Multiple sequence alignment - TraesCS1A01G243300

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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 TraesCS1A01G243300 chr1A 100.000 5941 0 0 1 5941 431775563 431781503 0.000000e+00 10972.0
1 TraesCS1A01G243300 chr1A 87.838 74 6 2 5166 5238 58289708 58289637 3.820000e-12 84.2
2 TraesCS1A01G243300 chr1B 95.399 2130 73 11 2983 5104 449389492 449391604 0.000000e+00 3367.0
3 TraesCS1A01G243300 chr1B 94.500 1709 61 16 889 2584 449387335 449389023 0.000000e+00 2604.0
4 TraesCS1A01G243300 chr1B 86.632 950 67 19 1 924 449363381 449364296 0.000000e+00 996.0
5 TraesCS1A01G243300 chr1B 96.528 576 20 0 5366 5941 449391919 449392494 0.000000e+00 953.0
6 TraesCS1A01G243300 chr1B 89.247 744 61 15 1 733 449364520 449365255 0.000000e+00 913.0
7 TraesCS1A01G243300 chr1B 95.045 222 9 2 2581 2801 449389280 449389500 1.230000e-91 348.0
8 TraesCS1A01G243300 chr1B 97.283 184 4 1 2803 2985 416664285 416664468 1.610000e-80 311.0
9 TraesCS1A01G243300 chr1B 89.714 175 10 3 3014 3182 449389363 449389535 3.610000e-52 217.0
10 TraesCS1A01G243300 chr1B 90.411 146 11 2 739 884 449386375 449386517 7.860000e-44 189.0
11 TraesCS1A01G243300 chr1B 87.407 135 11 1 2667 2801 449389528 449389656 3.710000e-32 150.0
12 TraesCS1A01G243300 chr1D 92.697 2273 76 32 3098 5312 333498348 333500588 0.000000e+00 3195.0
13 TraesCS1A01G243300 chr1D 95.300 2000 59 15 768 2763 333496010 333497978 0.000000e+00 3140.0
14 TraesCS1A01G243300 chr1D 96.348 575 21 0 5367 5941 333500584 333501158 0.000000e+00 946.0
15 TraesCS1A01G243300 chr1D 93.750 96 4 2 3014 3109 333497885 333497978 6.210000e-30 143.0
16 TraesCS1A01G243300 chr1D 95.455 44 2 0 2983 3026 333498398 333498441 2.970000e-08 71.3
17 TraesCS1A01G243300 chr7B 84.259 324 47 4 65 386 502651057 502651378 4.470000e-81 313.0
18 TraesCS1A01G243300 chr7B 97.268 183 4 1 2803 2984 168758378 168758196 5.780000e-80 309.0
19 TraesCS1A01G243300 chr7B 97.268 183 4 1 2803 2984 408258481 408258663 5.780000e-80 309.0
20 TraesCS1A01G243300 chr7B 84.722 72 8 3 5159 5230 297400652 297400584 1.070000e-07 69.4
21 TraesCS1A01G243300 chr5D 97.283 184 4 1 2803 2985 29066206 29066023 1.610000e-80 311.0
22 TraesCS1A01G243300 chr5D 97.283 184 4 1 2803 2985 204730093 204729910 1.610000e-80 311.0
23 TraesCS1A01G243300 chr5D 97.283 184 4 1 2803 2985 236022600 236022783 1.610000e-80 311.0
24 TraesCS1A01G243300 chr5B 97.283 184 4 1 2803 2985 454819604 454819787 1.610000e-80 311.0
25 TraesCS1A01G243300 chr2B 97.268 183 4 1 2803 2984 288485325 288485507 5.780000e-80 309.0
26 TraesCS1A01G243300 chr3B 95.385 195 5 4 2791 2984 23958442 23958251 2.080000e-79 307.0
27 TraesCS1A01G243300 chr3B 78.218 505 68 34 998 1466 794864564 794865062 9.740000e-73 285.0
28 TraesCS1A01G243300 chr3B 100.000 28 0 0 3198 3225 209598925 209598898 1.100000e-02 52.8
29 TraesCS1A01G243300 chr3A 78.571 504 61 32 998 1466 724053116 724053607 7.530000e-74 289.0
30 TraesCS1A01G243300 chrUn 78.439 487 70 23 998 1466 45750492 45750961 9.740000e-73 285.0
31 TraesCS1A01G243300 chr3D 91.453 117 9 1 4468 4583 191315710 191315594 6.160000e-35 159.0
32 TraesCS1A01G243300 chr3D 92.500 40 3 0 5191 5230 107075617 107075578 2.310000e-04 58.4
33 TraesCS1A01G243300 chr7A 84.932 73 6 5 5159 5230 391906577 391906645 1.070000e-07 69.4
34 TraesCS1A01G243300 chr6B 93.182 44 3 0 5187 5230 18737748 18737791 1.380000e-06 65.8
35 TraesCS1A01G243300 chr2D 100.000 35 0 0 5196 5230 372324242 372324276 1.380000e-06 65.8
36 TraesCS1A01G243300 chr7D 92.500 40 3 0 5191 5230 43214907 43214868 2.310000e-04 58.4
37 TraesCS1A01G243300 chr4A 92.500 40 3 0 5191 5230 651368074 651368035 2.310000e-04 58.4


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 TraesCS1A01G243300 chr1A 431775563 431781503 5940 False 10972.000000 10972 100.000000 1 5941 1 chr1A.!!$F1 5940
1 TraesCS1A01G243300 chr1B 449386375 449392494 6119 False 1118.285714 3367 92.714857 739 5941 7 chr1B.!!$F3 5202
2 TraesCS1A01G243300 chr1B 449363381 449365255 1874 False 954.500000 996 87.939500 1 924 2 chr1B.!!$F2 923
3 TraesCS1A01G243300 chr1D 333496010 333501158 5148 False 1499.060000 3195 94.710000 768 5941 5 chr1D.!!$F1 5173

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
