Multiple sequence alignment - TraesCS5B01G486900

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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 TraesCS5B01G486900 chr5B 100.000 3795 0 0 570 4364 658095497 658091703 0.000000e+00 7009.0
1 TraesCS5B01G486900 chr5B 100.000 341 0 0 1 341 658096066 658095726 7.960000e-177 630.0
2 TraesCS5B01G486900 chr5D 92.328 1877 80 33 923 2779 521715456 521713624 0.000000e+00 2610.0
3 TraesCS5B01G486900 chr5D 90.438 502 21 10 3003 3477 521713484 521712983 1.710000e-178 636.0
4 TraesCS5B01G486900 chr5D 87.640 445 24 14 3469 3897 521712961 521712532 5.070000e-134 488.0
5 TraesCS5B01G486900 chr5D 90.349 373 15 2 570 921 521716358 521715986 1.840000e-128 470.0
6 TraesCS5B01G486900 chr5D 93.773 273 7 4 73 341 521716813 521716547 6.800000e-108 401.0
7 TraesCS5B01G486900 chr5D 80.964 415 24 24 3954 4323 521712505 521712101 1.200000e-70 278.0
8 TraesCS5B01G486900 chr5D 93.684 95 3 3 2786 2880 521713573 521713482 5.890000e-29 139.0
9 TraesCS5B01G486900 chr5D 100.000 29 0 0 4318 4346 521712080 521712052 2.000000e-03 54.7
10 TraesCS5B01G486900 chr5A 89.127 2005 124 48 923 2878 650129915 650127956 0.000000e+00 2409.0
11 TraesCS5B01G486900 chr5A 89.125 377 12 17 3005 3362 650127948 650127582 4.010000e-120 442.0
12 TraesCS5B01G486900 chr5A 88.472 373 22 8 570 921 650130813 650130441 8.670000e-117 431.0
13 TraesCS5B01G486900 chr5A 87.419 310 23 10 35 341 650131604 650131308 4.180000e-90 342.0
14 TraesCS5B01G486900 chr5A 96.899 129 4 0 2878 3006 264419967 264419839 2.640000e-52 217.0
15 TraesCS5B01G486900 chr5A 77.262 431 43 27 3485 3891 650127447 650127048 7.400000e-48 202.0
16 TraesCS5B01G486900 chr5A 82.632 190 17 12 4173 4356 650126739 650126560 2.100000e-33 154.0
17 TraesCS5B01G486900 chr5A 78.767 146 14 10 3953 4081 650127021 650126876 1.010000e-11 82.4
18 TraesCS5B01G486900 chr4B 96.992 133 4 0 2876 3008 462241146 462241278 1.580000e-54 224.0
19 TraesCS5B01G486900 chr4B 96.899 129 4 0 2877 3005 105342448 105342320 2.640000e-52 217.0
20 TraesCS5B01G486900 chr4B 96.183 131 5 0 2878 3008 444101829 444101699 9.510000e-52 215.0
21 TraesCS5B01G486900 chr3B 95.035 141 6 1 2868 3007 699869858 699869998 2.040000e-53 220.0
22 TraesCS5B01G486900 chr7A 96.875 128 4 0 2878 3005 732841418 732841291 9.510000e-52 215.0
23 TraesCS5B01G486900 chr3A 94.928 138 5 2 2877 3014 93557082 93556947 9.510000e-52 215.0
24 TraesCS5B01G486900 chr7B 96.183 131 4 1 2879 3009 9790431 9790302 3.420000e-51 213.0
25 TraesCS5B01G486900 chr7B 96.183 131 4 1 2879 3009 9805102 9804973 3.420000e-51 213.0


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 TraesCS5B01G486900 chr5B 658091703 658096066 4363 True 3819.500000 7009 100.000000 1 4364 2 chr5B.!!$R1 4363
1 TraesCS5B01G486900 chr5D 521712052 521716813 4761 True 634.587500 2610 91.147000 73 4346 8 chr5D.!!$R1 4273
2 TraesCS5B01G486900 chr5A 650126560 650131604 5044 True 580.342857 2409 84.686286 35 4356 7 chr5A.!!$R2 4321

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
276 281 0.035630 CTCTTTCTCCCACTGGCCTG 60.036 60.0 8.29 8.29 0.00 4.85 F
924 1225 0.526662 GCTCGCAGTACAGTGGTAGT 59.473 55.0 0.00 0.00 33.36 2.73 F
2455 3333 0.037303 TCACTACGAGAACGACCCCT 59.963 55.0 0.00 0.00 42.66 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 3078 0.188342 ACAACTGGGCCAACAGGAAT 59.812 50.0 8.04 0.0 42.75 3.01 R
2466 3344 0.463474 GCCAAGCAGAGGATGAGGAC 60.463 60.0 0.00 0.0 0.00 3.85 R
4150 5247 0.175302 CTGCTCTGCTCCACTGTAGG 59.825 60.0 0.00 0.0 0.00 3.18 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
33 34 9.065871 GGTCATTTATCTCATTTTTCTCAAACG 57.934 33.333 0.00 0.00 0.00 3.60
34 35 9.612620 GTCATTTATCTCATTTTTCTCAAACGT 57.387 29.630 0.00 0.00 0.00 3.99
224 225 0.331278 TTACCTGTGATGCCCTTGGG 59.669 55.000 0.32 0.32 0.00 4.12
229 230 2.614969 TGATGCCCTTGGGCTCCT 60.615 61.111 28.37 14.88 35.66 3.69
276 281 0.035630 CTCTTTCTCCCACTGGCCTG 60.036 60.000 8.29 8.29 0.00 4.85
277 282 1.001641 CTTTCTCCCACTGGCCTGG 60.002 63.158 14.82 9.41 0.00 4.45
699 985 2.102357 CCCGATGACGACGACTGG 59.898 66.667 0.00 0.00 42.66 4.00
918 1219 2.878429 CGGAGCTCGCAGTACAGT 59.122 61.111 7.83 0.00 0.00 3.55
921 1222 1.587054 GAGCTCGCAGTACAGTGGT 59.413 57.895 0.00 0.00 0.00 4.16
922 1223 0.809385 GAGCTCGCAGTACAGTGGTA 59.191 55.000 0.00 0.00 0.00 3.25
923 1224 0.811915 AGCTCGCAGTACAGTGGTAG 59.188 55.000 0.00 0.00 0.00 3.18
924 1225 0.526662 GCTCGCAGTACAGTGGTAGT 59.473 55.000 0.00 0.00 33.36 2.73
925 1226 1.467713 GCTCGCAGTACAGTGGTAGTC 60.468 57.143 0.00 0.00 30.66 2.59
945 1784 3.551890 GTCAGTGCGCCGGATAATATATG 59.448 47.826 5.05 0.00 0.00 1.78
972 1811 4.451900 GTTTGTCCGATGGTTGATATCCT 58.548 43.478 0.00 0.00 0.00 3.24
989 1828 4.514585 TGTGGGTGGTGGTGGTGC 62.515 66.667 0.00 0.00 0.00 5.01
1174 2024 6.432783 AGCAGGCACACACACTAAAATTAATA 59.567 34.615 0.00 0.00 0.00 0.98
1175 2025 7.040062 AGCAGGCACACACACTAAAATTAATAA 60.040 33.333 0.00 0.00 0.00 1.40
1177 2027 9.638239 CAGGCACACACACTAAAATTAATAAAT 57.362 29.630 0.00 0.00 0.00 1.40
1274 2128 3.316308 ACAAGCTGTTCATGAACTTGACC 59.684 43.478 30.53 18.99 41.67 4.02
