Multiple sequence alignment - TraesCS3D01G218800

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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 TraesCS3D01G218800 chr3D 100.000 3286 0 0 1 3286 298056872 298060157 0.000000e+00 6069
1 TraesCS3D01G218800 chr3B 88.164 3050 143 77 362 3250 393227304 393230296 0.000000e+00 3432
2 TraesCS3D01G218800 chr3B 89.537 583 53 6 150 729 393225827 393226404 0.000000e+00 732
3 TraesCS3D01G218800 chr3A 89.974 1526 90 34 362 1851 395757090 395758588 0.000000e+00 1912
4 TraesCS3D01G218800 chr3A 89.655 899 47 24 1851 2735 395760870 395761736 0.000000e+00 1103
5 TraesCS3D01G218800 chr3A 90.449 534 44 5 2736 3266 395761768 395762297 0.000000e+00 697
6 TraesCS3D01G218800 chr7B 81.600 125 17 6 146 269 316019834 316019715 7.500000e-17 99


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 TraesCS3D01G218800 chr3D 298056872 298060157 3285 False 6069.000000 6069 100.0000 1 3286 1 chr3D.!!$F1 3285
1 TraesCS3D01G218800 chr3B 393225827 393230296 4469 False 2082.000000 3432 88.8505 150 3250 2 chr3B.!!$F1 3100
2 TraesCS3D01G218800 chr3A 395757090 395762297 5207 False 1237.333333 1912 90.0260 362 3266 3 chr3A.!!$F1 2904

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
31 32 0.040425 GCAACAAAACGCCGTCATCT 60.040 50.0 0.00 0.00 0.00 2.90 F
1118 2415 0.108186 CTCGCCATGGTGAGTAGCAA 60.108 55.0 36.95 12.89 44.90 3.91 F
1513 2858 0.304098 GCTACTCGTGCTCGTATCGT 59.696 55.0 8.17 4.61 38.33 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 5534 0.244450 CGGTGGCATGCAACTCAATT 59.756 50.0 24.21 0.0 0.00 2.32 R
2036 5671 0.250467 GCTCCTGCACCAAGTCAAGA 60.250 55.0 0.00 0.0 39.41 3.02 R
2977 6680 0.895100 GAGGGGCAGCATTTGTGTCA 60.895 55.0 0.00 0.0 0.00 3.58 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
28 29 2.409651 GGCAACAAAACGCCGTCA 59.590 55.556 0.00 0.00 38.82 4.35
29 30 1.007849 GGCAACAAAACGCCGTCAT 60.008 52.632 0.00 0.00 38.82 3.06
30 31 1.001745 GGCAACAAAACGCCGTCATC 61.002 55.000 0.00 0.00 38.82 2.92
31 32 0.040425 GCAACAAAACGCCGTCATCT 60.040 50.000 0.00 0.00 0.00 2.90
32 33 1.599419 GCAACAAAACGCCGTCATCTT 60.599 47.619 0.00 0.00 0.00 2.40
33 34 2.726633 CAACAAAACGCCGTCATCTTT 58.273 42.857 0.00 0.00 0.00 2.52
34 35 2.399396 ACAAAACGCCGTCATCTTTG 57.601 45.000 9.80 9.80 34.04 2.77
35 36 1.944024 ACAAAACGCCGTCATCTTTGA 59.056 42.857 16.42 0.00 32.57 2.69
47 48 4.159377 TCATCTTTGACAAAATCGCACC 57.841 40.909 1.62 0.00 0.00 5.01
48 49 3.567585 TCATCTTTGACAAAATCGCACCA 59.432 39.130 1.62 0.00 0.00 4.17
49 50 4.218200 TCATCTTTGACAAAATCGCACCAT 59.782 37.500 1.62 0.00 0.00 3.55
50 51 4.159377 TCTTTGACAAAATCGCACCATC 57.841 40.909 1.62 0.00 0.00 3.51
51 52 3.567585 TCTTTGACAAAATCGCACCATCA 59.432 39.130 1.62 0.00 0.00 3.07
52 53 4.218200 TCTTTGACAAAATCGCACCATCAT 59.782 37.500 1.62 0.00 0.00 2.45
53 54 3.763097 TGACAAAATCGCACCATCATC 57.237 42.857 0.00 0.00 0.00 2.92
54 55 3.346315 TGACAAAATCGCACCATCATCT 58.654 40.909 0.00 0.00 0.00 2.90
55 56 3.758023 TGACAAAATCGCACCATCATCTT 59.242 39.130 0.00 0.00 0.00 2.40
56 57 4.142622 TGACAAAATCGCACCATCATCTTC 60.143 41.667 0.00 0.00 0.00 2.87
57 58 3.129287 ACAAAATCGCACCATCATCTTCC 59.871 43.478 0.00 0.00 0.00 3.46
58 59 3.287867 AAATCGCACCATCATCTTCCT 57.712 42.857 0.00 0.00 0.00 3.36
59 60 2.540265 ATCGCACCATCATCTTCCTC 57.460 50.000 0.00 0.00 0.00 3.71
60 61 1.489481 TCGCACCATCATCTTCCTCT 58.511 50.000 0.00 0.00 0.00 3.69
61 62 1.410517 TCGCACCATCATCTTCCTCTC 59.589 52.381 0.00 0.00 0.00 3.20
62 63 1.411977 CGCACCATCATCTTCCTCTCT 59.588 52.381 0.00 0.00 0.00 3.10
63 64 2.158986 CGCACCATCATCTTCCTCTCTT 60.159 50.000 0.00 0.00 0.00 2.85
64 65 3.068732 CGCACCATCATCTTCCTCTCTTA 59.931 47.826 0.00 0.00 0.00 2.10
65 66 4.262377 CGCACCATCATCTTCCTCTCTTAT 60.262 45.833 0.00 0.00 0.00 1.73
66 67 5.237048 GCACCATCATCTTCCTCTCTTATC 58.763 45.833 0.00 0.00 0.00 1.75
67 68 5.468592 CACCATCATCTTCCTCTCTTATCG 58.531 45.833 0.00 0.00 0.00 2.92
68 69 5.010516 CACCATCATCTTCCTCTCTTATCGT 59.989 44.000 0.00 0.00 0.00 3.73
69 70 5.010516 ACCATCATCTTCCTCTCTTATCGTG 59.989 44.000 0.00 0.00 0.00 4.35
