Multiple sequence alignment - TraesCS4D01G211600

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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 TraesCS4D01G211600 chr4D 100.000 6005 0 0 1 6005 364027390 364033394 0 11090
1 TraesCS4D01G211600 chr4A 93.872 4928 197 45 1141 6005 100968381 100963496 0 7330
2 TraesCS4D01G211600 chr4A 88.486 1103 36 27 97 1141 100969495 100968426 0 1249
3 TraesCS4D01G211600 chr4B 94.325 3119 117 24 1140 4222 449503184 449506278 0 4724
4 TraesCS4D01G211600 chr4B 96.256 1095 28 4 4220 5303 449506307 449507399 0 1783
5 TraesCS4D01G211600 chr4B 89.927 1092 37 22 95 1143 449502081 449503142 0 1339
6 TraesCS4D01G211600 chr4B 92.898 704 39 4 5310 6005 449509609 449510309 0 1013


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 TraesCS4D01G211600 chr4D 364027390 364033394 6004 False 11090.00 11090 100.0000 1 6005 1 chr4D.!!$F1 6004
1 TraesCS4D01G211600 chr4A 100963496 100969495 5999 True 4289.50 7330 91.1790 97 6005 2 chr4A.!!$R1 5908
2 TraesCS4D01G211600 chr4B 449502081 449510309 8228 False 2214.75 4724 93.3515 95 6005 4 chr4B.!!$F1 5910

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
90 91 0.037232 GCTAGGCTGAGTTGAACGGT 60.037 55.000 0.00 0.00 0.00 4.83 F
355 373 0.249489 GCGTACTCTTCCCGCATCAT 60.249 55.000 0.00 0.00 46.26 2.45 F
400 423 1.005394 GTTCCCGCGTTTCTCCAGA 60.005 57.895 4.92 0.00 0.00 3.86 F
401 424 1.014564 GTTCCCGCGTTTCTCCAGAG 61.015 60.000 4.92 0.00 0.00 3.35 F
1124 1187 1.343510 TTTTACGTACTTCGGCGGCG 61.344 55.000 27.15 27.15 44.69 6.46 F
2001 2133 0.729116 GTGTCGGCTCATGATGGTTG 59.271 55.000 0.00 0.00 0.00 3.77 F
2612 2753 0.390735 AATGTAACCCTGTCCGTCGC 60.391 55.000 0.00 0.00 0.00 5.19 F
3950 4100 0.392193 GACCTCACCACATGCCTGAG 60.392 60.000 0.00 7.57 32.66 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1077 0.108329 AGTTCTGATTACCGTGGCCG 60.108 55.0 0.00 0.00 0.00 6.13 R
1612 1742 0.254178 CAATCAGGGTCAGGGTCAGG 59.746 60.0 0.00 0.00 0.00 3.86 R
1613 1743 0.393537 GCAATCAGGGTCAGGGTCAG 60.394 60.0 0.00 0.00 0.00 3.51 R
1899 2031 1.176527 CTTGTTCGGCACCATGGAAT 58.823 50.0 21.47 0.00 0.00 3.01 R
2593 2734 0.390735 GCGACGGACAGGGTTACATT 60.391 55.0 0.00 0.00 0.00 2.71 R
3950 4100 0.394565 ACAGACACAGGCCTCTTGTC 59.605 55.0 26.96 26.96 40.04 3.18 R
4292 4474 1.027357 GTAGCCTGCAATCATGTGGG 58.973 55.0 0.00 0.00 0.00 4.61 R
5412 7829 0.179468 TTATGTTGTAGAGGCCGCCC 59.821 55.0 5.55 0.00 0.00 6.13 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
17 18 2.514824 GGGATGAAGTGGGCGCTC 60.515 66.667 7.64 2.47 0.00 5.03
18 19 2.514824 GGATGAAGTGGGCGCTCC 60.515 66.667 3.94 6.36 0.00 4.70
19 20 2.892425 GATGAAGTGGGCGCTCCG 60.892 66.667 3.94 0.00 38.76 4.63
30 31 4.108902 CGCTCCGCTTAATGCTGA 57.891 55.556 0.00 0.00 40.11 4.26
31 32 1.638467 CGCTCCGCTTAATGCTGAC 59.362 57.895 0.00 0.00 40.11 3.51
