Multiple sequence alignment - TraesCS7D01G411200

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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 TraesCS7D01G411200 chr7D 100.000 3978 0 0 1 3978 530102178 530106155 0.000000e+00 7347.0
1 TraesCS7D01G411200 chr7D 89.737 380 26 8 55 433 530023626 530023993 1.290000e-129 473.0
2 TraesCS7D01G411200 chr7D 83.650 263 8 11 520 782 530024494 530024721 8.660000e-52 215.0
3 TraesCS7D01G411200 chr7D 94.915 59 3 0 1 59 530015911 530015969 4.230000e-15 93.5
4 TraesCS7D01G411200 chr7A 92.917 2866 150 14 849 3681 610433588 610436433 0.000000e+00 4119.0
5 TraesCS7D01G411200 chr7A 87.161 2251 244 25 854 3069 609548659 609550899 0.000000e+00 2514.0
6 TraesCS7D01G411200 chr7A 95.946 296 12 0 3683 3978 610436471 610436766 7.730000e-132 481.0
7 TraesCS7D01G411200 chr7A 90.583 223 14 4 55 277 609526763 609526978 5.030000e-74 289.0
8 TraesCS7D01G411200 chr7A 89.091 220 15 2 1008 1226 610432356 610432567 8.480000e-67 265.0
9 TraesCS7D01G411200 chr7A 83.270 263 9 12 520 782 609548265 609548492 4.030000e-50 209.0
10 TraesCS7D01G411200 chr7A 86.875 160 16 3 274 433 609547598 609547752 1.470000e-39 174.0
11 TraesCS7D01G411200 chr7A 93.056 72 5 0 782 853 610433106 610433177 5.440000e-19 106.0
12 TraesCS7D01G411200 chr7A 94.915 59 3 0 1 59 609519029 609519087 4.230000e-15 93.5
13 TraesCS7D01G411200 chr7B 91.477 2851 203 12 849 3681 568645656 568648484 0.000000e+00 3882.0
14 TraesCS7D01G411200 chr7B 89.366 2238 202 21 854 3069 568488075 568490298 0.000000e+00 2782.0
15 TraesCS7D01G411200 chr7B 88.987 454 28 8 1 445 568485369 568485809 3.500000e-150 542.0
16 TraesCS7D01G411200 chr7B 95.608 296 13 0 3683 3978 568648522 568648817 3.600000e-130 475.0
17 TraesCS7D01G411200 chr7B 95.789 95 3 1 691 785 568487627 568487720 6.890000e-33 152.0
18 TraesCS7D01G411200 chr7B 93.617 47 3 0 3193 3239 568637893 568637939 1.980000e-08 71.3
19 TraesCS7D01G411200 chr7B 93.617 47 3 0 3193 3239 568642466 568642512 1.980000e-08 71.3


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 TraesCS7D01G411200 chr7D 530102178 530106155 3977 False 7347.000000 7347 100.000000 1 3978 1 chr7D.!!$F2 3977
1 TraesCS7D01G411200 chr7D 530023626 530024721 1095 False 344.000000 473 86.693500 55 782 2 chr7D.!!$F3 727
2 TraesCS7D01G411200 chr7A 610432356 610436766 4410 False 1242.750000 4119 92.752500 782 3978 4 chr7A.!!$F4 3196
3 TraesCS7D01G411200 chr7A 609547598 609550899 3301 False 965.666667 2514 85.768667 274 3069 3 chr7A.!!$F3 2795
4 TraesCS7D01G411200 chr7B 568642466 568648817 6351 False 1476.100000 3882 93.567333 849 3978 3 chr7B.!!$F3 3129
5 TraesCS7D01G411200 chr7B 568485369 568490298 4929 False 1158.666667 2782 91.380667 1 3069 3 chr7B.!!$F2 3068

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
810 2929 0.179056 ATGAATAACTCACCGGCCGG 60.179 55.0 42.17 42.17 36.69 6.13 F
1724 4292 0.112606 TCAGTCACCGTCTCCTCCTT 59.887 55.0 0.00 0.00 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 4934 0.600057 CCCTCTCTTGCCTTTTGTGC 59.400 55.0 0.00 0.0 0.00 4.57 R
3305 5930 0.179134 CTCCCGGAACTTCTGCGTAG 60.179 60.0 0.73 0.0 37.12 3.51 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
31 32 3.777465 CAGAACATGCTTTGATCCCAG 57.223 47.619 0.00 0.00 0.00 4.45
37 38 3.521126 ACATGCTTTGATCCCAGTCTACT 59.479 43.478 0.00 0.00 0.00 2.57
50 51 7.973048 TCCCAGTCTACTATTAACATTGAGT 57.027 36.000 0.00 0.00 0.00 3.41
175 176 3.652869 TGGTCAAGACTCTCCAAATCCTT 59.347 43.478 0.00 0.00 0.00 3.36
199 200 9.994432 CTTCAATGGATATTACTCTTTGTCAAC 57.006 33.333 0.00 0.00 0.00 3.18
212 213 6.262273 ACTCTTTGTCAACGTCCAATAAACAT 59.738 34.615 0.00 0.00 0.00 2.71
216 217 6.567687 TGTCAACGTCCAATAAACATGAAT 57.432 33.333 0.00 0.00 0.00 2.57
221 231 6.691754 ACGTCCAATAAACATGAATGCATA 57.308 33.333 0.00 0.00 32.27 3.14
235 245 4.635324 TGAATGCATAATTGTGAGCGAAGA 59.365 37.500 6.35 0.00 0.00 2.87
238 248 3.750652 TGCATAATTGTGAGCGAAGACAA 59.249 39.130 6.35 0.00 36.54 3.18
257 267 9.760660 GAAGACAAACATAATCAAGTGTATGAC 57.239 33.333 0.00 0.00 32.94 3.06
271 281 6.590234 AGTGTATGACTGTGAGTGACAATA 57.410 37.500 0.00 0.00 32.80 1.90
340 350 3.382227 TGCAACATGATTCTATTGGGCTG 59.618 43.478 0.00 0.00 0.00 4.85
402 412 8.280258 TCATAGGATTAAATTGGTCTCCTCAT 57.720 34.615 0.00 0.00 37.51 2.90
