Multiple sequence alignment - TraesCS7D01G414100

Loading Multiple Alignment...

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 TraesCS7D01G414100 chr7D 100.000 4968 0 0 1 4968 532608869 532603902 0.000000e+00 9175.0
1 TraesCS7D01G414100 chr7D 100.000 30 0 0 2539 2568 532606263 532606234 6.950000e-04 56.5
2 TraesCS7D01G414100 chr7D 100.000 30 0 0 2607 2636 532606331 532606302 6.950000e-04 56.5
3 TraesCS7D01G414100 chr7B 88.615 3452 202 77 793 4122 572938839 572935457 0.000000e+00 4021.0
4 TraesCS7D01G414100 chr7B 92.627 746 33 13 1 734 572939574 572938839 0.000000e+00 1053.0
5 TraesCS7D01G414100 chr7B 90.547 201 19 0 1489 1689 374352418 374352618 2.950000e-67 267.0
6 TraesCS7D01G414100 chr7B 100.000 30 0 0 2607 2636 572937063 572937034 6.950000e-04 56.5
7 TraesCS7D01G414100 chr7A 90.708 1625 94 27 809 2401 612701109 612699510 0.000000e+00 2111.0
8 TraesCS7D01G414100 chr7A 85.958 1054 70 38 3178 4184 612698736 612697714 0.000000e+00 1055.0
9 TraesCS7D01G414100 chr7A 87.871 371 36 6 2807 3171 612699142 612698775 1.280000e-115 427.0
10 TraesCS7D01G414100 chr7A 82.216 343 44 12 5 330 612741161 612740819 3.790000e-71 279.0
11 TraesCS7D01G414100 chr7A 91.589 107 8 1 2468 2574 612699481 612699376 4.010000e-31 147.0
12 TraesCS7D01G414100 chr7A 100.000 32 0 0 2605 2636 612699413 612699382 5.370000e-05 60.2
13 TraesCS7D01G414100 chr6B 89.919 744 73 2 4224 4967 216699500 216698759 0.000000e+00 957.0
14 TraesCS7D01G414100 chr6B 91.144 271 24 0 1489 1759 483680460 483680190 7.860000e-98 368.0
15 TraesCS7D01G414100 chr6B 90.775 271 25 0 1489 1759 483731825 483731555 3.660000e-96 363.0
16 TraesCS7D01G414100 chr2D 89.474 760 67 9 4210 4967 187524768 187524020 0.000000e+00 948.0
17 TraesCS7D01G414100 chr2D 87.449 741 87 6 4228 4967 550629860 550629125 0.000000e+00 848.0
18 TraesCS7D01G414100 chr4A 89.247 744 79 1 4225 4967 86929258 86930001 0.000000e+00 929.0
19 TraesCS7D01G414100 chr3D 88.755 747 79 5 4224 4966 387152281 387151536 0.000000e+00 909.0
20 TraesCS7D01G414100 chr3B 87.995 758 83 4 4210 4967 363322419 363321670 0.000000e+00 889.0
21 TraesCS7D01G414100 chr3B 91.418 268 23 0 1489 1756 286474519 286474786 7.860000e-98 368.0
22 TraesCS7D01G414100 chr3B 90.411 146 14 0 1614 1759 205170896 205170751 5.080000e-45 193.0
23 TraesCS7D01G414100 chrUn 86.821 736 86 9 4240 4967 119816117 119815385 0.000000e+00 811.0
24 TraesCS7D01G414100 chr3A 86.821 736 85 11 4240 4967 319954052 319953321 0.000000e+00 811.0
25 TraesCS7D01G414100 chr2A 86.040 745 97 5 4224 4967 692037296 692036558 0.000000e+00 793.0
26 TraesCS7D01G414100 chr2B 93.865 163 10 0 1594 1756 756870721 756870883 3.840000e-61 246.0
27 TraesCS7D01G414100 chr5B 90.361 166 16 0 1594 1759 622453331 622453166 8.370000e-53 219.0
28 TraesCS7D01G414100 chr5B 94.167 120 7 0 1640 1759 653691945 653691826 3.050000e-42 183.0
29 TraesCS7D01G414100 chr5B 92.391 92 6 1 1494 1584 653692025 653691934 4.040000e-26 130.0


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 TraesCS7D01G414100 chr7D 532603902 532608869 4967 True 3096.000000 9175 100.000000 1 4968 3 chr7D.!!$R1 4967
1 TraesCS7D01G414100 chr7B 572935457 572939574 4117 True 1710.166667 4021 93.747333 1 4122 3 chr7B.!!$R1 4121
2 TraesCS7D01G414100 chr7A 612697714 612701109 3395 True 760.040000 2111 91.225200 809 4184 5 chr7A.!!$R2 3375
3 TraesCS7D01G414100 chr6B 216698759 216699500 741 True 957.000000 957 89.919000 4224 4967 1 chr6B.!!$R1 743
4 TraesCS7D01G414100 chr2D 187524020 187524768 748 True 948.000000 948 89.474000 4210 4967 1 chr2D.!!$R1 757
5 TraesCS7D01G414100 chr2D 550629125 550629860 735 True 848.000000 848 87.449000 4228 4967 1 chr2D.!!$R2 739
6 TraesCS7D01G414100 chr4A 86929258 86930001 743 False 929.000000 929 89.247000 4225 4967 1 chr4A.!!$F1 742
7 TraesCS7D01G414100 chr3D 387151536 387152281 745 True 909.000000 909 88.755000 4224 4966 1 chr3D.!!$R1 742
8 TraesCS7D01G414100 chr3B 363321670 363322419 749 True 889.000000 889 87.995000 4210 4967 1 chr3B.!!$R2 757
9 TraesCS7D01G414100 chrUn 119815385 119816117 732 True 811.000000 811 86.821000 4240 4967 1 chrUn.!!$R1 727
10 TraesCS7D01G414100 chr3A 319953321 319954052 731 True 811.000000 811 86.821000 4240 4967 1 chr3A.!!$R1 727
11 TraesCS7D01G414100 chr2A 692036558 692037296 738 True 793.000000 793 86.040000 4224 4967 1 chr2A.!!$R1 743

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
783 793 0.036765 TATCCACCCGCACACAGAAC 60.037 55.0 0.00 0.0 0.0 3.01 F
1215 1225 0.107081 TCTCTCCTCTCGATCGTCCC 59.893 60.0 15.94 0.0 0.0 4.46 F
2654 2732 0.251832 TCAGAGAAGTTCCCGGAGCT 60.252 55.0 0.73 0.0 0.0 4.09 F
3313 3485 0.031994 GGCTCTCATCTTCCTCGCTC 59.968 60.0 0.00 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 2307 0.035534 TTCGCCTAGCATTCCAAGCA 60.036 50.0 0.00 0.0 0.00 3.91 R
2798 2909 0.036765 TTCGCGGCCAGTATGAACTT 60.037 50.0 6.13 0.0 39.69 2.66 R
3562 3744 0.034186 GGGGCAGTTCACATGGATCA 60.034 55.0 0.00 0.0 0.00 2.92 R
4203 4430 0.105607 GATAGAGGTCGGGTCCCCTT 60.106 60.0 1.00 0.0 0.00 3.95 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
21 22 2.923426 GATGGCCCGTCAGATTGCGA 62.923 60.000 0.00 0.00 0.00 5.10
81 82 2.632377 ACAATGTTCCGCTCTACATGG 58.368 47.619 0.00 0.00 35.29 3.66
102 103 6.095432 TGGTGAATTTTGGAATGAACGATT 57.905 33.333 0.00 0.00 0.00 3.34
