Multiple sequence alignment - TraesCS3B01G048100

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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 TraesCS3B01G048100 chr3B 100.000 3648 0 0 1 3648 24384911 24388558 0.000000e+00 6737.0
1 TraesCS3B01G048100 chr3D 90.961 2102 129 25 1563 3648 16990528 16992584 0.000000e+00 2772.0
2 TraesCS3B01G048100 chr3D 95.255 548 23 3 926 1473 16989963 16990507 0.000000e+00 865.0
3 TraesCS3B01G048100 chr3D 87.865 684 67 11 1 678 16987008 16987681 0.000000e+00 789.0
4 TraesCS3B01G048100 chr3D 83.007 153 12 9 2314 2457 570054804 570054951 3.820000e-25 126.0
5 TraesCS3B01G048100 chr3D 92.754 69 4 1 1943 2011 16990972 16991039 8.340000e-17 99.0
6 TraesCS3B01G048100 chr3A 91.121 1284 78 15 1559 2828 19881658 19880397 0.000000e+00 1707.0
7 TraesCS3B01G048100 chr3A 85.494 1103 77 39 386 1478 19882817 19881788 0.000000e+00 1074.0
8 TraesCS3B01G048100 chr3A 88.509 409 45 2 1 408 19883051 19883458 9.100000e-136 494.0
9 TraesCS3B01G048100 chr3A 89.855 69 6 1 1943 2011 19881212 19881145 1.800000e-13 87.9
10 TraesCS3B01G048100 chr3A 83.333 78 8 3 1998 2074 19881281 19881208 2.350000e-07 67.6
11 TraesCS3B01G048100 chr6A 86.632 389 33 14 2106 2481 17939254 17939636 2.620000e-111 412.0
12 TraesCS3B01G048100 chr6D 73.449 693 109 44 2571 3229 17314173 17314824 1.340000e-44 191.0
13 TraesCS3B01G048100 chr6D 91.139 79 7 0 1 79 306067445 306067367 1.390000e-19 108.0
14 TraesCS3B01G048100 chr4A 93.407 91 6 0 2372 2462 533588065 533588155 6.350000e-28 135.0
15 TraesCS3B01G048100 chr4A 91.026 78 7 0 2 79 734418876 734418953 4.980000e-19 106.0
16 TraesCS3B01G048100 chr4A 89.873 79 8 0 1 79 572224210 572224132 6.440000e-18 102.0
17 TraesCS3B01G048100 chr1B 83.766 154 9 10 2314 2457 223365574 223365427 8.220000e-27 132.0
18 TraesCS3B01G048100 chr2A 81.699 153 14 8 2314 2457 595814143 595813996 8.280000e-22 115.0
19 TraesCS3B01G048100 chr2A 81.046 153 15 8 2314 2457 595854858 595854711 3.850000e-20 110.0
20 TraesCS3B01G048100 chr5A 81.046 153 15 8 2314 2457 269760079 269760226 3.850000e-20 110.0
21 TraesCS3B01G048100 chr7A 91.139 79 7 0 1 79 572844369 572844447 1.390000e-19 108.0
22 TraesCS3B01G048100 chr4D 91.139 79 7 0 1 79 378872165 378872243 1.390000e-19 108.0
23 TraesCS3B01G048100 chr4B 91.139 79 7 0 1 79 652239659 652239737 1.390000e-19 108.0
24 TraesCS3B01G048100 chr1A 91.139 79 7 0 1 79 104869388 104869466 1.390000e-19 108.0


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 TraesCS3B01G048100 chr3B 24384911 24388558 3647 False 6737.000 6737 100.00000 1 3648 1 chr3B.!!$F1 3647
1 TraesCS3B01G048100 chr3D 16987008 16992584 5576 False 1131.250 2772 91.70875 1 3648 4 chr3D.!!$F2 3647
2 TraesCS3B01G048100 chr3A 19880397 19882817 2420 True 734.125 1707 87.45075 386 2828 4 chr3A.!!$R1 2442

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
739 2759 0.397254 TCACTGCTAGAGGGTAGGCC 60.397 60.0 0.0 0.0 0.00 5.19 F
1385 3513 0.179468 GCCTCCCGCATGGTAAGTTA 59.821 55.0 0.0 0.0 37.47 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 4601 1.079819 CGGAGTCCGCACAACAGAT 60.080 57.895 20.5 0.0 41.17 2.9 R
3231 5427 0.100503 CCACGAATCAAAATCGGCCC 59.899 55.000 0.0 0.0 44.32 5.8 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
35 36 2.271800 CCACTAGTGGTTGAGAATCGC 58.728 52.381 30.57 0.00 45.53 4.58
39 40 2.568623 AGTGGTTGAGAATCGCCTTT 57.431 45.000 0.00 0.00 38.61 3.11
41 42 0.881118 TGGTTGAGAATCGCCTTTGC 59.119 50.000 0.00 0.00 38.61 3.68
61 62 7.605691 CCTTTGCGATATTATCTCAAGGAGAAT 59.394 37.037 15.97 0.00 42.27 2.40
66 67 7.692908 GATATTATCTCAAGGAGAATAGCGC 57.307 40.000 0.00 0.00 42.27 5.92
97 98 4.804139 CGTGGTAATACACATCTCTCCAAC 59.196 45.833 0.00 0.00 41.38 3.77
107 108 3.067461 ACATCTCTCCAACGATGACTAGC 59.933 47.826 6.29 0.00 39.43 3.42
112 113 1.134367 TCCAACGATGACTAGCTTCCG 59.866 52.381 0.00 0.00 0.00 4.30
118 119 3.693085 ACGATGACTAGCTTCCGTCTAAA 59.307 43.478 0.00 0.00 0.00 1.85
123 124 4.765856 TGACTAGCTTCCGTCTAAAGAAGT 59.234 41.667 0.00 0.00 41.29 3.01
137 138 9.254133 CGTCTAAAGAAGTGAACATCATGATAT 57.746 33.333 8.15 0.00 0.00 1.63
155 156 9.778741 TCATGATATATCCTTGTCTTTGGTTAC 57.221 33.333 10.25 0.00 0.00 2.50
202 203 5.335661 GCGGTTTACTTTGATCATTTGACCT 60.336 40.000 0.00 0.00 0.00 3.85
243 244 8.902540 TGATTGTTTATCTCGCCATAGTTATT 57.097 30.769 0.00 0.00 34.17 1.40
244 245 9.337396 TGATTGTTTATCTCGCCATAGTTATTT 57.663 29.630 0.00 0.00 34.17 1.40
