Multiple sequence alignment - TraesCS1B01G425800

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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 TraesCS1B01G425800 chr1B 100.000 3001 0 0 1 3001 652049013 652046013 0.000000e+00 5542.0
1 TraesCS1B01G425800 chr1B 89.463 1006 61 21 1159 2146 651913806 651912828 0.000000e+00 1229.0
2 TraesCS1B01G425800 chr1B 87.836 781 60 19 539 1302 652295476 652294714 0.000000e+00 883.0
3 TraesCS1B01G425800 chr1B 90.678 472 28 7 42 499 652296020 652296489 5.500000e-172 614.0
4 TraesCS1B01G425800 chr1B 85.825 515 53 7 1633 2146 652298204 652297709 2.050000e-146 529.0
5 TraesCS1B01G425800 chr1B 82.961 493 44 19 2536 3001 652297723 652297244 2.780000e-110 409.0
6 TraesCS1B01G425800 chr1B 96.689 151 5 0 1294 1444 652294303 652294153 4.970000e-63 252.0
7 TraesCS1B01G425800 chr1B 88.757 169 15 2 2837 3001 651912494 651912326 1.410000e-48 204.0
8 TraesCS1B01G425800 chr1B 80.508 118 17 5 644 761 17808672 17808561 5.330000e-13 86.1
9 TraesCS1B01G425800 chr1D 87.897 1636 131 32 539 2128 470031707 470030093 0.000000e+00 1862.0
10 TraesCS1B01G425800 chr1D 89.362 517 37 6 1 499 470032251 470032767 4.220000e-178 634.0
11 TraesCS1B01G425800 chr1D 88.556 367 34 6 2146 2509 328097002 328097363 3.550000e-119 438.0
12 TraesCS1B01G425800 chr1D 83.845 489 43 15 2536 3001 470033904 470033429 1.650000e-117 433.0
13 TraesCS1B01G425800 chr1D 88.435 147 11 4 2861 3001 469986434 469986288 3.980000e-39 172.0
14 TraesCS1B01G425800 chr1A 87.800 1582 118 36 541 2077 563599760 563598209 0.000000e+00 1783.0
15 TraesCS1B01G425800 chr1A 88.439 519 38 10 1 499 563603952 563604468 9.200000e-170 606.0
16 TraesCS1B01G425800 chr1A 83.976 493 43 18 2536 3001 563605715 563605232 9.870000e-120 440.0
17 TraesCS1B01G425800 chr1A 81.977 516 74 9 1 499 274480375 274480888 1.290000e-113 420.0
18 TraesCS1B01G425800 chr1A 85.908 369 48 3 2150 2515 104392617 104392250 1.010000e-104 390.0
19 TraesCS1B01G425800 chr1A 89.726 146 10 3 2861 3001 563597802 563597657 6.610000e-42 182.0
20 TraesCS1B01G425800 chr1A 83.529 85 7 5 667 751 587391503 587391426 4.150000e-09 73.1
21 TraesCS1B01G425800 chr5A 88.462 364 36 6 2176 2537 82302706 82303065 4.590000e-118 435.0
22 TraesCS1B01G425800 chr5A 82.143 112 12 2 644 755 368099392 368099495 4.120000e-14 89.8
23 TraesCS1B01G425800 chr5A 81.081 111 13 4 645 755 164161300 164161402 6.900000e-12 82.4
24 TraesCS1B01G425800 chr7A 81.923 520 73 10 1 502 553832469 553831953 1.290000e-113 420.0
25 TraesCS1B01G425800 chr7A 97.059 34 1 0 626 659 127042875 127042908 1.160000e-04 58.4
26 TraesCS1B01G425800 chr6A 81.503 519 77 10 1 502 616276259 616275743 2.780000e-110 409.0
27 TraesCS1B01G425800 chr3D 81.489 524 68 14 1 502 417829855 417829339 1.300000e-108 403.0
28 TraesCS1B01G425800 chr3D 84.289 401 49 12 2145 2540 4393126 4392735 2.180000e-101 379.0
29 TraesCS1B01G425800 chr5D 84.864 403 50 9 2145 2540 447434328 447433930 2.170000e-106 396.0
30 TraesCS1B01G425800 chr5D 78.814 118 19 4 644 761 348755360 348755249 1.150000e-09 75.0
31 TraesCS1B01G425800 chr5D 96.970 33 1 0 1359 1391 442010089 442010121 4.180000e-04 56.5
32 TraesCS1B01G425800 chr7D 84.691 405 50 10 2146 2544 606683477 606683079 7.800000e-106 394.0
33 TraesCS1B01G425800 chr7D 84.131 397 52 10 2150 2540 578817578 578817969 1.020000e-99 374.0
34 TraesCS1B01G425800 chr7D 84.906 106 11 5 644 747 191795304 191795406 5.290000e-18 102.0
35 TraesCS1B01G425800 chr3A 84.673 398 53 6 2146 2539 37835294 37835687 1.010000e-104 390.0
36 TraesCS1B01G425800 chr3A 77.538 325 56 8 192 499 363009680 363009356 2.380000e-41 180.0
37 TraesCS1B01G425800 chr2B 83.920 398 54 9 2146 2539 28879362 28878971 3.650000e-99 372.0
38 TraesCS1B01G425800 chr2B 80.508 118 13 5 644 761 154226646 154226539 6.900000e-12 82.4
39 TraesCS1B01G425800 chr2A 80.368 489 81 12 1 479 343911831 343912314 1.020000e-94 357.0
40 TraesCS1B01G425800 chr2A 91.250 80 6 1 546 624 519610200 519610121 1.140000e-19 108.0
41 TraesCS1B01G425800 chr7B 79.487 507 87 15 1 497 12738177 12738676 7.960000e-91 344.0
42 TraesCS1B01G425800 chr7B 83.673 98 11 4 1318 1413 10606061 10606155 1.480000e-13 87.9
43 TraesCS1B01G425800 chr3B 79.077 325 51 8 192 499 116852089 116851765 1.090000e-49 207.0
44 TraesCS1B01G425800 chr3B 78.769 325 52 8 192 499 116891931 116891607 5.070000e-48 202.0
45 TraesCS1B01G425800 chr3B 89.655 87 8 1 546 631 772639748 772639662 3.160000e-20 110.0
46 TraesCS1B01G425800 chr5B 78.659 328 53 8 189 499 83881355 83881682 5.070000e-48 202.0
47 TraesCS1B01G425800 chr5B 81.356 118 14 2 644 761 125794988 125794879 4.120000e-14 89.8
48 TraesCS1B01G425800 chr4A 83.036 112 11 2 644 755 63750026 63750129 8.860000e-16 95.3
49 TraesCS1B01G425800 chr4A 81.356 118 14 2 644 761 492346950 492346841 4.120000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G425800 chr1B 652046013 652049013 3000 True 5542.00 5542 100.00000 1 3001 1 chr1B.!!$R2 3000
1 TraesCS1B01G425800 chr1B 651912326 651913806 1480 True 716.50 1229 89.11000 1159 3001 2 chr1B.!!$R3 1842
2 TraesCS1B01G425800 chr1B 652294153 652298204 4051 True 518.25 883 88.32775 539 3001 4 chr1B.!!$R4 2462
3 TraesCS1B01G425800 chr1D 470030093 470033904 3811 True 1147.50 1862 85.87100 539 3001 2 chr1D.!!$R2 2462
4 TraesCS1B01G425800 chr1D 470032251 470032767 516 False 634.00 634 89.36200 1 499 1 chr1D.!!$F2 498
