Multiple sequence alignment - TraesCS1D01G255300

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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 TraesCS1D01G255300 chr1D 100.000 3178 0 0 1 3178 348009314 348012491 0.000000e+00 5869.0
1 TraesCS1D01G255300 chr1D 90.260 154 13 2 224 376 9436683 9436835 1.930000e-47 200.0
2 TraesCS1D01G255300 chr1B 95.736 1501 41 5 547 2035 469536548 469538037 0.000000e+00 2396.0
3 TraesCS1D01G255300 chr1B 91.087 561 40 3 3 554 469530234 469530793 0.000000e+00 750.0
4 TraesCS1D01G255300 chr1B 87.406 397 35 11 2066 2457 469538128 469538514 2.910000e-120 442.0
5 TraesCS1D01G255300 chr1B 82.609 115 16 4 416 527 420998956 420998843 7.250000e-17 99.0
6 TraesCS1D01G255300 chr1A 92.063 1638 75 23 436 2037 448814074 448815692 0.000000e+00 2254.0
7 TraesCS1D01G255300 chr1A 92.112 393 30 1 2066 2457 448815781 448816173 1.290000e-153 553.0
8 TraesCS1D01G255300 chr1A 91.083 157 9 4 224 376 10717615 10717770 1.160000e-49 207.0
9 TraesCS1D01G255300 chr5B 82.435 501 49 25 2684 3156 484892439 484892928 4.940000e-108 401.0
10 TraesCS1D01G255300 chr5B 90.123 162 16 0 26 187 377115873 377115712 8.930000e-51 211.0
11 TraesCS1D01G255300 chr5B 90.647 139 12 1 241 379 377089581 377089444 1.950000e-42 183.0
12 TraesCS1D01G255300 chr5B 77.564 156 28 7 383 535 670522901 670522750 1.570000e-13 87.9
13 TraesCS1D01G255300 chr4B 82.937 463 47 19 2737 3178 492226139 492225688 3.840000e-104 388.0
14 TraesCS1D01G255300 chr3D 82.276 457 59 16 2698 3145 82552502 82552945 2.990000e-100 375.0
15 TraesCS1D01G255300 chr7A 82.203 472 44 28 2699 3156 20152877 20153322 1.390000e-98 370.0
16 TraesCS1D01G255300 chr7D 81.263 475 55 27 2685 3143 399450822 399451278 1.400000e-93 353.0
17 TraesCS1D01G255300 chr7D 82.869 251 31 11 2914 3158 593025483 593025239 6.900000e-52 215.0
18 TraesCS1D01G255300 chr7D 84.545 110 12 5 435 541 448866672 448866565 1.560000e-18 104.0
19 TraesCS1D01G255300 chr7D 78.882 161 28 4 383 542 509568541 509568696 1.560000e-18 104.0
20 TraesCS1D01G255300 chr2A 93.048 187 13 0 1 187 767010565 767010379 1.120000e-69 274.0
21 TraesCS1D01G255300 chr2A 91.791 134 9 2 224 356 767010378 767010246 5.410000e-43 185.0
22 TraesCS1D01G255300 chr2D 80.720 389 42 23 2691 3069 614742207 614742572 4.040000e-69 272.0
23 TraesCS1D01G255300 chr5D 86.454 251 23 9 2914 3158 10789653 10789408 6.760000e-67 265.0
24 TraesCS1D01G255300 chr5D 83.582 268 27 8 2915 3178 445966627 445966881 5.300000e-58 235.0
25 TraesCS1D01G255300 chr5D 84.848 231 21 12 2928 3152 8971112 8971334 1.480000e-53 220.0
26 TraesCS1D01G255300 chr5D 81.633 147 23 4 394 539 522113407 522113264 5.570000e-23 119.0
27 TraesCS1D01G255300 chr4A 81.686 344 40 15 2813 3145 696222845 696223176 6.760000e-67 265.0
28 TraesCS1D01G255300 chr6D 79.108 426 55 23 2707 3110 138391723 138391310 2.430000e-66 263.0
29 TraesCS1D01G255300 chr2B 80.460 348 53 8 2814 3152 5102254 5102595 5.260000e-63 252.0
30 TraesCS1D01G255300 chr3A 86.449 214 21 8 2970 3178 580810922 580810712 8.870000e-56 228.0
31 TraesCS1D01G255300 chr5A 78.616 318 46 15 2872 3178 17821059 17821365 1.160000e-44 191.0
32 TraesCS1D01G255300 chr5A 81.061 132 15 8 412 541 44363933 44363810 2.610000e-16 97.1
33 TraesCS1D01G255300 chrUn 77.564 156 28 7 383 535 35127573 35127724 1.570000e-13 87.9
34 TraesCS1D01G255300 chr7B 77.160 162 29 6 383 542 537728879 537729034 1.570000e-13 87.9
35 TraesCS1D01G255300 chr6A 87.013 77 9 1 2574 2650 2907679 2907604 5.650000e-13 86.1


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 TraesCS1D01G255300 chr1D 348009314 348012491 3177 False 5869.0 5869 100.0000 1 3178 1 chr1D.!!$F2 3177
1 TraesCS1D01G255300 chr1B 469536548 469538514 1966 False 1419.0 2396 91.5710 547 2457 2 chr1B.!!$F2 1910
2 TraesCS1D01G255300 chr1B 469530234 469530793 559 False 750.0 750 91.0870 3 554 1 chr1B.!!$F1 551
3 TraesCS1D01G255300 chr1A 448814074 448816173 2099 False 1403.5 2254 92.0875 436 2457 2 chr1A.!!$F2 2021

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
357 367 0.531311 TGCACACAGAGAGCACACAG 60.531 55.0 0.0 0.0 38.96 3.66 F
1028 1055 0.037232 GGTGTTCTTCCCACTCTCGG 60.037 60.0 0.0 0.0 33.31 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1221 0.035152 TGATGTTGCCGCAGAAGGAT 60.035 50.0 0.0 0.0 0.0 3.24 R
2533 2639 0.105039 GATCAAGTAGGCGACCCAGG 59.895 60.0 0.0 0.0 0.0 4.45 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 8.273780 GGATTGAATACCAATATCACAGGATC 57.726 38.462 0.00 0.00 45.00 3.36
49 50 7.709947 TCTTGATATTCAGATTGAATGCCAAC 58.290 34.615 13.13 3.07 45.77 3.77
56 57 5.716094 TCAGATTGAATGCCAACATTTCTG 58.284 37.500 10.57 10.57 46.59 3.02
69 70 6.073819 GCCAACATTTCTGTTTGGATGTTTAC 60.074 38.462 3.75 0.00 43.05 2.01
84 85 5.277154 GGATGTTTACGTATTCGGAACATGG 60.277 44.000 21.32 0.00 46.65 3.66
158 159 5.355071 TCAAACTGAAGTATCCATGACATGC 59.645 40.000 10.10 0.00 0.00 4.06
159 160 3.813443 ACTGAAGTATCCATGACATGCC 58.187 45.455 10.10 0.00 0.00 4.40
163 164 3.889859 AGTATCCATGACATGCCCATT 57.110 42.857 10.10 0.00 0.00 3.16
214 223 7.353497 TCTTCTTACGAGTAATATCTTGAGCG 58.647 38.462 0.00 0.00 0.00 5.03
222 231 7.081349 CGAGTAATATCTTGAGCGAGAAAGAT 58.919 38.462 10.49 10.49 43.71 2.40