819 838 0.100682 CATCACACGACTACCCGGAG 59.899 60.000 0.73 0.0 0.00 4.63 F
1297 2140 1.006454 GCGAGGGCGTAAGTATCCC 60.006 63.158 0.00 0.0 40.36 3.85 F
2835 4009 0.725117 GCTAGGCGTTAATTGTGCGT 59.275 50.000 0.00 0.0 0.00 5.24 F
2928 4102 0.042274 GCACAATGCGTTTTGCCAAC 60.042 50.000 17.21 0.0 45.60 3.77 F
2936 4110 0.165944 CGTTTTGCCAACGCCTAGAG 59.834 55.000 5.44 0.0 36.82 2.43 F
2938 4112 1.241315 TTTTGCCAACGCCTAGAGCC 61.241 55.000 0.00 0.0 38.78 4.70 F
2951 4125 1.261938 TAGAGCCCAGGTGCGCTTAA 61.262 55.000 9.73 0.0 41.75 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 3124 2.611292 CTGCACTAGATAACTTGCAGGC 59.389 50.000 18.36 3.58 46.06 4.85 R
2909 4083 0.042274 GTTGGCAAAACGCATTGTGC 60.042 50.000 0.00 0.00 45.17 4.57 R
4112 5349 0.312102 GCCAGGCTCACAAACACTTC 59.688 55.000 3.29 0.00 0.00 3.01 R
4115 5352 0.746659 AAAGCCAGGCTCACAAACAC 59.253 50.000 16.53 0.00 38.25 3.32 R
4116 5353 1.484038 AAAAGCCAGGCTCACAAACA 58.516 45.000 16.53 0.00 38.25 2.83 R
4330 5567 7.291651 TGGGGTATGTCTTAATAGAACTTAGGG 59.708 40.741 0.00 0.00 30.65 3.53 R
4985 6403 1.619827 TGCCATGGCCTTCTTGAAAAG 59.380 47.619 33.44 0.00 42.75 2.27 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
26 27 6.493115 TGTAAAAAGAATGATCTTCAGGGCAA 59.507 34.615 0.00 0.00 45.19 4.52
44 45 3.960755 GGCAATGCCCCTAATTCTACTTT 59.039 43.478 14.47 0.00 44.06 2.66
45 46 4.038042 GGCAATGCCCCTAATTCTACTTTC 59.962 45.833 14.47 0.00 44.06 2.62
54 55 8.311109 GCCCCTAATTCTACTTTCATTGAAAAA 58.689 33.333 12.62 5.12 30.84 1.94
63 64 9.301153 TCTACTTTCATTGAAAAAGAAACAAGC 57.699 29.630 12.62 0.00 38.44 4.01
89 90 6.420903 CCGTGATGTAAAATGAGACGACATAT 59.579 38.462 0.00 0.00 31.03 1.78
98 99 8.506168 AAAATGAGACGACATATGGTAATTGT 57.494 30.769 7.80 0.00 0.00 2.71
127 128 3.160679 AGGCAGTGCTTACTTTCCATT 57.839 42.857 16.11 0.00 0.00 3.16
131 132 3.503748 GCAGTGCTTACTTTCCATTGTCT 59.496 43.478 8.18 0.00 0.00 3.41
132 133 4.695455 GCAGTGCTTACTTTCCATTGTCTA 59.305 41.667 8.18 0.00 0.00 2.59
193 194 9.589111 TTGTTTTTAGATGTTTAGGGTTGTTTC 57.411 29.630 0.00 0.00 0.00 2.78
194 195 8.750298 TGTTTTTAGATGTTTAGGGTTGTTTCA 58.250 29.630 0.00 0.00 0.00 2.69
294 295 5.986135 CCACCAGTTGATATACAGTAAGCTC 59.014 44.000 0.00 0.00 0.00 4.09
302 303 3.887621 ATACAGTAAGCTCGGCAAAGA 57.112 42.857 0.00 0.00 0.00 2.52
327 328 7.141363 AGCTAACAAAAGTTTGATCATGTGAC 58.859 34.615 10.66 0.00 40.55 3.67
342 343 8.710551 TGATCATGTGACATTTTACAAAATTGC 58.289 29.630 0.00 0.00 36.52 3.56
344 345 8.659925 TCATGTGACATTTTACAAAATTGCTT 57.340 26.923 0.00 0.00 36.52 3.91
381 382 0.606401 CAACAAGCATCTGGACGGGT 60.606 55.000 0.00 0.00 0.00 5.28
388 389 1.359848 CATCTGGACGGGTTCTTTCG 58.640 55.000 0.00 0.00 0.00 3.46
390 391 2.031465 TGGACGGGTTCTTTCGCC 59.969 61.111 0.00 0.00 0.00 5.54
392 393 3.785499 GACGGGTTCTTTCGCCGC 61.785 66.667 0.00 0.00 0.00 6.53
393 394 4.612412 ACGGGTTCTTTCGCCGCA 62.612 61.111 0.00 0.00 0.00 5.69
395 396 3.733960 GGGTTCTTTCGCCGCACC 61.734 66.667 0.00 0.00 0.00 5.01
396 397 2.668550 GGTTCTTTCGCCGCACCT 60.669 61.111 0.00 0.00 0.00 4.00
398 399 1.668151 GTTCTTTCGCCGCACCTCT 60.668 57.895 0.00 0.00 0.00 3.69
399 400 0.389426 GTTCTTTCGCCGCACCTCTA 60.389 55.000 0.00 0.00 0.00 2.43
405 424 2.028337 GCCGCACCTCTAGCTAGC 59.972 66.667 16.35 6.62 0.00 3.42
433 452 5.752955 GCAAATTTCTAGCACAACCTCAAAA 59.247 36.000 0.00 0.00 0.00 2.44
452 471 7.094334 CCTCAAAACCAAGTTTCTACCCTAATC 60.094 40.741 0.00 0.00 34.43 1.75
453 472 7.291566 TCAAAACCAAGTTTCTACCCTAATCA 58.708 34.615 0.00 0.00 34.43 2.57
472 491 9.323985 CCTAATCAAATTTGAACCTTTGTGAAA 57.676 29.630 23.91 0.00 41.13 2.69
480 499 3.761218 TGAACCTTTGTGAAAGAAGCACA 59.239 39.130 0.00 0.00 43.89 4.57
488 507 5.826601 TGTGAAAGAAGCACAACATACAA 57.173 34.783 0.00 0.00 42.75 2.41
491 510 6.094742 TGTGAAAGAAGCACAACATACAAGAA 59.905 34.615 0.00 0.00 42.75 2.52
553 572 3.124466 TGTCGTAAACATCAAAGATGGCG 59.876 43.478 11.29 9.50 31.20 5.69
592 611 6.648192 TGTGTTTCTTCAAATTCCCATGTTT 58.352 32.000 0.00 0.00 0.00 2.83
718 737 9.554724 TTTTAGAAAATGTGTCGATTATTCTGC 57.445 29.630 0.00 0.00 0.00 4.26
720 739 5.882557 AGAAAATGTGTCGATTATTCTGCCT 59.117 36.000 0.00 0.00 0.00 4.75
721 740 6.375455 AGAAAATGTGTCGATTATTCTGCCTT 59.625 34.615 0.00 0.00 0.00 4.35
725 744 5.938322 TGTGTCGATTATTCTGCCTTTTTC 58.062 37.500 0.00 0.00 0.00 2.29
