Multiple sequence alignment - TraesCS4A01G198600

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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 TraesCS4A01G198600 chr4A 100.000 3054 0 0 1 3054 484671134 484674187 0.000000e+00 5640.0
1 TraesCS4A01G198600 chr4D 90.821 1961 92 37 519 2437 95290886 95288972 0.000000e+00 2543.0
2 TraesCS4A01G198600 chr4D 94.260 453 13 4 2575 3027 95288960 95288521 0.000000e+00 680.0
3 TraesCS4A01G198600 chr4D 89.391 509 45 6 1 505 95291472 95290969 1.550000e-177 632.0
4 TraesCS4A01G198600 chr4B 89.542 1836 87 33 585 2359 134826114 134824323 0.000000e+00 2230.0
5 TraesCS4A01G198600 chr4B 92.277 505 15 10 2564 3054 134824241 134823747 0.000000e+00 695.0
6 TraesCS4A01G198600 chr4B 89.349 169 16 2 1 168 134853663 134853496 8.580000e-51 211.0
7 TraesCS4A01G198600 chrUn 86.512 215 22 4 1533 1747 67924636 67924843 2.370000e-56 230.0
8 TraesCS4A01G198600 chr1B 100.000 123 0 0 2435 2557 281029228 281029350 8.520000e-56 228.0
9 TraesCS4A01G198600 chr1B 100.000 120 0 0 2435 2554 8056517 8056636 3.960000e-54 222.0
10 TraesCS4A01G198600 chr1B 74.800 250 53 10 193 438 512786732 512786975 1.500000e-18 104.0
11 TraesCS4A01G198600 chr5A 86.385 213 22 4 1533 1745 278299834 278299629 3.060000e-55 226.0
12 TraesCS4A01G198600 chr5A 73.932 468 103 16 7 463 419214726 419214267 1.460000e-38 171.0
13 TraesCS4A01G198600 chr3A 100.000 121 0 0 2435 2555 708679246 708679126 1.100000e-54 224.0
14 TraesCS4A01G198600 chr3A 96.000 125 4 1 2435 2558 175958868 175958744 5.160000e-48 202.0
15 TraesCS4A01G198600 chr3A 72.297 444 100 18 10 440 28895412 28894979 1.920000e-22 117.0
16 TraesCS4A01G198600 chr7A 100.000 120 0 0 2435 2554 392931970 392931851 3.960000e-54 222.0
17 TraesCS4A01G198600 chr7A 73.866 463 97 19 7 455 640371725 640372177 2.440000e-36 163.0
18 TraesCS4A01G198600 chr7A 75.490 204 35 12 1538 1737 475962905 475962713 5.430000e-13 86.1
19 TraesCS4A01G198600 chr6B 100.000 120 0 0 2435 2554 190125430 190125311 3.960000e-54 222.0
20 TraesCS4A01G198600 chr6B 75.732 239 40 14 212 438 720143703 720143471 1.500000e-18 104.0
21 TraesCS4A01G198600 chr5B 100.000 120 0 0 2435 2554 669691385 669691504 3.960000e-54 222.0
22 TraesCS4A01G198600 chr3B 100.000 120 0 0 2435 2554 400377159 400377040 3.960000e-54 222.0
23 TraesCS4A01G198600 chr2B 95.968 124 5 0 2435 2558 793913756 793913633 5.160000e-48 202.0
24 TraesCS4A01G198600 chr1A 74.074 459 102 15 7 455 539709232 539708781 4.050000e-39 172.0
25 TraesCS4A01G198600 chr5D 72.104 423 102 13 28 438 486823532 486823114 2.490000e-21 113.0
26 TraesCS4A01G198600 chr7D 76.471 204 33 13 1538 1737 414087256 414087064 2.510000e-16 97.1
27 TraesCS4A01G198600 chr1D 82.609 115 13 5 347 455 59837061 59837174 9.010000e-16 95.3
28 TraesCS4A01G198600 chr7B 76.111 180 32 8 1560 1737 428483411 428483241 1.950000e-12 84.2


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 TraesCS4A01G198600 chr4A 484671134 484674187 3053 False 5640.0 5640 100.000000 1 3054 1 chr4A.!!$F1 3053
1 TraesCS4A01G198600 chr4D 95288521 95291472 2951 True 1285.0 2543 91.490667 1 3027 3 chr4D.!!$R1 3026
2 TraesCS4A01G198600 chr4B 134823747 134826114 2367 True 1462.5 2230 90.909500 585 3054 2 chr4B.!!$R2 2469

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
315 320 0.179129 GGATTTCACCGCTGCCATTG 60.179 55.000 0.0 0.0 0.00 2.82 F
367 372 1.134250 TGTTTCTGTAGGCTGTGTGCA 60.134 47.619 0.0 0.0 45.15 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1419 0.101219 CGTCATCGTCATCCAGCTCA 59.899 55.0 0.0 0.0 0.0 4.26 R
2145 2281 0.173481 GAAATTCCGGCCTTCCAAGC 59.827 55.0 0.0 0.0 0.0 4.01 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
33 34 0.539986 TAAGGGTGGAATCGTCTGCC 59.460 55.000 0.00 0.00 0.00 4.85
36 37 0.539986 GGGTGGAATCGTCTGCCTTA 59.460 55.000 0.00 0.00 0.00 2.69
40 41 3.808174 GGTGGAATCGTCTGCCTTATTAC 59.192 47.826 0.00 0.00 0.00 1.89
41 42 4.439057 GTGGAATCGTCTGCCTTATTACA 58.561 43.478 0.00 0.00 0.00 2.41
42 43 4.508124 GTGGAATCGTCTGCCTTATTACAG 59.492 45.833 0.00 0.00 35.15 2.74
53 57 2.290641 CCTTATTACAGCCGCATTGTCC 59.709 50.000 0.00 0.00 0.00 4.02
56 60 1.093972 TTACAGCCGCATTGTCCATG 58.906 50.000 0.00 0.00 35.73 3.66
64 68 4.584325 AGCCGCATTGTCCATGTATAAATT 59.416 37.500 0.00 0.00 34.98 1.82
65 69 4.681025 GCCGCATTGTCCATGTATAAATTG 59.319 41.667 0.00 0.00 34.98 2.32
86 90 8.789825 AATTGCATTATTTCTAATGGCAAACA 57.210 26.923 0.00 0.00 42.96 2.83
105 110 2.097466 ACACTTTCTTGTTTGCAGGTCG 59.903 45.455 0.00 0.00 0.00 4.79
110 115 1.748493 TCTTGTTTGCAGGTCGCTTTT 59.252 42.857 0.00 0.00 43.06 2.27
119 124 1.862201 CAGGTCGCTTTTCGTTGTACA 59.138 47.619 0.00 0.00 39.67 2.90
166 171 4.465632 TGCATCGAACATAGTACCAACT 57.534 40.909 0.00 0.00 39.91 3.16
177 182 6.765403 ACATAGTACCAACTGTTGCTTAAGA 58.235 36.000 14.94 0.00 36.36 2.10
184 189 1.806542 ACTGTTGCTTAAGATGGTGCG 59.193 47.619 6.67 0.00 0.00 5.34
189 194 1.202817 TGCTTAAGATGGTGCGTACGA 59.797 47.619 21.65 0.80 0.00 3.43
193 198 2.450609 AAGATGGTGCGTACGAGTTT 57.549 45.000 21.65 0.00 0.00 2.66
196 201 0.319083 ATGGTGCGTACGAGTTTGGA 59.681 50.000 21.65 0.00 0.00 3.53
200 205 1.180456 TGCGTACGAGTTTGGAGGGA 61.180 55.000 21.65 0.00 0.00 4.20
