Multiple sequence alignment - TraesCS4A01G072500

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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 TraesCS4A01G072500 chr4A 100.000 3397 0 0 1 3397 70322426 70319030 0.000000e+00 6274
1 TraesCS4A01G072500 chr4A 77.241 290 49 10 1254 1529 588441501 588441787 1.630000e-33 154
2 TraesCS4A01G072500 chr4D 94.072 2311 77 25 591 2872 388954063 388951784 0.000000e+00 3454
3 TraesCS4A01G072500 chr4D 91.272 401 27 6 162 558 388954536 388954140 1.070000e-149 540
4 TraesCS4A01G072500 chr4D 84.412 340 27 11 2901 3235 388951784 388951466 9.150000e-81 311
5 TraesCS4A01G072500 chr4D 98.361 61 0 1 3337 3397 123728507 123728448 4.640000e-19 106
6 TraesCS4A01G072500 chr4D 96.825 63 1 1 3335 3397 134971762 134971823 1.670000e-18 104
7 TraesCS4A01G072500 chr4B 95.062 1215 46 8 1561 2766 477237691 477236482 0.000000e+00 1899
8 TraesCS4A01G072500 chr4B 95.937 886 30 4 680 1563 477238650 477237769 0.000000e+00 1432
9 TraesCS4A01G072500 chr5B 87.255 204 19 6 2509 2709 7082730 7082929 3.410000e-55 226
10 TraesCS4A01G072500 chr2A 79.078 282 43 12 1254 1524 695827228 695826952 2.690000e-41 180
11 TraesCS4A01G072500 chrUn 98.413 63 0 1 3335 3397 381709085 381709024 3.580000e-20 110
12 TraesCS4A01G072500 chrUn 98.413 63 0 1 3335 3397 402971932 402971993 3.580000e-20 110
13 TraesCS4A01G072500 chr7D 98.413 63 0 1 3335 3397 203527488 203527427 3.580000e-20 110
14 TraesCS4A01G072500 chr7D 98.413 63 0 1 3335 3397 307179355 307179294 3.580000e-20 110
15 TraesCS4A01G072500 chr7D 98.413 63 0 1 3335 3397 381879320 381879259 3.580000e-20 110
16 TraesCS4A01G072500 chr3D 98.413 63 0 1 3335 3397 501894713 501894774 3.580000e-20 110
17 TraesCS4A01G072500 chr2D 98.413 63 0 1 3335 3397 635021795 635021856 3.580000e-20 110


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 TraesCS4A01G072500 chr4A 70319030 70322426 3396 True 6274.0 6274 100.000000 1 3397 1 chr4A.!!$R1 3396
1 TraesCS4A01G072500 chr4D 388951466 388954536 3070 True 1435.0 3454 89.918667 162 3235 3 chr4D.!!$R2 3073
2 TraesCS4A01G072500 chr4B 477236482 477238650 2168 True 1665.5 1899 95.499500 680 2766 2 chr4B.!!$R1 2086

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
558 562 0.250424 AAAAAGCACATGGGCCAAGC 60.250 50.000 18.42 15.76 0.0 4.01 F
781 844 1.002544 AGGAAAAGGAGCGAAGACCAG 59.997 52.381 0.00 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 1853 0.614979 AGAGCGGGTCCACATACACT 60.615 55.0 3.13 0.0 0.0 3.55 R
2668 2826 0.798159 CAATCGCACACAAGCAGCTA 59.202 50.0 0.00 0.0 0.0 3.32 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
29 30 9.988815 ATTTACATATTTTTGTTTACACCAGCA 57.011 25.926 0.00 0.00 0.00 4.41
30 31 9.817809 TTTACATATTTTTGTTTACACCAGCAA 57.182 25.926 0.00 0.00 0.00 3.91
31 32 7.707774 ACATATTTTTGTTTACACCAGCAAC 57.292 32.000 0.00 0.00 0.00 4.17
32 33 7.268586 ACATATTTTTGTTTACACCAGCAACA 58.731 30.769 0.00 0.00 0.00 3.33
33 34 7.930865 ACATATTTTTGTTTACACCAGCAACAT 59.069 29.630 0.00 0.00 30.64 2.71
34 35 8.772705 CATATTTTTGTTTACACCAGCAACATT 58.227 29.630 0.00 0.00 30.64 2.71
35 36 7.622893 ATTTTTGTTTACACCAGCAACATTT 57.377 28.000 0.00 0.00 30.64 2.32
36 37 7.440523 TTTTTGTTTACACCAGCAACATTTT 57.559 28.000 0.00 0.00 30.64 1.82
37 38 7.440523 TTTTGTTTACACCAGCAACATTTTT 57.559 28.000 0.00 0.00 30.64 1.94
38 39 8.547967 TTTTGTTTACACCAGCAACATTTTTA 57.452 26.923 0.00 0.00 30.64 1.52
39 40 8.723942 TTTGTTTACACCAGCAACATTTTTAT 57.276 26.923 0.00 0.00 30.64 1.40
40 41 9.817809 TTTGTTTACACCAGCAACATTTTTATA 57.182 25.926 0.00 0.00 30.64 0.98
41 42 9.988815 TTGTTTACACCAGCAACATTTTTATAT 57.011 25.926 0.00 0.00 30.64 0.86
46 47 8.116651 ACACCAGCAACATTTTTATATACACA 57.883 30.769 0.00 0.00 0.00 3.72
47 48 8.026607 ACACCAGCAACATTTTTATATACACAC 58.973 33.333 0.00 0.00 0.00 3.82
48 49 8.243426 CACCAGCAACATTTTTATATACACACT 58.757 33.333 0.00 0.00 0.00 3.55
49 50 8.802267 ACCAGCAACATTTTTATATACACACTT 58.198 29.630 0.00 0.00 0.00 3.16
116 117 9.120538 ACTTTTTGTATATTTCTCACACACACT 57.879 29.630 0.00 0.00 0.00 3.55
117 118 9.385902 CTTTTTGTATATTTCTCACACACACTG 57.614 33.333 0.00 0.00 0.00 3.66
118 119 8.445275 TTTTGTATATTTCTCACACACACTGT 57.555 30.769 0.00 0.00 0.00 3.55
119 120 9.549078 TTTTGTATATTTCTCACACACACTGTA 57.451 29.630 0.00 0.00 0.00 2.74
120 121 8.528917 TTGTATATTTCTCACACACACTGTAC 57.471 34.615 0.00 0.00 0.00 2.90
121 122 7.662897 TGTATATTTCTCACACACACTGTACA 58.337 34.615 0.00 0.00 0.00 2.90
122 123 8.311109 TGTATATTTCTCACACACACTGTACAT 58.689 33.333 0.00 0.00 0.00 2.29
123 124 9.151471 GTATATTTCTCACACACACTGTACATT 57.849 33.333 0.00 0.00 0.00 2.71
124 125 6.942532 ATTTCTCACACACACTGTACATTT 57.057 33.333 0.00 0.00 0.00 2.32
125 126 5.984233 TTCTCACACACACTGTACATTTC 57.016 39.130 0.00 0.00 0.00 2.17
126 127 5.017294 TCTCACACACACTGTACATTTCA 57.983 39.130 0.00 0.00 0.00 2.69
127 128 5.610398 TCTCACACACACTGTACATTTCAT 58.390 37.500 0.00 0.00 0.00 2.57
128 129 6.754193 TCTCACACACACTGTACATTTCATA 58.246 36.000 0.00 0.00 0.00 2.15
129 130 7.386059 TCTCACACACACTGTACATTTCATAT 58.614 34.615 0.00 0.00 0.00 1.78
130 131 8.527810 TCTCACACACACTGTACATTTCATATA 58.472 33.333 0.00 0.00 0.00 0.86
131 132 9.317936 CTCACACACACTGTACATTTCATATAT 57.682 33.333 0.00 0.00 0.00 0.86
325 327 4.574599 AAGAAAGAAAACGCTCAATGCT 57.425 36.364 0.00 0.00 40.11 3.79
