Multiple sequence alignment - TraesCS2A01G082600

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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 TraesCS2A01G082600 chr2A 100.000 3710 0 0 1 3710 37277694 37273985 0.000000e+00 6852.0
1 TraesCS2A01G082600 chr2A 86.910 741 69 15 950 1682 37269421 37270141 0.000000e+00 806.0
2 TraesCS2A01G082600 chr2A 89.384 292 17 7 2200 2482 37270718 37271004 4.560000e-94 355.0
3 TraesCS2A01G082600 chr2D 87.973 2561 165 56 1 2473 34344814 34342309 0.000000e+00 2891.0
4 TraesCS2A01G082600 chr2D 86.792 742 66 15 950 1682 34329576 34330294 0.000000e+00 798.0
5 TraesCS2A01G082600 chr2D 91.429 280 18 3 2195 2474 34330894 34331167 2.700000e-101 379.0
6 TraesCS2A01G082600 chr2D 91.489 188 15 1 2530 2717 34342190 34342004 1.320000e-64 257.0
7 TraesCS2A01G082600 chr2D 79.508 244 39 8 3300 3536 408456861 408457100 2.960000e-36 163.0
8 TraesCS2A01G082600 chr2B 91.275 1490 65 26 639 2099 56918021 56916568 0.000000e+00 1971.0
9 TraesCS2A01G082600 chr2B 89.093 816 38 21 2900 3710 56915852 56915083 0.000000e+00 966.0
10 TraesCS2A01G082600 chr2B 93.968 630 16 5 2134 2763 56916569 56915962 0.000000e+00 933.0
11 TraesCS2A01G082600 chr2B 87.297 740 64 15 950 1682 56899501 56900217 0.000000e+00 819.0
12 TraesCS2A01G082600 chr2B 90.459 283 16 4 2200 2474 56900807 56901086 2.720000e-96 363.0
13 TraesCS2A01G082600 chr2B 77.778 297 51 13 3200 3483 63847942 63848236 6.370000e-38 169.0
14 TraesCS2A01G082600 chr2B 89.231 130 3 2 2827 2947 56915961 56915834 6.420000e-33 152.0
15 TraesCS2A01G082600 chr3B 82.143 420 56 12 3138 3543 796548154 796548568 3.550000e-90 342.0
16 TraesCS2A01G082600 chr1A 81.524 433 56 11 3134 3543 27400539 27400970 5.940000e-88 335.0
17 TraesCS2A01G082600 chr1A 80.093 432 64 15 3135 3549 536300709 536301135 6.020000e-78 302.0
18 TraesCS2A01G082600 chr1A 80.795 302 49 8 3234 3529 463926359 463926657 1.040000e-55 228.0
19 TraesCS2A01G082600 chr3D 83.071 254 39 3 3138 3389 489734211 489733960 1.040000e-55 228.0
20 TraesCS2A01G082600 chr1D 81.034 290 44 7 3256 3543 358218429 358218149 1.730000e-53 220.0
21 TraesCS2A01G082600 chr7B 83.700 227 22 9 1943 2161 27077895 27078114 2.260000e-47 200.0
22 TraesCS2A01G082600 chrUn 79.381 291 43 11 3200 3476 345756078 345755791 4.890000e-44 189.0
23 TraesCS2A01G082600 chr5B 82.938 211 32 3 3268 3476 113823861 113824069 1.760000e-43 187.0
24 TraesCS2A01G082600 chr4B 81.250 80 8 6 2752 2829 40779503 40779429 1.440000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G082600 chr2A 37273985 37277694 3709 True 6852.0 6852 100.00000 1 3710 1 chr2A.!!$R1 3709
1 TraesCS2A01G082600 chr2A 37269421 37271004 1583 False 580.5 806 88.14700 950 2482 2 chr2A.!!$F1 1532
2 TraesCS2A01G082600 chr2D 34342004 34344814 2810 True 1574.0 2891 89.73100 1 2717 2 chr2D.!!$R1 2716
3 TraesCS2A01G082600 chr2D 34329576 34331167 1591 False 588.5 798 89.11050 950 2474 2 chr2D.!!$F2 1524
4 TraesCS2A01G082600 chr2B 56915083 56918021 2938 True 1005.5 1971 90.89175 639 3710 4 chr2B.!!$R1 3071
5 TraesCS2A01G082600 chr2B 56899501 56901086 1585 False 591.0 819 88.87800 950 2474 2 chr2B.!!$F2 1524

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
326 335 0.034089 CACTCCAAACCCCATCCTCC 60.034 60.0 0.00 0.0 0.00 4.30 F
608 618 0.322906 GCCCCAAGCTGAGCTAAAGT 60.323 55.0 7.68 0.0 38.25 2.66 F
1895 2122 0.467384 CATGGGACTGGCCACTCTAG 59.533 60.0 0.00 0.0 38.95 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 2122 0.247736 CCGATCACTATGGGCCTAGC 59.752 60.0 4.53 0.0 0.00 3.42 R
1898 2125 0.398522 TCACCGATCACTATGGGCCT 60.399 55.0 4.53 0.0 34.44 5.19 R
3146 3622 0.036022 AGAAGAAGCTCCAGTGCACC 59.964 55.0 14.63 0.0 34.99 5.01 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
23 24 2.483583 TGCCGTCACATTCAAAACAC 57.516 45.000 0.00 0.00 0.00 3.32
26 27 2.635444 CCGTCACATTCAAAACACGAC 58.365 47.619 0.00 0.00 0.00 4.34
47 48 5.119279 CGACTAACATGAACAAAGGAGACTG 59.881 44.000 0.00 0.00 42.68 3.51
48 49 5.308825 ACTAACATGAACAAAGGAGACTGG 58.691 41.667 0.00 0.00 42.68 4.00
49 50 2.508526 ACATGAACAAAGGAGACTGGC 58.491 47.619 0.00 0.00 42.68 4.85
56 57 0.765510 AAAGGAGACTGGCGAAAGGT 59.234 50.000 0.00 0.00 42.68 3.50
57 58 0.321996 AAGGAGACTGGCGAAAGGTC 59.678 55.000 0.00 0.00 42.68 3.85
67 68 2.998949 GAAAGGTCGGCCCCTGAT 59.001 61.111 0.08 0.00 34.19 2.90
71 72 2.444895 GGTCGGCCCCTGATCTCT 60.445 66.667 0.00 0.00 0.00 3.10
81 82 2.776536 CCCCTGATCTCTTGATGTCCTT 59.223 50.000 0.00 0.00 32.19 3.36
87 88 1.833630 TCTCTTGATGTCCTTCGCCAT 59.166 47.619 0.00 0.00 0.00 4.40
90 91 1.869767 CTTGATGTCCTTCGCCATAGC 59.130 52.381 0.00 0.00 0.00 2.97
91 92 0.106708 TGATGTCCTTCGCCATAGCC 59.893 55.000 0.00 0.00 34.57 3.93
93 94 2.280186 GTCCTTCGCCATAGCCGG 60.280 66.667 0.00 0.00 34.57 6.13
94 95 3.546543 TCCTTCGCCATAGCCGGG 61.547 66.667 2.18 0.00 34.57 5.73
95 96 3.546543 CCTTCGCCATAGCCGGGA 61.547 66.667 2.18 0.00 34.57 5.14
96 97 2.280186 CTTCGCCATAGCCGGGAC 60.280 66.667 2.18 0.00 34.57 4.46
97 98 3.809374 CTTCGCCATAGCCGGGACC 62.809 68.421 2.18 0.00 34.57 4.46
120 121 3.288964 GGAGAGTAGATTTGTCCCTCGA 58.711 50.000 0.00 0.00 0.00 4.04
122 123 2.683867 AGAGTAGATTTGTCCCTCGACG 59.316 50.000 0.00 0.00 42.37 5.12
126 127 0.672401 GATTTGTCCCTCGACGCCAA 60.672 55.000 0.00 0.00 42.37 4.52
149 150 8.424918 CCAAATTTAGCCTAGAGATAAGAGTGA 58.575 37.037 0.00 0.00 0.00 3.41