32 33 0.807667 CGCTCCGCTTAATGCTGACT 60.808 55.000 0.00 0.00 40.11 3.41
33 34 0.654683 GCTCCGCTTAATGCTGACTG 59.345 55.000 0.00 0.00 40.11 3.51
34 35 1.740380 GCTCCGCTTAATGCTGACTGA 60.740 52.381 0.00 0.00 40.11 3.41
35 36 2.831333 CTCCGCTTAATGCTGACTGAT 58.169 47.619 0.00 0.00 40.11 2.90
36 37 2.543012 CTCCGCTTAATGCTGACTGATG 59.457 50.000 0.00 0.00 40.11 3.07
37 38 2.093500 TCCGCTTAATGCTGACTGATGT 60.093 45.455 0.00 0.00 40.11 3.06
38 39 2.031314 CCGCTTAATGCTGACTGATGTG 59.969 50.000 0.00 0.00 40.11 3.21
39 40 2.538333 CGCTTAATGCTGACTGATGTGC 60.538 50.000 0.00 0.00 40.11 4.57
40 41 2.538333 GCTTAATGCTGACTGATGTGCG 60.538 50.000 0.00 0.00 38.95 5.34
41 42 2.385013 TAATGCTGACTGATGTGCGT 57.615 45.000 0.00 0.00 0.00 5.24
42 43 2.385013 AATGCTGACTGATGTGCGTA 57.615 45.000 0.00 0.00 0.00 4.42
43 44 2.609427 ATGCTGACTGATGTGCGTAT 57.391 45.000 0.00 0.00 0.00 3.06
44 45 3.733443 ATGCTGACTGATGTGCGTATA 57.267 42.857 0.00 0.00 0.00 1.47
45 46 3.518634 TGCTGACTGATGTGCGTATAA 57.481 42.857 0.00 0.00 0.00 0.98
46 47 3.855858 TGCTGACTGATGTGCGTATAAA 58.144 40.909 0.00 0.00 0.00 1.40
47 48 4.441792 TGCTGACTGATGTGCGTATAAAT 58.558 39.130 0.00 0.00 0.00 1.40
48 49 4.270808 TGCTGACTGATGTGCGTATAAATG 59.729 41.667 0.00 0.00 0.00 2.32
49 50 4.271049 GCTGACTGATGTGCGTATAAATGT 59.729 41.667 0.00 0.00 0.00 2.71
50 51 5.557136 GCTGACTGATGTGCGTATAAATGTC 60.557 44.000 0.00 0.00 0.00 3.06
51 52 4.808895 TGACTGATGTGCGTATAAATGTCC 59.191 41.667 0.00 0.00 0.00 4.02
52 53 3.802139 ACTGATGTGCGTATAAATGTCCG 59.198 43.478 0.00 0.00 0.00 4.79
53 54 3.127589 TGATGTGCGTATAAATGTCCGG 58.872 45.455 0.00 0.00 0.00 5.14
54 55 2.963548 TGTGCGTATAAATGTCCGGA 57.036 45.000 0.00 0.00 0.00 5.14
55 56 3.248495 TGTGCGTATAAATGTCCGGAA 57.752 42.857 5.23 0.00 0.00 4.30
56 57 2.931325 TGTGCGTATAAATGTCCGGAAC 59.069 45.455 5.23 0.59 0.00 3.62
57 58 2.931325 GTGCGTATAAATGTCCGGAACA 59.069 45.455 5.23 7.54 43.51 3.18
64 65 1.302949 ATGTCCGGAACATGGGTGG 59.697 57.895 5.23 0.00 47.00 4.61
65 66 2.045340 GTCCGGAACATGGGTGGG 60.045 66.667 5.23 0.00 0.00 4.61
66 67 2.530661 TCCGGAACATGGGTGGGT 60.531 61.111 0.00 0.00 0.00 4.51
67 68 2.361104 CCGGAACATGGGTGGGTG 60.361 66.667 0.00 0.00 0.00 4.61
68 69 2.434331 CGGAACATGGGTGGGTGT 59.566 61.111 0.00 0.00 0.00 4.16
69 70 1.971167 CGGAACATGGGTGGGTGTG 60.971 63.158 0.00 0.00 0.00 3.82
70 71 1.606313 GGAACATGGGTGGGTGTGG 60.606 63.158 0.00 0.00 0.00 4.17
71 72 1.606313 GAACATGGGTGGGTGTGGG 60.606 63.158 0.00 0.00 0.00 4.61
72 73 3.826265 AACATGGGTGGGTGTGGGC 62.826 63.158 0.00 0.00 0.00 5.36
73 74 3.983420 CATGGGTGGGTGTGGGCT 61.983 66.667 0.00 0.00 0.00 5.19
74 75 2.204228 ATGGGTGGGTGTGGGCTA 60.204 61.111 0.00 0.00 0.00 3.93
75 76 2.308722 ATGGGTGGGTGTGGGCTAG 61.309 63.158 0.00 0.00 0.00 3.42
76 77 3.728373 GGGTGGGTGTGGGCTAGG 61.728 72.222 0.00 0.00 0.00 3.02
77 78 4.426313 GGTGGGTGTGGGCTAGGC 62.426 72.222 8.00 8.00 0.00 3.93
