Multiple sequence alignment - TraesCS5B01G445700

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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 TraesCS5B01G445700 chr5B 100.000 3829 0 0 1 3829 617603009 617599181 0.000000e+00 7071.0
1 TraesCS5B01G445700 chr5B 85.389 1800 232 22 1072 2853 617436570 617434784 0.000000e+00 1838.0
2 TraesCS5B01G445700 chr5B 88.133 1146 133 2 1685 2829 617292578 617291435 0.000000e+00 1360.0
3 TraesCS5B01G445700 chr5B 79.126 709 100 34 970 1660 617293315 617292637 2.710000e-121 446.0
4 TraesCS5B01G445700 chr5B 85.517 290 41 1 3070 3358 78736121 78736410 6.220000e-78 302.0
5 TraesCS5B01G445700 chr5D 90.409 2273 148 35 706 2941 498291532 498289293 0.000000e+00 2926.0
6 TraesCS5B01G445700 chr5D 85.849 1802 214 31 1072 2852 498173624 498171843 0.000000e+00 1877.0
7 TraesCS5B01G445700 chr5D 89.248 1144 115 4 1711 2852 498085504 498084367 0.000000e+00 1424.0
8 TraesCS5B01G445700 chr5D 84.968 632 37 21 45 660 498292410 498291821 4.260000e-164 588.0
9 TraesCS5B01G445700 chr5A 88.262 1951 159 39 1042 2957 622460691 622458776 0.000000e+00 2270.0
10 TraesCS5B01G445700 chr5A 85.429 1901 223 43 978 2849 622394331 622392456 0.000000e+00 1927.0
11 TraesCS5B01G445700 chr5A 83.638 1913 233 55 970 2829 622234468 622232583 0.000000e+00 1725.0
12 TraesCS5B01G445700 chr5A 88.205 780 50 20 133 893 622461622 622460866 0.000000e+00 893.0
13 TraesCS5B01G445700 chr5A 77.686 363 45 18 3075 3428 50762167 50762502 5.050000e-44 189.0
14 TraesCS5B01G445700 chr5A 100.000 28 0 0 914 941 622460862 622460835 7.000000e-03 52.8
15 TraesCS5B01G445700 chr1B 82.955 1279 155 32 1095 2330 569519345 569520603 0.000000e+00 1096.0
16 TraesCS5B01G445700 chr1B 97.917 48 1 0 1 48 679818978 679818931 2.450000e-12 84.2
17 TraesCS5B01G445700 chr1B 100.000 44 0 0 1 44 367562199 367562242 8.820000e-12 82.4
18 TraesCS5B01G445700 chr3A 81.142 981 174 8 1778 2754 20557818 20556845 0.000000e+00 776.0
19 TraesCS5B01G445700 chr3B 81.378 784 103 30 3077 3829 679530197 679529426 1.970000e-167 599.0
20 TraesCS5B01G445700 chr3B 85.749 407 38 12 3434 3829 776548004 776547607 2.750000e-111 412.0
21 TraesCS5B01G445700 chr3B 93.220 59 1 3 1 58 809086362 809086306 2.450000e-12 84.2
22 TraesCS5B01G445700 chr7A 88.753 409 40 5 3424 3828 200235745 200236151 2.660000e-136 496.0
23 TraesCS5B01G445700 chr7A 84.409 372 44 7 3070 3428 547554535 547554165 1.690000e-93 353.0
24 TraesCS5B01G445700 chr7D 87.010 408 39 8 3428 3829 71844246 71843847 7.550000e-122 448.0
25 TraesCS5B01G445700 chr7D 96.104 77 2 1 2986 3061 11793688 11793764 1.440000e-24 124.0
26 TraesCS5B01G445700 chr7D 93.902 82 4 1 2984 3064 451886699 451886780 5.190000e-24 122.0
27 TraesCS5B01G445700 chr4D 86.275 408 50 3 3428 3829 51290412 51290005 4.540000e-119 438.0
28 TraesCS5B01G445700 chr4D 85.539 408 46 7 3427 3829 447331706 447331307 7.650000e-112 414.0
29 TraesCS5B01G445700 chr6B 86.275 408 44 8 3428 3829 163224482 163224081 2.110000e-117 433.0
30 TraesCS5B01G445700 chr6B 97.959 49 0 1 1 49 196869376 196869329 2.450000e-12 84.2
31 TraesCS5B01G445700 chr3D 86.835 395 42 6 3443 3829 512490711 512490319 2.110000e-117 433.0
32 TraesCS5B01G445700 chr3D 82.303 356 51 10 3082 3428 43656047 43655695 8.040000e-77 298.0
33 TraesCS5B01G445700 chr3D 80.978 368 61 5 3070 3428 495231876 495232243 2.250000e-72 283.0
34 TraesCS5B01G445700 chr6A 84.672 411 50 7 3428 3829 103683117 103682711 7.710000e-107 398.0
35 TraesCS5B01G445700 chr6A 96.825 63 2 0 2982 3044 502916578 502916640 5.230000e-19 106.0
36 TraesCS5B01G445700 chr2D 84.767 407 51 9 3428 3829 106357039 106356639 7.710000e-107 398.0
37 TraesCS5B01G445700 chr2D 84.054 370 46 11 3070 3428 106357458 106357091 1.020000e-90 344.0
38 TraesCS5B01G445700 chr2D 84.104 346 44 8 3092 3428 646352697 646352354 1.330000e-84 324.0
39 TraesCS5B01G445700 chr2D 100.000 44 0 0 1 44 90902119 90902162 8.820000e-12 82.4
40 TraesCS5B01G445700 chr4B 76.870 722 142 21 1849 2559 15753156 15753863 6.000000e-103 385.0
41 TraesCS5B01G445700 chr4B 85.135 370 37 10 3074 3428 559843574 559843208 2.810000e-96 363.0
42 TraesCS5B01G445700 chr2B 84.384 365 44 9 3070 3422 753831799 753832162 2.830000e-91 346.0
43 TraesCS5B01G445700 chr2B 97.917 48 1 0 1 48 108113121 108113074 2.450000e-12 84.2
44 TraesCS5B01G445700 chr2B 97.959 49 0 1 1 48 721245315 721245363 2.450000e-12 84.2
45 TraesCS5B01G445700 chr1A 83.696 368 50 9 3070 3428 20971429 20971063 4.740000e-89 339.0
46 TraesCS5B01G445700 chr6D 83.889 360 42 7 3070 3428 11443891 11444235 2.850000e-86 329.0
47 TraesCS5B01G445700 chr7B 85.811 296 35 5 3068 3358 44792749 44792456 1.340000e-79 307.0
48 TraesCS5B01G445700 chr7B 81.452 248 26 10 3195 3424 688816658 688816413 6.530000e-43 185.0
49 TraesCS5B01G445700 chr7B 100.000 45 0 0 1 45 200978418 200978462 2.450000e-12 84.2
50 TraesCS5B01G445700 chr7B 97.959 49 0 1 1 48 393178545 393178497 2.450000e-12 84.2
