Multiple sequence alignment - TraesCS4D01G113600

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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 TraesCS4D01G113600 chr4D 100.000 5593 0 0 1 5593 94263150 94257558 0.000000e+00 10329.0
1 TraesCS4D01G113600 chr4D 95.161 496 22 2 5100 5593 40798946 40799441 0.000000e+00 782.0
2 TraesCS4D01G113600 chr4D 81.421 732 119 12 2856 3580 93845566 93844845 2.900000e-162 582.0
3 TraesCS4D01G113600 chr4D 81.116 699 91 31 911 1578 93848170 93847482 6.420000e-144 521.0
4 TraesCS4D01G113600 chr4D 82.609 322 34 10 1911 2221 93846406 93846096 1.190000e-66 265.0
5 TraesCS4D01G113600 chr4D 84.556 259 39 1 2472 2729 93845882 93845624 7.190000e-64 255.0
6 TraesCS4D01G113600 chr4D 97.794 136 3 0 1785 1920 117644077 117643942 9.370000e-58 235.0
7 TraesCS4D01G113600 chr4B 94.564 2925 103 22 1912 4797 132855582 132852675 0.000000e+00 4470.0
8 TraesCS4D01G113600 chr4B 95.357 1120 44 5 465 1582 132856799 132855686 0.000000e+00 1773.0
9 TraesCS4D01G113600 chr4B 96.312 461 14 2 10 470 132858725 132858268 0.000000e+00 754.0
10 TraesCS4D01G113600 chr4B 81.700 694 91 27 911 1575 132338508 132337822 3.810000e-151 545.0
11 TraesCS4D01G113600 chr4B 89.643 280 13 5 4805 5072 132852623 132852348 5.370000e-90 342.0
12 TraesCS4D01G113600 chr4B 83.386 319 31 10 1911 2218 132336723 132336416 5.520000e-70 276.0
13 TraesCS4D01G113600 chr4B 85.328 259 37 1 2472 2729 132336195 132335937 3.320000e-67 267.0
14 TraesCS4D01G113600 chr4B 94.545 110 6 0 1679 1788 132855690 132855581 2.680000e-38 171.0
15 TraesCS4D01G113600 chr4A 94.505 2730 74 16 1912 4596 486640667 486643365 0.000000e+00 4141.0
16 TraesCS4D01G113600 chr4A 94.599 1796 58 16 1 1788 486638904 486640668 0.000000e+00 2743.0
17 TraesCS4D01G113600 chr4A 81.316 760 121 13 2830 3580 487864666 487865413 1.040000e-166 597.0
18 TraesCS4D01G113600 chr4A 81.530 693 94 26 911 1575 487862058 487862744 1.770000e-149 540.0
19 TraesCS4D01G113600 chr4A 89.437 284 14 7 4805 5072 486643963 486644246 1.490000e-90 344.0
20 TraesCS4D01G113600 chr4A 97.605 167 4 0 4637 4803 486643749 486643915 2.550000e-73 287.0
21 TraesCS4D01G113600 chr4A 82.663 323 32 11 1911 2221 487863862 487864172 1.190000e-66 265.0
22 TraesCS4D01G113600 chr4A 84.556 259 39 1 2472 2729 487864382 487864640 7.190000e-64 255.0
23 TraesCS4D01G113600 chr4A 95.495 111 4 1 2248 2358 101750483 101750374 5.760000e-40 176.0
24 TraesCS4D01G113600 chr4A 94.340 106 5 1 2253 2358 37306866 37306970 1.610000e-35 161.0
25 TraesCS4D01G113600 chr4A 94.340 106 5 1 2253 2358 150653313 150653417 1.610000e-35 161.0
26 TraesCS4D01G113600 chr2D 95.758 495 21 0 5099 5593 5110354 5109860 0.000000e+00 798.0
27 TraesCS4D01G113600 chr2D 86.521 549 66 7 2891 3434 433506432 433506977 1.040000e-166 597.0
28 TraesCS4D01G113600 chr2D 78.315 724 96 30 3925 4607 433507924 433508627 1.450000e-110 411.0
29 TraesCS4D01G113600 chr2D 87.440 207 23 2 2478 2683 433505984 433506188 9.370000e-58 235.0
30 TraesCS4D01G113600 chr2D 98.473 131 2 0 1784 1914 561025751 561025621 1.210000e-56 231.0
31 TraesCS4D01G113600 chr2D 79.503 322 41 15 1918 2219 433505192 433505508 7.340000e-49 206.0
32 TraesCS4D01G113600 chr7D 95.010 501 23 2 5095 5593 568366002 568365502 0.000000e+00 785.0
33 TraesCS4D01G113600 chr7D 93.478 46 2 1 2728 2772 101475459 101475414 3.620000e-07 67.6
34 TraesCS4D01G113600 chr6D 94.960 496 23 2 5100 5593 55902835 55902340 0.000000e+00 776.0
35 TraesCS4D01G113600 chr6D 92.810 153 8 3 1787 1938 54003174 54003324 9.430000e-53 219.0
36 TraesCS4D01G113600 chr2A 94.970 497 21 3 5099 5593 136642333 136642827 0.000000e+00 776.0
37 TraesCS4D01G113600 chr2A 86.314 548 68 6 2891 3434 553487089 553486545 1.740000e-164 590.0
38 TraesCS4D01G113600 chr2A 78.363 721 95 35 3928 4607 553485543 553484843 1.450000e-110 411.0
39 TraesCS4D01G113600 chr2A 87.755 196 21 2 2489 2683 553487385 553487192 5.640000e-55 226.0
40 TraesCS4D01G113600 chr2A 80.124 322 39 13 1918 2219 553488189 553487873 3.390000e-52 217.0
41 TraesCS4D01G113600 chr5D 94.578 498 25 2 5098 5593 254594518 254594021 0.000000e+00 769.0
42 TraesCS4D01G113600 chr5D 94.578 498 24 3 5099 5593 483581771 483581274 0.000000e+00 767.0
43 TraesCS4D01G113600 chr5D 96.117 103 3 1 2256 2358 509138381 509138280 3.470000e-37 167.0
44 TraesCS4D01G113600 chr5D 95.161 62 2 1 2728 2788 500865601 500865662 4.610000e-16 97.1
