Multiple sequence alignment - TraesCS2D01G255900

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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 TraesCS2D01G255900 chr2D 100.000 5773 0 0 1 5773 308981361 308987133 0.000000e+00 10661.0
1 TraesCS2D01G255900 chr2D 83.422 187 18 10 3964 4139 9603522 9603338 1.660000e-35 161.0
2 TraesCS2D01G255900 chr2D 82.873 181 24 6 3964 4139 330211942 330211764 7.750000e-34 156.0
3 TraesCS2D01G255900 chr2D 83.234 167 22 4 3964 4126 446315932 446315768 1.300000e-31 148.0
4 TraesCS2D01G255900 chr2D 88.889 117 9 2 753 867 127944251 127944365 2.170000e-29 141.0
5 TraesCS2D01G255900 chr2D 92.727 55 4 0 2 56 607601286 607601232 4.800000e-11 80.5
6 TraesCS2D01G255900 chr2A 96.218 4151 120 12 877 5018 430955102 430950980 0.000000e+00 6761.0
7 TraesCS2D01G255900 chr2A 95.527 693 24 7 39 728 535150127 535150815 0.000000e+00 1101.0
8 TraesCS2D01G255900 chr2A 96.258 481 13 3 5296 5773 430950649 430950171 0.000000e+00 784.0
9 TraesCS2D01G255900 chr2A 94.410 161 9 0 5004 5164 430950829 430950669 1.240000e-61 248.0
10 TraesCS2D01G255900 chr2A 80.556 180 29 6 3964 4139 377823093 377823270 3.630000e-27 134.0
11 TraesCS2D01G255900 chr2B 97.233 2891 66 4 870 3756 359315195 359312315 0.000000e+00 4883.0
12 TraesCS2D01G255900 chr2B 95.364 1359 52 8 3767 5119 359312204 359310851 0.000000e+00 2150.0
13 TraesCS2D01G255900 chr2B 95.542 673 25 5 57 728 20551791 20552459 0.000000e+00 1072.0
14 TraesCS2D01G255900 chr2B 95.027 563 14 5 5216 5773 359306121 359305568 0.000000e+00 872.0
15 TraesCS2D01G255900 chr2B 97.059 102 3 0 5116 5217 359306304 359306203 7.690000e-39 172.0
16 TraesCS2D01G255900 chr2B 89.565 115 8 2 755 867 26633614 26633502 6.030000e-30 143.0
17 TraesCS2D01G255900 chr5D 78.899 2616 490 50 1141 3716 479579793 479582386 0.000000e+00 1716.0
18 TraesCS2D01G255900 chr5D 81.111 180 24 8 3964 4139 399128379 399128552 1.010000e-27 135.0
19 TraesCS2D01G255900 chr5D 95.455 44 2 0 715 758 430534230 430534273 2.890000e-08 71.3
20 TraesCS2D01G255900 chr5B 96.137 673 23 3 57 728 600500469 600501139 0.000000e+00 1096.0
21 TraesCS2D01G255900 chr5B 89.344 122 6 5 755 873 415811262 415811379 4.660000e-31 147.0
22 TraesCS2D01G255900 chr5B 89.381 113 8 2 754 864 419246243 419246133 7.800000e-29 139.0
23 TraesCS2D01G255900 chr5B 95.349 43 2 0 714 756 61558555 61558513 1.040000e-07 69.4
24 TraesCS2D01G255900 chr5B 93.182 44 3 0 714 757 38863220 38863177 1.340000e-06 65.8
25 TraesCS2D01G255900 chr5B 92.857 42 3 0 717 758 338717768 338717727 1.740000e-05 62.1
26 TraesCS2D01G255900 chr5B 92.500 40 3 0 714 753 229127231 229127270 2.250000e-04 58.4
27 TraesCS2D01G255900 chr3B 95.852 675 22 5 54 728 576146347 576147015 0.000000e+00 1086.0
28 TraesCS2D01G255900 chr3B 95.833 672 25 3 57 728 545044462 545043794 0.000000e+00 1083.0
29 TraesCS2D01G255900 chr3B 95.556 675 28 2 54 728 745737221 745737893 0.000000e+00 1079.0
30 TraesCS2D01G255900 chr3B 95.287 679 27 5 50 728 531806824 531807497 0.000000e+00 1072.0
31 TraesCS2D01G255900 chr7A 95.542 673 27 3 56 728 586322001 586322670 0.000000e+00 1074.0
32 TraesCS2D01G255900 chr7A 89.362 47 5 0 715 761 26763647 26763693 6.250000e-05 60.2
33 TraesCS2D01G255900 chr4B 95.273 677 28 4 52 728 334178771 334179443 0.000000e+00 1070.0
34 TraesCS2D01G255900 chr4B 74.603 567 130 14 1619 2178 489090466 489089907 2.690000e-58 237.0
35 TraesCS2D01G255900 chr4B 95.349 43 2 0 714 756 159295921 159295879 1.040000e-07 69.4
36 TraesCS2D01G255900 chr4A 74.178 639 151 14 1547 2178 54109587 54108956 2.670000e-63 254.0
37 TraesCS2D01G255900 chr4A 92.857 56 4 0 1 56 744518417 744518362 1.330000e-11 82.4
38 TraesCS2D01G255900 chr4A 90.909 55 5 0 2 56 253447205 253447151 2.230000e-09 75.0
39 TraesCS2D01G255900 chr4D 75.137 547 126 10 1619 2160 397096641 397096100 1.240000e-61 248.0
40 TraesCS2D01G255900 chr4D 88.496 113 9 2 754 864 37496879 37496769 3.630000e-27 134.0
41 TraesCS2D01G255900 chr4D 88.496 113 9 3 754 864 508494764 508494874 3.630000e-27 134.0
42 TraesCS2D01G255900 chr4D 94.545 55 3 0 2 56 37496925 37496871 1.030000e-12 86.1
