Multiple sequence alignment - TraesCS1B01G078500

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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 TraesCS1B01G078500 chr1B 100.000 2722 0 0 1 2722 61489400 61486679 0.000000e+00 5027.0
1 TraesCS1B01G078500 chr1B 91.176 68 6 0 548 615 478575307 478575374 2.890000e-15 93.5
2 TraesCS1B01G078500 chr6B 99.569 464 2 0 1128 1591 476706339 476705876 0.000000e+00 846.0
3 TraesCS1B01G078500 chr6B 99.353 464 3 0 1128 1591 476707281 476706818 0.000000e+00 841.0
4 TraesCS1B01G078500 chr6B 99.352 463 3 0 1129 1591 476707751 476707289 0.000000e+00 839.0
5 TraesCS1B01G078500 chr6B 81.495 281 46 4 175 450 513884734 513885013 2.730000e-55 226.0
6 TraesCS1B01G078500 chr6B 82.000 100 16 2 549 647 35631963 35631865 1.740000e-12 84.2
7 TraesCS1B01G078500 chr7B 99.568 463 2 0 1129 1591 732519355 732519817 0.000000e+00 845.0
8 TraesCS1B01G078500 chr7B 95.327 107 3 2 441 545 479326992 479326886 4.660000e-38 169.0
9 TraesCS1B01G078500 chr7B 95.876 97 4 0 449 545 413721540 413721636 1.010000e-34 158.0
10 TraesCS1B01G078500 chr3A 99.568 463 2 0 1129 1591 729535302 729534840 0.000000e+00 845.0
11 TraesCS1B01G078500 chr3A 99.138 464 3 1 1129 1591 743550746 743550283 0.000000e+00 833.0
12 TraesCS1B01G078500 chr3B 99.143 467 4 0 1125 1591 807232847 807232381 0.000000e+00 841.0
13 TraesCS1B01G078500 chr2B 99.355 465 2 1 1128 1592 705606512 705606975 0.000000e+00 841.0
14 TraesCS1B01G078500 chr2B 82.432 296 49 3 157 450 507193604 507193898 3.480000e-64 255.0
15 TraesCS1B01G078500 chr2B 94.595 111 3 3 447 555 715928117 715928008 4.660000e-38 169.0
16 TraesCS1B01G078500 chr2B 93.805 113 4 3 448 559 440223766 440223876 1.680000e-37 167.0
17 TraesCS1B01G078500 chr2B 95.238 105 4 1 442 545 25123222 25123326 6.030000e-37 165.0
18 TraesCS1B01G078500 chr2B 91.176 68 6 0 548 615 765790049 765789982 2.890000e-15 93.5
19 TraesCS1B01G078500 chr4A 99.138 464 4 0 1129 1592 663199346 663199809 0.000000e+00 835.0
20 TraesCS1B01G078500 chr1A 90.986 588 34 10 544 1131 41341077 41340509 0.000000e+00 774.0
21 TraesCS1B01G078500 chr1A 90.986 588 34 10 544 1131 41349454 41348886 0.000000e+00 774.0
22 TraesCS1B01G078500 chr1A 89.890 455 32 6 1 450 41341521 41341076 8.450000e-160 573.0
23 TraesCS1B01G078500 chr1A 89.890 455 32 6 1 450 41349898 41349453 8.450000e-160 573.0
24 TraesCS1B01G078500 chr1A 94.068 354 11 3 2374 2722 41347833 41347485 1.860000e-146 529.0
25 TraesCS1B01G078500 chr1A 92.373 354 11 6 2374 2722 41391662 41392004 8.760000e-135 490.0
26 TraesCS1B01G078500 chr1A 96.313 217 8 0 2110 2326 41348173 41347957 9.270000e-95 357.0
27 TraesCS1B01G078500 chr1A 95.853 217 9 0 2110 2326 41391322 41391538 4.310000e-93 351.0
28 TraesCS1B01G078500 chr1A 92.952 227 9 3 1873 2098 41348437 41348217 9.400000e-85 324.0
29 TraesCS1B01G078500 chr1A 97.701 174 4 0 1592 1765 41340521 41340348 1.580000e-77 300.0
30 TraesCS1B01G078500 chr1A 97.701 174 4 0 1592 1765 41348898 41348725 1.580000e-77 300.0
31 TraesCS1B01G078500 chr1A 92.891 211 7 3 1889 2098 41391075 41391278 1.580000e-77 300.0
32 TraesCS1B01G078500 chrUn 94.068 354 11 3 2374 2722 354330679 354330331 1.860000e-146 529.0
33 TraesCS1B01G078500 chrUn 96.774 217 7 0 2110 2326 354331019 354330803 1.990000e-96 363.0
34 TraesCS1B01G078500 chrUn 93.392 227 9 2 1873 2098 354331284 354331063 5.620000e-87 331.0
35 TraesCS1B01G078500 chrUn 97.701 174 4 0 1592 1765 354331745 354331572 1.580000e-77 300.0
36 TraesCS1B01G078500 chrUn 99.167 120 1 0 1012 1131 354331852 354331733 1.640000e-52 217.0
37 TraesCS1B01G078500 chr1D 95.925 319 11 2 2404 2722 41495502 41495186 1.450000e-142 516.0
38 TraesCS1B01G078500 chr1D 89.737 419 17 18 714 1131 41497164 41496771 1.870000e-141 512.0
39 TraesCS1B01G078500 chr1D 94.574 258 9 4 1592 1847 41496783 41496529 7.060000e-106 394.0
40 TraesCS1B01G078500 chr1D 97.235 217 6 0 2110 2326 41495869 41495653 4.280000e-98 368.0
41 TraesCS1B01G078500 chr1D 84.615 182 22 4 1850 2029 41496223 41496046 2.790000e-40 176.0
42 TraesCS1B01G078500 chr2D 86.513 304 33 5 155 450 3093353 3093656 7.270000e-86 327.0
43 TraesCS1B01G078500 chr2D 85.099 302 41 4 155 453 430384757 430384457 3.410000e-79 305.0
44 TraesCS1B01G078500 chr2D 84.848 297 41 4 157 450 429692062 429692357 2.050000e-76 296.0
45 TraesCS1B01G078500 chr6D 86.242 298 32 5 160 450 28405495 28405790 5.660000e-82 315.0
46 TraesCS1B01G078500 chr2A 84.768 302 39 5 155 450 556108398 556108698 2.050000e-76 296.0
47 TraesCS1B01G078500 chr2A 95.146 103 5 0 444 546 498097585 498097687 2.170000e-36 163.0
48 TraesCS1B01G078500 chr2A 93.578 109 7 0 448 556 676184548 676184656 2.170000e-36 163.0
49 TraesCS1B01G078500 chr4D 97.030 101 3 0 446 546 122272837 122272737 1.300000e-38 171.0
50 TraesCS1B01G078500 chr7A 95.283 106 5 0 441 546 68887679 68887574 4.660000e-38 169.0
51 TraesCS1B01G078500 chr7A 86.792 53 6 1 549 600 66172631 66172579 1.050000e-04 58.4


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 TraesCS1B01G078500 chr1B 61486679 61489400 2721 True 5027.000000 5027 100.000000 1 2722 1 chr1B.!!$R1 2721
1 TraesCS1B01G078500 chr6B 476705876 476707751 1875 True 842.000000 846 99.424667 1128 1591 3 chr6B.!!$R2 463
2 TraesCS1B01G078500 chr1A 41340348 41341521 1173 True 549.000000 774 92.859000 1 1765 3 chr1A.!!$R1 1764
