Multiple sequence alignment - TraesCS1A01G121000

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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 TraesCS1A01G121000 chr1A 100.000 7587 0 0 1 7587 133411497 133419083 0.000000e+00 14011.0
1 TraesCS1A01G121000 chr1A 97.849 93 2 0 5959 6051 584082806 584082898 2.190000e-35 161.0
2 TraesCS1A01G121000 chr1A 79.787 188 30 5 3188 3373 556114822 556115003 6.180000e-26 130.0
3 TraesCS1A01G121000 chr1D 98.576 2879 34 6 3092 5968 122539230 122542103 0.000000e+00 5083.0
4 TraesCS1A01G121000 chr1D 98.606 1363 19 0 1476 2838 122537818 122539180 0.000000e+00 2412.0
5 TraesCS1A01G121000 chr1D 92.879 997 31 21 6049 7039 122542101 122543063 0.000000e+00 1411.0
6 TraesCS1A01G121000 chr1D 96.377 690 20 3 757 1442 122537142 122537830 0.000000e+00 1131.0
7 TraesCS1A01G121000 chr1D 86.201 616 62 10 134 729 122536361 122536973 0.000000e+00 645.0
8 TraesCS1A01G121000 chr1D 94.631 149 6 2 2842 2990 418199581 418199435 5.920000e-56 230.0
9 TraesCS1A01G121000 chr1D 98.246 57 1 0 2995 3051 122539174 122539230 4.840000e-17 100.0
10 TraesCS1A01G121000 chr1D 98.182 55 1 0 1 55 122536315 122536369 6.270000e-16 97.1
11 TraesCS1A01G121000 chr1D 95.652 46 2 0 6978 7023 122543057 122543102 2.940000e-09 75.0
12 TraesCS1A01G121000 chr1B 94.485 2992 95 22 2995 5949 186461094 186464052 0.000000e+00 4547.0
13 TraesCS1A01G121000 chr1B 95.876 1358 38 5 1482 2838 186459760 186461100 0.000000e+00 2182.0
14 TraesCS1A01G121000 chr1B 92.335 835 29 12 6061 6862 186464076 186464908 0.000000e+00 1155.0
15 TraesCS1A01G121000 chr1B 95.108 695 23 3 757 1440 186459072 186459766 0.000000e+00 1085.0
16 TraesCS1A01G121000 chr1B 85.847 756 80 9 1 735 186458161 186458910 0.000000e+00 778.0
17 TraesCS1A01G121000 chr1B 80.943 530 97 4 7056 7583 566553306 566553833 4.230000e-112 416.0
18 TraesCS1A01G121000 chr1B 84.865 370 39 5 3 360 186451069 186451433 2.600000e-94 357.0
19 TraesCS1A01G121000 chr1B 82.890 263 37 8 7058 7316 496511472 496511214 5.920000e-56 230.0
20 TraesCS1A01G121000 chr1B 92.035 113 5 4 5949 6059 47517330 47517440 1.020000e-33 156.0
21 TraesCS1A01G121000 chr1B 93.069 101 5 1 6941 7039 186467253 186467353 6.130000e-31 147.0
22 TraesCS1A01G121000 chr2D 95.370 540 20 3 7051 7587 55272982 55272445 0.000000e+00 854.0
23 TraesCS1A01G121000 chr2D 95.973 149 4 2 2842 2990 215831964 215831818 2.740000e-59 241.0
24 TraesCS1A01G121000 chr7B 78.987 533 108 4 7053 7584 713278306 713278835 2.010000e-95 361.0
25 TraesCS1A01G121000 chr7B 81.967 305 51 4 7053 7356 713260847 713261148 9.770000e-64 255.0
26 TraesCS1A01G121000 chr3D 95.973 149 4 2 2842 2990 26165698 26165844 2.740000e-59 241.0
27 TraesCS1A01G121000 chr7D 95.302 149 5 2 2842 2990 617790595 617790741 1.270000e-57 235.0
28 TraesCS1A01G121000 chr7D 90.435 115 10 1 5943 6056 89216161 89216047 4.740000e-32 150.0
29 TraesCS1A01G121000 chr5B 95.302 149 5 2 2842 2990 291787003 291786857 1.270000e-57 235.0
30 TraesCS1A01G121000 chr5B 87.121 132 11 4 5928 6054 74153064 74153194 2.210000e-30 145.0
31 TraesCS1A01G121000 chr6D 94.631 149 6 2 2842 2990 450832114 450831968 5.920000e-56 230.0
32 TraesCS1A01G121000 chr5D 94.631 149 6 2 2842 2990 257502285 257502139 5.920000e-56 230.0
33 TraesCS1A01G121000 chr5D 75.758 297 57 13 7045 7333 56130063 56130352 1.330000e-27 135.0
34 TraesCS1A01G121000 chr7A 93.960 149 7 2 2842 2990 428822322 428822176 2.760000e-54 224.0
35 TraesCS1A01G121000 chr7A 92.661 109 4 3 5953 6061 3013998 3014102 3.670000e-33 154.0
36 TraesCS1A01G121000 chr7A 100.000 28 0 0 6074 6101 32537801 32537828 1.400000e-02 52.8
37 TraesCS1A01G121000 chr3A 94.521 146 6 2 2845 2990 593355721 593355864 2.760000e-54 224.0
38 TraesCS1A01G121000 chr4B 75.406 431 98 7 7054 7481 459067020 459066595 1.290000e-47 202.0
39 TraesCS1A01G121000 chr4B 96.000 100 3 1 5953 6052 565213474 565213376 2.190000e-35 161.0
40 TraesCS1A01G121000 chr4B 78.169 142 23 6 7057 7194 671711395 671711532 4.880000e-12 84.2
41 TraesCS1A01G121000 chr2A 97.959 98 1 1 5963 6059 686840776 686840873 1.310000e-37 169.0
42 TraesCS1A01G121000 chr2A 91.150 113 8 2 5955 6066 166785083 166784972 1.320000e-32 152.0
43 TraesCS1A01G121000 chr6A 95.960 99 4 0 5953 6051 73454942 73454844 2.190000e-35 161.0
44 TraesCS1A01G121000 chr6B 74.126 286 55 14 7058 7333 89694730 89694454 4.840000e-17 100.0


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 TraesCS1A01G121000 chr1A 133411497 133419083 7586 False 14011.0000 14011 100.000000 1 7587 1 chr1A.!!$F1 7586
1 TraesCS1A01G121000 chr1D 122536315 122543102 6787 False 1369.2625 5083 95.589875 1 7039 8 chr1D.!!$F1 7038
2 TraesCS1A01G121000 chr1B 186458161 186467353 9192 False 1649.0000 4547 92.786667 1 7039 6 chr1B.!!$F4 7038
3 TraesCS1A01G121000 chr1B 566553306 566553833 527 False 416.0000 416 80.943000 7056 7583 1 chr1B.!!$F3 527
4 TraesCS1A01G121000 chr2D 55272445 55272982 537 True 854.0000 854 95.370000 7051 7587 1 chr2D.!!$R1 536
5 TraesCS1A01G121000 chr7B 713278306 713278835 529 False 361.0000 361 78.987000 7053 7584 1 chr7B.!!$F2 531

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
380 394 0.398318 GCTTCACCTGGAGTTGTCCT 59.602 55.000 0.00 0.0 44.30 3.85 F
