Multiple sequence alignment - TraesCS1D01G367200

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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 TraesCS1D01G367200 chr1D 100.000 3671 0 0 1 3671 447219863 447223533 0.000000e+00 6780.0
1 TraesCS1D01G367200 chr1B 94.051 2471 109 18 799 3242 612826386 612828845 0.000000e+00 3714.0
2 TraesCS1D01G367200 chr1B 98.305 59 1 0 750 808 612821769 612821827 1.800000e-18 104.0
3 TraesCS1D01G367200 chr1B 84.932 73 0 4 3284 3347 612828855 612828925 3.060000e-06 63.9
4 TraesCS1D01G367200 chr4B 87.274 2043 196 29 1091 3105 86757421 86755415 0.000000e+00 2274.0
5 TraesCS1D01G367200 chr4B 95.722 748 31 1 1 747 131358577 131359324 0.000000e+00 1203.0
6 TraesCS1D01G367200 chr4B 93.063 591 38 2 1 589 360554943 360554354 0.000000e+00 861.0
7 TraesCS1D01G367200 chr4A 89.272 1594 137 16 1091 2669 538887487 538885913 0.000000e+00 1965.0
8 TraesCS1D01G367200 chr4A 88.496 113 6 3 2712 2819 538885913 538885803 2.980000e-26 130.0
9 TraesCS1D01G367200 chr1A 95.983 1145 46 0 1092 2236 543041215 543042359 0.000000e+00 1860.0
10 TraesCS1D01G367200 chr1A 94.542 1136 36 9 2227 3347 543055406 543056530 0.000000e+00 1731.0
11 TraesCS1D01G367200 chr1A 91.725 858 56 6 872 1723 542869542 542868694 0.000000e+00 1177.0
12 TraesCS1D01G367200 chr1A 92.782 665 31 9 2056 2718 542868684 542868035 0.000000e+00 946.0
13 TraesCS1D01G367200 chr1A 76.720 945 181 31 1094 2023 58370299 58369379 1.180000e-134 490.0
14 TraesCS1D01G367200 chr1A 76.562 960 186 31 1079 2023 58479218 58480153 1.180000e-134 490.0
15 TraesCS1D01G367200 chr1A 87.123 365 30 11 2711 3069 542868000 542867647 7.390000e-107 398.0
16 TraesCS1D01G367200 chr1A 82.301 226 29 6 2859 3082 542867567 542867351 6.260000e-43 185.0
17 TraesCS1D01G367200 chr6D 97.878 754 13 3 1 753 293702723 293701972 0.000000e+00 1301.0
18 TraesCS1D01G367200 chr7B 94.548 752 40 1 1 752 742365177 742365927 0.000000e+00 1160.0
19 TraesCS1D01G367200 chr3B 93.351 752 38 6 1 745 602288384 602287638 0.000000e+00 1101.0
20 TraesCS1D01G367200 chr5D 89.880 751 65 4 3 752 378737633 378738373 0.000000e+00 955.0
21 TraesCS1D01G367200 chr5D 97.959 49 1 0 3346 3394 233974904 233974952 6.530000e-13 86.1
22 TraesCS1D01G367200 chr5D 92.982 57 4 0 3343 3399 494066919 494066975 2.350000e-12 84.2
23 TraesCS1D01G367200 chr5B 88.048 753 79 3 1 752 452959908 452960650 0.000000e+00 881.0
24 TraesCS1D01G367200 chr5B 77.391 690 135 17 1116 1799 396055173 396054499 1.240000e-104 390.0
25 TraesCS1D01G367200 chr5A 74.509 1526 330 43 1110 2612 438776289 438774800 3.130000e-170 608.0
26 TraesCS1D01G367200 chr5A 92.683 41 3 0 3354 3394 389718482 389718522 3.960000e-05 60.2
27 TraesCS1D01G367200 chr3D 81.152 764 122 19 1 751 441044394 441045148 8.780000e-166 593.0
28 TraesCS1D01G367200 chr3D 80.946 761 121 19 1 750 441039332 441040079 6.830000e-162 580.0
29 TraesCS1D01G367200 chr3A 91.228 57 5 0 3346 3402 717943465 717943521 1.090000e-10 78.7
30 TraesCS1D01G367200 chr3A 92.857 42 3 0 3353 3394 640371178 640371137 1.100000e-05 62.1
31 TraesCS1D01G367200 chr7D 91.071 56 5 0 3344 3399 191547124 191547179 3.930000e-10 76.8
32 TraesCS1D01G367200 chr4D 91.071 56 5 0 3344 3399 379253113 379253168 3.930000e-10 76.8


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 TraesCS1D01G367200 chr1D 447219863 447223533 3670 False 6780.00 6780 100.00000 1 3671 1 chr1D.!!$F1 3670
1 TraesCS1D01G367200 chr1B 612826386 612828925 2539 False 1888.95 3714 89.49150 799 3347 2 chr1B.!!$F2 2548
2 TraesCS1D01G367200 chr4B 86755415 86757421 2006 True 2274.00 2274 87.27400 1091 3105 1 chr4B.!!$R1 2014
3 TraesCS1D01G367200 chr4B 131358577 131359324 747 False 1203.00 1203 95.72200 1 747 1 chr4B.!!$F1 746
4 TraesCS1D01G367200 chr4B 360554354 360554943 589 True 861.00 861 93.06300 1 589 1 chr4B.!!$R2 588
5 TraesCS1D01G367200 chr4A 538885803 538887487 1684 True 1047.50 1965 88.88400 1091 2819 2 chr4A.!!$R1 1728
6 TraesCS1D01G367200 chr1A 543041215 543042359 1144 False 1860.00 1860 95.98300 1092 2236 1 chr1A.!!$F2 1144
7 TraesCS1D01G367200 chr1A 543055406 543056530 1124 False 1731.00 1731 94.54200 2227 3347 1 chr1A.!!$F3 1120
8 TraesCS1D01G367200 chr1A 542867351 542869542 2191 True 676.50 1177 88.48275 872 3082 4 chr1A.!!$R2 2210
9 TraesCS1D01G367200 chr1A 58369379 58370299 920 True 490.00 490 76.72000 1094 2023 1 chr1A.!!$R1 929
10 TraesCS1D01G367200 chr1A 58479218 58480153 935 False 490.00 490 76.56200 1079 2023 1 chr1A.!!$F1 944
11 TraesCS1D01G367200 chr6D 293701972 293702723 751 True 1301.00 1301 97.87800 1 753 1 chr6D.!!$R1 752
12 TraesCS1D01G367200 chr7B 742365177 742365927 750 False 1160.00 1160 94.54800 1 752 1 chr7B.!!$F1 751
13 TraesCS1D01G367200 chr3B 602287638 602288384 746 True 1101.00 1101 93.35100 1 745 1 chr3B.!!$R1 744