5 TraesCS1B01G425800 chr1A 563597657 563599760 2103 True 982.50 1783 88.76300 541 3001 2 chr1A.!!$R4 2460
6 TraesCS1B01G425800 chr1A 563603952 563604468 516 False 606.00 606 88.43900 1 499 1 chr1A.!!$F2 498
7 TraesCS1B01G425800 chr1A 274480375 274480888 513 False 420.00 420 81.97700 1 499 1 chr1A.!!$F1 498
8 TraesCS1B01G425800 chr7A 553831953 553832469 516 True 420.00 420 81.92300 1 502 1 chr7A.!!$R1 501
9 TraesCS1B01G425800 chr6A 616275743 616276259 516 True 409.00 409 81.50300 1 502 1 chr6A.!!$R1 501
10 TraesCS1B01G425800 chr3D 417829339 417829855 516 True 403.00 403 81.48900 1 502 1 chr3D.!!$R2 501

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
843 3128 0.468029 CCCAGGTCACAACTTTGCCT 60.468 55.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2513 5257 0.240945 GCACGTCCTGAACCAAATGG 59.759 55.0 0.0 0.0 42.17 3.16 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
50 53 6.389830 ACATAACAAAACAGTCATGCTTGA 57.610 33.333 0.00 0.00 0.00 3.02
132 135 3.244215 TGACGAGCTTCAAGGACAAGAAT 60.244 43.478 0.00 0.00 0.00 2.40
141 144 7.042335 GCTTCAAGGACAAGAATAAGTAGCTA 58.958 38.462 0.00 0.00 0.00 3.32
261 265 6.145048 GCAAGATATTATTCAAGGCATGCAAC 59.855 38.462 21.36 2.42 0.00 4.17
266 270 2.459060 TTCAAGGCATGCAACCATTG 57.541 45.000 21.36 14.78 0.00 2.82
342 349 8.871686 AAGATTTGGTCATAACTTTGTTGTTC 57.128 30.769 0.00 0.00 0.00 3.18
369 394 8.498054 TGCATCTATTAGAAAAACTTGAGAGG 57.502 34.615 0.00 0.00 0.00 3.69
434 459 5.075858 ACAAAGCATATTGGTCAACATGG 57.924 39.130 0.00 0.00 34.56 3.66
441 466 1.112315 TTGGTCAACATGGTGTGCCC 61.112 55.000 19.21 14.37 0.00 5.36
452 477 1.985159 TGGTGTGCCCTTTAGAGTGAT 59.015 47.619 0.00 0.00 0.00 3.06
499 524 4.370094 AAGTTGTCCCGGTTGGTTTATA 57.630 40.909 0.00 0.00 34.77 0.98
502 527 5.677567 AGTTGTCCCGGTTGGTTTATATAG 58.322 41.667 0.00 0.00 34.77 1.31
504 529 5.697082 TGTCCCGGTTGGTTTATATAGTT 57.303 39.130 0.00 0.00 34.77 2.24
506 531 5.045724 TGTCCCGGTTGGTTTATATAGTTGT 60.046 40.000 0.00 0.00 34.77 3.32
507 532 5.525012 GTCCCGGTTGGTTTATATAGTTGTC 59.475 44.000 0.00 0.00 34.77 3.18
508 533 4.818005 CCCGGTTGGTTTATATAGTTGTCC 59.182 45.833 0.00 0.00 0.00 4.02
509 534 4.818005 CCGGTTGGTTTATATAGTTGTCCC 59.182 45.833 0.00 0.00 0.00 4.46
511 536 5.526111 CGGTTGGTTTATATAGTTGTCCCAG 59.474 44.000 0.00 0.00 0.00 4.45
512 537 6.420638 GGTTGGTTTATATAGTTGTCCCAGT 58.579 40.000 0.00 0.00 0.00 4.00
513 538 6.888088 GGTTGGTTTATATAGTTGTCCCAGTT 59.112 38.462 0.00 0.00 0.00 3.16
514 539 7.148137 GGTTGGTTTATATAGTTGTCCCAGTTG 60.148 40.741 0.00 0.00 0.00 3.16
515 540 6.419791 TGGTTTATATAGTTGTCCCAGTTGG 58.580 40.000 0.00 0.00 0.00 3.77
517 542 6.888088 GGTTTATATAGTTGTCCCAGTTGGTT 59.112 38.462 0.00 0.00 34.77 3.67
519 544 9.452287 GTTTATATAGTTGTCCCAGTTGGTTTA 57.548 33.333 0.00 0.00 34.77 2.01
532 557 9.496873 TCCCAGTTGGTTTATATATATTCAACG 57.503 33.333 17.78 14.67 38.29 4.10
533 558 9.280174 CCCAGTTGGTTTATATATATTCAACGT 57.720 33.333 17.78 0.00 38.29 3.99
628 2891 2.195389 GCCAAATGCAGCCTGATCA 58.805 52.632 0.00 0.00 40.77 2.92
641 2904 6.379133 TGCAGCCTGATCATTTTAGAGATTTT 59.621 34.615 0.00 0.00 0.00 1.82
701 2982 7.189512 AGATTCACTTATTTTGCTTCGTATGC 58.810 34.615 0.00 0.00 0.00 3.14
712 2993 4.968626 TGCTTCGTATGCAGTTTATGTTG 58.031 39.130 0.00 0.00 35.31 3.33
727 3008 9.480053 CAGTTTATGTTGGAATGTTGAAATCTT 57.520 29.630 0.00 0.00 0.00 2.40
770 3051 8.140112 AGAAATGGAGAGTGTACTAGAAATGT 57.860 34.615 0.00 0.00 0.00 2.71
771 3052 9.256228 AGAAATGGAGAGTGTACTAGAAATGTA 57.744 33.333 0.00 0.00 0.00 2.29
772 3053 9.522804 GAAATGGAGAGTGTACTAGAAATGTAG 57.477 37.037 0.00 0.00 0.00 2.74
774 3055 9.696572 AATGGAGAGTGTACTAGAAATGTAGTA 57.303 33.333 0.00 0.00 34.91 1.82
775 3056 9.696572 ATGGAGAGTGTACTAGAAATGTAGTAA 57.303 33.333 0.00 0.00 37.27 2.24
776 3057 9.524496 TGGAGAGTGTACTAGAAATGTAGTAAA 57.476 33.333 0.00 0.00 37.27 2.01
841 3126 1.363807 GCCCAGGTCACAACTTTGC 59.636 57.895 0.00 0.00 0.00 3.68
843 3128 0.468029 CCCAGGTCACAACTTTGCCT 60.468 55.000 0.00 0.00 0.00 4.75
897 3183 2.239907 GTGGGAGAAGAAACTATGGCCT 59.760 50.000 3.32 0.00 0.00 5.19
940 3226 3.128764 TGCAACGACCAGTACTCATCTAG 59.871 47.826 0.00 0.00 0.00 2.43
947 3233 5.433526 GACCAGTACTCATCTAGACACTCT 58.566 45.833 0.00 0.00 0.00 3.24
953 3239 4.776349 ACTCATCTAGACACTCTCACGAT 58.224 43.478 0.00 0.00 0.00 3.73
1005 3292 3.452627 AGTAGCCACCCAAATCTAGTCTG 59.547 47.826 0.00 0.00 0.00 3.51
1031 3318 0.762461 CCTTGAACCAAAGCCCCCAA 60.762 55.000 0.00 0.00 0.00 4.12
1067 3368 1.918467 CTGCAGGAGAGCCATGGGAA 61.918 60.000 15.13 0.00 36.29 3.97
1075 3376 1.076024 AGAGCCATGGGAAGAAGCAAA 59.924 47.619 15.13 0.00 0.00 3.68
1077 3378 2.498885 GAGCCATGGGAAGAAGCAAAAT 59.501 45.455 15.13 0.00 0.00 1.82
1079 3380 2.027837 GCCATGGGAAGAAGCAAAATGT 60.028 45.455 15.13 0.00 0.00 2.71
1080 3381 3.853475 CCATGGGAAGAAGCAAAATGTC 58.147 45.455 2.85 0.00 0.00 3.06
1111 3412 1.717645 GCGATCGTGTGTTTACTCGTT 59.282 47.619 17.81 0.00 42.57 3.85
1216 3517 1.361543 TGCCTTCTGGGTCCTAGTACT 59.638 52.381 0.00 0.00 37.43 2.73
1225 3526 3.968649 TGGGTCCTAGTACTGTGTTTCAA 59.031 43.478 5.39 0.00 0.00 2.69
1415 4140 6.603237 TGTTGAGCGACAATTAATATGAGG 57.397 37.500 3.08 0.00 40.76 3.86
1416 4141 6.345298 TGTTGAGCGACAATTAATATGAGGA 58.655 36.000 3.08 0.00 40.76 3.71
1444 4169 1.840737 TGCTACTCTCTCAGTCCCAC 58.159 55.000 0.00 0.00 36.43 4.61
