Multiple sequence alignment - TraesCS3A01G495100

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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 TraesCS3A01G495100 chr3A 100.000 7231 0 0 1 7231 721261680 721254450 0.000000e+00 13354.0
1 TraesCS3A01G495100 chr3A 92.818 1824 104 15 1143 2965 721448494 721450291 0.000000e+00 2617.0
2 TraesCS3A01G495100 chr3A 87.635 2135 158 49 5004 7105 721452087 721454148 0.000000e+00 2383.0
3 TraesCS3A01G495100 chr3A 93.560 1087 48 9 3886 4955 721451007 721452088 0.000000e+00 1600.0
4 TraesCS3A01G495100 chr3A 94.100 678 34 4 2968 3642 721450347 721451021 0.000000e+00 1026.0
5 TraesCS3A01G495100 chr3A 91.250 240 21 0 3647 3886 543724260 543724499 1.950000e-85 327.0
6 TraesCS3A01G495100 chr3A 87.398 246 31 0 3643 3888 629665186 629665431 4.270000e-72 283.0
7 TraesCS3A01G495100 chr3A 81.788 302 35 7 768 1049 721448150 721448451 1.210000e-57 235.0
8 TraesCS3A01G495100 chr3B 96.449 6224 154 29 792 6996 791659241 791665416 0.000000e+00 10207.0
9 TraesCS3A01G495100 chr3B 89.565 1562 132 17 5064 6597 790745007 790743449 0.000000e+00 1953.0
10 TraesCS3A01G495100 chr3B 91.685 1395 75 16 1575 2967 790750577 790749222 0.000000e+00 1895.0
11 TraesCS3A01G495100 chr3B 92.406 1093 58 10 3886 4958 790748508 790747421 0.000000e+00 1535.0
12 TraesCS3A01G495100 chr3B 93.651 693 37 5 2953 3642 790749182 790748494 0.000000e+00 1029.0
13 TraesCS3A01G495100 chr3B 84.808 757 52 28 6389 7105 791286062 791286795 0.000000e+00 702.0
14 TraesCS3A01G495100 chr3B 83.895 683 100 6 2966 3642 791281877 791282555 1.700000e-180 643.0
15 TraesCS3A01G495100 chr3B 85.420 583 72 11 2966 3540 792070360 792070937 1.740000e-165 593.0
16 TraesCS3A01G495100 chr3B 90.200 449 32 6 1143 1583 790751644 790751200 6.290000e-160 575.0
17 TraesCS3A01G495100 chr3B 81.722 755 66 38 6389 7098 792105179 792105906 1.360000e-156 564.0
18 TraesCS3A01G495100 chr3B 86.910 466 55 6 3078 3540 792115634 792116096 1.080000e-142 518.0
19 TraesCS3A01G495100 chr3B 86.780 469 52 8 3078 3540 792154982 792155446 1.390000e-141 514.0
20 TraesCS3A01G495100 chr3B 79.791 767 76 43 6389 7105 792142448 792143185 1.090000e-132 484.0
21 TraesCS3A01G495100 chr3B 79.791 767 76 43 6389 7105 792180511 792181248 1.090000e-132 484.0
22 TraesCS3A01G495100 chr3B 79.477 765 82 41 6389 7105 792253773 792254510 2.360000e-129 473.0
23 TraesCS3A01G495100 chr3B 88.630 387 40 2 34 417 790753561 790753176 1.100000e-127 468.0
24 TraesCS3A01G495100 chr3B 92.361 288 19 2 6653 6937 790743450 790743163 2.430000e-109 407.0
25 TraesCS3A01G495100 chr3B 80.000 460 68 14 2520 2967 791281386 791281833 1.170000e-82 318.0
26 TraesCS3A01G495100 chr3B 86.364 242 33 0 3643 3884 377118371 377118130 1.550000e-66 265.0
27 TraesCS3A01G495100 chr3B 86.667 225 23 4 3891 4110 791282546 791282768 7.250000e-60 243.0
28 TraesCS3A01G495100 chr3B 81.609 261 40 7 2134 2392 791280872 791281126 7.350000e-50 209.0
29 TraesCS3A01G495100 chr3B 97.248 109 3 0 6997 7105 790742978 790742870 1.240000e-42 185.0
30 TraesCS3A01G495100 chr3B 80.400 250 38 7 4147 4387 740549443 740549196 5.760000e-41 180.0
31 TraesCS3A01G495100 chr3B 88.976 127 11 3 4169 4293 442637474 442637349 3.490000e-33 154.0
32 TraesCS3A01G495100 chr3B 94.937 79 4 0 978 1056 790751758 790751680 2.740000e-24 124.0
33 TraesCS3A01G495100 chr3B 97.015 67 2 0 5004 5070 790747425 790747359 5.930000e-21 113.0
34 TraesCS3A01G495100 chr3B 86.239 109 1 3 6997 7105 791665456 791665550 9.920000e-19 106.0
35 TraesCS3A01G495100 chr3B 95.161 62 3 0 719 780 790751976 790751915 1.660000e-16 99.0
36 TraesCS3A01G495100 chr3B 89.062 64 6 1 6937 6999 752687043 752687106 2.160000e-10 78.7
37 TraesCS3A01G495100 chr3B 93.878 49 3 0 7109 7157 790742411 790742363 2.800000e-09 75.0
38 TraesCS3A01G495100 chr3D 89.958 2141 158 25 5004 7105 590755806 590753684 0.000000e+00 2710.0
39 TraesCS3A01G495100 chr3D 90.696 1666 110 19 1079 2740 590764957 590763333 0.000000e+00 2176.0
40 TraesCS3A01G495100 chr3D 91.452 1088 61 15 3886 4958 590756872 590755802 0.000000e+00 1465.0
41 TraesCS3A01G495100 chr3D 92.024 677 38 8 2968 3642 590757520 590756858 0.000000e+00 937.0
42 TraesCS3A01G495100 chr3D 84.936 624 83 9 2966 3581 591039907 591040527 7.970000e-174 621.0
43 TraesCS3A01G495100 chr3D 93.705 413 20 6 573 982 590766318 590765909 1.330000e-171 614.0
44 TraesCS3A01G495100 chr3D 89.009 464 23 8 6538 6996 591042565 591043005 3.810000e-152 549.0
45 TraesCS3A01G495100 chr3D 96.121 232 9 0 2736 2967 590757805 590757574 5.290000e-101 379.0
46 TraesCS3A01G495100 chr3D 87.603 242 30 0 3643 3884 552668746 552668505 1.540000e-71 281.0
47 TraesCS3A01G495100 chr3D 88.554 166 15 4 413 574 507038577 507038742 1.590000e-46 198.0
48 TraesCS3A01G495100 chr3D 94.495 109 6 0 6997 7105 591043044 591043152 1.250000e-37 169.0
49 TraesCS3A01G495100 chr3D 90.000 120 9 1 301 417 590766437 590766318 1.260000e-32 152.0
50 TraesCS3A01G495100 chr3D 90.196 102 10 0 2291 2392 591039047 591039148 4.550000e-27 134.0
