Multiple sequence alignment - TraesCS7D01G396500

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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 TraesCS7D01G396500 chr7D 100.000 3103 0 0 1 3103 511212211 511215313 0.000000e+00 5731.0
1 TraesCS7D01G396500 chr7D 97.315 782 21 0 2322 3103 634746292 634747073 0.000000e+00 1328.0
2 TraesCS7D01G396500 chr7D 97.315 782 20 1 2322 3103 182568928 182569708 0.000000e+00 1327.0
3 TraesCS7D01G396500 chr7D 75.307 652 123 27 102 727 568358228 568358867 8.470000e-71 278.0
4 TraesCS7D01G396500 chr7D 100.000 42 0 0 1033 1074 64701892 64701933 9.230000e-11 78.7
5 TraesCS7D01G396500 chr2B 90.731 1327 105 10 1000 2324 749230827 749232137 0.000000e+00 1753.0
6 TraesCS7D01G396500 chr2B 84.738 629 87 6 1482 2102 749238549 749237922 3.400000e-174 621.0
7 TraesCS7D01G396500 chr2B 83.122 237 38 2 1483 1718 785311163 785311398 6.740000e-52 215.0
8 TraesCS7D01G396500 chr2D 90.580 1327 107 9 1000 2324 614843862 614845172 0.000000e+00 1742.0
9 TraesCS7D01G396500 chr2D 97.308 780 21 0 2322 3101 576874724 576873945 0.000000e+00 1325.0
10 TraesCS7D01G396500 chr2D 84.579 629 88 8 1482 2102 614853908 614853281 1.580000e-172 616.0
11 TraesCS7D01G396500 chr2D 82.386 721 110 14 1482 2198 649677318 649678025 2.050000e-171 612.0
12 TraesCS7D01G396500 chr2D 76.642 548 109 18 116 655 575958354 575958890 5.060000e-73 285.0
13 TraesCS7D01G396500 chr2D 93.373 166 11 0 832 997 81004757 81004922 2.390000e-61 246.0
14 TraesCS7D01G396500 chr3D 97.442 782 20 0 2322 3103 7350255 7351036 0.000000e+00 1334.0
15 TraesCS7D01G396500 chr3D 97.965 737 14 1 1 737 581968468 581969203 0.000000e+00 1277.0
16 TraesCS7D01G396500 chr3D 93.413 167 11 0 832 998 537154863 537154697 6.640000e-62 248.0
17 TraesCS7D01G396500 chr3D 92.353 170 13 0 824 993 595024968 595025137 3.090000e-60 243.0
18 TraesCS7D01G396500 chr1D 97.442 782 19 1 2322 3103 473897708 473898488 0.000000e+00 1332.0
19 TraesCS7D01G396500 chr1D 98.182 55 0 1 737 790 254438759 254438705 9.160000e-16 95.3
20 TraesCS7D01G396500 chr1D 98.182 55 0 1 737 790 273914601 273914655 9.160000e-16 95.3
21 TraesCS7D01G396500 chr1D 98.182 55 0 1 737 790 491425210 491425264 9.160000e-16 95.3
22 TraesCS7D01G396500 chr6D 97.318 783 20 1 2322 3103 35599861 35600643 0.000000e+00 1328.0
23 TraesCS7D01G396500 chr6D 97.187 782 22 0 2322 3103 204556373 204555592 0.000000e+00 1323.0
24 TraesCS7D01G396500 chr6D 96.081 740 28 1 1 739 25529755 25530494 0.000000e+00 1205.0
25 TraesCS7D01G396500 chr5D 97.187 782 22 0 2322 3103 505773951 505774732 0.000000e+00 1323.0
26 TraesCS7D01G396500 chr5D 94.479 163 9 0 831 993 53583239 53583077 5.140000e-63 252.0
27 TraesCS7D01G396500 chr5D 98.182 55 0 1 737 790 6173207 6173261 9.160000e-16 95.3
28 TraesCS7D01G396500 chr4D 97.187 782 22 0 2322 3103 504583960 504584741 0.000000e+00 1323.0
29 TraesCS7D01G396500 chr4D 91.398 744 45 9 1 741 264066344 264065617 0.000000e+00 1002.0
30 TraesCS7D01G396500 chr4A 94.723 739 36 1 1 739 183154703 183153968 0.000000e+00 1146.0
31 TraesCS7D01G396500 chr4A 93.939 165 10 0 829 993 517406468 517406632 1.850000e-62 250.0
32 TraesCS7D01G396500 chr2A 81.641 719 118 10 1482 2197 775186657 775185950 4.460000e-163 584.0
33 TraesCS7D01G396500 chr2A 93.023 172 11 1 829 1000 734270039 734269869 1.850000e-62 250.0
34 TraesCS7D01G396500 chr2A 73.560 382 85 14 365 740 719695018 719694647 6.980000e-27 132.0
35 TraesCS7D01G396500 chr3A 89.362 423 40 5 318 739 165724527 165724109 7.620000e-146 527.0
36 TraesCS7D01G396500 chr3A 93.939 165 10 0 829 993 365363941 365363777 1.850000e-62 250.0
37 TraesCS7D01G396500 chr5A 75.663 641 126 25 116 739 457052239 457052866 3.030000e-75 292.0
38 TraesCS7D01G396500 chr5A 76.364 110 26 0 1035 1144 618301645 618301754 3.340000e-05 60.2
39 TraesCS7D01G396500 chr5B 75.472 583 113 22 173 739 571451621 571451053 1.100000e-64 257.0
40 TraesCS7D01G396500 chr5B 79.683 315 57 6 1778 2088 610868136 610868447 1.450000e-53 220.0
41 TraesCS7D01G396500 chr4B 93.976 166 10 0 828 993 344463294 344463459 5.140000e-63 252.0
42 TraesCS7D01G396500 chr4B 94.444 162 9 0 832 993 135218049 135218210 1.850000e-62 250.0
43 TraesCS7D01G396500 chr4B 98.182 55 0 1 737 790 288361394 288361448 9.160000e-16 95.3
44 TraesCS7D01G396500 chr4B 98.182 55 0 1 737 790 308676041 308676095 9.160000e-16 95.3
45 TraesCS7D01G396500 chr1B 76.957 460 80 17 102 545 63971828 63971379 4.000000e-59 239.0
46 TraesCS7D01G396500 chrUn 98.182 55 0 1 737 790 425346425 425346479 9.160000e-16 95.3
47 TraesCS7D01G396500 chr6A 98.182 55 0 1 737 790 248917353 248917299 9.160000e-16 95.3
48 TraesCS7D01G396500 chr1A 98.182 55 0 1 737 790 554474584 554474638 9.160000e-16 95.3
49 TraesCS7D01G396500 chr3B 93.103 58 4 0 7 64 214612616 214612559 5.510000e-13 86.1
50 TraesCS7D01G396500 chr7B 100.000 33 0 0 1041 1073 6215919 6215951 9.290000e-06 62.1