43 TraesCS2D01G255900 chr1A 89.630 135 11 2 3964 4096 132412261 132412128 9.950000e-38 169.0
44 TraesCS2D01G255900 chr1A 89.286 56 6 0 1 56 344298118 344298173 2.890000e-08 71.3
45 TraesCS2D01G255900 chr3A 83.333 168 23 4 3964 4127 741196147 741195981 3.600000e-32 150.0
46 TraesCS2D01G255900 chr6A 88.793 116 9 3 754 867 436116702 436116589 7.800000e-29 139.0
47 TraesCS2D01G255900 chr3D 88.696 115 9 2 754 866 561766827 561766939 2.810000e-28 137.0
48 TraesCS2D01G255900 chr3D 93.023 43 3 0 715 757 309671397 309671439 4.830000e-06 63.9
49 TraesCS2D01G255900 chr7D 86.179 123 13 2 752 872 162984657 162984537 4.690000e-26 130.0
50 TraesCS2D01G255900 chr7B 94.545 55 3 0 2 56 553195610 553195556 1.030000e-12 86.1
51 TraesCS2D01G255900 chr7B 90.909 55 5 0 2 56 659649416 659649470 2.230000e-09 75.0
52 TraesCS2D01G255900 chr5A 95.238 42 1 1 714 755 148052197 148052157 1.340000e-06 65.8


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 TraesCS2D01G255900 chr2D 308981361 308987133 5772 False 10661.000000 10661 100.000000 1 5773 1 chr2D.!!$F2 5772
1 TraesCS2D01G255900 chr2A 430950171 430955102 4931 True 2597.666667 6761 95.628667 877 5773 3 chr2A.!!$R1 4896
2 TraesCS2D01G255900 chr2A 535150127 535150815 688 False 1101.000000 1101 95.527000 39 728 1 chr2A.!!$F2 689
3 TraesCS2D01G255900 chr2B 359310851 359315195 4344 True 3516.500000 4883 96.298500 870 5119 2 chr2B.!!$R3 4249
4 TraesCS2D01G255900 chr2B 20551791 20552459 668 False 1072.000000 1072 95.542000 57 728 1 chr2B.!!$F1 671
5 TraesCS2D01G255900 chr2B 359305568 359306304 736 True 522.000000 872 96.043000 5116 5773 2 chr2B.!!$R2 657
6 TraesCS2D01G255900 chr5D 479579793 479582386 2593 False 1716.000000 1716 78.899000 1141 3716 1 chr5D.!!$F3 2575
7 TraesCS2D01G255900 chr5B 600500469 600501139 670 False 1096.000000 1096 96.137000 57 728 1 chr5B.!!$F3 671
8 TraesCS2D01G255900 chr3B 576146347 576147015 668 False 1086.000000 1086 95.852000 54 728 1 chr3B.!!$F2 674
9 TraesCS2D01G255900 chr3B 545043794 545044462 668 True 1083.000000 1083 95.833000 57 728 1 chr3B.!!$R1 671
10 TraesCS2D01G255900 chr3B 745737221 745737893 672 False 1079.000000 1079 95.556000 54 728 1 chr3B.!!$F3 674
11 TraesCS2D01G255900 chr3B 531806824 531807497 673 False 1072.000000 1072 95.287000 50 728 1 chr3B.!!$F1 678
12 TraesCS2D01G255900 chr7A 586322001 586322670 669 False 1074.000000 1074 95.542000 56 728 1 chr7A.!!$F2 672
13 TraesCS2D01G255900 chr4B 334178771 334179443 672 False 1070.000000 1070 95.273000 52 728 1 chr4B.!!$F1 676
14 TraesCS2D01G255900 chr4B 489089907 489090466 559 True 237.000000 237 74.603000 1619 2178 1 chr4B.!!$R2 559
15 TraesCS2D01G255900 chr4A 54108956 54109587 631 True 254.000000 254 74.178000 1547 2178 1 chr4A.!!$R1 631
16 TraesCS2D01G255900 chr4D 397096100 397096641 541 True 248.000000 248 75.137000 1619 2160 1 chr4D.!!$R1 541

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
840 844 0.040781 ACAAAATCGCCGTCCGTTTG 60.041 50.000 0.00 0.00 38.28 2.93 F
864 868 0.255890 GCCCCATTGGAGTTGCTCTA 59.744 55.000 3.62 0.00 35.39 2.43 F
1826 1855 0.322816 GCAGAGCTGGGGAACATGAA 60.323 55.000 0.00 0.00 0.00 2.57 F
2751 2780 1.532078 TGGAGATATACCGCCGGCA 60.532 57.895 28.98 7.49 0.00 5.69 F
4233 4370 0.377554 CACTAGTAGCCGACCGTCTG 59.622 60.000 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1736 0.609957 TCTTCCCGGACAGCTCGTTA 60.610 55.0 0.73 0.0 0.00 3.18 R
2073 2102 0.691078 GGATGTCACCCCTGAGCCTA 60.691 60.0 0.00 0.0 0.00 3.93 R
3615 3644 0.803380 GCCCGAAATCAGCAACATGC 60.803 55.0 0.00 0.0 45.46 4.06 R
4694 4831 1.171308 GCTGCTCCTTTGCTTCATCA 58.829 50.0 0.00 0.0 0.00 3.07 R
5343 5737 0.037975 GGCAAGCAAACATGTGAGGG 60.038 55.0 0.00 0.0 0.00 4.30 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
27 28 2.203015 GGCCACGCCGACACATAT 60.203 61.111 0.00 0.00 39.62 1.78
28 29 2.534019 GGCCACGCCGACACATATG 61.534 63.158 0.00 0.00 39.62 1.78
29 30 2.534019 GCCACGCCGACACATATGG 61.534 63.158 7.80 0.00 0.00 2.74
30 31 1.142965 CCACGCCGACACATATGGA 59.857 57.895 7.80 0.00 0.00 3.41
31 32 0.249868 CCACGCCGACACATATGGAT 60.250 55.000 7.80 0.00 0.00 3.41
