Multiple sequence alignment - TraesCS3B01G315800

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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 TraesCS3B01G315800 chr3B 100.000 4087 0 0 1 4087 507302835 507298749 0.000000e+00 7548.0
1 TraesCS3B01G315800 chr3B 86.869 99 11 2 97 195 658388050 658388146 4.320000e-20 110.0
2 TraesCS3B01G315800 chr3D 91.923 2142 117 21 283 2381 390077133 390075005 0.000000e+00 2946.0
3 TraesCS3B01G315800 chr3D 89.905 1684 114 28 2438 4087 390074919 390073258 0.000000e+00 2117.0
4 TraesCS3B01G315800 chr3D 95.588 68 3 0 189 256 390077200 390077133 4.320000e-20 110.0
5 TraesCS3B01G315800 chr3A 92.162 1850 99 22 569 2381 510691841 510690001 0.000000e+00 2571.0
6 TraesCS3B01G315800 chr3A 89.727 1684 103 28 2438 4087 510689913 510688266 0.000000e+00 2087.0
7 TraesCS3B01G315800 chr1B 81.579 152 25 3 1351 1500 593837600 593837450 5.550000e-24 122.0
8 TraesCS3B01G315800 chr1A 82.353 136 22 2 1351 1485 534933235 534933101 2.580000e-22 117.0
9 TraesCS3B01G315800 chr1A 86.517 89 11 1 101 189 358735195 358735108 3.360000e-16 97.1
10 TraesCS3B01G315800 chr4B 85.859 99 12 2 97 195 175903816 175903720 2.010000e-18 104.0
11 TraesCS3B01G315800 chr1D 72.951 366 73 17 1351 1702 438228781 438228428 2.010000e-18 104.0
12 TraesCS3B01G315800 chr1D 87.209 86 10 1 102 187 18464929 18465013 3.360000e-16 97.1
13 TraesCS3B01G315800 chr7B 86.316 95 11 2 94 188 677294932 677295024 7.230000e-18 102.0
14 TraesCS3B01G315800 chr5A 83.636 110 14 4 89 197 29180182 29180076 2.600000e-17 100.0
15 TraesCS3B01G315800 chr2A 86.364 88 11 1 102 189 745406927 745406841 1.210000e-15 95.3
16 TraesCS3B01G315800 chr2A 86.047 86 11 1 102 187 753210725 753210641 1.560000e-14 91.6
17 TraesCS3B01G315800 chr7D 83.838 99 14 2 90 188 264750235 264750139 4.350000e-15 93.5


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 TraesCS3B01G315800 chr3B 507298749 507302835 4086 True 7548.000000 7548 100.0000 1 4087 1 chr3B.!!$R1 4086
1 TraesCS3B01G315800 chr3D 390073258 390077200 3942 True 1724.333333 2946 92.4720 189 4087 3 chr3D.!!$R1 3898
2 TraesCS3B01G315800 chr3A 510688266 510691841 3575 True 2329.000000 2571 90.9445 569 4087 2 chr3A.!!$R1 3518

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
50 51 0.251787 AGCCCCTTCACAATCCAACC 60.252 55.0 0.00 0.0 0.0 3.77 F
385 387 0.387929 TGACCTTCAAACTCGAGCGT 59.612 50.0 13.61 0.0 0.0 5.07 F
387 389 0.663568 ACCTTCAAACTCGAGCGTCG 60.664 55.0 13.61 0.0 42.1 5.12 F
1424 1450 0.924823 AGGCTTGCCATCCAGATCTT 59.075 50.0 14.54 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1599 0.036010 ACCTGTTCATCCCTTGCTCG 60.036 55.000 0.00 0.00 0.00 5.03 R
2269 2325 1.636148 ATGCAACCTGCTCAAATGGT 58.364 45.000 0.00 0.00 45.31 3.55 R
2381 2437 1.701847 AGAGCCCATCCACCATCATAC 59.298 52.381 0.00 0.00 0.00 2.39 R
3384 3516 0.179113 TGATGATAACGAGCTGCGCA 60.179 50.000 10.98 10.98 46.04 6.09 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
24 25 7.926674 TGAAGTCTGAAGCATGAATAATTGA 57.073 32.000 0.00 0.00 0.00 2.57
25 26 8.339344 TGAAGTCTGAAGCATGAATAATTGAA 57.661 30.769 0.00 0.00 0.00 2.69
26 27 8.963725 TGAAGTCTGAAGCATGAATAATTGAAT 58.036 29.630 0.00 0.00 0.00 2.57
36 37 9.359653 AGCATGAATAATTGAATATATAGCCCC 57.640 33.333 0.00 0.00 0.00 5.80
37 38 9.359653 GCATGAATAATTGAATATATAGCCCCT 57.640 33.333 0.00 0.00 0.00 4.79
45 46 8.814038 ATTGAATATATAGCCCCTTCACAATC 57.186 34.615 0.00 0.00 0.00 2.67
46 47 6.721318 TGAATATATAGCCCCTTCACAATCC 58.279 40.000 0.00 0.00 0.00 3.01
47 48 6.274436 TGAATATATAGCCCCTTCACAATCCA 59.726 38.462 0.00 0.00 0.00 3.41
48 49 6.718593 ATATATAGCCCCTTCACAATCCAA 57.281 37.500 0.00 0.00 0.00 3.53
49 50 2.507407 TAGCCCCTTCACAATCCAAC 57.493 50.000 0.00 0.00 0.00 3.77
50 51 0.251787 AGCCCCTTCACAATCCAACC 60.252 55.000 0.00 0.00 0.00 3.77
51 52 0.251787 GCCCCTTCACAATCCAACCT 60.252 55.000 0.00 0.00 0.00 3.50
52 53 1.827245 GCCCCTTCACAATCCAACCTT 60.827 52.381 0.00 0.00 0.00 3.50
53 54 2.171003 CCCCTTCACAATCCAACCTTC 58.829 52.381 0.00 0.00 0.00 3.46
54 55 2.225117 CCCCTTCACAATCCAACCTTCT 60.225 50.000 0.00 0.00 0.00 2.85
55 56 3.084786 CCCTTCACAATCCAACCTTCTC 58.915 50.000 0.00 0.00 0.00 2.87
56 57 3.498481 CCCTTCACAATCCAACCTTCTCA 60.498 47.826 0.00 0.00 0.00 3.27
57 58 4.144297 CCTTCACAATCCAACCTTCTCAA 58.856 43.478 0.00 0.00 0.00 3.02
58 59 4.217118 CCTTCACAATCCAACCTTCTCAAG 59.783 45.833 0.00 0.00 0.00 3.02
105 106 9.494271 TGAATCCATCATATTACAAAGCTACTC 57.506 33.333 0.00 0.00 31.50 2.59
106 107 8.854614 AATCCATCATATTACAAAGCTACTCC 57.145 34.615 0.00 0.00 0.00 3.85
107 108 6.769512 TCCATCATATTACAAAGCTACTCCC 58.230 40.000 0.00 0.00 0.00 4.30
108 109 6.558775 TCCATCATATTACAAAGCTACTCCCT 59.441 38.462 0.00 0.00 0.00 4.20
109 110 7.072454 TCCATCATATTACAAAGCTACTCCCTT 59.928 37.037 0.00 0.00 0.00 3.95
