Multiple sequence alignment - TraesCS7A01G053600

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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 TraesCS7A01G053600 chr7A 100.000 3651 0 0 1 3651 26025472 26029122 0.000000e+00 6743.0
1 TraesCS7A01G053600 chr7D 90.205 1562 104 12 1993 3528 25186699 25188237 0.000000e+00 1991.0
2 TraesCS7A01G053600 chr7D 96.644 1043 29 3 915 1953 25185582 25186622 0.000000e+00 1727.0
3 TraesCS7A01G053600 chr7D 87.021 678 34 22 2 661 25184718 25185359 0.000000e+00 715.0
4 TraesCS7A01G053600 chr7D 91.045 134 10 2 765 896 465477927 465477794 2.900000e-41 180.0
5 TraesCS7A01G053600 chr7D 90.244 123 9 2 3531 3651 25188166 25188287 1.360000e-34 158.0
6 TraesCS7A01G053600 chr7D 95.122 41 1 1 451 491 51551036 51550997 3.040000e-06 63.9
7 TraesCS7A01G053600 chrUn 94.904 1040 44 4 956 1987 327953157 327954195 0.000000e+00 1618.0
8 TraesCS7A01G053600 chrUn 94.808 1040 45 4 956 1987 326025942 326026980 0.000000e+00 1613.0
9 TraesCS7A01G053600 chrUn 95.346 967 45 0 1985 2951 326027054 326028020 0.000000e+00 1537.0
10 TraesCS7A01G053600 chrUn 95.346 967 45 0 1985 2951 327954269 327955235 0.000000e+00 1537.0
11 TraesCS7A01G053600 chrUn 95.346 967 45 0 1985 2951 339887747 339888713 0.000000e+00 1537.0
12 TraesCS7A01G053600 chrUn 95.140 967 47 0 1985 2951 349956177 349957143 0.000000e+00 1526.0
13 TraesCS7A01G053600 chrUn 96.500 800 28 0 2155 2954 387894895 387894096 0.000000e+00 1323.0
14 TraesCS7A01G053600 chrUn 95.611 638 28 0 1350 1987 339887036 339887673 0.000000e+00 1024.0
15 TraesCS7A01G053600 chrUn 95.174 373 18 0 1615 1987 349955731 349956103 1.130000e-164 590.0
16 TraesCS7A01G053600 chrUn 89.844 128 6 2 3531 3651 326028386 326028513 1.360000e-34 158.0
17 TraesCS7A01G053600 chrUn 89.844 128 6 2 3531 3651 327955601 327955728 1.360000e-34 158.0
18 TraesCS7A01G053600 chrUn 89.844 128 6 2 3531 3651 339889079 339889206 1.360000e-34 158.0
19 TraesCS7A01G053600 chrUn 89.844 128 6 2 3531 3651 349957509 349957636 1.360000e-34 158.0
20 TraesCS7A01G053600 chrUn 89.844 128 6 2 3531 3651 387893733 387893606 1.360000e-34 158.0
21 TraesCS7A01G053600 chr7B 92.424 132 10 0 765 896 490208132 490208001 4.810000e-44 189.0
22 TraesCS7A01G053600 chr7B 91.852 135 11 0 762 896 734071487 734071621 4.810000e-44 189.0
23 TraesCS7A01G053600 chr7B 86.885 122 15 1 659 780 198397111 198397231 6.360000e-28 135.0
24 TraesCS7A01G053600 chr7B 86.066 122 16 1 659 780 195946746 195946866 2.960000e-26 130.0
25 TraesCS7A01G053600 chr5B 90.370 135 13 0 762 896 313151812 313151946 1.040000e-40 178.0
26 TraesCS7A01G053600 chr5B 89.855 138 13 1 759 895 510535665 510535528 3.750000e-40 176.0
27 TraesCS7A01G053600 chr5B 85.593 118 17 0 663 780 392204730 392204847 1.380000e-24 124.0
28 TraesCS7A01G053600 chr1A 90.909 132 12 0 765 896 21328415 21328546 1.040000e-40 178.0
29 TraesCS7A01G053600 chr2D 90.909 132 11 1 765 896 296364190 296364060 3.750000e-40 176.0
30 TraesCS7A01G053600 chr2B 90.370 135 12 1 762 896 366017535 366017668 3.750000e-40 176.0
31 TraesCS7A01G053600 chr2B 84.615 117 15 3 652 766 701670391 701670506 2.980000e-21 113.0
32 TraesCS7A01G053600 chr2B 76.440 191 35 7 406 593 178315525 178315708 1.080000e-15 95.3
33 TraesCS7A01G053600 chr5D 89.130 138 15 0 759 896 299406162 299406025 4.850000e-39 172.0
34 TraesCS7A01G053600 chr5D 88.298 94 11 0 682 775 162216100 162216007 2.980000e-21 113.0
35 TraesCS7A01G053600 chr5D 89.583 48 2 2 526 570 308022778 308022731 1.420000e-04 58.4
36 TraesCS7A01G053600 chr1B 86.325 117 14 2 652 766 266640213 266640097 3.830000e-25 126.0
37 TraesCS7A01G053600 chr4B 85.246 122 16 2 659 780 500419563 500419682 1.380000e-24 124.0
38 TraesCS7A01G053600 chr4D 84.483 116 16 2 653 766 446720538 446720653 2.980000e-21 113.0
39 TraesCS7A01G053600 chr4D 79.279 111 12 9 504 606 2970981 2971088 2.350000e-07 67.6
40 TraesCS7A01G053600 chr3D 84.483 116 16 2 653 766 38473025 38473140 2.980000e-21 113.0
41 TraesCS7A01G053600 chr1D 75.194 258 40 15 403 646 443416370 443416617 2.320000e-17 100.0
42 TraesCS7A01G053600 chr4A 80.769 130 17 5 468 593 513345104 513344979 1.080000e-15 95.3
43 TraesCS7A01G053600 chr3B 84.043 94 7 4 468 559 122012827 122012740 2.340000e-12 84.2
44 TraesCS7A01G053600 chr3B 81.651 109 10 8 453 559 122081696 122081596 8.400000e-12 82.4
