Multiple sequence alignment - TraesCS7D01G141300

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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 TraesCS7D01G141300 chr7D 100.000 4517 0 0 1 4517 90407095 90411611 0.000000e+00 8342.0
1 TraesCS7D01G141300 chr7D 89.091 110 8 3 3058 3163 190163112 190163221 2.830000e-27 134.0
2 TraesCS7D01G141300 chr7D 84.211 133 14 5 3061 3188 478795417 478795287 6.140000e-24 122.0
3 TraesCS7D01G141300 chr7B 93.652 1150 41 16 1828 2964 41284857 41285987 0.000000e+00 1690.0
4 TraesCS7D01G141300 chr7B 93.678 870 37 7 2990 3852 41286060 41286918 0.000000e+00 1286.0
5 TraesCS7D01G141300 chr7B 90.067 745 55 8 1118 1843 41283933 41284677 0.000000e+00 948.0
6 TraesCS7D01G141300 chr7B 88.953 688 36 17 376 1054 41283276 41283932 0.000000e+00 813.0
7 TraesCS7D01G141300 chr7B 89.048 420 38 4 3855 4267 41287005 41287423 8.660000e-142 514.0
8 TraesCS7D01G141300 chr7B 93.411 258 13 4 4261 4515 41287446 41287702 3.300000e-101 379.0
9 TraesCS7D01G141300 chr7B 85.574 305 30 11 59 351 41282109 41282411 1.580000e-79 307.0
10 TraesCS7D01G141300 chr7B 89.524 105 8 2 3063 3165 478835036 478835139 3.670000e-26 130.0
11 TraesCS7D01G141300 chr7A 85.643 1205 90 35 60 1235 91639438 91640588 0.000000e+00 1190.0
12 TraesCS7D01G141300 chr7A 100.000 29 0 0 5 33 91638278 91638306 2.000000e-03 54.7
13 TraesCS7D01G141300 chr3A 82.538 1048 130 27 1144 2165 668582377 668583397 0.000000e+00 872.0
14 TraesCS7D01G141300 chr3A 87.285 755 54 22 2169 2898 668225720 668226457 0.000000e+00 824.0
15 TraesCS7D01G141300 chr3A 86.720 753 72 16 2161 2898 668583523 668584262 0.000000e+00 811.0
16 TraesCS7D01G141300 chr3A 81.449 911 88 42 3156 4006 668226732 668227621 0.000000e+00 671.0
17 TraesCS7D01G141300 chr3A 84.233 463 36 17 3583 4012 668584933 668585391 2.510000e-112 416.0
18 TraesCS7D01G141300 chr1D 85.116 860 56 30 2161 2964 226468071 226468914 0.000000e+00 813.0
19 TraesCS7D01G141300 chr1D 83.371 896 93 36 3156 4012 226469083 226469961 0.000000e+00 778.0
20 TraesCS7D01G141300 chr1D 80.376 744 89 34 3156 3845 208413220 208412480 3.120000e-141 512.0
21 TraesCS7D01G141300 chr1D 82.807 570 62 21 3337 3874 223164513 223165078 1.140000e-130 477.0
22 TraesCS7D01G141300 chr1D 82.883 555 69 14 3307 3838 227375832 227376383 4.090000e-130 475.0
23 TraesCS7D01G141300 chr1D 86.667 435 43 11 2483 2912 208415554 208415130 6.840000e-128 468.0
24 TraesCS7D01G141300 chr1D 79.649 570 72 29 3310 3838 226827660 226828226 1.980000e-98 370.0
25 TraesCS7D01G141300 chr1D 85.175 371 39 7 1372 1735 226467443 226467804 2.570000e-97 366.0
26 TraesCS7D01G141300 chr1D 79.913 458 58 17 3156 3583 226945065 226945518 5.680000e-79 305.0
27 TraesCS7D01G141300 chr1D 87.129 202 24 1 1966 2165 457844645 457844846 1.260000e-55 228.0
28 TraesCS7D01G141300 chr1D 84.024 169 21 4 1490 1657 227653059 227653222 1.680000e-34 158.0
29 TraesCS7D01G141300 chr1D 83.929 168 21 4 1491 1657 208410536 208410374 6.050000e-34 156.0
30 TraesCS7D01G141300 chr1D 82.840 169 16 5 3156 3311 227375636 227375804 6.090000e-29 139.0
31 TraesCS7D01G141300 chr1D 89.623 106 9 1 2062 2165 226467834 226467939 2.830000e-27 134.0
32 TraesCS7D01G141300 chr1D 81.875 160 26 3 1509 1667 477791020 477790863 1.020000e-26 132.0
33 TraesCS7D01G141300 chr3B 86.569 752 74 16 2161 2898 705148383 705149121 0.000000e+00 804.0
34 TraesCS7D01G141300 chr3B 81.690 923 80 51 3156 4012 705149395 705150294 0.000000e+00 686.0
35 TraesCS7D01G141300 chr3B 82.886 298 35 10 1877 2165 705147960 705148250 2.090000e-63 254.0
36 TraesCS7D01G141300 chr3D 84.809 836 82 26 2161 2964 532869905 532870727 0.000000e+00 798.0
37 TraesCS7D01G141300 chr3D 81.164 945 118 29 1269 2165 532868858 532869790 0.000000e+00 704.0
38 TraesCS7D01G141300 chr3D 81.385 924 81 49 3156 4011 532870911 532871811 0.000000e+00 669.0
39 TraesCS7D01G141300 chr3D 98.113 53 1 0 751 803 532868377 532868429 4.810000e-15 93.5
40 TraesCS7D01G141300 chr1A 84.930 856 53 34 2161 2964 293736477 293737308 0.000000e+00 797.0
41 TraesCS7D01G141300 chr1A 82.924 896 97 33 3156 4012 293737477 293738355 0.000000e+00 756.0
42 TraesCS7D01G141300 chr1A 83.395 542 62 18 3304 3821 294041598 294042135 1.140000e-130 477.0
43 TraesCS7D01G141300 chr1A 80.428 654 92 22 1519 2160 550216991 550217620 2.460000e-127 466.0
44 TraesCS7D01G141300 chr1A 78.893 777 92 47 3156 3874 290126434 290127196 1.140000e-125 460.0
45 TraesCS7D01G141300 chr1A 79.562 685 88 26 1519 2165 550298310 550298980 4.150000e-120 442.0