252 262 3.053455 GTGCGTGAGGAAGCATCTATAC 58.947 50.000 0.00 0.00 45.69 1.47
265 275 6.849085 AGCATCTATACTATCTTGGACCAG 57.151 41.667 0.00 0.00 0.00 4.00
340 350 4.884164 ACCTGCAATTAAAGTAGAGGATGC 59.116 41.667 0.00 0.00 0.00 3.91
344 354 5.123820 TGCAATTAAAGTAGAGGATGCACAC 59.876 40.000 0.00 0.00 37.61 3.82
357 367 0.531311 TGCACACAGAGAGCACACAG 60.531 55.000 0.00 0.00 38.96 3.66
371 381 2.503331 CACACAGGCACATAGGAACAA 58.497 47.619 0.00 0.00 0.00 2.83
380 390 3.500680 GCACATAGGAACAAACTCCGAAA 59.499 43.478 0.00 0.00 40.75 3.46
431 441 2.220479 AGGTAAGTAAATCGCGAGCC 57.780 50.000 16.66 6.33 0.00 4.70
438 448 2.538449 AGTAAATCGCGAGCCGTATTTG 59.462 45.455 16.66 0.00 38.35 2.32
444 454 3.386486 TCGCGAGCCGTATTTGATAAAT 58.614 40.909 3.71 0.00 38.35 1.40
527 542 2.162319 TACTCAGTTGCAATGCACGA 57.838 45.000 7.72 4.13 38.71 4.35
541 556 5.678483 GCAATGCACGAACAATTATCTAGTG 59.322 40.000 0.00 0.00 0.00 2.74
759 777 5.961272 ACAGTTTCAAAAGTTTAGGGTGTG 58.039 37.500 0.00 0.00 0.00 3.82
762 780 7.340999 ACAGTTTCAAAAGTTTAGGGTGTGTAT 59.659 33.333 0.00 0.00 0.00 2.29
808 834 4.143347 GGTGCAATCTACAATTTTGTTGCG 60.143 41.667 11.21 0.00 41.59 4.85
849 875 6.581712 AGATGTAAGAGAGAGCAAGAATTCC 58.418 40.000 0.65 0.00 0.00 3.01
874 900 5.171339 AGCAGTGGACATGAAGACTAATT 57.829 39.130 0.00 0.00 0.00 1.40
998 1025 4.222114 GTGCTGCTTTGTTGCTTAACTAG 58.778 43.478 0.00 0.00 0.00 2.57
999 1026 4.024048 GTGCTGCTTTGTTGCTTAACTAGA 60.024 41.667 0.00 0.00 0.00 2.43
1000 1027 4.578516 TGCTGCTTTGTTGCTTAACTAGAA 59.421 37.500 0.00 0.00 0.00 2.10
1001 1028 5.241506 TGCTGCTTTGTTGCTTAACTAGAAT 59.758 36.000 0.00 0.00 0.00 2.40
1028 1055 0.037232 GGTGTTCTTCCCACTCTCGG 60.037 60.000 0.00 0.00 33.31 4.63
1044 1071 3.357203 TCTCGGTCTTCTTGTATCAGCT 58.643 45.455 0.00 0.00 0.00 4.24
1059 1087 0.820891 CAGCTTCCACACACTTGGCT 60.821 55.000 0.00 0.00 36.48 4.75
1062 1102 1.813862 GCTTCCACACACTTGGCTGTA 60.814 52.381 0.00 0.00 36.48 2.74
1176 1221 3.424859 TCGATCACGACGTGCCGA 61.425 61.111 28.28 28.28 43.81 5.54
1997 2042 1.817209 CCCTTCTCGCCTCAGGTAC 59.183 63.158 0.00 0.00 0.00 3.34
1998 2043 1.677637 CCCTTCTCGCCTCAGGTACC 61.678 65.000 2.73 2.73 0.00 3.34
1999 2044 1.433879 CTTCTCGCCTCAGGTACCG 59.566 63.158 6.18 1.56 0.00 4.02
2000 2045 1.303888 TTCTCGCCTCAGGTACCGT 60.304 57.895 6.18 0.00 0.00 4.83
2037 2082 6.597832 AGTACATTTCAGTAGTCTCTTGCT 57.402 37.500 0.00 0.00 0.00 3.91
2040 2085 6.107901 ACATTTCAGTAGTCTCTTGCTTCT 57.892 37.500 0.00 0.00 0.00 2.85
2042 2087 7.671302 ACATTTCAGTAGTCTCTTGCTTCTTA 58.329 34.615 0.00 0.00 0.00 2.10
2043 2088 7.816995 ACATTTCAGTAGTCTCTTGCTTCTTAG 59.183 37.037 0.00 0.00 0.00 2.18
2053 2098 2.387309 GCTTCTTAGCTGCGATGCA 58.613 52.632 15.43 0.00 44.27 3.96
2057 2102 2.538512 TCTTAGCTGCGATGCATCAT 57.461 45.000 25.70 8.71 38.13 2.45
2058 2103 2.842457 TCTTAGCTGCGATGCATCATT 58.158 42.857 25.70 8.71 38.13 2.57
2059 2104 2.804527 TCTTAGCTGCGATGCATCATTC 59.195 45.455 25.70 14.24 38.13 2.67
2060 2105 1.516161 TAGCTGCGATGCATCATTCC 58.484 50.000 25.70 11.19 38.13 3.01
2061 2106 0.464916 AGCTGCGATGCATCATTCCA 60.465 50.000 25.70 14.87 38.13 3.53
2062 2107 0.596577 GCTGCGATGCATCATTCCAT 59.403 50.000 25.70 0.00 38.13 3.41
2064 2109 2.227149 GCTGCGATGCATCATTCCATAA 59.773 45.455 25.70 1.68 38.13 1.90
2095 2200 5.418310 TTTGGATGTTGTTTCGAGTTCTC 57.582 39.130 0.00 0.00 0.00 2.87
2098 2203 3.120511 GGATGTTGTTTCGAGTTCTCTGC 60.121 47.826 0.00 0.00 0.00 4.26
2122 2227 5.560375 CGCCTCTCATTTCATTTGCTGATAG 60.560 44.000 0.00 0.00 32.72 2.08
2125 2230 6.205076 CCTCTCATTTCATTTGCTGATAGAGG 59.795 42.308 0.00 0.00 38.85 3.69
2135 2240 1.334239 GCTGATAGAGGTGTCGCTACG 60.334 57.143 0.00 0.00 0.00 3.51
2140 2245 0.321387 AGAGGTGTCGCTACGTCTGA 60.321 55.000 11.51 0.00 42.35 3.27
2165 2270 2.963101 AGGATTGTCGTCCGGATCAATA 59.037 45.455 22.82 6.70 43.27 1.90
2174 2279 3.214328 GTCCGGATCAATAGCCAACATT 58.786 45.455 7.81 0.00 0.00 2.71
2206 2311 2.209273 TGTGTTCATCCAACAGTGACG 58.791 47.619 0.00 0.00 46.07 4.35
2217 2322 3.745912 AGTGACGACTGACGAGCA 58.254 55.556 6.52 1.52 45.77 4.26
2260 2365 3.687102 CCGTCTGGTGTACCGCCA 61.687 66.667 6.18 6.18 42.15 5.69
2263 2368 0.248907 CGTCTGGTGTACCGCCATAG 60.249 60.000 6.71 0.00 43.46 2.23
2311 2416 3.062099 GCGACTGAAATGTTTATCTGCGA 59.938 43.478 0.00 0.00 0.00 5.10
2360 2465 9.371136 CAGTGCCATATTACATTCGAAGTATAT 57.629 33.333 3.35 1.71 0.00 0.86
2380 2485 9.982651 AGTATATCTACAAAACATATGCGAGTT 57.017 29.630 1.58 0.00 0.00 3.01
2451 2557 0.099436 GATGTGGCTCCGTTTGCATC 59.901 55.000 0.00 0.00 0.00 3.91
2457 2563 0.166814 GCTCCGTTTGCATCTGTGAC 59.833 55.000 0.00 0.00 0.00 3.67
2458 2564 1.800805 CTCCGTTTGCATCTGTGACT 58.199 50.000 0.00 0.00 0.00 3.41
2459 2565 2.146342 CTCCGTTTGCATCTGTGACTT 58.854 47.619 0.00 0.00 0.00 3.01
2460 2566 1.872952 TCCGTTTGCATCTGTGACTTG 59.127 47.619 0.00 0.00 0.00 3.16
2461 2567 1.603802 CCGTTTGCATCTGTGACTTGT 59.396 47.619 0.00 0.00 0.00 3.16
2462 2568 2.602933 CCGTTTGCATCTGTGACTTGTG 60.603 50.000 0.00 0.00 0.00 3.33
2463 2569 2.287644 CGTTTGCATCTGTGACTTGTGA 59.712 45.455 0.00 0.00 0.00 3.58
2464 2570 3.605461 CGTTTGCATCTGTGACTTGTGAG 60.605 47.826 0.00 0.00 0.00 3.51
