Multiple sequence alignment - TraesCS6A01G417400

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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 TraesCS6A01G417400 chr6A 100.000 3470 0 0 1 3470 615782703 615779234 0.000000e+00 6408.0
1 TraesCS6A01G417400 chr6A 91.871 2116 98 24 594 2656 615791210 615793304 0.000000e+00 2887.0
2 TraesCS6A01G417400 chr6A 81.987 1077 154 25 789 1834 615947699 615948766 0.000000e+00 878.0
3 TraesCS6A01G417400 chr6A 91.687 409 11 4 2757 3165 615793306 615793691 2.360000e-151 545.0
4 TraesCS6A01G417400 chr6A 93.689 206 10 3 3210 3414 471195167 471195370 4.350000e-79 305.0
5 TraesCS6A01G417400 chr6A 78.481 474 30 34 44 494 615946961 615947385 9.620000e-61 244.0
6 TraesCS6A01G417400 chr6A 78.750 320 30 19 1 310 615790771 615791062 2.750000e-41 180.0
7 TraesCS6A01G417400 chr6A 94.118 68 4 0 3401 3468 53161395 53161462 1.700000e-18 104.0
8 TraesCS6A01G417400 chr6A 95.385 65 3 0 3404 3468 98181191 98181127 1.700000e-18 104.0
9 TraesCS6A01G417400 chr6B 92.597 2418 118 23 795 3165 719744846 719742443 0.000000e+00 3417.0
10 TraesCS6A01G417400 chr6B 90.579 2643 133 41 605 3165 719732728 719735336 0.000000e+00 3395.0
11 TraesCS6A01G417400 chr6B 78.872 1046 191 24 1055 2079 719910240 719909204 0.000000e+00 680.0
12 TraesCS6A01G417400 chr6B 85.161 310 13 9 12 310 719745556 719745269 1.580000e-73 287.0
13 TraesCS6A01G417400 chr6B 82.555 321 25 12 12 310 719732220 719732531 1.600000e-63 254.0
14 TraesCS6A01G417400 chr6B 81.877 309 15 9 12 310 719747731 719747454 4.510000e-54 222.0
15 TraesCS6A01G417400 chr6B 82.645 242 24 7 341 579 719745268 719745042 7.600000e-47 198.0
16 TraesCS6A01G417400 chr6B 87.879 99 2 1 212 310 719756744 719756656 1.320000e-19 108.0
17 TraesCS6A01G417400 chr6B 97.297 37 1 0 341 377 719756655 719756619 2.890000e-06 63.9
18 TraesCS6A01G417400 chr6B 92.105 38 3 0 2209 2246 719903398 719903361 2.000000e-03 54.7
19 TraesCS6A01G417400 chr6D 90.230 2129 107 30 594 2659 470975643 470977733 0.000000e+00 2686.0
20 TraesCS6A01G417400 chr6D 92.365 406 20 3 2760 3165 470977733 470978127 5.030000e-158 568.0
21 TraesCS6A01G417400 chr6D 76.628 522 50 30 341 849 471178343 471177881 4.510000e-54 222.0
22 TraesCS6A01G417400 chr6D 78.516 256 35 15 67 310 470975202 470975449 2.160000e-32 150.0
23 TraesCS6A01G417400 chr6D 91.919 99 3 1 421 519 470975510 470975603 2.170000e-27 134.0
24 TraesCS6A01G417400 chr6D 84.112 107 8 1 168 265 471178455 471178349 1.030000e-15 95.3
25 TraesCS6A01G417400 chr6D 87.931 58 3 3 2178 2235 450861466 450861519 8.040000e-07 65.8
26 TraesCS6A01G417400 chr3A 80.676 621 96 15 1769 2376 574346238 574345629 8.780000e-126 460.0
27 TraesCS6A01G417400 chr3A 93.548 217 11 3 3207 3422 651189302 651189516 1.550000e-83 320.0
28 TraesCS6A01G417400 chr3A 92.166 217 14 3 3207 3422 651155438 651155652 1.560000e-78 303.0
29 TraesCS6A01G417400 chr3A 93.237 207 11 3 3210 3414 76343839 76343634 5.630000e-78 302.0
30 TraesCS6A01G417400 chr3A 88.489 139 9 5 1872 2004 574344630 574344493 9.970000e-36 161.0
31 TraesCS6A01G417400 chr3A 93.750 96 5 1 1742 1837 574344730 574344636 3.610000e-30 143.0
32 TraesCS6A01G417400 chr3A 95.385 65 3 0 3404 3468 510692776 510692712 1.700000e-18 104.0
33 TraesCS6A01G417400 chr3A 94.030 67 4 0 3404 3470 240356855 240356789 6.130000e-18 102.0
34 TraesCS6A01G417400 chr2A 93.720 207 11 2 3210 3414 35678295 35678501 3.360000e-80 309.0
35 TraesCS6A01G417400 chr2A 93.237 207 12 2 3210 3414 519403790 519403996 1.560000e-78 303.0
36 TraesCS6A01G417400 chr2A 93.237 207 12 2 3210 3414 576447322 576447528 1.560000e-78 303.0
37 TraesCS6A01G417400 chr2A 93.204 206 13 1 3210 3414 443920917 443921122 5.630000e-78 302.0
38 TraesCS6A01G417400 chr5A 93.237 207 10 4 3210 3414 414976325 414976529 5.630000e-78 302.0
39 TraesCS6A01G417400 chr5A 95.455 66 3 0 3403 3468 16725711 16725776 4.740000e-19 106.0
40 TraesCS6A01G417400 chr5B 94.118 68 4 0 3401 3468 632157152 632157219 1.700000e-18 104.0
41 TraesCS6A01G417400 chr1A 94.118 68 4 0 3401 3468 51702761 51702828 1.700000e-18 104.0
42 TraesCS6A01G417400 chr1A 94.030 67 4 0 3404 3470 65260325 65260259 6.130000e-18 102.0
43 TraesCS6A01G417400 chr2D 94.030 67 4 0 3404 3470 562339835 562339769 6.130000e-18 102.0


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 TraesCS6A01G417400 chr6A 615779234 615782703 3469 True 6408.000000 6408 100.000000 1 3470 1 chr6A.!!$R2 3469
1 TraesCS6A01G417400 chr6A 615790771 615793691 2920 False 1204.000000 2887 87.436000 1 3165 3 chr6A.!!$F3 3164
2 TraesCS6A01G417400 chr6A 615946961 615948766 1805 False 561.000000 878 80.234000 44 1834 2 chr6A.!!$F4 1790
3 TraesCS6A01G417400 chr6B 719732220 719735336 3116 False 1824.500000 3395 86.567000 12 3165 2 chr6B.!!$F1 3153
4 TraesCS6A01G417400 chr6B 719742443 719747731 5288 True 1031.000000 3417 85.570000 12 3165 4 chr6B.!!$R3 3153
5 TraesCS6A01G417400 chr6B 719909204 719910240 1036 True 680.000000 680 78.872000 1055 2079 1 chr6B.!!$R2 1024
6 TraesCS6A01G417400 chr6D 470975202 470978127 2925 False 884.500000 2686 88.257500 67 3165 4 chr6D.!!$F2 3098
7 TraesCS6A01G417400 chr3A 574344493 574346238 1745 True 254.666667 460 87.638333 1742 2376 3 chr3A.!!$R4 634

