Multiple sequence alignment - TraesCS5D01G036600

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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 TraesCS5D01G036600 chr5D 100.000 2846 0 0 1 2846 35651225 35654070 0.000000e+00 5256.0
1 TraesCS5D01G036600 chr5D 90.113 708 48 11 1271 1975 521404560 521403872 0.000000e+00 900.0
2 TraesCS5D01G036600 chr5D 81.432 964 107 39 326 1251 521405469 521404540 0.000000e+00 723.0
3 TraesCS5D01G036600 chr5D 90.517 116 8 2 2215 2329 362966022 362966135 1.770000e-32 150.0
4 TraesCS5D01G036600 chr5D 86.726 113 14 1 2215 2326 484910185 484910073 1.070000e-24 124.0
5 TraesCS5D01G036600 chr5D 92.000 50 1 1 1973 2019 521403839 521403790 1.830000e-07 67.6
6 TraesCS5D01G036600 chrUn 88.977 2023 142 40 1 1970 318995347 318997341 0.000000e+00 2425.0
7 TraesCS5D01G036600 chrUn 91.397 1453 74 27 544 1970 271013744 271015171 0.000000e+00 1943.0
8 TraesCS5D01G036600 chrUn 91.397 1453 74 27 544 1970 280884431 280885858 0.000000e+00 1943.0
9 TraesCS5D01G036600 chrUn 91.049 1173 54 21 843 1970 397775233 397776399 0.000000e+00 1537.0
10 TraesCS5D01G036600 chrUn 87.389 563 64 7 1 559 271013171 271013730 8.600000e-180 640.0
11 TraesCS5D01G036600 chrUn 87.389 563 64 7 1 559 280883858 280884417 8.600000e-180 640.0
12 TraesCS5D01G036600 chrUn 84.000 600 79 13 1 594 273922843 273923431 6.890000e-156 560.0
13 TraesCS5D01G036600 chrUn 84.906 212 19 7 1973 2174 318997386 318997594 4.810000e-48 202.0
14 TraesCS5D01G036600 chrUn 84.906 212 19 7 1973 2174 397776444 397776652 4.810000e-48 202.0
15 TraesCS5D01G036600 chrUn 79.828 233 34 11 2283 2510 330097790 330098014 1.060000e-34 158.0
16 TraesCS5D01G036600 chrUn 79.828 233 34 11 2283 2510 330161458 330161682 1.060000e-34 158.0
17 TraesCS5D01G036600 chrUn 79.828 233 34 11 2283 2510 346940830 346941054 1.060000e-34 158.0
18 TraesCS5D01G036600 chrUn 79.828 233 34 11 2283 2510 442655186 442655410 1.060000e-34 158.0
19 TraesCS5D01G036600 chrUn 83.333 168 25 3 2344 2510 336148139 336147974 4.910000e-33 152.0
20 TraesCS5D01G036600 chrUn 79.399 233 35 11 2283 2510 350283097 350283321 4.910000e-33 152.0
21 TraesCS5D01G036600 chrUn 81.538 195 15 9 1973 2159 271015216 271015397 1.060000e-29 141.0
22 TraesCS5D01G036600 chrUn 81.538 195 15 9 1973 2159 280885903 280886084 1.060000e-29 141.0
23 TraesCS5D01G036600 chr5A 87.990 1632 94 53 634 2194 24197691 24199291 0.000000e+00 1834.0
24 TraesCS5D01G036600 chr5A 89.428 1381 68 35 874 2189 23907973 23906606 0.000000e+00 1670.0
25 TraesCS5D01G036600 chr5A 91.360 706 46 10 1275 1975 649784934 649784239 0.000000e+00 952.0
26 TraesCS5D01G036600 chr5A 84.290 662 50 26 634 1251 649785569 649784918 5.250000e-167 597.0
27 TraesCS5D01G036600 chr5A 85.981 214 18 9 634 839 23908180 23907971 4.770000e-53 219.0
28 TraesCS5D01G036600 chr5A 79.661 236 22 9 1973 2198 649784205 649783986 2.280000e-31 147.0
29 TraesCS5D01G036600 chr5A 88.542 96 10 1 2218 2312 626615051 626614956 6.440000e-22 115.0
30 TraesCS5D01G036600 chr5B 90.014 711 44 13 1271 1975 657722574 657721885 0.000000e+00 894.0
31 TraesCS5D01G036600 chr5B 89.286 84 4 5 2220 2301 130932005 130932085 1.800000e-17 100.0
32 TraesCS5D01G036600 chr3D 87.500 304 33 5 33 331 90831974 90831671 2.100000e-91 346.0
33 TraesCS5D01G036600 chr3D 84.894 331 42 8 9 333 29810532 29810204 7.600000e-86 327.0
34 TraesCS5D01G036600 chr1D 86.120 317 36 8 16 326 442369568 442369882 4.540000e-88 335.0
35 TraesCS5D01G036600 chr1D 86.498 237 30 1 2563 2799 291328484 291328250 2.810000e-65 259.0
36 TraesCS5D01G036600 chr1D 97.701 87 1 1 2479 2564 460308584 460308670 6.350000e-32 148.0
37 TraesCS5D01G036600 chr2B 86.218 312 37 6 6 312 503925506 503925816 1.630000e-87 333.0
38 TraesCS5D01G036600 chr4D 85.714 315 36 9 24 332 12696199 12695888 9.830000e-85 324.0
39 TraesCS5D01G036600 chr2D 91.667 168 13 1 2336 2503 536434972 536434806 6.130000e-57 231.0
40 TraesCS5D01G036600 chr2D 89.773 176 16 2 2333 2507 536436319 536436145 1.030000e-54 224.0
41 TraesCS5D01G036600 chr2D 89.535 172 17 1 2333 2504 536437667 536437497 1.720000e-52 217.0
42 TraesCS5D01G036600 chr2D 82.692 156 15 8 2196 2340 640589602 640589756 8.280000e-26 128.0
43 TraesCS5D01G036600 chr6B 88.679 106 11 1 2222 2326 27188879 27188984 8.280000e-26 128.0
44 TraesCS5D01G036600 chr2A 88.679 106 11 1 2222 2326 41223460 41223565 8.280000e-26 128.0
45 TraesCS5D01G036600 chr1B 85.366 123 16 2 2599 2720 554588785 554588664 2.980000e-25 126.0
46 TraesCS5D01G036600 chr7D 94.203 69 2 1 2194 2260 3793130 3793062 1.390000e-18 104.0
47 TraesCS5D01G036600 chr3B 92.593 54 4 0 2222 2275 362051827 362051774 8.450000e-11 78.7


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 TraesCS5D01G036600 chr5D 35651225 35654070 2845 False 5256.000000 5256 100.000000 1 2846 1 chr5D.!!$F1 2845