32 33 1.139989 CACGCCGACACATATGGATC 58.860 55.000 7.80 3.14 0.00 3.36
33 34 0.318699 ACGCCGACACATATGGATCG 60.319 55.000 18.82 18.82 0.00 3.69
35 36 2.827604 CCGACACATATGGATCGGC 58.172 57.895 27.06 7.90 46.75 5.54
36 37 1.008875 CCGACACATATGGATCGGCG 61.009 60.000 27.06 17.07 46.75 6.46
37 38 1.617755 CGACACATATGGATCGGCGC 61.618 60.000 18.27 0.00 0.00 6.53
38 39 1.617755 GACACATATGGATCGGCGCG 61.618 60.000 7.80 0.00 0.00 6.86
39 40 1.664649 CACATATGGATCGGCGCGT 60.665 57.895 8.43 0.00 0.00 6.01
40 41 1.069090 ACATATGGATCGGCGCGTT 59.931 52.632 8.43 0.00 0.00 4.84
41 42 1.221466 ACATATGGATCGGCGCGTTG 61.221 55.000 8.43 0.00 0.00 4.10
42 43 1.667830 ATATGGATCGGCGCGTTGG 60.668 57.895 8.43 0.00 0.00 3.77
43 44 2.094757 ATATGGATCGGCGCGTTGGA 62.095 55.000 8.43 2.80 0.00 3.53
44 45 2.964438 TATGGATCGGCGCGTTGGAC 62.964 60.000 8.43 0.00 0.00 4.02
507 510 9.476202 AGTCTACCAAATTTTGCAATTTTCTAC 57.524 29.630 0.00 0.00 40.09 2.59
508 511 9.255304 GTCTACCAAATTTTGCAATTTTCTACA 57.745 29.630 0.00 0.00 40.09 2.74
753 757 3.918544 CCCGTTTGGCCAGGTATG 58.081 61.111 5.11 0.95 0.00 2.39
754 758 2.414785 CCCGTTTGGCCAGGTATGC 61.415 63.158 5.11 0.00 0.00 3.14
755 759 1.378514 CCGTTTGGCCAGGTATGCT 60.379 57.895 5.11 0.00 0.00 3.79
756 760 1.656818 CCGTTTGGCCAGGTATGCTG 61.657 60.000 5.11 0.00 0.00 4.41
757 761 1.512694 GTTTGGCCAGGTATGCTGC 59.487 57.895 5.11 0.00 0.00 5.25
758 762 1.682005 TTTGGCCAGGTATGCTGCC 60.682 57.895 5.11 0.00 44.27 4.85
760 764 4.175337 GGCCAGGTATGCTGCCGA 62.175 66.667 0.00 0.00 33.59 5.54
761 765 2.897350 GCCAGGTATGCTGCCGAC 60.897 66.667 0.00 0.00 0.00 4.79
762 766 2.203070 CCAGGTATGCTGCCGACC 60.203 66.667 11.09 11.09 0.00 4.79
763 767 2.203070 CAGGTATGCTGCCGACCC 60.203 66.667 14.44 2.22 33.40 4.46
764 768 2.687200 AGGTATGCTGCCGACCCA 60.687 61.111 14.44 0.00 33.40 4.51
765 769 2.072487 AGGTATGCTGCCGACCCAT 61.072 57.895 14.44 0.00 33.40 4.00
766 770 0.762842 AGGTATGCTGCCGACCCATA 60.763 55.000 14.44 0.00 33.40 2.74
767 771 0.324943 GGTATGCTGCCGACCCATAT 59.675 55.000 8.48 0.00 0.00 1.78
768 772 1.676014 GGTATGCTGCCGACCCATATC 60.676 57.143 8.48 0.00 0.00 1.63
769 773 1.276421 GTATGCTGCCGACCCATATCT 59.724 52.381 0.00 0.00 0.00 1.98
770 774 1.644509 ATGCTGCCGACCCATATCTA 58.355 50.000 0.00 0.00 0.00 1.98
771 775 1.419381 TGCTGCCGACCCATATCTAA 58.581 50.000 0.00 0.00 0.00 2.10
772 776 1.765904 TGCTGCCGACCCATATCTAAA 59.234 47.619 0.00 0.00 0.00 1.85
773 777 2.171659 TGCTGCCGACCCATATCTAAAA 59.828 45.455 0.00 0.00 0.00 1.52
774 778 3.181445 TGCTGCCGACCCATATCTAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
775 779 4.041075 TGCTGCCGACCCATATCTAAAATA 59.959 41.667 0.00 0.00 0.00 1.40
776 780 4.392138 GCTGCCGACCCATATCTAAAATAC 59.608 45.833 0.00 0.00 0.00 1.89
777 781 5.547465 CTGCCGACCCATATCTAAAATACA 58.453 41.667 0.00 0.00 0.00 2.29
778 782 5.547465 TGCCGACCCATATCTAAAATACAG 58.453 41.667 0.00 0.00 0.00 2.74
779 783 4.935808 GCCGACCCATATCTAAAATACAGG 59.064 45.833 0.00 0.00 0.00 4.00
780 784 5.488341 CCGACCCATATCTAAAATACAGGG 58.512 45.833 0.00 0.00 40.88 4.45
781 785 4.935808 CGACCCATATCTAAAATACAGGGC 59.064 45.833 0.00 0.00 38.64 5.19
782 786 4.906618 ACCCATATCTAAAATACAGGGCG 58.093 43.478 0.00 0.00 38.64 6.13
783 787 4.261801 CCCATATCTAAAATACAGGGCGG 58.738 47.826 0.00 0.00 0.00 6.13
784 788 4.019681 CCCATATCTAAAATACAGGGCGGA 60.020 45.833 0.00 0.00 0.00 5.54
785 789 4.935808 CCATATCTAAAATACAGGGCGGAC 59.064 45.833 0.00 0.00 0.00 4.79
786 790 2.589798 TCTAAAATACAGGGCGGACG 57.410 50.000 0.00 0.00 0.00 4.79
787 791 0.935196 CTAAAATACAGGGCGGACGC 59.065 55.000 8.39 8.39 41.06 5.19
807 811 4.235762 GATGGGCGGCCGAGCTAA 62.236 66.667 33.48 9.33 37.29 3.09
808 812 3.750373 GATGGGCGGCCGAGCTAAA 62.750 63.158 33.48 7.67 37.29 1.85
809 813 3.120086 ATGGGCGGCCGAGCTAAAT 62.120 57.895 33.48 9.90 37.29 1.40
810 814 3.279875 GGGCGGCCGAGCTAAATG 61.280 66.667 33.48 0.00 37.29 2.32
811 815 3.279875 GGCGGCCGAGCTAAATGG 61.280 66.667 33.48 0.00 37.29 3.16
812 816 2.203015 GCGGCCGAGCTAAATGGA 60.203 61.111 33.48 0.00 0.00 3.41
813 817 2.534903 GCGGCCGAGCTAAATGGAC 61.535 63.158 33.48 1.41 0.00 4.02