203 208 1.264295 GTACGAGTTTGGAGGGAGGT 58.736 55.000 0.00 0.00 0.00 3.85
204 209 1.067071 GTACGAGTTTGGAGGGAGGTG 60.067 57.143 0.00 0.00 0.00 4.00
205 210 1.296715 CGAGTTTGGAGGGAGGTGG 59.703 63.158 0.00 0.00 0.00 4.61
206 211 1.481056 CGAGTTTGGAGGGAGGTGGT 61.481 60.000 0.00 0.00 0.00 4.16
209 214 0.250770 GTTTGGAGGGAGGTGGTCAC 60.251 60.000 0.00 0.00 0.00 3.67
226 231 2.291465 GTCACGGAGGTTTTTACCCAAC 59.709 50.000 0.00 0.00 0.00 3.77
233 238 6.947158 ACGGAGGTTTTTACCCAACATTAATA 59.053 34.615 0.00 0.00 0.00 0.98
238 243 8.092068 AGGTTTTTACCCAACATTAATAGCAAC 58.908 33.333 0.00 0.00 0.00 4.17
247 252 8.199449 CCCAACATTAATAGCAACATGATCTTT 58.801 33.333 0.00 0.00 0.00 2.52
260 265 6.319048 ACATGATCTTTAGATTGGTCCACT 57.681 37.500 0.00 0.00 34.37 4.00
266 271 5.805728 TCTTTAGATTGGTCCACTTTCTCC 58.194 41.667 0.00 0.00 0.00 3.71
268 273 6.729100 TCTTTAGATTGGTCCACTTTCTCCTA 59.271 38.462 0.00 0.00 0.00 2.94
272 277 5.669447 AGATTGGTCCACTTTCTCCTATGAT 59.331 40.000 0.00 0.00 0.00 2.45
287 292 9.521841 TTCTCCTATGATATAGACTTAGTGTGG 57.478 37.037 0.00 0.00 0.00 4.17
299 304 3.311402 ACTTAGTGTGGGTCCCATAGGAT 60.311 47.826 15.49 3.05 46.41 3.24
305 310 1.850345 TGGGTCCCATAGGATTTCACC 59.150 52.381 6.47 0.00 46.41 4.02
315 320 0.179129 GGATTTCACCGCTGCCATTG 60.179 55.000 0.00 0.00 0.00 2.82
321 326 3.049674 CCGCTGCCATTGTGTCGT 61.050 61.111 0.00 0.00 0.00 4.34
327 332 2.031683 GCTGCCATTGTGTCGTTATACC 59.968 50.000 0.00 0.00 0.00 2.73
364 369 3.560636 ACTTGTTTCTGTAGGCTGTGT 57.439 42.857 0.00 0.00 0.00 3.72
366 371 1.593196 TGTTTCTGTAGGCTGTGTGC 58.407 50.000 0.00 0.00 41.94 4.57
367 372 1.134250 TGTTTCTGTAGGCTGTGTGCA 60.134 47.619 0.00 0.00 45.15 4.57
375 380 3.134623 TGTAGGCTGTGTGCATAGCTATT 59.865 43.478 17.85 8.78 43.83 1.73
388 393 2.310779 AGCTATTCAGAGGCCGGATA 57.689 50.000 5.05 0.00 0.00 2.59
409 414 7.041721 GGATATCGCTTCATATGTATGTTCCA 58.958 38.462 1.90 0.00 35.26 3.53
459 464 7.429636 AAAGCATCATTTGTTGAAAAGATGG 57.570 32.000 12.25 0.00 43.13 3.51
465 470 7.014092 TCATTTGTTGAAAAGATGGTTTTGC 57.986 32.000 0.00 0.00 0.00 3.68
507 512 9.838339 ATGTAGGTATAGGATAAAATGCTATGC 57.162 33.333 10.22 8.88 42.78 3.14
509 514 9.892130 GTAGGTATAGGATAAAATGCTATGCTT 57.108 33.333 13.31 9.93 42.78 3.91
510 515 8.798859 AGGTATAGGATAAAATGCTATGCTTG 57.201 34.615 13.31 0.00 42.78 4.01
513 518 9.231297 GTATAGGATAAAATGCTATGCTTGGAA 57.769 33.333 10.22 0.00 42.78 3.53
514 519 6.645790 AGGATAAAATGCTATGCTTGGAAG 57.354 37.500 0.00 0.00 0.00 3.46
515 520 6.131961 AGGATAAAATGCTATGCTTGGAAGT 58.868 36.000 0.00 0.00 0.00 3.01
528 602 3.130340 GCTTGGAAGTTTGAAACAGTCCA 59.870 43.478 22.12 22.12 42.57 4.02
529 603 4.202151 GCTTGGAAGTTTGAAACAGTCCAT 60.202 41.667 24.79 0.00 43.25 3.41
540 614 8.999431 GTTTGAAACAGTCCATTAGTCTTGATA 58.001 33.333 2.68 0.00 0.00 2.15
543 617 7.180229 TGAAACAGTCCATTAGTCTTGATAGGA 59.820 37.037 0.00 0.00 0.00 2.94
588 662 4.676196 GCCTACGAACTCCTACGAAATTCA 60.676 45.833 0.00 0.00 0.00 2.57
605 679 6.147492 CGAAATTCATCAATTCAAAAGGCCAA 59.853 34.615 5.01 0.00 30.37 4.52
609 683 5.786311 TCATCAATTCAAAAGGCCAAAGAG 58.214 37.500 5.01 0.00 0.00 2.85
610 684 4.605640 TCAATTCAAAAGGCCAAAGAGG 57.394 40.909 5.01 0.00 41.84 3.69
680 754 5.567423 GCGTAACCACCGGTAGGATAAATAT 60.567 44.000 24.32 3.00 41.02 1.28
685 762 6.772605 ACCACCGGTAGGATAAATATAAACC 58.227 40.000 24.32 0.00 41.02 3.27
877 965 4.836825 TCTCTTAATTGCAGCAGCTACTT 58.163 39.130 1.76 0.00 42.74 2.24
890 978 1.477295 AGCTACTTTCTACCTCACGCC 59.523 52.381 0.00 0.00 0.00 5.68
1005 1116 2.119391 TGTGGGGTTCCAATGGGC 59.881 61.111 0.00 0.00 46.04 5.36
1251 1362 2.428544 ACCAGCTCGACTACATCTCT 57.571 50.000 0.00 0.00 0.00 3.10
1289 1400 2.254737 GACGACGAGGAGGAGGAGGA 62.255 65.000 0.00 0.00 0.00 3.71
1290 1401 1.525077 CGACGAGGAGGAGGAGGAG 60.525 68.421 0.00 0.00 0.00 3.69
1291 1402 1.152839 GACGAGGAGGAGGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1292 1403 1.619975 ACGAGGAGGAGGAGGAGGA 60.620 63.158 0.00 0.00 0.00 3.71
1293 1404 1.150536 CGAGGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1294 1405 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1326 1437 2.200067 CTTGAGCTGGATGACGATGAC 58.800 52.381 0.00 0.00 0.00 3.06
1362 1473 4.477975 GCGTCGGAGGAGTGGTCG 62.478 72.222 1.18 0.00 0.00 4.79
1663 1777 2.441051 AGGAGCTCCTCGTGTGGA 59.559 61.111 30.40 0.00 44.77 4.02
1768 1882 2.995872 GCTGGCGTCGTCCTCTTCT 61.996 63.158 0.00 0.00 0.00 2.85
1926 2040 3.774528 AGAGGAGCAATGCGGCGA 61.775 61.111 12.98 0.00 39.27 5.54
1927 2041 2.590007 GAGGAGCAATGCGGCGAT 60.590 61.111 12.98 0.00 39.27 4.58
2023 2155 2.022129 CGACAAGGCAGGTGACGAC 61.022 63.158 0.00 0.00 36.48 4.34
2024 2156 2.022129 GACAAGGCAGGTGACGACG 61.022 63.158 0.00 0.00 0.00 5.12
2025 2157 2.338620 CAAGGCAGGTGACGACGA 59.661 61.111 0.00 0.00 0.00 4.20
2037 2169 2.784380 GTGACGACGATCTTAGCATCAC 59.216 50.000 0.00 0.00 0.00 3.06
2038 2170 2.223502 TGACGACGATCTTAGCATCACC 60.224 50.000 0.00 0.00 0.00 4.02
2041 2173 2.033424 CGACGATCTTAGCATCACCAGA 59.967 50.000 0.00 0.00 0.00 3.86
2050 2182 1.171308 GCATCACCAGAAGTGCACAT 58.829 50.000 21.04 7.05 46.81 3.21
2067 2199 4.695455 TGCACATTAGCTTCTTGGTTAGTC 59.305 41.667 0.00 0.00 34.99 2.59