744 766 0.969409 GCAGGCTGGCAGGAAGATTT 60.969 55.000 17.64 0.0 0.00 2.17 F
799 963 0.974010 GACCCCACCCGTCAGATACA 60.974 60.000 0.00 0.0 0.00 2.29 F
2363 2539 0.108233 CACCAGAGGAGAAGCAGCTC 60.108 60.000 0.00 0.0 0.00 4.09 F
2873 3049 0.036388 TCTTGCCTTGGACGCTTAGG 60.036 55.000 0.00 0.0 0.00 2.69 F
2978 3154 0.179119 CACCTTAGGTCGCCTTACCG 60.179 60.000 0.00 0.0 44.77 4.02 F
4893 5103 0.251354 TTCTGCATGAGGAGGTCTGC 59.749 55.000 0.00 0.0 33.43 4.26 F
5259 5473 1.340017 GGCCAAGATAGAACTGGTGCA 60.340 52.381 0.00 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1420 0.179161 CAGTTCCGTACCGCAGAGAG 60.179 60.000 0.00 0.0 0.00 3.20 R
2363 2539 3.885297 CCCAATTATGGCCACTAACAGAG 59.115 47.826 8.16 0.0 46.09 3.35 R
2393 2569 4.558226 ACTCAGCTAACCATTGATGTCA 57.442 40.909 0.00 0.0 0.00 3.58 R
3297 3480 0.544357 AGGGACGTTCCTCATCACCA 60.544 55.000 10.55 0.0 36.57 4.17 R
4604 4789 3.035942 GCAAGTGCACAAGTAGAAAACG 58.964 45.455 21.04 0.0 41.59 3.60 R
4966 5176 3.345714 GCGCTCAAATTCAACATACTCG 58.654 45.455 0.00 0.0 0.00 4.18 R
5901 6116 0.333993 ATGCAGTTTGGGATGGAGCT 59.666 50.000 0.00 0.0 0.00 4.09 R
6979 9543 1.108727 CACAAAGACTTGGGCCAGCA 61.109 55.000 6.23 0.0 36.82 4.41 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
62 63 3.636231 CGGTGGGTGCTTCAGGGA 61.636 66.667 0.00 0.00 0.00 4.20
105 106 1.450211 GCGGAGGCAAATAGGGCTA 59.550 57.895 0.00 0.00 44.62 3.93
108 109 0.885150 GGAGGCAAATAGGGCTACGC 60.885 60.000 0.00 0.00 44.62 4.42
132 133 2.284276 TGGACGCGATGTGGGGTTA 61.284 57.895 15.93 0.00 32.74 2.85
168 169 1.990327 GGGTGGAGGGGAAGACTTTTA 59.010 52.381 0.00 0.00 0.00 1.52
170 171 3.181426 GGGTGGAGGGGAAGACTTTTAAA 60.181 47.826 0.00 0.00 0.00 1.52
224 237 7.498239 GGCCGAGAAGTATAATTTTTACTCCTT 59.502 37.037 0.00 0.00 0.00 3.36
332 345 4.338964 TCGATTATGGTTGCTCTTACGGTA 59.661 41.667 0.00 0.00 0.00 4.02
333 346 5.045215 CGATTATGGTTGCTCTTACGGTAA 58.955 41.667 0.00 0.00 0.00 2.85
335 348 3.975168 ATGGTTGCTCTTACGGTAAGT 57.025 42.857 23.27 3.25 37.10 2.24
340 353 4.274214 GGTTGCTCTTACGGTAAGTTTTGT 59.726 41.667 23.27 0.00 37.10 2.83
356 370 3.724508 TTTGTTTGCGTCCACATCATT 57.275 38.095 0.00 0.00 0.00 2.57
380 394 0.398318 GCTTCACCTGGAGTTGTCCT 59.602 55.000 0.00 0.00 44.30 3.85
382 396 2.038557 GCTTCACCTGGAGTTGTCCTTA 59.961 50.000 0.00 0.00 44.30 2.69
412 426 8.723942 TTATAAATGTTTGTTTGGTTGCTGTT 57.276 26.923 0.00 0.00 0.00 3.16
431 445 7.995289 TGCTGTTCTATGAAAAAGAAAACTCA 58.005 30.769 0.00 0.00 34.86 3.41
438 452 3.766591 TGAAAAAGAAAACTCACCTGGCA 59.233 39.130 0.00 0.00 0.00 4.92
441 455 5.712152 AAAAGAAAACTCACCTGGCATAG 57.288 39.130 0.00 0.00 0.00 2.23
479 493 5.379706 AATTAGCCTGGCTAGACTCATTT 57.620 39.130 26.04 8.11 42.34 2.32
576 590 2.159282 AGTGTATCGATGGGACGTTGAC 60.159 50.000 8.54 0.00 34.70 3.18
587 601 1.673920 GGACGTTGACTTTTTGCCTGA 59.326 47.619 0.00 0.00 0.00 3.86
615 631 6.311200 GGCAAACCTGTTCTATATTTTTGCAG 59.689 38.462 15.65 0.00 45.80 4.41
619 635 8.525290 AACCTGTTCTATATTTTTGCAGCTAT 57.475 30.769 0.00 0.00 0.00 2.97
647 663 2.265589 AGAACGAAACCGACCCATTT 57.734 45.000 0.00 0.00 0.00 2.32
658 674 2.292267 CGACCCATTTCTCTGGAATGG 58.708 52.381 9.97 9.97 38.69 3.16
661 677 3.950395 GACCCATTTCTCTGGAATGGAAG 59.050 47.826 16.83 5.94 38.69 3.46
663 679 3.698040 CCCATTTCTCTGGAATGGAAGTG 59.302 47.826 16.83 0.00 38.69 3.16
667 683 4.705110 TTCTCTGGAATGGAAGTGTTCA 57.295 40.909 0.00 0.00 0.00 3.18
668 684 4.916041 TCTCTGGAATGGAAGTGTTCAT 57.084 40.909 0.00 0.00 0.00 2.57
669 685 4.582869 TCTCTGGAATGGAAGTGTTCATG 58.417 43.478 0.00 0.00 0.00 3.07
670 686 3.689347 TCTGGAATGGAAGTGTTCATGG 58.311 45.455 0.00 0.00 0.00 3.66
679 701 4.202514 TGGAAGTGTTCATGGTATGGTTCA 60.203 41.667 0.00 0.00 0.00 3.18
681 703 5.418840 GGAAGTGTTCATGGTATGGTTCATT 59.581 40.000 0.00 0.00 0.00 2.57
729 751 2.667418 CCTGGTCTGTCTGGCAGG 59.333 66.667 15.73 0.00 45.08 4.85
734 756 4.025858 TCTGTCTGGCAGGCTGGC 62.026 66.667 31.94 31.94 45.08 4.85
742 764 2.274760 GCAGGCTGGCAGGAAGAT 59.725 61.111 17.64 0.00 0.00 2.40
743 765 1.379576 GCAGGCTGGCAGGAAGATT 60.380 57.895 17.64 0.00 0.00 2.40
744 766 0.969409 GCAGGCTGGCAGGAAGATTT 60.969 55.000 17.64 0.00 0.00 2.17
745 767 1.553706 CAGGCTGGCAGGAAGATTTT 58.446 50.000 17.64 0.00 0.00 1.82
746 768 2.726821 CAGGCTGGCAGGAAGATTTTA 58.273 47.619 17.64 0.00 0.00 1.52
747 769 2.424956 CAGGCTGGCAGGAAGATTTTAC 59.575 50.000 17.64 0.00 0.00 2.01
749 771 3.026694 GGCTGGCAGGAAGATTTTACAT 58.973 45.455 17.64 0.00 0.00 2.29
750 772 3.067320 GGCTGGCAGGAAGATTTTACATC 59.933 47.826 17.64 0.00 0.00 3.06
751 773 3.950395 GCTGGCAGGAAGATTTTACATCT 59.050 43.478 17.64 0.00 0.00 2.90
752 774 4.036144 GCTGGCAGGAAGATTTTACATCTC 59.964 45.833 17.64 0.00 0.00 2.75
754 776 3.002759 GGCAGGAAGATTTTACATCTCGC 59.997 47.826 0.00 0.00 0.00 5.03
799 963 0.974010 GACCCCACCCGTCAGATACA 60.974 60.000 0.00 0.00 0.00 2.29
1017 1189 2.363276 ATGACGGACGGCCACCTA 60.363 61.111 8.76 0.00 0.00 3.08
1188 1360 2.415512 GCTCGTCTAGCGGAATTTGTTT 59.584 45.455 6.71 0.00 42.53 2.83
1189 1361 3.615496 GCTCGTCTAGCGGAATTTGTTTA 59.385 43.478 6.71 0.00 42.53 2.01
1248 1420 1.362355 CACGCCAGGGTTTGTTTCC 59.638 57.895 0.00 0.00 0.00 3.13
