Multiple sequence alignment - TraesCS1D01G184500

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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 TraesCS1D01G184500 chr1D 100.000 5191 0 0 1 5191 254795148 254789958 0.000000e+00 9587.0
1 TraesCS1D01G184500 chr1B 92.879 1671 60 30 599 2241 357637939 357639578 0.000000e+00 2372.0
2 TraesCS1D01G184500 chr1B 91.168 1653 80 40 3559 5191 357640997 357642603 0.000000e+00 2183.0
3 TraesCS1D01G184500 chr1B 92.131 610 31 9 1 603 357637239 357637838 0.000000e+00 845.0
4 TraesCS1D01G184500 chr1B 88.772 285 11 6 2990 3273 357640536 357640800 3.880000e-86 329.0
5 TraesCS1D01G184500 chr1B 85.304 313 28 11 2592 2891 357640232 357640539 1.820000e-79 307.0
6 TraesCS1D01G184500 chr1B 90.517 116 8 3 2880 2992 647110478 647110593 3.240000e-32 150.0
7 TraesCS1D01G184500 chr1A 95.594 1339 24 13 723 2029 327018254 327016919 0.000000e+00 2113.0
8 TraesCS1D01G184500 chr1A 93.110 1103 51 10 3559 4644 327015761 327014667 0.000000e+00 1592.0
9 TraesCS1D01G184500 chr1A 90.842 546 25 9 1 540 327018842 327018316 0.000000e+00 708.0
10 TraesCS1D01G184500 chr1A 93.679 443 22 2 2991 3429 327016266 327015826 0.000000e+00 658.0
11 TraesCS1D01G184500 chr1A 88.262 443 26 11 4678 5120 327014667 327014251 1.670000e-139 507.0
12 TraesCS1D01G184500 chr1A 83.820 445 41 9 2083 2511 327016902 327016473 1.350000e-105 394.0
13 TraesCS1D01G184500 chr1A 91.429 210 9 4 2689 2890 327016475 327016267 3.960000e-71 279.0
14 TraesCS1D01G184500 chr1A 100.000 32 0 0 3450 3481 327015829 327015798 5.610000e-05 60.2
15 TraesCS1D01G184500 chr6B 86.090 798 103 6 995 1791 2772083 2772873 0.000000e+00 852.0
16 TraesCS1D01G184500 chr6B 86.108 799 99 11 996 1791 1133234 1132445 0.000000e+00 850.0
17 TraesCS1D01G184500 chr6B 87.391 571 70 2 3586 4155 1131985 1131416 0.000000e+00 654.0
18 TraesCS1D01G184500 chr6B 86.851 578 73 2 3579 4156 2772998 2773572 1.220000e-180 643.0
19 TraesCS1D01G184500 chrUn 90.297 639 62 0 1153 1791 329195308 329194670 0.000000e+00 837.0
20 TraesCS1D01G184500 chrUn 87.391 571 70 2 3586 4155 329194289 329193720 0.000000e+00 654.0
21 TraesCS1D01G184500 chrUn 84.672 137 17 4 2879 3011 15981944 15981808 3.260000e-27 134.0
22 TraesCS1D01G184500 chr3D 90.435 115 8 3 2886 2997 594424619 594424505 1.160000e-31 148.0
23 TraesCS1D01G184500 chr2D 91.743 109 6 3 2887 2992 71200756 71200864 1.160000e-31 148.0
24 TraesCS1D01G184500 chr2D 91.743 109 6 3 2888 2993 139026157 139026049 1.160000e-31 148.0
25 TraesCS1D01G184500 chr5A 89.744 117 9 3 2879 2992 657200311 657200427 4.190000e-31 147.0
26 TraesCS1D01G184500 chr4A 89.256 121 7 6 2877 2992 597328154 597328035 4.190000e-31 147.0
27 TraesCS1D01G184500 chr4A 90.991 111 7 3 2885 2992 733998430 733998320 4.190000e-31 147.0
28 TraesCS1D01G184500 chr6A 89.655 116 9 3 2884 2996 51405181 51405296 1.510000e-30 145.0


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 TraesCS1D01G184500 chr1D 254789958 254795148 5190 True 9587.0 9587 100.0000 1 5191 1 chr1D.!!$R1 5190
1 TraesCS1D01G184500 chr1B 357637239 357642603 5364 False 1207.2 2372 90.0508 1 5191 5 chr1B.!!$F2 5190
2 TraesCS1D01G184500 chr1A 327014251 327018842 4591 True 788.9 2113 92.0920 1 5120 8 chr1A.!!$R1 5119
3 TraesCS1D01G184500 chr6B 1131416 1133234 1818 True 752.0 850 86.7495 996 4155 2 chr6B.!!$R1 3159
4 TraesCS1D01G184500 chr6B 2772083 2773572 1489 False 747.5 852 86.4705 995 4156 2 chr6B.!!$F1 3161
5 TraesCS1D01G184500 chrUn 329193720 329195308 1588 True 745.5 837 88.8440 1153 4155 2 chrUn.!!$R2 3002

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
123 130 0.457853 CCGTGATCGTGATGGAACGT 60.458 55.0 0.00 0.0 43.96 3.99 F
1816 1961 0.753262 CATCCCGGAACTACTCCCAG 59.247 60.0 0.73 0.0 41.87 4.45 F
2892 3590 0.107654 GCTCACCCTCACATGTACCC 60.108 60.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2151 2.689471 GGTTGACTAAAAACGTGGGGTT 59.311 45.455 0.0 0.0 41.76 4.11 R
3432 4160 0.110486 GTTGGTGATGGTGAGTGGGT 59.890 55.000 0.0 0.0 0.00 4.51 R
4447 5187 0.040958 AAGCGTGCGAGCAAAAAGAG 60.041 50.000 0.0 0.0 40.15 2.85 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
123 130 0.457853 CCGTGATCGTGATGGAACGT 60.458 55.000 0.00 0.00 43.96 3.99
125 132 2.521996 CGTGATCGTGATGGAACGTAA 58.478 47.619 0.00 0.00 43.96 3.18
152 159 1.172812 AAAAAGTGGCGAGCCCAGAC 61.173 55.000 12.05 3.29 46.54 3.51
186 193 1.308998 CATCCTGATACGGTTTGCCC 58.691 55.000 0.00 0.00 0.00 5.36
208 215 0.886563 GGATGCTCACTTTTGCTGCT 59.113 50.000 0.00 0.00 0.00 4.24
273 280 4.045104 CGAATCGTCTATCTTTGTGGAGG 58.955 47.826 0.00 0.00 0.00 4.30
339 346 7.335422 GCTACTAGTAATGGTCGCCTTAGTATA 59.665 40.741 3.76 0.00 0.00 1.47
340 347 7.684937 ACTAGTAATGGTCGCCTTAGTATAG 57.315 40.000 0.00 0.00 0.00 1.31
341 348 5.979288 AGTAATGGTCGCCTTAGTATAGG 57.021 43.478 0.00 0.00 38.40 2.57
342 349 5.638133 AGTAATGGTCGCCTTAGTATAGGA 58.362 41.667 0.00 0.00 37.50 2.94
343 350 6.254522 AGTAATGGTCGCCTTAGTATAGGAT 58.745 40.000 0.00 0.00 37.50 3.24
403 410 1.535462 CTCTTTTCACCGCCGAACATT 59.465 47.619 0.00 0.00 0.00 2.71
516 524 7.065443 ACTGTCGCATAAAATTTACTCCCTTAC 59.935 37.037 0.00 0.00 0.00 2.34
557 565 2.502213 TTCTGCACGACGAAAGAAGA 57.498 45.000 0.00 0.00 0.00 2.87
567 575 6.687655 CACGACGAAAGAAGATTCTCATTAC 58.312 40.000 0.00 0.00 36.28 1.89
571 579 7.253486 CGACGAAAGAAGATTCTCATTACTCAC 60.253 40.741 0.00 0.00 36.28 3.51