173 174 4.418973 AGAATGGATGATCACCAGACAG 57.581 45.455 18.01 0.00 40.89 3.51
219 220 5.728351 TGGACTCAAGTTTGAAAGTTACG 57.272 39.130 0.00 0.00 36.64 3.18
335 336 7.215789 AGTTGGCATTCTAGAGAAGATATGTG 58.784 38.462 0.00 0.00 37.48 3.21
353 354 7.609146 AGATATGTGTGTGTTGTCAATCAGATT 59.391 33.333 0.00 0.00 0.00 2.40
618 627 6.555812 AAAACCGAAGATAACCAGAGAAAC 57.444 37.500 0.00 0.00 0.00 2.78
619 628 4.884668 ACCGAAGATAACCAGAGAAACA 57.115 40.909 0.00 0.00 0.00 2.83
628 637 7.837863 AGATAACCAGAGAAACACGAAGATAA 58.162 34.615 0.00 0.00 0.00 1.75
631 640 3.612860 CCAGAGAAACACGAAGATAACCG 59.387 47.826 0.00 0.00 0.00 4.44
632 641 3.612860 CAGAGAAACACGAAGATAACCGG 59.387 47.826 0.00 0.00 0.00 5.28
703 713 1.691337 TACATTACTGGGCCGGCCT 60.691 57.895 42.70 27.41 36.10 5.19
709 719 2.123425 CTGGGCCGGCCTAGTAGA 60.123 66.667 42.19 20.66 39.49 2.59
718 728 2.423898 GCCTAGTAGAGCCACGCCA 61.424 63.158 0.00 0.00 0.00 5.69
721 731 0.103208 CTAGTAGAGCCACGCCAAGG 59.897 60.000 0.00 0.00 0.00 3.61
732 742 3.077556 GCCAAGGGGAGCGAGAGA 61.078 66.667 0.00 0.00 35.59 3.10
733 743 2.439104 GCCAAGGGGAGCGAGAGAT 61.439 63.158 0.00 0.00 35.59 2.75
734 744 1.115930 GCCAAGGGGAGCGAGAGATA 61.116 60.000 0.00 0.00 35.59 1.98
735 745 0.965439 CCAAGGGGAGCGAGAGATAG 59.035 60.000 0.00 0.00 35.59 2.08
736 746 0.316841 CAAGGGGAGCGAGAGATAGC 59.683 60.000 0.00 0.00 0.00 2.97
742 752 3.763931 AGCGAGAGATAGCTCCCAT 57.236 52.632 3.92 0.00 42.30 4.00
743 753 1.255882 AGCGAGAGATAGCTCCCATG 58.744 55.000 3.92 0.00 42.30 3.66
744 754 0.965439 GCGAGAGATAGCTCCCATGT 59.035 55.000 3.92 0.00 42.30 3.21
745 755 1.336702 GCGAGAGATAGCTCCCATGTG 60.337 57.143 3.92 0.00 42.30 3.21
746 756 2.234143 CGAGAGATAGCTCCCATGTGA 58.766 52.381 3.92 0.00 42.30 3.58
747 757 2.228582 CGAGAGATAGCTCCCATGTGAG 59.771 54.545 3.92 0.11 42.30 3.51
748 758 3.495331 GAGAGATAGCTCCCATGTGAGA 58.505 50.000 9.61 0.00 42.30 3.27
749 759 3.894427 GAGAGATAGCTCCCATGTGAGAA 59.106 47.826 9.61 0.00 42.30 2.87
750 760 3.896888 AGAGATAGCTCCCATGTGAGAAG 59.103 47.826 9.61 0.00 42.30 2.85
751 761 3.640967 GAGATAGCTCCCATGTGAGAAGT 59.359 47.826 9.61 0.00 35.01 3.01
752 762 4.809193 AGATAGCTCCCATGTGAGAAGTA 58.191 43.478 9.61 0.00 34.11 2.24
753 763 4.832266 AGATAGCTCCCATGTGAGAAGTAG 59.168 45.833 9.61 0.00 34.11 2.57
754 764 2.114616 AGCTCCCATGTGAGAAGTAGG 58.885 52.381 9.61 0.00 34.11 3.18
755 765 1.474143 GCTCCCATGTGAGAAGTAGGC 60.474 57.143 9.61 0.00 34.11 3.93
756 766 1.139853 CTCCCATGTGAGAAGTAGGCC 59.860 57.143 0.00 0.00 34.11 5.19
757 767 0.181350 CCCATGTGAGAAGTAGGCCC 59.819 60.000 0.00 0.00 0.00 5.80
758 768 0.911769 CCATGTGAGAAGTAGGCCCA 59.088 55.000 0.00 0.00 0.00 5.36
759 769 1.281867 CCATGTGAGAAGTAGGCCCAA 59.718 52.381 0.00 0.00 0.00 4.12
760 770 2.290896 CCATGTGAGAAGTAGGCCCAAA 60.291 50.000 0.00 0.00 0.00 3.28
761 771 3.624777 CATGTGAGAAGTAGGCCCAAAT 58.375 45.455 0.00 0.00 0.00 2.32
762 772 4.385199 CCATGTGAGAAGTAGGCCCAAATA 60.385 45.833 0.00 0.00 0.00 1.40
763 773 4.919774 TGTGAGAAGTAGGCCCAAATAA 57.080 40.909 0.00 0.00 0.00 1.40
764 774 5.450818 TGTGAGAAGTAGGCCCAAATAAT 57.549 39.130 0.00 0.00 0.00 1.28
765 775 6.569127 TGTGAGAAGTAGGCCCAAATAATA 57.431 37.500 0.00 0.00 0.00 0.98
766 776 7.149202 TGTGAGAAGTAGGCCCAAATAATAT 57.851 36.000 0.00 0.00 0.00 1.28
767 777 7.224297 TGTGAGAAGTAGGCCCAAATAATATC 58.776 38.462 0.00 0.00 0.00 1.63
768 778 6.655425 GTGAGAAGTAGGCCCAAATAATATCC 59.345 42.308 0.00 0.00 0.00 2.59
769 779 6.331572 TGAGAAGTAGGCCCAAATAATATCCA 59.668 38.462 0.00 0.00 0.00 3.41
770 780 6.543735 AGAAGTAGGCCCAAATAATATCCAC 58.456 40.000 0.00 0.00 0.00 4.02
771 781 5.256806 AGTAGGCCCAAATAATATCCACC 57.743 43.478 0.00 0.00 0.00 4.61
772 782 3.542969 AGGCCCAAATAATATCCACCC 57.457 47.619 0.00 0.00 0.00 4.61
773 783 2.167662 GGCCCAAATAATATCCACCCG 58.832 52.381 0.00 0.00 0.00 5.28
774 784 1.544246 GCCCAAATAATATCCACCCGC 59.456 52.381 0.00 0.00 0.00 6.13
775 785 2.870175 CCCAAATAATATCCACCCGCA 58.130 47.619 0.00 0.00 0.00 5.69
776 786 2.556622 CCCAAATAATATCCACCCGCAC 59.443 50.000 0.00 0.00 0.00 5.34
777 787 3.218453 CCAAATAATATCCACCCGCACA 58.782 45.455 0.00 0.00 0.00 4.57
778 788 3.004315 CCAAATAATATCCACCCGCACAC 59.996 47.826 0.00 0.00 0.00 3.82
779 789 3.569194 AATAATATCCACCCGCACACA 57.431 42.857 0.00 0.00 0.00 3.72
780 790 2.613026 TAATATCCACCCGCACACAG 57.387 50.000 0.00 0.00 0.00 3.66
781 791 0.908910 AATATCCACCCGCACACAGA 59.091 50.000 0.00 0.00 0.00 3.41
782 792 0.908910 ATATCCACCCGCACACAGAA 59.091 50.000 0.00 0.00 0.00 3.02
783 793 0.036765 TATCCACCCGCACACAGAAC 60.037 55.000 0.00 0.00 0.00 3.01
784 794 1.768684 ATCCACCCGCACACAGAACT 61.769 55.000 0.00 0.00 0.00 3.01
785 795 2.253758 CCACCCGCACACAGAACTG 61.254 63.158 0.00 0.00 0.00 3.16
786 796 2.591715 ACCCGCACACAGAACTGC 60.592 61.111 1.46 0.00 0.00 4.40
787 797 2.281070 CCCGCACACAGAACTGCT 60.281 61.111 1.46 0.00 0.00 4.24
878 888 1.919956 CTCGCCACGACGTACTCCTT 61.920 60.000 0.00 0.00 0.00 3.36
925 935 2.440817 GGACGGGGGATCGGACATT 61.441 63.158 0.00 0.00 0.00 2.71
1188 1198 2.279120 CTCGCCAGTGAGATCGCC 60.279 66.667 1.90 0.00 38.28 5.54
1189 1199 2.755876 TCGCCAGTGAGATCGCCT 60.756 61.111 0.00 0.00 0.00 5.52
1190 1200 2.279120 CGCCAGTGAGATCGCCTC 60.279 66.667 0.00 0.00 42.30 4.70
1191 1201 2.780094 CGCCAGTGAGATCGCCTCT 61.780 63.158 0.00 0.00 42.44 3.69