366 370 2.544685 CTCATTCTGGGCTACTTGACG 58.455 52.381 0.00 0.00 0.00 4.35
394 398 1.007038 GCACCGTGTCTCGTTACCA 60.007 57.895 0.00 0.00 37.94 3.25
451 455 1.953686 TCCTTTTTGAGGCAAACTCCG 59.046 47.619 0.00 0.00 46.01 4.63
489 493 4.679373 ATGACCTGATATTTGAGCGACT 57.321 40.909 0.00 0.00 0.00 4.18
498 502 6.108687 TGATATTTGAGCGACTTCTTGTCAT 58.891 36.000 0.00 0.00 45.60 3.06
499 503 6.595326 TGATATTTGAGCGACTTCTTGTCATT 59.405 34.615 0.00 0.00 45.60 2.57
540 544 8.681486 TTGAGATTCAGTTGAGAATTTCTGAA 57.319 30.769 3.03 0.00 46.18 3.02
555 559 0.680618 CTGAAAAAGCACATGGGCCA 59.319 50.000 18.42 9.61 0.00 5.36
557 561 1.070445 TGAAAAAGCACATGGGCCAAG 59.930 47.619 18.42 9.37 0.00 3.61
558 562 0.250424 AAAAAGCACATGGGCCAAGC 60.250 50.000 18.42 15.76 0.00 4.01
575 579 5.694458 GGCCAAGCCCATTTTAATTATAACG 59.306 40.000 0.00 0.00 44.06 3.18
576 580 6.461788 GGCCAAGCCCATTTTAATTATAACGA 60.462 38.462 0.00 0.00 44.06 3.85
577 581 6.419710 GCCAAGCCCATTTTAATTATAACGAC 59.580 38.462 0.00 0.00 0.00 4.34
578 582 7.484975 CCAAGCCCATTTTAATTATAACGACA 58.515 34.615 0.00 0.00 0.00 4.35
579 583 8.141268 CCAAGCCCATTTTAATTATAACGACAT 58.859 33.333 0.00 0.00 0.00 3.06
580 584 9.180678 CAAGCCCATTTTAATTATAACGACATC 57.819 33.333 0.00 0.00 0.00 3.06
582 586 9.077885 AGCCCATTTTAATTATAACGACATCAT 57.922 29.630 0.00 0.00 0.00 2.45
652 702 5.308237 ACTCTGGCTTTCTTTTCTCTAAGGA 59.692 40.000 0.00 0.00 0.00 3.36
705 768 3.372822 GCCGAACGGACTCAAAATATCAA 59.627 43.478 17.63 0.00 37.50 2.57
781 844 1.002544 AGGAAAAGGAGCGAAGACCAG 59.997 52.381 0.00 0.00 0.00 4.00
787 850 1.009389 GGAGCGAAGACCAGAACACG 61.009 60.000 0.00 0.00 0.00 4.49
800 863 1.407618 AGAACACGCAAAAGGGGAAAC 59.592 47.619 0.00 0.00 0.00 2.78
967 1031 3.039526 CCTCCCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
1026 1090 1.152546 GAGCCCTCTCCTCCTCCTC 60.153 68.421 0.00 0.00 33.19 3.71
1290 1355 2.830264 CGGTGCGCCTTAGTTGTTA 58.170 52.632 15.69 0.00 0.00 2.41
1291 1356 1.149987 CGGTGCGCCTTAGTTGTTAA 58.850 50.000 15.69 0.00 0.00 2.01
1436 1504 2.750350 CTCCACCTCCCGTTGCTT 59.250 61.111 0.00 0.00 0.00 3.91
1462 1530 5.523916 CGGAGGACAAGGTATAAATTCTGTG 59.476 44.000 0.00 0.00 0.00 3.66
1497 1565 9.734620 GCATCTTATTGCTGTAAATTTGTATGA 57.265 29.630 0.00 0.00 39.57 2.15
1594 1742 6.316140 TGCTGTGTTGATGGTTATCAGAATAC 59.684 38.462 0.00 0.00 43.76 1.89
1605 1753 7.734942 TGGTTATCAGAATACATGATGTGCTA 58.265 34.615 8.61 0.00 37.91 3.49
1636 1784 7.732996 ACTGTATACTGTATGGTTACCAATCC 58.267 38.462 8.63 0.00 36.95 3.01
1641 1789 4.202223 ACTGTATGGTTACCAATCCGCTAG 60.202 45.833 8.63 3.22 36.95 3.42
1678 1826 3.750828 GCCTACTCAGACAAGAGGC 57.249 57.895 0.00 0.00 45.48 4.70
1705 1853 3.812609 TCATGCGAGCAGTTTTAAGAACA 59.187 39.130 3.58 0.00 0.00 3.18
1719 1867 3.418684 AAGAACAGTGTATGTGGACCC 57.581 47.619 0.00 0.00 43.00 4.46
1760 1910 3.923017 GCACACAGCTACTGGAAAAAT 57.077 42.857 0.00 0.00 41.15 1.82
1765 1916 6.621596 GCACACAGCTACTGGAAAAATTCTAG 60.622 42.308 2.39 2.39 41.05 2.43
1783 1934 9.875691 AAATTCTAGGGCTTTATGTGAAAAATC 57.124 29.630 0.00 0.00 0.00 2.17
1784 1935 8.593945 ATTCTAGGGCTTTATGTGAAAAATCA 57.406 30.769 0.00 0.00 0.00 2.57
1789 1941 6.041979 AGGGCTTTATGTGAAAAATCAGTGTT 59.958 34.615 0.00 0.00 0.00 3.32
1864 2018 7.815641 TGTTACATTGGTACTTCATCACATTG 58.184 34.615 0.00 0.00 0.00 2.82
1866 2020 8.511321 GTTACATTGGTACTTCATCACATTGAA 58.489 33.333 0.00 0.00 34.55 2.69
1920 2074 3.015327 ACTCAGCCTTGCAAATCTCATC 58.985 45.455 0.00 0.00 0.00 2.92
1945 2099 2.035066 GTGGAGCTGATTTGCTGTTGTT 59.965 45.455 0.00 0.00 44.17 2.83
2030 2184 7.386025 ACTTAATCTTTTGCATCTTCCTTTTGC 59.614 33.333 0.00 0.00 36.91 3.68
2087 2241 8.253810 TGTTTGTGACAATGGATGAAAGTAAAA 58.746 29.630 0.00 0.00 34.69 1.52
2174 2328 2.594592 GGGCGTGCTTGTGGAGTT 60.595 61.111 0.00 0.00 0.00 3.01
2177 2331 1.574702 GGCGTGCTTGTGGAGTTACC 61.575 60.000 0.00 0.00 39.54 2.85
2341 2497 4.517453 TGTGTACCCTTTCTCCGAAAATTG 59.483 41.667 0.00 0.00 0.00 2.32
2547 2703 2.158914 TCATGCTGCCATTATGTCGTCT 60.159 45.455 0.00 0.00 0.00 4.18
2667 2825 8.561738 TTATGAGTTTGAGAATTGGGAACTAC 57.438 34.615 0.00 0.00 31.24 2.73
2668 2826 6.187727 TGAGTTTGAGAATTGGGAACTACT 57.812 37.500 0.00 0.00 31.24 2.57
2669 2827 7.311092 TGAGTTTGAGAATTGGGAACTACTA 57.689 36.000 0.00 0.00 31.24 1.82
2695 2853 0.798159 TGTGTGCGATTGCTCATGTC 59.202 50.000 12.62 1.66 45.34 3.06
2700 2858 2.009108 CGATTGCTCATGTCGTGGG 58.991 57.895 0.00 0.00 0.00 4.61
2743 2901 7.121020 TCTGCTCAGTCTATCTGCTATAATCTG 59.879 40.741 0.00 0.00 43.32 2.90
2778 2938 3.181451 TGCTGTCTGTCAAATCCAGAAGT 60.181 43.478 0.00 0.00 40.44 3.01
2796 2956 8.772250 TCCAGAAGTGTCTTATTTGGATTCTAT 58.228 33.333 0.00 0.00 28.78 1.98
2816 2976 7.921786 TCTATAACCTGTGAATTGGAACTTG 57.078 36.000 0.00 0.00 0.00 3.16
2838 2999 6.442541 TGTTCCTATTTCCTTGTAGGTTCA 57.557 37.500 0.00 0.00 38.84 3.18
2882 3043 5.224821 TCCTGAAGGAATATGATCAGCTG 57.775 43.478 7.63 7.63 42.18 4.24
2883 3044 4.657504 TCCTGAAGGAATATGATCAGCTGT 59.342 41.667 14.67 0.42 42.18 4.40
2884 3045 5.131642 TCCTGAAGGAATATGATCAGCTGTT 59.868 40.000 14.67 5.03 42.18 3.16
2885 3046 5.826737 CCTGAAGGAATATGATCAGCTGTTT 59.173 40.000 14.67 2.24 38.34 2.83
2886 3047 6.994496 CCTGAAGGAATATGATCAGCTGTTTA 59.006 38.462 14.67 2.16 38.34 2.01
2887 3048 7.172875 CCTGAAGGAATATGATCAGCTGTTTAG 59.827 40.741 14.67 2.68 38.34 1.85
2888 3049 7.568349 TGAAGGAATATGATCAGCTGTTTAGT 58.432 34.615 14.67 0.90 0.00 2.24
