Multiple sequence alignment - TraesCS3D01G437000

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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 TraesCS3D01G437000 chr3D 100.000 4588 0 0 1 4588 548550813 548555400 0.000000e+00 8473.0
1 TraesCS3D01G437000 chr3D 87.292 1023 99 20 2678 3675 548572878 548573894 0.000000e+00 1140.0
2 TraesCS3D01G437000 chr3D 81.618 272 42 6 4 272 548569086 548569352 7.730000e-53 219.0
3 TraesCS3D01G437000 chr3D 92.593 81 6 0 4440 4520 548540362 548540442 2.900000e-22 117.0
4 TraesCS3D01G437000 chr3D 93.506 77 1 2 2610 2686 511352820 511352748 1.350000e-20 111.0
5 TraesCS3D01G437000 chr3D 93.333 75 3 1 2608 2680 603942479 603942405 4.850000e-20 110.0
6 TraesCS3D01G437000 chr3B 91.529 2845 138 46 809 3622 727156693 727159465 0.000000e+00 3823.0
7 TraesCS3D01G437000 chr3B 96.957 1380 40 2 3210 4588 727235061 727236439 0.000000e+00 2314.0
8 TraesCS3D01G437000 chr3B 96.444 1181 34 2 2034 3214 727228285 727229457 0.000000e+00 1941.0
9 TraesCS3D01G437000 chr3B 88.372 946 88 16 2748 3675 727330676 727331617 0.000000e+00 1118.0
10 TraesCS3D01G437000 chr3B 88.356 730 76 8 2897 3621 727264445 727265170 0.000000e+00 869.0
11 TraesCS3D01G437000 chr3B 94.384 552 24 3 1486 2036 727227413 727227958 0.000000e+00 841.0
12 TraesCS3D01G437000 chr3B 87.736 318 37 2 1 317 727152462 727152778 2.020000e-98 370.0
13 TraesCS3D01G437000 chr3B 82.394 284 42 3 3281 3562 726521915 726522192 1.650000e-59 241.0
14 TraesCS3D01G437000 chr3B 84.375 224 32 3 54 275 727323093 727323315 2.780000e-52 217.0
15 TraesCS3D01G437000 chr3B 75.466 322 54 18 997 1313 726781093 726781394 2.880000e-27 134.0
16 TraesCS3D01G437000 chr3B 92.105 76 3 2 2608 2680 811039689 811039614 2.260000e-18 104.0
17 TraesCS3D01G437000 chr3A 87.017 1009 108 11 2678 3675 686151176 686152172 0.000000e+00 1116.0
18 TraesCS3D01G437000 chr3A 76.447 985 139 52 1649 2610 686150260 686151174 9.050000e-122 448.0
19 TraesCS3D01G437000 chr3A 83.857 223 35 1 54 275 686141989 686142211 1.290000e-50 211.0
20 TraesCS3D01G437000 chr3A 85.227 88 13 0 4440 4527 686134219 686134306 1.760000e-14 91.6
21 TraesCS3D01G437000 chr7B 94.521 73 2 2 2610 2680 458364477 458364549 1.350000e-20 111.0
22 TraesCS3D01G437000 chr5A 95.588 68 2 1 2610 2677 588555632 588555698 1.750000e-19 108.0
23 TraesCS3D01G437000 chr7D 93.151 73 3 2 2610 2680 440585751 440585823 6.280000e-19 106.0
24 TraesCS3D01G437000 chr7D 92.000 75 2 1 2604 2678 530349288 530349358 8.120000e-18 102.0
25 TraesCS3D01G437000 chr2D 92.208 77 3 2 2607 2680 441760370 441760446 6.280000e-19 106.0


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 TraesCS3D01G437000 chr3D 548550813 548555400 4587 False 8473.0 8473 100.0000 1 4588 1 chr3D.!!$F2 4587
1 TraesCS3D01G437000 chr3D 548569086 548573894 4808 False 679.5 1140 84.4550 4 3675 2 chr3D.!!$F3 3671
2 TraesCS3D01G437000 chr3B 727235061 727236439 1378 False 2314.0 2314 96.9570 3210 4588 1 chr3B.!!$F3 1378
3 TraesCS3D01G437000 chr3B 727152462 727159465 7003 False 2096.5 3823 89.6325 1 3622 2 chr3B.!!$F7 3621
4 TraesCS3D01G437000 chr3B 727227413 727229457 2044 False 1391.0 1941 95.4140 1486 3214 2 chr3B.!!$F8 1728
5 TraesCS3D01G437000 chr3B 727330676 727331617 941 False 1118.0 1118 88.3720 2748 3675 1 chr3B.!!$F6 927
6 TraesCS3D01G437000 chr3B 727264445 727265170 725 False 869.0 869 88.3560 2897 3621 1 chr3B.!!$F4 724
7 TraesCS3D01G437000 chr3A 686150260 686152172 1912 False 782.0 1116 81.7320 1649 3675 2 chr3A.!!$F3 2026

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
819 4344 0.107456 ATCGATCATGGTGCCCAGTC 59.893 55.000 0.00 0.00 36.75 3.51 F
931 5059 0.110104 CAGCATCCATCCCCTTCCTC 59.890 60.000 0.00 0.00 0.00 3.71 F
1116 5259 0.250901 ACACTCAAGGCGAGCCAAAT 60.251 50.000 17.18 0.00 46.63 2.32 F
1318 5461 1.001974 TCACCGATGAGAGGTTTGGTG 59.998 52.381 2.86 2.86 45.27 4.17 F
1591 5822 1.303317 CCTCACCTTCCCCAAACCG 60.303 63.158 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2648 7253 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.0 46.66 5.19 R
3119 7748 6.116806 TCTAGATGTTGAGGTACTGACTCTC 58.883 44.000 0.00 0.0 41.55 3.20 R
3199 7828 4.022503 AGTTTGCTTCTTTCCAGCTTGATC 60.023 41.667 0.00 0.0 38.19 2.92 R
3500 8131 4.250464 CGAAGAAGCCCACAATGTTAGTA 58.750 43.478 0.00 0.0 0.00 1.82 R
3773 8417 4.834496 TGTACTTAGACTTCCTTTTCCCGA 59.166 41.667 0.00 0.0 0.00 5.14 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
48 49 6.985188 TTAACTATGACCAAGAAGTGATGC 57.015 37.500 0.00 0.00 0.00 3.91
55 56 1.179152 CAAGAAGTGATGCCATGCCA 58.821 50.000 0.00 0.00 0.00 4.92
92 94 2.091720 TCCTACCTTATAGACCACCGCA 60.092 50.000 0.00 0.00 0.00 5.69
112 114 3.663025 CAAATCCGCCACTTCCAATTTT 58.337 40.909 0.00 0.00 0.00 1.82
119 121 2.419990 GCCACTTCCAATTTTATGGCCC 60.420 50.000 0.00 0.00 45.59 5.80
121 123 2.107366 ACTTCCAATTTTATGGCCCGG 58.893 47.619 0.00 0.00 40.46 5.73
131 133 2.638480 TATGGCCCGGAGAGAAATTG 57.362 50.000 0.73 0.00 0.00 2.32
142 144 5.278463 CCGGAGAGAAATTGTTTGTGATGTT 60.278 40.000 0.00 0.00 0.00 2.71
