Multiple sequence alignment - TraesCS1B01G092200

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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 TraesCS1B01G092200 chr1B 100.000 3884 0 0 1 3884 94187800 94183917 0.000000e+00 7173.0
1 TraesCS1B01G092200 chr1B 88.162 718 80 4 1 717 111936909 111937622 0.000000e+00 850.0
2 TraesCS1B01G092200 chr1B 90.149 670 39 6 3242 3884 94200146 94199477 0.000000e+00 846.0
3 TraesCS1B01G092200 chr1B 89.666 629 37 12 892 1493 94208704 94208077 0.000000e+00 776.0
4 TraesCS1B01G092200 chr1B 85.215 629 59 17 1939 2547 94201894 94201280 1.980000e-172 616.0
5 TraesCS1B01G092200 chr1B 93.171 410 24 3 1511 1919 94208000 94207594 2.000000e-167 599.0
6 TraesCS1B01G092200 chr1B 84.450 373 35 16 2544 2895 94201254 94200884 2.870000e-91 346.0
7 TraesCS1B01G092200 chr1B 93.182 44 3 0 819 862 94208782 94208739 9.010000e-07 65.8
8 TraesCS1B01G092200 chr1B 94.444 36 2 0 3007 3042 94200522 94200487 5.420000e-04 56.5
9 TraesCS1B01G092200 chr1D 87.778 2021 124 54 1929 3884 58450090 58452052 0.000000e+00 2250.0
10 TraesCS1B01G092200 chr1D 88.301 718 79 4 1 717 408620936 408621649 0.000000e+00 856.0
11 TraesCS1B01G092200 chr1D 88.571 630 53 6 872 1484 58448917 58449544 0.000000e+00 747.0
12 TraesCS1B01G092200 chr1D 94.853 408 21 0 1512 1919 58449635 58450042 4.230000e-179 638.0
13 TraesCS1B01G092200 chr1A 91.189 976 44 20 2945 3884 57192038 57193007 0.000000e+00 1288.0
14 TraesCS1B01G092200 chr1A 90.966 642 34 9 875 1493 57394897 57394257 0.000000e+00 843.0
15 TraesCS1B01G092200 chr1A 87.790 647 60 8 872 1501 57189730 57190374 0.000000e+00 739.0
16 TraesCS1B01G092200 chr1A 86.348 586 54 10 1938 2508 57190916 57191490 1.980000e-172 616.0
17 TraesCS1B01G092200 chr1A 85.835 593 54 12 1938 2512 57393704 57393124 1.540000e-168 603.0
18 TraesCS1B01G092200 chr1A 92.402 408 27 4 1511 1917 57190445 57190849 2.600000e-161 579.0
19 TraesCS1B01G092200 chr1A 89.021 419 26 8 1515 1919 57394183 57393771 5.790000e-138 501.0
20 TraesCS1B01G092200 chr1A 85.476 420 30 17 2548 2938 57191557 57191974 3.610000e-110 409.0
21 TraesCS1B01G092200 chr1A 85.326 368 31 17 2548 2895 57393053 57392689 3.690000e-95 359.0
22 TraesCS1B01G092200 chr1A 90.909 55 4 1 874 928 57310191 57310138 5.380000e-09 73.1
23 TraesCS1B01G092200 chr1A 88.889 54 4 2 810 862 57189633 57189685 9.010000e-07 65.8
24 TraesCS1B01G092200 chr1A 91.489 47 3 1 817 862 57394998 57394952 3.240000e-06 63.9
25 TraesCS1B01G092200 chr1A 92.500 40 3 0 817 856 57310287 57310248 1.510000e-04 58.4
26 TraesCS1B01G092200 chr3D 88.595 719 76 5 1 717 580982887 580983601 0.000000e+00 869.0
27 TraesCS1B01G092200 chr7A 88.392 715 78 4 4 717 452644875 452644165 0.000000e+00 856.0
28 TraesCS1B01G092200 chr4B 88.022 718 82 4 1 717 70909659 70910373 0.000000e+00 846.0
29 TraesCS1B01G092200 chr7B 87.989 716 80 6 4 717 370947271 370946560 0.000000e+00 841.0
30 TraesCS1B01G092200 chr7B 87.639 720 81 8 1 717 737521597 737522311 0.000000e+00 830.0
31 TraesCS1B01G092200 chr7B 87.204 719 86 5 1 717 737217751 737218465 0.000000e+00 813.0
32 TraesCS1B01G092200 chr6A 87.151 716 86 5 4 717 8005528 8004817 0.000000e+00 808.0


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 TraesCS1B01G092200 chr1B 94183917 94187800 3883 True 7173.000000 7173 100.000000 1 3884 1 chr1B.!!$R1 3883
1 TraesCS1B01G092200 chr1B 111936909 111937622 713 False 850.000000 850 88.162000 1 717 1 chr1B.!!$F1 716
2 TraesCS1B01G092200 chr1B 94207594 94208782 1188 True 480.266667 776 92.006333 819 1919 3 chr1B.!!$R3 1100
3 TraesCS1B01G092200 chr1B 94199477 94201894 2417 True 466.125000 846 88.564500 1939 3884 4 chr1B.!!$R2 1945
4 TraesCS1B01G092200 chr1D 58448917 58452052 3135 False 1211.666667 2250 90.400667 872 3884 3 chr1D.!!$F2 3012
5 TraesCS1B01G092200 chr1D 408620936 408621649 713 False 856.000000 856 88.301000 1 717 1 chr1D.!!$F1 716
6 TraesCS1B01G092200 chr1A 57189633 57193007 3374 False 616.133333 1288 88.682333 810 3884 6 chr1A.!!$F1 3074
7 TraesCS1B01G092200 chr1A 57392689 57394998 2309 True 473.980000 843 88.527400 817 2895 5 chr1A.!!$R2 2078
8 TraesCS1B01G092200 chr3D 580982887 580983601 714 False 869.000000 869 88.595000 1 717 1 chr3D.!!$F1 716
9 TraesCS1B01G092200 chr7A 452644165 452644875 710 True 856.000000 856 88.392000 4 717 1 chr7A.!!$R1 713
10 TraesCS1B01G092200 chr4B 70909659 70910373 714 False 846.000000 846 88.022000 1 717 1 chr4B.!!$F1 716
11 TraesCS1B01G092200 chr7B 370946560 370947271 711 True 841.000000 841 87.989000 4 717 1 chr7B.!!$R1 713
12 TraesCS1B01G092200 chr7B 737521597 737522311 714 False 830.000000 830 87.639000 1 717 1 chr7B.!!$F2 716
13 TraesCS1B01G092200 chr7B 737217751 737218465 714 False 813.000000 813 87.204000 1 717 1 chr7B.!!$F1 716
14 TraesCS1B01G092200 chr6A 8004817 8005528 711 True 808.000000 808 87.151000 4 717 1 chr6A.!!$R1 713

