Multiple sequence alignment - TraesCS5B01G250800

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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 TraesCS5B01G250800 chr5B 100.000 4148 0 0 1 4148 432981686 432985833 0.000000e+00 7661.0
1 TraesCS5B01G250800 chr6B 92.790 2871 134 26 418 3252 12885997 12888830 0.000000e+00 4087.0
2 TraesCS5B01G250800 chr6B 91.070 2206 188 6 973 3172 13653949 13651747 0.000000e+00 2974.0
3 TraesCS5B01G250800 chr6B 89.684 2307 222 14 999 3296 26861804 26864103 0.000000e+00 2928.0
4 TraesCS5B01G250800 chr6B 89.911 337 17 6 1 337 12885681 12886000 6.410000e-113 418.0
5 TraesCS5B01G250800 chr6B 83.212 137 7 8 754 875 13654191 13654056 1.220000e-20 111.0
6 TraesCS5B01G250800 chr6A 87.999 2758 266 36 751 3457 7079332 7082075 0.000000e+00 3199.0
7 TraesCS5B01G250800 chr6A 90.280 2212 191 17 949 3149 7186852 7184654 0.000000e+00 2872.0
8 TraesCS5B01G250800 chr6A 88.552 2376 244 17 903 3259 7176070 7173704 0.000000e+00 2856.0
9 TraesCS5B01G250800 chr6A 87.472 886 77 11 3175 4039 7092340 7093212 0.000000e+00 990.0
10 TraesCS5B01G250800 chr6A 91.630 227 12 2 111 337 7063943 7064162 1.450000e-79 307.0
11 TraesCS5B01G250800 chr6A 82.178 303 32 10 3176 3457 7184661 7184360 1.490000e-59 241.0
12 TraesCS5B01G250800 chr6A 93.137 102 7 0 1 102 7063785 7063886 2.580000e-32 150.0
13 TraesCS5B01G250800 chrUn 91.044 2289 201 3 973 3259 79937079 79939365 0.000000e+00 3088.0
14 TraesCS5B01G250800 chrUn 88.520 2291 258 5 973 3259 80037167 80034878 0.000000e+00 2769.0
15 TraesCS5B01G250800 chrUn 89.764 127 6 4 558 680 79930142 79930265 5.550000e-34 156.0
16 TraesCS5B01G250800 chr7D 89.931 2324 224 8 942 3259 597677191 597674872 0.000000e+00 2987.0
17 TraesCS5B01G250800 chr6D 89.182 2237 231 10 966 3196 7346001 7343770 0.000000e+00 2780.0
18 TraesCS5B01G250800 chr6D 90.782 358 30 2 3684 4039 7342890 7342534 3.750000e-130 475.0
19 TraesCS5B01G250800 chr6D 92.715 151 11 0 3513 3663 7343420 7343270 6.980000e-53 219.0
20 TraesCS5B01G250800 chr6D 91.589 107 7 2 335 441 194007120 194007016 3.340000e-31 147.0
21 TraesCS5B01G250800 chr6D 98.000 50 1 0 582 631 7346370 7346321 2.050000e-13 87.9
22 TraesCS5B01G250800 chr6D 85.484 62 4 4 763 822 7359614 7359556 4.480000e-05 60.2
23 TraesCS5B01G250800 chr4B 95.192 104 3 2 325 426 443547457 443547354 3.320000e-36 163.0
24 TraesCS5B01G250800 chr4B 95.876 97 3 1 335 431 27246034 27245939 5.550000e-34 156.0
25 TraesCS5B01G250800 chr5A 95.960 99 3 1 329 426 48918170 48918072 4.290000e-35 159.0
26 TraesCS5B01G250800 chr7A 95.876 97 4 0 330 426 126943132 126943036 1.540000e-34 158.0
27 TraesCS5B01G250800 chr1B 95.050 101 4 1 321 420 632863380 632863280 1.540000e-34 158.0
28 TraesCS5B01G250800 chr7B 94.118 102 6 0 329 430 117797345 117797446 5.550000e-34 156.0
29 TraesCS5B01G250800 chr7B 92.727 110 3 5 315 420 451446859 451446967 2.000000e-33 154.0
30 TraesCS5B01G250800 chr3B 93.269 104 6 1 324 426 241399322 241399219 7.180000e-33 152.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G250800 chr5B 432981686 432985833 4147 False 7661.000 7661 100.00000 1 4148 1 chr5B.!!$F1 4147
1 TraesCS5B01G250800 chr6B 26861804 26864103 2299 False 2928.000 2928 89.68400 999 3296 1 chr6B.!!$F1 2297
2 TraesCS5B01G250800 chr6B 12885681 12888830 3149 False 2252.500 4087 91.35050 1 3252 2 chr6B.!!$F2 3251
3 TraesCS5B01G250800 chr6B 13651747 13654191 2444 True 1542.500 2974 87.14100 754 3172 2 chr6B.!!$R1 2418
4 TraesCS5B01G250800 chr6A 7079332 7082075 2743 False 3199.000 3199 87.99900 751 3457 1 chr6A.!!$F1 2706
5 TraesCS5B01G250800 chr6A 7173704 7176070 2366 True 2856.000 2856 88.55200 903 3259 1 chr6A.!!$R1 2356
6 TraesCS5B01G250800 chr6A 7184360 7186852 2492 True 1556.500 2872 86.22900 949 3457 2 chr6A.!!$R2 2508
7 TraesCS5B01G250800 chr6A 7092340 7093212 872 False 990.000 990 87.47200 3175 4039 1 chr6A.!!$F2 864
8 TraesCS5B01G250800 chrUn 79937079 79939365 2286 False 3088.000 3088 91.04400 973 3259 1 chrUn.!!$F2 2286
9 TraesCS5B01G250800 chrUn 80034878 80037167 2289 True 2769.000 2769 88.52000 973 3259 1 chrUn.!!$R1 2286
10 TraesCS5B01G250800 chr7D 597674872 597677191 2319 True 2987.000 2987 89.93100 942 3259 1 chr7D.!!$R1 2317
11 TraesCS5B01G250800 chr6D 7342534 7346370 3836 True 890.475 2780 92.66975 582 4039 4 chr6D.!!$R3 3457

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
90 91 0.415429 AGAGAAGCTTCAGGAGGGGA 59.585 55.000 27.57 0.0 0.00 4.81 F
1042 1165 0.171231 CGACAGACGCATCTTGGAGA 59.829 55.000 0.00 0.0 30.42 3.71 F
1850 1976 1.064685 GGAGGTGGATCGGGTTTTCAT 60.065 52.381 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 1334 0.963962 CACCTTGGCTCTTGCAACAT 59.036 50.0 0.00 0.0 41.91 2.71 R
2691 2820 0.611896 CCTTCCCGGCCAACATTTCT 60.612 55.0 2.24 0.0 0.00 2.52 R
3361 3583 0.112995 TGGAGGCCAAATGAACAGCT 59.887 50.0 5.01 0.0 0.00 4.24 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