1214 1224 1.069513 TCTCTCTCCTCTCGATCGTCC 59.930 57.143 15.94 0.00 0.00 4.79
1215 1225 0.107081 TCTCTCCTCTCGATCGTCCC 59.893 60.000 15.94 0.00 0.00 4.46
1221 1231 3.606662 CTCGATCGTCCCCCGCAT 61.607 66.667 15.94 0.00 36.19 4.73
1236 1250 1.299620 GCATACCCGCGACACGTAT 60.300 57.895 8.23 4.97 41.42 3.06
1292 1315 1.137614 GTCGCTGCAGAGATCGTCA 59.862 57.895 23.33 0.00 0.00 4.35
1411 1438 0.373716 GTCGACGCCATTGACAATCC 59.626 55.000 0.00 0.00 41.01 3.01
1667 1694 3.782244 GAGTGCTTCGCGGTGCTG 61.782 66.667 20.75 3.71 0.00 4.41
1844 1871 2.061220 CTGCCAGGTGAGGTTCAGA 58.939 57.895 0.00 0.00 0.00 3.27
1845 1872 0.321122 CTGCCAGGTGAGGTTCAGAC 60.321 60.000 0.00 0.00 0.00 3.51
1861 1889 2.095415 TCAGACCATCGTCGTGTTACTG 60.095 50.000 0.00 0.00 44.28 2.74
1907 1935 0.461548 TGCAAACATTCGTGCCCAAA 59.538 45.000 0.00 0.00 40.14 3.28
1908 1936 1.069823 TGCAAACATTCGTGCCCAAAT 59.930 42.857 0.00 0.00 40.14 2.32
1924 1954 3.006752 CCCAAATTTTACTGCAGCCTGAA 59.993 43.478 15.27 4.20 0.00 3.02
2060 2093 2.416027 CGTCTTCCTGCGATCTCTGAAA 60.416 50.000 0.00 0.00 0.00 2.69
2193 2243 5.713861 AGGAACTCTGGTACGTGTACTTATT 59.286 40.000 9.79 0.00 36.36 1.40
2194 2244 6.886459 AGGAACTCTGGTACGTGTACTTATTA 59.114 38.462 9.79 0.00 36.36 0.98
2195 2245 7.559170 AGGAACTCTGGTACGTGTACTTATTAT 59.441 37.037 9.79 0.00 36.36 1.28
2202 2252 6.602803 TGGTACGTGTACTTATTATGAGACCA 59.397 38.462 9.79 0.00 36.36 4.02
2228 2278 2.517959 TCTTCTGCATTTTCCCCTGTG 58.482 47.619 0.00 0.00 0.00 3.66
2241 2291 4.463050 TCCCCTGTGGAATTAACTGTTT 57.537 40.909 0.00 0.00 41.40 2.83
2242 2292 4.810345 TCCCCTGTGGAATTAACTGTTTT 58.190 39.130 0.00 0.00 41.40 2.43
2269 2331 1.927487 TTGATGGTGCTTGGAATGCT 58.073 45.000 0.00 0.00 37.94 3.79
2440 2514 5.163683 CCTTCAGGAGTATGTTTTGATGCTG 60.164 44.000 0.00 0.00 37.39 4.41
2442 2516 5.181009 TCAGGAGTATGTTTTGATGCTGAG 58.819 41.667 0.00 0.00 34.05 3.35
2462 2536 6.976925 GCTGAGATGATTTTATTTTCCCTGTG 59.023 38.462 0.00 0.00 0.00 3.66
2463 2537 7.363268 GCTGAGATGATTTTATTTTCCCTGTGT 60.363 37.037 0.00 0.00 0.00 3.72
2464 2538 8.421249 TGAGATGATTTTATTTTCCCTGTGTT 57.579 30.769 0.00 0.00 0.00 3.32
2465 2539 8.869109 TGAGATGATTTTATTTTCCCTGTGTTT 58.131 29.630 0.00 0.00 0.00 2.83
2466 2540 9.710900 GAGATGATTTTATTTTCCCTGTGTTTT 57.289 29.630 0.00 0.00 0.00 2.43
2507 2581 3.100658 TCGTTTCTTGTGACGATGGAA 57.899 42.857 0.00 0.00 42.67 3.53
2624 2702 3.206964 TGTCACGTTGCAAATAAGACCA 58.793 40.909 0.00 0.00 0.00 4.02
2635 2713 5.711506 TGCAAATAAGACCATTGTGAGTCAT 59.288 36.000 0.00 0.00 35.38 3.06
2644 2722 4.285517 ACCATTGTGAGTCATCAGAGAAGT 59.714 41.667 0.00 0.00 35.66 3.01
2646 2724 5.350914 CCATTGTGAGTCATCAGAGAAGTTC 59.649 44.000 0.00 0.00 35.66 3.01
2649 2727 2.493675 TGAGTCATCAGAGAAGTTCCCG 59.506 50.000 0.00 0.00 0.00 5.14
2654 2732 0.251832 TCAGAGAAGTTCCCGGAGCT 60.252 55.000 0.73 0.00 0.00 4.09
2664 2742 4.962155 AGTTCCCGGAGCTATTATTTCAG 58.038 43.478 0.73 0.00 0.00 3.02
2668 2746 5.145564 TCCCGGAGCTATTATTTCAGTAGT 58.854 41.667 0.73 0.00 0.00 2.73
2669 2747 5.243283 TCCCGGAGCTATTATTTCAGTAGTC 59.757 44.000 0.73 0.00 0.00 2.59
2692 2772 5.471456 TCTTTTCTCTGATCTCAAAAGTGCC 59.529 40.000 13.73 0.00 37.21 5.01
2757 2868 4.111916 CTGAAACGAACAAAATGCCAGTT 58.888 39.130 0.00 0.00 0.00 3.16
2782 2893 6.483687 ACATTGTCGTTTGAACTTGACTAAC 58.516 36.000 0.00 0.00 32.64 2.34
2785 2896 6.281848 TGTCGTTTGAACTTGACTAACATC 57.718 37.500 0.00 0.00 32.64 3.06
2787 2898 5.465724 GTCGTTTGAACTTGACTAACATCCT 59.534 40.000 0.00 0.00 0.00 3.24
2788 2899 5.465390 TCGTTTGAACTTGACTAACATCCTG 59.535 40.000 0.00 0.00 0.00 3.86
2790 2901 4.623932 TGAACTTGACTAACATCCTGCT 57.376 40.909 0.00 0.00 0.00 4.24
2792 2903 6.109156 TGAACTTGACTAACATCCTGCTAA 57.891 37.500 0.00 0.00 0.00 3.09
2793 2904 5.932303 TGAACTTGACTAACATCCTGCTAAC 59.068 40.000 0.00 0.00 0.00 2.34
2797 2908 6.595716 ACTTGACTAACATCCTGCTAACATTC 59.404 38.462 0.00 0.00 0.00 2.67
2798 2909 6.048732 TGACTAACATCCTGCTAACATTCA 57.951 37.500 0.00 0.00 0.00 2.57
2800 2911 6.595326 TGACTAACATCCTGCTAACATTCAAG 59.405 38.462 0.00 0.00 0.00 3.02
2801 2912 6.476378 ACTAACATCCTGCTAACATTCAAGT 58.524 36.000 0.00 0.00 0.00 3.16
2802 2913 6.942576 ACTAACATCCTGCTAACATTCAAGTT 59.057 34.615 0.00 0.00 35.55 2.66
2803 2914 5.886960 ACATCCTGCTAACATTCAAGTTC 57.113 39.130 0.00 0.00 33.07 3.01
2811 2939 5.123820 TGCTAACATTCAAGTTCATACTGGC 59.876 40.000 0.00 0.00 34.01 4.85
2821 2949 0.874175 TCATACTGGCCGCGAATTCG 60.874 55.000 23.34 23.34 43.27 3.34
2833 2961 1.324736 GCGAATTCGTGTGTCCTGATC 59.675 52.381 27.24 4.00 42.22 2.92
2898 3031 5.582689 ATTCTGGAATTCCGGTGAAATTC 57.417 39.130 28.69 15.43 43.01 2.17
2912 3045 4.051237 GTGAAATTCACTGGCTTTGGAAC 58.949 43.478 18.03 0.00 43.73 3.62
2935 3068 4.216257 CCAAATTGGTAGGAATATCGGCAG 59.784 45.833 3.34 0.00 31.35 4.85
2965 3098 2.843701 ACTGCAGACCAAGAAGAACAG 58.156 47.619 23.35 0.00 0.00 3.16
2971 3104 0.535102 ACCAAGAAGAACAGCCACCG 60.535 55.000 0.00 0.00 0.00 4.94
3076 3209 0.994995 CTGAGCTCAACGATGAACCG 59.005 55.000 18.85 0.00 34.49 4.44
3096 3229 0.762418 CAACCTACCACCACCACTGA 59.238 55.000 0.00 0.00 0.00 3.41
3125 3258 3.627577 CGATTTACTGGTAAGCTGCCAAT 59.372 43.478 10.93 4.53 35.32 3.16
3134 3267 2.211250 AAGCTGCCAATGTCTGTCAT 57.789 45.000 0.00 0.00 38.57 3.06
3161 3294 2.710096 TACAGCCCTGATGTTTAGCC 57.290 50.000 1.69 0.00 33.09 3.93
