Multiple sequence alignment - TraesCS3D01G003600

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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 TraesCS3D01G003600 chr3D 100.000 3667 0 0 1 3667 1609506 1605840 0.000000e+00 6772.0
1 TraesCS3D01G003600 chr3D 84.571 175 21 5 1042 1213 9291609 9291780 6.300000e-38 169.0
2 TraesCS3D01G003600 chr3B 93.697 1872 88 16 1 1846 5198410 5200277 0.000000e+00 2776.0
3 TraesCS3D01G003600 chr3B 93.504 1878 95 15 1 1855 3638081 3636208 0.000000e+00 2767.0
4 TraesCS3D01G003600 chr3B 90.998 1022 43 21 1980 2989 5200292 5201276 0.000000e+00 1332.0
5 TraesCS3D01G003600 chr3B 91.696 843 29 16 2159 2989 3636113 3635300 0.000000e+00 1131.0
6 TraesCS3D01G003600 chr3B 85.876 177 15 8 1042 1213 11601784 11601955 2.910000e-41 180.0
7 TraesCS3D01G003600 chr3A 92.607 1542 63 21 363 1886 7439378 7437870 0.000000e+00 2169.0
8 TraesCS3D01G003600 chr3A 86.735 1274 99 29 1941 3178 7437861 7436622 0.000000e+00 1352.0
9 TraesCS3D01G003600 chr3A 83.693 834 69 31 2187 2989 7436115 7435318 0.000000e+00 725.0
10 TraesCS3D01G003600 chr3A 82.469 559 58 20 3061 3593 7435271 7434727 1.550000e-123 453.0
11 TraesCS3D01G003600 chr3A 87.664 381 30 5 1 366 7439837 7439459 9.410000e-116 427.0
12 TraesCS3D01G003600 chr3A 83.422 187 25 5 1042 1225 11839309 11839126 6.300000e-38 169.0
13 TraesCS3D01G003600 chr7D 89.383 697 65 4 1121 1814 272591467 272592157 0.000000e+00 869.0
14 TraesCS3D01G003600 chr7D 85.354 792 46 29 2162 2911 272592669 272593432 0.000000e+00 756.0
15 TraesCS3D01G003600 chr7D 84.192 291 33 8 854 1131 272583212 272583502 1.680000e-68 270.0
16 TraesCS3D01G003600 chr7D 83.951 162 21 2 466 623 272582926 272583086 2.280000e-32 150.0
17 TraesCS3D01G003600 chr7A 86.533 750 46 22 2171 2893 306221554 306222275 0.000000e+00 774.0
18 TraesCS3D01G003600 chr7A 88.847 529 50 4 1289 1814 306221003 306221525 3.090000e-180 641.0
19 TraesCS3D01G003600 chr7A 92.126 127 10 0 1044 1170 306220874 306221000 2.910000e-41 180.0
20 TraesCS3D01G003600 chr7B 85.051 495 38 15 2443 2913 265471689 265471207 4.290000e-129 472.0
21 TraesCS3D01G003600 chr2A 89.766 342 32 3 1 341 613041426 613041765 5.620000e-118 435.0
22 TraesCS3D01G003600 chr5D 92.453 53 4 0 2994 3046 565716670 565716618 3.930000e-10 76.8
23 TraesCS3D01G003600 chr1B 95.745 47 2 0 2993 3039 601830338 601830384 3.930000e-10 76.8
24 TraesCS3D01G003600 chr1B 93.617 47 3 0 2993 3039 601899636 601899682 1.830000e-08 71.3
25 TraesCS3D01G003600 chr1B 100.000 38 0 0 3009 3046 636663274 636663311 1.830000e-08 71.3
26 TraesCS3D01G003600 chr1D 97.368 38 1 0 3009 3046 27920983 27920946 8.500000e-07 65.8
27 TraesCS3D01G003600 chr6A 100.000 30 0 0 1894 1923 197041131 197041102 5.120000e-04 56.5


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 TraesCS3D01G003600 chr3D 1605840 1609506 3666 True 6772.000000 6772 100.000000 1 3667 1 chr3D.!!$R1 3666
1 TraesCS3D01G003600 chr3B 5198410 5201276 2866 False 2054.000000 2776 92.347500 1 2989 2 chr3B.!!$F2 2988
2 TraesCS3D01G003600 chr3B 3635300 3638081 2781 True 1949.000000 2767 92.600000 1 2989 2 chr3B.!!$R1 2988
3 TraesCS3D01G003600 chr3A 7434727 7439837 5110 True 1025.200000 2169 86.633600 1 3593 5 chr3A.!!$R2 3592
4 TraesCS3D01G003600 chr7D 272591467 272593432 1965 False 812.500000 869 87.368500 1121 2911 2 chr7D.!!$F2 1790
5 TraesCS3D01G003600 chr7D 272582926 272583502 576 False 210.000000 270 84.071500 466 1131 2 chr7D.!!$F1 665
6 TraesCS3D01G003600 chr7A 306220874 306222275 1401 False 531.666667 774 89.168667 1044 2893 3 chr7A.!!$F1 1849

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
453 553 1.005215 CCTCTTGGGAGAAACATGGCT 59.995 52.381 0.00 0.0 41.86 4.75 F
1676 1818 0.245539 CTCAAGAAGTACCCCGCGAA 59.754 55.000 8.23 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2760 1.242076 GCGATGAAGCCCTGCATATT 58.758 50.0 0.00 0.0 0.0 1.28 R
3032 5042 0.035739 GGTGCACCCTCCGTAAAGAA 59.964 55.0 26.31 0.0 0.0 2.52 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
81 82 9.712359 AATCAGTACTTTAAACTCGTTCAAAAC 57.288 29.630 0.00 0.00 0.00 2.43
96 108 3.013921 TCAAAACATATTCAGGGTCGGC 58.986 45.455 0.00 0.00 0.00 5.54
128 141 5.178797 ACGGTCTATTCACCAAGAATTCAG 58.821 41.667 8.44 0.00 44.48 3.02
130 143 5.874810 CGGTCTATTCACCAAGAATTCAGAA 59.125 40.000 8.44 4.30 44.48 3.02
272 285 1.181786 ACGCTTCTCTCCTTCCTCAG 58.818 55.000 0.00 0.00 0.00 3.35