1493 4218 8.327941 TCTCCTTTTTGAAGTAGACATTGATG 57.672 34.615 0.00 0.00 0.00 3.07
1606 4347 1.448985 ACAATGTTTCCACGATCCCG 58.551 50.000 0.00 0.00 42.50 5.14
1838 4582 0.821711 TTGGCACCAGCTACCAACAC 60.822 55.000 5.77 0.00 38.52 3.32
1840 4584 0.323629 GGCACCAGCTACCAACACTA 59.676 55.000 0.00 0.00 41.70 2.74
1868 4612 8.250332 AGAGATGAAACTCTATGTGAAACTCTC 58.750 37.037 0.00 0.00 44.17 3.20
1966 4710 5.670792 ATGCATGGTTTGAAATCTCACAT 57.329 34.783 0.00 0.00 0.00 3.21
2021 4765 4.762289 AACTGGATCCCATTGAGAGTAC 57.238 45.455 9.90 0.00 30.82 2.73
2037 4781 1.202604 AGTACCCAAACCAGTGTGTCG 60.203 52.381 0.00 0.00 0.00 4.35
2056 4800 3.972502 GTCGGTTTGTTTATGTGCTTGTC 59.027 43.478 0.00 0.00 0.00 3.18
2077 4821 7.117241 TGTCTGTATTTTCTTTCGTTGCTAG 57.883 36.000 0.00 0.00 0.00 3.42
2078 4822 6.704493 TGTCTGTATTTTCTTTCGTTGCTAGT 59.296 34.615 0.00 0.00 0.00 2.57
2079 4823 7.225931 TGTCTGTATTTTCTTTCGTTGCTAGTT 59.774 33.333 0.00 0.00 0.00 2.24
2080 4824 7.530861 GTCTGTATTTTCTTTCGTTGCTAGTTG 59.469 37.037 0.00 0.00 0.00 3.16
2081 4825 6.140110 TGTATTTTCTTTCGTTGCTAGTTGC 58.860 36.000 0.00 0.00 43.25 4.17
2082 4826 4.893424 TTTTCTTTCGTTGCTAGTTGCT 57.107 36.364 0.00 0.00 43.37 3.91
2083 4827 5.994887 TTTTCTTTCGTTGCTAGTTGCTA 57.005 34.783 0.00 0.00 43.37 3.49
2146 4890 3.812262 TGATGTACTGCCATGATTGAGG 58.188 45.455 0.00 0.00 0.00 3.86
2147 4891 2.715749 TGTACTGCCATGATTGAGGG 57.284 50.000 0.00 0.00 0.00 4.30
2148 4892 2.195727 TGTACTGCCATGATTGAGGGA 58.804 47.619 0.00 0.00 0.00 4.20
2149 4893 2.575735 TGTACTGCCATGATTGAGGGAA 59.424 45.455 0.00 0.00 0.00 3.97
2150 4894 2.905415 ACTGCCATGATTGAGGGAAA 57.095 45.000 0.00 0.00 0.00 3.13
2151 4895 2.731572 ACTGCCATGATTGAGGGAAAG 58.268 47.619 0.00 0.00 0.00 2.62
2152 4896 2.042162 ACTGCCATGATTGAGGGAAAGT 59.958 45.455 0.00 0.00 0.00 2.66
2153 4897 2.426024 CTGCCATGATTGAGGGAAAGTG 59.574 50.000 0.00 0.00 0.00 3.16
2154 4898 1.135721 GCCATGATTGAGGGAAAGTGC 59.864 52.381 0.00 0.00 0.00 4.40
2155 4899 2.449464 CCATGATTGAGGGAAAGTGCA 58.551 47.619 0.00 0.00 0.00 4.57
2156 4900 3.028850 CCATGATTGAGGGAAAGTGCAT 58.971 45.455 0.00 0.00 0.00 3.96
2157 4901 3.067742 CCATGATTGAGGGAAAGTGCATC 59.932 47.826 0.00 0.00 0.00 3.91
2158 4902 2.358957 TGATTGAGGGAAAGTGCATCG 58.641 47.619 0.00 0.00 0.00 3.84
2159 4903 2.027285 TGATTGAGGGAAAGTGCATCGA 60.027 45.455 0.00 0.00 0.00 3.59
2160 4904 2.787473 TTGAGGGAAAGTGCATCGAT 57.213 45.000 0.00 0.00 0.00 3.59
2161 4905 2.028420 TGAGGGAAAGTGCATCGATG 57.972 50.000 21.27 21.27 0.00 3.84
2162 4906 1.554617 TGAGGGAAAGTGCATCGATGA 59.445 47.619 29.20 11.22 0.00 2.92
2163 4907 2.027285 TGAGGGAAAGTGCATCGATGAA 60.027 45.455 29.20 16.94 0.00 2.57
2164 4908 3.209410 GAGGGAAAGTGCATCGATGAAT 58.791 45.455 29.20 10.43 0.00 2.57
2165 4909 3.624777 AGGGAAAGTGCATCGATGAATT 58.375 40.909 29.20 13.09 0.00 2.17
2166 4910 3.629398 AGGGAAAGTGCATCGATGAATTC 59.371 43.478 29.20 18.68 0.00 2.17
2180 4924 6.153212 CGATGAATTCGGGTACATATGAAC 57.847 41.667 10.38 0.00 44.28 3.18
2181 4925 5.120208 CGATGAATTCGGGTACATATGAACC 59.880 44.000 10.38 7.31 44.28 3.62
2194 4938 8.931775 GGTACATATGAACCCATTTTGAAAAAC 58.068 33.333 10.38 0.00 34.31 2.43
2195 4939 9.482627 GTACATATGAACCCATTTTGAAAAACA 57.517 29.630 10.38 0.00 34.31 2.83
2196 4940 8.376889 ACATATGAACCCATTTTGAAAAACAC 57.623 30.769 10.38 0.00 34.31 3.32
2197 4941 7.989741 ACATATGAACCCATTTTGAAAAACACA 59.010 29.630 10.38 0.00 34.31 3.72
2198 4942 9.001542 CATATGAACCCATTTTGAAAAACACAT 57.998 29.630 0.00 0.00 34.31 3.21
2199 4943 7.878547 ATGAACCCATTTTGAAAAACACATT 57.121 28.000 0.00 0.00 0.00 2.71
2200 4944 7.693969 TGAACCCATTTTGAAAAACACATTT 57.306 28.000 0.00 0.00 0.00 2.32
2201 4945 7.756558 TGAACCCATTTTGAAAAACACATTTC 58.243 30.769 0.00 0.00 39.28 2.17
2202 4946 7.609532 TGAACCCATTTTGAAAAACACATTTCT 59.390 29.630 0.00 0.00 39.51 2.52
2203 4947 9.103861 GAACCCATTTTGAAAAACACATTTCTA 57.896 29.630 0.00 0.00 39.51 2.10
2204 4948 9.454859 AACCCATTTTGAAAAACACATTTCTAA 57.545 25.926 0.00 0.00 39.51 2.10
2205 4949 9.454859 ACCCATTTTGAAAAACACATTTCTAAA 57.545 25.926 10.24 10.24 43.15 1.85
2231 4975 8.137210 TGCTAAAATAAACTGAAAAAGGTTGC 57.863 30.769 0.00 0.00 36.16 4.17
2232 4976 7.766278 TGCTAAAATAAACTGAAAAAGGTTGCA 59.234 29.630 0.00 0.00 36.16 4.08
2233 4977 8.061857 GCTAAAATAAACTGAAAAAGGTTGCAC 58.938 33.333 0.00 0.00 36.16 4.57
2234 4978 6.582437 AAATAAACTGAAAAAGGTTGCACG 57.418 33.333 0.00 0.00 36.16 5.34
2235 4979 2.577449 AACTGAAAAAGGTTGCACGG 57.423 45.000 0.00 0.00 0.00 4.94
2236 4980 1.757682 ACTGAAAAAGGTTGCACGGA 58.242 45.000 0.00 0.00 0.00 4.69
2237 4981 1.676006 ACTGAAAAAGGTTGCACGGAG 59.324 47.619 0.00 0.00 0.00 4.63
2238 4982 1.946768 CTGAAAAAGGTTGCACGGAGA 59.053 47.619 0.00 0.00 0.00 3.71
2239 4983 1.673920 TGAAAAAGGTTGCACGGAGAC 59.326 47.619 0.00 0.00 0.00 3.36
2252 4996 3.233355 GGAGACGCCTTCATGTGTT 57.767 52.632 0.00 0.00 0.00 3.32
2253 4997 1.523758 GGAGACGCCTTCATGTGTTT 58.476 50.000 0.00 0.00 0.00 2.83
2254 4998 2.695359 GGAGACGCCTTCATGTGTTTA 58.305 47.619 0.00 0.00 0.00 2.01
2255 4999 3.270877 GGAGACGCCTTCATGTGTTTAT 58.729 45.455 0.00 0.00 0.00 1.40
2256 5000 3.063997 GGAGACGCCTTCATGTGTTTATG 59.936 47.826 0.00 0.00 0.00 1.90
2257 5001 3.674997 AGACGCCTTCATGTGTTTATGT 58.325 40.909 0.00 0.00 0.00 2.29
2258 5002 3.436704 AGACGCCTTCATGTGTTTATGTG 59.563 43.478 0.00 0.00 0.00 3.21