608 721 7.375834 AGAGATTTCAATGTTGACTACGTACA 58.624 34.615 0.00 0.00 36.83 2.90
615 728 5.591643 ATGTTGACTACGTACAAAGCAAG 57.408 39.130 0.63 0.00 0.00 4.01
632 745 2.061773 CAAGCTGAGTGAACCTACACG 58.938 52.381 0.00 0.00 44.35 4.49
636 749 2.732597 GCTGAGTGAACCTACACGCTAG 60.733 54.545 0.00 0.00 44.35 3.42
641 754 5.593095 TGAGTGAACCTACACGCTAGATTAT 59.407 40.000 0.00 0.00 44.35 1.28
699 812 1.443802 TGCATGCGTTACGATTTCCA 58.556 45.000 14.09 0.00 0.00 3.53
713 826 3.191162 CGATTTCCAGATCTTTTGGCACA 59.809 43.478 0.00 0.00 35.62 4.57
903 1033 6.401394 TGAATTCCTGATCATCGGCTATAAG 58.599 40.000 2.27 0.00 0.00 1.73
1816 1961 0.753262 CATCCCGGAACTACTCCCAG 59.247 60.000 0.73 0.00 41.87 4.45
1858 2015 2.722629 CACGCATGCAAAGACAAGAAAG 59.277 45.455 19.57 0.00 0.00 2.62
1961 2122 4.217118 AGTTCGACAAAGTCCATACGTACT 59.783 41.667 0.00 0.00 0.00 2.73
1962 2123 5.412594 AGTTCGACAAAGTCCATACGTACTA 59.587 40.000 0.00 0.00 32.00 1.82
1963 2124 5.221891 TCGACAAAGTCCATACGTACTAC 57.778 43.478 0.00 0.00 0.00 2.73
1964 2125 4.094887 TCGACAAAGTCCATACGTACTACC 59.905 45.833 0.00 0.00 0.00 3.18
1966 2127 5.294306 CGACAAAGTCCATACGTACTACCTA 59.706 44.000 0.00 0.00 0.00 3.08
1967 2128 6.510799 CGACAAAGTCCATACGTACTACCTAG 60.511 46.154 0.00 0.00 0.00 3.02
2029 2192 6.370718 GTCAACCGTCATCTTATTTAACTGGT 59.629 38.462 0.00 0.00 0.00 4.00
2030 2193 6.370442 TCAACCGTCATCTTATTTAACTGGTG 59.630 38.462 0.00 0.00 0.00 4.17
2031 2194 4.634443 ACCGTCATCTTATTTAACTGGTGC 59.366 41.667 0.00 0.00 0.00 5.01
2032 2195 4.260212 CCGTCATCTTATTTAACTGGTGCG 60.260 45.833 0.00 0.00 0.00 5.34
2033 2196 4.328983 CGTCATCTTATTTAACTGGTGCGT 59.671 41.667 0.00 0.00 0.00 5.24
2034 2197 5.517411 CGTCATCTTATTTAACTGGTGCGTA 59.483 40.000 0.00 0.00 0.00 4.42
2035 2198 6.035220 CGTCATCTTATTTAACTGGTGCGTAA 59.965 38.462 0.00 0.00 0.00 3.18
2036 2199 7.178074 GTCATCTTATTTAACTGGTGCGTAAC 58.822 38.462 0.00 0.00 0.00 2.50
2037 2200 5.766702 TCTTATTTAACTGGTGCGTAACG 57.233 39.130 0.00 0.00 0.00 3.18
2038 2201 5.229423 TCTTATTTAACTGGTGCGTAACGT 58.771 37.500 0.00 0.00 0.00 3.99
2039 2202 5.695816 TCTTATTTAACTGGTGCGTAACGTT 59.304 36.000 5.88 5.88 0.00 3.99
2040 2203 4.816786 ATTTAACTGGTGCGTAACGTTT 57.183 36.364 5.91 0.00 0.00 3.60
2041 2204 4.612932 TTTAACTGGTGCGTAACGTTTT 57.387 36.364 5.91 0.00 0.00 2.43
2042 2205 4.612932 TTAACTGGTGCGTAACGTTTTT 57.387 36.364 5.91 0.00 0.00 1.94
2043 2206 2.461897 ACTGGTGCGTAACGTTTTTG 57.538 45.000 5.91 0.00 0.00 2.44
2044 2207 1.738908 ACTGGTGCGTAACGTTTTTGT 59.261 42.857 5.91 0.00 0.00 2.83
2045 2208 2.935201 ACTGGTGCGTAACGTTTTTGTA 59.065 40.909 5.91 0.00 0.00 2.41
2046 2209 3.373439 ACTGGTGCGTAACGTTTTTGTAA 59.627 39.130 5.91 0.00 0.00 2.41
2047 2210 4.142730 ACTGGTGCGTAACGTTTTTGTAAA 60.143 37.500 5.91 0.00 0.00 2.01
2048 2211 4.726416 TGGTGCGTAACGTTTTTGTAAAA 58.274 34.783 5.91 0.00 0.00 1.52
2049 2212 4.556523 TGGTGCGTAACGTTTTTGTAAAAC 59.443 37.500 5.91 5.23 0.00 2.43
2050 2213 4.792702 GGTGCGTAACGTTTTTGTAAAACT 59.207 37.500 5.91 0.00 0.00 2.66
2051 2214 5.962423 GGTGCGTAACGTTTTTGTAAAACTA 59.038 36.000 5.91 0.00 0.00 2.24
2052 2215 6.139013 GGTGCGTAACGTTTTTGTAAAACTAG 59.861 38.462 5.91 0.00 0.00 2.57
2053 2216 6.682441 GTGCGTAACGTTTTTGTAAAACTAGT 59.318 34.615 5.91 0.00 0.00 2.57
2054 2217 7.843686 GTGCGTAACGTTTTTGTAAAACTAGTA 59.156 33.333 5.91 1.35 0.00 1.82
2055 2218 8.547069 TGCGTAACGTTTTTGTAAAACTAGTAT 58.453 29.630 5.91 0.00 0.00 2.12
2061 2224 9.848172 ACGTTTTTGTAAAACTAGTATACAACG 57.152 29.630 24.77 24.77 38.77 4.10
2062 2225 9.848172 CGTTTTTGTAAAACTAGTATACAACGT 57.152 29.630 23.54 0.00 38.77 3.99
2103 2293 2.163010 TCCGGACGTGTCATTAGTTCTC 59.837 50.000 0.00 0.00 0.00 2.87
2104 2294 2.094906 CCGGACGTGTCATTAGTTCTCA 60.095 50.000 0.00 0.00 0.00 3.27
2105 2295 3.571571 CGGACGTGTCATTAGTTCTCAA 58.428 45.455 0.00 0.00 0.00 3.02
2106 2296 3.985279 CGGACGTGTCATTAGTTCTCAAA 59.015 43.478 0.00 0.00 0.00 2.69
2270 2480 4.261801 GGCTGCATAGGTTCAACTAGAAA 58.738 43.478 0.50 0.00 38.13 2.52
2328 2538 4.771114 AACGGTCTGGAATAATGATGGA 57.229 40.909 0.00 0.00 0.00 3.41
2331 2541 6.433847 ACGGTCTGGAATAATGATGGAATA 57.566 37.500 0.00 0.00 0.00 1.75
2334 2544 5.352569 GGTCTGGAATAATGATGGAATAGCG 59.647 44.000 0.00 0.00 0.00 4.26
2347 2740 5.039920 TGGAATAGCGGTGAGTAGTACTA 57.960 43.478 1.88 0.00 0.00 1.82
2348 2741 5.628130 TGGAATAGCGGTGAGTAGTACTAT 58.372 41.667 5.75 0.00 0.00 2.12
2420 2823 3.572661 TTAGGAGAAACTGGTACCCCT 57.427 47.619 10.07 9.11 0.00 4.79
2516 2919 4.634012 TTACTTGTGCCTAACTGTGGAT 57.366 40.909 0.00 0.00 0.00 3.41
2518 2921 4.634012 ACTTGTGCCTAACTGTGGATAA 57.366 40.909 0.00 0.00 0.00 1.75
2543 2946 8.773404 AAAACACGTGCTCTATTTAGATTAGT 57.227 30.769 17.22 0.00 0.00 2.24
2549 2952 8.344098 ACGTGCTCTATTTAGATTAGTCACTAC 58.656 37.037 0.00 0.00 0.00 2.73
2556 2959 5.945144 TTAGATTAGTCACTACCCAACCC 57.055 43.478 0.00 0.00 0.00 4.11
2562 2965 1.280133 GTCACTACCCAACCCCCTAAC 59.720 57.143 0.00 0.00 0.00 2.34
2575 2980 2.094675 CCCCTAACCAAATCTGCAGTG 58.905 52.381 14.67 4.59 0.00 3.66
2594 2999 3.961408 AGTGGCTACCTTACTGATACTGG 59.039 47.826 0.00 0.00 0.00 4.00
2595 3000 3.958798 GTGGCTACCTTACTGATACTGGA 59.041 47.826 0.00 0.00 0.00 3.86
2691 3373 9.798994 ACTAAATTTTATACGGAGTGAGTACTG 57.201 33.333 0.00 0.00 45.73 2.74
2786 3471 1.878656 AAAGAGGCTCTCGACACGGG 61.879 60.000 19.03 0.00 35.36 5.28