2465 2571 2.916702 TGCATCTGTGACTTGTGAGT 57.083 45.000 0.00 0.00 39.32 3.41
2466 2572 2.486918 TGCATCTGTGACTTGTGAGTG 58.513 47.619 0.00 0.00 35.88 3.51
2467 2573 2.102925 TGCATCTGTGACTTGTGAGTGA 59.897 45.455 0.00 0.00 35.88 3.41
2468 2574 2.735663 GCATCTGTGACTTGTGAGTGAG 59.264 50.000 0.00 0.00 35.88 3.51
2469 2575 3.553715 GCATCTGTGACTTGTGAGTGAGA 60.554 47.826 0.00 0.00 35.88 3.27
2470 2576 3.717400 TCTGTGACTTGTGAGTGAGAC 57.283 47.619 0.00 0.00 35.88 3.36
2471 2577 2.033424 TCTGTGACTTGTGAGTGAGACG 59.967 50.000 0.00 0.00 35.88 4.18
2472 2578 2.021457 TGTGACTTGTGAGTGAGACGA 58.979 47.619 0.00 0.00 35.88 4.20
2473 2579 2.033424 TGTGACTTGTGAGTGAGACGAG 59.967 50.000 0.00 0.00 35.88 4.18
2474 2580 2.290916 GTGACTTGTGAGTGAGACGAGA 59.709 50.000 0.00 0.00 35.88 4.04
2475 2581 2.550180 TGACTTGTGAGTGAGACGAGAG 59.450 50.000 0.00 0.00 35.88 3.20
2476 2582 1.268352 ACTTGTGAGTGAGACGAGAGC 59.732 52.381 0.00 0.00 33.99 4.09
2477 2583 1.268079 CTTGTGAGTGAGACGAGAGCA 59.732 52.381 0.00 0.00 0.00 4.26
2478 2584 0.593618 TGTGAGTGAGACGAGAGCAC 59.406 55.000 0.00 0.00 0.00 4.40
2479 2585 0.878416 GTGAGTGAGACGAGAGCACT 59.122 55.000 0.00 0.00 44.87 4.40
2480 2586 2.077627 GTGAGTGAGACGAGAGCACTA 58.922 52.381 0.00 0.00 42.47 2.74
2481 2587 2.680841 GTGAGTGAGACGAGAGCACTAT 59.319 50.000 0.00 0.00 42.47 2.12
2482 2588 3.127895 GTGAGTGAGACGAGAGCACTATT 59.872 47.826 0.00 0.00 42.47 1.73
2483 2589 3.759086 TGAGTGAGACGAGAGCACTATTT 59.241 43.478 0.00 0.00 42.47 1.40
2484 2590 4.142578 TGAGTGAGACGAGAGCACTATTTC 60.143 45.833 0.00 0.00 42.47 2.17
2485 2591 4.013728 AGTGAGACGAGAGCACTATTTCT 58.986 43.478 0.00 0.00 40.79 2.52
2486 2592 4.095782 AGTGAGACGAGAGCACTATTTCTC 59.904 45.833 0.00 8.38 40.79 2.87
2487 2593 4.010349 TGAGACGAGAGCACTATTTCTCA 58.990 43.478 12.10 12.10 39.82 3.27
2488 2594 4.142578 TGAGACGAGAGCACTATTTCTCAC 60.143 45.833 12.10 1.61 39.82 3.51
2489 2595 3.759086 AGACGAGAGCACTATTTCTCACA 59.241 43.478 0.00 0.00 39.82 3.58
2490 2596 4.101942 GACGAGAGCACTATTTCTCACAG 58.898 47.826 0.00 0.00 39.82 3.66
2491 2597 3.119316 ACGAGAGCACTATTTCTCACAGG 60.119 47.826 0.00 0.00 39.82 4.00
2492 2598 3.129462 CGAGAGCACTATTTCTCACAGGA 59.871 47.826 2.84 0.00 39.82 3.86
2493 2599 4.380973 CGAGAGCACTATTTCTCACAGGAA 60.381 45.833 2.84 0.00 39.82 3.36
2494 2600 5.083533 AGAGCACTATTTCTCACAGGAAG 57.916 43.478 0.00 0.00 0.00 3.46
2495 2601 4.774726 AGAGCACTATTTCTCACAGGAAGA 59.225 41.667 0.00 0.00 0.00 2.87
2496 2602 5.083533 AGCACTATTTCTCACAGGAAGAG 57.916 43.478 0.00 0.00 34.42 2.85
2497 2603 4.774726 AGCACTATTTCTCACAGGAAGAGA 59.225 41.667 0.00 0.00 40.20 3.10
2520 2626 1.860078 AAAAAGAGCGTCGCTTCCG 59.140 52.632 22.67 0.00 39.88 4.30
2521 2627 1.566018 AAAAAGAGCGTCGCTTCCGG 61.566 55.000 22.67 0.00 39.88 5.14
2522 2628 3.934391 AAAGAGCGTCGCTTCCGGG 62.934 63.158 22.67 0.00 39.88 5.73
2524 2630 4.856607 GAGCGTCGCTTCCGGGAG 62.857 72.222 22.67 4.95 39.88 4.30
2542 2648 3.250986 GTTTCGAACCTGGGTCGC 58.749 61.111 28.59 11.78 0.00 5.19
2543 2649 2.031465 TTTCGAACCTGGGTCGCC 59.969 61.111 28.59 0.00 0.00 5.54
2544 2650 2.513259 TTTCGAACCTGGGTCGCCT 61.513 57.895 28.59 0.00 0.00 5.52
2545 2651 1.186917 TTTCGAACCTGGGTCGCCTA 61.187 55.000 28.59 13.61 0.00 3.93
2546 2652 1.880819 TTCGAACCTGGGTCGCCTAC 61.881 60.000 28.59 0.00 0.00 3.18
2547 2653 2.348888 CGAACCTGGGTCGCCTACT 61.349 63.158 22.53 0.00 0.00 2.57
2548 2654 1.885163 CGAACCTGGGTCGCCTACTT 61.885 60.000 22.53 0.00 0.00 2.24
2549 2655 0.391263 GAACCTGGGTCGCCTACTTG 60.391 60.000 0.00 0.00 0.00 3.16
2550 2656 0.834687 AACCTGGGTCGCCTACTTGA 60.835 55.000 0.00 0.00 0.00 3.02
2551 2657 0.617820 ACCTGGGTCGCCTACTTGAT 60.618 55.000 0.00 0.00 0.00 2.57
2552 2658 0.105039 CCTGGGTCGCCTACTTGATC 59.895 60.000 0.00 0.00 0.00 2.92
2553 2659 0.249073 CTGGGTCGCCTACTTGATCG 60.249 60.000 0.00 0.00 0.00 3.69
2554 2660 0.968901 TGGGTCGCCTACTTGATCGT 60.969 55.000 0.00 0.00 0.00 3.73
2555 2661 0.527817 GGGTCGCCTACTTGATCGTG 60.528 60.000 0.00 0.00 0.00 4.35
2556 2662 0.454600 GGTCGCCTACTTGATCGTGA 59.545 55.000 0.00 0.00 0.00 4.35
2557 2663 1.534175 GGTCGCCTACTTGATCGTGAG 60.534 57.143 0.00 0.00 0.00 3.51
2558 2664 0.738975 TCGCCTACTTGATCGTGAGG 59.261 55.000 0.00 0.00 0.00 3.86
2559 2665 0.249073 CGCCTACTTGATCGTGAGGG 60.249 60.000 5.28 0.00 0.00 4.30
2560 2666 0.530870 GCCTACTTGATCGTGAGGGC 60.531 60.000 3.71 3.71 0.00 5.19
2561 2667 0.824109 CCTACTTGATCGTGAGGGCA 59.176 55.000 0.00 0.00 0.00 5.36
2562 2668 1.202463 CCTACTTGATCGTGAGGGCAG 60.202 57.143 0.00 0.00 0.00 4.85
2563 2669 1.478510 CTACTTGATCGTGAGGGCAGT 59.521 52.381 0.00 0.00 0.00 4.40
2564 2670 0.687354 ACTTGATCGTGAGGGCAGTT 59.313 50.000 0.00 0.00 0.00 3.16
2565 2671 1.899814 ACTTGATCGTGAGGGCAGTTA 59.100 47.619 0.00 0.00 0.00 2.24
2566 2672 2.093973 ACTTGATCGTGAGGGCAGTTAG 60.094 50.000 0.00 0.00 0.00 2.34
2567 2673 0.175760 TGATCGTGAGGGCAGTTAGC 59.824 55.000 0.00 0.00 44.65 3.09
2581 2687 3.207354 TAGCCCACGCTAGACTGC 58.793 61.111 0.00 0.00 46.08 4.40
2582 2688 1.680989 TAGCCCACGCTAGACTGCA 60.681 57.895 0.00 0.00 46.08 4.41
2583 2689 1.667154 TAGCCCACGCTAGACTGCAG 61.667 60.000 13.48 13.48 46.08 4.41
2584 2690 2.973899 CCCACGCTAGACTGCAGT 59.026 61.111 21.88 21.88 0.00 4.40