51 TraesCS3A01G495100 chr3D 91.250 80 7 0 978 1057 590765879 590765800 7.670000e-20 110.0
52 TraesCS3A01G495100 chr3D 100.000 31 0 0 6941 6971 610564013 610564043 2.820000e-04 58.4
53 TraesCS3A01G495100 chr3D 100.000 28 0 0 6948 6975 133721527 133721554 1.300000e-02 52.8
54 TraesCS3A01G495100 chr1D 91.322 242 20 1 3643 3884 136364325 136364565 5.410000e-86 329.0
55 TraesCS3A01G495100 chr1D 87.500 168 17 3 419 582 127925491 127925324 2.660000e-44 191.0
56 TraesCS3A01G495100 chr1D 92.424 66 4 1 5187 5252 449466699 449466763 7.720000e-15 93.5
57 TraesCS3A01G495100 chr1D 89.855 69 6 1 5185 5252 421221504 421221436 3.590000e-13 87.9
58 TraesCS3A01G495100 chr5B 89.837 246 22 2 4145 4387 316714640 316714395 5.450000e-81 313.0
59 TraesCS3A01G495100 chr5B 91.525 59 4 1 6941 6999 490949145 490949202 6.010000e-11 80.5
60 TraesCS3A01G495100 chr7D 88.525 244 28 0 3643 3886 454085881 454086124 5.490000e-76 296.0
61 TraesCS3A01G495100 chr7D 97.500 40 1 0 6941 6980 619998628 619998667 1.300000e-07 69.4
62 TraesCS3A01G495100 chr7D 95.000 40 1 1 5197 5236 622102558 622102520 2.180000e-05 62.1
63 TraesCS3A01G495100 chr5D 88.163 245 21 3 4145 4387 385114395 385114157 1.190000e-72 285.0
64 TraesCS3A01G495100 chr5D 88.820 161 14 4 419 575 539916011 539915851 2.060000e-45 195.0
65 TraesCS3A01G495100 chr5D 89.474 57 6 0 6940 6996 482889428 482889484 1.010000e-08 73.1
66 TraesCS3A01G495100 chr5D 97.297 37 1 0 5189 5225 416626690 416626654 6.060000e-06 63.9
67 TraesCS3A01G495100 chr2B 89.035 228 17 6 4145 4370 391143037 391143258 7.150000e-70 276.0
68 TraesCS3A01G495100 chr2B 89.375 160 13 4 419 574 291855166 291855007 1.590000e-46 198.0
69 TraesCS3A01G495100 chr5A 86.831 243 32 0 3643 3885 537448394 537448152 9.240000e-69 272.0
70 TraesCS3A01G495100 chr1A 86.307 241 32 1 3643 3883 305339673 305339434 2.000000e-65 261.0
71 TraesCS3A01G495100 chr1A 92.424 66 4 1 5187 5252 544599651 544599715 7.720000e-15 93.5
72 TraesCS3A01G495100 chr1A 94.737 57 2 1 5185 5240 517515256 517515200 3.590000e-13 87.9
73 TraesCS3A01G495100 chr7A 95.139 144 5 2 4145 4286 552975527 552975384 7.300000e-55 226.0
74 TraesCS3A01G495100 chr4A 91.772 158 9 3 4134 4287 115567251 115567094 4.390000e-52 217.0
75 TraesCS3A01G495100 chr4A 88.415 164 13 6 419 577 621921631 621921793 7.400000e-45 193.0
76 TraesCS3A01G495100 chr7B 88.485 165 13 6 421 579 415436691 415436527 2.060000e-45 195.0
77 TraesCS3A01G495100 chr6B 88.095 168 14 6 412 574 600973126 600972960 2.060000e-45 195.0
78 TraesCS3A01G495100 chr6B 88.344 163 15 3 419 577 376888763 376888601 7.400000e-45 193.0
79 TraesCS3A01G495100 chr4B 87.719 171 15 5 408 574 535344990 535345158 2.060000e-45 195.0
80 TraesCS3A01G495100 chr4B 92.593 54 3 1 6941 6993 108410835 108410782 7.780000e-10 76.8
81 TraesCS3A01G495100 chr4B 100.000 32 0 0 6941 6972 659691672 659691703 7.830000e-05 60.2
82 TraesCS3A01G495100 chr2D 94.792 96 5 0 4292 4387 294545406 294545501 4.520000e-32 150.0
83 TraesCS3A01G495100 chr2D 96.296 54 2 0 5199 5252 425212648 425212701 9.990000e-14 89.8
84 TraesCS3A01G495100 chr2D 100.000 35 0 0 6941 6975 184404490 184404524 1.680000e-06 65.8
85 TraesCS3A01G495100 chr2D 94.737 38 2 0 6938 6975 43945965 43946002 7.830000e-05 60.2
86 TraesCS3A01G495100 chr1B 89.855 69 6 1 5185 5252 570521173 570521105 3.590000e-13 87.9
87 TraesCS3A01G495100 chr6A 90.741 54 4 1 6941 6993 144496975 144497028 3.620000e-08 71.3
88 TraesCS3A01G495100 chr6D 91.837 49 4 0 6941 6989 3442605 3442557 1.300000e-07 69.4


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 TraesCS3A01G495100 chr3A 721254450 721261680 7230 True 13354.000000 13354 100.000000 1 7231 1 chr3A.!!$R1 7230
1 TraesCS3A01G495100 chr3A 721448150 721454148 5998 False 1572.200000 2617 89.980200 768 7105 5 chr3A.!!$F3 6337
2 TraesCS3A01G495100 chr3B 791659241 791665550 6309 False 5156.500000 10207 91.344000 792 7105 2 chr3B.!!$F10 6313
3 TraesCS3A01G495100 chr3B 790742363 790753561 11198 True 704.833333 1953 93.061417 34 7157 12 chr3B.!!$R4 7123
4 TraesCS3A01G495100 chr3B 792070360 792070937 577 False 593.000000 593 85.420000 2966 3540 1 chr3B.!!$F2 574
5 TraesCS3A01G495100 chr3B 792105179 792105906 727 False 564.000000 564 81.722000 6389 7098 1 chr3B.!!$F3 709
6 TraesCS3A01G495100 chr3B 792142448 792143185 737 False 484.000000 484 79.791000 6389 7105 1 chr3B.!!$F5 716
7 TraesCS3A01G495100 chr3B 792180511 792181248 737 False 484.000000 484 79.791000 6389 7105 1 chr3B.!!$F7 716
8 TraesCS3A01G495100 chr3B 792253773 792254510 737 False 473.000000 473 79.477000 6389 7105 1 chr3B.!!$F8 716
9 TraesCS3A01G495100 chr3B 791280872 791286795 5923 False 423.000000 702 83.395800 2134 7105 5 chr3B.!!$F9 4971
10 TraesCS3A01G495100 chr3D 590753684 590757805 4121 True 1372.750000 2710 92.388750 2736 7105 4 chr3D.!!$R2 4369
11 TraesCS3A01G495100 chr3D 590763333 590766437 3104 True 763.000000 2176 91.412750 301 2740 4 chr3D.!!$R3 2439
12 TraesCS3A01G495100 chr3D 591039047 591043152 4105 False 368.250000 621 89.659000 2291 7105 4 chr3D.!!$F4 4814