3 TraesCS1B01G078500 chr1A 41347485 41349898 2413 True 476.166667 774 93.651667 1 2722 6 chr1A.!!$R2 2721
4 TraesCS1B01G078500 chr1A 41391075 41392004 929 False 380.333333 490 93.705667 1889 2722 3 chr1A.!!$F1 833
5 TraesCS1B01G078500 chrUn 354330331 354331852 1521 True 348.000000 529 96.220400 1012 2722 5 chrUn.!!$R1 1710
6 TraesCS1B01G078500 chr1D 41495186 41497164 1978 True 393.200000 516 92.417200 714 2722 5 chr1D.!!$R1 2008

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
641 647 0.107703 TGGATTGTGCCAGATCCGAC 60.108 55.0 3.37 0.0 43.86 4.79 F
1131 1137 0.034863 ATGGGCGTAACAACCGGAAT 60.035 50.0 9.46 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 2030 0.106149 CCTATGCACCCGGGTACTTC 59.894 60.0 29.72 16.18 0.00 3.01 R
2670 4316 0.811281 GAAAGGTCAGGCCATTTCGG 59.189 55.0 5.01 0.00 40.61 4.30 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
25 26 2.039298 TGGGGCCGGGGATATTGA 60.039 61.111 2.18 0.00 0.00 2.57
36 37 3.315191 CGGGGATATTGATTGGTTGTGAC 59.685 47.826 0.00 0.00 0.00 3.67
38 39 4.196193 GGGATATTGATTGGTTGTGACGA 58.804 43.478 0.00 0.00 0.00 4.20
118 119 3.044809 GTCGCTGGACGCTTGATTA 57.955 52.632 0.00 0.00 43.23 1.75
137 138 2.107141 GGTCGATCCAAGGGCTCG 59.893 66.667 2.31 2.31 35.97 5.03
138 139 2.722201 GGTCGATCCAAGGGCTCGT 61.722 63.158 8.18 0.00 35.97 4.18
154 155 2.797792 GCTCGTGGATCAGTCAGATGAC 60.798 54.545 4.77 4.77 45.08 3.06
166 167 3.760537 GTCAGATGACGTGTAGAGTTCC 58.239 50.000 0.00 0.00 35.12 3.62
171 172 0.172803 GACGTGTAGAGTTCCGCCAT 59.827 55.000 0.00 0.00 0.00 4.40
173 174 0.527817 CGTGTAGAGTTCCGCCATCC 60.528 60.000 0.00 0.00 0.00 3.51
180 181 4.015406 TTCCGCCATCCGTGCAGT 62.015 61.111 0.00 0.00 34.38 4.40
189 190 0.460284 ATCCGTGCAGTCGTTGGATC 60.460 55.000 0.00 0.00 34.37 3.36
196 197 1.741770 AGTCGTTGGATCGCCTTGC 60.742 57.895 0.00 0.00 34.31 4.01
203 204 1.153086 GGATCGCCTTGCTCCATGT 60.153 57.895 0.00 0.00 0.00 3.21
220 221 4.702020 TGTCGTCACACACACTCG 57.298 55.556 0.00 0.00 0.00 4.18
221 222 1.587876 TGTCGTCACACACACTCGC 60.588 57.895 0.00 0.00 0.00 5.03
222 223 1.587876 GTCGTCACACACACTCGCA 60.588 57.895 0.00 0.00 0.00 5.10
223 224 1.587876 TCGTCACACACACTCGCAC 60.588 57.895 0.00 0.00 0.00 5.34
224 225 1.876263 CGTCACACACACTCGCACA 60.876 57.895 0.00 0.00 0.00 4.57
225 226 1.636340 GTCACACACACTCGCACAC 59.364 57.895 0.00 0.00 0.00 3.82
226 227 1.876263 TCACACACACTCGCACACG 60.876 57.895 0.00 0.00 42.01 4.49
276 277 3.381590 GCCCCTTTACCTTATCTTGCAAG 59.618 47.826 20.81 20.81 0.00 4.01
279 280 5.501156 CCCTTTACCTTATCTTGCAAGAGT 58.499 41.667 31.14 24.71 38.66 3.24
281 282 6.763610 CCCTTTACCTTATCTTGCAAGAGTAG 59.236 42.308 31.14 26.93 38.66 2.57
282 283 6.763610 CCTTTACCTTATCTTGCAAGAGTAGG 59.236 42.308 35.46 35.46 41.60 3.18
393 394 6.872920 ACCTTTGTTGCAAAGAAAATCTACA 58.127 32.000 19.50 0.00 38.69 2.74
404 405 8.050170 GCAAAGAAAATCTACAACAAAAACTCG 58.950 33.333 0.00 0.00 0.00 4.18
453 459 8.856490 CAACCTATGTTGCAAAAATATACTCC 57.144 34.615 0.00 0.00 44.86 3.85
454 460 7.582667 ACCTATGTTGCAAAAATATACTCCC 57.417 36.000 0.00 0.00 0.00 4.30
455 461 7.354312 ACCTATGTTGCAAAAATATACTCCCT 58.646 34.615 0.00 0.00 0.00 4.20
456 462 7.502561 ACCTATGTTGCAAAAATATACTCCCTC 59.497 37.037 0.00 0.00 0.00 4.30
457 463 6.715347 ATGTTGCAAAAATATACTCCCTCC 57.285 37.500 0.00 0.00 0.00 4.30
458 464 5.575157 TGTTGCAAAAATATACTCCCTCCA 58.425 37.500 0.00 0.00 0.00 3.86
459 465 6.194235 TGTTGCAAAAATATACTCCCTCCAT 58.806 36.000 0.00 0.00 0.00 3.41
460 466 6.667414 TGTTGCAAAAATATACTCCCTCCATT 59.333 34.615 0.00 0.00 0.00 3.16
461 467 6.959639 TGCAAAAATATACTCCCTCCATTC 57.040 37.500 0.00 0.00 0.00 2.67
462 468 5.833131 TGCAAAAATATACTCCCTCCATTCC 59.167 40.000 0.00 0.00 0.00 3.01
463 469 5.833131 GCAAAAATATACTCCCTCCATTCCA 59.167 40.000 0.00 0.00 0.00 3.53
464 470 6.323739 GCAAAAATATACTCCCTCCATTCCAA 59.676 38.462 0.00 0.00 0.00 3.53
465 471 7.147742 GCAAAAATATACTCCCTCCATTCCAAA 60.148 37.037 0.00 0.00 0.00 3.28
466 472 8.757877 CAAAAATATACTCCCTCCATTCCAAAA 58.242 33.333 0.00 0.00 0.00 2.44
467 473 9.506042 AAAAATATACTCCCTCCATTCCAAAAT 57.494 29.630 0.00 0.00 0.00 1.82
469 475 9.813826 AAATATACTCCCTCCATTCCAAAATAG 57.186 33.333 0.00 0.00 0.00 1.73
470 476 8.757307 ATATACTCCCTCCATTCCAAAATAGA 57.243 34.615 0.00 0.00 0.00 1.98
471 477 7.654287 ATACTCCCTCCATTCCAAAATAGAT 57.346 36.000 0.00 0.00 0.00 1.98
472 478 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
473 479 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
474 480 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
475 481 5.433051 TCCCTCCATTCCAAAATAGATGACT 59.567 40.000 0.00 0.00 0.00 3.41
476 482 5.767168 CCCTCCATTCCAAAATAGATGACTC 59.233 44.000 0.00 0.00 0.00 3.36
477 483 6.359804 CCTCCATTCCAAAATAGATGACTCA 58.640 40.000 0.00 0.00 0.00 3.41
478 484 6.830324 CCTCCATTCCAAAATAGATGACTCAA 59.170 38.462 0.00 0.00 0.00 3.02
479 485 7.201767 CCTCCATTCCAAAATAGATGACTCAAC 60.202 40.741 0.00 0.00 0.00 3.18
480 486 7.405292 TCCATTCCAAAATAGATGACTCAACT 58.595 34.615 0.00 0.00 0.00 3.16
481 487 7.890127 TCCATTCCAAAATAGATGACTCAACTT 59.110 33.333 0.00 0.00 0.00 2.66
482 488 8.526147 CCATTCCAAAATAGATGACTCAACTTT 58.474 33.333 0.00 0.00 0.00 2.66
483 489 9.350357 CATTCCAAAATAGATGACTCAACTTTG 57.650 33.333 0.00 0.00 0.00 2.77