110 111 7.389053 CCATCATATTACAAAGCTACTCCCTTC 59.611 40.741 0.00 0.00 0.00 3.46
111 112 7.432148 TCATATTACAAAGCTACTCCCTTCA 57.568 36.000 0.00 0.00 0.00 3.02
112 113 8.034313 TCATATTACAAAGCTACTCCCTTCAT 57.966 34.615 0.00 0.00 0.00 2.57
113 114 9.154632 TCATATTACAAAGCTACTCCCTTCATA 57.845 33.333 0.00 0.00 0.00 2.15
114 115 9.778741 CATATTACAAAGCTACTCCCTTCATAA 57.221 33.333 0.00 0.00 0.00 1.90
116 117 7.916914 TTACAAAGCTACTCCCTTCATAAAC 57.083 36.000 0.00 0.00 0.00 2.01
117 118 6.128138 ACAAAGCTACTCCCTTCATAAACT 57.872 37.500 0.00 0.00 0.00 2.66
118 119 7.253905 ACAAAGCTACTCCCTTCATAAACTA 57.746 36.000 0.00 0.00 0.00 2.24
119 120 7.686434 ACAAAGCTACTCCCTTCATAAACTAA 58.314 34.615 0.00 0.00 0.00 2.24
120 121 8.329502 ACAAAGCTACTCCCTTCATAAACTAAT 58.670 33.333 0.00 0.00 0.00 1.73
121 122 9.832445 CAAAGCTACTCCCTTCATAAACTAATA 57.168 33.333 0.00 0.00 0.00 0.98
122 123 9.833917 AAAGCTACTCCCTTCATAAACTAATAC 57.166 33.333 0.00 0.00 0.00 1.89
123 124 8.548880 AGCTACTCCCTTCATAAACTAATACA 57.451 34.615 0.00 0.00 0.00 2.29
124 125 8.989131 AGCTACTCCCTTCATAAACTAATACAA 58.011 33.333 0.00 0.00 0.00 2.41
125 126 9.262358 GCTACTCCCTTCATAAACTAATACAAG 57.738 37.037 0.00 0.00 0.00 3.16
128 129 7.988028 ACTCCCTTCATAAACTAATACAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
129 130 7.857456 TCCCTTCATAAACTAATACAAGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
130 131 8.494433 TCCCTTCATAAACTAATACAAGAGCAT 58.506 33.333 0.00 0.00 0.00 3.79
131 132 9.125026 CCCTTCATAAACTAATACAAGAGCATT 57.875 33.333 0.00 0.00 0.00 3.56
255 256 8.744652 CCATCGGACTAAGTCTATAAAGATCAT 58.255 37.037 0.00 0.00 33.30 2.45
280 281 7.016361 AGAACGTACATCAATTATTCCTTGC 57.984 36.000 0.00 0.00 0.00 4.01
281 282 5.403897 ACGTACATCAATTATTCCTTGCG 57.596 39.130 0.00 0.00 0.00 4.85
301 302 2.739913 CGTGTCCGTTTGGTGTGAATAT 59.260 45.455 0.00 0.00 36.30 1.28
305 306 4.214545 TGTCCGTTTGGTGTGAATATTGTC 59.785 41.667 0.00 0.00 36.30 3.18
327 329 5.411669 GTCGACCCAAGTTTGATTATTCACT 59.588 40.000 3.51 0.00 0.00 3.41
364 366 6.381481 TGCTTCCACAATTTGATATGCTAG 57.619 37.500 2.79 0.00 0.00 3.42
365 367 6.121590 TGCTTCCACAATTTGATATGCTAGA 58.878 36.000 2.79 0.00 0.00 2.43
368 370 7.040892 GCTTCCACAATTTGATATGCTAGATGA 60.041 37.037 2.79 0.00 0.00 2.92
370 372 6.712095 TCCACAATTTGATATGCTAGATGACC 59.288 38.462 2.79 0.00 0.00 4.02
371 373 6.713903 CCACAATTTGATATGCTAGATGACCT 59.286 38.462 2.79 0.00 0.00 3.85
377 379 7.792374 TTGATATGCTAGATGACCTTCAAAC 57.208 36.000 0.00 0.00 0.00 2.93
385 387 0.387929 TGACCTTCAAACTCGAGCGT 59.612 50.000 13.61 0.00 0.00 5.07
387 389 0.663568 ACCTTCAAACTCGAGCGTCG 60.664 55.000 13.61 0.00 42.10 5.12
399 404 2.417586 TCGAGCGTCGTCAGAAGAATAA 59.582 45.455 7.16 0.00 41.35 1.40
402 407 3.502920 AGCGTCGTCAGAAGAATAACAG 58.497 45.455 0.00 0.00 0.00 3.16
410 415 6.861572 TCGTCAGAAGAATAACAGTTGTACAG 59.138 38.462 0.00 0.00 0.00 2.74
417 422 5.780793 AGAATAACAGTTGTACAGACTCCCT 59.219 40.000 0.00 0.00 0.00 4.20
440 453 1.377725 CTCCGTGGCTTGGAGCAAT 60.378 57.895 11.70 0.00 45.99 3.56
444 457 2.037687 TGGCTTGGAGCAATGGGG 59.962 61.111 2.04 0.00 44.75 4.96
446 459 1.305213 GGCTTGGAGCAATGGGGAA 60.305 57.895 2.04 0.00 44.75 3.97
466 479 7.176589 GGGAATCCCACTCTACTAGATTATG 57.823 44.000 14.67 0.00 44.65 1.90
488 501 1.006086 TGTGCAACATTATCCGCTCG 58.994 50.000 0.00 0.00 45.67 5.03
502 515 8.761497 CATTATCCGCTCGAAAAGACTTATTTA 58.239 33.333 0.00 0.00 0.00 1.40
506 519 6.035650 TCCGCTCGAAAAGACTTATTTACATG 59.964 38.462 0.00 0.00 0.00 3.21
507 520 6.035650 CCGCTCGAAAAGACTTATTTACATGA 59.964 38.462 0.00 0.00 0.00 3.07
508 521 6.895040 CGCTCGAAAAGACTTATTTACATGAC 59.105 38.462 0.00 0.00 0.00 3.06
520 533 9.485206 ACTTATTTACATGACGTAACTTGAAGT 57.515 29.630 0.00 0.00 39.84 3.01
545 558 1.084289 AAAGTTATGGCGCCGACTTC 58.916 50.000 30.39 17.79 31.57 3.01
555 568 1.803519 GCCGACTTCGCTGTCAGAG 60.804 63.158 3.32 0.00 36.82 3.35
567 580 3.403038 GCTGTCAGAGAAGCCTTGTAAA 58.597 45.455 3.32 0.00 33.12 2.01
574 587 3.648545 AGAGAAGCCTTGTAAACTCACCT 59.351 43.478 0.00 0.00 0.00 4.00
630 644 9.149225 CCATAATAATGAAGAAATCGAGAGAGG 57.851 37.037 0.00 0.00 38.42 3.69
690 704 2.107950 TAAATCAACCAGGCTCACCG 57.892 50.000 0.00 0.00 42.76 4.94
702 719 3.876914 CAGGCTCACCGCAAGAATATTTA 59.123 43.478 0.00 0.00 42.76 1.40
705 722 5.594317 AGGCTCACCGCAAGAATATTTATTT 59.406 36.000 0.00 0.00 42.76 1.40
706 723 6.770785 AGGCTCACCGCAAGAATATTTATTTA 59.229 34.615 0.00 0.00 42.76 1.40
709 726 7.266922 TCACCGCAAGAATATTTATTTACCC 57.733 36.000 0.00 0.00 43.02 3.69
759 778 2.162208 CACCACGGACATTGAGAAATGG 59.838 50.000 3.70 0.00 34.56 3.16
760 779 2.039746 ACCACGGACATTGAGAAATGGA 59.960 45.455 3.70 0.00 34.56 3.41
763 782 4.002982 CACGGACATTGAGAAATGGAGAA 58.997 43.478 3.70 0.00 34.56 2.87
768 787 5.819901 GGACATTGAGAAATGGAGAAGTAGG 59.180 44.000 3.70 0.00 34.56 3.18