29 30 0.804933 GCGAGGTATGGACGGTTGTC 60.805 60.000 0.00 0.00 44.72 3.18
40 41 3.050275 GGTTGTCTGCCACGCTCC 61.050 66.667 0.00 0.00 0.00 4.70
53 54 3.717294 GCTCCCGGGAAGCAAGGA 61.717 66.667 29.17 7.02 0.00 3.36
87 88 0.829990 GGGAGAGAAGCTTCAGGAGG 59.170 60.000 27.57 0.00 0.00 4.30
90 91 0.415429 AGAGAAGCTTCAGGAGGGGA 59.585 55.000 27.57 0.00 0.00 4.81
132 133 5.361427 TCGAAATATGGAAGCACCGAAATA 58.639 37.500 0.00 0.00 42.61 1.40
177 178 5.238432 GTGCCATCGATAAACCATGTATTCA 59.762 40.000 0.00 0.00 0.00 2.57
186 187 8.595533 CGATAAACCATGTATTCAATAGGATCG 58.404 37.037 0.00 0.00 0.00 3.69
193 194 7.310052 CCATGTATTCAATAGGATCGAAGGAGA 60.310 40.741 0.00 0.00 0.00 3.71
194 195 7.597288 TGTATTCAATAGGATCGAAGGAGAA 57.403 36.000 0.00 0.00 0.00 2.87
195 196 8.195165 TGTATTCAATAGGATCGAAGGAGAAT 57.805 34.615 0.00 0.00 0.00 2.40
196 197 8.090831 TGTATTCAATAGGATCGAAGGAGAATG 58.909 37.037 0.00 0.00 0.00 2.67
197 198 4.887748 TCAATAGGATCGAAGGAGAATGC 58.112 43.478 0.00 0.00 0.00 3.56
198 199 3.971245 ATAGGATCGAAGGAGAATGCC 57.029 47.619 0.00 0.00 0.00 4.40
199 200 1.500474 AGGATCGAAGGAGAATGCCA 58.500 50.000 0.00 0.00 0.00 4.92
200 201 1.415659 AGGATCGAAGGAGAATGCCAG 59.584 52.381 0.00 0.00 0.00 4.85
201 202 1.414181 GGATCGAAGGAGAATGCCAGA 59.586 52.381 0.00 0.00 0.00 3.86
202 203 2.038295 GGATCGAAGGAGAATGCCAGAT 59.962 50.000 0.00 0.00 0.00 2.90
246 247 3.485764 GGAGATGTTGCCTCCTTCC 57.514 57.895 0.00 0.00 45.18 3.46
249 250 1.556911 GAGATGTTGCCTCCTTCCTGA 59.443 52.381 0.00 0.00 0.00 3.86
262 263 3.319405 TCCTTCCTGAGAGCGTTATCATC 59.681 47.826 0.00 0.00 0.00 2.92
293 294 1.330213 GGCTACGACGAGGAGTTAGAC 59.670 57.143 0.00 0.00 31.77 2.59
312 313 0.734942 CTAGCCAACGTACACGGGTG 60.735 60.000 0.00 3.99 44.95 4.61
337 338 6.290294 AGTTGGGTTCGTGTAATATGTACT 57.710 37.500 0.00 0.00 0.00 2.73
338 339 6.335777 AGTTGGGTTCGTGTAATATGTACTC 58.664 40.000 0.00 0.00 0.00 2.59
339 340 5.266733 TGGGTTCGTGTAATATGTACTCC 57.733 43.478 0.00 0.00 0.00 3.85
340 341 4.099881 TGGGTTCGTGTAATATGTACTCCC 59.900 45.833 0.00 0.00 0.00 4.30
341 342 4.343239 GGGTTCGTGTAATATGTACTCCCT 59.657 45.833 0.00 0.00 0.00 4.20
342 343 5.508657 GGGTTCGTGTAATATGTACTCCCTC 60.509 48.000 0.00 0.00 0.00 4.30
343 344 5.508657 GGTTCGTGTAATATGTACTCCCTCC 60.509 48.000 0.00 0.00 0.00 4.30
344 345 3.817084 TCGTGTAATATGTACTCCCTCCG 59.183 47.826 0.00 0.00 0.00 4.63
345 346 3.567164 CGTGTAATATGTACTCCCTCCGT 59.433 47.826 0.00 0.00 0.00 4.69
346 347 4.037208 CGTGTAATATGTACTCCCTCCGTT 59.963 45.833 0.00 0.00 0.00 4.44
347 348 5.527033 GTGTAATATGTACTCCCTCCGTTC 58.473 45.833 0.00 0.00 0.00 3.95
348 349 4.586001 TGTAATATGTACTCCCTCCGTTCC 59.414 45.833 0.00 0.00 0.00 3.62
349 350 2.832643 TATGTACTCCCTCCGTTCCA 57.167 50.000 0.00 0.00 0.00 3.53
350 351 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
351 352 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
352 353 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
353 354 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
354 355 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
355 356 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
356 357 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
357 358 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
358 359 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
359 360 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
360 361 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
361 362 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
362 363 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
363 364 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
364 365 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
365 366 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
366 367 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
367 368 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
368 369 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
369 370 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
370 371 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
371 372 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
372 373 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
373 374 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
406 407 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
407 408 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
408 409 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
409 410 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
410 411 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
411 412 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
412 413 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
413 414 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
414 415 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
415 416 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