484 490 8.463930 TTCCAAAATAGATGACTCAACTTTGT 57.536 30.769 0.00 0.00 0.00 2.83
485 491 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
486 492 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
487 493 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
537 543 9.713684 AAATTAGGTCATCTATTTTGGAATGGA 57.286 29.630 0.00 0.00 37.20 3.41
538 544 8.930846 ATTAGGTCATCTATTTTGGAATGGAG 57.069 34.615 0.00 0.00 36.39 3.86
539 545 5.699143 AGGTCATCTATTTTGGAATGGAGG 58.301 41.667 0.00 0.00 36.39 4.30
540 546 4.829492 GGTCATCTATTTTGGAATGGAGGG 59.171 45.833 0.00 0.00 36.39 4.30
541 547 5.399038 GGTCATCTATTTTGGAATGGAGGGA 60.399 44.000 0.00 0.00 36.39 4.20
542 548 5.767168 GTCATCTATTTTGGAATGGAGGGAG 59.233 44.000 0.00 0.00 36.39 4.30
596 602 6.588373 TGTTTCTTTAACAAGACCTTTGTTGC 59.412 34.615 13.79 0.00 43.58 4.17
606 612 3.321111 AGACCTTTGTTGCGAAGTAGAGA 59.679 43.478 0.00 0.00 0.00 3.10
607 613 4.056050 GACCTTTGTTGCGAAGTAGAGAA 58.944 43.478 0.00 0.00 0.00 2.87
639 645 4.961637 TGGATTGTGCCAGATCCG 57.038 55.556 3.37 0.00 43.86 4.18
641 647 0.107703 TGGATTGTGCCAGATCCGAC 60.108 55.000 3.37 0.00 43.86 4.79
645 651 2.202756 GTGCCAGATCCGACGACC 60.203 66.667 0.00 0.00 0.00 4.79
647 653 1.077285 TGCCAGATCCGACGACCTA 60.077 57.895 0.00 0.00 0.00 3.08
648 654 0.467474 TGCCAGATCCGACGACCTAT 60.467 55.000 0.00 0.00 0.00 2.57
657 663 1.729470 CGACGACCTATGAGGCAGCT 61.729 60.000 0.00 0.00 39.63 4.24
666 672 5.372373 ACCTATGAGGCAGCTAATCTTTTC 58.628 41.667 0.00 0.00 39.63 2.29
671 677 6.017400 TGAGGCAGCTAATCTTTTCAAAAG 57.983 37.500 3.20 3.20 0.00 2.27
672 678 5.536161 TGAGGCAGCTAATCTTTTCAAAAGT 59.464 36.000 9.74 0.00 0.00 2.66
678 684 8.820933 GCAGCTAATCTTTTCAAAAGTTCTTTT 58.179 29.630 9.74 4.91 0.00 2.27
699 705 4.497473 TTTAAAGATCTGTTGGCCAACG 57.503 40.909 36.62 30.41 43.94 4.10
700 706 2.270352 AAAGATCTGTTGGCCAACGA 57.730 45.000 36.62 33.56 43.94 3.85
701 707 2.270352 AAGATCTGTTGGCCAACGAA 57.730 45.000 36.62 28.70 43.94 3.85
708 714 0.179163 GTTGGCCAACGAATAGCAGC 60.179 55.000 31.73 6.25 0.00 5.25
725 731 9.844257 GAATAGCAGCCTCCATATATTTATCTT 57.156 33.333 0.00 0.00 0.00 2.40
772 778 4.715523 CCACGCGGGGGACATGTT 62.716 66.667 22.99 0.00 0.00 2.71
774 780 4.715523 ACGCGGGGGACATGTTGG 62.716 66.667 12.47 0.00 0.00 3.77
806 812 1.200519 CCGATGGGAAAGGGTGAGTA 58.799 55.000 0.00 0.00 34.06 2.59
815 821 4.345547 GGGAAAGGGTGAGTAGAAGGATAG 59.654 50.000 0.00 0.00 0.00 2.08
860 866 4.892345 AGAGATGGAGAATCATGAGACGAA 59.108 41.667 0.09 0.00 37.81 3.85
878 884 1.251527 AAGGGAGACGCACGATCTGT 61.252 55.000 0.00 0.00 0.00 3.41
912 918 4.743975 TGCCGTCCGCGTATGCAA 62.744 61.111 4.92 0.00 42.97 4.08
954 960 3.187112 TCCCCCTAGTAGGTCCAAAAAG 58.813 50.000 15.26 0.00 31.93 2.27
1131 1137 0.034863 ATGGGCGTAACAACCGGAAT 60.035 50.000 9.46 0.00 0.00 3.01
1132 1138 0.956410 TGGGCGTAACAACCGGAATG 60.956 55.000 9.46 9.74 0.00 2.67
1184 1190 5.363868 CCTCACTATCCTAACACTCCAATGA 59.636 44.000 0.00 0.00 0.00 2.57
1433 1910 9.533831 AAATCTGTAAGTTTTATCCCACATTCT 57.466 29.630 0.00 0.00 34.30 2.40
1435 1912 9.614792 ATCTGTAAGTTTTATCCCACATTCTAC 57.385 33.333 0.00 0.00 33.76 2.59
1436 1913 8.598916 TCTGTAAGTTTTATCCCACATTCTACA 58.401 33.333 0.00 0.00 33.76 2.74
1437 1914 9.396022 CTGTAAGTTTTATCCCACATTCTACAT 57.604 33.333 0.00 0.00 0.00 2.29
1444 1921 8.677148 TTTATCCCACATTCTACATAGAAAGC 57.323 34.615 5.48 0.00 44.63 3.51
1445 1922 5.957771 TCCCACATTCTACATAGAAAGCT 57.042 39.130 5.48 0.00 44.63 3.74
1446 1923 6.313519 TCCCACATTCTACATAGAAAGCTT 57.686 37.500 5.48 0.00 44.63 3.74
1447 1924 6.721318 TCCCACATTCTACATAGAAAGCTTT 58.279 36.000 12.53 12.53 44.63 3.51
1448 1925 6.599244 TCCCACATTCTACATAGAAAGCTTTG 59.401 38.462 18.30 5.25 44.63 2.77
1449 1926 6.375455 CCCACATTCTACATAGAAAGCTTTGT 59.625 38.462 18.30 15.90 44.63 2.83
1450 1927 7.094205 CCCACATTCTACATAGAAAGCTTTGTT 60.094 37.037 18.30 7.23 44.63 2.83
1451 1928 7.752239 CCACATTCTACATAGAAAGCTTTGTTG 59.248 37.037 18.30 15.03 44.63 3.33
1452 1929 8.292448 CACATTCTACATAGAAAGCTTTGTTGT 58.708 33.333 18.30 19.36 44.63 3.32
1453 1930 8.292448 ACATTCTACATAGAAAGCTTTGTTGTG 58.708 33.333 18.30 16.43 44.63 3.33
1454 1931 6.241207 TCTACATAGAAAGCTTTGTTGTGC 57.759 37.500 18.30 0.25 37.47 4.57
1455 1932 5.997746 TCTACATAGAAAGCTTTGTTGTGCT 59.002 36.000 18.30 8.71 41.82 4.40
1456 1933 4.863491 ACATAGAAAGCTTTGTTGTGCTG 58.137 39.130 18.30 8.38 39.71 4.41
1457 1934 2.214387 AGAAAGCTTTGTTGTGCTGC 57.786 45.000 18.30 0.00 39.71 5.25
1458 1935 1.477700 AGAAAGCTTTGTTGTGCTGCA 59.522 42.857 18.30 0.00 39.71 4.41
1459 1936 2.094078 AGAAAGCTTTGTTGTGCTGCAA 60.094 40.909 18.30 0.00 39.71 4.08
1460 1937 2.383368 AAGCTTTGTTGTGCTGCAAA 57.617 40.000 2.77 0.00 39.71 3.68
1464 1941 3.644805 CTTTGTTGTGCTGCAAAGTTG 57.355 42.857 2.77 0.00 43.69 3.16
1465 1942 3.252400 CTTTGTTGTGCTGCAAAGTTGA 58.748 40.909 2.77 0.00 43.69 3.18
1466 1943 3.309961 TTGTTGTGCTGCAAAGTTGAA 57.690 38.095 2.77 0.00 39.03 2.69
1467 1944 2.878580 TGTTGTGCTGCAAAGTTGAAG 58.121 42.857 2.77 0.00 39.03 3.02
1468 1945 2.230992 TGTTGTGCTGCAAAGTTGAAGT 59.769 40.909 2.77 0.00 39.03 3.01
1469 1946 3.441922 TGTTGTGCTGCAAAGTTGAAGTA 59.558 39.130 2.77 0.00 39.03 2.24
1470 1947 3.691049 TGTGCTGCAAAGTTGAAGTAC 57.309 42.857 12.06 12.06 46.14 2.73
