Multiple sequence alignment - TraesCS2B01G333400

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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 TraesCS2B01G333400 chr2B 100.000 3794 0 0 1 3794 476560630 476564423 0.000000e+00 7007.0
1 TraesCS2B01G333400 chr2B 88.073 109 13 0 3617 3725 161410875 161410767 3.080000e-26 130.0
2 TraesCS2B01G333400 chr2D 95.461 2930 100 19 680 3598 402713831 402716738 0.000000e+00 4643.0
3 TraesCS2B01G333400 chr2D 86.477 562 41 18 1 542 402713005 402713551 5.460000e-163 584.0
4 TraesCS2B01G333400 chr2A 92.063 2268 107 32 661 2912 539970368 539972578 0.000000e+00 3123.0
5 TraesCS2B01G333400 chr2A 85.565 478 33 17 1 459 539967874 539968334 5.740000e-128 468.0
6 TraesCS2B01G333400 chr2A 77.841 176 26 8 490 655 539968337 539968509 3.120000e-16 97.1
7 TraesCS2B01G333400 chr4A 90.826 109 10 0 3617 3725 74167979 74168087 3.050000e-31 147.0
8 TraesCS2B01G333400 chr7D 89.908 109 11 0 3617 3725 397578520 397578628 1.420000e-29 141.0
9 TraesCS2B01G333400 chr7B 89.908 109 9 2 3618 3725 570465364 570465257 5.110000e-29 139.0
10 TraesCS2B01G333400 chr5A 89.524 105 11 0 3616 3720 294245019 294244915 2.380000e-27 134.0
11 TraesCS2B01G333400 chr4D 88.889 108 12 0 3618 3725 241799795 241799902 2.380000e-27 134.0
12 TraesCS2B01G333400 chr5D 90.000 100 10 0 3617 3716 315923170 315923269 3.080000e-26 130.0
13 TraesCS2B01G333400 chr5D 92.000 50 4 0 3745 3794 219646085 219646036 1.890000e-08 71.3
14 TraesCS2B01G333400 chr4B 87.963 108 13 0 3618 3725 300935273 300935166 1.110000e-25 128.0
15 TraesCS2B01G333400 chr4B 90.385 52 4 1 3744 3794 60326771 60326720 2.450000e-07 67.6
16 TraesCS2B01G333400 chr7A 83.333 144 17 5 3620 3760 416425221 416425082 3.980000e-25 126.0
17 TraesCS2B01G333400 chr1B 94.118 51 3 0 3744 3794 331419568 331419518 1.130000e-10 78.7
18 TraesCS2B01G333400 chr3D 93.750 48 3 0 3744 3791 29167299 29167346 5.260000e-09 73.1
19 TraesCS2B01G333400 chr6A 93.478 46 3 0 3744 3789 187733669 187733624 6.800000e-08 69.4
20 TraesCS2B01G333400 chr3B 89.474 57 3 3 3735 3791 576161118 576161171 6.800000e-08 69.4
21 TraesCS2B01G333400 chr6D 91.837 49 3 1 3744 3791 408903024 408903072 2.450000e-07 67.6
22 TraesCS2B01G333400 chr1D 93.333 45 3 0 3744 3788 246649983 246650027 2.450000e-07 67.6


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 TraesCS2B01G333400 chr2B 476560630 476564423 3793 False 7007.000000 7007 100.000000 1 3794 1 chr2B.!!$F1 3793
1 TraesCS2B01G333400 chr2D 402713005 402716738 3733 False 2613.500000 4643 90.969000 1 3598 2 chr2D.!!$F1 3597
2 TraesCS2B01G333400 chr2A 539967874 539972578 4704 False 1229.366667 3123 85.156333 1 2912 3 chr2A.!!$F1 2911

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
90 93 0.179215 CTGAGACGGTTGCGCAAATC 60.179 55.000 26.87 21.47 0.00 2.17 F
250 253 0.321919 CTGGGCTGCAACTGAGCTTA 60.322 55.000 0.50 0.00 36.63 3.09 F
452 472 0.880278 GCTGAACTCGACTGTTGCCA 60.880 55.000 0.00 0.00 0.00 4.92 F
914 2941 1.134907 TCGGATTTTCTACGCCACTCC 60.135 52.381 0.00 0.00 0.00 3.85 F
2159 4192 0.953727 GCTTTGTGCAGTGGTGATCA 59.046 50.000 0.00 0.00 42.31 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 3752 1.339438 ACATCGCCTTCTCTGCACATT 60.339 47.619 0.0 0.0 0.00 2.71 R
2159 4192 1.138568 CTCCTCAGCATCCTCCCATT 58.861 55.000 0.0 0.0 0.00 3.16 R
2160 4193 1.417288 GCTCCTCAGCATCCTCCCAT 61.417 60.000 0.0 0.0 46.06 4.00 R
2445 4478 1.902508 TCTTCATCCAGAAACTCGGCT 59.097 47.619 0.0 0.0 35.40 5.52 R
3315 5356 0.679505 AGCAGTTTGTCTAGGCACGA 59.320 50.000 0.0 0.0 0.00 4.35 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 4.106197 GGAGCTAATGAACGTACAGTGAG 58.894 47.826 0.00 0.00 0.00 3.51
83 86 0.586802 GGACAAACTGAGACGGTTGC 59.413 55.000 0.00 0.00 32.82 4.17
88 91 1.092921 AACTGAGACGGTTGCGCAAA 61.093 50.000 26.87 6.30 31.12 3.68
90 93 0.179215 CTGAGACGGTTGCGCAAATC 60.179 55.000 26.87 21.47 0.00 2.17
149 152 5.290493 TCAGTCAACAACATCCTACAGTT 57.710 39.130 0.00 0.00 0.00 3.16
190 193 6.732531 TTTTTCATCAGCTCTACATGTCAG 57.267 37.500 0.00 0.27 0.00 3.51
193 196 3.065925 TCATCAGCTCTACATGTCAGACG 59.934 47.826 0.00 0.00 0.00 4.18
250 253 0.321919 CTGGGCTGCAACTGAGCTTA 60.322 55.000 0.50 0.00 36.63 3.09
286 291 3.394674 TGTGGCTCGTTGACATTCTTA 57.605 42.857 0.00 0.00 35.31 2.10
296 301 5.290885 TCGTTGACATTCTTATGGAATCACG 59.709 40.000 0.00 0.00 42.20 4.35
299 304 5.912892 TGACATTCTTATGGAATCACGCTA 58.087 37.500 0.00 0.00 42.20 4.26
300 305 6.524734 TGACATTCTTATGGAATCACGCTAT 58.475 36.000 0.00 0.00 42.20 2.97
301 306 7.666623 TGACATTCTTATGGAATCACGCTATA 58.333 34.615 0.00 0.00 42.20 1.31
312 317 6.755141 TGGAATCACGCTATAAGACTTGTTAC 59.245 38.462 0.00 0.00 0.00 2.50
325 330 6.380079 AGACTTGTTACTGAAGGAATGGAT 57.620 37.500 0.00 0.00 0.00 3.41
353 358 6.590292 CACAGTTTTGAACTATCGTAGGACAT 59.410 38.462 0.00 0.00 40.46 3.06
354 359 6.590292 ACAGTTTTGAACTATCGTAGGACATG 59.410 38.462 0.00 0.00 40.46 3.21