779 798 3.532232 TGGAGAAGTAGGTGAGGGTATCT 59.468 47.826 0.00 0.00 0.00 1.98
792 811 5.989777 GTGAGGGTATCTACGCAAATACAAT 59.010 40.000 7.11 0.00 41.10 2.71
796 815 7.224297 AGGGTATCTACGCAAATACAATCATT 58.776 34.615 7.11 0.00 41.10 2.57
797 816 7.719633 AGGGTATCTACGCAAATACAATCATTT 59.280 33.333 7.11 0.00 41.10 2.32
808 827 6.594788 AATACAATCATTTGCAAGGTCTGT 57.405 33.333 0.00 4.08 36.22 3.41
810 829 7.701539 ATACAATCATTTGCAAGGTCTGTTA 57.298 32.000 0.00 0.00 36.22 2.41
811 830 6.017400 ACAATCATTTGCAAGGTCTGTTAG 57.983 37.500 0.00 0.00 36.22 2.34
813 832 2.819608 TCATTTGCAAGGTCTGTTAGGC 59.180 45.455 0.00 0.00 0.00 3.93
853 872 3.665675 ATCGCGGGAGAAGTGTGGC 62.666 63.158 6.13 0.00 0.00 5.01
959 978 4.507916 TCTCCTCGCTCCTCCCCG 62.508 72.222 0.00 0.00 0.00 5.73
1046 1066 1.651240 CTCGCAGAATTGGTGGCCAG 61.651 60.000 5.11 0.00 31.61 4.85
1271 1291 3.122111 GTCGTAAGTTCTTCAGCTTCTGC 59.878 47.826 0.00 0.00 37.93 4.26
1272 1292 3.005897 TCGTAAGTTCTTCAGCTTCTGCT 59.994 43.478 0.00 0.00 45.42 4.24
1302 1323 4.846779 GCACTCTTGTGGGAAAACAATA 57.153 40.909 0.00 0.00 43.97 1.90
1303 1324 4.546570 GCACTCTTGTGGGAAAACAATAC 58.453 43.478 0.00 0.00 43.97 1.89
1315 1336 5.077564 GGAAAACAATACTCTTTCCCCTGT 58.922 41.667 2.05 0.00 41.46 4.00
1317 1338 6.041637 GGAAAACAATACTCTTTCCCCTGTTT 59.958 38.462 2.05 0.00 41.46 2.83
1318 1339 7.418597 GGAAAACAATACTCTTTCCCCTGTTTT 60.419 37.037 9.14 9.14 44.07 2.43
1322 1348 6.492429 ACAATACTCTTTCCCCTGTTTTTACC 59.508 38.462 0.00 0.00 0.00 2.85
1328 1354 2.259012 TCCCCTGTTTTTACCGAGCTA 58.741 47.619 0.00 0.00 0.00 3.32
1335 1361 6.183360 CCCTGTTTTTACCGAGCTAATAACAG 60.183 42.308 16.89 16.89 41.07 3.16
1338 1364 8.156994 TGTTTTTACCGAGCTAATAACAGTTT 57.843 30.769 0.00 0.00 29.54 2.66
1409 1435 3.623060 CGTACTACAATTGCATGAAGGCT 59.377 43.478 5.05 0.00 34.04 4.58
1424 1450 0.924823 AGGCTTGCCATCCAGATCTT 59.075 50.000 14.54 0.00 0.00 2.40
1427 1453 1.878734 GCTTGCCATCCAGATCTTAGC 59.121 52.381 0.00 0.00 0.00 3.09
1504 1531 8.028938 CACGGTAAAATCCTGAGAAATGAAAAT 58.971 33.333 0.00 0.00 0.00 1.82
1507 1534 7.702348 GGTAAAATCCTGAGAAATGAAAATCGG 59.298 37.037 0.00 0.00 0.00 4.18
1509 1536 7.651027 AAATCCTGAGAAATGAAAATCGGAT 57.349 32.000 0.00 0.00 31.20 4.18
1512 1539 4.096833 CCTGAGAAATGAAAATCGGATGCA 59.903 41.667 0.00 0.00 0.00 3.96
1513 1540 5.393352 CCTGAGAAATGAAAATCGGATGCAA 60.393 40.000 0.00 0.00 0.00 4.08
1514 1541 6.023357 TGAGAAATGAAAATCGGATGCAAA 57.977 33.333 0.00 0.00 0.00 3.68
1554 1599 7.806690 TGCAATCTAATCTGTGAAGTTAACAC 58.193 34.615 8.61 2.22 38.55 3.32
1577 1622 3.450904 AGCAAGGGATGAACAGGTACTA 58.549 45.455 0.00 0.00 36.02 1.82
1796 1847 1.985614 CTCCCATCTGTGTGCAGGA 59.014 57.895 0.00 0.00 42.78 3.86
1922 1973 1.608055 CCATTGACAGTTGGTGAGCA 58.392 50.000 0.00 0.00 0.00 4.26
1940 1991 4.142337 TGAGCACCATGTCTGCATTATTTG 60.142 41.667 13.51 0.00 37.08 2.32
1954 2005 9.399797 TCTGCATTATTTGATTTGTATCTGTCT 57.600 29.630 0.00 0.00 0.00 3.41
2209 2260 9.261180 GCAGTTAGTTAATATGCAATCACTCTA 57.739 33.333 0.00 0.00 36.88 2.43
2338 2394 3.540617 TGATGTGTTCCGGATGGTAATG 58.459 45.455 4.15 0.00 36.30 1.90
2346 2402 5.046159 TGTTCCGGATGGTAATGTCTTTACT 60.046 40.000 4.15 0.00 40.14 2.24
2381 2437 9.991906 TTACATTTATATCCCCTAACTTTCTCG 57.008 33.333 0.00 0.00 0.00 4.04
2382 2438 8.030913 ACATTTATATCCCCTAACTTTCTCGT 57.969 34.615 0.00 0.00 0.00 4.18
2383 2439 9.151177 ACATTTATATCCCCTAACTTTCTCGTA 57.849 33.333 0.00 0.00 0.00 3.43
2389 2495 4.344102 TCCCCTAACTTTCTCGTATGATGG 59.656 45.833 0.00 0.00 0.00 3.51
2407 2513 0.250640 GGTGGATGGGCTCTATGCAG 60.251 60.000 0.00 0.00 45.15 4.41
2413 2524 2.627515 TGGGCTCTATGCAGTTCATC 57.372 50.000 0.00 0.00 45.15 2.92
2476 2587 5.424252 TCATCCTAAATACGTCCACCTTCTT 59.576 40.000 0.00 0.00 0.00 2.52
2492 2603 8.434392 TCCACCTTCTTAAGTTGTTATTACAGT 58.566 33.333 1.63 0.00 35.28 3.55
2622 2734 1.956477 GCTGGGAGAAAAGACAAGCAA 59.044 47.619 0.00 0.00 0.00 3.91
2643 2755 8.499403 AGCAAAAGTCTTGGTATAATTCTCTC 57.501 34.615 0.00 0.00 0.00 3.20
2706 2827 8.049721 AGGAAAGTTAGGATCATAAACTTCTGG 58.950 37.037 15.47 0.00 41.36 3.86
2711 2832 9.588096 AGTTAGGATCATAAACTTCTGGTTTTT 57.412 29.630 0.58 0.00 44.77 1.94
2712 2833 9.626045 GTTAGGATCATAAACTTCTGGTTTTTG 57.374 33.333 0.58 2.94 44.77 2.44
2738 2859 2.916640 TCAACTGCATGTGTCTTGTCA 58.083 42.857 0.00 0.00 0.00 3.58
2772 2893 5.502544 GCGTAATGTCTTGCAGAATAAGGTC 60.503 44.000 0.00 0.00 0.00 3.85
2797 2918 1.134007 TGCGGATGAGCCAAGATGATT 60.134 47.619 0.00 0.00 35.94 2.57
2877 2998 7.758495 AGAACGGTAAAACTAGCATATTTTGG 58.242 34.615 0.00 0.00 30.80 3.28
2880 3001 6.096282 ACGGTAAAACTAGCATATTTTGGCAT 59.904 34.615 0.00 0.00 30.80 4.40
2887 3008 6.567050 ACTAGCATATTTTGGCATTTGTCAG 58.433 36.000 0.00 0.00 0.00 3.51
2894 3015 1.960417 TGGCATTTGTCAGTTCGTCA 58.040 45.000 0.00 0.00 0.00 4.35