404 414 9.359653 CATAGGATTAAATTGGTCTCCTCATTT 57.640 33.333 0.00 0.00 37.51 2.32
433 443 1.386533 AGCTAATGATGCAGTGCACC 58.613 50.000 22.44 12.43 43.04 5.01
438 448 2.753043 GATGCAGTGCACCAGGGG 60.753 66.667 22.44 0.00 43.04 4.79
459 469 4.561735 GTGAAACCAGACCAAATTCGAA 57.438 40.909 0.00 0.00 0.00 3.71
460 470 4.287720 GTGAAACCAGACCAAATTCGAAC 58.712 43.478 0.00 0.00 0.00 3.95
461 471 3.002862 TGAAACCAGACCAAATTCGAACG 59.997 43.478 0.00 0.00 0.00 3.95
462 472 1.519408 ACCAGACCAAATTCGAACGG 58.481 50.000 0.00 4.10 0.00 4.44
463 473 1.071071 ACCAGACCAAATTCGAACGGA 59.929 47.619 15.09 0.00 0.00 4.69
465 475 3.055675 ACCAGACCAAATTCGAACGGATA 60.056 43.478 15.09 0.00 0.00 2.59
466 476 3.936453 CCAGACCAAATTCGAACGGATAA 59.064 43.478 15.09 0.00 0.00 1.75
490 500 5.867166 CGCTACCGTATCCTATTCTCTAAC 58.133 45.833 0.00 0.00 0.00 2.34
491 501 5.642919 CGCTACCGTATCCTATTCTCTAACT 59.357 44.000 0.00 0.00 0.00 2.24
495 505 9.896263 CTACCGTATCCTATTCTCTAACTTTTC 57.104 37.037 0.00 0.00 0.00 2.29
508 518 7.518188 TCTCTAACTTTTCTGGATTTGGAAGT 58.482 34.615 0.00 0.00 0.00 3.01
511 521 3.897505 ACTTTTCTGGATTTGGAAGTGGG 59.102 43.478 0.00 0.00 0.00 4.61
588 2707 5.089970 TGCTATCTTGCTAACATGTGAGT 57.910 39.130 12.02 0.00 0.00 3.41
606 2725 3.504520 TGAGTGTGTACGATGTAGCTTGA 59.495 43.478 0.00 0.00 0.00 3.02
607 2726 3.834610 AGTGTGTACGATGTAGCTTGAC 58.165 45.455 0.00 0.00 0.00 3.18
608 2727 2.921754 GTGTGTACGATGTAGCTTGACC 59.078 50.000 0.00 0.00 0.00 4.02
609 2728 2.182825 GTGTACGATGTAGCTTGACCG 58.817 52.381 0.00 0.00 0.00 4.79
610 2729 1.133598 TGTACGATGTAGCTTGACCGG 59.866 52.381 0.00 0.00 0.00 5.28
611 2730 1.402968 GTACGATGTAGCTTGACCGGA 59.597 52.381 9.46 0.00 0.00 5.14
612 2731 0.892755 ACGATGTAGCTTGACCGGAA 59.107 50.000 9.46 0.00 0.00 4.30
613 2732 1.480954 ACGATGTAGCTTGACCGGAAT 59.519 47.619 9.46 0.00 0.00 3.01
615 2734 2.540101 CGATGTAGCTTGACCGGAATTC 59.460 50.000 9.46 0.00 0.00 2.17
616 2735 2.396590 TGTAGCTTGACCGGAATTCC 57.603 50.000 15.01 15.01 0.00 3.01
617 2736 1.626321 TGTAGCTTGACCGGAATTCCA 59.374 47.619 24.09 1.39 35.14 3.53
618 2737 2.280628 GTAGCTTGACCGGAATTCCAG 58.719 52.381 24.09 15.63 35.14 3.86
621 2740 1.826385 CTTGACCGGAATTCCAGCTT 58.174 50.000 24.09 4.63 35.14 3.74
622 2741 1.470098 CTTGACCGGAATTCCAGCTTG 59.530 52.381 24.09 7.29 35.14 4.01
639 2758 6.324512 TCCAGCTTGACCATATGCAATTATTT 59.675 34.615 0.00 0.00 0.00 1.40
644 2763 7.707893 GCTTGACCATATGCAATTATTTGAAGT 59.292 33.333 0.00 0.00 34.60 3.01
662 2781 1.364328 AGTCTCTCCCTCCTGATTGGT 59.636 52.381 0.00 0.00 37.07 3.67
664 2783 1.127343 CTCTCCCTCCTGATTGGTCC 58.873 60.000 0.00 0.00 37.07 4.46
665 2784 0.687757 TCTCCCTCCTGATTGGTCCG 60.688 60.000 0.00 0.00 37.07 4.79
666 2785 0.978146 CTCCCTCCTGATTGGTCCGT 60.978 60.000 0.00 0.00 37.07 4.69
667 2786 0.546747 TCCCTCCTGATTGGTCCGTT 60.547 55.000 0.00 0.00 37.07 4.44
668 2787 0.328258 CCCTCCTGATTGGTCCGTTT 59.672 55.000 0.00 0.00 37.07 3.60
669 2788 1.679032 CCCTCCTGATTGGTCCGTTTC 60.679 57.143 0.00 0.00 37.07 2.78
671 2790 2.500098 CCTCCTGATTGGTCCGTTTCTA 59.500 50.000 0.00 0.00 37.07 2.10
672 2791 3.134804 CCTCCTGATTGGTCCGTTTCTAT 59.865 47.826 0.00 0.00 37.07 1.98
673 2792 4.344102 CCTCCTGATTGGTCCGTTTCTATA 59.656 45.833 0.00 0.00 37.07 1.31
674 2793 5.012148 CCTCCTGATTGGTCCGTTTCTATAT 59.988 44.000 0.00 0.00 37.07 0.86
675 2794 5.853936 TCCTGATTGGTCCGTTTCTATATG 58.146 41.667 0.00 0.00 37.07 1.78
677 2796 4.968259 TGATTGGTCCGTTTCTATATGGG 58.032 43.478 0.00 0.00 0.00 4.00
678 2797 2.922740 TGGTCCGTTTCTATATGGGC 57.077 50.000 0.00 0.00 0.00 5.36
679 2798 2.120312 TGGTCCGTTTCTATATGGGCA 58.880 47.619 0.00 0.00 30.09 5.36
681 2800 2.158871 GGTCCGTTTCTATATGGGCACA 60.159 50.000 0.00 0.00 30.09 4.57
686 2805 4.024048 CCGTTTCTATATGGGCACACATTC 60.024 45.833 0.00 0.00 32.39 2.67
785 2904 6.041511 TGGTGCATTATTGTGATTATTGTGC 58.958 36.000 0.00 0.00 0.00 4.57
786 2905 6.041511 GGTGCATTATTGTGATTATTGTGCA 58.958 36.000 0.00 0.00 37.69 4.57
788 2907 6.041511 TGCATTATTGTGATTATTGTGCACC 58.958 36.000 15.69 0.00 35.41 5.01
790 2909 6.702723 GCATTATTGTGATTATTGTGCACCAT 59.297 34.615 15.69 11.89 0.00 3.55
791 2910 7.866898 GCATTATTGTGATTATTGTGCACCATA 59.133 33.333 15.69 10.71 0.00 2.74
792 2911 9.917129 CATTATTGTGATTATTGTGCACCATAT 57.083 29.630 15.69 7.86 0.00 1.78
793 2912 9.917129 ATTATTGTGATTATTGTGCACCATATG 57.083 29.630 15.69 0.00 0.00 1.78