14 TraesCS1D01G367200 chr5D 378737633 378738373 740 False 955.00 955 89.88000 3 752 1 chr5D.!!$F2 749
15 TraesCS1D01G367200 chr5B 452959908 452960650 742 False 881.00 881 88.04800 1 752 1 chr5B.!!$F1 751
16 TraesCS1D01G367200 chr5B 396054499 396055173 674 True 390.00 390 77.39100 1116 1799 1 chr5B.!!$R1 683
17 TraesCS1D01G367200 chr5A 438774800 438776289 1489 True 608.00 608 74.50900 1110 2612 1 chr5A.!!$R1 1502
18 TraesCS1D01G367200 chr3D 441044394 441045148 754 False 593.00 593 81.15200 1 751 1 chr3D.!!$F2 750
19 TraesCS1D01G367200 chr3D 441039332 441040079 747 False 580.00 580 80.94600 1 750 1 chr3D.!!$F1 749

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
759 777 0.108329 TAACTTAGCTGGACGCAGGC 60.108 55.0 0.00 0.00 42.61 4.85 F
772 790 0.679640 CGCAGGCCTTGATACCCAAA 60.680 55.0 0.00 0.00 33.76 3.28 F
792 810 1.042559 AAATTGTATGCTGGGGCCCG 61.043 55.0 19.83 14.09 37.74 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2059 2.106166 TGGCGGTTTAGTCCAGGTAAAA 59.894 45.455 0.00 0.0 0.0 1.52 R
2632 2690 3.248024 ACCAGAACTACAGGAATCCACA 58.752 45.455 0.61 0.0 0.0 4.17 R
2763 2864 5.534654 AGATACAAAGTAGCAGCACCAAAAA 59.465 36.000 0.00 0.0 0.0 1.94 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
456 458 2.280552 AAGGGCTTACCGACGCTGA 61.281 57.895 0.00 0.00 46.96 4.26
658 667 2.564771 CCATGCCGTTGTATCTCACAT 58.435 47.619 0.00 0.00 36.90 3.21
677 686 3.139957 ACATGATCTCCCTGCTCTCTCTA 59.860 47.826 0.00 0.00 0.00 2.43
753 771 5.007136 GTGAGATTGCATAACTTAGCTGGAC 59.993 44.000 0.00 0.00 0.00 4.02
754 772 4.122776 AGATTGCATAACTTAGCTGGACG 58.877 43.478 0.00 0.00 0.00 4.79
755 773 1.651987 TGCATAACTTAGCTGGACGC 58.348 50.000 0.00 0.00 39.57 5.19
756 774 1.066502 TGCATAACTTAGCTGGACGCA 60.067 47.619 0.00 0.00 42.61 5.24
757 775 1.594862 GCATAACTTAGCTGGACGCAG 59.405 52.381 0.00 0.00 42.61 5.18
758 776 2.205074 CATAACTTAGCTGGACGCAGG 58.795 52.381 0.00 0.00 42.61 4.85
759 777 0.108329 TAACTTAGCTGGACGCAGGC 60.108 55.000 0.00 0.00 42.61 4.85
760 778 2.512515 CTTAGCTGGACGCAGGCC 60.513 66.667 0.00 0.00 42.61 5.19
761 779 3.003173 TTAGCTGGACGCAGGCCT 61.003 61.111 0.00 0.00 42.61 5.19
762 780 2.527951 CTTAGCTGGACGCAGGCCTT 62.528 60.000 0.00 0.00 42.61 4.35
763 781 2.803155 TTAGCTGGACGCAGGCCTTG 62.803 60.000 0.00 0.00 42.61 3.61
764 782 4.704833 GCTGGACGCAGGCCTTGA 62.705 66.667 0.00 0.00 38.92 3.02
765 783 2.270205 CTGGACGCAGGCCTTGAT 59.730 61.111 0.00 0.00 0.00 2.57
766 784 1.522092 CTGGACGCAGGCCTTGATA 59.478 57.895 0.00 0.00 0.00 2.15
767 785 0.811616 CTGGACGCAGGCCTTGATAC 60.812 60.000 0.00 0.00 0.00 2.24
768 786 1.523938 GGACGCAGGCCTTGATACC 60.524 63.158 0.00 0.00 0.00 2.73
769 787 1.523938 GACGCAGGCCTTGATACCC 60.524 63.158 0.00 0.00 0.00 3.69
770 788 2.252072 GACGCAGGCCTTGATACCCA 62.252 60.000 0.00 0.00 0.00 4.51
771 789 1.077787 CGCAGGCCTTGATACCCAA 60.078 57.895 0.00 0.00 0.00 4.12
772 790 0.679640 CGCAGGCCTTGATACCCAAA 60.680 55.000 0.00 0.00 33.76 3.28
773 791 1.555967 GCAGGCCTTGATACCCAAAA 58.444 50.000 0.00 0.00 33.76 2.44
774 792 1.899142 GCAGGCCTTGATACCCAAAAA 59.101 47.619 0.00 0.00 33.76 1.94
791 809 1.203237 AAAATTGTATGCTGGGGCCC 58.797 50.000 18.17 18.17 37.74 5.80
792 810 1.042559 AAATTGTATGCTGGGGCCCG 61.043 55.000 19.83 14.09 37.74 6.13
793 811 1.932156 AATTGTATGCTGGGGCCCGA 61.932 55.000 19.83 12.10 37.74 5.14
794 812 2.343475 ATTGTATGCTGGGGCCCGAG 62.343 60.000 28.58 28.58 37.74 4.63
795 813 4.256180 GTATGCTGGGGCCCGAGG 62.256 72.222 32.47 18.01 37.74 4.63
937 956 5.258622 CGCAATTTCAACTCCGATTAGAAG 58.741 41.667 0.00 0.00 0.00 2.85
957 976 1.153429 GCGAATCGTAGCCCCTGTT 60.153 57.895 4.07 0.00 0.00 3.16
1073 1098 1.425066 CCCCAATGCCTAGGATTGCTA 59.575 52.381 14.75 0.00 30.66 3.49
1564 1589 1.065997 AGGTTGTTGCCACCCCTACT 61.066 55.000 0.00 0.00 0.00 2.57
2000 2028 4.600576 TTGCGCACGTGAGCCTCA 62.601 61.111 35.78 20.26 40.22 3.86
2031 2059 3.966543 CCAACTGGAAGGGGGCGT 61.967 66.667 0.00 0.00 39.30 5.68
2051 2079 2.477845 TTTACCTGGACTAAACCGCC 57.522 50.000 0.00 0.00 0.00 6.13
2052 2080 1.350071 TTACCTGGACTAAACCGCCA 58.650 50.000 0.00 0.00 0.00 5.69
2632 2690 6.240894 TGAGCTTAATGTTGGAGAACTGAAT 58.759 36.000 0.00 0.00 32.79 2.57
2811 2916 1.135199 CCTGCTGAACAATGATGCCAC 60.135 52.381 0.00 0.00 0.00 5.01
2856 2973 7.831691 TGGTTTCTTGTTTTATGATCCTCAA 57.168 32.000 0.00 0.00 0.00 3.02
2878 3001 5.606348 AATTAGTTGTTGTCTTTTGGGCA 57.394 34.783 0.00 0.00 0.00 5.36
2883 3006 2.199652 TTGTCTTTTGGGCAGGCGG 61.200 57.895 0.00 0.00 0.00 6.13
2884 3007 2.282180 GTCTTTTGGGCAGGCGGA 60.282 61.111 0.00 0.00 0.00 5.54
2924 3050 6.861065 ATGCTGTACCGTTTAAATCCTATG 57.139 37.500 0.00 0.00 0.00 2.23
2927 3053 5.362105 TGTACCGTTTAAATCCTATGGCT 57.638 39.130 0.00 0.00 0.00 4.75
2928 3054 6.482898 TGTACCGTTTAAATCCTATGGCTA 57.517 37.500 0.00 0.00 0.00 3.93