78 79 3.330720 GTGGGTGTGGGCTAGGCT 61.331 66.667 16.80 0.00 0.00 4.58
79 80 3.329889 TGGGTGTGGGCTAGGCTG 61.330 66.667 16.80 0.00 0.00 4.85
80 81 3.009115 GGGTGTGGGCTAGGCTGA 61.009 66.667 16.80 0.02 0.00 4.26
81 82 2.586792 GGTGTGGGCTAGGCTGAG 59.413 66.667 16.80 0.00 0.00 3.35
82 83 2.294078 GGTGTGGGCTAGGCTGAGT 61.294 63.158 16.80 0.00 0.00 3.41
83 84 1.679898 GTGTGGGCTAGGCTGAGTT 59.320 57.895 16.80 0.00 0.00 3.01
84 85 0.674895 GTGTGGGCTAGGCTGAGTTG 60.675 60.000 16.80 0.00 0.00 3.16
85 86 0.835971 TGTGGGCTAGGCTGAGTTGA 60.836 55.000 16.80 0.00 0.00 3.18
86 87 0.324943 GTGGGCTAGGCTGAGTTGAA 59.675 55.000 16.80 0.00 0.00 2.69
87 88 0.324943 TGGGCTAGGCTGAGTTGAAC 59.675 55.000 16.80 0.00 0.00 3.18
88 89 0.741221 GGGCTAGGCTGAGTTGAACG 60.741 60.000 16.80 0.00 0.00 3.95
89 90 0.741221 GGCTAGGCTGAGTTGAACGG 60.741 60.000 9.46 0.00 0.00 4.44
90 91 0.037232 GCTAGGCTGAGTTGAACGGT 60.037 55.000 0.00 0.00 0.00 4.83
91 92 1.203994 GCTAGGCTGAGTTGAACGGTA 59.796 52.381 0.00 0.00 0.00 4.02
92 93 2.353406 GCTAGGCTGAGTTGAACGGTAA 60.353 50.000 0.00 0.00 0.00 2.85
93 94 2.165319 AGGCTGAGTTGAACGGTAAC 57.835 50.000 0.00 0.00 0.00 2.50
104 105 7.710044 TGAGTTGAACGGTAACATTGTTACTAA 59.290 33.333 29.24 17.78 0.00 2.24
131 132 2.413453 CGCTGGCTCTCTTGTTTAACTC 59.587 50.000 0.00 0.00 0.00 3.01
135 136 4.632153 TGGCTCTCTTGTTTAACTCTGTC 58.368 43.478 0.00 0.00 0.00 3.51
185 186 1.794714 ATTCGTGGATGACCCTAGCT 58.205 50.000 0.00 0.00 35.38 3.32
186 187 2.447408 TTCGTGGATGACCCTAGCTA 57.553 50.000 0.00 0.00 35.38 3.32
187 188 1.982660 TCGTGGATGACCCTAGCTAG 58.017 55.000 14.20 14.20 35.38 3.42
188 189 0.315568 CGTGGATGACCCTAGCTAGC 59.684 60.000 15.74 6.62 35.38 3.42
210 216 2.283604 TGGCTACCACCGAGCTCA 60.284 61.111 15.40 0.00 39.98 4.26
354 372 1.141019 GCGTACTCTTCCCGCATCA 59.859 57.895 0.00 0.00 46.26 3.07
355 373 0.249489 GCGTACTCTTCCCGCATCAT 60.249 55.000 0.00 0.00 46.26 2.45
357 375 1.772182 GTACTCTTCCCGCATCATCG 58.228 55.000 0.00 0.00 0.00 3.84
359 377 1.958205 CTCTTCCCGCATCATCGCC 60.958 63.158 0.00 0.00 0.00 5.54
360 378 2.974698 CTTCCCGCATCATCGCCC 60.975 66.667 0.00 0.00 0.00 6.13
361 379 4.908687 TTCCCGCATCATCGCCCG 62.909 66.667 0.00 0.00 0.00 6.13
395 418 4.692475 CCCCGTTCCCGCGTTTCT 62.692 66.667 4.92 0.00 0.00 2.52
396 419 3.116531 CCCGTTCCCGCGTTTCTC 61.117 66.667 4.92 0.00 0.00 2.87
397 420 3.116531 CCGTTCCCGCGTTTCTCC 61.117 66.667 4.92 0.00 0.00 3.71
398 421 2.356553 CGTTCCCGCGTTTCTCCA 60.357 61.111 4.92 0.00 0.00 3.86
399 422 2.380410 CGTTCCCGCGTTTCTCCAG 61.380 63.158 4.92 0.00 0.00 3.86
400 423 1.005394 GTTCCCGCGTTTCTCCAGA 60.005 57.895 4.92 0.00 0.00 3.86
401 424 1.014564 GTTCCCGCGTTTCTCCAGAG 61.015 60.000 4.92 0.00 0.00 3.35
402 425 2.781595 TTCCCGCGTTTCTCCAGAGC 62.782 60.000 4.92 0.00 0.00 4.09
403 426 2.048222 CCGCGTTTCTCCAGAGCA 60.048 61.111 4.92 0.00 0.00 4.26
432 455 8.568732 TCCACGAAAAACATAACAAAGAAATC 57.431 30.769 0.00 0.00 0.00 2.17