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
453 456 0.115745 ACGAGAAGGACCCCCAGTAA 59.884 55.0 0.00 0.0 33.88 2.24 F
578 582 0.319083 ACACCGGCGATGTTAACTGA 59.681 50.0 9.30 0.0 0.00 3.41 F
2324 2559 0.696143 TCTCCCAAGGGGTGTGTGAA 60.696 55.0 5.08 0.0 44.74 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2597 0.248377 GCGCTCATGCAGGTTTCATC 60.248 55.0 0.00 0.0 39.64 2.92 R
2374 2609 0.596083 GCTACATCGACAGCGCTCAT 60.596 55.0 7.13 0.0 37.46 2.90 R
3289 4098 0.674895 AATGCCAGCTTGGAGACGAC 60.675 55.0 6.40 0.0 40.96 4.34 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
36 37 5.889853 AGAAATGCTCAATGCTTCCATCTTA 59.110 36.000 0.00 0.00 43.37 2.10
38 39 6.726490 AATGCTCAATGCTTCCATCTTAAT 57.274 33.333 0.00 0.00 43.37 1.40
50 51 8.370940 TGCTTCCATCTTAATATCAACTAGAGG 58.629 37.037 0.00 0.00 0.00 3.69
75 76 4.658063 ACCTGTCCAAATAATCGTTTCCA 58.342 39.130 0.00 0.00 0.00 3.53
77 78 5.536916 ACCTGTCCAAATAATCGTTTCCAAA 59.463 36.000 0.00 0.00 0.00 3.28
111 112 7.138736 CCACAAACGAACAATCAGTTTCTAAT 58.861 34.615 0.00 0.00 41.51 1.73
126 127 5.829924 AGTTTCTAATATGATGGGCTTGTGG 59.170 40.000 0.00 0.00 0.00 4.17
138 139 2.504175 GGGCTTGTGGAGAGTAATACCA 59.496 50.000 0.00 0.00 0.00 3.25
186 187 1.741401 TTCCGCTTCATCCACGCTG 60.741 57.895 0.00 0.00 0.00 5.18
207 210 4.649088 GTTGCAAACCCCAGTATAATCC 57.351 45.455 0.00 0.00 42.21 3.01
210 213 2.227194 CAAACCCCAGTATAATCCCGC 58.773 52.381 0.00 0.00 0.00 6.13
229 232 4.112634 CCGCGAAGAAATGATCACTTCTA 58.887 43.478 19.01 0.00 38.16 2.10
233 236 5.525378 GCGAAGAAATGATCACTTCTACCAT 59.475 40.000 19.01 4.27 38.16 3.55
260 263 2.441164 GGCAACCACACCCACACA 60.441 61.111 0.00 0.00 0.00 3.72
261 264 2.781158 GGCAACCACACCCACACAC 61.781 63.158 0.00 0.00 0.00 3.82
268 271 1.817941 ACACCCACACACTCGCAAC 60.818 57.895 0.00 0.00 0.00 4.17
276 279 1.067693 CACACTCGCAACGCTAATGA 58.932 50.000 0.00 0.00 0.00 2.57
287 290 3.134574 ACGCTAATGACCTCCACAAAA 57.865 42.857 0.00 0.00 0.00 2.44
288 291 3.482436 ACGCTAATGACCTCCACAAAAA 58.518 40.909 0.00 0.00 0.00 1.94
324 327 5.757850 AATCTTAATGAACTCCGGATTGC 57.242 39.130 3.57 0.00 0.00 3.56
326 329 1.948104 TAATGAACTCCGGATTGCGG 58.052 50.000 10.75 10.75 0.00 5.69
343 346 1.606885 CGGGGCTGCCAATTCACAAT 61.607 55.000 22.05 0.00 0.00 2.71
381 384 5.205056 TCATTGGTACCAATAAACCCATCC 58.795 41.667 34.23 0.00 43.92 3.51
387 390 2.024369 ACCAATAAACCCATCCACCCTC 60.024 50.000 0.00 0.00 0.00 4.30
418 421 4.884668 TTGTTGGTAATCTCCGTCTTCT 57.115 40.909 0.00 0.00 0.00 2.85
432 435 6.153851 TCTCCGTCTTCTTATTGGTATGACAA 59.846 38.462 0.00 0.00 34.41 3.18
453 456 0.115745 ACGAGAAGGACCCCCAGTAA 59.884 55.000 0.00 0.00 33.88 2.24
475 479 9.476202 AGTAATTTTGAATAAACTCACAAAGGC 57.524 29.630 0.00 0.00 34.54 4.35
491 495 5.123027 CACAAAGGCAGAGATAGTTTCCTTC 59.877 44.000 0.00 0.00 33.22 3.46
503 507 4.759793 AGTTTCCTTCCCCTTACCAAAT 57.240 40.909 0.00 0.00 0.00 2.32
516 520 7.062957 CCCCTTACCAAATATCAAGTCATTCT 58.937 38.462 0.00 0.00 0.00 2.40
518 522 8.971073 CCCTTACCAAATATCAAGTCATTCTTT 58.029 33.333 0.00 0.00 33.63 2.52
550 554 7.256404 CCATGCCCTCCAAAACATGAATATAAT 60.256 37.037 0.00 0.00 41.93 1.28
553 557 9.206690 TGCCCTCCAAAACATGAATATAATTTA 57.793 29.630 0.00 0.00 0.00 1.40
578 582 0.319083 ACACCGGCGATGTTAACTGA 59.681 50.000 9.30 0.00 0.00 3.41
613 617 6.749923 AAGTAGCCAATCTAGCTTCAAAAG 57.250 37.500 0.00 0.00 41.83 2.27
616 620 7.796054 AGTAGCCAATCTAGCTTCAAAAGATA 58.204 34.615 0.00 0.00 41.83 1.98
717 721 5.123502 AGAGCATGAAACACACATTCATCTC 59.876 40.000 0.00 14.18 43.72 2.75
718 722 4.763279 AGCATGAAACACACATTCATCTCA 59.237 37.500 0.00 0.00 43.72 3.27
719 723 4.855388 GCATGAAACACACATTCATCTCAC 59.145 41.667 0.00 0.00 43.72 3.51
720 724 5.396484 CATGAAACACACATTCATCTCACC 58.604 41.667 0.00 0.00 43.72 4.02
721 725 4.459330 TGAAACACACATTCATCTCACCA 58.541 39.130 0.00 0.00 32.10 4.17
722 726 4.516321 TGAAACACACATTCATCTCACCAG 59.484 41.667 0.00 0.00 32.10 4.00
723 727 4.356405 AACACACATTCATCTCACCAGA 57.644 40.909 0.00 0.00 0.00 3.86
724 728 3.935315 ACACACATTCATCTCACCAGAG 58.065 45.455 0.00 0.00 43.48 3.35
725 729 2.676839 CACACATTCATCTCACCAGAGC 59.323 50.000 0.00 0.00 41.81 4.09
726 730 2.303890 ACACATTCATCTCACCAGAGCA 59.696 45.455 0.00 0.00 41.81 4.26
727 731 2.937149 CACATTCATCTCACCAGAGCAG 59.063 50.000 0.00 0.00 41.81 4.24
728 732 2.570752 ACATTCATCTCACCAGAGCAGT 59.429 45.455 0.00 0.00 41.81 4.40
729 733 3.196463 CATTCATCTCACCAGAGCAGTC 58.804 50.000 0.00 0.00 41.81 3.51
730 734 2.228545 TCATCTCACCAGAGCAGTCT 57.771 50.000 0.00 0.00 41.81 3.24
744 748 3.375782 GCAGTCTGCTTTTGGACAATT 57.624 42.857 17.89 0.00 40.96 2.32
745 749 3.721035 GCAGTCTGCTTTTGGACAATTT 58.279 40.909 17.89 0.00 40.96 1.82
746 750 3.492011 GCAGTCTGCTTTTGGACAATTTG 59.508 43.478 17.89 0.00 40.96 2.32
747 751 4.685924 CAGTCTGCTTTTGGACAATTTGT 58.314 39.130 0.63 0.63 35.18 2.83