2585 2691 1.153745 CCCACGCTAGACTGCAGTC 60.154 63.158 34.82 34.82 45.08 3.51
2596 2702 3.166489 GACTGCAGTCGCCTAAATAGT 57.834 47.619 29.84 0.00 37.32 2.12
2597 2703 4.303086 GACTGCAGTCGCCTAAATAGTA 57.697 45.455 29.84 0.00 37.32 1.82
2598 2704 4.291783 GACTGCAGTCGCCTAAATAGTAG 58.708 47.826 29.84 0.00 37.32 2.57
2599 2705 3.068307 ACTGCAGTCGCCTAAATAGTAGG 59.932 47.826 15.25 0.00 37.32 3.18
2600 2706 3.028850 TGCAGTCGCCTAAATAGTAGGT 58.971 45.455 1.57 0.00 37.06 3.08
2601 2707 3.067742 TGCAGTCGCCTAAATAGTAGGTC 59.932 47.826 1.57 0.00 37.06 3.85
2602 2708 3.852572 GCAGTCGCCTAAATAGTAGGTCG 60.853 52.174 1.57 5.80 37.06 4.79
2603 2709 2.883386 AGTCGCCTAAATAGTAGGTCGG 59.117 50.000 12.83 0.00 37.06 4.79
2604 2710 2.030451 GTCGCCTAAATAGTAGGTCGGG 60.030 54.545 12.83 0.00 37.06 5.14
2605 2711 1.336609 CGCCTAAATAGTAGGTCGGGC 60.337 57.143 1.57 0.00 37.06 6.13
2606 2712 1.001746 GCCTAAATAGTAGGTCGGGCC 59.998 57.143 0.00 0.00 37.06 5.80
2616 2722 3.950869 GGTCGGGCCTTCTTAAGTT 57.049 52.632 0.84 0.00 0.00 2.66
2617 2723 1.450025 GGTCGGGCCTTCTTAAGTTG 58.550 55.000 0.84 0.00 0.00 3.16
2618 2724 1.002773 GGTCGGGCCTTCTTAAGTTGA 59.997 52.381 0.84 0.00 0.00 3.18
2619 2725 2.551504 GGTCGGGCCTTCTTAAGTTGAA 60.552 50.000 0.84 0.00 0.00 2.69
2620 2726 3.143728 GTCGGGCCTTCTTAAGTTGAAA 58.856 45.455 0.84 0.00 0.00 2.69
2621 2727 3.058432 GTCGGGCCTTCTTAAGTTGAAAC 60.058 47.826 0.84 0.00 0.00 2.78
2622 2728 2.095919 CGGGCCTTCTTAAGTTGAAACG 60.096 50.000 0.84 0.00 0.00 3.60
2623 2729 3.143728 GGGCCTTCTTAAGTTGAAACGA 58.856 45.455 0.84 0.00 0.00 3.85
2624 2730 3.566742 GGGCCTTCTTAAGTTGAAACGAA 59.433 43.478 0.84 0.00 0.00 3.85
2625 2731 4.534168 GGCCTTCTTAAGTTGAAACGAAC 58.466 43.478 1.63 0.00 0.00 3.95
2626 2732 4.534168 GCCTTCTTAAGTTGAAACGAACC 58.466 43.478 1.63 0.00 0.00 3.62
2627 2733 4.769215 CCTTCTTAAGTTGAAACGAACCG 58.231 43.478 1.63 0.00 0.00 4.44
2628 2734 4.271776 CCTTCTTAAGTTGAAACGAACCGT 59.728 41.667 1.63 0.00 43.97 4.83
2629 2735 4.782252 TCTTAAGTTGAAACGAACCGTG 57.218 40.909 1.63 0.00 39.99 4.94
2630 2736 4.183101 TCTTAAGTTGAAACGAACCGTGT 58.817 39.130 1.63 0.00 39.99 4.49
2631 2737 4.630940 TCTTAAGTTGAAACGAACCGTGTT 59.369 37.500 1.63 0.00 39.99 3.32
2632 2738 3.835378 AAGTTGAAACGAACCGTGTTT 57.165 38.095 0.00 0.00 39.99 2.83
2637 2743 3.343380 GAAACGAACCGTGTTTCCATT 57.657 42.857 7.22 0.00 45.92 3.16
2638 2744 2.766970 AACGAACCGTGTTTCCATTG 57.233 45.000 0.00 0.00 39.99 2.82
2639 2745 1.670791 ACGAACCGTGTTTCCATTGT 58.329 45.000 0.00 0.00 39.18 2.71
2640 2746 2.018515 ACGAACCGTGTTTCCATTGTT 58.981 42.857 0.00 0.00 39.18 2.83
2641 2747 2.424246 ACGAACCGTGTTTCCATTGTTT 59.576 40.909 0.00 0.00 39.18 2.83
2642 2748 3.040099 CGAACCGTGTTTCCATTGTTTC 58.960 45.455 0.00 0.00 0.00 2.78
2643 2749 3.242936 CGAACCGTGTTTCCATTGTTTCT 60.243 43.478 0.00 0.00 0.00 2.52
2644 2750 4.678622 GAACCGTGTTTCCATTGTTTCTT 58.321 39.130 0.00 0.00 0.00 2.52
2645 2751 4.729227 ACCGTGTTTCCATTGTTTCTTT 57.271 36.364 0.00 0.00 0.00 2.52
2646 2752 5.079689 ACCGTGTTTCCATTGTTTCTTTT 57.920 34.783 0.00 0.00 0.00 2.27
2647 2753 5.106442 ACCGTGTTTCCATTGTTTCTTTTC 58.894 37.500 0.00 0.00 0.00 2.29
2648 2754 4.506288 CCGTGTTTCCATTGTTTCTTTTCC 59.494 41.667 0.00 0.00 0.00 3.13
2649 2755 5.105752 CGTGTTTCCATTGTTTCTTTTCCA 58.894 37.500 0.00 0.00 0.00 3.53
2650 2756 5.231991 CGTGTTTCCATTGTTTCTTTTCCAG 59.768 40.000 0.00 0.00 0.00 3.86
2651 2757 5.523552 GTGTTTCCATTGTTTCTTTTCCAGG 59.476 40.000 0.00 0.00 0.00 4.45
2652 2758 5.423610 TGTTTCCATTGTTTCTTTTCCAGGA 59.576 36.000 0.00 0.00 0.00 3.86
2653 2759 6.099557 TGTTTCCATTGTTTCTTTTCCAGGAT 59.900 34.615 0.00 0.00 0.00 3.24
2654 2760 6.745794 TTCCATTGTTTCTTTTCCAGGATT 57.254 33.333 0.00 0.00 0.00 3.01
2655 2761 6.745794 TCCATTGTTTCTTTTCCAGGATTT 57.254 33.333 0.00 0.00 0.00 2.17
2656 2762 7.135591 TCCATTGTTTCTTTTCCAGGATTTT 57.864 32.000 0.00 0.00 0.00 1.82
2657 2763 7.572814 TCCATTGTTTCTTTTCCAGGATTTTT 58.427 30.769 0.00 0.00 0.00 1.94
2658 2764 7.714813 TCCATTGTTTCTTTTCCAGGATTTTTC 59.285 33.333 0.00 0.00 0.00 2.29
2659 2765 7.498570 CCATTGTTTCTTTTCCAGGATTTTTCA 59.501 33.333 0.00 0.00 0.00 2.69
2660 2766 8.553696 CATTGTTTCTTTTCCAGGATTTTTCAG 58.446 33.333 0.00 0.00 0.00 3.02
2661 2767 7.181569 TGTTTCTTTTCCAGGATTTTTCAGT 57.818 32.000 0.00 0.00 0.00 3.41
2662 2768 7.619965 TGTTTCTTTTCCAGGATTTTTCAGTT 58.380 30.769 0.00 0.00 0.00 3.16
2663 2769 8.100164 TGTTTCTTTTCCAGGATTTTTCAGTTT 58.900 29.630 0.00 0.00 0.00 2.66
2664 2770 8.946085 GTTTCTTTTCCAGGATTTTTCAGTTTT 58.054 29.630 0.00 0.00 0.00 2.43
2665 2771 9.513906 TTTCTTTTCCAGGATTTTTCAGTTTTT 57.486 25.926 0.00 0.00 0.00 1.94
2842 2948 7.886191 TTTTCGTTTTCACTCTACATTTTCG 57.114 32.000 0.00 0.00 0.00 3.46
2843 2949 6.592798 TTCGTTTTCACTCTACATTTTCGT 57.407 33.333 0.00 0.00 0.00 3.85
2844 2950 7.697352 TTCGTTTTCACTCTACATTTTCGTA 57.303 32.000 0.00 0.00 0.00 3.43
2845 2951 7.878477 TCGTTTTCACTCTACATTTTCGTAT 57.122 32.000 0.00 0.00 0.00 3.06
2846 2952 8.969121 TCGTTTTCACTCTACATTTTCGTATA 57.031 30.769 0.00 0.00 0.00 1.47
2847 2953 9.577110 TCGTTTTCACTCTACATTTTCGTATAT 57.423 29.630 0.00 0.00 0.00 0.86
2848 2954 9.619727 CGTTTTCACTCTACATTTTCGTATATG 57.380 33.333 0.00 0.00 0.00 1.78
