Multiple sequence alignment - TraesCS3A01G151800

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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 TraesCS3A01G151800 chr3A 100.000 3062 0 0 1 3062 141909154 141912215 0.000000e+00 5655
1 TraesCS3A01G151800 chr3D 95.528 2102 56 14 634 2728 129396835 129398905 0.000000e+00 3326
2 TraesCS3A01G151800 chr3D 83.158 665 77 17 1 639 129394840 129395495 2.650000e-160 575
3 TraesCS3A01G151800 chr3B 90.473 2582 147 40 1 2559 183541680 183544185 0.000000e+00 3314
4 TraesCS3A01G151800 chr3B 79.898 587 85 21 6 567 732847623 732847045 1.710000e-107 399
5 TraesCS3A01G151800 chr3B 92.683 82 6 0 2542 2623 183544199 183544280 5.360000e-23 119
6 TraesCS3A01G151800 chr5B 81.385 462 75 9 6 463 504812721 504813175 1.730000e-97 366
7 TraesCS3A01G151800 chr7A 81.087 460 78 8 11 463 192846348 192846805 2.900000e-95 359
8 TraesCS3A01G151800 chr5D 80.632 475 82 9 10 477 438042656 438042185 2.900000e-95 359
9 TraesCS3A01G151800 chr5A 78.253 584 97 22 11 567 426572687 426572107 6.280000e-92 348
10 TraesCS3A01G151800 chr1D 80.086 467 87 5 6 469 427156601 427156138 2.920000e-90 342
11 TraesCS3A01G151800 chr6B 79.493 473 85 10 5 471 187957042 187957508 2.940000e-85 326


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 TraesCS3A01G151800 chr3A 141909154 141912215 3061 False 5655.0 5655 100.000 1 3062 1 chr3A.!!$F1 3061
1 TraesCS3A01G151800 chr3D 129394840 129398905 4065 False 1950.5 3326 89.343 1 2728 2 chr3D.!!$F1 2727
2 TraesCS3A01G151800 chr3B 183541680 183544280 2600 False 1716.5 3314 91.578 1 2623 2 chr3B.!!$F1 2622
3 TraesCS3A01G151800 chr3B 732847045 732847623 578 True 399.0 399 79.898 6 567 1 chr3B.!!$R1 561
4 TraesCS3A01G151800 chr5A 426572107 426572687 580 True 348.0 348 78.253 11 567 1 chr5A.!!$R1 556

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
444 459 0.179043 TACGACTTTGCTGGTTGCCA 60.179 50.0 0.0 0.0 42.0 4.92 F
1005 2391 0.029567 CGACTGAGCTACCGATGGAC 59.970 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 2658 2.437180 TCGCGGCGAGAAGAGGTA 60.437 61.111 22.69 0.0 0.0 3.08 R
2735 4171 1.408969 TTGGGCCCAAGTTCAGAAAC 58.591 50.000 34.07 0.0 35.5 2.78 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
69 70 2.795231 ACATGAGTGACTTCCATGGG 57.205 50.000 13.02 0.00 41.28 4.00
82 83 0.251916 CCATGGGGTTGCTACTCGAA 59.748 55.000 2.85 0.00 0.00 3.71
153 156 5.424757 GTTATACCTGGCAATGGCGATATA 58.575 41.667 1.51 1.84 42.47 0.86
170 173 7.809331 TGGCGATATATTTTCTTACGTCGTTAT 59.191 33.333 1.78 0.00 0.00 1.89
190 193 7.763985 TCGTTATCTTATTGAAGACATTGCTCA 59.236 33.333 0.00 0.00 44.50 4.26
253 257 0.616371 CCTTGTGGTTGGATCCGGTA 59.384 55.000 7.39 0.00 0.00 4.02
257 261 1.909986 TGTGGTTGGATCCGGTAATGA 59.090 47.619 7.39 0.00 0.00 2.57
296 304 2.832672 CCTTCTAAAGGCGTTGATGC 57.167 50.000 0.00 0.00 42.78 3.91
301 309 3.407698 TCTAAAGGCGTTGATGCTGAAA 58.592 40.909 0.00 0.00 34.52 2.69
339 347 2.909662 TGGTGTCATGAGATGGTTGGTA 59.090 45.455 0.00 0.00 0.00 3.25
342 351 2.505407 TGTCATGAGATGGTTGGTAGGG 59.495 50.000 0.00 0.00 0.00 3.53
371 380 6.183360 GGTCATTACTCTAGTTTGTCGATCCT 60.183 42.308 0.00 0.00 0.00 3.24
422 437 1.000506 GTCTACGCAGGACTTTGGTCA 59.999 52.381 0.00 0.00 43.77 4.02
437 452 5.351465 ACTTTGGTCATATACGACTTTGCTG 59.649 40.000 0.00 0.00 36.12 4.41
444 459 0.179043 TACGACTTTGCTGGTTGCCA 60.179 50.000 0.00 0.00 42.00 4.92
463 478 1.716581 CAACGTGTTTTTGCGTGTGTT 59.283 42.857 0.00 0.00 41.42 3.32
473 488 3.773860 TTGCGTGTGTTTGAGTTGATT 57.226 38.095 0.00 0.00 0.00 2.57
480 512 7.385478 TGCGTGTGTTTGAGTTGATTTAGTATA 59.615 33.333 0.00 0.00 0.00 1.47
481 513 8.388103 GCGTGTGTTTGAGTTGATTTAGTATAT 58.612 33.333 0.00 0.00 0.00 0.86
514 546 7.798516 CGGATGTTTGCTCATTGTATTATGTAC 59.201 37.037 0.00 0.00 0.00 2.90
515 547 8.840321 GGATGTTTGCTCATTGTATTATGTACT 58.160 33.333 0.00 0.00 0.00 2.73
540 575 3.232213 TGATGCTCCGTTTGAGTCTAC 57.768 47.619 0.00 0.00 43.48 2.59
551 586 5.929992 CCGTTTGAGTCTACAAAATCCACTA 59.070 40.000 0.00 0.00 40.62 2.74
558 593 8.154203 TGAGTCTACAAAATCCACTATTTGTCA 58.846 33.333 7.11 0.00 44.16 3.58
559 594 8.553459 AGTCTACAAAATCCACTATTTGTCAG 57.447 34.615 7.11 4.96 44.16 3.51
570 605 7.054124 TCCACTATTTGTCAGAAAAGAACAGT 58.946 34.615 0.00 0.00 0.00 3.55
585 621 3.673809 AGAACAGTCAGTAATTCGTTCGC 59.326 43.478 0.00 0.00 38.18 4.70
586 622 2.334838 ACAGTCAGTAATTCGTTCGCC 58.665 47.619 0.00 0.00 0.00 5.54
620 656 6.879367 TCATATCTGGAATGCTGGATGATA 57.121 37.500 0.00 0.00 0.00 2.15
630 666 4.128925 TGCTGGATGATAACTCAGTGAC 57.871 45.455 0.00 0.00 34.12 3.67
692 2073 2.782163 CATGATTTGCTCAGTGCTTCG 58.218 47.619 0.00 0.00 43.37 3.79
716 2101 4.876107 GTGTCAGTGATTCCATAACCGAAT 59.124 41.667 0.00 0.00 32.62 3.34
807 2193 7.201487 CCTTGATTAATAATTCGTCACGTGACA 60.201 37.037 39.14 26.15 44.99 3.58
856 2242 0.526211 TAGTGTACTGGCAGCTCACG 59.474 55.000 25.54 2.88 34.71 4.35
907 2293 1.924731 CTCCATCTCCCACGGCTATA 58.075 55.000 0.00 0.00 0.00 1.31
908 2294 2.461695 CTCCATCTCCCACGGCTATAT 58.538 52.381 0.00 0.00 0.00 0.86
909 2295 3.632333 CTCCATCTCCCACGGCTATATA 58.368 50.000 0.00 0.00 0.00 0.86
910 2296 4.219115 CTCCATCTCCCACGGCTATATAT 58.781 47.826 0.00 0.00 0.00 0.86
911 2297 5.386060 CTCCATCTCCCACGGCTATATATA 58.614 45.833 0.00 0.00 0.00 0.86
912 2298 5.773091 TCCATCTCCCACGGCTATATATAA 58.227 41.667 0.00 0.00 0.00 0.98
