Multiple sequence alignment - TraesCS4D01G324600

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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 TraesCS4D01G324600 chr4D 100.000 3286 0 0 1 3286 485162423 485165708 0.000000e+00 6069
1 TraesCS4D01G324600 chr4B 90.955 2355 121 37 1 2343 618346172 618348446 0.000000e+00 3085
2 TraesCS4D01G324600 chr4B 94.333 300 14 2 2817 3116 618348559 618348855 1.070000e-124 457
3 TraesCS4D01G324600 chr4B 89.908 218 21 1 2359 2575 90868542 90868759 2.500000e-71 279
4 TraesCS4D01G324600 chr4B 93.252 163 10 1 3107 3269 618349076 618349237 4.240000e-59 239
5 TraesCS4D01G324600 chr4B 91.489 94 8 0 2676 2769 618348470 618348563 2.660000e-26 130
6 TraesCS4D01G324600 chr5A 92.931 1457 67 12 861 2311 666203847 666205273 0.000000e+00 2087
7 TraesCS4D01G324600 chr5A 85.467 867 40 37 1 812 666202838 666203673 0.000000e+00 824
8 TraesCS4D01G324600 chr5A 93.833 454 20 6 2818 3269 666208935 666209382 0.000000e+00 676
9 TraesCS4D01G324600 chr5A 89.535 86 7 2 2263 2347 666205269 666205353 1.250000e-19 108
10 TraesCS4D01G324600 chr1D 91.667 216 16 2 2355 2569 214850073 214850287 6.890000e-77 298
11 TraesCS4D01G324600 chr1D 87.500 160 19 1 1983 2142 293291859 293292017 2.010000e-42 183
12 TraesCS4D01G324600 chr2B 90.868 219 18 2 2359 2575 35130787 35131005 3.210000e-75 292
13 TraesCS4D01G324600 chr2B 77.152 302 35 22 1371 1664 609202091 609201816 9.500000e-31 145
14 TraesCS4D01G324600 chr4A 89.954 219 20 2 2359 2575 655564612 655564394 6.940000e-72 281
15 TraesCS4D01G324600 chrUn 89.908 218 19 3 2354 2569 24293012 24293228 8.980000e-71 278
16 TraesCS4D01G324600 chr5B 89.498 219 21 2 2359 2575 527839557 527839339 3.230000e-70 276
17 TraesCS4D01G324600 chr3A 90.094 212 20 1 2359 2569 459051134 459050923 1.160000e-69 274
18 TraesCS4D01G324600 chr5D 89.671 213 20 2 2359 2569 533643423 533643211 1.500000e-68 270
19 TraesCS4D01G324600 chr2D 89.401 217 20 3 2355 2569 170533475 170533690 1.500000e-68 270
20 TraesCS4D01G324600 chr2D 76.144 306 39 23 1371 1668 517264488 517264209 2.660000e-26 130
21 TraesCS4D01G324600 chr1B 87.179 156 19 1 1983 2138 394116969 394117123 3.370000e-40 176
22 TraesCS4D01G324600 chr2A 76.159 302 38 22 1371 1664 661585615 661585340 9.570000e-26 128


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 TraesCS4D01G324600 chr4D 485162423 485165708 3285 False 6069.00 6069 100.00000 1 3286 1 chr4D.!!$F1 3285
1 TraesCS4D01G324600 chr4B 618346172 618349237 3065 False 977.75 3085 92.50725 1 3269 4 chr4B.!!$F2 3268
2 TraesCS4D01G324600 chr5A 666202838 666209382 6544 False 923.75 2087 90.44150 1 3269 4 chr5A.!!$F1 3268

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
863 1041 0.034476 CTCTGCAAGCTCAGTGTCCA 59.966 55.0 2.63 0.0 35.63 4.02 F
2020 2218 0.256464 GAGGAGGAGGACGAGAGGAA 59.744 60.0 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2349 0.108041 TCCTATCGGGCCGTCAAAAC 60.108 55.0 27.32 0.0 34.39 2.43 R
2960 6445 0.459585 CAGTTACGATCCCACCACCG 60.460 60.0 0.00 0.0 0.00 4.94 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
143 157 3.064987 GCGGTGGCGCTAGAGAAGA 62.065 63.158 7.64 0.00 0.00 2.87
148 162 1.204941 GTGGCGCTAGAGAAGAAAGGA 59.795 52.381 7.64 0.00 0.00 3.36
297 316 2.566057 TACGTGATGGCAACGGCGAT 62.566 55.000 16.62 0.00 41.52 4.58
298 317 2.404789 GTGATGGCAACGGCGATG 59.595 61.111 16.62 14.68 38.69 3.84
588 642 1.371558 GTGGAGGGTCAAGCTCGTT 59.628 57.895 0.00 0.00 0.00 3.85
591 645 1.183549 GGAGGGTCAAGCTCGTTCTA 58.816 55.000 0.00 0.00 0.00 2.10
592 646 1.549170 GGAGGGTCAAGCTCGTTCTAA 59.451 52.381 0.00 0.00 0.00 2.10
593 647 2.608268 GAGGGTCAAGCTCGTTCTAAC 58.392 52.381 0.00 0.00 0.00 2.34
662 725 3.504906 CACATTGTCCAACTTGATCTGCT 59.495 43.478 0.00 0.00 0.00 4.24
663 726 3.504906 ACATTGTCCAACTTGATCTGCTG 59.495 43.478 0.00 0.00 0.00 4.41
664 727 1.527034 TGTCCAACTTGATCTGCTGC 58.473 50.000 0.00 0.00 0.00 5.25
737 806 0.396417 TGGTCAACCCAACCAACCAG 60.396 55.000 0.00 0.00 43.72 4.00
800 869 4.617762 CGTACTTTACCCAGAGTCTTCCAC 60.618 50.000 0.00 0.00 0.00 4.02