814 818 1.153449 CGGCCGAGCTAAATGGACA 60.153 57.895 24.07 0.00 0.00 4.02
815 819 0.742990 CGGCCGAGCTAAATGGACAA 60.743 55.000 24.07 0.00 0.00 3.18
816 820 1.017387 GGCCGAGCTAAATGGACAAG 58.983 55.000 0.00 0.00 0.00 3.16
817 821 1.017387 GCCGAGCTAAATGGACAAGG 58.983 55.000 0.00 0.00 0.00 3.61
818 822 1.017387 CCGAGCTAAATGGACAAGGC 58.983 55.000 0.00 0.00 0.00 4.35
819 823 0.652592 CGAGCTAAATGGACAAGGCG 59.347 55.000 0.00 0.00 0.00 5.52
820 824 1.017387 GAGCTAAATGGACAAGGCGG 58.983 55.000 0.00 0.00 0.00 6.13
821 825 0.618458 AGCTAAATGGACAAGGCGGA 59.382 50.000 0.00 0.00 0.00 5.54
822 826 0.733150 GCTAAATGGACAAGGCGGAC 59.267 55.000 0.00 0.00 0.00 4.79
823 827 1.948611 GCTAAATGGACAAGGCGGACA 60.949 52.381 0.00 0.00 0.00 4.02
824 828 2.432444 CTAAATGGACAAGGCGGACAA 58.568 47.619 0.00 0.00 0.00 3.18
825 829 1.698506 AAATGGACAAGGCGGACAAA 58.301 45.000 0.00 0.00 0.00 2.83
826 830 1.698506 AATGGACAAGGCGGACAAAA 58.301 45.000 0.00 0.00 0.00 2.44
827 831 1.923356 ATGGACAAGGCGGACAAAAT 58.077 45.000 0.00 0.00 0.00 1.82
828 832 1.243902 TGGACAAGGCGGACAAAATC 58.756 50.000 0.00 0.00 0.00 2.17
829 833 0.168128 GGACAAGGCGGACAAAATCG 59.832 55.000 0.00 0.00 0.00 3.34
834 838 2.097728 GCGGACAAAATCGCCGTC 59.902 61.111 0.00 0.00 46.38 4.79
835 839 2.782615 CGGACAAAATCGCCGTCC 59.217 61.111 0.00 0.00 44.79 4.79
836 840 2.782615 GGACAAAATCGCCGTCCG 59.217 61.111 0.00 0.00 39.86 4.79
837 841 2.030958 GGACAAAATCGCCGTCCGT 61.031 57.895 0.00 0.00 39.86 4.69
838 842 1.571215 GGACAAAATCGCCGTCCGTT 61.571 55.000 0.00 0.00 39.86 4.44
839 843 0.236449 GACAAAATCGCCGTCCGTTT 59.764 50.000 0.00 0.00 38.35 3.60
840 844 0.040781 ACAAAATCGCCGTCCGTTTG 60.041 50.000 0.00 0.00 38.28 2.93
841 845 0.727793 CAAAATCGCCGTCCGTTTGG 60.728 55.000 0.00 0.00 38.35 3.28
842 846 1.858372 AAAATCGCCGTCCGTTTGGG 61.858 55.000 0.00 0.00 38.35 4.12
843 847 3.540367 AATCGCCGTCCGTTTGGGT 62.540 57.895 0.00 0.00 38.35 4.51
844 848 3.945304 ATCGCCGTCCGTTTGGGTC 62.945 63.158 0.00 0.00 38.35 4.46
858 862 2.355115 GGTCGCCCCATTGGAGTT 59.645 61.111 3.62 0.00 35.07 3.01
859 863 2.046285 GGTCGCCCCATTGGAGTTG 61.046 63.158 3.62 0.00 35.07 3.16
860 864 2.361104 TCGCCCCATTGGAGTTGC 60.361 61.111 3.62 0.53 35.07 4.17
861 865 2.361610 CGCCCCATTGGAGTTGCT 60.362 61.111 3.62 0.00 35.39 3.91
862 866 2.409870 CGCCCCATTGGAGTTGCTC 61.410 63.158 3.62 0.00 35.39 4.26
863 867 1.000396 GCCCCATTGGAGTTGCTCT 60.000 57.895 3.62 0.00 35.39 4.09
864 868 0.255890 GCCCCATTGGAGTTGCTCTA 59.744 55.000 3.62 0.00 35.39 2.43
865 869 1.340991 GCCCCATTGGAGTTGCTCTAA 60.341 52.381 3.62 0.00 35.57 2.10
866 870 2.687914 GCCCCATTGGAGTTGCTCTAAT 60.688 50.000 3.62 2.55 41.23 1.73
867 871 3.217626 CCCCATTGGAGTTGCTCTAATC 58.782 50.000 3.62 0.00 39.14 1.75
868 872 3.371917 CCCCATTGGAGTTGCTCTAATCA 60.372 47.826 3.62 0.00 39.14 2.57
873 877 7.166851 CCATTGGAGTTGCTCTAATCATCTAT 58.833 38.462 0.00 0.00 39.14 1.98
909 913 8.996024 TCTGTGTTTCGATAATTCTGTGAATA 57.004 30.769 0.00 0.00 0.00 1.75
910 914 9.430623 TCTGTGTTTCGATAATTCTGTGAATAA 57.569 29.630 0.00 0.00 0.00 1.40
1027 1035 1.159285 CCAAGAAATGAGCACGAGCA 58.841 50.000 7.77 0.00 45.49 4.26
1028 1036 1.129998 CCAAGAAATGAGCACGAGCAG 59.870 52.381 7.77 0.00 45.49 4.24
1029 1037 0.801251 AAGAAATGAGCACGAGCAGC 59.199 50.000 7.77 0.00 45.49 5.25
1030 1038 1.023513 AGAAATGAGCACGAGCAGCC 61.024 55.000 7.77 0.00 45.49 4.85
1485 1514 1.279271 CTCCTCACCCACCTTAACCTG 59.721 57.143 0.00 0.00 0.00 4.00
1510 1539 2.818169 AACCTGCTGAACGGCTCCA 61.818 57.895 7.15 0.00 0.00 3.86
1515 1544 3.036429 GCTGAACGGCTCCATCCCT 62.036 63.158 0.00 0.00 0.00 4.20
1826 1855 0.322816 GCAGAGCTGGGGAACATGAA 60.323 55.000 0.00 0.00 0.00 2.57
1842 1871 2.670934 AAGGAGCTTGTGCGGCTG 60.671 61.111 0.00 0.00 45.42 4.85
2004 2033 4.338327 GACCTGTCGAACAACGCT 57.662 55.556 0.00 0.00 42.26 5.07
2073 2102 2.884639 CCTGTTCAACCTGTTCCGAAAT 59.115 45.455 0.00 0.00 0.00 2.17
2668 2697 1.536709 GCAATTCATTCGATGGTGGCC 60.537 52.381 0.00 0.00 0.00 5.36
2751 2780 1.532078 TGGAGATATACCGCCGGCA 60.532 57.895 28.98 7.49 0.00 5.69
2876 2905 4.452455 GGACTTCTCATACAACAACCTGTG 59.548 45.833 0.00 0.00 0.00 3.66