746 765 9.953565 TTTTTCCTATCTAATACCCCATAATCG 57.046 33.333 0.00 0.00 0.00 3.34
747 766 7.670605 TTCCTATCTAATACCCCATAATCGG 57.329 40.000 0.00 0.00 0.00 4.18
811 830 3.990469 GTGTTCAATCTCATCACACGACT 59.010 43.478 0.00 0.00 0.00 4.18
816 835 1.092348 TCTCATCACACGACTACCCG 58.908 55.000 0.00 0.00 0.00 5.28
819 838 0.100682 CATCACACGACTACCCGGAG 59.899 60.000 0.73 0.00 0.00 4.63
887 913 1.070758 TGTTCAGGCTTCAGAGTCCAC 59.929 52.381 0.00 0.00 0.00 4.02
1185 2028 2.892425 CGGTCTGATTCGGCTGCC 60.892 66.667 9.11 9.11 0.00 4.85
1244 2087 2.104170 GAGACGGAGACCAAGGAGATT 58.896 52.381 0.00 0.00 0.00 2.40
1297 2140 1.006454 GCGAGGGCGTAAGTATCCC 60.006 63.158 0.00 0.00 40.36 3.85
1308 2153 2.624437 AAGTATCCCGCCGCGTCTTC 62.624 60.000 12.58 0.00 0.00 2.87
1355 2204 2.540383 TCTTGGCTCTGAGGCTTTCTA 58.460 47.619 28.26 8.32 41.96 2.10
1367 2216 5.118990 TGAGGCTTTCTATTCTTGATTCGG 58.881 41.667 0.00 0.00 0.00 4.30
1493 2342 2.988010 TCATCCCACGAATCAGAAGG 57.012 50.000 0.00 0.00 0.00 3.46
1591 2442 1.407437 CGAGCAGGGGAAGCAAAGTAT 60.407 52.381 0.00 0.00 0.00 2.12
1861 2773 4.406648 TGATGATGGTACTGGTTGCTAG 57.593 45.455 0.00 0.00 0.00 3.42
1862 2774 3.774766 TGATGATGGTACTGGTTGCTAGT 59.225 43.478 0.00 0.00 0.00 2.57
1863 2775 4.959839 TGATGATGGTACTGGTTGCTAGTA 59.040 41.667 0.00 0.00 0.00 1.82
1871 2783 3.728845 ACTGGTTGCTAGTACAAGTGTG 58.271 45.455 6.43 0.00 28.66 3.82
1880 2792 3.470645 AGTACAAGTGTGGTTCCTGAC 57.529 47.619 0.00 0.00 0.00 3.51
2003 2915 4.691685 GCAGACAATTTGCATGAATTTGGA 59.308 37.500 0.00 0.00 41.17 3.53
2043 2955 8.531530 CAGTGACTTTGTTGTTTTTATGCTAAC 58.468 33.333 0.00 0.00 0.00 2.34
2091 3003 7.472663 GCAGGATCTAACCTCTTGATAGACAAT 60.473 40.741 0.00 0.00 38.32 2.71
2212 3124 4.035208 GGTATTGCAGTGTTATCCTTTCGG 59.965 45.833 0.00 0.00 0.00 4.30
2214 3126 0.733150 GCAGTGTTATCCTTTCGGCC 59.267 55.000 0.00 0.00 0.00 6.13
2465 3378 9.715121 AATTGCTTATTTGATGTGATGAGTTTT 57.285 25.926 0.00 0.00 0.00 2.43
2700 3874 4.337274 TCATAATGTGAAGCTGGAGCATTG 59.663 41.667 13.06 2.95 45.16 2.82
2725 3899 4.944317 GGTAAAGAGAAACTAGCAGCCATT 59.056 41.667 0.00 0.00 0.00 3.16
2728 3902 2.751806 AGAGAAACTAGCAGCCATTTGC 59.248 45.455 0.00 0.00 44.41 3.68
2729 3903 2.489329 GAGAAACTAGCAGCCATTTGCA 59.511 45.455 0.52 0.00 46.47 4.08
2775 3949 7.369803 ACTAGAGATTGTACAATGTTGCAAG 57.630 36.000 25.42 17.13 0.00 4.01
2784 3958 5.418524 TGTACAATGTTGCAAGCTTATCCAT 59.581 36.000 0.00 0.00 0.00 3.41
2801 3975 4.790765 TCCATATCTATCTGACGGCAAG 57.209 45.455 0.00 0.00 0.00 4.01
2802 3976 4.152647 TCCATATCTATCTGACGGCAAGT 58.847 43.478 0.00 0.00 0.00 3.16
2803 3977 5.321927 TCCATATCTATCTGACGGCAAGTA 58.678 41.667 0.00 0.00 0.00 2.24
2804 3978 5.416013 TCCATATCTATCTGACGGCAAGTAG 59.584 44.000 0.00 0.00 0.00 2.57
2805 3979 5.184096 CCATATCTATCTGACGGCAAGTAGT 59.816 44.000 8.86 1.59 0.00 2.73
2806 3980 6.294787 CCATATCTATCTGACGGCAAGTAGTT 60.295 42.308 8.86 4.56 0.00 2.24
2807 3981 4.634184 TCTATCTGACGGCAAGTAGTTC 57.366 45.455 8.86 0.00 0.00 3.01
2808 3982 4.014406 TCTATCTGACGGCAAGTAGTTCA 58.986 43.478 8.86 0.00 0.00 3.18
2809 3983 3.678056 ATCTGACGGCAAGTAGTTCAA 57.322 42.857 0.00 0.00 0.00 2.69
2811 3985 3.799366 TCTGACGGCAAGTAGTTCAAAA 58.201 40.909 0.00 0.00 0.00 2.44
2812 3986 4.193090 TCTGACGGCAAGTAGTTCAAAAA 58.807 39.130 0.00 0.00 0.00 1.94
2835 4009 0.725117 GCTAGGCGTTAATTGTGCGT 59.275 50.000 0.00 0.00 0.00 5.24
2836 4010 1.129811 GCTAGGCGTTAATTGTGCGTT 59.870 47.619 0.00 0.00 0.00 4.84
2837 4011 2.413634 GCTAGGCGTTAATTGTGCGTTT 60.414 45.455 0.00 0.00 0.00 3.60
2838 4012 2.785713 AGGCGTTAATTGTGCGTTTT 57.214 40.000 0.00 0.00 0.00 2.43
2839 4013 2.389998 AGGCGTTAATTGTGCGTTTTG 58.610 42.857 0.00 0.00 0.00 2.44
2840 4014 1.136748 GGCGTTAATTGTGCGTTTTGC 60.137 47.619 0.00 0.00 46.70 3.68
2841 4015 1.136748 GCGTTAATTGTGCGTTTTGCC 60.137 47.619 0.00 0.00 45.60 4.52
2842 4016 2.120232 CGTTAATTGTGCGTTTTGCCA 58.880 42.857 0.00 0.00 45.60 4.92
2845 4019 0.873743 AATTGTGCGTTTTGCCACCG 60.874 50.000 0.00 0.00 45.60 4.94
2846 4020 4.560856 TGTGCGTTTTGCCACCGC 62.561 61.111 0.00 0.00 45.60 5.68
2849 4023 4.279043 GCGTTTTGCCACCGCCTT 62.279 61.111 0.00 0.00 41.50 4.35
2851 4025 2.661537 GTTTTGCCACCGCCTTGC 60.662 61.111 0.00 0.00 0.00 4.01