45 TraesCS7A01G053600 chr6A 81.443 97 11 7 465 559 2945352 2945261 5.060000e-09 73.1
46 TraesCS7A01G053600 chr6A 80.682 88 14 2 489 576 17771622 17771706 8.460000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G053600 chr7A 26025472 26029122 3650 False 6743.000000 6743 100.000000 1 3651 1 chr7A.!!$F1 3650
1 TraesCS7A01G053600 chr7D 25184718 25188287 3569 False 1147.750000 1991 91.028500 2 3651 4 chr7D.!!$F1 3649
2 TraesCS7A01G053600 chrUn 327953157 327955728 2571 False 1104.333333 1618 93.364667 956 3651 3 chrUn.!!$F2 2695
3 TraesCS7A01G053600 chrUn 326025942 326028513 2571 False 1102.666667 1613 93.332667 956 3651 3 chrUn.!!$F1 2695
4 TraesCS7A01G053600 chrUn 339887036 339889206 2170 False 906.333333 1537 93.600333 1350 3651 3 chrUn.!!$F3 2301
5 TraesCS7A01G053600 chrUn 349955731 349957636 1905 False 758.000000 1526 93.386000 1615 3651 3 chrUn.!!$F4 2036
6 TraesCS7A01G053600 chrUn 387893606 387894895 1289 True 740.500000 1323 93.172000 2155 3651 2 chrUn.!!$R1 1496

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
946 1024 1.211949 GCTGGGCCCTGTTCACTTATA 59.788 52.381 27.68 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2852 3015 0.31179 AACAAGTGCAGCATCAACGG 59.688 50.0 0.0 0.0 0.0 4.44 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.480981 CAGGATGTTCATTTTTGCTCTTGTTT 59.519 34.615 0.00 0.00 0.00 2.83
117 118 5.835819 TCCTTAGAGAGAGAGAGAGAGAGAG 59.164 48.000 0.00 0.00 0.00 3.20
127 128 4.534500 AGAGAGAGAGAGAGAGTTGTGGTA 59.466 45.833 0.00 0.00 0.00 3.25
141 142 3.926058 TGTGGTATTCTCTTAAGGGCC 57.074 47.619 1.85 0.00 0.00 5.80
153 154 4.196971 TCTTAAGGGCCTATTTTCTTCGC 58.803 43.478 6.41 0.00 0.00 4.70
154 155 2.507407 AAGGGCCTATTTTCTTCGCA 57.493 45.000 6.41 0.00 0.00 5.10
208 226 2.430332 CGACATTATTTGGCCAACCCAT 59.570 45.455 20.35 12.26 44.89 4.00
223 241 2.187958 ACCCATTACTGTAGCTGAGCA 58.812 47.619 7.39 0.00 0.00 4.26
229 247 2.847327 ACTGTAGCTGAGCATGTGTT 57.153 45.000 7.39 0.00 0.00 3.32
316 334 6.299922 TGGTTTTCTTTGGGTTTTCTTGTTT 58.700 32.000 0.00 0.00 0.00 2.83
317 335 6.428465 TGGTTTTCTTTGGGTTTTCTTGTTTC 59.572 34.615 0.00 0.00 0.00 2.78
322 340 8.684386 TTCTTTGGGTTTTCTTGTTTCTTTTT 57.316 26.923 0.00 0.00 0.00 1.94
323 341 8.317891 TCTTTGGGTTTTCTTGTTTCTTTTTC 57.682 30.769 0.00 0.00 0.00 2.29
324 342 8.154203 TCTTTGGGTTTTCTTGTTTCTTTTTCT 58.846 29.630 0.00 0.00 0.00 2.52
325 343 8.684386 TTTGGGTTTTCTTGTTTCTTTTTCTT 57.316 26.923 0.00 0.00 0.00 2.52
326 344 8.684386 TTGGGTTTTCTTGTTTCTTTTTCTTT 57.316 26.923 0.00 0.00 0.00 2.52
327 345 8.684386 TGGGTTTTCTTGTTTCTTTTTCTTTT 57.316 26.923 0.00 0.00 0.00 2.27
328 346 9.126151 TGGGTTTTCTTGTTTCTTTTTCTTTTT 57.874 25.926 0.00 0.00 0.00 1.94
365 383 4.935205 GGTTTTCTTTGTGCTTTTCTTGGT 59.065 37.500 0.00 0.00 0.00 3.67
608 627 6.450845 AATACATGTGTTGACATTTTTGCG 57.549 33.333 9.11 0.00 41.12 4.85
610 629 4.428209 ACATGTGTTGACATTTTTGCGAA 58.572 34.783 0.00 0.00 41.12 4.70
611 630 5.049167 ACATGTGTTGACATTTTTGCGAAT 58.951 33.333 0.00 0.00 41.12 3.34
612 631 6.212235 ACATGTGTTGACATTTTTGCGAATA 58.788 32.000 0.00 0.00 41.12 1.75
613 632 6.143758 ACATGTGTTGACATTTTTGCGAATAC 59.856 34.615 0.00 0.00 41.12 1.89
614 633 4.672862 TGTGTTGACATTTTTGCGAATACG 59.327 37.500 0.00 0.00 42.93 3.06
615 634 4.673311 GTGTTGACATTTTTGCGAATACGT 59.327 37.500 0.00 0.00 41.98 3.57
616 635 4.672862 TGTTGACATTTTTGCGAATACGTG 59.327 37.500 0.00 0.00 41.98 4.49
617 636 4.475763 TGACATTTTTGCGAATACGTGT 57.524 36.364 0.00 0.00 41.98 4.49
618 637 4.849883 TGACATTTTTGCGAATACGTGTT 58.150 34.783 0.00 0.00 41.98 3.32
672 691 8.562892 TCGACTTATTTTATAGTACTCCTTCCG 58.437 37.037 0.00 0.00 0.00 4.30
673 692 8.348507 CGACTTATTTTATAGTACTCCTTCCGT 58.651 37.037 0.00 0.00 0.00 4.69
693 712 5.126707 TCCGTTTCTAAATACTCCCTCTGTC 59.873 44.000 0.00 0.00 0.00 3.51
695 714 5.672503 GTTTCTAAATACTCCCTCTGTCCC 58.327 45.833 0.00 0.00 0.00 4.46
696 715 4.620086 TCTAAATACTCCCTCTGTCCCA 57.380 45.455 0.00 0.00 0.00 4.37
697 716 5.157770 TCTAAATACTCCCTCTGTCCCAT 57.842 43.478 0.00 0.00 0.00 4.00
698 717 6.289482 TCTAAATACTCCCTCTGTCCCATA 57.711 41.667 0.00 0.00 0.00 2.74
699 718 6.689561 TCTAAATACTCCCTCTGTCCCATAA 58.310 40.000 0.00 0.00 0.00 1.90
700 719 7.313731 TCTAAATACTCCCTCTGTCCCATAAT 58.686 38.462 0.00 0.00 0.00 1.28
701 720 8.461854 TCTAAATACTCCCTCTGTCCCATAATA 58.538 37.037 0.00 0.00 0.00 0.98
