Multiple sequence alignment - TraesCS1D01G379500

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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 TraesCS1D01G379500 chr1D 100.000 4081 0 0 1 4081 455747313 455751393 0.000000e+00 7537.0
1 TraesCS1D01G379500 chr1D 88.073 109 13 0 3886 3994 455765638 455765746 3.310000e-26 130.0
2 TraesCS1D01G379500 chr1B 95.030 3119 123 16 978 4079 626084135 626087238 0.000000e+00 4872.0
3 TraesCS1D01G379500 chr1B 87.663 843 45 19 3 833 626083183 626083978 0.000000e+00 926.0
4 TraesCS1D01G379500 chr1B 90.647 139 10 3 849 986 626084049 626084185 9.010000e-42 182.0
5 TraesCS1D01G379500 chr1B 97.368 38 0 1 2464 2501 626085545 626085581 3.410000e-06 63.9
6 TraesCS1D01G379500 chr1A 93.289 745 40 2 2653 3397 549289546 549290280 0.000000e+00 1090.0
7 TraesCS1D01G379500 chr1A 87.591 137 13 3 3886 4018 549312813 549312949 5.460000e-34 156.0
8 TraesCS1D01G379500 chrUn 79.806 926 165 15 2471 3380 134238342 134237423 0.000000e+00 654.0
9 TraesCS1D01G379500 chrUn 83.121 628 104 2 2471 3097 65118920 65118294 4.580000e-159 571.0
10 TraesCS1D01G379500 chr4B 80.420 858 154 11 2474 3320 666565300 666564446 3.440000e-180 641.0
11 TraesCS1D01G379500 chr3B 83.835 631 98 4 2476 3104 820286873 820286245 7.550000e-167 597.0
12 TraesCS1D01G379500 chr3B 83.955 617 95 4 2472 3086 820150460 820151074 4.540000e-164 588.0
13 TraesCS1D01G379500 chr3B 82.879 660 104 8 2451 3104 820447605 820446949 5.880000e-163 584.0
14 TraesCS1D01G379500 chr3B 79.538 606 114 10 1025 1625 820314708 820314108 1.360000e-114 424.0
15 TraesCS1D01G379500 chr3D 82.243 642 105 8 2451 3086 609585794 609585156 2.770000e-151 545.0
16 TraesCS1D01G379500 chr2B 81.553 618 102 11 2471 3082 4624341 4624952 2.190000e-137 499.0
17 TraesCS1D01G379500 chr6D 97.368 38 1 0 4029 4066 466624148 466624185 9.470000e-07 65.8
18 TraesCS1D01G379500 chr6D 94.872 39 2 0 4029 4067 346959026 346959064 1.220000e-05 62.1
19 TraesCS1D01G379500 chr6D 97.059 34 1 0 4034 4067 346959023 346958990 1.580000e-04 58.4


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 TraesCS1D01G379500 chr1D 455747313 455751393 4080 False 7537.000 7537 100.000 1 4081 1 chr1D.!!$F1 4080
1 TraesCS1D01G379500 chr1B 626083183 626087238 4055 False 1510.975 4872 92.677 3 4079 4 chr1B.!!$F1 4076
2 TraesCS1D01G379500 chr1A 549289546 549290280 734 False 1090.000 1090 93.289 2653 3397 1 chr1A.!!$F1 744
3 TraesCS1D01G379500 chrUn 134237423 134238342 919 True 654.000 654 79.806 2471 3380 1 chrUn.!!$R2 909
4 TraesCS1D01G379500 chrUn 65118294 65118920 626 True 571.000 571 83.121 2471 3097 1 chrUn.!!$R1 626
5 TraesCS1D01G379500 chr4B 666564446 666565300 854 True 641.000 641 80.420 2474 3320 1 chr4B.!!$R1 846
6 TraesCS1D01G379500 chr3B 820286245 820286873 628 True 597.000 597 83.835 2476 3104 1 chr3B.!!$R1 628
7 TraesCS1D01G379500 chr3B 820150460 820151074 614 False 588.000 588 83.955 2472 3086 1 chr3B.!!$F1 614
8 TraesCS1D01G379500 chr3B 820446949 820447605 656 True 584.000 584 82.879 2451 3104 1 chr3B.!!$R3 653
9 TraesCS1D01G379500 chr3B 820314108 820314708 600 True 424.000 424 79.538 1025 1625 1 chr3B.!!$R2 600
10 TraesCS1D01G379500 chr3D 609585156 609585794 638 True 545.000 545 82.243 2451 3086 1 chr3D.!!$R1 635
11 TraesCS1D01G379500 chr2B 4624341 4624952 611 False 499.000 499 81.553 2471 3082 1 chr2B.!!$F1 611

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
622 635 0.175531 TCGCAGATTCTTCATGCCGA 59.824 50.0 0.00 0.00 36.60 5.54 F
840 854 0.325272 GGTCAGGTGAGTCCCTTTCC 59.675 60.0 0.00 1.38 36.75 3.13 F
1203 1272 0.394762 CCATCCATGGTCACCAGGTG 60.395 60.0 14.19 14.19 43.05 4.00 F
1455 1524 0.463204 TGATAGCAGCAGAGCCTGAC 59.537 55.0 6.40 0.00 34.77 3.51 F
2274 2350 0.243907 TCGCTGCCTTACTGTCTCAC 59.756 55.0 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
1780 1849 0.107214 TCAATGATGGGCCGAGGAAC 60.107 55.000 0.00 0.0 0.00 3.62 R
1783 1852 0.758734 TAGTCAATGATGGGCCGAGG 59.241 55.000 0.00 0.0 0.00 4.63 R
2151 2227 1.837439 TGCGGTGTCCTCAGGATAAAT 59.163 47.619 0.00 0.0 32.73 1.40 R
2669 2747 1.880941 ATCCTCCAGGTAGGGTGAAC 58.119 55.000 5.39 0.0 37.24 3.18 R
