278 3395 262367720 262367839 1.630000e-33 154
8 TraesCS1A01G229800 chr5A 90.598 117 9 2 3281 3395 554172495 554172379 1.630000e-33 154
9 TraesCS1A01G229800 chr4A 95.133 678 33 0 1 678 684018150 684018827 0.000000e+00 1070
10 TraesCS1A01G229800 chr4A 94.993 679 32 2 1 678 21854876 21854199 0.000000e+00 1064
11 TraesCS1A01G229800 chr4A 94.838 678 35 0 1 678 684037940 684038617 0.000000e+00 1059
12 TraesCS1A01G229800 chr4A 94.690 678 36 0 1 678 628816928 628816251 0.000000e+00 1053
13 TraesCS1A01G229800 chr4A 93.103 116 7 1 3281 3395 5252376 5252261 5.830000e-38 169
14 TraesCS1A01G229800 chr2A 94.838 678 35 0 1 678 148863165 148863842 0.000000e+00 1059
15 TraesCS1A01G229800 chr2A 94.838 678 34 1 1 678 750327313 750326637 0.000000e+00 1057
16 TraesCS1A01G229800 chr6A 94.698 679 34 2 1 678 542387488 542386811 0.000000e+00 1053
17 TraesCS1A01G229800 chr6A 91.304 115 8 2 3283 3395 607984589 607984703 4.540000e-34 156
18 TraesCS1A01G229800 chr6A 90.598 117 9 2 3281 3395 257323529 257323645 1.630000e-33 154
19 TraesCS1A01G229800 chr2D 93.162 117 6 1 3281 3395 22500722 22500606 1.620000e-38 171
20 TraesCS1A01G229800 chr2D 91.453 117 8 2 3281 3395 59659625 59659509 3.510000e-35 159
21 TraesCS1A01G229800 chr4D 92.241 116 7 1 3282 3395 36535895 36536010 2.710000e-36 163
22 TraesCS1A01G229800 chr3D 90.598 117 9 2 3281 3395 388809880 388809764 1.630000e-33 154


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 TraesCS1A01G229800 chr1A 402276379 402279773 3394 True 6270.0 6270 100.0000 1 3395 1 chr1A.!!$R1 3394
1 TraesCS1A01G229800 chr1D 320582050 320584543 2493 False 1758.0 3022 92.0195 696 3212 2 chr1D.!!$F1 2516
2 TraesCS1A01G229800 chr1B 433597638 433599776 2138 False 1496.5 2745 93.0130 698 3120 2 chr1B.!!$F1 2422
3 TraesCS1A01G229800 chr5A 640950489 640951168 679 True 1099.0 1099 95.8820 1 678 1 chr5A.!!$R2 677
4 TraesCS1A01G229800 chr5A 482129615 482130298 683 False 1059.0 1059 94.5910 1 684 1 chr5A.!!$F2 683
5 TraesCS1A01G229800 chr4A 684018150 684018827 677 False 1070.0 1070 95.1330 1 678 1 chr4A.!!$F1 677
6 TraesCS1A01G229800 chr4A 21854199 21854876 677 True 1064.0 1064 94.9930 1 678 1 chr4A.!!$R2 677
7 TraesCS1A01G229800 chr4A 684037940 684038617 677 False 1059.0 1059 94.8380 1 678 1 chr4A.!!$F2 677
8 TraesCS1A01G229800 chr4A 628816251 628816928 677 True 1053.0 1053 94.6900 1 678 1 chr4A.!!$R3 677
9 TraesCS1A01G229800 chr2A 148863165 148863842 677 False 1059.0 1059 94.8380 1 678 1 chr2A.!!$F1 677
10 TraesCS1A01G229800 chr2A 750326637 750327313 676 True 1057.0 1057 94.8380 1 678 1 chr2A.!!$R1 677
11 TraesCS1A01G229800 chr6A 542386811 542387488 677 True 1053.0 1053 94.6980 1 678 1 chr6A.!!$R1 677

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
685 688 0.038166 GGTGGAGTTGGCATGAGGAA 59.962 55.0 0.0 0.0 0.0 3.36 F
1677 1706 0.032615 GAGGCAGAGGAGGAGGAGAA 60.033 60.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2070 0.100146 CGTGGTACCCGTAGAAGCTC 59.900 60.0 10.07 0.0 0.0 4.09 R
3228 3301 0.041663 GCGGCTTATTTATGCGCGAA 60.042 50.0 12.10 0.0 0.0 4.70 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
140 142 1.271597 GCTTTGGGAGGTGATGACTGT 60.272 52.381 0.00 0.00 0.00 3.55
235 238 4.934356 TCAAGGTGAAAATATTGAGCCCT 58.066 39.130 0.00 0.00 0.00 5.19
587 590 4.147449 CGGCCACCGCATCTCAGA 62.147 66.667 2.24 0.00 41.17 3.27
599 602 0.537188 ATCTCAGAACACGCCCGAAT 59.463 50.000 0.00 0.00 0.00 3.34
602 605 0.604073 TCAGAACACGCCCGAATACA 59.396 50.000 0.00 0.00 0.00 2.29
612 615 1.828595 GCCCGAATACAACCCCAAATT 59.171 47.619 0.00 0.00 0.00 1.82
624 627 2.256306 CCCCAAATTGCTACCCAAACT 58.744 47.619 0.00 0.00 36.92 2.66
684 687 1.685224 GGTGGAGTTGGCATGAGGA 59.315 57.895 0.00 0.00 0.00 3.71
685 688 0.038166 GGTGGAGTTGGCATGAGGAA 59.962 55.000 0.00 0.00 0.00 3.36
686 689 1.457346 GTGGAGTTGGCATGAGGAAG 58.543 55.000 0.00 0.00 0.00 3.46
687 690 1.003580 GTGGAGTTGGCATGAGGAAGA 59.996 52.381 0.00 0.00 0.00 2.87
688 691 1.280133 TGGAGTTGGCATGAGGAAGAG 59.720 52.381 0.00 0.00 0.00 2.85
689 692 1.556911 GGAGTTGGCATGAGGAAGAGA 59.443 52.381 0.00 0.00 0.00 3.10
690 693 2.626840 GAGTTGGCATGAGGAAGAGAC 58.373 52.381 0.00 0.00 0.00 3.36
691 694 1.980765 AGTTGGCATGAGGAAGAGACA 59.019 47.619 0.00 0.00 0.00 3.41
692 695 2.373169 AGTTGGCATGAGGAAGAGACAA 59.627 45.455 0.00 0.00 0.00 3.18
693 696 2.746362 GTTGGCATGAGGAAGAGACAAG 59.254 50.000 0.00 0.00 0.00 3.16
694 697 1.280133 TGGCATGAGGAAGAGACAAGG 59.720 52.381 0.00 0.00 0.00 3.61
904 917 4.974721 CCCAGGCCACCACCACAC 62.975 72.222 5.01 0.00 0.00 3.82