3167 3300 2.795329 CCCTGATGTTTAGCCAACTGT 58.205 47.619 0.00 0.00 36.21 3.55
3213 3379 2.237392 GGGTTTACATGAGGTGAGCTCT 59.763 50.000 16.19 0.00 0.00 4.09
3264 3430 3.211963 GCCCTGGCCATTGTAGCG 61.212 66.667 5.51 0.00 34.56 4.26
3275 3441 2.080693 CATTGTAGCGCCAGGTAACAA 58.919 47.619 2.29 6.15 41.41 2.83
3276 3442 1.803334 TTGTAGCGCCAGGTAACAAG 58.197 50.000 2.29 0.00 41.41 3.16
3300 3466 2.516460 CCATGCAGCTGGGCTCTC 60.516 66.667 17.12 0.00 36.40 3.20
3302 3468 1.152943 CATGCAGCTGGGCTCTCAT 60.153 57.895 17.12 6.13 36.40 2.90
3303 3469 1.148723 ATGCAGCTGGGCTCTCATC 59.851 57.895 17.12 0.00 36.40 2.92
3305 3471 1.224039 GCAGCTGGGCTCTCATCTT 59.776 57.895 17.12 0.00 36.40 2.40
3306 3472 0.814812 GCAGCTGGGCTCTCATCTTC 60.815 60.000 17.12 0.00 36.40 2.87
3307 3473 0.179051 CAGCTGGGCTCTCATCTTCC 60.179 60.000 5.57 0.00 36.40 3.46
3308 3474 0.326427 AGCTGGGCTCTCATCTTCCT 60.326 55.000 0.00 0.00 30.62 3.36
3309 3475 0.106521 GCTGGGCTCTCATCTTCCTC 59.893 60.000 0.00 0.00 0.00 3.71
3313 3485 0.031994 GGCTCTCATCTTCCTCGCTC 59.968 60.000 0.00 0.00 0.00 5.03
3343 3515 3.827898 CCTCCCTGCTCGTCGTCC 61.828 72.222 0.00 0.00 0.00 4.79
3355 3527 1.154205 CGTCGTCCCATGGATTCAGC 61.154 60.000 15.22 0.00 32.73 4.26
3356 3528 0.179000 GTCGTCCCATGGATTCAGCT 59.821 55.000 15.22 0.00 32.73 4.24
3359 3531 1.407299 CGTCCCATGGATTCAGCTCAA 60.407 52.381 15.22 0.00 32.73 3.02
3372 3544 2.386660 GCTCAACAGCCGCTGACTC 61.387 63.158 27.12 7.17 40.14 3.36
3390 3566 2.109774 CTCACTCTGCTCCATTCCTCT 58.890 52.381 0.00 0.00 0.00 3.69
3393 3569 1.554160 ACTCTGCTCCATTCCTCTGTG 59.446 52.381 0.00 0.00 0.00 3.66
3412 3591 3.006756 GCTCAGGTGGTAGCAGCGA 62.007 63.158 17.58 15.81 38.63 4.93
3540 3722 1.797025 ACTACGCAAAGAGCAGAACC 58.203 50.000 0.00 0.00 46.13 3.62
3547 3729 3.883744 AAGAGCAGAACCCCGTGCG 62.884 63.158 0.00 0.00 44.78 5.34
3553 3735 4.382320 GAACCCCGTGCGGCAGTA 62.382 66.667 1.18 0.00 0.00 2.74
3562 3744 0.748005 GTGCGGCAGTACCATCCATT 60.748 55.000 1.18 0.00 39.03 3.16
3563 3745 0.747644 TGCGGCAGTACCATCCATTG 60.748 55.000 0.00 0.00 39.03 2.82
3564 3746 0.463654 GCGGCAGTACCATCCATTGA 60.464 55.000 0.00 0.00 39.03 2.57
3565 3747 1.815408 GCGGCAGTACCATCCATTGAT 60.815 52.381 0.00 0.00 39.03 2.57
3567 3749 2.508526 GGCAGTACCATCCATTGATCC 58.491 52.381 0.00 0.00 38.86 3.36
3568 3750 2.158623 GGCAGTACCATCCATTGATCCA 60.159 50.000 0.00 0.00 38.86 3.41
3569 3751 3.499202 GGCAGTACCATCCATTGATCCAT 60.499 47.826 0.00 0.00 38.86 3.41
3570 3752 3.504906 GCAGTACCATCCATTGATCCATG 59.495 47.826 0.00 0.00 0.00 3.66
3573 3755 3.957508 ACCATCCATTGATCCATGTGA 57.042 42.857 6.08 3.85 0.00 3.58
3575 3757 3.956199 ACCATCCATTGATCCATGTGAAC 59.044 43.478 6.08 0.00 0.00 3.18
3576 3758 4.212716 CCATCCATTGATCCATGTGAACT 58.787 43.478 6.08 0.00 0.00 3.01
3577 3759 4.037565 CCATCCATTGATCCATGTGAACTG 59.962 45.833 6.08 0.98 0.00 3.16
3578 3760 3.018856 TCCATTGATCCATGTGAACTGC 58.981 45.455 6.08 0.00 0.00 4.40
3579 3761 2.100252 CCATTGATCCATGTGAACTGCC 59.900 50.000 6.08 0.00 0.00 4.85
3580 3762 1.838112 TTGATCCATGTGAACTGCCC 58.162 50.000 0.00 0.00 0.00 5.36
3581 3763 0.034186 TGATCCATGTGAACTGCCCC 60.034 55.000 0.00 0.00 0.00 5.80
3582 3764 0.753111 GATCCATGTGAACTGCCCCC 60.753 60.000 0.00 0.00 0.00 5.40
3583 3765 1.508667 ATCCATGTGAACTGCCCCCA 61.509 55.000 0.00 0.00 0.00 4.96
3584 3766 1.000739 CCATGTGAACTGCCCCCAT 59.999 57.895 0.00 0.00 0.00 4.00
3585 3767 0.258484 CCATGTGAACTGCCCCCATA 59.742 55.000 0.00 0.00 0.00 2.74
3586 3768 1.133388 CCATGTGAACTGCCCCCATAT 60.133 52.381 0.00 0.00 0.00 1.78
3587 3769 2.669781 CATGTGAACTGCCCCCATATT 58.330 47.619 0.00 0.00 0.00 1.28
3588 3770 2.917713 TGTGAACTGCCCCCATATTT 57.082 45.000 0.00 0.00 0.00 1.40
3589 3771 2.733956 TGTGAACTGCCCCCATATTTC 58.266 47.619 0.00 0.00 0.00 2.17
3593 3775 3.525609 TGAACTGCCCCCATATTTCTGTA 59.474 43.478 0.00 0.00 0.00 2.74
3601 3783 5.755849 CCCCCATATTTCTGTAACTCTGTT 58.244 41.667 0.00 0.00 0.00 3.16
3611 3793 4.099419 TCTGTAACTCTGTTCTCACTTGCA 59.901 41.667 0.00 0.00 0.00 4.08
3617 3799 0.592637 TGTTCTCACTTGCATTGCCG 59.407 50.000 6.12 0.00 0.00 5.69
3621 3803 4.041917 CACTTGCATTGCCGCCGT 62.042 61.111 6.12 0.00 0.00 5.68
3622 3804 3.294493 ACTTGCATTGCCGCCGTT 61.294 55.556 6.12 0.00 0.00 4.44
3796 3981 0.179076 AGATGTCGATGATGGCGCAA 60.179 50.000 10.83 0.00 0.00 4.85
3841 4032 2.180017 CTGCCGTTTCAGCATGCC 59.820 61.111 15.66 0.00 40.04 4.40
4109 4336 3.864789 ATCTTCTGACAAACCACACCT 57.135 42.857 0.00 0.00 0.00 4.00
4125 4352 5.597182 ACCACACCTCTACATTCGTACATAT 59.403 40.000 0.00 0.00 0.00 1.78
4167 4394 2.159599 CGCTGTTTTCATCTTCTGCCTC 60.160 50.000 0.00 0.00 0.00 4.70
4184 4411 2.287915 GCCTCCAATACAGCAACATACG 59.712 50.000 0.00 0.00 0.00 3.06
4185 4412 3.531538 CCTCCAATACAGCAACATACGT 58.468 45.455 0.00 0.00 0.00 3.57
4186 4413 4.689071 CCTCCAATACAGCAACATACGTA 58.311 43.478 0.00 0.00 0.00 3.57
4187 4414 4.745125 CCTCCAATACAGCAACATACGTAG 59.255 45.833 0.08 0.00 0.00 3.51
4230 4457 1.557832 CCCGACCTCTATCCCAACAAA 59.442 52.381 0.00 0.00 0.00 2.83
4235 4462 4.760204 CGACCTCTATCCCAACAAAAAGTT 59.240 41.667 0.00 0.00 42.42 2.66
4269 4496 1.067821 GGATGCACACAACCCGAAAAA 59.932 47.619 0.00 0.00 32.67 1.94
4326 4557 3.862267 GTGATCAACTCCTCTCAACATCG 59.138 47.826 0.00 0.00 0.00 3.84
4395 4630 0.868406 AAAAGCGACGCCTTCAAGAG 59.132 50.000 17.79 0.00 0.00 2.85