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
151 2364 0.396060 GAATAGCCCAGCCAGAGAGG 59.604 60.0 0.00 0.0 41.84 3.69 F
414 2660 0.442699 GCGCTGTGCTTACCTAACAC 59.557 55.0 5.84 0.0 41.73 3.32 F
1648 4064 0.518636 CACTTGCATCACCCAACTCG 59.481 55.0 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 3851 0.250513 GAGGGATCCAACAGCGAAGT 59.749 55.0 15.23 0.0 0.00 3.01 R
1872 4288 0.261696 ACAAACCACCAGCCTTCCTT 59.738 50.0 0.00 0.0 0.00 3.36 R
3358 6238 0.032117 TGAGACCCGTCCTGATGGAT 60.032 55.0 6.98 0.0 45.29 3.41 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
41 42 2.210116 CCGTTGGTTATCTGAATCCCG 58.790 52.381 0.00 0.00 0.00 5.14
42 43 2.210116 CGTTGGTTATCTGAATCCCGG 58.790 52.381 0.00 0.00 0.00 5.73
151 2364 0.396060 GAATAGCCCAGCCAGAGAGG 59.604 60.000 0.00 0.00 41.84 3.69
316 2553 4.862641 AACCCTAGCTGGTTCAACATAT 57.137 40.909 2.64 0.00 45.51 1.78
317 2554 4.423625 ACCCTAGCTGGTTCAACATATC 57.576 45.455 0.00 0.00 33.91 1.63
318 2555 4.040755 ACCCTAGCTGGTTCAACATATCT 58.959 43.478 0.00 0.00 33.91 1.98
319 2556 4.475016 ACCCTAGCTGGTTCAACATATCTT 59.525 41.667 0.00 0.00 33.91 2.40
320 2557 5.044846 ACCCTAGCTGGTTCAACATATCTTT 60.045 40.000 0.00 0.00 33.91 2.52
321 2558 5.297776 CCCTAGCTGGTTCAACATATCTTTG 59.702 44.000 0.00 0.00 0.00 2.77
322 2559 5.882557 CCTAGCTGGTTCAACATATCTTTGT 59.117 40.000 0.00 0.00 0.00 2.83
323 2560 6.375455 CCTAGCTGGTTCAACATATCTTTGTT 59.625 38.462 0.00 0.00 40.39 2.83
324 2561 6.655078 AGCTGGTTCAACATATCTTTGTTT 57.345 33.333 0.00 0.00 37.73 2.83
325 2562 6.681777 AGCTGGTTCAACATATCTTTGTTTC 58.318 36.000 0.00 0.00 37.73 2.78
326 2563 5.863935 GCTGGTTCAACATATCTTTGTTTCC 59.136 40.000 0.00 0.00 37.73 3.13
327 2564 6.294731 GCTGGTTCAACATATCTTTGTTTCCT 60.295 38.462 0.00 0.00 37.73 3.36
328 2565 7.595819 TGGTTCAACATATCTTTGTTTCCTT 57.404 32.000 0.00 0.00 37.73 3.36
329 2566 8.017418 TGGTTCAACATATCTTTGTTTCCTTT 57.983 30.769 0.00 0.00 37.73 3.11
330 2567 8.482128 TGGTTCAACATATCTTTGTTTCCTTTT 58.518 29.630 0.00 0.00 37.73 2.27
331 2568 9.325198 GGTTCAACATATCTTTGTTTCCTTTTT 57.675 29.630 0.00 0.00 37.73 1.94
377 2618 4.237724 GCTTCTTGGTTGGATGTTTTAGC 58.762 43.478 0.00 0.00 0.00 3.09
378 2619 4.261994 GCTTCTTGGTTGGATGTTTTAGCA 60.262 41.667 0.00 0.00 0.00 3.49
397 2638 1.524355 CAGATTCTGGCGTAAGATGCG 59.476 52.381 5.73 0.00 43.02 4.73
414 2660 0.442699 GCGCTGTGCTTACCTAACAC 59.557 55.000 5.84 0.00 41.73 3.32
495 2742 3.722147 CGATTTGGGATACTCTGACCTG 58.278 50.000 0.00 0.00 0.00 4.00
496 2743 3.384789 CGATTTGGGATACTCTGACCTGA 59.615 47.826 0.00 0.00 0.00 3.86
497 2744 4.698575 GATTTGGGATACTCTGACCTGAC 58.301 47.826 0.00 0.00 0.00 3.51
499 2746 1.646447 TGGGATACTCTGACCTGACCT 59.354 52.381 0.00 0.00 0.00 3.85
516 2833 3.138283 TGACCTGGATTCAGTTTTGGTCT 59.862 43.478 10.00 0.00 39.31 3.85
579 2896 7.816513 GGAATGGAATGGAAGAAAGAAAGAAAG 59.183 37.037 0.00 0.00 0.00 2.62
581 2898 7.896383 TGGAATGGAAGAAAGAAAGAAAGAA 57.104 32.000 0.00 0.00 0.00 2.52
582 2899 8.305046 TGGAATGGAAGAAAGAAAGAAAGAAA 57.695 30.769 0.00 0.00 0.00 2.52
587 2904 8.424274 TGGAAGAAAGAAAGAAAGAAAATTGC 57.576 30.769 0.00 0.00 0.00 3.56
588 2905 8.040132 TGGAAGAAAGAAAGAAAGAAAATTGCA 58.960 29.630 0.00 0.00 0.00 4.08
589 2906 8.331022 GGAAGAAAGAAAGAAAGAAAATTGCAC 58.669 33.333 0.00 0.00 0.00 4.57
591 2908 8.189709 AGAAAGAAAGAAAGAAAATTGCACAC 57.810 30.769 0.00 0.00 0.00 3.82
592 2909 8.037166 AGAAAGAAAGAAAGAAAATTGCACACT 58.963 29.630 0.00 0.00 0.00 3.55
650 2969 3.308035 TCATCGGTTAGAGGGCTAGAA 57.692 47.619 0.00 0.00 0.00 2.10
693 3047 6.640499 CAGATGTATACTGCTAGCAGAAAGAC 59.360 42.308 43.42 34.12 46.30 3.01
727 3090 4.318332 TCGAAATGTTCTGATGTGCTTCT 58.682 39.130 0.00 0.00 0.00 2.85
733 3096 6.585695 ATGTTCTGATGTGCTTCTCAAATT 57.414 33.333 0.00 0.00 0.00 1.82
777 3152 6.981722 ACACATTTCCATAACCAAGTTTCTC 58.018 36.000 0.00 0.00 0.00 2.87
778 3153 6.777580 ACACATTTCCATAACCAAGTTTCTCT 59.222 34.615 0.00 0.00 0.00 3.10
779 3154 7.287696 ACACATTTCCATAACCAAGTTTCTCTT 59.712 33.333 0.00 0.00 36.75 2.85
871 3250 8.409358 AAACTCTTGTTTTTAGTCTATGGCAT 57.591 30.769 4.88 4.88 43.13 4.40
990 3383 3.885297 AGGCATATATGTTTCACCTGCAC 59.115 43.478 14.14 0.00 0.00 4.57
994 3387 5.688621 GCATATATGTTTCACCTGCACAATG 59.311 40.000 14.14 0.00 0.00 2.82
1048 3456 7.126398 CGCCTTGTATTTCTTAATCTGCTTAC 58.874 38.462 0.00 0.00 0.00 2.34
1264 3680 4.365111 GCCACCACATGCCCCTCA 62.365 66.667 0.00 0.00 0.00 3.86
1383 3799 1.420138 TCTTCCTTGGACCAGTGGTTC 59.580 52.381 17.93 16.09 35.25 3.62
1435 3851 3.587933 GCCAACCGAAACACCGCA 61.588 61.111 0.00 0.00 0.00 5.69
1461 3877 3.244353 CGCTGTTGGATCCCTCAAGATAT 60.244 47.826 9.90 0.00 0.00 1.63
1463 3879 4.564041 CTGTTGGATCCCTCAAGATATCG 58.436 47.826 9.90 0.00 0.00 2.92
1519 3935 5.163509 TGGTAAGCTCATCTACTACTGCAAG 60.164 44.000 0.00 0.00 42.29 4.01
1571 3987 2.093973 GGTGACGATGTCTCAACTCCAT 60.094 50.000 0.00 0.00 33.15 3.41
1648 4064 0.518636 CACTTGCATCACCCAACTCG 59.481 55.000 0.00 0.00 0.00 4.18
1792 4208 4.560128 TCATTGTCTCGAATAGCTATGGC 58.440 43.478 7.09 1.89 39.06 4.40
1930 4362 0.250295 TCAGTTTGGGCGAGTTCCAG 60.250 55.000 0.00 0.00 35.48 3.86
2105 4543 2.352030 CGTACAGCTCGACCTTGGTTTA 60.352 50.000 0.00 0.00 0.00 2.01
2150 4597 0.390492 TCGCATGCAGGATAGACCAG 59.610 55.000 19.57 0.00 42.04 4.00
