Multiple sequence alignment - TraesCS1B01G205500

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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 TraesCS1B01G205500 chr1B 100.000 2666 0 0 1 2666 370044084 370046749 0.000000e+00 4924.0
1 TraesCS1B01G205500 chr1B 94.928 138 6 1 2173 2309 332086326 332086463 5.780000e-52 215.0
2 TraesCS1B01G205500 chr1D 91.533 1807 74 33 420 2180 268939046 268937273 0.000000e+00 2416.0
3 TraesCS1B01G205500 chr1D 91.471 340 22 2 4 338 268939406 268939069 6.720000e-126 460.0
4 TraesCS1B01G205500 chr1D 86.667 165 9 3 2304 2466 268937277 268937124 1.270000e-38 171.0
5 TraesCS1B01G205500 chr1D 87.356 87 9 2 359 444 60286445 60286360 6.070000e-17 99.0
6 TraesCS1B01G205500 chr1A 91.214 1104 51 19 600 1668 333912952 333914044 0.000000e+00 1459.0
7 TraesCS1B01G205500 chr1A 89.053 475 27 12 1729 2180 333914066 333914538 1.390000e-157 566.0
8 TraesCS1B01G205500 chr1A 89.916 357 15 9 1 338 333912203 333912557 8.760000e-120 440.0
9 TraesCS1B01G205500 chr1A 94.815 135 5 2 2172 2304 486045907 486045773 2.690000e-50 209.0
10 TraesCS1B01G205500 chr1A 85.465 172 13 4 422 593 333912582 333912741 4.560000e-38 169.0
11 TraesCS1B01G205500 chr1A 94.286 105 4 2 2537 2639 333914723 333914827 2.750000e-35 159.0
12 TraesCS1B01G205500 chr1A 79.894 189 7 8 2304 2462 333914534 333914721 2.810000e-20 110.0
13 TraesCS1B01G205500 chr4A 91.358 162 5 2 1 153 628854904 628854743 2.080000e-51 213.0
14 TraesCS1B01G205500 chr4A 94.366 71 4 0 357 427 95187537 95187467 2.810000e-20 110.0
15 TraesCS1B01G205500 chr2B 96.183 131 4 1 2178 2307 545760515 545760385 2.080000e-51 213.0
16 TraesCS1B01G205500 chr2B 95.489 133 5 1 2175 2306 776888870 776888738 7.480000e-51 211.0
17 TraesCS1B01G205500 chr2B 92.105 76 5 1 357 431 41129558 41129483 3.630000e-19 106.0
18 TraesCS1B01G205500 chr2B 93.651 63 4 0 276 338 545266718 545266780 7.860000e-16 95.3
19 TraesCS1B01G205500 chr3A 94.161 137 6 2 2174 2309 468726667 468726802 9.670000e-50 207.0
20 TraesCS1B01G205500 chr7B 95.385 130 5 1 2178 2306 140609532 140609403 3.480000e-49 206.0
21 TraesCS1B01G205500 chr7B 90.728 151 10 3 2177 2323 482861886 482861736 5.820000e-47 198.0
22 TraesCS1B01G205500 chr7B 92.208 77 5 1 357 432 611720274 611720350 1.010000e-19 108.0
23 TraesCS1B01G205500 chr6B 92.908 141 8 2 2168 2307 660665878 660666017 1.250000e-48 204.0
24 TraesCS1B01G205500 chr6B 93.651 63 4 0 276 338 562098574 562098636 7.860000e-16 95.3
25 TraesCS1B01G205500 chr6B 88.889 72 6 2 276 347 455419268 455419199 1.310000e-13 87.9
26 TraesCS1B01G205500 chr5B 88.272 162 14 4 2145 2304 596381233 596381391 3.500000e-44 189.0
27 TraesCS1B01G205500 chr7D 93.243 74 5 0 357 430 32381680 32381753 2.810000e-20 110.0
28 TraesCS1B01G205500 chr7D 92.208 77 5 1 357 433 602951544 602951469 1.010000e-19 108.0
29 TraesCS1B01G205500 chr7A 93.243 74 5 0 357 430 129876958 129877031 2.810000e-20 110.0
30 TraesCS1B01G205500 chr3B 93.151 73 5 0 357 429 156913504 156913576 1.010000e-19 108.0
31 TraesCS1B01G205500 chr3B 88.750 80 9 0 276 355 506196111 506196032 6.070000e-17 99.0
32 TraesCS1B01G205500 chr3B 92.188 64 5 0 276 339 245935476 245935539 1.020000e-14 91.6
33 TraesCS1B01G205500 chr6A 91.026 78 6 1 357 433 15768169 15768246 1.310000e-18 104.0
34 TraesCS1B01G205500 chr2D 95.000 60 3 0 280 339 633849182 633849123 7.860000e-16 95.3
35 TraesCS1B01G205500 chr5D 92.188 64 5 0 275 338 346639907 346639844 1.020000e-14 91.6
36 TraesCS1B01G205500 chr4D 92.000 50 1 1 1118 1164 497627995 497627946 1.710000e-07 67.6
37 TraesCS1B01G205500 chr4D 94.118 34 2 0 439 472 168219301 168219334 5.000000e-03 52.8


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 TraesCS1B01G205500 chr1B 370044084 370046749 2665 False 4924.000000 4924 100.000000 1 2666 1 chr1B.!!$F2 2665
1 TraesCS1B01G205500 chr1D 268937124 268939406 2282 True 1015.666667 2416 89.890333 4 2466 3 chr1D.!!$R2 2462
2 TraesCS1B01G205500 chr1A 333912203 333914827 2624 False 483.833333 1459 88.304667 1 2639 6 chr1A.!!$F1 2638

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
969 1218 0.256177 TCCAAGCCTCTCTCTCGCTA 59.744 55.0 0.0 0.0 31.12 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2601 0.106066 TACTCCCTCCGCCGGAAATA 60.106 55.0 7.5 0.0 0.0 1.4 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
51 56 4.576873 TGTAGATTCTGGAACTAGCTCGAG 59.423 45.833 8.45 8.45 0.00 4.04
137 147 1.900486 CCACCCGACTAATCCCCTATC 59.100 57.143 0.00 0.00 0.00 2.08
189 199 3.138283 TGACAGGTCTTTTGGGACTGAAT 59.862 43.478 0.65 0.00 36.55 2.57
191 201 5.014123 TGACAGGTCTTTTGGGACTGAATAT 59.986 40.000 0.65 0.00 36.55 1.28
192 202 5.892348 ACAGGTCTTTTGGGACTGAATATT 58.108 37.500 0.00 0.00 36.55 1.28
193 203 5.711976 ACAGGTCTTTTGGGACTGAATATTG 59.288 40.000 0.00 0.00 36.55 1.90
235 249 2.038557 GTCTTTCCCACTGCAAGGTCTA 59.961 50.000 4.33 0.00 39.30 2.59
274 293 5.811100 TCAGTAGAGAGTAGTACATGACACG 59.189 44.000 0.00 0.00 0.00 4.49