2929 3055 7.069877 TGTACCGTTTAAATCCTATGGCTAT 57.930 36.000 0.00 0.00 0.00 2.97
2930 3056 6.932400 TGTACCGTTTAAATCCTATGGCTATG 59.068 38.462 0.00 0.00 0.00 2.23
2968 3094 3.030291 TGTCAAAATGCCTGAACTGGTT 58.970 40.909 0.00 0.00 0.00 3.67
3132 3548 8.773404 ATATTACCTCCGTATGAAAATGTAGC 57.227 34.615 0.00 0.00 0.00 3.58
3133 3549 3.454375 ACCTCCGTATGAAAATGTAGCG 58.546 45.455 0.00 0.00 0.00 4.26
3254 3690 4.079558 AGGGTTGAGGTAATTCTGCATGAT 60.080 41.667 0.00 0.00 0.00 2.45
3257 3693 4.090761 TGAGGTAATTCTGCATGATCCC 57.909 45.455 0.00 0.00 0.00 3.85
3274 3713 3.130280 TCCCCTAGAAACACGTTTTCC 57.870 47.619 15.14 0.00 32.11 3.13
3347 3795 2.731572 TCCGGAGTGGACTAAGTAAGG 58.268 52.381 0.00 0.00 43.74 2.69
3348 3796 1.755380 CCGGAGTGGACTAAGTAAGGG 59.245 57.143 0.00 0.00 42.00 3.95
3349 3797 1.136500 CGGAGTGGACTAAGTAAGGGC 59.864 57.143 0.00 0.00 0.00 5.19
3350 3798 2.185387 GGAGTGGACTAAGTAAGGGCA 58.815 52.381 0.00 0.00 0.00 5.36
3351 3799 2.093606 GGAGTGGACTAAGTAAGGGCAC 60.094 54.545 0.00 0.00 0.00 5.01
3352 3800 1.549170 AGTGGACTAAGTAAGGGCACG 59.451 52.381 0.00 0.00 0.00 5.34
3353 3801 1.274447 GTGGACTAAGTAAGGGCACGT 59.726 52.381 0.00 0.00 0.00 4.49
3354 3802 2.493278 GTGGACTAAGTAAGGGCACGTA 59.507 50.000 0.00 0.00 0.00 3.57
3355 3803 2.493278 TGGACTAAGTAAGGGCACGTAC 59.507 50.000 3.60 3.60 32.61 3.67
3356 3804 2.493278 GGACTAAGTAAGGGCACGTACA 59.507 50.000 14.63 0.00 34.54 2.90
3357 3805 3.056607 GGACTAAGTAAGGGCACGTACAA 60.057 47.826 14.63 1.22 34.54 2.41
3358 3806 4.382362 GGACTAAGTAAGGGCACGTACAAT 60.382 45.833 14.63 5.34 34.54 2.71
3359 3807 4.501071 ACTAAGTAAGGGCACGTACAATG 58.499 43.478 14.63 5.86 34.54 2.82
3360 3808 1.734163 AGTAAGGGCACGTACAATGC 58.266 50.000 14.63 10.03 42.62 3.56
3361 3809 1.002659 AGTAAGGGCACGTACAATGCA 59.997 47.619 14.63 0.00 45.27 3.96
3362 3810 2.014128 GTAAGGGCACGTACAATGCAT 58.986 47.619 18.09 0.00 45.27 3.96
3363 3811 2.411628 AAGGGCACGTACAATGCATA 57.588 45.000 18.09 0.00 45.27 3.14
3364 3812 1.953559 AGGGCACGTACAATGCATAG 58.046 50.000 18.09 0.00 45.27 2.23
3365 3813 0.307760 GGGCACGTACAATGCATAGC 59.692 55.000 18.09 3.75 45.27 2.97
3366 3814 0.307760 GGCACGTACAATGCATAGCC 59.692 55.000 18.09 1.71 45.27 3.93
3367 3815 0.307760 GCACGTACAATGCATAGCCC 59.692 55.000 12.96 0.00 42.88 5.19
3368 3816 1.953559 CACGTACAATGCATAGCCCT 58.046 50.000 0.00 0.00 0.00 5.19
3369 3817 2.805295 GCACGTACAATGCATAGCCCTA 60.805 50.000 12.96 0.00 42.88 3.53
3370 3818 3.059884 CACGTACAATGCATAGCCCTAG 58.940 50.000 0.00 0.00 0.00 3.02
3371 3819 2.037251 ACGTACAATGCATAGCCCTAGG 59.963 50.000 0.00 0.06 0.00 3.02
3372 3820 2.612972 CGTACAATGCATAGCCCTAGGG 60.613 54.545 24.89 24.89 38.57 3.53
3373 3821 1.522900 ACAATGCATAGCCCTAGGGT 58.477 50.000 28.96 17.54 37.65 4.34
3374 3822 1.143684 ACAATGCATAGCCCTAGGGTG 59.856 52.381 28.96 19.89 37.65 4.61
3375 3823 1.421268 CAATGCATAGCCCTAGGGTGA 59.579 52.381 28.96 17.32 37.65 4.02
3376 3824 2.040813 CAATGCATAGCCCTAGGGTGAT 59.959 50.000 28.96 18.79 37.65 3.06
3377 3825 1.059098 TGCATAGCCCTAGGGTGATG 58.941 55.000 28.96 28.13 37.65 3.07
3378 3826 0.322008 GCATAGCCCTAGGGTGATGC 60.322 60.000 34.54 34.54 43.10 3.91
3379 3827 0.326264 CATAGCCCTAGGGTGATGCC 59.674 60.000 28.96 11.17 37.65 4.40
3380 3828 0.194587 ATAGCCCTAGGGTGATGCCT 59.805 55.000 28.96 17.85 37.65 4.75
3381 3829 0.471971 TAGCCCTAGGGTGATGCCTC 60.472 60.000 28.96 9.64 37.65 4.70
3382 3830 2.072487 GCCCTAGGGTGATGCCTCA 61.072 63.158 28.96 0.00 37.65 3.86
3383 3831 1.422161 GCCCTAGGGTGATGCCTCAT 61.422 60.000 28.96 0.00 37.65 2.90
3384 3832 2.030027 CCCTAGGGTGATGCCTCATA 57.970 55.000 20.88 0.00 37.43 2.15
3385 3833 1.625818 CCCTAGGGTGATGCCTCATAC 59.374 57.143 20.88 0.00 37.43 2.39
3386 3834 1.273606 CCTAGGGTGATGCCTCATACG 59.726 57.143 0.00 0.00 37.43 3.06
3387 3835 0.679505 TAGGGTGATGCCTCATACGC 59.320 55.000 0.00 0.00 37.43 4.42
3388 3836 1.598130 GGGTGATGCCTCATACGCC 60.598 63.158 0.00 0.00 37.43 5.68
3389 3837 1.146041 GGTGATGCCTCATACGCCA 59.854 57.895 0.00 0.00 32.98 5.69
3390 3838 0.250467 GGTGATGCCTCATACGCCAT 60.250 55.000 0.00 0.00 32.98 4.40
3391 3839 0.870393 GTGATGCCTCATACGCCATG 59.130 55.000 0.00 0.00 32.98 3.66
3392 3840 0.469494 TGATGCCTCATACGCCATGT 59.531 50.000 0.00 0.00 35.96 3.21
3393 3841 1.691434 TGATGCCTCATACGCCATGTA 59.309 47.619 0.00 0.00 35.96 2.29
3394 3842 2.289010 TGATGCCTCATACGCCATGTAG 60.289 50.000 0.00 0.00 36.25 2.74
3395 3843 0.392706 TGCCTCATACGCCATGTAGG 59.607 55.000 0.00 9.69 36.25 3.18
3396 3844 0.679505 GCCTCATACGCCATGTAGGA 59.320 55.000 14.67 1.76 41.27 2.94
3397 3845 1.276421 GCCTCATACGCCATGTAGGAT 59.724 52.381 14.67 0.00 42.46 3.24
3398 3846 2.675317 GCCTCATACGCCATGTAGGATC 60.675 54.545 14.67 0.00 42.46 3.36
3399 3847 2.562738 CCTCATACGCCATGTAGGATCA 59.437 50.000 0.00 0.00 42.46 2.92