905 918 4.974721 CCAGGCCACCACCACACC 62.975 72.222 5.01 0.00 0.00 4.16
906 919 4.202574 CAGGCCACCACCACACCA 62.203 66.667 5.01 0.00 0.00 4.17
907 920 4.204028 AGGCCACCACCACACCAC 62.204 66.667 5.01 0.00 0.00 4.16
908 921 4.514585 GGCCACCACCACACCACA 62.515 66.667 0.00 0.00 0.00 4.17
915 928 2.430332 CACCACCACACCACAGAAAAAT 59.570 45.455 0.00 0.00 0.00 1.82
1468 1491 1.169661 CCTCGTCATCCTCCTCCTCG 61.170 65.000 0.00 0.00 0.00 4.63
1530 1556 4.399395 CGCAGAGCCTGAGCCCAA 62.399 66.667 6.40 0.00 41.25 4.12
1540 1566 2.044946 GAGCCCAAACCCAGCGAT 60.045 61.111 0.00 0.00 0.00 4.58
1674 1703 1.309347 CAGAGGCAGAGGAGGAGGA 59.691 63.158 0.00 0.00 0.00 3.71
1675 1704 0.756442 CAGAGGCAGAGGAGGAGGAG 60.756 65.000 0.00 0.00 0.00 3.69
1676 1705 0.923729 AGAGGCAGAGGAGGAGGAGA 60.924 60.000 0.00 0.00 0.00 3.71
1677 1706 0.032615 GAGGCAGAGGAGGAGGAGAA 60.033 60.000 0.00 0.00 0.00 2.87
1681 1710 0.325110 CAGAGGAGGAGGAGAAGCCA 60.325 60.000 0.00 0.00 40.02 4.75
2149 2178 3.449227 CCGCTCTACGCCTGACCA 61.449 66.667 0.00 0.00 41.76 4.02
2158 2187 3.325753 GCCTGACCACCTGCTCCT 61.326 66.667 0.00 0.00 0.00 3.69
2235 2264 1.504647 ATCGATCGCCAAGCAGCATG 61.505 55.000 11.09 0.00 40.87 4.06
2311 2341 3.040763 GCTCCGAGCGATGCATCC 61.041 66.667 20.87 13.29 0.00 3.51
2337 2367 7.515841 CGTTCTCTTGTATCTTTTCATCCGATG 60.516 40.741 1.55 1.55 0.00 3.84
2338 2368 6.878317 TCTCTTGTATCTTTTCATCCGATGT 58.122 36.000 8.24 0.00 0.00 3.06
2339 2369 8.007405 TCTCTTGTATCTTTTCATCCGATGTA 57.993 34.615 8.24 0.00 0.00 2.29
2455 2485 5.139435 TGACGAGTTCTGATTCACAATCT 57.861 39.130 0.00 0.00 38.72 2.40
2488 2519 3.002656 CAGCTATGTTCTGCAATTACCGG 59.997 47.826 0.00 0.00 0.00 5.28
2530 2561 3.972227 CACCACACTGCTAGGTGC 58.028 61.111 0.00 0.00 45.39 5.01
2531 2562 1.672356 CACCACACTGCTAGGTGCC 60.672 63.158 0.00 0.00 45.39 5.01
2536 2568 0.252284 ACACTGCTAGGTGCCTAGGT 60.252 55.000 22.52 12.53 44.48 3.08
2542 2574 1.049402 CTAGGTGCCTAGGTTAGGGC 58.951 60.000 15.67 0.00 46.32 5.19
2562 2594 2.223735 GCTGATCATCCTTGTTGGCATG 60.224 50.000 0.00 0.00 35.26 4.06
2564 2596 1.068127 GATCATCCTTGTTGGCATGCC 59.932 52.381 30.54 30.54 35.26 4.40
2608 2643 4.448210 TCCGATTATCTTAAGCCACAACC 58.552 43.478 0.00 0.00 0.00 3.77
2613 2648 1.896220 TCTTAAGCCACAACCTGCAG 58.104 50.000 6.78 6.78 0.00 4.41
2704 2739 5.106157 CCAGAAAAAGAAGTTGTCTGTGTGT 60.106 40.000 5.72 0.00 36.40 3.72
2752 2787 1.434696 GCAATTGGCACCGATCCTG 59.565 57.895 7.72 0.00 43.97 3.86
2777 2817 2.124695 GCGTGGGATTCCTCACCC 60.125 66.667 14.80 0.00 45.74 4.61
2778 2818 2.670148 GCGTGGGATTCCTCACCCT 61.670 63.158 14.80 0.00 45.74 4.34
2779 2819 1.221840 CGTGGGATTCCTCACCCTG 59.778 63.158 14.80 2.74 45.74 4.45
2780 2820 1.609783 GTGGGATTCCTCACCCTGG 59.390 63.158 2.01 0.00 45.74 4.45
2781 2821 2.308722 TGGGATTCCTCACCCTGGC 61.309 63.158 2.01 0.00 45.74 4.85
2782 2822 2.003548 GGGATTCCTCACCCTGGCT 61.004 63.158 2.01 0.00 42.56 4.75
2783 2823 1.225704 GGATTCCTCACCCTGGCTG 59.774 63.158 0.00 0.00 0.00 4.85
2784 2824 1.452833 GATTCCTCACCCTGGCTGC 60.453 63.158 0.00 0.00 0.00 5.25
2785 2825 2.900671 GATTCCTCACCCTGGCTGCC 62.901 65.000 12.87 12.87 0.00 4.85
2806 2872 2.180017 CGCTGCTTCCATGCAACC 59.820 61.111 0.00 0.00 42.83 3.77
2816 2882 5.105797 TGCTTCCATGCAACCAAGTTAATAG 60.106 40.000 0.00 0.00 40.29 1.73
2817 2883 5.105756 GCTTCCATGCAACCAAGTTAATAGT 60.106 40.000 0.00 0.00 0.00 2.12
2818 2884 6.094881 GCTTCCATGCAACCAAGTTAATAGTA 59.905 38.462 0.00 0.00 0.00 1.82
2819 2885 7.201821 GCTTCCATGCAACCAAGTTAATAGTAT 60.202 37.037 0.00 0.00 0.00 2.12
2820 2886 9.337396 CTTCCATGCAACCAAGTTAATAGTATA 57.663 33.333 0.00 0.00 0.00 1.47
2821 2887 9.860650 TTCCATGCAACCAAGTTAATAGTATAT 57.139 29.630 0.00 0.00 0.00 0.86
2822 2888 9.860650 TCCATGCAACCAAGTTAATAGTATATT 57.139 29.630 0.00 0.00 0.00 1.28
2846 2912 6.507023 TCATTCCAGTTCAAAAAGAAAGAGC 58.493 36.000 0.00 0.00 38.13 4.09
2847 2913 6.322201 TCATTCCAGTTCAAAAAGAAAGAGCT 59.678 34.615 0.00 0.00 38.13 4.09
2848 2914 7.502226 TCATTCCAGTTCAAAAAGAAAGAGCTA 59.498 33.333 0.00 0.00 38.13 3.32
2849 2915 7.639113 TTCCAGTTCAAAAAGAAAGAGCTAA 57.361 32.000 0.00 0.00 38.13 3.09
2850 2916 7.823745 TCCAGTTCAAAAAGAAAGAGCTAAT 57.176 32.000 0.00 0.00 38.13 1.73
2851 2917 8.918202 TCCAGTTCAAAAAGAAAGAGCTAATA 57.082 30.769 0.00 0.00 38.13 0.98
2871 2937 7.310237 GCTAATATTCATTCCCTTTGCCATCAT 60.310 37.037 0.00 0.00 0.00 2.45
2872 2938 4.950205 ATTCATTCCCTTTGCCATCATC 57.050 40.909 0.00 0.00 0.00 2.92
2884 2950 1.596203 CATCATCTGGTGCCGCGAT 60.596 57.895 8.23 0.00 0.00 4.58
