Multiple sequence alignment - TraesCS5B01G208700

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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 TraesCS5B01G208700 chr5B 100.000 5029 0 0 1 5029 378521474 378516446 0.000000e+00 9287.0
1 TraesCS5B01G208700 chr5B 93.000 100 2 5 2236 2333 369334444 369334348 1.890000e-29 141.0
2 TraesCS5B01G208700 chr5D 91.438 1857 71 34 453 2243 326129800 326127966 0.000000e+00 2468.0
3 TraesCS5B01G208700 chr5D 93.649 1417 49 14 2334 3737 326127971 326126583 0.000000e+00 2080.0
4 TraesCS5B01G208700 chr5D 92.140 598 24 15 3682 4271 326126590 326126008 0.000000e+00 822.0
5 TraesCS5B01G208700 chr5D 87.517 729 46 21 4304 5005 326125661 326124951 0.000000e+00 800.0
6 TraesCS5B01G208700 chr5D 87.199 539 39 12 227 742 326130701 326130170 2.020000e-163 586.0
7 TraesCS5B01G208700 chr5D 88.983 236 12 7 1 226 326130972 326130741 3.830000e-71 279.0
8 TraesCS5B01G208700 chr5A 85.904 1880 116 70 435 2243 430487955 430489756 0.000000e+00 1866.0
9 TraesCS5B01G208700 chr5A 86.434 774 72 19 2563 3307 430490013 430490782 0.000000e+00 817.0
10 TraesCS5B01G208700 chr5A 92.440 582 24 17 3682 4251 430491320 430491893 0.000000e+00 813.0
11 TraesCS5B01G208700 chr5A 86.265 597 46 25 4425 5005 430501993 430502569 2.570000e-172 616.0
12 TraesCS5B01G208700 chr5A 91.411 326 15 7 3425 3737 430491002 430491327 7.730000e-118 435.0
13 TraesCS5B01G208700 chr5A 90.654 214 15 3 2332 2541 430489749 430489961 3.830000e-71 279.0
14 TraesCS5B01G208700 chr5A 82.353 238 11 13 1 209 430487185 430487420 1.440000e-40 178.0
15 TraesCS5B01G208700 chr1B 89.423 104 6 2 2235 2333 166562983 166563086 5.290000e-25 126.0
16 TraesCS5B01G208700 chr1B 87.850 107 8 4 2235 2336 166563087 166562981 2.460000e-23 121.0
17 TraesCS5B01G208700 chr1B 83.495 103 10 6 2236 2335 349352507 349352409 6.930000e-14 89.8
18 TraesCS5B01G208700 chr7D 84.466 103 11 5 2236 2336 277746361 277746262 4.140000e-16 97.1
19 TraesCS5B01G208700 chr7D 84.314 102 7 8 2236 2333 168427489 168427393 1.930000e-14 91.6
20 TraesCS5B01G208700 chr6B 83.178 107 11 7 2232 2335 693916547 693916445 1.930000e-14 91.6
21 TraesCS5B01G208700 chr2D 84.158 101 9 6 2236 2333 371164052 371163956 1.930000e-14 91.6
22 TraesCS5B01G208700 chr3D 83.495 103 8 8 2236 2334 445343050 445342953 2.490000e-13 87.9


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 TraesCS5B01G208700 chr5B 378516446 378521474 5028 True 9287.000000 9287 100.000000 1 5029 1 chr5B.!!$R2 5028
1 TraesCS5B01G208700 chr5D 326124951 326130972 6021 True 1172.500000 2468 90.154333 1 5005 6 chr5D.!!$R1 5004
2 TraesCS5B01G208700 chr5A 430487185 430491893 4708 False 731.333333 1866 88.199333 1 4251 6 chr5A.!!$F2 4250
3 TraesCS5B01G208700 chr5A 430501993 430502569 576 False 616.000000 616 86.265000 4425 5005 1 chr5A.!!$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
269 637 0.516877 CTCGTCGCTGGCAAATTCAA 59.483 50.000 0.00 0.0 0.00 2.69 F
270 638 1.131126 CTCGTCGCTGGCAAATTCAAT 59.869 47.619 0.00 0.0 0.00 2.57 F
297 673 1.255667 CCTGCAGCAGCCTTTTCCAT 61.256 55.000 17.81 0.0 41.13 3.41 F
648 1053 1.339151 TGCACTCGCACTCTCTCTCTA 60.339 52.381 0.00 0.0 45.36 2.43 F
1790 2936 0.249911 GCATTATTCCGACGAGGGCT 60.250 55.000 0.00 0.0 41.52 5.19 F
3602 4949 1.137872 AGCTGCTTCAGTATCCCTTCG 59.862 52.381 0.00 0.0 33.43 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 2573 0.036388 GCTCGAATCCCCAGAACACA 60.036 55.0 0.00 0.00 0.00 3.72 R
1659 2799 0.604780 CAACTGACAGGGCCACTCAG 60.605 60.0 22.47 22.47 34.85 3.35 R
1677 2818 0.664224 CGCTTCCATACATGCATGCA 59.336 50.0 26.53 25.04 0.00 3.96 R
2315 3483 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.00 0.00 3.28 R
3771 5175 0.250901 GGGACCTTGAAGCAGCTGAA 60.251 55.0 20.43 0.98 0.00 3.02 R
4583 6334 0.035820 GGCCCAACGGTCAGTGAATA 60.036 55.0 0.00 0.00 32.15 1.75 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
70 86 1.876263 CGCGTCAGTGTGTGTGTCA 60.876 57.895 0.00 0.00 0.00 3.58
91 107 1.069090 GTGGTTGCGTCTCTGTCCA 59.931 57.895 0.00 0.00 0.00 4.02
100 116 0.957888 GTCTCTGTCCAAGCAAGCCC 60.958 60.000 0.00 0.00 0.00 5.19
129 155 1.006102 CTCGTTCTGTCCCGTTGCT 60.006 57.895 0.00 0.00 0.00 3.91
196 232 4.640855 CCACCGTCACGCTCGTGT 62.641 66.667 19.95 0.27 45.55 4.49
197 233 3.394874 CACCGTCACGCTCGTGTG 61.395 66.667 19.95 14.08 45.55 3.82
198 234 3.588906 ACCGTCACGCTCGTGTGA 61.589 61.111 19.95 12.70 46.15 3.58
202 238 4.068280 TCACGCTCGTGTGAGGTA 57.932 55.556 19.95 0.00 43.62 3.08
269 637 0.516877 CTCGTCGCTGGCAAATTCAA 59.483 50.000 0.00 0.00 0.00 2.69
270 638 1.131126 CTCGTCGCTGGCAAATTCAAT 59.869 47.619 0.00 0.00 0.00 2.57
271 639 1.539388 TCGTCGCTGGCAAATTCAATT 59.461 42.857 0.00 0.00 0.00 2.32
272 640 1.650153 CGTCGCTGGCAAATTCAATTG 59.350 47.619 0.00 0.00 0.00 2.32
296 672 1.904865 CCTGCAGCAGCCTTTTCCA 60.905 57.895 17.81 0.00 41.13 3.53