51 TraesCS5B01G445700 chr4A 82.778 360 42 8 3070 3428 602909686 602909346 1.730000e-78 303.0
52 TraesCS5B01G445700 chr4A 84.277 159 16 4 3278 3428 713998739 713998896 3.080000e-31 147.0
53 TraesCS5B01G445700 chrUn 85.135 296 38 6 3068 3358 93147297 93147591 8.040000e-77 298.0
54 TraesCS5B01G445700 chrUn 96.250 80 2 1 2986 3064 269655001 269654922 3.100000e-26 130.0
55 TraesCS5B01G445700 chrUn 96.250 80 2 1 2986 3064 291404140 291404061 3.100000e-26 130.0
56 TraesCS5B01G445700 chr2A 93.671 79 2 2 2986 3061 694646476 694646398 8.690000e-22 115.0


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 TraesCS5B01G445700 chr5B 617599181 617603009 3828 True 7071.000000 7071 100.000000 1 3829 1 chr5B.!!$R2 3828
1 TraesCS5B01G445700 chr5B 617434784 617436570 1786 True 1838.000000 1838 85.389000 1072 2853 1 chr5B.!!$R1 1781
2 TraesCS5B01G445700 chr5B 617291435 617293315 1880 True 903.000000 1360 83.629500 970 2829 2 chr5B.!!$R3 1859
3 TraesCS5B01G445700 chr5D 498171843 498173624 1781 True 1877.000000 1877 85.849000 1072 2852 1 chr5D.!!$R2 1780
4 TraesCS5B01G445700 chr5D 498289293 498292410 3117 True 1757.000000 2926 87.688500 45 2941 2 chr5D.!!$R3 2896
5 TraesCS5B01G445700 chr5D 498084367 498085504 1137 True 1424.000000 1424 89.248000 1711 2852 1 chr5D.!!$R1 1141
6 TraesCS5B01G445700 chr5A 622392456 622394331 1875 True 1927.000000 1927 85.429000 978 2849 1 chr5A.!!$R2 1871
7 TraesCS5B01G445700 chr5A 622232583 622234468 1885 True 1725.000000 1725 83.638000 970 2829 1 chr5A.!!$R1 1859
8 TraesCS5B01G445700 chr5A 622458776 622461622 2846 True 1071.933333 2270 92.155667 133 2957 3 chr5A.!!$R3 2824
9 TraesCS5B01G445700 chr1B 569519345 569520603 1258 False 1096.000000 1096 82.955000 1095 2330 1 chr1B.!!$F2 1235
10 TraesCS5B01G445700 chr3A 20556845 20557818 973 True 776.000000 776 81.142000 1778 2754 1 chr3A.!!$R1 976
11 TraesCS5B01G445700 chr3B 679529426 679530197 771 True 599.000000 599 81.378000 3077 3829 1 chr3B.!!$R1 752
12 TraesCS5B01G445700 chr2D 106356639 106357458 819 True 371.000000 398 84.410500 3070 3829 2 chr2D.!!$R2 759
13 TraesCS5B01G445700 chr4B 15753156 15753863 707 False 385.000000 385 76.870000 1849 2559 1 chr4B.!!$F1 710

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
99 100 0.040246 CCGAGCTAAGCTACTACCGC 60.040 60.0 0.00 0.00 39.88 5.68 F
345 355 0.103208 ATGAACCGATCAGTCGCTCC 59.897 55.0 0.00 0.00 46.32 4.70 F
1192 1556 0.107312 CCTGCACAATGAGGAGGAGG 60.107 60.0 12.46 3.08 46.42 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1030 1343 0.108329 ACCGTATGTGTGCCACTAGC 60.108 55.0 0.0 0.0 44.14 3.42 R
1303 1673 0.110486 GTGACCCCAGGCTTCAAGAA 59.890 55.0 0.0 0.0 0.00 2.52 R
3048 3571 0.034896 AGTGCTGAACCTGTAACCGG 59.965 55.0 0.0 0.0 0.00 5.28 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
23 24 6.388259 CCCATAAAGTTAAAACGTGCATTG 57.612 37.500 0.00 0.00 0.00 2.82
24 25 5.164002 CCCATAAAGTTAAAACGTGCATTGC 60.164 40.000 0.46 0.46 0.00 3.56
25 26 5.403766 CCATAAAGTTAAAACGTGCATTGCA 59.596 36.000 7.38 7.38 35.60 4.08
96 97 2.574450 AGGACCGAGCTAAGCTACTAC 58.426 52.381 0.00 0.00 39.88 2.73
98 99 1.263752 GACCGAGCTAAGCTACTACCG 59.736 57.143 0.00 0.00 39.88 4.02
99 100 0.040246 CCGAGCTAAGCTACTACCGC 60.040 60.000 0.00 0.00 39.88 5.68
100 101 0.945813 CGAGCTAAGCTACTACCGCT 59.054 55.000 0.00 0.00 39.88 5.52
102 103 2.733517 GAGCTAAGCTACTACCGCTTG 58.266 52.381 7.46 0.10 46.36 4.01
103 104 1.202428 AGCTAAGCTACTACCGCTTGC 60.202 52.381 7.46 8.67 46.36 4.01
104 105 1.854227 CTAAGCTACTACCGCTTGCC 58.146 55.000 7.46 0.00 46.36 4.52
109 116 2.557490 AGCTACTACCGCTTGCCTATAC 59.443 50.000 0.00 0.00 32.98 1.47
124 131 9.208022 GCTTGCCTATACAAAAGAAAAAGAAAT 57.792 29.630 0.00 0.00 0.00 2.17
139 146 3.243359 AGAAATCACATGGGTTGGTGT 57.757 42.857 0.00 0.00 36.43 4.16
331 341 4.431894 TCATCGCGACGAAAATATGAAC 57.568 40.909 12.93 0.00 39.99 3.18
332 342 3.244345 TCATCGCGACGAAAATATGAACC 59.756 43.478 12.93 0.00 39.99 3.62
337 347 3.244345 GCGACGAAAATATGAACCGATCA 59.756 43.478 0.00 0.00 43.67 2.92
338 348 4.606232 GCGACGAAAATATGAACCGATCAG 60.606 45.833 0.00 0.00 42.53 2.90
345 355 0.103208 ATGAACCGATCAGTCGCTCC 59.897 55.000 0.00 0.00 46.32 4.70
347 357 2.938539 GAACCGATCAGTCGCTCCCG 62.939 65.000 0.00 0.00 46.32 5.14
348 358 4.933064 CCGATCAGTCGCTCCCGC 62.933 72.222 0.00 0.00 46.32 6.13
402 416 3.432933 GCTTAACGTGATTAAACCGGTCA 59.567 43.478 8.04 0.00 32.26 4.02
431 449 0.826715 AGCTAGCAGGCAAGATTCGA 59.173 50.000 18.83 0.00 34.17 3.71
432 450 1.415659 AGCTAGCAGGCAAGATTCGAT 59.584 47.619 18.83 0.00 34.17 3.59
436 454 0.302890 GCAGGCAAGATTCGATCACG 59.697 55.000 0.00 0.00 41.26 4.35
450 468 0.456221 ATCACGATCGTCCTGTCCAC 59.544 55.000 19.84 0.00 0.00 4.02
455 473 0.179161 GATCGTCCTGTCCACACTCG 60.179 60.000 0.00 0.00 0.00 4.18
456 474 0.608308 ATCGTCCTGTCCACACTCGA 60.608 55.000 0.00 0.00 0.00 4.04
545 563 4.523813 ACGCTTTAACTGAACACGAATTG 58.476 39.130 0.00 0.00 0.00 2.32
549 567 5.173131 GCTTTAACTGAACACGAATTGGTTG 59.827 40.000 0.00 0.00 0.00 3.77