355 360 6.590292 CAGTTTTGAACTATCGTAGGACATGT 59.410 38.462 0.00 0.00 40.46 3.21
356 361 6.812160 AGTTTTGAACTATCGTAGGACATGTC 59.188 38.462 17.91 17.91 40.69 3.06
357 362 5.907866 TTGAACTATCGTAGGACATGTCA 57.092 39.130 26.47 6.73 0.00 3.58
376 381 8.046708 ACATGTCATACTAGTTGCTCCATTTTA 58.953 33.333 0.00 0.00 0.00 1.52
386 403 9.309516 CTAGTTGCTCCATTTTACGTTATCTTA 57.690 33.333 0.00 0.00 0.00 2.10
405 422 4.782691 TCTTAGTTGGATCCCATTGTCTGA 59.217 41.667 9.90 0.00 31.53 3.27
415 432 4.018490 TCCCATTGTCTGATGGTTGAATG 58.982 43.478 3.47 0.00 44.17 2.67
417 434 4.142315 CCCATTGTCTGATGGTTGAATGTC 60.142 45.833 3.47 0.00 44.17 3.06
419 436 5.047872 CCATTGTCTGATGGTTGAATGTCAA 60.048 40.000 0.00 0.00 41.37 3.18
423 440 7.053316 TGTCTGATGGTTGAATGTCAATTTT 57.947 32.000 0.00 0.00 38.79 1.82
427 444 7.014518 TCTGATGGTTGAATGTCAATTTTCACT 59.985 33.333 0.00 0.00 38.79 3.41
439 456 6.091986 TGTCAATTTTCACTTTTTGGCTGAAC 59.908 34.615 0.00 0.00 0.00 3.18
452 472 0.880278 GCTGAACTCGACTGTTGCCA 60.880 55.000 0.00 0.00 0.00 4.92
473 493 2.572104 ACAAATCTAAGGACGCTTCCCT 59.428 45.455 5.45 0.00 44.10 4.20
475 495 1.867363 ATCTAAGGACGCTTCCCTGT 58.133 50.000 5.45 0.00 44.10 4.00
482 502 1.369625 GACGCTTCCCTGTTGTATGG 58.630 55.000 0.00 0.00 0.00 2.74
488 508 4.021102 CTTCCCTGTTGTATGGAAGTGT 57.979 45.455 8.93 0.00 46.53 3.55
505 525 5.163332 GGAAGTGTAGGAGAAAATATCCGGT 60.163 44.000 0.00 0.00 42.02 5.28
525 549 4.031028 GGTGAGATGCAATTTCGAATTCG 58.969 43.478 21.78 21.78 41.45 3.34
564 588 8.915057 AGTGAGAATGTCATTATAATTCAGGG 57.085 34.615 0.00 0.00 37.56 4.45
567 685 8.159447 TGAGAATGTCATTATAATTCAGGGGAG 58.841 37.037 0.00 0.00 33.61 4.30
579 697 5.734031 ATTCAGGGGAGTAAATAAAGCCT 57.266 39.130 0.00 0.00 0.00 4.58
581 699 4.108570 TCAGGGGAGTAAATAAAGCCTGA 58.891 43.478 0.00 0.00 0.00 3.86
584 702 3.945921 GGGGAGTAAATAAAGCCTGACAC 59.054 47.826 0.00 0.00 0.00 3.67
585 703 3.621715 GGGAGTAAATAAAGCCTGACACG 59.378 47.826 0.00 0.00 0.00 4.49
587 705 4.329256 GGAGTAAATAAAGCCTGACACGAC 59.671 45.833 0.00 0.00 0.00 4.34
589 707 5.488341 AGTAAATAAAGCCTGACACGACAT 58.512 37.500 0.00 0.00 0.00 3.06
593 711 3.402628 AAAGCCTGACACGACATTAGT 57.597 42.857 0.00 0.00 0.00 2.24
634 752 9.955208 TCATCATTATACATTGCTGAATTTGTC 57.045 29.630 0.00 0.00 0.00 3.18
635 753 9.738832 CATCATTATACATTGCTGAATTTGTCA 57.261 29.630 0.00 0.00 34.17 3.58
677 2666 9.968743 AAAACGATATTTCTAGAACGTCATTTC 57.031 29.630 16.32 7.11 33.59 2.17
678 2667 7.695869 ACGATATTTCTAGAACGTCATTTCC 57.304 36.000 4.18 0.00 0.00 3.13
679 2668 7.490000 ACGATATTTCTAGAACGTCATTTCCT 58.510 34.615 4.18 0.00 0.00 3.36
680 2669 7.980099 ACGATATTTCTAGAACGTCATTTCCTT 59.020 33.333 4.18 0.00 0.00 3.36
792 2817 1.278985 TGTGATCTGGTTTCAGCGGAT 59.721 47.619 0.00 0.00 43.73 4.18
801 2826 4.584874 TGGTTTCAGCGGATATTTTCTCA 58.415 39.130 0.00 0.00 0.00 3.27
805 2830 7.035612 GGTTTCAGCGGATATTTTCTCAAAAT 58.964 34.615 0.23 0.23 43.19 1.82
806 2831 7.545615 GGTTTCAGCGGATATTTTCTCAAAATT 59.454 33.333 0.00 0.00 41.16 1.82
807 2832 9.567848 GTTTCAGCGGATATTTTCTCAAAATTA 57.432 29.630 0.00 0.00 41.16 1.40
808 2833 9.787532 TTTCAGCGGATATTTTCTCAAAATTAG 57.212 29.630 0.00 0.00 41.16 1.73
809 2834 8.731275 TCAGCGGATATTTTCTCAAAATTAGA 57.269 30.769 0.00 0.00 41.16 2.10
811 2836 9.956720 CAGCGGATATTTTCTCAAAATTAGAAT 57.043 29.630 0.00 0.00 41.16 2.40
849 2876 3.058293 TGCGTACTTGCAGAAATTTCAGG 60.058 43.478 19.99 12.34 40.62 3.86
850 2877 3.058224 GCGTACTTGCAGAAATTTCAGGT 60.058 43.478 19.99 9.23 34.15 4.00
852 2879 5.334569 GCGTACTTGCAGAAATTTCAGGTAA 60.335 40.000 19.99 14.79 34.15 2.85
856 2883 5.928264 ACTTGCAGAAATTTCAGGTAATTGC 59.072 36.000 19.99 17.47 0.00 3.56
857 2884 4.819769 TGCAGAAATTTCAGGTAATTGCC 58.180 39.130 19.99 4.07 0.00 4.52
860 2887 5.349543 GCAGAAATTTCAGGTAATTGCCTTG 59.650 40.000 19.99 7.26 36.58 3.61
861 2888 5.870978 CAGAAATTTCAGGTAATTGCCTTGG 59.129 40.000 19.99 2.88 36.58 3.61
862 2889 5.543790 AGAAATTTCAGGTAATTGCCTTGGT 59.456 36.000 19.99 0.00 36.58 3.67
864 2891 2.969821 TCAGGTAATTGCCTTGGTGT 57.030 45.000 13.03 0.00 36.58 4.16
865 2892 3.237268 TCAGGTAATTGCCTTGGTGTT 57.763 42.857 13.03 0.00 36.58 3.32
866 2893 3.571590 TCAGGTAATTGCCTTGGTGTTT 58.428 40.909 13.03 0.00 36.58 2.83
867 2894 3.572255 TCAGGTAATTGCCTTGGTGTTTC 59.428 43.478 13.03 0.00 36.58 2.78
868 2895 3.573967 CAGGTAATTGCCTTGGTGTTTCT 59.426 43.478 13.03 0.00 36.58 2.52
869 2896 3.826729 AGGTAATTGCCTTGGTGTTTCTC 59.173 43.478 9.62 0.00 34.71 2.87
870 2897 3.572255 GGTAATTGCCTTGGTGTTTCTCA 59.428 43.478 5.16 0.00 0.00 3.27
871 2898 4.038642 GGTAATTGCCTTGGTGTTTCTCAA 59.961 41.667 5.16 0.00 0.00 3.02
872 2899 4.326504 AATTGCCTTGGTGTTTCTCAAG 57.673 40.909 0.00 0.00 39.83 3.02
879 2906 1.748493 TGGTGTTTCTCAAGGTGCAAC 59.252 47.619 0.00 0.00 0.00 4.17
883 2910 2.423185 TGTTTCTCAAGGTGCAACTGTG 59.577 45.455 4.19 6.30 36.74 3.66