3615 3644 3.748048 TCCTTGACTCTGATTTTGAAGCG 59.252 43.478 0.00 0.00 0.00 4.68
3724 3753 7.118971 GCTATATTGCTCCAGGTAAAAGATCAG 59.881 40.741 1.60 0.00 0.00 2.90
3756 3785 9.869757 ATTACAGTTTGGAAATGCTTATAAACC 57.130 29.630 0.00 0.00 0.00 3.27
3758 3787 7.906327 ACAGTTTGGAAATGCTTATAAACCAT 58.094 30.769 0.00 0.00 0.00 3.55
3759 3788 9.030452 ACAGTTTGGAAATGCTTATAAACCATA 57.970 29.630 0.00 0.00 0.00 2.74
3802 3931 9.346725 GTCTCAAAAATTATCCATGTTCAGTTC 57.653 33.333 0.00 0.00 0.00 3.01
3818 3948 6.262944 TGTTCAGTTCATTATTGTTGTCTGCT 59.737 34.615 0.00 0.00 0.00 4.24
3830 3960 4.923893 TGTTGTCTGCTGTTGAATTTCAG 58.076 39.130 0.00 0.00 35.12 3.02
3852 3982 8.498054 TCAGTTCCTTATTTCTGATGCTTTAG 57.502 34.615 0.00 0.00 32.95 1.85
3899 4029 7.606456 TCTGTTATTTTCTAGTCCATGTTCCAC 59.394 37.037 0.00 0.00 0.00 4.02
3914 4044 9.703892 TCCATGTTCCACTTTTACATTTTTATG 57.296 29.630 0.00 0.00 30.45 1.90
4105 4239 6.519679 AAAAGAATATAAAACCCCCGACAC 57.480 37.500 0.00 0.00 0.00 3.67
4142 4278 4.094590 GTCATATATAGGACCGACACCTCG 59.905 50.000 15.15 0.00 38.76 4.63
4233 4370 0.377554 CACTAGTAGCCGACCGTCTG 59.622 60.000 0.00 0.00 0.00 3.51
4252 4389 5.655488 GTCTGTCTGTACAAGCAGATACAT 58.345 41.667 23.36 0.00 45.81 2.29
4260 4397 9.890629 TCTGTACAAGCAGATACATTAATCTTT 57.109 29.630 0.00 0.00 40.23 2.52
4279 4416 5.356426 TCTTTCATCGAACTGTCACTTTGA 58.644 37.500 0.00 0.00 0.00 2.69
4432 4569 2.103771 ACTGGATCAAGATGATGACGGG 59.896 50.000 3.42 0.00 37.20 5.28
4694 4831 0.106519 AAACTGTGGAGCCTGCAACT 60.107 50.000 0.00 0.00 0.00 3.16
4748 4885 1.080434 GAGCTCGCCGTCTTCACTT 60.080 57.895 0.00 0.00 0.00 3.16
4784 4921 4.060900 TCAGCATCTGAAGAACTGTCAAC 58.939 43.478 11.38 0.00 37.57 3.18
4859 4996 5.938125 TCTTAAGGTTTGGTATGCTGTTCTC 59.062 40.000 1.85 0.00 0.00 2.87
5080 5387 2.356022 CCATCCAGTGTGGCATCTAACA 60.356 50.000 0.00 0.00 37.47 2.41
5081 5388 3.346315 CATCCAGTGTGGCATCTAACAA 58.654 45.455 0.00 0.00 37.47 2.83
5165 5472 3.181488 TGTGTTCAAATGAGCAGGTGTTG 60.181 43.478 0.00 0.00 35.96 3.33
5213 5520 9.309516 TGTAACTCAAGACTTTTAACTACAGTG 57.690 33.333 0.00 0.00 0.00 3.66
5237 5627 7.704472 GTGTTATTTGTCAGTGGTCAAAATTCA 59.296 33.333 14.67 11.62 36.05 2.57
5246 5636 6.150976 TCAGTGGTCAAAATTCATATGTGGTC 59.849 38.462 1.90 0.00 0.00 4.02
5258 5648 1.187974 ATGTGGTCGGTCCGTCAATA 58.812 50.000 11.88 0.00 39.52 1.90
5259 5649 0.528924 TGTGGTCGGTCCGTCAATAG 59.471 55.000 11.88 0.00 39.52 1.73
5291 5685 7.476540 TCTCTGGTACAAAGTGTATGTGTAT 57.523 36.000 0.00 0.00 38.70 2.29
5292 5686 7.320399 TCTCTGGTACAAAGTGTATGTGTATG 58.680 38.462 0.00 0.00 38.70 2.39
5293 5687 6.999950 TCTGGTACAAAGTGTATGTGTATGT 58.000 36.000 0.00 0.00 38.70 2.29
5294 5688 8.124808 TCTGGTACAAAGTGTATGTGTATGTA 57.875 34.615 0.00 0.00 38.70 2.29
5295 5689 8.755028 TCTGGTACAAAGTGTATGTGTATGTAT 58.245 33.333 0.00 0.00 38.70 2.29
5421 5818 5.109210 TGCTTGGAACGTGAGATTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
5766 6168 4.335315 CACAAGAAACAGTAAGCAACCAGA 59.665 41.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.203015 ATATGTGTCGGCGTGGCC 60.203 61.111 6.85 0.00 46.75 5.36
11 12 2.534019 CCATATGTGTCGGCGTGGC 61.534 63.158 6.85 0.00 0.00 5.01
14 15 0.318699 CGATCCATATGTGTCGGCGT 60.319 55.000 6.85 0.00 0.00 5.68
15 16 1.008875 CCGATCCATATGTGTCGGCG 61.009 60.000 24.24 0.00 45.80 6.46
16 17 2.827604 CCGATCCATATGTGTCGGC 58.172 57.895 24.24 0.00 45.80 5.54
18 19 1.617755 GCGCCGATCCATATGTGTCG 61.618 60.000 15.96 15.96 0.00 4.35
19 20 1.617755 CGCGCCGATCCATATGTGTC 61.618 60.000 0.00 0.00 0.00 3.67
20 21 1.664649 CGCGCCGATCCATATGTGT 60.665 57.895 0.00 0.00 0.00 3.72
21 22 1.221466 AACGCGCCGATCCATATGTG 61.221 55.000 5.73 0.00 0.00 3.21
22 23 1.069090 AACGCGCCGATCCATATGT 59.931 52.632 5.73 0.00 0.00 2.29
23 24 1.492873 CAACGCGCCGATCCATATG 59.507 57.895 5.73 0.00 0.00 1.78
24 25 1.667830 CCAACGCGCCGATCCATAT 60.668 57.895 5.73 0.00 0.00 1.78
25 26 2.279851 CCAACGCGCCGATCCATA 60.280 61.111 5.73 0.00 0.00 2.74
26 27 4.155733 TCCAACGCGCCGATCCAT 62.156 61.111 5.73 0.00 0.00 3.41
41 42 3.190323 TATAGTCGGCAGCGCGTCC 62.190 63.158 8.43 6.30 0.00 4.79
42 43 1.726322 CTATAGTCGGCAGCGCGTC 60.726 63.158 8.43 0.00 0.00 5.19