644 662 2.526304 AGCTAGCTTTCGTGTTGTGA 57.474 45.000 12.68 0.00 0.00 3.58
675 693 0.320508 TCACTCAAGAGCAGCAGCAG 60.321 55.000 3.17 0.00 45.49 4.24
676 694 1.671704 ACTCAAGAGCAGCAGCAGC 60.672 57.895 3.17 0.46 45.49 5.25
677 695 1.671379 CTCAAGAGCAGCAGCAGCA 60.671 57.895 12.92 0.00 45.49 4.41
678 696 1.640210 CTCAAGAGCAGCAGCAGCAG 61.640 60.000 12.92 0.00 45.49 4.24
687 705 2.668550 CAGCAGCAGCAGCACAGA 60.669 61.111 12.92 0.00 45.49 3.41
688 706 2.358860 AGCAGCAGCAGCACAGAG 60.359 61.111 12.92 0.00 45.49 3.35
689 707 2.358369 GCAGCAGCAGCACAGAGA 60.358 61.111 4.63 0.00 45.49 3.10
690 708 2.392181 GCAGCAGCAGCACAGAGAG 61.392 63.158 4.63 0.00 45.49 3.20
691 709 1.292541 CAGCAGCAGCACAGAGAGA 59.707 57.895 3.17 0.00 45.49 3.10
692 710 0.738063 CAGCAGCAGCACAGAGAGAG 60.738 60.000 3.17 0.00 45.49 3.20
693 711 0.899253 AGCAGCAGCACAGAGAGAGA 60.899 55.000 3.17 0.00 45.49 3.10
694 712 0.458889 GCAGCAGCACAGAGAGAGAG 60.459 60.000 0.00 0.00 41.58 3.20
695 713 1.175654 CAGCAGCACAGAGAGAGAGA 58.824 55.000 0.00 0.00 0.00 3.10
696 714 1.133598 CAGCAGCACAGAGAGAGAGAG 59.866 57.143 0.00 0.00 0.00 3.20
702 720 3.118482 AGCACAGAGAGAGAGAGAGAGAG 60.118 52.174 0.00 0.00 0.00 3.20
814 1108 4.291783 GACTCAACTGTGTCTGTCTGTAC 58.708 47.826 4.97 0.00 36.10 2.90
825 1119 3.003897 GTCTGTCTGTACCCATCTCGATC 59.996 52.174 0.00 0.00 0.00 3.69
877 1171 0.661020 CCCTTTAAATACCGCAGCCG 59.339 55.000 0.00 0.00 0.00 5.52
896 1190 1.094785 GCCGGAAAGAGCTGCATTAA 58.905 50.000 5.05 0.00 0.00 1.40
941 1241 2.547211 CAGACCACAACAGAAAGAGCTG 59.453 50.000 0.00 0.00 41.63 4.24
952 1264 3.065786 CAGAAAGAGCTGTGCTTGTTTCA 59.934 43.478 20.32 0.00 40.84 2.69
955 1267 3.475566 AGAGCTGTGCTTGTTTCACTA 57.524 42.857 0.00 0.00 39.88 2.74
960 1272 4.023707 AGCTGTGCTTGTTTCACTATTCAC 60.024 41.667 0.00 0.00 33.89 3.18
1062 1413 1.324435 CATACGGTGAGTTCATGCGTG 59.676 52.381 0.00 0.00 0.00 5.34
1065 1416 0.713883 CGGTGAGTTCATGCGTGTAC 59.286 55.000 7.55 7.55 0.00 2.90
1074 1425 2.616960 TCATGCGTGTACCTCATTCAC 58.383 47.619 5.68 0.00 0.00 3.18
1129 1481 4.680237 TGAACCTGGACGGCAGCG 62.680 66.667 0.00 0.00 35.61 5.18
1192 1556 0.107312 CCTGCACAATGAGGAGGAGG 60.107 60.000 12.46 3.08 46.42 4.30
1201 1565 4.804420 AGGAGGAGGCGGCCATCA 62.804 66.667 23.09 0.00 0.00 3.07
1306 1676 4.435436 TGATCACGCGCGGCTTCT 62.435 61.111 35.22 9.87 0.00 2.85
1412 1803 3.251245 GTCACTATGGACGACGATGAGAT 59.749 47.826 0.00 0.00 0.00 2.75
1572 1966 1.592669 GGTCATGGATCTCCGCGTG 60.593 63.158 4.92 0.00 39.43 5.34
1574 1968 0.384309 GTCATGGATCTCCGCGTGTA 59.616 55.000 4.92 0.00 39.43 2.90
1630 2024 2.894126 GAGGAGAAGACTGACAAGGTGA 59.106 50.000 0.00 0.00 0.00 4.02
1631 2025 2.896685 AGGAGAAGACTGACAAGGTGAG 59.103 50.000 0.00 0.00 0.00 3.51
1632 2026 2.894126 GGAGAAGACTGACAAGGTGAGA 59.106 50.000 0.00 0.00 0.00 3.27
1633 2027 3.056891 GGAGAAGACTGACAAGGTGAGAG 60.057 52.174 0.00 0.00 0.00 3.20
1664 2059 1.065782 ACGTAACCACCTGCATGCATA 60.066 47.619 22.97 6.59 0.00 3.14
1666 2061 2.643551 GTAACCACCTGCATGCATACT 58.356 47.619 22.97 3.24 0.00 2.12
1667 2062 1.466856 AACCACCTGCATGCATACTG 58.533 50.000 22.97 15.59 0.00 2.74
1671 2066 1.669265 CACCTGCATGCATACTGTCTG 59.331 52.381 22.97 6.58 0.00 3.51
1673 2068 1.669265 CCTGCATGCATACTGTCTGTG 59.331 52.381 22.97 4.99 0.00 3.66
1674 2069 1.669265 CTGCATGCATACTGTCTGTGG 59.331 52.381 22.97 0.21 0.00 4.17
1677 2072 1.399440 CATGCATACTGTCTGTGGCAC 59.601 52.381 11.55 11.55 40.96 5.01
1678 2073 0.670239 TGCATACTGTCTGTGGCACG 60.670 55.000 13.77 8.10 36.08 5.34
1688 2164 4.248402 GTGGCACGCAGTAACGTA 57.752 55.556 0.00 0.00 46.34 3.57
1691 2167 1.072391 TGGCACGCAGTAACGTAATG 58.928 50.000 0.00 0.00 46.34 1.90
1694 2174 2.285602 GGCACGCAGTAACGTAATGATG 60.286 50.000 0.00 0.00 46.34 3.07
1698 2178 3.918258 GCAGTAACGTAATGATGCGAA 57.082 42.857 0.00 0.00 38.11 4.70
1877 2380 1.071471 CAACCACTTCGACTGGGCT 59.929 57.895 12.06 0.00 32.45 5.19
1889 2392 1.205893 GACTGGGCTGTCTTCGAGAAT 59.794 52.381 4.44 0.00 34.39 2.40
2567 3070 2.534011 TGGGGGTTCATGCAGGGA 60.534 61.111 0.00 0.00 0.00 4.20
2569 3072 1.380380 GGGGGTTCATGCAGGGAAG 60.380 63.158 0.00 0.00 0.00 3.46
2706 3209 1.135774 GCGACGGGAATTTCAAGTTCC 60.136 52.381 2.98 2.98 43.52 3.62
2708 3211 2.419667 GACGGGAATTTCAAGTTCCGA 58.580 47.619 13.52 0.00 44.87 4.55
2741 3244 2.418976 CAGATACTTCGTCGAGGTCACA 59.581 50.000 13.80 0.00 0.00 3.58
2811 3320 1.837051 AACACGCCTCTCCTGGTGA 60.837 57.895 0.85 0.00 39.82 4.02
2857 3366 5.687780 TCACGGTGGATCTATCTACACTTA 58.312 41.667 8.50 0.00 39.70 2.24
2950 3473 7.534085 TGACACGTTAAGGAATAATAAGCTG 57.466 36.000 1.43 0.00 0.00 4.24
2951 3474 6.036735 TGACACGTTAAGGAATAATAAGCTGC 59.963 38.462 1.43 0.00 0.00 5.25
2952 3475 6.113411 ACACGTTAAGGAATAATAAGCTGCT 58.887 36.000 0.00 0.00 0.00 4.24
2953 3476 6.258068 ACACGTTAAGGAATAATAAGCTGCTC 59.742 38.462 1.00 0.00 0.00 4.26
2954 3477 6.480320 CACGTTAAGGAATAATAAGCTGCTCT 59.520 38.462 1.00 0.00 0.00 4.09