748 752 5.111293 CAGTCTGCTTTTGGACAATTTGTT 58.889 37.500 3.08 0.00 35.18 2.83
749 753 5.232838 CAGTCTGCTTTTGGACAATTTGTTC 59.767 40.000 3.08 1.75 35.18 3.18
750 754 5.105392 AGTCTGCTTTTGGACAATTTGTTCA 60.105 36.000 6.41 6.41 33.18 3.18
751 755 5.754890 GTCTGCTTTTGGACAATTTGTTCAT 59.245 36.000 11.27 0.00 35.46 2.57
752 756 6.258507 GTCTGCTTTTGGACAATTTGTTCATT 59.741 34.615 11.27 0.00 35.46 2.57
753 757 6.822676 TCTGCTTTTGGACAATTTGTTCATTT 59.177 30.769 11.27 0.00 35.46 2.32
754 758 7.984050 TCTGCTTTTGGACAATTTGTTCATTTA 59.016 29.630 11.27 0.00 35.46 1.40
755 759 8.140677 TGCTTTTGGACAATTTGTTCATTTAG 57.859 30.769 11.27 9.74 35.46 1.85
756 760 7.226325 TGCTTTTGGACAATTTGTTCATTTAGG 59.774 33.333 11.27 2.96 35.46 2.69
757 761 7.307930 GCTTTTGGACAATTTGTTCATTTAGGG 60.308 37.037 11.27 1.67 35.46 3.53
758 762 6.739331 TTGGACAATTTGTTCATTTAGGGT 57.261 33.333 11.27 0.00 35.46 4.34
759 763 6.739331 TGGACAATTTGTTCATTTAGGGTT 57.261 33.333 6.41 0.00 29.19 4.11
760 764 7.130681 TGGACAATTTGTTCATTTAGGGTTT 57.869 32.000 6.41 0.00 29.19 3.27
761 765 7.569240 TGGACAATTTGTTCATTTAGGGTTTT 58.431 30.769 6.41 0.00 29.19 2.43
762 766 8.049721 TGGACAATTTGTTCATTTAGGGTTTTT 58.950 29.630 6.41 0.00 29.19 1.94
763 767 8.341903 GGACAATTTGTTCATTTAGGGTTTTTG 58.658 33.333 3.08 0.00 0.00 2.44
764 768 8.219546 ACAATTTGTTCATTTAGGGTTTTTGG 57.780 30.769 0.00 0.00 0.00 3.28
765 769 8.049721 ACAATTTGTTCATTTAGGGTTTTTGGA 58.950 29.630 0.00 0.00 0.00 3.53
766 770 8.341903 CAATTTGTTCATTTAGGGTTTTTGGAC 58.658 33.333 0.00 0.00 0.00 4.02
767 771 6.546428 TTGTTCATTTAGGGTTTTTGGACA 57.454 33.333 0.00 0.00 0.00 4.02
768 772 6.546428 TGTTCATTTAGGGTTTTTGGACAA 57.454 33.333 0.00 0.00 0.00 3.18
769 773 7.130681 TGTTCATTTAGGGTTTTTGGACAAT 57.869 32.000 0.00 0.00 0.00 2.71
770 774 7.569240 TGTTCATTTAGGGTTTTTGGACAATT 58.431 30.769 0.00 0.00 0.00 2.32
771 775 7.713073 TGTTCATTTAGGGTTTTTGGACAATTC 59.287 33.333 0.00 0.00 0.00 2.17
772 776 6.451393 TCATTTAGGGTTTTTGGACAATTCG 58.549 36.000 0.00 0.00 0.00 3.34
773 777 4.857509 TTAGGGTTTTTGGACAATTCGG 57.142 40.909 0.00 0.00 0.00 4.30
774 778 2.673258 AGGGTTTTTGGACAATTCGGT 58.327 42.857 0.00 0.00 0.00 4.69
775 779 2.364002 AGGGTTTTTGGACAATTCGGTG 59.636 45.455 0.00 0.00 0.00 4.94
776 780 2.131972 GGTTTTTGGACAATTCGGTGC 58.868 47.619 0.00 0.00 0.00 5.01
777 781 2.223947 GGTTTTTGGACAATTCGGTGCT 60.224 45.455 0.00 0.00 0.00 4.40
778 782 3.453424 GTTTTTGGACAATTCGGTGCTT 58.547 40.909 0.00 0.00 0.00 3.91
779 783 3.810310 TTTTGGACAATTCGGTGCTTT 57.190 38.095 0.00 0.00 0.00 3.51
780 784 3.810310 TTTGGACAATTCGGTGCTTTT 57.190 38.095 0.00 0.00 0.00 2.27
781 785 3.810310 TTGGACAATTCGGTGCTTTTT 57.190 38.095 0.00 0.00 0.00 1.94
802 806 2.798976 TTGAGCTGTCAATTTGGTGC 57.201 45.000 0.00 0.00 37.79 5.01
803 807 1.985473 TGAGCTGTCAATTTGGTGCT 58.015 45.000 0.00 10.00 0.00 4.40
804 808 3.138884 TGAGCTGTCAATTTGGTGCTA 57.861 42.857 0.00 1.11 0.00 3.49
805 809 3.076621 TGAGCTGTCAATTTGGTGCTAG 58.923 45.455 0.00 0.00 0.00 3.42
806 810 3.077359 GAGCTGTCAATTTGGTGCTAGT 58.923 45.455 0.00 0.00 0.00 2.57
807 811 3.077359 AGCTGTCAATTTGGTGCTAGTC 58.923 45.455 8.96 0.00 0.00 2.59
808 812 3.077359 GCTGTCAATTTGGTGCTAGTCT 58.923 45.455 0.00 0.00 0.00 3.24
809 813 3.126000 GCTGTCAATTTGGTGCTAGTCTC 59.874 47.826 0.00 0.00 0.00 3.36
810 814 4.573900 CTGTCAATTTGGTGCTAGTCTCT 58.426 43.478 0.00 0.00 0.00 3.10
811 815 4.318332 TGTCAATTTGGTGCTAGTCTCTG 58.682 43.478 0.00 0.00 0.00 3.35
812 816 4.202357 TGTCAATTTGGTGCTAGTCTCTGT 60.202 41.667 0.00 0.00 0.00 3.41
813 817 4.757149 GTCAATTTGGTGCTAGTCTCTGTT 59.243 41.667 0.00 0.00 0.00 3.16
814 818 5.239525 GTCAATTTGGTGCTAGTCTCTGTTT 59.760 40.000 0.00 0.00 0.00 2.83
815 819 5.470098 TCAATTTGGTGCTAGTCTCTGTTTC 59.530 40.000 0.00 0.00 0.00 2.78
847 852 1.618343 CGATTTCTTGGGCCAAAAGGT 59.382 47.619 21.28 7.00 0.00 3.50
850 855 4.618227 CGATTTCTTGGGCCAAAAGGTTAG 60.618 45.833 21.28 6.61 0.00 2.34
938 991 2.584608 GGCTATCCACCACGCACT 59.415 61.111 0.00 0.00 0.00 4.40
939 992 1.815421 GGCTATCCACCACGCACTG 60.815 63.158 0.00 0.00 0.00 3.66
1029 1097 2.680352 ACCACGAGCCGTCTCCAT 60.680 61.111 0.00 0.00 38.32 3.41
1382 1455 2.158445 GGCTACCTATCTCCTCTCCACA 60.158 54.545 0.00 0.00 0.00 4.17
1428 1502 5.578336 TGCCGATATGAAATGATTCTCGATC 59.422 40.000 0.00 0.00 34.48 3.69
1494 1577 6.073873 GCTAATCTGAACCTCAATTCTCGATG 60.074 42.308 0.00 0.00 0.00 3.84
1501 1590 4.012374 ACCTCAATTCTCGATGCAACATT 58.988 39.130 0.00 0.00 0.00 2.71
1507 1596 6.583427 TCAATTCTCGATGCAACATTTTTCAG 59.417 34.615 0.00 0.00 0.00 3.02
1536 1683 2.097466 ACTGCTGTTGTGCTTGTTACAC 59.903 45.455 0.00 0.00 38.55 2.90
1540 1696 1.403679 TGTTGTGCTTGTTACACCTGC 59.596 47.619 0.00 0.00 37.22 4.85
1548 1704 4.083537 TGCTTGTTACACCTGCTAATTTCG 60.084 41.667 5.94 0.00 0.00 3.46
1733 1889 3.189287 CACCTCTTCTGCCATGTTTACAC 59.811 47.826 0.00 0.00 0.00 2.90
