Multiple sequence alignment - TraesCS5A01G220500

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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 TraesCS5A01G220500 chr5A 100.000 3810 0 0 1 3810 437034060 437037869 0.000000e+00 7036.0
1 TraesCS5A01G220500 chr5A 97.006 167 5 0 2923 3089 535156933 535156767 8.060000e-72 281.0
2 TraesCS5A01G220500 chr5D 87.349 1486 88 44 603 2017 335869654 335871110 0.000000e+00 1611.0
3 TraesCS5A01G220500 chr5D 93.640 912 43 11 2017 2917 335873131 335874038 0.000000e+00 1349.0
4 TraesCS5A01G220500 chr5D 88.817 617 39 16 3094 3701 335874039 335874634 0.000000e+00 730.0
5 TraesCS5A01G220500 chr5D 86.667 480 47 6 1 475 335869059 335869526 2.030000e-142 516.0
6 TraesCS5A01G220500 chr5B 90.434 1244 72 14 1711 2918 393834843 393836075 0.000000e+00 1594.0
7 TraesCS5A01G220500 chr5B 86.014 858 58 27 475 1289 393830455 393831293 0.000000e+00 863.0
8 TraesCS5A01G220500 chr5B 88.869 566 39 7 3108 3663 393836099 393836650 0.000000e+00 675.0
9 TraesCS5A01G220500 chr5B 91.283 413 31 4 1 408 393829943 393830355 3.320000e-155 558.0
10 TraesCS5A01G220500 chr5B 88.938 226 16 6 1323 1539 393831361 393831586 1.740000e-68 270.0
11 TraesCS5A01G220500 chr5B 93.750 48 3 0 1673 1720 393832606 393832653 5.280000e-09 73.1
12 TraesCS5A01G220500 chr1A 99.398 166 1 0 2922 3087 501034128 501034293 6.190000e-78 302.0
13 TraesCS5A01G220500 chr1A 99.398 166 1 0 2922 3087 501034718 501034883 6.190000e-78 302.0
14 TraesCS5A01G220500 chr1A 96.988 166 5 0 2922 3087 53691643 53691478 2.900000e-71 279.0
15 TraesCS5A01G220500 chr1A 93.889 180 11 0 2914 3093 32549217 32549396 4.850000e-69 272.0
16 TraesCS5A01G220500 chr2A 99.394 165 1 0 2923 3087 661453981 661453817 2.220000e-77 300.0
17 TraesCS5A01G220500 chr6A 96.471 170 6 0 2922 3091 610234315 610234146 8.060000e-72 281.0
18 TraesCS5A01G220500 chr6A 96.386 166 6 0 2923 3088 613273428 613273263 1.350000e-69 274.0
19 TraesCS5A01G220500 chr3A 96.970 165 5 0 2923 3087 491454119 491454283 1.040000e-70 278.0


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 TraesCS5A01G220500 chr5A 437034060 437037869 3809 False 7036.000000 7036 100.000000 1 3810 1 chr5A.!!$F1 3809
1 TraesCS5A01G220500 chr5D 335869059 335874634 5575 False 1051.500000 1611 89.118250 1 3701 4 chr5D.!!$F1 3700
2 TraesCS5A01G220500 chr5B 393829943 393836650 6707 False 672.183333 1594 89.881333 1 3663 6 chr5B.!!$F1 3662
3 TraesCS5A01G220500 chr1A 501034128 501034883 755 False 302.000000 302 99.398000 2922 3087 2 chr1A.!!$F2 165

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
754 832 0.326264 AGGGGAACATGAGTCACAGC 59.674 55.0 0.0 0.0 0.00 4.40 F
1617 1784 0.326143 TGCATAGGCCCACTAGGTCA 60.326 55.0 0.0 0.0 45.84 4.02 F
2599 7942 0.179097 TGTCTGTGTGCAGCGTGTTA 60.179 50.0 0.0 0.0 42.29 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 7370 0.248621 CCTGAAAATGGCCGCGAATC 60.249 55.0 8.23 0.0 0.00 2.52 R
2785 8128 0.812811 GGCATCTCGAAGCATCAGCA 60.813 55.0 6.51 0.0 45.49 4.41 R
3738 9653 0.855349 GGCATGTCGAAGTATCAGCG 59.145 55.0 0.00 0.0 0.00 5.18 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
36 37 2.435234 GGTGCATTCGCCGTGGTA 60.435 61.111 0.00 0.00 37.32 3.25
73 74 4.536526 TGTGGGGCAAAGCAGGCA 62.537 61.111 0.00 0.00 35.46 4.75
135 136 0.616111 AGAAGACATGGTCGGGCTCT 60.616 55.000 0.00 0.00 37.67 4.09
167 168 2.285154 CGGAAAGTACGATCACCGC 58.715 57.895 0.00 0.00 43.32 5.68
189 190 1.078143 GCTCCTGGCGGACAAGAAT 60.078 57.895 0.00 0.00 34.92 2.40
191 192 0.462759 CTCCTGGCGGACAAGAATCC 60.463 60.000 0.00 0.00 34.92 3.01
204 205 5.450137 GGACAAGAATCCGATCGAGAAGTAA 60.450 44.000 18.66 0.00 0.00 2.24
224 229 7.158099 AGTAATGGCTCTACAATTTTGGAAC 57.842 36.000 0.00 0.00 0.00 3.62
246 251 2.305343 AGCCAGTGATCTTTCTCAGCTT 59.695 45.455 0.00 0.00 28.67 3.74
253 258 4.505922 GTGATCTTTCTCAGCTTATGGTCG 59.494 45.833 0.00 0.00 0.00 4.79
262 267 2.009774 AGCTTATGGTCGCATGTGTTC 58.990 47.619 6.09 1.19 0.00 3.18
270 276 1.391485 GTCGCATGTGTTCTGTAGCTG 59.609 52.381 6.09 0.00 0.00 4.24
273 279 1.741706 GCATGTGTTCTGTAGCTGCAT 59.258 47.619 4.51 0.00 0.00 3.96
284 290 3.976169 TGTAGCTGCATGGTTGTTTTTC 58.024 40.909 0.00 0.00 0.00 2.29
312 318 1.893801 AGTACTAGTGTGCTGGTGGAC 59.106 52.381 5.39 0.00 37.73 4.02
323 329 2.117206 GGTGGACCATGTGGCCAA 59.883 61.111 7.24 0.00 40.99 4.52
325 331 2.283101 TGGACCATGTGGCCAAGC 60.283 61.111 7.24 0.00 38.06 4.01
353 363 2.413796 TGTCGCCGCTAATGTACAAAAG 59.586 45.455 0.00 1.20 0.00 2.27
360 370 6.142817 GCCGCTAATGTACAAAAGATAATGG 58.857 40.000 0.00 0.52 0.00 3.16
406 416 4.102681 CGAATTTAAGATGAGGTAGGGGGT 59.897 45.833 0.00 0.00 0.00 4.95
407 417 5.377478 GAATTTAAGATGAGGTAGGGGGTG 58.623 45.833 0.00 0.00 0.00 4.61
408 418 2.489528 TAAGATGAGGTAGGGGGTGG 57.510 55.000 0.00 0.00 0.00 4.61
409 419 0.327576 AAGATGAGGTAGGGGGTGGG 60.328 60.000 0.00 0.00 0.00 4.61
410 420 1.770518 GATGAGGTAGGGGGTGGGG 60.771 68.421 0.00 0.00 0.00 4.96
411 421 3.362946 ATGAGGTAGGGGGTGGGGG 62.363 68.421 0.00 0.00 0.00 5.40
434 444 1.201987 CGTGCTTACCAATTACGGCAC 60.202 52.381 0.00 0.00 44.16 5.01
468 483 1.514003 TTCGGTGCGCTACAATCAAA 58.486 45.000 9.73 0.00 0.00 2.69
469 484 1.732941 TCGGTGCGCTACAATCAAAT 58.267 45.000 9.73 0.00 0.00 2.32
470 485 1.663643 TCGGTGCGCTACAATCAAATC 59.336 47.619 9.73 0.00 0.00 2.17