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 TraesCS7D01G396500 chr7D 511212211 511215313 3102 False 5731 5731 100.000 1 3103 1 chr7D.!!$F3 3102
1 TraesCS7D01G396500 chr7D 634746292 634747073 781 False 1328 1328 97.315 2322 3103 1 chr7D.!!$F5 781
2 TraesCS7D01G396500 chr7D 182568928 182569708 780 False 1327 1327 97.315 2322 3103 1 chr7D.!!$F2 781
3 TraesCS7D01G396500 chr7D 568358228 568358867 639 False 278 278 75.307 102 727 1 chr7D.!!$F4 625
4 TraesCS7D01G396500 chr2B 749230827 749232137 1310 False 1753 1753 90.731 1000 2324 1 chr2B.!!$F1 1324
5 TraesCS7D01G396500 chr2B 749237922 749238549 627 True 621 621 84.738 1482 2102 1 chr2B.!!$R1 620
6 TraesCS7D01G396500 chr2D 614843862 614845172 1310 False 1742 1742 90.580 1000 2324 1 chr2D.!!$F3 1324
7 TraesCS7D01G396500 chr2D 576873945 576874724 779 True 1325 1325 97.308 2322 3101 1 chr2D.!!$R1 779
8 TraesCS7D01G396500 chr2D 614853281 614853908 627 True 616 616 84.579 1482 2102 1 chr2D.!!$R2 620
9 TraesCS7D01G396500 chr2D 649677318 649678025 707 False 612 612 82.386 1482 2198 1 chr2D.!!$F4 716
10 TraesCS7D01G396500 chr2D 575958354 575958890 536 False 285 285 76.642 116 655 1 chr2D.!!$F2 539
11 TraesCS7D01G396500 chr3D 7350255 7351036 781 False 1334 1334 97.442 2322 3103 1 chr3D.!!$F1 781
12 TraesCS7D01G396500 chr3D 581968468 581969203 735 False 1277 1277 97.965 1 737 1 chr3D.!!$F2 736
13 TraesCS7D01G396500 chr1D 473897708 473898488 780 False 1332 1332 97.442 2322 3103 1 chr1D.!!$F2 781
14 TraesCS7D01G396500 chr6D 35599861 35600643 782 False 1328 1328 97.318 2322 3103 1 chr6D.!!$F2 781
15 TraesCS7D01G396500 chr6D 204555592 204556373 781 True 1323 1323 97.187 2322 3103 1 chr6D.!!$R1 781
16 TraesCS7D01G396500 chr6D 25529755 25530494 739 False 1205 1205 96.081 1 739 1 chr6D.!!$F1 738
17 TraesCS7D01G396500 chr5D 505773951 505774732 781 False 1323 1323 97.187 2322 3103 1 chr5D.!!$F2 781
18 TraesCS7D01G396500 chr4D 504583960 504584741 781 False 1323 1323 97.187 2322 3103 1 chr4D.!!$F1 781
19 TraesCS7D01G396500 chr4D 264065617 264066344 727 True 1002 1002 91.398 1 741 1 chr4D.!!$R1 740
20 TraesCS7D01G396500 chr4A 183153968 183154703 735 True 1146 1146 94.723 1 739 1 chr4A.!!$R1 738
21 TraesCS7D01G396500 chr2A 775185950 775186657 707 True 584 584 81.641 1482 2197 1 chr2A.!!$R3 715
22 TraesCS7D01G396500 chr5A 457052239 457052866 627 False 292 292 75.663 116 739 1 chr5A.!!$F1 623
23 TraesCS7D01G396500 chr5B 571451053 571451621 568 True 257 257 75.472 173 739 1 chr5B.!!$R1 566

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
310 323 0.172578 TCGTTGCATCCTCGGTACAG 59.827 55.0 0.00 0.0 0.0 2.74 F
1312 1348 0.037232 GCTACCGGTGCAGAAACTCT 60.037 55.0 19.93 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1629 0.031857 CAGATGACCTAGCAGCGAGG 59.968 60.0 19.47 19.47 40.22 4.63 R
3037 3081 0.535335 TCCGGTATGGACAGTTGAGC 59.465 55.0 0.00 0.00 43.74 4.26 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
178 185 7.033791 GTCATGCTCATCAACTGAAATCAAAT 58.966 34.615 0.00 0.00 32.14 2.32
310 323 0.172578 TCGTTGCATCCTCGGTACAG 59.827 55.000 0.00 0.00 0.00 2.74
401 424 2.437895 GGCGGCAAGGAGGTTACC 60.438 66.667 3.07 0.00 0.00 2.85
575 610 0.764890 CCCCTGTTTCCTCACTGTGA 59.235 55.000 10.50 10.50 0.00 3.58
620 656 5.133221 ACAGGTCTTGTTTATTTCTGCTGT 58.867 37.500 0.00 0.00 36.31 4.40
682 718 2.496070 CCCTGACTAGTTCAATCCGACA 59.504 50.000 0.00 0.00 32.21 4.35
741 777 4.063967 CGCCTATCGCCGCCCATA 62.064 66.667 0.00 0.00 0.00 2.74
742 778 2.125512 GCCTATCGCCGCCCATAG 60.126 66.667 0.00 0.00 0.00 2.23
743 779 2.579201 CCTATCGCCGCCCATAGG 59.421 66.667 8.14 8.14 36.60 2.57
744 780 1.982395 CCTATCGCCGCCCATAGGA 60.982 63.158 14.36 0.00 43.18 2.94
745 781 1.330655 CCTATCGCCGCCCATAGGAT 61.331 60.000 14.36 0.53 43.18 3.24
746 782 1.399714 CTATCGCCGCCCATAGGATA 58.600 55.000 0.00 0.00 33.47 2.59
747 783 1.964223 CTATCGCCGCCCATAGGATAT 59.036 52.381 0.00 0.00 33.47 1.63
748 784 2.082140 ATCGCCGCCCATAGGATATA 57.918 50.000 0.00 0.00 33.47 0.86
749 785 1.399714 TCGCCGCCCATAGGATATAG 58.600 55.000 0.00 0.00 33.47 1.31
750 786 0.389391 CGCCGCCCATAGGATATAGG 59.611 60.000 0.00 0.00 33.47 2.57
751 787 1.789523 GCCGCCCATAGGATATAGGA 58.210 55.000 0.00 0.00 33.47 2.94
752 788 2.330216 GCCGCCCATAGGATATAGGAT 58.670 52.381 0.00 0.00 33.47 3.24
753 789 2.300437 GCCGCCCATAGGATATAGGATC 59.700 54.545 0.00 0.00 33.47 3.36
754 790 2.900546 CCGCCCATAGGATATAGGATCC 59.099 54.545 2.48 2.48 38.47 3.36
756 792 4.227197 CGCCCATAGGATATAGGATCCTT 58.773 47.826 22.03 10.49 45.78 3.36
757 793 4.039730 CGCCCATAGGATATAGGATCCTTG 59.960 50.000 22.03 9.26 45.78 3.61
758 794 4.349342 GCCCATAGGATATAGGATCCTTGG 59.651 50.000 22.03 17.97 45.78 3.61
759 795 4.910304 CCCATAGGATATAGGATCCTTGGG 59.090 50.000 23.44 23.44 45.78 4.12
760 796 5.792858 CCATAGGATATAGGATCCTTGGGA 58.207 45.833 22.03 0.99 45.78 4.37
761 797 5.843421 CCATAGGATATAGGATCCTTGGGAG 59.157 48.000 22.03 1.69 45.78 4.30