3806 3901 1.649664 CAAGGAGATGAGAGCCAACG 58.350 55.000 0.00 0.0 0.00 4.10 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
39 40 4.241590 ACAGTGTATGCATTTGGTTGTG 57.758 40.909 3.54 0.00 0.00 3.33
53 54 1.405105 GGTTGTGCGCATGGATATGTT 59.595 47.619 15.91 0.00 36.65 2.71
54 55 2.159254 GGTTGTGCGCATGGATATGTTT 60.159 45.455 15.91 0.00 36.65 2.83
55 56 2.847959 TGTGCGCATGGATATGTTTG 57.152 45.000 15.91 0.00 36.65 2.93
56 57 1.404748 TGTGCGCATGGATATGTTTGG 59.595 47.619 15.91 0.00 36.65 3.28
57 58 1.675483 GTGCGCATGGATATGTTTGGA 59.325 47.619 15.91 0.00 36.65 3.53
58 59 1.675483 TGCGCATGGATATGTTTGGAC 59.325 47.619 5.66 0.00 36.65 4.02
59 60 1.001378 GCGCATGGATATGTTTGGACC 60.001 52.381 0.30 0.00 36.65 4.46
60 61 2.296792 CGCATGGATATGTTTGGACCA 58.703 47.619 0.00 0.00 36.65 4.02
61 62 2.886523 CGCATGGATATGTTTGGACCAT 59.113 45.455 0.00 0.00 41.25 3.55
64 65 4.812403 ATGGATATGTTTGGACCATGGA 57.188 40.909 21.47 0.00 39.45 3.41
65 66 4.169059 TGGATATGTTTGGACCATGGAG 57.831 45.455 21.47 0.00 0.00 3.86
101 102 6.137794 ACATTTTTCGTATGGTGTTGTTGA 57.862 33.333 0.00 0.00 0.00 3.18
102 103 6.205784 ACATTTTTCGTATGGTGTTGTTGAG 58.794 36.000 0.00 0.00 0.00 3.02
108 109 9.438228 TTTTCGTATGGTGTTGTTGAGATATTA 57.562 29.630 0.00 0.00 0.00 0.98
116 117 9.325198 TGGTGTTGTTGAGATATTACATGATAC 57.675 33.333 0.00 0.00 0.00 2.24
216 217 2.189594 TGGCAAAGAGGTCATCACAG 57.810 50.000 0.00 0.00 0.00 3.66
217 218 0.807496 GGCAAAGAGGTCATCACAGC 59.193 55.000 0.00 0.00 0.00 4.40
222 223 2.486472 AGAGGTCATCACAGCAAAGG 57.514 50.000 0.00 0.00 0.00 3.11
263 264 8.527810 CAAACATAAATTTGGCTACCCTTAAGA 58.472 33.333 3.36 0.00 36.17 2.10
383 395 1.066303 CTGAGTGCTAGGATGACGACC 59.934 57.143 0.00 0.00 0.00 4.79
390 402 2.259618 CTAGGATGACGACCGTGTTTG 58.740 52.381 0.00 0.00 0.00 2.93
391 403 0.949105 AGGATGACGACCGTGTTTGC 60.949 55.000 0.00 0.00 0.00 3.68
408 421 2.808523 TGCGGAGTCATCATCAGATC 57.191 50.000 0.00 0.00 30.20 2.75
416 429 4.197750 AGTCATCATCAGATCAAAGGTGC 58.802 43.478 0.00 0.00 30.20 5.01
422 435 0.445436 CAGATCAAAGGTGCAGTCGC 59.555 55.000 0.00 0.00 39.24 5.19
444 457 2.730382 TGGCTGATCAAATGTCATGCT 58.270 42.857 0.00 0.00 0.00 3.79
524 537 1.452108 GGCATTAGTTCAGCGGGCT 60.452 57.895 0.00 0.00 0.00 5.19
551 564 8.825745 TCCAAATTTTGTCTAATTTTGCAGAAC 58.174 29.630 8.26 0.00 35.98 3.01
552 565 8.829612 CCAAATTTTGTCTAATTTTGCAGAACT 58.170 29.630 8.26 0.00 35.98 3.01
553 566 9.640974 CAAATTTTGTCTAATTTTGCAGAACTG 57.359 29.630 0.78 0.00 35.98 3.16
554 567 7.951530 ATTTTGTCTAATTTTGCAGAACTGG 57.048 32.000 3.99 0.00 0.00 4.00
555 568 6.707440 TTTGTCTAATTTTGCAGAACTGGA 57.293 33.333 3.99 0.00 0.00 3.86
556 569 5.689383 TGTCTAATTTTGCAGAACTGGAC 57.311 39.130 7.80 7.80 0.00 4.02
557 570 5.129634 TGTCTAATTTTGCAGAACTGGACA 58.870 37.500 12.48 12.48 0.00 4.02
558 571 5.239306 TGTCTAATTTTGCAGAACTGGACAG 59.761 40.000 12.48 0.00 0.00 3.51
604 617 3.380954 GGTAACTGTACTGCCTCCTACTC 59.619 52.174 0.00 0.00 0.00 2.59
614 627 1.410882 GCCTCCTACTCGCAGATTCTT 59.589 52.381 0.00 0.00 33.89 2.52
619 632 2.799412 CCTACTCGCAGATTCTTCATGC 59.201 50.000 0.00 0.00 33.89 4.06
622 635 0.175531 TCGCAGATTCTTCATGCCGA 59.824 50.000 0.00 0.00 36.60 5.54
655 668 0.589729 GTGCGCGCATTTATGGTCAG 60.590 55.000 38.62 0.00 0.00 3.51
656 669 1.024046 TGCGCGCATTTATGGTCAGT 61.024 50.000 33.09 0.00 0.00 3.41
670 683 8.677148 TTTATGGTCAGTGAATATAAAGAGGC 57.323 34.615 14.45 0.00 0.00 4.70
701 714 5.413309 TGTTTTTCATCAACTGGTTGGTT 57.587 34.783 12.65 0.03 40.78 3.67
702 715 5.174395 TGTTTTTCATCAACTGGTTGGTTG 58.826 37.500 12.65 10.80 45.42 3.77
703 716 3.451141 TTTCATCAACTGGTTGGTTGC 57.549 42.857 12.65 0.00 44.19 4.17
704 717 2.363306 TCATCAACTGGTTGGTTGCT 57.637 45.000 12.65 0.00 44.19 3.91
705 718 2.665165 TCATCAACTGGTTGGTTGCTT 58.335 42.857 12.65 0.00 44.19 3.91
706 719 2.622942 TCATCAACTGGTTGGTTGCTTC 59.377 45.455 12.65 0.00 44.19 3.86
744 757 9.083422 CCACTATATGTATAGATATCCCACTGG 57.917 40.741 12.71 4.38 38.30 4.00
755 768 7.552050 AGATATCCCACTGGAAGAGAATTAG 57.448 40.000 0.00 0.00 45.98 1.73
756 769 7.079048 AGATATCCCACTGGAAGAGAATTAGT 58.921 38.462 0.00 0.00 45.98 2.24
757 770 8.235230 AGATATCCCACTGGAAGAGAATTAGTA 58.765 37.037 0.00 0.00 45.98 1.82