629 656 3.112709 GCCGGGATCGCGCTAATC 61.113 66.667 25.28 8.51 34.56 1.75
760 787 3.121030 CCTTTCTGTCGCGGCCAG 61.121 66.667 8.89 14.25 0.00 4.85
814 850 3.711782 CCCCCTCTTCCCCTCCCT 61.712 72.222 0.00 0.00 0.00 4.20
896 938 3.849953 GTGATCGCCGCCGTTGTC 61.850 66.667 0.00 0.00 35.54 3.18
1032 1077 3.321497 CTCGAGGGCTTATAATCAGTGC 58.679 50.000 3.91 0.00 0.00 4.40
1046 1091 2.435234 GTGCGGCCACGGTAATCA 60.435 61.111 2.24 0.00 41.36 2.57
1047 1092 2.125310 TGCGGCCACGGTAATCAG 60.125 61.111 2.24 0.00 41.36 2.90
1069 1132 7.524294 CAGAACTCTCTGCTCTTCTATTTTC 57.476 40.000 0.00 0.00 42.66 2.29
1084 1147 2.973419 TTTTCATTACCGTTGCCGTC 57.027 45.000 0.00 0.00 0.00 4.79
1094 1157 4.634703 TTGCCGTCCGTGCATGGT 62.635 61.111 24.24 0.00 38.76 3.55
1124 1187 1.343510 TTTTACGTACTTCGGCGGCG 61.344 55.000 27.15 27.15 44.69 6.46
1125 1188 3.681961 TTACGTACTTCGGCGGCGG 62.682 63.158 31.73 18.65 44.69 6.13
1153 1261 4.091509 CGTCGTTCTCCTTTCGATTTGAAT 59.908 41.667 0.00 0.00 36.22 2.57
1171 1279 1.792006 ATCGTGAGGTCGTTTCAACC 58.208 50.000 0.00 0.00 37.03 3.77
1488 1617 9.484326 CAAATTATGTTGCAATCAATCAATGTG 57.516 29.630 0.59 6.36 34.29 3.21
1549 1678 6.208204 GCATGCTATATTCACAAGAGGGAAAT 59.792 38.462 11.37 0.00 0.00 2.17
1612 1742 2.094182 TCCGCCAAGATAGTGACTGAAC 60.094 50.000 0.00 0.00 0.00 3.18
1613 1743 2.271800 CGCCAAGATAGTGACTGAACC 58.728 52.381 0.00 0.00 0.00 3.62
1614 1744 2.093973 CGCCAAGATAGTGACTGAACCT 60.094 50.000 0.00 0.00 0.00 3.50
1615 1745 3.265791 GCCAAGATAGTGACTGAACCTG 58.734 50.000 0.00 0.00 0.00 4.00
1616 1746 3.055819 GCCAAGATAGTGACTGAACCTGA 60.056 47.826 0.00 0.00 0.00 3.86
1617 1747 4.499183 CCAAGATAGTGACTGAACCTGAC 58.501 47.826 0.00 0.00 0.00 3.51
1714 1845 1.945394 GTGATTAGGACGGCGTAGAGA 59.055 52.381 14.74 0.00 0.00 3.10
1808 1939 2.857592 ATTCCGCATTTGTCATCTGC 57.142 45.000 0.00 0.00 0.00 4.26
1854 1986 8.656849 CCATTAAGCGCCTAATAGTAACAATAG 58.343 37.037 10.82 0.00 0.00 1.73
1887 2019 5.186198 AGGATGTAGTTAAGCGCTGATTTT 58.814 37.500 12.58 0.00 0.00 1.82
1899 2031 4.458989 AGCGCTGATTTTATTTGAGTGGAA 59.541 37.500 10.39 0.00 0.00 3.53
1938 2070 4.592485 AGAACAGTTCCTGTAGTCTGTG 57.408 45.455 9.85 0.00 44.62 3.66
1996 2128 1.135915 GTCAGAGTGTCGGCTCATGAT 59.864 52.381 0.00 0.00 37.94 2.45
2001 2133 0.729116 GTGTCGGCTCATGATGGTTG 59.271 55.000 0.00 0.00 0.00 3.77
2147 2283 3.211045 GACATTTCGCTTGGGCCTATTA 58.789 45.455 4.53 0.00 34.44 0.98
2148 2284 3.821033 GACATTTCGCTTGGGCCTATTAT 59.179 43.478 4.53 0.00 34.44 1.28
2307 2443 3.351450 GGCAACAAGAACCGGTCC 58.649 61.111 8.04 0.00 0.00 4.46
2388 2525 4.158949 CCTGAAATTCCATTGCATGAGTCA 59.841 41.667 0.00 0.00 0.00 3.41
2402 2539 4.655027 CATGAGTCACATTCAATTCACCG 58.345 43.478 0.00 0.00 37.07 4.94
2413 2550 5.398603 TTCAATTCACCGCCACATTTATT 57.601 34.783 0.00 0.00 0.00 1.40
2426 2563 6.563422 GCCACATTTATTCAAGCACTTCATA 58.437 36.000 0.00 0.00 0.00 2.15
