Multiple sequence alignment - TraesCS1A01G321400

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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 TraesCS1A01G321400 chr1A 100.000 3081 0 0 1 3081 511637236 511634156 0.000000e+00 5690.0
1 TraesCS1A01G321400 chr1A 87.791 1548 85 38 864 2363 512040399 512038908 0.000000e+00 1716.0
2 TraesCS1A01G321400 chr1A 91.098 865 69 5 1 865 512041304 512040448 0.000000e+00 1164.0
3 TraesCS1A01G321400 chr1A 90.603 862 79 2 4 865 512019497 512018638 0.000000e+00 1142.0
4 TraesCS1A01G321400 chr1A 89.177 887 72 14 1 865 511791647 511790763 0.000000e+00 1085.0
5 TraesCS1A01G321400 chr1A 84.917 663 59 28 1516 2174 512461280 512460655 1.560000e-177 632.0
6 TraesCS1A01G321400 chr1A 85.041 488 37 5 1152 1606 512018426 512017942 6.020000e-127 464.0
7 TraesCS1A01G321400 chr1A 90.055 362 12 7 859 1219 511790719 511790381 6.060000e-122 448.0
8 TraesCS1A01G321400 chr1A 90.311 289 18 8 2049 2332 511784853 511784570 1.350000e-98 370.0
9 TraesCS1A01G321400 chr1A 85.926 270 13 6 1082 1335 512462033 512461773 6.550000e-67 265.0
10 TraesCS1A01G321400 chr1A 93.636 110 7 0 1330 1439 512461850 512461741 6.830000e-37 165.0
11 TraesCS1A01G321400 chr1A 92.793 111 5 1 1430 1540 511789786 511789679 1.140000e-34 158.0
12 TraesCS1A01G321400 chr1A 91.743 109 8 1 1009 1116 512018530 512018422 1.910000e-32 150.0
13 TraesCS1A01G321400 chr1D 89.455 2532 169 50 1 2449 415054925 415052409 0.000000e+00 3107.0
14 TraesCS1A01G321400 chr1D 91.040 1663 74 38 859 2460 414942003 414940355 0.000000e+00 2176.0
15 TraesCS1A01G321400 chr1D 86.963 721 80 8 1 720 415039979 415039272 0.000000e+00 798.0
16 TraesCS1A01G321400 chr1D 86.078 668 53 16 1511 2174 415145634 415145003 0.000000e+00 682.0
17 TraesCS1A01G321400 chr1D 83.288 730 89 19 42 766 414942988 414942287 2.590000e-180 641.0
18 TraesCS1A01G321400 chr1D 85.350 628 56 14 855 1468 415059116 415058511 4.360000e-173 617.0
19 TraesCS1A01G321400 chr1D 84.954 545 47 14 1605 2149 416986038 416986547 1.270000e-143 520.0
20 TraesCS1A01G321400 chr1D 92.742 248 9 4 1088 1335 415146343 415146105 1.760000e-92 350.0
21 TraesCS1A01G321400 chr1D 87.500 232 25 2 635 862 416931092 416931323 6.550000e-67 265.0
22 TraesCS1A01G321400 chr1D 92.727 110 8 0 1330 1439 415146182 415146073 3.180000e-35 159.0
23 TraesCS1A01G321400 chr1D 74.083 436 66 23 257 688 415158459 415158067 5.360000e-28 135.0
24 TraesCS1A01G321400 chr1B 91.067 1500 92 20 859 2339 560789409 560787933 0.000000e+00 1989.0
25 TraesCS1A01G321400 chr1B 86.203 848 109 6 23 865 560790297 560789453 0.000000e+00 911.0
26 TraesCS1A01G321400 chr1B 83.165 790 69 29 1511 2282 561157088 561156345 0.000000e+00 664.0
27 TraesCS1A01G321400 chr1B 84.771 545 55 14 1605 2149 563847816 563848332 3.520000e-144 521.0
28 TraesCS1A01G321400 chr1B 80.079 763 77 37 1516 2268 561256458 561255761 5.930000e-137 497.0
29 TraesCS1A01G321400 chr1B 88.987 227 24 1 2712 2937 560786591 560786365 2.340000e-71 279.0
30 TraesCS1A01G321400 chr1B 79.684 443 44 15 1015 1425 563847319 563847747 8.410000e-71 278.0
31 TraesCS1A01G321400 chr1B 85.211 284 13 4 1072 1335 561257224 561256950 6.550000e-67 265.0
32 TraesCS1A01G321400 chr1B 84.588 279 21 7 1079 1335 561157849 561157571 1.100000e-64 257.0
33 TraesCS1A01G321400 chr1B 84.082 245 28 7 2719 2954 47204933 47204691 3.090000e-55 226.0
34 TraesCS1A01G321400 chr1B 94.615 130 1 3 2343 2470 560787711 560787586 2.420000e-46 196.0
35 TraesCS1A01G321400 chr1B 91.367 139 5 3 2584 2715 560787531 560787393 1.890000e-42 183.0
36 TraesCS1A01G321400 chr1B 97.059 34 0 1 904 936 563787164 563787197 4.290000e-04 56.5
37 TraesCS1A01G321400 chr1B 97.059 34 0 1 904 936 563847189 563847222 4.290000e-04 56.5
38 TraesCS1A01G321400 chrUn 90.404 198 19 0 634 831 305657929 305658126 8.470000e-66 261.0
39 TraesCS1A01G321400 chrUn 90.404 198 19 0 634 831 394107049 394106852 8.470000e-66 261.0
40 TraesCS1A01G321400 chr3D 85.333 225 31 2 2713 2937 559226479 559226257 6.640000e-57 231.0
41 TraesCS1A01G321400 chr6D 83.843 229 31 6 2715 2937 4238927 4239155 2.410000e-51 213.0
42 TraesCS1A01G321400 chr6D 81.070 243 28 8 2713 2938 467161057 467161298 8.780000e-41 178.0
43 TraesCS1A01G321400 chr6D 85.714 91 10 3 2709 2798 25727458 25727370 3.270000e-15 93.5
44 TraesCS1A01G321400 chr7A 82.128 235 30 8 2713 2937 19165412 19165644 1.130000e-44 191.0
45 TraesCS1A01G321400 chr7A 90.541 74 5 2 2508 2581 722599694 722599623 2.530000e-16 97.1
46 TraesCS1A01G321400 chr7A 90.411 73 3 3 2510 2581 106813350 106813281 3.270000e-15 93.5
47 TraesCS1A01G321400 chr5D 80.827 266 24 12 2713 2953 548292498 548292761 1.890000e-42 183.0
48 TraesCS1A01G321400 chr5D 91.071 56 5 0 2768 2823 66298719 66298664 3.290000e-10 76.8
49 TraesCS1A01G321400 chr5D 93.478 46 2 1 2885 2929 481641618 481641663 1.980000e-07 67.6
50 TraesCS1A01G321400 chr5D 91.304 46 4 0 2885 2930 498184903 498184858 2.560000e-06 63.9
51 TraesCS1A01G321400 chr2B 79.848 263 25 15 2714 2952 109211256 109210998 1.900000e-37 167.0
52 TraesCS1A01G321400 chr2B 90.667 75 5 2 2507 2581 376149172 376149244 7.030000e-17 99.0
53 TraesCS1A01G321400 chr3A 78.017 232 31 11 2713 2926 94185951 94185722 8.970000e-26 128.0
54 TraesCS1A01G321400 chr3A 91.781 73 5 1 2510 2581 141041325 141041253 1.950000e-17 100.0
55 TraesCS1A01G321400 chr2A 92.000 75 4 2 2508 2581 89486322 89486249 1.510000e-18 104.0