759 772 6.945636 TCCCACTGGAAGAGAATTAGTAAA 57.054 37.500 0.00 0.00 37.86 2.01
761 774 6.271391 TCCCACTGGAAGAGAATTAGTAAACA 59.729 38.462 0.00 0.00 37.86 2.83
762 775 6.595716 CCCACTGGAAGAGAATTAGTAAACAG 59.404 42.308 0.00 0.00 37.43 3.16
763 776 6.092807 CCACTGGAAGAGAATTAGTAAACAGC 59.907 42.308 0.00 0.00 37.43 4.40
764 777 6.650807 CACTGGAAGAGAATTAGTAAACAGCA 59.349 38.462 0.00 0.00 37.43 4.41
765 778 6.651225 ACTGGAAGAGAATTAGTAAACAGCAC 59.349 38.462 0.00 0.00 37.43 4.40
766 779 5.637810 TGGAAGAGAATTAGTAAACAGCACG 59.362 40.000 0.00 0.00 0.00 5.34
767 780 5.867716 GGAAGAGAATTAGTAAACAGCACGA 59.132 40.000 0.00 0.00 0.00 4.35
768 781 6.367969 GGAAGAGAATTAGTAAACAGCACGAA 59.632 38.462 0.00 0.00 0.00 3.85
769 782 6.952935 AGAGAATTAGTAAACAGCACGAAG 57.047 37.500 0.00 0.00 0.00 3.79
770 783 5.348997 AGAGAATTAGTAAACAGCACGAAGC 59.651 40.000 0.00 0.00 46.19 3.86
792 805 5.789643 CTAGCTAGCATTTCTCTTCTCCT 57.210 43.478 18.83 0.00 0.00 3.69
822 836 1.705186 TCCAGTCCCTTTCCTTTGAGG 59.295 52.381 0.00 0.00 36.46 3.86
833 847 1.971357 TCCTTTGAGGTCAGGTGAGTC 59.029 52.381 0.00 0.00 36.53 3.36
834 848 1.002544 CCTTTGAGGTCAGGTGAGTCC 59.997 57.143 0.00 0.00 0.00 3.85
838 852 1.353091 GAGGTCAGGTGAGTCCCTTT 58.647 55.000 0.00 0.00 36.75 3.11
840 854 0.325272 GGTCAGGTGAGTCCCTTTCC 59.675 60.000 0.00 1.38 36.75 3.13
841 855 1.353091 GTCAGGTGAGTCCCTTTCCT 58.647 55.000 0.00 0.00 36.75 3.36
844 858 2.106511 TCAGGTGAGTCCCTTTCCTTTG 59.893 50.000 0.00 0.00 36.75 2.77
845 859 2.106511 CAGGTGAGTCCCTTTCCTTTGA 59.893 50.000 0.00 0.00 36.75 2.69
846 860 2.373502 AGGTGAGTCCCTTTCCTTTGAG 59.626 50.000 0.00 0.00 36.75 3.02
847 861 2.553247 GGTGAGTCCCTTTCCTTTGAGG 60.553 54.545 0.00 0.00 36.46 3.86
851 920 2.158460 AGTCCCTTTCCTTTGAGGTTGG 60.158 50.000 0.00 0.00 36.53 3.77
871 940 4.728534 TGGATAATTTTGCGGAACTTTCG 58.271 39.130 0.00 0.00 0.00 3.46
882 951 4.082081 TGCGGAACTTTCGGAGTAGAATTA 60.082 41.667 0.99 0.00 37.72 1.40
914 983 8.560374 GCTCGGTTAATTTAGCAGATTTTCTAT 58.440 33.333 0.00 0.00 35.05 1.98
948 1017 6.894339 TTTTTCCTCCTCCACAGTTAAATC 57.106 37.500 0.00 0.00 0.00 2.17
949 1018 5.576563 TTTCCTCCTCCACAGTTAAATCA 57.423 39.130 0.00 0.00 0.00 2.57
950 1019 5.576563 TTCCTCCTCCACAGTTAAATCAA 57.423 39.130 0.00 0.00 0.00 2.57
951 1020 5.165961 TCCTCCTCCACAGTTAAATCAAG 57.834 43.478 0.00 0.00 0.00 3.02
952 1021 4.844085 TCCTCCTCCACAGTTAAATCAAGA 59.156 41.667 0.00 0.00 0.00 3.02
953 1022 5.488919 TCCTCCTCCACAGTTAAATCAAGAT 59.511 40.000 0.00 0.00 0.00 2.40
954 1023 6.672218 TCCTCCTCCACAGTTAAATCAAGATA 59.328 38.462 0.00 0.00 0.00 1.98
955 1024 7.348274 TCCTCCTCCACAGTTAAATCAAGATAT 59.652 37.037 0.00 0.00 0.00 1.63
956 1025 7.443575 CCTCCTCCACAGTTAAATCAAGATATG 59.556 40.741 0.00 0.00 0.00 1.78
957 1026 7.282585 TCCTCCACAGTTAAATCAAGATATGG 58.717 38.462 0.00 0.00 0.00 2.74
958 1027 7.127186 TCCTCCACAGTTAAATCAAGATATGGA 59.873 37.037 0.00 0.00 0.00 3.41
959 1028 7.941238 CCTCCACAGTTAAATCAAGATATGGAT 59.059 37.037 0.00 0.00 32.33 3.41
960 1029 8.681486 TCCACAGTTAAATCAAGATATGGATG 57.319 34.615 0.00 0.00 0.00 3.51
961 1030 7.720957 TCCACAGTTAAATCAAGATATGGATGG 59.279 37.037 0.00 0.00 0.00 3.51
962 1031 7.365741 CACAGTTAAATCAAGATATGGATGGC 58.634 38.462 0.00 0.00 0.00 4.40
963 1032 7.013559 CACAGTTAAATCAAGATATGGATGGCA 59.986 37.037 0.00 0.00 0.00 4.92
964 1033 7.230108 ACAGTTAAATCAAGATATGGATGGCAG 59.770 37.037 0.00 0.00 0.00 4.85
965 1034 7.446319 CAGTTAAATCAAGATATGGATGGCAGA 59.554 37.037 0.00 0.00 0.00 4.26
966 1035 7.446625 AGTTAAATCAAGATATGGATGGCAGAC 59.553 37.037 0.00 0.00 0.00 3.51
967 1036 4.987963 ATCAAGATATGGATGGCAGACA 57.012 40.909 0.00 0.00 0.00 3.41
968 1037 4.776435 TCAAGATATGGATGGCAGACAA 57.224 40.909 0.00 0.00 0.00 3.18
969 1038 5.314718 TCAAGATATGGATGGCAGACAAT 57.685 39.130 0.00 0.00 0.00 2.71
970 1039 6.438186 TCAAGATATGGATGGCAGACAATA 57.562 37.500 0.00 0.00 0.00 1.90
971 1040 6.233434 TCAAGATATGGATGGCAGACAATAC 58.767 40.000 0.00 0.00 0.00 1.89
972 1041 5.830799 AGATATGGATGGCAGACAATACA 57.169 39.130 0.00 0.00 0.00 2.29
973 1042 6.384342 AGATATGGATGGCAGACAATACAT 57.616 37.500 0.00 0.00 0.00 2.29
974 1043 6.413052 AGATATGGATGGCAGACAATACATC 58.587 40.000 0.00 0.00 39.11 3.06