2914 3035 3.723154 TCAGATCATTTGGGATCCCATCA 59.277 43.478 34.21 23.44 46.64 3.07
2927 3048 2.867624 TCCCATCATTTGCCTATCTGC 58.132 47.619 0.00 0.00 0.00 4.26
2943 3065 4.592485 ATCTGCGTTCTAATACTCCTGG 57.408 45.455 0.00 0.00 0.00 4.45
2945 3067 3.767673 TCTGCGTTCTAATACTCCTGGTT 59.232 43.478 0.00 0.00 0.00 3.67
2979 3101 4.039730 CAGAAGAGGACACAAAGGAGAGAA 59.960 45.833 0.00 0.00 0.00 2.87
2993 3115 2.512515 AGAATGAAGCGAGCGGCC 60.513 61.111 0.00 0.00 45.17 6.13
3040 3162 0.756294 TCGAGGAAAGGTGCAGACAA 59.244 50.000 0.00 0.00 0.00 3.18
3067 3189 4.597507 TCCTACATTCAAACTTCCAGAGGT 59.402 41.667 0.00 0.00 0.00 3.85
3097 3219 3.515562 ACCAGGAGTGAGAAGAGAACAT 58.484 45.455 0.00 0.00 0.00 2.71
3111 3233 5.654603 AGAGAACATGGTCGTTACACATA 57.345 39.130 4.80 0.00 0.00 2.29
3209 3331 2.520982 TCCCGCCCTCGATTCGAT 60.521 61.111 9.54 0.00 38.10 3.59
3300 3422 8.497745 AGGATACAGATTCCAGATGTAAAACAT 58.502 33.333 0.00 0.00 39.98 2.71
3359 3491 2.803956 CCTCGACGGTGTGTGTAAAATT 59.196 45.455 0.00 0.00 0.00 1.82
3369 3501 6.334202 GGTGTGTGTAAAATTCAAGTGGAAA 58.666 36.000 0.00 0.00 39.39 3.13
3377 3509 7.714377 TGTAAAATTCAAGTGGAAATGTGCATT 59.286 29.630 0.00 0.00 39.39 3.56
3382 3514 5.916318 TCAAGTGGAAATGTGCATTTTCTT 58.084 33.333 18.75 13.60 40.77 2.52
3384 3516 6.822676 TCAAGTGGAAATGTGCATTTTCTTTT 59.177 30.769 18.75 7.98 40.77 2.27
3385 3517 6.607735 AGTGGAAATGTGCATTTTCTTTTG 57.392 33.333 18.75 0.00 40.77 2.44
3386 3518 5.007921 AGTGGAAATGTGCATTTTCTTTTGC 59.992 36.000 18.75 10.01 40.77 3.68
3388 3520 3.524763 AATGTGCATTTTCTTTTGCGC 57.475 38.095 0.00 0.00 46.76 6.09
3390 3522 2.565367 GTGCATTTTCTTTTGCGCAG 57.435 45.000 11.31 0.00 46.07 5.18
3406 3538 3.867055 CGCAGCTCGTTATCATCAAAT 57.133 42.857 0.00 0.00 0.00 2.32
3407 3539 3.538780 CGCAGCTCGTTATCATCAAATG 58.461 45.455 0.00 0.00 0.00 2.32
3408 3540 3.294943 GCAGCTCGTTATCATCAAATGC 58.705 45.455 0.00 0.00 0.00 3.56
3409 3541 3.851105 GCAGCTCGTTATCATCAAATGCC 60.851 47.826 0.00 0.00 0.00 4.40
3410 3542 2.880890 AGCTCGTTATCATCAAATGCCC 59.119 45.455 0.00 0.00 0.00 5.36
3411 3543 2.349817 GCTCGTTATCATCAAATGCCCG 60.350 50.000 0.00 0.00 0.00 6.13
3412 3544 1.601903 TCGTTATCATCAAATGCCCGC 59.398 47.619 0.00 0.00 0.00 6.13
3413 3545 1.333308 CGTTATCATCAAATGCCCGCA 59.667 47.619 0.00 0.00 0.00 5.69
3414 3546 2.731217 GTTATCATCAAATGCCCGCAC 58.269 47.619 0.00 0.00 0.00 5.34
3415 3547 2.049888 TATCATCAAATGCCCGCACA 57.950 45.000 0.00 0.00 0.00 4.57
3416 3548 1.184431 ATCATCAAATGCCCGCACAA 58.816 45.000 0.00 0.00 0.00 3.33
3535 3677 6.199908 CGTACCAAATTGCAAGATTTTGAACA 59.800 34.615 20.41 6.75 36.36 3.18
3540 3682 6.476243 AATTGCAAGATTTTGAACAGATGC 57.524 33.333 4.94 0.00 36.36 3.91
3543 3685 4.278919 TGCAAGATTTTGAACAGATGCAGA 59.721 37.500 0.00 0.00 37.61 4.26
3549 3691 2.574006 TGAACAGATGCAGAGCCTTT 57.426 45.000 0.00 0.00 0.00 3.11
3563 3705 1.137872 AGCCTTTATCTGACCGAGCAG 59.862 52.381 0.00 0.00 37.24 4.24
3569 3711 1.830587 ATCTGACCGAGCAGGCAACA 61.831 55.000 4.95 0.00 46.52 3.33
3734 3876 2.028337 GGATCCGCTCTTCTCGCC 59.972 66.667 0.00 0.00 0.00 5.54
3776 3918 1.750778 ACGCATTTGGGATGTTGATCC 59.249 47.619 1.25 0.00 46.99 3.36
3779 3921 2.482490 GCATTTGGGATGTTGATCCTGC 60.482 50.000 0.00 0.00 46.88 4.85
3796 3938 2.034066 CTTCCTGGGCGGCTTCAA 59.966 61.111 9.56 0.00 0.00 2.69
3803 3945 2.391389 GGGCGGCTTCAACTCTTCG 61.391 63.158 9.56 0.00 0.00 3.79
3807 3949 1.355066 CGGCTTCAACTCTTCGGAGC 61.355 60.000 0.00 0.00 45.43 4.70
3808 3950 0.320771 GGCTTCAACTCTTCGGAGCA 60.321 55.000 0.00 0.00 45.43 4.26
3900 4042 1.373570 GTCGCCCTCCATTTCTTCTG 58.626 55.000 0.00 0.00 0.00 3.02
3901 4043 0.392998 TCGCCCTCCATTTCTTCTGC 60.393 55.000 0.00 0.00 0.00 4.26
3920 4065 5.977635 TCTGCTAGCTTCTTGTTGCTATTA 58.022 37.500 17.23 0.00 40.43 0.98
3930 4075 4.158949 TCTTGTTGCTATTACTACAGGCGA 59.841 41.667 0.00 0.00 0.00 5.54
3932 4077 3.446161 TGTTGCTATTACTACAGGCGACT 59.554 43.478 0.00 0.00 46.44 4.18
3993 4146 2.238521 GGCCATGTCTGAAGTTTGGAA 58.761 47.619 0.00 0.00 0.00 3.53
4012 4165 3.546724 GAATGGGGGAGAGCTTTTACTC 58.453 50.000 0.00 0.00 36.91 2.59
4053 4206 1.374758 CTCGGTGCTTCTGGTCACC 60.375 63.158 1.54 1.54 46.95 4.02
4070 4223 1.463444 CACCGAATGACCGAAAAGTCC 59.537 52.381 0.00 0.00 35.83 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.926674 TCAATTATTCATGCTTCAGACTTCA 57.073 32.000 0.00 0.00 0.00 3.02
10 11 9.359653 GGGGCTATATATTCAATTATTCATGCT 57.640 33.333 0.00 0.00 0.00 3.79
11 12 9.359653 AGGGGCTATATATTCAATTATTCATGC 57.640 33.333 0.00 0.00 0.00 4.06
19 20 9.247861 GATTGTGAAGGGGCTATATATTCAATT 57.752 33.333 0.00 0.00 32.13 2.32
20 21 7.836183 GGATTGTGAAGGGGCTATATATTCAAT 59.164 37.037 0.00 0.00 32.13 2.57
21 22 7.175104 GGATTGTGAAGGGGCTATATATTCAA 58.825 38.462 0.00 0.00 32.13 2.69
22 23 6.274436 TGGATTGTGAAGGGGCTATATATTCA 59.726 38.462 0.00 0.00 0.00 2.57
