Multiple sequence alignment - TraesCS6D01G148600

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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 TraesCS6D01G148600 chr6D 100.000 2990 0 0 1 2990 121581460 121578471 0.000000e+00 5522.0
1 TraesCS6D01G148600 chr6D 92.750 1738 80 29 580 2297 121064069 121065780 0.000000e+00 2470.0
2 TraesCS6D01G148600 chr6D 95.604 1433 43 8 743 2164 121225298 121226721 0.000000e+00 2279.0
3 TraesCS6D01G148600 chr6D 88.168 262 27 2 2348 2605 456946308 456946047 2.890000e-80 309.0
4 TraesCS6D01G148600 chr6D 87.405 262 27 4 2349 2605 426154723 426154463 2.250000e-76 296.0
5 TraesCS6D01G148600 chr6D 93.548 124 6 2 584 707 121220502 121220623 1.830000e-42 183.0
6 TraesCS6D01G148600 chr6D 80.870 230 21 5 2667 2896 121066194 121066400 3.080000e-35 159.0
7 TraesCS6D01G148600 chr6D 98.214 56 1 0 2164 2219 121261056 121261111 6.820000e-17 99.0
8 TraesCS6D01G148600 chr6B 93.796 1644 64 15 580 2219 213488744 213487135 0.000000e+00 2436.0
9 TraesCS6D01G148600 chr6B 93.718 1576 66 11 742 2301 212159940 212158382 0.000000e+00 2331.0
10 TraesCS6D01G148600 chr6B 87.814 279 20 7 2333 2605 147680310 147680040 6.220000e-82 315.0
11 TraesCS6D01G148600 chr6B 90.476 189 17 1 2797 2985 212151230 212151043 6.400000e-62 248.0
12 TraesCS6D01G148600 chr6B 84.536 97 11 2 580 676 212160037 212159945 3.170000e-15 93.5
13 TraesCS6D01G148600 chr6A 95.519 1473 45 11 753 2219 158318094 158316637 0.000000e+00 2335.0
14 TraesCS6D01G148600 chr6A 95.922 1275 46 2 742 2016 162891716 162890448 0.000000e+00 2061.0
15 TraesCS6D01G148600 chr6A 95.928 835 28 2 729 1563 158455198 158454370 0.000000e+00 1349.0
16 TraesCS6D01G148600 chr6A 86.364 836 104 8 997 1827 60973177 60972347 0.000000e+00 904.0
17 TraesCS6D01G148600 chr6A 90.512 664 28 14 1558 2219 158449078 158448448 0.000000e+00 845.0
18 TraesCS6D01G148600 chr6A 93.333 240 10 4 1984 2219 162890449 162890212 1.710000e-92 350.0
19 TraesCS6D01G148600 chr6A 87.410 278 27 6 2333 2605 89894848 89894574 2.240000e-81 313.0
20 TraesCS6D01G148600 chr6A 90.503 179 12 4 581 755 158318760 158318583 6.450000e-57 231.0
21 TraesCS6D01G148600 chr6A 88.125 160 12 5 580 739 162891978 162891826 1.830000e-42 183.0
22 TraesCS6D01G148600 chr6A 80.702 171 19 5 2726 2896 158313513 158313357 1.460000e-23 121.0
23 TraesCS6D01G148600 chr4D 86.499 837 101 9 997 1827 323097953 323097123 0.000000e+00 909.0
24 TraesCS6D01G148600 chr3D 90.820 610 25 10 1 581 185712930 185713537 0.000000e+00 787.0
25 TraesCS6D01G148600 chr3D 87.681 276 27 6 2336 2605 369414437 369414163 6.220000e-82 315.0
26 TraesCS6D01G148600 chr3D 87.786 262 28 2 2349 2606 65538908 65539169 1.350000e-78 303.0
27 TraesCS6D01G148600 chr7A 89.465 598 33 12 1 571 455908203 455908797 0.000000e+00 728.0
28 TraesCS6D01G148600 chr7A 89.298 598 31 13 1 571 455928263 455928854 0.000000e+00 719.0
29 TraesCS6D01G148600 chr7A 86.989 269 30 3 2342 2605 646560178 646560446 6.270000e-77 298.0
30 TraesCS6D01G148600 chrUn 88.380 611 37 14 2 588 305994447 305993847 0.000000e+00 704.0
31 TraesCS6D01G148600 chrUn 88.380 611 37 14 2 588 314905643 314906243 0.000000e+00 704.0
32 TraesCS6D01G148600 chrUn 88.380 611 37 14 2 588 382171697 382172297 0.000000e+00 704.0
33 TraesCS6D01G148600 chrUn 83.871 93 11 2 2218 2306 267452864 267452956 5.310000e-13 86.1
34 TraesCS6D01G148600 chrUn 83.871 93 11 2 2218 2306 340256232 340256324 5.310000e-13 86.1
35 TraesCS6D01G148600 chr2D 85.714 609 50 16 2 581 446540455 446539855 2.550000e-170 608.0
36 TraesCS6D01G148600 chr4B 88.723 470 41 9 115 581 255670231 255670691 5.600000e-157 564.0
37 TraesCS6D01G148600 chr5B 83.224 608 63 8 2 582 34378180 34378775 3.420000e-144 521.0
38 TraesCS6D01G148600 chr5B 86.170 470 54 6 115 582 71864215 71864675 5.760000e-137 497.0
39 TraesCS6D01G148600 chr5B 83.871 93 11 2 2218 2306 392087762 392087854 5.310000e-13 86.1
40 TraesCS6D01G148600 chr5B 83.871 93 11 2 2218 2306 392127799 392127891 5.310000e-13 86.1
41 TraesCS6D01G148600 chr5B 97.222 36 1 0 2800 2835 284835315 284835280 8.950000e-06 62.1
42 TraesCS6D01G148600 chr7B 87.413 286 28 7 2328 2605 203133081 203132796 3.720000e-84 322.0
43 TraesCS6D01G148600 chr3B 88.679 265 25 3 2346 2605 480377206 480376942 4.810000e-83 318.0
