Multiple sequence alignment - TraesCS2D01G128700

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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 TraesCS2D01G128700 chr2D 100.000 5036 0 0 1 5036 74973854 74978889 0.000000e+00 9300.0
1 TraesCS2D01G128700 chr2D 86.550 513 26 12 17 494 142672710 142672206 4.470000e-145 525.0
2 TraesCS2D01G128700 chr2D 85.882 510 36 15 14 494 542195710 542196212 1.250000e-140 510.0
3 TraesCS2D01G128700 chr2D 90.741 54 3 2 4814 4866 469261287 469261235 2.520000e-08 71.3
4 TraesCS2D01G128700 chr2B 92.126 2540 111 35 499 3009 114322321 114324800 0.000000e+00 3500.0
5 TraesCS2D01G128700 chr2B 92.095 1050 40 8 3007 4050 114324923 114325935 0.000000e+00 1439.0
6 TraesCS2D01G128700 chr2B 84.906 795 80 23 2333 3103 787811700 787812478 0.000000e+00 767.0
7 TraesCS2D01G128700 chr2B 84.071 791 87 20 2336 3103 289174244 289173470 0.000000e+00 726.0
8 TraesCS2D01G128700 chr2B 90.055 181 13 4 3186 3362 289173454 289173275 3.920000e-56 230.0
9 TraesCS2D01G128700 chr2B 91.089 101 7 1 2043 2141 247368638 247368538 8.790000e-28 135.0
10 TraesCS2D01G128700 chr2B 94.915 59 3 0 4433 4491 114325978 114325920 5.370000e-15 93.5
11 TraesCS2D01G128700 chr2B 94.737 57 3 0 4605 4661 114372897 114372953 6.940000e-14 89.8
12 TraesCS2D01G128700 chr2A 93.061 1225 61 11 3055 4275 74146545 74147749 0.000000e+00 1770.0
13 TraesCS2D01G128700 chr2A 96.060 863 28 6 1863 2721 74145379 74146239 0.000000e+00 1400.0
14 TraesCS2D01G128700 chr2A 89.468 864 49 14 973 1824 74144553 74145386 0.000000e+00 1053.0
15 TraesCS2D01G128700 chr2A 92.237 438 15 13 494 913 74143231 74143667 2.010000e-168 603.0
16 TraesCS2D01G128700 chr2A 80.614 717 75 40 3038 3745 348989999 348990660 3.500000e-136 496.0
17 TraesCS2D01G128700 chr2A 86.707 331 33 5 4266 4586 74149484 74149813 1.720000e-94 357.0
18 TraesCS2D01G128700 chr2A 96.316 190 7 0 2719 2908 74146362 74146551 3.790000e-81 313.0
19 TraesCS2D01G128700 chr2A 90.260 154 15 0 2333 2486 348989813 348989966 8.550000e-48 202.0
20 TraesCS2D01G128700 chr2A 89.831 118 12 0 4683 4800 74150197 74150314 8.730000e-33 152.0
21 TraesCS2D01G128700 chr2A 94.048 84 5 0 2058 2141 28816559 28816476 1.470000e-25 128.0
22 TraesCS2D01G128700 chr2A 94.118 85 4 1 2057 2141 182009050 182008967 1.470000e-25 128.0
23 TraesCS2D01G128700 chr7A 88.515 653 48 11 2333 2971 299533125 299533764 0.000000e+00 765.0
24 TraesCS2D01G128700 chr7A 82.312 571 59 33 3186 3744 299533921 299534461 1.650000e-124 457.0
25 TraesCS2D01G128700 chr7A 88.889 99 10 1 4489 4586 127844200 127844298 2.460000e-23 121.0
26 TraesCS2D01G128700 chr7A 94.737 38 2 0 4832 4869 643428893 643428930 5.440000e-05 60.2
27 TraesCS2D01G128700 chr3D 84.522 827 69 25 2333 3122 304401524 304402328 0.000000e+00 763.0
28 TraesCS2D01G128700 chr3D 82.294 802 93 21 2593 3352 406690205 406690999 0.000000e+00 649.0
29 TraesCS2D01G128700 chr3D 89.173 508 28 9 14 494 361757040 361757547 4.310000e-170 608.0
30 TraesCS2D01G128700 chr3D 82.632 570 55 32 3186 3744 304402329 304402865 9.880000e-127 464.0
31 TraesCS2D01G128700 chr3D 85.263 475 37 9 43 496 110275232 110274770 4.590000e-125 459.0
32 TraesCS2D01G128700 chr3D 87.500 264 27 5 1799 2061 500225859 500225601 2.950000e-77 300.0
33 TraesCS2D01G128700 chr3D 87.006 177 14 2 2140 2316 500225602 500225435 1.850000e-44 191.0
34 TraesCS2D01G128700 chr3D 86.029 136 12 7 3476 3607 406691013 406691145 6.800000e-29 139.0
35 TraesCS2D01G128700 chr3D 100.000 29 0 0 4838 4866 252841300 252841272 3.000000e-03 54.7
36 TraesCS2D01G128700 chr7B 82.332 832 69 33 2333 3122 555322811 555323606 0.000000e+00 651.0
37 TraesCS2D01G128700 chr7B 80.972 720 58 49 3038 3745 272694866 272695518 9.740000e-137 497.0
38 TraesCS2D01G128700 chr7B 82.281 570 59 29 3186 3744 555323607 555324145 5.940000e-124 455.0
39 TraesCS2D01G128700 chr7B 87.452 263 27 5 1794 2055 270096231 270096488 1.060000e-76 298.0
40 TraesCS2D01G128700 chr7B 91.667 96 8 0 4489 4584 88645241 88645336 3.160000e-27 134.0
41 TraesCS2D01G128700 chrUn 87.023 524 28 15 14 504 132104841 132105357 5.700000e-154 555.0
42 TraesCS2D01G128700 chrUn 91.379 116 9 1 2140 2255 87853248 87853134 1.880000e-34 158.0
43 TraesCS2D01G128700 chr1D 87.160 514 30 15 14 494 202560192 202560702 7.370000e-153 551.0
44 TraesCS2D01G128700 chr1D 85.354 198 24 4 2732 2924 296169462 296169265 3.070000e-47 200.0
45 TraesCS2D01G128700 chr1D 76.372 419 65 21 1094 1505 296170945 296170554 1.430000e-45 195.0
46 TraesCS2D01G128700 chr1D 91.111 90 6 2 2057 2145 451978872 451978960 2.460000e-23 121.0
47 TraesCS2D01G128700 chr1D 90.411 73 6 1 4514 4586 411526878 411526949 1.490000e-15 95.3
48 TraesCS2D01G128700 chr1D 82.143 84 8 7 4821 4898 495123845 495123763 1.170000e-06 65.8
49 TraesCS2D01G128700 chr7D 86.756 521 28 11 14 496 180706550 180707067 4.430000e-150 542.0
50 TraesCS2D01G128700 chr7D 86.381 514 32 6 14 494 365394936 365395444 1.240000e-145 527.0
51 TraesCS2D01G128700 chr7D 87.212 477 31 8 49 497 596593395 596592921 2.690000e-142 516.0
52 TraesCS2D01G128700 chr7D 79.781 366 43 13 1691 2055 561813419 561813754 2.340000e-58 237.0
53 TraesCS2D01G128700 chr7D 88.793 116 12 1 2140 2255 561813756 561813870 1.890000e-29 141.0
54 TraesCS2D01G128700 chr7D 87.755 98 11 1 4490 4586 127203871 127203968 4.120000e-21 113.0
55 TraesCS2D01G128700 chr5A 86.667 510 39 11 14 494 451448322 451447813 5.740000e-149 538.0
56 TraesCS2D01G128700 chr5A 86.567 469 41 7 2517 2971 186993160 186993620 9.740000e-137 497.0
57 TraesCS2D01G128700 chr5A 85.156 512 39 16 14 494 524635621 524635116 1.630000e-134 490.0
