Multiple sequence alignment - TraesCS3A01G201800

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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 TraesCS3A01G201800 chr3A 100.000 3818 0 0 548 4365 337883317 337879500 0.000000e+00 7051.0
1 TraesCS3A01G201800 chr3A 100.000 115 0 0 1 115 337883864 337883750 3.420000e-51 213.0
2 TraesCS3A01G201800 chr3D 93.949 2925 90 23 1304 4171 246326818 246329712 0.000000e+00 4340.0
3 TraesCS3A01G201800 chr3D 93.250 637 12 13 649 1285 246326228 246326833 0.000000e+00 909.0
4 TraesCS3A01G201800 chr3D 84.722 72 10 1 4287 4357 113181107 113181036 2.180000e-08 71.3
5 TraesCS3A01G201800 chr3D 100.000 36 0 0 548 583 246326186 246326221 2.820000e-07 67.6
6 TraesCS3A01G201800 chr3B 92.620 1084 41 20 2793 3865 331553572 331552517 0.000000e+00 1522.0
7 TraesCS3A01G201800 chr3B 93.271 862 32 8 1939 2776 331554413 331553554 0.000000e+00 1247.0
8 TraesCS3A01G201800 chr3B 93.760 625 24 10 1304 1915 331555094 331554472 0.000000e+00 924.0
9 TraesCS3A01G201800 chr3B 91.134 688 20 9 610 1285 331555737 331555079 0.000000e+00 894.0
10 TraesCS3A01G201800 chr3B 95.985 274 8 2 3900 4171 331543544 331543272 4.010000e-120 442.0
11 TraesCS3A01G201800 chr3B 95.000 40 2 0 557 596 331555758 331555719 3.640000e-06 63.9
12 TraesCS3A01G201800 chr7D 82.656 369 56 8 2988 3352 197150528 197150892 1.960000e-83 320.0
13 TraesCS3A01G201800 chr7D 87.879 99 12 0 4171 4269 16791191 16791289 2.760000e-22 117.0
14 TraesCS3A01G201800 chr7D 100.000 35 0 0 1842 1876 88191149 88191115 1.010000e-06 65.8
15 TraesCS3A01G201800 chr7A 82.114 369 58 8 2988 3352 206582238 206582602 4.240000e-80 309.0
16 TraesCS3A01G201800 chr7A 100.000 34 0 0 1842 1875 670237278 670237245 3.640000e-06 63.9
17 TraesCS3A01G201800 chr4A 87.719 114 12 1 4172 4285 261553779 261553668 9.850000e-27 132.0
18 TraesCS3A01G201800 chr4A 84.848 99 14 1 4171 4269 169692015 169691918 9.990000e-17 99.0
19 TraesCS3A01G201800 chr2B 87.879 99 12 0 4171 4269 348101628 348101726 2.760000e-22 117.0
20 TraesCS3A01G201800 chr2B 81.897 116 18 2 4170 4285 793313597 793313485 1.290000e-15 95.3
21 TraesCS3A01G201800 chr2B 97.368 38 0 1 1842 1878 448376709 448376672 3.640000e-06 63.9
22 TraesCS3A01G201800 chr1B 86.111 108 12 2 4171 4278 427342524 427342628 3.570000e-21 113.0
23 TraesCS3A01G201800 chr4D 84.348 115 16 1 4171 4285 31055774 31055886 1.280000e-20 111.0
24 TraesCS3A01G201800 chr4D 83.193 119 17 2 4167 4285 108202875 108202760 5.970000e-19 106.0
25 TraesCS3A01G201800 chr4D 90.278 72 6 1 4287 4357 108185645 108185574 4.650000e-15 93.5
26 TraesCS3A01G201800 chr4D 87.500 72 8 1 4287 4357 31656676 31656605 1.010000e-11 82.4
27 TraesCS3A01G201800 chr7B 90.278 72 6 1 4287 4357 624799903 624799832 4.650000e-15 93.5
28 TraesCS3A01G201800 chr6B 88.889 72 7 1 4287 4357 61133279 61133208 2.160000e-13 87.9
29 TraesCS3A01G201800 chr2D 89.394 66 7 0 4300 4365 310430658 310430723 2.800000e-12 84.2
30 TraesCS3A01G201800 chr2D 88.571 70 7 1 4297 4365 333222369 333222438 2.800000e-12 84.2
31 TraesCS3A01G201800 chr1A 89.394 66 7 0 4300 4365 524372854 524372919 2.800000e-12 84.2
32 TraesCS3A01G201800 chr1A 100.000 32 0 0 1843 1874 403030365 403030396 4.710000e-05 60.2
33 TraesCS3A01G201800 chr5D 85.714 70 6 3 4297 4365 28154140 28154074 2.180000e-08 71.3
34 TraesCS3A01G201800 chr5D 93.617 47 2 1 4172 4218 214621941 214621986 7.830000e-08 69.4
35 TraesCS3A01G201800 chrUn 100.000 33 0 0 1842 1874 418283635 418283603 1.310000e-05 62.1
36 TraesCS3A01G201800 chr1D 100.000 33 0 0 1842 1874 431815681 431815713 1.310000e-05 62.1
37 TraesCS3A01G201800 chr6A 87.755 49 4 2 1827 1874 81256047 81256094 6.100000e-04 56.5


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 TraesCS3A01G201800 chr3A 337879500 337883864 4364 True 3632.00 7051 100.000 1 4365 2 chr3A.!!$R1 4364
1 TraesCS3A01G201800 chr3D 246326186 246329712 3526 False 1772.20 4340 95.733 548 4171 3 chr3D.!!$F1 3623
2 TraesCS3A01G201800 chr3B 331552517 331555758 3241 True 930.18 1522 93.157 557 3865 5 chr3B.!!$R2 3308

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
714 715 0.178861 TGCTTCTCCCCCTCCTCTTT 60.179 55.0 0.0 0.0 0.00 2.52 F
1285 1335 0.173708 GTCGTGGCCGAGAGAGATTT 59.826 55.0 0.0 0.0 45.26 2.17 F
1286 1336 0.895530 TCGTGGCCGAGAGAGATTTT 59.104 50.0 0.0 0.0 38.40 1.82 F
1514 1564 0.901580 CCAAGGGAAAGCCAGCATGT 60.902 55.0 0.0 0.0 35.15 3.21 F
2347 2471 0.916086 AGCGGATGGATGGTTGGTTA 59.084 50.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 2404 0.034089 AATGTTACCCCTGCTGCTCC 60.034 55.000 0.00 0.00 0.00 4.70 R
2362 2494 0.798159 CGTGCTGCATACACACACAT 59.202 50.000 17.29 0.00 37.93 3.21 R
2507 2639 2.350522 GATGGTGTTGAGATCGTTGCT 58.649 47.619 0.00 0.00 0.00 3.91 R
2596 2729 3.134127 GTTGTCCCTGCCATCCGC 61.134 66.667 0.00 0.00 38.31 5.54 R
4124 4300 0.034767 CATCTTGGCAGGGCTCTGAA 60.035 55.000 20.53 2.03 43.49 3.02 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
29 30 3.403558 GGCGCCTCCCCTTCTCTT 61.404 66.667 22.15 0.00 0.00 2.85
30 31 2.671682 GCGCCTCCCCTTCTCTTT 59.328 61.111 0.00 0.00 0.00 2.52
31 32 1.623542 GGCGCCTCCCCTTCTCTTTA 61.624 60.000 22.15 0.00 0.00 1.85
32 33 0.470341 GCGCCTCCCCTTCTCTTTAT 59.530 55.000 0.00 0.00 0.00 1.40
33 34 1.541452 GCGCCTCCCCTTCTCTTTATC 60.541 57.143 0.00 0.00 0.00 1.75