2079 2211 2.410785 GGTTAGTCAACCGGCAAAAC 57.589 50.000 0.00 0.00 44.74 2.43
2100 2232 5.494632 ACGTCATCGGTTTTCTTTTCTTT 57.505 34.783 0.00 0.00 41.85 2.52
2114 2246 8.438676 TTTCTTTTCTTTGAGATCTCGAAAGT 57.561 30.769 27.94 0.00 32.96 2.66
2115 2247 8.438676 TTCTTTTCTTTGAGATCTCGAAAGTT 57.561 30.769 27.94 0.00 32.96 2.66
2145 2281 1.714899 CCTGTTTGATTAGCGGCCCG 61.715 60.000 0.00 0.00 0.00 6.13
2165 2301 1.544724 CTTGGAAGGCCGGAATTTCA 58.455 50.000 5.05 0.00 36.79 2.69
2185 2321 2.949447 ACAAGAATTTGTGCTCCCTGT 58.051 42.857 0.00 0.00 45.54 4.00
2186 2322 3.299503 ACAAGAATTTGTGCTCCCTGTT 58.700 40.909 0.00 0.00 45.54 3.16
2187 2323 3.706086 ACAAGAATTTGTGCTCCCTGTTT 59.294 39.130 0.00 0.00 45.54 2.83
2188 2324 4.162131 ACAAGAATTTGTGCTCCCTGTTTT 59.838 37.500 0.00 0.00 45.54 2.43
2219 2355 2.902484 CTCGTGAAATTTTCGCTTTCCG 59.098 45.455 17.86 5.07 38.02 4.30
2239 2375 4.945292 CGAACAATCGCAACAAAATTCA 57.055 36.364 0.00 0.00 42.96 2.57
2240 2376 5.499268 CGAACAATCGCAACAAAATTCAT 57.501 34.783 0.00 0.00 42.96 2.57
2241 2377 5.299622 CGAACAATCGCAACAAAATTCATG 58.700 37.500 0.00 0.00 42.96 3.07
2242 2378 5.116831 CGAACAATCGCAACAAAATTCATGA 59.883 36.000 0.00 0.00 42.96 3.07
2243 2379 6.183360 CGAACAATCGCAACAAAATTCATGAT 60.183 34.615 0.00 0.00 42.96 2.45
2247 2383 8.597227 ACAATCGCAACAAAATTCATGATAATG 58.403 29.630 0.00 0.00 0.00 1.90
2249 2385 6.331845 TCGCAACAAAATTCATGATAATGCT 58.668 32.000 0.00 0.00 0.00 3.79
2252 2388 6.685403 GCAACAAAATTCATGATAATGCTTGC 59.315 34.615 0.00 3.26 0.00 4.01
2255 2391 7.970384 ACAAAATTCATGATAATGCTTGCTTG 58.030 30.769 0.00 0.00 0.00 4.01
2264 2400 6.457355 TGATAATGCTTGCTTGTTTGTTCAT 58.543 32.000 0.00 0.00 0.00 2.57
2329 2469 8.899771 CGGAGTATTTACAAATATTTTGGAGGT 58.100 33.333 0.00 0.00 33.79 3.85
2356 2496 4.073201 GAGCCTGGAGGGATCCAA 57.927 61.111 15.23 0.00 44.19 3.53
2359 2499 0.625683 AGCCTGGAGGGATCCAATGT 60.626 55.000 15.23 0.00 39.61 2.71
2360 2500 1.140312 GCCTGGAGGGATCCAATGTA 58.860 55.000 15.23 0.00 39.61 2.29
2361 2501 1.202818 GCCTGGAGGGATCCAATGTAC 60.203 57.143 15.23 0.00 39.61 2.90
2362 2502 2.126882 CCTGGAGGGATCCAATGTACA 58.873 52.381 15.23 0.00 39.61 2.90
2363 2503 2.105477 CCTGGAGGGATCCAATGTACAG 59.895 54.545 15.23 10.59 39.61 2.74
2364 2504 2.774234 CTGGAGGGATCCAATGTACAGT 59.226 50.000 15.23 0.00 39.61 3.55
2366 2506 4.566837 TGGAGGGATCCAATGTACAGTAT 58.433 43.478 15.23 0.00 36.74 2.12
2367 2507 4.347876 TGGAGGGATCCAATGTACAGTATG 59.652 45.833 15.23 0.37 38.55 2.39
2368 2508 4.593206 GGAGGGATCCAATGTACAGTATGA 59.407 45.833 15.23 0.00 39.69 2.15
2370 2510 4.039245 AGGGATCCAATGTACAGTATGACG 59.961 45.833 15.23 0.00 39.69 4.35
2371 2511 3.741344 GGATCCAATGTACAGTATGACGC 59.259 47.826 6.95 0.00 39.69 5.19
2373 2513 4.400529 TCCAATGTACAGTATGACGCAT 57.599 40.909 0.33 0.00 39.69 4.73
2386 2535 2.888594 TGACGCATTAGTTGTAGGCTC 58.111 47.619 0.00 0.00 0.00 4.70
2390 2539 2.101582 CGCATTAGTTGTAGGCTCCTCT 59.898 50.000 0.00 0.00 0.00 3.69
2437 2587 5.411361 TCAATACTGTCGCAAGCTTAAACAT 59.589 36.000 0.00 0.00 37.18 2.71
2438 2588 6.592220 TCAATACTGTCGCAAGCTTAAACATA 59.408 34.615 0.00 0.44 37.18 2.29
2439 2589 4.663636 ACTGTCGCAAGCTTAAACATAC 57.336 40.909 0.00 0.00 37.18 2.39
2440 2590 3.122948 ACTGTCGCAAGCTTAAACATACG 59.877 43.478 0.00 0.00 37.18 3.06
2441 2591 3.318886 TGTCGCAAGCTTAAACATACGA 58.681 40.909 0.00 0.00 37.18 3.43
2442 2592 3.741856 TGTCGCAAGCTTAAACATACGAA 59.258 39.130 0.00 0.00 37.18 3.85
2443 2593 4.390603 TGTCGCAAGCTTAAACATACGAAT 59.609 37.500 0.00 0.00 37.18 3.34
2444 2594 5.106869 TGTCGCAAGCTTAAACATACGAATT 60.107 36.000 0.00 0.00 37.18 2.17
2445 2595 5.793457 GTCGCAAGCTTAAACATACGAATTT 59.207 36.000 0.00 0.00 37.18 1.82
2446 2596 5.792962 TCGCAAGCTTAAACATACGAATTTG 59.207 36.000 0.00 0.00 37.18 2.32
2447 2597 5.792962 CGCAAGCTTAAACATACGAATTTGA 59.207 36.000 0.00 0.00 0.00 2.69
2448 2598 6.236941 CGCAAGCTTAAACATACGAATTTGAC 60.237 38.462 0.00 0.00 0.00 3.18
2449 2599 6.580791 GCAAGCTTAAACATACGAATTTGACA 59.419 34.615 0.00 0.00 0.00 3.58
2450 2600 7.114247 GCAAGCTTAAACATACGAATTTGACAA 59.886 33.333 0.00 0.00 0.00 3.18
2451 2601 9.128107 CAAGCTTAAACATACGAATTTGACAAT 57.872 29.630 0.00 0.00 0.00 2.71
2452 2602 8.673626 AGCTTAAACATACGAATTTGACAATG 57.326 30.769 0.00 3.27 0.00 2.82
2453 2603 8.296713 AGCTTAAACATACGAATTTGACAATGT 58.703 29.630 0.00 3.85 0.00 2.71
2454 2604 9.549509 GCTTAAACATACGAATTTGACAATGTA 57.450 29.630 0.00 0.00 0.00 2.29
2458 2608 9.959749 AAACATACGAATTTGACAATGTACTTT 57.040 25.926 0.00 0.00 0.00 2.66
2459 2609 8.948853 ACATACGAATTTGACAATGTACTTTG 57.051 30.769 17.42 17.42 0.00 2.77
2460 2610 8.564574 ACATACGAATTTGACAATGTACTTTGT 58.435 29.630 22.93 22.93 42.37 2.83
2461 2611 8.839914 CATACGAATTTGACAATGTACTTTGTG 58.160 33.333 26.50 14.97 39.85 3.33
2462 2612 6.791303 ACGAATTTGACAATGTACTTTGTGT 58.209 32.000 26.50 15.49 39.85 3.72
2463 2613 7.921787 ACGAATTTGACAATGTACTTTGTGTA 58.078 30.769 26.50 15.00 39.85 2.90
2464 2614 8.399425 ACGAATTTGACAATGTACTTTGTGTAA 58.601 29.630 26.50 19.84 39.85 2.41
2465 2615 8.891928 CGAATTTGACAATGTACTTTGTGTAAG 58.108 33.333 26.50 10.87 39.85 2.34
2468 2618 8.903570 TTTGACAATGTACTTTGTGTAAGTTG 57.096 30.769 26.50 1.58 44.73 3.16