4414 4649 0.657840 GAGAAACAGTGCACAAGCGT 59.342 50.000 21.04 7.51 46.23 5.07
4518 4753 1.341285 CCAGGCACATCCAATGAAGGA 60.341 52.381 0.00 0.00 43.01 3.36
4549 4785 3.963129 AGTTTTCACCCTGAAAGTCACA 58.037 40.909 0.00 0.00 45.77 3.58
4585 4822 6.117975 AGGAGCATCACCAAAAATGAAATT 57.882 33.333 0.00 0.00 34.92 1.82
4660 4899 0.760567 TGGCTGACTCCATCGCCTAT 60.761 55.000 0.00 0.00 43.37 2.57
4753 4992 2.315925 AATCGAGATGCCGACATGTT 57.684 45.000 0.00 0.00 41.70 2.71
4771 5010 1.070175 GTTCCATGGTGTCGACAAACG 60.070 52.381 21.95 9.09 44.09 3.60
4895 5134 0.176219 AGTTCCGGAACACGTCAACA 59.824 50.000 40.66 5.52 43.47 3.33
4897 5136 0.176219 TTCCGGAACACGTCAACAGT 59.824 50.000 14.35 0.00 42.24 3.55
4906 5145 3.191669 ACACGTCAACAGTCAAATCGAA 58.808 40.909 0.00 0.00 0.00 3.71
4912 5151 4.932200 GTCAACAGTCAAATCGAAGAGGAT 59.068 41.667 0.00 0.00 43.63 3.24
4926 5165 4.637977 CGAAGAGGATCGATCATGGAGATA 59.362 45.833 25.93 0.00 45.48 1.98
4928 5167 6.349694 CGAAGAGGATCGATCATGGAGATAAA 60.350 42.308 25.93 0.00 45.48 1.40
4967 5206 2.107041 TACAAGGACCGCCACCACAG 62.107 60.000 0.00 0.00 36.29 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 8.514136 TTACAATCGTTCATTCCAAAATTCAC 57.486 30.769 0.00 0.00 0.00 3.18
146 147 5.419788 TCTGGTGATCATCCATTCTTTTTGG 59.580 40.000 14.78 3.89 34.26 3.28
173 174 4.155644 AGCCTTAGTATACCGATAACTCGC 59.844 45.833 0.00 0.00 43.66 5.03
219 220 0.818040 ACACAAAAGACCCGGTGCTC 60.818 55.000 0.00 0.00 34.69 4.26
335 336 7.171508 TCACTTCTAATCTGATTGACAACACAC 59.828 37.037 13.01 0.00 0.00 3.82
590 598 8.488651 TCTCTGGTTATCTTCGGTTTTATTTC 57.511 34.615 0.00 0.00 0.00 2.17
592 600 8.727910 GTTTCTCTGGTTATCTTCGGTTTTATT 58.272 33.333 0.00 0.00 0.00 1.40
593 601 7.881232 TGTTTCTCTGGTTATCTTCGGTTTTAT 59.119 33.333 0.00 0.00 0.00 1.40
594 602 7.172019 GTGTTTCTCTGGTTATCTTCGGTTTTA 59.828 37.037 0.00 0.00 0.00 1.52
599 607 3.612860 CGTGTTTCTCTGGTTATCTTCGG 59.387 47.826 0.00 0.00 0.00 4.30
600 608 4.482386 TCGTGTTTCTCTGGTTATCTTCG 58.518 43.478 0.00 0.00 0.00 3.79
601 609 6.157211 TCTTCGTGTTTCTCTGGTTATCTTC 58.843 40.000 0.00 0.00 0.00 2.87
602 610 6.097915 TCTTCGTGTTTCTCTGGTTATCTT 57.902 37.500 0.00 0.00 0.00 2.40
618 627 2.373540 TTCCACCGGTTATCTTCGTG 57.626 50.000 2.97 0.00 0.00 4.35
619 628 2.037511 TGTTTCCACCGGTTATCTTCGT 59.962 45.455 2.97 0.00 0.00 3.85
674 684 0.911769 AGTAATGTAGCTGCAGGGCA 59.088 50.000 17.12 0.00 36.92 5.36
703 713 1.327690 CCCTTGGCGTGGCTCTACTA 61.328 60.000 0.00 0.00 0.00 1.82
718 728 0.187361 AGCTATCTCTCGCTCCCCTT 59.813 55.000 0.00 0.00 0.00 3.95
724 734 1.255882 CATGGGAGCTATCTCTCGCT 58.744 55.000 8.82 0.00 42.87 4.93
726 736 2.228582 CTCACATGGGAGCTATCTCTCG 59.771 54.545 13.06 0.00 42.87 4.04
728 738 3.609256 TCTCACATGGGAGCTATCTCT 57.391 47.619 20.74 0.00 39.31 3.10
732 742 3.900601 CCTACTTCTCACATGGGAGCTAT 59.099 47.826 20.74 9.73 34.84 2.97
733 743 3.300388 CCTACTTCTCACATGGGAGCTA 58.700 50.000 20.74 9.57 34.84 3.32
734 744 2.114616 CCTACTTCTCACATGGGAGCT 58.885 52.381 20.74 7.42 34.84 4.09
735 745 1.474143 GCCTACTTCTCACATGGGAGC 60.474 57.143 20.74 3.52 34.84 4.70
736 746 1.139853 GGCCTACTTCTCACATGGGAG 59.860 57.143 19.51 19.51 36.21 4.30
737 747 1.204146 GGCCTACTTCTCACATGGGA 58.796 55.000 0.00 0.00 0.00 4.37
738 748 0.181350 GGGCCTACTTCTCACATGGG 59.819 60.000 0.84 0.00 0.00 4.00
739 749 0.911769 TGGGCCTACTTCTCACATGG 59.088 55.000 4.53 0.00 0.00 3.66
740 750 2.787473 TTGGGCCTACTTCTCACATG 57.213 50.000 4.53 0.00 0.00 3.21
741 751 5.450818 TTATTTGGGCCTACTTCTCACAT 57.549 39.130 4.53 0.00 0.00 3.21
742 752 4.919774 TTATTTGGGCCTACTTCTCACA 57.080 40.909 4.53 0.00 0.00 3.58
743 753 6.655425 GGATATTATTTGGGCCTACTTCTCAC 59.345 42.308 4.53 0.00 0.00 3.51
744 754 6.331572 TGGATATTATTTGGGCCTACTTCTCA 59.668 38.462 4.53 0.00 0.00 3.27
745 755 6.655425 GTGGATATTATTTGGGCCTACTTCTC 59.345 42.308 4.53 0.00 0.00 2.87
746 756 6.467339 GGTGGATATTATTTGGGCCTACTTCT 60.467 42.308 4.53 0.00 0.00 2.85
747 757 5.710567 GGTGGATATTATTTGGGCCTACTTC 59.289 44.000 4.53 0.00 0.00 3.01
748 758 5.459094 GGGTGGATATTATTTGGGCCTACTT 60.459 44.000 4.53 0.00 0.00 2.24
749 759 4.044191 GGGTGGATATTATTTGGGCCTACT 59.956 45.833 4.53 0.00 0.00 2.57
750 760 4.341487 GGGTGGATATTATTTGGGCCTAC 58.659 47.826 4.53 0.00 0.00 3.18
751 761 3.009695 CGGGTGGATATTATTTGGGCCTA 59.990 47.826 4.53 0.00 0.00 3.93
752 762 2.225017 CGGGTGGATATTATTTGGGCCT 60.225 50.000 4.53 0.00 0.00 5.19
753 763 2.167662 CGGGTGGATATTATTTGGGCC 58.832 52.381 0.00 0.00 0.00 5.80
754 764 1.544246 GCGGGTGGATATTATTTGGGC 59.456 52.381 0.00 0.00 0.00 5.36
755 765 2.556622 GTGCGGGTGGATATTATTTGGG 59.443 50.000 0.00 0.00 0.00 4.12
756 766 3.004315 GTGTGCGGGTGGATATTATTTGG 59.996 47.826 0.00 0.00 0.00 3.28
757 767 3.629855 TGTGTGCGGGTGGATATTATTTG 59.370 43.478 0.00 0.00 0.00 2.32
758 768 3.882888 CTGTGTGCGGGTGGATATTATTT 59.117 43.478 0.00 0.00 0.00 1.40
759 769 3.135712 TCTGTGTGCGGGTGGATATTATT 59.864 43.478 0.00 0.00 0.00 1.40
760 770 2.703536 TCTGTGTGCGGGTGGATATTAT 59.296 45.455 0.00 0.00 0.00 1.28
761 771 2.112190 TCTGTGTGCGGGTGGATATTA 58.888 47.619 0.00 0.00 0.00 0.98
762 772 0.908910 TCTGTGTGCGGGTGGATATT 59.091 50.000 0.00 0.00 0.00 1.28
763 773 0.908910 TTCTGTGTGCGGGTGGATAT 59.091 50.000 0.00 0.00 0.00 1.63
764 774 0.036765 GTTCTGTGTGCGGGTGGATA 60.037 55.000 0.00 0.00 0.00 2.59