794 2913 7.585579 ATTGTGATTATTGTGCACCATATGA 57.414 32.000 15.69 0.00 0.00 2.15
795 2914 7.401955 TTGTGATTATTGTGCACCATATGAA 57.598 32.000 15.69 0.23 0.00 2.57
796 2915 7.585579 TGTGATTATTGTGCACCATATGAAT 57.414 32.000 15.69 8.66 0.00 2.57
797 2916 8.688747 TGTGATTATTGTGCACCATATGAATA 57.311 30.769 15.69 7.63 0.00 1.75
799 2918 9.398170 GTGATTATTGTGCACCATATGAATAAC 57.602 33.333 15.69 5.62 0.00 1.89
800 2919 9.353431 TGATTATTGTGCACCATATGAATAACT 57.647 29.630 15.69 6.96 0.00 2.24
802 2921 8.744568 TTATTGTGCACCATATGAATAACTCA 57.255 30.769 15.69 0.00 38.81 3.41
803 2922 6.435430 TTGTGCACCATATGAATAACTCAC 57.565 37.500 15.69 3.34 36.69 3.51
805 2924 4.024893 GTGCACCATATGAATAACTCACCG 60.025 45.833 5.22 0.00 36.69 4.94
806 2925 3.498397 GCACCATATGAATAACTCACCGG 59.502 47.826 3.65 0.00 36.69 5.28
807 2926 3.498397 CACCATATGAATAACTCACCGGC 59.502 47.826 0.00 0.00 36.69 6.13
809 2928 2.519377 TATGAATAACTCACCGGCCG 57.481 50.000 21.04 21.04 36.69 6.13
810 2929 0.179056 ATGAATAACTCACCGGCCGG 60.179 55.000 42.17 42.17 36.69 6.13
811 2930 2.124860 AATAACTCACCGGCCGGC 60.125 61.111 43.58 21.18 39.32 6.13
813 2932 2.869503 AATAACTCACCGGCCGGCTG 62.870 60.000 43.58 35.39 39.32 4.85
825 2944 4.399395 CGGCTGCCCTGAGCTCAA 62.399 66.667 18.85 1.24 44.23 3.02
826 2945 2.274760 GGCTGCCCTGAGCTCAAT 59.725 61.111 18.85 0.00 44.23 2.57
827 2946 1.379576 GGCTGCCCTGAGCTCAATT 60.380 57.895 18.85 0.00 44.23 2.32
828 2947 1.664321 GGCTGCCCTGAGCTCAATTG 61.664 60.000 18.85 9.95 44.23 2.32
829 2948 0.679002 GCTGCCCTGAGCTCAATTGA 60.679 55.000 18.85 8.12 44.23 2.57
830 2949 1.830279 CTGCCCTGAGCTCAATTGAA 58.170 50.000 18.85 2.60 44.23 2.69
831 2950 2.165167 CTGCCCTGAGCTCAATTGAAA 58.835 47.619 18.85 0.79 44.23 2.69
834 2953 2.821969 GCCCTGAGCTCAATTGAAAGAA 59.178 45.455 18.85 0.00 38.99 2.52
835 2954 3.366781 GCCCTGAGCTCAATTGAAAGAAC 60.367 47.826 18.85 0.95 38.99 3.01
836 2955 3.822735 CCCTGAGCTCAATTGAAAGAACA 59.177 43.478 18.85 5.22 0.00 3.18
837 2956 4.320788 CCCTGAGCTCAATTGAAAGAACAC 60.321 45.833 18.85 0.00 0.00 3.32
838 2957 4.320788 CCTGAGCTCAATTGAAAGAACACC 60.321 45.833 18.85 0.00 0.00 4.16
840 2959 3.565307 AGCTCAATTGAAAGAACACCCA 58.435 40.909 9.88 0.00 0.00 4.51
841 2960 3.960102 AGCTCAATTGAAAGAACACCCAA 59.040 39.130 9.88 0.00 0.00 4.12
842 2961 4.038402 AGCTCAATTGAAAGAACACCCAAG 59.962 41.667 9.88 0.00 0.00 3.61
843 2962 4.202151 GCTCAATTGAAAGAACACCCAAGT 60.202 41.667 9.88 0.00 0.00 3.16
867 3433 9.110502 AGTGCAAATTATTTTTAAAACCCGAAA 57.889 25.926 0.00 0.00 0.00 3.46
916 3482 3.554934 TCATGGTACCAAGCCAATGATC 58.445 45.455 20.76 0.00 39.72 2.92
925 3491 0.682209 AGCCAATGATCCAGTGCACC 60.682 55.000 14.63 0.00 0.00 5.01
942 3508 3.201045 TGCACCCATATAAGTAGCACCAA 59.799 43.478 0.00 0.00 0.00 3.67
945 3511 5.411669 GCACCCATATAAGTAGCACCAATAC 59.588 44.000 0.00 0.00 0.00 1.89
951 3517 7.309255 CCATATAAGTAGCACCAATACGAGACT 60.309 40.741 0.00 0.00 0.00 3.24
991 3559 9.128404 ACATATGCATTTGTTTCTCACTCATAT 57.872 29.630 15.98 0.00 0.00 1.78
1062 3630 3.020627 CTGCATAGCTTCAGCCGC 58.979 61.111 0.00 0.00 43.38 6.53
1089 3657 7.078228 TCAGTAGATATGTTGTCGATTCGATG 58.922 38.462 12.54 1.85 38.42 3.84
1104 3672 6.584942 TCGATTCGATGGTTTTTATCTATCGG 59.415 38.462 4.29 0.00 43.11 4.18
1161 3729 2.026822 ACTGTCCTACTTCCTTGCCATG 60.027 50.000 0.00 0.00 0.00 3.66
1216 3784 3.515602 AACCAAGCAATCCTGAGTTCT 57.484 42.857 0.00 0.00 0.00 3.01
1362 3930 2.237392 AGGAGGGGAGATCTTTGTTTCG 59.763 50.000 0.00 0.00 0.00 3.46
1550 4118 6.459923 AGAAATGTACAGAGTTGAAGAGGAC 58.540 40.000 0.33 0.00 0.00 3.85
1552 4120 4.855715 TGTACAGAGTTGAAGAGGACTG 57.144 45.455 0.00 0.00 0.00 3.51
1553 4121 4.470602 TGTACAGAGTTGAAGAGGACTGA 58.529 43.478 0.00 0.00 0.00 3.41
1554 4122 4.893524 TGTACAGAGTTGAAGAGGACTGAA 59.106 41.667 0.00 0.00 0.00 3.02
1566 4134 3.900601 AGAGGACTGAATCTGTCAAGTGT 59.099 43.478 19.37 2.50 35.22 3.55
1569 4137 5.059833 AGGACTGAATCTGTCAAGTGTTTC 58.940 41.667 19.37 2.64 35.22 2.78
1573 4141 3.807622 TGAATCTGTCAAGTGTTTCGGAC 59.192 43.478 0.00 0.00 31.51 4.79
1579 4147 2.869801 GTCAAGTGTTTCGGACATGTGA 59.130 45.455 1.15 0.00 41.10 3.58
1596 4164 4.098914 TGTGATCTTTGGGTACTTTGCT 57.901 40.909 0.00 0.00 0.00 3.91
1717 4285 3.351794 TCTCACTATCAGTCACCGTCT 57.648 47.619 0.00 0.00 0.00 4.18