211 213 0.818296 AGCATACACTCCAGGTCGAC 59.182 55.000 7.13 7.13 0.00 4.20
212 214 0.179108 GCATACACTCCAGGTCGACC 60.179 60.000 27.67 27.67 0.00 4.79
215 217 3.760035 CACTCCAGGTCGACCCGG 61.760 72.222 28.25 28.25 38.74 5.73
238 240 0.811219 CGAGCTTGGCGATCCATTCA 60.811 55.000 0.00 0.00 43.05 2.57
239 241 0.942962 GAGCTTGGCGATCCATTCAG 59.057 55.000 0.00 0.00 43.05 3.02
256 258 8.101309 TCCATTCAGGATTAAATAACCAGAGA 57.899 34.615 0.00 0.00 43.07 3.10
276 278 3.633986 AGAACCCTTGAAACAAGAGCAAG 59.366 43.478 12.25 0.00 38.90 4.01
278 280 3.631250 ACCCTTGAAACAAGAGCAAGAA 58.369 40.909 12.25 0.00 41.03 2.52
282 328 4.980434 CCTTGAAACAAGAGCAAGAACATG 59.020 41.667 12.25 0.00 41.03 3.21
286 332 3.885484 ACAAGAGCAAGAACATGTTCG 57.115 42.857 28.18 18.28 43.97 3.95
317 364 2.936919 TCACAGGTCAGTGATTGCTT 57.063 45.000 0.00 0.00 43.18 3.91
321 368 3.567164 CACAGGTCAGTGATTGCTTTTCT 59.433 43.478 0.00 0.00 42.05 2.52
323 370 3.057736 CAGGTCAGTGATTGCTTTTCTGG 60.058 47.826 0.00 0.00 0.00 3.86
328 375 4.402155 TCAGTGATTGCTTTTCTGGTTTGT 59.598 37.500 0.00 0.00 0.00 2.83
330 377 5.687285 CAGTGATTGCTTTTCTGGTTTGTAC 59.313 40.000 0.00 0.00 0.00 2.90
340 387 5.570234 TTCTGGTTTGTACACAGGAAAAC 57.430 39.130 10.97 5.03 33.19 2.43
341 388 4.850680 TCTGGTTTGTACACAGGAAAACT 58.149 39.130 10.97 0.00 33.90 2.66
342 389 5.258051 TCTGGTTTGTACACAGGAAAACTT 58.742 37.500 10.97 0.00 33.90 2.66
346 393 6.033966 GGTTTGTACACAGGAAAACTTCAAG 58.966 40.000 0.00 0.00 33.90 3.02
347 394 4.893424 TGTACACAGGAAAACTTCAAGC 57.107 40.909 0.00 0.00 0.00 4.01
348 395 4.523083 TGTACACAGGAAAACTTCAAGCT 58.477 39.130 0.00 0.00 0.00 3.74
349 396 5.676552 TGTACACAGGAAAACTTCAAGCTA 58.323 37.500 0.00 0.00 0.00 3.32
350 397 5.758296 TGTACACAGGAAAACTTCAAGCTAG 59.242 40.000 0.00 0.00 0.00 3.42
351 398 3.565902 ACACAGGAAAACTTCAAGCTAGC 59.434 43.478 6.62 6.62 0.00 3.42
352 399 2.808543 ACAGGAAAACTTCAAGCTAGCG 59.191 45.455 9.55 0.00 0.00 4.26
353 400 3.067106 CAGGAAAACTTCAAGCTAGCGA 58.933 45.455 9.55 0.00 0.00 4.93
354 401 3.686726 CAGGAAAACTTCAAGCTAGCGAT 59.313 43.478 9.55 0.00 0.00 4.58
355 402 4.870426 CAGGAAAACTTCAAGCTAGCGATA 59.130 41.667 9.55 0.00 0.00 2.92
356 403 4.870991 AGGAAAACTTCAAGCTAGCGATAC 59.129 41.667 9.55 0.00 0.00 2.24
357 404 4.630069 GGAAAACTTCAAGCTAGCGATACA 59.370 41.667 9.55 0.00 0.00 2.29
358 405 5.121768 GGAAAACTTCAAGCTAGCGATACAA 59.878 40.000 9.55 0.00 0.00 2.41
360 677 4.720649 ACTTCAAGCTAGCGATACAAGA 57.279 40.909 9.55 0.00 0.00 3.02
361 678 4.425520 ACTTCAAGCTAGCGATACAAGAC 58.574 43.478 9.55 0.00 0.00 3.01
369 686 4.737765 GCTAGCGATACAAGACAGAGAAAG 59.262 45.833 0.00 0.00 0.00 2.62
382 699 7.246171 AGACAGAGAAAGCAGAAATTACCTA 57.754 36.000 0.00 0.00 0.00 3.08
386 703 7.179338 ACAGAGAAAGCAGAAATTACCTAGAGA 59.821 37.037 0.00 0.00 0.00 3.10
387 704 8.037758 CAGAGAAAGCAGAAATTACCTAGAGAA 58.962 37.037 0.00 0.00 0.00 2.87
388 705 8.257306 AGAGAAAGCAGAAATTACCTAGAGAAG 58.743 37.037 0.00 0.00 0.00 2.85
389 706 6.821160 AGAAAGCAGAAATTACCTAGAGAAGC 59.179 38.462 0.00 0.00 0.00 3.86
392 709 6.345298 AGCAGAAATTACCTAGAGAAGCTTC 58.655 40.000 19.11 19.11 0.00 3.86
393 710 6.070538 AGCAGAAATTACCTAGAGAAGCTTCA 60.071 38.462 27.57 7.01 0.00 3.02
394 711 6.257630 GCAGAAATTACCTAGAGAAGCTTCAG 59.742 42.308 27.57 16.06 0.00 3.02
396 713 8.203485 CAGAAATTACCTAGAGAAGCTTCAGAT 58.797 37.037 27.57 14.98 0.00 2.90
397 714 9.427821 AGAAATTACCTAGAGAAGCTTCAGATA 57.572 33.333 27.57 15.29 0.00 1.98
399 716 9.427821 AAATTACCTAGAGAAGCTTCAGATAGA 57.572 33.333 27.57 10.82 0.00 1.98
401 718 6.899393 ACCTAGAGAAGCTTCAGATAGATG 57.101 41.667 27.57 14.95 0.00 2.90
402 719 6.372931 ACCTAGAGAAGCTTCAGATAGATGT 58.627 40.000 27.57 15.47 0.00 3.06
403 720 6.838612 ACCTAGAGAAGCTTCAGATAGATGTT 59.161 38.462 27.57 3.15 0.00 2.71
405 722 9.023962 CCTAGAGAAGCTTCAGATAGATGTTAT 57.976 37.037 27.57 2.38 0.00 1.89
408 725 6.686630 AGAAGCTTCAGATAGATGTTATCCG 58.313 40.000 27.57 0.00 0.00 4.18
409 726 4.815269 AGCTTCAGATAGATGTTATCCGC 58.185 43.478 0.00 0.00 0.00 5.54
410 727 4.281941 AGCTTCAGATAGATGTTATCCGCA 59.718 41.667 0.00 0.00 0.00 5.69
412 729 4.179926 TCAGATAGATGTTATCCGCAGC 57.820 45.455 0.00 0.00 0.00 5.25
415 827 2.820059 TAGATGTTATCCGCAGCTGG 57.180 50.000 17.12 5.50 34.25 4.85
423 835 1.680522 ATCCGCAGCTGGGTAGTGAG 61.681 60.000 26.94 12.28 0.00 3.51
433 845 0.456628 GGGTAGTGAGGAAGACGAGC 59.543 60.000 0.00 0.00 0.00 5.03
465 881 0.975556 TTATCCGCAGCTGGGAGACA 60.976 55.000 30.57 13.42 36.91 3.41
486 902 3.983988 CAGGTCGTCTAATGATTCCATCG 59.016 47.826 0.00 0.00 31.40 3.84
491 907 3.121328 CGTCTAATGATTCCATCGAACGC 60.121 47.826 0.00 0.00 31.40 4.84
492 908 3.184581 GTCTAATGATTCCATCGAACGCC 59.815 47.826 0.00 0.00 31.40 5.68
493 909 2.036958 AATGATTCCATCGAACGCCA 57.963 45.000 0.00 0.00 31.40 5.69
494 910 2.260844 ATGATTCCATCGAACGCCAT 57.739 45.000 0.00 0.00 0.00 4.40
495 911 1.298602 TGATTCCATCGAACGCCATG 58.701 50.000 0.00 0.00 0.00 3.66
498 914 1.599576 TCCATCGAACGCCATGGAA 59.400 52.632 18.40 0.00 44.68 3.53