44 TraesCS6D01G148600 chr2A 81.457 302 21 13 2 277 162563481 162563189 6.490000e-52 215.0


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 TraesCS6D01G148600 chr6D 121578471 121581460 2989 True 5522.000000 5522 100.000 1 2990 1 chr6D.!!$R1 2989
1 TraesCS6D01G148600 chr6D 121225298 121226721 1423 False 2279.000000 2279 95.604 743 2164 1 chr6D.!!$F2 1421
2 TraesCS6D01G148600 chr6D 121064069 121066400 2331 False 1314.500000 2470 86.810 580 2896 2 chr6D.!!$F4 2316
3 TraesCS6D01G148600 chr6B 213487135 213488744 1609 True 2436.000000 2436 93.796 580 2219 1 chr6B.!!$R3 1639
4 TraesCS6D01G148600 chr6B 212158382 212160037 1655 True 1212.250000 2331 89.127 580 2301 2 chr6B.!!$R4 1721
5 TraesCS6D01G148600 chr6A 158454370 158455198 828 True 1349.000000 1349 95.928 729 1563 1 chr6A.!!$R4 834
6 TraesCS6D01G148600 chr6A 60972347 60973177 830 True 904.000000 904 86.364 997 1827 1 chr6A.!!$R1 830
7 TraesCS6D01G148600 chr6A 158313357 158318760 5403 True 895.666667 2335 88.908 581 2896 3 chr6A.!!$R5 2315
8 TraesCS6D01G148600 chr6A 162890212 162891978 1766 True 864.666667 2061 92.460 580 2219 3 chr6A.!!$R6 1639
9 TraesCS6D01G148600 chr6A 158448448 158449078 630 True 845.000000 845 90.512 1558 2219 1 chr6A.!!$R3 661
10 TraesCS6D01G148600 chr4D 323097123 323097953 830 True 909.000000 909 86.499 997 1827 1 chr4D.!!$R1 830
11 TraesCS6D01G148600 chr3D 185712930 185713537 607 False 787.000000 787 90.820 1 581 1 chr3D.!!$F2 580
12 TraesCS6D01G148600 chr7A 455908203 455908797 594 False 728.000000 728 89.465 1 571 1 chr7A.!!$F1 570
13 TraesCS6D01G148600 chr7A 455928263 455928854 591 False 719.000000 719 89.298 1 571 1 chr7A.!!$F2 570
14 TraesCS6D01G148600 chrUn 305993847 305994447 600 True 704.000000 704 88.380 2 588 1 chrUn.!!$R1 586
15 TraesCS6D01G148600 chrUn 314905643 314906243 600 False 704.000000 704 88.380 2 588 1 chrUn.!!$F2 586
16 TraesCS6D01G148600 chrUn 382171697 382172297 600 False 704.000000 704 88.380 2 588 1 chrUn.!!$F4 586
17 TraesCS6D01G148600 chr2D 446539855 446540455 600 True 608.000000 608 85.714 2 581 1 chr2D.!!$R1 579
18 TraesCS6D01G148600 chr5B 34378180 34378775 595 False 521.000000 521 83.224 2 582 1 chr5B.!!$F1 580

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
934 1593 0.829333 AACTCATCGAGCAGCTCCAT 59.171 50.0 17.16 6.78 32.04 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 3349 0.038067 TCGCCCAAAGAATCGTCGAA 60.038 50.0 0.0 0.0 0.0 3.71 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
107 111 7.710044 TGTGAAAGCAAACAATGTAACATGAAT 59.290 29.630 0.00 0.00 0.00 2.57
553 589 9.736023 CATTTAACTTTATGAAATGCTAGTCCC 57.264 33.333 0.00 0.00 34.72 4.46
555 591 5.450818 ACTTTATGAAATGCTAGTCCCCA 57.549 39.130 0.00 0.00 0.00 4.96
560 596 2.575735 TGAAATGCTAGTCCCCACATCA 59.424 45.455 0.00 0.00 0.00 3.07
730 774 4.526262 AGCGACATGAGCCTCTAAGATTAT 59.474 41.667 0.00 0.00 34.64 1.28
731 775 5.712446 AGCGACATGAGCCTCTAAGATTATA 59.288 40.000 0.00 0.00 34.64 0.98
732 776 6.033341 GCGACATGAGCCTCTAAGATTATAG 58.967 44.000 0.00 0.00 0.00 1.31
834 1479 1.239347 AAGCGTCTTTTTCCTCAGCC 58.761 50.000 0.00 0.00 0.00 4.85
886 1539 3.226777 AGAAGTCTCGCCACTGCTATAT 58.773 45.455 0.00 0.00 29.38 0.86
887 1540 3.639094 AGAAGTCTCGCCACTGCTATATT 59.361 43.478 0.00 0.00 29.38 1.28
888 1541 4.827835 AGAAGTCTCGCCACTGCTATATTA 59.172 41.667 0.00 0.00 29.38 0.98
889 1542 5.478679 AGAAGTCTCGCCACTGCTATATTAT 59.521 40.000 0.00 0.00 29.38 1.28
890 1543 6.659668 AGAAGTCTCGCCACTGCTATATTATA 59.340 38.462 0.00 0.00 29.38 0.98
934 1593 0.829333 AACTCATCGAGCAGCTCCAT 59.171 50.000 17.16 6.78 32.04 3.41
1821 2491 4.564406 GGTGAGGTCATCAACTCTGTCATT 60.564 45.833 0.00 0.00 42.83 2.57
2068 2770 3.511146 TCGTGGTAAATTCCCTACTCGTT 59.489 43.478 0.00 0.00 0.00 3.85
2219 2933 9.926158 AAATAATGTGTGATTTGAAGTGCAATA 57.074 25.926 0.00 0.00 36.15 1.90
2222 2936 6.000891 TGTGTGATTTGAAGTGCAATACTC 57.999 37.500 0.00 0.00 39.18 2.59
2240 2960 7.201696 GCAATACTCCATCCGTCTCAAAATAAA 60.202 37.037 0.00 0.00 0.00 1.40
2242 2962 6.927294 ACTCCATCCGTCTCAAAATAAATC 57.073 37.500 0.00 0.00 0.00 2.17
2244 2964 7.112779 ACTCCATCCGTCTCAAAATAAATCTT 58.887 34.615 0.00 0.00 0.00 2.40