913 2299 5.597182 TCCATCTCCCACGGCTATATATAAC 59.403 44.000 0.00 0.00 0.00 1.89
921 2307 9.423964 TCCCACGGCTATATATAACATATAACA 57.576 33.333 0.00 0.00 0.00 2.41
986 2372 3.414700 CGGCGTCAAGTGAGCACC 61.415 66.667 0.00 0.00 0.00 5.01
999 2385 2.202623 GCACCGACTGAGCTACCG 60.203 66.667 0.00 0.00 0.00 4.02
1005 2391 0.029567 CGACTGAGCTACCGATGGAC 59.970 60.000 0.00 0.00 0.00 4.02
1011 2397 1.598130 GCTACCGATGGACCATGGC 60.598 63.158 12.99 4.47 0.00 4.40
1131 2526 1.231928 GACCTCCTCCTCCTCCTCC 59.768 68.421 0.00 0.00 0.00 4.30
1263 2658 1.965219 CGACAGGGACTCGTTCCTT 59.035 57.895 0.00 0.00 45.09 3.36
1296 2691 1.153901 CGACTACGCCACCATCGTT 60.154 57.895 0.00 0.00 40.89 3.85
1439 2834 0.036875 AAAAAGAGCCCTCTCCACGG 59.963 55.000 0.00 0.00 39.39 4.94
1440 2835 2.470938 AAAAGAGCCCTCTCCACGGC 62.471 60.000 0.00 0.00 46.09 5.68
1542 2937 1.374758 CTTCAGCACCTCGGACACC 60.375 63.158 0.00 0.00 0.00 4.16
2097 3495 2.159170 GGCTATCCACTCACTCACTCAC 60.159 54.545 0.00 0.00 0.00 3.51
2098 3496 2.757868 GCTATCCACTCACTCACTCACT 59.242 50.000 0.00 0.00 0.00 3.41
2099 3497 3.181491 GCTATCCACTCACTCACTCACTC 60.181 52.174 0.00 0.00 0.00 3.51
2100 3498 2.364972 TCCACTCACTCACTCACTCA 57.635 50.000 0.00 0.00 0.00 3.41
2265 3667 5.127356 GGTTCTGCTGTAATGTACTCCTAGT 59.873 44.000 0.00 0.00 0.00 2.57
2266 3668 6.320672 GGTTCTGCTGTAATGTACTCCTAGTA 59.679 42.308 0.00 0.00 0.00 1.82
2350 3752 2.305009 GGATTCAGATTTGGCCAGAGG 58.695 52.381 5.11 0.00 0.00 3.69
2467 3869 2.491770 TTTGCGCTTCCCCTGCCATA 62.492 55.000 9.73 0.00 0.00 2.74
2476 3878 0.986019 CCCCTGCCATACCACCACTA 60.986 60.000 0.00 0.00 0.00 2.74
2481 3883 1.277842 TGCCATACCACCACTACACTG 59.722 52.381 0.00 0.00 0.00 3.66
2503 3905 2.279935 TTACCCTTTGTGTCGGCAAT 57.720 45.000 0.00 0.00 0.00 3.56
2537 3942 2.240500 GGATGCTCGCCATGTCGAC 61.241 63.158 9.11 9.11 33.29 4.20
2546 3982 2.991190 TCGCCATGTCGACTTTAAAGAC 59.009 45.455 21.92 14.39 33.02 3.01
2547 3983 2.734606 CGCCATGTCGACTTTAAAGACA 59.265 45.455 21.92 15.39 46.99 3.41
2572 4008 1.878953 ATAATCGTTCATCGGTGCCC 58.121 50.000 0.00 0.00 40.32 5.36
2632 4068 9.148104 ACGTATCATGTAGACTTAACCTTTTTC 57.852 33.333 0.00 0.00 0.00 2.29
2633 4069 9.146984 CGTATCATGTAGACTTAACCTTTTTCA 57.853 33.333 0.00 0.00 0.00 2.69
2675 4111 8.849490 CATGGTTAAACAATGAGTAACATTTCG 58.151 33.333 0.00 0.00 45.60 3.46
2677 4113 6.307077 GGTTAAACAATGAGTAACATTTCGCC 59.693 38.462 10.97 0.00 45.60 5.54
2681 4117 6.751514 ACAATGAGTAACATTTCGCCAATA 57.248 33.333 0.00 0.00 45.60 1.90
2682 4118 6.785191 ACAATGAGTAACATTTCGCCAATAG 58.215 36.000 0.00 0.00 45.60 1.73
2683 4119 6.597672 ACAATGAGTAACATTTCGCCAATAGA 59.402 34.615 0.00 0.00 45.60 1.98
2684 4120 7.120579 ACAATGAGTAACATTTCGCCAATAGAA 59.879 33.333 0.00 0.00 45.60 2.10
2752 4188 3.439440 AGTTTCTGAACTTGGGCCC 57.561 52.632 17.59 17.59 43.48 5.80
2753 4189 0.555769 AGTTTCTGAACTTGGGCCCA 59.444 50.000 24.45 24.45 43.48 5.36
2754 4190 1.063266 AGTTTCTGAACTTGGGCCCAA 60.063 47.619 34.90 34.90 43.48 4.12
2755 4191 1.970640 GTTTCTGAACTTGGGCCCAAT 59.029 47.619 37.10 24.30 35.20 3.16
2756 4192 3.161866 GTTTCTGAACTTGGGCCCAATA 58.838 45.455 37.10 21.42 35.20 1.90
2757 4193 3.756082 TTCTGAACTTGGGCCCAATAT 57.244 42.857 37.10 27.48 35.20 1.28
2758 4194 3.297134 TCTGAACTTGGGCCCAATATC 57.703 47.619 37.10 32.69 35.20 1.63
2759 4195 2.091885 TCTGAACTTGGGCCCAATATCC 60.092 50.000 37.10 24.36 35.20 2.59
2760 4196 1.643286 TGAACTTGGGCCCAATATCCA 59.357 47.619 37.10 26.43 35.20 3.41
2761 4197 2.247111 TGAACTTGGGCCCAATATCCAT 59.753 45.455 37.10 18.86 35.20 3.41
2762 4198 3.308401 GAACTTGGGCCCAATATCCATT 58.692 45.455 37.10 22.30 35.20 3.16
2763 4199 3.419732 ACTTGGGCCCAATATCCATTT 57.580 42.857 37.10 11.35 35.20 2.32
2764 4200 3.734926 ACTTGGGCCCAATATCCATTTT 58.265 40.909 37.10 10.31 35.20 1.82
2765 4201 4.110824 ACTTGGGCCCAATATCCATTTTT 58.889 39.130 37.10 8.79 35.20 1.94
2766 4202 4.164030 ACTTGGGCCCAATATCCATTTTTC 59.836 41.667 37.10 0.00 35.20 2.29
2767 4203 4.006247 TGGGCCCAATATCCATTTTTCT 57.994 40.909 26.33 0.00 0.00 2.52
2768 4204 5.149584 TGGGCCCAATATCCATTTTTCTA 57.850 39.130 26.33 0.00 0.00 2.10
2769 4205 4.898861 TGGGCCCAATATCCATTTTTCTAC 59.101 41.667 26.33 0.00 0.00 2.59
2770 4206 4.283467 GGGCCCAATATCCATTTTTCTACC 59.717 45.833 19.95 0.00 0.00 3.18
2771 4207 4.283467 GGCCCAATATCCATTTTTCTACCC 59.717 45.833 0.00 0.00 0.00 3.69
2772 4208 4.022329 GCCCAATATCCATTTTTCTACCCG 60.022 45.833 0.00 0.00 0.00 5.28
2773 4209 5.381757 CCCAATATCCATTTTTCTACCCGA 58.618 41.667 0.00 0.00 0.00 5.14
2774 4210 5.473504 CCCAATATCCATTTTTCTACCCGAG 59.526 44.000 0.00 0.00 0.00 4.63
2775 4211 5.048713 CCAATATCCATTTTTCTACCCGAGC 60.049 44.000 0.00 0.00 0.00 5.03
2776 4212 3.933861 ATCCATTTTTCTACCCGAGCT 57.066 42.857 0.00 0.00 0.00 4.09
2777 4213 3.713826 TCCATTTTTCTACCCGAGCTT 57.286 42.857 0.00 0.00 0.00 3.74
2778 4214 4.829872 TCCATTTTTCTACCCGAGCTTA 57.170 40.909 0.00 0.00 0.00 3.09
2779 4215 5.367945 TCCATTTTTCTACCCGAGCTTAT 57.632 39.130 0.00 0.00 0.00 1.73
2780 4216 5.365619 TCCATTTTTCTACCCGAGCTTATC 58.634 41.667 0.00 0.00 0.00 1.75
2781 4217 5.130477 TCCATTTTTCTACCCGAGCTTATCT 59.870 40.000 0.00 0.00 0.00 1.98
2782 4218 5.237344 CCATTTTTCTACCCGAGCTTATCTG 59.763 44.000 0.00 0.00 0.00 2.90
2783 4219 5.670792 TTTTTCTACCCGAGCTTATCTGA 57.329 39.130 0.00 0.00 0.00 3.27
2784 4220 5.871396 TTTTCTACCCGAGCTTATCTGAT 57.129 39.130 0.00 0.00 0.00 2.90
2785 4221 5.455056 TTTCTACCCGAGCTTATCTGATC 57.545 43.478 0.00 0.00 0.00 2.92