2955 3478 7.652105 CACGTTAAGGAATAATAAGCTGCTCTA 59.348 37.037 1.00 0.00 0.00 2.43
2956 3479 8.368668 ACGTTAAGGAATAATAAGCTGCTCTAT 58.631 33.333 1.00 0.67 0.00 1.98
2957 3480 8.865001 CGTTAAGGAATAATAAGCTGCTCTATC 58.135 37.037 1.00 0.00 0.00 2.08
2958 3481 9.157104 GTTAAGGAATAATAAGCTGCTCTATCC 57.843 37.037 1.00 5.76 0.00 2.59
2959 3482 7.566658 AAGGAATAATAAGCTGCTCTATCCT 57.433 36.000 1.00 7.96 0.00 3.24
2960 3483 7.181569 AGGAATAATAAGCTGCTCTATCCTC 57.818 40.000 1.00 0.00 0.00 3.71
2961 3484 6.959366 AGGAATAATAAGCTGCTCTATCCTCT 59.041 38.462 1.00 0.00 0.00 3.69
2962 3485 8.119246 AGGAATAATAAGCTGCTCTATCCTCTA 58.881 37.037 1.00 0.00 0.00 2.43
2963 3486 8.923270 GGAATAATAAGCTGCTCTATCCTCTAT 58.077 37.037 1.00 0.00 0.00 1.98
2964 3487 9.748708 GAATAATAAGCTGCTCTATCCTCTATG 57.251 37.037 1.00 0.00 0.00 2.23
2965 3488 9.486123 AATAATAAGCTGCTCTATCCTCTATGA 57.514 33.333 1.00 0.00 0.00 2.15
2966 3489 6.773976 ATAAGCTGCTCTATCCTCTATGAC 57.226 41.667 1.00 0.00 0.00 3.06
2967 3490 4.111255 AGCTGCTCTATCCTCTATGACA 57.889 45.455 0.00 0.00 0.00 3.58
2968 3491 3.826157 AGCTGCTCTATCCTCTATGACAC 59.174 47.826 0.00 0.00 0.00 3.67
2969 3492 3.826157 GCTGCTCTATCCTCTATGACACT 59.174 47.826 0.00 0.00 0.00 3.55
2970 3493 5.007034 GCTGCTCTATCCTCTATGACACTA 58.993 45.833 0.00 0.00 0.00 2.74
2971 3494 5.106317 GCTGCTCTATCCTCTATGACACTAC 60.106 48.000 0.00 0.00 0.00 2.73
2972 3495 6.194285 TGCTCTATCCTCTATGACACTACT 57.806 41.667 0.00 0.00 0.00 2.57
2973 3496 6.234920 TGCTCTATCCTCTATGACACTACTC 58.765 44.000 0.00 0.00 0.00 2.59
2974 3497 6.043822 TGCTCTATCCTCTATGACACTACTCT 59.956 42.308 0.00 0.00 0.00 3.24
2975 3498 6.940298 GCTCTATCCTCTATGACACTACTCTT 59.060 42.308 0.00 0.00 0.00 2.85
2976 3499 7.119262 GCTCTATCCTCTATGACACTACTCTTC 59.881 44.444 0.00 0.00 0.00 2.87
2977 3500 7.455058 TCTATCCTCTATGACACTACTCTTCC 58.545 42.308 0.00 0.00 0.00 3.46
2978 3501 5.718801 TCCTCTATGACACTACTCTTCCT 57.281 43.478 0.00 0.00 0.00 3.36
2979 3502 6.826632 TCCTCTATGACACTACTCTTCCTA 57.173 41.667 0.00 0.00 0.00 2.94
2980 3503 7.209340 TCCTCTATGACACTACTCTTCCTAA 57.791 40.000 0.00 0.00 0.00 2.69
2981 3504 7.817440 TCCTCTATGACACTACTCTTCCTAAT 58.183 38.462 0.00 0.00 0.00 1.73
2982 3505 8.282982 TCCTCTATGACACTACTCTTCCTAATT 58.717 37.037 0.00 0.00 0.00 1.40
2983 3506 8.919145 CCTCTATGACACTACTCTTCCTAATTT 58.081 37.037 0.00 0.00 0.00 1.82
3010 3533 5.570234 TTTTGACGAAAAACAGCCTTAGT 57.430 34.783 0.00 0.00 32.72 2.24
3011 3534 4.545823 TTGACGAAAAACAGCCTTAGTG 57.454 40.909 0.00 0.00 0.00 2.74
3012 3535 2.289547 TGACGAAAAACAGCCTTAGTGC 59.710 45.455 0.00 0.00 0.00 4.40
3013 3536 2.548480 GACGAAAAACAGCCTTAGTGCT 59.452 45.455 0.00 0.00 44.00 4.40
3023 3546 4.978083 AGCCTTAGTGCTGATTTCATTG 57.022 40.909 0.00 0.00 40.90 2.82
3024 3547 3.129988 AGCCTTAGTGCTGATTTCATTGC 59.870 43.478 0.00 0.00 40.90 3.56
3025 3548 3.119388 GCCTTAGTGCTGATTTCATTGCA 60.119 43.478 0.00 0.00 0.00 4.08
3026 3549 4.618927 GCCTTAGTGCTGATTTCATTGCAA 60.619 41.667 0.00 0.00 37.17 4.08
3027 3550 5.657474 CCTTAGTGCTGATTTCATTGCAAT 58.343 37.500 5.99 5.99 37.17 3.56
3028 3551 6.681120 GCCTTAGTGCTGATTTCATTGCAATA 60.681 38.462 12.53 0.00 37.17 1.90
3029 3552 7.259882 CCTTAGTGCTGATTTCATTGCAATAA 58.740 34.615 12.53 4.20 41.46 1.40
3031 3554 6.519679 AGTGCTGATTTCATTGCAATAAGA 57.480 33.333 12.53 3.26 37.17 2.10
3032 3555 6.561614 AGTGCTGATTTCATTGCAATAAGAG 58.438 36.000 12.53 5.66 37.17 2.85
3033 3556 6.376299 AGTGCTGATTTCATTGCAATAAGAGA 59.624 34.615 12.53 2.05 37.17 3.10
3034 3557 7.031372 GTGCTGATTTCATTGCAATAAGAGAA 58.969 34.615 12.53 8.66 37.17 2.87
3035 3558 7.543172 GTGCTGATTTCATTGCAATAAGAGAAA 59.457 33.333 19.15 19.15 37.17 2.52
3036 3559 7.758076 TGCTGATTTCATTGCAATAAGAGAAAG 59.242 33.333 20.60 12.55 32.12 2.62
3037 3560 7.222224 GCTGATTTCATTGCAATAAGAGAAAGG 59.778 37.037 20.60 15.63 0.00 3.11
3038 3561 7.037438 TGATTTCATTGCAATAAGAGAAAGGC 58.963 34.615 20.60 16.63 0.00 4.35
3039 3562 4.989279 TCATTGCAATAAGAGAAAGGCC 57.011 40.909 12.53 0.00 0.00 5.19
3040 3563 4.343231 TCATTGCAATAAGAGAAAGGCCA 58.657 39.130 12.53 0.00 0.00 5.36
3041 3564 4.771577 TCATTGCAATAAGAGAAAGGCCAA 59.228 37.500 12.53 0.00 0.00 4.52
3042 3565 4.789012 TTGCAATAAGAGAAAGGCCAAG 57.211 40.909 5.01 0.00 0.00 3.61
3043 3566 4.032960 TGCAATAAGAGAAAGGCCAAGA 57.967 40.909 5.01 0.00 0.00 3.02
3044 3567 3.758554 TGCAATAAGAGAAAGGCCAAGAC 59.241 43.478 5.01 0.00 0.00 3.01
3045 3568 3.181506 GCAATAAGAGAAAGGCCAAGACG 60.182 47.826 5.01 0.00 0.00 4.18
3046 3569 2.762535 TAAGAGAAAGGCCAAGACGG 57.237 50.000 5.01 0.00 38.11 4.79
3055 3578 2.435410 CCAAGACGGCCCGGTTAC 60.435 66.667 8.57 0.00 0.00 2.50
3056 3579 2.344500 CAAGACGGCCCGGTTACA 59.656 61.111 8.57 0.00 0.00 2.41
3057 3580 1.740296 CAAGACGGCCCGGTTACAG 60.740 63.158 8.57 0.00 0.00 2.74
3058 3581 2.951101 AAGACGGCCCGGTTACAGG 61.951 63.158 8.57 0.00 0.00 4.00
3059 3582 3.698820 GACGGCCCGGTTACAGGT 61.699 66.667 8.57 0.00 0.00 4.00
3060 3583 3.243816 ACGGCCCGGTTACAGGTT 61.244 61.111 8.57 0.00 0.00 3.50