46 TraesCS7D01G141300 chr1A 80.339 295 39 8 3583 3874 338593456 338593178 5.920000e-49 206.0
47 TraesCS7D01G141300 chr1A 80.139 287 25 15 506 780 293730714 293730980 7.720000e-43 185.0
48 TraesCS7D01G141300 chr1A 83.432 169 22 4 1490 1657 294514182 294514345 7.830000e-33 152.0
49 TraesCS7D01G141300 chr1A 82.249 169 17 7 3156 3311 294041406 294041574 2.830000e-27 134.0
50 TraesCS7D01G141300 chr1A 80.447 179 29 6 1490 1667 574273358 574273185 1.020000e-26 132.0
51 TraesCS7D01G141300 chr1A 83.721 129 14 6 3037 3162 590991980 590991856 1.030000e-21 115.0
52 TraesCS7D01G141300 chr1B 87.354 427 46 6 2474 2898 327343227 327343647 2.440000e-132 483.0
53 TraesCS7D01G141300 chr1B 83.005 559 67 15 3304 3838 327229803 327230357 8.790000e-132 481.0
54 TraesCS7D01G141300 chr1B 80.055 727 80 35 3156 3823 322475508 322476228 3.160000e-131 479.0
55 TraesCS7D01G141300 chr1B 79.730 740 89 31 3156 3838 326914158 326914893 3.160000e-131 479.0
56 TraesCS7D01G141300 chr1B 82.801 564 65 18 3304 3839 327345400 327345959 4.090000e-130 475.0
57 TraesCS7D01G141300 chr1B 84.615 169 20 4 1490 1657 327347926 327348089 3.620000e-36 163.0
58 TraesCS7D01G141300 chr1B 82.123 179 26 3 1490 1667 665246284 665246111 1.010000e-31 148.0
59 TraesCS7D01G141300 chr1B 86.885 122 14 1 2046 2165 627782091 627782212 7.880000e-28 135.0
60 TraesCS7D01G141300 chr1B 90.625 96 7 1 3063 3156 518802184 518802089 4.740000e-25 126.0
61 TraesCS7D01G141300 chr1B 81.065 169 19 7 3156 3311 327229611 327229779 6.140000e-24 122.0
62 TraesCS7D01G141300 chr4D 90.816 98 7 1 3064 3159 50462599 50462502 3.670000e-26 130.0
63 TraesCS7D01G141300 chr2A 90.816 98 7 1 3063 3158 85601289 85601386 3.670000e-26 130.0
64 TraesCS7D01G141300 chr2B 89.109 101 8 3 3060 3158 272682308 272682407 6.140000e-24 122.0


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 TraesCS7D01G141300 chr7D 90407095 90411611 4516 False 8342.000000 8342 100.000000 1 4517 1 chr7D.!!$F1 4516
1 TraesCS7D01G141300 chr7B 41282109 41287702 5593 False 848.142857 1690 90.626143 59 4515 7 chr7B.!!$F2 4456
2 TraesCS7D01G141300 chr7A 91638278 91640588 2310 False 622.350000 1190 92.821500 5 1235 2 chr7A.!!$F1 1230
3 TraesCS7D01G141300 chr3A 668225720 668227621 1901 False 747.500000 824 84.367000 2169 4006 2 chr3A.!!$F1 1837
4 TraesCS7D01G141300 chr3A 668582377 668585391 3014 False 699.666667 872 84.497000 1144 4012 3 chr3A.!!$F2 2868
5 TraesCS7D01G141300 chr1D 226467443 226469961 2518 False 522.750000 813 85.821250 1372 4012 4 chr1D.!!$F6 2640
6 TraesCS7D01G141300 chr1D 223164513 223165078 565 False 477.000000 477 82.807000 3337 3874 1 chr1D.!!$F1 537
7 TraesCS7D01G141300 chr1D 208410374 208415554 5180 True 378.666667 512 83.657333 1491 3845 3 chr1D.!!$R2 2354
8 TraesCS7D01G141300 chr1D 226827660 226828226 566 False 370.000000 370 79.649000 3310 3838 1 chr1D.!!$F2 528
9 TraesCS7D01G141300 chr1D 227375636 227376383 747 False 307.000000 475 82.861500 3156 3838 2 chr1D.!!$F7 682
10 TraesCS7D01G141300 chr3B 705147960 705150294 2334 False 581.333333 804 83.715000 1877 4012 3 chr3B.!!$F1 2135
11 TraesCS7D01G141300 chr3D 532868377 532871811 3434 False 566.125000 798 86.367750 751 4011 4 chr3D.!!$F1 3260
12 TraesCS7D01G141300 chr1A 293736477 293738355 1878 False 776.500000 797 83.927000 2161 4012 2 chr1A.!!$F6 1851
13 TraesCS7D01G141300 chr1A 550216991 550217620 629 False 466.000000 466 80.428000 1519 2160 1 chr1A.!!$F4 641
14 TraesCS7D01G141300 chr1A 290126434 290127196 762 False 460.000000 460 78.893000 3156 3874 1 chr1A.!!$F1 718
15 TraesCS7D01G141300 chr1A 550298310 550298980 670 False 442.000000 442 79.562000 1519 2165 1 chr1A.!!$F5 646
16 TraesCS7D01G141300 chr1A 294041406 294042135 729 False 305.500000 477 82.822000 3156 3821 2 chr1A.!!$F7 665
17 TraesCS7D01G141300 chr1B 322475508 322476228 720 False 479.000000 479 80.055000 3156 3823 1 chr1B.!!$F1 667
18 TraesCS7D01G141300 chr1B 326914158 326914893 735 False 479.000000 479 79.730000 3156 3838 1 chr1B.!!$F2 682
19 TraesCS7D01G141300 chr1B 327343227 327348089 4862 False 373.666667 483 84.923333 1490 3839 3 chr1B.!!$F5 2349
20 TraesCS7D01G141300 chr1B 327229611 327230357 746 False 301.500000 481 82.035000 3156 3838 2 chr1B.!!$F4 682

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
806 2780 0.247145 CATTCTCGCAAACCGTACGC 60.247 55.0 10.49 0.0 38.35 4.42 F
1466 3561 0.178068 TGAGAACTATTCTGCGCCCC 59.822 55.0 4.18 0.0 40.87 5.80 F