1724 4292 0.112606 TCAGTCACCGTCTCCTCCTT 59.887 55.000 0.00 0.00 0.00 3.36
1728 4296 1.118965 TCACCGTCTCCTCCTTTGCA 61.119 55.000 0.00 0.00 0.00 4.08
1746 4314 2.034879 AAATGCAGGACTCGTGCCG 61.035 57.895 18.65 0.00 43.45 5.69
1929 4497 2.206576 ACCCTGAGGAAGTGCATTTC 57.793 50.000 13.21 13.21 36.73 2.17
1945 4513 3.549070 GCATTTCGCTAATTTGCTTCCTG 59.451 43.478 10.13 4.23 37.77 3.86
1952 4520 0.318120 AATTTGCTTCCTGGGTTGCG 59.682 50.000 0.00 0.00 0.00 4.85
1959 4527 1.990160 TTCCTGGGTTGCGGACTGTT 61.990 55.000 0.00 0.00 0.00 3.16
1977 4545 3.877508 CTGTTTTTCTCTCCTCAACGGTT 59.122 43.478 0.00 0.00 0.00 4.44
1988 4556 2.811799 AACGGTTGTTGGCCTTGC 59.188 55.556 3.32 0.00 36.81 4.01
2164 4735 7.092891 CCCCTGCCATTATAGTACTATTCATCA 60.093 40.741 20.21 11.10 0.00 3.07
2199 4770 6.413052 AGTTCATGACTGAATAGCACTTCAT 58.587 36.000 0.00 0.00 43.08 2.57
2283 4857 5.630264 TCTCAAATTCATGTGCGACAATTTG 59.370 36.000 16.29 16.29 36.18 2.32
2357 4931 3.808174 GGAGATACTAAAACCACCGATGC 59.192 47.826 0.00 0.00 0.00 3.91
2360 4934 1.722011 ACTAAAACCACCGATGCGAG 58.278 50.000 0.00 0.00 0.00 5.03
2399 4982 1.336755 GTCGTTGGTGCAGAATTTGGT 59.663 47.619 0.00 0.00 0.00 3.67
2542 5125 7.025365 CAGGTGTGTTATTCTTTCATGTGATG 58.975 38.462 0.00 0.00 0.00 3.07
2629 5219 6.377996 AGACTAGACATAAATGGCAATTGCAA 59.622 34.615 30.32 21.81 44.36 4.08
2672 5262 9.005777 ACTTAATTTATAAACCGAGCACTTTGA 57.994 29.630 0.00 0.00 0.00 2.69
2727 5328 7.689446 AACTTAGAAGGCAAAATCTTACTCC 57.311 36.000 0.00 0.00 0.00 3.85
2938 5544 5.126067 GTCATGCTCTATGGAAGGCTTAAA 58.874 41.667 0.00 0.00 37.39 1.52
2986 5592 6.867519 TCCTGGAAAGTATGATACAGTTGA 57.132 37.500 5.28 0.00 0.00 3.18
2997 5603 8.251721 AGTATGATACAGTTGACCAAGACTAAC 58.748 37.037 5.28 0.00 0.00 2.34
3003 5609 6.771188 CAGTTGACCAAGACTAACTGTAAG 57.229 41.667 0.00 0.00 42.94 2.34
3031 5637 2.817258 TGTGCCAAACTGGTATAACTGC 59.183 45.455 0.00 0.00 40.46 4.40
3032 5638 3.081804 GTGCCAAACTGGTATAACTGCT 58.918 45.455 0.00 0.00 40.46 4.24
3107 5717 1.357420 TGTAGGTGGATGTTGGGCATT 59.643 47.619 0.00 0.00 38.06 3.56
3121 5731 5.187687 GTTGGGCATTCAATGGAAATCATT 58.812 37.500 0.00 0.00 46.24 2.57
3128 5738 9.280174 GGCATTCAATGGAAATCATTTATCAAT 57.720 29.630 0.00 0.00 43.04 2.57
3147 5757 0.884259 TGTGTGGCATCTTGACGTGG 60.884 55.000 0.00 0.00 0.00 4.94
3203 5813 8.836413 TGAATTCTTATTCTTATTGTTAGGGCG 58.164 33.333 7.05 0.00 40.68 6.13
3245 5863 9.655769 CACACAATTTACAATATAGATGTGAGC 57.344 33.333 9.29 0.00 39.30 4.26
3246 5864 8.551205 ACACAATTTACAATATAGATGTGAGCG 58.449 33.333 9.29 0.00 39.30 5.03
3281 5906 5.499139 TTATAAGCACAGCTAATGTTGCC 57.501 39.130 0.00 0.00 41.41 4.52
3290 5915 5.068198 CACAGCTAATGTTGCCCTATCATTT 59.932 40.000 0.00 0.00 41.41 2.32
3304 5929 9.375974 TGCCCTATCATTTTAGTACATACTACT 57.624 33.333 0.00 0.00 38.43 2.57
3305 5930 9.857957 GCCCTATCATTTTAGTACATACTACTC 57.142 37.037 0.00 0.00 38.43 2.59
3331 5956 3.586892 CAGAAGTTCCGGGAGAAACTAC 58.413 50.000 0.00 0.00 35.85 2.73
3420 6046 7.728532 ACCTTGGTATATTTTGTTGAGGTCTTT 59.271 33.333 0.00 0.00 29.42 2.52
3439 6065 5.751509 GTCTTTAAAAGGCGTTCCACAATTT 59.248 36.000 0.00 0.00 33.74 1.82
3440 6066 6.919115 GTCTTTAAAAGGCGTTCCACAATTTA 59.081 34.615 0.00 0.00 33.74 1.40
3441 6067 7.597369 GTCTTTAAAAGGCGTTCCACAATTTAT 59.403 33.333 0.00 0.00 33.74 1.40
3442 6068 7.810759 TCTTTAAAAGGCGTTCCACAATTTATC 59.189 33.333 0.00 0.00 33.74 1.75
3443 6069 3.757745 AAGGCGTTCCACAATTTATCG 57.242 42.857 0.00 0.00 33.74 2.92
3444 6070 2.980568 AGGCGTTCCACAATTTATCGA 58.019 42.857 0.00 0.00 33.74 3.59
3445 6071 2.936498 AGGCGTTCCACAATTTATCGAG 59.064 45.455 0.00 0.00 33.74 4.04
3446 6072 2.676342 GGCGTTCCACAATTTATCGAGT 59.324 45.455 0.00 0.00 0.00 4.18
3447 6073 3.126343 GGCGTTCCACAATTTATCGAGTT 59.874 43.478 0.00 0.00 0.00 3.01
3448 6074 4.330620 GGCGTTCCACAATTTATCGAGTTA 59.669 41.667 0.00 0.00 0.00 2.24
3449 6075 5.253335 GCGTTCCACAATTTATCGAGTTAC 58.747 41.667 0.00 0.00 0.00 2.50
3450 6076 5.063060 GCGTTCCACAATTTATCGAGTTACT 59.937 40.000 0.00 0.00 0.00 2.24
3451 6077 6.466812 CGTTCCACAATTTATCGAGTTACTG 58.533 40.000 0.00 0.00 0.00 2.74
3452 6078 6.309494 CGTTCCACAATTTATCGAGTTACTGA 59.691 38.462 0.00 0.00 0.00 3.41
3513 6139 3.308595 CACGTCTGAGTTTTGCACTAACA 59.691 43.478 12.09 0.00 35.01 2.41
3526 6152 5.309323 TGCACTAACACATAATTGCTTCC 57.691 39.130 0.00 0.00 0.00 3.46