151 152 9.427821 AAATTTAGCCTAGAGATAAGAGTGAGA 57.572 33.333 0.00 0.00 0.00 3.27
161 162 7.555087 AGAGATAAGAGTGAGACAATCAAAGG 58.445 38.462 0.00 0.00 40.43 3.11
164 165 4.963318 AGAGTGAGACAATCAAAGGTCA 57.037 40.909 0.00 0.00 40.43 4.02
186 187 5.536497 AGGATAATGTTCCTGGAACCTTT 57.464 39.130 31.00 25.55 44.63 3.11
187 188 6.652205 AGGATAATGTTCCTGGAACCTTTA 57.348 37.500 31.00 26.54 44.63 1.85
188 189 6.663734 AGGATAATGTTCCTGGAACCTTTAG 58.336 40.000 31.00 0.00 44.63 1.85
189 190 6.217693 AGGATAATGTTCCTGGAACCTTTAGT 59.782 38.462 31.00 17.24 44.63 2.24
206 207 5.334879 CCTTTAGTTCCCACAAACAAGATCG 60.335 44.000 0.00 0.00 0.00 3.69
268 269 2.038863 ACCCCTCAATGTGTCCACTA 57.961 50.000 0.00 0.00 0.00 2.74
273 282 3.244561 CCCTCAATGTGTCCACTACAACT 60.245 47.826 0.00 0.00 40.63 3.16
298 307 2.695585 AGACAAGAACCAAGGGAGTCT 58.304 47.619 0.00 0.00 0.00 3.24
310 319 1.288335 AGGGAGTCTCGGATAACCACT 59.712 52.381 0.00 0.00 35.59 4.00
316 325 3.056035 AGTCTCGGATAACCACTCCAAAC 60.056 47.826 0.00 0.00 35.59 2.93
318 327 1.279846 TCGGATAACCACTCCAAACCC 59.720 52.381 0.00 0.00 35.59 4.11
326 335 0.034089 CACTCCAAACCCCATCCTCC 60.034 60.000 0.00 0.00 0.00 4.30
327 336 1.224592 CTCCAAACCCCATCCTCCG 59.775 63.158 0.00 0.00 0.00 4.63
328 337 1.229690 TCCAAACCCCATCCTCCGA 60.230 57.895 0.00 0.00 0.00 4.55
337 346 2.667470 CCCATCCTCCGAGAAGAACTA 58.333 52.381 0.00 0.00 0.00 2.24
339 348 2.035321 CCATCCTCCGAGAAGAACTAGC 59.965 54.545 0.00 0.00 0.00 3.42
346 355 5.163499 CCTCCGAGAAGAACTAGCAAATACT 60.163 44.000 0.00 0.00 0.00 2.12
374 383 0.409092 ATTGACTTGCACCATCCCCA 59.591 50.000 0.00 0.00 0.00 4.96
382 391 2.530661 ACCATCCCCACCGGTGAA 60.531 61.111 36.07 20.30 0.00 3.18
398 408 2.497273 GGTGAAGGACCCATTTTGGATG 59.503 50.000 0.00 0.00 40.96 3.51
412 422 1.909700 TGGATGTGAAGAACCAAGGC 58.090 50.000 0.00 0.00 0.00 4.35
417 427 2.150719 TGAAGAACCAAGGCCGGGA 61.151 57.895 21.64 0.00 0.00 5.14
440 450 1.821216 GCTTAAGCCAGGCAGTAACA 58.179 50.000 17.00 0.00 34.31 2.41
441 451 1.468914 GCTTAAGCCAGGCAGTAACAC 59.531 52.381 17.00 1.35 34.31 3.32
445 455 1.285280 AGCCAGGCAGTAACACCATA 58.715 50.000 15.80 0.00 0.00 2.74
446 456 1.846439 AGCCAGGCAGTAACACCATAT 59.154 47.619 15.80 0.00 0.00 1.78
447 457 3.045634 AGCCAGGCAGTAACACCATATA 58.954 45.455 15.80 0.00 0.00 0.86
448 458 3.652869 AGCCAGGCAGTAACACCATATAT 59.347 43.478 15.80 0.00 0.00 0.86
449 459 4.003648 GCCAGGCAGTAACACCATATATC 58.996 47.826 6.55 0.00 0.00 1.63
450 460 4.504864 GCCAGGCAGTAACACCATATATCA 60.505 45.833 6.55 0.00 0.00 2.15
451 461 5.620206 CCAGGCAGTAACACCATATATCAA 58.380 41.667 0.00 0.00 0.00 2.57
452 462 5.470098 CCAGGCAGTAACACCATATATCAAC 59.530 44.000 0.00 0.00 0.00 3.18
471 481 2.704572 ACGAGGCAAGATTTTCTCCAG 58.295 47.619 0.00 0.00 0.00 3.86
476 486 4.583871 AGGCAAGATTTTCTCCAGTACTG 58.416 43.478 16.34 16.34 0.00 2.74
520 530 9.709495 CTCCTAAATTTTGAACATGGAATTCAA 57.291 29.630 7.93 6.00 42.78 2.69
538 548 3.565307 TCAAACAGCCAGAGGAAATTGT 58.435 40.909 0.00 0.00 0.00 2.71
539 549 3.318839 TCAAACAGCCAGAGGAAATTGTG 59.681 43.478 0.00 0.00 0.00 3.33
542 552 3.565307 ACAGCCAGAGGAAATTGTGAAA 58.435 40.909 0.00 0.00 0.00 2.69
545 555 3.823304 AGCCAGAGGAAATTGTGAAAGTC 59.177 43.478 0.00 0.00 0.00 3.01
551 561 7.386851 CAGAGGAAATTGTGAAAGTCCTAGTA 58.613 38.462 0.00 0.00 38.85 1.82
584 594 0.578683 CTTGTGCATGTAGATCGCCG 59.421 55.000 0.00 0.00 0.00 6.46
586 596 0.741915 TGTGCATGTAGATCGCCGTA 59.258 50.000 0.00 0.00 0.00 4.02
588 598 1.787155 GTGCATGTAGATCGCCGTAAG 59.213 52.381 0.00 0.00 0.00 2.34
607 617 1.034292 GGCCCCAAGCTGAGCTAAAG 61.034 60.000 7.68 0.39 38.25 1.85
608 618 0.322906 GCCCCAAGCTGAGCTAAAGT 60.323 55.000 7.68 0.00 38.25 2.66
610 620 2.618045 GCCCCAAGCTGAGCTAAAGTAA 60.618 50.000 7.68 0.00 38.25 2.24
611 621 3.274288 CCCCAAGCTGAGCTAAAGTAAG 58.726 50.000 7.68 0.00 38.25 2.34
612 622 2.680339 CCCAAGCTGAGCTAAAGTAAGC 59.320 50.000 7.68 0.00 38.25 3.09
613 623 2.680339 CCAAGCTGAGCTAAAGTAAGCC 59.320 50.000 7.68 0.00 43.86 4.35
616 639 4.227864 AGCTGAGCTAAAGTAAGCCAAT 57.772 40.909 4.49 0.00 43.86 3.16
619 642 4.513318 GCTGAGCTAAAGTAAGCCAATAGG 59.487 45.833 0.00 0.00 43.86 2.57
694 717 2.791383 CCATCAAACGGCAAACTTGA 57.209 45.000 0.00 0.00 33.82 3.02
695 718 2.664916 CCATCAAACGGCAAACTTGAG 58.335 47.619 0.00 0.00 32.87 3.02
696 719 2.053627 CATCAAACGGCAAACTTGAGC 58.946 47.619 0.00 0.00 32.87 4.26
697 720 1.388547 TCAAACGGCAAACTTGAGCT 58.611 45.000 0.00 0.00 0.00 4.09
699 722 2.946329 TCAAACGGCAAACTTGAGCTAA 59.054 40.909 0.00 0.00 0.00 3.09
700 723 3.378742 TCAAACGGCAAACTTGAGCTAAA 59.621 39.130 0.00 0.00 0.00 1.85
701 724 4.037446 TCAAACGGCAAACTTGAGCTAAAT 59.963 37.500 0.00 0.00 0.00 1.40
876 909 3.059597 GGCGTACAGAATCATTTCCATCG 60.060 47.826 0.00 0.00 31.84 3.84
889 922 5.125257 TCATTTCCATCGCAGAAATTAAGCA 59.875 36.000 4.90 0.00 43.58 3.91
923 956 1.542030 ACACTCACTCACTCGATCACC 59.458 52.381 0.00 0.00 0.00 4.02
924 957 1.815613 CACTCACTCACTCGATCACCT 59.184 52.381 0.00 0.00 0.00 4.00
925 958 3.010420 CACTCACTCACTCGATCACCTA 58.990 50.000 0.00 0.00 0.00 3.08
926 959 3.011119 ACTCACTCACTCGATCACCTAC 58.989 50.000 0.00 0.00 0.00 3.18
927 960 2.356382 CTCACTCACTCGATCACCTACC 59.644 54.545 0.00 0.00 0.00 3.18
928 961 2.026169 TCACTCACTCGATCACCTACCT 60.026 50.000 0.00 0.00 0.00 3.08
930 963 3.562141 CACTCACTCGATCACCTACCTAG 59.438 52.174 0.00 0.00 0.00 3.02
978 1019 4.220821 ACACACATACACACTAGCTAAGCT 59.779 41.667 0.00 0.00 43.41 3.74