1389 1564 6.619801 ACAGATTGGAAACTCAACTACAAC 57.380 37.500 0.00 0.00 0.00 3.32
1403 1578 4.207891 ACTACAACCAGGCACTAATCTG 57.792 45.455 0.00 0.00 36.02 2.90
1432 1607 5.125356 TCGAGGAACATGTTCATGCAATAT 58.875 37.500 33.42 12.82 41.20 1.28
1667 1842 7.798596 ATTCTCCTTATCACTGTTTAGCATG 57.201 36.000 0.00 0.00 0.00 4.06
1763 1938 9.129209 GGTTCATATCTTTTTGAAACTTAGTGC 57.871 33.333 0.00 0.00 36.76 4.40
1764 1939 9.899226 GTTCATATCTTTTTGAAACTTAGTGCT 57.101 29.630 0.00 0.00 33.90 4.40
2363 2539 0.108233 CACCAGAGGAGAAGCAGCTC 60.108 60.000 0.00 0.00 0.00 4.09
2393 2569 2.124693 CCATAATTGGGGCGCGGTT 61.125 57.895 8.83 0.00 39.56 4.44
2635 2811 3.700863 ACTACAGGGGCTAATGAGGTA 57.299 47.619 0.00 0.00 0.00 3.08
2782 2958 9.352784 CCAACATTGGTGTGTATATTTAAACTG 57.647 33.333 0.20 0.00 43.43 3.16
2837 3013 4.700213 TCTTATTAGTTTCCTTGCCTGTGC 59.300 41.667 0.00 0.00 38.26 4.57
2838 3014 1.616159 TTAGTTTCCTTGCCTGTGCC 58.384 50.000 0.00 0.00 36.33 5.01
2839 3015 0.771127 TAGTTTCCTTGCCTGTGCCT 59.229 50.000 0.00 0.00 36.33 4.75
2840 3016 0.771127 AGTTTCCTTGCCTGTGCCTA 59.229 50.000 0.00 0.00 36.33 3.93
2841 3017 1.355720 AGTTTCCTTGCCTGTGCCTAT 59.644 47.619 0.00 0.00 36.33 2.57
2842 3018 1.474077 GTTTCCTTGCCTGTGCCTATG 59.526 52.381 0.00 0.00 36.33 2.23
2843 3019 0.698238 TTCCTTGCCTGTGCCTATGT 59.302 50.000 0.00 0.00 36.33 2.29
2844 3020 0.698238 TCCTTGCCTGTGCCTATGTT 59.302 50.000 0.00 0.00 36.33 2.71
2845 3021 1.075374 TCCTTGCCTGTGCCTATGTTT 59.925 47.619 0.00 0.00 36.33 2.83
2846 3022 1.895131 CCTTGCCTGTGCCTATGTTTT 59.105 47.619 0.00 0.00 36.33 2.43
2847 3023 2.299867 CCTTGCCTGTGCCTATGTTTTT 59.700 45.455 0.00 0.00 36.33 1.94
2848 3024 3.509575 CCTTGCCTGTGCCTATGTTTTTA 59.490 43.478 0.00 0.00 36.33 1.52
2849 3025 4.021544 CCTTGCCTGTGCCTATGTTTTTAA 60.022 41.667 0.00 0.00 36.33 1.52
2850 3026 4.782019 TGCCTGTGCCTATGTTTTTAAG 57.218 40.909 0.00 0.00 36.33 1.85
2851 3027 3.509575 TGCCTGTGCCTATGTTTTTAAGG 59.490 43.478 0.00 0.00 36.33 2.69
2857 3033 4.696899 GCCTATGTTTTTAAGGCGTCTT 57.303 40.909 7.72 7.72 45.82 3.01
2858 3034 4.412207 GCCTATGTTTTTAAGGCGTCTTG 58.588 43.478 13.69 0.00 45.82 3.02
2859 3035 4.412207 CCTATGTTTTTAAGGCGTCTTGC 58.588 43.478 13.69 0.00 45.38 4.01
2869 3045 2.357517 CGTCTTGCCTTGGACGCT 60.358 61.111 2.72 0.00 46.23 5.07
2870 3046 1.961277 CGTCTTGCCTTGGACGCTT 60.961 57.895 2.72 0.00 46.23 4.68
2871 3047 0.669318 CGTCTTGCCTTGGACGCTTA 60.669 55.000 2.72 0.00 46.23 3.09
2872 3048 1.079503 GTCTTGCCTTGGACGCTTAG 58.920 55.000 0.00 0.00 0.00 2.18
2873 3049 0.036388 TCTTGCCTTGGACGCTTAGG 60.036 55.000 0.00 0.00 0.00 2.69
2908 3084 3.084070 GGCAGTGCCTTACAAATATGC 57.916 47.619 27.48 0.00 46.69 3.14
2909 3085 2.223805 GGCAGTGCCTTACAAATATGCC 60.224 50.000 27.48 0.00 46.69 4.40
2910 3086 2.223805 GCAGTGCCTTACAAATATGCCC 60.224 50.000 2.85 0.00 0.00 5.36
2911 3087 2.033299 CAGTGCCTTACAAATATGCCCG 59.967 50.000 0.00 0.00 0.00 6.13
2912 3088 1.028905 TGCCTTACAAATATGCCCGC 58.971 50.000 0.00 0.00 0.00 6.13
2913 3089 0.313987 GCCTTACAAATATGCCCGCC 59.686 55.000 0.00 0.00 0.00 6.13
2914 3090 1.981256 CCTTACAAATATGCCCGCCT 58.019 50.000 0.00 0.00 0.00 5.52
2915 3091 2.306847 CCTTACAAATATGCCCGCCTT 58.693 47.619 0.00 0.00 0.00 4.35
2916 3092 3.482436 CCTTACAAATATGCCCGCCTTA 58.518 45.455 0.00 0.00 0.00 2.69
2917 3093 3.502211 CCTTACAAATATGCCCGCCTTAG 59.498 47.826 0.00 0.00 0.00 2.18
2918 3094 1.981256 ACAAATATGCCCGCCTTAGG 58.019 50.000 0.00 0.00 0.00 2.69
2971 3147 4.187056 GTGCTCACCTTAGGTCGC 57.813 61.111 13.38 13.38 31.02 5.19
2972 3148 1.448013 GTGCTCACCTTAGGTCGCC 60.448 63.158 16.41 7.13 31.02 5.54
2973 3149 1.609501 TGCTCACCTTAGGTCGCCT 60.610 57.895 16.41 3.87 37.71 5.52
2974 3150 1.192146 TGCTCACCTTAGGTCGCCTT 61.192 55.000 16.41 0.00 34.61 4.35
2975 3151 0.822164 GCTCACCTTAGGTCGCCTTA 59.178 55.000 0.00 0.00 34.61 2.69
2976 3152 1.471153 GCTCACCTTAGGTCGCCTTAC 60.471 57.143 0.00 0.00 34.61 2.34
2977 3153 1.136500 CTCACCTTAGGTCGCCTTACC 59.864 57.143 0.00 0.00 40.06 2.85
2978 3154 0.179119 CACCTTAGGTCGCCTTACCG 60.179 60.000 0.00 0.00 44.77 4.02
2979 3155 1.227176 CCTTAGGTCGCCTTACCGC 60.227 63.158 3.71 0.00 44.77 5.68
2980 3156 1.227176 CTTAGGTCGCCTTACCGCC 60.227 63.158 3.71 0.00 44.77 6.13
2981 3157 1.673808 CTTAGGTCGCCTTACCGCCT 61.674 60.000 3.71 0.00 44.77 5.52
2982 3158 1.259840 TTAGGTCGCCTTACCGCCTT 61.260 55.000 3.71 0.00 44.77 4.35
2983 3159 0.395586 TAGGTCGCCTTACCGCCTTA 60.396 55.000 3.71 0.00 44.77 2.69
2984 3160 1.218854 GGTCGCCTTACCGCCTTAA 59.781 57.895 0.00 0.00 0.00 1.85
2985 3161 0.391528 GGTCGCCTTACCGCCTTAAA 60.392 55.000 0.00 0.00 0.00 1.52
2986 3162 1.441738 GTCGCCTTACCGCCTTAAAA 58.558 50.000 0.00 0.00 0.00 1.52
2987 3163 1.805943 GTCGCCTTACCGCCTTAAAAA 59.194 47.619 0.00 0.00 0.00 1.94
2988 3164 1.805943 TCGCCTTACCGCCTTAAAAAC 59.194 47.619 0.00 0.00 0.00 2.43
2989 3165 1.536331 CGCCTTACCGCCTTAAAAACA 59.464 47.619 0.00 0.00 0.00 2.83
2990 3166 2.162809 CGCCTTACCGCCTTAAAAACAT 59.837 45.455 0.00 0.00 0.00 2.71
2991 3167 3.374678 CGCCTTACCGCCTTAAAAACATA 59.625 43.478 0.00 0.00 0.00 2.29
2992 3168 4.495184 CGCCTTACCGCCTTAAAAACATAG 60.495 45.833 0.00 0.00 0.00 2.23
2993 3169 4.732647 GCCTTACCGCCTTAAAAACATAGC 60.733 45.833 0.00 0.00 0.00 2.97