2247 2967 7.829211 TCCATCCGTCTCAAAATAAATCTTTCT 59.171 33.333 0.00 0.00 0.00 2.52
2250 2970 7.816640 TCCGTCTCAAAATAAATCTTTCTTGG 58.183 34.615 0.00 0.00 0.00 3.61
2301 3025 8.451748 CAAAGCTAAGACACTTATTTTAGGACC 58.548 37.037 0.00 0.00 0.00 4.46
2302 3026 6.338937 AGCTAAGACACTTATTTTAGGACCG 58.661 40.000 0.00 0.00 0.00 4.79
2303 3027 6.154021 AGCTAAGACACTTATTTTAGGACCGA 59.846 38.462 0.00 0.00 0.00 4.69
2304 3028 6.476053 GCTAAGACACTTATTTTAGGACCGAG 59.524 42.308 0.00 0.00 0.00 4.63
2305 3029 5.340439 AGACACTTATTTTAGGACCGAGG 57.660 43.478 0.00 0.00 0.00 4.63
2306 3030 5.021458 AGACACTTATTTTAGGACCGAGGA 58.979 41.667 0.00 0.00 0.00 3.71
2307 3031 5.482878 AGACACTTATTTTAGGACCGAGGAA 59.517 40.000 0.00 0.00 0.00 3.36
2308 3032 5.731591 ACACTTATTTTAGGACCGAGGAAG 58.268 41.667 0.00 0.00 0.00 3.46
2309 3033 5.247792 ACACTTATTTTAGGACCGAGGAAGT 59.752 40.000 0.00 0.00 0.00 3.01
2310 3034 6.438425 ACACTTATTTTAGGACCGAGGAAGTA 59.562 38.462 0.00 0.00 0.00 2.24
2311 3035 6.755607 CACTTATTTTAGGACCGAGGAAGTAC 59.244 42.308 0.00 0.00 0.00 2.73
2312 3036 6.666980 ACTTATTTTAGGACCGAGGAAGTACT 59.333 38.462 0.00 0.00 31.73 2.73
2313 3037 7.836183 ACTTATTTTAGGACCGAGGAAGTACTA 59.164 37.037 0.00 0.00 28.99 1.82
2314 3038 8.593945 TTATTTTAGGACCGAGGAAGTACTAA 57.406 34.615 0.00 0.00 38.58 2.24
2315 3039 6.916360 TTTTAGGACCGAGGAAGTACTAAA 57.084 37.500 0.00 4.58 44.93 1.85
2316 3040 7.486407 TTTTAGGACCGAGGAAGTACTAAAT 57.514 36.000 8.69 0.00 45.55 1.40
2317 3041 8.593945 TTTTAGGACCGAGGAAGTACTAAATA 57.406 34.615 8.69 0.08 45.55 1.40
2318 3042 8.593945 TTTAGGACCGAGGAAGTACTAAATAA 57.406 34.615 0.00 0.00 42.85 1.40
2319 3043 8.773033 TTAGGACCGAGGAAGTACTAAATAAT 57.227 34.615 0.00 0.00 37.64 1.28
2320 3044 9.866655 TTAGGACCGAGGAAGTACTAAATAATA 57.133 33.333 0.00 0.00 37.64 0.98
2321 3045 8.175925 AGGACCGAGGAAGTACTAAATAATAC 57.824 38.462 0.00 0.00 0.00 1.89
2322 3046 8.003629 AGGACCGAGGAAGTACTAAATAATACT 58.996 37.037 0.00 0.00 32.93 2.12
2323 3047 8.081025 GGACCGAGGAAGTACTAAATAATACTG 58.919 40.741 0.00 0.00 31.93 2.74
2324 3048 7.432059 ACCGAGGAAGTACTAAATAATACTGC 58.568 38.462 0.00 0.00 31.93 4.40
2325 3049 6.867293 CCGAGGAAGTACTAAATAATACTGCC 59.133 42.308 0.00 0.00 44.76 4.85
2326 3050 6.867293 CGAGGAAGTACTAAATAATACTGCCC 59.133 42.308 0.00 0.00 45.33 5.36
2327 3051 6.756221 AGGAAGTACTAAATAATACTGCCCG 58.244 40.000 0.00 0.00 45.33 6.13
2328 3052 5.407691 GGAAGTACTAAATAATACTGCCCGC 59.592 44.000 0.00 0.00 40.21 6.13
2329 3053 5.540400 AGTACTAAATAATACTGCCCGCA 57.460 39.130 0.00 0.00 30.34 5.69
2330 3054 5.920903 AGTACTAAATAATACTGCCCGCAA 58.079 37.500 0.00 0.00 30.34 4.85
2331 3055 6.350906 AGTACTAAATAATACTGCCCGCAAA 58.649 36.000 0.00 0.00 30.34 3.68
2332 3056 6.824704 AGTACTAAATAATACTGCCCGCAAAA 59.175 34.615 0.00 0.00 30.34 2.44
2333 3057 6.518208 ACTAAATAATACTGCCCGCAAAAA 57.482 33.333 0.00 0.00 0.00 1.94
2361 3085 9.978044 AAGTACTAAATAATACTCCATCCGTTC 57.022 33.333 0.00 0.00 31.15 3.95
2362 3086 8.583296 AGTACTAAATAATACTCCATCCGTTCC 58.417 37.037 0.00 0.00 0.00 3.62
2363 3087 7.613551 ACTAAATAATACTCCATCCGTTCCT 57.386 36.000 0.00 0.00 0.00 3.36
2364 3088 8.030913 ACTAAATAATACTCCATCCGTTCCTT 57.969 34.615 0.00 0.00 0.00 3.36
2365 3089 8.491958 ACTAAATAATACTCCATCCGTTCCTTT 58.508 33.333 0.00 0.00 0.00 3.11
2366 3090 9.991906 CTAAATAATACTCCATCCGTTCCTTTA 57.008 33.333 0.00 0.00 0.00 1.85
2374 3098 8.030913 ACTCCATCCGTTCCTTTATATAAAGT 57.969 34.615 26.18 9.54 40.73 2.66
2375 3099 7.931948 ACTCCATCCGTTCCTTTATATAAAGTG 59.068 37.037 26.18 19.46 40.73 3.16
2376 3100 7.798071 TCCATCCGTTCCTTTATATAAAGTGT 58.202 34.615 26.18 7.86 40.73 3.55
2377 3101 8.926374 TCCATCCGTTCCTTTATATAAAGTGTA 58.074 33.333 26.18 13.48 40.73 2.90
2378 3102 9.720769 CCATCCGTTCCTTTATATAAAGTGTAT 57.279 33.333 26.18 12.60 40.73 2.29
2408 3132 9.985318 TTTTTCAAAAGTCAAAGTGCATATTTG 57.015 25.926 16.97 16.97 38.68 2.32
2409 3133 8.939201 TTTCAAAAGTCAAAGTGCATATTTGA 57.061 26.923 20.11 20.11 42.73 2.69
2414 3138 4.944962 TCAAAGTGCATATTTGACCGAG 57.055 40.909 20.11 1.55 40.72 4.63
2415 3139 4.323417 TCAAAGTGCATATTTGACCGAGT 58.677 39.130 20.11 0.00 40.72 4.18
2416 3140 4.759693 TCAAAGTGCATATTTGACCGAGTT 59.240 37.500 20.11 0.00 40.72 3.01
2417 3141 5.240623 TCAAAGTGCATATTTGACCGAGTTT 59.759 36.000 20.11 0.00 40.72 2.66