1781 1942 7.600231 TTGATCTCTGCATCTCTTCTCTTAT 57.400 36.000 0.00 0.00 0.00 1.73
1796 1957 7.272978 TCTTCTCTTATAAATTTCAGGTCCGG 58.727 38.462 0.00 0.00 0.00 5.14
1806 1967 1.000019 CAGGTCCGGGTACTCCAGA 60.000 63.158 0.00 0.00 34.36 3.86
1872 2033 3.331478 CACCAATTGCTAATGGCCAAA 57.669 42.857 10.96 0.00 40.51 3.28
1919 2080 7.715657 AGTTCATTGCAAGTCAGACATTTTAA 58.284 30.769 4.94 0.00 0.00 1.52
1927 2088 5.982890 AGTCAGACATTTTAACCATTGGG 57.017 39.130 7.78 0.00 41.29 4.12
1952 2161 5.419542 TGCAGAATTAACTTAGCGTGATCT 58.580 37.500 0.00 0.00 0.00 2.75
1953 2162 6.569780 TGCAGAATTAACTTAGCGTGATCTA 58.430 36.000 0.00 0.00 0.00 1.98
1973 2182 9.877178 TGATCTATGGTCTTCTTTTTCTTACTC 57.123 33.333 0.00 0.00 0.00 2.59
2025 2234 2.953821 CGCTTTCGTGCCAATGGT 59.046 55.556 0.00 0.00 0.00 3.55
2064 2273 2.159627 GTGAATTCTGTAACACTGCCCG 59.840 50.000 7.05 0.00 0.00 6.13
2313 2543 5.192927 TGCAATACCTTTATGTCTCCCAAG 58.807 41.667 0.00 0.00 0.00 3.61
2314 2544 4.580580 GCAATACCTTTATGTCTCCCAAGG 59.419 45.833 0.00 0.00 41.52 3.61
2315 2545 5.133221 CAATACCTTTATGTCTCCCAAGGG 58.867 45.833 0.00 0.00 40.27 3.95
2316 2546 1.923148 ACCTTTATGTCTCCCAAGGGG 59.077 52.381 5.08 0.00 46.11 4.79
2317 2547 1.923148 CCTTTATGTCTCCCAAGGGGT 59.077 52.381 5.08 0.00 44.74 4.95
2324 2559 0.696143 TCTCCCAAGGGGTGTGTGAA 60.696 55.000 5.08 0.00 44.74 3.18
2332 2567 4.526262 CCAAGGGGTGTGTGAAATCAATTA 59.474 41.667 0.00 0.00 0.00 1.40
2359 2594 9.905713 AGCAAACTGGAATTGTATAATCTTCTA 57.094 29.630 0.00 0.00 0.00 2.10
2360 2595 9.937175 GCAAACTGGAATTGTATAATCTTCTAC 57.063 33.333 0.00 0.00 0.00 2.59
2374 2609 4.890158 TCTTCTACTGATGAAACCTGCA 57.110 40.909 0.00 0.00 0.00 4.41
2380 2615 1.063616 CTGATGAAACCTGCATGAGCG 59.936 52.381 0.00 0.00 46.23 5.03
2381 2616 0.248377 GATGAAACCTGCATGAGCGC 60.248 55.000 0.00 0.00 46.23 5.92
2391 2626 0.871592 GCATGAGCGCTGTCGATGTA 60.872 55.000 18.48 0.00 38.10 2.29
2392 2627 1.126890 CATGAGCGCTGTCGATGTAG 58.873 55.000 18.48 0.00 38.10 2.74
2397 2632 1.056103 GCGCTGTCGATGTAGCATAG 58.944 55.000 16.14 4.88 39.87 2.23
2398 2633 1.056103 CGCTGTCGATGTAGCATAGC 58.944 55.000 16.14 0.00 39.87 2.97
2402 2637 3.304257 CTGTCGATGTAGCATAGCTGTC 58.696 50.000 0.00 0.00 40.10 3.51
2403 2638 2.687935 TGTCGATGTAGCATAGCTGTCA 59.312 45.455 0.00 1.87 40.10 3.58
2404 2639 3.130340 TGTCGATGTAGCATAGCTGTCAA 59.870 43.478 0.00 0.00 40.10 3.18
2405 2640 4.202151 TGTCGATGTAGCATAGCTGTCAAT 60.202 41.667 0.00 0.00 40.10 2.57
2406 2641 4.384247 GTCGATGTAGCATAGCTGTCAATC 59.616 45.833 0.00 0.00 40.10 2.67
2423 2658 7.699812 GCTGTCAATCAATAGATCTTGAAAACC 59.300 37.037 0.00 0.00 38.55 3.27
2453 2688 2.373169 TCAGCCAAACTTGACCAGATCT 59.627 45.455 0.00 0.00 0.00 2.75
2454 2689 2.486982 CAGCCAAACTTGACCAGATCTG 59.513 50.000 16.24 16.24 0.00 2.90
2485 2720 3.826157 TGCTCCTTGAATGGTTAGGTTTG 59.174 43.478 0.00 0.00 0.00 2.93
2491 2726 5.716703 CCTTGAATGGTTAGGTTTGAATCCT 59.283 40.000 0.00 0.00 38.91 3.24
2494 2729 2.432444 TGGTTAGGTTTGAATCCTGCG 58.568 47.619 5.08 0.00 36.60 5.18
2505 2740 0.678048 AATCCTGCGTTGGAGCTTCC 60.678 55.000 4.95 0.00 39.78 3.46
2512 2747 0.237498 CGTTGGAGCTTCCGGAAAAC 59.763 55.000 19.39 17.19 40.17 2.43
2513 2748 0.596577 GTTGGAGCTTCCGGAAAACC 59.403 55.000 19.39 19.92 40.17 3.27
2515 2750 0.476771 TGGAGCTTCCGGAAAACCTT 59.523 50.000 19.39 1.80 40.17 3.50
2517 2752 2.307686 TGGAGCTTCCGGAAAACCTTAT 59.692 45.455 19.39 0.00 40.17 1.73
2518 2753 2.943690 GGAGCTTCCGGAAAACCTTATC 59.056 50.000 19.39 8.11 0.00 1.75
2519 2754 3.370633 GGAGCTTCCGGAAAACCTTATCT 60.371 47.826 19.39 5.15 0.00 1.98
2521 2756 2.943690 GCTTCCGGAAAACCTTATCTCC 59.056 50.000 19.39 0.00 0.00 3.71
2522 2757 3.370633 GCTTCCGGAAAACCTTATCTCCT 60.371 47.826 19.39 0.00 0.00 3.69
2529 2764 6.412214 CGGAAAACCTTATCTCCTTTCCTTA 58.588 40.000 9.51 0.00 41.84 2.69
2543 2778 7.017254 TCTCCTTTCCTTAGCCTAAAAGAGAAA 59.983 37.037 0.00 0.00 31.81 2.52
2583 2860 0.327924 TCAAGGATCACATGGGCGTT 59.672 50.000 0.00 0.00 0.00 4.84
2592 2869 1.665679 CACATGGGCGTTGATCTGTAC 59.334 52.381 0.00 0.00 0.00 2.90
2601 2878 2.205074 GTTGATCTGTACATGGAGCCG 58.795 52.381 0.00 0.00 0.00 5.52
2616 2893 4.000988 TGGAGCCGAATTTTGAAGACTAC 58.999 43.478 0.00 0.00 0.00 2.73
2629 2906 1.479709 AGACTACAGCTGCCAGGTAG 58.520 55.000 15.27 17.07 40.19 3.18
2632 2909 2.432510 GACTACAGCTGCCAGGTAGAAT 59.567 50.000 22.46 8.04 38.26 2.40
2646 2933 6.515696 GCCAGGTAGAATAAATTCAGGAATGC 60.516 42.308 5.55 0.00 39.23 3.56
2648 2935 7.232127 CCAGGTAGAATAAATTCAGGAATGCAT 59.768 37.037 0.00 0.00 39.23 3.96
2649 2936 8.080417 CAGGTAGAATAAATTCAGGAATGCATG 58.920 37.037 0.00 0.00 39.23 4.06
2651 2938 9.066892 GGTAGAATAAATTCAGGAATGCATGTA 57.933 33.333 0.00 0.00 39.23 2.29
2672 2960 9.740239 CATGTATTGCTATGCTAAAACAGAAAT 57.260 29.630 0.00 0.00 0.00 2.17
2673 2961 9.956720 ATGTATTGCTATGCTAAAACAGAAATC 57.043 29.630 0.00 0.00 0.00 2.17