2786 4222 4.374689 TCTACCCGAGCTTATCTGATCT 57.625 45.455 0.00 0.00 0.00 2.75
2787 4223 4.328536 TCTACCCGAGCTTATCTGATCTC 58.671 47.826 0.00 0.00 0.00 2.75
2788 4224 1.883275 ACCCGAGCTTATCTGATCTCG 59.117 52.381 16.10 16.10 45.50 4.04
2795 4231 5.767269 GAGCTTATCTGATCTCGATGAACA 58.233 41.667 0.00 0.00 0.00 3.18
2796 4232 5.771469 AGCTTATCTGATCTCGATGAACAG 58.229 41.667 12.65 12.65 44.06 3.16
2797 4233 5.301551 AGCTTATCTGATCTCGATGAACAGT 59.698 40.000 16.05 9.85 43.43 3.55
2798 4234 5.982516 GCTTATCTGATCTCGATGAACAGTT 59.017 40.000 16.05 12.52 43.43 3.16
2799 4235 7.013750 AGCTTATCTGATCTCGATGAACAGTTA 59.986 37.037 16.05 11.86 43.43 2.24
2800 4236 7.649705 GCTTATCTGATCTCGATGAACAGTTAA 59.350 37.037 16.05 15.97 43.43 2.01
2801 4237 9.689976 CTTATCTGATCTCGATGAACAGTTAAT 57.310 33.333 16.05 9.23 43.43 1.40
2855 4291 6.892658 TTTTTAGGAAGATGTTTAGCTGCA 57.107 33.333 1.02 0.00 0.00 4.41
2856 4292 7.466746 TTTTTAGGAAGATGTTTAGCTGCAT 57.533 32.000 1.02 0.00 0.00 3.96
2857 4293 6.441093 TTTAGGAAGATGTTTAGCTGCATG 57.559 37.500 1.02 0.00 0.00 4.06
2858 4294 4.226427 AGGAAGATGTTTAGCTGCATGA 57.774 40.909 1.02 0.00 0.00 3.07
2859 4295 4.197750 AGGAAGATGTTTAGCTGCATGAG 58.802 43.478 1.02 0.00 0.00 2.90
2860 4296 3.314635 GGAAGATGTTTAGCTGCATGAGG 59.685 47.826 1.02 0.00 0.00 3.86
2861 4297 3.641434 AGATGTTTAGCTGCATGAGGT 57.359 42.857 1.02 0.00 36.09 3.85
2862 4298 4.760530 AGATGTTTAGCTGCATGAGGTA 57.239 40.909 1.02 0.00 33.31 3.08
2863 4299 5.301835 AGATGTTTAGCTGCATGAGGTAT 57.698 39.130 1.02 0.00 34.59 2.73
2864 4300 5.061853 AGATGTTTAGCTGCATGAGGTATG 58.938 41.667 1.02 0.00 39.88 2.39
2865 4301 4.220693 TGTTTAGCTGCATGAGGTATGT 57.779 40.909 1.02 0.00 39.08 2.29
2866 4302 4.588899 TGTTTAGCTGCATGAGGTATGTT 58.411 39.130 1.02 0.00 39.08 2.71
2867 4303 5.009631 TGTTTAGCTGCATGAGGTATGTTT 58.990 37.500 1.02 0.00 39.08 2.83
2868 4304 5.123820 TGTTTAGCTGCATGAGGTATGTTTC 59.876 40.000 1.02 0.00 39.08 2.78
2869 4305 3.354948 AGCTGCATGAGGTATGTTTCA 57.645 42.857 1.02 0.00 39.08 2.69
2870 4306 3.689347 AGCTGCATGAGGTATGTTTCAA 58.311 40.909 1.02 0.00 39.08 2.69
2871 4307 4.275810 AGCTGCATGAGGTATGTTTCAAT 58.724 39.130 1.02 0.00 39.08 2.57
2872 4308 4.708421 AGCTGCATGAGGTATGTTTCAATT 59.292 37.500 1.02 0.00 39.08 2.32
2873 4309 5.186409 AGCTGCATGAGGTATGTTTCAATTT 59.814 36.000 1.02 0.00 39.08 1.82
2874 4310 5.870978 GCTGCATGAGGTATGTTTCAATTTT 59.129 36.000 0.00 0.00 39.08 1.82
2875 4311 6.035327 GCTGCATGAGGTATGTTTCAATTTTC 59.965 38.462 0.00 0.00 39.08 2.29
2876 4312 6.990798 TGCATGAGGTATGTTTCAATTTTCA 58.009 32.000 0.00 0.00 39.08 2.69
2877 4313 7.092079 TGCATGAGGTATGTTTCAATTTTCAG 58.908 34.615 0.00 0.00 39.08 3.02
2878 4314 6.035327 GCATGAGGTATGTTTCAATTTTCAGC 59.965 38.462 0.00 0.00 39.08 4.26
2879 4315 5.698832 TGAGGTATGTTTCAATTTTCAGCG 58.301 37.500 0.00 0.00 0.00 5.18
2880 4316 5.240623 TGAGGTATGTTTCAATTTTCAGCGT 59.759 36.000 0.00 0.00 0.00 5.07
2881 4317 5.460646 AGGTATGTTTCAATTTTCAGCGTG 58.539 37.500 0.00 0.00 0.00 5.34
2882 4318 5.009610 AGGTATGTTTCAATTTTCAGCGTGT 59.990 36.000 0.00 0.00 0.00 4.49
2883 4319 5.689961 GGTATGTTTCAATTTTCAGCGTGTT 59.310 36.000 0.00 0.00 0.00 3.32
2884 4320 6.200097 GGTATGTTTCAATTTTCAGCGTGTTT 59.800 34.615 0.00 0.00 0.00 2.83
2885 4321 5.447478 TGTTTCAATTTTCAGCGTGTTTG 57.553 34.783 0.00 0.00 0.00 2.93
2886 4322 4.328440 TGTTTCAATTTTCAGCGTGTTTGG 59.672 37.500 0.00 0.00 0.00 3.28
2887 4323 4.377839 TTCAATTTTCAGCGTGTTTGGA 57.622 36.364 0.00 0.00 0.00 3.53
2888 4324 3.701241 TCAATTTTCAGCGTGTTTGGAC 58.299 40.909 0.00 0.00 0.00 4.02
2889 4325 3.129462 TCAATTTTCAGCGTGTTTGGACA 59.871 39.130 0.00 0.00 0.00 4.02
2890 4326 4.050553 CAATTTTCAGCGTGTTTGGACAT 58.949 39.130 0.00 0.00 38.23 3.06
2891 4327 3.791973 TTTTCAGCGTGTTTGGACATT 57.208 38.095 0.00 0.00 38.23 2.71
2892 4328 3.791973 TTTCAGCGTGTTTGGACATTT 57.208 38.095 0.00 0.00 38.23 2.32
2893 4329 2.772568 TCAGCGTGTTTGGACATTTG 57.227 45.000 0.00 0.00 38.23 2.32
2894 4330 2.293170 TCAGCGTGTTTGGACATTTGA 58.707 42.857 0.00 0.00 38.23 2.69
2895 4331 2.290367 TCAGCGTGTTTGGACATTTGAG 59.710 45.455 0.00 0.00 38.23 3.02
2896 4332 2.033299 CAGCGTGTTTGGACATTTGAGT 59.967 45.455 0.00 0.00 38.23 3.41
2897 4333 3.249799 CAGCGTGTTTGGACATTTGAGTA 59.750 43.478 0.00 0.00 38.23 2.59
2898 4334 3.498397 AGCGTGTTTGGACATTTGAGTAG 59.502 43.478 0.00 0.00 38.23 2.57
2899 4335 3.810373 CGTGTTTGGACATTTGAGTAGC 58.190 45.455 0.00 0.00 38.23 3.58
2900 4336 3.498397 CGTGTTTGGACATTTGAGTAGCT 59.502 43.478 0.00 0.00 38.23 3.32
2901 4337 4.377431 CGTGTTTGGACATTTGAGTAGCTC 60.377 45.833 0.00 0.00 38.23 4.09
2902 4338 4.072131 TGTTTGGACATTTGAGTAGCTCC 58.928 43.478 0.00 0.00 0.00 4.70
2903 4339 3.350219 TTGGACATTTGAGTAGCTCCC 57.650 47.619 0.00 0.00 0.00 4.30
2904 4340 2.265367 TGGACATTTGAGTAGCTCCCA 58.735 47.619 0.00 0.00 0.00 4.37
2905 4341 2.237143 TGGACATTTGAGTAGCTCCCAG 59.763 50.000 0.00 0.00 0.00 4.45
2906 4342 2.284190 GACATTTGAGTAGCTCCCAGC 58.716 52.381 0.00 0.00 42.84 4.85
2907 4343 1.630369 ACATTTGAGTAGCTCCCAGCA 59.370 47.619 0.00 0.00 45.56 4.41
2908 4344 2.040278 ACATTTGAGTAGCTCCCAGCAA 59.960 45.455 0.00 0.00 45.56 3.91
2909 4345 2.949177 TTTGAGTAGCTCCCAGCAAA 57.051 45.000 0.00 0.00 45.56 3.68
2910 4346 2.949177 TTGAGTAGCTCCCAGCAAAA 57.051 45.000 0.00 0.00 45.56 2.44
2911 4347 2.949177 TGAGTAGCTCCCAGCAAAAA 57.051 45.000 0.00 0.00 45.56 1.94