909 2936 1.925052 CGCTCGGATTTTCTACGCC 59.075 57.895 0.00 0.00 0.00 5.68
914 2941 1.134907 TCGGATTTTCTACGCCACTCC 60.135 52.381 0.00 0.00 0.00 3.85
916 2943 2.706890 GGATTTTCTACGCCACTCCAA 58.293 47.619 0.00 0.00 0.00 3.53
918 2945 3.065371 GGATTTTCTACGCCACTCCAATG 59.935 47.826 0.00 0.00 0.00 2.82
920 2947 2.093306 TTCTACGCCACTCCAATGTG 57.907 50.000 0.00 0.00 37.66 3.21
921 2948 1.262417 TCTACGCCACTCCAATGTGA 58.738 50.000 0.00 0.00 40.12 3.58
926 2953 2.224426 ACGCCACTCCAATGTGAAGTTA 60.224 45.455 0.00 0.00 40.12 2.24
928 2955 3.412386 GCCACTCCAATGTGAAGTTAGT 58.588 45.455 0.00 0.00 40.12 2.24
933 2960 6.128172 CCACTCCAATGTGAAGTTAGTTGATC 60.128 42.308 0.00 0.00 40.12 2.92
934 2961 6.427853 CACTCCAATGTGAAGTTAGTTGATCA 59.572 38.462 0.00 0.00 40.12 2.92
935 2962 6.652481 ACTCCAATGTGAAGTTAGTTGATCAG 59.348 38.462 0.00 0.00 0.00 2.90
936 2963 5.412594 TCCAATGTGAAGTTAGTTGATCAGC 59.587 40.000 0.50 0.50 0.00 4.26
1722 3752 5.924356 ACATACAATGTTATCATGGACGGA 58.076 37.500 0.00 0.00 41.63 4.69
1872 3902 3.253677 CGGACGTTGAGGAGCTTATAGAT 59.746 47.826 0.00 0.00 0.00 1.98
1886 3916 5.248020 AGCTTATAGATGAGATGTTCAGGGG 59.752 44.000 0.00 0.00 39.68 4.79
2131 4164 8.619683 ACCTAAGACCACTACCTATAACATTT 57.380 34.615 0.00 0.00 0.00 2.32
2159 4192 0.953727 GCTTTGTGCAGTGGTGATCA 59.046 50.000 0.00 0.00 42.31 2.92
2160 4193 1.337703 GCTTTGTGCAGTGGTGATCAA 59.662 47.619 0.00 0.00 42.31 2.57
2223 4256 8.733458 CAAACTGATCAACTTCCAGATATTTCA 58.267 33.333 0.00 0.00 0.00 2.69
2291 4324 4.212214 GCTGAAGGCCATCGAAGTATTTAG 59.788 45.833 5.01 0.00 34.27 1.85
2445 4478 8.079211 ACTCAGAGGTAAAATATGAGCTGTTA 57.921 34.615 1.53 0.00 39.15 2.41
2448 4481 6.203723 CAGAGGTAAAATATGAGCTGTTAGCC 59.796 42.308 0.00 0.00 43.77 3.93
2466 4499 2.503356 AGCCGAGTTTCTGGATGAAGAT 59.497 45.455 0.00 0.00 35.89 2.40
2565 4598 6.318900 ACAATACAATACTCTTAGGGCTTTGC 59.681 38.462 0.00 0.00 0.00 3.68
2574 4607 1.851304 TAGGGCTTTGCAGAAATGGG 58.149 50.000 0.00 0.00 0.00 4.00
2584 4617 5.549742 TTGCAGAAATGGGAAAACAGATT 57.450 34.783 0.00 0.00 0.00 2.40
2640 4673 1.268896 GGTTGCATGCCTGATGAATCG 60.269 52.381 16.68 0.00 33.31 3.34
2647 4680 3.885724 TGCCTGATGAATCGACTTACA 57.114 42.857 0.00 0.00 0.00 2.41
2648 4681 3.521560 TGCCTGATGAATCGACTTACAC 58.478 45.455 0.00 0.00 0.00 2.90
2673 4706 3.167485 ACTCATTGATGGTTTGGCACAT 58.833 40.909 0.00 0.00 39.30 3.21
2996 5035 2.433604 TCTTGCAATTTTGGCTGGTCAA 59.566 40.909 0.00 0.00 0.00 3.18
2997 5036 3.071312 TCTTGCAATTTTGGCTGGTCAAT 59.929 39.130 0.00 0.00 0.00 2.57
2998 5037 3.042871 TGCAATTTTGGCTGGTCAATC 57.957 42.857 0.00 0.00 0.00 2.67
2999 5038 2.367894 TGCAATTTTGGCTGGTCAATCA 59.632 40.909 0.00 0.00 0.00 2.57
3043 5084 6.271488 ACAAAATATCAGTGTGTGGGAATG 57.729 37.500 0.00 0.00 0.00 2.67
3109 5150 6.436843 TTTTGACCTTGAGTCTGAAACTTC 57.563 37.500 0.00 0.00 46.46 3.01
3209 5250 3.572661 TGGGACTAAAACTAGGGAGGT 57.427 47.619 0.00 0.00 0.00 3.85
3247 5288 6.389830 TGTTGTATGTCTGCTGATGTTTTT 57.610 33.333 0.00 0.00 0.00 1.94
3311 5352 1.216990 AGGGTGGAGCCAGGATTTAG 58.783 55.000 0.00 0.00 39.65 1.85
3312 5353 0.183731 GGGTGGAGCCAGGATTTAGG 59.816 60.000 0.00 0.00 39.65 2.69
3339 5380 2.497675 TGCCTAGACAAACTGCTAGAGG 59.502 50.000 0.00 0.00 36.97 3.69
3456 5498 9.609950 TTTCTCTTTTCTTTTTGCACAAAAATG 57.390 25.926 18.64 13.57 45.69 2.32
3457 5499 7.242783 TCTCTTTTCTTTTTGCACAAAAATGC 58.757 30.769 18.64 0.00 45.69 3.56
3459 5501 3.940657 TCTTTTTGCACAAAAATGCCG 57.059 38.095 18.64 9.54 45.69 5.69
3556 5599 9.574458 TCGTTGAAAATGAAAAACAAAGTATGA 57.426 25.926 0.00 0.00 39.27 2.15
3598 5641 8.362464 ACAGAACAGAGGACTTTACATATACA 57.638 34.615 0.00 0.00 0.00 2.29
3599 5642 8.812972 ACAGAACAGAGGACTTTACATATACAA 58.187 33.333 0.00 0.00 0.00 2.41
3600 5643 9.307121 CAGAACAGAGGACTTTACATATACAAG 57.693 37.037 0.00 0.00 0.00 3.16
3601 5644 7.982354 AGAACAGAGGACTTTACATATACAAGC 59.018 37.037 0.00 0.00 0.00 4.01
3602 5645 7.425224 ACAGAGGACTTTACATATACAAGCT 57.575 36.000 0.00 0.00 0.00 3.74
3603 5646 7.852263 ACAGAGGACTTTACATATACAAGCTT 58.148 34.615 0.00 0.00 0.00 3.74
3604 5647 8.978472 ACAGAGGACTTTACATATACAAGCTTA 58.022 33.333 0.00 0.00 0.00 3.09
3605 5648 9.817809 CAGAGGACTTTACATATACAAGCTTAA 57.182 33.333 0.00 0.00 0.00 1.85
3622 5665 8.893727 ACAAGCTTAATGTATGAATTGTACTCC 58.106 33.333 0.00 0.00 0.00 3.85
3623 5666 9.113838 CAAGCTTAATGTATGAATTGTACTCCT 57.886 33.333 0.00 0.00 0.00 3.69
3624 5667 9.686683 AAGCTTAATGTATGAATTGTACTCCTT 57.313 29.630 0.00 0.00 0.00 3.36
3625 5668 9.331282 AGCTTAATGTATGAATTGTACTCCTTC 57.669 33.333 0.00 0.00 0.00 3.46
3626 5669 8.560374 GCTTAATGTATGAATTGTACTCCTTCC 58.440 37.037 0.00 0.00 0.00 3.46
3627 5670 9.613428 CTTAATGTATGAATTGTACTCCTTCCA 57.387 33.333 0.00 0.00 0.00 3.53
3629 5672 8.682936 AATGTATGAATTGTACTCCTTCCATC 57.317 34.615 0.00 0.00 0.00 3.51
3630 5673 6.591935 TGTATGAATTGTACTCCTTCCATCC 58.408 40.000 0.00 0.00 0.00 3.51