2891 2957 2.369257 CTGGTGCCGCGATATCCACT 62.369 60.000 8.23 0.00 0.00 4.00
2894 2960 2.430921 GCCGCGATATCCACTCCG 60.431 66.667 8.23 0.00 0.00 4.63
2895 2961 2.430921 CCGCGATATCCACTCCGC 60.431 66.667 8.23 0.00 43.68 5.54
2905 2975 1.717194 TCCACTCCGCGTTGTTTATC 58.283 50.000 4.92 0.00 0.00 1.75
2906 2976 0.725117 CCACTCCGCGTTGTTTATCC 59.275 55.000 4.92 0.00 0.00 2.59
2915 2985 0.096454 GTTGTTTATCCGTGGCGAGC 59.904 55.000 0.00 0.00 0.00 5.03
2987 3057 2.223947 TGGTTCGTACGGATGGATGATG 60.224 50.000 16.52 0.00 0.00 3.07
3095 3167 1.627550 GCGTTGCTTCTCCGAGGTTC 61.628 60.000 0.00 0.00 0.00 3.62
3096 3168 0.038159 CGTTGCTTCTCCGAGGTTCT 60.038 55.000 0.00 0.00 0.00 3.01
3097 3169 1.605712 CGTTGCTTCTCCGAGGTTCTT 60.606 52.381 0.00 0.00 0.00 2.52
3167 3240 0.108520 AATCACGATACAACCCGCGT 60.109 50.000 4.92 0.00 37.48 6.01
3196 3269 6.850752 AAAACAGGGACGAAATTAATCCAT 57.149 33.333 0.00 0.00 33.87 3.41
3216 3289 8.655935 ATCCATAAACATCTTTTTCCTGAACT 57.344 30.769 0.00 0.00 0.00 3.01
3217 3290 8.110860 TCCATAAACATCTTTTTCCTGAACTC 57.889 34.615 0.00 0.00 0.00 3.01
3218 3291 7.944554 TCCATAAACATCTTTTTCCTGAACTCT 59.055 33.333 0.00 0.00 0.00 3.24
3219 3292 8.025445 CCATAAACATCTTTTTCCTGAACTCTG 58.975 37.037 0.00 0.00 0.00 3.35
3220 3293 8.571336 CATAAACATCTTTTTCCTGAACTCTGT 58.429 33.333 0.00 0.00 0.00 3.41
3221 3294 7.410120 AAACATCTTTTTCCTGAACTCTGTT 57.590 32.000 0.00 0.00 0.00 3.16
3222 3295 6.382869 ACATCTTTTTCCTGAACTCTGTTG 57.617 37.500 0.00 0.00 0.00 3.33
3223 3296 4.900635 TCTTTTTCCTGAACTCTGTTGC 57.099 40.909 0.00 0.00 0.00 4.17
3224 3297 3.632145 TCTTTTTCCTGAACTCTGTTGCC 59.368 43.478 0.00 0.00 0.00 4.52
3225 3298 3.297134 TTTTCCTGAACTCTGTTGCCT 57.703 42.857 0.00 0.00 0.00 4.75
3226 3299 2.260844 TTCCTGAACTCTGTTGCCTG 57.739 50.000 0.00 0.00 0.00 4.85
3227 3300 1.131638 TCCTGAACTCTGTTGCCTGT 58.868 50.000 0.00 0.00 0.00 4.00
3228 3301 1.490490 TCCTGAACTCTGTTGCCTGTT 59.510 47.619 0.00 0.00 0.00 3.16
3229 3302 2.092429 TCCTGAACTCTGTTGCCTGTTT 60.092 45.455 0.00 0.00 0.00 2.83
3230 3303 2.291741 CCTGAACTCTGTTGCCTGTTTC 59.708 50.000 0.00 0.00 0.00 2.78
3231 3304 1.939934 TGAACTCTGTTGCCTGTTTCG 59.060 47.619 0.00 0.00 0.00 3.46
3232 3305 0.663153 AACTCTGTTGCCTGTTTCGC 59.337 50.000 0.00 0.00 0.00 4.70
3233 3306 1.205064 CTCTGTTGCCTGTTTCGCG 59.795 57.895 0.00 0.00 0.00 5.87
3234 3307 2.427410 CTGTTGCCTGTTTCGCGC 60.427 61.111 0.00 0.00 0.00 6.86
3235 3308 3.179869 CTGTTGCCTGTTTCGCGCA 62.180 57.895 8.75 0.00 0.00 6.09
3236 3309 2.255252 GTTGCCTGTTTCGCGCAT 59.745 55.556 8.75 0.00 31.44 4.73
3237 3310 1.231296 TGTTGCCTGTTTCGCGCATA 61.231 50.000 8.75 0.00 31.44 3.14
3238 3311 0.109964 GTTGCCTGTTTCGCGCATAA 60.110 50.000 8.75 0.00 31.44 1.90
3239 3312 0.593618 TTGCCTGTTTCGCGCATAAA 59.406 45.000 8.75 4.27 31.44 1.40
3240 3313 0.808125 TGCCTGTTTCGCGCATAAAT 59.192 45.000 8.75 0.00 0.00 1.40
3241 3314 2.010497 TGCCTGTTTCGCGCATAAATA 58.990 42.857 8.75 4.84 0.00 1.40
3242 3315 2.420372 TGCCTGTTTCGCGCATAAATAA 59.580 40.909 8.75 0.00 0.00 1.40
3243 3316 3.035942 GCCTGTTTCGCGCATAAATAAG 58.964 45.455 8.75 9.10 0.00 1.73
3244 3317 3.035942 CCTGTTTCGCGCATAAATAAGC 58.964 45.455 8.75 0.00 0.00 3.09
3245 3318 3.035942 CTGTTTCGCGCATAAATAAGCC 58.964 45.455 8.75 0.00 0.00 4.35
3246 3319 2.034076 GTTTCGCGCATAAATAAGCCG 58.966 47.619 8.75 0.00 0.00 5.52
3247 3320 0.041663 TTCGCGCATAAATAAGCCGC 60.042 50.000 8.75 0.00 0.00 6.53
3248 3321 1.440353 CGCGCATAAATAAGCCGCC 60.440 57.895 8.75 0.00 0.00 6.13
3249 3322 1.652012 GCGCATAAATAAGCCGCCA 59.348 52.632 0.30 0.00 0.00 5.69
3250 3323 0.240945 GCGCATAAATAAGCCGCCAT 59.759 50.000 0.30 0.00 0.00 4.40
3251 3324 1.466950 GCGCATAAATAAGCCGCCATA 59.533 47.619 0.30 0.00 0.00 2.74
3252 3325 2.097466 GCGCATAAATAAGCCGCCATAT 59.903 45.455 0.30 0.00 0.00 1.78
3253 3326 3.427503 GCGCATAAATAAGCCGCCATATT 60.428 43.478 0.30 0.00 0.00 1.28
3254 3327 4.201871 GCGCATAAATAAGCCGCCATATTA 60.202 41.667 0.30 0.00 0.00 0.98
3255 3328 5.501715 CGCATAAATAAGCCGCCATATTAG 58.498 41.667 0.77 0.00 0.00 1.73
3256 3329 5.273944 GCATAAATAAGCCGCCATATTAGC 58.726 41.667 0.77 2.86 0.00 3.09
3265 3338 1.328439 GCCATATTAGCGTCTCGTCG 58.672 55.000 0.00 0.00 0.00 5.12
3274 3347 2.430493 CGTCTCGTCGCACAAATGA 58.570 52.632 0.00 0.00 0.00 2.57
3275 3348 0.091344 CGTCTCGTCGCACAAATGAC 59.909 55.000 0.00 0.00 0.00 3.06
3276 3349 1.136690 GTCTCGTCGCACAAATGACA 58.863 50.000 0.00 0.00 34.78 3.58
3277 3350 1.525197 GTCTCGTCGCACAAATGACAA 59.475 47.619 0.00 0.00 34.78 3.18