273 274 5.428253 ACACACCTTTATATTCTGCATCGT 58.572 37.500 0.00 0.00 0.00 3.73
285 286 4.450082 TCTGCATCGTCTAAACTTGCTA 57.550 40.909 0.00 0.00 34.84 3.49
295 296 8.766000 TCGTCTAAACTTGCTAATAATCAACA 57.234 30.769 0.00 0.00 0.00 3.33
324 325 8.706322 AAATATGTATTTGTCCCTATTCACCC 57.294 34.615 0.00 0.00 34.79 4.61
325 326 4.513406 TGTATTTGTCCCTATTCACCCC 57.487 45.455 0.00 0.00 0.00 4.95
335 336 1.276140 TATTCACCCCCGTCCCCTTG 61.276 60.000 0.00 0.00 0.00 3.61
344 345 3.007542 GTCCCCTTGGGTCCATCC 58.992 66.667 4.84 0.00 44.74 3.51
345 346 1.928567 GTCCCCTTGGGTCCATCCA 60.929 63.158 4.84 0.00 44.74 3.41
354 355 1.846439 TGGGTCCATCCAGATCCTTTC 59.154 52.381 0.00 0.00 37.96 2.62
355 356 1.846439 GGGTCCATCCAGATCCTTTCA 59.154 52.381 0.00 0.00 33.89 2.69
366 367 3.436704 CAGATCCTTTCAGCGTTGCTAAA 59.563 43.478 0.00 0.00 36.40 1.85
376 377 2.685897 AGCGTTGCTAAAAGACCAAACA 59.314 40.909 0.00 0.00 36.99 2.83
423 424 0.459489 GCCCATTAGCGATTTTGCCA 59.541 50.000 0.00 0.00 34.65 4.92
438 439 5.429681 TTTTGCCAACCTACTGCTATAGA 57.570 39.130 3.21 0.00 0.00 1.98
447 448 6.927294 ACCTACTGCTATAGAATTTTGTGC 57.073 37.500 3.21 0.00 0.00 4.57
448 449 6.414732 ACCTACTGCTATAGAATTTTGTGCA 58.585 36.000 3.21 0.00 0.00 4.57
507 509 0.468400 AAGTTTTTGCCGGGCCACTA 60.468 50.000 17.97 0.00 0.00 2.74
515 517 1.833049 CCGGGCCACTACTAGAGGG 60.833 68.421 4.39 0.00 0.00 4.30
560 565 5.422214 ACCAGCTACTGTGCTACTAAAAT 57.578 39.130 4.79 0.00 41.98 1.82
660 665 8.817092 AAATGTCCCGAAATTTAAGAATAGGA 57.183 30.769 0.00 0.00 0.00 2.94
701 2721 5.482908 AGAATAGGATTTGCCGTATAGCAG 58.517 41.667 0.00 0.00 45.13 4.24
735 2755 4.184649 TCATCATCACTGCTAGAGGGTA 57.815 45.455 0.00 0.00 0.00 3.69
739 2759 0.397254 TCACTGCTAGAGGGTAGGCC 60.397 60.000 0.00 0.00 0.00 5.19
793 2815 4.331968 TCGGCTTGTAGACAAATGGAAAT 58.668 39.130 0.00 0.00 35.15 2.17
807 2869 8.055279 ACAAATGGAAATTAGATATATGCCGG 57.945 34.615 0.00 0.00 0.00 6.13
847 2967 0.865769 AACGCACGGATTGTCTCAAC 59.134 50.000 0.00 0.00 0.00 3.18
848 2968 0.949105 ACGCACGGATTGTCTCAACC 60.949 55.000 0.00 0.00 0.00 3.77
851 2971 1.606668 GCACGGATTGTCTCAACCAAA 59.393 47.619 0.00 0.00 0.00 3.28
878 2998 4.329462 AAAAGAGAGAGAGAAACAGCGT 57.671 40.909 0.00 0.00 0.00 5.07
879 2999 5.455056 AAAAGAGAGAGAGAAACAGCGTA 57.545 39.130 0.00 0.00 0.00 4.42
880 3000 4.428615 AAGAGAGAGAGAAACAGCGTAC 57.571 45.455 0.00 0.00 0.00 3.67
881 3001 3.413327 AGAGAGAGAGAAACAGCGTACA 58.587 45.455 0.00 0.00 0.00 2.90
1214 3334 1.004918 CGACAACTTCTCCGCCCTT 60.005 57.895 0.00 0.00 0.00 3.95
1382 3510 2.588877 CGCCTCCCGCATGGTAAG 60.589 66.667 0.00 0.00 37.30 2.34
1383 3511 2.590092 GCCTCCCGCATGGTAAGT 59.410 61.111 0.00 0.00 37.47 2.24
1384 3512 1.077716 GCCTCCCGCATGGTAAGTT 60.078 57.895 0.00 0.00 37.47 2.66
1385 3513 0.179468 GCCTCCCGCATGGTAAGTTA 59.821 55.000 0.00 0.00 37.47 2.24
1387 3515 1.485066 CCTCCCGCATGGTAAGTTAGT 59.515 52.381 0.00 0.00 34.77 2.24
1388 3516 2.696707 CCTCCCGCATGGTAAGTTAGTA 59.303 50.000 0.00 0.00 34.77 1.82
1389 3517 3.133362 CCTCCCGCATGGTAAGTTAGTAA 59.867 47.826 0.00 0.00 34.77 2.24
1390 3518 4.117685 CTCCCGCATGGTAAGTTAGTAAC 58.882 47.826 4.78 4.78 34.77 2.50
1391 3519 2.861935 CCCGCATGGTAAGTTAGTAACG 59.138 50.000 7.38 0.00 36.23 3.18
1392 3520 3.429272 CCCGCATGGTAAGTTAGTAACGA 60.429 47.826 7.38 0.00 36.23 3.85
1393 3521 3.549070 CCGCATGGTAAGTTAGTAACGAC 59.451 47.826 7.38 9.41 36.23 4.34
1394 3522 3.239026 CGCATGGTAAGTTAGTAACGACG 59.761 47.826 7.38 0.00 36.23 5.12
1395 3523 4.414852 GCATGGTAAGTTAGTAACGACGA 58.585 43.478 0.00 7.62 36.23 4.20
1447 3575 5.278512 GGAGATTTGTTTCTTCCCACTGTTC 60.279 44.000 0.00 0.00 0.00 3.18
1448 3576 4.275936 AGATTTGTTTCTTCCCACTGTTCG 59.724 41.667 0.00 0.00 0.00 3.95
1483 3616 3.821841 CAAAATTGGAGTCGTGCCTTAC 58.178 45.455 0.00 0.00 0.00 2.34
1489 3622 2.000447 GGAGTCGTGCCTTACATCAAC 59.000 52.381 0.00 0.00 0.00 3.18
1490 3623 2.611971 GGAGTCGTGCCTTACATCAACA 60.612 50.000 0.00 0.00 0.00 3.33
1493 3626 1.155889 CGTGCCTTACATCAACAGCA 58.844 50.000 0.00 0.00 0.00 4.41
1497 3630 1.885887 GCCTTACATCAACAGCACCAA 59.114 47.619 0.00 0.00 0.00 3.67
1498 3631 2.095059 GCCTTACATCAACAGCACCAAG 60.095 50.000 0.00 0.00 0.00 3.61
1499 3632 3.149196 CCTTACATCAACAGCACCAAGT 58.851 45.455 0.00 0.00 0.00 3.16
1501 3634 2.346766 ACATCAACAGCACCAAGTCA 57.653 45.000 0.00 0.00 0.00 3.41
1502 3635 2.867624 ACATCAACAGCACCAAGTCAT 58.132 42.857 0.00 0.00 0.00 3.06
1505 3638 5.012239 ACATCAACAGCACCAAGTCATTAT 58.988 37.500 0.00 0.00 0.00 1.28
1506 3639 6.179756 ACATCAACAGCACCAAGTCATTATA 58.820 36.000 0.00 0.00 0.00 0.98