3631 5674 5.983333 ATGAATTGTACTCCTTCCATCCT 57.017 39.130 0.00 0.00 0.00 3.24
3632 5675 5.102953 TGAATTGTACTCCTTCCATCCTG 57.897 43.478 0.00 0.00 0.00 3.86
3633 5676 4.782691 TGAATTGTACTCCTTCCATCCTGA 59.217 41.667 0.00 0.00 0.00 3.86
3634 5677 5.250543 TGAATTGTACTCCTTCCATCCTGAA 59.749 40.000 0.00 0.00 0.00 3.02
3635 5678 5.983333 ATTGTACTCCTTCCATCCTGAAT 57.017 39.130 0.00 0.00 0.00 2.57
3636 5679 5.779241 TTGTACTCCTTCCATCCTGAATT 57.221 39.130 0.00 0.00 0.00 2.17
3637 5680 6.884472 TTGTACTCCTTCCATCCTGAATTA 57.116 37.500 0.00 0.00 0.00 1.40
3638 5681 6.235231 TGTACTCCTTCCATCCTGAATTAC 57.765 41.667 0.00 0.00 0.00 1.89
3639 5682 5.964477 TGTACTCCTTCCATCCTGAATTACT 59.036 40.000 0.00 0.00 0.00 2.24
3640 5683 6.443849 TGTACTCCTTCCATCCTGAATTACTT 59.556 38.462 0.00 0.00 0.00 2.24
3641 5684 5.749462 ACTCCTTCCATCCTGAATTACTTG 58.251 41.667 0.00 0.00 0.00 3.16
3642 5685 5.251700 ACTCCTTCCATCCTGAATTACTTGT 59.748 40.000 0.00 0.00 0.00 3.16
3643 5686 6.139679 TCCTTCCATCCTGAATTACTTGTT 57.860 37.500 0.00 0.00 0.00 2.83
3644 5687 5.945784 TCCTTCCATCCTGAATTACTTGTTG 59.054 40.000 0.00 0.00 0.00 3.33
3645 5688 5.393461 CCTTCCATCCTGAATTACTTGTTGC 60.393 44.000 0.00 0.00 0.00 4.17
3646 5689 4.661222 TCCATCCTGAATTACTTGTTGCA 58.339 39.130 0.00 0.00 0.00 4.08
3647 5690 4.701651 TCCATCCTGAATTACTTGTTGCAG 59.298 41.667 0.00 0.00 0.00 4.41
3648 5691 4.701651 CCATCCTGAATTACTTGTTGCAGA 59.298 41.667 0.00 0.00 0.00 4.26
3649 5692 5.392380 CCATCCTGAATTACTTGTTGCAGAC 60.392 44.000 0.00 0.00 0.00 3.51
3650 5693 4.713553 TCCTGAATTACTTGTTGCAGACA 58.286 39.130 0.00 0.00 36.19 3.41
3651 5694 5.316167 TCCTGAATTACTTGTTGCAGACAT 58.684 37.500 0.00 0.00 38.26 3.06
3652 5695 5.181811 TCCTGAATTACTTGTTGCAGACATG 59.818 40.000 10.96 10.96 38.26 3.21
3653 5696 5.375417 TGAATTACTTGTTGCAGACATGG 57.625 39.130 14.65 8.92 38.26 3.66
3654 5697 5.069318 TGAATTACTTGTTGCAGACATGGA 58.931 37.500 14.65 7.41 38.26 3.41
3655 5698 5.711506 TGAATTACTTGTTGCAGACATGGAT 59.288 36.000 14.65 8.59 38.26 3.41
3656 5699 5.571784 ATTACTTGTTGCAGACATGGATG 57.428 39.130 14.65 0.00 38.26 3.51
3657 5700 2.867624 ACTTGTTGCAGACATGGATGT 58.132 42.857 14.65 0.00 45.16 3.06
3658 5701 4.019792 ACTTGTTGCAGACATGGATGTA 57.980 40.909 14.65 0.00 41.95 2.29
3659 5702 4.592942 ACTTGTTGCAGACATGGATGTAT 58.407 39.130 14.65 0.00 41.95 2.29
3660 5703 4.637534 ACTTGTTGCAGACATGGATGTATC 59.362 41.667 14.65 0.00 41.95 2.24
3661 5704 4.492494 TGTTGCAGACATGGATGTATCT 57.508 40.909 0.00 0.00 41.95 1.98
3662 5705 5.612725 TGTTGCAGACATGGATGTATCTA 57.387 39.130 0.00 0.00 41.95 1.98
3663 5706 5.604565 TGTTGCAGACATGGATGTATCTAG 58.395 41.667 0.00 0.00 41.95 2.43
3664 5707 5.363580 TGTTGCAGACATGGATGTATCTAGA 59.636 40.000 0.00 0.00 41.95 2.43
3665 5708 6.042437 TGTTGCAGACATGGATGTATCTAGAT 59.958 38.462 10.73 10.73 41.95 1.98
3666 5709 6.034161 TGCAGACATGGATGTATCTAGATG 57.966 41.667 15.79 0.00 41.95 2.90
3667 5710 5.541484 TGCAGACATGGATGTATCTAGATGT 59.459 40.000 15.79 3.21 41.95 3.06
3668 5711 6.721208 TGCAGACATGGATGTATCTAGATGTA 59.279 38.462 15.79 4.44 41.95 2.29
3669 5712 7.398332 TGCAGACATGGATGTATCTAGATGTAT 59.602 37.037 15.79 9.11 41.95 2.29
3670 5713 8.256605 GCAGACATGGATGTATCTAGATGTATT 58.743 37.037 15.79 0.00 41.95 1.89
3700 5743 9.988815 AGTTCTAGATACATCCATTTATGTGAC 57.011 33.333 0.00 0.00 40.29 3.67
3701 5744 9.764363 GTTCTAGATACATCCATTTATGTGACA 57.236 33.333 0.00 0.00 40.29 3.58
3703 5746 9.987272 TCTAGATACATCCATTTATGTGACAAG 57.013 33.333 0.00 0.00 40.29 3.16
3704 5747 9.770097 CTAGATACATCCATTTATGTGACAAGT 57.230 33.333 0.00 0.00 40.29 3.16
3710 5753 8.397906 ACATCCATTTATGTGACAAGTAATTCG 58.602 33.333 0.00 0.00 38.65 3.34
3711 5754 7.315247 TCCATTTATGTGACAAGTAATTCGG 57.685 36.000 0.00 0.00 0.00 4.30
3712 5755 6.317642 TCCATTTATGTGACAAGTAATTCGGG 59.682 38.462 0.00 0.00 0.00 5.14
3713 5756 6.317642 CCATTTATGTGACAAGTAATTCGGGA 59.682 38.462 0.00 0.00 0.00 5.14
3714 5757 6.730960 TTTATGTGACAAGTAATTCGGGAC 57.269 37.500 0.00 0.00 0.00 4.46
3731 5774 3.993920 GGGACGAAGGTAGTAACAAACA 58.006 45.455 0.00 0.00 0.00 2.83
3732 5775 4.379652 GGGACGAAGGTAGTAACAAACAA 58.620 43.478 0.00 0.00 0.00 2.83
3733 5776 4.999311 GGGACGAAGGTAGTAACAAACAAT 59.001 41.667 0.00 0.00 0.00 2.71
3734 5777 5.471116 GGGACGAAGGTAGTAACAAACAATT 59.529 40.000 0.00 0.00 0.00 2.32
3735 5778 6.650390 GGGACGAAGGTAGTAACAAACAATTA 59.350 38.462 0.00 0.00 0.00 1.40
3736 5779 7.335171 GGGACGAAGGTAGTAACAAACAATTAT 59.665 37.037 0.00 0.00 0.00 1.28
3737 5780 9.369904 GGACGAAGGTAGTAACAAACAATTATA 57.630 33.333 0.00 0.00 0.00 0.98
3751 5794 9.326413 ACAAACAATTATATAGTTCTCCTTCCG 57.674 33.333 0.00 0.00 0.00 4.30
3752 5795 9.326413 CAAACAATTATATAGTTCTCCTTCCGT 57.674 33.333 0.00 0.00 0.00 4.69
3753 5796 9.901172 AAACAATTATATAGTTCTCCTTCCGTT 57.099 29.630 0.00 0.00 0.00 4.44
3754 5797 9.543783 AACAATTATATAGTTCTCCTTCCGTTC 57.456 33.333 0.00 0.00 0.00 3.95