297 673 1.255667 CCTGCAGCAGCCTTTTCCAT 61.256 55.000 17.81 0.00 41.13 3.41
309 687 3.440173 GCCTTTTCCATCATCAAACTCGA 59.560 43.478 0.00 0.00 0.00 4.04
328 706 5.643348 ACTCGACACTATTTGCAATTGATCA 59.357 36.000 10.34 0.00 0.00 2.92
354 738 1.461127 GCTACCAAGTGTTTGAGCTCG 59.539 52.381 9.64 0.00 36.36 5.03
377 761 5.616204 CGATAATCATCGCTCCAACGTACTA 60.616 44.000 0.00 0.00 46.80 1.82
380 764 3.534554 TCATCGCTCCAACGTACTACTA 58.465 45.455 0.00 0.00 0.00 1.82
381 765 3.310774 TCATCGCTCCAACGTACTACTAC 59.689 47.826 0.00 0.00 0.00 2.73
382 766 2.977914 TCGCTCCAACGTACTACTACT 58.022 47.619 0.00 0.00 0.00 2.57
384 768 2.223203 CGCTCCAACGTACTACTACTGG 60.223 54.545 0.00 0.00 0.00 4.00
387 771 2.041620 TCCAACGTACTACTACTGGGGT 59.958 50.000 0.00 0.00 0.00 4.95
415 799 4.418328 TTGGCATTACGGGCGGCT 62.418 61.111 9.56 0.00 35.84 5.52
416 800 4.849310 TGGCATTACGGGCGGCTC 62.849 66.667 9.56 0.00 35.84 4.70
494 882 2.961721 CGGACCCATCGCACATCG 60.962 66.667 0.00 0.00 40.15 3.84
524 912 3.123620 GGACAAGCGCAGGCAGAG 61.124 66.667 11.47 0.00 43.41 3.35
604 1009 4.569719 TTCTCTCTCATTAAACCCCACC 57.430 45.455 0.00 0.00 0.00 4.61
648 1053 1.339151 TGCACTCGCACTCTCTCTCTA 60.339 52.381 0.00 0.00 45.36 2.43
649 1054 1.740585 GCACTCGCACTCTCTCTCTAA 59.259 52.381 0.00 0.00 38.36 2.10
650 1055 2.162608 GCACTCGCACTCTCTCTCTAAA 59.837 50.000 0.00 0.00 38.36 1.85
651 1056 3.730662 GCACTCGCACTCTCTCTCTAAAG 60.731 52.174 0.00 0.00 38.36 1.85
746 1818 1.803289 GCCTCCGCCTTCATTTCAC 59.197 57.895 0.00 0.00 0.00 3.18
971 2072 2.221918 GCTAAGCCTAAGCCCTCCA 58.778 57.895 0.00 0.00 41.25 3.86
973 2074 1.501582 CTAAGCCTAAGCCCTCCAGT 58.498 55.000 0.00 0.00 41.25 4.00
985 2086 2.601067 TCCAGTTCCGGGCGTGTA 60.601 61.111 0.00 0.00 0.00 2.90
1232 2343 2.443255 TCCCTCTTCCTTTGACTTTGCT 59.557 45.455 0.00 0.00 0.00 3.91
1319 2434 2.767505 AGTAGTAGCAGTTGTTGGTGC 58.232 47.619 0.00 0.00 39.78 5.01
1326 2441 1.392589 CAGTTGTTGGTGCTGAAGGT 58.607 50.000 0.00 0.00 32.39 3.50
1409 2533 8.840321 TCAATTCTTTATTAATCTACTGCTGCC 58.160 33.333 0.00 0.00 0.00 4.85
1410 2534 8.844244 CAATTCTTTATTAATCTACTGCTGCCT 58.156 33.333 0.00 0.00 0.00 4.75
1446 2573 5.185442 GCTAGTAGGGTTATTTATCTCGGCT 59.815 44.000 0.00 0.00 0.00 5.52
1493 2620 4.195334 CTGCGAATGGGGAGGGGG 62.195 72.222 0.00 0.00 0.00 5.40
1656 2796 4.704965 CAGTGACCAGTGATGATGATGAT 58.295 43.478 0.00 0.00 33.67 2.45
1657 2797 4.511826 CAGTGACCAGTGATGATGATGATG 59.488 45.833 0.00 0.00 33.67 3.07
1658 2798 4.407945 AGTGACCAGTGATGATGATGATGA 59.592 41.667 0.00 0.00 0.00 2.92
1659 2799 4.510711 GTGACCAGTGATGATGATGATGAC 59.489 45.833 0.00 0.00 0.00 3.06
1660 2800 4.407945 TGACCAGTGATGATGATGATGACT 59.592 41.667 0.00 0.00 0.00 3.41
1677 2818 1.757306 CTGAGTGGCCCTGTCAGTT 59.243 57.895 14.98 0.00 34.24 3.16
1728 2869 1.470098 CCGTTCTTGCTTGCTTGCTAT 59.530 47.619 3.47 0.00 0.00 2.97
1730 2871 2.730090 CGTTCTTGCTTGCTTGCTATGG 60.730 50.000 3.47 0.00 0.00 2.74
1731 2872 1.466856 TCTTGCTTGCTTGCTATGGG 58.533 50.000 3.47 0.00 0.00 4.00
1782 2928 1.092921 GTGGCCACGCATTATTCCGA 61.093 55.000 22.49 0.00 0.00 4.55
1785 2931 1.149361 GCCACGCATTATTCCGACGA 61.149 55.000 0.00 0.00 0.00 4.20
1787 2933 0.852777 CACGCATTATTCCGACGAGG 59.147 55.000 0.00 0.00 42.97 4.63
1789 2935 1.557443 CGCATTATTCCGACGAGGGC 61.557 60.000 0.00 0.00 41.52 5.19
1790 2936 0.249911 GCATTATTCCGACGAGGGCT 60.250 55.000 0.00 0.00 41.52 5.19
1791 2937 1.784525 CATTATTCCGACGAGGGCTC 58.215 55.000 0.00 0.00 41.52 4.70
1839 2985 2.302733 AGCTTTGGGGCTTTTTATGTGG 59.697 45.455 0.00 0.00 39.86 4.17
1979 3141 1.457346 ATGCCTTTGTGCTAGCAGTC 58.543 50.000 20.03 8.15 38.89 3.51
2075 3237 3.615849 GCATCCATTTGCTAGCACTAC 57.384 47.619 19.17 0.00 39.57 2.73
2222 3390 9.451002 AATTTTCCACATTCATGCATATCAAAA 57.549 25.926 0.00 0.00 0.00 2.44
2240 3408 6.992063 TCAAAATGCAGAAAGATCTACTCC 57.008 37.500 0.00 0.00 33.50 3.85
2241 3409 5.882557 TCAAAATGCAGAAAGATCTACTCCC 59.117 40.000 0.00 0.00 33.50 4.30
2242 3410 5.707066 AAATGCAGAAAGATCTACTCCCT 57.293 39.130 0.00 0.00 33.50 4.20
2243 3411 4.953940 ATGCAGAAAGATCTACTCCCTC 57.046 45.455 0.00 0.00 33.50 4.30
2244 3412 3.034635 TGCAGAAAGATCTACTCCCTCC 58.965 50.000 0.00 0.00 33.50 4.30
2245 3413 2.035321 GCAGAAAGATCTACTCCCTCCG 59.965 54.545 0.00 0.00 33.50 4.63
2246 3414 3.292460 CAGAAAGATCTACTCCCTCCGT 58.708 50.000 0.00 0.00 33.50 4.69
2247 3415 3.702045 CAGAAAGATCTACTCCCTCCGTT 59.298 47.826 0.00 0.00 33.50 4.44
2248 3416 3.955551 AGAAAGATCTACTCCCTCCGTTC 59.044 47.826 0.00 0.00 32.88 3.95
2249 3417 2.368311 AGATCTACTCCCTCCGTTCC 57.632 55.000 0.00 0.00 0.00 3.62
2250 3418 1.569548 AGATCTACTCCCTCCGTTCCA 59.430 52.381 0.00 0.00 0.00 3.53
2251 3419 2.024273 AGATCTACTCCCTCCGTTCCAA 60.024 50.000 0.00 0.00 0.00 3.53
2252 3420 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
2253 3421 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
2254 3422 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