341 361 7.542534 TTGTCACGTTTTAGTGTATTTCAGT 57.457 32.000 0.00 0.00 42.40 3.41
342 362 7.542534 TGTCACGTTTTAGTGTATTTCAGTT 57.457 32.000 0.00 0.00 42.40 3.16
343 363 7.976826 TGTCACGTTTTAGTGTATTTCAGTTT 58.023 30.769 0.00 0.00 42.40 2.66
344 364 7.906010 TGTCACGTTTTAGTGTATTTCAGTTTG 59.094 33.333 0.00 0.00 42.40 2.93
348 368 9.872757 ACGTTTTAGTGTATTTCAGTTTGTATG 57.127 29.630 0.00 0.00 0.00 2.39
356 376 7.822822 GTGTATTTCAGTTTGTATGTACTCCCT 59.177 37.037 0.00 0.00 0.00 4.20
357 377 7.822334 TGTATTTCAGTTTGTATGTACTCCCTG 59.178 37.037 0.00 0.00 0.00 4.45
358 378 5.818678 TTCAGTTTGTATGTACTCCCTGT 57.181 39.130 0.00 0.00 0.00 4.00
359 379 6.921486 TTCAGTTTGTATGTACTCCCTGTA 57.079 37.500 0.00 0.00 0.00 2.74
360 380 6.921486 TCAGTTTGTATGTACTCCCTGTAA 57.079 37.500 0.00 0.00 32.25 2.41
361 381 6.931838 TCAGTTTGTATGTACTCCCTGTAAG 58.068 40.000 0.00 0.00 32.25 2.34
362 382 6.722590 TCAGTTTGTATGTACTCCCTGTAAGA 59.277 38.462 0.00 0.00 34.07 2.10
363 383 7.399191 TCAGTTTGTATGTACTCCCTGTAAGAT 59.601 37.037 0.00 0.00 34.07 2.40
364 384 7.492669 CAGTTTGTATGTACTCCCTGTAAGATG 59.507 40.741 0.00 0.00 34.07 2.90
365 385 7.399191 AGTTTGTATGTACTCCCTGTAAGATGA 59.601 37.037 0.00 0.00 34.07 2.92
366 386 7.914427 TTGTATGTACTCCCTGTAAGATGAT 57.086 36.000 0.00 0.00 34.07 2.45
367 387 7.914427 TGTATGTACTCCCTGTAAGATGATT 57.086 36.000 0.00 0.00 34.07 2.57
368 388 8.319057 TGTATGTACTCCCTGTAAGATGATTT 57.681 34.615 0.00 0.00 34.07 2.17
369 389 8.768397 TGTATGTACTCCCTGTAAGATGATTTT 58.232 33.333 0.00 0.00 34.07 1.82
370 390 9.614792 GTATGTACTCCCTGTAAGATGATTTTT 57.385 33.333 0.00 0.00 34.07 1.94
371 391 7.921786 TGTACTCCCTGTAAGATGATTTTTG 57.078 36.000 0.00 0.00 34.07 2.44
372 392 7.685481 TGTACTCCCTGTAAGATGATTTTTGA 58.315 34.615 0.00 0.00 34.07 2.69
373 393 7.606456 TGTACTCCCTGTAAGATGATTTTTGAC 59.394 37.037 0.00 0.00 34.07 3.18
374 394 6.542821 ACTCCCTGTAAGATGATTTTTGACA 58.457 36.000 0.00 0.00 34.07 3.58
375 395 6.431234 ACTCCCTGTAAGATGATTTTTGACAC 59.569 38.462 0.00 0.00 34.07 3.67
376 396 6.542821 TCCCTGTAAGATGATTTTTGACACT 58.457 36.000 0.00 0.00 34.07 3.55
377 397 7.685481 TCCCTGTAAGATGATTTTTGACACTA 58.315 34.615 0.00 0.00 34.07 2.74
378 398 7.606456 TCCCTGTAAGATGATTTTTGACACTAC 59.394 37.037 0.00 0.00 34.07 2.73
379 399 7.390440 CCCTGTAAGATGATTTTTGACACTACA 59.610 37.037 0.00 0.00 34.07 2.74
380 400 8.230486 CCTGTAAGATGATTTTTGACACTACAC 58.770 37.037 0.00 0.00 34.07 2.90
381 401 8.902540 TGTAAGATGATTTTTGACACTACACT 57.097 30.769 0.00 0.00 0.00 3.55
382 402 9.990360 TGTAAGATGATTTTTGACACTACACTA 57.010 29.630 0.00 0.00 0.00 2.74
433 453 7.256012 GGGACAGAGGGAGTAGTTTATATTGAG 60.256 44.444 0.00 0.00 0.00 3.02
434 454 7.256012 GGACAGAGGGAGTAGTTTATATTGAGG 60.256 44.444 0.00 0.00 0.00 3.86
435 455 7.133483 ACAGAGGGAGTAGTTTATATTGAGGT 58.867 38.462 0.00 0.00 0.00 3.85
436 456 8.287350 ACAGAGGGAGTAGTTTATATTGAGGTA 58.713 37.037 0.00 0.00 0.00 3.08
437 457 8.578151 CAGAGGGAGTAGTTTATATTGAGGTAC 58.422 40.741 0.00 0.00 0.00 3.34
468 491 9.396022 AGAAACATCTTATATTTGTGAACGGAT 57.604 29.630 0.00 0.00 0.00 4.18
492 515 3.864243 AGGGTAACACGATTTGCGAATA 58.136 40.909 0.00 0.00 44.66 1.75
499 522 5.095691 ACACGATTTGCGAATATGATTCC 57.904 39.130 14.58 0.00 44.57 3.01
564 587 0.664166 TTCGGTCGGCGTGTAGTTTC 60.664 55.000 6.85 0.00 0.00 2.78
597 626 6.019398 GCAAATGCGAATGATCATCATTTTGA 60.019 34.615 22.07 7.09 46.20 2.69
616 849 5.762825 TTGACCTATATCCACTGTACGAC 57.237 43.478 0.00 0.00 0.00 4.34
806 1043 0.952280 TCGCTTCAGAGACGTCAACT 59.048 50.000 19.50 13.54 0.00 3.16
872 1112 4.641094 CCGCCTCTATATTATCTTCCTCGT 59.359 45.833 0.00 0.00 0.00 4.18
873 1113 5.449314 CCGCCTCTATATTATCTTCCTCGTG 60.449 48.000 0.00 0.00 0.00 4.35
912 1153 3.414700 GCCTCGGTTCACACGCAG 61.415 66.667 0.00 0.00 0.00 5.18
913 1154 3.414700 CCTCGGTTCACACGCAGC 61.415 66.667 0.00 0.00 0.00 5.25
914 1155 2.356313 CTCGGTTCACACGCAGCT 60.356 61.111 0.00 0.00 0.00 4.24
916 1157 1.344942 CTCGGTTCACACGCAGCTAC 61.345 60.000 0.00 0.00 0.00 3.58
917 1158 2.716828 CGGTTCACACGCAGCTACG 61.717 63.158 4.40 4.40 39.50 3.51
968 1217 0.396974 ATCCAAGCCTCTCTCTCGCT 60.397 55.000 0.00 0.00 0.00 4.93
969 1218 0.256177 TCCAAGCCTCTCTCTCGCTA 59.744 55.000 0.00 0.00 31.12 4.26
970 1219 1.133637 TCCAAGCCTCTCTCTCGCTAT 60.134 52.381 0.00 0.00 31.12 2.97
991 1240 4.893601 TCGCGCACCGTCAACCAA 62.894 61.111 8.75 0.00 38.35 3.67
992 1241 4.659874 CGCGCACCGTCAACCAAC 62.660 66.667 8.75 0.00 0.00 3.77
993 1242 4.322385 GCGCACCGTCAACCAACC 62.322 66.667 0.30 0.00 0.00 3.77
1128 1383 0.103208 GCTCCACGTCCTTCATCGAT 59.897 55.000 0.00 0.00 0.00 3.59
1323 1590 4.855596 GTGTCCTACGTGTCGTCC 57.144 61.111 0.00 0.00 41.54 4.79
1668 1944 1.859427 GACGACAGGACGTGTAGGCA 61.859 60.000 9.09 0.00 46.52 4.75
1671 1947 1.228769 ACAGGACGTGTAGGCAGGA 60.229 57.895 0.00 0.00 37.75 3.86
1675 1951 1.136984 GACGTGTAGGCAGGACGAG 59.863 63.158 0.00 0.00 36.90 4.18
1676 1952 2.202623 CGTGTAGGCAGGACGAGC 60.203 66.667 0.00 0.00 35.05 5.03