812 881 3.607741 AGTCTTCCACAGCAAGATGATG 58.392 45.455 0.00 0.00 40.09 3.07
813 882 3.262660 AGTCTTCCACAGCAAGATGATGA 59.737 43.478 2.23 0.00 35.45 2.92
814 883 4.080469 AGTCTTCCACAGCAAGATGATGAT 60.080 41.667 2.23 0.00 35.45 2.45
815 884 4.639310 GTCTTCCACAGCAAGATGATGATT 59.361 41.667 2.23 0.00 35.45 2.57
817 886 4.224991 TCCACAGCAAGATGATGATTCA 57.775 40.909 2.23 0.00 35.45 2.57
818 887 3.943381 TCCACAGCAAGATGATGATTCAC 59.057 43.478 2.23 0.00 35.45 3.18
821 890 3.284617 CAGCAAGATGATGATTCACCCA 58.715 45.455 0.00 0.00 35.45 4.51
824 893 2.621998 CAAGATGATGATTCACCCAGGC 59.378 50.000 0.00 0.00 33.85 4.85
826 895 1.144503 GATGATGATTCACCCAGGCCT 59.855 52.381 0.00 0.00 33.85 5.19
827 896 0.256752 TGATGATTCACCCAGGCCTG 59.743 55.000 26.87 26.87 0.00 4.85
828 897 4.422266 ATGATGATTCACCCAGGCCTGG 62.422 54.545 40.71 40.71 41.07 4.45
862 1040 2.838286 CTCTGCAAGCTCAGTGTCC 58.162 57.895 2.63 0.00 35.63 4.02
863 1041 0.034476 CTCTGCAAGCTCAGTGTCCA 59.966 55.000 2.63 0.00 35.63 4.02
865 1043 1.134128 TCTGCAAGCTCAGTGTCCAAA 60.134 47.619 2.63 0.00 35.63 3.28
866 1044 1.266175 CTGCAAGCTCAGTGTCCAAAG 59.734 52.381 0.00 0.00 0.00 2.77
867 1045 1.312815 GCAAGCTCAGTGTCCAAAGT 58.687 50.000 0.00 0.00 0.00 2.66
869 1047 2.564771 CAAGCTCAGTGTCCAAAGTGA 58.435 47.619 0.00 0.00 0.00 3.41
958 1152 0.995132 ATCCACTCATCCCCATGCCA 60.995 55.000 0.00 0.00 0.00 4.92
1013 1211 3.427573 ACACCACCCTATAAAAACAGCC 58.572 45.455 0.00 0.00 0.00 4.85
1095 1293 1.290324 CGCCGGGATCGATCATCTT 59.710 57.895 25.93 0.00 39.00 2.40
1099 1297 1.067283 CCGGGATCGATCATCTTCAGG 60.067 57.143 25.93 14.20 39.00 3.86
1100 1298 1.067283 CGGGATCGATCATCTTCAGGG 60.067 57.143 25.93 1.74 39.00 4.45
1102 1300 2.836981 GGGATCGATCATCTTCAGGGAT 59.163 50.000 25.93 0.00 0.00 3.85
1103 1301 3.118811 GGGATCGATCATCTTCAGGGATC 60.119 52.174 25.93 4.51 35.28 3.36
1104 1302 3.513119 GGATCGATCATCTTCAGGGATCA 59.487 47.826 25.93 0.00 37.81 2.92
1105 1303 4.161942 GGATCGATCATCTTCAGGGATCAT 59.838 45.833 25.93 0.00 37.81 2.45
1106 1304 4.797800 TCGATCATCTTCAGGGATCATC 57.202 45.455 0.00 0.00 37.81 2.92
1107 1305 4.414677 TCGATCATCTTCAGGGATCATCT 58.585 43.478 0.00 0.00 37.81 2.90
1108 1306 4.837298 TCGATCATCTTCAGGGATCATCTT 59.163 41.667 0.00 0.00 37.81 2.40
1109 1307 5.047448 TCGATCATCTTCAGGGATCATCTTC 60.047 44.000 0.00 0.00 37.81 2.87
1110 1308 5.279356 CGATCATCTTCAGGGATCATCTTCA 60.279 44.000 0.00 0.00 37.81 3.02
1111 1309 5.548181 TCATCTTCAGGGATCATCTTCAG 57.452 43.478 0.00 0.00 0.00 3.02
1112 1310 4.347292 TCATCTTCAGGGATCATCTTCAGG 59.653 45.833 0.00 0.00 0.00 3.86
1113 1311 3.999603 TCTTCAGGGATCATCTTCAGGA 58.000 45.455 0.00 0.00 0.00 3.86
1114 1312 3.708631 TCTTCAGGGATCATCTTCAGGAC 59.291 47.826 0.00 0.00 0.00 3.85
1115 1313 3.411454 TCAGGGATCATCTTCAGGACT 57.589 47.619 0.00 0.00 0.00 3.85
1116 1314 3.729108 TCAGGGATCATCTTCAGGACTT 58.271 45.455 0.00 0.00 0.00 3.01
1553 1751 3.844090 GAGGCGCTCCTGTCCCTC 61.844 72.222 7.64 0.00 44.46 4.30
1694 1892 4.452733 GCCCTCTCCCACCGTTCG 62.453 72.222 0.00 0.00 0.00 3.95
2020 2218 0.256464 GAGGAGGAGGACGAGAGGAA 59.744 60.000 0.00 0.00 0.00 3.36
2151 2349 1.580845 CCTCACGCCCTGCTTTTGAG 61.581 60.000 0.00 0.00 0.00 3.02
2152 2350 0.886490 CTCACGCCCTGCTTTTGAGT 60.886 55.000 0.00 0.00 0.00 3.41
2153 2351 0.465460 TCACGCCCTGCTTTTGAGTT 60.465 50.000 0.00 0.00 0.00 3.01
2154 2352 0.385390 CACGCCCTGCTTTTGAGTTT 59.615 50.000 0.00 0.00 0.00 2.66
2155 2353 1.111277 ACGCCCTGCTTTTGAGTTTT 58.889 45.000 0.00 0.00 0.00 2.43
2156 2354 1.202405 ACGCCCTGCTTTTGAGTTTTG 60.202 47.619 0.00 0.00 0.00 2.44
2157 2355 1.066908 CGCCCTGCTTTTGAGTTTTGA 59.933 47.619 0.00 0.00 0.00 2.69
2163 2361 1.868109 GCTTTTGAGTTTTGACGGCCC 60.868 52.381 0.00 0.00 0.00 5.80
2168 2366 1.287425 GAGTTTTGACGGCCCGATAG 58.713 55.000 11.71 0.00 0.00 2.08
2192 2390 6.094048 AGGACAATGTGGATTAGTTTGATTCG 59.906 38.462 0.00 0.00 0.00 3.34
2208 2406 9.442047 AGTTTGATTCGATTGATCTTTCTTAGT 57.558 29.630 0.00 0.00 0.00 2.24
2253 2451 7.550551 ACATGATGTACAGAGATCGTTTCAAAT 59.449 33.333 0.00 0.00 0.00 2.32