702 721 9.273137 CTAAATACTCCCTCTGTCCCATAATAT 57.727 37.037 0.00 0.00 0.00 1.28
704 723 8.846423 AATACTCCCTCTGTCCCATAATATAG 57.154 38.462 0.00 0.00 0.00 1.31
705 724 5.594777 ACTCCCTCTGTCCCATAATATAGG 58.405 45.833 0.00 0.00 0.00 2.57
706 725 5.318889 ACTCCCTCTGTCCCATAATATAGGA 59.681 44.000 0.00 0.00 0.00 2.94
707 726 5.843469 TCCCTCTGTCCCATAATATAGGAG 58.157 45.833 0.00 0.00 0.00 3.69
708 727 4.407296 CCCTCTGTCCCATAATATAGGAGC 59.593 50.000 0.00 0.00 0.00 4.70
709 728 4.098654 CCTCTGTCCCATAATATAGGAGCG 59.901 50.000 0.00 0.00 0.00 5.03
710 729 4.673968 TCTGTCCCATAATATAGGAGCGT 58.326 43.478 0.00 0.00 0.00 5.07
711 730 5.084519 TCTGTCCCATAATATAGGAGCGTT 58.915 41.667 0.00 0.00 0.00 4.84
712 731 5.542635 TCTGTCCCATAATATAGGAGCGTTT 59.457 40.000 0.00 0.00 0.00 3.60
713 732 6.042781 TCTGTCCCATAATATAGGAGCGTTTT 59.957 38.462 0.00 0.00 0.00 2.43
714 733 6.597562 TGTCCCATAATATAGGAGCGTTTTT 58.402 36.000 0.00 0.00 0.00 1.94
715 734 6.485313 TGTCCCATAATATAGGAGCGTTTTTG 59.515 38.462 0.00 0.00 0.00 2.44
716 735 6.708949 GTCCCATAATATAGGAGCGTTTTTGA 59.291 38.462 0.00 0.00 0.00 2.69
717 736 7.390718 GTCCCATAATATAGGAGCGTTTTTGAT 59.609 37.037 0.00 0.00 0.00 2.57
718 737 8.598916 TCCCATAATATAGGAGCGTTTTTGATA 58.401 33.333 0.00 0.00 0.00 2.15
719 738 8.665685 CCCATAATATAGGAGCGTTTTTGATAC 58.334 37.037 0.00 0.00 0.00 2.24
720 739 9.436957 CCATAATATAGGAGCGTTTTTGATACT 57.563 33.333 0.00 0.00 0.00 2.12
728 747 8.235359 AGGAGCGTTTTTGATACTATACTAGT 57.765 34.615 0.00 0.00 42.68 2.57
729 748 8.136165 AGGAGCGTTTTTGATACTATACTAGTG 58.864 37.037 5.39 0.00 39.81 2.74
730 749 7.096147 GGAGCGTTTTTGATACTATACTAGTGC 60.096 40.741 5.39 0.00 39.81 4.40
731 750 6.700520 AGCGTTTTTGATACTATACTAGTGCC 59.299 38.462 5.39 0.00 39.81 5.01
732 751 6.477688 GCGTTTTTGATACTATACTAGTGCCA 59.522 38.462 5.39 0.00 39.81 4.92
733 752 7.010738 GCGTTTTTGATACTATACTAGTGCCAA 59.989 37.037 5.39 0.00 39.81 4.52
734 753 8.875803 CGTTTTTGATACTATACTAGTGCCAAA 58.124 33.333 5.39 2.97 39.81 3.28
738 757 7.997107 TGATACTATACTAGTGCCAAAAACG 57.003 36.000 5.39 0.00 39.81 3.60
739 758 7.549839 TGATACTATACTAGTGCCAAAAACGT 58.450 34.615 5.39 0.00 39.81 3.99
740 759 8.036575 TGATACTATACTAGTGCCAAAAACGTT 58.963 33.333 5.39 0.00 39.81 3.99
741 760 6.716898 ACTATACTAGTGCCAAAAACGTTC 57.283 37.500 5.39 0.00 37.69 3.95
742 761 6.461640 ACTATACTAGTGCCAAAAACGTTCT 58.538 36.000 5.39 0.00 37.69 3.01
743 762 6.932960 ACTATACTAGTGCCAAAAACGTTCTT 59.067 34.615 5.39 0.00 37.69 2.52
744 763 8.090214 ACTATACTAGTGCCAAAAACGTTCTTA 58.910 33.333 5.39 0.00 37.69 2.10
745 764 7.916914 ATACTAGTGCCAAAAACGTTCTTAT 57.083 32.000 5.39 0.00 0.00 1.73
747 766 7.916914 ACTAGTGCCAAAAACGTTCTTATAT 57.083 32.000 0.00 0.00 0.00 0.86
748 767 8.331730 ACTAGTGCCAAAAACGTTCTTATATT 57.668 30.769 0.00 0.00 0.00 1.28
749 768 9.439500 ACTAGTGCCAAAAACGTTCTTATATTA 57.561 29.630 0.00 0.00 0.00 0.98
752 771 8.188139 AGTGCCAAAAACGTTCTTATATTATGG 58.812 33.333 0.00 3.63 0.00 2.74
753 772 7.434013 GTGCCAAAAACGTTCTTATATTATGGG 59.566 37.037 0.00 0.00 0.00 4.00
754 773 7.339721 TGCCAAAAACGTTCTTATATTATGGGA 59.660 33.333 0.00 1.11 0.00 4.37
755 774 7.646526 GCCAAAAACGTTCTTATATTATGGGAC 59.353 37.037 0.00 0.00 0.00 4.46
775 794 7.064229 TGGGACAAAGGAAGTATAAGTGTTTT 58.936 34.615 0.00 0.00 31.92 2.43
815 835 3.871594 ACTACATACGGAGCAAAATGAGC 59.128 43.478 0.00 0.00 0.00 4.26
825 845 4.260538 GGAGCAAAATGAGCGAATCTACAG 60.261 45.833 0.00 0.00 37.01 2.74
832 852 8.443160 CAAAATGAGCGAATCTACAGTCTAAAA 58.557 33.333 0.00 0.00 0.00 1.52
874 896 4.996788 TGTAGTCCTTACCGAAATCTCC 57.003 45.455 0.00 0.00 0.00 3.71
876 898 4.401519 TGTAGTCCTTACCGAAATCTCCAG 59.598 45.833 0.00 0.00 0.00 3.86
882 904 4.870991 CCTTACCGAAATCTCCAGAAAGAC 59.129 45.833 0.00 0.00 0.00 3.01
883 905 5.337652 CCTTACCGAAATCTCCAGAAAGACT 60.338 44.000 0.00 0.00 0.00 3.24
884 906 4.625607 ACCGAAATCTCCAGAAAGACTT 57.374 40.909 0.00 0.00 0.00 3.01
946 1024 1.211949 GCTGGGCCCTGTTCACTTATA 59.788 52.381 27.68 0.00 0.00 0.98
947 1025 2.158608 GCTGGGCCCTGTTCACTTATAT 60.159 50.000 27.68 0.00 0.00 0.86
1020 1100 0.902984 TGGAGGAAGTGAAGCGGCTA 60.903 55.000 1.35 0.00 0.00 3.93
1261 1344 1.273552 CCTTCACCTTCCTCCTCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
1638 1724 2.042831 GGTGCAGCCGAATGAGCTT 61.043 57.895 4.03 0.00 38.95 3.74
1689 1775 2.037847 GTTGGGGCCATGGAGCTT 59.962 61.111 18.40 0.00 0.00 3.74