2312 4768 3.924686 GCACTGGCTTCATCTGAAATTTG 59.075 43.478 0.00 0.00 36.96 2.32
2328 4784 2.978156 TTTGCCTTTGAGATCCAGGT 57.022 45.000 0.00 0.00 0.00 4.00
2343 4799 5.600484 AGATCCAGGTAGTAGAGATTGGTTG 59.400 44.000 0.00 0.00 0.00 3.77
2461 4948 1.810755 GGTGTTGGCACTAGCTTTACC 59.189 52.381 0.00 0.00 44.65 2.85
2592 5086 0.671781 CAGCGTCTCCCCTGTTTCAG 60.672 60.000 0.00 0.00 0.00 3.02
2602 5096 1.266989 CCCTGTTTCAGCGAGGAAAAC 59.733 52.381 3.87 1.02 38.41 2.43
2631 5125 6.486657 ACATTTCTGCTTGTACTTGAGCTTTA 59.513 34.615 14.46 2.05 39.60 1.85
2650 5145 7.923888 AGCTTTATGTGTATAAGCTTGTCATG 58.076 34.615 9.86 0.00 33.45 3.07
2661 5158 5.473066 AAGCTTGTCATGGTTTGCTAAAT 57.527 34.783 0.00 0.00 0.00 1.40
2714 5494 8.294577 GGATTAGTTGGTGTAAACCTTAGTTTG 58.705 37.037 3.10 0.00 45.77 2.93
2792 5576 3.491619 GCGCCTCATCTCAGTGAAGATAA 60.492 47.826 0.00 0.00 34.21 1.75
2801 5585 8.331740 TCATCTCAGTGAAGATAAAAATTCCCT 58.668 33.333 0.00 0.00 34.21 4.20
2802 5586 7.928307 TCTCAGTGAAGATAAAAATTCCCTG 57.072 36.000 0.00 0.00 33.73 4.45
2803 5587 7.689299 TCTCAGTGAAGATAAAAATTCCCTGA 58.311 34.615 0.00 1.27 37.52 3.86
2806 5590 8.108999 TCAGTGAAGATAAAAATTCCCTGATGA 58.891 33.333 0.00 0.00 35.77 2.92
2891 5683 3.506067 GGCCACTGCAGTTTAGTTATGTT 59.494 43.478 18.94 0.00 40.13 2.71
3022 5895 8.632906 ATTTTCATTGCATCTAGCTAGCTATT 57.367 30.769 24.36 12.57 45.94 1.73
3165 6045 0.931702 TTTGTTTCTTTCTCGCGCGA 59.068 45.000 32.60 32.60 0.00 5.87
3166 6046 0.506932 TTGTTTCTTTCTCGCGCGAG 59.493 50.000 45.23 45.23 43.21 5.03
3167 6047 0.596600 TGTTTCTTTCTCGCGCGAGT 60.597 50.000 46.69 0.00 42.49 4.18
3168 6048 0.179272 GTTTCTTTCTCGCGCGAGTG 60.179 55.000 46.69 36.92 42.49 3.51
3169 6049 1.282248 TTTCTTTCTCGCGCGAGTGG 61.282 55.000 46.69 36.48 42.49 4.00
3170 6050 2.126463 CTTTCTCGCGCGAGTGGA 60.126 61.111 46.69 33.93 42.49 4.02
3171 6051 2.430244 TTTCTCGCGCGAGTGGAC 60.430 61.111 46.69 0.51 42.49 4.02
3172 6052 3.202216 TTTCTCGCGCGAGTGGACA 62.202 57.895 46.69 31.58 42.49 4.02
3173 6053 3.610791 TTCTCGCGCGAGTGGACAG 62.611 63.158 46.69 28.71 42.49 3.51
3174 6054 4.103103 CTCGCGCGAGTGGACAGA 62.103 66.667 43.16 16.34 43.13 3.41
3175 6055 3.610791 CTCGCGCGAGTGGACAGAA 62.611 63.158 43.16 15.58 43.13 3.02
3176 6056 3.470567 CGCGCGAGTGGACAGAAC 61.471 66.667 28.94 0.00 38.12 3.01
3177 6057 3.470567 GCGCGAGTGGACAGAACG 61.471 66.667 12.10 0.00 0.00 3.95
3178 6058 2.050351 CGCGAGTGGACAGAACGT 60.050 61.111 0.00 0.00 0.00 3.99
3179 6059 2.081212 CGCGAGTGGACAGAACGTC 61.081 63.158 0.00 0.00 44.57 4.34
3180 6060 1.286260 GCGAGTGGACAGAACGTCT 59.714 57.895 0.00 0.00 44.70 4.18
3192 6072 3.670625 CAGAACGTCTGGTTTTATGGGA 58.329 45.455 7.01 0.00 40.71 4.37
3193 6073 4.261801 CAGAACGTCTGGTTTTATGGGAT 58.738 43.478 7.01 0.00 40.71 3.85
3198 6078 3.761752 CGTCTGGTTTTATGGGATTGGTT 59.238 43.478 0.00 0.00 0.00 3.67
3199 6079 4.944930 CGTCTGGTTTTATGGGATTGGTTA 59.055 41.667 0.00 0.00 0.00 2.85
3201 6081 5.359860 GTCTGGTTTTATGGGATTGGTTAGG 59.640 44.000 0.00 0.00 0.00 2.69
3202 6082 5.015817 TCTGGTTTTATGGGATTGGTTAGGT 59.984 40.000 0.00 0.00 0.00 3.08
3203 6083 5.265989 TGGTTTTATGGGATTGGTTAGGTC 58.734 41.667 0.00 0.00 0.00 3.85
3204 6084 5.015817 TGGTTTTATGGGATTGGTTAGGTCT 59.984 40.000 0.00 0.00 0.00 3.85
3208 6088 2.124411 TGGGATTGGTTAGGTCTAGGC 58.876 52.381 0.00 0.00 0.00 3.93
3209 6089 1.070289 GGGATTGGTTAGGTCTAGGCG 59.930 57.143 0.00 0.00 0.00 5.52
3213 6093 1.941377 TGGTTAGGTCTAGGCGGAAA 58.059 50.000 0.00 0.00 0.00 3.13
3214 6094 2.259012 TGGTTAGGTCTAGGCGGAAAA 58.741 47.619 0.00 0.00 0.00 2.29
3215 6095 2.235402 TGGTTAGGTCTAGGCGGAAAAG 59.765 50.000 0.00 0.00 0.00 2.27
3217 6097 3.055602 GGTTAGGTCTAGGCGGAAAAGAA 60.056 47.826 0.00 0.00 0.00 2.52
3218 6098 4.383880 GGTTAGGTCTAGGCGGAAAAGAAT 60.384 45.833 0.00 0.00 0.00 2.40
3219 6099 5.183969 GTTAGGTCTAGGCGGAAAAGAATT 58.816 41.667 0.00 0.00 0.00 2.17
3220 6100 3.875125 AGGTCTAGGCGGAAAAGAATTC 58.125 45.455 0.00 0.00 0.00 2.17
3221 6101 3.519913 AGGTCTAGGCGGAAAAGAATTCT 59.480 43.478 0.88 0.88 0.00 2.40
3222 6102 4.715297 AGGTCTAGGCGGAAAAGAATTCTA 59.285 41.667 8.75 0.00 0.00 2.10
3224 6104 5.467063 GGTCTAGGCGGAAAAGAATTCTATG 59.533 44.000 8.75 0.00 0.00 2.23
3225 6105 6.281405 GTCTAGGCGGAAAAGAATTCTATGA 58.719 40.000 8.75 0.00 0.00 2.15
3226 6106 6.422400 GTCTAGGCGGAAAAGAATTCTATGAG 59.578 42.308 8.75 1.27 0.00 2.90
3227 6107 5.359194 AGGCGGAAAAGAATTCTATGAGA 57.641 39.130 8.75 0.00 0.00 3.27
3229 6109 5.994668 AGGCGGAAAAGAATTCTATGAGATC 59.005 40.000 8.75 1.58 0.00 2.75
3230 6110 5.760253 GGCGGAAAAGAATTCTATGAGATCA 59.240 40.000 8.75 0.00 0.00 2.92
3234 6114 7.170658 CGGAAAAGAATTCTATGAGATCAGGTC 59.829 40.741 8.75 0.00 0.00 3.85
3235 6115 8.210265 GGAAAAGAATTCTATGAGATCAGGTCT 58.790 37.037 8.75 0.00 40.81 3.85
3242 6122 4.320910 AGATCAGGTCTCACGCGA 57.679 55.556 15.93 0.00 28.45 5.87
3243 6123 2.102554 AGATCAGGTCTCACGCGAG 58.897 57.895 15.93 4.59 40.98 5.03
3244 6124 0.393132 AGATCAGGTCTCACGCGAGA 60.393 55.000 15.93 10.37 46.28 4.04
3250 6130 3.197614 TCTCACGCGAGACCCATC 58.802 61.111 15.93 0.00 43.55 3.51
3252 6132 2.362503 TCACGCGAGACCCATCCT 60.363 61.111 15.93 0.00 0.00 3.24
3254 6134 2.362503 ACGCGAGACCCATCCTGA 60.363 61.111 15.93 0.00 0.00 3.86