2284 2482 6.305693 AGATTGTAATTAGGCGAAATGCTC 57.694 37.500 0.00 0.00 45.43 4.26
2347 2589 5.461078 CCAAATTTTGCAGTTGTTCTCTCTG 59.539 40.000 3.50 0.00 0.00 3.35
2349 2591 5.841957 ATTTTGCAGTTGTTCTCTCTGTT 57.158 34.783 0.00 0.00 0.00 3.16
2352 2594 3.995199 TGCAGTTGTTCTCTCTGTTAGG 58.005 45.455 0.00 0.00 0.00 2.69
2353 2595 2.739379 GCAGTTGTTCTCTCTGTTAGGC 59.261 50.000 0.00 0.00 0.00 3.93
2354 2596 3.556004 GCAGTTGTTCTCTCTGTTAGGCT 60.556 47.826 0.00 0.00 0.00 4.58
2355 2597 4.322049 GCAGTTGTTCTCTCTGTTAGGCTA 60.322 45.833 0.00 0.00 0.00 3.93
2356 2598 5.784177 CAGTTGTTCTCTCTGTTAGGCTAA 58.216 41.667 2.04 2.04 0.00 3.09
2357 2599 5.866633 CAGTTGTTCTCTCTGTTAGGCTAAG 59.133 44.000 7.33 0.00 0.00 2.18
2358 2600 5.046950 AGTTGTTCTCTCTGTTAGGCTAAGG 60.047 44.000 7.33 4.13 0.00 2.69
2359 2601 4.417437 TGTTCTCTCTGTTAGGCTAAGGT 58.583 43.478 7.33 0.00 0.00 3.50
2360 2602 5.577100 TGTTCTCTCTGTTAGGCTAAGGTA 58.423 41.667 7.33 0.00 0.00 3.08
2361 2603 5.418209 TGTTCTCTCTGTTAGGCTAAGGTAC 59.582 44.000 7.33 0.00 0.00 3.34
2363 2605 5.438833 TCTCTCTGTTAGGCTAAGGTACTC 58.561 45.833 7.33 0.00 38.49 2.59
2364 2606 4.534797 TCTCTGTTAGGCTAAGGTACTCC 58.465 47.826 7.33 0.00 38.49 3.85
2365 2607 3.637694 CTCTGTTAGGCTAAGGTACTCCC 59.362 52.174 7.33 0.00 38.49 4.30
2367 2609 3.637694 CTGTTAGGCTAAGGTACTCCCTC 59.362 52.174 7.33 0.00 45.47 4.30
2368 2610 2.964464 GTTAGGCTAAGGTACTCCCTCC 59.036 54.545 7.33 0.00 45.47 4.30
2369 2611 1.016415 AGGCTAAGGTACTCCCTCCA 58.984 55.000 0.00 0.00 45.47 3.86
2370 2612 1.581149 AGGCTAAGGTACTCCCTCCAT 59.419 52.381 0.00 0.00 45.47 3.41
2373 2615 2.369203 GCTAAGGTACTCCCTCCATTCC 59.631 54.545 0.00 0.00 45.47 3.01
2378 2620 3.923425 AGGTACTCCCTCCATTCCTTTTT 59.077 43.478 0.00 0.00 40.71 1.94
2386 2628 3.343617 CTCCATTCCTTTTTACTCCGCA 58.656 45.455 0.00 0.00 0.00 5.69
2390 2632 6.833041 TCCATTCCTTTTTACTCCGCATATA 58.167 36.000 0.00 0.00 0.00 0.86
2391 2633 7.284074 TCCATTCCTTTTTACTCCGCATATAA 58.716 34.615 0.00 0.00 0.00 0.98
2392 2634 7.444183 TCCATTCCTTTTTACTCCGCATATAAG 59.556 37.037 0.00 0.00 0.00 1.73
2393 2635 7.444183 CCATTCCTTTTTACTCCGCATATAAGA 59.556 37.037 0.00 0.00 0.00 2.10
2395 2637 8.974060 TTCCTTTTTACTCCGCATATAAGATT 57.026 30.769 0.00 0.00 0.00 2.40
2402 4495 8.683550 TTACTCCGCATATAAGATTTATGTCG 57.316 34.615 0.00 0.00 31.13 4.35
2405 4498 8.035394 ACTCCGCATATAAGATTTATGTCGAAT 58.965 33.333 0.00 0.00 32.95 3.34
2423 4516 8.388319 TGTCGAATCAAACTTTACAAACTTTG 57.612 30.769 0.00 0.00 0.00 2.77
2424 4517 8.237949 TGTCGAATCAAACTTTACAAACTTTGA 58.762 29.630 8.55 10.11 36.16 2.69
2426 4519 9.445786 TCGAATCAAACTTTACAAACTTTGATC 57.554 29.630 16.09 11.52 38.89 2.92
2427 4520 9.232082 CGAATCAAACTTTACAAACTTTGATCA 57.768 29.630 16.09 0.00 38.89 2.92
2432 4525 9.520204 CAAACTTTACAAACTTTGATCAGATGT 57.480 29.630 8.55 0.00 0.00 3.06
2433 4526 9.520204 AAACTTTACAAACTTTGATCAGATGTG 57.480 29.630 8.55 0.00 0.00 3.21
2434 4527 8.225603 ACTTTACAAACTTTGATCAGATGTGT 57.774 30.769 8.55 0.00 0.00 3.72
2518 5907 6.773638 TGAATCTAGAGATATTCCTTTGGCC 58.226 40.000 0.00 0.00 33.73 5.36
2523 5912 5.975988 AGAGATATTCCTTTGGCCTTGTA 57.024 39.130 3.32 0.00 0.00 2.41
2524 5913 6.327386 AGAGATATTCCTTTGGCCTTGTAA 57.673 37.500 3.32 0.00 0.00 2.41
2525 5914 6.731467 AGAGATATTCCTTTGGCCTTGTAAA 58.269 36.000 3.32 0.00 0.00 2.01
2529 5918 4.864704 TTCCTTTGGCCTTGTAAATGTC 57.135 40.909 3.32 0.00 0.00 3.06
2531 5920 2.817258 CCTTTGGCCTTGTAAATGTCGA 59.183 45.455 3.32 0.00 0.00 4.20
2533 5922 4.082245 CCTTTGGCCTTGTAAATGTCGATT 60.082 41.667 3.32 0.00 0.00 3.34
2536 5925 5.461032 TGGCCTTGTAAATGTCGATTTTT 57.539 34.783 3.32 0.00 33.63 1.94
2571 5960 9.753674 AGTTTGATCAAAATAGGGATACTTCAA 57.246 29.630 22.07 0.00 31.33 2.69
2573 5962 9.753674 TTTGATCAAAATAGGGATACTTCAAGT 57.246 29.630 18.45 0.00 0.00 3.16
2574 5963 9.753674 TTGATCAAAATAGGGATACTTCAAGTT 57.246 29.630 5.45 0.00 0.00 2.66
2582 5971 9.950496 AATAGGGATACTTCAAGTTATATGCAG 57.050 33.333 0.00 0.00 0.00 4.41
2584 5973 7.445945 AGGGATACTTCAAGTTATATGCAGAC 58.554 38.462 0.00 0.00 0.00 3.51