43 44 2.331805 CTATAGTCGGCAGCGCGT 59.668 61.111 8.43 0.00 0.00 6.01
44 45 3.100191 GCTATAGTCGGCAGCGCG 61.100 66.667 0.00 0.00 0.00 6.86
45 46 2.018866 CAGCTATAGTCGGCAGCGC 61.019 63.158 0.00 0.00 40.29 5.92
46 47 1.372251 CCAGCTATAGTCGGCAGCG 60.372 63.158 0.84 0.00 40.29 5.18
47 48 1.666234 GCCAGCTATAGTCGGCAGC 60.666 63.158 22.49 1.93 44.25 5.25
48 49 1.005630 GGCCAGCTATAGTCGGCAG 60.006 63.158 26.20 2.82 46.75 4.85
49 50 1.334384 TTGGCCAGCTATAGTCGGCA 61.334 55.000 26.20 17.54 46.75 5.69
50 51 0.179056 TTTGGCCAGCTATAGTCGGC 60.179 55.000 20.41 20.41 44.10 5.54
51 52 1.583054 GTTTGGCCAGCTATAGTCGG 58.417 55.000 5.11 3.54 0.00 4.79
52 53 1.209128 CGTTTGGCCAGCTATAGTCG 58.791 55.000 5.11 0.00 0.00 4.18
53 54 1.583054 CCGTTTGGCCAGCTATAGTC 58.417 55.000 5.11 0.00 0.00 2.59
300 302 7.746034 CACTAATAAAATACGCATGCACTATGG 59.254 37.037 19.57 2.13 37.26 2.74
421 424 7.864108 TGTACATCATTAAAACTCCCATCTG 57.136 36.000 0.00 0.00 0.00 2.90
527 531 5.769484 TTGTAATACCTTTGAAAACGGCA 57.231 34.783 0.00 0.00 0.00 5.69
578 582 4.379243 CGTTGGAGGACGCTGGCT 62.379 66.667 0.00 0.00 36.12 4.75
736 740 2.414785 GCATACCTGGCCAAACGGG 61.415 63.158 7.01 7.12 42.81 5.28
737 741 1.378514 AGCATACCTGGCCAAACGG 60.379 57.895 7.01 7.56 0.00 4.44
738 742 1.802636 CAGCATACCTGGCCAAACG 59.197 57.895 7.01 0.00 37.93 3.60
739 743 1.512694 GCAGCATACCTGGCCAAAC 59.487 57.895 7.01 0.00 42.03 2.93
740 744 4.016838 GCAGCATACCTGGCCAAA 57.983 55.556 7.01 0.00 42.03 3.28
745 749 2.203070 GGTCGGCAGCATACCTGG 60.203 66.667 7.93 0.00 42.03 4.45
746 750 2.203070 GGGTCGGCAGCATACCTG 60.203 66.667 13.57 0.00 44.67 4.00
747 751 0.762842 TATGGGTCGGCAGCATACCT 60.763 55.000 13.57 0.24 33.59 3.08
748 752 0.324943 ATATGGGTCGGCAGCATACC 59.675 55.000 6.82 6.82 0.00 2.73
749 753 1.276421 AGATATGGGTCGGCAGCATAC 59.724 52.381 0.00 0.00 0.00 2.39
750 754 1.644509 AGATATGGGTCGGCAGCATA 58.355 50.000 0.00 0.00 0.00 3.14
751 755 1.644509 TAGATATGGGTCGGCAGCAT 58.355 50.000 0.00 0.00 0.00 3.79
752 756 1.419381 TTAGATATGGGTCGGCAGCA 58.581 50.000 0.00 0.00 0.00 4.41
753 757 2.543777 TTTAGATATGGGTCGGCAGC 57.456 50.000 0.00 0.00 0.00 5.25
754 758 5.547465 TGTATTTTAGATATGGGTCGGCAG 58.453 41.667 0.00 0.00 0.00 4.85
755 759 5.512404 CCTGTATTTTAGATATGGGTCGGCA 60.512 44.000 0.00 0.00 0.00 5.69
756 760 4.935808 CCTGTATTTTAGATATGGGTCGGC 59.064 45.833 0.00 0.00 0.00 5.54
757 761 5.488341 CCCTGTATTTTAGATATGGGTCGG 58.512 45.833 0.00 0.00 0.00 4.79
758 762 4.935808 GCCCTGTATTTTAGATATGGGTCG 59.064 45.833 0.00 0.00 36.00 4.79
759 763 4.935808 CGCCCTGTATTTTAGATATGGGTC 59.064 45.833 0.00 0.00 36.00 4.46
760 764 4.263331 CCGCCCTGTATTTTAGATATGGGT 60.263 45.833 0.00 0.00 36.00 4.51
761 765 4.019681 TCCGCCCTGTATTTTAGATATGGG 60.020 45.833 0.00 0.00 36.63 4.00
762 766 4.935808 GTCCGCCCTGTATTTTAGATATGG 59.064 45.833 0.00 0.00 0.00 2.74
763 767 4.625742 CGTCCGCCCTGTATTTTAGATATG 59.374 45.833 0.00 0.00 0.00 1.78
764 768 4.817517 CGTCCGCCCTGTATTTTAGATAT 58.182 43.478 0.00 0.00 0.00 1.63
765 769 3.553508 GCGTCCGCCCTGTATTTTAGATA 60.554 47.826 0.00 0.00 34.56 1.98
766 770 2.805657 GCGTCCGCCCTGTATTTTAGAT 60.806 50.000 0.00 0.00 34.56 1.98
767 771 1.472026 GCGTCCGCCCTGTATTTTAGA 60.472 52.381 0.00 0.00 34.56 2.10
768 772 0.935196 GCGTCCGCCCTGTATTTTAG 59.065 55.000 0.00 0.00 34.56 1.85
769 773 3.068574 GCGTCCGCCCTGTATTTTA 57.931 52.632 0.00 0.00 34.56 1.52
770 774 3.899395 GCGTCCGCCCTGTATTTT 58.101 55.556 0.00 0.00 34.56 1.82
790 794 3.750373 TTTAGCTCGGCCGCCCATC 62.750 63.158 23.51 7.05 0.00 3.51
791 795 3.120086 ATTTAGCTCGGCCGCCCAT 62.120 57.895 23.51 8.83 0.00 4.00
792 796 3.792736 ATTTAGCTCGGCCGCCCA 61.793 61.111 23.51 1.50 0.00 5.36
793 797 3.279875 CATTTAGCTCGGCCGCCC 61.280 66.667 23.51 13.90 0.00 6.13
794 798 3.279875 CCATTTAGCTCGGCCGCC 61.280 66.667 23.51 14.31 0.00 6.13
795 799 2.203015 TCCATTTAGCTCGGCCGC 60.203 61.111 23.51 7.56 0.00 6.53
796 800 0.742990 TTGTCCATTTAGCTCGGCCG 60.743 55.000 22.12 22.12 0.00 6.13
797 801 1.017387 CTTGTCCATTTAGCTCGGCC 58.983 55.000 0.00 0.00 0.00 6.13
798 802 1.017387 CCTTGTCCATTTAGCTCGGC 58.983 55.000 0.00 0.00 0.00 5.54