3400 3848 3.367806 CCTCATACGCCATGTAGGATCAG 60.368 52.174 0.00 0.00 42.46 2.90
3401 3849 3.496331 TCATACGCCATGTAGGATCAGA 58.504 45.455 0.00 0.00 38.83 3.27
3402 3850 3.895041 TCATACGCCATGTAGGATCAGAA 59.105 43.478 0.00 0.00 38.83 3.02
3403 3851 4.343814 TCATACGCCATGTAGGATCAGAAA 59.656 41.667 0.00 0.00 38.83 2.52
3404 3852 3.627395 ACGCCATGTAGGATCAGAAAA 57.373 42.857 0.00 0.00 41.22 2.29
3405 3853 3.950397 ACGCCATGTAGGATCAGAAAAA 58.050 40.909 0.00 0.00 41.22 1.94
3428 3876 7.836479 AAAATAGGATCGGTTAGTAGTAGCT 57.164 36.000 0.00 0.00 0.00 3.32
3429 3877 8.930846 AAAATAGGATCGGTTAGTAGTAGCTA 57.069 34.615 0.00 0.00 0.00 3.32
3430 3878 8.564509 AAATAGGATCGGTTAGTAGTAGCTAG 57.435 38.462 0.00 0.00 0.00 3.42
3431 3879 4.325972 AGGATCGGTTAGTAGTAGCTAGC 58.674 47.826 6.62 6.62 0.00 3.42
3432 3880 4.070716 GGATCGGTTAGTAGTAGCTAGCA 58.929 47.826 18.83 0.00 0.00 3.49
3433 3881 4.701171 GGATCGGTTAGTAGTAGCTAGCAT 59.299 45.833 18.83 4.86 0.00 3.79
3434 3882 5.183522 GGATCGGTTAGTAGTAGCTAGCATT 59.816 44.000 18.83 4.13 0.00 3.56
3435 3883 6.373774 GGATCGGTTAGTAGTAGCTAGCATTA 59.626 42.308 18.83 3.08 0.00 1.90
3436 3884 7.067251 GGATCGGTTAGTAGTAGCTAGCATTAT 59.933 40.741 18.83 2.12 0.00 1.28
3437 3885 7.142306 TCGGTTAGTAGTAGCTAGCATTATG 57.858 40.000 18.83 0.00 0.00 1.90
3438 3886 6.150641 TCGGTTAGTAGTAGCTAGCATTATGG 59.849 42.308 18.83 0.00 0.00 2.74
3439 3887 6.625300 CGGTTAGTAGTAGCTAGCATTATGGG 60.625 46.154 18.83 0.00 0.00 4.00
3440 3888 6.436532 GGTTAGTAGTAGCTAGCATTATGGGA 59.563 42.308 18.83 0.00 0.00 4.37
3441 3889 7.363094 GGTTAGTAGTAGCTAGCATTATGGGAG 60.363 44.444 18.83 0.00 0.00 4.30
3442 3890 5.893500 AGTAGTAGCTAGCATTATGGGAGA 58.106 41.667 18.83 0.00 0.00 3.71
3443 3891 6.315714 AGTAGTAGCTAGCATTATGGGAGAA 58.684 40.000 18.83 0.00 0.00 2.87
3444 3892 6.782988 AGTAGTAGCTAGCATTATGGGAGAAA 59.217 38.462 18.83 0.00 0.00 2.52
3445 3893 6.500589 AGTAGCTAGCATTATGGGAGAAAA 57.499 37.500 18.83 0.00 0.00 2.29
3446 3894 6.900194 AGTAGCTAGCATTATGGGAGAAAAA 58.100 36.000 18.83 0.00 0.00 1.94
3469 3917 8.837099 AAAATCAATATAGATTCCCCAACACA 57.163 30.769 0.00 0.00 37.24 3.72
3470 3918 9.438163 AAAATCAATATAGATTCCCCAACACAT 57.562 29.630 0.00 0.00 37.24 3.21
3471 3919 8.641498 AATCAATATAGATTCCCCAACACATC 57.359 34.615 0.00 0.00 33.03 3.06
3472 3920 7.147958 TCAATATAGATTCCCCAACACATCA 57.852 36.000 0.00 0.00 0.00 3.07
3473 3921 7.758609 TCAATATAGATTCCCCAACACATCAT 58.241 34.615 0.00 0.00 0.00 2.45
3474 3922 7.666804 TCAATATAGATTCCCCAACACATCATG 59.333 37.037 0.00 0.00 0.00 3.07
3475 3923 2.381911 AGATTCCCCAACACATCATGC 58.618 47.619 0.00 0.00 0.00 4.06
3476 3924 2.101783 GATTCCCCAACACATCATGCA 58.898 47.619 0.00 0.00 0.00 3.96
3477 3925 1.548081 TTCCCCAACACATCATGCAG 58.452 50.000 0.00 0.00 0.00 4.41
3478 3926 0.405198 TCCCCAACACATCATGCAGT 59.595 50.000 0.00 0.00 0.00 4.40
3479 3927 0.528924 CCCCAACACATCATGCAGTG 59.471 55.000 13.62 13.62 41.40 3.66
3480 3928 0.108992 CCCAACACATCATGCAGTGC 60.109 55.000 8.58 8.58 39.30 4.40
3481 3929 0.455464 CCAACACATCATGCAGTGCG 60.455 55.000 11.20 0.00 39.30 5.34
3482 3930 1.068832 CAACACATCATGCAGTGCGC 61.069 55.000 11.20 0.00 39.30 6.09
3483 3931 2.277057 CACATCATGCAGTGCGCG 60.277 61.111 11.20 0.00 46.97 6.86
3484 3932 4.170062 ACATCATGCAGTGCGCGC 62.170 61.111 27.26 27.26 46.97 6.86
3485 3933 3.872728 CATCATGCAGTGCGCGCT 61.873 61.111 33.29 19.72 46.97 5.92
3486 3934 3.570638 ATCATGCAGTGCGCGCTC 61.571 61.111 33.29 28.81 46.97 5.03
3490 3938 3.738429 ATGCAGTGCGCGCTCCATA 62.738 57.895 33.29 16.98 46.97 2.74
3491 3939 3.634072 GCAGTGCGCGCTCCATAG 61.634 66.667 33.29 18.50 0.00 2.23
3492 3940 2.963854 CAGTGCGCGCTCCATAGG 60.964 66.667 33.29 11.77 0.00 2.57
3493 3941 3.147595 AGTGCGCGCTCCATAGGA 61.148 61.111 33.29 5.92 0.00 2.94
3494 3942 2.202878 GTGCGCGCTCCATAGGAA 60.203 61.111 33.29 5.03 0.00 3.36
3495 3943 1.595382 GTGCGCGCTCCATAGGAAT 60.595 57.895 33.29 0.00 0.00 3.01
3496 3944 1.146041 TGCGCGCTCCATAGGAATT 59.854 52.632 33.29 0.00 0.00 2.17
3497 3945 1.159713 TGCGCGCTCCATAGGAATTG 61.160 55.000 33.29 0.00 0.00 2.32
3498 3946 0.880278 GCGCGCTCCATAGGAATTGA 60.880 55.000 26.67 0.00 0.00 2.57
3499 3947 1.581934 CGCGCTCCATAGGAATTGAA 58.418 50.000 5.56 0.00 0.00 2.69
3500 3948 1.261619 CGCGCTCCATAGGAATTGAAC 59.738 52.381 5.56 0.00 0.00 3.18
3501 3949 2.288666 GCGCTCCATAGGAATTGAACA 58.711 47.619 0.00 0.00 0.00 3.18
3502 3950 2.032178 GCGCTCCATAGGAATTGAACAC 59.968 50.000 0.00 0.00 0.00 3.32
3503 3951 2.285220 CGCTCCATAGGAATTGAACACG 59.715 50.000 0.00 0.00 0.00 4.49
3504 3952 3.531538 GCTCCATAGGAATTGAACACGA 58.468 45.455 0.00 0.00 0.00 4.35
3505 3953 3.557595 GCTCCATAGGAATTGAACACGAG 59.442 47.826 0.00 0.00 0.00 4.18
3506 3954 4.680708 GCTCCATAGGAATTGAACACGAGA 60.681 45.833 0.00 0.00 0.00 4.04