1 TraesCS5D01G036600 chr5D 521403790 521405469 1679 True 563.533333 900 87.848333 326 2019 3 chr5D.!!$R2 1693
2 TraesCS5D01G036600 chrUn 318995347 318997594 2247 False 1313.500000 2425 86.941500 1 2174 2 chrUn.!!$F9 2173
3 TraesCS5D01G036600 chrUn 271013171 271015397 2226 False 908.000000 1943 86.774667 1 2159 3 chrUn.!!$F7 2158
4 TraesCS5D01G036600 chrUn 280883858 280886084 2226 False 908.000000 1943 86.774667 1 2159 3 chrUn.!!$F8 2158
5 TraesCS5D01G036600 chrUn 397775233 397776652 1419 False 869.500000 1537 87.977500 843 2174 2 chrUn.!!$F10 1331
6 TraesCS5D01G036600 chrUn 273922843 273923431 588 False 560.000000 560 84.000000 1 594 1 chrUn.!!$F1 593
7 TraesCS5D01G036600 chr5A 24197691 24199291 1600 False 1834.000000 1834 87.990000 634 2194 1 chr5A.!!$F1 1560
8 TraesCS5D01G036600 chr5A 23906606 23908180 1574 True 944.500000 1670 87.704500 634 2189 2 chr5A.!!$R2 1555
9 TraesCS5D01G036600 chr5A 649783986 649785569 1583 True 565.333333 952 85.103667 634 2198 3 chr5A.!!$R3 1564
10 TraesCS5D01G036600 chr5B 657721885 657722574 689 True 894.000000 894 90.014000 1271 1975 1 chr5B.!!$R1 704
11 TraesCS5D01G036600 chr2D 536434806 536437667 2861 True 224.000000 231 90.325000 2333 2507 3 chr2D.!!$R1 174

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
27 28 1.208535 TGGATCCGGTATTTGCTCGTT 59.791 47.619 7.39 0.0 0.00 3.85 F
114 115 1.480789 TCTGTGCGCTGGTCCTATAA 58.519 50.000 9.73 0.0 0.00 0.98 F
174 176 1.600636 TTTTGCCGGCTCCAGTGAG 60.601 57.895 29.70 0.0 41.84 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1304 0.105862 CCCTCCACGATGGGGTAGTA 60.106 60.000 0.0 0.0 35.80 1.82 R
1597 1748 1.905215 CTTGACCTCCACAGACATCCT 59.095 52.381 0.0 0.0 0.00 3.24 R
2032 2291 2.850647 GAGACGCATAGTTCGGTAACAC 59.149 50.000 0.0 0.0 38.12 3.32 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
25 26 1.217882 GTGGATCCGGTATTTGCTCG 58.782 55.000 7.39 0.00 0.00 5.03
27 28 1.208535 TGGATCCGGTATTTGCTCGTT 59.791 47.619 7.39 0.00 0.00 3.85
29 30 3.118702 TGGATCCGGTATTTGCTCGTTTA 60.119 43.478 7.39 0.00 0.00 2.01
63 64 3.760580 ACAAGATGGATCCTTCCGATC 57.239 47.619 21.04 11.62 45.89 3.69
65 66 3.070734 ACAAGATGGATCCTTCCGATCTG 59.929 47.826 21.04 13.81 45.90 2.90
79 80 4.810790 TCCGATCTGAACTTCTCTTCAAC 58.189 43.478 0.00 0.00 29.66 3.18
82 83 4.561105 GATCTGAACTTCTCTTCAACGGT 58.439 43.478 0.00 0.00 29.66 4.83
84 85 3.383505 TCTGAACTTCTCTTCAACGGTGA 59.616 43.478 0.00 0.00 29.66 4.02
86 87 3.118920 TGAACTTCTCTTCAACGGTGACA 60.119 43.478 0.44 0.00 31.90 3.58
101 102 2.477863 GGTGACAGTTGTTGTTCTGTGC 60.478 50.000 2.54 0.00 43.64 4.57
114 115 1.480789 TCTGTGCGCTGGTCCTATAA 58.519 50.000 9.73 0.00 0.00 0.98
115 116 1.828595 TCTGTGCGCTGGTCCTATAAA 59.171 47.619 9.73 0.00 0.00 1.40
125 126 5.509840 CGCTGGTCCTATAAAGTCTTAGCAT 60.510 44.000 0.00 0.00 0.00 3.79
126 127 5.698545 GCTGGTCCTATAAAGTCTTAGCATG 59.301 44.000 0.00 0.00 0.00 4.06
128 129 6.817184 TGGTCCTATAAAGTCTTAGCATGAC 58.183 40.000 0.00 0.00 34.88 3.06
134 135 7.380065 CCTATAAAGTCTTAGCATGACGACTTC 59.620 40.741 15.09 0.00 43.65 3.01
174 176 1.600636 TTTTGCCGGCTCCAGTGAG 60.601 57.895 29.70 0.00 41.84 3.51
183 185 3.940480 TCCAGTGAGGGAGGGGCA 61.940 66.667 0.00 0.00 38.24 5.36
249 252 3.570125 TCGCTAGGTGTCTATGAATCTGG 59.430 47.826 0.00 0.00 0.00 3.86
311 314 8.387813 TCATGATTGATGATGGATAGATTGGAA 58.612 33.333 0.00 0.00 36.06 3.53
312 315 8.678199 CATGATTGATGATGGATAGATTGGAAG 58.322 37.037 0.00 0.00 33.31 3.46
313 316 7.981142 TGATTGATGATGGATAGATTGGAAGA 58.019 34.615 0.00 0.00 0.00 2.87
322 325 7.718334 TGGATAGATTGGAAGATTATCGCTA 57.282 36.000 0.00 0.00 0.00 4.26
337 340 9.042008 AGATTATCGCTAAAATAAAAGCTCGAA 57.958 29.630 0.00 0.00 36.56 3.71
340 343 4.933400 TCGCTAAAATAAAAGCTCGAACCT 59.067 37.500 0.00 0.00 36.56 3.50
490 499 2.688446 CGGGCCATCGAGCTTATATCTA 59.312 50.000 4.39 0.00 0.00 1.98
563 608 8.939929 GTTTATTTGAGAGAGATCATGTGTCAA 58.060 33.333 0.00 0.00 0.00 3.18
602 650 4.611310 AAAGAGTGTCATCATGCAATCG 57.389 40.909 0.00 0.00 35.23 3.34
684 741 6.889494 TCACAAATGCTTGCACAATATTTTG 58.111 32.000 12.58 12.58 35.84 2.44
987 1108 2.463653 CGCACGTTTTCACAAATCACAG 59.536 45.455 0.00 0.00 0.00 3.66
1469 1605 2.045926 GGATGACAAGGCGCTGGT 60.046 61.111 7.64 2.60 0.00 4.00
1597 1748 3.440173 GGTTAATAACAAGCTGCAGCAGA 59.560 43.478 38.24 19.26 45.16 4.26
1614 1765 1.480137 CAGAGGATGTCTGTGGAGGTC 59.520 57.143 0.00 0.00 46.89 3.85
1877 2060 1.464608 CACACATCACATGTTCCGTCC 59.535 52.381 0.00 0.00 42.70 4.79
1912 2107 3.708403 TCTGCATTGACCATTGAGTCT 57.292 42.857 0.00 0.00 37.66 3.24
2032 2291 3.454082 AGACCTATTCCTTTGCTCCTCAG 59.546 47.826 0.00 0.00 0.00 3.35
2104 2374 2.490902 GGGGGAACTCCAACAATCTGTT 60.491 50.000 0.00 0.00 42.08 3.16