2886 3584 1.153289 GCGATGCTCACCCTCACAT 60.153 57.895 0.00 0.00 0.00 3.21
2887 3585 1.434622 GCGATGCTCACCCTCACATG 61.435 60.000 0.00 0.00 0.00 3.21
2888 3586 0.107993 CGATGCTCACCCTCACATGT 60.108 55.000 0.00 0.00 0.00 3.21
2889 3587 1.136891 CGATGCTCACCCTCACATGTA 59.863 52.381 0.00 0.00 0.00 2.29
2890 3588 2.555199 GATGCTCACCCTCACATGTAC 58.445 52.381 0.00 0.00 0.00 2.90
2891 3589 0.613260 TGCTCACCCTCACATGTACC 59.387 55.000 0.00 0.00 0.00 3.34
2892 3590 0.107654 GCTCACCCTCACATGTACCC 60.108 60.000 0.00 0.00 0.00 3.69
2893 3591 0.541863 CTCACCCTCACATGTACCCC 59.458 60.000 0.00 0.00 0.00 4.95
2894 3592 0.118346 TCACCCTCACATGTACCCCT 59.882 55.000 0.00 0.00 0.00 4.79
2895 3593 0.541863 CACCCTCACATGTACCCCTC 59.458 60.000 0.00 0.00 0.00 4.30
2896 3594 0.976073 ACCCTCACATGTACCCCTCG 60.976 60.000 0.00 0.00 0.00 4.63
2897 3595 0.976073 CCCTCACATGTACCCCTCGT 60.976 60.000 0.00 0.00 0.00 4.18
2898 3596 0.902531 CCTCACATGTACCCCTCGTT 59.097 55.000 0.00 0.00 0.00 3.85
2899 3597 1.134788 CCTCACATGTACCCCTCGTTC 60.135 57.143 0.00 0.00 0.00 3.95
2900 3598 0.528924 TCACATGTACCCCTCGTTCG 59.471 55.000 0.00 0.00 0.00 3.95
2901 3599 0.528924 CACATGTACCCCTCGTTCGA 59.471 55.000 0.00 0.00 0.00 3.71
2902 3600 1.067425 CACATGTACCCCTCGTTCGAA 60.067 52.381 0.00 0.00 0.00 3.71
2903 3601 1.619827 ACATGTACCCCTCGTTCGAAA 59.380 47.619 0.00 0.00 0.00 3.46
2904 3602 2.235402 ACATGTACCCCTCGTTCGAAAT 59.765 45.455 0.00 0.00 0.00 2.17
2905 3603 3.267483 CATGTACCCCTCGTTCGAAATT 58.733 45.455 0.00 0.00 0.00 1.82
2906 3604 4.081531 ACATGTACCCCTCGTTCGAAATTA 60.082 41.667 0.00 0.00 0.00 1.40
2907 3605 3.848726 TGTACCCCTCGTTCGAAATTAC 58.151 45.455 0.00 0.00 0.00 1.89
2908 3606 3.511146 TGTACCCCTCGTTCGAAATTACT 59.489 43.478 0.00 0.00 0.00 2.24
2909 3607 3.690475 ACCCCTCGTTCGAAATTACTT 57.310 42.857 0.00 0.00 0.00 2.24
2910 3608 3.332034 ACCCCTCGTTCGAAATTACTTG 58.668 45.455 0.00 0.00 0.00 3.16
2911 3609 3.244318 ACCCCTCGTTCGAAATTACTTGT 60.244 43.478 0.00 0.00 0.00 3.16
2912 3610 3.370061 CCCCTCGTTCGAAATTACTTGTC 59.630 47.826 0.00 0.00 0.00 3.18
2913 3611 3.060363 CCCTCGTTCGAAATTACTTGTCG 59.940 47.826 0.00 0.00 36.12 4.35
2914 3612 3.481467 CCTCGTTCGAAATTACTTGTCGC 60.481 47.826 0.00 0.00 34.80 5.19
2915 3613 3.051327 TCGTTCGAAATTACTTGTCGCA 58.949 40.909 0.00 0.00 34.80 5.10
2916 3614 3.490155 TCGTTCGAAATTACTTGTCGCAA 59.510 39.130 0.00 0.00 34.80 4.85
2917 3615 4.025896 TCGTTCGAAATTACTTGTCGCAAA 60.026 37.500 0.00 0.00 34.80 3.68
2918 3616 4.667061 CGTTCGAAATTACTTGTCGCAAAA 59.333 37.500 0.00 0.00 34.80 2.44
2919 3617 5.169915 CGTTCGAAATTACTTGTCGCAAAAA 59.830 36.000 0.00 0.00 34.80 1.94
2920 3618 6.129561 CGTTCGAAATTACTTGTCGCAAAAAT 60.130 34.615 0.00 0.00 34.80 1.82
2921 3619 6.667981 TCGAAATTACTTGTCGCAAAAATG 57.332 33.333 0.00 0.00 34.80 2.32
2922 3620 5.627367 TCGAAATTACTTGTCGCAAAAATGG 59.373 36.000 0.00 0.00 34.80 3.16
2923 3621 5.627367 CGAAATTACTTGTCGCAAAAATGGA 59.373 36.000 0.00 0.00 0.00 3.41
2924 3622 6.307800 CGAAATTACTTGTCGCAAAAATGGAT 59.692 34.615 0.00 0.00 0.00 3.41
2925 3623 6.949578 AATTACTTGTCGCAAAAATGGATG 57.050 33.333 0.00 0.00 0.00 3.51
2926 3624 5.446143 TTACTTGTCGCAAAAATGGATGT 57.554 34.783 0.00 0.00 0.00 3.06
2927 3625 6.561737 TTACTTGTCGCAAAAATGGATGTA 57.438 33.333 0.00 0.00 0.00 2.29
2928 3626 5.643379 ACTTGTCGCAAAAATGGATGTAT 57.357 34.783 0.00 0.00 0.00 2.29
2929 3627 5.640732 ACTTGTCGCAAAAATGGATGTATC 58.359 37.500 0.00 0.00 0.00 2.24
2930 3628 5.415701 ACTTGTCGCAAAAATGGATGTATCT 59.584 36.000 0.00 0.00 0.00 1.98
2931 3629 6.597672 ACTTGTCGCAAAAATGGATGTATCTA 59.402 34.615 0.00 0.00 0.00 1.98
2932 3630 6.603237 TGTCGCAAAAATGGATGTATCTAG 57.397 37.500 0.00 0.00 0.00 2.43
2933 3631 6.345298 TGTCGCAAAAATGGATGTATCTAGA 58.655 36.000 0.00 0.00 0.00 2.43
2934 3632 6.257849 TGTCGCAAAAATGGATGTATCTAGAC 59.742 38.462 0.00 0.00 0.00 2.59
2935 3633 5.462068 TCGCAAAAATGGATGTATCTAGACG 59.538 40.000 0.00 0.00 0.00 4.18
2936 3634 5.234329 CGCAAAAATGGATGTATCTAGACGT 59.766 40.000 0.00 0.00 0.00 4.34
2937 3635 6.419710 CGCAAAAATGGATGTATCTAGACGTA 59.580 38.462 0.00 0.00 0.00 3.57
2938 3636 7.116376 CGCAAAAATGGATGTATCTAGACGTAT 59.884 37.037 0.00 0.00 0.00 3.06
2939 3637 8.774586 GCAAAAATGGATGTATCTAGACGTATT 58.225 33.333 0.00 0.00 0.00 1.89
2983 3681 9.586150 CATTTCCGAGATAAATAATTCTGAACG 57.414 33.333 0.00 0.00 0.00 3.95
2984 3682 7.709269 TTCCGAGATAAATAATTCTGAACGG 57.291 36.000 0.00 0.00 37.37 4.44
2985 3683 7.046292 TCCGAGATAAATAATTCTGAACGGA 57.954 36.000 0.00 0.00 41.49 4.69
2986 3684 7.145985 TCCGAGATAAATAATTCTGAACGGAG 58.854 38.462 0.00 0.00 39.48 4.63
2987 3685 6.366332 CCGAGATAAATAATTCTGAACGGAGG 59.634 42.308 0.00 0.00 38.09 4.30
2988 3686 7.145985 CGAGATAAATAATTCTGAACGGAGGA 58.854 38.462 0.00 0.00 0.00 3.71
2997 3697 1.399791 CTGAACGGAGGAGTACGTACC 59.600 57.143 21.80 13.02 43.31 3.34
2999 3699 2.019984 GAACGGAGGAGTACGTACCAT 58.980 52.381 21.80 11.18 43.31 3.55
3023 3723 0.896019 ACTCGTCTGTAGCCAGCAGT 60.896 55.000 0.00 0.00 38.66 4.40
3024 3724 0.457509 CTCGTCTGTAGCCAGCAGTG 60.458 60.000 0.00 0.00 38.66 3.66
3042 3742 4.558496 GCAGTGGCTACTTATCTCTAGCTG 60.558 50.000 0.00 0.00 36.41 4.24
3048 3748 1.067821 ACTTATCTCTAGCTGGTGCGC 59.932 52.381 0.00 0.00 45.42 6.09
3078 3779 2.564458 CTAACCCGTTTTGGCCGC 59.436 61.111 0.00 0.00 35.87 6.53
3110 3811 4.720902 CCTCGCATGCCACCACCA 62.721 66.667 13.15 0.00 0.00 4.17
