Multiple sequence alignment - TraesCS6D01G366500

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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 TraesCS6D01G366500 chr6D 100.000 9282 0 0 1 9282 454929681 454938962 0.000000e+00 17141.0
1 TraesCS6D01G366500 chr6D 88.742 151 16 1 7954 8104 218393524 218393673 5.720000e-42 183.0
2 TraesCS6D01G366500 chr6D 87.417 151 18 1 7954 8104 467084170 467084021 1.240000e-38 172.0
3 TraesCS6D01G366500 chr6D 88.889 54 4 2 713 766 366708963 366709014 2.160000e-06 65.8
4 TraesCS6D01G366500 chr6A 96.364 3988 114 12 1012 4973 601222045 601226027 0.000000e+00 6532.0
5 TraesCS6D01G366500 chr6A 93.178 3723 160 42 4973 8636 601226107 601229794 0.000000e+00 5382.0
6 TraesCS6D01G366500 chr6A 89.165 683 40 5 8630 9278 601229841 601230523 0.000000e+00 821.0
7 TraesCS6D01G366500 chr6A 98.261 115 2 0 767 881 601221562 601221676 1.580000e-47 202.0
8 TraesCS6D01G366500 chr6A 87.640 89 7 4 8608 8693 381109462 381109549 5.930000e-17 100.0
9 TraesCS6D01G366500 chr6A 90.909 44 3 1 717 760 50868315 50868357 3.620000e-04 58.4
10 TraesCS6D01G366500 chr6B 95.912 3963 116 16 883 4812 692024541 692028490 0.000000e+00 6379.0
11 TraesCS6D01G366500 chr6B 89.395 2395 127 49 6194 8510 692030102 692032447 0.000000e+00 2898.0
12 TraesCS6D01G366500 chr6B 96.858 1305 21 8 4904 6198 692028489 692029783 0.000000e+00 2165.0
13 TraesCS6D01G366500 chr6B 87.417 151 18 1 7954 8104 489430839 489430690 1.240000e-38 172.0
14 TraesCS6D01G366500 chr6B 85.156 128 12 5 765 888 692024248 692024372 3.520000e-24 124.0
15 TraesCS6D01G366500 chr6B 86.408 103 11 3 9182 9282 73428613 73428512 9.850000e-20 110.0
16 TraesCS6D01G366500 chr6B 90.741 54 3 2 713 766 59821918 59821867 4.650000e-08 71.3
17 TraesCS6D01G366500 chr5A 85.483 3217 319 64 2126 5266 88025097 88028241 0.000000e+00 3217.0
18 TraesCS6D01G366500 chr5A 84.352 818 94 22 1147 1935 88023854 88024666 0.000000e+00 771.0
19 TraesCS6D01G366500 chr5A 80.022 926 117 35 5291 6177 88028309 88029205 2.850000e-174 623.0
20 TraesCS6D01G366500 chr5A 80.651 522 65 18 6372 6882 88029418 88029914 1.140000e-98 372.0
21 TraesCS6D01G366500 chr5A 83.333 138 15 3 1979 2116 88024681 88024810 4.550000e-23 121.0
22 TraesCS6D01G366500 chr5A 92.105 76 4 2 8611 8685 446749266 446749192 1.270000e-18 106.0
23 TraesCS6D01G366500 chr5A 87.805 82 3 5 7094 7175 88030122 88030196 1.280000e-13 89.8
24 TraesCS6D01G366500 chr5D 86.650 2824 273 50 2126 4889 94065682 94068461 0.000000e+00 3031.0
25 TraesCS6D01G366500 chr5D 88.125 960 94 10 3640 4579 9377195 9378154 0.000000e+00 1123.0
26 TraesCS6D01G366500 chr5D 88.141 936 102 6 3808 4737 9371663 9372595 0.000000e+00 1105.0
27 TraesCS6D01G366500 chr5D 86.688 924 102 6 3818 4737 9353900 9354806 0.000000e+00 1005.0
28 TraesCS6D01G366500 chr5D 83.234 1002 120 30 1147 2116 94064408 94065393 0.000000e+00 876.0
29 TraesCS6D01G366500 chr5D 87.835 485 43 14 2985 3465 9376677 9377149 1.050000e-153 555.0
30 TraesCS6D01G366500 chr5D 87.629 485 45 12 2985 3465 9353427 9353900 4.900000e-152 549.0
31 TraesCS6D01G366500 chr5D 80.505 554 57 22 5642 6177 94069290 94069810 2.450000e-100 377.0
32 TraesCS6D01G366500 chr5D 86.643 277 32 3 5359 5632 94068958 94069232 1.510000e-77 302.0
33 TraesCS6D01G366500 chr5D 91.391 151 10 3 2985 3134 9371508 9371656 4.390000e-48 204.0
34 TraesCS6D01G366500 chr5D 79.239 289 42 7 4993 5266 94068521 94068806 1.590000e-42 185.0
35 TraesCS6D01G366500 chr5D 90.698 86 7 1 9197 9282 425065728 425065812 7.620000e-21 113.0
36 TraesCS6D01G366500 chr5D 87.805 82 3 5 7094 7175 94070729 94070803 1.280000e-13 89.8
37 TraesCS6D01G366500 chr5B 87.544 1686 134 33 2126 3778 101416634 101418276 0.000000e+00 1881.0
38 TraesCS6D01G366500 chr5B 83.951 1483 187 26 3808 5266 101418402 101419857 0.000000e+00 1373.0
39 TraesCS6D01G366500 chr5B 83.250 997 120 29 1152 2116 101415361 101416342 0.000000e+00 872.0
40 TraesCS6D01G366500 chr5B 82.098 715 76 24 5291 5976 101419925 101420616 1.750000e-156 564.0
41 TraesCS6D01G366500 chr5B 81.144 472 60 15 6372 6838 101421054 101421501 1.480000e-92 351.0
42 TraesCS6D01G366500 chr5B 79.803 203 28 2 1 190 479618206 479618004 1.630000e-27 135.0
43 TraesCS6D01G366500 chr5B 91.463 82 7 0 9194 9275 642304988 642305069 7.620000e-21 113.0
44 TraesCS6D01G366500 chr5B 92.105 76 4 2 8608 8682 597850971 597851045 1.270000e-18 106.0