2889 3050 8.049117 TGAAGGAATATGATCAGCTGTTTAGTT 58.951 33.333 14.67 3.31 0.00 2.24
2890 3051 9.547753 GAAGGAATATGATCAGCTGTTTAGTTA 57.452 33.333 14.67 0.33 0.00 2.24
2891 3052 9.553064 AAGGAATATGATCAGCTGTTTAGTTAG 57.447 33.333 14.67 0.00 0.00 2.34
2892 3053 7.659390 AGGAATATGATCAGCTGTTTAGTTAGC 59.341 37.037 14.67 0.00 40.18 3.09
2893 3054 7.095017 GGAATATGATCAGCTGTTTAGTTAGCC 60.095 40.741 14.67 3.81 40.76 3.93
2894 3055 4.551702 TGATCAGCTGTTTAGTTAGCCA 57.448 40.909 14.67 0.00 40.76 4.75
2895 3056 4.905429 TGATCAGCTGTTTAGTTAGCCAA 58.095 39.130 14.67 0.00 40.76 4.52
2896 3057 4.695455 TGATCAGCTGTTTAGTTAGCCAAC 59.305 41.667 14.67 0.00 40.76 3.77
2897 3058 4.079980 TCAGCTGTTTAGTTAGCCAACA 57.920 40.909 14.67 0.00 40.76 3.33
2898 3059 4.456535 TCAGCTGTTTAGTTAGCCAACAA 58.543 39.130 14.67 0.00 40.76 2.83
2899 3060 4.274950 TCAGCTGTTTAGTTAGCCAACAAC 59.725 41.667 14.67 0.00 40.76 3.32
2963 3127 3.508793 CCATGGATGGTTATGGATTGCTC 59.491 47.826 5.56 0.00 45.32 4.26
2966 3130 4.464008 TGGATGGTTATGGATTGCTCTTC 58.536 43.478 0.00 0.00 0.00 2.87
2977 3141 4.081476 TGGATTGCTCTTCGATTTCAGAGA 60.081 41.667 14.62 0.00 39.21 3.10
2978 3142 4.872691 GGATTGCTCTTCGATTTCAGAGAA 59.127 41.667 14.62 2.44 39.21 2.87
2986 3150 5.934043 TCTTCGATTTCAGAGAAATGAAGCA 59.066 36.000 22.54 15.75 40.16 3.91
2992 3156 2.005451 CAGAGAAATGAAGCAGACCCG 58.995 52.381 0.00 0.00 0.00 5.28
2994 3158 1.734465 GAGAAATGAAGCAGACCCGTG 59.266 52.381 0.00 0.00 0.00 4.94
3001 3165 4.932789 GCAGACCCGTGCTTATGA 57.067 55.556 0.00 0.00 40.54 2.15
3002 3166 2.384203 GCAGACCCGTGCTTATGAC 58.616 57.895 0.00 0.00 40.54 3.06
3003 3167 0.108138 GCAGACCCGTGCTTATGACT 60.108 55.000 0.00 0.00 40.54 3.41
3004 3168 1.136305 GCAGACCCGTGCTTATGACTA 59.864 52.381 0.00 0.00 40.54 2.59
3028 3192 9.777297 CTATAATAAATGGGGGAATGTTTTTGG 57.223 33.333 0.00 0.00 0.00 3.28
3029 3193 6.461577 AATAAATGGGGGAATGTTTTTGGT 57.538 33.333 0.00 0.00 0.00 3.67
3030 3194 4.805140 AAATGGGGGAATGTTTTTGGTT 57.195 36.364 0.00 0.00 0.00 3.67
3031 3195 4.805140 AATGGGGGAATGTTTTTGGTTT 57.195 36.364 0.00 0.00 0.00 3.27
3032 3196 3.567478 TGGGGGAATGTTTTTGGTTTG 57.433 42.857 0.00 0.00 0.00 2.93
3033 3197 2.173569 TGGGGGAATGTTTTTGGTTTGG 59.826 45.455 0.00 0.00 0.00 3.28
3034 3198 2.488167 GGGGGAATGTTTTTGGTTTGGG 60.488 50.000 0.00 0.00 0.00 4.12
3035 3199 2.488167 GGGGAATGTTTTTGGTTTGGGG 60.488 50.000 0.00 0.00 0.00 4.96
3036 3200 2.439880 GGGAATGTTTTTGGTTTGGGGA 59.560 45.455 0.00 0.00 0.00 4.81
3037 3201 3.117851 GGGAATGTTTTTGGTTTGGGGAA 60.118 43.478 0.00 0.00 0.00 3.97
3038 3202 4.447034 GGGAATGTTTTTGGTTTGGGGAAT 60.447 41.667 0.00 0.00 0.00 3.01
3039 3203 5.136828 GGAATGTTTTTGGTTTGGGGAATT 58.863 37.500 0.00 0.00 0.00 2.17
3063 3227 1.839994 CTCATCTAGCAGACCCCCAAA 59.160 52.381 0.00 0.00 0.00 3.28
3126 3290 6.707440 TGTTTTCTTTCTTGCCTATTGACA 57.293 33.333 0.00 0.00 0.00 3.58
3133 3297 4.574674 TCTTGCCTATTGACAATGAGGT 57.425 40.909 11.05 0.00 0.00 3.85
3150 3314 1.583495 GGTCAGTACTTTTGCCGCCC 61.583 60.000 0.00 0.00 0.00 6.13
3151 3315 1.302993 TCAGTACTTTTGCCGCCCC 60.303 57.895 0.00 0.00 0.00 5.80
3152 3316 2.035155 AGTACTTTTGCCGCCCCC 59.965 61.111 0.00 0.00 0.00 5.40
3184 3348 2.155065 CCCCCACTTCCAACTCAGT 58.845 57.895 0.00 0.00 0.00 3.41
3185 3349 0.478507 CCCCCACTTCCAACTCAGTT 59.521 55.000 0.00 0.00 0.00 3.16
3186 3350 1.609208 CCCCACTTCCAACTCAGTTG 58.391 55.000 10.91 10.91 42.49 3.16
3187 3351 1.133792 CCCCACTTCCAACTCAGTTGT 60.134 52.381 16.50 0.00 41.41 3.32
3188 3352 2.222027 CCCACTTCCAACTCAGTTGTC 58.778 52.381 16.50 0.00 41.41 3.18
3189 3353 1.867233 CCACTTCCAACTCAGTTGTCG 59.133 52.381 16.50 6.61 41.41 4.35
3207 3372 6.260936 AGTTGTCGAACTTCATTGAGAATGTT 59.739 34.615 0.00 0.00 39.56 2.71
3216 3381 2.673775 TTGAGAATGTTGGCCTGGAA 57.326 45.000 3.32 0.00 0.00 3.53
3223 3388 2.027625 GTTGGCCTGGAAGTCGACG 61.028 63.158 10.46 0.00 0.00 5.12
3227 3392 2.178521 CCTGGAAGTCGACGACGG 59.821 66.667 21.44 12.74 37.67 4.79
3235 3400 3.744719 TCGACGACGGCAAGGAGG 61.745 66.667 7.55 0.00 40.21 4.30
3236 3401 3.744719 CGACGACGGCAAGGAGGA 61.745 66.667 0.00 0.00 35.72 3.71
3237 3402 2.126031 GACGACGGCAAGGAGGAC 60.126 66.667 0.00 0.00 0.00 3.85
3238 3403 3.644399 GACGACGGCAAGGAGGACC 62.644 68.421 0.00 0.00 0.00 4.46
3253 3418 4.524318 ACCTATTCGGTGGCGGCG 62.524 66.667 0.51 0.51 46.80 6.46
3254 3419 4.215742 CCTATTCGGTGGCGGCGA 62.216 66.667 12.98 0.00 0.00 5.54
3255 3420 2.960129 CTATTCGGTGGCGGCGAC 60.960 66.667 12.98 9.31 0.00 5.19
3267 3432 4.296265 GGCGACGACCCTGAAAAT 57.704 55.556 0.00 0.00 0.00 1.82
3268 3433 3.446507 GGCGACGACCCTGAAAATA 57.553 52.632 0.00 0.00 0.00 1.40
3269 3434 1.004595 GGCGACGACCCTGAAAATAC 58.995 55.000 0.00 0.00 0.00 1.89
3270 3435 1.004595 GCGACGACCCTGAAAATACC 58.995 55.000 0.00 0.00 0.00 2.73
3271 3436 1.274596 CGACGACCCTGAAAATACCG 58.725 55.000 0.00 0.00 0.00 4.02
3272 3437 1.004595 GACGACCCTGAAAATACCGC 58.995 55.000 0.00 0.00 0.00 5.68
3273 3438 0.392060 ACGACCCTGAAAATACCGCC 60.392 55.000 0.00 0.00 0.00 6.13
3274 3439 0.391927 CGACCCTGAAAATACCGCCA 60.392 55.000 0.00 0.00 0.00 5.69
3275 3440 1.092348 GACCCTGAAAATACCGCCAC 58.908 55.000 0.00 0.00 0.00 5.01
3276 3441 0.675522 ACCCTGAAAATACCGCCACG 60.676 55.000 0.00 0.00 0.00 4.94
3277 3442 0.675522 CCCTGAAAATACCGCCACGT 60.676 55.000 0.00 0.00 0.00 4.49