1960 4301 0.029163 TCCCATCCCATTCCCAGCTA 60.029 55.0 0.00 0.0 0.00 3.32 F
3158 7616 0.696501 TTTTGGGCCAGAGGGAGTAC 59.303 55.0 6.23 0.0 35.59 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 4292 0.036732 CACTTGCAGGTAGCTGGGAA 59.963 55.000 22.69 10.32 45.94 3.97 R
2740 5315 1.134946 GTTCATGGCCCAAGTGTATGC 59.865 52.381 0.00 0.00 0.00 3.14 R
3384 7941 2.107378 TGTACCTGTTGGCAAGAATGGA 59.893 45.455 9.29 0.00 36.63 3.41 R
4390 10251 0.258774 ACAGGGCAACAAGACTTGGT 59.741 50.000 19.16 10.30 36.46 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.598416 ACAGAGCAAACCTTTAAGCTTTT 57.402 34.783 3.20 0.00 37.48 2.27
35 36 5.360999 ACAGAGCAAACCTTTAAGCTTTTCT 59.639 36.000 3.20 0.00 37.48 2.52
37 38 7.231519 ACAGAGCAAACCTTTAAGCTTTTCTAT 59.768 33.333 3.20 0.00 37.48 1.98
38 39 7.752686 CAGAGCAAACCTTTAAGCTTTTCTATC 59.247 37.037 3.20 0.00 37.48 2.08
39 40 7.448469 AGAGCAAACCTTTAAGCTTTTCTATCA 59.552 33.333 3.20 0.00 37.48 2.15
40 41 7.371159 AGCAAACCTTTAAGCTTTTCTATCAC 58.629 34.615 3.20 0.00 32.52 3.06
42 43 7.114953 GCAAACCTTTAAGCTTTTCTATCACAC 59.885 37.037 3.20 0.00 0.00 3.82
43 44 6.481954 ACCTTTAAGCTTTTCTATCACACG 57.518 37.500 3.20 0.00 0.00 4.49
44 45 5.106673 ACCTTTAAGCTTTTCTATCACACGC 60.107 40.000 3.20 0.00 0.00 5.34
45 46 4.939509 TTAAGCTTTTCTATCACACGCC 57.060 40.909 3.20 0.00 0.00 5.68
55 332 1.028330 ATCACACGCCTGGCATGAAG 61.028 55.000 22.94 13.19 0.00 3.02
56 333 3.058160 ACACGCCTGGCATGAAGC 61.058 61.111 22.94 0.00 44.65 3.86
107 1215 5.976458 ACATCTGAAAAGAAAAGGCAAACA 58.024 33.333 0.00 0.00 0.00 2.83
142 1255 8.504812 AAGTTGCCATACAAAAAGAAAATTGT 57.495 26.923 0.00 0.00 40.82 2.71
218 1332 1.276989 TCCGGACTTACCATGTGTTCC 59.723 52.381 0.00 0.00 38.90 3.62
219 1333 1.002659 CCGGACTTACCATGTGTTCCA 59.997 52.381 0.00 0.00 38.90 3.53
221 1335 2.711542 GGACTTACCATGTGTTCCAGG 58.288 52.381 0.00 0.00 38.79 4.45
224 1338 4.080526 GGACTTACCATGTGTTCCAGGTAT 60.081 45.833 0.00 0.00 36.57 2.73
225 1339 4.843728 ACTTACCATGTGTTCCAGGTATG 58.156 43.478 0.00 0.00 36.57 2.39
226 1340 4.534500 ACTTACCATGTGTTCCAGGTATGA 59.466 41.667 0.00 0.00 36.57 2.15
227 1341 3.350219 ACCATGTGTTCCAGGTATGAC 57.650 47.619 0.00 0.00 31.32 3.06
307 1428 1.444933 TCCTCCCCGCAAATGGATAT 58.555 50.000 0.00 0.00 0.00 1.63
337 1466 5.657470 TGAATGACAGCGAAAGTATATGC 57.343 39.130 0.00 0.00 0.00 3.14
458 2427 1.135315 CCAGAAATCACTTGCCGCG 59.865 57.895 0.00 0.00 0.00 6.46
459 2428 1.298157 CCAGAAATCACTTGCCGCGA 61.298 55.000 8.23 0.00 0.00 5.87
462 2431 1.009829 GAAATCACTTGCCGCGAGAT 58.990 50.000 14.92 0.00 0.00 2.75
471 2440 2.024871 CCGCGAGATCCACGAGTC 59.975 66.667 8.23 0.00 0.00 3.36
598 2571 1.719600 CAGGTCTTTCTCCTGCTTCG 58.280 55.000 0.00 0.00 44.46 3.79
645 2618 3.087031 AGATTAGAGGGTTTCGACGACA 58.913 45.455 0.00 0.00 0.00 4.35
655 2628 1.214367 TTCGACGACAACTTTCAGGC 58.786 50.000 0.00 0.00 0.00 4.85
659 2632 2.993899 CGACGACAACTTTCAGGCTAAT 59.006 45.455 0.00 0.00 0.00 1.73
663 2636 2.742053 GACAACTTTCAGGCTAATGCGA 59.258 45.455 0.00 0.00 40.82 5.10
664 2637 2.484264 ACAACTTTCAGGCTAATGCGAC 59.516 45.455 0.00 0.00 40.82 5.19
665 2638 2.472695 ACTTTCAGGCTAATGCGACA 57.527 45.000 0.00 0.00 40.82 4.35
666 2639 2.991250 ACTTTCAGGCTAATGCGACAT 58.009 42.857 0.00 0.00 40.82 3.06
667 2640 3.347216 ACTTTCAGGCTAATGCGACATT 58.653 40.909 9.46 9.46 40.82 2.71
668 2641 3.127548 ACTTTCAGGCTAATGCGACATTG 59.872 43.478 13.17 6.52 40.82 2.82
669 2642 1.016627 TCAGGCTAATGCGACATTGC 58.983 50.000 13.17 13.18 40.82 3.56
670 2643 0.316442 CAGGCTAATGCGACATTGCG 60.316 55.000 13.17 7.10 40.82 4.85
671 2644 0.461870 AGGCTAATGCGACATTGCGA 60.462 50.000 13.17 0.00 40.82 5.10
714 2687 2.894763 TCGTTTGAGAAAGAACCGGA 57.105 45.000 9.46 0.00 0.00 5.14
717 2690 3.006537 TCGTTTGAGAAAGAACCGGATCT 59.993 43.478 9.46 9.03 0.00 2.75
806 2780 0.247145 CATTCTCGCAAACCGTACGC 60.247 55.000 10.49 0.00 38.35 4.42
958 2950 2.362077 AGGCGCCATGATTAATTTCACC 59.638 45.455 31.54 0.00 0.00 4.02
971 2963 2.727123 TTTCACCTGCAGACCAAGAA 57.273 45.000 17.39 8.57 0.00 2.52
1028 3020 1.144057 CCGGGAGCACAGGTATGTC 59.856 63.158 0.00 0.00 37.65 3.06
1066 3058 4.631131 ACTTCAGACATCGTGTTCATGAA 58.369 39.130 3.38 3.38 31.53 2.57
1067 3059 4.687948 ACTTCAGACATCGTGTTCATGAAG 59.312 41.667 8.80 22.13 43.49 3.02
1070 3062 5.056480 TCAGACATCGTGTTCATGAAGTTT 58.944 37.500 8.80 0.00 0.00 2.66
1071 3063 5.527214 TCAGACATCGTGTTCATGAAGTTTT 59.473 36.000 8.80 0.00 0.00 2.43
1072 3064 5.622448 CAGACATCGTGTTCATGAAGTTTTG 59.378 40.000 8.80 6.14 0.00 2.44