2469 2619 6.491394 TGACAATGTACTTTGTGTAAGTTGC 58.509 36.000 26.50 12.99 44.73 4.17
2470 2620 6.094186 TGACAATGTACTTTGTGTAAGTTGCA 59.906 34.615 26.50 14.96 44.73 4.08
2471 2621 7.038154 ACAATGTACTTTGTGTAAGTTGCAT 57.962 32.000 22.31 0.00 44.73 3.96
2472 2622 6.917477 ACAATGTACTTTGTGTAAGTTGCATG 59.083 34.615 22.31 0.00 44.73 4.06
2473 2623 6.633500 ATGTACTTTGTGTAAGTTGCATGT 57.367 33.333 0.00 0.00 44.73 3.21
2474 2624 6.055231 TGTACTTTGTGTAAGTTGCATGTC 57.945 37.500 0.00 0.00 44.73 3.06
2475 2625 5.586643 TGTACTTTGTGTAAGTTGCATGTCA 59.413 36.000 0.00 0.00 44.73 3.58
2476 2626 5.772825 ACTTTGTGTAAGTTGCATGTCAT 57.227 34.783 0.00 0.00 44.73 3.06
2477 2627 6.875948 ACTTTGTGTAAGTTGCATGTCATA 57.124 33.333 0.00 0.00 44.73 2.15
2478 2628 7.452880 ACTTTGTGTAAGTTGCATGTCATAT 57.547 32.000 0.00 0.00 44.73 1.78
2479 2629 8.560355 ACTTTGTGTAAGTTGCATGTCATATA 57.440 30.769 0.00 0.00 44.73 0.86
2480 2630 9.177608 ACTTTGTGTAAGTTGCATGTCATATAT 57.822 29.630 0.00 0.00 44.73 0.86
2489 2639 8.859236 AGTTGCATGTCATATATTATTGCTCT 57.141 30.769 0.00 0.00 0.00 4.09
2490 2640 9.948964 AGTTGCATGTCATATATTATTGCTCTA 57.051 29.630 0.00 0.00 0.00 2.43
2505 2655 9.971922 ATTATTGCTCTAATATTTGGTCAAAGC 57.028 29.630 0.00 0.00 33.32 3.51
2506 2656 7.651027 ATTGCTCTAATATTTGGTCAAAGCT 57.349 32.000 0.00 0.00 33.32 3.74
2507 2657 8.752005 ATTGCTCTAATATTTGGTCAAAGCTA 57.248 30.769 0.00 0.00 33.32 3.32
2508 2658 7.792374 TGCTCTAATATTTGGTCAAAGCTAG 57.208 36.000 0.00 0.00 33.32 3.42
2509 2659 6.260936 TGCTCTAATATTTGGTCAAAGCTAGC 59.739 38.462 6.62 6.62 33.32 3.42
2510 2660 6.293680 GCTCTAATATTTGGTCAAAGCTAGCC 60.294 42.308 12.13 0.00 33.32 3.93
2511 2661 6.900194 TCTAATATTTGGTCAAAGCTAGCCT 58.100 36.000 12.13 0.00 33.32 4.58
2512 2662 7.346471 TCTAATATTTGGTCAAAGCTAGCCTT 58.654 34.615 12.13 0.71 33.32 4.35
2513 2663 5.841957 ATATTTGGTCAAAGCTAGCCTTG 57.158 39.130 18.30 18.30 33.01 3.61
2514 2664 2.949177 TTGGTCAAAGCTAGCCTTGA 57.051 45.000 22.11 22.11 33.01 3.02
2515 2665 2.949177 TGGTCAAAGCTAGCCTTGAA 57.051 45.000 26.34 12.38 33.01 2.69
2516 2666 3.222173 TGGTCAAAGCTAGCCTTGAAA 57.778 42.857 26.34 16.68 33.01 2.69
2517 2667 3.561143 TGGTCAAAGCTAGCCTTGAAAA 58.439 40.909 26.34 16.37 33.01 2.29
2518 2668 3.957497 TGGTCAAAGCTAGCCTTGAAAAA 59.043 39.130 26.34 14.22 33.01 1.94
2519 2669 4.202111 TGGTCAAAGCTAGCCTTGAAAAAC 60.202 41.667 26.34 16.08 33.01 2.43
2520 2670 3.975035 GTCAAAGCTAGCCTTGAAAAACG 59.025 43.478 26.34 1.13 33.01 3.60
2521 2671 3.630312 TCAAAGCTAGCCTTGAAAAACGT 59.370 39.130 23.37 0.00 33.01 3.99
2522 2672 4.817464 TCAAAGCTAGCCTTGAAAAACGTA 59.183 37.500 23.37 1.52 33.01 3.57
2523 2673 5.472137 TCAAAGCTAGCCTTGAAAAACGTAT 59.528 36.000 23.37 0.00 33.01 3.06
2524 2674 5.959618 AAGCTAGCCTTGAAAAACGTATT 57.040 34.783 12.13 0.00 30.99 1.89
2525 2675 7.173562 TCAAAGCTAGCCTTGAAAAACGTATTA 59.826 33.333 23.37 0.00 33.01 0.98
2526 2676 6.663944 AGCTAGCCTTGAAAAACGTATTAG 57.336 37.500 12.13 0.00 0.00 1.73
2527 2677 5.585047 AGCTAGCCTTGAAAAACGTATTAGG 59.415 40.000 12.13 0.00 0.00 2.69
2528 2678 4.696899 AGCCTTGAAAAACGTATTAGGC 57.303 40.909 15.18 15.18 45.38 3.93
2529 2679 3.442625 AGCCTTGAAAAACGTATTAGGCC 59.557 43.478 17.66 0.00 46.01 5.19
2530 2680 3.428452 GCCTTGAAAAACGTATTAGGCCC 60.428 47.826 13.21 0.00 40.55 5.80
2531 2681 4.014406 CCTTGAAAAACGTATTAGGCCCT 58.986 43.478 0.00 0.00 0.00 5.19
2532 2682 5.187687 CCTTGAAAAACGTATTAGGCCCTA 58.812 41.667 0.00 0.00 0.00 3.53
2533 2683 5.826208 CCTTGAAAAACGTATTAGGCCCTAT 59.174 40.000 0.00 0.00 0.00 2.57
2534 2684 6.993902 CCTTGAAAAACGTATTAGGCCCTATA 59.006 38.462 0.00 0.00 0.00 1.31
2535 2685 7.664318 CCTTGAAAAACGTATTAGGCCCTATAT 59.336 37.037 0.00 0.00 0.00 0.86
2536 2686 9.715121 CTTGAAAAACGTATTAGGCCCTATATA 57.285 33.333 0.00 0.00 0.00 0.86
2537 2687 9.715121 TTGAAAAACGTATTAGGCCCTATATAG 57.285 33.333 0.00 2.46 0.00 1.31
2538 2688 9.092338 TGAAAAACGTATTAGGCCCTATATAGA 57.908 33.333 11.53 0.00 0.00 1.98
2540 2690 9.886132 AAAAACGTATTAGGCCCTATATAGATG 57.114 33.333 11.53 3.39 0.00 2.90
2541 2691 7.598759 AACGTATTAGGCCCTATATAGATGG 57.401 40.000 11.53 6.04 0.00 3.51
2542 2692 6.919158 ACGTATTAGGCCCTATATAGATGGA 58.081 40.000 11.53 0.00 0.00 3.41
2543 2693 7.359849 ACGTATTAGGCCCTATATAGATGGAA 58.640 38.462 11.53 0.00 0.00 3.53
2544 2694 7.506261 ACGTATTAGGCCCTATATAGATGGAAG 59.494 40.741 11.53 0.00 0.00 3.46
2545 2695 7.039644 CGTATTAGGCCCTATATAGATGGAAGG 60.040 44.444 11.53 3.94 0.00 3.46
2546 2696 4.994411 AGGCCCTATATAGATGGAAGGA 57.006 45.455 11.53 0.00 0.00 3.36
2547 2697 4.889780 AGGCCCTATATAGATGGAAGGAG 58.110 47.826 11.53 0.00 0.00 3.69
2548 2698 3.970640 GGCCCTATATAGATGGAAGGAGG 59.029 52.174 11.53 1.87 0.00 4.30
2549 2699 3.970640 GCCCTATATAGATGGAAGGAGGG 59.029 52.174 11.53 3.52 44.52 4.30
2550 2700 4.327010 GCCCTATATAGATGGAAGGAGGGA 60.327 50.000 11.53 0.00 44.48 4.20
2551 2701 5.463154 CCCTATATAGATGGAAGGAGGGAG 58.537 50.000 11.53 0.00 44.48 4.30
2552 2702 5.042979 CCCTATATAGATGGAAGGAGGGAGT 60.043 48.000 11.53 0.00 44.48 3.85
2553 2703 6.162420 CCCTATATAGATGGAAGGAGGGAGTA 59.838 46.154 11.53 0.00 44.48 2.59
2554 2704 7.064229 CCTATATAGATGGAAGGAGGGAGTAC 58.936 46.154 11.53 0.00 0.00 2.73
2555 2705 4.834406 ATAGATGGAAGGAGGGAGTACA 57.166 45.455 0.00 0.00 0.00 2.90