45 TraesCS6D01G366500 chr5B 85.366 82 2 6 7094 7175 101421744 101421815 9.990000e-10 76.8
46 TraesCS6D01G366500 chr5B 95.652 46 1 1 721 766 591643737 591643693 1.290000e-08 73.1
47 TraesCS6D01G366500 chr5B 87.302 63 7 1 715 776 51960697 51960635 4.650000e-08 71.3
48 TraesCS6D01G366500 chr5B 90.566 53 3 2 713 764 579593537 579593588 1.670000e-07 69.4
49 TraesCS6D01G366500 chr5B 90.000 50 4 1 715 763 455802703 455802654 7.780000e-06 63.9
50 TraesCS6D01G366500 chr2B 84.408 1629 194 24 3138 4743 371892632 371894223 0.000000e+00 1546.0
51 TraesCS6D01G366500 chr2B 83.030 825 72 24 1 767 296084407 296083593 0.000000e+00 686.0
52 TraesCS6D01G366500 chr3D 87.443 653 64 8 2985 3633 170178432 170177794 0.000000e+00 736.0
53 TraesCS6D01G366500 chr3D 92.857 126 9 0 2924 3049 170178551 170178426 5.720000e-42 183.0
54 TraesCS6D01G366500 chr3D 80.882 204 27 4 1 192 462545659 462545456 5.810000e-32 150.0
55 TraesCS6D01G366500 chr3A 86.772 567 61 7 3073 3634 207777239 207776682 3.680000e-173 619.0
56 TraesCS6D01G366500 chr3A 89.888 89 8 1 9194 9282 735599439 735599526 7.620000e-21 113.0
57 TraesCS6D01G366500 chr3B 90.066 151 14 1 7954 8104 151199134 151199283 2.640000e-45 195.0
58 TraesCS6D01G366500 chr3B 89.344 122 12 1 1 122 798409893 798410013 1.610000e-32 152.0
59 TraesCS6D01G366500 chr2D 89.474 152 14 2 7954 8104 524963648 524963798 3.420000e-44 191.0
60 TraesCS6D01G366500 chr1A 88.079 151 17 1 7954 8104 39438989 39438840 2.660000e-40 178.0
61 TraesCS6D01G366500 chr1A 91.667 72 4 2 8611 8681 64565605 64565535 2.130000e-16 99.0
62 TraesCS6D01G366500 chr7A 85.143 175 18 6 7955 8124 1528645 1528816 1.240000e-38 172.0
63 TraesCS6D01G366500 chr7A 87.500 88 7 4 8593 8678 465769175 465769260 2.130000e-16 99.0
64 TraesCS6D01G366500 chr7A 90.566 53 3 2 713 764 289118650 289118701 1.670000e-07 69.4
65 TraesCS6D01G366500 chr4B 89.888 89 8 1 9194 9282 629957840 629957927 7.620000e-21 113.0
66 TraesCS6D01G366500 chr4B 87.368 95 10 2 9183 9275 35064856 35064950 3.540000e-19 108.0
67 TraesCS6D01G366500 chr7B 78.736 174 31 5 7951 8122 54907443 54907274 2.740000e-20 111.0
68 TraesCS6D01G366500 chr7B 89.873 79 6 2 8605 8682 446142996 446143073 5.930000e-17 100.0
69 TraesCS6D01G366500 chr7B 90.566 53 3 2 713 764 7841035 7841086 1.670000e-07 69.4
70 TraesCS6D01G366500 chrUn 88.764 89 10 0 9194 9282 264394227 264394315 9.850000e-20 110.0
71 TraesCS6D01G366500 chr4A 90.123 81 8 0 9197 9277 87416023 87415943 1.270000e-18 106.0
72 TraesCS6D01G366500 chr4A 90.244 82 5 3 8598 8678 222527739 222527818 4.580000e-18 104.0
73 TraesCS6D01G366500 chr1D 93.056 72 3 2 8608 8678 494172172 494172242 4.580000e-18 104.0
74 TraesCS6D01G366500 chr1D 93.617 47 2 1 719 765 468838565 468838520 1.670000e-07 69.4
75 TraesCS6D01G366500 chr2A 90.769 65 6 0 700 764 12151084 12151148 4.620000e-13 87.9
76 TraesCS6D01G366500 chr2A 90.625 64 6 0 701 764 33653139 33653076 1.660000e-12 86.1


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 TraesCS6D01G366500 chr6D 454929681 454938962 9281 False 17141.000000 17141 100.000000 1 9282 1 chr6D.!!$F3 9281
1 TraesCS6D01G366500 chr6A 601221562 601230523 8961 False 3234.250000 6532 94.242000 767 9278 4 chr6A.!!$F3 8511
2 TraesCS6D01G366500 chr6B 692024248 692032447 8199 False 2891.500000 6379 91.830250 765 8510 4 chr6B.!!$F1 7745
3 TraesCS6D01G366500 chr5A 88023854 88030196 6342 False 865.633333 3217 83.607667 1147 7175 6 chr5A.!!$F1 6028
4 TraesCS6D01G366500 chr5D 9376677 9378154 1477 False 839.000000 1123 87.980000 2985 4579 2 chr5D.!!$F4 1594
5 TraesCS6D01G366500 chr5D 94064408 94070803 6395 False 810.133333 3031 84.012667 1147 7175 6 chr5D.!!$F5 6028
6 TraesCS6D01G366500 chr5D 9353427 9354806 1379 False 777.000000 1005 87.158500 2985 4737 2 chr5D.!!$F2 1752
7 TraesCS6D01G366500 chr5D 9371508 9372595 1087 False 654.500000 1105 89.766000 2985 4737 2 chr5D.!!$F3 1752
8 TraesCS6D01G366500 chr5B 101415361 101421815 6454 False 852.966667 1881 83.892167 1152 7175 6 chr5B.!!$F4 6023
9 TraesCS6D01G366500 chr2B 371892632 371894223 1591 False 1546.000000 1546 84.408000 3138 4743 1 chr2B.!!$F1 1605
10 TraesCS6D01G366500 chr2B 296083593 296084407 814 True 686.000000 686 83.030000 1 767 1 chr2B.!!$R1 766
11 TraesCS6D01G366500 chr3D 170177794 170178551 757 True 459.500000 736 90.150000 2924 3633 2 chr3D.!!$R2 709
12 TraesCS6D01G366500 chr3A 207776682 207777239 557 True 619.000000 619 86.772000 3073 3634 1 chr3A.!!$R1 561