1073 3065 4.290155 ACATCGTGTTCATGAAGTTTTGC 58.710 39.130 8.80 0.00 0.00 3.68
1074 3066 4.202000 ACATCGTGTTCATGAAGTTTTGCA 60.202 37.500 8.80 0.00 0.00 4.08
1076 3068 4.289342 TCGTGTTCATGAAGTTTTGCATG 58.711 39.130 8.80 7.77 42.41 4.06
1077 3069 4.043750 CGTGTTCATGAAGTTTTGCATGT 58.956 39.130 8.80 0.00 41.88 3.21
1078 3070 4.085466 CGTGTTCATGAAGTTTTGCATGTG 60.085 41.667 8.80 0.00 41.88 3.21
1079 3071 4.805192 GTGTTCATGAAGTTTTGCATGTGT 59.195 37.500 8.80 0.00 41.88 3.72
1080 3072 5.976534 GTGTTCATGAAGTTTTGCATGTGTA 59.023 36.000 8.80 0.00 41.88 2.90
1081 3073 6.142798 GTGTTCATGAAGTTTTGCATGTGTAG 59.857 38.462 8.80 0.00 41.88 2.74
1082 3074 4.797471 TCATGAAGTTTTGCATGTGTAGC 58.203 39.130 0.00 0.00 41.88 3.58
1083 3075 4.520111 TCATGAAGTTTTGCATGTGTAGCT 59.480 37.500 0.00 0.00 41.88 3.32
1084 3076 4.488126 TGAAGTTTTGCATGTGTAGCTC 57.512 40.909 0.00 0.00 0.00 4.09
1085 3077 4.136796 TGAAGTTTTGCATGTGTAGCTCT 58.863 39.130 0.00 0.00 0.00 4.09
1086 3078 5.304778 TGAAGTTTTGCATGTGTAGCTCTA 58.695 37.500 0.00 0.00 0.00 2.43
1087 3079 5.762711 TGAAGTTTTGCATGTGTAGCTCTAA 59.237 36.000 0.00 0.00 0.00 2.10
1088 3080 6.262049 TGAAGTTTTGCATGTGTAGCTCTAAA 59.738 34.615 0.00 0.00 0.00 1.85
1089 3081 6.246420 AGTTTTGCATGTGTAGCTCTAAAG 57.754 37.500 0.00 0.00 0.00 1.85
1090 3082 5.765182 AGTTTTGCATGTGTAGCTCTAAAGT 59.235 36.000 0.00 0.00 0.00 2.66
1091 3083 5.862924 TTTGCATGTGTAGCTCTAAAGTC 57.137 39.130 0.00 0.00 0.00 3.01
1092 3084 4.535526 TGCATGTGTAGCTCTAAAGTCA 57.464 40.909 0.00 0.00 0.00 3.41
1093 3085 4.498241 TGCATGTGTAGCTCTAAAGTCAG 58.502 43.478 0.00 0.00 0.00 3.51
1094 3086 3.868077 GCATGTGTAGCTCTAAAGTCAGG 59.132 47.826 0.00 0.00 0.00 3.86
1095 3087 4.437239 CATGTGTAGCTCTAAAGTCAGGG 58.563 47.826 0.00 0.00 0.00 4.45
1096 3088 3.507411 TGTGTAGCTCTAAAGTCAGGGT 58.493 45.455 0.00 0.00 0.00 4.34
1097 3089 3.901844 TGTGTAGCTCTAAAGTCAGGGTT 59.098 43.478 0.00 0.00 0.00 4.11
1159 3151 9.384764 AGTCAGGTTACAGATAGCTTTAAATTC 57.615 33.333 0.00 0.00 0.00 2.17
1166 3158 9.959721 TTACAGATAGCTTTAAATTCAGGAAGT 57.040 29.630 0.00 0.00 0.00 3.01
1192 3187 0.729116 CCTCACCATCGTGCATGTTC 59.271 55.000 5.68 0.00 40.04 3.18
1247 3242 6.776744 TGCTGATCCTAATGCTTATTCATCT 58.223 36.000 0.00 0.00 0.00 2.90
1267 3333 9.817809 TTCATCTGAACCAATAGTAGATACAAC 57.182 33.333 0.00 0.00 0.00 3.32
1298 3367 8.545472 ACTTATACATGTAAAAGTGGCCTCTTA 58.455 33.333 19.95 5.39 31.20 2.10
1407 3498 3.638160 AGTGGTTGCTTGTCACAAATCAT 59.362 39.130 0.00 0.00 34.17 2.45
1462 3557 5.046529 ACATAGCTTGAGAACTATTCTGCG 58.953 41.667 0.00 0.00 40.87 5.18
1466 3561 0.178068 TGAGAACTATTCTGCGCCCC 59.822 55.000 4.18 0.00 40.87 5.80
1477 3572 3.518068 GCGCCCCTCCATTTTCCG 61.518 66.667 0.00 0.00 0.00 4.30
1587 3684 6.778821 TCAAATGGAAGGTTCATGACTTCTA 58.221 36.000 19.77 16.31 42.05 2.10
1588 3685 6.655003 TCAAATGGAAGGTTCATGACTTCTAC 59.345 38.462 19.77 6.08 42.05 2.59
1691 3801 5.120986 TCGCAATAGCAACTTTAATCAACGA 59.879 36.000 0.00 0.00 42.27 3.85
1794 3911 7.353414 TGTTTACCCAGAAATCATGTTTCAA 57.647 32.000 17.36 5.54 0.00 2.69
1913 4251 8.757982 AATGTTAGGCTTGATTCAGTTATGAT 57.242 30.769 0.00 0.00 34.73 2.45
1951 4292 4.033009 GTTTCCTTCAATTCCCATCCCAT 58.967 43.478 0.00 0.00 0.00 4.00
1952 4293 4.351110 TTCCTTCAATTCCCATCCCATT 57.649 40.909 0.00 0.00 0.00 3.16
1954 4295 2.967887 CCTTCAATTCCCATCCCATTCC 59.032 50.000 0.00 0.00 0.00 3.01
1955 4296 2.773525 TCAATTCCCATCCCATTCCC 57.226 50.000 0.00 0.00 0.00 3.97
1956 4297 1.935913 TCAATTCCCATCCCATTCCCA 59.064 47.619 0.00 0.00 0.00 4.37
1957 4298 2.091166 TCAATTCCCATCCCATTCCCAG 60.091 50.000 0.00 0.00 0.00 4.45
1958 4299 0.189327 ATTCCCATCCCATTCCCAGC 59.811 55.000 0.00 0.00 0.00 4.85
1959 4300 0.925720 TTCCCATCCCATTCCCAGCT 60.926 55.000 0.00 0.00 0.00 4.24
1960 4301 0.029163 TCCCATCCCATTCCCAGCTA 60.029 55.000 0.00 0.00 0.00 3.32
2137 4514 2.605837 TGCAAAGGTACTCGTGAACA 57.394 45.000 0.00 0.00 38.49 3.18
2167 4689 7.473735 TTTTAACTGCATCCATCCAATTACA 57.526 32.000 0.00 0.00 0.00 2.41
2228 4752 2.233271 AGTTTGTCCGTCGACCTTCTA 58.767 47.619 10.58 0.00 38.32 2.10
2338 4899 1.144913 TGCTAACTGGGGTGAAAGCTT 59.855 47.619 0.00 0.00 31.79 3.74
2388 4955 7.104043 AGTTGATTATGTGTCATTTGGGATG 57.896 36.000 0.00 0.00 0.00 3.51
2395 4962 4.942852 TGTGTCATTTGGGATGTTTTCAC 58.057 39.130 0.00 0.00 0.00 3.18
2400 4967 7.169140 GTGTCATTTGGGATGTTTTCACTTTAC 59.831 37.037 0.00 0.00 0.00 2.01
2401 4968 7.147828 TGTCATTTGGGATGTTTTCACTTTACA 60.148 33.333 0.00 0.00 0.00 2.41
2402 4969 7.708752 GTCATTTGGGATGTTTTCACTTTACAA 59.291 33.333 0.00 0.00 0.00 2.41