23 24 6.721318 TGGATTGTGAAGGGGCTATATATTC 58.279 40.000 0.00 0.00 0.00 1.75
24 25 6.718593 TGGATTGTGAAGGGGCTATATATT 57.281 37.500 0.00 0.00 0.00 1.28
25 26 6.485171 GTTGGATTGTGAAGGGGCTATATAT 58.515 40.000 0.00 0.00 0.00 0.86
26 27 5.222048 GGTTGGATTGTGAAGGGGCTATATA 60.222 44.000 0.00 0.00 0.00 0.86
27 28 4.447762 GGTTGGATTGTGAAGGGGCTATAT 60.448 45.833 0.00 0.00 0.00 0.86
28 29 3.117663 GGTTGGATTGTGAAGGGGCTATA 60.118 47.826 0.00 0.00 0.00 1.31
29 30 2.358195 GGTTGGATTGTGAAGGGGCTAT 60.358 50.000 0.00 0.00 0.00 2.97
30 31 1.005450 GGTTGGATTGTGAAGGGGCTA 59.995 52.381 0.00 0.00 0.00 3.93
31 32 0.251787 GGTTGGATTGTGAAGGGGCT 60.252 55.000 0.00 0.00 0.00 5.19
32 33 0.251787 AGGTTGGATTGTGAAGGGGC 60.252 55.000 0.00 0.00 0.00 5.80
33 34 2.171003 GAAGGTTGGATTGTGAAGGGG 58.829 52.381 0.00 0.00 0.00 4.79
34 35 3.084786 GAGAAGGTTGGATTGTGAAGGG 58.915 50.000 0.00 0.00 0.00 3.95
35 36 3.754965 TGAGAAGGTTGGATTGTGAAGG 58.245 45.455 0.00 0.00 0.00 3.46
36 37 4.217118 CCTTGAGAAGGTTGGATTGTGAAG 59.783 45.833 0.00 0.00 43.95 3.02
37 38 4.144297 CCTTGAGAAGGTTGGATTGTGAA 58.856 43.478 0.00 0.00 43.95 3.18
38 39 3.754965 CCTTGAGAAGGTTGGATTGTGA 58.245 45.455 0.00 0.00 43.95 3.58
67 68 6.862469 ATGATGGATTCATGGTGTCTTTTT 57.138 33.333 0.00 0.00 43.60 1.94
68 69 8.543293 AATATGATGGATTCATGGTGTCTTTT 57.457 30.769 0.00 0.00 44.90 2.27
69 70 9.071276 GTAATATGATGGATTCATGGTGTCTTT 57.929 33.333 0.00 0.00 44.90 2.52
70 71 8.219868 TGTAATATGATGGATTCATGGTGTCTT 58.780 33.333 0.00 0.00 44.90 3.01
71 72 7.748677 TGTAATATGATGGATTCATGGTGTCT 58.251 34.615 0.00 0.00 44.90 3.41
72 73 7.984422 TGTAATATGATGGATTCATGGTGTC 57.016 36.000 0.00 0.00 44.90 3.67
73 74 8.765488 TTTGTAATATGATGGATTCATGGTGT 57.235 30.769 0.00 0.00 44.90 4.16
74 75 7.811236 GCTTTGTAATATGATGGATTCATGGTG 59.189 37.037 0.00 0.00 44.90 4.17
75 76 7.727186 AGCTTTGTAATATGATGGATTCATGGT 59.273 33.333 0.00 0.00 44.90 3.55
76 77 8.118976 AGCTTTGTAATATGATGGATTCATGG 57.881 34.615 0.00 0.00 44.90 3.66
79 80 9.494271 GAGTAGCTTTGTAATATGATGGATTCA 57.506 33.333 0.00 0.00 39.12 2.57
80 81 8.940952 GGAGTAGCTTTGTAATATGATGGATTC 58.059 37.037 0.00 0.00 0.00 2.52
81 82 7.885399 GGGAGTAGCTTTGTAATATGATGGATT 59.115 37.037 0.00 0.00 0.00 3.01
82 83 7.238514 AGGGAGTAGCTTTGTAATATGATGGAT 59.761 37.037 0.00 0.00 0.00 3.41
83 84 6.558775 AGGGAGTAGCTTTGTAATATGATGGA 59.441 38.462 0.00 0.00 0.00 3.41
84 85 6.773638 AGGGAGTAGCTTTGTAATATGATGG 58.226 40.000 0.00 0.00 0.00 3.51
85 86 7.933577 TGAAGGGAGTAGCTTTGTAATATGATG 59.066 37.037 0.00 0.00 0.00 3.07
86 87 8.034313 TGAAGGGAGTAGCTTTGTAATATGAT 57.966 34.615 0.00 0.00 0.00 2.45
87 88 7.432148 TGAAGGGAGTAGCTTTGTAATATGA 57.568 36.000 0.00 0.00 0.00 2.15
88 89 9.778741 TTATGAAGGGAGTAGCTTTGTAATATG 57.221 33.333 0.00 0.00 0.00 1.78
90 91 9.609346 GTTTATGAAGGGAGTAGCTTTGTAATA 57.391 33.333 0.00 0.00 0.00 0.98
91 92 8.329502 AGTTTATGAAGGGAGTAGCTTTGTAAT 58.670 33.333 0.00 0.00 0.00 1.89
92 93 7.686434 AGTTTATGAAGGGAGTAGCTTTGTAA 58.314 34.615 0.00 0.00 0.00 2.41
93 94 7.253905 AGTTTATGAAGGGAGTAGCTTTGTA 57.746 36.000 0.00 0.00 0.00 2.41
94 95 6.128138 AGTTTATGAAGGGAGTAGCTTTGT 57.872 37.500 0.00 0.00 0.00 2.83
95 96 8.738645 ATTAGTTTATGAAGGGAGTAGCTTTG 57.261 34.615 0.00 0.00 0.00 2.77
96 97 9.833917 GTATTAGTTTATGAAGGGAGTAGCTTT 57.166 33.333 0.00 0.00 0.00 3.51
97 98 8.989131 TGTATTAGTTTATGAAGGGAGTAGCTT 58.011 33.333 0.00 0.00 0.00 3.74
98 99 8.548880 TGTATTAGTTTATGAAGGGAGTAGCT 57.451 34.615 0.00 0.00 0.00 3.32
99 100 9.262358 CTTGTATTAGTTTATGAAGGGAGTAGC 57.738 37.037 0.00 0.00 0.00 3.58
102 103 7.988028 GCTCTTGTATTAGTTTATGAAGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
103 104 7.987458 TGCTCTTGTATTAGTTTATGAAGGGAG 59.013 37.037 0.00 0.00 0.00 4.30
104 105 7.857456 TGCTCTTGTATTAGTTTATGAAGGGA 58.143 34.615 0.00 0.00 0.00 4.20
105 106 8.682936 ATGCTCTTGTATTAGTTTATGAAGGG 57.317 34.615 0.00 0.00 0.00 3.95
255 256 7.042992 CGCAAGGAATAATTGATGTACGTTCTA 60.043 37.037 0.00 0.00 0.00 2.10
256 257 6.238103 CGCAAGGAATAATTGATGTACGTTCT 60.238 38.462 0.00 0.00 0.00 3.01
257 258 5.901884 CGCAAGGAATAATTGATGTACGTTC 59.098 40.000 0.00 0.00 0.00 3.95
258 259 5.353123 ACGCAAGGAATAATTGATGTACGTT 59.647 36.000 0.00 0.00 46.39 3.99
259 260 4.873827 ACGCAAGGAATAATTGATGTACGT 59.126 37.500 0.00 0.00 46.39 3.57
260 261 5.197549 CACGCAAGGAATAATTGATGTACG 58.802 41.667 0.00 0.00 46.39 3.67
261 262 6.119144 ACACGCAAGGAATAATTGATGTAC 57.881 37.500 0.00 0.00 46.39 2.90
262 263 5.295787 GGACACGCAAGGAATAATTGATGTA 59.704 40.000 0.00 0.00 46.39 2.29
263 264 4.096382 GGACACGCAAGGAATAATTGATGT 59.904 41.667 0.00 0.00 46.39 3.06
264 265 4.601019 GGACACGCAAGGAATAATTGATG 58.399 43.478 0.00 0.00 46.39 3.07
265 266 3.312421 CGGACACGCAAGGAATAATTGAT 59.688 43.478 0.00 0.00 46.39 2.57
266 267 2.675844 CGGACACGCAAGGAATAATTGA 59.324 45.455 0.00 0.00 46.39 2.57