2862 4036 2.179267 GCCTTGCGCTTTACTGCC 59.821 61.111 9.73 0.00 0.00 4.85
2863 4037 2.625823 GCCTTGCGCTTTACTGCCA 61.626 57.895 9.73 0.00 0.00 4.92
2864 4038 1.956043 CCTTGCGCTTTACTGCCAA 59.044 52.632 9.73 0.00 0.00 4.52
2866 4040 1.666888 CCTTGCGCTTTACTGCCAAAG 60.667 52.381 9.73 0.00 38.34 2.77
2874 4048 2.107950 TTACTGCCAAAGCGCATACT 57.892 45.000 11.47 0.00 44.31 2.12
2875 4049 2.107950 TACTGCCAAAGCGCATACTT 57.892 45.000 11.47 0.00 44.31 2.24
2876 4050 2.107950 ACTGCCAAAGCGCATACTTA 57.892 45.000 11.47 0.00 44.31 2.24
2877 4051 2.643551 ACTGCCAAAGCGCATACTTAT 58.356 42.857 11.47 0.00 44.31 1.73
2878 4052 2.355756 ACTGCCAAAGCGCATACTTATG 59.644 45.455 11.47 0.00 44.31 1.90
2903 4077 5.966636 CAGTTATGCACAGATTAAGCGTA 57.033 39.130 0.00 0.00 0.00 4.42
2905 4079 5.520288 CAGTTATGCACAGATTAAGCGTAGT 59.480 40.000 0.00 0.00 32.03 2.73
2908 4082 7.926555 AGTTATGCACAGATTAAGCGTAGTTAT 59.073 33.333 0.00 0.00 32.03 1.89
2909 4083 5.966636 TGCACAGATTAAGCGTAGTTATG 57.033 39.130 0.00 0.00 0.00 1.90
2910 4084 4.270084 TGCACAGATTAAGCGTAGTTATGC 59.730 41.667 0.00 0.00 38.47 3.14
2911 4085 4.270084 GCACAGATTAAGCGTAGTTATGCA 59.730 41.667 6.16 0.00 40.60 3.96
2912 4086 5.728255 CACAGATTAAGCGTAGTTATGCAC 58.272 41.667 6.16 0.00 40.60 4.57
2913 4087 5.290885 CACAGATTAAGCGTAGTTATGCACA 59.709 40.000 6.16 0.00 40.60 4.57
2915 4089 6.538742 ACAGATTAAGCGTAGTTATGCACAAT 59.461 34.615 6.16 4.67 40.60 2.71
2917 4091 3.405170 AAGCGTAGTTATGCACAATGC 57.595 42.857 6.16 0.00 45.29 3.56
2926 4100 4.024698 GCACAATGCGTTTTGCCA 57.975 50.000 17.21 0.00 45.60 4.92
2928 4102 0.042274 GCACAATGCGTTTTGCCAAC 60.042 50.000 17.21 0.00 45.60 3.77
2934 4108 4.838959 CGTTTTGCCAACGCCTAG 57.161 55.556 5.44 0.00 36.82 3.02
2935 4109 2.240230 CGTTTTGCCAACGCCTAGA 58.760 52.632 5.44 0.00 36.82 2.43
2936 4110 0.165944 CGTTTTGCCAACGCCTAGAG 59.834 55.000 5.44 0.00 36.82 2.43
2938 4112 1.241315 TTTTGCCAACGCCTAGAGCC 61.241 55.000 0.00 0.00 38.78 4.70
2939 4113 3.622060 TTGCCAACGCCTAGAGCCC 62.622 63.158 0.00 0.00 38.78 5.19
2940 4114 4.096003 GCCAACGCCTAGAGCCCA 62.096 66.667 0.00 0.00 38.78 5.36
2941 4115 2.187946 CCAACGCCTAGAGCCCAG 59.812 66.667 0.00 0.00 38.78 4.45
2942 4116 2.187946 CAACGCCTAGAGCCCAGG 59.812 66.667 0.00 0.00 38.78 4.45
2944 4118 2.660064 AACGCCTAGAGCCCAGGTG 61.660 63.158 7.63 7.63 46.98 4.00
2945 4119 4.537433 CGCCTAGAGCCCAGGTGC 62.537 72.222 0.00 0.00 36.90 5.01
2947 4121 4.537433 CCTAGAGCCCAGGTGCGC 62.537 72.222 0.00 0.00 36.02 6.09
2949 4123 3.003173 TAGAGCCCAGGTGCGCTT 61.003 61.111 9.73 0.00 41.75 4.68
2950 4124 1.676678 CTAGAGCCCAGGTGCGCTTA 61.677 60.000 9.73 0.00 41.75 3.09
2951 4125 1.261938 TAGAGCCCAGGTGCGCTTAA 61.262 55.000 9.73 0.00 41.75 1.85
2952 4126 2.045926 AGCCCAGGTGCGCTTAAG 60.046 61.111 9.73 0.00 36.02 1.85
2953 4127 3.815396 GCCCAGGTGCGCTTAAGC 61.815 66.667 17.83 17.83 37.78 3.09
3096 4305 2.351706 GTGTAACACACCTGGGGAAA 57.648 50.000 1.10 0.00 43.05 3.13
3188 4406 5.799978 ACTACTCGGGGAATATCTCCTAT 57.200 43.478 0.00 0.00 44.68 2.57
3192 4410 5.757988 ACTCGGGGAATATCTCCTATAGAC 58.242 45.833 0.00 0.00 44.68 2.59
3236 4454 5.969423 TCCTACAACAAATCGTACTTAGGG 58.031 41.667 0.00 0.00 29.89 3.53
3531 4750 6.119536 TCTACTTTGCAAGAGAAACCTGAAA 58.880 36.000 13.35 0.00 0.00 2.69
3542 4761 7.323052 AGAGAAACCTGAAATTAACTCCTCT 57.677 36.000 0.00 0.00 0.00 3.69
3591 4810 3.003275 TCTTCAAAATGTGCGTGGTTCTC 59.997 43.478 0.00 0.00 0.00 2.87
3656 4878 5.752712 CAGTTCTTTACTTTGAGGCACTTC 58.247 41.667 0.00 0.00 33.95 3.01
3729 4958 6.096673 TGAACTTGTAGTCTACTGCAATCA 57.903 37.500 12.99 11.90 45.12 2.57
3961 5190 6.942532 TCATCTTTTGTACTTGAAGCTTGT 57.057 33.333 2.10 0.00 0.00 3.16
3994 5223 2.762745 TCGGAAGAGTGTTTGCTTACC 58.237 47.619 0.00 0.00 34.84 2.85
3995 5224 2.103432 TCGGAAGAGTGTTTGCTTACCA 59.897 45.455 0.00 0.00 34.84 3.25
4052 5281 3.776969 TCTGCTGGAGAGGATGTTAACAT 59.223 43.478 20.93 20.93 39.70 2.71
4092 5327 3.952535 AGTTGCTTCTTGTTTGCTTACG 58.047 40.909 0.00 0.00 0.00 3.18
4111 5348 9.051679 TGCTTACGTTTATATGCTTTGATATGT 57.948 29.630 0.00 0.00 0.00 2.29
4112 5349 9.318041 GCTTACGTTTATATGCTTTGATATGTG 57.682 33.333 0.00 0.00 0.00 3.21
4116 5353 9.109393 ACGTTTATATGCTTTGATATGTGAAGT 57.891 29.630 0.00 0.00 0.00 3.01
4330 5567 1.331756 CTCGTGGCTTGCCATAATCAC 59.668 52.381 17.86 2.76 0.00 3.06