2994 3170 4.201980 CCTTACCGCCTTAAAAACATAGCC 60.202 45.833 0.00 0.00 0.00 3.93
2995 3171 2.097036 ACCGCCTTAAAAACATAGCCC 58.903 47.619 0.00 0.00 0.00 5.19
2996 3172 2.291346 ACCGCCTTAAAAACATAGCCCT 60.291 45.455 0.00 0.00 0.00 5.19
2997 3173 2.099098 CCGCCTTAAAAACATAGCCCTG 59.901 50.000 0.00 0.00 0.00 4.45
2998 3174 2.752903 CGCCTTAAAAACATAGCCCTGT 59.247 45.455 0.00 0.00 0.00 4.00
2999 3175 3.427503 CGCCTTAAAAACATAGCCCTGTG 60.428 47.826 0.00 0.00 0.00 3.66
3040 3216 5.525378 CGGCTATAGCTGTTCTTTCAATCTT 59.475 40.000 23.20 0.00 42.29 2.40
3057 3233 9.487790 TTTCAATCTTGTTTTAGGCATTTAAGG 57.512 29.630 0.00 0.00 0.00 2.69
3080 3256 2.226962 AACTAGCTCCGGTGGTTAGA 57.773 50.000 14.11 0.00 33.34 2.10
3162 3345 3.921104 TGAGCACCATCTAGAGGATTCT 58.079 45.455 5.84 0.00 37.46 2.40
3167 3350 4.617995 GCACCATCTAGAGGATTCTGATCG 60.618 50.000 5.84 0.00 34.79 3.69
3297 3480 7.839680 ACCAACTTCAAATACTCAATTCCTT 57.160 32.000 0.00 0.00 0.00 3.36
3947 4130 6.054860 ACTTGGCTACAGTTCTTGTATGAT 57.945 37.500 0.00 0.00 41.30 2.45
4153 4336 6.431234 ACCTATTTCACCTCAAAGTTGATCAC 59.569 38.462 0.00 0.00 36.46 3.06
4219 4403 3.859411 TTTGTTTTCCTTTGTCAGCGT 57.141 38.095 0.00 0.00 0.00 5.07
4526 4711 6.633500 TTCTGCTTGCAAGTATGTTTAGTT 57.367 33.333 26.55 0.00 0.00 2.24
4527 4712 6.000891 TCTGCTTGCAAGTATGTTTAGTTG 57.999 37.500 26.55 8.14 40.36 3.16
4893 5103 0.251354 TTCTGCATGAGGAGGTCTGC 59.749 55.000 0.00 0.00 33.43 4.26
5259 5473 1.340017 GGCCAAGATAGAACTGGTGCA 60.340 52.381 0.00 0.00 0.00 4.57
5362 5576 6.372659 TGAAGAAAGTGATGAAGAGGTATTGC 59.627 38.462 0.00 0.00 0.00 3.56
5399 5613 2.551459 GCTCTTGCTTGCCTATATGGTG 59.449 50.000 0.00 0.00 35.60 4.17
5401 5615 3.808728 TCTTGCTTGCCTATATGGTGAC 58.191 45.455 0.00 0.00 38.35 3.67
5436 5650 8.424628 TGCGTAATTTGTTTACTTGTAAATCG 57.575 30.769 8.87 7.18 38.44 3.34
5616 5831 3.799281 ACCTGAACCAAAACACATGTG 57.201 42.857 24.25 24.25 0.00 3.21
5617 5832 2.430332 ACCTGAACCAAAACACATGTGG 59.570 45.455 28.64 13.85 38.46 4.17
5901 6116 7.012515 ACAAAATTGTAATCTGAACACGTACCA 59.987 33.333 0.00 0.00 40.16 3.25
5972 6194 8.519526 TGAAACATGTTTTTCATATGTACTCCC 58.480 33.333 24.02 6.88 39.94 4.30
5973 6195 8.650143 AAACATGTTTTTCATATGTACTCCCT 57.350 30.769 18.13 0.00 34.18 4.20
5974 6196 7.865706 ACATGTTTTTCATATGTACTCCCTC 57.134 36.000 1.90 0.00 33.57 4.30
5975 6197 6.828785 ACATGTTTTTCATATGTACTCCCTCC 59.171 38.462 1.90 0.00 33.57 4.30
5976 6198 5.424757 TGTTTTTCATATGTACTCCCTCCG 58.575 41.667 1.90 0.00 0.00 4.63
5977 6199 5.046159 TGTTTTTCATATGTACTCCCTCCGT 60.046 40.000 1.90 0.00 0.00 4.69
5978 6200 6.154877 TGTTTTTCATATGTACTCCCTCCGTA 59.845 38.462 1.90 0.00 0.00 4.02
5979 6201 6.795144 TTTTCATATGTACTCCCTCCGTAA 57.205 37.500 1.90 0.00 0.00 3.18
5980 6202 6.795144 TTTCATATGTACTCCCTCCGTAAA 57.205 37.500 1.90 0.00 0.00 2.01
5981 6203 5.779529 TCATATGTACTCCCTCCGTAAAC 57.220 43.478 1.90 0.00 0.00 2.01
5982 6204 5.452255 TCATATGTACTCCCTCCGTAAACT 58.548 41.667 1.90 0.00 0.00 2.66
5983 6205 6.604171 TCATATGTACTCCCTCCGTAAACTA 58.396 40.000 1.90 0.00 0.00 2.24
5984 6206 7.062322 TCATATGTACTCCCTCCGTAAACTAA 58.938 38.462 1.90 0.00 0.00 2.24
5985 6207 7.727186 TCATATGTACTCCCTCCGTAAACTAAT 59.273 37.037 1.90 0.00 0.00 1.73
5986 6208 9.017509 CATATGTACTCCCTCCGTAAACTAATA 57.982 37.037 0.00 0.00 0.00 0.98
5987 6209 9.765295 ATATGTACTCCCTCCGTAAACTAATAT 57.235 33.333 0.00 0.00 0.00 1.28
5989 6211 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
5990 6212 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
5991 6213 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
5992 6214 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
5993 6215 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
5994 6216 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
5995 6217 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
5996 6218 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
5997 6219 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
5998 6220 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
5999 6221 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
6000 6222 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
6012 6234 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
6013 6235 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
6027 6249 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
6028 6250 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
6029 6251 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
6030 6252 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
6045 6267 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
6046 6268 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
6047 6269 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
6048 6270 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
6049 6271 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
6146 6368 9.796120 TGTTTTTGACGAATTTTAGTTCATTCT 57.204 25.926 0.00 0.00 0.00 2.40
6148 6370 9.796120 TTTTTGACGAATTTTAGTTCATTCTGT 57.204 25.926 0.00 0.00 0.00 3.41
6218 6442 2.254546 TCTCAAGACATTTGGCGTGT 57.745 45.000 0.00 0.00 34.09 4.49
6219 6443 1.872952 TCTCAAGACATTTGGCGTGTG 59.127 47.619 0.00 0.00 34.09 3.82