2403 4970 8.428063 TCATTTGGGATGTTTTCACTTTACAAT 58.572 29.630 0.00 0.00 0.00 2.71
2404 4971 9.054922 CATTTGGGATGTTTTCACTTTACAATT 57.945 29.630 0.00 0.00 0.00 2.32
2405 4972 9.625747 ATTTGGGATGTTTTCACTTTACAATTT 57.374 25.926 0.00 0.00 0.00 1.82
2669 5244 4.656112 TGTCTCTTCTCCTGAAAAGAAGGT 59.344 41.667 11.73 0.00 46.37 3.50
2740 5315 3.757947 AGAAGGGGTTCATTAAAGGGG 57.242 47.619 0.00 0.00 0.00 4.79
2752 5327 2.818751 TAAAGGGGCATACACTTGGG 57.181 50.000 0.00 0.00 0.00 4.12
2852 5428 7.948357 TGTATACATCTGGGTAGTTACATCAC 58.052 38.462 0.08 0.00 0.00 3.06
2928 5617 6.125029 CAGTCCTTCATATTCCAACTGGATT 58.875 40.000 0.00 0.00 44.98 3.01
2966 5661 9.770097 TCTCTAATCATTCAACCAAGATATGAC 57.230 33.333 0.00 0.00 0.00 3.06
2967 5662 9.551734 CTCTAATCATTCAACCAAGATATGACA 57.448 33.333 0.00 0.00 0.00 3.58
2968 5663 9.330063 TCTAATCATTCAACCAAGATATGACAC 57.670 33.333 0.00 0.00 0.00 3.67
2969 5664 9.334947 CTAATCATTCAACCAAGATATGACACT 57.665 33.333 0.00 0.00 0.00 3.55
2970 5665 8.585471 AATCATTCAACCAAGATATGACACTT 57.415 30.769 0.00 0.00 0.00 3.16
2971 5666 9.685276 AATCATTCAACCAAGATATGACACTTA 57.315 29.630 0.00 0.00 0.00 2.24
2972 5667 9.857656 ATCATTCAACCAAGATATGACACTTAT 57.142 29.630 0.00 0.00 0.00 1.73
2976 5671 8.506168 TCAACCAAGATATGACACTTATTTCC 57.494 34.615 0.00 0.00 0.00 3.13
2978 5673 8.960591 CAACCAAGATATGACACTTATTTCCTT 58.039 33.333 0.00 0.00 0.00 3.36
3073 7525 3.497332 TCCTTATCATGTACTCCCTCCG 58.503 50.000 0.00 0.00 0.00 4.63
3082 7534 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3158 7616 0.696501 TTTTGGGCCAGAGGGAGTAC 59.303 55.000 6.23 0.00 35.59 2.73
3333 7877 6.480524 TTCTGATTTCAGTAACCAATCACG 57.519 37.500 7.42 0.00 44.12 4.35
3443 8000 2.135933 GGTGACAAGTACAGCACTGAC 58.864 52.381 4.31 0.00 37.63 3.51
3461 8018 2.072298 GACTGCCTCAGCTTGTACTTG 58.928 52.381 0.00 0.00 40.80 3.16
3626 8233 8.977412 TGTAACCTCATGATTACAGTTGATCTA 58.023 33.333 14.96 0.00 36.59 1.98
3686 8331 1.716503 AGTTGGGGATGGCCTAACTTT 59.283 47.619 3.32 0.00 37.90 2.66
3845 8492 5.738619 TGTGTCTTCATCCTAGCAGTTAA 57.261 39.130 0.00 0.00 0.00 2.01
3852 8506 7.703197 GTCTTCATCCTAGCAGTTAAGAGTTAC 59.297 40.741 0.00 0.00 0.00 2.50
3907 9725 4.988540 TGTTCTTATGTTCACAAGGAGTCG 59.011 41.667 0.00 0.00 0.00 4.18
3919 9737 5.409520 TCACAAGGAGTCGAGAAATGATTTG 59.590 40.000 0.00 0.00 0.00 2.32
3920 9738 4.154918 ACAAGGAGTCGAGAAATGATTTGC 59.845 41.667 0.00 0.00 0.00 3.68
3928 9746 6.037610 AGTCGAGAAATGATTTGCAGGTATTC 59.962 38.462 0.00 0.00 0.00 1.75
3941 9759 5.419542 TGCAGGTATTCTTGTCTGTGATAC 58.580 41.667 0.00 0.00 0.00 2.24
3981 9803 5.163703 TGCGTCAATGTTGTCAGTTAAGTTT 60.164 36.000 0.00 0.00 0.00 2.66
4016 9838 6.745794 TGTGTATGGTTCCATGATCATCTA 57.254 37.500 4.86 0.00 0.00 1.98
4025 9847 6.294473 GTTCCATGATCATCTATGTTGGACT 58.706 40.000 4.86 0.00 31.83 3.85
4052 9874 2.497273 ACATTTTACATGCCTGCCCTTC 59.503 45.455 0.00 0.00 0.00 3.46
4062 9884 1.247567 CCTGCCCTTCGTGTCATTTT 58.752 50.000 0.00 0.00 0.00 1.82
4068 9890 2.350388 CCCTTCGTGTCATTTTTGACCG 60.350 50.000 3.84 7.04 37.99 4.79
4087 9910 3.444388 ACCGGTTTTGCTCTGTTTTAACA 59.556 39.130 0.00 0.00 37.37 2.41
4092 9915 4.647424 TTTGCTCTGTTTTAACACCTGG 57.353 40.909 0.00 0.00 34.70 4.45
4109 9932 3.527665 ACCTGGTATTTTGGCATCCTACT 59.472 43.478 0.00 0.00 0.00 2.57
4111 9934 4.580580 CCTGGTATTTTGGCATCCTACTTC 59.419 45.833 0.00 0.00 0.00 3.01
4119 9942 4.842531 TGGCATCCTACTTCTTTCATGA 57.157 40.909 0.00 0.00 0.00 3.07
4156 9979 1.078848 GCATCCTGACGAGTTGCCT 60.079 57.895 0.00 0.00 0.00 4.75
4209 10034 4.910195 TGTATTGGCTCTGATGTGACTTT 58.090 39.130 0.00 0.00 0.00 2.66
4213 10038 7.611467 TGTATTGGCTCTGATGTGACTTTTATT 59.389 33.333 0.00 0.00 0.00 1.40
4216 10041 7.994425 TGGCTCTGATGTGACTTTTATTTTA 57.006 32.000 0.00 0.00 0.00 1.52
4289 10147 5.042593 TGTGCAAATGTGTTTTCTGTCATC 58.957 37.500 0.00 0.00 0.00 2.92
4310 10168 3.149196 CAATTCACTTAGTGGGTGCACT 58.851 45.455 17.98 0.00 39.08 4.40
4330 10188 6.603237 CACTGAGTGTGTACATCAAAAGAA 57.397 37.500 4.01 0.00 41.53 2.52
4336 10194 6.729187 AGTGTGTACATCAAAAGAAAAGAGC 58.271 36.000 0.00 0.00 0.00 4.09
4337 10195 5.915196 GTGTGTACATCAAAAGAAAAGAGCC 59.085 40.000 0.00 0.00 0.00 4.70
4416 10277 2.430694 GTCTTGTTGCCCTGTTTTTCCT 59.569 45.455 0.00 0.00 0.00 3.36
4420 10281 2.834549 TGTTGCCCTGTTTTTCCTTTGA 59.165 40.909 0.00 0.00 0.00 2.69
4456 10317 0.737715 GTCCATTTCGTCGAGCAGCT 60.738 55.000 0.00 0.00 0.00 4.24
4474 10335 2.150809 CTGCGGCGCATACTGAATCG 62.151 60.000 36.35 16.43 38.13 3.34