471 486 1.592110 CGGTGCGCTACAATCAAATCG 60.592 52.381 9.73 0.00 0.00 3.34
472 487 1.396996 GGTGCGCTACAATCAAATCGT 59.603 47.619 9.73 0.00 0.00 3.73
473 488 2.605818 GGTGCGCTACAATCAAATCGTA 59.394 45.455 9.73 0.00 0.00 3.43
517 570 1.789464 GCTTCTTGACTGACACTGACG 59.211 52.381 0.00 0.00 0.00 4.35
555 626 2.936919 TGTGCATTTCTCCAGTCAGT 57.063 45.000 0.00 0.00 0.00 3.41
560 631 5.046663 TGTGCATTTCTCCAGTCAGTATGTA 60.047 40.000 0.00 0.00 37.40 2.29
561 632 6.051717 GTGCATTTCTCCAGTCAGTATGTAT 58.948 40.000 0.00 0.00 37.40 2.29
562 633 6.018425 GTGCATTTCTCCAGTCAGTATGTATG 60.018 42.308 0.00 0.00 37.40 2.39
563 634 6.051717 GCATTTCTCCAGTCAGTATGTATGT 58.948 40.000 0.00 0.00 37.40 2.29
564 635 6.540189 GCATTTCTCCAGTCAGTATGTATGTT 59.460 38.462 0.00 0.00 37.40 2.71
565 636 7.254590 GCATTTCTCCAGTCAGTATGTATGTTC 60.255 40.741 0.00 0.00 37.40 3.18
566 637 6.850752 TTCTCCAGTCAGTATGTATGTTCA 57.149 37.500 0.00 0.00 37.40 3.18
567 638 6.456795 TCTCCAGTCAGTATGTATGTTCAG 57.543 41.667 0.00 0.00 37.40 3.02
568 639 5.952347 TCTCCAGTCAGTATGTATGTTCAGT 59.048 40.000 0.00 0.00 37.40 3.41
569 640 6.095580 TCTCCAGTCAGTATGTATGTTCAGTC 59.904 42.308 0.00 0.00 37.40 3.51
570 641 5.952347 TCCAGTCAGTATGTATGTTCAGTCT 59.048 40.000 0.00 0.00 37.40 3.24
571 642 7.116736 TCCAGTCAGTATGTATGTTCAGTCTA 58.883 38.462 0.00 0.00 37.40 2.59
572 643 7.283354 TCCAGTCAGTATGTATGTTCAGTCTAG 59.717 40.741 0.00 0.00 37.40 2.43
573 644 7.421599 CAGTCAGTATGTATGTTCAGTCTAGG 58.578 42.308 0.00 0.00 37.40 3.02
574 645 6.039941 AGTCAGTATGTATGTTCAGTCTAGGC 59.960 42.308 0.00 0.00 37.40 3.93
575 646 5.891551 TCAGTATGTATGTTCAGTCTAGGCA 59.108 40.000 0.00 0.00 37.40 4.75
576 647 6.379988 TCAGTATGTATGTTCAGTCTAGGCAA 59.620 38.462 0.00 0.00 37.40 4.52
577 648 7.069950 TCAGTATGTATGTTCAGTCTAGGCAAT 59.930 37.037 0.00 0.00 37.40 3.56
578 649 8.360390 CAGTATGTATGTTCAGTCTAGGCAATA 58.640 37.037 0.00 0.00 0.00 1.90
585 656 4.327982 TCAGTCTAGGCAATAGTCATGC 57.672 45.455 0.00 0.00 43.08 4.06
586 657 3.963374 TCAGTCTAGGCAATAGTCATGCT 59.037 43.478 0.00 0.00 43.34 3.79
591 662 3.641434 AGGCAATAGTCATGCTGAACT 57.359 42.857 0.00 0.00 43.34 3.01
603 674 1.448540 CTGAACTAGTGCCAGGCGG 60.449 63.158 7.03 0.00 0.00 6.13
687 764 1.475751 CGCCAGCCAATTCAGGATAGT 60.476 52.381 0.00 0.00 0.00 2.12
754 832 0.326264 AGGGGAACATGAGTCACAGC 59.674 55.000 0.00 0.00 0.00 4.40
761 839 1.202639 ACATGAGTCACAGCACCGAAA 60.203 47.619 0.00 0.00 0.00 3.46
767 845 0.944386 TCACAGCACCGAAAAGAAGC 59.056 50.000 0.00 0.00 0.00 3.86
775 853 2.031682 CACCGAAAAGAAGCACAAGAGG 60.032 50.000 0.00 0.00 0.00 3.69
817 895 4.476361 GGCGAAAATTCCAAGCCG 57.524 55.556 0.00 0.00 38.28 5.52
824 908 1.384222 AAATTCCAAGCCGGGCGATC 61.384 55.000 14.39 0.00 34.36 3.69
881 965 4.355437 CGCTCAACTCTTTATCTCATCGT 58.645 43.478 0.00 0.00 0.00 3.73
887 971 6.602009 TCAACTCTTTATCTCATCGTCTGGTA 59.398 38.462 0.00 0.00 0.00 3.25
888 972 6.627395 ACTCTTTATCTCATCGTCTGGTAG 57.373 41.667 0.00 0.00 0.00 3.18
889 973 5.009210 ACTCTTTATCTCATCGTCTGGTAGC 59.991 44.000 0.00 0.00 0.00 3.58
917 1002 1.281656 GACTGCAAAACCCGAACCG 59.718 57.895 0.00 0.00 0.00 4.44
1292 1408 3.528370 CTCCCTCGCCAGGTACGG 61.528 72.222 0.00 0.00 38.30 4.02
1300 1416 4.732106 CCAGGTACGGCTCGATTC 57.268 61.111 1.50 0.00 0.00 2.52
1308 1424 4.162690 GGCTCGATTCCGGCACCT 62.163 66.667 0.00 0.00 34.94 4.00
1310 1426 2.464459 GCTCGATTCCGGCACCTTG 61.464 63.158 0.00 0.00 36.24 3.61
1312 1428 3.864686 CGATTCCGGCACCTTGCG 61.865 66.667 0.00 0.00 46.21 4.85
1313 1429 4.179579 GATTCCGGCACCTTGCGC 62.180 66.667 0.00 0.00 46.21 6.09
1318 1434 2.511373 CGGCACCTTGCGCTGATA 60.511 61.111 9.73 0.00 46.21 2.15
1328 1481 2.793278 TGCGCTGATACGATACATGT 57.207 45.000 9.73 2.69 34.06 3.21
1331 1484 2.664698 GCGCTGATACGATACATGTCGA 60.665 50.000 13.28 0.00 44.06 4.20
1350 1503 4.505217 CGATGTTGCAGCGCGACC 62.505 66.667 12.10 0.00 41.86 4.79
1491 1644 1.687493 CTCCTCCCCTTTCTCCGCT 60.687 63.158 0.00 0.00 0.00 5.52
1492 1645 1.681486 CTCCTCCCCTTTCTCCGCTC 61.681 65.000 0.00 0.00 0.00 5.03
1517 1684 2.289532 GGTGCCTCAGACAGAGCCT 61.290 63.158 0.00 0.00 43.31 4.58
1535 1702 2.125106 GCTGGCCGTCCGATTTCT 60.125 61.111 0.00 0.00 34.14 2.52
1539 1706 1.017177 TGGCCGTCCGATTTCTTTCG 61.017 55.000 0.00 0.00 38.83 3.46
1572 1739 8.628882 TTTTTGAGAAAAGTCCGATTTCTTTC 57.371 30.769 3.33 0.00 44.81 2.62
1573 1740 5.591643 TGAGAAAAGTCCGATTTCTTTCG 57.408 39.130 3.33 0.00 44.81 3.46
1574 1741 5.054477 TGAGAAAAGTCCGATTTCTTTCGT 58.946 37.500 3.33 0.00 44.81 3.85
1575 1742 5.526111 TGAGAAAAGTCCGATTTCTTTCGTT 59.474 36.000 3.33 0.00 44.81 3.85
1576 1743 5.748592 AGAAAAGTCCGATTTCTTTCGTTG 58.251 37.500 0.00 0.00 42.85 4.10
1577 1744 4.483476 AAAGTCCGATTTCTTTCGTTGG 57.517 40.909 0.00 0.00 37.42 3.77
1578 1745 3.121738 AGTCCGATTTCTTTCGTTGGT 57.878 42.857 0.00 0.00 37.42 3.67
1598 1765 3.933332 GGTCGCTTGTAGCTACTCATTTT 59.067 43.478 23.84 0.00 39.60 1.82
1599 1766 4.201724 GGTCGCTTGTAGCTACTCATTTTG 60.202 45.833 23.84 8.22 39.60 2.44
1600 1767 3.370978 TCGCTTGTAGCTACTCATTTTGC 59.629 43.478 23.84 14.85 39.60 3.68
1601 1768 3.125146 CGCTTGTAGCTACTCATTTTGCA 59.875 43.478 23.84 0.00 39.60 4.08
1611 1778 2.291800 ACTCATTTTGCATAGGCCCACT 60.292 45.455 0.00 0.00 40.13 4.00
1614 1781 2.435372 TTTTGCATAGGCCCACTAGG 57.565 50.000 0.00 0.00 40.13 3.02
1615 1782 1.295020 TTTGCATAGGCCCACTAGGT 58.705 50.000 0.00 0.00 40.13 3.08