45 TraesCS4D01G113600 chr1D 94.433 503 22 3 5096 5593 458720952 458720451 0.000000e+00 769.0
46 TraesCS4D01G113600 chr3D 94.223 502 26 3 5095 5593 1835397 1835898 0.000000e+00 763.0
47 TraesCS4D01G113600 chr3D 92.683 164 6 4 1782 1940 283321256 283321094 1.210000e-56 231.0
48 TraesCS4D01G113600 chr2B 88.560 507 53 5 2891 3395 511276313 511276816 1.330000e-170 610.0
49 TraesCS4D01G113600 chr2B 76.591 880 128 41 3775 4607 511277632 511278480 4.030000e-111 412.0
50 TraesCS4D01G113600 chr2B 84.576 389 44 10 881 1254 511273348 511273735 6.840000e-99 372.0
51 TraesCS4D01G113600 chr2B 96.403 139 4 1 1783 1920 25022321 25022459 1.570000e-55 228.0
52 TraesCS4D01G113600 chr2B 86.538 208 23 3 2477 2683 511276008 511276211 2.030000e-54 224.0
53 TraesCS4D01G113600 chr2B 83.613 238 32 6 1917 2151 511275147 511275380 3.390000e-52 217.0
54 TraesCS4D01G113600 chr3B 99.248 133 1 0 1782 1914 741865981 741865849 2.010000e-59 241.0
55 TraesCS4D01G113600 chr3B 93.878 147 7 2 1775 1920 749091031 749090886 2.620000e-53 220.0
56 TraesCS4D01G113600 chr3B 89.516 124 8 5 2246 2366 698611526 698611405 9.700000e-33 152.0
57 TraesCS4D01G113600 chr7A 98.496 133 2 0 1782 1914 15084525 15084393 9.370000e-58 235.0
58 TraesCS4D01G113600 chr6B 94.595 148 6 2 1785 1932 582866939 582867084 1.570000e-55 228.0
59 TraesCS4D01G113600 chr1B 94.340 106 4 2 2253 2358 368410400 368410503 1.610000e-35 161.0
60 TraesCS4D01G113600 chr6A 90.000 120 9 3 2239 2358 214179497 214179613 9.700000e-33 152.0
61 TraesCS4D01G113600 chr5A 100.000 28 0 0 2743 2770 413415565 413415538 1.000000e-02 52.8


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 TraesCS4D01G113600 chr4D 94257558 94263150 5592 True 10329.000000 10329 100.000000 1 5593 1 chr4D.!!$R1 5592
1 TraesCS4D01G113600 chr4D 93844845 93848170 3325 True 405.750000 582 82.425500 911 3580 4 chr4D.!!$R3 2669
2 TraesCS4D01G113600 chr4B 132852348 132858725 6377 True 1502.000000 4470 94.084200 10 5072 5 chr4B.!!$R2 5062
3 TraesCS4D01G113600 chr4B 132335937 132338508 2571 True 362.666667 545 83.471333 911 2729 3 chr4B.!!$R1 1818
4 TraesCS4D01G113600 chr4A 486638904 486644246 5342 False 1878.750000 4141 94.036500 1 5072 4 chr4A.!!$F3 5071
5 TraesCS4D01G113600 chr4A 487862058 487865413 3355 False 414.250000 597 82.516250 911 3580 4 chr4A.!!$F4 2669
6 TraesCS4D01G113600 chr2D 433505192 433508627 3435 False 362.250000 597 82.944750 1918 4607 4 chr2D.!!$F1 2689
7 TraesCS4D01G113600 chr7D 568365502 568366002 500 True 785.000000 785 95.010000 5095 5593 1 chr7D.!!$R2 498
8 TraesCS4D01G113600 chr2A 553484843 553488189 3346 True 361.000000 590 83.139000 1918 4607 4 chr2A.!!$R1 2689
9 TraesCS4D01G113600 chr1D 458720451 458720952 501 True 769.000000 769 94.433000 5096 5593 1 chr1D.!!$R1 497
10 TraesCS4D01G113600 chr3D 1835397 1835898 501 False 763.000000 763 94.223000 5095 5593 1 chr3D.!!$F1 498
11 TraesCS4D01G113600 chr2B 511273348 511278480 5132 False 367.000000 610 83.975600 881 4607 5 chr2B.!!$F2 3726

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
239 244 0.179189 GTGCGATTGTGCCTGCTAAC 60.179 55.000 0.0 0.0 0.00 2.34 F
1640 4285 0.321919 GGCCACTCATGCTTGTCAGA 60.322 55.000 0.0 0.0 0.00 3.27 F
1807 4465 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.0 0.0 0.00 2.17 F
3545 6905 0.879765 GCTGTTGCTTGATGTGCTCT 59.120 50.000 0.0 0.0 36.03 4.09 F
4373 8288 1.764723 CATGGAGTGGAGATGGCTGTA 59.235 52.381 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 4446 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.0 0.00 4.30 R
3034 6371 1.774639 CAAGCGCATTTTGAGCAACT 58.225 45.000 11.47 0.0 45.82 3.16 R
3595 7376 3.347216 GTTCACATGGTATGCTCCTGTT 58.653 45.455 0.00 0.0 0.00 3.16 R
4432 8380 0.099082 GTTCTCTGCCGTCCGAGTAG 59.901 60.000 0.00 0.0 0.00 2.57 R
5224 9583 0.112995 ATGAATGCCCACACACCAGT 59.887 50.000 0.00 0.0 0.00 4.00 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
179 184 7.306866 CCGATTTGTTTATCTTCCGAGATCTTC 60.307 40.741 0.00 0.00 41.68 2.87
180 185 7.436673 CGATTTGTTTATCTTCCGAGATCTTCT 59.563 37.037 0.00 0.00 41.68 2.85
181 186 9.103861 GATTTGTTTATCTTCCGAGATCTTCTT 57.896 33.333 0.00 0.00 41.68 2.52
239 244 0.179189 GTGCGATTGTGCCTGCTAAC 60.179 55.000 0.00 0.00 0.00 2.34
343 348 3.520290 ACTCGCTTTAATCATGACGGA 57.480 42.857 0.00 0.00 0.00 4.69
379 384 0.668096 AATCGTAACCGCGTGCTCAA 60.668 50.000 4.92 0.00 0.00 3.02
450 455 7.722949 AGCCAAATTTCAAGAGGAATTCATA 57.277 32.000 7.93 0.00 34.91 2.15