3256 6136 1.300465 CGCGAGACCCATCCTGATG 60.300 63.158 0.00 0.00 38.51 3.07
3270 6150 1.409101 CCTGATGGATGACATGTGGCA 60.409 52.381 1.15 0.00 40.72 4.92
3272 6152 2.956333 CTGATGGATGACATGTGGCATT 59.044 45.455 1.15 0.00 45.42 3.56
3274 6154 2.510928 TGGATGACATGTGGCATTCA 57.489 45.000 1.15 5.70 46.54 2.57
3288 6168 5.170021 GTGGCATTCACAAATCATAAAGCA 58.830 37.500 0.00 0.00 45.39 3.91
3289 6169 5.813672 GTGGCATTCACAAATCATAAAGCAT 59.186 36.000 0.00 0.00 45.39 3.79
3290 6170 6.019318 GTGGCATTCACAAATCATAAAGCATC 60.019 38.462 0.00 0.00 45.39 3.91
3294 6174 4.608269 TCACAAATCATAAAGCATCCCCA 58.392 39.130 0.00 0.00 0.00 4.96
3296 6176 3.706086 ACAAATCATAAAGCATCCCCACC 59.294 43.478 0.00 0.00 0.00 4.61
3297 6177 2.683211 ATCATAAAGCATCCCCACCC 57.317 50.000 0.00 0.00 0.00 4.61
3299 6179 1.929494 TCATAAAGCATCCCCACCCTT 59.071 47.619 0.00 0.00 0.00 3.95
3300 6180 2.091885 TCATAAAGCATCCCCACCCTTC 60.092 50.000 0.00 0.00 0.00 3.46
3301 6181 1.377690 TAAAGCATCCCCACCCTTCA 58.622 50.000 0.00 0.00 0.00 3.02
3302 6182 0.251787 AAAGCATCCCCACCCTTCAC 60.252 55.000 0.00 0.00 0.00 3.18
3303 6183 1.142688 AAGCATCCCCACCCTTCACT 61.143 55.000 0.00 0.00 0.00 3.41
3305 6185 0.623723 GCATCCCCACCCTTCACTTA 59.376 55.000 0.00 0.00 0.00 2.24
3306 6186 1.005450 GCATCCCCACCCTTCACTTAA 59.995 52.381 0.00 0.00 0.00 1.85
3308 6188 3.773560 CATCCCCACCCTTCACTTAAAA 58.226 45.455 0.00 0.00 0.00 1.52
3309 6189 4.352893 CATCCCCACCCTTCACTTAAAAT 58.647 43.478 0.00 0.00 0.00 1.82
3310 6190 4.042271 TCCCCACCCTTCACTTAAAATC 57.958 45.455 0.00 0.00 0.00 2.17
3311 6191 3.399644 TCCCCACCCTTCACTTAAAATCA 59.600 43.478 0.00 0.00 0.00 2.57
3312 6192 3.763897 CCCCACCCTTCACTTAAAATCAG 59.236 47.826 0.00 0.00 0.00 2.90
3313 6193 3.763897 CCCACCCTTCACTTAAAATCAGG 59.236 47.826 0.00 0.00 0.00 3.86
3314 6194 3.763897 CCACCCTTCACTTAAAATCAGGG 59.236 47.826 0.20 0.20 45.85 4.45
3315 6195 3.763897 CACCCTTCACTTAAAATCAGGGG 59.236 47.826 6.99 0.00 44.82 4.79
3318 6198 4.273318 CCTTCACTTAAAATCAGGGGGAG 58.727 47.826 0.00 0.00 0.00 4.30
3319 6199 4.018415 CCTTCACTTAAAATCAGGGGGAGA 60.018 45.833 0.00 0.00 0.00 3.71
3320 6200 4.844349 TCACTTAAAATCAGGGGGAGAG 57.156 45.455 0.00 0.00 0.00 3.20
3321 6201 3.054361 TCACTTAAAATCAGGGGGAGAGC 60.054 47.826 0.00 0.00 0.00 4.09
3322 6202 2.092914 ACTTAAAATCAGGGGGAGAGCG 60.093 50.000 0.00 0.00 0.00 5.03
3323 6203 1.874129 TAAAATCAGGGGGAGAGCGA 58.126 50.000 0.00 0.00 0.00 4.93
3325 6205 1.216990 AAATCAGGGGGAGAGCGATT 58.783 50.000 0.00 0.00 0.00 3.34
3326 6206 2.103153 AATCAGGGGGAGAGCGATTA 57.897 50.000 0.00 0.00 0.00 1.75
3328 6208 0.556258 TCAGGGGGAGAGCGATTAGA 59.444 55.000 0.00 0.00 0.00 2.10
3329 6209 1.148027 TCAGGGGGAGAGCGATTAGAT 59.852 52.381 0.00 0.00 0.00 1.98
3330 6210 1.274728 CAGGGGGAGAGCGATTAGATG 59.725 57.143 0.00 0.00 0.00 2.90
3331 6211 0.036858 GGGGGAGAGCGATTAGATGC 60.037 60.000 0.00 0.00 0.00 3.91
3332 6212 0.972883 GGGGAGAGCGATTAGATGCT 59.027 55.000 0.00 0.00 45.90 3.79
3333 6213 1.346068 GGGGAGAGCGATTAGATGCTT 59.654 52.381 0.00 0.00 42.60 3.91
3334 6214 2.224402 GGGGAGAGCGATTAGATGCTTT 60.224 50.000 0.00 0.00 42.60 3.51
3336 6216 3.462021 GGAGAGCGATTAGATGCTTTGT 58.538 45.455 0.00 0.00 42.60 2.83
3337 6217 3.247173 GGAGAGCGATTAGATGCTTTGTG 59.753 47.826 0.00 0.00 42.60 3.33
3338 6218 4.115516 GAGAGCGATTAGATGCTTTGTGA 58.884 43.478 0.00 0.00 42.60 3.58
3342 6222 5.847304 AGCGATTAGATGCTTTGTGATCTA 58.153 37.500 0.00 0.00 38.57 1.98
3344 6224 6.368243 AGCGATTAGATGCTTTGTGATCTATG 59.632 38.462 0.00 0.00 38.57 2.23
3345 6225 6.367149 GCGATTAGATGCTTTGTGATCTATGA 59.633 38.462 0.00 0.00 32.47 2.15
3347 6227 8.933807 CGATTAGATGCTTTGTGATCTATGAAT 58.066 33.333 0.00 0.00 32.47 2.57
3349 6229 6.315091 AGATGCTTTGTGATCTATGAATGC 57.685 37.500 0.00 0.00 0.00 3.56
3350 6230 4.906065 TGCTTTGTGATCTATGAATGCC 57.094 40.909 0.00 0.00 0.00 4.40
3351 6231 4.271661 TGCTTTGTGATCTATGAATGCCA 58.728 39.130 0.00 0.00 0.00 4.92
3352 6232 4.096833 TGCTTTGTGATCTATGAATGCCAC 59.903 41.667 0.00 0.00 0.00 5.01
3353 6233 4.787563 GCTTTGTGATCTATGAATGCCACG 60.788 45.833 0.00 0.00 0.00 4.94
3354 6234 3.541996 TGTGATCTATGAATGCCACGT 57.458 42.857 0.00 0.00 0.00 4.49
3355 6235 3.197265 TGTGATCTATGAATGCCACGTG 58.803 45.455 9.08 9.08 0.00 4.49
3356 6236 3.198068 GTGATCTATGAATGCCACGTGT 58.802 45.455 15.65 0.00 0.00 4.49
3357 6237 3.246226 GTGATCTATGAATGCCACGTGTC 59.754 47.826 15.65 0.98 0.00 3.67
3358 6238 3.118811 TGATCTATGAATGCCACGTGTCA 60.119 43.478 15.65 8.63 0.00 3.58
3359 6239 3.541996 TCTATGAATGCCACGTGTCAT 57.458 42.857 19.43 19.43 35.05 3.06
3360 6240 3.457234 TCTATGAATGCCACGTGTCATC 58.543 45.455 19.16 11.02 32.99 2.92
3361 6241 1.382522 ATGAATGCCACGTGTCATCC 58.617 50.000 13.12 0.00 0.00 3.51
3362 6242 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.000 13.12 2.86 0.00 3.41
3363 6243 1.339920 TGAATGCCACGTGTCATCCAT 60.340 47.619 13.12 0.00 0.00 3.41
3364 6244 1.331756 GAATGCCACGTGTCATCCATC 59.668 52.381 13.12 3.25 0.00 3.51
3365 6245 0.252761 ATGCCACGTGTCATCCATCA 59.747 50.000 15.65 0.00 0.00 3.07
3366 6246 0.391528 TGCCACGTGTCATCCATCAG 60.392 55.000 15.65 0.00 0.00 2.90
3367 6247 1.091771 GCCACGTGTCATCCATCAGG 61.092 60.000 15.65 0.00 0.00 3.86
3376 6256 4.356979 TCCATCAGGACGGGTCTC 57.643 61.111 0.00 0.00 39.61 3.36