6607 6862 1.698506 TTGGAAGATTGGCCGTTGTT 58.301 45.000 0.00 0.00 0.00 2.83
6652 6907 2.769663 TGGTACAAGTAGGCATCCGATT 59.230 45.455 0.00 0.00 31.92 3.34
6687 6942 2.037772 GTGACTGTTGAGGTGTGATCCT 59.962 50.000 0.00 0.00 40.97 3.24
6690 6945 4.246458 GACTGTTGAGGTGTGATCCTTAC 58.754 47.826 0.00 0.00 38.02 2.34
6702 6957 3.927142 GTGATCCTTACCGTTTCTGAGTG 59.073 47.826 0.00 0.00 0.00 3.51
6706 6961 2.729882 CCTTACCGTTTCTGAGTGAACG 59.270 50.000 13.80 13.80 33.88 3.95
6792 7047 1.727857 GCCAGGTGTTTTATTCGCACG 60.728 52.381 0.00 0.00 34.25 5.34
6908 7269 8.795842 TTGAACCATTAAATGACTAATACCGT 57.204 30.769 0.00 0.00 0.00 4.83
6979 9543 0.392060 GTTCGCCCTCCCATAACGTT 60.392 55.000 5.88 5.88 0.00 3.99
6982 9546 1.077716 GCCCTCCCATAACGTTGCT 60.078 57.895 11.99 0.00 0.00 3.91
7026 9645 2.429610 TCCTCTAATGACCAACGCTACC 59.570 50.000 0.00 0.00 0.00 3.18
7030 9649 2.311124 AATGACCAACGCTACCTAGC 57.689 50.000 0.00 0.00 45.62 3.42
7031 9650 1.486211 ATGACCAACGCTACCTAGCT 58.514 50.000 2.91 0.00 46.85 3.32
7032 9651 0.530744 TGACCAACGCTACCTAGCTG 59.469 55.000 0.00 0.00 46.85 4.24
7034 9653 1.747355 GACCAACGCTACCTAGCTGTA 59.253 52.381 0.00 0.00 46.85 2.74
7035 9654 2.165030 GACCAACGCTACCTAGCTGTAA 59.835 50.000 0.00 0.00 46.85 2.41
7036 9655 2.094338 ACCAACGCTACCTAGCTGTAAC 60.094 50.000 0.00 0.00 46.85 2.50
7037 9656 2.537401 CAACGCTACCTAGCTGTAACC 58.463 52.381 0.00 0.00 46.85 2.85
7038 9657 0.737219 ACGCTACCTAGCTGTAACCG 59.263 55.000 0.00 0.00 46.85 4.44
7039 9658 0.737219 CGCTACCTAGCTGTAACCGT 59.263 55.000 0.00 0.00 46.85 4.83
7040 9659 1.268437 CGCTACCTAGCTGTAACCGTC 60.268 57.143 0.00 0.00 46.85 4.79
7041 9660 2.022934 GCTACCTAGCTGTAACCGTCT 58.977 52.381 0.00 0.00 45.62 4.18
7042 9661 2.426381 GCTACCTAGCTGTAACCGTCTT 59.574 50.000 0.00 0.00 45.62 3.01
7043 9662 3.119209 GCTACCTAGCTGTAACCGTCTTT 60.119 47.826 0.00 0.00 45.62 2.52
7044 9663 4.096984 GCTACCTAGCTGTAACCGTCTTTA 59.903 45.833 0.00 0.00 45.62 1.85
7045 9664 5.221204 GCTACCTAGCTGTAACCGTCTTTAT 60.221 44.000 0.00 0.00 45.62 1.40
7046 9665 5.007385 ACCTAGCTGTAACCGTCTTTATG 57.993 43.478 0.00 0.00 0.00 1.90
7047 9666 3.802685 CCTAGCTGTAACCGTCTTTATGC 59.197 47.826 0.00 0.00 0.00 3.14
7048 9667 3.328382 AGCTGTAACCGTCTTTATGCA 57.672 42.857 0.00 0.00 0.00 3.96
7049 9668 3.000727 AGCTGTAACCGTCTTTATGCAC 58.999 45.455 0.00 0.00 0.00 4.57
7050 9669 3.000727 GCTGTAACCGTCTTTATGCACT 58.999 45.455 0.00 0.00 0.00 4.40
7051 9670 4.081862 AGCTGTAACCGTCTTTATGCACTA 60.082 41.667 0.00 0.00 0.00 2.74
7052 9671 4.628333 GCTGTAACCGTCTTTATGCACTAA 59.372 41.667 0.00 0.00 0.00 2.24
7053 9672 5.220416 GCTGTAACCGTCTTTATGCACTAAG 60.220 44.000 0.00 0.00 0.00 2.18
7054 9673 5.786311 TGTAACCGTCTTTATGCACTAAGT 58.214 37.500 8.90 0.00 0.00 2.24
7055 9674 6.225318 TGTAACCGTCTTTATGCACTAAGTT 58.775 36.000 8.90 1.61 0.00 2.66
7056 9675 6.707161 TGTAACCGTCTTTATGCACTAAGTTT 59.293 34.615 8.90 3.29 0.00 2.66
7106 9726 4.811908 TCATTCGAAACAACGGTCATAGA 58.188 39.130 0.00 0.00 0.00 1.98
7128 9748 1.064017 ACACTGTTTGGGTCATGTGGT 60.064 47.619 0.00 0.00 0.00 4.16
7156 9776 3.695830 ACCAAACATGTCGACCTACAT 57.304 42.857 14.12 0.00 40.75 2.29
7165 9785 8.410673 AACATGTCGACCTACATCTAGATTAT 57.589 34.615 14.12 0.00 38.01 1.28
7256 9878 1.949465 AAACTCCCACAACGAGTCAC 58.051 50.000 0.00 0.00 39.69 3.67
7290 9912 2.054453 GGCAGCATTTGGACCTCCC 61.054 63.158 0.00 0.00 34.29 4.30
7330 9953 0.758734 CACCACTCCTTGACAGTCCA 59.241 55.000 0.00 0.00 0.00 4.02
7400 10023 3.871594 GCTTCACGGTATGCATAAGTCTT 59.128 43.478 8.28 0.00 0.00 3.01
7457 10080 1.329256 GCCGAGGAGCCTAGATACAA 58.671 55.000 0.00 0.00 0.00 2.41
7468 10091 3.565902 GCCTAGATACAAACCAGATTGGC 59.434 47.826 0.00 0.00 42.67 4.52
7516 10142 0.892755 ACGACGGGATCTTGCTACAA 59.107 50.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.003233 GACTCCCTGAAGCACCCAC 60.003 63.158 0.00 0.00 0.00 4.61
87 88 0.885150 GTAGCCCTATTTGCCTCCGC 60.885 60.000 0.00 0.00 0.00 5.54
108 109 1.807165 CACATCGCGTCCACTCTGG 60.807 63.158 5.77 0.00 39.43 3.86
110 111 2.573869 CCACATCGCGTCCACTCT 59.426 61.111 5.77 0.00 0.00 3.24
132 133 2.198426 CCTTGGTTGCACCCACCT 59.802 61.111 0.70 0.00 37.50 4.00
168 169 1.740296 CTCGCCAACCGACCGATTT 60.740 57.895 0.00 0.00 41.89 2.17
170 171 4.814294 GCTCGCCAACCGACCGAT 62.814 66.667 0.00 0.00 41.89 4.18
239 252 3.962718 CCCTAATTGGCACATGGAAGATT 59.037 43.478 0.00 0.00 39.30 2.40
244 257 2.358090 CCTTCCCTAATTGGCACATGGA 60.358 50.000 0.00 0.00 39.30 3.41
246 259 3.017048 TCCTTCCCTAATTGGCACATG 57.983 47.619 0.00 0.00 39.30 3.21
248 261 3.534357 TTTCCTTCCCTAATTGGCACA 57.466 42.857 0.00 0.00 0.00 4.57
316 329 3.756933 AACTTACCGTAAGAGCAACCA 57.243 42.857 22.48 0.00 39.09 3.67
332 345 3.119316 TGATGTGGACGCAAACAAAACTT 60.119 39.130 0.00 0.00 0.00 2.66
333 346 2.425312 TGATGTGGACGCAAACAAAACT 59.575 40.909 0.00 0.00 0.00 2.66
335 348 3.724508 ATGATGTGGACGCAAACAAAA 57.275 38.095 0.00 0.00 0.00 2.44
356 370 3.096092 ACAACTCCAGGTGAAGCAAAAA 58.904 40.909 0.00 0.00 0.00 1.94
363 377 2.637872 CCTAAGGACAACTCCAGGTGAA 59.362 50.000 0.00 0.00 39.39 3.18
382 396 9.430623 GCAACCAAACAAACATTTATAATACCT 57.569 29.630 0.00 0.00 0.00 3.08
410 424 7.862873 CCAGGTGAGTTTTCTTTTTCATAGAAC 59.137 37.037 0.00 0.00 31.68 3.01