975 1044 3.929955 TGGATGGCAGACAATACATCA 57.070 42.857 0.00 0.00 41.03 3.07
976 1045 3.812262 TGGATGGCAGACAATACATCAG 58.188 45.455 0.00 0.00 41.03 2.90
977 1046 2.551459 GGATGGCAGACAATACATCAGC 59.449 50.000 0.00 0.00 41.03 4.26
978 1047 2.785540 TGGCAGACAATACATCAGCA 57.214 45.000 0.00 0.00 30.65 4.41
979 1048 2.635714 TGGCAGACAATACATCAGCAG 58.364 47.619 0.00 0.00 30.65 4.24
980 1049 1.332997 GGCAGACAATACATCAGCAGC 59.667 52.381 0.00 0.00 30.65 5.25
981 1050 2.286872 GCAGACAATACATCAGCAGCT 58.713 47.619 0.00 0.00 0.00 4.24
982 1051 3.461061 GCAGACAATACATCAGCAGCTA 58.539 45.455 0.00 0.00 0.00 3.32
983 1052 3.493877 GCAGACAATACATCAGCAGCTAG 59.506 47.826 0.00 0.00 0.00 3.42
984 1053 4.691175 CAGACAATACATCAGCAGCTAGT 58.309 43.478 0.00 0.00 0.00 2.57
985 1054 5.114780 CAGACAATACATCAGCAGCTAGTT 58.885 41.667 0.00 0.00 0.00 2.24
986 1055 6.276091 CAGACAATACATCAGCAGCTAGTTA 58.724 40.000 0.00 0.00 0.00 2.24
998 1067 8.599055 TCAGCAGCTAGTTAAATCAAGATATG 57.401 34.615 0.00 0.00 0.00 1.78
999 1068 7.658982 TCAGCAGCTAGTTAAATCAAGATATGG 59.341 37.037 0.00 0.00 0.00 2.74
1003 1072 9.716531 CAGCTAGTTAAATCAAGATATGGATGA 57.283 33.333 0.00 0.00 0.00 2.92
1154 1223 6.721704 AAGCATTCTTCTTGGAAAAACTCT 57.278 33.333 0.00 0.00 0.00 3.24
1203 1272 0.394762 CCATCCATGGTCACCAGGTG 60.395 60.000 14.19 14.19 43.05 4.00
1309 1378 1.296392 CGTGGCTGGGTCTCATTGA 59.704 57.895 0.00 0.00 0.00 2.57
1320 1389 4.838423 TGGGTCTCATTGACTTCTGTCTTA 59.162 41.667 0.00 0.00 44.74 2.10
1335 1404 0.666913 TCTTACTCCGATGCTACCGC 59.333 55.000 0.00 0.00 0.00 5.68
1455 1524 0.463204 TGATAGCAGCAGAGCCTGAC 59.537 55.000 6.40 0.00 34.77 3.51
1608 1677 3.025866 GCATGCTGCAGCTACAAAC 57.974 52.632 36.61 17.60 44.26 2.93
1735 1804 6.205464 AGCATATTTGATGTTATGGTTCCTCG 59.795 38.462 0.00 0.00 33.91 4.63
1760 1829 6.253746 GCTTTTGCATCTACAGTATCAGTTG 58.746 40.000 0.00 0.00 46.58 3.16
1786 1855 2.098117 CCAAAGGCAATCATCGTTCCTC 59.902 50.000 0.00 0.00 0.00 3.71
1789 1858 1.643832 GCAATCATCGTTCCTCGGC 59.356 57.895 0.00 0.00 40.32 5.54
1798 1874 1.439353 CGTTCCTCGGCCCATCATTG 61.439 60.000 0.00 0.00 35.71 2.82
1811 1887 4.560108 GCCCATCATTGACTAATTCATGCC 60.560 45.833 0.00 0.00 32.84 4.40
1833 1909 6.716628 TGCCTCTTGACTATTTTTCAGACATT 59.283 34.615 0.00 0.00 0.00 2.71
1914 1990 1.956477 ACACCAGCAAGATTGGTTGTC 59.044 47.619 0.00 0.00 46.57 3.18
1978 2054 8.877864 ACATGATTGTTCTTTAGGGTATGAAA 57.122 30.769 0.00 0.00 29.55 2.69
1996 2072 6.849588 ATGAAATGAGCACAAAAGGTTTTC 57.150 33.333 0.00 0.00 0.00 2.29
2041 2117 4.122046 TCGAGGTCATATTGATGTTGCTG 58.878 43.478 0.00 0.00 34.41 4.41
2094 2170 7.439655 GCTCCTTATTGTCAAGTAGATAACCAG 59.560 40.741 0.00 0.00 29.65 4.00
2126 2202 8.777578 TGGACACTCCTACATACAACTATAAT 57.222 34.615 0.00 0.00 37.46 1.28
2127 2203 9.209048 TGGACACTCCTACATACAACTATAATT 57.791 33.333 0.00 0.00 37.46 1.40
2148 2224 5.627499 TTAACAATCATGCAGAGTTCACC 57.373 39.130 0.00 0.00 0.00 4.02
2151 2227 2.743664 CAATCATGCAGAGTTCACCGAA 59.256 45.455 0.00 0.00 0.00 4.30
2212 2288 4.081198 ACATGCAAGACAACCAAGGAAAAA 60.081 37.500 0.00 0.00 0.00 1.94
2274 2350 0.243907 TCGCTGCCTTACTGTCTCAC 59.756 55.000 0.00 0.00 0.00 3.51
2337 2413 1.338020 GCAACTTGGGAACTGTGGAAG 59.662 52.381 0.00 0.00 0.00 3.46
2355 2431 4.016444 GGAAGGTCATACAGAATGCCAAA 58.984 43.478 0.00 0.00 42.53 3.28
2358 2434 4.666512 AGGTCATACAGAATGCCAAAACT 58.333 39.130 0.00 0.00 42.53 2.66
2381 2457 8.707938 ACTTTAAACTGGGTACGTATGTTATC 57.292 34.615 0.00 0.00 0.00 1.75
2417 2493 7.197703 TGTAGAATGAATTGTGCATGCTTATG 58.802 34.615 20.33 0.00 33.67 1.90
2418 2494 5.597806 AGAATGAATTGTGCATGCTTATGG 58.402 37.500 20.33 0.00 26.69 2.74
2855 2933 8.289939 ACGAGTTCTTGGTTTACTATAGATCA 57.710 34.615 6.78 0.00 0.00 2.92
3026 3104 0.674895 GCGAATGGCCTGTCTTGAGT 60.675 55.000 3.32 0.00 34.80 3.41
3087 3165 2.549064 TGACATTGTGTGACCTCAGG 57.451 50.000 0.00 0.00 0.00 3.86
3273 3361 7.377766 TCCACTTAAACTAAATGCAGTGATC 57.622 36.000 0.00 0.00 34.74 2.92
3442 3532 4.932200 ACTGTTGAGCACTAGTAAGATTGC 59.068 41.667 0.00 0.00 35.08 3.56
3507 3597 8.662141 GTCTGTTTATAACAAATACCGATGTGT 58.338 33.333 0.00 0.00 41.61 3.72
3568 3660 3.951115 CTTGCAAGCAGAAGCACAA 57.049 47.368 14.65 0.00 45.49 3.33