3377 6257 1.386550 TCCATCAGGACGGGTCTCA 59.613 57.895 0.00 0.00 39.61 3.27
3378 6258 0.032117 TCCATCAGGACGGGTCTCAT 60.032 55.000 0.00 0.00 39.61 2.90
3379 6259 0.390860 CCATCAGGACGGGTCTCATC 59.609 60.000 0.00 0.00 36.89 2.92
3380 6260 1.407936 CATCAGGACGGGTCTCATCT 58.592 55.000 0.00 0.00 0.00 2.90
3381 6261 1.068281 CATCAGGACGGGTCTCATCTG 59.932 57.143 0.00 0.00 0.00 2.90
3382 6262 1.142748 CAGGACGGGTCTCATCTGC 59.857 63.158 0.00 0.00 0.00 4.26
3383 6263 1.000993 AGGACGGGTCTCATCTGCT 59.999 57.895 0.00 0.00 0.00 4.24
3384 6264 0.259065 AGGACGGGTCTCATCTGCTA 59.741 55.000 0.00 0.00 0.00 3.49
3385 6265 1.112113 GGACGGGTCTCATCTGCTAA 58.888 55.000 0.00 0.00 0.00 3.09
3386 6266 1.202428 GGACGGGTCTCATCTGCTAAC 60.202 57.143 0.00 0.00 0.00 2.34
3387 6267 0.824759 ACGGGTCTCATCTGCTAACC 59.175 55.000 0.00 0.00 0.00 2.85
3388 6268 0.249073 CGGGTCTCATCTGCTAACCG 60.249 60.000 0.00 0.00 0.00 4.44
3389 6269 0.824759 GGGTCTCATCTGCTAACCGT 59.175 55.000 0.00 0.00 0.00 4.83
3390 6270 1.471676 GGGTCTCATCTGCTAACCGTG 60.472 57.143 0.00 0.00 0.00 4.94
3391 6271 1.476891 GGTCTCATCTGCTAACCGTGA 59.523 52.381 0.00 0.00 0.00 4.35
3392 6272 2.480416 GGTCTCATCTGCTAACCGTGAG 60.480 54.545 0.00 0.00 38.07 3.51
3393 6273 2.423892 GTCTCATCTGCTAACCGTGAGA 59.576 50.000 0.00 0.00 41.99 3.27
3394 6274 3.067461 GTCTCATCTGCTAACCGTGAGAT 59.933 47.826 6.65 0.00 44.77 2.75
3395 6275 3.316588 TCTCATCTGCTAACCGTGAGATC 59.683 47.826 0.00 0.00 40.06 2.75
3396 6276 3.291584 TCATCTGCTAACCGTGAGATCT 58.708 45.455 0.00 0.00 0.00 2.75
3397 6277 3.067320 TCATCTGCTAACCGTGAGATCTG 59.933 47.826 0.00 0.00 0.00 2.90
3398 6278 1.751351 TCTGCTAACCGTGAGATCTGG 59.249 52.381 0.00 0.00 0.00 3.86
3399 6279 1.478510 CTGCTAACCGTGAGATCTGGT 59.521 52.381 0.00 0.00 37.68 4.00
3400 6280 1.476891 TGCTAACCGTGAGATCTGGTC 59.523 52.381 0.00 0.00 34.11 4.02
3401 6281 1.751924 GCTAACCGTGAGATCTGGTCT 59.248 52.381 0.00 0.00 40.81 3.85
3417 6297 9.282569 AGATCTGGTCTCATATAATTTTTGCTC 57.717 33.333 0.00 0.00 28.45 4.26
3418 6298 7.807977 TCTGGTCTCATATAATTTTTGCTCC 57.192 36.000 0.00 0.00 0.00 4.70
3419 6299 6.772716 TCTGGTCTCATATAATTTTTGCTCCC 59.227 38.462 0.00 0.00 0.00 4.30
3420 6300 5.530915 TGGTCTCATATAATTTTTGCTCCCG 59.469 40.000 0.00 0.00 0.00 5.14
3421 6301 5.452777 GTCTCATATAATTTTTGCTCCCGC 58.547 41.667 0.00 0.00 0.00 6.13
3422 6302 4.518970 TCTCATATAATTTTTGCTCCCGCC 59.481 41.667 0.00 0.00 34.43 6.13
3423 6303 3.252215 TCATATAATTTTTGCTCCCGCCG 59.748 43.478 0.00 0.00 34.43 6.46
3424 6304 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
3425 6305 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
3426 6306 2.093537 AATTTTTGCTCCCGCCGCAA 62.094 50.000 0.00 0.00 44.83 4.85
3427 6307 1.887344 ATTTTTGCTCCCGCCGCAAT 61.887 50.000 5.33 0.00 45.67 3.56
3428 6308 2.485188 TTTTTGCTCCCGCCGCAATC 62.485 55.000 5.33 0.00 45.67 2.67
3454 6334 9.897744 CGGTCTTAATAGTTAAATATACGGTCA 57.102 33.333 0.00 0.00 0.00 4.02
3461 6341 9.826574 AATAGTTAAATATACGGTCAAAGCTGA 57.173 29.630 0.00 0.00 0.00 4.26
3462 6342 9.826574 ATAGTTAAATATACGGTCAAAGCTGAA 57.173 29.630 0.00 0.00 31.88 3.02
3463 6343 8.556213 AGTTAAATATACGGTCAAAGCTGAAA 57.444 30.769 0.00 0.00 31.88 2.69
3464 6344 8.448615 AGTTAAATATACGGTCAAAGCTGAAAC 58.551 33.333 0.00 0.00 31.88 2.78
3465 6345 6.811253 AAATATACGGTCAAAGCTGAAACA 57.189 33.333 0.00 0.00 31.88 2.83
3466 6346 5.796350 ATATACGGTCAAAGCTGAAACAC 57.204 39.130 0.00 0.00 31.88 3.32
3467 6347 0.655733 ACGGTCAAAGCTGAAACACG 59.344 50.000 0.00 0.00 31.88 4.49
3468 6348 0.934496 CGGTCAAAGCTGAAACACGA 59.066 50.000 0.00 0.00 31.88 4.35
3469 6349 1.070577 CGGTCAAAGCTGAAACACGAG 60.071 52.381 0.00 0.00 31.88 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 141 0.693049 TCTTCTTCTTGGGAGGGTGC 59.307 55.000 0.00 0.00 0.00 5.01
328 2565 6.931790 TCATCCATCCAATCCAAAGAAAAA 57.068 33.333 0.00 0.00 0.00 1.94
329 2566 6.931790 TTCATCCATCCAATCCAAAGAAAA 57.068 33.333 0.00 0.00 0.00 2.29
330 2567 6.183360 CGATTCATCCATCCAATCCAAAGAAA 60.183 38.462 0.00 0.00 0.00 2.52
331 2568 5.300034 CGATTCATCCATCCAATCCAAAGAA 59.700 40.000 0.00 0.00 0.00 2.52
332 2569 4.823442 CGATTCATCCATCCAATCCAAAGA 59.177 41.667 0.00 0.00 0.00 2.52
333 2570 4.558095 GCGATTCATCCATCCAATCCAAAG 60.558 45.833 0.00 0.00 0.00 2.77
334 2571 3.318839 GCGATTCATCCATCCAATCCAAA 59.681 43.478 0.00 0.00 0.00 3.28
335 2572 2.886523 GCGATTCATCCATCCAATCCAA 59.113 45.455 0.00 0.00 0.00 3.53
336 2573 2.107031 AGCGATTCATCCATCCAATCCA 59.893 45.455 0.00 0.00 0.00 3.41
337 2574 2.787994 AGCGATTCATCCATCCAATCC 58.212 47.619 0.00 0.00 0.00 3.01
338 2575 4.070716 AGAAGCGATTCATCCATCCAATC 58.929 43.478 16.78 0.00 0.00 2.67
339 2576 4.096190 AGAAGCGATTCATCCATCCAAT 57.904 40.909 16.78 0.00 0.00 3.16
344 2581 3.287867 ACCAAGAAGCGATTCATCCAT 57.712 42.857 16.78 0.00 0.00 3.41
377 2618 1.524355 CGCATCTTACGCCAGAATCTG 59.476 52.381 2.68 2.68 0.00 2.90
378 2619 1.858091 CGCATCTTACGCCAGAATCT 58.142 50.000 0.00 0.00 0.00 2.40
414 2660 6.480763 TCAATCTACTCTAGATCTAGCCCTG 58.519 44.000 22.81 14.81 44.44 4.45
425 2671 7.658167 TCGATTAGTCCACTCAATCTACTCTAG 59.342 40.741 0.00 0.00 0.00 2.43
495 2742 3.503748 CAGACCAAAACTGAATCCAGGTC 59.496 47.826 0.00 0.00 39.98 3.85
496 2743 3.117512 ACAGACCAAAACTGAATCCAGGT 60.118 43.478 0.00 0.00 43.46 4.00