1020 1061 3.411351 GCGTCGCCGAAGAAAGCA 61.411 61.111 5.75 0.00 35.63 3.91
1098 1142 1.687493 CTTCCTCCTCGGCCTCCTT 60.687 63.158 0.00 0.00 0.00 3.36
1137 1181 4.063967 CGCTGGACCCACGTAGCA 62.064 66.667 6.56 0.00 35.98 3.49
1140 1184 1.897423 CTGGACCCACGTAGCATCA 59.103 57.895 0.00 0.00 0.00 3.07
1509 1562 3.782443 CGGCACCTGACCTACCCC 61.782 72.222 0.00 0.00 0.00 4.95
1524 1577 2.342279 CCCGAGAACTTCACGGCA 59.658 61.111 19.05 0.00 46.83 5.69
1704 1782 2.284190 GCATTCTCCTGCCTACAAGTC 58.716 52.381 0.00 0.00 36.10 3.01
1727 1809 7.040409 AGTCTGGTTAACCTGTTCATTTCATTC 60.040 37.037 24.78 6.06 36.48 2.67
1765 1960 9.701098 CTTTAGTGAACTGGTAATTGTAGTGTA 57.299 33.333 0.00 0.00 0.00 2.90
1766 1961 9.701098 TTTAGTGAACTGGTAATTGTAGTGTAG 57.299 33.333 0.00 0.00 0.00 2.74
1767 1962 7.299246 AGTGAACTGGTAATTGTAGTGTAGT 57.701 36.000 0.00 0.00 0.00 2.73
1768 1963 8.413309 AGTGAACTGGTAATTGTAGTGTAGTA 57.587 34.615 0.00 0.00 0.00 1.82
1770 1965 9.480053 GTGAACTGGTAATTGTAGTGTAGTAAA 57.520 33.333 0.00 0.00 0.00 2.01
1771 1966 9.480053 TGAACTGGTAATTGTAGTGTAGTAAAC 57.520 33.333 0.00 0.00 0.00 2.01
1772 1967 9.702494 GAACTGGTAATTGTAGTGTAGTAAACT 57.298 33.333 0.00 0.00 0.00 2.66
1773 1968 9.485206 AACTGGTAATTGTAGTGTAGTAAACTG 57.515 33.333 2.99 0.00 0.00 3.16
1776 1971 7.874016 TGGTAATTGTAGTGTAGTAAACTGGTG 59.126 37.037 2.99 0.00 0.00 4.17
1786 1981 7.172703 AGTGTAGTAAACTGGTGATTAAGTTGC 59.827 37.037 0.00 0.00 36.75 4.17
1788 1983 6.313744 AGTAAACTGGTGATTAAGTTGCAC 57.686 37.500 0.00 0.00 36.75 4.57
1790 1985 4.836125 AACTGGTGATTAAGTTGCACTG 57.164 40.909 0.00 0.00 35.34 3.66
1791 1986 2.554032 ACTGGTGATTAAGTTGCACTGC 59.446 45.455 0.00 0.00 33.25 4.40
1792 1987 1.535028 TGGTGATTAAGTTGCACTGCG 59.465 47.619 0.00 0.00 33.25 5.18
1794 1989 1.135689 GTGATTAAGTTGCACTGCGGG 60.136 52.381 0.00 0.00 0.00 6.13
1795 1990 1.165270 GATTAAGTTGCACTGCGGGT 58.835 50.000 0.00 0.00 0.00 5.28
1796 1991 2.289756 TGATTAAGTTGCACTGCGGGTA 60.290 45.455 0.00 0.00 0.00 3.69
1871 2091 2.546778 AGCAAATAATGTGCATGCAGC 58.453 42.857 23.41 18.06 44.74 5.25
1887 2114 3.534056 GCATGGCATGGGACTGGC 61.534 66.667 27.48 8.72 41.78 4.85
1888 2115 2.836360 CATGGCATGGGACTGGCC 60.836 66.667 19.80 0.00 45.75 5.36
1891 2118 4.052518 GGCATGGGACTGGCCACT 62.053 66.667 0.00 0.00 45.10 4.00
1892 2119 2.439156 GCATGGGACTGGCCACTC 60.439 66.667 0.00 1.65 38.95 3.51
1893 2120 2.976490 GCATGGGACTGGCCACTCT 61.976 63.158 0.00 0.00 38.95 3.24
1894 2121 1.626356 GCATGGGACTGGCCACTCTA 61.626 60.000 0.00 0.00 38.95 2.43
1895 2122 0.467384 CATGGGACTGGCCACTCTAG 59.533 60.000 0.00 0.00 38.95 2.43
1896 2123 1.341156 ATGGGACTGGCCACTCTAGC 61.341 60.000 0.00 0.00 38.95 3.42
1898 2125 0.397254 GGGACTGGCCACTCTAGCTA 60.397 60.000 0.00 0.00 38.95 3.32
1900 2127 1.036707 GACTGGCCACTCTAGCTAGG 58.963 60.000 20.58 13.33 42.63 3.02
1901 2128 1.045911 ACTGGCCACTCTAGCTAGGC 61.046 60.000 20.58 16.14 42.63 3.93
2069 2365 2.825836 CACCATCCTCCGCTTGCC 60.826 66.667 0.00 0.00 0.00 4.52
2101 2397 1.324718 CGAGTGTCGGTAGAAACGTG 58.675 55.000 0.00 0.00 39.59 4.49
2102 2398 1.694639 GAGTGTCGGTAGAAACGTGG 58.305 55.000 0.00 0.00 39.59 4.94
2104 2400 1.000938 AGTGTCGGTAGAAACGTGGAC 60.001 52.381 0.00 0.00 39.59 4.02
2105 2401 0.040157 TGTCGGTAGAAACGTGGACG 60.040 55.000 0.00 0.00 46.33 4.79
2106 2402 0.238289 GTCGGTAGAAACGTGGACGA 59.762 55.000 6.12 0.00 43.02 4.20
2107 2403 0.518636 TCGGTAGAAACGTGGACGAG 59.481 55.000 6.12 0.00 43.02 4.18
2108 2404 1.069378 CGGTAGAAACGTGGACGAGC 61.069 60.000 6.12 0.00 43.02 5.03
2110 2406 0.110056 GTAGAAACGTGGACGAGCGA 60.110 55.000 6.12 0.00 43.02 4.93
2111 2407 0.167470 TAGAAACGTGGACGAGCGAG 59.833 55.000 6.12 0.00 43.02 5.03
2121 2429 1.599667 GGACGAGCGAGCGAATGATTA 60.600 52.381 4.36 0.00 34.83 1.75
2124 2432 0.432738 GAGCGAGCGAATGATTAGCG 59.567 55.000 4.66 0.00 35.78 4.26
2132 2450 2.160091 GCGAATGATTAGCGCTAACGAG 60.160 50.000 30.92 18.84 46.53 4.18
2138 2492 5.177725 TGATTAGCGCTAACGAGACATTA 57.822 39.130 30.92 8.43 43.93 1.90
2189 2543 2.223112 CGTTACTGTGCATGAATGGAGC 60.223 50.000 0.00 0.00 0.00 4.70
2190 2544 2.749076 GTTACTGTGCATGAATGGAGCA 59.251 45.455 0.00 0.00 35.63 4.26
2493 2853 6.155737 AGGTACTGTAACTCCGTAATTGGATT 59.844 38.462 0.00 0.00 37.18 3.01
2494 2854 7.342799 AGGTACTGTAACTCCGTAATTGGATTA 59.657 37.037 0.00 0.00 37.18 1.75
2495 2855 8.146412 GGTACTGTAACTCCGTAATTGGATTAT 58.854 37.037 0.00 0.00 37.41 1.28
2503 2863 8.795842 ACTCCGTAATTGGATTATAAAACACA 57.204 30.769 0.00 0.00 37.41 3.72
2622 3060 4.036804 GTGCAACGATTGGCCGCA 62.037 61.111 0.00 0.00 0.00 5.69
2661 3099 2.280865 GGAATGCCCGATCCCGAC 60.281 66.667 0.00 0.00 38.22 4.79
2724 3162 5.279006 CGCTACCTAGATTGCTCTGGATAAA 60.279 44.000 0.00 0.00 31.92 1.40
2725 3163 6.573289 CGCTACCTAGATTGCTCTGGATAAAT 60.573 42.308 0.00 0.00 31.92 1.40
2726 3164 6.593382 GCTACCTAGATTGCTCTGGATAAATG 59.407 42.308 0.00 0.00 31.92 2.32
2727 3165 6.753913 ACCTAGATTGCTCTGGATAAATGA 57.246 37.500 0.00 0.00 31.92 2.57
2728 3166 7.327064 ACCTAGATTGCTCTGGATAAATGAT 57.673 36.000 0.00 0.00 31.92 2.45
2729 3167 8.441311 ACCTAGATTGCTCTGGATAAATGATA 57.559 34.615 0.00 0.00 31.92 2.15
2731 3169 9.902684 CCTAGATTGCTCTGGATAAATGATAAT 57.097 33.333 0.00 0.00 31.92 1.28
2734 3172 9.976776 AGATTGCTCTGGATAAATGATAATCAT 57.023 29.630 0.00 0.00 39.09 2.45
2763 3201 5.339477 ACATATACCTACCCACATACTCCC 58.661 45.833 0.00 0.00 0.00 4.30