2556 2706 3.715648 AGATGGAAGGAGGGAGTACAT 57.284 47.619 0.00 0.00 0.00 2.29
2557 2707 4.014273 AGATGGAAGGAGGGAGTACATT 57.986 45.455 0.00 0.00 0.00 2.71
2558 2708 3.970640 AGATGGAAGGAGGGAGTACATTC 59.029 47.826 0.00 0.00 0.00 2.67
2559 2709 3.199442 TGGAAGGAGGGAGTACATTCA 57.801 47.619 0.00 0.00 0.00 2.57
2560 2710 3.736094 TGGAAGGAGGGAGTACATTCAT 58.264 45.455 0.00 0.00 0.00 2.57
2561 2711 4.111577 TGGAAGGAGGGAGTACATTCATT 58.888 43.478 0.00 0.00 0.00 2.57
2562 2712 4.164221 TGGAAGGAGGGAGTACATTCATTC 59.836 45.833 0.00 0.74 31.61 2.67
2573 2723 7.309012 GGGAGTACATTCATTCATTCATCCATG 60.309 40.741 0.00 0.00 0.00 3.66
2595 2746 4.571984 TGATCCATCAATTACTGCGAGTTG 59.428 41.667 0.00 0.00 33.08 3.16
2723 2879 5.848036 GTCGATGCACAGACATATTTAATGC 59.152 40.000 15.92 0.00 37.34 3.56
2815 2971 1.066358 GGCAGTAGGACTAACCACCAC 60.066 57.143 0.00 0.00 42.04 4.16
2816 2972 1.900486 GCAGTAGGACTAACCACCACT 59.100 52.381 0.00 0.00 42.04 4.00
2817 2973 2.353803 GCAGTAGGACTAACCACCACTG 60.354 54.545 0.00 0.00 42.63 3.66
2848 3004 2.852413 CGTGGTGATGTGATTAGACGAC 59.148 50.000 0.00 0.00 0.00 4.34
2849 3005 2.852413 GTGGTGATGTGATTAGACGACG 59.148 50.000 0.00 0.00 0.00 5.12
2850 3006 2.750712 TGGTGATGTGATTAGACGACGA 59.249 45.455 0.00 0.00 0.00 4.20
2871 3027 5.088739 CGAAGTACGTGTACCTAATTTCGT 58.911 41.667 16.71 0.00 35.69 3.85
2879 3035 5.164022 CGTGTACCTAATTTCGTTGTTCTCC 60.164 44.000 0.00 0.00 0.00 3.71
2880 3036 4.925054 TGTACCTAATTTCGTTGTTCTCCG 59.075 41.667 0.00 0.00 0.00 4.63
2881 3037 3.999046 ACCTAATTTCGTTGTTCTCCGT 58.001 40.909 0.00 0.00 0.00 4.69
2882 3038 3.992427 ACCTAATTTCGTTGTTCTCCGTC 59.008 43.478 0.00 0.00 0.00 4.79
2885 3041 1.860676 TTTCGTTGTTCTCCGTCTGG 58.139 50.000 0.00 0.00 0.00 3.86
3042 3209 1.620739 ATGACTGATCGCACAGGGCT 61.621 55.000 11.91 0.00 41.59 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.057734 GACGATTCCACCCTTATAAGCG 58.942 50.000 6.99 1.01 36.84 4.68
12 13 2.367567 GGCAGACGATTCCACCCTTATA 59.632 50.000 0.00 0.00 0.00 0.98
23 24 3.467803 GGCTGTAATAAGGCAGACGATT 58.532 45.455 0.00 0.00 42.15 3.34
25 26 2.596904 GGCTGTAATAAGGCAGACGA 57.403 50.000 0.00 0.00 42.15 4.20
33 34 2.942376 TGGACAATGCGGCTGTAATAAG 59.058 45.455 0.00 0.00 0.00 1.73
36 37 1.677576 CATGGACAATGCGGCTGTAAT 59.322 47.619 0.00 0.00 0.00 1.89
40 41 1.311859 ATACATGGACAATGCGGCTG 58.688 50.000 0.00 0.00 40.22 4.85
41 42 2.928801 TATACATGGACAATGCGGCT 57.071 45.000 0.00 0.00 40.22 5.52
42 43 3.980646 TTTATACATGGACAATGCGGC 57.019 42.857 0.00 0.00 40.22 6.53
64 68 6.934056 AGTGTTTGCCATTAGAAATAATGCA 58.066 32.000 0.00 0.00 36.41 3.96
65 69 7.832503 AAGTGTTTGCCATTAGAAATAATGC 57.167 32.000 3.04 0.85 36.41 3.56
86 90 1.065551 GCGACCTGCAAACAAGAAAGT 59.934 47.619 0.00 0.00 45.45 2.66
105 110 3.805971 AGTAGGTGTGTACAACGAAAAGC 59.194 43.478 0.00 0.00 38.92 3.51
110 115 4.389890 ACAAAGTAGGTGTGTACAACGA 57.610 40.909 0.00 0.00 38.92 3.85
119 124 6.376299 TCGTAGATCACATACAAAGTAGGTGT 59.624 38.462 17.87 8.56 31.91 4.16
151 156 5.941948 AAGCAACAGTTGGTACTATGTTC 57.058 39.130 18.21 0.00 41.14 3.18
166 171 1.890876 ACGCACCATCTTAAGCAACA 58.109 45.000 0.00 0.00 0.00 3.33
177 182 0.319083 TCCAAACTCGTACGCACCAT 59.681 50.000 11.24 0.00 0.00 3.55
184 189 1.067071 CACCTCCCTCCAAACTCGTAC 60.067 57.143 0.00 0.00 0.00 3.67
189 194 0.401395 TGACCACCTCCCTCCAAACT 60.401 55.000 0.00 0.00 0.00 2.66
193 198 2.603473 CGTGACCACCTCCCTCCA 60.603 66.667 0.00 0.00 0.00 3.86
196 201 2.283966 CTCCGTGACCACCTCCCT 60.284 66.667 0.00 0.00 0.00 4.20
200 205 0.549469 AAAAACCTCCGTGACCACCT 59.451 50.000 0.00 0.00 0.00 4.00
203 208 1.202794 GGGTAAAAACCTCCGTGACCA 60.203 52.381 0.00 0.00 0.00 4.02
204 209 1.202794 TGGGTAAAAACCTCCGTGACC 60.203 52.381 0.00 0.00 0.00 4.02
205 210 2.259266 TGGGTAAAAACCTCCGTGAC 57.741 50.000 0.00 0.00 0.00 3.67
206 211 2.092538 TGTTGGGTAAAAACCTCCGTGA 60.093 45.455 0.00 0.00 0.00 4.35
209 214 5.708877 TTAATGTTGGGTAAAAACCTCCG 57.291 39.130 0.00 0.00 0.00 4.63
233 238 5.591877 GGACCAATCTAAAGATCATGTTGCT 59.408 40.000 0.00 0.00 32.75 3.91
238 243 7.555554 AGAAAGTGGACCAATCTAAAGATCATG 59.444 37.037 0.00 0.00 32.75 3.07
247 252 6.202331 TCATAGGAGAAAGTGGACCAATCTA 58.798 40.000 0.00 0.00 0.00 1.98
266 271 7.122948 GGGACCCACACTAAGTCTATATCATAG 59.877 44.444 5.33 0.00 0.00 2.23
268 273 5.780793 GGGACCCACACTAAGTCTATATCAT 59.219 44.000 5.33 0.00 0.00 2.45
272 277 4.613265 TGGGACCCACACTAAGTCTATA 57.387 45.455 9.95 0.00 0.00 1.31
286 291 1.202770 CGGTGAAATCCTATGGGACCC 60.203 57.143 2.45 2.45 45.43 4.46
287 292 1.814248 GCGGTGAAATCCTATGGGACC 60.814 57.143 0.00 0.00 45.43 4.46
299 304 1.106351 ACACAATGGCAGCGGTGAAA 61.106 50.000 20.69 5.35 35.33 2.69
305 310 0.726827 ATAACGACACAATGGCAGCG 59.273 50.000 0.00 0.00 0.00 5.18
364 369 1.001293 CGGCCTCTGAATAGCTATGCA 59.999 52.381 13.99 13.99 0.00 3.96
366 371 1.895798 TCCGGCCTCTGAATAGCTATG 59.104 52.381 7.09 0.00 0.00 2.23
367 372 2.310779 TCCGGCCTCTGAATAGCTAT 57.689 50.000 0.00 0.00 0.00 2.97
375 380 0.827925 AAGCGATATCCGGCCTCTGA 60.828 55.000 0.00 0.00 39.04 3.27
388 393 5.858381 AGTGGAACATACATATGAAGCGAT 58.142 37.500 10.38 0.00 44.52 4.58
440 445 7.282675 TGCAAAACCATCTTTTCAACAAATGAT 59.717 29.630 0.00 0.00 38.03 2.45