2255 3423 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
2256 3424 4.778958 TCTACTCCCTCCGTTCCAAAATAA 59.221 41.667 0.00 0.00 0.00 1.40
2257 3425 3.951663 ACTCCCTCCGTTCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
2258 3426 3.329814 ACTCCCTCCGTTCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
2259 3427 3.681593 TCCCTCCGTTCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
2260 3428 3.328343 TCCCTCCGTTCCAAAATAAGTGA 59.672 43.478 0.00 0.00 0.00 3.41
2261 3429 3.439129 CCCTCCGTTCCAAAATAAGTGAC 59.561 47.826 0.00 0.00 0.00 3.67
2262 3430 4.324267 CCTCCGTTCCAAAATAAGTGACT 58.676 43.478 0.00 0.00 0.00 3.41
2263 3431 4.392138 CCTCCGTTCCAAAATAAGTGACTC 59.608 45.833 0.00 0.00 0.00 3.36
2264 3432 4.963373 TCCGTTCCAAAATAAGTGACTCA 58.037 39.130 0.00 0.00 0.00 3.41
2265 3433 5.369833 TCCGTTCCAAAATAAGTGACTCAA 58.630 37.500 0.00 0.00 0.00 3.02
2266 3434 5.823570 TCCGTTCCAAAATAAGTGACTCAAA 59.176 36.000 0.00 0.00 0.00 2.69
2267 3435 6.319152 TCCGTTCCAAAATAAGTGACTCAAAA 59.681 34.615 0.00 0.00 0.00 2.44
2268 3436 6.975772 CCGTTCCAAAATAAGTGACTCAAAAA 59.024 34.615 0.00 0.00 0.00 1.94
2269 3437 7.651704 CCGTTCCAAAATAAGTGACTCAAAAAT 59.348 33.333 0.00 0.00 0.00 1.82
2270 3438 8.479280 CGTTCCAAAATAAGTGACTCAAAAATG 58.521 33.333 0.00 0.00 0.00 2.32
2271 3439 9.528018 GTTCCAAAATAAGTGACTCAAAAATGA 57.472 29.630 0.00 0.00 0.00 2.57
2272 3440 9.528018 TTCCAAAATAAGTGACTCAAAAATGAC 57.472 29.630 0.00 0.00 0.00 3.06
2273 3441 8.912988 TCCAAAATAAGTGACTCAAAAATGACT 58.087 29.630 0.00 0.00 0.00 3.41
2274 3442 9.185192 CCAAAATAAGTGACTCAAAAATGACTC 57.815 33.333 0.00 0.00 0.00 3.36
2275 3443 9.734620 CAAAATAAGTGACTCAAAAATGACTCA 57.265 29.630 0.00 0.00 0.00 3.41
2277 3445 9.736023 AAATAAGTGACTCAAAAATGACTCAAC 57.264 29.630 0.00 0.00 0.00 3.18
2278 3446 8.682936 ATAAGTGACTCAAAAATGACTCAACT 57.317 30.769 0.00 0.00 0.00 3.16
2279 3447 7.396540 AAGTGACTCAAAAATGACTCAACTT 57.603 32.000 0.00 0.00 0.00 2.66
2280 3448 7.396540 AGTGACTCAAAAATGACTCAACTTT 57.603 32.000 0.00 0.00 0.00 2.66
2281 3449 7.253422 AGTGACTCAAAAATGACTCAACTTTG 58.747 34.615 8.79 8.79 0.00 2.77
2282 3450 7.029563 GTGACTCAAAAATGACTCAACTTTGT 58.970 34.615 12.53 0.54 0.00 2.83
2283 3451 8.181573 GTGACTCAAAAATGACTCAACTTTGTA 58.818 33.333 12.53 3.94 0.00 2.41
2284 3452 8.181573 TGACTCAAAAATGACTCAACTTTGTAC 58.818 33.333 12.53 0.00 0.00 2.90
2285 3453 8.281212 ACTCAAAAATGACTCAACTTTGTACT 57.719 30.769 12.53 0.48 0.00 2.73
2286 3454 9.391006 ACTCAAAAATGACTCAACTTTGTACTA 57.609 29.630 12.53 0.00 0.00 1.82
2288 3456 9.997482 TCAAAAATGACTCAACTTTGTACTAAC 57.003 29.630 12.53 0.00 0.00 2.34
2289 3457 9.781834 CAAAAATGACTCAACTTTGTACTAACA 57.218 29.630 0.00 0.00 0.00 2.41
2292 3460 8.732746 AATGACTCAACTTTGTACTAACAAGT 57.267 30.769 0.00 0.00 45.99 3.16
2293 3461 8.732746 ATGACTCAACTTTGTACTAACAAGTT 57.267 30.769 0.00 1.30 45.99 2.66
2294 3462 7.970384 TGACTCAACTTTGTACTAACAAGTTG 58.030 34.615 21.81 21.81 45.99 3.16
2295 3463 7.820386 TGACTCAACTTTGTACTAACAAGTTGA 59.180 33.333 25.13 25.13 46.71 3.18
2296 3464 7.971455 ACTCAACTTTGTACTAACAAGTTGAC 58.029 34.615 24.12 0.00 45.68 3.18
2297 3465 7.822822 ACTCAACTTTGTACTAACAAGTTGACT 59.177 33.333 24.12 17.88 45.68 3.41
2298 3466 8.193250 TCAACTTTGTACTAACAAGTTGACTC 57.807 34.615 24.12 0.00 45.68 3.36
2299 3467 7.820386 TCAACTTTGTACTAACAAGTTGACTCA 59.180 33.333 24.12 12.65 45.68 3.41
2300 3468 7.535489 ACTTTGTACTAACAAGTTGACTCAC 57.465 36.000 10.54 1.61 45.99 3.51
2301 3469 7.328737 ACTTTGTACTAACAAGTTGACTCACT 58.671 34.615 10.54 0.00 45.99 3.41
2302 3470 7.822822 ACTTTGTACTAACAAGTTGACTCACTT 59.177 33.333 10.54 0.00 45.99 3.16
2303 3471 8.556213 TTTGTACTAACAAGTTGACTCACTTT 57.444 30.769 10.54 0.00 45.99 2.66
2304 3472 8.556213 TTGTACTAACAAGTTGACTCACTTTT 57.444 30.769 10.54 0.00 40.69 2.27
2305 3473 7.970384 TGTACTAACAAGTTGACTCACTTTTG 58.030 34.615 10.54 0.00 34.60 2.44
2306 3474 7.820386 TGTACTAACAAGTTGACTCACTTTTGA 59.180 33.333 10.54 0.00 34.60 2.69
2320 3488 6.633500 TCACTTTTGAGTCACTATTTTGGG 57.367 37.500 0.00 0.00 0.00 4.12
2321 3489 6.361433 TCACTTTTGAGTCACTATTTTGGGA 58.639 36.000 0.00 0.00 0.00 4.37
2322 3490 6.262273 TCACTTTTGAGTCACTATTTTGGGAC 59.738 38.462 0.00 0.00 0.00 4.46
2323 3491 5.238650 ACTTTTGAGTCACTATTTTGGGACG 59.761 40.000 0.00 0.00 35.49 4.79
2324 3492 3.328382 TGAGTCACTATTTTGGGACGG 57.672 47.619 0.00 0.00 35.49 4.79
2325 3493 2.901192 TGAGTCACTATTTTGGGACGGA 59.099 45.455 0.00 0.00 35.49 4.69
2326 3494 3.056107 TGAGTCACTATTTTGGGACGGAG 60.056 47.826 0.00 0.00 35.49 4.63
2327 3495 2.236395 AGTCACTATTTTGGGACGGAGG 59.764 50.000 0.00 0.00 35.49 4.30
2328 3496 1.557832 TCACTATTTTGGGACGGAGGG 59.442 52.381 0.00 0.00 0.00 4.30
2329 3497 1.557832 CACTATTTTGGGACGGAGGGA 59.442 52.381 0.00 0.00 0.00 4.20
2330 3498 1.838077 ACTATTTTGGGACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
2340 3508 2.374839 GGACGGAGGGAGTACTACCTAT 59.625 54.545 27.44 15.31 46.12 2.57