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
130 150 0.173935 CTACAACCGGTACCATCGCA 59.826 55.000 8.00 0.00 0.00 5.10 F
1009 1350 1.182667 GGTAAAAGGCATGACCCACC 58.817 55.000 0.00 0.00 40.58 4.61 F
1610 1974 1.451207 GTCATGTATGGCCGTGGCA 60.451 57.895 13.76 7.13 44.11 4.92 F
1726 2098 1.672145 GGCCGGTTGACTAGAACTGAC 60.672 57.143 1.90 0.00 34.59 3.51 F
2112 2485 1.745087 GCTGTGCCTGCTTAGCAATAA 59.255 47.619 8.68 0.00 43.02 1.40 F
3747 4528 0.677731 TGTTGAGCCTGGCTGCATAC 60.678 55.000 28.82 20.27 39.88 2.39 F
4155 5037 1.520787 GAGTAATGCCGACCACCCG 60.521 63.158 0.00 0.00 0.00 5.28 F
4383 5277 2.362077 CCTTGGTTACATATGGGCAAGC 59.638 50.000 7.80 8.18 0.00 4.01 F
5746 6859 3.550842 GGGGTCATGCGCTTTTTGATATC 60.551 47.826 9.73 0.00 0.00 1.63 F
6285 7768 0.449786 TTGTTGTGTTGGTGCACGAG 59.550 50.000 11.45 0.00 41.94 4.18 F
7438 9047 1.133637 TGGCTGGTGCTTCCAAGTAAA 60.134 47.619 3.15 0.00 46.59 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1040 1381 0.459078 GTCGTACCTGGGCTTAGGAC 59.541 60.000 13.9 0.0 40.42 3.85 R
1899 2271 1.404391 CCATCACAATCTCTTGCTGGC 59.596 52.381 0.0 0.0 35.69 4.85 R
2910 3595 2.005451 GGCACTCAAGATACTGCACTG 58.995 52.381 0.0 0.0 0.00 3.66 R
3156 3899 4.463891 CCTGATGCCTTGTAAATTCCTTGT 59.536 41.667 0.0 0.0 0.00 3.16 R
3892 4771 2.107950 TTGAATAGGCAGGGACAACG 57.892 50.000 0.0 0.0 0.00 4.10 R
4632 5528 4.039124 AGGGTAAACAAATCAGCAAAGTGG 59.961 41.667 0.0 0.0 0.00 4.00 R
5232 6231 4.957684 ACTAGTTAATTATCGGCAGGCT 57.042 40.909 0.0 0.0 0.00 4.58 R
6285 7768 0.539518 GAGGCCCTTCCAAGAGTCTC 59.460 60.000 0.0 0.0 37.29 3.36 R
7312 8921 0.109781 CCTCACGGGCAAATGTTTCG 60.110 55.000 0.0 0.0 0.00 3.46 R
7662 9296 1.106285 GCAACCCACATGATCCCTTC 58.894 55.000 0.0 0.0 0.00 3.46 R
8888 10634 0.325296 AGGTCGGGCTCTTGGACATA 60.325 55.000 0.0 0.0 32.39 2.29 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
30 31 1.659098 CGACAGCGGAAAATCTACCAC 59.341 52.381 0.00 0.00 0.00 4.16
38 39 3.121544 GGAAAATCTACCACCGACGATC 58.878 50.000 0.00 0.00 0.00 3.69
86 87 2.430921 GACGAGCGGCGATATGGG 60.431 66.667 12.98 0.00 44.57 4.00
126 146 2.863132 TTTGCTACAACCGGTACCAT 57.137 45.000 8.00 0.00 0.00 3.55
130 150 0.173935 CTACAACCGGTACCATCGCA 59.826 55.000 8.00 0.00 0.00 5.10
139 159 3.365291 TACCATCGCAGTGACCGCC 62.365 63.158 0.00 0.00 0.00 6.13
197 217 2.845550 CGACGGATGCTGGGATCGA 61.846 63.158 0.00 0.00 0.00 3.59
204 224 1.277273 GATGCTGGGATCGATGATGGA 59.723 52.381 0.54 0.00 0.00 3.41
223 269 5.295431 TGGATCTGTTTTTGCTACAATCG 57.705 39.130 0.00 0.00 0.00 3.34
241 287 7.016361 ACAATCGATAATCACAAAAGCTACC 57.984 36.000 0.00 0.00 0.00 3.18
245 291 4.332543 CGATAATCACAAAAGCTACCAGCA 59.667 41.667 0.38 0.00 45.56 4.41
250 296 3.503363 TCACAAAAGCTACCAGCAATGAG 59.497 43.478 0.38 0.00 45.56 2.90
263 309 3.894351 GCAATGAGCATTTTTGCTACG 57.106 42.857 0.00 0.00 46.36 3.51
285 331 4.473520 CTGACGGGAAGGCGGCAT 62.474 66.667 13.08 0.00 0.00 4.40
293 339 3.360956 GAAGGCGGCATTGGCAAGG 62.361 63.158 13.08 7.66 43.71 3.61
296 342 4.376176 GCGGCATTGGCAAGGCAA 62.376 61.111 33.88 11.56 43.71 4.52
297 343 2.125832 CGGCATTGGCAAGGCAAG 60.126 61.111 33.88 24.08 43.71 4.01
325 371 4.589046 TGGAACGGCCATGTGTTT 57.411 50.000 2.24 0.00 43.33 2.83
376 422 2.675056 GCAACCTGAGCTGCGACTG 61.675 63.158 0.00 0.00 0.00 3.51
475 543 2.667536 CGCACTGGAGCTGCAACT 60.668 61.111 9.92 0.00 34.00 3.16
477 545 1.895707 GCACTGGAGCTGCAACTGT 60.896 57.895 9.92 0.39 34.56 3.55
496 565 3.938048 GGCACCATATTGCTGGCA 58.062 55.556 0.00 0.00 42.56 4.92
692 763 2.095461 TCCAGATCTGACGAACCAGAG 58.905 52.381 24.62 3.19 45.27 3.35
695 766 3.181495 CCAGATCTGACGAACCAGAGTAC 60.181 52.174 24.62 0.00 45.27 2.73
921 1168 3.006537 AGCATGCAAGCTTTGTTCAATCT 59.993 39.130 21.98 0.00 43.70 2.40
985 1326 3.520290 ACGAATCGACATCCTAAAGCA 57.480 42.857 10.55 0.00 0.00 3.91
986 1327 3.857052 ACGAATCGACATCCTAAAGCAA 58.143 40.909 10.55 0.00 0.00 3.91
987 1328 3.865745 ACGAATCGACATCCTAAAGCAAG 59.134 43.478 10.55 0.00 0.00 4.01
988 1329 4.112634 CGAATCGACATCCTAAAGCAAGA 58.887 43.478 0.00 0.00 0.00 3.02
989 1330 4.566759 CGAATCGACATCCTAAAGCAAGAA 59.433 41.667 0.00 0.00 0.00 2.52
990 1331 5.276584 CGAATCGACATCCTAAAGCAAGAAG 60.277 44.000 0.00 0.00 0.00 2.85
991 1332 3.861840 TCGACATCCTAAAGCAAGAAGG 58.138 45.455 0.00 0.00 0.00 3.46
992 1333 3.260884 TCGACATCCTAAAGCAAGAAGGT 59.739 43.478 0.00 0.00 0.00 3.50