1677 1953 2.202623 GTGTAGGCAGGACGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
1678 1954 4.129737 TGTAGGCAGGACGAGCGC 62.130 66.667 0.00 0.00 0.00 5.92
1679 1955 3.827898 GTAGGCAGGACGAGCGCT 61.828 66.667 11.27 11.27 0.00 5.92
1680 1956 3.518998 TAGGCAGGACGAGCGCTC 61.519 66.667 27.64 27.64 0.00 5.03
1700 1976 0.032678 CGCTCTGGCATAGATCGGTT 59.967 55.000 3.79 0.00 40.40 4.44
1708 1984 1.539929 GCATAGATCGGTTGCTGCTCT 60.540 52.381 0.00 0.00 33.61 4.09
1711 1987 2.191128 AGATCGGTTGCTGCTCTTTT 57.809 45.000 0.00 0.00 0.00 2.27
1738 2018 2.303163 TGATTTCCGGTGTACATCCG 57.697 50.000 22.29 22.29 46.49 4.18
1748 2028 4.468095 GGTGTACATCCGATTTGCATAC 57.532 45.455 0.00 0.00 0.00 2.39
1750 2030 3.799963 GTGTACATCCGATTTGCATACGA 59.200 43.478 0.00 0.00 0.00 3.43
1781 2061 8.011673 TGAGTGTATAGCGTATACGTTATGAAC 58.988 37.037 32.26 28.17 43.68 3.18
1783 2063 8.013947 AGTGTATAGCGTATACGTTATGAACTG 58.986 37.037 32.26 4.25 43.68 3.16
1872 2159 3.324846 TGATGAAGCTACCTGTCACTGTT 59.675 43.478 0.00 0.00 0.00 3.16
1880 2167 1.762957 ACCTGTCACTGTTACTGTGCT 59.237 47.619 15.92 0.00 34.16 4.40
1904 2201 1.404391 TGCTAAGGACGAGATTCGGTC 59.596 52.381 3.37 3.24 45.59 4.79
1921 2218 5.441709 TCGGTCCAAAGGAAATTGTTAAC 57.558 39.130 0.00 0.00 31.38 2.01
1973 2270 3.961477 TTGCCATGATTATGTGCGTAC 57.039 42.857 0.00 0.00 34.93 3.67
1991 2296 6.128710 GCGTACTATATATGTATGCATGCG 57.871 41.667 21.79 0.00 46.38 4.73
2002 2307 2.515523 GCATGCGTCAGGCCAGAT 60.516 61.111 5.01 0.00 42.61 2.90
2012 2317 1.507742 TCAGGCCAGATAGACCCCATA 59.492 52.381 5.01 0.00 0.00 2.74
2090 2400 2.915137 TTTTCCCCGGCAAGGCAC 60.915 61.111 0.00 0.00 39.21 5.01
2091 2401 3.740495 TTTTCCCCGGCAAGGCACA 62.740 57.895 0.00 0.00 39.21 4.57
2092 2402 3.521765 TTTCCCCGGCAAGGCACAT 62.522 57.895 0.00 0.00 39.21 3.21
2093 2403 3.521765 TTCCCCGGCAAGGCACATT 62.522 57.895 0.00 0.00 39.21 2.71
2094 2404 2.044451 CCCCGGCAAGGCACATTA 60.044 61.111 0.00 0.00 39.21 1.90
2120 2437 8.107095 ACTAAAACTCATTCAAACCTATAGGCA 58.893 33.333 19.25 0.00 39.32 4.75
2126 2443 3.827008 TCAAACCTATAGGCAGCTGAG 57.173 47.619 20.43 4.99 39.32 3.35
2133 2450 3.181488 CCTATAGGCAGCTGAGATCGATG 60.181 52.174 20.43 0.00 0.00 3.84
2175 2492 0.878523 CCAAGTCGCCGAGTCAAACA 60.879 55.000 0.00 0.00 0.00 2.83
2176 2493 1.148310 CAAGTCGCCGAGTCAAACAT 58.852 50.000 0.00 0.00 0.00 2.71
2177 2494 2.333926 CAAGTCGCCGAGTCAAACATA 58.666 47.619 0.00 0.00 0.00 2.29
2178 2495 2.930040 CAAGTCGCCGAGTCAAACATAT 59.070 45.455 0.00 0.00 0.00 1.78
2179 2496 4.109766 CAAGTCGCCGAGTCAAACATATA 58.890 43.478 0.00 0.00 0.00 0.86
2180 2497 3.703420 AGTCGCCGAGTCAAACATATAC 58.297 45.455 0.00 0.00 0.00 1.47
2181 2498 3.380637 AGTCGCCGAGTCAAACATATACT 59.619 43.478 0.00 0.00 0.00 2.12
2182 2499 3.729716 GTCGCCGAGTCAAACATATACTC 59.270 47.826 0.00 0.00 36.99 2.59
2183 2500 3.630769 TCGCCGAGTCAAACATATACTCT 59.369 43.478 0.00 0.00 37.97 3.24
2184 2501 3.975670 CGCCGAGTCAAACATATACTCTC 59.024 47.826 0.00 0.00 37.97 3.20
2185 2502 4.261238 CGCCGAGTCAAACATATACTCTCT 60.261 45.833 0.00 0.00 37.97 3.10
2186 2503 5.216648 GCCGAGTCAAACATATACTCTCTC 58.783 45.833 0.00 0.00 37.97 3.20
2187 2504 5.764131 CCGAGTCAAACATATACTCTCTCC 58.236 45.833 0.00 0.00 37.97 3.71
2188 2505 5.444983 CGAGTCAAACATATACTCTCTCCG 58.555 45.833 0.00 0.00 37.97 4.63
2189 2506 5.007823 CGAGTCAAACATATACTCTCTCCGT 59.992 44.000 0.00 0.00 37.97 4.69
2190 2507 6.380095 AGTCAAACATATACTCTCTCCGTC 57.620 41.667 0.00 0.00 0.00 4.79
2191 2508 5.299782 AGTCAAACATATACTCTCTCCGTCC 59.700 44.000 0.00 0.00 0.00 4.79
2192 2509 4.275196 TCAAACATATACTCTCTCCGTCCG 59.725 45.833 0.00 0.00 0.00 4.79
2193 2510 3.766068 ACATATACTCTCTCCGTCCGA 57.234 47.619 0.00 0.00 0.00 4.55
2194 2511 4.082665 ACATATACTCTCTCCGTCCGAA 57.917 45.455 0.00 0.00 0.00 4.30
2195 2512 4.458397 ACATATACTCTCTCCGTCCGAAA 58.542 43.478 0.00 0.00 0.00 3.46
2196 2513 4.885907 ACATATACTCTCTCCGTCCGAAAA 59.114 41.667 0.00 0.00 0.00 2.29
2197 2514 5.535406 ACATATACTCTCTCCGTCCGAAAAT 59.465 40.000 0.00 0.00 0.00 1.82
2198 2515 6.713903 ACATATACTCTCTCCGTCCGAAAATA 59.286 38.462 0.00 0.00 0.00 1.40
2199 2516 3.779271 ACTCTCTCCGTCCGAAAATAC 57.221 47.619 0.00 0.00 0.00 1.89
2200 2517 3.354467 ACTCTCTCCGTCCGAAAATACT 58.646 45.455 0.00 0.00 0.00 2.12
2201 2518 3.762823 ACTCTCTCCGTCCGAAAATACTT 59.237 43.478 0.00 0.00 0.00 2.24
2202 2519 4.106029 TCTCTCCGTCCGAAAATACTTG 57.894 45.455 0.00 0.00 0.00 3.16
2203 2520 3.508793 TCTCTCCGTCCGAAAATACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
2204 2521 3.841643 TCTCCGTCCGAAAATACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
2205 2522 3.256383 TCTCCGTCCGAAAATACTTGTCA 59.744 43.478 0.00 0.00 0.00 3.58
2206 2523 4.081862 TCTCCGTCCGAAAATACTTGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