499 915 0.461870 TCCATCGAACGCCATGGAAG 60.462 55.000 18.40 11.25 44.68 3.46
500 916 0.461870 CCATCGAACGCCATGGAAGA 60.462 55.000 18.40 6.72 42.11 2.87
502 918 1.737236 CATCGAACGCCATGGAAGAAA 59.263 47.619 18.40 0.00 0.00 2.52
503 919 2.107950 TCGAACGCCATGGAAGAAAT 57.892 45.000 18.40 0.76 0.00 2.17
504 920 3.254470 TCGAACGCCATGGAAGAAATA 57.746 42.857 18.40 0.00 0.00 1.40
506 922 3.118920 TCGAACGCCATGGAAGAAATAGA 60.119 43.478 18.40 0.59 0.00 1.98
507 923 3.001330 CGAACGCCATGGAAGAAATAGAC 59.999 47.826 18.40 0.00 0.00 2.59
508 924 2.919228 ACGCCATGGAAGAAATAGACC 58.081 47.619 18.40 0.00 0.00 3.85
510 926 2.222027 GCCATGGAAGAAATAGACCCG 58.778 52.381 18.40 0.00 0.00 5.28
511 927 2.222027 CCATGGAAGAAATAGACCCGC 58.778 52.381 5.56 0.00 0.00 6.13
512 928 2.158755 CCATGGAAGAAATAGACCCGCT 60.159 50.000 5.56 0.00 0.00 5.52
513 929 2.691409 TGGAAGAAATAGACCCGCTG 57.309 50.000 0.00 0.00 0.00 5.18
517 933 4.897076 TGGAAGAAATAGACCCGCTGTATA 59.103 41.667 0.00 0.00 0.00 1.47
519 935 6.042781 TGGAAGAAATAGACCCGCTGTATAAT 59.957 38.462 0.00 0.00 0.00 1.28
559 3174 7.770801 TTATGTGAGATGTGTAATGTACTGC 57.229 36.000 0.00 0.00 0.00 4.40
561 3176 5.546526 TGTGAGATGTGTAATGTACTGCAA 58.453 37.500 0.00 0.00 0.00 4.08
576 3191 1.461127 CTGCAAGTGAACGGCTACTTC 59.539 52.381 0.00 0.00 35.08 3.01
577 3192 1.070134 TGCAAGTGAACGGCTACTTCT 59.930 47.619 0.00 0.00 35.08 2.85
579 3194 2.924290 GCAAGTGAACGGCTACTTCTAG 59.076 50.000 0.00 0.00 35.08 2.43
580 3195 3.614390 GCAAGTGAACGGCTACTTCTAGT 60.614 47.826 0.00 0.00 35.08 2.57
582 3197 4.437772 AGTGAACGGCTACTTCTAGTTC 57.562 45.455 0.28 0.28 40.90 3.01
583 3198 3.825014 AGTGAACGGCTACTTCTAGTTCA 59.175 43.478 5.37 5.37 45.78 3.18
585 3200 4.553323 TGAACGGCTACTTCTAGTTCAAC 58.447 43.478 6.83 0.00 45.24 3.18
588 3203 3.169733 CGGCTACTTCTAGTTCAACGTC 58.830 50.000 0.00 0.00 0.00 4.34
590 3205 3.169733 GCTACTTCTAGTTCAACGTCCG 58.830 50.000 0.00 0.00 0.00 4.79
591 3206 3.365767 GCTACTTCTAGTTCAACGTCCGT 60.366 47.826 0.00 0.00 0.00 4.69
592 3207 4.142816 GCTACTTCTAGTTCAACGTCCGTA 60.143 45.833 0.00 0.00 0.00 4.02
593 3208 4.152607 ACTTCTAGTTCAACGTCCGTAC 57.847 45.455 0.00 0.00 0.00 3.67
594 3209 3.565482 ACTTCTAGTTCAACGTCCGTACA 59.435 43.478 0.00 0.00 0.00 2.90
597 3212 5.125100 TCTAGTTCAACGTCCGTACAATT 57.875 39.130 0.00 0.00 0.00 2.32
598 3213 4.919168 TCTAGTTCAACGTCCGTACAATTG 59.081 41.667 3.24 3.24 0.00 2.32
600 3215 2.529780 TCAACGTCCGTACAATTGGT 57.470 45.000 10.83 0.00 0.00 3.67
601 3216 2.836262 TCAACGTCCGTACAATTGGTT 58.164 42.857 10.83 0.00 0.00 3.67
602 3217 3.987547 TCAACGTCCGTACAATTGGTTA 58.012 40.909 10.83 0.00 0.00 2.85
603 3218 3.989167 TCAACGTCCGTACAATTGGTTAG 59.011 43.478 10.83 0.00 0.00 2.34
604 3219 2.963432 ACGTCCGTACAATTGGTTAGG 58.037 47.619 10.83 7.68 0.00 2.69
605 3220 2.273557 CGTCCGTACAATTGGTTAGGG 58.726 52.381 10.83 9.12 0.00 3.53
606 3221 2.094078 CGTCCGTACAATTGGTTAGGGA 60.094 50.000 10.83 11.23 0.00 4.20
608 3223 2.093341 TCCGTACAATTGGTTAGGGAGC 60.093 50.000 10.83 0.00 0.00 4.70
609 3224 2.093128 CCGTACAATTGGTTAGGGAGCT 60.093 50.000 10.83 0.00 0.00 4.09
611 3226 2.808906 ACAATTGGTTAGGGAGCTCC 57.191 50.000 25.59 25.59 0.00 4.70
612 3227 1.065418 ACAATTGGTTAGGGAGCTCCG 60.065 52.381 26.36 10.80 41.52 4.63
613 3228 1.209504 CAATTGGTTAGGGAGCTCCGA 59.790 52.381 26.36 14.23 41.52 4.55
614 3229 1.123928 ATTGGTTAGGGAGCTCCGAG 58.876 55.000 26.36 0.00 41.52 4.63
615 3230 0.252103 TTGGTTAGGGAGCTCCGAGT 60.252 55.000 26.36 15.59 41.52 4.18
616 3231 0.627451 TGGTTAGGGAGCTCCGAGTA 59.373 55.000 26.36 14.56 41.52 2.59
617 3232 1.031235 GGTTAGGGAGCTCCGAGTAC 58.969 60.000 26.36 19.28 41.52 2.73
618 3233 1.684248 GGTTAGGGAGCTCCGAGTACA 60.684 57.143 26.36 4.19 41.52 2.90
620 3235 2.694109 GTTAGGGAGCTCCGAGTACATT 59.306 50.000 26.36 6.76 41.52 2.71
621 3236 1.867363 AGGGAGCTCCGAGTACATTT 58.133 50.000 26.36 0.56 41.52 2.32
622 3237 2.188817 AGGGAGCTCCGAGTACATTTT 58.811 47.619 26.36 0.00 41.52 1.82
623 3238 2.168728 AGGGAGCTCCGAGTACATTTTC 59.831 50.000 26.36 7.86 41.52 2.29
624 3239 2.552031 GGAGCTCCGAGTACATTTTCC 58.448 52.381 19.06 0.00 0.00 3.13
625 3240 2.194271 GAGCTCCGAGTACATTTTCCG 58.806 52.381 0.87 0.00 0.00 4.30
626 3241 1.549170 AGCTCCGAGTACATTTTCCGT 59.451 47.619 0.00 0.00 0.00 4.69
627 3242 1.925185 GCTCCGAGTACATTTTCCGTC 59.075 52.381 0.00 0.00 0.00 4.79
628 3243 2.537401 CTCCGAGTACATTTTCCGTCC 58.463 52.381 0.00 0.00 0.00 4.79
629 3244 1.135315 TCCGAGTACATTTTCCGTCCG 60.135 52.381 0.00 0.00 0.00 4.79
630 3245 1.403249 CCGAGTACATTTTCCGTCCGT 60.403 52.381 0.00 0.00 0.00 4.69
631 3246 1.916000 CGAGTACATTTTCCGTCCGTC 59.084 52.381 0.00 0.00 0.00 4.79
632 3247 2.265683 GAGTACATTTTCCGTCCGTCC 58.734 52.381 0.00 0.00 0.00 4.79
634 3249 2.037511 AGTACATTTTCCGTCCGTCCAA 59.962 45.455 0.00 0.00 0.00 3.53
635 3250 1.232119 ACATTTTCCGTCCGTCCAAC 58.768 50.000 0.00 0.00 0.00 3.77
636 3251 0.165079 CATTTTCCGTCCGTCCAACG 59.835 55.000 0.00 0.00 42.11 4.10
637 3252 0.249996 ATTTTCCGTCCGTCCAACGT 60.250 50.000 0.00 0.00 40.58 3.99
638 3253 0.875474 TTTTCCGTCCGTCCAACGTC 60.875 55.000 0.00 0.00 40.58 4.34