2764 3202 5.077441 ACATATACCTACCCACATACTCCCT 59.923 44.000 0.00 0.00 0.00 4.20
2765 3203 2.473576 ACCTACCCACATACTCCCTC 57.526 55.000 0.00 0.00 0.00 4.30
2766 3204 1.062352 ACCTACCCACATACTCCCTCC 60.062 57.143 0.00 0.00 0.00 4.30
2767 3205 1.329256 CTACCCACATACTCCCTCCG 58.671 60.000 0.00 0.00 0.00 4.63
2768 3206 0.632835 TACCCACATACTCCCTCCGT 59.367 55.000 0.00 0.00 0.00 4.69
2769 3207 0.252558 ACCCACATACTCCCTCCGTT 60.253 55.000 0.00 0.00 0.00 4.44
2770 3208 0.464452 CCCACATACTCCCTCCGTTC 59.536 60.000 0.00 0.00 0.00 3.95
2771 3209 0.464452 CCACATACTCCCTCCGTTCC 59.536 60.000 0.00 0.00 0.00 3.62
2772 3210 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2773 3211 1.553248 CACATACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
2774 3212 2.027561 CACATACTCCCTCCGTTCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
2775 3213 2.844348 ACATACTCCCTCCGTTCCAAAT 59.156 45.455 0.00 0.00 0.00 2.32
2776 3214 3.265995 ACATACTCCCTCCGTTCCAAATT 59.734 43.478 0.00 0.00 0.00 1.82
2777 3215 4.472108 ACATACTCCCTCCGTTCCAAATTA 59.528 41.667 0.00 0.00 0.00 1.40
2778 3216 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2779 3217 2.277084 CTCCCTCCGTTCCAAATTACG 58.723 52.381 0.00 0.00 37.50 3.18
2780 3218 1.624813 TCCCTCCGTTCCAAATTACGT 59.375 47.619 0.00 0.00 36.09 3.57
2781 3219 2.830923 TCCCTCCGTTCCAAATTACGTA 59.169 45.455 0.00 0.00 36.09 3.57
2782 3220 2.931969 CCCTCCGTTCCAAATTACGTAC 59.068 50.000 0.00 0.00 36.09 3.67
2783 3221 3.368739 CCCTCCGTTCCAAATTACGTACT 60.369 47.826 0.00 0.00 36.09 2.73
2784 3222 4.248058 CCTCCGTTCCAAATTACGTACTT 58.752 43.478 0.00 0.00 36.09 2.24
2785 3223 4.092383 CCTCCGTTCCAAATTACGTACTTG 59.908 45.833 0.00 2.10 36.09 3.16
2786 3224 4.630111 TCCGTTCCAAATTACGTACTTGT 58.370 39.130 13.04 0.00 36.09 3.16
2787 3225 4.685628 TCCGTTCCAAATTACGTACTTGTC 59.314 41.667 13.04 5.40 36.09 3.18
2788 3226 4.433283 CCGTTCCAAATTACGTACTTGTCG 60.433 45.833 13.04 13.06 36.09 4.35
2789 3227 4.148696 CGTTCCAAATTACGTACTTGTCGT 59.851 41.667 13.04 0.00 43.86 4.34
2790 3228 5.368374 GTTCCAAATTACGTACTTGTCGTG 58.632 41.667 13.04 3.10 41.62 4.35
2791 3229 3.989167 TCCAAATTACGTACTTGTCGTGG 59.011 43.478 13.04 10.32 41.62 4.94
2792 3230 3.742369 CCAAATTACGTACTTGTCGTGGT 59.258 43.478 13.04 0.00 41.62 4.16
2793 3231 4.211794 CCAAATTACGTACTTGTCGTGGTT 59.788 41.667 13.04 0.00 41.62 3.67
2794 3232 5.277442 CCAAATTACGTACTTGTCGTGGTTT 60.277 40.000 13.04 0.58 41.62 3.27
2795 3233 5.989551 AATTACGTACTTGTCGTGGTTTT 57.010 34.783 0.00 0.00 41.62 2.43
2796 3234 5.989551 ATTACGTACTTGTCGTGGTTTTT 57.010 34.783 0.00 0.00 41.62 1.94
2797 3235 3.661758 ACGTACTTGTCGTGGTTTTTG 57.338 42.857 0.00 0.00 40.07 2.44
2798 3236 3.002102 ACGTACTTGTCGTGGTTTTTGT 58.998 40.909 0.00 0.00 40.07 2.83
2799 3237 3.436359 ACGTACTTGTCGTGGTTTTTGTT 59.564 39.130 0.00 0.00 40.07 2.83
2800 3238 4.023783 CGTACTTGTCGTGGTTTTTGTTC 58.976 43.478 0.00 0.00 0.00 3.18
2801 3239 4.435784 CGTACTTGTCGTGGTTTTTGTTCA 60.436 41.667 0.00 0.00 0.00 3.18
2802 3240 4.506886 ACTTGTCGTGGTTTTTGTTCAA 57.493 36.364 0.00 0.00 0.00 2.69
2803 3241 4.872664 ACTTGTCGTGGTTTTTGTTCAAA 58.127 34.783 0.00 0.00 0.00 2.69
2804 3242 5.474825 ACTTGTCGTGGTTTTTGTTCAAAT 58.525 33.333 0.00 0.00 0.00 2.32
2805 3243 5.929415 ACTTGTCGTGGTTTTTGTTCAAATT 59.071 32.000 0.00 0.00 0.00 1.82
2806 3244 5.769967 TGTCGTGGTTTTTGTTCAAATTG 57.230 34.783 0.00 0.00 0.00 2.32
2807 3245 5.230942 TGTCGTGGTTTTTGTTCAAATTGT 58.769 33.333 0.00 0.00 0.00 2.71
2808 3246 6.387465 TGTCGTGGTTTTTGTTCAAATTGTA 58.613 32.000 0.00 0.00 0.00 2.41
2809 3247 6.866770 TGTCGTGGTTTTTGTTCAAATTGTAA 59.133 30.769 0.00 0.00 0.00 2.41
2810 3248 7.545965 TGTCGTGGTTTTTGTTCAAATTGTAAT 59.454 29.630 0.00 0.00 0.00 1.89
2811 3249 8.384365 GTCGTGGTTTTTGTTCAAATTGTAATT 58.616 29.630 0.00 0.00 0.00 1.40
2812 3250 8.936864 TCGTGGTTTTTGTTCAAATTGTAATTT 58.063 25.926 0.00 0.00 39.07 1.82
2862 3300 1.348594 GATCGCAACACGGCTAAGC 59.651 57.895 0.00 0.00 43.89 3.09
2972 3446 1.195448 CAAGTAGCTTTCCGTGCACAG 59.805 52.381 18.64 5.51 0.00 3.66
2980 3454 1.441738 TTCCGTGCACAGTGATCATG 58.558 50.000 18.64 1.05 0.00 3.07
2988 3462 2.672760 GCACAGTGATCATGCATGCAAA 60.673 45.455 26.68 16.55 39.23 3.68
3049 3525 3.153919 GTTGCCTTATTGAGTTCACCCA 58.846 45.455 0.00 0.00 0.00 4.51
3050 3526 3.071874 TGCCTTATTGAGTTCACCCAG 57.928 47.619 0.00 0.00 0.00 4.45
3110 3586 5.307976 TGCTCAGTCATACTATAGGCCAAAT 59.692 40.000 5.01 0.00 0.00 2.32
3121 3597 1.981256 AGGCCAAATTGTCTCACGTT 58.019 45.000 5.01 0.00 0.00 3.99
3136 3612 1.760613 CACGTTGATAGGGGGCTAGAA 59.239 52.381 0.00 0.00 0.00 2.10
3146 3622 1.614413 GGGGGCTAGAAGACGTATCTG 59.386 57.143 12.36 5.25 34.48 2.90
3147 3623 1.614413 GGGGCTAGAAGACGTATCTGG 59.386 57.143 12.36 10.70 34.48 3.86
3153 3629 2.171840 AGAAGACGTATCTGGTGCACT 58.828 47.619 17.98 0.00 34.48 4.40
3165 3641 0.036022 GGTGCACTGGAGCTTCTTCT 59.964 55.000 17.98 0.00 34.99 2.85
3167 3643 0.604780 TGCACTGGAGCTTCTTCTGC 60.605 55.000 0.00 0.00 34.99 4.26
3282 3759 9.949174 AATTCAAATTTAAACTCCAAACAATGC 57.051 25.926 0.00 0.00 0.00 3.56
3283 3760 8.729805 TTCAAATTTAAACTCCAAACAATGCT 57.270 26.923 0.00 0.00 0.00 3.79
3284 3761 8.364129 TCAAATTTAAACTCCAAACAATGCTC 57.636 30.769 0.00 0.00 0.00 4.26
3285 3762 7.168972 TCAAATTTAAACTCCAAACAATGCTCG 59.831 33.333 0.00 0.00 0.00 5.03
3286 3763 5.759506 TTTAAACTCCAAACAATGCTCGA 57.240 34.783 0.00 0.00 0.00 4.04