416 417 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
417 418 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
418 419 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
419 420 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
420 421 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
438 439 1.640428 ACACACTCATGCGTATTCGG 58.360 50.000 0.00 0.00 37.56 4.30
504 505 9.996554 ATTCCTACCCAAAAATAAAACAAAGAG 57.003 29.630 0.00 0.00 0.00 2.85
505 506 7.438564 TCCTACCCAAAAATAAAACAAAGAGC 58.561 34.615 0.00 0.00 0.00 4.09
506 507 7.070074 TCCTACCCAAAAATAAAACAAAGAGCA 59.930 33.333 0.00 0.00 0.00 4.26
507 508 7.384932 CCTACCCAAAAATAAAACAAAGAGCAG 59.615 37.037 0.00 0.00 0.00 4.24
508 509 6.649155 ACCCAAAAATAAAACAAAGAGCAGT 58.351 32.000 0.00 0.00 0.00 4.40
509 510 6.761242 ACCCAAAAATAAAACAAAGAGCAGTC 59.239 34.615 0.00 0.00 0.00 3.51
510 511 6.202762 CCCAAAAATAAAACAAAGAGCAGTCC 59.797 38.462 0.00 0.00 0.00 3.85
511 512 6.986231 CCAAAAATAAAACAAAGAGCAGTCCT 59.014 34.615 0.00 0.00 0.00 3.85
512 513 7.495606 CCAAAAATAAAACAAAGAGCAGTCCTT 59.504 33.333 0.00 0.00 0.00 3.36
513 514 8.542953 CAAAAATAAAACAAAGAGCAGTCCTTC 58.457 33.333 0.00 0.00 0.00 3.46
514 515 6.959639 AATAAAACAAAGAGCAGTCCTTCA 57.040 33.333 0.00 0.00 0.00 3.02
515 516 6.959639 ATAAAACAAAGAGCAGTCCTTCAA 57.040 33.333 0.00 0.00 0.00 2.69
516 517 4.907879 AAACAAAGAGCAGTCCTTCAAG 57.092 40.909 0.00 0.00 0.00 3.02
517 518 3.567478 ACAAAGAGCAGTCCTTCAAGT 57.433 42.857 0.00 0.00 0.00 3.16
520 521 3.305398 AAGAGCAGTCCTTCAAGTACG 57.695 47.619 0.00 0.00 0.00 3.67
536 537 6.050432 TCAAGTACGTATGGTGTGAAGTTTT 58.950 36.000 0.00 0.00 0.00 2.43
577 578 8.047413 TCAGTTAGTTCACGATACAGATACAA 57.953 34.615 0.00 0.00 0.00 2.41
578 579 7.966753 TCAGTTAGTTCACGATACAGATACAAC 59.033 37.037 0.00 0.00 0.00 3.32
580 581 8.521176 AGTTAGTTCACGATACAGATACAACTT 58.479 33.333 0.00 0.00 0.00 2.66
581 582 8.796278 GTTAGTTCACGATACAGATACAACTTC 58.204 37.037 0.00 0.00 0.00 3.01
582 583 7.159322 AGTTCACGATACAGATACAACTTCT 57.841 36.000 0.00 0.00 0.00 2.85
583 584 7.603651 AGTTCACGATACAGATACAACTTCTT 58.396 34.615 0.00 0.00 0.00 2.52
584 585 7.755822 AGTTCACGATACAGATACAACTTCTTC 59.244 37.037 0.00 0.00 0.00 2.87
585 586 7.392494 TCACGATACAGATACAACTTCTTCT 57.608 36.000 0.00 0.00 0.00 2.85
586 587 7.827701 TCACGATACAGATACAACTTCTTCTT 58.172 34.615 0.00 0.00 0.00 2.52
683 697 4.475135 GCGTTGAGGCCCTCTCCC 62.475 72.222 12.94 0.00 41.76 4.30
992 1105 0.465278 GAGGGATTCTTCAGGCCAGC 60.465 60.000 5.01 0.00 0.00 4.85
1042 1165 0.171231 CGACAGACGCATCTTGGAGA 59.829 55.000 0.00 0.00 30.42 3.71
1142 1265 2.768344 TGGGCCTTCCTCGATCCC 60.768 66.667 4.53 0.00 37.49 3.85
1211 1334 1.671742 GCGTCTCCCTCTTCAACCA 59.328 57.895 0.00 0.00 0.00 3.67
1610 1736 3.507162 TGATGGCTTGTTGAAAGAGGA 57.493 42.857 0.00 0.00 0.00 3.71
1795 1921 7.070696 TGCCAGATGTTACCACATATACTAGTT 59.929 37.037 0.00 0.00 44.22 2.24
1850 1976 1.064685 GGAGGTGGATCGGGTTTTCAT 60.065 52.381 0.00 0.00 0.00 2.57
1949 2075 3.517100 AGATGCACAGAAGCTAGGAAGAA 59.483 43.478 0.00 0.00 34.99 2.52
1977 2103 2.133281 TCATGATCAGTTTGGGCCAG 57.867 50.000 6.23 0.00 0.00 4.85
2305 2431 5.069251 ACTGAAGGGTTAGTTCCTGATATCG 59.931 44.000 0.00 0.00 34.34 2.92
2408 2537 1.750399 GCGGCATCTGTCCCAACAT 60.750 57.895 0.00 0.00 34.13 2.71
2420 2549 4.385825 TGTCCCAACATAGTGTTCTTCAC 58.614 43.478 0.00 0.00 46.46 3.18
2528 2657 6.889198 AGCCTGATGTGTGTACTTATAACAT 58.111 36.000 0.00 0.00 34.28 2.71
2679 2808 7.239438 AGAATGGAAGGATAGATGATGCATTT 58.761 34.615 0.00 0.00 33.12 2.32
2691 2820 6.751157 AGATGATGCATTTGTTGTTTTCAGA 58.249 32.000 0.00 0.00 0.00 3.27
2808 2937 3.737559 TTGTTTGATGGTATCTGGGCT 57.262 42.857 0.00 0.00 0.00 5.19
2898 3027 9.639563 TCTCTACAAGAGTCTGATGATCTATTT 57.360 33.333 0.00 0.00 42.83 1.40
2899 3028 9.681692 CTCTACAAGAGTCTGATGATCTATTTG 57.318 37.037 0.00 0.00 37.57 2.32
2940 3070 0.679505 GTGCTGCCGACTCCCATATA 59.320 55.000 0.00 0.00 0.00 0.86
2941 3071 1.070134 GTGCTGCCGACTCCCATATAA 59.930 52.381 0.00 0.00 0.00 0.98
3111 3241 8.364142 CAGGAATATAAAGAGTTACTCCCTGAG 58.636 40.741 18.60 0.73 35.52 3.35
3114 3244 9.974980 GAATATAAAGAGTTACTCCCTGAGAAG 57.025 37.037 8.96 0.00 33.32 2.85
3172 3302 8.885693 AAACCTTTTCTAGAGATTTTGCCTAT 57.114 30.769 0.00 0.00 0.00 2.57
3173 3303 8.885693 AACCTTTTCTAGAGATTTTGCCTATT 57.114 30.769 0.00 0.00 0.00 1.73
3199 3401 0.032815 GGACTGCTAATCGAGGCCTC 59.967 60.000 23.79 23.79 34.09 4.70
3203 3405 0.179111 TGCTAATCGAGGCCTCAACG 60.179 55.000 31.67 19.29 0.00 4.10
3211 3415 1.069906 CGAGGCCTCAACGTTTCTTTG 60.070 52.381 31.67 7.51 0.00 2.77
3212 3416 1.947456 GAGGCCTCAACGTTTCTTTGT 59.053 47.619 28.43 0.00 0.00 2.83
3215 3419 2.350484 GGCCTCAACGTTTCTTTGTAGC 60.350 50.000 0.00 0.00 0.00 3.58
3218 3422 4.527564 CCTCAACGTTTCTTTGTAGCTTG 58.472 43.478 0.00 0.00 0.00 4.01
3223 3427 3.058224 ACGTTTCTTTGTAGCTTGCATCC 60.058 43.478 0.00 0.00 0.00 3.51