34 35 1.762957 CGCCTCCCCTTCTCTTTATCA 59.237 52.381 0.00 0.00 0.00 2.15
35 36 2.170607 CGCCTCCCCTTCTCTTTATCAA 59.829 50.000 0.00 0.00 0.00 2.57
36 37 3.370527 CGCCTCCCCTTCTCTTTATCAAA 60.371 47.826 0.00 0.00 0.00 2.69
37 38 4.600062 GCCTCCCCTTCTCTTTATCAAAA 58.400 43.478 0.00 0.00 0.00 2.44
38 39 4.642437 GCCTCCCCTTCTCTTTATCAAAAG 59.358 45.833 0.00 0.00 42.99 2.27
39 40 4.642437 CCTCCCCTTCTCTTTATCAAAAGC 59.358 45.833 0.00 0.00 41.64 3.51
40 41 4.261801 TCCCCTTCTCTTTATCAAAAGCG 58.738 43.478 0.00 0.00 41.64 4.68
41 42 3.181496 CCCCTTCTCTTTATCAAAAGCGC 60.181 47.826 0.00 0.00 41.64 5.92
42 43 3.440173 CCCTTCTCTTTATCAAAAGCGCA 59.560 43.478 11.47 0.00 41.64 6.09
43 44 4.406943 CCTTCTCTTTATCAAAAGCGCAC 58.593 43.478 11.47 0.00 41.64 5.34
44 45 4.406943 CTTCTCTTTATCAAAAGCGCACC 58.593 43.478 11.47 0.00 41.64 5.01
45 46 2.747446 TCTCTTTATCAAAAGCGCACCC 59.253 45.455 11.47 0.00 41.64 4.61
46 47 1.816224 TCTTTATCAAAAGCGCACCCC 59.184 47.619 11.47 0.00 41.64 4.95
47 48 0.523966 TTTATCAAAAGCGCACCCCG 59.476 50.000 11.47 0.00 40.75 5.73
48 49 0.321741 TTATCAAAAGCGCACCCCGA 60.322 50.000 11.47 0.00 40.02 5.14
49 50 1.022451 TATCAAAAGCGCACCCCGAC 61.022 55.000 11.47 0.00 40.02 4.79
50 51 4.038080 CAAAAGCGCACCCCGACC 62.038 66.667 11.47 0.00 40.02 4.79
69 70 2.041596 GGCCCCACCCCTACACTA 59.958 66.667 0.00 0.00 0.00 2.74
70 71 2.070650 GGCCCCACCCCTACACTAG 61.071 68.421 0.00 0.00 0.00 2.57
71 72 2.070650 GCCCCACCCCTACACTAGG 61.071 68.421 0.00 0.00 45.81 3.02
595 596 9.458727 CCATAAGCACCTATGAATAAGAATGAT 57.541 33.333 2.90 0.00 31.94 2.45
598 599 8.757982 AAGCACCTATGAATAAGAATGATTGT 57.242 30.769 0.00 0.00 0.00 2.71
599 600 8.388484 AGCACCTATGAATAAGAATGATTGTC 57.612 34.615 0.00 0.00 0.00 3.18
600 601 8.216423 AGCACCTATGAATAAGAATGATTGTCT 58.784 33.333 0.00 0.00 0.00 3.41
601 602 8.502387 GCACCTATGAATAAGAATGATTGTCTC 58.498 37.037 0.00 0.00 0.00 3.36
602 603 9.551734 CACCTATGAATAAGAATGATTGTCTCA 57.448 33.333 0.00 0.00 38.53 3.27
645 646 5.798125 ATGGTGATGGATATATAGCTCCG 57.202 43.478 0.00 0.00 34.05 4.63
699 700 4.070552 GCGGGAGGACGAGTGCTT 62.071 66.667 0.00 0.00 35.47 3.91
700 701 2.182030 CGGGAGGACGAGTGCTTC 59.818 66.667 0.00 0.00 35.47 3.86
701 702 2.344203 CGGGAGGACGAGTGCTTCT 61.344 63.158 3.11 0.00 35.47 2.85
702 703 1.513622 GGGAGGACGAGTGCTTCTC 59.486 63.158 3.11 0.00 39.62 2.87
703 704 1.513622 GGAGGACGAGTGCTTCTCC 59.486 63.158 0.00 0.00 39.84 3.71
704 705 1.513622 GAGGACGAGTGCTTCTCCC 59.486 63.158 0.00 1.89 39.84 4.30
712 713 1.306568 GTGCTTCTCCCCCTCCTCT 60.307 63.158 0.00 0.00 0.00 3.69
714 715 0.178861 TGCTTCTCCCCCTCCTCTTT 60.179 55.000 0.00 0.00 0.00 2.52
745 749 4.775253 TCCTCCTCCTTCTTCTTCTTCTTC 59.225 45.833 0.00 0.00 0.00 2.87
746 750 4.777366 CCTCCTCCTTCTTCTTCTTCTTCT 59.223 45.833 0.00 0.00 0.00 2.85
747 751 5.248248 CCTCCTCCTTCTTCTTCTTCTTCTT 59.752 44.000 0.00 0.00 0.00 2.52
748 752 6.353404 TCCTCCTTCTTCTTCTTCTTCTTC 57.647 41.667 0.00 0.00 0.00 2.87
749 753 6.081356 TCCTCCTTCTTCTTCTTCTTCTTCT 58.919 40.000 0.00 0.00 0.00 2.85
750 754 6.556874 TCCTCCTTCTTCTTCTTCTTCTTCTT 59.443 38.462 0.00 0.00 0.00 2.52
751 755 6.873605 CCTCCTTCTTCTTCTTCTTCTTCTTC 59.126 42.308 0.00 0.00 0.00 2.87
752 756 7.256296 CCTCCTTCTTCTTCTTCTTCTTCTTCT 60.256 40.741 0.00 0.00 0.00 2.85
753 757 8.028652 TCCTTCTTCTTCTTCTTCTTCTTCTT 57.971 34.615 0.00 0.00 0.00 2.52
856 860 1.352622 TGGCTGGAGTGGACAGGTTT 61.353 55.000 0.00 0.00 36.48 3.27
883 887 2.386779 GAGTACTAGTCCCAACTCCCC 58.613 57.143 11.09 0.00 36.92 4.81
947 951 1.078356 CACAGGAGCATCAGCAGCT 60.078 57.895 0.00 0.00 46.82 4.24
1239 1255 2.786495 CGATCGCCCTACTGCCAGT 61.786 63.158 0.26 1.54 0.00 4.00
1240 1256 1.227380 GATCGCCCTACTGCCAGTG 60.227 63.158 7.83 0.00 0.00 3.66
1241 1257 1.676678 GATCGCCCTACTGCCAGTGA 61.677 60.000 7.83 0.00 0.00 3.41
1242 1258 1.961180 ATCGCCCTACTGCCAGTGAC 61.961 60.000 7.83 0.00 0.00 3.67
1243 1259 2.942796 CGCCCTACTGCCAGTGACA 61.943 63.158 7.83 0.00 0.00 3.58
1244 1260 1.078848 GCCCTACTGCCAGTGACAG 60.079 63.158 7.83 4.72 41.08 3.51
1264 1280 1.804151 GTGTTGCTGCAATTCGGTCTA 59.196 47.619 19.11 0.00 0.00 2.59
1285 1335 0.173708 GTCGTGGCCGAGAGAGATTT 59.826 55.000 0.00 0.00 45.26 2.17
1286 1336 0.895530 TCGTGGCCGAGAGAGATTTT 59.104 50.000 0.00 0.00 38.40 1.82
1287 1337 1.275291 TCGTGGCCGAGAGAGATTTTT 59.725 47.619 0.00 0.00 38.40 1.94
1308 1358 3.541713 TTTTTGCGGTGGGTGGCC 61.542 61.111 0.00 0.00 0.00 5.36
1315 1365 3.319198 GGTGGGTGGCCGAGAGAA 61.319 66.667 0.00 0.00 0.00 2.87
1316 1366 2.747686 GTGGGTGGCCGAGAGAAA 59.252 61.111 0.00 0.00 0.00 2.52
1317 1367 1.299976 GTGGGTGGCCGAGAGAAAT 59.700 57.895 0.00 0.00 0.00 2.17
1514 1564 0.901580 CCAAGGGAAAGCCAGCATGT 60.902 55.000 0.00 0.00 35.15 3.21
1807 1857 2.608546 CGAGGTCCGTAGTCTACTCTTG 59.391 54.545 8.37 1.77 0.00 3.02
1808 1858 3.608796 GAGGTCCGTAGTCTACTCTTGT 58.391 50.000 8.37 0.00 0.00 3.16
1809 1859 3.345414 AGGTCCGTAGTCTACTCTTGTG 58.655 50.000 8.37 0.00 0.00 3.33
1810 1860 3.080319 GGTCCGTAGTCTACTCTTGTGT 58.920 50.000 8.37 0.00 0.00 3.72
1811 1861 3.126686 GGTCCGTAGTCTACTCTTGTGTC 59.873 52.174 8.37 0.00 0.00 3.67
1812 1862 4.002316 GTCCGTAGTCTACTCTTGTGTCT 58.998 47.826 8.37 0.00 0.00 3.41
1813 1863 4.455190 GTCCGTAGTCTACTCTTGTGTCTT 59.545 45.833 8.37 0.00 0.00 3.01