762 798 4.360425 AGGATATAGGATCCTTGGGAGG 57.640 50.000 22.03 0.00 45.78 4.30
772 808 2.381752 CCTTGGGAGGAACTTTTGGT 57.618 50.000 0.00 0.00 46.74 3.67
773 809 3.518992 CCTTGGGAGGAACTTTTGGTA 57.481 47.619 0.00 0.00 46.74 3.25
774 810 3.839778 CCTTGGGAGGAACTTTTGGTAA 58.160 45.455 0.00 0.00 46.74 2.85
775 811 4.416516 CCTTGGGAGGAACTTTTGGTAAT 58.583 43.478 0.00 0.00 46.74 1.89
776 812 4.220602 CCTTGGGAGGAACTTTTGGTAATG 59.779 45.833 0.00 0.00 46.74 1.90
777 813 3.773560 TGGGAGGAACTTTTGGTAATGG 58.226 45.455 0.00 0.00 41.55 3.16
778 814 2.496070 GGGAGGAACTTTTGGTAATGGC 59.504 50.000 0.00 0.00 41.55 4.40
779 815 2.496070 GGAGGAACTTTTGGTAATGGCC 59.504 50.000 0.00 0.00 41.55 5.36
780 816 3.431415 GAGGAACTTTTGGTAATGGCCT 58.569 45.455 3.32 0.00 41.55 5.19
781 817 3.832490 GAGGAACTTTTGGTAATGGCCTT 59.168 43.478 3.32 0.00 41.55 4.35
782 818 3.578282 AGGAACTTTTGGTAATGGCCTTG 59.422 43.478 3.32 0.00 27.25 3.61
783 819 3.576550 GGAACTTTTGGTAATGGCCTTGA 59.423 43.478 3.32 0.00 0.00 3.02
784 820 4.222810 GGAACTTTTGGTAATGGCCTTGAT 59.777 41.667 3.32 0.00 0.00 2.57
785 821 5.405935 AACTTTTGGTAATGGCCTTGATC 57.594 39.130 3.32 0.00 0.00 2.92
786 822 3.769300 ACTTTTGGTAATGGCCTTGATCC 59.231 43.478 3.32 2.25 0.00 3.36
787 823 3.756082 TTTGGTAATGGCCTTGATCCT 57.244 42.857 3.32 0.00 0.00 3.24
788 824 3.297134 TTGGTAATGGCCTTGATCCTC 57.703 47.619 3.32 0.00 0.00 3.71
789 825 2.492025 TGGTAATGGCCTTGATCCTCT 58.508 47.619 3.32 0.00 0.00 3.69
790 826 2.173356 TGGTAATGGCCTTGATCCTCTG 59.827 50.000 3.32 0.00 0.00 3.35
791 827 2.173569 GGTAATGGCCTTGATCCTCTGT 59.826 50.000 3.32 0.00 0.00 3.41
792 828 3.372025 GGTAATGGCCTTGATCCTCTGTT 60.372 47.826 3.32 0.00 0.00 3.16
793 829 4.141482 GGTAATGGCCTTGATCCTCTGTTA 60.141 45.833 3.32 0.00 0.00 2.41
794 830 4.591321 AATGGCCTTGATCCTCTGTTAA 57.409 40.909 3.32 0.00 0.00 2.01
795 831 3.350219 TGGCCTTGATCCTCTGTTAAC 57.650 47.619 3.32 0.00 0.00 2.01
796 832 2.642311 TGGCCTTGATCCTCTGTTAACA 59.358 45.455 8.28 8.28 0.00 2.41
797 833 3.010420 GGCCTTGATCCTCTGTTAACAC 58.990 50.000 3.59 0.00 0.00 3.32
798 834 3.010420 GCCTTGATCCTCTGTTAACACC 58.990 50.000 3.59 0.00 0.00 4.16
799 835 3.559171 GCCTTGATCCTCTGTTAACACCA 60.559 47.826 3.59 0.00 0.00 4.17
800 836 4.848357 CCTTGATCCTCTGTTAACACCAT 58.152 43.478 3.59 0.00 0.00 3.55
801 837 5.256474 CCTTGATCCTCTGTTAACACCATT 58.744 41.667 3.59 0.00 0.00 3.16
802 838 6.414732 CCTTGATCCTCTGTTAACACCATTA 58.585 40.000 3.59 0.00 0.00 1.90
803 839 7.056635 CCTTGATCCTCTGTTAACACCATTAT 58.943 38.462 3.59 0.00 0.00 1.28
804 840 7.227512 CCTTGATCCTCTGTTAACACCATTATC 59.772 40.741 3.59 5.43 0.00 1.75
805 841 6.591935 TGATCCTCTGTTAACACCATTATCC 58.408 40.000 3.59 0.00 0.00 2.59
806 842 6.157820 TGATCCTCTGTTAACACCATTATCCA 59.842 38.462 3.59 0.00 0.00 3.41
807 843 6.575244 TCCTCTGTTAACACCATTATCCAT 57.425 37.500 3.59 0.00 0.00 3.41
808 844 6.969043 TCCTCTGTTAACACCATTATCCATT 58.031 36.000 3.59 0.00 0.00 3.16
809 845 8.096621 TCCTCTGTTAACACCATTATCCATTA 57.903 34.615 3.59 0.00 0.00 1.90
810 846 8.210946 TCCTCTGTTAACACCATTATCCATTAG 58.789 37.037 3.59 0.00 0.00 1.73
811 847 7.041098 CCTCTGTTAACACCATTATCCATTAGC 60.041 40.741 3.59 0.00 0.00 3.09
812 848 6.770785 TCTGTTAACACCATTATCCATTAGCC 59.229 38.462 3.59 0.00 0.00 3.93
813 849 5.830991 TGTTAACACCATTATCCATTAGCCC 59.169 40.000 3.59 0.00 0.00 5.19
814 850 4.814224 AACACCATTATCCATTAGCCCT 57.186 40.909 0.00 0.00 0.00 5.19
815 851 4.104383 ACACCATTATCCATTAGCCCTG 57.896 45.455 0.00 0.00 0.00 4.45
816 852 2.821969 CACCATTATCCATTAGCCCTGC 59.178 50.000 0.00 0.00 0.00 4.85
817 853 2.446666 ACCATTATCCATTAGCCCTGCA 59.553 45.455 0.00 0.00 0.00 4.41
818 854 3.117169 ACCATTATCCATTAGCCCTGCAA 60.117 43.478 0.00 0.00 0.00 4.08
819 855 4.091549 CCATTATCCATTAGCCCTGCAAT 58.908 43.478 0.00 0.00 0.00 3.56
820 856 5.222316 ACCATTATCCATTAGCCCTGCAATA 60.222 40.000 0.00 0.00 0.00 1.90
821 857 5.359009 CCATTATCCATTAGCCCTGCAATAG 59.641 44.000 0.00 0.00 0.00 1.73
822 858 2.957402 TCCATTAGCCCTGCAATAGG 57.043 50.000 0.00 0.00 46.88 2.57
837 873 7.296628 CTGCAATAGGATAGGATATACTCCC 57.703 44.000 0.00 0.00 46.27 4.30
838 874 6.998112 TGCAATAGGATAGGATATACTCCCT 58.002 40.000 12.14 12.14 46.27 4.20
839 875 7.069986 TGCAATAGGATAGGATATACTCCCTC 58.930 42.308 11.10 0.00 46.27 4.30
840 876 6.495526 GCAATAGGATAGGATATACTCCCTCC 59.504 46.154 11.10 7.37 46.27 4.30
841 877 4.799715 AGGATAGGATATACTCCCTCCG 57.200 50.000 0.00 0.00 46.27 4.63
842 878 4.120681 AGGATAGGATATACTCCCTCCGT 58.879 47.826 0.00 0.00 46.27 4.69
843 879 4.544968 AGGATAGGATATACTCCCTCCGTT 59.455 45.833 0.00 0.00 46.27 4.44
844 880 5.016459 AGGATAGGATATACTCCCTCCGTTT 59.984 44.000 0.00 0.00 46.27 3.60
845 881 5.360429 GGATAGGATATACTCCCTCCGTTTC 59.640 48.000 0.00 0.00 46.27 2.78
846 882 4.472690 AGGATATACTCCCTCCGTTTCT 57.527 45.455 0.00 0.00 46.27 2.52
847 883 5.595814 AGGATATACTCCCTCCGTTTCTA 57.404 43.478 0.00 0.00 46.27 2.10
848 884 5.961897 AGGATATACTCCCTCCGTTTCTAA 58.038 41.667 0.00 0.00 46.27 2.10