1285 2139 8.880750 GTTCATGAACTTGACCCTAATTAGTAC 58.119 37.037 27.66 0.00 38.25 2.73
1297 2151 8.834004 ACCCTAATTAGTACTAGATGTGACAA 57.166 34.615 11.50 0.00 0.00 3.18
1309 2163 1.159713 TGTGACAAGGCAGCTGTTCG 61.160 55.000 16.64 4.33 0.00 3.95
1423 2278 9.559958 CATCAAGTTAATCCATGTTGTTAGTTC 57.440 33.333 0.00 0.00 0.00 3.01
1475 2335 1.913762 CCACTTCCCCCGACACTCT 60.914 63.158 0.00 0.00 0.00 3.24
1507 2367 7.119699 CAGACATCTATTTGGAGCAACTGTTAA 59.880 37.037 0.00 0.00 0.00 2.01
1508 2368 7.665559 AGACATCTATTTGGAGCAACTGTTAAA 59.334 33.333 0.00 0.00 0.00 1.52
1509 2369 7.820648 ACATCTATTTGGAGCAACTGTTAAAG 58.179 34.615 0.00 0.00 0.00 1.85
1510 2370 6.817765 TCTATTTGGAGCAACTGTTAAAGG 57.182 37.500 0.00 0.00 0.00 3.11
1511 2371 6.303839 TCTATTTGGAGCAACTGTTAAAGGT 58.696 36.000 0.00 0.00 0.00 3.50
1512 2372 5.869649 ATTTGGAGCAACTGTTAAAGGTT 57.130 34.783 0.00 0.00 0.00 3.50
1513 2373 4.911514 TTGGAGCAACTGTTAAAGGTTC 57.088 40.909 0.00 0.00 0.00 3.62
1516 2376 3.004419 GGAGCAACTGTTAAAGGTTCCAC 59.996 47.826 6.60 0.00 0.00 4.02
1529 2391 8.709646 GTTAAAGGTTCCACATATATGATCGAC 58.290 37.037 19.63 11.35 0.00 4.20
1729 2603 6.239600 GCAAGGTACTGTGATTATCCCTGATA 60.240 42.308 0.00 0.00 40.86 2.15
1730 2604 7.527868 GCAAGGTACTGTGATTATCCCTGATAT 60.528 40.741 0.00 0.00 40.86 1.63
1731 2605 7.726033 AGGTACTGTGATTATCCCTGATATC 57.274 40.000 0.00 0.00 37.18 1.63
1732 2606 6.670027 AGGTACTGTGATTATCCCTGATATCC 59.330 42.308 0.00 0.00 37.18 2.59
1734 2608 6.365970 ACTGTGATTATCCCTGATATCCAC 57.634 41.667 0.00 0.00 32.80 4.02
1735 2609 5.846164 ACTGTGATTATCCCTGATATCCACA 59.154 40.000 0.00 13.50 36.20 4.17
1736 2610 6.503217 ACTGTGATTATCCCTGATATCCACAT 59.497 38.462 14.09 0.00 37.01 3.21
1738 2612 8.448068 TGTGATTATCCCTGATATCCACATTA 57.552 34.615 0.00 0.00 35.01 1.90
1739 2613 8.889445 TGTGATTATCCCTGATATCCACATTAA 58.111 33.333 0.00 0.00 35.01 1.40
1742 2616 8.700145 ATTATCCCTGATATCCACATTAAGGA 57.300 34.615 0.00 0.00 39.97 3.36
1743 2617 8.518720 TTATCCCTGATATCCACATTAAGGAA 57.481 34.615 0.00 0.00 38.93 3.36
1755 2629 5.222631 CACATTAAGGAAGCTCACAAAACC 58.777 41.667 0.00 0.00 0.00 3.27
1776 2650 2.860735 CTCCTTAATTTCCGCTCACTCG 59.139 50.000 0.00 0.00 0.00 4.18
1914 2788 2.417651 CGCCGAAAATGAGGGTACTACA 60.418 50.000 0.00 0.00 0.00 2.74
1915 2789 3.602483 GCCGAAAATGAGGGTACTACAA 58.398 45.455 0.00 0.00 0.00 2.41
1916 2790 3.373130 GCCGAAAATGAGGGTACTACAAC 59.627 47.826 0.00 0.00 0.00 3.32
1977 2851 8.373981 CACCCAAGTCTTATCTCATTGATATCT 58.626 37.037 3.98 0.00 37.48 1.98
1979 2853 9.434420 CCCAAGTCTTATCTCATTGATATCTTC 57.566 37.037 3.98 0.00 37.48 2.87
2027 2901 4.515361 CTGATGCTCTTGACTTGGATCTT 58.485 43.478 0.00 0.00 31.33 2.40
2073 2947 3.177600 CCAAGCGGGACAACATCG 58.822 61.111 0.00 0.00 40.01 3.84
2145 3019 6.365970 TGCTCTCTTCTCAGGTAAAGAAAT 57.634 37.500 0.00 0.00 32.60 2.17
2146 3020 6.773638 TGCTCTCTTCTCAGGTAAAGAAATT 58.226 36.000 0.00 0.00 32.60 1.82
2188 3062 4.825085 ACTAGCTAGCTCAGTGGTTAGATC 59.175 45.833 23.26 0.00 0.00 2.75
2189 3063 2.621055 AGCTAGCTCAGTGGTTAGATCG 59.379 50.000 12.68 0.00 0.00 3.69
2190 3064 2.860582 GCTAGCTCAGTGGTTAGATCGC 60.861 54.545 7.70 0.00 0.00 4.58
2191 3065 1.479709 AGCTCAGTGGTTAGATCGCT 58.520 50.000 0.00 0.00 0.00 4.93
2192 3066 1.135915 AGCTCAGTGGTTAGATCGCTG 59.864 52.381 0.00 0.00 42.29 5.18
2193 3067 1.804372 GCTCAGTGGTTAGATCGCTGG 60.804 57.143 2.30 0.00 41.53 4.85
2196 3070 2.766263 TCAGTGGTTAGATCGCTGGAAT 59.234 45.455 2.30 0.00 41.53 3.01
2197 3071 3.958147 TCAGTGGTTAGATCGCTGGAATA 59.042 43.478 2.30 0.00 41.53 1.75
2198 3072 4.038042 TCAGTGGTTAGATCGCTGGAATAG 59.962 45.833 2.30 0.00 41.53 1.73
2199 3073 4.038042 CAGTGGTTAGATCGCTGGAATAGA 59.962 45.833 0.00 0.00 38.62 1.98
2298 3173 8.241367 CCTAAACTTACGATATTTGTGCCTTTT 58.759 33.333 0.00 0.00 0.00 2.27
2367 3242 0.953471 TCAACATGGCACGGCAGTAC 60.953 55.000 0.00 0.00 0.00 2.73
2455 3333 0.037303 TCACTACGAGAACGACCCCT 59.963 55.000 0.00 0.00 42.66 4.79
2465 3343 1.219824 AACGACCCCTCCTCCTCCTA 61.220 60.000 0.00 0.00 0.00 2.94
2466 3344 1.151908 CGACCCCTCCTCCTCCTAG 59.848 68.421 0.00 0.00 0.00 3.02
2472 3350 1.227249 CCTCCTCCTCCTAGTCCTCA 58.773 60.000 0.00 0.00 0.00 3.86
2485 3363 0.463474 GTCCTCATCCTCTGCTTGGC 60.463 60.000 0.00 0.00 0.00 4.52
2522 3400 4.752101 AGCTTACTGAAACTGTTGCTACTG 59.248 41.667 0.00 3.77 0.00 2.74
2610 3489 7.855784 ATTAAGGTTTCCATGTTTCTTTCCT 57.144 32.000 0.00 0.00 0.00 3.36
2611 3490 5.535753 AAGGTTTCCATGTTTCTTTCCTG 57.464 39.130 0.00 0.00 0.00 3.86
2613 3492 3.641436 GGTTTCCATGTTTCTTTCCTGGT 59.359 43.478 0.00 0.00 0.00 4.00
2614 3493 4.501400 GGTTTCCATGTTTCTTTCCTGGTG 60.501 45.833 0.00 0.00 0.00 4.17
2644 3524 1.808411 TGCCTGCTCTCCTAAAAACG 58.192 50.000 0.00 0.00 0.00 3.60
2646 3526 1.464997 GCCTGCTCTCCTAAAAACGTG 59.535 52.381 0.00 0.00 0.00 4.49
2657 3537 4.271533 TCCTAAAAACGTGTACAAGTGCTG 59.728 41.667 15.32 4.84 0.00 4.41
2663 3543 2.806244 ACGTGTACAAGTGCTGGAATTC 59.194 45.455 13.87 0.00 0.00 2.17
2683 3563 4.042271 TCTGGGTGTAGTGATGTGTCTA 57.958 45.455 0.00 0.00 0.00 2.59
2727 3607 2.849473 TGAAACGAAACGCAAGCTTTTC 59.151 40.909 12.39 12.39 45.62 2.29