639 3254 2.697992 TTTCCGTCCGTCCAACGTCC 62.698 60.000 0.00 0.00 40.58 4.79
640 3255 4.729856 CCGTCCGTCCAACGTCCC 62.730 72.222 0.00 0.00 40.58 4.46
641 3256 4.729856 CGTCCGTCCAACGTCCCC 62.730 72.222 0.00 0.00 40.58 4.81
642 3257 3.308705 GTCCGTCCAACGTCCCCT 61.309 66.667 0.00 0.00 40.58 4.79
644 3259 2.047560 CCGTCCAACGTCCCCTTC 60.048 66.667 0.00 0.00 40.58 3.46
645 3260 2.738480 CGTCCAACGTCCCCTTCA 59.262 61.111 0.00 0.00 36.74 3.02
647 3747 0.321298 CGTCCAACGTCCCCTTCAAT 60.321 55.000 0.00 0.00 36.74 2.57
651 3751 2.372504 TCCAACGTCCCCTTCAATTACA 59.627 45.455 0.00 0.00 0.00 2.41
655 3755 2.307686 ACGTCCCCTTCAATTACACCAT 59.692 45.455 0.00 0.00 0.00 3.55
657 3757 3.288092 GTCCCCTTCAATTACACCATCC 58.712 50.000 0.00 0.00 0.00 3.51
660 3760 4.016666 TCCCCTTCAATTACACCATCCAAT 60.017 41.667 0.00 0.00 0.00 3.16
661 3761 4.099881 CCCCTTCAATTACACCATCCAATG 59.900 45.833 0.00 0.00 0.00 2.82
677 3777 1.200020 CAATGGAGAAAAGGGACGTGC 59.800 52.381 0.00 0.00 0.00 5.34
678 3778 0.673644 ATGGAGAAAAGGGACGTGCG 60.674 55.000 0.00 0.00 0.00 5.34
682 3782 1.128692 GAGAAAAGGGACGTGCGATTG 59.871 52.381 0.00 0.00 0.00 2.67
686 3786 0.670546 AAGGGACGTGCGATTGTCTG 60.671 55.000 0.00 0.00 35.45 3.51
688 3788 2.740714 GGACGTGCGATTGTCTGGC 61.741 63.158 0.00 0.00 35.45 4.85
689 3789 1.738099 GACGTGCGATTGTCTGGCT 60.738 57.895 0.00 0.00 32.37 4.75
690 3790 0.457853 GACGTGCGATTGTCTGGCTA 60.458 55.000 0.00 0.00 32.37 3.93
691 3791 0.736325 ACGTGCGATTGTCTGGCTAC 60.736 55.000 0.00 0.00 0.00 3.58
692 3792 0.458543 CGTGCGATTGTCTGGCTACT 60.459 55.000 0.00 0.00 0.00 2.57
693 3793 1.726853 GTGCGATTGTCTGGCTACTT 58.273 50.000 0.00 0.00 0.00 2.24
694 3794 1.661112 GTGCGATTGTCTGGCTACTTC 59.339 52.381 0.00 0.00 0.00 3.01
697 3797 3.181486 TGCGATTGTCTGGCTACTTCTAG 60.181 47.826 0.00 0.00 0.00 2.43
698 3798 3.181485 GCGATTGTCTGGCTACTTCTAGT 60.181 47.826 0.00 0.00 0.00 2.57
701 3801 4.803098 TTGTCTGGCTACTTCTAGTTCC 57.197 45.455 0.00 0.00 0.00 3.62
702 3802 3.774734 TGTCTGGCTACTTCTAGTTCCA 58.225 45.455 0.00 0.00 31.77 3.53
703 3803 3.510360 TGTCTGGCTACTTCTAGTTCCAC 59.490 47.826 0.00 0.00 30.25 4.02
706 3806 2.895404 TGGCTACTTCTAGTTCCACGTT 59.105 45.455 0.00 0.00 28.96 3.99
707 3807 3.322828 TGGCTACTTCTAGTTCCACGTTT 59.677 43.478 0.00 0.00 28.96 3.60
721 3956 3.127895 TCCACGTTTCAAGTTTGAACTGG 59.872 43.478 6.79 11.16 45.99 4.00
726 3961 4.202010 CGTTTCAAGTTTGAACTGGTCCAT 60.202 41.667 6.79 0.00 45.99 3.41
728 3963 4.163441 TCAAGTTTGAACTGGTCCATCA 57.837 40.909 0.00 0.00 39.66 3.07
729 3964 4.531854 TCAAGTTTGAACTGGTCCATCAA 58.468 39.130 4.11 4.11 39.66 2.57
773 4261 2.604046 AATTAGTGCAGCTAGGACCG 57.396 50.000 0.00 0.00 39.79 4.79
777 4265 1.185618 AGTGCAGCTAGGACCGTTCA 61.186 55.000 0.00 0.00 39.79 3.18
782 4270 1.053424 AGCTAGGACCGTTCAACCAA 58.947 50.000 0.00 0.00 0.00 3.67
786 4274 1.395635 AGGACCGTTCAACCAAAACC 58.604 50.000 0.00 0.00 0.00 3.27
795 4283 4.682787 GTTCAACCAAAACCAAGAGAAGG 58.317 43.478 0.00 0.00 0.00 3.46
811 4336 4.163078 AGAGAAGGTTCAATCGATCATGGT 59.837 41.667 0.00 0.00 0.00 3.55
817 4342 0.949397 CAATCGATCATGGTGCCCAG 59.051 55.000 0.00 0.00 36.75 4.45
818 4343 0.548031 AATCGATCATGGTGCCCAGT 59.452 50.000 0.00 0.00 36.75 4.00
819 4344 0.107456 ATCGATCATGGTGCCCAGTC 59.893 55.000 0.00 0.00 36.75 3.51
834 4359 1.068281 CCAGTCCCATCTGATGACTCG 59.932 57.143 18.92 4.70 37.25 4.18
839 4891 1.537776 CCCATCTGATGACTCGCTGTC 60.538 57.143 18.92 2.16 45.54 3.51
859 4911 1.546834 GCGTAGTCATCACCTCGAAC 58.453 55.000 0.00 0.00 0.00 3.95
863 4915 2.680312 AGTCATCACCTCGAACCATG 57.320 50.000 0.00 0.00 0.00 3.66
878 4930 7.657354 CCTCGAACCATGATTTAGACATAATCA 59.343 37.037 0.00 0.00 43.80 2.57
879 4931 8.593492 TCGAACCATGATTTAGACATAATCAG 57.407 34.615 0.00 0.00 43.15 2.90
880 4932 7.657354 TCGAACCATGATTTAGACATAATCAGG 59.343 37.037 0.00 0.00 43.15 3.86
881 4933 7.442364 CGAACCATGATTTAGACATAATCAGGT 59.558 37.037 0.00 0.00 43.15 4.00
920 5048 1.961394 GACCGTATACCTCAGCATCCA 59.039 52.381 0.00 0.00 0.00 3.41
921 5049 2.563179 GACCGTATACCTCAGCATCCAT 59.437 50.000 0.00 0.00 0.00 3.41
922 5050 2.563179 ACCGTATACCTCAGCATCCATC 59.437 50.000 0.00 0.00 0.00 3.51
931 5059 0.110104 CAGCATCCATCCCCTTCCTC 59.890 60.000 0.00 0.00 0.00 3.71
935 5063 0.699231 ATCCATCCCCTTCCTCACCC 60.699 60.000 0.00 0.00 0.00 4.61
937 5065 2.044620 ATCCCCTTCCTCACCCCC 59.955 66.667 0.00 0.00 0.00 5.40
983 5112 1.227002 CGACGGAAGAAGCCTAGCC 60.227 63.158 0.00 0.00 0.00 3.93
992 5135 1.150135 AGAAGCCTAGCCCTATAGCCA 59.850 52.381 0.00 0.00 0.00 4.75
994 5137 1.872773 AGCCTAGCCCTATAGCCATC 58.127 55.000 0.00 0.00 0.00 3.51
1046 5189 4.124238 CTCGAGACCACTACTCTCCTTAG 58.876 52.174 6.58 0.00 31.92 2.18
1116 5259 0.250901 ACACTCAAGGCGAGCCAAAT 60.251 50.000 17.18 0.00 46.63 2.32
1305 5448 7.090173 CCAGTTTCAACATAATTTTCACCGAT 58.910 34.615 0.00 0.00 0.00 4.18
1318 5461 1.001974 TCACCGATGAGAGGTTTGGTG 59.998 52.381 2.86 2.86 45.27 4.17
1333 5486 5.244178 AGGTTTGGTGTTTTTACACTTGTGA 59.756 36.000 7.83 0.00 40.28 3.58