3111 3812 3.434319 CTCGCATGCCACCACCAC 61.434 66.667 13.15 0.00 0.00 4.16
3195 3899 1.585521 GTCCATGGACGACGCTACG 60.586 63.158 28.52 0.00 35.30 3.51
3317 4045 1.599518 GAACGGTGCACATCCCACA 60.600 57.895 20.43 0.00 34.94 4.17
3349 4077 2.592102 TTGGTCCGTAGTAGTCCTGT 57.408 50.000 0.00 0.00 0.00 4.00
3365 4093 0.745486 CTGTCATGGCATCGCTCCAA 60.745 55.000 0.00 0.00 37.13 3.53
3366 4094 0.745486 TGTCATGGCATCGCTCCAAG 60.745 55.000 0.00 0.00 37.13 3.61
3380 4108 3.499737 CAAGCGGTGCCGATGGTC 61.500 66.667 15.45 0.00 42.83 4.02
3394 4122 0.606401 ATGGTCTCTTGTGGTTGCGG 60.606 55.000 0.00 0.00 0.00 5.69
3429 4157 1.735571 GCGATACACCGAACCAAACAT 59.264 47.619 0.00 0.00 0.00 2.71
3430 4158 2.475519 GCGATACACCGAACCAAACATG 60.476 50.000 0.00 0.00 0.00 3.21
3432 4160 3.433957 CGATACACCGAACCAAACATGAA 59.566 43.478 0.00 0.00 0.00 2.57
3435 4163 1.000717 CACCGAACCAAACATGAACCC 60.001 52.381 0.00 0.00 0.00 4.11
3436 4164 1.323412 CCGAACCAAACATGAACCCA 58.677 50.000 0.00 0.00 0.00 4.51
3438 4166 1.953686 CGAACCAAACATGAACCCACT 59.046 47.619 0.00 0.00 0.00 4.00
3439 4167 2.031157 CGAACCAAACATGAACCCACTC 60.031 50.000 0.00 0.00 0.00 3.51
3440 4168 2.746279 ACCAAACATGAACCCACTCA 57.254 45.000 0.00 0.00 0.00 3.41
3441 4169 2.306847 ACCAAACATGAACCCACTCAC 58.693 47.619 0.00 0.00 0.00 3.51
3442 4170 1.613437 CCAAACATGAACCCACTCACC 59.387 52.381 0.00 0.00 0.00 4.02
3443 4171 2.305928 CAAACATGAACCCACTCACCA 58.694 47.619 0.00 0.00 0.00 4.17
3444 4172 2.892852 CAAACATGAACCCACTCACCAT 59.107 45.455 0.00 0.00 0.00 3.55
3445 4173 2.496899 ACATGAACCCACTCACCATC 57.503 50.000 0.00 0.00 0.00 3.51
3446 4174 1.704628 ACATGAACCCACTCACCATCA 59.295 47.619 0.00 0.00 0.00 3.07
3447 4175 2.086869 CATGAACCCACTCACCATCAC 58.913 52.381 0.00 0.00 0.00 3.06
3448 4176 0.400213 TGAACCCACTCACCATCACC 59.600 55.000 0.00 0.00 0.00 4.02
3449 4177 0.400213 GAACCCACTCACCATCACCA 59.600 55.000 0.00 0.00 0.00 4.17
3450 4178 0.850100 AACCCACTCACCATCACCAA 59.150 50.000 0.00 0.00 0.00 3.67
3451 4179 0.110486 ACCCACTCACCATCACCAAC 59.890 55.000 0.00 0.00 0.00 3.77
3452 4180 0.110295 CCCACTCACCATCACCAACA 59.890 55.000 0.00 0.00 0.00 3.33
3495 4223 6.485830 ACTTGCATGTAGTATCATGTAGGT 57.514 37.500 2.92 6.68 44.68 3.08
3497 4225 8.195165 ACTTGCATGTAGTATCATGTAGGTAT 57.805 34.615 2.92 0.00 43.94 2.73
3499 4227 6.398095 TGCATGTAGTATCATGTAGGTATGC 58.602 40.000 0.00 0.00 44.68 3.14
3501 4229 7.044181 GCATGTAGTATCATGTAGGTATGCAT 58.956 38.462 3.79 3.79 44.68 3.96
3503 4231 6.398095 TGTAGTATCATGTAGGTATGCATGC 58.602 40.000 11.82 11.82 45.92 4.06
3506 4234 6.111382 AGTATCATGTAGGTATGCATGCATC 58.889 40.000 35.35 24.63 45.92 3.91
3507 4235 4.628963 TCATGTAGGTATGCATGCATCT 57.371 40.909 35.35 27.48 45.92 2.90
3508 4236 4.320870 TCATGTAGGTATGCATGCATCTG 58.679 43.478 35.35 20.21 45.92 2.90
3509 4237 4.040706 TCATGTAGGTATGCATGCATCTGA 59.959 41.667 35.35 21.81 45.92 3.27
3510 4238 3.732212 TGTAGGTATGCATGCATCTGAC 58.268 45.455 35.35 26.48 37.82 3.51
3511 4239 3.134442 TGTAGGTATGCATGCATCTGACA 59.866 43.478 35.35 27.95 37.82 3.58
3512 4240 3.286329 AGGTATGCATGCATCTGACAA 57.714 42.857 35.35 15.39 37.82 3.18
3513 4241 3.623703 AGGTATGCATGCATCTGACAAA 58.376 40.909 35.35 14.61 37.82 2.83
3515 4243 4.277672 AGGTATGCATGCATCTGACAAATC 59.722 41.667 35.35 17.17 37.82 2.17
3542 4270 3.441572 ACCTATGTGAAATCTTGCAGCAC 59.558 43.478 0.00 0.00 0.00 4.40
3543 4271 3.181493 CCTATGTGAAATCTTGCAGCACC 60.181 47.826 0.00 0.00 0.00 5.01
3544 4272 1.985473 TGTGAAATCTTGCAGCACCT 58.015 45.000 0.00 0.00 0.00 4.00
3545 4273 1.610038 TGTGAAATCTTGCAGCACCTG 59.390 47.619 0.00 0.00 34.12 4.00
3546 4274 1.881973 GTGAAATCTTGCAGCACCTGA 59.118 47.619 0.00 0.00 32.44 3.86
3547 4275 1.881973 TGAAATCTTGCAGCACCTGAC 59.118 47.619 0.00 0.00 32.44 3.51
3548 4276 2.157738 GAAATCTTGCAGCACCTGACT 58.842 47.619 0.00 0.00 32.44 3.41
3549 4277 1.818642 AATCTTGCAGCACCTGACTC 58.181 50.000 0.00 0.00 32.44 3.36
3550 4278 0.689055 ATCTTGCAGCACCTGACTCA 59.311 50.000 0.00 0.00 32.44 3.41
3551 4279 0.034476 TCTTGCAGCACCTGACTCAG 59.966 55.000 0.00 0.00 32.44 3.35
3552 4280 1.575576 CTTGCAGCACCTGACTCAGC 61.576 60.000 0.00 0.00 32.44 4.26
3553 4281 2.031616 GCAGCACCTGACTCAGCA 59.968 61.111 0.00 0.00 32.44 4.41
3554 4282 1.376942 GCAGCACCTGACTCAGCAT 60.377 57.895 0.00 0.00 32.44 3.79
3555 4283 0.959372 GCAGCACCTGACTCAGCATT 60.959 55.000 0.00 0.00 32.44 3.56
3556 4284 0.803117 CAGCACCTGACTCAGCATTG 59.197 55.000 0.00 0.00 32.44 2.82
3557 4285 0.322277 AGCACCTGACTCAGCATTGG 60.322 55.000 0.00 0.00 0.00 3.16
3565 4293 4.160439 CCTGACTCAGCATTGGAGTAGTAA 59.840 45.833 0.00 0.00 45.21 2.24
4206 4934 2.435059 GACGACCCAAGAGGCTGC 60.435 66.667 0.00 0.00 40.58 5.25
4293 5033 2.225068 GCTAAGTAAGCGCCATCTGA 57.775 50.000 2.29 0.00 42.53 3.27
4295 5035 3.134458 GCTAAGTAAGCGCCATCTGAAT 58.866 45.455 2.29 0.00 42.53 2.57
4299 5039 2.169352 AGTAAGCGCCATCTGAATCTGT 59.831 45.455 2.29 0.00 0.00 3.41
4318 5058 2.240414 TGTTCAGATGGATGGACATGCT 59.760 45.455 5.43 0.00 33.64 3.79
4447 5187 1.401905 GTCAACTGCCATCCCGATTTC 59.598 52.381 0.00 0.00 0.00 2.17
4454 5194 3.430453 TGCCATCCCGATTTCTCTTTTT 58.570 40.909 0.00 0.00 0.00 1.94
4482 5222 1.266891 CGCTTCGATTCTGCGTTTACC 60.267 52.381 12.27 0.00 44.00 2.85
4489 5229 0.533308 TTCTGCGTTTACCGTGGCTT 60.533 50.000 0.00 0.00 39.32 4.35
4517 5257 4.839121 TGTCCATACCAACACCAGAATAC 58.161 43.478 0.00 0.00 0.00 1.89