2427 2564 6.473455 GCCACATTTATTCAAGCACTTCATAC 59.527 38.462 0.00 0.00 0.00 2.39
2432 2569 9.722056 CATTTATTCAAGCACTTCATACTAACC 57.278 33.333 0.00 0.00 0.00 2.85
2452 2589 4.380531 ACCTATTTTGTGCGATCATCGAT 58.619 39.130 12.38 0.00 43.74 3.59
2580 2721 1.892209 AGCCAAACGTCCTAAAGGTG 58.108 50.000 0.00 0.00 36.34 4.00
2591 2732 4.506654 CGTCCTAAAGGTGCACATATACAC 59.493 45.833 20.43 4.93 36.34 2.90
2606 2747 6.260050 CACATATACACCAATGTAACCCTGTC 59.740 42.308 0.00 0.00 44.47 3.51
2612 2753 0.390735 AATGTAACCCTGTCCGTCGC 60.391 55.000 0.00 0.00 0.00 5.19
2624 2765 3.479269 CGTCGCGCCTTTCTGGTC 61.479 66.667 0.00 0.00 38.35 4.02
2627 2768 1.959226 TCGCGCCTTTCTGGTCAAC 60.959 57.895 0.00 0.00 38.35 3.18
2628 2769 1.961277 CGCGCCTTTCTGGTCAACT 60.961 57.895 0.00 0.00 38.35 3.16
2633 2774 3.190874 CGCCTTTCTGGTCAACTATCTC 58.809 50.000 0.00 0.00 38.35 2.75
2634 2775 3.190874 GCCTTTCTGGTCAACTATCTCG 58.809 50.000 0.00 0.00 38.35 4.04
2636 2777 4.177026 CCTTTCTGGTCAACTATCTCGTG 58.823 47.826 0.00 0.00 0.00 4.35
2637 2778 4.082190 CCTTTCTGGTCAACTATCTCGTGA 60.082 45.833 0.00 0.00 0.00 4.35
2648 2791 6.150474 TCAACTATCTCGTGACAGTGTGATTA 59.850 38.462 0.00 0.00 29.29 1.75
2837 2980 1.000866 GCCTTTCCTCCAATGCCCT 59.999 57.895 0.00 0.00 0.00 5.19
2861 3004 7.226720 CCTTGAAAGAGCTAGTGTGTAAAGAAA 59.773 37.037 0.00 0.00 0.00 2.52
2863 3006 6.482308 TGAAAGAGCTAGTGTGTAAAGAAACC 59.518 38.462 0.00 0.00 0.00 3.27
2957 3100 3.939740 ATGTACTGGCATCCTCAATGT 57.060 42.857 0.00 0.00 37.71 2.71
2978 3121 0.884704 TCCGTTGCTCTTCTTGCACC 60.885 55.000 0.00 0.00 40.40 5.01
3056 3201 1.000717 CGGCGGGAATTGAACTGTTTT 60.001 47.619 0.00 0.00 0.00 2.43
3109 3257 7.444183 TCCTTTAAACTGTATTCAGGTGTCTTG 59.556 37.037 4.24 0.00 41.20 3.02
3126 3274 6.294010 GGTGTCTTGGAAAATAGAAAGTGACC 60.294 42.308 0.00 0.00 0.00 4.02
3142 3292 2.289820 GTGACCGTCACCCTTTTTCTTC 59.710 50.000 19.30 0.00 41.37 2.87
3143 3293 2.092861 TGACCGTCACCCTTTTTCTTCA 60.093 45.455 0.00 0.00 0.00 3.02
3145 3295 3.146847 ACCGTCACCCTTTTTCTTCATC 58.853 45.455 0.00 0.00 0.00 2.92
3146 3296 3.181443 ACCGTCACCCTTTTTCTTCATCT 60.181 43.478 0.00 0.00 0.00 2.90
3147 3297 3.821033 CCGTCACCCTTTTTCTTCATCTT 59.179 43.478 0.00 0.00 0.00 2.40
3148 3298 4.278419 CCGTCACCCTTTTTCTTCATCTTT 59.722 41.667 0.00 0.00 0.00 2.52
3149 3299 5.215160 CGTCACCCTTTTTCTTCATCTTTG 58.785 41.667 0.00 0.00 0.00 2.77
3150 3300 5.221048 CGTCACCCTTTTTCTTCATCTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
3151 3301 6.017440 CGTCACCCTTTTTCTTCATCTTTGTA 60.017 38.462 0.00 0.00 0.00 2.41
3192 3342 1.305219 GCGCAGAGCCATACCACAAA 61.305 55.000 0.30 0.00 40.81 2.83
3208 3358 3.569701 CCACAAATTGTGCTACAAGGAGT 59.430 43.478 19.82 3.77 46.51 3.85
3275 3425 2.493675 TCTCTGAATGAACTCCGTCTGG 59.506 50.000 0.00 0.00 0.00 3.86
3440 3590 2.279918 GACCGCACACCTCGTTGT 60.280 61.111 0.00 0.00 0.00 3.32