318 332 5.110814 TCACCCCTCTATGTTTGTATTGG 57.889 43.478 0.00 0.00 0.00 3.16
324 341 5.123820 CCCTCTATGTTTGTATTGGTGTGTG 59.876 44.000 0.00 0.00 0.00 3.82
333 350 5.933187 TGTATTGGTGTGTGTTCATGTAC 57.067 39.130 0.00 0.00 0.00 2.90
341 358 3.562141 TGTGTGTTCATGTACGGAAAAGG 59.438 43.478 1.79 0.00 0.00 3.11
357 374 8.040716 ACGGAAAAGGTTGACATCTTATAAAG 57.959 34.615 0.00 0.00 0.00 1.85
435 535 1.472728 CCGGTAGTGCGCTATTTTCCT 60.473 52.381 10.75 0.00 0.00 3.36
453 553 1.005215 CCTCTTGGGAGAAACATGGCT 59.995 52.381 0.00 0.00 41.86 4.75
454 554 2.239654 CCTCTTGGGAGAAACATGGCTA 59.760 50.000 0.00 0.00 41.86 3.93
462 562 3.691609 GGAGAAACATGGCTAGGAAAGTG 59.308 47.826 0.00 0.00 0.00 3.16
535 641 5.701290 AGCTGTTGATGTTTAGTACTGGTTC 59.299 40.000 5.39 0.00 0.00 3.62
661 767 1.344438 ACGACATTGACAGCTCTGGAA 59.656 47.619 1.66 0.00 34.19 3.53
664 770 3.438087 CGACATTGACAGCTCTGGAAAAT 59.562 43.478 1.66 0.00 34.19 1.82
705 811 3.555527 TCTCAGGAATCTTGAGGCATG 57.444 47.619 20.02 0.00 0.00 4.06
724 831 2.693210 TGCATGATAGGAGTGGGATGA 58.307 47.619 0.00 0.00 0.00 2.92
728 835 2.694397 TGATAGGAGTGGGATGAAGGG 58.306 52.381 0.00 0.00 0.00 3.95
934 1067 2.093658 GTCCTCTCTCTCGTCTCTCAGT 60.094 54.545 0.00 0.00 0.00 3.41
1359 1498 1.450312 CATCCAGAACTCCGTGCCC 60.450 63.158 0.00 0.00 0.00 5.36
1514 1653 2.280186 CATCTTCGCCCCTACCGC 60.280 66.667 0.00 0.00 0.00 5.68
1515 1654 3.547513 ATCTTCGCCCCTACCGCC 61.548 66.667 0.00 0.00 0.00 6.13
1593 1735 2.032681 AAGAACTGGACGCTGGGC 59.967 61.111 0.00 0.00 0.00 5.36
1676 1818 0.245539 CTCAAGAAGTACCCCGCGAA 59.754 55.000 8.23 0.00 0.00 4.70
1794 1936 1.587054 CGGCTCCGAAGTCTTCACT 59.413 57.895 12.99 0.00 42.83 3.41
1823 1967 4.789095 ACGCCGTAAGCATTTATTAGTG 57.211 40.909 0.00 0.00 44.04 2.74
1846 1990 9.826574 AGTGTCCTATATAATTTCGCAGTTAAA 57.173 29.630 0.00 0.00 0.00 1.52
1976 2121 8.918202 TGGAATCCCAATCACATACTAATTAC 57.082 34.615 0.00 0.00 40.09 1.89
2005 2150 5.188555 ACTCTCTATCTGAGGTGCAAATGAA 59.811 40.000 0.00 0.00 42.86 2.57
2008 2153 7.114754 TCTCTATCTGAGGTGCAAATGAAAAT 58.885 34.615 0.00 0.00 42.86 1.82
2105 2251 0.461548 TGTCAGGATCACCGATCTGC 59.538 55.000 4.12 0.00 38.91 4.26
2107 2253 0.461548 TCAGGATCACCGATCTGCAC 59.538 55.000 4.12 0.00 38.91 4.57
2126 2272 3.188667 GCACCAGTACTCCTTTAGCAAAC 59.811 47.826 0.00 0.00 0.00 2.93
2266 2728 4.646040 TGATTATGCAAATGTAAGCTGGCT 59.354 37.500 0.00 0.00 0.00 4.75
2345 2807 1.809619 GGCGTTCGCAGTGCAGATA 60.810 57.895 16.83 2.57 0.00 1.98
2468 2930 3.606662 CTCGGCGGGATCATCGGT 61.607 66.667 0.00 0.00 0.00 4.69
2681 3152 5.857822 ACGTCTGAAACTTAATTGCTACC 57.142 39.130 0.00 0.00 0.00 3.18
2682 3153 5.548406 ACGTCTGAAACTTAATTGCTACCT 58.452 37.500 0.00 0.00 0.00 3.08
2683 3154 6.694447 ACGTCTGAAACTTAATTGCTACCTA 58.306 36.000 0.00 0.00 0.00 3.08
2684 3155 6.812160 ACGTCTGAAACTTAATTGCTACCTAG 59.188 38.462 0.00 0.00 0.00 3.02
2706 3178 0.732880 ACCGTCGCTTCTCAACGATG 60.733 55.000 0.00 0.00 43.27 3.84
2709 3181 1.799181 CGTCGCTTCTCAACGATGGAT 60.799 52.381 0.00 0.00 40.69 3.41
2712 3184 2.002586 CGCTTCTCAACGATGGATTGT 58.997 47.619 0.00 0.00 0.00 2.71
2905 4915 9.658799 CTTGATGTATTGGTACCCTATCTAATG 57.341 37.037 10.07 0.00 0.00 1.90
2945 4955 5.520748 AGGGTTTGTTCACTATGGATTCT 57.479 39.130 0.00 0.00 0.00 2.40
2946 4956 6.636454 AGGGTTTGTTCACTATGGATTCTA 57.364 37.500 0.00 0.00 0.00 2.10
2947 4957 6.415573 AGGGTTTGTTCACTATGGATTCTAC 58.584 40.000 0.00 0.00 0.00 2.59
2948 4958 5.293569 GGGTTTGTTCACTATGGATTCTACG 59.706 44.000 0.00 0.00 0.00 3.51
2949 4959 5.873164 GGTTTGTTCACTATGGATTCTACGT 59.127 40.000 0.00 0.00 0.00 3.57
2950 4960 7.037438 GGTTTGTTCACTATGGATTCTACGTA 58.963 38.462 0.00 0.00 0.00 3.57
2959 4969 9.395707 CACTATGGATTCTACGTACTTAATGTC 57.604 37.037 0.00 0.00 0.00 3.06
2964 4974 9.128404 TGGATTCTACGTACTTAATGTCTACAT 57.872 33.333 0.00 0.00 38.41 2.29
2965 4975 9.609950 GGATTCTACGTACTTAATGTCTACATC 57.390 37.037 0.00 0.00 35.10 3.06
2989 4999 8.500837 TCGTTTTTGCAATCAGTAATTAAGTG 57.499 30.769 0.00 0.00 0.00 3.16
2990 5000 7.114247 TCGTTTTTGCAATCAGTAATTAAGTGC 59.886 33.333 0.00 2.01 0.00 4.40
2991 5001 7.509797 GTTTTTGCAATCAGTAATTAAGTGCC 58.490 34.615 0.00 0.00 0.00 5.01
2992 5002 4.981806 TGCAATCAGTAATTAAGTGCCC 57.018 40.909 5.81 0.00 0.00 5.36
2993 5003 3.699038 TGCAATCAGTAATTAAGTGCCCC 59.301 43.478 5.81 0.00 0.00 5.80
2994 5004 3.954258 GCAATCAGTAATTAAGTGCCCCT 59.046 43.478 0.00 0.00 0.00 4.79