2418 3142 4.946784 AGTGCATATTTGACCGAGTTTC 57.053 40.909 0.00 0.00 0.00 2.78
2419 3143 4.579869 AGTGCATATTTGACCGAGTTTCT 58.420 39.130 0.00 0.00 0.00 2.52
2420 3144 5.730550 AGTGCATATTTGACCGAGTTTCTA 58.269 37.500 0.00 0.00 0.00 2.10
2421 3145 5.812642 AGTGCATATTTGACCGAGTTTCTAG 59.187 40.000 0.00 0.00 0.00 2.43
2422 3146 5.810587 GTGCATATTTGACCGAGTTTCTAGA 59.189 40.000 0.00 0.00 0.00 2.43
2423 3147 6.312918 GTGCATATTTGACCGAGTTTCTAGAA 59.687 38.462 0.00 0.00 0.00 2.10
2424 3148 6.876789 TGCATATTTGACCGAGTTTCTAGAAA 59.123 34.615 13.99 13.99 0.00 2.52
2425 3149 7.389330 TGCATATTTGACCGAGTTTCTAGAAAA 59.611 33.333 19.30 1.34 31.33 2.29
2426 3150 8.234546 GCATATTTGACCGAGTTTCTAGAAAAA 58.765 33.333 19.30 8.14 31.33 1.94
2429 3153 7.562454 TTTGACCGAGTTTCTAGAAAAATGT 57.438 32.000 19.30 13.52 31.33 2.71
2430 3154 8.665643 TTTGACCGAGTTTCTAGAAAAATGTA 57.334 30.769 19.30 1.35 31.33 2.29
2431 3155 8.842358 TTGACCGAGTTTCTAGAAAAATGTAT 57.158 30.769 19.30 4.41 31.33 2.29
2432 3156 9.932207 TTGACCGAGTTTCTAGAAAAATGTATA 57.068 29.630 19.30 2.67 31.33 1.47
2433 3157 9.932207 TGACCGAGTTTCTAGAAAAATGTATAA 57.068 29.630 19.30 0.55 31.33 0.98
2565 3289 6.843069 AACATTTAAATGGTTGACTTGCAC 57.157 33.333 27.43 0.00 40.70 4.57
2566 3290 4.981674 ACATTTAAATGGTTGACTTGCACG 59.018 37.500 27.43 2.64 40.70 5.34
2567 3291 4.902443 TTTAAATGGTTGACTTGCACGA 57.098 36.364 0.00 0.00 0.00 4.35
2568 3292 2.774439 AAATGGTTGACTTGCACGAC 57.226 45.000 0.00 0.00 0.00 4.34
2569 3293 1.674359 AATGGTTGACTTGCACGACA 58.326 45.000 0.00 0.00 0.00 4.35
2570 3294 1.674359 ATGGTTGACTTGCACGACAA 58.326 45.000 4.10 4.10 36.62 3.18
2571 3295 1.674359 TGGTTGACTTGCACGACAAT 58.326 45.000 10.85 0.00 37.72 2.71
2572 3296 1.601903 TGGTTGACTTGCACGACAATC 59.398 47.619 10.85 10.85 37.72 2.67
2573 3297 1.398451 GGTTGACTTGCACGACAATCG 60.398 52.381 10.85 0.00 46.93 3.34
2574 3298 1.525197 GTTGACTTGCACGACAATCGA 59.475 47.619 10.85 0.00 43.74 3.59
2575 3299 2.078849 TGACTTGCACGACAATCGAT 57.921 45.000 5.04 0.00 43.74 3.59
2576 3300 3.224884 TGACTTGCACGACAATCGATA 57.775 42.857 5.04 0.00 43.74 2.92
2577 3301 2.921121 TGACTTGCACGACAATCGATAC 59.079 45.455 5.04 0.00 43.74 2.24
2578 3302 2.921121 GACTTGCACGACAATCGATACA 59.079 45.455 5.04 0.00 43.74 2.29
2579 3303 2.666508 ACTTGCACGACAATCGATACAC 59.333 45.455 5.04 0.00 43.74 2.90
2580 3304 1.635844 TGCACGACAATCGATACACC 58.364 50.000 5.04 0.00 43.74 4.16
2581 3305 1.203758 TGCACGACAATCGATACACCT 59.796 47.619 5.04 0.00 43.74 4.00
2582 3306 2.268298 GCACGACAATCGATACACCTT 58.732 47.619 5.04 0.00 43.74 3.50
2583 3307 3.119424 TGCACGACAATCGATACACCTTA 60.119 43.478 5.04 0.00 43.74 2.69
2584 3308 4.049186 GCACGACAATCGATACACCTTAT 58.951 43.478 5.04 0.00 43.74 1.73
2585 3309 5.217393 GCACGACAATCGATACACCTTATA 58.783 41.667 5.04 0.00 43.74 0.98
2586 3310 5.116680 GCACGACAATCGATACACCTTATAC 59.883 44.000 5.04 0.00 43.74 1.47
2587 3311 6.436261 CACGACAATCGATACACCTTATACT 58.564 40.000 5.04 0.00 43.74 2.12
2588 3312 6.577800 CACGACAATCGATACACCTTATACTC 59.422 42.308 5.04 0.00 43.74 2.59
2589 3313 6.485984 ACGACAATCGATACACCTTATACTCT 59.514 38.462 5.04 0.00 43.74 3.24
2590 3314 6.797513 CGACAATCGATACACCTTATACTCTG 59.202 42.308 0.00 0.00 43.74 3.35
2591 3315 7.520131 CGACAATCGATACACCTTATACTCTGT 60.520 40.741 0.00 0.00 43.74 3.41
2595 3319 9.570468 AATCGATACACCTTATACTCTGTAAGA 57.430 33.333 0.00 0.00 43.69 2.10
2619 3343 2.351455 GGAGTAAGAAAGAGCAGTGCC 58.649 52.381 12.58 3.25 0.00 5.01
2641 3365 1.737236 TGCATTCGACGATTCTTTGGG 59.263 47.619 0.00 0.00 0.00 4.12
2643 3367 1.006832 ATTCGACGATTCTTTGGGCG 58.993 50.000 0.00 0.00 0.00 6.13
2651 3375 1.406539 GATTCTTTGGGCGATGCATGT 59.593 47.619 2.46 0.00 0.00 3.21
2652 3376 0.527113 TTCTTTGGGCGATGCATGTG 59.473 50.000 2.46 0.00 0.00 3.21
2663 6574 3.328505 CGATGCATGTGCCATAGACATA 58.671 45.455 2.46 0.00 41.18 2.29
2665 6576 3.843893 TGCATGTGCCATAGACATAGT 57.156 42.857 2.07 0.00 41.18 2.12
2713 6633 2.403252 ACCCCAGTTTTGCTATCTCG 57.597 50.000 0.00 0.00 0.00 4.04
2714 6634 1.017387 CCCCAGTTTTGCTATCTCGC 58.983 55.000 0.00 0.00 0.00 5.03
2715 6635 1.678728 CCCCAGTTTTGCTATCTCGCA 60.679 52.381 0.00 0.00 38.31 5.10
2722 6642 1.448985 TTGCTATCTCGCAACCAACC 58.551 50.000 0.00 0.00 44.30 3.77