3061 3584 2.435410 CGGCCCGGTTACAGGTTC 60.435 66.667 0.00 0.00 0.00 3.62
3062 3585 2.751688 GGCCCGGTTACAGGTTCA 59.248 61.111 0.00 0.00 0.00 3.18
3063 3586 1.376812 GGCCCGGTTACAGGTTCAG 60.377 63.158 0.00 0.00 0.00 3.02
3064 3587 2.038837 GCCCGGTTACAGGTTCAGC 61.039 63.158 0.00 0.00 0.00 4.26
3065 3588 1.373435 CCCGGTTACAGGTTCAGCA 59.627 57.895 0.00 0.00 0.00 4.41
3066 3589 0.953960 CCCGGTTACAGGTTCAGCAC 60.954 60.000 0.00 0.00 0.00 4.40
3067 3590 0.034896 CCGGTTACAGGTTCAGCACT 59.965 55.000 0.00 0.00 0.00 4.40
3068 3591 1.542547 CCGGTTACAGGTTCAGCACTT 60.543 52.381 0.00 0.00 0.00 3.16
3084 3607 7.227049 TCAGCACTTTCCCTAATTTTAAAGG 57.773 36.000 0.00 0.00 34.07 3.11
3134 3657 2.302587 ATTGGGTCACCCGATTTTGT 57.697 45.000 10.32 0.00 45.09 2.83
3136 3659 2.298729 ATTGGGTCACCCGATTTTGTTG 59.701 45.455 10.32 0.00 45.09 3.33
3156 3679 3.146066 TGGGGACAACAATTTCTCGAAG 58.854 45.455 0.00 0.00 37.44 3.79
3168 3691 3.412981 TTCTCGAAGCTCTCTCATTCG 57.587 47.619 0.38 0.38 45.37 3.34
3181 3704 7.593273 AGCTCTCTCATTCGATTCTTTTATACG 59.407 37.037 0.00 0.00 0.00 3.06
3217 3740 9.914131 GCTTTCTAATTTTTAAGGTCTCACAAT 57.086 29.630 0.00 0.00 0.00 2.71
3231 3754 8.697507 AGGTCTCACAATTAATTGAAGTCTTT 57.302 30.769 30.18 14.82 40.14 2.52
3283 3808 4.100808 TGGGTCAACAATTTTTCAAGGAGG 59.899 41.667 0.00 0.00 0.00 4.30
3359 3887 9.877137 TTCAATTCGATTATGGTATTCAATTCG 57.123 29.630 0.00 0.00 0.00 3.34
3400 3935 6.127952 CGGGCCAATCATTTTTCAAATCAATT 60.128 34.615 4.39 0.00 0.00 2.32
3407 3942 7.280730 TCATTTTTCAAATCAATTAGCAGCG 57.719 32.000 0.00 0.00 0.00 5.18
3409 3947 6.689178 TTTTTCAAATCAATTAGCAGCGAC 57.311 33.333 0.00 0.00 0.00 5.19
3411 3949 2.351418 TCAAATCAATTAGCAGCGACCG 59.649 45.455 0.00 0.00 0.00 4.79
3424 3962 1.208776 AGCGACCGGCCTATAAAAACT 59.791 47.619 0.00 0.00 45.17 2.66
3430 4020 5.050567 CGACCGGCCTATAAAAACTTATGAC 60.051 44.000 0.00 0.00 0.00 3.06
3445 4035 9.448438 AAAACTTATGACACTGTAGCATCAATA 57.552 29.630 0.00 0.00 0.00 1.90
3456 4046 7.599998 CACTGTAGCATCAATATAGTACATGCA 59.400 37.037 15.05 0.00 41.98 3.96
3457 4047 8.150296 ACTGTAGCATCAATATAGTACATGCAA 58.850 33.333 15.05 3.97 41.98 4.08
3466 4056 2.273370 AGTACATGCAACTACCGACG 57.727 50.000 0.00 0.00 0.00 5.12
3467 4057 1.814394 AGTACATGCAACTACCGACGA 59.186 47.619 0.00 0.00 0.00 4.20
3469 4059 1.710013 ACATGCAACTACCGACGAAG 58.290 50.000 0.00 0.00 0.00 3.79
3489 4079 7.768240 ACGAAGAAATTTCCCCACATAAATAC 58.232 34.615 14.61 0.00 0.00 1.89
3499 4089 6.110707 TCCCCACATAAATACGAGTTTCTTC 58.889 40.000 0.00 0.00 0.00 2.87
3512 4102 3.395639 AGTTTCTTCGCGGATAACACAA 58.604 40.909 6.13 0.00 0.00 3.33
3533 4123 1.207791 ATCACATCGAGAAAGGCCCT 58.792 50.000 0.00 0.00 0.00 5.19
3540 4130 2.193127 TCGAGAAAGGCCCTCCAAATA 58.807 47.619 0.00 0.00 33.74 1.40
3543 4133 3.954258 CGAGAAAGGCCCTCCAAATAATT 59.046 43.478 0.00 0.00 33.74 1.40
3581 4171 5.418840 ACAAAACACACTCCATCATATTCCC 59.581 40.000 0.00 0.00 0.00 3.97
3586 4176 0.987294 CTCCATCATATTCCCGCCCT 59.013 55.000 0.00 0.00 0.00 5.19
3587 4177 2.187958 CTCCATCATATTCCCGCCCTA 58.812 52.381 0.00 0.00 0.00 3.53
3604 4194 4.212636 CGCCCTACCAAACTAAATATTCCG 59.787 45.833 0.00 0.00 0.00 4.30
3625 4215 5.008217 TCCGTCAATTCCAAAATATAAGCGG 59.992 40.000 0.00 0.00 34.97 5.52
3665 4259 7.435192 GTCAAATTCCTTTACTTTGACCAAGTG 59.565 37.037 13.65 0.00 46.62 3.16
3670 4264 4.338118 CCTTTACTTTGACCAAGTGCAGAA 59.662 41.667 2.25 0.00 45.98 3.02
3672 4266 2.722094 ACTTTGACCAAGTGCAGAACA 58.278 42.857 0.00 0.00 44.70 3.18
3697 4291 7.718272 AAAAATGACAACATCCACAAGATTG 57.282 32.000 0.00 0.00 35.50 2.67
3702 4296 5.008911 TGACAACATCCACAAGATTGAACAG 59.991 40.000 0.00 0.00 30.59 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.164002 GCAATGCACGTTTTAACTTTATGGG 60.164 40.000 0.00 0.00 0.00 4.00
1 2 5.403766 TGCAATGCACGTTTTAACTTTATGG 59.596 36.000 2.72 0.00 31.71 2.74
2 3 6.445267 TGCAATGCACGTTTTAACTTTATG 57.555 33.333 2.72 0.00 31.71 1.90
23 24 8.462143 AATAATACTAGTATGTATGCACGTGC 57.538 34.615 33.11 33.11 42.50 5.34
55 56 9.387257 GGTCCTTTTTATTTAGAAGATAACCGA 57.613 33.333 0.00 0.00 0.00 4.69
56 57 8.333186 CGGTCCTTTTTATTTAGAAGATAACCG 58.667 37.037 0.00 0.00 36.02 4.44
57 58 9.387257 TCGGTCCTTTTTATTTAGAAGATAACC 57.613 33.333 0.00 0.00 0.00 2.85
59 60 9.106070 GCTCGGTCCTTTTTATTTAGAAGATAA 57.894 33.333 0.00 0.00 0.00 1.75
61 62 7.339482 AGCTCGGTCCTTTTTATTTAGAAGAT 58.661 34.615 0.00 0.00 0.00 2.40
63 64 6.986904 AGCTCGGTCCTTTTTATTTAGAAG 57.013 37.500 0.00 0.00 0.00 2.85
77 78 1.608109 GGTAGTAGCTTAGCTCGGTCC 59.392 57.143 11.09 6.35 40.44 4.46
79 80 1.307097 CGGTAGTAGCTTAGCTCGGT 58.693 55.000 11.09 0.00 40.44 4.69
96 97 4.695217 TTTCTTTTGTATAGGCAAGCGG 57.305 40.909 0.00 0.00 0.00 5.52
98 99 8.587952 TTTCTTTTTCTTTTGTATAGGCAAGC 57.412 30.769 0.00 0.00 0.00 4.01
101 102 9.691362 GTGATTTCTTTTTCTTTTGTATAGGCA 57.309 29.630 0.00 0.00 0.00 4.75
102 103 9.691362 TGTGATTTCTTTTTCTTTTGTATAGGC 57.309 29.630 0.00 0.00 0.00 3.93
109 116 7.790823 ACCCATGTGATTTCTTTTTCTTTTG 57.209 32.000 0.00 0.00 0.00 2.44