1710 1796 1.062044 GGGAGGAAGGTGGAGGAGTAT 60.062 57.143 0.00 0.00 0.00 2.12
1791 1877 1.180456 CCAAGTGTGGCAGCATCCAA 61.180 55.000 0.00 0.00 38.35 3.53
1819 1905 0.681243 GCAGGTGTTTCAGGGGATCC 60.681 60.000 1.92 1.92 0.00 3.36
1915 2001 3.005791 ACTTGCCTTGTTCCATAAGTTGC 59.994 43.478 0.00 0.00 0.00 4.17
1965 2051 9.826574 TGTATTTTACTCCTATATTTTCGCACT 57.173 29.630 0.00 0.00 0.00 4.40
1969 2055 9.656040 TTTTACTCCTATATTTTCGCACTAACA 57.344 29.630 0.00 0.00 0.00 2.41
1972 2058 7.272978 ACTCCTATATTTTCGCACTAACACAT 58.727 34.615 0.00 0.00 0.00 3.21
1981 2067 4.314961 TCGCACTAACACATCATCACTTT 58.685 39.130 0.00 0.00 0.00 2.66
1994 2156 2.346766 TCACTTTCTTGCCTTGCTCA 57.653 45.000 0.00 0.00 0.00 4.26
1997 2159 3.254166 TCACTTTCTTGCCTTGCTCATTC 59.746 43.478 0.00 0.00 0.00 2.67
2002 2164 1.743958 CTTGCCTTGCTCATTCCTCAG 59.256 52.381 0.00 0.00 0.00 3.35
2015 2177 4.042062 TCATTCCTCAGTGTGGAACTTGAT 59.958 41.667 25.04 9.49 45.10 2.57
2116 2278 1.177401 GAGGTTTGGTGGATGAAGGC 58.823 55.000 0.00 0.00 0.00 4.35
2134 2296 1.996191 GGCAAGCTACTCTTCAACTCG 59.004 52.381 0.00 0.00 31.27 4.18
2140 2302 3.764434 AGCTACTCTTCAACTCGATGGAA 59.236 43.478 0.00 0.00 0.00 3.53
2143 2305 2.300152 ACTCTTCAACTCGATGGAAGCA 59.700 45.455 13.16 5.19 38.29 3.91
2215 2377 3.075005 GGGCGTGCTGGTCTCCTA 61.075 66.667 0.00 0.00 0.00 2.94
2238 2400 7.547370 CCTAAATGAAGCCTACAGTATGATAGC 59.453 40.741 0.00 0.00 39.69 2.97
2261 2423 2.976490 ATGCCAGTGGAGCCTGACC 61.976 63.158 15.20 0.00 34.23 4.02
2324 2486 3.177487 GGAAACGTAGAACTAGCGGAAG 58.823 50.000 0.00 0.00 0.00 3.46
2325 2487 3.366781 GGAAACGTAGAACTAGCGGAAGT 60.367 47.826 0.00 0.00 0.00 3.01
2639 2801 3.494398 GGAACAGCTGTTTCTGTCACCTA 60.494 47.826 31.58 0.00 45.77 3.08
2709 2871 1.838112 TCTGTGATTGCCCATGAACC 58.162 50.000 0.00 0.00 0.00 3.62
2789 2952 4.491676 CAACAGAAGGAATGCCAAATCAG 58.508 43.478 0.00 0.00 36.29 2.90
2816 2979 1.000896 GTAGCACCACCTGGGCATT 60.001 57.895 0.00 0.00 42.05 3.56
2852 3015 6.275335 TCTTGCTGCTATAAATCAAAATGGC 58.725 36.000 0.00 0.00 0.00 4.40
2857 3020 5.347342 TGCTATAAATCAAAATGGCCGTTG 58.653 37.500 11.94 9.14 0.00 4.10
2864 3027 0.390209 AAAATGGCCGTTGATGCTGC 60.390 50.000 11.94 0.00 0.00 5.25
2865 3028 1.534336 AAATGGCCGTTGATGCTGCA 61.534 50.000 11.94 4.13 0.00 4.41
2870 3033 1.951510 CCGTTGATGCTGCACTTGT 59.048 52.632 3.57 0.00 0.00 3.16
2888 3051 6.243551 CACTTGTTATTAAGATGCACAGACG 58.756 40.000 0.00 0.00 0.00 4.18
2942 3105 5.249622 TCAAGATACATCCCAACAAGGTACA 59.750 40.000 0.00 0.00 34.66 2.90
2951 3114 7.122650 ACATCCCAACAAGGTACATTTATTCTG 59.877 37.037 0.00 0.00 34.66 3.02
2973 3136 7.505258 TCTGGAATAATGAAATCCACATACGA 58.495 34.615 0.00 0.00 38.30 3.43
2981 3144 5.977635 TGAAATCCACATACGAGAACTGAT 58.022 37.500 0.00 0.00 0.00 2.90
2986 3149 6.073327 TCCACATACGAGAACTGATATGAC 57.927 41.667 0.00 0.00 0.00 3.06
3000 3163 7.545362 ACTGATATGACAAGTAAATGAGCAC 57.455 36.000 0.00 0.00 0.00 4.40
3017 3180 5.470368 TGAGCACAGAGTACAGAAACATAC 58.530 41.667 0.00 0.00 0.00 2.39
3031 3205 4.275936 AGAAACATACAGTTGTGTTGAGGC 59.724 41.667 5.14 0.00 41.19 4.70
3069 3243 0.596577 CTGTGTGCTTCATTGCTGCT 59.403 50.000 0.00 0.00 0.00 4.24
3119 3293 0.612174 GCCAACCCTCCTTTCCCTTC 60.612 60.000 0.00 0.00 0.00 3.46
3124 3298 1.203622 ACCCTCCTTTCCCTTCTGGAT 60.204 52.381 0.00 0.00 44.66 3.41
3172 3346 0.536006 ACCTGCAACAACTCTGAGGC 60.536 55.000 9.85 2.86 0.00 4.70
3198 3372 6.888105 AGTTTTCCCAAAAGAACATCATTGT 58.112 32.000 0.00 0.00 37.82 2.71
3204 3378 6.775142 TCCCAAAAGAACATCATTGTCAGTTA 59.225 34.615 0.00 0.00 34.06 2.24
3205 3379 7.040478 TCCCAAAAGAACATCATTGTCAGTTAG 60.040 37.037 0.00 0.00 34.06 2.34
3207 3381 8.137437 CCAAAAGAACATCATTGTCAGTTAGTT 58.863 33.333 0.00 0.00 34.06 2.24
3217 3396 1.597663 GTCAGTTAGTTGCGCTGTTGT 59.402 47.619 9.73 0.00 0.00 3.32
3218 3397 2.798283 GTCAGTTAGTTGCGCTGTTGTA 59.202 45.455 9.73 0.00 0.00 2.41
3222 3401 4.862574 CAGTTAGTTGCGCTGTTGTATAGA 59.137 41.667 9.73 0.00 0.00 1.98
3225 3404 2.233922 AGTTGCGCTGTTGTATAGAGGT 59.766 45.455 9.73 0.00 0.00 3.85
3227 3406 1.548719 TGCGCTGTTGTATAGAGGTGT 59.451 47.619 9.73 0.00 0.00 4.16
3228 3407 2.028476 TGCGCTGTTGTATAGAGGTGTT 60.028 45.455 9.73 0.00 0.00 3.32
3229 3408 3.193903 TGCGCTGTTGTATAGAGGTGTTA 59.806 43.478 9.73 0.00 0.00 2.41
3230 3409 3.797256 GCGCTGTTGTATAGAGGTGTTAG 59.203 47.826 0.00 0.00 0.00 2.34
3231 3410 4.677250 GCGCTGTTGTATAGAGGTGTTAGT 60.677 45.833 0.00 0.00 0.00 2.24