849 885 6.379579 AGGATATACTCCCTCCGTTTCTAAA 58.620 40.000 0.00 0.00 46.27 1.85
850 886 7.017531 AGGATATACTCCCTCCGTTTCTAAAT 58.982 38.462 0.00 0.00 46.27 1.40
851 887 8.175431 AGGATATACTCCCTCCGTTTCTAAATA 58.825 37.037 0.00 0.00 46.27 1.40
852 888 8.979534 GGATATACTCCCTCCGTTTCTAAATAT 58.020 37.037 0.00 0.00 38.19 1.28
856 892 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
857 893 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
858 894 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
859 895 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
860 896 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
861 897 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
879 915 8.380742 AGTCTTTTTAGAGATTCCACTATGGA 57.619 34.615 0.00 0.00 46.61 3.41
894 930 8.598202 TCCACTATGGACTACATACAAAGTAA 57.402 34.615 0.00 0.00 42.67 2.24
895 931 9.038072 TCCACTATGGACTACATACAAAGTAAA 57.962 33.333 0.00 0.00 42.67 2.01
896 932 9.661563 CCACTATGGACTACATACAAAGTAAAA 57.338 33.333 0.00 0.00 40.96 1.52
901 937 9.959721 ATGGACTACATACAAAGTAAAATGAGT 57.040 29.630 0.00 0.00 38.26 3.41
902 938 9.214957 TGGACTACATACAAAGTAAAATGAGTG 57.785 33.333 0.00 0.00 0.00 3.51
903 939 9.431887 GGACTACATACAAAGTAAAATGAGTGA 57.568 33.333 0.00 0.00 0.00 3.41
908 944 9.295825 ACATACAAAGTAAAATGAGTGAATCCA 57.704 29.630 0.00 0.00 0.00 3.41
909 945 9.559958 CATACAAAGTAAAATGAGTGAATCCAC 57.440 33.333 0.00 0.00 43.50 4.02
910 946 7.581213 ACAAAGTAAAATGAGTGAATCCACA 57.419 32.000 0.00 0.00 45.54 4.17
911 947 7.425606 ACAAAGTAAAATGAGTGAATCCACAC 58.574 34.615 0.00 0.00 45.54 3.82
924 960 8.723942 AGTGAATCCACACTCTAAAATATGTC 57.276 34.615 0.00 0.00 46.36 3.06
925 961 8.543774 AGTGAATCCACACTCTAAAATATGTCT 58.456 33.333 0.00 0.00 46.36 3.41
926 962 9.817809 GTGAATCCACACTCTAAAATATGTCTA 57.182 33.333 0.00 0.00 42.72 2.59
988 1024 9.868160 AAAAGACTTATATTTAGGAATGGAGGG 57.132 33.333 0.00 0.00 0.00 4.30
989 1025 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
990 1026 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
991 1027 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
992 1028 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
993 1029 9.684702 ACTTATATTTAGGAATGGAGGGAGTAA 57.315 33.333 0.00 0.00 0.00 2.24
1022 1058 1.068055 GGCAGATGAGTGCAAGGTTTG 60.068 52.381 0.00 0.00 45.93 2.93
1057 1093 4.222336 AGATGAGAGAGGGTCATACTTGG 58.778 47.826 0.00 0.00 34.69 3.61
1088 1124 0.687354 GGACACTCAAGAGCCAAGGA 59.313 55.000 0.00 0.00 0.00 3.36
1089 1125 1.338579 GGACACTCAAGAGCCAAGGAG 60.339 57.143 0.00 0.00 0.00 3.69
1092 1128 0.324285 ACTCAAGAGCCAAGGAGCTG 59.676 55.000 0.00 0.00 45.15 4.24
1094 1130 0.767375 TCAAGAGCCAAGGAGCTGTT 59.233 50.000 0.00 0.00 46.38 3.16
1104 1140 0.538287 AGGAGCTGTTCAACAAGGGC 60.538 55.000 0.00 0.00 0.00 5.19
1120 1156 0.107654 GGGCGAGTACATGGCTTCTT 60.108 55.000 10.08 0.00 32.34 2.52
1131 1167 1.149101 TGGCTTCTTCCCCTTTCAGT 58.851 50.000 0.00 0.00 0.00 3.41
1132 1168 1.499007 TGGCTTCTTCCCCTTTCAGTT 59.501 47.619 0.00 0.00 0.00 3.16
1146 1182 3.374042 TTCAGTTTTGGAGGTCACCAA 57.626 42.857 0.00 0.00 46.44 3.67
1152 1188 2.765689 TTGGAGGTCACCAATGGTTT 57.234 45.000 0.16 0.00 43.79 3.27
1153 1189 1.993956 TGGAGGTCACCAATGGTTTG 58.006 50.000 0.16 0.00 36.96 2.93
1154 1190 0.603065 GGAGGTCACCAATGGTTTGC 59.397 55.000 0.16 0.00 31.02 3.68
1176 1212 4.424061 GGTGTATTACCCAAACGGAAAC 57.576 45.455 0.00 0.00 44.15 2.78
1204 1240 3.242936 CGACTCGGAAAAACATGTTGGTT 60.243 43.478 12.82 9.61 0.00 3.67
1222 1258 3.006003 TGGTTACAACATACTCGTGAGCA 59.994 43.478 0.00 0.00 0.00 4.26
1231 1267 1.800805 ACTCGTGAGCATGGTTCTTG 58.199 50.000 0.00 0.00 0.00 3.02
1237 1273 3.425359 CGTGAGCATGGTTCTTGATTCAC 60.425 47.826 0.00 0.00 31.96 3.18
1239 1275 2.424956 GAGCATGGTTCTTGATTCACCC 59.575 50.000 0.00 0.00 0.00 4.61
1242 1278 2.178912 TGGTTCTTGATTCACCCGAC 57.821 50.000 0.00 0.00 0.00 4.79
1261 1297 2.633860 GCCAAGGATATCAAGGCGG 58.366 57.895 14.12 4.59 35.42 6.13
1275 1311 2.438868 AGGCGGAAGTCAAATTTTGC 57.561 45.000 4.19 0.57 38.99 3.68
1276 1312 1.059942 GGCGGAAGTCAAATTTTGCG 58.940 50.000 4.19 3.44 40.45 4.85
1281 1317 4.533222 CGGAAGTCAAATTTTGCGTACTT 58.467 39.130 12.11 12.11 34.13 2.24
1283 1319 4.148174 GGAAGTCAAATTTTGCGTACTTGC 59.852 41.667 15.47 14.62 30.53 4.01
1284 1320 4.300189 AGTCAAATTTTGCGTACTTGCA 57.700 36.364 4.19 0.00 44.61 4.08
1299 1335 1.225376 TTGCAAAGGACGTGCTACCG 61.225 55.000 10.98 2.80 42.69 4.02
1312 1348 0.037232 GCTACCGGTGCAGAAACTCT 60.037 55.000 19.93 0.00 0.00 3.24
1329 1365 1.139734 CTGCTGTACCGTCGCTGAT 59.860 57.895 0.00 0.00 0.00 2.90
1332 1368 1.999051 CTGTACCGTCGCTGATTGC 59.001 57.895 0.00 0.00 38.57 3.56
1340 1376 1.372582 GTCGCTGATTGCATCTTCCA 58.627 50.000 0.00 0.00 43.06 3.53
1359 1395 3.057596 TCCAACGGAAAGATTCAACATGC 60.058 43.478 0.00 0.00 0.00 4.06
1362 1398 2.416547 ACGGAAAGATTCAACATGCGAG 59.583 45.455 0.00 0.00 0.00 5.03