3549 6175 2.413112 GACGTGAACATGTGGTGATCAG 59.587 50.000 0.00 0.00 39.88 2.90
3574 6200 8.677300 AGTTCATGCGAAGAAATAATTGTACAT 58.323 29.630 0.00 0.00 0.00 2.29
3578 6204 6.027131 TGCGAAGAAATAATTGTACATGCAC 58.973 36.000 0.00 0.00 0.00 4.57
3637 6263 3.455990 ACACACAAATCATGCAAAGCA 57.544 38.095 0.00 0.00 44.86 3.91
3638 6264 3.386486 ACACACAAATCATGCAAAGCAG 58.614 40.909 0.00 0.00 43.65 4.24
3666 6292 4.321899 GCCATTCAGTTGCTGGTTATTGAA 60.322 41.667 0.00 0.00 32.42 2.69
3667 6293 5.782047 CCATTCAGTTGCTGGTTATTGAAA 58.218 37.500 0.00 0.00 31.51 2.69
3681 6307 5.863935 GGTTATTGAAATCACTGAACCTTGC 59.136 40.000 10.75 0.00 33.05 4.01
3684 6310 3.149196 TGAAATCACTGAACCTTGCCTC 58.851 45.455 0.00 0.00 0.00 4.70
3714 6376 9.747898 ATCAATAACAATAACAGGTTTACCTCA 57.252 29.630 0.00 0.00 46.65 3.86
3788 6450 2.778270 GGCCCTATTAGAAGTCCCAGTT 59.222 50.000 0.00 0.00 0.00 3.16
3799 6461 1.349688 AGTCCCAGTTGTATCCGCAAA 59.650 47.619 0.00 0.00 0.00 3.68
3833 6495 4.890581 GGACTCATCTTACCTCTTCAGCTA 59.109 45.833 0.00 0.00 0.00 3.32
3912 6574 5.273944 CAAGCAACAAACTAGAAAGTGACC 58.726 41.667 0.00 0.00 35.62 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 176 7.822334 ACGTTGACAAAGAGTAATATCCATTGA 59.178 33.333 8.17 0.00 0.00 2.57
199 200 8.481641 CAATTATGCATTCATGTTTATTGGACG 58.518 33.333 3.54 0.00 34.22 4.79
212 213 4.635324 TCTTCGCTCACAATTATGCATTCA 59.365 37.500 3.54 0.00 0.00 2.57
216 217 3.333804 TGTCTTCGCTCACAATTATGCA 58.666 40.909 0.00 0.00 0.00 3.96
221 231 4.836125 ATGTTTGTCTTCGCTCACAATT 57.164 36.364 0.00 0.00 32.60 2.32
235 245 8.506437 CACAGTCATACACTTGATTATGTTTGT 58.494 33.333 0.00 0.00 30.26 2.83
238 248 8.097038 ACTCACAGTCATACACTTGATTATGTT 58.903 33.333 0.00 0.00 30.26 2.71
316 326 3.491447 GCCCAATAGAATCATGTTGCACC 60.491 47.826 0.00 0.00 0.00 5.01
340 350 8.937634 ATTTAAAAATTGATCATCAGACAGCC 57.062 30.769 0.00 0.00 0.00 4.85
373 383 8.166726 AGGAGACCAATTTAATCCTATGATTCC 58.833 37.037 0.00 0.00 41.44 3.01
402 412 6.125719 TGCATCATTAGCTTGGTACCATAAA 58.874 36.000 17.17 8.21 0.00 1.40
404 414 5.163205 ACTGCATCATTAGCTTGGTACCATA 60.163 40.000 17.17 2.00 0.00 2.74
405 415 4.139786 CTGCATCATTAGCTTGGTACCAT 58.860 43.478 17.17 3.16 0.00 3.55
406 416 3.054434 ACTGCATCATTAGCTTGGTACCA 60.054 43.478 11.60 11.60 0.00 3.25
433 443 0.184933 TTGGTCTGGTTTCACCCCTG 59.815 55.000 0.00 0.00 37.50 4.45
438 448 4.287720 GTTCGAATTTGGTCTGGTTTCAC 58.712 43.478 0.00 0.00 0.00 3.18
446 456 3.615496 CGTTATCCGTTCGAATTTGGTCT 59.385 43.478 0.00 0.05 0.00 3.85
449 459 2.350498 AGCGTTATCCGTTCGAATTTGG 59.650 45.455 0.00 4.34 39.32 3.28
451 461 3.553105 GGTAGCGTTATCCGTTCGAATTT 59.447 43.478 0.00 0.00 39.32 1.82
453 463 2.735823 GGTAGCGTTATCCGTTCGAAT 58.264 47.619 0.00 0.00 39.32 3.34
454 464 1.531677 CGGTAGCGTTATCCGTTCGAA 60.532 52.381 6.07 0.00 39.51 3.71
455 465 0.027979 CGGTAGCGTTATCCGTTCGA 59.972 55.000 6.07 0.00 39.51 3.71
456 466 2.488079 CGGTAGCGTTATCCGTTCG 58.512 57.895 6.07 0.00 39.51 3.95
461 471 5.356470 AGAATAGGATACGGTAGCGTTATCC 59.644 44.000 28.92 28.92 46.39 2.59
462 472 6.315891 AGAGAATAGGATACGGTAGCGTTATC 59.684 42.308 26.37 22.00 46.39 1.75
463 473 6.179040 AGAGAATAGGATACGGTAGCGTTAT 58.821 40.000 26.37 13.88 46.39 1.89
465 475 4.396522 AGAGAATAGGATACGGTAGCGTT 58.603 43.478 26.37 13.16 46.39 4.84
466 476 4.018484 AGAGAATAGGATACGGTAGCGT 57.982 45.455 24.61 24.61 46.39 5.07
470 480 9.638176 AGAAAAGTTAGAGAATAGGATACGGTA 57.362 33.333 0.00 0.00 46.39 4.02
471 481 8.414778 CAGAAAAGTTAGAGAATAGGATACGGT 58.585 37.037 0.00 0.00 46.39 4.83
485 495 6.490040 CCACTTCCAAATCCAGAAAAGTTAGA 59.510 38.462 0.00 0.00 0.00 2.10
486 496 6.294731 CCCACTTCCAAATCCAGAAAAGTTAG 60.295 42.308 0.00 0.00 0.00 2.34
490 500 4.021981 GTCCCACTTCCAAATCCAGAAAAG 60.022 45.833 0.00 0.00 0.00 2.27
491 501 3.895041 GTCCCACTTCCAAATCCAGAAAA 59.105 43.478 0.00 0.00 0.00 2.29
495 505 1.453155 CGTCCCACTTCCAAATCCAG 58.547 55.000 0.00 0.00 0.00 3.86
500 510 0.608035 GCATCCGTCCCACTTCCAAA 60.608 55.000 0.00 0.00 0.00 3.28
508 518 2.549064 CATATTCTGCATCCGTCCCA 57.451 50.000 0.00 0.00 0.00 4.37
588 2707 2.414957 CGGTCAAGCTACATCGTACACA 60.415 50.000 0.00 0.00 0.00 3.72
606 2725 0.322546 GGTCAAGCTGGAATTCCGGT 60.323 55.000 29.82 21.10 44.34 5.28
607 2726 0.322456 TGGTCAAGCTGGAATTCCGG 60.322 55.000 26.56 26.56 45.30 5.14