4478 10339 1.334689 CGGCGCATACTGAATCGACTA 60.335 52.381 10.83 0.00 0.00 2.59
4516 10377 2.338620 GAGGCGGCCAACAAAACC 59.661 61.111 23.09 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.502136 AAAGGTTTGCTCTGTATCTTAAGC 57.498 37.500 0.00 0.00 35.31 3.09
33 34 0.179076 CATGCCAGGCGTGTGATAGA 60.179 55.000 23.98 0.00 40.30 1.98
35 36 0.251634 TTCATGCCAGGCGTGTGATA 59.748 50.000 29.45 10.83 44.84 2.15
37 38 1.672030 CTTCATGCCAGGCGTGTGA 60.672 57.895 29.45 19.24 44.84 3.58
38 39 2.872557 CTTCATGCCAGGCGTGTG 59.127 61.111 29.45 20.31 44.84 3.82
39 40 3.058160 GCTTCATGCCAGGCGTGT 61.058 61.111 29.45 5.76 44.84 4.49
40 41 2.332362 GATGCTTCATGCCAGGCGTG 62.332 60.000 25.99 25.99 45.79 5.34
42 43 2.719979 GATGCTTCATGCCAGGCG 59.280 61.111 7.03 0.00 42.00 5.52
43 44 1.455217 AGGATGCTTCATGCCAGGC 60.455 57.895 3.66 3.66 42.00 4.85
44 45 0.106868 TCAGGATGCTTCATGCCAGG 60.107 55.000 9.21 0.00 42.00 4.45
45 46 1.022735 GTCAGGATGCTTCATGCCAG 58.977 55.000 9.21 0.00 42.00 4.85
118 1226 7.768120 TGACAATTTTCTTTTTGTATGGCAACT 59.232 29.630 0.00 0.00 36.25 3.16
119 1227 7.914465 TGACAATTTTCTTTTTGTATGGCAAC 58.086 30.769 0.00 0.00 36.25 4.17
165 1278 3.923461 GCAAGTATAGTGATGCGAGGATC 59.077 47.826 0.00 0.00 0.00 3.36
199 1313 1.002659 TGGAACACATGGTAAGTCCGG 59.997 52.381 0.00 0.00 39.52 5.14
204 1318 4.876107 GTCATACCTGGAACACATGGTAAG 59.124 45.833 0.00 0.00 36.84 2.34
218 1332 5.068723 ACGACCCTAATAAGTGTCATACCTG 59.931 44.000 0.00 0.00 0.00 4.00
219 1333 5.068723 CACGACCCTAATAAGTGTCATACCT 59.931 44.000 0.00 0.00 0.00 3.08
221 1335 6.140303 TCACGACCCTAATAAGTGTCATAC 57.860 41.667 0.00 0.00 34.71 2.39
224 1338 3.119245 GCTCACGACCCTAATAAGTGTCA 60.119 47.826 0.00 0.00 34.71 3.58
225 1339 3.130693 AGCTCACGACCCTAATAAGTGTC 59.869 47.826 0.00 0.00 34.71 3.67
226 1340 3.097614 AGCTCACGACCCTAATAAGTGT 58.902 45.455 0.00 0.00 34.71 3.55
227 1341 3.802948 AGCTCACGACCCTAATAAGTG 57.197 47.619 0.00 0.00 0.00 3.16
307 1428 5.700832 ACTTTCGCTGTCATTCATGTTTCTA 59.299 36.000 0.00 0.00 0.00 2.10
353 1482 6.418057 TTTGACAGCACCCTCAATATTTTT 57.582 33.333 0.00 0.00 0.00 1.94
355 1484 6.891908 ACTATTTGACAGCACCCTCAATATTT 59.108 34.615 0.00 0.00 0.00 1.40
356 1485 6.426587 ACTATTTGACAGCACCCTCAATATT 58.573 36.000 0.00 0.00 0.00 1.28
358 1487 5.435686 ACTATTTGACAGCACCCTCAATA 57.564 39.130 0.00 0.00 0.00 1.90
359 1488 4.307032 ACTATTTGACAGCACCCTCAAT 57.693 40.909 0.00 0.00 0.00 2.57
360 1489 3.788227 ACTATTTGACAGCACCCTCAA 57.212 42.857 0.00 0.00 0.00 3.02
362 1491 5.880332 TCAATTACTATTTGACAGCACCCTC 59.120 40.000 0.00 0.00 0.00 4.30
365 1494 6.974622 CCAATCAATTACTATTTGACAGCACC 59.025 38.462 0.00 0.00 36.02 5.01
368 1497 9.722056 CTAACCAATCAATTACTATTTGACAGC 57.278 33.333 0.00 0.00 36.02 4.40
369 1498 9.722056 GCTAACCAATCAATTACTATTTGACAG 57.278 33.333 0.00 0.00 36.02 3.51
370 1499 8.394877 CGCTAACCAATCAATTACTATTTGACA 58.605 33.333 0.00 0.00 36.02 3.58
371 1500 8.395633 ACGCTAACCAATCAATTACTATTTGAC 58.604 33.333 0.00 0.00 36.02 3.18
374 1503 8.736244 ACAACGCTAACCAATCAATTACTATTT 58.264 29.630 0.00 0.00 0.00 1.40
458 2427 3.181485 CCTAACCAAGACTCGTGGATCTC 60.181 52.174 16.99 0.00 39.62 2.75
459 2428 2.761208 CCTAACCAAGACTCGTGGATCT 59.239 50.000 16.99 4.61 39.62 2.75
462 2431 2.297698 TCCTAACCAAGACTCGTGGA 57.702 50.000 16.99 0.00 39.62 4.02
471 2440 1.771255 AGGCTGCCTATCCTAACCAAG 59.229 52.381 21.98 0.00 28.47 3.61
513 2486 3.701205 TTGTTGGAGCTGCTAGATGAA 57.299 42.857 6.82 0.00 0.00 2.57
517 2490 1.795768 CGTTTGTTGGAGCTGCTAGA 58.204 50.000 6.82 0.00 0.00 2.43
593 2566 1.790481 GCGCAAACATAAGGACGAAGC 60.790 52.381 0.30 0.00 0.00 3.86
598 2571 2.084546 AGAAGGCGCAAACATAAGGAC 58.915 47.619 10.83 0.00 0.00 3.85
645 2618 2.778299 TGTCGCATTAGCCTGAAAGTT 58.222 42.857 0.00 0.00 37.52 2.66
655 2628 3.551890 ACTAAGTCGCAATGTCGCATTAG 59.448 43.478 5.03 13.44 35.40 1.73
659 2632 2.640346 TACTAAGTCGCAATGTCGCA 57.360 45.000 0.00 0.00 0.00 5.10
663 2636 3.873910 AGCCAATACTAAGTCGCAATGT 58.126 40.909 0.00 0.00 0.00 2.71
664 2637 4.882671 AAGCCAATACTAAGTCGCAATG 57.117 40.909 0.00 0.00 0.00 2.82
665 2638 5.186198 AGAAAGCCAATACTAAGTCGCAAT 58.814 37.500 0.00 0.00 0.00 3.56
666 2639 4.575885 AGAAAGCCAATACTAAGTCGCAA 58.424 39.130 0.00 0.00 0.00 4.85
667 2640 4.202245 AGAAAGCCAATACTAAGTCGCA 57.798 40.909 0.00 0.00 0.00 5.10
668 2641 4.201822 CCAAGAAAGCCAATACTAAGTCGC 60.202 45.833 0.00 0.00 0.00 5.19
669 2642 4.332819 CCCAAGAAAGCCAATACTAAGTCG 59.667 45.833 0.00 0.00 0.00 4.18