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
235 236 0.319405 AAGGTCTGCAAGGCAAATGC 59.681 50.000 0.0 0.0 43.51 3.56 F
417 421 0.531532 CACCCGCTCTCCAGCTTATG 60.532 60.000 0.0 0.0 44.40 1.90 F
597 601 1.064946 CAAGCTAGGAGCCTCGACG 59.935 63.158 0.0 0.0 43.77 5.12 F
2243 4848 1.150536 GTGGAAGAAGTGGGTGGCA 59.849 57.895 0.0 0.0 0.00 4.92 F
2245 4850 1.352622 TGGAAGAAGTGGGTGGCAGT 61.353 55.000 0.0 0.0 0.00 4.40 F
3652 6470 2.155539 GTGCAACAAATTCGCAATGACC 59.844 45.455 0.0 0.0 37.41 4.02 F
5240 11676 0.543883 TGCCAAAATAAGCTGCCCCA 60.544 50.000 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 4201 0.802494 GTAATGCACACGACCCCTTG 59.198 55.000 0.00 0.00 0.00 3.61 R
2243 4848 1.280133 CTCACCACATCCATCCACACT 59.720 52.381 0.00 0.00 0.00 3.55 R
2245 4850 1.361204 ACTCACCACATCCATCCACA 58.639 50.000 0.00 0.00 0.00 4.17 R
3665 6483 0.039618 ATTGGTCGAAGGGGTTGCAT 59.960 50.000 0.00 0.00 0.00 3.96 R
3666 6484 0.178975 AATTGGTCGAAGGGGTTGCA 60.179 50.000 0.00 0.00 0.00 4.08 R
5399 11839 1.062525 GCCATGAATTCGCGACACC 59.937 57.895 9.15 0.32 0.00 4.16 R
6422 13025 2.166829 CATGAATCCCAACGGTTTCCA 58.833 47.619 0.00 0.00 37.14 3.53 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
22 23 4.979943 TGTACCAATGCATGTACCAATG 57.020 40.909 19.26 5.34 37.19 2.82
32 33 4.979943 CATGTACCAATGCATGTACCAA 57.020 40.909 19.26 7.14 42.28 3.67
45 46 1.202867 TGTACCAATGGCTCACTTGCA 60.203 47.619 0.00 0.00 34.04 4.08
46 47 1.200020 GTACCAATGGCTCACTTGCAC 59.800 52.381 0.00 0.00 34.04 4.57
49 50 2.969806 AATGGCTCACTTGCACGCG 61.970 57.895 3.53 3.53 34.04 6.01
71 72 0.392863 CGATGGTGTGCCCTGAATGA 60.393 55.000 0.00 0.00 0.00 2.57
94 95 4.309950 GGCGTGGGGACAACGACT 62.310 66.667 0.00 0.00 46.06 4.18
109 110 2.989824 ACTAGGGTGAGCGCGTGT 60.990 61.111 8.43 0.00 0.00 4.49
122 123 2.524300 GCGTGTGTTAGGCGAGAAA 58.476 52.632 0.00 0.00 0.00 2.52
140 141 6.220201 CGAGAAAGATAAGGGAAGGAGAATC 58.780 44.000 0.00 0.00 0.00 2.52
144 145 4.810345 AGATAAGGGAAGGAGAATCGAGT 58.190 43.478 0.00 0.00 34.37 4.18
151 152 0.681564 AGGAGAATCGAGTCCGTGCT 60.682 55.000 9.63 0.00 37.97 4.40
154 155 1.941294 GAGAATCGAGTCCGTGCTCTA 59.059 52.381 9.63 0.00 37.05 2.43
167 168 0.615331 TGCTCTACTGCAAGGAAGGG 59.385 55.000 0.00 0.00 40.29 3.95
193 194 4.442893 CCAGTAATTGCTCCCGTGATTCTA 60.443 45.833 0.00 0.00 0.00 2.10
195 196 2.246719 ATTGCTCCCGTGATTCTAGC 57.753 50.000 0.00 0.00 0.00 3.42
206 207 2.633481 GTGATTCTAGCGGGGGTATTCT 59.367 50.000 0.00 0.00 0.00 2.40
221 222 4.640647 GGGTATTCTCATCCAAACAAGGTC 59.359 45.833 0.00 0.00 0.00 3.85
233 234 1.708341 ACAAGGTCTGCAAGGCAAAT 58.292 45.000 0.00 0.00 43.51 2.32
235 236 0.319405 AAGGTCTGCAAGGCAAATGC 59.681 50.000 0.00 0.00 43.51 3.56
244 245 1.135315 CAAGGCAAATGCGCACTACAT 60.135 47.619 14.90 0.00 43.26 2.29
248 249 2.290367 GGCAAATGCGCACTACATATCA 59.710 45.455 14.90 0.00 43.26 2.15
249 250 3.243035 GGCAAATGCGCACTACATATCAA 60.243 43.478 14.90 0.00 43.26 2.57
294 295 6.610020 TGCACACTATATAAAGGTACAGAGGT 59.390 38.462 0.00 0.00 0.00 3.85
326 327 3.018598 TCAGAAGAAGAACACGAGCTG 57.981 47.619 0.00 0.00 0.00 4.24
363 367 1.270147 CGACACGAGAAGGGAAAGGTT 60.270 52.381 0.00 0.00 0.00 3.50
372 376 3.981375 AGAAGGGAAAGGTTGAACTAGGT 59.019 43.478 0.00 0.00 0.00 3.08
416 420 1.690219 CCACCCGCTCTCCAGCTTAT 61.690 60.000 0.00 0.00 44.40 1.73
417 421 0.531532 CACCCGCTCTCCAGCTTATG 60.532 60.000 0.00 0.00 44.40 1.90
418 422 1.596477 CCCGCTCTCCAGCTTATGC 60.596 63.158 0.00 0.00 44.40 3.14
431 435 3.220674 GCTTATGCTCCCTTCATTCCT 57.779 47.619 0.00 0.00 36.03 3.36
432 436 4.357918 GCTTATGCTCCCTTCATTCCTA 57.642 45.455 0.00 0.00 36.03 2.94
433 437 4.718961 GCTTATGCTCCCTTCATTCCTAA 58.281 43.478 0.00 0.00 36.03 2.69
434 438 5.133221 GCTTATGCTCCCTTCATTCCTAAA 58.867 41.667 0.00 0.00 36.03 1.85
435 439 5.772169 GCTTATGCTCCCTTCATTCCTAAAT 59.228 40.000 0.00 0.00 36.03 1.40
436 440 6.942576 GCTTATGCTCCCTTCATTCCTAAATA 59.057 38.462 0.00 0.00 36.03 1.40
437 441 7.613411 GCTTATGCTCCCTTCATTCCTAAATAT 59.387 37.037 0.00 0.00 36.03 1.28
441 445 8.045720 TGCTCCCTTCATTCCTAAATATAAGT 57.954 34.615 0.00 0.00 0.00 2.24
442 446 8.157476 TGCTCCCTTCATTCCTAAATATAAGTC 58.843 37.037 0.00 0.00 0.00 3.01
443 447 8.379331 GCTCCCTTCATTCCTAAATATAAGTCT 58.621 37.037 0.00 0.00 0.00 3.24
466 470 9.897744 GTCTTTGTAAAGATTTCACATGAATCA 57.102 29.630 9.98 0.00 45.83 2.57
467 471 9.897744 TCTTTGTAAAGATTTCACATGAATCAC 57.102 29.630 0.00 0.00 39.95 3.06
468 472 9.681692 CTTTGTAAAGATTTCACATGAATCACA 57.318 29.630 0.00 0.00 38.28 3.58
477 481 9.961265 GATTTCACATGAATCACATATGAATGT 57.039 29.630 10.38 6.43 46.96 2.71
506 510 7.129457 AGATGCATTTTAGAGTGTAGATCCA 57.871 36.000 0.00 0.00 0.00 3.41
507 511 7.743749 AGATGCATTTTAGAGTGTAGATCCAT 58.256 34.615 0.00 0.00 0.00 3.41
508 512 8.216423 AGATGCATTTTAGAGTGTAGATCCATT 58.784 33.333 0.00 0.00 0.00 3.16
509 513 8.757982 ATGCATTTTAGAGTGTAGATCCATTT 57.242 30.769 0.00 0.00 0.00 2.32
510 514 9.851686 ATGCATTTTAGAGTGTAGATCCATTTA 57.148 29.630 0.00 0.00 0.00 1.40
511 515 9.851686 TGCATTTTAGAGTGTAGATCCATTTAT 57.148 29.630 0.00 0.00 0.00 1.40