1342 5495 8.588789 GTGTTTTTACACTTGTGAATTTGTACC 58.411 33.333 7.83 0.00 37.62 3.34
1346 5499 5.751243 ACACTTGTGAATTTGTACCACTC 57.249 39.130 7.83 0.00 0.00 3.51
1354 5507 6.493115 TGTGAATTTGTACCACTCCATTGATT 59.507 34.615 0.00 0.00 0.00 2.57
1355 5508 7.029563 GTGAATTTGTACCACTCCATTGATTC 58.970 38.462 0.00 0.00 0.00 2.52
1374 5599 7.346208 TGATTCACACTTGTTAACTATGTCG 57.654 36.000 7.22 4.54 0.00 4.35
1459 5690 3.152341 CATAAGAGATGGTGAATGGGCC 58.848 50.000 0.00 0.00 0.00 5.80
1564 5795 3.798954 CTGGGAGCTCCGAATCCGC 62.799 68.421 26.36 11.16 38.76 5.54
1591 5822 1.303317 CCTCACCTTCCCCAAACCG 60.303 63.158 0.00 0.00 0.00 4.44
1730 5961 2.039084 CACTGTCCTCTAAAACTGCCCT 59.961 50.000 0.00 0.00 0.00 5.19
2009 6251 6.896969 AGACTGTACGTACTCTTGTCTAAAC 58.103 40.000 26.32 12.00 32.44 2.01
2013 6255 4.152607 ACGTACTCTTGTCTAAACCGAC 57.847 45.455 0.00 0.00 34.52 4.79
2059 6630 7.509318 TGAGCAGGAGGTTATAGCTTAGAAATA 59.491 37.037 0.00 0.00 35.36 1.40
2644 7249 7.655732 CGTCCCATAATGTAAGATATGTGTCAA 59.344 37.037 0.00 0.00 0.00 3.18
3119 7748 6.942532 TGGAGGAAAAGAATTTGATATCCG 57.057 37.500 0.00 0.00 39.02 4.18
3171 7800 4.036262 GTGACAATTAGAAGTGGTGTTGCA 59.964 41.667 0.00 0.00 0.00 4.08
3199 7828 6.427853 TGACTCAATTGTGTTCTCCTACATTG 59.572 38.462 13.95 0.00 0.00 2.82
3301 7930 7.436673 CACCACATTGCTAGTTCTATCTACTTC 59.563 40.741 0.00 0.00 0.00 3.01
3500 8131 2.526888 TCAGTGTCCCTCTTACGGAT 57.473 50.000 0.00 0.00 0.00 4.18
3564 8195 2.882927 TGCGATAGGAGTTTATGCGT 57.117 45.000 0.00 0.00 0.00 5.24
3642 8284 2.032981 GGCATCTTATGGGTTGCCG 58.967 57.895 0.00 0.00 44.58 5.69
3656 8300 1.933853 GTTGCCGTGGTCTCATGTATC 59.066 52.381 0.00 0.00 0.00 2.24
3677 8321 5.257082 TCACTACTTGTTTCCCTTTTTGC 57.743 39.130 0.00 0.00 0.00 3.68
3679 8323 5.362430 TCACTACTTGTTTCCCTTTTTGCAT 59.638 36.000 0.00 0.00 0.00 3.96
3773 8417 4.574674 TTCTGAAGTGGGCAGACATAAT 57.425 40.909 0.00 0.00 41.72 1.28
3789 8433 5.189934 AGACATAATCGGGAAAAGGAAGTCT 59.810 40.000 0.00 0.00 0.00 3.24
3847 8491 9.005777 TCAACTTTAATGTCAAACCAGGTATAC 57.994 33.333 0.00 0.00 0.00 1.47
3906 8551 7.776618 TGAAGAGTGATAAGTAAGGAGAACA 57.223 36.000 0.00 0.00 0.00 3.18
3927 8572 4.278919 ACATTGCACAACATTCACTGATCA 59.721 37.500 0.00 0.00 0.00 2.92
4069 8714 6.252599 TCAACCTAAAGATAGCATCCATGT 57.747 37.500 0.00 0.00 0.00 3.21
4099 8744 4.568152 ACACACCTTAAACTGAACATGC 57.432 40.909 0.00 0.00 0.00 4.06
4126 8771 4.691860 AATATTTGATAGCTCGCCATGC 57.308 40.909 0.00 0.00 0.00 4.06
4220 8865 2.899339 GCAGCTTCGGATGGAGCC 60.899 66.667 0.00 0.00 0.00 4.70
4254 8899 3.244561 ACAAGCCAGTTGCAGTACAGTAT 60.245 43.478 0.00 0.00 44.83 2.12
4318 8963 2.190578 CCCAGCAAGGATCCGACC 59.809 66.667 5.98 0.00 41.22 4.79
4321 8966 4.514577 AGCAAGGATCCGACCGCG 62.515 66.667 5.98 0.00 34.73 6.46
4331 8976 1.010908 CCGACCGCGAAAAACGTTT 60.011 52.632 8.23 7.96 44.60 3.60
4557 9202 0.180171 TGGATGATTGGTGCCTACGG 59.820 55.000 0.00 0.00 0.00 4.02
4568 9213 0.390603 TGCCTACGGTTTGATGGTCG 60.391 55.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.250727 TCTAAACAGTGGCAGGGCAC 60.251 55.000 17.21 17.21 0.00 5.01
92 94 5.418676 CATAAAATTGGAAGTGGCGGATTT 58.581 37.500 0.00 0.00 0.00 2.17
112 114 1.843851 ACAATTTCTCTCCGGGCCATA 59.156 47.619 4.39 0.00 0.00 2.74
119 121 5.362556 ACATCACAAACAATTTCTCTCCG 57.637 39.130 0.00 0.00 0.00 4.63
121 123 8.633075 TGAAAACATCACAAACAATTTCTCTC 57.367 30.769 0.00 0.00 31.50 3.20
131 133 7.992180 ATCACTTCTTGAAAACATCACAAAC 57.008 32.000 0.00 0.00 37.92 2.93
142 144 4.637276 TCTGCCGTTATCACTTCTTGAAA 58.363 39.130 0.00 0.00 37.92 2.69
215 217 3.567797 GATCGCCAAGCTCGTGCC 61.568 66.667 5.73 0.00 40.80 5.01
238 240 6.910259 AGGGTTCTCTGGTTATTTAATCCT 57.090 37.500 0.00 0.00 0.00 3.24
239 241 7.116736 TCAAGGGTTCTCTGGTTATTTAATCC 58.883 38.462 0.00 0.00 0.00 3.01
253 255 3.214328 TGCTCTTGTTTCAAGGGTTCTC 58.786 45.455 10.43 0.00 0.00 2.87
256 258 3.631250 TCTTGCTCTTGTTTCAAGGGTT 58.369 40.909 10.43 0.00 38.13 4.11
286 332 2.747989 TGACCTGTGATCACGTCTCTAC 59.252 50.000 24.95 13.14 33.17 2.59
299 346 3.567164 AGAAAAGCAATCACTGACCTGTG 59.433 43.478 1.26 1.26 39.15 3.66
307 354 5.359576 TGTACAAACCAGAAAAGCAATCACT 59.640 36.000 0.00 0.00 0.00 3.41
317 364 5.712917 AGTTTTCCTGTGTACAAACCAGAAA 59.287 36.000 12.30 8.13 30.72 2.52
321 368 5.010933 TGAAGTTTTCCTGTGTACAAACCA 58.989 37.500 0.00 0.00 30.72 3.67
323 370 5.515270 GCTTGAAGTTTTCCTGTGTACAAAC 59.485 40.000 0.00 0.00 0.00 2.93
328 375 4.755123 GCTAGCTTGAAGTTTTCCTGTGTA 59.245 41.667 7.70 0.00 0.00 2.90
330 377 3.364366 CGCTAGCTTGAAGTTTTCCTGTG 60.364 47.826 13.93 0.00 0.00 3.66
340 387 4.424626 TGTCTTGTATCGCTAGCTTGAAG 58.575 43.478 13.93 7.67 0.00 3.02
341 388 4.157840 TCTGTCTTGTATCGCTAGCTTGAA 59.842 41.667 13.93 0.00 0.00 2.69
342 389 3.694566 TCTGTCTTGTATCGCTAGCTTGA 59.305 43.478 13.93 3.75 0.00 3.02
346 393 3.972950 TCTCTGTCTTGTATCGCTAGC 57.027 47.619 4.06 4.06 0.00 3.42
347 394 4.737765 GCTTTCTCTGTCTTGTATCGCTAG 59.262 45.833 0.00 0.00 0.00 3.42
348 395 4.157840 TGCTTTCTCTGTCTTGTATCGCTA 59.842 41.667 0.00 0.00 0.00 4.26