267 268 2.418628 ACGGACACGCAAGGAATAATTG 59.581 45.455 0.00 0.00 46.04 2.32
268 269 2.706890 ACGGACACGCAAGGAATAATT 58.293 42.857 0.00 0.00 46.04 1.40
269 270 2.396590 ACGGACACGCAAGGAATAAT 57.603 45.000 0.00 0.00 46.04 1.28
270 271 2.172851 AACGGACACGCAAGGAATAA 57.827 45.000 0.00 0.00 46.04 1.40
271 272 1.801771 CAAACGGACACGCAAGGAATA 59.198 47.619 0.00 0.00 46.04 1.75
272 273 0.591170 CAAACGGACACGCAAGGAAT 59.409 50.000 0.00 0.00 46.04 3.01
273 274 1.440938 CCAAACGGACACGCAAGGAA 61.441 55.000 0.00 0.00 46.04 3.36
274 275 1.890041 CCAAACGGACACGCAAGGA 60.890 57.895 0.00 0.00 46.04 3.36
275 276 2.184167 ACCAAACGGACACGCAAGG 61.184 57.895 0.00 0.00 46.04 3.61
276 277 1.010125 CACCAAACGGACACGCAAG 60.010 57.895 0.00 0.00 46.04 4.01
277 278 1.745864 ACACCAAACGGACACGCAA 60.746 52.632 0.00 0.00 46.04 4.85
278 279 2.125065 ACACCAAACGGACACGCA 60.125 55.556 0.00 0.00 46.04 5.24
279 280 1.707239 TTCACACCAAACGGACACGC 61.707 55.000 0.00 0.00 46.04 5.34
281 282 4.023536 ACAATATTCACACCAAACGGACAC 60.024 41.667 0.00 0.00 0.00 3.67
301 302 5.765677 TGAATAATCAAACTTGGGTCGACAA 59.234 36.000 18.91 2.86 30.99 3.18
305 306 5.411361 TGAGTGAATAATCAAACTTGGGTCG 59.589 40.000 0.00 0.00 37.30 4.79
339 341 5.839621 AGCATATCAAATTGTGGAAGCATC 58.160 37.500 0.00 0.00 0.00 3.91
364 366 1.656095 CGCTCGAGTTTGAAGGTCATC 59.344 52.381 15.13 0.00 0.00 2.92
365 367 1.000955 ACGCTCGAGTTTGAAGGTCAT 59.999 47.619 15.13 0.00 0.00 3.06
368 370 0.663568 CGACGCTCGAGTTTGAAGGT 60.664 55.000 15.13 1.14 43.74 3.50
370 372 0.703466 GACGACGCTCGAGTTTGAAG 59.297 55.000 15.13 3.95 43.74 3.02
371 373 0.029700 TGACGACGCTCGAGTTTGAA 59.970 50.000 15.13 0.00 43.74 2.69
377 379 0.166161 TTCTTCTGACGACGCTCGAG 59.834 55.000 8.45 8.45 43.74 4.04
385 387 6.741109 TGTACAACTGTTATTCTTCTGACGA 58.259 36.000 0.00 0.00 0.00 4.20
387 389 7.868415 AGTCTGTACAACTGTTATTCTTCTGAC 59.132 37.037 9.11 2.39 0.00 3.51
399 404 1.887198 CGAGGGAGTCTGTACAACTGT 59.113 52.381 13.23 0.00 0.00 3.55
402 407 3.018149 AGATCGAGGGAGTCTGTACAAC 58.982 50.000 0.00 0.00 0.00 3.32
410 415 1.448922 CCACGGAGATCGAGGGAGTC 61.449 65.000 0.00 0.00 44.19 3.36
417 422 1.680989 TCCAAGCCACGGAGATCGA 60.681 57.895 0.00 0.00 42.43 3.59
444 457 7.233389 TGCATAATCTAGTAGAGTGGGATTC 57.767 40.000 10.34 0.00 0.00 2.52
446 459 6.728164 ACATGCATAATCTAGTAGAGTGGGAT 59.272 38.462 10.34 6.38 0.00 3.85
466 479 1.066002 AGCGGATAATGTTGCACATGC 59.934 47.619 0.00 0.00 37.97 4.06
475 488 4.124851 AGTCTTTTCGAGCGGATAATGT 57.875 40.909 0.00 0.00 0.00 2.71
484 497 6.895040 CGTCATGTAAATAAGTCTTTTCGAGC 59.105 38.462 0.00 0.00 0.00 5.03
502 515 5.597806 TCAAGACTTCAAGTTACGTCATGT 58.402 37.500 0.00 0.00 0.00 3.21
506 519 7.001695 ACTTTTCAAGACTTCAAGTTACGTC 57.998 36.000 0.00 0.00 0.00 4.34
507 520 6.980051 ACTTTTCAAGACTTCAAGTTACGT 57.020 33.333 0.00 0.00 0.00 3.57
508 521 9.370126 CATAACTTTTCAAGACTTCAAGTTACG 57.630 33.333 17.99 11.38 40.79 3.18
520 533 1.466950 CGGCGCCATAACTTTTCAAGA 59.533 47.619 28.98 0.00 0.00 3.02
545 558 0.320247 ACAAGGCTTCTCTGACAGCG 60.320 55.000 0.00 0.00 36.85 5.18
555 568 2.226674 GCAGGTGAGTTTACAAGGCTTC 59.773 50.000 0.00 0.00 0.00 3.86
599 613 5.791974 CGATTTCTTCATTATTATGGCTGCG 59.208 40.000 0.00 0.00 32.40 5.18
630 644 6.092944 TCAAATGCAAGCCATCATCAAATTTC 59.907 34.615 0.00 0.00 31.43 2.17
662 676 8.708742 GTGAGCCTGGTTGATTTAAAATAAAAC 58.291 33.333 0.00 0.00 0.00 2.43
672 686 1.244019 GCGGTGAGCCTGGTTGATTT 61.244 55.000 0.00 0.00 40.81 2.17
673 687 1.675641 GCGGTGAGCCTGGTTGATT 60.676 57.895 0.00 0.00 40.81 2.57
759 778 4.756135 CGTAGATACCCTCACCTACTTCTC 59.244 50.000 0.00 0.00 31.78 2.87
760 779 4.716794 CGTAGATACCCTCACCTACTTCT 58.283 47.826 0.00 0.00 31.78 2.85
763 782 2.174210 TGCGTAGATACCCTCACCTACT 59.826 50.000 0.00 0.00 31.78 2.57
768 787 4.940463 TGTATTTGCGTAGATACCCTCAC 58.060 43.478 10.87 0.00 0.00 3.51
792 811 2.819608 GCCTAACAGACCTTGCAAATGA 59.180 45.455 0.00 0.00 0.00 2.57
796 815 0.394938 TCGCCTAACAGACCTTGCAA 59.605 50.000 0.00 0.00 0.00 4.08
797 816 0.394938 TTCGCCTAACAGACCTTGCA 59.605 50.000 0.00 0.00 0.00 4.08
806 825 1.342174 ACCGTTCTTCTTCGCCTAACA 59.658 47.619 0.00 0.00 0.00 2.41
808 827 1.337447 CCACCGTTCTTCTTCGCCTAA 60.337 52.381 0.00 0.00 0.00 2.69
810 829 1.004918 CCACCGTTCTTCTTCGCCT 60.005 57.895 0.00 0.00 0.00 5.52
811 830 1.005394 TCCACCGTTCTTCTTCGCC 60.005 57.895 0.00 0.00 0.00 5.54
813 832 2.433868 TTCTCCACCGTTCTTCTTCG 57.566 50.000 0.00 0.00 0.00 3.79
878 897 2.050077 GCTGCGTTTTCCTGGCAC 60.050 61.111 0.00 0.00 32.46 5.01
959 978 4.388499 TTTCGGTGCGAGGGAGGC 62.388 66.667 0.00 0.00 37.14 4.70
984 1004 1.541233 GCCATCGGGTAGAGGATGTTG 60.541 57.143 0.98 0.00 38.66 3.33
1032 1052 1.384191 GGACCTGGCCACCAATTCT 59.616 57.895 0.00 0.00 30.80 2.40
1035 1055 1.814292 AATGGGACCTGGCCACCAAT 61.814 55.000 16.15 5.92 36.44 3.16