1471 1948 3.691049 GTGCTGCAAAGTTGAAGTACA 57.309 42.857 13.61 0.00 45.51 2.90
1472 1949 4.027572 GTGCTGCAAAGTTGAAGTACAA 57.972 40.909 13.61 0.00 45.51 2.41
1473 1950 4.420168 GTGCTGCAAAGTTGAAGTACAAA 58.580 39.130 13.61 0.00 45.51 2.83
1474 1951 4.862018 GTGCTGCAAAGTTGAAGTACAAAA 59.138 37.500 13.61 0.00 45.51 2.44
1475 1952 5.519927 GTGCTGCAAAGTTGAAGTACAAAAT 59.480 36.000 13.61 0.00 45.51 1.82
1476 1953 6.695278 GTGCTGCAAAGTTGAAGTACAAAATA 59.305 34.615 13.61 0.00 45.51 1.40
1477 1954 6.695278 TGCTGCAAAGTTGAAGTACAAAATAC 59.305 34.615 0.00 0.00 40.36 1.89
1478 1955 6.695278 GCTGCAAAGTTGAAGTACAAAATACA 59.305 34.615 1.02 0.00 40.36 2.29
1479 1956 7.382218 GCTGCAAAGTTGAAGTACAAAATACAT 59.618 33.333 1.02 0.00 40.36 2.29
1480 1957 8.572828 TGCAAAGTTGAAGTACAAAATACATG 57.427 30.769 0.00 0.00 40.36 3.21
1481 1958 8.194104 TGCAAAGTTGAAGTACAAAATACATGT 58.806 29.630 2.69 2.69 40.36 3.21
1482 1959 9.030301 GCAAAGTTGAAGTACAAAATACATGTT 57.970 29.630 2.30 0.00 40.36 2.71
1526 2003 7.725610 AAGAGAAAATTATTTGCACGAATCG 57.274 32.000 0.00 0.00 0.00 3.34
1527 2004 6.842163 AGAGAAAATTATTTGCACGAATCGT 58.158 32.000 0.96 0.96 42.36 3.73
1537 2014 3.832704 ACGAATCGTGATGCAGGAA 57.167 47.368 7.77 0.00 39.18 3.36
1538 2015 2.315925 ACGAATCGTGATGCAGGAAT 57.684 45.000 7.77 0.00 39.18 3.01
1539 2016 1.935873 ACGAATCGTGATGCAGGAATG 59.064 47.619 7.77 0.00 39.18 2.67
1540 2017 2.204237 CGAATCGTGATGCAGGAATGA 58.796 47.619 0.00 0.00 32.06 2.57
1541 2018 2.220363 CGAATCGTGATGCAGGAATGAG 59.780 50.000 0.00 0.00 32.06 2.90
1542 2019 2.996249 ATCGTGATGCAGGAATGAGT 57.004 45.000 0.00 0.00 32.06 3.41
1543 2020 2.014335 TCGTGATGCAGGAATGAGTG 57.986 50.000 0.00 0.00 0.00 3.51
1544 2021 1.012086 CGTGATGCAGGAATGAGTGG 58.988 55.000 0.00 0.00 0.00 4.00
1545 2022 1.676916 CGTGATGCAGGAATGAGTGGT 60.677 52.381 0.00 0.00 0.00 4.16
1546 2023 2.440409 GTGATGCAGGAATGAGTGGTT 58.560 47.619 0.00 0.00 0.00 3.67
1547 2024 2.163010 GTGATGCAGGAATGAGTGGTTG 59.837 50.000 0.00 0.00 0.00 3.77
1548 2025 1.747355 GATGCAGGAATGAGTGGTTGG 59.253 52.381 0.00 0.00 0.00 3.77
1549 2026 0.770499 TGCAGGAATGAGTGGTTGGA 59.230 50.000 0.00 0.00 0.00 3.53
1550 2027 1.355381 TGCAGGAATGAGTGGTTGGAT 59.645 47.619 0.00 0.00 0.00 3.41
1551 2028 2.575735 TGCAGGAATGAGTGGTTGGATA 59.424 45.455 0.00 0.00 0.00 2.59
1552 2029 3.010027 TGCAGGAATGAGTGGTTGGATAA 59.990 43.478 0.00 0.00 0.00 1.75
1553 2030 3.629398 GCAGGAATGAGTGGTTGGATAAG 59.371 47.826 0.00 0.00 0.00 1.73
1554 2031 4.626287 GCAGGAATGAGTGGTTGGATAAGA 60.626 45.833 0.00 0.00 0.00 2.10
1555 2032 5.500234 CAGGAATGAGTGGTTGGATAAGAA 58.500 41.667 0.00 0.00 0.00 2.52
1556 2033 5.587844 CAGGAATGAGTGGTTGGATAAGAAG 59.412 44.000 0.00 0.00 0.00 2.85
1557 2034 5.251700 AGGAATGAGTGGTTGGATAAGAAGT 59.748 40.000 0.00 0.00 0.00 3.01
1558 2035 6.443849 AGGAATGAGTGGTTGGATAAGAAGTA 59.556 38.462 0.00 0.00 0.00 2.24
1559 2036 6.539103 GGAATGAGTGGTTGGATAAGAAGTAC 59.461 42.308 0.00 0.00 0.00 2.73
1560 2037 5.416271 TGAGTGGTTGGATAAGAAGTACC 57.584 43.478 0.00 0.00 0.00 3.34
1561 2038 4.224370 TGAGTGGTTGGATAAGAAGTACCC 59.776 45.833 0.00 0.00 0.00 3.69
1562 2039 3.197116 AGTGGTTGGATAAGAAGTACCCG 59.803 47.826 0.00 0.00 0.00 5.28
1563 2040 2.502538 TGGTTGGATAAGAAGTACCCGG 59.497 50.000 0.00 0.00 0.00 5.73
1564 2041 2.158856 GGTTGGATAAGAAGTACCCGGG 60.159 54.545 22.25 22.25 0.00 5.73
1565 2042 2.502947 GTTGGATAAGAAGTACCCGGGT 59.497 50.000 32.66 32.66 0.00 5.28
1566 2043 2.112998 TGGATAAGAAGTACCCGGGTG 58.887 52.381 36.97 6.22 0.00 4.61
1567 2044 1.202615 GGATAAGAAGTACCCGGGTGC 60.203 57.143 36.97 34.59 0.00 5.01
1568 2045 1.483415 GATAAGAAGTACCCGGGTGCA 59.517 52.381 38.49 21.38 33.14 4.57
1569 2046 1.575419 TAAGAAGTACCCGGGTGCAT 58.425 50.000 38.49 30.24 33.14 3.96
1570 2047 1.575419 AAGAAGTACCCGGGTGCATA 58.425 50.000 38.49 17.40 33.14 3.14
1571 2048 1.120530 AGAAGTACCCGGGTGCATAG 58.879 55.000 38.49 7.31 33.14 2.23
1572 2049 0.106149 GAAGTACCCGGGTGCATAGG 59.894 60.000 38.49 6.51 33.14 2.57
1573 2050 1.979619 AAGTACCCGGGTGCATAGGC 61.980 60.000 38.49 18.29 41.68 3.93
1574 2051 2.041301 TACCCGGGTGCATAGGCT 60.041 61.111 36.97 8.21 41.91 4.58
1575 2052 2.138179 TACCCGGGTGCATAGGCTC 61.138 63.158 36.97 0.00 41.91 4.70
1576 2053 2.599139 TACCCGGGTGCATAGGCTCT 62.599 60.000 36.97 6.74 41.91 4.09
1577 2054 1.837051 CCCGGGTGCATAGGCTCTA 60.837 63.158 14.18 0.00 41.91 2.43
1578 2055 1.407656 CCCGGGTGCATAGGCTCTAA 61.408 60.000 14.18 0.00 41.91 2.10
1579 2056 0.468226 CCGGGTGCATAGGCTCTAAA 59.532 55.000 0.00 0.00 41.91 1.85
1580 2057 1.134220 CCGGGTGCATAGGCTCTAAAA 60.134 52.381 0.00 0.00 41.91 1.52
1581 2058 1.940613 CGGGTGCATAGGCTCTAAAAC 59.059 52.381 0.00 0.00 41.91 2.43
1582 2059 2.679639 CGGGTGCATAGGCTCTAAAACA 60.680 50.000 0.00 0.00 41.91 2.83
1583 2060 3.555966 GGGTGCATAGGCTCTAAAACAT 58.444 45.455 0.00 0.00 41.91 2.71
1584 2061 3.316308 GGGTGCATAGGCTCTAAAACATG 59.684 47.826 0.00 0.00 41.91 3.21
1585 2062 3.947834 GGTGCATAGGCTCTAAAACATGT 59.052 43.478 0.00 0.00 41.91 3.21
1586 2063 4.399303 GGTGCATAGGCTCTAAAACATGTT 59.601 41.667 4.92 4.92 41.91 2.71
1587 2064 5.105756 GGTGCATAGGCTCTAAAACATGTTT 60.106 40.000 18.13 18.13 41.91 2.83
1588 2065 6.389906 GTGCATAGGCTCTAAAACATGTTTT 58.610 36.000 32.63 32.63 42.11 2.43
1589 2066 6.528072 GTGCATAGGCTCTAAAACATGTTTTC 59.472 38.462 33.71 21.47 40.89 2.29