3755 5798 8.701895 ACAATTATATAGTTCTCCTTCCGTTCA 58.298 33.333 0.00 0.00 0.00 3.18
3756 5799 8.979574 CAATTATATAGTTCTCCTTCCGTTCAC 58.020 37.037 0.00 0.00 0.00 3.18
3757 5800 7.649533 TTATATAGTTCTCCTTCCGTTCACA 57.350 36.000 0.00 0.00 0.00 3.58
3758 5801 4.884668 ATAGTTCTCCTTCCGTTCACAA 57.115 40.909 0.00 0.00 0.00 3.33
3759 5802 3.553828 AGTTCTCCTTCCGTTCACAAA 57.446 42.857 0.00 0.00 0.00 2.83
3760 5803 4.086706 AGTTCTCCTTCCGTTCACAAAT 57.913 40.909 0.00 0.00 0.00 2.32
3761 5804 5.223449 AGTTCTCCTTCCGTTCACAAATA 57.777 39.130 0.00 0.00 0.00 1.40
3762 5805 5.805728 AGTTCTCCTTCCGTTCACAAATAT 58.194 37.500 0.00 0.00 0.00 1.28
3763 5806 6.942976 AGTTCTCCTTCCGTTCACAAATATA 58.057 36.000 0.00 0.00 0.00 0.86
3764 5807 7.391620 AGTTCTCCTTCCGTTCACAAATATAA 58.608 34.615 0.00 0.00 0.00 0.98
3765 5808 7.549488 AGTTCTCCTTCCGTTCACAAATATAAG 59.451 37.037 0.00 0.00 0.00 1.73
3766 5809 7.177832 TCTCCTTCCGTTCACAAATATAAGA 57.822 36.000 0.00 0.00 0.00 2.10
3767 5810 7.792032 TCTCCTTCCGTTCACAAATATAAGAT 58.208 34.615 0.00 0.00 0.00 2.40
3768 5811 7.710907 TCTCCTTCCGTTCACAAATATAAGATG 59.289 37.037 0.00 0.00 0.00 2.90
3769 5812 7.335627 TCCTTCCGTTCACAAATATAAGATGT 58.664 34.615 0.00 0.00 0.00 3.06
3770 5813 7.827236 TCCTTCCGTTCACAAATATAAGATGTT 59.173 33.333 0.00 0.00 0.00 2.71
3771 5814 8.122952 CCTTCCGTTCACAAATATAAGATGTTC 58.877 37.037 0.00 0.00 0.00 3.18
3772 5815 8.786826 TTCCGTTCACAAATATAAGATGTTCT 57.213 30.769 0.00 0.00 0.00 3.01
3773 5816 9.878667 TTCCGTTCACAAATATAAGATGTTCTA 57.121 29.630 0.00 0.00 0.00 2.10
3774 5817 9.529325 TCCGTTCACAAATATAAGATGTTCTAG 57.471 33.333 0.00 0.00 0.00 2.43
3775 5818 8.276325 CCGTTCACAAATATAAGATGTTCTAGC 58.724 37.037 0.00 0.00 0.00 3.42
3776 5819 9.035607 CGTTCACAAATATAAGATGTTCTAGCT 57.964 33.333 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.397564 TTTGGTAACCGGTCACCTCC 59.602 55.000 27.52 15.70 35.73 4.30
83 86 2.791383 TGGTGTTTCTTGGATTTGCG 57.209 45.000 0.00 0.00 0.00 4.85
88 91 4.528206 GGAGGAAAATGGTGTTTCTTGGAT 59.472 41.667 0.00 0.00 37.60 3.41
90 93 3.305335 CGGAGGAAAATGGTGTTTCTTGG 60.305 47.826 0.00 0.00 37.60 3.61
208 211 2.027653 CCAATGTTACGCCCCCAAAATT 60.028 45.455 0.00 0.00 0.00 1.82
209 212 1.552792 CCAATGTTACGCCCCCAAAAT 59.447 47.619 0.00 0.00 0.00 1.82
212 215 1.979693 GCCAATGTTACGCCCCCAA 60.980 57.895 0.00 0.00 0.00 4.12
250 253 4.084287 AGCCACAAAATCATCACAGTGAT 58.916 39.130 10.53 10.53 40.44 3.06
286 291 5.918608 ACAAGTCTTATAGCGTGATTCCAT 58.081 37.500 0.00 0.00 0.00 3.41
296 301 8.821894 CATTCCTTCAGTAACAAGTCTTATAGC 58.178 37.037 0.00 0.00 0.00 2.97
299 304 7.918076 TCCATTCCTTCAGTAACAAGTCTTAT 58.082 34.615 0.00 0.00 0.00 1.73
300 305 7.311092 TCCATTCCTTCAGTAACAAGTCTTA 57.689 36.000 0.00 0.00 0.00 2.10
301 306 6.187727 TCCATTCCTTCAGTAACAAGTCTT 57.812 37.500 0.00 0.00 0.00 3.01
312 317 3.947868 ACTGTGACATCCATTCCTTCAG 58.052 45.455 0.00 0.00 0.00 3.02
353 358 6.533723 CGTAAAATGGAGCAACTAGTATGACA 59.466 38.462 0.00 0.00 0.00 3.58
354 359 6.534079 ACGTAAAATGGAGCAACTAGTATGAC 59.466 38.462 0.00 0.00 0.00 3.06
355 360 6.636705 ACGTAAAATGGAGCAACTAGTATGA 58.363 36.000 0.00 0.00 0.00 2.15
356 361 6.903883 ACGTAAAATGGAGCAACTAGTATG 57.096 37.500 0.00 0.00 0.00 2.39
357 362 9.257651 GATAACGTAAAATGGAGCAACTAGTAT 57.742 33.333 0.00 0.00 0.00 2.12
376 381 5.888982 ATGGGATCCAACTAAGATAACGT 57.111 39.130 15.23 0.00 36.95 3.99
386 403 3.372349 CCATCAGACAATGGGATCCAACT 60.372 47.826 15.23 0.00 42.19 3.16
405 422 8.735692 AAAAGTGAAAATTGACATTCAACCAT 57.264 26.923 0.00 0.00 39.45 3.55
415 432 6.313658 AGTTCAGCCAAAAAGTGAAAATTGAC 59.686 34.615 0.00 0.00 32.15 3.18
417 434 6.508404 CGAGTTCAGCCAAAAAGTGAAAATTG 60.508 38.462 0.00 0.00 32.15 2.32
419 436 5.043248 CGAGTTCAGCCAAAAAGTGAAAAT 58.957 37.500 0.00 0.00 32.15 1.82
423 440 2.612212 GTCGAGTTCAGCCAAAAAGTGA 59.388 45.455 0.00 0.00 0.00 3.41
427 444 2.639065 ACAGTCGAGTTCAGCCAAAAA 58.361 42.857 0.00 0.00 0.00 1.94
452 472 2.572104 AGGGAAGCGTCCTTAGATTTGT 59.428 45.455 18.54 0.00 44.28 2.83
473 493 6.428083 TTTCTCCTACACTTCCATACAACA 57.572 37.500 0.00 0.00 0.00 3.33
475 495 9.832445 GATATTTTCTCCTACACTTCCATACAA 57.168 33.333 0.00 0.00 0.00 2.41
482 502 5.753921 CACCGGATATTTTCTCCTACACTTC 59.246 44.000 9.46 0.00 0.00 3.01
486 506 5.205821 TCTCACCGGATATTTTCTCCTACA 58.794 41.667 9.46 0.00 0.00 2.74
488 508 5.279506 GCATCTCACCGGATATTTTCTCCTA 60.280 44.000 9.46 0.00 0.00 2.94
542 566 8.160106 ACTCCCCTGAATTATAATGACATTCTC 58.840 37.037 3.36 0.00 0.00 2.87
543 567 8.050316 ACTCCCCTGAATTATAATGACATTCT 57.950 34.615 3.36 0.00 0.00 2.40
544 568 9.793259 TTACTCCCCTGAATTATAATGACATTC 57.207 33.333 3.36 0.00 0.00 2.67
553 577 8.955794 AGGCTTTATTTACTCCCCTGAATTATA 58.044 33.333 0.00 0.00 0.00 0.98
554 578 7.725844 CAGGCTTTATTTACTCCCCTGAATTAT 59.274 37.037 0.00 0.00 40.52 1.28
555 579 7.060421 CAGGCTTTATTTACTCCCCTGAATTA 58.940 38.462 0.00 0.00 40.52 1.40
558 582 4.538490 TCAGGCTTTATTTACTCCCCTGAA 59.462 41.667 4.15 0.00 42.99 3.02