58 TraesCS2D01G128700 chr5A 79.883 512 63 32 3252 3744 186993801 186994291 6.250000e-89 339.0
59 TraesCS2D01G128700 chr5A 87.692 65 4 3 4802 4865 391993215 391993276 6.990000e-09 73.1
60 TraesCS2D01G128700 chr5A 94.737 38 2 0 4829 4866 537951756 537951719 5.440000e-05 60.2
61 TraesCS2D01G128700 chr1A 87.633 469 34 9 2517 2971 267347953 267348411 1.610000e-144 523.0
62 TraesCS2D01G128700 chr1A 87.420 469 36 9 2517 2971 272010410 272009951 7.470000e-143 518.0
63 TraesCS2D01G128700 chr1A 82.794 587 56 24 3038 3618 554812807 554813354 2.730000e-132 483.0
64 TraesCS2D01G128700 chr1A 92.174 115 4 4 3252 3362 267348592 267348705 1.880000e-34 158.0
65 TraesCS2D01G128700 chr5D 85.741 526 34 12 14 506 115652205 115651688 7.470000e-143 518.0
66 TraesCS2D01G128700 chr5D 85.271 516 36 15 14 498 381789064 381789570 3.500000e-136 496.0
67 TraesCS2D01G128700 chr5D 90.789 228 18 3 268 494 269734188 269734413 8.190000e-78 302.0
68 TraesCS2D01G128700 chr4A 81.119 715 69 41 3041 3745 290583468 290582810 3.480000e-141 512.0
69 TraesCS2D01G128700 chr4A 81.967 488 46 22 45 494 621412952 621413435 4.760000e-100 375.0
70 TraesCS2D01G128700 chr4A 90.728 151 14 0 2336 2486 290583654 290583504 8.550000e-48 202.0
71 TraesCS2D01G128700 chr4A 78.037 214 37 8 4066 4272 449983453 449983663 5.290000e-25 126.0
72 TraesCS2D01G128700 chr4D 85.490 510 43 12 16 496 503911410 503911917 2.090000e-138 503.0
73 TraesCS2D01G128700 chr4D 85.549 519 31 15 14 498 505324150 505324658 2.090000e-138 503.0
74 TraesCS2D01G128700 chr4D 88.776 98 9 2 2045 2141 5067814 5067910 8.860000e-23 119.0
75 TraesCS2D01G128700 chr4D 100.000 29 0 0 4838 4866 340081936 340081908 3.000000e-03 54.7
76 TraesCS2D01G128700 chr3A 84.570 512 45 10 14 497 698149440 698148935 1.270000e-130 477.0
77 TraesCS2D01G128700 chr3A 89.216 102 10 1 4489 4589 208796067 208795966 5.290000e-25 126.0
78 TraesCS2D01G128700 chr3A 100.000 33 0 0 4823 4855 53546200 53546168 1.510000e-05 62.1
79 TraesCS2D01G128700 chr3B 82.514 366 52 8 1691 2055 18216698 18217052 1.360000e-80 311.0
80 TraesCS2D01G128700 chr3B 82.941 340 46 8 1714 2051 521511846 521512175 3.810000e-76 296.0
81 TraesCS2D01G128700 chr3B 89.655 116 9 2 2140 2255 18217054 18217166 1.460000e-30 145.0
82 TraesCS2D01G128700 chr1B 77.475 404 53 20 1106 1497 397670167 397669790 1.840000e-49 207.0
83 TraesCS2D01G128700 chr1B 84.848 198 25 3 2732 2924 397668654 397668457 1.430000e-45 195.0
84 TraesCS2D01G128700 chr1B 85.311 177 17 3 2140 2316 495807089 495806922 1.860000e-39 174.0
85 TraesCS2D01G128700 chr1B 89.216 102 10 1 2057 2157 597156804 597156905 5.290000e-25 126.0
86 TraesCS2D01G128700 chr1B 82.979 94 14 2 4498 4590 40876536 40876444 3.230000e-12 84.2
87 TraesCS2D01G128700 chr6B 90.909 88 7 1 2054 2141 85383677 85383763 3.190000e-22 117.0
88 TraesCS2D01G128700 chr6B 91.071 56 4 1 4811 4866 182142444 182142390 1.940000e-09 75.0
89 TraesCS2D01G128700 chr6B 91.489 47 3 1 4821 4866 664896111 664896065 4.210000e-06 63.9
90 TraesCS2D01G128700 chr5B 84.848 99 14 1 4489 4586 87164469 87164371 1.150000e-16 99.0
91 TraesCS2D01G128700 chr6D 93.478 46 1 2 4824 4868 354064396 354064352 3.250000e-07 67.6


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 TraesCS2D01G128700 chr2D 74973854 74978889 5035 False 9300.000000 9300 100.000000 1 5036 1 chr2D.!!$F1 5035
1 TraesCS2D01G128700 chr2D 142672206 142672710 504 True 525.000000 525 86.550000 17 494 1 chr2D.!!$R1 477
2 TraesCS2D01G128700 chr2D 542195710 542196212 502 False 510.000000 510 85.882000 14 494 1 chr2D.!!$F2 480
3 TraesCS2D01G128700 chr2B 114322321 114325935 3614 False 2469.500000 3500 92.110500 499 4050 2 chr2B.!!$F3 3551
4 TraesCS2D01G128700 chr2B 787811700 787812478 778 False 767.000000 767 84.906000 2333 3103 1 chr2B.!!$F2 770
5 TraesCS2D01G128700 chr2B 289173275 289174244 969 True 478.000000 726 87.063000 2336 3362 2 chr2B.!!$R3 1026
6 TraesCS2D01G128700 chr2A 74143231 74150314 7083 False 806.857143 1770 91.954286 494 4800 7 chr2A.!!$F1 4306
7 TraesCS2D01G128700 chr2A 348989813 348990660 847 False 349.000000 496 85.437000 2333 3745 2 chr2A.!!$F2 1412
8 TraesCS2D01G128700 chr7A 299533125 299534461 1336 False 611.000000 765 85.413500 2333 3744 2 chr7A.!!$F3 1411
9 TraesCS2D01G128700 chr3D 304401524 304402865 1341 False 613.500000 763 83.577000 2333 3744 2 chr3D.!!$F2 1411
10 TraesCS2D01G128700 chr3D 361757040 361757547 507 False 608.000000 608 89.173000 14 494 1 chr3D.!!$F1 480
11 TraesCS2D01G128700 chr3D 406690205 406691145 940 False 394.000000 649 84.161500 2593 3607 2 chr3D.!!$F3 1014
12 TraesCS2D01G128700 chr7B 555322811 555324145 1334 False 553.000000 651 82.306500 2333 3744 2 chr7B.!!$F4 1411
13 TraesCS2D01G128700 chr7B 272694866 272695518 652 False 497.000000 497 80.972000 3038 3745 1 chr7B.!!$F3 707
14 TraesCS2D01G128700 chrUn 132104841 132105357 516 False 555.000000 555 87.023000 14 504 1 chrUn.!!$F1 490
15 TraesCS2D01G128700 chr1D 202560192 202560702 510 False 551.000000 551 87.160000 14 494 1 chr1D.!!$F1 480
16 TraesCS2D01G128700 chr7D 180706550 180707067 517 False 542.000000 542 86.756000 14 496 1 chr7D.!!$F2 482
17 TraesCS2D01G128700 chr7D 365394936 365395444 508 False 527.000000 527 86.381000 14 494 1 chr7D.!!$F3 480
18 TraesCS2D01G128700 chr5A 451447813 451448322 509 True 538.000000 538 86.667000 14 494 1 chr5A.!!$R1 480
19 TraesCS2D01G128700 chr5A 524635116 524635621 505 True 490.000000 490 85.156000 14 494 1 chr5A.!!$R2 480
20 TraesCS2D01G128700 chr5A 186993160 186994291 1131 False 418.000000 497 83.225000 2517 3744 2 chr5A.!!$F2 1227
21 TraesCS2D01G128700 chr1A 554812807 554813354 547 False 483.000000 483 82.794000 3038 3618 1 chr1A.!!$F1 580
