Multiple sequence alignment - TraesCS5B01G204500

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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 TraesCS5B01G204500 chr5B 100.000 3039 0 0 1 3039 372247696 372250734 0.000000e+00 5613
1 TraesCS5B01G204500 chr5B 89.577 307 19 3 1670 1976 372249072 372249365 7.950000e-101 377
2 TraesCS5B01G204500 chr5B 89.577 307 19 3 1377 1670 372249365 372249671 7.950000e-101 377
3 TraesCS5B01G204500 chr5D 90.935 2824 175 43 1 2777 321615195 321617984 0.000000e+00 3722
4 TraesCS5B01G204500 chr5D 90.879 307 15 3 1670 1976 321616588 321616881 1.700000e-107 399
5 TraesCS5B01G204500 chr5D 88.179 313 18 6 1377 1670 321616881 321617193 3.730000e-94 355
6 TraesCS5B01G204500 chr5D 82.264 265 43 2 2311 2575 393074893 393075153 3.050000e-55 226
7 TraesCS5B01G204500 chr5A 90.421 2495 142 41 1 2445 415674278 415676725 0.000000e+00 3193
8 TraesCS5B01G204500 chr5A 90.878 296 15 3 1681 1976 415675676 415675959 1.320000e-103 387
9 TraesCS5B01G204500 chr5A 87.540 313 20 7 1377 1670 415675959 415676271 8.070000e-91 344
10 TraesCS5B01G204500 chr2D 84.402 468 73 0 2310 2777 595273243 595273710 7.680000e-126 460
11 TraesCS5B01G204500 chr2D 88.841 233 22 3 2546 2777 552543425 552543654 1.780000e-72 283
12 TraesCS5B01G204500 chr2D 80.377 265 44 4 2776 3039 329491624 329491881 8.600000e-46 195
13 TraesCS5B01G204500 chr2D 79.856 139 26 2 2262 2399 594646234 594646371 1.930000e-17 100
14 TraesCS5B01G204500 chr7D 84.110 472 70 5 2307 2777 13303525 13303058 4.620000e-123 451
15 TraesCS5B01G204500 chr7D 80.995 442 70 7 2349 2777 110320053 110319613 3.750000e-89 339
16 TraesCS5B01G204500 chr7D 83.404 235 34 3 2777 3010 596609574 596609804 2.370000e-51 213
17 TraesCS5B01G204500 chr7D 80.153 262 44 5 2779 3039 424813670 424813924 4.000000e-44 189
18 TraesCS5B01G204500 chr3B 85.990 414 54 4 2363 2775 106970206 106970616 1.000000e-119 440
19 TraesCS5B01G204500 chr3B 81.200 250 37 7 2792 3039 294057018 294056777 3.090000e-45 193
20 TraesCS5B01G204500 chr3B 80.524 267 34 12 2779 3039 718634160 718633906 4.000000e-44 189
21 TraesCS5B01G204500 chr6B 83.585 463 74 1 2313 2775 524061918 524061458 1.670000e-117 433
22 TraesCS5B01G204500 chr6D 80.842 475 85 4 2307 2777 354226083 354226555 4.790000e-98 368
23 TraesCS5B01G204500 chr6D 82.129 263 40 6 2779 3039 160787208 160787465 5.100000e-53 219
24 TraesCS5B01G204500 chr7B 80.123 488 72 8 2450 2916 534507561 534508044 1.040000e-89 340
25 TraesCS5B01G204500 chr7B 75.636 472 81 25 2265 2713 573266819 573267279 1.430000e-48 204
26 TraesCS5B01G204500 chr7B 80.077 261 47 3 2779 3039 77567973 77568228 4.000000e-44 189
27 TraesCS5B01G204500 chr3A 80.534 262 43 6 2779 3039 133966322 133966576 8.600000e-46 195
28 TraesCS5B01G204500 chr1A 81.982 222 35 5 2263 2482 570865373 570865591 1.860000e-42 183
29 TraesCS5B01G204500 chr1A 79.389 262 46 5 2779 3039 146756869 146757123 8.660000e-41 178
30 TraesCS5B01G204500 chr2B 83.030 165 19 7 2262 2422 672317082 672316923 1.140000e-29 141


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 TraesCS5B01G204500 chr5B 372247696 372250734 3038 False 2122.333333 5613 93.051333 1 3039 3 chr5B.!!$F1 3038
1 TraesCS5B01G204500 chr5D 321615195 321617984 2789 False 1492.000000 3722 89.997667 1 2777 3 chr5D.!!$F2 2776
2 TraesCS5B01G204500 chr5A 415674278 415676725 2447 False 1308.000000 3193 89.613000 1 2445 3 chr5A.!!$F1 2444

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
278 298 0.103208 GTCTCCGGTAGTGCCTCATG 59.897 60.0 0.00 0.00 34.25 3.07 F
388 412 0.178970 GAGCAATCATGGCCAGGGAT 60.179 55.0 18.94 16.76 0.00 3.85 F
452 476 1.287730 CGAGAACCAGCTGTGTCTGC 61.288 60.0 18.36 10.48 32.87 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1767 1823 0.036952 TTCAGCCTTCTTCTCTGCCG 60.037 55.000 0.00 0.0 0.00 5.69 R
1825 1887 0.461693 CAACTGCTAGCTGCTCCTCC 60.462 60.000 20.35 0.0 43.37 4.30 R
2299 2367 1.067416 GTATCCGCCGACAGATGCA 59.933 57.895 0.00 0.0 0.00 3.96 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
27 28 2.048603 GGGCCAGGCTACTGCTTTG 61.049 63.158 12.43 0.00 43.53 2.77
33 34 3.815396 GCTACTGCTTTGCCCCGC 61.815 66.667 0.00 0.00 36.03 6.13
70 78 0.834612 GTATGTCCATGGAACCCGGA 59.165 55.000 18.20 0.00 0.00 5.14
85 93 3.676216 GGAAAATGTTCCCGGCGT 58.324 55.556 6.01 0.00 46.84 5.68
113 121 4.383861 CGGAGGTGCTGCTGCTGA 62.384 66.667 17.00 0.00 40.48 4.26
115 123 1.378250 GGAGGTGCTGCTGCTGATT 60.378 57.895 17.00 0.00 40.48 2.57
116 124 0.964358 GGAGGTGCTGCTGCTGATTT 60.964 55.000 17.00 0.00 40.48 2.17
117 125 0.450983 GAGGTGCTGCTGCTGATTTC 59.549 55.000 17.00 4.18 40.48 2.17
118 126 0.964358 AGGTGCTGCTGCTGATTTCC 60.964 55.000 17.00 9.09 40.48 3.13
135 150 0.394192 TCCCACTGTTGCTGTCAGAG 59.606 55.000 3.32 0.00 36.81 3.35
151 166 2.469274 AGAGTGCCTCTGAATGTGTG 57.531 50.000 4.16 0.00 39.62 3.82
155 170 2.105477 AGTGCCTCTGAATGTGTGAACT 59.895 45.455 0.00 0.00 0.00 3.01