4518 5258 4.534500 TGTCCATACCAACACCAGAATACT 59.466 41.667 0.00 0.00 0.00 2.12
4523 5263 4.273148 ACCAACACCAGAATACTCTGTC 57.727 45.455 0.00 0.00 46.71 3.51
4559 5302 7.227910 AGCTACAGTTAGTTATCTAGTCAGAGC 59.772 40.741 0.00 0.00 33.22 4.09
4561 5304 7.948034 ACAGTTAGTTATCTAGTCAGAGCTT 57.052 36.000 0.00 0.00 33.22 3.74
4648 5394 5.581126 ACATGTCTCTTTTCTGCACAAAA 57.419 34.783 0.00 0.00 0.00 2.44
4676 5424 7.444703 AGGGTATCTCTCTGCTCTTTATTTT 57.555 36.000 0.00 0.00 0.00 1.82
4683 5431 7.907389 TCTCTCTGCTCTTTATTTTAGGTTGA 58.093 34.615 0.00 0.00 0.00 3.18
4978 5730 9.754382 AAAAATCAGATTTGCATATGTATGACC 57.246 29.630 9.24 0.00 35.45 4.02
5073 5825 6.385033 GGTAGTGTACTTGTCGTTATTCAGT 58.615 40.000 0.00 0.00 0.00 3.41
5074 5826 6.525976 GGTAGTGTACTTGTCGTTATTCAGTC 59.474 42.308 0.00 0.00 0.00 3.51
5075 5827 6.080648 AGTGTACTTGTCGTTATTCAGTCA 57.919 37.500 0.00 0.00 0.00 3.41
5076 5828 6.509656 AGTGTACTTGTCGTTATTCAGTCAA 58.490 36.000 0.00 0.00 0.00 3.18
5077 5829 6.982141 AGTGTACTTGTCGTTATTCAGTCAAA 59.018 34.615 0.00 0.00 0.00 2.69
5078 5830 7.656137 AGTGTACTTGTCGTTATTCAGTCAAAT 59.344 33.333 0.00 0.00 0.00 2.32
5079 5831 7.950496 GTGTACTTGTCGTTATTCAGTCAAATC 59.050 37.037 0.00 0.00 0.00 2.17
5093 5845 3.620374 AGTCAAATCTCACATGTCATCGC 59.380 43.478 0.00 0.00 0.00 4.58
5099 5851 1.460743 CTCACATGTCATCGCGTTTGT 59.539 47.619 5.77 0.00 0.00 2.83
5100 5852 1.459209 TCACATGTCATCGCGTTTGTC 59.541 47.619 5.77 4.11 0.00 3.18
5111 5863 2.113289 CGCGTTTGTCGTGGAATTTTT 58.887 42.857 0.00 0.00 44.94 1.94
5113 5865 2.217620 GCGTTTGTCGTGGAATTTTTGG 59.782 45.455 0.00 0.00 42.13 3.28
5114 5866 3.696898 CGTTTGTCGTGGAATTTTTGGA 58.303 40.909 0.00 0.00 34.52 3.53
5115 5867 3.728718 CGTTTGTCGTGGAATTTTTGGAG 59.271 43.478 0.00 0.00 34.52 3.86
5116 5868 4.496673 CGTTTGTCGTGGAATTTTTGGAGA 60.497 41.667 0.00 0.00 34.52 3.71
5117 5869 5.528870 GTTTGTCGTGGAATTTTTGGAGAT 58.471 37.500 0.00 0.00 0.00 2.75
5118 5870 6.566942 CGTTTGTCGTGGAATTTTTGGAGATA 60.567 38.462 0.00 0.00 34.52 1.98
5156 5908 4.059773 TCTATTTGAATGGCCTTGGGTT 57.940 40.909 3.32 0.00 0.00 4.11
5168 5920 2.224402 GCCTTGGGTTTTATGTTTGCCA 60.224 45.455 0.00 0.00 0.00 4.92
5169 5921 3.558958 GCCTTGGGTTTTATGTTTGCCAT 60.559 43.478 0.00 0.00 37.58 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 193 1.129998 CAGCAAAAGTGAGCATCCGAG 59.870 52.381 0.00 0.00 0.00 4.63
208 215 3.541632 GCCGTGAATCTTCCCAAATCTA 58.458 45.455 0.00 0.00 0.00 1.98
273 280 3.194861 TGCATGCTAATTCTGGTACGTC 58.805 45.455 20.33 0.00 0.00 4.34
339 346 0.983378 AAACGCAGGCCTCCTATCCT 60.983 55.000 0.00 0.00 29.64 3.24
340 347 0.533085 GAAACGCAGGCCTCCTATCC 60.533 60.000 0.00 0.00 29.64 2.59
341 348 0.876342 CGAAACGCAGGCCTCCTATC 60.876 60.000 0.00 0.00 29.64 2.08
342 349 1.144057 CGAAACGCAGGCCTCCTAT 59.856 57.895 0.00 0.00 29.64 2.57
343 350 2.577059 CGAAACGCAGGCCTCCTA 59.423 61.111 0.00 0.00 29.64 2.94
403 410 2.295909 GCAAACCAGGTTCAATGCACTA 59.704 45.455 18.89 0.00 30.22 2.74
477 485 2.769387 CGACAGTTCGTAACAGCATG 57.231 50.000 0.00 0.00 40.61 4.06
536 544 3.191669 TCTTCTTTCGTCGTGCAGAAAA 58.808 40.909 0.00 0.00 36.14 2.29
540 548 2.989840 AGAATCTTCTTTCGTCGTGCAG 59.010 45.455 0.00 0.00 32.55 4.41
541 549 2.987149 GAGAATCTTCTTTCGTCGTGCA 59.013 45.455 0.00 0.00 37.73 4.57
542 550 2.987149 TGAGAATCTTCTTTCGTCGTGC 59.013 45.455 0.00 0.00 37.73 5.34
543 551 5.769967 AATGAGAATCTTCTTTCGTCGTG 57.230 39.130 0.00 0.00 37.73 4.35
544 552 6.622549 AGTAATGAGAATCTTCTTTCGTCGT 58.377 36.000 0.00 0.00 37.73 4.34
545 553 6.747739 TGAGTAATGAGAATCTTCTTTCGTCG 59.252 38.462 0.00 0.00 37.73 5.12
546 554 7.253486 CGTGAGTAATGAGAATCTTCTTTCGTC 60.253 40.741 0.00 0.00 37.73 4.20
547 555 6.528423 CGTGAGTAATGAGAATCTTCTTTCGT 59.472 38.462 0.00 0.00 37.73 3.85
548 556 6.020281 CCGTGAGTAATGAGAATCTTCTTTCG 60.020 42.308 0.00 0.00 37.73 3.46
553 561 6.137794 TCTCCGTGAGTAATGAGAATCTTC 57.862 41.667 1.60 0.00 34.92 2.87
555 563 6.531503 TTTCTCCGTGAGTAATGAGAATCT 57.468 37.500 0.00 0.00 41.87 2.40
567 575 9.534565 TTGAAATCTCTTATATTTCTCCGTGAG 57.465 33.333 9.27 0.00 41.72 3.51
600 713 3.121944 CACTCAGCTTGCTTTGTACGTAG 59.878 47.826 0.00 0.00 0.00 3.51
604 717 3.304057 GGTTCACTCAGCTTGCTTTGTAC 60.304 47.826 0.00 0.00 0.00 2.90
608 721 2.355010 AGGTTCACTCAGCTTGCTTT 57.645 45.000 0.00 0.00 0.00 3.51
615 728 0.038159 AGCGTGTAGGTTCACTCAGC 60.038 55.000 0.00 0.00 36.33 4.26
641 754 7.668469 TCCTCGAGCCTTTTATGTATATAGACA 59.332 37.037 6.99 2.07 0.00 3.41
660 773 4.631377 TGCATCATGTTTTACTTCCTCGAG 59.369 41.667 5.13 5.13 0.00 4.04
662 775 4.944962 TGCATCATGTTTTACTTCCTCG 57.055 40.909 0.00 0.00 0.00 4.63
714 827 7.264221 TGACAAGTGTAATGTTGAGCATTTTT 58.736 30.769 0.00 0.00 44.82 1.94
715 828 6.804677 TGACAAGTGTAATGTTGAGCATTTT 58.195 32.000 0.00 0.00 44.82 1.82
1989 2151 2.689471 GGTTGACTAAAAACGTGGGGTT 59.311 45.455 0.00 0.00 41.76 4.11
2029 2192 6.770076 ACTAGTTTTACAAAAACGTTACGCA 58.230 32.000 4.09 0.00 35.42 5.24
2030 2193 8.918175 ATACTAGTTTTACAAAAACGTTACGC 57.082 30.769 4.09 0.00 35.42 4.42
2035 2198 9.848172 CGTTGTATACTAGTTTTACAAAAACGT 57.152 29.630 22.57 5.66 37.52 3.99
2036 2199 9.848172 ACGTTGTATACTAGTTTTACAAAAACG 57.152 29.630 22.57 22.88 37.52 3.60
2050 2213 9.135843 GCAATGCTATTCATACGTTGTATACTA 57.864 33.333 4.17 0.00 34.33 1.82
2051 2214 7.872993 AGCAATGCTATTCATACGTTGTATACT 59.127 33.333 5.69 0.00 36.99 2.12