1616 1783 0.837272 TTGCATAGGCCCACTAGGTC 59.163 55.000 0.00 0.00 42.50 3.85
1617 1784 0.326143 TGCATAGGCCCACTAGGTCA 60.326 55.000 0.00 0.00 45.84 4.02
1619 1786 1.794714 CATAGGCCCACTAGGTCAGT 58.205 55.000 0.00 0.00 45.84 3.41
1620 1787 1.689273 CATAGGCCCACTAGGTCAGTC 59.311 57.143 0.00 0.00 45.84 3.51
1636 1821 3.084039 TCAGTCAGCCCATTGATTGTTC 58.916 45.455 0.00 0.00 36.52 3.18
1647 1832 1.212751 GATTGTTCGGGCTTGTGGC 59.787 57.895 0.00 0.00 40.90 5.01
1654 1839 2.644992 GGGCTTGTGGCTTTCGTG 59.355 61.111 0.00 0.00 41.46 4.35
1708 2794 1.006571 TGGAGTGACTCGAAACGCC 60.007 57.895 6.50 7.97 36.85 5.68
1862 5148 4.767255 AAGCTTCTCGGCGCCCTG 62.767 66.667 23.46 14.27 37.29 4.45
1890 5176 2.509336 CGACCGATGACTGGGTGC 60.509 66.667 0.00 0.00 36.46 5.01
1989 5275 2.802247 GCACCTTGGCTTGAAAACATTC 59.198 45.455 0.00 0.00 0.00 2.67
1995 5281 3.237746 TGGCTTGAAAACATTCATCCCA 58.762 40.909 6.61 6.61 32.59 4.37
2003 5289 6.690530 TGAAAACATTCATCCCATTTCTGTC 58.309 36.000 0.00 0.00 0.00 3.51
2007 5293 5.573219 ACATTCATCCCATTTCTGTCAGAA 58.427 37.500 11.36 11.36 31.28 3.02
2009 5295 6.096423 ACATTCATCCCATTTCTGTCAGAATG 59.904 38.462 15.95 14.57 43.11 2.67
2056 7364 5.457799 GCGATTGATTGGTTTCTGAATGATG 59.542 40.000 0.00 0.00 0.00 3.07
2062 7370 7.712797 TGATTGGTTTCTGAATGATGATGATG 58.287 34.615 0.00 0.00 0.00 3.07
2063 7371 7.558444 TGATTGGTTTCTGAATGATGATGATGA 59.442 33.333 0.00 0.00 0.00 2.92
2064 7372 7.891498 TTGGTTTCTGAATGATGATGATGAT 57.109 32.000 0.00 0.00 0.00 2.45
2065 7373 7.891498 TGGTTTCTGAATGATGATGATGATT 57.109 32.000 0.00 0.00 0.00 2.57
2071 7379 1.150827 TGATGATGATGATTCGCGGC 58.849 50.000 6.13 0.00 0.00 6.53
2110 7418 5.290386 GTCTGTAAATCCTACCTTGATCCG 58.710 45.833 0.00 0.00 0.00 4.18
2113 7421 2.918712 AATCCTACCTTGATCCGCTG 57.081 50.000 0.00 0.00 0.00 5.18
2215 7523 4.959723 AGATCTGGAAGCTTGCTTCTATC 58.040 43.478 27.48 24.64 34.06 2.08
2311 7631 5.233957 TGTTGTTCTGAACTGTGTTGATG 57.766 39.130 20.18 0.00 0.00 3.07
2321 7641 7.278646 TCTGAACTGTGTTGATGTATAATGAGC 59.721 37.037 0.00 0.00 0.00 4.26
2331 7651 4.235079 TGTATAATGAGCTTGGCCACTT 57.765 40.909 3.88 0.00 0.00 3.16
2418 7738 1.322442 GCATATCAGTGAAAGGCCCC 58.678 55.000 0.00 0.00 0.00 5.80
2470 7790 3.694734 GCGGTCATCACAACAATATTGG 58.305 45.455 19.37 5.37 0.00 3.16
2472 7792 3.489059 CGGTCATCACAACAATATTGGCC 60.489 47.826 19.37 0.00 0.00 5.36
2537 7880 4.109050 GACTGAACTTCCTATTCTGCTCG 58.891 47.826 0.00 0.00 0.00 5.03
2572 7915 2.870411 GCTACCGTGGATGATGTTTACC 59.130 50.000 0.00 0.00 0.00 2.85
2599 7942 0.179097 TGTCTGTGTGCAGCGTGTTA 60.179 50.000 0.00 0.00 42.29 2.41
2611 7954 3.517602 CAGCGTGTTAGGTGCTATTGTA 58.482 45.455 0.00 0.00 37.15 2.41
2656 7999 2.684927 GCTGTGGGGTAAAGCTGATGAT 60.685 50.000 0.00 0.00 34.05 2.45
2663 8006 2.540361 GGTAAAGCTGATGATGCAAGCG 60.540 50.000 1.82 0.00 0.00 4.68
2767 8110 5.846203 ACCAATCTTTCAGAACCATTGTTG 58.154 37.500 10.48 2.43 33.97 3.33
2785 8128 3.749088 TGTTGTTATCTGAAAACGCGGAT 59.251 39.130 12.47 4.66 37.61 4.18
2810 8153 1.372582 TGCTTCGAGATGCCAATGAC 58.627 50.000 8.22 0.00 0.00 3.06
2816 8159 1.674441 CGAGATGCCAATGACATTGCT 59.326 47.619 20.69 12.92 38.92 3.91
2818 8161 2.426024 GAGATGCCAATGACATTGCTGT 59.574 45.455 20.69 9.32 38.92 4.40
2843 8187 7.617041 TTTTTAGAATCAGCTTCTAGCCTTC 57.383 36.000 0.00 0.00 45.07 3.46
2846 8190 3.449018 AGAATCAGCTTCTAGCCTTCGAA 59.551 43.478 0.00 0.00 43.77 3.71
2877 8221 9.539194 AATGATCCCTTTTTCTGATACTTCTTT 57.461 29.630 0.00 0.00 0.00 2.52
2908 8256 5.226396 TGCTTGTTGCCAAAATATGTGTAC 58.774 37.500 0.00 0.00 42.00 2.90
3087 8435 2.501316 GGGACCATGCTAAAATTTGCCT 59.499 45.455 0.00 0.00 0.00 4.75
3090 8438 5.003160 GGACCATGCTAAAATTTGCCTTTT 58.997 37.500 0.00 0.00 33.17 2.27
3091 8439 5.122239 GGACCATGCTAAAATTTGCCTTTTC 59.878 40.000 0.00 0.00 31.15 2.29
3092 8440 5.003160 ACCATGCTAAAATTTGCCTTTTCC 58.997 37.500 0.00 0.00 31.15 3.13
3126 9017 2.723746 GCCAATGGCCATGCTACG 59.276 61.111 21.63 6.21 44.06 3.51
3136 9034 2.943033 GGCCATGCTACGTTATCAAACT 59.057 45.455 0.00 0.00 33.15 2.66
3163 9061 1.397343 CTAGCTGTCTGCACAATGCTG 59.603 52.381 0.00 1.80 45.31 4.41
3175 9073 0.806868 CAATGCTGAATGTGCCGAGT 59.193 50.000 0.00 0.00 0.00 4.18
3259 9157 5.532779 GGGAACATGGAAGATATTGGAAGAC 59.467 44.000 0.00 0.00 0.00 3.01
3297 9199 7.566879 AGGACTGAGACCTATGTTAAGAATGAT 59.433 37.037 0.55 0.00 35.84 2.45
3332 9241 1.273886 GAGAGTCACACAGAAGGGACC 59.726 57.143 0.00 0.00 0.00 4.46
3417 9326 8.715191 ATCTCTTCAATGTTTACTCATGAGTC 57.285 34.615 31.09 17.71 42.54 3.36
3418 9327 7.670364 TCTCTTCAATGTTTACTCATGAGTCA 58.330 34.615 31.09 22.56 42.54 3.41
3419 9328 8.316946 TCTCTTCAATGTTTACTCATGAGTCAT 58.683 33.333 31.09 23.68 42.54 3.06
3462 9371 6.441924 TCTTCCTTCATGAAGAACTCCATACT 59.558 38.462 32.49 0.00 45.78 2.12
3463 9372 5.982356 TCCTTCATGAAGAACTCCATACTG 58.018 41.667 32.49 13.77 40.79 2.74
3464 9373 5.104776 TCCTTCATGAAGAACTCCATACTGG 60.105 44.000 32.49 14.64 40.79 4.00
3465 9374 4.760530 TCATGAAGAACTCCATACTGGG 57.239 45.455 0.00 0.00 38.32 4.45
3466 9375 4.361783 TCATGAAGAACTCCATACTGGGA 58.638 43.478 0.00 0.00 38.32 4.37
3482 9391 1.527370 GGAGTGGGAGGTATGCACC 59.473 63.158 0.00 0.00 46.19 5.01
3494 9403 2.427095 GGTATGCACCAACTTCATTCCC 59.573 50.000 0.00 0.00 45.04 3.97
3614 9529 1.153489 CTGTCACCATCGGCCTCTG 60.153 63.158 0.00 0.00 0.00 3.35