2585 5974 7.291182 AGGGATACTTCAAGTTATATGCAGACT 59.709 37.037 0.00 0.00 0.00 3.24
2586 5975 8.585881 GGGATACTTCAAGTTATATGCAGACTA 58.414 37.037 0.00 0.00 0.00 2.59
2621 6106 5.717178 AGGAGTAATCATGGCGTATACTCAT 59.283 40.000 19.56 13.97 42.59 2.90
2622 6107 6.037098 GGAGTAATCATGGCGTATACTCATC 58.963 44.000 19.56 7.41 42.59 2.92
2623 6108 6.127591 GGAGTAATCATGGCGTATACTCATCT 60.128 42.308 19.56 0.00 42.59 2.90
2624 6109 7.233389 AGTAATCATGGCGTATACTCATCTT 57.767 36.000 0.56 4.28 0.00 2.40
2625 6110 7.316640 AGTAATCATGGCGTATACTCATCTTC 58.683 38.462 0.56 0.00 0.00 2.87
2626 6111 5.728637 ATCATGGCGTATACTCATCTTCA 57.271 39.130 0.56 0.00 0.00 3.02
2627 6112 5.728637 TCATGGCGTATACTCATCTTCAT 57.271 39.130 0.56 0.00 0.00 2.57
2628 6113 6.101650 TCATGGCGTATACTCATCTTCATT 57.898 37.500 0.56 0.00 0.00 2.57
2629 6114 6.159293 TCATGGCGTATACTCATCTTCATTC 58.841 40.000 0.56 0.00 0.00 2.67
2630 6115 4.546570 TGGCGTATACTCATCTTCATTCG 58.453 43.478 0.56 0.00 0.00 3.34
2631 6116 3.365220 GGCGTATACTCATCTTCATTCGC 59.635 47.826 0.56 0.00 36.73 4.70
2632 6117 3.365220 GCGTATACTCATCTTCATTCGCC 59.635 47.826 0.56 0.00 32.99 5.54
2633 6118 4.546570 CGTATACTCATCTTCATTCGCCA 58.453 43.478 0.56 0.00 0.00 5.69
2634 6119 4.982295 CGTATACTCATCTTCATTCGCCAA 59.018 41.667 0.56 0.00 0.00 4.52
2635 6120 5.462068 CGTATACTCATCTTCATTCGCCAAA 59.538 40.000 0.56 0.00 0.00 3.28
2636 6121 6.019075 CGTATACTCATCTTCATTCGCCAAAA 60.019 38.462 0.56 0.00 0.00 2.44
2637 6122 6.757897 ATACTCATCTTCATTCGCCAAAAA 57.242 33.333 0.00 0.00 0.00 1.94
2638 6123 5.051891 ACTCATCTTCATTCGCCAAAAAG 57.948 39.130 0.00 0.00 0.00 2.27
2639 6124 4.761739 ACTCATCTTCATTCGCCAAAAAGA 59.238 37.500 0.00 0.00 0.00 2.52
2640 6125 5.106396 ACTCATCTTCATTCGCCAAAAAGAG 60.106 40.000 0.00 0.00 30.16 2.85
2641 6126 5.003160 TCATCTTCATTCGCCAAAAAGAGA 58.997 37.500 0.00 0.00 30.16 3.10
2642 6127 5.473162 TCATCTTCATTCGCCAAAAAGAGAA 59.527 36.000 0.00 0.00 30.16 2.87
2643 6128 5.766150 TCTTCATTCGCCAAAAAGAGAAA 57.234 34.783 0.00 0.00 0.00 2.52
2644 6129 5.762045 TCTTCATTCGCCAAAAAGAGAAAG 58.238 37.500 0.00 0.00 0.00 2.62
2645 6130 4.503741 TCATTCGCCAAAAAGAGAAAGG 57.496 40.909 0.00 0.00 0.00 3.11
2646 6131 3.888930 TCATTCGCCAAAAAGAGAAAGGT 59.111 39.130 0.00 0.00 0.00 3.50
2647 6132 5.067273 TCATTCGCCAAAAAGAGAAAGGTA 58.933 37.500 0.00 0.00 0.00 3.08
2648 6133 5.710099 TCATTCGCCAAAAAGAGAAAGGTAT 59.290 36.000 0.00 0.00 0.00 2.73
2649 6134 6.882140 TCATTCGCCAAAAAGAGAAAGGTATA 59.118 34.615 0.00 0.00 0.00 1.47
2650 6135 6.490566 TTCGCCAAAAAGAGAAAGGTATAC 57.509 37.500 0.00 0.00 0.00 1.47
2651 6136 5.801380 TCGCCAAAAAGAGAAAGGTATACT 58.199 37.500 2.25 0.00 0.00 2.12
2652 6137 5.873164 TCGCCAAAAAGAGAAAGGTATACTC 59.127 40.000 2.25 0.00 0.00 2.59
2653 6138 5.875359 CGCCAAAAAGAGAAAGGTATACTCT 59.125 40.000 2.25 0.00 41.86 3.24
2679 6164 4.664150 TTTTGCGATGGAAGAAAAAGGT 57.336 36.364 0.00 0.00 0.00 3.50
2680 6165 3.641437 TTGCGATGGAAGAAAAAGGTG 57.359 42.857 0.00 0.00 0.00 4.00
2681 6166 2.582052 TGCGATGGAAGAAAAAGGTGT 58.418 42.857 0.00 0.00 0.00 4.16
2682 6167 3.745799 TGCGATGGAAGAAAAAGGTGTA 58.254 40.909 0.00 0.00 0.00 2.90
2683 6168 3.500680 TGCGATGGAAGAAAAAGGTGTAC 59.499 43.478 0.00 0.00 0.00 2.90
2684 6169 3.751698 GCGATGGAAGAAAAAGGTGTACT 59.248 43.478 0.00 0.00 0.00 2.73
2685 6170 4.142881 GCGATGGAAGAAAAAGGTGTACTC 60.143 45.833 0.00 0.00 0.00 2.59
2686 6171 4.392138 CGATGGAAGAAAAAGGTGTACTCC 59.608 45.833 5.81 5.81 0.00 3.85
2694 6179 2.715763 AAGGTGTACTCCTCTTGGGA 57.284 50.000 16.59 0.00 42.77 4.37
2769 6254 3.829601 TCCGGTGACATAAGCCAATTTTT 59.170 39.130 0.00 0.00 0.00 1.94
2788 6273 3.414549 TTTCACTTTTTGTCCGACAGC 57.585 42.857 0.64 0.00 0.00 4.40
2789 6274 2.031258 TCACTTTTTGTCCGACAGCA 57.969 45.000 0.64 0.00 0.00 4.41
2790 6275 2.360844 TCACTTTTTGTCCGACAGCAA 58.639 42.857 0.64 0.00 0.00 3.91
2791 6276 2.948979 TCACTTTTTGTCCGACAGCAAT 59.051 40.909 0.64 0.00 0.00 3.56
2792 6277 3.044986 CACTTTTTGTCCGACAGCAATG 58.955 45.455 0.64 4.57 0.00 2.82
2793 6278 2.687935 ACTTTTTGTCCGACAGCAATGT 59.312 40.909 0.64 5.12 0.00 2.71