497 2744 3.490348 ACAGACCAAAACTGAATCCAGG 58.510 45.455 0.00 0.00 44.60 4.45
499 2746 5.420421 TCAAAACAGACCAAAACTGAATCCA 59.580 36.000 0.00 0.00 38.55 3.41
516 2833 2.159707 GCGCTCGAATTAGCTCAAAACA 60.160 45.455 0.00 0.00 40.49 2.83
579 2896 6.892310 AGTTTCTCAAAGTGTGCAATTTTC 57.108 33.333 0.00 0.00 0.00 2.29
581 2898 6.633856 AGAAGTTTCTCAAAGTGTGCAATTT 58.366 32.000 0.00 0.00 29.94 1.82
582 2899 6.212888 AGAAGTTTCTCAAAGTGTGCAATT 57.787 33.333 0.00 0.00 29.94 2.32
650 2969 5.047021 ACATCTGTACATCTACAAGTGCTGT 60.047 40.000 0.00 0.00 42.47 4.40
661 2980 6.717084 TGCTAGCAGTATACATCTGTACATCT 59.283 38.462 14.93 0.00 35.60 2.90
693 3047 4.867047 AGAACATTTCGATGCTAGTGTCTG 59.133 41.667 0.00 0.00 34.02 3.51
733 3096 9.675464 AATGTGTCCTCCGTTTTATTTTATCTA 57.325 29.630 0.00 0.00 0.00 1.98
786 3161 8.822805 TGTTCAGGTTCAGAATAAGGTAATACT 58.177 33.333 0.00 0.00 0.00 2.12
787 3162 8.880750 GTGTTCAGGTTCAGAATAAGGTAATAC 58.119 37.037 0.00 0.00 0.00 1.89
867 3246 2.908688 AACAACCAAAGGAACATGCC 57.091 45.000 0.00 0.00 0.00 4.40
871 3250 9.137459 TCAGATAAATAAACAACCAAAGGAACA 57.863 29.630 0.00 0.00 0.00 3.18
990 3383 2.411628 TCGGAACCATGGGTACATTG 57.588 50.000 13.91 0.00 33.12 2.82
994 3387 3.876341 TGTTAATCGGAACCATGGGTAC 58.124 45.455 18.09 10.02 33.12 3.34
1372 3788 1.277557 AGCTCATGAGAACCACTGGTC 59.722 52.381 27.04 4.27 33.12 4.02
1435 3851 0.250513 GAGGGATCCAACAGCGAAGT 59.749 55.000 15.23 0.00 0.00 3.01
1461 3877 5.817296 CCAATAAATGTCATCTTCTCCACGA 59.183 40.000 0.00 0.00 0.00 4.35
1463 3879 7.040823 GGATCCAATAAATGTCATCTTCTCCAC 60.041 40.741 6.95 0.00 0.00 4.02
1519 3935 1.269723 TCGATGATGCGACAGTATCCC 59.730 52.381 0.00 0.00 38.49 3.85
1558 3974 1.902508 GGGAGACATGGAGTTGAGACA 59.097 52.381 0.00 0.00 0.00 3.41
1571 3987 1.891933 TTAGCATGGGATGGGAGACA 58.108 50.000 0.00 0.00 0.00 3.41
1648 4064 1.476891 TCGGTACTGACAAGGAGATGC 59.523 52.381 0.00 0.00 0.00 3.91
1825 4241 1.401905 GTTTTTATCTCCTGCAGGCCG 59.598 52.381 28.91 20.39 34.44 6.13
1872 4288 0.261696 ACAAACCACCAGCCTTCCTT 59.738 50.000 0.00 0.00 0.00 3.36
1930 4362 2.740714 GGTTGACATGTCGAGGCGC 61.741 63.158 20.54 0.00 0.00 6.53
2027 4463 0.960364 TCCGGGCTCATGCAAGAAAC 60.960 55.000 0.00 0.00 41.91 2.78
2105 4543 1.696336 CCTGCCACACAGCCTATAGAT 59.304 52.381 0.00 0.00 45.78 1.98
2150 4597 3.862063 CTGCAGGTTCAACGCGTGC 62.862 63.158 14.98 11.03 44.84 5.34
2294 4750 3.167485 AGGCAAATTTCAGATGAAGCCA 58.833 40.909 19.67 0.00 41.41 4.75
2307 4763 3.782992 ACCTGGATCTCAAAGGCAAATT 58.217 40.909 0.00 0.00 34.18 1.82
2312 4768 3.961408 TCTACTACCTGGATCTCAAAGGC 59.039 47.826 0.00 0.00 34.18 4.35
2328 4784 4.253685 GCAGCAACAACCAATCTCTACTA 58.746 43.478 0.00 0.00 0.00 1.82
2343 4799 3.885297 ACATATTCTACCCATGCAGCAAC 59.115 43.478 0.00 0.00 0.00 4.17
2461 4948 7.611213 AAAACCGGATAACTGAGTTATTCTG 57.389 36.000 18.03 14.77 38.62 3.02
2548 5038 7.823799 TGAACATATGCTACTTTCATCACAGAA 59.176 33.333 1.58 0.00 0.00 3.02
2602 5096 6.621596 GCTCAAGTACAAGCAGAAATGTTAGG 60.622 42.308 9.31 0.00 38.42 2.69
2631 5125 6.625740 GCAAACCATGACAAGCTTATACACAT 60.626 38.462 0.00 0.00 0.00 3.21
2650 5145 1.892474 TCCACTGCCATTTAGCAAACC 59.108 47.619 0.00 0.00 43.52 3.27
2661 5158 2.092968 GTGTATCATCCTTCCACTGCCA 60.093 50.000 0.00 0.00 0.00 4.92
2702 5482 9.251440 GGGACCTATATTTTCAAACTAAGGTTT 57.749 33.333 0.00 0.00 45.35 3.27
2792 5576 5.205821 TGCATCAGATCATCAGGGAATTTT 58.794 37.500 0.00 0.00 0.00 1.82
2801 5585 6.038271 CAGAATTTCACTGCATCAGATCATCA 59.962 38.462 0.29 0.00 35.18 3.07
2802 5586 6.431278 CAGAATTTCACTGCATCAGATCATC 58.569 40.000 0.29 0.00 35.18 2.92
2803 5587 6.378710 CAGAATTTCACTGCATCAGATCAT 57.621 37.500 0.29 0.00 35.18 2.45
2845 5637 6.536941 CCAGTCCTCTAGCTAAACTGAAAATC 59.463 42.308 19.21 0.00 39.72 2.17
2862 5654 2.046507 CTGCAGTGGCCAGTCCTC 60.047 66.667 11.12 3.52 40.13 3.71
2891 5683 6.100279 AGTTGCATAATTCACTAGGATGAGGA 59.900 38.462 0.00 0.00 0.00 3.71
3022 5895 3.505480 ATTTTCCTTTTGGCATGGCAA 57.495 38.095 29.00 29.00 40.12 4.52
3170 6050 3.071892 TCCCATAAAACCAGACGTTCTGT 59.928 43.478 12.10 0.00 42.80 3.41
3171 6051 3.670625 TCCCATAAAACCAGACGTTCTG 58.329 45.455 7.72 7.72 43.91 3.02
3172 6052 4.569719 ATCCCATAAAACCAGACGTTCT 57.430 40.909 0.00 0.00 31.78 3.01
3173 6053 4.142469 CCAATCCCATAAAACCAGACGTTC 60.142 45.833 0.00 0.00 31.78 3.95
3174 6054 3.761752 CCAATCCCATAAAACCAGACGTT 59.238 43.478 0.00 0.00 35.70 3.99
3175 6055 3.245122 ACCAATCCCATAAAACCAGACGT 60.245 43.478 0.00 0.00 0.00 4.34
3176 6056 3.352648 ACCAATCCCATAAAACCAGACG 58.647 45.455 0.00 0.00 0.00 4.18
3177 6057 5.359860 CCTAACCAATCCCATAAAACCAGAC 59.640 44.000 0.00 0.00 0.00 3.51
3178 6058 5.015817 ACCTAACCAATCCCATAAAACCAGA 59.984 40.000 0.00 0.00 0.00 3.86
3179 6059 5.269189 ACCTAACCAATCCCATAAAACCAG 58.731 41.667 0.00 0.00 0.00 4.00
3180 6060 5.015817 AGACCTAACCAATCCCATAAAACCA 59.984 40.000 0.00 0.00 0.00 3.67
3181 6061 5.516044 AGACCTAACCAATCCCATAAAACC 58.484 41.667 0.00 0.00 0.00 3.27
3183 6063 6.636336 GCCTAGACCTAACCAATCCCATAAAA 60.636 42.308 0.00 0.00 0.00 1.52
3184 6064 5.163131 GCCTAGACCTAACCAATCCCATAAA 60.163 44.000 0.00 0.00 0.00 1.40
3185 6065 4.349930 GCCTAGACCTAACCAATCCCATAA 59.650 45.833 0.00 0.00 0.00 1.90
3186 6066 3.908103 GCCTAGACCTAACCAATCCCATA 59.092 47.826 0.00 0.00 0.00 2.74