2995 5005 4.036852 GCAATCAGTAATTAAGTGCCCCTC 59.963 45.833 0.00 0.00 0.00 4.30
2996 5006 5.440610 CAATCAGTAATTAAGTGCCCCTCT 58.559 41.667 0.00 0.00 0.00 3.69
2997 5007 4.487714 TCAGTAATTAAGTGCCCCTCTG 57.512 45.455 0.00 0.00 0.00 3.35
2998 5008 3.844211 TCAGTAATTAAGTGCCCCTCTGT 59.156 43.478 0.00 0.00 0.00 3.41
2999 5009 5.027460 TCAGTAATTAAGTGCCCCTCTGTA 58.973 41.667 0.00 0.00 0.00 2.74
3002 5012 6.316390 CAGTAATTAAGTGCCCCTCTGTAAAG 59.684 42.308 0.00 0.00 0.00 1.85
3006 5016 4.388577 AAGTGCCCCTCTGTAAAGAAAT 57.611 40.909 0.00 0.00 0.00 2.17
3009 5019 6.079712 AGTGCCCCTCTGTAAAGAAATATT 57.920 37.500 0.00 0.00 0.00 1.28
3012 5022 7.054751 GTGCCCCTCTGTAAAGAAATATTAGT 58.945 38.462 0.00 0.00 0.00 2.24
3013 5023 7.012421 GTGCCCCTCTGTAAAGAAATATTAGTG 59.988 40.741 0.00 0.00 0.00 2.74
3016 5026 9.495572 CCCCTCTGTAAAGAAATATTAGTGATC 57.504 37.037 0.00 0.00 0.00 2.92
3045 5055 8.822652 ACGTTATTATATTTCTTTACGGAGGG 57.177 34.615 0.00 0.00 32.54 4.30
3046 5056 8.424133 ACGTTATTATATTTCTTTACGGAGGGT 58.576 33.333 0.00 0.00 32.54 4.34
3047 5057 8.706035 CGTTATTATATTTCTTTACGGAGGGTG 58.294 37.037 0.00 0.00 0.00 4.61
3048 5058 8.501580 GTTATTATATTTCTTTACGGAGGGTGC 58.498 37.037 0.00 0.00 0.00 5.01
3051 5061 0.035739 TTCTTTACGGAGGGTGCACC 59.964 55.000 28.57 28.57 40.67 5.01
3064 5074 1.024271 GTGCACCTTGTTCAGCTTCA 58.976 50.000 5.22 0.00 0.00 3.02
3074 5084 1.125021 GTTCAGCTTCACATCGACACG 59.875 52.381 0.00 0.00 0.00 4.49
3078 5088 1.136690 GCTTCACATCGACACGAACA 58.863 50.000 0.00 0.00 39.99 3.18
3084 5094 1.270094 ACATCGACACGAACATGTGGT 60.270 47.619 0.00 0.00 44.21 4.16
3085 5095 1.126662 CATCGACACGAACATGTGGTG 59.873 52.381 22.10 22.10 44.21 4.17
3095 5105 1.300963 CATGTGGTGGGTCCTCCTG 59.699 63.158 9.22 0.00 37.07 3.86
3096 5106 1.925455 ATGTGGTGGGTCCTCCTGG 60.925 63.158 9.22 0.00 37.07 4.45
3157 5167 0.605319 TTCCGCAATGACACTCACCC 60.605 55.000 0.00 0.00 0.00 4.61
3158 5168 2.040544 CCGCAATGACACTCACCCC 61.041 63.158 0.00 0.00 0.00 4.95
3159 5169 2.390599 CGCAATGACACTCACCCCG 61.391 63.158 0.00 0.00 0.00 5.73
3160 5170 2.690778 GCAATGACACTCACCCCGC 61.691 63.158 0.00 0.00 0.00 6.13
3161 5171 1.003355 CAATGACACTCACCCCGCT 60.003 57.895 0.00 0.00 0.00 5.52
3163 5173 1.480212 AATGACACTCACCCCGCTCA 61.480 55.000 0.00 0.00 0.00 4.26
3164 5174 2.048127 GACACTCACCCCGCTCAC 60.048 66.667 0.00 0.00 0.00 3.51
3165 5175 3.591254 GACACTCACCCCGCTCACC 62.591 68.421 0.00 0.00 0.00 4.02
3166 5176 3.314331 CACTCACCCCGCTCACCT 61.314 66.667 0.00 0.00 0.00 4.00
3168 5178 1.229082 ACTCACCCCGCTCACCTTA 60.229 57.895 0.00 0.00 0.00 2.69
3169 5179 1.218316 CTCACCCCGCTCACCTTAC 59.782 63.158 0.00 0.00 0.00 2.34
3170 5180 1.229082 TCACCCCGCTCACCTTACT 60.229 57.895 0.00 0.00 0.00 2.24
3174 5194 1.305930 CCCCGCTCACCTTACTTTGC 61.306 60.000 0.00 0.00 0.00 3.68
3175 5195 1.635663 CCCGCTCACCTTACTTTGCG 61.636 60.000 0.00 0.00 42.52 4.85
3182 5202 4.003648 CTCACCTTACTTTGCGGATTTCT 58.996 43.478 0.00 0.00 0.00 2.52
3183 5203 4.394729 TCACCTTACTTTGCGGATTTCTT 58.605 39.130 0.00 0.00 0.00 2.52
3190 5210 7.010275 CCTTACTTTGCGGATTTCTTACTCTAC 59.990 40.741 0.00 0.00 0.00 2.59
3199 5219 7.255173 GCGGATTTCTTACTCTACACTCATAGA 60.255 40.741 0.00 0.00 0.00 1.98
3200 5220 8.788806 CGGATTTCTTACTCTACACTCATAGAT 58.211 37.037 0.00 0.00 30.77 1.98
3238 5258 8.761575 ATTAAAATGCAAACACTATGTCTTGG 57.238 30.769 0.00 0.00 0.00 3.61
3240 5260 2.580962 TGCAAACACTATGTCTTGGCA 58.419 42.857 0.00 0.00 0.00 4.92
3243 5263 3.191162 GCAAACACTATGTCTTGGCATCA 59.809 43.478 0.00 0.00 0.00 3.07
3267 5287 1.077285 TCTCCTCACATACCGGCGA 60.077 57.895 9.30 0.00 0.00 5.54
3268 5288 1.101635 TCTCCTCACATACCGGCGAG 61.102 60.000 9.30 0.06 0.00 5.03
3269 5289 1.379443 TCCTCACATACCGGCGAGT 60.379 57.895 9.30 7.43 0.00 4.18
3280 5300 1.337167 ACCGGCGAGTTACCTTGTAAC 60.337 52.381 9.30 8.68 0.00 2.50
3335 5359 9.615660 TTGAGTAATATATACAAGTGGGGATCT 57.384 33.333 0.00 0.00 0.00 2.75
3354 5378 5.782845 GGATCTTCTACCCCAGATGACTTAT 59.217 44.000 0.00 0.00 39.52 1.73
3356 5380 6.732896 TCTTCTACCCCAGATGACTTATTC 57.267 41.667 0.00 0.00 33.65 1.75
3362 5386 6.840780 ACCCCAGATGACTTATTCAAAAAG 57.159 37.500 0.00 0.00 37.92 2.27
3365 5389 7.508977 ACCCCAGATGACTTATTCAAAAAGAAA 59.491 33.333 0.00 0.00 40.22 2.52
3366 5390 8.367156 CCCCAGATGACTTATTCAAAAAGAAAA 58.633 33.333 0.00 0.00 40.22 2.29
3367 5391 9.762933 CCCAGATGACTTATTCAAAAAGAAAAA 57.237 29.630 0.00 0.00 40.22 1.94