70 71 5.468592 CATCATCTTCCTCTCTTATCGTGG 58.531 45.833 0.00 0.00 0.00 4.94
71 72 3.319405 TCATCTTCCTCTCTTATCGTGGC 59.681 47.826 0.00 0.00 0.00 5.01
72 73 2.735151 TCTTCCTCTCTTATCGTGGCA 58.265 47.619 0.00 0.00 0.00 4.92
73 74 3.096852 TCTTCCTCTCTTATCGTGGCAA 58.903 45.455 0.00 0.00 0.00 4.52
74 75 3.706594 TCTTCCTCTCTTATCGTGGCAAT 59.293 43.478 0.00 0.00 0.00 3.56
75 76 3.735237 TCCTCTCTTATCGTGGCAATC 57.265 47.619 0.00 0.00 0.00 2.67
76 77 3.031013 TCCTCTCTTATCGTGGCAATCA 58.969 45.455 0.00 0.00 0.00 2.57
77 78 3.450817 TCCTCTCTTATCGTGGCAATCAA 59.549 43.478 0.00 0.00 0.00 2.57
78 79 4.081142 TCCTCTCTTATCGTGGCAATCAAA 60.081 41.667 0.00 0.00 0.00 2.69
79 80 4.272018 CCTCTCTTATCGTGGCAATCAAAG 59.728 45.833 0.00 0.00 0.00 2.77
80 81 5.084818 TCTCTTATCGTGGCAATCAAAGA 57.915 39.130 0.00 0.00 0.00 2.52
81 82 5.674525 TCTCTTATCGTGGCAATCAAAGAT 58.325 37.500 0.00 0.00 0.00 2.40
82 83 5.525012 TCTCTTATCGTGGCAATCAAAGATG 59.475 40.000 0.00 0.00 0.00 2.90
83 84 5.427378 TCTTATCGTGGCAATCAAAGATGA 58.573 37.500 0.00 0.00 40.57 2.92
84 85 5.879777 TCTTATCGTGGCAATCAAAGATGAA 59.120 36.000 0.00 0.00 39.49 2.57
85 86 4.627611 ATCGTGGCAATCAAAGATGAAG 57.372 40.909 0.00 0.00 39.49 3.02
86 87 2.162208 TCGTGGCAATCAAAGATGAAGC 59.838 45.455 0.00 0.00 39.49 3.86
87 88 2.163010 CGTGGCAATCAAAGATGAAGCT 59.837 45.455 0.00 0.00 39.49 3.74
88 89 3.730061 CGTGGCAATCAAAGATGAAGCTC 60.730 47.826 0.00 0.00 39.49 4.09
89 90 3.192001 GTGGCAATCAAAGATGAAGCTCA 59.808 43.478 0.00 0.00 39.49 4.26
90 91 3.192001 TGGCAATCAAAGATGAAGCTCAC 59.808 43.478 0.00 0.00 39.49 3.51
91 92 3.442977 GGCAATCAAAGATGAAGCTCACT 59.557 43.478 0.00 0.00 39.49 3.41
92 93 4.438472 GGCAATCAAAGATGAAGCTCACTC 60.438 45.833 0.00 0.00 39.49 3.51
93 94 4.438472 GCAATCAAAGATGAAGCTCACTCC 60.438 45.833 0.00 0.00 39.49 3.85
94 95 4.840716 ATCAAAGATGAAGCTCACTCCT 57.159 40.909 0.00 0.00 39.49 3.69
95 96 3.935315 TCAAAGATGAAGCTCACTCCTG 58.065 45.455 0.00 0.00 30.99 3.86
96 97 3.008330 CAAAGATGAAGCTCACTCCTGG 58.992 50.000 0.00 0.00 0.00 4.45
97 98 1.202330 AGATGAAGCTCACTCCTGGG 58.798 55.000 0.00 0.00 0.00 4.45
98 99 0.463474 GATGAAGCTCACTCCTGGGC 60.463 60.000 0.00 0.00 45.38 5.36
99 100 1.919600 ATGAAGCTCACTCCTGGGCC 61.920 60.000 0.00 0.00 46.34 5.80
100 101 3.672295 GAAGCTCACTCCTGGGCCG 62.672 68.421 0.00 0.00 46.34 6.13
102 103 4.767255 GCTCACTCCTGGGCCGTG 62.767 72.222 0.00 0.23 38.04 4.94
103 104 4.087892 CTCACTCCTGGGCCGTGG 62.088 72.222 8.88 8.88 0.00 4.94
115 116 4.504916 CCGTGGCAGGAGCTCGAG 62.505 72.222 8.45 8.45 41.70 4.04
116 117 4.504916 CGTGGCAGGAGCTCGAGG 62.505 72.222 15.58 0.29 41.70 4.63
117 118 3.071206 GTGGCAGGAGCTCGAGGA 61.071 66.667 15.58 0.00 41.70 3.71
118 119 2.283894 TGGCAGGAGCTCGAGGAA 60.284 61.111 15.58 0.00 41.70 3.36
119 120 1.687146 TGGCAGGAGCTCGAGGAAT 60.687 57.895 15.58 0.00 41.70 3.01
120 121 1.227497 GGCAGGAGCTCGAGGAATG 60.227 63.158 15.58 0.82 41.70 2.67
121 122 1.680522 GGCAGGAGCTCGAGGAATGA 61.681 60.000 15.58 0.00 41.70 2.57
122 123 0.176680 GCAGGAGCTCGAGGAATGAA 59.823 55.000 15.58 0.00 37.91 2.57
123 124 1.933247 CAGGAGCTCGAGGAATGAAC 58.067 55.000 15.58 0.00 0.00 3.18
124 125 1.205655 CAGGAGCTCGAGGAATGAACA 59.794 52.381 15.58 0.00 0.00 3.18
125 126 1.205893 AGGAGCTCGAGGAATGAACAC 59.794 52.381 15.58 0.00 0.00 3.32
126 127 1.066858 GGAGCTCGAGGAATGAACACA 60.067 52.381 15.58 0.00 0.00 3.72
127 128 2.419297 GGAGCTCGAGGAATGAACACAT 60.419 50.000 15.58 0.00 0.00 3.21
128 129 2.863137 GAGCTCGAGGAATGAACACATC 59.137 50.000 15.58 0.00 0.00 3.06
129 130 2.499289 AGCTCGAGGAATGAACACATCT 59.501 45.455 15.58 0.00 0.00 2.90
130 131 3.055530 AGCTCGAGGAATGAACACATCTT 60.056 43.478 15.58 0.00 0.00 2.40
131 132 3.686726 GCTCGAGGAATGAACACATCTTT 59.313 43.478 15.58 0.00 0.00 2.52
132 133 4.154918 GCTCGAGGAATGAACACATCTTTT 59.845 41.667 15.58 0.00 0.00 2.27
133 134 5.335191 GCTCGAGGAATGAACACATCTTTTT 60.335 40.000 15.58 0.00 0.00 1.94
162 163 3.246226 CGGAATCGAGGAATGAACACATC 59.754 47.826 0.00 0.00 39.00 3.06
167 168 6.662865 ATCGAGGAATGAACACATCTATCT 57.337 37.500 0.00 0.00 0.00 1.98