3278 3443 1.161843 CCTGAAAATACCGCCACGTT 58.838 50.000 0.00 0.00 0.00 3.99
3279 3444 1.135803 CCTGAAAATACCGCCACGTTG 60.136 52.381 0.00 0.00 0.00 4.10
3280 3445 0.875728 TGAAAATACCGCCACGTTGG 59.124 50.000 0.00 0.00 41.55 3.77
3281 3446 0.876399 GAAAATACCGCCACGTTGGT 59.124 50.000 8.74 8.74 40.46 3.67
3282 3447 0.876399 AAAATACCGCCACGTTGGTC 59.124 50.000 7.13 0.00 40.46 4.02
3283 3448 1.293267 AAATACCGCCACGTTGGTCG 61.293 55.000 7.13 9.52 40.46 4.79
3284 3449 2.157305 AATACCGCCACGTTGGTCGA 62.157 55.000 7.13 0.00 40.46 4.20
3285 3450 2.824071 ATACCGCCACGTTGGTCGAC 62.824 60.000 7.13 7.13 40.46 4.20
3287 3452 4.986587 CGCCACGTTGGTCGACGA 62.987 66.667 16.53 1.86 45.47 4.20
3288 3453 3.400590 GCCACGTTGGTCGACGAC 61.401 66.667 19.70 19.70 45.47 4.34
3298 3463 4.427793 TCGACGACGACACGAATG 57.572 55.556 5.75 0.00 43.81 2.67
3299 3464 1.570967 TCGACGACGACACGAATGT 59.429 52.632 5.75 0.00 43.81 2.71
3300 3465 0.723459 TCGACGACGACACGAATGTG 60.723 55.000 5.75 0.00 43.81 3.21
3308 3473 3.966215 CACGAATGTGCGGTTCCT 58.034 55.556 0.00 0.00 39.67 3.36
3309 3474 1.497278 CACGAATGTGCGGTTCCTG 59.503 57.895 0.00 0.00 39.67 3.86
3310 3475 1.671054 ACGAATGTGCGGTTCCTGG 60.671 57.895 0.00 0.00 35.12 4.45
3311 3476 1.671054 CGAATGTGCGGTTCCTGGT 60.671 57.895 0.00 0.00 0.00 4.00
3312 3477 1.635663 CGAATGTGCGGTTCCTGGTC 61.636 60.000 0.00 0.00 0.00 4.02
3313 3478 1.303317 AATGTGCGGTTCCTGGTCC 60.303 57.895 0.00 0.00 0.00 4.46
3318 3483 4.003788 CGGTTCCTGGTCCGTGCT 62.004 66.667 19.06 0.00 41.58 4.40
3319 3484 2.047179 GGTTCCTGGTCCGTGCTC 60.047 66.667 0.00 0.00 0.00 4.26
3320 3485 2.047179 GTTCCTGGTCCGTGCTCC 60.047 66.667 0.00 0.00 0.00 4.70
3321 3486 2.203788 TTCCTGGTCCGTGCTCCT 60.204 61.111 0.00 0.00 0.00 3.69
3322 3487 2.283529 TTCCTGGTCCGTGCTCCTC 61.284 63.158 0.00 0.00 0.00 3.71
3323 3488 2.681778 CCTGGTCCGTGCTCCTCT 60.682 66.667 0.00 0.00 0.00 3.69
3324 3489 2.575993 CTGGTCCGTGCTCCTCTG 59.424 66.667 0.00 0.00 0.00 3.35
3325 3490 3.655810 CTGGTCCGTGCTCCTCTGC 62.656 68.421 0.00 0.00 0.00 4.26
3326 3491 4.459089 GGTCCGTGCTCCTCTGCC 62.459 72.222 0.00 0.00 0.00 4.85
3327 3492 3.695606 GTCCGTGCTCCTCTGCCA 61.696 66.667 0.00 0.00 0.00 4.92
3328 3493 2.922503 TCCGTGCTCCTCTGCCAA 60.923 61.111 0.00 0.00 0.00 4.52
3329 3494 2.743928 CCGTGCTCCTCTGCCAAC 60.744 66.667 0.00 0.00 0.00 3.77
3330 3495 3.114616 CGTGCTCCTCTGCCAACG 61.115 66.667 0.00 0.00 0.00 4.10
3331 3496 3.426568 GTGCTCCTCTGCCAACGC 61.427 66.667 0.00 0.00 0.00 4.84
3332 3497 4.704833 TGCTCCTCTGCCAACGCC 62.705 66.667 0.00 0.00 0.00 5.68
3333 3498 4.704833 GCTCCTCTGCCAACGCCA 62.705 66.667 0.00 0.00 0.00 5.69
3334 3499 2.270205 CTCCTCTGCCAACGCCAT 59.730 61.111 0.00 0.00 0.00 4.40
3335 3500 2.046023 TCCTCTGCCAACGCCATG 60.046 61.111 0.00 0.00 0.00 3.66
3336 3501 3.136123 CCTCTGCCAACGCCATGG 61.136 66.667 7.63 7.63 43.70 3.66
3337 3502 3.136123 CTCTGCCAACGCCATGGG 61.136 66.667 15.13 6.26 41.01 4.00
3338 3503 3.925630 CTCTGCCAACGCCATGGGT 62.926 63.158 15.13 6.98 41.01 4.51
3339 3504 3.443045 CTGCCAACGCCATGGGTC 61.443 66.667 15.13 0.00 41.01 4.46
3340 3505 4.277009 TGCCAACGCCATGGGTCA 62.277 61.111 15.13 1.84 41.01 4.02
3341 3506 2.988684 GCCAACGCCATGGGTCAA 60.989 61.111 15.13 0.00 41.01 3.18
3342 3507 2.569354 GCCAACGCCATGGGTCAAA 61.569 57.895 15.13 0.00 41.01 2.69
3343 3508 1.586028 CCAACGCCATGGGTCAAAG 59.414 57.895 15.13 1.85 36.79 2.77
3344 3509 0.893270 CCAACGCCATGGGTCAAAGA 60.893 55.000 15.13 0.00 36.79 2.52
3345 3510 0.523072 CAACGCCATGGGTCAAAGAG 59.477 55.000 15.13 0.00 0.00 2.85
3346 3511 0.609131 AACGCCATGGGTCAAAGAGG 60.609 55.000 15.13 0.00 0.00 3.69
3347 3512 2.409870 CGCCATGGGTCAAAGAGGC 61.410 63.158 15.13 0.00 38.73 4.70
3348 3513 2.054453 GCCATGGGTCAAAGAGGCC 61.054 63.158 15.13 0.00 43.09 5.19
3349 3514 1.693640 CCATGGGTCAAAGAGGCCT 59.306 57.895 3.86 3.86 43.45 5.19
3350 3515 0.682209 CCATGGGTCAAAGAGGCCTG 60.682 60.000 12.00 0.00 43.45 4.85
3351 3516 1.000396 ATGGGTCAAAGAGGCCTGC 60.000 57.895 12.00 1.09 43.45 4.85
3352 3517 1.504275 ATGGGTCAAAGAGGCCTGCT 61.504 55.000 12.00 4.06 43.45 4.24
3353 3518 0.840288 TGGGTCAAAGAGGCCTGCTA 60.840 55.000 12.00 0.00 43.45 3.49
3354 3519 0.107459 GGGTCAAAGAGGCCTGCTAG 60.107 60.000 12.00 4.23 43.45 3.42
3355 3520 0.107459 GGTCAAAGAGGCCTGCTAGG 60.107 60.000 12.00 3.48 39.61 3.02
3356 3521 0.615850 GTCAAAGAGGCCTGCTAGGT 59.384 55.000 12.00 0.00 37.80 3.08
3357 3522 0.615331 TCAAAGAGGCCTGCTAGGTG 59.385 55.000 12.00 7.01 37.80 4.00
3358 3523 0.615331 CAAAGAGGCCTGCTAGGTGA 59.385 55.000 12.00 0.00 37.80 4.02
3359 3524 0.908198 AAAGAGGCCTGCTAGGTGAG 59.092 55.000 12.00 0.00 37.80 3.51
3360 3525 0.041833 AAGAGGCCTGCTAGGTGAGA 59.958 55.000 12.00 0.00 37.80 3.27
3361 3526 0.396974 AGAGGCCTGCTAGGTGAGAG 60.397 60.000 12.00 0.00 37.80 3.20
3362 3527 2.026945 GAGGCCTGCTAGGTGAGAGC 62.027 65.000 12.00 0.00 37.80 4.09
3363 3528 2.503546 GCCTGCTAGGTGAGAGCC 59.496 66.667 4.45 0.00 39.30 4.70
3364 3529 2.063378 GCCTGCTAGGTGAGAGCCT 61.063 63.158 4.45 0.00 39.30 4.58
3365 3530 1.621672 GCCTGCTAGGTGAGAGCCTT 61.622 60.000 4.45 0.00 39.30 4.35
3366 3531 0.908198 CCTGCTAGGTGAGAGCCTTT 59.092 55.000 0.00 0.00 39.30 3.11
3367 3532 1.134551 CCTGCTAGGTGAGAGCCTTTC 60.135 57.143 0.00 0.00 39.30 2.62
3368 3533 1.552337 CTGCTAGGTGAGAGCCTTTCA 59.448 52.381 0.00 0.00 39.30 2.69
3369 3534 2.170187 CTGCTAGGTGAGAGCCTTTCAT 59.830 50.000 0.00 0.00 39.30 2.57