2481 3649 5.622007 GCTGCATTGCAAACTAGTATTCCAA 60.622 40.000 13.18 0.00 38.41 3.53
2484 3652 7.385267 TGCATTGCAAACTAGTATTCCAATTT 58.615 30.769 9.33 0.00 34.76 1.82
2642 3844 7.639113 TGTCAGTTTGGTCTCTGTAAATTTT 57.361 32.000 0.00 0.00 33.89 1.82
2725 3931 1.747355 CCCCACTTGCATCAGAACATC 59.253 52.381 0.00 0.00 0.00 3.06
2781 3987 7.343357 TCTTGGGTTTCATCCTTAAACGATAT 58.657 34.615 0.00 0.00 37.64 1.63
2782 3988 8.487848 TCTTGGGTTTCATCCTTAAACGATATA 58.512 33.333 0.00 0.00 37.64 0.86
2837 4043 3.996032 GCTAAATGCTTGAGTGAACTCG 58.004 45.455 6.01 0.00 41.23 4.18
2851 4058 3.366422 GTGAACTCGAGCACAATTCTCTC 59.634 47.826 13.61 0.89 35.19 3.20
2915 4143 7.307989 CCCTTAATTTCTTATACATGTCGCCAG 60.308 40.741 0.00 0.00 0.00 4.85
2923 4151 1.781786 ACATGTCGCCAGTATCCTCT 58.218 50.000 0.00 0.00 0.00 3.69
2955 4183 7.170658 TGCTTTTATTTTGTCCATTGTTACAGC 59.829 33.333 0.00 0.00 0.00 4.40
2958 4186 5.806654 ATTTTGTCCATTGTTACAGCCTT 57.193 34.783 0.00 0.00 0.00 4.35
3008 4244 7.293018 CGTGTACAATACTTTTCAGGGTAAAC 58.707 38.462 0.00 0.00 0.00 2.01
3052 4288 4.407945 AGACCCGCTAATACCAATGTAAGT 59.592 41.667 0.00 0.00 0.00 2.24
3065 4301 6.441222 ACCAATGTAAGTCCCTCTATACTCA 58.559 40.000 0.00 0.00 0.00 3.41
3092 4328 6.860080 ACATCCTATTTCTTTGAAGCATGTG 58.140 36.000 0.00 0.00 0.00 3.21
3286 4524 6.320171 CAAGAGAAAATGACATTGCAGTAGG 58.680 40.000 0.34 0.00 0.00 3.18
3309 4547 8.466617 AGGAGATAACACTATGAAAGATACGT 57.533 34.615 0.00 0.00 0.00 3.57
3366 4683 5.473066 GGCATGATAGTTATTTGCCCAAT 57.527 39.130 0.00 0.00 45.63 3.16
3367 4684 5.232463 GGCATGATAGTTATTTGCCCAATG 58.768 41.667 0.00 0.00 45.63 2.82
3378 4695 2.889170 TGCCCAATGCTTGTAACCTA 57.111 45.000 0.00 0.00 42.00 3.08
3379 4696 3.380471 TGCCCAATGCTTGTAACCTAT 57.620 42.857 0.00 0.00 42.00 2.57
3381 4698 2.290641 GCCCAATGCTTGTAACCTATCG 59.709 50.000 0.00 0.00 36.87 2.92
3383 4700 4.699637 CCCAATGCTTGTAACCTATCGTA 58.300 43.478 0.00 0.00 0.00 3.43
3384 4701 4.750098 CCCAATGCTTGTAACCTATCGTAG 59.250 45.833 0.00 0.00 0.00 3.51
3455 4796 3.365820 GCAAATGTTTTTCCTGCAGATCG 59.634 43.478 17.39 0.00 0.00 3.69
3509 4850 1.322538 CCTGCCAATGCCTACCAACC 61.323 60.000 0.00 0.00 36.33 3.77
3592 4939 1.516365 AACTGCTGCAGCTGCTTCAG 61.516 55.000 36.41 36.41 42.72 3.02
3593 4940 1.966972 CTGCTGCAGCTGCTTCAGT 60.967 57.895 36.61 0.00 42.66 3.41
3602 4949 1.137872 AGCTGCTTCAGTATCCCTTCG 59.862 52.381 0.00 0.00 33.43 3.79
3620 4967 1.438814 GTGCTGCAAACCAAGCTGT 59.561 52.632 2.77 0.00 34.00 4.40
3716 5069 3.112709 GAGTGCGGCTCGTGTTCC 61.113 66.667 0.00 0.00 34.13 3.62
3786 5190 0.522180 CTGCTTCAGCTGCTTCAAGG 59.478 55.000 9.47 0.00 42.66 3.61
3808 5212 4.740062 CAAATGCTCGTGCGCGCA 62.740 61.111 33.09 33.09 43.34 6.09
4046 5450 2.200373 AAGTTAGGCCACATGGTGTC 57.800 50.000 5.01 0.00 37.57 3.67
4047 5451 1.064003 AGTTAGGCCACATGGTGTCA 58.936 50.000 5.01 0.00 37.57 3.58
4049 5453 1.812571 GTTAGGCCACATGGTGTCAAG 59.187 52.381 5.01 0.00 37.57 3.02
4050 5454 0.322456 TAGGCCACATGGTGTCAAGC 60.322 55.000 5.01 0.00 37.57 4.01
4052 5456 1.604593 GCCACATGGTGTCAAGCCT 60.605 57.895 0.00 0.00 37.57 4.58
4055 5459 1.270550 CCACATGGTGTCAAGCCTTTC 59.729 52.381 0.00 0.00 0.00 2.62
4075 5479 7.217906 CCTTTCTCTCTTTTGGTAGTAGTTGT 58.782 38.462 0.00 0.00 0.00 3.32
4109 5514 3.636764 CTGTTTAAGCCTCTGTTTGGGTT 59.363 43.478 0.00 0.00 45.72 4.11
4126 5532 3.869473 TTCGTTCGGGGCCTTGACG 62.869 63.158 16.15 16.15 0.00 4.35
4258 5671 6.754193 TGTCAACCATTTTACAGGGATTTTC 58.246 36.000 0.00 0.00 0.00 2.29
4264 5677 8.902540 ACCATTTTACAGGGATTTTCTTTTTC 57.097 30.769 0.00 0.00 0.00 2.29
4265 5678 8.713971 ACCATTTTACAGGGATTTTCTTTTTCT 58.286 29.630 0.00 0.00 0.00 2.52
4266 5679 9.559732 CCATTTTACAGGGATTTTCTTTTTCTT 57.440 29.630 0.00 0.00 0.00 2.52
4294 5707 9.491675 TTTTTATTCATGAGACACATTTGCATT 57.508 25.926 0.00 0.00 37.07 3.56
4297 5710 9.738832 TTATTCATGAGACACATTTGCATTATG 57.261 29.630 0.00 7.56 37.07 1.90
4298 5711 7.393841 TTCATGAGACACATTTGCATTATGA 57.606 32.000 14.28 0.64 37.07 2.15
4299 5712 7.576861 TCATGAGACACATTTGCATTATGAT 57.423 32.000 14.28 4.21 37.07 2.45
4301 5714 6.051646 TGAGACACATTTGCATTATGATCG 57.948 37.500 14.28 6.51 0.00 3.69
4303 5716 4.577693 AGACACATTTGCATTATGATCGCT 59.422 37.500 14.28 5.25 0.00 4.93
4304 5717 5.759763 AGACACATTTGCATTATGATCGCTA 59.240 36.000 14.28 0.00 0.00 4.26
4334 6062 9.458727 AAACTAATCATGATCACTTTCATCACT 57.541 29.630 9.06 0.00 34.09 3.41
4335 6063 8.434733 ACTAATCATGATCACTTTCATCACTG 57.565 34.615 9.06 0.00 34.09 3.66
4340 6068 8.620116 TCATGATCACTTTCATCACTGTTAAA 57.380 30.769 0.00 0.00 34.09 1.52
4401 6129 1.127951 CGACCAGTTTTATGGCGTCAC 59.872 52.381 0.00 0.00 44.80 3.67
4577 6328 2.363147 AGAGTCACTCGCTCCCCC 60.363 66.667 0.00 0.00 35.36 5.40
4583 6334 2.120718 ACTCGCTCCCCCAGTCTT 59.879 61.111 0.00 0.00 0.00 3.01
4641 6392 0.504384 CGAGTCAGTCAGTTTGTGCG 59.496 55.000 0.00 0.00 0.00 5.34