139 146 2.926586 GCACAGATCGAGTTGCTACACA 60.927 50.000 0.13 0.00 0.00 3.72
431 449 0.456221 GTGGACAGGACGATCGTGAT 59.544 55.000 28.12 10.98 35.94 3.06
432 450 0.891904 TGTGGACAGGACGATCGTGA 60.892 55.000 28.12 0.00 35.94 4.35
436 454 0.179161 CGAGTGTGGACAGGACGATC 60.179 60.000 0.00 0.00 0.00 3.69
443 461 1.202348 TGTGCTATCGAGTGTGGACAG 59.798 52.381 0.00 0.00 0.00 3.51
450 468 1.474478 ACTGGTCTGTGCTATCGAGTG 59.526 52.381 0.00 0.00 0.00 3.51
455 473 3.179830 CGTGTAACTGGTCTGTGCTATC 58.820 50.000 0.00 0.00 31.75 2.08
456 474 2.674177 GCGTGTAACTGGTCTGTGCTAT 60.674 50.000 0.00 0.00 31.75 2.97
529 547 3.628032 TGCAACCAATTCGTGTTCAGTTA 59.372 39.130 0.00 0.00 0.00 2.24
533 551 2.483583 GTGCAACCAATTCGTGTTCA 57.516 45.000 0.00 0.00 0.00 3.18
644 662 4.754114 GCTCTTGAGTGACAGTGAAGATTT 59.246 41.667 11.91 0.00 0.00 2.17
675 693 0.458889 CTCTCTCTCTGTGCTGCTGC 60.459 60.000 8.89 8.89 40.20 5.25
676 694 1.133598 CTCTCTCTCTCTGTGCTGCTG 59.866 57.143 0.00 0.00 0.00 4.41
677 695 1.004628 TCTCTCTCTCTCTGTGCTGCT 59.995 52.381 0.00 0.00 0.00 4.24
678 696 1.402968 CTCTCTCTCTCTCTGTGCTGC 59.597 57.143 0.00 0.00 0.00 5.25
679 697 2.941064 CTCTCTCTCTCTCTCTGTGCTG 59.059 54.545 0.00 0.00 0.00 4.41
680 698 2.840038 TCTCTCTCTCTCTCTCTGTGCT 59.160 50.000 0.00 0.00 0.00 4.40
681 699 3.118629 TCTCTCTCTCTCTCTCTCTGTGC 60.119 52.174 0.00 0.00 0.00 4.57
682 700 4.403752 TCTCTCTCTCTCTCTCTCTCTGTG 59.596 50.000 0.00 0.00 0.00 3.66
683 701 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
684 702 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
685 703 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
686 704 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
687 705 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
688 706 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
689 707 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
690 708 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
691 709 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
692 710 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
693 711 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
694 712 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
695 713 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
696 714 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
702 720 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
825 1119 1.722852 GCCGTCGATCGATGTCTCG 60.723 63.158 29.97 22.84 46.41 4.04
855 1149 2.583143 GCTGCGGTATTTAAAGGGGAT 58.417 47.619 0.00 0.00 0.00 3.85
877 1171 1.094785 TTAATGCAGCTCTTTCCGGC 58.905 50.000 0.00 0.00 0.00 6.13
896 1190 4.588106 CACTCTGAGTATGGGTGATGAGAT 59.412 45.833 10.47 0.00 0.00 2.75
941 1241 5.821204 AGTTGTGAATAGTGAAACAAGCAC 58.179 37.500 0.00 0.00 41.43 4.40
952 1264 2.253610 TGACCGGGAGTTGTGAATAGT 58.746 47.619 6.32 0.00 0.00 2.12
955 1267 2.711542 GATTGACCGGGAGTTGTGAAT 58.288 47.619 6.32 0.00 0.00 2.57
960 1272 4.201951 CCGATTGACCGGGAGTTG 57.798 61.111 6.32 0.00 45.43 3.16
981 1293 2.738147 CTTACACGAGTGGAAGCGG 58.262 57.895 14.44 0.00 43.75 5.52
986 1298 1.204704 CTGCCATCTTACACGAGTGGA 59.795 52.381 8.19 0.00 34.19 4.02
1030 1343 0.108329 ACCGTATGTGTGCCACTAGC 60.108 55.000 0.00 0.00 44.14 3.42
1059 1410 2.412870 TGCAAGTGAATGAGGTACACG 58.587 47.619 0.00 0.00 39.19 4.49
1062 1413 3.127548 CACCATGCAAGTGAATGAGGTAC 59.872 47.826 13.52 0.00 37.42 3.34
1065 1416 1.135199 GCACCATGCAAGTGAATGAGG 60.135 52.381 20.92 2.11 44.26 3.86
1289 1659 3.932580 AAGAAGCCGCGCGTGATCA 62.933 57.895 29.95 0.00 0.00 2.92
1303 1673 0.110486 GTGACCCCAGGCTTCAAGAA 59.890 55.000 0.00 0.00 0.00 2.52
1306 1676 1.122632 TACGTGACCCCAGGCTTCAA 61.123 55.000 0.00 0.00 0.00 2.69
1412 1803 1.834856 CTCCACCTGCAGGCTCTCAA 61.835 60.000 33.06 11.30 39.32 3.02
1461 1852 1.526887 GCCCATGATCTCCGTCCAA 59.473 57.895 0.00 0.00 0.00 3.53
1539 1933 1.144691 TGACCTTGATGTCAACCCCA 58.855 50.000 0.00 0.00 42.06 4.96
1572 1966 1.136984 CTCGCGGTCTGTCTGGTAC 59.863 63.158 6.13 0.00 0.00 3.34
1574 1968 3.374402 CCTCGCGGTCTGTCTGGT 61.374 66.667 6.13 0.00 0.00 4.00
1609 2003 2.894126 TCACCTTGTCAGTCTTCTCCTC 59.106 50.000 0.00 0.00 0.00 3.71
1614 2008 3.613910 GCTCTCTCACCTTGTCAGTCTTC 60.614 52.174 0.00 0.00 0.00 2.87
1630 2024 0.526211 TTACGTCGTGCATGCTCTCT 59.474 50.000 20.33 0.00 0.00 3.10
1631 2025 0.640768 GTTACGTCGTGCATGCTCTC 59.359 55.000 20.33 10.02 0.00 3.20
1632 2026 0.736325 GGTTACGTCGTGCATGCTCT 60.736 55.000 20.33 1.75 0.00 4.09
1633 2027 1.011968 TGGTTACGTCGTGCATGCTC 61.012 55.000 20.33 14.84 0.00 4.26
1664 2059 1.744320 TACTGCGTGCCACAGACAGT 61.744 55.000 16.34 16.34 43.60 3.55
1666 2061 0.878523 GTTACTGCGTGCCACAGACA 60.879 55.000 4.89 0.00 38.55 3.41
1667 2062 1.860078 GTTACTGCGTGCCACAGAC 59.140 57.895 4.89 0.00 38.55 3.51
1671 2066 1.073177 ATTACGTTACTGCGTGCCAC 58.927 50.000 0.00 0.00 45.33 5.01
1673 2068 1.352114 TCATTACGTTACTGCGTGCC 58.648 50.000 0.00 0.00 45.33 5.01
1674 2069 2.845764 GCATCATTACGTTACTGCGTGC 60.846 50.000 0.00 0.27 45.33 5.34