1009 1350 1.182667 GGTAAAAGGCATGACCCACC 58.817 55.000 0.00 0.00 40.58 4.61
1040 1381 2.916702 AAGCCTGAAAAAGCCCAAAG 57.083 45.000 0.00 0.00 0.00 2.77
1141 1482 3.173151 CCAAAGCTAAACCTTCCCCAAT 58.827 45.455 0.00 0.00 0.00 3.16
1151 1492 3.589627 TTCCCCAATCCCTCCCCGT 62.590 63.158 0.00 0.00 0.00 5.28
1546 1910 3.770040 CGGGAGATGGCCGTCACA 61.770 66.667 26.70 0.00 0.00 3.58
1610 1974 1.451207 GTCATGTATGGCCGTGGCA 60.451 57.895 13.76 7.13 44.11 4.92
1653 2017 2.420129 CCTTCCTGTGGATTACGAAGGG 60.420 54.545 6.30 0.00 40.44 3.95
1681 2045 7.875554 TGCAGTATTAATTGTAGTGTCTGTTGA 59.124 33.333 0.00 0.00 0.00 3.18
1726 2098 1.672145 GGCCGGTTGACTAGAACTGAC 60.672 57.143 1.90 0.00 34.59 3.51
1772 2144 2.441375 CTGGGGAAAATTTTGGGGTGTT 59.559 45.455 8.47 0.00 0.00 3.32
1870 2242 2.247358 CCATTTGGTACTGGTTGCCTT 58.753 47.619 0.00 0.00 0.00 4.35
1898 2270 6.790319 AGTGTGGACTTGGGAAATAATTACT 58.210 36.000 0.00 0.00 0.00 2.24
1899 2271 6.659242 AGTGTGGACTTGGGAAATAATTACTG 59.341 38.462 0.00 0.00 0.00 2.74
2112 2485 1.745087 GCTGTGCCTGCTTAGCAATAA 59.255 47.619 8.68 0.00 43.02 1.40
2127 2786 3.565482 AGCAATAATATCACGTGCCCTTG 59.435 43.478 11.67 9.27 35.80 3.61
2267 2931 7.065324 TCGTTTACACTTTCAGTTGTTTCATCT 59.935 33.333 0.00 0.00 0.00 2.90
2529 3193 8.677870 ATTATGAGGATAAGGCAGATAACTCT 57.322 34.615 0.00 0.00 0.00 3.24
2567 3231 6.942576 ACAATTGATAAGGATATACTGGCCAC 59.057 38.462 13.59 0.00 0.00 5.01
2583 3247 3.039011 GGCCACTAATCCTACTCTCCAA 58.961 50.000 0.00 0.00 0.00 3.53
2859 3537 7.311408 GGTTTACTAGTTGACGATGTAAGTCT 58.689 38.462 0.00 0.00 39.24 3.24
2868 3546 4.021456 TGACGATGTAAGTCTGTTCACCAT 60.021 41.667 0.00 0.00 39.24 3.55
2910 3595 9.415544 AGACAAGAAAACATGATGCTTATTTTC 57.584 29.630 0.00 9.61 38.81 2.29
3192 3935 1.734707 GCATCAGGTACGCGTAGTTGT 60.735 52.381 21.25 8.77 0.00 3.32
3430 4207 6.431543 AGGTCTATAGGTATGTCATCGTTGAG 59.568 42.308 0.00 0.00 30.85 3.02
3438 4215 5.221263 GGTATGTCATCGTTGAGTCCTGTAT 60.221 44.000 0.00 0.00 30.85 2.29
3442 4219 6.873997 TGTCATCGTTGAGTCCTGTATAATT 58.126 36.000 0.00 0.00 30.85 1.40
3747 4528 0.677731 TGTTGAGCCTGGCTGCATAC 60.678 55.000 28.82 20.27 39.88 2.39
4000 4879 9.440761 ACTAATTCTGGAATTACAGATAGTCCT 57.559 33.333 21.14 3.20 46.07 3.85
4155 5037 1.520787 GAGTAATGCCGACCACCCG 60.521 63.158 0.00 0.00 0.00 5.28
4221 5104 9.162764 GTATTCTTCTATTCTTAGTTGGTGCAA 57.837 33.333 0.00 0.00 0.00 4.08
4266 5157 3.186409 CGTTACTGTGGTTGTCAGGATTG 59.814 47.826 0.00 0.00 37.25 2.67
4302 5193 5.295292 CCTGGTGATACATTTGTCATGTCTC 59.705 44.000 0.00 0.00 33.76 3.36
4304 5195 4.271049 GGTGATACATTTGTCATGTCTCGG 59.729 45.833 0.00 0.00 33.76 4.63
4305 5196 4.870426 GTGATACATTTGTCATGTCTCGGT 59.130 41.667 0.00 0.00 33.76 4.69
4320 5213 9.173021 TCATGTCTCGGTTTTATAATCATTGTT 57.827 29.630 0.00 0.00 0.00 2.83
4383 5277 2.362077 CCTTGGTTACATATGGGCAAGC 59.638 50.000 7.80 8.18 0.00 4.01
4632 5528 6.052360 GGGATTCTCATACTCCTTTTGTCTC 58.948 44.000 0.00 0.00 0.00 3.36
4646 5542 5.452356 CCTTTTGTCTCCACTTTGCTGATTT 60.452 40.000 0.00 0.00 0.00 2.17
4794 5690 8.511321 TGTGAATGCCTACTAAATGTAAACAAG 58.489 33.333 0.00 0.00 0.00 3.16
4813 5710 6.851222 ACAAGTATGCACATATAAGTCAGC 57.149 37.500 0.00 0.00 0.00 4.26
4816 5713 6.119240 AGTATGCACATATAAGTCAGCCAT 57.881 37.500 0.00 0.00 0.00 4.40
4833 5730 5.045213 TCAGCCATCCTAAGTATGGTTTGAA 60.045 40.000 4.18 0.00 44.87 2.69
4860 5757 9.793259 CTGGACAACATATTACTTATGGGTAAT 57.207 33.333 9.15 9.15 41.80 1.89
4881 5778 5.582439 ATGCGCTATAGTTCTCATTTTCG 57.418 39.130 9.73 0.00 0.00 3.46
4950 5850 5.727515 GCTGCAAAGGACATTTTGTTTTGTC 60.728 40.000 0.00 0.00 39.62 3.18
5049 6031 6.109156 TGAAGTAGCTGGAAGTAATGTTCA 57.891 37.500 0.00 0.00 35.30 3.18
5136 6128 6.479660 ACTGTTTTTGCTGGTAATGTTCATTG 59.520 34.615 8.11 0.00 0.00 2.82
5232 6231 5.527951 TGCGGTGTCTTGTTCTAATTTTACA 59.472 36.000 0.00 0.00 0.00 2.41
5238 6237 6.086871 GTCTTGTTCTAATTTTACAGCCTGC 58.913 40.000 0.00 0.00 0.00 4.85
5349 6401 6.809869 AGAGTATGCCCATTCTTTATTTTGC 58.190 36.000 0.00 0.00 0.00 3.68
5746 6859 3.550842 GGGGTCATGCGCTTTTTGATATC 60.551 47.826 9.73 0.00 0.00 1.63
6285 7768 0.449786 TTGTTGTGTTGGTGCACGAG 59.550 50.000 11.45 0.00 41.94 4.18
6331 7814 4.204799 GTGGTTGTCAAGTTTTAGGTCCT 58.795 43.478 0.00 0.00 0.00 3.85
6432 7976 7.587037 AATGGATTATTTCGTGATGGTGATT 57.413 32.000 0.00 0.00 0.00 2.57
6544 8088 6.796426 TCGATTTCGATTACAGATGAGTTCT 58.204 36.000 0.00 0.00 44.22 3.01