2674 2962 9.177608 TGTATTGCTATGCTAAAACAGAAATCT 57.822 29.630 0.00 0.00 0.00 2.40
2675 2963 9.657121 GTATTGCTATGCTAAAACAGAAATCTC 57.343 33.333 0.00 0.00 0.00 2.75
2676 2964 6.349973 TGCTATGCTAAAACAGAAATCTCG 57.650 37.500 0.00 0.00 0.00 4.04
2677 2965 5.201181 GCTATGCTAAAACAGAAATCTCGC 58.799 41.667 0.00 0.00 0.00 5.03
2679 2967 2.415168 TGCTAAAACAGAAATCTCGCGG 59.585 45.455 6.13 0.00 0.00 6.46
2680 2968 2.223044 GCTAAAACAGAAATCTCGCGGG 60.223 50.000 6.13 1.01 0.00 6.13
2681 2969 0.521735 AAAACAGAAATCTCGCGGGC 59.478 50.000 6.13 0.00 0.00 6.13
2703 2994 4.662145 CATGCTCGTGTTTATCCCTTTTC 58.338 43.478 0.00 0.00 0.00 2.29
2704 2995 3.745799 TGCTCGTGTTTATCCCTTTTCA 58.254 40.909 0.00 0.00 0.00 2.69
2726 3032 2.992543 CAACCAAATGCCACCAATAACG 59.007 45.455 0.00 0.00 0.00 3.18
2730 3037 2.859538 CAAATGCCACCAATAACGATGC 59.140 45.455 0.00 0.00 0.00 3.91
2736 3043 2.009051 CACCAATAACGATGCTGCTCA 58.991 47.619 0.00 0.00 0.00 4.26
2791 3098 4.643387 ACACCGACAAGGCCCTGC 62.643 66.667 0.00 0.00 46.52 4.85
2793 3100 3.884774 ACCGACAAGGCCCTGCAA 61.885 61.111 0.00 0.00 46.52 4.08
2811 3118 2.242043 CAAGAACCCTGCTTGGACATT 58.758 47.619 0.00 0.00 39.18 2.71
2915 3222 3.932710 TCTGAAAGGACGCACATGATAAC 59.067 43.478 0.00 0.00 0.00 1.89
2926 3237 7.011828 ACGCACATGATAACTAAAATGGTAC 57.988 36.000 0.00 0.00 0.00 3.34
2979 3562 1.078143 CTGCTTCACCTGGGGCTAC 60.078 63.158 0.00 0.00 0.00 3.58
3049 3663 6.098679 CCTAGCTGAACTGTATAGCATGATC 58.901 44.000 15.60 0.00 39.84 2.92
3146 3767 5.078411 AGTTGAATCTCGTATTGTCTGCT 57.922 39.130 0.00 0.00 0.00 4.24
3175 3911 2.874086 GCAAAGCAAAGAATTGGCACTT 59.126 40.909 0.00 0.00 37.02 3.16
3176 3912 3.059393 GCAAAGCAAAGAATTGGCACTTC 60.059 43.478 9.36 9.36 37.02 3.01
3177 3913 3.391506 AAGCAAAGAATTGGCACTTCC 57.608 42.857 13.27 0.00 37.02 3.46
3178 3914 1.620323 AGCAAAGAATTGGCACTTCCC 59.380 47.619 13.27 1.57 37.02 3.97
3179 3915 1.620323 GCAAAGAATTGGCACTTCCCT 59.380 47.619 13.27 0.00 37.02 4.20
3180 3916 2.611224 GCAAAGAATTGGCACTTCCCTG 60.611 50.000 13.27 11.64 37.02 4.45
3191 3927 2.341257 CACTTCCCTGATGTTCTGTCG 58.659 52.381 0.00 0.00 0.00 4.35
3269 4078 4.080638 AGGGATCCTGTTCTCAGATTTGTC 60.081 45.833 12.58 0.00 43.76 3.18
3289 4098 0.926155 CTTGCGTGTCCATCTCATCG 59.074 55.000 0.00 0.00 0.00 3.84
3312 4133 0.986527 TCTCCAAGCTGGCATTCTGA 59.013 50.000 0.00 0.00 37.47 3.27
3314 4135 0.694771 TCCAAGCTGGCATTCTGAGT 59.305 50.000 0.00 0.00 37.47 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.735354 GCATTGAGCATTTCTAGGTTGATGG 60.735 44.000 0.00 0.00 44.79 3.51
36 37 5.836358 GGACAGGTCTCCTCTAGTTGATATT 59.164 44.000 0.00 0.00 0.00 1.28
38 39 4.229812 TGGACAGGTCTCCTCTAGTTGATA 59.770 45.833 0.00 0.00 0.00 2.15
48 49 3.775316 ACGATTATTTGGACAGGTCTCCT 59.225 43.478 0.00 0.00 0.00 3.69
50 51 5.064834 GGAAACGATTATTTGGACAGGTCTC 59.935 44.000 0.00 0.00 0.00 3.36
77 78 1.407618 GTTCGTTTGTGGCCTCCTTTT 59.592 47.619 3.32 0.00 0.00 2.27
84 85 1.336755 ACTGATTGTTCGTTTGTGGCC 59.663 47.619 0.00 0.00 0.00 5.36
93 94 8.285394 CCCATCATATTAGAAACTGATTGTTCG 58.715 37.037 0.00 0.00 38.03 3.95
111 112 2.481441 ACTCTCCACAAGCCCATCATA 58.519 47.619 0.00 0.00 0.00 2.15
126 127 6.592870 AGGGCTTTACATTGGTATTACTCTC 58.407 40.000 0.00 0.00 0.00 3.20
159 160 2.159028 GGATGAAGCGGAACTTAGAGCT 60.159 50.000 0.00 0.00 39.29 4.09
186 187 3.383505 GGGATTATACTGGGGTTTGCAAC 59.616 47.826 0.00 0.00 0.00 4.17
199 200 5.637810 TGATCATTTCTTCGCGGGATTATAC 59.362 40.000 6.13 0.00 0.00 1.47
207 210 2.932614 AGAAGTGATCATTTCTTCGCGG 59.067 45.455 23.59 0.00 41.36 6.46
210 213 8.706936 CATATGGTAGAAGTGATCATTTCTTCG 58.293 37.037 30.97 13.96 41.36 3.79
260 263 0.246635 AGGTCATTAGCGTTGCGAGT 59.753 50.000 0.00 0.00 0.00 4.18
261 264 0.924090 GAGGTCATTAGCGTTGCGAG 59.076 55.000 0.00 0.00 0.00 5.03
268 271 4.701956 ATTTTTGTGGAGGTCATTAGCG 57.298 40.909 0.00 0.00 0.00 4.26
276 279 4.141756 TGTTGATGCAATTTTTGTGGAGGT 60.142 37.500 0.00 0.00 0.00 3.85
324 327 1.606885 ATTGTGAATTGGCAGCCCCG 61.607 55.000 9.64 0.00 35.87 5.73
326 329 2.477845 AAATTGTGAATTGGCAGCCC 57.522 45.000 9.64 0.00 0.00 5.19
355 358 6.537453 TGGGTTTATTGGTACCAATGATTG 57.463 37.500 38.99 0.00 45.15 2.67
356 359 6.326323 GGATGGGTTTATTGGTACCAATGATT 59.674 38.462 38.99 23.15 45.15 2.57
357 360 5.838521 GGATGGGTTTATTGGTACCAATGAT 59.161 40.000 38.99 23.48 45.15 2.45
361 364 4.345854 GTGGATGGGTTTATTGGTACCAA 58.654 43.478 28.95 28.95 40.47 3.67
367 370 2.244769 AGAGGGTGGATGGGTTTATTGG 59.755 50.000 0.00 0.00 0.00 3.16
370 373 2.136026 GGAGAGGGTGGATGGGTTTAT 58.864 52.381 0.00 0.00 0.00 1.40
371 374 1.082194 AGGAGAGGGTGGATGGGTTTA 59.918 52.381 0.00 0.00 0.00 2.01
381 384 3.412386 CAACAAAGGTAAGGAGAGGGTG 58.588 50.000 0.00 0.00 0.00 4.61
407 410 5.655090 TGTCATACCAATAAGAAGACGGAGA 59.345 40.000 0.00 0.00 0.00 3.71