22 TraesCS2D01G128700 chr1A 267347953 267348705 752 False 340.500000 523 89.903500 2517 3362 2 chr1A.!!$F2 845
23 TraesCS2D01G128700 chr5D 115651688 115652205 517 True 518.000000 518 85.741000 14 506 1 chr5D.!!$R1 492
24 TraesCS2D01G128700 chr5D 381789064 381789570 506 False 496.000000 496 85.271000 14 498 1 chr5D.!!$F2 484
25 TraesCS2D01G128700 chr4A 290582810 290583654 844 True 357.000000 512 85.923500 2336 3745 2 chr4A.!!$R1 1409
26 TraesCS2D01G128700 chr4D 503911410 503911917 507 False 503.000000 503 85.490000 16 496 1 chr4D.!!$F2 480
27 TraesCS2D01G128700 chr4D 505324150 505324658 508 False 503.000000 503 85.549000 14 498 1 chr4D.!!$F3 484
28 TraesCS2D01G128700 chr3A 698148935 698149440 505 True 477.000000 477 84.570000 14 497 1 chr3A.!!$R3 483
29 TraesCS2D01G128700 chr1B 397668457 397670167 1710 True 201.000000 207 81.161500 1106 2924 2 chr1B.!!$R3 1818

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
654 829 0.956633 CAGCTGTGTTCACATTGCCT 59.043 50.000 5.25 0.0 0.00 4.75 F
1556 2671 1.725641 TAGATGCGCAACACTGAAGG 58.274 50.000 17.11 0.0 0.00 3.46 F
1567 2682 2.306847 ACACTGAAGGCCGACAAAATT 58.693 42.857 0.00 0.0 0.00 1.82 F
2838 4346 0.611896 GTGGTCCCTGGAACATTGGG 60.612 60.000 7.28 0.0 44.26 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 2844 1.191489 TGTGGATCGAGGCTGTTGGA 61.191 55.000 0.00 0.0 0.00 3.53 R
2374 3612 1.407979 CTCGGCGTATACCTTGGACTT 59.592 52.381 6.85 0.0 0.00 3.01 R
2862 4372 1.760613 CTTACTTCGGTATGGCCTGGA 59.239 52.381 3.32 0.0 34.25 3.86 R
4084 5802 0.176449 CATGGTCGTGATGCAGAGGA 59.824 55.000 0.00 0.0 0.00 3.71 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
476 651 2.526110 GAAGGCCTTTGTGGGGGT 59.474 61.111 21.54 0.00 36.00 4.95
511 686 3.068873 GCTCTTAGATGATCCGAGTTGGT 59.931 47.826 0.00 0.00 39.52 3.67
579 754 1.130373 CGAAGGCGCAAATGAGCTTAA 59.870 47.619 10.83 0.00 40.76 1.85
588 763 3.550561 CAAATGAGCTTAAAACGTGCGA 58.449 40.909 0.00 0.00 0.00 5.10
589 764 3.455619 AATGAGCTTAAAACGTGCGAG 57.544 42.857 0.00 0.00 0.00 5.03
625 800 2.421399 GGGGAATCTGCTTGCCTGC 61.421 63.158 1.85 0.00 44.46 4.85
654 829 0.956633 CAGCTGTGTTCACATTGCCT 59.043 50.000 5.25 0.00 0.00 4.75
799 975 8.543774 ACTGTTTTCCATCTACAGAAGTGATAT 58.456 33.333 8.32 0.00 41.33 1.63
863 1062 6.707608 TGTGGATATATCATGCAAACTCAGAC 59.292 38.462 14.60 0.00 0.00 3.51
948 2005 2.880890 CCCATGCTCCTATTAAGTGCAC 59.119 50.000 9.40 9.40 34.56 4.57
949 2006 3.434167 CCCATGCTCCTATTAAGTGCACT 60.434 47.826 15.25 15.25 34.56 4.40
951 2008 4.752101 CCATGCTCCTATTAAGTGCACTAC 59.248 45.833 22.01 2.14 34.56 2.73
953 2010 5.263968 TGCTCCTATTAAGTGCACTACTC 57.736 43.478 22.01 2.92 39.18 2.59
954 2011 4.709886 TGCTCCTATTAAGTGCACTACTCA 59.290 41.667 22.01 4.65 39.18 3.41
955 2012 5.163509 TGCTCCTATTAAGTGCACTACTCAG 60.164 44.000 22.01 14.64 39.18 3.35
956 2013 5.163499 GCTCCTATTAAGTGCACTACTCAGT 60.163 44.000 22.01 5.66 39.18 3.41
958 2015 7.330900 TCCTATTAAGTGCACTACTCAGTAC 57.669 40.000 22.01 0.00 39.18 2.73
959 2016 7.117397 TCCTATTAAGTGCACTACTCAGTACT 58.883 38.462 22.01 3.16 39.18 2.73
960 2017 7.282675 TCCTATTAAGTGCACTACTCAGTACTC 59.717 40.741 22.01 0.00 39.18 2.59
961 2018 6.835819 ATTAAGTGCACTACTCAGTACTCA 57.164 37.500 22.01 0.00 39.18 3.41
962 2019 4.775058 AAGTGCACTACTCAGTACTCAG 57.225 45.455 22.01 0.00 39.18 3.35
963 2020 4.022413 AGTGCACTACTCAGTACTCAGA 57.978 45.455 20.16 0.00 33.17 3.27
964 2021 4.006989 AGTGCACTACTCAGTACTCAGAG 58.993 47.826 20.16 4.67 33.17 3.35
965 2022 4.004314 GTGCACTACTCAGTACTCAGAGA 58.996 47.826 10.32 0.00 35.83 3.10
966 2023 4.004314 TGCACTACTCAGTACTCAGAGAC 58.996 47.826 15.23 0.00 35.83 3.36
967 2024 4.004314 GCACTACTCAGTACTCAGAGACA 58.996 47.826 15.23 4.04 35.83 3.41
968 2025 4.094294 GCACTACTCAGTACTCAGAGACAG 59.906 50.000 15.23 13.06 35.83 3.51
969 2026 4.094294 CACTACTCAGTACTCAGAGACAGC 59.906 50.000 15.23 0.00 35.83 4.40
970 2027 3.147553 ACTCAGTACTCAGAGACAGCA 57.852 47.619 15.23 0.00 35.83 4.41
971 2028 3.491342 ACTCAGTACTCAGAGACAGCAA 58.509 45.455 15.23 0.00 35.83 3.91
972 2029 4.085733 ACTCAGTACTCAGAGACAGCAAT 58.914 43.478 15.23 0.00 35.83 3.56
973 2030 5.257262 ACTCAGTACTCAGAGACAGCAATA 58.743 41.667 15.23 0.00 35.83 1.90
974 2031 5.890985 ACTCAGTACTCAGAGACAGCAATAT 59.109 40.000 15.23 0.00 35.83 1.28
975 2032 6.141560 TCAGTACTCAGAGACAGCAATATG 57.858 41.667 3.79 0.00 0.00 1.78
978 2035 6.915300 CAGTACTCAGAGACAGCAATATGTAC 59.085 42.308 3.79 0.00 32.25 2.90
981 2038 7.646548 ACTCAGAGACAGCAATATGTACTTA 57.353 36.000 3.79 0.00 32.25 2.24
995 2052 4.690184 TGTACTTATCGAACGAGCTCAA 57.310 40.909 15.40 0.00 0.00 3.02
1505 2585 2.098117 GGCACTGCAGGTAACATCATTC 59.902 50.000 19.93 0.00 41.41 2.67
1532 2647 3.525537 TCTAGCTGCAACTAATCAGTGC 58.474 45.455 1.02 0.00 34.36 4.40
1538 2653 4.201812 GCTGCAACTAATCAGTGCGATTTA 60.202 41.667 0.00 0.00 41.83 1.40
1553 2668 2.348362 CGATTTAGATGCGCAACACTGA 59.652 45.455 17.11 8.59 0.00 3.41
1556 2671 1.725641 TAGATGCGCAACACTGAAGG 58.274 50.000 17.11 0.00 0.00 3.46
1558 2673 2.533391 GATGCGCAACACTGAAGGCC 62.533 60.000 17.11 0.00 0.00 5.19
1567 2682 2.306847 ACACTGAAGGCCGACAAAATT 58.693 42.857 0.00 0.00 0.00 1.82
1568 2683 2.693074 ACACTGAAGGCCGACAAAATTT 59.307 40.909 0.00 0.00 0.00 1.82
1569 2684 3.243401 ACACTGAAGGCCGACAAAATTTC 60.243 43.478 0.00 0.00 0.00 2.17
1628 2824 8.821894 GGAGTTCATGTTATCTCTGTACATTTC 58.178 37.037 0.00 0.00 30.45 2.17
1748 2948 4.082408 ACGACGATCTTCCTGTATGAACAA 60.082 41.667 0.00 0.00 34.49 2.83
1789 2992 7.491696 CCTCTTTAACTTCCTCCAGTAAATACG 59.508 40.741 0.00 0.00 0.00 3.06