1371 1407 4.466567 TTCAACATGCGAGTACTTTGTG 57.533 40.909 0.00 0.00 0.00 3.33
1373 1409 3.740832 TCAACATGCGAGTACTTTGTGAG 59.259 43.478 0.00 0.00 0.00 3.51
1374 1410 2.688507 ACATGCGAGTACTTTGTGAGG 58.311 47.619 0.00 0.00 0.00 3.86
1375 1411 2.037251 ACATGCGAGTACTTTGTGAGGT 59.963 45.455 0.00 0.00 0.00 3.85
1398 1434 0.965363 ATGTTTTTGAGCGGCCCGAT 60.965 50.000 7.68 0.00 0.00 4.18
1450 1486 4.202121 GGTGCGACCTAACTATCATCAAGA 60.202 45.833 0.00 0.00 34.73 3.02
1451 1487 5.348986 GTGCGACCTAACTATCATCAAGAA 58.651 41.667 0.00 0.00 0.00 2.52
1452 1488 5.986135 GTGCGACCTAACTATCATCAAGAAT 59.014 40.000 0.00 0.00 0.00 2.40
1563 1599 0.748450 ACGTCACCTTTCTTGTCGGA 59.252 50.000 0.00 0.00 31.03 4.55
1569 1605 0.912486 CCTTTCTTGTCGGAGGGGAT 59.088 55.000 0.00 0.00 0.00 3.85
1588 1624 3.394606 GGATAAGTTCTTGGCCCATAGGA 59.605 47.826 0.00 0.00 33.47 2.94
1593 1629 1.048601 TCTTGGCCCATAGGATCGTC 58.951 55.000 0.00 0.00 33.47 4.20
1611 1647 0.106469 TCCTCGCTGCTAGGTCATCT 60.106 55.000 18.46 0.00 35.48 2.90
1650 1686 2.176273 CGGCGCCATGAAGGAGAAG 61.176 63.158 28.98 0.37 40.01 2.85
1653 1689 0.678048 GCGCCATGAAGGAGAAGGTT 60.678 55.000 0.00 0.00 40.01 3.50
1662 1698 6.660949 CCATGAAGGAGAAGGTTAACAATCTT 59.339 38.462 8.10 1.55 41.22 2.40
1691 1727 0.181350 AAGGAGATGGAACCCGATGC 59.819 55.000 0.00 0.00 0.00 3.91
1709 1745 2.671177 CGTTCAGGTGCTTGCTCCG 61.671 63.158 7.88 4.28 0.00 4.63
1727 1763 5.109903 GCTCCGTTTCATATACACTGACTT 58.890 41.667 0.00 0.00 0.00 3.01
1729 1765 6.032956 TCCGTTTCATATACACTGACTTGT 57.967 37.500 0.00 0.00 0.00 3.16
1743 1779 3.817084 CTGACTTGTTGCCTGATCTTCAA 59.183 43.478 0.00 0.00 0.00 2.69
1750 1789 3.581024 TGCCTGATCTTCAAAACATGC 57.419 42.857 0.00 0.00 0.00 4.06
1873 1915 3.365820 GCACAAGTTATGCAGCAACATTC 59.634 43.478 14.42 0.00 42.88 2.67
2060 2103 2.158900 GCTAATTGCTAGTCTCCTGCCA 60.159 50.000 0.00 0.00 38.95 4.92
2128 2171 3.119637 GGTGGTTTAGTATTGTTGCGCAT 60.120 43.478 12.75 0.00 0.00 4.73
2149 2192 8.840867 GCGCATGCATAAGTTAGTTTTAATATC 58.159 33.333 19.57 0.00 42.15 1.63
2204 2247 1.490621 GCATGTGTGCCTCAACAAAC 58.509 50.000 0.00 0.00 45.76 2.93
2213 2256 2.750166 TGCCTCAACAAACGAAAAGTGA 59.250 40.909 0.00 0.00 0.00 3.41
2215 2258 3.730715 GCCTCAACAAACGAAAAGTGATG 59.269 43.478 0.00 0.00 0.00 3.07
2224 2267 7.703328 ACAAACGAAAAGTGATGTCTATGTTT 58.297 30.769 0.00 0.00 30.73 2.83
2225 2268 7.643764 ACAAACGAAAAGTGATGTCTATGTTTG 59.356 33.333 0.00 0.00 44.65 2.93
2226 2269 6.861065 ACGAAAAGTGATGTCTATGTTTGT 57.139 33.333 0.00 0.00 0.00 2.83
2227 2270 7.259290 ACGAAAAGTGATGTCTATGTTTGTT 57.741 32.000 0.00 0.00 0.00 2.83
2228 2271 8.373048 ACGAAAAGTGATGTCTATGTTTGTTA 57.627 30.769 0.00 0.00 0.00 2.41
2247 2290 4.134563 GTTAGTTCCTTGCTGGTTCTGAA 58.865 43.478 0.00 0.00 37.07 3.02
2248 2291 2.576615 AGTTCCTTGCTGGTTCTGAAC 58.423 47.619 12.05 12.05 37.07 3.18
2252 2295 2.951642 TCCTTGCTGGTTCTGAACTTTG 59.048 45.455 19.05 10.86 37.07 2.77
2255 2298 4.338118 CCTTGCTGGTTCTGAACTTTGTTA 59.662 41.667 19.05 2.08 0.00 2.41
2263 2306 5.681543 GGTTCTGAACTTTGTTAGCGAAAAG 59.318 40.000 19.05 0.00 38.95 2.27
2281 2324 9.654663 AGCGAAAAGAGAAACTTGTATATACTT 57.345 29.630 13.89 0.00 38.98 2.24
2308 2351 0.616891 ACTGAGATGCATGAGTGGCA 59.383 50.000 2.46 0.00 46.66 4.92
2312 2355 1.453379 GATGCATGAGTGGCAGCCT 60.453 57.895 14.15 0.00 45.68 4.58
2313 2356 0.179037 GATGCATGAGTGGCAGCCTA 60.179 55.000 14.15 0.00 45.68 3.93
2320 2363 1.415289 TGAGTGGCAGCCTATGATCTG 59.585 52.381 14.15 0.00 0.00 2.90
2470 2513 4.508551 TTGATGAGGGTATGCTTGTCAT 57.491 40.909 0.00 0.00 39.17 3.06
2511 2554 5.337578 TGACATCGACCAAGACAATATGA 57.662 39.130 0.00 0.00 0.00 2.15
2690 2733 4.774660 TGGTAGACAAAACCCACTACAA 57.225 40.909 0.00 0.00 37.52 2.41
2790 2833 8.547967 TCTACAATCAAACTCCTCAACATTAC 57.452 34.615 0.00 0.00 0.00 1.89
3002 3046 4.102996 TGATGTATCAGAATGGCAGCCTTA 59.897 41.667 14.15 0.00 36.16 2.69
3037 3081 6.378564 ACATATATCCAGGTCATCCTACGAAG 59.621 42.308 0.00 0.00 43.07 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
401 424 5.063438 CCTTCAACCATGTCTTACATACGTG 59.937 44.000 0.00 0.00 36.53 4.49
575 610 0.607620 CAACCATTGTTTCGCCCCAT 59.392 50.000 0.00 0.00 30.42 4.00
620 656 1.548128 CCCCCACCAAATGAACCGTTA 60.548 52.381 0.00 0.00 0.00 3.18
682 718 2.844839 GCCGGTCTATCCCCAGCT 60.845 66.667 1.90 0.00 0.00 4.24
753 789 2.381752 ACCAAAAGTTCCTCCCAAGG 57.618 50.000 0.00 0.00 44.89 3.61
754 790 4.220602 CCATTACCAAAAGTTCCTCCCAAG 59.779 45.833 0.00 0.00 0.00 3.61
755 791 4.156477 CCATTACCAAAAGTTCCTCCCAA 58.844 43.478 0.00 0.00 0.00 4.12
756 792 3.773560 CCATTACCAAAAGTTCCTCCCA 58.226 45.455 0.00 0.00 0.00 4.37
757 793 2.496070 GCCATTACCAAAAGTTCCTCCC 59.504 50.000 0.00 0.00 0.00 4.30
758 794 2.496070 GGCCATTACCAAAAGTTCCTCC 59.504 50.000 0.00 0.00 0.00 4.30
759 795 3.431415 AGGCCATTACCAAAAGTTCCTC 58.569 45.455 5.01 0.00 0.00 3.71
760 796 3.542969 AGGCCATTACCAAAAGTTCCT 57.457 42.857 5.01 0.00 0.00 3.36