1507 3640 6.094048 ACATCAACAGCACCAAGTCATTATAC 59.906 38.462 0.00 0.00 0.00 1.47
1508 3641 5.555966 TCAACAGCACCAAGTCATTATACA 58.444 37.500 0.00 0.00 0.00 2.29
1509 3642 6.000840 TCAACAGCACCAAGTCATTATACAA 58.999 36.000 0.00 0.00 0.00 2.41
1510 3643 6.149308 TCAACAGCACCAAGTCATTATACAAG 59.851 38.462 0.00 0.00 0.00 3.16
1511 3644 4.396166 ACAGCACCAAGTCATTATACAAGC 59.604 41.667 0.00 0.00 0.00 4.01
1512 3645 4.637534 CAGCACCAAGTCATTATACAAGCT 59.362 41.667 0.00 0.00 0.00 3.74
1513 3646 5.817296 CAGCACCAAGTCATTATACAAGCTA 59.183 40.000 0.00 0.00 0.00 3.32
1515 3648 7.657354 CAGCACCAAGTCATTATACAAGCTATA 59.343 37.037 0.00 0.00 0.00 1.31
1532 3697 6.292389 AGCTATAAATTTGACATCACTCGC 57.708 37.500 0.00 0.00 0.00 5.03
1553 3718 5.985530 TCGCAGTGAGATTGGTTATTATGAG 59.014 40.000 0.00 0.00 0.00 2.90
1556 3721 7.148672 CGCAGTGAGATTGGTTATTATGAGATC 60.149 40.741 0.00 0.00 0.00 2.75
1597 3774 4.580995 TCGAAACAGTAAAGCCCAATTGAA 59.419 37.500 7.12 0.00 0.00 2.69
1610 3787 5.044846 AGCCCAATTGAATGGTAGTAGAAGT 60.045 40.000 7.12 0.00 38.91 3.01
1629 3810 7.296628 AGAAGTCTAAGCTATCCCTGTATTG 57.703 40.000 0.00 0.00 0.00 1.90
1657 3838 0.951558 ACTTGTAGCACAAAAGCCCG 59.048 50.000 3.84 0.00 37.69 6.13
1663 3844 1.661509 GCACAAAAGCCCGCAAGTC 60.662 57.895 0.00 0.00 0.00 3.01
1718 3899 3.998341 GCAACCAGCATGAAAATGAATGT 59.002 39.130 0.00 0.00 44.79 2.71
2003 4187 4.984161 GTGCTGCAATTGTAACAAGTTGAT 59.016 37.500 10.54 0.00 0.00 2.57
2034 4218 0.822164 GGACTACCTTAGCTTCGGCA 59.178 55.000 0.00 0.00 44.74 5.69
2334 4518 2.988010 TGAAGTGCTCAGTCAACAGT 57.012 45.000 0.00 0.00 0.00 3.55
2417 4601 3.838317 AGTTGGAGGCACATTACTACTCA 59.162 43.478 0.00 0.00 0.00 3.41
2538 4722 4.156556 TGATTCTTTACAAGGCTGTCATGC 59.843 41.667 0.00 0.00 36.96 4.06
2568 4752 9.381033 TGCATTTACCTTTAGCGTTAACTTATA 57.619 29.630 3.71 0.00 0.00 0.98
2575 4759 7.820872 ACCTTTAGCGTTAACTTATAGAAGCAA 59.179 33.333 3.71 0.00 35.97 3.91
2578 4762 9.595823 TTTAGCGTTAACTTATAGAAGCAAGAT 57.404 29.630 3.71 0.00 35.97 2.40
2666 4850 4.627741 GCATAGTCCAAGGAAATACCACCA 60.628 45.833 0.00 0.00 42.04 4.17
2691 4875 4.626172 GTCGAACAAGGACTTAATGACTCC 59.374 45.833 0.00 0.00 0.00 3.85
2696 4880 4.102524 ACAAGGACTTAATGACTCCACACA 59.897 41.667 0.00 0.00 0.00 3.72
2729 4913 5.677319 TGAGTAGAAGGAACCATAACCAG 57.323 43.478 0.00 0.00 0.00 4.00
2762 4946 8.142994 AGATTAGTATTAAAACATGGCTGTCG 57.857 34.615 0.00 0.00 33.36 4.35
2776 4960 2.603560 GGCTGTCGTTGCTTGATACTAC 59.396 50.000 0.00 0.00 0.00 2.73
2806 4995 6.709018 AGCAATACTTTTATTTACGCCCAT 57.291 33.333 0.00 0.00 0.00 4.00
2825 5014 1.375013 GTGCCCTGCATGCCTTTTG 60.375 57.895 16.68 0.14 41.91 2.44
2855 5044 2.097825 GATGCATTCTGCTTCCCTTGT 58.902 47.619 0.00 0.00 45.31 3.16
2856 5045 2.877097 TGCATTCTGCTTCCCTTGTA 57.123 45.000 0.34 0.00 45.31 2.41
2857 5046 2.715046 TGCATTCTGCTTCCCTTGTAG 58.285 47.619 0.34 0.00 45.31 2.74
2858 5047 2.040278 TGCATTCTGCTTCCCTTGTAGT 59.960 45.455 0.34 0.00 45.31 2.73
2888 5078 9.624697 TTGTCTTTATGATCAACAAATAACTGC 57.375 29.630 0.00 0.00 0.00 4.40
2924 5114 3.348119 CCTCCTGTTTCCCTAAAGAAGC 58.652 50.000 0.00 0.00 0.00 3.86
2972 5168 5.912955 ACTTAGTTAACTGTTTGCGATTTGC 59.087 36.000 18.56 0.00 46.70 3.68
2987 5183 3.436704 CGATTTGCAGGCAGAGAACTTAA 59.563 43.478 0.00 0.00 0.00 1.85
2990 5186 6.183360 CGATTTGCAGGCAGAGAACTTAAATA 60.183 38.462 0.00 0.00 0.00 1.40
3018 5214 7.760794 TGAATAGTTCATGAACCATGCATTTTC 59.239 33.333 30.34 20.83 41.18 2.29
3021 5217 5.244402 AGTTCATGAACCATGCATTTTCTGA 59.756 36.000 30.34 13.45 41.18 3.27
3042 5238 6.377429 TCTGAGGACGTATAGAAGTTCATGTT 59.623 38.462 5.50 0.00 0.00 2.71
3045 5241 7.544566 TGAGGACGTATAGAAGTTCATGTTTTC 59.455 37.037 5.50 0.00 0.00 2.29
3072 5268 2.679355 TTCCAATTGACGAGTTTGCG 57.321 45.000 7.12 0.00 37.29 4.85
3076 5272 1.463056 CAATTGACGAGTTTGCGGCTA 59.537 47.619 0.00 0.00 40.74 3.93
3086 5282 2.236395 AGTTTGCGGCTATCAGGTTAGT 59.764 45.455 0.00 0.00 0.00 2.24
3087 5283 3.007635 GTTTGCGGCTATCAGGTTAGTT 58.992 45.455 0.00 0.00 0.00 2.24
3088 5284 2.309528 TGCGGCTATCAGGTTAGTTG 57.690 50.000 0.00 0.00 0.00 3.16
3089 5285 1.828595 TGCGGCTATCAGGTTAGTTGA 59.171 47.619 0.00 0.00 0.00 3.18
3090 5286 2.235155 TGCGGCTATCAGGTTAGTTGAA 59.765 45.455 0.00 0.00 0.00 2.69
3091 5287 2.866762 GCGGCTATCAGGTTAGTTGAAG 59.133 50.000 0.00 0.00 0.00 3.02
3092 5288 3.430374 GCGGCTATCAGGTTAGTTGAAGA 60.430 47.826 0.00 0.00 0.00 2.87
3093 5289 4.755411 CGGCTATCAGGTTAGTTGAAGAA 58.245 43.478 0.00 0.00 0.00 2.52