412 426 6.016276 GCCAGGTGAGTTTTCTTTTTCATAGA 60.016 38.462 0.00 0.00 0.00 1.98
431 445 5.193679 GGTACAAAGAAATCTATGCCAGGT 58.806 41.667 0.00 0.00 0.00 4.00
438 452 9.269453 GGCTAATTACGGTACAAAGAAATCTAT 57.731 33.333 0.00 0.00 0.00 1.98
441 455 7.407337 CAGGCTAATTACGGTACAAAGAAATC 58.593 38.462 0.00 0.00 0.00 2.17
479 493 0.746563 GCCAGGCTAATTACCGTGCA 60.747 55.000 3.29 0.00 0.00 4.57
507 521 2.038269 GCCAGGCGTCCGAATTTGA 61.038 57.895 0.00 0.00 0.00 2.69
509 523 2.750237 GGCCAGGCGTCCGAATTT 60.750 61.111 5.00 0.00 0.00 1.82
587 601 7.577616 GCAAAAATATAGAACAGGTTTGCCTCT 60.578 37.037 6.90 0.00 44.97 3.69
615 631 5.957796 CGGTTTCGTTCTTGTATTTGATAGC 59.042 40.000 0.00 0.00 0.00 2.97
619 635 4.211794 GGTCGGTTTCGTTCTTGTATTTGA 59.788 41.667 0.00 0.00 37.69 2.69
624 640 1.411977 TGGGTCGGTTTCGTTCTTGTA 59.588 47.619 0.00 0.00 37.69 2.41
628 644 2.148768 GAAATGGGTCGGTTTCGTTCT 58.851 47.619 0.00 0.00 37.69 3.01
647 663 4.566278 CCATGAACACTTCCATTCCAGAGA 60.566 45.833 0.00 0.00 0.00 3.10
658 674 6.515272 AATGAACCATACCATGAACACTTC 57.485 37.500 0.00 0.00 0.00 3.01
679 701 3.237268 TGAAGGGTGTGCTTGGTTAAT 57.763 42.857 0.00 0.00 0.00 1.40
681 703 2.107378 TGATGAAGGGTGTGCTTGGTTA 59.893 45.455 0.00 0.00 0.00 2.85
688 710 0.537143 TGTGGTGATGAAGGGTGTGC 60.537 55.000 0.00 0.00 0.00 4.57
729 751 3.950395 AGATGTAAAATCTTCCTGCCAGC 59.050 43.478 0.00 0.00 0.00 4.85
730 752 4.272018 CGAGATGTAAAATCTTCCTGCCAG 59.728 45.833 0.00 0.00 0.00 4.85
731 753 4.191544 CGAGATGTAAAATCTTCCTGCCA 58.808 43.478 0.00 0.00 0.00 4.92
732 754 3.002759 GCGAGATGTAAAATCTTCCTGCC 59.997 47.826 0.00 0.00 0.00 4.85
734 756 3.865745 ACGCGAGATGTAAAATCTTCCTG 59.134 43.478 15.93 0.00 0.00 3.86
735 757 4.113354 GACGCGAGATGTAAAATCTTCCT 58.887 43.478 15.93 0.00 0.00 3.36
736 758 3.245519 GGACGCGAGATGTAAAATCTTCC 59.754 47.826 15.93 0.00 0.00 3.46
737 759 4.113354 AGGACGCGAGATGTAAAATCTTC 58.887 43.478 15.93 0.00 0.00 2.87
738 760 4.124851 AGGACGCGAGATGTAAAATCTT 57.875 40.909 15.93 0.00 0.00 2.40
739 761 3.802948 AGGACGCGAGATGTAAAATCT 57.197 42.857 15.93 0.00 0.00 2.40
740 762 3.863424 TGAAGGACGCGAGATGTAAAATC 59.137 43.478 15.93 0.00 0.00 2.17
742 764 3.306917 TGAAGGACGCGAGATGTAAAA 57.693 42.857 15.93 0.00 0.00 1.52
743 765 3.444916 GATGAAGGACGCGAGATGTAAA 58.555 45.455 15.93 0.00 0.00 2.01
744 766 2.540973 CGATGAAGGACGCGAGATGTAA 60.541 50.000 15.93 0.00 0.00 2.41
745 767 1.002792 CGATGAAGGACGCGAGATGTA 60.003 52.381 15.93 0.00 0.00 2.29
746 768 0.248661 CGATGAAGGACGCGAGATGT 60.249 55.000 15.93 0.00 0.00 3.06
747 769 0.248661 ACGATGAAGGACGCGAGATG 60.249 55.000 15.93 0.00 0.00 2.90
749 771 1.428219 GACGATGAAGGACGCGAGA 59.572 57.895 15.93 0.00 0.00 4.04
750 772 1.934956 CGACGATGAAGGACGCGAG 60.935 63.158 15.93 0.00 33.69 5.03
751 773 2.099638 CGACGATGAAGGACGCGA 59.900 61.111 15.93 0.00 33.69 5.87
752 774 2.949678 CCGACGATGAAGGACGCG 60.950 66.667 3.53 3.53 0.00 6.01
754 776 4.379221 GTCCGACGATGAAGGACG 57.621 61.111 0.00 0.00 43.96 4.79
1017 1189 2.941415 GCCGAGGGAGATGTTGTTGAAT 60.941 50.000 0.00 0.00 0.00 2.57
1188 1360 1.735571 GCCGTTCTGAAAAATCCGCTA 59.264 47.619 0.00 0.00 0.00 4.26
1189 1361 0.521735 GCCGTTCTGAAAAATCCGCT 59.478 50.000 0.00 0.00 0.00 5.52
1235 1407 1.882623 GCAGAGAGGAAACAAACCCTG 59.117 52.381 0.00 0.00 31.84 4.45
1248 1420 0.179161 CAGTTCCGTACCGCAGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
1369 1544 5.048713 CCTGGTTGTAGTTGAGTTTCCAATC 60.049 44.000 0.00 0.00 0.00 2.67
1403 1578 2.289565 GAACATGTTCCTCGAATCCCC 58.710 52.381 25.26 0.00 33.64 4.81
1483 1658 8.137437 GGTAGCAATTGCACAAGACATTTATAT 58.863 33.333 30.89 7.95 45.16 0.86
1484 1659 7.121907 TGGTAGCAATTGCACAAGACATTTATA 59.878 33.333 30.89 8.03 45.16 0.98
1485 1660 6.071447 TGGTAGCAATTGCACAAGACATTTAT 60.071 34.615 30.89 9.03 45.16 1.40
1486 1661 5.242615 TGGTAGCAATTGCACAAGACATTTA 59.757 36.000 30.89 8.74 45.16 1.40
1487 1662 4.039004 TGGTAGCAATTGCACAAGACATTT 59.961 37.500 30.89 9.74 45.16 2.32
1656 1831 4.445453 TCACATCTAGGCATGCTAAACAG 58.555 43.478 18.92 7.80 0.00 3.16
1667 1842 5.182001 ACAAGTGTTTCAATCACATCTAGGC 59.818 40.000 1.48 0.00 38.16 3.93
2363 2539 3.885297 CCCAATTATGGCCACTAACAGAG 59.115 47.826 8.16 0.00 46.09 3.35
2393 2569 4.558226 ACTCAGCTAACCATTGATGTCA 57.442 40.909 0.00 0.00 0.00 3.58
2635 2811 8.377799 TGATCAATATATACAGGCAGACAACAT 58.622 33.333 0.00 0.00 0.00 2.71
2837 3013 4.412207 GCAAGACGCCTTAAAAACATAGG 58.588 43.478 0.00 0.00 32.94 2.57
2853 3029 1.079503 CTAAGCGTCCAAGGCAAGAC 58.920 55.000 0.00 0.00 0.00 3.01
2854 3030 0.036388 CCTAAGCGTCCAAGGCAAGA 60.036 55.000 0.00 0.00 0.00 3.02
2855 3031 2.471255 CCTAAGCGTCCAAGGCAAG 58.529 57.895 0.00 0.00 0.00 4.01
2856 3032 4.713946 CCTAAGCGTCCAAGGCAA 57.286 55.556 0.00 0.00 0.00 4.52
2874 3050 4.545706 TGCCAGGGCGCCTTATCG 62.546 66.667 28.56 10.79 45.51 2.92
2875 3051 2.592861 CTGCCAGGGCGCCTTATC 60.593 66.667 28.56 14.20 45.51 1.75
2876 3052 3.411517 ACTGCCAGGGCGCCTTAT 61.412 61.111 28.56 10.23 45.51 1.73
2877 3053 4.408821 CACTGCCAGGGCGCCTTA 62.409 66.667 28.56 2.14 45.51 2.69
2889 3065 2.223805 GGGCATATTTGTAAGGCACTGC 60.224 50.000 0.00 0.00 40.86 4.40
2890 3066 2.033299 CGGGCATATTTGTAAGGCACTG 59.967 50.000 0.00 0.00 40.86 3.66