3519 3669 1.341383 GGAGATGAATGCTTGGGGTGT 60.341 52.381 0.00 0.00 0.00 4.16
3609 3759 0.620556 ATTGCCTCTCCAACCACGAT 59.379 50.000 0.00 0.00 0.00 3.73
3865 4015 6.017934 TGCAAAGTGAGTTCTTATGTTCAGTC 60.018 38.462 0.00 0.00 0.00 3.51
3886 4036 1.255600 GATCGGTCGAAGCAAATCGTC 59.744 52.381 0.00 1.87 43.19 4.20
3950 4100 0.392193 GACCTCACCACATGCCTGAG 60.392 60.000 0.00 7.57 32.66 3.35
4117 4268 1.477558 CCAGGATTGGTGGACATAGGC 60.478 57.143 0.00 0.00 39.79 3.93
4374 4556 1.897398 GCGCCTCAAAGGTACGTGTG 61.897 60.000 0.00 0.00 37.80 3.82
4417 4599 4.073293 ACCTTCTACGGCCATATTTCTG 57.927 45.455 2.24 0.00 0.00 3.02
4419 4601 4.080526 ACCTTCTACGGCCATATTTCTGTT 60.081 41.667 2.24 0.00 0.00 3.16
4421 4603 5.465724 CCTTCTACGGCCATATTTCTGTTAC 59.534 44.000 2.24 0.00 0.00 2.50
4466 4651 1.334869 CGATTAATGGCACCTTCAGGC 59.665 52.381 0.00 0.00 39.32 4.85
4706 4891 0.518636 CCAATGACACCTCAACAGCG 59.481 55.000 0.00 0.00 0.00 5.18
4793 4978 5.286267 ACCATATACGTTTAACTGGAGGG 57.714 43.478 11.25 0.00 0.00 4.30
4850 5035 5.735285 ATCGGAGAAATGCAGAGATCATA 57.265 39.130 0.00 0.00 43.58 2.15
4885 5070 5.426689 AGGAGATGAATGTGCTACAGAAA 57.573 39.130 0.00 0.00 0.00 2.52
4997 5182 7.072961 AGGATGGAAGGTGTAATAAGATGACAT 59.927 37.037 0.00 0.00 0.00 3.06
4998 5183 8.375506 GGATGGAAGGTGTAATAAGATGACATA 58.624 37.037 0.00 0.00 0.00 2.29
5028 5213 8.746052 AAATACCAATGTAACTAGCAGCATTA 57.254 30.769 0.00 0.00 31.29 1.90
5194 5389 3.243771 CCATTAACCTCGAATCCTACGCT 60.244 47.826 0.00 0.00 0.00 5.07
5236 5431 5.589367 ACCTATCCATTAGCACCAATCAT 57.411 39.130 0.00 0.00 0.00 2.45
5296 5503 5.509501 GCAAGTCAGAAATGGAACCAAATGA 60.510 40.000 0.00 0.00 0.00 2.57
5303 5510 6.755141 CAGAAATGGAACCAAATGACATCATC 59.245 38.462 0.00 0.00 35.10 2.92
5304 5511 6.438108 AGAAATGGAACCAAATGACATCATCA 59.562 34.615 0.00 0.00 43.13 3.07
5345 7759 6.513393 CGAAGCATCAAACAGAGTTTACCTTT 60.513 38.462 0.00 0.00 0.00 3.11
5388 7805 1.202794 TGCTGTGGATCAGTTCTTGCA 60.203 47.619 0.00 0.00 45.23 4.08
5397 7814 4.507710 GATCAGTTCTTGCAGTCCATACA 58.492 43.478 0.00 0.00 0.00 2.29
5398 7815 3.930336 TCAGTTCTTGCAGTCCATACAG 58.070 45.455 0.00 0.00 0.00 2.74
5431 7848 0.179468 GGGCGGCCTCTACAACATAA 59.821 55.000 22.87 0.00 0.00 1.90
5491 7908 3.066621 TGTCTTCACCATGAGTTGTTTGC 59.933 43.478 0.00 0.00 0.00 3.68
5507 7924 8.722342 AGTTGTTTGCGTATGTTTTTATGTAG 57.278 30.769 0.00 0.00 0.00 2.74
5517 7934 3.754323 TGTTTTTATGTAGAAGGCCACCG 59.246 43.478 5.01 0.00 0.00 4.94
5547 7964 6.286758 TGCAGGATAAGAAACAAAAATGCAA 58.713 32.000 0.00 0.00 37.04 4.08
5554 7971 9.679596 GATAAGAAACAAAAATGCAATCAATCG 57.320 29.630 0.00 0.00 0.00 3.34
5562 7979 3.558931 ATGCAATCAATCGGTCCAGTA 57.441 42.857 0.00 0.00 0.00 2.74
5570 7987 7.409697 CAATCAATCGGTCCAGTAATAAACAG 58.590 38.462 0.00 0.00 0.00 3.16
5625 8042 7.734942 TGATAGAAGTACATAATCACCATGCA 58.265 34.615 0.00 0.00 0.00 3.96