2105 2375 3.230976 GGGGAACTCCAACAATCTGTTT 58.769 45.455 0.00 0.00 38.77 2.83
2198 2489 5.695851 ATTGTAAGCTCTCCACTTTGTTG 57.304 39.130 0.00 0.00 0.00 3.33
2199 2490 3.476552 TGTAAGCTCTCCACTTTGTTGG 58.523 45.455 0.00 0.00 38.10 3.77
2200 2491 3.135712 TGTAAGCTCTCCACTTTGTTGGA 59.864 43.478 0.00 0.00 43.83 3.53
2201 2492 3.297134 AAGCTCTCCACTTTGTTGGAA 57.703 42.857 0.00 0.00 45.37 3.53
2202 2493 3.515602 AGCTCTCCACTTTGTTGGAAT 57.484 42.857 0.00 0.00 45.37 3.01
2203 2494 4.640771 AGCTCTCCACTTTGTTGGAATA 57.359 40.909 0.00 0.00 45.37 1.75
2204 2495 4.985538 AGCTCTCCACTTTGTTGGAATAA 58.014 39.130 0.00 0.00 45.37 1.40
2205 2496 5.006386 AGCTCTCCACTTTGTTGGAATAAG 58.994 41.667 0.00 0.00 45.37 1.73
2206 2497 4.379918 GCTCTCCACTTTGTTGGAATAAGC 60.380 45.833 5.55 5.55 45.37 3.09
2207 2498 4.079253 TCTCCACTTTGTTGGAATAAGCC 58.921 43.478 0.00 0.00 45.37 4.35
2208 2499 3.826157 CTCCACTTTGTTGGAATAAGCCA 59.174 43.478 0.00 0.00 45.37 4.75
2209 2500 3.572255 TCCACTTTGTTGGAATAAGCCAC 59.428 43.478 0.00 0.00 43.04 5.01
2210 2501 3.564511 CACTTTGTTGGAATAAGCCACG 58.435 45.455 0.00 0.00 37.75 4.94
2211 2502 2.556622 ACTTTGTTGGAATAAGCCACGG 59.443 45.455 0.00 0.00 37.75 4.94
2212 2503 0.885196 TTGTTGGAATAAGCCACGGC 59.115 50.000 0.00 0.00 37.75 5.68
2322 2613 3.136123 CAGGGGAAGCGTGGCATG 61.136 66.667 1.31 1.31 0.00 4.06
2323 2614 3.650950 AGGGGAAGCGTGGCATGT 61.651 61.111 8.75 0.00 0.00 3.21
2324 2615 3.443045 GGGGAAGCGTGGCATGTG 61.443 66.667 8.75 0.00 0.00 3.21
2325 2616 2.672996 GGGAAGCGTGGCATGTGT 60.673 61.111 8.75 0.00 0.00 3.72
2326 2617 2.562912 GGAAGCGTGGCATGTGTG 59.437 61.111 8.75 0.00 0.00 3.82
2327 2618 2.260869 GGAAGCGTGGCATGTGTGT 61.261 57.895 8.75 0.00 0.00 3.72
2328 2619 1.207593 GAAGCGTGGCATGTGTGTC 59.792 57.895 8.75 0.00 0.00 3.67
2329 2620 1.227943 AAGCGTGGCATGTGTGTCT 60.228 52.632 8.75 0.00 0.00 3.41
2330 2621 1.230635 AAGCGTGGCATGTGTGTCTC 61.231 55.000 8.75 0.00 0.00 3.36
2331 2622 1.960763 GCGTGGCATGTGTGTCTCA 60.961 57.895 8.75 0.00 0.00 3.27
2338 2629 1.400629 GCATGTGTGTCTCATGTGTGC 60.401 52.381 11.52 0.00 42.94 4.57
2360 2651 2.508928 CCGAGTTGTGGGGTGTGT 59.491 61.111 0.00 0.00 0.00 3.72
2361 2652 1.749665 CCGAGTTGTGGGGTGTGTA 59.250 57.895 0.00 0.00 0.00 2.90
2364 4003 1.270625 CGAGTTGTGGGGTGTGTATGT 60.271 52.381 0.00 0.00 0.00 2.29
2373 4012 4.162698 GTGGGGTGTGTATGTATTGGAGTA 59.837 45.833 0.00 0.00 0.00 2.59
2375 4014 4.202326 GGGGTGTGTATGTATTGGAGTAGG 60.202 50.000 0.00 0.00 0.00 3.18
2386 4025 0.898320 TGGAGTAGGTCTGCAGCTTC 59.102 55.000 9.47 0.00 39.51 3.86
2416 4055 3.857854 CGTGGACGAGCTGCATGC 61.858 66.667 11.82 11.82 43.02 4.06
2433 4072 2.183300 CAGTAGCGGCCGTTGCTA 59.817 61.111 30.04 18.51 43.71 3.49
2447 4086 4.832608 GCTACCCGTTGGAGCCCG 62.833 72.222 0.00 0.00 32.09 6.13
2505 4144 4.148825 GAGGCGTGCGGATCAGGT 62.149 66.667 0.00 0.00 33.35 4.00
2506 4145 4.457496 AGGCGTGCGGATCAGGTG 62.457 66.667 0.00 0.00 33.35 4.00
2507 4146 4.760047 GGCGTGCGGATCAGGTGT 62.760 66.667 0.00 0.00 33.35 4.16
2509 4148 3.490759 CGTGCGGATCAGGTGTGC 61.491 66.667 0.00 0.00 0.00 4.57
2510 4149 2.358615 GTGCGGATCAGGTGTGCA 60.359 61.111 0.00 0.00 0.00 4.57
2511 4150 1.746615 GTGCGGATCAGGTGTGCAT 60.747 57.895 0.00 0.00 37.93 3.96
2512 4151 1.746239 TGCGGATCAGGTGTGCATG 60.746 57.895 0.00 0.00 0.00 4.06
2513 4152 3.104766 CGGATCAGGTGTGCATGC 58.895 61.111 11.82 11.82 0.00 4.06
2514 4153 1.746239 CGGATCAGGTGTGCATGCA 60.746 57.895 18.46 18.46 0.00 3.96
2515 4154 1.712018 CGGATCAGGTGTGCATGCAG 61.712 60.000 23.41 9.30 0.00 4.41
2516 4155 1.432251 GATCAGGTGTGCATGCAGC 59.568 57.895 23.41 16.84 45.96 5.25
2525 4164 2.944429 GCATGCAGCATAGCGAGG 59.056 61.111 14.21 0.00 44.79 4.63
2526 4165 2.944429 CATGCAGCATAGCGAGGC 59.056 61.111 7.82 0.00 37.31 4.70
2527 4166 2.664185 ATGCAGCATAGCGAGGCG 60.664 61.111 5.94 0.00 37.47 5.52
2528 4167 3.451556 ATGCAGCATAGCGAGGCGT 62.452 57.895 5.94 0.00 37.47 5.68
2529 4168 3.634072 GCAGCATAGCGAGGCGTG 61.634 66.667 0.00 0.00 37.47 5.34
2530 4169 3.634072 CAGCATAGCGAGGCGTGC 61.634 66.667 11.31 11.31 42.23 5.34
2531 4170 4.147449 AGCATAGCGAGGCGTGCA 62.147 61.111 18.22 0.00 43.51 4.57
2532 4171 3.634072 GCATAGCGAGGCGTGCAG 61.634 66.667 13.44 0.00 41.79 4.41
2533 4172 2.963854 CATAGCGAGGCGTGCAGG 60.964 66.667 1.01 1.01 33.85 4.85
2534 4173 3.461773 ATAGCGAGGCGTGCAGGT 61.462 61.111 8.40 0.00 33.85 4.00
2535 4174 3.432051 ATAGCGAGGCGTGCAGGTC 62.432 63.158 1.99 1.99 33.85 3.85
2562 4201 3.207669 GGAAGAGCTGCATGGCCG 61.208 66.667 1.02 0.00 0.00 6.13
2563 4202 2.124983 GAAGAGCTGCATGGCCGA 60.125 61.111 1.02 0.00 0.00 5.54
2564 4203 2.124819 AAGAGCTGCATGGCCGAG 60.125 61.111 1.02 0.00 0.00 4.63
2566 4205 2.437359 GAGCTGCATGGCCGAGTT 60.437 61.111 1.02 0.00 0.00 3.01