1677 2072 2.264207 CGCATCATTACGTTACTGCG 57.736 50.000 11.70 11.70 45.05 5.18
1678 2073 3.306166 AGTTCGCATCATTACGTTACTGC 59.694 43.478 0.00 0.00 0.00 4.40
1680 2075 4.110482 GGAGTTCGCATCATTACGTTACT 58.890 43.478 0.00 0.00 0.00 2.24
1688 2164 3.243301 GCATCAATGGAGTTCGCATCATT 60.243 43.478 0.00 0.00 0.00 2.57
1691 2167 1.672363 TGCATCAATGGAGTTCGCATC 59.328 47.619 0.00 0.00 0.00 3.91
1694 2174 0.379669 CCTGCATCAATGGAGTTCGC 59.620 55.000 10.14 0.00 43.71 4.70
1698 2178 2.117156 GCGCCTGCATCAATGGAGT 61.117 57.895 10.14 0.00 43.71 3.85
1877 2380 3.256879 ACTTGAGCTCATTCTCGAAGACA 59.743 43.478 19.04 0.00 35.90 3.41
1889 2392 1.070134 GTGTGGTACCACTTGAGCTCA 59.930 52.381 37.91 13.74 46.30 4.26
2027 2530 0.890996 GGTTCTTGACCCACTGCTGG 60.891 60.000 0.00 0.00 43.06 4.85
2048 2551 1.070758 GACTTCAGCTGGTCCTTGTCA 59.929 52.381 15.13 0.00 0.00 3.58
2113 2616 1.012486 GTCGTAGTGCGGGAACTTGG 61.012 60.000 0.00 0.00 41.72 3.61
2283 2786 2.924922 TATTTCTCCGGCGTCGCGTC 62.925 60.000 11.75 0.00 34.56 5.19
2300 2803 4.570663 GCGACCTGCTCGGCGTAT 62.571 66.667 6.85 0.00 43.18 3.06
2540 3043 2.776526 AACCCCCAGAGCACCACA 60.777 61.111 0.00 0.00 0.00 4.17
2543 3046 1.379044 CATGAACCCCCAGAGCACC 60.379 63.158 0.00 0.00 0.00 5.01
2567 3070 4.349503 TCCTGCCGCCACATGCTT 62.350 61.111 0.00 0.00 38.05 3.91
2696 3199 1.142060 TGGAAGCCTCGGAACTTGAAA 59.858 47.619 0.00 0.00 0.00 2.69
2706 3209 2.016393 TATCTGCCGTGGAAGCCTCG 62.016 60.000 0.00 0.00 39.77 4.63
2708 3211 0.978146 AGTATCTGCCGTGGAAGCCT 60.978 55.000 0.00 0.00 0.00 4.58
2944 3467 5.475220 GTGTCATAGAGGATAGAGCAGCTTA 59.525 44.000 0.00 0.00 0.00 3.09
2945 3468 4.280677 GTGTCATAGAGGATAGAGCAGCTT 59.719 45.833 0.00 0.00 0.00 3.74
2946 3469 3.826157 GTGTCATAGAGGATAGAGCAGCT 59.174 47.826 0.00 0.00 0.00 4.24
2950 3473 6.472887 AGAGTAGTGTCATAGAGGATAGAGC 58.527 44.000 0.00 0.00 0.00 4.09
2951 3474 7.606456 GGAAGAGTAGTGTCATAGAGGATAGAG 59.394 44.444 0.00 0.00 0.00 2.43
2952 3475 7.293771 AGGAAGAGTAGTGTCATAGAGGATAGA 59.706 40.741 0.00 0.00 0.00 1.98
2953 3476 7.458397 AGGAAGAGTAGTGTCATAGAGGATAG 58.542 42.308 0.00 0.00 0.00 2.08
2954 3477 7.395525 AGGAAGAGTAGTGTCATAGAGGATA 57.604 40.000 0.00 0.00 0.00 2.59
2955 3478 6.274322 AGGAAGAGTAGTGTCATAGAGGAT 57.726 41.667 0.00 0.00 0.00 3.24
2956 3479 5.718801 AGGAAGAGTAGTGTCATAGAGGA 57.281 43.478 0.00 0.00 0.00 3.71
2957 3480 8.472007 AATTAGGAAGAGTAGTGTCATAGAGG 57.528 38.462 0.00 0.00 0.00 3.69
2987 3510 5.802956 CACTAAGGCTGTTTTTCGTCAAAAA 59.197 36.000 0.00 0.00 38.84 1.94
2988 3511 5.336744 CACTAAGGCTGTTTTTCGTCAAAA 58.663 37.500 0.00 0.00 31.50 2.44
2989 3512 4.732355 GCACTAAGGCTGTTTTTCGTCAAA 60.732 41.667 0.00 0.00 0.00 2.69
2990 3513 3.242936 GCACTAAGGCTGTTTTTCGTCAA 60.243 43.478 0.00 0.00 0.00 3.18
2991 3514 2.289547 GCACTAAGGCTGTTTTTCGTCA 59.710 45.455 0.00 0.00 0.00 4.35
2992 3515 2.548480 AGCACTAAGGCTGTTTTTCGTC 59.452 45.455 0.00 0.00 43.89 4.20
2993 3516 2.572290 AGCACTAAGGCTGTTTTTCGT 58.428 42.857 0.00 0.00 43.89 3.85
3003 3526 3.119388 TGCAATGAAATCAGCACTAAGGC 60.119 43.478 0.00 0.00 33.21 4.35
3004 3527 4.707030 TGCAATGAAATCAGCACTAAGG 57.293 40.909 0.00 0.00 33.21 2.69
3005 3528 8.186163 TCTTATTGCAATGAAATCAGCACTAAG 58.814 33.333 22.27 18.49 43.57 2.18
3006 3529 8.054152 TCTTATTGCAATGAAATCAGCACTAA 57.946 30.769 22.27 2.45 37.06 2.24
3007 3530 7.553760 TCTCTTATTGCAATGAAATCAGCACTA 59.446 33.333 22.27 0.00 37.06 2.74
3008 3531 6.376299 TCTCTTATTGCAATGAAATCAGCACT 59.624 34.615 22.27 0.00 37.06 4.40
3009 3532 6.558009 TCTCTTATTGCAATGAAATCAGCAC 58.442 36.000 22.27 0.00 37.06 4.40
3010 3533 6.762702 TCTCTTATTGCAATGAAATCAGCA 57.237 33.333 22.27 0.00 35.80 4.41
3011 3534 7.222224 CCTTTCTCTTATTGCAATGAAATCAGC 59.778 37.037 22.27 0.00 0.00 4.26
3012 3535 7.222224 GCCTTTCTCTTATTGCAATGAAATCAG 59.778 37.037 22.27 13.52 0.00 2.90
3013 3536 7.037438 GCCTTTCTCTTATTGCAATGAAATCA 58.963 34.615 22.27 0.00 0.00 2.57
3014 3537 6.478016 GGCCTTTCTCTTATTGCAATGAAATC 59.522 38.462 22.27 14.67 0.00 2.17
3015 3538 6.070653 TGGCCTTTCTCTTATTGCAATGAAAT 60.071 34.615 22.27 0.00 0.00 2.17
3016 3539 5.245751 TGGCCTTTCTCTTATTGCAATGAAA 59.754 36.000 22.27 19.11 0.00 2.69
3017 3540 4.771577 TGGCCTTTCTCTTATTGCAATGAA 59.228 37.500 22.27 13.30 0.00 2.57
3018 3541 4.343231 TGGCCTTTCTCTTATTGCAATGA 58.657 39.130 22.27 13.07 0.00 2.57
3019 3542 4.724074 TGGCCTTTCTCTTATTGCAATG 57.276 40.909 22.27 6.31 0.00 2.82
3020 3543 5.018809 TCTTGGCCTTTCTCTTATTGCAAT 58.981 37.500 17.56 17.56 0.00 3.56
3021 3544 4.218417 GTCTTGGCCTTTCTCTTATTGCAA 59.782 41.667 3.32 0.00 0.00 4.08
3022 3545 3.758554 GTCTTGGCCTTTCTCTTATTGCA 59.241 43.478 3.32 0.00 0.00 4.08
3023 3546 3.181506 CGTCTTGGCCTTTCTCTTATTGC 60.182 47.826 3.32 0.00 0.00 3.56
3024 3547 3.375299 CCGTCTTGGCCTTTCTCTTATTG 59.625 47.826 3.32 0.00 0.00 1.90
3025 3548 3.610911 CCGTCTTGGCCTTTCTCTTATT 58.389 45.455 3.32 0.00 0.00 1.40
3026 3549 3.268023 CCGTCTTGGCCTTTCTCTTAT 57.732 47.619 3.32 0.00 0.00 1.73