3187 6067 2.711547 GCCTAGACCTAACCAATCCCAT 59.288 50.000 0.00 0.00 0.00 4.00
3189 6069 1.070289 CGCCTAGACCTAACCAATCCC 59.930 57.143 0.00 0.00 0.00 3.85
3190 6070 1.070289 CCGCCTAGACCTAACCAATCC 59.930 57.143 0.00 0.00 0.00 3.01
3192 6072 2.170012 TCCGCCTAGACCTAACCAAT 57.830 50.000 0.00 0.00 0.00 3.16
3193 6073 1.941377 TTCCGCCTAGACCTAACCAA 58.059 50.000 0.00 0.00 0.00 3.67
3198 6078 4.715297 AGAATTCTTTTCCGCCTAGACCTA 59.285 41.667 0.88 0.00 0.00 3.08
3199 6079 3.519913 AGAATTCTTTTCCGCCTAGACCT 59.480 43.478 0.88 0.00 0.00 3.85
3201 6081 6.281405 TCATAGAATTCTTTTCCGCCTAGAC 58.719 40.000 14.36 0.00 0.00 2.59
3202 6082 6.323996 TCTCATAGAATTCTTTTCCGCCTAGA 59.676 38.462 14.36 2.09 0.00 2.43
3203 6083 6.516718 TCTCATAGAATTCTTTTCCGCCTAG 58.483 40.000 14.36 0.00 0.00 3.02
3204 6084 6.479972 TCTCATAGAATTCTTTTCCGCCTA 57.520 37.500 14.36 0.00 0.00 3.93
3208 6088 6.989169 ACCTGATCTCATAGAATTCTTTTCCG 59.011 38.462 14.36 0.00 0.00 4.30
3209 6089 8.210265 AGACCTGATCTCATAGAATTCTTTTCC 58.790 37.037 14.36 0.00 28.16 3.13
3225 6105 0.393132 TCTCGCGTGAGACCTGATCT 60.393 55.000 24.28 0.00 46.25 2.75
3226 6106 2.099143 TCTCGCGTGAGACCTGATC 58.901 57.895 24.28 0.00 46.25 2.92
3227 6107 4.320910 TCTCGCGTGAGACCTGAT 57.679 55.556 24.28 0.00 46.25 2.90
3234 6114 2.105128 GGATGGGTCTCGCGTGAG 59.895 66.667 19.99 19.99 43.99 3.51
3235 6115 2.362503 AGGATGGGTCTCGCGTGA 60.363 61.111 5.77 6.33 0.00 4.35
3236 6116 2.021068 ATCAGGATGGGTCTCGCGTG 62.021 60.000 5.77 3.13 36.16 5.34
3238 6118 1.300465 CATCAGGATGGGTCTCGCG 60.300 63.158 0.00 0.00 36.16 5.87
3250 6130 1.315690 GCCACATGTCATCCATCAGG 58.684 55.000 0.00 0.00 0.00 3.86
3252 6132 2.740506 ATGCCACATGTCATCCATCA 57.259 45.000 0.00 0.00 0.00 3.07
3254 6134 2.691526 GTGAATGCCACATGTCATCCAT 59.308 45.455 0.00 0.00 45.03 3.41
3256 6136 2.857592 GTGAATGCCACATGTCATCC 57.142 50.000 0.00 0.00 45.03 3.51
3265 6145 5.170021 TGCTTTATGATTTGTGAATGCCAC 58.830 37.500 0.00 0.00 45.88 5.01
3266 6146 5.402997 TGCTTTATGATTTGTGAATGCCA 57.597 34.783 0.00 0.00 0.00 4.92
3267 6147 5.464389 GGATGCTTTATGATTTGTGAATGCC 59.536 40.000 0.00 0.00 0.00 4.40
3268 6148 5.464389 GGGATGCTTTATGATTTGTGAATGC 59.536 40.000 0.00 0.00 0.00 3.56
3270 6150 5.662208 TGGGGATGCTTTATGATTTGTGAAT 59.338 36.000 0.00 0.00 0.00 2.57
3271 6151 5.022122 TGGGGATGCTTTATGATTTGTGAA 58.978 37.500 0.00 0.00 0.00 3.18
3272 6152 4.402155 GTGGGGATGCTTTATGATTTGTGA 59.598 41.667 0.00 0.00 0.00 3.58
3274 6154 3.706086 GGTGGGGATGCTTTATGATTTGT 59.294 43.478 0.00 0.00 0.00 2.83
3276 6156 3.051880 AGGGTGGGGATGCTTTATGATTT 60.052 43.478 0.00 0.00 0.00 2.17
3278 6158 2.146998 AGGGTGGGGATGCTTTATGAT 58.853 47.619 0.00 0.00 0.00 2.45
3279 6159 1.607225 AGGGTGGGGATGCTTTATGA 58.393 50.000 0.00 0.00 0.00 2.15
3280 6160 2.310538 GAAGGGTGGGGATGCTTTATG 58.689 52.381 0.00 0.00 0.00 1.90
3281 6161 1.929494 TGAAGGGTGGGGATGCTTTAT 59.071 47.619 0.00 0.00 0.00 1.40
3283 6163 0.251787 GTGAAGGGTGGGGATGCTTT 60.252 55.000 0.00 0.00 0.00 3.51
3286 6166 0.623723 TAAGTGAAGGGTGGGGATGC 59.376 55.000 0.00 0.00 0.00 3.91
3288 6168 4.045334 TGATTTTAAGTGAAGGGTGGGGAT 59.955 41.667 0.00 0.00 0.00 3.85
3289 6169 3.399644 TGATTTTAAGTGAAGGGTGGGGA 59.600 43.478 0.00 0.00 0.00 4.81
3290 6170 3.763897 CTGATTTTAAGTGAAGGGTGGGG 59.236 47.826 0.00 0.00 0.00 4.96
3294 6174 3.245622 CCCCCTGATTTTAAGTGAAGGGT 60.246 47.826 12.05 0.00 42.47 4.34
3296 6176 4.018415 TCTCCCCCTGATTTTAAGTGAAGG 60.018 45.833 0.00 0.00 0.00 3.46
3297 6177 5.179452 TCTCCCCCTGATTTTAAGTGAAG 57.821 43.478 0.00 0.00 0.00 3.02
3299 6179 3.054361 GCTCTCCCCCTGATTTTAAGTGA 60.054 47.826 0.00 0.00 0.00 3.41
3300 6180 3.282885 GCTCTCCCCCTGATTTTAAGTG 58.717 50.000 0.00 0.00 0.00 3.16
3301 6181 2.092914 CGCTCTCCCCCTGATTTTAAGT 60.093 50.000 0.00 0.00 0.00 2.24
3302 6182 2.170607 TCGCTCTCCCCCTGATTTTAAG 59.829 50.000 0.00 0.00 0.00 1.85
3303 6183 2.193127 TCGCTCTCCCCCTGATTTTAA 58.807 47.619 0.00 0.00 0.00 1.52
3305 6185 1.216990 ATCGCTCTCCCCCTGATTTT 58.783 50.000 0.00 0.00 0.00 1.82
3306 6186 1.216990 AATCGCTCTCCCCCTGATTT 58.783 50.000 0.00 0.00 0.00 2.17
3308 6188 1.148027 TCTAATCGCTCTCCCCCTGAT 59.852 52.381 0.00 0.00 0.00 2.90
3309 6189 0.556258 TCTAATCGCTCTCCCCCTGA 59.444 55.000 0.00 0.00 0.00 3.86
3310 6190 1.274728 CATCTAATCGCTCTCCCCCTG 59.725 57.143 0.00 0.00 0.00 4.45
3311 6191 1.638529 CATCTAATCGCTCTCCCCCT 58.361 55.000 0.00 0.00 0.00 4.79
3312 6192 0.036858 GCATCTAATCGCTCTCCCCC 60.037 60.000 0.00 0.00 0.00 5.40
3313 6193 0.972883 AGCATCTAATCGCTCTCCCC 59.027 55.000 0.00 0.00 31.16 4.81
3314 6194 2.805099 CAAAGCATCTAATCGCTCTCCC 59.195 50.000 0.00 0.00 37.54 4.30
3315 6195 3.247173 CACAAAGCATCTAATCGCTCTCC 59.753 47.826 0.00 0.00 37.54 3.71
3318 6198 4.749099 AGATCACAAAGCATCTAATCGCTC 59.251 41.667 0.00 0.00 37.54 5.03
3319 6199 4.701765 AGATCACAAAGCATCTAATCGCT 58.298 39.130 0.00 0.00 41.20 4.93
3320 6200 6.367149 TCATAGATCACAAAGCATCTAATCGC 59.633 38.462 0.00 0.00 35.66 4.58
3321 6201 7.880059 TCATAGATCACAAAGCATCTAATCG 57.120 36.000 0.00 0.00 35.66 3.34
3323 6203 8.512956 GCATTCATAGATCACAAAGCATCTAAT 58.487 33.333 0.00 0.00 35.66 1.73
3325 6205 6.429078 GGCATTCATAGATCACAAAGCATCTA 59.571 38.462 0.00 0.00 36.32 1.98
3326 6206 5.241064 GGCATTCATAGATCACAAAGCATCT 59.759 40.000 0.00 0.00 33.75 2.90