443 448 6.998968 TGCAAAACCATCTTTTCAACAAAT 57.001 29.167 0.00 0.00 0.00 2.32
493 498 7.975616 TCAAACTTCCAAGCATAGCATTTTATC 59.024 33.333 0.00 0.00 0.00 1.75
505 510 3.130340 GGACTGTTTCAAACTTCCAAGCA 59.870 43.478 13.81 0.00 35.54 3.91
507 512 4.981806 TGGACTGTTTCAAACTTCCAAG 57.018 40.909 17.41 3.06 39.65 3.61
509 514 6.126409 ACTAATGGACTGTTTCAAACTTCCA 58.874 36.000 20.38 20.38 43.63 3.53
510 515 6.486993 AGACTAATGGACTGTTTCAAACTTCC 59.513 38.462 12.41 12.41 35.83 3.46
513 518 7.054124 TCAAGACTAATGGACTGTTTCAAACT 58.946 34.615 1.10 0.00 0.00 2.66
514 519 7.259290 TCAAGACTAATGGACTGTTTCAAAC 57.741 36.000 0.00 0.00 0.00 2.93
515 520 9.219603 CTATCAAGACTAATGGACTGTTTCAAA 57.780 33.333 0.00 0.00 0.00 2.69
554 628 5.699915 AGGAGTTCGTAGGCTTTTAGTTTTC 59.300 40.000 0.00 0.00 0.00 2.29
570 644 6.589830 ATTGATGAATTTCGTAGGAGTTCG 57.410 37.500 0.00 0.00 0.00 3.95
588 662 4.594491 ACCTCTTTGGCCTTTTGAATTGAT 59.406 37.500 3.32 0.00 40.22 2.57
621 695 4.009002 CCCAATTTGGAATGCGGATTTTT 58.991 39.130 17.24 0.00 40.96 1.94
625 699 2.157640 TCCCAATTTGGAATGCGGAT 57.842 45.000 17.24 0.00 40.96 4.18
680 754 1.203994 GTGTCAGCTAGCTCCGGTTTA 59.796 52.381 16.15 0.00 0.00 2.01
685 762 1.729470 ATCCGTGTCAGCTAGCTCCG 61.729 60.000 16.15 14.16 0.00 4.63
687 764 1.135139 TGAATCCGTGTCAGCTAGCTC 59.865 52.381 16.15 5.23 0.00 4.09
877 965 3.766691 GGGCGGCGTGAGGTAGAA 61.767 66.667 9.37 0.00 0.00 2.10
1308 1419 0.101219 CGTCATCGTCATCCAGCTCA 59.899 55.000 0.00 0.00 0.00 4.26
1326 1437 1.795177 GGTCGTCGTCGAGAAACCG 60.795 63.158 4.68 0.00 46.96 4.44
1752 1866 2.962569 CAGAAGAGGACGACGCCA 59.037 61.111 10.28 0.00 0.00 5.69
1901 2015 1.800805 CATTGCTCCTCTGTCGTTGT 58.199 50.000 0.00 0.00 0.00 3.32
2023 2155 4.052159 ACTTCTGGTGATGCTAAGATCG 57.948 45.455 0.00 0.00 0.00 3.69
2037 2169 3.341823 AGAAGCTAATGTGCACTTCTGG 58.658 45.455 19.41 5.46 45.35 3.86
2038 2170 4.379186 CCAAGAAGCTAATGTGCACTTCTG 60.379 45.833 19.41 11.15 46.13 3.02
2041 2173 3.490348 ACCAAGAAGCTAATGTGCACTT 58.510 40.909 19.41 9.21 34.34 3.16
2067 2199 0.724453 CGATGACGTTTTGCCGGTTG 60.724 55.000 1.90 0.00 34.56 3.77
2079 2211 5.507077 TCAAAGAAAAGAAAACCGATGACG 58.493 37.500 0.00 0.00 39.43 4.35
2090 2222 8.438676 AACTTTCGAGATCTCAAAGAAAAGAA 57.561 30.769 31.98 20.09 34.68 2.52
2091 2223 7.928706 AGAACTTTCGAGATCTCAAAGAAAAGA 59.071 33.333 31.98 16.69 34.68 2.52
2092 2224 8.082334 AGAACTTTCGAGATCTCAAAGAAAAG 57.918 34.615 31.98 25.83 34.68 2.27
2093 2225 8.979574 GTAGAACTTTCGAGATCTCAAAGAAAA 58.020 33.333 31.98 19.84 34.68 2.29
2094 2226 7.326305 CGTAGAACTTTCGAGATCTCAAAGAAA 59.674 37.037 31.98 25.58 34.68 2.52
2095 2227 6.802348 CGTAGAACTTTCGAGATCTCAAAGAA 59.198 38.462 31.98 22.12 34.68 2.52
2096 2228 6.315551 CGTAGAACTTTCGAGATCTCAAAGA 58.684 40.000 31.98 18.83 34.68 2.52
2097 2229 5.513495 CCGTAGAACTTTCGAGATCTCAAAG 59.487 44.000 27.83 27.83 35.66 2.77
2100 2232 3.181499 GCCGTAGAACTTTCGAGATCTCA 60.181 47.826 22.31 7.11 0.00 3.27
2114 2246 2.886134 AAACAGGGCCGCCGTAGAA 61.886 57.895 3.84 0.00 0.00 2.10
2115 2247 3.315949 AAACAGGGCCGCCGTAGA 61.316 61.111 3.84 0.00 0.00 2.59
2145 2281 0.173481 GAAATTCCGGCCTTCCAAGC 59.827 55.000 0.00 0.00 0.00 4.01
2153 2289 3.592898 AATTCTTGTGAAATTCCGGCC 57.407 42.857 0.00 0.00 35.63 6.13
2180 2316 3.317993 ACGAGAATTTGGTGAAAACAGGG 59.682 43.478 0.00 0.00 0.00 4.45
2181 2317 4.036262 TCACGAGAATTTGGTGAAAACAGG 59.964 41.667 0.00 0.00 37.72 4.00
2187 2323 6.416455 CGAAAATTTCACGAGAATTTGGTGAA 59.584 34.615 6.53 12.87 45.83 3.18
2188 2324 5.912396 CGAAAATTTCACGAGAATTTGGTGA 59.088 36.000 6.53 3.84 38.80 4.02
2219 2355 6.450845 TCATGAATTTTGTTGCGATTGTTC 57.549 33.333 0.00 0.00 0.00 3.18
2230 2366 7.604927 ACAAGCAAGCATTATCATGAATTTTGT 59.395 29.630 0.00 0.00 31.07 2.83
2232 2368 8.556213 AACAAGCAAGCATTATCATGAATTTT 57.444 26.923 0.00 0.00 31.07 1.82
2233 2369 8.447833 CAAACAAGCAAGCATTATCATGAATTT 58.552 29.630 0.00 0.00 31.07 1.82
2234 2370 7.604927 ACAAACAAGCAAGCATTATCATGAATT 59.395 29.630 0.00 0.00 31.07 2.17
2235 2371 7.101054 ACAAACAAGCAAGCATTATCATGAAT 58.899 30.769 0.00 0.00 31.07 2.57
2236 2372 6.457355 ACAAACAAGCAAGCATTATCATGAA 58.543 32.000 0.00 0.00 31.07 2.57
2237 2373 6.028146 ACAAACAAGCAAGCATTATCATGA 57.972 33.333 0.00 0.00 31.07 3.07
2238 2374 6.366604 TGAACAAACAAGCAAGCATTATCATG 59.633 34.615 0.00 0.00 0.00 3.07
2239 2375 6.457355 TGAACAAACAAGCAAGCATTATCAT 58.543 32.000 0.00 0.00 0.00 2.45
2240 2376 5.840715 TGAACAAACAAGCAAGCATTATCA 58.159 33.333 0.00 0.00 0.00 2.15
2241 2377 6.810182 AGATGAACAAACAAGCAAGCATTATC 59.190 34.615 0.00 0.00 0.00 1.75
2242 2378 6.694447 AGATGAACAAACAAGCAAGCATTAT 58.306 32.000 0.00 0.00 0.00 1.28
2243 2379 6.016024 AGAGATGAACAAACAAGCAAGCATTA 60.016 34.615 0.00 0.00 0.00 1.90
2247 2383 4.225208 GAGAGATGAACAAACAAGCAAGC 58.775 43.478 0.00 0.00 0.00 4.01
2249 2385 4.464008 AGGAGAGATGAACAAACAAGCAA 58.536 39.130 0.00 0.00 0.00 3.91
2252 2388 6.624352 TTGAAGGAGAGATGAACAAACAAG 57.376 37.500 0.00 0.00 0.00 3.16
2255 2391 8.877808 AAAAATTGAAGGAGAGATGAACAAAC 57.122 30.769 0.00 0.00 0.00 2.93
2285 2421 4.141711 ACTCCGTATGTGGTATCAGCATTT 60.142 41.667 0.00 0.00 0.00 2.32
2286 2422 3.388024 ACTCCGTATGTGGTATCAGCATT 59.612 43.478 0.00 0.00 0.00 3.56