180 181 6.912426 ACACATCTATCTCTCCTGTAACCTA 58.088 40.000 0.00 0.00 0.00 3.08
256 259 0.727398 GCCTCGCCATTCTTGTGTAC 59.273 55.000 0.00 0.00 0.00 2.90
261 264 0.168128 GCCATTCTTGTGTACGTGGC 59.832 55.000 0.00 0.00 44.37 5.01
266 269 0.878523 TCTTGTGTACGTGGCTGTGC 60.879 55.000 0.00 0.00 0.00 4.57
274 277 2.032528 GTGGCTGTGCTGCTACCA 59.967 61.111 0.00 0.16 38.28 3.25
291 294 4.586841 GCTACCATGTACTCTCTTCATCCT 59.413 45.833 0.00 0.00 0.00 3.24
309 312 8.557592 TTCATCCTCTATCAATGCAATGATAC 57.442 34.615 18.52 0.00 40.44 2.24
322 325 1.029681 ATGATACGCTGCTACGTCCA 58.970 50.000 7.85 8.28 44.43 4.02
324 327 0.661552 GATACGCTGCTACGTCCAGA 59.338 55.000 17.42 0.66 44.43 3.86
352 355 7.496529 AAAATGATACGCTGCTATGTGTATT 57.503 32.000 0.00 0.00 41.81 1.89
353 356 8.601845 AAAATGATACGCTGCTATGTGTATTA 57.398 30.769 0.00 8.25 41.81 0.98
393 397 7.394016 TGTCTCAAGCAGGTTTCTGATATTTA 58.606 34.615 0.00 0.00 43.49 1.40
396 400 5.590259 TCAAGCAGGTTTCTGATATTTAGCC 59.410 40.000 0.00 0.00 43.49 3.93
397 401 5.116084 AGCAGGTTTCTGATATTTAGCCA 57.884 39.130 0.00 0.00 43.49 4.75
403 407 5.006746 GGTTTCTGATATTTAGCCAGTCACG 59.993 44.000 0.00 0.00 0.00 4.35
549 1816 1.833787 AAACCACGCCGGACATAGGT 61.834 55.000 5.05 1.49 38.63 3.08
556 1823 0.243095 GCCGGACATAGGTCGGTATC 59.757 60.000 5.05 0.34 45.28 2.24
793 2063 0.466555 CCTCTCCTCCTACCACCTCG 60.467 65.000 0.00 0.00 0.00 4.63
826 2108 3.699538 GGATATTTTCCTTTTCCCGCACT 59.300 43.478 0.00 0.00 41.78 4.40
855 2137 1.012486 GCCTTTATATACGCCGCGCT 61.012 55.000 13.88 2.91 0.00 5.92
896 2181 2.752238 CGCTGTCTCTCCCCGTCT 60.752 66.667 0.00 0.00 0.00 4.18
897 2182 2.766400 CGCTGTCTCTCCCCGTCTC 61.766 68.421 0.00 0.00 0.00 3.36
898 2183 2.766400 GCTGTCTCTCCCCGTCTCG 61.766 68.421 0.00 0.00 0.00 4.04
899 2184 1.377463 CTGTCTCTCCCCGTCTCGT 60.377 63.158 0.00 0.00 0.00 4.18
900 2185 1.370587 CTGTCTCTCCCCGTCTCGTC 61.371 65.000 0.00 0.00 0.00 4.20
915 2200 2.105128 GTCTCAGGTCGCCATCGG 59.895 66.667 0.00 0.00 36.13 4.18
917 2202 1.680989 TCTCAGGTCGCCATCGGAA 60.681 57.895 0.00 0.00 36.13 4.30
1118 2415 0.108186 CTCGCCATGGTGAGTAGCAA 60.108 55.000 36.95 12.89 44.90 3.91
1301 2627 2.313317 CGAGGCATACCAGGGTACTTA 58.687 52.381 0.00 0.00 39.06 2.24
1302 2628 2.897969 CGAGGCATACCAGGGTACTTAT 59.102 50.000 0.00 0.00 39.06 1.73
1303 2629 3.323979 CGAGGCATACCAGGGTACTTATT 59.676 47.826 0.00 0.00 39.06 1.40
1304 2630 4.560919 CGAGGCATACCAGGGTACTTATTC 60.561 50.000 0.00 0.00 39.06 1.75
1306 2632 4.593634 AGGCATACCAGGGTACTTATTCTC 59.406 45.833 0.00 0.00 39.06 2.87
1307 2633 4.593634 GGCATACCAGGGTACTTATTCTCT 59.406 45.833 0.00 0.00 35.26 3.10
1308 2634 5.071923 GGCATACCAGGGTACTTATTCTCTT 59.928 44.000 0.00 0.00 35.26 2.85
1312 2655 9.144298 CATACCAGGGTACTTATTCTCTTTCTA 57.856 37.037 0.00 0.00 33.01 2.10
1313 2656 7.421087 ACCAGGGTACTTATTCTCTTTCTAC 57.579 40.000 0.00 0.00 0.00 2.59
1464 2809 4.184629 CCAAGAAGAGGTCGAGGTAATTG 58.815 47.826 0.00 0.00 0.00 2.32
1473 2818 6.042552 AGAGGTCGAGGTAATTGATTGATGAT 59.957 38.462 0.00 0.00 0.00 2.45
1485 2830 5.885230 TGATTGATGATTTTGCTTCTCGT 57.115 34.783 0.00 0.00 0.00 4.18
1486 2831 6.983474 TGATTGATGATTTTGCTTCTCGTA 57.017 33.333 0.00 0.00 0.00 3.43
1487 2832 7.376435 TGATTGATGATTTTGCTTCTCGTAA 57.624 32.000 0.00 0.00 0.00 3.18
1511 2856 2.303707 GAGCTACTCGTGCTCGTATC 57.696 55.000 8.17 0.00 45.73 2.24
1512 2857 0.582482 AGCTACTCGTGCTCGTATCG 59.418 55.000 8.17 0.00 35.67 2.92
1513 2858 0.304098 GCTACTCGTGCTCGTATCGT 59.696 55.000 8.17 4.61 38.33 3.73
1514 2859 1.524355 GCTACTCGTGCTCGTATCGTA 59.476 52.381 8.17 5.44 38.33 3.43
1515 2860 2.157279 GCTACTCGTGCTCGTATCGTAT 59.843 50.000 8.17 0.00 38.33 3.06
1630 2975 2.385803 CCACCGTTGGTAGAGAGGTAT 58.614 52.381 0.00 0.00 38.23 2.73
1634 2979 3.950395 ACCGTTGGTAGAGAGGTATGTAC 59.050 47.826 0.00 0.00 32.11 2.90
1636 2981 3.624861 CGTTGGTAGAGAGGTATGTACGT 59.375 47.826 0.00 0.00 0.00 3.57
1637 2982 4.811024 CGTTGGTAGAGAGGTATGTACGTA 59.189 45.833 0.00 0.00 0.00 3.57
1668 3015 3.897141 AATGTTCATCATGCATGCCAA 57.103 38.095 22.25 10.80 36.81 4.52