600 2079 5.886992 TGTTTCATGAATGATCTGCATGTC 58.113 37.500 9.40 11.72 40.12 3.06
602 2081 2.546789 TCATGAATGATCTGCATGTCGC 59.453 45.455 16.81 0.00 40.12 5.19
729 2208 0.682209 ATGATGGGCAGGCAGTTCAC 60.682 55.000 0.00 0.00 0.00 3.18
790 2269 5.928839 CCTTCATCGTTATAATCTGGGACTG 59.071 44.000 0.00 0.00 0.00 3.51
949 2437 4.265893 TGTTAAGTTTGCAGAGGTGACAA 58.734 39.130 0.00 0.00 0.00 3.18
964 2457 9.853555 CAGAGGTGACAATATATATCTCACTTC 57.146 37.037 22.79 22.79 37.92 3.01
1339 2853 7.254227 TGTTTTCATGTTTGTGTAGACTACC 57.746 36.000 10.14 2.63 0.00 3.18
1608 4253 3.265737 AGCCCCAGTGTTGTACATTGATA 59.734 43.478 0.00 0.00 37.96 2.15
1640 4285 0.321919 GGCCACTCATGCTTGTCAGA 60.322 55.000 0.00 0.00 0.00 3.27
1677 4322 2.504175 GCAACCTAGGGTACATCCTTGA 59.496 50.000 14.81 0.00 38.30 3.02
1783 4441 7.276658 TGTTTATGAATCGCTAAATGTCCCTA 58.723 34.615 0.00 0.00 0.00 3.53
1789 4447 8.362464 TGAATCGCTAAATGTCCCTATATACT 57.638 34.615 0.00 0.00 0.00 2.12
1790 4448 8.467598 TGAATCGCTAAATGTCCCTATATACTC 58.532 37.037 0.00 0.00 0.00 2.59
1791 4449 6.770746 TCGCTAAATGTCCCTATATACTCC 57.229 41.667 0.00 0.00 0.00 3.85
1792 4450 5.655532 TCGCTAAATGTCCCTATATACTCCC 59.344 44.000 0.00 0.00 0.00 4.30
1793 4451 5.657302 CGCTAAATGTCCCTATATACTCCCT 59.343 44.000 0.00 0.00 0.00 4.20
1794 4452 6.183360 CGCTAAATGTCCCTATATACTCCCTC 60.183 46.154 0.00 0.00 0.00 4.30
1795 4453 6.098552 GCTAAATGTCCCTATATACTCCCTCC 59.901 46.154 0.00 0.00 0.00 4.30
1796 4454 3.733883 TGTCCCTATATACTCCCTCCG 57.266 52.381 0.00 0.00 0.00 4.63
1797 4455 2.991713 TGTCCCTATATACTCCCTCCGT 59.008 50.000 0.00 0.00 0.00 4.69
1798 4456 3.009916 TGTCCCTATATACTCCCTCCGTC 59.990 52.174 0.00 0.00 0.00 4.79
1799 4457 2.579860 TCCCTATATACTCCCTCCGTCC 59.420 54.545 0.00 0.00 0.00 4.79
1800 4458 2.357986 CCCTATATACTCCCTCCGTCCC 60.358 59.091 0.00 0.00 0.00 4.46
1801 4459 2.310945 CCTATATACTCCCTCCGTCCCA 59.689 54.545 0.00 0.00 0.00 4.37
1802 4460 3.245514 CCTATATACTCCCTCCGTCCCAA 60.246 52.174 0.00 0.00 0.00 4.12
1803 4461 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
1804 4462 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1805 4463 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1806 4464 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1807 4465 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1808 4466 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1809 4467 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1810 4468 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1811 4469 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1812 4470 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1813 4471 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1814 4472 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1815 4473 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1816 4474 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1817 4475 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1818 4476 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1819 4477 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1820 4478 7.244192 CGTCCCAAAATTCTTGTCTTAGATTC 58.756 38.462 0.00 0.00 0.00 2.52
1821 4479 7.244192 GTCCCAAAATTCTTGTCTTAGATTCG 58.756 38.462 0.00 0.00 0.00 3.34
1822 4480 6.940298 TCCCAAAATTCTTGTCTTAGATTCGT 59.060 34.615 0.00 0.00 0.00 3.85
1823 4481 7.119262 TCCCAAAATTCTTGTCTTAGATTCGTC 59.881 37.037 0.00 0.00 0.00 4.20
1824 4482 7.119846 CCCAAAATTCTTGTCTTAGATTCGTCT 59.880 37.037 0.00 0.00 0.00 4.18
1825 4483 9.151471 CCAAAATTCTTGTCTTAGATTCGTCTA 57.849 33.333 0.00 0.00 0.00 2.59
1831 4489 8.074474 TCTTGTCTTAGATTCGTCTAGATACG 57.926 38.462 0.00 0.00 44.19 3.06
1832 4490 6.782298 TGTCTTAGATTCGTCTAGATACGG 57.218 41.667 0.00 0.00 43.05 4.02
1833 4491 6.519382 TGTCTTAGATTCGTCTAGATACGGA 58.481 40.000 0.00 0.00 43.05 4.69
1834 4492 7.160049 TGTCTTAGATTCGTCTAGATACGGAT 58.840 38.462 0.00 0.00 43.73 4.18
1835 4493 7.117956 TGTCTTAGATTCGTCTAGATACGGATG 59.882 40.741 2.64 0.00 41.14 3.51
1836 4494 7.118101 GTCTTAGATTCGTCTAGATACGGATGT 59.882 40.741 2.64 1.92 41.14 3.06
1837 4495 8.309656 TCTTAGATTCGTCTAGATACGGATGTA 58.690 37.037 2.64 1.02 41.14 2.29
1838 4496 9.100554 CTTAGATTCGTCTAGATACGGATGTAT 57.899 37.037 2.64 0.00 41.14 2.29
1854 4512 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
1855 4513 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