4642 6393 0.861837 GAGTCAGTCAGTTTGTGCGG 59.138 55.000 0.00 0.00 0.00 5.69
4669 6427 3.103911 GTTGTCGCCCGTGTCGAG 61.104 66.667 0.00 0.00 36.56 4.04
4677 6435 4.907034 CCGTGTCGAGATCGGCCG 62.907 72.222 22.12 22.12 44.42 6.13
4693 6451 3.630148 CGGCGCCATTAGCACGAG 61.630 66.667 28.98 0.98 42.29 4.18
4694 6452 2.511600 GGCGCCATTAGCACGAGT 60.512 61.111 24.80 0.00 44.04 4.18
4695 6453 2.526120 GGCGCCATTAGCACGAGTC 61.526 63.158 24.80 0.00 44.04 3.36
4696 6454 2.860628 GCGCCATTAGCACGAGTCG 61.861 63.158 11.85 11.85 44.04 4.18
4697 6455 2.860628 CGCCATTAGCACGAGTCGC 61.861 63.158 13.59 0.00 44.04 5.19
4698 6456 1.519455 GCCATTAGCACGAGTCGCT 60.519 57.895 13.59 5.01 42.97 4.93
4831 6590 0.607489 ACATCTTCCAGTGCTGTGCC 60.607 55.000 0.00 0.00 0.00 5.01
5010 6785 3.987404 GCATTCCTCTGCGTGGTT 58.013 55.556 0.00 0.00 31.49 3.67
5011 6786 1.796796 GCATTCCTCTGCGTGGTTC 59.203 57.895 0.00 0.00 31.49 3.62
5012 6787 1.970917 GCATTCCTCTGCGTGGTTCG 61.971 60.000 0.00 0.00 43.12 3.95
5013 6788 0.670546 CATTCCTCTGCGTGGTTCGT 60.671 55.000 0.00 0.00 42.13 3.85
5014 6789 0.670546 ATTCCTCTGCGTGGTTCGTG 60.671 55.000 0.00 0.00 42.13 4.35
5015 6790 2.709125 TTCCTCTGCGTGGTTCGTGG 62.709 60.000 0.00 0.00 42.13 4.94
5016 6791 2.338620 CTCTGCGTGGTTCGTGGA 59.661 61.111 0.00 0.00 42.13 4.02
5017 6792 1.079819 CTCTGCGTGGTTCGTGGAT 60.080 57.895 0.00 0.00 42.13 3.41
5018 6793 0.670546 CTCTGCGTGGTTCGTGGATT 60.671 55.000 0.00 0.00 42.13 3.01
5019 6794 0.669318 TCTGCGTGGTTCGTGGATTC 60.669 55.000 0.00 0.00 42.13 2.52
5020 6795 1.635663 CTGCGTGGTTCGTGGATTCC 61.636 60.000 0.00 0.00 42.13 3.01
5021 6796 1.375523 GCGTGGTTCGTGGATTCCT 60.376 57.895 3.95 0.00 42.13 3.36
5022 6797 0.953960 GCGTGGTTCGTGGATTCCTT 60.954 55.000 3.95 0.00 42.13 3.36
5023 6798 1.519408 CGTGGTTCGTGGATTCCTTT 58.481 50.000 3.95 0.00 34.52 3.11
5024 6799 1.196808 CGTGGTTCGTGGATTCCTTTG 59.803 52.381 3.95 0.00 34.52 2.77
5025 6800 2.227194 GTGGTTCGTGGATTCCTTTGT 58.773 47.619 3.95 0.00 0.00 2.83
5026 6801 2.031157 GTGGTTCGTGGATTCCTTTGTG 60.031 50.000 3.95 0.00 0.00 3.33
5027 6802 1.539827 GGTTCGTGGATTCCTTTGTGG 59.460 52.381 3.95 0.00 37.10 4.17
5028 6803 1.068541 GTTCGTGGATTCCTTTGTGGC 60.069 52.381 3.95 0.00 35.26 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 86 0.249489 GACAGAGACGCAACCACACT 60.249 55.000 0.00 0.00 0.00 3.55
91 107 2.187946 CCTCGATCGGGCTTGCTT 59.812 61.111 16.41 0.00 0.00 3.91
129 155 2.437716 GGAAAAGCCATCCGCGGA 60.438 61.111 33.12 33.12 44.76 5.54
237 597 1.001597 GCGACGAGTGGGGAATAGTAG 60.002 57.143 0.00 0.00 0.00 2.57
269 637 1.035932 GCTGCTGCAGGGTGATCAAT 61.036 55.000 29.05 0.00 39.41 2.57
270 638 1.676635 GCTGCTGCAGGGTGATCAA 60.677 57.895 29.05 0.00 39.41 2.57
271 639 2.045634 GCTGCTGCAGGGTGATCA 60.046 61.111 29.05 2.34 39.41 2.92
272 640 2.827642 GGCTGCTGCAGGGTGATC 60.828 66.667 29.05 12.33 41.91 2.92
296 672 5.643348 TGCAAATAGTGTCGAGTTTGATGAT 59.357 36.000 9.80 0.00 34.38 2.45
297 673 4.994217 TGCAAATAGTGTCGAGTTTGATGA 59.006 37.500 9.80 0.00 34.38 2.92
309 687 5.948162 AGGAGTGATCAATTGCAAATAGTGT 59.052 36.000 1.71 0.00 0.00 3.55
328 706 2.438021 TCAAACACTTGGTAGCAGGAGT 59.562 45.455 11.37 6.16 33.01 3.85
354 738 4.547532 AGTACGTTGGAGCGATGATTATC 58.452 43.478 0.00 0.00 35.59 1.75
377 761 3.538387 AGGAAACCAATACCCCAGTAGT 58.462 45.455 0.00 0.00 0.00 2.73
380 764 2.225267 CCAAGGAAACCAATACCCCAGT 60.225 50.000 0.00 0.00 0.00 4.00
381 765 2.456577 CCAAGGAAACCAATACCCCAG 58.543 52.381 0.00 0.00 0.00 4.45
382 766 1.551329 GCCAAGGAAACCAATACCCCA 60.551 52.381 0.00 0.00 0.00 4.96
384 768 1.931635 TGCCAAGGAAACCAATACCC 58.068 50.000 0.00 0.00 0.00 3.69
387 771 3.697045 CCGTAATGCCAAGGAAACCAATA 59.303 43.478 0.00 0.00 0.00 1.90
415 799 3.650950 GAGCCAGCCCAACAGGGA 61.651 66.667 4.37 0.00 46.20 4.20
511 899 4.774503 GAGCCTCTGCCTGCGCTT 62.775 66.667 9.73 0.00 38.69 4.68
514 902 3.889134 TTGTGAGCCTCTGCCTGCG 62.889 63.158 0.00 0.00 38.69 5.18
515 903 2.033141 TTGTGAGCCTCTGCCTGC 59.967 61.111 0.00 0.00 38.69 4.85
516 904 0.673022 GACTTGTGAGCCTCTGCCTG 60.673 60.000 0.00 0.00 38.69 4.85
519 907 1.287730 CGTGACTTGTGAGCCTCTGC 61.288 60.000 0.00 0.00 37.95 4.26
520 908 0.315251 TCGTGACTTGTGAGCCTCTG 59.685 55.000 0.00 0.00 0.00 3.35
521 909 1.040646 TTCGTGACTTGTGAGCCTCT 58.959 50.000 0.00 0.00 0.00 3.69
522 910 1.140816 GTTCGTGACTTGTGAGCCTC 58.859 55.000 0.00 0.00 0.00 4.70
523 911 0.249911 GGTTCGTGACTTGTGAGCCT 60.250 55.000 0.00 0.00 31.12 4.58
524 912 1.557443 CGGTTCGTGACTTGTGAGCC 61.557 60.000 0.00 0.00 0.00 4.70
526 914 1.557443 GCCGGTTCGTGACTTGTGAG 61.557 60.000 1.90 0.00 0.00 3.51
563 968 0.827368 AGAAGATCAAGGGAGGACGC 59.173 55.000 0.00 0.00 0.00 5.19
648 1053 1.232621 GCGCGTGGGGTTTAGACTTT 61.233 55.000 8.43 0.00 0.00 2.66
649 1054 1.670083 GCGCGTGGGGTTTAGACTT 60.670 57.895 8.43 0.00 0.00 3.01
650 1055 2.047560 GCGCGTGGGGTTTAGACT 60.048 61.111 8.43 0.00 0.00 3.24