2207 2524 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2208 2525 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2209 2526 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2210 2527 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2211 2528 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2212 2529 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2213 2530 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2214 2531 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2215 2532 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2216 2533 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2224 2541 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
2276 2593 9.713684 AGATACATTCCCTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
2279 2596 8.378115 ACATTCCCTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 0.00 2.92
2280 2597 8.260114 ACATTCCCTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 0.00 3.06
2281 2598 7.789202 TTCCCTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
2282 2599 7.789202 TCCCTTTTATCCATTTTGATGACAA 57.211 32.000 0.00 0.00 0.00 3.18
2283 2600 7.839907 TCCCTTTTATCCATTTTGATGACAAG 58.160 34.615 0.00 0.00 37.32 3.16
2284 2601 7.454380 TCCCTTTTATCCATTTTGATGACAAGT 59.546 33.333 0.00 0.00 37.32 3.16
2285 2602 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
2291 2608 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2292 2609 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2293 2610 4.695217 TTTGATGACAAGTATTTCCGGC 57.305 40.909 0.00 0.00 37.32 6.13
2294 2611 2.276201 TGATGACAAGTATTTCCGGCG 58.724 47.619 0.00 0.00 0.00 6.46
2295 2612 1.597663 GATGACAAGTATTTCCGGCGG 59.402 52.381 22.51 22.51 0.00 6.13
2296 2613 0.609151 TGACAAGTATTTCCGGCGGA 59.391 50.000 27.46 27.46 0.00 5.54
2297 2614 1.287425 GACAAGTATTTCCGGCGGAG 58.713 55.000 29.30 17.66 31.21 4.63
2298 2615 0.107848 ACAAGTATTTCCGGCGGAGG 60.108 55.000 29.30 15.00 31.21 4.30
2299 2616 0.814010 CAAGTATTTCCGGCGGAGGG 60.814 60.000 29.30 10.49 31.21 4.30
2300 2617 0.979187 AAGTATTTCCGGCGGAGGGA 60.979 55.000 29.30 18.88 31.21 4.20
2301 2618 1.069258 GTATTTCCGGCGGAGGGAG 59.931 63.158 29.30 0.00 34.45 4.30
2302 2619 1.382146 TATTTCCGGCGGAGGGAGT 60.382 57.895 29.30 13.87 34.45 3.85
2398 2734 3.069074 CGTTCCATACGGACAATACGA 57.931 47.619 0.00 0.00 46.42 3.43
2407 2743 3.531538 ACGGACAATACGATGCAATCTT 58.468 40.909 0.00 0.00 42.58 2.40
2408 2744 3.555956 ACGGACAATACGATGCAATCTTC 59.444 43.478 0.00 0.00 42.58 2.87
2410 2746 3.876914 GGACAATACGATGCAATCTTCCA 59.123 43.478 0.00 0.00 42.58 3.53
2411 2747 4.335315 GGACAATACGATGCAATCTTCCAA 59.665 41.667 0.00 0.00 42.58 3.53
2412 2748 5.163663 GGACAATACGATGCAATCTTCCAAA 60.164 40.000 0.00 0.00 42.58 3.28
2413 2749 6.455360 ACAATACGATGCAATCTTCCAAAT 57.545 33.333 0.00 0.00 42.58 2.32
2414 2750 6.267817 ACAATACGATGCAATCTTCCAAATG 58.732 36.000 0.00 0.00 42.58 2.32
2415 2751 3.155093 ACGATGCAATCTTCCAAATGC 57.845 42.857 0.00 0.00 42.58 3.56
2441 2786 1.069204 AGTAGATACGCACAGGGCATG 59.931 52.381 0.00 0.00 45.17 4.06
2451 2798 1.064906 CACAGGGCATGGAACTCAGAT 60.065 52.381 3.46 0.00 0.00 2.90
2455 2802 3.881688 CAGGGCATGGAACTCAGATTAAG 59.118 47.826 0.00 0.00 0.00 1.85
2466 2813 9.605275 TGGAACTCAGATTAAGATCATTTGTAG 57.395 33.333 0.00 0.00 34.60 2.74
2467 2814 9.606631 GGAACTCAGATTAAGATCATTTGTAGT 57.393 33.333 0.00 0.00 34.60 2.73
2469 2816 8.430801 ACTCAGATTAAGATCATTTGTAGTGC 57.569 34.615 0.00 0.00 34.60 4.40
2470 2817 8.263640 ACTCAGATTAAGATCATTTGTAGTGCT 58.736 33.333 0.00 0.00 34.60 4.40
2471 2818 8.654230 TCAGATTAAGATCATTTGTAGTGCTC 57.346 34.615 0.00 0.00 34.60 4.26
2472 2819 8.481314 TCAGATTAAGATCATTTGTAGTGCTCT 58.519 33.333 0.00 0.00 34.60 4.09
2473 2820 9.755804 CAGATTAAGATCATTTGTAGTGCTCTA 57.244 33.333 0.00 0.00 34.60 2.43
2474 2821 9.757227 AGATTAAGATCATTTGTAGTGCTCTAC 57.243 33.333 17.14 17.14 39.54 2.59
2475 2822 9.757227 GATTAAGATCATTTGTAGTGCTCTACT 57.243 33.333 22.64 4.09 38.57 2.57
2480 2827 8.508062 AGATCATTTGTAGTGCTCTACTATACG 58.492 37.037 22.64 10.51 43.44 3.06
2481 2828 6.436261 TCATTTGTAGTGCTCTACTATACGC 58.564 40.000 22.64 0.03 43.44 4.42
2482 2829 5.823209 TTTGTAGTGCTCTACTATACGCA 57.177 39.130 22.64 2.45 43.44 5.24
2483 2830 5.419760 TTGTAGTGCTCTACTATACGCAG 57.580 43.478 22.64 0.00 43.44 5.18
2484 2831 3.813724 TGTAGTGCTCTACTATACGCAGG 59.186 47.826 22.64 0.00 43.44 4.85
2485 2832 3.210232 AGTGCTCTACTATACGCAGGA 57.790 47.619 0.00 0.00 38.04 3.86
2486 2833 3.757270 AGTGCTCTACTATACGCAGGAT 58.243 45.455 0.00 0.00 38.04 3.24
2487 2834 4.145807 AGTGCTCTACTATACGCAGGATT 58.854 43.478 0.00 0.00 38.04 3.01
2488 2835 4.022762 AGTGCTCTACTATACGCAGGATTG 60.023 45.833 0.00 0.00 38.04 2.67
2489 2836 3.255888 TGCTCTACTATACGCAGGATTGG 59.744 47.826 0.00 0.00 0.00 3.16
2490 2837 3.506455 GCTCTACTATACGCAGGATTGGA 59.494 47.826 0.00 0.00 0.00 3.53
2491 2838 4.022242 GCTCTACTATACGCAGGATTGGAA 60.022 45.833 0.00 0.00 0.00 3.53
2492 2839 5.336849 GCTCTACTATACGCAGGATTGGAAT 60.337 44.000 0.00 0.00 0.00 3.01
2493 2840 6.268825 TCTACTATACGCAGGATTGGAATC 57.731 41.667 0.00 0.00 34.66 2.52
2494 2841 4.955811 ACTATACGCAGGATTGGAATCA 57.044 40.909 1.94 0.00 37.15 2.57