3392 5416 7.380536 ACAAAGACATGCAATACAATGTTGAT 58.619 30.769 0.00 0.00 0.00 2.57
3410 5434 7.825331 TGTTGATCCTCTAGTATAAGGTGAG 57.175 40.000 0.00 0.00 34.12 3.51
3415 5439 6.716934 TCCTCTAGTATAAGGTGAGCAAAG 57.283 41.667 0.00 0.00 34.12 2.77
3416 5440 6.432581 TCCTCTAGTATAAGGTGAGCAAAGA 58.567 40.000 0.00 0.00 34.12 2.52
3417 5441 6.895756 TCCTCTAGTATAAGGTGAGCAAAGAA 59.104 38.462 0.00 0.00 34.12 2.52
3418 5442 7.565398 TCCTCTAGTATAAGGTGAGCAAAGAAT 59.435 37.037 0.00 0.00 34.12 2.40
3419 5443 8.207545 CCTCTAGTATAAGGTGAGCAAAGAATT 58.792 37.037 0.00 0.00 0.00 2.17
3429 5453 5.119125 GGTGAGCAAAGAATTAATGCACAAC 59.881 40.000 9.95 9.22 41.17 3.32
3433 5457 6.457355 AGCAAAGAATTAATGCACAACATCA 58.543 32.000 10.95 0.00 42.45 3.07
3435 5459 8.252417 AGCAAAGAATTAATGCACAACATCATA 58.748 29.630 10.95 0.00 42.45 2.15
3469 5494 8.771920 ACATCACATATCTCGTTTTGTAAAGA 57.228 30.769 0.00 0.00 0.00 2.52
3498 5523 5.003804 ACAACCATGTTCATGTAGGAAGAC 58.996 41.667 11.13 0.00 35.91 3.01
3532 5557 6.041751 GGCTGGAGCTAGATAGGTAAAAACTA 59.958 42.308 0.00 0.00 41.70 2.24
3533 5558 6.924612 GCTGGAGCTAGATAGGTAAAAACTAC 59.075 42.308 0.00 0.00 38.21 2.73
3536 5561 6.924612 GGAGCTAGATAGGTAAAAACTACTGC 59.075 42.308 0.00 0.00 33.58 4.40
3573 5609 3.534056 GCCACATCCAGCCATGCC 61.534 66.667 0.00 0.00 0.00 4.40
3588 5624 0.457851 ATGCCGACCGAGAGAAAGAG 59.542 55.000 0.00 0.00 0.00 2.85
3593 5629 2.414824 CCGACCGAGAGAAAGAGAAGTG 60.415 54.545 0.00 0.00 0.00 3.16
3594 5630 2.414824 CGACCGAGAGAAAGAGAAGTGG 60.415 54.545 0.00 0.00 0.00 4.00
3595 5631 1.896465 ACCGAGAGAAAGAGAAGTGGG 59.104 52.381 0.00 0.00 0.00 4.61
3596 5632 2.171840 CCGAGAGAAAGAGAAGTGGGA 58.828 52.381 0.00 0.00 0.00 4.37
3597 5633 2.165437 CCGAGAGAAAGAGAAGTGGGAG 59.835 54.545 0.00 0.00 0.00 4.30
3598 5634 2.165437 CGAGAGAAAGAGAAGTGGGAGG 59.835 54.545 0.00 0.00 0.00 4.30
3599 5635 2.499693 GAGAGAAAGAGAAGTGGGAGGG 59.500 54.545 0.00 0.00 0.00 4.30
3600 5636 1.557371 GAGAAAGAGAAGTGGGAGGGG 59.443 57.143 0.00 0.00 0.00 4.79
3601 5637 0.621082 GAAAGAGAAGTGGGAGGGGG 59.379 60.000 0.00 0.00 0.00 5.40
3602 5638 1.501654 AAAGAGAAGTGGGAGGGGGC 61.502 60.000 0.00 0.00 0.00 5.80
3603 5639 3.787001 GAGAAGTGGGAGGGGGCG 61.787 72.222 0.00 0.00 0.00 6.13
3604 5640 4.332543 AGAAGTGGGAGGGGGCGA 62.333 66.667 0.00 0.00 0.00 5.54
3605 5641 3.327404 GAAGTGGGAGGGGGCGAA 61.327 66.667 0.00 0.00 0.00 4.70
3606 5642 2.856988 AAGTGGGAGGGGGCGAAA 60.857 61.111 0.00 0.00 0.00 3.46
3607 5643 2.420466 GAAGTGGGAGGGGGCGAAAA 62.420 60.000 0.00 0.00 0.00 2.29
3608 5644 2.675423 GTGGGAGGGGGCGAAAAC 60.675 66.667 0.00 0.00 0.00 2.43
3609 5645 2.856988 TGGGAGGGGGCGAAAACT 60.857 61.111 0.00 0.00 0.00 2.66
3610 5646 2.361230 GGGAGGGGGCGAAAACTG 60.361 66.667 0.00 0.00 0.00 3.16
3611 5647 2.434774 GGAGGGGGCGAAAACTGT 59.565 61.111 0.00 0.00 0.00 3.55
3612 5648 1.681076 GGAGGGGGCGAAAACTGTA 59.319 57.895 0.00 0.00 0.00 2.74
3613 5649 0.037160 GGAGGGGGCGAAAACTGTAA 59.963 55.000 0.00 0.00 0.00 2.41
3614 5650 1.546099 GGAGGGGGCGAAAACTGTAAA 60.546 52.381 0.00 0.00 0.00 2.01
3615 5651 2.443416 GAGGGGGCGAAAACTGTAAAT 58.557 47.619 0.00 0.00 0.00 1.40
3616 5652 2.163613 GAGGGGGCGAAAACTGTAAATG 59.836 50.000 0.00 0.00 0.00 2.32
3617 5653 1.890489 GGGGGCGAAAACTGTAAATGT 59.110 47.619 0.00 0.00 0.00 2.71
3618 5654 2.297880 GGGGGCGAAAACTGTAAATGTT 59.702 45.455 0.00 0.00 0.00 2.71
3619 5655 3.313690 GGGGCGAAAACTGTAAATGTTG 58.686 45.455 0.00 0.00 0.00 3.33
3620 5656 3.243602 GGGGCGAAAACTGTAAATGTTGT 60.244 43.478 0.00 0.00 0.00 3.32
3621 5657 4.023021 GGGGCGAAAACTGTAAATGTTGTA 60.023 41.667 0.00 0.00 0.00 2.41
3622 5658 4.913345 GGGCGAAAACTGTAAATGTTGTAC 59.087 41.667 0.00 0.00 0.00 2.90
3623 5659 4.609708 GGCGAAAACTGTAAATGTTGTACG 59.390 41.667 0.00 0.00 0.00 3.67
3624 5660 5.433855 GCGAAAACTGTAAATGTTGTACGA 58.566 37.500 0.00 0.00 0.00 3.43
3625 5661 5.558888 GCGAAAACTGTAAATGTTGTACGAG 59.441 40.000 0.00 0.00 0.00 4.18
3626 5662 5.558888 CGAAAACTGTAAATGTTGTACGAGC 59.441 40.000 0.00 0.00 0.00 5.03
3627 5663 5.994887 AAACTGTAAATGTTGTACGAGCA 57.005 34.783 0.00 0.00 0.00 4.26
3628 5664 4.985044 ACTGTAAATGTTGTACGAGCAC 57.015 40.909 0.00 0.00 0.00 4.40
3629 5665 3.744426 ACTGTAAATGTTGTACGAGCACC 59.256 43.478 0.00 0.00 0.00 5.01
3630 5666 3.729966 TGTAAATGTTGTACGAGCACCA 58.270 40.909 0.00 0.00 0.00 4.17
3631 5667 4.320023 TGTAAATGTTGTACGAGCACCAT 58.680 39.130 0.00 0.00 0.00 3.55