3278 3351 2.033236 GTCTCGTCGCACAAATGACAAA 60.033 45.455 0.00 0.00 34.78 2.83
3279 3352 2.609916 TCTCGTCGCACAAATGACAAAA 59.390 40.909 0.00 0.00 34.78 2.44
3280 3353 3.064134 TCTCGTCGCACAAATGACAAAAA 59.936 39.130 0.00 0.00 34.78 1.94
3281 3354 3.102276 TCGTCGCACAAATGACAAAAAC 58.898 40.909 0.00 0.00 34.78 2.43
3282 3355 3.105203 CGTCGCACAAATGACAAAAACT 58.895 40.909 0.00 0.00 34.78 2.66
3283 3356 4.034163 TCGTCGCACAAATGACAAAAACTA 59.966 37.500 0.00 0.00 34.78 2.24
3284 3357 4.144051 CGTCGCACAAATGACAAAAACTAC 59.856 41.667 0.00 0.00 34.78 2.73
3285 3358 4.439776 GTCGCACAAATGACAAAAACTACC 59.560 41.667 0.00 0.00 35.20 3.18
3286 3359 3.733727 CGCACAAATGACAAAAACTACCC 59.266 43.478 0.00 0.00 0.00 3.69
3287 3360 4.688021 GCACAAATGACAAAAACTACCCA 58.312 39.130 0.00 0.00 0.00 4.51
3288 3361 4.506288 GCACAAATGACAAAAACTACCCAC 59.494 41.667 0.00 0.00 0.00 4.61
3289 3362 5.655488 CACAAATGACAAAAACTACCCACA 58.345 37.500 0.00 0.00 0.00 4.17
3290 3363 5.748152 CACAAATGACAAAAACTACCCACAG 59.252 40.000 0.00 0.00 0.00 3.66
3291 3364 5.420739 ACAAATGACAAAAACTACCCACAGT 59.579 36.000 0.00 0.00 0.00 3.55
3292 3365 5.514274 AATGACAAAAACTACCCACAGTG 57.486 39.130 0.00 0.00 0.00 3.66
3293 3366 4.223556 TGACAAAAACTACCCACAGTGA 57.776 40.909 0.62 0.00 0.00 3.41
3294 3367 4.590918 TGACAAAAACTACCCACAGTGAA 58.409 39.130 0.62 0.00 0.00 3.18
3295 3368 5.010933 TGACAAAAACTACCCACAGTGAAA 58.989 37.500 0.62 0.00 0.00 2.69
3296 3369 5.124776 TGACAAAAACTACCCACAGTGAAAG 59.875 40.000 0.62 0.00 0.00 2.62
3297 3370 5.014202 ACAAAAACTACCCACAGTGAAAGT 58.986 37.500 0.62 0.00 0.00 2.66
3298 3371 6.181908 ACAAAAACTACCCACAGTGAAAGTA 58.818 36.000 0.62 0.26 0.00 2.24
3299 3372 6.660094 ACAAAAACTACCCACAGTGAAAGTAA 59.340 34.615 0.62 0.00 0.00 2.24
3300 3373 6.688637 AAAACTACCCACAGTGAAAGTAAC 57.311 37.500 0.62 0.00 0.00 2.50
3301 3374 5.362105 AACTACCCACAGTGAAAGTAACA 57.638 39.130 0.62 0.00 0.00 2.41
3302 3375 5.562298 ACTACCCACAGTGAAAGTAACAT 57.438 39.130 0.62 0.00 0.00 2.71
3303 3376 6.675413 ACTACCCACAGTGAAAGTAACATA 57.325 37.500 0.62 0.00 0.00 2.29
3304 3377 6.698380 ACTACCCACAGTGAAAGTAACATAG 58.302 40.000 0.62 0.00 0.00 2.23
3305 3378 4.906618 ACCCACAGTGAAAGTAACATAGG 58.093 43.478 0.62 0.00 0.00 2.57
3306 3379 4.349930 ACCCACAGTGAAAGTAACATAGGT 59.650 41.667 0.62 0.00 0.00 3.08
3307 3380 4.695455 CCCACAGTGAAAGTAACATAGGTG 59.305 45.833 0.62 0.00 0.00 4.00
3308 3381 4.695455 CCACAGTGAAAGTAACATAGGTGG 59.305 45.833 0.62 0.00 0.00 4.61
3309 3382 5.305585 CACAGTGAAAGTAACATAGGTGGT 58.694 41.667 0.00 0.00 0.00 4.16
3310 3383 6.460781 CACAGTGAAAGTAACATAGGTGGTA 58.539 40.000 0.00 0.00 0.00 3.25
3311 3384 6.932400 CACAGTGAAAGTAACATAGGTGGTAA 59.068 38.462 0.00 0.00 0.00 2.85
3312 3385 6.932960 ACAGTGAAAGTAACATAGGTGGTAAC 59.067 38.462 0.00 0.00 0.00 2.50
3329 3402 5.353938 TGGTAACATCACGTTTATCTAGGC 58.646 41.667 0.00 0.00 46.17 3.93
3330 3403 5.105269 TGGTAACATCACGTTTATCTAGGCA 60.105 40.000 0.00 0.00 46.17 4.75
3331 3404 5.813672 GGTAACATCACGTTTATCTAGGCAA 59.186 40.000 0.00 0.00 39.14 4.52
3332 3405 6.314400 GGTAACATCACGTTTATCTAGGCAAA 59.686 38.462 0.00 0.00 39.14 3.68
3333 3406 6.811253 AACATCACGTTTATCTAGGCAAAA 57.189 33.333 0.00 0.00 32.35 2.44
3334 3407 7.391148 AACATCACGTTTATCTAGGCAAAAT 57.609 32.000 0.00 0.00 32.35 1.82
3335 3408 8.500753 AACATCACGTTTATCTAGGCAAAATA 57.499 30.769 0.00 0.00 32.35 1.40
3336 3409 8.500753 ACATCACGTTTATCTAGGCAAAATAA 57.499 30.769 0.00 0.00 0.00 1.40
3337 3410 8.952278 ACATCACGTTTATCTAGGCAAAATAAA 58.048 29.630 0.00 0.00 0.00 1.40
3338 3411 9.950680 CATCACGTTTATCTAGGCAAAATAAAT 57.049 29.630 0.00 0.00 30.14 1.40
3339 3412 9.950680 ATCACGTTTATCTAGGCAAAATAAATG 57.049 29.630 9.76 9.76 37.65 2.32
3340 3413 9.168451 TCACGTTTATCTAGGCAAAATAAATGA 57.832 29.630 15.05 6.58 36.25 2.57
3341 3414 9.950680 CACGTTTATCTAGGCAAAATAAATGAT 57.049 29.630 15.05 0.00 36.25 2.45
3342 3415 9.950680 ACGTTTATCTAGGCAAAATAAATGATG 57.049 29.630 15.05 3.77 36.25 3.07
3343 3416 9.950680 CGTTTATCTAGGCAAAATAAATGATGT 57.049 29.630 7.04 0.00 35.39 3.06
3346 3419 6.147864 TCTAGGCAAAATAAATGATGTGGC 57.852 37.500 0.00 0.00 32.08 5.01
3347 3420 4.822685 AGGCAAAATAAATGATGTGGCA 57.177 36.364 0.00 0.00 33.54 4.92
3348 3421 5.362105 AGGCAAAATAAATGATGTGGCAT 57.638 34.783 0.00 0.00 33.54 4.40
3349 3422 5.120399 AGGCAAAATAAATGATGTGGCATG 58.880 37.500 0.00 0.00 33.54 4.06
3350 3423 4.877251 GGCAAAATAAATGATGTGGCATGT 59.123 37.500 0.00 0.00 32.18 3.21
3351 3424 6.047870 GGCAAAATAAATGATGTGGCATGTA 58.952 36.000 0.00 0.00 32.18 2.29