3287 3764 3.904136 AAACTCCAAACAATGCTCGAG 57.096 42.857 8.45 8.45 0.00 4.04
3288 3765 2.839486 ACTCCAAACAATGCTCGAGA 57.161 45.000 18.75 1.31 0.00 4.04
3291 3768 2.143122 TCCAAACAATGCTCGAGACAC 58.857 47.619 18.75 0.00 0.00 3.67
3303 3780 4.214437 GCTCGAGACACAAAAATGACAAG 58.786 43.478 18.75 0.00 0.00 3.16
3366 3843 9.698309 CCAACTTGTCCTATATACTATTCAGTG 57.302 37.037 0.00 0.00 36.14 3.66
3368 3845 7.897864 ACTTGTCCTATATACTATTCAGTGCC 58.102 38.462 0.00 0.00 36.14 5.01
3491 3968 3.405823 CATTTGGAAATGTGCCAAGGT 57.594 42.857 4.24 0.00 45.39 3.50
3492 3969 4.533919 CATTTGGAAATGTGCCAAGGTA 57.466 40.909 4.24 0.00 45.39 3.08
3493 3970 4.497300 CATTTGGAAATGTGCCAAGGTAG 58.503 43.478 4.24 0.00 45.39 3.18
3494 3971 2.969821 TGGAAATGTGCCAAGGTAGT 57.030 45.000 0.00 0.00 31.13 2.73
3495 3972 2.790433 TGGAAATGTGCCAAGGTAGTC 58.210 47.619 0.00 0.00 31.13 2.59
3496 3973 2.092323 GGAAATGTGCCAAGGTAGTCC 58.908 52.381 0.00 0.00 0.00 3.85
3497 3974 2.554344 GGAAATGTGCCAAGGTAGTCCA 60.554 50.000 0.00 0.00 35.89 4.02
3498 3975 2.496899 AATGTGCCAAGGTAGTCCAG 57.503 50.000 0.00 0.00 35.89 3.86
3499 3976 1.362224 ATGTGCCAAGGTAGTCCAGT 58.638 50.000 0.00 0.00 35.89 4.00
3500 3977 0.396435 TGTGCCAAGGTAGTCCAGTG 59.604 55.000 0.00 0.00 35.89 3.66
3501 3978 0.955919 GTGCCAAGGTAGTCCAGTGC 60.956 60.000 0.00 0.00 35.89 4.40
3502 3979 1.374947 GCCAAGGTAGTCCAGTGCA 59.625 57.895 0.00 0.00 35.89 4.57
3503 3980 0.955919 GCCAAGGTAGTCCAGTGCAC 60.956 60.000 9.40 9.40 35.89 4.57
3504 3981 0.687354 CCAAGGTAGTCCAGTGCACT 59.313 55.000 15.25 15.25 35.89 4.40
3505 3982 1.609061 CCAAGGTAGTCCAGTGCACTG 60.609 57.143 35.15 35.15 43.40 3.66
3529 4006 0.957395 CACAAGAAGCTCCGGTGCAT 60.957 55.000 28.68 18.66 34.99 3.96
3624 4101 2.309613 AGCACCATGTTTCTCTGCAAA 58.690 42.857 0.00 0.00 0.00 3.68
3625 4102 2.694628 AGCACCATGTTTCTCTGCAAAA 59.305 40.909 0.00 0.00 0.00 2.44
3675 4152 6.509317 TCGAGAATTTGCACATTGTTTTTC 57.491 33.333 2.08 0.00 0.00 2.29
3687 4164 2.285827 TGTTTTTCCCGCAAACACAG 57.714 45.000 0.00 0.00 38.84 3.66
3696 4173 1.272784 CGCAAACACAGTGCATGCAG 61.273 55.000 23.41 13.42 42.33 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.268285 CGTGTTTTGAATGTGACGGCA 60.268 47.619 0.00 0.00 0.00 5.69
23 24 5.119279 CAGTCTCCTTTGTTCATGTTAGTCG 59.881 44.000 0.00 0.00 0.00 4.18
26 27 4.154918 GCCAGTCTCCTTTGTTCATGTTAG 59.845 45.833 0.00 0.00 0.00 2.34
49 50 2.925162 GATCAGGGGCCGACCTTTCG 62.925 65.000 0.00 0.00 45.44 3.46
56 57 0.399091 ATCAAGAGATCAGGGGCCGA 60.399 55.000 0.00 0.00 0.00 5.54
57 58 0.250209 CATCAAGAGATCAGGGGCCG 60.250 60.000 0.00 0.00 30.20 6.13
65 66 2.159043 TGGCGAAGGACATCAAGAGATC 60.159 50.000 0.00 0.00 30.20 2.75
67 68 1.266178 TGGCGAAGGACATCAAGAGA 58.734 50.000 0.00 0.00 0.00 3.10
71 72 1.475034 GGCTATGGCGAAGGACATCAA 60.475 52.381 0.00 0.00 37.28 2.57
91 92 0.467659 AATCTACTCTCCCGGTCCCG 60.468 60.000 0.00 0.00 39.44 5.14
93 94 2.101082 GACAAATCTACTCTCCCGGTCC 59.899 54.545 0.00 0.00 0.00 4.46
94 95 2.101082 GGACAAATCTACTCTCCCGGTC 59.899 54.545 0.00 0.00 0.00 4.79
95 96 2.108970 GGACAAATCTACTCTCCCGGT 58.891 52.381 0.00 0.00 0.00 5.28
96 97 1.413077 GGGACAAATCTACTCTCCCGG 59.587 57.143 0.00 0.00 31.41 5.73
97 98 2.362717 GAGGGACAAATCTACTCTCCCG 59.637 54.545 0.00 0.00 44.84 5.14
98 99 2.362717 CGAGGGACAAATCTACTCTCCC 59.637 54.545 0.00 0.00 41.03 4.30
99 100 3.067040 GTCGAGGGACAAATCTACTCTCC 59.933 52.174 0.00 0.00 42.91 3.71
105 106 0.458669 GGCGTCGAGGGACAAATCTA 59.541 55.000 7.31 0.00 43.61 1.98
120 121 3.906720 TCTCTAGGCTAAATTTGGCGT 57.093 42.857 22.50 22.50 35.26 5.68
122 123 7.172361 CACTCTTATCTCTAGGCTAAATTTGGC 59.828 40.741 17.48 17.48 0.00 4.52
126 127 8.856103 GTCTCACTCTTATCTCTAGGCTAAATT 58.144 37.037 0.00 0.00 0.00 1.82
149 150 6.725364 ACATTATCCTGACCTTTGATTGTCT 58.275 36.000 0.00 0.00 32.67 3.41
151 152 6.378280 GGAACATTATCCTGACCTTTGATTGT 59.622 38.462 0.00 0.00 36.50 2.71
164 165 7.257419 AACTAAAGGTTCCAGGAACATTATCCT 60.257 37.037 28.20 17.12 44.00 3.24
181 182 4.862371 TCTTGTTTGTGGGAACTAAAGGT 58.138 39.130 0.00 0.00 0.00 3.50
186 187 3.071479 GCGATCTTGTTTGTGGGAACTA 58.929 45.455 0.00 0.00 0.00 2.24
187 188 1.880027 GCGATCTTGTTTGTGGGAACT 59.120 47.619 0.00 0.00 0.00 3.01
188 189 1.068541 GGCGATCTTGTTTGTGGGAAC 60.069 52.381 0.00 0.00 0.00 3.62
189 190 1.202879 AGGCGATCTTGTTTGTGGGAA 60.203 47.619 0.00 0.00 0.00 3.97
221 222 3.647590 ACCCTTGAAATGTTTGAGGCATT 59.352 39.130 0.00 0.00 38.09 3.56
227 228 1.691434 GGCCACCCTTGAAATGTTTGA 59.309 47.619 0.00 0.00 0.00 2.69
231 232 1.047801 GTTGGCCACCCTTGAAATGT 58.952 50.000 3.88 0.00 0.00 2.71
268 269 4.150897 TGGTTCTTGTCTTGCTAGTTGT 57.849 40.909 0.00 0.00 0.00 3.32
273 282 2.708861 TCCCTTGGTTCTTGTCTTGCTA 59.291 45.455 0.00 0.00 0.00 3.49
298 307 1.279846 GGGTTTGGAGTGGTTATCCGA 59.720 52.381 0.00 0.00 39.91 4.55
310 319 1.229690 TCGGAGGATGGGGTTTGGA 60.230 57.895 0.00 0.00 0.00 3.53
316 325 0.466124 GTTCTTCTCGGAGGATGGGG 59.534 60.000 4.96 0.00 0.00 4.96
318 327 2.035321 GCTAGTTCTTCTCGGAGGATGG 59.965 54.545 4.96 0.00 0.00 3.51
339 348 6.183360 GCAAGTCAATTTGGATGCAGTATTTG 60.183 38.462 13.43 0.00 34.10 2.32
346 355 2.288948 GGTGCAAGTCAATTTGGATGCA 60.289 45.455 15.69 15.69 41.08 3.96
354 363 1.203162 TGGGGATGGTGCAAGTCAATT 60.203 47.619 0.00 0.00 0.00 2.32
382 391 3.075882 TCTTCACATCCAAAATGGGTCCT 59.924 43.478 0.00 0.00 38.32 3.85
398 408 1.971695 CCCGGCCTTGGTTCTTCAC 60.972 63.158 0.00 0.00 0.00 3.18