3507 3955 4.755411 TCCATAGGAATTGAACACGAGAC 58.245 43.478 0.00 0.00 0.00 3.36
3508 3956 3.871594 CCATAGGAATTGAACACGAGACC 59.128 47.826 0.00 0.00 0.00 3.85
3509 3957 4.383118 CCATAGGAATTGAACACGAGACCT 60.383 45.833 0.00 0.00 0.00 3.85
3510 3958 3.771577 AGGAATTGAACACGAGACCTT 57.228 42.857 0.00 0.00 0.00 3.50
3511 3959 3.665190 AGGAATTGAACACGAGACCTTC 58.335 45.455 0.00 0.00 0.00 3.46
3512 3960 3.325135 AGGAATTGAACACGAGACCTTCT 59.675 43.478 0.00 0.00 0.00 2.85
3513 3961 4.065789 GGAATTGAACACGAGACCTTCTT 58.934 43.478 0.00 0.00 0.00 2.52
3514 3962 5.011738 AGGAATTGAACACGAGACCTTCTTA 59.988 40.000 0.00 0.00 0.00 2.10
3515 3963 5.120363 GGAATTGAACACGAGACCTTCTTAC 59.880 44.000 0.00 0.00 0.00 2.34
3516 3964 3.655276 TGAACACGAGACCTTCTTACC 57.345 47.619 0.00 0.00 0.00 2.85
3517 3965 2.030540 TGAACACGAGACCTTCTTACCG 60.031 50.000 0.00 0.00 0.00 4.02
3518 3966 0.886563 ACACGAGACCTTCTTACCGG 59.113 55.000 0.00 0.00 0.00 5.28
3519 3967 0.172803 CACGAGACCTTCTTACCGGG 59.827 60.000 6.32 0.00 0.00 5.73
3520 3968 0.038744 ACGAGACCTTCTTACCGGGA 59.961 55.000 6.32 0.00 0.00 5.14
3521 3969 1.180029 CGAGACCTTCTTACCGGGAA 58.820 55.000 6.32 0.97 0.00 3.97
3522 3970 1.547372 CGAGACCTTCTTACCGGGAAA 59.453 52.381 6.32 0.00 0.00 3.13
3523 3971 2.673326 CGAGACCTTCTTACCGGGAAAC 60.673 54.545 6.32 0.00 0.00 2.78
3524 3972 2.566279 GAGACCTTCTTACCGGGAAACT 59.434 50.000 6.32 0.00 0.00 2.66
3525 3973 3.766051 GAGACCTTCTTACCGGGAAACTA 59.234 47.826 6.32 0.00 0.00 2.24
3526 3974 3.513119 AGACCTTCTTACCGGGAAACTAC 59.487 47.826 6.32 0.00 0.00 2.73
3527 3975 3.242011 ACCTTCTTACCGGGAAACTACA 58.758 45.455 6.32 0.00 0.00 2.74
3528 3976 3.260128 ACCTTCTTACCGGGAAACTACAG 59.740 47.826 6.32 0.00 0.00 2.74
3529 3977 3.259902 CTTCTTACCGGGAAACTACAGC 58.740 50.000 6.32 0.00 0.00 4.40
3530 3978 2.532843 TCTTACCGGGAAACTACAGCT 58.467 47.619 6.32 0.00 0.00 4.24
3531 3979 2.494870 TCTTACCGGGAAACTACAGCTC 59.505 50.000 6.32 0.00 0.00 4.09
3532 3980 1.188863 TACCGGGAAACTACAGCTCC 58.811 55.000 6.32 0.00 0.00 4.70
3533 3981 0.544595 ACCGGGAAACTACAGCTCCT 60.545 55.000 6.32 0.00 0.00 3.69
3534 3982 1.272872 ACCGGGAAACTACAGCTCCTA 60.273 52.381 6.32 0.00 0.00 2.94
3535 3983 1.136500 CCGGGAAACTACAGCTCCTAC 59.864 57.143 0.00 0.00 0.00 3.18
3536 3984 1.136500 CGGGAAACTACAGCTCCTACC 59.864 57.143 0.00 0.00 0.00 3.18
3537 3985 2.185387 GGGAAACTACAGCTCCTACCA 58.815 52.381 0.00 0.00 0.00 3.25
3538 3986 2.093606 GGGAAACTACAGCTCCTACCAC 60.094 54.545 0.00 0.00 0.00 4.16
3539 3987 2.832733 GGAAACTACAGCTCCTACCACT 59.167 50.000 0.00 0.00 0.00 4.00
3540 3988 4.021916 GGAAACTACAGCTCCTACCACTA 58.978 47.826 0.00 0.00 0.00 2.74
3541 3989 4.142204 GGAAACTACAGCTCCTACCACTAC 60.142 50.000 0.00 0.00 0.00 2.73
3542 3990 3.733883 ACTACAGCTCCTACCACTACA 57.266 47.619 0.00 0.00 0.00 2.74
3543 3991 4.043608 ACTACAGCTCCTACCACTACAA 57.956 45.455 0.00 0.00 0.00 2.41
3544 3992 3.762823 ACTACAGCTCCTACCACTACAAC 59.237 47.826 0.00 0.00 0.00 3.32
3545 3993 1.900486 ACAGCTCCTACCACTACAACC 59.100 52.381 0.00 0.00 0.00 3.77
3546 3994 1.899814 CAGCTCCTACCACTACAACCA 59.100 52.381 0.00 0.00 0.00 3.67
3547 3995 2.301870 CAGCTCCTACCACTACAACCAA 59.698 50.000 0.00 0.00 0.00 3.67
3548 3996 3.055094 CAGCTCCTACCACTACAACCAAT 60.055 47.826 0.00 0.00 0.00 3.16
3549 3997 4.161565 CAGCTCCTACCACTACAACCAATA 59.838 45.833 0.00 0.00 0.00 1.90
3550 3998 4.406003 AGCTCCTACCACTACAACCAATAG 59.594 45.833 0.00 0.00 0.00 1.73
3551 3999 4.694339 CTCCTACCACTACAACCAATAGC 58.306 47.826 0.00 0.00 0.00 2.97
3552 4000 4.359105 TCCTACCACTACAACCAATAGCT 58.641 43.478 0.00 0.00 0.00 3.32
3553 4001 5.521696 TCCTACCACTACAACCAATAGCTA 58.478 41.667 0.00 0.00 0.00 3.32
3554 4002 5.361857 TCCTACCACTACAACCAATAGCTAC 59.638 44.000 0.00 0.00 0.00 3.58
3555 4003 5.363005 CCTACCACTACAACCAATAGCTACT 59.637 44.000 0.00 0.00 0.00 2.57
3556 4004 6.548622 CCTACCACTACAACCAATAGCTACTA 59.451 42.308 0.00 0.00 0.00 1.82
3557 4005 7.232941 CCTACCACTACAACCAATAGCTACTAT 59.767 40.741 0.00 0.00 0.00 2.12
3558 4006 7.433537 ACCACTACAACCAATAGCTACTATT 57.566 36.000 0.00 0.00 37.16 1.73
3589 4037 8.989653 TTTTTGAAACCGTTTTTACAGATTCT 57.010 26.923 0.00 0.00 0.00 2.40
3598 4046 9.503399 ACCGTTTTTACAGATTCTAATTTCTCT 57.497 29.630 0.00 0.00 0.00 3.10
3599 4047 9.760660 CCGTTTTTACAGATTCTAATTTCTCTG 57.239 33.333 0.00 0.00 40.71 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.449967 TAGCCCGAGGTGGACTTCCA 62.450 60.000 0.00 0.00 45.30 3.53
380 382 1.528776 GAGGACGCGTATCTCCCCT 60.529 63.158 23.53 19.49 0.00 4.79
456 458 1.104630 GACCGGAAGTCGAGGAAGAT 58.895 55.000 9.46 0.00 42.43 2.40
658 667 4.141065 TGAATAGAGAGAGCAGGGAGATCA 60.141 45.833 0.00 0.00 34.30 2.92
753 771 0.679640 TTTGGGTATCAAGGCCTGCG 60.680 55.000 5.69 0.00 36.62 5.18
754 772 1.555967 TTTTGGGTATCAAGGCCTGC 58.444 50.000 5.69 0.00 36.62 4.85