3247 3451 6.014584 CCCCCAAGCTTTTCTTTTTGTAGTAT 60.015 38.462 0.00 0.00 31.27 2.12
3298 3502 7.699878 ACTAATAATTCTGGGAGGAACTTGTT 58.300 34.615 0.00 0.00 41.55 2.83
3299 3503 8.832735 ACTAATAATTCTGGGAGGAACTTGTTA 58.167 33.333 0.00 0.00 41.55 2.41
3300 3504 9.331282 CTAATAATTCTGGGAGGAACTTGTTAG 57.669 37.037 0.00 0.00 41.55 2.34
3301 3505 5.584551 AATTCTGGGAGGAACTTGTTAGT 57.415 39.130 0.00 0.00 41.55 2.24
3302 3506 6.697641 AATTCTGGGAGGAACTTGTTAGTA 57.302 37.500 0.00 0.00 41.55 1.82
3303 3507 5.740290 TTCTGGGAGGAACTTGTTAGTAG 57.260 43.478 0.00 0.00 41.55 2.57
3304 3508 4.748701 TCTGGGAGGAACTTGTTAGTAGT 58.251 43.478 0.00 0.00 41.55 2.73
3306 3510 4.485875 TGGGAGGAACTTGTTAGTAGTGA 58.514 43.478 0.00 0.00 41.55 3.41
3308 3512 5.546499 TGGGAGGAACTTGTTAGTAGTGAAT 59.454 40.000 0.00 0.00 41.55 2.57
3309 3513 5.875359 GGGAGGAACTTGTTAGTAGTGAATG 59.125 44.000 0.00 0.00 41.55 2.67
3323 3545 3.589988 AGTGAATGTCTGATGAACGACC 58.410 45.455 0.00 0.00 0.00 4.79
3361 3583 2.356125 GGCTGCCTTCTACTTCAATGGA 60.356 50.000 12.43 0.00 0.00 3.41
3367 3589 4.583871 CCTTCTACTTCAATGGAGCTGTT 58.416 43.478 0.00 0.00 0.00 3.16
3379 3601 0.813821 GAGCTGTTCATTTGGCCTCC 59.186 55.000 3.32 0.00 0.00 4.30
3427 3649 7.884816 TTTGTTAGTCTTCGATTTCACCTAG 57.115 36.000 0.00 0.00 0.00 3.02
3459 3684 2.076863 CGCCCTTTTCCTTGTCTACTG 58.923 52.381 0.00 0.00 0.00 2.74
3477 3702 9.588096 TGTCTACTGTAATGATGGACATATACT 57.412 33.333 2.37 0.00 38.38 2.12
3603 3828 1.230324 GTGGACTCACTGAAGTTGCC 58.770 55.000 0.00 0.00 40.58 4.52
3669 3894 3.452755 TGGGAACATGCAGTATAGACG 57.547 47.619 0.00 0.00 33.40 4.18
3719 4303 8.601476 CATATCTGTCACATGATTATTCATCGG 58.399 37.037 0.00 0.00 40.70 4.18
3872 4458 9.614792 AATGACATATAAGTCTTAACTTGTCCC 57.385 33.333 19.68 7.18 45.37 4.46
3893 4479 5.365605 TCCCAGTTCTCTTCTTGTAAACTGA 59.634 40.000 13.51 0.00 46.09 3.41
3899 4485 8.646900 AGTTCTCTTCTTGTAAACTGATCTTCT 58.353 33.333 0.00 0.00 0.00 2.85
3930 4516 8.037758 CAGAGACACAAACTAAGGTATCAGATT 58.962 37.037 0.00 0.00 0.00 2.40
3931 4517 9.256228 AGAGACACAAACTAAGGTATCAGATTA 57.744 33.333 0.00 0.00 0.00 1.75
3933 4519 9.823647 AGACACAAACTAAGGTATCAGATTATG 57.176 33.333 0.00 0.00 0.00 1.90
3947 4533 5.869579 TCAGATTATGGCATCTTTACTCCC 58.130 41.667 1.65 0.00 30.50 4.30
3948 4534 5.369404 TCAGATTATGGCATCTTTACTCCCA 59.631 40.000 1.65 0.00 30.50 4.37
3963 4549 4.718940 ACTCCCACTTGTTTTTGTTCAG 57.281 40.909 0.00 0.00 0.00 3.02
3970 4556 6.203723 CCCACTTGTTTTTGTTCAGTTTTTGA 59.796 34.615 0.00 0.00 0.00 2.69
3989 4576 9.811995 GTTTTTGAGTGGTTTTACTAGGAATTT 57.188 29.630 0.00 0.00 0.00 1.82
4039 4626 6.752168 AGGAGGTGATGTTTCTTCAATTTTG 58.248 36.000 0.00 0.00 0.00 2.44
4040 4627 5.928264 GGAGGTGATGTTTCTTCAATTTTGG 59.072 40.000 0.00 0.00 0.00 3.28
4041 4628 6.462909 GGAGGTGATGTTTCTTCAATTTTGGT 60.463 38.462 0.00 0.00 0.00 3.67
4042 4629 6.888105 AGGTGATGTTTCTTCAATTTTGGTT 58.112 32.000 0.00 0.00 0.00 3.67
4043 4630 8.017418 AGGTGATGTTTCTTCAATTTTGGTTA 57.983 30.769 0.00 0.00 0.00 2.85
4044 4631 7.926018 AGGTGATGTTTCTTCAATTTTGGTTAC 59.074 33.333 0.00 0.00 0.00 2.50
4045 4632 7.926018 GGTGATGTTTCTTCAATTTTGGTTACT 59.074 33.333 0.00 0.00 0.00 2.24
4046 4633 9.959749 GTGATGTTTCTTCAATTTTGGTTACTA 57.040 29.630 0.00 0.00 0.00 1.82
4048 4635 9.626045 GATGTTTCTTCAATTTTGGTTACTAGG 57.374 33.333 0.00 0.00 0.00 3.02
4049 4636 8.754991 TGTTTCTTCAATTTTGGTTACTAGGA 57.245 30.769 0.00 0.00 0.00 2.94
4050 4637 9.191479 TGTTTCTTCAATTTTGGTTACTAGGAA 57.809 29.630 0.00 0.00 0.00 3.36
4051 4638 9.678941 GTTTCTTCAATTTTGGTTACTAGGAAG 57.321 33.333 0.00 0.00 0.00 3.46
4052 4639 7.996098 TCTTCAATTTTGGTTACTAGGAAGG 57.004 36.000 0.00 0.00 32.32 3.46
4053 4640 7.751646 TCTTCAATTTTGGTTACTAGGAAGGA 58.248 34.615 0.00 0.00 32.32 3.36
4054 4641 8.390921 TCTTCAATTTTGGTTACTAGGAAGGAT 58.609 33.333 0.00 0.00 32.32 3.24
4055 4642 7.938140 TCAATTTTGGTTACTAGGAAGGATG 57.062 36.000 0.00 0.00 0.00 3.51
4056 4643 7.695055 TCAATTTTGGTTACTAGGAAGGATGA 58.305 34.615 0.00 0.00 0.00 2.92
4057 4644 8.336235 TCAATTTTGGTTACTAGGAAGGATGAT 58.664 33.333 0.00 0.00 0.00 2.45
4058 4645 8.408601 CAATTTTGGTTACTAGGAAGGATGATG 58.591 37.037 0.00 0.00 0.00 3.07
4059 4646 4.689612 TGGTTACTAGGAAGGATGATGC 57.310 45.455 0.00 0.00 0.00 3.91
4060 4647 4.298626 TGGTTACTAGGAAGGATGATGCT 58.701 43.478 0.00 0.00 0.00 3.79
4061 4648 4.721776 TGGTTACTAGGAAGGATGATGCTT 59.278 41.667 0.00 0.00 0.00 3.91
4062 4649 5.059833 GGTTACTAGGAAGGATGATGCTTG 58.940 45.833 3.26 0.00 0.00 4.01
4063 4650 3.205784 ACTAGGAAGGATGATGCTTGC 57.794 47.619 10.06 10.06 36.46 4.01
4064 4651 2.776536 ACTAGGAAGGATGATGCTTGCT 59.223 45.455 22.49 22.49 46.87 3.91
4065 4652 2.822707 AGGAAGGATGATGCTTGCTT 57.177 45.000 14.51 0.27 43.27 3.91
4066 4653 3.097342 AGGAAGGATGATGCTTGCTTT 57.903 42.857 14.51 0.00 43.27 3.51
4067 4654 3.438183 AGGAAGGATGATGCTTGCTTTT 58.562 40.909 14.51 0.00 43.27 2.27