56 TraesCS1A01G321400 chr6A 88.372 86 8 2 2713 2798 23849249 23849166 5.440000e-18 102.0
57 TraesCS1A01G321400 chr7B 91.667 72 4 2 2510 2581 589938038 589938107 7.030000e-17 99.0
58 TraesCS1A01G321400 chr6B 91.549 71 4 2 2511 2581 22733668 22733736 2.530000e-16 97.1
59 TraesCS1A01G321400 chr5A 91.549 71 5 1 2512 2581 532036113 532036043 2.530000e-16 97.1
60 TraesCS1A01G321400 chr2D 89.333 75 6 2 2507 2581 199881331 199881403 3.270000e-15 93.5
61 TraesCS1A01G321400 chr7D 93.333 45 3 0 2885 2929 12386923 12386967 1.980000e-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 TraesCS1A01G321400 chr1A 511634156 511637236 3080 True 5690.000000 5690 100.000000 1 3081 1 chr1A.!!$R1 3080
1 TraesCS1A01G321400 chr1A 512038908 512041304 2396 True 1440.000000 1716 89.444500 1 2363 2 chr1A.!!$R5 2362
2 TraesCS1A01G321400 chr1A 512017942 512019497 1555 True 585.333333 1142 89.129000 4 1606 3 chr1A.!!$R4 1602
3 TraesCS1A01G321400 chr1A 511789679 511791647 1968 True 563.666667 1085 90.675000 1 1540 3 chr1A.!!$R3 1539
4 TraesCS1A01G321400 chr1A 512460655 512462033 1378 True 354.000000 632 88.159667 1082 2174 3 chr1A.!!$R6 1092
5 TraesCS1A01G321400 chr1D 415052409 415059116 6707 True 1862.000000 3107 87.402500 1 2449 2 chr1D.!!$R4 2448
6 TraesCS1A01G321400 chr1D 414940355 414942988 2633 True 1408.500000 2176 87.164000 42 2460 2 chr1D.!!$R3 2418
7 TraesCS1A01G321400 chr1D 415039272 415039979 707 True 798.000000 798 86.963000 1 720 1 chr1D.!!$R1 719
8 TraesCS1A01G321400 chr1D 416986038 416986547 509 False 520.000000 520 84.954000 1605 2149 1 chr1D.!!$F2 544
9 TraesCS1A01G321400 chr1D 415145003 415146343 1340 True 397.000000 682 90.515667 1088 2174 3 chr1D.!!$R5 1086
10 TraesCS1A01G321400 chr1B 560786365 560790297 3932 True 711.600000 1989 90.447800 23 2937 5 chr1B.!!$R2 2914
11 TraesCS1A01G321400 chr1B 561156345 561157849 1504 True 460.500000 664 83.876500 1079 2282 2 chr1B.!!$R3 1203
12 TraesCS1A01G321400 chr1B 561255761 561257224 1463 True 381.000000 497 82.645000 1072 2268 2 chr1B.!!$R4 1196
13 TraesCS1A01G321400 chr1B 563847189 563848332 1143 False 285.166667 521 87.171333 904 2149 3 chr1B.!!$F2 1245

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
471 4669 0.038251 TCTCTTCTGATGCGCAACGT 60.038 50.0 17.11 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 8043 0.031585 CCGGATCGACGAGGCAATTA 59.968 55.0 3.01 0.0 35.47 1.4 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
19 4211 0.990374 AATGAGAAGCCAGCCTCACT 59.010 50.000 0.00 0.00 41.59 3.41
20 4212 0.990374 ATGAGAAGCCAGCCTCACTT 59.010 50.000 0.00 0.00 41.59 3.16
36 4228 3.276857 TCACTTTCGCGTCTACTAGGAT 58.723 45.455 5.77 0.00 0.00 3.24
64 4256 3.636231 CCCCACGCCTGGTCAAGA 61.636 66.667 0.86 0.00 35.46 3.02
80 4272 1.939934 CAAGAAGGAGTCGTTGCACAA 59.060 47.619 2.13 0.00 0.00 3.33
186 4381 1.379044 GGCCAGGTCACCATGAAGG 60.379 63.158 0.00 0.00 45.67 3.46
268 4466 4.111016 CACGCGTCGCCAGGACTA 62.111 66.667 9.86 0.00 43.79 2.59
334 4532 1.215382 CCGTGAAGATGTCCGAGCA 59.785 57.895 0.00 0.00 0.00 4.26
340 4538 2.125912 GATGTCCGAGCAGCACGT 60.126 61.111 11.46 0.00 0.00 4.49
411 4609 5.977129 AGTACACAATTGTTTTTGCAGCTAC 59.023 36.000 8.77 0.00 37.15 3.58
471 4669 0.038251 TCTCTTCTGATGCGCAACGT 60.038 50.000 17.11 0.00 0.00 3.99
473 4671 1.510623 CTTCTGATGCGCAACGTGC 60.511 57.895 17.11 2.09 40.69 5.34
591 4810 2.050714 GCGAAGACGTCCGTCACA 60.051 61.111 20.57 0.00 46.76 3.58
632 4851 1.926561 CTCACAAAGATCGGCGATGA 58.073 50.000 29.20 17.36 0.00 2.92
674 4895 3.503363 CCACAGTTGATTTTGCAGCTAGA 59.497 43.478 0.00 0.00 0.00 2.43
711 4932 3.508012 ACACGGGCATTTATTTACAGCAA 59.492 39.130 0.00 0.00 0.00 3.91
812 5176 7.676004 TGCCTAAATATCATATCGAGGTGAAA 58.324 34.615 6.61 0.00 0.00 2.69
833 5197 8.689972 GTGAAAATTATGAGAAGATGGAATGGT 58.310 33.333 0.00 0.00 0.00 3.55
903 5317 2.960688 GCCCCACCTGTCTGTCTCC 61.961 68.421 0.00 0.00 0.00 3.71
953 5368 1.523095 GTAAATCAGCATCTCGGCGAC 59.477 52.381 4.99 0.00 39.27 5.19
1041 5488 2.505777 CTCAGCTCTCACCACGCG 60.506 66.667 3.53 3.53 0.00 6.01
1486 6767 2.815647 GTGCAGCAGGTACTCCGC 60.816 66.667 0.00 0.00 34.60 5.54
1487 6768 4.435436 TGCAGCAGGTACTCCGCG 62.435 66.667 0.00 0.00 34.60 6.46
1622 6943 2.355108 GCTTGGCAGATAGAGGAACACA 60.355 50.000 0.00 0.00 0.00 3.72
1630 6951 0.617820 TAGAGGAACACAGGCCCCTC 60.618 60.000 13.94 13.94 44.14 4.30
1762 7095 3.323115 AGCTCGGCATCATTCATCTAGAA 59.677 43.478 0.00 0.00 41.28 2.10
1765 7098 5.871524 GCTCGGCATCATTCATCTAGAATTA 59.128 40.000 0.00 0.00 44.48 1.40
1766 7099 6.369890 GCTCGGCATCATTCATCTAGAATTAA 59.630 38.462 0.00 0.00 44.48 1.40
1767 7100 7.065563 GCTCGGCATCATTCATCTAGAATTAAT 59.934 37.037 0.00 0.00 44.48 1.40
1768 7101 8.484641 TCGGCATCATTCATCTAGAATTAATC 57.515 34.615 0.00 0.00 44.48 1.75
1871 7216 2.690452 CGGAGGGGAGGAAGGAGA 59.310 66.667 0.00 0.00 0.00 3.71
1911 7264 2.780094 CGACGAGGATCAGCAGCCT 61.780 63.158 0.00 0.00 37.18 4.58
1999 7355 1.457643 CGATGGCTCCCTGGACCTA 60.458 63.158 0.00 0.00 0.00 3.08
2298 7687 3.179010 CATGCATGCTACTGTATTCGC 57.821 47.619 20.33 0.00 0.00 4.70
2314 7703 3.768468 TTCGCGTTTCTTTCCTTTTGT 57.232 38.095 5.77 0.00 0.00 2.83
2371 7986 1.227823 CCTCACTCACCCACGCAAA 60.228 57.895 0.00 0.00 0.00 3.68
2413 8028 1.895798 GATGAGGAGGAGTGTGTGTGA 59.104 52.381 0.00 0.00 0.00 3.58
2414 8029 1.788229 TGAGGAGGAGTGTGTGTGAA 58.212 50.000 0.00 0.00 0.00 3.18
2415 8030 2.329267 TGAGGAGGAGTGTGTGTGAAT 58.671 47.619 0.00 0.00 0.00 2.57