1590 2067 5.739161 GCATAGGCTCTAAAACATGTTTTCG 59.261 40.000 33.71 28.00 39.12 3.46
1591 2068 4.766404 AGGCTCTAAAACATGTTTTCGG 57.234 40.909 33.71 26.53 41.39 4.30
1592 2069 4.142038 AGGCTCTAAAACATGTTTTCGGT 58.858 39.130 33.71 17.24 41.39 4.69
1593 2070 5.310451 AGGCTCTAAAACATGTTTTCGGTA 58.690 37.500 33.71 18.91 41.39 4.02
1594 2071 5.766174 AGGCTCTAAAACATGTTTTCGGTAA 59.234 36.000 33.71 18.58 41.39 2.85
1595 2072 5.854866 GGCTCTAAAACATGTTTTCGGTAAC 59.145 40.000 33.71 20.67 41.39 2.50
1596 2073 6.432107 GCTCTAAAACATGTTTTCGGTAACA 58.568 36.000 33.71 17.32 41.39 2.41
1597 2074 6.913673 GCTCTAAAACATGTTTTCGGTAACAA 59.086 34.615 33.71 16.69 41.39 2.83
1598 2075 7.096763 GCTCTAAAACATGTTTTCGGTAACAAC 60.097 37.037 33.71 14.72 41.39 3.32
1599 2076 7.194962 TCTAAAACATGTTTTCGGTAACAACC 58.805 34.615 33.71 0.00 41.39 3.77
1751 2228 6.650807 CCTCTGCTTTTTGACTAACTGATACA 59.349 38.462 0.00 0.00 0.00 2.29
1769 2246 2.888594 ACATAATCTCCCAACGACACG 58.111 47.619 0.00 0.00 0.00 4.49
1770 2247 2.232941 ACATAATCTCCCAACGACACGT 59.767 45.455 0.00 0.00 43.97 4.49
1785 2262 4.021544 ACGACACGTAATTTAACCCCTGTA 60.022 41.667 0.00 0.00 38.73 2.74
1844 2386 3.438087 CCACTCCAGATTGATGTTGTGAC 59.562 47.826 0.00 0.00 0.00 3.67
1856 2671 0.463116 GTTGTGACCAACCCGTCTGT 60.463 55.000 0.00 0.00 44.25 3.41
1866 2681 2.878406 CAACCCGTCTGTCTGTTTCAAT 59.122 45.455 0.00 0.00 0.00 2.57
1867 2682 3.208747 ACCCGTCTGTCTGTTTCAATT 57.791 42.857 0.00 0.00 0.00 2.32
1868 2683 3.551846 ACCCGTCTGTCTGTTTCAATTT 58.448 40.909 0.00 0.00 0.00 1.82
1902 2717 9.998106 AAATATATCGTAGTATTTTCAGCAGGT 57.002 29.630 0.00 0.00 28.78 4.00
1907 2722 4.436050 CGTAGTATTTTCAGCAGGTGCAAG 60.436 45.833 4.48 0.00 45.16 4.01
1908 2723 2.821969 AGTATTTTCAGCAGGTGCAAGG 59.178 45.455 4.48 0.00 45.16 3.61
1909 2724 0.319405 ATTTTCAGCAGGTGCAAGGC 59.681 50.000 4.48 0.00 45.16 4.35
1912 2727 0.828762 TTCAGCAGGTGCAAGGCAAT 60.829 50.000 4.48 0.00 41.47 3.56
1913 2728 1.214589 CAGCAGGTGCAAGGCAATC 59.785 57.895 4.48 0.00 41.47 2.67
1958 2775 7.781056 TCATCCTATTTTCCCTATTTGTTTGC 58.219 34.615 0.00 0.00 0.00 3.68
1967 2784 9.579932 TTTTCCCTATTTGTTTGCCATTATTTT 57.420 25.926 0.00 0.00 0.00 1.82
1998 2815 6.314648 CGTTCAATCATTCTCTCCTTCAATGA 59.685 38.462 0.00 0.00 40.07 2.57
2096 2913 9.854668 ACTAGACAACATATGAGATGTACTACT 57.145 33.333 10.38 7.28 0.00 2.57
2099 2916 9.854668 AGACAACATATGAGATGTACTACTACT 57.145 33.333 10.38 1.17 0.00 2.57
2281 3221 5.964958 CTTCAGGAAGTTTTCTAATGCCA 57.035 39.130 0.83 0.00 33.87 4.92
2306 3246 3.009805 ACATTGGTAACCCTTGTCCCTAC 59.990 47.826 0.00 0.00 0.00 3.18
2341 3321 7.634671 TCATTTATACTAGTTGGACGAGTCA 57.365 36.000 0.00 0.00 35.66 3.41
2381 3511 9.683069 AGCAATTTTCAATACACTTTGTTAGAG 57.317 29.630 0.00 0.00 0.00 2.43
2382 3512 9.463443 GCAATTTTCAATACACTTTGTTAGAGT 57.537 29.630 0.00 0.00 0.00 3.24
2433 3652 2.213499 CCGCATGTCTCTAAACCCATC 58.787 52.381 0.00 0.00 0.00 3.51
2550 4084 6.772716 TGAGCCCATAGTTTGAGGAATATTTC 59.227 38.462 0.00 0.00 0.00 2.17
2621 4267 7.943413 TGTACATACTAGCAACAAAACGTAA 57.057 32.000 0.00 0.00 0.00 3.18
2654 4300 3.325135 ACCTAGGCAGCCTGATAATACAC 59.675 47.826 25.59 0.00 34.61 2.90
2670 4316 0.038159 ACACACTCTTCGCCTAGTGC 60.038 55.000 9.78 0.00 45.65 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.622942 CACAACCAATCAATATCCCCGG 59.377 50.000 0.00 0.00 0.00 5.73
25 26 1.282248 CGAGCGTCGTCACAACCAAT 61.282 55.000 0.00 0.00 34.72 3.16
68 69 4.736896 ACGGAGTCGCCCTTTCGC 62.737 66.667 0.00 0.00 29.74 4.70
118 119 2.683933 AGCCCTTGGATCGACCGT 60.684 61.111 0.00 0.00 42.61 4.83
137 138 2.094494 ACACGTCATCTGACTGATCCAC 60.094 50.000 8.57 0.00 42.66 4.02
138 139 2.171003 ACACGTCATCTGACTGATCCA 58.829 47.619 8.57 0.00 42.66 3.41
154 155 0.527817 GGATGGCGGAACTCTACACG 60.528 60.000 0.00 0.00 0.00 4.49
171 172 1.080093 GATCCAACGACTGCACGGA 60.080 57.895 1.59 0.00 37.61 4.69
173 174 3.071459 GCGATCCAACGACTGCACG 62.071 63.158 0.00 0.00 39.31 5.34
180 181 1.447838 GAGCAAGGCGATCCAACGA 60.448 57.895 0.00 0.00 35.09 3.85
182 183 0.749454 ATGGAGCAAGGCGATCCAAC 60.749 55.000 2.82 0.00 45.82 3.77
189 190 2.743752 CGACACATGGAGCAAGGCG 61.744 63.158 0.00 0.00 0.00 5.52
203 204 1.587876 GCGAGTGTGTGTGACGACA 60.588 57.895 0.00 0.00 0.00 4.35
220 221 0.445043 GGAAATAACGGACCGTGTGC 59.555 55.000 22.53 7.69 39.99 4.57
221 222 1.081094 GGGAAATAACGGACCGTGTG 58.919 55.000 22.53 0.00 39.99 3.82
222 223 0.978907 AGGGAAATAACGGACCGTGT 59.021 50.000 22.53 13.15 39.99 4.49
223 224 1.735571 CAAGGGAAATAACGGACCGTG 59.264 52.381 22.53 0.00 39.99 4.94
224 225 1.947212 GCAAGGGAAATAACGGACCGT 60.947 52.381 15.37 15.37 43.97 4.83
225 226 0.730840 GCAAGGGAAATAACGGACCG 59.269 55.000 13.61 13.61 0.00 4.79
226 227 1.100510 GGCAAGGGAAATAACGGACC 58.899 55.000 0.00 0.00 0.00 4.46
276 277 1.244816 GGTTTGCAACACCCCTACTC 58.755 55.000 15.77 0.00 0.00 2.59
279 280 1.626686 CATGGTTTGCAACACCCCTA 58.373 50.000 20.83 8.97 32.71 3.53
281 282 1.370810 CCATGGTTTGCAACACCCC 59.629 57.895 20.83 10.96 32.71 4.95
282 283 1.301637 GCCATGGTTTGCAACACCC 60.302 57.895 14.67 12.97 32.71 4.61
302 303 1.908065 AAGTTGCAGTTGTCGTTTGC 58.092 45.000 0.00 0.00 38.30 3.68
311 312 5.343249 CAAAAGCTTGTCTAAGTTGCAGTT 58.657 37.500 0.00 0.00 36.27 3.16
373 374 8.539770 TTTGTTGTAGATTTTCTTTGCAACAA 57.460 26.923 19.09 19.09 42.76 2.83