2796 3702 2.173569 ACTTGGTTTCTCCTGTGAGCTT 59.826 45.455 0.00 0.00 38.58 3.74
2802 3733 1.123861 TCTCCTGTGAGCTTGCACCT 61.124 55.000 3.31 0.00 38.58 4.00
2809 3740 0.473755 TGAGCTTGCACCTCCTTTCA 59.526 50.000 10.22 0.00 0.00 2.69
2847 3778 2.685100 GTCCTCCGGTTCTTACAGTTG 58.315 52.381 0.00 0.00 0.00 3.16
2880 3811 5.419542 TCCATGACACAGCTTTAGATGTAC 58.580 41.667 0.00 0.00 43.53 2.90
2881 3812 5.187772 TCCATGACACAGCTTTAGATGTACT 59.812 40.000 0.00 0.00 43.53 2.73
2882 3813 5.521735 CCATGACACAGCTTTAGATGTACTC 59.478 44.000 0.00 0.12 43.53 2.59
2883 3814 5.073311 TGACACAGCTTTAGATGTACTCC 57.927 43.478 0.00 0.00 43.53 3.85
2884 3815 4.081642 TGACACAGCTTTAGATGTACTCCC 60.082 45.833 0.00 0.00 43.53 4.30
2885 3816 4.097418 ACACAGCTTTAGATGTACTCCCT 58.903 43.478 0.00 0.00 43.53 4.20
2886 3817 4.160626 ACACAGCTTTAGATGTACTCCCTC 59.839 45.833 0.00 0.00 43.53 4.30
2887 3818 3.707102 ACAGCTTTAGATGTACTCCCTCC 59.293 47.826 0.00 0.00 43.55 4.30
2888 3819 2.959707 AGCTTTAGATGTACTCCCTCCG 59.040 50.000 0.00 0.00 0.00 4.63
2889 3820 2.694109 GCTTTAGATGTACTCCCTCCGT 59.306 50.000 0.00 0.00 0.00 4.69
2890 3821 3.132467 GCTTTAGATGTACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
2891 3822 4.737055 GCTTTAGATGTACTCCCTCCGTTC 60.737 50.000 0.00 0.00 0.00 3.95
2892 3823 2.830651 AGATGTACTCCCTCCGTTCT 57.169 50.000 0.00 0.00 0.00 3.01
2893 3824 2.379972 AGATGTACTCCCTCCGTTCTG 58.620 52.381 0.00 0.00 0.00 3.02
2894 3825 2.025226 AGATGTACTCCCTCCGTTCTGA 60.025 50.000 0.00 0.00 0.00 3.27
2895 3826 2.297698 TGTACTCCCTCCGTTCTGAA 57.702 50.000 0.00 0.00 0.00 3.02
2896 3827 2.816411 TGTACTCCCTCCGTTCTGAAT 58.184 47.619 0.00 0.00 0.00 2.57
2897 3828 3.170717 TGTACTCCCTCCGTTCTGAATT 58.829 45.455 0.00 0.00 0.00 2.17
2898 3829 4.346730 TGTACTCCCTCCGTTCTGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
2899 3830 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2900 3831 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2901 3832 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2902 3833 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2903 3834 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2904 3835 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2905 3836 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2906 3837 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
2907 3838 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.00 0.00 2.10
2908 3839 6.872020 CCTCCGTTCTGAATTACTTGTCTTAA 59.128 38.462 0.00 0.00 0.00 1.85
2909 3840 7.386848 CCTCCGTTCTGAATTACTTGTCTTAAA 59.613 37.037 0.00 0.00 0.00 1.52
2910 3841 8.842358 TCCGTTCTGAATTACTTGTCTTAAAT 57.158 30.769 0.00 0.00 0.00 1.40
2911 3842 9.280174 TCCGTTCTGAATTACTTGTCTTAAATT 57.720 29.630 0.00 0.00 0.00 1.82
2912 3843 9.893305 CCGTTCTGAATTACTTGTCTTAAATTT 57.107 29.630 0.00 0.00 0.00 1.82
2924 3855 9.367444 ACTTGTCTTAAATTTGTCTAGATACGG 57.633 33.333 0.00 0.00 0.00 4.02
2925 3856 9.582431 CTTGTCTTAAATTTGTCTAGATACGGA 57.418 33.333 0.00 0.00 0.00 4.69
2927 3858 9.529325 TGTCTTAAATTTGTCTAGATACGGATG 57.471 33.333 0.00 0.00 0.00 3.51
2928 3859 9.530633 GTCTTAAATTTGTCTAGATACGGATGT 57.469 33.333 0.00 0.00 0.00 3.06
2946 3877 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
2947 3878 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
2948 3879 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
2949 3880 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
2952 3883 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
2953 3884 9.887406 GTATCTAGACTCATTTTAGTGCTAGAC 57.113 37.037 0.00 0.00 38.10 2.59
2954 3885 7.939784 TCTAGACTCATTTTAGTGCTAGACA 57.060 36.000 0.00 0.00 34.69 3.41
2955 3886 8.526667 TCTAGACTCATTTTAGTGCTAGACAT 57.473 34.615 0.00 0.00 34.69 3.06
2956 3887 9.628500 TCTAGACTCATTTTAGTGCTAGACATA 57.372 33.333 0.00 0.00 34.69 2.29
2959 3890 9.142014 AGACTCATTTTAGTGCTAGACATATCT 57.858 33.333 0.00 0.00 39.15 1.98
2960 3891 9.190858 GACTCATTTTAGTGCTAGACATATCTG 57.809 37.037 0.00 0.00 36.29 2.90
2961 3892 8.700051 ACTCATTTTAGTGCTAGACATATCTGT 58.300 33.333 0.00 0.00 38.67 3.41
2969 3900 8.786826 AGTGCTAGACATATCTGTATCTAGAC 57.213 38.462 10.56 6.51 34.21 2.59
2970 3901 8.379331 AGTGCTAGACATATCTGTATCTAGACA 58.621 37.037 10.56 5.96 34.21 3.41
2971 3902 9.004717 GTGCTAGACATATCTGTATCTAGACAA 57.995 37.037 10.56 0.00 34.21 3.18
2972 3903 9.574516 TGCTAGACATATCTGTATCTAGACAAA 57.425 33.333 10.56 0.00 34.21 2.83
2976 3907 9.508642 AGACATATCTGTATCTAGACAAATCGA 57.491 33.333 0.00 0.00 35.14 3.59
2981 3912 7.625828 TCTGTATCTAGACAAATCGAAGACA 57.374 36.000 0.00 0.00 42.51 3.41
2982 3913 8.051901 TCTGTATCTAGACAAATCGAAGACAA 57.948 34.615 0.00 0.00 42.51 3.18
2983 3914 8.184848 TCTGTATCTAGACAAATCGAAGACAAG 58.815 37.037 0.00 0.00 42.51 3.16
2984 3915 7.827701 TGTATCTAGACAAATCGAAGACAAGT 58.172 34.615 0.00 0.00 42.51 3.16
2985 3916 8.953313 TGTATCTAGACAAATCGAAGACAAGTA 58.047 33.333 0.00 0.00 42.51 2.24
2986 3917 9.784680 GTATCTAGACAAATCGAAGACAAGTAA 57.215 33.333 0.00 0.00 42.51 2.24
2988 3919 9.877178 ATCTAGACAAATCGAAGACAAGTAATT 57.123 29.630 0.00 0.00 42.51 1.40