6554 8098 4.778534 CAGATGAGTTCTGTGCCATTTT 57.221 40.909 0.00 0.00 45.79 1.82
6571 8117 9.288124 GTGCCATTTTTATTTATTTTTGGATGC 57.712 29.630 0.00 0.00 0.00 3.91
6669 8219 6.603237 TGATAATCTTGTATTGAACGCAGG 57.397 37.500 0.00 0.00 0.00 4.85
6776 8326 9.505995 GAGTCCGATAAAGTTTTTGTTAAACAA 57.494 29.630 0.00 0.00 36.11 2.83
7153 8758 1.331138 GAAGACGACGAGGATGACGAT 59.669 52.381 0.00 0.00 34.70 3.73
7306 8915 1.340502 GGAGGGCAAAAGAAGAGAGGG 60.341 57.143 0.00 0.00 0.00 4.30
7307 8916 1.352687 GAGGGCAAAAGAAGAGAGGGT 59.647 52.381 0.00 0.00 0.00 4.34
7312 8921 2.431454 CAAAAGAAGAGAGGGTGGAGC 58.569 52.381 0.00 0.00 0.00 4.70
7433 9042 2.202395 GCTTGGCTGGTGCTTCCAA 61.202 57.895 3.15 0.00 46.59 3.53
7435 9044 1.229927 TTGGCTGGTGCTTCCAAGT 59.770 52.632 3.15 0.00 46.59 3.16
7438 9047 1.133637 TGGCTGGTGCTTCCAAGTAAA 60.134 47.619 3.15 0.00 46.59 2.01
7720 9354 3.373565 CCTCAAAAGGGCCACGGC 61.374 66.667 6.18 0.00 39.21 5.68
7772 9409 0.032267 CTCGTCGGATCCCCTAAAGC 59.968 60.000 6.06 0.00 0.00 3.51
8016 9692 7.601073 TTACATACAGAGCAAAATGAGTGAG 57.399 36.000 0.00 0.00 0.00 3.51
8017 9693 4.940046 ACATACAGAGCAAAATGAGTGAGG 59.060 41.667 0.00 0.00 0.00 3.86
8081 9757 9.704098 GTCTGTATTAAAATCTCTAAAAAGGCG 57.296 33.333 0.00 0.00 0.00 5.52
8186 9862 1.267574 ATGGAGAGAAGCTTCCGGCA 61.268 55.000 22.81 3.13 44.79 5.69
8211 9887 0.806868 CCGTACGTCTCTGTTAGGCA 59.193 55.000 15.21 0.00 0.00 4.75
8218 9894 1.540267 GTCTCTGTTAGGCACGTCTCA 59.460 52.381 0.00 0.00 0.00 3.27
8313 9989 2.921754 GACTCGACGGTATTGACCTTTG 59.078 50.000 0.00 0.00 44.46 2.77
8339 10015 1.202268 GCACGTAGAACCGAGCATACT 60.202 52.381 0.00 0.00 42.73 2.12
8340 10016 2.451132 CACGTAGAACCGAGCATACTG 58.549 52.381 0.00 0.00 0.00 2.74
8361 10037 5.516339 ACTGCGAAAAGAAGACAACATTTTG 59.484 36.000 0.00 0.00 38.83 2.44
8362 10038 5.645624 TGCGAAAAGAAGACAACATTTTGA 58.354 33.333 0.00 0.00 36.48 2.69
8363 10039 5.514914 TGCGAAAAGAAGACAACATTTTGAC 59.485 36.000 0.00 0.00 36.48 3.18
8364 10040 5.514914 GCGAAAAGAAGACAACATTTTGACA 59.485 36.000 0.00 0.00 36.48 3.58
8367 10043 8.051909 CGAAAAGAAGACAACATTTTGACATTG 58.948 33.333 0.00 0.00 36.48 2.82
8368 10044 9.086336 GAAAAGAAGACAACATTTTGACATTGA 57.914 29.630 0.00 0.00 36.48 2.57
8369 10045 9.603921 AAAAGAAGACAACATTTTGACATTGAT 57.396 25.926 0.00 0.00 36.48 2.57
8371 10047 8.583810 AGAAGACAACATTTTGACATTGATTG 57.416 30.769 0.00 0.00 36.48 2.67
8379 10055 6.014840 ACATTTTGACATTGATTGGAAGAGCT 60.015 34.615 0.00 0.00 0.00 4.09
8446 10122 8.862325 AATACTTACAAGGATGTCACATTTGA 57.138 30.769 8.87 0.00 41.05 2.69
8592 10281 5.435291 AGCCAATCTATATAGAATGCCAGC 58.565 41.667 18.72 16.54 35.69 4.85
8602 10291 3.146104 AGAATGCCAGCAGTACAAAGT 57.854 42.857 0.00 0.00 0.00 2.66
8603 10292 3.490348 AGAATGCCAGCAGTACAAAGTT 58.510 40.909 0.00 0.00 0.00 2.66
8636 10326 5.186992 ACAAAAGCCTTTAGTCCAAACAAGT 59.813 36.000 0.00 0.00 0.00 3.16
8649 10392 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
8652 10395 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
8660 10403 3.310193 GGGTAGGCTAGAGGTGAAATCT 58.690 50.000 0.00 0.00 0.00 2.40
8678 10421 5.398603 AATCTATAAGATCTCGCCACCAG 57.601 43.478 0.00 0.00 32.89 4.00
8749 10495 2.275318 GGCTGATCTTCCTCTCAAACG 58.725 52.381 0.00 0.00 0.00 3.60
8768 10514 1.744522 CGGATTGATGTCACATTGCCA 59.255 47.619 0.00 0.00 0.00 4.92
8795 10541 3.365265 CCAACGCCAGAGCCAACC 61.365 66.667 0.00 0.00 34.57 3.77
8840 10586 2.133520 AGTCATCAAGGCCATGATCCT 58.866 47.619 20.39 15.54 37.96 3.24
8844 10590 3.055602 TCATCAAGGCCATGATCCTATCG 60.056 47.826 20.39 8.73 37.96 2.92
8877 10623 4.438148 TCGATGAAGAAGTTGTCACAACA 58.562 39.130 22.66 0.86 0.00 3.33
8888 10634 3.213206 TGTCACAACAGAAAGAGCCAT 57.787 42.857 0.00 0.00 0.00 4.40
8902 10648 0.475906 AGCCATATGTCCAAGAGCCC 59.524 55.000 1.24 0.00 0.00 5.19
8938 10684 4.454678 TCAATAAATCTCGCAAGCCTCAT 58.545 39.130 0.00 0.00 37.18 2.90
8969 10722 2.413837 GTGGACGCATCAACTTAGTGT 58.586 47.619 0.00 0.00 0.00 3.55
8970 10723 2.412089 GTGGACGCATCAACTTAGTGTC 59.588 50.000 0.00 0.00 40.91 3.67
8979 10732 0.246635 AACTTAGTGTCGATGCGGCT 59.753 50.000 0.00 0.00 30.55 5.52
8991 10744 4.344865 GCGGCTGAAGGACCCCAA 62.345 66.667 0.00 0.00 0.00 4.12
9037 10790 2.551270 TCCTGCAAACCCTAGTCTCAT 58.449 47.619 0.00 0.00 0.00 2.90
9057 10823 4.346709 TCATTATCCAGAATCTACGCCCAA 59.653 41.667 0.00 0.00 0.00 4.12
9082 10848 3.560105 TCATCCACAAACAACACCATCA 58.440 40.909 0.00 0.00 0.00 3.07