1831 1881 6.098266 TGTGTCTTGTCATGCCATACTACTAT 59.902 38.462 0.00 0.00 0.00 2.12
1945 2052 3.747854 TGGTTGCTGAATGAAATTGCA 57.252 38.095 0.00 0.00 36.07 4.08
2108 2226 1.975660 TGCCGTTGCTTTTACTCCTT 58.024 45.000 0.00 0.00 38.71 3.36
2110 2228 1.199327 GCCGTTGCTTTTACTCCTTCC 59.801 52.381 0.00 0.00 33.53 3.46
2280 2404 5.978814 AGGGAGTAGTAATTAACTGCAGTG 58.021 41.667 22.49 0.00 42.81 3.66
2302 2426 3.555966 GAGCAGCAGGGGTAACATTAAT 58.444 45.455 0.00 0.00 39.74 1.40
2347 2471 0.916086 AGCGGATGGATGGTTGGTTA 59.084 50.000 0.00 0.00 0.00 2.85
2362 2494 5.833667 TGGTTGGTTATTGAAATGGTGTGTA 59.166 36.000 0.00 0.00 0.00 2.90
2507 2639 1.448893 GTTATCGGCGGCACCTTCA 60.449 57.895 10.53 0.00 35.61 3.02
2595 2728 0.251386 TCTGGTCTCTGCTCTCGGTT 60.251 55.000 0.00 0.00 0.00 4.44
2596 2729 0.108898 CTGGTCTCTGCTCTCGGTTG 60.109 60.000 0.00 0.00 0.00 3.77
2697 2830 1.228154 GGACAACTCGCCCAGGTTT 60.228 57.895 0.00 0.00 0.00 3.27
2775 2908 7.640240 CGTCTGTCTGGTAAAAGAAAAGAAAAG 59.360 37.037 0.00 0.00 0.00 2.27
3055 3188 1.004394 GTGGGTTACTGGCCTAGCTTT 59.996 52.381 3.32 0.00 0.00 3.51
3514 3659 6.157123 ACAGTTTATTTTCCAACCAAAGGGAA 59.843 34.615 0.00 0.00 41.27 3.97
3528 3673 1.657804 AGGGAAGGTGGGTTCACTAG 58.342 55.000 0.00 0.00 38.48 2.57
3537 3689 5.128205 AGGTGGGTTCACTAGTTGTAAAAC 58.872 41.667 0.00 0.00 43.17 2.43
3551 3703 4.927267 TGTAAAACATGGGTCTCCTGAT 57.073 40.909 0.00 0.00 0.00 2.90
3559 3711 2.182827 TGGGTCTCCTGATCTCAACAG 58.817 52.381 0.00 0.00 35.43 3.16
3591 3743 6.806120 AGCTTCGTTTCAAAAACAATGTAC 57.194 33.333 3.72 0.00 0.00 2.90
3592 3744 6.560711 AGCTTCGTTTCAAAAACAATGTACT 58.439 32.000 0.00 0.00 0.00 2.73
3593 3745 7.699566 AGCTTCGTTTCAAAAACAATGTACTA 58.300 30.769 0.00 0.00 0.00 1.82
3594 3746 7.642586 AGCTTCGTTTCAAAAACAATGTACTAC 59.357 33.333 0.00 0.00 0.00 2.73
3595 3747 7.642586 GCTTCGTTTCAAAAACAATGTACTACT 59.357 33.333 0.00 0.00 0.00 2.57
3596 3748 8.829514 TTCGTTTCAAAAACAATGTACTACTG 57.170 30.769 0.00 0.00 0.00 2.74
3597 3749 7.976826 TCGTTTCAAAAACAATGTACTACTGT 58.023 30.769 0.00 0.00 0.00 3.55
3598 3750 9.096160 TCGTTTCAAAAACAATGTACTACTGTA 57.904 29.630 0.00 0.00 0.00 2.74
3599 3751 9.150653 CGTTTCAAAAACAATGTACTACTGTAC 57.849 33.333 0.00 0.00 46.74 2.90
3617 3769 4.404640 TGTACTAGTGTAGCCAACTCAGT 58.595 43.478 5.39 0.00 0.00 3.41
3618 3770 5.563592 TGTACTAGTGTAGCCAACTCAGTA 58.436 41.667 5.39 0.00 0.00 2.74
3619 3771 5.646793 TGTACTAGTGTAGCCAACTCAGTAG 59.353 44.000 5.39 0.00 39.54 2.57
3620 3772 4.664392 ACTAGTGTAGCCAACTCAGTAGT 58.336 43.478 0.00 0.00 40.93 2.73
3674 3834 4.392445 GCATCAATTGTTTATTGCCAAGCA 59.608 37.500 5.13 0.00 42.79 3.91
3724 3884 5.228665 GGTTCTTCACTTACTGGACAGTAC 58.771 45.833 11.46 0.41 43.02 2.73
3725 3885 5.010820 GGTTCTTCACTTACTGGACAGTACT 59.989 44.000 11.46 0.00 43.02 2.73
3729 3889 6.430308 TCTTCACTTACTGGACAGTACTGTAG 59.570 42.308 27.98 23.34 45.05 2.74
3757 3917 1.135972 ACATGAATCACGCTTCAACGC 60.136 47.619 0.00 0.00 38.55 4.84
3784 3944 2.731217 ACATTTGAAGCAAAGACGCAC 58.269 42.857 0.00 0.00 36.76 5.34
3800 3960 4.096003 ACATACCGCGCCTGCCTT 62.096 61.111 0.00 0.00 38.08 4.35
3802 3962 4.891727 ATACCGCGCCTGCCTTCG 62.892 66.667 0.00 0.00 38.08 3.79
3814 3974 0.178975 TGCCTTCGTGGGGAAACAAT 60.179 50.000 0.05 0.00 33.34 2.71
3855 4015 3.369381 CACGGAATGGAGCACTAGG 57.631 57.895 0.00 0.00 0.00 3.02
3865 4025 3.995636 TGGAGCACTAGGGTATTTCTCT 58.004 45.455 0.00 0.00 0.00 3.10
3877 4045 5.196165 AGGGTATTTCTCTGGAGTAGTAGGT 59.804 44.000 0.00 0.00 0.00 3.08
3888 4056 8.023021 TCTGGAGTAGTAGGTAGTATCGTTTA 57.977 38.462 0.00 0.00 0.00 2.01
3898 4066 9.578439 GTAGGTAGTATCGTTTATTTTGTCACT 57.422 33.333 0.00 0.00 0.00 3.41
3955 4129 1.753073 CTTCCATCCATGTTTCCCTGC 59.247 52.381 0.00 0.00 0.00 4.85
3957 4131 0.819582 CCATCCATGTTTCCCTGCAC 59.180 55.000 0.00 0.00 0.00 4.57
4019 4193 0.460284 CTATCACCTGGACCACACGC 60.460 60.000 0.00 0.00 0.00 5.34
4032 4206 1.598685 ACACGCCCCGTTCGAATTT 60.599 52.632 0.00 0.00 38.32 1.82
4037 4211 1.260561 CGCCCCGTTCGAATTTGATAG 59.739 52.381 0.00 0.00 0.00 2.08
4045 4219 4.025647 CGTTCGAATTTGATAGCTCCTTCC 60.026 45.833 0.00 0.00 0.00 3.46
4046 4220 3.717707 TCGAATTTGATAGCTCCTTCCG 58.282 45.455 0.00 0.00 0.00 4.30
4047 4221 3.132289 TCGAATTTGATAGCTCCTTCCGT 59.868 43.478 0.00 0.00 0.00 4.69
4051 4225 6.036735 CGAATTTGATAGCTCCTTCCGTTTTA 59.963 38.462 0.00 0.00 0.00 1.52
4052 4226 6.679327 ATTTGATAGCTCCTTCCGTTTTAC 57.321 37.500 0.00 0.00 0.00 2.01
4053 4227 5.416271 TTGATAGCTCCTTCCGTTTTACT 57.584 39.130 0.00 0.00 0.00 2.24
4054 4228 6.534475 TTGATAGCTCCTTCCGTTTTACTA 57.466 37.500 0.00 0.00 0.00 1.82
4055 4229 6.534475 TGATAGCTCCTTCCGTTTTACTAA 57.466 37.500 0.00 0.00 0.00 2.24
4096 4272 2.440539 AACGAGAAGGCACACTGTAG 57.559 50.000 0.00 0.00 0.00 2.74
4103 4279 3.580458 AGAAGGCACACTGTAGAGAATGT 59.420 43.478 0.00 0.00 0.00 2.71
4109 4285 5.874810 GGCACACTGTAGAGAATGTCATAAA 59.125 40.000 0.00 0.00 0.00 1.40
4124 4300 3.192633 GTCATAAACCCGATTTGCCAACT 59.807 43.478 0.00 0.00 0.00 3.16
4161 4337 6.543465 CCAAGATGTGAGAGCCAATTACAATA 59.457 38.462 0.00 0.00 0.00 1.90
4164 4340 7.512130 AGATGTGAGAGCCAATTACAATATGA 58.488 34.615 0.00 0.00 0.00 2.15
4165 4341 6.925610 TGTGAGAGCCAATTACAATATGAC 57.074 37.500 0.00 0.00 0.00 3.06
4166 4342 5.523552 TGTGAGAGCCAATTACAATATGACG 59.476 40.000 0.00 0.00 0.00 4.35