2495 2842 5.489792 ACTATACGCAGGATTGGAATCAT 57.510 39.130 1.94 0.00 37.15 2.45
2496 2843 5.482908 ACTATACGCAGGATTGGAATCATC 58.517 41.667 1.94 0.00 37.15 2.92
2497 2844 1.972872 ACGCAGGATTGGAATCATCC 58.027 50.000 1.94 0.00 46.76 3.51
2498 2845 1.492176 ACGCAGGATTGGAATCATCCT 59.508 47.619 1.94 0.00 46.70 3.24
2501 2848 2.671896 AGGATTGGAATCATCCTGGC 57.328 50.000 1.76 0.00 46.70 4.85
2502 2849 1.854939 AGGATTGGAATCATCCTGGCA 59.145 47.619 1.76 0.00 46.70 4.92
2503 2850 2.449730 AGGATTGGAATCATCCTGGCAT 59.550 45.455 1.76 0.00 46.70 4.40
2504 2851 2.561419 GGATTGGAATCATCCTGGCATG 59.439 50.000 1.94 0.00 46.70 4.06
2505 2852 1.405872 TTGGAATCATCCTGGCATGC 58.594 50.000 9.90 9.90 46.70 4.06
2506 2853 0.259356 TGGAATCATCCTGGCATGCA 59.741 50.000 21.36 4.79 46.70 3.96
2507 2854 1.342175 TGGAATCATCCTGGCATGCAA 60.342 47.619 21.36 7.49 46.70 4.08
2508 2855 1.968493 GGAATCATCCTGGCATGCAAT 59.032 47.619 21.36 4.14 42.93 3.56
2509 2856 2.367567 GGAATCATCCTGGCATGCAATT 59.632 45.455 21.36 6.77 42.93 2.32
2510 2857 3.181458 GGAATCATCCTGGCATGCAATTT 60.181 43.478 21.36 0.94 42.93 1.82
2511 2858 4.448210 GAATCATCCTGGCATGCAATTTT 58.552 39.130 21.36 1.47 0.00 1.82
2512 2859 3.530265 TCATCCTGGCATGCAATTTTC 57.470 42.857 21.36 0.64 0.00 2.29
2513 2860 3.101437 TCATCCTGGCATGCAATTTTCT 58.899 40.909 21.36 0.00 0.00 2.52
2514 2861 3.516300 TCATCCTGGCATGCAATTTTCTT 59.484 39.130 21.36 0.00 0.00 2.52
2515 2862 4.020039 TCATCCTGGCATGCAATTTTCTTT 60.020 37.500 21.36 0.00 0.00 2.52
2516 2863 4.354893 TCCTGGCATGCAATTTTCTTTT 57.645 36.364 21.36 0.00 0.00 2.27
2517 2864 4.716794 TCCTGGCATGCAATTTTCTTTTT 58.283 34.783 21.36 0.00 0.00 1.94
2559 2906 0.109342 ATGCAATTAGGCGGGAGAGG 59.891 55.000 0.00 0.00 36.28 3.69
2575 2924 3.852578 GGAGAGGGAGAGAGAGAGGATAT 59.147 52.174 0.00 0.00 0.00 1.63
2596 2945 2.358247 ACATGGACCGTTCACCGC 60.358 61.111 0.00 0.00 34.38 5.68
2626 2975 2.039787 TACCCCTCCCGACATGCA 59.960 61.111 0.00 0.00 0.00 3.96
2655 3004 3.141488 CGGGACCAGAGACCGGAG 61.141 72.222 9.46 0.00 43.69 4.63
2656 3005 3.462678 GGGACCAGAGACCGGAGC 61.463 72.222 9.46 0.00 0.00 4.70
2657 3006 3.462678 GGACCAGAGACCGGAGCC 61.463 72.222 9.46 0.00 0.00 4.70
2658 3007 2.680352 GACCAGAGACCGGAGCCA 60.680 66.667 9.46 0.00 0.00 4.75
2659 3008 2.203788 ACCAGAGACCGGAGCCAA 60.204 61.111 9.46 0.00 0.00 4.52
2660 3009 1.613630 ACCAGAGACCGGAGCCAAT 60.614 57.895 9.46 0.00 0.00 3.16
2661 3010 0.325296 ACCAGAGACCGGAGCCAATA 60.325 55.000 9.46 0.00 0.00 1.90
2662 3011 0.830648 CCAGAGACCGGAGCCAATAA 59.169 55.000 9.46 0.00 0.00 1.40
2663 3012 1.417890 CCAGAGACCGGAGCCAATAAT 59.582 52.381 9.46 0.00 0.00 1.28
2664 3013 2.487934 CAGAGACCGGAGCCAATAATG 58.512 52.381 9.46 0.00 0.00 1.90
2665 3014 2.119495 AGAGACCGGAGCCAATAATGT 58.881 47.619 9.46 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 56 2.159476 CCTATCATGTTGCCATATGCGC 60.159 50.000 0.00 0.00 45.60 6.09
254 268 4.510571 TGCGTGTCATGTACTACTCTCTA 58.489 43.478 0.00 0.00 0.00 2.43
308 328 8.997621 ACACTAAAACGTGACAATATACATCT 57.002 30.769 0.00 0.00 38.27 2.90
323 343 9.872757 ACATACAAACTGAAATACACTAAAACG 57.127 29.630 0.00 0.00 0.00 3.60
338 358 6.931838 TCTTACAGGGAGTACATACAAACTG 58.068 40.000 0.00 0.00 30.91 3.16
339 359 7.399191 TCATCTTACAGGGAGTACATACAAACT 59.601 37.037 0.00 0.00 30.91 2.66
340 360 7.553334 TCATCTTACAGGGAGTACATACAAAC 58.447 38.462 0.00 0.00 30.91 2.93
341 361 7.727578 TCATCTTACAGGGAGTACATACAAA 57.272 36.000 0.00 0.00 30.91 2.83
342 362 7.914427 ATCATCTTACAGGGAGTACATACAA 57.086 36.000 0.00 0.00 30.91 2.41
343 363 7.914427 AATCATCTTACAGGGAGTACATACA 57.086 36.000 0.00 0.00 30.91 2.29
344 364 9.614792 AAAAATCATCTTACAGGGAGTACATAC 57.385 33.333 0.00 0.00 30.91 2.39
348 368 7.606456 TGTCAAAAATCATCTTACAGGGAGTAC 59.394 37.037 0.00 0.00 30.91 2.73
350 370 6.431234 GTGTCAAAAATCATCTTACAGGGAGT 59.569 38.462 0.00 0.00 0.00 3.85
351 371 6.656693 AGTGTCAAAAATCATCTTACAGGGAG 59.343 38.462 0.00 0.00 0.00 4.30
352 372 6.542821 AGTGTCAAAAATCATCTTACAGGGA 58.457 36.000 0.00 0.00 0.00 4.20
356 376 8.902540 AGTGTAGTGTCAAAAATCATCTTACA 57.097 30.769 0.00 0.00 0.00 2.41
389 409 9.326413 CTCTGTCCCATAATATAAGACGTTTTT 57.674 33.333 0.00 0.00 0.00 1.94
390 410 7.931948 CCTCTGTCCCATAATATAAGACGTTTT 59.068 37.037 0.00 0.00 0.00 2.43
391 411 7.442656 CCTCTGTCCCATAATATAAGACGTTT 58.557 38.462 0.00 0.00 0.00 3.60
392 412 6.014499 CCCTCTGTCCCATAATATAAGACGTT 60.014 42.308 0.00 0.00 0.00 3.99
393 413 5.480772 CCCTCTGTCCCATAATATAAGACGT 59.519 44.000 0.00 0.00 0.00 4.34
394 414 5.715279 TCCCTCTGTCCCATAATATAAGACG 59.285 44.000 0.00 0.00 0.00 4.18
395 415 6.726764 ACTCCCTCTGTCCCATAATATAAGAC 59.273 42.308 0.00 0.00 0.00 3.01
396 416 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
397 417 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
398 418 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
399 419 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
400 420 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