3352 3425 6.538021 GGCAAAATAAATGATGTGGCATGTAA 59.462 34.615 0.00 0.00 32.18 2.41
3353 3426 7.227116 GGCAAAATAAATGATGTGGCATGTAAT 59.773 33.333 0.00 0.00 32.18 1.89
3354 3427 8.614346 GCAAAATAAATGATGTGGCATGTAATT 58.386 29.630 0.00 0.00 0.00 1.40
3361 3434 9.887629 AAATGATGTGGCATGTAATTAATGAAA 57.112 25.926 0.00 0.00 0.00 2.69
3362 3435 9.887629 AATGATGTGGCATGTAATTAATGAAAA 57.112 25.926 0.00 0.00 0.00 2.29
3363 3436 9.887629 ATGATGTGGCATGTAATTAATGAAAAA 57.112 25.926 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.202976 ACACTCTCTTGCATTTGGGCT 60.203 47.619 0.00 0.00 34.04 5.19
235 238 4.966787 GGCCGGGTCTTGGTGCAA 62.967 66.667 2.18 0.00 0.00 4.08
511 514 3.818773 CTGTCCGTTAGGGTCAAAAATGT 59.181 43.478 0.00 0.00 38.33 2.71
520 523 1.412649 CCCTATCCTGTCCGTTAGGGT 60.413 57.143 5.83 0.00 43.98 4.34
525 528 0.988832 TTTGCCCTATCCTGTCCGTT 59.011 50.000 0.00 0.00 0.00 4.44
583 586 0.604073 TGTATTCGGGCGTGTTCTGA 59.396 50.000 0.00 0.00 0.00 3.27
587 590 0.956902 GGGTTGTATTCGGGCGTGTT 60.957 55.000 0.00 0.00 0.00 3.32
599 602 2.110188 TGGGTAGCAATTTGGGGTTGTA 59.890 45.455 0.00 0.00 0.00 2.41
602 605 2.370519 GTTTGGGTAGCAATTTGGGGTT 59.629 45.455 0.00 0.00 0.00 4.11
612 615 3.559171 GGATTCTGTCAGTTTGGGTAGCA 60.559 47.826 0.00 0.00 0.00 3.49
678 681 1.836802 GCCTCCTTGTCTCTTCCTCAT 59.163 52.381 0.00 0.00 0.00 2.90
684 687 2.022718 ACAGAGCCTCCTTGTCTCTT 57.977 50.000 0.00 0.00 35.19 2.85
685 688 1.622811 CAACAGAGCCTCCTTGTCTCT 59.377 52.381 0.00 0.00 37.66 3.10
686 689 1.338579 CCAACAGAGCCTCCTTGTCTC 60.339 57.143 0.00 0.00 0.00 3.36
687 690 0.689623 CCAACAGAGCCTCCTTGTCT 59.310 55.000 0.00 0.00 0.00 3.41
688 691 0.687354 TCCAACAGAGCCTCCTTGTC 59.313 55.000 0.00 0.00 0.00 3.18
689 692 1.072965 CTTCCAACAGAGCCTCCTTGT 59.927 52.381 0.00 0.00 0.00 3.16
690 693 1.349026 TCTTCCAACAGAGCCTCCTTG 59.651 52.381 0.00 0.00 0.00 3.61
691 694 1.734655 TCTTCCAACAGAGCCTCCTT 58.265 50.000 0.00 0.00 0.00 3.36
692 695 1.734655 TTCTTCCAACAGAGCCTCCT 58.265 50.000 0.00 0.00 0.00 3.69
693 696 2.290577 ACATTCTTCCAACAGAGCCTCC 60.291 50.000 0.00 0.00 0.00 4.30
694 697 3.064900 ACATTCTTCCAACAGAGCCTC 57.935 47.619 0.00 0.00 0.00 4.70
831 834 4.873827 TCTTGTCGTTACAAAACTCTTGCT 59.126 37.500 0.00 0.00 44.79 3.91
904 917 3.131933 TGGTTGTGTCCATTTTTCTGTGG 59.868 43.478 0.00 0.00 36.82 4.17
905 918 4.111916 GTGGTTGTGTCCATTTTTCTGTG 58.888 43.478 0.00 0.00 39.81 3.66
906 919 3.132111 GGTGGTTGTGTCCATTTTTCTGT 59.868 43.478 0.00 0.00 39.81 3.41
907 920 3.492482 GGGTGGTTGTGTCCATTTTTCTG 60.492 47.826 0.00 0.00 39.81 3.02
908 921 2.698274 GGGTGGTTGTGTCCATTTTTCT 59.302 45.455 0.00 0.00 39.81 2.52
915 928 1.923006 TTTCGGGGTGGTTGTGTCCA 61.923 55.000 0.00 0.00 34.85 4.02
1041 1055 3.376935 ATCTCCTTGTGCTCCGCGG 62.377 63.158 22.12 22.12 0.00 6.46
1116 1139 2.284995 GCTCCACCACCTCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
1509 1532 4.828925 GCTCAGGCTCTGCGGTCC 62.829 72.222 0.00 0.00 35.22 4.46
1516 1542 2.759795 GGTTTGGGCTCAGGCTCT 59.240 61.111 0.00 0.00 40.19 4.09
1517 1543 2.361737 GGGTTTGGGCTCAGGCTC 60.362 66.667 0.00 0.00 39.89 4.70
1520 1546 2.677875 GCTGGGTTTGGGCTCAGG 60.678 66.667 0.00 0.00 37.44 3.86
1522 1548 2.905996 ATCGCTGGGTTTGGGCTCA 61.906 57.895 0.00 0.00 0.00 4.26
1528 1554 1.210931 CAGTGCATCGCTGGGTTTG 59.789 57.895 0.00 0.00 38.21 2.93
1662 1691 0.325110 TGGCTTCTCCTCCTCCTCTG 60.325 60.000 0.00 0.00 35.26 3.35
1663 1692 0.325203 GTGGCTTCTCCTCCTCCTCT 60.325 60.000 0.00 0.00 35.26 3.69
1664 1693 1.334384 GGTGGCTTCTCCTCCTCCTC 61.334 65.000 0.00 0.00 43.58 3.71
2041 2070 0.100146 CGTGGTACCCGTAGAAGCTC 59.900 60.000 10.07 0.00 0.00 4.09
2149 2178 2.997897 GACCGGACAGGAGCAGGT 60.998 66.667 9.46 0.00 45.00 4.00
2210 2239 2.279451 TTGGCGATCGATCCAGCG 60.279 61.111 21.57 9.72 33.32 5.18
2250 2279 2.395690 CACGCACCGAATTCTCGC 59.604 61.111 3.52 2.44 44.04 5.03
2302 2332 1.645034 ACAAGAGAACGGATGCATCG 58.355 50.000 20.15 16.86 0.00 3.84
2311 2341 5.805486 TCGGATGAAAAGATACAAGAGAACG 59.195 40.000 0.00 0.00 0.00 3.95
2337 2367 4.339814 AGCATCAGCCAGAGTTACTACTAC 59.660 45.833 0.00 0.00 43.56 2.73
2338 2368 4.537751 AGCATCAGCCAGAGTTACTACTA 58.462 43.478 0.00 0.00 43.56 1.82
2339 2369 3.370104 AGCATCAGCCAGAGTTACTACT 58.630 45.455 0.00 0.00 43.56 2.57
2428 2458 2.029020 TGAATCAGAACTCGTCAGGGTG 60.029 50.000 0.00 0.00 0.00 4.61
2455 2485 0.752658 ACATAGCTGCATAGGACGCA 59.247 50.000 1.02 0.00 37.88 5.24
2488 2519 4.208666 GGAGCAAAGAACGTAATCGGTATC 59.791 45.833 0.00 0.00 41.85 2.24
2501 2532 1.064758 AGTGTGGTGTGGAGCAAAGAA 60.065 47.619 0.00 0.00 0.00 2.52