2287 2423 2.965831 ACTCCGTATGTGGTATCAGCAT 59.034 45.455 0.00 0.00 0.00 3.79
2288 2424 2.384828 ACTCCGTATGTGGTATCAGCA 58.615 47.619 0.00 0.00 0.00 4.41
2290 2426 7.654568 TGTAAATACTCCGTATGTGGTATCAG 58.345 38.462 0.00 0.00 0.00 2.90
2318 2458 5.818857 GCTCCAACGTTATACCTCCAAAATA 59.181 40.000 0.00 0.00 0.00 1.40
2323 2463 1.483415 GGCTCCAACGTTATACCTCCA 59.517 52.381 0.00 0.00 0.00 3.86
2326 2466 1.485066 CCAGGCTCCAACGTTATACCT 59.515 52.381 0.00 2.82 0.00 3.08
2329 2469 1.760613 CCTCCAGGCTCCAACGTTATA 59.239 52.381 0.00 0.00 0.00 0.98
2332 2472 2.750350 CCTCCAGGCTCCAACGTT 59.250 61.111 0.00 0.00 0.00 3.99
2333 2473 3.322466 CCCTCCAGGCTCCAACGT 61.322 66.667 0.00 0.00 0.00 3.99
2353 2493 5.753438 ACTAATGCGTCATACTGTACATTGG 59.247 40.000 0.00 9.14 33.71 3.16
2356 2496 6.338146 ACAACTAATGCGTCATACTGTACAT 58.662 36.000 0.00 0.00 0.00 2.29
2359 2499 6.500910 CCTACAACTAATGCGTCATACTGTA 58.499 40.000 0.00 0.00 0.00 2.74
2360 2500 5.348986 CCTACAACTAATGCGTCATACTGT 58.651 41.667 0.00 0.00 0.00 3.55
2361 2501 4.209288 GCCTACAACTAATGCGTCATACTG 59.791 45.833 0.00 0.00 0.00 2.74
2362 2502 4.099573 AGCCTACAACTAATGCGTCATACT 59.900 41.667 0.00 0.00 0.00 2.12
2363 2503 4.369182 AGCCTACAACTAATGCGTCATAC 58.631 43.478 0.00 0.00 0.00 2.39
2364 2504 4.500887 GGAGCCTACAACTAATGCGTCATA 60.501 45.833 0.00 0.00 0.00 2.15
2366 2506 2.418197 GGAGCCTACAACTAATGCGTCA 60.418 50.000 0.00 0.00 0.00 4.35
2367 2507 2.159085 AGGAGCCTACAACTAATGCGTC 60.159 50.000 0.00 0.00 0.00 5.19
2368 2508 1.831736 AGGAGCCTACAACTAATGCGT 59.168 47.619 0.00 0.00 0.00 5.24
2370 2510 3.828875 AGAGGAGCCTACAACTAATGC 57.171 47.619 0.00 0.00 0.00 3.56
2371 2511 6.640518 TGTTTAGAGGAGCCTACAACTAATG 58.359 40.000 0.00 0.00 0.00 1.90
2373 2513 5.187186 CCTGTTTAGAGGAGCCTACAACTAA 59.813 44.000 0.00 0.00 34.69 2.24
2386 2535 7.463961 TCAAGTAAGTACTCCTGTTTAGAGG 57.536 40.000 0.00 0.00 34.99 3.69
2405 2554 5.617751 GCTTGCGACAGTATTGATTTCAAGT 60.618 40.000 0.00 0.00 39.47 3.16
2407 2556 4.455533 AGCTTGCGACAGTATTGATTTCAA 59.544 37.500 0.00 0.00 40.51 2.69
2437 2587 7.921787 ACACAAAGTACATTGTCAAATTCGTA 58.078 30.769 13.29 0.00 41.44 3.43
2438 2588 6.791303 ACACAAAGTACATTGTCAAATTCGT 58.209 32.000 13.29 4.57 41.44 3.85
2439 2589 8.775220 TTACACAAAGTACATTGTCAAATTCG 57.225 30.769 13.29 3.98 41.44 3.34
2440 2590 9.730420 ACTTACACAAAGTACATTGTCAAATTC 57.270 29.630 13.29 0.00 46.85 2.17
2463 2613 9.293404 AGAGCAATAATATATGACATGCAACTT 57.707 29.630 10.78 0.00 34.89 2.66
2464 2614 8.859236 AGAGCAATAATATATGACATGCAACT 57.141 30.769 10.78 7.52 34.89 3.16
2479 2629 9.971922 GCTTTGACCAAATATTAGAGCAATAAT 57.028 29.630 0.00 0.00 32.84 1.28
2480 2630 9.189156 AGCTTTGACCAAATATTAGAGCAATAA 57.811 29.630 0.00 0.00 32.84 1.40
2481 2631 8.752005 AGCTTTGACCAAATATTAGAGCAATA 57.248 30.769 0.00 0.00 33.62 1.90
2482 2632 7.651027 AGCTTTGACCAAATATTAGAGCAAT 57.349 32.000 0.00 0.00 0.00 3.56
2483 2633 7.201732 GCTAGCTTTGACCAAATATTAGAGCAA 60.202 37.037 7.70 0.00 0.00 3.91
2484 2634 6.260936 GCTAGCTTTGACCAAATATTAGAGCA 59.739 38.462 7.70 0.00 0.00 4.26
2485 2635 6.293680 GGCTAGCTTTGACCAAATATTAGAGC 60.294 42.308 15.72 0.00 0.00 4.09
2486 2636 6.995091 AGGCTAGCTTTGACCAAATATTAGAG 59.005 38.462 15.72 0.00 0.00 2.43
2487 2637 6.900194 AGGCTAGCTTTGACCAAATATTAGA 58.100 36.000 15.72 0.00 0.00 2.10
2488 2638 7.283127 TCAAGGCTAGCTTTGACCAAATATTAG 59.717 37.037 31.68 8.03 37.17 1.73
2489 2639 7.116075 TCAAGGCTAGCTTTGACCAAATATTA 58.884 34.615 31.68 11.27 37.17 0.98
2490 2640 5.951747 TCAAGGCTAGCTTTGACCAAATATT 59.048 36.000 31.68 0.00 37.17 1.28
2491 2641 5.509498 TCAAGGCTAGCTTTGACCAAATAT 58.491 37.500 31.68 0.00 37.17 1.28
2492 2642 4.917385 TCAAGGCTAGCTTTGACCAAATA 58.083 39.130 31.68 13.24 37.17 1.40
2493 2643 3.766545 TCAAGGCTAGCTTTGACCAAAT 58.233 40.909 31.68 0.00 37.17 2.32
2494 2644 3.222173 TCAAGGCTAGCTTTGACCAAA 57.778 42.857 31.68 14.56 37.17 3.28
2495 2645 2.949177 TCAAGGCTAGCTTTGACCAA 57.051 45.000 31.68 14.90 37.17 3.67
2496 2646 2.949177 TTCAAGGCTAGCTTTGACCA 57.051 45.000 34.22 21.97 40.81 4.02
2497 2647 4.299155 GTTTTTCAAGGCTAGCTTTGACC 58.701 43.478 34.22 21.03 40.81 4.02
2498 2648 3.975035 CGTTTTTCAAGGCTAGCTTTGAC 59.025 43.478 34.22 24.06 40.81 3.18
2499 2649 3.630312 ACGTTTTTCAAGGCTAGCTTTGA 59.370 39.130 31.68 31.68 39.67 2.69
2500 2650 3.964909 ACGTTTTTCAAGGCTAGCTTTG 58.035 40.909 28.50 28.50 34.83 2.77
2501 2651 5.959618 ATACGTTTTTCAAGGCTAGCTTT 57.040 34.783 15.72 11.02 0.00 3.51
2502 2652 5.959618 AATACGTTTTTCAAGGCTAGCTT 57.040 34.783 15.72 3.40 0.00 3.74
2503 2653 5.585047 CCTAATACGTTTTTCAAGGCTAGCT 59.415 40.000 15.72 0.00 0.00 3.32
2504 2654 5.729732 GCCTAATACGTTTTTCAAGGCTAGC 60.730 44.000 18.33 6.04 43.70 3.42
2505 2655 5.220796 GGCCTAATACGTTTTTCAAGGCTAG 60.221 44.000 22.26 3.45 45.79 3.42
2506 2656 4.637091 GGCCTAATACGTTTTTCAAGGCTA 59.363 41.667 22.26 0.00 45.79 3.93
2507 2657 3.442625 GGCCTAATACGTTTTTCAAGGCT 59.557 43.478 22.26 0.00 45.79 4.58
2508 2658 3.428452 GGGCCTAATACGTTTTTCAAGGC 60.428 47.826 17.70 17.70 45.79 4.35
2509 2659 4.014406 AGGGCCTAATACGTTTTTCAAGG 58.986 43.478 2.82 0.00 0.00 3.61
2510 2660 6.937436 ATAGGGCCTAATACGTTTTTCAAG 57.063 37.500 18.91 0.00 0.00 3.02