1036 1056 2.439553 GAATGGGACCTGGCCACCAA 62.440 60.000 16.15 3.51 36.44 3.67
1046 1066 1.915983 GTGGAGGAGGAATGGGACC 59.084 63.158 0.00 0.00 0.00 4.46
1125 1145 2.032071 CGGTGGCGGTCTTTCCTT 59.968 61.111 0.00 0.00 0.00 3.36
1130 1150 3.692406 GTCTCCGGTGGCGGTCTT 61.692 66.667 0.00 0.00 0.00 3.01
1271 1291 1.979469 CACAAGAGTGCGAACGAGTAG 59.021 52.381 0.00 0.00 39.21 2.57
1272 1292 1.335597 CCACAAGAGTGCGAACGAGTA 60.336 52.381 0.00 0.00 44.53 2.59
1302 1323 3.136992 TCGGTAAAAACAGGGGAAAGAGT 59.863 43.478 0.00 0.00 0.00 3.24
1303 1324 3.746940 TCGGTAAAAACAGGGGAAAGAG 58.253 45.455 0.00 0.00 0.00 2.85
1315 1336 8.611654 AGAAACTGTTATTAGCTCGGTAAAAA 57.388 30.769 0.00 0.00 0.00 1.94
1317 1338 6.815142 GGAGAAACTGTTATTAGCTCGGTAAA 59.185 38.462 0.00 0.00 0.00 2.01
1318 1339 6.071221 TGGAGAAACTGTTATTAGCTCGGTAA 60.071 38.462 0.00 0.00 0.00 2.85
1322 1348 5.812642 ACATGGAGAAACTGTTATTAGCTCG 59.187 40.000 0.00 0.00 0.00 5.03
1328 1354 8.463930 TCTGAAAACATGGAGAAACTGTTATT 57.536 30.769 0.00 0.00 33.01 1.40
1335 1361 4.488879 GGCATCTGAAAACATGGAGAAAC 58.511 43.478 0.00 0.00 0.00 2.78
1338 1364 2.358957 CGGCATCTGAAAACATGGAGA 58.641 47.619 0.00 0.00 0.00 3.71
1409 1435 1.202687 CCGCTAAGATCTGGATGGCAA 60.203 52.381 0.00 0.00 0.00 4.52
1504 1531 3.513662 CAAATTGCTCATTTGCATCCGA 58.486 40.909 8.44 0.00 44.18 4.55
1541 1583 2.869801 CCTTGCTCGTGTTAACTTCACA 59.130 45.455 7.22 0.00 35.79 3.58
1542 1584 2.223377 CCCTTGCTCGTGTTAACTTCAC 59.777 50.000 7.22 0.00 0.00 3.18
1554 1599 0.036010 ACCTGTTCATCCCTTGCTCG 60.036 55.000 0.00 0.00 0.00 5.03
1577 1622 4.096003 CGCTGGATGGGGTCGGTT 62.096 66.667 0.00 0.00 0.00 4.44
1765 1816 4.225942 ACAGATGGGAGCAGAACTTGAATA 59.774 41.667 0.00 0.00 0.00 1.75
1769 1820 2.082231 CACAGATGGGAGCAGAACTTG 58.918 52.381 0.00 0.00 0.00 3.16
1796 1847 7.038154 ACACACATTAGCACAGTTTTTACAT 57.962 32.000 0.00 0.00 0.00 2.29
1922 1973 6.938507 ACAAATCAAATAATGCAGACATGGT 58.061 32.000 0.00 0.00 36.36 3.55
1940 1991 8.400947 TGTTACGGTAGTAGACAGATACAAATC 58.599 37.037 0.00 0.00 33.87 2.17
1954 2005 6.892658 TTCAGTAGGTTTGTTACGGTAGTA 57.107 37.500 0.00 0.00 0.00 1.82
2266 2322 2.961741 TGCAACCTGCTCAAATGGTAAA 59.038 40.909 0.00 0.00 45.31 2.01
2269 2325 1.636148 ATGCAACCTGCTCAAATGGT 58.364 45.000 0.00 0.00 45.31 3.55
2365 2421 5.012148 CCATCATACGAGAAAGTTAGGGGAT 59.988 44.000 0.00 0.00 0.00 3.85
2381 2437 1.701847 AGAGCCCATCCACCATCATAC 59.298 52.381 0.00 0.00 0.00 2.39
2382 2438 2.123018 AGAGCCCATCCACCATCATA 57.877 50.000 0.00 0.00 0.00 2.15
2383 2439 2.123018 TAGAGCCCATCCACCATCAT 57.877 50.000 0.00 0.00 0.00 2.45
2389 2495 0.471617 ACTGCATAGAGCCCATCCAC 59.528 55.000 0.00 0.00 44.83 4.02
2443 2554 9.621629 TGGACGTATTTAGGATGAACATTAATT 57.378 29.630 0.00 0.00 0.00 1.40
2444 2555 9.052759 GTGGACGTATTTAGGATGAACATTAAT 57.947 33.333 0.00 0.00 0.00 1.40
2445 2556 7.496591 GGTGGACGTATTTAGGATGAACATTAA 59.503 37.037 0.00 0.00 0.00 1.40
2446 2557 6.987992 GGTGGACGTATTTAGGATGAACATTA 59.012 38.462 0.00 0.00 0.00 1.90
2447 2558 5.820947 GGTGGACGTATTTAGGATGAACATT 59.179 40.000 0.00 0.00 0.00 2.71
2448 2559 5.130477 AGGTGGACGTATTTAGGATGAACAT 59.870 40.000 0.00 0.00 0.00 2.71
2449 2560 4.468510 AGGTGGACGTATTTAGGATGAACA 59.531 41.667 0.00 0.00 0.00 3.18
2450 2561 5.019785 AGGTGGACGTATTTAGGATGAAC 57.980 43.478 0.00 0.00 0.00 3.18
2451 2562 5.424252 AGAAGGTGGACGTATTTAGGATGAA 59.576 40.000 0.00 0.00 0.00 2.57
2452 2563 4.960469 AGAAGGTGGACGTATTTAGGATGA 59.040 41.667 0.00 0.00 0.00 2.92
2453 2564 5.277857 AGAAGGTGGACGTATTTAGGATG 57.722 43.478 0.00 0.00 0.00 3.51
2454 2565 5.952347 AAGAAGGTGGACGTATTTAGGAT 57.048 39.130 0.00 0.00 0.00 3.24
2455 2566 6.438425 ACTTAAGAAGGTGGACGTATTTAGGA 59.562 38.462 10.09 0.00 0.00 2.94
2456 2567 6.637657 ACTTAAGAAGGTGGACGTATTTAGG 58.362 40.000 10.09 0.00 0.00 2.69
2492 2603 6.765403 ACTGTGGTTTAAACTGCATAGAGTA 58.235 36.000 20.30 0.35 0.00 2.59
2622 2734 8.750298 TCGAAGAGAGAATTATACCAAGACTTT 58.250 33.333 0.00 0.00 0.00 2.66
2643 2755 8.993121 ACATATAAAGAAAGCCATGTATCGAAG 58.007 33.333 0.00 0.00 0.00 3.79
2706 2827 6.642131 ACACATGCAGTTGATATGTCAAAAAC 59.358 34.615 6.45 0.00 45.38 2.43
2711 2832 4.835678 AGACACATGCAGTTGATATGTCA 58.164 39.130 10.43 0.00 37.93 3.58
2712 2833 5.122869 ACAAGACACATGCAGTTGATATGTC 59.877 40.000 4.40 3.47 33.06 3.06
2738 2859 1.759445 AGACATTACGCAGAGGCTCAT 59.241 47.619 18.26 1.50 38.10 2.90
2772 2893 1.153107 TTGGCTCATCCGCATCCTG 60.153 57.895 0.00 0.00 37.80 3.86
2797 2918 2.642311 TCCATGAACTGCCCTTGTTAGA 59.358 45.455 0.00 0.00 0.00 2.10
2877 2998 3.433274 TGATCTGACGAACTGACAAATGC 59.567 43.478 0.00 0.00 0.00 3.56
2880 3001 5.049474 CCAAATGATCTGACGAACTGACAAA 60.049 40.000 0.00 0.00 0.00 2.83
2887 3008 3.561725 GGATCCCAAATGATCTGACGAAC 59.438 47.826 0.00 0.00 40.80 3.95
2914 3035 6.525629 AGTATTAGAACGCAGATAGGCAAAT 58.474 36.000 0.00 0.00 0.00 2.32