1682 3029 3.319755 CATGCCAAACTTTGATTCGCTT 58.680 40.909 2.87 0.00 0.00 4.68
1721 3069 4.411256 TTAGAGTTTGAACCCAACTCGT 57.589 40.909 7.07 0.52 36.48 4.18
1733 3081 6.265196 TGAACCCAACTCGTCTACTTACTTTA 59.735 38.462 0.00 0.00 0.00 1.85
1777 3125 9.103861 CTGTAAATCAGTTCTCCTATTTCCTTC 57.896 37.037 0.00 0.00 39.17 3.46
1900 5532 9.239002 CAACAACCGTGATATTTTTGTAAGAAA 57.761 29.630 0.00 0.00 30.28 2.52
1901 5533 9.804758 AACAACCGTGATATTTTTGTAAGAAAA 57.195 25.926 0.00 0.00 33.46 2.29
1902 5534 9.804758 ACAACCGTGATATTTTTGTAAGAAAAA 57.195 25.926 0.00 0.00 32.75 1.94
1977 5612 5.104941 TCCATGTAGATCAAACCGAATGTCT 60.105 40.000 0.00 0.00 0.00 3.41
2008 5643 0.885879 TTCTGCTGCATGCCTGAAAG 59.114 50.000 16.68 6.41 42.00 2.62
2029 5664 2.675348 GGCTGAAGCTATCACTGACAAC 59.325 50.000 1.74 0.00 41.70 3.32
2030 5665 2.675348 GCTGAAGCTATCACTGACAACC 59.325 50.000 0.00 0.00 38.21 3.77
2381 6024 0.543883 TTGCAGAGACTGGGAGAGCT 60.544 55.000 0.00 0.00 31.21 4.09
2399 6042 1.403780 GCTATTCACAGGGAACGTCGT 60.404 52.381 0.00 0.00 38.60 4.34
2457 6105 1.450312 CCCACTGGATGAGCGGAAC 60.450 63.158 0.00 0.00 0.00 3.62
2584 6232 2.682856 AGACGTGATGTTTTGCACTGTT 59.317 40.909 0.00 0.00 32.98 3.16
2585 6233 3.128589 AGACGTGATGTTTTGCACTGTTT 59.871 39.130 0.00 0.00 32.98 2.83
2587 6235 3.857093 ACGTGATGTTTTGCACTGTTTTC 59.143 39.130 0.00 0.00 32.98 2.29
2589 6237 5.163703 ACGTGATGTTTTGCACTGTTTTCTA 60.164 36.000 0.00 0.00 32.98 2.10
2590 6238 5.396362 CGTGATGTTTTGCACTGTTTTCTAG 59.604 40.000 0.00 0.00 32.98 2.43
2591 6239 6.265577 GTGATGTTTTGCACTGTTTTCTAGT 58.734 36.000 0.00 0.00 32.44 2.57
2593 6241 6.751425 TGATGTTTTGCACTGTTTTCTAGTTG 59.249 34.615 0.00 0.00 0.00 3.16
2594 6242 6.260870 TGTTTTGCACTGTTTTCTAGTTGA 57.739 33.333 0.00 0.00 0.00 3.18
2595 6243 6.090129 TGTTTTGCACTGTTTTCTAGTTGAC 58.910 36.000 0.00 0.00 0.00 3.18
2625 6280 0.937304 CTGACACGTGTTGGAGTTGG 59.063 55.000 24.26 3.55 0.00 3.77
2681 6343 3.173151 TCATCTAGAACCTGCTTGTCCA 58.827 45.455 0.00 0.00 0.00 4.02
2685 6347 1.966451 GAACCTGCTTGTCCACCCG 60.966 63.158 0.00 0.00 0.00 5.28
2703 6372 1.398390 CCGCTTGTTATCTGGTTCTGC 59.602 52.381 0.00 0.00 0.00 4.26
2735 6404 0.931702 TGCGTGAACGTAACCAACAG 59.068 50.000 4.59 0.00 42.22 3.16
2736 6405 1.210870 GCGTGAACGTAACCAACAGA 58.789 50.000 4.59 0.00 42.22 3.41
2737 6406 1.796459 GCGTGAACGTAACCAACAGAT 59.204 47.619 4.59 0.00 42.22 2.90
2738 6407 2.222445 GCGTGAACGTAACCAACAGATT 59.778 45.455 4.59 0.00 42.22 2.40
2739 6408 3.429543 GCGTGAACGTAACCAACAGATTA 59.570 43.478 4.59 0.00 42.22 1.75
2740 6409 4.664891 GCGTGAACGTAACCAACAGATTAC 60.665 45.833 4.59 0.00 42.22 1.89
2790 6493 2.413310 ATATGTGGTTCGGTTGGGTC 57.587 50.000 0.00 0.00 0.00 4.46
2903 6606 1.702957 ACCAGCAACTAAGGCTTGGTA 59.297 47.619 16.99 0.00 40.23 3.25
2977 6680 3.453717 TGAGATCTGCCTGTTAGCAATCT 59.546 43.478 0.00 9.43 43.52 2.40
3010 6713 0.539051 CCCCTCCGGATGATGATAGC 59.461 60.000 3.57 0.00 0.00 2.97
3012 6715 1.566211 CCTCCGGATGATGATAGCCT 58.434 55.000 3.57 0.00 0.00 4.58
3015 6718 1.002430 TCCGGATGATGATAGCCTTGC 59.998 52.381 0.00 0.00 0.00 4.01
3030 6733 2.360165 GCCTTGCTATCCATGTCTTTGG 59.640 50.000 0.00 0.00 38.18 3.28
3113 6816 3.083997 GACCTGGATCCGCACCCT 61.084 66.667 7.39 0.00 0.00 4.34
3119 6822 3.785859 GATCCGCACCCTCTGCCA 61.786 66.667 0.00 0.00 43.84 4.92
3164 6885 4.462280 CCTTACCCGCCACCGTCC 62.462 72.222 0.00 0.00 0.00 4.79
3197 6930 1.291272 GCCAGAGCCAAAGCCAAAG 59.709 57.895 0.00 0.00 41.25 2.77
3200 6933 1.154688 AGAGCCAAAGCCAAAGCCT 59.845 52.632 0.00 0.00 41.25 4.58
3201 6934 0.897401 AGAGCCAAAGCCAAAGCCTC 60.897 55.000 0.00 0.00 41.25 4.70
3227 6972 4.020617 CCTGAGCCACAGCCGGAA 62.021 66.667 5.05 0.00 44.52 4.30
3230 6975 4.329545 GAGCCACAGCCGGAACCA 62.330 66.667 5.05 0.00 41.25 3.67
3236 6981 4.020617 CAGCCGGAACCAGAGCCA 62.021 66.667 5.05 0.00 0.00 4.75
3243 6988 1.376553 GAACCAGAGCCAGAGCCAC 60.377 63.158 0.00 0.00 41.25 5.01
3244 6989 3.245668 AACCAGAGCCAGAGCCACG 62.246 63.158 0.00 0.00 41.25 4.94
3262 7007 2.601367 GCCAGAGCCAAAGCCCAA 60.601 61.111 0.00 0.00 41.25 4.12
3263 7008 2.643232 GCCAGAGCCAAAGCCCAAG 61.643 63.158 0.00 0.00 41.25 3.61