4727 6145 2.516930 CAAGGTGGCGGCTATGGG 60.517 66.667 11.43 0.00 0.00 4.00
4862 6280 2.203209 CCTTATGGTCCTGGCGGC 60.203 66.667 0.00 0.00 0.00 6.53
4863 6281 2.588877 CTTATGGTCCTGGCGGCG 60.589 66.667 0.51 0.51 0.00 6.46
4864 6282 4.169696 TTATGGTCCTGGCGGCGG 62.170 66.667 11.58 11.58 0.00 6.13
4985 6403 7.830739 ACCATGTCATGTAGATTTCTTTTTCC 58.169 34.615 11.84 0.00 0.00 3.13
5041 6459 4.214119 CCATGATAAGTGGAAACCTATGCG 59.786 45.833 0.00 0.00 39.12 4.73
5104 6523 6.395426 TTTTGCTGGGCTTGATATGATAAG 57.605 37.500 0.00 0.00 0.00 1.73
5105 6524 3.415212 TGCTGGGCTTGATATGATAAGC 58.585 45.455 0.00 0.00 46.45 3.09
5106 6525 3.073503 TGCTGGGCTTGATATGATAAGCT 59.926 43.478 12.85 0.00 46.40 3.74
5108 6527 5.221904 TGCTGGGCTTGATATGATAAGCTAA 60.222 40.000 12.85 4.57 46.40 3.09
5109 6528 5.884792 GCTGGGCTTGATATGATAAGCTAAT 59.115 40.000 12.85 0.00 46.40 1.73
5111 6530 7.094032 GCTGGGCTTGATATGATAAGCTAATTT 60.094 37.037 12.85 0.00 46.40 1.82
5194 6640 7.979444 AAAACACAGCAACATATAGTACACT 57.021 32.000 0.00 0.00 0.00 3.55
5288 6797 6.122964 AGAAGCTTATTTGGGGACATACTTC 58.877 40.000 0.00 0.00 42.32 3.01
5319 6828 9.965902 AATTTGAAATGGAGAGAATGTAGTAGT 57.034 29.630 0.00 0.00 0.00 2.73
5320 6829 8.777865 TTTGAAATGGAGAGAATGTAGTAGTG 57.222 34.615 0.00 0.00 0.00 2.74
5321 6830 6.341316 TGAAATGGAGAGAATGTAGTAGTGC 58.659 40.000 0.00 0.00 0.00 4.40
5322 6831 4.576216 ATGGAGAGAATGTAGTAGTGCG 57.424 45.455 0.00 0.00 0.00 5.34
5324 6833 3.377485 TGGAGAGAATGTAGTAGTGCGTC 59.623 47.826 0.00 0.00 0.00 5.19
5325 6834 3.546417 GGAGAGAATGTAGTAGTGCGTCG 60.546 52.174 0.00 0.00 0.00 5.12
5326 6835 3.008330 AGAGAATGTAGTAGTGCGTCGT 58.992 45.455 0.00 0.00 0.00 4.34
5327 6836 3.063725 AGAGAATGTAGTAGTGCGTCGTC 59.936 47.826 0.00 0.00 0.00 4.20
5328 6837 2.745821 AGAATGTAGTAGTGCGTCGTCA 59.254 45.455 0.00 0.00 0.00 4.35
5329 6838 2.539346 ATGTAGTAGTGCGTCGTCAC 57.461 50.000 10.56 10.56 37.24 3.67
5331 6840 1.196127 TGTAGTAGTGCGTCGTCACTG 59.804 52.381 23.61 0.00 45.95 3.66
5332 6841 0.800631 TAGTAGTGCGTCGTCACTGG 59.199 55.000 23.61 0.00 45.95 4.00
5334 6843 0.170561 GTAGTGCGTCGTCACTGGAT 59.829 55.000 23.61 7.96 45.95 3.41
5335 6844 0.885879 TAGTGCGTCGTCACTGGATT 59.114 50.000 23.61 7.68 45.95 3.01
5336 6845 0.033504 AGTGCGTCGTCACTGGATTT 59.966 50.000 17.59 0.00 44.88 2.17
5338 6847 1.263217 GTGCGTCGTCACTGGATTTTT 59.737 47.619 11.08 0.00 34.29 1.94
5472 6981 0.034896 TGTCCTTGCCCGTCTTCTTC 59.965 55.000 0.00 0.00 0.00 2.87
5715 7224 3.420943 GCGGCATTGCGGAAGTAT 58.579 55.556 19.15 0.00 0.00 2.12
5919 7428 4.908687 ACGTTGAGCAGCGCCACA 62.909 61.111 2.29 0.00 38.63 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 6.672593 TCAATGAAAGTAGAATTAGGGGCAT 58.327 36.000 0.00 0.00 0.00 4.40
41 42 6.509997 CGGGCTTGTTTCTTTTTCAATGAAAG 60.510 38.462 8.51 0.00 35.87 2.62
44 45 4.142049 ACGGGCTTGTTTCTTTTTCAATGA 60.142 37.500 0.00 0.00 0.00 2.57
45 46 4.025813 CACGGGCTTGTTTCTTTTTCAATG 60.026 41.667 0.00 0.00 0.00 2.82
54 55 2.851263 TACATCACGGGCTTGTTTCT 57.149 45.000 0.00 0.00 0.00 2.52
59 60 3.689161 TCTCATTTTACATCACGGGCTTG 59.311 43.478 0.00 0.00 0.00 4.01
63 64 3.306166 GTCGTCTCATTTTACATCACGGG 59.694 47.826 0.00 0.00 0.00 5.28
89 90 3.196039 TGCCTAGTAGCGAACAATTACCA 59.804 43.478 0.00 0.00 34.65 3.25
98 99 0.895530 AAGCACTGCCTAGTAGCGAA 59.104 50.000 0.00 0.00 36.62 4.70
131 132 9.261035 TGTCCCAGCAATTTTAAAATCCTTATA 57.739 29.630 13.68 0.00 0.00 0.98
132 133 8.144862 TGTCCCAGCAATTTTAAAATCCTTAT 57.855 30.769 13.68 0.00 0.00 1.73
182 183 7.676893 TCTTATCTAAGGTCTGAAACAACCCTA 59.323 37.037 0.00 0.00 36.11 3.53
188 189 8.088981 GTCACTTCTTATCTAAGGTCTGAAACA 58.911 37.037 0.00 0.00 34.14 2.83
189 190 8.308207 AGTCACTTCTTATCTAAGGTCTGAAAC 58.692 37.037 0.00 0.00 34.14 2.78
193 194 8.514330 AGTAGTCACTTCTTATCTAAGGTCTG 57.486 38.462 0.00 0.00 34.14 3.51
238 239 8.190122 GCACATGTCATGGTAAATATGAAAAGA 58.810 33.333 17.08 0.00 36.41 2.52
254 255 2.105006 GTGGTCTCAGCACATGTCAT 57.895 50.000 0.00 0.00 45.26 3.06
294 295 3.626028 ACTTTTGTTAGCTCTTTGCCG 57.374 42.857 0.00 0.00 44.23 5.69
302 303 7.141363 GTCACATGATCAAACTTTTGTTAGCT 58.859 34.615 0.00 0.00 42.67 3.32
306 307 8.721019 AAATGTCACATGATCAAACTTTTGTT 57.279 26.923 0.00 0.00 45.94 2.83
344 345 6.377327 TTGTTGTTGTTTTGGCAAGAAAAA 57.623 29.167 0.00 0.00 34.23 1.94