3620 9535 1.227380 CCATCGGCCTCTGTGTAGC 60.227 63.158 0.00 0.00 0.00 3.58
3623 9538 4.162690 CGGCCTCTGTGTAGCCCC 62.163 72.222 0.00 0.00 44.13 5.80
3649 9564 4.202409 GGGGTAAAGAAGATGATGGAGAGG 60.202 50.000 0.00 0.00 0.00 3.69
3674 9589 5.982516 GTGAGAGCATGGTAGAACAAGATAG 59.017 44.000 0.00 0.00 0.00 2.08
3701 9616 7.268199 TCGTTGTAAAAGTAGAGAGTGAGAA 57.732 36.000 0.00 0.00 0.00 2.87
3702 9617 7.137426 TCGTTGTAAAAGTAGAGAGTGAGAAC 58.863 38.462 0.00 0.00 0.00 3.01
3703 9618 6.916387 CGTTGTAAAAGTAGAGAGTGAGAACA 59.084 38.462 0.00 0.00 0.00 3.18
3704 9619 7.434307 CGTTGTAAAAGTAGAGAGTGAGAACAA 59.566 37.037 0.00 0.00 0.00 2.83
3705 9620 9.262358 GTTGTAAAAGTAGAGAGTGAGAACAAT 57.738 33.333 0.00 0.00 0.00 2.71
3706 9621 9.477484 TTGTAAAAGTAGAGAGTGAGAACAATC 57.523 33.333 0.00 0.00 40.77 2.67
3707 9622 8.088981 TGTAAAAGTAGAGAGTGAGAACAATCC 58.911 37.037 0.00 0.00 41.28 3.01
3708 9623 6.926630 AAAGTAGAGAGTGAGAACAATCCT 57.073 37.500 0.00 0.00 41.28 3.24
3709 9624 6.926630 AAGTAGAGAGTGAGAACAATCCTT 57.073 37.500 0.00 0.00 41.28 3.36
3710 9625 6.524101 AGTAGAGAGTGAGAACAATCCTTC 57.476 41.667 0.00 0.00 41.28 3.46
3711 9626 6.013379 AGTAGAGAGTGAGAACAATCCTTCA 58.987 40.000 0.00 0.00 41.28 3.02
3712 9627 5.404466 AGAGAGTGAGAACAATCCTTCAG 57.596 43.478 0.00 0.00 41.28 3.02
3713 9628 5.083122 AGAGAGTGAGAACAATCCTTCAGA 58.917 41.667 0.00 0.00 41.28 3.27
3714 9629 5.185635 AGAGAGTGAGAACAATCCTTCAGAG 59.814 44.000 0.00 0.00 41.28 3.35
3715 9630 3.932089 GAGTGAGAACAATCCTTCAGAGC 59.068 47.826 0.00 0.00 35.45 4.09
3716 9631 3.006247 GTGAGAACAATCCTTCAGAGCC 58.994 50.000 0.00 0.00 0.00 4.70
3717 9632 2.639347 TGAGAACAATCCTTCAGAGCCA 59.361 45.455 0.00 0.00 0.00 4.75
3718 9633 3.265221 TGAGAACAATCCTTCAGAGCCAT 59.735 43.478 0.00 0.00 0.00 4.40
3719 9634 4.263639 TGAGAACAATCCTTCAGAGCCATT 60.264 41.667 0.00 0.00 0.00 3.16
3720 9635 4.015084 AGAACAATCCTTCAGAGCCATTG 58.985 43.478 0.00 0.00 32.20 2.82
3721 9636 3.446442 ACAATCCTTCAGAGCCATTGT 57.554 42.857 0.00 0.00 33.44 2.71
3722 9637 3.771216 ACAATCCTTCAGAGCCATTGTT 58.229 40.909 0.00 0.00 34.04 2.83
3723 9638 4.922206 ACAATCCTTCAGAGCCATTGTTA 58.078 39.130 0.00 0.00 34.04 2.41
3724 9639 5.513233 ACAATCCTTCAGAGCCATTGTTAT 58.487 37.500 0.00 0.00 34.04 1.89
3725 9640 5.591877 ACAATCCTTCAGAGCCATTGTTATC 59.408 40.000 0.00 0.00 34.04 1.75
3726 9641 5.643421 ATCCTTCAGAGCCATTGTTATCT 57.357 39.130 0.00 0.00 0.00 1.98
3727 9642 4.774124 TCCTTCAGAGCCATTGTTATCTG 58.226 43.478 0.00 0.00 40.42 2.90
3728 9643 4.471025 TCCTTCAGAGCCATTGTTATCTGA 59.529 41.667 8.02 8.02 44.78 3.27
3732 9647 6.500684 TCAGAGCCATTGTTATCTGAAAAC 57.499 37.500 9.15 0.00 43.81 2.43
3733 9648 5.122239 TCAGAGCCATTGTTATCTGAAAACG 59.878 40.000 9.15 0.00 43.81 3.60
3734 9649 5.003804 AGAGCCATTGTTATCTGAAAACGT 58.996 37.500 0.00 0.00 0.00 3.99
3735 9650 5.046910 AGCCATTGTTATCTGAAAACGTG 57.953 39.130 0.00 0.00 0.00 4.49
3736 9651 4.759693 AGCCATTGTTATCTGAAAACGTGA 59.240 37.500 0.00 0.00 0.00 4.35
3737 9652 5.240623 AGCCATTGTTATCTGAAAACGTGAA 59.759 36.000 0.00 0.00 0.00 3.18
3738 9653 5.342259 GCCATTGTTATCTGAAAACGTGAAC 59.658 40.000 0.00 0.00 0.00 3.18
3739 9654 5.563751 CCATTGTTATCTGAAAACGTGAACG 59.436 40.000 0.40 0.40 46.33 3.95
3740 9655 4.123276 TGTTATCTGAAAACGTGAACGC 57.877 40.909 2.11 0.00 44.43 4.84
3741 9656 3.805422 TGTTATCTGAAAACGTGAACGCT 59.195 39.130 2.11 0.00 44.43 5.07
3742 9657 2.949714 ATCTGAAAACGTGAACGCTG 57.050 45.000 2.11 0.00 44.43 5.18
3743 9658 1.929230 TCTGAAAACGTGAACGCTGA 58.071 45.000 2.11 0.00 44.43 4.26
3744 9659 2.479837 TCTGAAAACGTGAACGCTGAT 58.520 42.857 2.11 0.00 44.43 2.90
3745 9660 3.644823 TCTGAAAACGTGAACGCTGATA 58.355 40.909 2.11 0.00 44.43 2.15
3746 9661 3.427528 TCTGAAAACGTGAACGCTGATAC 59.572 43.478 2.11 0.00 44.43 2.24
3747 9662 3.386486 TGAAAACGTGAACGCTGATACT 58.614 40.909 2.11 0.00 44.43 2.12
3748 9663 3.805422 TGAAAACGTGAACGCTGATACTT 59.195 39.130 2.11 0.00 44.43 2.24
3749 9664 4.084745 TGAAAACGTGAACGCTGATACTTC 60.085 41.667 2.11 0.00 44.43 3.01
3750 9665 1.614385 ACGTGAACGCTGATACTTCG 58.386 50.000 2.11 0.00 44.43 3.79
3751 9666 1.198408 ACGTGAACGCTGATACTTCGA 59.802 47.619 2.11 0.00 44.43 3.71
3752 9667 1.578023 CGTGAACGCTGATACTTCGAC 59.422 52.381 0.00 0.00 0.00 4.20
3753 9668 2.592194 GTGAACGCTGATACTTCGACA 58.408 47.619 0.00 0.00 0.00 4.35
3754 9669 3.179830 GTGAACGCTGATACTTCGACAT 58.820 45.455 0.00 0.00 0.00 3.06
3755 9670 3.000674 GTGAACGCTGATACTTCGACATG 60.001 47.826 0.00 0.00 0.00 3.21
3756 9671 1.560923 ACGCTGATACTTCGACATGC 58.439 50.000 0.00 0.00 0.00 4.06
3757 9672 0.855349 CGCTGATACTTCGACATGCC 59.145 55.000 0.00 0.00 0.00 4.40
3758 9673 1.802508 CGCTGATACTTCGACATGCCA 60.803 52.381 0.00 0.00 0.00 4.92
3759 9674 2.279741 GCTGATACTTCGACATGCCAA 58.720 47.619 0.00 0.00 0.00 4.52
3760 9675 2.030946 GCTGATACTTCGACATGCCAAC 59.969 50.000 0.00 0.00 0.00 3.77
3761 9676 2.267426 TGATACTTCGACATGCCAACG 58.733 47.619 0.00 0.00 0.00 4.10
3762 9677 2.094442 TGATACTTCGACATGCCAACGA 60.094 45.455 0.00 0.00 0.00 3.85
3763 9678 2.665649 TACTTCGACATGCCAACGAT 57.334 45.000 0.00 0.00 36.02 3.73
3764 9679 2.665649 ACTTCGACATGCCAACGATA 57.334 45.000 0.00 0.00 36.02 2.92
3765 9680 2.540515 ACTTCGACATGCCAACGATAG 58.459 47.619 0.00 3.54 46.19 2.08
3766 9681 1.860950 CTTCGACATGCCAACGATAGG 59.139 52.381 0.00 0.00 43.77 2.57
3767 9682 1.107945 TCGACATGCCAACGATAGGA 58.892 50.000 0.00 0.00 43.77 2.94