2794 6279 3.880490 ACTTTTTGTCCGACAGCAATGTA 59.120 39.130 0.64 0.00 0.00 2.29
2795 6280 4.518970 ACTTTTTGTCCGACAGCAATGTAT 59.481 37.500 0.64 0.00 0.00 2.29
2796 6281 5.009610 ACTTTTTGTCCGACAGCAATGTATT 59.990 36.000 0.64 0.00 0.00 1.89
2797 6282 5.446143 TTTTGTCCGACAGCAATGTATTT 57.554 34.783 0.64 0.00 0.00 1.40
2798 6283 5.446143 TTTGTCCGACAGCAATGTATTTT 57.554 34.783 0.64 0.00 0.00 1.82
2799 6284 5.446143 TTGTCCGACAGCAATGTATTTTT 57.554 34.783 0.64 0.00 0.00 1.94
2844 6329 7.324354 TGTGTGTGTCGATAAGTTAGCTATA 57.676 36.000 0.00 0.00 0.00 1.31
2845 6330 7.937649 TGTGTGTGTCGATAAGTTAGCTATAT 58.062 34.615 0.00 0.00 0.00 0.86
2846 6331 7.860872 TGTGTGTGTCGATAAGTTAGCTATATG 59.139 37.037 0.00 0.00 0.00 1.78
2847 6332 6.861572 TGTGTGTCGATAAGTTAGCTATATGC 59.138 38.462 0.00 0.00 43.29 3.14
2865 6350 2.977914 TGCTCTGCCATCTTCAACTAC 58.022 47.619 0.00 0.00 0.00 2.73
2879 6364 1.993370 CAACTACTGCCGAGTGTAAGC 59.007 52.381 0.00 0.00 33.21 3.09
2960 6445 3.433615 GCTTGAATATCATAGGCCGACAC 59.566 47.826 0.00 0.00 0.00 3.67
3064 6549 7.364144 CCAGGATTATTCCAAGAAAGAAAAGGG 60.364 40.741 6.44 0.00 45.30 3.95
3073 6559 2.092323 GAAAGAAAAGGGATGGACGGG 58.908 52.381 0.00 0.00 0.00 5.28
3074 6560 1.368374 AAGAAAAGGGATGGACGGGA 58.632 50.000 0.00 0.00 0.00 5.14
3116 6602 8.004801 CAGATTCCCTAACCCACCTTTATATTT 58.995 37.037 0.00 0.00 0.00 1.40
3117 6603 8.225416 AGATTCCCTAACCCACCTTTATATTTC 58.775 37.037 0.00 0.00 0.00 2.17
3125 6841 5.190677 CCCACCTTTATATTTCGTGGAAGT 58.809 41.667 6.11 0.00 45.62 3.01
3269 6985 6.582677 TCCAACAATACCGTGAATTGAAAT 57.417 33.333 8.17 0.00 37.68 2.17
3270 6986 6.987386 TCCAACAATACCGTGAATTGAAATT 58.013 32.000 8.17 0.00 37.68 1.82
3271 6987 7.437748 TCCAACAATACCGTGAATTGAAATTT 58.562 30.769 8.17 0.00 37.68 1.82
3272 6988 7.383572 TCCAACAATACCGTGAATTGAAATTTG 59.616 33.333 0.00 3.57 37.68 2.32
3273 6989 7.383572 CCAACAATACCGTGAATTGAAATTTGA 59.616 33.333 0.00 0.00 37.68 2.69
3274 6990 8.759641 CAACAATACCGTGAATTGAAATTTGAA 58.240 29.630 0.00 0.00 37.68 2.69
3275 6991 8.879342 ACAATACCGTGAATTGAAATTTGAAA 57.121 26.923 0.00 0.00 37.68 2.69
3276 6992 8.977505 ACAATACCGTGAATTGAAATTTGAAAG 58.022 29.630 0.00 0.00 37.68 2.62
3277 6993 9.190858 CAATACCGTGAATTGAAATTTGAAAGA 57.809 29.630 0.00 0.00 36.61 2.52
3278 6994 8.742554 ATACCGTGAATTGAAATTTGAAAGAC 57.257 30.769 0.00 0.00 0.00 3.01
3279 6995 5.983118 ACCGTGAATTGAAATTTGAAAGACC 59.017 36.000 0.00 0.00 0.00 3.85
3280 6996 5.982516 CCGTGAATTGAAATTTGAAAGACCA 59.017 36.000 0.00 0.00 0.00 4.02
3281 6997 6.074356 CCGTGAATTGAAATTTGAAAGACCAC 60.074 38.462 0.00 0.81 0.00 4.16
3282 6998 6.344936 CGTGAATTGAAATTTGAAAGACCACG 60.345 38.462 15.88 15.88 32.21 4.94
3283 6999 6.475402 GTGAATTGAAATTTGAAAGACCACGT 59.525 34.615 0.00 0.00 0.00 4.49
3284 7000 6.695278 TGAATTGAAATTTGAAAGACCACGTC 59.305 34.615 0.00 0.00 0.00 4.34
3285 7001 4.203950 TGAAATTTGAAAGACCACGTCG 57.796 40.909 0.00 0.00 37.67 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 149 4.717280 GGGGACATCTTCCTTTCTTCTCTA 59.283 45.833 0.00 0.00 45.09 2.43
143 157 0.249398 CGACGGGGACATCTTCCTTT 59.751 55.000 0.00 0.00 45.09 3.11
148 162 2.882876 CGACGACGGGGACATCTT 59.117 61.111 0.00 0.00 35.72 2.40
315 334 4.974721 CCAAACGCTGCCCCACCT 62.975 66.667 0.00 0.00 0.00 4.00
323 342 3.294493 CCACCCACCCAAACGCTG 61.294 66.667 0.00 0.00 0.00 5.18
346 365 2.426752 GAGATCGCTCGCTCGCTC 60.427 66.667 0.00 0.00 0.00 5.03
504 523 6.115448 ACAGAAACCAAAGAGTAGTATGCT 57.885 37.500 0.00 0.00 0.00 3.79
598 657 1.083401 GTTGACTTGTGTGCGAGCG 60.083 57.895 0.00 0.00 0.00 5.03
662 725 2.817844 TCAAACTCGAGTAGTAGCAGCA 59.182 45.455 20.39 0.00 37.50 4.41
663 726 3.119779 AGTCAAACTCGAGTAGTAGCAGC 60.120 47.826 20.39 4.35 37.50 5.25
664 727 4.154375 TCAGTCAAACTCGAGTAGTAGCAG 59.846 45.833 20.39 6.92 37.50 4.24
737 806 5.594724 TGTACGTGTACAATACCTTTTGC 57.405 39.130 10.27 0.00 42.49 3.68
800 869 3.284617 TGGGTGAATCATCATCTTGCTG 58.715 45.455 0.00 0.00 36.86 4.41
826 895 3.333219 CAAGGAGCCCAGAGCCCA 61.333 66.667 0.00 0.00 45.47 5.36