3614 3706 9.823647 AATCCTTATAGATATATCACGGCAAAG 57.176 33.333 15.08 8.70 0.00 2.77
3694 3789 8.919145 TGTAAGGACCACAAAATCACTAAATTT 58.081 29.630 0.00 0.00 0.00 1.82
3697 3792 9.758651 AAGGACCACAAAATCACTAAATTTTAC 57.241 29.630 0.00 0.00 36.86 2.01
3731 3826 5.126061 ACAACAAATCAGGAGCCATGAATAC 59.874 40.000 0.00 0.00 0.00 1.89
3745 3840 7.329499 AGCCATGAATACTAATGATAGCAGAG 58.671 38.462 0.00 0.00 31.96 3.35
3806 3901 0.831307 ACCCGGATCAAGGACTTAGC 59.169 55.000 0.73 0.00 0.00 3.09
3878 3973 1.673337 GCAGTGCTGTCTGATGGCA 60.673 57.895 8.18 0.00 37.61 4.92
3920 4015 2.930826 TGGTTCTCAGTTTCTGGGTC 57.069 50.000 0.00 0.00 33.01 4.46
3921 4016 2.123589 TGGTTCTCAGTTTCTGGGTCA 58.876 47.619 0.00 0.00 33.01 4.02
3936 4032 4.225717 TCTGGGTCAAGATTGTGATGATGA 59.774 41.667 0.00 0.00 0.00 2.92
3981 4077 7.121759 CCTGAAACAGAACAGGTATCATTTCAT 59.878 37.037 0.00 0.00 45.82 2.57
4007 4103 6.188407 TCAGTTATACTACTGCCTCTGTTCT 58.812 40.000 0.00 0.00 44.10 3.01
4019 4115 5.809001 TGCCTCTGTTCTGAAATAAGTGAT 58.191 37.500 0.00 0.00 0.00 3.06
4024 4120 5.412594 TCTGTTCTGAAATAAGTGATGTGGC 59.587 40.000 0.00 0.00 0.00 5.01
4045 4141 7.232534 TGTGGCTTTAATCTGAACTAAAACCAT 59.767 33.333 15.21 0.00 36.28 3.55
4046 4142 7.542130 GTGGCTTTAATCTGAACTAAAACCATG 59.458 37.037 15.21 0.00 36.28 3.66
4066 4162 3.334691 TGCCACTTATTTCCGAACAGAG 58.665 45.455 0.00 0.00 0.00 3.35
4079 4175 3.058224 CCGAACAGAGTTTGCTAAAAGGG 60.058 47.826 0.00 0.00 0.00 3.95
4080 4176 3.609409 CGAACAGAGTTTGCTAAAAGGGC 60.609 47.826 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.988493 GCACAACCAAATGCATACACTG 59.012 45.455 0.00 0.00 41.65 3.66
26 27 0.944788 CATGCGCACAACCAAATGCA 60.945 50.000 14.90 0.00 42.17 3.96
39 40 1.001378 GGTCCAAACATATCCATGCGC 60.001 52.381 0.00 0.00 35.39 6.09
53 54 3.332187 TGGATTGTAACTCCATGGTCCAA 59.668 43.478 12.58 8.88 37.87 3.53
54 55 2.916269 TGGATTGTAACTCCATGGTCCA 59.084 45.455 12.58 11.88 37.87 4.02
55 56 3.644966 TGGATTGTAACTCCATGGTCC 57.355 47.619 12.58 9.20 37.87 4.46
56 57 6.119536 TGTATTGGATTGTAACTCCATGGTC 58.880 40.000 12.58 0.00 42.26 4.02
57 58 6.073447 TGTATTGGATTGTAACTCCATGGT 57.927 37.500 12.58 0.00 42.26 3.55
58 59 7.587037 AATGTATTGGATTGTAACTCCATGG 57.413 36.000 4.97 4.97 42.26 3.66
59 60 9.874205 AAAAATGTATTGGATTGTAACTCCATG 57.126 29.630 0.00 0.00 42.26 3.66
61 62 8.240682 CGAAAAATGTATTGGATTGTAACTCCA 58.759 33.333 0.00 0.00 41.03 3.86
62 63 8.241367 ACGAAAAATGTATTGGATTGTAACTCC 58.759 33.333 0.00 0.00 0.00 3.85
78 79 6.038825 TCTCAACAACACCATACGAAAAATGT 59.961 34.615 0.00 0.00 0.00 2.71
206 207 3.063997 CGAATACCTTTGCTGTGATGACC 59.936 47.826 0.00 0.00 0.00 4.02
216 217 4.501071 TGGTTAGAGACGAATACCTTTGC 58.499 43.478 0.00 0.00 0.00 3.68
217 218 6.425721 TGTTTGGTTAGAGACGAATACCTTTG 59.574 38.462 0.00 0.00 0.00 2.77
249 250 3.520721 GGTTAAGGTCTTAAGGGTAGCCA 59.479 47.826 14.62 0.00 35.90 4.75
255 256 3.844804 AGAGGTGGTTAAGGTCTTAAGGG 59.155 47.826 1.85 0.00 35.90 3.95
263 264 6.697641 TCTAAATTGAGAGGTGGTTAAGGT 57.302 37.500 0.00 0.00 0.00 3.50
383 395 1.061131 GATGATGACTCCGCAAACACG 59.939 52.381 0.00 0.00 0.00 4.49
390 402 2.808523 TGATCTGATGATGACTCCGC 57.191 50.000 0.00 0.00 32.19 5.54
391 403 4.056740 CCTTTGATCTGATGATGACTCCG 58.943 47.826 0.00 0.00 32.19 4.63
400 413 2.350804 CGACTGCACCTTTGATCTGATG 59.649 50.000 0.00 0.00 0.00 3.07
416 429 1.089112 TTTGATCAGCCATGCGACTG 58.911 50.000 0.00 3.03 35.15 3.51
422 435 3.068165 AGCATGACATTTGATCAGCCATG 59.932 43.478 0.00 14.79 34.66 3.66
429 442 3.887110 TCCATGGAGCATGACATTTGATC 59.113 43.478 11.44 0.00 43.81 2.92
444 457 5.251932 TCCCACTAAACTAATGTTCCATGGA 59.748 40.000 11.44 11.44 35.14 3.41
501 514 2.292267 CCGCTGAACTAATGCCAGAAT 58.708 47.619 0.00 0.00 0.00 2.40
504 517 1.718757 GCCCGCTGAACTAATGCCAG 61.719 60.000 0.00 0.00 0.00 4.85
524 537 8.954950 TCTGCAAAATTAGACAAAATTTGGAA 57.045 26.923 10.71 2.01 38.68 3.53
594 607 1.036707 AGAATCTGCGAGTAGGAGGC 58.963 55.000 0.00 0.00 38.98 4.70
604 617 1.224075 ATCGGCATGAAGAATCTGCG 58.776 50.000 0.00 0.00 36.76 5.18
614 627 3.264998 TGTGAAGATCAATCGGCATGA 57.735 42.857 0.00 0.00 0.00 3.07
619 632 2.286008 CGCACATGTGAAGATCAATCGG 60.286 50.000 29.80 0.00 0.00 4.18