2892 3068 1.269051 GCGGGCATATTTGTAAGGCAC 60.269 52.381 0.00 0.00 0.00 5.01
2893 3069 1.028905 GCGGGCATATTTGTAAGGCA 58.971 50.000 0.00 0.00 0.00 4.75
2894 3070 0.313987 GGCGGGCATATTTGTAAGGC 59.686 55.000 0.00 0.00 0.00 4.35
2895 3071 1.981256 AGGCGGGCATATTTGTAAGG 58.019 50.000 3.78 0.00 0.00 2.69
2896 3072 3.502211 CCTAAGGCGGGCATATTTGTAAG 59.498 47.826 3.78 0.00 0.00 2.34
2897 3073 3.482436 CCTAAGGCGGGCATATTTGTAA 58.518 45.455 3.78 0.00 0.00 2.41
2898 3074 3.134574 CCTAAGGCGGGCATATTTGTA 57.865 47.619 3.78 0.00 0.00 2.41
2899 3075 1.981256 CCTAAGGCGGGCATATTTGT 58.019 50.000 3.78 0.00 0.00 2.83
2941 3117 3.775654 AGCACCACCCGCTCTAGC 61.776 66.667 0.00 0.00 33.35 3.42
2954 3130 1.448013 GGCGACCTAAGGTGAGCAC 60.448 63.158 0.00 0.00 37.58 4.40
2955 3131 1.192146 AAGGCGACCTAAGGTGAGCA 61.192 55.000 0.00 0.00 37.58 4.26
2956 3132 0.822164 TAAGGCGACCTAAGGTGAGC 59.178 55.000 0.00 0.00 35.25 4.26
2957 3133 1.136500 GGTAAGGCGACCTAAGGTGAG 59.864 57.143 4.54 0.00 35.25 3.51
2958 3134 1.188863 GGTAAGGCGACCTAAGGTGA 58.811 55.000 4.54 0.00 35.25 4.02
2959 3135 0.179119 CGGTAAGGCGACCTAAGGTG 60.179 60.000 9.52 0.00 35.25 4.00
2960 3136 1.953231 GCGGTAAGGCGACCTAAGGT 61.953 60.000 9.52 0.00 39.44 3.50
2961 3137 1.227176 GCGGTAAGGCGACCTAAGG 60.227 63.158 9.52 0.00 37.34 2.69
2962 3138 1.227176 GGCGGTAAGGCGACCTAAG 60.227 63.158 9.52 0.00 37.34 2.18
2963 3139 2.894919 GGCGGTAAGGCGACCTAA 59.105 61.111 9.52 0.00 37.34 2.69
2971 3147 4.201980 GGCTATGTTTTTAAGGCGGTAAGG 60.202 45.833 0.00 0.00 0.00 2.69
2972 3148 4.201980 GGGCTATGTTTTTAAGGCGGTAAG 60.202 45.833 0.00 0.00 36.71 2.34
2973 3149 3.695556 GGGCTATGTTTTTAAGGCGGTAA 59.304 43.478 0.00 0.00 36.71 2.85
2974 3150 3.054213 AGGGCTATGTTTTTAAGGCGGTA 60.054 43.478 0.00 0.00 36.71 4.02
2975 3151 2.097036 GGGCTATGTTTTTAAGGCGGT 58.903 47.619 0.00 0.00 36.71 5.68
2976 3152 2.099098 CAGGGCTATGTTTTTAAGGCGG 59.901 50.000 0.00 0.00 36.71 6.13
2977 3153 2.752903 ACAGGGCTATGTTTTTAAGGCG 59.247 45.455 0.00 0.00 36.71 5.52
2978 3154 3.676049 GCACAGGGCTATGTTTTTAAGGC 60.676 47.826 0.00 0.00 40.25 4.35
2979 3155 3.509575 TGCACAGGGCTATGTTTTTAAGG 59.490 43.478 0.00 0.00 45.15 2.69
2980 3156 4.485163 GTGCACAGGGCTATGTTTTTAAG 58.515 43.478 13.17 0.00 45.15 1.85
2981 3157 3.057876 CGTGCACAGGGCTATGTTTTTAA 60.058 43.478 18.64 0.00 45.15 1.52
2982 3158 2.486203 CGTGCACAGGGCTATGTTTTTA 59.514 45.455 18.64 0.00 45.15 1.52
2983 3159 1.269448 CGTGCACAGGGCTATGTTTTT 59.731 47.619 18.64 0.00 45.15 1.94
2984 3160 0.881118 CGTGCACAGGGCTATGTTTT 59.119 50.000 18.64 0.00 45.15 2.43
2985 3161 0.250727 ACGTGCACAGGGCTATGTTT 60.251 50.000 18.64 0.00 45.15 2.83
2986 3162 0.611200 TACGTGCACAGGGCTATGTT 59.389 50.000 18.64 0.00 45.15 2.71
2987 3163 0.611200 TTACGTGCACAGGGCTATGT 59.389 50.000 18.64 6.32 45.15 2.29
2988 3164 1.732941 TTTACGTGCACAGGGCTATG 58.267 50.000 18.64 0.00 45.15 2.23
2989 3165 2.290071 ACTTTTACGTGCACAGGGCTAT 60.290 45.455 18.64 0.00 45.15 2.97
2990 3166 1.071071 ACTTTTACGTGCACAGGGCTA 59.929 47.619 18.64 0.00 45.15 3.93
2991 3167 0.179029 ACTTTTACGTGCACAGGGCT 60.179 50.000 18.64 0.00 45.15 5.19
2992 3168 0.666374 AACTTTTACGTGCACAGGGC 59.334 50.000 18.64 0.00 45.13 5.19
2993 3169 4.472286 CATAAACTTTTACGTGCACAGGG 58.528 43.478 18.64 2.84 0.00 4.45
2994 3170 3.911964 GCATAAACTTTTACGTGCACAGG 59.088 43.478 18.64 3.67 31.99 4.00
2995 3171 3.597825 CGCATAAACTTTTACGTGCACAG 59.402 43.478 18.64 12.16 31.45 3.66
2996 3172 3.546617 CGCATAAACTTTTACGTGCACA 58.453 40.909 18.64 0.00 31.45 4.57
2997 3173 2.906161 CCGCATAAACTTTTACGTGCAC 59.094 45.455 6.82 6.82 31.45 4.57
2998 3174 2.666069 GCCGCATAAACTTTTACGTGCA 60.666 45.455 0.00 0.00 31.45 4.57
2999 3175 1.908889 GCCGCATAAACTTTTACGTGC 59.091 47.619 0.00 0.00 0.00 5.34
3040 3216 9.444600 CTAGTTAGACCTTAAATGCCTAAAACA 57.555 33.333 0.00 0.00 0.00 2.83
3054 3230 2.100989 CACCGGAGCTAGTTAGACCTT 58.899 52.381 9.46 0.00 0.00 3.50
3057 3233 1.472188 ACCACCGGAGCTAGTTAGAC 58.528 55.000 9.46 0.00 0.00 2.59
3080 3256 9.036980 GGAAAGTGTATCTCCTATGTATATGGT 57.963 37.037 0.00 0.00 0.00 3.55
3162 3345 7.731882 TGTAAGATTTTTGTGGTAACGATCA 57.268 32.000 0.00 0.00 42.51 2.92
3297 3480 0.544357 AGGGACGTTCCTCATCACCA 60.544 55.000 10.55 0.00 36.57 4.17
3922 4105 5.932303 TCATACAAGAACTGTAGCCAAGTTC 59.068 40.000 13.28 13.28 43.78 3.01
4219 4403 9.177608 AGAGCACTTGATAATTAAAGCATGTAA 57.822 29.630 0.00 0.00 0.00 2.41
4477 4661 5.741962 ATGCATGTCAGTAGCTCTATGAT 57.258 39.130 0.00 0.00 0.00 2.45
4526 4711 7.750229 ATTCAGTTCAGTAAAGCATTCTTCA 57.250 32.000 0.00 0.00 0.00 3.02
4595 4780 6.537301 TGCACAAGTAGAAAACGGAATATAGG 59.463 38.462 0.00 0.00 0.00 2.57
4596 4781 7.277981 AGTGCACAAGTAGAAAACGGAATATAG 59.722 37.037 21.04 0.00 0.00 1.31
4597 4782 7.101054 AGTGCACAAGTAGAAAACGGAATATA 58.899 34.615 21.04 0.00 0.00 0.86
4598 4783 5.938125 AGTGCACAAGTAGAAAACGGAATAT 59.062 36.000 21.04 0.00 0.00 1.28
4599 4784 5.302360 AGTGCACAAGTAGAAAACGGAATA 58.698 37.500 21.04 0.00 0.00 1.75
4600 4785 4.134563 AGTGCACAAGTAGAAAACGGAAT 58.865 39.130 21.04 0.00 0.00 3.01
4602 4787 3.188159 AGTGCACAAGTAGAAAACGGA 57.812 42.857 21.04 0.00 0.00 4.69
4603 4788 3.617669 CAAGTGCACAAGTAGAAAACGG 58.382 45.455 21.04 0.00 0.00 4.44