2723 6643 0.739462 TGCTATCTCGCAACCAACCG 60.739 55.000 0.00 0.00 36.89 4.44
2724 6644 0.459585 GCTATCTCGCAACCAACCGA 60.460 55.000 0.00 0.00 0.00 4.69
2733 6653 2.031508 CGCAACCAACCGACAAATACTT 60.032 45.455 0.00 0.00 0.00 2.24
2737 6657 4.094830 ACCAACCGACAAATACTTCCTT 57.905 40.909 0.00 0.00 0.00 3.36
2738 6658 5.231702 ACCAACCGACAAATACTTCCTTA 57.768 39.130 0.00 0.00 0.00 2.69
2742 6662 6.128363 CCAACCGACAAATACTTCCTTAGTTC 60.128 42.308 0.00 0.00 38.33 3.01
2793 6713 9.734620 TTTCTGAATTGGATATATTTTGAAGCG 57.265 29.630 0.00 0.00 0.00 4.68
2794 6714 7.362662 TCTGAATTGGATATATTTTGAAGCGC 58.637 34.615 0.00 0.00 0.00 5.92
2796 6716 7.715657 TGAATTGGATATATTTTGAAGCGCTT 58.284 30.769 25.35 25.35 0.00 4.68
2797 6717 8.196771 TGAATTGGATATATTTTGAAGCGCTTT 58.803 29.630 25.84 10.54 0.00 3.51
2798 6718 9.677567 GAATTGGATATATTTTGAAGCGCTTTA 57.322 29.630 25.84 18.49 0.00 1.85
2799 6719 9.683069 AATTGGATATATTTTGAAGCGCTTTAG 57.317 29.630 25.84 0.00 0.00 1.85
2800 6720 7.801716 TGGATATATTTTGAAGCGCTTTAGT 57.198 32.000 25.84 12.25 0.00 2.24
2801 6721 7.639039 TGGATATATTTTGAAGCGCTTTAGTG 58.361 34.615 25.84 0.00 0.00 2.74
2819 6739 7.588488 GCTTTAGTGCGTTTGTTTACTCATTTA 59.412 33.333 0.00 0.00 0.00 1.40
2896 6816 4.894114 AGGTGATAGTTAGTAAGCCGACAT 59.106 41.667 0.00 0.00 0.00 3.06
2897 6817 4.982916 GGTGATAGTTAGTAAGCCGACATG 59.017 45.833 0.00 0.00 0.00 3.21
2898 6818 4.444720 GTGATAGTTAGTAAGCCGACATGC 59.555 45.833 0.00 0.00 0.00 4.06
2899 6819 4.098807 TGATAGTTAGTAAGCCGACATGCA 59.901 41.667 0.00 0.00 0.00 3.96
2900 6820 3.328382 AGTTAGTAAGCCGACATGCAA 57.672 42.857 0.00 0.00 0.00 4.08
2901 6821 3.262420 AGTTAGTAAGCCGACATGCAAG 58.738 45.455 0.00 0.00 0.00 4.01
2902 6822 3.000727 GTTAGTAAGCCGACATGCAAGT 58.999 45.455 0.00 0.00 0.00 3.16
2903 6823 4.081862 AGTTAGTAAGCCGACATGCAAGTA 60.082 41.667 0.00 0.00 0.00 2.24
2904 6824 3.543680 AGTAAGCCGACATGCAAGTAT 57.456 42.857 0.00 0.00 0.00 2.12
2905 6825 4.665833 AGTAAGCCGACATGCAAGTATA 57.334 40.909 0.00 0.00 0.00 1.47
2906 6826 5.215252 AGTAAGCCGACATGCAAGTATAT 57.785 39.130 0.00 0.00 0.00 0.86
2907 6827 6.340962 AGTAAGCCGACATGCAAGTATATA 57.659 37.500 0.00 0.00 0.00 0.86
2908 6828 6.390721 AGTAAGCCGACATGCAAGTATATAG 58.609 40.000 0.00 0.00 0.00 1.31
2909 6829 4.873746 AGCCGACATGCAAGTATATAGT 57.126 40.909 0.00 0.00 0.00 2.12
2910 6830 5.977489 AGCCGACATGCAAGTATATAGTA 57.023 39.130 0.00 0.00 0.00 1.82
2911 6831 6.340962 AGCCGACATGCAAGTATATAGTAA 57.659 37.500 0.00 0.00 0.00 2.24
2912 6832 6.390721 AGCCGACATGCAAGTATATAGTAAG 58.609 40.000 0.00 0.00 0.00 2.34
2913 6833 6.208797 AGCCGACATGCAAGTATATAGTAAGA 59.791 38.462 0.00 0.00 0.00 2.10
2914 6834 6.866770 GCCGACATGCAAGTATATAGTAAGAA 59.133 38.462 0.00 0.00 0.00 2.52
2915 6835 7.062371 GCCGACATGCAAGTATATAGTAAGAAG 59.938 40.741 0.00 0.00 0.00 2.85
2916 6836 8.297426 CCGACATGCAAGTATATAGTAAGAAGA 58.703 37.037 0.00 0.00 0.00 2.87
2917 6837 9.847706 CGACATGCAAGTATATAGTAAGAAGAT 57.152 33.333 0.00 0.00 0.00 2.40
2961 6881 8.668510 TCTAAATGGATTGAGAAATAGTCAGC 57.331 34.615 0.00 0.00 0.00 4.26
2962 6882 6.705863 AAATGGATTGAGAAATAGTCAGCC 57.294 37.500 0.00 0.00 0.00 4.85
2963 6883 4.842531 TGGATTGAGAAATAGTCAGCCA 57.157 40.909 0.00 0.00 31.51 4.75
2964 6884 5.378230 TGGATTGAGAAATAGTCAGCCAT 57.622 39.130 0.00 0.00 29.96 4.40
2965 6885 6.499106 TGGATTGAGAAATAGTCAGCCATA 57.501 37.500 0.00 0.00 29.96 2.74
2966 6886 6.899089 TGGATTGAGAAATAGTCAGCCATAA 58.101 36.000 0.00 0.00 29.96 1.90
2967 6887 7.345691 TGGATTGAGAAATAGTCAGCCATAAA 58.654 34.615 0.00 0.00 29.96 1.40
2968 6888 7.833682 TGGATTGAGAAATAGTCAGCCATAAAA 59.166 33.333 0.00 0.00 29.96 1.52
2969 6889 8.686334 GGATTGAGAAATAGTCAGCCATAAAAA 58.314 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
318 348 9.605955 TTATGATCACTCGTGTTGTTTAAATTG 57.394 29.630 0.00 0.00 0.00 2.32
421 451 6.143438 CGTAGTTCTATCTTCAACACGTTTGT 59.857 38.462 9.31 0.00 37.67 2.83
439 469 8.739649 ATGTAAGACTACTTCAAACGTAGTTC 57.260 34.615 4.56 0.00 45.44 3.01
553 589 3.443045 GTGGCCCGCTTGATGTGG 61.443 66.667 0.00 0.00 45.60 4.17
555 591 1.228552 AAAGTGGCCCGCTTGATGT 60.229 52.632 10.93 0.00 34.24 3.06
560 596 1.675641 CTAGCAAAGTGGCCCGCTT 60.676 57.895 3.03 3.03 35.58 4.68
608 644 3.260632 TCTCCAAACATGAATGAGGACGA 59.739 43.478 0.00 0.00 0.00 4.20