1856 4514 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
1857 4515 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
1867 4525 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
1868 4526 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
1869 4527 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
1870 4528 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
1871 4529 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
1872 4530 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
1873 4531 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
1874 4532 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
1875 4533 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
1876 4534 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
1877 4535 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
1878 4536 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
1879 4537 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
1880 4538 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
1881 4539 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
1888 4546 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
1889 4547 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
1891 4549 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
1892 4550 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
1900 4558 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1901 4559 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1902 4560 9.093458 ACAAATCTAAGACAAGAATTTTGGGAT 57.907 29.630 0.00 0.00 33.04 3.85
1903 4561 9.362539 CAAATCTAAGACAAGAATTTTGGGATG 57.637 33.333 5.68 0.00 28.49 3.51
1904 4562 7.651027 ATCTAAGACAAGAATTTTGGGATGG 57.349 36.000 5.68 0.00 0.00 3.51
1905 4563 6.789268 TCTAAGACAAGAATTTTGGGATGGA 58.211 36.000 5.68 0.00 0.00 3.41
1906 4564 5.990120 AAGACAAGAATTTTGGGATGGAG 57.010 39.130 5.68 0.00 0.00 3.86
1907 4565 4.347607 AGACAAGAATTTTGGGATGGAGG 58.652 43.478 5.68 0.00 0.00 4.30
1908 4566 3.444029 ACAAGAATTTTGGGATGGAGGG 58.556 45.455 5.68 0.00 0.00 4.30
1909 4567 3.077391 ACAAGAATTTTGGGATGGAGGGA 59.923 43.478 5.68 0.00 0.00 4.20
1910 4568 3.677156 AGAATTTTGGGATGGAGGGAG 57.323 47.619 0.00 0.00 0.00 4.30
1911 4569 2.929043 AGAATTTTGGGATGGAGGGAGT 59.071 45.455 0.00 0.00 0.00 3.85
1912 4570 4.119155 AGAATTTTGGGATGGAGGGAGTA 58.881 43.478 0.00 0.00 0.00 2.59
2438 5461 6.434018 GCAGAAGAGATATGCAGTCTTTTT 57.566 37.500 5.93 4.67 45.64 1.94
2496 5659 5.295787 TGCTCGTTGTAAGTTCTCAATGTTT 59.704 36.000 10.59 0.00 33.78 2.83
2731 6038 4.461198 CTTGTTTCCCCACACTTCTACTT 58.539 43.478 0.00 0.00 0.00 2.24
2759 6067 7.514721 TCCTTCCCATATATAAGAGCGTTTTT 58.485 34.615 0.00 0.00 0.00 1.94
2760 6068 7.444183 TCCTTCCCATATATAAGAGCGTTTTTG 59.556 37.037 0.00 0.00 0.00 2.44
2761 6069 7.444183 CCTTCCCATATATAAGAGCGTTTTTGA 59.556 37.037 0.00 0.00 0.00 2.69
2762 6070 7.724305 TCCCATATATAAGAGCGTTTTTGAC 57.276 36.000 0.00 0.00 0.00 3.18
2763 6071 7.276658 TCCCATATATAAGAGCGTTTTTGACA 58.723 34.615 0.00 0.00 0.00 3.58
2764 6072 7.225931 TCCCATATATAAGAGCGTTTTTGACAC 59.774 37.037 0.00 0.00 0.00 3.67
2765 6073 7.226720 CCCATATATAAGAGCGTTTTTGACACT 59.773 37.037 0.00 0.00 0.00 3.55
2766 6074 9.256477 CCATATATAAGAGCGTTTTTGACACTA 57.744 33.333 0.00 0.00 0.00 2.74
2769 6077 4.795970 AAGAGCGTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
2770 6078 2.544267 AGAGCGTTTTTGACACTAGTGC 59.456 45.455 22.90 15.35 0.00 4.40
2788 6108 5.683876 AGTGCGCTCTTATATTATGGGAT 57.316 39.130 9.73 0.00 0.00 3.85
3515 6875 2.302157 AGTGTAGGTTGCCTAGGTCAAC 59.698 50.000 27.43 27.43 42.13 3.18
3545 6905 0.879765 GCTGTTGCTTGATGTGCTCT 59.120 50.000 0.00 0.00 36.03 4.09
3547 6907 2.485426 GCTGTTGCTTGATGTGCTCTAA 59.515 45.455 0.00 0.00 36.03 2.10
3594 7375 2.367567 GGGATACGCTAGGGAATGTCAA 59.632 50.000 14.59 0.00 37.60 3.18
3595 7376 3.181458 GGGATACGCTAGGGAATGTCAAA 60.181 47.826 14.59 0.00 37.60 2.69
3909 7781 5.773680 AGTACTCCAGTAACATACACACACT 59.226 40.000 0.00 0.00 31.52 3.55
3912 7784 6.453092 ACTCCAGTAACATACACACACTAAC 58.547 40.000 0.00 0.00 0.00 2.34
4092 7983 2.857592 GCGTCATGCTCATGGAAATT 57.142 45.000 9.69 0.00 41.73 1.82
4111 8002 7.232534 TGGAAATTATCAAGCACCTAAACAGTT 59.767 33.333 0.00 0.00 0.00 3.16
4123 8014 4.286032 ACCTAAACAGTTGAGCATGGTAGA 59.714 41.667 0.00 0.00 0.00 2.59
4373 8288 1.764723 CATGGAGTGGAGATGGCTGTA 59.235 52.381 0.00 0.00 0.00 2.74
4434 8382 4.077184 CCCCGCACCAGAACGCTA 62.077 66.667 0.00 0.00 0.00 4.26