771 789 1.559219 GGGCCCCAGCATACAATTTTT 59.441 47.619 12.23 0.00 42.56 1.94
772 790 1.203237 GGGCCCCAGCATACAATTTT 58.797 50.000 12.23 0.00 42.56 1.82
773 791 1.042559 CGGGCCCCAGCATACAATTT 61.043 55.000 18.66 0.00 42.56 1.82
774 792 1.455587 CGGGCCCCAGCATACAATT 60.456 57.895 18.66 0.00 42.56 2.32
775 793 2.195683 CGGGCCCCAGCATACAAT 59.804 61.111 18.66 0.00 42.56 2.71
776 794 3.012119 TCGGGCCCCAGCATACAA 61.012 61.111 18.66 0.00 42.56 2.41
777 795 3.479203 CTCGGGCCCCAGCATACA 61.479 66.667 18.66 0.00 42.56 2.29
778 796 4.256180 CCTCGGGCCCCAGCATAC 62.256 72.222 18.66 0.00 42.56 2.39
783 801 3.242291 GATACCCTCGGGCCCCAG 61.242 72.222 18.66 14.15 39.32 4.45
784 802 4.892291 GGATACCCTCGGGCCCCA 62.892 72.222 18.66 0.85 39.32 4.96
788 806 3.394635 TTTGCGGATACCCTCGGGC 62.395 63.158 0.82 0.00 39.32 6.13
789 807 1.523032 GTTTGCGGATACCCTCGGG 60.523 63.158 0.00 0.00 42.03 5.14
790 808 1.523032 GGTTTGCGGATACCCTCGG 60.523 63.158 5.21 0.00 0.00 4.63
791 809 0.391927 TTGGTTTGCGGATACCCTCG 60.392 55.000 13.64 0.00 33.34 4.63
792 810 1.471287 GTTTGGTTTGCGGATACCCTC 59.529 52.381 13.64 1.36 33.34 4.30
793 811 1.541379 GTTTGGTTTGCGGATACCCT 58.459 50.000 13.64 0.00 33.34 4.34
794 812 0.528924 GGTTTGGTTTGCGGATACCC 59.471 55.000 13.64 0.00 33.34 3.69
795 813 1.249407 TGGTTTGGTTTGCGGATACC 58.751 50.000 9.60 9.60 34.93 2.73
796 814 3.488553 GCTATGGTTTGGTTTGCGGATAC 60.489 47.826 0.00 0.00 0.00 2.24
797 815 2.685897 GCTATGGTTTGGTTTGCGGATA 59.314 45.455 0.00 0.00 0.00 2.59
937 956 1.300233 CAGGGGCTACGATTCGCTC 60.300 63.158 5.86 0.00 0.00 5.03
2031 2059 2.106166 TGGCGGTTTAGTCCAGGTAAAA 59.894 45.455 0.00 0.00 0.00 1.52
2052 2080 4.355437 CTGAATCAAGAAGTCGCGATAGT 58.645 43.478 14.06 0.00 39.35 2.12
2632 2690 3.248024 ACCAGAACTACAGGAATCCACA 58.752 45.455 0.61 0.00 0.00 4.17
2760 2861 5.772521 ACAAAGTAGCAGCACCAAAAATAG 58.227 37.500 0.00 0.00 0.00 1.73
2763 2864 5.534654 AGATACAAAGTAGCAGCACCAAAAA 59.465 36.000 0.00 0.00 0.00 1.94
2811 2916 7.092137 ACCATGATATTCCAATCATATTGCG 57.908 36.000 0.00 0.00 43.23 4.85
2856 2973 5.453198 CCTGCCCAAAAGACAACAACTAATT 60.453 40.000 0.00 0.00 0.00 1.40
2924 3050 8.356000 ACAGTCTAATAAGAGGATACATAGCC 57.644 38.462 0.00 0.00 41.41 3.93
2968 3094 5.670485 TGACTGCTCTTCTCAGTTTACAAA 58.330 37.500 0.00 0.00 44.09 2.83
3122 3538 4.453136 TCACCTAAACACCGCTACATTTTC 59.547 41.667 0.00 0.00 0.00 2.29
3132 3548 4.625742 CAGTGTAGATTCACCTAAACACCG 59.374 45.833 0.00 0.00 38.91 4.94
3133 3549 5.548406 ACAGTGTAGATTCACCTAAACACC 58.452 41.667 0.00 0.00 38.91 4.16
3254 3690 2.707257 AGGAAAACGTGTTTCTAGGGGA 59.293 45.455 0.00 0.00 31.45 4.81
3257 3693 3.995048 GGAGAGGAAAACGTGTTTCTAGG 59.005 47.826 0.00 0.00 31.45 3.02
3347 3795 0.307760 GGCTATGCATTGTACGTGCC 59.692 55.000 17.26 4.38 41.83 5.01
3348 3796 0.307760 GGGCTATGCATTGTACGTGC 59.692 55.000 3.54 14.20 42.81 5.34
3349 3797 1.953559 AGGGCTATGCATTGTACGTG 58.046 50.000 3.54 0.00 0.00 4.49
3350 3798 2.037251 CCTAGGGCTATGCATTGTACGT 59.963 50.000 3.54 5.08 0.00 3.57
3351 3799 2.612972 CCCTAGGGCTATGCATTGTACG 60.613 54.545 16.90 0.00 0.00 3.67
3352 3800 2.372172 ACCCTAGGGCTATGCATTGTAC 59.628 50.000 28.88 0.22 39.32 2.90
3353 3801 2.371841 CACCCTAGGGCTATGCATTGTA 59.628 50.000 28.88 0.00 39.32 2.41
3354 3802 1.143684 CACCCTAGGGCTATGCATTGT 59.856 52.381 28.88 0.30 39.32 2.71
3355 3803 1.421268 TCACCCTAGGGCTATGCATTG 59.579 52.381 28.88 15.66 39.32 2.82
3356 3804 1.819753 TCACCCTAGGGCTATGCATT 58.180 50.000 28.88 2.02 39.32 3.56
3357 3805 1.632409 CATCACCCTAGGGCTATGCAT 59.368 52.381 28.88 3.79 39.32 3.96
3358 3806 1.059098 CATCACCCTAGGGCTATGCA 58.941 55.000 28.88 9.23 39.32 3.96
3359 3807 0.322008 GCATCACCCTAGGGCTATGC 60.322 60.000 34.95 34.95 44.06 3.14
3360 3808 0.326264 GGCATCACCCTAGGGCTATG 59.674 60.000 28.88 28.17 39.32 2.23
3361 3809 0.194587 AGGCATCACCCTAGGGCTAT 59.805 55.000 28.88 18.18 40.58 2.97
3362 3810 0.471971 GAGGCATCACCCTAGGGCTA 60.472 60.000 28.88 16.57 40.58 3.93
3363 3811 1.768077 GAGGCATCACCCTAGGGCT 60.768 63.158 28.88 15.44 40.58 5.19
3364 3812 1.422161 ATGAGGCATCACCCTAGGGC 61.422 60.000 28.88 13.14 38.57 5.19
3365 3813 1.625818 GTATGAGGCATCACCCTAGGG 59.374 57.143 27.36 27.36 38.57 3.53
3366 3814 1.273606 CGTATGAGGCATCACCCTAGG 59.726 57.143 1.71 0.06 38.57 3.02
3367 3815 1.337260 GCGTATGAGGCATCACCCTAG 60.337 57.143 1.71 0.00 38.57 3.02
3368 3816 0.679505 GCGTATGAGGCATCACCCTA 59.320 55.000 1.71 0.00 38.57 3.53
3369 3817 1.447643 GCGTATGAGGCATCACCCT 59.552 57.895 1.71 0.00 38.57 4.34
3370 3818 1.598130 GGCGTATGAGGCATCACCC 60.598 63.158 1.71 0.00 38.57 4.61
3371 3819 1.146041 TGGCGTATGAGGCATCACC 59.854 57.895 1.71 0.16 41.94 4.02
3372 3820 4.855105 TGGCGTATGAGGCATCAC 57.145 55.556 1.71 0.00 41.94 3.06
3377 3825 0.679505 TCCTACATGGCGTATGAGGC 59.320 55.000 8.47 0.00 39.21 4.70