5644 8061 1.545706 AAGGACGAGGCAGGAGGAAC 61.546 60.000 0.00 0.00 0.00 3.62
5677 8094 7.724061 ACTTTTACAATGTCAGACCCAGTAATT 59.276 33.333 0.00 0.00 0.00 1.40
5678 8095 9.226606 CTTTTACAATGTCAGACCCAGTAATTA 57.773 33.333 0.00 0.00 0.00 1.40
5694 8111 6.418956 CAGTAATTATGCAACATCGGTACAC 58.581 40.000 0.00 0.00 0.00 2.90
5773 8193 8.879759 GGATCGATACATCAGAAAGTTTAACAA 58.120 33.333 1.67 0.00 0.00 2.83
5774 8194 9.690434 GATCGATACATCAGAAAGTTTAACAAC 57.310 33.333 0.00 0.00 0.00 3.32
5775 8195 8.596271 TCGATACATCAGAAAGTTTAACAACA 57.404 30.769 0.00 0.00 35.05 3.33
5799 8223 8.043113 ACAGAGAAGATAGTGCAACATAAATCA 58.957 33.333 0.00 0.00 41.43 2.57
5815 8239 6.264067 ACATAAATCAAGATAGAGCTTTGGCC 59.736 38.462 0.00 0.00 39.73 5.36
5877 8301 6.030734 AGATCCAGGATCCATATCAAGATGT 58.969 40.000 24.02 0.00 39.66 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.514824 GAGCGCCCACTTCATCCC 60.515 66.667 2.29 0.00 0.00 3.85
1 2 2.514824 GGAGCGCCCACTTCATCC 60.515 66.667 2.29 0.00 34.14 3.51
2 3 2.892425 CGGAGCGCCCACTTCATC 60.892 66.667 2.29 0.00 34.14 2.92
19 20 2.538333 CGCACATCAGTCAGCATTAAGC 60.538 50.000 0.00 0.00 46.19 3.09
20 21 2.674852 ACGCACATCAGTCAGCATTAAG 59.325 45.455 0.00 0.00 0.00 1.85
21 22 2.698803 ACGCACATCAGTCAGCATTAA 58.301 42.857 0.00 0.00 0.00 1.40
22 23 2.385013 ACGCACATCAGTCAGCATTA 57.615 45.000 0.00 0.00 0.00 1.90
23 24 2.385013 TACGCACATCAGTCAGCATT 57.615 45.000 0.00 0.00 0.00 3.56
24 25 2.609427 ATACGCACATCAGTCAGCAT 57.391 45.000 0.00 0.00 0.00 3.79
25 26 3.518634 TTATACGCACATCAGTCAGCA 57.481 42.857 0.00 0.00 0.00 4.41
26 27 4.271049 ACATTTATACGCACATCAGTCAGC 59.729 41.667 0.00 0.00 0.00 4.26
27 28 5.050769 GGACATTTATACGCACATCAGTCAG 60.051 44.000 0.00 0.00 0.00 3.51
28 29 4.808895 GGACATTTATACGCACATCAGTCA 59.191 41.667 0.00 0.00 0.00 3.41
29 30 4.085055 CGGACATTTATACGCACATCAGTC 60.085 45.833 0.00 0.00 0.00 3.51
30 31 3.802139 CGGACATTTATACGCACATCAGT 59.198 43.478 0.00 0.00 0.00 3.41
31 32 3.184379 CCGGACATTTATACGCACATCAG 59.816 47.826 0.00 0.00 0.00 2.90
32 33 3.127589 CCGGACATTTATACGCACATCA 58.872 45.455 0.00 0.00 0.00 3.07
33 34 3.386486 TCCGGACATTTATACGCACATC 58.614 45.455 0.00 0.00 0.00 3.06
34 35 3.462483 TCCGGACATTTATACGCACAT 57.538 42.857 0.00 0.00 0.00 3.21
35 36 2.931325 GTTCCGGACATTTATACGCACA 59.069 45.455 1.83 0.00 0.00 4.57
36 37 2.931325 TGTTCCGGACATTTATACGCAC 59.069 45.455 1.83 0.00 32.00 5.34
37 38 3.248495 TGTTCCGGACATTTATACGCA 57.752 42.857 1.83 0.00 32.00 5.24
38 39 3.059188 CCATGTTCCGGACATTTATACGC 60.059 47.826 1.83 0.00 46.80 4.42
39 40 3.496884 CCCATGTTCCGGACATTTATACG 59.503 47.826 1.83 0.00 46.80 3.06
40 41 4.274950 CACCCATGTTCCGGACATTTATAC 59.725 45.833 1.83 0.00 46.80 1.47
41 42 4.456535 CACCCATGTTCCGGACATTTATA 58.543 43.478 1.83 0.00 46.80 0.98
42 43 3.287222 CACCCATGTTCCGGACATTTAT 58.713 45.455 1.83 0.00 46.80 1.40
43 44 2.619332 CCACCCATGTTCCGGACATTTA 60.619 50.000 1.83 0.00 46.80 1.40