3370 3535 3.374764 TGCTAGGTGAGAGCCTTTCATA 58.625 45.455 0.00 0.00 39.30 2.15
3371 3536 3.386078 TGCTAGGTGAGAGCCTTTCATAG 59.614 47.826 0.00 0.00 39.30 2.23
3375 3540 3.390639 AGGTGAGAGCCTTTCATAGGATG 59.609 47.826 0.00 0.00 44.54 3.51
3376 3541 3.495806 GGTGAGAGCCTTTCATAGGATGG 60.496 52.174 0.00 0.00 44.54 3.51
3377 3542 3.135530 GTGAGAGCCTTTCATAGGATGGT 59.864 47.826 0.00 0.00 44.54 3.55
3378 3543 3.135348 TGAGAGCCTTTCATAGGATGGTG 59.865 47.826 0.00 0.00 44.54 4.17
3379 3544 2.158696 AGAGCCTTTCATAGGATGGTGC 60.159 50.000 0.00 0.00 44.54 5.01
3380 3545 3.072688 GAGCCTTTCATAGGATGGTGCC 61.073 54.545 0.00 0.00 44.54 5.01
3382 3547 2.620251 CTTTCATAGGATGGTGCCGA 57.380 50.000 0.00 0.00 0.00 5.54
3383 3548 2.917933 CTTTCATAGGATGGTGCCGAA 58.082 47.619 0.00 0.00 0.00 4.30
3384 3549 3.278574 CTTTCATAGGATGGTGCCGAAA 58.721 45.455 0.00 0.00 0.00 3.46
3385 3550 3.358111 TTCATAGGATGGTGCCGAAAA 57.642 42.857 0.00 0.00 0.00 2.29
3386 3551 2.917933 TCATAGGATGGTGCCGAAAAG 58.082 47.619 0.00 0.00 0.00 2.27
3387 3552 1.334869 CATAGGATGGTGCCGAAAAGC 59.665 52.381 0.00 0.00 0.00 3.51
3388 3553 0.393808 TAGGATGGTGCCGAAAAGCC 60.394 55.000 0.00 0.00 0.00 4.35
3389 3554 1.678970 GGATGGTGCCGAAAAGCCT 60.679 57.895 0.00 0.00 0.00 4.58
3390 3555 0.393808 GGATGGTGCCGAAAAGCCTA 60.394 55.000 0.00 0.00 0.00 3.93
3391 3556 1.680338 GATGGTGCCGAAAAGCCTAT 58.320 50.000 0.00 0.00 0.00 2.57
3392 3557 1.604278 GATGGTGCCGAAAAGCCTATC 59.396 52.381 0.00 0.00 0.00 2.08
3393 3558 0.326595 TGGTGCCGAAAAGCCTATCA 59.673 50.000 0.00 0.00 0.00 2.15
3394 3559 1.064758 TGGTGCCGAAAAGCCTATCAT 60.065 47.619 0.00 0.00 0.00 2.45
3395 3560 2.171659 TGGTGCCGAAAAGCCTATCATA 59.828 45.455 0.00 0.00 0.00 2.15
3396 3561 3.181445 TGGTGCCGAAAAGCCTATCATAT 60.181 43.478 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.988815 TGCTGGTGTAAACAAAAATATGTAAAT 57.011 25.926 0.00 0.00 32.02 1.40
4 5 9.817809 TTGCTGGTGTAAACAAAAATATGTAAA 57.182 25.926 0.00 0.00 32.02 2.01
5 6 9.250624 GTTGCTGGTGTAAACAAAAATATGTAA 57.749 29.630 0.00 0.00 32.02 2.41
6 7 8.414003 TGTTGCTGGTGTAAACAAAAATATGTA 58.586 29.630 0.00 0.00 31.16 2.29
7 8 7.268586 TGTTGCTGGTGTAAACAAAAATATGT 58.731 30.769 0.00 0.00 31.16 2.29
8 9 7.706281 TGTTGCTGGTGTAAACAAAAATATG 57.294 32.000 0.00 0.00 31.16 1.78
9 10 8.900983 AATGTTGCTGGTGTAAACAAAAATAT 57.099 26.923 0.00 0.00 37.36 1.28
10 11 8.723942 AAATGTTGCTGGTGTAAACAAAAATA 57.276 26.923 0.00 0.00 37.36 1.40
11 12 7.622893 AAATGTTGCTGGTGTAAACAAAAAT 57.377 28.000 0.00 0.00 37.36 1.82
12 13 7.440523 AAAATGTTGCTGGTGTAAACAAAAA 57.559 28.000 0.00 0.00 37.36 1.94
13 14 7.440523 AAAAATGTTGCTGGTGTAAACAAAA 57.559 28.000 0.00 0.00 37.36 2.44
14 15 8.723942 ATAAAAATGTTGCTGGTGTAAACAAA 57.276 26.923 0.00 0.00 37.36 2.83
15 16 9.988815 ATATAAAAATGTTGCTGGTGTAAACAA 57.011 25.926 0.00 0.00 37.36 2.83
20 21 9.232473 TGTGTATATAAAAATGTTGCTGGTGTA 57.768 29.630 0.00 0.00 0.00 2.90
21 22 8.026607 GTGTGTATATAAAAATGTTGCTGGTGT 58.973 33.333 0.00 0.00 0.00 4.16
22 23 8.243426 AGTGTGTATATAAAAATGTTGCTGGTG 58.757 33.333 0.00 0.00 0.00 4.17
23 24 8.348285 AGTGTGTATATAAAAATGTTGCTGGT 57.652 30.769 0.00 0.00 0.00 4.00
90 91 9.120538 AGTGTGTGTGAGAAATATACAAAAAGT 57.879 29.630 0.00 0.00 0.00 2.66
91 92 9.385902 CAGTGTGTGTGAGAAATATACAAAAAG 57.614 33.333 0.00 0.00 0.00 2.27
92 93 8.898761 ACAGTGTGTGTGAGAAATATACAAAAA 58.101 29.630 0.00 0.00 38.28 1.94
93 94 8.445275 ACAGTGTGTGTGAGAAATATACAAAA 57.555 30.769 0.00 0.00 38.28 2.44
94 95 8.984764 GTACAGTGTGTGTGAGAAATATACAAA 58.015 33.333 5.88 0.00 40.69 2.83
95 96 8.145122 TGTACAGTGTGTGTGAGAAATATACAA 58.855 33.333 5.88 0.00 40.69 2.41
96 97 7.662897 TGTACAGTGTGTGTGAGAAATATACA 58.337 34.615 5.88 0.00 40.69 2.29
97 98 8.703604 ATGTACAGTGTGTGTGAGAAATATAC 57.296 34.615 5.88 0.00 40.69 1.47
98 99 9.719355 AAATGTACAGTGTGTGTGAGAAATATA 57.281 29.630 5.88 0.00 40.69 0.86
99 100 8.621532 AAATGTACAGTGTGTGTGAGAAATAT 57.378 30.769 5.88 0.00 40.69 1.28
100 101 7.713073 TGAAATGTACAGTGTGTGTGAGAAATA 59.287 33.333 5.88 0.00 40.69 1.40
101 102 6.542005 TGAAATGTACAGTGTGTGTGAGAAAT 59.458 34.615 5.88 0.00 40.69 2.17
102 103 5.877564 TGAAATGTACAGTGTGTGTGAGAAA 59.122 36.000 5.88 0.00 40.69 2.52
103 104 5.423886 TGAAATGTACAGTGTGTGTGAGAA 58.576 37.500 5.88 0.00 40.69 2.87
104 105 5.017294 TGAAATGTACAGTGTGTGTGAGA 57.983 39.130 5.88 0.00 40.69 3.27
105 106 5.929697 ATGAAATGTACAGTGTGTGTGAG 57.070 39.130 5.88 0.00 40.69 3.51
191 192 7.584847 CAGATTTGAAAAATGTTGAACATGCAC 59.415 33.333 12.09 5.08 37.97 4.57
192 193 7.280428 ACAGATTTGAAAAATGTTGAACATGCA 59.720 29.630 12.09 5.58 37.97 3.96
193 194 7.632721 ACAGATTTGAAAAATGTTGAACATGC 58.367 30.769 12.09 3.07 37.97 4.06
196 197 9.814899 ACATACAGATTTGAAAAATGTTGAACA 57.185 25.926 0.00 0.00 0.00 3.18
302 304 5.641777 GCATTGAGCGTTTTCTTTCTTTT 57.358 34.783 0.00 0.00 0.00 2.27
394 398 1.394618 GGGCGTGACTATGTCTCTCT 58.605 55.000 0.00 0.00 33.15 3.10
523 527 6.753279 TGTGCTTTTTCAGAAATTCTCAACTG 59.247 34.615 0.00 0.00 0.00 3.16
540 544 1.372307 GCTTGGCCCATGTGCTTTT 59.628 52.632 0.00 0.00 0.00 2.27
555 559 8.908903 TGATGTCGTTATAATTAAAATGGGCTT 58.091 29.630 0.00 0.00 0.00 4.35
580 584 9.806203 TGTCAGGAAAAAGCAATAATCAATATG 57.194 29.630 0.00 0.00 0.00 1.78
589 593 9.859427 CTGATTATTTGTCAGGAAAAAGCAATA 57.141 29.630 0.00 0.00 39.48 1.90
590 594 8.587608 TCTGATTATTTGTCAGGAAAAAGCAAT 58.412 29.630 3.58 0.00 42.58 3.56