559 583 4.080526 GTCAGGCTTTATTTACTCCCCTGA 60.081 45.833 2.57 2.57 43.53 3.86
560 584 4.200092 GTCAGGCTTTATTTACTCCCCTG 58.800 47.826 0.00 0.00 39.68 4.45
562 586 3.945921 GTGTCAGGCTTTATTTACTCCCC 59.054 47.826 0.00 0.00 0.00 4.81
563 587 3.621715 CGTGTCAGGCTTTATTTACTCCC 59.378 47.826 0.00 0.00 0.00 4.30
564 588 4.329256 GTCGTGTCAGGCTTTATTTACTCC 59.671 45.833 0.00 0.00 0.00 3.85
567 685 5.796350 ATGTCGTGTCAGGCTTTATTTAC 57.204 39.130 0.00 0.00 0.00 2.01
576 694 2.363788 TCACTAATGTCGTGTCAGGC 57.636 50.000 0.00 0.00 34.14 4.85
577 695 5.408299 TCATTTTCACTAATGTCGTGTCAGG 59.592 40.000 0.00 0.00 36.95 3.86
579 697 6.852858 TTCATTTTCACTAATGTCGTGTCA 57.147 33.333 0.00 0.00 36.95 3.58
655 791 7.932120 AGGAAATGACGTTCTAGAAATATCG 57.068 36.000 6.78 9.11 0.00 2.92
739 2763 8.859090 ACTCAGTGAAATCATGTTTGGAAATTA 58.141 29.630 0.00 0.00 0.00 1.40
742 2766 6.713762 ACTCAGTGAAATCATGTTTGGAAA 57.286 33.333 0.00 0.00 0.00 3.13
849 2876 4.846779 TGAGAAACACCAAGGCAATTAC 57.153 40.909 0.00 0.00 0.00 1.89
850 2877 5.452078 CTTGAGAAACACCAAGGCAATTA 57.548 39.130 0.00 0.00 36.90 1.40
857 2884 2.023673 TGCACCTTGAGAAACACCAAG 58.976 47.619 0.00 0.00 39.43 3.61
860 2887 2.024414 AGTTGCACCTTGAGAAACACC 58.976 47.619 0.00 0.00 0.00 4.16
861 2888 2.423538 ACAGTTGCACCTTGAGAAACAC 59.576 45.455 0.00 0.00 0.00 3.32
862 2889 2.423185 CACAGTTGCACCTTGAGAAACA 59.577 45.455 0.00 0.00 0.00 2.83
879 2906 2.127496 CGAGCGCAAACAGCACAG 60.127 61.111 11.47 0.00 46.13 3.66
883 2910 0.387239 AAAATCCGAGCGCAAACAGC 60.387 50.000 11.47 0.00 40.87 4.40
884 2911 1.197721 AGAAAATCCGAGCGCAAACAG 59.802 47.619 11.47 0.00 0.00 3.16
891 2918 0.804544 TGGCGTAGAAAATCCGAGCG 60.805 55.000 0.00 0.00 0.00 5.03
895 2922 1.287425 GGAGTGGCGTAGAAAATCCG 58.713 55.000 0.00 0.00 0.00 4.18
909 2936 6.427853 TGATCAACTAACTTCACATTGGAGTG 59.572 38.462 0.00 0.00 40.85 3.51
914 2941 6.245115 TGCTGATCAACTAACTTCACATTG 57.755 37.500 0.00 0.00 0.00 2.82
916 2943 4.394300 GCTGCTGATCAACTAACTTCACAT 59.606 41.667 0.00 0.00 0.00 3.21
918 2945 3.181526 CGCTGCTGATCAACTAACTTCAC 60.182 47.826 0.00 0.00 0.00 3.18
920 2947 2.349886 CCGCTGCTGATCAACTAACTTC 59.650 50.000 0.00 0.00 0.00 3.01
921 2948 2.350522 CCGCTGCTGATCAACTAACTT 58.649 47.619 0.00 0.00 0.00 2.66
926 2953 1.744368 CTGCCGCTGCTGATCAACT 60.744 57.895 0.70 0.00 38.61 3.16
928 2955 3.129502 GCTGCCGCTGCTGATCAA 61.130 61.111 14.47 0.00 38.61 2.57
1048 3078 1.867487 AGTAGGAGGGAGGGGGTGT 60.867 63.158 0.00 0.00 0.00 4.16
1722 3752 1.339438 ACATCGCCTTCTCTGCACATT 60.339 47.619 0.00 0.00 0.00 2.71
1731 3761 2.579201 CCGTCCACATCGCCTTCT 59.421 61.111 0.00 0.00 0.00 2.85
1761 3791 2.033424 GTGAGAAGGCAAGGTGTTCAAC 59.967 50.000 0.00 0.00 0.00 3.18
1872 3902 2.649312 ACAATTCCCCCTGAACATCTCA 59.351 45.455 0.00 0.00 35.31 3.27
1886 3916 2.513897 CGCTCGGGGGACAATTCC 60.514 66.667 0.00 0.00 41.95 3.01
2103 4136 9.719433 ATGTTATAGGTAGTGGTCTTAGGTTTA 57.281 33.333 0.00 0.00 0.00 2.01
2131 4164 2.618241 CACTGCACAAAGCCTTCACTAA 59.382 45.455 0.00 0.00 44.83 2.24
2159 4192 1.138568 CTCCTCAGCATCCTCCCATT 58.861 55.000 0.00 0.00 0.00 3.16
2160 4193 1.417288 GCTCCTCAGCATCCTCCCAT 61.417 60.000 0.00 0.00 46.06 4.00
2223 4256 7.577303 AGATACCAATGAGTGTATTGAATGGT 58.423 34.615 0.00 0.00 39.79 3.55
2445 4478 1.902508 TCTTCATCCAGAAACTCGGCT 59.097 47.619 0.00 0.00 35.40 5.52
2448 4481 7.493971 ACTTTATCATCTTCATCCAGAAACTCG 59.506 37.037 0.00 0.00 35.40 4.18
2466 4499 5.569355 TGGATTGCCTCTTCAACTTTATCA 58.431 37.500 0.00 0.00 34.31 2.15
2565 4598 6.870769 AGCATAATCTGTTTTCCCATTTCTG 58.129 36.000 0.00 0.00 0.00 3.02
2640 4673 9.601217 AAACCATCAATGAGTATAGTGTAAGTC 57.399 33.333 0.00 0.00 0.00 3.01
2647 4680 5.590259 GTGCCAAACCATCAATGAGTATAGT 59.410 40.000 0.00 0.00 0.00 2.12
2648 4681 5.589855 TGTGCCAAACCATCAATGAGTATAG 59.410 40.000 0.00 0.00 0.00 1.31
2673 4706 3.317406 TGCCTCCTTCATATAGCCTTCA 58.683 45.455 0.00 0.00 0.00 3.02
2850 4889 4.402793 CAGTGTGTAAGCACTATCCTACCT 59.597 45.833 0.00 0.00 46.81 3.08
2962 5001 9.590451 CCAAAATTGCAAGATAATTGAGTACAT 57.410 29.630 4.94 0.00 0.00 2.29
2970 5009 5.807909 ACCAGCCAAAATTGCAAGATAATT 58.192 33.333 4.94 0.00 0.00 1.40
2996 5035 7.822334 TGTTAAACTATCCACGAAGATTGTGAT 59.178 33.333 0.00 0.00 39.73 3.06
2997 5036 7.156000 TGTTAAACTATCCACGAAGATTGTGA 58.844 34.615 0.00 0.00 39.73 3.58
2998 5037 7.359262 TGTTAAACTATCCACGAAGATTGTG 57.641 36.000 0.00 0.00 33.41 3.33
2999 5038 7.972832 TTGTTAAACTATCCACGAAGATTGT 57.027 32.000 0.00 0.00 34.34 2.71
3037 5078 9.710900 GGTTTAATCCATCATATTTTCATTCCC 57.289 33.333 0.00 0.00 0.00 3.97
3109 5150 4.741321 AAATTACCAACCATCCATGCAG 57.259 40.909 0.00 0.00 0.00 4.41
3188 5229 3.878086 ACCTCCCTAGTTTTAGTCCCAA 58.122 45.455 0.00 0.00 0.00 4.12
3209 5250 6.237901 ACATACAACATTCCAGCTACTTGAA 58.762 36.000 0.00 0.00 0.00 2.69
3282 5323 1.339151 GGCTCCACCCTTGTAAGTCAG 60.339 57.143 0.00 0.00 0.00 3.51