428 438 5.227569 TGATATATGGTGTTACTGCCTGG 57.772 43.478 0.00 0.00 0.00 4.45
432 442 5.405571 CCTCGTTGATATATGGTGTTACTGC 59.594 44.000 0.00 0.00 0.00 4.40
433 443 5.405571 GCCTCGTTGATATATGGTGTTACTG 59.594 44.000 0.00 0.00 0.00 2.74
434 444 5.069914 TGCCTCGTTGATATATGGTGTTACT 59.930 40.000 0.00 0.00 0.00 2.24
435 445 5.294356 TGCCTCGTTGATATATGGTGTTAC 58.706 41.667 0.00 0.00 0.00 2.50
437 447 4.415881 TGCCTCGTTGATATATGGTGTT 57.584 40.909 0.00 0.00 0.00 3.32
439 449 4.631131 TCTTGCCTCGTTGATATATGGTG 58.369 43.478 0.00 0.00 0.00 4.17
440 450 4.955811 TCTTGCCTCGTTGATATATGGT 57.044 40.909 0.00 0.00 0.00 3.55
441 451 6.808008 AAATCTTGCCTCGTTGATATATGG 57.192 37.500 0.00 0.00 0.00 2.74
445 455 5.529060 GGAGAAAATCTTGCCTCGTTGATAT 59.471 40.000 0.00 0.00 0.00 1.63
446 456 4.876107 GGAGAAAATCTTGCCTCGTTGATA 59.124 41.667 0.00 0.00 0.00 2.15
447 457 3.691609 GGAGAAAATCTTGCCTCGTTGAT 59.308 43.478 0.00 0.00 0.00 2.57
448 458 3.074412 GGAGAAAATCTTGCCTCGTTGA 58.926 45.455 0.00 0.00 0.00 3.18
449 459 2.813754 TGGAGAAAATCTTGCCTCGTTG 59.186 45.455 0.00 0.00 0.00 4.10
450 460 3.077359 CTGGAGAAAATCTTGCCTCGTT 58.923 45.455 0.00 0.00 0.00 3.85
451 461 2.039084 ACTGGAGAAAATCTTGCCTCGT 59.961 45.455 0.00 0.00 0.00 4.18
452 462 2.704572 ACTGGAGAAAATCTTGCCTCG 58.295 47.619 0.00 0.00 0.00 4.63
471 481 6.522946 AGAAACCTTACTCAGAAACCAGTAC 58.477 40.000 0.00 0.00 0.00 2.73
489 499 7.666623 TCCATGTTCAAAATTTAGGAGAAACC 58.333 34.615 0.00 0.00 39.35 3.27
510 520 3.094572 CCTCTGGCTGTTTGAATTCCAT 58.905 45.455 2.27 0.00 0.00 3.41
511 521 2.108075 TCCTCTGGCTGTTTGAATTCCA 59.892 45.455 2.27 0.00 0.00 3.53
520 530 3.228188 TCACAATTTCCTCTGGCTGTT 57.772 42.857 0.00 0.00 0.00 3.16
524 534 3.057245 GGACTTTCACAATTTCCTCTGGC 60.057 47.826 0.00 0.00 0.00 4.85
563 573 2.798145 CGGCGATCTACATGCACAAGTA 60.798 50.000 0.00 0.00 0.00 2.24
564 574 1.656652 GGCGATCTACATGCACAAGT 58.343 50.000 0.00 0.00 0.00 3.16
584 594 1.750780 GCTCAGCTTGGGGCCTTAC 60.751 63.158 0.84 0.00 43.05 2.34
586 596 1.500783 TTAGCTCAGCTTGGGGCCTT 61.501 55.000 3.31 0.00 43.05 4.35
588 598 1.000896 TTTAGCTCAGCTTGGGGCC 60.001 57.895 3.31 0.00 43.05 5.80
592 602 2.680339 GGCTTACTTTAGCTCAGCTTGG 59.320 50.000 3.31 0.00 40.44 3.61
596 606 4.513318 CCTATTGGCTTACTTTAGCTCAGC 59.487 45.833 0.00 0.00 40.99 4.26
612 622 2.863809 AGCGGGATAAAAGCCTATTGG 58.136 47.619 0.00 0.00 0.00 3.16
613 623 4.918810 AAAGCGGGATAAAAGCCTATTG 57.081 40.909 0.00 0.00 0.00 1.90
616 639 9.969001 ATTAATATAAAGCGGGATAAAAGCCTA 57.031 29.630 0.00 0.00 0.00 3.93
679 702 3.347958 TTAGCTCAAGTTTGCCGTTTG 57.652 42.857 0.00 0.00 0.00 2.93
684 707 7.469260 TCGTTTATATTTAGCTCAAGTTTGCC 58.531 34.615 0.00 0.00 0.00 4.52
692 715 7.217200 AGAATGCCTCGTTTATATTTAGCTCA 58.783 34.615 0.00 0.00 0.00 4.26
693 716 7.600752 AGAGAATGCCTCGTTTATATTTAGCTC 59.399 37.037 0.00 0.00 46.49 4.09
694 717 7.445945 AGAGAATGCCTCGTTTATATTTAGCT 58.554 34.615 0.00 0.00 46.49 3.32
695 718 7.659652 AGAGAATGCCTCGTTTATATTTAGC 57.340 36.000 0.00 0.00 46.49 3.09
822 854 6.183360 GGAAAGTTGGAATTGATGGATGTAGG 60.183 42.308 0.00 0.00 0.00 3.18
876 909 3.190535 TCGGGTCTTTGCTTAATTTCTGC 59.809 43.478 0.00 0.00 0.00 4.26
889 922 1.691976 TGAGTGTGTGATCGGGTCTTT 59.308 47.619 0.00 0.00 0.00 2.52
923 956 1.361993 CAGCAGAGCGGCTAGGTAG 59.638 63.158 0.60 0.00 43.68 3.18
924 957 2.786495 GCAGCAGAGCGGCTAGGTA 61.786 63.158 0.60 0.00 45.50 3.08
925 958 4.154347 GCAGCAGAGCGGCTAGGT 62.154 66.667 0.60 1.04 45.50 3.08
1509 1562 1.337817 CGTCTGCCGTGAAGTTCTCG 61.338 60.000 18.05 18.05 33.67 4.04
1704 1782 6.086222 CGAATGAAATGAACAGGTTAACCAG 58.914 40.000 26.26 20.65 38.89 4.00
1727 1809 3.604065 TCACTAAAGGATCGATCGACG 57.396 47.619 22.06 8.03 44.09 5.12
1765 1960 6.313744 GTGCAACTTAATCACCAGTTTACT 57.686 37.500 0.00 0.00 30.48 2.24
1786 1981 3.119101 ACTCTGAATTACTACCCGCAGTG 60.119 47.826 0.00 0.00 0.00 3.66
1788 1983 3.802948 ACTCTGAATTACTACCCGCAG 57.197 47.619 0.00 0.00 0.00 5.18
1790 1985 2.608090 GCAACTCTGAATTACTACCCGC 59.392 50.000 0.00 0.00 0.00 6.13
1791 1986 3.617263 GTGCAACTCTGAATTACTACCCG 59.383 47.826 0.00 0.00 0.00 5.28
1792 1987 3.939592 GGTGCAACTCTGAATTACTACCC 59.060 47.826 0.00 0.00 36.74 3.69
1794 1989 4.575885 TGGGTGCAACTCTGAATTACTAC 58.424 43.478 0.00 0.00 38.97 2.73
1795 1990 4.832248 CTGGGTGCAACTCTGAATTACTA 58.168 43.478 0.00 0.00 38.76 1.82
1796 1991 3.679389 CTGGGTGCAACTCTGAATTACT 58.321 45.455 0.00 0.00 38.76 2.24
1871 2091 2.836360 GGCCAGTCCCATGCCATG 60.836 66.667 0.00 0.00 44.70 3.66
1880 2107 1.036707 CTAGCTAGAGTGGCCAGTCC 58.963 60.000 32.69 19.75 0.00 3.85
1887 2114 2.175202 CTATGGGCCTAGCTAGAGTGG 58.825 57.143 22.70 7.37 0.00 4.00
1888 2115 2.560542 CACTATGGGCCTAGCTAGAGTG 59.439 54.545 22.70 20.06 32.59 3.51
1889 2116 2.447429 TCACTATGGGCCTAGCTAGAGT 59.553 50.000 22.70 12.95 0.00 3.24
1890 2117 3.162147 TCACTATGGGCCTAGCTAGAG 57.838 52.381 22.70 12.31 0.00 2.43
1891 2118 3.702792 GATCACTATGGGCCTAGCTAGA 58.297 50.000 22.70 1.99 0.00 2.43
1892 2119 2.425312 CGATCACTATGGGCCTAGCTAG 59.575 54.545 14.20 14.20 0.00 3.42
1893 2120 2.447443 CGATCACTATGGGCCTAGCTA 58.553 52.381 4.53 0.00 0.00 3.32
1894 2121 1.261480 CGATCACTATGGGCCTAGCT 58.739 55.000 4.53 0.00 0.00 3.32
1895 2122 0.247736 CCGATCACTATGGGCCTAGC 59.752 60.000 4.53 0.00 0.00 3.42
1896 2123 1.273606 CACCGATCACTATGGGCCTAG 59.726 57.143 4.53 6.78 34.44 3.02
1898 2125 0.398522 TCACCGATCACTATGGGCCT 60.399 55.000 4.53 0.00 34.44 5.19