2567 4206 1.153369 GAGCTGCATGGCCGAGTTA 60.153 57.895 1.02 0.00 0.00 2.24
2569 4208 0.107017 AGCTGCATGGCCGAGTTAAT 60.107 50.000 1.02 0.00 0.00 1.40
2570 4209 0.740737 GCTGCATGGCCGAGTTAATT 59.259 50.000 0.00 0.00 0.00 1.40
2572 4211 2.287009 GCTGCATGGCCGAGTTAATTAC 60.287 50.000 0.00 0.00 0.00 1.89
2574 4213 3.550820 TGCATGGCCGAGTTAATTACAT 58.449 40.909 0.00 0.00 0.00 2.29
2575 4214 4.709250 TGCATGGCCGAGTTAATTACATA 58.291 39.130 0.00 0.00 0.00 2.29
2577 4216 4.994852 GCATGGCCGAGTTAATTACATAGA 59.005 41.667 0.00 0.00 0.00 1.98
2578 4217 5.468746 GCATGGCCGAGTTAATTACATAGAA 59.531 40.000 0.00 0.00 0.00 2.10
2579 4218 6.347725 GCATGGCCGAGTTAATTACATAGAAG 60.348 42.308 0.00 0.00 0.00 2.85
2580 4219 6.229936 TGGCCGAGTTAATTACATAGAAGT 57.770 37.500 0.00 0.00 0.00 3.01
2581 4220 7.350744 TGGCCGAGTTAATTACATAGAAGTA 57.649 36.000 0.00 0.00 0.00 2.24
2582 4221 7.205297 TGGCCGAGTTAATTACATAGAAGTAC 58.795 38.462 0.00 0.00 0.00 2.73
2584 4223 8.571336 GGCCGAGTTAATTACATAGAAGTACTA 58.429 37.037 0.00 0.00 35.42 1.82
2585 4224 9.392021 GCCGAGTTAATTACATAGAAGTACTAC 57.608 37.037 0.00 0.00 33.62 2.73
2598 4237 1.825474 AGTACTACACTTCGGCATGCT 59.175 47.619 18.92 0.00 31.59 3.79
2599 4238 1.927174 GTACTACACTTCGGCATGCTG 59.073 52.381 21.02 21.02 0.00 4.41
2600 4239 0.321671 ACTACACTTCGGCATGCTGT 59.678 50.000 25.42 18.91 0.00 4.40
2601 4240 1.548719 ACTACACTTCGGCATGCTGTA 59.451 47.619 25.42 19.02 0.00 2.74
2604 4494 1.806542 ACACTTCGGCATGCTGTAAAG 59.193 47.619 25.42 22.77 0.00 1.85
2605 4495 1.131126 CACTTCGGCATGCTGTAAAGG 59.869 52.381 25.42 10.09 0.00 3.11
2614 4504 4.022849 GGCATGCTGTAAAGGATTGGTATC 60.023 45.833 18.92 0.00 0.00 2.24
2615 4505 4.580167 GCATGCTGTAAAGGATTGGTATCA 59.420 41.667 11.37 0.00 32.09 2.15
2616 4506 5.506317 GCATGCTGTAAAGGATTGGTATCAC 60.506 44.000 11.37 0.00 32.09 3.06
2620 4510 6.156256 TGCTGTAAAGGATTGGTATCACTAGT 59.844 38.462 0.00 0.00 32.09 2.57
2623 4513 8.319057 TGTAAAGGATTGGTATCACTAGTCAT 57.681 34.615 0.00 0.00 32.09 3.06
2651 4541 7.843490 TTTTACATGTTAGTACCATCTCTGC 57.157 36.000 2.30 0.00 0.00 4.26
2653 4543 3.181475 ACATGTTAGTACCATCTCTGCGG 60.181 47.826 0.00 0.00 0.00 5.69
2654 4544 1.136305 TGTTAGTACCATCTCTGCGGC 59.864 52.381 0.00 0.00 0.00 6.53
2655 4545 1.409427 GTTAGTACCATCTCTGCGGCT 59.591 52.381 0.00 0.00 0.00 5.52
2656 4546 2.621998 GTTAGTACCATCTCTGCGGCTA 59.378 50.000 0.00 0.00 0.00 3.93
2657 4547 1.776662 AGTACCATCTCTGCGGCTAA 58.223 50.000 0.00 0.00 0.00 3.09
2658 4548 2.320781 AGTACCATCTCTGCGGCTAAT 58.679 47.619 0.00 0.00 0.00 1.73
2659 4549 2.700897 AGTACCATCTCTGCGGCTAATT 59.299 45.455 0.00 0.00 0.00 1.40
2661 4551 1.210478 ACCATCTCTGCGGCTAATTGT 59.790 47.619 0.00 0.00 0.00 2.71
2662 4552 2.292267 CCATCTCTGCGGCTAATTGTT 58.708 47.619 0.00 0.00 0.00 2.83
2664 4554 1.086696 TCTCTGCGGCTAATTGTTGC 58.913 50.000 0.00 0.00 0.00 4.17
2665 4555 0.804364 CTCTGCGGCTAATTGTTGCA 59.196 50.000 0.00 0.00 0.00 4.08
2666 4556 1.199789 CTCTGCGGCTAATTGTTGCAA 59.800 47.619 0.00 0.00 34.78 4.08
2667 4557 1.611006 TCTGCGGCTAATTGTTGCAAA 59.389 42.857 0.00 0.00 34.78 3.68
2668 4558 2.035193 TCTGCGGCTAATTGTTGCAAAA 59.965 40.909 0.00 0.00 34.78 2.44
2669 4559 2.131183 TGCGGCTAATTGTTGCAAAAC 58.869 42.857 0.00 0.00 31.69 2.43
2670 4560 2.131183 GCGGCTAATTGTTGCAAAACA 58.869 42.857 0.00 0.00 0.00 2.83
2671 4561 2.155539 GCGGCTAATTGTTGCAAAACAG 59.844 45.455 0.00 0.00 33.73 3.16
2672 4562 3.380142 CGGCTAATTGTTGCAAAACAGT 58.620 40.909 0.00 0.00 33.73 3.55
2673 4563 3.425193 CGGCTAATTGTTGCAAAACAGTC 59.575 43.478 0.00 0.00 33.73 3.51
2674 4564 4.620982 GGCTAATTGTTGCAAAACAGTCT 58.379 39.130 0.00 0.00 33.73 3.24
2675 4565 4.445385 GGCTAATTGTTGCAAAACAGTCTG 59.555 41.667 0.00 0.00 33.73 3.51
2676 4566 4.445385 GCTAATTGTTGCAAAACAGTCTGG 59.555 41.667 0.00 0.00 33.73 3.86
2677 4567 2.957491 TTGTTGCAAAACAGTCTGGG 57.043 45.000 0.00 0.00 33.73 4.45
2678 4568 0.459489 TGTTGCAAAACAGTCTGGGC 59.541 50.000 0.00 3.21 0.00 5.36
2679 4569 0.249447 GTTGCAAAACAGTCTGGGCC 60.249 55.000 0.00 0.00 0.00 5.80
2681 4571 0.469705 TGCAAAACAGTCTGGGCCAT 60.470 50.000 6.72 0.00 0.00 4.40
2683 4573 1.331214 CAAAACAGTCTGGGCCATGT 58.669 50.000 6.72 5.95 0.00 3.21
2684 4574 2.513753 CAAAACAGTCTGGGCCATGTA 58.486 47.619 6.72 0.00 0.00 2.29
2685 4575 3.091545 CAAAACAGTCTGGGCCATGTAT 58.908 45.455 6.72 0.00 0.00 2.29
2686 4576 4.269183 CAAAACAGTCTGGGCCATGTATA 58.731 43.478 6.72 0.00 0.00 1.47
2687 4577 4.584638 AAACAGTCTGGGCCATGTATAA 57.415 40.909 6.72 0.00 0.00 0.98
2688 4578 4.584638 AACAGTCTGGGCCATGTATAAA 57.415 40.909 6.72 0.00 0.00 1.40
2690 4580 3.265737 ACAGTCTGGGCCATGTATAAACA 59.734 43.478 6.72 0.00 40.69 2.83
2693 4583 2.237643 TCTGGGCCATGTATAAACACGT 59.762 45.455 6.72 0.00 38.78 4.49
2694 4584 3.451540 TCTGGGCCATGTATAAACACGTA 59.548 43.478 6.72 0.00 38.78 3.57