592 596 7.523293 TCTGATTATTTGTCAGGAAAAAGCA 57.477 32.000 3.58 0.00 42.58 3.91
608 658 9.887629 CCAGAGTGCATCTTATTATCTGATTAT 57.112 33.333 0.00 0.00 35.47 1.28
781 844 1.847818 GTTTCCCCTTTTGCGTGTTC 58.152 50.000 0.00 0.00 0.00 3.18
787 850 3.005367 TGATTCTTCGTTTCCCCTTTTGC 59.995 43.478 0.00 0.00 0.00 3.68
800 863 3.540359 GCGATTGTCTTCGTGATTCTTCG 60.540 47.826 0.00 0.00 41.16 3.79
917 981 2.610859 GTGGGGAGGGAGCTTGGA 60.611 66.667 0.00 0.00 0.00 3.53
1026 1090 1.793134 CGAGGTACGGAATCGGGAGG 61.793 65.000 0.00 0.00 41.39 4.30
1273 1337 2.095919 CAGTTAACAACTAAGGCGCACC 60.096 50.000 10.83 0.00 40.46 5.01
1290 1355 3.255642 CACGGGGATTGAAATCAACAGTT 59.744 43.478 5.46 0.00 38.86 3.16
1291 1356 2.819608 CACGGGGATTGAAATCAACAGT 59.180 45.455 5.46 2.20 38.86 3.55
1436 1504 4.163458 AGAATTTATACCTTGTCCTCCGCA 59.837 41.667 0.00 0.00 0.00 5.69
1497 1565 1.339055 ACCACATCACGCAAGCTACAT 60.339 47.619 0.00 0.00 45.62 2.29
1636 1784 3.600388 ACTCAAACTTCCAATCCTAGCG 58.400 45.455 0.00 0.00 0.00 4.26
1641 1789 4.273318 AGGCATACTCAAACTTCCAATCC 58.727 43.478 0.00 0.00 0.00 3.01
1668 1816 1.949547 GCATGAGCAAGCCTCTTGTCT 60.950 52.381 0.00 5.99 43.82 3.41
1705 1853 0.614979 AGAGCGGGTCCACATACACT 60.615 55.000 3.13 0.00 0.00 3.55
1719 1867 4.388773 TGCTGATACAAACAGTTAAGAGCG 59.611 41.667 0.00 0.00 37.64 5.03
1757 1907 9.875691 GATTTTTCACATAAAGCCCTAGAATTT 57.124 29.630 0.00 0.00 0.00 1.82
1760 1910 7.669722 ACTGATTTTTCACATAAAGCCCTAGAA 59.330 33.333 0.00 0.00 0.00 2.10
1765 1916 5.783111 ACACTGATTTTTCACATAAAGCCC 58.217 37.500 0.00 0.00 0.00 5.19
1826 1978 4.022068 CCAATGTAACAGGATGCAACAACT 60.022 41.667 0.00 0.00 42.53 3.16
1827 1979 4.236935 CCAATGTAACAGGATGCAACAAC 58.763 43.478 0.00 0.00 42.53 3.32
1920 2074 1.136147 GCAAATCAGCTCCACTGCG 59.864 57.895 0.00 0.00 46.76 5.18
1936 2090 6.631971 TGTCAAGATTAATGAACAACAGCA 57.368 33.333 0.00 0.00 0.00 4.41
2087 2241 7.559486 TCATACAACAGATGAGCTCAATAAGT 58.441 34.615 22.50 16.14 0.00 2.24
2177 2331 1.526575 AACAAGCAATGACCGGCCTG 61.527 55.000 0.00 0.00 0.00 4.85
2275 2431 6.457528 GGCAGTTGTATAGAAAATCAGCAGAC 60.458 42.308 0.00 0.00 0.00 3.51
2341 2497 8.547894 GTGATTCACAAAATTTAAAACAGGGTC 58.452 33.333 11.93 0.00 34.08 4.46
2667 2825 1.081892 AATCGCACACAAGCAGCTAG 58.918 50.000 0.00 0.00 0.00 3.42
2668 2826 0.798159 CAATCGCACACAAGCAGCTA 59.202 50.000 0.00 0.00 0.00 3.32
2669 2827 1.577922 CAATCGCACACAAGCAGCT 59.422 52.632 0.00 0.00 0.00 4.24
2695 2853 2.552315 ACAAGCACAAAGATAACCCACG 59.448 45.455 0.00 0.00 0.00 4.94
2700 2858 5.113502 AGCAGAACAAGCACAAAGATAAC 57.886 39.130 0.00 0.00 0.00 1.89
2778 2938 9.613428 CACAGGTTATAGAATCCAAATAAGACA 57.387 33.333 0.00 0.00 0.00 3.41
2796 2956 6.385649 GAACAAGTTCCAATTCACAGGTTA 57.614 37.500 1.51 0.00 33.64 2.85
2816 2976 7.498239 GGTATGAACCTACAAGGAAATAGGAAC 59.502 40.741 4.33 0.00 43.08 3.62
2871 3032 6.233905 TGGCTAACTAAACAGCTGATCATA 57.766 37.500 23.35 6.54 37.91 2.15
2872 3033 5.102953 TGGCTAACTAAACAGCTGATCAT 57.897 39.130 23.35 5.64 37.91 2.45
2873 3034 4.551702 TGGCTAACTAAACAGCTGATCA 57.448 40.909 23.35 3.09 37.91 2.92
2874 3035 4.695455 TGTTGGCTAACTAAACAGCTGATC 59.305 41.667 23.35 0.00 37.91 2.92
2875 3036 4.651778 TGTTGGCTAACTAAACAGCTGAT 58.348 39.130 23.35 5.41 37.91 2.90
2876 3037 4.079980 TGTTGGCTAACTAAACAGCTGA 57.920 40.909 23.35 0.00 37.91 4.26
2877 3038 4.275936 AGTTGTTGGCTAACTAAACAGCTG 59.724 41.667 13.48 13.48 41.78 4.24
2878 3039 4.461198 AGTTGTTGGCTAACTAAACAGCT 58.539 39.130 14.47 0.00 39.56 4.24
2879 3040 4.830826 AGTTGTTGGCTAACTAAACAGC 57.169 40.909 14.47 0.00 36.66 4.40
2880 3041 6.038271 ACAGAAGTTGTTGGCTAACTAAACAG 59.962 38.462 14.47 5.73 37.39 3.16
2881 3042 5.883673 ACAGAAGTTGTTGGCTAACTAAACA 59.116 36.000 14.47 0.00 37.39 2.83
2882 3043 6.373186 ACAGAAGTTGTTGGCTAACTAAAC 57.627 37.500 14.47 10.73 37.39 2.01
2897 3058 7.680730 ACTCATAATACAGACCAACAGAAGTT 58.319 34.615 0.00 0.00 38.88 2.66
2898 3059 7.246171 ACTCATAATACAGACCAACAGAAGT 57.754 36.000 0.00 0.00 0.00 3.01
2899 3060 9.823647 ATTACTCATAATACAGACCAACAGAAG 57.176 33.333 0.00 0.00 0.00 2.85
2963 3127 6.091849 TCTGCTTCATTTCTCTGAAATCGAAG 59.908 38.462 22.61 22.61 34.86 3.79
2966 3130 5.447010 GGTCTGCTTCATTTCTCTGAAATCG 60.447 44.000 2.92 1.11 34.86 3.34
2977 3141 0.250901 AGCACGGGTCTGCTTCATTT 60.251 50.000 0.00 0.00 45.64 2.32
2978 3142 1.376466 AGCACGGGTCTGCTTCATT 59.624 52.632 0.00 0.00 45.64 2.57
2986 3150 7.534723 TTATTATAGTCATAAGCACGGGTCT 57.465 36.000 0.00 0.00 30.22 3.85
2992 3156 8.107095 TCCCCCATTTATTATAGTCATAAGCAC 58.893 37.037 0.00 0.00 30.22 4.40
2994 3158 9.700831 ATTCCCCCATTTATTATAGTCATAAGC 57.299 33.333 0.00 0.00 30.22 3.09
2998 3162 9.897040 AAACATTCCCCCATTTATTATAGTCAT 57.103 29.630 0.00 0.00 0.00 3.06
2999 3163 9.722317 AAAACATTCCCCCATTTATTATAGTCA 57.278 29.630 0.00 0.00 0.00 3.41
3002 3166 9.777297 CCAAAAACATTCCCCCATTTATTATAG 57.223 33.333 0.00 0.00 0.00 1.31
3003 3167 9.285359 ACCAAAAACATTCCCCCATTTATTATA 57.715 29.630 0.00 0.00 0.00 0.98
3004 3168 8.168905 ACCAAAAACATTCCCCCATTTATTAT 57.831 30.769 0.00 0.00 0.00 1.28
3021 3185 5.373222 AGCTAAATTCCCCAAACCAAAAAC 58.627 37.500 0.00 0.00 0.00 2.43
3027 3191 4.281657 AGATGAGCTAAATTCCCCAAACC 58.718 43.478 0.00 0.00 0.00 3.27
3028 3192 6.625873 CTAGATGAGCTAAATTCCCCAAAC 57.374 41.667 0.00 0.00 0.00 2.93