2259 5003 2.095263 ACGCCTTCATGTGTTTATGTGC 60.095 45.455 0.00 0.00 0.00 4.57
2260 5004 2.518949 GCCTTCATGTGTTTATGTGCG 58.481 47.619 0.00 0.00 0.00 5.34
2261 5005 2.095263 GCCTTCATGTGTTTATGTGCGT 60.095 45.455 0.00 0.00 0.00 5.24
2262 5006 3.491356 CCTTCATGTGTTTATGTGCGTG 58.509 45.455 0.00 0.00 0.00 5.34
2263 5007 2.610219 TCATGTGTTTATGTGCGTGC 57.390 45.000 0.00 0.00 0.00 5.34
2264 5008 1.876156 TCATGTGTTTATGTGCGTGCA 59.124 42.857 0.00 0.00 0.00 4.57
2265 5009 2.487372 TCATGTGTTTATGTGCGTGCAT 59.513 40.909 0.00 0.12 0.00 3.96
2266 5010 3.686726 TCATGTGTTTATGTGCGTGCATA 59.313 39.130 0.00 0.00 0.00 3.14
2267 5011 4.154918 TCATGTGTTTATGTGCGTGCATAA 59.845 37.500 0.00 8.87 38.94 1.90
2268 5012 4.489679 TGTGTTTATGTGCGTGCATAAA 57.510 36.364 16.73 16.73 44.33 1.40
2269 5013 4.471373 TGTGTTTATGTGCGTGCATAAAG 58.529 39.130 19.36 0.00 45.96 1.85
2270 5014 4.023622 TGTGTTTATGTGCGTGCATAAAGT 60.024 37.500 19.36 0.00 45.96 2.66
2271 5015 4.915085 GTGTTTATGTGCGTGCATAAAGTT 59.085 37.500 19.36 0.00 45.96 2.66
2272 5016 5.401079 GTGTTTATGTGCGTGCATAAAGTTT 59.599 36.000 19.36 0.00 45.96 2.66
2273 5017 5.627367 TGTTTATGTGCGTGCATAAAGTTTC 59.373 36.000 19.36 12.21 45.96 2.78
2274 5018 2.308347 TGTGCGTGCATAAAGTTTCG 57.692 45.000 0.00 0.00 0.00 3.46
2275 5019 1.600013 TGTGCGTGCATAAAGTTTCGT 59.400 42.857 0.00 0.00 0.00 3.85
2276 5020 1.969256 GTGCGTGCATAAAGTTTCGTG 59.031 47.619 0.00 0.00 0.00 4.35
2277 5021 1.069568 TGCGTGCATAAAGTTTCGTGG 60.070 47.619 0.00 0.00 0.00 4.94
2278 5022 1.195900 GCGTGCATAAAGTTTCGTGGA 59.804 47.619 0.00 0.00 0.00 4.02
2279 5023 2.350007 GCGTGCATAAAGTTTCGTGGAA 60.350 45.455 0.00 0.00 0.00 3.53
2280 5024 3.850374 GCGTGCATAAAGTTTCGTGGAAA 60.850 43.478 0.00 0.00 0.00 3.13
2281 5025 4.283678 CGTGCATAAAGTTTCGTGGAAAA 58.716 39.130 0.00 0.00 33.14 2.29
2282 5026 4.735822 CGTGCATAAAGTTTCGTGGAAAAA 59.264 37.500 0.00 0.00 33.14 1.94
2283 5027 5.401079 CGTGCATAAAGTTTCGTGGAAAAAT 59.599 36.000 0.00 0.00 33.14 1.82
2284 5028 6.579292 CGTGCATAAAGTTTCGTGGAAAAATA 59.421 34.615 0.00 0.00 33.14 1.40
2285 5029 7.113684 CGTGCATAAAGTTTCGTGGAAAAATAA 59.886 33.333 0.00 0.00 33.14 1.40
2286 5030 8.921670 GTGCATAAAGTTTCGTGGAAAAATAAT 58.078 29.630 0.00 0.00 33.14 1.28
2287 5031 9.482627 TGCATAAAGTTTCGTGGAAAAATAATT 57.517 25.926 0.00 0.00 33.14 1.40
2379 5123 3.972950 TTTTTGCGGAGACAAATCGAA 57.027 38.095 0.00 0.00 39.18 3.71
2380 5124 3.536158 TTTTGCGGAGACAAATCGAAG 57.464 42.857 0.00 0.00 39.18 3.79
2381 5125 2.448926 TTGCGGAGACAAATCGAAGA 57.551 45.000 0.00 0.00 45.75 2.87
2382 5126 1.996292 TGCGGAGACAAATCGAAGAG 58.004 50.000 0.00 0.00 43.63 2.85
2383 5127 1.544246 TGCGGAGACAAATCGAAGAGA 59.456 47.619 0.00 0.00 43.63 3.10
2384 5128 1.921230 GCGGAGACAAATCGAAGAGAC 59.079 52.381 0.00 0.00 43.63 3.36
2385 5129 2.671351 GCGGAGACAAATCGAAGAGACA 60.671 50.000 0.00 0.00 43.63 3.41
2386 5130 3.775202 CGGAGACAAATCGAAGAGACAT 58.225 45.455 0.00 0.00 43.63 3.06
2387 5131 4.177026 CGGAGACAAATCGAAGAGACATT 58.823 43.478 0.00 0.00 43.63 2.71
2388 5132 4.627467 CGGAGACAAATCGAAGAGACATTT 59.373 41.667 0.00 0.00 43.63 2.32
2389 5133 5.120830 CGGAGACAAATCGAAGAGACATTTT 59.879 40.000 0.00 0.00 43.63 1.82
2390 5134 6.347725 CGGAGACAAATCGAAGAGACATTTTT 60.348 38.462 0.00 0.00 43.63 1.94
2413 5157 3.041874 CAAAACTTTGTGCCGTGCA 57.958 47.368 0.00 0.00 35.60 4.57
2504 5248 9.566432 TTAAAATGCATATTTCAAAAAGTGGGT 57.434 25.926 0.00 0.00 35.50 4.51
2505 5249 7.437793 AAATGCATATTTCAAAAAGTGGGTG 57.562 32.000 0.00 0.00 30.85 4.61
2506 5250 4.314121 TGCATATTTCAAAAAGTGGGTGC 58.686 39.130 0.00 0.00 0.00 5.01
2507 5251 4.202295 TGCATATTTCAAAAAGTGGGTGCA 60.202 37.500 0.00 0.00 36.62 4.57
2508 5252 4.937015 GCATATTTCAAAAAGTGGGTGCAT 59.063 37.500 0.00 0.00 0.00 3.96
2509 5253 6.105333 GCATATTTCAAAAAGTGGGTGCATA 58.895 36.000 0.00 0.00 0.00 3.14
2510 5254 6.762661 GCATATTTCAAAAAGTGGGTGCATAT 59.237 34.615 0.00 0.00 0.00 1.78
2511 5255 7.254522 GCATATTTCAAAAAGTGGGTGCATATG 60.255 37.037 0.00 0.00 0.00 1.78
2512 5256 3.591196 TCAAAAAGTGGGTGCATATGC 57.409 42.857 21.09 21.09 42.50 3.14
2513 5257 2.233431 TCAAAAAGTGGGTGCATATGCC 59.767 45.455 24.54 15.25 41.18 4.40
2514 5258 1.194218 AAAAGTGGGTGCATATGCCC 58.806 50.000 24.54 22.41 45.04 5.36
2519 5263 3.993382 GGGTGCATATGCCCATTTG 57.007 52.632 26.58 0.00 44.23 2.32
2520 5264 0.393820 GGGTGCATATGCCCATTTGG 59.606 55.000 26.58 0.00 44.23 3.28
2521 5265 1.122227 GGTGCATATGCCCATTTGGT 58.878 50.000 24.54 0.00 41.18 3.67
2522 5266 1.485895 GGTGCATATGCCCATTTGGTT 59.514 47.619 24.54 0.00 41.18 3.67
2523 5267 2.483538 GGTGCATATGCCCATTTGGTTC 60.484 50.000 24.54 0.00 41.18 3.62
2524 5268 2.168106 GTGCATATGCCCATTTGGTTCA 59.832 45.455 24.54 0.00 41.18 3.18
2525 5269 2.431419 TGCATATGCCCATTTGGTTCAG 59.569 45.455 24.54 0.00 41.18 3.02
2526 5270 2.224113 GCATATGCCCATTTGGTTCAGG 60.224 50.000 17.26 0.00 36.04 3.86
2527 5271 3.298619 CATATGCCCATTTGGTTCAGGA 58.701 45.455 0.00 0.00 36.04 3.86
2528 5272 1.560505 ATGCCCATTTGGTTCAGGAC 58.439 50.000 0.00 0.00 36.04 3.85
2529 5273 0.893270 TGCCCATTTGGTTCAGGACG 60.893 55.000 0.00 0.00 36.04 4.79
2530 5274 0.893727 GCCCATTTGGTTCAGGACGT 60.894 55.000 0.00 0.00 36.04 4.34
2531 5275 0.881118 CCCATTTGGTTCAGGACGTG 59.119 55.000 0.00 0.00 0.00 4.49
2532 5276 0.240945 CCATTTGGTTCAGGACGTGC 59.759 55.000 0.00 0.00 0.00 5.34