622 635 1.063027 CGCGCACATGTGAAGATCAAT 59.937 47.619 29.80 0.00 0.00 2.57
655 668 8.903820 ACAACCAATAAGCCTCTTTATATTCAC 58.096 33.333 0.00 0.00 0.00 3.18
656 669 9.474313 AACAACCAATAAGCCTCTTTATATTCA 57.526 29.630 0.00 0.00 0.00 2.57
670 683 7.710475 ACCAGTTGATGAAAAACAACCAATAAG 59.290 33.333 0.00 0.00 44.79 1.73
701 714 0.469494 TGGACAGACAAGCAGAAGCA 59.531 50.000 0.00 0.00 45.49 3.91
702 715 0.871057 GTGGACAGACAAGCAGAAGC 59.129 55.000 0.00 0.00 42.56 3.86
703 716 2.540265 AGTGGACAGACAAGCAGAAG 57.460 50.000 0.00 0.00 0.00 2.85
704 717 5.187772 ACATATAGTGGACAGACAAGCAGAA 59.812 40.000 0.00 0.00 0.00 3.02
705 718 4.711846 ACATATAGTGGACAGACAAGCAGA 59.288 41.667 0.00 0.00 0.00 4.26
706 719 5.016051 ACATATAGTGGACAGACAAGCAG 57.984 43.478 0.00 0.00 0.00 4.24
744 757 6.946229 TCGTGCTGTTTACTAATTCTCTTC 57.054 37.500 0.00 0.00 0.00 2.87
770 783 5.068987 ACAGGAGAAGAGAAATGCTAGCTAG 59.931 44.000 16.84 16.84 0.00 3.42
771 784 4.959210 ACAGGAGAAGAGAAATGCTAGCTA 59.041 41.667 17.23 2.58 0.00 3.32
772 785 3.774216 ACAGGAGAAGAGAAATGCTAGCT 59.226 43.478 17.23 0.00 0.00 3.32
773 786 3.870419 CACAGGAGAAGAGAAATGCTAGC 59.130 47.826 8.10 8.10 0.00 3.42
774 787 4.161189 TCCACAGGAGAAGAGAAATGCTAG 59.839 45.833 0.00 0.00 0.00 3.42
775 788 4.096681 TCCACAGGAGAAGAGAAATGCTA 58.903 43.478 0.00 0.00 0.00 3.49
808 822 1.425448 ACCTGACCTCAAAGGAAAGGG 59.575 52.381 17.29 9.21 42.17 3.95
822 836 1.353091 AGGAAAGGGACTCACCTGAC 58.647 55.000 0.00 0.00 40.99 3.51
833 847 2.675658 TCCAACCTCAAAGGAAAGGG 57.324 50.000 0.00 0.00 37.67 3.95
834 848 6.857437 AATTATCCAACCTCAAAGGAAAGG 57.143 37.500 0.00 0.00 37.67 3.11
838 852 5.336372 CGCAAAATTATCCAACCTCAAAGGA 60.336 40.000 0.00 0.00 37.67 3.36
840 854 4.864247 CCGCAAAATTATCCAACCTCAAAG 59.136 41.667 0.00 0.00 0.00 2.77
841 855 4.524714 TCCGCAAAATTATCCAACCTCAAA 59.475 37.500 0.00 0.00 0.00 2.69
844 858 4.157840 AGTTCCGCAAAATTATCCAACCTC 59.842 41.667 0.00 0.00 0.00 3.85
845 859 4.086457 AGTTCCGCAAAATTATCCAACCT 58.914 39.130 0.00 0.00 0.00 3.50
846 860 4.450082 AGTTCCGCAAAATTATCCAACC 57.550 40.909 0.00 0.00 0.00 3.77
847 861 5.060446 CGAAAGTTCCGCAAAATTATCCAAC 59.940 40.000 0.00 0.00 0.00 3.77
851 920 4.976987 TCCGAAAGTTCCGCAAAATTATC 58.023 39.130 0.00 0.00 0.00 1.75
871 940 4.039366 ACCGAGCTCCATTAATTCTACTCC 59.961 45.833 8.47 0.00 0.00 3.85
882 951 4.523083 TGCTAAATTAACCGAGCTCCATT 58.477 39.130 8.47 5.22 35.89 3.16
930 999 5.165961 TCTTGATTTAACTGTGGAGGAGG 57.834 43.478 0.00 0.00 0.00 4.30
937 1006 7.013559 TGCCATCCATATCTTGATTTAACTGTG 59.986 37.037 0.00 0.00 0.00 3.66
938 1007 7.062322 TGCCATCCATATCTTGATTTAACTGT 58.938 34.615 0.00 0.00 0.00 3.55
946 1015 4.987963 TGTCTGCCATCCATATCTTGAT 57.012 40.909 0.00 0.00 0.00 2.57
947 1016 4.776435 TTGTCTGCCATCCATATCTTGA 57.224 40.909 0.00 0.00 0.00 3.02
948 1017 5.999600 TGTATTGTCTGCCATCCATATCTTG 59.000 40.000 0.00 0.00 0.00 3.02
949 1018 6.191657 TGTATTGTCTGCCATCCATATCTT 57.808 37.500 0.00 0.00 0.00 2.40
950 1019 5.830799 TGTATTGTCTGCCATCCATATCT 57.169 39.130 0.00 0.00 0.00 1.98
951 1020 6.175471 TGATGTATTGTCTGCCATCCATATC 58.825 40.000 0.00 0.00 34.22 1.63
952 1021 6.130692 TGATGTATTGTCTGCCATCCATAT 57.869 37.500 0.00 0.00 34.22 1.78
953 1022 5.554070 CTGATGTATTGTCTGCCATCCATA 58.446 41.667 0.00 0.00 34.22 2.74
954 1023 4.395625 CTGATGTATTGTCTGCCATCCAT 58.604 43.478 0.00 0.00 34.22 3.41
955 1024 3.812262 CTGATGTATTGTCTGCCATCCA 58.188 45.455 0.00 0.00 34.22 3.41
956 1025 2.551459 GCTGATGTATTGTCTGCCATCC 59.449 50.000 0.00 0.00 35.34 3.51
957 1026 3.208594 TGCTGATGTATTGTCTGCCATC 58.791 45.455 0.00 0.00 39.08 3.51
958 1027 3.211865 CTGCTGATGTATTGTCTGCCAT 58.788 45.455 0.00 0.00 39.08 4.40
959 1028 2.635714 CTGCTGATGTATTGTCTGCCA 58.364 47.619 0.00 0.00 39.08 4.92
960 1029 1.332997 GCTGCTGATGTATTGTCTGCC 59.667 52.381 0.00 0.00 39.08 4.85
961 1030 2.286872 AGCTGCTGATGTATTGTCTGC 58.713 47.619 0.00 0.00 39.91 4.26
962 1031 4.691175 ACTAGCTGCTGATGTATTGTCTG 58.309 43.478 13.43 0.00 0.00 3.51
963 1032 5.350504 AACTAGCTGCTGATGTATTGTCT 57.649 39.130 13.43 0.00 0.00 3.41
964 1033 7.539712 TTTAACTAGCTGCTGATGTATTGTC 57.460 36.000 13.43 0.00 0.00 3.18