197 212 4.012374 TGCTGGTTTCAATCTTCATCTCC 58.988 43.478 0.00 0.00 0.00 3.71
198 213 3.064545 GCTGGTTTCAATCTTCATCTCCG 59.935 47.826 0.00 0.00 0.00 4.63
224 241 0.247736 CCGTAGCAGAAGGTCTTGCT 59.752 55.000 4.30 4.30 35.86 3.91
239 256 1.004044 CTTGCTTGTCCCTGTCCAGAT 59.996 52.381 0.00 0.00 0.00 2.90
275 295 0.108756 GTTGTCTCCGGTAGTGCCTC 60.109 60.000 0.00 0.00 34.25 4.70
278 298 0.103208 GTCTCCGGTAGTGCCTCATG 59.897 60.000 0.00 0.00 34.25 3.07
288 308 1.905215 AGTGCCTCATGCTCAACTACT 59.095 47.619 0.00 0.00 42.00 2.57
364 388 9.223099 GATTCCAAATTCCAAGAACAATGATTT 57.777 29.630 0.00 0.00 0.00 2.17
388 412 0.178970 GAGCAATCATGGCCAGGGAT 60.179 55.000 18.94 16.76 0.00 3.85
452 476 1.287730 CGAGAACCAGCTGTGTCTGC 61.288 60.000 18.36 10.48 32.87 4.26
594 629 2.558380 AAATTCCGGAGCCTGCCCTC 62.558 60.000 3.34 0.00 0.00 4.30
665 715 1.481871 TGGGCAGCAGGTAGTACTAC 58.518 55.000 22.53 22.53 35.40 2.73
806 856 6.149973 TCCTTGCATTGCAGCATAGATTATAC 59.850 38.462 11.76 0.00 45.19 1.47
807 857 6.150641 CCTTGCATTGCAGCATAGATTATACT 59.849 38.462 11.76 0.00 45.19 2.12
809 859 7.838771 TGCATTGCAGCATAGATTATACTAG 57.161 36.000 7.38 0.00 40.11 2.57
811 861 6.314648 GCATTGCAGCATAGATTATACTAGCA 59.685 38.462 3.15 0.00 0.00 3.49
812 862 7.465647 GCATTGCAGCATAGATTATACTAGCAG 60.466 40.741 3.15 0.00 0.00 4.24
813 863 6.596309 TGCAGCATAGATTATACTAGCAGT 57.404 37.500 0.00 0.00 0.00 4.40
814 864 7.703058 TGCAGCATAGATTATACTAGCAGTA 57.297 36.000 0.00 0.00 34.82 2.74
815 865 7.539436 TGCAGCATAGATTATACTAGCAGTAC 58.461 38.462 0.00 0.00 32.84 2.73
816 866 6.975772 GCAGCATAGATTATACTAGCAGTACC 59.024 42.308 0.00 0.00 32.84 3.34
913 963 2.993899 GCCGCTGCATATAACGAATACT 59.006 45.455 0.00 0.00 37.47 2.12
914 964 3.432252 GCCGCTGCATATAACGAATACTT 59.568 43.478 0.00 0.00 37.47 2.24
957 1012 2.501723 TGTTCCTGGCTATCTGGTTCTC 59.498 50.000 0.00 0.00 36.08 2.87
1039 1094 2.191400 AGCCTGCTGATCTCAAGGTAA 58.809 47.619 9.10 0.00 0.00 2.85
1090 1145 3.007973 GCGGAGAAGAAGGTCGCCT 62.008 63.158 0.00 0.00 40.44 5.52
1175 1230 2.104792 TGCTCAAAGAGGTACACAGCTT 59.895 45.455 0.00 0.00 30.99 3.74
1176 1231 2.481952 GCTCAAAGAGGTACACAGCTTG 59.518 50.000 0.00 0.00 30.99 4.01
1205 1260 5.056894 TCCTCTTCACTCGCTACTTTAAC 57.943 43.478 0.00 0.00 0.00 2.01
1208 1263 4.224433 TCTTCACTCGCTACTTTAACACG 58.776 43.478 0.00 0.00 0.00 4.49
1231 1286 4.320057 GGTGACAGAAGAGCATGTTTTGAG 60.320 45.833 0.00 0.00 27.76 3.02
1257 1312 2.549754 CAGTTGCGGACATGTTCTCTTT 59.450 45.455 0.00 0.00 0.00 2.52
1346 1402 1.745653 GCAGCAGGGGATTTCTAACAC 59.254 52.381 0.00 0.00 0.00 3.32
1363 1419 3.669939 ACACCCCCTTTTATCTGGATG 57.330 47.619 0.00 0.00 0.00 3.51
1364 1420 2.310538 CACCCCCTTTTATCTGGATGC 58.689 52.381 0.00 0.00 0.00 3.91
1365 1421 1.929494 ACCCCCTTTTATCTGGATGCA 59.071 47.619 0.00 0.00 0.00 3.96
1366 1422 2.310538 CCCCCTTTTATCTGGATGCAC 58.689 52.381 0.00 0.00 0.00 4.57
1535 1591 1.442769 TGAAAATGGAGCGACAGAGC 58.557 50.000 0.00 0.00 37.41 4.09
1614 1670 2.202987 GGAGCCAGAGGATGCACG 60.203 66.667 0.00 0.00 27.57 5.34
1642 1698 2.873649 GCAGGTGGTGGAAGAAGAGAAG 60.874 54.545 0.00 0.00 0.00 2.85
1692 1748 8.603181 GGTTGCAATTTATCTTTATGCGATTTT 58.397 29.630 0.59 0.00 39.81 1.82
1719 1775 6.661377 ACTTCATGAGTCAAGAAGCTCTACTA 59.339 38.462 29.11 0.25 41.16 1.82
1749 1805 2.726760 CCTTTTGACAGAACGACGAGAG 59.273 50.000 0.00 0.00 0.00 3.20
1765 1821 3.384014 GAGTGACGTCGAGGCTCCG 62.384 68.421 11.62 10.25 0.00 4.63
1792 1854 3.007831 CAGAGAAGAAGGCTGAAGAACCT 59.992 47.826 0.00 0.00 38.14 3.50
1825 1887 1.201855 GCTGATGAAAGTGAAGCGACG 60.202 52.381 0.00 0.00 0.00 5.12
1925 1987 1.415659 CAGAGGATCCCCAGACACATC 59.584 57.143 8.55 0.00 33.66 3.06
1950 2012 2.777692 AGGTGGTGGAAGAAGAGAAACA 59.222 45.455 0.00 0.00 0.00 2.83
2117 2179 2.844946 TCTTGTTCATTTCCGTGCTGA 58.155 42.857 0.00 0.00 0.00 4.26
2120 2182 3.347958 TGTTCATTTCCGTGCTGAAAC 57.652 42.857 0.00 0.00 37.08 2.78
2194 2262 9.280174 CCGGTGGTGTAATATAGATTTTATTGT 57.720 33.333 0.00 0.00 0.00 2.71
2218 2286 6.876257 GTCATTTCTCTGTTTATGTCACCTCT 59.124 38.462 0.00 0.00 0.00 3.69
2222 2290 6.030548 TCTCTGTTTATGTCACCTCTTCAG 57.969 41.667 0.00 0.00 0.00 3.02
2223 2291 5.540337 TCTCTGTTTATGTCACCTCTTCAGT 59.460 40.000 0.00 0.00 0.00 3.41
2224 2292 6.719829 TCTCTGTTTATGTCACCTCTTCAGTA 59.280 38.462 0.00 0.00 0.00 2.74
2225 2293 6.688578 TCTGTTTATGTCACCTCTTCAGTAC 58.311 40.000 0.00 0.00 0.00 2.73
2226 2294 6.266786 TCTGTTTATGTCACCTCTTCAGTACA 59.733 38.462 0.00 0.00 0.00 2.90
2233 2301 5.648526 TGTCACCTCTTCAGTACACTAGATC 59.351 44.000 0.00 0.00 0.00 2.75
2273 2341 2.834638 ATGCAACCTTAGGGCATCTT 57.165 45.000 8.81 0.00 44.41 2.40
2277 2345 3.026694 GCAACCTTAGGGCATCTTCAAT 58.973 45.455 2.32 0.00 35.63 2.57
2279 2347 4.019174 CAACCTTAGGGCATCTTCAATGT 58.981 43.478 2.32 0.00 35.63 2.71
2286 2354 1.678728 GGCATCTTCAATGTCGACCCA 60.679 52.381 14.12 0.00 0.00 4.51
2294 2362 4.927978 TCAATGTCGACCCACAAATTTT 57.072 36.364 14.12 0.00 0.00 1.82
2299 2367 3.146847 GTCGACCCACAAATTTTCTCCT 58.853 45.455 3.51 0.00 0.00 3.69