2052 2215 8.018677 AGCAATGCTATTCATACGTTGTATAC 57.981 34.615 5.69 0.00 36.99 1.47
2053 2216 8.601845 AAGCAATGCTATTCATACGTTGTATA 57.398 30.769 8.68 0.00 38.25 1.47
2054 2217 7.496529 AAGCAATGCTATTCATACGTTGTAT 57.503 32.000 8.68 0.00 38.25 2.29
2055 2218 6.918892 AAGCAATGCTATTCATACGTTGTA 57.081 33.333 8.68 0.00 38.25 2.41
2056 2219 5.818136 AAGCAATGCTATTCATACGTTGT 57.182 34.783 8.68 0.00 38.25 3.32
2057 2220 6.968904 AGAAAAGCAATGCTATTCATACGTTG 59.031 34.615 8.68 0.00 38.25 4.10
2058 2221 7.088589 AGAAAAGCAATGCTATTCATACGTT 57.911 32.000 8.68 0.00 38.25 3.99
2059 2222 6.238484 GGAGAAAAGCAATGCTATTCATACGT 60.238 38.462 8.68 0.00 38.25 3.57
2060 2223 6.138761 GGAGAAAAGCAATGCTATTCATACG 58.861 40.000 8.68 0.00 38.25 3.06
2061 2224 6.138761 CGGAGAAAAGCAATGCTATTCATAC 58.861 40.000 8.68 0.00 38.25 2.39
2062 2225 5.239306 CCGGAGAAAAGCAATGCTATTCATA 59.761 40.000 8.68 0.00 38.25 2.15
2063 2226 4.037208 CCGGAGAAAAGCAATGCTATTCAT 59.963 41.667 8.68 0.00 38.25 2.57
2064 2227 3.378112 CCGGAGAAAAGCAATGCTATTCA 59.622 43.478 8.68 0.00 38.25 2.57
2065 2228 3.627577 TCCGGAGAAAAGCAATGCTATTC 59.372 43.478 8.68 4.01 38.25 1.75
2066 2229 3.378427 GTCCGGAGAAAAGCAATGCTATT 59.622 43.478 8.68 2.41 38.25 1.73
2067 2230 2.945668 GTCCGGAGAAAAGCAATGCTAT 59.054 45.455 8.68 0.00 38.25 2.97
2133 2325 4.133820 CTGTTTGGGTGTGTCAAGTGATA 58.866 43.478 0.00 0.00 0.00 2.15
2322 2532 3.296854 ACTACTCACCGCTATTCCATCA 58.703 45.455 0.00 0.00 0.00 3.07
2374 2777 3.610040 ACTCAACGCTGTTCCATCATA 57.390 42.857 0.00 0.00 0.00 2.15
2483 2886 9.943163 GTTAGGCACAAGTAATAGTACTAGTAC 57.057 37.037 25.77 25.77 39.79 2.73
2486 2889 8.684520 ACAGTTAGGCACAAGTAATAGTACTAG 58.315 37.037 8.85 0.00 39.79 2.57
2501 2904 5.458015 GTGTTTTTATCCACAGTTAGGCAC 58.542 41.667 0.00 0.00 0.00 5.01
2518 2921 8.773404 ACTAATCTAAATAGAGCACGTGTTTT 57.227 30.769 18.38 9.22 35.50 2.43
2542 2945 1.280133 GTTAGGGGGTTGGGTAGTGAC 59.720 57.143 0.00 0.00 0.00 3.67
2543 2946 1.660242 GTTAGGGGGTTGGGTAGTGA 58.340 55.000 0.00 0.00 0.00 3.41
2549 2952 1.361197 AGATTTGGTTAGGGGGTTGGG 59.639 52.381 0.00 0.00 0.00 4.12
2556 2959 2.094675 CCACTGCAGATTTGGTTAGGG 58.905 52.381 23.35 1.93 0.00 3.53
2562 2965 1.098050 GGTAGCCACTGCAGATTTGG 58.902 55.000 23.35 18.91 41.13 3.28
2575 2980 6.011481 ACTATCCAGTATCAGTAAGGTAGCC 58.989 44.000 0.00 0.00 31.45 3.93
2668 3278 9.798994 CTACAGTACTCACTCCGTATAAAATTT 57.201 33.333 0.00 0.00 30.46 1.82
2674 3284 5.757320 GCTTCTACAGTACTCACTCCGTATA 59.243 44.000 0.00 0.00 30.46 1.47
2675 3285 4.575645 GCTTCTACAGTACTCACTCCGTAT 59.424 45.833 0.00 0.00 30.46 3.06
2691 3373 3.307242 CCGCTACTGAATTGTGCTTCTAC 59.693 47.826 0.00 0.00 0.00 2.59
2786 3471 2.666190 TGCAACAGTGAGAGGCGC 60.666 61.111 0.00 0.00 0.00 6.53
2833 3530 0.250727 TCCTTTTGGCCTTGTCTCCG 60.251 55.000 3.32 0.00 40.12 4.63
2886 3584 3.511146 AGTAATTTCGAACGAGGGGTACA 59.489 43.478 0.00 0.00 0.00 2.90
2887 3585 4.115401 AGTAATTTCGAACGAGGGGTAC 57.885 45.455 0.00 0.00 0.00 3.34
2888 3586 4.021192 ACAAGTAATTTCGAACGAGGGGTA 60.021 41.667 0.00 0.00 0.00 3.69
2889 3587 3.244318 ACAAGTAATTTCGAACGAGGGGT 60.244 43.478 0.00 0.00 0.00 4.95
2890 3588 3.332034 ACAAGTAATTTCGAACGAGGGG 58.668 45.455 0.00 0.00 0.00 4.79
2891 3589 3.060363 CGACAAGTAATTTCGAACGAGGG 59.940 47.826 0.00 0.00 34.62 4.30
2892 3590 3.481467 GCGACAAGTAATTTCGAACGAGG 60.481 47.826 0.00 0.00 34.62 4.63
2893 3591 3.120616 TGCGACAAGTAATTTCGAACGAG 59.879 43.478 0.00 0.00 34.62 4.18
2894 3592 3.051327 TGCGACAAGTAATTTCGAACGA 58.949 40.909 0.00 0.00 34.62 3.85
2895 3593 3.427516 TGCGACAAGTAATTTCGAACG 57.572 42.857 0.00 0.00 34.62 3.95
2896 3594 6.485253 TTTTTGCGACAAGTAATTTCGAAC 57.515 33.333 0.00 0.00 34.62 3.95
2897 3595 6.143118 CCATTTTTGCGACAAGTAATTTCGAA 59.857 34.615 0.00 0.00 34.62 3.71
2898 3596 5.627367 CCATTTTTGCGACAAGTAATTTCGA 59.373 36.000 10.25 0.00 34.62 3.71
2899 3597 5.627367 TCCATTTTTGCGACAAGTAATTTCG 59.373 36.000 0.00 4.05 35.82 3.46
2900 3598 7.116233 ACATCCATTTTTGCGACAAGTAATTTC 59.884 33.333 0.00 0.00 0.00 2.17
2901 3599 6.928492 ACATCCATTTTTGCGACAAGTAATTT 59.072 30.769 0.00 0.00 0.00 1.82
2902 3600 6.454795 ACATCCATTTTTGCGACAAGTAATT 58.545 32.000 0.00 0.00 0.00 1.40
2903 3601 6.024552 ACATCCATTTTTGCGACAAGTAAT 57.975 33.333 0.00 0.00 0.00 1.89
2904 3602 5.446143 ACATCCATTTTTGCGACAAGTAA 57.554 34.783 0.00 0.00 0.00 2.24
2905 3603 6.597672 AGATACATCCATTTTTGCGACAAGTA 59.402 34.615 0.00 0.00 0.00 2.24
2906 3604 5.415701 AGATACATCCATTTTTGCGACAAGT 59.584 36.000 0.00 0.00 0.00 3.16
2907 3605 5.883661 AGATACATCCATTTTTGCGACAAG 58.116 37.500 0.00 0.00 0.00 3.16
2908 3606 5.895636 AGATACATCCATTTTTGCGACAA 57.104 34.783 0.00 0.00 0.00 3.18
2909 3607 6.257849 GTCTAGATACATCCATTTTTGCGACA 59.742 38.462 0.00 0.00 0.00 4.35
2910 3608 6.562270 CGTCTAGATACATCCATTTTTGCGAC 60.562 42.308 0.00 0.00 0.00 5.19
2911 3609 5.462068 CGTCTAGATACATCCATTTTTGCGA 59.538 40.000 0.00 0.00 0.00 5.10
2912 3610 5.234329 ACGTCTAGATACATCCATTTTTGCG 59.766 40.000 0.00 0.00 0.00 4.85
2913 3611 6.604735 ACGTCTAGATACATCCATTTTTGC 57.395 37.500 0.00 0.00 0.00 3.68
2957 3655 9.586150 CGTTCAGAATTATTTATCTCGGAAATG 57.414 33.333 0.00 0.00 0.00 2.32
2958 3656 8.774586 CCGTTCAGAATTATTTATCTCGGAAAT 58.225 33.333 0.00 0.00 34.35 2.17
2959 3657 7.982919 TCCGTTCAGAATTATTTATCTCGGAAA 59.017 33.333 0.00 0.00 36.94 3.13
2960 3658 7.494211 TCCGTTCAGAATTATTTATCTCGGAA 58.506 34.615 0.00 0.00 36.94 4.30