799 803 1.017387 GCCTTGTCCATTTAGCTCGG 58.983 55.000 0.00 0.00 0.00 4.63
800 804 0.652592 CGCCTTGTCCATTTAGCTCG 59.347 55.000 0.00 0.00 0.00 5.03
801 805 1.017387 CCGCCTTGTCCATTTAGCTC 58.983 55.000 0.00 0.00 0.00 4.09
802 806 0.618458 TCCGCCTTGTCCATTTAGCT 59.382 50.000 0.00 0.00 0.00 3.32
803 807 0.733150 GTCCGCCTTGTCCATTTAGC 59.267 55.000 0.00 0.00 0.00 3.09
804 808 2.107950 TGTCCGCCTTGTCCATTTAG 57.892 50.000 0.00 0.00 0.00 1.85
805 809 2.570415 TTGTCCGCCTTGTCCATTTA 57.430 45.000 0.00 0.00 0.00 1.40
806 810 1.698506 TTTGTCCGCCTTGTCCATTT 58.301 45.000 0.00 0.00 0.00 2.32
807 811 1.698506 TTTTGTCCGCCTTGTCCATT 58.301 45.000 0.00 0.00 0.00 3.16
808 812 1.818674 GATTTTGTCCGCCTTGTCCAT 59.181 47.619 0.00 0.00 0.00 3.41
809 813 1.243902 GATTTTGTCCGCCTTGTCCA 58.756 50.000 0.00 0.00 0.00 4.02
810 814 0.168128 CGATTTTGTCCGCCTTGTCC 59.832 55.000 0.00 0.00 0.00 4.02
811 815 0.454452 GCGATTTTGTCCGCCTTGTC 60.454 55.000 0.00 0.00 45.06 3.18
812 816 1.579429 GCGATTTTGTCCGCCTTGT 59.421 52.632 0.00 0.00 45.06 3.16
813 817 4.458164 GCGATTTTGTCCGCCTTG 57.542 55.556 0.00 0.00 45.06 3.61
819 823 1.571215 AACGGACGGCGATTTTGTCC 61.571 55.000 16.62 8.05 46.91 4.02
820 824 0.236449 AAACGGACGGCGATTTTGTC 59.764 50.000 16.62 0.00 0.00 3.18
821 825 0.040781 CAAACGGACGGCGATTTTGT 60.041 50.000 16.62 1.09 0.00 2.83
822 826 0.727793 CCAAACGGACGGCGATTTTG 60.728 55.000 16.62 15.66 0.00 2.44
823 827 1.577421 CCAAACGGACGGCGATTTT 59.423 52.632 16.62 3.87 0.00 1.82
824 828 2.329614 CCCAAACGGACGGCGATTT 61.330 57.895 16.62 5.62 0.00 2.17
825 829 2.744709 CCCAAACGGACGGCGATT 60.745 61.111 16.62 0.00 0.00 3.34
826 830 3.945304 GACCCAAACGGACGGCGAT 62.945 63.158 16.62 0.00 34.64 4.58
827 831 4.668118 GACCCAAACGGACGGCGA 62.668 66.667 16.62 0.00 34.64 5.54
842 846 2.700773 GCAACTCCAATGGGGCGAC 61.701 63.158 0.00 0.00 36.21 5.19
843 847 2.361104 GCAACTCCAATGGGGCGA 60.361 61.111 0.00 0.00 36.21 5.54
844 848 2.361610 AGCAACTCCAATGGGGCG 60.362 61.111 0.00 0.00 36.21 6.13
845 849 0.255890 TAGAGCAACTCCAATGGGGC 59.744 55.000 0.00 0.00 36.21 5.80
846 850 2.806945 TTAGAGCAACTCCAATGGGG 57.193 50.000 0.00 0.00 38.37 4.96
847 851 3.889815 TGATTAGAGCAACTCCAATGGG 58.110 45.455 0.00 0.00 0.00 4.00
848 852 5.374921 AGATGATTAGAGCAACTCCAATGG 58.625 41.667 0.00 0.00 0.00 3.16
849 853 8.618702 AATAGATGATTAGAGCAACTCCAATG 57.381 34.615 0.00 0.00 0.00 2.82
850 854 9.638176 AAAATAGATGATTAGAGCAACTCCAAT 57.362 29.630 0.00 0.00 0.00 3.16
851 855 9.466497 AAAAATAGATGATTAGAGCAACTCCAA 57.534 29.630 0.00 0.00 0.00 3.53
909 913 6.839134 TCCTAGGCCTCTTTTCTTTTTCTTTT 59.161 34.615 9.68 0.00 0.00 2.27
910 914 6.373759 TCCTAGGCCTCTTTTCTTTTTCTTT 58.626 36.000 9.68 0.00 0.00 2.52
911 915 5.953571 TCCTAGGCCTCTTTTCTTTTTCTT 58.046 37.500 9.68 0.00 0.00 2.52
912 916 5.584551 TCCTAGGCCTCTTTTCTTTTTCT 57.415 39.130 9.68 0.00 0.00 2.52
913 917 5.946377 TCATCCTAGGCCTCTTTTCTTTTTC 59.054 40.000 9.68 0.00 0.00 2.29
914 918 5.712446 GTCATCCTAGGCCTCTTTTCTTTTT 59.288 40.000 9.68 0.00 0.00 1.94
1027 1035 0.106217 GAGAGGAGCAGAGGTAGGCT 60.106 60.000 0.00 0.00 44.48 4.58
1028 1036 1.112916 GGAGAGGAGCAGAGGTAGGC 61.113 65.000 0.00 0.00 0.00 3.93
1029 1037 0.469144 GGGAGAGGAGCAGAGGTAGG 60.469 65.000 0.00 0.00 0.00 3.18
1030 1038 0.555769 AGGGAGAGGAGCAGAGGTAG 59.444 60.000 0.00 0.00 0.00 3.18
1479 1508 0.250727 GCAGGTTGCTGGACAGGTTA 60.251 55.000 1.01 0.00 40.96 2.85
1544 1573 6.767524 TGTTGTTGTACAAATCAAGAACCT 57.232 33.333 10.51 0.00 43.53 3.50
1707 1736 0.609957 TCTTCCCGGACAGCTCGTTA 60.610 55.000 0.73 0.00 0.00 3.18
1806 1835 1.203441 TCATGTTCCCCAGCTCTGCT 61.203 55.000 0.00 0.00 40.77 4.24
1826 1855 4.711949 CCAGCCGCACAAGCTCCT 62.712 66.667 0.00 0.00 38.95 3.69
2073 2102 0.691078 GGATGTCACCCCTGAGCCTA 60.691 60.000 0.00 0.00 0.00 3.93
2472 2501 3.738481 CCCCCAAGATTCGGCCCA 61.738 66.667 0.00 0.00 0.00 5.36
2751 2780 2.620115 CAGTATCCGCATGCCTGAAATT 59.380 45.455 13.15 0.00 0.00 1.82
3019 3048 3.935993 GCTTGAGGCTACTGGACAA 57.064 52.632 0.00 0.00 38.06 3.18
3615 3644 0.803380 GCCCGAAATCAGCAACATGC 60.803 55.000 0.00 0.00 45.46 4.06
3724 3753 5.183904 AGCATTTCCAAACTGTAATGAGGAC 59.816 40.000 4.80 0.00 31.29 3.85