3632 5668 3.829886 AAATGTTGTACGAGCACCATG 57.170 42.857 0.00 0.00 0.00 3.66
3633 5669 1.737838 ATGTTGTACGAGCACCATGG 58.262 50.000 11.19 11.19 0.00 3.66
3634 5670 0.394938 TGTTGTACGAGCACCATGGT 59.605 50.000 13.00 13.00 0.00 3.55
3643 5679 3.443045 CACCATGGTGCCCGCTTC 61.443 66.667 31.13 0.00 39.39 3.86
3644 5680 4.740822 ACCATGGTGCCCGCTTCC 62.741 66.667 18.99 0.00 0.00 3.46
3645 5681 4.738998 CCATGGTGCCCGCTTCCA 62.739 66.667 2.57 6.63 35.64 3.53
3646 5682 2.676121 CATGGTGCCCGCTTCCAA 60.676 61.111 7.89 0.00 34.80 3.53
3647 5683 2.117206 ATGGTGCCCGCTTCCAAA 59.883 55.556 7.89 0.00 34.80 3.28
3648 5684 1.532794 ATGGTGCCCGCTTCCAAAA 60.533 52.632 7.89 0.00 34.80 2.44
3649 5685 1.535204 ATGGTGCCCGCTTCCAAAAG 61.535 55.000 7.89 0.00 34.80 2.27
3650 5686 1.901464 GGTGCCCGCTTCCAAAAGA 60.901 57.895 0.00 0.00 34.14 2.52
3651 5687 1.250840 GGTGCCCGCTTCCAAAAGAT 61.251 55.000 0.00 0.00 34.14 2.40
3652 5688 0.171231 GTGCCCGCTTCCAAAAGATC 59.829 55.000 0.00 0.00 34.14 2.75
3653 5689 0.251121 TGCCCGCTTCCAAAAGATCA 60.251 50.000 0.00 0.00 34.14 2.92
3654 5690 0.171231 GCCCGCTTCCAAAAGATCAC 59.829 55.000 0.00 0.00 34.14 3.06
3655 5691 1.826385 CCCGCTTCCAAAAGATCACT 58.174 50.000 0.00 0.00 34.14 3.41
3656 5692 2.162681 CCCGCTTCCAAAAGATCACTT 58.837 47.619 0.00 0.00 38.05 3.16
3657 5693 2.558359 CCCGCTTCCAAAAGATCACTTT 59.442 45.455 0.00 0.00 46.64 2.66
3658 5694 3.568538 CCGCTTCCAAAAGATCACTTTG 58.431 45.455 11.48 11.48 44.32 2.77
3659 5695 3.004734 CCGCTTCCAAAAGATCACTTTGT 59.995 43.478 15.30 0.00 44.32 2.83
3660 5696 4.215399 CCGCTTCCAAAAGATCACTTTGTA 59.785 41.667 15.30 1.89 44.32 2.41
3661 5697 5.147162 CGCTTCCAAAAGATCACTTTGTAC 58.853 41.667 15.30 0.00 44.32 2.90
3662 5698 5.147162 GCTTCCAAAAGATCACTTTGTACG 58.853 41.667 15.30 3.53 44.32 3.67
3663 5699 5.049680 GCTTCCAAAAGATCACTTTGTACGA 60.050 40.000 15.30 6.60 44.32 3.43
3664 5700 6.539649 TTCCAAAAGATCACTTTGTACGAG 57.460 37.500 15.30 0.00 44.32 4.18
3665 5701 4.994852 TCCAAAAGATCACTTTGTACGAGG 59.005 41.667 15.30 0.00 44.32 4.63
3666 5702 4.378459 CCAAAAGATCACTTTGTACGAGGC 60.378 45.833 15.30 0.00 44.32 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 8.603242 ACGAGTTTAAAGTACTGATTTCACAT 57.397 30.769 0.00 0.00 0.00 3.21
81 82 1.134098 ACAAGGCCGACCCTGAATATG 60.134 52.381 0.00 0.00 45.62 1.78
96 108 4.998672 TGGTGAATAGACCGTTAAACAAGG 59.001 41.667 0.00 0.00 39.07 3.61
292 305 7.228706 CCAATACAAACATAGAGGGGTGAATAC 59.771 40.741 0.00 0.00 0.00 1.89
296 309 4.538490 ACCAATACAAACATAGAGGGGTGA 59.462 41.667 0.00 0.00 0.00 4.02
297 310 4.640201 CACCAATACAAACATAGAGGGGTG 59.360 45.833 0.00 0.00 36.49 4.61
318 332 4.523813 CTTTTCCGTACATGAACACACAC 58.476 43.478 0.00 0.00 0.00 3.82
324 341 4.273969 TGTCAACCTTTTCCGTACATGAAC 59.726 41.667 0.00 0.00 0.00 3.18
333 350 8.263940 TCTTTATAAGATGTCAACCTTTTCCG 57.736 34.615 0.00 0.00 31.20 4.30
435 535 2.239654 CCTAGCCATGTTTCTCCCAAGA 59.760 50.000 0.00 0.00 0.00 3.02
453 553 4.389374 CTTTGTTCAGCTCCACTTTCCTA 58.611 43.478 0.00 0.00 0.00 2.94
454 554 3.217626 CTTTGTTCAGCTCCACTTTCCT 58.782 45.455 0.00 0.00 0.00 3.36
462 562 1.032014 TGTTGGCTTTGTTCAGCTCC 58.968 50.000 0.00 0.00 39.97 4.70
514 616 4.449743 GCGAACCAGTACTAAACATCAACA 59.550 41.667 0.00 0.00 0.00 3.33
535 641 1.528586 CACTTGAGTTCTTCACTGGCG 59.471 52.381 0.00 0.00 35.01 5.69
661 767 8.915036 AGATCACAGTCGGAAGTATAGTAATTT 58.085 33.333 0.00 0.00 0.00 1.82
664 770 7.052248 TGAGATCACAGTCGGAAGTATAGTAA 58.948 38.462 0.00 0.00 0.00 2.24
705 811 3.558746 CCTTCATCCCACTCCTATCATGC 60.559 52.174 0.00 0.00 0.00 4.06
724 831 3.691297 ATAGGCCGACCGACCCCTT 62.691 63.158 0.00 0.00 42.76 3.95
1593 1735 1.299468 GCCGATGAGGTAGACGCAG 60.299 63.158 0.00 0.00 43.70 5.18
1794 1936 1.971481 TGCTTACGGCGTAGAGGATA 58.029 50.000 20.01 3.20 45.43 2.59
1923 2068 9.026074 GCCTAATATAAGAGCGTTTAGATCATC 57.974 37.037 0.00 0.00 37.82 2.92
1924 2069 7.982354 GGCCTAATATAAGAGCGTTTAGATCAT 59.018 37.037 0.00 0.00 37.82 2.45
1925 2070 7.178628 AGGCCTAATATAAGAGCGTTTAGATCA 59.821 37.037 1.29 0.00 37.82 2.92
1926 2071 7.489757 CAGGCCTAATATAAGAGCGTTTAGATC 59.510 40.741 3.98 0.00 35.01 2.75
1927 2072 7.324178 CAGGCCTAATATAAGAGCGTTTAGAT 58.676 38.462 3.98 0.00 0.00 1.98
1928 2073 6.295123 CCAGGCCTAATATAAGAGCGTTTAGA 60.295 42.308 3.98 0.00 0.00 2.10
1929 2074 5.869888 CCAGGCCTAATATAAGAGCGTTTAG 59.130 44.000 3.98 0.00 0.00 1.85
1930 2075 5.541101 TCCAGGCCTAATATAAGAGCGTTTA 59.459 40.000 3.98 0.00 0.00 2.01