2851 2957 9.863845 TTTCACTCTACATTTTCGTATATGTCA 57.136 29.630 1.65 0.00 36.46 3.58
2852 2958 9.863845 TTCACTCTACATTTTCGTATATGTCAA 57.136 29.630 1.65 0.00 36.46 3.18
2853 2959 9.863845 TCACTCTACATTTTCGTATATGTCAAA 57.136 29.630 1.65 0.00 36.46 2.69
2905 3011 5.743026 TTTGTACACACGTTCATCATTGT 57.257 34.783 0.00 0.00 0.00 2.71
2906 3012 4.723879 TGTACACACGTTCATCATTGTG 57.276 40.909 0.00 0.00 44.09 3.33
2907 3013 2.686558 ACACACGTTCATCATTGTGC 57.313 45.000 0.56 0.00 42.60 4.57
2908 3014 1.069973 ACACACGTTCATCATTGTGCG 60.070 47.619 0.56 0.00 42.60 5.34
2909 3015 1.194322 CACACGTTCATCATTGTGCGA 59.806 47.619 0.00 0.00 35.79 5.10
2910 3016 1.870402 ACACGTTCATCATTGTGCGAA 59.130 42.857 0.00 0.00 35.79 4.70
2911 3017 2.233355 CACGTTCATCATTGTGCGAAC 58.767 47.619 0.00 0.00 35.50 3.95
2913 3019 1.250476 GTTCATCATTGTGCGAACGC 58.750 50.000 12.33 12.33 42.35 4.84
2914 3020 1.135972 GTTCATCATTGTGCGAACGCT 60.136 47.619 19.32 0.00 42.51 5.07
2915 3021 1.155889 TCATCATTGTGCGAACGCTT 58.844 45.000 19.32 0.52 42.51 4.68
2916 3022 2.342179 TCATCATTGTGCGAACGCTTA 58.658 42.857 19.32 6.34 42.51 3.09
2917 3023 2.935849 TCATCATTGTGCGAACGCTTAT 59.064 40.909 19.32 7.83 42.51 1.73
2918 3024 3.373748 TCATCATTGTGCGAACGCTTATT 59.626 39.130 19.32 3.49 42.51 1.40
2919 3025 3.383546 TCATTGTGCGAACGCTTATTC 57.616 42.857 19.32 6.41 42.51 1.75
2920 3026 2.739379 TCATTGTGCGAACGCTTATTCA 59.261 40.909 19.32 8.54 42.51 2.57
2921 3027 3.187432 TCATTGTGCGAACGCTTATTCAA 59.813 39.130 19.32 15.12 42.51 2.69
2922 3028 2.587612 TGTGCGAACGCTTATTCAAC 57.412 45.000 19.32 8.39 42.51 3.18
2923 3029 1.867865 TGTGCGAACGCTTATTCAACA 59.132 42.857 19.32 10.71 42.51 3.33
2924 3030 2.482336 TGTGCGAACGCTTATTCAACAT 59.518 40.909 19.32 0.00 42.51 2.71
2925 3031 3.058570 TGTGCGAACGCTTATTCAACATT 60.059 39.130 19.32 0.00 42.51 2.71
2926 3032 3.911964 GTGCGAACGCTTATTCAACATTT 59.088 39.130 19.32 0.00 42.51 2.32
2927 3033 4.381566 GTGCGAACGCTTATTCAACATTTT 59.618 37.500 19.32 0.00 42.51 1.82
2928 3034 4.979197 TGCGAACGCTTATTCAACATTTTT 59.021 33.333 19.32 0.00 42.51 1.94
2929 3035 5.116377 TGCGAACGCTTATTCAACATTTTTC 59.884 36.000 19.32 0.00 42.51 2.29
2930 3036 5.116377 GCGAACGCTTATTCAACATTTTTCA 59.884 36.000 11.97 0.00 38.26 2.69
2931 3037 6.345408 GCGAACGCTTATTCAACATTTTTCAA 60.345 34.615 11.97 0.00 38.26 2.69
2932 3038 7.551340 CGAACGCTTATTCAACATTTTTCAAA 58.449 30.769 0.00 0.00 0.00 2.69
2933 3039 8.213812 CGAACGCTTATTCAACATTTTTCAAAT 58.786 29.630 0.00 0.00 0.00 2.32
2936 3042 9.691362 ACGCTTATTCAACATTTTTCAAATACT 57.309 25.926 0.00 0.00 0.00 2.12
2996 3102 9.834628 TCAATAATTTCCAAATACTCGTTCAAC 57.165 29.630 0.00 0.00 0.00 3.18
2997 3103 9.619316 CAATAATTTCCAAATACTCGTTCAACA 57.381 29.630 0.00 0.00 0.00 3.33
3001 3107 9.541143 AATTTCCAAATACTCGTTCAACATTTT 57.459 25.926 0.00 0.00 0.00 1.82
3002 3108 8.934507 TTTCCAAATACTCGTTCAACATTTTT 57.065 26.923 0.00 0.00 0.00 1.94
3003 3109 8.568732 TTCCAAATACTCGTTCAACATTTTTC 57.431 30.769 0.00 0.00 0.00 2.29
3004 3110 7.708051 TCCAAATACTCGTTCAACATTTTTCA 58.292 30.769 0.00 0.00 0.00 2.69
3005 3111 8.191446 TCCAAATACTCGTTCAACATTTTTCAA 58.809 29.630 0.00 0.00 0.00 2.69
3006 3112 8.812329 CCAAATACTCGTTCAACATTTTTCAAA 58.188 29.630 0.00 0.00 0.00 2.69
3012 3118 9.581099 ACTCGTTCAACATTTTTCAAAATACTT 57.419 25.926 0.00 0.00 36.52 2.24
3013 3119 9.833894 CTCGTTCAACATTTTTCAAAATACTTG 57.166 29.630 0.00 3.65 36.52 3.16
3014 3120 9.360093 TCGTTCAACATTTTTCAAAATACTTGT 57.640 25.926 0.00 0.00 36.52 3.16
3015 3121 9.965748 CGTTCAACATTTTTCAAAATACTTGTT 57.034 25.926 0.00 0.00 36.52 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.105829 AGATCCTGTGATATTGGTATTCAATCC 58.894 37.037 0.00 0.00 44.32 3.01
1 2 9.512588 AAGATCCTGTGATATTGGTATTCAATC 57.487 33.333 0.00 0.00 44.32 2.67
21 22 7.176165 TGGCATTCAATCTGAATATCAAGATCC 59.824 37.037 1.71 0.00 44.60 3.36
25 26 7.485810 TGTTGGCATTCAATCTGAATATCAAG 58.514 34.615 12.69 0.65 44.60 3.02
34 35 5.475719 ACAGAAATGTTGGCATTCAATCTG 58.524 37.500 22.22 22.22 44.71 2.90
49 50 8.964420 AATACGTAAACATCCAAACAGAAATG 57.036 30.769 0.00 0.00 0.00 2.32
56 57 5.783100 TCCGAATACGTAAACATCCAAAC 57.217 39.130 0.00 0.00 37.88 2.93
69 70 3.517602 TCAAGTCCATGTTCCGAATACG 58.482 45.455 0.00 0.00 39.43 3.06
82 83 5.357878 GCATTCAACCTCAATATCAAGTCCA 59.642 40.000 0.00 0.00 0.00 4.02
84 85 5.357878 TGGCATTCAACCTCAATATCAAGTC 59.642 40.000 0.00 0.00 0.00 3.01
214 223 2.223203 CGCACATGCTTCCATCTTTCTC 60.223 50.000 1.82 0.00 39.32 2.87
222 231 1.672030 CCTCACGCACATGCTTCCA 60.672 57.895 1.82 0.00 39.32 3.53
238 247 6.439058 GGTCCAAGATAGTATAGATGCTTCCT 59.561 42.308 0.00 0.00 0.00 3.36
252 262 8.043710 AGTTGTATTCTTTCTGGTCCAAGATAG 58.956 37.037 0.00 0.00 0.00 2.08
324 334 6.155221 TCTCTGTGTGCATCCTCTACTTTAAT 59.845 38.462 0.00 0.00 0.00 1.40
340 350 1.226686 GCCTGTGTGCTCTCTGTGTG 61.227 60.000 0.00 0.00 0.00 3.82
344 354 0.321387 ATGTGCCTGTGTGCTCTCTG 60.321 55.000 0.00 0.00 0.00 3.35
357 367 1.737793 CGGAGTTTGTTCCTATGTGCC 59.262 52.381 0.00 0.00 34.96 5.01
409 419 2.718027 GCTCGCGATTTACTTACCTACG 59.282 50.000 10.36 0.00 0.00 3.51
425 435 9.769093 AATAAATATTTATCAAATACGGCTCGC 57.231 29.630 18.72 0.00 36.27 5.03