3768 9683 1.067060 TCGACATGCCAACGATAGGAG 59.933 52.381 0.00 0.00 43.77 3.69
3769 9684 1.202417 CGACATGCCAACGATAGGAGT 60.202 52.381 0.00 0.00 43.77 3.85
3770 9685 2.034179 CGACATGCCAACGATAGGAGTA 59.966 50.000 0.00 0.00 43.77 2.59
3771 9686 3.305403 CGACATGCCAACGATAGGAGTAT 60.305 47.826 0.00 0.00 43.77 2.12
3772 9687 4.632153 GACATGCCAACGATAGGAGTATT 58.368 43.478 0.00 0.00 43.77 1.89
3773 9688 4.380531 ACATGCCAACGATAGGAGTATTG 58.619 43.478 0.00 0.00 43.77 1.90
3774 9689 2.833794 TGCCAACGATAGGAGTATTGC 58.166 47.619 0.00 0.00 43.77 3.56
3775 9690 2.169561 TGCCAACGATAGGAGTATTGCA 59.830 45.455 0.00 0.00 43.77 4.08
3776 9691 2.544267 GCCAACGATAGGAGTATTGCAC 59.456 50.000 0.00 0.00 43.77 4.57
3777 9692 3.741388 GCCAACGATAGGAGTATTGCACT 60.741 47.826 0.00 0.00 43.77 4.40
3778 9693 4.500887 GCCAACGATAGGAGTATTGCACTA 60.501 45.833 0.00 0.00 43.77 2.74
3779 9694 5.223382 CCAACGATAGGAGTATTGCACTAG 58.777 45.833 0.00 0.00 43.77 2.57
3780 9695 4.506886 ACGATAGGAGTATTGCACTAGC 57.493 45.455 0.00 0.00 43.77 3.42
3781 9696 3.889538 ACGATAGGAGTATTGCACTAGCA 59.110 43.478 0.00 0.00 46.84 3.49
3797 9712 7.227992 GCACTAGCACTACTCTAAAAATCTG 57.772 40.000 0.00 0.00 41.58 2.90
3798 9713 6.237969 GCACTAGCACTACTCTAAAAATCTGC 60.238 42.308 0.00 0.00 41.58 4.26
3799 9714 6.256757 CACTAGCACTACTCTAAAAATCTGCC 59.743 42.308 0.00 0.00 0.00 4.85
3800 9715 5.428184 AGCACTACTCTAAAAATCTGCCT 57.572 39.130 0.00 0.00 0.00 4.75
3801 9716 5.810095 AGCACTACTCTAAAAATCTGCCTT 58.190 37.500 0.00 0.00 0.00 4.35
3802 9717 5.877564 AGCACTACTCTAAAAATCTGCCTTC 59.122 40.000 0.00 0.00 0.00 3.46
3803 9718 5.220491 GCACTACTCTAAAAATCTGCCTTCG 60.220 44.000 0.00 0.00 0.00 3.79
3804 9719 5.292101 CACTACTCTAAAAATCTGCCTTCGG 59.708 44.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.075005 ACGATGTACAGCCCGGCT 61.075 61.111 5.94 5.94 40.77 5.52
73 74 2.657237 CCTCGGGCTCTTGACGTT 59.343 61.111 0.00 0.00 0.00 3.99
98 99 2.969238 CCAGATCATCGGCGTGCC 60.969 66.667 6.85 0.00 0.00 5.01
184 185 5.533482 CCATTACTTCTCGATCGGATTCTT 58.467 41.667 16.41 0.00 0.00 2.52
186 187 3.675698 GCCATTACTTCTCGATCGGATTC 59.324 47.826 16.41 0.00 0.00 2.52
189 190 2.293677 GAGCCATTACTTCTCGATCGGA 59.706 50.000 16.41 8.74 0.00 4.55
191 192 3.634568 AGAGCCATTACTTCTCGATCG 57.365 47.619 9.36 9.36 32.42 3.69
204 205 4.082026 GCTGTTCCAAAATTGTAGAGCCAT 60.082 41.667 0.00 0.00 0.00 4.40
224 229 2.008329 GCTGAGAAAGATCACTGGCTG 58.992 52.381 0.00 0.00 0.00 4.85
246 251 2.760634 ACAGAACACATGCGACCATA 57.239 45.000 0.00 0.00 0.00 2.74
253 258 1.159285 TGCAGCTACAGAACACATGC 58.841 50.000 0.00 0.00 0.00 4.06
262 267 3.648339 AAAACAACCATGCAGCTACAG 57.352 42.857 0.00 0.00 0.00 2.74
270 276 1.611491 TCCCTCGAAAAACAACCATGC 59.389 47.619 0.00 0.00 0.00 4.06
273 279 2.171870 ACTCTCCCTCGAAAAACAACCA 59.828 45.455 0.00 0.00 0.00 3.67
284 290 1.671845 GCACACTAGTACTCTCCCTCG 59.328 57.143 0.00 0.00 0.00 4.63
325 331 2.940890 ATTAGCGGCGACACCATGGG 62.941 60.000 18.09 7.72 39.03 4.00
326 332 1.523711 ATTAGCGGCGACACCATGG 60.524 57.895 12.98 11.19 39.03 3.66
330 340 0.458889 TGTACATTAGCGGCGACACC 60.459 55.000 12.98 0.00 0.00 4.16
331 341 1.352114 TTGTACATTAGCGGCGACAC 58.648 50.000 12.98 0.00 0.00 3.67
353 363 5.514914 CACAACAACATTTACGGCCATTATC 59.485 40.000 2.24 0.00 0.00 1.75
360 370 2.606065 GGGACACAACAACATTTACGGC 60.606 50.000 0.00 0.00 0.00 5.68
408 418 3.655350 ATTGGTAAGCACGGCCCCC 62.655 63.158 0.00 0.00 0.00 5.40
409 419 0.394625 TAATTGGTAAGCACGGCCCC 60.395 55.000 0.00 0.00 0.00 5.80
410 420 0.736636 GTAATTGGTAAGCACGGCCC 59.263 55.000 0.00 0.00 0.00 5.80
411 421 0.375803 CGTAATTGGTAAGCACGGCC 59.624 55.000 0.00 0.00 0.00 6.13
412 422 0.375803 CCGTAATTGGTAAGCACGGC 59.624 55.000 1.08 0.00 44.78 5.68
414 424 1.080298 TGCCGTAATTGGTAAGCACG 58.920 50.000 0.00 0.00 0.00 5.34
415 425 2.537639 GTGCCGTAATTGGTAAGCAC 57.462 50.000 0.00 0.00 43.14 4.40
456 466 5.696260 TTCTGTACGATTTGATTGTAGCG 57.304 39.130 0.00 0.00 30.00 4.26
468 483 3.673594 CGCCTCTGAAGTTTCTGTACGAT 60.674 47.826 0.00 0.00 0.00 3.73
469 484 2.351447 CGCCTCTGAAGTTTCTGTACGA 60.351 50.000 0.00 0.00 0.00 3.43
470 485 1.986378 CGCCTCTGAAGTTTCTGTACG 59.014 52.381 0.00 0.00 0.00 3.67
471 486 3.299340 TCGCCTCTGAAGTTTCTGTAC 57.701 47.619 0.00 0.00 0.00 2.90
472 487 4.220821 AGATTCGCCTCTGAAGTTTCTGTA 59.779 41.667 0.00 0.00 0.00 2.74
473 488 2.910688 TTCGCCTCTGAAGTTTCTGT 57.089 45.000 0.00 0.00 0.00 3.41
524 581 2.992689 TGCACAATGGCTGCAGGG 60.993 61.111 17.12 0.00 39.76 4.45
532 589 2.821378 TGACTGGAGAAATGCACAATGG 59.179 45.455 0.00 0.00 0.00 3.16
555 626 8.478775 ACTATTGCCTAGACTGAACATACATA 57.521 34.615 0.00 0.00 0.00 2.29
560 631 5.939764 TGACTATTGCCTAGACTGAACAT 57.060 39.130 0.00 0.00 0.00 2.71
561 632 5.664457 CATGACTATTGCCTAGACTGAACA 58.336 41.667 0.00 0.00 0.00 3.18
562 633 4.509600 GCATGACTATTGCCTAGACTGAAC 59.490 45.833 0.00 0.00 33.95 3.18
563 634 4.406972 AGCATGACTATTGCCTAGACTGAA 59.593 41.667 0.00 0.00 41.06 3.02
564 635 3.963374 AGCATGACTATTGCCTAGACTGA 59.037 43.478 0.00 0.00 41.06 3.41
565 636 4.056740 CAGCATGACTATTGCCTAGACTG 58.943 47.826 0.00 0.00 41.06 3.51
566 637 3.963374 TCAGCATGACTATTGCCTAGACT 59.037 43.478 0.00 0.00 42.56 3.24
567 638 4.327982 TCAGCATGACTATTGCCTAGAC 57.672 45.455 0.00 0.00 42.56 2.59
585 656 1.448540 CCGCCTGGCACTAGTTCAG 60.449 63.158 20.29 13.40 0.00 3.02