517 521 9.905713 TTAGAGTGTAGATCCATTTATTTTGCT 57.094 29.630 0.00 0.00 0.00 3.91
518 522 8.443953 AGAGTGTAGATCCATTTATTTTGCTC 57.556 34.615 0.00 0.00 0.00 4.26
519 523 7.500559 AGAGTGTAGATCCATTTATTTTGCTCC 59.499 37.037 0.00 0.00 0.00 4.70
520 524 6.260936 AGTGTAGATCCATTTATTTTGCTCCG 59.739 38.462 0.00 0.00 0.00 4.63
521 525 6.038271 GTGTAGATCCATTTATTTTGCTCCGT 59.962 38.462 0.00 0.00 0.00 4.69
522 526 7.225931 GTGTAGATCCATTTATTTTGCTCCGTA 59.774 37.037 0.00 0.00 0.00 4.02
523 527 7.936847 TGTAGATCCATTTATTTTGCTCCGTAT 59.063 33.333 0.00 0.00 0.00 3.06
524 528 9.431887 GTAGATCCATTTATTTTGCTCCGTATA 57.568 33.333 0.00 0.00 0.00 1.47
528 532 9.959721 ATCCATTTATTTTGCTCCGTATATAGT 57.040 29.630 0.00 0.00 0.00 2.12
529 533 9.431887 TCCATTTATTTTGCTCCGTATATAGTC 57.568 33.333 0.00 0.00 0.00 2.59
530 534 9.436957 CCATTTATTTTGCTCCGTATATAGTCT 57.563 33.333 0.00 0.00 0.00 3.24
566 570 9.582431 TCTTACAAAGACTTATATTCAGGAACG 57.418 33.333 0.00 0.00 31.20 3.95
567 571 8.712285 TTACAAAGACTTATATTCAGGAACGG 57.288 34.615 0.00 0.00 0.00 4.44
568 572 6.113411 ACAAAGACTTATATTCAGGAACGGG 58.887 40.000 0.00 0.00 0.00 5.28
569 573 4.957684 AGACTTATATTCAGGAACGGGG 57.042 45.455 0.00 0.00 0.00 5.73
570 574 4.553678 AGACTTATATTCAGGAACGGGGA 58.446 43.478 0.00 0.00 0.00 4.81
571 575 4.589374 AGACTTATATTCAGGAACGGGGAG 59.411 45.833 0.00 0.00 0.00 4.30
597 601 1.064946 CAAGCTAGGAGCCTCGACG 59.935 63.158 0.00 0.00 43.77 5.12
1123 3082 4.143333 CGCCGATCCCTTCACGGT 62.143 66.667 0.00 0.00 46.95 4.83
1551 3519 1.609208 ACTTTGGCATGGACAGTCAC 58.391 50.000 2.17 0.00 0.00 3.67
1566 3534 3.699538 ACAGTCACTGTGATCCGCTATTA 59.300 43.478 10.48 0.00 43.63 0.98
1811 4412 5.046304 CACAAGTAATATGGATCGGAGGGAT 60.046 44.000 0.00 0.00 38.35 3.85
1915 4516 5.319043 TCTTTGTCACCTTTGGTCCTTAT 57.681 39.130 0.00 0.00 31.02 1.73
1916 4517 6.442541 TCTTTGTCACCTTTGGTCCTTATA 57.557 37.500 0.00 0.00 31.02 0.98
1952 4557 3.057969 TGGCTGGATATAAGCGGATTG 57.942 47.619 4.29 0.00 41.78 2.67
2120 4725 5.278169 CCACAATGTGAACAGAAGGAAGAAG 60.278 44.000 15.91 0.00 35.23 2.85
2121 4726 4.276926 ACAATGTGAACAGAAGGAAGAAGC 59.723 41.667 0.00 0.00 0.00 3.86
2177 4782 3.482598 CGCTCAATCGTCTTAAACAGCAG 60.483 47.826 0.00 0.00 0.00 4.24
2243 4848 1.150536 GTGGAAGAAGTGGGTGGCA 59.849 57.895 0.00 0.00 0.00 4.92
2245 4850 1.352622 TGGAAGAAGTGGGTGGCAGT 61.353 55.000 0.00 0.00 0.00 4.40
2492 5216 6.624352 AATGATTCTGATTATCAACACCGG 57.376 37.500 0.00 0.00 35.77 5.28
3222 6032 6.558771 TGTGATTCACCTCAATTTACTGTG 57.441 37.500 14.05 0.00 32.73 3.66
3261 6075 7.721399 AGTTTCCTCACAAGACATGAACTTATT 59.279 33.333 0.00 0.00 0.00 1.40
3633 6451 6.446781 AAATTAATCTGGTGAGCATCTGTG 57.553 37.500 0.00 0.00 34.92 3.66
3652 6470 2.155539 GTGCAACAAATTCGCAATGACC 59.844 45.455 0.00 0.00 37.41 4.02
3728 6546 1.339438 TGAAGCTAAGCTCTGGGCAAG 60.339 52.381 0.74 0.00 44.79 4.01
3815 6633 1.544691 GACTGTAACCGCTCCTCTTCA 59.455 52.381 0.00 0.00 0.00 3.02
3876 6694 3.434637 GCAAGTCTTTTGCGTTTTCTCA 58.565 40.909 0.00 0.00 35.58 3.27
3916 6735 5.600669 ACAAATACTTCCCTCCTTCCTTT 57.399 39.130 0.00 0.00 0.00 3.11
4353 8413 2.957402 TGGCTCACCAAGTCTTTCAT 57.043 45.000 0.00 0.00 45.37 2.57
4424 8484 9.723601 ATAAGTTTGCCATACATTTTTCATTGT 57.276 25.926 0.00 0.00 0.00 2.71
4447 8507 3.485216 GGTTTCGACTATGCCATGTTTCG 60.485 47.826 0.00 0.00 0.00 3.46
4514 8574 6.493115 TCCATTGGCCTGTAATTATATTGTGG 59.507 38.462 3.32 0.00 0.00 4.17
4537 8597 4.909696 TGTTATGTTGACCAAGGTGTTG 57.090 40.909 0.00 0.00 0.00 3.33
4923 8998 3.021695 TCCGATCCATAGAAAGTGTCGT 58.978 45.455 0.00 0.00 0.00 4.34
4963 9038 8.747538 ACTGAACTAACCTTAATTCAAACTGT 57.252 30.769 0.00 0.00 31.00 3.55
5107 11540 5.125578 TCTCTAGCATACGTGTCATTCTTGT 59.874 40.000 0.00 0.00 0.00 3.16
5240 11676 0.543883 TGCCAAAATAAGCTGCCCCA 60.544 50.000 0.00 0.00 0.00 4.96
5298 11735 4.024048 AGGTTAGTGTCAACATTTGCGAAG 60.024 41.667 0.00 0.00 0.00 3.79
5399 11839 1.402968 CCAATTCGTGCTTGGGAGATG 59.597 52.381 5.77 0.00 39.62 2.90
5466 11907 4.853924 AAGGTGCATCAGTTTTTACAGG 57.146 40.909 0.00 0.00 0.00 4.00
5653 12094 6.955851 TCTTTCTTGAAATTGGATTGGGAGAT 59.044 34.615 0.00 0.00 0.00 2.75
5780 12224 5.338871 CCCAGACTTGGTAGCTATTGGTTTA 60.339 44.000 0.00 0.00 43.40 2.01
6194 12663 3.749954 GCATGGGCAGAAATCTACATCCT 60.750 47.826 0.00 0.00 40.72 3.24
6332 12928 3.881937 AATTCTCATTCCAAGGCTTGC 57.118 42.857 21.77 0.00 0.00 4.01
6361 12964 5.128033 TCCAAATGGATGCCTTCTTCATA 57.872 39.130 0.00 0.00 39.78 2.15
6422 13025 7.308830 CCAGAGTTTGCTTAGCATTAGAGTTTT 60.309 37.037 8.05 0.00 38.76 2.43
6577 13210 3.366374 GCTTCAGGAGTTGCATTTGGTAC 60.366 47.826 0.00 0.00 0.00 3.34
6597 13236 6.719370 TGGTACCAGCTTTCTTTGTTGATATT 59.281 34.615 11.60 0.00 0.00 1.28
6675 13314 6.708054 ACATAACTGAATAATCTGTGCTAGGC 59.292 38.462 0.00 0.00 37.74 3.93
6823 13464 3.462982 TGTAGTATTAGGCGGCACATTG 58.537 45.455 13.08 0.00 0.00 2.82
6824 13465 3.133183 TGTAGTATTAGGCGGCACATTGA 59.867 43.478 13.08 0.00 0.00 2.57
6863 13506 2.043227 AGGAGTAGATAGCACAAGCCC 58.957 52.381 0.00 0.00 43.56 5.19