3094 5290 4.567159 CGGCTATCAGGTTAGTTGAAGAAC 59.433 45.833 0.00 0.00 0.00 3.01
3095 5291 5.624738 CGGCTATCAGGTTAGTTGAAGAACT 60.625 44.000 0.00 0.00 44.90 3.01
3096 5292 6.174049 GGCTATCAGGTTAGTTGAAGAACTT 58.826 40.000 0.00 0.00 39.56 2.66
3097 5293 6.092807 GGCTATCAGGTTAGTTGAAGAACTTG 59.907 42.308 0.00 0.00 39.56 3.16
3098 5294 6.092807 GCTATCAGGTTAGTTGAAGAACTTGG 59.907 42.308 0.00 0.00 39.56 3.61
3099 5295 5.367945 TCAGGTTAGTTGAAGAACTTGGT 57.632 39.130 0.00 0.00 39.56 3.67
3138 5334 5.025453 AGTGCCTGGATGGATTTAAAACAT 58.975 37.500 0.00 8.08 38.35 2.71
3143 5339 9.023962 TGCCTGGATGGATTTAAAACATATATC 57.976 33.333 0.00 2.38 38.35 1.63
3171 5367 5.815222 AGGGAAATTTGAAACAAAACTTCGG 59.185 36.000 0.00 0.00 0.00 4.30
3175 5371 3.859411 TTGAAACAAAACTTCGGTGCT 57.141 38.095 0.00 0.00 0.00 4.40
3196 5392 3.947834 CTGAAATCATGGGAACTGTACCC 59.052 47.826 0.00 0.00 46.87 3.69
3201 5397 3.976758 GGGAACTGTACCCAACGC 58.023 61.111 0.00 0.00 46.05 4.84
3203 5399 0.535553 GGGAACTGTACCCAACGCAA 60.536 55.000 0.00 0.00 46.05 4.85
3204 5400 0.589708 GGAACTGTACCCAACGCAAC 59.410 55.000 0.00 0.00 0.00 4.17
3205 5401 1.301423 GAACTGTACCCAACGCAACA 58.699 50.000 0.00 0.00 0.00 3.33
3206 5402 1.671845 GAACTGTACCCAACGCAACAA 59.328 47.619 0.00 0.00 0.00 2.83
3207 5403 1.018910 ACTGTACCCAACGCAACAAC 58.981 50.000 0.00 0.00 0.00 3.32
3208 5404 1.305201 CTGTACCCAACGCAACAACT 58.695 50.000 0.00 0.00 0.00 3.16
3209 5405 1.673920 CTGTACCCAACGCAACAACTT 59.326 47.619 0.00 0.00 0.00 2.66
3210 5406 2.873472 CTGTACCCAACGCAACAACTTA 59.127 45.455 0.00 0.00 0.00 2.24
3211 5407 3.276857 TGTACCCAACGCAACAACTTAA 58.723 40.909 0.00 0.00 0.00 1.85
3212 5408 2.855660 ACCCAACGCAACAACTTAAC 57.144 45.000 0.00 0.00 0.00 2.01
3213 5409 2.371306 ACCCAACGCAACAACTTAACT 58.629 42.857 0.00 0.00 0.00 2.24
3214 5410 2.356695 ACCCAACGCAACAACTTAACTC 59.643 45.455 0.00 0.00 0.00 3.01
3215 5411 2.616842 CCCAACGCAACAACTTAACTCT 59.383 45.455 0.00 0.00 0.00 3.24
3216 5412 3.066203 CCCAACGCAACAACTTAACTCTT 59.934 43.478 0.00 0.00 0.00 2.85
3217 5413 4.439563 CCCAACGCAACAACTTAACTCTTT 60.440 41.667 0.00 0.00 0.00 2.52
3218 5414 4.499040 CCAACGCAACAACTTAACTCTTTG 59.501 41.667 0.00 0.00 0.00 2.77
3230 5426 7.631717 ACTTAACTCTTTGACTTGCTCTTTT 57.368 32.000 0.00 0.00 0.00 2.27
3231 5427 7.475840 ACTTAACTCTTTGACTTGCTCTTTTG 58.524 34.615 0.00 0.00 0.00 2.44
3250 5446 0.100503 GGGCCGATTTTGATTCGTGG 59.899 55.000 0.00 0.00 34.85 4.94
3258 5454 3.859411 TTTTGATTCGTGGGTAATGGC 57.141 42.857 0.00 0.00 0.00 4.40
3272 5468 7.174253 CGTGGGTAATGGCTACAAACATTATAT 59.826 37.037 0.00 0.00 40.46 0.86
3273 5469 8.296713 GTGGGTAATGGCTACAAACATTATATG 58.703 37.037 0.00 0.00 40.46 1.78
3295 5491 5.680619 TGACAAGTGTCTCAACCATTAACT 58.319 37.500 12.43 0.00 44.99 2.24
3306 5502 3.385193 ACCATTAACTTTTGCAGCCAC 57.615 42.857 0.00 0.00 0.00 5.01
3329 5525 5.664908 ACTCATGGTTTCAGGATATCTCTGT 59.335 40.000 16.20 0.12 32.96 3.41
3333 5529 6.627087 TGGTTTCAGGATATCTCTGTCTTT 57.373 37.500 16.20 0.00 34.15 2.52
3337 5533 4.537751 TCAGGATATCTCTGTCTTTCCGT 58.462 43.478 16.20 0.00 34.15 4.69
3341 5537 2.100605 ATCTCTGTCTTTCCGTTGGC 57.899 50.000 0.00 0.00 0.00 4.52
3344 5540 0.250295 TCTGTCTTTCCGTTGGCAGG 60.250 55.000 0.00 0.00 0.00 4.85
3347 5543 0.034896 GTCTTTCCGTTGGCAGGAGA 59.965 55.000 0.00 0.00 39.22 3.71
3348 5544 0.321671 TCTTTCCGTTGGCAGGAGAG 59.678 55.000 6.92 6.92 40.27 3.20
3349 5545 1.301677 CTTTCCGTTGGCAGGAGAGC 61.302 60.000 1.12 0.00 39.22 4.09
3352 5548 3.123620 CGTTGGCAGGAGAGCAGC 61.124 66.667 0.00 0.00 35.83 5.25
3376 5574 2.479566 CTTAAGGAGCTGTGCAAGGA 57.520 50.000 0.00 0.00 0.00 3.36
3390 5588 2.205074 GCAAGGACATGGTCGATGTAG 58.795 52.381 0.00 0.00 45.90 2.74
3393 5591 2.111384 AGGACATGGTCGATGTAGCTT 58.889 47.619 0.00 0.00 45.90 3.74
3405 5603 6.128391 GGTCGATGTAGCTTGTGTAAAAATCA 60.128 38.462 0.00 0.00 0.00 2.57
3413 5611 9.177304 GTAGCTTGTGTAAAAATCACCTTAAAC 57.823 33.333 0.00 0.00 35.25 2.01
3447 5645 5.554822 TTTCCAACGATGTTGTATTAGCC 57.445 39.130 8.68 0.00 0.00 3.93
3457 5655 7.600375 ACGATGTTGTATTAGCCATTGAGATAG 59.400 37.037 0.00 0.00 0.00 2.08
3467 5667 4.100189 AGCCATTGAGATAGCGTTCTAGTT 59.900 41.667 0.00 0.00 0.00 2.24
3472 5672 6.374565 TTGAGATAGCGTTCTAGTTCCTAC 57.625 41.667 0.00 0.00 0.00 3.18
3486 5686 5.224821 AGTTCCTACCCTGTTGTTCTAAC 57.775 43.478 0.00 0.00 0.00 2.34
3490 5690 5.152934 TCCTACCCTGTTGTTCTAACTTCT 58.847 41.667 0.00 0.00 0.00 2.85