3264 7009 2.643232 CCAGAGCCAAAGCCCAAGC 61.643 63.158 0.00 0.00 41.25 4.01
3265 7010 2.283460 AGAGCCAAAGCCCAAGCC 60.283 61.111 0.00 0.00 41.25 4.35
3266 7011 2.283460 GAGCCAAAGCCCAAGCCT 60.283 61.111 0.00 0.00 41.25 4.58
3267 7012 2.283460 AGCCAAAGCCCAAGCCTC 60.283 61.111 0.00 0.00 41.25 4.70
3268 7013 2.601367 GCCAAAGCCCAAGCCTCA 60.601 61.111 0.00 0.00 41.25 3.86
3269 7014 2.643232 GCCAAAGCCCAAGCCTCAG 61.643 63.158 0.00 0.00 41.25 3.35
3270 7015 2.643232 CCAAAGCCCAAGCCTCAGC 61.643 63.158 0.00 0.00 41.25 4.26
3271 7016 2.283460 AAAGCCCAAGCCTCAGCC 60.283 61.111 0.00 0.00 41.25 4.85
3272 7017 2.849962 AAAGCCCAAGCCTCAGCCT 61.850 57.895 0.00 0.00 41.25 4.58
3273 7018 3.580604 AAGCCCAAGCCTCAGCCTG 62.581 63.158 0.00 0.00 41.25 4.85
3274 7019 4.039092 GCCCAAGCCTCAGCCTGA 62.039 66.667 0.00 0.00 41.25 3.86
3275 7020 2.271497 CCCAAGCCTCAGCCTGAG 59.729 66.667 14.99 14.99 43.91 3.35
3276 7021 2.438075 CCAAGCCTCAGCCTGAGC 60.438 66.667 16.49 11.53 42.98 4.26
3277 7022 2.438075 CAAGCCTCAGCCTGAGCC 60.438 66.667 16.49 5.24 42.98 4.70
3278 7023 2.610233 AAGCCTCAGCCTGAGCCT 60.610 61.111 16.49 7.92 42.98 4.58
3279 7024 2.969162 AAGCCTCAGCCTGAGCCTG 61.969 63.158 16.49 4.20 42.98 4.85
3280 7025 3.397439 GCCTCAGCCTGAGCCTGA 61.397 66.667 16.49 0.00 42.98 3.86
3281 7026 2.901813 CCTCAGCCTGAGCCTGAG 59.098 66.667 16.49 13.12 42.98 3.35
3282 7027 2.187424 CTCAGCCTGAGCCTGAGC 59.813 66.667 9.13 0.00 37.72 4.26
3283 7028 3.388703 CTCAGCCTGAGCCTGAGCC 62.389 68.421 9.13 0.00 37.72 4.70
3284 7029 3.714001 CAGCCTGAGCCTGAGCCA 61.714 66.667 0.00 0.00 41.25 4.75
3285 7030 3.715097 AGCCTGAGCCTGAGCCAC 61.715 66.667 0.00 0.00 41.25 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.827368 TTTGTTGCCACCAAAGGGAC 59.173 50.000 0.00 0.00 38.05 4.46
1 2 1.208293 GTTTTGTTGCCACCAAAGGGA 59.792 47.619 0.00 0.00 38.05 4.20
2 3 1.662517 GTTTTGTTGCCACCAAAGGG 58.337 50.000 0.00 0.00 41.29 3.95
3 4 1.285578 CGTTTTGTTGCCACCAAAGG 58.714 50.000 0.00 0.00 33.67 3.11
4 5 0.649993 GCGTTTTGTTGCCACCAAAG 59.350 50.000 0.00 0.00 33.67 2.77
5 6 2.755929 GCGTTTTGTTGCCACCAAA 58.244 47.368 0.00 0.00 31.68 3.28
6 7 4.504132 GCGTTTTGTTGCCACCAA 57.496 50.000 0.00 0.00 0.00 3.67
12 13 0.040425 AGATGACGGCGTTTTGTTGC 60.040 50.000 16.19 0.00 0.00 4.17
13 14 2.399396 AAGATGACGGCGTTTTGTTG 57.601 45.000 16.19 0.00 0.00 3.33
14 15 2.356382 TCAAAGATGACGGCGTTTTGTT 59.644 40.909 25.28 14.54 32.22 2.83
15 16 1.944024 TCAAAGATGACGGCGTTTTGT 59.056 42.857 25.28 10.05 32.22 2.83
16 17 2.307049 GTCAAAGATGACGGCGTTTTG 58.693 47.619 22.31 22.31 45.94 2.44
17 18 2.681152 GTCAAAGATGACGGCGTTTT 57.319 45.000 16.19 7.91 45.94 2.43
26 27 3.567585 TGGTGCGATTTTGTCAAAGATGA 59.432 39.130 0.00 0.00 0.00 2.92
27 28 3.899734 TGGTGCGATTTTGTCAAAGATG 58.100 40.909 0.00 0.00 0.00 2.90
28 29 4.218200 TGATGGTGCGATTTTGTCAAAGAT 59.782 37.500 0.00 0.00 0.00 2.40
29 30 3.567585 TGATGGTGCGATTTTGTCAAAGA 59.432 39.130 0.00 0.00 0.00 2.52
30 31 3.899734 TGATGGTGCGATTTTGTCAAAG 58.100 40.909 0.00 0.00 0.00 2.77
31 32 3.998099 TGATGGTGCGATTTTGTCAAA 57.002 38.095 0.00 0.00 0.00 2.69
32 33 3.758023 AGATGATGGTGCGATTTTGTCAA 59.242 39.130 0.00 0.00 0.00 3.18
33 34 3.346315 AGATGATGGTGCGATTTTGTCA 58.654 40.909 0.00 0.00 0.00 3.58
34 35 4.346129 GAAGATGATGGTGCGATTTTGTC 58.654 43.478 0.00 0.00 0.00 3.18
35 36 3.129287 GGAAGATGATGGTGCGATTTTGT 59.871 43.478 0.00 0.00 0.00 2.83
36 37 3.379372 AGGAAGATGATGGTGCGATTTTG 59.621 43.478 0.00 0.00 0.00 2.44
37 38 3.624777 AGGAAGATGATGGTGCGATTTT 58.375 40.909 0.00 0.00 0.00 1.82
38 39 3.118112 AGAGGAAGATGATGGTGCGATTT 60.118 43.478 0.00 0.00 0.00 2.17
39 40 2.437281 AGAGGAAGATGATGGTGCGATT 59.563 45.455 0.00 0.00 0.00 3.34
40 41 2.036992 GAGAGGAAGATGATGGTGCGAT 59.963 50.000 0.00 0.00 0.00 4.58
41 42 1.410517 GAGAGGAAGATGATGGTGCGA 59.589 52.381 0.00 0.00 0.00 5.10
42 43 1.411977 AGAGAGGAAGATGATGGTGCG 59.588 52.381 0.00 0.00 0.00 5.34
43 44 3.557228 AAGAGAGGAAGATGATGGTGC 57.443 47.619 0.00 0.00 0.00 5.01
44 45 5.010516 ACGATAAGAGAGGAAGATGATGGTG 59.989 44.000 0.00 0.00 0.00 4.17