4435 8383 2.813908 CCCGCACCAGAACGCTAC 60.814 66.667 0.00 0.00 0.00 3.58
4436 8384 2.261671 CCGCACCAGAACGCTACT 59.738 61.111 0.00 0.00 0.00 2.57
4437 8385 1.805945 CCGCACCAGAACGCTACTC 60.806 63.158 0.00 0.00 0.00 2.59
4438 8386 2.152699 CGCACCAGAACGCTACTCG 61.153 63.158 0.00 0.00 45.38 4.18
4439 8387 1.805945 GCACCAGAACGCTACTCGG 60.806 63.158 0.00 0.00 43.86 4.63
4440 8388 1.880894 CACCAGAACGCTACTCGGA 59.119 57.895 0.00 0.00 43.86 4.55
4441 8389 0.456312 CACCAGAACGCTACTCGGAC 60.456 60.000 0.00 0.00 43.86 4.79
4442 8390 1.226323 CCAGAACGCTACTCGGACG 60.226 63.158 0.00 0.00 43.86 4.79
4443 8391 1.226323 CAGAACGCTACTCGGACGG 60.226 63.158 0.00 0.00 43.86 4.79
4444 8392 2.578981 GAACGCTACTCGGACGGC 60.579 66.667 0.00 0.00 43.86 5.68
4445 8393 3.332493 GAACGCTACTCGGACGGCA 62.332 63.158 0.00 0.00 43.86 5.69
4446 8394 3.338126 AACGCTACTCGGACGGCAG 62.338 63.158 0.00 0.00 43.86 4.85
4447 8395 3.506096 CGCTACTCGGACGGCAGA 61.506 66.667 0.00 0.00 33.78 4.26
4448 8396 2.409651 GCTACTCGGACGGCAGAG 59.590 66.667 17.51 17.51 41.39 3.35
4449 8397 2.113433 GCTACTCGGACGGCAGAGA 61.113 63.158 25.91 7.83 38.43 3.10
4570 8521 1.179174 TATGATCACGGCGAGAGGGG 61.179 60.000 16.62 0.00 0.00 4.79
4676 8970 6.599244 TGATATGTTGGGAGATTTGAACTGTC 59.401 38.462 0.00 0.00 0.00 3.51
4803 9097 5.954296 AATTGTGTGAAATGGAGACTCTG 57.046 39.130 1.74 0.00 0.00 3.35
4856 9196 3.837146 CCATGTGTAGGGAGAGATGCTAT 59.163 47.826 0.00 0.00 0.00 2.97
4893 9238 5.516696 CAGATGGTGTACATTCTGTTAGACG 59.483 44.000 18.23 0.00 40.72 4.18
4904 9249 2.101415 TCTGTTAGACGGATCATGCTGG 59.899 50.000 0.00 0.00 0.00 4.85
4963 9315 3.990469 ACAAGATTACAGAACTCGCACTG 59.010 43.478 0.00 0.00 39.65 3.66
4990 9342 4.482990 TCATGCACTATCCATCCAGTCTA 58.517 43.478 0.00 0.00 0.00 2.59
5072 9431 2.325583 TGTCTGGACCAGAACAACAC 57.674 50.000 25.93 13.24 42.46 3.32
5073 9432 1.134220 TGTCTGGACCAGAACAACACC 60.134 52.381 25.93 11.96 42.46 4.16
5074 9433 0.472471 TCTGGACCAGAACAACACCC 59.528 55.000 22.30 0.00 37.57 4.61
5075 9434 0.182537 CTGGACCAGAACAACACCCA 59.817 55.000 17.22 0.00 32.44 4.51
5076 9435 0.106918 TGGACCAGAACAACACCCAC 60.107 55.000 0.00 0.00 0.00 4.61
5077 9436 0.182775 GGACCAGAACAACACCCACT 59.817 55.000 0.00 0.00 0.00 4.00
5078 9437 1.418637 GGACCAGAACAACACCCACTA 59.581 52.381 0.00 0.00 0.00 2.74
5079 9438 2.039879 GGACCAGAACAACACCCACTAT 59.960 50.000 0.00 0.00 0.00 2.12
5080 9439 3.497942 GGACCAGAACAACACCCACTATT 60.498 47.826 0.00 0.00 0.00 1.73
5081 9440 3.486383 ACCAGAACAACACCCACTATTG 58.514 45.455 0.00 0.00 0.00 1.90
5082 9441 2.228822 CCAGAACAACACCCACTATTGC 59.771 50.000 0.00 0.00 0.00 3.56
5083 9442 2.884012 CAGAACAACACCCACTATTGCA 59.116 45.455 0.00 0.00 0.00 4.08
5084 9443 3.507233 CAGAACAACACCCACTATTGCAT 59.493 43.478 0.00 0.00 0.00 3.96
5085 9444 4.022068 CAGAACAACACCCACTATTGCATT 60.022 41.667 0.00 0.00 0.00 3.56
5086 9445 4.588528 AGAACAACACCCACTATTGCATTT 59.411 37.500 0.00 0.00 0.00 2.32
5087 9446 5.772672 AGAACAACACCCACTATTGCATTTA 59.227 36.000 0.00 0.00 0.00 1.40
5088 9447 5.385509 ACAACACCCACTATTGCATTTAC 57.614 39.130 0.00 0.00 0.00 2.01
5089 9448 5.076873 ACAACACCCACTATTGCATTTACT 58.923 37.500 0.00 0.00 0.00 2.24
5090 9449 6.242396 ACAACACCCACTATTGCATTTACTA 58.758 36.000 0.00 0.00 0.00 1.82
5091 9450 6.717540 ACAACACCCACTATTGCATTTACTAA 59.282 34.615 0.00 0.00 0.00 2.24
5092 9451 7.396055 ACAACACCCACTATTGCATTTACTAAT 59.604 33.333 0.00 0.00 0.00 1.73
5093 9452 7.333528 ACACCCACTATTGCATTTACTAATG 57.666 36.000 0.00 0.00 43.28 1.90
5094 9453 7.116075 ACACCCACTATTGCATTTACTAATGA 58.884 34.615 2.25 0.00 43.12 2.57
5095 9454 7.613801 ACACCCACTATTGCATTTACTAATGAA 59.386 33.333 2.25 0.00 43.12 2.57
5096 9455 8.465999 CACCCACTATTGCATTTACTAATGAAA 58.534 33.333 2.25 0.00 42.21 2.69
5097 9456 9.200817 ACCCACTATTGCATTTACTAATGAAAT 57.799 29.630 8.65 8.65 46.89 2.17
5116 9475 3.661758 ATACGAAAACATTAACGCCCG 57.338 42.857 0.00 0.00 0.00 6.13
5208 9567 2.033236 CGCGTTCTAGCAGTTTTTGTGA 60.033 45.455 0.00 0.00 36.85 3.58
5221 9580 0.753867 TTTGTGAGCCACGTAGGACA 59.246 50.000 8.04 4.80 41.22 4.02
5224 9583 1.139256 TGTGAGCCACGTAGGACAAAA 59.861 47.619 8.04 0.00 41.22 2.44
5329 9691 0.449786 CACACCAGTTTTCACGCACA 59.550 50.000 0.00 0.00 0.00 4.57
5462 9824 5.758924 CCCTAGTTTTGTTTGTAAGCAGAC 58.241 41.667 0.00 0.00 0.00 3.51
5464 9826 5.235616 CCTAGTTTTGTTTGTAAGCAGACGA 59.764 40.000 0.00 0.00 32.96 4.20