2961 3659 7.046292 TCCGTTCAGAATTATTTATCTCGGA 57.954 36.000 0.00 0.00 37.30 4.55
2962 3660 6.366332 CCTCCGTTCAGAATTATTTATCTCGG 59.634 42.308 0.00 0.00 33.97 4.63
2963 3661 7.145985 TCCTCCGTTCAGAATTATTTATCTCG 58.854 38.462 0.00 0.00 0.00 4.04
2964 3662 8.145122 ACTCCTCCGTTCAGAATTATTTATCTC 58.855 37.037 0.00 0.00 0.00 2.75
2965 3663 8.024145 ACTCCTCCGTTCAGAATTATTTATCT 57.976 34.615 0.00 0.00 0.00 1.98
2966 3664 9.194271 GTACTCCTCCGTTCAGAATTATTTATC 57.806 37.037 0.00 0.00 0.00 1.75
2967 3665 7.866393 CGTACTCCTCCGTTCAGAATTATTTAT 59.134 37.037 0.00 0.00 0.00 1.40
2968 3666 7.148018 ACGTACTCCTCCGTTCAGAATTATTTA 60.148 37.037 0.00 0.00 32.50 1.40
2969 3667 6.040878 CGTACTCCTCCGTTCAGAATTATTT 58.959 40.000 0.00 0.00 0.00 1.40
2970 3668 5.126707 ACGTACTCCTCCGTTCAGAATTATT 59.873 40.000 0.00 0.00 32.50 1.40
2971 3669 4.643784 ACGTACTCCTCCGTTCAGAATTAT 59.356 41.667 0.00 0.00 32.50 1.28
2972 3670 4.012374 ACGTACTCCTCCGTTCAGAATTA 58.988 43.478 0.00 0.00 32.50 1.40
2973 3671 2.824341 ACGTACTCCTCCGTTCAGAATT 59.176 45.455 0.00 0.00 32.50 2.17
2974 3672 2.444421 ACGTACTCCTCCGTTCAGAAT 58.556 47.619 0.00 0.00 32.50 2.40
2975 3673 1.901591 ACGTACTCCTCCGTTCAGAA 58.098 50.000 0.00 0.00 32.50 3.02
2976 3674 2.350522 GTACGTACTCCTCCGTTCAGA 58.649 52.381 18.47 0.00 38.43 3.27
2977 3675 1.399791 GGTACGTACTCCTCCGTTCAG 59.600 57.143 24.07 0.00 38.43 3.02
2978 3676 1.271325 TGGTACGTACTCCTCCGTTCA 60.271 52.381 24.07 8.35 38.43 3.18
2979 3677 1.453155 TGGTACGTACTCCTCCGTTC 58.547 55.000 24.07 5.85 38.43 3.95
2980 3678 1.747355 CATGGTACGTACTCCTCCGTT 59.253 52.381 24.07 0.00 38.43 4.44
2981 3679 1.065199 TCATGGTACGTACTCCTCCGT 60.065 52.381 24.07 6.86 40.87 4.69
2982 3680 1.602851 CTCATGGTACGTACTCCTCCG 59.397 57.143 24.07 8.35 0.00 4.63
2983 3681 2.652590 ACTCATGGTACGTACTCCTCC 58.347 52.381 24.07 8.84 0.00 4.30
2984 3682 4.809815 GTACTCATGGTACGTACTCCTC 57.190 50.000 24.07 9.00 40.90 3.71
2997 3697 2.683362 TGGCTACAGACGAGTACTCATG 59.317 50.000 22.37 18.12 0.00 3.07
2999 3699 2.484742 TGGCTACAGACGAGTACTCA 57.515 50.000 22.37 0.99 0.00 3.41
3023 3723 3.891977 CACCAGCTAGAGATAAGTAGCCA 59.108 47.826 0.00 0.00 42.32 4.75
3024 3724 3.305744 GCACCAGCTAGAGATAAGTAGCC 60.306 52.174 0.00 0.00 42.32 3.93
3311 4039 4.653341 ACCAAAGAAAATGAATGTGTGGGA 59.347 37.500 0.00 0.00 0.00 4.37
3317 4045 5.768164 ACTACGGACCAAAGAAAATGAATGT 59.232 36.000 0.00 0.00 0.00 2.71
3349 4077 1.820906 GCTTGGAGCGATGCCATGA 60.821 57.895 0.00 0.00 34.90 3.07
3365 4093 4.148825 GAGACCATCGGCACCGCT 62.149 66.667 3.66 0.00 39.59 5.52
3366 4094 3.665675 AAGAGACCATCGGCACCGC 62.666 63.158 3.66 0.00 39.59 5.68
3380 4108 1.535860 CCAAAACCGCAACCACAAGAG 60.536 52.381 0.00 0.00 0.00 2.85
3394 4122 1.644786 ATCGCGCTAGGCACCAAAAC 61.645 55.000 5.56 0.00 43.84 2.43
3429 4157 0.400213 GGTGATGGTGAGTGGGTTCA 59.600 55.000 0.00 0.00 0.00 3.18
3430 4158 0.400213 TGGTGATGGTGAGTGGGTTC 59.600 55.000 0.00 0.00 0.00 3.62
3432 4160 0.110486 GTTGGTGATGGTGAGTGGGT 59.890 55.000 0.00 0.00 0.00 4.51
3435 4163 2.687425 TGTTTGTTGGTGATGGTGAGTG 59.313 45.455 0.00 0.00 0.00 3.51
3436 4164 3.011566 TGTTTGTTGGTGATGGTGAGT 57.988 42.857 0.00 0.00 0.00 3.41
3438 4166 3.130164 CAGTTGTTTGTTGGTGATGGTGA 59.870 43.478 0.00 0.00 0.00 4.02
3439 4167 3.130164 TCAGTTGTTTGTTGGTGATGGTG 59.870 43.478 0.00 0.00 0.00 4.17
3440 4168 3.360867 TCAGTTGTTTGTTGGTGATGGT 58.639 40.909 0.00 0.00 0.00 3.55
3441 4169 4.279169 AGATCAGTTGTTTGTTGGTGATGG 59.721 41.667 0.00 0.00 0.00 3.51
3442 4170 5.240183 AGAGATCAGTTGTTTGTTGGTGATG 59.760 40.000 0.00 0.00 0.00 3.07
3443 4171 5.380043 AGAGATCAGTTGTTTGTTGGTGAT 58.620 37.500 0.00 0.00 0.00 3.06
3444 4172 4.780815 AGAGATCAGTTGTTTGTTGGTGA 58.219 39.130 0.00 0.00 0.00 4.02
3445 4173 4.319046 CGAGAGATCAGTTGTTTGTTGGTG 60.319 45.833 0.00 0.00 0.00 4.17
3446 4174 3.809832 CGAGAGATCAGTTGTTTGTTGGT 59.190 43.478 0.00 0.00 0.00 3.67
3447 4175 3.364366 GCGAGAGATCAGTTGTTTGTTGG 60.364 47.826 0.00 0.00 0.00 3.77
3448 4176 3.248363 TGCGAGAGATCAGTTGTTTGTTG 59.752 43.478 0.00 0.00 0.00 3.33
3449 4177 3.466836 TGCGAGAGATCAGTTGTTTGTT 58.533 40.909 0.00 0.00 0.00 2.83
3450 4178 3.111853 TGCGAGAGATCAGTTGTTTGT 57.888 42.857 0.00 0.00 0.00 2.83
3451 4179 4.024556 AGTTTGCGAGAGATCAGTTGTTTG 60.025 41.667 0.00 0.00 0.00 2.93
3452 4180 4.130118 AGTTTGCGAGAGATCAGTTGTTT 58.870 39.130 0.00 0.00 0.00 2.83
3481 4209 6.603940 TGCATGCATACCTACATGATACTA 57.396 37.500 18.46 0.00 45.23 1.82
3483 4211 6.036844 CAGATGCATGCATACCTACATGATAC 59.963 42.308 32.27 15.08 45.23 2.24
3485 4213 4.941873 CAGATGCATGCATACCTACATGAT 59.058 41.667 32.27 7.50 45.23 2.45
3486 4214 4.040706 TCAGATGCATGCATACCTACATGA 59.959 41.667 32.27 21.52 45.23 3.07
3487 4215 4.153655 GTCAGATGCATGCATACCTACATG 59.846 45.833 32.27 19.90 45.19 3.21
3488 4216 4.202388 TGTCAGATGCATGCATACCTACAT 60.202 41.667 32.27 9.74 36.70 2.29
3491 4219 4.420522 TTGTCAGATGCATGCATACCTA 57.579 40.909 32.27 15.60 36.70 3.08
3492 4220 3.286329 TTGTCAGATGCATGCATACCT 57.714 42.857 32.27 22.69 36.70 3.08
3493 4221 4.037089 TGATTTGTCAGATGCATGCATACC 59.963 41.667 32.27 20.80 36.70 2.73
3495 4223 5.533154 TGATGATTTGTCAGATGCATGCATA 59.467 36.000 32.27 15.33 36.70 3.14
3497 4225 3.697045 TGATGATTTGTCAGATGCATGCA 59.303 39.130 25.04 25.04 0.00 3.96
3499 4227 5.041287 GGTTGATGATTTGTCAGATGCATG 58.959 41.667 2.46 0.00 0.00 4.06