3491 5691 6.317312 TCCTACCCTGTTGTTCTAACTTCTA 58.683 40.000 0.00 0.00 0.00 2.10
3492 5692 6.210185 TCCTACCCTGTTGTTCTAACTTCTAC 59.790 42.308 0.00 0.00 0.00 2.59
3498 5698 7.599245 CCCTGTTGTTCTAACTTCTACTAGTTG 59.401 40.741 0.00 0.00 38.72 3.16
3509 5709 8.937634 AACTTCTACTAGTTGTTTTTCGAAGA 57.062 30.769 0.00 0.00 37.00 2.87
3512 5712 9.798885 CTTCTACTAGTTGTTTTTCGAAGATTG 57.201 33.333 0.00 0.00 35.04 2.67
3524 5724 6.480524 TTTCGAAGATTGTTACCATGTCTG 57.519 37.500 0.00 0.00 35.04 3.51
3543 5743 0.961019 GCTTCCATGAGGTGTTTGCA 59.039 50.000 0.00 0.00 35.89 4.08
3545 5745 2.028748 GCTTCCATGAGGTGTTTGCATT 60.029 45.455 0.00 0.00 35.89 3.56
3547 5747 3.159213 TCCATGAGGTGTTTGCATTCT 57.841 42.857 0.00 0.00 35.89 2.40
3551 5751 1.872952 TGAGGTGTTTGCATTCTCGTG 59.127 47.619 0.00 0.00 33.52 4.35
3555 5755 2.310577 GTGTTTGCATTCTCGTGCTTC 58.689 47.619 0.00 0.00 45.27 3.86
3563 5763 3.669023 GCATTCTCGTGCTTCTTTTCTGG 60.669 47.826 0.00 0.00 41.82 3.86
3564 5764 1.512926 TCTCGTGCTTCTTTTCTGGC 58.487 50.000 0.00 0.00 0.00 4.85
3565 5765 1.070758 TCTCGTGCTTCTTTTCTGGCT 59.929 47.619 0.00 0.00 0.00 4.75
3566 5766 1.876156 CTCGTGCTTCTTTTCTGGCTT 59.124 47.619 0.00 0.00 0.00 4.35
3567 5767 2.291741 CTCGTGCTTCTTTTCTGGCTTT 59.708 45.455 0.00 0.00 0.00 3.51
3568 5768 2.687935 TCGTGCTTCTTTTCTGGCTTTT 59.312 40.909 0.00 0.00 0.00 2.27
3569 5769 3.045688 CGTGCTTCTTTTCTGGCTTTTC 58.954 45.455 0.00 0.00 0.00 2.29
3570 5770 3.384668 GTGCTTCTTTTCTGGCTTTTCC 58.615 45.455 0.00 0.00 0.00 3.13
3571 5771 2.034558 TGCTTCTTTTCTGGCTTTTCCG 59.965 45.455 0.00 0.00 37.80 4.30
3572 5772 2.608016 GCTTCTTTTCTGGCTTTTCCGG 60.608 50.000 0.00 0.00 42.90 5.14
3609 5809 6.122850 TCCATTTTCTGCGAGTATCATTTG 57.877 37.500 0.00 0.00 33.17 2.32
3615 5815 5.339008 TCTGCGAGTATCATTTGTAACCT 57.661 39.130 0.00 0.00 33.17 3.50
3617 5817 6.504398 TCTGCGAGTATCATTTGTAACCTAG 58.496 40.000 0.00 0.00 33.17 3.02
3618 5818 6.320418 TCTGCGAGTATCATTTGTAACCTAGA 59.680 38.462 0.00 0.00 33.17 2.43
3623 5823 6.583562 AGTATCATTTGTAACCTAGACCTGC 58.416 40.000 0.00 0.00 0.00 4.85
3629 5829 4.216411 TGTAACCTAGACCTGCAATTCC 57.784 45.455 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.459066 TCTCCTTGAGATAATATCGCAAAGG 58.541 40.000 17.57 18.38 45.93 3.11
39 40 7.261325 GCTATTCTCCTTGAGATAATATCGCA 58.739 38.462 2.55 2.55 38.56 5.10
41 42 6.416455 GCGCTATTCTCCTTGAGATAATATCG 59.584 42.308 0.00 0.95 38.56 2.92
43 44 6.095580 TCGCGCTATTCTCCTTGAGATAATAT 59.904 38.462 5.56 0.00 38.56 1.28
45 46 4.218635 TCGCGCTATTCTCCTTGAGATAAT 59.781 41.667 5.56 0.00 38.56 1.28
82 83 4.017126 AGTCATCGTTGGAGAGATGTGTA 58.983 43.478 5.51 0.00 43.34 2.90
97 98 3.965292 TTAGACGGAAGCTAGTCATCG 57.035 47.619 16.04 2.17 39.67 3.84
107 108 5.926542 TGATGTTCACTTCTTTAGACGGAAG 59.073 40.000 0.00 0.00 43.02 3.46
118 119 9.722184 CAAGGATATATCATGATGTTCACTTCT 57.278 33.333 18.72 3.19 0.00 2.85
179 180 6.254281 AGGTCAAATGATCAAAGTAAACCG 57.746 37.500 0.00 0.00 0.00 4.44
182 183 7.048629 TGCAAGGTCAAATGATCAAAGTAAA 57.951 32.000 0.00 0.00 0.00 2.01
189 190 7.407393 TGATTAATGCAAGGTCAAATGATCA 57.593 32.000 0.00 0.00 0.00 2.92
271 272 9.820229 TTTGTTGATTATTAGCAAGTTTAGACG 57.180 29.630 0.00 0.00 28.79 4.18
300 301 7.238710 GGGGTGAATAGGGACAAATACATATT 58.761 38.462 0.00 0.00 0.00 1.28
302 303 5.073965 GGGGGTGAATAGGGACAAATACATA 59.926 44.000 0.00 0.00 0.00 2.29
303 304 4.141018 GGGGGTGAATAGGGACAAATACAT 60.141 45.833 0.00 0.00 0.00 2.29
310 311 0.979187 GACGGGGGTGAATAGGGACA 60.979 60.000 0.00 0.00 0.00 4.02
311 312 1.693152 GGACGGGGGTGAATAGGGAC 61.693 65.000 0.00 0.00 0.00 4.46
312 313 1.383525 GGACGGGGGTGAATAGGGA 60.384 63.158 0.00 0.00 0.00 4.20
335 336 1.846439 TGAAAGGATCTGGATGGACCC 59.154 52.381 0.00 0.00 38.00 4.46
338 339 1.139654 CGCTGAAAGGATCTGGATGGA 59.860 52.381 0.00 0.00 0.00 3.41
344 345 1.446907 AGCAACGCTGAAAGGATCTG 58.553 50.000 0.00 0.00 37.57 2.90
345 346 3.334583 TTAGCAACGCTGAAAGGATCT 57.665 42.857 0.00 0.00 40.10 2.75
354 355 3.042887 GTTTGGTCTTTTAGCAACGCTG 58.957 45.455 0.00 0.00 44.95 5.18
355 356 2.685897 TGTTTGGTCTTTTAGCAACGCT 59.314 40.909 0.00 0.00 44.95 5.07
366 367 0.105760 TGGGGTGCATGTTTGGTCTT 60.106 50.000 0.00 0.00 0.00 3.01
376 377 1.566298 GGAGAGAAGGTGGGGTGCAT 61.566 60.000 0.00 0.00 0.00 3.96
423 424 6.884295 TGCACAAAATTCTATAGCAGTAGGTT 59.116 34.615 0.00 0.00 0.00 3.50
485 486 1.663388 GGCCCGGCAAAAACTTTCG 60.663 57.895 12.58 0.00 0.00 3.46
507 509 2.706190 ACAGCTCAACAAACCCTCTAGT 59.294 45.455 0.00 0.00 0.00 2.57