965 1034 7.770433 TGATTTAACTAGCTGCTGATGTATTGT 59.230 33.333 13.43 0.00 0.00 2.71
966 1035 8.146479 TGATTTAACTAGCTGCTGATGTATTG 57.854 34.615 13.43 0.00 0.00 1.90
967 1036 8.737168 TTGATTTAACTAGCTGCTGATGTATT 57.263 30.769 13.43 0.26 0.00 1.89
968 1037 8.206867 TCTTGATTTAACTAGCTGCTGATGTAT 58.793 33.333 13.43 0.00 0.00 2.29
969 1038 7.555965 TCTTGATTTAACTAGCTGCTGATGTA 58.444 34.615 13.43 0.00 0.00 2.29
970 1039 6.409704 TCTTGATTTAACTAGCTGCTGATGT 58.590 36.000 13.43 5.71 0.00 3.06
971 1040 6.915544 TCTTGATTTAACTAGCTGCTGATG 57.084 37.500 13.43 5.05 0.00 3.07
972 1041 9.217278 CATATCTTGATTTAACTAGCTGCTGAT 57.783 33.333 13.43 4.31 0.00 2.90
973 1042 7.658982 CCATATCTTGATTTAACTAGCTGCTGA 59.341 37.037 13.43 0.00 0.00 4.26
974 1043 7.658982 TCCATATCTTGATTTAACTAGCTGCTG 59.341 37.037 13.43 4.99 0.00 4.41
975 1044 7.739825 TCCATATCTTGATTTAACTAGCTGCT 58.260 34.615 7.57 7.57 0.00 4.24
976 1045 7.969536 TCCATATCTTGATTTAACTAGCTGC 57.030 36.000 0.00 0.00 0.00 5.25
977 1046 9.716531 TCATCCATATCTTGATTTAACTAGCTG 57.283 33.333 0.00 0.00 0.00 4.24
978 1047 9.717942 GTCATCCATATCTTGATTTAACTAGCT 57.282 33.333 0.00 0.00 0.00 3.32
979 1048 9.494271 TGTCATCCATATCTTGATTTAACTAGC 57.506 33.333 0.00 0.00 0.00 3.42
982 1051 9.553064 GTCTGTCATCCATATCTTGATTTAACT 57.447 33.333 0.00 0.00 0.00 2.24
983 1052 9.330063 TGTCTGTCATCCATATCTTGATTTAAC 57.670 33.333 0.00 0.00 0.00 2.01
984 1053 9.904198 TTGTCTGTCATCCATATCTTGATTTAA 57.096 29.630 0.00 0.00 0.00 1.52
986 1055 8.991783 ATTGTCTGTCATCCATATCTTGATTT 57.008 30.769 0.00 0.00 0.00 2.17
998 1067 4.445453 TGCTGATGTATTGTCTGTCATCC 58.555 43.478 0.00 0.00 36.75 3.51
999 1068 4.025061 GCTGCTGATGTATTGTCTGTCATC 60.025 45.833 0.00 0.00 37.68 2.92
1003 1072 3.623906 AGCTGCTGATGTATTGTCTGT 57.376 42.857 0.00 0.00 0.00 3.41
1154 1223 2.203480 GGCAGGTGTTCCCTTGCA 60.203 61.111 0.00 0.00 42.73 4.08
1203 1272 0.318614 CCACCACATCCGTGCAAAAC 60.319 55.000 0.00 0.00 42.17 2.43
1309 1378 3.093057 AGCATCGGAGTAAGACAGAAGT 58.907 45.455 0.00 0.00 0.00 3.01
1335 1404 1.734477 CTCACTCAACCGCCGTGAG 60.734 63.158 3.45 3.45 45.75 3.51
1455 1524 0.320683 TGGTCACATGCTTCGACAGG 60.321 55.000 0.00 0.00 0.00 4.00
1546 1615 3.126831 CCGCATGACTAGAATCTGGAAC 58.873 50.000 0.00 0.00 0.00 3.62
1608 1677 1.522569 GGTCTCACCTCCATTCCCG 59.477 63.158 0.00 0.00 34.73 5.14
1634 1703 9.862371 ACACTATATTACTGTAATCTATGCTGC 57.138 33.333 15.84 0.00 0.00 5.25
1668 1737 2.053865 CCCATGGCCGCTTTGATGT 61.054 57.895 6.09 0.00 0.00 3.06
1669 1738 1.111116 ATCCCATGGCCGCTTTGATG 61.111 55.000 6.09 0.00 0.00 3.07
1677 1746 2.985957 AATTTTCAATCCCATGGCCG 57.014 45.000 6.09 0.00 0.00 6.13
1678 1747 4.408596 TCCTAAATTTTCAATCCCATGGCC 59.591 41.667 6.09 0.00 0.00 5.36
1716 1785 3.013921 GCCGAGGAACCATAACATCAAA 58.986 45.455 0.00 0.00 0.00 2.69
1728 1797 1.168714 AGATGCAAAAGCCGAGGAAC 58.831 50.000 0.00 0.00 0.00 3.62
1735 1804 4.878397 ACTGATACTGTAGATGCAAAAGCC 59.122 41.667 0.00 0.00 0.00 4.35
1780 1849 0.107214 TCAATGATGGGCCGAGGAAC 60.107 55.000 0.00 0.00 0.00 3.62
1782 1851 0.982852 AGTCAATGATGGGCCGAGGA 60.983 55.000 0.00 0.00 0.00 3.71
1783 1852 0.758734 TAGTCAATGATGGGCCGAGG 59.241 55.000 0.00 0.00 0.00 4.63
1786 1855 3.213506 TGAATTAGTCAATGATGGGCCG 58.786 45.455 0.00 0.00 31.51 6.13
1789 1858 4.831155 AGGCATGAATTAGTCAATGATGGG 59.169 41.667 0.00 0.00 40.50 4.00
1798 1874 8.443953 AAATAGTCAAGAGGCATGAATTAGTC 57.556 34.615 0.00 0.00 0.00 2.59
1811 1887 7.814642 AGCAATGTCTGAAAAATAGTCAAGAG 58.185 34.615 0.00 0.00 0.00 2.85
1833 1909 5.588246 TCGCATCCTCATAATTTTTGTAGCA 59.412 36.000 0.00 0.00 0.00 3.49
1845 1921 3.494924 CCATTTCAGGTCGCATCCTCATA 60.495 47.826 0.00 0.00 35.37 2.15
1978 2054 2.368548 GGGGAAAACCTTTTGTGCTCAT 59.631 45.455 0.00 0.00 40.03 2.90
2041 2117 7.106239 TCAGGACAATGTTTAAGAATCTCTCC 58.894 38.462 0.00 0.00 0.00 3.71
2094 2170 1.906574 TGTAGGAGTGTCCAACCATCC 59.093 52.381 0.00 0.00 39.61 3.51
2126 2202 4.154015 CGGTGAACTCTGCATGATTGTTAA 59.846 41.667 0.00 0.00 0.00 2.01
2127 2203 3.684305 CGGTGAACTCTGCATGATTGTTA 59.316 43.478 0.00 0.00 0.00 2.41
2145 2221 3.871594 GTGTCCTCAGGATAAATTCGGTG 59.128 47.826 0.00 0.00 32.73 4.94
2146 2222 3.118371 GGTGTCCTCAGGATAAATTCGGT 60.118 47.826 0.00 0.00 32.73 4.69