2530 2561 2.569404 GGATGATCAGCCCTAACCTAGG 59.431 54.545 19.66 7.41 45.81 3.02
2531 2562 3.515562 AGGATGATCAGCCCTAACCTAG 58.484 50.000 26.11 0.00 37.67 3.02
2536 2568 3.371917 CCAACAAGGATGATCAGCCCTAA 60.372 47.826 26.11 0.00 41.22 2.69
2542 2574 2.223735 GCATGCCAACAAGGATGATCAG 60.224 50.000 6.36 0.00 41.22 2.90
2562 2594 1.667154 GGAGGATTCAAAAGCCCGGC 61.667 60.000 0.00 0.00 37.80 6.13
2564 2596 1.037579 GGGGAGGATTCAAAAGCCCG 61.038 60.000 0.00 0.00 37.80 6.13
2608 2643 0.471617 ATGCTAGCCCTAACCTGCAG 59.528 55.000 13.29 6.78 33.87 4.41
2613 2648 2.224402 CCTCTTGATGCTAGCCCTAACC 60.224 54.545 13.29 0.00 0.00 2.85
2674 2709 7.711339 ACAGACAACTTCTTTTTCTGGTAGTAG 59.289 37.037 5.43 0.00 38.42 2.57
2675 2710 7.494625 CACAGACAACTTCTTTTTCTGGTAGTA 59.505 37.037 5.43 0.00 38.42 1.82
2676 2711 6.316390 CACAGACAACTTCTTTTTCTGGTAGT 59.684 38.462 5.43 0.00 38.42 2.73
2677 2712 6.316390 ACACAGACAACTTCTTTTTCTGGTAG 59.684 38.462 5.43 0.00 38.42 3.18
2682 2717 6.183360 CGTACACACAGACAACTTCTTTTTCT 60.183 38.462 0.00 0.00 28.96 2.52
2683 2718 5.957796 CGTACACACAGACAACTTCTTTTTC 59.042 40.000 0.00 0.00 28.96 2.29
2752 2787 1.384222 GGAATCCCACGCAATCCCAC 61.384 60.000 0.00 0.00 0.00 4.61
2787 2827 3.751246 TTGCATGGAAGCAGCGGC 61.751 61.111 0.00 0.00 46.54 6.53
2789 2829 2.144833 TTGGTTGCATGGAAGCAGCG 62.145 55.000 27.00 0.00 46.54 5.18
2790 2830 0.389426 CTTGGTTGCATGGAAGCAGC 60.389 55.000 27.00 6.50 46.54 5.25
2820 2886 7.654923 GCTCTTTCTTTTTGAACTGGAATGAAT 59.345 33.333 0.00 0.00 33.88 2.57
2821 2887 6.980397 GCTCTTTCTTTTTGAACTGGAATGAA 59.020 34.615 0.00 0.00 33.88 2.57
2822 2888 6.322201 AGCTCTTTCTTTTTGAACTGGAATGA 59.678 34.615 0.00 0.00 33.88 2.57
2823 2889 6.510536 AGCTCTTTCTTTTTGAACTGGAATG 58.489 36.000 0.00 0.00 33.88 2.67
2824 2890 6.721704 AGCTCTTTCTTTTTGAACTGGAAT 57.278 33.333 0.00 0.00 33.88 3.01
2825 2891 7.639113 TTAGCTCTTTCTTTTTGAACTGGAA 57.361 32.000 0.00 0.00 33.88 3.53
2826 2892 7.823745 ATTAGCTCTTTCTTTTTGAACTGGA 57.176 32.000 0.00 0.00 33.88 3.86
2835 2901 9.706529 AGGGAATGAATATTAGCTCTTTCTTTT 57.293 29.630 0.00 0.00 0.00 2.27
2836 2902 9.706529 AAGGGAATGAATATTAGCTCTTTCTTT 57.293 29.630 0.00 0.00 0.00 2.52
2837 2903 9.706529 AAAGGGAATGAATATTAGCTCTTTCTT 57.293 29.630 0.00 0.00 0.00 2.52
2838 2904 9.129532 CAAAGGGAATGAATATTAGCTCTTTCT 57.870 33.333 0.00 0.00 0.00 2.52
2839 2905 7.864882 GCAAAGGGAATGAATATTAGCTCTTTC 59.135 37.037 0.00 0.00 0.00 2.62
2840 2906 7.201947 GGCAAAGGGAATGAATATTAGCTCTTT 60.202 37.037 0.00 0.00 0.00 2.52
2841 2907 6.266330 GGCAAAGGGAATGAATATTAGCTCTT 59.734 38.462 0.00 0.00 0.00 2.85
2842 2908 5.772169 GGCAAAGGGAATGAATATTAGCTCT 59.228 40.000 0.00 0.00 0.00 4.09
2843 2909 5.536161 TGGCAAAGGGAATGAATATTAGCTC 59.464 40.000 0.00 0.00 0.00 4.09
2844 2910 5.457686 TGGCAAAGGGAATGAATATTAGCT 58.542 37.500 0.00 0.00 0.00 3.32
2845 2911 5.789643 TGGCAAAGGGAATGAATATTAGC 57.210 39.130 0.00 0.00 0.00 3.09
2846 2912 7.528996 TGATGGCAAAGGGAATGAATATTAG 57.471 36.000 0.00 0.00 0.00 1.73
2847 2913 7.951806 AGATGATGGCAAAGGGAATGAATATTA 59.048 33.333 0.00 0.00 0.00 0.98
2848 2914 6.785963 AGATGATGGCAAAGGGAATGAATATT 59.214 34.615 0.00 0.00 0.00 1.28
2849 2915 6.210784 CAGATGATGGCAAAGGGAATGAATAT 59.789 38.462 0.00 0.00 0.00 1.28
2850 2916 5.537295 CAGATGATGGCAAAGGGAATGAATA 59.463 40.000 0.00 0.00 0.00 1.75
2851 2917 4.344102 CAGATGATGGCAAAGGGAATGAAT 59.656 41.667 0.00 0.00 0.00 2.57
2871 2937 2.131067 TGGATATCGCGGCACCAGA 61.131 57.895 6.13 0.00 0.00 3.86
2872 2938 1.956170 GTGGATATCGCGGCACCAG 60.956 63.158 6.13 0.00 0.00 4.00
2884 2950 3.450578 GATAAACAACGCGGAGTGGATA 58.549 45.455 12.47 3.88 45.78 2.59
2891 2957 1.015085 CCACGGATAAACAACGCGGA 61.015 55.000 12.47 0.00 31.92 5.54
2894 2960 1.225908 CGCCACGGATAAACAACGC 60.226 57.895 0.00 0.00 0.00 4.84
2895 2961 0.368907 CTCGCCACGGATAAACAACG 59.631 55.000 0.00 0.00 0.00 4.10
2896 2962 0.096454 GCTCGCCACGGATAAACAAC 59.904 55.000 0.00 0.00 0.00 3.32
2906 2976 4.838486 GTCGGAGAGCTCGCCACG 62.838 72.222 32.15 20.71 36.95 4.94
2933 3003 3.984193 ATCTGCCTGCCGCTTGGAC 62.984 63.158 7.09 0.67 38.78 4.02
2987 3057 2.704190 TCTCATATCTCCTCCCCACC 57.296 55.000 0.00 0.00 0.00 4.61
3053 3125 5.106237 GCATCAAATATCTGCAATCTCCTCC 60.106 44.000 0.00 0.00 35.96 4.30
3054 3126 5.390673 CGCATCAAATATCTGCAATCTCCTC 60.391 44.000 0.00 0.00 35.64 3.71
3055 3127 4.454847 CGCATCAAATATCTGCAATCTCCT 59.545 41.667 0.00 0.00 35.64 3.69
3122 3194 9.402320 TGTATGCCTGATTAAGTAAGCAATAAA 57.598 29.630 0.00 0.00 33.35 1.40