827 896 4.811364 GCAAGGAGCCCAGAGCCC 62.811 72.222 0.00 0.00 45.47 5.19
1075 1273 1.734477 GATGATCGATCCCGGCGTG 60.734 63.158 22.31 0.00 36.24 5.34
1095 1293 3.411454 AGTCCTGAAGATGATCCCTGA 57.589 47.619 0.00 0.00 0.00 3.86
1099 1297 3.118482 TGCTGAAGTCCTGAAGATGATCC 60.118 47.826 0.00 0.00 0.00 3.36
1100 1298 4.134379 TGCTGAAGTCCTGAAGATGATC 57.866 45.455 0.00 0.00 0.00 2.92
1102 1300 3.867600 GCTTGCTGAAGTCCTGAAGATGA 60.868 47.826 0.00 0.00 0.00 2.92
1103 1301 2.419324 GCTTGCTGAAGTCCTGAAGATG 59.581 50.000 0.00 0.00 0.00 2.90
1104 1302 2.617532 GGCTTGCTGAAGTCCTGAAGAT 60.618 50.000 0.00 0.00 0.00 2.40
1105 1303 1.271054 GGCTTGCTGAAGTCCTGAAGA 60.271 52.381 0.00 0.00 0.00 2.87
1106 1304 1.163554 GGCTTGCTGAAGTCCTGAAG 58.836 55.000 0.00 0.00 0.00 3.02
1107 1305 0.603707 CGGCTTGCTGAAGTCCTGAA 60.604 55.000 0.00 0.00 29.07 3.02
1108 1306 1.004560 CGGCTTGCTGAAGTCCTGA 60.005 57.895 0.00 0.00 29.07 3.86
1109 1307 2.037136 CCGGCTTGCTGAAGTCCTG 61.037 63.158 2.59 0.00 29.07 3.86
1110 1308 2.217038 TCCGGCTTGCTGAAGTCCT 61.217 57.895 0.00 0.00 29.07 3.85
1111 1309 2.035442 GTCCGGCTTGCTGAAGTCC 61.035 63.158 0.00 0.00 29.07 3.85
1112 1310 2.383527 CGTCCGGCTTGCTGAAGTC 61.384 63.158 0.00 0.00 0.00 3.01
1113 1311 2.357517 CGTCCGGCTTGCTGAAGT 60.358 61.111 0.00 0.00 0.00 3.01
1114 1312 3.793144 GCGTCCGGCTTGCTGAAG 61.793 66.667 0.00 0.00 39.11 3.02
1115 1313 4.617520 TGCGTCCGGCTTGCTGAA 62.618 61.111 12.53 0.00 44.05 3.02
1340 1538 4.873129 CCGATCCACTCCGTGCCG 62.873 72.222 0.00 0.00 31.34 5.69
1394 1592 3.695606 TGGAGCAGGTCGGTGAGC 61.696 66.667 0.00 0.00 0.00 4.26
1679 1877 2.261671 CACGAACGGTGGGAGAGG 59.738 66.667 0.00 0.00 43.16 3.69
1826 2024 4.519274 GTCAATGCGCGCGATGCA 62.519 61.111 37.18 25.09 46.97 3.96
2151 2349 0.108041 TCCTATCGGGCCGTCAAAAC 60.108 55.000 27.32 0.00 34.39 2.43
2152 2350 0.108041 GTCCTATCGGGCCGTCAAAA 60.108 55.000 27.32 6.22 34.39 2.44
2153 2351 1.259142 TGTCCTATCGGGCCGTCAAA 61.259 55.000 27.32 6.68 32.45 2.69
2154 2352 1.259142 TTGTCCTATCGGGCCGTCAA 61.259 55.000 27.32 17.71 32.45 3.18
2155 2353 1.046472 ATTGTCCTATCGGGCCGTCA 61.046 55.000 27.32 13.80 32.45 4.35
2156 2354 0.600255 CATTGTCCTATCGGGCCGTC 60.600 60.000 27.32 10.80 32.45 4.79
2157 2355 1.335132 ACATTGTCCTATCGGGCCGT 61.335 55.000 27.32 15.73 32.45 5.68
2163 2361 6.761242 TCAAACTAATCCACATTGTCCTATCG 59.239 38.462 0.00 0.00 0.00 2.92
2168 2366 6.093495 TCGAATCAAACTAATCCACATTGTCC 59.907 38.462 0.00 0.00 0.00 4.02
2177 2375 9.657121 GAAAGATCAATCGAATCAAACTAATCC 57.343 33.333 0.00 0.00 0.00 3.01
2182 2380 9.442047 ACTAAGAAAGATCAATCGAATCAAACT 57.558 29.630 0.00 0.00 0.00 2.66
2192 2390 9.980780 GCTACAGAAAACTAAGAAAGATCAATC 57.019 33.333 0.00 0.00 0.00 2.67
2208 2406 8.882736 CATCATGTATACACAAGCTACAGAAAA 58.117 33.333 7.96 0.00 38.42 2.29
2212 2410 7.920682 TGTACATCATGTATACACAAGCTACAG 59.079 37.037 7.96 0.00 38.42 2.74
2253 2451 5.870433 TCGCCTAATTACAATCTCGTTTCAA 59.130 36.000 0.00 0.00 0.00 2.69
2357 2599 4.317530 AAAAAGGAATGGAGGGAGTACC 57.682 45.455 0.00 0.00 40.67 3.34
2358 2600 6.063496 AGTAAAAAGGAATGGAGGGAGTAC 57.937 41.667 0.00 0.00 0.00 2.73
2359 2601 5.191124 GGAGTAAAAAGGAATGGAGGGAGTA 59.809 44.000 0.00 0.00 0.00 2.59
2360 2602 4.018324 GGAGTAAAAAGGAATGGAGGGAGT 60.018 45.833 0.00 0.00 0.00 3.85
2361 2603 4.527944 GGAGTAAAAAGGAATGGAGGGAG 58.472 47.826 0.00 0.00 0.00 4.30
2362 2604 3.054655 CGGAGTAAAAAGGAATGGAGGGA 60.055 47.826 0.00 0.00 0.00 4.20
2363 2605 3.279434 CGGAGTAAAAAGGAATGGAGGG 58.721 50.000 0.00 0.00 0.00 4.30
2364 2606 2.683362 GCGGAGTAAAAAGGAATGGAGG 59.317 50.000 0.00 0.00 0.00 4.30
2365 2607 3.343617 TGCGGAGTAAAAAGGAATGGAG 58.656 45.455 0.00 0.00 0.00 3.86
2366 2608 3.426787 TGCGGAGTAAAAAGGAATGGA 57.573 42.857 0.00 0.00 0.00 3.41
2367 2609 7.444183 TCTTATATGCGGAGTAAAAAGGAATGG 59.556 37.037 0.00 0.00 0.00 3.16
2368 2610 8.378172 TCTTATATGCGGAGTAAAAAGGAATG 57.622 34.615 0.00 0.00 0.00 2.67
2369 2611 9.574516 AATCTTATATGCGGAGTAAAAAGGAAT 57.425 29.630 0.00 0.00 0.00 3.01
2370 2612 8.974060 AATCTTATATGCGGAGTAAAAAGGAA 57.026 30.769 0.00 0.00 0.00 3.36