2416 8031 2.705658 TGAGGAGGAGTGTGTGTGAATT 59.294 45.455 0.00 0.00 0.00 2.17
2418 8033 4.346709 TGAGGAGGAGTGTGTGTGAATTTA 59.653 41.667 0.00 0.00 0.00 1.40
2419 8034 4.642429 AGGAGGAGTGTGTGTGAATTTAC 58.358 43.478 0.00 0.00 0.00 2.01
2421 8036 4.452455 GGAGGAGTGTGTGTGAATTTACAG 59.548 45.833 2.84 0.00 0.00 2.74
2424 8039 3.462982 AGTGTGTGTGAATTTACAGCGA 58.537 40.909 2.84 0.00 0.00 4.93
2427 8042 4.152402 GTGTGTGTGAATTTACAGCGAGAT 59.848 41.667 2.84 0.00 0.00 2.75
2428 8043 4.754618 TGTGTGTGAATTTACAGCGAGATT 59.245 37.500 2.84 0.00 0.00 2.40
2470 8087 3.909430 ACAGCAGCATCATTTTTGTCAG 58.091 40.909 0.00 0.00 0.00 3.51
2471 8088 2.666508 CAGCAGCATCATTTTTGTCAGC 59.333 45.455 0.00 0.00 0.00 4.26
2472 8089 2.297880 AGCAGCATCATTTTTGTCAGCA 59.702 40.909 0.00 0.00 0.00 4.41
2473 8090 3.056107 AGCAGCATCATTTTTGTCAGCAT 60.056 39.130 0.00 0.00 0.00 3.79
2474 8091 4.158949 AGCAGCATCATTTTTGTCAGCATA 59.841 37.500 0.00 0.00 0.00 3.14
2475 8092 4.266976 GCAGCATCATTTTTGTCAGCATAC 59.733 41.667 0.00 0.00 0.00 2.39
2478 8095 5.865552 AGCATCATTTTTGTCAGCATACAAC 59.134 36.000 3.61 0.00 39.02 3.32
2480 8097 6.183360 GCATCATTTTTGTCAGCATACAACTG 60.183 38.462 3.61 3.40 39.02 3.16
2481 8098 6.389830 TCATTTTTGTCAGCATACAACTGT 57.610 33.333 3.61 0.00 39.02 3.55
2482 8099 6.437928 TCATTTTTGTCAGCATACAACTGTC 58.562 36.000 3.61 0.00 39.02 3.51
2483 8100 4.829064 TTTTGTCAGCATACAACTGTCC 57.171 40.909 3.61 0.00 39.02 4.02
2484 8101 3.483808 TTGTCAGCATACAACTGTCCA 57.516 42.857 0.17 0.00 34.50 4.02
2485 8102 2.766313 TGTCAGCATACAACTGTCCAC 58.234 47.619 0.00 0.00 36.50 4.02
2506 8138 5.107530 CCACTGCAATGTTTAAAACGATTGG 60.108 40.000 13.62 5.18 33.97 3.16
2513 8145 8.318167 GCAATGTTTAAAACGATTGGCTAATAC 58.682 33.333 13.62 0.00 33.97 1.89
2514 8146 9.567848 CAATGTTTAAAACGATTGGCTAATACT 57.432 29.630 0.00 0.00 31.87 2.12
2515 8147 9.783256 AATGTTTAAAACGATTGGCTAATACTC 57.217 29.630 0.00 0.00 0.00 2.59
2516 8148 7.754625 TGTTTAAAACGATTGGCTAATACTCC 58.245 34.615 0.00 0.00 0.00 3.85
2517 8149 6.930667 TTAAAACGATTGGCTAATACTCCC 57.069 37.500 0.00 0.00 0.00 4.30
2518 8150 4.772886 AAACGATTGGCTAATACTCCCT 57.227 40.909 0.00 0.00 0.00 4.20
2519 8151 4.338379 AACGATTGGCTAATACTCCCTC 57.662 45.455 0.00 0.00 0.00 4.30
2520 8152 3.577919 ACGATTGGCTAATACTCCCTCT 58.422 45.455 0.00 0.00 0.00 3.69
2521 8153 3.322254 ACGATTGGCTAATACTCCCTCTG 59.678 47.826 0.00 0.00 0.00 3.35
2522 8154 3.322254 CGATTGGCTAATACTCCCTCTGT 59.678 47.826 0.00 0.00 0.00 3.41
2523 8155 4.202264 CGATTGGCTAATACTCCCTCTGTT 60.202 45.833 0.00 0.00 0.00 3.16
2524 8156 5.685075 CGATTGGCTAATACTCCCTCTGTTT 60.685 44.000 0.00 0.00 0.00 2.83
2525 8157 4.755266 TGGCTAATACTCCCTCTGTTTC 57.245 45.455 0.00 0.00 0.00 2.78
2526 8158 4.101114 TGGCTAATACTCCCTCTGTTTCA 58.899 43.478 0.00 0.00 0.00 2.69
2527 8159 4.534500 TGGCTAATACTCCCTCTGTTTCAA 59.466 41.667 0.00 0.00 0.00 2.69
2528 8160 5.013704 TGGCTAATACTCCCTCTGTTTCAAA 59.986 40.000 0.00 0.00 0.00 2.69
2529 8161 5.944007 GGCTAATACTCCCTCTGTTTCAAAA 59.056 40.000 0.00 0.00 0.00 2.44
2530 8162 6.603599 GGCTAATACTCCCTCTGTTTCAAAAT 59.396 38.462 0.00 0.00 0.00 1.82
2531 8163 7.773690 GGCTAATACTCCCTCTGTTTCAAAATA 59.226 37.037 0.00 0.00 0.00 1.40
2532 8164 8.831550 GCTAATACTCCCTCTGTTTCAAAATAG 58.168 37.037 0.00 0.00 0.00 1.73
2535 8167 8.970859 ATACTCCCTCTGTTTCAAAATAGATG 57.029 34.615 2.91 1.27 35.92 2.90
2536 8168 7.020827 ACTCCCTCTGTTTCAAAATAGATGA 57.979 36.000 2.91 3.20 35.92 2.92
2537 8169 6.881602 ACTCCCTCTGTTTCAAAATAGATGAC 59.118 38.462 2.91 0.00 35.92 3.06
2538 8170 6.180472 TCCCTCTGTTTCAAAATAGATGACC 58.820 40.000 2.91 0.00 35.92 4.02
2539 8171 5.358160 CCCTCTGTTTCAAAATAGATGACCC 59.642 44.000 2.91 0.00 35.92 4.46
2540 8172 6.183347 CCTCTGTTTCAAAATAGATGACCCT 58.817 40.000 2.91 0.00 35.92 4.34
2541 8173 7.338710 CCTCTGTTTCAAAATAGATGACCCTA 58.661 38.462 2.91 0.00 35.92 3.53
2542 8174 7.995488 CCTCTGTTTCAAAATAGATGACCCTAT 59.005 37.037 2.91 0.00 35.92 2.57
2545 8177 9.838339 CTGTTTCAAAATAGATGACCCTATAGT 57.162 33.333 0.00 0.00 29.67 2.12
2557 8189 9.490083 AGATGACCCTATAGTTAGTACAAAGTT 57.510 33.333 0.00 0.00 0.00 2.66
2558 8190 9.530633 GATGACCCTATAGTTAGTACAAAGTTG 57.469 37.037 0.00 0.00 0.00 3.16
2559 8191 8.654485 TGACCCTATAGTTAGTACAAAGTTGA 57.346 34.615 0.00 0.00 0.00 3.18
2560 8192 8.746530 TGACCCTATAGTTAGTACAAAGTTGAG 58.253 37.037 0.00 0.00 0.00 3.02
2561 8193 8.661752 ACCCTATAGTTAGTACAAAGTTGAGT 57.338 34.615 0.00 0.00 0.00 3.41
2562 8194 8.747471 ACCCTATAGTTAGTACAAAGTTGAGTC 58.253 37.037 0.00 0.00 0.00 3.36
2563 8195 8.746530 CCCTATAGTTAGTACAAAGTTGAGTCA 58.253 37.037 0.00 0.00 0.00 3.41
2573 8205 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2574 8206 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2575 8207 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2576 8208 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2577 8209 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2578 8210 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2579 8211 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2580 8212 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2581 8213 5.186992 TGAGTCATCTATTTTGGAACGGAGA 59.813 40.000 0.00 0.00 0.00 3.71
2582 8214 6.049955 AGTCATCTATTTTGGAACGGAGAA 57.950 37.500 0.00 0.00 0.00 2.87
2583 8215 6.472887 AGTCATCTATTTTGGAACGGAGAAA 58.527 36.000 0.00 0.00 0.00 2.52
2584 8216 6.940298 AGTCATCTATTTTGGAACGGAGAAAA 59.060 34.615 0.00 0.00 0.00 2.29
2585 8217 7.611855 AGTCATCTATTTTGGAACGGAGAAAAT 59.388 33.333 0.00 0.00 34.49 1.82