608 2727 1.755179 ATGGTCAAGCTGGAATTCCG 58.245 50.000 19.57 14.67 39.43 4.30
609 2728 3.005155 GCATATGGTCAAGCTGGAATTCC 59.995 47.826 18.17 18.17 0.00 3.01
610 2729 3.633525 TGCATATGGTCAAGCTGGAATTC 59.366 43.478 4.56 0.00 0.00 2.17
611 2730 3.634504 TGCATATGGTCAAGCTGGAATT 58.365 40.909 4.56 0.00 0.00 2.17
612 2731 3.301794 TGCATATGGTCAAGCTGGAAT 57.698 42.857 4.56 0.00 0.00 3.01
613 2732 2.804986 TGCATATGGTCAAGCTGGAA 57.195 45.000 4.56 0.00 0.00 3.53
615 2734 5.717078 ATAATTGCATATGGTCAAGCTGG 57.283 39.130 4.56 0.00 0.00 4.85
616 2735 7.204604 TCAAATAATTGCATATGGTCAAGCTG 58.795 34.615 4.56 0.00 36.45 4.24
617 2736 7.350744 TCAAATAATTGCATATGGTCAAGCT 57.649 32.000 4.56 0.00 36.45 3.74
618 2737 7.707893 ACTTCAAATAATTGCATATGGTCAAGC 59.292 33.333 4.56 0.00 36.45 4.01
621 2740 8.523915 AGACTTCAAATAATTGCATATGGTCA 57.476 30.769 4.56 0.00 36.45 4.02
622 2741 8.844244 AGAGACTTCAAATAATTGCATATGGTC 58.156 33.333 4.56 0.00 36.45 4.02
639 2758 3.102972 CAATCAGGAGGGAGAGACTTCA 58.897 50.000 0.00 0.00 0.00 3.02
644 2763 1.343478 GGACCAATCAGGAGGGAGAGA 60.343 57.143 0.00 0.00 41.22 3.10
662 2781 2.502130 TGTGTGCCCATATAGAAACGGA 59.498 45.455 0.00 0.00 0.00 4.69
664 2783 4.024048 GGAATGTGTGCCCATATAGAAACG 60.024 45.833 0.00 0.00 0.00 3.60
665 2784 5.009010 CAGGAATGTGTGCCCATATAGAAAC 59.991 44.000 0.00 0.00 0.00 2.78
666 2785 5.132502 CAGGAATGTGTGCCCATATAGAAA 58.867 41.667 0.00 0.00 0.00 2.52
667 2786 4.717877 CAGGAATGTGTGCCCATATAGAA 58.282 43.478 0.00 0.00 0.00 2.10
668 2787 3.496692 GCAGGAATGTGTGCCCATATAGA 60.497 47.826 0.00 0.00 33.29 1.98
669 2788 2.816087 GCAGGAATGTGTGCCCATATAG 59.184 50.000 0.00 0.00 33.29 1.31
671 2790 1.063792 TGCAGGAATGTGTGCCCATAT 60.064 47.619 0.00 0.00 39.04 1.78
672 2791 0.330941 TGCAGGAATGTGTGCCCATA 59.669 50.000 0.00 0.00 39.04 2.74
673 2792 0.968901 CTGCAGGAATGTGTGCCCAT 60.969 55.000 5.57 0.00 39.04 4.00
674 2793 1.604308 CTGCAGGAATGTGTGCCCA 60.604 57.895 5.57 0.00 39.04 5.36
675 2794 1.181098 AACTGCAGGAATGTGTGCCC 61.181 55.000 19.93 0.00 39.04 5.36
677 2796 0.665369 GCAACTGCAGGAATGTGTGC 60.665 55.000 19.93 11.24 41.59 4.57
678 2797 3.484524 GCAACTGCAGGAATGTGTG 57.515 52.632 19.93 5.27 41.59 3.82
785 2904 3.498397 GCCGGTGAGTTATTCATATGGTG 59.502 47.826 1.90 0.00 38.29 4.17
786 2905 3.496160 GGCCGGTGAGTTATTCATATGGT 60.496 47.826 1.90 0.00 38.29 3.55
787 2906 3.074412 GGCCGGTGAGTTATTCATATGG 58.926 50.000 1.90 0.00 38.29 2.74
788 2907 2.736721 CGGCCGGTGAGTTATTCATATG 59.263 50.000 20.10 0.00 38.29 1.78
790 2909 1.069513 CCGGCCGGTGAGTTATTCATA 59.930 52.381 36.64 0.00 38.29 2.15
791 2910 0.179056 CCGGCCGGTGAGTTATTCAT 60.179 55.000 36.64 0.00 38.29 2.57
792 2911 1.219664 CCGGCCGGTGAGTTATTCA 59.780 57.895 36.64 0.00 0.00 2.57
793 2912 2.178235 GCCGGCCGGTGAGTTATTC 61.178 63.158 42.53 20.88 37.65 1.75
794 2913 2.124860 GCCGGCCGGTGAGTTATT 60.125 61.111 42.53 0.00 37.65 1.40
795 2914 3.081409 AGCCGGCCGGTGAGTTAT 61.081 61.111 42.53 18.61 37.65 1.89
796 2915 4.077184 CAGCCGGCCGGTGAGTTA 62.077 66.667 42.53 0.00 42.92 2.24
809 2928 1.379576 AATTGAGCTCAGGGCAGCC 60.380 57.895 17.43 1.26 44.79 4.85
810 2929 0.679002 TCAATTGAGCTCAGGGCAGC 60.679 55.000 17.43 0.00 44.79 5.25
811 2930 1.830279 TTCAATTGAGCTCAGGGCAG 58.170 50.000 17.43 6.92 44.79 4.85
813 2932 2.440409 TCTTTCAATTGAGCTCAGGGC 58.560 47.619 17.43 0.00 42.19 5.19
814 2933 3.822735 TGTTCTTTCAATTGAGCTCAGGG 59.177 43.478 17.43 10.48 0.00 4.45
815 2934 4.320788 GGTGTTCTTTCAATTGAGCTCAGG 60.321 45.833 17.43 10.84 0.00 3.86
816 2935 4.320788 GGGTGTTCTTTCAATTGAGCTCAG 60.321 45.833 17.43 5.77 0.00 3.35
817 2936 3.569701 GGGTGTTCTTTCAATTGAGCTCA 59.430 43.478 13.74 13.74 0.00 4.26
818 2937 3.569701 TGGGTGTTCTTTCAATTGAGCTC 59.430 43.478 6.82 6.82 0.00 4.09
819 2938 3.565307 TGGGTGTTCTTTCAATTGAGCT 58.435 40.909 8.41 0.00 0.00 4.09
821 2940 5.284079 CACTTGGGTGTTCTTTCAATTGAG 58.716 41.667 8.41 0.00 38.54 3.02
824 2943 3.450457 TGCACTTGGGTGTTCTTTCAATT 59.550 39.130 0.00 0.00 44.65 2.32
825 2944 3.030291 TGCACTTGGGTGTTCTTTCAAT 58.970 40.909 0.00 0.00 44.65 2.57
826 2945 2.451490 TGCACTTGGGTGTTCTTTCAA 58.549 42.857 0.00 0.00 44.65 2.69
827 2946 2.136298 TGCACTTGGGTGTTCTTTCA 57.864 45.000 0.00 0.00 44.65 2.69
828 2947 3.518634 TTTGCACTTGGGTGTTCTTTC 57.481 42.857 0.00 0.00 44.65 2.62
829 2948 4.486125 AATTTGCACTTGGGTGTTCTTT 57.514 36.364 0.00 0.00 44.65 2.52