412 415 7.033791 TCGTCTTGTCATACCAATAAGAAGAC 58.966 38.462 0.00 0.00 33.27 3.01
418 421 6.153851 TCCTTCTCGTCTTGTCATACCAATAA 59.846 38.462 0.00 0.00 0.00 1.40
432 435 1.305381 CTGGGGGTCCTTCTCGTCT 60.305 63.158 0.00 0.00 0.00 4.18
453 456 7.725251 TCTGCCTTTGTGAGTTTATTCAAAAT 58.275 30.769 0.00 0.00 31.07 1.82
475 479 5.163290 GGTAAGGGGAAGGAAACTATCTCTG 60.163 48.000 0.00 0.00 42.68 3.35
491 495 7.062957 AGAATGACTTGATATTTGGTAAGGGG 58.937 38.462 0.00 0.00 0.00 4.79
550 554 0.319083 ATCGCCGGTGTGTGAGTAAA 59.681 50.000 16.01 0.00 0.00 2.01
553 557 2.048222 CATCGCCGGTGTGTGAGT 60.048 61.111 16.01 0.00 0.00 3.41
559 563 0.319083 TCAGTTAACATCGCCGGTGT 59.681 50.000 16.01 0.00 0.00 4.16
616 620 8.592809 GGAACTTACCAGATGATGAGATATTCT 58.407 37.037 0.00 0.00 0.00 2.40
644 648 0.391966 GTATGGCGGTAAGGGAGGTC 59.608 60.000 0.00 0.00 0.00 3.85
671 675 1.296715 GAGATGTCCCAAGGCGTGT 59.703 57.895 0.00 0.00 0.00 4.49
724 728 3.375782 AATTGTCCAAAAGCAGACTGC 57.624 42.857 20.12 20.12 45.46 4.40
725 729 4.685924 ACAAATTGTCCAAAAGCAGACTG 58.314 39.130 0.00 0.00 34.02 3.51
726 730 5.105392 TGAACAAATTGTCCAAAAGCAGACT 60.105 36.000 0.00 0.00 34.02 3.24
727 731 5.108517 TGAACAAATTGTCCAAAAGCAGAC 58.891 37.500 0.00 0.00 0.00 3.51
728 732 5.336150 TGAACAAATTGTCCAAAAGCAGA 57.664 34.783 0.00 0.00 0.00 4.26
729 733 6.607735 AATGAACAAATTGTCCAAAAGCAG 57.392 33.333 0.00 0.00 0.00 4.24
730 734 6.998968 AAATGAACAAATTGTCCAAAAGCA 57.001 29.167 0.00 0.00 0.00 3.91
731 735 7.307930 CCCTAAATGAACAAATTGTCCAAAAGC 60.308 37.037 0.00 0.00 0.00 3.51
732 736 7.714813 ACCCTAAATGAACAAATTGTCCAAAAG 59.285 33.333 0.00 0.00 0.00 2.27
733 737 7.569240 ACCCTAAATGAACAAATTGTCCAAAA 58.431 30.769 0.00 0.00 0.00 2.44
734 738 7.130681 ACCCTAAATGAACAAATTGTCCAAA 57.869 32.000 0.00 0.00 0.00 3.28
735 739 6.739331 ACCCTAAATGAACAAATTGTCCAA 57.261 33.333 0.00 0.00 0.00 3.53
736 740 6.739331 AACCCTAAATGAACAAATTGTCCA 57.261 33.333 0.00 0.00 0.00 4.02
737 741 8.341903 CAAAAACCCTAAATGAACAAATTGTCC 58.658 33.333 0.00 0.00 0.00 4.02
738 742 8.341903 CCAAAAACCCTAAATGAACAAATTGTC 58.658 33.333 0.00 0.00 0.00 3.18
739 743 8.049721 TCCAAAAACCCTAAATGAACAAATTGT 58.950 29.630 0.00 0.00 0.00 2.71
740 744 8.341903 GTCCAAAAACCCTAAATGAACAAATTG 58.658 33.333 0.00 0.00 0.00 2.32
741 745 8.049721 TGTCCAAAAACCCTAAATGAACAAATT 58.950 29.630 0.00 0.00 0.00 1.82
742 746 7.569240 TGTCCAAAAACCCTAAATGAACAAAT 58.431 30.769 0.00 0.00 0.00 2.32
743 747 6.947464 TGTCCAAAAACCCTAAATGAACAAA 58.053 32.000 0.00 0.00 0.00 2.83
744 748 6.546428 TGTCCAAAAACCCTAAATGAACAA 57.454 33.333 0.00 0.00 0.00 2.83
745 749 6.546428 TTGTCCAAAAACCCTAAATGAACA 57.454 33.333 0.00 0.00 0.00 3.18
746 750 7.095816 CGAATTGTCCAAAAACCCTAAATGAAC 60.096 37.037 0.00 0.00 0.00 3.18
747 751 6.926272 CGAATTGTCCAAAAACCCTAAATGAA 59.074 34.615 0.00 0.00 0.00 2.57
748 752 6.451393 CGAATTGTCCAAAAACCCTAAATGA 58.549 36.000 0.00 0.00 0.00 2.57
749 753 5.637387 CCGAATTGTCCAAAAACCCTAAATG 59.363 40.000 0.00 0.00 0.00 2.32
750 754 5.305902 ACCGAATTGTCCAAAAACCCTAAAT 59.694 36.000 0.00 0.00 0.00 1.40
751 755 4.650131 ACCGAATTGTCCAAAAACCCTAAA 59.350 37.500 0.00 0.00 0.00 1.85
752 756 4.038162 CACCGAATTGTCCAAAAACCCTAA 59.962 41.667 0.00 0.00 0.00 2.69
753 757 3.570550 CACCGAATTGTCCAAAAACCCTA 59.429 43.478 0.00 0.00 0.00 3.53
754 758 2.364002 CACCGAATTGTCCAAAAACCCT 59.636 45.455 0.00 0.00 0.00 4.34
755 759 2.749776 CACCGAATTGTCCAAAAACCC 58.250 47.619 0.00 0.00 0.00 4.11
756 760 2.131972 GCACCGAATTGTCCAAAAACC 58.868 47.619 0.00 0.00 0.00 3.27
757 761 3.092334 AGCACCGAATTGTCCAAAAAC 57.908 42.857 0.00 0.00 0.00 2.43
758 762 3.810310 AAGCACCGAATTGTCCAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
759 763 3.810310 AAAGCACCGAATTGTCCAAAA 57.190 38.095 0.00 0.00 0.00 2.44
760 764 3.810310 AAAAGCACCGAATTGTCCAAA 57.190 38.095 0.00 0.00 0.00 3.28
761 765 3.810310 AAAAAGCACCGAATTGTCCAA 57.190 38.095 0.00 0.00 0.00 3.53
780 784 3.870419 GCACCAAATTGACAGCTCAAAAA 59.130 39.130 0.00 0.00 39.90 1.94
781 785 3.132646 AGCACCAAATTGACAGCTCAAAA 59.867 39.130 0.00 0.00 39.90 2.44
782 786 2.694628 AGCACCAAATTGACAGCTCAAA 59.305 40.909 0.00 0.00 39.90 2.69
783 787 2.309613 AGCACCAAATTGACAGCTCAA 58.690 42.857 0.00 0.00 40.77 3.02
784 788 1.985473 AGCACCAAATTGACAGCTCA 58.015 45.000 0.00 0.00 0.00 4.26
785 789 3.077359 ACTAGCACCAAATTGACAGCTC 58.923 45.455 9.32 0.00 33.83 4.09
786 790 3.077359 GACTAGCACCAAATTGACAGCT 58.923 45.455 10.48 10.48 36.20 4.24
787 791 3.077359 AGACTAGCACCAAATTGACAGC 58.923 45.455 0.00 0.00 0.00 4.40
788 792 4.391216 CAGAGACTAGCACCAAATTGACAG 59.609 45.833 0.00 0.00 0.00 3.51
789 793 4.202357 ACAGAGACTAGCACCAAATTGACA 60.202 41.667 0.00 0.00 0.00 3.58
790 794 4.319177 ACAGAGACTAGCACCAAATTGAC 58.681 43.478 0.00 0.00 0.00 3.18
791 795 4.623932 ACAGAGACTAGCACCAAATTGA 57.376 40.909 0.00 0.00 0.00 2.57
792 796 5.335191 GGAAACAGAGACTAGCACCAAATTG 60.335 44.000 0.00 0.00 0.00 2.32