2378 2620 8.047413 TCGACATAAATCTTATATGCGGAGTA 57.953 34.615 0.00 0.00 34.75 2.59
2409 4502 8.225603 ACACATCTGATCAAAGTTTGTAAAGT 57.774 30.769 15.08 4.27 0.00 2.66
2491 4584 9.950496 GCCAAAGGAATATCTCTAGATTCATTA 57.050 33.333 4.62 0.00 36.59 1.90
2492 4585 7.887495 GGCCAAAGGAATATCTCTAGATTCATT 59.113 37.037 0.00 2.83 38.55 2.57
2494 4587 6.560304 AGGCCAAAGGAATATCTCTAGATTCA 59.440 38.462 5.01 0.00 35.45 2.57
2495 4588 7.014988 AGGCCAAAGGAATATCTCTAGATTC 57.985 40.000 5.01 0.00 36.05 2.52
2496 4589 7.147230 ACAAGGCCAAAGGAATATCTCTAGATT 60.147 37.037 5.01 0.00 36.05 2.40
2497 4590 6.331307 ACAAGGCCAAAGGAATATCTCTAGAT 59.669 38.462 5.01 0.00 38.51 1.98
2499 4592 5.934781 ACAAGGCCAAAGGAATATCTCTAG 58.065 41.667 5.01 0.00 0.00 2.43
2500 4593 5.975988 ACAAGGCCAAAGGAATATCTCTA 57.024 39.130 5.01 0.00 0.00 2.43
2505 4598 6.183360 CGACATTTACAAGGCCAAAGGAATAT 60.183 38.462 5.01 0.00 0.00 1.28
2507 4600 4.082245 CGACATTTACAAGGCCAAAGGAAT 60.082 41.667 5.01 0.00 0.00 3.01
2509 4602 2.817258 CGACATTTACAAGGCCAAAGGA 59.183 45.455 5.01 0.00 0.00 3.36
2511 4604 4.701956 ATCGACATTTACAAGGCCAAAG 57.298 40.909 5.01 0.00 0.00 2.77
2512 4605 5.461032 AAATCGACATTTACAAGGCCAAA 57.539 34.783 5.01 0.00 29.81 3.28
2513 4606 5.461032 AAAATCGACATTTACAAGGCCAA 57.539 34.783 5.01 0.00 31.51 4.52
2548 5937 9.753674 AACTTGAAGTATCCCTATTTTGATCAA 57.246 29.630 3.38 3.38 0.00 2.57
2557 5946 9.326489 TCTGCATATAACTTGAAGTATCCCTAT 57.674 33.333 0.00 0.00 0.00 2.57
2558 5947 8.585881 GTCTGCATATAACTTGAAGTATCCCTA 58.414 37.037 0.00 0.00 0.00 3.53
2559 5948 7.291182 AGTCTGCATATAACTTGAAGTATCCCT 59.709 37.037 0.00 0.00 0.00 4.20
2560 5949 7.445945 AGTCTGCATATAACTTGAAGTATCCC 58.554 38.462 0.00 0.00 0.00 3.85
2561 5950 9.982651 TTAGTCTGCATATAACTTGAAGTATCC 57.017 33.333 0.00 0.00 0.00 2.59
2588 5977 4.157840 GCCATGATTACTCCTTCCGTTTTT 59.842 41.667 0.00 0.00 0.00 1.94
2592 5981 1.202533 CGCCATGATTACTCCTTCCGT 60.203 52.381 0.00 0.00 0.00 4.69
2593 5982 1.202533 ACGCCATGATTACTCCTTCCG 60.203 52.381 0.00 0.00 0.00 4.30
2594 5983 2.622064 ACGCCATGATTACTCCTTCC 57.378 50.000 0.00 0.00 0.00 3.46
2595 5984 6.026947 AGTATACGCCATGATTACTCCTTC 57.973 41.667 0.00 0.00 0.00 3.46
2596 5985 5.538813 TGAGTATACGCCATGATTACTCCTT 59.461 40.000 4.03 0.00 33.54 3.36
2597 5986 5.077564 TGAGTATACGCCATGATTACTCCT 58.922 41.667 4.03 0.00 33.54 3.69
2598 5987 5.386958 TGAGTATACGCCATGATTACTCC 57.613 43.478 4.03 0.00 33.54 3.85
2599 5988 6.857956 AGATGAGTATACGCCATGATTACTC 58.142 40.000 15.38 4.24 34.66 2.59
2602 5991 7.227049 TGAAGATGAGTATACGCCATGATTA 57.773 36.000 15.38 2.73 0.00 1.75
2608 6093 4.546570 CGAATGAAGATGAGTATACGCCA 58.453 43.478 4.03 4.01 0.00 5.69
2609 6094 3.365220 GCGAATGAAGATGAGTATACGCC 59.635 47.826 4.03 0.00 37.13 5.68
2621 6106 5.278463 CCTTTCTCTTTTTGGCGAATGAAGA 60.278 40.000 7.31 7.31 0.00 2.87
2622 6107 4.919754 CCTTTCTCTTTTTGGCGAATGAAG 59.080 41.667 0.00 0.00 0.00 3.02
2623 6108 4.340950 ACCTTTCTCTTTTTGGCGAATGAA 59.659 37.500 0.00 0.00 0.00 2.57
2624 6109 3.888930 ACCTTTCTCTTTTTGGCGAATGA 59.111 39.130 0.00 0.00 0.00 2.57
2625 6110 4.243007 ACCTTTCTCTTTTTGGCGAATG 57.757 40.909 0.00 0.00 0.00 2.67
2626 6111 6.884836 AGTATACCTTTCTCTTTTTGGCGAAT 59.115 34.615 0.00 0.00 0.00 3.34
2627 6112 6.235664 AGTATACCTTTCTCTTTTTGGCGAA 58.764 36.000 0.00 0.00 0.00 4.70
2628 6113 5.801380 AGTATACCTTTCTCTTTTTGGCGA 58.199 37.500 0.00 0.00 0.00 5.54
2629 6114 5.875359 AGAGTATACCTTTCTCTTTTTGGCG 59.125 40.000 0.00 0.00 35.37 5.69
2630 6115 7.689446 AAGAGTATACCTTTCTCTTTTTGGC 57.311 36.000 0.00 0.00 43.24 4.52
2657 6142 4.808364 CACCTTTTTCTTCCATCGCAAAAA 59.192 37.500 0.00 0.00 0.00 1.94
2658 6143 4.142049 ACACCTTTTTCTTCCATCGCAAAA 60.142 37.500 0.00 0.00 0.00 2.44
2659 6144 3.383185 ACACCTTTTTCTTCCATCGCAAA 59.617 39.130 0.00 0.00 0.00 3.68
2660 6145 2.955660 ACACCTTTTTCTTCCATCGCAA 59.044 40.909 0.00 0.00 0.00 4.85
2661 6146 2.582052 ACACCTTTTTCTTCCATCGCA 58.418 42.857 0.00 0.00 0.00 5.10
2662 6147 3.751698 AGTACACCTTTTTCTTCCATCGC 59.248 43.478 0.00 0.00 0.00 4.58