2932 4368 5.365403 AAAAACTCGGTTCGAATATTGCA 57.635 34.783 0.00 0.00 34.74 4.08
2933 4369 4.336532 AAACTCGGTTCGAATATTGCAC 57.663 40.909 0.00 0.00 34.74 4.57
2934 4370 2.967362 ACTCGGTTCGAATATTGCACA 58.033 42.857 0.00 0.00 34.74 4.57
2935 4371 3.331150 ACTCGGTTCGAATATTGCACAA 58.669 40.909 0.00 0.00 34.74 3.33
2936 4372 3.749088 ACTCGGTTCGAATATTGCACAAA 59.251 39.130 0.00 0.00 34.74 2.83
2937 4373 4.073169 TCGGTTCGAATATTGCACAAAC 57.927 40.909 0.00 0.00 31.06 2.93
2938 4374 3.498777 TCGGTTCGAATATTGCACAAACA 59.501 39.130 0.00 0.00 31.06 2.83
2939 4375 4.023963 TCGGTTCGAATATTGCACAAACAA 60.024 37.500 0.00 0.00 31.06 2.83
2940 4376 4.856487 CGGTTCGAATATTGCACAAACAAT 59.144 37.500 0.00 0.00 42.73 2.71
2941 4377 6.024664 CGGTTCGAATATTGCACAAACAATA 58.975 36.000 0.00 0.00 44.36 1.90
2942 4378 6.524933 CGGTTCGAATATTGCACAAACAATAA 59.475 34.615 0.00 0.00 43.68 1.40
2943 4379 7.061210 CGGTTCGAATATTGCACAAACAATAAA 59.939 33.333 0.00 0.00 43.68 1.40
2944 4380 8.159709 GGTTCGAATATTGCACAAACAATAAAC 58.840 33.333 0.00 2.34 43.68 2.01
2945 4381 8.911662 GTTCGAATATTGCACAAACAATAAACT 58.088 29.630 0.00 0.00 43.68 2.66
2946 4382 9.469807 TTCGAATATTGCACAAACAATAAACTT 57.530 25.926 0.00 0.00 43.68 2.66
2947 4383 9.469807 TCGAATATTGCACAAACAATAAACTTT 57.530 25.926 0.00 0.00 43.68 2.66
2952 4388 5.790547 TGCACAAACAATAAACTTTTTCGC 58.209 33.333 0.00 0.00 0.00 4.70
2953 4389 5.348724 TGCACAAACAATAAACTTTTTCGCA 59.651 32.000 0.00 0.00 0.00 5.10
2954 4390 5.895889 GCACAAACAATAAACTTTTTCGCAG 59.104 36.000 0.00 0.00 0.00 5.18
2955 4391 6.237701 GCACAAACAATAAACTTTTTCGCAGA 60.238 34.615 0.00 0.00 0.00 4.26
2956 4392 7.110511 CACAAACAATAAACTTTTTCGCAGAC 58.889 34.615 0.00 0.00 34.32 3.51
2957 4393 6.254804 ACAAACAATAAACTTTTTCGCAGACC 59.745 34.615 0.00 0.00 34.32 3.85
2958 4394 4.866921 ACAATAAACTTTTTCGCAGACCC 58.133 39.130 0.00 0.00 34.32 4.46
2959 4395 4.583073 ACAATAAACTTTTTCGCAGACCCT 59.417 37.500 0.00 0.00 34.32 4.34
2960 4396 5.154222 CAATAAACTTTTTCGCAGACCCTC 58.846 41.667 0.00 0.00 34.32 4.30
2961 4397 2.341846 AACTTTTTCGCAGACCCTCA 57.658 45.000 0.00 0.00 34.32 3.86
2962 4398 2.341846 ACTTTTTCGCAGACCCTCAA 57.658 45.000 0.00 0.00 34.32 3.02
2963 4399 2.863809 ACTTTTTCGCAGACCCTCAAT 58.136 42.857 0.00 0.00 34.32 2.57
2964 4400 3.222603 ACTTTTTCGCAGACCCTCAATT 58.777 40.909 0.00 0.00 34.32 2.32
2965 4401 3.636764 ACTTTTTCGCAGACCCTCAATTT 59.363 39.130 0.00 0.00 34.32 1.82
2966 4402 4.099419 ACTTTTTCGCAGACCCTCAATTTT 59.901 37.500 0.00 0.00 34.32 1.82
2967 4403 4.664150 TTTTCGCAGACCCTCAATTTTT 57.336 36.364 0.00 0.00 34.32 1.94
2994 4430 6.338214 TGATAGCTAATCAGATGTCCAGAC 57.662 41.667 0.00 0.00 39.77 3.51
2995 4431 5.835280 TGATAGCTAATCAGATGTCCAGACA 59.165 40.000 2.42 2.42 41.64 3.41
2996 4432 6.496218 TGATAGCTAATCAGATGTCCAGACAT 59.504 38.462 12.98 12.98 45.58 3.06
2997 4433 6.812656 GATAGCTAATCAGATGTCCAGACATG 59.187 42.308 17.67 6.54 41.86 3.21
2998 4434 7.309683 GATAGCTAATCAGATGTCCAGACATGA 60.310 40.741 17.67 11.62 41.86 3.07
3008 4444 5.648178 TGTCCAGACATGATGAAAATTGG 57.352 39.130 0.00 0.00 36.21 3.16
3009 4445 5.078949 TGTCCAGACATGATGAAAATTGGT 58.921 37.500 0.00 0.00 36.21 3.67
3010 4446 6.244654 TGTCCAGACATGATGAAAATTGGTA 58.755 36.000 0.00 0.00 36.21 3.25
3011 4447 6.891361 TGTCCAGACATGATGAAAATTGGTAT 59.109 34.615 0.00 0.00 36.21 2.73
3012 4448 7.148035 TGTCCAGACATGATGAAAATTGGTATG 60.148 37.037 0.00 0.00 36.21 2.39
3013 4449 7.067372 GTCCAGACATGATGAAAATTGGTATGA 59.933 37.037 0.00 0.00 0.00 2.15
3014 4450 7.614974 TCCAGACATGATGAAAATTGGTATGAA 59.385 33.333 0.00 0.00 0.00 2.57
3015 4451 7.703621 CCAGACATGATGAAAATTGGTATGAAC 59.296 37.037 0.00 0.00 0.00 3.18
3016 4452 8.245491 CAGACATGATGAAAATTGGTATGAACA 58.755 33.333 0.00 0.00 0.00 3.18
3017 4453 8.974238 AGACATGATGAAAATTGGTATGAACAT 58.026 29.630 0.00 0.00 0.00 2.71
3018 4454 9.241317 GACATGATGAAAATTGGTATGAACATC 57.759 33.333 0.00 0.00 35.13 3.06
3019 4455 8.751242 ACATGATGAAAATTGGTATGAACATCA 58.249 29.630 0.00 0.00 43.89 3.07
3020 4456 9.027129 CATGATGAAAATTGGTATGAACATCAC 57.973 33.333 0.00 0.00 43.05 3.06
3021 4457 8.120140 TGATGAAAATTGGTATGAACATCACA 57.880 30.769 0.00 0.00 38.17 3.58
3022 4458 8.028354 TGATGAAAATTGGTATGAACATCACAC 58.972 33.333 0.00 0.00 38.17 3.82
3023 4459 7.282332 TGAAAATTGGTATGAACATCACACA 57.718 32.000 0.00 0.00 0.00 3.72
3024 4460 7.144661 TGAAAATTGGTATGAACATCACACAC 58.855 34.615 0.00 0.00 0.00 3.82
3025 4461 6.899393 AAATTGGTATGAACATCACACACT 57.101 33.333 0.00 0.00 0.00 3.55
3026 4462 6.500684 AATTGGTATGAACATCACACACTC 57.499 37.500 0.00 0.00 0.00 3.51
3027 4463 4.615588 TGGTATGAACATCACACACTCA 57.384 40.909 0.00 0.00 0.00 3.41
3028 4464 4.967036 TGGTATGAACATCACACACTCAA 58.033 39.130 0.00 0.00 0.00 3.02
3029 4465 5.372373 TGGTATGAACATCACACACTCAAA 58.628 37.500 0.00 0.00 0.00 2.69
3030 4466 5.238432 TGGTATGAACATCACACACTCAAAC 59.762 40.000 0.00 0.00 0.00 2.93
3031 4467 5.238432 GGTATGAACATCACACACTCAAACA 59.762 40.000 0.00 0.00 0.00 2.83
3032 4468 6.072508 GGTATGAACATCACACACTCAAACAT 60.073 38.462 0.00 0.00 0.00 2.71
3033 4469 5.422666 TGAACATCACACACTCAAACATC 57.577 39.130 0.00 0.00 0.00 3.06
3034 4470 5.125356 TGAACATCACACACTCAAACATCT 58.875 37.500 0.00 0.00 0.00 2.90
3035 4471 5.237127 TGAACATCACACACTCAAACATCTC 59.763 40.000 0.00 0.00 0.00 2.75
3036 4472 4.965814 ACATCACACACTCAAACATCTCT 58.034 39.130 0.00 0.00 0.00 3.10