448 454 6.619437 TCATCTATTTTGGAATGGAGGGAGTA 59.381 38.462 0.00 0.00 36.39 2.59
449 455 5.433051 TCATCTATTTTGGAATGGAGGGAGT 59.567 40.000 0.00 0.00 36.39 3.85
450 456 5.767168 GTCATCTATTTTGGAATGGAGGGAG 59.233 44.000 0.00 0.00 36.39 4.30
451 457 5.433051 AGTCATCTATTTTGGAATGGAGGGA 59.567 40.000 0.00 0.00 36.39 4.20
452 458 5.699143 AGTCATCTATTTTGGAATGGAGGG 58.301 41.667 0.00 0.00 36.39 4.30
453 459 6.359804 TGAGTCATCTATTTTGGAATGGAGG 58.640 40.000 0.00 0.00 36.39 4.30
454 460 7.555554 AGTTGAGTCATCTATTTTGGAATGGAG 59.444 37.037 1.70 0.00 36.39 3.86
455 461 7.405292 AGTTGAGTCATCTATTTTGGAATGGA 58.595 34.615 1.70 0.00 37.20 3.41
456 462 7.636150 AGTTGAGTCATCTATTTTGGAATGG 57.364 36.000 1.70 0.00 0.00 3.16
457 463 9.350357 CAAAGTTGAGTCATCTATTTTGGAATG 57.650 33.333 4.14 0.00 35.65 2.67
458 464 9.082313 ACAAAGTTGAGTCATCTATTTTGGAAT 57.918 29.630 14.35 0.00 40.00 3.01
459 465 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
460 466 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
461 467 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
511 517 9.713684 TCCATTCCAAAATAGATGACCTAATTT 57.286 29.630 0.00 0.00 32.23 1.82
512 518 9.359653 CTCCATTCCAAAATAGATGACCTAATT 57.640 33.333 0.00 0.00 0.00 1.40
513 519 7.946776 CCTCCATTCCAAAATAGATGACCTAAT 59.053 37.037 0.00 0.00 0.00 1.73
514 520 7.290061 CCTCCATTCCAAAATAGATGACCTAA 58.710 38.462 0.00 0.00 0.00 2.69
515 521 6.183361 CCCTCCATTCCAAAATAGATGACCTA 60.183 42.308 0.00 0.00 0.00 3.08
516 522 5.399497 CCCTCCATTCCAAAATAGATGACCT 60.399 44.000 0.00 0.00 0.00 3.85
517 523 4.829492 CCCTCCATTCCAAAATAGATGACC 59.171 45.833 0.00 0.00 0.00 4.02
518 524 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
519 525 5.433051 ACTCCCTCCATTCCAAAATAGATGA 59.567 40.000 0.00 0.00 0.00 2.92
520 526 5.699143 ACTCCCTCCATTCCAAAATAGATG 58.301 41.667 0.00 0.00 0.00 2.90
521 527 7.654287 ATACTCCCTCCATTCCAAAATAGAT 57.346 36.000 0.00 0.00 0.00 1.98
522 528 7.465900 AATACTCCCTCCATTCCAAAATAGA 57.534 36.000 0.00 0.00 0.00 1.98
523 529 9.236006 CATAATACTCCCTCCATTCCAAAATAG 57.764 37.037 0.00 0.00 0.00 1.73
524 530 7.669722 GCATAATACTCCCTCCATTCCAAAATA 59.330 37.037 0.00 0.00 0.00 1.40
525 531 6.494835 GCATAATACTCCCTCCATTCCAAAAT 59.505 38.462 0.00 0.00 0.00 1.82
526 532 5.833131 GCATAATACTCCCTCCATTCCAAAA 59.167 40.000 0.00 0.00 0.00 2.44
527 533 5.103728 TGCATAATACTCCCTCCATTCCAAA 60.104 40.000 0.00 0.00 0.00 3.28
528 534 4.415179 TGCATAATACTCCCTCCATTCCAA 59.585 41.667 0.00 0.00 0.00 3.53
529 535 3.980022 TGCATAATACTCCCTCCATTCCA 59.020 43.478 0.00 0.00 0.00 3.53
530 536 4.640771 TGCATAATACTCCCTCCATTCC 57.359 45.455 0.00 0.00 0.00 3.01
531 537 5.376625 TGTTGCATAATACTCCCTCCATTC 58.623 41.667 0.00 0.00 0.00 2.67
532 538 5.387113 TGTTGCATAATACTCCCTCCATT 57.613 39.130 0.00 0.00 0.00 3.16
533 539 5.589367 ATGTTGCATAATACTCCCTCCAT 57.411 39.130 0.00 0.00 0.00 3.41
534 540 6.296026 GTTATGTTGCATAATACTCCCTCCA 58.704 40.000 5.08 0.00 0.00 3.86
535 541 5.705905 GGTTATGTTGCATAATACTCCCTCC 59.294 44.000 5.08 0.00 0.00 4.30
536 542 6.534634 AGGTTATGTTGCATAATACTCCCTC 58.465 40.000 5.08 0.00 0.00 4.30
537 543 6.515512 AGGTTATGTTGCATAATACTCCCT 57.484 37.500 5.08 4.24 0.00 4.20
538 544 7.068226 ACAAAGGTTATGTTGCATAATACTCCC 59.932 37.037 5.08 2.35 0.00 4.30
539 545 7.996385 ACAAAGGTTATGTTGCATAATACTCC 58.004 34.615 5.08 2.64 0.00 3.85
578 584 4.396790 ACTTCGCAACAAAGGTCTTGTTAA 59.603 37.500 2.75 0.00 40.30 2.01
579 585 3.942748 ACTTCGCAACAAAGGTCTTGTTA 59.057 39.130 2.75 0.00 40.30 2.41
585 591 3.650139 TCTCTACTTCGCAACAAAGGTC 58.350 45.455 0.00 0.00 0.00 3.85
592 598 5.847670 AATGTCTTTCTCTACTTCGCAAC 57.152 39.130 0.00 0.00 0.00 4.17
595 601 5.005875 GGCTTAATGTCTTTCTCTACTTCGC 59.994 44.000 0.00 0.00 0.00 4.70
596 602 6.035112 GTGGCTTAATGTCTTTCTCTACTTCG 59.965 42.308 0.00 0.00 0.00 3.79
606 612 5.047802 CACAATCCAGTGGCTTAATGTCTTT 60.048 40.000 3.51 0.00 35.88 2.52
607 613 4.460382 CACAATCCAGTGGCTTAATGTCTT 59.540 41.667 3.51 0.00 35.88 3.01
634 640 0.241481 GCCTCATAGGTCGTCGGATC 59.759 60.000 0.00 0.00 37.80 3.36
639 645 1.319541 TAGCTGCCTCATAGGTCGTC 58.680 55.000 0.00 0.00 37.80 4.20
641 647 2.560542 AGATTAGCTGCCTCATAGGTCG 59.439 50.000 0.00 0.00 37.80 4.79
645 651 6.932356 TTGAAAAGATTAGCTGCCTCATAG 57.068 37.500 0.00 0.00 0.00 2.23
647 653 6.210185 ACTTTTGAAAAGATTAGCTGCCTCAT 59.790 34.615 23.14 0.00 0.00 2.90
648 654 5.536161 ACTTTTGAAAAGATTAGCTGCCTCA 59.464 36.000 23.14 0.00 0.00 3.86
678 684 4.138290 TCGTTGGCCAACAGATCTTTAAA 58.862 39.130 39.91 16.47 41.20 1.52
680 686 3.410631 TCGTTGGCCAACAGATCTTTA 57.589 42.857 39.91 17.66 41.20 1.85
683 689 2.496899 ATTCGTTGGCCAACAGATCT 57.503 45.000 39.91 25.29 41.20 2.75
685 691 2.017049 GCTATTCGTTGGCCAACAGAT 58.983 47.619 39.91 32.91 41.20 2.90
686 692 1.271108 TGCTATTCGTTGGCCAACAGA 60.271 47.619 39.91 33.38 41.20 3.41
687 693 1.131126 CTGCTATTCGTTGGCCAACAG 59.869 52.381 39.91 31.18 41.20 3.16
688 694 1.164411 CTGCTATTCGTTGGCCAACA 58.836 50.000 39.91 26.63 41.20 3.33
689 695 0.179163 GCTGCTATTCGTTGGCCAAC 60.179 55.000 34.48 34.48 37.92 3.77
690 696 1.312371 GGCTGCTATTCGTTGGCCAA 61.312 55.000 16.05 16.05 39.38 4.52
691 697 1.748879 GGCTGCTATTCGTTGGCCA 60.749 57.895 0.00 0.00 39.38 5.36
692 698 1.440145 GAGGCTGCTATTCGTTGGCC 61.440 60.000 0.00 0.00 39.82 5.36