2663 6148 4.392138 GGAGTACACCTTTTTCTTCCATCG 59.608 45.833 1.54 0.00 0.00 3.84
2664 6149 5.561679 AGGAGTACACCTTTTTCTTCCATC 58.438 41.667 5.96 0.00 36.86 3.51
2665 6150 5.310857 AGAGGAGTACACCTTTTTCTTCCAT 59.689 40.000 13.49 0.00 40.73 3.41
2666 6151 4.658901 AGAGGAGTACACCTTTTTCTTCCA 59.341 41.667 13.49 0.00 40.73 3.53
2667 6152 5.230323 AGAGGAGTACACCTTTTTCTTCC 57.770 43.478 13.49 0.00 40.73 3.46
2668 6153 5.470437 CCAAGAGGAGTACACCTTTTTCTTC 59.530 44.000 13.49 0.00 40.73 2.87
2669 6154 5.377478 CCAAGAGGAGTACACCTTTTTCTT 58.623 41.667 13.49 9.16 40.73 2.52
2670 6155 4.202472 CCCAAGAGGAGTACACCTTTTTCT 60.202 45.833 13.49 3.31 40.73 2.52
2671 6156 4.072839 CCCAAGAGGAGTACACCTTTTTC 58.927 47.826 13.49 0.90 40.73 2.29
2672 6157 3.720002 TCCCAAGAGGAGTACACCTTTTT 59.280 43.478 13.49 8.47 40.93 1.94
2673 6158 3.323775 TCCCAAGAGGAGTACACCTTTT 58.676 45.455 13.49 11.08 40.93 2.27
2674 6159 2.986050 TCCCAAGAGGAGTACACCTTT 58.014 47.619 13.49 4.85 40.93 3.11
2675 6160 2.715763 TCCCAAGAGGAGTACACCTT 57.284 50.000 13.49 1.20 40.93 3.50
2684 6169 3.593442 TTCAAAAAGCTCCCAAGAGGA 57.407 42.857 0.00 0.00 44.91 3.71
2685 6170 4.625028 CTTTTCAAAAAGCTCCCAAGAGG 58.375 43.478 2.51 0.00 40.79 3.69
2708 6193 6.255453 CCGTAATGGCAATTGAACCAAATAAG 59.745 38.462 10.34 8.02 39.96 1.73
2716 6201 5.705902 ACTTTACCGTAATGGCAATTGAAC 58.294 37.500 10.34 1.30 43.94 3.18
2769 6254 2.360844 TGCTGTCGGACAAAAAGTGAA 58.639 42.857 12.54 0.00 0.00 3.18
2771 6256 2.842208 TTGCTGTCGGACAAAAAGTG 57.158 45.000 12.54 0.42 0.00 3.16
2772 6257 2.687935 ACATTGCTGTCGGACAAAAAGT 59.312 40.909 12.54 9.67 0.00 2.66
2773 6258 3.354089 ACATTGCTGTCGGACAAAAAG 57.646 42.857 12.54 9.09 0.00 2.27
2774 6259 5.446143 AATACATTGCTGTCGGACAAAAA 57.554 34.783 12.54 9.59 36.79 1.94
2775 6260 5.446143 AAATACATTGCTGTCGGACAAAA 57.554 34.783 12.54 9.94 36.79 2.44
2776 6261 5.446143 AAAATACATTGCTGTCGGACAAA 57.554 34.783 12.54 5.02 36.79 2.83
2777 6262 5.446143 AAAAATACATTGCTGTCGGACAA 57.554 34.783 12.54 0.00 36.79 3.18
2810 6295 4.686839 TCGACACACACAACATGAAAAA 57.313 36.364 0.00 0.00 0.00 1.94
2811 6296 4.891627 ATCGACACACACAACATGAAAA 57.108 36.364 0.00 0.00 0.00 2.29
2812 6297 5.525745 ACTTATCGACACACACAACATGAAA 59.474 36.000 0.00 0.00 0.00 2.69
2813 6298 5.053811 ACTTATCGACACACACAACATGAA 58.946 37.500 0.00 0.00 0.00 2.57
2814 6299 4.627058 ACTTATCGACACACACAACATGA 58.373 39.130 0.00 0.00 0.00 3.07
2815 6300 4.990543 ACTTATCGACACACACAACATG 57.009 40.909 0.00 0.00 0.00 3.21
2816 6301 5.120208 GCTAACTTATCGACACACACAACAT 59.880 40.000 0.00 0.00 0.00 2.71
2817 6302 4.446385 GCTAACTTATCGACACACACAACA 59.554 41.667 0.00 0.00 0.00 3.33
2818 6303 4.684703 AGCTAACTTATCGACACACACAAC 59.315 41.667 0.00 0.00 0.00 3.32
2819 6304 4.878439 AGCTAACTTATCGACACACACAA 58.122 39.130 0.00 0.00 0.00 3.33
2844 6329 2.803030 AGTTGAAGATGGCAGAGCAT 57.197 45.000 0.00 0.00 0.00 3.79
2845 6330 2.568956 AGTAGTTGAAGATGGCAGAGCA 59.431 45.455 0.00 0.00 0.00 4.26
2846 6331 2.935201 CAGTAGTTGAAGATGGCAGAGC 59.065 50.000 0.00 0.00 0.00 4.09
2847 6332 2.935201 GCAGTAGTTGAAGATGGCAGAG 59.065 50.000 0.00 0.00 0.00 3.35
2848 6333 2.355108 GGCAGTAGTTGAAGATGGCAGA 60.355 50.000 0.00 0.00 36.53 4.26
2857 6342 3.859627 GCTTACACTCGGCAGTAGTTGAA 60.860 47.826 0.00 0.00 0.00 2.69
2865 6350 1.073216 CAGTCGCTTACACTCGGCAG 61.073 60.000 0.00 0.00 32.00 4.85
2879 6364 5.679906 CAAGAGTCCAAATGTAAACAGTCG 58.320 41.667 0.00 0.00 0.00 4.18
2960 6445 0.459585 CAGTTACGATCCCACCACCG 60.460 60.000 0.00 0.00 0.00 4.94
3064 6549 2.683362 GGTGAGATTTTTCCCGTCCATC 59.317 50.000 0.00 0.00 0.00 3.51
3073 6559 2.795329 TCTGCCTGGGTGAGATTTTTC 58.205 47.619 0.00 0.00 0.00 2.29
3074 6560 2.978156 TCTGCCTGGGTGAGATTTTT 57.022 45.000 0.00 0.00 0.00 1.94
3116 6602 3.325425 TGTAAAATCTCCCACTTCCACGA 59.675 43.478 0.00 0.00 0.00 4.35
3117 6603 3.670625 TGTAAAATCTCCCACTTCCACG 58.329 45.455 0.00 0.00 0.00 4.94
3125 6841 3.788227 AGTGCACTGTAAAATCTCCCA 57.212 42.857 20.97 0.00 0.00 4.37
3221 6937 3.423154 GCGAAGGAAGGTGGCACG 61.423 66.667 12.17 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.