641 646 6.923508 GGCAAATCCTATTCTTAAATTTCGGG 59.076 38.462 0.00 0.00 0.00 5.14
671 676 5.360591 ACGGCAAATCCTATTCTTGTCTAG 58.639 41.667 0.00 0.00 0.00 2.43
672 677 5.353394 ACGGCAAATCCTATTCTTGTCTA 57.647 39.130 0.00 0.00 0.00 2.59
673 678 4.222124 ACGGCAAATCCTATTCTTGTCT 57.778 40.909 0.00 0.00 0.00 3.41
674 679 6.128526 GCTATACGGCAAATCCTATTCTTGTC 60.129 42.308 0.00 0.00 0.00 3.18
675 680 5.701290 GCTATACGGCAAATCCTATTCTTGT 59.299 40.000 0.00 0.00 0.00 3.16
676 681 5.700832 TGCTATACGGCAAATCCTATTCTTG 59.299 40.000 0.00 0.00 39.43 3.02
709 2729 5.172205 CCTCTAGCAGTGATGATGATGATG 58.828 45.833 0.00 0.00 0.00 3.07
710 2730 4.223255 CCCTCTAGCAGTGATGATGATGAT 59.777 45.833 0.00 0.00 0.00 2.45
711 2731 3.577415 CCCTCTAGCAGTGATGATGATGA 59.423 47.826 0.00 0.00 0.00 2.92
712 2732 3.324268 ACCCTCTAGCAGTGATGATGATG 59.676 47.826 0.00 0.00 0.00 3.07
713 2733 3.585360 ACCCTCTAGCAGTGATGATGAT 58.415 45.455 0.00 0.00 0.00 2.45
714 2734 3.037851 ACCCTCTAGCAGTGATGATGA 57.962 47.619 0.00 0.00 0.00 2.92
715 2735 3.257873 CCTACCCTCTAGCAGTGATGATG 59.742 52.174 0.00 0.00 0.00 3.07
739 2759 3.492353 ATGGACCGGGCCCATCAG 61.492 66.667 27.91 9.75 40.16 2.90
793 2815 2.438021 GGATGGGCCGGCATATATCTAA 59.562 50.000 30.85 2.66 0.00 2.10
801 2823 3.958860 GCTAGGATGGGCCGGCAT 61.959 66.667 30.85 14.88 43.43 4.40
807 2869 0.324275 TTTGTTGGGCTAGGATGGGC 60.324 55.000 0.00 0.00 43.03 5.36
861 2981 3.426963 CCTGTACGCTGTTTCTCTCTCTC 60.427 52.174 0.00 0.00 0.00 3.20
862 2982 2.490115 CCTGTACGCTGTTTCTCTCTCT 59.510 50.000 0.00 0.00 0.00 3.10
864 2984 1.546476 CCCTGTACGCTGTTTCTCTCT 59.454 52.381 0.00 0.00 0.00 3.10
865 2985 1.404315 CCCCTGTACGCTGTTTCTCTC 60.404 57.143 0.00 0.00 0.00 3.20
866 2986 0.608640 CCCCTGTACGCTGTTTCTCT 59.391 55.000 0.00 0.00 0.00 3.10
868 2988 0.320697 GTCCCCTGTACGCTGTTTCT 59.679 55.000 0.00 0.00 0.00 2.52
869 2989 0.034337 TGTCCCCTGTACGCTGTTTC 59.966 55.000 0.00 0.00 0.00 2.78
870 2990 0.034896 CTGTCCCCTGTACGCTGTTT 59.965 55.000 0.00 0.00 0.00 2.83
871 2991 1.671742 CTGTCCCCTGTACGCTGTT 59.328 57.895 0.00 0.00 0.00 3.16
872 2992 2.943978 GCTGTCCCCTGTACGCTGT 61.944 63.158 0.00 0.00 0.00 4.40
873 2993 2.125512 GCTGTCCCCTGTACGCTG 60.126 66.667 0.00 0.00 0.00 5.18
874 2994 3.391382 GGCTGTCCCCTGTACGCT 61.391 66.667 0.00 0.00 0.00 5.07
875 2995 4.814294 CGGCTGTCCCCTGTACGC 62.814 72.222 0.00 0.00 0.00 4.42
876 2996 4.814294 GCGGCTGTCCCCTGTACG 62.814 72.222 0.00 0.00 0.00 3.67
877 2997 3.702048 TGCGGCTGTCCCCTGTAC 61.702 66.667 0.00 0.00 0.00 2.90
878 2998 3.702048 GTGCGGCTGTCCCCTGTA 61.702 66.667 0.00 0.00 0.00 2.74
1214 3334 0.595567 GTACGCGGGCGATGTTGATA 60.596 55.000 20.98 0.00 42.83 2.15
1391 3519 2.089349 GCAGTGAGGCGAGTTCGTC 61.089 63.158 0.00 0.00 45.56 4.20
1392 3520 2.049063 GCAGTGAGGCGAGTTCGT 60.049 61.111 3.27 0.00 42.22 3.85
1393 3521 2.811317 GGCAGTGAGGCGAGTTCG 60.811 66.667 0.00 0.00 43.27 3.95
1394 3522 2.435059 GGGCAGTGAGGCGAGTTC 60.435 66.667 0.00 0.00 45.36 3.01
1395 3523 3.241530 TGGGCAGTGAGGCGAGTT 61.242 61.111 0.00 0.00 45.36 3.01
1448 3576 3.186205 CCAATTTTGGGCACGACAATTTC 59.814 43.478 1.14 0.00 44.70 2.17
1483 3616 3.928727 AATGACTTGGTGCTGTTGATG 57.071 42.857 0.00 0.00 0.00 3.07
1489 3622 4.637534 AGCTTGTATAATGACTTGGTGCTG 59.362 41.667 0.00 0.00 0.00 4.41
1490 3623 4.848357 AGCTTGTATAATGACTTGGTGCT 58.152 39.130 0.00 0.00 0.00 4.40
1505 3638 8.817100 CGAGTGATGTCAAATTTATAGCTTGTA 58.183 33.333 0.00 0.00 0.00 2.41
1506 3639 7.677276 GCGAGTGATGTCAAATTTATAGCTTGT 60.677 37.037 0.00 0.00 0.00 3.16
1507 3640 6.630443 GCGAGTGATGTCAAATTTATAGCTTG 59.370 38.462 0.00 0.00 0.00 4.01
1508 3641 6.316140 TGCGAGTGATGTCAAATTTATAGCTT 59.684 34.615 0.00 0.00 0.00 3.74
1509 3642 5.817296 TGCGAGTGATGTCAAATTTATAGCT 59.183 36.000 0.00 0.00 0.00 3.32
1510 3643 6.048073 TGCGAGTGATGTCAAATTTATAGC 57.952 37.500 0.00 0.00 0.00 2.97
1511 3644 7.239166 ACTGCGAGTGATGTCAAATTTATAG 57.761 36.000 0.00 0.00 0.00 1.31
1528 3693 5.985530 TCATAATAACCAATCTCACTGCGAG 59.014 40.000 0.00 0.00 43.80 5.03
1530 3695 5.985530 TCTCATAATAACCAATCTCACTGCG 59.014 40.000 0.00 0.00 0.00 5.18
1553 3718 8.581057 TTCGATCTTCATTGCTAGTTTAGATC 57.419 34.615 0.00 0.00 35.41 2.75
1556 3721 7.963981 TGTTTCGATCTTCATTGCTAGTTTAG 58.036 34.615 0.00 0.00 0.00 1.85
1597 3774 6.949463 GGGATAGCTTAGACTTCTACTACCAT 59.051 42.308 0.00 0.00 0.00 3.55
1610 3787 6.213600 GGGATTCAATACAGGGATAGCTTAGA 59.786 42.308 0.00 0.00 0.00 2.10
1629 3810 2.778299 TGTGCTACAAGTGTGGGATTC 58.222 47.619 0.00 0.00 0.00 2.52