45 46 5.010516 CACGATAAGAGAGGAAGATGATGGT 59.989 44.000 0.00 0.00 0.00 3.55
46 47 5.468592 CACGATAAGAGAGGAAGATGATGG 58.531 45.833 0.00 0.00 0.00 3.51
47 48 5.468592 CCACGATAAGAGAGGAAGATGATG 58.531 45.833 0.00 0.00 0.00 3.07
48 49 4.021544 GCCACGATAAGAGAGGAAGATGAT 60.022 45.833 0.00 0.00 0.00 2.45
49 50 3.319405 GCCACGATAAGAGAGGAAGATGA 59.681 47.826 0.00 0.00 0.00 2.92
50 51 3.068732 TGCCACGATAAGAGAGGAAGATG 59.931 47.826 0.00 0.00 0.00 2.90
51 52 3.300388 TGCCACGATAAGAGAGGAAGAT 58.700 45.455 0.00 0.00 0.00 2.40
52 53 2.735151 TGCCACGATAAGAGAGGAAGA 58.265 47.619 0.00 0.00 0.00 2.87
53 54 3.526931 TTGCCACGATAAGAGAGGAAG 57.473 47.619 0.00 0.00 0.00 3.46
54 55 3.450817 TGATTGCCACGATAAGAGAGGAA 59.549 43.478 0.00 0.00 0.00 3.36
55 56 3.031013 TGATTGCCACGATAAGAGAGGA 58.969 45.455 0.00 0.00 0.00 3.71
56 57 3.459232 TGATTGCCACGATAAGAGAGG 57.541 47.619 0.00 0.00 0.00 3.69
57 58 5.111989 TCTTTGATTGCCACGATAAGAGAG 58.888 41.667 0.00 0.00 0.00 3.20
58 59 5.084818 TCTTTGATTGCCACGATAAGAGA 57.915 39.130 0.00 0.00 0.00 3.10
59 60 5.525012 TCATCTTTGATTGCCACGATAAGAG 59.475 40.000 0.00 0.00 0.00 2.85
60 61 5.427378 TCATCTTTGATTGCCACGATAAGA 58.573 37.500 0.00 0.00 0.00 2.10
61 62 5.739752 TCATCTTTGATTGCCACGATAAG 57.260 39.130 0.00 0.00 0.00 1.73
62 63 5.449041 GCTTCATCTTTGATTGCCACGATAA 60.449 40.000 0.00 0.00 0.00 1.75
63 64 4.035558 GCTTCATCTTTGATTGCCACGATA 59.964 41.667 0.00 0.00 0.00 2.92
64 65 3.181493 GCTTCATCTTTGATTGCCACGAT 60.181 43.478 0.00 0.00 0.00 3.73
65 66 2.162208 GCTTCATCTTTGATTGCCACGA 59.838 45.455 0.00 0.00 0.00 4.35
66 67 2.163010 AGCTTCATCTTTGATTGCCACG 59.837 45.455 0.00 0.00 34.32 4.94
67 68 3.192001 TGAGCTTCATCTTTGATTGCCAC 59.808 43.478 0.00 0.00 34.32 5.01
68 69 3.192001 GTGAGCTTCATCTTTGATTGCCA 59.808 43.478 0.00 0.00 34.32 4.92
69 70 3.442977 AGTGAGCTTCATCTTTGATTGCC 59.557 43.478 0.00 0.00 34.32 4.52
70 71 4.438472 GGAGTGAGCTTCATCTTTGATTGC 60.438 45.833 0.00 0.00 34.13 3.56
71 72 4.942483 AGGAGTGAGCTTCATCTTTGATTG 59.058 41.667 0.00 0.00 0.00 2.67
72 73 4.942483 CAGGAGTGAGCTTCATCTTTGATT 59.058 41.667 0.00 0.00 0.00 2.57
73 74 4.515361 CAGGAGTGAGCTTCATCTTTGAT 58.485 43.478 0.00 0.00 0.00 2.57
74 75 3.307269 CCAGGAGTGAGCTTCATCTTTGA 60.307 47.826 0.00 0.00 0.00 2.69
75 76 3.008330 CCAGGAGTGAGCTTCATCTTTG 58.992 50.000 0.00 0.00 0.00 2.77
76 77 2.026449 CCCAGGAGTGAGCTTCATCTTT 60.026 50.000 0.00 0.00 0.00 2.52
77 78 1.558756 CCCAGGAGTGAGCTTCATCTT 59.441 52.381 0.00 0.00 0.00 2.40
78 79 1.202330 CCCAGGAGTGAGCTTCATCT 58.798 55.000 0.00 0.00 0.00 2.90
79 80 0.463474 GCCCAGGAGTGAGCTTCATC 60.463 60.000 0.00 0.00 0.00 2.92
80 81 1.606531 GCCCAGGAGTGAGCTTCAT 59.393 57.895 0.00 0.00 0.00 2.57
81 82 2.596851 GGCCCAGGAGTGAGCTTCA 61.597 63.158 0.00 0.00 0.00 3.02
82 83 2.270527 GGCCCAGGAGTGAGCTTC 59.729 66.667 0.00 0.00 0.00 3.86
83 84 3.710722 CGGCCCAGGAGTGAGCTT 61.711 66.667 0.00 0.00 0.00 3.74
85 86 4.767255 CACGGCCCAGGAGTGAGC 62.767 72.222 0.00 0.00 38.06 4.26
86 87 4.087892 CCACGGCCCAGGAGTGAG 62.088 72.222 9.07 0.00 38.06 3.51
98 99 4.504916 CTCGAGCTCCTGCCACGG 62.505 72.222 8.47 0.00 40.80 4.94
99 100 4.504916 CCTCGAGCTCCTGCCACG 62.505 72.222 6.99 0.00 40.80 4.94
100 101 1.965754 ATTCCTCGAGCTCCTGCCAC 61.966 60.000 6.99 0.00 40.80 5.01
101 102 1.687146 ATTCCTCGAGCTCCTGCCA 60.687 57.895 6.99 0.00 40.80 4.92
102 103 1.227497 CATTCCTCGAGCTCCTGCC 60.227 63.158 6.99 0.00 40.80 4.85
103 104 0.176680 TTCATTCCTCGAGCTCCTGC 59.823 55.000 6.99 0.00 40.05 4.85
104 105 1.205655 TGTTCATTCCTCGAGCTCCTG 59.794 52.381 6.99 0.53 0.00 3.86
105 106 1.205893 GTGTTCATTCCTCGAGCTCCT 59.794 52.381 6.99 0.00 0.00 3.69
106 107 1.066858 TGTGTTCATTCCTCGAGCTCC 60.067 52.381 6.99 0.00 0.00 4.70
107 108 2.370281 TGTGTTCATTCCTCGAGCTC 57.630 50.000 6.99 2.73 0.00 4.09
108 109 2.499289 AGATGTGTTCATTCCTCGAGCT 59.501 45.455 6.99 0.00 34.06 4.09
109 110 2.898705 AGATGTGTTCATTCCTCGAGC 58.101 47.619 6.99 0.00 34.06 5.03
110 111 5.869753 AAAAGATGTGTTCATTCCTCGAG 57.130 39.130 5.13 5.13 34.06 4.04
134 135 3.078097 TCATTCCTCGATTCCGCAAAAA 58.922 40.909 0.00 0.00 35.37 1.94