2305 2373 3.512724 CCCACAAATTTTCTCCTGCATCT 59.487 43.478 0.00 0.00 0.00 2.90
2309 2377 4.083110 ACAAATTTTCTCCTGCATCTGTCG 60.083 41.667 0.00 0.00 0.00 4.35
2310 2378 2.099141 TTTTCTCCTGCATCTGTCGG 57.901 50.000 0.00 0.00 0.00 4.79
2315 2383 2.107750 CTGCATCTGTCGGCGGAT 59.892 61.111 5.25 5.25 41.16 4.18
2343 2411 3.224324 GAGGCCGCTATCCGACCA 61.224 66.667 0.00 0.00 42.55 4.02
2344 2412 2.524394 AGGCCGCTATCCGACCAT 60.524 61.111 0.00 0.00 42.55 3.55
2346 2414 1.215647 GGCCGCTATCCGACCATAG 59.784 63.158 0.00 0.00 39.53 2.23
2350 2418 1.446272 GCTATCCGACCATAGCCGC 60.446 63.158 8.89 0.00 43.86 6.53
2351 2419 1.964448 CTATCCGACCATAGCCGCA 59.036 57.895 0.00 0.00 0.00 5.69
2370 2438 5.060940 GCCGCACATATTTCAAACTCTTTTC 59.939 40.000 0.00 0.00 0.00 2.29
2400 2468 4.704540 ACCGGATGAAATTCATGCAAACTA 59.295 37.500 23.55 0.00 44.18 2.24
2402 2470 5.066375 CCGGATGAAATTCATGCAAACTAGA 59.934 40.000 23.55 0.00 44.18 2.43
2413 2481 5.941058 TCATGCAAACTAGACCGGATTTTAA 59.059 36.000 9.46 0.00 0.00 1.52
2426 2494 6.557110 ACCGGATTTTAAATAAACATGACGG 58.443 36.000 9.46 0.00 40.69 4.79
2441 2509 4.522405 ACATGACGGATTTCATTCAAACCA 59.478 37.500 0.00 0.00 33.74 3.67
2448 2516 6.072673 ACGGATTTCATTCAAACCAGACTAAC 60.073 38.462 0.00 0.00 0.00 2.34
2497 2565 6.968335 TCAACTAAAAACAAAACCGAACTAGC 59.032 34.615 0.00 0.00 0.00 3.42
2501 2569 6.644248 AAAAACAAAACCGAACTAGCCTAT 57.356 33.333 0.00 0.00 0.00 2.57
2502 2570 5.622770 AAACAAAACCGAACTAGCCTATG 57.377 39.130 0.00 0.00 0.00 2.23
2540 2608 4.808414 ATCCATTCCGACGACATGATAT 57.192 40.909 0.00 0.00 0.00 1.63
2560 2628 1.558294 TCCTCGACTAGTCTACTGCCA 59.442 52.381 20.34 0.00 0.00 4.92
2579 2647 4.867599 CCGCGGCGGGTCTCTAAC 62.868 72.222 32.80 0.00 44.15 2.34
2584 2652 2.694760 GGCGGGTCTCTAACGTCGT 61.695 63.158 0.00 0.00 0.00 4.34
2595 2663 0.899253 TAACGTCGTCCCCATGACCA 60.899 55.000 0.00 0.00 41.18 4.02
2596 2664 1.760479 AACGTCGTCCCCATGACCAA 61.760 55.000 0.00 0.00 41.18 3.67
2600 2668 1.125093 TCGTCCCCATGACCAACAGT 61.125 55.000 0.00 0.00 41.18 3.55
2611 2679 2.515398 CAACAGTGGTGAGGCCCA 59.485 61.111 0.38 0.00 36.04 5.36
2614 2682 1.352622 AACAGTGGTGAGGCCCAGAA 61.353 55.000 0.00 0.00 34.43 3.02
2626 2694 3.048600 AGGCCCAGAAGTATATGCTTCA 58.951 45.455 28.32 0.00 45.28 3.02
2639 2707 2.616969 GCTTCAGCACAAAGGACGA 58.383 52.632 0.00 0.00 41.59 4.20
2652 2720 2.722201 GGACGACTCGCTTCCCCAT 61.722 63.158 0.00 0.00 0.00 4.00
2654 2722 2.278857 CGACTCGCTTCCCCATCG 60.279 66.667 0.00 0.00 0.00 3.84
2659 2727 2.109799 CGCTTCCCCATCGCTCAT 59.890 61.111 0.00 0.00 0.00 2.90
2671 2739 1.519455 CGCTCATCGGAGTGGAACC 60.519 63.158 0.00 0.00 45.78 3.62
2688 2756 3.126879 CGCCGCCTGATGCTTCAA 61.127 61.111 3.65 0.00 38.05 2.69
2689 2757 2.475466 CGCCGCCTGATGCTTCAAT 61.475 57.895 3.65 0.00 38.05 2.57
2746 2814 3.526430 GGTTGGTTCTTAGGTAAGGGGAT 59.474 47.826 0.00 0.00 34.14 3.85
2747 2815 4.524053 GTTGGTTCTTAGGTAAGGGGATG 58.476 47.826 0.00 0.00 34.14 3.51
2760 2828 4.504596 GGATGATGGTGGCCGGCA 62.505 66.667 30.85 12.04 0.00 5.69
2761 2829 2.903855 GATGATGGTGGCCGGCAG 60.904 66.667 30.85 0.00 0.00 4.85
2777 2845 2.203788 AGGAGGGCAAGACACCGA 60.204 61.111 0.00 0.00 0.00 4.69
2778 2846 2.047179 GGAGGGCAAGACACCGAC 60.047 66.667 0.00 0.00 0.00 4.79
2779 2847 2.047179 GAGGGCAAGACACCGACC 60.047 66.667 0.00 0.00 0.00 4.79
2780 2848 2.526873 AGGGCAAGACACCGACCT 60.527 61.111 0.00 0.00 0.00 3.85
2781 2849 2.113243 GAGGGCAAGACACCGACCTT 62.113 60.000 0.00 0.00 0.00 3.50
2782 2850 1.671379 GGGCAAGACACCGACCTTC 60.671 63.158 0.00 0.00 0.00 3.46
2783 2851 1.070786 GGCAAGACACCGACCTTCA 59.929 57.895 0.00 0.00 0.00 3.02
2784 2852 0.321653 GGCAAGACACCGACCTTCAT 60.322 55.000 0.00 0.00 0.00 2.57
2785 2853 0.798776 GCAAGACACCGACCTTCATG 59.201 55.000 0.00 0.00 0.00 3.07
2786 2854 1.442769 CAAGACACCGACCTTCATGG 58.557 55.000 0.00 0.00 42.93 3.66
2787 2855 0.324943 AAGACACCGACCTTCATGGG 59.675 55.000 0.00 0.00 41.11 4.00
2788 2856 0.544357 AGACACCGACCTTCATGGGA 60.544 55.000 0.00 0.00 41.11 4.37
2789 2857 0.391263 GACACCGACCTTCATGGGAC 60.391 60.000 0.00 0.00 41.11 4.46
2790 2858 1.078426 CACCGACCTTCATGGGACC 60.078 63.158 0.00 0.00 41.11 4.46
2791 2859 2.298661 ACCGACCTTCATGGGACCC 61.299 63.158 2.45 2.45 41.11 4.46
2792 2860 2.297895 CCGACCTTCATGGGACCCA 61.298 63.158 17.73 17.73 41.11 4.51
2793 2861 1.682849 CGACCTTCATGGGACCCAA 59.317 57.895 19.58 0.00 41.11 4.12
2794 2862 0.392998 CGACCTTCATGGGACCCAAG 60.393 60.000 19.58 14.31 41.11 3.61
2795 2863 0.681243 GACCTTCATGGGACCCAAGC 60.681 60.000 19.58 0.00 41.11 4.01
2796 2864 1.750399 CCTTCATGGGACCCAAGCG 60.750 63.158 19.58 9.52 36.95 4.68
2797 2865 1.750399 CTTCATGGGACCCAAGCGG 60.750 63.158 19.58 7.90 36.95 5.52
2798 2866 3.936772 TTCATGGGACCCAAGCGGC 62.937 63.158 19.58 0.00 36.95 6.53
2819 2887 3.709567 GGCCTCCCGTGTTCTACT 58.290 61.111 0.00 0.00 0.00 2.57
2820 2888 1.980844 GGCCTCCCGTGTTCTACTT 59.019 57.895 0.00 0.00 0.00 2.24
2821 2889 0.108281 GGCCTCCCGTGTTCTACTTC 60.108 60.000 0.00 0.00 0.00 3.01