3097 3261 9.044150 CAATAGGCAAGAAAGAAAACATTTCAA 57.956 29.630 5.71 0.00 38.79 2.69
3104 3268 7.867403 TCATTGTCAATAGGCAAGAAAGAAAAC 59.133 33.333 0.00 0.00 0.00 2.43
3126 3290 3.074412 CGGCAAAAGTACTGACCTCATT 58.926 45.455 0.00 0.00 0.00 2.57
3133 3297 1.302993 GGGGCGGCAAAAGTACTGA 60.303 57.895 12.47 0.00 0.00 3.41
3150 3314 2.138831 GGGGTTAGGACGCTAGGGG 61.139 68.421 11.95 0.00 38.65 4.79
3151 3315 2.138831 GGGGGTTAGGACGCTAGGG 61.139 68.421 5.05 5.05 38.65 3.53
3152 3316 3.547247 GGGGGTTAGGACGCTAGG 58.453 66.667 0.00 0.00 38.65 3.02
3175 3339 3.194861 TGAAGTTCGACAACTGAGTTGG 58.805 45.455 27.01 12.06 46.50 3.77
3177 3341 5.116180 TCAATGAAGTTCGACAACTGAGTT 58.884 37.500 0.00 0.00 42.45 3.01
3178 3342 4.693283 TCAATGAAGTTCGACAACTGAGT 58.307 39.130 0.00 0.00 42.45 3.41
3179 3343 4.984785 TCTCAATGAAGTTCGACAACTGAG 59.015 41.667 0.00 8.67 42.45 3.35
3182 3346 5.760253 ACATTCTCAATGAAGTTCGACAACT 59.240 36.000 3.24 0.00 42.21 3.16
3183 3347 5.990408 ACATTCTCAATGAAGTTCGACAAC 58.010 37.500 3.24 0.00 41.46 3.32
3184 3348 6.429624 CAACATTCTCAATGAAGTTCGACAA 58.570 36.000 3.24 0.00 41.46 3.18
3185 3349 5.049474 CCAACATTCTCAATGAAGTTCGACA 60.049 40.000 3.24 0.00 41.46 4.35
3186 3350 5.385617 CCAACATTCTCAATGAAGTTCGAC 58.614 41.667 3.24 0.00 41.46 4.20
3187 3351 4.083324 GCCAACATTCTCAATGAAGTTCGA 60.083 41.667 3.24 0.00 41.46 3.71
3188 3352 4.161333 GCCAACATTCTCAATGAAGTTCG 58.839 43.478 3.24 0.00 41.46 3.95
3189 3353 4.219288 AGGCCAACATTCTCAATGAAGTTC 59.781 41.667 5.01 0.00 41.46 3.01
3207 3372 2.599281 TCGTCGACTTCCAGGCCA 60.599 61.111 14.70 0.00 0.00 5.36
3216 3381 2.979197 CTCCTTGCCGTCGTCGACT 61.979 63.158 22.18 0.00 39.71 4.18
3223 3388 0.831307 AATAGGTCCTCCTTGCCGTC 59.169 55.000 0.00 0.00 42.12 4.79
3227 3392 3.688553 CCGAATAGGTCCTCCTTGC 57.311 57.895 0.00 0.00 42.12 4.01
3238 3403 2.960129 GTCGCCGCCACCGAATAG 60.960 66.667 0.00 0.00 36.36 1.73
3239 3404 4.858433 CGTCGCCGCCACCGAATA 62.858 66.667 0.00 0.00 36.36 1.75
3249 3414 0.458889 TATTTTCAGGGTCGTCGCCG 60.459 55.000 0.00 0.00 0.00 6.46
3250 3415 1.004595 GTATTTTCAGGGTCGTCGCC 58.995 55.000 0.00 0.00 0.00 5.54
3251 3416 1.004595 GGTATTTTCAGGGTCGTCGC 58.995 55.000 0.00 0.00 0.00 5.19
3252 3417 1.274596 CGGTATTTTCAGGGTCGTCG 58.725 55.000 0.00 0.00 0.00 5.12
3253 3418 1.004595 GCGGTATTTTCAGGGTCGTC 58.995 55.000 0.00 0.00 0.00 4.20
3254 3419 0.392060 GGCGGTATTTTCAGGGTCGT 60.392 55.000 0.00 0.00 0.00 4.34
3255 3420 0.391927 TGGCGGTATTTTCAGGGTCG 60.392 55.000 0.00 0.00 0.00 4.79
3256 3421 1.092348 GTGGCGGTATTTTCAGGGTC 58.908 55.000 0.00 0.00 0.00 4.46
3257 3422 0.675522 CGTGGCGGTATTTTCAGGGT 60.676 55.000 0.00 0.00 0.00 4.34
3258 3423 0.675522 ACGTGGCGGTATTTTCAGGG 60.676 55.000 0.00 0.00 0.00 4.45
3259 3424 1.135803 CAACGTGGCGGTATTTTCAGG 60.136 52.381 0.00 0.00 0.00 3.86
3260 3425 1.135803 CCAACGTGGCGGTATTTTCAG 60.136 52.381 0.00 0.00 0.00 3.02
3261 3426 0.875728 CCAACGTGGCGGTATTTTCA 59.124 50.000 0.00 0.00 0.00 2.69
3262 3427 0.876399 ACCAACGTGGCGGTATTTTC 59.124 50.000 2.89 0.00 42.67 2.29
3263 3428 0.876399 GACCAACGTGGCGGTATTTT 59.124 50.000 4.67 0.00 42.67 1.82
3264 3429 1.293267 CGACCAACGTGGCGGTATTT 61.293 55.000 4.67 0.00 42.67 1.40
3265 3430 1.738830 CGACCAACGTGGCGGTATT 60.739 57.895 4.67 0.00 42.67 1.89
3266 3431 2.125832 CGACCAACGTGGCGGTAT 60.126 61.111 4.67 0.00 42.67 2.73
3267 3432 3.293714 TCGACCAACGTGGCGGTA 61.294 61.111 0.88 0.00 42.67 4.02
3268 3433 4.955774 GTCGACCAACGTGGCGGT 62.956 66.667 3.51 2.71 42.67 5.68
3270 3435 4.986587 TCGTCGACCAACGTGGCG 62.987 66.667 10.58 0.00 42.67 5.69
3271 3436 3.400590 GTCGTCGACCAACGTGGC 61.401 66.667 14.60 0.00 42.67 5.01
3272 3437 3.095278 CGTCGTCGACCAACGTGG 61.095 66.667 22.94 4.35 45.02 4.94
3273 3438 2.051971 TCGTCGTCGACCAACGTG 60.052 61.111 27.23 8.42 43.08 4.49
3281 3446 0.723459 CACATTCGTGTCGTCGTCGA 60.723 55.000 0.00 0.00 38.41 4.20
3282 3447 1.688848 CACATTCGTGTCGTCGTCG 59.311 57.895 0.00 0.00 38.41 5.12
3283 3448 1.411089 GCACATTCGTGTCGTCGTC 59.589 57.895 0.00 0.00 45.50 4.20
3284 3449 2.362047 CGCACATTCGTGTCGTCGT 61.362 57.895 0.00 0.00 45.50 4.34
3285 3450 2.386491 CGCACATTCGTGTCGTCG 59.614 61.111 0.00 0.00 45.50 5.12
3286 3451 1.554042 AACCGCACATTCGTGTCGTC 61.554 55.000 0.00 0.00 45.50 4.20
3287 3452 1.554042 GAACCGCACATTCGTGTCGT 61.554 55.000 0.00 0.00 45.50 4.34
3288 3453 1.129809 GAACCGCACATTCGTGTCG 59.870 57.895 0.00 0.00 45.50 4.35
3289 3454 0.949105 AGGAACCGCACATTCGTGTC 60.949 55.000 0.00 0.00 45.50 3.67
3290 3455 1.070786 AGGAACCGCACATTCGTGT 59.929 52.632 0.00 0.00 45.50 4.49
3291 3456 1.497278 CAGGAACCGCACATTCGTG 59.503 57.895 0.00 0.00 46.56 4.35
3292 3457 1.671054 CCAGGAACCGCACATTCGT 60.671 57.895 0.00 0.00 0.00 3.85
3293 3458 1.635663 GACCAGGAACCGCACATTCG 61.636 60.000 0.00 0.00 0.00 3.34
3294 3459 1.305930 GGACCAGGAACCGCACATTC 61.306 60.000 0.00 0.00 0.00 2.67
3295 3460 1.303317 GGACCAGGAACCGCACATT 60.303 57.895 0.00 0.00 0.00 2.71
3296 3461 2.351276 GGACCAGGAACCGCACAT 59.649 61.111 0.00 0.00 0.00 3.21
3297 3462 4.308458 CGGACCAGGAACCGCACA 62.308 66.667 14.63 0.00 42.55 4.57
3302 3467 2.047179 GAGCACGGACCAGGAACC 60.047 66.667 0.00 0.00 0.00 3.62
3303 3468 2.047179 GGAGCACGGACCAGGAAC 60.047 66.667 0.00 0.00 0.00 3.62
3304 3469 2.203788 AGGAGCACGGACCAGGAA 60.204 61.111 0.00 0.00 0.00 3.36
3305 3470 2.680352 GAGGAGCACGGACCAGGA 60.680 66.667 0.00 0.00 0.00 3.86