586 657 2.662596 CCGCCTGGCACTAGTTCA 59.337 61.111 20.29 0.00 0.00 3.18
603 674 2.026301 ATCCGTTAGCTCGCTCGC 59.974 61.111 0.00 0.00 0.00 5.03
604 675 0.248498 TTCATCCGTTAGCTCGCTCG 60.248 55.000 0.00 0.00 0.00 5.03
605 676 1.922570 TTTCATCCGTTAGCTCGCTC 58.077 50.000 0.00 0.00 0.00 5.03
606 677 2.380084 TTTTCATCCGTTAGCTCGCT 57.620 45.000 0.00 0.00 0.00 4.93
667 744 1.233019 CTATCCTGAATTGGCTGGCG 58.767 55.000 0.00 0.00 0.00 5.69
687 764 0.106619 GCCCGAGTTCTCCTCTCCTA 60.107 60.000 0.00 0.00 38.11 2.94
718 795 5.796502 TCCCCTCTAATCAATTGGTTTCT 57.203 39.130 9.68 0.00 0.00 2.52
754 832 2.031682 CCTCTTGTGCTTCTTTTCGGTG 60.032 50.000 0.00 0.00 0.00 4.94
761 839 3.777106 TCATGTCCTCTTGTGCTTCTT 57.223 42.857 0.00 0.00 0.00 2.52
767 845 3.683340 CACAGTGATCATGTCCTCTTGTG 59.317 47.826 0.00 1.19 0.00 3.33
775 853 5.808042 AAAGTATGCACAGTGATCATGTC 57.192 39.130 4.15 0.97 0.00 3.06
859 943 4.355437 ACGATGAGATAAAGAGTTGAGCG 58.645 43.478 0.00 0.00 0.00 5.03
860 944 5.458452 CAGACGATGAGATAAAGAGTTGAGC 59.542 44.000 0.00 0.00 0.00 4.26
861 945 5.976534 CCAGACGATGAGATAAAGAGTTGAG 59.023 44.000 0.00 0.00 0.00 3.02
862 946 5.419155 ACCAGACGATGAGATAAAGAGTTGA 59.581 40.000 0.00 0.00 0.00 3.18
866 950 5.009110 TGCTACCAGACGATGAGATAAAGAG 59.991 44.000 0.00 0.00 0.00 2.85
881 965 1.055849 TCAAACCAGCTGCTACCAGA 58.944 50.000 8.66 0.00 41.77 3.86
889 973 2.195922 GTTTTGCAGTCAAACCAGCTG 58.804 47.619 6.78 6.78 41.48 4.24
917 1002 6.019398 AGGTTTTGCGTGCTAATTTTGTTTAC 60.019 34.615 0.00 0.00 0.00 2.01
998 1083 3.417224 CCATCGCCATCGCCATCG 61.417 66.667 0.00 0.00 35.26 3.84
999 1084 3.730761 GCCATCGCCATCGCCATC 61.731 66.667 0.00 0.00 35.26 3.51
1004 1089 3.417224 CCATCGCCATCGCCATCG 61.417 66.667 0.00 0.00 35.26 3.84
1005 1090 3.730761 GCCATCGCCATCGCCATC 61.731 66.667 0.00 0.00 35.26 3.51
1252 1368 1.990614 GGAAGAGGAGGGCGAAGGT 60.991 63.158 0.00 0.00 0.00 3.50
1292 1408 2.125106 AAGGTGCCGGAATCGAGC 60.125 61.111 5.05 0.00 39.00 5.03
1293 1409 2.464459 GCAAGGTGCCGGAATCGAG 61.464 63.158 5.05 0.00 37.42 4.04
1294 1410 2.435938 GCAAGGTGCCGGAATCGA 60.436 61.111 5.05 0.00 37.42 3.59
1296 1412 4.179579 GCGCAAGGTGCCGGAATC 62.180 66.667 5.05 0.00 41.12 2.52
1308 1424 3.049912 GACATGTATCGTATCAGCGCAA 58.950 45.455 11.47 0.00 0.00 4.85
1310 1426 1.644295 CGACATGTATCGTATCAGCGC 59.356 52.381 0.00 0.00 37.33 5.92
1312 1428 3.781323 CGATCGACATGTATCGTATCAGC 59.219 47.826 18.66 0.00 42.80 4.26
1313 1429 5.204673 TCGATCGACATGTATCGTATCAG 57.795 43.478 23.48 13.10 44.11 2.90
1315 1431 5.561070 ACATCGATCGACATGTATCGTATC 58.439 41.667 22.06 15.21 44.11 2.24
1316 1432 5.547181 ACATCGATCGACATGTATCGTAT 57.453 39.130 22.06 15.58 44.11 3.06
1317 1433 5.144359 CAACATCGATCGACATGTATCGTA 58.856 41.667 22.06 14.41 44.11 3.43
1318 1434 3.898517 ACATCGATCGACATGTATCGT 57.101 42.857 22.06 12.75 44.11 3.73
1328 1481 2.516589 GCGCTGCAACATCGATCGA 61.517 57.895 21.86 21.86 0.00 3.59
1331 1484 2.509111 TCGCGCTGCAACATCGAT 60.509 55.556 5.56 0.00 0.00 3.59
1350 1503 3.448686 CATGAAGTAGAAGTACTGCCCG 58.551 50.000 0.00 0.00 39.60 6.13
1504 1671 1.218585 CCAGCAGGCTCTGTCTGAG 59.781 63.158 18.66 2.46 45.33 3.35
1517 1684 2.435938 GAAATCGGACGGCCAGCA 60.436 61.111 8.76 0.00 0.00 4.41
1547 1714 7.431084 CGAAAGAAATCGGACTTTTCTCAAAAA 59.569 33.333 6.97 0.00 41.38 1.94
1548 1715 6.910433 CGAAAGAAATCGGACTTTTCTCAAAA 59.090 34.615 6.97 0.00 41.38 2.44
1549 1716 6.037830 ACGAAAGAAATCGGACTTTTCTCAAA 59.962 34.615 6.97 0.00 46.82 2.69
1550 1717 5.526111 ACGAAAGAAATCGGACTTTTCTCAA 59.474 36.000 6.97 0.00 46.82 3.02
1551 1718 5.054477 ACGAAAGAAATCGGACTTTTCTCA 58.946 37.500 6.97 0.00 46.82 3.27
1552 1719 5.593183 ACGAAAGAAATCGGACTTTTCTC 57.407 39.130 6.97 0.00 46.82 2.87
1553 1720 5.277828 CCAACGAAAGAAATCGGACTTTTCT 60.278 40.000 1.65 1.65 46.82 2.52
1554 1721 4.909880 CCAACGAAAGAAATCGGACTTTTC 59.090 41.667 1.59 0.00 46.82 2.29
1555 1722 4.337274 ACCAACGAAAGAAATCGGACTTTT 59.663 37.500 1.59 0.00 46.82 2.27
1556 1723 3.881089 ACCAACGAAAGAAATCGGACTTT 59.119 39.130 1.59 0.00 46.82 2.66
1557 1724 3.473625 ACCAACGAAAGAAATCGGACTT 58.526 40.909 1.59 0.00 46.82 3.01
1558 1725 3.064931 GACCAACGAAAGAAATCGGACT 58.935 45.455 1.59 0.00 46.82 3.85
1559 1726 2.159881 CGACCAACGAAAGAAATCGGAC 60.160 50.000 1.59 0.00 46.82 4.79
1560 1727 2.063266 CGACCAACGAAAGAAATCGGA 58.937 47.619 1.59 0.00 46.82 4.55
1561 1728 1.463528 GCGACCAACGAAAGAAATCGG 60.464 52.381 1.59 0.00 46.82 4.18
1563 1730 3.226347 CAAGCGACCAACGAAAGAAATC 58.774 45.455 0.00 0.00 45.77 2.17
1564 1731 2.616842 ACAAGCGACCAACGAAAGAAAT 59.383 40.909 0.00 0.00 45.77 2.17
1565 1732 2.011222 ACAAGCGACCAACGAAAGAAA 58.989 42.857 0.00 0.00 45.77 2.52
1566 1733 1.658994 ACAAGCGACCAACGAAAGAA 58.341 45.000 0.00 0.00 45.77 2.52
1567 1734 2.400399 CTACAAGCGACCAACGAAAGA 58.600 47.619 0.00 0.00 45.77 2.52
1568 1735 1.136336 GCTACAAGCGACCAACGAAAG 60.136 52.381 0.00 0.00 45.77 2.62
1569 1736 0.863144 GCTACAAGCGACCAACGAAA 59.137 50.000 0.00 0.00 45.77 3.46
1570 1737 2.524300 GCTACAAGCGACCAACGAA 58.476 52.632 0.00 0.00 45.77 3.85
1571 1738 3.711278 AGTAGCTACAAGCGACCAACGA 61.711 50.000 25.28 0.00 46.10 3.85
1572 1739 1.402456 AGTAGCTACAAGCGACCAACG 60.402 52.381 25.28 0.00 46.10 4.10
1573 1740 2.260481 GAGTAGCTACAAGCGACCAAC 58.740 52.381 25.28 0.00 46.10 3.77
1574 1741 1.890489 TGAGTAGCTACAAGCGACCAA 59.110 47.619 25.28 0.00 46.10 3.67