2822 2890 0.896226 GCCTCCCGTGTTCTACTTCT 59.104 55.000 0.00 0.00 0.00 2.85
2823 2891 1.135053 GCCTCCCGTGTTCTACTTCTC 60.135 57.143 0.00 0.00 0.00 2.87
2824 2892 1.477295 CCTCCCGTGTTCTACTTCTCC 59.523 57.143 0.00 0.00 0.00 3.71
2825 2893 2.448453 CTCCCGTGTTCTACTTCTCCT 58.552 52.381 0.00 0.00 0.00 3.69
2826 2894 2.424246 CTCCCGTGTTCTACTTCTCCTC 59.576 54.545 0.00 0.00 0.00 3.71
2827 2895 1.132643 CCCGTGTTCTACTTCTCCTCG 59.867 57.143 0.00 0.00 0.00 4.63
2828 2896 2.082231 CCGTGTTCTACTTCTCCTCGA 58.918 52.381 0.00 0.00 0.00 4.04
2829 2897 2.683867 CCGTGTTCTACTTCTCCTCGAT 59.316 50.000 0.00 0.00 0.00 3.59
2830 2898 3.875727 CCGTGTTCTACTTCTCCTCGATA 59.124 47.826 0.00 0.00 0.00 2.92
2831 2899 4.334759 CCGTGTTCTACTTCTCCTCGATAA 59.665 45.833 0.00 0.00 0.00 1.75
2832 2900 5.008811 CCGTGTTCTACTTCTCCTCGATAAT 59.991 44.000 0.00 0.00 0.00 1.28
2833 2901 5.910166 CGTGTTCTACTTCTCCTCGATAATG 59.090 44.000 0.00 0.00 0.00 1.90
2834 2902 6.210078 GTGTTCTACTTCTCCTCGATAATGG 58.790 44.000 0.00 0.00 0.00 3.16
2835 2903 5.221263 TGTTCTACTTCTCCTCGATAATGGC 60.221 44.000 0.00 0.00 0.00 4.40
2836 2904 2.802787 ACTTCTCCTCGATAATGGCG 57.197 50.000 0.00 0.00 0.00 5.69
2837 2905 1.341531 ACTTCTCCTCGATAATGGCGG 59.658 52.381 0.00 0.00 0.00 6.13
2838 2906 0.033504 TTCTCCTCGATAATGGCGGC 59.966 55.000 0.00 0.00 0.00 6.53
2839 2907 1.734477 CTCCTCGATAATGGCGGCG 60.734 63.158 0.51 0.51 0.00 6.46
2840 2908 2.142357 CTCCTCGATAATGGCGGCGA 62.142 60.000 12.98 0.00 0.00 5.54
2841 2909 1.734477 CCTCGATAATGGCGGCGAG 60.734 63.158 12.98 0.00 47.00 5.03
2842 2910 2.375766 CTCGATAATGGCGGCGAGC 61.376 63.158 12.98 0.00 42.82 5.03
2852 2920 4.505217 CGGCGAGCATGAACGTGC 62.505 66.667 0.00 10.54 45.38 5.34
2858 2926 4.465512 GCATGAACGTGCTGGCCG 62.466 66.667 11.15 0.00 41.82 6.13
2859 2927 4.465512 CATGAACGTGCTGGCCGC 62.466 66.667 11.92 11.92 39.77 6.53
2860 2928 4.704833 ATGAACGTGCTGGCCGCT 62.705 61.111 18.14 0.72 40.11 5.52
2861 2929 3.309436 ATGAACGTGCTGGCCGCTA 62.309 57.895 18.14 4.84 40.11 4.26
2862 2930 3.188786 GAACGTGCTGGCCGCTAG 61.189 66.667 18.14 14.19 40.11 3.42
2869 2937 4.914420 CTGGCCGCTAGCTCGTCG 62.914 72.222 13.93 0.00 43.05 5.12
2871 2939 3.967335 GGCCGCTAGCTCGTCGAT 61.967 66.667 13.93 0.00 43.05 3.59
2872 2940 2.614446 GGCCGCTAGCTCGTCGATA 61.614 63.158 13.93 0.00 43.05 2.92
2873 2941 1.502640 GCCGCTAGCTCGTCGATAT 59.497 57.895 13.93 0.00 38.99 1.63
2874 2942 0.521659 GCCGCTAGCTCGTCGATATC 60.522 60.000 13.93 0.00 38.99 1.63
2875 2943 0.097325 CCGCTAGCTCGTCGATATCC 59.903 60.000 13.93 0.00 0.00 2.59
2876 2944 0.247340 CGCTAGCTCGTCGATATCCG 60.247 60.000 13.93 0.00 40.25 4.18
2877 2945 0.521659 GCTAGCTCGTCGATATCCGC 60.522 60.000 7.70 0.00 38.37 5.54
2878 2946 0.247340 CTAGCTCGTCGATATCCGCG 60.247 60.000 0.00 0.00 38.47 6.46
2879 2947 2.236803 TAGCTCGTCGATATCCGCGC 62.237 60.000 0.00 0.00 37.58 6.86
2880 2948 2.251371 CTCGTCGATATCCGCGCA 59.749 61.111 8.75 0.00 37.58 6.09
2881 2949 2.051614 TCGTCGATATCCGCGCAC 60.052 61.111 8.75 0.00 37.58 5.34
2882 2950 3.097728 CGTCGATATCCGCGCACC 61.098 66.667 8.75 0.00 38.37 5.01
2883 2951 2.733593 GTCGATATCCGCGCACCC 60.734 66.667 8.75 0.00 38.37 4.61
2884 2952 4.337060 TCGATATCCGCGCACCCG 62.337 66.667 8.75 1.53 38.37 5.28
2893 2961 4.103103 GCGCACCCGGCTTCTTTC 62.103 66.667 0.30 0.00 41.67 2.62
2894 2962 2.358737 CGCACCCGGCTTCTTTCT 60.359 61.111 0.00 0.00 41.67 2.52
2895 2963 2.391389 CGCACCCGGCTTCTTTCTC 61.391 63.158 0.00 0.00 41.67 2.87
2896 2964 1.003233 GCACCCGGCTTCTTTCTCT 60.003 57.895 0.00 0.00 40.25 3.10
2897 2965 1.301677 GCACCCGGCTTCTTTCTCTG 61.302 60.000 0.00 0.00 40.25 3.35
2898 2966 1.003233 ACCCGGCTTCTTTCTCTGC 60.003 57.895 0.00 0.00 0.00 4.26
2899 2967 1.746991 CCCGGCTTCTTTCTCTGCC 60.747 63.158 0.00 0.00 41.76 4.85
2900 2968 1.298014 CCGGCTTCTTTCTCTGCCT 59.702 57.895 0.00 0.00 42.90 4.75
2901 2969 1.023513 CCGGCTTCTTTCTCTGCCTG 61.024 60.000 0.00 0.00 42.90 4.85
2902 2970 1.642952 CGGCTTCTTTCTCTGCCTGC 61.643 60.000 0.00 0.00 42.90 4.85
2903 2971 0.607489 GGCTTCTTTCTCTGCCTGCA 60.607 55.000 0.00 0.00 41.92 4.41
2904 2972 1.461559 GCTTCTTTCTCTGCCTGCAT 58.538 50.000 0.00 0.00 0.00 3.96
2905 2973 1.132643 GCTTCTTTCTCTGCCTGCATG 59.867 52.381 0.00 0.00 0.00 4.06
2906 2974 1.743958 CTTCTTTCTCTGCCTGCATGG 59.256 52.381 0.00 0.00 39.35 3.66
2915 2983 2.590007 CCTGCATGGCGAGGCTAC 60.590 66.667 6.95 0.00 0.00 3.58
2916 2984 2.963854 CTGCATGGCGAGGCTACG 60.964 66.667 6.95 0.00 0.00 3.51
2917 2985 3.723235 CTGCATGGCGAGGCTACGT 62.723 63.158 6.95 0.00 35.59 3.57
2918 2986 2.349969 CTGCATGGCGAGGCTACGTA 62.350 60.000 6.95 0.00 35.59 3.57
2919 2987 1.949631 GCATGGCGAGGCTACGTAC 60.950 63.158 0.00 0.00 35.59 3.67
2920 2988 1.657487 CATGGCGAGGCTACGTACG 60.657 63.158 15.01 15.01 35.59 3.67
2921 2989 2.117156 ATGGCGAGGCTACGTACGT 61.117 57.895 25.98 25.98 35.59 3.57
2922 2990 2.277756 GGCGAGGCTACGTACGTG 60.278 66.667 30.25 19.92 35.59 4.49
2923 2991 2.948134 GCGAGGCTACGTACGTGC 60.948 66.667 30.25 27.11 35.59 5.34