670 2643 4.096532 GCCCAAGAAAGCCAATACTAAGTC 59.903 45.833 0.00 0.00 0.00 3.01
671 2644 4.017126 GCCCAAGAAAGCCAATACTAAGT 58.983 43.478 0.00 0.00 0.00 2.24
714 2687 6.133356 AGTCGGGAGATTAGAAAGAAGAGAT 58.867 40.000 0.00 0.00 43.27 2.75
717 2690 5.480772 ACAAGTCGGGAGATTAGAAAGAAGA 59.519 40.000 0.00 0.00 43.27 2.87
806 2780 0.248458 GCCACAACGCGGAATTATGG 60.248 55.000 12.47 5.91 0.00 2.74
906 2894 6.014156 AGGGCATAGTGGATAAGATGTCTAAC 60.014 42.308 0.00 0.00 0.00 2.34
958 2950 4.384056 TCTTCTTTCTTCTTGGTCTGCAG 58.616 43.478 7.63 7.63 0.00 4.41
971 2963 1.632920 CTGCCCCTTCCTCTTCTTTCT 59.367 52.381 0.00 0.00 0.00 2.52
1028 3020 1.200020 GAAGTTGAATTGGGCGGACAG 59.800 52.381 0.00 0.00 0.00 3.51
1066 3058 5.765182 ACTTTAGAGCTACACATGCAAAACT 59.235 36.000 0.00 0.00 0.00 2.66
1067 3059 6.002062 ACTTTAGAGCTACACATGCAAAAC 57.998 37.500 0.00 0.00 0.00 2.43
1070 3062 4.893608 TGACTTTAGAGCTACACATGCAA 58.106 39.130 0.00 0.00 0.00 4.08
1071 3063 4.498241 CTGACTTTAGAGCTACACATGCA 58.502 43.478 0.00 0.00 0.00 3.96
1072 3064 3.868077 CCTGACTTTAGAGCTACACATGC 59.132 47.826 0.00 0.00 0.00 4.06
1073 3065 4.081420 ACCCTGACTTTAGAGCTACACATG 60.081 45.833 0.00 0.00 0.00 3.21
1074 3066 4.097418 ACCCTGACTTTAGAGCTACACAT 58.903 43.478 0.00 0.00 0.00 3.21
1076 3068 4.538746 AACCCTGACTTTAGAGCTACAC 57.461 45.455 0.00 0.00 0.00 2.90
1077 3069 5.081728 TGTAACCCTGACTTTAGAGCTACA 58.918 41.667 0.00 0.00 0.00 2.74
1078 3070 5.418209 TCTGTAACCCTGACTTTAGAGCTAC 59.582 44.000 0.00 0.00 0.00 3.58
1079 3071 5.577100 TCTGTAACCCTGACTTTAGAGCTA 58.423 41.667 0.00 0.00 0.00 3.32
1080 3072 4.417437 TCTGTAACCCTGACTTTAGAGCT 58.583 43.478 0.00 0.00 0.00 4.09
1081 3073 4.803098 TCTGTAACCCTGACTTTAGAGC 57.197 45.455 0.00 0.00 0.00 4.09
1082 3074 6.322712 AGCTATCTGTAACCCTGACTTTAGAG 59.677 42.308 0.00 0.00 0.00 2.43
1083 3075 6.195700 AGCTATCTGTAACCCTGACTTTAGA 58.804 40.000 0.00 0.00 0.00 2.10
1084 3076 6.472686 AGCTATCTGTAACCCTGACTTTAG 57.527 41.667 0.00 0.00 0.00 1.85
1085 3077 6.869206 AAGCTATCTGTAACCCTGACTTTA 57.131 37.500 0.00 0.00 0.00 1.85
1086 3078 5.763876 AAGCTATCTGTAACCCTGACTTT 57.236 39.130 0.00 0.00 0.00 2.66
1087 3079 5.763876 AAAGCTATCTGTAACCCTGACTT 57.236 39.130 0.00 0.00 0.00 3.01
1088 3080 6.869206 TTAAAGCTATCTGTAACCCTGACT 57.131 37.500 0.00 0.00 0.00 3.41
1089 3081 8.507524 AATTTAAAGCTATCTGTAACCCTGAC 57.492 34.615 0.00 0.00 0.00 3.51
1090 3082 9.528489 AAAATTTAAAGCTATCTGTAACCCTGA 57.472 29.630 0.00 0.00 0.00 3.86
1091 3083 9.573133 CAAAATTTAAAGCTATCTGTAACCCTG 57.427 33.333 0.00 0.00 0.00 4.45
1092 3084 8.251026 GCAAAATTTAAAGCTATCTGTAACCCT 58.749 33.333 0.00 0.00 0.00 4.34
1093 3085 8.032451 TGCAAAATTTAAAGCTATCTGTAACCC 58.968 33.333 10.34 0.00 0.00 4.11
1094 3086 8.980143 TGCAAAATTTAAAGCTATCTGTAACC 57.020 30.769 10.34 0.00 0.00 2.85
1097 3089 9.571810 CACATGCAAAATTTAAAGCTATCTGTA 57.428 29.630 0.00 0.00 0.00 2.74
1159 3151 1.528129 GTGAGGGCAAGAACTTCCTG 58.472 55.000 0.55 0.00 0.00 3.86
1166 3158 2.066340 ACGATGGTGAGGGCAAGAA 58.934 52.632 0.00 0.00 0.00 2.52
1192 3187 4.036498 GCATTCAGAGGGATTCAGTTCATG 59.964 45.833 0.00 0.00 0.00 3.07
1266 3332 9.813446 GCCACTTTTACATGTATAAGTAGTAGT 57.187 33.333 29.49 13.24 35.93 2.73
1267 3333 9.257651 GGCCACTTTTACATGTATAAGTAGTAG 57.742 37.037 29.49 20.86 35.93 2.57
1332 3408 1.408822 GGCAGGGATACAAAGGACAGG 60.409 57.143 0.00 0.00 39.74 4.00
1462 3557 1.037579 CCTTCGGAAAATGGAGGGGC 61.038 60.000 0.00 0.00 0.00 5.80
1466 3561 4.009675 TGTTCATCCTTCGGAAAATGGAG 58.990 43.478 10.95 2.30 34.34 3.86
1477 3572 9.696917 AACAACTCAAAATTATGTTCATCCTTC 57.303 29.630 0.00 0.00 28.61 3.46
1504 3599 4.401925 CTGAAATTTCCACAGAAGGAGGT 58.598 43.478 15.48 0.00 39.25 3.85
1587 3684 0.454620 CTTCGTCTCAAGTAGCGCGT 60.455 55.000 8.43 0.00 0.00 6.01
1588 3685 1.134530 CCTTCGTCTCAAGTAGCGCG 61.135 60.000 0.00 0.00 0.00 6.86
1772 3889 8.187913 TGATTGAAACATGATTTCTGGGTAAA 57.812 30.769 16.46 6.77 0.00 2.01
1812 3929 6.272318 GGTTTGTGAGATTGTGAATTTGTGA 58.728 36.000 0.00 0.00 0.00 3.58
1891 4229 8.462016 ACAAATCATAACTGAATCAAGCCTAAC 58.538 33.333 0.00 0.00 34.37 2.34
1913 4251 7.340256 TGAAGGAAACCAAGTAAGTCTACAAA 58.660 34.615 0.00 0.00 0.00 2.83
1951 4292 0.036732 CACTTGCAGGTAGCTGGGAA 59.963 55.000 22.69 10.32 45.94 3.97
1952 4293 0.835971 TCACTTGCAGGTAGCTGGGA 60.836 55.000 22.69 0.74 45.94 4.37
1954 4295 0.322975 AGTCACTTGCAGGTAGCTGG 59.677 55.000 22.69 9.33 45.94 4.85
1955 4296 1.674221 GGAGTCACTTGCAGGTAGCTG 60.674 57.143 17.67 17.67 45.94 4.24
1956 4297 0.610687 GGAGTCACTTGCAGGTAGCT 59.389 55.000 0.00 2.46 45.94 3.32