5477 9839 3.385577 AGCAGACGACAACTCTCTTTTC 58.614 45.455 0.00 0.00 0.00 2.29
5530 9892 1.746615 CAACTGCCCTAGCGTGCAT 60.747 57.895 0.00 0.00 44.31 3.96
5547 9909 5.818720 GTGCATGTAAGCAGATGGCAACC 62.819 52.174 0.00 0.00 46.69 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 184 8.876790 AGAAGCAATTTGAACAAGAAAAAGAAG 58.123 29.630 0.00 0.00 0.00 2.85
180 185 8.658609 CAGAAGCAATTTGAACAAGAAAAAGAA 58.341 29.630 0.00 0.00 0.00 2.52
181 186 7.201548 GCAGAAGCAATTTGAACAAGAAAAAGA 60.202 33.333 0.00 0.00 41.58 2.52
370 375 0.388520 GACCCCAAAATTGAGCACGC 60.389 55.000 0.00 0.00 0.00 5.34
429 434 7.490402 GCCACTATGAATTCCTCTTGAAATTTG 59.510 37.037 2.27 0.00 36.33 2.32
450 455 3.451178 ACTCGATATTACAAGTGGCCACT 59.549 43.478 33.20 33.20 44.94 4.00
600 2079 6.292168 CCATTTACAAGGATAACGAGTTAGCG 60.292 42.308 5.35 0.00 32.65 4.26
602 2081 7.438459 CCTCCATTTACAAGGATAACGAGTTAG 59.562 40.741 2.08 0.00 32.53 2.34
729 2208 6.528321 TGTCCATATAGCTCTGAATCTTTGG 58.472 40.000 0.00 0.00 0.00 3.28
790 2269 1.000938 GCATGCAAAGGATTCCGGATC 60.001 52.381 14.21 5.08 0.00 3.36
964 2457 6.146347 CCTCTTTTCTTCTAAAGAACCTGACG 59.854 42.308 1.73 0.00 46.53 4.35
1191 2686 4.997395 TGAAGAAAGGTGCAGTATGACTTC 59.003 41.667 0.00 0.00 39.69 3.01
1339 2853 8.675504 AGAAATCAAGCTATCAGAAAATGACAG 58.324 33.333 0.00 0.00 41.91 3.51
1500 3029 4.632153 AGAGTACAACACTGTCATCAACC 58.368 43.478 0.00 0.00 37.72 3.77
1608 4253 2.916934 TGAGTGGCCCCTAAAGTAACAT 59.083 45.455 0.00 0.00 0.00 2.71
1677 4322 7.725844 AGTTTGATCTTTTCTGTTCTACCCAAT 59.274 33.333 0.00 0.00 0.00 3.16
1783 4441 3.339713 TTTGGGACGGAGGGAGTATAT 57.660 47.619 0.00 0.00 0.00 0.86
1788 4446 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1789 4447 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
1790 4448 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1791 4449 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1792 4450 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1793 4451 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1794 4452 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1795 4453 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1796 4454 7.094762 ACGAATCTAAGACAAGAATTTTGGGAC 60.095 37.037 0.00 0.00 0.00 4.46
1797 4455 6.940298 ACGAATCTAAGACAAGAATTTTGGGA 59.060 34.615 0.00 0.00 0.00 4.37
1798 4456 7.119846 AGACGAATCTAAGACAAGAATTTTGGG 59.880 37.037 0.00 0.00 31.46 4.12
1799 4457 8.034058 AGACGAATCTAAGACAAGAATTTTGG 57.966 34.615 0.00 0.00 31.46 3.28
1805 4463 8.549548 CGTATCTAGACGAATCTAAGACAAGAA 58.450 37.037 0.00 0.00 45.82 2.52
1806 4464 7.171167 CCGTATCTAGACGAATCTAAGACAAGA 59.829 40.741 5.60 0.00 45.82 3.02
1807 4465 7.171167 TCCGTATCTAGACGAATCTAAGACAAG 59.829 40.741 5.60 0.00 45.82 3.16
1808 4466 6.988580 TCCGTATCTAGACGAATCTAAGACAA 59.011 38.462 5.60 0.00 45.82 3.18
1809 4467 6.519382 TCCGTATCTAGACGAATCTAAGACA 58.481 40.000 5.60 0.00 45.82 3.41
1810 4468 7.118101 ACATCCGTATCTAGACGAATCTAAGAC 59.882 40.741 5.60 0.00 45.82 3.01
1811 4469 7.160049 ACATCCGTATCTAGACGAATCTAAGA 58.840 38.462 5.60 0.00 45.82 2.10
1812 4470 7.367159 ACATCCGTATCTAGACGAATCTAAG 57.633 40.000 5.60 0.00 45.82 2.18
1828 4486 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
1829 4487 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
1830 4488 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
1831 4489 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
1841 4499 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
1842 4500 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
1843 4501 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
1844 4502 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
1845 4503 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
1846 4504 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
1847 4505 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
1848 4506 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
1849 4507 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
1850 4508 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
1851 4509 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
1852 4510 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
1853 4511 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
1854 4512 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
1855 4513 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
1862 4520 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