6865 13508 3.117093 AGGAGTAGATAGCACAAGCCCTA 60.117 47.826 0.00 0.00 43.56 3.53
6916 13562 1.243342 TGGGAATCAAGTGCCTTGCG 61.243 55.000 9.35 0.00 40.84 4.85
7105 13876 2.738213 AAGGACCGCTGCTCTGGTTG 62.738 60.000 0.00 0.00 38.99 3.77
7106 13877 2.743928 GACCGCTGCTCTGGTTGG 60.744 66.667 0.00 0.00 38.99 3.77
7108 13879 2.743928 CCGCTGCTCTGGTTGGAC 60.744 66.667 0.00 0.00 0.00 4.02
7109 13880 2.345244 CGCTGCTCTGGTTGGACT 59.655 61.111 0.00 0.00 0.00 3.85
7110 13881 1.302033 CGCTGCTCTGGTTGGACTT 60.302 57.895 0.00 0.00 0.00 3.01
7111 13882 1.294659 CGCTGCTCTGGTTGGACTTC 61.295 60.000 0.00 0.00 0.00 3.01
7123 14349 4.099266 TGGTTGGACTTCATTTCTTGTTGG 59.901 41.667 0.00 0.00 0.00 3.77
7126 14352 4.277476 TGGACTTCATTTCTTGTTGGTGT 58.723 39.130 0.00 0.00 0.00 4.16
7157 14383 2.154462 AGTTGAAGAGTCCAAATGGCG 58.846 47.619 0.00 0.00 34.44 5.69
7158 14384 1.200020 GTTGAAGAGTCCAAATGGCGG 59.800 52.381 0.00 0.00 34.44 6.13
7159 14385 0.960364 TGAAGAGTCCAAATGGCGGC 60.960 55.000 0.00 0.00 34.44 6.53
7160 14386 0.960364 GAAGAGTCCAAATGGCGGCA 60.960 55.000 16.34 16.34 34.44 5.69
7161 14387 0.539438 AAGAGTCCAAATGGCGGCAA 60.539 50.000 18.31 0.00 34.44 4.52
7162 14388 0.323725 AGAGTCCAAATGGCGGCAAT 60.324 50.000 18.31 4.06 34.44 3.56
7163 14389 0.532115 GAGTCCAAATGGCGGCAATT 59.468 50.000 18.31 12.02 34.44 2.32
7164 14390 0.975887 AGTCCAAATGGCGGCAATTT 59.024 45.000 18.31 9.53 34.44 1.82
7165 14391 1.077915 GTCCAAATGGCGGCAATTTG 58.922 50.000 28.18 28.18 42.24 2.32
7166 14392 0.972134 TCCAAATGGCGGCAATTTGA 59.028 45.000 33.82 22.07 44.30 2.69
7167 14393 1.554160 TCCAAATGGCGGCAATTTGAT 59.446 42.857 33.82 5.74 44.30 2.57
7168 14394 1.666700 CCAAATGGCGGCAATTTGATG 59.333 47.619 33.82 19.79 44.30 3.07
7169 14395 1.062880 CAAATGGCGGCAATTTGATGC 59.937 47.619 30.31 2.77 44.30 3.91
7170 14396 0.538118 AATGGCGGCAATTTGATGCT 59.462 45.000 18.31 0.00 45.68 3.79
7171 14397 0.538118 ATGGCGGCAATTTGATGCTT 59.462 45.000 18.31 0.00 45.68 3.91
7172 14398 1.180907 TGGCGGCAATTTGATGCTTA 58.819 45.000 10.22 0.00 45.68 3.09
7173 14399 1.135141 TGGCGGCAATTTGATGCTTAC 60.135 47.619 10.22 0.00 45.68 2.34
7174 14400 1.134946 GGCGGCAATTTGATGCTTACT 59.865 47.619 3.07 0.00 45.68 2.24
7175 14401 2.417243 GGCGGCAATTTGATGCTTACTT 60.417 45.455 3.07 0.00 45.68 2.24
7176 14402 2.599973 GCGGCAATTTGATGCTTACTTG 59.400 45.455 0.00 0.00 45.68 3.16
7177 14403 3.836949 CGGCAATTTGATGCTTACTTGT 58.163 40.909 0.00 0.00 45.68 3.16
7178 14404 3.609373 CGGCAATTTGATGCTTACTTGTG 59.391 43.478 0.00 0.00 45.68 3.33
7179 14405 4.615682 CGGCAATTTGATGCTTACTTGTGA 60.616 41.667 0.00 0.00 45.68 3.58
7180 14406 5.229423 GGCAATTTGATGCTTACTTGTGAA 58.771 37.500 0.00 0.00 45.68 3.18
7181 14407 5.870978 GGCAATTTGATGCTTACTTGTGAAT 59.129 36.000 0.00 0.00 45.68 2.57
7182 14408 7.035004 GGCAATTTGATGCTTACTTGTGAATA 58.965 34.615 0.00 0.00 45.68 1.75
7183 14409 7.707893 GGCAATTTGATGCTTACTTGTGAATAT 59.292 33.333 0.00 0.00 45.68 1.28
7184 14410 8.537223 GCAATTTGATGCTTACTTGTGAATATG 58.463 33.333 0.00 0.00 43.06 1.78
7185 14411 9.577110 CAATTTGATGCTTACTTGTGAATATGT 57.423 29.630 0.00 0.00 0.00 2.29
7187 14413 8.969121 TTTGATGCTTACTTGTGAATATGTTG 57.031 30.769 0.00 0.00 0.00 3.33
7188 14414 7.686438 TGATGCTTACTTGTGAATATGTTGT 57.314 32.000 0.00 0.00 0.00 3.32
7189 14415 7.529158 TGATGCTTACTTGTGAATATGTTGTG 58.471 34.615 0.00 0.00 0.00 3.33
7190 14416 7.390162 TGATGCTTACTTGTGAATATGTTGTGA 59.610 33.333 0.00 0.00 0.00 3.58
7191 14417 7.686438 TGCTTACTTGTGAATATGTTGTGAT 57.314 32.000 0.00 0.00 0.00 3.06
7192 14418 7.529158 TGCTTACTTGTGAATATGTTGTGATG 58.471 34.615 0.00 0.00 0.00 3.07
7193 14419 7.174772 TGCTTACTTGTGAATATGTTGTGATGT 59.825 33.333 0.00 0.00 0.00 3.06
7194 14420 7.482743 GCTTACTTGTGAATATGTTGTGATGTG 59.517 37.037 0.00 0.00 0.00 3.21
7195 14421 6.882610 ACTTGTGAATATGTTGTGATGTGT 57.117 33.333 0.00 0.00 0.00 3.72
7196 14422 7.275888 ACTTGTGAATATGTTGTGATGTGTT 57.724 32.000 0.00 0.00 0.00 3.32
7197 14423 7.715657 ACTTGTGAATATGTTGTGATGTGTTT 58.284 30.769 0.00 0.00 0.00 2.83
7198 14424 7.648908 ACTTGTGAATATGTTGTGATGTGTTTG 59.351 33.333 0.00 0.00 0.00 2.93
7199 14425 7.269477 TGTGAATATGTTGTGATGTGTTTGA 57.731 32.000 0.00 0.00 0.00 2.69
7200 14426 7.361894 TGTGAATATGTTGTGATGTGTTTGAG 58.638 34.615 0.00 0.00 0.00 3.02
7201 14427 6.803320 GTGAATATGTTGTGATGTGTTTGAGG 59.197 38.462 0.00 0.00 0.00 3.86
7202 14428 6.714356 TGAATATGTTGTGATGTGTTTGAGGA 59.286 34.615 0.00 0.00 0.00 3.71
7203 14429 7.394077 TGAATATGTTGTGATGTGTTTGAGGAT 59.606 33.333 0.00 0.00 0.00 3.24
7204 14430 8.806429 AATATGTTGTGATGTGTTTGAGGATA 57.194 30.769 0.00 0.00 0.00 2.59
7205 14431 5.940192 TGTTGTGATGTGTTTGAGGATAC 57.060 39.130 0.00 0.00 0.00 2.24
7206 14432 5.372373 TGTTGTGATGTGTTTGAGGATACA 58.628 37.500 0.00 0.00 41.41 2.29
7207 14433 5.825151 TGTTGTGATGTGTTTGAGGATACAA 59.175 36.000 0.00 0.00 41.41 2.41
7208 14434 6.489700 TGTTGTGATGTGTTTGAGGATACAAT 59.510 34.615 0.00 0.00 41.41 2.71
7209 14435 7.663493 TGTTGTGATGTGTTTGAGGATACAATA 59.337 33.333 0.00 0.00 41.41 1.90
7210 14436 8.511321 GTTGTGATGTGTTTGAGGATACAATAA 58.489 33.333 0.00 0.00 41.41 1.40