3232 3411 5.408356 CGCTGTTGTATAGAGGTGTTAGTT 58.592 41.667 0.00 0.00 0.00 2.24
3233 3412 5.288712 CGCTGTTGTATAGAGGTGTTAGTTG 59.711 44.000 0.00 0.00 0.00 3.16
3234 3413 5.063564 GCTGTTGTATAGAGGTGTTAGTTGC 59.936 44.000 0.00 0.00 0.00 4.17
3235 3414 5.165676 TGTTGTATAGAGGTGTTAGTTGCG 58.834 41.667 0.00 0.00 0.00 4.85
3236 3415 3.777478 TGTATAGAGGTGTTAGTTGCGC 58.223 45.455 0.00 0.00 0.00 6.09
3237 3416 3.446161 TGTATAGAGGTGTTAGTTGCGCT 59.554 43.478 9.73 0.00 0.00 5.92
3238 3417 2.363788 TAGAGGTGTTAGTTGCGCTG 57.636 50.000 9.73 0.00 0.00 5.18
3239 3418 0.393077 AGAGGTGTTAGTTGCGCTGT 59.607 50.000 9.73 0.00 0.00 4.40
3240 3419 1.202651 AGAGGTGTTAGTTGCGCTGTT 60.203 47.619 9.73 0.00 0.00 3.16
3241 3420 1.602377 GAGGTGTTAGTTGCGCTGTTT 59.398 47.619 9.73 0.00 0.00 2.83
3242 3421 1.602377 AGGTGTTAGTTGCGCTGTTTC 59.398 47.619 9.73 0.00 0.00 2.78
3243 3422 1.332375 GGTGTTAGTTGCGCTGTTTCA 59.668 47.619 9.73 0.00 0.00 2.69
3244 3423 2.031157 GGTGTTAGTTGCGCTGTTTCAT 60.031 45.455 9.73 0.00 0.00 2.57
3245 3424 3.187637 GGTGTTAGTTGCGCTGTTTCATA 59.812 43.478 9.73 0.00 0.00 2.15
3246 3425 4.394795 GTGTTAGTTGCGCTGTTTCATAG 58.605 43.478 9.73 0.00 0.00 2.23
3247 3426 4.151689 GTGTTAGTTGCGCTGTTTCATAGA 59.848 41.667 9.73 0.00 0.00 1.98
3248 3427 4.388773 TGTTAGTTGCGCTGTTTCATAGAG 59.611 41.667 9.73 0.00 0.00 2.43
3249 3428 2.350522 AGTTGCGCTGTTTCATAGAGG 58.649 47.619 9.73 0.00 0.00 3.69
3250 3429 2.076863 GTTGCGCTGTTTCATAGAGGT 58.923 47.619 9.73 0.00 0.00 3.85
3313 3500 2.304180 CCAGTGGTCTTGAGAACCAGAT 59.696 50.000 0.00 0.00 33.74 2.90
3314 3501 3.332919 CAGTGGTCTTGAGAACCAGATG 58.667 50.000 0.00 0.00 33.74 2.90
3318 3505 5.485353 AGTGGTCTTGAGAACCAGATGATAA 59.515 40.000 0.00 0.00 33.74 1.75
3320 3507 6.825721 GTGGTCTTGAGAACCAGATGATAATT 59.174 38.462 0.00 0.00 33.74 1.40
3348 3535 2.744202 AGGTGCATCTCGTTTCATGAAC 59.256 45.455 7.89 2.92 34.82 3.18
3390 3577 0.608130 CGTCCCTCCTGATGTGTTCA 59.392 55.000 0.00 0.00 0.00 3.18
3393 3580 3.274288 GTCCCTCCTGATGTGTTCAATC 58.726 50.000 0.00 0.00 32.78 2.67
3396 3583 1.325640 CTCCTGATGTGTTCAATCGCG 59.674 52.381 0.00 0.00 32.78 5.87
3397 3584 1.078709 CCTGATGTGTTCAATCGCGT 58.921 50.000 5.77 0.00 32.78 6.01
3400 3587 3.124466 CCTGATGTGTTCAATCGCGTTTA 59.876 43.478 5.77 0.00 32.78 2.01
3401 3588 4.201812 CCTGATGTGTTCAATCGCGTTTAT 60.202 41.667 5.77 0.00 32.78 1.40
3477 3670 1.553248 TGTTTATAGCTCCCGTGCACT 59.447 47.619 16.19 0.00 34.99 4.40
3503 3696 2.555757 GGATGCAGCAATTATCTGGACC 59.444 50.000 3.51 6.63 34.78 4.46
3511 3704 3.023832 CAATTATCTGGACCGGCCTTTT 58.976 45.455 14.76 3.76 37.63 2.27
3512 3705 2.891191 TTATCTGGACCGGCCTTTTT 57.109 45.000 14.76 2.31 37.63 1.94
3541 3734 9.665719 TTGTCAAGATCTATGTTGTTTATAGCA 57.334 29.630 0.00 0.00 33.29 3.49
3542 3735 9.098355 TGTCAAGATCTATGTTGTTTATAGCAC 57.902 33.333 0.00 0.00 33.29 4.40
3543 3736 8.552034 GTCAAGATCTATGTTGTTTATAGCACC 58.448 37.037 0.00 0.00 33.29 5.01
3544 3737 7.715249 TCAAGATCTATGTTGTTTATAGCACCC 59.285 37.037 0.00 0.00 33.29 4.61
3545 3738 6.223852 AGATCTATGTTGTTTATAGCACCCG 58.776 40.000 0.00 0.00 0.00 5.28
3546 3739 5.347620 TCTATGTTGTTTATAGCACCCGT 57.652 39.130 0.00 0.00 0.00 5.28
3547 3740 5.113383 TCTATGTTGTTTATAGCACCCGTG 58.887 41.667 0.00 0.00 0.00 4.94
3617 3812 7.872113 AGATCTATGTTGGAATCTTGGAAAC 57.128 36.000 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.014840 ACAAGAGCAAAAATGAACATCCTGAT 60.015 34.615 0.00 0.00 0.00 2.90
95 96 6.549364 ACTCTCTCTCTCTCTCTCTCTCTAAG 59.451 46.154 0.00 0.00 0.00 2.18
96 97 6.436027 ACTCTCTCTCTCTCTCTCTCTCTAA 58.564 44.000 0.00 0.00 0.00 2.10
99 100 5.105146 ACAACTCTCTCTCTCTCTCTCTCTC 60.105 48.000 0.00 0.00 0.00 3.20
100 101 4.780021 ACAACTCTCTCTCTCTCTCTCTCT 59.220 45.833 0.00 0.00 0.00 3.10
101 102 4.872691 CACAACTCTCTCTCTCTCTCTCTC 59.127 50.000 0.00 0.00 0.00 3.20
102 103 4.323792 CCACAACTCTCTCTCTCTCTCTCT 60.324 50.000 0.00 0.00 0.00 3.10
103 104 3.941483 CCACAACTCTCTCTCTCTCTCTC 59.059 52.174 0.00 0.00 0.00 3.20
104 105 3.330701 ACCACAACTCTCTCTCTCTCTCT 59.669 47.826 0.00 0.00 0.00 3.10
105 106 3.686016 ACCACAACTCTCTCTCTCTCTC 58.314 50.000 0.00 0.00 0.00 3.20
117 118 4.876679 GCCCTTAAGAGAATACCACAACTC 59.123 45.833 3.36 0.00 0.00 3.01
127 128 6.768381 CGAAGAAAATAGGCCCTTAAGAGAAT 59.232 38.462 3.36 0.00 0.00 2.40
141 142 6.870965 ACATATAGCTCCTGCGAAGAAAATAG 59.129 38.462 0.00 0.00 45.42 1.73