1575 1742 1.541379 TGAGTAGCTACAAGCGACCA 58.459 50.000 25.28 8.49 46.10 4.02
1576 1743 2.873133 ATGAGTAGCTACAAGCGACC 57.127 50.000 25.28 6.23 46.10 4.79
1598 1765 0.326143 TGACCTAGTGGGCCTATGCA 60.326 55.000 4.53 0.00 42.00 3.96
1599 1766 0.394565 CTGACCTAGTGGGCCTATGC 59.605 60.000 4.53 0.00 42.00 3.14
1600 1767 1.689273 GACTGACCTAGTGGGCCTATG 59.311 57.143 4.53 0.00 42.00 2.23
1601 1768 1.291033 TGACTGACCTAGTGGGCCTAT 59.709 52.381 4.53 0.00 42.00 2.57
1611 1778 1.951209 TCAATGGGCTGACTGACCTA 58.049 50.000 5.73 0.00 46.68 3.08
1614 1781 2.440409 ACAATCAATGGGCTGACTGAC 58.560 47.619 0.00 0.00 0.00 3.51
1615 1782 2.885135 ACAATCAATGGGCTGACTGA 57.115 45.000 0.00 0.00 0.00 3.41
1616 1783 2.159476 CGAACAATCAATGGGCTGACTG 60.159 50.000 0.00 0.00 0.00 3.51
1617 1784 2.086869 CGAACAATCAATGGGCTGACT 58.913 47.619 0.00 0.00 0.00 3.41
1619 1786 1.462616 CCGAACAATCAATGGGCTGA 58.537 50.000 0.00 0.00 0.00 4.26
1620 1787 0.457035 CCCGAACAATCAATGGGCTG 59.543 55.000 0.00 0.00 32.09 4.85
1636 1821 2.978010 ACGAAAGCCACAAGCCCG 60.978 61.111 0.00 0.00 45.47 6.13
1708 2794 1.271054 GGGAATGGGATGATCGGTCAG 60.271 57.143 3.97 0.00 37.87 3.51
1817 5103 1.372582 TGAAGAACGCCATGAGCATC 58.627 50.000 0.00 0.00 44.04 3.91
1890 5176 2.336809 GAGGTAGATGCCGCCTCG 59.663 66.667 0.00 0.00 39.29 4.63
1989 5275 4.097437 CCACATTCTGACAGAAATGGGATG 59.903 45.833 28.59 20.81 39.24 3.51
1995 5281 6.713762 TTTTGTCCACATTCTGACAGAAAT 57.286 33.333 21.29 10.33 42.05 2.17
2003 5289 6.680810 ACATACACATTTTGTCCACATTCTG 58.319 36.000 0.00 0.00 39.91 3.02
2007 5293 5.769662 ACAGACATACACATTTTGTCCACAT 59.230 36.000 0.00 0.00 40.46 3.21
2009 5295 5.451908 CACAGACATACACATTTTGTCCAC 58.548 41.667 0.00 0.00 40.46 4.02
2056 7364 0.877071 AATGGCCGCGAATCATCATC 59.123 50.000 8.23 0.00 0.00 2.92
2062 7370 0.248621 CCTGAAAATGGCCGCGAATC 60.249 55.000 8.23 0.00 0.00 2.52
2063 7371 0.965363 ACCTGAAAATGGCCGCGAAT 60.965 50.000 8.23 0.00 0.00 3.34
2064 7372 0.321741 TACCTGAAAATGGCCGCGAA 60.322 50.000 8.23 0.00 0.00 4.70
2065 7373 1.022451 GTACCTGAAAATGGCCGCGA 61.022 55.000 8.23 0.00 0.00 5.87
2071 7379 2.290071 ACAGACCGGTACCTGAAAATGG 60.290 50.000 25.55 4.24 34.65 3.16
2110 7418 2.270986 CCAGGTTGCCAAGGACAGC 61.271 63.158 0.00 0.00 0.00 4.40
2113 7421 0.251341 ACATCCAGGTTGCCAAGGAC 60.251 55.000 0.00 0.00 33.90 3.85
2182 7490 4.100808 AGCTTCCAGATCTCCATGTAGTTC 59.899 45.833 0.00 0.00 0.00 3.01
2293 7606 8.935844 TCATTATACATCAACACAGTTCAGAAC 58.064 33.333 5.00 5.00 0.00 3.01
2311 7631 5.588648 TGTTAAGTGGCCAAGCTCATTATAC 59.411 40.000 7.24 0.00 0.00 1.47
2321 7641 2.948979 TCAGTGTTGTTAAGTGGCCAAG 59.051 45.455 7.24 0.00 0.00 3.61
2331 7651 6.312426 CCTGCAAAAATTGTTCAGTGTTGTTA 59.688 34.615 0.00 0.00 0.00 2.41
2418 7738 4.384547 GGTGTAAAAATTGCGCTGTAAAGG 59.615 41.667 9.73 0.00 0.00 3.11
2470 7790 3.112709 GTGAAGGACGAGCGTGGC 61.113 66.667 0.00 0.00 0.00 5.01
2537 7880 4.049186 CACGGTAGCAGTGATTATGTACC 58.951 47.826 10.14 0.00 41.83 3.34
2599 7942 5.280215 GCCTAGGATGATTACAATAGCACCT 60.280 44.000 14.75 0.00 0.00 4.00
2611 7954 4.413520 ACAACATACAGGCCTAGGATGATT 59.586 41.667 25.45 16.13 0.00 2.57
2663 8006 4.512914 GATGGCCAGCCCCTCACC 62.513 72.222 10.76 0.00 34.56 4.02
2688 8031 6.615088 TGCTCTAAAATGCTTTCAGAATCAC 58.385 36.000 0.00 0.00 0.00 3.06
2767 8110 2.351726 AGCATCCGCGTTTTCAGATAAC 59.648 45.455 4.92 0.00 45.49 1.89
2785 8128 0.812811 GGCATCTCGAAGCATCAGCA 60.813 55.000 6.51 0.00 45.49 4.41
2919 8267 4.380867 GGGACCATGTTAAAACTGCTCATG 60.381 45.833 0.00 0.00 36.60 3.07
2920 8268 3.763897 GGGACCATGTTAAAACTGCTCAT 59.236 43.478 0.00 0.00 0.00 2.90
2934 8282 1.696097 CGGGGGTAAGAGGGACCATG 61.696 65.000 0.00 0.00 38.86 3.66
3087 8435 5.046663 GGCCAAGAACTATCAAATGGGAAAA 60.047 40.000 0.00 0.00 30.82 2.29
3090 8438 3.011144 TGGCCAAGAACTATCAAATGGGA 59.989 43.478 0.61 0.00 30.82 4.37
3091 8439 3.364549 TGGCCAAGAACTATCAAATGGG 58.635 45.455 0.61 0.00 30.82 4.00
3092 8440 5.353938 CATTGGCCAAGAACTATCAAATGG 58.646 41.667 24.94 0.00 32.36 3.16
3126 9017 6.639671 CAGCTAGACTGTGAGTTTGATAAC 57.360 41.667 0.00 0.00 41.86 1.89
3163 9061 6.092259 GGGTCAAATATATACTCGGCACATTC 59.908 42.308 0.00 0.00 0.00 2.67
3175 9073 5.013079 CCTGACTGGCTGGGTCAAATATATA 59.987 44.000 0.00 0.00 42.15 0.86
3416 9325 9.832445 GGAAGAGTTTAGGTAATATTGTCATGA 57.168 33.333 0.00 0.00 0.00 3.07
3417 9326 9.838339 AGGAAGAGTTTAGGTAATATTGTCATG 57.162 33.333 0.00 0.00 0.00 3.07
3419 9328 9.886132 GAAGGAAGAGTTTAGGTAATATTGTCA 57.114 33.333 0.00 0.00 0.00 3.58
3462 9371 1.082019 TGCATACCTCCCACTCCCA 59.918 57.895 0.00 0.00 0.00 4.37
3463 9372 1.527370 GTGCATACCTCCCACTCCC 59.473 63.158 0.00 0.00 0.00 4.30
3464 9373 1.527370 GGTGCATACCTCCCACTCC 59.473 63.158 0.00 0.00 43.97 3.85
3482 9391 3.954258 GGACCTAATGGGGAATGAAGTTG 59.046 47.826 0.00 0.00 40.03 3.16
3494 9403 1.916181 AGGGTTCAGTGGACCTAATGG 59.084 52.381 20.41 0.00 37.34 3.16
3573 9488 2.536365 CCTAATACGCTGCGTGAAAGA 58.464 47.619 35.11 17.27 41.39 2.52
3623 9538 3.118408 TCCATCATCTTCTTTACCCCACG 60.118 47.826 0.00 0.00 0.00 4.94
3632 9547 3.710677 CTCACCCTCTCCATCATCTTCTT 59.289 47.826 0.00 0.00 0.00 2.52
3649 9564 3.055819 TCTTGTTCTACCATGCTCTCACC 60.056 47.826 0.00 0.00 0.00 4.02
3674 9589 5.862323 TCACTCTCTACTTTTACAACGATGC 59.138 40.000 0.00 0.00 0.00 3.91
3701 9616 3.446442 ACAATGGCTCTGAAGGATTGT 57.554 42.857 0.00 0.00 0.00 2.71