2989 3920 9.706691 TCTAGACAAATCGAAGACAAGTAATTT 57.293 29.630 0.00 0.00 42.51 1.82
2990 3921 9.746711 CTAGACAAATCGAAGACAAGTAATTTG 57.253 33.333 0.00 0.00 42.51 2.32
2991 3922 7.584987 AGACAAATCGAAGACAAGTAATTTGG 58.415 34.615 9.60 0.00 42.51 3.28
2992 3923 7.444183 AGACAAATCGAAGACAAGTAATTTGGA 59.556 33.333 9.60 0.00 42.51 3.53
2993 3924 7.936584 ACAAATCGAAGACAAGTAATTTGGAA 58.063 30.769 9.60 0.00 42.51 3.53
2994 3925 7.860872 ACAAATCGAAGACAAGTAATTTGGAAC 59.139 33.333 9.60 0.00 42.51 3.62
2995 3926 5.585500 TCGAAGACAAGTAATTTGGAACG 57.415 39.130 0.00 0.00 41.25 3.95
2996 3927 4.449743 TCGAAGACAAGTAATTTGGAACGG 59.550 41.667 0.00 0.00 41.25 4.44
2997 3928 4.449743 CGAAGACAAGTAATTTGGAACGGA 59.550 41.667 0.00 0.00 41.25 4.69
2998 3929 5.389516 CGAAGACAAGTAATTTGGAACGGAG 60.390 44.000 0.00 0.00 41.25 4.63
2999 3930 4.324267 AGACAAGTAATTTGGAACGGAGG 58.676 43.478 0.00 0.00 41.25 4.30
3000 3931 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
3001 3932 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
3002 3933 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3003 3934 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3004 3935 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
3022 3956 4.425520 GAGTAGCTTGCTTAGGTGTAGTG 58.574 47.826 0.00 0.00 35.80 2.74
3040 3974 1.559682 GTGGTACCCTGATCACATGGT 59.440 52.381 10.07 10.70 44.73 3.55
3111 4045 2.773745 GCTTGCATGCACGGCCATA 61.774 57.895 22.58 2.30 0.00 2.74
3129 4063 3.380004 CCATAACTTGACGCTCTCTCTCT 59.620 47.826 0.00 0.00 0.00 3.10
3153 4107 4.463879 CAGGTGCAGGAGAGGCCG 62.464 72.222 0.00 0.00 43.43 6.13
3395 4357 3.123620 CTCTGCTTGCTCGGCCAC 61.124 66.667 2.24 0.00 0.00 5.01
3433 4397 1.227527 TGTGTGTTGGAGGTGCTCG 60.228 57.895 0.00 0.00 0.00 5.03
3447 4411 2.050895 CTCGCGCCTCATCGGTAG 60.051 66.667 0.00 0.00 34.25 3.18
3462 4426 1.533731 CGGTAGCCGTTGTTGTGAATT 59.466 47.619 0.00 0.00 42.73 2.17
3463 4427 2.737783 CGGTAGCCGTTGTTGTGAATTA 59.262 45.455 0.00 0.00 42.73 1.40
3466 4430 5.329493 GGTAGCCGTTGTTGTGAATTAATC 58.671 41.667 0.00 0.00 0.00 1.75
3467 4431 4.078363 AGCCGTTGTTGTGAATTAATCG 57.922 40.909 0.00 0.00 0.00 3.34
3481 4478 0.535335 TAATCGGAGTGTGACTGGCC 59.465 55.000 0.00 0.00 0.00 5.36
3482 4479 2.185310 AATCGGAGTGTGACTGGCCC 62.185 60.000 0.00 0.00 0.00 5.80
3492 4489 3.927481 GACTGGCCCAGGCTGGTTC 62.927 68.421 30.68 21.74 36.41 3.62
3544 4547 1.258982 CATCGTGGCTGCTCGTTATTC 59.741 52.381 14.48 0.00 0.00 1.75
3582 4585 3.011566 TGCTCAAGTTTCCCAAACAGA 57.988 42.857 2.16 0.00 43.79 3.41
3583 4586 2.687935 TGCTCAAGTTTCCCAAACAGAC 59.312 45.455 2.16 0.00 43.79 3.51
3584 4587 2.952310 GCTCAAGTTTCCCAAACAGACT 59.048 45.455 2.16 0.00 43.79 3.24
3585 4588 3.003793 GCTCAAGTTTCCCAAACAGACTC 59.996 47.826 2.16 0.00 43.79 3.36
3638 4641 3.217321 ATGCATGCATGGGTCACAT 57.783 47.368 31.74 17.93 41.57 3.21
3650 4654 3.372730 TCACATTGCGCCCTTGCC 61.373 61.111 4.18 0.00 0.00 4.52
3659 4663 4.760047 GCCCTTGCCGAAGAGCGA 62.760 66.667 0.00 0.00 44.57 4.93
3660 4664 2.815647 CCCTTGCCGAAGAGCGAC 60.816 66.667 0.00 0.00 44.57 5.19
3735 4757 1.377202 CGGTGATTGACAGGTGGGG 60.377 63.158 0.00 0.00 0.00 4.96
3809 4831 0.614979 TGAGGTGAGGTGAGTAGGCC 60.615 60.000 0.00 0.00 0.00 5.19
3813 4835 3.155167 GAGGTGAGTAGGCCGGGG 61.155 72.222 2.18 0.00 0.00 5.73
3851 4873 0.461870 TCGTTGCCATCCTCCATTCG 60.462 55.000 0.00 0.00 0.00 3.34
3885 4912 2.544590 ATTGATGGGCCGTAACCGCA 62.545 55.000 0.00 0.00 0.00 5.69
3894 4921 1.805945 CGTAACCGCAGCTGGAGTC 60.806 63.158 17.12 0.00 0.00 3.36
3897 4924 2.486636 TAACCGCAGCTGGAGTCGTG 62.487 60.000 17.12 7.05 0.00 4.35
3898 4925 4.363990 CCGCAGCTGGAGTCGTGT 62.364 66.667 17.12 0.00 0.00 4.49
3899 4926 2.807045 CGCAGCTGGAGTCGTGTC 60.807 66.667 17.12 0.00 0.00 3.67
3900 4927 2.340078 GCAGCTGGAGTCGTGTCA 59.660 61.111 17.12 0.00 0.00 3.58
3901 4928 2.024319 GCAGCTGGAGTCGTGTCAC 61.024 63.158 17.12 0.00 0.00 3.67
3904 4931 0.753262 AGCTGGAGTCGTGTCACTTT 59.247 50.000 0.65 0.00 0.00 2.66
3918 4945 3.181423 TGTCACTTTTAGCCAATCCCCTT 60.181 43.478 0.00 0.00 0.00 3.95
3919 4946 3.444034 GTCACTTTTAGCCAATCCCCTTC 59.556 47.826 0.00 0.00 0.00 3.46
3920 4947 3.075283 TCACTTTTAGCCAATCCCCTTCA 59.925 43.478 0.00 0.00 0.00 3.02
3921 4948 4.026052 CACTTTTAGCCAATCCCCTTCAT 58.974 43.478 0.00 0.00 0.00 2.57
3922 4949 4.467438 CACTTTTAGCCAATCCCCTTCATT 59.533 41.667 0.00 0.00 0.00 2.57
3923 4950 5.656416 CACTTTTAGCCAATCCCCTTCATTA 59.344 40.000 0.00 0.00 0.00 1.90
3924 4951 6.324770 CACTTTTAGCCAATCCCCTTCATTAT 59.675 38.462 0.00 0.00 0.00 1.28
3926 4953 7.402941 ACTTTTAGCCAATCCCCTTCATTATTT 59.597 33.333 0.00 0.00 0.00 1.40
3927 4954 7.747809 TTTAGCCAATCCCCTTCATTATTTT 57.252 32.000 0.00 0.00 0.00 1.82
3928 4955 7.747809 TTAGCCAATCCCCTTCATTATTTTT 57.252 32.000 0.00 0.00 0.00 1.94
3947 4974 4.552883 TTTTTCCCTTTTCCCTTCCTCT 57.447 40.909 0.00 0.00 0.00 3.69
3948 4975 4.552883 TTTTCCCTTTTCCCTTCCTCTT 57.447 40.909 0.00 0.00 0.00 2.85
3949 4976 3.808834 TTCCCTTTTCCCTTCCTCTTC 57.191 47.619 0.00 0.00 0.00 2.87
3950 4977 2.713595 TCCCTTTTCCCTTCCTCTTCA 58.286 47.619 0.00 0.00 0.00 3.02