2533 5277 0.240945 CATTTGGTTCAGGACGTGCC 59.759 55.000 2.38 0.00 0.00 5.01
2534 5278 1.234615 ATTTGGTTCAGGACGTGCCG 61.235 55.000 2.38 0.00 43.43 5.69
2535 5279 2.313051 TTTGGTTCAGGACGTGCCGA 62.313 55.000 2.38 0.00 43.43 5.54
2536 5280 2.737376 GGTTCAGGACGTGCCGAC 60.737 66.667 2.38 0.00 43.43 4.79
2537 5281 2.338984 GTTCAGGACGTGCCGACT 59.661 61.111 2.38 0.00 43.43 4.18
2538 5282 1.733399 GTTCAGGACGTGCCGACTC 60.733 63.158 2.38 0.00 43.43 3.36
2539 5283 2.927580 TTCAGGACGTGCCGACTCC 61.928 63.158 2.38 0.00 43.43 3.85
2540 5284 3.680786 CAGGACGTGCCGACTCCA 61.681 66.667 2.38 0.00 43.43 3.86
2541 5285 2.680352 AGGACGTGCCGACTCCAT 60.680 61.111 2.38 0.00 43.43 3.41
2542 5286 2.509336 GGACGTGCCGACTCCATG 60.509 66.667 0.00 0.00 0.00 3.66
2543 5287 2.571757 GACGTGCCGACTCCATGA 59.428 61.111 0.00 0.00 0.00 3.07
2544 5288 1.141881 GACGTGCCGACTCCATGAT 59.858 57.895 0.00 0.00 0.00 2.45
2545 5289 0.460284 GACGTGCCGACTCCATGATT 60.460 55.000 0.00 0.00 0.00 2.57
2546 5290 0.740868 ACGTGCCGACTCCATGATTG 60.741 55.000 0.00 0.00 0.00 2.67
2547 5291 0.460109 CGTGCCGACTCCATGATTGA 60.460 55.000 0.00 0.00 0.00 2.57
2548 5292 1.293924 GTGCCGACTCCATGATTGAG 58.706 55.000 0.00 0.00 35.92 3.02
2557 5301 8.147058 GCCGACTCCATGATTGAGATATAATAT 58.853 37.037 0.01 0.00 33.95 1.28
2558 5302 9.689976 CCGACTCCATGATTGAGATATAATATC 57.310 37.037 0.01 0.00 33.95 1.63
2603 5349 9.761504 CTATGGATATAAACTCTGAGCATATGG 57.238 37.037 4.19 0.00 0.00 2.74
2604 5350 7.559335 TGGATATAAACTCTGAGCATATGGT 57.441 36.000 7.23 7.23 0.00 3.55
2607 5353 8.097038 GGATATAAACTCTGAGCATATGGTTCA 58.903 37.037 9.14 7.70 35.29 3.18
2608 5354 8.839310 ATATAAACTCTGAGCATATGGTTCAC 57.161 34.615 9.14 0.00 32.86 3.18
2611 5357 2.862536 CTCTGAGCATATGGTTCACGTG 59.137 50.000 9.94 9.94 32.86 4.49
2623 5369 4.900684 TGGTTCACGTGATATTCTTTGGA 58.099 39.130 20.80 0.00 0.00 3.53
2625 5371 4.094442 GGTTCACGTGATATTCTTTGGACC 59.906 45.833 20.80 15.42 0.00 4.46
2658 5414 5.437289 TTGACCTCATGTTGTTTGATGTC 57.563 39.130 0.00 0.00 38.48 3.06
2663 5419 4.224433 CTCATGTTGTTTGATGTCTGTGC 58.776 43.478 0.00 0.00 0.00 4.57
2702 5458 4.987912 GGATCTTGTTTTCCGCATTTTCAA 59.012 37.500 0.00 0.00 0.00 2.69
2704 5460 6.147656 GGATCTTGTTTTCCGCATTTTCAATT 59.852 34.615 0.00 0.00 0.00 2.32
2706 5462 7.636259 TCTTGTTTTCCGCATTTTCAATTAG 57.364 32.000 0.00 0.00 0.00 1.73
2708 5464 5.537188 TGTTTTCCGCATTTTCAATTAGCT 58.463 33.333 0.00 0.00 0.00 3.32
2711 5467 4.882671 TCCGCATTTTCAATTAGCTCTC 57.117 40.909 0.00 0.00 0.00 3.20
2712 5468 4.517285 TCCGCATTTTCAATTAGCTCTCT 58.483 39.130 0.00 0.00 0.00 3.10
2713 5469 5.670485 TCCGCATTTTCAATTAGCTCTCTA 58.330 37.500 0.00 0.00 0.00 2.43
2745 5504 2.364632 TGATATGCCGGGTGTTTTGAG 58.635 47.619 2.18 0.00 0.00 3.02
2758 5517 5.175127 GGTGTTTTGAGCTCCTTTTTGAAA 58.825 37.500 12.15 0.00 0.00 2.69
2762 5521 6.589907 TGTTTTGAGCTCCTTTTTGAAAAGAC 59.410 34.615 12.15 1.59 46.39 3.01
2765 5524 6.469782 TGAGCTCCTTTTTGAAAAGACAAT 57.530 33.333 12.15 2.00 46.39 2.71
2766 5525 6.507023 TGAGCTCCTTTTTGAAAAGACAATC 58.493 36.000 12.15 9.73 46.39 2.67
2767 5526 5.847304 AGCTCCTTTTTGAAAAGACAATCC 58.153 37.500 15.79 1.42 46.39 3.01
2771 5538 6.270064 TCCTTTTTGAAAAGACAATCCGTTC 58.730 36.000 15.79 0.00 46.39 3.95
2782 5549 6.560253 AGACAATCCGTTCATATTTATGGC 57.440 37.500 0.00 0.00 34.50 4.40
2787 5554 4.888917 TCCGTTCATATTTATGGCATCGA 58.111 39.130 1.65 0.00 34.50 3.59
2814 5581 4.097418 ACAAGTCTGGGCTACTACTTCAT 58.903 43.478 0.00 0.00 29.93 2.57
2845 5612 4.869297 CGCCCATTTTCTGCAATATTCAAA 59.131 37.500 0.00 0.00 0.00 2.69
2904 5777 0.108615 GCATGTGTCTAGCAGTCCGT 60.109 55.000 0.00 0.00 0.00 4.69
2950 5823 6.301486 TCTACCATTAGCCGATAACTAGTCA 58.699 40.000 0.00 0.00 0.00 3.41
2951 5824 5.864418 ACCATTAGCCGATAACTAGTCAA 57.136 39.130 0.00 0.00 0.00 3.18
2957 5830 2.601763 GCCGATAACTAGTCAACAACGG 59.398 50.000 14.72 14.72 40.60 4.44
2959 5832 3.855950 CCGATAACTAGTCAACAACGGTC 59.144 47.826 0.00 0.00 34.39 4.79
2970 5843 1.152989 ACAACGGTCGCGCTTAAACA 61.153 50.000 5.56 0.00 0.00 2.83
2972 5845 1.562575 AACGGTCGCGCTTAAACAGG 61.563 55.000 5.56 0.00 0.00 4.00
2982 5855 1.266989 GCTTAAACAGGCGAGCACTTT 59.733 47.619 0.00 0.00 35.29 2.66
2993 5866 6.936900 ACAGGCGAGCACTTTTGATATATATT 59.063 34.615 0.00 0.00 0.00 1.28
2995 5868 8.935844 CAGGCGAGCACTTTTGATATATATTTA 58.064 33.333 0.00 0.00 0.00 1.40
2997 5870 9.922305 GGCGAGCACTTTTGATATATATTTATC 57.078 33.333 6.30 6.30 0.00 1.75
2998 5871 9.922305 GCGAGCACTTTTGATATATATTTATCC 57.078 33.333 9.78 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.781056 ACTGTTTTGTTATGTTTTCCATGTCT 58.219 30.769 0.00 0.00 34.86 3.41
18 19 7.551585 TGACTGTTTTGTTATGTTTTCCATGT 58.448 30.769 0.00 0.00 34.86 3.21
132 135 6.985645 TCAACCGAACTTTGTTTAGCTACTTA 59.014 34.615 0.00 0.00 0.00 2.24
141 144 5.379732 TCTTTGTCAACCGAACTTTGTTT 57.620 34.783 0.00 0.00 0.00 2.83
253 257 0.245539 AGAGCACAATGGTTGCATGC 59.754 50.000 11.82 11.82 34.08 4.06
261 265 0.038744 AGGTTGGGAGAGCACAATGG 59.961 55.000 0.00 0.00 40.07 3.16
266 270 3.350219 TCAAATAGGTTGGGAGAGCAC 57.650 47.619 0.00 0.00 37.85 4.40
342 349 9.932699 CTCTCAAGTTTTTCTAATAGATGCATG 57.067 33.333 2.46 0.00 0.00 4.06
369 394 8.040727 ACAAATAAATTACCCTTCTTCATTGGC 58.959 33.333 0.00 0.00 0.00 4.52
423 448 1.530419 GGGCACACCATGTTGACCA 60.530 57.895 0.00 0.00 39.85 4.02
434 459 2.094182 TCGATCACTCTAAAGGGCACAC 60.094 50.000 0.00 0.00 0.00 3.82