731 775 9.925268 CTTTTACGTGTTTGAAAATGTAGTACT 57.075 29.630 0.00 0.00 0.00 2.73
732 776 9.706846 ACTTTTACGTGTTTGAAAATGTAGTAC 57.293 29.630 0.00 0.00 0.00 2.73
934 1593 2.254546 AAATGTGTGCCTCTGAACGA 57.745 45.000 0.00 0.00 0.00 3.85
1806 2476 2.094894 GGCGACAATGACAGAGTTGATG 59.905 50.000 0.00 0.00 0.00 3.07
1959 2629 1.856265 GCTCTTTGGTGGCCAACTCG 61.856 60.000 24.13 10.27 43.82 4.18
2068 2770 3.579709 ACACGCACAAACATCAAAACAA 58.420 36.364 0.00 0.00 0.00 2.83
2219 2933 6.653989 AGATTTATTTTGAGACGGATGGAGT 58.346 36.000 0.00 0.00 0.00 3.85
2222 2936 7.989826 AGAAAGATTTATTTTGAGACGGATGG 58.010 34.615 0.00 0.00 0.00 3.51
2263 2987 7.868415 AGTGTCTTAGCTTTGTACTGACTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
2275 2999 8.451748 GGTCCTAAAATAAGTGTCTTAGCTTTG 58.548 37.037 0.00 0.00 0.00 2.77
2280 3004 6.979238 CCTCGGTCCTAAAATAAGTGTCTTAG 59.021 42.308 0.00 0.00 0.00 2.18
2301 3025 6.867293 GGGCAGTATTATTTAGTACTTCCTCG 59.133 42.308 0.00 0.00 34.14 4.63
2302 3026 6.867293 CGGGCAGTATTATTTAGTACTTCCTC 59.133 42.308 0.00 1.08 34.14 3.71
2303 3027 6.740681 GCGGGCAGTATTATTTAGTACTTCCT 60.741 42.308 0.00 0.00 34.14 3.36
2304 3028 5.407691 GCGGGCAGTATTATTTAGTACTTCC 59.592 44.000 0.00 1.92 33.36 3.46
2305 3029 5.987347 TGCGGGCAGTATTATTTAGTACTTC 59.013 40.000 0.00 0.00 0.00 3.01
2306 3030 5.920903 TGCGGGCAGTATTATTTAGTACTT 58.079 37.500 0.00 0.00 0.00 2.24
2307 3031 5.540400 TGCGGGCAGTATTATTTAGTACT 57.460 39.130 0.00 0.00 0.00 2.73
2308 3032 6.607735 TTTGCGGGCAGTATTATTTAGTAC 57.392 37.500 0.00 0.00 0.00 2.73
2309 3033 7.627298 TTTTTGCGGGCAGTATTATTTAGTA 57.373 32.000 0.00 0.00 0.00 1.82
2310 3034 6.518208 TTTTTGCGGGCAGTATTATTTAGT 57.482 33.333 0.00 0.00 0.00 2.24
2335 3059 9.978044 GAACGGATGGAGTATTATTTAGTACTT 57.022 33.333 0.00 0.00 30.19 2.24
2336 3060 8.583296 GGAACGGATGGAGTATTATTTAGTACT 58.417 37.037 0.00 0.00 32.33 2.73
2337 3061 8.583296 AGGAACGGATGGAGTATTATTTAGTAC 58.417 37.037 0.00 0.00 0.00 2.73
2338 3062 8.716674 AGGAACGGATGGAGTATTATTTAGTA 57.283 34.615 0.00 0.00 0.00 1.82
2339 3063 7.613551 AGGAACGGATGGAGTATTATTTAGT 57.386 36.000 0.00 0.00 0.00 2.24
2340 3064 8.904099 AAAGGAACGGATGGAGTATTATTTAG 57.096 34.615 0.00 0.00 0.00 1.85
2348 3072 9.151177 ACTTTATATAAAGGAACGGATGGAGTA 57.849 33.333 29.82 0.00 45.23 2.59
2349 3073 7.931948 CACTTTATATAAAGGAACGGATGGAGT 59.068 37.037 29.82 9.96 45.23 3.85
2350 3074 7.931948 ACACTTTATATAAAGGAACGGATGGAG 59.068 37.037 29.82 9.43 45.23 3.86
2351 3075 7.798071 ACACTTTATATAAAGGAACGGATGGA 58.202 34.615 29.82 0.00 45.23 3.41
2352 3076 9.720769 ATACACTTTATATAAAGGAACGGATGG 57.279 33.333 29.82 14.64 45.23 3.51
2382 3106 9.985318 CAAATATGCACTTTGACTTTTGAAAAA 57.015 25.926 15.26 0.00 35.99 1.94
2383 3107 9.376075 TCAAATATGCACTTTGACTTTTGAAAA 57.624 25.926 17.82 0.00 37.61 2.29
2384 3108 8.939201 TCAAATATGCACTTTGACTTTTGAAA 57.061 26.923 17.82 0.00 37.61 2.69
2393 3117 4.323417 ACTCGGTCAAATATGCACTTTGA 58.677 39.130 17.82 17.82 39.60 2.69
2394 3118 4.685169 ACTCGGTCAAATATGCACTTTG 57.315 40.909 14.51 14.51 35.41 2.77
2395 3119 5.473504 AGAAACTCGGTCAAATATGCACTTT 59.526 36.000 0.00 0.00 0.00 2.66
2396 3120 5.003804 AGAAACTCGGTCAAATATGCACTT 58.996 37.500 0.00 0.00 0.00 3.16
2397 3121 4.579869 AGAAACTCGGTCAAATATGCACT 58.420 39.130 0.00 0.00 0.00 4.40
2398 3122 4.946784 AGAAACTCGGTCAAATATGCAC 57.053 40.909 0.00 0.00 0.00 4.57
2399 3123 5.972935 TCTAGAAACTCGGTCAAATATGCA 58.027 37.500 0.00 0.00 0.00 3.96
2400 3124 6.903883 TTCTAGAAACTCGGTCAAATATGC 57.096 37.500 1.68 0.00 0.00 3.14
2403 3127 9.280174 ACATTTTTCTAGAAACTCGGTCAAATA 57.720 29.630 17.51 0.00 0.00 1.40
2404 3128 8.166422 ACATTTTTCTAGAAACTCGGTCAAAT 57.834 30.769 17.51 9.12 0.00 2.32
2405 3129 7.562454 ACATTTTTCTAGAAACTCGGTCAAA 57.438 32.000 17.51 7.22 0.00 2.69
2406 3130 8.842358 ATACATTTTTCTAGAAACTCGGTCAA 57.158 30.769 17.51 7.92 0.00 3.18
2407 3131 9.932207 TTATACATTTTTCTAGAAACTCGGTCA 57.068 29.630 17.51 0.00 0.00 4.02
2533 3257 9.474920 GTCAACCATTTAAATGTTTGATCAAGA 57.525 29.630 31.32 14.52 45.38 3.02
2534 3258 9.480053 AGTCAACCATTTAAATGTTTGATCAAG 57.520 29.630 31.32 15.44 45.38 3.02
2535 3259 9.829507 AAGTCAACCATTTAAATGTTTGATCAA 57.170 25.926 31.32 15.36 45.38 2.57