3285 5326 0.693049 CTGGCTCCACCCTTGTAAGT 59.307 55.000 0.00 0.00 37.83 2.24
3312 5353 1.394917 CAGTTTGTCTAGGCACGATGC 59.605 52.381 0.00 0.00 44.08 3.91
3313 5354 1.394917 GCAGTTTGTCTAGGCACGATG 59.605 52.381 0.00 0.00 0.00 3.84
3314 5355 1.276421 AGCAGTTTGTCTAGGCACGAT 59.724 47.619 0.00 0.00 0.00 3.73
3315 5356 0.679505 AGCAGTTTGTCTAGGCACGA 59.320 50.000 0.00 0.00 0.00 4.35
3316 5357 2.094700 TCTAGCAGTTTGTCTAGGCACG 60.095 50.000 0.00 0.00 34.52 5.34
3362 5403 2.861935 GAGAAGGTTGAACACGAACGAA 59.138 45.455 0.00 0.00 0.00 3.85
3363 5404 2.466846 GAGAAGGTTGAACACGAACGA 58.533 47.619 0.00 0.00 0.00 3.85
3364 5405 1.525619 GGAGAAGGTTGAACACGAACG 59.474 52.381 0.00 0.00 0.00 3.95
3365 5406 2.544267 CTGGAGAAGGTTGAACACGAAC 59.456 50.000 0.00 0.00 0.00 3.95
3442 5484 1.661341 AGCGGCATTTTTGTGCAAAA 58.339 40.000 1.45 6.04 46.81 2.44
3455 5497 5.606505 TCATCACAGTAAATTATAGCGGCA 58.393 37.500 1.45 0.00 0.00 5.69
3456 5498 6.018262 TGTTCATCACAGTAAATTATAGCGGC 60.018 38.462 0.00 0.00 0.00 6.53
3457 5499 7.477144 TGTTCATCACAGTAAATTATAGCGG 57.523 36.000 0.00 0.00 0.00 5.52
3506 5549 7.361201 CGATAGCCCATACTGGTTTCATTATTG 60.361 40.741 0.00 0.00 35.17 1.90
3526 5569 8.539674 ACTTTGTTTTTCATTTTCAACGATAGC 58.460 29.630 0.00 0.00 42.67 2.97
3531 5574 9.618410 GTCATACTTTGTTTTTCATTTTCAACG 57.382 29.630 0.00 0.00 0.00 4.10
3598 5641 9.686683 AAGGAGTACAATTCATACATTAAGCTT 57.313 29.630 3.48 3.48 0.00 3.74
3599 5642 9.331282 GAAGGAGTACAATTCATACATTAAGCT 57.669 33.333 0.00 0.00 0.00 3.74
3600 5643 8.560374 GGAAGGAGTACAATTCATACATTAAGC 58.440 37.037 0.00 0.00 0.00 3.09
3601 5644 9.613428 TGGAAGGAGTACAATTCATACATTAAG 57.387 33.333 0.00 0.00 0.00 1.85
3603 5646 9.778741 GATGGAAGGAGTACAATTCATACATTA 57.221 33.333 0.00 0.00 0.00 1.90
3604 5647 7.721399 GGATGGAAGGAGTACAATTCATACATT 59.279 37.037 0.00 0.00 0.00 2.71
3605 5648 7.072961 AGGATGGAAGGAGTACAATTCATACAT 59.927 37.037 0.00 0.00 0.00 2.29
3606 5649 6.386927 AGGATGGAAGGAGTACAATTCATACA 59.613 38.462 0.00 0.00 0.00 2.29
3607 5650 6.708054 CAGGATGGAAGGAGTACAATTCATAC 59.292 42.308 0.00 0.00 0.00 2.39
3608 5651 6.615316 TCAGGATGGAAGGAGTACAATTCATA 59.385 38.462 0.00 0.00 36.16 2.15
3609 5652 5.429762 TCAGGATGGAAGGAGTACAATTCAT 59.570 40.000 0.00 0.00 36.16 2.57
3610 5653 4.782691 TCAGGATGGAAGGAGTACAATTCA 59.217 41.667 0.00 0.00 36.16 2.57
3611 5654 5.359194 TCAGGATGGAAGGAGTACAATTC 57.641 43.478 0.00 0.00 36.16 2.17
3612 5655 5.779241 TTCAGGATGGAAGGAGTACAATT 57.221 39.130 0.00 0.00 36.16 2.32
3613 5656 5.983333 ATTCAGGATGGAAGGAGTACAAT 57.017 39.130 0.00 0.00 36.16 2.71
3614 5657 5.779241 AATTCAGGATGGAAGGAGTACAA 57.221 39.130 0.00 0.00 36.16 2.41
3615 5658 5.964477 AGTAATTCAGGATGGAAGGAGTACA 59.036 40.000 0.00 0.00 36.16 2.90
3616 5659 6.487299 AGTAATTCAGGATGGAAGGAGTAC 57.513 41.667 0.00 0.00 36.16 2.73
3617 5660 6.443849 ACAAGTAATTCAGGATGGAAGGAGTA 59.556 38.462 0.00 0.00 36.16 2.59
3618 5661 5.251700 ACAAGTAATTCAGGATGGAAGGAGT 59.748 40.000 0.00 0.00 36.16 3.85
3619 5662 5.749462 ACAAGTAATTCAGGATGGAAGGAG 58.251 41.667 0.00 0.00 36.16 3.69
3620 5663 5.779241 ACAAGTAATTCAGGATGGAAGGA 57.221 39.130 0.00 0.00 36.16 3.36
3621 5664 5.393461 GCAACAAGTAATTCAGGATGGAAGG 60.393 44.000 0.00 0.00 36.16 3.46
3622 5665 5.183713 TGCAACAAGTAATTCAGGATGGAAG 59.816 40.000 0.00 0.00 36.16 3.46
3623 5666 5.076182 TGCAACAAGTAATTCAGGATGGAA 58.924 37.500 0.00 0.00 36.16 3.53
3624 5667 4.661222 TGCAACAAGTAATTCAGGATGGA 58.339 39.130 0.00 0.00 36.16 3.41
3625 5668 4.701651 TCTGCAACAAGTAATTCAGGATGG 59.298 41.667 0.00 0.00 36.16 3.51
3626 5669 5.181811 TGTCTGCAACAAGTAATTCAGGATG 59.818 40.000 0.00 0.00 34.03 3.51
3627 5670 5.316167 TGTCTGCAACAAGTAATTCAGGAT 58.684 37.500 0.00 0.00 34.03 3.24
3628 5671 4.713553 TGTCTGCAACAAGTAATTCAGGA 58.286 39.130 0.00 0.00 34.03 3.86
3629 5672 5.396484 CATGTCTGCAACAAGTAATTCAGG 58.604 41.667 5.94 0.00 42.37 3.86
3630 5673 5.181811 TCCATGTCTGCAACAAGTAATTCAG 59.818 40.000 5.94 0.00 42.37 3.02
3631 5674 5.069318 TCCATGTCTGCAACAAGTAATTCA 58.931 37.500 5.94 0.00 42.37 2.57
3632 5675 5.627499 TCCATGTCTGCAACAAGTAATTC 57.373 39.130 5.94 0.00 42.37 2.17
3633 5676 5.477984 ACATCCATGTCTGCAACAAGTAATT 59.522 36.000 5.94 0.00 42.37 1.40
3634 5677 5.012239 ACATCCATGTCTGCAACAAGTAAT 58.988 37.500 5.94 0.00 42.37 1.89
3635 5678 4.397420 ACATCCATGTCTGCAACAAGTAA 58.603 39.130 5.94 0.00 42.37 2.24
3636 5679 4.019792 ACATCCATGTCTGCAACAAGTA 57.980 40.909 5.94 0.00 42.37 2.24
3637 5680 2.867624 ACATCCATGTCTGCAACAAGT 58.132 42.857 5.94 0.00 42.37 3.16
3638 5681 4.880120 AGATACATCCATGTCTGCAACAAG 59.120 41.667 5.94 2.56 42.37 3.16
3639 5682 4.847198 AGATACATCCATGTCTGCAACAA 58.153 39.130 5.94 0.00 42.37 2.83
3640 5683 4.492494 AGATACATCCATGTCTGCAACA 57.508 40.909 0.00 4.56 41.97 3.33
3641 5684 5.847304 TCTAGATACATCCATGTCTGCAAC 58.153 41.667 0.00 0.00 41.97 4.17
3642 5685 6.042437 ACATCTAGATACATCCATGTCTGCAA 59.958 38.462 4.54 0.00 41.97 4.08