761 797 3.576550 TCAAGGCCATTACCAAAAGTTCC 59.423 43.478 5.01 0.00 0.00 3.62
762 798 4.864704 TCAAGGCCATTACCAAAAGTTC 57.135 40.909 5.01 0.00 0.00 3.01
763 799 4.222810 GGATCAAGGCCATTACCAAAAGTT 59.777 41.667 5.01 0.00 0.00 2.66
764 800 3.769300 GGATCAAGGCCATTACCAAAAGT 59.231 43.478 5.01 0.00 0.00 2.66
765 801 4.026052 AGGATCAAGGCCATTACCAAAAG 58.974 43.478 5.01 0.00 0.00 2.27
766 802 4.023291 GAGGATCAAGGCCATTACCAAAA 58.977 43.478 5.01 0.00 33.17 2.44
767 803 3.269381 AGAGGATCAAGGCCATTACCAAA 59.731 43.478 5.01 0.00 37.82 3.28
768 804 2.852449 AGAGGATCAAGGCCATTACCAA 59.148 45.455 5.01 0.00 37.82 3.67
769 805 2.173356 CAGAGGATCAAGGCCATTACCA 59.827 50.000 5.01 0.00 37.82 3.25
770 806 2.173569 ACAGAGGATCAAGGCCATTACC 59.826 50.000 5.01 1.24 37.82 2.85
771 807 3.567478 ACAGAGGATCAAGGCCATTAC 57.433 47.619 5.01 0.00 37.82 1.89
772 808 5.045213 TGTTAACAGAGGATCAAGGCCATTA 60.045 40.000 5.01 0.00 37.82 1.90
773 809 4.263905 TGTTAACAGAGGATCAAGGCCATT 60.264 41.667 5.01 0.00 37.82 3.16
774 810 3.266772 TGTTAACAGAGGATCAAGGCCAT 59.733 43.478 5.01 0.00 37.82 4.40
775 811 2.642311 TGTTAACAGAGGATCAAGGCCA 59.358 45.455 5.01 0.00 37.82 5.36
776 812 3.010420 GTGTTAACAGAGGATCAAGGCC 58.990 50.000 8.98 0.00 37.82 5.19
777 813 3.010420 GGTGTTAACAGAGGATCAAGGC 58.990 50.000 8.98 0.00 37.82 4.35
778 814 4.286297 TGGTGTTAACAGAGGATCAAGG 57.714 45.455 8.98 0.00 37.82 3.61
779 815 7.227512 GGATAATGGTGTTAACAGAGGATCAAG 59.772 40.741 8.98 0.00 37.82 3.02
780 816 7.054124 GGATAATGGTGTTAACAGAGGATCAA 58.946 38.462 8.98 0.00 37.82 2.57
781 817 6.157820 TGGATAATGGTGTTAACAGAGGATCA 59.842 38.462 8.98 1.83 37.82 2.92
782 818 6.591935 TGGATAATGGTGTTAACAGAGGATC 58.408 40.000 8.98 8.41 0.00 3.36
783 819 6.575244 TGGATAATGGTGTTAACAGAGGAT 57.425 37.500 8.98 0.00 0.00 3.24
784 820 6.575244 ATGGATAATGGTGTTAACAGAGGA 57.425 37.500 8.98 0.00 0.00 3.71
785 821 7.041098 GCTAATGGATAATGGTGTTAACAGAGG 60.041 40.741 8.98 0.00 0.00 3.69
786 822 7.041098 GGCTAATGGATAATGGTGTTAACAGAG 60.041 40.741 8.98 0.00 0.00 3.35
787 823 6.770785 GGCTAATGGATAATGGTGTTAACAGA 59.229 38.462 8.98 0.00 0.00 3.41
788 824 6.016276 GGGCTAATGGATAATGGTGTTAACAG 60.016 42.308 8.98 0.00 0.00 3.16
789 825 5.830991 GGGCTAATGGATAATGGTGTTAACA 59.169 40.000 3.59 3.59 0.00 2.41
790 826 6.016276 CAGGGCTAATGGATAATGGTGTTAAC 60.016 42.308 0.00 0.00 0.00 2.01
791 827 6.068010 CAGGGCTAATGGATAATGGTGTTAA 58.932 40.000 0.00 0.00 0.00 2.01
792 828 5.630121 CAGGGCTAATGGATAATGGTGTTA 58.370 41.667 0.00 0.00 0.00 2.41
793 829 4.473444 CAGGGCTAATGGATAATGGTGTT 58.527 43.478 0.00 0.00 0.00 3.32
794 830 3.751893 GCAGGGCTAATGGATAATGGTGT 60.752 47.826 0.00 0.00 0.00 4.16
795 831 2.821969 GCAGGGCTAATGGATAATGGTG 59.178 50.000 0.00 0.00 0.00 4.17
796 832 2.446666 TGCAGGGCTAATGGATAATGGT 59.553 45.455 0.00 0.00 0.00 3.55
797 833 3.159213 TGCAGGGCTAATGGATAATGG 57.841 47.619 0.00 0.00 0.00 3.16
798 834 5.359009 CCTATTGCAGGGCTAATGGATAATG 59.641 44.000 0.00 0.00 41.26 1.90
799 835 5.253798 TCCTATTGCAGGGCTAATGGATAAT 59.746 40.000 0.00 0.00 45.58 1.28
800 836 4.601420 TCCTATTGCAGGGCTAATGGATAA 59.399 41.667 0.00 0.00 45.58 1.75
801 837 4.175172 TCCTATTGCAGGGCTAATGGATA 58.825 43.478 0.00 0.00 45.58 2.59
802 838 2.988859 TCCTATTGCAGGGCTAATGGAT 59.011 45.455 0.00 0.00 45.58 3.41
803 839 2.417652 TCCTATTGCAGGGCTAATGGA 58.582 47.619 0.00 0.00 45.58 3.41
804 840 2.957402 TCCTATTGCAGGGCTAATGG 57.043 50.000 0.00 0.00 45.58 3.16
805 841 4.225942 TCCTATCCTATTGCAGGGCTAATG 59.774 45.833 0.00 0.00 45.58 1.90
806 842 4.438913 TCCTATCCTATTGCAGGGCTAAT 58.561 43.478 0.00 0.00 45.58 1.73
807 843 3.869310 TCCTATCCTATTGCAGGGCTAA 58.131 45.455 0.00 0.00 45.58 3.09
808 844 3.560357 TCCTATCCTATTGCAGGGCTA 57.440 47.619 0.00 0.00 45.58 3.93
809 845 2.422939 TCCTATCCTATTGCAGGGCT 57.577 50.000 0.00 0.00 45.58 5.19
810 846 5.604650 AGTATATCCTATCCTATTGCAGGGC 59.395 44.000 0.00 0.00 45.58 5.19
811 847 6.268847 GGAGTATATCCTATCCTATTGCAGGG 59.731 46.154 0.00 0.00 45.64 4.45
812 848 7.296628 GGAGTATATCCTATCCTATTGCAGG 57.703 44.000 0.00 0.00 45.64 4.85
830 866 9.377238 ACTTATATTTAGAAACGGAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
831 867 8.773033 ACTTATATTTAGAAACGGAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
832 868 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
833 869 7.953752 AGACTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
834 870 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
835 871 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
853 889 8.826765 TCCATAGTGGAATCTCTAAAAAGACTT 58.173 33.333 0.00 0.00 45.00 3.01
854 890 8.380742 TCCATAGTGGAATCTCTAAAAAGACT 57.619 34.615 0.00 0.00 45.00 3.24
869 905 8.598202 TTACTTTGTATGTAGTCCATAGTGGA 57.402 34.615 0.00 0.00 45.98 4.02
870 906 9.661563 TTTTACTTTGTATGTAGTCCATAGTGG 57.338 33.333 0.00 0.00 36.71 4.00
875 911 9.959721 ACTCATTTTACTTTGTATGTAGTCCAT 57.040 29.630 0.00 0.00 37.58 3.41
876 912 9.214957 CACTCATTTTACTTTGTATGTAGTCCA 57.785 33.333 0.00 0.00 0.00 4.02