2536 3260 9.258826 CAAGTCAACCATTTAAATGTTTGATCA 57.741 29.630 31.32 15.64 45.38 2.92
2537 3261 8.223100 GCAAGTCAACCATTTAAATGTTTGATC 58.777 33.333 31.32 25.32 45.38 2.92
2538 3262 7.714377 TGCAAGTCAACCATTTAAATGTTTGAT 59.286 29.630 31.32 20.16 45.38 2.57
2539 3263 7.010923 GTGCAAGTCAACCATTTAAATGTTTGA 59.989 33.333 27.60 27.60 42.89 2.69
2540 3264 7.125113 GTGCAAGTCAACCATTTAAATGTTTG 58.875 34.615 24.73 24.73 39.34 2.93
2541 3265 6.019156 CGTGCAAGTCAACCATTTAAATGTTT 60.019 34.615 23.24 14.99 34.60 2.83
2542 3266 5.461737 CGTGCAAGTCAACCATTTAAATGTT 59.538 36.000 23.24 15.56 34.60 2.71
2543 3267 4.981674 CGTGCAAGTCAACCATTTAAATGT 59.018 37.500 23.24 11.22 34.60 2.71
2544 3268 5.116983 GTCGTGCAAGTCAACCATTTAAATG 59.883 40.000 19.40 19.40 36.17 2.32
2545 3269 5.219633 GTCGTGCAAGTCAACCATTTAAAT 58.780 37.500 0.00 0.00 0.00 1.40
2546 3270 4.096532 TGTCGTGCAAGTCAACCATTTAAA 59.903 37.500 0.00 0.00 0.00 1.52
2547 3271 3.628032 TGTCGTGCAAGTCAACCATTTAA 59.372 39.130 0.00 0.00 0.00 1.52
2548 3272 3.206964 TGTCGTGCAAGTCAACCATTTA 58.793 40.909 0.00 0.00 0.00 1.40
2549 3273 2.020720 TGTCGTGCAAGTCAACCATTT 58.979 42.857 0.00 0.00 0.00 2.32
2550 3274 1.674359 TGTCGTGCAAGTCAACCATT 58.326 45.000 0.00 0.00 0.00 3.16
2551 3275 1.674359 TTGTCGTGCAAGTCAACCAT 58.326 45.000 8.07 0.00 32.52 3.55
2552 3276 1.601903 GATTGTCGTGCAAGTCAACCA 59.398 47.619 13.54 0.00 40.86 3.67
2553 3277 1.398451 CGATTGTCGTGCAAGTCAACC 60.398 52.381 13.54 4.35 40.86 3.77
2554 3278 1.525197 TCGATTGTCGTGCAAGTCAAC 59.475 47.619 13.54 7.86 41.35 3.18
2555 3279 1.859383 TCGATTGTCGTGCAAGTCAA 58.141 45.000 13.62 13.62 41.35 3.18
2556 3280 2.078849 ATCGATTGTCGTGCAAGTCA 57.921 45.000 0.00 0.00 41.35 3.41
2557 3281 2.921121 TGTATCGATTGTCGTGCAAGTC 59.079 45.455 1.71 0.00 41.35 3.01
2558 3282 2.666508 GTGTATCGATTGTCGTGCAAGT 59.333 45.455 1.71 0.00 41.35 3.16
2559 3283 2.029244 GGTGTATCGATTGTCGTGCAAG 59.971 50.000 1.71 0.00 41.35 4.01
2560 3284 1.996898 GGTGTATCGATTGTCGTGCAA 59.003 47.619 1.71 0.00 41.35 4.08
2561 3285 1.203758 AGGTGTATCGATTGTCGTGCA 59.796 47.619 1.71 0.00 41.35 4.57
2562 3286 1.922570 AGGTGTATCGATTGTCGTGC 58.077 50.000 1.71 0.00 41.35 5.34
2563 3287 6.436261 AGTATAAGGTGTATCGATTGTCGTG 58.564 40.000 1.71 0.00 41.35 4.35
2564 3288 6.485984 AGAGTATAAGGTGTATCGATTGTCGT 59.514 38.462 1.71 0.00 41.35 4.34
2565 3289 6.797513 CAGAGTATAAGGTGTATCGATTGTCG 59.202 42.308 1.71 0.00 42.10 4.35
2566 3290 7.649973 ACAGAGTATAAGGTGTATCGATTGTC 58.350 38.462 1.71 0.00 0.00 3.18
2567 3291 7.584122 ACAGAGTATAAGGTGTATCGATTGT 57.416 36.000 1.71 0.00 0.00 2.71
2568 3292 9.613957 CTTACAGAGTATAAGGTGTATCGATTG 57.386 37.037 1.71 0.00 0.00 2.67
2569 3293 9.570468 TCTTACAGAGTATAAGGTGTATCGATT 57.430 33.333 1.71 0.00 31.65 3.34
2570 3294 9.221933 CTCTTACAGAGTATAAGGTGTATCGAT 57.778 37.037 2.16 2.16 37.57 3.59
2571 3295 8.427276 TCTCTTACAGAGTATAAGGTGTATCGA 58.573 37.037 0.75 0.00 42.83 3.59
2572 3296 8.604640 TCTCTTACAGAGTATAAGGTGTATCG 57.395 38.462 0.75 0.00 42.83 2.92
2573 3297 9.005777 CCTCTCTTACAGAGTATAAGGTGTATC 57.994 40.741 0.75 0.00 46.85 2.24
2574 3298 7.945664 CCCTCTCTTACAGAGTATAAGGTGTAT 59.054 40.741 0.75 0.00 46.85 2.29
2575 3299 7.128418 TCCCTCTCTTACAGAGTATAAGGTGTA 59.872 40.741 0.75 0.00 46.85 2.90
2576 3300 6.068971 TCCCTCTCTTACAGAGTATAAGGTGT 60.069 42.308 0.75 0.00 46.85 4.16
2577 3301 6.366340 TCCCTCTCTTACAGAGTATAAGGTG 58.634 44.000 0.75 0.00 46.85 4.00
2578 3302 6.160814 ACTCCCTCTCTTACAGAGTATAAGGT 59.839 42.308 0.75 0.00 46.85 3.50
2579 3303 6.607019 ACTCCCTCTCTTACAGAGTATAAGG 58.393 44.000 0.75 0.89 46.85 2.69
2580 3304 9.280174 CTTACTCCCTCTCTTACAGAGTATAAG 57.720 40.741 0.75 0.00 46.85 1.73
2581 3305 9.000978 TCTTACTCCCTCTCTTACAGAGTATAA 57.999 37.037 0.75 0.00 46.85 0.98
2582 3306 8.564364 TCTTACTCCCTCTCTTACAGAGTATA 57.436 38.462 0.75 0.00 46.85 1.47
2583 3307 7.454553 TCTTACTCCCTCTCTTACAGAGTAT 57.545 40.000 0.75 0.00 46.85 2.12
2584 3308 6.887886 TCTTACTCCCTCTCTTACAGAGTA 57.112 41.667 0.75 0.00 46.85 2.59
2585 3309 5.782677 TCTTACTCCCTCTCTTACAGAGT 57.217 43.478 0.75 0.00 46.85 3.24
2587 3311 6.791371 TCTTTCTTACTCCCTCTCTTACAGA 58.209 40.000 0.00 0.00 0.00 3.41
2588 3312 6.405397 GCTCTTTCTTACTCCCTCTCTTACAG 60.405 46.154 0.00 0.00 0.00 2.74