208 226 3.961480 ACACATGCTCAGCTACAGTAA 57.039 42.857 0.00 0.00 0.00 2.24
285 303 8.204160 AGAAAACCCAAAGAAAACCATAGAAAG 58.796 33.333 0.00 0.00 0.00 2.62
290 308 7.189079 ACAAGAAAACCCAAAGAAAACCATA 57.811 32.000 0.00 0.00 0.00 2.74
298 316 8.154203 AGAAAAAGAAACAAGAAAACCCAAAGA 58.846 29.630 0.00 0.00 0.00 2.52
341 359 4.934602 CCAAGAAAAGCACAAAGAAAACCA 59.065 37.500 0.00 0.00 0.00 3.67
355 373 3.793797 ACCGGTGAAAACCAAGAAAAG 57.206 42.857 6.12 0.00 0.00 2.27
356 374 4.538746 AAACCGGTGAAAACCAAGAAAA 57.461 36.364 8.52 0.00 0.00 2.29
365 383 7.731882 AAAAAGAAAGAAAAACCGGTGAAAA 57.268 28.000 8.52 0.00 0.00 2.29
391 409 6.199531 TGTGTACGAAAAGTAGATGTGTGTTC 59.800 38.462 0.00 0.00 35.72 3.18
583 602 7.862873 TCGCAAAAATGTCAACACATGTATTTA 59.137 29.630 0.00 0.00 42.89 1.40
659 678 8.814038 AGTATTTAGAAACGGAAGGAGTACTA 57.186 34.615 0.00 0.00 0.00 1.82
660 679 7.147932 GGAGTATTTAGAAACGGAAGGAGTACT 60.148 40.741 0.00 0.00 0.00 2.73
661 680 6.977502 GGAGTATTTAGAAACGGAAGGAGTAC 59.022 42.308 0.00 0.00 0.00 2.73
662 681 6.097412 GGGAGTATTTAGAAACGGAAGGAGTA 59.903 42.308 0.00 0.00 0.00 2.59
663 682 5.105023 GGGAGTATTTAGAAACGGAAGGAGT 60.105 44.000 0.00 0.00 0.00 3.85
664 683 5.128991 AGGGAGTATTTAGAAACGGAAGGAG 59.871 44.000 0.00 0.00 0.00 3.69
665 684 5.028131 AGGGAGTATTTAGAAACGGAAGGA 58.972 41.667 0.00 0.00 0.00 3.36
666 685 5.128991 AGAGGGAGTATTTAGAAACGGAAGG 59.871 44.000 0.00 0.00 0.00 3.46
667 686 6.043411 CAGAGGGAGTATTTAGAAACGGAAG 58.957 44.000 0.00 0.00 0.00 3.46
668 687 5.482878 ACAGAGGGAGTATTTAGAAACGGAA 59.517 40.000 0.00 0.00 0.00 4.30
669 688 5.021458 ACAGAGGGAGTATTTAGAAACGGA 58.979 41.667 0.00 0.00 0.00 4.69
670 689 5.340439 ACAGAGGGAGTATTTAGAAACGG 57.660 43.478 0.00 0.00 0.00 4.44
671 690 5.349809 GGACAGAGGGAGTATTTAGAAACG 58.650 45.833 0.00 0.00 0.00 3.60
672 691 5.189145 TGGGACAGAGGGAGTATTTAGAAAC 59.811 44.000 0.00 0.00 0.00 2.78
673 692 5.347124 TGGGACAGAGGGAGTATTTAGAAA 58.653 41.667 0.00 0.00 0.00 2.52
674 693 4.955335 TGGGACAGAGGGAGTATTTAGAA 58.045 43.478 0.00 0.00 0.00 2.10
675 694 4.620086 TGGGACAGAGGGAGTATTTAGA 57.380 45.455 0.00 0.00 0.00 2.10
693 712 7.687941 ATCAAAAACGCTCCTATATTATGGG 57.312 36.000 0.00 0.00 0.00 4.00
719 738 6.963049 AGAACGTTTTTGGCACTAGTATAG 57.037 37.500 0.46 0.00 46.50 1.31
721 740 7.916914 ATAAGAACGTTTTTGGCACTAGTAT 57.083 32.000 13.87 0.00 0.00 2.12
722 741 9.439500 AATATAAGAACGTTTTTGGCACTAGTA 57.561 29.630 13.87 0.00 0.00 1.82
723 742 7.916914 ATATAAGAACGTTTTTGGCACTAGT 57.083 32.000 13.87 0.00 0.00 2.57
726 745 8.188139 CCATAATATAAGAACGTTTTTGGCACT 58.812 33.333 13.87 0.00 0.00 4.40
727 746 7.434013 CCCATAATATAAGAACGTTTTTGGCAC 59.566 37.037 13.87 0.00 0.00 5.01
728 747 7.339721 TCCCATAATATAAGAACGTTTTTGGCA 59.660 33.333 13.87 0.01 0.00 4.92
729 748 7.646526 GTCCCATAATATAAGAACGTTTTTGGC 59.353 37.037 13.87 0.00 0.00 4.52
730 749 8.679100 TGTCCCATAATATAAGAACGTTTTTGG 58.321 33.333 13.87 5.54 0.00 3.28
734 753 8.899771 CCTTTGTCCCATAATATAAGAACGTTT 58.100 33.333 0.46 0.00 0.00 3.60
735 754 8.269317 TCCTTTGTCCCATAATATAAGAACGTT 58.731 33.333 0.00 0.00 0.00 3.99
736 755 7.798071 TCCTTTGTCCCATAATATAAGAACGT 58.202 34.615 0.00 0.00 0.00 3.99
737 756 8.671384 TTCCTTTGTCCCATAATATAAGAACG 57.329 34.615 0.00 0.00 0.00 3.95
738 757 9.628500 ACTTCCTTTGTCCCATAATATAAGAAC 57.372 33.333 0.00 0.00 0.00 3.01
746 765 8.557450 ACACTTATACTTCCTTTGTCCCATAAT 58.443 33.333 0.00 0.00 0.00 1.28
747 766 7.924541 ACACTTATACTTCCTTTGTCCCATAA 58.075 34.615 0.00 0.00 0.00 1.90
748 767 7.504926 ACACTTATACTTCCTTTGTCCCATA 57.495 36.000 0.00 0.00 0.00 2.74
749 768 6.388619 ACACTTATACTTCCTTTGTCCCAT 57.611 37.500 0.00 0.00 0.00 4.00
750 769 5.836024 ACACTTATACTTCCTTTGTCCCA 57.164 39.130 0.00 0.00 0.00 4.37
751 770 7.520451 AAAACACTTATACTTCCTTTGTCCC 57.480 36.000 0.00 0.00 0.00 4.46
767 786 7.505585 TCCACATTGGAATCTCTAAAAACACTT 59.494 33.333 0.00 0.00 45.00 3.16
768 787 7.004086 TCCACATTGGAATCTCTAAAAACACT 58.996 34.615 0.00 0.00 45.00 3.55
784 803 3.717707 CTCCGTATGTAGTCCACATTGG 58.282 50.000 0.00 0.00 46.01 3.16
788 807 1.842052 TGCTCCGTATGTAGTCCACA 58.158 50.000 0.00 0.00 42.69 4.17
789 808 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
790 809 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
802 822 3.623060 TGTAGATTCGCTCATTTTGCTCC 59.377 43.478 0.00 0.00 0.00 4.70