1957 4298 0.321671 TGGAGTCACTTGCAGGTAGC 59.678 55.000 0.00 0.00 45.96 3.58
1958 4299 2.839486 TTGGAGTCACTTGCAGGTAG 57.161 50.000 0.00 0.00 0.00 3.18
1959 4300 2.810400 GCTTTGGAGTCACTTGCAGGTA 60.810 50.000 0.00 0.00 0.00 3.08
1960 4301 1.972872 CTTTGGAGTCACTTGCAGGT 58.027 50.000 0.00 0.00 0.00 4.00
2146 4523 7.201902 GGAAATGTAATTGGATGGATGCAGTTA 60.202 37.037 0.00 0.00 36.10 2.24
2151 4528 4.344679 TGGGAAATGTAATTGGATGGATGC 59.655 41.667 0.00 0.00 36.10 3.91
2167 4689 6.418057 TCAAGCAACTTGTTAATGGGAAAT 57.582 33.333 7.18 0.00 41.66 2.17
2669 5244 2.687935 GCCTTCTTCTGAACCACAACAA 59.312 45.455 0.00 0.00 0.00 2.83
2740 5315 1.134946 GTTCATGGCCCAAGTGTATGC 59.865 52.381 0.00 0.00 0.00 3.14
2752 5327 5.122711 CCAATTCAAGGAAATTGTTCATGGC 59.877 40.000 8.15 0.00 42.50 4.40
2947 5642 9.685276 AATAAGTGTCATATCTTGGTTGAATGA 57.315 29.630 0.00 0.00 0.00 2.57
2951 5646 8.328758 AGGAAATAAGTGTCATATCTTGGTTGA 58.671 33.333 0.00 0.00 0.00 3.18
3073 7525 7.039313 AGAAAGTTGACACTTATTTTGGGAC 57.961 36.000 0.00 0.00 42.89 4.46
3108 7562 7.982919 TGTCACAGCTTTAGTAGAACTTTGTAA 59.017 33.333 0.00 0.00 0.00 2.41
3118 7576 8.230486 CCAAAATAAGTGTCACAGCTTTAGTAG 58.770 37.037 5.62 0.00 0.00 2.57
3127 7585 2.890311 TGGCCCAAAATAAGTGTCACAG 59.110 45.455 5.62 0.00 0.00 3.66
3158 7616 6.674066 ACAAGAACCGTTTGTACCAAATATG 58.326 36.000 0.00 0.00 37.02 1.78
3333 7877 7.771183 TGCTTGGGAAAATGTATATCAAGAAC 58.229 34.615 0.00 0.00 33.96 3.01
3384 7941 2.107378 TGTACCTGTTGGCAAGAATGGA 59.893 45.455 9.29 0.00 36.63 3.41
3443 8000 2.175878 ACAAGTACAAGCTGAGGCAG 57.824 50.000 0.00 0.00 41.70 4.85
3461 8018 2.297597 CTCATCCGAGGTATCCAGGAAC 59.702 54.545 0.00 0.00 36.51 3.62
3626 8233 3.686016 ACCTGCGATCACCATAAAAGTT 58.314 40.909 0.00 0.00 0.00 2.66
3686 8331 4.042809 TCCTTGAGTTTCTTGAGCCCAATA 59.957 41.667 0.00 0.00 0.00 1.90
3845 8492 8.928448 ACAACACCATCTCATATATGTAACTCT 58.072 33.333 12.42 0.00 0.00 3.24
3852 8506 6.528321 AGTCCACAACACCATCTCATATATG 58.472 40.000 6.36 6.36 0.00 1.78
3907 9725 7.542025 ACAAGAATACCTGCAAATCATTTCTC 58.458 34.615 0.00 0.00 0.00 2.87
3919 9737 5.665459 AGTATCACAGACAAGAATACCTGC 58.335 41.667 0.00 0.00 0.00 4.85
3941 9759 8.559536 ACATTGACGCACTTCCAAATAATATAG 58.440 33.333 0.00 0.00 0.00 1.31
3958 9776 4.468095 ACTTAACTGACAACATTGACGC 57.532 40.909 0.00 0.00 0.00 5.19
3981 9803 3.342719 ACCATACACATCATGCAAACGA 58.657 40.909 0.00 0.00 0.00 3.85
4016 9838 2.592102 AATGTCCAGCAGTCCAACAT 57.408 45.000 0.00 0.00 32.15 2.71
4025 9847 2.492881 CAGGCATGTAAAATGTCCAGCA 59.507 45.455 0.00 0.00 0.00 4.41
4052 9874 2.766970 AACCGGTCAAAAATGACACG 57.233 45.000 8.04 10.73 40.38 4.49
4062 9884 1.757682 AACAGAGCAAAACCGGTCAA 58.242 45.000 8.04 0.00 35.83 3.18
4068 9890 4.803613 CAGGTGTTAAAACAGAGCAAAACC 59.196 41.667 0.00 0.00 40.05 3.27
4087 9910 3.527665 AGTAGGATGCCAAAATACCAGGT 59.472 43.478 0.00 0.00 0.00 4.00
4092 9915 7.391148 TGAAAGAAGTAGGATGCCAAAATAC 57.609 36.000 0.00 0.00 0.00 1.89
4119 9942 9.590451 CAGGATGCAAGACAAATGTTAATTAAT 57.410 29.630 0.31 0.00 0.00 1.40
4133 9956 1.728971 CAACTCGTCAGGATGCAAGAC 59.271 52.381 0.00 0.00 34.76 3.01
4138 9961 3.490890 GGCAACTCGTCAGGATGC 58.509 61.111 0.00 0.00 36.39 3.91
4156 9979 4.579753 ACCCACGGAAAAATTAGTCGAAAA 59.420 37.500 0.00 0.00 0.00 2.29
4185 10008 5.108187 AGTCACATCAGAGCCAATACAAT 57.892 39.130 0.00 0.00 0.00 2.71
4209 10034 9.321562 GGTCGTCAATATTCAGGAGTAAAATAA 57.678 33.333 0.00 0.00 0.00 1.40
4213 10038 6.540438 AGGTCGTCAATATTCAGGAGTAAA 57.460 37.500 0.00 0.00 0.00 2.01
4216 10041 4.466370 TGAAGGTCGTCAATATTCAGGAGT 59.534 41.667 0.00 0.00 0.00 3.85
4289 10147 3.559238 GTGCACCCACTAAGTGAATTG 57.441 47.619 5.22 0.00 38.93 2.32
4310 10168 7.467267 GCTCTTTTCTTTTGATGTACACACTCA 60.467 37.037 0.00 0.00 0.00 3.41
4327 10185 1.308998 CAACACACCGGCTCTTTTCT 58.691 50.000 0.00 0.00 0.00 2.52
4330 10188 2.193536 GGCAACACACCGGCTCTTT 61.194 57.895 0.00 0.00 0.00 2.52
4382 10243 3.769536 CAACAAGACTTGGTTGTGTTCC 58.230 45.455 19.16 0.00 38.17 3.62
4390 10251 0.258774 ACAGGGCAACAAGACTTGGT 59.741 50.000 19.16 10.30 36.46 3.67
4416 10277 2.361757 CACACAGGCCAACAAGATCAAA 59.638 45.455 5.01 0.00 0.00 2.69
4420 10281 1.609208 GACACACAGGCCAACAAGAT 58.391 50.000 5.01 0.00 0.00 2.40
4456 10317 2.237066 CGATTCAGTATGCGCCGCA 61.237 57.895 16.69 16.69 44.86 5.69
4474 10335 3.919216 TGCTCTCTCACTGCTTTTAGTC 58.081 45.455 0.00 0.00 0.00 2.59
4478 10339 2.883386 CCTTTGCTCTCTCACTGCTTTT 59.117 45.455 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.