877 913 9.431887 TCACTCATTTTACTTTGTATGTAGTCC 57.568 33.333 0.00 0.00 0.00 3.85
882 918 9.295825 TGGATTCACTCATTTTACTTTGTATGT 57.704 29.630 0.00 0.00 0.00 2.29
883 919 9.559958 GTGGATTCACTCATTTTACTTTGTATG 57.440 33.333 0.00 0.00 40.58 2.39
884 920 9.295825 TGTGGATTCACTCATTTTACTTTGTAT 57.704 29.630 5.55 0.00 43.94 2.29
885 921 8.564574 GTGTGGATTCACTCATTTTACTTTGTA 58.435 33.333 5.55 0.00 43.94 2.41
886 922 7.285401 AGTGTGGATTCACTCATTTTACTTTGT 59.715 33.333 5.55 0.00 44.07 2.83
887 923 7.651808 AGTGTGGATTCACTCATTTTACTTTG 58.348 34.615 5.55 0.00 44.07 2.77
888 924 7.823745 AGTGTGGATTCACTCATTTTACTTT 57.176 32.000 5.55 0.00 44.07 2.66
900 936 8.723942 AGACATATTTTAGAGTGTGGATTCAC 57.276 34.615 0.00 0.00 43.87 3.18
962 998 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
963 999 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
964 1000 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
965 1001 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
966 1002 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
967 1003 9.684702 TTACTCCCTCCATTCCTAAATATAAGT 57.315 33.333 0.00 0.00 0.00 2.24
977 1013 8.394040 CCATTAATTATTACTCCCTCCATTCCT 58.606 37.037 0.00 0.00 0.00 3.36
978 1014 7.122799 GCCATTAATTATTACTCCCTCCATTCC 59.877 40.741 0.00 0.00 0.00 3.01
979 1015 7.669722 TGCCATTAATTATTACTCCCTCCATTC 59.330 37.037 0.00 0.00 0.00 2.67
980 1016 7.534852 TGCCATTAATTATTACTCCCTCCATT 58.465 34.615 0.00 0.00 0.00 3.16
981 1017 7.018550 TCTGCCATTAATTATTACTCCCTCCAT 59.981 37.037 0.00 0.00 0.00 3.41
982 1018 6.331572 TCTGCCATTAATTATTACTCCCTCCA 59.668 38.462 0.00 0.00 0.00 3.86
983 1019 6.779860 TCTGCCATTAATTATTACTCCCTCC 58.220 40.000 0.00 0.00 0.00 4.30
984 1020 8.103305 TCATCTGCCATTAATTATTACTCCCTC 58.897 37.037 0.00 0.00 0.00 4.30
985 1021 7.988937 TCATCTGCCATTAATTATTACTCCCT 58.011 34.615 0.00 0.00 0.00 4.20
986 1022 7.885399 ACTCATCTGCCATTAATTATTACTCCC 59.115 37.037 0.00 0.00 0.00 4.30
987 1023 8.725148 CACTCATCTGCCATTAATTATTACTCC 58.275 37.037 0.00 0.00 0.00 3.85
988 1024 8.233190 GCACTCATCTGCCATTAATTATTACTC 58.767 37.037 0.00 0.00 0.00 2.59
989 1025 7.720957 TGCACTCATCTGCCATTAATTATTACT 59.279 33.333 0.00 0.00 36.21 2.24
990 1026 7.874940 TGCACTCATCTGCCATTAATTATTAC 58.125 34.615 0.00 0.00 36.21 1.89
991 1027 8.462589 TTGCACTCATCTGCCATTAATTATTA 57.537 30.769 0.00 0.00 36.21 0.98
992 1028 6.964807 TGCACTCATCTGCCATTAATTATT 57.035 33.333 0.00 0.00 36.21 1.40
993 1029 6.015688 CCTTGCACTCATCTGCCATTAATTAT 60.016 38.462 0.00 0.00 36.21 1.28
994 1030 5.300034 CCTTGCACTCATCTGCCATTAATTA 59.700 40.000 0.00 0.00 36.21 1.40
995 1031 4.098960 CCTTGCACTCATCTGCCATTAATT 59.901 41.667 0.00 0.00 36.21 1.40
996 1032 3.635373 CCTTGCACTCATCTGCCATTAAT 59.365 43.478 0.00 0.00 36.21 1.40
997 1033 3.018856 CCTTGCACTCATCTGCCATTAA 58.981 45.455 0.00 0.00 36.21 1.40
998 1034 2.025981 ACCTTGCACTCATCTGCCATTA 60.026 45.455 0.00 0.00 36.21 1.90
1022 1058 5.378292 TCTCTCATCTATATTCACGGCAC 57.622 43.478 0.00 0.00 0.00 5.01
1057 1093 4.220821 TCTTGAGTGTCCATCTACCTTGAC 59.779 45.833 0.00 0.00 0.00 3.18
1088 1124 0.886490 CTCGCCCTTGTTGAACAGCT 60.886 55.000 0.00 0.00 0.00 4.24
1089 1125 1.166531 ACTCGCCCTTGTTGAACAGC 61.167 55.000 0.00 0.00 0.00 4.40
1092 1128 1.873698 TGTACTCGCCCTTGTTGAAC 58.126 50.000 0.00 0.00 0.00 3.18
1094 1130 1.338674 CCATGTACTCGCCCTTGTTGA 60.339 52.381 0.00 0.00 0.00 3.18
1104 1140 1.473434 GGGGAAGAAGCCATGTACTCG 60.473 57.143 0.00 0.00 0.00 4.18
1120 1156 1.856920 ACCTCCAAAACTGAAAGGGGA 59.143 47.619 0.00 0.00 39.30 4.81
1173 1209 0.102844 TTTCCGAGTCGTCACCGTTT 59.897 50.000 12.31 0.00 35.01 3.60
1174 1210 0.102844 TTTTCCGAGTCGTCACCGTT 59.897 50.000 12.31 0.00 35.01 4.44
1175 1211 0.102844 TTTTTCCGAGTCGTCACCGT 59.897 50.000 12.31 0.00 35.01 4.83
1176 1212 0.505655 GTTTTTCCGAGTCGTCACCG 59.494 55.000 12.31 0.00 0.00 4.94
1177 1213 1.574134 TGTTTTTCCGAGTCGTCACC 58.426 50.000 12.31 0.00 0.00 4.02
1178 1214 2.542595 ACATGTTTTTCCGAGTCGTCAC 59.457 45.455 12.31 1.21 0.00 3.67
1179 1215 2.828877 ACATGTTTTTCCGAGTCGTCA 58.171 42.857 12.31 0.00 0.00 4.35
1180 1216 3.541711 CAACATGTTTTTCCGAGTCGTC 58.458 45.455 8.77 0.00 0.00 4.20
1181 1217 2.289547 CCAACATGTTTTTCCGAGTCGT 59.710 45.455 8.77 0.00 0.00 4.34
1182 1218 2.289547 ACCAACATGTTTTTCCGAGTCG 59.710 45.455 8.77 5.29 0.00 4.18
1204 1240 3.194755 ACCATGCTCACGAGTATGTTGTA 59.805 43.478 19.53 0.00 45.97 2.41
1218 1254 2.424956 GGGTGAATCAAGAACCATGCTC 59.575 50.000 0.00 0.00 35.56 4.26
1222 1258 2.711542 GTCGGGTGAATCAAGAACCAT 58.288 47.619 0.00 0.00 35.56 3.55
1231 1267 2.106683 CCTTGGCGTCGGGTGAATC 61.107 63.158 0.00 0.00 0.00 2.52
1237 1273 0.105964 TTGATATCCTTGGCGTCGGG 59.894 55.000 0.00 0.00 0.00 5.14
1239 1275 1.502231 CCTTGATATCCTTGGCGTCG 58.498 55.000 0.00 0.00 0.00 5.12
1260 1296 4.148174 GCAAGTACGCAAAATTTGACTTCC 59.852 41.667 10.26 0.00 0.00 3.46
1261 1297 4.737765 TGCAAGTACGCAAAATTTGACTTC 59.262 37.500 10.26 5.85 39.45 3.01