1931 2076 4.347000 TCCAGGCCTAATATAAGAGCGTTT 59.653 41.667 3.98 0.00 0.00 3.60
1932 2077 3.901844 TCCAGGCCTAATATAAGAGCGTT 59.098 43.478 3.98 0.00 0.00 4.84
1933 2078 3.507411 TCCAGGCCTAATATAAGAGCGT 58.493 45.455 3.98 0.00 0.00 5.07
1934 2079 4.537135 TTCCAGGCCTAATATAAGAGCG 57.463 45.455 3.98 0.00 0.00 5.03
1935 2080 5.432645 GGATTCCAGGCCTAATATAAGAGC 58.567 45.833 3.98 0.00 0.00 4.09
1936 2081 5.488919 TGGGATTCCAGGCCTAATATAAGAG 59.511 44.000 3.98 0.00 38.32 2.85
1937 2082 5.420455 TGGGATTCCAGGCCTAATATAAGA 58.580 41.667 3.98 0.00 38.32 2.10
1938 2083 5.779241 TGGGATTCCAGGCCTAATATAAG 57.221 43.478 3.98 0.00 38.32 1.73
1939 2084 6.276806 TGATTGGGATTCCAGGCCTAATATAA 59.723 38.462 3.98 0.00 45.04 0.98
1948 2093 2.077687 ATGTGATTGGGATTCCAGGC 57.922 50.000 4.80 0.00 45.04 4.85
2008 2153 8.090788 ACCTCTACTCCTTTAGCAAATTATCA 57.909 34.615 0.00 0.00 0.00 2.15
2105 2251 4.642429 AGTTTGCTAAAGGAGTACTGGTG 58.358 43.478 0.00 0.00 0.00 4.17
2107 2253 7.783042 ACTATAGTTTGCTAAAGGAGTACTGG 58.217 38.462 0.00 0.00 0.00 4.00
2157 2604 3.332919 CCTTCCACTCACTGACTTGATG 58.667 50.000 0.00 0.00 0.00 3.07
2266 2728 3.391965 GTTTTCATTTGCCATGTCAGCA 58.608 40.909 0.00 0.00 38.81 4.41
2298 2760 1.242076 GCGATGAAGCCCTGCATATT 58.758 50.000 0.00 0.00 0.00 1.28
2468 2930 2.891936 GTGATGATGAGCGCGGCA 60.892 61.111 8.83 4.86 0.00 5.69
2553 3015 2.899339 GGAGGAAGCTGCCGATGC 60.899 66.667 4.63 0.00 38.26 3.91
2639 3110 2.037367 TCGGAGGTGGTGGAGGAG 59.963 66.667 0.00 0.00 0.00 3.69
2681 3152 1.015109 TGAGAAGCGACGGTAGCTAG 58.985 55.000 16.10 0.00 45.31 3.42
2682 3153 1.131883 GTTGAGAAGCGACGGTAGCTA 59.868 52.381 16.10 0.00 45.31 3.32
2684 3155 2.360794 GTTGAGAAGCGACGGTAGC 58.639 57.895 4.99 4.99 0.00 3.58
2686 3157 1.466866 CATCGTTGAGAAGCGACGGTA 60.467 52.381 0.00 0.00 45.77 4.02
2693 3164 3.002791 TCACAATCCATCGTTGAGAAGC 58.997 45.455 0.00 0.00 0.00 3.86
2706 3178 5.774498 AACAAGAAAACTCCTCACAATCC 57.226 39.130 0.00 0.00 0.00 3.01
2709 3181 9.581099 GAATTTAAACAAGAAAACTCCTCACAA 57.419 29.630 0.00 0.00 0.00 3.33
2712 3184 8.413229 CCTGAATTTAAACAAGAAAACTCCTCA 58.587 33.333 0.00 0.00 0.00 3.86
2945 4955 9.624697 AAAAACGATGTAGACATTAAGTACGTA 57.375 29.630 5.57 0.00 36.57 3.57
2946 4956 8.430063 CAAAAACGATGTAGACATTAAGTACGT 58.570 33.333 0.00 0.00 36.57 3.57
2947 4957 7.421613 GCAAAAACGATGTAGACATTAAGTACG 59.578 37.037 0.00 0.00 36.57 3.67
2948 4958 8.225107 TGCAAAAACGATGTAGACATTAAGTAC 58.775 33.333 0.00 0.00 36.57 2.73
2949 4959 8.312896 TGCAAAAACGATGTAGACATTAAGTA 57.687 30.769 0.00 0.00 36.57 2.24
2950 4960 7.197071 TGCAAAAACGATGTAGACATTAAGT 57.803 32.000 0.00 0.00 36.57 2.24
2959 4969 8.673626 AATTACTGATTGCAAAAACGATGTAG 57.326 30.769 1.71 0.00 0.00 2.74
2964 4974 7.114247 GCACTTAATTACTGATTGCAAAAACGA 59.886 33.333 1.71 0.00 0.00 3.85
2965 4975 7.219922 GCACTTAATTACTGATTGCAAAAACG 58.780 34.615 1.71 0.00 0.00 3.60
2989 4999 7.280356 TCACTAATATTTCTTTACAGAGGGGC 58.720 38.462 0.00 0.00 0.00 5.80
2990 5000 9.495572 GATCACTAATATTTCTTTACAGAGGGG 57.504 37.037 0.00 0.00 0.00 4.79
3019 5029 9.264719 CCCTCCGTAAAGAAATATAATAACGTT 57.735 33.333 5.88 5.88 0.00 3.99
3020 5030 8.424133 ACCCTCCGTAAAGAAATATAATAACGT 58.576 33.333 0.00 0.00 0.00 3.99
3021 5031 8.706035 CACCCTCCGTAAAGAAATATAATAACG 58.294 37.037 0.00 0.00 0.00 3.18
3024 5034 7.658575 GTGCACCCTCCGTAAAGAAATATAATA 59.341 37.037 5.22 0.00 0.00 0.98
3025 5035 6.485648 GTGCACCCTCCGTAAAGAAATATAAT 59.514 38.462 5.22 0.00 0.00 1.28
3026 5036 5.818857 GTGCACCCTCCGTAAAGAAATATAA 59.181 40.000 5.22 0.00 0.00 0.98
3027 5037 5.362263 GTGCACCCTCCGTAAAGAAATATA 58.638 41.667 5.22 0.00 0.00 0.86
3028 5038 4.196971 GTGCACCCTCCGTAAAGAAATAT 58.803 43.478 5.22 0.00 0.00 1.28
3029 5039 3.602483 GTGCACCCTCCGTAAAGAAATA 58.398 45.455 5.22 0.00 0.00 1.40
3030 5040 2.433436 GTGCACCCTCCGTAAAGAAAT 58.567 47.619 5.22 0.00 0.00 2.17
3031 5041 1.543871 GGTGCACCCTCCGTAAAGAAA 60.544 52.381 26.31 0.00 0.00 2.52
3032 5042 0.035739 GGTGCACCCTCCGTAAAGAA 59.964 55.000 26.31 0.00 0.00 2.52
3033 5043 0.834687 AGGTGCACCCTCCGTAAAGA 60.835 55.000 32.29 0.00 40.71 2.52
3034 5044 0.036306 AAGGTGCACCCTCCGTAAAG 59.964 55.000 32.29 0.00 45.47 1.85
3035 5045 0.250553 CAAGGTGCACCCTCCGTAAA 60.251 55.000 32.29 0.00 45.47 2.01
3036 5046 1.373435 CAAGGTGCACCCTCCGTAA 59.627 57.895 32.29 0.00 45.47 3.18
3037 5047 1.412453 AACAAGGTGCACCCTCCGTA 61.412 55.000 32.29 0.00 45.47 4.02