401 421 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
402 422 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
403 423 4.348020 AACTACTCCCTCTGTCCCATAA 57.652 45.455 0.00 0.00 0.00 1.90
404 424 4.348020 AAACTACTCCCTCTGTCCCATA 57.652 45.455 0.00 0.00 0.00 2.74
405 425 2.950990 AACTACTCCCTCTGTCCCAT 57.049 50.000 0.00 0.00 0.00 4.00
406 426 2.715763 AAACTACTCCCTCTGTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
407 427 6.553852 TCAATATAAACTACTCCCTCTGTCCC 59.446 42.308 0.00 0.00 0.00 4.46
408 428 7.256012 CCTCAATATAAACTACTCCCTCTGTCC 60.256 44.444 0.00 0.00 0.00 4.02
409 429 7.288158 ACCTCAATATAAACTACTCCCTCTGTC 59.712 40.741 0.00 0.00 0.00 3.51
410 430 7.133483 ACCTCAATATAAACTACTCCCTCTGT 58.867 38.462 0.00 0.00 0.00 3.41
411 431 7.604657 ACCTCAATATAAACTACTCCCTCTG 57.395 40.000 0.00 0.00 0.00 3.35
412 432 8.512813 AGTACCTCAATATAAACTACTCCCTCT 58.487 37.037 0.00 0.00 0.00 3.69
413 433 8.709272 AGTACCTCAATATAAACTACTCCCTC 57.291 38.462 0.00 0.00 0.00 4.30
443 466 9.438291 CATCCGTTCACAAATATAAGATGTTTC 57.562 33.333 0.00 0.00 0.00 2.78
468 491 2.029200 TCGCAAATCGTGTTACCCTACA 60.029 45.455 0.00 0.00 39.67 2.74
492 515 7.372451 TCTAAATTTCGTCAAACGGAATCAT 57.628 32.000 6.48 2.66 45.99 2.45
499 522 4.611366 GGTTGCTCTAAATTTCGTCAAACG 59.389 41.667 0.00 0.00 44.19 3.60
564 587 3.959943 TCATTCGCATTTGCATCATCTG 58.040 40.909 3.13 0.00 42.21 2.90
597 626 4.529897 TGTGTCGTACAGTGGATATAGGT 58.470 43.478 0.00 0.00 33.42 3.08
806 1043 6.127730 GGAAAAGAGAAGAAACAAACAGACCA 60.128 38.462 0.00 0.00 0.00 4.02
872 1112 4.680237 CGGAAGTGAGTGGCGCCA 62.680 66.667 29.03 29.03 0.00 5.69
912 1153 1.941975 GAGGACTCAGAGGTACGTAGC 59.058 57.143 16.85 16.85 0.00 3.58
913 1154 2.937799 GTGAGGACTCAGAGGTACGTAG 59.062 54.545 1.56 0.00 40.75 3.51
914 1155 2.570752 AGTGAGGACTCAGAGGTACGTA 59.429 50.000 1.56 0.00 40.75 3.57
916 1157 2.116827 AGTGAGGACTCAGAGGTACG 57.883 55.000 1.56 0.00 40.75 3.67
968 1217 1.655885 TTGACGGTGCGCGAGGTATA 61.656 55.000 12.10 0.00 0.00 1.47
969 1218 2.997075 TTGACGGTGCGCGAGGTAT 61.997 57.895 12.10 0.00 0.00 2.73
970 1219 3.672447 TTGACGGTGCGCGAGGTA 61.672 61.111 12.10 0.00 0.00 3.08
989 1238 1.883084 GCCTCCATAGACGCGGTTG 60.883 63.158 12.47 1.66 0.00 3.77
991 1240 3.537874 GGCCTCCATAGACGCGGT 61.538 66.667 12.47 0.00 0.00 5.68
992 1241 3.214250 GAGGCCTCCATAGACGCGG 62.214 68.421 23.19 0.00 0.00 6.46
993 1242 2.336809 GAGGCCTCCATAGACGCG 59.663 66.667 23.19 3.53 0.00 6.01
1128 1383 4.853142 AGCTCCGCGGGGTCCATA 62.853 66.667 28.92 3.05 33.83 2.74
1188 1443 2.725312 GGCAGCCTCCTCGTCATCA 61.725 63.158 3.29 0.00 0.00 3.07
1323 1590 2.202892 GCGGAGTAGAAAGCGGGG 60.203 66.667 0.00 0.00 0.00 5.73
1423 1696 3.077556 CAGGAGGCGCAGGTACCT 61.078 66.667 9.21 9.21 39.65 3.08
1678 1954 3.810579 GATCTATGCCAGAGCGGAG 57.189 57.895 0.00 0.00 44.31 4.63
1682 1958 1.506493 CAACCGATCTATGCCAGAGC 58.494 55.000 0.00 0.00 36.48 4.09
1683 1959 1.069823 AGCAACCGATCTATGCCAGAG 59.930 52.381 9.70 0.00 40.93 3.35
1684 1960 1.123077 AGCAACCGATCTATGCCAGA 58.877 50.000 9.70 0.00 40.93 3.86
1685 1961 1.224075 CAGCAACCGATCTATGCCAG 58.776 55.000 9.70 1.89 40.93 4.85
1686 1962 0.815213 GCAGCAACCGATCTATGCCA 60.815 55.000 9.70 0.00 40.93 4.92
1687 1963 0.533755 AGCAGCAACCGATCTATGCC 60.534 55.000 9.70 0.00 40.93 4.40
1688 1964 0.864455 GAGCAGCAACCGATCTATGC 59.136 55.000 0.00 6.22 40.34 3.14
1689 1965 2.522836 AGAGCAGCAACCGATCTATG 57.477 50.000 0.00 0.00 0.00 2.23
1690 1966 3.550437 AAAGAGCAGCAACCGATCTAT 57.450 42.857 0.00 0.00 0.00 1.98
1691 1967 3.002791 CAAAAGAGCAGCAACCGATCTA 58.997 45.455 0.00 0.00 0.00 1.98
1700 1976 2.964464 TCAAAATCCCAAAAGAGCAGCA 59.036 40.909 0.00 0.00 0.00 4.41
1708 1984 4.101741 ACACCGGAAATCAAAATCCCAAAA 59.898 37.500 9.46 0.00 31.73 2.44
1711 1987 2.883026 ACACCGGAAATCAAAATCCCA 58.117 42.857 9.46 0.00 31.73 4.37
1738 2018 4.641954 CACTCAAGTGTCGTATGCAAATC 58.358 43.478 1.88 0.00 40.96 2.17
1880 2167 2.477357 CGAATCTCGTCCTTAGCAACGA 60.477 50.000 7.61 7.61 44.91 3.85
1904 2201 7.480542 CGTATCTTCGTTAACAATTTCCTTTGG 59.519 37.037 6.39 0.00 0.00 3.28
1921 2218 2.159366 AGGACAGAAGTGCGTATCTTCG 60.159 50.000 9.05 7.56 43.93 3.79
1973 2270 5.176406 GCCTGACGCATGCATACATATATAG 59.824 44.000 19.57 0.00 37.47 1.31
1991 2296 0.691078 TGGGGTCTATCTGGCCTGAC 60.691 60.000 15.36 9.29 41.10 3.51
2002 2307 3.668141 TGACCTAACGTATGGGGTCTA 57.332 47.619 21.20 11.05 45.85 2.59
2012 2317 3.492011 GTCGATGTTTGTTGACCTAACGT 59.508 43.478 0.00 0.00 42.34 3.99
2093 2403 9.609346 GCCTATAGGTTTGAATGAGTTTTAGTA 57.391 33.333 20.10 0.00 37.57 1.82
2094 2404 8.107095 TGCCTATAGGTTTGAATGAGTTTTAGT 58.893 33.333 20.10 0.00 37.57 2.24
2120 2437 2.064434 TGACCTCATCGATCTCAGCT 57.936 50.000 0.00 0.00 0.00 4.24
2126 2443 0.385751 TCGGCTTGACCTCATCGATC 59.614 55.000 0.00 0.00 35.61 3.69
2133 2450 1.737008 GGTCGTTCGGCTTGACCTC 60.737 63.158 3.46 0.00 46.86 3.85
2175 2492 6.941436 AGTATTTTCGGACGGAGAGAGTATAT 59.059 38.462 0.00 0.00 0.00 0.86
2176 2493 6.294473 AGTATTTTCGGACGGAGAGAGTATA 58.706 40.000 0.00 0.00 0.00 1.47