2695 4585 4.101898 TCTGGGCCATGTATAAACACGTAT 59.898 41.667 6.72 0.00 38.78 3.06
2696 4586 4.783055 TGGGCCATGTATAAACACGTATT 58.217 39.130 0.00 0.00 38.78 1.89
2699 4589 5.277634 GGGCCATGTATAAACACGTATTGAC 60.278 44.000 4.39 0.00 38.78 3.18
2713 4603 3.481028 CGTATTGACGTTGTATCTGACCG 59.519 47.826 0.00 0.00 44.31 4.79
2715 4605 0.108992 TGACGTTGTATCTGACCGGC 60.109 55.000 0.00 0.00 0.00 6.13
2716 4606 0.172803 GACGTTGTATCTGACCGGCT 59.827 55.000 0.00 0.00 0.00 5.52
2718 4608 0.806102 CGTTGTATCTGACCGGCTGG 60.806 60.000 11.02 11.02 42.84 4.85
2719 4609 0.462047 GTTGTATCTGACCGGCTGGG 60.462 60.000 18.00 4.46 40.75 4.45
2721 4611 3.161450 TATCTGACCGGCTGGGCC 61.161 66.667 17.09 7.16 46.01 5.80
2731 4621 2.356278 GCTGGGCCCATCTGTCAA 59.644 61.111 28.82 0.00 0.00 3.18
2732 4622 2.048603 GCTGGGCCCATCTGTCAAC 61.049 63.158 28.82 3.64 0.00 3.18
2733 4623 1.379916 CTGGGCCCATCTGTCAACA 59.620 57.895 28.82 0.00 0.00 3.33
2734 4624 0.679002 CTGGGCCCATCTGTCAACAG 60.679 60.000 28.82 5.25 45.08 3.16
2736 4626 2.048603 GGCCCATCTGTCAACAGCC 61.049 63.158 5.25 0.21 43.46 4.85
2737 4627 1.303561 GCCCATCTGTCAACAGCCA 60.304 57.895 5.25 0.00 43.46 4.75
2738 4628 0.895100 GCCCATCTGTCAACAGCCAA 60.895 55.000 5.25 0.00 43.46 4.52
2739 4629 1.843368 CCCATCTGTCAACAGCCAAT 58.157 50.000 5.25 0.00 43.46 3.16
2740 4630 2.173519 CCCATCTGTCAACAGCCAATT 58.826 47.619 5.25 0.00 43.46 2.32
2741 4631 2.564062 CCCATCTGTCAACAGCCAATTT 59.436 45.455 5.25 0.00 43.46 1.82
2742 4632 3.581755 CCATCTGTCAACAGCCAATTTG 58.418 45.455 5.25 0.00 43.46 2.32
2772 4662 3.990959 TTTTGCAGAAAACCCCTTTGT 57.009 38.095 0.00 0.00 0.00 2.83
2774 4664 5.422214 TTTTGCAGAAAACCCCTTTGTTA 57.578 34.783 0.00 0.00 0.00 2.41
2775 4665 5.622346 TTTGCAGAAAACCCCTTTGTTAT 57.378 34.783 0.00 0.00 0.00 1.89
2776 4666 6.732896 TTTGCAGAAAACCCCTTTGTTATA 57.267 33.333 0.00 0.00 0.00 0.98
2777 4667 6.732896 TTGCAGAAAACCCCTTTGTTATAA 57.267 33.333 0.00 0.00 0.00 0.98
2779 4669 5.836358 TGCAGAAAACCCCTTTGTTATAAGT 59.164 36.000 0.00 0.00 0.00 2.24
2780 4670 6.325286 TGCAGAAAACCCCTTTGTTATAAGTT 59.675 34.615 0.00 0.00 0.00 2.66
2781 4671 7.147637 TGCAGAAAACCCCTTTGTTATAAGTTT 60.148 33.333 0.00 0.00 0.00 2.66
2782 4672 8.361889 GCAGAAAACCCCTTTGTTATAAGTTTA 58.638 33.333 0.00 0.00 0.00 2.01
2788 4678 9.596308 AACCCCTTTGTTATAAGTTTATTCACT 57.404 29.630 0.00 0.00 0.00 3.41
2789 4679 9.239551 ACCCCTTTGTTATAAGTTTATTCACTC 57.760 33.333 0.00 0.00 0.00 3.51
2790 4680 9.238368 CCCCTTTGTTATAAGTTTATTCACTCA 57.762 33.333 0.00 0.00 0.00 3.41
2799 4689 4.969484 AGTTTATTCACTCAAAGTCCCGT 58.031 39.130 0.00 0.00 0.00 5.28
2800 4690 5.374071 AGTTTATTCACTCAAAGTCCCGTT 58.626 37.500 0.00 0.00 0.00 4.44
2801 4691 5.238650 AGTTTATTCACTCAAAGTCCCGTTG 59.761 40.000 0.00 0.00 0.00 4.10
2802 4692 1.305201 TTCACTCAAAGTCCCGTTGC 58.695 50.000 0.00 0.00 0.00 4.17
2803 4693 0.468226 TCACTCAAAGTCCCGTTGCT 59.532 50.000 0.00 0.00 0.00 3.91
2804 4694 0.588252 CACTCAAAGTCCCGTTGCTG 59.412 55.000 0.00 0.00 0.00 4.41
2806 5447 1.856265 CTCAAAGTCCCGTTGCTGGC 61.856 60.000 0.00 0.00 0.00 4.85
2838 5479 4.415332 TCGCCTCGACCTCGTTGC 62.415 66.667 0.00 0.00 40.80 4.17
2841 5482 3.382832 CCTCGACCTCGTTGCCCT 61.383 66.667 0.00 0.00 40.80 5.19
2842 5483 2.182030 CTCGACCTCGTTGCCCTC 59.818 66.667 0.00 0.00 40.80 4.30
2844 5485 4.452733 CGACCTCGTTGCCCTCCC 62.453 72.222 0.00 0.00 34.11 4.30
2845 5486 4.097361 GACCTCGTTGCCCTCCCC 62.097 72.222 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.655733 CAAATACCGGATCCACGTGC 59.344 55.000 9.46 0.00 0.00 5.34
25 26 7.744715 CCATCTTGTAGACACACGAAAATAAAC 59.255 37.037 0.00 0.00 36.61 2.01
27 28 7.156000 TCCATCTTGTAGACACACGAAAATAA 58.844 34.615 0.00 0.00 36.61 1.40
29 30 5.547465 TCCATCTTGTAGACACACGAAAAT 58.453 37.500 0.00 0.00 36.61 1.82
63 64 3.491267 GTCACCGTTGAAGAGAAGTTCAG 59.509 47.826 5.50 0.00 37.72 3.02
65 66 3.454375 TGTCACCGTTGAAGAGAAGTTC 58.546 45.455 0.00 0.00 31.90 3.01
79 80 2.006888 ACAGAACAACAACTGTCACCG 58.993 47.619 0.00 0.00 42.61 4.94
82 83 1.396648 CGCACAGAACAACAACTGTCA 59.603 47.619 0.00 0.00 44.07 3.58
84 85 0.098728 GCGCACAGAACAACAACTGT 59.901 50.000 0.30 0.00 46.32 3.55
86 87 0.378257 CAGCGCACAGAACAACAACT 59.622 50.000 11.47 0.00 0.00 3.16
101 102 4.202121 TGCTAAGACTTTATAGGACCAGCG 60.202 45.833 0.00 0.00 0.00 5.18
115 116 2.166664 GGGAAGTCGTCATGCTAAGACT 59.833 50.000 6.44 6.44 44.81 3.24
125 126 0.536687 AGACAGTCGGGAAGTCGTCA 60.537 55.000 0.00 0.00 37.36 4.35
126 127 1.130186 GTAGACAGTCGGGAAGTCGTC 59.870 57.143 0.00 0.00 37.36 4.20
128 129 1.451067 AGTAGACAGTCGGGAAGTCG 58.549 55.000 0.00 0.00 37.36 4.18
134 135 3.255149 ACTTGTTGTAGTAGACAGTCGGG 59.745 47.826 0.00 0.00 39.88 5.14
213 215 1.130749 CTAGCGACGACTACAAGCACT 59.869 52.381 0.00 0.00 0.00 4.40