4068 4655 3.836562 AGGAAGGATGATGCTTGCTTTTT 59.163 39.130 14.51 0.00 43.27 1.94
4087 4674 4.370364 TTTTCTCACACTTTGCTGGAAC 57.630 40.909 0.00 0.00 0.00 3.62
4088 4675 3.281727 TTCTCACACTTTGCTGGAACT 57.718 42.857 0.00 0.00 0.00 3.01
4089 4676 2.564771 TCTCACACTTTGCTGGAACTG 58.435 47.619 0.00 0.00 0.00 3.16
4090 4677 2.092968 TCTCACACTTTGCTGGAACTGT 60.093 45.455 0.00 0.00 0.00 3.55
4091 4678 2.684881 CTCACACTTTGCTGGAACTGTT 59.315 45.455 0.00 0.00 0.00 3.16
4092 4679 2.423185 TCACACTTTGCTGGAACTGTTG 59.577 45.455 0.00 0.00 0.00 3.33
4093 4680 1.134946 ACACTTTGCTGGAACTGTTGC 59.865 47.619 4.98 4.98 0.00 4.17
4094 4681 0.746659 ACTTTGCTGGAACTGTTGCC 59.253 50.000 9.61 5.93 0.00 4.52
4095 4682 0.746063 CTTTGCTGGAACTGTTGCCA 59.254 50.000 9.61 9.87 0.00 4.92
4096 4683 0.459489 TTTGCTGGAACTGTTGCCAC 59.541 50.000 9.61 2.35 0.00 5.01
4097 4684 0.395586 TTGCTGGAACTGTTGCCACT 60.396 50.000 9.61 0.00 0.00 4.00
4098 4685 1.102809 TGCTGGAACTGTTGCCACTG 61.103 55.000 9.61 2.74 0.00 3.66
4099 4686 1.656441 CTGGAACTGTTGCCACTGC 59.344 57.895 9.61 0.00 38.26 4.40
4100 4687 1.799258 CTGGAACTGTTGCCACTGCC 61.799 60.000 9.61 0.00 36.33 4.85
4101 4688 1.827789 GGAACTGTTGCCACTGCCA 60.828 57.895 0.00 0.00 36.33 4.92
4102 4689 1.656441 GAACTGTTGCCACTGCCAG 59.344 57.895 0.00 0.00 36.33 4.85
4103 4690 2.412037 GAACTGTTGCCACTGCCAGC 62.412 60.000 0.00 0.00 36.33 4.85
4104 4691 2.596631 CTGTTGCCACTGCCAGCT 60.597 61.111 0.00 0.00 36.33 4.24
4105 4692 1.302752 CTGTTGCCACTGCCAGCTA 60.303 57.895 0.00 0.00 36.33 3.32
4106 4693 0.679002 CTGTTGCCACTGCCAGCTAT 60.679 55.000 0.00 0.00 36.33 2.97
4107 4694 0.617935 TGTTGCCACTGCCAGCTATA 59.382 50.000 0.00 0.00 36.33 1.31
4108 4695 1.212688 TGTTGCCACTGCCAGCTATAT 59.787 47.619 0.00 0.00 36.33 0.86
4109 4696 1.876156 GTTGCCACTGCCAGCTATATC 59.124 52.381 0.00 0.00 36.33 1.63
4110 4697 1.427809 TGCCACTGCCAGCTATATCT 58.572 50.000 0.00 0.00 36.33 1.98
4111 4698 2.608623 TGCCACTGCCAGCTATATCTA 58.391 47.619 0.00 0.00 36.33 1.98
4112 4699 2.564504 TGCCACTGCCAGCTATATCTAG 59.435 50.000 0.00 0.00 36.33 2.43
4113 4700 5.186469 TGCCACTGCCAGCTATATCTAGC 62.186 52.174 1.94 1.94 43.09 3.42
4131 4718 6.225981 TCTAGCAGATCTTTATGAACAGCA 57.774 37.500 0.00 0.00 33.57 4.41
4132 4719 6.824553 TCTAGCAGATCTTTATGAACAGCAT 58.175 36.000 0.00 0.00 41.08 3.79
4133 4720 7.955918 TCTAGCAGATCTTTATGAACAGCATA 58.044 34.615 0.00 0.00 38.44 3.14
4134 4721 8.087136 TCTAGCAGATCTTTATGAACAGCATAG 58.913 37.037 0.00 0.00 40.40 2.23
4135 4722 5.469421 AGCAGATCTTTATGAACAGCATAGC 59.531 40.000 0.00 0.00 40.40 2.97
4136 4723 5.237996 GCAGATCTTTATGAACAGCATAGCA 59.762 40.000 0.00 0.00 40.40 3.49
4137 4724 6.238566 GCAGATCTTTATGAACAGCATAGCAA 60.239 38.462 0.00 0.00 40.40 3.91
4138 4725 7.680350 GCAGATCTTTATGAACAGCATAGCAAA 60.680 37.037 0.00 0.00 40.40 3.68
4139 4726 8.350722 CAGATCTTTATGAACAGCATAGCAAAT 58.649 33.333 0.00 0.00 40.40 2.32
4140 4727 9.565090 AGATCTTTATGAACAGCATAGCAAATA 57.435 29.630 0.00 0.00 40.40 1.40
4141 4728 9.604626 GATCTTTATGAACAGCATAGCAAATAC 57.395 33.333 0.00 0.00 40.40 1.89
4142 4729 8.504812 TCTTTATGAACAGCATAGCAAATACA 57.495 30.769 0.00 0.00 40.40 2.29
4143 4730 8.955388 TCTTTATGAACAGCATAGCAAATACAA 58.045 29.630 0.00 0.00 40.40 2.41
4144 4731 9.571810 CTTTATGAACAGCATAGCAAATACAAA 57.428 29.630 0.00 0.00 40.40 2.83
4146 4733 7.997107 ATGAACAGCATAGCAAATACAAATG 57.003 32.000 0.00 0.00 34.82 2.32
4147 4734 7.155655 TGAACAGCATAGCAAATACAAATGA 57.844 32.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.764890 TATCCATCCTTGCTTCCCGG 59.235 55.000 0.00 0.00 0.00 5.73
68 69 0.829990 CCTCCTGAAGCTTCTCTCCC 59.170 60.000 26.09 0.58 0.00 4.30
69 70 0.829990 CCCTCCTGAAGCTTCTCTCC 59.170 60.000 26.09 1.35 0.00 3.71
104 105 3.254166 GGTGCTTCCATATTTCGATGCAT 59.746 43.478 0.00 0.00 40.12 3.96
109 110 2.971660 TCGGTGCTTCCATATTTCGA 57.028 45.000 0.00 0.00 35.57 3.71
132 133 5.064707 GCACTACACCATCAAATACAATCGT 59.935 40.000 0.00 0.00 0.00 3.73
177 178 3.648067 TGGCATTCTCCTTCGATCCTATT 59.352 43.478 0.00 0.00 0.00 1.73
186 187 2.092753 TCCACATCTGGCATTCTCCTTC 60.093 50.000 0.00 0.00 37.49 3.46
193 194 1.033746 CCGCTTCCACATCTGGCATT 61.034 55.000 0.00 0.00 37.49 3.56
194 195 1.452651 CCGCTTCCACATCTGGCAT 60.453 57.895 0.00 0.00 37.49 4.40
195 196 2.046023 CCGCTTCCACATCTGGCA 60.046 61.111 0.00 0.00 37.49 4.92
196 197 2.825836 CCCGCTTCCACATCTGGC 60.826 66.667 0.00 0.00 37.49 4.85
197 198 2.825836 GCCCGCTTCCACATCTGG 60.826 66.667 0.00 0.00 39.23 3.86
198 199 2.825836 GGCCCGCTTCCACATCTG 60.826 66.667 0.00 0.00 0.00 2.90
199 200 4.473520 CGGCCCGCTTCCACATCT 62.474 66.667 0.00 0.00 0.00 2.90
211 212 2.830370 CTTTGATGAGCCCGGCCC 60.830 66.667 5.55 0.00 0.00 5.80
246 247 2.389059 CCACGATGATAACGCTCTCAG 58.611 52.381 0.00 0.00 0.00 3.35
249 250 0.249489 GCCCACGATGATAACGCTCT 60.249 55.000 0.00 0.00 0.00 4.09
274 275 2.278854 AGTCTAACTCCTCGTCGTAGC 58.721 52.381 0.00 0.00 0.00 3.58