2177 2494 5.131784 AGTATTTTCGGACGGAGAGAGTAT 58.868 41.667 0.00 0.00 0.00 2.12
2178 2495 4.521146 AGTATTTTCGGACGGAGAGAGTA 58.479 43.478 0.00 0.00 0.00 2.59
2179 2496 3.354467 AGTATTTTCGGACGGAGAGAGT 58.646 45.455 0.00 0.00 0.00 3.24
2180 2497 4.106197 CAAGTATTTTCGGACGGAGAGAG 58.894 47.826 0.00 0.00 0.00 3.20
2181 2498 3.508793 ACAAGTATTTTCGGACGGAGAGA 59.491 43.478 0.00 0.00 0.00 3.10
2182 2499 3.846360 ACAAGTATTTTCGGACGGAGAG 58.154 45.455 0.00 0.00 0.00 3.20
2183 2500 3.256383 TGACAAGTATTTTCGGACGGAGA 59.744 43.478 0.00 0.00 0.00 3.71
2184 2501 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2185 2502 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2186 2503 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2187 2504 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2188 2505 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
2189 2506 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2190 2507 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
2191 2508 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
2198 2515 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
2250 2567 9.713684 TCAAAATGGATAAAAGGGAATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
2253 2570 9.486123 TCATCAAAATGGATAAAAGGGAATGTA 57.514 29.630 0.00 0.00 33.42 2.29
2254 2571 8.260114 GTCATCAAAATGGATAAAAGGGAATGT 58.740 33.333 0.00 0.00 33.42 2.71
2255 2572 8.259411 TGTCATCAAAATGGATAAAAGGGAATG 58.741 33.333 0.00 0.00 33.42 2.67
2256 2573 8.378115 TGTCATCAAAATGGATAAAAGGGAAT 57.622 30.769 0.00 0.00 33.42 3.01
2257 2574 7.789202 TGTCATCAAAATGGATAAAAGGGAA 57.211 32.000 0.00 0.00 33.42 3.97
2258 2575 7.454380 ACTTGTCATCAAAATGGATAAAAGGGA 59.546 33.333 0.00 0.00 33.42 4.20
2259 2576 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
2265 2582 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2266 2583 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2267 2584 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2268 2585 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2269 2586 5.516339 GCCGGAAATACTTGTCATCAAAATG 59.484 40.000 5.05 0.00 32.87 2.32
2270 2587 5.650543 GCCGGAAATACTTGTCATCAAAAT 58.349 37.500 5.05 0.00 32.87 1.82
2271 2588 4.378978 CGCCGGAAATACTTGTCATCAAAA 60.379 41.667 5.05 0.00 32.87 2.44
2272 2589 3.126171 CGCCGGAAATACTTGTCATCAAA 59.874 43.478 5.05 0.00 32.87 2.69
2273 2590 2.675844 CGCCGGAAATACTTGTCATCAA 59.324 45.455 5.05 0.00 0.00 2.57
2274 2591 2.276201 CGCCGGAAATACTTGTCATCA 58.724 47.619 5.05 0.00 0.00 3.07
2275 2592 1.597663 CCGCCGGAAATACTTGTCATC 59.402 52.381 5.05 0.00 0.00 2.92
2276 2593 1.208535 TCCGCCGGAAATACTTGTCAT 59.791 47.619 1.70 0.00 0.00 3.06
2277 2594 0.609151 TCCGCCGGAAATACTTGTCA 59.391 50.000 1.70 0.00 0.00 3.58
2278 2595 1.287425 CTCCGCCGGAAATACTTGTC 58.713 55.000 7.50 0.00 0.00 3.18
2279 2596 0.107848 CCTCCGCCGGAAATACTTGT 60.108 55.000 7.50 0.00 0.00 3.16
2280 2597 0.814010 CCCTCCGCCGGAAATACTTG 60.814 60.000 7.50 0.00 0.00 3.16
2281 2598 0.979187 TCCCTCCGCCGGAAATACTT 60.979 55.000 7.50 0.00 0.00 2.24
2282 2599 1.382146 TCCCTCCGCCGGAAATACT 60.382 57.895 7.50 0.00 0.00 2.12
2283 2600 1.069258 CTCCCTCCGCCGGAAATAC 59.931 63.158 7.50 0.00 0.00 1.89
2284 2601 0.106066 TACTCCCTCCGCCGGAAATA 60.106 55.000 7.50 0.00 0.00 1.40
2285 2602 0.763223 ATACTCCCTCCGCCGGAAAT 60.763 55.000 7.50 0.00 0.00 2.17
2286 2603 0.106066 TATACTCCCTCCGCCGGAAA 60.106 55.000 7.50 0.00 0.00 3.13
2287 2604 0.113776 ATATACTCCCTCCGCCGGAA 59.886 55.000 7.50 0.00 0.00 4.30
2288 2605 0.994247 TATATACTCCCTCCGCCGGA 59.006 55.000 5.05 5.37 0.00 5.14
2289 2606 1.390565 CTATATACTCCCTCCGCCGG 58.609 60.000 0.00 0.00 0.00 6.13
2290 2607 0.739561 GCTATATACTCCCTCCGCCG 59.260 60.000 0.00 0.00 0.00 6.46
2291 2608 1.751924 CAGCTATATACTCCCTCCGCC 59.248 57.143 0.00 0.00 0.00 6.13
2292 2609 1.135333 GCAGCTATATACTCCCTCCGC 59.865 57.143 0.00 0.00 0.00 5.54
2293 2610 2.164624 GTGCAGCTATATACTCCCTCCG 59.835 54.545 0.00 0.00 0.00 4.63
2294 2611 3.165875 TGTGCAGCTATATACTCCCTCC 58.834 50.000 0.00 0.00 0.00 4.30
2295 2612 3.829601 ACTGTGCAGCTATATACTCCCTC 59.170 47.826 0.00 0.00 0.00 4.30
2296 2613 3.850752 ACTGTGCAGCTATATACTCCCT 58.149 45.455 0.00 0.00 0.00 4.20
2297 2614 4.039245 TCAACTGTGCAGCTATATACTCCC 59.961 45.833 0.00 0.00 0.00 4.30
2298 2615 5.201713 TCAACTGTGCAGCTATATACTCC 57.798 43.478 0.00 0.00 0.00 3.85
2299 2616 6.925718 TGAATCAACTGTGCAGCTATATACTC 59.074 38.462 0.00 0.00 0.00 2.59
2300 2617 6.820335 TGAATCAACTGTGCAGCTATATACT 58.180 36.000 0.00 0.00 0.00 2.12
2301 2618 7.664082 ATGAATCAACTGTGCAGCTATATAC 57.336 36.000 0.00 0.00 0.00 1.47
2302 2619 9.948964 ATAATGAATCAACTGTGCAGCTATATA 57.051 29.630 0.00 0.00 0.00 0.86
2407 2743 5.049828 CGTATCTACTGTCATGCATTTGGA 58.950 41.667 0.00 0.00 0.00 3.53
2408 2744 4.319046 GCGTATCTACTGTCATGCATTTGG 60.319 45.833 0.00 0.00 0.00 3.28
2410 2746 4.271049 GTGCGTATCTACTGTCATGCATTT 59.729 41.667 0.00 0.00 33.25 2.32