307 310 9.120538 AGCTTTTATTTTAGCGATAATCTTCCA 57.879 29.630 0.00 0.00 42.18 3.53
309 312 9.307451 CGAGCTTTTATTTTAGCGATAATCTTC 57.693 33.333 0.00 0.00 42.18 2.87
311 314 8.589335 TCGAGCTTTTATTTTAGCGATAATCT 57.411 30.769 0.00 0.00 42.18 2.40
312 315 9.093390 GTTCGAGCTTTTATTTTAGCGATAATC 57.907 33.333 0.00 0.00 42.18 1.75
313 316 8.068380 GGTTCGAGCTTTTATTTTAGCGATAAT 58.932 33.333 0.00 0.00 42.18 1.28
317 320 4.933400 AGGTTCGAGCTTTTATTTTAGCGA 59.067 37.500 0.00 0.00 42.18 4.93
322 325 7.309012 GGGTTTCTAGGTTCGAGCTTTTATTTT 60.309 37.037 0.00 0.00 0.00 1.82
337 340 1.977685 CGGGTTCGGGTTTCTAGGT 59.022 57.895 0.00 0.00 0.00 3.08
436 439 5.658468 CCCGAGTTACCTTAAAACTAGAGG 58.342 45.833 0.00 0.00 37.31 3.69
478 487 5.871465 GCTTGGGCTTTAGATATAAGCTC 57.129 43.478 8.27 5.36 46.85 4.09
584 630 4.129878 CATCGATTGCATGATGACACTC 57.870 45.455 15.32 0.00 43.68 3.51
597 645 6.693761 TTTTTGAGACAAATGCATCGATTG 57.306 33.333 0.00 3.60 0.00 2.67
630 678 5.756195 TTCTAAGATATGTGCATGCAACC 57.244 39.130 24.58 12.00 0.00 3.77
663 719 5.090083 GCCAAAATATTGTGCAAGCATTTG 58.910 37.500 0.00 4.00 34.69 2.32
684 741 7.976135 ACTTGATGTTATTCAGATATCTGCC 57.024 36.000 25.27 11.90 43.46 4.85
857 940 4.874396 ACCGCTTAAAGTGCCTCTTTATAC 59.126 41.667 10.52 6.62 44.72 1.47
863 946 0.685097 TGACCGCTTAAAGTGCCTCT 59.315 50.000 0.00 0.00 0.00 3.69
987 1108 1.090052 CCTCCATCGCGTTTCCCTTC 61.090 60.000 5.77 0.00 0.00 3.46
1171 1304 0.105862 CCCTCCACGATGGGGTAGTA 60.106 60.000 0.00 0.00 35.80 1.82
1469 1605 2.974489 GACGACGGCTCGAACTCCA 61.974 63.158 12.16 0.00 43.06 3.86
1597 1748 1.905215 CTTGACCTCCACAGACATCCT 59.095 52.381 0.00 0.00 0.00 3.24
1614 1765 3.365265 GTCTTGGCGCCCCACTTG 61.365 66.667 26.77 7.53 41.97 3.16
1877 2060 5.587443 TCAATGCAGATCTGTAAACCTGATG 59.413 40.000 23.38 10.88 32.43 3.07
1912 2107 4.097741 GGAGTACCATGCATGCAACATAAA 59.902 41.667 26.68 5.59 35.97 1.40
2032 2291 2.850647 GAGACGCATAGTTCGGTAACAC 59.149 50.000 0.00 0.00 38.12 3.32
2195 2486 1.303091 ACGCCGTGGCTTATTCCAAC 61.303 55.000 9.55 0.00 37.96 3.77
2198 2489 3.098555 CACGCCGTGGCTTATTCC 58.901 61.111 9.90 0.00 39.32 3.01
2305 2596 3.136123 CATGCCACGCTTCCCCTG 61.136 66.667 0.00 0.00 0.00 4.45
2306 2597 3.650950 ACATGCCACGCTTCCCCT 61.651 61.111 0.00 0.00 0.00 4.79
2307 2598 3.443045 CACATGCCACGCTTCCCC 61.443 66.667 0.00 0.00 0.00 4.81
2308 2599 2.672996 ACACATGCCACGCTTCCC 60.673 61.111 0.00 0.00 0.00 3.97
2309 2600 2.187599 GACACACATGCCACGCTTCC 62.188 60.000 0.00 0.00 0.00 3.46
2310 2601 1.207593 GACACACATGCCACGCTTC 59.792 57.895 0.00 0.00 0.00 3.86
2311 2602 1.227943 AGACACACATGCCACGCTT 60.228 52.632 0.00 0.00 0.00 4.68
2312 2603 1.669115 GAGACACACATGCCACGCT 60.669 57.895 0.00 0.00 0.00 5.07
2313 2604 1.300971 ATGAGACACACATGCCACGC 61.301 55.000 0.00 0.00 0.00 5.34
2314 2605 0.445043 CATGAGACACACATGCCACG 59.555 55.000 0.00 0.00 38.58 4.94
2315 2606 1.198408 CACATGAGACACACATGCCAC 59.802 52.381 0.00 0.00 45.95 5.01
2316 2607 1.202794 ACACATGAGACACACATGCCA 60.203 47.619 0.00 0.00 45.95 4.92
2317 2608 1.198408 CACACATGAGACACACATGCC 59.802 52.381 0.00 0.00 45.95 4.40
2318 2609 1.400629 GCACACATGAGACACACATGC 60.401 52.381 0.00 0.00 45.95 4.06
2319 2610 2.095919 CAGCACACATGAGACACACATG 60.096 50.000 0.00 0.00 46.96 3.21
2320 2611 2.148768 CAGCACACATGAGACACACAT 58.851 47.619 0.00 0.00 0.00 3.21
2321 2612 1.138661 TCAGCACACATGAGACACACA 59.861 47.619 0.00 0.00 0.00 3.72
2322 2613 1.528586 GTCAGCACACATGAGACACAC 59.471 52.381 0.00 0.00 34.38 3.82
2323 2614 1.541015 GGTCAGCACACATGAGACACA 60.541 52.381 0.00 0.00 35.34 3.72
2324 2615 1.151668 GGTCAGCACACATGAGACAC 58.848 55.000 0.00 0.00 35.34 3.67
2325 2616 0.035317 GGGTCAGCACACATGAGACA 59.965 55.000 0.00 0.00 35.34 3.41
2326 2617 1.016130 CGGGTCAGCACACATGAGAC 61.016 60.000 0.00 0.00 33.81 3.36
2327 2618 1.184970 TCGGGTCAGCACACATGAGA 61.185 55.000 0.00 0.00 0.00 3.27
2328 2619 0.738762 CTCGGGTCAGCACACATGAG 60.739 60.000 0.00 0.00 0.00 2.90
2329 2620 1.293179 CTCGGGTCAGCACACATGA 59.707 57.895 0.00 0.00 0.00 3.07
2330 2621 0.603707 AACTCGGGTCAGCACACATG 60.604 55.000 0.00 0.00 0.00 3.21
2331 2622 0.603707 CAACTCGGGTCAGCACACAT 60.604 55.000 0.00 0.00 0.00 3.21
2338 2629 2.347490 CCCCACAACTCGGGTCAG 59.653 66.667 0.00 0.00 42.77 3.51
2356 2647 5.163447 GCAGACCTACTCCAATACATACACA 60.163 44.000 0.00 0.00 0.00 3.72
2360 2651 4.039245 GCTGCAGACCTACTCCAATACATA 59.961 45.833 20.43 0.00 0.00 2.29
2361 2652 3.181461 GCTGCAGACCTACTCCAATACAT 60.181 47.826 20.43 0.00 0.00 2.29
2364 4003 2.752030 AGCTGCAGACCTACTCCAATA 58.248 47.619 20.43 0.00 0.00 1.90
2373 4012 4.400961 GCGGGAAGCTGCAGACCT 62.401 66.667 20.43 2.30 44.04 3.85
2375 4014 3.642778 TACGCGGGAAGCTGCAGAC 62.643 63.158 20.43 9.11 45.59 3.51
2416 4055 2.183300 TAGCAACGGCCGCTACTG 59.817 61.111 28.58 18.42 42.56 2.74