830 2949 5.806654 ATAATTTGCACTTGGGTGTTCTT 57.193 34.783 0.00 0.00 44.65 2.52
831 2950 5.806654 AATAATTTGCACTTGGGTGTTCT 57.193 34.783 0.00 0.00 44.65 3.01
834 2953 8.738645 TTTAAAAATAATTTGCACTTGGGTGT 57.261 26.923 0.00 0.00 44.65 4.16
835 2954 9.444534 GTTTTAAAAATAATTTGCACTTGGGTG 57.555 29.630 1.31 0.00 45.53 4.61
836 2955 8.625651 GGTTTTAAAAATAATTTGCACTTGGGT 58.374 29.630 1.31 0.00 0.00 4.51
837 2956 8.079203 GGGTTTTAAAAATAATTTGCACTTGGG 58.921 33.333 1.31 0.00 0.00 4.12
838 2957 7.800847 CGGGTTTTAAAAATAATTTGCACTTGG 59.199 33.333 1.31 0.00 0.00 3.61
840 2959 8.664211 TCGGGTTTTAAAAATAATTTGCACTT 57.336 26.923 1.31 0.00 0.00 3.16
841 2960 8.664211 TTCGGGTTTTAAAAATAATTTGCACT 57.336 26.923 1.31 0.00 0.00 4.40
842 2961 9.885934 ATTTCGGGTTTTAAAAATAATTTGCAC 57.114 25.926 1.31 0.00 0.00 4.57
916 3482 3.181455 TGCTACTTATATGGGTGCACTGG 60.181 47.826 17.98 0.00 0.00 4.00
925 3491 6.807230 GTCTCGTATTGGTGCTACTTATATGG 59.193 42.308 0.00 0.00 0.00 2.74
942 3508 6.374613 TGTCTGTGACAAGATAAGTCTCGTAT 59.625 38.462 0.00 0.00 39.78 3.06
945 3511 5.048153 TGTCTGTGACAAGATAAGTCTCG 57.952 43.478 0.00 0.00 39.78 4.04
951 3517 8.400186 CAAATGCATATGTCTGTGACAAGATAA 58.600 33.333 0.00 0.00 45.96 1.75
991 3559 2.525124 CCCGGCCCATGGTGCTATA 61.525 63.158 20.31 0.00 0.00 1.31
1062 3630 7.078228 TCGAATCGACAACATATCTACTGATG 58.922 38.462 0.00 0.00 34.32 3.07
1089 3657 4.317628 GCGACGAACCGATAGATAAAAACC 60.318 45.833 0.00 0.00 39.76 3.27
1161 3729 3.707102 AGAGGACTGAACCAAGTATAGCC 59.293 47.826 0.00 0.00 0.00 3.93
1216 3784 5.132502 CAACATGTCAATATAAGGAGGGCA 58.867 41.667 0.00 0.00 0.00 5.36
1362 3930 2.366916 TCTAAGCATGAGGCCTAAGAGC 59.633 50.000 4.42 7.33 46.50 4.09
1550 4118 4.058124 TCCGAAACACTTGACAGATTCAG 58.942 43.478 0.00 0.00 34.94 3.02
1552 4120 3.807622 TGTCCGAAACACTTGACAGATTC 59.192 43.478 0.00 0.00 33.09 2.52
1553 4121 3.804036 TGTCCGAAACACTTGACAGATT 58.196 40.909 0.00 0.00 33.09 2.40
1554 4122 3.469008 TGTCCGAAACACTTGACAGAT 57.531 42.857 0.00 0.00 33.09 2.90
1566 4134 3.081061 CCCAAAGATCACATGTCCGAAA 58.919 45.455 0.00 0.00 0.00 3.46
1569 4137 2.113860 ACCCAAAGATCACATGTCCG 57.886 50.000 0.00 0.00 0.00 4.79
1573 4141 4.460382 AGCAAAGTACCCAAAGATCACATG 59.540 41.667 0.00 0.00 0.00 3.21
1579 4147 4.098914 TCACAGCAAAGTACCCAAAGAT 57.901 40.909 0.00 0.00 0.00 2.40
1728 4296 3.987404 GGCACGAGTCCTGCATTT 58.013 55.556 14.80 0.00 36.27 2.32
1746 4314 6.373774 AGAAGATGACCATGTTCTCATTTGTC 59.626 38.462 14.33 0.00 44.92 3.18
1929 4497 1.463674 ACCCAGGAAGCAAATTAGCG 58.536 50.000 0.00 0.00 40.15 4.26
1945 4513 1.001706 GAGAAAAACAGTCCGCAACCC 60.002 52.381 0.00 0.00 0.00 4.11
1952 4520 3.495001 CGTTGAGGAGAGAAAAACAGTCC 59.505 47.826 0.00 0.00 0.00 3.85
1959 4527 3.553828 ACAACCGTTGAGGAGAGAAAA 57.446 42.857 18.19 0.00 45.00 2.29
1977 4545 3.608662 GCTGCTGCAAGGCCAACA 61.609 61.111 11.11 0.00 39.41 3.33
2215 4788 9.561069 AGTACCTACCAATCAAATGATATGAAC 57.439 33.333 0.00 0.00 33.73 3.18
2231 4804 6.295462 CCAAAGCAAGTAAGTAGTACCTACCA 60.295 42.308 5.59 0.00 37.65 3.25
2232 4805 6.071165 TCCAAAGCAAGTAAGTAGTACCTACC 60.071 42.308 5.59 0.00 37.65 3.18
2283 4857 3.127721 GCAAATACCTGAGACCAAGAAGC 59.872 47.826 0.00 0.00 0.00 3.86
2357 4931 1.196354 CTCTCTTGCCTTTTGTGCTCG 59.804 52.381 0.00 0.00 0.00 5.03
2360 4934 0.600057 CCCTCTCTTGCCTTTTGTGC 59.400 55.000 0.00 0.00 0.00 4.57
2399 4982 4.349682 ACCCGAGCGGTGAGAATA 57.650 55.556 8.25 0.00 46.09 1.75
2550 5133 7.290248 TCCATCTTTAGGGAGAGTAATGTAAGG 59.710 40.741 0.00 0.00 30.39 2.69
2582 5172 4.417426 ACGCTACCATTGCCTTACTAAT 57.583 40.909 0.00 0.00 0.00 1.73
2647 5237 9.490663 CTCAAAGTGCTCGGTTTATAAATTAAG 57.509 33.333 0.31 1.00 0.00 1.85
2654 5244 5.168569 CAGACTCAAAGTGCTCGGTTTATA 58.831 41.667 0.00 0.00 0.00 0.98
2661 5251 1.194098 CTTGCAGACTCAAAGTGCTCG 59.806 52.381 0.00 0.00 38.09 5.03
2672 5262 2.408050 CGTGTTTAGCTCTTGCAGACT 58.592 47.619 0.00 0.00 42.74 3.24
2750 5356 8.334632 ACTGCAAAACAAAGCATACAAAATTAC 58.665 29.630 0.00 0.00 40.42 1.89
2938 5544 3.276846 GTGGACACCGCAAACGCT 61.277 61.111 0.00 0.00 38.22 5.07
2944 5550 0.398696 ATTTACCTGTGGACACCGCA 59.601 50.000 4.03 4.03 42.15 5.69
2986 5592 2.976882 TGCCCTTACAGTTAGTCTTGGT 59.023 45.455 0.00 0.00 0.00 3.67
3031 5637 1.136690 TTCGTCTTGCAAGTACGCAG 58.863 50.000 30.00 16.99 44.14 5.18