2411 2747 3.804325 GTGCGTATCTACTGTCATGCATT 59.196 43.478 0.00 0.00 33.25 3.56
2412 2748 3.181476 TGTGCGTATCTACTGTCATGCAT 60.181 43.478 0.00 0.00 33.25 3.96
2413 2749 2.165437 TGTGCGTATCTACTGTCATGCA 59.835 45.455 0.00 0.00 0.00 3.96
2414 2750 2.791560 CTGTGCGTATCTACTGTCATGC 59.208 50.000 0.00 0.00 0.00 4.06
2415 2751 3.375642 CCTGTGCGTATCTACTGTCATG 58.624 50.000 0.00 0.00 0.00 3.07
2441 2786 9.606631 ACTACAAATGATCTTAATCTGAGTTCC 57.393 33.333 0.00 0.00 32.75 3.62
2466 2813 4.230657 CAATCCTGCGTATAGTAGAGCAC 58.769 47.826 0.00 0.00 35.59 4.40
2467 2814 3.255888 CCAATCCTGCGTATAGTAGAGCA 59.744 47.826 0.00 0.00 38.03 4.26
2468 2815 3.506455 TCCAATCCTGCGTATAGTAGAGC 59.494 47.826 0.00 0.00 34.21 4.09
2469 2816 5.707242 TTCCAATCCTGCGTATAGTAGAG 57.293 43.478 0.00 0.00 34.21 2.43
2470 2817 5.773176 TGATTCCAATCCTGCGTATAGTAGA 59.227 40.000 0.00 0.00 34.50 2.59
2471 2818 6.025749 TGATTCCAATCCTGCGTATAGTAG 57.974 41.667 0.00 0.00 34.50 2.57
2472 2819 6.351033 GGATGATTCCAATCCTGCGTATAGTA 60.351 42.308 0.00 0.00 42.12 1.82
2473 2820 4.955811 TGATTCCAATCCTGCGTATAGT 57.044 40.909 0.00 0.00 34.50 2.12
2474 2821 4.872691 GGATGATTCCAATCCTGCGTATAG 59.127 45.833 0.00 0.00 42.12 1.31
2475 2822 4.532126 AGGATGATTCCAATCCTGCGTATA 59.468 41.667 4.18 0.00 45.30 1.47
2476 2823 3.328931 AGGATGATTCCAATCCTGCGTAT 59.671 43.478 4.18 0.00 45.30 3.06
2477 2824 2.705658 AGGATGATTCCAATCCTGCGTA 59.294 45.455 4.18 0.00 45.30 4.42
2478 2825 1.492176 AGGATGATTCCAATCCTGCGT 59.508 47.619 4.18 0.00 45.30 5.24
2479 2826 2.267174 AGGATGATTCCAATCCTGCG 57.733 50.000 4.18 0.00 45.30 5.18
2482 2829 1.854939 TGCCAGGATGATTCCAATCCT 59.145 47.619 0.00 0.00 45.30 3.24
2483 2830 2.369983 TGCCAGGATGATTCCAATCC 57.630 50.000 0.00 0.00 45.30 3.01
2484 2831 2.029290 GCATGCCAGGATGATTCCAATC 60.029 50.000 6.36 0.00 45.30 2.67
2485 2832 1.968493 GCATGCCAGGATGATTCCAAT 59.032 47.619 6.36 0.00 45.30 3.16
2486 2833 1.342175 TGCATGCCAGGATGATTCCAA 60.342 47.619 16.68 0.00 45.30 3.53
2487 2834 0.259356 TGCATGCCAGGATGATTCCA 59.741 50.000 16.68 0.00 45.30 3.53
2488 2835 1.405872 TTGCATGCCAGGATGATTCC 58.594 50.000 16.68 0.00 39.69 3.01
2489 2836 3.746045 AATTGCATGCCAGGATGATTC 57.254 42.857 16.68 0.00 39.69 2.52
2490 2837 4.163458 AGAAAATTGCATGCCAGGATGATT 59.837 37.500 16.68 3.85 39.69 2.57
2491 2838 3.709653 AGAAAATTGCATGCCAGGATGAT 59.290 39.130 16.68 0.00 39.69 2.45
2492 2839 3.101437 AGAAAATTGCATGCCAGGATGA 58.899 40.909 16.68 0.00 39.69 2.92
2493 2840 3.536956 AGAAAATTGCATGCCAGGATG 57.463 42.857 16.68 0.00 0.00 3.51
2494 2841 4.563140 AAAGAAAATTGCATGCCAGGAT 57.437 36.364 16.68 1.03 0.00 3.24
2495 2842 4.354893 AAAAGAAAATTGCATGCCAGGA 57.645 36.364 16.68 0.00 0.00 3.86
2517 2864 6.219417 TGCCAAGATGTTTCTCAAAAAGAA 57.781 33.333 0.00 0.00 42.35 2.52
2518 2865 5.850557 TGCCAAGATGTTTCTCAAAAAGA 57.149 34.783 0.00 0.00 0.00 2.52
2519 2866 5.107220 GCATGCCAAGATGTTTCTCAAAAAG 60.107 40.000 6.36 0.00 0.00 2.27
2520 2867 4.751098 GCATGCCAAGATGTTTCTCAAAAA 59.249 37.500 6.36 0.00 0.00 1.94
2521 2868 4.202233 TGCATGCCAAGATGTTTCTCAAAA 60.202 37.500 16.68 0.00 0.00 2.44
2522 2869 3.321396 TGCATGCCAAGATGTTTCTCAAA 59.679 39.130 16.68 0.00 0.00 2.69
2523 2870 2.892215 TGCATGCCAAGATGTTTCTCAA 59.108 40.909 16.68 0.00 0.00 3.02
2524 2871 2.516906 TGCATGCCAAGATGTTTCTCA 58.483 42.857 16.68 0.00 0.00 3.27
2525 2872 3.581024 TTGCATGCCAAGATGTTTCTC 57.419 42.857 16.68 0.00 0.00 2.87
2526 2873 4.546829 AATTGCATGCCAAGATGTTTCT 57.453 36.364 16.68 0.00 36.76 2.52
2527 2874 4.807304 CCTAATTGCATGCCAAGATGTTTC 59.193 41.667 16.68 0.00 36.76 2.78
2528 2875 4.761975 CCTAATTGCATGCCAAGATGTTT 58.238 39.130 16.68 3.55 36.76 2.83
2529 2876 3.431207 GCCTAATTGCATGCCAAGATGTT 60.431 43.478 16.68 0.00 36.76 2.71
2530 2877 2.101917 GCCTAATTGCATGCCAAGATGT 59.898 45.455 16.68 0.00 36.76 3.06
2531 2878 2.750948 GCCTAATTGCATGCCAAGATG 58.249 47.619 16.68 0.91 36.76 2.90
2532 2879 1.338973 CGCCTAATTGCATGCCAAGAT 59.661 47.619 16.68 1.03 36.76 2.40
2533 2880 0.740149 CGCCTAATTGCATGCCAAGA 59.260 50.000 16.68 0.00 36.76 3.02
2534 2881 0.249155 CCGCCTAATTGCATGCCAAG 60.249 55.000 16.68 6.95 36.76 3.61
2535 2882 1.674764 CCCGCCTAATTGCATGCCAA 61.675 55.000 16.68 10.06 37.94 4.52
2559 2906 3.008594 TGTCGGATATCCTCTCTCTCTCC 59.991 52.174 19.61 0.00 0.00 3.71
2575 2924 1.290955 GTGAACGGTCCATGTCGGA 59.709 57.895 0.00 0.00 43.61 4.55
2639 2988 3.462678 GCTCCGGTCTCTGGTCCC 61.463 72.222 0.00 0.00 0.00 4.46
2640 2989 3.462678 GGCTCCGGTCTCTGGTCC 61.463 72.222 0.00 0.00 0.00 4.46
2641 2990 1.617947 ATTGGCTCCGGTCTCTGGTC 61.618 60.000 0.00 0.00 0.00 4.02
2642 2991 0.325296 TATTGGCTCCGGTCTCTGGT 60.325 55.000 0.00 0.00 0.00 4.00
2643 2992 0.830648 TTATTGGCTCCGGTCTCTGG 59.169 55.000 0.00 0.00 0.00 3.86
2644 2993 2.158900 ACATTATTGGCTCCGGTCTCTG 60.159 50.000 0.00 0.00 0.00 3.35
2645 2994 2.119495 ACATTATTGGCTCCGGTCTCT 58.881 47.619 0.00 0.00 0.00 3.10
2646 2995 2.622064 ACATTATTGGCTCCGGTCTC 57.378 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.