3037 4473 4.993584 ACATCACACACTCAAACATCTCTC 59.006 41.667 0.00 0.00 0.00 3.20
3038 4474 4.670896 TCACACACTCAAACATCTCTCA 57.329 40.909 0.00 0.00 0.00 3.27
3039 4475 5.219343 TCACACACTCAAACATCTCTCAT 57.781 39.130 0.00 0.00 0.00 2.90
3040 4476 4.992951 TCACACACTCAAACATCTCTCATG 59.007 41.667 0.00 0.00 0.00 3.07
3041 4477 4.753610 CACACACTCAAACATCTCTCATGT 59.246 41.667 0.00 0.00 0.00 3.21
3042 4478 4.993584 ACACACTCAAACATCTCTCATGTC 59.006 41.667 0.00 0.00 0.00 3.06
3043 4479 4.992951 CACACTCAAACATCTCTCATGTCA 59.007 41.667 0.00 0.00 0.00 3.58
3044 4480 5.467735 CACACTCAAACATCTCTCATGTCAA 59.532 40.000 0.00 0.00 0.00 3.18
3045 4481 6.148976 CACACTCAAACATCTCTCATGTCAAT 59.851 38.462 0.00 0.00 0.00 2.57
3046 4482 6.370994 ACACTCAAACATCTCTCATGTCAATC 59.629 38.462 0.00 0.00 0.00 2.67
3047 4483 6.594547 CACTCAAACATCTCTCATGTCAATCT 59.405 38.462 0.00 0.00 0.00 2.40
3048 4484 6.594547 ACTCAAACATCTCTCATGTCAATCTG 59.405 38.462 0.00 0.00 0.00 2.90
3049 4485 6.704310 TCAAACATCTCTCATGTCAATCTGA 58.296 36.000 0.00 0.00 0.00 3.27
3050 4486 7.163441 TCAAACATCTCTCATGTCAATCTGAA 58.837 34.615 0.00 0.00 0.00 3.02
3051 4487 6.981762 AACATCTCTCATGTCAATCTGAAC 57.018 37.500 0.00 0.00 0.00 3.18
3052 4488 6.297080 ACATCTCTCATGTCAATCTGAACT 57.703 37.500 0.00 0.00 0.00 3.01
3053 4489 6.709281 ACATCTCTCATGTCAATCTGAACTT 58.291 36.000 0.00 0.00 0.00 2.66
3054 4490 7.166851 ACATCTCTCATGTCAATCTGAACTTT 58.833 34.615 0.00 0.00 0.00 2.66
3055 4491 7.664731 ACATCTCTCATGTCAATCTGAACTTTT 59.335 33.333 0.00 0.00 0.00 2.27
3056 4492 8.512956 CATCTCTCATGTCAATCTGAACTTTTT 58.487 33.333 0.00 0.00 0.00 1.94
3057 4493 8.092521 TCTCTCATGTCAATCTGAACTTTTTC 57.907 34.615 0.00 0.00 0.00 2.29
3058 4494 7.935755 TCTCTCATGTCAATCTGAACTTTTTCT 59.064 33.333 0.00 0.00 32.36 2.52
3059 4495 9.212641 CTCTCATGTCAATCTGAACTTTTTCTA 57.787 33.333 0.00 0.00 32.36 2.10
3060 4496 9.212641 TCTCATGTCAATCTGAACTTTTTCTAG 57.787 33.333 0.00 0.00 32.36 2.43
3061 4497 8.908786 TCATGTCAATCTGAACTTTTTCTAGT 57.091 30.769 0.00 0.00 32.36 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.338674 TGTTCGAGTAGCAACCCCATG 60.339 52.381 0.00 0.00 0.00 3.66
69 70 1.012486 CGGGTGTTCGAGTAGCAACC 61.012 60.000 5.66 5.66 42.56 3.77
82 83 3.063084 GAGCTCGAGACCGGGTGT 61.063 66.667 18.75 0.00 38.83 4.16
190 193 7.566879 ACCTTGGAGATCAGTTTGAGTATATCT 59.433 37.037 0.00 0.00 0.00 1.98
293 301 2.293399 GGACGACAAGGTTTTTCAGCAT 59.707 45.455 0.00 0.00 0.00 3.79
296 304 3.315191 ACATGGACGACAAGGTTTTTCAG 59.685 43.478 0.00 0.00 0.00 3.02
301 309 1.133915 ACCACATGGACGACAAGGTTT 60.134 47.619 4.53 0.00 38.94 3.27
339 347 6.672657 ACAAACTAGAGTAATGACCATACCCT 59.327 38.462 0.00 0.00 0.00 4.34
342 351 7.478322 TCGACAAACTAGAGTAATGACCATAC 58.522 38.462 0.00 0.00 0.00 2.39
411 426 5.220605 GCAAAGTCGTATATGACCAAAGTCC 60.221 44.000 19.37 1.45 42.81 3.85
437 452 0.371989 GCAAAAACACGTTGGCAACC 59.628 50.000 23.68 7.21 0.00 3.77
444 459 2.053282 AACACACGCAAAAACACGTT 57.947 40.000 0.00 0.00 41.32 3.99
480 512 6.767902 ACAATGAGCAAACATCCGACTTATAT 59.232 34.615 0.00 0.00 0.00 0.86
481 513 6.112734 ACAATGAGCAAACATCCGACTTATA 58.887 36.000 0.00 0.00 0.00 0.98
483 515 4.323417 ACAATGAGCAAACATCCGACTTA 58.677 39.130 0.00 0.00 0.00 2.24
485 517 2.783135 ACAATGAGCAAACATCCGACT 58.217 42.857 0.00 0.00 0.00 4.18
514 546 4.075763 CTCAAACGGAGCATCAAGAAAG 57.924 45.455 0.00 0.00 36.69 2.62
540 575 9.748708 TTCTTTTCTGACAAATAGTGGATTTTG 57.251 29.630 0.00 0.00 35.45 2.44
551 586 8.506168 TTACTGACTGTTCTTTTCTGACAAAT 57.494 30.769 0.00 0.00 0.00 2.32
558 593 7.306632 CGAACGAATTACTGACTGTTCTTTTCT 60.307 37.037 0.00 0.00 34.93 2.52
559 594 6.786103 CGAACGAATTACTGACTGTTCTTTTC 59.214 38.462 0.00 0.00 34.93 2.29
564 599 3.181533 GGCGAACGAATTACTGACTGTTC 60.182 47.826 0.00 0.00 34.03 3.18
570 605 0.609151 TGGGGCGAACGAATTACTGA 59.391 50.000 0.00 0.00 0.00 3.41
585 621 4.286707 TCCAGATATGATATACGGTGGGG 58.713 47.826 0.00 0.00 0.00 4.96
586 622 5.932619 TTCCAGATATGATATACGGTGGG 57.067 43.478 0.00 0.00 0.00 4.61
620 656 7.552687 TGAAACAGATTTTAGTGTCACTGAGTT 59.447 33.333 16.03 4.83 27.37 3.01
630 666 7.095439 GGACTGACTCTGAAACAGATTTTAGTG 60.095 40.741 14.60 0.00 39.92 2.74
692 2073 2.936498 CGGTTATGGAATCACTGACACC 59.064 50.000 0.00 0.00 28.06 4.16
716 2101 5.657826 ATGTTTTGGCATGTATGTAAGCA 57.342 34.783 0.00 0.00 0.00 3.91
807 2193 1.219522 GAGCCGTGCGTACAAAGTGT 61.220 55.000 4.09 0.00 0.00 3.55
856 2242 3.092301 AGGAAGGTTTGAAATGGCTAGC 58.908 45.455 6.04 6.04 0.00 3.42
907 2293 6.978659 CGAGCCATCGGTGTTATATGTTATAT 59.021 38.462 0.00 0.00 45.39 0.86
908 2294 6.327154 CGAGCCATCGGTGTTATATGTTATA 58.673 40.000 0.00 0.00 45.39 0.98
909 2295 5.168569 CGAGCCATCGGTGTTATATGTTAT 58.831 41.667 0.00 0.00 45.39 1.89
910 2296 4.552355 CGAGCCATCGGTGTTATATGTTA 58.448 43.478 0.00 0.00 45.39 2.41
911 2297 3.390135 CGAGCCATCGGTGTTATATGTT 58.610 45.455 0.00 0.00 45.39 2.71
912 2298 3.026630 CGAGCCATCGGTGTTATATGT 57.973 47.619 0.00 0.00 45.39 2.29
986 2372 0.029567 GTCCATCGGTAGCTCAGTCG 59.970 60.000 0.00 0.00 0.00 4.18
1263 2658 2.437180 TCGCGGCGAGAAGAGGTA 60.437 61.111 22.69 0.00 0.00 3.08
1439 2834 3.127533 GGTGGTGCCGATGACTGC 61.128 66.667 0.00 0.00 0.00 4.40
1617 3012 2.771372 GCTTCTGGAGGAGGAGAAGAAT 59.229 50.000 11.95 0.00 45.51 2.40
2097 3495 4.392940 CTGGGGCTGGATTAATAACTGAG 58.607 47.826 0.00 0.00 0.00 3.35
2098 3496 3.138283 CCTGGGGCTGGATTAATAACTGA 59.862 47.826 0.00 0.00 0.00 3.41