4167 4343 5.523916 GTGAGAGCCAATTACAATATGACGT 59.476 40.000 0.00 0.00 0.00 4.34
4173 4349 5.391523 GCCAATTACAATATGACGTGTGTGT 60.392 40.000 0.00 0.00 0.00 3.72
4174 4350 6.607689 CCAATTACAATATGACGTGTGTGTT 58.392 36.000 0.00 0.00 0.00 3.32
4175 4351 6.522855 CCAATTACAATATGACGTGTGTGTTG 59.477 38.462 0.00 0.00 0.00 3.33
4176 4352 7.294473 CAATTACAATATGACGTGTGTGTTGA 58.706 34.615 0.00 0.00 0.00 3.18
4177 4353 4.990543 ACAATATGACGTGTGTGTTGAG 57.009 40.909 0.00 0.00 0.00 3.02
4178 4354 4.377021 ACAATATGACGTGTGTGTTGAGT 58.623 39.130 0.00 0.00 0.00 3.41
4179 4355 5.534407 ACAATATGACGTGTGTGTTGAGTA 58.466 37.500 0.00 0.00 0.00 2.59
4180 4356 6.163476 ACAATATGACGTGTGTGTTGAGTAT 58.837 36.000 0.00 0.00 0.00 2.12
4181 4357 7.317390 ACAATATGACGTGTGTGTTGAGTATA 58.683 34.615 0.00 0.00 0.00 1.47
4182 4358 7.979537 ACAATATGACGTGTGTGTTGAGTATAT 59.020 33.333 0.00 0.00 0.00 0.86
4183 4359 9.458374 CAATATGACGTGTGTGTTGAGTATATA 57.542 33.333 0.00 0.00 0.00 0.86
4186 4362 8.942338 ATGACGTGTGTGTTGAGTATATATTT 57.058 30.769 0.00 0.00 0.00 1.40
4187 4363 8.766000 TGACGTGTGTGTTGAGTATATATTTT 57.234 30.769 0.00 0.00 0.00 1.82
4188 4364 8.652463 TGACGTGTGTGTTGAGTATATATTTTG 58.348 33.333 0.00 0.00 0.00 2.44
4189 4365 8.542497 ACGTGTGTGTTGAGTATATATTTTGT 57.458 30.769 0.00 0.00 0.00 2.83
4190 4366 8.440059 ACGTGTGTGTTGAGTATATATTTTGTG 58.560 33.333 0.00 0.00 0.00 3.33
4191 4367 8.440059 CGTGTGTGTTGAGTATATATTTTGTGT 58.560 33.333 0.00 0.00 0.00 3.72
4194 4370 9.061610 GTGTGTTGAGTATATATTTTGTGTTGC 57.938 33.333 0.00 0.00 0.00 4.17
4195 4371 8.787852 TGTGTTGAGTATATATTTTGTGTTGCA 58.212 29.630 0.00 0.00 0.00 4.08
4196 4372 9.787532 GTGTTGAGTATATATTTTGTGTTGCAT 57.212 29.630 0.00 0.00 0.00 3.96
4197 4373 9.786105 TGTTGAGTATATATTTTGTGTTGCATG 57.214 29.630 0.00 0.00 0.00 4.06
4198 4374 9.787532 GTTGAGTATATATTTTGTGTTGCATGT 57.212 29.630 0.00 0.00 0.00 3.21
4207 4383 7.739022 ATTTTGTGTTGCATGTATATTCGTG 57.261 32.000 0.00 0.00 0.00 4.35
4208 4384 5.871465 TTGTGTTGCATGTATATTCGTGT 57.129 34.783 3.81 0.00 0.00 4.49
4209 4385 5.871465 TGTGTTGCATGTATATTCGTGTT 57.129 34.783 3.81 0.00 0.00 3.32
4210 4386 5.626211 TGTGTTGCATGTATATTCGTGTTG 58.374 37.500 3.81 0.00 0.00 3.33
4211 4387 5.180304 TGTGTTGCATGTATATTCGTGTTGT 59.820 36.000 3.81 0.00 0.00 3.32
4212 4388 6.369065 TGTGTTGCATGTATATTCGTGTTGTA 59.631 34.615 3.81 0.00 0.00 2.41
4213 4389 6.899771 GTGTTGCATGTATATTCGTGTTGTAG 59.100 38.462 3.81 0.00 0.00 2.74
4214 4390 5.651172 TGCATGTATATTCGTGTTGTAGC 57.349 39.130 3.81 0.00 0.00 3.58
4215 4391 4.509970 TGCATGTATATTCGTGTTGTAGCC 59.490 41.667 3.81 0.00 0.00 3.93
4216 4392 4.084013 GCATGTATATTCGTGTTGTAGCCC 60.084 45.833 3.81 0.00 0.00 5.19
4217 4393 4.739587 TGTATATTCGTGTTGTAGCCCA 57.260 40.909 0.00 0.00 0.00 5.36
4218 4394 5.284861 TGTATATTCGTGTTGTAGCCCAT 57.715 39.130 0.00 0.00 0.00 4.00
4219 4395 5.294356 TGTATATTCGTGTTGTAGCCCATC 58.706 41.667 0.00 0.00 0.00 3.51
4220 4396 4.689612 ATATTCGTGTTGTAGCCCATCT 57.310 40.909 0.00 0.00 0.00 2.90
4221 4397 2.851263 TTCGTGTTGTAGCCCATCTT 57.149 45.000 0.00 0.00 0.00 2.40
4222 4398 2.380084 TCGTGTTGTAGCCCATCTTC 57.620 50.000 0.00 0.00 0.00 2.87
4223 4399 1.899814 TCGTGTTGTAGCCCATCTTCT 59.100 47.619 0.00 0.00 0.00 2.85
4224 4400 3.093814 TCGTGTTGTAGCCCATCTTCTA 58.906 45.455 0.00 0.00 0.00 2.10
4225 4401 3.119245 TCGTGTTGTAGCCCATCTTCTAC 60.119 47.826 0.00 0.00 36.58 2.59
4226 4402 3.119101 CGTGTTGTAGCCCATCTTCTACT 60.119 47.826 0.00 0.00 36.88 2.57
4227 4403 4.434520 GTGTTGTAGCCCATCTTCTACTC 58.565 47.826 0.00 0.00 36.88 2.59
4228 4404 3.451178 TGTTGTAGCCCATCTTCTACTCC 59.549 47.826 0.00 0.00 36.88 3.85
4229 4405 3.689872 TGTAGCCCATCTTCTACTCCT 57.310 47.619 0.00 0.00 36.88 3.69
4230 4406 3.300388 TGTAGCCCATCTTCTACTCCTG 58.700 50.000 0.00 0.00 36.88 3.86
4231 4407 2.559381 AGCCCATCTTCTACTCCTGT 57.441 50.000 0.00 0.00 0.00 4.00
4232 4408 3.689872 AGCCCATCTTCTACTCCTGTA 57.310 47.619 0.00 0.00 0.00 2.74
4233 4409 4.206244 AGCCCATCTTCTACTCCTGTAT 57.794 45.455 0.00 0.00 0.00 2.29
4234 4410 5.340891 AGCCCATCTTCTACTCCTGTATA 57.659 43.478 0.00 0.00 0.00 1.47
4235 4411 5.329399 AGCCCATCTTCTACTCCTGTATAG 58.671 45.833 0.00 0.00 0.00 1.31
4236 4412 5.081032 GCCCATCTTCTACTCCTGTATAGT 58.919 45.833 0.00 0.00 0.00 2.12
4237 4413 5.540719 GCCCATCTTCTACTCCTGTATAGTT 59.459 44.000 0.00 0.00 0.00 2.24
4238 4414 6.294843 GCCCATCTTCTACTCCTGTATAGTTC 60.295 46.154 0.00 0.00 0.00 3.01
4239 4415 6.778069 CCCATCTTCTACTCCTGTATAGTTCA 59.222 42.308 0.00 0.00 0.00 3.18
4240 4416 7.287927 CCCATCTTCTACTCCTGTATAGTTCAA 59.712 40.741 0.00 0.00 0.00 2.69
4241 4417 8.356657 CCATCTTCTACTCCTGTATAGTTCAAG 58.643 40.741 0.00 0.00 0.00 3.02
4242 4418 8.908903 CATCTTCTACTCCTGTATAGTTCAAGT 58.091 37.037 0.00 0.00 0.00 3.16
4243 4419 8.880991 TCTTCTACTCCTGTATAGTTCAAGTT 57.119 34.615 0.00 0.00 0.00 2.66
4244 4420 8.958506 TCTTCTACTCCTGTATAGTTCAAGTTC 58.041 37.037 0.00 0.00 0.00 3.01
4245 4421 8.645814 TTCTACTCCTGTATAGTTCAAGTTCA 57.354 34.615 0.00 0.00 0.00 3.18
4246 4422 8.282455 TCTACTCCTGTATAGTTCAAGTTCAG 57.718 38.462 0.00 0.00 0.00 3.02
4247 4423 8.107729 TCTACTCCTGTATAGTTCAAGTTCAGA 58.892 37.037 0.00 0.00 0.00 3.27
4248 4424 6.926313 ACTCCTGTATAGTTCAAGTTCAGAC 58.074 40.000 0.00 0.00 0.00 3.51