1972 3202 9.783256 GAAACATAATGGTTGACAGGTAATTAC 57.217 33.333 7.09 7.09 0.00 1.89
1984 3214 4.526262 ACAGGTAATTACATGCCAAGCAAA 59.474 37.500 25.76 0.00 43.62 3.68
1985 3215 5.011533 ACAGGTAATTACATGCCAAGCAAAA 59.988 36.000 25.76 0.00 43.62 2.44
2055 3286 8.911247 AAAAGTTCAGTTTAAGCACAAAGTAG 57.089 30.769 0.00 0.00 0.00 2.57
2067 3299 4.082136 AGCACAAAGTAGTACTACCTCTGC 60.082 45.833 25.97 24.09 36.75 4.26
2070 3302 5.047943 CACAAAGTAGTACTACCTCTGCACT 60.048 44.000 25.97 7.10 36.75 4.40
2083 3315 8.136165 ACTACCTCTGCACTAAAATATAAGACG 58.864 37.037 0.00 0.00 0.00 4.18
2149 3381 4.646492 GGTACGGAGGGAGTAGTATTGAAA 59.354 45.833 0.00 0.00 0.00 2.69
2191 3423 8.258007 TGTGACATGAAGGAAGTAAGTAATAGG 58.742 37.037 0.00 0.00 0.00 2.57
2224 3456 6.715344 CACATATGTGTAGTTTACCGTTGT 57.285 37.500 24.91 0.00 40.96 3.32
2226 3458 7.231607 CACATATGTGTAGTTTACCGTTGTTC 58.768 38.462 24.91 0.00 40.96 3.18
2257 3490 4.314740 TTTTTGGTCGGAACCTTGAATG 57.685 40.909 0.00 0.00 46.60 2.67
2267 3500 3.703052 GGAACCTTGAATGCTTGATGGAT 59.297 43.478 0.00 0.00 0.00 3.41
2269 3502 5.537674 GGAACCTTGAATGCTTGATGGATAT 59.462 40.000 0.00 0.00 0.00 1.63
2466 3704 4.326826 ACCCACATGTATGTTCAGACTTG 58.673 43.478 0.00 10.41 39.39 3.16
2746 4251 3.193267 TGCTTTATGATGTTTGCCCTGAC 59.807 43.478 0.00 0.00 0.00 3.51
2838 4346 0.611896 GTGGTCCCTGGAACATTGGG 60.612 60.000 7.28 0.00 44.26 4.12
2862 4372 9.136323 GGGAATGATTTTGAACTTATCCATACT 57.864 33.333 0.00 0.00 0.00 2.12
2895 4405 5.855045 ACCGAAGTAAGAAACTCAACTCAT 58.145 37.500 0.00 0.00 37.50 2.90
2971 4485 3.948473 GGATTAAAGAGGAGTTGGGCTTC 59.052 47.826 0.00 0.00 0.00 3.86
3358 5025 2.915869 AGTACAATCCACCCTTCTCCA 58.084 47.619 0.00 0.00 0.00 3.86
3363 5030 4.310740 ACAATCCACCCTTCTCCATAGAT 58.689 43.478 0.00 0.00 0.00 1.98
3382 5049 7.758980 CCATAGATTTCCTATCTCAAGTGATCG 59.241 40.741 0.00 0.00 35.96 3.69
3544 5258 7.658575 GCATCCCTTCATTATTGCATACAAAAT 59.341 33.333 0.00 0.00 39.77 1.82
3588 5303 5.048083 TCAGTTTGATACCTGGATTTGCAAC 60.048 40.000 0.00 0.00 0.00 4.17
3766 5484 2.286242 CGCATCTTGTGATCACATGCTC 60.286 50.000 33.50 23.01 41.52 4.26
3770 5488 0.392863 TTGTGATCACATGCTCCCCG 60.393 55.000 28.32 0.00 41.52 5.73
3880 5598 7.450014 TCCAAACATCATGTATTGTGGTACTTT 59.550 33.333 0.00 0.00 0.00 2.66
3881 5599 8.735315 CCAAACATCATGTATTGTGGTACTTTA 58.265 33.333 0.00 0.00 0.00 1.85
3912 5630 3.264193 TCTCCAAGATGTACAAGGCATGT 59.736 43.478 0.00 0.00 46.36 3.21
3967 5685 6.098124 TGGATCATCCCGCAAAAGAAAATATT 59.902 34.615 0.00 0.00 35.03 1.28
3969 5687 7.169813 GGATCATCCCGCAAAAGAAAATATTTC 59.830 37.037 0.10 0.00 0.00 2.17
4005 5723 7.816031 CAGATTGTACAAGCAAGGAAATCATTT 59.184 33.333 24.55 0.00 0.00 2.32
4030 5748 6.631962 AGTCAGTTTAGTAGACCAAGCATAC 58.368 40.000 0.00 0.00 32.82 2.39
4044 5762 4.574828 CCAAGCATACGTAGCAATACCTTT 59.425 41.667 15.98 1.62 0.00 3.11
4050 5768 6.238374 GCATACGTAGCAATACCTTTGTGATT 60.238 38.462 0.08 0.00 0.00 2.57
4051 5769 7.678690 GCATACGTAGCAATACCTTTGTGATTT 60.679 37.037 0.08 0.00 0.00 2.17
4052 5770 6.569179 ACGTAGCAATACCTTTGTGATTTT 57.431 33.333 0.00 0.00 0.00 1.82
4053 5771 6.977213 ACGTAGCAATACCTTTGTGATTTTT 58.023 32.000 0.00 0.00 0.00 1.94
4083 5801 5.715434 TTTTGAAAAGAAGGATAACCCCG 57.285 39.130 0.00 0.00 36.73 5.73
4084 5802 4.376225 TTGAAAAGAAGGATAACCCCGT 57.624 40.909 0.00 0.00 36.73 5.28
4090 5809 1.413077 GAAGGATAACCCCGTCCTCTG 59.587 57.143 0.00 0.00 43.94 3.35
4096 5815 2.185310 AACCCCGTCCTCTGCATCAC 62.185 60.000 0.00 0.00 0.00 3.06
4112 5831 1.512522 CACGACCATGCATGCAACG 60.513 57.895 26.68 26.14 0.00 4.10
4124 5843 8.306038 ACCATGCATGCAACGATAAATTATTAT 58.694 29.630 26.68 0.00 34.40 1.28
4155 5874 3.052455 TCTAGCAGCCGAAAAACATCA 57.948 42.857 0.00 0.00 0.00 3.07
4160 5879 1.339610 CAGCCGAAAAACATCAACCCA 59.660 47.619 0.00 0.00 0.00 4.51
4170 5890 2.699954 ACATCAACCCAGAGTAAAGCG 58.300 47.619 0.00 0.00 0.00 4.68
4180 5900 5.535030 ACCCAGAGTAAAGCGAAAAGAAAAT 59.465 36.000 0.00 0.00 0.00 1.82
4189 5909 1.132453 CGAAAAGAAAATCCGAGGCCC 59.868 52.381 0.00 0.00 0.00 5.80
4190 5910 2.447443 GAAAAGAAAATCCGAGGCCCT 58.553 47.619 0.00 0.00 0.00 5.19
4208 5928 2.415625 CCCTATGCCTCGCGATAGTAAC 60.416 54.545 10.36 0.00 39.35 2.50
4211 5931 0.306840 TGCCTCGCGATAGTAACTCG 59.693 55.000 10.36 0.00 39.11 4.18
4216 5936 2.009051 TCGCGATAGTAACTCGACCAA 58.991 47.619 3.71 0.00 38.38 3.67
4221 5941 5.108480 CGCGATAGTAACTCGACCAAATAAC 60.108 44.000 0.00 0.00 38.38 1.89
4230 5950 4.285260 ACTCGACCAAATAACCACTAACCT 59.715 41.667 0.00 0.00 0.00 3.50
4243 5963 7.500720 AACCACTAACCTTATGTTACAACAC 57.499 36.000 0.00 0.00 42.51 3.32
4246 5966 6.592607 CCACTAACCTTATGTTACAACACGAT 59.407 38.462 0.00 0.00 42.51 3.73
4248 5968 9.309516 CACTAACCTTATGTTACAACACGATAT 57.690 33.333 0.00 0.00 42.51 1.63
4249 5969 9.525409 ACTAACCTTATGTTACAACACGATATC 57.475 33.333 0.00 0.00 42.51 1.63
4253 5973 8.879759 ACCTTATGTTACAACACGATATCAAAG 58.120 33.333 3.12 0.00 42.51 2.77
4269 7733 7.692291 CGATATCAAAGCGAAAAATACACAACT 59.308 33.333 3.12 0.00 0.00 3.16
4282 7746 5.793030 ATACACAACTCCTAGACTATGGC 57.207 43.478 0.00 0.00 0.00 4.40
4299 7764 1.021968 GGCGAGTCAACACAAGGTTT 58.978 50.000 0.00 0.00 37.72 3.27
4304 7769 4.201881 GCGAGTCAACACAAGGTTTAACTT 60.202 41.667 0.00 0.00 37.72 2.66
4311 7776 5.684550 ACACAAGGTTTAACTTCGGATTC 57.315 39.130 0.00 0.00 0.00 2.52
4319 7784 4.417426 TTAACTTCGGATTCTCATCCCC 57.583 45.455 0.00 0.00 46.06 4.81
4325 7790 2.576191 TCGGATTCTCATCCCCAAAGTT 59.424 45.455 0.00 0.00 46.06 2.66
4342 7808 6.327934 CCAAAGTTAAGCTTCAATCCATCAG 58.672 40.000 0.00 0.00 36.17 2.90
4353 7819 2.054232 ATCCATCAGCTTCAGCAAGG 57.946 50.000 0.75 0.00 45.16 3.61