2924 2992 2.646862 CGAGGCTACGTACGTGCG 60.647 66.667 30.25 24.57 37.94 5.34
2925 2993 2.948134 GAGGCTACGTACGTGCGC 60.948 66.667 30.25 28.00 34.88 6.09
2926 2994 3.672255 GAGGCTACGTACGTGCGCA 62.672 63.158 31.42 12.77 34.88 6.09
2927 2995 2.581409 GGCTACGTACGTGCGCAT 60.581 61.111 31.42 10.20 34.88 4.73
2928 2996 2.574222 GGCTACGTACGTGCGCATC 61.574 63.158 31.42 19.09 34.88 3.91
2929 2997 2.902383 GCTACGTACGTGCGCATCG 61.902 63.158 30.25 24.02 34.88 3.84
2960 3028 4.767255 GGTCGCAGGTGCTGGAGG 62.767 72.222 0.00 0.00 39.32 4.30
2967 3035 3.702048 GGTGCTGGAGGCGTGGTA 61.702 66.667 0.00 0.00 45.43 3.25
2968 3036 2.434359 GTGCTGGAGGCGTGGTAC 60.434 66.667 0.00 0.00 45.43 3.34
2969 3037 4.063967 TGCTGGAGGCGTGGTACG 62.064 66.667 0.00 0.00 45.88 3.67
2970 3038 3.755628 GCTGGAGGCGTGGTACGA 61.756 66.667 5.44 0.00 46.05 3.43
2997 3065 4.831307 GTCGACGGCAGCGACGAT 62.831 66.667 14.99 0.00 46.85 3.73
2998 3066 4.829518 TCGACGGCAGCGACGATG 62.830 66.667 9.11 9.11 35.20 3.84
3018 3086 4.760047 CGTGCCGCCAAGCTACCT 62.760 66.667 0.00 0.00 0.00 3.08
3019 3087 3.127533 GTGCCGCCAAGCTACCTG 61.128 66.667 0.00 0.00 0.00 4.00
3020 3088 3.318384 TGCCGCCAAGCTACCTGA 61.318 61.111 0.00 0.00 0.00 3.86
3021 3089 2.820037 GCCGCCAAGCTACCTGAC 60.820 66.667 0.00 0.00 0.00 3.51
3022 3090 2.509336 CCGCCAAGCTACCTGACG 60.509 66.667 0.00 0.00 0.00 4.35
3023 3091 2.261671 CGCCAAGCTACCTGACGT 59.738 61.111 0.00 0.00 0.00 4.34
3024 3092 2.094659 CGCCAAGCTACCTGACGTG 61.095 63.158 0.00 0.00 0.00 4.49
3025 3093 1.004918 GCCAAGCTACCTGACGTGT 60.005 57.895 0.00 0.00 0.00 4.49
3026 3094 1.014564 GCCAAGCTACCTGACGTGTC 61.015 60.000 0.00 0.00 0.00 3.67
3027 3095 0.732880 CCAAGCTACCTGACGTGTCG 60.733 60.000 0.00 0.00 0.00 4.35
3028 3096 0.732880 CAAGCTACCTGACGTGTCGG 60.733 60.000 0.00 1.73 35.77 4.79
3029 3097 2.488087 AAGCTACCTGACGTGTCGGC 62.488 60.000 0.00 0.00 34.69 5.54
3030 3098 2.181021 CTACCTGACGTGTCGGCC 59.819 66.667 0.00 0.00 31.60 6.13
3031 3099 2.282674 TACCTGACGTGTCGGCCT 60.283 61.111 0.00 0.00 31.60 5.19
3032 3100 2.543687 CTACCTGACGTGTCGGCCTG 62.544 65.000 0.00 0.00 31.60 4.85
3033 3101 4.742201 CCTGACGTGTCGGCCTGG 62.742 72.222 0.00 0.00 31.60 4.45
3034 3102 3.680786 CTGACGTGTCGGCCTGGA 61.681 66.667 0.00 0.00 31.60 3.86
3035 3103 3.633094 CTGACGTGTCGGCCTGGAG 62.633 68.421 0.00 0.00 31.60 3.86
3038 3106 4.680237 CGTGTCGGCCTGGAGCAA 62.680 66.667 0.00 0.00 46.50 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.048603 CAAAGCAGTAGCCTGGCCC 61.049 63.158 16.57 6.44 43.56 5.80
27 28 2.679996 ATCCTTGTTTGGCGGGGC 60.680 61.111 0.00 0.00 0.00 5.80
33 34 0.673437 ACGGCAACATCCTTGTTTGG 59.327 50.000 0.00 0.00 43.57 3.28
70 78 1.606903 TACAACGCCGGGAACATTTT 58.393 45.000 2.18 0.00 0.00 1.82
85 93 2.811431 CAGCACCTCCGTTGAATTACAA 59.189 45.455 0.00 0.00 36.02 2.41
113 121 2.158623 TCTGACAGCAACAGTGGGAAAT 60.159 45.455 0.00 0.00 36.81 2.17
115 123 0.836606 TCTGACAGCAACAGTGGGAA 59.163 50.000 0.00 0.00 36.81 3.97
116 124 0.394192 CTCTGACAGCAACAGTGGGA 59.606 55.000 0.00 0.00 36.81 4.37
117 125 0.107456 ACTCTGACAGCAACAGTGGG 59.893 55.000 0.00 0.00 36.81 4.61
118 126 1.224075 CACTCTGACAGCAACAGTGG 58.776 55.000 12.17 0.00 33.98 4.00
135 150 2.498167 AGTTCACACATTCAGAGGCAC 58.502 47.619 0.00 0.00 0.00 5.01
151 166 2.096218 CAGAAACACGGCTTGCTAGTTC 60.096 50.000 0.00 0.00 0.00 3.01
155 170 1.565156 CGCAGAAACACGGCTTGCTA 61.565 55.000 0.00 0.00 37.54 3.49
197 212 0.165944 CTTCTGCTACGGCCAAAACG 59.834 55.000 2.24 0.00 37.74 3.60
198 213 0.521735 CCTTCTGCTACGGCCAAAAC 59.478 55.000 2.24 0.00 37.74 2.43
224 241 8.713708 TTTTATTTTAATCTGGACAGGGACAA 57.286 30.769 0.00 0.00 0.00 3.18
239 256 8.785946 CGGAGACAACTAACCCTTTTATTTTAA 58.214 33.333 0.00 0.00 0.00 1.52
261 279 1.227380 GCATGAGGCACTACCGGAG 60.227 63.158 9.46 3.52 46.52 4.63
364 388 2.028876 CTGGCCATGATTGCTCATCAA 58.971 47.619 5.51 0.00 45.45 2.57
415 439 2.817258 CTCGTTGTTAATTTGGCCCTCA 59.183 45.455 0.00 0.00 0.00 3.86
452 476 5.067954 TCTGGCAGAATGGTAATCATCATG 58.932 41.667 16.28 0.00 34.44 3.07
483 507 3.266636 ACGTCCGTGCATAATGATTCAA 58.733 40.909 0.00 0.00 0.00 2.69
513 541 1.937546 GCCCTTTCCCGTTCATGCTG 61.938 60.000 0.00 0.00 0.00 4.41
541 576 3.612115 TAGCACCCGGCCACTAGGT 62.612 63.158 2.24 0.00 46.50 3.08
550 585 4.388499 ACCGCAACTAGCACCCGG 62.388 66.667 0.00 0.00 46.13 5.73
552 587 2.746277 CCACCGCAACTAGCACCC 60.746 66.667 0.00 0.00 46.13 4.61
553 588 0.320946 TAACCACCGCAACTAGCACC 60.321 55.000 0.00 0.00 46.13 5.01
554 589 1.076332 CTAACCACCGCAACTAGCAC 58.924 55.000 0.00 0.00 46.13 4.40
555 590 0.036765 CCTAACCACCGCAACTAGCA 60.037 55.000 0.00 0.00 46.13 3.49
806 856 1.539065 CGGCCAAGATGGTACTGCTAG 60.539 57.143 2.24 0.00 40.46 3.42
807 857 0.464036 CGGCCAAGATGGTACTGCTA 59.536 55.000 2.24 0.00 40.46 3.49
809 859 1.819632 CCGGCCAAGATGGTACTGC 60.820 63.158 2.24 0.00 40.46 4.40
811 861 2.590092 GCCGGCCAAGATGGTACT 59.410 61.111 18.11 0.00 40.46 2.73