1863 4521 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
1865 4523 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
1866 4524 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
1874 4532 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1875 4533 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1876 4534 8.477419 TCCCAAAATTCTTGTCTTAGATTTGT 57.523 30.769 0.00 0.00 28.79 2.83
1877 4535 9.362539 CATCCCAAAATTCTTGTCTTAGATTTG 57.637 33.333 0.00 0.00 29.84 2.32
1878 4536 8.534496 CCATCCCAAAATTCTTGTCTTAGATTT 58.466 33.333 0.00 0.00 0.00 2.17
1879 4537 7.895429 TCCATCCCAAAATTCTTGTCTTAGATT 59.105 33.333 0.00 0.00 0.00 2.40
1880 4538 7.413446 TCCATCCCAAAATTCTTGTCTTAGAT 58.587 34.615 0.00 0.00 0.00 1.98
1881 4539 6.789268 TCCATCCCAAAATTCTTGTCTTAGA 58.211 36.000 0.00 0.00 0.00 2.10
1882 4540 6.096001 CCTCCATCCCAAAATTCTTGTCTTAG 59.904 42.308 0.00 0.00 0.00 2.18
1883 4541 5.951747 CCTCCATCCCAAAATTCTTGTCTTA 59.048 40.000 0.00 0.00 0.00 2.10
1884 4542 4.774200 CCTCCATCCCAAAATTCTTGTCTT 59.226 41.667 0.00 0.00 0.00 3.01
1885 4543 4.347607 CCTCCATCCCAAAATTCTTGTCT 58.652 43.478 0.00 0.00 0.00 3.41
1886 4544 3.448660 CCCTCCATCCCAAAATTCTTGTC 59.551 47.826 0.00 0.00 0.00 3.18
1887 4545 3.077391 TCCCTCCATCCCAAAATTCTTGT 59.923 43.478 0.00 0.00 0.00 3.16
1888 4546 3.703052 CTCCCTCCATCCCAAAATTCTTG 59.297 47.826 0.00 0.00 0.00 3.02
1889 4547 3.337909 ACTCCCTCCATCCCAAAATTCTT 59.662 43.478 0.00 0.00 0.00 2.52
1890 4548 2.929043 ACTCCCTCCATCCCAAAATTCT 59.071 45.455 0.00 0.00 0.00 2.40
1891 4549 3.388552 ACTCCCTCCATCCCAAAATTC 57.611 47.619 0.00 0.00 0.00 2.17
1892 4550 4.482025 TGATACTCCCTCCATCCCAAAATT 59.518 41.667 0.00 0.00 0.00 1.82
1893 4551 4.054369 TGATACTCCCTCCATCCCAAAAT 58.946 43.478 0.00 0.00 0.00 1.82
1894 4552 3.459598 CTGATACTCCCTCCATCCCAAAA 59.540 47.826 0.00 0.00 0.00 2.44
1895 4553 3.048600 CTGATACTCCCTCCATCCCAAA 58.951 50.000 0.00 0.00 0.00 3.28
1896 4554 2.022035 ACTGATACTCCCTCCATCCCAA 60.022 50.000 0.00 0.00 0.00 4.12
1897 4555 1.580658 ACTGATACTCCCTCCATCCCA 59.419 52.381 0.00 0.00 0.00 4.37
1898 4556 2.407340 ACTGATACTCCCTCCATCCC 57.593 55.000 0.00 0.00 0.00 3.85
1899 4557 4.282195 CAGTAACTGATACTCCCTCCATCC 59.718 50.000 0.00 0.00 43.12 3.51
1900 4558 4.262249 GCAGTAACTGATACTCCCTCCATC 60.262 50.000 0.00 0.00 43.12 3.51
1901 4559 3.643792 GCAGTAACTGATACTCCCTCCAT 59.356 47.826 0.00 0.00 43.12 3.41
1902 4560 3.031736 GCAGTAACTGATACTCCCTCCA 58.968 50.000 0.00 0.00 43.12 3.86
1903 4561 3.031736 TGCAGTAACTGATACTCCCTCC 58.968 50.000 0.00 0.00 43.12 4.30
1904 4562 4.946478 ATGCAGTAACTGATACTCCCTC 57.054 45.455 0.00 0.00 43.12 4.30
1905 4563 6.808321 TTTATGCAGTAACTGATACTCCCT 57.192 37.500 0.00 0.00 43.12 4.20
1906 4564 9.726438 ATAATTTATGCAGTAACTGATACTCCC 57.274 33.333 0.00 0.00 43.12 4.30
1965 4627 5.105392 GCCATTCACCATAAGGAAAACATGA 60.105 40.000 0.00 0.00 38.69 3.07
2309 5039 5.034797 TGTAGATTCACTCATTTCGCTACG 58.965 41.667 0.00 0.00 31.97 3.51
2405 5135 5.515626 GCATATCTCTTCTGCAAAGCAAAAG 59.484 40.000 0.00 0.00 37.89 2.27
2438 5461 4.250464 GCTGTAGGCTATACACACAACAA 58.750 43.478 0.00 0.00 38.06 2.83
2496 5659 4.652421 TGTCTGTAGGTTACAACGAACA 57.348 40.909 0.00 0.22 38.38 3.18
2731 6038 4.956700 CGCTCTTATATATGGGAAGGAGGA 59.043 45.833 0.00 0.00 0.00 3.71
2759 6067 5.515797 AATATAAGAGCGCACTAGTGTCA 57.484 39.130 23.44 0.19 0.00 3.58
2760 6068 6.528423 CCATAATATAAGAGCGCACTAGTGTC 59.472 42.308 23.44 13.49 0.00 3.67
2761 6069 6.390721 CCATAATATAAGAGCGCACTAGTGT 58.609 40.000 23.44 4.36 0.00 3.55
2762 6070 5.807520 CCCATAATATAAGAGCGCACTAGTG 59.192 44.000 18.93 18.93 0.00 2.74
2763 6071 5.715279 TCCCATAATATAAGAGCGCACTAGT 59.285 40.000 11.47 3.49 0.00 2.57
2764 6072 6.208988 TCCCATAATATAAGAGCGCACTAG 57.791 41.667 11.47 0.00 0.00 2.57
2765 6073 6.406961 CCATCCCATAATATAAGAGCGCACTA 60.407 42.308 11.47 0.00 0.00 2.74
2766 6074 5.423015 CATCCCATAATATAAGAGCGCACT 58.577 41.667 11.47 5.59 0.00 4.40
2767 6075 4.572389 CCATCCCATAATATAAGAGCGCAC 59.428 45.833 11.47 2.25 0.00 5.34
2768 6076 4.469586 TCCATCCCATAATATAAGAGCGCA 59.530 41.667 11.47 0.00 0.00 6.09
2769 6077 5.023533 TCCATCCCATAATATAAGAGCGC 57.976 43.478 0.00 0.00 0.00 5.92
2770 6078 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
2788 6108 4.329638 TTGGCAGAATAATTTCCCTCCA 57.670 40.909 0.00 0.00 31.84 3.86
2848 6177 4.977739 TCTTGTCATAGGAATCAGGGGATT 59.022 41.667 0.00 0.00 46.27 3.01