651 1056 3.122971 GGCGCGTGGGGTTTAGAC 61.123 66.667 8.43 0.00 0.00 2.59
746 1818 1.205893 GAGTAGAGCAGGTGGTGGAAG 59.794 57.143 0.00 0.00 0.00 3.46
971 2072 0.896940 TCTCTTACACGCCCGGAACT 60.897 55.000 0.73 0.00 0.00 3.01
973 2074 1.180456 TGTCTCTTACACGCCCGGAA 61.180 55.000 0.73 0.00 31.43 4.30
985 2086 2.307098 CCCCCATGTCTCTTTGTCTCTT 59.693 50.000 0.00 0.00 0.00 2.85
1197 2308 0.813210 GAGGGAGGAGCAATGAAGCG 60.813 60.000 0.00 0.00 40.15 4.68
1232 2343 7.177568 TCGGATCTTGTTTTAAAAATGGGATCA 59.822 33.333 21.81 8.14 31.68 2.92
1302 2417 1.140852 TCAGCACCAACAACTGCTACT 59.859 47.619 0.00 0.00 41.97 2.57
1304 2419 2.221169 CTTCAGCACCAACAACTGCTA 58.779 47.619 0.00 0.00 41.97 3.49
1313 2428 1.300620 CGTCGACCTTCAGCACCAA 60.301 57.895 10.58 0.00 0.00 3.67
1319 2434 2.087009 GGCGTTCGTCGACCTTCAG 61.087 63.158 10.58 0.00 42.54 3.02
1409 2533 3.505680 CCCTACTAGCTACAGATGCAGAG 59.494 52.174 0.00 0.00 0.00 3.35
1410 2534 3.117474 ACCCTACTAGCTACAGATGCAGA 60.117 47.826 0.00 0.00 0.00 4.26
1446 2573 0.036388 GCTCGAATCCCCAGAACACA 60.036 55.000 0.00 0.00 0.00 3.72
1523 2653 2.125512 GATTGTCTGCGCCGAGGT 60.126 61.111 4.18 0.00 0.00 3.85
1526 2656 4.812476 CCGGATTGTCTGCGCCGA 62.812 66.667 4.18 0.00 46.29 5.54
1656 2796 1.459348 TGACAGGGCCACTCAGTCA 60.459 57.895 6.18 8.91 36.92 3.41
1657 2797 1.294780 CTGACAGGGCCACTCAGTC 59.705 63.158 18.04 12.24 0.00 3.51
1658 2798 1.056700 AACTGACAGGGCCACTCAGT 61.057 55.000 23.54 23.54 42.62 3.41
1659 2799 0.604780 CAACTGACAGGGCCACTCAG 60.605 60.000 22.47 22.47 34.85 3.35
1660 2800 1.451504 CAACTGACAGGGCCACTCA 59.548 57.895 6.18 4.48 0.00 3.41
1677 2818 0.664224 CGCTTCCATACATGCATGCA 59.336 50.000 26.53 25.04 0.00 3.96
1728 2869 1.993391 GTGCCCAGGCTACTACCCA 60.993 63.158 10.58 0.00 42.51 4.51
1730 2871 2.499685 CGTGCCCAGGCTACTACC 59.500 66.667 10.58 0.00 42.51 3.18
1731 2872 2.499685 CCGTGCCCAGGCTACTAC 59.500 66.667 10.58 0.00 42.51 2.73
1792 2938 4.166011 GCCCATCAACGCACGAGC 62.166 66.667 0.00 0.00 37.42 5.03
1793 2939 2.434884 AGCCCATCAACGCACGAG 60.435 61.111 0.00 0.00 0.00 4.18
1794 2940 2.741985 CAGCCCATCAACGCACGA 60.742 61.111 0.00 0.00 0.00 4.35
1795 2941 4.465512 GCAGCCCATCAACGCACG 62.466 66.667 0.00 0.00 0.00 5.34
1797 2943 4.657408 TGGCAGCCCATCAACGCA 62.657 61.111 9.64 0.00 35.79 5.24
1839 2985 5.931724 CCCCATGGAAAAACACAAAATCTAC 59.068 40.000 15.22 0.00 0.00 2.59
2222 3390 3.645687 GGAGGGAGTAGATCTTTCTGCAT 59.354 47.826 16.34 11.66 37.08 3.96
2235 3403 4.533311 ACTTATTTTGGAACGGAGGGAGTA 59.467 41.667 0.00 0.00 0.00 2.59
2236 3404 3.329814 ACTTATTTTGGAACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
2237 3405 3.689649 CACTTATTTTGGAACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
2238 3406 3.328343 TCACTTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
2239 3407 3.439129 GTCACTTATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
2240 3408 4.324267 AGTCACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
2241 3409 4.994852 TGAGTCACTTATTTTGGAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
2242 3410 4.963373 TGAGTCACTTATTTTGGAACGGA 58.037 39.130 0.00 0.00 0.00 4.69
2243 3411 5.682943 TTGAGTCACTTATTTTGGAACGG 57.317 39.130 0.00 0.00 0.00 4.44
2244 3412 7.979115 TTTTTGAGTCACTTATTTTGGAACG 57.021 32.000 0.00 0.00 0.00 3.95
2245 3413 9.528018 TCATTTTTGAGTCACTTATTTTGGAAC 57.472 29.630 0.00 0.00 0.00 3.62
2246 3414 9.528018 GTCATTTTTGAGTCACTTATTTTGGAA 57.472 29.630 0.00 0.00 0.00 3.53
2247 3415 8.912988 AGTCATTTTTGAGTCACTTATTTTGGA 58.087 29.630 0.00 0.00 0.00 3.53
2248 3416 9.185192 GAGTCATTTTTGAGTCACTTATTTTGG 57.815 33.333 0.00 0.00 37.98 3.28
2249 3417 9.734620 TGAGTCATTTTTGAGTCACTTATTTTG 57.265 29.630 8.96 0.00 41.68 2.44
2251 3419 9.736023 GTTGAGTCATTTTTGAGTCACTTATTT 57.264 29.630 11.91 0.00 44.92 1.40
2252 3420 9.125026 AGTTGAGTCATTTTTGAGTCACTTATT 57.875 29.630 11.91 0.00 44.92 1.40
2253 3421 8.682936 AGTTGAGTCATTTTTGAGTCACTTAT 57.317 30.769 11.91 0.00 44.92 1.73
2254 3422 8.506168 AAGTTGAGTCATTTTTGAGTCACTTA 57.494 30.769 11.91 0.00 44.92 2.24
2255 3423 7.396540 AAGTTGAGTCATTTTTGAGTCACTT 57.603 32.000 11.91 13.95 44.92 3.16
2256 3424 7.094205 ACAAAGTTGAGTCATTTTTGAGTCACT 60.094 33.333 24.96 8.36 44.92 3.41
2257 3425 7.029563 ACAAAGTTGAGTCATTTTTGAGTCAC 58.970 34.615 24.96 6.53 44.92 3.67
2258 3426 7.156876 ACAAAGTTGAGTCATTTTTGAGTCA 57.843 32.000 24.96 8.96 43.96 3.41
2259 3427 8.398665 AGTACAAAGTTGAGTCATTTTTGAGTC 58.601 33.333 24.96 17.22 38.42 3.36
2260 3428 8.281212 AGTACAAAGTTGAGTCATTTTTGAGT 57.719 30.769 24.96 13.32 33.98 3.41
2262 3430 9.997482 GTTAGTACAAAGTTGAGTCATTTTTGA 57.003 29.630 24.96 13.02 33.98 2.69
2263 3431 9.781834 TGTTAGTACAAAGTTGAGTCATTTTTG 57.218 29.630 20.05 20.05 35.47 2.44
2266 3434 9.174166 ACTTGTTAGTACAAAGTTGAGTCATTT 57.826 29.630 0.00 0.00 43.33 2.32
2267 3435 8.732746 ACTTGTTAGTACAAAGTTGAGTCATT 57.267 30.769 0.00 0.00 43.33 2.57
2268 3436 8.612619 CAACTTGTTAGTACAAAGTTGAGTCAT 58.387 33.333 24.42 2.42 44.75 3.06