812 862 2.516225 GGCCGGCCAAGATGGTAC 60.516 66.667 40.73 8.62 40.46 3.34
813 863 2.690881 AGGCCGGCCAAGATGGTA 60.691 61.111 45.13 0.00 40.46 3.25
814 864 4.115199 GAGGCCGGCCAAGATGGT 62.115 66.667 45.13 25.09 40.46 3.55
815 865 2.916527 ATTGAGGCCGGCCAAGATGG 62.917 60.000 45.13 0.00 41.55 3.51
816 866 1.454479 ATTGAGGCCGGCCAAGATG 60.454 57.895 45.13 0.00 38.92 2.90
916 966 3.952675 CCCACACACACGCAGCAC 61.953 66.667 0.00 0.00 0.00 4.40
918 968 3.952675 CACCCACACACACGCAGC 61.953 66.667 0.00 0.00 0.00 5.25
957 1012 2.125912 CGAGGGTTGACAGAGGCG 60.126 66.667 0.00 0.00 0.00 5.52
1090 1145 1.077140 TTTCAGCCACAGCCACACA 60.077 52.632 0.00 0.00 41.25 3.72
1130 1185 2.750637 TGAGAGACCTCCGGCGAC 60.751 66.667 9.30 0.00 38.66 5.19
1175 1230 3.067106 GCGAGTGAAGAGGAAATCAACA 58.933 45.455 0.00 0.00 0.00 3.33
1176 1231 3.330267 AGCGAGTGAAGAGGAAATCAAC 58.670 45.455 0.00 0.00 0.00 3.18
1205 1260 1.073964 CATGCTCTTCTGTCACCGTG 58.926 55.000 0.00 0.00 0.00 4.94
1208 1263 3.565482 TCAAAACATGCTCTTCTGTCACC 59.435 43.478 0.00 0.00 0.00 4.02
1231 1286 1.156736 ACATGTCCGCAACTGCTAAC 58.843 50.000 0.00 0.00 39.32 2.34
1346 1402 2.310538 GTGCATCCAGATAAAAGGGGG 58.689 52.381 0.00 0.00 0.00 5.40
1363 1419 0.171007 AATTGCAGCATACACCGTGC 59.829 50.000 0.00 0.00 42.81 5.34
1364 1420 2.634982 AAATTGCAGCATACACCGTG 57.365 45.000 0.00 0.00 0.00 4.94
1365 1421 6.633500 AATATAAATTGCAGCATACACCGT 57.367 33.333 0.00 0.00 0.00 4.83
1366 1422 7.218773 GCATAATATAAATTGCAGCATACACCG 59.781 37.037 0.00 0.00 35.22 4.94
1515 1571 1.806542 GCTCTGTCGCTCCATTTTCAA 59.193 47.619 0.00 0.00 0.00 2.69
1535 1591 1.367599 GGCTCAACTGCTAGCTGCTG 61.368 60.000 20.35 18.26 44.70 4.41
1642 1698 1.293924 CTGAATCAGGATCCACACGC 58.706 55.000 15.82 0.56 0.00 5.34
1692 1748 4.282957 AGAGCTTCTTGACTCATGAAGTGA 59.717 41.667 24.85 1.87 43.20 3.41
1698 1754 8.196771 AGATTTAGTAGAGCTTCTTGACTCATG 58.803 37.037 0.00 0.00 35.28 3.07
1719 1775 4.023707 CGTTCTGTCAAAAGGAGCAGATTT 60.024 41.667 0.00 0.00 35.26 2.17
1749 1805 4.477975 CCGGAGCCTCGACGTCAC 62.478 72.222 17.16 1.42 0.00 3.67
1765 1821 2.821810 GCCTTCTTCTCTGCCGCC 60.822 66.667 0.00 0.00 0.00 6.13
1767 1823 0.036952 TTCAGCCTTCTTCTCTGCCG 60.037 55.000 0.00 0.00 0.00 5.69
1815 1877 2.507324 GCTCCTCCGTCGCTTCAC 60.507 66.667 0.00 0.00 0.00 3.18
1825 1887 0.461693 CAACTGCTAGCTGCTCCTCC 60.462 60.000 20.35 0.00 43.37 4.30
1950 2012 4.778579 CTGAACTGAATCAGGATCCACAT 58.221 43.478 15.82 1.62 42.52 3.21
2137 2203 7.795272 GCAATGCATACACAGAAAAAGAAAAAG 59.205 33.333 0.00 0.00 0.00 2.27
2138 2204 7.279536 TGCAATGCATACACAGAAAAAGAAAAA 59.720 29.630 2.72 0.00 31.71 1.94
2139 2205 6.760298 TGCAATGCATACACAGAAAAAGAAAA 59.240 30.769 2.72 0.00 31.71 2.29
2140 2206 6.279123 TGCAATGCATACACAGAAAAAGAAA 58.721 32.000 2.72 0.00 31.71 2.52
2141 2207 5.840715 TGCAATGCATACACAGAAAAAGAA 58.159 33.333 2.72 0.00 31.71 2.52
2142 2208 5.450592 TGCAATGCATACACAGAAAAAGA 57.549 34.783 2.72 0.00 31.71 2.52
2194 2262 7.009179 AGAGGTGACATAAACAGAGAAATGA 57.991 36.000 0.00 0.00 0.00 2.57
2211 2279 6.068461 AGATCTAGTGTACTGAAGAGGTGA 57.932 41.667 0.00 0.00 0.00 4.02
2212 2280 6.767524 AAGATCTAGTGTACTGAAGAGGTG 57.232 41.667 0.00 0.00 0.00 4.00
2223 2291 9.516314 CGTCAAATGACAATAAGATCTAGTGTA 57.484 33.333 13.51 0.00 44.99 2.90
2224 2292 7.492669 CCGTCAAATGACAATAAGATCTAGTGT 59.507 37.037 13.51 0.11 44.99 3.55
2225 2293 7.492669 ACCGTCAAATGACAATAAGATCTAGTG 59.507 37.037 13.51 0.00 44.99 2.74
2226 2294 7.556844 ACCGTCAAATGACAATAAGATCTAGT 58.443 34.615 13.51 0.00 44.99 2.57
2233 2301 7.026562 TGCATAAACCGTCAAATGACAATAAG 58.973 34.615 13.51 0.00 44.99 1.73
2273 2341 4.582656 AGAAAATTTGTGGGTCGACATTGA 59.417 37.500 18.91 0.00 0.00 2.57
2277 2345 2.882137 GGAGAAAATTTGTGGGTCGACA 59.118 45.455 18.91 0.00 0.00 4.35
2279 2347 3.146066 CAGGAGAAAATTTGTGGGTCGA 58.854 45.455 0.00 0.00 0.00 4.20
2286 2354 4.083110 CGACAGATGCAGGAGAAAATTTGT 60.083 41.667 0.00 0.00 0.00 2.83
2294 2362 2.895680 GCCGACAGATGCAGGAGA 59.104 61.111 0.00 0.00 0.00 3.71
2299 2367 1.067416 GTATCCGCCGACAGATGCA 59.933 57.895 0.00 0.00 0.00 3.96
2305 2373 2.725641 CATCCGTATCCGCCGACA 59.274 61.111 0.00 0.00 0.00 4.35
2310 2378 3.916392 CTCCCGCATCCGTATCCGC 62.916 68.421 0.00 0.00 0.00 5.54
2339 2407 3.138304 TGAAATATGTGCGGCTATGGTC 58.862 45.455 0.00 0.00 0.00 4.02
2343 2411 5.126067 AGAGTTTGAAATATGTGCGGCTAT 58.874 37.500 0.00 0.00 0.00 2.97
2344 2412 4.513442 AGAGTTTGAAATATGTGCGGCTA 58.487 39.130 0.00 0.00 0.00 3.93
2346 2414 3.764885 AGAGTTTGAAATATGTGCGGC 57.235 42.857 0.00 0.00 0.00 6.53
2350 2418 8.870160 TGTTGGAAAAGAGTTTGAAATATGTG 57.130 30.769 0.00 0.00 0.00 3.21
2351 2419 9.883142 TTTGTTGGAAAAGAGTTTGAAATATGT 57.117 25.926 0.00 0.00 0.00 2.29
2370 2438 4.250116 TGAATTTCATCCGGTTTGTTGG 57.750 40.909 0.00 0.00 0.00 3.77
2400 2468 7.414762 CCGTCATGTTTATTTAAAATCCGGTCT 60.415 37.037 0.00 0.00 0.00 3.85
2402 2470 6.374894 TCCGTCATGTTTATTTAAAATCCGGT 59.625 34.615 0.00 0.00 0.00 5.28
2413 2481 9.139174 GTTTGAATGAAATCCGTCATGTTTATT 57.861 29.630 0.00 0.00 38.28 1.40