4249 4425 6.071278 ACTCCTGTATAGTTCAAGTTCAGACC 60.071 42.308 0.00 0.00 0.00 3.85
4250 4426 6.017192 TCCTGTATAGTTCAAGTTCAGACCT 58.983 40.000 0.00 0.00 0.00 3.85
4251 4427 7.179966 TCCTGTATAGTTCAAGTTCAGACCTA 58.820 38.462 0.00 0.00 0.00 3.08
4252 4428 7.839705 TCCTGTATAGTTCAAGTTCAGACCTAT 59.160 37.037 0.00 0.00 0.00 2.57
4253 4429 8.138712 CCTGTATAGTTCAAGTTCAGACCTATC 58.861 40.741 0.00 0.00 0.00 2.08
4254 4430 8.008513 TGTATAGTTCAAGTTCAGACCTATCC 57.991 38.462 0.00 0.00 0.00 2.59
4255 4431 7.839705 TGTATAGTTCAAGTTCAGACCTATCCT 59.160 37.037 0.00 0.00 0.00 3.24
4256 4432 5.413309 AGTTCAAGTTCAGACCTATCCTG 57.587 43.478 0.00 0.00 0.00 3.86
4257 4433 4.841246 AGTTCAAGTTCAGACCTATCCTGT 59.159 41.667 0.00 0.00 33.57 4.00
4258 4434 6.017192 AGTTCAAGTTCAGACCTATCCTGTA 58.983 40.000 0.00 0.00 33.57 2.74
4259 4435 6.497259 AGTTCAAGTTCAGACCTATCCTGTAA 59.503 38.462 0.00 0.00 33.57 2.41
4260 4436 7.181125 AGTTCAAGTTCAGACCTATCCTGTAAT 59.819 37.037 0.00 0.00 33.57 1.89
4261 4437 7.496346 TCAAGTTCAGACCTATCCTGTAATT 57.504 36.000 0.00 0.00 33.57 1.40
4262 4438 8.603898 TCAAGTTCAGACCTATCCTGTAATTA 57.396 34.615 0.00 0.00 33.57 1.40
4263 4439 9.213777 TCAAGTTCAGACCTATCCTGTAATTAT 57.786 33.333 0.00 0.00 33.57 1.28
4292 4468 1.656441 GCACAAGCACCTTGACTGG 59.344 57.895 11.56 0.69 43.42 4.00
4293 4469 1.799258 GCACAAGCACCTTGACTGGG 61.799 60.000 11.56 0.00 43.42 4.45
4294 4470 0.466189 CACAAGCACCTTGACTGGGT 60.466 55.000 11.56 0.00 43.42 4.51
4295 4471 0.258774 ACAAGCACCTTGACTGGGTT 59.741 50.000 11.56 0.00 43.42 4.11
4296 4472 0.954452 CAAGCACCTTGACTGGGTTC 59.046 55.000 0.00 0.00 43.42 3.62
4297 4473 0.178990 AAGCACCTTGACTGGGTTCC 60.179 55.000 0.00 0.00 34.44 3.62
4298 4474 1.603739 GCACCTTGACTGGGTTCCC 60.604 63.158 0.12 0.12 34.44 3.97
4299 4475 1.302511 CACCTTGACTGGGTTCCCG 60.303 63.158 3.27 1.34 34.44 5.14
4300 4476 2.351276 CCTTGACTGGGTTCCCGG 59.649 66.667 14.57 14.57 38.41 5.73
4310 4486 3.767806 GTTCCCGGTCCCCGTCTC 61.768 72.222 0.00 0.00 46.80 3.36
4316 4492 4.077180 GGTCCCCGTCTCCCTCCT 62.077 72.222 0.00 0.00 0.00 3.69
4317 4493 2.698075 GGTCCCCGTCTCCCTCCTA 61.698 68.421 0.00 0.00 0.00 2.94
4318 4494 1.455402 GTCCCCGTCTCCCTCCTAC 60.455 68.421 0.00 0.00 0.00 3.18
4319 4495 2.518825 CCCCGTCTCCCTCCTACG 60.519 72.222 0.00 0.00 36.42 3.51
4320 4496 2.593978 CCCGTCTCCCTCCTACGA 59.406 66.667 0.00 0.00 38.89 3.43
4321 4497 1.526455 CCCGTCTCCCTCCTACGAG 60.526 68.421 0.00 0.00 38.89 4.18
4331 4507 0.457851 CTCCTACGAGGTTGAGCTGG 59.542 60.000 0.00 0.00 36.53 4.85
4332 4508 1.153549 CCTACGAGGTTGAGCTGGC 60.154 63.158 0.00 0.00 0.00 4.85
4333 4509 1.517257 CTACGAGGTTGAGCTGGCG 60.517 63.158 0.00 0.00 0.00 5.69
4334 4510 2.890847 CTACGAGGTTGAGCTGGCGG 62.891 65.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.623542 TAAAGAGAAGGGGAGGCGCC 61.624 60.000 21.89 21.89 36.67 6.53
13 14 0.470341 ATAAAGAGAAGGGGAGGCGC 59.530 55.000 0.00 0.00 0.00 6.53
14 15 1.762957 TGATAAAGAGAAGGGGAGGCG 59.237 52.381 0.00 0.00 0.00 5.52
15 16 3.933861 TTGATAAAGAGAAGGGGAGGC 57.066 47.619 0.00 0.00 0.00 4.70
16 17 4.642437 GCTTTTGATAAAGAGAAGGGGAGG 59.358 45.833 2.02 0.00 42.78 4.30
17 18 4.333926 CGCTTTTGATAAAGAGAAGGGGAG 59.666 45.833 2.02 0.00 41.87 4.30
18 19 4.261801 CGCTTTTGATAAAGAGAAGGGGA 58.738 43.478 2.02 0.00 41.87 4.81
19 20 3.181496 GCGCTTTTGATAAAGAGAAGGGG 60.181 47.826 0.00 0.00 41.87 4.79
20 21 3.440173 TGCGCTTTTGATAAAGAGAAGGG 59.560 43.478 9.73 0.00 41.87 3.95
21 22 4.406943 GTGCGCTTTTGATAAAGAGAAGG 58.593 43.478 9.73 0.00 41.87 3.46
22 23 4.406943 GGTGCGCTTTTGATAAAGAGAAG 58.593 43.478 9.73 0.00 41.87 2.85
23 24 3.190535 GGGTGCGCTTTTGATAAAGAGAA 59.809 43.478 9.73 0.00 41.87 2.87
24 25 2.747446 GGGTGCGCTTTTGATAAAGAGA 59.253 45.455 9.73 0.00 41.87 3.10
25 26 2.159379 GGGGTGCGCTTTTGATAAAGAG 60.159 50.000 9.73 0.01 42.78 2.85
26 27 1.816224 GGGGTGCGCTTTTGATAAAGA 59.184 47.619 9.73 0.00 42.78 2.52
27 28 1.467374 CGGGGTGCGCTTTTGATAAAG 60.467 52.381 9.73 0.00 42.97 1.85
28 29 0.523966 CGGGGTGCGCTTTTGATAAA 59.476 50.000 9.73 0.00 0.00 1.40
29 30 0.321741 TCGGGGTGCGCTTTTGATAA 60.322 50.000 9.73 0.00 0.00 1.75
30 31 1.022451 GTCGGGGTGCGCTTTTGATA 61.022 55.000 9.73 0.00 0.00 2.15
31 32 2.033448 TCGGGGTGCGCTTTTGAT 59.967 55.556 9.73 0.00 0.00 2.57
32 33 2.975799 GTCGGGGTGCGCTTTTGA 60.976 61.111 9.73 0.00 0.00 2.69
33 34 4.038080 GGTCGGGGTGCGCTTTTG 62.038 66.667 9.73 0.00 0.00 2.44
51 52 3.988050 TAGTGTAGGGGTGGGGCCG 62.988 68.421 0.00 0.00 38.44 6.13
52 53 2.041596 TAGTGTAGGGGTGGGGCC 59.958 66.667 0.00 0.00 0.00 5.80
53 54 2.070650 CCTAGTGTAGGGGTGGGGC 61.071 68.421 0.00 0.00 42.42 5.80
54 55 0.398664 CTCCTAGTGTAGGGGTGGGG 60.399 65.000 0.08 0.00 46.24 4.96
55 56 0.635009 TCTCCTAGTGTAGGGGTGGG 59.365 60.000 0.00 0.00 46.94 4.61
56 57 2.074729 CTCTCCTAGTGTAGGGGTGG 57.925 60.000 0.00 0.00 46.94 4.61
57 58 1.569548 TCCTCTCCTAGTGTAGGGGTG 59.430 57.143 0.00 0.00 46.94 4.61
58 59 1.854280 CTCCTCTCCTAGTGTAGGGGT 59.146 57.143 0.00 0.00 46.94 4.95
60 61 5.327737 AATACTCCTCTCCTAGTGTAGGG 57.672 47.826 0.08 0.00 46.24 3.53
606 607 8.917088 CCATCACCATTCTTATTCATAGGTTTT 58.083 33.333 0.00 0.00 0.00 2.43
607 608 8.281531 TCCATCACCATTCTTATTCATAGGTTT 58.718 33.333 0.00 0.00 0.00 3.27
608 609 7.815383 TCCATCACCATTCTTATTCATAGGTT 58.185 34.615 0.00 0.00 0.00 3.50
609 610 7.392766 TCCATCACCATTCTTATTCATAGGT 57.607 36.000 0.00 0.00 0.00 3.08