765 775 1.302511 GTTCTGTGTGCGGGTGGAT 60.303 57.895 0.00 0.00 0.00 3.41
766 776 2.110213 GTTCTGTGTGCGGGTGGA 59.890 61.111 0.00 0.00 0.00 4.02
767 777 2.111043 AGTTCTGTGTGCGGGTGG 59.889 61.111 0.00 0.00 0.00 4.61
768 778 2.896801 GCAGTTCTGTGTGCGGGTG 61.897 63.158 1.78 0.00 0.00 4.61
769 779 2.591715 GCAGTTCTGTGTGCGGGT 60.592 61.111 1.78 0.00 0.00 5.28
770 780 2.281070 AGCAGTTCTGTGTGCGGG 60.281 61.111 1.78 0.00 44.78 6.13
771 781 2.610694 CCAGCAGTTCTGTGTGCGG 61.611 63.158 1.78 0.00 44.78 5.69
772 782 2.610694 CCCAGCAGTTCTGTGTGCG 61.611 63.158 1.78 0.00 44.78 5.34
773 783 2.263741 CCCCAGCAGTTCTGTGTGC 61.264 63.158 1.78 0.00 41.25 4.57
774 784 1.149174 ACCCCAGCAGTTCTGTGTG 59.851 57.895 1.78 0.62 41.25 3.82
775 785 1.149174 CACCCCAGCAGTTCTGTGT 59.851 57.895 1.78 0.00 41.25 3.72
776 786 1.601759 CCACCCCAGCAGTTCTGTG 60.602 63.158 1.78 0.00 41.25 3.66
777 787 2.833913 CCCACCCCAGCAGTTCTGT 61.834 63.158 1.78 0.00 41.25 3.41
778 788 2.034687 CCCACCCCAGCAGTTCTG 59.965 66.667 0.00 0.00 42.49 3.02
779 789 3.971702 GCCCACCCCAGCAGTTCT 61.972 66.667 0.00 0.00 0.00 3.01
806 816 6.183360 TGGACGGATTTTAATTCATTCTCGTG 60.183 38.462 0.00 0.00 0.00 4.35
878 888 3.573772 CTGGCTTGGTCGTGCTCGA 62.574 63.158 6.80 6.80 44.12 4.04
907 917 2.440817 AATGTCCGATCCCCCGTCC 61.441 63.158 0.00 0.00 0.00 4.79
908 918 1.227556 CAATGTCCGATCCCCCGTC 60.228 63.158 0.00 0.00 0.00 4.79
909 919 2.742116 CCAATGTCCGATCCCCCGT 61.742 63.158 0.00 0.00 0.00 5.28
910 920 2.111043 CCAATGTCCGATCCCCCG 59.889 66.667 0.00 0.00 0.00 5.73
911 921 1.148498 GTCCAATGTCCGATCCCCC 59.852 63.158 0.00 0.00 0.00 5.40
912 922 0.179045 CTGTCCAATGTCCGATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
913 923 0.830648 TCTGTCCAATGTCCGATCCC 59.169 55.000 0.00 0.00 0.00 3.85
925 935 2.604686 AGCCGGCTTCTCTGTCCA 60.605 61.111 27.08 0.00 0.00 4.02
1188 1198 2.039418 TCGAGAGGAGAGAGAGGAGAG 58.961 57.143 0.00 0.00 0.00 3.20
1189 1199 2.168458 TCGAGAGGAGAGAGAGGAGA 57.832 55.000 0.00 0.00 0.00 3.71
1190 1200 2.610479 CGATCGAGAGGAGAGAGAGGAG 60.610 59.091 10.26 0.00 0.00 3.69
1191 1201 1.343142 CGATCGAGAGGAGAGAGAGGA 59.657 57.143 10.26 0.00 0.00 3.71
1192 1202 1.070134 ACGATCGAGAGGAGAGAGAGG 59.930 57.143 24.34 0.00 0.00 3.69
1193 1203 2.404215 GACGATCGAGAGGAGAGAGAG 58.596 57.143 24.34 0.00 0.00 3.20
1194 1204 1.069513 GGACGATCGAGAGGAGAGAGA 59.930 57.143 24.34 0.00 0.00 3.10
1195 1205 1.508632 GGACGATCGAGAGGAGAGAG 58.491 60.000 24.34 0.00 0.00 3.20
1196 1206 0.107081 GGGACGATCGAGAGGAGAGA 59.893 60.000 24.34 0.00 0.00 3.10
1197 1207 0.887387 GGGGACGATCGAGAGGAGAG 60.887 65.000 24.34 0.00 0.00 3.20
1221 1231 0.179166 GAACATACGTGTCGCGGGTA 60.179 55.000 6.13 4.45 46.52 3.69
1231 1241 2.029290 GGTGACTGGTCAGAACATACGT 60.029 50.000 3.47 0.00 40.75 3.57
1271 1294 2.959071 GATCTCTGCAGCGACGGC 60.959 66.667 8.90 0.00 40.37 5.68
1272 1295 2.653448 CGATCTCTGCAGCGACGG 60.653 66.667 8.90 0.00 0.00 4.79
1274 1297 0.865218 CTGACGATCTCTGCAGCGAC 60.865 60.000 8.90 7.69 0.00 5.19
1278 1301 2.229589 GCGCTGACGATCTCTGCAG 61.230 63.158 7.63 7.63 42.57 4.41
1411 1438 0.460109 TCCATCAATGCGAGTGTCCG 60.460 55.000 0.00 0.00 0.00 4.79
1844 1871 1.884579 AGTCAGTAACACGACGATGGT 59.115 47.619 0.00 0.00 37.23 3.55
1845 1872 2.251040 CAGTCAGTAACACGACGATGG 58.749 52.381 0.00 0.00 37.23 3.51
1907 1935 3.350833 CTCCTTCAGGCTGCAGTAAAAT 58.649 45.455 16.64 0.00 34.44 1.82
1908 1936 2.783135 CTCCTTCAGGCTGCAGTAAAA 58.217 47.619 16.64 4.34 34.44 1.52
2060 2093 5.046304 TCAACGATGGAGGAGAAGAGAAAAT 60.046 40.000 0.00 0.00 0.00 1.82
2193 2243 3.849911 CAGAAGAAACGCTGGTCTCATA 58.150 45.455 0.00 0.00 0.00 2.15
2194 2244 2.693069 CAGAAGAAACGCTGGTCTCAT 58.307 47.619 0.00 0.00 0.00 2.90
2195 2245 1.873903 GCAGAAGAAACGCTGGTCTCA 60.874 52.381 0.00 0.00 32.83 3.27
2202 2252 2.029918 GGGAAAATGCAGAAGAAACGCT 60.030 45.455 0.00 0.00 0.00 5.07
2241 2291 3.058450 CAAGCACCATCAATTCGCAAAA 58.942 40.909 0.00 0.00 0.00 2.44
2242 2292 2.609984 CCAAGCACCATCAATTCGCAAA 60.610 45.455 0.00 0.00 0.00 3.68
2244 2294 0.527113 CCAAGCACCATCAATTCGCA 59.473 50.000 0.00 0.00 0.00 5.10
2245 2295 0.810648 TCCAAGCACCATCAATTCGC 59.189 50.000 0.00 0.00 0.00 4.70
2246 2296 3.441163 CATTCCAAGCACCATCAATTCG 58.559 45.455 0.00 0.00 0.00 3.34
2249 2299 2.463752 AGCATTCCAAGCACCATCAAT 58.536 42.857 0.00 0.00 0.00 2.57
2251 2301 2.646930 CTAGCATTCCAAGCACCATCA 58.353 47.619 0.00 0.00 0.00 3.07
2252 2302 1.952296 CCTAGCATTCCAAGCACCATC 59.048 52.381 0.00 0.00 0.00 3.51
2254 2304 0.680921 GCCTAGCATTCCAAGCACCA 60.681 55.000 0.00 0.00 0.00 4.17
2255 2305 1.718757 CGCCTAGCATTCCAAGCACC 61.719 60.000 0.00 0.00 0.00 5.01
2256 2306 0.744414 TCGCCTAGCATTCCAAGCAC 60.744 55.000 0.00 0.00 0.00 4.40
2257 2307 0.035534 TTCGCCTAGCATTCCAAGCA 60.036 50.000 0.00 0.00 0.00 3.91
2258 2308 0.659957 CTTCGCCTAGCATTCCAAGC 59.340 55.000 0.00 0.00 0.00 4.01
2424 2488 7.876936 AATCATCTCAGCATCAAAACATACT 57.123 32.000 0.00 0.00 0.00 2.12
2428 2492 9.932207 AAATAAAATCATCTCAGCATCAAAACA 57.068 25.926 0.00 0.00 0.00 2.83
2434 2508 7.866393 CAGGGAAAATAAAATCATCTCAGCATC 59.134 37.037 0.00 0.00 0.00 3.91
2440 2514 9.710900 AAAACACAGGGAAAATAAAATCATCTC 57.289 29.630 0.00 0.00 0.00 2.75
2442 2516 9.271828 ACAAAACACAGGGAAAATAAAATCATC 57.728 29.630 0.00 0.00 0.00 2.92
2462 2536 2.857748 CGGTGGCTGAAGAAAACAAAAC 59.142 45.455 0.00 0.00 0.00 2.43