4356 7822 1.612462 CCATCAGCTTCAGCAAGGACA 60.612 52.381 0.75 0.00 45.16 4.02
4357 7823 2.366533 CATCAGCTTCAGCAAGGACAT 58.633 47.619 0.75 0.00 45.16 3.06
4359 7825 0.809385 CAGCTTCAGCAAGGACATGG 59.191 55.000 0.75 0.00 45.16 3.66
4361 7827 1.798735 CTTCAGCAAGGACATGGCG 59.201 57.895 0.00 0.00 0.00 5.69
4379 7845 4.799473 CAGGCGCGCGTCAACATG 62.799 66.667 37.48 22.17 0.00 3.21
4384 7850 2.502510 GCGCGTCAACATGGCTTG 60.503 61.111 8.43 0.00 0.00 4.01
4423 7893 4.717629 CCGGAGCGCAAGTCGTCA 62.718 66.667 11.47 0.00 41.07 4.35
4480 7954 1.339610 TGAACAAAAGCAATCACCCCG 59.660 47.619 0.00 0.00 0.00 5.73
4517 7991 4.318021 CACGTGCAGCACAGTGGC 62.318 66.667 28.36 5.69 36.27 5.01
4528 8002 4.463879 CAGTGGCTCTGGCGGAGG 62.464 72.222 24.11 6.92 42.08 4.30
4542 8016 0.671251 CGGAGGTCTCATGTCTAGCC 59.329 60.000 0.14 0.00 0.00 3.93
4544 8018 2.487445 CGGAGGTCTCATGTCTAGCCTA 60.487 54.545 0.14 0.00 0.00 3.93
4545 8019 2.888414 GGAGGTCTCATGTCTAGCCTAC 59.112 54.545 0.14 0.00 0.00 3.18
4562 8036 3.215151 CCTACTGCTACTGGATCGAAGA 58.785 50.000 0.00 0.00 45.75 2.87
4569 8043 0.904649 ACTGGATCGAAGATGGTGCA 59.095 50.000 0.00 0.00 45.12 4.57
4577 8051 1.609208 GAAGATGGTGCAACAGTGGT 58.391 50.000 11.62 0.00 39.98 4.16
4586 8060 1.075482 CAACAGTGGTGGGAGGCAT 59.925 57.895 0.00 0.00 0.00 4.40
4601 8389 5.534654 TGGGAGGCATGCAAAAATATACTAC 59.465 40.000 21.36 4.20 0.00 2.73
4603 8391 6.265422 GGGAGGCATGCAAAAATATACTACTT 59.735 38.462 21.36 0.00 0.00 2.24
4654 8442 0.320771 GAGACCATGACGCCACAGTT 60.321 55.000 0.00 0.00 0.00 3.16
4663 8451 4.120331 GCCACAGTTCATGGGCGC 62.120 66.667 0.00 0.00 37.73 6.53
4664 8452 3.803082 CCACAGTTCATGGGCGCG 61.803 66.667 0.00 0.00 33.18 6.86
4665 8453 4.465512 CACAGTTCATGGGCGCGC 62.466 66.667 25.94 25.94 0.00 6.86
4668 8456 4.722700 AGTTCATGGGCGCGCCTT 62.723 61.111 45.23 31.59 36.10 4.35
4669 8457 3.747976 GTTCATGGGCGCGCCTTT 61.748 61.111 45.23 31.23 36.10 3.11
4670 8458 2.988684 TTCATGGGCGCGCCTTTT 60.989 55.556 45.23 28.71 36.10 2.27
4671 8459 2.569354 TTCATGGGCGCGCCTTTTT 61.569 52.632 45.23 26.23 36.10 1.94
4690 8478 1.967319 TTTTAGATCCTCATGGGCGC 58.033 50.000 0.00 0.00 34.39 6.53
4701 8489 3.814615 ATGGGCGCGCCTATGTCTG 62.815 63.158 42.93 0.00 35.89 3.51
4715 8503 0.681733 TGTCTGGCTTGACAGGAGAC 59.318 55.000 3.41 0.00 41.43 3.36
4716 8504 0.389166 GTCTGGCTTGACAGGAGACG 60.389 60.000 3.41 0.00 38.98 4.18
4717 8505 1.739562 CTGGCTTGACAGGAGACGC 60.740 63.158 0.00 0.00 34.84 5.19
4724 8512 1.214062 GACAGGAGACGCAGGACAG 59.786 63.158 0.00 0.00 0.00 3.51
4800 8588 9.147732 ACAACCTCATTTAATTCCTTTTCTTCT 57.852 29.630 0.00 0.00 0.00 2.85
4860 8648 9.558396 AAGAATGTTAATCAAGCATTTGGAAAA 57.442 25.926 0.00 0.00 33.56 2.29
4861 8649 9.558396 AGAATGTTAATCAAGCATTTGGAAAAA 57.442 25.926 0.00 0.00 33.56 1.94
4959 8747 9.601971 TGTAATAAGAAAGTTGAACATAAACGC 57.398 29.630 0.00 0.00 32.65 4.84
4960 8748 9.601971 GTAATAAGAAAGTTGAACATAAACGCA 57.398 29.630 0.00 0.00 32.65 5.24
4963 8751 9.769093 ATAAGAAAGTTGAACATAAACGCATAC 57.231 29.630 0.00 0.00 32.65 2.39
4964 8752 7.197071 AGAAAGTTGAACATAAACGCATACA 57.803 32.000 0.00 0.00 32.65 2.29
4965 8753 7.816640 AGAAAGTTGAACATAAACGCATACAT 58.183 30.769 0.00 0.00 32.65 2.29
4966 8754 8.296713 AGAAAGTTGAACATAAACGCATACATT 58.703 29.630 0.00 0.00 32.65 2.71
4967 8755 8.810652 AAAGTTGAACATAAACGCATACATTT 57.189 26.923 0.00 0.00 32.65 2.32
4968 8756 8.810652 AAGTTGAACATAAACGCATACATTTT 57.189 26.923 0.00 0.00 32.65 1.82
4969 8757 8.226543 AGTTGAACATAAACGCATACATTTTG 57.773 30.769 0.00 0.00 32.65 2.44
4970 8758 8.079203 AGTTGAACATAAACGCATACATTTTGA 58.921 29.630 0.00 0.00 32.65 2.69
4971 8759 8.695284 GTTGAACATAAACGCATACATTTTGAA 58.305 29.630 0.00 0.00 0.00 2.69
4972 8760 8.978564 TGAACATAAACGCATACATTTTGAAT 57.021 26.923 0.00 0.00 0.00 2.57
4976 8764 9.502145 ACATAAACGCATACATTTTGAATAGTG 57.498 29.630 0.00 0.00 0.00 2.74
4977 8765 9.715123 CATAAACGCATACATTTTGAATAGTGA 57.285 29.630 0.00 0.00 0.00 3.41
4979 8767 8.619146 AAACGCATACATTTTGAATAGTGATG 57.381 30.769 0.00 0.00 0.00 3.07
4980 8768 7.320443 ACGCATACATTTTGAATAGTGATGT 57.680 32.000 0.00 0.00 35.36 3.06
4981 8769 7.761409 ACGCATACATTTTGAATAGTGATGTT 58.239 30.769 0.00 0.00 33.42 2.71
4982 8770 8.243426 ACGCATACATTTTGAATAGTGATGTTT 58.757 29.630 0.00 0.00 33.42 2.83
4983 8771 9.715123 CGCATACATTTTGAATAGTGATGTTTA 57.285 29.630 0.00 0.00 33.42 2.01
4987 8775 8.970691 ACATTTTGAATAGTGATGTTTACTGC 57.029 30.769 0.00 0.00 0.00 4.40
4988 8776 8.796475 ACATTTTGAATAGTGATGTTTACTGCT 58.204 29.630 0.00 0.00 0.00 4.24
4989 8777 9.282247 CATTTTGAATAGTGATGTTTACTGCTC 57.718 33.333 0.00 0.00 0.00 4.26
4990 8778 6.647212 TTGAATAGTGATGTTTACTGCTCG 57.353 37.500 0.00 0.00 0.00 5.03
4991 8779 5.961272 TGAATAGTGATGTTTACTGCTCGA 58.039 37.500 0.00 0.00 0.00 4.04
4992 8780 5.805486 TGAATAGTGATGTTTACTGCTCGAC 59.195 40.000 0.00 0.00 0.00 4.20
4993 8781 3.660501 AGTGATGTTTACTGCTCGACA 57.339 42.857 0.00 0.00 0.00 4.35
4994 8782 3.318017 AGTGATGTTTACTGCTCGACAC 58.682 45.455 0.00 0.00 0.00 3.67
4995 8783 2.090658 GTGATGTTTACTGCTCGACACG 59.909 50.000 0.00 0.00 0.00 4.49
4996 8784 2.030628 TGATGTTTACTGCTCGACACGA 60.031 45.455 0.00 0.00 0.00 4.35
4997 8785 2.717580 TGTTTACTGCTCGACACGAT 57.282 45.000 0.00 0.00 34.61 3.73
4998 8786 3.021269 TGTTTACTGCTCGACACGATT 57.979 42.857 0.00 0.00 34.61 3.34
4999 8787 2.984471 TGTTTACTGCTCGACACGATTC 59.016 45.455 0.00 0.00 34.61 2.52
5000 8788 2.984471 GTTTACTGCTCGACACGATTCA 59.016 45.455 0.00 0.00 34.61 2.57
5001 8789 3.291809 TTACTGCTCGACACGATTCAA 57.708 42.857 0.00 0.00 34.61 2.69
5002 8790 2.370281 ACTGCTCGACACGATTCAAT 57.630 45.000 0.00 0.00 34.61 2.57
5003 8791 1.995484 ACTGCTCGACACGATTCAATG 59.005 47.619 0.00 0.00 34.61 2.82