135 136 2.705730 TCATTCCTCGATTCCGCAAAA 58.294 42.857 0.00 0.00 35.37 2.44
136 137 2.394930 TCATTCCTCGATTCCGCAAA 57.605 45.000 0.00 0.00 35.37 3.68
137 138 2.006888 GTTCATTCCTCGATTCCGCAA 58.993 47.619 0.00 0.00 35.37 4.85
138 139 1.066502 TGTTCATTCCTCGATTCCGCA 60.067 47.619 0.00 0.00 35.37 5.69
139 140 1.327764 GTGTTCATTCCTCGATTCCGC 59.672 52.381 0.00 0.00 35.37 5.54
140 141 2.616960 TGTGTTCATTCCTCGATTCCG 58.383 47.619 0.00 0.00 37.07 4.30
141 142 4.446371 AGATGTGTTCATTCCTCGATTCC 58.554 43.478 0.00 0.00 34.06 3.01
142 143 7.151308 AGATAGATGTGTTCATTCCTCGATTC 58.849 38.462 0.00 0.00 34.06 2.52
143 144 7.015098 AGAGATAGATGTGTTCATTCCTCGATT 59.985 37.037 0.00 0.00 34.06 3.34
144 145 6.493115 AGAGATAGATGTGTTCATTCCTCGAT 59.507 38.462 0.00 0.00 34.06 3.59
145 146 5.830457 AGAGATAGATGTGTTCATTCCTCGA 59.170 40.000 0.00 0.00 34.06 4.04
146 147 6.083098 AGAGATAGATGTGTTCATTCCTCG 57.917 41.667 0.00 0.00 34.06 4.63
147 148 6.267471 AGGAGAGATAGATGTGTTCATTCCTC 59.733 42.308 0.00 0.00 30.23 3.71
148 149 6.041865 CAGGAGAGATAGATGTGTTCATTCCT 59.958 42.308 0.00 0.00 33.94 3.36
180 181 2.703536 CAGCCCCCAAACCTAAAAGTTT 59.296 45.455 0.00 0.00 40.57 2.66
190 191 2.574018 GGTTGCTCAGCCCCCAAAC 61.574 63.158 0.00 0.00 0.00 2.93
242 245 0.168128 GCCACGTACACAAGAATGGC 59.832 55.000 0.00 0.00 45.26 4.40
256 259 3.121030 GGTAGCAGCACAGCCACG 61.121 66.667 0.00 0.00 34.23 4.94
261 264 2.167281 AGAGTACATGGTAGCAGCACAG 59.833 50.000 0.00 0.00 0.00 3.66
266 269 4.991153 TGAAGAGAGTACATGGTAGCAG 57.009 45.455 0.00 0.00 0.00 4.24
274 277 8.805175 CATTGATAGAGGATGAAGAGAGTACAT 58.195 37.037 0.00 0.00 0.00 2.29
291 294 4.152938 GCAGCGTATCATTGCATTGATAGA 59.847 41.667 24.60 9.88 38.83 1.98
309 312 1.144969 TTTTTCTGGACGTAGCAGCG 58.855 50.000 0.00 0.00 37.94 5.18
329 332 7.872993 ACTAATACACATAGCAGCGTATCATTT 59.127 33.333 0.00 0.00 0.00 2.32
368 372 3.777106 ATCAGAAACCTGCTTGAGACA 57.223 42.857 0.00 0.00 0.00 3.41
369 373 6.749923 AAATATCAGAAACCTGCTTGAGAC 57.250 37.500 0.00 0.00 0.00 3.36
393 397 2.288886 GGTTACTTCTTCGTGACTGGCT 60.289 50.000 0.00 0.00 0.00 4.75
396 400 4.238761 TCTGGTTACTTCTTCGTGACTG 57.761 45.455 0.00 0.00 0.00 3.51
397 401 4.262079 CCTTCTGGTTACTTCTTCGTGACT 60.262 45.833 0.00 0.00 0.00 3.41
403 407 7.764901 ACGATATTTCCTTCTGGTTACTTCTTC 59.235 37.037 0.00 0.00 34.23 2.87
491 1758 2.196749 CGTGTGCATATGTGTCTCTCC 58.803 52.381 4.29 0.00 0.00 3.71
492 1759 1.590238 GCGTGTGCATATGTGTCTCTC 59.410 52.381 4.29 0.00 42.15 3.20
502 1769 4.460683 GGACCCGGCGTGTGCATA 62.461 66.667 9.35 0.00 45.35 3.14
521 1788 1.969589 GGCGTGGTTTTGATCCGGT 60.970 57.895 0.00 0.00 0.00 5.28
549 1816 1.461091 GCCCCACATCGAGATACCGA 61.461 60.000 0.00 0.00 43.16 4.69
684 1954 0.776451 CGGGAAAATATCTCGCGTCG 59.224 55.000 5.77 0.00 46.67 5.12
793 2063 1.381165 AAAATATCCGCGTGGCCACC 61.381 55.000 29.95 20.55 34.14 4.61
795 2065 1.098712 GGAAAATATCCGCGTGGCCA 61.099 55.000 11.05 0.00 38.79 5.36
896 2181 2.761195 CGATGGCGACCTGAGACGA 61.761 63.158 0.00 0.00 40.82 4.20
897 2182 2.278206 CGATGGCGACCTGAGACG 60.278 66.667 0.00 0.00 40.82 4.18
898 2183 1.945354 TTCCGATGGCGACCTGAGAC 61.945 60.000 0.00 0.00 40.82 3.36
899 2184 1.680989 TTCCGATGGCGACCTGAGA 60.681 57.895 0.00 0.00 40.82 3.27
900 2185 1.519455 GTTCCGATGGCGACCTGAG 60.519 63.158 0.00 0.00 40.82 3.35
915 2200 0.672711 GGTTCCTGCTACCGGTGTTC 60.673 60.000 19.93 6.48 0.00 3.18
917 2202 2.590114 GGGTTCCTGCTACCGGTGT 61.590 63.158 19.93 0.00 36.49 4.16
922 2207 0.177373 CGTTAGGGGTTCCTGCTACC 59.823 60.000 0.00 0.00 44.61 3.18
950 2236 4.027295 GCTACAAACAATCTCGTGATCTCG 60.027 45.833 10.84 10.84 31.51 4.04
957 2243 4.327357 CGATCAAGCTACAAACAATCTCGT 59.673 41.667 0.00 0.00 0.00 4.18
1118 2415 2.677037 CGGAAGCACCCGTTAAAGAGAT 60.677 50.000 8.42 0.00 44.23 2.75
1150 2471 6.688578 AGATAAACGTCAAACTCTGCTTCTA 58.311 36.000 0.00 0.00 0.00 2.10
1464 2809 9.935682 TTATTACGAGAAGCAAAATCATCAATC 57.064 29.630 0.00 0.00 0.00 2.67
1473 2818 6.985188 AGCTCATTATTACGAGAAGCAAAA 57.015 33.333 0.00 0.00 0.00 2.44
1510 2855 3.800949 GCCCATGGTCAATACGAATACGA 60.801 47.826 11.73 0.00 42.66 3.43