514 529 4.858692 AGATAATTGTTCGTGCATTGCAAC 59.141 37.500 13.94 8.93 41.47 4.17
521 536 9.589111 TTAATACACTAGATAATTGTTCGTGCA 57.411 29.630 0.00 0.00 0.00 4.57
746 764 8.715190 ACCAAAAATATACACACCCTAAACTT 57.285 30.769 0.00 0.00 0.00 2.66
849 875 3.144506 AGTCTTCATGTCCACTGCTTTG 58.855 45.455 0.00 0.00 0.00 2.77
900 927 3.385111 TCTTTTTCGGGGCTTTTGCTTTA 59.615 39.130 0.00 0.00 46.54 1.85
998 1025 3.119352 GGGAAGAACACCTGCATTCATTC 60.119 47.826 0.94 2.42 0.00 2.67
999 1026 2.827921 GGGAAGAACACCTGCATTCATT 59.172 45.455 0.94 0.00 0.00 2.57
1000 1027 2.225091 TGGGAAGAACACCTGCATTCAT 60.225 45.455 0.94 0.00 0.00 2.57
1001 1028 1.144708 TGGGAAGAACACCTGCATTCA 59.855 47.619 0.94 0.00 0.00 2.57
1028 1055 4.390297 GTGTGGAAGCTGATACAAGAAGAC 59.610 45.833 0.00 0.00 0.00 3.01
1044 1071 2.294074 GTTACAGCCAAGTGTGTGGAA 58.706 47.619 0.00 0.00 41.65 3.53
1059 1087 1.824230 GCCATTGATTGCCCTGTTACA 59.176 47.619 0.00 0.00 0.00 2.41
1062 1102 1.892338 CGCCATTGATTGCCCTGTT 59.108 52.632 0.00 0.00 0.00 3.16
1176 1221 0.035152 TGATGTTGCCGCAGAAGGAT 60.035 50.000 0.00 0.00 0.00 3.24
1689 1734 1.681327 GTACCCCTCGCACTGGAGA 60.681 63.158 0.00 0.00 36.08 3.71
1968 2013 0.107945 CGAGAAGGGCCAAGAGAAGG 60.108 60.000 6.18 0.00 0.00 3.46
1997 2042 7.919313 AATGTACTACGTCAATATGTTACGG 57.081 36.000 0.00 0.00 40.81 4.02
1998 2043 9.012448 TGAAATGTACTACGTCAATATGTTACG 57.988 33.333 0.00 0.00 42.17 3.18
2037 2082 2.314323 TGATGCATCGCAGCTAAGAA 57.686 45.000 21.34 0.00 45.80 2.52
2040 2085 1.875514 GGAATGATGCATCGCAGCTAA 59.124 47.619 21.34 2.58 45.80 3.09
2042 2087 0.464916 TGGAATGATGCATCGCAGCT 60.465 50.000 21.34 4.03 45.80 4.24
2043 2088 0.596577 ATGGAATGATGCATCGCAGC 59.403 50.000 21.34 10.54 45.81 5.25
2045 2090 3.742385 TCTTATGGAATGATGCATCGCA 58.258 40.909 21.34 6.37 44.86 5.10
2046 2091 4.634883 AGATCTTATGGAATGATGCATCGC 59.365 41.667 21.34 12.91 38.66 4.58
2047 2092 5.873164 TCAGATCTTATGGAATGATGCATCG 59.127 40.000 21.34 4.30 38.66 3.84
2048 2093 7.683437 TTCAGATCTTATGGAATGATGCATC 57.317 36.000 20.14 20.14 38.66 3.91
2051 2096 7.813148 CCAAATTCAGATCTTATGGAATGATGC 59.187 37.037 6.75 0.00 30.87 3.91
2052 2097 9.074576 TCCAAATTCAGATCTTATGGAATGATG 57.925 33.333 6.75 8.66 32.84 3.07
2053 2098 9.824216 ATCCAAATTCAGATCTTATGGAATGAT 57.176 29.630 12.91 7.13 38.82 2.45
2057 2102 8.689061 CAACATCCAAATTCAGATCTTATGGAA 58.311 33.333 12.91 5.92 38.82 3.53
2058 2103 7.835682 ACAACATCCAAATTCAGATCTTATGGA 59.164 33.333 11.83 11.83 39.59 3.41
2059 2104 8.004087 ACAACATCCAAATTCAGATCTTATGG 57.996 34.615 0.00 0.00 0.00 2.74
2060 2105 9.865321 AAACAACATCCAAATTCAGATCTTATG 57.135 29.630 0.00 0.00 0.00 1.90
2062 2107 8.236586 CGAAACAACATCCAAATTCAGATCTTA 58.763 33.333 0.00 0.00 0.00 2.10
2064 2109 6.430925 TCGAAACAACATCCAAATTCAGATCT 59.569 34.615 0.00 0.00 0.00 2.75
2095 2200 2.793933 CAAATGAAATGAGAGGCGCAG 58.206 47.619 10.83 0.00 0.00 5.18
2098 2203 2.421073 TCAGCAAATGAAATGAGAGGCG 59.579 45.455 0.00 0.00 34.02 5.52
2122 2227 0.733729 ATCAGACGTAGCGACACCTC 59.266 55.000 0.00 0.00 0.00 3.85
2125 2230 0.456142 TGCATCAGACGTAGCGACAC 60.456 55.000 0.00 0.00 0.00 3.67
2135 2240 1.929836 GACGACAATCCTGCATCAGAC 59.070 52.381 0.00 0.00 32.44 3.51
2140 2245 1.153369 CCGGACGACAATCCTGCAT 60.153 57.895 0.00 0.00 36.52 3.96
2165 2270 1.852067 GACGCCGTCAAATGTTGGCT 61.852 55.000 13.23 4.65 45.36 4.75
2174 2279 0.530870 TGAACACATGACGCCGTCAA 60.531 50.000 25.07 7.94 45.96 3.18
2217 2322 0.546122 TAATCATGGCGGCAGGAACT 59.454 50.000 29.94 21.16 43.88 3.01
2222 2327 0.886490 GGAGGTAATCATGGCGGCAG 60.886 60.000 19.29 9.89 0.00 4.85
2360 2465 8.942338 ATTCTAACTCGCATATGTTTTGTAGA 57.058 30.769 4.29 4.40 0.00 2.59
2451 2557 2.033424 TCGTCTCACTCACAAGTCACAG 59.967 50.000 0.00 0.00 31.71 3.66
2457 2563 1.268079 TGCTCTCGTCTCACTCACAAG 59.732 52.381 0.00 0.00 0.00 3.16
2458 2564 1.001268 GTGCTCTCGTCTCACTCACAA 60.001 52.381 0.00 0.00 0.00 3.33
2459 2565 0.593618 GTGCTCTCGTCTCACTCACA 59.406 55.000 0.00 0.00 0.00 3.58
2460 2566 0.878416 AGTGCTCTCGTCTCACTCAC 59.122 55.000 0.00 0.00 36.42 3.51
2461 2567 2.474410 TAGTGCTCTCGTCTCACTCA 57.526 50.000 0.00 0.00 40.96 3.41
2462 2568 4.095782 AGAAATAGTGCTCTCGTCTCACTC 59.904 45.833 0.00 0.00 40.96 3.51
2463 2569 4.013728 AGAAATAGTGCTCTCGTCTCACT 58.986 43.478 0.00 0.00 42.89 3.41
2464 2570 4.142578 TGAGAAATAGTGCTCTCGTCTCAC 60.143 45.833 16.14 0.00 40.89 3.51
2465 2571 4.010349 TGAGAAATAGTGCTCTCGTCTCA 58.990 43.478 16.14 16.14 40.89 3.27
2466 2572 4.142578 TGTGAGAAATAGTGCTCTCGTCTC 60.143 45.833 0.00 12.77 40.89 3.36
2467 2573 3.759086 TGTGAGAAATAGTGCTCTCGTCT 59.241 43.478 0.00 0.00 40.89 4.18
2468 2574 4.098055 TGTGAGAAATAGTGCTCTCGTC 57.902 45.455 0.00 0.00 40.89 4.20
2469 2575 3.119316 CCTGTGAGAAATAGTGCTCTCGT 60.119 47.826 0.00 0.00 40.89 4.18
2470 2576 3.129462 TCCTGTGAGAAATAGTGCTCTCG 59.871 47.826 0.00 0.00 40.89 4.04
2471 2577 4.727507 TCCTGTGAGAAATAGTGCTCTC 57.272 45.455 0.00 0.00 38.87 3.20
2472 2578 4.774726 TCTTCCTGTGAGAAATAGTGCTCT 59.225 41.667 0.00 0.00 32.44 4.09
2473 2579 5.078411 TCTTCCTGTGAGAAATAGTGCTC 57.922 43.478 0.00 0.00 0.00 4.26
2474 2580 4.774726 TCTCTTCCTGTGAGAAATAGTGCT 59.225 41.667 0.00 0.00 37.59 4.40
2475 2581 5.078411 TCTCTTCCTGTGAGAAATAGTGC 57.922 43.478 0.00 0.00 37.59 4.40