348 349 2.999355 GCTTGTTGTTGTTTTGGCAAGA 59.001 40.909 0.00 0.00 36.41 3.02
349 350 2.740981 TGCTTGTTGTTGTTTTGGCAAG 59.259 40.909 0.00 0.00 37.12 4.01
358 359 1.603802 CGTCCAGATGCTTGTTGTTGT 59.396 47.619 0.00 0.00 0.00 3.32
381 382 0.108804 CTAGAGGTGCGGCGAAAGAA 60.109 55.000 12.98 0.00 0.00 2.52
388 389 2.028337 GCTAGCTAGAGGTGCGGC 59.972 66.667 25.15 3.10 35.28 6.53
390 391 0.248825 CACTGCTAGCTAGAGGTGCG 60.249 60.000 25.15 8.26 35.28 5.34
392 393 0.820226 TGCACTGCTAGCTAGAGGTG 59.180 55.000 27.46 27.46 33.61 4.00
393 394 1.561643 TTGCACTGCTAGCTAGAGGT 58.438 50.000 25.15 17.36 0.00 3.85
395 396 4.874966 AGAAATTTGCACTGCTAGCTAGAG 59.125 41.667 25.15 18.98 0.00 2.43
396 397 4.836825 AGAAATTTGCACTGCTAGCTAGA 58.163 39.130 25.15 8.65 0.00 2.43
398 399 4.572389 GCTAGAAATTTGCACTGCTAGCTA 59.428 41.667 17.23 1.31 44.39 3.32
399 400 3.376546 GCTAGAAATTTGCACTGCTAGCT 59.623 43.478 17.23 0.00 44.39 3.32
427 446 7.447238 TGATTAGGGTAGAAACTTGGTTTTGAG 59.553 37.037 0.00 0.00 35.77 3.02
433 452 8.585018 CAAATTTGATTAGGGTAGAAACTTGGT 58.415 33.333 13.08 0.00 0.00 3.67
452 471 7.148440 TGCTTCTTTCACAAAGGTTCAAATTTG 60.148 33.333 12.15 12.15 41.22 2.32
453 472 6.878389 TGCTTCTTTCACAAAGGTTCAAATTT 59.122 30.769 0.00 0.00 39.01 1.82
472 491 6.017109 ACGATTTTCTTGTATGTTGTGCTTCT 60.017 34.615 0.00 0.00 0.00 2.85
488 507 8.674607 GGGATTCTTTGTATTGTACGATTTTCT 58.325 33.333 0.00 0.00 0.00 2.52
491 510 7.827236 TGAGGGATTCTTTGTATTGTACGATTT 59.173 33.333 0.00 0.00 0.00 2.17
535 554 3.171277 GCACGCCATCTTTGATGTTTAC 58.829 45.455 6.78 0.00 0.00 2.01
553 572 6.843069 AGAAACACAACAATAAAATGGCAC 57.157 33.333 0.00 0.00 0.00 5.01
607 626 7.382218 GTGGACCTATGAAAAACAAACTCAATG 59.618 37.037 0.00 0.00 0.00 2.82
608 627 7.069331 TGTGGACCTATGAAAAACAAACTCAAT 59.931 33.333 0.00 0.00 0.00 2.57
657 676 9.053840 TGCAACATTACAATCATGTCAAATTTT 57.946 25.926 0.00 0.00 41.05 1.82
658 677 8.497554 GTGCAACATTACAATCATGTCAAATTT 58.502 29.630 0.00 0.00 37.67 1.82
659 678 7.874016 AGTGCAACATTACAATCATGTCAAATT 59.126 29.630 0.00 0.00 41.43 1.82
660 679 7.380536 AGTGCAACATTACAATCATGTCAAAT 58.619 30.769 0.00 0.00 41.43 2.32
661 680 6.747125 AGTGCAACATTACAATCATGTCAAA 58.253 32.000 0.00 0.00 41.43 2.69
662 681 6.330004 AGTGCAACATTACAATCATGTCAA 57.670 33.333 0.00 0.00 41.43 3.18
663 682 5.963176 AGTGCAACATTACAATCATGTCA 57.037 34.783 0.00 0.00 41.43 3.58
664 683 8.915871 ATAAAGTGCAACATTACAATCATGTC 57.084 30.769 0.00 0.00 41.43 3.06
665 684 9.709495 AAATAAAGTGCAACATTACAATCATGT 57.291 25.926 0.00 0.00 41.43 3.21
695 714 7.047891 AGGCAGAATAATCGACACATTTTCTA 58.952 34.615 0.00 0.00 0.00 2.10
697 716 6.124088 AGGCAGAATAATCGACACATTTTC 57.876 37.500 0.00 0.00 0.00 2.29
720 739 9.953565 CGATTATGGGGTATTAGATAGGAAAAA 57.046 33.333 0.00 0.00 0.00 1.94
721 740 8.545472 CCGATTATGGGGTATTAGATAGGAAAA 58.455 37.037 0.00 0.00 0.00 2.29
725 744 7.670605 TTCCGATTATGGGGTATTAGATAGG 57.329 40.000 0.00 0.00 0.00 2.57
756 775 3.439129 CGGTGTTTCTATCTGTTTTCCCC 59.561 47.826 0.00 0.00 0.00 4.81
757 776 4.320870 TCGGTGTTTCTATCTGTTTTCCC 58.679 43.478 0.00 0.00 0.00 3.97
758 777 5.934935 TTCGGTGTTTCTATCTGTTTTCC 57.065 39.130 0.00 0.00 0.00 3.13
759 778 6.631636 GTGTTTCGGTGTTTCTATCTGTTTTC 59.368 38.462 0.00 0.00 0.00 2.29
761 780 5.277154 CGTGTTTCGGTGTTTCTATCTGTTT 60.277 40.000 0.00 0.00 35.71 2.83
762 781 4.210537 CGTGTTTCGGTGTTTCTATCTGTT 59.789 41.667 0.00 0.00 35.71 3.16
763 782 3.739300 CGTGTTTCGGTGTTTCTATCTGT 59.261 43.478 0.00 0.00 35.71 3.41
764 783 3.423123 GCGTGTTTCGGTGTTTCTATCTG 60.423 47.826 0.00 0.00 40.26 2.90
793 812 3.130516 GGGTAGTCGTGTGATGAGATTGA 59.869 47.826 0.00 0.00 0.00 2.57
816 835 1.930908 ATCGTGTCCGTCCGTTCTCC 61.931 60.000 0.00 0.00 35.01 3.71
819 838 0.387622 TCAATCGTGTCCGTCCGTTC 60.388 55.000 0.00 0.00 35.01 3.95
824 843 1.429463 AAGCTTCAATCGTGTCCGTC 58.571 50.000 0.00 0.00 35.01 4.79
887 913 2.347490 CCGAAGAGGGGTGTGGTG 59.653 66.667 0.00 0.00 35.97 4.17
1160 2003 1.540267 CCGAATCAGACCGACGGATAT 59.460 52.381 23.38 0.00 45.31 1.63
1164 2007 2.582498 GCCGAATCAGACCGACGG 60.582 66.667 13.61 13.61 45.26 4.79
1244 2087 0.458543 GGATCTTCTTGAGCGCGACA 60.459 55.000 12.10 6.26 30.59 4.35
1297 2140 2.943653 AAAAAGGAAGACGCGGCG 59.056 55.556 22.36 22.36 0.00 6.46