2463 2537 2.159170 CCGGTGGCTGAAGAAAACAAAA 60.159 45.455 0.00 0.00 0.00 2.44
2464 2538 1.407258 CCGGTGGCTGAAGAAAACAAA 59.593 47.619 0.00 0.00 0.00 2.83
2465 2539 1.028905 CCGGTGGCTGAAGAAAACAA 58.971 50.000 0.00 0.00 0.00 2.83
2466 2540 1.452145 GCCGGTGGCTGAAGAAAACA 61.452 55.000 1.90 0.00 46.69 2.83
2507 2581 3.295973 GGGAGCTTCTCTGATGTACTCT 58.704 50.000 0.00 0.00 0.00 3.24
2624 2702 5.486526 GGAACTTCTCTGATGACTCACAAT 58.513 41.667 0.00 0.00 0.00 2.71
2635 2713 0.251832 AGCTCCGGGAACTTCTCTGA 60.252 55.000 0.00 0.00 0.00 3.27
2644 2722 5.601313 ACTACTGAAATAATAGCTCCGGGAA 59.399 40.000 0.00 0.00 0.00 3.97
2646 2724 5.244178 AGACTACTGAAATAATAGCTCCGGG 59.756 44.000 0.00 0.00 0.00 5.73
2649 2727 9.825109 AGAAAAGACTACTGAAATAATAGCTCC 57.175 33.333 0.00 0.00 0.00 4.70
2664 2742 8.707839 CACTTTTGAGATCAGAGAAAAGACTAC 58.292 37.037 18.00 0.00 37.52 2.73
2668 2746 5.471456 GGCACTTTTGAGATCAGAGAAAAGA 59.529 40.000 18.00 0.00 37.52 2.52
2669 2747 5.472820 AGGCACTTTTGAGATCAGAGAAAAG 59.527 40.000 12.98 12.98 39.99 2.27
2740 2821 4.846779 ATGTAACTGGCATTTTGTTCGT 57.153 36.364 0.00 0.00 0.00 3.85
2742 2823 5.116983 CGACAATGTAACTGGCATTTTGTTC 59.883 40.000 0.00 0.00 34.68 3.18
2757 2868 7.278203 TGTTAGTCAAGTTCAAACGACAATGTA 59.722 33.333 0.00 0.00 0.00 2.29
2782 2893 5.885230 TGAACTTGAATGTTAGCAGGATG 57.115 39.130 0.00 0.00 40.87 3.51
2785 2896 6.183360 CCAGTATGAACTTGAATGTTAGCAGG 60.183 42.308 0.00 0.00 39.69 4.85
2787 2898 5.123820 GCCAGTATGAACTTGAATGTTAGCA 59.876 40.000 0.00 0.00 39.69 3.49
2788 2899 5.449177 GGCCAGTATGAACTTGAATGTTAGC 60.449 44.000 0.00 0.00 39.69 3.09
2790 2901 4.634004 CGGCCAGTATGAACTTGAATGTTA 59.366 41.667 2.24 0.00 39.69 2.41
2792 2903 3.009723 CGGCCAGTATGAACTTGAATGT 58.990 45.455 2.24 0.00 39.69 2.71
2793 2904 2.223340 GCGGCCAGTATGAACTTGAATG 60.223 50.000 2.24 0.00 39.69 2.67
2797 2908 0.739462 TCGCGGCCAGTATGAACTTG 60.739 55.000 6.13 0.00 39.69 3.16
2798 2909 0.036765 TTCGCGGCCAGTATGAACTT 60.037 50.000 6.13 0.00 39.69 2.66
2800 2911 1.003866 GAATTCGCGGCCAGTATGAAC 60.004 52.381 6.13 0.00 39.69 3.18
2801 2912 1.295792 GAATTCGCGGCCAGTATGAA 58.704 50.000 6.13 0.00 39.69 2.57
2802 2913 0.874175 CGAATTCGCGGCCAGTATGA 60.874 55.000 15.93 0.00 39.69 2.15
2803 2914 1.151777 ACGAATTCGCGGCCAGTATG 61.152 55.000 27.03 0.00 44.43 2.39
2811 2939 1.736645 AGGACACACGAATTCGCGG 60.737 57.895 27.03 20.92 44.43 6.46
2821 2949 7.226720 TCAGTAAAAGAAAAGATCAGGACACAC 59.773 37.037 0.00 0.00 0.00 3.82
2898 3031 3.132925 CAATTTGGTTCCAAAGCCAGTG 58.867 45.455 19.48 10.16 38.98 3.66
2912 3045 4.141287 TGCCGATATTCCTACCAATTTGG 58.859 43.478 14.02 14.02 45.02 3.28
2921 3054 2.009681 TCCAGCTGCCGATATTCCTA 57.990 50.000 8.66 0.00 0.00 2.94
2935 3068 0.105778 GGTCTGCAGTAGGATCCAGC 59.894 60.000 15.82 12.61 0.00 4.85
2999 3132 1.140312 TCCTCCACTGCAGGTTCTTT 58.860 50.000 19.93 0.00 32.20 2.52
3044 3177 2.667418 CTCAGGTGCAGAGTGGGG 59.333 66.667 0.00 0.00 0.00 4.96
3076 3209 0.889186 CAGTGGTGGTGGTAGGTTGC 60.889 60.000 0.00 0.00 0.00 4.17
3096 3229 5.291128 CAGCTTACCAGTAAATCGAAATCGT 59.709 40.000 2.41 0.00 40.80 3.73
3125 3258 4.576053 GGCTGTATAATGCAATGACAGACA 59.424 41.667 18.06 4.91 44.16 3.41
3134 3267 4.169059 ACATCAGGGCTGTATAATGCAA 57.831 40.909 0.00 0.00 0.00 4.08
3142 3275 1.912731 TGGCTAAACATCAGGGCTGTA 59.087 47.619 0.00 0.00 0.00 2.74
3144 3277 1.474077 GTTGGCTAAACATCAGGGCTG 59.526 52.381 0.00 0.00 38.75 4.85
3161 3294 1.464608 CACACCGGCAGATAACAGTTG 59.535 52.381 0.00 0.00 0.00 3.16
3167 3300 0.394938 ACACACACACCGGCAGATAA 59.605 50.000 0.00 0.00 0.00 1.75
3226 3392 1.803519 GTGCGTTGCTCTCCTCGAG 60.804 63.158 5.13 5.13 42.88 4.04
3264 3430 1.202348 GGAACATGCTTGTTACCTGGC 59.798 52.381 17.09 4.79 46.01 4.85
3300 3466 1.472376 GGAAGTGGAGCGAGGAAGATG 60.472 57.143 0.00 0.00 0.00 2.90
3302 3468 1.258445 GGGAAGTGGAGCGAGGAAGA 61.258 60.000 0.00 0.00 0.00 2.87
3303 3469 1.219393 GGGAAGTGGAGCGAGGAAG 59.781 63.158 0.00 0.00 0.00 3.46
3305 3471 1.984570 CTGGGAAGTGGAGCGAGGA 60.985 63.158 0.00 0.00 0.00 3.71
3306 3472 2.581354 CTGGGAAGTGGAGCGAGG 59.419 66.667 0.00 0.00 0.00 4.63
3307 3473 2.125350 GCTGGGAAGTGGAGCGAG 60.125 66.667 0.00 0.00 0.00 5.03
3308 3474 2.604686 AGCTGGGAAGTGGAGCGA 60.605 61.111 0.00 0.00 37.81 4.93
3309 3475 2.125350 GAGCTGGGAAGTGGAGCG 60.125 66.667 0.00 0.00 37.81 5.03
3313 3485 2.674220 GGGAGGAGCTGGGAAGTGG 61.674 68.421 0.00 0.00 0.00 4.00
3343 3515 1.404391 GCTGTTGAGCTGAATCCATGG 59.596 52.381 4.97 4.97 42.52 3.66
3355 3527 1.005748 TGAGTCAGCGGCTGTTGAG 60.006 57.895 27.63 3.83 35.89 3.02
3356 3528 1.300931 GTGAGTCAGCGGCTGTTGA 60.301 57.895 27.63 8.15 32.44 3.18
3359 3531 1.905843 AGAGTGAGTCAGCGGCTGT 60.906 57.895 27.63 11.36 32.61 4.40
3365 3537 0.536260 ATGGAGCAGAGTGAGTCAGC 59.464 55.000 0.00 0.00 37.96 4.26
3372 3544 1.554160 ACAGAGGAATGGAGCAGAGTG 59.446 52.381 0.00 0.00 0.00 3.51
3390 3566 1.830587 CTGCTACCACCTGAGCCACA 61.831 60.000 0.00 0.00 37.94 4.17
3393 3569 2.124942 GCTGCTACCACCTGAGCC 60.125 66.667 0.00 0.00 37.94 4.70
3431 3613 1.667724 GAAGATCCAGCCATGTCAACG 59.332 52.381 0.00 0.00 0.00 4.10
3540 3722 4.467084 ATGGTACTGCCGCACGGG 62.467 66.667 11.65 0.00 41.21 5.28
3547 3729 2.158623 TGGATCAATGGATGGTACTGCC 60.159 50.000 0.00 0.00 32.67 4.85
3551 3733 4.717877 TCACATGGATCAATGGATGGTAC 58.282 43.478 14.72 0.00 32.67 3.34