3027 3550 2.762535 CCGTCTTGGCCTTTCTCTTA 57.237 50.000 3.32 0.00 0.00 2.10
3028 3551 3.633361 CCGTCTTGGCCTTTCTCTT 57.367 52.632 3.32 0.00 0.00 2.85
3038 3561 2.435410 GTAACCGGGCCGTCTTGG 60.435 66.667 26.32 11.62 42.50 3.61
3039 3562 1.740296 CTGTAACCGGGCCGTCTTG 60.740 63.158 26.32 12.04 0.00 3.02
3040 3563 2.660802 CTGTAACCGGGCCGTCTT 59.339 61.111 26.32 17.48 0.00 3.01
3041 3564 3.387947 CCTGTAACCGGGCCGTCT 61.388 66.667 26.32 13.78 0.00 4.18
3042 3565 3.244281 AACCTGTAACCGGGCCGTC 62.244 63.158 26.32 12.45 41.25 4.79
3043 3566 3.243816 AACCTGTAACCGGGCCGT 61.244 61.111 26.32 10.07 41.25 5.68
3044 3567 2.435410 GAACCTGTAACCGGGCCG 60.435 66.667 21.46 21.46 41.25 6.13
3045 3568 1.376812 CTGAACCTGTAACCGGGCC 60.377 63.158 6.32 0.00 41.25 5.80
3046 3569 2.038837 GCTGAACCTGTAACCGGGC 61.039 63.158 6.32 0.00 41.25 6.13
3047 3570 0.953960 GTGCTGAACCTGTAACCGGG 60.954 60.000 6.32 0.00 43.41 5.73
3048 3571 0.034896 AGTGCTGAACCTGTAACCGG 59.965 55.000 0.00 0.00 0.00 5.28
3049 3572 1.878953 AAGTGCTGAACCTGTAACCG 58.121 50.000 0.00 0.00 0.00 4.44
3050 3573 2.552743 GGAAAGTGCTGAACCTGTAACC 59.447 50.000 0.00 0.00 0.00 2.85
3051 3574 2.552743 GGGAAAGTGCTGAACCTGTAAC 59.447 50.000 0.00 0.00 0.00 2.50
3052 3575 2.441750 AGGGAAAGTGCTGAACCTGTAA 59.558 45.455 0.00 0.00 0.00 2.41
3053 3576 2.054799 AGGGAAAGTGCTGAACCTGTA 58.945 47.619 0.00 0.00 0.00 2.74
3054 3577 0.846693 AGGGAAAGTGCTGAACCTGT 59.153 50.000 0.00 0.00 0.00 4.00
3055 3578 2.859165 TAGGGAAAGTGCTGAACCTG 57.141 50.000 0.00 0.00 0.00 4.00
3056 3579 4.388577 AATTAGGGAAAGTGCTGAACCT 57.611 40.909 0.00 0.00 0.00 3.50
3057 3580 5.468540 AAAATTAGGGAAAGTGCTGAACC 57.531 39.130 0.00 0.00 0.00 3.62
3058 3581 7.598869 CCTTTAAAATTAGGGAAAGTGCTGAAC 59.401 37.037 0.00 0.00 0.00 3.18
3059 3582 7.666623 CCTTTAAAATTAGGGAAAGTGCTGAA 58.333 34.615 0.00 0.00 0.00 3.02
3060 3583 7.227049 CCTTTAAAATTAGGGAAAGTGCTGA 57.773 36.000 0.00 0.00 0.00 4.26
3084 3607 4.759183 GGAGACCTCAATTGATTATGAGCC 59.241 45.833 8.96 1.82 41.36 4.70
3134 3657 3.216187 TCGAGAAATTGTTGTCCCCAA 57.784 42.857 0.00 0.00 0.00 4.12
3136 3659 2.095212 GCTTCGAGAAATTGTTGTCCCC 60.095 50.000 0.00 0.00 0.00 4.81
3139 3662 4.688413 AGAGAGCTTCGAGAAATTGTTGTC 59.312 41.667 0.00 0.00 0.00 3.18
3140 3663 4.636249 AGAGAGCTTCGAGAAATTGTTGT 58.364 39.130 0.00 0.00 0.00 3.32
3153 3676 6.660887 AAAAGAATCGAATGAGAGAGCTTC 57.339 37.500 0.00 0.00 0.00 3.86
3156 3679 7.591795 TCGTATAAAAGAATCGAATGAGAGAGC 59.408 37.037 0.00 0.00 0.00 4.09
3225 3748 9.396022 TGAGTGACTCTTTTTGAATTAAAGACT 57.604 29.630 14.42 0.00 36.86 3.24
3346 3874 9.964303 CAAAATCCATAATCGAATTGAATACCA 57.036 29.630 0.00 0.00 0.00 3.25
3358 3886 3.119849 GGCCCGATCAAAATCCATAATCG 60.120 47.826 0.00 0.00 39.05 3.34
3359 3887 3.826157 TGGCCCGATCAAAATCCATAATC 59.174 43.478 0.00 0.00 0.00 1.75
3361 3889 3.304911 TGGCCCGATCAAAATCCATAA 57.695 42.857 0.00 0.00 0.00 1.90
3362 3890 3.304911 TTGGCCCGATCAAAATCCATA 57.695 42.857 0.00 0.00 0.00 2.74
3363 3891 2.157640 TTGGCCCGATCAAAATCCAT 57.842 45.000 0.00 0.00 0.00 3.41
3365 3893 2.031120 TGATTGGCCCGATCAAAATCC 58.969 47.619 11.44 0.00 32.02 3.01
3400 3935 0.824595 TTATAGGCCGGTCGCTGCTA 60.825 55.000 1.90 0.00 37.74 3.49
3407 3942 5.818857 TGTCATAAGTTTTTATAGGCCGGTC 59.181 40.000 0.00 0.00 0.00 4.79
3409 3947 5.820947 AGTGTCATAAGTTTTTATAGGCCGG 59.179 40.000 0.00 0.00 0.00 6.13
3411 3949 7.625828 ACAGTGTCATAAGTTTTTATAGGCC 57.374 36.000 0.00 0.00 0.00 5.19
3430 4020 7.599998 TGCATGTACTATATTGATGCTACAGTG 59.400 37.037 11.82 0.00 40.11 3.66
3445 4035 3.628942 TCGTCGGTAGTTGCATGTACTAT 59.371 43.478 11.38 0.00 31.31 2.12
3456 4046 3.999001 GGGAAATTTCTTCGTCGGTAGTT 59.001 43.478 17.42 0.00 0.00 2.24
3457 4047 3.593096 GGGAAATTTCTTCGTCGGTAGT 58.407 45.455 17.42 0.00 0.00 2.73
3466 4056 7.992008 TCGTATTTATGTGGGGAAATTTCTTC 58.008 34.615 17.42 10.43 0.00 2.87
3467 4057 7.614192 ACTCGTATTTATGTGGGGAAATTTCTT 59.386 33.333 17.42 0.16 0.00 2.52
3469 4059 7.329588 ACTCGTATTTATGTGGGGAAATTTC 57.670 36.000 9.83 9.83 0.00 2.17
3489 4079 2.027688 GTGTTATCCGCGAAGAAACTCG 59.972 50.000 8.23 0.00 41.84 4.18
3499 4089 3.463533 TGTGATTTTGTGTTATCCGCG 57.536 42.857 0.00 0.00 0.00 6.46
3512 4102 2.025887 AGGGCCTTTCTCGATGTGATTT 60.026 45.455 0.00 0.00 0.00 2.17
3557 4147 5.418840 GGGAATATGATGGAGTGTGTTTTGT 59.581 40.000 0.00 0.00 0.00 2.83
3558 4148 5.449041 CGGGAATATGATGGAGTGTGTTTTG 60.449 44.000 0.00 0.00 0.00 2.44
3576 4166 1.587066 TAGTTTGGTAGGGCGGGAAT 58.413 50.000 0.00 0.00 0.00 3.01
3578 4168 1.360185 TTTAGTTTGGTAGGGCGGGA 58.640 50.000 0.00 0.00 0.00 5.14
3581 4171 4.212636 CGGAATATTTAGTTTGGTAGGGCG 59.787 45.833 0.00 0.00 0.00 6.13
3586 4176 8.895737 GGAATTGACGGAATATTTAGTTTGGTA 58.104 33.333 0.00 0.00 0.00 3.25
3587 4177 7.394923 TGGAATTGACGGAATATTTAGTTTGGT 59.605 33.333 0.00 0.00 0.00 3.67
3680 4274 5.132502 TCTGTTCAATCTTGTGGATGTTGT 58.867 37.500 0.00 0.00 34.45 3.32


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

AutoCloner maintained by Alex Coulton.