3378 3826 2.562738 TGATCCTACATGGCGTATGAGG 59.437 50.000 8.47 9.87 39.21 3.86
3379 3827 3.507622 TCTGATCCTACATGGCGTATGAG 59.492 47.826 8.47 2.95 39.21 2.90
3380 3828 3.496331 TCTGATCCTACATGGCGTATGA 58.504 45.455 8.47 0.00 39.21 2.15
3381 3829 3.942130 TCTGATCCTACATGGCGTATG 57.058 47.619 0.00 1.05 42.68 2.39
3382 3830 4.955811 TTTCTGATCCTACATGGCGTAT 57.044 40.909 0.00 0.00 35.26 3.06
3383 3831 4.746535 TTTTCTGATCCTACATGGCGTA 57.253 40.909 0.00 0.00 35.26 4.42
3384 3832 3.627395 TTTTCTGATCCTACATGGCGT 57.373 42.857 0.00 0.00 35.26 5.68
3403 3851 8.247666 AGCTACTACTAACCGATCCTATTTTT 57.752 34.615 0.00 0.00 0.00 1.94
3404 3852 7.836479 AGCTACTACTAACCGATCCTATTTT 57.164 36.000 0.00 0.00 0.00 1.82
3405 3853 7.121020 GCTAGCTACTACTAACCGATCCTATTT 59.879 40.741 7.70 0.00 0.00 1.40
3406 3854 6.598850 GCTAGCTACTACTAACCGATCCTATT 59.401 42.308 7.70 0.00 0.00 1.73
3407 3855 6.114767 GCTAGCTACTACTAACCGATCCTAT 58.885 44.000 7.70 0.00 0.00 2.57
3408 3856 5.012458 TGCTAGCTACTACTAACCGATCCTA 59.988 44.000 17.23 0.00 0.00 2.94
3409 3857 4.202440 TGCTAGCTACTACTAACCGATCCT 60.202 45.833 17.23 0.00 0.00 3.24
3410 3858 4.070716 TGCTAGCTACTACTAACCGATCC 58.929 47.826 17.23 0.00 0.00 3.36
3411 3859 5.883503 ATGCTAGCTACTACTAACCGATC 57.116 43.478 17.23 0.00 0.00 3.69
3412 3860 7.148052 CCATAATGCTAGCTACTACTAACCGAT 60.148 40.741 17.23 0.00 0.00 4.18
3413 3861 6.150641 CCATAATGCTAGCTACTACTAACCGA 59.849 42.308 17.23 0.00 0.00 4.69
3414 3862 6.323266 CCATAATGCTAGCTACTACTAACCG 58.677 44.000 17.23 0.00 0.00 4.44
3415 3863 6.436532 TCCCATAATGCTAGCTACTACTAACC 59.563 42.308 17.23 0.00 0.00 2.85
3416 3864 7.393796 TCTCCCATAATGCTAGCTACTACTAAC 59.606 40.741 17.23 0.00 0.00 2.34
3417 3865 7.467650 TCTCCCATAATGCTAGCTACTACTAA 58.532 38.462 17.23 0.00 0.00 2.24
3418 3866 7.029053 TCTCCCATAATGCTAGCTACTACTA 57.971 40.000 17.23 0.00 0.00 1.82
3419 3867 5.893500 TCTCCCATAATGCTAGCTACTACT 58.106 41.667 17.23 0.00 0.00 2.57
3420 3868 6.591750 TTCTCCCATAATGCTAGCTACTAC 57.408 41.667 17.23 0.00 0.00 2.73
3421 3869 7.612065 TTTTCTCCCATAATGCTAGCTACTA 57.388 36.000 17.23 4.92 0.00 1.82
3422 3870 6.500589 TTTTCTCCCATAATGCTAGCTACT 57.499 37.500 17.23 2.62 0.00 2.57
3443 3891 9.265862 TGTGTTGGGGAATCTATATTGATTTTT 57.734 29.630 12.68 0.00 36.86 1.94
3444 3892 8.837099 TGTGTTGGGGAATCTATATTGATTTT 57.163 30.769 12.68 0.00 36.86 1.82
3445 3893 9.082313 GATGTGTTGGGGAATCTATATTGATTT 57.918 33.333 12.68 0.00 36.86 2.17
3446 3894 8.226810 TGATGTGTTGGGGAATCTATATTGATT 58.773 33.333 11.50 11.50 39.14 2.57
3447 3895 7.758609 TGATGTGTTGGGGAATCTATATTGAT 58.241 34.615 0.00 0.00 0.00 2.57
3448 3896 7.147958 TGATGTGTTGGGGAATCTATATTGA 57.852 36.000 0.00 0.00 0.00 2.57
3449 3897 7.576287 GCATGATGTGTTGGGGAATCTATATTG 60.576 40.741 0.00 0.00 0.00 1.90
3450 3898 6.435277 GCATGATGTGTTGGGGAATCTATATT 59.565 38.462 0.00 0.00 0.00 1.28
3451 3899 5.948162 GCATGATGTGTTGGGGAATCTATAT 59.052 40.000 0.00 0.00 0.00 0.86
3452 3900 5.163109 TGCATGATGTGTTGGGGAATCTATA 60.163 40.000 0.00 0.00 0.00 1.31
3453 3901 4.147321 GCATGATGTGTTGGGGAATCTAT 58.853 43.478 0.00 0.00 0.00 1.98
3454 3902 3.053768 TGCATGATGTGTTGGGGAATCTA 60.054 43.478 0.00 0.00 0.00 1.98
3455 3903 2.291735 TGCATGATGTGTTGGGGAATCT 60.292 45.455 0.00 0.00 0.00 2.40
3456 3904 2.100252 CTGCATGATGTGTTGGGGAATC 59.900 50.000 0.00 0.00 0.00 2.52
3457 3905 2.104967 CTGCATGATGTGTTGGGGAAT 58.895 47.619 0.00 0.00 0.00 3.01
3458 3906 1.203038 ACTGCATGATGTGTTGGGGAA 60.203 47.619 0.00 0.00 0.00 3.97
3459 3907 0.405198 ACTGCATGATGTGTTGGGGA 59.595 50.000 0.00 0.00 0.00 4.81
3460 3908 0.528924 CACTGCATGATGTGTTGGGG 59.471 55.000 0.00 0.00 0.00 4.96
3461 3909 0.108992 GCACTGCATGATGTGTTGGG 60.109 55.000 16.25 0.00 36.63 4.12
3462 3910 0.455464 CGCACTGCATGATGTGTTGG 60.455 55.000 16.25 6.32 36.63 3.77
3463 3911 1.068832 GCGCACTGCATGATGTGTTG 61.069 55.000 0.30 11.74 45.45 3.33
3464 3912 1.210931 GCGCACTGCATGATGTGTT 59.789 52.632 0.30 0.00 45.45 3.32
3465 3913 2.872557 GCGCACTGCATGATGTGT 59.127 55.556 0.30 0.00 45.45 3.72
3466 3914 2.277057 CGCGCACTGCATGATGTG 60.277 61.111 8.75 12.33 46.97 3.21
3467 3915 4.170062 GCGCGCACTGCATGATGT 62.170 61.111 29.10 0.00 46.97 3.06
3468 3916 3.785252 GAGCGCGCACTGCATGATG 62.785 63.158 35.10 0.00 46.97 3.07
3469 3917 3.570638 GAGCGCGCACTGCATGAT 61.571 61.111 35.10 8.99 46.97 2.45
3473 3921 4.449568 TATGGAGCGCGCACTGCA 62.450 61.111 35.10 25.17 46.97 4.41
3474 3922 3.634072 CTATGGAGCGCGCACTGC 61.634 66.667 35.10 19.77 41.47 4.40
3475 3923 2.906182 TTCCTATGGAGCGCGCACTG 62.906 60.000 35.10 17.22 31.21 3.66
3476 3924 2.032860 ATTCCTATGGAGCGCGCACT 62.033 55.000 35.10 14.51 31.21 4.40
3477 3925 1.160329 AATTCCTATGGAGCGCGCAC 61.160 55.000 35.10 27.93 31.21 5.34
3478 3926 1.146041 AATTCCTATGGAGCGCGCA 59.854 52.632 35.10 13.97 31.21 6.09