848 868 5.824624 AGATTTCGGTAAGGACTACATACGA 59.175 40.000 0.00 0.00 31.45 3.43
856 876 3.709587 TCTGGAGATTTCGGTAAGGACT 58.290 45.455 0.00 0.00 0.00 3.85
859 879 4.870991 GTCTTTCTGGAGATTTCGGTAAGG 59.129 45.833 0.00 0.00 0.00 2.69
860 880 5.725362 AGTCTTTCTGGAGATTTCGGTAAG 58.275 41.667 0.00 0.00 0.00 2.34
862 882 5.740290 AAGTCTTTCTGGAGATTTCGGTA 57.260 39.130 0.00 0.00 0.00 4.02
863 883 4.625607 AAGTCTTTCTGGAGATTTCGGT 57.374 40.909 0.00 0.00 0.00 4.69
864 884 8.894768 AATATAAGTCTTTCTGGAGATTTCGG 57.105 34.615 0.00 0.00 29.76 4.30
905 983 3.617775 GCGGCCTTCTCTCTAAAAAGACT 60.618 47.826 0.00 0.00 0.00 3.24
906 984 2.673862 GCGGCCTTCTCTCTAAAAAGAC 59.326 50.000 0.00 0.00 0.00 3.01
909 987 2.615493 CCAGCGGCCTTCTCTCTAAAAA 60.615 50.000 0.00 0.00 0.00 1.94
910 988 1.066143 CCAGCGGCCTTCTCTCTAAAA 60.066 52.381 0.00 0.00 0.00 1.52
911 989 0.537188 CCAGCGGCCTTCTCTCTAAA 59.463 55.000 0.00 0.00 0.00 1.85
912 990 1.330655 CCCAGCGGCCTTCTCTCTAA 61.331 60.000 0.00 0.00 0.00 2.10
913 991 1.758514 CCCAGCGGCCTTCTCTCTA 60.759 63.158 0.00 0.00 0.00 2.43
946 1024 3.873910 CCCATCCAAGTGTAAGTCGAAT 58.126 45.455 0.00 0.00 0.00 3.34
947 1025 2.614481 GCCCATCCAAGTGTAAGTCGAA 60.614 50.000 0.00 0.00 0.00 3.71
1140 1223 4.361971 AGGAGGCGGTCGTGGAGA 62.362 66.667 0.00 0.00 0.00 3.71
1227 1310 0.616111 TGAAGGAGAGAGGGGTGAGC 60.616 60.000 0.00 0.00 0.00 4.26
1600 1686 2.204291 TGCCCCCTCCCACATCTT 60.204 61.111 0.00 0.00 0.00 2.40
1689 1775 1.081092 CTCCTCCACCTTCCTCCCA 59.919 63.158 0.00 0.00 0.00 4.37
1732 1818 2.897271 TTGGCCACATACACATTCCT 57.103 45.000 3.88 0.00 0.00 3.36
1733 1819 2.481795 GCATTGGCCACATACACATTCC 60.482 50.000 3.88 0.00 0.00 3.01
1791 1877 1.322442 GAAACACCTGCCAAGCTCTT 58.678 50.000 0.00 0.00 0.00 2.85
1819 1905 2.052941 GAGATCTCGCCGACGACG 60.053 66.667 7.04 0.00 45.12 5.12
1955 2041 5.412594 AGTGATGATGTGTTAGTGCGAAAAT 59.587 36.000 0.00 0.00 0.00 1.82
1957 2043 4.314961 AGTGATGATGTGTTAGTGCGAAA 58.685 39.130 0.00 0.00 0.00 3.46
1960 2046 4.389992 AGAAAGTGATGATGTGTTAGTGCG 59.610 41.667 0.00 0.00 0.00 5.34
1965 2051 5.316167 AGGCAAGAAAGTGATGATGTGTTA 58.684 37.500 0.00 0.00 0.00 2.41
1969 2055 3.057033 GCAAGGCAAGAAAGTGATGATGT 60.057 43.478 0.00 0.00 0.00 3.06
1972 2058 2.816087 GAGCAAGGCAAGAAAGTGATGA 59.184 45.455 0.00 0.00 0.00 2.92
1981 2067 1.352017 TGAGGAATGAGCAAGGCAAGA 59.648 47.619 0.00 0.00 0.00 3.02
1994 2156 4.647564 ATCAAGTTCCACACTGAGGAAT 57.352 40.909 10.72 0.00 46.08 3.01
1997 2159 4.013267 AGAATCAAGTTCCACACTGAGG 57.987 45.455 0.00 0.00 37.56 3.86
2002 2164 9.612620 CAGTAAAATAAGAATCAAGTTCCACAC 57.387 33.333 0.00 0.00 37.56 3.82
2015 2177 8.547967 GTCATCTGGACACAGTAAAATAAGAA 57.452 34.615 0.00 0.00 46.19 2.52
2116 2278 3.862267 CCATCGAGTTGAAGAGTAGCTTG 59.138 47.826 0.00 0.00 36.83 4.01
2134 2296 7.225734 GGAGTAAGACTAAATTCTGCTTCCATC 59.774 40.741 0.00 0.00 0.00 3.51
2140 2302 7.246171 TCTTGGAGTAAGACTAAATTCTGCT 57.754 36.000 0.00 0.00 40.43 4.24
2143 2305 8.750298 TCGATTCTTGGAGTAAGACTAAATTCT 58.250 33.333 0.00 0.00 44.84 2.40
2215 2377 6.830912 TGCTATCATACTGTAGGCTTCATTT 58.169 36.000 0.00 0.00 0.00 2.32
2238 2400 2.707849 GGCTCCACTGGCATGCTTG 61.708 63.158 18.92 12.90 0.00 4.01
2261 2423 3.866582 GGCTCCCCAGATGACGGG 61.867 72.222 0.00 0.00 44.07 5.28
2324 2486 8.089115 AGAAAGATGAGTTTGTTTACTGCTAC 57.911 34.615 0.00 0.00 0.00 3.58
2325 2487 7.116376 CGAGAAAGATGAGTTTGTTTACTGCTA 59.884 37.037 0.00 0.00 0.00 3.49
2694 2856 1.001020 AGCGGTTCATGGGCAATCA 60.001 52.632 0.00 0.00 0.00 2.57
2709 2871 3.181477 ACTTGGAAGATCAGATCAGAGCG 60.181 47.826 13.14 0.00 0.00 5.03
2816 2979 2.632028 AGCAGCAAGAAGAGAAGAGTCA 59.368 45.455 0.00 0.00 0.00 3.41
2852 3015 0.311790 AACAAGTGCAGCATCAACGG 59.688 50.000 0.00 0.00 0.00 4.44
2857 3020 5.684626 GCATCTTAATAACAAGTGCAGCATC 59.315 40.000 0.00 0.00 35.00 3.91
2864 3027 6.090763 TCGTCTGTGCATCTTAATAACAAGTG 59.909 38.462 0.00 0.00 0.00 3.16
2865 3028 6.090898 GTCGTCTGTGCATCTTAATAACAAGT 59.909 38.462 0.00 0.00 0.00 3.16
2870 3033 4.109766 CGGTCGTCTGTGCATCTTAATAA 58.890 43.478 0.00 0.00 0.00 1.40
2888 3051 1.656095 CTTCGTCTGCAATTCTCGGTC 59.344 52.381 0.00 0.00 0.00 4.79
2951 3114 7.962964 TCTCGTATGTGGATTTCATTATTCC 57.037 36.000 0.00 0.00 0.00 3.01
2973 3136 8.043113 TGCTCATTTACTTGTCATATCAGTTCT 58.957 33.333 0.00 0.00 0.00 3.01
2981 3144 6.701340 ACTCTGTGCTCATTTACTTGTCATA 58.299 36.000 0.00 0.00 0.00 2.15