3501 4229 4.338012 AGGTTGATGATTTGTCAGATGCA 58.662 39.130 0.00 0.00 0.00 3.96
3502 4230 4.978083 AGGTTGATGATTTGTCAGATGC 57.022 40.909 0.00 0.00 0.00 3.91
3503 4231 7.281549 TCACATAGGTTGATGATTTGTCAGATG 59.718 37.037 0.00 0.00 0.00 2.90
3506 4234 6.990341 TCACATAGGTTGATGATTTGTCAG 57.010 37.500 0.00 0.00 0.00 3.51
3507 4235 7.757941 TTTCACATAGGTTGATGATTTGTCA 57.242 32.000 0.00 0.00 0.00 3.58
3508 4236 8.680903 AGATTTCACATAGGTTGATGATTTGTC 58.319 33.333 0.00 0.00 0.00 3.18
3509 4237 8.585471 AGATTTCACATAGGTTGATGATTTGT 57.415 30.769 0.00 0.00 0.00 2.83
3510 4238 9.297586 CAAGATTTCACATAGGTTGATGATTTG 57.702 33.333 0.00 0.00 0.00 2.32
3511 4239 7.977853 GCAAGATTTCACATAGGTTGATGATTT 59.022 33.333 0.00 0.00 0.00 2.17
3512 4240 7.123098 TGCAAGATTTCACATAGGTTGATGATT 59.877 33.333 0.00 0.00 0.00 2.57
3513 4241 6.604396 TGCAAGATTTCACATAGGTTGATGAT 59.396 34.615 0.00 0.00 0.00 2.45
3515 4243 6.198650 TGCAAGATTTCACATAGGTTGATG 57.801 37.500 0.00 0.00 0.00 3.07
3542 4270 2.499289 ACTACTCCAATGCTGAGTCAGG 59.501 50.000 21.54 5.65 41.97 3.86
3543 4271 3.883830 ACTACTCCAATGCTGAGTCAG 57.116 47.619 16.21 16.21 41.97 3.51
3544 4272 5.422012 TCATTACTACTCCAATGCTGAGTCA 59.578 40.000 0.00 0.00 41.97 3.41
3545 4273 5.751028 GTCATTACTACTCCAATGCTGAGTC 59.249 44.000 0.00 0.00 41.97 3.36
3546 4274 5.423610 AGTCATTACTACTCCAATGCTGAGT 59.576 40.000 0.00 0.00 44.85 3.41
3547 4275 5.911752 AGTCATTACTACTCCAATGCTGAG 58.088 41.667 0.00 0.00 32.84 3.35
3548 4276 5.939764 AGTCATTACTACTCCAATGCTGA 57.060 39.130 0.00 0.00 32.84 4.26
3549 4277 7.041721 TGTTAGTCATTACTACTCCAATGCTG 58.958 38.462 0.00 0.00 37.94 4.41
3550 4278 7.182817 TGTTAGTCATTACTACTCCAATGCT 57.817 36.000 0.00 0.00 37.94 3.79
3551 4279 7.549488 ACTTGTTAGTCATTACTACTCCAATGC 59.451 37.037 0.00 0.00 37.94 3.56
3552 4280 8.873830 CACTTGTTAGTCATTACTACTCCAATG 58.126 37.037 0.00 0.00 37.94 2.82
3553 4281 8.594550 ACACTTGTTAGTCATTACTACTCCAAT 58.405 33.333 0.00 0.00 37.94 3.16
3554 4282 7.959175 ACACTTGTTAGTCATTACTACTCCAA 58.041 34.615 0.00 0.00 37.94 3.53
3555 4283 7.534723 ACACTTGTTAGTCATTACTACTCCA 57.465 36.000 0.00 0.00 37.94 3.86
3556 4284 8.086522 TCAACACTTGTTAGTCATTACTACTCC 58.913 37.037 0.00 0.00 37.94 3.85
3557 4285 8.913656 GTCAACACTTGTTAGTCATTACTACTC 58.086 37.037 0.00 0.00 37.94 2.59
3565 4293 5.408604 GGAATCGTCAACACTTGTTAGTCAT 59.591 40.000 0.00 0.00 36.32 3.06
4206 4934 1.206578 CAGCGCTTGGTGGTTTACG 59.793 57.895 7.50 0.00 37.45 3.18
4293 5033 4.849813 TGTCCATCCATCTGAACAGATT 57.150 40.909 13.69 0.00 45.31 2.40
4295 5035 3.683564 GCATGTCCATCCATCTGAACAGA 60.684 47.826 6.98 6.98 42.37 3.41
4299 5039 3.713248 ACTAGCATGTCCATCCATCTGAA 59.287 43.478 0.00 0.00 0.00 3.02
4318 5058 1.144969 GCGTGCTGCTTAACACACTA 58.855 50.000 0.00 0.00 41.73 2.74
4338 5078 4.563140 ACGCTCCCCAAAGACTAATTTA 57.437 40.909 0.00 0.00 0.00 1.40
4339 5079 3.434940 ACGCTCCCCAAAGACTAATTT 57.565 42.857 0.00 0.00 0.00 1.82
4340 5080 3.518303 AGTACGCTCCCCAAAGACTAATT 59.482 43.478 0.00 0.00 0.00 1.40
4399 5139 2.037902 TCACTGACAGGAAATTACGCCA 59.962 45.455 7.51 0.00 0.00 5.69
4447 5187 0.040958 AAGCGTGCGAGCAAAAAGAG 60.041 50.000 0.00 0.00 40.15 2.85
4454 5194 2.432456 AATCGAAGCGTGCGAGCA 60.432 55.556 6.01 0.00 41.49 4.26
4476 5216 3.173247 GCAACAAGCCACGGTAAAC 57.827 52.632 0.00 0.00 37.23 2.01
4538 5278 8.894731 TGTAAGCTCTGACTAGATAACTAACTG 58.105 37.037 0.00 0.00 31.21 3.16
4543 5283 7.685641 GCCATTGTAAGCTCTGACTAGATAACT 60.686 40.741 0.00 0.00 31.21 2.24
4544 5284 6.422400 GCCATTGTAAGCTCTGACTAGATAAC 59.578 42.308 0.00 0.00 31.21 1.89
4545 5285 6.098266 TGCCATTGTAAGCTCTGACTAGATAA 59.902 38.462 0.00 0.00 31.21 1.75
4559 5302 4.940046 AGTTCAGAGACATGCCATTGTAAG 59.060 41.667 0.00 0.00 0.00 2.34
4561 5304 4.507710 GAGTTCAGAGACATGCCATTGTA 58.492 43.478 0.00 0.00 0.00 2.41
4615 5361 5.938438 AAAGAGACATGTTGCTTTCTCTC 57.062 39.130 16.55 9.14 43.26 3.20
4648 5394 2.092103 AGAGCAGAGAGATACCCTTCGT 60.092 50.000 0.00 0.00 0.00 3.85
4676 5424 7.201661 GCCAATATTAAACACGACATCAACCTA 60.202 37.037 0.00 0.00 0.00 3.08
4683 5431 5.554822 AACGCCAATATTAAACACGACAT 57.445 34.783 0.00 0.00 0.00 3.06
4989 5741 7.383361 GTTCGTCAATGTAATTTGCAATTAGC 58.617 34.615 0.00 0.00 38.09 3.09
4990 5742 7.591407 CGTTCGTCAATGTAATTTGCAATTAG 58.409 34.615 0.00 0.00 31.22 1.73
4991 5743 6.032985 GCGTTCGTCAATGTAATTTGCAATTA 59.967 34.615 0.00 0.00 31.22 1.40
4995 5747 3.230355 GCGTTCGTCAATGTAATTTGCA 58.770 40.909 0.00 0.00 31.22 4.08
5073 5825 2.604462 CGCGATGACATGTGAGATTTGA 59.396 45.455 1.15 0.00 0.00 2.69
5074 5826 2.349580 ACGCGATGACATGTGAGATTTG 59.650 45.455 15.93 0.00 0.00 2.32
5075 5827 2.621338 ACGCGATGACATGTGAGATTT 58.379 42.857 15.93 0.00 0.00 2.17
5076 5828 2.299993 ACGCGATGACATGTGAGATT 57.700 45.000 15.93 0.00 0.00 2.40
5077 5829 2.299993 AACGCGATGACATGTGAGAT 57.700 45.000 15.93 0.00 0.00 2.75
5078 5830 1.726248 CAAACGCGATGACATGTGAGA 59.274 47.619 15.93 0.00 0.00 3.27
5079 5831 1.460743 ACAAACGCGATGACATGTGAG 59.539 47.619 15.93 0.00 0.00 3.51
5099 5851 6.152661 AGCATTTATCTCCAAAAATTCCACGA 59.847 34.615 0.00 0.00 0.00 4.35
5100 5852 6.254157 CAGCATTTATCTCCAAAAATTCCACG 59.746 38.462 0.00 0.00 0.00 4.94
5111 5863 1.683943 GCCTGCAGCATTTATCTCCA 58.316 50.000 8.66 0.00 42.97 3.86
5156 5908 8.218338 ACATTGAACAAAATGGCAAACATAAA 57.782 26.923 0.00 0.00 41.06 1.40


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

AutoCloner maintained by Alex Coulton.