2586 8218 8.889717 GTCATCTATTTTGGAACGGAGAAAATA 58.110 33.333 0.00 0.00 32.78 1.40
2587 8219 9.456147 TCATCTATTTTGGAACGGAGAAAATAA 57.544 29.630 0.00 0.00 33.37 1.40
2588 8220 9.722056 CATCTATTTTGGAACGGAGAAAATAAG 57.278 33.333 0.00 0.00 33.37 1.73
2677 8309 0.537188 ACAGTGCGGGATAAGTGAGG 59.463 55.000 0.00 0.00 0.00 3.86
2681 8313 0.907704 TGCGGGATAAGTGAGGGTGT 60.908 55.000 0.00 0.00 0.00 4.16
2715 8354 6.871492 TGGACGCATACATACATACAATAAGG 59.129 38.462 0.00 0.00 0.00 2.69
2753 9198 6.090783 GGAACAAAATAATTTCGGACCTCAC 58.909 40.000 0.00 0.00 0.00 3.51
2767 9212 3.938963 GGACCTCACTGAAATATGCGAAA 59.061 43.478 0.00 0.00 0.00 3.46
2865 9310 8.746922 TTATGTTGAAATCAGTTTGAATCTGC 57.253 30.769 0.00 0.00 33.48 4.26
2868 9313 5.633830 TGAAATCAGTTTGAATCTGCCTC 57.366 39.130 0.00 0.00 33.48 4.70
2869 9314 5.319453 TGAAATCAGTTTGAATCTGCCTCT 58.681 37.500 0.00 0.00 33.48 3.69
2874 9319 7.951347 ATCAGTTTGAATCTGCCTCTAAATT 57.049 32.000 0.00 0.00 33.48 1.82
2877 9322 7.448161 TCAGTTTGAATCTGCCTCTAAATTTCA 59.552 33.333 0.00 0.00 33.48 2.69
2883 9328 5.772393 TCTGCCTCTAAATTTCAGGGTTA 57.228 39.130 14.97 2.24 0.00 2.85
2888 9333 8.201242 TGCCTCTAAATTTCAGGGTTAAAAAT 57.799 30.769 14.97 0.00 0.00 1.82
2898 9343 9.647797 ATTTCAGGGTTAAAAATATTTCGAACC 57.352 29.630 23.74 23.74 35.59 3.62
2900 9345 8.411991 TCAGGGTTAAAAATATTTCGAACCTT 57.588 30.769 27.21 22.32 36.14 3.50
2902 9347 9.563898 CAGGGTTAAAAATATTTCGAACCTTAC 57.436 33.333 27.21 18.21 36.14 2.34
2904 9349 9.563898 GGGTTAAAAATATTTCGAACCTTACTG 57.436 33.333 27.21 0.00 36.14 2.74
2913 9358 5.712217 TTCGAACCTTACTGAAATATGCG 57.288 39.130 0.00 0.00 0.00 4.73
2921 9366 8.050778 ACCTTACTGAAATATGCGAAATTTCA 57.949 30.769 17.99 15.75 46.08 2.69
2951 9396 7.758613 TTCACTGAAACGAAATTTTTAACCC 57.241 32.000 0.00 0.00 0.00 4.11
2952 9397 7.102847 TCACTGAAACGAAATTTTTAACCCT 57.897 32.000 0.00 0.00 0.00 4.34
2953 9398 7.548967 TCACTGAAACGAAATTTTTAACCCTT 58.451 30.769 0.00 0.00 0.00 3.95
2954 9399 8.684520 TCACTGAAACGAAATTTTTAACCCTTA 58.315 29.630 0.00 0.00 0.00 2.69
2955 9400 8.748582 CACTGAAACGAAATTTTTAACCCTTAC 58.251 33.333 0.00 0.00 0.00 2.34
2956 9401 8.468399 ACTGAAACGAAATTTTTAACCCTTACA 58.532 29.630 0.00 0.00 0.00 2.41
2957 9402 9.471084 CTGAAACGAAATTTTTAACCCTTACAT 57.529 29.630 0.00 0.00 0.00 2.29
2958 9403 9.819267 TGAAACGAAATTTTTAACCCTTACATT 57.181 25.926 0.00 0.00 0.00 2.71
2960 9405 9.819267 AAACGAAATTTTTAACCCTTACATTCA 57.181 25.926 0.00 0.00 0.00 2.57
2961 9406 9.990360 AACGAAATTTTTAACCCTTACATTCAT 57.010 25.926 0.00 0.00 0.00 2.57
2962 9407 9.990360 ACGAAATTTTTAACCCTTACATTCATT 57.010 25.926 0.00 0.00 0.00 2.57
2967 9412 9.927668 ATTTTTAACCCTTACATTCATTGACAG 57.072 29.630 0.00 0.00 0.00 3.51
2968 9413 6.509418 TTAACCCTTACATTCATTGACAGC 57.491 37.500 0.00 0.00 0.00 4.40
2969 9414 4.032960 ACCCTTACATTCATTGACAGCA 57.967 40.909 0.00 0.00 0.00 4.41
2970 9415 3.758554 ACCCTTACATTCATTGACAGCAC 59.241 43.478 0.00 0.00 0.00 4.40
2971 9416 4.012374 CCCTTACATTCATTGACAGCACT 58.988 43.478 0.00 0.00 0.00 4.40
2972 9417 4.095483 CCCTTACATTCATTGACAGCACTC 59.905 45.833 0.00 0.00 0.00 3.51
2973 9418 4.095483 CCTTACATTCATTGACAGCACTCC 59.905 45.833 0.00 0.00 0.00 3.85
2974 9419 3.144657 ACATTCATTGACAGCACTCCA 57.855 42.857 0.00 0.00 0.00 3.86
2975 9420 3.693807 ACATTCATTGACAGCACTCCAT 58.306 40.909 0.00 0.00 0.00 3.41
2976 9421 3.442625 ACATTCATTGACAGCACTCCATG 59.557 43.478 0.00 0.00 0.00 3.66
2986 9431 1.568025 CACTCCATGCATGCGATCG 59.432 57.895 21.69 11.69 0.00 3.69
2987 9432 0.877213 CACTCCATGCATGCGATCGA 60.877 55.000 21.69 11.40 0.00 3.59
2988 9433 0.034476 ACTCCATGCATGCGATCGAT 59.966 50.000 21.69 0.00 0.00 3.59
2989 9434 0.720027 CTCCATGCATGCGATCGATC 59.280 55.000 21.69 15.68 0.00 3.69
2990 9435 0.033781 TCCATGCATGCGATCGATCA 59.966 50.000 24.40 8.77 0.00 2.92
2991 9436 0.442699 CCATGCATGCGATCGATCAG 59.557 55.000 24.40 17.27 0.00 2.90
2992 9437 0.179222 CATGCATGCGATCGATCAGC 60.179 55.000 24.40 24.91 0.00 4.26
2993 9438 0.320508 ATGCATGCGATCGATCAGCT 60.321 50.000 28.97 18.35 0.00 4.24
2994 9439 1.219522 TGCATGCGATCGATCAGCTG 61.220 55.000 28.97 25.00 0.00 4.24
2995 9440 0.942884 GCATGCGATCGATCAGCTGA 60.943 55.000 28.97 20.79 0.00 4.26
2996 9441 1.711206 CATGCGATCGATCAGCTGAT 58.289 50.000 29.09 29.09 37.51 2.90
2997 9442 1.390463 CATGCGATCGATCAGCTGATG 59.610 52.381 33.33 23.09 34.37 3.07
2998 9443 0.942884 TGCGATCGATCAGCTGATGC 60.943 55.000 33.33 27.10 34.37 3.91
2999 9444 0.942884 GCGATCGATCAGCTGATGCA 60.943 55.000 33.33 19.02 42.74 3.96
3000 9445 1.494824 CGATCGATCAGCTGATGCAA 58.505 50.000 33.33 17.81 42.74 4.08
3001 9446 1.456165 CGATCGATCAGCTGATGCAAG 59.544 52.381 33.33 19.88 42.74 4.01
3002 9447 1.799403 GATCGATCAGCTGATGCAAGG 59.201 52.381 33.33 16.01 42.74 3.61
3003 9448 0.179065 TCGATCAGCTGATGCAAGGG 60.179 55.000 33.33 14.37 42.74 3.95
3004 9449 1.783031 CGATCAGCTGATGCAAGGGC 61.783 60.000 33.33 15.64 42.74 5.19
3014 9459 4.074647 GCAAGGGCACTTACGGTT 57.925 55.556 0.00 0.00 40.72 4.44
3015 9460 1.579429 GCAAGGGCACTTACGGTTG 59.421 57.895 0.00 0.00 40.72 3.77
3016 9461 0.887387 GCAAGGGCACTTACGGTTGA 60.887 55.000 0.00 0.00 40.72 3.18
3017 9462 0.872388 CAAGGGCACTTACGGTTGAC 59.128 55.000 0.00 0.00 34.49 3.18
3018 9463 0.470766 AAGGGCACTTACGGTTGACA 59.529 50.000 0.00 0.00 34.49 3.58
3019 9464 0.470766 AGGGCACTTACGGTTGACAA 59.529 50.000 0.00 0.00 0.00 3.18
3020 9465 1.073284 AGGGCACTTACGGTTGACAAT 59.927 47.619 0.00 0.00 0.00 2.71