2099 3497 3.138283 TCCTGGGGCTGGATTAATAACTG 59.862 47.826 0.00 0.00 0.00 3.16
2100 3498 3.138468 GTCCTGGGGCTGGATTAATAACT 59.862 47.826 0.00 0.00 34.19 2.24
2265 3667 7.628234 AGCCAAGAACAGTAGTACTACTAGTA 58.372 38.462 30.34 1.89 43.98 1.82
2266 3668 6.483405 AGCCAAGAACAGTAGTACTACTAGT 58.517 40.000 30.34 25.57 43.98 2.57
2267 3669 6.824704 AGAGCCAAGAACAGTAGTACTACTAG 59.175 42.308 30.34 25.04 43.98 2.57
2350 3752 3.433540 AAACAAAACCCACGGCGCC 62.434 57.895 19.07 19.07 0.00 6.53
2467 3869 3.434024 GGGTAAAACAGTGTAGTGGTGGT 60.434 47.826 0.00 0.00 0.00 4.16
2476 3878 3.375922 CGACACAAAGGGTAAAACAGTGT 59.624 43.478 0.00 0.00 40.96 3.55
2481 3883 1.677052 TGCCGACACAAAGGGTAAAAC 59.323 47.619 0.00 0.00 0.00 2.43
2503 3905 5.576774 CGAGCATCCGAGCATAATACAATAA 59.423 40.000 0.00 0.00 36.85 1.40
2546 3982 5.003402 GCACCGATGAACGATTATTTGTTTG 59.997 40.000 0.00 0.00 45.77 2.93
2547 3983 5.092781 GCACCGATGAACGATTATTTGTTT 58.907 37.500 0.00 0.00 45.77 2.83
2572 4008 9.750882 CATGAATCGCACAAATATAATCTACTG 57.249 33.333 0.00 0.00 0.00 2.74
2735 4171 1.408969 TTGGGCCCAAGTTCAGAAAC 58.591 50.000 34.07 0.00 35.50 2.78
2736 4172 2.397044 ATTGGGCCCAAGTTCAGAAA 57.603 45.000 38.82 16.53 39.47 2.52
2737 4173 3.627237 GGATATTGGGCCCAAGTTCAGAA 60.627 47.826 38.82 17.32 39.47 3.02
2738 4174 2.091885 GGATATTGGGCCCAAGTTCAGA 60.092 50.000 38.82 18.14 39.47 3.27
2739 4175 2.310538 GGATATTGGGCCCAAGTTCAG 58.689 52.381 38.82 0.00 39.47 3.02
2740 4176 1.643286 TGGATATTGGGCCCAAGTTCA 59.357 47.619 38.82 30.52 39.47 3.18
2741 4177 2.452600 TGGATATTGGGCCCAAGTTC 57.547 50.000 38.82 33.33 39.47 3.01
2742 4178 3.419732 AATGGATATTGGGCCCAAGTT 57.580 42.857 38.82 28.87 39.47 2.66
2743 4179 3.419732 AAATGGATATTGGGCCCAAGT 57.580 42.857 38.82 30.03 39.47 3.16
2744 4180 4.409901 AGAAAAATGGATATTGGGCCCAAG 59.590 41.667 38.82 0.00 39.47 3.61
2745 4181 4.369872 AGAAAAATGGATATTGGGCCCAA 58.630 39.130 38.72 38.72 40.47 4.12
2746 4182 4.006247 AGAAAAATGGATATTGGGCCCA 57.994 40.909 24.45 24.45 0.00 5.36
2747 4183 4.283467 GGTAGAAAAATGGATATTGGGCCC 59.717 45.833 17.59 17.59 0.00 5.80
2748 4184 4.283467 GGGTAGAAAAATGGATATTGGGCC 59.717 45.833 0.00 0.00 0.00 5.80
2749 4185 4.022329 CGGGTAGAAAAATGGATATTGGGC 60.022 45.833 0.00 0.00 0.00 5.36
2750 4186 5.381757 TCGGGTAGAAAAATGGATATTGGG 58.618 41.667 0.00 0.00 0.00 4.12
2751 4187 5.048713 GCTCGGGTAGAAAAATGGATATTGG 60.049 44.000 0.00 0.00 0.00 3.16
2752 4188 5.765182 AGCTCGGGTAGAAAAATGGATATTG 59.235 40.000 0.00 0.00 0.00 1.90
2753 4189 5.941788 AGCTCGGGTAGAAAAATGGATATT 58.058 37.500 0.00 0.00 0.00 1.28
2754 4190 5.568620 AGCTCGGGTAGAAAAATGGATAT 57.431 39.130 0.00 0.00 0.00 1.63
2755 4191 5.367945 AAGCTCGGGTAGAAAAATGGATA 57.632 39.130 0.00 0.00 0.00 2.59
2756 4192 3.933861 AGCTCGGGTAGAAAAATGGAT 57.066 42.857 0.00 0.00 0.00 3.41
2757 4193 3.713826 AAGCTCGGGTAGAAAAATGGA 57.286 42.857 0.00 0.00 0.00 3.41
2758 4194 5.237344 CAGATAAGCTCGGGTAGAAAAATGG 59.763 44.000 0.00 0.00 0.00 3.16
2759 4195 6.049149 TCAGATAAGCTCGGGTAGAAAAATG 58.951 40.000 0.00 0.00 0.00 2.32
2760 4196 6.235231 TCAGATAAGCTCGGGTAGAAAAAT 57.765 37.500 0.00 0.00 0.00 1.82
2761 4197 5.670792 TCAGATAAGCTCGGGTAGAAAAA 57.329 39.130 0.00 0.00 0.00 1.94
2762 4198 5.598830 AGATCAGATAAGCTCGGGTAGAAAA 59.401 40.000 0.00 0.00 0.00 2.29
2763 4199 5.141182 AGATCAGATAAGCTCGGGTAGAAA 58.859 41.667 0.00 0.00 0.00 2.52
2764 4200 4.730966 AGATCAGATAAGCTCGGGTAGAA 58.269 43.478 0.00 0.00 0.00 2.10
2765 4201 4.328536 GAGATCAGATAAGCTCGGGTAGA 58.671 47.826 0.00 0.00 0.00 2.59
2766 4202 3.126171 CGAGATCAGATAAGCTCGGGTAG 59.874 52.174 10.75 0.00 44.58 3.18
2767 4203 3.075148 CGAGATCAGATAAGCTCGGGTA 58.925 50.000 10.75 0.00 44.58 3.69
2768 4204 1.883275 CGAGATCAGATAAGCTCGGGT 59.117 52.381 10.75 0.00 44.58 5.28
2769 4205 2.627863 CGAGATCAGATAAGCTCGGG 57.372 55.000 10.75 0.00 44.58 5.14
2772 4208 5.767269 TGTTCATCGAGATCAGATAAGCTC 58.233 41.667 0.00 0.00 0.00 4.09
2773 4209 5.301551 ACTGTTCATCGAGATCAGATAAGCT 59.698 40.000 20.31 0.00 43.66 3.74
2774 4210 5.527951 ACTGTTCATCGAGATCAGATAAGC 58.472 41.667 20.31 0.00 43.66 3.09
2775 4211 9.689976 ATTAACTGTTCATCGAGATCAGATAAG 57.310 33.333 20.31 0.00 43.66 1.73
2832 4268 6.892658 TGCAGCTAAACATCTTCCTAAAAA 57.107 33.333 0.00 0.00 0.00 1.94
2833 4269 6.658816 TCATGCAGCTAAACATCTTCCTAAAA 59.341 34.615 0.00 0.00 0.00 1.52
2834 4270 6.179756 TCATGCAGCTAAACATCTTCCTAAA 58.820 36.000 0.00 0.00 0.00 1.85
2835 4271 5.744171 TCATGCAGCTAAACATCTTCCTAA 58.256 37.500 0.00 0.00 0.00 2.69
2836 4272 5.357742 TCATGCAGCTAAACATCTTCCTA 57.642 39.130 0.00 0.00 0.00 2.94
2837 4273 4.197750 CTCATGCAGCTAAACATCTTCCT 58.802 43.478 0.00 0.00 0.00 3.36
2838 4274 3.314635 CCTCATGCAGCTAAACATCTTCC 59.685 47.826 0.00 0.00 0.00 3.46
2839 4275 3.944015 ACCTCATGCAGCTAAACATCTTC 59.056 43.478 0.00 0.00 0.00 2.87
2840 4276 3.960571 ACCTCATGCAGCTAAACATCTT 58.039 40.909 0.00 0.00 0.00 2.40
2841 4277 3.641434 ACCTCATGCAGCTAAACATCT 57.359 42.857 0.00 0.00 0.00 2.90
2842 4278 4.818546 ACATACCTCATGCAGCTAAACATC 59.181 41.667 0.00 0.00 38.29 3.06
2843 4279 4.785301 ACATACCTCATGCAGCTAAACAT 58.215 39.130 0.00 0.00 38.29 2.71
2844 4280 4.220693 ACATACCTCATGCAGCTAAACA 57.779 40.909 0.00 0.00 38.29 2.83
2845 4281 5.123820 TGAAACATACCTCATGCAGCTAAAC 59.876 40.000 0.00 0.00 38.29 2.01
2846 4282 5.252547 TGAAACATACCTCATGCAGCTAAA 58.747 37.500 0.00 0.00 38.29 1.85