349 396 3.056536 TGCTTTCTCTGTCTTGTATCGCT 60.057 43.478 0.00 0.00 0.00 4.93
350 397 3.254060 TGCTTTCTCTGTCTTGTATCGC 58.746 45.455 0.00 0.00 0.00 4.58
351 398 4.738124 TCTGCTTTCTCTGTCTTGTATCG 58.262 43.478 0.00 0.00 0.00 2.92
352 399 7.608308 ATTTCTGCTTTCTCTGTCTTGTATC 57.392 36.000 0.00 0.00 0.00 2.24
353 400 7.992754 AATTTCTGCTTTCTCTGTCTTGTAT 57.007 32.000 0.00 0.00 0.00 2.29
354 401 7.387948 GGTAATTTCTGCTTTCTCTGTCTTGTA 59.612 37.037 0.00 0.00 0.00 2.41
355 402 6.205658 GGTAATTTCTGCTTTCTCTGTCTTGT 59.794 38.462 0.00 0.00 0.00 3.16
356 403 6.429385 AGGTAATTTCTGCTTTCTCTGTCTTG 59.571 38.462 0.00 0.00 0.00 3.02
357 404 6.538263 AGGTAATTTCTGCTTTCTCTGTCTT 58.462 36.000 0.00 0.00 0.00 3.01
358 405 6.120507 AGGTAATTTCTGCTTTCTCTGTCT 57.879 37.500 0.00 0.00 0.00 3.41
360 677 7.179338 TCTCTAGGTAATTTCTGCTTTCTCTGT 59.821 37.037 0.00 0.00 0.00 3.41
361 678 7.551585 TCTCTAGGTAATTTCTGCTTTCTCTG 58.448 38.462 0.00 0.00 0.00 3.35
369 686 6.109359 TGAAGCTTCTCTAGGTAATTTCTGC 58.891 40.000 26.09 0.00 33.29 4.26
382 699 7.309133 CGGATAACATCTATCTGAAGCTTCTCT 60.309 40.741 26.09 13.33 33.30 3.10
386 703 5.221521 TGCGGATAACATCTATCTGAAGCTT 60.222 40.000 0.00 0.00 33.30 3.74
387 704 4.281941 TGCGGATAACATCTATCTGAAGCT 59.718 41.667 5.03 0.00 33.30 3.74
388 705 4.560128 TGCGGATAACATCTATCTGAAGC 58.440 43.478 5.03 1.78 33.30 3.86
389 706 4.624882 GCTGCGGATAACATCTATCTGAAG 59.375 45.833 0.00 4.87 38.47 3.02
392 709 3.925299 CAGCTGCGGATAACATCTATCTG 59.075 47.826 0.00 0.00 34.33 2.90
393 710 3.056250 CCAGCTGCGGATAACATCTATCT 60.056 47.826 8.66 0.00 0.00 1.98
394 711 3.257393 CCAGCTGCGGATAACATCTATC 58.743 50.000 8.66 0.00 0.00 2.08
396 713 1.344438 CCCAGCTGCGGATAACATCTA 59.656 52.381 8.66 0.00 0.00 1.98
397 714 0.107456 CCCAGCTGCGGATAACATCT 59.893 55.000 8.66 0.00 0.00 2.90
399 716 1.070758 CTACCCAGCTGCGGATAACAT 59.929 52.381 23.24 6.62 0.00 2.71
401 718 0.464452 ACTACCCAGCTGCGGATAAC 59.536 55.000 23.24 0.00 0.00 1.89
402 719 0.464036 CACTACCCAGCTGCGGATAA 59.536 55.000 23.24 10.32 0.00 1.75
403 720 0.396556 TCACTACCCAGCTGCGGATA 60.397 55.000 23.24 12.81 0.00 2.59
405 722 2.283604 TCACTACCCAGCTGCGGA 60.284 61.111 23.24 5.67 0.00 5.54
406 723 2.185350 CTCACTACCCAGCTGCGG 59.815 66.667 8.66 13.80 0.00 5.69
408 725 0.107945 CTTCCTCACTACCCAGCTGC 60.108 60.000 8.66 0.00 0.00 5.25
409 726 1.205893 GTCTTCCTCACTACCCAGCTG 59.794 57.143 6.78 6.78 0.00 4.24
410 727 1.562783 GTCTTCCTCACTACCCAGCT 58.437 55.000 0.00 0.00 0.00 4.24
412 729 1.746220 CTCGTCTTCCTCACTACCCAG 59.254 57.143 0.00 0.00 0.00 4.45
415 827 1.465794 AGCTCGTCTTCCTCACTACC 58.534 55.000 0.00 0.00 0.00 3.18
465 881 3.889538 TCGATGGAATCATTAGACGACCT 59.110 43.478 0.00 0.00 45.97 3.85
476 892 1.298602 CATGGCGTTCGATGGAATCA 58.701 50.000 0.00 0.00 45.97 2.57
479 895 1.599576 TCCATGGCGTTCGATGGAA 59.400 52.632 6.96 0.00 44.22 3.53
480 896 0.461870 CTTCCATGGCGTTCGATGGA 60.462 55.000 6.96 10.23 45.27 3.41
482 898 1.368641 TTCTTCCATGGCGTTCGATG 58.631 50.000 6.96 0.00 0.00 3.84
486 902 3.312697 GGTCTATTTCTTCCATGGCGTTC 59.687 47.826 6.96 0.00 0.00 3.95
491 907 2.158755 AGCGGGTCTATTTCTTCCATGG 60.159 50.000 4.97 4.97 0.00 3.66
492 908 2.874701 CAGCGGGTCTATTTCTTCCATG 59.125 50.000 0.00 0.00 0.00 3.66
493 909 2.505819 ACAGCGGGTCTATTTCTTCCAT 59.494 45.455 0.00 0.00 0.00 3.41
494 910 1.906574 ACAGCGGGTCTATTTCTTCCA 59.093 47.619 0.00 0.00 0.00 3.53
495 911 2.693267 ACAGCGGGTCTATTTCTTCC 57.307 50.000 0.00 0.00 0.00 3.46
540 989 5.639082 CACTTGCAGTACATTACACATCTCA 59.361 40.000 0.00 0.00 0.00 3.27
546 995 4.377022 CCGTTCACTTGCAGTACATTACAC 60.377 45.833 0.00 0.00 0.00 2.90
548 997 3.424433 GCCGTTCACTTGCAGTACATTAC 60.424 47.826 0.00 0.00 0.00 1.89
550 999 1.535462 GCCGTTCACTTGCAGTACATT 59.465 47.619 0.00 0.00 0.00 2.71
553 3168 1.725164 GTAGCCGTTCACTTGCAGTAC 59.275 52.381 0.00 0.00 0.00 2.73
558 3173 1.797025 AGAAGTAGCCGTTCACTTGC 58.203 50.000 0.00 0.00 35.17 4.01
559 3174 4.175787 ACTAGAAGTAGCCGTTCACTTG 57.824 45.455 0.00 0.00 35.17 3.16
561 3176 3.825014 TGAACTAGAAGTAGCCGTTCACT 59.175 43.478 0.00 0.00 39.03 3.41
564 3179 3.607209 CGTTGAACTAGAAGTAGCCGTTC 59.393 47.826 0.00 0.00 35.69 3.95
565 3180 3.005155 ACGTTGAACTAGAAGTAGCCGTT 59.995 43.478 0.00 0.00 0.00 4.44
566 3181 2.555757 ACGTTGAACTAGAAGTAGCCGT 59.444 45.455 0.00 0.00 0.00 5.68
576 3191 4.090930 CCAATTGTACGGACGTTGAACTAG 59.909 45.833 15.14 0.00 0.00 2.57
577 3192 3.989167 CCAATTGTACGGACGTTGAACTA 59.011 43.478 15.14 0.00 0.00 2.24
579 3194 2.545106 ACCAATTGTACGGACGTTGAAC 59.455 45.455 15.14 0.00 0.00 3.18
580 3195 2.836262 ACCAATTGTACGGACGTTGAA 58.164 42.857 15.14 0.00 0.00 2.69
582 3197 3.123959 CCTAACCAATTGTACGGACGTTG 59.876 47.826 1.57 8.36 0.00 4.10
583 3198 3.328505 CCTAACCAATTGTACGGACGTT 58.671 45.455 1.57 2.27 0.00 3.99
585 3200 2.094078 TCCCTAACCAATTGTACGGACG 60.094 50.000 4.43 0.00 0.00 4.79
588 3203 2.093128 AGCTCCCTAACCAATTGTACGG 60.093 50.000 4.43 0.00 0.00 4.02
590 3205 3.542648 GGAGCTCCCTAACCAATTGTAC 58.457 50.000 23.19 0.00 0.00 2.90
591 3206 2.169769 CGGAGCTCCCTAACCAATTGTA 59.830 50.000 27.20 0.00 0.00 2.41