3021 9466 1.199097 GGGCACTTACGGTTGACAATG 59.801 52.381 0.00 0.00 0.00 2.82
3022 9467 1.401018 GGCACTTACGGTTGACAATGC 60.401 52.381 0.00 0.00 0.00 3.56
3023 9468 1.535462 GCACTTACGGTTGACAATGCT 59.465 47.619 0.00 0.00 0.00 3.79
3024 9469 2.665519 GCACTTACGGTTGACAATGCTG 60.666 50.000 0.00 0.00 0.00 4.41
3025 9470 2.095768 CACTTACGGTTGACAATGCTGG 60.096 50.000 0.00 0.00 0.00 4.85
3026 9471 2.151202 CTTACGGTTGACAATGCTGGT 58.849 47.619 0.00 0.00 0.00 4.00
3027 9472 1.518325 TACGGTTGACAATGCTGGTG 58.482 50.000 0.00 0.00 0.00 4.17
3028 9473 1.081242 CGGTTGACAATGCTGGTGC 60.081 57.895 0.00 0.00 40.20 5.01
3029 9474 1.518056 CGGTTGACAATGCTGGTGCT 61.518 55.000 0.00 0.00 40.48 4.40
3030 9475 0.242017 GGTTGACAATGCTGGTGCTC 59.758 55.000 0.00 0.00 40.48 4.26
3031 9476 1.242076 GTTGACAATGCTGGTGCTCT 58.758 50.000 0.00 0.00 40.48 4.09
3032 9477 1.198637 GTTGACAATGCTGGTGCTCTC 59.801 52.381 0.00 0.00 40.48 3.20
3033 9478 0.397564 TGACAATGCTGGTGCTCTCA 59.602 50.000 0.00 0.00 40.48 3.27
3034 9479 1.202794 TGACAATGCTGGTGCTCTCAA 60.203 47.619 0.00 0.00 40.48 3.02
3035 9480 2.089980 GACAATGCTGGTGCTCTCAAT 58.910 47.619 0.00 0.00 40.48 2.57
3036 9481 2.089980 ACAATGCTGGTGCTCTCAATC 58.910 47.619 0.00 0.00 40.48 2.67
3037 9482 1.063616 CAATGCTGGTGCTCTCAATCG 59.936 52.381 0.00 0.00 40.48 3.34
3038 9483 0.251354 ATGCTGGTGCTCTCAATCGT 59.749 50.000 0.00 0.00 40.48 3.73
3039 9484 0.390340 TGCTGGTGCTCTCAATCGTC 60.390 55.000 0.00 0.00 40.48 4.20
3040 9485 0.390340 GCTGGTGCTCTCAATCGTCA 60.390 55.000 0.00 0.00 36.03 4.35
3041 9486 1.941209 GCTGGTGCTCTCAATCGTCAA 60.941 52.381 0.00 0.00 36.03 3.18
3042 9487 1.998315 CTGGTGCTCTCAATCGTCAAG 59.002 52.381 0.00 0.00 0.00 3.02
3043 9488 1.344438 TGGTGCTCTCAATCGTCAAGT 59.656 47.619 0.00 0.00 0.00 3.16
3044 9489 2.224281 TGGTGCTCTCAATCGTCAAGTT 60.224 45.455 0.00 0.00 0.00 2.66
3045 9490 2.413453 GGTGCTCTCAATCGTCAAGTTC 59.587 50.000 0.00 0.00 0.00 3.01
3046 9491 3.321497 GTGCTCTCAATCGTCAAGTTCT 58.679 45.455 0.00 0.00 0.00 3.01
3047 9492 3.743396 GTGCTCTCAATCGTCAAGTTCTT 59.257 43.478 0.00 0.00 0.00 2.52
3048 9493 3.990469 TGCTCTCAATCGTCAAGTTCTTC 59.010 43.478 0.00 0.00 0.00 2.87
3049 9494 3.990469 GCTCTCAATCGTCAAGTTCTTCA 59.010 43.478 0.00 0.00 0.00 3.02
3050 9495 4.091220 GCTCTCAATCGTCAAGTTCTTCAG 59.909 45.833 0.00 0.00 0.00 3.02
3051 9496 3.990469 TCTCAATCGTCAAGTTCTTCAGC 59.010 43.478 0.00 0.00 0.00 4.26
3052 9497 3.727726 TCAATCGTCAAGTTCTTCAGCA 58.272 40.909 0.00 0.00 0.00 4.41
3053 9498 3.494626 TCAATCGTCAAGTTCTTCAGCAC 59.505 43.478 0.00 0.00 0.00 4.40
3054 9499 2.890808 TCGTCAAGTTCTTCAGCACT 57.109 45.000 0.00 0.00 0.00 4.40
3055 9500 4.521130 ATCGTCAAGTTCTTCAGCACTA 57.479 40.909 0.00 0.00 0.00 2.74
3056 9501 3.902150 TCGTCAAGTTCTTCAGCACTAG 58.098 45.455 0.00 0.00 0.00 2.57
3057 9502 3.318275 TCGTCAAGTTCTTCAGCACTAGT 59.682 43.478 0.00 0.00 0.00 2.57
3058 9503 4.051922 CGTCAAGTTCTTCAGCACTAGTT 58.948 43.478 0.00 0.00 0.00 2.24
3059 9504 5.009310 TCGTCAAGTTCTTCAGCACTAGTTA 59.991 40.000 0.00 0.00 0.00 2.24
3060 9505 5.117287 CGTCAAGTTCTTCAGCACTAGTTAC 59.883 44.000 0.00 0.00 0.00 2.50
3061 9506 5.983720 GTCAAGTTCTTCAGCACTAGTTACA 59.016 40.000 0.00 0.00 0.00 2.41
3062 9507 6.647067 GTCAAGTTCTTCAGCACTAGTTACAT 59.353 38.462 0.00 0.00 0.00 2.29
3063 9508 6.646653 TCAAGTTCTTCAGCACTAGTTACATG 59.353 38.462 0.00 0.00 0.00 3.21
3064 9509 6.102897 AGTTCTTCAGCACTAGTTACATGT 57.897 37.500 2.69 2.69 0.00 3.21
3065 9510 7.228314 AGTTCTTCAGCACTAGTTACATGTA 57.772 36.000 0.08 0.08 0.00 2.29
3066 9511 7.091443 AGTTCTTCAGCACTAGTTACATGTAC 58.909 38.462 4.68 1.30 0.00 2.90
3067 9512 6.584185 TCTTCAGCACTAGTTACATGTACA 57.416 37.500 4.68 0.00 0.00 2.90
3068 9513 6.621613 TCTTCAGCACTAGTTACATGTACAG 58.378 40.000 4.68 5.97 0.00 2.74
3069 9514 4.744570 TCAGCACTAGTTACATGTACAGC 58.255 43.478 4.68 3.96 0.00 4.40
3070 9515 4.219725 TCAGCACTAGTTACATGTACAGCA 59.780 41.667 4.68 0.00 0.00 4.41
3071 9516 4.929211 CAGCACTAGTTACATGTACAGCAA 59.071 41.667 4.68 0.00 0.00 3.91
3072 9517 5.582269 CAGCACTAGTTACATGTACAGCAAT 59.418 40.000 4.68 0.00 0.00 3.56
3073 9518 5.582269 AGCACTAGTTACATGTACAGCAATG 59.418 40.000 4.68 0.00 0.00 2.82
3074 9519 5.727791 GCACTAGTTACATGTACAGCAATGC 60.728 44.000 4.68 8.06 0.00 3.56
3075 9520 5.351189 CACTAGTTACATGTACAGCAATGCA 59.649 40.000 8.35 0.00 0.00 3.96
3076 9521 6.037500 CACTAGTTACATGTACAGCAATGCAT 59.962 38.462 8.35 0.00 0.00 3.96
3077 9522 5.239359 AGTTACATGTACAGCAATGCATG 57.761 39.130 8.35 14.10 45.22 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 4211 1.952296 GGGATCCTAGTAGACGCGAAA 59.048 52.381 15.93 0.00 0.00 3.46
20 4212 1.602311 GGGATCCTAGTAGACGCGAA 58.398 55.000 15.93 0.00 0.00 4.70
64 4256 2.076863 GCTATTGTGCAACGACTCCTT 58.923 47.619 0.00 0.00 42.39 3.36
80 4272 1.542030 CGATCGAACTAGCCCAGCTAT 59.458 52.381 10.26 0.00 40.54 2.97
106 4300 0.528017 GAGGCGAGATGACAGTGACA 59.472 55.000 0.00 0.00 0.00 3.58
168 4362 1.379044 CCTTCATGGTGACCTGGCC 60.379 63.158 2.11 0.00 0.00 5.36
268 4466 1.658686 CTCTGTTAGCGCGAGGACCT 61.659 60.000 12.10 0.00 0.00 3.85
471 4669 1.002257 AATGCTGGTCGGTGATGCA 60.002 52.632 0.00 0.00 38.05 3.96
473 4671 2.009108 CGAATGCTGGTCGGTGATG 58.991 57.895 0.00 0.00 34.85 3.07
674 4895 4.041075 TGCCCGTGTATATATGTCCAATGT 59.959 41.667 0.00 0.00 0.00 2.71
722 4943 8.122952 CGAAACAAGAGAAAATATATCACCCAC 58.877 37.037 0.00 0.00 0.00 4.61
779 5142 9.554395 TCGATATGATATTTAGGCAAGAAACAA 57.446 29.630 0.00 0.00 0.00 2.83