9106 10872 5.227593 AGATGGGAAGGCTCTAGGAAATAA 58.772 41.667 0.00 0.00 0.00 1.40
9109 10875 6.341408 TGGGAAGGCTCTAGGAAATAAAAT 57.659 37.500 0.00 0.00 0.00 1.82
9155 10931 6.303839 TGACTATAAGTTTGGTCAGGCTTTT 58.696 36.000 0.00 0.00 34.38 2.27
9188 10965 2.381445 AAGGCAGAGGCTTAGTGCT 58.619 52.632 14.61 0.00 46.45 4.40
9225 11002 8.856490 ACGAATCTGGATGTAATTTTTATTGC 57.144 30.769 0.00 0.00 0.00 3.56
9227 11004 8.961092 CGAATCTGGATGTAATTTTTATTGCTG 58.039 33.333 0.00 0.00 0.00 4.41
9233 11010 7.816995 TGGATGTAATTTTTATTGCTGGTGTTC 59.183 33.333 0.00 0.00 0.00 3.18
9243 11020 1.009675 CTGGTGTTCGTTGCACTGC 60.010 57.895 0.00 0.00 37.07 4.40
9264 11041 4.337274 TGCCATGATTGATGATGAACAGAC 59.663 41.667 0.00 0.00 33.31 3.51
9267 11044 5.505819 CCATGATTGATGATGAACAGACTGC 60.506 44.000 1.25 0.00 33.31 4.40
9281 11058 3.442441 CTGCAAGTTTTCCCCGCA 58.558 55.556 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.007608 GGTGGTAGATTTTCCGCTGTC 58.992 52.381 0.00 0.00 34.96 3.51
12 13 1.674817 CGGTGGTAGATTTTCCGCTGT 60.675 52.381 0.00 0.00 36.28 4.40
19 20 2.424601 TCGATCGTCGGTGGTAGATTTT 59.575 45.455 15.94 0.00 40.88 1.82
23 24 1.671979 ATTCGATCGTCGGTGGTAGA 58.328 50.000 15.94 0.00 40.88 2.59
30 31 0.315382 GCAGCAAATTCGATCGTCGG 60.315 55.000 15.94 3.06 40.88 4.79
38 39 2.088178 GCCGGTTGCAGCAAATTCG 61.088 57.895 10.11 13.71 40.77 3.34
95 96 0.098200 GTAGCAAAAATCCGGGTCGC 59.902 55.000 0.00 0.00 0.00 5.19
101 102 1.538075 ACCGGTTGTAGCAAAAATCCG 59.462 47.619 0.00 0.00 36.85 4.18
161 181 1.711060 CGTCGAGGTCTCAGCTCCTC 61.711 65.000 8.78 8.78 44.65 3.71
197 217 6.839124 TTGTAGCAAAAACAGATCCATCAT 57.161 33.333 0.00 0.00 0.00 2.45
204 224 8.892723 TGATTATCGATTGTAGCAAAAACAGAT 58.107 29.630 1.71 0.00 0.00 2.90
223 269 5.818136 TGCTGGTAGCTTTTGTGATTATC 57.182 39.130 0.00 0.00 42.97 1.75
245 291 4.675510 CCATCGTAGCAAAAATGCTCATT 58.324 39.130 6.59 0.00 45.00 2.57
250 296 2.159393 TCAGCCATCGTAGCAAAAATGC 60.159 45.455 0.00 0.00 0.00 3.56
252 298 2.095853 CGTCAGCCATCGTAGCAAAAAT 59.904 45.455 0.00 0.00 0.00 1.82
263 309 2.514824 GCCTTCCCGTCAGCCATC 60.515 66.667 0.00 0.00 0.00 3.51
285 331 2.345124 AAAAATGCTTGCCTTGCCAA 57.655 40.000 0.00 0.00 0.00 4.52
325 371 1.670791 AAGTCGCCGGTCAAAGAAAA 58.329 45.000 1.90 0.00 0.00 2.29
328 374 1.670791 AAAAAGTCGCCGGTCAAAGA 58.329 45.000 1.90 0.00 0.00 2.52
348 394 0.317160 CTCAGGTTGCTGGTCGTACA 59.683 55.000 0.00 0.00 0.00 2.90
349 395 1.014564 GCTCAGGTTGCTGGTCGTAC 61.015 60.000 0.00 0.00 0.00 3.67
350 396 1.185618 AGCTCAGGTTGCTGGTCGTA 61.186 55.000 0.00 0.00 39.56 3.43
371 417 4.742201 CTCCCGTGGCACCAGTCG 62.742 72.222 12.86 0.00 0.00 4.18
458 504 2.667536 AGTTGCAGCTCCAGTGCG 60.668 61.111 0.00 0.00 44.35 5.34
475 543 0.683828 CCAGCAATATGGTGCCCACA 60.684 55.000 4.10 0.00 46.14 4.17
477 545 1.757731 GCCAGCAATATGGTGCCCA 60.758 57.895 4.10 0.00 46.14 5.36
486 554 1.199789 CTGCGTTTCTTGCCAGCAATA 59.800 47.619 5.38 0.00 37.38 1.90
554 623 0.964860 TGCATATTGCCTGTTGCCGT 60.965 50.000 0.00 0.00 44.23 5.68
559 628 1.416243 CCCCATGCATATTGCCTGTT 58.584 50.000 0.00 0.00 44.23 3.16
563 632 2.652530 CGCCCCATGCATATTGCC 59.347 61.111 0.00 0.00 44.23 4.52
564 633 2.048877 GCGCCCCATGCATATTGC 60.049 61.111 0.00 0.77 45.29 3.56
594 663 4.758251 CACCCGCATCTCACGCCA 62.758 66.667 0.00 0.00 0.00 5.69
626 695 3.361977 GCAACACCGGTCGCCATT 61.362 61.111 2.59 0.00 0.00 3.16
643 712 0.113190 ACCCCAAAGGCTCCTTCTTG 59.887 55.000 1.05 0.00 40.58 3.02
671 742 2.493675 CTCTGGTTCGTCAGATCTGGAA 59.506 50.000 22.42 15.35 42.19 3.53
672 743 2.095461 CTCTGGTTCGTCAGATCTGGA 58.905 52.381 22.42 10.07 42.19 3.86
681 752 5.585445 TCAGATTCTAGTACTCTGGTTCGTC 59.415 44.000 0.00 0.00 37.57 4.20
692 763 1.001597 CGGGCCGTCAGATTCTAGTAC 60.002 57.143 19.97 0.00 0.00 2.73
695 766 1.300233 GCGGGCCGTCAGATTCTAG 60.300 63.158 28.82 0.00 0.00 2.43
798 869 3.997681 TGCTTCGGTTCATCGACAATTTA 59.002 39.130 0.00 0.00 39.01 1.40
881 955 4.946784 TGCTCGATTTTAGAGAAAAGGC 57.053 40.909 0.00 0.00 37.94 4.35
934 1187 1.275010 TGTGCAGATCGAACTTGCCTA 59.725 47.619 14.13 3.59 0.00 3.93
985 1326 3.181423 TGGGTCATGCCTTTTACCTTCTT 60.181 43.478 6.20 0.00 37.43 2.52
986 1327 2.378547 TGGGTCATGCCTTTTACCTTCT 59.621 45.455 6.20 0.00 37.43 2.85
987 1328 2.492088 GTGGGTCATGCCTTTTACCTTC 59.508 50.000 6.20 0.00 37.43 3.46
988 1329 2.525368 GTGGGTCATGCCTTTTACCTT 58.475 47.619 6.20 0.00 37.43 3.50
989 1330 1.272480 GGTGGGTCATGCCTTTTACCT 60.272 52.381 6.20 0.00 37.43 3.08