3951 4978 2.375509 TCCCTTTTCCCTTCCTCTTCAC 59.624 50.000 0.00 0.00 0.00 3.18
4028 5070 0.864455 CGCTAGCCAGCTATCTTTGC 59.136 55.000 9.66 0.00 46.26 3.68
4030 5072 1.475751 GCTAGCCAGCTATCTTTGCCA 60.476 52.381 2.29 0.00 44.93 4.92
4047 5108 2.453497 ACCCACCCACCCATCCAA 60.453 61.111 0.00 0.00 0.00 3.53
4080 5150 6.380274 TCCACAATAGCAAAGCTAGTAGTACT 59.620 38.462 8.14 8.14 44.66 2.73
4155 5252 3.906660 GTGCAGCACACTACCTACA 57.093 52.632 21.22 0.00 46.41 2.74
4156 5253 1.714794 GTGCAGCACACTACCTACAG 58.285 55.000 21.22 0.00 46.41 2.74
4157 5254 1.000955 GTGCAGCACACTACCTACAGT 59.999 52.381 21.22 0.00 46.41 3.55
4165 5277 2.447443 CACTACCTACAGTGGAGCAGA 58.553 52.381 8.75 0.00 41.88 4.26
4167 5279 1.407258 CTACCTACAGTGGAGCAGAGC 59.593 57.143 0.00 0.00 0.00 4.09
4170 5282 0.894141 CTACAGTGGAGCAGAGCAGT 59.106 55.000 0.00 0.00 0.00 4.40
4171 5283 2.095461 CTACAGTGGAGCAGAGCAGTA 58.905 52.381 0.00 0.00 0.00 2.74
4299 5428 3.551407 GAGCGATCCCCACCCTCC 61.551 72.222 0.00 0.00 0.00 4.30
4346 5501 3.639008 CGCGAACTGCACTGCACA 61.639 61.111 0.00 0.00 46.97 4.57
4347 5502 2.051882 GCGAACTGCACTGCACAC 60.052 61.111 0.00 0.00 45.45 3.82
4348 5503 2.537560 GCGAACTGCACTGCACACT 61.538 57.895 0.00 0.00 45.45 3.55
4350 5505 0.877649 CGAACTGCACTGCACACTCT 60.878 55.000 0.00 0.00 33.79 3.24
4351 5506 0.585357 GAACTGCACTGCACACTCTG 59.415 55.000 0.00 0.00 33.79 3.35
4359 5514 3.563842 GCACACTCTGCAGCTCAG 58.436 61.111 9.47 3.83 46.29 3.35
4360 5515 2.678956 GCACACTCTGCAGCTCAGC 61.679 63.158 9.47 5.54 46.29 4.26
4361 5516 1.004799 CACACTCTGCAGCTCAGCT 60.005 57.895 9.47 0.00 42.56 4.24
4362 5517 1.015085 CACACTCTGCAGCTCAGCTC 61.015 60.000 9.47 0.00 42.56 4.09
4363 5518 1.292541 CACTCTGCAGCTCAGCTCA 59.707 57.895 9.47 0.00 42.56 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.065871 CGTTTGAGAAAAATGAGATAAATGACC 57.934 33.333 0.00 0.00 0.00 4.02
8 9 9.612620 ACGTTTGAGAAAAATGAGATAAATGAC 57.387 29.630 0.00 0.00 0.00 3.06
38 39 8.201242 AGGTAAATGCCTCCTTTCAATAAAAA 57.799 30.769 0.00 0.00 32.39 1.94
39 40 7.790782 AGGTAAATGCCTCCTTTCAATAAAA 57.209 32.000 0.00 0.00 32.39 1.52
40 41 7.234577 ACAAGGTAAATGCCTCCTTTCAATAAA 59.765 33.333 0.00 0.00 39.22 1.40
41 42 6.723977 ACAAGGTAAATGCCTCCTTTCAATAA 59.276 34.615 0.00 0.00 39.22 1.40
42 43 6.152661 CACAAGGTAAATGCCTCCTTTCAATA 59.847 38.462 0.00 0.00 39.22 1.90
43 44 5.047092 CACAAGGTAAATGCCTCCTTTCAAT 60.047 40.000 0.00 0.00 39.22 2.57
44 45 4.280677 CACAAGGTAAATGCCTCCTTTCAA 59.719 41.667 0.00 0.00 39.22 2.69
48 49 2.378547 TCCACAAGGTAAATGCCTCCTT 59.621 45.455 0.00 0.00 41.53 3.36
61 62 3.731652 TCAACATTTTGCTCCACAAGG 57.268 42.857 0.00 0.00 40.06 3.61
155 156 4.404098 CTACGCCCACACACCCCC 62.404 72.222 0.00 0.00 0.00 5.40
201 202 3.157087 CAAGGGCATCACAGGTAAACTT 58.843 45.455 0.00 0.00 0.00 2.66
224 225 2.065906 GAGATGGGACGTCGAGGAGC 62.066 65.000 12.85 3.27 0.00 4.70
229 230 1.592400 AAAGCGAGATGGGACGTCGA 61.592 55.000 9.92 0.00 35.70 4.20
279 284 4.467107 GACGAGGAGAGGGGGCCT 62.467 72.222 0.84 0.00 37.18 5.19
918 1219 4.063967 CCGGCGCACTGACTACCA 62.064 66.667 10.83 0.00 0.00 3.25
921 1222 1.037493 ATTATCCGGCGCACTGACTA 58.963 50.000 10.83 0.00 0.00 2.59
922 1223 1.037493 TATTATCCGGCGCACTGACT 58.963 50.000 10.83 0.00 0.00 3.41
923 1224 2.080286 ATATTATCCGGCGCACTGAC 57.920 50.000 10.83 0.00 0.00 3.51
924 1225 3.430236 CCATATATTATCCGGCGCACTGA 60.430 47.826 10.83 1.80 0.00 3.41
925 1226 2.866156 CCATATATTATCCGGCGCACTG 59.134 50.000 10.83 0.00 0.00 3.66
945 1784 0.538746 AACCATCGGACAAACCACCC 60.539 55.000 0.00 0.00 38.90 4.61
972 1811 4.514585 GCACCACCACCACCCACA 62.515 66.667 0.00 0.00 0.00 4.17
989 1828 3.057033 CCAGTTCCTCATCTGGCAAAAAG 60.057 47.826 0.00 0.00 43.45 2.27
1205 2058 9.363763 CTTGTACTGTATATGGCATCTGATTAG 57.636 37.037 1.65 0.00 0.00 1.73
1212 2065 7.813148 ACGTAATCTTGTACTGTATATGGCATC 59.187 37.037 1.65 0.00 0.00 3.91
1244 2097 6.040166 AGTTCATGAACAGCTTGTGAATTTCT 59.960 34.615 33.92 10.09 43.47 2.52
1274 2128 7.868415 GCCTTGTCACATCTAGTACTAATTAGG 59.132 40.741 16.73 0.00 0.00 2.69
1285 2139 2.277969 CAGCTGCCTTGTCACATCTAG 58.722 52.381 0.00 0.00 0.00 2.43
1309 2163 3.425758 GGCTAATTAAACGTCCACAGCAC 60.426 47.826 0.00 0.00 0.00 4.40
1357 2211 7.122650 CCAGCTAAGATTATGTTTCAAAAGGGA 59.877 37.037 0.00 0.00 0.00 4.20
1423 2278 2.972505 AACACAGGACGCGCCAAG 60.973 61.111 19.30 13.92 40.02 3.61
1475 2335 4.577693 GCTCCAAATAGATGTCTGCAATCA 59.422 41.667 0.00 0.00 0.00 2.57
1507 2367 6.672266 AGTCGATCATATATGTGGAACCTT 57.328 37.500 12.42 0.00 34.36 3.50
1508 2368 6.042093 ACAAGTCGATCATATATGTGGAACCT 59.958 38.462 12.42 1.21 34.36 3.50
1509 2369 6.223852 ACAAGTCGATCATATATGTGGAACC 58.776 40.000 12.42 0.00 34.36 3.62
1510 2370 6.366332 GGACAAGTCGATCATATATGTGGAAC 59.634 42.308 12.42 7.54 37.35 3.62
1511 2371 6.041523 TGGACAAGTCGATCATATATGTGGAA 59.958 38.462 12.42 0.00 0.00 3.53
1512 2372 5.538433 TGGACAAGTCGATCATATATGTGGA 59.462 40.000 12.42 5.94 0.00 4.02
1513 2373 5.783111 TGGACAAGTCGATCATATATGTGG 58.217 41.667 12.42 3.82 0.00 4.17
1516 2376 7.713764 TGTTTGGACAAGTCGATCATATATG 57.286 36.000 6.36 6.36 31.49 1.78
1729 2603 4.574674 TGTGAGCTTCCTTAATGTGGAT 57.425 40.909 0.00 0.00 33.09 3.41