693 699 1.440145 GGAGGCTGCTATTCGTTGGC 61.440 60.000 0.00 0.00 0.00 4.52
694 700 0.107703 TGGAGGCTGCTATTCGTTGG 60.108 55.000 7.74 0.00 0.00 3.77
695 701 1.959042 ATGGAGGCTGCTATTCGTTG 58.041 50.000 7.74 0.00 0.00 4.10
696 702 5.683876 ATATATGGAGGCTGCTATTCGTT 57.316 39.130 7.74 0.00 0.00 3.85
697 703 5.683876 AATATATGGAGGCTGCTATTCGT 57.316 39.130 7.74 0.00 0.00 3.85
698 704 8.147058 AGATAAATATATGGAGGCTGCTATTCG 58.853 37.037 7.74 0.00 0.00 3.34
699 705 9.844257 AAGATAAATATATGGAGGCTGCTATTC 57.156 33.333 7.74 0.00 0.00 1.75
741 747 3.243336 CCGCGTGGCTTATTAGAGATAC 58.757 50.000 0.00 0.00 0.00 2.24
806 812 4.842948 TGCTTGCATCTATCCTATCCTTCT 59.157 41.667 0.00 0.00 0.00 2.85
815 821 2.799412 CTCGTTCTGCTTGCATCTATCC 59.201 50.000 0.00 0.00 0.00 2.59
860 866 1.251527 AACAGATCGTGCGTCTCCCT 61.252 55.000 0.00 0.00 0.00 4.20
912 918 7.147426 GGGGGAGTATTTATAGTTACTGGTTGT 60.147 40.741 0.00 0.00 0.00 3.32
954 960 4.710167 AGGGTTACGCCGTTGCCC 62.710 66.667 17.57 17.57 39.60 5.36
1131 1137 3.506844 TGCATAAGCTCACAAAATCTGCA 59.493 39.130 0.00 0.00 42.74 4.41
1132 1138 3.855950 GTGCATAAGCTCACAAAATCTGC 59.144 43.478 0.00 0.00 42.74 4.26
1184 1190 3.937706 GTGTAGCACAGATCTCAAAGCAT 59.062 43.478 0.00 0.00 34.08 3.79
1407 1884 9.533831 AGAATGTGGGATAAAACTTACAGATTT 57.466 29.630 0.00 0.00 0.00 2.17
1409 1886 9.614792 GTAGAATGTGGGATAAAACTTACAGAT 57.385 33.333 0.00 0.00 0.00 2.90
1410 1887 8.598916 TGTAGAATGTGGGATAAAACTTACAGA 58.401 33.333 0.00 0.00 0.00 3.41
1411 1888 8.786826 TGTAGAATGTGGGATAAAACTTACAG 57.213 34.615 0.00 0.00 0.00 2.74
1418 1895 9.120538 GCTTTCTATGTAGAATGTGGGATAAAA 57.879 33.333 13.77 0.00 41.52 1.52
1419 1896 8.494433 AGCTTTCTATGTAGAATGTGGGATAAA 58.506 33.333 13.77 0.00 41.52 1.40
1420 1897 8.034313 AGCTTTCTATGTAGAATGTGGGATAA 57.966 34.615 13.77 0.00 41.52 1.75
1421 1898 7.618019 AGCTTTCTATGTAGAATGTGGGATA 57.382 36.000 13.77 0.00 41.52 2.59
1422 1899 6.506538 AGCTTTCTATGTAGAATGTGGGAT 57.493 37.500 13.77 0.00 41.52 3.85
1423 1900 5.957771 AGCTTTCTATGTAGAATGTGGGA 57.042 39.130 13.77 0.00 41.52 4.37
1424 1901 6.375455 ACAAAGCTTTCTATGTAGAATGTGGG 59.625 38.462 9.23 0.00 41.52 4.61
1425 1902 7.383102 ACAAAGCTTTCTATGTAGAATGTGG 57.617 36.000 9.23 0.00 41.52 4.17
1426 1903 8.292448 ACAACAAAGCTTTCTATGTAGAATGTG 58.708 33.333 9.23 2.02 41.52 3.21
1427 1904 8.292448 CACAACAAAGCTTTCTATGTAGAATGT 58.708 33.333 9.23 3.70 41.52 2.71
1428 1905 7.272084 GCACAACAAAGCTTTCTATGTAGAATG 59.728 37.037 9.23 3.07 41.52 2.67
1429 1906 7.175641 AGCACAACAAAGCTTTCTATGTAGAAT 59.824 33.333 9.23 0.00 41.52 2.40
1430 1907 6.486657 AGCACAACAAAGCTTTCTATGTAGAA 59.513 34.615 9.23 0.00 38.01 2.10
1431 1908 5.997746 AGCACAACAAAGCTTTCTATGTAGA 59.002 36.000 9.23 0.00 38.01 2.59
1432 1909 6.082338 CAGCACAACAAAGCTTTCTATGTAG 58.918 40.000 9.23 10.01 39.50 2.74
1433 1910 5.562696 GCAGCACAACAAAGCTTTCTATGTA 60.563 40.000 9.23 0.00 39.50 2.29
1434 1911 4.794003 GCAGCACAACAAAGCTTTCTATGT 60.794 41.667 9.23 11.49 39.50 2.29
1435 1912 3.671928 GCAGCACAACAAAGCTTTCTATG 59.328 43.478 9.23 10.85 39.50 2.23
1436 1913 3.318839 TGCAGCACAACAAAGCTTTCTAT 59.681 39.130 9.23 0.00 39.50 1.98
1437 1914 2.687425 TGCAGCACAACAAAGCTTTCTA 59.313 40.909 9.23 0.00 39.50 2.10
1438 1915 1.477700 TGCAGCACAACAAAGCTTTCT 59.522 42.857 9.23 0.00 39.50 2.52
1439 1916 1.925229 TGCAGCACAACAAAGCTTTC 58.075 45.000 9.23 0.00 39.50 2.62
1440 1917 2.383368 TTGCAGCACAACAAAGCTTT 57.617 40.000 5.69 5.69 39.50 3.51
1441 1918 2.273557 CTTTGCAGCACAACAAAGCTT 58.726 42.857 0.00 0.00 44.32 3.74
1442 1919 1.930567 CTTTGCAGCACAACAAAGCT 58.069 45.000 0.00 0.00 44.32 3.74
1445 1922 3.309961 TCAACTTTGCAGCACAACAAA 57.690 38.095 0.00 0.00 38.23 2.83
1446 1923 3.252400 CTTCAACTTTGCAGCACAACAA 58.748 40.909 0.00 0.00 38.23 2.83
1447 1924 2.230992 ACTTCAACTTTGCAGCACAACA 59.769 40.909 0.00 0.00 38.23 3.33
1448 1925 2.879826 ACTTCAACTTTGCAGCACAAC 58.120 42.857 0.00 0.00 38.23 3.32
1449 1926 3.441922 TGTACTTCAACTTTGCAGCACAA 59.558 39.130 0.00 0.00 36.13 3.33
1450 1927 3.013219 TGTACTTCAACTTTGCAGCACA 58.987 40.909 0.00 0.00 27.73 4.57
1451 1928 3.691049 TGTACTTCAACTTTGCAGCAC 57.309 42.857 0.00 0.00 0.00 4.40
1452 1929 4.710423 TTTGTACTTCAACTTTGCAGCA 57.290 36.364 0.00 0.00 35.61 4.41
1453 1930 6.695278 TGTATTTTGTACTTCAACTTTGCAGC 59.305 34.615 0.00 0.00 35.61 5.25
1454 1931 8.693504 CATGTATTTTGTACTTCAACTTTGCAG 58.306 33.333 0.00 0.00 35.61 4.41
1455 1932 8.194104 ACATGTATTTTGTACTTCAACTTTGCA 58.806 29.630 0.00 0.00 35.61 4.08
1456 1933 8.574196 ACATGTATTTTGTACTTCAACTTTGC 57.426 30.769 0.00 0.00 35.61 3.68
1500 1977 8.638565 CGATTCGTGCAAATAATTTTCTCTTTT 58.361 29.630 0.00 0.00 0.00 2.27
1501 1978 7.807907 ACGATTCGTGCAAATAATTTTCTCTTT 59.192 29.630 11.56 0.00 39.18 2.52
1502 1979 7.305474 ACGATTCGTGCAAATAATTTTCTCTT 58.695 30.769 11.56 0.00 39.18 2.85
1503 1980 6.842163 ACGATTCGTGCAAATAATTTTCTCT 58.158 32.000 11.56 0.00 39.18 3.10
1519 1996 1.935873 CATTCCTGCATCACGATTCGT 59.064 47.619 5.75 5.75 42.36 3.85
1520 1997 2.204237 TCATTCCTGCATCACGATTCG 58.796 47.619 4.14 4.14 0.00 3.34
1521 1998 3.002042 CACTCATTCCTGCATCACGATTC 59.998 47.826 0.00 0.00 0.00 2.52
1522 1999 2.941064 CACTCATTCCTGCATCACGATT 59.059 45.455 0.00 0.00 0.00 3.34
1523 2000 2.558378 CACTCATTCCTGCATCACGAT 58.442 47.619 0.00 0.00 0.00 3.73