7211 14437 8.806429 TGTGATGTGTTTGAGGATACAATAAT 57.194 30.769 0.00 0.00 41.41 1.28
7212 14438 9.898152 TGTGATGTGTTTGAGGATACAATAATA 57.102 29.630 0.00 0.00 41.41 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.202141 GCATTGGTACATGCATTGGTACAT 60.202 41.667 22.02 10.32 41.21 2.29
1 2 3.130164 GCATTGGTACATGCATTGGTACA 59.870 43.478 22.02 8.85 41.21 2.90
2 3 3.130164 TGCATTGGTACATGCATTGGTAC 59.870 43.478 14.93 15.59 43.71 3.34
3 4 3.359950 TGCATTGGTACATGCATTGGTA 58.640 40.909 14.93 0.00 43.71 3.25
4 5 2.177734 TGCATTGGTACATGCATTGGT 58.822 42.857 14.93 0.00 43.71 3.67
5 6 2.963548 TGCATTGGTACATGCATTGG 57.036 45.000 14.93 0.00 43.71 3.16
10 11 2.687425 TGGTACATGCATTGGTACATGC 59.313 45.455 22.02 10.46 46.08 4.06
12 13 4.341806 CCATTGGTACATGCATTGGTACAT 59.658 41.667 22.02 10.32 41.21 2.29
13 14 3.698539 CCATTGGTACATGCATTGGTACA 59.301 43.478 22.02 8.85 41.21 2.90
14 15 3.490761 GCCATTGGTACATGCATTGGTAC 60.491 47.826 15.59 15.59 39.30 3.34
15 16 2.692557 GCCATTGGTACATGCATTGGTA 59.307 45.455 11.86 3.41 39.30 3.25
16 17 1.481772 GCCATTGGTACATGCATTGGT 59.518 47.619 11.86 4.33 39.30 3.67
17 18 1.758280 AGCCATTGGTACATGCATTGG 59.242 47.619 4.26 1.02 39.30 3.16
18 19 2.427812 TGAGCCATTGGTACATGCATTG 59.572 45.455 4.26 0.00 39.30 2.82
19 20 2.428171 GTGAGCCATTGGTACATGCATT 59.572 45.455 4.26 0.00 39.30 3.56
20 21 2.026641 GTGAGCCATTGGTACATGCAT 58.973 47.619 4.26 0.00 39.30 3.96
21 22 1.004628 AGTGAGCCATTGGTACATGCA 59.995 47.619 4.26 0.00 39.30 3.96
22 23 1.755179 AGTGAGCCATTGGTACATGC 58.245 50.000 4.26 0.00 39.30 4.06
23 24 2.159338 GCAAGTGAGCCATTGGTACATG 60.159 50.000 4.26 6.23 39.30 3.21
24 25 2.094675 GCAAGTGAGCCATTGGTACAT 58.905 47.619 4.26 0.00 39.30 2.29
25 26 1.202867 TGCAAGTGAGCCATTGGTACA 60.203 47.619 4.26 2.39 0.00 2.90
26 27 1.200020 GTGCAAGTGAGCCATTGGTAC 59.800 52.381 4.26 2.00 0.00 3.34
27 28 1.533625 GTGCAAGTGAGCCATTGGTA 58.466 50.000 4.26 0.00 0.00 3.25
28 29 1.518056 CGTGCAAGTGAGCCATTGGT 61.518 55.000 4.26 0.00 0.00 3.67
29 30 1.210931 CGTGCAAGTGAGCCATTGG 59.789 57.895 0.00 0.00 0.00 3.16
30 31 1.443194 GCGTGCAAGTGAGCCATTG 60.443 57.895 0.59 0.00 0.00 2.82
31 32 2.956987 GCGTGCAAGTGAGCCATT 59.043 55.556 0.59 0.00 0.00 3.16
32 33 3.425713 CGCGTGCAAGTGAGCCAT 61.426 61.111 7.47 0.00 0.00 4.40
87 88 1.805945 GCGCTCACCCTAGTCGTTG 60.806 63.158 0.00 0.00 0.00 4.10
89 90 3.812019 CGCGCTCACCCTAGTCGT 61.812 66.667 5.56 0.00 0.00 4.34
94 95 1.525718 TAACACACGCGCTCACCCTA 61.526 55.000 5.73 0.00 0.00 3.53
109 110 4.028131 TCCCTTATCTTTCTCGCCTAACA 58.972 43.478 0.00 0.00 0.00 2.41
122 123 4.810345 ACTCGATTCTCCTTCCCTTATCT 58.190 43.478 0.00 0.00 0.00 1.98
140 141 1.226435 GCAGTAGAGCACGGACTCG 60.226 63.158 1.82 0.00 41.77 4.18
151 152 1.628846 GGTTCCCTTCCTTGCAGTAGA 59.371 52.381 0.00 0.00 0.00 2.59
154 155 0.111253 CTGGTTCCCTTCCTTGCAGT 59.889 55.000 0.00 0.00 0.00 4.40
167 168 1.737793 CACGGGAGCAATTACTGGTTC 59.262 52.381 0.00 0.00 35.35 3.62
171 172 3.535561 AGAATCACGGGAGCAATTACTG 58.464 45.455 0.00 0.00 0.00 2.74
177 178 0.179111 CGCTAGAATCACGGGAGCAA 60.179 55.000 0.00 0.00 32.55 3.91
193 194 0.399949 TGGATGAGAATACCCCCGCT 60.400 55.000 0.00 0.00 0.00 5.52
195 196 2.092646 TGTTTGGATGAGAATACCCCCG 60.093 50.000 0.00 0.00 0.00 5.73
206 207 2.655090 TGCAGACCTTGTTTGGATGA 57.345 45.000 0.00 0.00 0.00 2.92
221 222 2.048970 TGCGCATTTGCCTTGCAG 60.049 55.556 5.66 0.00 40.61 4.41
233 234 6.616017 TCAAAATTTTGATATGTAGTGCGCA 58.384 32.000 26.01 5.66 41.88 6.09
289 290 6.723339 TCTTCTGAAGTTAGCTACTACCTCT 58.277 40.000 16.43 0.00 35.54 3.69
326 327 1.531578 GTCGCCAGTTTCACTTTCCTC 59.468 52.381 0.00 0.00 0.00 3.71
345 349 1.766496 TCAACCTTTCCCTTCTCGTGT 59.234 47.619 0.00 0.00 0.00 4.49
347 351 2.438392 AGTTCAACCTTTCCCTTCTCGT 59.562 45.455 0.00 0.00 0.00 4.18
349 353 4.041815 ACCTAGTTCAACCTTTCCCTTCTC 59.958 45.833 0.00 0.00 0.00 2.87
372 376 3.510388 TGGCACGACAAATGAACAAAA 57.490 38.095 0.00 0.00 0.00 2.44
382 386 1.169661 GGTGGATGTTGGCACGACAA 61.170 55.000 0.00 0.00 0.00 3.18
386 390 3.430862 CGGGTGGATGTTGGCACG 61.431 66.667 0.00 0.00 0.00 5.34
416 420 8.045720 ACTTATATTTAGGAATGAAGGGAGCA 57.954 34.615 0.00 0.00 30.05 4.26
417 421 8.379331 AGACTTATATTTAGGAATGAAGGGAGC 58.621 37.037 0.00 0.00 30.05 4.70
440 444 9.897744 TGATTCATGTGAAATCTTTACAAAGAC 57.102 29.630 6.56 0.00 40.51 3.01
441 445 9.897744 GTGATTCATGTGAAATCTTTACAAAGA 57.102 29.630 6.85 6.85 41.21 2.52
442 446 9.681692 TGTGATTCATGTGAAATCTTTACAAAG 57.318 29.630 0.00 0.00 37.61 2.77
480 484 8.874156 TGGATCTACACTCTAAAATGCATCTAT 58.126 33.333 0.00 0.00 0.00 1.98
481 485 8.250143 TGGATCTACACTCTAAAATGCATCTA 57.750 34.615 0.00 0.00 0.00 1.98
482 486 7.129457 TGGATCTACACTCTAAAATGCATCT 57.871 36.000 0.00 0.00 0.00 2.90
483 487 7.976135 ATGGATCTACACTCTAAAATGCATC 57.024 36.000 0.00 0.00 0.00 3.91
484 488 8.757982 AAATGGATCTACACTCTAAAATGCAT 57.242 30.769 0.00 0.00 0.00 3.96
485 489 9.851686 ATAAATGGATCTACACTCTAAAATGCA 57.148 29.630 0.00 0.00 0.00 3.96
491 495 9.905713 AGCAAAATAAATGGATCTACACTCTAA 57.094 29.630 0.00 0.00 0.00 2.10