1657 3838 8.520835 TTACATGATAACTGATATCGACTTGC 57.479 34.615 0.00 0.00 42.91 4.01
1718 3899 3.268334 ACATTTTCACCCTAGCCATACCA 59.732 43.478 0.00 0.00 0.00 3.25
1772 3953 6.263617 AGACCTTACCGAACTGATCTCTATTC 59.736 42.308 0.00 0.00 0.00 1.75
1778 3959 6.793505 AAATAGACCTTACCGAACTGATCT 57.206 37.500 0.00 0.00 0.00 2.75
1966 4150 1.308047 CAGCACTAATTATGGCGCCA 58.692 50.000 34.80 34.80 0.00 5.69
2003 4187 3.083122 AGGTAGTCCTCGCTTCTTGTA 57.917 47.619 0.00 0.00 40.58 2.41
2334 4518 3.023119 GCATTCTCTCTGTCTCCTCTGA 58.977 50.000 0.00 0.00 0.00 3.27
2417 4601 1.079819 CGGAGTCCGCACAACAGAT 60.080 57.895 20.50 0.00 41.17 2.90
2538 4722 4.419522 ACGCTAAAGGTAAATGCAACAG 57.580 40.909 0.00 0.00 0.00 3.16
2588 4772 9.106070 GTACCCTCATTAAACTATTGTACCAAG 57.894 37.037 0.00 0.00 0.00 3.61
2606 4790 4.265856 ACAGACATAGATGGTACCCTCA 57.734 45.455 18.17 5.99 0.00 3.86
2691 4875 6.662414 TCTACTCAAAAGTTTGACTGTGTG 57.338 37.500 2.32 0.00 41.88 3.82
2696 4880 6.542735 GGTTCCTTCTACTCAAAAGTTTGACT 59.457 38.462 2.32 0.00 41.88 3.41
2701 4885 7.447545 GGTTATGGTTCCTTCTACTCAAAAGTT 59.552 37.037 0.00 0.00 36.92 2.66
2729 4913 9.301153 CATGTTTTAATACTAATCTTGGTTGCC 57.699 33.333 0.00 0.00 0.00 4.52
2762 4946 5.786401 CTTGTGGAGTAGTATCAAGCAAC 57.214 43.478 0.00 0.00 31.19 4.17
2776 4960 7.218204 GCGTAAATAAAAGTATTGCTTGTGGAG 59.782 37.037 0.00 0.00 37.52 3.86
2806 4995 1.837947 AAAAGGCATGCAGGGCACA 60.838 52.632 27.20 0.00 43.04 4.57
2941 5131 9.048446 TCGCAAACAGTTAACTAAGTTCTTTAT 57.952 29.630 8.04 0.00 0.00 1.40
2943 5133 7.311364 TCGCAAACAGTTAACTAAGTTCTTT 57.689 32.000 8.04 0.00 0.00 2.52
2945 5135 7.492352 AATCGCAAACAGTTAACTAAGTTCT 57.508 32.000 8.04 0.00 0.00 3.01
2946 5136 7.357287 GCAAATCGCAAACAGTTAACTAAGTTC 60.357 37.037 8.04 0.00 41.79 3.01
2947 5137 6.416750 GCAAATCGCAAACAGTTAACTAAGTT 59.583 34.615 8.04 6.65 41.79 2.66
2948 5138 5.912955 GCAAATCGCAAACAGTTAACTAAGT 59.087 36.000 8.04 0.00 41.79 2.24
2949 5139 6.362632 GCAAATCGCAAACAGTTAACTAAG 57.637 37.500 8.04 0.00 41.79 2.18
2965 5161 1.446907 AGTTCTCTGCCTGCAAATCG 58.553 50.000 0.00 0.00 0.00 3.34
3009 5205 6.161855 TCTATACGTCCTCAGAAAATGCAT 57.838 37.500 0.00 0.00 0.00 3.96
3018 5214 6.137794 ACATGAACTTCTATACGTCCTCAG 57.862 41.667 0.00 0.00 0.00 3.35
3021 5217 6.530534 CGAAAACATGAACTTCTATACGTCCT 59.469 38.462 0.00 0.00 0.00 3.85
3042 5238 8.259049 ACTCGTCAATTGGAAATTATACGAAA 57.741 30.769 13.47 0.00 37.62 3.46
3045 5241 7.044966 GCAAACTCGTCAATTGGAAATTATACG 60.045 37.037 5.42 5.69 0.00 3.06
3072 5268 5.735766 AGTTCTTCAACTAACCTGATAGCC 58.264 41.667 0.00 0.00 41.39 3.93
3076 5272 5.941788 ACCAAGTTCTTCAACTAACCTGAT 58.058 37.500 0.00 0.00 42.45 2.90
3086 5282 3.068024 GTGCCATCAACCAAGTTCTTCAA 59.932 43.478 0.00 0.00 0.00 2.69
3087 5283 2.622942 GTGCCATCAACCAAGTTCTTCA 59.377 45.455 0.00 0.00 0.00 3.02
3088 5284 2.622942 TGTGCCATCAACCAAGTTCTTC 59.377 45.455 0.00 0.00 0.00 2.87
3089 5285 2.665165 TGTGCCATCAACCAAGTTCTT 58.335 42.857 0.00 0.00 0.00 2.52
3090 5286 2.363306 TGTGCCATCAACCAAGTTCT 57.637 45.000 0.00 0.00 0.00 3.01
3091 5287 4.022416 TGTTATGTGCCATCAACCAAGTTC 60.022 41.667 0.00 0.00 0.00 3.01
3092 5288 3.894427 TGTTATGTGCCATCAACCAAGTT 59.106 39.130 0.00 0.00 0.00 2.66
3093 5289 3.495331 TGTTATGTGCCATCAACCAAGT 58.505 40.909 0.00 0.00 0.00 3.16
3094 5290 4.022068 ACTTGTTATGTGCCATCAACCAAG 60.022 41.667 0.00 0.00 0.00 3.61
3095 5291 3.894427 ACTTGTTATGTGCCATCAACCAA 59.106 39.130 0.00 0.00 0.00 3.67
3096 5292 3.255395 CACTTGTTATGTGCCATCAACCA 59.745 43.478 0.00 0.00 0.00 3.67
3097 5293 3.836949 CACTTGTTATGTGCCATCAACC 58.163 45.455 0.00 0.00 0.00 3.77
3169 5365 1.133025 GTTCCCATGATTTCAGCACCG 59.867 52.381 0.00 0.00 0.00 4.94
3171 5367 2.821969 ACAGTTCCCATGATTTCAGCAC 59.178 45.455 0.00 0.00 0.00 4.40
3175 5371 3.963129 GGGTACAGTTCCCATGATTTCA 58.037 45.455 10.42 0.00 44.05 2.69
3196 5392 5.227184 GTCAAAGAGTTAAGTTGTTGCGTTG 59.773 40.000 3.24 0.00 0.00 4.10
3197 5393 5.123344 AGTCAAAGAGTTAAGTTGTTGCGTT 59.877 36.000 3.24 0.00 0.00 4.84
3198 5394 4.634443 AGTCAAAGAGTTAAGTTGTTGCGT 59.366 37.500 3.24 0.00 0.00 5.24
3199 5395 5.156804 AGTCAAAGAGTTAAGTTGTTGCG 57.843 39.130 3.24 0.00 0.00 4.85
3200 5396 5.230097 GCAAGTCAAAGAGTTAAGTTGTTGC 59.770 40.000 0.00 0.00 31.43 4.17
3201 5397 6.555315 AGCAAGTCAAAGAGTTAAGTTGTTG 58.445 36.000 0.00 2.09 0.00 3.33
3203 5399 6.116126 AGAGCAAGTCAAAGAGTTAAGTTGT 58.884 36.000 0.00 0.00 0.00 3.32
3204 5400 6.610741 AGAGCAAGTCAAAGAGTTAAGTTG 57.389 37.500 0.00 0.00 0.00 3.16