3702 9617 5.826737 AGATAACAATGGCTCTGAAGGATTG 59.173 40.000 0.00 0.00 0.00 2.67
3703 9618 5.826737 CAGATAACAATGGCTCTGAAGGATT 59.173 40.000 3.82 0.00 37.85 3.01
3704 9619 5.131642 TCAGATAACAATGGCTCTGAAGGAT 59.868 40.000 8.52 0.00 40.73 3.24
3705 9620 4.471025 TCAGATAACAATGGCTCTGAAGGA 59.529 41.667 8.52 0.00 40.73 3.36
3706 9621 4.774124 TCAGATAACAATGGCTCTGAAGG 58.226 43.478 8.52 0.00 40.73 3.46
3709 9624 5.122239 CGTTTTCAGATAACAATGGCTCTGA 59.878 40.000 7.33 7.33 41.65 3.27
3710 9625 5.106555 ACGTTTTCAGATAACAATGGCTCTG 60.107 40.000 4.82 3.56 37.14 3.35
3711 9626 5.003804 ACGTTTTCAGATAACAATGGCTCT 58.996 37.500 4.82 0.00 0.00 4.09
3712 9627 5.088739 CACGTTTTCAGATAACAATGGCTC 58.911 41.667 4.82 0.00 0.00 4.70
3713 9628 4.759693 TCACGTTTTCAGATAACAATGGCT 59.240 37.500 4.82 0.00 0.00 4.75
3714 9629 5.041951 TCACGTTTTCAGATAACAATGGC 57.958 39.130 4.82 0.00 0.00 4.40
3715 9630 5.563751 CGTTCACGTTTTCAGATAACAATGG 59.436 40.000 4.82 0.00 34.11 3.16
3716 9631 5.058008 GCGTTCACGTTTTCAGATAACAATG 59.942 40.000 0.62 2.66 42.22 2.82
3717 9632 5.049680 AGCGTTCACGTTTTCAGATAACAAT 60.050 36.000 0.62 0.00 42.22 2.71
3718 9633 4.271533 AGCGTTCACGTTTTCAGATAACAA 59.728 37.500 0.62 0.00 42.22 2.83
3719 9634 3.805422 AGCGTTCACGTTTTCAGATAACA 59.195 39.130 0.62 0.00 42.22 2.41
3720 9635 4.084745 TCAGCGTTCACGTTTTCAGATAAC 60.085 41.667 0.62 0.00 42.22 1.89
3721 9636 4.052608 TCAGCGTTCACGTTTTCAGATAA 58.947 39.130 0.62 0.00 42.22 1.75
3722 9637 3.644823 TCAGCGTTCACGTTTTCAGATA 58.355 40.909 0.62 0.00 42.22 1.98
3723 9638 2.479837 TCAGCGTTCACGTTTTCAGAT 58.520 42.857 0.62 0.00 42.22 2.90
3724 9639 1.929230 TCAGCGTTCACGTTTTCAGA 58.071 45.000 0.62 0.00 42.22 3.27
3725 9640 2.949714 ATCAGCGTTCACGTTTTCAG 57.050 45.000 0.62 0.00 42.22 3.02
3726 9641 3.386486 AGTATCAGCGTTCACGTTTTCA 58.614 40.909 0.62 0.00 42.22 2.69
3727 9642 4.383679 GAAGTATCAGCGTTCACGTTTTC 58.616 43.478 0.62 0.00 42.22 2.29
3728 9643 3.121126 CGAAGTATCAGCGTTCACGTTTT 60.121 43.478 0.62 0.00 42.22 2.43
3729 9644 2.407361 CGAAGTATCAGCGTTCACGTTT 59.593 45.455 0.62 0.00 42.22 3.60
3730 9645 1.983605 CGAAGTATCAGCGTTCACGTT 59.016 47.619 0.62 0.00 42.22 3.99
3731 9646 1.198408 TCGAAGTATCAGCGTTCACGT 59.802 47.619 0.62 0.00 42.22 4.49
3732 9647 1.578023 GTCGAAGTATCAGCGTTCACG 59.422 52.381 0.00 0.00 43.27 4.35
3733 9648 2.592194 TGTCGAAGTATCAGCGTTCAC 58.408 47.619 0.00 0.00 0.00 3.18
3734 9649 3.179048 CATGTCGAAGTATCAGCGTTCA 58.821 45.455 0.00 0.00 0.00 3.18
3735 9650 2.034507 GCATGTCGAAGTATCAGCGTTC 60.035 50.000 0.00 0.00 0.00 3.95
3736 9651 1.927174 GCATGTCGAAGTATCAGCGTT 59.073 47.619 0.00 0.00 0.00 4.84
3737 9652 1.560923 GCATGTCGAAGTATCAGCGT 58.439 50.000 0.00 0.00 0.00 5.07
3738 9653 0.855349 GGCATGTCGAAGTATCAGCG 59.145 55.000 0.00 0.00 0.00 5.18
3739 9654 1.939974 TGGCATGTCGAAGTATCAGC 58.060 50.000 0.00 0.00 0.00 4.26
3740 9655 2.282555 CGTTGGCATGTCGAAGTATCAG 59.717 50.000 0.00 0.00 0.00 2.90
3741 9656 2.094442 TCGTTGGCATGTCGAAGTATCA 60.094 45.455 0.22 0.00 0.00 2.15
3742 9657 2.536365 TCGTTGGCATGTCGAAGTATC 58.464 47.619 0.22 0.00 0.00 2.24
3743 9658 2.665649 TCGTTGGCATGTCGAAGTAT 57.334 45.000 0.22 0.00 0.00 2.12
3744 9659 2.665649 ATCGTTGGCATGTCGAAGTA 57.334 45.000 12.27 0.00 37.16 2.24
3745 9660 2.540515 CTATCGTTGGCATGTCGAAGT 58.459 47.619 12.27 2.67 37.16 3.01
3746 9661 1.860950 CCTATCGTTGGCATGTCGAAG 59.139 52.381 12.27 0.00 37.16 3.79
3747 9662 1.478916 TCCTATCGTTGGCATGTCGAA 59.521 47.619 12.27 0.00 37.16 3.71
3748 9663 1.067060 CTCCTATCGTTGGCATGTCGA 59.933 52.381 11.06 11.06 37.96 4.20
3749 9664 1.202417 ACTCCTATCGTTGGCATGTCG 60.202 52.381 0.00 0.00 0.00 4.35
3750 9665 2.604046 ACTCCTATCGTTGGCATGTC 57.396 50.000 0.00 0.00 0.00 3.06
3751 9666 4.380531 CAATACTCCTATCGTTGGCATGT 58.619 43.478 0.00 0.00 0.00 3.21
3752 9667 3.187227 GCAATACTCCTATCGTTGGCATG 59.813 47.826 0.00 0.00 0.00 4.06
3753 9668 3.181455 TGCAATACTCCTATCGTTGGCAT 60.181 43.478 0.00 0.00 0.00 4.40
3754 9669 2.169561 TGCAATACTCCTATCGTTGGCA 59.830 45.455 0.00 0.00 0.00 4.92
3755 9670 2.544267 GTGCAATACTCCTATCGTTGGC 59.456 50.000 0.00 0.00 0.00 4.52
3756 9671 4.060038 AGTGCAATACTCCTATCGTTGG 57.940 45.455 0.00 0.00 33.17 3.77
3757 9672 4.681942 GCTAGTGCAATACTCCTATCGTTG 59.318 45.833 0.00 0.00 40.89 4.10
3758 9673 4.872664 GCTAGTGCAATACTCCTATCGTT 58.127 43.478 0.00 0.00 40.89 3.85
3759 9674 4.506886 GCTAGTGCAATACTCCTATCGT 57.493 45.455 0.00 0.00 40.89 3.73
3773 9688 6.237969 GCAGATTTTTAGAGTAGTGCTAGTGC 60.238 42.308 0.00 0.00 40.20 4.40
3774 9689 6.256757 GGCAGATTTTTAGAGTAGTGCTAGTG 59.743 42.308 0.00 0.00 0.00 2.74
3775 9690 6.155393 AGGCAGATTTTTAGAGTAGTGCTAGT 59.845 38.462 0.00 0.00 0.00 2.57
3776 9691 6.578023 AGGCAGATTTTTAGAGTAGTGCTAG 58.422 40.000 0.00 0.00 0.00 3.42
3777 9692 6.546428 AGGCAGATTTTTAGAGTAGTGCTA 57.454 37.500 0.00 0.00 0.00 3.49
3778 9693 5.428184 AGGCAGATTTTTAGAGTAGTGCT 57.572 39.130 0.00 0.00 0.00 4.40
3779 9694 5.220491 CGAAGGCAGATTTTTAGAGTAGTGC 60.220 44.000 0.00 0.00 0.00 4.40
3780 9695 5.292101 CCGAAGGCAGATTTTTAGAGTAGTG 59.708 44.000 0.00 0.00 46.14 2.74
3781 9696 5.420409 CCGAAGGCAGATTTTTAGAGTAGT 58.580 41.667 0.00 0.00 46.14 2.73
3782 9697 5.975410 CCGAAGGCAGATTTTTAGAGTAG 57.025 43.478 0.00 0.00 46.14 2.57


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

AutoCloner maintained by Alex Coulton.