492 496 9.547753 GAGCAAAATAAATGGATCTACACTCTA 57.452 33.333 0.00 0.00 0.00 2.43
493 497 7.500559 GGAGCAAAATAAATGGATCTACACTCT 59.499 37.037 0.00 0.00 0.00 3.24
494 498 7.519008 CGGAGCAAAATAAATGGATCTACACTC 60.519 40.741 0.00 0.00 0.00 3.51
495 499 6.260936 CGGAGCAAAATAAATGGATCTACACT 59.739 38.462 0.00 0.00 0.00 3.55
496 500 6.038271 ACGGAGCAAAATAAATGGATCTACAC 59.962 38.462 0.00 0.00 0.00 2.90
497 501 6.119536 ACGGAGCAAAATAAATGGATCTACA 58.880 36.000 0.00 0.00 0.00 2.74
498 502 6.619801 ACGGAGCAAAATAAATGGATCTAC 57.380 37.500 0.00 0.00 0.00 2.59
502 506 9.959721 ACTATATACGGAGCAAAATAAATGGAT 57.040 29.630 0.00 0.00 0.00 3.41
503 507 9.431887 GACTATATACGGAGCAAAATAAATGGA 57.568 33.333 0.00 0.00 0.00 3.41
504 508 9.436957 AGACTATATACGGAGCAAAATAAATGG 57.563 33.333 0.00 0.00 0.00 3.16
540 544 9.582431 CGTTCCTGAATATAAGTCTTTGTAAGA 57.418 33.333 0.00 0.00 34.51 2.10
541 545 8.818057 CCGTTCCTGAATATAAGTCTTTGTAAG 58.182 37.037 0.00 0.00 0.00 2.34
542 546 7.767198 CCCGTTCCTGAATATAAGTCTTTGTAA 59.233 37.037 0.00 0.00 0.00 2.41
543 547 7.270047 CCCGTTCCTGAATATAAGTCTTTGTA 58.730 38.462 0.00 0.00 0.00 2.41
544 548 6.113411 CCCGTTCCTGAATATAAGTCTTTGT 58.887 40.000 0.00 0.00 0.00 2.83
545 549 5.527582 CCCCGTTCCTGAATATAAGTCTTTG 59.472 44.000 0.00 0.00 0.00 2.77
546 550 5.427481 TCCCCGTTCCTGAATATAAGTCTTT 59.573 40.000 0.00 0.00 0.00 2.52
547 551 4.966805 TCCCCGTTCCTGAATATAAGTCTT 59.033 41.667 0.00 0.00 0.00 3.01
548 552 4.553678 TCCCCGTTCCTGAATATAAGTCT 58.446 43.478 0.00 0.00 0.00 3.24
549 553 4.344390 ACTCCCCGTTCCTGAATATAAGTC 59.656 45.833 0.00 0.00 0.00 3.01
550 554 4.296056 ACTCCCCGTTCCTGAATATAAGT 58.704 43.478 0.00 0.00 0.00 2.24
551 555 4.957684 ACTCCCCGTTCCTGAATATAAG 57.042 45.455 0.00 0.00 0.00 1.73
552 556 7.897030 TGATATACTCCCCGTTCCTGAATATAA 59.103 37.037 0.00 0.00 0.00 0.98
553 557 7.341256 GTGATATACTCCCCGTTCCTGAATATA 59.659 40.741 0.00 0.00 0.00 0.86
554 558 6.154706 GTGATATACTCCCCGTTCCTGAATAT 59.845 42.308 0.00 0.00 0.00 1.28
555 559 5.479375 GTGATATACTCCCCGTTCCTGAATA 59.521 44.000 0.00 0.00 0.00 1.75
556 560 4.283722 GTGATATACTCCCCGTTCCTGAAT 59.716 45.833 0.00 0.00 0.00 2.57
557 561 3.640029 GTGATATACTCCCCGTTCCTGAA 59.360 47.826 0.00 0.00 0.00 3.02
558 562 3.228453 GTGATATACTCCCCGTTCCTGA 58.772 50.000 0.00 0.00 0.00 3.86
559 563 2.963101 TGTGATATACTCCCCGTTCCTG 59.037 50.000 0.00 0.00 0.00 3.86
560 564 3.323774 TGTGATATACTCCCCGTTCCT 57.676 47.619 0.00 0.00 0.00 3.36
561 565 3.802675 GCTTGTGATATACTCCCCGTTCC 60.803 52.174 0.00 0.00 0.00 3.62
562 566 3.069729 AGCTTGTGATATACTCCCCGTTC 59.930 47.826 0.00 0.00 0.00 3.95
563 567 3.039011 AGCTTGTGATATACTCCCCGTT 58.961 45.455 0.00 0.00 0.00 4.44
564 568 2.679082 AGCTTGTGATATACTCCCCGT 58.321 47.619 0.00 0.00 0.00 5.28
565 569 3.193691 CCTAGCTTGTGATATACTCCCCG 59.806 52.174 0.00 0.00 0.00 5.73
566 570 4.417437 TCCTAGCTTGTGATATACTCCCC 58.583 47.826 0.00 0.00 0.00 4.81
567 571 4.081917 GCTCCTAGCTTGTGATATACTCCC 60.082 50.000 0.00 0.00 38.45 4.30
568 572 4.081917 GGCTCCTAGCTTGTGATATACTCC 60.082 50.000 0.00 0.00 41.99 3.85
569 573 4.770010 AGGCTCCTAGCTTGTGATATACTC 59.230 45.833 0.00 0.00 41.99 2.59
570 574 4.746466 AGGCTCCTAGCTTGTGATATACT 58.254 43.478 0.00 0.00 41.99 2.12
571 575 4.380023 CGAGGCTCCTAGCTTGTGATATAC 60.380 50.000 9.32 0.00 41.99 1.47
1551 3519 6.726258 TTAATGCATAATAGCGGATCACAG 57.274 37.500 0.00 0.00 37.31 3.66
1602 4201 0.802494 GTAATGCACACGACCCCTTG 59.198 55.000 0.00 0.00 0.00 3.61
1811 4412 5.412286 CACATGTTGAATCATGGTGTACTGA 59.588 40.000 0.00 0.00 46.39 3.41
1915 4516 7.531857 TCCAGCCATTTACAAGAAAACAATA 57.468 32.000 0.00 0.00 0.00 1.90
1916 4517 6.418057 TCCAGCCATTTACAAGAAAACAAT 57.582 33.333 0.00 0.00 0.00 2.71
1952 4557 8.942338 AGTTTGTTCTAAAGGGAAAAACATTC 57.058 30.769 0.00 0.00 33.75 2.67
2177 4782 1.398390 CGGTTATCCTCACAAGCTTGC 59.602 52.381 26.27 6.38 0.00 4.01
2243 4848 1.280133 CTCACCACATCCATCCACACT 59.720 52.381 0.00 0.00 0.00 3.55
2245 4850 1.361204 ACTCACCACATCCATCCACA 58.639 50.000 0.00 0.00 0.00 4.17
2321 4926 3.738429 CTCGTCATGCGGGATGGCA 62.738 63.158 14.45 0.00 45.67 4.92
2492 5216 2.269241 GCAGAGGGCACAGGTACC 59.731 66.667 2.73 2.73 43.97 3.34
2906 5660 4.319177 GAAGACTTACTGGCAATCTGTGT 58.681 43.478 0.00 0.00 0.00 3.72
3184 5994 6.403636 GGTGAATCACAAATAGCAACCTACAG 60.404 42.308 15.86 0.00 35.86 2.74
3261 6075 4.600692 TGCACTTTCAGTAAGAGCTACA 57.399 40.909 9.90 0.00 46.64 2.74
3633 6451 1.386412 CGGTCATTGCGAATTTGTTGC 59.614 47.619 0.00 0.00 37.12 4.17
3657 6475 1.200020 GAAGGGGTTGCATCGTTGAAG 59.800 52.381 0.00 0.00 0.00 3.02
3665 6483 0.039618 ATTGGTCGAAGGGGTTGCAT 59.960 50.000 0.00 0.00 0.00 3.96
3666 6484 0.178975 AATTGGTCGAAGGGGTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
3815 6633 6.613153 AAGATAGAGTTTGTTACAGCCTCT 57.387 37.500 16.26 16.26 36.52 3.69
3916 6735 4.014569 TGATGAACCACAAAGATTCGGA 57.985 40.909 0.00 0.00 0.00 4.55
4353 8413 1.623279 CCGGGTAAAGGAGGAGGGTTA 60.623 57.143 0.00 0.00 0.00 2.85
4424 8484 2.779755 ACATGGCATAGTCGAAACCA 57.220 45.000 0.00 0.00 34.28 3.67