618 619 8.928448 GGAGCTATATATCCATCACCATTCTTA 58.072 37.037 0.00 0.00 35.54 2.10
619 620 7.418368 CGGAGCTATATATCCATCACCATTCTT 60.418 40.741 3.79 0.00 35.14 2.52
620 621 6.041409 CGGAGCTATATATCCATCACCATTCT 59.959 42.308 3.79 0.00 35.14 2.40
621 622 6.183360 ACGGAGCTATATATCCATCACCATTC 60.183 42.308 3.79 0.00 35.14 2.67
622 623 5.663106 ACGGAGCTATATATCCATCACCATT 59.337 40.000 3.79 0.00 35.14 3.16
623 624 5.211973 ACGGAGCTATATATCCATCACCAT 58.788 41.667 3.79 0.00 35.14 3.55
624 625 4.610333 ACGGAGCTATATATCCATCACCA 58.390 43.478 3.79 0.00 35.14 4.17
625 626 4.890581 AGACGGAGCTATATATCCATCACC 59.109 45.833 2.27 0.00 35.14 4.02
626 627 5.277586 CGAGACGGAGCTATATATCCATCAC 60.278 48.000 2.27 0.00 35.14 3.06
660 661 1.118838 AGCAAAGATCTCTCCCTCCG 58.881 55.000 0.00 0.00 0.00 4.63
699 700 1.398799 AGAGAAAGAGGAGGGGGAGA 58.601 55.000 0.00 0.00 0.00 3.71
700 701 2.262266 AAGAGAAAGAGGAGGGGGAG 57.738 55.000 0.00 0.00 0.00 4.30
701 702 2.114506 AGAAAGAGAAAGAGGAGGGGGA 59.885 50.000 0.00 0.00 0.00 4.81
702 703 2.503765 GAGAAAGAGAAAGAGGAGGGGG 59.496 54.545 0.00 0.00 0.00 5.40
703 704 2.503765 GGAGAAAGAGAAAGAGGAGGGG 59.496 54.545 0.00 0.00 0.00 4.79
704 705 3.449918 AGGAGAAAGAGAAAGAGGAGGG 58.550 50.000 0.00 0.00 0.00 4.30
712 713 4.757692 AGAAGGAGGAGGAGAAAGAGAAA 58.242 43.478 0.00 0.00 0.00 2.52
714 715 4.045334 AGAAGAAGGAGGAGGAGAAAGAGA 59.955 45.833 0.00 0.00 0.00 3.10
745 749 5.539955 TCAATCCCTTTTCCCAAAGAAGAAG 59.460 40.000 0.00 0.00 41.97 2.85
746 750 5.463154 TCAATCCCTTTTCCCAAAGAAGAA 58.537 37.500 0.00 0.00 41.97 2.52
747 751 5.073437 TCAATCCCTTTTCCCAAAGAAGA 57.927 39.130 0.00 0.00 41.97 2.87
748 752 6.168389 CAATCAATCCCTTTTCCCAAAGAAG 58.832 40.000 0.00 0.00 41.97 2.85
749 753 5.512921 GCAATCAATCCCTTTTCCCAAAGAA 60.513 40.000 0.00 0.00 41.97 2.52
750 754 4.020307 GCAATCAATCCCTTTTCCCAAAGA 60.020 41.667 0.00 0.00 41.97 2.52
751 755 4.256110 GCAATCAATCCCTTTTCCCAAAG 58.744 43.478 0.00 0.00 39.45 2.77
752 756 3.306641 CGCAATCAATCCCTTTTCCCAAA 60.307 43.478 0.00 0.00 0.00 3.28
753 757 2.233431 CGCAATCAATCCCTTTTCCCAA 59.767 45.455 0.00 0.00 0.00 4.12
810 814 3.126225 GTGGCAGCTCAGCTCAGC 61.126 66.667 0.00 0.00 36.40 4.26
856 860 1.180029 GGGACTAGTACTCGCCACAA 58.820 55.000 4.77 0.00 0.00 3.33
883 887 4.712425 GCCTGCCGCTTGTTGCTG 62.712 66.667 0.00 0.00 40.11 4.41
969 973 0.761187 TCTGTGCCTGTGAAGCTTCT 59.239 50.000 26.09 0.00 0.00 2.85
1140 1156 2.754658 CGCCTGTACCTCCGGAGT 60.755 66.667 29.25 19.19 0.00 3.85
1243 1259 0.593128 GACCGAATTGCAGCAACACT 59.407 50.000 10.85 0.00 0.00 3.55
1244 1260 0.593128 AGACCGAATTGCAGCAACAC 59.407 50.000 10.85 6.65 0.00 3.32
1264 1280 2.559922 ATCTCTCTCGGCCACGACCT 62.560 60.000 2.24 0.00 45.59 3.85
1291 1341 3.541713 GGCCACCCACCGCAAAAA 61.542 61.111 0.00 0.00 0.00 1.94
1298 1348 2.198304 ATTTCTCTCGGCCACCCACC 62.198 60.000 2.24 0.00 0.00 4.61
1299 1349 0.322546 AATTTCTCTCGGCCACCCAC 60.323 55.000 2.24 0.00 0.00 4.61
1300 1350 1.281419 TAATTTCTCTCGGCCACCCA 58.719 50.000 2.24 0.00 0.00 4.51
1301 1351 2.014857 GTTAATTTCTCTCGGCCACCC 58.985 52.381 2.24 0.00 0.00 4.61
1302 1352 2.014857 GGTTAATTTCTCTCGGCCACC 58.985 52.381 2.24 0.00 0.00 4.61
1303 1353 1.664151 CGGTTAATTTCTCTCGGCCAC 59.336 52.381 2.24 0.00 0.00 5.01
1304 1354 1.276989 ACGGTTAATTTCTCTCGGCCA 59.723 47.619 2.24 0.00 0.00 5.36
1305 1355 1.664151 CACGGTTAATTTCTCTCGGCC 59.336 52.381 0.00 0.00 0.00 6.13
1306 1356 1.664151 CCACGGTTAATTTCTCTCGGC 59.336 52.381 0.00 0.00 0.00 5.54
1307 1357 2.671396 CACCACGGTTAATTTCTCTCGG 59.329 50.000 0.00 0.00 0.00 4.63
1308 1358 2.093783 GCACCACGGTTAATTTCTCTCG 59.906 50.000 0.00 0.00 0.00 4.04
1309 1359 3.335579 AGCACCACGGTTAATTTCTCTC 58.664 45.455 0.00 0.00 0.00 3.20
1310 1360 3.335579 GAGCACCACGGTTAATTTCTCT 58.664 45.455 0.00 0.00 0.00 3.10
1311 1361 2.093783 CGAGCACCACGGTTAATTTCTC 59.906 50.000 0.00 0.00 0.00 2.87
1312 1362 2.073816 CGAGCACCACGGTTAATTTCT 58.926 47.619 0.00 0.00 0.00 2.52
1313 1363 1.802365 ACGAGCACCACGGTTAATTTC 59.198 47.619 0.00 0.00 34.93 2.17
1314 1364 1.886886 ACGAGCACCACGGTTAATTT 58.113 45.000 0.00 0.00 34.93 1.82
1315 1365 1.533731 CAACGAGCACCACGGTTAATT 59.466 47.619 0.00 0.00 34.93 1.40
1316 1366 1.153353 CAACGAGCACCACGGTTAAT 58.847 50.000 0.00 0.00 34.93 1.40
1317 1367 0.881159 CCAACGAGCACCACGGTTAA 60.881 55.000 0.00 0.00 34.93 2.01
1514 1564 9.667107 CCAAGACTTGGTTAACTAATCAATCTA 57.333 33.333 23.92 0.00 45.93 1.98
1807 1857 4.759782 AGTAGTATGGCATGACAAGACAC 58.240 43.478 4.70 8.15 0.00 3.67
1808 1858 6.731292 ATAGTAGTATGGCATGACAAGACA 57.269 37.500 4.70 0.00 0.00 3.41
1809 1859 7.887381 ACTATAGTAGTATGGCATGACAAGAC 58.113 38.462 4.70 7.15 37.23 3.01
1810 1860 9.011095 GTACTATAGTAGTATGGCATGACAAGA 57.989 37.037 4.70 0.00 42.68 3.02
1811 1861 9.015367 AGTACTATAGTAGTATGGCATGACAAG 57.985 37.037 17.07 0.00 42.68 3.16
1812 1862 8.935614 AGTACTATAGTAGTATGGCATGACAA 57.064 34.615 17.07 0.00 42.68 3.18
1813 1863 8.935614 AAGTACTATAGTAGTATGGCATGACA 57.064 34.615 18.53 2.18 42.68 3.58
1945 2052 2.717639 AAGCATCATTTAGCGGAGGT 57.282 45.000 0.00 0.00 44.89 3.85
2108 2226 0.461548 CTCTGCGGATGTTAGCTGGA 59.538 55.000 0.00 0.00 33.89 3.86
2110 2228 1.850377 CTCTCTGCGGATGTTAGCTG 58.150 55.000 0.00 0.00 0.00 4.24
2210 2334 9.498307 ACACTACGTTAATGTCAAAAAGAAAAG 57.502 29.630 2.93 0.00 0.00 2.27