3192 3265 7.944554 AGAGTTCAGGAAAAAGATGTTTATGGA 59.055 33.333 0.00 0.00 0.00 3.41
3196 3269 8.405531 CAACAGAGTTCAGGAAAAAGATGTTTA 58.594 33.333 0.00 0.00 0.00 2.01
3208 3281 1.131638 ACAGGCAACAGAGTTCAGGA 58.868 50.000 0.00 0.00 41.41 3.86
3210 3283 2.032549 CGAAACAGGCAACAGAGTTCAG 60.033 50.000 0.00 0.00 41.41 3.02
3211 3284 1.939934 CGAAACAGGCAACAGAGTTCA 59.060 47.619 0.00 0.00 41.41 3.18
3212 3285 1.334149 GCGAAACAGGCAACAGAGTTC 60.334 52.381 0.00 0.00 41.41 3.01
3213 3286 0.663153 GCGAAACAGGCAACAGAGTT 59.337 50.000 0.00 0.00 41.41 3.01
3214 3287 1.498865 CGCGAAACAGGCAACAGAGT 61.499 55.000 0.00 0.00 41.41 3.24
3215 3288 1.205064 CGCGAAACAGGCAACAGAG 59.795 57.895 0.00 0.00 41.41 3.35
3216 3289 2.892334 GCGCGAAACAGGCAACAGA 61.892 57.895 12.10 0.00 41.41 3.41
3217 3290 2.427410 GCGCGAAACAGGCAACAG 60.427 61.111 12.10 0.00 41.41 3.16
3218 3291 1.231296 TATGCGCGAAACAGGCAACA 61.231 50.000 12.10 0.00 40.49 3.33
3219 3292 0.109964 TTATGCGCGAAACAGGCAAC 60.110 50.000 12.10 0.00 40.49 4.17
3220 3293 0.593618 TTTATGCGCGAAACAGGCAA 59.406 45.000 12.10 0.00 40.49 4.52
3221 3294 0.808125 ATTTATGCGCGAAACAGGCA 59.192 45.000 12.10 0.00 41.48 4.75
3222 3295 2.748461 TATTTATGCGCGAAACAGGC 57.252 45.000 12.10 0.00 0.00 4.85
3223 3296 3.035942 GCTTATTTATGCGCGAAACAGG 58.964 45.455 12.10 0.62 0.00 4.00
3224 3297 3.035942 GGCTTATTTATGCGCGAAACAG 58.964 45.455 12.10 9.44 0.00 3.16
3225 3298 2.537931 CGGCTTATTTATGCGCGAAACA 60.538 45.455 12.10 0.00 0.00 2.83
3226 3299 2.034076 CGGCTTATTTATGCGCGAAAC 58.966 47.619 12.10 0.00 0.00 2.78
3227 3300 1.595976 GCGGCTTATTTATGCGCGAAA 60.596 47.619 12.10 6.31 0.00 3.46
3228 3301 0.041663 GCGGCTTATTTATGCGCGAA 60.042 50.000 12.10 0.00 0.00 4.70
3229 3302 1.567537 GCGGCTTATTTATGCGCGA 59.432 52.632 12.10 0.00 0.00 5.87
3230 3303 1.440353 GGCGGCTTATTTATGCGCG 60.440 57.895 0.00 0.00 32.61 6.86
3231 3304 0.240945 ATGGCGGCTTATTTATGCGC 59.759 50.000 11.43 0.00 0.00 6.09
3232 3305 4.355543 AATATGGCGGCTTATTTATGCG 57.644 40.909 20.22 0.00 0.00 4.73
3233 3306 5.273944 GCTAATATGGCGGCTTATTTATGC 58.726 41.667 27.48 23.75 0.00 3.14
3246 3319 1.328439 CGACGAGACGCTAATATGGC 58.672 55.000 0.00 0.00 0.00 4.40
3256 3329 0.091344 GTCATTTGTGCGACGAGACG 59.909 55.000 0.00 0.00 0.00 4.18
3257 3330 1.136690 TGTCATTTGTGCGACGAGAC 58.863 50.000 0.00 0.00 34.78 3.36
3258 3331 1.859383 TTGTCATTTGTGCGACGAGA 58.141 45.000 0.00 0.00 34.78 4.04
3259 3332 2.661504 TTTGTCATTTGTGCGACGAG 57.338 45.000 0.00 0.00 34.78 4.18
3260 3333 3.102276 GTTTTTGTCATTTGTGCGACGA 58.898 40.909 0.00 0.00 34.78 4.20
3261 3334 3.105203 AGTTTTTGTCATTTGTGCGACG 58.895 40.909 0.00 0.00 34.78 5.12
3262 3335 4.439776 GGTAGTTTTTGTCATTTGTGCGAC 59.560 41.667 0.00 0.00 0.00 5.19
3263 3336 4.498345 GGGTAGTTTTTGTCATTTGTGCGA 60.498 41.667 0.00 0.00 0.00 5.10
3264 3337 3.733727 GGGTAGTTTTTGTCATTTGTGCG 59.266 43.478 0.00 0.00 0.00 5.34
3265 3338 4.506288 GTGGGTAGTTTTTGTCATTTGTGC 59.494 41.667 0.00 0.00 0.00 4.57
3266 3339 5.655488 TGTGGGTAGTTTTTGTCATTTGTG 58.345 37.500 0.00 0.00 0.00 3.33
3267 3340 5.420739 ACTGTGGGTAGTTTTTGTCATTTGT 59.579 36.000 0.00 0.00 0.00 2.83
3268 3341 5.748152 CACTGTGGGTAGTTTTTGTCATTTG 59.252 40.000 0.00 0.00 0.00 2.32
3269 3342 5.654650 TCACTGTGGGTAGTTTTTGTCATTT 59.345 36.000 8.11 0.00 0.00 2.32
3270 3343 5.197451 TCACTGTGGGTAGTTTTTGTCATT 58.803 37.500 8.11 0.00 0.00 2.57
3271 3344 4.787551 TCACTGTGGGTAGTTTTTGTCAT 58.212 39.130 8.11 0.00 0.00 3.06
3272 3345 4.223556 TCACTGTGGGTAGTTTTTGTCA 57.776 40.909 8.11 0.00 0.00 3.58
3273 3346 5.124936 ACTTTCACTGTGGGTAGTTTTTGTC 59.875 40.000 8.11 0.00 0.00 3.18
3274 3347 5.014202 ACTTTCACTGTGGGTAGTTTTTGT 58.986 37.500 8.11 0.00 0.00 2.83
3275 3348 5.576447 ACTTTCACTGTGGGTAGTTTTTG 57.424 39.130 8.11 0.00 0.00 2.44
3276 3349 6.660094 TGTTACTTTCACTGTGGGTAGTTTTT 59.340 34.615 8.11 0.00 0.00 1.94
3277 3350 6.181908 TGTTACTTTCACTGTGGGTAGTTTT 58.818 36.000 8.11 0.00 0.00 2.43
3278 3351 5.747342 TGTTACTTTCACTGTGGGTAGTTT 58.253 37.500 8.11 0.00 0.00 2.66
3279 3352 5.362105 TGTTACTTTCACTGTGGGTAGTT 57.638 39.130 8.11 0.00 0.00 2.24
3280 3353 5.562298 ATGTTACTTTCACTGTGGGTAGT 57.438 39.130 8.11 10.87 0.00 2.73
3281 3354 6.106673 CCTATGTTACTTTCACTGTGGGTAG 58.893 44.000 8.11 5.69 0.00 3.18
3282 3355 5.544948 ACCTATGTTACTTTCACTGTGGGTA 59.455 40.000 8.11 6.54 0.00 3.69
3283 3356 4.349930 ACCTATGTTACTTTCACTGTGGGT 59.650 41.667 8.11 7.45 0.00 4.51
3284 3357 4.695455 CACCTATGTTACTTTCACTGTGGG 59.305 45.833 8.11 0.00 0.00 4.61
3285 3358 4.695455 CCACCTATGTTACTTTCACTGTGG 59.305 45.833 8.11 0.00 0.00 4.17