2502 2608 1.566018 CCGGAAGCGACGCTCTTTTT 61.566 55.000 24.69 6.77 38.25 1.94
2503 2609 2.027625 CCGGAAGCGACGCTCTTTT 61.028 57.895 24.69 7.23 38.25 2.27
2504 2610 2.432628 CCGGAAGCGACGCTCTTT 60.433 61.111 24.69 7.67 38.25 2.52
2505 2611 4.436998 CCCGGAAGCGACGCTCTT 62.437 66.667 24.69 8.56 38.25 2.85
2507 2613 4.856607 CTCCCGGAAGCGACGCTC 62.857 72.222 24.69 15.91 38.25 5.03
2510 2616 3.584868 AAACCTCCCGGAAGCGACG 62.585 63.158 0.73 0.00 0.00 5.12
2511 2617 1.740664 GAAACCTCCCGGAAGCGAC 60.741 63.158 0.73 0.00 0.00 5.19
2512 2618 2.660802 GAAACCTCCCGGAAGCGA 59.339 61.111 0.73 0.00 0.00 4.93
2513 2619 2.775032 TTCGAAACCTCCCGGAAGCG 62.775 60.000 0.73 0.00 0.00 4.68
2514 2620 1.004200 TTCGAAACCTCCCGGAAGC 60.004 57.895 0.73 0.00 0.00 3.86
2515 2621 2.836944 GTTCGAAACCTCCCGGAAG 58.163 57.895 0.73 0.00 0.00 3.46
2525 2631 2.322830 GGCGACCCAGGTTCGAAAC 61.323 63.158 11.22 4.63 0.00 2.78
2526 2632 1.186917 TAGGCGACCCAGGTTCGAAA 61.187 55.000 11.22 0.00 0.00 3.46
2527 2633 1.607178 TAGGCGACCCAGGTTCGAA 60.607 57.895 11.22 0.00 0.00 3.71
2528 2634 2.036098 TAGGCGACCCAGGTTCGA 59.964 61.111 11.22 0.00 0.00 3.71
2529 2635 1.885163 AAGTAGGCGACCCAGGTTCG 61.885 60.000 1.08 1.08 0.00 3.95
2530 2636 0.391263 CAAGTAGGCGACCCAGGTTC 60.391 60.000 0.00 0.00 0.00 3.62
2531 2637 0.834687 TCAAGTAGGCGACCCAGGTT 60.835 55.000 0.00 0.00 0.00 3.50
2532 2638 0.617820 ATCAAGTAGGCGACCCAGGT 60.618 55.000 0.00 0.00 0.00 4.00
2533 2639 0.105039 GATCAAGTAGGCGACCCAGG 59.895 60.000 0.00 0.00 0.00 4.45
2534 2640 0.249073 CGATCAAGTAGGCGACCCAG 60.249 60.000 0.00 0.00 0.00 4.45
2535 2641 0.968901 ACGATCAAGTAGGCGACCCA 60.969 55.000 0.00 0.00 0.00 4.51
2536 2642 0.527817 CACGATCAAGTAGGCGACCC 60.528 60.000 0.00 0.00 0.00 4.46
2537 2643 0.454600 TCACGATCAAGTAGGCGACC 59.545 55.000 0.00 0.00 0.00 4.79
2538 2644 1.534175 CCTCACGATCAAGTAGGCGAC 60.534 57.143 0.00 0.00 0.00 5.19
2539 2645 0.738975 CCTCACGATCAAGTAGGCGA 59.261 55.000 0.00 0.00 0.00 5.54
2540 2646 0.249073 CCCTCACGATCAAGTAGGCG 60.249 60.000 0.00 0.00 0.00 5.52
2541 2647 0.530870 GCCCTCACGATCAAGTAGGC 60.531 60.000 0.00 0.00 0.00 3.93
2542 2648 0.824109 TGCCCTCACGATCAAGTAGG 59.176 55.000 0.00 0.00 0.00 3.18
2543 2649 1.478510 ACTGCCCTCACGATCAAGTAG 59.521 52.381 0.00 0.00 0.00 2.57
2544 2650 1.557099 ACTGCCCTCACGATCAAGTA 58.443 50.000 0.00 0.00 0.00 2.24
2545 2651 0.687354 AACTGCCCTCACGATCAAGT 59.313 50.000 0.00 0.00 0.00 3.16
2546 2652 2.544685 CTAACTGCCCTCACGATCAAG 58.455 52.381 0.00 0.00 0.00 3.02
2547 2653 1.405526 GCTAACTGCCCTCACGATCAA 60.406 52.381 0.00 0.00 35.15 2.57
2548 2654 0.175760 GCTAACTGCCCTCACGATCA 59.824 55.000 0.00 0.00 35.15 2.92
2549 2655 2.979130 GCTAACTGCCCTCACGATC 58.021 57.895 0.00 0.00 35.15 3.69
2566 2672 2.510238 CTGCAGTCTAGCGTGGGC 60.510 66.667 5.25 0.00 37.31 5.36
2567 2673 1.153745 GACTGCAGTCTAGCGTGGG 60.154 63.158 34.54 0.00 41.65 4.61
2568 2674 1.515088 CGACTGCAGTCTAGCGTGG 60.515 63.158 36.78 20.25 42.66 4.94
2569 2675 2.155194 GCGACTGCAGTCTAGCGTG 61.155 63.158 36.78 24.17 42.66 5.34
2570 2676 2.179517 GCGACTGCAGTCTAGCGT 59.820 61.111 36.78 8.79 42.66 5.07
2571 2677 1.715862 TAGGCGACTGCAGTCTAGCG 61.716 60.000 36.78 27.69 45.35 4.26
2572 2678 0.456221 TTAGGCGACTGCAGTCTAGC 59.544 55.000 36.78 32.38 45.35 3.42
2573 2679 2.941453 TTTAGGCGACTGCAGTCTAG 57.059 50.000 36.78 26.08 45.35 2.43
2574 2680 3.952323 ACTATTTAGGCGACTGCAGTCTA 59.048 43.478 36.78 23.55 45.35 2.59
2575 2681 2.761208 ACTATTTAGGCGACTGCAGTCT 59.239 45.455 36.78 24.52 45.35 3.24
2576 2682 3.166489 ACTATTTAGGCGACTGCAGTC 57.834 47.619 32.73 32.73 45.35 3.51
2577 2683 3.068307 CCTACTATTTAGGCGACTGCAGT 59.932 47.826 21.88 21.88 45.35 4.40
2578 2684 3.068307 ACCTACTATTTAGGCGACTGCAG 59.932 47.826 13.48 13.48 45.35 4.41
2579 2685 3.028850 ACCTACTATTTAGGCGACTGCA 58.971 45.455 0.00 0.00 45.35 4.41
2580 2686 3.640592 GACCTACTATTTAGGCGACTGC 58.359 50.000 0.00 0.00 43.88 4.40
2581 2687 3.304525 CCGACCTACTATTTAGGCGACTG 60.305 52.174 0.00 0.00 43.88 3.51
2583 2689 2.030451 CCCGACCTACTATTTAGGCGAC 60.030 54.545 12.68 0.00 38.25 5.19
2584 2690 2.233271 CCCGACCTACTATTTAGGCGA 58.767 52.381 12.68 0.00 38.25 5.54
2585 2691 1.336609 GCCCGACCTACTATTTAGGCG 60.337 57.143 0.00 2.98 38.25 5.52
2586 2692 1.001746 GGCCCGACCTACTATTTAGGC 59.998 57.143 0.00 0.00 38.25 3.93
2598 2704 1.002773 TCAACTTAAGAAGGCCCGACC 59.997 52.381 10.09 0.00 39.61 4.79
2599 2705 2.467566 TCAACTTAAGAAGGCCCGAC 57.532 50.000 10.09 0.00 0.00 4.79
2600 2706 3.143728 GTTTCAACTTAAGAAGGCCCGA 58.856 45.455 10.09 0.00 0.00 5.14
2601 2707 2.095919 CGTTTCAACTTAAGAAGGCCCG 60.096 50.000 10.09 1.02 0.00 6.13
2602 2708 3.143728 TCGTTTCAACTTAAGAAGGCCC 58.856 45.455 10.09 0.00 0.00 5.80
2603 2709 4.534168 GTTCGTTTCAACTTAAGAAGGCC 58.466 43.478 10.09 0.00 0.00 5.19
2604 2710 4.534168 GGTTCGTTTCAACTTAAGAAGGC 58.466 43.478 10.09 0.00 0.00 4.35
2605 2711 4.271776 ACGGTTCGTTTCAACTTAAGAAGG 59.728 41.667 10.09 0.00 36.35 3.46
2606 2712 5.195379 CACGGTTCGTTTCAACTTAAGAAG 58.805 41.667 10.09 0.89 38.32 2.85
2607 2713 4.630940 ACACGGTTCGTTTCAACTTAAGAA 59.369 37.500 10.09 0.00 38.32 2.52
2608 2714 4.183101 ACACGGTTCGTTTCAACTTAAGA 58.817 39.130 10.09 0.00 38.32 2.10