1730 2604 4.365514 TTGTGAGCTTCCTTAATGTGGA 57.634 40.909 0.00 0.00 0.00 4.02
1731 2605 5.222631 GTTTTGTGAGCTTCCTTAATGTGG 58.777 41.667 0.00 0.00 0.00 4.17
1732 2606 5.010012 AGGTTTTGTGAGCTTCCTTAATGTG 59.990 40.000 0.00 0.00 0.00 3.21
1734 2608 5.335976 GGAGGTTTTGTGAGCTTCCTTAATG 60.336 44.000 0.00 0.00 0.00 1.90
1735 2609 4.767409 GGAGGTTTTGTGAGCTTCCTTAAT 59.233 41.667 0.00 0.00 0.00 1.40
1736 2610 4.141251 AGGAGGTTTTGTGAGCTTCCTTAA 60.141 41.667 0.00 0.00 0.00 1.85
1738 2612 2.175715 AGGAGGTTTTGTGAGCTTCCTT 59.824 45.455 0.00 0.00 0.00 3.36
1739 2613 1.777272 AGGAGGTTTTGTGAGCTTCCT 59.223 47.619 0.00 0.00 0.00 3.36
1742 2616 6.239317 GGAAATTAAGGAGGTTTTGTGAGCTT 60.239 38.462 0.00 0.00 0.00 3.74
1743 2617 5.243954 GGAAATTAAGGAGGTTTTGTGAGCT 59.756 40.000 0.00 0.00 0.00 4.09
1755 2629 2.860735 CGAGTGAGCGGAAATTAAGGAG 59.139 50.000 0.00 0.00 0.00 3.69
1776 2650 4.095483 CCAAATCCAACATGACACTAGAGC 59.905 45.833 0.00 0.00 0.00 4.09
1914 2788 3.733337 GACAGGTGAGACTGATTGTGTT 58.267 45.455 0.00 0.00 40.97 3.32
1915 2789 2.288457 CGACAGGTGAGACTGATTGTGT 60.288 50.000 0.00 0.00 40.97 3.72
1916 2790 2.029918 TCGACAGGTGAGACTGATTGTG 60.030 50.000 0.00 0.00 40.97 3.33
1977 2851 7.030165 TCAACAATTGCTAAGAAAACAACGAA 58.970 30.769 5.05 0.00 0.00 3.85
1979 2853 6.804534 TCAACAATTGCTAAGAAAACAACG 57.195 33.333 5.05 0.00 0.00 4.10
2027 2901 1.514087 GGTAGGTTGCGACATCCGA 59.486 57.895 6.39 0.00 41.76 4.55
2073 2947 1.375013 TTAACTGAAGGCCGGCGAC 60.375 57.895 22.54 14.55 0.00 5.19
2173 3047 1.565305 CAGCGATCTAACCACTGAGC 58.435 55.000 0.00 0.00 0.00 4.26
2204 3078 0.188342 ACAACTGGGCCAACAGGAAT 59.812 50.000 8.04 0.00 42.75 3.01
2298 3173 4.309933 CTCATTGGCTACAGCGATATCAA 58.690 43.478 3.12 0.00 43.26 2.57
2367 3242 2.359602 CTGGTGCTGCTGAGGTGG 60.360 66.667 0.00 0.00 0.00 4.61
2455 3333 1.783979 GGATGAGGACTAGGAGGAGGA 59.216 57.143 0.00 0.00 0.00 3.71
2465 3343 1.202330 CCAAGCAGAGGATGAGGACT 58.798 55.000 0.00 0.00 0.00 3.85
2466 3344 0.463474 GCCAAGCAGAGGATGAGGAC 60.463 60.000 0.00 0.00 0.00 3.85
2540 3418 5.751680 ACTGAAATGTCATCAACAGTTTCG 58.248 37.500 11.27 0.00 45.60 3.46
2550 3428 7.992180 ACTTGTCAAAAACTGAAATGTCATC 57.008 32.000 0.00 0.00 35.22 2.92
2553 3431 7.810766 TGAACTTGTCAAAAACTGAAATGTC 57.189 32.000 0.00 0.00 35.22 3.06
2610 3489 2.754552 GCAGGCATGATTAGTTTCACCA 59.245 45.455 0.62 0.00 0.00 4.17
2611 3490 3.019564 AGCAGGCATGATTAGTTTCACC 58.980 45.455 0.62 0.00 0.00 4.02
2613 3492 4.194640 GAGAGCAGGCATGATTAGTTTCA 58.805 43.478 0.62 0.00 0.00 2.69
2614 3493 3.563390 GGAGAGCAGGCATGATTAGTTTC 59.437 47.826 0.62 0.00 0.00 2.78
2644 3524 3.189287 CCAGAATTCCAGCACTTGTACAC 59.811 47.826 0.65 0.00 0.00 2.90
2646 3526 2.749621 CCCAGAATTCCAGCACTTGTAC 59.250 50.000 0.65 0.00 0.00 2.90
2657 3537 3.941483 CACATCACTACACCCAGAATTCC 59.059 47.826 0.65 0.00 0.00 3.01
2663 3543 5.105351 TCAATAGACACATCACTACACCCAG 60.105 44.000 0.00 0.00 0.00 4.45
2727 3607 0.926155 CATGAGACGAGATGCCAACG 59.074 55.000 0.00 0.00 0.00 4.10
2728 3608 1.134699 TCCATGAGACGAGATGCCAAC 60.135 52.381 0.00 0.00 0.00 3.77
2779 3667 0.877743 GCAAGCTCACAGGAGAAACC 59.122 55.000 0.00 0.00 44.26 3.27
2785 3691 3.567308 AGGTGCAAGCTCACAGGA 58.433 55.556 7.75 0.00 44.61 3.86
2847 3778 0.811616 GTGTCATGGAGGACGGATGC 60.812 60.000 0.00 0.00 40.72 3.91
2880 3811 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2881 3812 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2882 3813 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2883 3814 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
2884 3815 7.884816 TTAAGACAAGTAATTCAGAACGGAG 57.115 36.000 0.00 0.00 0.00 4.63
2885 3816 8.842358 ATTTAAGACAAGTAATTCAGAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
2886 3817 9.893305 AAATTTAAGACAAGTAATTCAGAACGG 57.107 29.630 0.00 0.00 0.00 4.44
2898 3829 9.367444 CCGTATCTAGACAAATTTAAGACAAGT 57.633 33.333 0.00 0.00 0.00 3.16
2899 3830 9.582431 TCCGTATCTAGACAAATTTAAGACAAG 57.418 33.333 0.00 0.00 0.00 3.16
2901 3832 9.529325 CATCCGTATCTAGACAAATTTAAGACA 57.471 33.333 0.00 0.00 0.00 3.41
2902 3833 9.530633 ACATCCGTATCTAGACAAATTTAAGAC 57.469 33.333 0.00 0.00 0.00 3.01
2920 3851 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
2921 3852 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
2922 3853 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
2923 3854 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
2926 3857 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
2927 3858 9.887406 GTCTAGCACTAAAATGAGTCTAGATAC 57.113 37.037 0.00 0.00 37.86 2.24
2928 3859 9.628500 TGTCTAGCACTAAAATGAGTCTAGATA 57.372 33.333 0.00 8.96 37.86 1.98
2929 3860 8.526667 TGTCTAGCACTAAAATGAGTCTAGAT 57.473 34.615 0.00 0.00 37.86 1.98
2930 3861 7.939784 TGTCTAGCACTAAAATGAGTCTAGA 57.060 36.000 0.00 0.00 35.79 2.43
2933 3864 9.142014 AGATATGTCTAGCACTAAAATGAGTCT 57.858 33.333 0.00 0.00 31.36 3.24
2934 3865 9.190858 CAGATATGTCTAGCACTAAAATGAGTC 57.809 37.037 0.00 0.00 32.09 3.36
2935 3866 8.700051 ACAGATATGTCTAGCACTAAAATGAGT 58.300 33.333 0.00 0.00 32.09 3.41