2426 2494 6.797033 CGTGTTAGTCTGGTTTGAATGAAATC 59.203 38.462 0.00 0.00 0.00 2.17
2434 2502 3.547054 AACCGTGTTAGTCTGGTTTGA 57.453 42.857 0.00 0.00 41.80 2.69
2441 2509 5.467735 GTCCAAAATGTAACCGTGTTAGTCT 59.532 40.000 0.00 0.00 0.00 3.24
2448 2516 7.810282 TGAAAATATGTCCAAAATGTAACCGTG 59.190 33.333 0.00 0.00 0.00 4.94
2478 2546 4.994907 AGGCTAGTTCGGTTTTGTTTTT 57.005 36.364 0.00 0.00 0.00 1.94
2484 2552 2.640184 GCCATAGGCTAGTTCGGTTTT 58.360 47.619 0.00 0.00 46.69 2.43
2504 2572 0.246360 TGGATATATGCCGACGCTGG 59.754 55.000 1.35 0.00 35.36 4.85
2506 2574 2.418746 GGAATGGATATATGCCGACGCT 60.419 50.000 1.35 0.00 35.36 5.07
2510 2578 2.159296 CGTCGGAATGGATATATGCCGA 60.159 50.000 3.76 3.76 44.60 5.54
2513 2581 3.845178 TGTCGTCGGAATGGATATATGC 58.155 45.455 0.00 0.00 0.00 3.14
2516 2584 5.914898 ATCATGTCGTCGGAATGGATATA 57.085 39.130 7.82 0.00 0.00 0.86
2540 2608 1.558294 TGGCAGTAGACTAGTCGAGGA 59.442 52.381 17.07 1.75 34.09 3.71
2584 2652 1.767036 CCACTGTTGGTCATGGGGA 59.233 57.895 0.00 0.00 38.23 4.81
2595 2663 1.352622 TTCTGGGCCTCACCACTGTT 61.353 55.000 4.53 0.00 42.05 3.16
2596 2664 1.770110 TTCTGGGCCTCACCACTGT 60.770 57.895 4.53 0.00 42.05 3.55
2600 2668 2.561209 TATACTTCTGGGCCTCACCA 57.439 50.000 4.53 0.00 42.05 4.17
2607 2675 2.810852 GCTGAAGCATATACTTCTGGGC 59.189 50.000 18.86 14.54 45.20 5.36
2626 2694 1.664965 GCGAGTCGTCCTTTGTGCT 60.665 57.895 15.08 0.00 0.00 4.40
2629 2697 0.319641 GGAAGCGAGTCGTCCTTTGT 60.320 55.000 15.08 0.00 39.80 2.83
2639 2707 3.077556 AGCGATGGGGAAGCGAGT 61.078 61.111 0.00 0.00 41.20 4.18
2652 2720 1.511305 GTTCCACTCCGATGAGCGA 59.489 57.895 0.00 0.00 42.74 4.93
2654 2722 4.522971 GGTTCCACTCCGATGAGC 57.477 61.111 0.00 0.00 42.74 4.26
2688 2756 2.040779 GGACCCTTCCCCTCCGAT 60.041 66.667 0.00 0.00 35.57 4.18
2741 2809 4.586235 CCGGCCACCATCATCCCC 62.586 72.222 2.24 0.00 0.00 4.81
2747 2815 4.864334 CTCCTGCCGGCCACCATC 62.864 72.222 26.77 0.00 0.00 3.51
2760 2828 2.203788 TCGGTGTCTTGCCCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
2761 2829 2.047179 GTCGGTGTCTTGCCCTCC 60.047 66.667 0.00 0.00 0.00 4.30
2777 2845 1.384191 GCTTGGGTCCCATGAAGGT 59.616 57.895 24.71 0.00 31.53 3.50
2778 2846 1.750399 CGCTTGGGTCCCATGAAGG 60.750 63.158 24.71 10.72 31.53 3.46
2779 2847 1.750399 CCGCTTGGGTCCCATGAAG 60.750 63.158 24.71 14.81 31.53 3.02
2780 2848 2.354729 CCGCTTGGGTCCCATGAA 59.645 61.111 24.71 4.30 31.53 2.57
2781 2849 4.424711 GCCGCTTGGGTCCCATGA 62.425 66.667 24.71 5.05 38.44 3.07
2800 2868 3.766691 TAGAACACGGGAGGCCGC 61.767 66.667 0.00 0.00 36.58 6.53
2801 2869 1.885163 AAGTAGAACACGGGAGGCCG 61.885 60.000 0.00 0.00 39.31 6.13
2802 2870 0.108281 GAAGTAGAACACGGGAGGCC 60.108 60.000 0.00 0.00 0.00 5.19
2803 2871 0.896226 AGAAGTAGAACACGGGAGGC 59.104 55.000 0.00 0.00 0.00 4.70
2804 2872 1.477295 GGAGAAGTAGAACACGGGAGG 59.523 57.143 0.00 0.00 0.00 4.30
2805 2873 2.424246 GAGGAGAAGTAGAACACGGGAG 59.576 54.545 0.00 0.00 0.00 4.30
2806 2874 2.444421 GAGGAGAAGTAGAACACGGGA 58.556 52.381 0.00 0.00 0.00 5.14
2807 2875 1.132643 CGAGGAGAAGTAGAACACGGG 59.867 57.143 0.00 0.00 0.00 5.28
2808 2876 2.082231 TCGAGGAGAAGTAGAACACGG 58.918 52.381 0.00 0.00 0.00 4.94
2809 2877 5.481200 TTATCGAGGAGAAGTAGAACACG 57.519 43.478 0.00 0.00 0.00 4.49
2810 2878 6.210078 CCATTATCGAGGAGAAGTAGAACAC 58.790 44.000 0.00 0.00 0.00 3.32
2811 2879 5.221263 GCCATTATCGAGGAGAAGTAGAACA 60.221 44.000 0.00 0.00 0.00 3.18
2812 2880 5.224135 GCCATTATCGAGGAGAAGTAGAAC 58.776 45.833 0.00 0.00 0.00 3.01
2813 2881 4.023107 CGCCATTATCGAGGAGAAGTAGAA 60.023 45.833 0.00 0.00 0.00 2.10
2814 2882 3.502595 CGCCATTATCGAGGAGAAGTAGA 59.497 47.826 0.00 0.00 0.00 2.59
2815 2883 3.366476 CCGCCATTATCGAGGAGAAGTAG 60.366 52.174 0.00 0.00 0.00 2.57
2816 2884 2.557056 CCGCCATTATCGAGGAGAAGTA 59.443 50.000 0.00 0.00 0.00 2.24
2817 2885 1.341531 CCGCCATTATCGAGGAGAAGT 59.658 52.381 0.00 0.00 0.00 3.01
2818 2886 1.937108 GCCGCCATTATCGAGGAGAAG 60.937 57.143 0.00 0.00 0.00 2.85
2819 2887 0.033504 GCCGCCATTATCGAGGAGAA 59.966 55.000 0.00 0.00 0.00 2.87
2820 2888 1.666011 GCCGCCATTATCGAGGAGA 59.334 57.895 0.00 0.00 0.00 3.71
2821 2889 1.734477 CGCCGCCATTATCGAGGAG 60.734 63.158 0.00 0.00 0.00 3.69
2822 2890 2.142357 CTCGCCGCCATTATCGAGGA 62.142 60.000 2.91 0.00 43.13 3.71
2823 2891 1.734477 CTCGCCGCCATTATCGAGG 60.734 63.158 2.91 0.00 43.13 4.63
2824 2892 3.848142 CTCGCCGCCATTATCGAG 58.152 61.111 0.00 0.00 41.66 4.04
2825 2893 2.355837 GCTCGCCGCCATTATCGA 60.356 61.111 0.00 0.00 0.00 3.59
2826 2894 2.029288 ATGCTCGCCGCCATTATCG 61.029 57.895 0.00 0.00 38.05 2.92
2827 2895 0.950555 TCATGCTCGCCGCCATTATC 60.951 55.000 0.00 0.00 38.05 1.75
2828 2896 0.534877 TTCATGCTCGCCGCCATTAT 60.535 50.000 0.00 0.00 38.05 1.28
2829 2897 1.153269 TTCATGCTCGCCGCCATTA 60.153 52.632 0.00 0.00 38.05 1.90
2830 2898 2.438254 TTCATGCTCGCCGCCATT 60.438 55.556 0.00 0.00 38.05 3.16
2831 2899 3.204827 GTTCATGCTCGCCGCCAT 61.205 61.111 0.00 0.00 38.05 4.40