2986 3149 6.159293 TCTGTACTCTGTGCTCATTTACTTG 58.841 40.000 0.00 0.00 0.00 3.16
3000 3163 6.701841 ACACAACTGTATGTTTCTGTACTCTG 59.298 38.462 0.00 0.00 36.63 3.35
3017 3180 8.131100 CCAAATTATATAGCCTCAACACAACTG 58.869 37.037 0.00 0.00 0.00 3.16
3031 3205 8.338259 GCACACAGACTCAACCAAATTATATAG 58.662 37.037 0.00 0.00 0.00 1.31
3080 3254 1.739562 CCGCCTCTGCTCAAGACAC 60.740 63.158 0.00 0.00 34.43 3.67
3083 3257 3.011635 GCTCCGCCTCTGCTCAAGA 62.012 63.158 0.00 0.00 34.43 3.02
3119 3293 1.551430 TGCCAAATGCCAAAGATCCAG 59.449 47.619 0.00 0.00 40.16 3.86
3124 3298 4.888326 ATAACTTGCCAAATGCCAAAGA 57.112 36.364 0.00 0.00 40.16 2.52
3165 3339 0.762418 TTGGGAAAACTCGCCTCAGA 59.238 50.000 0.00 0.00 0.00 3.27
3167 3341 1.953686 CTTTTGGGAAAACTCGCCTCA 59.046 47.619 0.00 0.00 0.00 3.86
3172 3346 5.181690 TGATGTTCTTTTGGGAAAACTCG 57.818 39.130 0.00 0.00 0.00 4.18
3198 3372 1.948104 ACAACAGCGCAACTAACTGA 58.052 45.000 11.47 0.00 35.38 3.41
3204 3378 2.233922 ACCTCTATACAACAGCGCAACT 59.766 45.455 11.47 0.00 0.00 3.16
3205 3379 2.348666 CACCTCTATACAACAGCGCAAC 59.651 50.000 11.47 0.00 0.00 4.17
3207 3381 1.548719 ACACCTCTATACAACAGCGCA 59.451 47.619 11.47 0.00 0.00 6.09
3217 3396 3.446161 ACAGCGCAACTAACACCTCTATA 59.554 43.478 11.47 0.00 0.00 1.31
3218 3397 2.233922 ACAGCGCAACTAACACCTCTAT 59.766 45.455 11.47 0.00 0.00 1.98
3222 3401 1.602377 GAAACAGCGCAACTAACACCT 59.398 47.619 11.47 0.00 0.00 4.00
3225 3404 4.311606 TCTATGAAACAGCGCAACTAACA 58.688 39.130 11.47 2.67 0.00 2.41
3227 3406 3.932710 CCTCTATGAAACAGCGCAACTAA 59.067 43.478 11.47 0.00 0.00 2.24
3228 3407 3.056107 ACCTCTATGAAACAGCGCAACTA 60.056 43.478 11.47 0.00 0.00 2.24
3229 3408 2.289694 ACCTCTATGAAACAGCGCAACT 60.290 45.455 11.47 0.00 0.00 3.16
3230 3409 2.076863 ACCTCTATGAAACAGCGCAAC 58.923 47.619 11.47 0.00 0.00 4.17
3231 3410 2.076100 CACCTCTATGAAACAGCGCAA 58.924 47.619 11.47 0.00 0.00 4.85
3232 3411 1.675714 CCACCTCTATGAAACAGCGCA 60.676 52.381 11.47 0.00 0.00 6.09
3233 3412 1.009829 CCACCTCTATGAAACAGCGC 58.990 55.000 0.00 0.00 0.00 5.92
3234 3413 2.386661 ACCACCTCTATGAAACAGCG 57.613 50.000 0.00 0.00 0.00 5.18
3235 3414 3.437049 GTCAACCACCTCTATGAAACAGC 59.563 47.826 0.00 0.00 0.00 4.40
3236 3415 4.003648 GGTCAACCACCTCTATGAAACAG 58.996 47.826 0.00 0.00 42.84 3.16
3237 3416 4.015872 GGTCAACCACCTCTATGAAACA 57.984 45.455 0.00 0.00 42.84 2.83
3249 3428 3.050275 GCTCGGCAGGTCAACCAC 61.050 66.667 1.33 0.00 38.89 4.16
3250 3429 4.329545 GGCTCGGCAGGTCAACCA 62.330 66.667 1.33 0.00 38.89 3.67
3298 3485 7.050377 TGGAATTATCATCTGGTTCTCAAGAC 58.950 38.462 0.00 0.00 0.00 3.01
3313 3500 5.263599 AGATGCACCTTGTTGGAATTATCA 58.736 37.500 0.00 0.00 39.71 2.15
3314 3501 5.504665 CGAGATGCACCTTGTTGGAATTATC 60.505 44.000 0.00 0.00 39.71 1.75
3318 3505 2.086869 CGAGATGCACCTTGTTGGAAT 58.913 47.619 0.00 0.00 39.71 3.01
3320 3507 0.396435 ACGAGATGCACCTTGTTGGA 59.604 50.000 0.00 0.00 39.71 3.53
3367 3554 1.990060 ACATCAGGAGGGACGGTGG 60.990 63.158 0.00 0.00 0.00 4.61
3390 3577 9.567848 AAATCAAATTGAGTAATAAACGCGATT 57.432 25.926 15.93 10.83 42.04 3.34
3487 3680 0.947244 GCCGGTCCAGATAATTGCTG 59.053 55.000 1.90 3.82 0.00 4.41
3489 3682 0.179018 AGGCCGGTCCAGATAATTGC 60.179 55.000 15.92 0.00 37.29 3.56
3491 3684 3.382083 AAAAGGCCGGTCCAGATAATT 57.618 42.857 15.92 0.00 37.29 1.40
3515 3708 9.665719 TGCTATAAACAACATAGATCTTGACAA 57.334 29.630 0.00 0.00 0.00 3.18
3516 3709 9.098355 GTGCTATAAACAACATAGATCTTGACA 57.902 33.333 0.00 0.00 0.00 3.58
3517 3710 8.552034 GGTGCTATAAACAACATAGATCTTGAC 58.448 37.037 0.00 0.00 0.00 3.18
3518 3711 7.715249 GGGTGCTATAAACAACATAGATCTTGA 59.285 37.037 0.00 0.00 0.00 3.02
3519 3712 7.307396 CGGGTGCTATAAACAACATAGATCTTG 60.307 40.741 0.00 1.85 0.00 3.02
3520 3713 6.706270 CGGGTGCTATAAACAACATAGATCTT 59.294 38.462 0.00 0.00 0.00 2.40
3521 3714 6.183360 ACGGGTGCTATAAACAACATAGATCT 60.183 38.462 0.00 0.00 0.00 2.75
3522 3715 5.989777 ACGGGTGCTATAAACAACATAGATC 59.010 40.000 0.00 0.00 0.00 2.75
3523 3716 5.758296 CACGGGTGCTATAAACAACATAGAT 59.242 40.000 0.00 0.00 0.00 1.98
3524 3717 5.113383 CACGGGTGCTATAAACAACATAGA 58.887 41.667 0.00 0.00 0.00 1.98
3525 3718 5.403897 CACGGGTGCTATAAACAACATAG 57.596 43.478 0.00 0.00 0.00 2.23
3617 3812 6.662414 TTATTATGTTCTCCAAACGAGCAG 57.338 37.500 0.00 0.00 38.62 4.24


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

AutoCloner maintained by Alex Coulton.