3038 5048 2.676163 GAACAAGGTGCACCCTCCGT 62.676 60.000 32.29 20.20 45.47 4.69
3039 5049 1.966451 GAACAAGGTGCACCCTCCG 60.966 63.158 32.29 19.54 45.47 4.63
3040 5050 0.890996 CTGAACAAGGTGCACCCTCC 60.891 60.000 32.29 16.86 45.47 4.30
3041 5051 1.518903 GCTGAACAAGGTGCACCCTC 61.519 60.000 32.29 22.11 45.47 4.30
3043 5053 1.109323 AAGCTGAACAAGGTGCACCC 61.109 55.000 32.29 16.87 36.51 4.61
3044 5054 0.312102 GAAGCTGAACAAGGTGCACC 59.688 55.000 29.22 29.22 36.51 5.01
3045 5055 1.024271 TGAAGCTGAACAAGGTGCAC 58.976 50.000 8.80 8.80 37.00 4.57
3046 5056 1.024271 GTGAAGCTGAACAAGGTGCA 58.976 50.000 0.00 0.00 39.78 4.57
3047 5057 1.024271 TGTGAAGCTGAACAAGGTGC 58.976 50.000 0.00 0.00 36.51 5.01
3048 5058 2.096069 CGATGTGAAGCTGAACAAGGTG 60.096 50.000 5.88 0.00 36.51 4.00
3051 5061 2.802247 TGTCGATGTGAAGCTGAACAAG 59.198 45.455 5.88 4.30 0.00 3.16
3056 5066 0.596082 TCGTGTCGATGTGAAGCTGA 59.404 50.000 0.00 0.00 0.00 4.26
3057 5067 1.125021 GTTCGTGTCGATGTGAAGCTG 59.875 52.381 0.00 0.00 35.23 4.24
3059 5069 1.136690 TGTTCGTGTCGATGTGAAGC 58.863 50.000 0.00 0.00 35.23 3.86
3064 5074 1.270094 ACCACATGTTCGTGTCGATGT 60.270 47.619 0.00 0.00 35.23 3.06
3074 5084 0.322546 GGAGGACCCACCACATGTTC 60.323 60.000 0.00 0.00 42.04 3.18
3078 5088 1.925455 CCAGGAGGACCCACCACAT 60.925 63.158 5.35 0.00 42.04 3.21
3084 5094 2.692368 GATGGCCAGGAGGACCCA 60.692 66.667 13.05 0.00 45.14 4.51
3085 5095 2.003548 AAGATGGCCAGGAGGACCC 61.004 63.158 13.05 0.00 45.14 4.46
3108 5118 4.912187 GGCGTTTCTTGAGTCTCAAATTTC 59.088 41.667 15.97 6.98 35.73 2.17
3116 5126 2.872858 GACTTTGGCGTTTCTTGAGTCT 59.127 45.455 0.00 0.00 31.73 3.24
3117 5127 2.872858 AGACTTTGGCGTTTCTTGAGTC 59.127 45.455 0.00 0.00 33.93 3.36
3157 5167 1.787847 CGCAAAGTAAGGTGAGCGG 59.212 57.895 0.00 0.00 41.30 5.52
3158 5168 0.669318 TCCGCAAAGTAAGGTGAGCG 60.669 55.000 0.00 0.00 44.24 5.03
3159 5169 1.739067 ATCCGCAAAGTAAGGTGAGC 58.261 50.000 0.00 0.00 0.00 4.26
3160 5170 4.003648 AGAAATCCGCAAAGTAAGGTGAG 58.996 43.478 0.00 0.00 0.00 3.51
3161 5171 4.015872 AGAAATCCGCAAAGTAAGGTGA 57.984 40.909 0.00 0.00 0.00 4.02
3163 5173 5.557866 AGTAAGAAATCCGCAAAGTAAGGT 58.442 37.500 0.00 0.00 0.00 3.50
3164 5174 5.875359 AGAGTAAGAAATCCGCAAAGTAAGG 59.125 40.000 0.00 0.00 0.00 2.69
3165 5175 6.969828 AGAGTAAGAAATCCGCAAAGTAAG 57.030 37.500 0.00 0.00 0.00 2.34
3166 5176 7.330208 GTGTAGAGTAAGAAATCCGCAAAGTAA 59.670 37.037 0.00 0.00 0.00 2.24
3168 5178 5.638234 GTGTAGAGTAAGAAATCCGCAAAGT 59.362 40.000 0.00 0.00 0.00 2.66
3169 5179 5.869888 AGTGTAGAGTAAGAAATCCGCAAAG 59.130 40.000 0.00 0.00 0.00 2.77
3170 5180 5.790593 AGTGTAGAGTAAGAAATCCGCAAA 58.209 37.500 0.00 0.00 0.00 3.68
3174 5194 8.155821 TCTATGAGTGTAGAGTAAGAAATCCG 57.844 38.462 0.00 0.00 0.00 4.18
3209 5229 9.979578 AGACATAGTGTTTGCATTTTAATTTGA 57.020 25.926 0.00 0.00 0.00 2.69
3213 5233 7.331687 GCCAAGACATAGTGTTTGCATTTTAAT 59.668 33.333 0.00 0.00 0.00 1.40
3215 5235 6.155827 GCCAAGACATAGTGTTTGCATTTTA 58.844 36.000 0.00 0.00 0.00 1.52
3220 5240 2.580962 TGCCAAGACATAGTGTTTGCA 58.419 42.857 2.39 2.39 0.00 4.08
3238 5258 2.103373 TGTGAGGAGAGGTAGTGATGC 58.897 52.381 0.00 0.00 0.00 3.91
3240 5260 4.475345 GGTATGTGAGGAGAGGTAGTGAT 58.525 47.826 0.00 0.00 0.00 3.06
3243 5263 2.423088 CCGGTATGTGAGGAGAGGTAGT 60.423 54.545 0.00 0.00 0.00 2.73
3268 5288 7.141363 TCGAGTTACAAGAGTTACAAGGTAAC 58.859 38.462 10.47 10.47 40.30 2.50
3269 5289 7.275888 TCGAGTTACAAGAGTTACAAGGTAA 57.724 36.000 0.00 0.00 29.96 2.85
3280 5300 5.326200 ACCATAGGTTCGAGTTACAAGAG 57.674 43.478 0.00 0.00 27.29 2.85
3330 5354 3.582164 AGTCATCTGGGGTAGAAGATCC 58.418 50.000 0.00 0.00 39.30 3.36
3335 5359 6.884472 TTGAATAAGTCATCTGGGGTAGAA 57.116 37.500 0.00 0.00 39.30 2.10
3354 5378 8.092521 TGCATGTCTTTGTTTTTCTTTTTGAA 57.907 26.923 0.00 0.00 0.00 2.69
3356 5380 8.898983 ATTGCATGTCTTTGTTTTTCTTTTTG 57.101 26.923 0.00 0.00 0.00 2.44
3362 5386 8.550376 ACATTGTATTGCATGTCTTTGTTTTTC 58.450 29.630 0.00 0.00 0.00 2.29
3365 5389 7.710044 TCAACATTGTATTGCATGTCTTTGTTT 59.290 29.630 0.00 0.00 0.00 2.83
3366 5390 7.208777 TCAACATTGTATTGCATGTCTTTGTT 58.791 30.769 0.00 0.00 0.00 2.83
3367 5391 6.747125 TCAACATTGTATTGCATGTCTTTGT 58.253 32.000 0.00 0.00 0.00 2.83
3368 5392 7.009815 GGATCAACATTGTATTGCATGTCTTTG 59.990 37.037 0.00 0.00 0.00 2.77
3369 5393 7.037438 GGATCAACATTGTATTGCATGTCTTT 58.963 34.615 0.00 0.00 0.00 2.52
3370 5394 6.379133 AGGATCAACATTGTATTGCATGTCTT 59.621 34.615 0.00 0.00 0.00 3.01