275 276 3.490526 GCTAGTCTAACTCCTCGTCGTAG 59.509 52.174 0.00 0.00 0.00 3.51
276 277 3.452474 GCTAGTCTAACTCCTCGTCGTA 58.548 50.000 0.00 0.00 0.00 3.43
277 278 2.278854 GCTAGTCTAACTCCTCGTCGT 58.721 52.381 0.00 0.00 0.00 4.34
278 279 1.598601 GGCTAGTCTAACTCCTCGTCG 59.401 57.143 0.00 0.00 0.00 5.12
279 280 2.641305 TGGCTAGTCTAACTCCTCGTC 58.359 52.381 0.00 0.00 0.00 4.20
280 281 2.754002 GTTGGCTAGTCTAACTCCTCGT 59.246 50.000 0.00 0.00 33.86 4.18
293 294 0.734942 CACCCGTGTACGTTGGCTAG 60.735 60.000 0.00 0.00 37.74 3.42
312 313 4.510571 ACATATTACACGAACCCAACTCC 58.489 43.478 0.00 0.00 0.00 3.85
337 338 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
338 339 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
339 340 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
340 341 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
341 342 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
342 343 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
343 344 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
344 345 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
345 346 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
346 347 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
347 348 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
380 381 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
381 382 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
382 383 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
383 384 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
384 385 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
385 386 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
386 387 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
387 388 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
388 389 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
389 390 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
390 391 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
391 392 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
392 393 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
393 394 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
394 395 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
395 396 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
396 397 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
397 398 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
398 399 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
399 400 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
400 401 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
401 402 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
402 403 1.345415 GTGTACTCCCTCCGTTCCAAA 59.655 52.381 0.00 0.00 0.00 3.28
403 404 0.971386 GTGTACTCCCTCCGTTCCAA 59.029 55.000 0.00 0.00 0.00 3.53
404 405 0.178955 TGTGTACTCCCTCCGTTCCA 60.179 55.000 0.00 0.00 0.00 3.53
405 406 0.245813 GTGTGTACTCCCTCCGTTCC 59.754 60.000 0.00 0.00 0.00 3.62
406 407 1.201880 GAGTGTGTACTCCCTCCGTTC 59.798 57.143 0.00 0.00 46.14 3.95
407 408 1.254954 GAGTGTGTACTCCCTCCGTT 58.745 55.000 0.00 0.00 46.14 4.44
408 409 2.958513 GAGTGTGTACTCCCTCCGT 58.041 57.895 0.00 0.00 46.14 4.69
420 421 1.921243 TCCGAATACGCATGAGTGTG 58.079 50.000 12.80 0.00 39.22 3.82
449 450 7.122204 GGAGCACCCACTTACAACTTATTTATT 59.878 37.037 0.00 0.00 34.14 1.40
451 452 5.941647 GGAGCACCCACTTACAACTTATTTA 59.058 40.000 0.00 0.00 34.14 1.40
454 455 3.951663 GGAGCACCCACTTACAACTTAT 58.048 45.455 0.00 0.00 34.14 1.73
503 504 3.119101 CCATACGTACTTGAAGGACTGCT 60.119 47.826 5.94 0.00 0.00 4.24
504 505 3.187700 CCATACGTACTTGAAGGACTGC 58.812 50.000 5.94 0.00 0.00 4.40
505 506 4.174009 CACCATACGTACTTGAAGGACTG 58.826 47.826 5.94 2.16 0.00 3.51
506 507 3.830755 ACACCATACGTACTTGAAGGACT 59.169 43.478 5.94 0.00 0.00 3.85
507 508 3.924686 CACACCATACGTACTTGAAGGAC 59.075 47.826 0.00 0.00 0.00 3.85
508 509 3.827876 TCACACCATACGTACTTGAAGGA 59.172 43.478 0.00 0.00 0.00 3.36
509 510 4.182693 TCACACCATACGTACTTGAAGG 57.817 45.455 0.00 0.00 0.00 3.46
510 511 5.227908 ACTTCACACCATACGTACTTGAAG 58.772 41.667 20.72 20.72 39.12 3.02
511 512 5.204409 ACTTCACACCATACGTACTTGAA 57.796 39.130 0.00 2.08 0.00 2.69
512 513 4.859304 ACTTCACACCATACGTACTTGA 57.141 40.909 0.00 0.00 0.00 3.02
513 514 5.917541 AAACTTCACACCATACGTACTTG 57.082 39.130 0.00 0.00 0.00 3.16
514 515 6.930667 AAAAACTTCACACCATACGTACTT 57.069 33.333 0.00 0.00 0.00 2.24
577 578 2.491693 CTCGGCTCTCTCAAGAAGAAGT 59.508 50.000 0.00 0.00 32.23 3.01
578 579 2.159254 CCTCGGCTCTCTCAAGAAGAAG 60.159 54.545 0.00 0.00 32.23 2.85
580 581 1.272203 ACCTCGGCTCTCTCAAGAAGA 60.272 52.381 0.00 0.00 0.00 2.87
581 582 1.134175 GACCTCGGCTCTCTCAAGAAG 59.866 57.143 0.00 0.00 0.00 2.85
582 583 1.178276 GACCTCGGCTCTCTCAAGAA 58.822 55.000 0.00 0.00 0.00 2.52
583 584 0.329931 AGACCTCGGCTCTCTCAAGA 59.670 55.000 0.00 0.00 0.00 3.02