3479 3927 0.880278 TCAATTCCTATGGAGCGCGC 60.880 55.000 26.66 26.66 31.21 6.86
3480 3928 1.261619 GTTCAATTCCTATGGAGCGCG 59.738 52.381 0.00 0.00 31.21 6.86
3481 3929 2.032178 GTGTTCAATTCCTATGGAGCGC 59.968 50.000 0.00 0.00 31.21 5.92
3482 3930 2.285220 CGTGTTCAATTCCTATGGAGCG 59.715 50.000 0.00 0.00 31.21 5.03
3483 3931 3.531538 TCGTGTTCAATTCCTATGGAGC 58.468 45.455 0.00 0.00 31.21 4.70
3484 3932 4.806247 GTCTCGTGTTCAATTCCTATGGAG 59.194 45.833 0.00 0.00 31.21 3.86
3485 3933 4.382685 GGTCTCGTGTTCAATTCCTATGGA 60.383 45.833 0.00 0.00 0.00 3.41
3486 3934 3.871594 GGTCTCGTGTTCAATTCCTATGG 59.128 47.826 0.00 0.00 0.00 2.74
3487 3935 4.759782 AGGTCTCGTGTTCAATTCCTATG 58.240 43.478 0.00 0.00 0.00 2.23
3488 3936 5.187967 AGAAGGTCTCGTGTTCAATTCCTAT 59.812 40.000 0.00 0.00 0.00 2.57
3489 3937 4.527038 AGAAGGTCTCGTGTTCAATTCCTA 59.473 41.667 0.00 0.00 0.00 2.94
3490 3938 3.325135 AGAAGGTCTCGTGTTCAATTCCT 59.675 43.478 0.00 0.00 0.00 3.36
3491 3939 3.665190 AGAAGGTCTCGTGTTCAATTCC 58.335 45.455 0.00 0.00 0.00 3.01
3492 3940 5.120363 GGTAAGAAGGTCTCGTGTTCAATTC 59.880 44.000 0.00 0.00 0.00 2.17
3493 3941 4.995487 GGTAAGAAGGTCTCGTGTTCAATT 59.005 41.667 0.00 0.00 0.00 2.32
3494 3942 4.566987 GGTAAGAAGGTCTCGTGTTCAAT 58.433 43.478 0.00 0.00 0.00 2.57
3495 3943 3.551454 CGGTAAGAAGGTCTCGTGTTCAA 60.551 47.826 0.00 0.00 0.00 2.69
3496 3944 2.030540 CGGTAAGAAGGTCTCGTGTTCA 60.031 50.000 0.00 0.00 0.00 3.18
3497 3945 2.593257 CGGTAAGAAGGTCTCGTGTTC 58.407 52.381 0.00 0.00 0.00 3.18
3498 3946 1.271656 CCGGTAAGAAGGTCTCGTGTT 59.728 52.381 0.00 0.00 0.00 3.32
3499 3947 0.886563 CCGGTAAGAAGGTCTCGTGT 59.113 55.000 0.00 0.00 0.00 4.49
3500 3948 0.172803 CCCGGTAAGAAGGTCTCGTG 59.827 60.000 0.00 0.00 0.00 4.35
3501 3949 0.038744 TCCCGGTAAGAAGGTCTCGT 59.961 55.000 0.00 0.00 0.00 4.18
3502 3950 1.180029 TTCCCGGTAAGAAGGTCTCG 58.820 55.000 0.00 0.00 0.00 4.04
3503 3951 2.566279 AGTTTCCCGGTAAGAAGGTCTC 59.434 50.000 0.00 0.00 0.00 3.36
3504 3952 2.617658 AGTTTCCCGGTAAGAAGGTCT 58.382 47.619 0.00 0.00 0.00 3.85
3505 3953 3.259123 TGTAGTTTCCCGGTAAGAAGGTC 59.741 47.826 0.00 0.00 0.00 3.85
3506 3954 3.242011 TGTAGTTTCCCGGTAAGAAGGT 58.758 45.455 0.00 0.00 0.00 3.50
3507 3955 3.858247 CTGTAGTTTCCCGGTAAGAAGG 58.142 50.000 0.00 0.00 0.00 3.46
3508 3956 3.056035 AGCTGTAGTTTCCCGGTAAGAAG 60.056 47.826 0.00 0.00 0.00 2.85
3509 3957 2.901839 AGCTGTAGTTTCCCGGTAAGAA 59.098 45.455 0.00 0.00 0.00 2.52
3510 3958 2.494870 GAGCTGTAGTTTCCCGGTAAGA 59.505 50.000 0.00 0.00 0.00 2.10
3511 3959 2.418334 GGAGCTGTAGTTTCCCGGTAAG 60.418 54.545 0.00 0.00 0.00 2.34
3512 3960 1.551883 GGAGCTGTAGTTTCCCGGTAA 59.448 52.381 0.00 0.00 0.00 2.85
3513 3961 1.188863 GGAGCTGTAGTTTCCCGGTA 58.811 55.000 0.00 0.00 0.00 4.02
3514 3962 0.544595 AGGAGCTGTAGTTTCCCGGT 60.545 55.000 0.00 0.00 0.00 5.28
3515 3963 1.136500 GTAGGAGCTGTAGTTTCCCGG 59.864 57.143 0.00 0.00 0.00 5.73
3516 3964 1.136500 GGTAGGAGCTGTAGTTTCCCG 59.864 57.143 0.00 0.00 0.00 5.14
3517 3965 2.093606 GTGGTAGGAGCTGTAGTTTCCC 60.094 54.545 0.00 0.00 0.00 3.97
3518 3966 2.832733 AGTGGTAGGAGCTGTAGTTTCC 59.167 50.000 0.00 0.00 0.00 3.13
3519 3967 4.461781 TGTAGTGGTAGGAGCTGTAGTTTC 59.538 45.833 0.00 0.00 0.00 2.78
3520 3968 4.413760 TGTAGTGGTAGGAGCTGTAGTTT 58.586 43.478 0.00 0.00 0.00 2.66
3521 3969 4.043608 TGTAGTGGTAGGAGCTGTAGTT 57.956 45.455 0.00 0.00 0.00 2.24
3522 3970 3.733883 TGTAGTGGTAGGAGCTGTAGT 57.266 47.619 0.00 0.00 0.00 2.73
3523 3971 3.130693 GGTTGTAGTGGTAGGAGCTGTAG 59.869 52.174 0.00 0.00 0.00 2.74
3524 3972 3.094572 GGTTGTAGTGGTAGGAGCTGTA 58.905 50.000 0.00 0.00 0.00 2.74
3525 3973 1.900486 GGTTGTAGTGGTAGGAGCTGT 59.100 52.381 0.00 0.00 0.00 4.40
3526 3974 1.899814 TGGTTGTAGTGGTAGGAGCTG 59.100 52.381 0.00 0.00 0.00 4.24
3527 3975 2.320681 TGGTTGTAGTGGTAGGAGCT 57.679 50.000 0.00 0.00 0.00 4.09
3528 3976 3.629142 ATTGGTTGTAGTGGTAGGAGC 57.371 47.619 0.00 0.00 0.00 4.70
3529 3977 4.406003 AGCTATTGGTTGTAGTGGTAGGAG 59.594 45.833 0.00 0.00 0.00 3.69
3530 3978 4.359105 AGCTATTGGTTGTAGTGGTAGGA 58.641 43.478 0.00 0.00 0.00 2.94
3531 3979 4.755266 AGCTATTGGTTGTAGTGGTAGG 57.245 45.455 0.00 0.00 0.00 3.18
3532 3980 6.466885 AGTAGCTATTGGTTGTAGTGGTAG 57.533 41.667 0.00 0.00 0.00 3.18
3533 3981 8.418662 CAATAGTAGCTATTGGTTGTAGTGGTA 58.581 37.037 16.80 0.00 45.42 3.25
3534 3982 7.272978 CAATAGTAGCTATTGGTTGTAGTGGT 58.727 38.462 16.80 0.00 45.42 4.16
3535 3983 7.715265 CAATAGTAGCTATTGGTTGTAGTGG 57.285 40.000 16.80 0.00 45.42 4.00
3564 4012 8.989653 AGAATCTGTAAAAACGGTTTCAAAAA 57.010 26.923 6.57 0.00 30.86 1.94
3572 4020 9.503399 AGAGAAATTAGAATCTGTAAAAACGGT 57.497 29.630 0.00 0.00 0.00 4.83
3573 4021 9.760660 CAGAGAAATTAGAATCTGTAAAAACGG 57.239 33.333 0.00 0.00 35.52 4.44


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

AutoCloner maintained by Alex Coulton.