1316 2161 5.951747 CCAAGAACATCATTTAGGGAAGGAA 59.048 40.000 0.00 0.00 30.98 3.36
1317 2162 5.509498 CCAAGAACATCATTTAGGGAAGGA 58.491 41.667 0.00 0.00 31.87 3.36
1318 2163 4.098501 GCCAAGAACATCATTTAGGGAAGG 59.901 45.833 0.00 0.00 0.00 3.46
1319 2164 4.952335 AGCCAAGAACATCATTTAGGGAAG 59.048 41.667 0.00 0.00 0.00 3.46
1320 2165 4.934356 AGCCAAGAACATCATTTAGGGAA 58.066 39.130 0.00 0.00 0.00 3.97
1321 2166 4.228210 AGAGCCAAGAACATCATTTAGGGA 59.772 41.667 0.00 0.00 0.00 4.20
1322 2167 4.337555 CAGAGCCAAGAACATCATTTAGGG 59.662 45.833 0.00 0.00 0.00 3.53
1355 2204 1.398390 GAACTGCGCCGAATCAAGAAT 59.602 47.619 4.18 0.00 0.00 2.40
1367 2216 1.883084 CCGTGATAGGGAACTGCGC 60.883 63.158 0.00 0.00 43.88 6.09
1493 2342 5.402270 GCAGTTAACAACCAAACATGATGTC 59.598 40.000 8.61 0.00 0.00 3.06
1861 2773 3.188159 TGTCAGGAACCACACTTGTAC 57.812 47.619 0.00 0.00 0.00 2.90
1862 2774 5.554437 TTATGTCAGGAACCACACTTGTA 57.446 39.130 0.00 0.00 0.00 2.41
1863 2775 4.431416 TTATGTCAGGAACCACACTTGT 57.569 40.909 0.00 0.00 0.00 3.16
1880 2792 6.048509 TGTAGCACTGGTACATGACATTATG 58.951 40.000 15.58 0.00 40.80 1.90
2003 2915 6.318648 ACAAAGTCACTGTCACAACATAACAT 59.681 34.615 0.00 0.00 34.13 2.71
2043 2955 7.099266 TGCAGGAGTAAATTTTGATACATGG 57.901 36.000 0.00 0.00 0.00 3.66
2091 3003 4.103469 TCAGCCAGTTTTAAGTTACCCTCA 59.897 41.667 0.00 0.00 0.00 3.86
2212 3124 2.611292 CTGCACTAGATAACTTGCAGGC 59.389 50.000 18.36 3.58 46.06 4.85
2700 3874 4.185394 GGCTGCTAGTTTCTCTTTACCTC 58.815 47.826 0.00 0.00 0.00 3.85
2775 3949 5.163509 TGCCGTCAGATAGATATGGATAAGC 60.164 44.000 0.00 0.00 0.00 3.09
2784 3958 5.826208 TGAACTACTTGCCGTCAGATAGATA 59.174 40.000 0.00 0.00 0.00 1.98
2817 3991 3.465122 AAACGCACAATTAACGCCTAG 57.535 42.857 0.00 0.00 0.00 3.02
2820 3994 1.136748 GCAAAACGCACAATTAACGCC 60.137 47.619 0.00 0.00 41.79 5.68
2822 3996 2.097637 GTGGCAAAACGCACAATTAACG 60.098 45.455 0.00 0.00 45.17 3.18
2823 3997 2.219903 GGTGGCAAAACGCACAATTAAC 59.780 45.455 0.00 0.00 45.17 2.01
2824 3998 2.474816 GGTGGCAAAACGCACAATTAA 58.525 42.857 0.00 0.00 45.17 1.40
2825 3999 1.600663 CGGTGGCAAAACGCACAATTA 60.601 47.619 0.00 0.00 45.17 1.40
2826 4000 0.873743 CGGTGGCAAAACGCACAATT 60.874 50.000 0.00 0.00 45.17 2.32
2827 4001 1.299773 CGGTGGCAAAACGCACAAT 60.300 52.632 0.00 0.00 45.17 2.71
2845 4019 2.141122 TTGGCAGTAAAGCGCAAGGC 62.141 55.000 11.47 3.90 44.05 4.35
2846 4020 0.313672 TTTGGCAGTAAAGCGCAAGG 59.686 50.000 11.47 0.00 38.28 3.61
2847 4021 1.689959 CTTTGGCAGTAAAGCGCAAG 58.310 50.000 11.47 0.00 31.62 4.01
2848 4022 3.863681 CTTTGGCAGTAAAGCGCAA 57.136 47.368 11.47 0.00 31.62 4.85
2881 4055 4.864916 ACGCTTAATCTGTGCATAACTG 57.135 40.909 0.00 0.00 0.00 3.16
2882 4056 5.661458 ACTACGCTTAATCTGTGCATAACT 58.339 37.500 0.00 0.00 0.00 2.24
2884 4058 7.307160 GCATAACTACGCTTAATCTGTGCATAA 60.307 37.037 0.00 0.00 0.00 1.90
2886 4060 5.050091 GCATAACTACGCTTAATCTGTGCAT 60.050 40.000 0.00 0.00 0.00 3.96
2888 4062 4.270084 TGCATAACTACGCTTAATCTGTGC 59.730 41.667 0.00 0.00 0.00 4.57
2889 4063 5.290885 TGTGCATAACTACGCTTAATCTGTG 59.709 40.000 0.00 0.00 0.00 3.66
2890 4064 5.416083 TGTGCATAACTACGCTTAATCTGT 58.584 37.500 0.00 0.00 0.00 3.41
2891 4065 5.966636 TGTGCATAACTACGCTTAATCTG 57.033 39.130 0.00 0.00 0.00 2.90
2892 4066 6.511767 GCATTGTGCATAACTACGCTTAATCT 60.512 38.462 0.00 0.00 44.26 2.40
2893 4067 5.621228 GCATTGTGCATAACTACGCTTAATC 59.379 40.000 0.00 0.00 44.26 1.75
2894 4068 5.510671 GCATTGTGCATAACTACGCTTAAT 58.489 37.500 0.00 0.00 44.26 1.40
2895 4069 4.493382 CGCATTGTGCATAACTACGCTTAA 60.493 41.667 0.00 0.00 45.36 1.85
2896 4070 3.000825 CGCATTGTGCATAACTACGCTTA 59.999 43.478 0.00 0.00 45.36 3.09
2900 4074 3.383546 AACGCATTGTGCATAACTACG 57.616 42.857 0.00 5.47 45.36 3.51
2901 4075 4.201485 GCAAAACGCATTGTGCATAACTAC 60.201 41.667 2.07 0.00 45.36 2.73
2903 4077 2.730928 GCAAAACGCATTGTGCATAACT 59.269 40.909 2.07 0.00 45.36 2.24
2905 4079 2.064762 GGCAAAACGCATTGTGCATAA 58.935 42.857 10.25 0.00 45.36 1.90
2908 4082 0.460811 TTGGCAAAACGCATTGTGCA 60.461 45.000 10.25 0.00 45.36 4.57
2909 4083 0.042274 GTTGGCAAAACGCATTGTGC 60.042 50.000 0.00 0.00 45.17 4.57
2910 4084 0.229247 CGTTGGCAAAACGCATTGTG 59.771 50.000 0.00 0.00 45.17 3.33
2911 4085 2.587574 CGTTGGCAAAACGCATTGT 58.412 47.368 0.00 0.00 45.17 2.71