584 585 0.738389 GAGACCTCGGCTCTCTCAAG 59.262 60.000 7.74 0.00 32.75 3.02
585 586 2.875188 GAGACCTCGGCTCTCTCAA 58.125 57.895 7.74 0.00 32.75 3.02
586 587 4.647825 GAGACCTCGGCTCTCTCA 57.352 61.111 7.74 0.00 32.75 3.27
638 652 4.534141 TCCCGTATTTCCGCCGCC 62.534 66.667 0.00 0.00 0.00 6.13
639 653 2.965462 CTCCCGTATTTCCGCCGC 60.965 66.667 0.00 0.00 0.00 6.53
640 654 1.881252 CACTCCCGTATTTCCGCCG 60.881 63.158 0.00 0.00 0.00 6.46
641 655 1.523032 CCACTCCCGTATTTCCGCC 60.523 63.158 0.00 0.00 0.00 6.13
642 656 2.178235 GCCACTCCCGTATTTCCGC 61.178 63.158 0.00 0.00 0.00 5.54
692 706 1.688311 GCCTTTGGTTTCCCCTATCCC 60.688 57.143 0.00 0.00 0.00 3.85
992 1105 1.592669 CGGCGGCTCATAGTTCCAG 60.593 63.158 7.61 0.00 0.00 3.86
1042 1165 2.434702 GGTACCGATCCTTGATGTTCCT 59.565 50.000 0.00 0.00 0.00 3.36
1211 1334 0.963962 CACCTTGGCTCTTGCAACAT 59.036 50.000 0.00 0.00 41.91 2.71
1610 1736 1.985159 TGTAAGCTTGGTCCACCTCAT 59.015 47.619 9.86 0.00 36.82 2.90
1850 1976 8.999431 GTTGAACACCATTTCTAGACATTTCTA 58.001 33.333 0.00 0.00 32.75 2.10
1949 2075 6.596497 GCCCAAACTGATCATGAAATCAAAAT 59.404 34.615 0.00 0.00 35.32 1.82
1977 2103 5.376854 TGTAGGTAGTAACAGTCGGTTTC 57.623 43.478 0.00 0.00 40.96 2.78
2420 2549 1.762708 AAGGCGGTCCATAATTGTGG 58.237 50.000 14.77 14.77 40.76 4.17
2528 2657 7.914427 ATGAACAAGTATCCACCTATCAGTA 57.086 36.000 0.00 0.00 0.00 2.74
2679 2808 5.108517 GCCAACATTTCTCTGAAAACAACA 58.891 37.500 0.00 0.00 0.00 3.33
2691 2820 0.611896 CCTTCCCGGCCAACATTTCT 60.612 55.000 2.24 0.00 0.00 2.52
2743 2872 1.336755 ACCTTTAAGCAACGCACCAAG 59.663 47.619 0.00 0.00 0.00 3.61
2898 3027 6.825213 CACATCCATTCTTCTCCATAGAAACA 59.175 38.462 0.00 0.00 41.19 2.83
2899 3028 6.238593 GCACATCCATTCTTCTCCATAGAAAC 60.239 42.308 0.00 0.00 41.19 2.78
2965 3095 1.074248 GCACCTCCCCTTTCCGAAA 59.926 57.895 0.00 0.00 0.00 3.46
3050 3180 2.042686 AGCAAGTGCAGTCAACAAGA 57.957 45.000 6.00 0.00 45.16 3.02
3111 3241 5.365619 TGTTCCAGAAAAGAGTGGTACTTC 58.634 41.667 0.00 0.00 35.66 3.01
3114 3244 4.065789 CCTGTTCCAGAAAAGAGTGGTAC 58.934 47.826 0.00 0.00 35.32 3.34
3172 3302 5.175859 CCTCGATTAGCAGTCCAAAGTAAA 58.824 41.667 0.00 0.00 0.00 2.01
3173 3303 4.755411 CCTCGATTAGCAGTCCAAAGTAA 58.245 43.478 0.00 0.00 0.00 2.24
3199 3401 3.690422 TGCAAGCTACAAAGAAACGTTG 58.310 40.909 0.00 0.00 0.00 4.10
3203 3405 3.367395 GGGGATGCAAGCTACAAAGAAAC 60.367 47.826 0.00 0.00 0.00 2.78
3211 3415 1.387295 GCTTGGGGGATGCAAGCTAC 61.387 60.000 1.10 0.00 45.43 3.58
3212 3416 1.076777 GCTTGGGGGATGCAAGCTA 60.077 57.895 1.10 0.00 45.43 3.32
3215 3419 0.978907 AAAAGCTTGGGGGATGCAAG 59.021 50.000 0.00 0.00 0.00 4.01
3218 3422 1.269958 AAGAAAAGCTTGGGGGATGC 58.730 50.000 0.00 0.00 34.93 3.91
3223 3427 5.276461 ACTACAAAAAGAAAAGCTTGGGG 57.724 39.130 0.00 0.00 36.80 4.96
3267 3471 8.706521 GTTCCTCCCAGAATTATTAGTAAGAGT 58.293 37.037 0.00 0.00 0.00 3.24
3277 3481 7.272144 ACTAACAAGTTCCTCCCAGAATTAT 57.728 36.000 0.00 0.00 0.00 1.28
3298 3502 6.404403 GGTCGTTCATCAGACATTCACTACTA 60.404 42.308 0.00 0.00 39.01 1.82
3299 3503 5.403246 GTCGTTCATCAGACATTCACTACT 58.597 41.667 0.00 0.00 37.34 2.57
3300 3504 4.563184 GGTCGTTCATCAGACATTCACTAC 59.437 45.833 0.00 0.00 39.01 2.73
3301 3505 4.219725 TGGTCGTTCATCAGACATTCACTA 59.780 41.667 0.00 0.00 39.01 2.74
3302 3506 3.006859 TGGTCGTTCATCAGACATTCACT 59.993 43.478 0.00 0.00 39.01 3.41
3303 3507 3.325870 TGGTCGTTCATCAGACATTCAC 58.674 45.455 0.00 0.00 39.01 3.18
3304 3508 3.676291 TGGTCGTTCATCAGACATTCA 57.324 42.857 0.00 0.00 39.01 2.57
3306 3510 4.186926 CAGATGGTCGTTCATCAGACATT 58.813 43.478 17.82 0.27 44.30 2.71
3308 3512 2.562738 ACAGATGGTCGTTCATCAGACA 59.437 45.455 17.82 0.00 44.30 3.41
3309 3513 2.926200 CACAGATGGTCGTTCATCAGAC 59.074 50.000 17.82 0.00 44.30 3.51
3323 3545 4.214971 GGCAGCCATATAGAAACACAGATG 59.785 45.833 6.55 0.00 0.00 2.90
3361 3583 0.112995 TGGAGGCCAAATGAACAGCT 59.887 50.000 5.01 0.00 0.00 4.24
3367 3589 1.635487 AGCTTAGTGGAGGCCAAATGA 59.365 47.619 5.01 0.00 34.18 2.57
3408 3630 9.798994 GAATTTACTAGGTGAAATCGAAGACTA 57.201 33.333 0.00 0.00 42.51 2.59
3415 3637 7.391786 CGTTGAGAATTTACTAGGTGAAATCG 58.608 38.462 0.00 0.00 0.00 3.34
3421 3643 3.621715 GGGCGTTGAGAATTTACTAGGTG 59.378 47.826 0.00 0.00 0.00 4.00
3427 3649 4.217767 AGGAAAAGGGCGTTGAGAATTTAC 59.782 41.667 0.00 0.00 0.00 2.01
3477 3702 9.987272 CTCACATTATGAAGTGGTGAATATCTA 57.013 33.333 0.00 0.00 37.96 1.98
3493 3718 4.701651 TGCCAAAGGTCTTCTCACATTATG 59.298 41.667 0.00 0.00 0.00 1.90
3543 3768 7.719778 TCATATCATGATCAGCTGTAAACAC 57.280 36.000 12.53 1.13 33.59 3.32
3603 3828 7.254932 GGGAATATAGAAACTAACTTGCTGCTG 60.255 40.741 0.00 0.00 0.00 4.41
3676 3901 6.885918 ACAGATATGTTGATCATTGTTCACCA 59.114 34.615 0.00 0.00 37.91 4.17
3816 4402 9.431887 GAGAGACAACCTTGTTTACACATATTA 57.568 33.333 0.00 0.00 42.43 0.98
3860 4446 5.859495 AGAAGAGAACTGGGACAAGTTAAG 58.141 41.667 0.00 0.00 38.70 1.85