2493 4132 1.746615 ATGCACACCTGATCCGCAC 60.747 57.895 0.00 0.00 35.02 5.34
2509 4148 2.944429 GCCTCGCTATGCTGCATG 59.056 61.111 24.59 14.98 0.00 4.06
2510 4149 2.664185 CGCCTCGCTATGCTGCAT 60.664 61.111 20.18 20.18 0.00 3.96
2511 4150 4.147449 ACGCCTCGCTATGCTGCA 62.147 61.111 4.13 4.13 0.00 4.41
2512 4151 3.634072 CACGCCTCGCTATGCTGC 61.634 66.667 0.00 0.00 0.00 5.25
2513 4152 3.634072 GCACGCCTCGCTATGCTG 61.634 66.667 3.33 0.00 36.08 4.41
2514 4153 4.147449 TGCACGCCTCGCTATGCT 62.147 61.111 10.02 0.00 38.52 3.79
2515 4154 3.634072 CTGCACGCCTCGCTATGC 61.634 66.667 3.54 3.54 38.31 3.14
2516 4155 2.963854 CCTGCACGCCTCGCTATG 60.964 66.667 0.00 0.00 0.00 2.23
2517 4156 3.432051 GACCTGCACGCCTCGCTAT 62.432 63.158 0.00 0.00 0.00 2.97
2518 4157 4.129737 GACCTGCACGCCTCGCTA 62.130 66.667 0.00 0.00 0.00 4.26
2532 4171 4.452733 CTTCCACGAGGCCCGACC 62.453 72.222 18.74 0.00 41.76 4.79
2533 4172 3.358076 CTCTTCCACGAGGCCCGAC 62.358 68.421 18.74 1.57 41.76 4.79
2534 4173 3.068691 CTCTTCCACGAGGCCCGA 61.069 66.667 18.74 0.00 41.76 5.14
2535 4174 4.821589 GCTCTTCCACGAGGCCCG 62.822 72.222 11.48 11.48 45.44 6.13
2536 4175 3.394836 AGCTCTTCCACGAGGCCC 61.395 66.667 0.00 0.00 33.74 5.80
2537 4176 2.125350 CAGCTCTTCCACGAGGCC 60.125 66.667 0.00 0.00 33.74 5.19
2538 4177 2.817396 GCAGCTCTTCCACGAGGC 60.817 66.667 0.00 0.00 33.74 4.70
2578 4217 1.825474 AGCATGCCGAAGTGTAGTACT 59.175 47.619 15.66 0.00 42.89 2.73
2579 4218 1.927174 CAGCATGCCGAAGTGTAGTAC 59.073 52.381 15.66 0.00 0.00 2.73
2580 4219 1.548719 ACAGCATGCCGAAGTGTAGTA 59.451 47.619 15.66 0.00 42.53 1.82
2581 4220 0.321671 ACAGCATGCCGAAGTGTAGT 59.678 50.000 15.66 0.00 42.53 2.73
2582 4221 2.293677 TACAGCATGCCGAAGTGTAG 57.706 50.000 15.66 0.00 42.53 2.74
2584 4223 1.806542 CTTTACAGCATGCCGAAGTGT 59.193 47.619 15.66 14.25 42.53 3.55
2585 4224 1.131126 CCTTTACAGCATGCCGAAGTG 59.869 52.381 15.66 8.30 42.53 3.16
2586 4225 1.003118 TCCTTTACAGCATGCCGAAGT 59.997 47.619 15.66 10.81 42.53 3.01
2588 4227 2.418368 ATCCTTTACAGCATGCCGAA 57.582 45.000 15.66 2.98 42.53 4.30
2590 4229 1.066002 CCAATCCTTTACAGCATGCCG 59.934 52.381 15.66 6.75 42.53 5.69
2591 4230 2.102578 ACCAATCCTTTACAGCATGCC 58.897 47.619 15.66 0.00 42.53 4.40
2593 4232 5.824624 AGTGATACCAATCCTTTACAGCATG 59.175 40.000 0.00 0.00 46.00 4.06
2594 4233 6.006275 AGTGATACCAATCCTTTACAGCAT 57.994 37.500 0.00 0.00 0.00 3.79
2595 4234 5.435686 AGTGATACCAATCCTTTACAGCA 57.564 39.130 0.00 0.00 0.00 4.41
2596 4235 6.583562 ACTAGTGATACCAATCCTTTACAGC 58.416 40.000 0.00 0.00 0.00 4.40
2598 4237 7.727578 TGACTAGTGATACCAATCCTTTACA 57.272 36.000 0.00 0.00 0.00 2.41
2626 4516 7.064134 CGCAGAGATGGTACTAACATGTAAAAA 59.936 37.037 0.00 0.00 0.00 1.94
2627 4517 6.533723 CGCAGAGATGGTACTAACATGTAAAA 59.466 38.462 0.00 0.00 0.00 1.52
2630 4520 4.037565 CCGCAGAGATGGTACTAACATGTA 59.962 45.833 0.00 0.00 0.00 2.29
2631 4521 3.181475 CCGCAGAGATGGTACTAACATGT 60.181 47.826 0.00 0.00 0.00 3.21
2632 4522 3.384668 CCGCAGAGATGGTACTAACATG 58.615 50.000 0.00 0.00 0.00 3.21
2633 4523 2.224066 GCCGCAGAGATGGTACTAACAT 60.224 50.000 0.00 0.00 0.00 2.71
2634 4524 1.136305 GCCGCAGAGATGGTACTAACA 59.864 52.381 0.00 0.00 0.00 2.41
2636 4526 1.776662 AGCCGCAGAGATGGTACTAA 58.223 50.000 0.00 0.00 0.00 2.24
2637 4527 2.651382 TAGCCGCAGAGATGGTACTA 57.349 50.000 0.00 0.00 0.00 1.82
2638 4528 1.776662 TTAGCCGCAGAGATGGTACT 58.223 50.000 0.00 0.00 0.00 2.73
2640 4530 2.434336 ACAATTAGCCGCAGAGATGGTA 59.566 45.455 0.00 0.00 0.00 3.25
2641 4531 1.210478 ACAATTAGCCGCAGAGATGGT 59.790 47.619 0.00 0.00 0.00 3.55
2642 4532 1.959042 ACAATTAGCCGCAGAGATGG 58.041 50.000 0.00 0.00 0.00 3.51
2643 4533 2.540361 GCAACAATTAGCCGCAGAGATG 60.540 50.000 0.00 0.00 0.00 2.90
2644 4534 1.672881 GCAACAATTAGCCGCAGAGAT 59.327 47.619 0.00 0.00 0.00 2.75
2645 4535 1.086696 GCAACAATTAGCCGCAGAGA 58.913 50.000 0.00 0.00 0.00 3.10
2646 4536 0.804364 TGCAACAATTAGCCGCAGAG 59.196 50.000 0.00 0.00 0.00 3.35
2647 4537 1.242989 TTGCAACAATTAGCCGCAGA 58.757 45.000 0.00 0.00 33.48 4.26
2649 4539 2.131183 GTTTTGCAACAATTAGCCGCA 58.869 42.857 0.00 0.00 32.54 5.69
2650 4540 2.131183 TGTTTTGCAACAATTAGCCGC 58.869 42.857 0.00 0.00 40.10 6.53
2651 4541 3.380142 ACTGTTTTGCAACAATTAGCCG 58.620 40.909 0.00 0.00 42.53 5.52
2653 4543 4.445385 CCAGACTGTTTTGCAACAATTAGC 59.555 41.667 0.00 0.00 42.53 3.09
2654 4544 4.984161 CCCAGACTGTTTTGCAACAATTAG 59.016 41.667 0.00 3.47 42.53 1.73
2655 4545 4.739137 GCCCAGACTGTTTTGCAACAATTA 60.739 41.667 0.00 0.00 42.53 1.40
2656 4546 3.795877 CCCAGACTGTTTTGCAACAATT 58.204 40.909 0.00 0.00 42.53 2.32
2657 4547 2.483538 GCCCAGACTGTTTTGCAACAAT 60.484 45.455 0.00 0.00 42.53 2.71
2658 4548 1.134848 GCCCAGACTGTTTTGCAACAA 60.135 47.619 0.00 0.00 42.53 2.83