2943 3874 9.878667 GTCTAGATACAGATATGTCTAGCACTA 57.121 37.037 10.05 1.82 39.21 2.74
2944 3875 8.379331 TGTCTAGATACAGATATGTCTAGCACT 58.621 37.037 10.05 0.94 39.21 4.40
2945 3876 8.554835 TGTCTAGATACAGATATGTCTAGCAC 57.445 38.462 10.05 9.68 39.21 4.40
2946 3877 9.574516 TTTGTCTAGATACAGATATGTCTAGCA 57.425 33.333 10.05 8.99 39.21 3.49
2950 3881 9.508642 TCGATTTGTCTAGATACAGATATGTCT 57.491 33.333 0.00 0.00 34.14 3.41
2955 3886 9.338622 TGTCTTCGATTTGTCTAGATACAGATA 57.661 33.333 0.00 0.00 0.00 1.98
2956 3887 8.226819 TGTCTTCGATTTGTCTAGATACAGAT 57.773 34.615 0.00 0.00 0.00 2.90
2957 3888 7.625828 TGTCTTCGATTTGTCTAGATACAGA 57.374 36.000 0.00 0.00 0.00 3.41
2958 3889 7.971168 ACTTGTCTTCGATTTGTCTAGATACAG 59.029 37.037 0.00 0.00 0.00 2.74
2959 3890 7.827701 ACTTGTCTTCGATTTGTCTAGATACA 58.172 34.615 0.00 0.00 0.00 2.29
2960 3891 9.784680 TTACTTGTCTTCGATTTGTCTAGATAC 57.215 33.333 0.00 0.00 0.00 2.24
2962 3893 9.877178 AATTACTTGTCTTCGATTTGTCTAGAT 57.123 29.630 0.00 0.00 0.00 1.98
2963 3894 9.706691 AAATTACTTGTCTTCGATTTGTCTAGA 57.293 29.630 0.00 0.00 0.00 2.43
2964 3895 9.746711 CAAATTACTTGTCTTCGATTTGTCTAG 57.253 33.333 0.00 0.00 32.62 2.43
2965 3896 8.717821 CCAAATTACTTGTCTTCGATTTGTCTA 58.282 33.333 0.00 0.00 34.40 2.59
2966 3897 7.444183 TCCAAATTACTTGTCTTCGATTTGTCT 59.556 33.333 0.00 0.00 34.40 3.41
2967 3898 7.581476 TCCAAATTACTTGTCTTCGATTTGTC 58.419 34.615 0.00 0.00 34.40 3.18
2968 3899 7.504924 TCCAAATTACTTGTCTTCGATTTGT 57.495 32.000 0.00 0.00 34.40 2.83
2969 3900 7.059488 CGTTCCAAATTACTTGTCTTCGATTTG 59.941 37.037 0.00 0.00 35.40 2.32
2970 3901 7.075741 CGTTCCAAATTACTTGTCTTCGATTT 58.924 34.615 0.00 0.00 32.65 2.17
2971 3902 6.348213 CCGTTCCAAATTACTTGTCTTCGATT 60.348 38.462 0.00 0.00 32.65 3.34
2972 3903 5.121768 CCGTTCCAAATTACTTGTCTTCGAT 59.878 40.000 0.00 0.00 32.65 3.59
2973 3904 4.449743 CCGTTCCAAATTACTTGTCTTCGA 59.550 41.667 0.00 0.00 32.65 3.71
2974 3905 4.449743 TCCGTTCCAAATTACTTGTCTTCG 59.550 41.667 0.00 0.00 32.65 3.79
2975 3906 5.106673 CCTCCGTTCCAAATTACTTGTCTTC 60.107 44.000 0.00 0.00 32.65 2.87
2976 3907 4.760204 CCTCCGTTCCAAATTACTTGTCTT 59.240 41.667 0.00 0.00 32.65 3.01
2977 3908 4.324267 CCTCCGTTCCAAATTACTTGTCT 58.676 43.478 0.00 0.00 32.65 3.41
2978 3909 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
2979 3910 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
2980 3911 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
2981 3912 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
2982 3913 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2983 3914 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2984 3915 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
2985 3916 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
2986 3917 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
2987 3918 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2988 3919 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2989 3920 0.252103 AAGCTACTCCCTCCGTTCCA 60.252 55.000 0.00 0.00 0.00 3.53
2990 3921 0.175989 CAAGCTACTCCCTCCGTTCC 59.824 60.000 0.00 0.00 0.00 3.62
2991 3922 0.460459 GCAAGCTACTCCCTCCGTTC 60.460 60.000 0.00 0.00 0.00 3.95
2992 3923 0.905337 AGCAAGCTACTCCCTCCGTT 60.905 55.000 0.00 0.00 0.00 4.44
2993 3924 0.905337 AAGCAAGCTACTCCCTCCGT 60.905 55.000 0.00 0.00 0.00 4.69
2994 3925 1.067821 CTAAGCAAGCTACTCCCTCCG 59.932 57.143 0.00 0.00 0.00 4.63
2995 3926 1.414550 CCTAAGCAAGCTACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
2996 3927 2.112190 ACCTAAGCAAGCTACTCCCTC 58.888 52.381 0.00 0.00 0.00 4.30
2997 3928 1.834263 CACCTAAGCAAGCTACTCCCT 59.166 52.381 0.00 0.00 0.00 4.20
2998 3929 1.555533 ACACCTAAGCAAGCTACTCCC 59.444 52.381 0.00 0.00 0.00 4.30
2999 3930 3.447944 ACTACACCTAAGCAAGCTACTCC 59.552 47.826 0.00 0.00 0.00 3.85
3000 3931 4.425520 CACTACACCTAAGCAAGCTACTC 58.574 47.826 0.00 0.00 0.00 2.59
3001 3932 3.195825 CCACTACACCTAAGCAAGCTACT 59.804 47.826 0.00 0.00 0.00 2.57
3002 3933 3.056035 ACCACTACACCTAAGCAAGCTAC 60.056 47.826 0.00 0.00 0.00 3.58
3003 3934 3.170717 ACCACTACACCTAAGCAAGCTA 58.829 45.455 0.00 0.00 0.00 3.32
3004 3935 1.978580 ACCACTACACCTAAGCAAGCT 59.021 47.619 0.00 0.00 0.00 3.74
3040 3974 4.695455 GTGTCTACCAAGAATAAAGCTGCA 59.305 41.667 1.02 0.00 32.16 4.41
3095 4029 0.964860 AGTTATGGCCGTGCATGCAA 60.965 50.000 24.58 6.73 0.00 4.08
3111 4045 2.487762 CTGAGAGAGAGAGCGTCAAGTT 59.512 50.000 0.00 0.00 0.00 2.66
3414 4376 1.498865 CGAGCACCTCCAACACACAC 61.499 60.000 0.00 0.00 0.00 3.82
3447 4411 3.120130 TCCGATTAATTCACAACAACGGC 60.120 43.478 0.00 0.00 38.11 5.68
3449 4413 5.079406 CACTCCGATTAATTCACAACAACG 58.921 41.667 0.00 0.00 0.00 4.10
3462 4426 0.535335 GGCCAGTCACACTCCGATTA 59.465 55.000 0.00 0.00 0.00 1.75
3463 4427 1.296715 GGCCAGTCACACTCCGATT 59.703 57.895 0.00 0.00 0.00 3.34
3466 4430 3.596066 CTGGGCCAGTCACACTCCG 62.596 68.421 25.74 0.00 0.00 4.63
3467 4431 2.348998 CTGGGCCAGTCACACTCC 59.651 66.667 25.74 0.00 0.00 3.85
3481 4478 2.993853 GGAGAGGAACCAGCCTGG 59.006 66.667 9.83 9.83 45.02 4.45
3482 4479 2.581354 CGGAGAGGAACCAGCCTG 59.419 66.667 0.00 0.00 38.73 4.85
3528 4531 3.044809 TCGAATAACGAGCAGCCAC 57.955 52.632 0.00 0.00 46.45 5.01