4604 4789 3.035942 GCAAGTGCACAAGTAGAAAACG 58.964 45.455 21.04 0.00 41.59 3.60
4893 5103 7.615582 TTAGGCATGTCAGAAATGTAGAAAG 57.384 36.000 0.00 0.00 0.00 2.62
4966 5176 3.345714 GCGCTCAAATTCAACATACTCG 58.654 45.455 0.00 0.00 0.00 4.18
5259 5473 1.670406 CTGAAGAGCAGCCGCAACT 60.670 57.895 0.00 0.00 42.27 3.16
5384 5598 1.070134 TCCGTCACCATATAGGCAAGC 59.930 52.381 0.00 0.00 43.14 4.01
5399 5613 4.565564 ACAAATTACGCATTCTACTCCGTC 59.434 41.667 0.00 0.00 35.36 4.79
5401 5615 5.464965 AACAAATTACGCATTCTACTCCG 57.535 39.130 0.00 0.00 0.00 4.63
5436 5650 8.092687 TCCTGAAGTTGGAATAAGTTACAGTAC 58.907 37.037 0.00 0.00 27.72 2.73
5634 5849 9.833182 GGAAGATTTCTGAAACAAGAAGTTATC 57.167 33.333 4.73 0.00 40.26 1.75
5873 6088 7.022055 ACGTGTTCAGATTACAATTTTGTCA 57.978 32.000 0.00 0.00 42.35 3.58
5901 6116 0.333993 ATGCAGTTTGGGATGGAGCT 59.666 50.000 0.00 0.00 0.00 4.09
5968 6190 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
5969 6191 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
5970 6192 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
5971 6193 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
5972 6194 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
5973 6195 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
5974 6196 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
5986 6208 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
5987 6209 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
5988 6210 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
5989 6211 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
6003 6225 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
6004 6226 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
6019 6241 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
6020 6242 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
6021 6243 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
6022 6244 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
6023 6245 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
6034 6256 8.612145 ACCAAATAAATACTCCCTCTGTAAACT 58.388 33.333 0.00 0.00 0.00 2.66
6035 6257 8.803397 ACCAAATAAATACTCCCTCTGTAAAC 57.197 34.615 0.00 0.00 0.00 2.01
6146 6368 4.085357 AGAAACCATAGACTGCAACACA 57.915 40.909 0.00 0.00 0.00 3.72
6147 6369 5.643777 ACATAGAAACCATAGACTGCAACAC 59.356 40.000 0.00 0.00 0.00 3.32
6148 6370 5.804639 ACATAGAAACCATAGACTGCAACA 58.195 37.500 0.00 0.00 0.00 3.33
6218 6442 5.042593 CACTGTTTGCTTAATTTGACAGCA 58.957 37.500 0.00 0.00 41.85 4.41
6219 6443 4.445385 CCACTGTTTGCTTAATTTGACAGC 59.555 41.667 0.00 0.00 38.37 4.40
6418 6671 8.788806 ACAATTGGAAATGATTAACACGAGTTA 58.211 29.630 10.83 0.99 39.15 2.24
6607 6862 4.021456 TGACTCGAAAGTATGCTCCTTTCA 60.021 41.667 17.42 8.46 45.14 2.69
6652 6907 5.011635 TCAACAGTCACTACAGCCAAGATAA 59.988 40.000 0.00 0.00 0.00 1.75
6687 6942 3.713858 TCGTTCACTCAGAAACGGTAA 57.286 42.857 14.27 0.00 38.13 2.85
6690 6945 2.739292 TCTTCGTTCACTCAGAAACGG 58.261 47.619 14.27 3.37 38.13 4.44
6702 6957 7.648510 CCTACATATCCTAACTGTTCTTCGTTC 59.351 40.741 0.00 0.00 0.00 3.95
6706 6961 7.927092 GGAACCTACATATCCTAACTGTTCTTC 59.073 40.741 0.00 0.00 32.37 2.87
6773 7028 1.727857 GCGTGCGAATAAAACACCTGG 60.728 52.381 0.00 0.00 0.00 4.45
6881 7242 7.855904 CGGTATTAGTCATTTAATGGTTCAAGC 59.144 37.037 5.02 0.00 0.00 4.01
6908 7269 1.795768 GTCAACGGCTCATTCTGTGA 58.204 50.000 0.00 0.00 35.05 3.58
6979 9543 1.108727 CACAAAGACTTGGGCCAGCA 61.109 55.000 6.23 0.00 36.82 4.41
7026 9645 4.267928 GTGCATAAAGACGGTTACAGCTAG 59.732 45.833 0.00 0.00 0.00 3.42
7030 9649 5.867716 ACTTAGTGCATAAAGACGGTTACAG 59.132 40.000 15.55 0.00 0.00 2.74
7031 9650 5.786311 ACTTAGTGCATAAAGACGGTTACA 58.214 37.500 15.55 0.00 0.00 2.41
7032 9651 6.716898 AACTTAGTGCATAAAGACGGTTAC 57.283 37.500 15.55 0.00 0.00 2.50
7034 9653 6.628919 AAAACTTAGTGCATAAAGACGGTT 57.371 33.333 15.55 0.85 0.00 4.44
7035 9654 6.628919 AAAAACTTAGTGCATAAAGACGGT 57.371 33.333 15.55 0.00 0.00 4.83
7060 9679 8.729756 TGAATAAAGATGCGAGATTTCTCAAAA 58.270 29.630 8.23 0.00 43.00 2.44
7064 9683 7.739477 CGAATGAATAAAGATGCGAGATTTCTC 59.261 37.037 0.00 0.00 39.55 2.87
7106 9726 3.181434 ACCACATGACCCAAACAGTGTAT 60.181 43.478 0.00 0.00 0.00 2.29
7128 9748 1.240256 GACATGTTTGGTTGGGCGTA 58.760 50.000 0.00 0.00 0.00 4.42
7165 9785 6.090898 GCTCGTAATCTCTTCAAGTTTGCTTA 59.909 38.462 0.00 0.00 32.87 3.09
7177 9799 9.482627 CTTTAATTATGAGGCTCGTAATCTCTT 57.517 33.333 31.74 22.70 37.53 2.85
7178 9800 8.643324 ACTTTAATTATGAGGCTCGTAATCTCT 58.357 33.333 31.74 22.49 37.53 3.10
7186 9808 6.144080 CGTAGGAACTTTAATTATGAGGCTCG 59.856 42.308 10.42 0.00 41.75 5.03
7243 9865 4.690748 ACATGAAATAGTGACTCGTTGTGG 59.309 41.667 0.00 0.00 0.00 4.17
7256 9878 7.444629 AATGCTGCCATAGTACATGAAATAG 57.555 36.000 0.00 0.00 0.00 1.73
7290 9912 2.113860 ATGACATCAACAAGGGGACG 57.886 50.000 0.00 0.00 0.00 4.79
7457 10080 0.112995 TTGCAGAGGCCAATCTGGTT 59.887 50.000 20.38 0.00 45.66 3.67
7468 10091 0.801251 GTAGCAGCTGTTTGCAGAGG 59.199 55.000 16.64 0.00 46.47 3.69
7516 10142 4.636648 TGTGAAAGTAAACGTTGATGGTGT 59.363 37.500 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.