2280 2404 0.034089 AATGTTACCCCTGCTGCTCC 60.034 55.000 0.00 0.00 0.00 4.70
2341 2465 7.014711 ACACATACACACCATTTCAATAACCAA 59.985 33.333 0.00 0.00 0.00 3.67
2347 2471 5.301551 ACACACACATACACACCATTTCAAT 59.698 36.000 0.00 0.00 0.00 2.57
2362 2494 0.798159 CGTGCTGCATACACACACAT 59.202 50.000 17.29 0.00 37.93 3.21
2507 2639 2.350522 GATGGTGTTGAGATCGTTGCT 58.649 47.619 0.00 0.00 0.00 3.91
2596 2729 3.134127 GTTGTCCCTGCCATCCGC 61.134 66.667 0.00 0.00 38.31 5.54
2794 2927 9.739276 AATTCAAACCCTTTTCTTTTCTTTTCT 57.261 25.926 0.00 0.00 0.00 2.52
3310 3443 4.213513 CGTAGTAGAAGTAGTTCCCCCAT 58.786 47.826 6.68 0.00 32.48 4.00
3433 3578 7.679638 GCACAACTGTAGAAGATGAACAACTTT 60.680 37.037 0.00 0.00 33.09 2.66
3480 3625 6.476243 TGGAAAATAAACTGTAGAAGACGC 57.524 37.500 0.00 0.00 0.00 5.19
3514 3659 5.128205 GTTTTACAACTAGTGAACCCACCT 58.872 41.667 0.00 0.00 44.22 4.00
3528 3673 4.394729 TCAGGAGACCCATGTTTTACAAC 58.605 43.478 0.00 0.00 33.88 3.32
3537 3689 2.502947 TGTTGAGATCAGGAGACCCATG 59.497 50.000 0.00 0.00 33.88 3.66
3551 3703 4.320275 CGAAGCTACACTACACTGTTGAGA 60.320 45.833 0.00 0.00 0.00 3.27
3559 3711 5.646467 TTTGAAACGAAGCTACACTACAC 57.354 39.130 0.00 0.00 0.00 2.90
3591 3743 5.646793 TGAGTTGGCTACACTAGTACAGTAG 59.353 44.000 12.39 12.39 34.98 2.57
3592 3744 5.563592 TGAGTTGGCTACACTAGTACAGTA 58.436 41.667 0.00 0.00 34.98 2.74
3593 3745 4.404640 TGAGTTGGCTACACTAGTACAGT 58.595 43.478 0.00 0.00 38.32 3.55
3594 3746 4.459685 ACTGAGTTGGCTACACTAGTACAG 59.540 45.833 0.00 0.00 0.00 2.74
3595 3747 4.404640 ACTGAGTTGGCTACACTAGTACA 58.595 43.478 0.00 0.00 0.00 2.90
3596 3748 5.647225 ACTACTGAGTTGGCTACACTAGTAC 59.353 44.000 0.00 0.00 28.61 2.73
3597 3749 5.813383 ACTACTGAGTTGGCTACACTAGTA 58.187 41.667 0.00 6.03 28.61 1.82
3598 3750 4.664392 ACTACTGAGTTGGCTACACTAGT 58.336 43.478 1.24 5.23 28.61 2.57
3599 3751 5.881443 AGTACTACTGAGTTGGCTACACTAG 59.119 44.000 0.00 0.00 37.10 2.57
3600 3752 5.813383 AGTACTACTGAGTTGGCTACACTA 58.187 41.667 0.00 0.00 37.10 2.74
3601 3753 4.664392 AGTACTACTGAGTTGGCTACACT 58.336 43.478 0.00 0.00 37.10 3.55
3617 3769 6.892485 TGTAGTATGTGCTGGAGTAGTACTA 58.108 40.000 1.88 0.00 41.93 1.82
3618 3770 5.752650 TGTAGTATGTGCTGGAGTAGTACT 58.247 41.667 1.37 1.37 41.93 2.73
3619 3771 6.439599 CATGTAGTATGTGCTGGAGTAGTAC 58.560 44.000 0.00 0.00 41.78 2.73
3620 3772 5.009710 GCATGTAGTATGTGCTGGAGTAGTA 59.990 44.000 0.00 0.00 36.02 1.82
3674 3834 2.029828 AGAGAGACACAACGAGCGATTT 60.030 45.455 0.00 0.00 0.00 2.17
3724 3884 6.851837 GCGTGATTCATGTACTACTACTACAG 59.148 42.308 7.67 0.00 0.00 2.74
3725 3885 6.541278 AGCGTGATTCATGTACTACTACTACA 59.459 38.462 7.67 0.00 0.00 2.74
3729 3889 6.263344 TGAAGCGTGATTCATGTACTACTAC 58.737 40.000 7.67 0.00 34.31 2.73
3757 3917 4.025480 GTCTTTGCTTCAAATGTTGCTTGG 60.025 41.667 0.00 0.00 32.70 3.61
3784 3944 3.272334 GAAGGCAGGCGCGGTATG 61.272 66.667 8.83 0.00 39.92 2.39
3796 3956 0.526211 GATTGTTTCCCCACGAAGGC 59.474 55.000 0.00 0.00 35.39 4.35
3800 3960 2.166829 CAATGGATTGTTTCCCCACGA 58.833 47.619 0.00 0.00 44.77 4.35
3802 3962 4.824479 AATCAATGGATTGTTTCCCCAC 57.176 40.909 0.00 0.00 44.77 4.61
3814 3974 1.031571 GGTCTGGCGCAATCAATGGA 61.032 55.000 10.83 0.00 0.00 3.41
3855 4015 7.289310 ACTACCTACTACTCCAGAGAAATACC 58.711 42.308 0.70 0.00 0.00 2.73
3865 4025 9.632638 AAATAAACGATACTACCTACTACTCCA 57.367 33.333 0.00 0.00 0.00 3.86
3877 4045 7.762615 CCCTGAGTGACAAAATAAACGATACTA 59.237 37.037 0.00 0.00 0.00 1.82
3888 4056 1.548582 CCTGGCCCTGAGTGACAAAAT 60.549 52.381 0.00 0.00 0.00 1.82
3896 4064 1.142688 ACAAATCCCTGGCCCTGAGT 61.143 55.000 0.00 0.00 0.00 3.41
3898 4066 1.691219 GACAAATCCCTGGCCCTGA 59.309 57.895 0.00 0.00 0.00 3.86
3955 4129 4.931601 TCAGTAGATGCTTGTGCTTTAGTG 59.068 41.667 0.00 0.00 40.48 2.74
3957 4131 6.314648 TGAATCAGTAGATGCTTGTGCTTTAG 59.685 38.462 0.00 0.00 40.48 1.85
4019 4193 2.544267 GAGCTATCAAATTCGAACGGGG 59.456 50.000 0.00 0.00 0.00 5.73
4032 4206 6.534475 TTAGTAAAACGGAAGGAGCTATCA 57.466 37.500 0.00 0.00 0.00 2.15
4096 4272 5.273944 GCAAATCGGGTTTATGACATTCTC 58.726 41.667 0.00 0.00 0.00 2.87
4103 4279 3.426615 AGTTGGCAAATCGGGTTTATGA 58.573 40.909 0.00 0.00 0.00 2.15
4109 4285 1.202879 TCTGAAGTTGGCAAATCGGGT 60.203 47.619 17.99 0.00 0.00 5.28
4124 4300 0.034767 CATCTTGGCAGGGCTCTGAA 60.035 55.000 20.53 2.03 43.49 3.02
4161 4337 8.942338 AAATATATACTCAACACACACGTCAT 57.058 30.769 0.00 0.00 0.00 3.06
4164 4340 8.440059 CACAAAATATATACTCAACACACACGT 58.560 33.333 0.00 0.00 0.00 4.49
4165 4341 8.440059 ACACAAAATATATACTCAACACACACG 58.560 33.333 0.00 0.00 0.00 4.49
4181 4357 9.449550 CACGAATATACATGCAACACAAAATAT 57.550 29.630 0.00 0.00 0.00 1.28
4182 4358 8.454894 ACACGAATATACATGCAACACAAAATA 58.545 29.630 0.00 0.00 0.00 1.40
4183 4359 7.312154 ACACGAATATACATGCAACACAAAAT 58.688 30.769 0.00 0.00 0.00 1.82
4184 4360 6.673106 ACACGAATATACATGCAACACAAAA 58.327 32.000 0.00 0.00 0.00 2.44
4185 4361 6.247727 ACACGAATATACATGCAACACAAA 57.752 33.333 0.00 0.00 0.00 2.83
4186 4362 5.871465 ACACGAATATACATGCAACACAA 57.129 34.783 0.00 0.00 0.00 3.33
4187 4363 5.180304 ACAACACGAATATACATGCAACACA 59.820 36.000 0.00 0.00 0.00 3.72
4188 4364 5.627172 ACAACACGAATATACATGCAACAC 58.373 37.500 0.00 0.00 0.00 3.32
4189 4365 5.871465 ACAACACGAATATACATGCAACA 57.129 34.783 0.00 0.00 0.00 3.33