793 797 4.762251 GGAAACAGAGACTAGCACCAAATT 59.238 41.667 0.00 0.00 0.00 1.82
794 798 4.042187 AGGAAACAGAGACTAGCACCAAAT 59.958 41.667 0.00 0.00 0.00 2.32
795 799 3.391296 AGGAAACAGAGACTAGCACCAAA 59.609 43.478 0.00 0.00 0.00 3.28
796 800 2.972713 AGGAAACAGAGACTAGCACCAA 59.027 45.455 0.00 0.00 0.00 3.67
797 801 2.609747 AGGAAACAGAGACTAGCACCA 58.390 47.619 0.00 0.00 0.00 4.17
798 802 3.686916 AAGGAAACAGAGACTAGCACC 57.313 47.619 0.00 0.00 0.00 5.01
799 803 3.748568 CCAAAGGAAACAGAGACTAGCAC 59.251 47.826 0.00 0.00 0.00 4.40
800 804 3.807209 GCCAAAGGAAACAGAGACTAGCA 60.807 47.826 0.00 0.00 0.00 3.49
801 805 2.744741 GCCAAAGGAAACAGAGACTAGC 59.255 50.000 0.00 0.00 0.00 3.42
802 806 2.996621 CGCCAAAGGAAACAGAGACTAG 59.003 50.000 0.00 0.00 0.00 2.57
803 807 2.289444 CCGCCAAAGGAAACAGAGACTA 60.289 50.000 0.00 0.00 0.00 2.59
804 808 1.543429 CCGCCAAAGGAAACAGAGACT 60.543 52.381 0.00 0.00 0.00 3.24
805 809 0.875059 CCGCCAAAGGAAACAGAGAC 59.125 55.000 0.00 0.00 0.00 3.36
806 810 0.762418 TCCGCCAAAGGAAACAGAGA 59.238 50.000 0.00 0.00 37.36 3.10
807 811 1.740025 GATCCGCCAAAGGAAACAGAG 59.260 52.381 0.00 0.00 44.50 3.35
808 812 1.821216 GATCCGCCAAAGGAAACAGA 58.179 50.000 0.00 0.00 44.50 3.41
809 813 0.447801 CGATCCGCCAAAGGAAACAG 59.552 55.000 0.00 0.00 44.50 3.16
810 814 0.035598 TCGATCCGCCAAAGGAAACA 59.964 50.000 0.00 0.00 44.50 2.83
811 815 1.379527 ATCGATCCGCCAAAGGAAAC 58.620 50.000 0.00 0.00 44.50 2.78
812 816 2.122783 AATCGATCCGCCAAAGGAAA 57.877 45.000 0.00 0.00 44.50 3.13
813 817 2.014128 GAAATCGATCCGCCAAAGGAA 58.986 47.619 0.00 0.00 44.50 3.36
814 818 1.209504 AGAAATCGATCCGCCAAAGGA 59.790 47.619 0.00 0.00 45.54 3.36
815 819 1.668419 AGAAATCGATCCGCCAAAGG 58.332 50.000 0.00 0.00 0.00 3.11
939 992 1.098712 TTGGCCTGTGACAAACCGTC 61.099 55.000 3.32 0.00 45.61 4.79
1070 1138 2.683933 GGGCTGAGGAGGACGGAA 60.684 66.667 0.00 0.00 0.00 4.30
1283 1351 0.382515 CGGAAGAAGGCGAGTAGGAG 59.617 60.000 0.00 0.00 0.00 3.69
1288 1356 4.083862 GCCCGGAAGAAGGCGAGT 62.084 66.667 0.73 0.00 39.87 4.18
1382 1455 5.006941 GCACTGAACAAAAATCACTTGCATT 59.993 36.000 0.00 0.00 33.71 3.56
1428 1502 0.321564 TTCTGCAGTCAACCCCATCG 60.322 55.000 14.67 0.00 0.00 3.84
1494 1577 6.892310 AGTGAAAGAACTGAAAAATGTTGC 57.108 33.333 0.00 0.00 0.00 4.17
1507 1596 2.098117 AGCACAACAGCAGTGAAAGAAC 59.902 45.455 0.00 0.00 39.30 3.01
1536 1683 4.025061 CAGAGAATGAGCGAAATTAGCAGG 60.025 45.833 0.27 0.00 37.01 4.85
1540 1696 6.531594 TGTGTACAGAGAATGAGCGAAATTAG 59.468 38.462 0.00 0.00 0.00 1.73
1548 1704 3.999663 AGCTTTGTGTACAGAGAATGAGC 59.000 43.478 6.73 1.41 30.38 4.26
1758 1919 8.703378 TTATAAGAGAAGAGATGCAGAGATCA 57.297 34.615 0.00 0.00 0.00 2.92
1781 1942 3.198417 GGAGTACCCGGACCTGAAATTTA 59.802 47.826 0.73 0.00 0.00 1.40
1796 1957 1.275573 GGGAACAGTGTCTGGAGTACC 59.724 57.143 0.00 0.00 35.51 3.34
1872 2033 3.138839 TCACCTACCATCATGGATGCAAT 59.861 43.478 11.90 0.00 40.96 3.56
1919 2080 2.497273 GTTAATTCTGCAGCCCAATGGT 59.503 45.455 9.47 0.00 0.00 3.55
1927 2088 3.370978 TCACGCTAAGTTAATTCTGCAGC 59.629 43.478 9.47 0.00 0.00 5.25
1952 2161 7.663827 TCACGAGTAAGAAAAAGAAGACCATA 58.336 34.615 0.00 0.00 0.00 2.74
1953 2162 6.522054 TCACGAGTAAGAAAAAGAAGACCAT 58.478 36.000 0.00 0.00 0.00 3.55
2025 2234 1.887854 CACTGAACATGTGCCCATCAA 59.112 47.619 0.00 0.00 0.00 2.57
2064 2273 2.480419 CACTTGACAACGACTTCCCATC 59.520 50.000 0.00 0.00 0.00 3.51
2313 2543 4.021544 TGCTTAATTGATTTCACACACCCC 60.022 41.667 0.00 0.00 0.00 4.95
2314 2544 5.132897 TGCTTAATTGATTTCACACACCC 57.867 39.130 0.00 0.00 0.00 4.61
2315 2545 6.701400 AGTTTGCTTAATTGATTTCACACACC 59.299 34.615 0.00 0.00 0.00 4.16
2316 2546 7.306749 CCAGTTTGCTTAATTGATTTCACACAC 60.307 37.037 0.00 0.00 0.00 3.82
2317 2547 6.700960 CCAGTTTGCTTAATTGATTTCACACA 59.299 34.615 0.00 0.00 0.00 3.72
2332 2567 9.247861 AGAAGATTATACAATTCCAGTTTGCTT 57.752 29.630 0.00 0.00 0.00 3.91
2356 2591 4.763073 CTCATGCAGGTTTCATCAGTAGA 58.237 43.478 0.00 0.00 0.00 2.59
2359 2594 2.089980 GCTCATGCAGGTTTCATCAGT 58.910 47.619 0.00 0.00 39.41 3.41
2360 2595 1.063616 CGCTCATGCAGGTTTCATCAG 59.936 52.381 0.00 0.00 39.64 2.90
2361 2596 1.089112 CGCTCATGCAGGTTTCATCA 58.911 50.000 0.00 0.00 39.64 3.07
2362 2597 0.248377 GCGCTCATGCAGGTTTCATC 60.248 55.000 0.00 0.00 39.64 2.92
2363 2598 0.679002 AGCGCTCATGCAGGTTTCAT 60.679 50.000 2.64 0.00 39.64 2.57
2374 2609 0.596083 GCTACATCGACAGCGCTCAT 60.596 55.000 7.13 0.00 37.46 2.90
2380 2615 2.057316 CAGCTATGCTACATCGACAGC 58.943 52.381 8.22 8.22 36.40 4.40
2381 2616 3.243201 TGACAGCTATGCTACATCGACAG 60.243 47.826 0.00 0.00 36.40 3.51
2391 2626 7.006865 AGATCTATTGATTGACAGCTATGCT 57.993 36.000 0.00 0.00 33.94 3.79
2392 2627 7.387122 TCAAGATCTATTGATTGACAGCTATGC 59.613 37.037 0.00 0.00 34.31 3.14
2397 2632 7.699812 GGTTTTCAAGATCTATTGATTGACAGC 59.300 37.037 0.00 0.00 38.90 4.40