2927 3048 6.475727 CACATGTAACCAGGAGTATTAGAACG 59.524 42.308 0.00 0.00 0.00 3.95
2943 3065 5.758296 TGTCCTCTTCTGTTTCACATGTAAC 59.242 40.000 0.00 0.65 0.00 2.50
2945 3067 5.163353 TGTGTCCTCTTCTGTTTCACATGTA 60.163 40.000 0.00 0.00 31.03 2.29
3003 3125 2.339728 GAGTATTCTCGCCATCTCCG 57.660 55.000 0.00 0.00 0.00 4.63
3040 3162 3.330701 TGGAAGTTTGAATGTAGGAGGCT 59.669 43.478 0.00 0.00 0.00 4.58
3067 3189 0.541063 TCACTCCTGGTTGGACGCTA 60.541 55.000 0.00 0.00 40.56 4.26
3111 3233 5.596845 ACGCTTCATAAAACCACACATTTT 58.403 33.333 0.00 0.00 33.85 1.82
3209 3331 6.859017 TGATTTACAGATACTGCTAACACGA 58.141 36.000 0.00 0.00 34.37 4.35
3300 3422 2.027561 GGGCCACTGTCTATTGTACACA 60.028 50.000 4.39 0.00 0.00 3.72
3359 3491 5.534207 AGAAAATGCACATTTCCACTTGA 57.466 34.783 18.37 0.00 39.88 3.02
3369 3501 2.477375 CTGCGCAAAAGAAAATGCACAT 59.523 40.909 13.05 0.00 42.68 3.21
3377 3509 0.380378 AACGAGCTGCGCAAAAGAAA 59.620 45.000 13.05 0.00 46.04 2.52
3382 3514 1.327460 GATGATAACGAGCTGCGCAAA 59.673 47.619 13.05 0.00 46.04 3.68
3384 3516 0.179113 TGATGATAACGAGCTGCGCA 60.179 50.000 10.98 10.98 46.04 6.09
3385 3517 0.930310 TTGATGATAACGAGCTGCGC 59.070 50.000 0.00 0.00 46.04 6.09
3388 3520 3.304257 GGGCATTTGATGATAACGAGCTG 60.304 47.826 0.00 0.00 0.00 4.24
3389 3521 2.880890 GGGCATTTGATGATAACGAGCT 59.119 45.455 0.00 0.00 0.00 4.09
3390 3522 2.349817 CGGGCATTTGATGATAACGAGC 60.350 50.000 0.00 0.00 0.00 5.03
3391 3523 2.349817 GCGGGCATTTGATGATAACGAG 60.350 50.000 0.00 0.00 0.00 4.18
3392 3524 1.601903 GCGGGCATTTGATGATAACGA 59.398 47.619 0.00 0.00 0.00 3.85
3393 3525 1.333308 TGCGGGCATTTGATGATAACG 59.667 47.619 0.00 0.00 0.00 3.18
3394 3526 2.098934 TGTGCGGGCATTTGATGATAAC 59.901 45.455 0.00 0.00 0.00 1.89
3395 3527 2.373224 TGTGCGGGCATTTGATGATAA 58.627 42.857 0.00 0.00 0.00 1.75
3396 3528 2.049888 TGTGCGGGCATTTGATGATA 57.950 45.000 0.00 0.00 0.00 2.15
3397 3529 1.184431 TTGTGCGGGCATTTGATGAT 58.816 45.000 0.00 0.00 0.00 2.45
3398 3530 1.135053 CATTGTGCGGGCATTTGATGA 60.135 47.619 0.00 0.00 0.00 2.92
3399 3531 1.135053 TCATTGTGCGGGCATTTGATG 60.135 47.619 0.00 0.16 0.00 3.07
3400 3532 1.184431 TCATTGTGCGGGCATTTGAT 58.816 45.000 0.00 0.00 0.00 2.57
3401 3533 0.964700 TTCATTGTGCGGGCATTTGA 59.035 45.000 0.00 0.00 0.00 2.69
3402 3534 1.793258 TTTCATTGTGCGGGCATTTG 58.207 45.000 0.00 0.00 0.00 2.32
3403 3535 2.348660 CATTTCATTGTGCGGGCATTT 58.651 42.857 0.00 0.00 0.00 2.32
3404 3536 2.008045 GCATTTCATTGTGCGGGCATT 61.008 47.619 0.00 0.00 0.00 3.56
3405 3537 0.460635 GCATTTCATTGTGCGGGCAT 60.461 50.000 0.00 0.00 0.00 4.40
3406 3538 1.079956 GCATTTCATTGTGCGGGCA 60.080 52.632 0.00 0.00 0.00 5.36
3407 3539 3.784746 GCATTTCATTGTGCGGGC 58.215 55.556 0.00 0.00 0.00 6.13
3412 3544 1.265568 GAGCTGCGCATTTCATTGTG 58.734 50.000 12.24 0.00 0.00 3.33
3413 3545 0.883153 TGAGCTGCGCATTTCATTGT 59.117 45.000 12.24 0.00 0.00 2.71
3414 3546 2.203800 ATGAGCTGCGCATTTCATTG 57.796 45.000 23.41 8.30 0.00 2.82
3415 3547 2.292569 CCTATGAGCTGCGCATTTCATT 59.707 45.455 29.80 18.99 32.83 2.57
3416 3548 1.878088 CCTATGAGCTGCGCATTTCAT 59.122 47.619 28.49 28.49 34.81 2.57
3535 3677 3.181456 GGTCAGATAAAGGCTCTGCATCT 60.181 47.826 0.00 0.00 39.98 2.90
3540 3682 2.801342 GCTCGGTCAGATAAAGGCTCTG 60.801 54.545 0.00 0.00 41.23 3.35
3543 3685 1.137872 CTGCTCGGTCAGATAAAGGCT 59.862 52.381 0.00 0.00 36.19 4.58
3549 3691 0.175760 GTTGCCTGCTCGGTCAGATA 59.824 55.000 6.44 0.00 36.19 1.98
3563 3705 2.677524 TGGGCTCATGCTGTTGCC 60.678 61.111 0.00 0.00 44.22 4.52
3569 3711 3.005539 AGGTCGTGGGCTCATGCT 61.006 61.111 0.00 0.00 39.59 3.79
3710 3852 0.105778 GAAGAGCGGATCCAGGAAGG 59.894 60.000 13.41 0.00 39.47 3.46
3716 3858 2.786495 GGCGAGAAGAGCGGATCCA 61.786 63.158 13.41 0.00 35.00 3.41
3734 3876 4.436998 GACGAGGTGACGCTGGGG 62.437 72.222 0.00 0.00 36.70 4.96
3776 3918 4.729918 AAGCCGCCCAGGAAGCAG 62.730 66.667 0.00 0.00 45.00 4.24
3779 3921 2.034066 TTGAAGCCGCCCAGGAAG 59.966 61.111 0.00 0.00 45.00 3.46
3796 3938 0.320247 CAAGCAGTGCTCCGAAGAGT 60.320 55.000 20.03 0.00 42.59 3.24
3803 3945 2.866028 CGCTTCAAGCAGTGCTCC 59.134 61.111 20.03 4.01 42.58 4.70
3807 3949 4.748679 GCCGCGCTTCAAGCAGTG 62.749 66.667 10.73 8.82 42.58 3.66
3900 4042 6.757010 TGTAGTAATAGCAACAAGAAGCTAGC 59.243 38.462 6.62 6.62 45.53 3.42
3901 4043 7.436673 CCTGTAGTAATAGCAACAAGAAGCTAG 59.563 40.741 0.00 0.00 45.53 3.42
3920 4065 3.391382 GCCCCAGTCGCCTGTAGT 61.391 66.667 0.00 0.00 36.95 2.73
3930 4075 0.112412 AAATTCCACTTCGCCCCAGT 59.888 50.000 0.00 0.00 0.00 4.00
3932 4077 0.897863 CCAAATTCCACTTCGCCCCA 60.898 55.000 0.00 0.00 0.00 4.96
3993 4146 1.847088 GGAGTAAAAGCTCTCCCCCAT 59.153 52.381 7.79 0.00 42.96 4.00
4053 4206 1.463444 GGTGGACTTTTCGGTCATTCG 59.537 52.381 0.00 0.00 37.91 3.34


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

AutoCloner maintained by Alex Coulton.