3034 6371 1.774639 CAAGCGCATTTTGAGCAACT 58.225 45.000 11.47 0.00 45.82 3.16
3594 7375 3.719268 TCACATGGTATGCTCCTGTTT 57.281 42.857 0.00 0.00 0.00 2.83
3595 7376 3.347216 GTTCACATGGTATGCTCCTGTT 58.653 45.455 0.00 0.00 0.00 3.16
3909 7781 3.706600 AAAGAATAGCACGGGTGGTTA 57.293 42.857 8.95 0.00 41.96 2.85
3912 7784 2.420022 CTGAAAAGAATAGCACGGGTGG 59.580 50.000 0.43 0.00 0.00 4.61
4092 7983 4.695455 GCTCAACTGTTTAGGTGCTTGATA 59.305 41.667 4.10 0.00 41.55 2.15
4111 8002 4.066614 GGGGGTCTACCATGCTCA 57.933 61.111 0.81 0.00 42.91 4.26
4235 8150 8.608317 GCTTTCACTTTATCCTTGTCTATCTTC 58.392 37.037 0.00 0.00 0.00 2.87
4373 8288 4.703897 TGTCGTGTTTCTTCTCATCCTTT 58.296 39.130 0.00 0.00 0.00 3.11
4429 8377 3.812019 CTGCCGTCCGAGTAGCGT 61.812 66.667 0.00 0.00 38.67 5.07
4430 8378 3.456431 CTCTGCCGTCCGAGTAGCG 62.456 68.421 0.00 0.00 40.47 4.26
4431 8379 1.654954 TTCTCTGCCGTCCGAGTAGC 61.655 60.000 0.00 0.00 0.00 3.58
4432 8380 0.099082 GTTCTCTGCCGTCCGAGTAG 59.901 60.000 0.00 0.00 0.00 2.57
4433 8381 1.642037 CGTTCTCTGCCGTCCGAGTA 61.642 60.000 0.00 0.00 0.00 2.59
4434 8382 2.963371 GTTCTCTGCCGTCCGAGT 59.037 61.111 0.00 0.00 0.00 4.18
4435 8383 2.202492 CGTTCTCTGCCGTCCGAG 60.202 66.667 0.00 0.00 0.00 4.63
4436 8384 4.415332 GCGTTCTCTGCCGTCCGA 62.415 66.667 0.00 0.00 0.00 4.55
4443 8391 2.202676 CTCCTCGGCGTTCTCTGC 60.203 66.667 6.85 0.00 0.00 4.26
4444 8392 2.492090 CCTCCTCGGCGTTCTCTG 59.508 66.667 6.85 0.00 0.00 3.35
4445 8393 2.756283 CCCTCCTCGGCGTTCTCT 60.756 66.667 6.85 0.00 0.00 3.10
4446 8394 4.516195 GCCCTCCTCGGCGTTCTC 62.516 72.222 6.85 0.00 39.64 2.87
4570 8521 2.038387 TGATCTCGCCCTTTTAAGGC 57.962 50.000 2.87 0.00 45.10 4.35
4617 8568 1.802880 CGATTGTTCTACGCAGGGGAG 60.803 57.143 0.00 0.00 0.00 4.30
4618 8569 0.174845 CGATTGTTCTACGCAGGGGA 59.825 55.000 0.00 0.00 0.00 4.81
4621 8572 0.739462 TGCCGATTGTTCTACGCAGG 60.739 55.000 0.00 0.00 0.00 4.85
4622 8573 0.647410 CTGCCGATTGTTCTACGCAG 59.353 55.000 0.00 0.00 0.00 5.18
4856 9196 2.743664 CACCATCTGATCGCACAAAAGA 59.256 45.455 0.00 0.00 0.00 2.52
4904 9249 0.179134 CTTCCAGTGACCGGATCGAC 60.179 60.000 9.46 0.00 30.99 4.20
5087 9446 9.269415 GCGTTAATGTTTTCGTATTTCATTAGT 57.731 29.630 0.00 0.00 34.17 2.24
5088 9447 8.730427 GGCGTTAATGTTTTCGTATTTCATTAG 58.270 33.333 0.00 0.00 34.17 1.73
5089 9448 7.697291 GGGCGTTAATGTTTTCGTATTTCATTA 59.303 33.333 0.00 0.00 32.27 1.90
5090 9449 6.528774 GGGCGTTAATGTTTTCGTATTTCATT 59.471 34.615 0.00 0.00 34.02 2.57
5091 9450 6.031471 GGGCGTTAATGTTTTCGTATTTCAT 58.969 36.000 0.00 0.00 0.00 2.57
5092 9451 5.392286 GGGCGTTAATGTTTTCGTATTTCA 58.608 37.500 0.00 0.00 0.00 2.69
5093 9452 4.492998 CGGGCGTTAATGTTTTCGTATTTC 59.507 41.667 0.00 0.00 0.00 2.17
5094 9453 4.405196 CGGGCGTTAATGTTTTCGTATTT 58.595 39.130 0.00 0.00 0.00 1.40
5095 9454 3.728566 GCGGGCGTTAATGTTTTCGTATT 60.729 43.478 0.00 0.00 0.00 1.89
5096 9455 2.223089 GCGGGCGTTAATGTTTTCGTAT 60.223 45.455 0.00 0.00 0.00 3.06
5097 9456 1.128321 GCGGGCGTTAATGTTTTCGTA 59.872 47.619 0.00 0.00 0.00 3.43
5098 9457 0.110101 GCGGGCGTTAATGTTTTCGT 60.110 50.000 0.00 0.00 0.00 3.85
5099 9458 0.110147 TGCGGGCGTTAATGTTTTCG 60.110 50.000 0.00 0.00 0.00 3.46
5100 9459 1.333115 GTGCGGGCGTTAATGTTTTC 58.667 50.000 0.00 0.00 0.00 2.29
5107 9466 3.339464 CACACGTGCGGGCGTTAA 61.339 61.111 17.22 0.00 43.83 2.01
5208 9567 1.542547 CCAGTTTTGTCCTACGTGGCT 60.543 52.381 0.00 0.00 35.26 4.75
5221 9580 1.412343 GAATGCCCACACACCAGTTTT 59.588 47.619 0.00 0.00 0.00 2.43
5224 9583 0.112995 ATGAATGCCCACACACCAGT 59.887 50.000 0.00 0.00 0.00 4.00
5329 9691 3.252284 CACACCAGCCCCCTCTGT 61.252 66.667 0.00 0.00 32.32 3.41
5351 9713 2.147958 GTGTGGGCGAAGTGATAAACA 58.852 47.619 0.00 0.00 0.00 2.83
5415 9777 0.322456 TGCCATGTACCCTGCAGAAC 60.322 55.000 17.39 10.92 0.00 3.01
5445 9807 4.948608 TGTCGTCTGCTTACAAACAAAA 57.051 36.364 0.00 0.00 0.00 2.44
5450 9812 4.049186 GAGAGTTGTCGTCTGCTTACAAA 58.951 43.478 0.00 0.00 35.08 2.83
5462 9824 1.000506 TCGGGGAAAAGAGAGTTGTCG 59.999 52.381 0.00 0.00 0.00 4.35
5464 9826 2.047830 ACTCGGGGAAAAGAGAGTTGT 58.952 47.619 0.00 0.00 40.64 3.32
5477 9839 1.178534 AAACACATGGCAACTCGGGG 61.179 55.000 0.00 0.00 37.61 5.73
5530 9892 0.698238 AGGGTTGCCATCTGCTTACA 59.302 50.000 0.00 0.00 42.00 2.41
5547 9909 3.989817 GCAGTTGCCATGTAAAAGAAAGG 59.010 43.478 0.00 0.00 34.31 3.11


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

AutoCloner maintained by Alex Coulton.