5004 8792 2.262211 CTGCTCGACACGATTCAATGA 58.738 47.619 0.00 0.00 34.61 2.57
5005 8793 2.862536 CTGCTCGACACGATTCAATGAT 59.137 45.455 0.00 0.00 34.61 2.45
5006 8794 2.604462 TGCTCGACACGATTCAATGATG 59.396 45.455 0.00 0.00 34.61 3.07
5007 8795 2.860136 GCTCGACACGATTCAATGATGA 59.140 45.455 0.00 0.00 34.61 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.151022 CCTCCCTCTCCCGTGAGC 61.151 72.222 0.00 0.00 38.58 4.26
8 9 2.443016 CCCTCCCTCTCCCGTGAG 60.443 72.222 0.00 0.00 40.17 3.51
9 10 4.779733 GCCCTCCCTCTCCCGTGA 62.780 72.222 0.00 0.00 0.00 4.35
10 11 4.787280 AGCCCTCCCTCTCCCGTG 62.787 72.222 0.00 0.00 0.00 4.94
11 12 4.467107 GAGCCCTCCCTCTCCCGT 62.467 72.222 0.00 0.00 0.00 5.28
76 79 1.227664 CCGAGCTCTACCTCTCCCA 59.772 63.158 12.85 0.00 0.00 4.37
511 686 4.282496 TCAAAAAGAAGGTAAGGGCAACA 58.718 39.130 0.00 0.00 39.74 3.33
554 729 1.511887 CATTTGCGCCTTCGAACGG 60.512 57.895 4.18 9.23 38.10 4.44
579 754 0.038159 CTCCTCCTTCTCGCACGTTT 60.038 55.000 0.00 0.00 0.00 3.60
588 763 0.695347 CTTTGCCACCTCCTCCTTCT 59.305 55.000 0.00 0.00 0.00 2.85
589 764 0.322906 CCTTTGCCACCTCCTCCTTC 60.323 60.000 0.00 0.00 0.00 3.46
625 800 3.046087 CACAGCTGCAGACACGGG 61.046 66.667 20.43 0.00 0.00 5.28
654 829 4.036734 GCTGTTGAATTTGACTTCAGTCCA 59.963 41.667 4.48 0.00 44.15 4.02
799 975 7.661127 AACAAGCACACGTATTATCAGTTTA 57.339 32.000 0.00 0.00 0.00 2.01
800 976 6.554334 AACAAGCACACGTATTATCAGTTT 57.446 33.333 0.00 0.00 0.00 2.66
801 977 6.426937 AGAAACAAGCACACGTATTATCAGTT 59.573 34.615 0.00 0.00 0.00 3.16
813 989 2.297701 TGGGAGAAGAAACAAGCACAC 58.702 47.619 0.00 0.00 0.00 3.82
814 990 2.727123 TGGGAGAAGAAACAAGCACA 57.273 45.000 0.00 0.00 0.00 4.57
948 2005 4.257731 TGCTGTCTCTGAGTACTGAGTAG 58.742 47.826 9.29 9.90 41.02 2.57
949 2006 4.287766 TGCTGTCTCTGAGTACTGAGTA 57.712 45.455 9.29 0.00 41.02 2.59
951 2008 4.717233 ATTGCTGTCTCTGAGTACTGAG 57.283 45.455 0.00 0.00 41.39 3.35
953 2010 5.900425 ACATATTGCTGTCTCTGAGTACTG 58.100 41.667 0.00 7.06 0.00 2.74
954 2011 6.831353 AGTACATATTGCTGTCTCTGAGTACT 59.169 38.462 4.32 0.00 35.10 2.73
955 2012 7.033530 AGTACATATTGCTGTCTCTGAGTAC 57.966 40.000 4.32 2.82 0.00 2.73
956 2013 7.646548 AAGTACATATTGCTGTCTCTGAGTA 57.353 36.000 4.32 0.00 0.00 2.59
958 2015 7.536964 CGATAAGTACATATTGCTGTCTCTGAG 59.463 40.741 0.00 0.00 0.00 3.35
959 2016 7.228706 TCGATAAGTACATATTGCTGTCTCTGA 59.771 37.037 0.00 0.00 0.00 3.27
960 2017 7.363431 TCGATAAGTACATATTGCTGTCTCTG 58.637 38.462 0.00 0.00 0.00 3.35
961 2018 7.511959 TCGATAAGTACATATTGCTGTCTCT 57.488 36.000 0.00 0.00 0.00 3.10
962 2019 7.149112 CGTTCGATAAGTACATATTGCTGTCTC 60.149 40.741 0.00 0.00 0.00 3.36
963 2020 6.637254 CGTTCGATAAGTACATATTGCTGTCT 59.363 38.462 0.00 0.00 0.00 3.41
964 2021 6.635641 TCGTTCGATAAGTACATATTGCTGTC 59.364 38.462 0.00 0.00 0.00 3.51
965 2022 6.500910 TCGTTCGATAAGTACATATTGCTGT 58.499 36.000 0.00 0.00 0.00 4.40
966 2023 6.399039 GCTCGTTCGATAAGTACATATTGCTG 60.399 42.308 0.00 0.00 0.00 4.41
967 2024 5.629849 GCTCGTTCGATAAGTACATATTGCT 59.370 40.000 0.00 0.00 0.00 3.91
968 2025 5.629849 AGCTCGTTCGATAAGTACATATTGC 59.370 40.000 0.00 0.00 0.00 3.56
969 2026 6.856426 TGAGCTCGTTCGATAAGTACATATTG 59.144 38.462 9.64 0.00 0.00 1.90
970 2027 6.967135 TGAGCTCGTTCGATAAGTACATATT 58.033 36.000 9.64 0.00 0.00 1.28
971 2028 6.555812 TGAGCTCGTTCGATAAGTACATAT 57.444 37.500 9.64 0.00 0.00 1.78
972 2029 5.996669 TGAGCTCGTTCGATAAGTACATA 57.003 39.130 9.64 0.00 0.00 2.29
973 2030 4.895224 TGAGCTCGTTCGATAAGTACAT 57.105 40.909 9.64 0.00 0.00 2.29
974 2031 4.659088 CTTGAGCTCGTTCGATAAGTACA 58.341 43.478 9.64 0.00 0.00 2.90
975 2032 3.482833 GCTTGAGCTCGTTCGATAAGTAC 59.517 47.826 9.64 0.00 38.21 2.73
1323 2403 2.496070 AGATCAGGCGCAAAGTAGTACA 59.504 45.455 10.83 0.00 0.00 2.90
1473 2553 1.673665 GCAGTGCCTTGGTCCTCTG 60.674 63.158 2.85 0.00 0.00 3.35
1505 2585 2.680312 TAGTTGCAGCTAGAAGCAGG 57.320 50.000 6.14 0.00 45.56 4.85
1511 2591 3.525537 GCACTGATTAGTTGCAGCTAGA 58.474 45.455 10.34 3.13 34.07 2.43
1532 2647 2.348362 TCAGTGTTGCGCATCTAAATCG 59.652 45.455 12.75 0.00 0.00 3.34
1538 2653 1.580845 GCCTTCAGTGTTGCGCATCT 61.581 55.000 12.75 7.75 0.00 2.90
1553 2668 1.324383 ACGGAAATTTTGTCGGCCTT 58.676 45.000 0.00 0.00 0.00 4.35
1556 2671 2.348125 GCAAAACGGAAATTTTGTCGGC 60.348 45.455 11.43 6.78 46.68 5.54
1558 2673 4.770351 AAGCAAAACGGAAATTTTGTCG 57.230 36.364 11.43 0.23 46.68 4.35
1567 2682 6.385649 ACTATTCTTGAAAGCAAAACGGAA 57.614 33.333 0.00 0.00 32.73 4.30
1568 2683 6.385649 AACTATTCTTGAAAGCAAAACGGA 57.614 33.333 0.00 0.00 32.73 4.69
1569 2684 7.323656 CAGTAACTATTCTTGAAAGCAAAACGG 59.676 37.037 0.00 0.00 32.73 4.44
1648 2844 1.191489 TGTGGATCGAGGCTGTTGGA 61.191 55.000 0.00 0.00 0.00 3.53
1789 2992 5.351189 ACACAACTTTTTGGTGCTGAATTTC 59.649 36.000 0.00 0.00 36.69 2.17
1845 3055 8.476447 TGAAACACATCACGTATATAGGGTAAA 58.524 33.333 7.32 0.00 0.00 2.01
1846 3056 8.009622 TGAAACACATCACGTATATAGGGTAA 57.990 34.615 7.32 0.00 0.00 2.85
1847 3057 7.255695 CCTGAAACACATCACGTATATAGGGTA 60.256 40.741 7.32 0.00 0.00 3.69
1848 3058 6.462487 CCTGAAACACATCACGTATATAGGGT 60.462 42.308 7.32 0.00 0.00 4.34
1849 3059 5.926542 CCTGAAACACATCACGTATATAGGG 59.073 44.000 7.32 0.00 0.00 3.53
1972 3202 4.813027 ACTTCATAGTTTTGCTTGGCATG 58.187 39.130 0.00 0.00 38.76 4.06
1984 3214 2.389715 CCGAGGGGAGACTTCATAGTT 58.610 52.381 0.00 0.00 32.00 2.24
1985 3215 2.030045 GCCGAGGGGAGACTTCATAGT 61.030 57.143 0.00 0.00 33.93 2.12
2067 3299 9.607285 ACTGCAAAAACGTCTTATATTTTAGTG 57.393 29.630 0.00 0.00 0.00 2.74
2164 3396 9.823647 CTATTACTTACTTCCTTCATGTCACAT 57.176 33.333 0.00 0.00 0.00 3.21