3756 3785 6.980397 TGAGACAGTGCTATGTGTTGTATATG 59.020 38.462 0.00 0.00 32.25 1.78
3758 3787 6.524101 TGAGACAGTGCTATGTGTTGTATA 57.476 37.500 0.00 0.00 32.25 1.47
3759 3788 5.405935 TGAGACAGTGCTATGTGTTGTAT 57.594 39.130 0.00 0.00 32.25 2.29
3760 3789 4.864704 TGAGACAGTGCTATGTGTTGTA 57.135 40.909 0.00 0.00 32.25 2.41
3761 3790 3.751479 TGAGACAGTGCTATGTGTTGT 57.249 42.857 0.00 0.00 32.25 3.32
3763 3792 6.639632 ATTTTTGAGACAGTGCTATGTGTT 57.360 33.333 0.00 0.00 32.25 3.32
3764 3793 6.639632 AATTTTTGAGACAGTGCTATGTGT 57.360 33.333 0.00 0.00 32.25 3.72
3772 3901 8.298854 TGAACATGGATAATTTTTGAGACAGTG 58.701 33.333 0.00 0.00 0.00 3.66
3802 3931 7.878477 AATTCAACAGCAGACAACAATAATG 57.122 32.000 0.00 0.00 0.00 1.90
3818 3948 9.130661 TCAGAAATAAGGAACTGAAATTCAACA 57.869 29.630 0.00 0.00 40.86 3.33
3830 3960 9.384764 AGTACTAAAGCATCAGAAATAAGGAAC 57.615 33.333 0.00 0.00 0.00 3.62
3875 4005 7.458397 AGTGGAACATGGACTAGAAAATAACA 58.542 34.615 0.00 0.00 44.52 2.41
3960 4090 1.436983 GCGCCCCTTATCGGAAACAG 61.437 60.000 0.00 0.00 33.16 3.16
4007 4137 4.466827 TGCTCATCATGCTTTGTATCCAT 58.533 39.130 0.00 0.00 0.00 3.41
4008 4138 3.888583 TGCTCATCATGCTTTGTATCCA 58.111 40.909 0.00 0.00 0.00 3.41
4105 4239 6.975197 CCTATATATGACTAGTGTTGCCGATG 59.025 42.308 0.00 0.00 0.00 3.84
4193 4330 5.888161 AGTGAAGTGAGTGGAAAGAACAAAT 59.112 36.000 0.00 0.00 0.00 2.32
4205 4342 2.747989 TCGGCTACTAGTGAAGTGAGTG 59.252 50.000 5.39 0.00 39.39 3.51
4252 4389 7.962964 AAGTGACAGTTCGATGAAAGATTAA 57.037 32.000 0.00 0.00 0.00 1.40
4260 4397 6.429624 CAAATTCAAAGTGACAGTTCGATGA 58.570 36.000 0.00 0.00 0.00 2.92
4279 4416 4.679662 AGTATACGCGTACTCTGCAAATT 58.320 39.130 23.19 3.87 28.99 1.82
4432 4569 1.704641 AACCTGCTCCCTTTTGGAAC 58.295 50.000 0.00 0.00 44.57 3.62
4694 4831 1.171308 GCTGCTCCTTTGCTTCATCA 58.829 50.000 0.00 0.00 0.00 3.07
4748 4885 1.883678 TGCTGATGAGATTGGGAGGA 58.116 50.000 0.00 0.00 0.00 3.71
4784 4921 9.381033 TGACAAAATAAATGGCAATAATTCAGG 57.619 29.630 0.00 0.00 31.44 3.86
4834 4971 5.705905 AGAACAGCATACCAAACCTTAAGAC 59.294 40.000 3.36 0.00 0.00 3.01
4840 4977 3.679389 CAGAGAACAGCATACCAAACCT 58.321 45.455 0.00 0.00 0.00 3.50
4859 4996 0.532417 GCCAGAGACCTATGCTGCAG 60.532 60.000 10.11 10.11 0.00 4.41
4866 5003 5.026790 ACAACTAGAAAGCCAGAGACCTAT 58.973 41.667 0.00 0.00 0.00 2.57
4960 5097 8.816894 TCTTGATTGTAACAGGAAAGTAGAGAT 58.183 33.333 0.00 0.00 0.00 2.75
5080 5387 6.829229 TCTTGATTGATTTGCAGAGTCATT 57.171 33.333 0.00 0.00 0.00 2.57
5081 5388 7.406031 AATCTTGATTGATTTGCAGAGTCAT 57.594 32.000 0.00 0.00 33.33 3.06
5165 5472 4.979197 CAGTGCAGTACTAGATCCGAATTC 59.021 45.833 0.00 0.00 37.60 2.17
5213 5520 8.816640 ATGAATTTTGACCACTGACAAATAAC 57.183 30.769 0.00 0.00 36.34 1.89
5226 5616 4.398044 ACCGACCACATATGAATTTTGACC 59.602 41.667 10.38 0.00 0.00 4.02
5237 5627 1.187974 TTGACGGACCGACCACATAT 58.812 50.000 23.38 0.00 38.90 1.78
5246 5636 1.067582 GGCCTCTATTGACGGACCG 59.932 63.158 13.61 13.61 0.00 4.79
5291 5685 4.141287 GCAGCACCCCATAAACATATACA 58.859 43.478 0.00 0.00 0.00 2.29
5292 5686 4.141287 TGCAGCACCCCATAAACATATAC 58.859 43.478 0.00 0.00 0.00 1.47
5293 5687 4.445557 TGCAGCACCCCATAAACATATA 57.554 40.909 0.00 0.00 0.00 0.86
5294 5688 3.311167 TGCAGCACCCCATAAACATAT 57.689 42.857 0.00 0.00 0.00 1.78
5295 5689 2.757868 GTTGCAGCACCCCATAAACATA 59.242 45.455 0.00 0.00 0.00 2.29
5296 5690 1.550072 GTTGCAGCACCCCATAAACAT 59.450 47.619 0.00 0.00 0.00 2.71
5297 5691 0.965439 GTTGCAGCACCCCATAAACA 59.035 50.000 0.00 0.00 0.00 2.83
5298 5692 1.202348 GAGTTGCAGCACCCCATAAAC 59.798 52.381 2.55 0.00 0.00 2.01
5299 5693 1.202989 TGAGTTGCAGCACCCCATAAA 60.203 47.619 2.55 0.00 0.00 1.40
5300 5694 0.403655 TGAGTTGCAGCACCCCATAA 59.596 50.000 2.55 0.00 0.00 1.90
5301 5695 0.403655 TTGAGTTGCAGCACCCCATA 59.596 50.000 2.55 0.00 0.00 2.74
5302 5696 1.153524 TTGAGTTGCAGCACCCCAT 59.846 52.632 2.55 0.00 0.00 4.00
5343 5737 0.037975 GGCAAGCAAACATGTGAGGG 60.038 55.000 0.00 0.00 0.00 4.30
5421 5818 0.602372 GCTTCGGCTGATCAGATCCC 60.602 60.000 27.04 16.37 38.08 3.85


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

AutoCloner maintained by Alex Coulton.