2589 3313 5.419471 GCTCTTTCTTACTCCCTCTCTTACA 59.581 44.000 0.00 0.00 0.00 2.41
2590 3314 5.419471 TGCTCTTTCTTACTCCCTCTCTTAC 59.581 44.000 0.00 0.00 0.00 2.34
2591 3315 5.580998 TGCTCTTTCTTACTCCCTCTCTTA 58.419 41.667 0.00 0.00 0.00 2.10
2595 3319 3.513515 CACTGCTCTTTCTTACTCCCTCT 59.486 47.826 0.00 0.00 0.00 3.69
2619 3343 3.357021 CCAAAGAATCGTCGAATGCATG 58.643 45.455 0.00 0.00 0.00 4.06
2625 3349 0.038067 TCGCCCAAAGAATCGTCGAA 60.038 50.000 0.00 0.00 0.00 3.71
2626 3350 0.174845 ATCGCCCAAAGAATCGTCGA 59.825 50.000 0.00 0.00 0.00 4.20
2651 3375 1.754226 TCGCACACTATGTCTATGGCA 59.246 47.619 0.00 0.00 0.00 4.92
2652 3376 2.509052 TCGCACACTATGTCTATGGC 57.491 50.000 0.00 0.00 0.00 4.40
2654 3378 3.711086 AGCTTCGCACACTATGTCTATG 58.289 45.455 0.00 0.00 0.00 2.23
2658 3732 3.706698 TGATAGCTTCGCACACTATGTC 58.293 45.455 0.00 0.00 0.00 3.06
2663 6574 2.932614 GTTGATGATAGCTTCGCACACT 59.067 45.455 0.00 0.00 0.00 3.55
2665 6576 3.251479 AGTTGATGATAGCTTCGCACA 57.749 42.857 0.00 0.00 0.00 4.57
2681 6592 4.736126 AACTGGGGTTTTCAAGAAGTTG 57.264 40.909 0.00 0.00 31.21 3.16
2713 6633 3.561503 GAAGTATTTGTCGGTTGGTTGC 58.438 45.455 0.00 0.00 0.00 4.17
2714 6634 3.818773 AGGAAGTATTTGTCGGTTGGTTG 59.181 43.478 0.00 0.00 0.00 3.77
2715 6635 4.094830 AGGAAGTATTTGTCGGTTGGTT 57.905 40.909 0.00 0.00 0.00 3.67
2716 6636 3.782656 AGGAAGTATTTGTCGGTTGGT 57.217 42.857 0.00 0.00 0.00 3.67
2717 6637 5.243207 ACTAAGGAAGTATTTGTCGGTTGG 58.757 41.667 0.00 0.00 36.36 3.77
2718 6638 6.128363 GGAACTAAGGAAGTATTTGTCGGTTG 60.128 42.308 0.00 0.00 37.50 3.77
2719 6639 5.936372 GGAACTAAGGAAGTATTTGTCGGTT 59.064 40.000 0.00 0.00 37.50 4.44
2720 6640 5.485620 GGAACTAAGGAAGTATTTGTCGGT 58.514 41.667 0.00 0.00 37.50 4.69
2721 6641 4.565564 CGGAACTAAGGAAGTATTTGTCGG 59.434 45.833 0.00 0.00 37.50 4.79
2722 6642 5.404946 TCGGAACTAAGGAAGTATTTGTCG 58.595 41.667 0.00 0.00 37.50 4.35
2723 6643 7.845066 ATTCGGAACTAAGGAAGTATTTGTC 57.155 36.000 0.00 0.00 37.50 3.18
2724 6644 9.901172 ATAATTCGGAACTAAGGAAGTATTTGT 57.099 29.630 0.00 0.00 37.50 2.83
2776 6696 7.639039 CACTAAAGCGCTTCAAAATATATCCA 58.361 34.615 25.24 0.00 0.00 3.41
2778 6698 7.540362 GCACTAAAGCGCTTCAAAATATATC 57.460 36.000 25.24 1.81 0.00 1.63
2793 6713 4.839796 TGAGTAAACAAACGCACTAAAGC 58.160 39.130 0.00 0.00 0.00 3.51
2794 6714 7.908193 AAATGAGTAAACAAACGCACTAAAG 57.092 32.000 0.00 0.00 31.81 1.85
2796 6716 8.614346 ACTTAAATGAGTAAACAAACGCACTAA 58.386 29.630 0.00 0.00 31.81 2.24
2797 6717 8.145316 ACTTAAATGAGTAAACAAACGCACTA 57.855 30.769 0.00 0.00 31.81 2.74
2798 6718 7.023197 ACTTAAATGAGTAAACAAACGCACT 57.977 32.000 0.00 0.00 31.81 4.40
2799 6719 6.358822 GGACTTAAATGAGTAAACAAACGCAC 59.641 38.462 0.00 0.00 31.81 5.34
2800 6720 6.432107 GGACTTAAATGAGTAAACAAACGCA 58.568 36.000 0.00 0.00 33.60 5.24
2801 6721 5.562623 CGGACTTAAATGAGTAAACAAACGC 59.437 40.000 0.00 0.00 0.00 4.84
2802 6722 6.652245 ACGGACTTAAATGAGTAAACAAACG 58.348 36.000 0.00 0.00 0.00 3.60
2805 6725 8.836268 ACATACGGACTTAAATGAGTAAACAA 57.164 30.769 0.00 0.00 0.00 2.83
2843 6763 6.260050 TCCAAATTGTAGGACGCTTGAATATC 59.740 38.462 0.00 0.00 0.00 1.63
2846 6766 4.331968 TCCAAATTGTAGGACGCTTGAAT 58.668 39.130 0.00 0.00 0.00 2.57
2848 6768 3.410631 TCCAAATTGTAGGACGCTTGA 57.589 42.857 0.00 0.00 0.00 3.02
2854 6774 5.300792 TCACCTTTGTTCCAAATTGTAGGAC 59.699 40.000 0.00 0.00 32.62 3.85
2875 6795 4.444720 GCATGTCGGCTTACTAACTATCAC 59.555 45.833 0.00 0.00 0.00 3.06
2881 6801 3.000727 ACTTGCATGTCGGCTTACTAAC 58.999 45.455 0.00 0.00 34.04 2.34
2935 6855 9.113838 GCTGACTATTTCTCAATCCATTTAGAA 57.886 33.333 0.00 0.00 0.00 2.10
2936 6856 7.716998 GGCTGACTATTTCTCAATCCATTTAGA 59.283 37.037 0.00 0.00 0.00 2.10
2937 6857 7.500227 TGGCTGACTATTTCTCAATCCATTTAG 59.500 37.037 0.00 0.00 0.00 1.85
2938 6858 7.345691 TGGCTGACTATTTCTCAATCCATTTA 58.654 34.615 0.00 0.00 0.00 1.40
2939 6859 6.189859 TGGCTGACTATTTCTCAATCCATTT 58.810 36.000 0.00 0.00 0.00 2.32
2940 6860 5.759059 TGGCTGACTATTTCTCAATCCATT 58.241 37.500 0.00 0.00 0.00 3.16
2941 6861 5.378230 TGGCTGACTATTTCTCAATCCAT 57.622 39.130 0.00 0.00 0.00 3.41
2942 6862 4.842531 TGGCTGACTATTTCTCAATCCA 57.157 40.909 0.00 0.00 0.00 3.41
2943 6863 7.807977 TTTATGGCTGACTATTTCTCAATCC 57.192 36.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.