3286 3359 5.305585 ACCACCTATGTTACTTTCACTGTG 58.694 41.667 0.17 0.17 0.00 3.66
3287 3360 5.562298 ACCACCTATGTTACTTTCACTGT 57.438 39.130 0.00 0.00 0.00 3.55
3288 3361 6.932400 TGTTACCACCTATGTTACTTTCACTG 59.068 38.462 0.00 0.00 0.00 3.66
3289 3362 7.069877 TGTTACCACCTATGTTACTTTCACT 57.930 36.000 0.00 0.00 0.00 3.41
3290 3363 7.604927 TGATGTTACCACCTATGTTACTTTCAC 59.395 37.037 0.00 0.00 0.00 3.18
3291 3364 7.604927 GTGATGTTACCACCTATGTTACTTTCA 59.395 37.037 0.00 0.00 0.00 2.69
3292 3365 7.201496 CGTGATGTTACCACCTATGTTACTTTC 60.201 40.741 0.00 0.00 0.00 2.62
3293 3366 6.592607 CGTGATGTTACCACCTATGTTACTTT 59.407 38.462 0.00 0.00 0.00 2.66
3294 3367 6.103997 CGTGATGTTACCACCTATGTTACTT 58.896 40.000 0.00 0.00 0.00 2.24
3295 3368 5.186409 ACGTGATGTTACCACCTATGTTACT 59.814 40.000 0.00 0.00 0.00 2.24
3296 3369 5.413499 ACGTGATGTTACCACCTATGTTAC 58.587 41.667 0.00 0.00 0.00 2.50
3297 3370 5.664294 ACGTGATGTTACCACCTATGTTA 57.336 39.130 0.00 0.00 0.00 2.41
3298 3371 4.546829 ACGTGATGTTACCACCTATGTT 57.453 40.909 0.00 0.00 0.00 2.71
3299 3372 4.546829 AACGTGATGTTACCACCTATGT 57.453 40.909 0.00 0.00 39.61 2.29
3300 3373 6.984474 AGATAAACGTGATGTTACCACCTATG 59.016 38.462 0.00 0.00 40.84 2.23
3301 3374 7.120923 AGATAAACGTGATGTTACCACCTAT 57.879 36.000 0.00 0.00 40.84 2.57
3302 3375 6.534475 AGATAAACGTGATGTTACCACCTA 57.466 37.500 0.00 0.00 40.84 3.08
3303 3376 5.416271 AGATAAACGTGATGTTACCACCT 57.584 39.130 0.00 0.00 40.84 4.00
3304 3377 5.751990 CCTAGATAAACGTGATGTTACCACC 59.248 44.000 0.00 0.00 40.84 4.61
3305 3378 5.233689 GCCTAGATAAACGTGATGTTACCAC 59.766 44.000 0.00 0.00 40.84 4.16
3306 3379 5.105269 TGCCTAGATAAACGTGATGTTACCA 60.105 40.000 0.00 0.00 40.84 3.25
3307 3380 5.353938 TGCCTAGATAAACGTGATGTTACC 58.646 41.667 0.00 0.00 40.84 2.85
3308 3381 6.897259 TTGCCTAGATAAACGTGATGTTAC 57.103 37.500 0.00 0.00 40.84 2.50
3309 3382 7.908827 TTTTGCCTAGATAAACGTGATGTTA 57.091 32.000 0.00 0.00 40.84 2.41
3310 3383 6.811253 TTTTGCCTAGATAAACGTGATGTT 57.189 33.333 0.00 0.00 44.59 2.71
3311 3384 8.500753 TTATTTTGCCTAGATAAACGTGATGT 57.499 30.769 0.00 0.00 0.00 3.06
3312 3385 9.950680 ATTTATTTTGCCTAGATAAACGTGATG 57.049 29.630 0.00 0.00 30.59 3.07
3313 3386 9.950680 CATTTATTTTGCCTAGATAAACGTGAT 57.049 29.630 0.00 0.00 30.59 3.06
3314 3387 9.168451 TCATTTATTTTGCCTAGATAAACGTGA 57.832 29.630 0.00 0.00 30.59 4.35
3315 3388 9.950680 ATCATTTATTTTGCCTAGATAAACGTG 57.049 29.630 0.00 0.00 30.59 4.49
3316 3389 9.950680 CATCATTTATTTTGCCTAGATAAACGT 57.049 29.630 0.00 0.00 30.59 3.99
3317 3390 9.950680 ACATCATTTATTTTGCCTAGATAAACG 57.049 29.630 0.00 0.00 30.59 3.60
3320 3393 8.359642 GCCACATCATTTATTTTGCCTAGATAA 58.640 33.333 0.00 0.00 0.00 1.75
3321 3394 7.505248 TGCCACATCATTTATTTTGCCTAGATA 59.495 33.333 0.00 0.00 0.00 1.98
3322 3395 6.324512 TGCCACATCATTTATTTTGCCTAGAT 59.675 34.615 0.00 0.00 0.00 1.98
3323 3396 5.655974 TGCCACATCATTTATTTTGCCTAGA 59.344 36.000 0.00 0.00 0.00 2.43
3324 3397 5.904941 TGCCACATCATTTATTTTGCCTAG 58.095 37.500 0.00 0.00 0.00 3.02
3325 3398 5.929058 TGCCACATCATTTATTTTGCCTA 57.071 34.783 0.00 0.00 0.00 3.93
3326 3399 4.822685 TGCCACATCATTTATTTTGCCT 57.177 36.364 0.00 0.00 0.00 4.75
3327 3400 4.877251 ACATGCCACATCATTTATTTTGCC 59.123 37.500 0.00 0.00 0.00 4.52
3328 3401 7.536895 TTACATGCCACATCATTTATTTTGC 57.463 32.000 0.00 0.00 0.00 3.68
3335 3408 9.887629 TTTCATTAATTACATGCCACATCATTT 57.112 25.926 0.00 0.00 0.00 2.32
3336 3409 9.887629 TTTTCATTAATTACATGCCACATCATT 57.112 25.926 0.00 0.00 0.00 2.57
3337 3410 9.887629 TTTTTCATTAATTACATGCCACATCAT 57.112 25.926 0.00 0.00 0.00 2.45
3362 3435 7.883311 ACTAGCTATGTTACCACATGTCTTTTT 59.117 33.333 0.00 0.00 43.92 1.94
3363 3436 7.394816 ACTAGCTATGTTACCACATGTCTTTT 58.605 34.615 0.00 0.00 43.92 2.27
3364 3437 6.947464 ACTAGCTATGTTACCACATGTCTTT 58.053 36.000 0.00 0.00 43.92 2.52
3365 3438 6.546428 ACTAGCTATGTTACCACATGTCTT 57.454 37.500 0.00 0.00 43.92 3.01
3366 3439 6.546428 AACTAGCTATGTTACCACATGTCT 57.454 37.500 0.00 0.00 43.92 3.41
3367 3440 7.435488 CAGTAACTAGCTATGTTACCACATGTC 59.565 40.741 25.92 11.54 46.31 3.06
3368 3441 7.093465 ACAGTAACTAGCTATGTTACCACATGT 60.093 37.037 25.92 22.41 46.31 3.21
3369 3442 7.265673 ACAGTAACTAGCTATGTTACCACATG 58.734 38.462 25.92 22.03 46.31 3.21
3370 3443 7.419711 ACAGTAACTAGCTATGTTACCACAT 57.580 36.000 25.92 14.84 46.31 3.21
3371 3444 6.845758 ACAGTAACTAGCTATGTTACCACA 57.154 37.500 25.92 6.86 46.31 4.17


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

AutoCloner maintained by Alex Coulton.