592 3207 1.065418 CGGAGCTCCCTAACCAATTGT 60.065 52.381 27.20 0.00 0.00 2.71
593 3208 1.209504 TCGGAGCTCCCTAACCAATTG 59.790 52.381 27.20 8.85 0.00 2.32
594 3209 1.486726 CTCGGAGCTCCCTAACCAATT 59.513 52.381 27.20 0.00 0.00 2.32
597 3212 0.627451 TACTCGGAGCTCCCTAACCA 59.373 55.000 27.20 4.78 0.00 3.67
598 3213 1.031235 GTACTCGGAGCTCCCTAACC 58.969 60.000 27.20 8.81 0.00 2.85
600 3215 2.750141 ATGTACTCGGAGCTCCCTAA 57.250 50.000 27.20 11.79 0.00 2.69
601 3216 2.750141 AATGTACTCGGAGCTCCCTA 57.250 50.000 27.20 14.41 0.00 3.53
602 3217 1.867363 AAATGTACTCGGAGCTCCCT 58.133 50.000 27.20 12.02 0.00 4.20
603 3218 2.552031 GAAAATGTACTCGGAGCTCCC 58.448 52.381 27.20 12.95 0.00 4.30
604 3219 2.552031 GGAAAATGTACTCGGAGCTCC 58.448 52.381 23.79 23.79 0.00 4.70
605 3220 2.194271 CGGAAAATGTACTCGGAGCTC 58.806 52.381 4.71 4.71 0.00 4.09
606 3221 1.549170 ACGGAAAATGTACTCGGAGCT 59.451 47.619 4.58 0.00 0.00 4.09
608 3223 2.537401 GGACGGAAAATGTACTCGGAG 58.463 52.381 2.83 2.83 0.00 4.63
609 3224 1.135315 CGGACGGAAAATGTACTCGGA 60.135 52.381 0.00 0.00 0.00 4.55
611 3226 1.916000 GACGGACGGAAAATGTACTCG 59.084 52.381 0.00 0.00 0.00 4.18
612 3227 2.265683 GGACGGACGGAAAATGTACTC 58.734 52.381 0.00 0.00 0.00 2.59
613 3228 1.619827 TGGACGGACGGAAAATGTACT 59.380 47.619 0.00 0.00 0.00 2.73
614 3229 2.083167 TGGACGGACGGAAAATGTAC 57.917 50.000 0.00 0.00 0.00 2.90
615 3230 2.415776 GTTGGACGGACGGAAAATGTA 58.584 47.619 0.00 0.00 0.00 2.29
616 3231 1.232119 GTTGGACGGACGGAAAATGT 58.768 50.000 0.00 0.00 0.00 2.71
617 3232 0.165079 CGTTGGACGGACGGAAAATG 59.835 55.000 0.00 0.00 38.08 2.32
618 3233 2.535588 CGTTGGACGGACGGAAAAT 58.464 52.632 0.00 0.00 38.08 1.82
629 3244 1.905637 AATTGAAGGGGACGTTGGAC 58.094 50.000 0.00 0.00 36.18 4.02
630 3245 2.372504 TGTAATTGAAGGGGACGTTGGA 59.627 45.455 0.00 0.00 36.18 3.53
631 3246 2.486592 GTGTAATTGAAGGGGACGTTGG 59.513 50.000 0.00 0.00 36.18 3.77
632 3247 2.486592 GGTGTAATTGAAGGGGACGTTG 59.513 50.000 0.00 0.00 36.18 4.10
634 3249 1.700739 TGGTGTAATTGAAGGGGACGT 59.299 47.619 0.00 0.00 0.00 4.34
635 3250 2.483014 TGGTGTAATTGAAGGGGACG 57.517 50.000 0.00 0.00 0.00 4.79
636 3251 3.288092 GGATGGTGTAATTGAAGGGGAC 58.712 50.000 0.00 0.00 0.00 4.46
637 3252 2.922955 TGGATGGTGTAATTGAAGGGGA 59.077 45.455 0.00 0.00 0.00 4.81
638 3253 3.380471 TGGATGGTGTAATTGAAGGGG 57.620 47.619 0.00 0.00 0.00 4.79
639 3254 4.099881 CCATTGGATGGTGTAATTGAAGGG 59.900 45.833 0.00 0.00 45.54 3.95
640 3255 5.266733 CCATTGGATGGTGTAATTGAAGG 57.733 43.478 0.00 0.00 45.54 3.46
655 3755 1.702957 ACGTCCCTTTTCTCCATTGGA 59.297 47.619 5.05 5.05 0.00 3.53
657 3757 1.200020 GCACGTCCCTTTTCTCCATTG 59.800 52.381 0.00 0.00 0.00 2.82
660 3760 1.301401 CGCACGTCCCTTTTCTCCA 60.301 57.895 0.00 0.00 0.00 3.86
661 3761 0.391263 ATCGCACGTCCCTTTTCTCC 60.391 55.000 0.00 0.00 0.00 3.71
665 3765 0.872388 GACAATCGCACGTCCCTTTT 59.128 50.000 0.00 0.00 0.00 2.27
670 3770 2.740714 GCCAGACAATCGCACGTCC 61.741 63.158 0.00 0.00 32.33 4.79
673 3773 0.458543 AGTAGCCAGACAATCGCACG 60.459 55.000 0.00 0.00 0.00 5.34
677 3777 4.640789 ACTAGAAGTAGCCAGACAATCG 57.359 45.455 0.00 0.00 0.00 3.34
678 3778 5.105310 TGGAACTAGAAGTAGCCAGACAATC 60.105 44.000 0.00 0.00 31.71 2.67
682 3782 3.427773 CGTGGAACTAGAAGTAGCCAGAC 60.428 52.174 0.00 0.00 34.71 3.51
686 3786 3.589495 AACGTGGAACTAGAAGTAGCC 57.411 47.619 0.00 0.00 31.75 3.93
688 3788 6.214399 ACTTGAAACGTGGAACTAGAAGTAG 58.786 40.000 0.00 0.00 31.75 2.57
689 3789 6.152932 ACTTGAAACGTGGAACTAGAAGTA 57.847 37.500 0.00 0.00 31.75 2.24
690 3790 5.019785 ACTTGAAACGTGGAACTAGAAGT 57.980 39.130 0.00 0.00 31.75 3.01
691 3791 5.986004 AACTTGAAACGTGGAACTAGAAG 57.014 39.130 0.00 0.00 31.75 2.85
692 3792 5.875910 TCAAACTTGAAACGTGGAACTAGAA 59.124 36.000 0.00 0.00 33.55 2.10
693 3793 5.421277 TCAAACTTGAAACGTGGAACTAGA 58.579 37.500 0.00 0.00 33.55 2.43
694 3794 5.728351 TCAAACTTGAAACGTGGAACTAG 57.272 39.130 0.00 0.00 33.55 2.57
706 3806 4.531854 TGATGGACCAGTTCAAACTTGAA 58.468 39.130 0.00 0.69 44.31 2.69
707 3807 4.163441 TGATGGACCAGTTCAAACTTGA 57.837 40.909 0.00 0.00 37.08 3.02
726 3961 3.688235 TGTGTCTGATGCATCCAATTGA 58.312 40.909 23.67 10.94 0.00 2.57
728 3963 4.274978 TGATGTGTCTGATGCATCCAATT 58.725 39.130 23.67 5.79 38.47 2.32
729 3964 3.893521 TGATGTGTCTGATGCATCCAAT 58.106 40.909 23.67 10.37 38.47 3.16
744 4209 7.227314 TCCTAGCTGCACTAATTATTTGATGTG 59.773 37.037 1.02 0.00 0.00 3.21
773 4261 4.159693 ACCTTCTCTTGGTTTTGGTTGAAC 59.840 41.667 0.00 0.00 33.34 3.18
777 4265 4.349365 TGAACCTTCTCTTGGTTTTGGTT 58.651 39.130 0.00 0.00 46.59 3.67
782 4270 4.714632 TCGATTGAACCTTCTCTTGGTTT 58.285 39.130 0.00 0.00 46.59 3.27
786 4274 5.007430 CCATGATCGATTGAACCTTCTCTTG 59.993 44.000 0.00 0.00 0.00 3.02
795 4283 2.763249 GGCACCATGATCGATTGAAC 57.237 50.000 0.00 0.00 0.00 3.18
811 4336 0.621280 TCATCAGATGGGACTGGGCA 60.621 55.000 10.67 0.00 38.31 5.36
817 4342 0.749649 AGCGAGTCATCAGATGGGAC 59.250 55.000 10.67 2.48 0.00 4.46
818 4343 0.749049 CAGCGAGTCATCAGATGGGA 59.251 55.000 10.67 0.00 0.00 4.37