2847 4283 4.842574 TGAAACATACCTCATGCAGCTAA 58.157 39.130 0.00 0.00 38.29 3.09
2848 4284 4.486125 TGAAACATACCTCATGCAGCTA 57.514 40.909 0.00 0.00 38.29 3.32
2849 4285 3.354948 TGAAACATACCTCATGCAGCT 57.645 42.857 0.00 0.00 38.29 4.24
2850 4286 4.644103 ATTGAAACATACCTCATGCAGC 57.356 40.909 0.00 0.00 38.29 5.25
2851 4287 7.092079 TGAAAATTGAAACATACCTCATGCAG 58.908 34.615 0.00 0.00 38.29 4.41
2852 4288 6.990798 TGAAAATTGAAACATACCTCATGCA 58.009 32.000 0.00 0.00 38.29 3.96
2853 4289 6.035327 GCTGAAAATTGAAACATACCTCATGC 59.965 38.462 0.00 0.00 38.29 4.06
2854 4290 6.252015 CGCTGAAAATTGAAACATACCTCATG 59.748 38.462 0.00 0.00 40.78 3.07
2855 4291 6.071952 ACGCTGAAAATTGAAACATACCTCAT 60.072 34.615 0.00 0.00 0.00 2.90
2856 4292 5.240623 ACGCTGAAAATTGAAACATACCTCA 59.759 36.000 0.00 0.00 0.00 3.86
2857 4293 5.569059 CACGCTGAAAATTGAAACATACCTC 59.431 40.000 0.00 0.00 0.00 3.85
2858 4294 5.009610 ACACGCTGAAAATTGAAACATACCT 59.990 36.000 0.00 0.00 0.00 3.08
2859 4295 5.219633 ACACGCTGAAAATTGAAACATACC 58.780 37.500 0.00 0.00 0.00 2.73
2860 4296 6.747659 AACACGCTGAAAATTGAAACATAC 57.252 33.333 0.00 0.00 0.00 2.39
2861 4297 6.199908 CCAAACACGCTGAAAATTGAAACATA 59.800 34.615 0.00 0.00 0.00 2.29
2862 4298 5.006552 CCAAACACGCTGAAAATTGAAACAT 59.993 36.000 0.00 0.00 0.00 2.71
2863 4299 4.328440 CCAAACACGCTGAAAATTGAAACA 59.672 37.500 0.00 0.00 0.00 2.83
2864 4300 4.564769 TCCAAACACGCTGAAAATTGAAAC 59.435 37.500 0.00 0.00 0.00 2.78
2865 4301 4.564769 GTCCAAACACGCTGAAAATTGAAA 59.435 37.500 0.00 0.00 0.00 2.69
2866 4302 4.109050 GTCCAAACACGCTGAAAATTGAA 58.891 39.130 0.00 0.00 0.00 2.69
2867 4303 3.129462 TGTCCAAACACGCTGAAAATTGA 59.871 39.130 0.00 0.00 0.00 2.57
2868 4304 3.443037 TGTCCAAACACGCTGAAAATTG 58.557 40.909 0.00 0.00 0.00 2.32
2869 4305 3.791973 TGTCCAAACACGCTGAAAATT 57.208 38.095 0.00 0.00 0.00 1.82
2870 4306 4.320608 AATGTCCAAACACGCTGAAAAT 57.679 36.364 0.00 0.00 38.48 1.82
2871 4307 3.791973 AATGTCCAAACACGCTGAAAA 57.208 38.095 0.00 0.00 38.48 2.29
2872 4308 3.129462 TCAAATGTCCAAACACGCTGAAA 59.871 39.130 0.00 0.00 38.48 2.69
2873 4309 2.685388 TCAAATGTCCAAACACGCTGAA 59.315 40.909 0.00 0.00 38.48 3.02
2874 4310 2.290367 CTCAAATGTCCAAACACGCTGA 59.710 45.455 0.00 0.00 38.48 4.26
2875 4311 2.033299 ACTCAAATGTCCAAACACGCTG 59.967 45.455 0.00 0.00 38.48 5.18
2876 4312 2.297701 ACTCAAATGTCCAAACACGCT 58.702 42.857 0.00 0.00 38.48 5.07
2877 4313 2.774439 ACTCAAATGTCCAAACACGC 57.226 45.000 0.00 0.00 38.48 5.34
2878 4314 3.498397 AGCTACTCAAATGTCCAAACACG 59.502 43.478 0.00 0.00 38.48 4.49
2879 4315 4.083271 GGAGCTACTCAAATGTCCAAACAC 60.083 45.833 0.00 0.00 33.06 3.32
2880 4316 4.072131 GGAGCTACTCAAATGTCCAAACA 58.928 43.478 0.00 0.00 34.14 2.83
2881 4317 3.440522 GGGAGCTACTCAAATGTCCAAAC 59.559 47.826 0.00 0.00 31.08 2.93
2882 4318 3.073798 TGGGAGCTACTCAAATGTCCAAA 59.926 43.478 0.00 0.00 31.08 3.28
2883 4319 2.642311 TGGGAGCTACTCAAATGTCCAA 59.358 45.455 0.00 0.00 31.08 3.53
2884 4320 2.237143 CTGGGAGCTACTCAAATGTCCA 59.763 50.000 0.00 0.00 31.08 4.02
2885 4321 2.911484 CTGGGAGCTACTCAAATGTCC 58.089 52.381 0.00 0.00 31.08 4.02
2886 4322 2.284190 GCTGGGAGCTACTCAAATGTC 58.716 52.381 0.00 0.00 38.45 3.06
2887 4323 1.630369 TGCTGGGAGCTACTCAAATGT 59.370 47.619 0.00 0.00 42.97 2.71
2888 4324 2.408271 TGCTGGGAGCTACTCAAATG 57.592 50.000 0.00 0.00 42.97 2.32
2889 4325 3.439857 TTTGCTGGGAGCTACTCAAAT 57.560 42.857 0.00 0.00 42.97 2.32
2890 4326 2.949177 TTTGCTGGGAGCTACTCAAA 57.051 45.000 0.00 1.73 42.97 2.69
2891 4327 2.949177 TTTTGCTGGGAGCTACTCAA 57.051 45.000 0.00 0.00 42.97 3.02
2892 4328 2.949177 TTTTTGCTGGGAGCTACTCA 57.051 45.000 0.00 0.00 42.97 3.41
2910 4346 5.151389 GTGCAATATTCGAACCGAGTTTTT 58.849 37.500 0.00 0.00 37.14 1.94
2911 4347 4.214545 TGTGCAATATTCGAACCGAGTTTT 59.785 37.500 0.00 0.00 37.14 2.43
2912 4348 3.749088 TGTGCAATATTCGAACCGAGTTT 59.251 39.130 0.00 0.00 37.14 2.66
2913 4349 3.331150 TGTGCAATATTCGAACCGAGTT 58.669 40.909 0.00 0.00 37.14 3.01
2914 4350 2.967362 TGTGCAATATTCGAACCGAGT 58.033 42.857 0.00 0.00 37.14 4.18
2915 4351 4.088648 GTTTGTGCAATATTCGAACCGAG 58.911 43.478 0.00 0.00 37.14 4.63
2916 4352 3.498777 TGTTTGTGCAATATTCGAACCGA 59.501 39.130 0.00 0.00 0.00 4.69
2917 4353 3.816091 TGTTTGTGCAATATTCGAACCG 58.184 40.909 0.00 0.00 0.00 4.44
2918 4354 7.804614 TTATTGTTTGTGCAATATTCGAACC 57.195 32.000 0.00 0.00 39.95 3.62
2919 4355 8.911662 AGTTTATTGTTTGTGCAATATTCGAAC 58.088 29.630 0.00 0.00 39.95 3.95
2920 4356 9.469807 AAGTTTATTGTTTGTGCAATATTCGAA 57.530 25.926 0.00 0.00 39.95 3.71
2921 4357 9.469807 AAAGTTTATTGTTTGTGCAATATTCGA 57.530 25.926 0.00 0.00 39.95 3.71
2926 4362 8.058915 GCGAAAAAGTTTATTGTTTGTGCAATA 58.941 29.630 0.00 0.00 39.50 1.90
2927 4363 6.904543 GCGAAAAAGTTTATTGTTTGTGCAAT 59.095 30.769 0.00 0.00 41.42 3.56
2928 4364 6.128553 TGCGAAAAAGTTTATTGTTTGTGCAA 60.129 30.769 0.00 0.00 0.00 4.08
2929 4365 5.348724 TGCGAAAAAGTTTATTGTTTGTGCA 59.651 32.000 0.00 0.00 0.00 4.57
2930 4366 5.790547 TGCGAAAAAGTTTATTGTTTGTGC 58.209 33.333 0.00 0.00 0.00 4.57
2931 4367 7.110511 GTCTGCGAAAAAGTTTATTGTTTGTG 58.889 34.615 0.00 0.00 0.00 3.33
2932 4368 6.254804 GGTCTGCGAAAAAGTTTATTGTTTGT 59.745 34.615 0.00 0.00 0.00 2.83
2933 4369 6.292114 GGGTCTGCGAAAAAGTTTATTGTTTG 60.292 38.462 0.00 0.00 0.00 2.93
2934 4370 5.751509 GGGTCTGCGAAAAAGTTTATTGTTT 59.248 36.000 0.00 0.00 0.00 2.83
2935 4371 5.068591 AGGGTCTGCGAAAAAGTTTATTGTT 59.931 36.000 0.00 0.00 0.00 2.83