2609 2715 4.525411 ACACGGTTCGTTTCAACTTAAG 57.475 40.909 0.00 0.00 38.32 1.85
2610 2716 4.943142 AACACGGTTCGTTTCAACTTAA 57.057 36.364 0.00 0.00 38.32 1.85
2611 2717 4.943142 AAACACGGTTCGTTTCAACTTA 57.057 36.364 0.00 0.00 38.32 2.24
2612 2718 3.835378 AAACACGGTTCGTTTCAACTT 57.165 38.095 0.00 0.00 38.32 2.66
2629 2735 5.912892 TCCTGGAAAAGAAACAATGGAAAC 58.087 37.500 0.00 0.00 0.00 2.78
2630 2736 6.745794 ATCCTGGAAAAGAAACAATGGAAA 57.254 33.333 0.00 0.00 0.00 3.13
2631 2737 6.745794 AATCCTGGAAAAGAAACAATGGAA 57.254 33.333 0.00 0.00 0.00 3.53
2632 2738 6.745794 AAATCCTGGAAAAGAAACAATGGA 57.254 33.333 0.00 0.00 0.00 3.41
2633 2739 7.498570 TGAAAAATCCTGGAAAAGAAACAATGG 59.501 33.333 0.00 0.00 0.00 3.16
2634 2740 8.436046 TGAAAAATCCTGGAAAAGAAACAATG 57.564 30.769 0.00 0.00 0.00 2.82
2635 2741 8.267183 ACTGAAAAATCCTGGAAAAGAAACAAT 58.733 29.630 0.00 0.00 0.00 2.71
2636 2742 7.619965 ACTGAAAAATCCTGGAAAAGAAACAA 58.380 30.769 0.00 0.00 0.00 2.83
2637 2743 7.181569 ACTGAAAAATCCTGGAAAAGAAACA 57.818 32.000 0.00 0.00 0.00 2.83
2638 2744 8.492673 AAACTGAAAAATCCTGGAAAAGAAAC 57.507 30.769 0.00 0.00 0.00 2.78
2639 2745 9.513906 AAAAACTGAAAAATCCTGGAAAAGAAA 57.486 25.926 0.00 0.00 0.00 2.52
2817 2923 7.964011 ACGAAAATGTAGAGTGAAAACGAAAAA 59.036 29.630 0.00 0.00 0.00 1.94
2818 2924 7.465989 ACGAAAATGTAGAGTGAAAACGAAAA 58.534 30.769 0.00 0.00 0.00 2.29
2819 2925 7.007313 ACGAAAATGTAGAGTGAAAACGAAA 57.993 32.000 0.00 0.00 0.00 3.46
2820 2926 6.592798 ACGAAAATGTAGAGTGAAAACGAA 57.407 33.333 0.00 0.00 0.00 3.85
2821 2927 7.878477 ATACGAAAATGTAGAGTGAAAACGA 57.122 32.000 0.00 0.00 0.00 3.85
2822 2928 9.619727 CATATACGAAAATGTAGAGTGAAAACG 57.380 33.333 0.00 0.00 0.00 3.60
2825 2931 9.863845 TGACATATACGAAAATGTAGAGTGAAA 57.136 29.630 0.00 0.00 36.48 2.69
2826 2932 9.863845 TTGACATATACGAAAATGTAGAGTGAA 57.136 29.630 0.00 0.00 36.48 3.18
2827 2933 9.863845 TTTGACATATACGAAAATGTAGAGTGA 57.136 29.630 0.00 0.00 36.48 3.41
2881 2987 6.470556 CACAATGATGAACGTGTGTACAAAAA 59.529 34.615 0.00 0.00 0.00 1.94
2882 2988 5.968261 CACAATGATGAACGTGTGTACAAAA 59.032 36.000 0.00 0.00 0.00 2.44
2883 2989 5.506181 CACAATGATGAACGTGTGTACAAA 58.494 37.500 0.00 0.00 0.00 2.83
2884 2990 4.553742 GCACAATGATGAACGTGTGTACAA 60.554 41.667 0.00 0.00 0.00 2.41
2885 2991 3.059257 GCACAATGATGAACGTGTGTACA 60.059 43.478 0.00 0.00 0.00 2.90
2886 2992 3.479006 GCACAATGATGAACGTGTGTAC 58.521 45.455 0.00 0.00 0.00 2.90
2887 2993 2.156697 CGCACAATGATGAACGTGTGTA 59.843 45.455 0.00 0.00 35.64 2.90
2888 2994 1.069973 CGCACAATGATGAACGTGTGT 60.070 47.619 0.00 0.00 35.64 3.72
2889 2995 1.194322 TCGCACAATGATGAACGTGTG 59.806 47.619 0.00 0.00 40.39 3.82
2890 2996 1.507562 TCGCACAATGATGAACGTGT 58.492 45.000 0.00 0.00 32.75 4.49
2891 2997 2.233355 GTTCGCACAATGATGAACGTG 58.767 47.619 0.00 0.00 32.38 4.49
2892 2998 2.594529 GTTCGCACAATGATGAACGT 57.405 45.000 0.00 0.00 32.38 3.99
2894 3000 1.135972 AGCGTTCGCACAATGATGAAC 60.136 47.619 18.95 0.00 37.84 3.18
2895 3001 1.155889 AGCGTTCGCACAATGATGAA 58.844 45.000 18.95 0.00 0.00 2.57
2896 3002 1.155889 AAGCGTTCGCACAATGATGA 58.844 45.000 18.95 0.00 0.00 2.92
2897 3003 2.804421 TAAGCGTTCGCACAATGATG 57.196 45.000 18.95 0.00 0.00 3.07
2898 3004 3.373748 TGAATAAGCGTTCGCACAATGAT 59.626 39.130 18.95 0.00 0.00 2.45
2899 3005 2.739379 TGAATAAGCGTTCGCACAATGA 59.261 40.909 18.95 0.00 0.00 2.57
2900 3006 3.116063 TGAATAAGCGTTCGCACAATG 57.884 42.857 18.95 0.00 0.00 2.82
2901 3007 3.058570 TGTTGAATAAGCGTTCGCACAAT 60.059 39.130 18.95 6.55 0.00 2.71
2902 3008 2.288186 TGTTGAATAAGCGTTCGCACAA 59.712 40.909 18.95 12.67 0.00 3.33
2903 3009 1.867865 TGTTGAATAAGCGTTCGCACA 59.132 42.857 18.95 9.59 0.00 4.57
2904 3010 2.587612 TGTTGAATAAGCGTTCGCAC 57.412 45.000 18.95 7.20 0.00 5.34
2905 3011 3.822594 AATGTTGAATAAGCGTTCGCA 57.177 38.095 18.95 0.00 0.00 5.10
2906 3012 5.116377 TGAAAAATGTTGAATAAGCGTTCGC 59.884 36.000 9.24 9.24 0.00 4.70
2907 3013 6.667981 TGAAAAATGTTGAATAAGCGTTCG 57.332 33.333 0.00 0.00 0.00 3.95
2910 3016 9.691362 AGTATTTGAAAAATGTTGAATAAGCGT 57.309 25.926 0.00 0.00 0.00 5.07
2970 3076 9.834628 GTTGAACGAGTATTTGGAAATTATTGA 57.165 29.630 0.00 0.00 0.00 2.57
2971 3077 9.619316 TGTTGAACGAGTATTTGGAAATTATTG 57.381 29.630 0.00 0.00 0.00 1.90
2975 3081 9.541143 AAAATGTTGAACGAGTATTTGGAAATT 57.459 25.926 0.00 0.00 0.00 1.82
2976 3082 9.541143 AAAAATGTTGAACGAGTATTTGGAAAT 57.459 25.926 0.00 0.00 0.00 2.17
2977 3083 8.934507 AAAAATGTTGAACGAGTATTTGGAAA 57.065 26.923 0.00 0.00 0.00 3.13
2978 3084 8.191446 TGAAAAATGTTGAACGAGTATTTGGAA 58.809 29.630 0.00 0.00 0.00 3.53
2979 3085 7.708051 TGAAAAATGTTGAACGAGTATTTGGA 58.292 30.769 0.00 0.00 0.00 3.53
2980 3086 7.922505 TGAAAAATGTTGAACGAGTATTTGG 57.077 32.000 0.00 0.00 0.00 3.28
2986 3092 9.581099 AAGTATTTTGAAAAATGTTGAACGAGT 57.419 25.926 10.56 0.00 38.90 4.18
2987 3093 9.833894 CAAGTATTTTGAAAAATGTTGAACGAG 57.166 29.630 10.56 0.00 38.90 4.18
2988 3094 9.360093 ACAAGTATTTTGAAAAATGTTGAACGA 57.640 25.926 20.83 0.00 38.90 3.85
2989 3095 9.965748 AACAAGTATTTTGAAAAATGTTGAACG 57.034 25.926 20.83 0.00 38.90 3.95


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

AutoCloner maintained by Alex Coulton.