1900 2127 3.678056 TTATCACCGATCACTATGGGC 57.322 47.619 0.00 0.00 34.44 5.36
1901 2128 7.112452 TCATATTATCACCGATCACTATGGG 57.888 40.000 0.00 0.00 37.04 4.00
2101 2397 0.872021 AATCATTCGCTCGCTCGTCC 60.872 55.000 0.00 0.00 0.00 4.79
2102 2398 1.711298 CTAATCATTCGCTCGCTCGTC 59.289 52.381 0.00 0.00 0.00 4.20
2104 2400 0.432738 GCTAATCATTCGCTCGCTCG 59.567 55.000 0.00 0.00 0.00 5.03
2105 2401 0.432738 CGCTAATCATTCGCTCGCTC 59.567 55.000 0.00 0.00 0.00 5.03
2106 2402 1.552348 GCGCTAATCATTCGCTCGCT 61.552 55.000 0.00 0.00 44.79 4.93
2107 2403 1.154763 GCGCTAATCATTCGCTCGC 60.155 57.895 0.00 0.00 44.79 5.03
2121 2429 4.868171 TCAAATTAATGTCTCGTTAGCGCT 59.132 37.500 17.26 17.26 38.14 5.92
2124 2432 7.693952 TGGATTCAAATTAATGTCTCGTTAGC 58.306 34.615 0.00 0.00 0.00 3.09
2127 2435 8.739039 TGAATGGATTCAAATTAATGTCTCGTT 58.261 29.630 0.00 0.00 43.26 3.85
2128 2436 8.279970 TGAATGGATTCAAATTAATGTCTCGT 57.720 30.769 0.00 0.00 43.26 4.18
2495 2855 9.307121 CATTGTTCCAGTGTTTTATGTGTTTTA 57.693 29.630 0.00 0.00 0.00 1.52
2496 2856 7.821846 ACATTGTTCCAGTGTTTTATGTGTTTT 59.178 29.630 0.00 0.00 30.29 2.43
2497 2857 7.327214 ACATTGTTCCAGTGTTTTATGTGTTT 58.673 30.769 0.00 0.00 30.29 2.83
2498 2858 6.872920 ACATTGTTCCAGTGTTTTATGTGTT 58.127 32.000 0.00 0.00 30.29 3.32
2499 2859 6.463995 ACATTGTTCCAGTGTTTTATGTGT 57.536 33.333 0.00 0.00 30.29 3.72
2500 2860 6.420604 GGAACATTGTTCCAGTGTTTTATGTG 59.579 38.462 33.75 0.00 42.66 3.21
2501 2861 6.097554 TGGAACATTGTTCCAGTGTTTTATGT 59.902 34.615 36.29 2.53 42.66 2.29
2502 2862 6.511416 TGGAACATTGTTCCAGTGTTTTATG 58.489 36.000 36.29 1.86 42.66 1.90
2503 2863 6.723298 TGGAACATTGTTCCAGTGTTTTAT 57.277 33.333 36.29 0.00 42.66 1.40
2622 3060 2.028294 TCTCGACTCGTTGTACTCCTCT 60.028 50.000 0.00 0.00 0.00 3.69
2661 3099 0.463204 ACACCATGATCTCCGAGCAG 59.537 55.000 0.00 0.00 29.44 4.24
2736 3174 9.878737 GGAGTATGTGGGTAGGTATATGTATAT 57.121 37.037 0.00 0.00 0.00 0.86
2737 3175 8.284435 GGGAGTATGTGGGTAGGTATATGTATA 58.716 40.741 0.00 0.00 0.00 1.47
2738 3176 7.035320 AGGGAGTATGTGGGTAGGTATATGTAT 60.035 40.741 0.00 0.00 0.00 2.29
2739 3177 6.278719 AGGGAGTATGTGGGTAGGTATATGTA 59.721 42.308 0.00 0.00 0.00 2.29
2740 3178 5.077441 AGGGAGTATGTGGGTAGGTATATGT 59.923 44.000 0.00 0.00 0.00 2.29
2741 3179 5.590818 AGGGAGTATGTGGGTAGGTATATG 58.409 45.833 0.00 0.00 0.00 1.78
2763 3201 4.687483 ACAAGTACGTAATTTGGAACGGAG 59.313 41.667 19.38 4.80 43.25 4.63
2764 3202 4.630111 ACAAGTACGTAATTTGGAACGGA 58.370 39.130 19.38 0.00 43.25 4.69
2765 3203 4.433283 CGACAAGTACGTAATTTGGAACGG 60.433 45.833 19.38 5.95 43.25 4.44
2766 3204 4.148696 ACGACAAGTACGTAATTTGGAACG 59.851 41.667 19.38 20.21 42.17 3.95
2767 3205 5.368374 CACGACAAGTACGTAATTTGGAAC 58.632 41.667 19.38 12.02 42.07 3.62
2768 3206 4.448395 CCACGACAAGTACGTAATTTGGAA 59.552 41.667 15.68 0.00 42.07 3.53
2769 3207 3.989167 CCACGACAAGTACGTAATTTGGA 59.011 43.478 15.68 0.00 42.07 3.53
2770 3208 3.742369 ACCACGACAAGTACGTAATTTGG 59.258 43.478 18.01 18.01 42.07 3.28
2771 3209 4.977741 ACCACGACAAGTACGTAATTTG 57.022 40.909 5.37 11.78 42.07 2.32
2772 3210 5.989551 AAACCACGACAAGTACGTAATTT 57.010 34.783 5.37 0.00 42.07 1.82
2773 3211 5.989551 AAAACCACGACAAGTACGTAATT 57.010 34.783 1.75 1.75 42.07 1.40
2774 3212 5.294060 ACAAAAACCACGACAAGTACGTAAT 59.706 36.000 0.00 0.00 42.07 1.89
2775 3213 4.629200 ACAAAAACCACGACAAGTACGTAA 59.371 37.500 0.00 0.00 42.07 3.18
2776 3214 4.180057 ACAAAAACCACGACAAGTACGTA 58.820 39.130 0.00 0.00 42.07 3.57
2777 3215 3.002102 ACAAAAACCACGACAAGTACGT 58.998 40.909 0.00 0.00 44.83 3.57
2778 3216 3.661758 ACAAAAACCACGACAAGTACG 57.338 42.857 0.00 0.00 0.00 3.67
2779 3217 4.972201 TGAACAAAAACCACGACAAGTAC 58.028 39.130 0.00 0.00 0.00 2.73
2780 3218 5.624344 TTGAACAAAAACCACGACAAGTA 57.376 34.783 0.00 0.00 0.00 2.24
2781 3219 4.506886 TTGAACAAAAACCACGACAAGT 57.493 36.364 0.00 0.00 0.00 3.16
2782 3220 6.128688 ACAATTTGAACAAAAACCACGACAAG 60.129 34.615 2.79 0.00 33.56 3.16
2783 3221 5.696724 ACAATTTGAACAAAAACCACGACAA 59.303 32.000 2.79 0.00 33.56 3.18
2784 3222 5.230942 ACAATTTGAACAAAAACCACGACA 58.769 33.333 2.79 0.00 33.56 4.35
2785 3223 5.771602 ACAATTTGAACAAAAACCACGAC 57.228 34.783 2.79 0.00 33.56 4.34
2786 3224 8.480643 AATTACAATTTGAACAAAAACCACGA 57.519 26.923 2.79 0.00 33.56 4.35
2801 3239 8.250143 ACTCCCTCTGTTTCAAATTACAATTT 57.750 30.769 0.00 0.00 39.07 1.82
2802 3240 7.839680 ACTCCCTCTGTTTCAAATTACAATT 57.160 32.000 0.00 0.00 0.00 2.32
2803 3241 7.942341 TGTACTCCCTCTGTTTCAAATTACAAT 59.058 33.333 0.00 0.00 0.00 2.71
2804 3242 7.284074 TGTACTCCCTCTGTTTCAAATTACAA 58.716 34.615 0.00 0.00 0.00 2.41
2805 3243 6.833041 TGTACTCCCTCTGTTTCAAATTACA 58.167 36.000 0.00 0.00 0.00 2.41
2806 3244 7.390718 ACATGTACTCCCTCTGTTTCAAATTAC 59.609 37.037 0.00 0.00 0.00 1.89
2807 3245 7.458397 ACATGTACTCCCTCTGTTTCAAATTA 58.542 34.615 0.00 0.00 0.00 1.40
2808 3246 6.306987 ACATGTACTCCCTCTGTTTCAAATT 58.693 36.000 0.00 0.00 0.00 1.82
2809 3247 5.880901 ACATGTACTCCCTCTGTTTCAAAT 58.119 37.500 0.00 0.00 0.00 2.32
2810 3248 5.071788 AGACATGTACTCCCTCTGTTTCAAA 59.928 40.000 0.00 0.00 0.00 2.69
2811 3249 4.593206 AGACATGTACTCCCTCTGTTTCAA 59.407 41.667 0.00 0.00 0.00 2.69
2812 3250 4.160329 AGACATGTACTCCCTCTGTTTCA 58.840 43.478 0.00 0.00 0.00 2.69
2813 3251 4.810191 AGACATGTACTCCCTCTGTTTC 57.190 45.455 0.00 0.00 0.00 2.78
2814 3252 5.395768 GCATAGACATGTACTCCCTCTGTTT 60.396 44.000 0.00 0.00 34.40 2.83