1275 1311 0.110823 GCACGTCCTTTGCAAGTACG 60.111 55.000 21.35 21.35 45.00 3.67
1276 1312 1.226746 AGCACGTCCTTTGCAAGTAC 58.773 50.000 0.00 0.00 42.83 2.73
1281 1317 1.666553 CGGTAGCACGTCCTTTGCA 60.667 57.895 0.00 0.00 42.83 4.08
1283 1319 1.005394 ACCGGTAGCACGTCCTTTG 60.005 57.895 4.49 0.00 0.00 2.77
1284 1320 1.005394 CACCGGTAGCACGTCCTTT 60.005 57.895 6.87 0.00 0.00 3.11
1292 1328 0.320421 GAGTTTCTGCACCGGTAGCA 60.320 55.000 23.99 23.99 40.19 3.49
1312 1348 0.735978 CAATCAGCGACGGTACAGCA 60.736 55.000 0.00 0.00 0.00 4.41
1314 1350 1.999051 GCAATCAGCGACGGTACAG 59.001 57.895 0.00 0.00 0.00 2.74
1329 1365 2.857483 TCTTTCCGTTGGAAGATGCAA 58.143 42.857 0.00 0.00 43.06 4.08
1332 1368 5.048782 TGTTGAATCTTTCCGTTGGAAGATG 60.049 40.000 0.00 0.00 43.06 2.90
1340 1376 2.811431 TCGCATGTTGAATCTTTCCGTT 59.189 40.909 0.00 0.00 0.00 4.44
1359 1395 1.616865 TCCCACCTCACAAAGTACTCG 59.383 52.381 0.00 0.00 0.00 4.18
1362 1398 3.418684 ACATCCCACCTCACAAAGTAC 57.581 47.619 0.00 0.00 0.00 2.73
1371 1407 1.200020 CGCTCAAAAACATCCCACCTC 59.800 52.381 0.00 0.00 0.00 3.85
1373 1409 0.243636 CCGCTCAAAAACATCCCACC 59.756 55.000 0.00 0.00 0.00 4.61
1374 1410 0.388520 GCCGCTCAAAAACATCCCAC 60.389 55.000 0.00 0.00 0.00 4.61
1375 1411 1.531739 GGCCGCTCAAAAACATCCCA 61.532 55.000 0.00 0.00 0.00 4.37
1563 1599 0.927029 GGGCCAAGAACTTATCCCCT 59.073 55.000 4.39 0.00 31.20 4.79
1569 1605 3.071023 CGATCCTATGGGCCAAGAACTTA 59.929 47.826 11.89 0.00 0.00 2.24
1588 1624 1.448922 GACCTAGCAGCGAGGACGAT 61.449 60.000 27.02 5.31 42.66 3.73
1593 1629 0.031857 CAGATGACCTAGCAGCGAGG 59.968 60.000 19.47 19.47 40.22 4.63
1611 1647 2.427453 GAGGAGCTCCGTCTTGAATACA 59.573 50.000 26.95 0.00 42.08 2.29
1653 1689 9.300681 ATCTCCTTGATTTCAACAAGATTGTTA 57.699 29.630 10.43 0.00 44.92 2.41
1662 1698 4.766891 GGTTCCATCTCCTTGATTTCAACA 59.233 41.667 0.00 0.00 32.05 3.33
1691 1727 2.671177 CGGAGCAAGCACCTGAACG 61.671 63.158 6.94 0.00 0.00 3.95
1709 1745 6.149474 AGGCAACAAGTCAGTGTATATGAAAC 59.851 38.462 0.00 0.00 41.41 2.78
1727 1763 4.796946 GCATGTTTTGAAGATCAGGCAACA 60.797 41.667 0.00 0.00 37.51 3.33
1729 1765 3.306225 GGCATGTTTTGAAGATCAGGCAA 60.306 43.478 0.00 0.00 38.95 4.52
1743 1779 1.895131 CCTTGGTTGCTAGGCATGTTT 59.105 47.619 0.00 0.00 38.76 2.83
1750 1789 0.678048 GCCTCACCTTGGTTGCTAGG 60.678 60.000 0.00 0.00 37.56 3.02
1773 1812 0.752658 TAGCCATCACCACATCTCGG 59.247 55.000 0.00 0.00 0.00 4.63
1990 2032 2.167662 TCAGATGCTCGTAACCAGTGA 58.832 47.619 0.00 0.00 0.00 3.41
1991 2033 2.654749 TCAGATGCTCGTAACCAGTG 57.345 50.000 0.00 0.00 0.00 3.66
1992 2034 2.826128 TCTTCAGATGCTCGTAACCAGT 59.174 45.455 0.00 0.00 0.00 4.00
1993 2035 3.443037 CTCTTCAGATGCTCGTAACCAG 58.557 50.000 0.00 0.00 0.00 4.00
2060 2103 2.418368 TGGCCGCTTTCATTGTATCT 57.582 45.000 0.00 0.00 0.00 1.98
2105 2148 2.226912 GCGCAACAATACTAAACCACCA 59.773 45.455 0.30 0.00 0.00 4.17
2204 2247 8.495949 ACTAACAAACATAGACATCACTTTTCG 58.504 33.333 0.00 0.00 0.00 3.46
2213 2256 6.942576 AGCAAGGAACTAACAAACATAGACAT 59.057 34.615 0.00 0.00 38.49 3.06
2215 2258 6.348540 CCAGCAAGGAACTAACAAACATAGAC 60.349 42.308 0.00 0.00 38.49 2.59
2224 2267 3.135712 TCAGAACCAGCAAGGAACTAACA 59.864 43.478 1.83 0.00 38.49 2.41
2225 2268 3.740115 TCAGAACCAGCAAGGAACTAAC 58.260 45.455 1.83 0.00 38.49 2.34
2226 2269 4.134563 GTTCAGAACCAGCAAGGAACTAA 58.865 43.478 1.29 0.00 38.49 2.24
2227 2270 3.391296 AGTTCAGAACCAGCAAGGAACTA 59.609 43.478 9.85 0.00 42.07 2.24
2228 2271 3.372025 AAGTTCAGAACCAGCAAGGAACT 60.372 43.478 9.85 0.00 44.77 3.01
2247 2290 6.679327 AGTTTCTCTTTTCGCTAACAAAGT 57.321 33.333 0.00 0.00 32.67 2.66
2248 2291 6.967199 ACAAGTTTCTCTTTTCGCTAACAAAG 59.033 34.615 0.00 0.00 33.63 2.77
2255 2298 9.654663 AAGTATATACAAGTTTCTCTTTTCGCT 57.345 29.630 15.18 0.00 33.63 4.93
2281 2324 6.595326 CCACTCATGCATCTCAGTAAGTAAAA 59.405 38.462 0.00 0.00 0.00 1.52
2298 2341 2.038689 AGATCATAGGCTGCCACTCATG 59.961 50.000 22.65 16.92 0.00 3.07
2308 2351 5.245531 TCGTTTCAAAACAGATCATAGGCT 58.754 37.500 6.45 0.00 38.81 4.58
2310 2353 7.364522 TCTTCGTTTCAAAACAGATCATAGG 57.635 36.000 6.45 0.00 38.81 2.57
2313 2356 9.533253 AATTTTCTTCGTTTCAAAACAGATCAT 57.467 25.926 6.45 0.00 38.81 2.45
2320 2363 7.520119 AGGTGAATTTTCTTCGTTTCAAAAC 57.480 32.000 0.00 0.00 35.59 2.43
2422 2465 5.394883 CCATACATCTTGCAAAATGCTTCCT 60.395 40.000 12.71 0.00 45.31 3.36
2511 2554 4.217550 CGTATCAACAAGGACCCAAATGTT 59.782 41.667 0.00 0.00 36.49 2.71
2655 2698 3.055747 TGTCTACCATGTTCCGCACATTA 60.056 43.478 0.00 0.00 44.40 1.90
2690 2733 1.183549 AGTTAACTCGGAGCCATCGT 58.816 50.000 1.12 0.00 0.00 3.73
2790 2833 2.866156 CACTAGTGGCATGTATTGACCG 59.134 50.000 15.49 0.00 29.16 4.79
3002 3046 7.402054 TGACCTGGATATATGTTCAAAACACT 58.598 34.615 0.00 0.00 45.50 3.55
3037 3081 0.535335 TCCGGTATGGACAGTTGAGC 59.465 55.000 0.00 0.00 43.74 4.26


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

AutoCloner maintained by Alex Coulton.