990 1331 1.182667 GGTGGGTCATGCCTTTTACC 58.817 55.000 6.20 0.00 37.43 2.85
991 1332 1.182667 GGGTGGGTCATGCCTTTTAC 58.817 55.000 6.20 2.27 37.43 2.01
992 1333 0.780637 TGGGTGGGTCATGCCTTTTA 59.219 50.000 6.20 0.00 37.43 1.52
1040 1381 0.459078 GTCGTACCTGGGCTTAGGAC 59.541 60.000 13.90 0.00 40.42 3.85
1438 1802 0.612453 AGACGAAGACCTCCTCCACC 60.612 60.000 0.00 0.00 0.00 4.61
1610 1974 5.191323 AGGATGGAGATCAGAAACTCACAAT 59.809 40.000 0.00 2.09 35.17 2.71
1653 2017 6.313905 ACAGACACTACAATTAATACTGCAGC 59.686 38.462 15.27 0.00 0.00 5.25
1726 2098 5.673068 GCTTCAGTTTCACATATGCTCACTG 60.673 44.000 14.46 14.46 32.33 3.66
1772 2144 6.387192 TCCTTCCTTGAATGAACTGGAATA 57.613 37.500 0.00 0.00 36.39 1.75
1809 2181 7.050377 ACCTGGAATGACATGAAGTTATACAG 58.950 38.462 0.00 0.00 34.21 2.74
1898 2270 2.089201 CATCACAATCTCTTGCTGGCA 58.911 47.619 0.00 0.00 35.69 4.92
1899 2271 1.404391 CCATCACAATCTCTTGCTGGC 59.596 52.381 0.00 0.00 35.69 4.85
1944 2317 3.084039 TGAATGCTAGGTTTTGCTCTGG 58.916 45.455 0.00 0.00 0.00 3.86
2112 2485 3.153919 ACAAAACAAGGGCACGTGATAT 58.846 40.909 22.23 0.00 0.00 1.63
2127 2786 4.260334 GCGACAGCTATTAGGACAAAAC 57.740 45.455 0.00 0.00 41.01 2.43
2583 3247 5.242393 GCAGACCTCCATGTTATTATGCAAT 59.758 40.000 0.00 0.00 0.00 3.56
2859 3537 4.041567 ACATAGGTCAACTGATGGTGAACA 59.958 41.667 1.90 0.00 0.00 3.18
2868 3546 6.911250 TCTTGTCTTACATAGGTCAACTGA 57.089 37.500 0.00 0.00 0.00 3.41
2910 3595 2.005451 GGCACTCAAGATACTGCACTG 58.995 52.381 0.00 0.00 0.00 3.66
3114 3857 6.533819 TGACAGTTACCAAAAGATAACACG 57.466 37.500 0.00 0.00 34.36 4.49
3156 3899 4.463891 CCTGATGCCTTGTAAATTCCTTGT 59.536 41.667 0.00 0.00 0.00 3.16
3192 3935 4.776349 TCTTTGTGGCTCTTTTCAGTACA 58.224 39.130 0.00 0.00 0.00 2.90
3240 3990 6.975196 TTTTGAGGAATGAATCAAGGAACA 57.025 33.333 0.00 0.00 36.81 3.18
3446 4223 8.635765 ACAGTTCATATGTAAAGGTGATGTTT 57.364 30.769 1.90 0.00 0.00 2.83
3869 4748 8.842358 ACGACATTCTTTCCAACTTTAATCTA 57.158 30.769 0.00 0.00 0.00 1.98
3892 4771 2.107950 TTGAATAGGCAGGGACAACG 57.892 50.000 0.00 0.00 0.00 4.10
4000 4879 5.664294 TTTTAGGGTATGCAGACTTACGA 57.336 39.130 11.87 0.00 0.00 3.43
4221 5104 5.506815 CGCAAGCATGGATTACAGAAATCAT 60.507 40.000 0.00 0.00 45.05 2.45
4302 5193 7.328249 ACAGCAACAACAATGATTATAAAACCG 59.672 33.333 0.00 0.00 0.00 4.44
4304 5195 9.410556 AGACAGCAACAACAATGATTATAAAAC 57.589 29.630 0.00 0.00 0.00 2.43
4320 5213 7.439356 GTCTAAGCAATATCATAGACAGCAACA 59.561 37.037 6.86 0.00 42.33 3.33
4383 5277 3.458189 GTCCTGAATTCCAGTATCACCG 58.542 50.000 2.27 0.00 41.33 4.94
4632 5528 4.039124 AGGGTAAACAAATCAGCAAAGTGG 59.961 41.667 0.00 0.00 0.00 4.00
4794 5690 5.352569 GGATGGCTGACTTATATGTGCATAC 59.647 44.000 0.00 0.00 0.00 2.39
4816 5713 5.308497 TGTCCAGTTCAAACCATACTTAGGA 59.692 40.000 0.00 0.00 0.00 2.94
4833 5730 7.208064 ACCCATAAGTAATATGTTGTCCAGT 57.792 36.000 0.00 0.00 39.90 4.00
4860 5757 4.430007 ACGAAAATGAGAACTATAGCGCA 58.570 39.130 11.47 0.00 0.00 6.09
4881 5778 7.430502 GCTTGCATATCATTACTGTCTCAAAAC 59.569 37.037 0.00 0.00 0.00 2.43
5136 6128 7.066766 AGAGTGTTAATCCAAATTCAGATGCTC 59.933 37.037 0.00 0.00 0.00 4.26
5182 6174 9.726438 AAACAACTTTCATACTCTATACAAGCT 57.274 29.630 0.00 0.00 0.00 3.74
5232 6231 4.957684 ACTAGTTAATTATCGGCAGGCT 57.042 40.909 0.00 0.00 0.00 4.58
6285 7768 0.539518 GAGGCCCTTCCAAGAGTCTC 59.460 60.000 0.00 0.00 37.29 3.36
6571 8117 6.129115 GCAGTGCAAACAAAACTACATATGTG 60.129 38.462 18.81 10.62 0.00 3.21
6669 8219 6.267928 TCCTTATCATAGAGGTAAGGCAAGAC 59.732 42.308 8.89 0.00 42.61 3.01
7153 8758 4.509616 CTCTCCGACTCTACTCTTCTTCA 58.490 47.826 0.00 0.00 0.00 3.02
7306 8915 0.388520 GGGCAAATGTTTCGCTCCAC 60.389 55.000 0.00 0.00 0.00 4.02
7307 8916 1.861542 CGGGCAAATGTTTCGCTCCA 61.862 55.000 0.00 0.00 0.00 3.86
7312 8921 0.109781 CCTCACGGGCAAATGTTTCG 60.110 55.000 0.00 0.00 0.00 3.46
7438 9047 6.127451 ACAGCAAGTAAAACAAGTAGGCTTTT 60.127 34.615 0.00 0.00 31.49 2.27
7446 9055 4.278419 GGATGGACAGCAAGTAAAACAAGT 59.722 41.667 0.00 0.00 0.00 3.16
7662 9296 1.106285 GCAACCCACATGATCCCTTC 58.894 55.000 0.00 0.00 0.00 3.46
7982 9655 7.984422 TTGCTCTGTATGTAATCCATATTGG 57.016 36.000 0.00 0.00 38.29 3.16
8081 9757 5.050567 CGCTCCCTCCGTTTTATAAATGTAC 60.051 44.000 0.00 0.00 0.00 2.90
8090 9766 3.615224 AAATACGCTCCCTCCGTTTTA 57.385 42.857 0.00 0.00 39.88 1.52
8091 9767 2.484742 AAATACGCTCCCTCCGTTTT 57.515 45.000 0.00 0.00 39.88 2.43