812 5176 9.125026 GTGTAACCATTCCATCTTCTCATAATT 57.875 33.333 0.00 0.00 0.00 1.40
815 5179 6.097696 TCGTGTAACCATTCCATCTTCTCATA 59.902 38.462 0.00 0.00 0.00 2.15
833 5197 0.885879 ACTCCGCTCATGTCGTGTAA 59.114 50.000 8.72 0.00 0.00 2.41
903 5317 3.052082 CACTCGCCAGCCAACAGG 61.052 66.667 0.00 0.00 0.00 4.00
953 5368 3.848830 CGGGCGTGTGTGCGTATG 61.849 66.667 0.00 0.00 35.06 2.39
1486 6767 2.754658 AGTGGACTAGACGGGCCG 60.755 66.667 27.06 27.06 0.00 6.13
1487 6768 2.893398 CAGTGGACTAGACGGGCC 59.107 66.667 0.00 0.00 0.00 5.80
1488 6769 2.167398 TTGCAGTGGACTAGACGGGC 62.167 60.000 0.00 0.00 0.00 6.13
1489 6770 0.320374 TTTGCAGTGGACTAGACGGG 59.680 55.000 0.00 0.00 0.00 5.28
1490 6771 2.386661 ATTTGCAGTGGACTAGACGG 57.613 50.000 0.00 0.00 0.00 4.79
1493 6774 8.461222 CAAAATGAATATTTGCAGTGGACTAGA 58.539 33.333 0.00 0.00 36.65 2.43
1494 6775 8.246180 ACAAAATGAATATTTGCAGTGGACTAG 58.754 33.333 0.00 0.00 40.58 2.57
1495 6776 8.121305 ACAAAATGAATATTTGCAGTGGACTA 57.879 30.769 0.00 0.00 40.58 2.59
1581 6896 1.553248 CCCACCATCGTCTTTGTAGGA 59.447 52.381 0.00 0.00 0.00 2.94
1762 7095 4.876107 CACCAGTTAGTTCTGCCGATTAAT 59.124 41.667 0.00 0.00 34.47 1.40
1765 7098 2.301870 TCACCAGTTAGTTCTGCCGATT 59.698 45.455 0.00 0.00 34.47 3.34
1766 7099 1.899814 TCACCAGTTAGTTCTGCCGAT 59.100 47.619 0.00 0.00 34.47 4.18
1767 7100 1.272490 CTCACCAGTTAGTTCTGCCGA 59.728 52.381 0.00 0.00 34.47 5.54
1768 7101 1.000955 ACTCACCAGTTAGTTCTGCCG 59.999 52.381 0.00 0.00 34.47 5.69
1871 7216 1.067821 GAAGAACTCGATCTCCCGCAT 59.932 52.381 0.00 0.00 0.00 4.73
1983 7339 0.474660 GGATAGGTCCAGGGAGCCAT 60.475 60.000 13.58 6.03 44.42 4.40
2295 7684 5.427036 AATACAAAAGGAAAGAAACGCGA 57.573 34.783 15.93 0.00 0.00 5.87
2314 7703 9.672086 GGCATTGCTACGATAATTACAAAAATA 57.328 29.630 8.82 0.00 0.00 1.40
2371 7986 7.890127 TCATCAAAGTTAATCACCTTCAAGGAT 59.110 33.333 11.59 0.00 37.67 3.24
2413 8028 6.511767 CGAGGCAATTAATCTCGCTGTAAATT 60.512 38.462 10.88 0.00 42.70 1.82
2414 8029 5.050091 CGAGGCAATTAATCTCGCTGTAAAT 60.050 40.000 10.88 0.00 42.70 1.40
2415 8030 4.270084 CGAGGCAATTAATCTCGCTGTAAA 59.730 41.667 10.88 0.00 42.70 2.01
2416 8031 3.802139 CGAGGCAATTAATCTCGCTGTAA 59.198 43.478 10.88 0.00 42.70 2.41
2418 8033 2.205074 CGAGGCAATTAATCTCGCTGT 58.795 47.619 10.88 0.00 42.70 4.40
2419 8034 2.937994 CGAGGCAATTAATCTCGCTG 57.062 50.000 10.88 0.00 42.70 5.18
2424 8039 3.654414 GGATCGACGAGGCAATTAATCT 58.346 45.455 3.01 0.00 0.00 2.40
2427 8042 1.537348 CCGGATCGACGAGGCAATTAA 60.537 52.381 3.01 0.00 35.47 1.40
2428 8043 0.031585 CCGGATCGACGAGGCAATTA 59.968 55.000 3.01 0.00 35.47 1.40
2470 8087 1.522668 TGCAGTGGACAGTTGTATGC 58.477 50.000 0.00 0.00 0.00 3.14
2471 8088 3.503363 ACATTGCAGTGGACAGTTGTATG 59.497 43.478 14.25 0.00 0.00 2.39
2472 8089 3.754965 ACATTGCAGTGGACAGTTGTAT 58.245 40.909 14.25 0.00 0.00 2.29
2473 8090 3.207265 ACATTGCAGTGGACAGTTGTA 57.793 42.857 14.25 0.00 0.00 2.41
2474 8091 2.057137 ACATTGCAGTGGACAGTTGT 57.943 45.000 14.25 0.00 0.00 3.32
2475 8092 3.441496 AAACATTGCAGTGGACAGTTG 57.559 42.857 14.25 0.00 0.00 3.16
2478 8095 4.440758 CGTTTTAAACATTGCAGTGGACAG 59.559 41.667 14.25 0.00 0.00 3.51
2480 8097 4.602995 TCGTTTTAAACATTGCAGTGGAC 58.397 39.130 14.25 1.98 0.00 4.02
2481 8098 4.902443 TCGTTTTAAACATTGCAGTGGA 57.098 36.364 14.25 0.00 0.00 4.02
2482 8099 5.107530 CCAATCGTTTTAAACATTGCAGTGG 60.108 40.000 14.25 8.84 33.00 4.00
2483 8100 5.612276 GCCAATCGTTTTAAACATTGCAGTG 60.612 40.000 18.46 7.79 33.00 3.66
2484 8101 4.447389 GCCAATCGTTTTAAACATTGCAGT 59.553 37.500 18.46 0.00 33.00 4.40
2485 8102 4.685628 AGCCAATCGTTTTAAACATTGCAG 59.314 37.500 18.46 11.90 33.00 4.41
2506 8138 7.631717 ATTTTGAAACAGAGGGAGTATTAGC 57.368 36.000 0.00 0.00 0.00 3.09
2513 8145 6.317391 GGTCATCTATTTTGAAACAGAGGGAG 59.683 42.308 0.00 0.00 0.00 4.30
2514 8146 6.180472 GGTCATCTATTTTGAAACAGAGGGA 58.820 40.000 0.00 0.00 0.00 4.20
2515 8147 5.358160 GGGTCATCTATTTTGAAACAGAGGG 59.642 44.000 0.00 0.00 0.00 4.30
2516 8148 6.183347 AGGGTCATCTATTTTGAAACAGAGG 58.817 40.000 0.00 0.00 0.00 3.69
2517 8149 8.970859 ATAGGGTCATCTATTTTGAAACAGAG 57.029 34.615 0.00 0.00 0.00 3.35
2519 8151 9.838339 ACTATAGGGTCATCTATTTTGAAACAG 57.162 33.333 4.43 0.00 32.70 3.16
2531 8163 9.490083 AACTTTGTACTAACTATAGGGTCATCT 57.510 33.333 4.43 0.00 33.15 2.90
2532 8164 9.530633 CAACTTTGTACTAACTATAGGGTCATC 57.469 37.037 4.43 0.00 33.15 2.92
2533 8165 9.263446 TCAACTTTGTACTAACTATAGGGTCAT 57.737 33.333 4.43 0.00 33.15 3.06
2534 8166 8.654485 TCAACTTTGTACTAACTATAGGGTCA 57.346 34.615 4.43 0.00 33.15 4.02
2535 8167 8.747471 ACTCAACTTTGTACTAACTATAGGGTC 58.253 37.037 4.43 0.00 33.15 4.46
2536 8168 8.661752 ACTCAACTTTGTACTAACTATAGGGT 57.338 34.615 4.43 2.96 33.15 4.34
2537 8169 8.746530 TGACTCAACTTTGTACTAACTATAGGG 58.253 37.037 4.43 0.00 33.15 3.53
2547 8179 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2548 8180 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2549 8181 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2550 8182 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2551 8183 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2552 8184 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2553 8185 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2554 8186 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2555 8187 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2556 8188 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2557 8189 5.186992 TCTCCGTTCCAAAATAGATGACTCA 59.813 40.000 0.00 0.00 0.00 3.41