2398 2633 8.954350 AGGTTTTCAAGATCTATTGATTGACAG 58.046 33.333 0.00 0.00 38.90 3.51
2429 2664 0.843309 TGGTCAAGTTTGGCTGAGGA 59.157 50.000 0.00 0.00 32.28 3.71
2430 2665 1.202806 TCTGGTCAAGTTTGGCTGAGG 60.203 52.381 0.00 0.00 32.28 3.86
2432 2667 2.373169 AGATCTGGTCAAGTTTGGCTGA 59.627 45.455 0.00 0.00 32.28 4.26
2434 2669 2.553904 CCAGATCTGGTCAAGTTTGGCT 60.554 50.000 30.55 0.00 45.53 4.75
2435 2670 1.815003 CCAGATCTGGTCAAGTTTGGC 59.185 52.381 30.55 0.00 45.53 4.52
2458 2693 2.957402 ACCATTCAAGGAGCACTTCA 57.043 45.000 0.00 0.00 37.29 3.02
2462 2697 3.073274 ACCTAACCATTCAAGGAGCAC 57.927 47.619 0.00 0.00 34.34 4.40
2485 2720 0.729690 GAAGCTCCAACGCAGGATTC 59.270 55.000 0.00 0.00 36.99 2.52
2491 2726 2.668185 TTTCCGGAAGCTCCAACGCA 62.668 55.000 17.97 0.00 35.91 5.24
2494 2729 0.596577 GGTTTTCCGGAAGCTCCAAC 59.403 55.000 17.97 17.33 35.91 3.77
2512 2747 6.749036 TTAGGCTAAGGAAAGGAGATAAGG 57.251 41.667 2.04 0.00 0.00 2.69
2513 2748 8.487028 TCTTTTAGGCTAAGGAAAGGAGATAAG 58.513 37.037 14.19 8.31 31.69 1.73
2515 2750 7.844779 TCTCTTTTAGGCTAAGGAAAGGAGATA 59.155 37.037 14.67 0.00 39.18 1.98
2517 2752 6.023603 TCTCTTTTAGGCTAAGGAAAGGAGA 58.976 40.000 14.67 14.67 40.75 3.71
2518 2753 6.301169 TCTCTTTTAGGCTAAGGAAAGGAG 57.699 41.667 14.19 12.80 37.53 3.69
2519 2754 6.697641 TTCTCTTTTAGGCTAAGGAAAGGA 57.302 37.500 14.19 9.35 31.69 3.36
2559 2836 2.424956 GCCCATGTGATCCTTGAAGAAC 59.575 50.000 0.00 0.00 0.00 3.01
2583 2860 1.775385 TCGGCTCCATGTACAGATCA 58.225 50.000 0.33 0.00 0.00 2.92
2592 2869 3.441572 AGTCTTCAAAATTCGGCTCCATG 59.558 43.478 0.00 0.00 0.00 3.66
2601 2878 4.216257 TGGCAGCTGTAGTCTTCAAAATTC 59.784 41.667 16.64 0.00 0.00 2.17
2616 2893 4.883585 TGAATTTATTCTACCTGGCAGCTG 59.116 41.667 10.11 10.11 37.67 4.24
2646 2933 9.740239 ATTTCTGTTTTAGCATAGCAATACATG 57.260 29.630 0.00 0.00 0.00 3.21
2648 2935 9.177608 AGATTTCTGTTTTAGCATAGCAATACA 57.822 29.630 0.00 0.00 0.00 2.29
2649 2936 9.657121 GAGATTTCTGTTTTAGCATAGCAATAC 57.343 33.333 0.00 0.00 0.00 1.89
2651 2938 7.412853 CGAGATTTCTGTTTTAGCATAGCAAT 58.587 34.615 0.00 0.00 0.00 3.56
2665 2953 1.091771 CATGCCCGCGAGATTTCTGT 61.092 55.000 8.23 0.00 0.00 3.41
2668 2956 2.110734 GAGCATGCCCGCGAGATTTC 62.111 60.000 15.66 0.00 36.85 2.17
2671 2959 4.957684 CGAGCATGCCCGCGAGAT 62.958 66.667 15.66 0.00 36.85 2.75
2676 2964 1.714899 ATAAACACGAGCATGCCCGC 61.715 55.000 22.32 7.13 0.00 6.13
2677 2965 0.304705 GATAAACACGAGCATGCCCG 59.695 55.000 20.79 20.79 0.00 6.13
2679 2967 0.663153 GGGATAAACACGAGCATGCC 59.337 55.000 15.66 4.99 0.00 4.40
2680 2968 1.668419 AGGGATAAACACGAGCATGC 58.332 50.000 10.51 10.51 0.00 4.06
2681 2969 4.155826 TGAAAAGGGATAAACACGAGCATG 59.844 41.667 0.00 0.00 0.00 4.06
2690 2978 6.073276 GCATTTGGTTGTGAAAAGGGATAAAC 60.073 38.462 0.00 0.00 0.00 2.01
2703 2994 2.547299 ATTGGTGGCATTTGGTTGTG 57.453 45.000 0.00 0.00 0.00 3.33
2704 2995 3.553922 CGTTATTGGTGGCATTTGGTTGT 60.554 43.478 0.00 0.00 0.00 3.32
2736 3043 3.491447 GCACTCCAAAGTTGAACTGCAAT 60.491 43.478 0.00 0.00 39.03 3.56
2791 3098 1.915141 ATGTCCAAGCAGGGTTCTTG 58.085 50.000 0.00 0.00 40.31 3.02
2793 3100 2.242043 CAAATGTCCAAGCAGGGTTCT 58.758 47.619 0.00 0.00 38.24 3.01
2811 3118 2.623718 CGTCTCGCGTTTGTGCAA 59.376 55.556 5.77 0.00 35.54 4.08
2926 3237 8.068380 CCATTGCTGCATCATATCTAATATTCG 58.932 37.037 1.84 0.00 0.00 3.34
2933 3244 3.754850 GCACCATTGCTGCATCATATCTA 59.245 43.478 1.84 0.00 46.17 1.98
2934 3245 2.557056 GCACCATTGCTGCATCATATCT 59.443 45.455 1.84 0.00 46.17 1.98
2935 3246 2.942710 GCACCATTGCTGCATCATATC 58.057 47.619 1.84 0.00 46.17 1.63
2979 3562 7.042187 GCATACAAATCCATCTTCAGTCTAGTG 60.042 40.741 0.00 0.00 0.00 2.74
3049 3663 0.097499 CATGTGGCGTGTATGTGCAG 59.903 55.000 0.00 0.00 0.00 4.41
3146 3767 5.523188 CCAATTCTTTGCTTTGCTTGTACAA 59.477 36.000 8.28 8.28 0.00 2.41
3175 3911 1.924731 AGACGACAGAACATCAGGGA 58.075 50.000 0.00 0.00 0.00 4.20
3176 3912 2.751166 AAGACGACAGAACATCAGGG 57.249 50.000 0.00 0.00 0.00 4.45
3177 3913 4.500837 CGATAAAGACGACAGAACATCAGG 59.499 45.833 0.00 0.00 0.00 3.86
3178 3914 4.027295 GCGATAAAGACGACAGAACATCAG 60.027 45.833 0.00 0.00 0.00 2.90
3179 3915 3.857665 GCGATAAAGACGACAGAACATCA 59.142 43.478 0.00 0.00 0.00 3.07
3180 3916 4.027295 CAGCGATAAAGACGACAGAACATC 60.027 45.833 0.00 0.00 0.00 3.06
3191 3927 1.588861 GCTTCCGTCAGCGATAAAGAC 59.411 52.381 0.00 0.00 41.33 3.01
3269 4078 1.293924 GATGAGATGGACACGCAAGG 58.706 55.000 0.00 0.00 46.39 3.61
3289 4098 0.674895 AATGCCAGCTTGGAGACGAC 60.675 55.000 6.40 0.00 40.96 4.34
3312 4133 5.184892 AGTGGCAGAATGGAATCTAAACT 57.815 39.130 0.00 0.00 35.86 2.66
3314 4135 8.439971 ACATATAGTGGCAGAATGGAATCTAAA 58.560 33.333 0.00 0.00 35.86 1.85
3787 4625 1.515954 CTCCCCGACGTACATTGCT 59.484 57.895 0.00 0.00 0.00 3.91
3813 4651 1.062886 ACTCATCAGGGGGAATCTCGA 60.063 52.381 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.