2936 4372 4.583073 AGGGTCTGCGAAAAAGTTTATTGT 59.417 37.500 0.00 0.00 0.00 2.71
2937 4373 5.121221 AGGGTCTGCGAAAAAGTTTATTG 57.879 39.130 0.00 0.00 0.00 1.90
2938 4374 4.825085 TGAGGGTCTGCGAAAAAGTTTATT 59.175 37.500 0.00 0.00 0.00 1.40
2939 4375 4.394729 TGAGGGTCTGCGAAAAAGTTTAT 58.605 39.130 0.00 0.00 0.00 1.40
2940 4376 3.811083 TGAGGGTCTGCGAAAAAGTTTA 58.189 40.909 0.00 0.00 0.00 2.01
2941 4377 2.650322 TGAGGGTCTGCGAAAAAGTTT 58.350 42.857 0.00 0.00 0.00 2.66
2942 4378 2.341846 TGAGGGTCTGCGAAAAAGTT 57.658 45.000 0.00 0.00 0.00 2.66
2943 4379 2.341846 TTGAGGGTCTGCGAAAAAGT 57.658 45.000 0.00 0.00 0.00 2.66
2944 4380 3.923017 AATTGAGGGTCTGCGAAAAAG 57.077 42.857 0.00 0.00 0.00 2.27
2945 4381 4.664150 AAAATTGAGGGTCTGCGAAAAA 57.336 36.364 0.00 0.00 0.00 1.94
2946 4382 4.664150 AAAAATTGAGGGTCTGCGAAAA 57.336 36.364 0.00 0.00 0.00 2.29
2970 4406 6.015603 TGTCTGGACATCTGATTAGCTATCAG 60.016 42.308 19.19 19.19 46.74 2.90
2971 4407 5.835280 TGTCTGGACATCTGATTAGCTATCA 59.165 40.000 0.00 0.10 37.37 2.15
2972 4408 6.338214 TGTCTGGACATCTGATTAGCTATC 57.662 41.667 0.00 0.00 36.21 2.08
2986 4422 5.078949 ACCAATTTTCATCATGTCTGGACA 58.921 37.500 5.87 5.87 46.44 4.02
2987 4423 5.649782 ACCAATTTTCATCATGTCTGGAC 57.350 39.130 0.00 0.00 0.00 4.02
2988 4424 7.118060 TCATACCAATTTTCATCATGTCTGGA 58.882 34.615 0.00 0.00 0.00 3.86
2989 4425 7.337480 TCATACCAATTTTCATCATGTCTGG 57.663 36.000 0.00 0.00 0.00 3.86
2990 4426 8.245491 TGTTCATACCAATTTTCATCATGTCTG 58.755 33.333 0.00 0.00 0.00 3.51
2991 4427 8.352137 TGTTCATACCAATTTTCATCATGTCT 57.648 30.769 0.00 0.00 0.00 3.41
2992 4428 9.241317 GATGTTCATACCAATTTTCATCATGTC 57.759 33.333 0.00 0.00 33.18 3.06
2993 4429 8.751242 TGATGTTCATACCAATTTTCATCATGT 58.249 29.630 0.00 0.00 36.56 3.21
2994 4430 9.027129 GTGATGTTCATACCAATTTTCATCATG 57.973 33.333 0.00 0.00 41.06 3.07
2995 4431 8.751242 TGTGATGTTCATACCAATTTTCATCAT 58.249 29.630 0.00 0.00 41.06 2.45
2996 4432 8.028354 GTGTGATGTTCATACCAATTTTCATCA 58.972 33.333 0.00 0.00 38.27 3.07
2997 4433 8.028354 TGTGTGATGTTCATACCAATTTTCATC 58.972 33.333 2.55 0.00 37.65 2.92
2998 4434 7.814107 GTGTGTGATGTTCATACCAATTTTCAT 59.186 33.333 2.55 0.00 37.65 2.57
2999 4435 7.014134 AGTGTGTGATGTTCATACCAATTTTCA 59.986 33.333 2.55 0.00 37.65 2.69
3000 4436 7.370383 AGTGTGTGATGTTCATACCAATTTTC 58.630 34.615 2.55 0.00 37.65 2.29
3001 4437 7.014134 TGAGTGTGTGATGTTCATACCAATTTT 59.986 33.333 2.55 0.00 37.65 1.82
3002 4438 6.489700 TGAGTGTGTGATGTTCATACCAATTT 59.510 34.615 2.55 0.00 37.65 1.82
3003 4439 6.003326 TGAGTGTGTGATGTTCATACCAATT 58.997 36.000 2.55 0.00 37.65 2.32
3004 4440 5.559770 TGAGTGTGTGATGTTCATACCAAT 58.440 37.500 2.55 0.00 37.65 3.16
3005 4441 4.967036 TGAGTGTGTGATGTTCATACCAA 58.033 39.130 2.55 0.00 37.65 3.67
3006 4442 4.615588 TGAGTGTGTGATGTTCATACCA 57.384 40.909 2.55 0.00 37.65 3.25
3007 4443 5.238432 TGTTTGAGTGTGTGATGTTCATACC 59.762 40.000 2.55 0.00 37.65 2.73
3008 4444 6.299023 TGTTTGAGTGTGTGATGTTCATAC 57.701 37.500 0.00 0.00 38.72 2.39
3009 4445 6.936335 AGATGTTTGAGTGTGTGATGTTCATA 59.064 34.615 0.00 0.00 0.00 2.15
3010 4446 5.766670 AGATGTTTGAGTGTGTGATGTTCAT 59.233 36.000 0.00 0.00 0.00 2.57
3011 4447 5.125356 AGATGTTTGAGTGTGTGATGTTCA 58.875 37.500 0.00 0.00 0.00 3.18
3012 4448 5.468072 AGAGATGTTTGAGTGTGTGATGTTC 59.532 40.000 0.00 0.00 0.00 3.18
3013 4449 5.371526 AGAGATGTTTGAGTGTGTGATGTT 58.628 37.500 0.00 0.00 0.00 2.71
3014 4450 4.965814 AGAGATGTTTGAGTGTGTGATGT 58.034 39.130 0.00 0.00 0.00 3.06
3015 4451 4.992951 TGAGAGATGTTTGAGTGTGTGATG 59.007 41.667 0.00 0.00 0.00 3.07
3016 4452 5.219343 TGAGAGATGTTTGAGTGTGTGAT 57.781 39.130 0.00 0.00 0.00 3.06
3017 4453 4.670896 TGAGAGATGTTTGAGTGTGTGA 57.329 40.909 0.00 0.00 0.00 3.58
3018 4454 4.753610 ACATGAGAGATGTTTGAGTGTGTG 59.246 41.667 0.00 0.00 0.00 3.82
3019 4455 4.965814 ACATGAGAGATGTTTGAGTGTGT 58.034 39.130 0.00 0.00 0.00 3.72
3020 4456 4.992951 TGACATGAGAGATGTTTGAGTGTG 59.007 41.667 0.00 0.00 31.52 3.82
3021 4457 5.219343 TGACATGAGAGATGTTTGAGTGT 57.781 39.130 0.00 0.00 31.52 3.55
3022 4458 6.594547 AGATTGACATGAGAGATGTTTGAGTG 59.405 38.462 0.00 0.00 31.52 3.51
3023 4459 6.594547 CAGATTGACATGAGAGATGTTTGAGT 59.405 38.462 0.00 0.00 31.52 3.41
3024 4460 6.817140 TCAGATTGACATGAGAGATGTTTGAG 59.183 38.462 0.00 0.00 31.52 3.02
3025 4461 6.704310 TCAGATTGACATGAGAGATGTTTGA 58.296 36.000 0.00 0.00 31.52 2.69
3026 4462 6.980051 TCAGATTGACATGAGAGATGTTTG 57.020 37.500 0.00 0.00 31.52 2.93
3027 4463 7.166851 AGTTCAGATTGACATGAGAGATGTTT 58.833 34.615 0.00 0.00 31.52 2.83
3028 4464 6.709281 AGTTCAGATTGACATGAGAGATGTT 58.291 36.000 0.00 0.00 31.52 2.71
3029 4465 6.297080 AGTTCAGATTGACATGAGAGATGT 57.703 37.500 0.00 0.00 34.52 3.06
3030 4466 7.612668 AAAGTTCAGATTGACATGAGAGATG 57.387 36.000 0.00 0.00 0.00 2.90
3031 4467 8.632906 AAAAAGTTCAGATTGACATGAGAGAT 57.367 30.769 0.00 0.00 0.00 2.75
3032 4468 7.935755 AGAAAAAGTTCAGATTGACATGAGAGA 59.064 33.333 0.00 0.00 36.09 3.10
3033 4469 8.097078 AGAAAAAGTTCAGATTGACATGAGAG 57.903 34.615 0.00 0.00 36.09 3.20
3034 4470 9.212641 CTAGAAAAAGTTCAGATTGACATGAGA 57.787 33.333 0.00 0.00 36.09 3.27
3035 4471 8.997323 ACTAGAAAAAGTTCAGATTGACATGAG 58.003 33.333 0.00 0.00 36.09 2.90
3036 4472 8.908786 ACTAGAAAAAGTTCAGATTGACATGA 57.091 30.769 0.00 0.00 36.09 3.07


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

AutoCloner maintained by Alex Coulton.