2558 8190 5.661458 TCTCCGTTCCAAAATAGATGACTC 58.339 41.667 0.00 0.00 0.00 3.36
2559 8191 5.677319 TCTCCGTTCCAAAATAGATGACT 57.323 39.130 0.00 0.00 0.00 3.41
2560 8192 6.737254 TTTCTCCGTTCCAAAATAGATGAC 57.263 37.500 0.00 0.00 0.00 3.06
2561 8193 7.938140 ATTTTCTCCGTTCCAAAATAGATGA 57.062 32.000 0.00 0.00 29.78 2.92
2562 8194 9.722056 CTTATTTTCTCCGTTCCAAAATAGATG 57.278 33.333 0.00 0.00 34.83 2.90
2563 8195 9.462606 ACTTATTTTCTCCGTTCCAAAATAGAT 57.537 29.630 0.00 0.00 34.83 1.98
2564 8196 8.726988 CACTTATTTTCTCCGTTCCAAAATAGA 58.273 33.333 0.00 0.00 34.83 1.98
2565 8197 7.484959 GCACTTATTTTCTCCGTTCCAAAATAG 59.515 37.037 0.00 0.00 34.83 1.73
2566 8198 7.309920 GCACTTATTTTCTCCGTTCCAAAATA 58.690 34.615 0.00 0.00 33.02 1.40
2567 8199 6.156519 GCACTTATTTTCTCCGTTCCAAAAT 58.843 36.000 0.00 0.00 34.75 1.82
2568 8200 5.508320 GGCACTTATTTTCTCCGTTCCAAAA 60.508 40.000 0.00 0.00 0.00 2.44
2569 8201 4.022676 GGCACTTATTTTCTCCGTTCCAAA 60.023 41.667 0.00 0.00 0.00 3.28
2570 8202 3.504520 GGCACTTATTTTCTCCGTTCCAA 59.495 43.478 0.00 0.00 0.00 3.53
2571 8203 3.078837 GGCACTTATTTTCTCCGTTCCA 58.921 45.455 0.00 0.00 0.00 3.53
2572 8204 3.078837 TGGCACTTATTTTCTCCGTTCC 58.921 45.455 0.00 0.00 0.00 3.62
2573 8205 3.426292 GCTGGCACTTATTTTCTCCGTTC 60.426 47.826 0.00 0.00 0.00 3.95
2574 8206 2.488153 GCTGGCACTTATTTTCTCCGTT 59.512 45.455 0.00 0.00 0.00 4.44
2575 8207 2.084546 GCTGGCACTTATTTTCTCCGT 58.915 47.619 0.00 0.00 0.00 4.69
2576 8208 2.083774 TGCTGGCACTTATTTTCTCCG 58.916 47.619 0.00 0.00 0.00 4.63
2577 8209 4.036852 GGTATGCTGGCACTTATTTTCTCC 59.963 45.833 0.00 0.00 0.00 3.71
2578 8210 4.640201 TGGTATGCTGGCACTTATTTTCTC 59.360 41.667 0.00 0.00 0.00 2.87
2579 8211 4.399303 GTGGTATGCTGGCACTTATTTTCT 59.601 41.667 0.00 0.00 0.00 2.52
2580 8212 4.399303 AGTGGTATGCTGGCACTTATTTTC 59.601 41.667 0.00 0.00 0.00 2.29
2581 8213 4.158394 CAGTGGTATGCTGGCACTTATTTT 59.842 41.667 0.00 0.00 0.00 1.82
2582 8214 3.696051 CAGTGGTATGCTGGCACTTATTT 59.304 43.478 0.00 0.00 0.00 1.40
2583 8215 3.282021 CAGTGGTATGCTGGCACTTATT 58.718 45.455 0.00 0.00 0.00 1.40
2584 8216 2.239654 ACAGTGGTATGCTGGCACTTAT 59.760 45.455 0.00 0.00 38.22 1.73
2585 8217 1.628340 ACAGTGGTATGCTGGCACTTA 59.372 47.619 0.00 0.00 38.22 2.24
2586 8218 0.401738 ACAGTGGTATGCTGGCACTT 59.598 50.000 0.00 0.00 38.22 3.16
2587 8219 0.036010 GACAGTGGTATGCTGGCACT 60.036 55.000 0.00 0.00 41.45 4.40
2588 8220 1.026718 GGACAGTGGTATGCTGGCAC 61.027 60.000 0.00 0.00 43.52 5.01
2660 8292 0.617820 ACCCTCACTTATCCCGCACT 60.618 55.000 0.00 0.00 0.00 4.40
2681 8313 7.690952 TGTATGTATGCGTCCAGTGTATATA 57.309 36.000 0.00 0.00 0.00 0.86
2691 8323 6.872020 ACCTTATTGTATGTATGTATGCGTCC 59.128 38.462 0.00 0.00 0.00 4.79
2692 8324 7.884816 ACCTTATTGTATGTATGTATGCGTC 57.115 36.000 0.00 0.00 0.00 5.19
2730 9175 6.801862 CAGTGAGGTCCGAAATTATTTTGTTC 59.198 38.462 4.45 0.00 0.00 3.18
2858 9303 5.196695 ACCCTGAAATTTAGAGGCAGATTC 58.803 41.667 9.42 0.00 0.00 2.52
2874 9319 8.411991 AGGTTCGAAATATTTTTAACCCTGAA 57.588 30.769 26.41 10.89 36.60 3.02
2877 9322 9.524496 AGTAAGGTTCGAAATATTTTTAACCCT 57.476 29.630 26.41 21.07 36.60 4.34
2888 9333 7.707464 TCGCATATTTCAGTAAGGTTCGAAATA 59.293 33.333 0.00 0.00 41.82 1.40
2893 9338 5.712217 TTCGCATATTTCAGTAAGGTTCG 57.288 39.130 0.00 0.00 0.00 3.95
2941 9386 9.927668 CTGTCAATGAATGTAAGGGTTAAAAAT 57.072 29.630 0.00 0.00 0.00 1.82
2942 9387 7.870445 GCTGTCAATGAATGTAAGGGTTAAAAA 59.130 33.333 0.00 0.00 0.00 1.94
2943 9388 7.014711 TGCTGTCAATGAATGTAAGGGTTAAAA 59.985 33.333 0.00 0.00 0.00 1.52
2944 9389 6.491745 TGCTGTCAATGAATGTAAGGGTTAAA 59.508 34.615 0.00 0.00 0.00 1.52
2945 9390 6.007076 TGCTGTCAATGAATGTAAGGGTTAA 58.993 36.000 0.00 0.00 0.00 2.01
2946 9391 5.414454 GTGCTGTCAATGAATGTAAGGGTTA 59.586 40.000 0.00 0.00 0.00 2.85
2947 9392 4.218417 GTGCTGTCAATGAATGTAAGGGTT 59.782 41.667 0.00 0.00 0.00 4.11
2948 9393 3.758554 GTGCTGTCAATGAATGTAAGGGT 59.241 43.478 0.00 0.00 0.00 4.34
2949 9394 4.012374 AGTGCTGTCAATGAATGTAAGGG 58.988 43.478 0.00 0.00 0.00 3.95
2950 9395 4.095483 GGAGTGCTGTCAATGAATGTAAGG 59.905 45.833 0.00 0.00 0.00 2.69
2951 9396 4.696877 TGGAGTGCTGTCAATGAATGTAAG 59.303 41.667 0.00 0.00 0.00 2.34
2952 9397 4.650734 TGGAGTGCTGTCAATGAATGTAA 58.349 39.130 0.00 0.00 0.00 2.41
2953 9398 4.284829 TGGAGTGCTGTCAATGAATGTA 57.715 40.909 0.00 0.00 0.00 2.29
2954 9399 3.144657 TGGAGTGCTGTCAATGAATGT 57.855 42.857 0.00 0.00 0.00 2.71
2955 9400 4.028852 CATGGAGTGCTGTCAATGAATG 57.971 45.455 0.00 0.00 0.00 2.67
2968 9413 0.877213 TCGATCGCATGCATGGAGTG 60.877 55.000 27.34 17.12 0.00 3.51
2969 9414 0.034476 ATCGATCGCATGCATGGAGT 59.966 50.000 27.34 12.43 0.00 3.85
2970 9415 0.720027 GATCGATCGCATGCATGGAG 59.280 55.000 27.34 10.66 0.00 3.86
2971 9416 0.033781 TGATCGATCGCATGCATGGA 59.966 50.000 27.34 21.50 0.00 3.41
2972 9417 0.442699 CTGATCGATCGCATGCATGG 59.557 55.000 27.34 17.21 0.00 3.66
2973 9418 0.179222 GCTGATCGATCGCATGCATG 60.179 55.000 26.34 22.70 0.00 4.06
2974 9419 0.320508 AGCTGATCGATCGCATGCAT 60.321 50.000 29.97 10.35 0.00 3.96
2975 9420 1.068585 AGCTGATCGATCGCATGCA 59.931 52.632 29.97 11.92 0.00 3.96
2976 9421 0.942884 TCAGCTGATCGATCGCATGC 60.943 55.000 29.97 24.38 0.00 4.06
2977 9422 1.390463 CATCAGCTGATCGATCGCATG 59.610 52.381 29.97 23.91 31.21 4.06
2978 9423 1.711206 CATCAGCTGATCGATCGCAT 58.289 50.000 29.97 19.39 31.21 4.73
2979 9424 0.942884 GCATCAGCTGATCGATCGCA 60.943 55.000 29.97 18.41 37.91 5.10