2269 3437 7.820386 TCAACTTGTTAGTACAAAGTTGAGTCA 59.180 33.333 25.84 14.37 45.06 3.41
2270 3438 8.193250 TCAACTTGTTAGTACAAAGTTGAGTC 57.807 34.615 25.84 0.00 45.06 3.36
2273 3441 7.820386 TGAGTCAACTTGTTAGTACAAAGTTGA 59.180 33.333 25.84 25.84 46.08 3.18
2274 3442 7.903431 GTGAGTCAACTTGTTAGTACAAAGTTG 59.097 37.037 23.56 23.56 43.33 3.16
2275 3443 7.822822 AGTGAGTCAACTTGTTAGTACAAAGTT 59.177 33.333 0.00 9.07 43.33 2.66
2276 3444 7.328737 AGTGAGTCAACTTGTTAGTACAAAGT 58.671 34.615 0.00 0.00 43.33 2.66
2277 3445 7.772332 AGTGAGTCAACTTGTTAGTACAAAG 57.228 36.000 0.00 0.00 43.33 2.77
2278 3446 8.556213 AAAGTGAGTCAACTTGTTAGTACAAA 57.444 30.769 0.00 0.00 43.33 2.83
2279 3447 8.447833 CAAAAGTGAGTCAACTTGTTAGTACAA 58.552 33.333 0.00 0.00 40.28 2.41
2280 3448 7.820386 TCAAAAGTGAGTCAACTTGTTAGTACA 59.180 33.333 0.00 0.00 40.28 2.90
2281 3449 8.193250 TCAAAAGTGAGTCAACTTGTTAGTAC 57.807 34.615 0.00 0.00 40.28 2.73
2282 3450 8.420374 CTCAAAAGTGAGTCAACTTGTTAGTA 57.580 34.615 0.00 0.00 45.44 1.82
2283 3451 7.308782 CTCAAAAGTGAGTCAACTTGTTAGT 57.691 36.000 0.00 0.00 45.44 2.24
2297 3465 6.262273 GTCCCAAAATAGTGACTCAAAAGTGA 59.738 38.462 0.00 0.00 35.28 3.41
2298 3466 6.438763 GTCCCAAAATAGTGACTCAAAAGTG 58.561 40.000 0.00 0.00 35.28 3.16
2299 3467 5.238650 CGTCCCAAAATAGTGACTCAAAAGT 59.761 40.000 0.00 0.00 38.88 2.66
2300 3468 5.334879 CCGTCCCAAAATAGTGACTCAAAAG 60.335 44.000 0.00 0.00 0.00 2.27
2301 3469 4.517453 CCGTCCCAAAATAGTGACTCAAAA 59.483 41.667 0.00 0.00 0.00 2.44
2302 3470 4.069304 CCGTCCCAAAATAGTGACTCAAA 58.931 43.478 0.00 0.00 0.00 2.69
2303 3471 3.325425 TCCGTCCCAAAATAGTGACTCAA 59.675 43.478 0.00 0.00 0.00 3.02
2304 3472 2.901192 TCCGTCCCAAAATAGTGACTCA 59.099 45.455 0.00 0.00 0.00 3.41
2305 3473 3.522553 CTCCGTCCCAAAATAGTGACTC 58.477 50.000 0.00 0.00 0.00 3.36
2306 3474 2.236395 CCTCCGTCCCAAAATAGTGACT 59.764 50.000 0.00 0.00 0.00 3.41
2307 3475 2.629051 CCTCCGTCCCAAAATAGTGAC 58.371 52.381 0.00 0.00 0.00 3.67
2308 3476 1.557832 CCCTCCGTCCCAAAATAGTGA 59.442 52.381 0.00 0.00 0.00 3.41
2309 3477 1.557832 TCCCTCCGTCCCAAAATAGTG 59.442 52.381 0.00 0.00 0.00 2.74
2310 3478 1.838077 CTCCCTCCGTCCCAAAATAGT 59.162 52.381 0.00 0.00 0.00 2.12
2311 3479 1.838077 ACTCCCTCCGTCCCAAAATAG 59.162 52.381 0.00 0.00 0.00 1.73
2312 3480 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2313 3481 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2314 3482 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2315 3483 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2316 3484 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2317 3485 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
2318 3486 0.467106 GGTAGTACTCCCTCCGTCCC 60.467 65.000 0.00 0.00 0.00 4.46
2319 3487 0.550432 AGGTAGTACTCCCTCCGTCC 59.450 60.000 0.11 0.00 0.00 4.79
2320 3488 3.786368 ATAGGTAGTACTCCCTCCGTC 57.214 52.381 10.79 0.00 32.08 4.79
2321 3489 4.041444 CACTATAGGTAGTACTCCCTCCGT 59.959 50.000 10.79 4.07 39.12 4.69
2322 3490 4.565236 CCACTATAGGTAGTACTCCCTCCG 60.565 54.167 10.79 3.45 39.12 4.63
2323 3491 4.263860 CCCACTATAGGTAGTACTCCCTCC 60.264 54.167 10.79 4.42 39.12 4.30
2324 3492 4.353489 ACCCACTATAGGTAGTACTCCCTC 59.647 50.000 10.79 0.00 39.12 4.30
2325 3493 4.106019 CACCCACTATAGGTAGTACTCCCT 59.894 50.000 12.22 12.22 39.12 4.20
2326 3494 4.105377 TCACCCACTATAGGTAGTACTCCC 59.895 50.000 0.00 0.00 39.12 4.30
2327 3495 5.069318 GTCACCCACTATAGGTAGTACTCC 58.931 50.000 0.00 0.48 39.12 3.85
2328 3496 5.939447 AGTCACCCACTATAGGTAGTACTC 58.061 45.833 0.00 0.00 39.12 2.59
2329 3497 5.990713 AGTCACCCACTATAGGTAGTACT 57.009 43.478 4.43 0.00 39.12 2.73
2330 3498 7.123247 TCAAAAGTCACCCACTATAGGTAGTAC 59.877 40.741 4.43 0.00 39.12 2.73
2340 3508 6.261381 GTGTTTATGTCAAAAGTCACCCACTA 59.739 38.462 0.00 0.00 32.30 2.74
2725 3931 8.141909 TCACTCCCAAATGAACTCGTATAATAG 58.858 37.037 0.00 0.00 0.00 1.73
2781 3987 7.607607 TCAGCTATTTCAACTTCAAGAGCAATA 59.392 33.333 0.00 0.00 0.00 1.90
2782 3988 6.432162 TCAGCTATTTCAACTTCAAGAGCAAT 59.568 34.615 0.00 0.00 0.00 3.56
2837 4043 2.727298 GCTTTGCGAGAGAATTGTGCTC 60.727 50.000 0.00 0.00 0.00 4.26
2915 4143 9.294030 CAAAATAAAAGCATTGTGAGAGGATAC 57.706 33.333 0.00 0.00 0.00 2.24
2923 4151 7.714377 ACAATGGACAAAATAAAAGCATTGTGA 59.286 29.630 1.23 0.00 38.69 3.58
2969 4197 4.600692 TGTACACGGATATTAGCAGCAT 57.399 40.909 0.00 0.00 0.00 3.79
3052 4288 8.798975 AATAGGATGTTTTGAGTATAGAGGGA 57.201 34.615 0.00 0.00 0.00 4.20
3065 4301 8.370182 ACATGCTTCAAAGAAATAGGATGTTTT 58.630 29.630 0.00 0.00 44.02 2.43
3092 4328 3.374678 TGGTTCCGTCAAAAACACACTAC 59.625 43.478 0.00 0.00 0.00 2.73
3366 4683 3.382546 GTCCCTACGATAGGTTACAAGCA 59.617 47.826 9.33 0.00 44.73 3.91
3367 4684 3.974912 GTCCCTACGATAGGTTACAAGC 58.025 50.000 9.33 0.00 44.73 4.01
3381 4698 3.068307 ACAGATGAATACTGCGTCCCTAC 59.932 47.826 0.00 0.00 38.74 3.18