819 4344 0.463204 ACAGCGAGTCATCAGATGGG 59.537 55.000 10.67 0.00 0.00 4.00
834 4359 1.140407 GGTGATGACTACGCGACAGC 61.140 60.000 15.93 10.71 40.74 4.40
839 4891 0.098200 TTCGAGGTGATGACTACGCG 59.902 55.000 3.53 3.53 0.00 6.01
842 4894 3.130516 TCATGGTTCGAGGTGATGACTAC 59.869 47.826 0.00 0.00 0.00 2.73
844 4896 2.179427 TCATGGTTCGAGGTGATGACT 58.821 47.619 0.00 0.00 0.00 3.41
859 4911 7.226441 TCCACCTGATTATGTCTAAATCATGG 58.774 38.462 10.26 10.26 41.28 3.66
863 4915 7.933577 TGTCATCCACCTGATTATGTCTAAATC 59.066 37.037 0.00 0.00 34.55 2.17
878 4930 1.734655 ACTGGACTTGTCATCCACCT 58.265 50.000 3.08 0.00 41.47 4.00
879 4931 2.154462 CAACTGGACTTGTCATCCACC 58.846 52.381 3.08 0.00 41.47 4.61
880 4932 2.154462 CCAACTGGACTTGTCATCCAC 58.846 52.381 3.08 0.00 41.47 4.02
881 4933 2.054021 TCCAACTGGACTTGTCATCCA 58.946 47.619 3.08 0.00 44.20 3.41
905 4994 2.114323 AGGGGATGGATGCTGAGGTATA 59.886 50.000 0.00 0.00 0.00 1.47
909 4998 0.110104 GAAGGGGATGGATGCTGAGG 59.890 60.000 0.00 0.00 0.00 3.86
920 5048 2.044620 GGGGGTGAGGAAGGGGAT 59.955 66.667 0.00 0.00 0.00 3.85
947 5076 1.275291 TCGTCGCTTTGGAAGAGGATT 59.725 47.619 0.00 0.00 0.00 3.01
983 5112 2.719739 CCATGGCTTGATGGCTATAGG 58.280 52.381 0.00 0.00 42.34 2.57
992 5135 3.961225 TTGGCGGCCATGGCTTGAT 62.961 57.895 34.70 0.00 41.60 2.57
994 5137 4.137872 CTTGGCGGCCATGGCTTG 62.138 66.667 34.70 27.07 41.60 4.01
1046 5189 3.679389 TCCTTTTGCTGGATCTCTTGAC 58.321 45.455 0.00 0.00 0.00 3.18
1128 5271 1.593070 GCATGCAAAGACGATACAGCG 60.593 52.381 14.21 0.00 37.29 5.18
1164 5307 1.920574 CAGTCATGAACGACGATGGAC 59.079 52.381 0.00 2.00 40.98 4.02
1305 5448 5.258051 AGTGTAAAAACACCAAACCTCTCA 58.742 37.500 5.09 0.00 41.26 3.27
1318 5461 8.588789 GTGGTACAAATTCACAAGTGTAAAAAC 58.411 33.333 0.00 0.00 44.16 2.43
1333 5486 6.493115 TGTGAATCAATGGAGTGGTACAAATT 59.507 34.615 0.00 0.00 44.16 1.82
1342 5495 5.443185 AACAAGTGTGAATCAATGGAGTG 57.557 39.130 0.00 0.00 0.00 3.51
1346 5499 8.514594 ACATAGTTAACAAGTGTGAATCAATGG 58.485 33.333 8.61 0.00 0.00 3.16
1354 5507 8.821147 ATTAACGACATAGTTAACAAGTGTGA 57.179 30.769 8.61 0.00 45.67 3.58
1355 5508 8.922676 AGATTAACGACATAGTTAACAAGTGTG 58.077 33.333 8.61 0.00 45.67 3.82
1374 5599 7.502561 ACCTAAATAGCATCCCACAAGATTAAC 59.497 37.037 0.00 0.00 0.00 2.01
1459 5690 2.747460 CCGGTGCCACCAGTGATG 60.747 66.667 15.45 0.00 38.47 3.07
1841 6072 8.677148 AACAGTAATGTGTATGAACTTGTCTT 57.323 30.769 0.00 0.00 0.00 3.01
1888 6119 7.489574 TTTTGGTTGGATAGAATTTGCAAAC 57.510 32.000 15.41 2.49 33.25 2.93
1927 6158 8.090214 ACAGATAGTCAAAATGTTGGGAATTTG 58.910 33.333 0.00 0.00 35.29 2.32
1933 6172 6.207417 ACTTCACAGATAGTCAAAATGTTGGG 59.793 38.462 0.00 0.00 35.29 4.12
2009 6251 2.806244 CTGGTCTTGTAAAGGTTGTCGG 59.194 50.000 0.00 0.00 46.24 4.79
2013 6255 4.703897 TCAGTCTGGTCTTGTAAAGGTTG 58.296 43.478 0.00 0.00 46.24 3.77
2407 7009 5.293569 GTGTACATTAGGAAATGACCCGAAG 59.706 44.000 0.00 0.00 44.50 3.79
2644 7249 4.331717 CGTCCCATAATGTAAGACGCTTTT 59.668 41.667 0.00 0.00 43.07 2.27
2648 7253 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.00 46.66 5.19
3119 7748 6.116806 TCTAGATGTTGAGGTACTGACTCTC 58.883 44.000 0.00 0.00 41.55 3.20
3171 7800 6.998074 TGTAGGAGAACACAATTGAGTCAATT 59.002 34.615 22.70 22.70 43.71 2.32
3185 7814 5.181009 CAGCTTGATCAATGTAGGAGAACA 58.819 41.667 8.96 0.00 0.00 3.18
3199 7828 4.022503 AGTTTGCTTCTTTCCAGCTTGATC 60.023 41.667 0.00 0.00 38.19 2.92
3500 8131 4.250464 CGAAGAAGCCCACAATGTTAGTA 58.750 43.478 0.00 0.00 0.00 1.82
3642 8284 5.967088 ACAAGTAGTGATACATGAGACCAC 58.033 41.667 0.00 2.02 0.00 4.16
3656 8300 5.004922 TGCAAAAAGGGAAACAAGTAGTG 57.995 39.130 0.00 0.00 0.00 2.74
3677 8321 8.118976 AGGATATGCATTCCAGACAATAAATG 57.881 34.615 22.09 0.00 35.59 2.32
3679 8323 7.391554 GCTAGGATATGCATTCCAGACAATAAA 59.608 37.037 22.09 0.00 35.59 1.40
3773 8417 4.834496 TGTACTTAGACTTCCTTTTCCCGA 59.166 41.667 0.00 0.00 0.00 5.14
3847 8491 9.335891 CTATCTCGAATATTTGTGCTAGTACAG 57.664 37.037 13.56 1.15 0.00 2.74
3906 8551 5.456548 TTGATCAGTGAATGTTGTGCAAT 57.543 34.783 0.00 0.00 0.00 3.56
4069 8714 7.925043 TCAGTTTAAGGTGTGTTTTTAGTGA 57.075 32.000 0.00 0.00 0.00 3.41
4099 8744 4.092968 GGCGAGCTATCAAATATTAACGGG 59.907 45.833 0.00 0.00 0.00 5.28
4182 8827 4.016444 GCCCCATGTTTGTCTTCAGATTA 58.984 43.478 0.00 0.00 0.00 1.75
4220 8865 1.102809 TGGCTTGTGGCTGACAACAG 61.103 55.000 0.00 0.00 39.78 3.16
4254 8899 3.637769 AGCAAACTGGGTGTTTTCCTTA 58.362 40.909 0.00 0.00 45.69 2.69
4318 8963 1.116436 TGCATGAAACGTTTTTCGCG 58.884 45.000 15.89 0.00 43.71 5.87
4321 8966 5.772032 GCATTTTGCATGAAACGTTTTTC 57.228 34.783 15.89 3.82 44.26 2.29
4399 9044 5.622770 ACGCTGGTTTCGATAAAATTTCT 57.377 34.783 0.00 0.00 0.00 2.52
4400 9045 6.513317 CAAACGCTGGTTTCGATAAAATTTC 58.487 36.000 0.00 0.00 44.32 2.17
4408 9053 0.881118 ATGCAAACGCTGGTTTCGAT 59.119 45.000 0.00 0.00 44.32 3.59
4538 9183 0.180171 CCGTAGGCACCAATCATCCA 59.820 55.000 0.00 0.00 46.14 3.41


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

AutoCloner maintained by Alex Coulton.