3553 3735 3.956199 GTTCACATGGATCAATGGATGGT 59.044 43.478 14.72 0.00 32.67 3.55
3562 3744 0.034186 GGGGCAGTTCACATGGATCA 60.034 55.000 0.00 0.00 0.00 2.92
3563 3745 0.753111 GGGGGCAGTTCACATGGATC 60.753 60.000 0.00 0.00 0.00 3.36
3564 3746 1.307647 GGGGGCAGTTCACATGGAT 59.692 57.895 0.00 0.00 0.00 3.41
3565 3747 1.508667 ATGGGGGCAGTTCACATGGA 61.509 55.000 0.00 0.00 0.00 3.41
3567 3749 2.369983 ATATGGGGGCAGTTCACATG 57.630 50.000 0.00 0.00 0.00 3.21
3568 3750 3.052642 AGAAATATGGGGGCAGTTCACAT 60.053 43.478 0.00 0.00 0.00 3.21
3569 3751 2.311542 AGAAATATGGGGGCAGTTCACA 59.688 45.455 0.00 0.00 0.00 3.58
3570 3752 2.689983 CAGAAATATGGGGGCAGTTCAC 59.310 50.000 0.00 0.00 0.00 3.18
3573 3755 4.017499 AGTTACAGAAATATGGGGGCAGTT 60.017 41.667 0.00 0.00 0.00 3.16
3575 3757 4.137543 GAGTTACAGAAATATGGGGGCAG 58.862 47.826 0.00 0.00 0.00 4.85
3576 3758 3.785887 AGAGTTACAGAAATATGGGGGCA 59.214 43.478 0.00 0.00 0.00 5.36
3577 3759 4.137543 CAGAGTTACAGAAATATGGGGGC 58.862 47.826 0.00 0.00 0.00 5.80
3578 3760 5.373812 ACAGAGTTACAGAAATATGGGGG 57.626 43.478 0.00 0.00 0.00 5.40
3579 3761 6.653989 AGAACAGAGTTACAGAAATATGGGG 58.346 40.000 0.00 0.00 0.00 4.96
3580 3762 7.278868 GTGAGAACAGAGTTACAGAAATATGGG 59.721 40.741 0.00 0.00 0.00 4.00
3581 3763 8.037758 AGTGAGAACAGAGTTACAGAAATATGG 58.962 37.037 0.00 0.00 0.00 2.74
3582 3764 8.994429 AGTGAGAACAGAGTTACAGAAATATG 57.006 34.615 0.00 0.00 0.00 1.78
3583 3765 9.429359 CAAGTGAGAACAGAGTTACAGAAATAT 57.571 33.333 0.00 0.00 0.00 1.28
3584 3766 7.385205 GCAAGTGAGAACAGAGTTACAGAAATA 59.615 37.037 0.00 0.00 0.00 1.40
3585 3767 6.203723 GCAAGTGAGAACAGAGTTACAGAAAT 59.796 38.462 0.00 0.00 0.00 2.17
3586 3768 5.523916 GCAAGTGAGAACAGAGTTACAGAAA 59.476 40.000 0.00 0.00 0.00 2.52
3587 3769 5.050490 GCAAGTGAGAACAGAGTTACAGAA 58.950 41.667 0.00 0.00 0.00 3.02
3588 3770 4.099419 TGCAAGTGAGAACAGAGTTACAGA 59.901 41.667 0.00 0.00 0.00 3.41
3589 3771 4.371786 TGCAAGTGAGAACAGAGTTACAG 58.628 43.478 0.00 0.00 0.00 2.74
3593 3775 3.004106 GCAATGCAAGTGAGAACAGAGTT 59.996 43.478 0.00 0.00 30.28 3.01
3601 3783 2.334946 GGCGGCAATGCAAGTGAGA 61.335 57.895 7.79 0.00 30.28 3.27
3611 3793 1.876497 AAAGCATCAACGGCGGCAAT 61.876 50.000 13.24 0.00 36.08 3.56
3617 3799 0.039256 TGCAAGAAAGCATCAACGGC 60.039 50.000 0.00 0.00 40.11 5.68
3621 3803 0.604578 GGCCTGCAAGAAAGCATCAA 59.395 50.000 0.00 0.00 44.68 2.57
3622 3804 1.588824 CGGCCTGCAAGAAAGCATCA 61.589 55.000 0.00 0.00 44.68 3.07
3671 3853 4.764336 CGCCGCGTCCTCGTACAA 62.764 66.667 4.92 0.00 39.49 2.41
3796 3981 1.531423 CAAACATCTCCTGCTGCTGT 58.469 50.000 0.00 0.00 0.00 4.40
4125 4352 3.865164 CGCTGCTGATGTAGTGATGTTTA 59.135 43.478 0.00 0.00 38.42 2.01
4167 4394 6.037726 TGTACTACGTATGTTGCTGTATTGG 58.962 40.000 0.00 0.00 0.00 3.16
4198 4425 1.352017 GAGGTCGGGTCCCCTTAAAAA 59.648 52.381 1.00 0.00 0.00 1.94
4199 4426 0.986527 GAGGTCGGGTCCCCTTAAAA 59.013 55.000 1.00 0.00 0.00 1.52
4200 4427 0.117742 AGAGGTCGGGTCCCCTTAAA 59.882 55.000 1.00 0.00 0.00 1.52
4201 4428 1.009997 TAGAGGTCGGGTCCCCTTAA 58.990 55.000 1.00 0.00 0.00 1.85
4202 4429 1.146566 GATAGAGGTCGGGTCCCCTTA 59.853 57.143 1.00 0.00 0.00 2.69
4203 4430 0.105607 GATAGAGGTCGGGTCCCCTT 60.106 60.000 1.00 0.00 0.00 3.95
4204 4431 1.542679 GATAGAGGTCGGGTCCCCT 59.457 63.158 1.00 0.00 0.00 4.79
4205 4432 1.533513 GGATAGAGGTCGGGTCCCC 60.534 68.421 1.00 0.00 0.00 4.81
4206 4433 1.533513 GGGATAGAGGTCGGGTCCC 60.534 68.421 0.00 0.00 41.55 4.46
4207 4434 0.398098 TTGGGATAGAGGTCGGGTCC 60.398 60.000 0.00 0.00 0.00 4.46
4208 4435 0.751452 GTTGGGATAGAGGTCGGGTC 59.249 60.000 0.00 0.00 0.00 4.46
4220 4447 7.176589 TGTCTTTGTAACTTTTTGTTGGGAT 57.823 32.000 0.00 0.00 39.55 3.85
4221 4448 6.591750 TGTCTTTGTAACTTTTTGTTGGGA 57.408 33.333 0.00 0.00 39.55 4.37
4222 4449 7.841915 AATGTCTTTGTAACTTTTTGTTGGG 57.158 32.000 0.00 0.00 39.55 4.12
4230 4457 8.082242 GTGCATCCTAAATGTCTTTGTAACTTT 58.918 33.333 0.00 0.00 0.00 2.66
4235 4462 6.000840 TGTGTGCATCCTAAATGTCTTTGTA 58.999 36.000 0.00 0.00 0.00 2.41
4296 4527 0.169009 GGAGTTGATCACTTTGGCGC 59.831 55.000 0.00 0.00 35.01 6.53
4326 4557 0.749649 TTTGATGGTGGTTGTGTGCC 59.250 50.000 0.00 0.00 0.00 5.01
4395 4630 0.657840 ACGCTTGTGCACTGTTTCTC 59.342 50.000 19.41 0.00 39.64 2.87
4492 4727 5.122707 TCATTGGATGTGCCTGGTAATTA 57.877 39.130 0.00 0.00 37.63 1.40
4497 4732 1.617804 CCTTCATTGGATGTGCCTGGT 60.618 52.381 0.00 0.00 37.63 4.00
4518 4753 4.165372 TCAGGGTGAAAACTTAAGGTCTGT 59.835 41.667 7.53 0.00 0.00 3.41
4528 4763 3.963129 TGTGACTTTCAGGGTGAAAACT 58.037 40.909 3.82 0.00 44.69 2.66
4569 4805 6.514947 CACAGGAGAATTTCATTTTTGGTGA 58.485 36.000 0.00 0.00 0.00 4.02
4585 4822 4.025858 GGGCAGCAGCACAGGAGA 62.026 66.667 2.65 0.00 45.91 3.71
4669 4908 1.343069 GGAGGATCAGTAAGGCGGAT 58.657 55.000 0.00 0.00 36.25 4.18
4753 4992 0.389757 TCGTTTGTCGACACCATGGA 59.610 50.000 19.90 8.70 44.01 3.41
4843 5082 2.439507 TCTTGCCCAAGGATATCTGGAC 59.560 50.000 11.66 2.05 38.88 4.02
4906 5145 6.629963 GCATTTATCTCCATGATCGATCCTCT 60.630 42.308 22.31 4.76 36.65 3.69
4912 5151 3.006859 ACGGCATTTATCTCCATGATCGA 59.993 43.478 0.00 0.00 36.65 3.59
4921 5160 2.135139 TCGCATCACGGCATTTATCTC 58.865 47.619 0.00 0.00 43.89 2.75


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

AutoCloner maintained by Alex Coulton.