3032 5638 1.724623 GATTCGTCTTGCAAGTACGCA 59.275 47.619 30.00 24.88 41.03 5.24
3090 5700 0.409092 TGAATGCCCAACATCCACCT 59.591 50.000 0.00 0.00 38.34 4.00
3107 5717 9.589111 CACACATTGATAAATGATTTCCATTGA 57.411 29.630 9.95 0.00 44.28 2.57
3121 5731 4.094739 CGTCAAGATGCCACACATTGATAA 59.905 41.667 0.00 0.00 39.84 1.75
3128 5738 0.884259 CCACGTCAAGATGCCACACA 60.884 55.000 0.00 0.00 0.00 3.72
3203 5813 7.933215 AATTGTGTGAAGTAATACTAACCCC 57.067 36.000 0.00 0.00 0.00 4.95
3239 5857 0.973632 ATAGGGTGTCAACGCTCACA 59.026 50.000 0.00 0.00 45.89 3.58
3240 5858 2.094762 AATAGGGTGTCAACGCTCAC 57.905 50.000 0.00 0.00 45.89 3.51
3241 5859 2.851263 AAATAGGGTGTCAACGCTCA 57.149 45.000 0.00 0.00 45.89 4.26
3242 5860 5.050295 GCTTATAAATAGGGTGTCAACGCTC 60.050 44.000 0.00 0.00 45.89 5.03
3244 5862 4.573201 TGCTTATAAATAGGGTGTCAACGC 59.427 41.667 0.00 0.00 39.48 4.84
3245 5863 5.583061 TGTGCTTATAAATAGGGTGTCAACG 59.417 40.000 0.00 0.00 0.00 4.10
3246 5864 6.458342 GCTGTGCTTATAAATAGGGTGTCAAC 60.458 42.308 0.00 0.00 0.00 3.18
3290 5915 7.984050 ACTTCTGCGTAGAGTAGTATGTACTAA 59.016 37.037 6.12 0.00 40.20 2.24
3304 5929 0.609957 TCCCGGAACTTCTGCGTAGA 60.610 55.000 0.73 0.00 37.12 2.59
3305 5930 0.179134 CTCCCGGAACTTCTGCGTAG 60.179 60.000 0.73 0.00 37.12 3.51
3306 5931 0.609957 TCTCCCGGAACTTCTGCGTA 60.610 55.000 0.73 0.00 37.12 4.42
3307 5932 1.469335 TTCTCCCGGAACTTCTGCGT 61.469 55.000 0.73 0.00 37.12 5.24
3308 5933 0.320421 TTTCTCCCGGAACTTCTGCG 60.320 55.000 0.73 0.00 38.86 5.18
3309 5934 1.157585 GTTTCTCCCGGAACTTCTGC 58.842 55.000 0.73 0.00 33.13 4.26
3339 5964 9.860898 GGCTTTGAGTTTCAATAATTAAGTGAT 57.139 29.630 3.74 0.00 36.11 3.06
3341 5966 9.132521 CAGGCTTTGAGTTTCAATAATTAAGTG 57.867 33.333 0.00 0.00 36.11 3.16
3352 5977 4.704540 TCAAACTTCAGGCTTTGAGTTTCA 59.295 37.500 13.64 2.77 36.19 2.69
3420 6046 5.411977 TCGATAAATTGTGGAACGCCTTTTA 59.588 36.000 0.00 0.00 42.39 1.52
3439 6065 6.315642 CCTGTTGACTAGTCAGTAACTCGATA 59.684 42.308 23.97 4.18 41.13 2.92
3440 6066 5.124138 CCTGTTGACTAGTCAGTAACTCGAT 59.876 44.000 23.97 0.00 41.13 3.59
3441 6067 4.454847 CCTGTTGACTAGTCAGTAACTCGA 59.545 45.833 23.97 5.64 41.13 4.04
3442 6068 4.724303 CCTGTTGACTAGTCAGTAACTCG 58.276 47.826 23.97 14.44 41.13 4.18
3443 6069 4.022242 TGCCTGTTGACTAGTCAGTAACTC 60.022 45.833 23.97 13.78 41.13 3.01
3444 6070 3.895656 TGCCTGTTGACTAGTCAGTAACT 59.104 43.478 23.97 0.00 41.13 2.24
3445 6071 4.022242 TCTGCCTGTTGACTAGTCAGTAAC 60.022 45.833 23.97 19.68 41.13 2.50
3446 6072 4.149598 TCTGCCTGTTGACTAGTCAGTAA 58.850 43.478 23.97 13.38 41.13 2.24
3447 6073 3.759086 CTCTGCCTGTTGACTAGTCAGTA 59.241 47.826 23.97 16.14 41.13 2.74
3448 6074 2.560542 CTCTGCCTGTTGACTAGTCAGT 59.439 50.000 23.97 0.00 41.13 3.41
3449 6075 2.673610 GCTCTGCCTGTTGACTAGTCAG 60.674 54.545 23.97 14.43 41.13 3.51
3450 6076 1.273606 GCTCTGCCTGTTGACTAGTCA 59.726 52.381 21.74 21.74 37.91 3.41
3451 6077 1.273606 TGCTCTGCCTGTTGACTAGTC 59.726 52.381 16.32 16.32 0.00 2.59
3452 6078 1.342074 TGCTCTGCCTGTTGACTAGT 58.658 50.000 0.00 0.00 0.00 2.57
3513 6139 2.006888 CACGTCCGGAAGCAATTATGT 58.993 47.619 17.91 0.00 0.00 2.29
3526 6152 0.598942 TCACCACATGTTCACGTCCG 60.599 55.000 0.00 0.00 0.00 4.79
3549 6175 8.736742 CATGTACAATTATTTCTTCGCATGAAC 58.263 33.333 0.00 0.00 33.88 3.18
3574 6200 2.359850 GGCCTTCCGTGATGTGCA 60.360 61.111 0.00 0.00 0.00 4.57
3578 6204 1.746615 CTGGTGGCCTTCCGTGATG 60.747 63.158 3.32 0.00 34.14 3.07
3637 6263 2.355513 CCAGCAACTGAATGGCTCTACT 60.356 50.000 0.00 0.00 35.27 2.57
3638 6264 2.012673 CCAGCAACTGAATGGCTCTAC 58.987 52.381 0.00 0.00 35.27 2.59
3666 6292 1.425066 TGGAGGCAAGGTTCAGTGATT 59.575 47.619 0.00 0.00 0.00 2.57
3667 6293 1.067295 TGGAGGCAAGGTTCAGTGAT 58.933 50.000 0.00 0.00 0.00 3.06
3681 6307 8.924511 ACCTGTTATTGTTATTGATATGGAGG 57.075 34.615 0.00 0.00 0.00 4.30
3714 6376 6.183360 TGGAAAGTCATTGCTCACTGAAAATT 60.183 34.615 0.00 0.00 0.00 1.82
3788 6450 4.142271 CCAAAGGCTATTTTTGCGGATACA 60.142 41.667 0.00 0.00 34.88 2.29
3799 6461 6.069381 AGGTAAGATGAGTCCAAAGGCTATTT 60.069 38.462 0.00 0.00 0.00 1.40
3833 6495 7.362401 GCTGTTGTTACATCTTGATTGATCCTT 60.362 37.037 0.00 0.00 32.86 3.36
3898 6560 4.202367 CCCTCAGTTGGTCACTTTCTAGTT 60.202 45.833 0.00 0.00 30.92 2.24


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

AutoCloner maintained by Alex Coulton.