1511 2856 2.478894 GCCCATGGTCAATACGAATACG 59.521 50.000 11.73 0.00 45.75 3.06
1512 2857 2.478894 CGCCCATGGTCAATACGAATAC 59.521 50.000 11.73 0.00 0.00 1.89
1513 2858 2.103432 ACGCCCATGGTCAATACGAATA 59.897 45.455 11.73 0.00 0.00 1.75
1514 2859 1.134220 ACGCCCATGGTCAATACGAAT 60.134 47.619 11.73 0.00 0.00 3.34
1515 2860 0.250793 ACGCCCATGGTCAATACGAA 59.749 50.000 11.73 0.00 0.00 3.85
1668 3015 5.527582 ACACTACAAGAAGCGAATCAAAGTT 59.472 36.000 0.00 0.00 0.00 2.66
1682 3029 7.540474 ACTCTAAAATCTCCACACTACAAGA 57.460 36.000 0.00 0.00 0.00 3.02
1733 3081 8.691661 ATTTACAGTTCAGACATACCAAACTT 57.308 30.769 0.00 0.00 0.00 2.66
1830 3178 8.258007 TCATGATTGTTCTAGATCCTAACGTTT 58.742 33.333 5.91 0.00 0.00 3.60
1831 3179 7.707035 GTCATGATTGTTCTAGATCCTAACGTT 59.293 37.037 5.88 5.88 0.00 3.99
1900 5532 2.769893 GGTGGCATGCAACTCAATTTT 58.230 42.857 24.21 0.00 0.00 1.82
1901 5533 1.337074 CGGTGGCATGCAACTCAATTT 60.337 47.619 24.21 0.00 0.00 1.82
1902 5534 0.244450 CGGTGGCATGCAACTCAATT 59.756 50.000 24.21 0.00 0.00 2.32
1907 5539 4.972733 TGGCGGTGGCATGCAACT 62.973 61.111 24.21 0.00 42.47 3.16
1977 5612 1.949525 GCAGCAGAACCAGTTTCTCAA 59.050 47.619 0.00 0.00 43.23 3.02
2008 5643 2.675348 GTTGTCAGTGATAGCTTCAGCC 59.325 50.000 0.00 0.00 43.38 4.85
2009 5644 2.675348 GGTTGTCAGTGATAGCTTCAGC 59.325 50.000 0.00 0.00 42.49 4.26
2010 5645 3.265791 GGGTTGTCAGTGATAGCTTCAG 58.734 50.000 0.00 0.00 34.17 3.02
2011 5646 2.027192 GGGGTTGTCAGTGATAGCTTCA 60.027 50.000 0.00 0.00 0.00 3.02
2012 5647 2.633488 GGGGTTGTCAGTGATAGCTTC 58.367 52.381 0.00 0.00 0.00 3.86
2013 5648 1.282157 GGGGGTTGTCAGTGATAGCTT 59.718 52.381 0.00 0.00 0.00 3.74
2014 5649 0.912486 GGGGGTTGTCAGTGATAGCT 59.088 55.000 0.00 0.00 0.00 3.32
2015 5650 3.478540 GGGGGTTGTCAGTGATAGC 57.521 57.895 0.00 0.00 0.00 2.97
2036 5671 0.250467 GCTCCTGCACCAAGTCAAGA 60.250 55.000 0.00 0.00 39.41 3.02
2381 6024 1.670674 GCACGACGTTCCCTGTGAATA 60.671 52.381 0.00 0.00 34.90 1.75
2457 6105 9.804758 AACTAGAAATATCTACCGTCTTCTTTG 57.195 33.333 0.00 0.00 37.10 2.77
2606 6261 0.937304 CCAACTCCAACACGTGTCAG 59.063 55.000 23.61 19.35 0.00 3.51
2681 6343 1.628846 AGAACCAGATAACAAGCGGGT 59.371 47.619 0.00 0.00 0.00 5.28
2685 6347 2.436417 TGGCAGAACCAGATAACAAGC 58.564 47.619 0.00 0.00 46.36 4.01
2703 6372 1.063006 CACGCATCATTCGGCTTGG 59.937 57.895 0.00 0.00 0.00 3.61
2759 6462 5.163561 CCGAACCACATATTAGTGCCATTTT 60.164 40.000 0.00 0.00 38.18 1.82
2790 6493 2.746362 CTCTGTTTCTGCAAAGCTAGGG 59.254 50.000 0.00 0.00 0.00 3.53
2903 6606 7.624549 ACATCGCCTTATATATGAACTGGATT 58.375 34.615 0.00 0.00 0.00 3.01
2977 6680 0.895100 GAGGGGCAGCATTTGTGTCA 60.895 55.000 0.00 0.00 0.00 3.58
3010 6713 3.624777 ACCAAAGACATGGATAGCAAGG 58.375 45.455 0.00 0.00 43.54 3.61
3012 6715 4.406456 ACAACCAAAGACATGGATAGCAA 58.594 39.130 0.00 0.00 43.54 3.91
3015 6718 5.241506 ACACAACAACCAAAGACATGGATAG 59.758 40.000 0.00 0.00 43.54 2.08
3030 6733 1.039856 ATTGCAGGGGACACAACAAC 58.960 50.000 0.00 0.00 32.44 3.32
3146 6849 4.462280 GACGGTGGCGGGTAAGGG 62.462 72.222 0.00 0.00 0.00 3.95
3227 6972 3.699894 CGTGGCTCTGGCTCTGGT 61.700 66.667 0.00 0.00 38.73 4.00
3246 6991 2.643232 GCTTGGGCTTTGGCTCTGG 61.643 63.158 0.00 0.00 40.19 3.86
3249 6994 2.283460 AGGCTTGGGCTTTGGCTC 60.283 61.111 0.00 0.00 39.89 4.70
3252 6997 2.643232 GCTGAGGCTTGGGCTTTGG 61.643 63.158 0.00 0.00 38.98 3.28
3253 6998 2.643232 GGCTGAGGCTTGGGCTTTG 61.643 63.158 0.00 0.00 38.98 2.77
3254 6999 2.283460 GGCTGAGGCTTGGGCTTT 60.283 61.111 0.00 0.00 38.98 3.51
3255 7000 3.263259 AGGCTGAGGCTTGGGCTT 61.263 61.111 1.28 0.00 38.98 4.35
3256 7001 4.044439 CAGGCTGAGGCTTGGGCT 62.044 66.667 9.42 10.08 41.09 5.19
3257 7002 3.991725 CTCAGGCTGAGGCTTGGGC 62.992 68.421 32.31 6.19 44.26 5.36
3258 7003 2.271497 CTCAGGCTGAGGCTTGGG 59.729 66.667 32.31 9.78 44.26 4.12
3259 7004 2.438075 GCTCAGGCTGAGGCTTGG 60.438 66.667 37.73 18.69 44.43 3.61
3268 7013 3.715097 GTGGCTCAGGCTCAGGCT 61.715 66.667 14.06 0.00 39.66 4.58


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

AutoCloner maintained by Alex Coulton.