3328 6208 4.891168 TGGCATTCATAGATCACAAAGCAT 59.109 37.500 0.00 0.00 0.00 3.79
3329 6209 4.096833 GTGGCATTCATAGATCACAAAGCA 59.903 41.667 0.00 0.00 0.00 3.91
3330 6210 4.604976 GTGGCATTCATAGATCACAAAGC 58.395 43.478 0.00 0.00 0.00 3.51
3331 6211 4.333649 ACGTGGCATTCATAGATCACAAAG 59.666 41.667 0.00 0.00 0.00 2.77
3332 6212 4.094739 CACGTGGCATTCATAGATCACAAA 59.905 41.667 7.95 0.00 0.00 2.83
3333 6213 3.622612 CACGTGGCATTCATAGATCACAA 59.377 43.478 7.95 0.00 0.00 3.33
3334 6214 3.197265 CACGTGGCATTCATAGATCACA 58.803 45.455 7.95 0.00 0.00 3.58
3336 6216 3.118811 TGACACGTGGCATTCATAGATCA 60.119 43.478 23.03 6.48 0.00 2.92
3337 6217 3.457234 TGACACGTGGCATTCATAGATC 58.543 45.455 23.03 3.54 0.00 2.75
3338 6218 3.541996 TGACACGTGGCATTCATAGAT 57.458 42.857 23.03 0.00 0.00 1.98
3342 6222 1.339920 TGGATGACACGTGGCATTCAT 60.340 47.619 36.64 26.22 43.95 2.57
3344 6224 1.331756 GATGGATGACACGTGGCATTC 59.668 52.381 36.07 34.16 45.42 2.67
3345 6225 1.339920 TGATGGATGACACGTGGCATT 60.340 47.619 36.07 22.11 45.42 3.56
3347 6227 0.391528 CTGATGGATGACACGTGGCA 60.392 55.000 29.28 29.28 37.54 4.92
3348 6228 1.091771 CCTGATGGATGACACGTGGC 61.092 60.000 21.57 19.24 34.57 5.01
3349 6229 0.536724 TCCTGATGGATGACACGTGG 59.463 55.000 21.57 1.66 37.46 4.94
3350 6230 1.645034 GTCCTGATGGATGACACGTG 58.355 55.000 15.48 15.48 45.29 4.49
3357 6237 0.390860 GAGACCCGTCCTGATGGATG 59.609 60.000 6.98 0.00 45.29 3.51
3358 6238 0.032117 TGAGACCCGTCCTGATGGAT 60.032 55.000 6.98 0.00 45.29 3.41
3359 6239 0.032117 ATGAGACCCGTCCTGATGGA 60.032 55.000 6.98 0.00 39.90 3.41
3360 6240 0.390860 GATGAGACCCGTCCTGATGG 59.609 60.000 0.00 0.00 37.23 3.51
3361 6241 1.068281 CAGATGAGACCCGTCCTGATG 59.932 57.143 0.00 0.00 0.00 3.07
3362 6242 1.407936 CAGATGAGACCCGTCCTGAT 58.592 55.000 0.00 0.00 0.00 2.90
3363 6243 1.323271 GCAGATGAGACCCGTCCTGA 61.323 60.000 0.00 0.00 0.00 3.86
3364 6244 1.142748 GCAGATGAGACCCGTCCTG 59.857 63.158 0.00 0.00 0.00 3.86
3365 6245 0.259065 TAGCAGATGAGACCCGTCCT 59.741 55.000 0.00 0.00 0.00 3.85
3366 6246 1.112113 TTAGCAGATGAGACCCGTCC 58.888 55.000 0.00 0.00 0.00 4.79
3367 6247 1.202428 GGTTAGCAGATGAGACCCGTC 60.202 57.143 0.00 0.00 0.00 4.79
3368 6248 0.824759 GGTTAGCAGATGAGACCCGT 59.175 55.000 0.00 0.00 0.00 5.28
3369 6249 0.249073 CGGTTAGCAGATGAGACCCG 60.249 60.000 0.00 0.00 0.00 5.28
3370 6250 0.824759 ACGGTTAGCAGATGAGACCC 59.175 55.000 0.00 0.00 0.00 4.46
3371 6251 1.476891 TCACGGTTAGCAGATGAGACC 59.523 52.381 0.00 0.00 0.00 3.85
3372 6252 2.423892 TCTCACGGTTAGCAGATGAGAC 59.576 50.000 6.10 0.00 40.59 3.36
3373 6253 2.723273 TCTCACGGTTAGCAGATGAGA 58.277 47.619 6.10 6.10 42.63 3.27
3374 6254 3.317711 AGATCTCACGGTTAGCAGATGAG 59.682 47.826 0.00 0.00 38.51 2.90
3375 6255 3.067320 CAGATCTCACGGTTAGCAGATGA 59.933 47.826 0.00 0.00 0.00 2.92
3376 6256 3.379240 CAGATCTCACGGTTAGCAGATG 58.621 50.000 0.00 0.00 0.00 2.90
3377 6257 2.363680 CCAGATCTCACGGTTAGCAGAT 59.636 50.000 0.00 0.00 0.00 2.90
3378 6258 1.751351 CCAGATCTCACGGTTAGCAGA 59.249 52.381 0.00 0.00 0.00 4.26
3379 6259 1.478510 ACCAGATCTCACGGTTAGCAG 59.521 52.381 0.00 0.00 0.00 4.24
3380 6260 1.476891 GACCAGATCTCACGGTTAGCA 59.523 52.381 4.80 0.00 31.63 3.49
3381 6261 1.751924 AGACCAGATCTCACGGTTAGC 59.248 52.381 4.80 0.00 28.16 3.09
3391 6271 9.282569 GAGCAAAAATTATATGAGACCAGATCT 57.717 33.333 0.00 0.00 41.91 2.75
3392 6272 8.510505 GGAGCAAAAATTATATGAGACCAGATC 58.489 37.037 0.00 0.00 0.00 2.75
3393 6273 7.449704 GGGAGCAAAAATTATATGAGACCAGAT 59.550 37.037 0.00 0.00 0.00 2.90
3394 6274 6.772716 GGGAGCAAAAATTATATGAGACCAGA 59.227 38.462 0.00 0.00 0.00 3.86
3395 6275 6.293626 CGGGAGCAAAAATTATATGAGACCAG 60.294 42.308 0.00 0.00 0.00 4.00
3396 6276 5.530915 CGGGAGCAAAAATTATATGAGACCA 59.469 40.000 0.00 0.00 0.00 4.02
3397 6277 6.002062 CGGGAGCAAAAATTATATGAGACC 57.998 41.667 0.00 0.00 0.00 3.85
3428 6308 9.897744 TGACCGTATATTTAACTATTAAGACCG 57.102 33.333 0.00 0.00 0.00 4.79
3435 6315 9.826574 TCAGCTTTGACCGTATATTTAACTATT 57.173 29.630 0.00 0.00 0.00 1.73
3436 6316 9.826574 TTCAGCTTTGACCGTATATTTAACTAT 57.173 29.630 0.00 0.00 0.00 2.12
3437 6317 9.656040 TTTCAGCTTTGACCGTATATTTAACTA 57.344 29.630 0.00 0.00 0.00 2.24
3438 6318 8.448615 GTTTCAGCTTTGACCGTATATTTAACT 58.551 33.333 0.00 0.00 0.00 2.24
3439 6319 8.231837 TGTTTCAGCTTTGACCGTATATTTAAC 58.768 33.333 0.00 0.00 0.00 2.01
3440 6320 8.231837 GTGTTTCAGCTTTGACCGTATATTTAA 58.768 33.333 0.00 0.00 0.00 1.52
3441 6321 7.412129 CGTGTTTCAGCTTTGACCGTATATTTA 60.412 37.037 0.00 0.00 0.00 1.40
3442 6322 6.608610 GTGTTTCAGCTTTGACCGTATATTT 58.391 36.000 0.00 0.00 0.00 1.40
3443 6323 5.163893 CGTGTTTCAGCTTTGACCGTATATT 60.164 40.000 0.00 0.00 0.00 1.28
3444 6324 4.328983 CGTGTTTCAGCTTTGACCGTATAT 59.671 41.667 0.00 0.00 0.00 0.86
3445 6325 3.676172 CGTGTTTCAGCTTTGACCGTATA 59.324 43.478 0.00 0.00 0.00 1.47
3446 6326 2.478894 CGTGTTTCAGCTTTGACCGTAT 59.521 45.455 0.00 0.00 0.00 3.06
3447 6327 1.862201 CGTGTTTCAGCTTTGACCGTA 59.138 47.619 0.00 0.00 0.00 4.02
3448 6328 0.655733 CGTGTTTCAGCTTTGACCGT 59.344 50.000 0.00 0.00 0.00 4.83
3449 6329 0.934496 TCGTGTTTCAGCTTTGACCG 59.066 50.000 0.00 0.00 0.00 4.79
3450 6330 2.670401 CTCGTGTTTCAGCTTTGACC 57.330 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.