2834 2902 4.505217 CACGTTCATGCTCGCCGC 62.505 66.667 8.75 0.00 39.77 6.53
2835 2903 4.505217 GCACGTTCATGCTCGCCG 62.505 66.667 8.75 3.27 42.62 6.46
2841 2909 4.465512 CGGCCAGCACGTTCATGC 62.466 66.667 2.24 0.00 46.50 4.06
2852 2920 4.914420 CGACGAGCTAGCGGCCAG 62.914 72.222 9.55 2.87 43.05 4.85
2854 2922 1.924320 ATATCGACGAGCTAGCGGCC 61.924 60.000 9.55 0.00 43.05 6.13
2855 2923 0.521659 GATATCGACGAGCTAGCGGC 60.522 60.000 9.55 4.76 42.19 6.53
2856 2924 0.097325 GGATATCGACGAGCTAGCGG 59.903 60.000 9.55 8.21 35.12 5.52
2857 2925 0.247340 CGGATATCGACGAGCTAGCG 60.247 60.000 9.55 0.00 42.43 4.26
2858 2926 0.521659 GCGGATATCGACGAGCTAGC 60.522 60.000 6.62 6.62 42.43 3.42
2859 2927 0.247340 CGCGGATATCGACGAGCTAG 60.247 60.000 3.01 0.00 42.43 3.42
2860 2928 1.785951 CGCGGATATCGACGAGCTA 59.214 57.895 3.01 0.00 42.43 3.32
2861 2929 2.556792 CGCGGATATCGACGAGCT 59.443 61.111 3.01 0.00 42.43 4.09
2863 2931 2.075489 GTGCGCGGATATCGACGAG 61.075 63.158 17.26 9.72 42.43 4.18
2864 2932 2.051614 GTGCGCGGATATCGACGA 60.052 61.111 17.26 0.00 42.43 4.20
2865 2933 3.097728 GGTGCGCGGATATCGACG 61.098 66.667 8.83 10.66 42.43 5.12
2866 2934 2.733593 GGGTGCGCGGATATCGAC 60.734 66.667 8.83 0.00 42.43 4.20
2867 2935 4.337060 CGGGTGCGCGGATATCGA 62.337 66.667 8.83 0.00 42.43 3.59
2878 2946 1.003233 AGAGAAAGAAGCCGGGTGC 60.003 57.895 7.07 4.63 41.71 5.01
2879 2947 1.301677 GCAGAGAAAGAAGCCGGGTG 61.302 60.000 7.07 0.00 0.00 4.61
2880 2948 1.003233 GCAGAGAAAGAAGCCGGGT 60.003 57.895 0.00 0.00 0.00 5.28
2881 2949 1.746991 GGCAGAGAAAGAAGCCGGG 60.747 63.158 2.18 0.00 37.41 5.73
2882 2950 3.896479 GGCAGAGAAAGAAGCCGG 58.104 61.111 0.00 0.00 37.41 6.13
2885 2953 1.132643 CATGCAGGCAGAGAAAGAAGC 59.867 52.381 0.00 0.00 0.00 3.86
2886 2954 1.743958 CCATGCAGGCAGAGAAAGAAG 59.256 52.381 0.00 0.00 0.00 2.85
2887 2955 1.830279 CCATGCAGGCAGAGAAAGAA 58.170 50.000 0.00 0.00 0.00 2.52
2888 2956 3.564262 CCATGCAGGCAGAGAAAGA 57.436 52.632 0.00 0.00 0.00 2.52
2898 2966 2.590007 GTAGCCTCGCCATGCAGG 60.590 66.667 0.00 0.00 41.84 4.85
2899 2967 2.349969 TACGTAGCCTCGCCATGCAG 62.350 60.000 0.00 0.00 0.00 4.41
2900 2968 2.419739 TACGTAGCCTCGCCATGCA 61.420 57.895 0.00 0.00 0.00 3.96
2901 2969 1.949631 GTACGTAGCCTCGCCATGC 60.950 63.158 0.00 0.00 0.00 4.06
2902 2970 1.657487 CGTACGTAGCCTCGCCATG 60.657 63.158 7.22 0.00 0.00 3.66
2903 2971 2.117156 ACGTACGTAGCCTCGCCAT 61.117 57.895 21.41 0.00 0.00 4.40
2904 2972 2.747460 ACGTACGTAGCCTCGCCA 60.747 61.111 21.41 0.00 0.00 5.69
2905 2973 2.277756 CACGTACGTAGCCTCGCC 60.278 66.667 22.34 0.00 0.00 5.54
2906 2974 2.948134 GCACGTACGTAGCCTCGC 60.948 66.667 22.34 15.31 0.00 5.03
2907 2975 2.646862 CGCACGTACGTAGCCTCG 60.647 66.667 22.34 14.78 0.00 4.63
2908 2976 2.931713 ATGCGCACGTACGTAGCCTC 62.932 60.000 31.40 23.00 34.88 4.70
2909 2977 2.931713 GATGCGCACGTACGTAGCCT 62.932 60.000 31.40 25.81 34.88 4.58
2910 2978 2.574222 GATGCGCACGTACGTAGCC 61.574 63.158 31.40 23.34 34.88 3.93
2911 2979 2.902383 CGATGCGCACGTACGTAGC 61.902 63.158 29.46 29.46 34.88 3.58
2912 2980 3.199564 CGATGCGCACGTACGTAG 58.800 61.111 22.34 18.52 34.88 3.51
2950 3018 3.702048 TACCACGCCTCCAGCACC 61.702 66.667 0.00 0.00 44.04 5.01
2951 3019 2.434359 GTACCACGCCTCCAGCAC 60.434 66.667 0.00 0.00 44.04 4.40
2952 3020 4.063967 CGTACCACGCCTCCAGCA 62.064 66.667 0.00 0.00 44.04 4.41
2953 3021 3.755628 TCGTACCACGCCTCCAGC 61.756 66.667 0.00 0.00 42.21 4.85
2954 3022 2.181021 GTCGTACCACGCCTCCAG 59.819 66.667 0.00 0.00 42.21 3.86
2955 3023 3.740397 CGTCGTACCACGCCTCCA 61.740 66.667 0.00 0.00 42.21 3.86
2962 3030 3.170585 GACGCTGCGTCGTACCAC 61.171 66.667 35.10 15.06 46.56 4.16
3002 3070 3.127533 CAGGTAGCTTGGCGGCAC 61.128 66.667 12.92 0.00 34.17 5.01
3003 3071 3.318384 TCAGGTAGCTTGGCGGCA 61.318 61.111 7.97 7.97 34.17 5.69
3004 3072 2.820037 GTCAGGTAGCTTGGCGGC 60.820 66.667 0.00 0.00 0.00 6.53
3005 3073 2.509336 CGTCAGGTAGCTTGGCGG 60.509 66.667 2.96 0.00 39.79 6.13
3007 3075 1.004918 ACACGTCAGGTAGCTTGGC 60.005 57.895 0.00 0.00 0.00 4.52
3008 3076 0.732880 CGACACGTCAGGTAGCTTGG 60.733 60.000 0.00 0.00 0.00 3.61
3009 3077 0.732880 CCGACACGTCAGGTAGCTTG 60.733 60.000 0.00 0.00 0.00 4.01
3010 3078 1.585006 CCGACACGTCAGGTAGCTT 59.415 57.895 0.00 0.00 0.00 3.74
3011 3079 2.991076 GCCGACACGTCAGGTAGCT 61.991 63.158 0.00 0.00 0.00 3.32
3012 3080 2.506438 GCCGACACGTCAGGTAGC 60.506 66.667 0.00 0.00 0.00 3.58
3013 3081 2.181021 GGCCGACACGTCAGGTAG 59.819 66.667 0.00 0.00 0.00 3.18
3014 3082 2.282674 AGGCCGACACGTCAGGTA 60.283 61.111 0.00 0.00 0.00 3.08
3015 3083 3.991051 CAGGCCGACACGTCAGGT 61.991 66.667 0.00 0.00 0.00 4.00
3016 3084 4.742201 CCAGGCCGACACGTCAGG 62.742 72.222 0.00 1.41 0.00 3.86
3017 3085 3.633094 CTCCAGGCCGACACGTCAG 62.633 68.421 0.00 0.00 0.00 3.51
3018 3086 3.680786 CTCCAGGCCGACACGTCA 61.681 66.667 0.00 0.00 0.00 4.35
3021 3089 4.680237 TTGCTCCAGGCCGACACG 62.680 66.667 0.00 0.00 40.92 4.49


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

AutoCloner maintained by Alex Coulton.