3306 3471 2.681778 AGAGGAGCACGGACCAGG 60.682 66.667 0.00 0.00 0.00 4.45
3307 3472 2.575993 CAGAGGAGCACGGACCAG 59.424 66.667 0.00 0.00 0.00 4.00
3308 3473 3.695606 GCAGAGGAGCACGGACCA 61.696 66.667 0.00 0.00 0.00 4.02
3309 3474 4.459089 GGCAGAGGAGCACGGACC 62.459 72.222 0.00 0.00 35.83 4.46
3310 3475 3.240134 TTGGCAGAGGAGCACGGAC 62.240 63.158 0.00 0.00 35.83 4.79
3311 3476 2.922503 TTGGCAGAGGAGCACGGA 60.923 61.111 0.00 0.00 35.83 4.69
3312 3477 2.743928 GTTGGCAGAGGAGCACGG 60.744 66.667 0.00 0.00 35.83 4.94
3313 3478 3.114616 CGTTGGCAGAGGAGCACG 61.115 66.667 0.00 0.00 35.83 5.34
3314 3479 3.426568 GCGTTGGCAGAGGAGCAC 61.427 66.667 0.00 0.00 39.62 4.40
3315 3480 4.704833 GGCGTTGGCAGAGGAGCA 62.705 66.667 0.00 0.00 42.47 4.26
3316 3481 3.984193 ATGGCGTTGGCAGAGGAGC 62.984 63.158 0.00 0.00 42.43 4.70
3317 3482 2.110967 CATGGCGTTGGCAGAGGAG 61.111 63.158 0.00 0.00 42.43 3.69
3318 3483 2.046023 CATGGCGTTGGCAGAGGA 60.046 61.111 0.00 0.00 42.43 3.71
3319 3484 3.136123 CCATGGCGTTGGCAGAGG 61.136 66.667 0.00 0.08 42.43 3.69
3320 3485 3.136123 CCCATGGCGTTGGCAGAG 61.136 66.667 6.09 0.00 42.43 3.35
3321 3486 3.918253 GACCCATGGCGTTGGCAGA 62.918 63.158 6.09 0.00 42.43 4.26
3322 3487 3.443045 GACCCATGGCGTTGGCAG 61.443 66.667 6.09 0.00 42.43 4.85
3323 3488 3.799286 TTGACCCATGGCGTTGGCA 62.799 57.895 6.09 0.00 43.52 4.92
3324 3489 2.490993 CTTTGACCCATGGCGTTGGC 62.491 60.000 6.09 0.00 35.29 4.52
3325 3490 0.893270 TCTTTGACCCATGGCGTTGG 60.893 55.000 6.09 0.00 36.46 3.77
3326 3491 0.523072 CTCTTTGACCCATGGCGTTG 59.477 55.000 6.09 0.00 0.00 4.10
3327 3492 0.609131 CCTCTTTGACCCATGGCGTT 60.609 55.000 6.09 0.00 0.00 4.84
3328 3493 1.002134 CCTCTTTGACCCATGGCGT 60.002 57.895 6.09 5.83 0.00 5.68
3329 3494 2.409870 GCCTCTTTGACCCATGGCG 61.410 63.158 6.09 2.02 0.00 5.69
3330 3495 2.054453 GGCCTCTTTGACCCATGGC 61.054 63.158 6.09 0.00 39.61 4.40
3331 3496 0.682209 CAGGCCTCTTTGACCCATGG 60.682 60.000 0.00 4.14 0.00 3.66
3332 3497 1.318158 GCAGGCCTCTTTGACCCATG 61.318 60.000 0.00 0.00 0.00 3.66
3333 3498 1.000396 GCAGGCCTCTTTGACCCAT 60.000 57.895 0.00 0.00 0.00 4.00
3334 3499 0.840288 TAGCAGGCCTCTTTGACCCA 60.840 55.000 0.00 0.00 0.00 4.51
3335 3500 0.107459 CTAGCAGGCCTCTTTGACCC 60.107 60.000 0.00 0.00 0.00 4.46
3336 3501 0.107459 CCTAGCAGGCCTCTTTGACC 60.107 60.000 0.00 0.00 0.00 4.02
3337 3502 0.615850 ACCTAGCAGGCCTCTTTGAC 59.384 55.000 0.00 0.00 39.63 3.18
3338 3503 0.615331 CACCTAGCAGGCCTCTTTGA 59.385 55.000 0.00 0.00 39.63 2.69
3339 3504 0.615331 TCACCTAGCAGGCCTCTTTG 59.385 55.000 0.00 0.00 39.63 2.77
3340 3505 0.908198 CTCACCTAGCAGGCCTCTTT 59.092 55.000 0.00 0.00 39.63 2.52
3341 3506 0.041833 TCTCACCTAGCAGGCCTCTT 59.958 55.000 0.00 0.00 39.63 2.85
3342 3507 0.396974 CTCTCACCTAGCAGGCCTCT 60.397 60.000 0.00 6.08 39.63 3.69
3343 3508 2.026945 GCTCTCACCTAGCAGGCCTC 62.027 65.000 0.00 0.00 39.63 4.70
3344 3509 2.063378 GCTCTCACCTAGCAGGCCT 61.063 63.158 0.00 0.00 39.63 5.19
3345 3510 2.503546 GCTCTCACCTAGCAGGCC 59.496 66.667 0.00 0.00 39.63 5.19
3346 3511 1.621672 AAGGCTCTCACCTAGCAGGC 61.622 60.000 2.50 0.00 39.93 4.85
3347 3512 0.908198 AAAGGCTCTCACCTAGCAGG 59.092 55.000 0.00 1.16 39.93 4.85
3348 3513 1.552337 TGAAAGGCTCTCACCTAGCAG 59.448 52.381 0.00 0.00 39.93 4.24
3349 3514 1.644509 TGAAAGGCTCTCACCTAGCA 58.355 50.000 0.00 0.00 39.93 3.49
3350 3515 2.998316 ATGAAAGGCTCTCACCTAGC 57.002 50.000 0.00 0.00 39.93 3.42
3351 3516 4.219115 TCCTATGAAAGGCTCTCACCTAG 58.781 47.826 0.00 0.00 46.10 3.02
3352 3517 4.265856 TCCTATGAAAGGCTCTCACCTA 57.734 45.455 0.00 0.00 46.10 3.08
3353 3518 3.121929 TCCTATGAAAGGCTCTCACCT 57.878 47.619 0.00 0.00 46.10 4.00
3354 3519 3.495806 CCATCCTATGAAAGGCTCTCACC 60.496 52.174 0.00 0.00 46.10 4.02
3355 3520 3.135530 ACCATCCTATGAAAGGCTCTCAC 59.864 47.826 0.00 0.00 46.10 3.51
3356 3521 3.135348 CACCATCCTATGAAAGGCTCTCA 59.865 47.826 0.00 0.00 46.10 3.27
3357 3522 3.737850 CACCATCCTATGAAAGGCTCTC 58.262 50.000 0.00 0.00 46.10 3.20
3358 3523 2.158696 GCACCATCCTATGAAAGGCTCT 60.159 50.000 0.00 0.00 46.10 4.09
3359 3524 2.225467 GCACCATCCTATGAAAGGCTC 58.775 52.381 0.00 0.00 46.10 4.70
3360 3525 1.133668 GGCACCATCCTATGAAAGGCT 60.134 52.381 0.00 0.00 46.10 4.58
3361 3526 1.322442 GGCACCATCCTATGAAAGGC 58.678 55.000 0.00 0.00 46.10 4.35
3363 3528 2.620251 TCGGCACCATCCTATGAAAG 57.380 50.000 0.00 0.00 0.00 2.62
3364 3529 3.358111 TTTCGGCACCATCCTATGAAA 57.642 42.857 0.00 0.00 0.00 2.69
3365 3530 3.278574 CTTTTCGGCACCATCCTATGAA 58.721 45.455 0.00 0.00 0.00 2.57
3366 3531 2.917933 CTTTTCGGCACCATCCTATGA 58.082 47.619 0.00 0.00 0.00 2.15
3367 3532 1.334869 GCTTTTCGGCACCATCCTATG 59.665 52.381 0.00 0.00 0.00 2.23
3368 3533 1.680338 GCTTTTCGGCACCATCCTAT 58.320 50.000 0.00 0.00 0.00 2.57
3369 3534 0.393808 GGCTTTTCGGCACCATCCTA 60.394 55.000 0.00 0.00 38.25 2.94
3370 3535 1.678970 GGCTTTTCGGCACCATCCT 60.679 57.895 0.00 0.00 38.25 3.24
3371 3536 0.393808 TAGGCTTTTCGGCACCATCC 60.394 55.000 0.00 0.00 41.46 3.51
3372 3537 1.604278 GATAGGCTTTTCGGCACCATC 59.396 52.381 0.00 0.00 41.46 3.51
3373 3538 1.064758 TGATAGGCTTTTCGGCACCAT 60.065 47.619 0.00 0.00 41.46 3.55
3374 3539 0.326595 TGATAGGCTTTTCGGCACCA 59.673 50.000 0.00 0.00 41.46 4.17
3375 3540 1.680338 ATGATAGGCTTTTCGGCACC 58.320 50.000 0.00 0.00 41.46 5.01


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

AutoCloner maintained by Alex Coulton.