2917 4091 0.165944 CTCTAGGCGTTGGCAAAACG 59.834 55.000 16.88 16.88 45.56 3.60
2918 4092 0.109735 GCTCTAGGCGTTGGCAAAAC 60.110 55.000 0.00 0.00 42.47 2.43
2919 4093 1.241315 GGCTCTAGGCGTTGGCAAAA 61.241 55.000 0.00 0.00 42.47 2.44
2920 4094 1.674322 GGCTCTAGGCGTTGGCAAA 60.674 57.895 0.00 0.00 42.47 3.68
2921 4095 2.046314 GGCTCTAGGCGTTGGCAA 60.046 61.111 0.00 0.00 42.47 4.52
2923 4097 4.096003 TGGGCTCTAGGCGTTGGC 62.096 66.667 0.00 0.00 42.94 4.52
2924 4098 2.187946 CTGGGCTCTAGGCGTTGG 59.812 66.667 0.00 0.00 42.94 3.77
2926 4100 2.284699 ACCTGGGCTCTAGGCGTT 60.285 61.111 0.00 0.00 42.94 4.84
2928 4102 4.537433 GCACCTGGGCTCTAGGCG 62.537 72.222 0.00 0.00 42.94 5.52
2972 4146 5.752892 TGTGTTGCCGTCATAGTTAAAAA 57.247 34.783 0.00 0.00 0.00 1.94
2973 4147 5.106475 GGATGTGTTGCCGTCATAGTTAAAA 60.106 40.000 0.00 0.00 0.00 1.52
2974 4148 4.393680 GGATGTGTTGCCGTCATAGTTAAA 59.606 41.667 0.00 0.00 0.00 1.52
2975 4149 3.936453 GGATGTGTTGCCGTCATAGTTAA 59.064 43.478 0.00 0.00 0.00 2.01
2976 4150 3.196901 AGGATGTGTTGCCGTCATAGTTA 59.803 43.478 0.00 0.00 0.00 2.24
2977 4151 2.027192 AGGATGTGTTGCCGTCATAGTT 60.027 45.455 0.00 0.00 0.00 2.24
2979 4153 2.315925 AGGATGTGTTGCCGTCATAG 57.684 50.000 0.00 0.00 0.00 2.23
2980 4154 2.764010 AGTAGGATGTGTTGCCGTCATA 59.236 45.455 0.00 0.00 0.00 2.15
2981 4155 1.555075 AGTAGGATGTGTTGCCGTCAT 59.445 47.619 0.00 0.00 0.00 3.06
2982 4156 0.973632 AGTAGGATGTGTTGCCGTCA 59.026 50.000 0.00 0.00 0.00 4.35
2983 4157 2.953466 TAGTAGGATGTGTTGCCGTC 57.047 50.000 0.00 0.00 0.00 4.79
2984 4158 3.906720 AATAGTAGGATGTGTTGCCGT 57.093 42.857 0.00 0.00 0.00 5.68
2986 4160 6.267496 ACAAAAATAGTAGGATGTGTTGCC 57.733 37.500 0.00 0.00 0.00 4.52
2987 4161 8.040716 AGTACAAAAATAGTAGGATGTGTTGC 57.959 34.615 0.00 0.00 0.00 4.17
3036 4210 5.776173 TTACCTAGATGCTCTAGCTTCAC 57.224 43.478 17.16 1.77 43.89 3.18
3056 4230 6.414732 ACACATGGCTGCTAGTTTATCTTTA 58.585 36.000 0.00 0.00 0.00 1.85
3060 4234 5.584649 TGTTACACATGGCTGCTAGTTTATC 59.415 40.000 0.00 0.00 0.00 1.75
3089 4263 6.442541 TTGTACAATCTCTAGTTTTCCCCA 57.557 37.500 3.59 0.00 0.00 4.96
3095 4304 7.744087 TGCAACATTGTACAATCTCTAGTTT 57.256 32.000 18.25 2.52 0.00 2.66
3096 4305 7.744087 TTGCAACATTGTACAATCTCTAGTT 57.256 32.000 18.25 15.10 0.00 2.24
3400 4618 6.644248 ATTTGTTTCCCTACTGTAACCAAC 57.356 37.500 0.00 0.00 0.00 3.77
3531 4750 6.614906 AGATGAATGAGGACAGAGGAGTTAAT 59.385 38.462 0.00 0.00 0.00 1.40
3729 4958 2.093106 AGAGACAAGCGGATTACTCGT 58.907 47.619 6.69 0.00 32.33 4.18
3925 5154 8.979574 AGTACAAAAGATGAAAAGAGAAGTACG 58.020 33.333 0.00 0.00 33.99 3.67
3928 5157 9.396022 TCAAGTACAAAAGATGAAAAGAGAAGT 57.604 29.630 0.00 0.00 0.00 3.01
3931 5160 8.345565 GCTTCAAGTACAAAAGATGAAAAGAGA 58.654 33.333 0.00 0.00 30.37 3.10
3932 5161 8.348507 AGCTTCAAGTACAAAAGATGAAAAGAG 58.651 33.333 0.00 0.00 30.37 2.85
3933 5162 8.225603 AGCTTCAAGTACAAAAGATGAAAAGA 57.774 30.769 0.00 0.00 30.37 2.52
3994 5223 7.920151 TGAAAATCAAAACTAGAACCACACATG 59.080 33.333 0.00 0.00 0.00 3.21
3995 5224 8.006298 TGAAAATCAAAACTAGAACCACACAT 57.994 30.769 0.00 0.00 0.00 3.21
4052 5281 3.175594 ACTATACCTTTGACGGGTCCAA 58.824 45.455 0.00 0.00 38.19 3.53
4111 5348 1.679139 CCAGGCTCACAAACACTTCA 58.321 50.000 0.00 0.00 0.00 3.02
4112 5349 0.312102 GCCAGGCTCACAAACACTTC 59.688 55.000 3.29 0.00 0.00 3.01
4115 5352 0.746659 AAAGCCAGGCTCACAAACAC 59.253 50.000 16.53 0.00 38.25 3.32
4116 5353 1.484038 AAAAGCCAGGCTCACAAACA 58.516 45.000 16.53 0.00 38.25 2.83
4330 5567 7.291651 TGGGGTATGTCTTAATAGAACTTAGGG 59.708 40.741 0.00 0.00 30.65 3.53
4985 6403 1.619827 TGCCATGGCCTTCTTGAAAAG 59.380 47.619 33.44 0.00 42.75 2.27
5104 6523 9.976511 AGGACCAAACTAAAACTTTAAATTAGC 57.023 29.630 6.88 0.00 31.34 3.09
5314 6823 0.887836 TCCAGTGACGACGCACTACT 60.888 55.000 19.56 6.39 46.80 2.57
5315 6824 0.170561 ATCCAGTGACGACGCACTAC 59.829 55.000 19.56 4.44 46.80 2.73
5319 6828 1.588674 AAAAATCCAGTGACGACGCA 58.411 45.000 0.62 0.00 0.00 5.24
5404 6913 5.786264 ACCTCGACAATATTTCGACCTAT 57.214 39.130 14.57 0.00 40.51 2.57
5410 6919 4.181578 ACCTGAACCTCGACAATATTTCG 58.818 43.478 11.44 11.44 37.85 3.46
5615 7124 4.996434 GCTCCGGGATGGCGGATG 62.996 72.222 0.00 0.00 37.80 3.51
5896 7405 1.775344 CGCTGCTCAACGTGTACAG 59.225 57.895 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.