2659 4549 0.459489 GCCCAGACTGTTTTGCAACA 59.541 50.000 0.00 0.00 40.82 3.33
2661 4551 0.685785 TGGCCCAGACTGTTTTGCAA 60.686 50.000 0.00 0.00 0.00 4.08
2662 4552 0.469705 ATGGCCCAGACTGTTTTGCA 60.470 50.000 0.00 0.00 0.00 4.08
2664 4554 1.331214 ACATGGCCCAGACTGTTTTG 58.669 50.000 0.00 0.00 0.00 2.44
2665 4555 2.969821 TACATGGCCCAGACTGTTTT 57.030 45.000 0.00 0.00 0.00 2.43
2666 4556 4.584638 TTATACATGGCCCAGACTGTTT 57.415 40.909 0.00 0.00 0.00 2.83
2667 4557 4.263727 TGTTTATACATGGCCCAGACTGTT 60.264 41.667 0.00 0.00 0.00 3.16
2668 4558 3.265737 TGTTTATACATGGCCCAGACTGT 59.734 43.478 0.00 0.00 0.00 3.55
2669 4559 3.627577 GTGTTTATACATGGCCCAGACTG 59.372 47.826 0.00 0.00 36.50 3.51
2670 4560 3.681594 CGTGTTTATACATGGCCCAGACT 60.682 47.826 0.00 0.00 37.58 3.24
2671 4561 2.612212 CGTGTTTATACATGGCCCAGAC 59.388 50.000 0.00 0.00 37.58 3.51
2672 4562 2.237643 ACGTGTTTATACATGGCCCAGA 59.762 45.455 0.00 0.00 44.05 3.86
2673 4563 2.639065 ACGTGTTTATACATGGCCCAG 58.361 47.619 0.00 0.00 44.05 4.45
2674 4564 2.791347 ACGTGTTTATACATGGCCCA 57.209 45.000 0.00 0.00 44.05 5.36
2675 4565 4.817464 TCAATACGTGTTTATACATGGCCC 59.183 41.667 0.00 0.00 44.05 5.80
2676 4566 5.557514 CGTCAATACGTGTTTATACATGGCC 60.558 44.000 9.86 0.00 44.05 5.36
2677 4567 5.428770 CGTCAATACGTGTTTATACATGGC 58.571 41.667 9.86 0.00 44.05 4.40
2693 4583 3.735820 GCCGGTCAGATACAACGTCAATA 60.736 47.826 1.90 0.00 0.00 1.90
2694 4584 2.888594 CCGGTCAGATACAACGTCAAT 58.111 47.619 0.00 0.00 0.00 2.57
2695 4585 1.670674 GCCGGTCAGATACAACGTCAA 60.671 52.381 1.90 0.00 0.00 3.18
2696 4586 0.108992 GCCGGTCAGATACAACGTCA 60.109 55.000 1.90 0.00 0.00 4.35
2699 4589 0.806102 CCAGCCGGTCAGATACAACG 60.806 60.000 1.90 0.00 0.00 4.10
2700 4590 0.462047 CCCAGCCGGTCAGATACAAC 60.462 60.000 1.90 0.00 0.00 3.32
2701 4591 1.904771 CCCAGCCGGTCAGATACAA 59.095 57.895 1.90 0.00 0.00 2.41
2702 4592 2.731571 GCCCAGCCGGTCAGATACA 61.732 63.158 1.90 0.00 0.00 2.29
2715 4605 0.679002 CTGTTGACAGATGGGCCCAG 60.679 60.000 31.97 19.59 46.59 4.45
2716 4606 1.379916 CTGTTGACAGATGGGCCCA 59.620 57.895 30.92 30.92 46.59 5.36
2718 4608 2.048603 GGCTGTTGACAGATGGGCC 61.049 63.158 14.98 0.00 46.59 5.80
2719 4609 0.895100 TTGGCTGTTGACAGATGGGC 60.895 55.000 14.98 1.92 46.59 5.36
2721 4611 3.581755 CAAATTGGCTGTTGACAGATGG 58.418 45.455 14.98 0.00 46.59 3.51
2722 4612 3.581755 CCAAATTGGCTGTTGACAGATG 58.418 45.455 14.98 3.73 46.59 2.90
2723 4613 3.947910 CCAAATTGGCTGTTGACAGAT 57.052 42.857 14.98 0.00 46.59 2.90
2751 4641 4.293662 ACAAAGGGGTTTTCTGCAAAAA 57.706 36.364 0.00 0.00 33.17 1.94
2753 4643 3.990959 AACAAAGGGGTTTTCTGCAAA 57.009 38.095 0.00 0.00 0.00 3.68
2754 4644 6.325286 ACTTATAACAAAGGGGTTTTCTGCAA 59.675 34.615 0.00 0.00 32.29 4.08
2756 4646 6.340962 ACTTATAACAAAGGGGTTTTCTGC 57.659 37.500 0.00 0.00 32.29 4.26
2762 4652 9.596308 AGTGAATAAACTTATAACAAAGGGGTT 57.404 29.630 0.00 0.00 34.81 4.11
2764 4654 9.238368 TGAGTGAATAAACTTATAACAAAGGGG 57.762 33.333 0.00 0.00 0.00 4.79
2772 4662 9.158233 CGGGACTTTGAGTGAATAAACTTATAA 57.842 33.333 0.00 0.00 0.00 0.98
2774 4664 7.166167 ACGGGACTTTGAGTGAATAAACTTAT 58.834 34.615 0.00 0.00 0.00 1.73
2775 4665 6.527423 ACGGGACTTTGAGTGAATAAACTTA 58.473 36.000 0.00 0.00 0.00 2.24
2776 4666 5.374071 ACGGGACTTTGAGTGAATAAACTT 58.626 37.500 0.00 0.00 0.00 2.66
2777 4667 4.969484 ACGGGACTTTGAGTGAATAAACT 58.031 39.130 0.00 0.00 0.00 2.66
2779 4669 4.023536 GCAACGGGACTTTGAGTGAATAAA 60.024 41.667 0.00 0.00 40.19 1.40
2780 4670 3.500680 GCAACGGGACTTTGAGTGAATAA 59.499 43.478 0.00 0.00 40.19 1.40
2781 4671 3.071479 GCAACGGGACTTTGAGTGAATA 58.929 45.455 0.00 0.00 40.19 1.75
2782 4672 1.880027 GCAACGGGACTTTGAGTGAAT 59.120 47.619 0.00 0.00 40.19 2.57
2783 4673 1.134220 AGCAACGGGACTTTGAGTGAA 60.134 47.619 0.00 0.00 40.19 3.18
2784 4674 0.468226 AGCAACGGGACTTTGAGTGA 59.532 50.000 0.00 0.00 40.19 3.41
2785 4675 0.588252 CAGCAACGGGACTTTGAGTG 59.412 55.000 0.00 0.00 40.19 3.51
2786 4676 0.535102 CCAGCAACGGGACTTTGAGT 60.535 55.000 0.00 0.00 40.19 3.41
2787 4677 1.856265 GCCAGCAACGGGACTTTGAG 61.856 60.000 0.00 0.00 40.19 3.02
2788 4678 1.896660 GCCAGCAACGGGACTTTGA 60.897 57.895 0.00 0.00 40.19 2.69
2789 4679 1.856265 GAGCCAGCAACGGGACTTTG 61.856 60.000 0.00 0.00 40.76 2.77
2790 4680 1.600916 GAGCCAGCAACGGGACTTT 60.601 57.895 0.00 0.00 0.00 2.66
2791 4681 2.032681 GAGCCAGCAACGGGACTT 59.967 61.111 0.00 0.00 0.00 3.01
2792 4682 4.379243 CGAGCCAGCAACGGGACT 62.379 66.667 0.00 0.00 0.00 3.85
2821 5462 4.415332 GCAACGAGGTCGAGGCGA 62.415 66.667 6.35 0.00 43.02 5.54
2825 5466 2.182030 GAGGGCAACGAGGTCGAG 59.818 66.667 6.35 0.00 43.02 4.04
2826 5467 3.379445 GGAGGGCAACGAGGTCGA 61.379 66.667 6.35 0.00 43.02 4.20


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

AutoCloner maintained by Alex Coulton.