3872 4458 8.600449 AAGATCAGTTTACAAGAAGAGAACTG 57.400 34.615 7.93 7.93 45.17 3.16
3893 4479 5.305644 AGTTTGTGTCTCTGTACCAGAAGAT 59.694 40.000 0.00 0.00 40.18 2.40
3899 4485 4.652421 ACCTTAGTTTGTGTCTCTGTACCA 59.348 41.667 0.00 0.00 0.00 3.25
3918 4504 8.664079 AGTAAAGATGCCATAATCTGATACCTT 58.336 33.333 0.00 0.00 36.99 3.50
3930 4516 4.227300 ACAAGTGGGAGTAAAGATGCCATA 59.773 41.667 0.00 0.00 40.55 2.74
3931 4517 3.010584 ACAAGTGGGAGTAAAGATGCCAT 59.989 43.478 0.00 0.00 40.55 4.40
3933 4519 3.073274 ACAAGTGGGAGTAAAGATGCC 57.927 47.619 0.00 0.00 0.00 4.40
3947 4533 7.793427 CACTCAAAAACTGAACAAAAACAAGTG 59.207 33.333 0.00 0.00 32.17 3.16
3948 4534 7.042119 CCACTCAAAAACTGAACAAAAACAAGT 60.042 33.333 0.00 0.00 32.17 3.16
3963 4549 9.811995 AAATTCCTAGTAAAACCACTCAAAAAC 57.188 29.630 0.00 0.00 0.00 2.43
3970 4556 6.266786 CACCCAAAATTCCTAGTAAAACCACT 59.733 38.462 0.00 0.00 0.00 4.00
3989 4576 6.289834 TGAGTCGAAAGTATTTAACACCCAA 58.710 36.000 0.00 0.00 39.27 4.12
4039 4626 4.965200 AGCATCATCCTTCCTAGTAACC 57.035 45.455 0.00 0.00 0.00 2.85
4040 4627 4.513318 GCAAGCATCATCCTTCCTAGTAAC 59.487 45.833 0.00 0.00 0.00 2.50
4041 4628 4.410228 AGCAAGCATCATCCTTCCTAGTAA 59.590 41.667 0.00 0.00 0.00 2.24
4042 4629 3.969976 AGCAAGCATCATCCTTCCTAGTA 59.030 43.478 0.00 0.00 0.00 1.82
4043 4630 2.776536 AGCAAGCATCATCCTTCCTAGT 59.223 45.455 0.00 0.00 0.00 2.57
4044 4631 3.488778 AGCAAGCATCATCCTTCCTAG 57.511 47.619 0.00 0.00 0.00 3.02
4045 4632 3.939740 AAGCAAGCATCATCCTTCCTA 57.060 42.857 0.00 0.00 0.00 2.94
4046 4633 2.822707 AAGCAAGCATCATCCTTCCT 57.177 45.000 0.00 0.00 0.00 3.36
4047 4634 3.881937 AAAAGCAAGCATCATCCTTCC 57.118 42.857 0.00 0.00 0.00 3.46
4065 4652 4.462483 AGTTCCAGCAAAGTGTGAGAAAAA 59.538 37.500 0.00 0.00 0.00 1.94
4066 4653 4.016444 AGTTCCAGCAAAGTGTGAGAAAA 58.984 39.130 0.00 0.00 0.00 2.29
4067 4654 3.378112 CAGTTCCAGCAAAGTGTGAGAAA 59.622 43.478 0.00 0.00 0.00 2.52
4068 4655 2.945008 CAGTTCCAGCAAAGTGTGAGAA 59.055 45.455 0.00 0.00 0.00 2.87
4069 4656 2.092968 ACAGTTCCAGCAAAGTGTGAGA 60.093 45.455 6.27 0.00 40.44 3.27
4070 4657 2.292267 ACAGTTCCAGCAAAGTGTGAG 58.708 47.619 6.27 0.00 40.44 3.51
4071 4658 2.418368 ACAGTTCCAGCAAAGTGTGA 57.582 45.000 6.27 0.00 40.44 3.58
4072 4659 2.801063 CAACAGTTCCAGCAAAGTGTG 58.199 47.619 7.48 1.13 40.94 3.82
4073 4660 1.134946 GCAACAGTTCCAGCAAAGTGT 59.865 47.619 2.24 2.24 43.05 3.55
4074 4661 1.536709 GGCAACAGTTCCAGCAAAGTG 60.537 52.381 0.00 0.00 35.98 3.16
4075 4662 0.746659 GGCAACAGTTCCAGCAAAGT 59.253 50.000 0.00 0.00 0.00 2.66
4076 4663 0.746063 TGGCAACAGTTCCAGCAAAG 59.254 50.000 0.00 0.00 46.17 2.77
4077 4664 2.893441 TGGCAACAGTTCCAGCAAA 58.107 47.368 0.00 0.00 46.17 3.68
4078 4665 4.674306 TGGCAACAGTTCCAGCAA 57.326 50.000 0.00 0.00 46.17 3.91
4089 4676 1.876156 GATATAGCTGGCAGTGGCAAC 59.124 52.381 20.97 16.38 43.71 4.17
4090 4677 1.770658 AGATATAGCTGGCAGTGGCAA 59.229 47.619 20.97 6.41 43.71 4.52
4091 4678 1.427809 AGATATAGCTGGCAGTGGCA 58.572 50.000 19.44 19.44 43.71 4.92
4092 4679 2.676463 GCTAGATATAGCTGGCAGTGGC 60.676 54.545 20.00 10.30 41.44 5.01
4093 4680 2.564504 TGCTAGATATAGCTGGCAGTGG 59.435 50.000 23.13 0.00 45.65 4.00
4094 4681 3.949842 TGCTAGATATAGCTGGCAGTG 57.050 47.619 23.13 0.00 45.65 3.66
4098 4685 5.596836 AAGATCTGCTAGATATAGCTGGC 57.403 43.478 18.37 18.37 43.20 4.85
4099 4686 8.911965 TCATAAAGATCTGCTAGATATAGCTGG 58.088 37.037 21.51 13.95 43.20 4.85
4105 4692 8.591940 TGCTGTTCATAAAGATCTGCTAGATAT 58.408 33.333 0.00 0.00 39.93 1.63
4106 4693 7.955918 TGCTGTTCATAAAGATCTGCTAGATA 58.044 34.615 0.00 0.00 39.93 1.98
4107 4694 6.824553 TGCTGTTCATAAAGATCTGCTAGAT 58.175 36.000 0.00 0.00 39.93 1.98
4108 4695 6.225981 TGCTGTTCATAAAGATCTGCTAGA 57.774 37.500 0.00 0.00 39.93 2.43
4109 4696 7.148606 GCTATGCTGTTCATAAAGATCTGCTAG 60.149 40.741 0.00 0.00 39.93 3.42
4110 4697 6.648310 GCTATGCTGTTCATAAAGATCTGCTA 59.352 38.462 0.00 0.00 39.93 3.49
4111 4698 5.469421 GCTATGCTGTTCATAAAGATCTGCT 59.531 40.000 0.00 0.00 39.93 4.24
4112 4699 5.237996 TGCTATGCTGTTCATAAAGATCTGC 59.762 40.000 0.00 0.00 39.78 4.26
4113 4700 6.856135 TGCTATGCTGTTCATAAAGATCTG 57.144 37.500 0.00 0.00 37.22 2.90
4114 4701 7.870509 TTTGCTATGCTGTTCATAAAGATCT 57.129 32.000 0.00 0.00 37.22 2.75
4115 4702 9.604626 GTATTTGCTATGCTGTTCATAAAGATC 57.395 33.333 0.00 0.00 37.22 2.75
4116 4703 9.123902 TGTATTTGCTATGCTGTTCATAAAGAT 57.876 29.630 0.00 0.00 37.22 2.40
4117 4704 8.504812 TGTATTTGCTATGCTGTTCATAAAGA 57.495 30.769 0.00 0.00 37.22 2.52
4118 4705 9.571810 TTTGTATTTGCTATGCTGTTCATAAAG 57.428 29.630 0.00 0.00 37.22 1.85
4120 4707 9.518906 CATTTGTATTTGCTATGCTGTTCATAA 57.481 29.630 0.00 0.00 37.22 1.90
4121 4708 8.901793 TCATTTGTATTTGCTATGCTGTTCATA 58.098 29.630 0.00 0.00 36.63 2.15
4122 4709 7.774134 TCATTTGTATTTGCTATGCTGTTCAT 58.226 30.769 0.00 0.00 39.17 2.57
4123 4710 7.155655 TCATTTGTATTTGCTATGCTGTTCA 57.844 32.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.