2148 2224 3.123804 CGGTGTCCTCAGGATAAATTCG 58.876 50.000 0.00 0.00 32.73 3.34
2151 2227 1.837439 TGCGGTGTCCTCAGGATAAAT 59.163 47.619 0.00 0.00 32.73 1.40
2172 2248 3.301642 GCATGTTAATGACTTTGCGAAGC 59.698 43.478 13.93 7.32 46.17 3.86
2212 2288 2.706190 GGACTGCATAATGTAGAGGGGT 59.294 50.000 0.00 0.00 34.09 4.95
2274 2350 8.398665 TCGATCATTGTTACATCTATATCCTCG 58.601 37.037 0.00 0.00 0.00 4.63
2337 2413 5.391312 AAGTTTTGGCATTCTGTATGACC 57.609 39.130 0.00 0.29 42.03 4.02
2355 2431 9.154847 GATAACATACGTACCCAGTTTAAAGTT 57.845 33.333 0.00 0.00 0.00 2.66
2358 2434 9.723601 AAAGATAACATACGTACCCAGTTTAAA 57.276 29.630 0.00 0.00 0.00 1.52
2394 2470 6.321945 ACCATAAGCATGCACAATTCATTCTA 59.678 34.615 21.98 0.00 0.00 2.10
2403 2479 5.445069 ACCTTATACCATAAGCATGCACAA 58.555 37.500 21.98 4.64 0.00 3.33
2417 2493 6.243216 TCTGGGTACAAATGACCTTATACC 57.757 41.667 0.00 0.00 37.13 2.73
2418 2494 7.990886 TCATTCTGGGTACAAATGACCTTATAC 59.009 37.037 0.00 0.00 37.13 1.47
2669 2747 1.880941 ATCCTCCAGGTAGGGTGAAC 58.119 55.000 5.39 0.00 37.24 3.18
2855 2933 7.575720 GCAAACCACATGAGCTTCTTAGTAAAT 60.576 37.037 0.00 0.00 0.00 1.40
3026 3104 3.992943 TTTCCCAGCCGAAATCTAAGA 57.007 42.857 0.00 0.00 0.00 2.10
3087 3165 6.708949 TGTTACAAGGACCAGAAGACAAATAC 59.291 38.462 0.00 0.00 0.00 1.89
3273 3361 5.406649 GCATGAATTATCTCTAGAGACCGG 58.593 45.833 24.62 0.00 40.75 5.28
3341 3431 8.463930 TTTTATGGTTTCATGACAACTCTCTT 57.536 30.769 15.60 5.61 34.96 2.85
3342 3432 8.463930 TTTTTATGGTTTCATGACAACTCTCT 57.536 30.769 15.60 5.92 34.96 3.10
3402 3492 7.497249 GCTCAACAGTACCTGAATTCTTCATAT 59.503 37.037 7.05 0.00 39.30 1.78
3403 3493 6.818644 GCTCAACAGTACCTGAATTCTTCATA 59.181 38.462 7.05 0.00 39.30 2.15
3405 3495 4.997395 GCTCAACAGTACCTGAATTCTTCA 59.003 41.667 7.05 0.00 38.17 3.02
3406 3496 4.997395 TGCTCAACAGTACCTGAATTCTTC 59.003 41.667 7.05 0.00 35.18 2.87
3407 3497 4.757149 GTGCTCAACAGTACCTGAATTCTT 59.243 41.667 7.05 0.00 35.18 2.52
3408 3498 4.040952 AGTGCTCAACAGTACCTGAATTCT 59.959 41.667 7.05 0.00 35.92 2.40
3409 3499 4.319177 AGTGCTCAACAGTACCTGAATTC 58.681 43.478 0.00 0.00 35.92 2.17
3442 3532 3.306973 AGTCGATACATTCATTGCACGTG 59.693 43.478 12.28 12.28 0.00 4.49
3492 3582 9.781834 CAATTATTTGTACACATCGGTATTTGT 57.218 29.630 0.00 0.00 31.14 2.83
3493 3583 9.232082 CCAATTATTTGTACACATCGGTATTTG 57.768 33.333 0.00 0.00 0.00 2.32
3494 3584 8.962679 ACCAATTATTTGTACACATCGGTATTT 58.037 29.630 0.00 0.00 0.00 1.40
3495 3585 8.514330 ACCAATTATTTGTACACATCGGTATT 57.486 30.769 0.00 0.00 0.00 1.89
3563 3655 6.806249 TGCTGTTTTACAAGCTAATATTGTGC 59.194 34.615 0.00 2.80 40.92 4.57
3568 3660 8.525290 AGGATTGCTGTTTTACAAGCTAATAT 57.475 30.769 0.00 0.00 32.89 1.28
3584 3676 7.383572 GCCGTGATATATCTATAAGGATTGCTG 59.616 40.741 13.79 0.00 0.00 4.41
3585 3677 7.069950 TGCCGTGATATATCTATAAGGATTGCT 59.930 37.037 13.79 0.00 0.00 3.91
3614 3706 7.812648 TGTGCTTTAAAATGTACAGGTCATAC 58.187 34.615 0.33 0.00 0.00 2.39
3618 3710 9.289303 CATATTGTGCTTTAAAATGTACAGGTC 57.711 33.333 0.33 0.00 32.22 3.85
3665 3760 5.385198 AGTGATTTTGTGGTCCTTACATGT 58.615 37.500 2.69 2.69 0.00 3.21
3697 3792 7.542130 GGCTCCTGATTTGTTGTAATAAAAGTG 59.458 37.037 0.00 0.00 0.00 3.16
3731 3826 7.225784 ACACTATGTCCTCTGCTATCATTAG 57.774 40.000 0.00 0.00 0.00 1.73
3745 3840 7.843490 TGCTTCAACTTATTACACTATGTCC 57.157 36.000 0.00 0.00 0.00 4.02
3806 3901 1.649664 CAAGGAGATGAGAGCCAACG 58.350 55.000 0.00 0.00 0.00 4.10
3878 3973 2.103263 GGAGCAACAGATACCTCGGATT 59.897 50.000 0.00 0.00 0.00 3.01
3920 4015 4.725359 TGCGTTTCATCATCACAATCTTG 58.275 39.130 0.00 0.00 0.00 3.02
3921 4016 5.124297 TCATGCGTTTCATCATCACAATCTT 59.876 36.000 0.00 0.00 31.79 2.40
3936 4032 2.629656 GCTGTGGCCTCATGCGTTT 61.630 57.895 8.18 0.00 42.61 3.60
4007 4103 8.461222 CAGATTAAAGCCACATCACTTATTTCA 58.539 33.333 0.00 0.00 0.00 2.69
4019 4115 6.547880 TGGTTTTAGTTCAGATTAAAGCCACA 59.452 34.615 14.47 1.09 40.68 4.17
4024 4120 7.542130 GTGGCATGGTTTTAGTTCAGATTAAAG 59.458 37.037 0.00 0.00 0.00 1.85
4045 4141 3.244422 ACTCTGTTCGGAAATAAGTGGCA 60.244 43.478 0.00 0.00 0.00 4.92
4046 4142 3.335579 ACTCTGTTCGGAAATAAGTGGC 58.664 45.455 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.