2815 3253 4.100189 GCATAGACATGTACTCCCTCTGTT 59.900 45.833 0.00 0.00 34.40 3.16
2816 3254 3.639094 GCATAGACATGTACTCCCTCTGT 59.361 47.826 0.00 0.00 34.40 3.41
2817 3255 3.638627 TGCATAGACATGTACTCCCTCTG 59.361 47.826 0.00 0.00 34.40 3.35
2818 3256 3.639094 GTGCATAGACATGTACTCCCTCT 59.361 47.826 0.00 0.00 42.57 3.69
2819 3257 3.551046 CGTGCATAGACATGTACTCCCTC 60.551 52.174 0.00 0.00 43.38 4.30
2820 3258 2.362397 CGTGCATAGACATGTACTCCCT 59.638 50.000 0.00 0.00 43.38 4.20
2821 3259 2.100916 ACGTGCATAGACATGTACTCCC 59.899 50.000 0.00 0.00 43.38 4.30
2822 3260 3.438297 ACGTGCATAGACATGTACTCC 57.562 47.619 0.00 0.00 43.38 3.85
2823 3261 4.421058 TCAACGTGCATAGACATGTACTC 58.579 43.478 0.00 0.00 43.38 2.59
2824 3262 4.450082 TCAACGTGCATAGACATGTACT 57.550 40.909 0.00 0.37 43.38 2.73
2825 3263 4.085568 CGATCAACGTGCATAGACATGTAC 60.086 45.833 0.00 0.00 42.47 2.90
2862 3300 2.488153 GCTGGGTAGCTAACAAAACCTG 59.512 50.000 11.71 0.24 46.57 4.00
2972 3446 4.868171 AGACAAATTTGCATGCATGATCAC 59.132 37.500 30.64 12.74 0.00 3.06
3018 3494 8.907222 AACTCAATAAGGCAACAATCATTTTT 57.093 26.923 0.00 0.00 41.41 1.94
3028 3504 3.153919 TGGGTGAACTCAATAAGGCAAC 58.846 45.455 0.00 0.00 0.00 4.17
3049 3525 1.369625 GTATAGTGCGCTTTGTGGCT 58.630 50.000 9.73 0.00 0.00 4.75
3050 3526 0.377203 GGTATAGTGCGCTTTGTGGC 59.623 55.000 9.73 0.00 0.00 5.01
3110 3586 1.553248 CCCCCTATCAACGTGAGACAA 59.447 52.381 0.00 0.00 0.00 3.18
3121 3597 1.217183 ACGTCTTCTAGCCCCCTATCA 59.783 52.381 0.00 0.00 0.00 2.15
3136 3612 0.532573 CCAGTGCACCAGATACGTCT 59.467 55.000 14.63 0.00 34.14 4.18
3146 3622 0.036022 AGAAGAAGCTCCAGTGCACC 59.964 55.000 14.63 0.00 34.99 5.01
3147 3623 1.155042 CAGAAGAAGCTCCAGTGCAC 58.845 55.000 9.40 9.40 34.99 4.57
3153 3629 0.532573 CGGTAGCAGAAGAAGCTCCA 59.467 55.000 0.00 0.00 42.32 3.86
3217 3694 5.065218 GGTTCATGTCTTTTCGATGCACTAT 59.935 40.000 0.00 0.00 0.00 2.12
3226 3703 6.073276 TGACAACATAGGTTCATGTCTTTTCG 60.073 38.462 11.00 0.00 38.19 3.46
3270 3747 2.158449 GTGTCTCGAGCATTGTTTGGAG 59.842 50.000 7.81 0.00 0.00 3.86
3272 3749 1.872952 TGTGTCTCGAGCATTGTTTGG 59.127 47.619 7.81 0.00 0.00 3.28
3273 3750 3.607422 TTGTGTCTCGAGCATTGTTTG 57.393 42.857 7.81 0.00 0.00 2.93
3274 3751 4.630894 TTTTGTGTCTCGAGCATTGTTT 57.369 36.364 7.81 0.00 0.00 2.83
3275 3752 4.630894 TTTTTGTGTCTCGAGCATTGTT 57.369 36.364 7.81 0.00 0.00 2.83
3276 3753 4.275689 TCATTTTTGTGTCTCGAGCATTGT 59.724 37.500 7.81 0.00 0.00 2.71
3277 3754 4.614284 GTCATTTTTGTGTCTCGAGCATTG 59.386 41.667 7.81 3.07 0.00 2.82
3278 3755 4.275689 TGTCATTTTTGTGTCTCGAGCATT 59.724 37.500 7.81 0.00 0.00 3.56
3279 3756 3.814842 TGTCATTTTTGTGTCTCGAGCAT 59.185 39.130 7.81 0.00 0.00 3.79
3280 3757 3.202097 TGTCATTTTTGTGTCTCGAGCA 58.798 40.909 7.81 6.50 0.00 4.26
3281 3758 3.878086 TGTCATTTTTGTGTCTCGAGC 57.122 42.857 7.81 3.58 0.00 5.03
3282 3759 5.200454 CACTTGTCATTTTTGTGTCTCGAG 58.800 41.667 5.93 5.93 0.00 4.04
3283 3760 4.634004 ACACTTGTCATTTTTGTGTCTCGA 59.366 37.500 0.00 0.00 37.29 4.04
3284 3761 4.730042 CACACTTGTCATTTTTGTGTCTCG 59.270 41.667 0.00 0.00 39.46 4.04
3285 3762 5.739161 GTCACACTTGTCATTTTTGTGTCTC 59.261 40.000 0.00 0.00 39.46 3.36
3286 3763 5.182950 TGTCACACTTGTCATTTTTGTGTCT 59.817 36.000 0.00 0.00 39.46 3.41
3287 3764 5.398169 TGTCACACTTGTCATTTTTGTGTC 58.602 37.500 0.00 0.00 39.46 3.67
3288 3765 5.384063 TGTCACACTTGTCATTTTTGTGT 57.616 34.783 0.00 0.00 41.75 3.72
3303 3780 7.176515 TGGCCCATTATCATATTAATGTCACAC 59.823 37.037 0.00 0.00 37.71 3.82
3366 3843 8.856490 ATAGATACAAAAATGACAAATTCGGC 57.144 30.769 0.00 0.00 0.00 5.54
3394 3871 9.699985 TGTCACAAAAATTCAAATCAAAATTCG 57.300 25.926 0.00 0.00 0.00 3.34
3423 3900 7.930217 AGCGCATTCACATAACATTAAAGTAT 58.070 30.769 11.47 0.00 0.00 2.12
3456 3933 8.838365 CATTTCCAAATGTTTGAAAAATCTGGA 58.162 29.630 0.00 0.00 40.61 3.86
3486 3963 1.800805 CAGTGCACTGGACTACCTTG 58.199 55.000 34.65 9.83 40.20 3.61
3499 3976 1.882912 CTTCTTGTGCTACCAGTGCA 58.117 50.000 0.00 0.00 38.19 4.57
3500 3977 0.519077 GCTTCTTGTGCTACCAGTGC 59.481 55.000 0.00 0.00 0.00 4.40
3501 3978 2.072298 GAGCTTCTTGTGCTACCAGTG 58.928 52.381 0.00 0.00 41.30 3.66
3502 3979 1.002544 GGAGCTTCTTGTGCTACCAGT 59.997 52.381 0.00 0.00 41.30 4.00
3503 3980 1.731720 GGAGCTTCTTGTGCTACCAG 58.268 55.000 0.00 0.00 41.30 4.00
3504 3981 0.037326 CGGAGCTTCTTGTGCTACCA 60.037 55.000 0.00 0.00 41.30 3.25
3505 3982 0.741221 CCGGAGCTTCTTGTGCTACC 60.741 60.000 0.00 0.00 41.30 3.18
3506 3983 0.037232 ACCGGAGCTTCTTGTGCTAC 60.037 55.000 9.46 0.00 41.30 3.58
3507 3984 0.037326 CACCGGAGCTTCTTGTGCTA 60.037 55.000 9.46 0.00 41.30 3.49
3508 3985 1.302033 CACCGGAGCTTCTTGTGCT 60.302 57.895 9.46 0.00 44.24 4.40
3509 3986 2.970974 GCACCGGAGCTTCTTGTGC 61.971 63.158 17.33 17.55 44.53 4.57
3510 3987 0.957395 ATGCACCGGAGCTTCTTGTG 60.957 55.000 24.52 7.08 34.99 3.33
3511 3988 0.674895 GATGCACCGGAGCTTCTTGT 60.675 55.000 25.68 7.19 36.20 3.16
3512 3989 0.674581 TGATGCACCGGAGCTTCTTG 60.675 55.000 30.14 10.81 38.90 3.02
3529 4006 2.781757 TCCCCCTAGAGAACGTATCTGA 59.218 50.000 12.26 0.04 38.96 3.27
3585 4062 4.917415 GTGCTATGTTGTTTGAATGACACC 59.083 41.667 0.00 0.00 0.00 4.16
3662 4139 1.576356 TTGCGGGAAAAACAATGTGC 58.424 45.000 0.00 0.00 0.00 4.57
3675 4152 1.372004 CATGCACTGTGTTTGCGGG 60.372 57.895 9.86 0.00 43.34 6.13


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

AutoCloner maintained by Alex Coulton.