452 477 8.262715 TGATTGCAAAAATAAGTCACTATCGA 57.737 30.769 1.71 0.00 0.00 3.59
506 531 9.496873 CGTTGAATATATATAAACCAACTGGGA 57.503 33.333 20.58 0.00 41.15 4.37
507 532 9.280174 ACGTTGAATATATATAAACCAACTGGG 57.720 33.333 20.58 13.71 44.81 4.45
566 2825 4.093011 TCCAAGGATAACATGGTTTTGGG 58.907 43.478 12.97 0.00 35.48 4.12
567 2826 5.736951 TTCCAAGGATAACATGGTTTTGG 57.263 39.130 0.00 3.83 35.66 3.28
701 2982 9.480053 AAGATTTCAACATTCCAACATAAACTG 57.520 29.630 0.00 0.00 0.00 3.16
790 3075 1.740296 GGGATGTTACGTGCACGCT 60.740 57.895 37.35 25.67 44.43 5.07
819 3104 2.672996 GTTGTGACCTGGGCGCAT 60.673 61.111 18.00 0.00 0.00 4.73
897 3183 1.798223 CGTGAAACCAAAGCAGATCGA 59.202 47.619 0.00 0.00 0.00 3.59
924 3210 5.433526 AGAGTGTCTAGATGAGTACTGGTC 58.566 45.833 0.00 0.00 0.00 4.02
947 3233 8.863872 TTTATACTAGGAGATGATGATCGTGA 57.136 34.615 0.00 0.00 33.34 4.35
981 3268 5.128827 CAGACTAGATTTGGGTGGCTACTAA 59.871 44.000 0.00 0.00 0.00 2.24
991 3278 3.432890 GGGCTTCTCAGACTAGATTTGGG 60.433 52.174 0.00 0.00 0.00 4.12
1005 3292 1.270826 GCTTTGGTTCAAGGGCTTCTC 59.729 52.381 0.00 0.00 0.00 2.87
1067 3368 4.041444 ACTCTCCAGAGACATTTTGCTTCT 59.959 41.667 10.68 0.00 44.74 2.85
1075 3376 1.550327 TCGCACTCTCCAGAGACATT 58.450 50.000 10.68 0.00 44.74 2.71
1077 3378 1.098869 GATCGCACTCTCCAGAGACA 58.901 55.000 10.68 0.00 44.74 3.41
1079 3380 0.393132 ACGATCGCACTCTCCAGAGA 60.393 55.000 16.60 1.33 44.74 3.10
1111 3412 3.931631 CTCCAGGACCAGCCCCAGA 62.932 68.421 0.00 0.00 37.37 3.86
1136 3437 1.192146 TCCACGCCCTCTACTTGCTT 61.192 55.000 0.00 0.00 0.00 3.91
1216 3517 2.575694 AGTTTGCGCATTGAAACACA 57.424 40.000 21.16 0.00 35.00 3.72
1225 3526 1.174712 AGCCACAGAAGTTTGCGCAT 61.175 50.000 12.75 0.00 0.00 4.73
1319 4039 4.993028 AGTATATGAGACAGGAGGGAGTC 58.007 47.826 0.00 0.00 35.02 3.36
1393 4118 6.073548 CCTCCTCATATTAATTGTCGCTCAAC 60.074 42.308 0.00 0.00 38.97 3.18
1415 4140 6.472887 ACTGAGAGAGTAGCATATACTCCTC 58.527 44.000 17.50 17.50 43.61 3.71
1416 4141 6.448369 ACTGAGAGAGTAGCATATACTCCT 57.552 41.667 10.61 8.08 43.61 3.69
1444 4169 7.830201 AGATAGTATATACTTCCTTCGTCCCAG 59.170 40.741 20.21 0.00 37.73 4.45
1489 4214 7.669722 ACTTGGGAAAATACTCTTTTAGCATCA 59.330 33.333 0.00 0.00 0.00 3.07
1493 4218 9.622004 GTAAACTTGGGAAAATACTCTTTTAGC 57.378 33.333 0.00 0.00 0.00 3.09
1588 4329 1.732941 TCGGGATCGTGGAAACATTG 58.267 50.000 0.00 0.00 46.14 2.82
1599 4340 3.581755 TCACAACTACTTTTCGGGATCG 58.418 45.455 0.00 0.00 37.82 3.69
1635 4377 5.801350 TCATCTGCCAAAACGAAATAGAG 57.199 39.130 0.00 0.00 0.00 2.43
1840 4584 9.213799 GAGTTTCACATAGAGTTTCATCTCTTT 57.786 33.333 1.61 0.00 43.46 2.52
1868 4612 2.315925 ACTATCACAAGCATCACCGG 57.684 50.000 0.00 0.00 0.00 5.28
1953 4697 5.534207 AACTTTGGCATGTGAGATTTCAA 57.466 34.783 0.00 0.00 34.49 2.69
1960 4704 4.201753 CGAGACATAACTTTGGCATGTGAG 60.202 45.833 0.00 0.00 33.16 3.51
1966 4710 1.003118 AGGCGAGACATAACTTTGGCA 59.997 47.619 0.00 0.00 0.00 4.92
2021 4765 0.750182 AACCGACACACTGGTTTGGG 60.750 55.000 0.00 0.00 46.04 4.12
2037 4781 4.932146 ACAGACAAGCACATAAACAAACC 58.068 39.130 0.00 0.00 0.00 3.27
2056 4800 6.303259 GCAACTAGCAACGAAAGAAAATACAG 59.697 38.462 0.00 0.00 44.79 2.74
2077 4821 9.669353 CACCATGATATCTTTTATTGTAGCAAC 57.331 33.333 3.98 0.00 0.00 4.17
2078 4822 8.849168 CCACCATGATATCTTTTATTGTAGCAA 58.151 33.333 3.98 0.00 0.00 3.91
2079 4823 8.217111 TCCACCATGATATCTTTTATTGTAGCA 58.783 33.333 3.98 0.00 0.00 3.49
2080 4824 8.621532 TCCACCATGATATCTTTTATTGTAGC 57.378 34.615 3.98 0.00 0.00 3.58
2082 4826 9.013229 GCATCCACCATGATATCTTTTATTGTA 57.987 33.333 3.98 0.00 33.80 2.41
2083 4827 7.039504 GGCATCCACCATGATATCTTTTATTGT 60.040 37.037 3.98 0.00 33.80 2.71
2158 4902 5.411669 GGGTTCATATGTACCCGAATTCATC 59.588 44.000 28.62 8.38 44.05 2.92
2159 4903 5.313712 GGGTTCATATGTACCCGAATTCAT 58.686 41.667 28.62 0.00 44.05 2.57
2160 4904 4.710324 GGGTTCATATGTACCCGAATTCA 58.290 43.478 28.62 0.00 44.05 2.57
2168 4912 8.931775 GTTTTTCAAAATGGGTTCATATGTACC 58.068 33.333 20.26 20.26 35.09 3.34
2169 4913 9.482627 TGTTTTTCAAAATGGGTTCATATGTAC 57.517 29.630 1.90 3.04 32.44 2.90
2170 4914 9.482627 GTGTTTTTCAAAATGGGTTCATATGTA 57.517 29.630 1.90 0.00 32.44 2.29
2171 4915 7.989741 TGTGTTTTTCAAAATGGGTTCATATGT 59.010 29.630 1.90 0.00 32.44 2.29
2172 4916 8.375608 TGTGTTTTTCAAAATGGGTTCATATG 57.624 30.769 0.00 0.00 32.44 1.78
2173 4917 9.571816 AATGTGTTTTTCAAAATGGGTTCATAT 57.428 25.926 0.00 0.00 32.44 1.78
2174 4918 8.970859 AATGTGTTTTTCAAAATGGGTTCATA 57.029 26.923 0.00 0.00 32.44 2.15
2175 4919 7.878547 AATGTGTTTTTCAAAATGGGTTCAT 57.121 28.000 0.00 0.00 34.56 2.57
2176 4920 7.609532 AGAAATGTGTTTTTCAAAATGGGTTCA 59.390 29.630 0.00 0.00 37.93 3.18
2177 4921 7.984391 AGAAATGTGTTTTTCAAAATGGGTTC 58.016 30.769 0.00 0.00 37.93 3.62
2178 4922 7.936496 AGAAATGTGTTTTTCAAAATGGGTT 57.064 28.000 0.00 0.00 37.93 4.11
2179 4923 9.454859 TTTAGAAATGTGTTTTTCAAAATGGGT 57.545 25.926 0.00 0.00 37.93 4.51
2205 4949 8.773645 GCAACCTTTTTCAGTTTATTTTAGCAT 58.226 29.630 0.00 0.00 0.00 3.79
2206 4950 7.766278 TGCAACCTTTTTCAGTTTATTTTAGCA 59.234 29.630 0.00 0.00 0.00 3.49
2207 4951 8.061857 GTGCAACCTTTTTCAGTTTATTTTAGC 58.938 33.333 0.00 0.00 0.00 3.09
2208 4952 8.265998 CGTGCAACCTTTTTCAGTTTATTTTAG 58.734 33.333 0.00 0.00 0.00 1.85
2209 4953 7.222999 CCGTGCAACCTTTTTCAGTTTATTTTA 59.777 33.333 0.00 0.00 0.00 1.52