3205 5401 7.631717 AAAGAGCAAGTCAAAGAGTTAAGTT 57.368 32.000 0.00 0.00 0.00 2.66
3206 5402 7.415653 CCAAAAGAGCAAGTCAAAGAGTTAAGT 60.416 37.037 0.00 0.00 0.00 2.24
3207 5403 6.914757 CCAAAAGAGCAAGTCAAAGAGTTAAG 59.085 38.462 0.00 0.00 0.00 1.85
3208 5404 6.183360 CCCAAAAGAGCAAGTCAAAGAGTTAA 60.183 38.462 0.00 0.00 0.00 2.01
3209 5405 5.299279 CCCAAAAGAGCAAGTCAAAGAGTTA 59.701 40.000 0.00 0.00 0.00 2.24
3210 5406 4.098501 CCCAAAAGAGCAAGTCAAAGAGTT 59.901 41.667 0.00 0.00 0.00 3.01
3211 5407 3.633986 CCCAAAAGAGCAAGTCAAAGAGT 59.366 43.478 0.00 0.00 0.00 3.24
3212 5408 3.551659 GCCCAAAAGAGCAAGTCAAAGAG 60.552 47.826 0.00 0.00 0.00 2.85
3213 5409 2.362077 GCCCAAAAGAGCAAGTCAAAGA 59.638 45.455 0.00 0.00 0.00 2.52
3214 5410 2.546584 GGCCCAAAAGAGCAAGTCAAAG 60.547 50.000 0.00 0.00 0.00 2.77
3215 5411 1.412343 GGCCCAAAAGAGCAAGTCAAA 59.588 47.619 0.00 0.00 0.00 2.69
3216 5412 1.039856 GGCCCAAAAGAGCAAGTCAA 58.960 50.000 0.00 0.00 0.00 3.18
3217 5413 1.172180 CGGCCCAAAAGAGCAAGTCA 61.172 55.000 0.00 0.00 0.00 3.41
3218 5414 0.889186 TCGGCCCAAAAGAGCAAGTC 60.889 55.000 0.00 0.00 0.00 3.01
3230 5426 0.808125 CACGAATCAAAATCGGCCCA 59.192 50.000 0.00 0.00 44.32 5.36
3231 5427 0.100503 CCACGAATCAAAATCGGCCC 59.899 55.000 0.00 0.00 44.32 5.80
3235 5431 4.597079 CCATTACCCACGAATCAAAATCG 58.403 43.478 0.00 0.00 45.47 3.34
3250 5446 9.062524 TGTCATATAATGTTTGTAGCCATTACC 57.937 33.333 0.00 0.00 36.62 2.85
3273 5469 6.619801 AAGTTAATGGTTGAGACACTTGTC 57.380 37.500 0.77 0.77 45.08 3.18
3306 5502 6.041865 AGACAGAGATATCCTGAAACCATGAG 59.958 42.308 21.15 0.00 35.69 2.90
3322 5518 1.347707 TGCCAACGGAAAGACAGAGAT 59.652 47.619 0.00 0.00 0.00 2.75
3329 5525 0.321671 CTCTCCTGCCAACGGAAAGA 59.678 55.000 0.00 0.00 0.00 2.52
3333 5529 2.922503 TGCTCTCCTGCCAACGGA 60.923 61.111 0.00 0.00 0.00 4.69
3337 5533 4.399395 CCGCTGCTCTCCTGCCAA 62.399 66.667 0.00 0.00 35.20 4.52
3344 5540 2.509336 TTAAGCGCCGCTGCTCTC 60.509 61.111 14.52 0.00 46.60 3.20
3348 5544 3.567797 CTCCTTAAGCGCCGCTGC 61.568 66.667 14.52 1.31 39.62 5.25
3349 5545 3.567797 GCTCCTTAAGCGCCGCTG 61.568 66.667 14.52 0.00 42.21 5.18
3369 5565 0.324614 ACATCGACCATGTCCTTGCA 59.675 50.000 0.00 0.00 42.62 4.08
3390 5588 9.908152 ATAGTTTAAGGTGATTTTTACACAAGC 57.092 29.630 0.00 0.00 39.65 4.01
3425 5623 5.004448 TGGCTAATACAACATCGTTGGAAA 58.996 37.500 11.26 0.00 0.00 3.13
3427 5625 4.209307 TGGCTAATACAACATCGTTGGA 57.791 40.909 11.26 2.97 0.00 3.53
3428 5626 5.065859 TCAATGGCTAATACAACATCGTTGG 59.934 40.000 11.26 0.00 0.00 3.77
3429 5627 6.037062 TCTCAATGGCTAATACAACATCGTTG 59.963 38.462 5.34 5.34 0.00 4.10
3431 5629 5.670485 TCTCAATGGCTAATACAACATCGT 58.330 37.500 0.00 0.00 0.00 3.73
3432 5630 6.791887 ATCTCAATGGCTAATACAACATCG 57.208 37.500 0.00 0.00 0.00 3.84
3447 5645 5.837437 AGGAACTAGAACGCTATCTCAATG 58.163 41.667 0.00 0.00 36.02 2.82
3457 5655 1.823610 ACAGGGTAGGAACTAGAACGC 59.176 52.381 0.00 0.00 44.14 4.84
3467 5667 5.152934 AGAAGTTAGAACAACAGGGTAGGA 58.847 41.667 0.00 0.00 0.00 2.94
3472 5672 7.229581 ACTAGTAGAAGTTAGAACAACAGGG 57.770 40.000 3.59 0.00 0.00 4.45
3486 5686 9.798885 CAATCTTCGAAAAACAACTAGTAGAAG 57.201 33.333 3.59 2.56 35.31 2.85
3491 5691 8.340443 GGTAACAATCTTCGAAAAACAACTAGT 58.660 33.333 0.00 0.00 0.00 2.57
3492 5692 8.709496 GGTAACAATCTTCGAAAAACAACTAG 57.291 34.615 0.00 0.00 0.00 2.57
3512 5712 3.609853 TCATGGAAGCAGACATGGTAAC 58.390 45.455 12.55 0.00 43.49 2.50
3524 5724 0.961019 TGCAAACACCTCATGGAAGC 59.039 50.000 0.00 0.00 37.04 3.86
3543 5743 2.485814 GCCAGAAAAGAAGCACGAGAAT 59.514 45.455 0.00 0.00 0.00 2.40
3545 5745 1.070758 AGCCAGAAAAGAAGCACGAGA 59.929 47.619 0.00 0.00 0.00 4.04
3547 5747 1.967319 AAGCCAGAAAAGAAGCACGA 58.033 45.000 0.00 0.00 0.00 4.35
3551 5751 2.608016 CCGGAAAAGCCAGAAAAGAAGC 60.608 50.000 0.00 0.00 35.94 3.86
3555 5755 3.496898 GCCGGAAAAGCCAGAAAAG 57.503 52.632 5.05 0.00 35.94 2.27
3579 5779 0.026803 CGCAGAAAATGGAGTAGCGC 59.973 55.000 0.00 0.00 37.20 5.92
3580 5780 1.590238 CTCGCAGAAAATGGAGTAGCG 59.410 52.381 0.00 0.00 44.45 4.26
3609 5809 4.192317 CTGGAATTGCAGGTCTAGGTTAC 58.808 47.826 18.52 0.00 0.00 2.50
3615 5815 0.255890 GGCCTGGAATTGCAGGTCTA 59.744 55.000 37.06 0.11 39.92 2.59
3617 5817 2.054453 GGGCCTGGAATTGCAGGTC 61.054 63.158 37.06 36.18 42.18 3.85
3618 5818 2.037847 GGGCCTGGAATTGCAGGT 59.962 61.111 37.06 0.00 40.58 4.00
3623 5823 1.180029 CTGTTCAGGGCCTGGAATTG 58.820 55.000 32.23 13.93 31.51 2.32


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

AutoCloner maintained by Alex Coulton.