4447 8507 9.532697 CAAAATGTATAAGCAAATGAAAGCAAC 57.467 29.630 0.00 0.00 0.00 4.17
4514 8574 4.911514 ACACCTTGGTCAACATAACAAC 57.088 40.909 0.00 0.00 0.00 3.32
4523 8583 8.380099 AGAGTATTATTACAACACCTTGGTCAA 58.620 33.333 0.00 0.00 0.00 3.18
4923 8998 9.216117 GGTTAGTTCAGTCTTAATTCAAAGCTA 57.784 33.333 0.00 0.00 0.00 3.32
4963 9038 5.014123 ACTCCCTCAATCCAAATAAGTGTCA 59.986 40.000 0.00 0.00 0.00 3.58
5138 11573 1.734465 GCATGAGTGGGAAAGAAGTCG 59.266 52.381 0.00 0.00 0.00 4.18
5240 11676 3.115390 ACATGGTCAGTAAGCTGGGTAT 58.885 45.455 0.00 0.00 42.78 2.73
5298 11735 1.133025 CTCCCACATCAAAATGCCGAC 59.867 52.381 0.00 0.00 36.26 4.79
5399 11839 1.062525 GCCATGAATTCGCGACACC 59.937 57.895 9.15 0.32 0.00 4.16
5653 12094 1.135489 GCTCCTGTAACGACGACATCA 60.135 52.381 0.00 0.00 0.00 3.07
5772 12216 4.270008 CCAAGAGGAATCGGTAAACCAAT 58.730 43.478 0.00 0.00 36.89 3.16
5780 12224 0.613777 GACACCCAAGAGGAATCGGT 59.386 55.000 0.00 0.00 39.89 4.69
6194 12663 3.002791 CGCTAGTTCTTCCATTTGCTCA 58.997 45.455 0.00 0.00 0.00 4.26
6302 12776 8.680903 GCCTTGGAATGAGAATTATACATATGG 58.319 37.037 7.80 0.00 0.00 2.74
6322 12918 3.891422 TGGAATTTATGCAAGCCTTGG 57.109 42.857 6.57 0.00 0.00 3.61
6383 12986 5.098211 GCAAACTCTGGAATGATTTACAGC 58.902 41.667 6.10 0.00 42.66 4.40
6422 13025 2.166829 CATGAATCCCAACGGTTTCCA 58.833 47.619 0.00 0.00 37.14 3.53
6577 13210 8.822652 AAGAAAATATCAACAAAGAAAGCTGG 57.177 30.769 0.00 0.00 0.00 4.85
6675 13314 4.034510 GGTGCAGCTAAAGTTACAGCTATG 59.965 45.833 9.07 3.81 46.26 2.23
6823 13464 6.599638 ACTCCTTTTTACACTCAGCCATATTC 59.400 38.462 0.00 0.00 0.00 1.75
6824 13465 6.485171 ACTCCTTTTTACACTCAGCCATATT 58.515 36.000 0.00 0.00 0.00 1.28
6863 13506 5.156355 GTGCAAATGTCACACAAATCCTAG 58.844 41.667 0.00 0.00 34.43 3.02
6865 13508 3.384146 TGTGCAAATGTCACACAAATCCT 59.616 39.130 0.00 0.00 41.11 3.24
6916 13562 9.221775 GTAAATAGTAATTACATGCACTTGTGC 57.778 33.333 17.65 17.73 34.22 4.57
6976 13707 9.825109 GCCTATCTTTTAGATCACTCTTTAGTT 57.175 33.333 0.00 0.00 36.20 2.24
7105 13876 4.338118 TGACACCAACAAGAAATGAAGTCC 59.662 41.667 0.00 0.00 0.00 3.85
7106 13877 5.163663 TGTGACACCAACAAGAAATGAAGTC 60.164 40.000 2.45 0.00 0.00 3.01
7108 13879 5.247507 TGTGACACCAACAAGAAATGAAG 57.752 39.130 2.45 0.00 0.00 3.02
7109 13880 5.651387 TTGTGACACCAACAAGAAATGAA 57.349 34.783 2.45 0.00 0.00 2.57
7110 13881 5.359292 TGATTGTGACACCAACAAGAAATGA 59.641 36.000 2.45 0.00 0.00 2.57
7111 13882 5.590145 TGATTGTGACACCAACAAGAAATG 58.410 37.500 2.45 0.00 0.00 2.32
7123 14349 4.380531 TCTTCAACTCCTGATTGTGACAC 58.619 43.478 0.00 0.00 32.78 3.67
7126 14352 4.262635 GGACTCTTCAACTCCTGATTGTGA 60.263 45.833 0.00 0.00 32.78 3.58
7157 14383 4.808558 TCACAAGTAAGCATCAAATTGCC 58.191 39.130 0.00 0.00 43.83 4.52
7158 14384 6.956299 ATTCACAAGTAAGCATCAAATTGC 57.044 33.333 0.00 0.00 43.09 3.56
7159 14385 9.577110 ACATATTCACAAGTAAGCATCAAATTG 57.423 29.630 0.00 0.00 0.00 2.32
7161 14387 9.577110 CAACATATTCACAAGTAAGCATCAAAT 57.423 29.630 0.00 0.00 0.00 2.32
7162 14388 8.575589 ACAACATATTCACAAGTAAGCATCAAA 58.424 29.630 0.00 0.00 0.00 2.69
7163 14389 8.022550 CACAACATATTCACAAGTAAGCATCAA 58.977 33.333 0.00 0.00 0.00 2.57
7164 14390 7.390162 TCACAACATATTCACAAGTAAGCATCA 59.610 33.333 0.00 0.00 0.00 3.07
7165 14391 7.751732 TCACAACATATTCACAAGTAAGCATC 58.248 34.615 0.00 0.00 0.00 3.91
7166 14392 7.686438 TCACAACATATTCACAAGTAAGCAT 57.314 32.000 0.00 0.00 0.00 3.79
7167 14393 7.174772 ACATCACAACATATTCACAAGTAAGCA 59.825 33.333 0.00 0.00 0.00 3.91
7168 14394 7.482743 CACATCACAACATATTCACAAGTAAGC 59.517 37.037 0.00 0.00 0.00 3.09
7169 14395 8.506437 ACACATCACAACATATTCACAAGTAAG 58.494 33.333 0.00 0.00 0.00 2.34
7170 14396 8.389779 ACACATCACAACATATTCACAAGTAA 57.610 30.769 0.00 0.00 0.00 2.24
7171 14397 7.977789 ACACATCACAACATATTCACAAGTA 57.022 32.000 0.00 0.00 0.00 2.24
7172 14398 6.882610 ACACATCACAACATATTCACAAGT 57.117 33.333 0.00 0.00 0.00 3.16
7173 14399 7.861872 TCAAACACATCACAACATATTCACAAG 59.138 33.333 0.00 0.00 0.00 3.16
7174 14400 7.710896 TCAAACACATCACAACATATTCACAA 58.289 30.769 0.00 0.00 0.00 3.33
7175 14401 7.269477 TCAAACACATCACAACATATTCACA 57.731 32.000 0.00 0.00 0.00 3.58
7176 14402 6.803320 CCTCAAACACATCACAACATATTCAC 59.197 38.462 0.00 0.00 0.00 3.18
7177 14403 6.714356 TCCTCAAACACATCACAACATATTCA 59.286 34.615 0.00 0.00 0.00 2.57
7178 14404 7.144722 TCCTCAAACACATCACAACATATTC 57.855 36.000 0.00 0.00 0.00 1.75
7179 14405 7.707624 ATCCTCAAACACATCACAACATATT 57.292 32.000 0.00 0.00 0.00 1.28
7180 14406 7.828717 TGTATCCTCAAACACATCACAACATAT 59.171 33.333 0.00 0.00 0.00 1.78
7181 14407 7.164803 TGTATCCTCAAACACATCACAACATA 58.835 34.615 0.00 0.00 0.00 2.29
7182 14408 6.003326 TGTATCCTCAAACACATCACAACAT 58.997 36.000 0.00 0.00 0.00 2.71
7183 14409 5.372373 TGTATCCTCAAACACATCACAACA 58.628 37.500 0.00 0.00 0.00 3.33
7184 14410 5.940192 TGTATCCTCAAACACATCACAAC 57.060 39.130 0.00 0.00 0.00 3.32
7185 14411 8.628630 TTATTGTATCCTCAAACACATCACAA 57.371 30.769 0.00 0.00 0.00 3.33
7186 14412 8.806429 ATTATTGTATCCTCAAACACATCACA 57.194 30.769 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.