2210 4954 6.036626 CCGTGCAACCTTTTTCAGTTTATTTT 59.963 34.615 0.00 0.00 0.00 1.82
2211 4955 5.522097 CCGTGCAACCTTTTTCAGTTTATTT 59.478 36.000 0.00 0.00 0.00 1.40
2212 4956 5.047188 CCGTGCAACCTTTTTCAGTTTATT 58.953 37.500 0.00 0.00 0.00 1.40
2213 4957 4.339814 TCCGTGCAACCTTTTTCAGTTTAT 59.660 37.500 0.00 0.00 0.00 1.40
2214 4958 3.695060 TCCGTGCAACCTTTTTCAGTTTA 59.305 39.130 0.00 0.00 0.00 2.01
2215 4959 2.494073 TCCGTGCAACCTTTTTCAGTTT 59.506 40.909 0.00 0.00 0.00 2.66
2216 4960 2.096248 TCCGTGCAACCTTTTTCAGTT 58.904 42.857 0.00 0.00 0.00 3.16
2217 4961 1.676006 CTCCGTGCAACCTTTTTCAGT 59.324 47.619 0.00 0.00 0.00 3.41
2218 4962 1.946768 TCTCCGTGCAACCTTTTTCAG 59.053 47.619 0.00 0.00 0.00 3.02
2219 4963 1.673920 GTCTCCGTGCAACCTTTTTCA 59.326 47.619 0.00 0.00 0.00 2.69
2220 4964 1.333791 CGTCTCCGTGCAACCTTTTTC 60.334 52.381 0.00 0.00 0.00 2.29
2221 4965 0.661020 CGTCTCCGTGCAACCTTTTT 59.339 50.000 0.00 0.00 0.00 1.94
2222 4966 1.782028 GCGTCTCCGTGCAACCTTTT 61.782 55.000 0.00 0.00 36.15 2.27
2223 4967 2.251642 GCGTCTCCGTGCAACCTTT 61.252 57.895 0.00 0.00 36.15 3.11
2224 4968 2.665185 GCGTCTCCGTGCAACCTT 60.665 61.111 0.00 0.00 36.15 3.50
2225 4969 4.681978 GGCGTCTCCGTGCAACCT 62.682 66.667 0.00 0.00 36.15 3.50
2226 4970 4.681978 AGGCGTCTCCGTGCAACC 62.682 66.667 0.00 0.00 40.77 3.77
2227 4971 2.665185 AAGGCGTCTCCGTGCAAC 60.665 61.111 0.00 0.00 40.77 4.17
2228 4972 2.357034 GAAGGCGTCTCCGTGCAA 60.357 61.111 0.00 0.00 40.77 4.08
2229 4973 2.942796 ATGAAGGCGTCTCCGTGCA 61.943 57.895 1.41 0.00 40.77 4.57
2230 4974 2.125512 ATGAAGGCGTCTCCGTGC 60.126 61.111 1.41 0.00 40.77 5.34
2231 4975 1.079819 ACATGAAGGCGTCTCCGTG 60.080 57.895 0.00 0.00 40.77 4.94
2232 4976 1.079819 CACATGAAGGCGTCTCCGT 60.080 57.895 0.00 0.00 40.77 4.69
2233 4977 0.670546 AACACATGAAGGCGTCTCCG 60.671 55.000 0.00 0.00 40.77 4.63
2234 4978 1.523758 AAACACATGAAGGCGTCTCC 58.476 50.000 0.00 0.00 0.00 3.71
2235 4979 3.684788 ACATAAACACATGAAGGCGTCTC 59.315 43.478 0.00 0.00 0.00 3.36
2236 4980 3.436704 CACATAAACACATGAAGGCGTCT 59.563 43.478 0.00 0.00 0.00 4.18
2237 4981 3.747193 CACATAAACACATGAAGGCGTC 58.253 45.455 0.00 0.00 0.00 5.19
2238 4982 2.095263 GCACATAAACACATGAAGGCGT 60.095 45.455 0.00 0.00 0.00 5.68
2239 4983 2.518949 GCACATAAACACATGAAGGCG 58.481 47.619 0.00 0.00 0.00 5.52
2240 4984 2.095263 ACGCACATAAACACATGAAGGC 60.095 45.455 0.00 0.00 0.00 4.35
2241 4985 3.491356 CACGCACATAAACACATGAAGG 58.509 45.455 0.00 0.00 0.00 3.46
2242 4986 2.910482 GCACGCACATAAACACATGAAG 59.090 45.455 0.00 0.00 0.00 3.02
2243 4987 2.291741 TGCACGCACATAAACACATGAA 59.708 40.909 0.00 0.00 0.00 2.57
2244 4988 1.876156 TGCACGCACATAAACACATGA 59.124 42.857 0.00 0.00 0.00 3.07
2245 4989 2.328655 TGCACGCACATAAACACATG 57.671 45.000 0.00 0.00 0.00 3.21
2246 4990 4.693538 TTATGCACGCACATAAACACAT 57.306 36.364 7.94 0.00 39.07 3.21
2247 4991 4.023622 ACTTTATGCACGCACATAAACACA 60.024 37.500 15.64 1.48 43.90 3.72
2248 4992 4.472286 ACTTTATGCACGCACATAAACAC 58.528 39.130 15.64 0.00 43.90 3.32
2249 4993 4.757799 ACTTTATGCACGCACATAAACA 57.242 36.364 15.64 2.31 43.90 2.83
2250 4994 5.219768 CGAAACTTTATGCACGCACATAAAC 60.220 40.000 15.64 8.32 43.90 2.01
2251 4995 4.848841 CGAAACTTTATGCACGCACATAAA 59.151 37.500 17.56 17.56 45.59 1.40
2252 4996 4.083749 ACGAAACTTTATGCACGCACATAA 60.084 37.500 6.61 6.61 40.00 1.90
2253 4997 3.433957 ACGAAACTTTATGCACGCACATA 59.566 39.130 0.00 0.00 0.00 2.29
2254 4998 2.225491 ACGAAACTTTATGCACGCACAT 59.775 40.909 0.00 0.00 0.00 3.21
2255 4999 1.600013 ACGAAACTTTATGCACGCACA 59.400 42.857 0.00 0.00 0.00 4.57
2256 5000 1.969256 CACGAAACTTTATGCACGCAC 59.031 47.619 0.00 0.00 0.00 5.34
2257 5001 1.069568 CCACGAAACTTTATGCACGCA 60.070 47.619 0.00 0.00 0.00 5.24
2258 5002 1.195900 TCCACGAAACTTTATGCACGC 59.804 47.619 0.00 0.00 0.00 5.34
2259 5003 3.529634 TTCCACGAAACTTTATGCACG 57.470 42.857 0.00 0.00 0.00 5.34
2260 5004 6.763303 ATTTTTCCACGAAACTTTATGCAC 57.237 33.333 0.00 0.00 30.83 4.57
2261 5005 9.482627 AATTATTTTTCCACGAAACTTTATGCA 57.517 25.926 0.00 0.00 30.83 3.96
2359 5103 3.562141 TCTTCGATTTGTCTCCGCAAAAA 59.438 39.130 0.00 0.00 41.03 1.94
2360 5104 3.135225 TCTTCGATTTGTCTCCGCAAAA 58.865 40.909 0.00 0.00 41.03 2.44
2361 5105 2.736721 CTCTTCGATTTGTCTCCGCAAA 59.263 45.455 0.00 0.00 41.77 3.68
2362 5106 2.029380 TCTCTTCGATTTGTCTCCGCAA 60.029 45.455 0.00 0.00 0.00 4.85
2363 5107 1.544246 TCTCTTCGATTTGTCTCCGCA 59.456 47.619 0.00 0.00 0.00 5.69
2364 5108 1.921230 GTCTCTTCGATTTGTCTCCGC 59.079 52.381 0.00 0.00 0.00 5.54
2365 5109 3.217599 TGTCTCTTCGATTTGTCTCCG 57.782 47.619 0.00 0.00 0.00 4.63
2366 5110 6.487689 AAAATGTCTCTTCGATTTGTCTCC 57.512 37.500 0.00 0.00 0.00 3.71
2395 5139 3.041874 TGCACGGCACAAAGTTTTG 57.958 47.368 3.17 3.17 43.62 2.44
2412 5156 8.829612 ACATATACATGTTCACATATGTGTGTG 58.170 33.333 30.03 24.28 45.00 3.82
2413 5157 8.962884 ACATATACATGTTCACATATGTGTGT 57.037 30.769 30.03 27.01 45.00 3.72
2478 5222 9.566432 ACCCACTTTTTGAAATATGCATTTTAA 57.434 25.926 3.54 0.00 34.44 1.52
2479 5223 8.997323 CACCCACTTTTTGAAATATGCATTTTA 58.003 29.630 3.54 0.00 34.44 1.52
2480 5224 7.521910 GCACCCACTTTTTGAAATATGCATTTT 60.522 33.333 3.54 0.00 34.44 1.82
2481 5225 6.072563 GCACCCACTTTTTGAAATATGCATTT 60.073 34.615 3.54 0.00 37.06 2.32
2482 5226 5.412286 GCACCCACTTTTTGAAATATGCATT 59.588 36.000 3.54 0.00 0.00 3.56