2511 2661 9.715121 CTATATAGGGCCTAATACGTTTTTCAA 57.285 33.333 18.91 0.00 0.00 2.69
2512 2662 9.092338 TCTATATAGGGCCTAATACGTTTTTCA 57.908 33.333 18.91 0.00 0.00 2.69
2514 2664 9.886132 CATCTATATAGGGCCTAATACGTTTTT 57.114 33.333 18.91 0.00 0.00 1.94
2515 2665 8.483758 CCATCTATATAGGGCCTAATACGTTTT 58.516 37.037 18.91 0.30 0.00 2.43
2516 2666 7.842743 TCCATCTATATAGGGCCTAATACGTTT 59.157 37.037 18.91 1.12 0.00 3.60
2517 2667 7.359849 TCCATCTATATAGGGCCTAATACGTT 58.640 38.462 18.91 1.94 0.00 3.99
2518 2668 6.919158 TCCATCTATATAGGGCCTAATACGT 58.081 40.000 18.91 2.76 0.00 3.57
2519 2669 7.039644 CCTTCCATCTATATAGGGCCTAATACG 60.040 44.444 18.91 7.12 0.00 3.06
2520 2670 8.011290 TCCTTCCATCTATATAGGGCCTAATAC 58.989 40.741 18.91 0.00 0.00 1.89
2521 2671 8.138306 TCCTTCCATCTATATAGGGCCTAATA 57.862 38.462 18.91 14.53 0.00 0.98
2522 2672 7.009960 TCCTTCCATCTATATAGGGCCTAAT 57.990 40.000 18.91 14.19 0.00 1.73
2523 2673 6.432190 TCCTTCCATCTATATAGGGCCTAA 57.568 41.667 18.91 7.61 0.00 2.69
2524 2674 5.103043 CCTCCTTCCATCTATATAGGGCCTA 60.103 48.000 17.16 17.16 0.00 3.93
2525 2675 4.327332 CCTCCTTCCATCTATATAGGGCCT 60.327 50.000 12.58 12.58 0.00 5.19
2526 2676 3.970640 CCTCCTTCCATCTATATAGGGCC 59.029 52.174 9.89 0.00 0.00 5.80
2527 2677 3.970640 CCCTCCTTCCATCTATATAGGGC 59.029 52.174 9.89 0.00 36.30 5.19
2528 2678 5.042979 ACTCCCTCCTTCCATCTATATAGGG 60.043 48.000 9.89 4.49 43.23 3.53
2529 2679 6.098716 ACTCCCTCCTTCCATCTATATAGG 57.901 45.833 9.89 0.00 0.00 2.57
2530 2680 7.644062 TGTACTCCCTCCTTCCATCTATATAG 58.356 42.308 3.10 3.10 0.00 1.31
2531 2681 7.599353 TGTACTCCCTCCTTCCATCTATATA 57.401 40.000 0.00 0.00 0.00 0.86
2532 2682 6.485388 TGTACTCCCTCCTTCCATCTATAT 57.515 41.667 0.00 0.00 0.00 0.86
2533 2683 5.942977 TGTACTCCCTCCTTCCATCTATA 57.057 43.478 0.00 0.00 0.00 1.31
2534 2684 4.834406 TGTACTCCCTCCTTCCATCTAT 57.166 45.455 0.00 0.00 0.00 1.98
2535 2685 4.834406 ATGTACTCCCTCCTTCCATCTA 57.166 45.455 0.00 0.00 0.00 1.98
2536 2686 3.715648 ATGTACTCCCTCCTTCCATCT 57.284 47.619 0.00 0.00 0.00 2.90
2537 2687 3.711704 TGAATGTACTCCCTCCTTCCATC 59.288 47.826 0.00 0.00 0.00 3.51
2538 2688 3.736094 TGAATGTACTCCCTCCTTCCAT 58.264 45.455 0.00 0.00 0.00 3.41
2539 2689 3.199442 TGAATGTACTCCCTCCTTCCA 57.801 47.619 0.00 0.00 0.00 3.53
2540 2690 4.164221 TGAATGAATGTACTCCCTCCTTCC 59.836 45.833 0.00 0.00 0.00 3.46
2541 2691 5.359194 TGAATGAATGTACTCCCTCCTTC 57.641 43.478 0.00 0.00 0.00 3.46
2542 2692 5.983333 ATGAATGAATGTACTCCCTCCTT 57.017 39.130 0.00 0.00 0.00 3.36
2543 2693 5.429762 TGAATGAATGAATGTACTCCCTCCT 59.570 40.000 0.00 0.00 0.00 3.69
2544 2694 5.684704 TGAATGAATGAATGTACTCCCTCC 58.315 41.667 0.00 0.00 0.00 4.30
2545 2695 6.429385 GGATGAATGAATGAATGTACTCCCTC 59.571 42.308 0.00 0.00 0.00 4.30
2546 2696 6.126390 TGGATGAATGAATGAATGTACTCCCT 60.126 38.462 0.00 0.00 0.00 4.20
2547 2697 6.064060 TGGATGAATGAATGAATGTACTCCC 58.936 40.000 0.00 0.00 0.00 4.30
2548 2698 7.446319 TCATGGATGAATGAATGAATGTACTCC 59.554 37.037 0.00 0.00 33.63 3.85
2549 2699 8.387190 TCATGGATGAATGAATGAATGTACTC 57.613 34.615 0.00 0.00 33.63 2.59
2550 2700 8.935614 ATCATGGATGAATGAATGAATGTACT 57.064 30.769 0.00 0.00 39.90 2.73
2551 2701 8.242053 GGATCATGGATGAATGAATGAATGTAC 58.758 37.037 0.00 0.00 39.90 2.90
2552 2702 7.945664 TGGATCATGGATGAATGAATGAATGTA 59.054 33.333 0.00 0.00 39.90 2.29
2553 2703 6.780522 TGGATCATGGATGAATGAATGAATGT 59.219 34.615 0.00 0.00 39.90 2.71
2554 2704 7.227049 TGGATCATGGATGAATGAATGAATG 57.773 36.000 0.00 0.00 39.90 2.67
2555 2705 7.673926 TGATGGATCATGGATGAATGAATGAAT 59.326 33.333 0.00 0.00 39.90 2.57
2556 2706 7.007723 TGATGGATCATGGATGAATGAATGAA 58.992 34.615 0.00 0.00 39.90 2.57
2557 2707 6.548321 TGATGGATCATGGATGAATGAATGA 58.452 36.000 0.00 0.00 39.90 2.57
2558 2708 6.834168 TGATGGATCATGGATGAATGAATG 57.166 37.500 0.00 0.00 39.90 2.67
2559 2709 8.435931 AATTGATGGATCATGGATGAATGAAT 57.564 30.769 0.00 0.00 39.90 2.57
2560 2710 7.849322 AATTGATGGATCATGGATGAATGAA 57.151 32.000 0.00 0.00 39.90 2.57
2561 2711 8.168058 AGTAATTGATGGATCATGGATGAATGA 58.832 33.333 0.00 0.00 40.69 2.57
2562 2712 8.244113 CAGTAATTGATGGATCATGGATGAATG 58.756 37.037 0.00 0.00 40.69 2.67
2573 2723 4.553547 GCAACTCGCAGTAATTGATGGATC 60.554 45.833 0.00 0.00 41.79 3.36
2595 2746 0.528684 GTCGGTGCCTCATCAGTAGC 60.529 60.000 0.00 0.00 0.00 3.58
2723 2879 1.163420 TTGGCTTGTGGTGCTGTACG 61.163 55.000 0.00 0.00 0.00 3.67
2767 2923 1.070615 TGTGTACGCAGGCACATGT 59.929 52.632 4.65 0.00 41.06 3.21
2848 3004 5.088739 ACGAAATTAGGTACACGTACTTCG 58.911 41.667 18.95 18.95 46.00 3.79
2849 3005 6.363357 ACAACGAAATTAGGTACACGTACTTC 59.637 38.462 7.25 2.66 36.36 3.01
2850 3006 6.215845 ACAACGAAATTAGGTACACGTACTT 58.784 36.000 7.25 2.48 36.36 2.24
2871 3027 2.043992 TCTTTCCCAGACGGAGAACAA 58.956 47.619 0.00 0.00 43.39 2.83
2944 3100 4.320275 CGTCTCGCCTGCTAATCAATACTA 60.320 45.833 0.00 0.00 0.00 1.82
2945 3101 3.551046 CGTCTCGCCTGCTAATCAATACT 60.551 47.826 0.00 0.00 0.00 2.12
2946 3102 2.726760 CGTCTCGCCTGCTAATCAATAC 59.273 50.000 0.00 0.00 0.00 1.89
3011 3170 0.170339 TCAGTCATCACACGCTACCG 59.830 55.000 0.00 0.00 41.14 4.02


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

AutoCloner maintained by Alex Coulton.