4190 4366 5.901884 GCTACAACACGAATATACATGCAAC 59.098 40.000 0.00 0.00 0.00 4.17
4191 4367 5.007234 GGCTACAACACGAATATACATGCAA 59.993 40.000 0.00 0.00 0.00 4.08
4192 4368 4.509970 GGCTACAACACGAATATACATGCA 59.490 41.667 0.00 0.00 0.00 3.96
4193 4369 4.084013 GGGCTACAACACGAATATACATGC 60.084 45.833 0.00 0.00 0.00 4.06
4194 4370 5.053811 TGGGCTACAACACGAATATACATG 58.946 41.667 0.00 0.00 0.00 3.21
4195 4371 5.284861 TGGGCTACAACACGAATATACAT 57.715 39.130 0.00 0.00 0.00 2.29
4196 4372 4.739587 TGGGCTACAACACGAATATACA 57.260 40.909 0.00 0.00 0.00 2.29
4197 4373 5.539048 AGATGGGCTACAACACGAATATAC 58.461 41.667 0.00 0.00 0.00 1.47
4198 4374 5.801531 AGATGGGCTACAACACGAATATA 57.198 39.130 0.00 0.00 0.00 0.86
4199 4375 4.689612 AGATGGGCTACAACACGAATAT 57.310 40.909 0.00 0.00 0.00 1.28
4200 4376 4.161565 AGAAGATGGGCTACAACACGAATA 59.838 41.667 0.00 0.00 0.00 1.75
4201 4377 3.055094 AGAAGATGGGCTACAACACGAAT 60.055 43.478 0.00 0.00 0.00 3.34
4202 4378 2.301870 AGAAGATGGGCTACAACACGAA 59.698 45.455 0.00 0.00 0.00 3.85
4203 4379 1.899814 AGAAGATGGGCTACAACACGA 59.100 47.619 0.00 0.00 0.00 4.35
4204 4380 2.386661 AGAAGATGGGCTACAACACG 57.613 50.000 0.00 0.00 0.00 4.49
4205 4381 4.434520 GAGTAGAAGATGGGCTACAACAC 58.565 47.826 0.00 0.00 39.48 3.32
4206 4382 3.451178 GGAGTAGAAGATGGGCTACAACA 59.549 47.826 0.00 0.00 39.48 3.33
4207 4383 3.707102 AGGAGTAGAAGATGGGCTACAAC 59.293 47.826 0.00 0.00 39.48 3.32
4208 4384 3.706594 CAGGAGTAGAAGATGGGCTACAA 59.293 47.826 0.00 0.00 39.48 2.41
4209 4385 3.300388 CAGGAGTAGAAGATGGGCTACA 58.700 50.000 0.00 0.00 39.48 2.74
4210 4386 3.301274 ACAGGAGTAGAAGATGGGCTAC 58.699 50.000 0.00 0.00 37.77 3.58
4211 4387 3.689872 ACAGGAGTAGAAGATGGGCTA 57.310 47.619 0.00 0.00 0.00 3.93
4212 4388 2.559381 ACAGGAGTAGAAGATGGGCT 57.441 50.000 0.00 0.00 0.00 5.19
4213 4389 5.081032 ACTATACAGGAGTAGAAGATGGGC 58.919 45.833 0.00 0.00 32.86 5.36
4214 4390 6.778069 TGAACTATACAGGAGTAGAAGATGGG 59.222 42.308 0.00 0.00 32.86 4.00
4215 4391 7.825331 TGAACTATACAGGAGTAGAAGATGG 57.175 40.000 0.00 0.00 32.86 3.51
4216 4392 8.908903 ACTTGAACTATACAGGAGTAGAAGATG 58.091 37.037 0.00 0.00 32.86 2.90
4217 4393 9.482175 AACTTGAACTATACAGGAGTAGAAGAT 57.518 33.333 0.00 0.00 32.86 2.40
4218 4394 8.880991 AACTTGAACTATACAGGAGTAGAAGA 57.119 34.615 0.00 0.00 32.86 2.87
4219 4395 8.740906 TGAACTTGAACTATACAGGAGTAGAAG 58.259 37.037 0.00 0.00 32.86 2.85
4220 4396 8.645814 TGAACTTGAACTATACAGGAGTAGAA 57.354 34.615 0.00 0.00 32.86 2.10
4221 4397 8.107729 TCTGAACTTGAACTATACAGGAGTAGA 58.892 37.037 0.00 0.00 32.86 2.59
4222 4398 8.185505 GTCTGAACTTGAACTATACAGGAGTAG 58.814 40.741 0.00 0.00 32.86 2.57
4223 4399 7.122353 GGTCTGAACTTGAACTATACAGGAGTA 59.878 40.741 0.00 0.00 34.10 2.59
4224 4400 6.071278 GGTCTGAACTTGAACTATACAGGAGT 60.071 42.308 0.00 0.00 0.00 3.85
4225 4401 6.153680 AGGTCTGAACTTGAACTATACAGGAG 59.846 42.308 0.00 0.00 28.44 3.69
4226 4402 6.017192 AGGTCTGAACTTGAACTATACAGGA 58.983 40.000 0.00 0.00 28.44 3.86
4227 4403 6.287589 AGGTCTGAACTTGAACTATACAGG 57.712 41.667 0.00 0.00 28.44 4.00
4228 4404 8.138712 GGATAGGTCTGAACTTGAACTATACAG 58.861 40.741 0.00 0.00 42.49 2.74
4229 4405 7.839705 AGGATAGGTCTGAACTTGAACTATACA 59.160 37.037 0.00 0.00 43.86 2.29
4230 4406 8.138712 CAGGATAGGTCTGAACTTGAACTATAC 58.861 40.741 0.00 3.52 42.49 1.47
4231 4407 7.839705 ACAGGATAGGTCTGAACTTGAACTATA 59.160 37.037 0.00 0.00 42.49 1.31
4232 4408 6.670027 ACAGGATAGGTCTGAACTTGAACTAT 59.330 38.462 0.00 1.49 44.37 2.12
4233 4409 6.017192 ACAGGATAGGTCTGAACTTGAACTA 58.983 40.000 0.00 0.00 38.00 2.24
4234 4410 4.841246 ACAGGATAGGTCTGAACTTGAACT 59.159 41.667 0.00 0.00 36.22 3.01
4235 4411 5.153950 ACAGGATAGGTCTGAACTTGAAC 57.846 43.478 0.00 0.00 36.22 3.18
4236 4412 6.928348 TTACAGGATAGGTCTGAACTTGAA 57.072 37.500 0.00 0.00 36.22 2.69
4237 4413 7.496346 AATTACAGGATAGGTCTGAACTTGA 57.504 36.000 0.00 0.00 36.22 3.02
4274 4450 1.656441 CCAGTCAAGGTGCTTGTGC 59.344 57.895 0.00 0.00 41.66 4.57
4275 4451 0.466189 ACCCAGTCAAGGTGCTTGTG 60.466 55.000 0.00 0.00 41.66 3.33
4276 4452 0.258774 AACCCAGTCAAGGTGCTTGT 59.741 50.000 0.00 0.00 41.66 3.16
4277 4453 0.954452 GAACCCAGTCAAGGTGCTTG 59.046 55.000 0.00 0.00 42.25 4.01
4278 4454 0.178990 GGAACCCAGTCAAGGTGCTT 60.179 55.000 0.00 0.00 37.78 3.91
4279 4455 1.456287 GGAACCCAGTCAAGGTGCT 59.544 57.895 0.00 0.00 37.78 4.40
4280 4456 4.081050 GGAACCCAGTCAAGGTGC 57.919 61.111 0.00 0.00 37.78 5.01
4300 4476 1.455402 GTAGGAGGGAGACGGGGAC 60.455 68.421 0.00 0.00 0.00 4.46
4301 4477 3.013631 GTAGGAGGGAGACGGGGA 58.986 66.667 0.00 0.00 0.00 4.81
4302 4478 2.518825 CGTAGGAGGGAGACGGGG 60.519 72.222 0.00 0.00 33.01 5.73
4303 4479 1.526455 CTCGTAGGAGGGAGACGGG 60.526 68.421 4.45 0.00 36.61 5.28
4304 4480 4.144418 CTCGTAGGAGGGAGACGG 57.856 66.667 4.45 0.00 36.61 4.79
4312 4488 0.457851 CCAGCTCAACCTCGTAGGAG 59.542 60.000 5.43 5.43 37.67 3.69
4313 4489 1.605058 GCCAGCTCAACCTCGTAGGA 61.605 60.000 7.76 0.00 37.67 2.94
4314 4490 1.153549 GCCAGCTCAACCTCGTAGG 60.154 63.158 0.00 0.03 42.49 3.18
4315 4491 1.517257 CGCCAGCTCAACCTCGTAG 60.517 63.158 0.00 0.00 0.00 3.51
4316 4492 2.571757 CGCCAGCTCAACCTCGTA 59.428 61.111 0.00 0.00 0.00 3.43
4317 4493 4.379243 CCGCCAGCTCAACCTCGT 62.379 66.667 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.