2220 3452 7.270834 CGACCAAAAATCAATTAACGAACAAC 58.729 34.615 0.00 0.00 0.00 3.32
2221 3453 6.418226 CCGACCAAAAATCAATTAACGAACAA 59.582 34.615 0.00 0.00 0.00 2.83
2223 3455 6.144175 TCCGACCAAAAATCAATTAACGAAC 58.856 36.000 0.00 0.00 0.00 3.95
2224 3456 6.315091 TCCGACCAAAAATCAATTAACGAA 57.685 33.333 0.00 0.00 0.00 3.85
2226 3458 5.343860 GGTTCCGACCAAAAATCAATTAACG 59.656 40.000 0.00 0.00 45.77 3.18
2374 3612 1.407979 CTCGGCGTATACCTTGGACTT 59.592 52.381 6.85 0.00 0.00 3.01
2746 4251 4.220533 GCAAGGTTATTGCAGCAGATAG 57.779 45.455 7.67 0.00 44.34 2.08
2862 4372 1.760613 CTTACTTCGGTATGGCCTGGA 59.239 52.381 3.32 0.00 34.25 3.86
2926 4436 8.934023 TCCATAAACTTCTCCATAACAAAAGT 57.066 30.769 0.00 0.00 0.00 2.66
2971 4485 1.964608 TAGTGCAGCCAGCTAGCCAG 61.965 60.000 12.13 3.90 45.94 4.85
3010 4539 5.548056 GGAGAGGATGGGGTTGATAATCTTA 59.452 44.000 0.00 0.00 0.00 2.10
3011 4540 4.352298 GGAGAGGATGGGGTTGATAATCTT 59.648 45.833 0.00 0.00 0.00 2.40
3022 4676 2.310052 AGAAAAACTGGAGAGGATGGGG 59.690 50.000 0.00 0.00 0.00 4.96
3358 5025 8.642935 TCGATCACTTGAGATAGGAAATCTAT 57.357 34.615 0.00 0.00 41.14 1.98
3363 5030 5.067936 GGTCTCGATCACTTGAGATAGGAAA 59.932 44.000 1.99 0.00 42.61 3.13
3588 5303 3.247006 CCGAATATCTTACGGGATGGG 57.753 52.381 0.00 0.00 42.48 4.00
3766 5484 3.857157 TTCTGGAATCCTTATTCGGGG 57.143 47.619 0.00 0.00 42.16 5.73
3770 5488 7.448777 GGTCCCTTTATTCTGGAATCCTTATTC 59.551 40.741 0.00 0.00 40.77 1.75
3881 5599 9.253832 CCTTGTACATCTTGGAGAGAGATATAT 57.746 37.037 0.00 0.00 37.93 0.86
3882 5600 7.177568 GCCTTGTACATCTTGGAGAGAGATATA 59.822 40.741 0.00 0.00 37.93 0.86
3952 5670 6.011277 GCAAGCAGAAATATTTTCTTTTGCG 58.989 36.000 21.00 6.58 37.09 4.85
4005 5723 6.852420 ATGCTTGGTCTACTAAACTGACTA 57.148 37.500 0.00 0.00 0.00 2.59
4021 5739 3.728845 AGGTATTGCTACGTATGCTTGG 58.271 45.455 15.00 0.00 0.00 3.61
4064 5782 3.307904 GGACGGGGTTATCCTTCTTTTCA 60.308 47.826 0.00 0.00 35.33 2.69
4065 5783 3.054582 AGGACGGGGTTATCCTTCTTTTC 60.055 47.826 0.00 0.00 43.09 2.29
4071 5789 1.497161 CAGAGGACGGGGTTATCCTT 58.503 55.000 0.00 0.00 45.74 3.36
4080 5798 2.202797 CGTGATGCAGAGGACGGG 60.203 66.667 0.00 0.00 0.00 5.28
4083 5801 0.176680 ATGGTCGTGATGCAGAGGAC 59.823 55.000 11.19 11.19 0.00 3.85
4084 5802 0.176449 CATGGTCGTGATGCAGAGGA 59.824 55.000 0.00 0.00 0.00 3.71
4090 5809 1.298863 GCATGCATGGTCGTGATGC 60.299 57.895 27.34 8.13 45.45 3.91
4096 5815 0.936600 TATCGTTGCATGCATGGTCG 59.063 50.000 27.34 21.61 0.00 4.79
4124 5843 2.097954 CGGCTGCTAGATTTTGCATTCA 59.902 45.455 0.00 0.00 38.59 2.57
4137 5856 2.227865 GGTTGATGTTTTTCGGCTGCTA 59.772 45.455 0.00 0.00 0.00 3.49
4138 5857 1.000274 GGTTGATGTTTTTCGGCTGCT 60.000 47.619 0.00 0.00 0.00 4.24
4155 5874 4.081322 TCTTTTCGCTTTACTCTGGGTT 57.919 40.909 0.00 0.00 0.00 4.11
4160 5879 5.699458 TCGGATTTTCTTTTCGCTTTACTCT 59.301 36.000 0.00 0.00 0.00 3.24
4170 5890 2.447443 AGGGCCTCGGATTTTCTTTTC 58.553 47.619 0.00 0.00 0.00 2.29
4189 5909 3.725305 CGAGTTACTATCGCGAGGCATAG 60.725 52.174 16.66 13.82 32.81 2.23
4190 5910 2.159037 CGAGTTACTATCGCGAGGCATA 59.841 50.000 16.66 0.19 32.81 3.14
4208 5928 4.828829 AGGTTAGTGGTTATTTGGTCGAG 58.171 43.478 0.00 0.00 0.00 4.04
4211 5931 7.933215 ACATAAGGTTAGTGGTTATTTGGTC 57.067 36.000 0.00 0.00 0.00 4.02
4216 5936 9.796180 TGTTGTAACATAAGGTTAGTGGTTATT 57.204 29.630 0.00 0.00 42.44 1.40
4221 5941 5.927689 TCGTGTTGTAACATAAGGTTAGTGG 59.072 40.000 0.26 0.00 42.44 4.00
4230 5950 7.275999 TCGCTTTGATATCGTGTTGTAACATAA 59.724 33.333 0.26 0.00 41.59 1.90
4241 5961 6.958752 TGTGTATTTTTCGCTTTGATATCGTG 59.041 34.615 0.00 0.00 0.00 4.35
4243 5963 7.692291 AGTTGTGTATTTTTCGCTTTGATATCG 59.308 33.333 0.00 0.00 0.00 2.92
4246 5966 7.174253 AGGAGTTGTGTATTTTTCGCTTTGATA 59.826 33.333 0.00 0.00 0.00 2.15
4248 5968 5.298276 AGGAGTTGTGTATTTTTCGCTTTGA 59.702 36.000 0.00 0.00 0.00 2.69
4249 5969 5.519722 AGGAGTTGTGTATTTTTCGCTTTG 58.480 37.500 0.00 0.00 0.00 2.77
4253 5973 5.638234 AGTCTAGGAGTTGTGTATTTTTCGC 59.362 40.000 0.00 0.00 0.00 4.70
4269 7733 2.950309 GTTGACTCGCCATAGTCTAGGA 59.050 50.000 9.24 0.00 45.12 2.94
4282 7746 5.479716 AAGTTAAACCTTGTGTTGACTCG 57.520 39.130 0.00 0.00 37.23 4.18
4299 7764 3.380393 TGGGGATGAGAATCCGAAGTTA 58.620 45.455 0.00 0.00 41.63 2.24
4304 7769 2.196595 ACTTTGGGGATGAGAATCCGA 58.803 47.619 0.00 0.00 41.63 4.55
4311 7776 4.335416 TGAAGCTTAACTTTGGGGATGAG 58.665 43.478 0.00 0.00 39.29 2.90
4319 7784 5.803967 GCTGATGGATTGAAGCTTAACTTTG 59.196 40.000 0.00 0.00 39.29 2.77
4342 7808 1.509923 GCCATGTCCTTGCTGAAGC 59.490 57.895 0.00 0.00 42.50 3.86
4374 7840 5.221601 ACGAGATCTATGATCAAGCCATGTT 60.222 40.000 0.00 0.00 0.00 2.71
4379 7845 4.250116 ACACGAGATCTATGATCAAGCC 57.750 45.455 12.35 0.00 0.00 4.35
4382 7848 6.535150 GGTGAAAACACGAGATCTATGATCAA 59.465 38.462 12.35 0.00 0.00 2.57
4384 7850 5.174035 CGGTGAAAACACGAGATCTATGATC 59.826 44.000 12.35 8.32 0.00 2.92
4423 7893 2.582052 TGCCTTTTCCACGACTTCAAT 58.418 42.857 0.00 0.00 0.00 2.57
4499 7973 4.318021 CCACTGTGCTGCACGTGC 62.318 66.667 32.44 33.11 37.46 5.34
4507 7981 4.694233 CGCCAGAGCCACTGTGCT 62.694 66.667 1.29 3.33 46.37 4.40
4510 7984 3.699894 CTCCGCCAGAGCCACTGT 61.700 66.667 7.55 0.00 44.40 3.55
4517 7991 1.326213 ACATGAGACCTCCGCCAGAG 61.326 60.000 0.00 0.00 42.83 3.35
4523 7997 0.671251 GGCTAGACATGAGACCTCCG 59.329 60.000 0.00 0.00 0.00 4.63
4524 7998 2.080654 AGGCTAGACATGAGACCTCC 57.919 55.000 0.00 0.00 0.00 4.30
4528 8002 3.363341 GCAGTAGGCTAGACATGAGAC 57.637 52.381 0.00 0.00 40.25 3.36
4542 8016 4.320861 CCATCTTCGATCCAGTAGCAGTAG 60.321 50.000 0.00 0.00 0.00 2.57
4544 8018 2.363680 CCATCTTCGATCCAGTAGCAGT 59.636 50.000 0.00 0.00 0.00 4.40