8186 9862 1.177256 ACAGAGACGTACGGGCACTT 61.177 55.000 21.06 0.00 0.00 3.16
8211 9887 1.896220 TACGTTAGGTGGTGAGACGT 58.104 50.000 0.00 5.19 46.97 4.34
8218 9894 6.379133 TCAAGTCATCTTATACGTTAGGTGGT 59.621 38.462 0.00 0.00 32.07 4.16
8313 9989 2.436115 GGTTCTACGTGCCAGGGC 60.436 66.667 2.62 2.62 42.35 5.19
8339 10015 5.514914 GTCAAAATGTTGTCTTCTTTTCGCA 59.485 36.000 0.00 0.00 36.07 5.10
8340 10016 5.514914 TGTCAAAATGTTGTCTTCTTTTCGC 59.485 36.000 0.00 0.00 36.07 4.70
8346 10022 7.654520 CCAATCAATGTCAAAATGTTGTCTTCT 59.345 33.333 0.00 0.00 36.07 2.85
8347 10023 7.652909 TCCAATCAATGTCAAAATGTTGTCTTC 59.347 33.333 0.00 0.00 36.07 2.87
8352 10028 7.359765 GCTCTTCCAATCAATGTCAAAATGTTG 60.360 37.037 0.00 0.00 35.95 3.33
8353 10029 6.647895 GCTCTTCCAATCAATGTCAAAATGTT 59.352 34.615 0.00 0.00 0.00 2.71
8361 10037 3.063180 CACGAGCTCTTCCAATCAATGTC 59.937 47.826 12.85 0.00 0.00 3.06
8362 10038 3.005554 CACGAGCTCTTCCAATCAATGT 58.994 45.455 12.85 0.00 0.00 2.71
8363 10039 2.223203 GCACGAGCTCTTCCAATCAATG 60.223 50.000 12.85 0.00 37.91 2.82
8364 10040 2.012673 GCACGAGCTCTTCCAATCAAT 58.987 47.619 12.85 0.00 37.91 2.57
8379 10055 0.653636 GTGGTTTCAAACGAGCACGA 59.346 50.000 11.40 0.00 42.66 4.35
8391 10067 1.893137 GGGAACATTCTGGGTGGTTTC 59.107 52.381 0.00 0.00 0.00 2.78
8520 10209 8.893563 ACTTACATTTTGGGATGGAAGAATTA 57.106 30.769 14.87 0.00 46.48 1.40
8574 10263 7.724490 TGTACTGCTGGCATTCTATATAGAT 57.276 36.000 13.22 1.69 31.40 1.98
8583 10272 3.923017 AACTTTGTACTGCTGGCATTC 57.077 42.857 0.00 0.00 0.00 2.67
8592 10281 6.627395 TTGTTGATGGGTAACTTTGTACTG 57.373 37.500 0.00 0.00 0.00 2.74
8602 10291 5.836358 ACTAAAGGCTTTTGTTGATGGGTAA 59.164 36.000 18.93 0.00 0.00 2.85
8603 10292 5.390387 ACTAAAGGCTTTTGTTGATGGGTA 58.610 37.500 18.93 0.00 0.00 3.69
8636 10326 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
8649 10392 6.096695 GGCGAGATCTTATAGATTTCACCTC 58.903 44.000 0.00 1.64 36.00 3.85
8652 10395 5.635700 GGTGGCGAGATCTTATAGATTTCAC 59.364 44.000 0.00 0.00 36.07 3.18
8660 10403 3.759086 CTAGCTGGTGGCGAGATCTTATA 59.241 47.826 0.00 0.00 44.66 0.98
8706 10449 5.243730 CCCACATGGACTTCAGTGTAATTTT 59.756 40.000 0.00 0.00 37.39 1.82
8720 10463 1.673168 GAAGATCAGCCCACATGGAC 58.327 55.000 0.00 0.00 37.39 4.02
8723 10466 1.489649 AGAGGAAGATCAGCCCACATG 59.510 52.381 0.00 0.00 0.00 3.21
8724 10467 1.767681 GAGAGGAAGATCAGCCCACAT 59.232 52.381 0.00 0.00 0.00 3.21
8749 10495 3.018856 TCTGGCAATGTGACATCAATCC 58.981 45.455 0.00 0.00 33.12 3.01
8768 10514 4.681978 GGCGTTGGAGCGGTGTCT 62.682 66.667 0.00 0.00 38.18 3.41
8795 10541 4.260907 CCCGCTCATGATCAACAATGTTAG 60.261 45.833 0.00 0.00 0.00 2.34
8840 10586 5.473504 TCTTCATCGAGACAATGATCCGATA 59.526 40.000 0.00 0.00 37.81 2.92
8844 10590 5.355596 ACTTCTTCATCGAGACAATGATCC 58.644 41.667 0.00 0.00 33.36 3.36
8854 10600 4.507756 TGTTGTGACAACTTCTTCATCGAG 59.492 41.667 26.50 0.00 31.49 4.04
8877 10623 4.685575 GCTCTTGGACATATGGCTCTTTCT 60.686 45.833 8.85 0.00 0.00 2.52
8888 10634 0.325296 AGGTCGGGCTCTTGGACATA 60.325 55.000 0.00 0.00 32.39 2.29
8902 10648 8.642885 CGAGATTTATTGATTATTGAGAGGTCG 58.357 37.037 0.00 0.00 0.00 4.79
8938 10684 4.155733 CGTCCACCTATGCCGGCA 62.156 66.667 34.80 34.80 0.00 5.69
8969 10722 2.184322 GTCCTTCAGCCGCATCGA 59.816 61.111 0.00 0.00 0.00 3.59
8970 10723 2.892425 GGTCCTTCAGCCGCATCG 60.892 66.667 0.00 0.00 0.00 3.84
8979 10732 2.352561 TCCTACATTGGGGTCCTTCA 57.647 50.000 0.00 0.00 0.00 3.02
8991 10744 2.186903 CGTGGCGGCTTCCTACAT 59.813 61.111 11.43 0.00 0.00 2.29
9037 10790 4.974645 ATTGGGCGTAGATTCTGGATAA 57.025 40.909 0.00 0.00 0.00 1.75
9057 10823 6.436847 TGATGGTGTTGTTTGTGGATGATTAT 59.563 34.615 0.00 0.00 0.00 1.28
9082 10848 2.877154 TCCTAGAGCCTTCCCATCTT 57.123 50.000 0.00 0.00 0.00 2.40
9166 10943 2.911484 CACTAAGCCTCTGCCTTTAGG 58.089 52.381 0.00 0.00 38.69 2.69
9209 10986 7.540745 ACGAACACCAGCAATAAAAATTACATC 59.459 33.333 0.00 0.00 0.00 3.06
9224 11001 1.009675 CAGTGCAACGAACACCAGC 60.010 57.895 0.00 0.00 45.86 4.85
9225 11002 1.009675 GCAGTGCAACGAACACCAG 60.010 57.895 11.09 0.00 45.86 4.00
9227 11004 1.795170 ATGGCAGTGCAACGAACACC 61.795 55.000 18.61 0.00 45.86 4.16
9233 11010 0.522626 TCAATCATGGCAGTGCAACG 59.477 50.000 18.61 0.00 45.86 4.10
9243 11020 5.505819 GCAGTCTGTTCATCATCAATCATGG 60.506 44.000 0.93 0.00 32.64 3.66
9264 11041 3.442441 TGCGGGGAAAACTTGCAG 58.558 55.556 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.