2483 5227 4.937015 GCACCCACTTTTTGAAATATGCAT 59.063 37.500 3.79 3.79 0.00 3.96
2484 5228 4.202295 TGCACCCACTTTTTGAAATATGCA 60.202 37.500 0.00 0.00 37.03 3.96
2485 5229 4.314121 TGCACCCACTTTTTGAAATATGC 58.686 39.130 0.00 0.00 0.00 3.14
2486 5230 7.254522 GCATATGCACCCACTTTTTGAAATATG 60.255 37.037 22.84 0.00 41.59 1.78
2487 5231 6.762661 GCATATGCACCCACTTTTTGAAATAT 59.237 34.615 22.84 0.00 41.59 1.28
2488 5232 6.105333 GCATATGCACCCACTTTTTGAAATA 58.895 36.000 22.84 0.00 41.59 1.40
2489 5233 4.937015 GCATATGCACCCACTTTTTGAAAT 59.063 37.500 22.84 0.00 41.59 2.17
2490 5234 4.314121 GCATATGCACCCACTTTTTGAAA 58.686 39.130 22.84 0.00 41.59 2.69
2491 5235 3.306641 GGCATATGCACCCACTTTTTGAA 60.307 43.478 28.07 0.00 44.36 2.69
2492 5236 2.233431 GGCATATGCACCCACTTTTTGA 59.767 45.455 28.07 0.00 44.36 2.69
2493 5237 2.620242 GGCATATGCACCCACTTTTTG 58.380 47.619 28.07 0.00 44.36 2.44
2494 5238 1.554617 GGGCATATGCACCCACTTTTT 59.445 47.619 28.07 0.00 46.22 1.94
2495 5239 1.194218 GGGCATATGCACCCACTTTT 58.806 50.000 28.07 0.00 46.22 2.27
2496 5240 2.900547 GGGCATATGCACCCACTTT 58.099 52.632 28.07 0.00 46.22 2.66
2497 5241 4.684623 GGGCATATGCACCCACTT 57.315 55.556 28.07 0.00 46.22 3.16
2501 5245 0.393820 CCAAATGGGCATATGCACCC 59.606 55.000 26.74 19.95 45.73 4.61
2502 5246 1.122227 ACCAAATGGGCATATGCACC 58.878 50.000 26.74 23.82 45.73 5.01
2503 5247 2.168106 TGAACCAAATGGGCATATGCAC 59.832 45.455 28.07 25.88 46.69 4.57
2504 5248 2.431419 CTGAACCAAATGGGCATATGCA 59.569 45.455 28.07 10.14 44.36 3.96
2505 5249 2.224113 CCTGAACCAAATGGGCATATGC 60.224 50.000 19.79 19.79 42.05 3.14
2506 5250 3.068590 GTCCTGAACCAAATGGGCATATG 59.931 47.826 4.17 0.00 42.05 1.78
2507 5251 3.299503 GTCCTGAACCAAATGGGCATAT 58.700 45.455 4.17 0.00 42.05 1.78
2508 5252 2.733956 GTCCTGAACCAAATGGGCATA 58.266 47.619 4.17 0.00 42.05 3.14
2509 5253 1.560505 GTCCTGAACCAAATGGGCAT 58.439 50.000 4.17 0.00 42.05 4.40
2510 5254 0.893270 CGTCCTGAACCAAATGGGCA 60.893 55.000 4.17 1.07 42.05 5.36
2511 5255 0.893727 ACGTCCTGAACCAAATGGGC 60.894 55.000 4.17 0.00 42.05 5.36
2512 5256 0.881118 CACGTCCTGAACCAAATGGG 59.119 55.000 4.17 0.00 44.81 4.00
2513 5257 0.240945 GCACGTCCTGAACCAAATGG 59.759 55.000 0.00 0.00 42.17 3.16
2514 5258 0.240945 GGCACGTCCTGAACCAAATG 59.759 55.000 0.00 0.00 0.00 2.32
2515 5259 2.641197 GGCACGTCCTGAACCAAAT 58.359 52.632 0.00 0.00 0.00 2.32
2516 5260 4.150994 GGCACGTCCTGAACCAAA 57.849 55.556 0.00 0.00 0.00 3.28
2529 5273 1.134699 TCTCAATCATGGAGTCGGCAC 60.135 52.381 0.00 0.00 34.04 5.01
2530 5274 1.194218 TCTCAATCATGGAGTCGGCA 58.806 50.000 0.00 0.00 34.04 5.69
2531 5275 2.540265 ATCTCAATCATGGAGTCGGC 57.460 50.000 0.00 0.00 34.04 5.54
2532 5276 9.689976 GATATTATATCTCAATCATGGAGTCGG 57.310 37.037 5.06 0.00 34.04 4.79
2575 5319 9.720874 ATATGCTCAGAGTTTATATCCATAGGA 57.279 33.333 0.00 0.00 35.55 2.94
2603 5349 4.935808 AGGTCCAAAGAATATCACGTGAAC 59.064 41.667 24.13 11.56 0.00 3.18
2604 5350 5.160607 AGGTCCAAAGAATATCACGTGAA 57.839 39.130 24.13 12.36 0.00 3.18
2607 5353 9.326413 CTAATTAAGGTCCAAAGAATATCACGT 57.674 33.333 0.00 0.00 0.00 4.49
2608 5354 8.774586 CCTAATTAAGGTCCAAAGAATATCACG 58.225 37.037 0.00 0.00 40.94 4.35
2645 5401 3.016031 ACAGCACAGACATCAAACAACA 58.984 40.909 0.00 0.00 0.00 3.33
2658 5414 4.487948 CCATTTCATGGTTTACAGCACAG 58.512 43.478 0.00 0.00 45.54 3.66
2686 5442 5.863935 AGAGCTAATTGAAAATGCGGAAAAC 59.136 36.000 0.00 0.00 0.00 2.43
2706 5462 8.279103 GCATATCAACAAAATACTGTAGAGAGC 58.721 37.037 0.00 0.00 0.00 4.09
2708 5464 7.438160 CGGCATATCAACAAAATACTGTAGAGA 59.562 37.037 0.00 0.00 0.00 3.10
2711 5467 6.293407 CCCGGCATATCAACAAAATACTGTAG 60.293 42.308 0.00 0.00 0.00 2.74
2712 5468 5.529430 CCCGGCATATCAACAAAATACTGTA 59.471 40.000 0.00 0.00 0.00 2.74
2713 5469 4.338118 CCCGGCATATCAACAAAATACTGT 59.662 41.667 0.00 0.00 0.00 3.55
2721 5480 2.208132 AACACCCGGCATATCAACAA 57.792 45.000 0.00 0.00 0.00 2.83
2745 5504 4.681483 CGGATTGTCTTTTCAAAAAGGAGC 59.319 41.667 13.68 6.82 44.22 4.70
2758 5517 6.545666 TGCCATAAATATGAACGGATTGTCTT 59.454 34.615 1.98 0.00 35.75 3.01
2762 5521 6.023435 CGATGCCATAAATATGAACGGATTG 58.977 40.000 1.98 0.00 35.75 2.67
2765 5524 4.888917 TCGATGCCATAAATATGAACGGA 58.111 39.130 1.98 0.00 35.75 4.69
2766 5525 5.351189 TGATCGATGCCATAAATATGAACGG 59.649 40.000 0.54 0.00 35.75 4.44
2767 5526 6.407475 TGATCGATGCCATAAATATGAACG 57.593 37.500 0.54 0.00 35.75 3.95
2771 5538 8.077991 ACTTGTTTGATCGATGCCATAAATATG 58.922 33.333 0.54 0.96 0.00 1.78
2782 5549 2.096496 GCCCAGACTTGTTTGATCGATG 59.904 50.000 0.54 0.00 0.00 3.84
2787 5554 4.532521 AGTAGTAGCCCAGACTTGTTTGAT 59.467 41.667 0.00 0.00 0.00 2.57
2814 5581 2.165437 GCAGAAAATGGGCGGTTTCATA 59.835 45.455 8.32 0.00 36.41 2.15
2845 5612 3.119459 ACTTCTATGCGTCGAACATGTCT 60.119 43.478 11.45 0.00 0.00 3.41
2904 5777 2.835156 TGGAGACATGGTGGAAATACGA 59.165 45.455 0.00 0.00 33.40 3.43
2950 5823 0.041926 GTTTAAGCGCGACCGTTGTT 60.042 50.000 12.10 0.00 36.67 2.83
2951 5824 1.152989 TGTTTAAGCGCGACCGTTGT 61.153 50.000 12.10 0.00 36.67 3.32
2957 5830 2.095843 CGCCTGTTTAAGCGCGAC 59.904 61.111 12.10 0.04 46.50 5.19
2970 5843 7.986085 AAATATATATCAAAAGTGCTCGCCT 57.014 32.000 0.00 0.00 0.00 5.52
2972 5845 9.922305 GGATAAATATATATCAAAAGTGCTCGC 57.078 33.333 0.00 0.00 34.58 5.03


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

AutoCloner maintained by Alex Coulton.