3383 4700 2.111384 ACAGATGAATACTGCGTCCCT 58.889 47.619 0.00 0.00 38.74 4.20
3384 4701 2.604046 ACAGATGAATACTGCGTCCC 57.396 50.000 0.00 0.00 38.74 4.46
3385 4702 3.491267 GCTAACAGATGAATACTGCGTCC 59.509 47.826 0.00 0.00 38.74 4.79
3387 4704 4.115516 CAGCTAACAGATGAATACTGCGT 58.884 43.478 0.00 0.00 38.74 5.24
3388 4705 4.363138 TCAGCTAACAGATGAATACTGCG 58.637 43.478 0.00 0.00 37.74 5.18
3395 4712 2.935238 GCGGGTTCAGCTAACAGATGAA 60.935 50.000 2.89 2.89 46.92 2.57
3396 4713 1.405526 GCGGGTTCAGCTAACAGATGA 60.406 52.381 0.00 0.00 39.09 2.92
3397 4714 1.009829 GCGGGTTCAGCTAACAGATG 58.990 55.000 0.00 0.00 40.08 2.90
3399 4716 1.295423 GGCGGGTTCAGCTAACAGA 59.705 57.895 0.00 0.00 40.08 3.41
3401 4718 2.349755 GGGCGGGTTCAGCTAACA 59.650 61.111 0.00 0.00 40.08 2.41
3402 4719 1.745489 CTGGGCGGGTTCAGCTAAC 60.745 63.158 0.00 0.00 37.36 2.34
3434 4775 4.797471 TCGATCTGCAGGAAAAACATTTG 58.203 39.130 15.13 0.00 0.00 2.32
3509 4850 1.035139 AGCACCTTGGTCTTTTGCAG 58.965 50.000 0.00 0.00 35.57 4.41
3560 4901 2.952245 CAGTTCAGGCTGCAGCAC 59.048 61.111 37.63 26.85 44.36 4.40
3571 4912 1.512996 GAAGCAGCTGCAGCAGTTCA 61.513 55.000 38.24 0.00 45.16 3.18
3592 4939 1.130561 GTTTGCAGCACGAAGGGATAC 59.869 52.381 0.00 0.00 0.00 2.24
3593 4940 1.448985 GTTTGCAGCACGAAGGGATA 58.551 50.000 0.00 0.00 0.00 2.59
3602 4949 0.872881 CACAGCTTGGTTTGCAGCAC 60.873 55.000 0.00 0.00 38.61 4.40
3620 4967 2.558286 GCAGCACTCAAAGCAGCCA 61.558 57.895 0.00 0.00 38.40 4.75
3771 5175 0.250901 GGGACCTTGAAGCAGCTGAA 60.251 55.000 20.43 0.98 0.00 3.02
3786 5190 2.877691 GCACGAGCATTTGGGGAC 59.122 61.111 0.00 0.00 41.58 4.46
3808 5212 0.882042 CGACTGGCAGTTGAAGCACT 60.882 55.000 27.50 0.00 31.05 4.40
4046 5450 5.066593 ACTACCAAAAGAGAGAAAGGCTTG 58.933 41.667 0.00 0.00 0.00 4.01
4047 5451 5.311844 ACTACCAAAAGAGAGAAAGGCTT 57.688 39.130 0.00 0.00 0.00 4.35
4049 5453 5.795972 ACTACTACCAAAAGAGAGAAAGGC 58.204 41.667 0.00 0.00 0.00 4.35
4050 5454 7.217906 ACAACTACTACCAAAAGAGAGAAAGG 58.782 38.462 0.00 0.00 0.00 3.11
4052 5456 8.019656 AGACAACTACTACCAAAAGAGAGAAA 57.980 34.615 0.00 0.00 0.00 2.52
4055 5459 7.711339 ACAAAGACAACTACTACCAAAAGAGAG 59.289 37.037 0.00 0.00 0.00 3.20
4099 5504 1.512156 CCCCGAACGAACCCAAACAG 61.512 60.000 0.00 0.00 0.00 3.16
4109 5514 4.367023 CGTCAAGGCCCCGAACGA 62.367 66.667 10.97 0.00 0.00 3.85
4277 5690 6.665465 CGATCATAATGCAAATGTGTCTCAT 58.335 36.000 11.05 0.00 38.57 2.90
4278 5691 5.504501 GCGATCATAATGCAAATGTGTCTCA 60.505 40.000 11.05 0.00 0.00 3.27
4283 5696 7.682593 TTTTAGCGATCATAATGCAAATGTG 57.317 32.000 11.05 3.39 0.00 3.21
4309 6037 8.890718 CAGTGATGAAAGTGATCATGATTAGTT 58.109 33.333 10.14 12.01 40.08 2.24
4311 6039 8.434733 ACAGTGATGAAAGTGATCATGATTAG 57.565 34.615 10.14 0.00 40.08 1.73
4316 6044 9.681692 TTTTTAACAGTGATGAAAGTGATCATG 57.318 29.630 0.00 0.00 40.08 3.07
4353 6081 8.839343 GTTTTTCCTCAAAACCATGAAAATGAT 58.161 29.630 0.00 0.00 46.05 2.45
4369 6097 2.702592 ACTGGTCGTGTTTTTCCTCA 57.297 45.000 0.00 0.00 0.00 3.86
4381 6109 1.127951 GTGACGCCATAAAACTGGTCG 59.872 52.381 0.00 0.00 39.83 4.79
4552 6303 2.202544 GAGTGACTCTGGCTCGCG 60.203 66.667 5.12 0.00 0.00 5.87
4557 6308 2.183046 GGAGCGAGTGACTCTGGC 59.817 66.667 11.26 7.67 45.98 4.85
4558 6309 2.716017 GGGGAGCGAGTGACTCTGG 61.716 68.421 11.26 0.00 34.46 3.86
4559 6310 2.716017 GGGGGAGCGAGTGACTCTG 61.716 68.421 11.26 5.62 34.46 3.35
4560 6311 2.363147 GGGGGAGCGAGTGACTCT 60.363 66.667 11.26 0.00 34.46 3.24
4577 6328 3.679980 CCAACGGTCAGTGAATAAGACTG 59.320 47.826 0.00 0.00 42.79 3.51
4583 6334 0.035820 GGCCCAACGGTCAGTGAATA 60.036 55.000 0.00 0.00 32.15 1.75
4641 6392 4.072088 CGACAACACCGCGCTTCC 62.072 66.667 5.56 0.00 0.00 3.46
4642 6393 4.719616 GCGACAACACCGCGCTTC 62.720 66.667 5.56 0.00 46.53 3.86
4649 6407 3.343421 GACACGGGCGACAACACC 61.343 66.667 0.00 0.00 0.00 4.16
4651 6409 3.834447 CTCGACACGGGCGACAACA 62.834 63.158 0.01 0.00 33.71 3.33
4653 6411 2.537792 GATCTCGACACGGGCGACAA 62.538 60.000 0.01 0.00 33.71 3.18
4659 6417 4.570663 GGCCGATCTCGACACGGG 62.571 72.222 17.58 3.55 45.66 5.28
4661 6419 4.907034 CCGGCCGATCTCGACACG 62.907 72.222 30.73 0.44 43.02 4.49
4679 6437 2.860628 GCGACTCGTGCTAATGGCG 61.861 63.158 0.00 0.00 45.43 5.69
4685 6443 3.428282 TCGCAGCGACTCGTGCTA 61.428 61.111 15.11 9.10 41.72 3.49
4935 6704 4.008933 GCTCGTGGAGGTGGCTGT 62.009 66.667 0.00 0.00 0.00 4.40
5005 6780 2.031157 CACAAAGGAATCCACGAACCAC 60.031 50.000 0.61 0.00 0.00 4.16
5006 6781 2.226330 CACAAAGGAATCCACGAACCA 58.774 47.619 0.61 0.00 0.00 3.67
5007 6782 1.539827 CCACAAAGGAATCCACGAACC 59.460 52.381 0.61 0.00 41.22 3.62
5008 6783 1.068541 GCCACAAAGGAATCCACGAAC 60.069 52.381 0.61 0.00 41.22 3.95
5009 6784 1.243902 GCCACAAAGGAATCCACGAA 58.756 50.000 0.61 0.00 41.22 3.85
5010 6785 2.941210 GCCACAAAGGAATCCACGA 58.059 52.632 0.61 0.00 41.22 4.35


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

AutoCloner maintained by Alex Coulton.