1524 2001 1.405933 CCACTCATTCCTGCATCACGA 60.406 52.381 0.00 0.00 0.00 4.35
1525 2002 1.012086 CCACTCATTCCTGCATCACG 58.988 55.000 0.00 0.00 0.00 4.35
1526 2003 2.119801 ACCACTCATTCCTGCATCAC 57.880 50.000 0.00 0.00 0.00 3.06
1527 2004 2.439409 CAACCACTCATTCCTGCATCA 58.561 47.619 0.00 0.00 0.00 3.07
1528 2005 1.747355 CCAACCACTCATTCCTGCATC 59.253 52.381 0.00 0.00 0.00 3.91
1529 2006 1.355381 TCCAACCACTCATTCCTGCAT 59.645 47.619 0.00 0.00 0.00 3.96
1530 2007 0.770499 TCCAACCACTCATTCCTGCA 59.230 50.000 0.00 0.00 0.00 4.41
1531 2008 2.134789 ATCCAACCACTCATTCCTGC 57.865 50.000 0.00 0.00 0.00 4.85
1532 2009 5.102953 TCTTATCCAACCACTCATTCCTG 57.897 43.478 0.00 0.00 0.00 3.86
1533 2010 5.251700 ACTTCTTATCCAACCACTCATTCCT 59.748 40.000 0.00 0.00 0.00 3.36
1534 2011 5.501156 ACTTCTTATCCAACCACTCATTCC 58.499 41.667 0.00 0.00 0.00 3.01
1535 2012 6.539103 GGTACTTCTTATCCAACCACTCATTC 59.461 42.308 0.00 0.00 0.00 2.67
1536 2013 6.415573 GGTACTTCTTATCCAACCACTCATT 58.584 40.000 0.00 0.00 0.00 2.57
1537 2014 5.104485 GGGTACTTCTTATCCAACCACTCAT 60.104 44.000 0.00 0.00 29.98 2.90
1538 2015 4.224370 GGGTACTTCTTATCCAACCACTCA 59.776 45.833 0.00 0.00 29.98 3.41
1539 2016 4.679905 CGGGTACTTCTTATCCAACCACTC 60.680 50.000 0.00 0.00 28.52 3.51
1540 2017 3.197116 CGGGTACTTCTTATCCAACCACT 59.803 47.826 0.00 0.00 28.52 4.00
1541 2018 3.528532 CGGGTACTTCTTATCCAACCAC 58.471 50.000 0.00 0.00 28.52 4.16
1542 2019 2.502538 CCGGGTACTTCTTATCCAACCA 59.497 50.000 0.00 0.00 28.52 3.67
1543 2020 2.158856 CCCGGGTACTTCTTATCCAACC 60.159 54.545 14.18 0.00 28.52 3.77
1544 2021 2.502947 ACCCGGGTACTTCTTATCCAAC 59.497 50.000 29.13 0.00 28.52 3.77
1545 2022 2.502538 CACCCGGGTACTTCTTATCCAA 59.497 50.000 29.72 0.00 28.52 3.53
1546 2023 2.112998 CACCCGGGTACTTCTTATCCA 58.887 52.381 29.72 0.00 28.52 3.41
1547 2024 1.202615 GCACCCGGGTACTTCTTATCC 60.203 57.143 29.72 0.62 0.00 2.59
1548 2025 1.483415 TGCACCCGGGTACTTCTTATC 59.517 52.381 29.72 7.38 0.00 1.75
1549 2026 1.575419 TGCACCCGGGTACTTCTTAT 58.425 50.000 29.72 0.00 0.00 1.73
1550 2027 1.575419 ATGCACCCGGGTACTTCTTA 58.425 50.000 29.72 4.16 0.00 2.10
1551 2028 1.485066 CTATGCACCCGGGTACTTCTT 59.515 52.381 29.72 15.50 0.00 2.52
1552 2029 1.120530 CTATGCACCCGGGTACTTCT 58.879 55.000 29.72 12.40 0.00 2.85
1553 2030 0.106149 CCTATGCACCCGGGTACTTC 59.894 60.000 29.72 16.18 0.00 3.01
1554 2031 1.979619 GCCTATGCACCCGGGTACTT 61.980 60.000 29.72 21.78 37.47 2.24
1555 2032 2.440817 GCCTATGCACCCGGGTACT 61.441 63.158 29.72 16.37 37.47 2.73
1556 2033 2.110420 GCCTATGCACCCGGGTAC 59.890 66.667 29.72 23.40 37.47 3.34
1557 2034 2.041301 AGCCTATGCACCCGGGTA 60.041 61.111 29.72 13.39 41.13 3.69
1558 2035 2.599139 TAGAGCCTATGCACCCGGGT 62.599 60.000 24.16 24.16 41.13 5.28
1559 2036 1.407656 TTAGAGCCTATGCACCCGGG 61.408 60.000 22.25 22.25 41.13 5.73
1560 2037 0.468226 TTTAGAGCCTATGCACCCGG 59.532 55.000 0.00 0.00 41.13 5.73
1561 2038 1.940613 GTTTTAGAGCCTATGCACCCG 59.059 52.381 0.00 0.00 41.13 5.28
1562 2039 2.999331 TGTTTTAGAGCCTATGCACCC 58.001 47.619 0.00 0.00 41.13 4.61
1563 2040 3.947834 ACATGTTTTAGAGCCTATGCACC 59.052 43.478 0.00 0.00 41.13 5.01
1564 2041 5.567138 AACATGTTTTAGAGCCTATGCAC 57.433 39.130 4.92 0.00 41.13 4.57
1565 2042 6.588719 AAAACATGTTTTAGAGCCTATGCA 57.411 33.333 30.29 0.00 40.61 3.96
1566 2043 5.739161 CGAAAACATGTTTTAGAGCCTATGC 59.261 40.000 31.09 16.24 42.26 3.14
1567 2044 6.128007 ACCGAAAACATGTTTTAGAGCCTATG 60.128 38.462 32.83 21.24 42.26 2.23
1568 2045 5.944007 ACCGAAAACATGTTTTAGAGCCTAT 59.056 36.000 32.83 14.06 42.26 2.57
1569 2046 5.310451 ACCGAAAACATGTTTTAGAGCCTA 58.690 37.500 32.83 0.00 42.26 3.93
1570 2047 4.142038 ACCGAAAACATGTTTTAGAGCCT 58.858 39.130 32.83 15.32 42.26 4.58
1571 2048 4.499037 ACCGAAAACATGTTTTAGAGCC 57.501 40.909 32.83 21.28 42.26 4.70
1572 2049 6.432107 TGTTACCGAAAACATGTTTTAGAGC 58.568 36.000 32.83 21.57 42.26 4.09
1573 2050 7.377662 GGTTGTTACCGAAAACATGTTTTAGAG 59.622 37.037 32.83 26.04 39.04 2.43
1574 2051 7.194962 GGTTGTTACCGAAAACATGTTTTAGA 58.805 34.615 32.83 18.69 39.04 2.10
1575 2052 7.384358 GGTTGTTACCGAAAACATGTTTTAG 57.616 36.000 31.09 29.17 39.04 1.85
1590 2067 3.991999 GGGCTTCCGGTTGTTACC 58.008 61.111 0.00 0.00 41.33 2.85
1751 2228 4.724074 TTACGTGTCGTTGGGAGATTAT 57.276 40.909 0.00 0.00 41.54 1.28
1844 2386 1.226746 GAAACAGACAGACGGGTTGG 58.773 55.000 0.00 0.00 0.00 3.77
1877 2692 9.424319 CACCTGCTGAAAATACTACGATATATT 57.576 33.333 0.00 0.00 0.00 1.28
1886 2701 4.009675 CCTTGCACCTGCTGAAAATACTA 58.990 43.478 0.00 0.00 42.66 1.82
1902 2717 4.782019 AAAATACTTCGATTGCCTTGCA 57.218 36.364 0.00 0.00 36.47 4.08
1967 2784 6.003950 AGGAGAGAATGATTGAACGGAAAAA 58.996 36.000 0.00 0.00 0.00 1.94
2281 3221 2.514803 GACAAGGGTTACCAATGTGCT 58.485 47.619 14.51 0.00 38.64 4.40
2460 3969 9.942850 AAATGGTCCTGAAAATACTTTAAATGG 57.057 29.630 0.00 0.00 0.00 3.16
2621 4267 5.894393 CAGGCTGCCTAGGTACTATGTATAT 59.106 44.000 22.90 0.00 41.70 0.86
2626 4272 2.598565 TCAGGCTGCCTAGGTACTATG 58.401 52.381 22.90 6.66 41.70 2.23
2637 4283 3.134458 GAGTGTGTATTATCAGGCTGCC 58.866 50.000 11.65 11.65 0.00 4.85
2654 4300 4.504132 GGCACTAGGCGAAGAGTG 57.496 61.111 6.65 6.65 46.16 3.51
2670 4316 0.811281 GAAAGGTCAGGCCATTTCGG 59.189 55.000 5.01 0.00 40.61 4.30


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

AutoCloner maintained by Alex Coulton.