2980 9425 0.942884 TGCATCAGCTGATCGATCGC 60.943 55.000 26.44 24.17 42.74 4.58
2981 9426 1.456165 CTTGCATCAGCTGATCGATCG 59.544 52.381 26.44 15.60 42.74 3.69
2982 9427 1.799403 CCTTGCATCAGCTGATCGATC 59.201 52.381 26.44 18.72 42.74 3.69
2983 9428 1.542767 CCCTTGCATCAGCTGATCGAT 60.543 52.381 26.44 3.64 42.74 3.59
2984 9429 0.179065 CCCTTGCATCAGCTGATCGA 60.179 55.000 26.44 18.04 42.74 3.59
2985 9430 1.783031 GCCCTTGCATCAGCTGATCG 61.783 60.000 26.44 20.80 42.74 3.69
2986 9431 0.750546 TGCCCTTGCATCAGCTGATC 60.751 55.000 26.44 19.78 44.23 2.92
2987 9432 1.305287 TGCCCTTGCATCAGCTGAT 59.695 52.632 23.75 23.75 44.23 2.90
2988 9433 2.758434 TGCCCTTGCATCAGCTGA 59.242 55.556 20.79 20.79 44.23 4.26
2997 9442 0.887387 TCAACCGTAAGTGCCCTTGC 60.887 55.000 0.00 0.00 38.26 4.01
2998 9443 0.872388 GTCAACCGTAAGTGCCCTTG 59.128 55.000 0.00 0.00 31.89 3.61
2999 9444 0.470766 TGTCAACCGTAAGTGCCCTT 59.529 50.000 0.00 0.00 34.56 3.95
3000 9445 0.470766 TTGTCAACCGTAAGTGCCCT 59.529 50.000 0.00 0.00 0.00 5.19
3001 9446 1.199097 CATTGTCAACCGTAAGTGCCC 59.801 52.381 0.00 0.00 0.00 5.36
3002 9447 1.401018 GCATTGTCAACCGTAAGTGCC 60.401 52.381 0.00 0.00 0.00 5.01
3003 9448 1.535462 AGCATTGTCAACCGTAAGTGC 59.465 47.619 0.00 0.00 0.00 4.40
3004 9449 2.095768 CCAGCATTGTCAACCGTAAGTG 60.096 50.000 0.00 0.00 0.00 3.16
3005 9450 2.151202 CCAGCATTGTCAACCGTAAGT 58.849 47.619 0.00 0.00 0.00 2.24
3006 9451 2.095768 CACCAGCATTGTCAACCGTAAG 60.096 50.000 0.00 0.00 0.00 2.34
3007 9452 1.876799 CACCAGCATTGTCAACCGTAA 59.123 47.619 0.00 0.00 0.00 3.18
3008 9453 1.518325 CACCAGCATTGTCAACCGTA 58.482 50.000 0.00 0.00 0.00 4.02
3009 9454 1.795170 GCACCAGCATTGTCAACCGT 61.795 55.000 0.00 0.00 41.58 4.83
3010 9455 1.081242 GCACCAGCATTGTCAACCG 60.081 57.895 0.00 0.00 41.58 4.44
3011 9456 0.242017 GAGCACCAGCATTGTCAACC 59.758 55.000 0.00 0.00 45.49 3.77
3012 9457 1.198637 GAGAGCACCAGCATTGTCAAC 59.801 52.381 0.00 0.00 45.49 3.18
3013 9458 1.202794 TGAGAGCACCAGCATTGTCAA 60.203 47.619 0.00 0.00 45.49 3.18
3014 9459 0.397564 TGAGAGCACCAGCATTGTCA 59.602 50.000 0.00 0.00 45.49 3.58
3015 9460 1.527034 TTGAGAGCACCAGCATTGTC 58.473 50.000 0.00 0.00 45.49 3.18
3016 9461 2.089980 GATTGAGAGCACCAGCATTGT 58.910 47.619 0.00 0.00 45.49 2.71
3017 9462 1.063616 CGATTGAGAGCACCAGCATTG 59.936 52.381 0.00 0.00 45.49 2.82
3018 9463 1.339438 ACGATTGAGAGCACCAGCATT 60.339 47.619 0.00 0.00 45.49 3.56
3019 9464 0.251354 ACGATTGAGAGCACCAGCAT 59.749 50.000 0.00 0.00 45.49 3.79
3020 9465 0.390340 GACGATTGAGAGCACCAGCA 60.390 55.000 0.00 0.00 45.49 4.41
3021 9466 0.390340 TGACGATTGAGAGCACCAGC 60.390 55.000 0.00 0.00 42.56 4.85
3022 9467 1.998315 CTTGACGATTGAGAGCACCAG 59.002 52.381 0.00 0.00 0.00 4.00
3023 9468 1.344438 ACTTGACGATTGAGAGCACCA 59.656 47.619 0.00 0.00 0.00 4.17
3024 9469 2.086054 ACTTGACGATTGAGAGCACC 57.914 50.000 0.00 0.00 0.00 5.01
3025 9470 3.321497 AGAACTTGACGATTGAGAGCAC 58.679 45.455 0.00 0.00 0.00 4.40
3026 9471 3.667497 AGAACTTGACGATTGAGAGCA 57.333 42.857 0.00 0.00 0.00 4.26
3027 9472 3.990469 TGAAGAACTTGACGATTGAGAGC 59.010 43.478 0.00 0.00 0.00 4.09
3028 9473 4.091220 GCTGAAGAACTTGACGATTGAGAG 59.909 45.833 0.00 0.00 0.00 3.20
3029 9474 3.990469 GCTGAAGAACTTGACGATTGAGA 59.010 43.478 0.00 0.00 0.00 3.27
3030 9475 3.742882 TGCTGAAGAACTTGACGATTGAG 59.257 43.478 0.00 0.00 0.00 3.02
3031 9476 3.494626 GTGCTGAAGAACTTGACGATTGA 59.505 43.478 0.00 0.00 0.00 2.57
3032 9477 3.496130 AGTGCTGAAGAACTTGACGATTG 59.504 43.478 0.00 0.00 26.38 2.67
3033 9478 3.733337 AGTGCTGAAGAACTTGACGATT 58.267 40.909 0.00 0.00 26.38 3.34
3034 9479 3.393089 AGTGCTGAAGAACTTGACGAT 57.607 42.857 0.00 0.00 26.38 3.73
3035 9480 2.890808 AGTGCTGAAGAACTTGACGA 57.109 45.000 0.00 0.00 26.38 4.20
3036 9481 3.643763 ACTAGTGCTGAAGAACTTGACG 58.356 45.455 6.87 0.00 35.12 4.35
3037 9482 5.983720 TGTAACTAGTGCTGAAGAACTTGAC 59.016 40.000 6.87 0.00 35.12 3.18
3038 9483 6.156748 TGTAACTAGTGCTGAAGAACTTGA 57.843 37.500 6.87 0.00 35.12 3.02
3039 9484 6.425114 ACATGTAACTAGTGCTGAAGAACTTG 59.575 38.462 0.00 0.00 35.12 3.16
3040 9485 6.525629 ACATGTAACTAGTGCTGAAGAACTT 58.474 36.000 0.00 0.00 35.12 2.66
3041 9486 6.102897 ACATGTAACTAGTGCTGAAGAACT 57.897 37.500 0.00 0.00 37.72 3.01
3042 9487 6.866770 TGTACATGTAACTAGTGCTGAAGAAC 59.133 38.462 7.25 0.00 0.00 3.01
3043 9488 6.988522 TGTACATGTAACTAGTGCTGAAGAA 58.011 36.000 7.25 0.00 0.00 2.52
3044 9489 6.584185 TGTACATGTAACTAGTGCTGAAGA 57.416 37.500 7.25 0.00 0.00 2.87
3045 9490 5.289675 GCTGTACATGTAACTAGTGCTGAAG 59.710 44.000 7.25 0.00 0.00 3.02
3046 9491 5.168569 GCTGTACATGTAACTAGTGCTGAA 58.831 41.667 7.25 0.00 0.00 3.02
3047 9492 4.219725 TGCTGTACATGTAACTAGTGCTGA 59.780 41.667 7.25 0.00 0.00 4.26
3048 9493 4.494484 TGCTGTACATGTAACTAGTGCTG 58.506 43.478 7.25 0.00 0.00 4.41
3049 9494 4.801330 TGCTGTACATGTAACTAGTGCT 57.199 40.909 7.25 0.00 0.00 4.40
3050 9495 5.727791 GCATTGCTGTACATGTAACTAGTGC 60.728 44.000 7.25 10.25 0.00 4.40
3051 9496 5.351189 TGCATTGCTGTACATGTAACTAGTG 59.649 40.000 7.25 4.38 0.00 2.74
3052 9497 5.487433 TGCATTGCTGTACATGTAACTAGT 58.513 37.500 7.25 0.00 0.00 2.57
3053 9498 6.424683 CATGCATTGCTGTACATGTAACTAG 58.575 40.000 7.25 7.78 36.11 2.57
3054 9499 6.362210 CATGCATTGCTGTACATGTAACTA 57.638 37.500 7.25 0.00 36.11 2.24
3055 9500 5.239359 CATGCATTGCTGTACATGTAACT 57.761 39.130 7.25 0.00 36.11 2.24


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

AutoCloner maintained by Alex Coulton.