3371 5395 5.889853 AGGATCAACATTGTATTGCATGTCT 59.110 36.000 0.00 0.00 0.00 3.41
3372 5396 6.039047 AGAGGATCAACATTGTATTGCATGTC 59.961 38.462 0.00 0.00 37.82 3.06
3373 5397 5.889853 AGAGGATCAACATTGTATTGCATGT 59.110 36.000 0.00 0.00 37.82 3.21
3392 5416 6.432581 TCTTTGCTCACCTTATACTAGAGGA 58.567 40.000 0.00 0.00 36.84 3.71
3405 5429 4.808558 TGTGCATTAATTCTTTGCTCACC 58.191 39.130 0.00 0.00 35.62 4.02
3410 5434 6.709145 TGATGTTGTGCATTAATTCTTTGC 57.291 33.333 0.00 1.38 38.06 3.68
3417 5441 9.483916 CCATGATTTATGATGTTGTGCATTAAT 57.516 29.630 0.00 0.00 39.21 1.40
3418 5442 8.693625 TCCATGATTTATGATGTTGTGCATTAA 58.306 29.630 0.00 0.00 39.21 1.40
3419 5443 8.136800 GTCCATGATTTATGATGTTGTGCATTA 58.863 33.333 0.00 0.00 39.21 1.90
3433 5457 8.316946 ACGAGATATGTGATGTCCATGATTTAT 58.683 33.333 0.00 0.00 0.00 1.40
3435 5459 6.528321 ACGAGATATGTGATGTCCATGATTT 58.472 36.000 0.00 0.00 0.00 2.17
3469 5494 6.945435 TCCTACATGAACATGGTTGTTTGTAT 59.055 34.615 17.25 0.00 46.01 2.29
3472 5497 5.703978 TCCTACATGAACATGGTTGTTTG 57.296 39.130 17.25 0.01 46.01 2.93
3493 5518 0.954452 CCAGCCCAACAACTGTCTTC 59.046 55.000 0.00 0.00 31.76 2.87
3498 5523 0.036732 TAGCTCCAGCCCAACAACTG 59.963 55.000 0.00 0.00 43.38 3.16
3536 5561 3.072468 CTTGGGCTGCCACATGGG 61.072 66.667 22.05 0.00 40.85 4.00
3573 5609 2.414824 CCACTTCTCTTTCTCTCGGTCG 60.415 54.545 0.00 0.00 0.00 4.79
3588 5624 2.420466 TTTTCGCCCCCTCCCACTTC 62.420 60.000 0.00 0.00 0.00 3.01
3593 5629 1.844544 TACAGTTTTCGCCCCCTCCC 61.845 60.000 0.00 0.00 0.00 4.30
3594 5630 0.037160 TTACAGTTTTCGCCCCCTCC 59.963 55.000 0.00 0.00 0.00 4.30
3595 5631 1.900245 TTTACAGTTTTCGCCCCCTC 58.100 50.000 0.00 0.00 0.00 4.30
3596 5632 2.167662 CATTTACAGTTTTCGCCCCCT 58.832 47.619 0.00 0.00 0.00 4.79
3597 5633 1.890489 ACATTTACAGTTTTCGCCCCC 59.110 47.619 0.00 0.00 0.00 5.40
3598 5634 3.243602 ACAACATTTACAGTTTTCGCCCC 60.244 43.478 0.00 0.00 0.00 5.80
3599 5635 3.972403 ACAACATTTACAGTTTTCGCCC 58.028 40.909 0.00 0.00 0.00 6.13
3600 5636 4.609708 CGTACAACATTTACAGTTTTCGCC 59.390 41.667 0.00 0.00 0.00 5.54
3601 5637 5.433855 TCGTACAACATTTACAGTTTTCGC 58.566 37.500 0.00 0.00 0.00 4.70
3602 5638 5.558888 GCTCGTACAACATTTACAGTTTTCG 59.441 40.000 0.00 0.00 0.00 3.46
3603 5639 6.356190 GTGCTCGTACAACATTTACAGTTTTC 59.644 38.462 0.00 0.00 0.00 2.29
3604 5640 6.196571 GTGCTCGTACAACATTTACAGTTTT 58.803 36.000 0.00 0.00 0.00 2.43
3605 5641 5.277634 GGTGCTCGTACAACATTTACAGTTT 60.278 40.000 0.00 0.00 0.00 2.66
3606 5642 4.212636 GGTGCTCGTACAACATTTACAGTT 59.787 41.667 0.00 0.00 0.00 3.16
3607 5643 3.744426 GGTGCTCGTACAACATTTACAGT 59.256 43.478 0.00 0.00 0.00 3.55
3608 5644 3.743911 TGGTGCTCGTACAACATTTACAG 59.256 43.478 0.00 0.00 30.61 2.74
3609 5645 3.729966 TGGTGCTCGTACAACATTTACA 58.270 40.909 0.00 0.00 30.61 2.41
3610 5646 4.436852 CCATGGTGCTCGTACAACATTTAC 60.437 45.833 2.57 0.00 45.70 2.01
3611 5647 3.687212 CCATGGTGCTCGTACAACATTTA 59.313 43.478 2.57 0.00 45.70 1.40
3612 5648 2.487762 CCATGGTGCTCGTACAACATTT 59.512 45.455 2.57 0.00 45.70 2.32
3613 5649 2.083774 CCATGGTGCTCGTACAACATT 58.916 47.619 2.57 0.00 45.70 2.71
3615 5651 0.394938 ACCATGGTGCTCGTACAACA 59.605 50.000 18.99 0.85 42.54 3.33
3616 5652 0.796312 CACCATGGTGCTCGTACAAC 59.204 55.000 31.13 0.00 39.39 3.32
3617 5653 3.225272 CACCATGGTGCTCGTACAA 57.775 52.632 31.13 0.00 39.39 2.41
3633 5669 0.171231 GATCTTTTGGAAGCGGGCAC 59.829 55.000 0.00 0.00 32.75 5.01
3634 5670 0.251121 TGATCTTTTGGAAGCGGGCA 60.251 50.000 0.00 0.00 32.75 5.36
3635 5671 0.171231 GTGATCTTTTGGAAGCGGGC 59.829 55.000 0.00 0.00 32.75 6.13
3636 5672 1.826385 AGTGATCTTTTGGAAGCGGG 58.174 50.000 0.00 0.00 32.75 6.13
3637 5673 3.004734 ACAAAGTGATCTTTTGGAAGCGG 59.995 43.478 20.08 2.55 41.31 5.52
3638 5674 4.228912 ACAAAGTGATCTTTTGGAAGCG 57.771 40.909 20.08 0.00 41.31 4.68
3639 5675 5.049680 TCGTACAAAGTGATCTTTTGGAAGC 60.050 40.000 20.08 6.94 41.31 3.86
3640 5676 6.347725 CCTCGTACAAAGTGATCTTTTGGAAG 60.348 42.308 20.08 16.10 41.31 3.46
3641 5677 5.468746 CCTCGTACAAAGTGATCTTTTGGAA 59.531 40.000 20.08 10.24 41.31 3.53
3642 5678 4.994852 CCTCGTACAAAGTGATCTTTTGGA 59.005 41.667 20.08 13.23 41.31 3.53
3643 5679 4.378459 GCCTCGTACAAAGTGATCTTTTGG 60.378 45.833 20.08 5.72 41.31 3.28
3644 5680 4.712763 GCCTCGTACAAAGTGATCTTTTG 58.287 43.478 16.62 16.62 41.31 2.44


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

AutoCloner maintained by Alex Coulton.