4545 8019 2.363680 ACCATCTTCGATCCAGTAGCAG 59.636 50.000 0.00 0.00 0.00 4.24
4562 8036 1.531365 CCCACCACTGTTGCACCAT 60.531 57.895 0.00 0.00 0.00 3.55
4569 8043 1.075482 CATGCCTCCCACCACTGTT 59.925 57.895 0.00 0.00 0.00 3.16
4577 8051 4.545678 AGTATATTTTTGCATGCCTCCCA 58.454 39.130 16.68 0.00 0.00 4.37
4609 8397 8.326529 CCAACCTTTCTCCCTCTAATTAGTTTA 58.673 37.037 12.19 0.00 0.00 2.01
4654 8442 2.988684 AAAAAGGCGCGCCCATGA 60.989 55.556 44.47 0.00 36.58 3.07
4670 8458 2.297701 GCGCCCATGAGGATCTAAAAA 58.702 47.619 0.00 0.00 38.24 1.94
4671 8459 1.810031 CGCGCCCATGAGGATCTAAAA 60.810 52.381 0.00 0.00 38.24 1.52
4672 8460 0.249868 CGCGCCCATGAGGATCTAAA 60.250 55.000 0.00 0.00 38.24 1.85
4673 8461 1.367471 CGCGCCCATGAGGATCTAA 59.633 57.895 0.00 0.00 38.24 2.10
4674 8462 3.051210 CGCGCCCATGAGGATCTA 58.949 61.111 0.00 0.00 38.24 1.98
4675 8463 4.615815 GCGCGCCCATGAGGATCT 62.616 66.667 23.24 0.00 38.24 2.75
4679 8467 4.320456 ATAGGCGCGCCCATGAGG 62.320 66.667 44.47 0.00 36.58 3.86
4680 8468 3.046087 CATAGGCGCGCCCATGAG 61.046 66.667 43.23 27.24 36.58 2.90
4682 8470 3.349006 GACATAGGCGCGCCCATG 61.349 66.667 43.37 43.37 36.58 3.66
4683 8471 3.550431 AGACATAGGCGCGCCCAT 61.550 61.111 44.47 35.54 36.58 4.00
4684 8472 4.529219 CAGACATAGGCGCGCCCA 62.529 66.667 44.47 34.90 36.58 5.36
4701 8489 1.739562 CTGCGTCTCCTGTCAAGCC 60.740 63.158 0.00 0.00 0.00 4.35
4709 8497 3.386237 GGCTGTCCTGCGTCTCCT 61.386 66.667 0.00 0.00 0.00 3.69
4710 8498 3.363844 GAGGCTGTCCTGCGTCTCC 62.364 68.421 0.00 0.00 44.46 3.71
4717 8505 3.978723 CTCACGCGAGGCTGTCCTG 62.979 68.421 15.93 0.00 44.46 3.86
4731 8519 4.500116 GGTCTCGCGCTCCCTCAC 62.500 72.222 5.56 0.00 0.00 3.51
4772 8560 7.670364 AGAAAAGGAATTAAATGAGGTTGTGG 58.330 34.615 0.00 0.00 0.00 4.17
4834 8622 9.558396 TTTTCCAAATGCTTGATTAACATTCTT 57.442 25.926 0.00 0.00 33.01 2.52
4835 8623 9.558396 TTTTTCCAAATGCTTGATTAACATTCT 57.442 25.926 0.00 0.00 33.01 2.40
4933 8721 9.601971 GCGTTTATGTTCAACTTTCTTATTACA 57.398 29.630 0.00 0.00 0.00 2.41
4934 8722 9.601971 TGCGTTTATGTTCAACTTTCTTATTAC 57.398 29.630 0.00 0.00 0.00 1.89
4937 8725 9.769093 GTATGCGTTTATGTTCAACTTTCTTAT 57.231 29.630 0.00 0.00 0.00 1.73
4938 8726 8.775527 TGTATGCGTTTATGTTCAACTTTCTTA 58.224 29.630 0.00 0.00 0.00 2.10
4939 8727 7.644490 TGTATGCGTTTATGTTCAACTTTCTT 58.356 30.769 0.00 0.00 0.00 2.52
4940 8728 7.197071 TGTATGCGTTTATGTTCAACTTTCT 57.803 32.000 0.00 0.00 0.00 2.52
4941 8729 8.447787 AATGTATGCGTTTATGTTCAACTTTC 57.552 30.769 0.00 0.00 0.00 2.62
4942 8730 8.810652 AAATGTATGCGTTTATGTTCAACTTT 57.189 26.923 0.00 0.00 32.52 2.66
4943 8731 8.698854 CAAAATGTATGCGTTTATGTTCAACTT 58.301 29.630 1.14 0.00 33.79 2.66
4944 8732 8.079203 TCAAAATGTATGCGTTTATGTTCAACT 58.921 29.630 1.14 0.00 33.79 3.16
4945 8733 8.221801 TCAAAATGTATGCGTTTATGTTCAAC 57.778 30.769 1.14 0.00 33.79 3.18
4946 8734 8.803201 TTCAAAATGTATGCGTTTATGTTCAA 57.197 26.923 1.14 0.00 33.79 2.69
4947 8735 8.978564 ATTCAAAATGTATGCGTTTATGTTCA 57.021 26.923 1.14 0.00 33.79 3.18
4950 8738 9.502145 CACTATTCAAAATGTATGCGTTTATGT 57.498 29.630 1.14 0.00 33.79 2.29
4951 8739 9.715123 TCACTATTCAAAATGTATGCGTTTATG 57.285 29.630 1.14 3.61 33.79 1.90
4953 8741 9.715123 CATCACTATTCAAAATGTATGCGTTTA 57.285 29.630 1.14 0.00 33.79 2.01
4954 8742 8.243426 ACATCACTATTCAAAATGTATGCGTTT 58.757 29.630 0.00 0.00 35.51 3.60
4955 8743 7.761409 ACATCACTATTCAAAATGTATGCGTT 58.239 30.769 0.00 0.00 0.00 4.84
4956 8744 7.320443 ACATCACTATTCAAAATGTATGCGT 57.680 32.000 0.00 0.00 0.00 5.24
4957 8745 8.619146 AAACATCACTATTCAAAATGTATGCG 57.381 30.769 0.00 0.00 30.71 4.73
4962 8750 8.796475 AGCAGTAAACATCACTATTCAAAATGT 58.204 29.630 0.00 0.00 32.15 2.71
4963 8751 9.282247 GAGCAGTAAACATCACTATTCAAAATG 57.718 33.333 0.00 0.00 0.00 2.32
4964 8752 8.177663 CGAGCAGTAAACATCACTATTCAAAAT 58.822 33.333 0.00 0.00 0.00 1.82
4965 8753 7.386573 TCGAGCAGTAAACATCACTATTCAAAA 59.613 33.333 0.00 0.00 0.00 2.44
4966 8754 6.871492 TCGAGCAGTAAACATCACTATTCAAA 59.129 34.615 0.00 0.00 0.00 2.69
4967 8755 6.310467 GTCGAGCAGTAAACATCACTATTCAA 59.690 38.462 0.00 0.00 0.00 2.69
4968 8756 5.805486 GTCGAGCAGTAAACATCACTATTCA 59.195 40.000 0.00 0.00 0.00 2.57
4969 8757 5.805486 TGTCGAGCAGTAAACATCACTATTC 59.195 40.000 0.00 0.00 0.00 1.75
4970 8758 5.577164 GTGTCGAGCAGTAAACATCACTATT 59.423 40.000 0.00 0.00 0.00 1.73
4971 8759 5.103000 GTGTCGAGCAGTAAACATCACTAT 58.897 41.667 0.00 0.00 0.00 2.12
4972 8760 4.482386 GTGTCGAGCAGTAAACATCACTA 58.518 43.478 0.00 0.00 0.00 2.74
4973 8761 3.318017 GTGTCGAGCAGTAAACATCACT 58.682 45.455 0.00 0.00 0.00 3.41
4974 8762 2.090658 CGTGTCGAGCAGTAAACATCAC 59.909 50.000 0.00 0.00 0.00 3.06
4975 8763 2.030628 TCGTGTCGAGCAGTAAACATCA 60.031 45.455 0.00 0.00 0.00 3.07
4976 8764 2.592194 TCGTGTCGAGCAGTAAACATC 58.408 47.619 0.00 0.00 0.00 3.06
4977 8765 2.717580 TCGTGTCGAGCAGTAAACAT 57.282 45.000 0.00 0.00 0.00 2.71
4978 8766 2.717580 ATCGTGTCGAGCAGTAAACA 57.282 45.000 0.00 0.00 39.91 2.83
4979 8767 2.984471 TGAATCGTGTCGAGCAGTAAAC 59.016 45.455 0.00 0.00 39.91 2.01
4980 8768 3.291809 TGAATCGTGTCGAGCAGTAAA 57.708 42.857 0.00 0.00 39.91 2.01
4981 8769 3.291809 TTGAATCGTGTCGAGCAGTAA 57.708 42.857 0.00 0.00 39.91 2.24
4982 8770 3.119637 TCATTGAATCGTGTCGAGCAGTA 60.120 43.478 0.00 0.00 39.91 2.74
4983 8771 1.995484 CATTGAATCGTGTCGAGCAGT 59.005 47.619 0.00 0.00 39.91 4.40
4984 8772 2.262211 TCATTGAATCGTGTCGAGCAG 58.738 47.619 0.00 0.00 39.91 4.24
4985 8773 2.362169 TCATTGAATCGTGTCGAGCA 57.638 45.000 0.00 0.00 39.91 4.26
4986 8774 2.860136 TCATCATTGAATCGTGTCGAGC 59.140 45.455 0.00 0.00 39.91 5.03


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

AutoCloner maintained by Alex Coulton.