3643 5686 5.541484 ACATCTAGATACATCCATGTCTGCA 59.459 40.000 4.54 0.00 41.97 4.41
3644 5687 6.035368 ACATCTAGATACATCCATGTCTGC 57.965 41.667 4.54 0.00 41.97 4.26
3674 5717 9.988815 GTCACATAAATGGATGTATCTAGAACT 57.011 33.333 0.00 0.00 37.99 3.01
3675 5718 9.764363 TGTCACATAAATGGATGTATCTAGAAC 57.236 33.333 0.00 0.00 37.99 3.01
3677 5720 9.987272 CTTGTCACATAAATGGATGTATCTAGA 57.013 33.333 0.00 0.00 37.99 2.43
3678 5721 9.770097 ACTTGTCACATAAATGGATGTATCTAG 57.230 33.333 0.00 0.00 37.99 2.43
3684 5727 8.397906 CGAATTACTTGTCACATAAATGGATGT 58.602 33.333 0.00 0.00 40.78 3.06
3685 5728 7.857389 CCGAATTACTTGTCACATAAATGGATG 59.143 37.037 0.00 0.00 0.00 3.51
3686 5729 7.013274 CCCGAATTACTTGTCACATAAATGGAT 59.987 37.037 0.00 0.00 0.00 3.41
3687 5730 6.317642 CCCGAATTACTTGTCACATAAATGGA 59.682 38.462 0.00 0.00 0.00 3.41
3688 5731 6.317642 TCCCGAATTACTTGTCACATAAATGG 59.682 38.462 0.00 0.00 0.00 3.16
3689 5732 7.186804 GTCCCGAATTACTTGTCACATAAATG 58.813 38.462 0.00 0.00 0.00 2.32
3690 5733 6.036735 CGTCCCGAATTACTTGTCACATAAAT 59.963 38.462 0.00 0.00 0.00 1.40
3691 5734 5.349270 CGTCCCGAATTACTTGTCACATAAA 59.651 40.000 0.00 0.00 0.00 1.40
3692 5735 4.865925 CGTCCCGAATTACTTGTCACATAA 59.134 41.667 0.00 0.00 0.00 1.90
3693 5736 4.158209 TCGTCCCGAATTACTTGTCACATA 59.842 41.667 0.00 0.00 31.06 2.29
3694 5737 3.056393 TCGTCCCGAATTACTTGTCACAT 60.056 43.478 0.00 0.00 31.06 3.21
3695 5738 2.296752 TCGTCCCGAATTACTTGTCACA 59.703 45.455 0.00 0.00 31.06 3.58
3696 5739 2.950433 TCGTCCCGAATTACTTGTCAC 58.050 47.619 0.00 0.00 31.06 3.67
3697 5740 3.581755 CTTCGTCCCGAATTACTTGTCA 58.418 45.455 0.00 0.00 44.85 3.58
3698 5741 2.928116 CCTTCGTCCCGAATTACTTGTC 59.072 50.000 0.00 0.00 44.85 3.18
3699 5742 2.301009 ACCTTCGTCCCGAATTACTTGT 59.699 45.455 0.00 0.00 44.85 3.16
3700 5743 2.968675 ACCTTCGTCCCGAATTACTTG 58.031 47.619 0.00 0.00 44.85 3.16
3701 5744 3.766051 ACTACCTTCGTCCCGAATTACTT 59.234 43.478 0.00 0.00 44.85 2.24
3702 5745 3.359950 ACTACCTTCGTCCCGAATTACT 58.640 45.455 0.00 0.00 44.85 2.24
3703 5746 3.790152 ACTACCTTCGTCCCGAATTAC 57.210 47.619 0.00 0.00 44.85 1.89
3704 5747 4.704540 TGTTACTACCTTCGTCCCGAATTA 59.295 41.667 0.00 0.00 44.85 1.40
3705 5748 3.511146 TGTTACTACCTTCGTCCCGAATT 59.489 43.478 0.00 0.00 44.85 2.17
3706 5749 3.091545 TGTTACTACCTTCGTCCCGAAT 58.908 45.455 0.00 0.00 44.85 3.34
3707 5750 2.513753 TGTTACTACCTTCGTCCCGAA 58.486 47.619 0.00 0.00 43.75 4.30
3708 5751 2.198827 TGTTACTACCTTCGTCCCGA 57.801 50.000 0.00 0.00 0.00 5.14
3709 5752 2.989166 GTTTGTTACTACCTTCGTCCCG 59.011 50.000 0.00 0.00 0.00 5.14
3710 5753 3.993920 TGTTTGTTACTACCTTCGTCCC 58.006 45.455 0.00 0.00 0.00 4.46
3711 5754 6.549912 AATTGTTTGTTACTACCTTCGTCC 57.450 37.500 0.00 0.00 0.00 4.79
3725 5768 9.326413 CGGAAGGAGAACTATATAATTGTTTGT 57.674 33.333 0.00 0.00 0.00 2.83
3726 5769 9.326413 ACGGAAGGAGAACTATATAATTGTTTG 57.674 33.333 0.00 0.00 0.00 2.93
3727 5770 9.901172 AACGGAAGGAGAACTATATAATTGTTT 57.099 29.630 0.00 0.00 0.00 2.83
3728 5771 9.543783 GAACGGAAGGAGAACTATATAATTGTT 57.456 33.333 0.00 0.00 0.00 2.83
3729 5772 8.701895 TGAACGGAAGGAGAACTATATAATTGT 58.298 33.333 0.00 0.00 0.00 2.71
3730 5773 8.979574 GTGAACGGAAGGAGAACTATATAATTG 58.020 37.037 0.00 0.00 0.00 2.32
3731 5774 8.701895 TGTGAACGGAAGGAGAACTATATAATT 58.298 33.333 0.00 0.00 0.00 1.40
3732 5775 8.246430 TGTGAACGGAAGGAGAACTATATAAT 57.754 34.615 0.00 0.00 0.00 1.28
3733 5776 7.649533 TGTGAACGGAAGGAGAACTATATAA 57.350 36.000 0.00 0.00 0.00 0.98
3734 5777 7.649533 TTGTGAACGGAAGGAGAACTATATA 57.350 36.000 0.00 0.00 0.00 0.86
3735 5778 6.540438 TTGTGAACGGAAGGAGAACTATAT 57.460 37.500 0.00 0.00 0.00 0.86
3736 5779 5.988310 TTGTGAACGGAAGGAGAACTATA 57.012 39.130 0.00 0.00 0.00 1.31
3737 5780 4.884668 TTGTGAACGGAAGGAGAACTAT 57.115 40.909 0.00 0.00 0.00 2.12
3738 5781 4.675976 TTTGTGAACGGAAGGAGAACTA 57.324 40.909 0.00 0.00 0.00 2.24
3739 5782 3.553828 TTTGTGAACGGAAGGAGAACT 57.446 42.857 0.00 0.00 0.00 3.01
3740 5783 7.548075 TCTTATATTTGTGAACGGAAGGAGAAC 59.452 37.037 0.00 0.00 0.00 3.01
3741 5784 7.617225 TCTTATATTTGTGAACGGAAGGAGAA 58.383 34.615 0.00 0.00 0.00 2.87
3742 5785 7.177832 TCTTATATTTGTGAACGGAAGGAGA 57.822 36.000 0.00 0.00 0.00 3.71
3743 5786 7.495934 ACATCTTATATTTGTGAACGGAAGGAG 59.504 37.037 0.00 0.00 0.00 3.69
3744 5787 7.335627 ACATCTTATATTTGTGAACGGAAGGA 58.664 34.615 0.00 0.00 0.00 3.36
3745 5788 7.553881 ACATCTTATATTTGTGAACGGAAGG 57.446 36.000 0.00 0.00 0.00 3.46
3746 5789 8.883731 AGAACATCTTATATTTGTGAACGGAAG 58.116 33.333 0.00 0.00 0.00 3.46
3747 5790 8.786826 AGAACATCTTATATTTGTGAACGGAA 57.213 30.769 0.00 0.00 0.00 4.30
3748 5791 9.529325 CTAGAACATCTTATATTTGTGAACGGA 57.471 33.333 0.00 0.00 0.00 4.69
3749 5792 8.276325 GCTAGAACATCTTATATTTGTGAACGG 58.724 37.037 0.00 0.00 0.00 4.44
3750 5793 9.035607 AGCTAGAACATCTTATATTTGTGAACG 57.964 33.333 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.