3627 4630 2.491152 GGCGCAATGTGACCCATG 59.509 61.111 10.83 0.00 32.82 3.66
3632 4635 2.126346 GCAAGGGCGCAATGTGAC 60.126 61.111 10.83 0.00 0.00 3.67
3650 4654 0.660595 ACAACAGACGTCGCTCTTCG 60.661 55.000 10.46 0.00 40.15 3.79
3659 4663 2.352342 CCAACGGTAAAACAACAGACGT 59.648 45.455 0.00 0.00 34.25 4.34
3660 4664 2.352342 ACCAACGGTAAAACAACAGACG 59.648 45.455 0.00 0.00 32.11 4.18
3720 4742 2.763215 GGCCCCACCTGTCAATCA 59.237 61.111 0.00 0.00 34.51 2.57
3809 4831 4.143333 CACTGACCGCCTACCCCG 62.143 72.222 0.00 0.00 0.00 5.73
3813 4835 2.000447 GAACAATCACTGACCGCCTAC 59.000 52.381 0.00 0.00 0.00 3.18
3851 4873 3.155167 AATCGGAGGTCGCTCCCC 61.155 66.667 3.78 0.34 40.31 4.81
3864 4891 1.495584 CGGTTACGGCCCATCAATCG 61.496 60.000 0.00 0.00 36.18 3.34
3885 4912 0.753262 AAAGTGACACGACTCCAGCT 59.247 50.000 0.00 0.00 0.00 4.24
3894 4921 2.161609 GGGATTGGCTAAAAGTGACACG 59.838 50.000 0.00 0.00 0.00 4.49
3897 4924 3.087370 AGGGGATTGGCTAAAAGTGAC 57.913 47.619 0.00 0.00 0.00 3.67
3898 4925 3.075283 TGAAGGGGATTGGCTAAAAGTGA 59.925 43.478 0.00 0.00 0.00 3.41
3899 4926 3.430453 TGAAGGGGATTGGCTAAAAGTG 58.570 45.455 0.00 0.00 0.00 3.16
3900 4927 3.825908 TGAAGGGGATTGGCTAAAAGT 57.174 42.857 0.00 0.00 0.00 2.66
3901 4928 6.983906 ATAATGAAGGGGATTGGCTAAAAG 57.016 37.500 0.00 0.00 0.00 2.27
3904 4931 7.747809 AAAAATAATGAAGGGGATTGGCTAA 57.252 32.000 0.00 0.00 0.00 3.09
3926 4953 4.552883 AGAGGAAGGGAAAAGGGAAAAA 57.447 40.909 0.00 0.00 0.00 1.94
3927 4954 4.078863 TGAAGAGGAAGGGAAAAGGGAAAA 60.079 41.667 0.00 0.00 0.00 2.29
3928 4955 3.465588 TGAAGAGGAAGGGAAAAGGGAAA 59.534 43.478 0.00 0.00 0.00 3.13
3930 4957 2.375509 GTGAAGAGGAAGGGAAAAGGGA 59.624 50.000 0.00 0.00 0.00 4.20
3932 4959 3.797559 AGTGAAGAGGAAGGGAAAAGG 57.202 47.619 0.00 0.00 0.00 3.11
3933 4960 4.718961 TGAAGTGAAGAGGAAGGGAAAAG 58.281 43.478 0.00 0.00 0.00 2.27
3934 4961 4.788925 TGAAGTGAAGAGGAAGGGAAAA 57.211 40.909 0.00 0.00 0.00 2.29
3935 4962 4.788925 TTGAAGTGAAGAGGAAGGGAAA 57.211 40.909 0.00 0.00 0.00 3.13
3936 4963 4.263506 GGATTGAAGTGAAGAGGAAGGGAA 60.264 45.833 0.00 0.00 0.00 3.97
3937 4964 3.264450 GGATTGAAGTGAAGAGGAAGGGA 59.736 47.826 0.00 0.00 0.00 4.20
3938 4965 3.615155 GGATTGAAGTGAAGAGGAAGGG 58.385 50.000 0.00 0.00 0.00 3.95
3939 4966 3.615155 GGGATTGAAGTGAAGAGGAAGG 58.385 50.000 0.00 0.00 0.00 3.46
3940 4967 3.265791 CGGGATTGAAGTGAAGAGGAAG 58.734 50.000 0.00 0.00 0.00 3.46
3941 4968 2.615493 GCGGGATTGAAGTGAAGAGGAA 60.615 50.000 0.00 0.00 0.00 3.36
3942 4969 1.066143 GCGGGATTGAAGTGAAGAGGA 60.066 52.381 0.00 0.00 0.00 3.71
3943 4970 1.339055 TGCGGGATTGAAGTGAAGAGG 60.339 52.381 0.00 0.00 0.00 3.69
3944 4971 1.734465 GTGCGGGATTGAAGTGAAGAG 59.266 52.381 0.00 0.00 0.00 2.85
3945 4972 1.071542 TGTGCGGGATTGAAGTGAAGA 59.928 47.619 0.00 0.00 0.00 2.87
3946 4973 1.466167 CTGTGCGGGATTGAAGTGAAG 59.534 52.381 0.00 0.00 0.00 3.02
3947 4974 1.202758 ACTGTGCGGGATTGAAGTGAA 60.203 47.619 0.00 0.00 0.00 3.18
3948 4975 0.396435 ACTGTGCGGGATTGAAGTGA 59.604 50.000 0.00 0.00 0.00 3.41
3949 4976 0.518636 CACTGTGCGGGATTGAAGTG 59.481 55.000 0.00 0.00 0.00 3.16
3950 4977 0.396435 TCACTGTGCGGGATTGAAGT 59.604 50.000 2.12 0.00 0.00 3.01
3951 4978 1.466167 CTTCACTGTGCGGGATTGAAG 59.534 52.381 2.12 0.00 37.81 3.02
4028 5070 4.060667 GGATGGGTGGGTGGGTGG 62.061 72.222 0.00 0.00 0.00 4.61
4030 5072 2.453497 TTGGATGGGTGGGTGGGT 60.453 61.111 0.00 0.00 0.00 4.51
4043 5104 3.688126 GCTATTGTGGATGGATGGTTGGA 60.688 47.826 0.00 0.00 0.00 3.53
4047 5108 3.668141 TTGCTATTGTGGATGGATGGT 57.332 42.857 0.00 0.00 0.00 3.55
4148 5245 1.272480 TGCTCTGCTCCACTGTAGGTA 60.272 52.381 0.00 0.00 0.00 3.08
4149 5246 0.542938 TGCTCTGCTCCACTGTAGGT 60.543 55.000 0.00 0.00 0.00 3.08
4150 5247 0.175302 CTGCTCTGCTCCACTGTAGG 59.825 60.000 0.00 0.00 0.00 3.18
4151 5248 0.894141 ACTGCTCTGCTCCACTGTAG 59.106 55.000 0.00 0.00 0.00 2.74
4152 5249 2.095461 CTACTGCTCTGCTCCACTGTA 58.905 52.381 0.00 0.00 0.00 2.74
4153 5250 0.894141 CTACTGCTCTGCTCCACTGT 59.106 55.000 0.00 0.00 0.00 3.55
4155 5252 1.612395 GGCTACTGCTCTGCTCCACT 61.612 60.000 0.00 0.00 39.59 4.00
4156 5253 1.153469 GGCTACTGCTCTGCTCCAC 60.153 63.158 0.00 0.00 39.59 4.02
4157 5254 2.362369 GGGCTACTGCTCTGCTCCA 61.362 63.158 0.00 0.00 36.57 3.86
4158 5255 2.308968 CTGGGCTACTGCTCTGCTCC 62.309 65.000 0.00 0.00 41.13 4.70
4167 5279 4.537433 GCTCCGGCTGGGCTACTG 62.537 72.222 12.87 0.00 35.24 2.74
4231 5348 4.607606 CATGCATGCTCTGGCGCG 62.608 66.667 20.33 0.00 42.25 6.86
4280 5409 2.765807 AGGGTGGGGATCGCTCTG 60.766 66.667 9.90 0.00 34.94 3.35
4281 5410 2.444895 GAGGGTGGGGATCGCTCT 60.445 66.667 9.90 2.92 39.87 4.09
4282 5411 3.551407 GGAGGGTGGGGATCGCTC 61.551 72.222 9.90 3.66 41.85 5.03
4283 5412 3.642741 AAGGAGGGTGGGGATCGCT 62.643 63.158 9.90 0.00 0.00 4.93
4284 5413 2.680370 AAAGGAGGGTGGGGATCGC 61.680 63.158 0.06 0.06 0.00 4.58
4286 5415 1.615262 CCAAAGGAGGGTGGGGATC 59.385 63.158 0.00 0.00 0.00 3.36
4299 5428 3.000080 GACGCACGAGTCGCCAAAG 62.000 63.158 13.59 2.53 0.00 2.77


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

AutoCloner maintained by Alex Coulton.