44 45 1.544724 CACCCATGTTCCGGACATTT 58.455 50.000 1.83 0.00 46.80 2.32
45 46 0.323360 CCACCCATGTTCCGGACATT 60.323 55.000 1.83 0.00 46.80 2.71
47 48 2.753701 CCACCCATGTTCCGGACA 59.246 61.111 1.83 6.40 43.71 4.02
48 49 2.045340 CCCACCCATGTTCCGGAC 60.045 66.667 1.83 0.00 0.00 4.79
49 50 2.530661 ACCCACCCATGTTCCGGA 60.531 61.111 0.00 0.00 0.00 5.14
50 51 2.361104 CACCCACCCATGTTCCGG 60.361 66.667 0.00 0.00 0.00 5.14
51 52 1.971167 CACACCCACCCATGTTCCG 60.971 63.158 0.00 0.00 0.00 4.30
52 53 1.606313 CCACACCCACCCATGTTCC 60.606 63.158 0.00 0.00 0.00 3.62
53 54 1.606313 CCCACACCCACCCATGTTC 60.606 63.158 0.00 0.00 0.00 3.18
54 55 2.525592 CCCACACCCACCCATGTT 59.474 61.111 0.00 0.00 0.00 2.71
55 56 4.299796 GCCCACACCCACCCATGT 62.300 66.667 0.00 0.00 0.00 3.21
56 57 2.556840 CTAGCCCACACCCACCCATG 62.557 65.000 0.00 0.00 0.00 3.66
57 58 2.204228 TAGCCCACACCCACCCAT 60.204 61.111 0.00 0.00 0.00 4.00
58 59 2.933287 CTAGCCCACACCCACCCA 60.933 66.667 0.00 0.00 0.00 4.51
59 60 3.728373 CCTAGCCCACACCCACCC 61.728 72.222 0.00 0.00 0.00 4.61
60 61 4.426313 GCCTAGCCCACACCCACC 62.426 72.222 0.00 0.00 0.00 4.61
61 62 3.330720 AGCCTAGCCCACACCCAC 61.331 66.667 0.00 0.00 0.00 4.61
62 63 3.329889 CAGCCTAGCCCACACCCA 61.330 66.667 0.00 0.00 0.00 4.51
63 64 3.009115 TCAGCCTAGCCCACACCC 61.009 66.667 0.00 0.00 0.00 4.61
64 65 1.842381 AACTCAGCCTAGCCCACACC 61.842 60.000 0.00 0.00 0.00 4.16
65 66 0.674895 CAACTCAGCCTAGCCCACAC 60.675 60.000 0.00 0.00 0.00 3.82
66 67 0.835971 TCAACTCAGCCTAGCCCACA 60.836 55.000 0.00 0.00 0.00 4.17
67 68 0.324943 TTCAACTCAGCCTAGCCCAC 59.675 55.000 0.00 0.00 0.00 4.61
68 69 0.324943 GTTCAACTCAGCCTAGCCCA 59.675 55.000 0.00 0.00 0.00 5.36
69 70 0.741221 CGTTCAACTCAGCCTAGCCC 60.741 60.000 0.00 0.00 0.00 5.19
70 71 0.741221 CCGTTCAACTCAGCCTAGCC 60.741 60.000 0.00 0.00 0.00 3.93
71 72 0.037232 ACCGTTCAACTCAGCCTAGC 60.037 55.000 0.00 0.00 0.00 3.42
72 73 3.251571 GTTACCGTTCAACTCAGCCTAG 58.748 50.000 0.00 0.00 0.00 3.02
73 74 2.629137 TGTTACCGTTCAACTCAGCCTA 59.371 45.455 0.00 0.00 0.00 3.93
74 75 1.414919 TGTTACCGTTCAACTCAGCCT 59.585 47.619 0.00 0.00 0.00 4.58
75 76 1.873698 TGTTACCGTTCAACTCAGCC 58.126 50.000 0.00 0.00 0.00 4.85
76 77 3.250040 ACAATGTTACCGTTCAACTCAGC 59.750 43.478 0.00 0.00 0.00 4.26
77 78 5.418310 AACAATGTTACCGTTCAACTCAG 57.582 39.130 0.00 0.00 0.00 3.35
78 79 6.050432 AGTAACAATGTTACCGTTCAACTCA 58.950 36.000 26.93 0.00 0.00 3.41
79 80 6.535274 AGTAACAATGTTACCGTTCAACTC 57.465 37.500 26.93 4.25 0.00 3.01
80 81 8.500773 CATTAGTAACAATGTTACCGTTCAACT 58.499 33.333 26.93 13.99 32.33 3.16
81 82 8.284693 ACATTAGTAACAATGTTACCGTTCAAC 58.715 33.333 26.93 7.79 44.75 3.18
82 83 8.380743 ACATTAGTAACAATGTTACCGTTCAA 57.619 30.769 26.93 15.92 44.75 2.69
83 84 7.966246 ACATTAGTAACAATGTTACCGTTCA 57.034 32.000 26.93 11.30 44.75 3.18
93 94 5.064707 AGCCAGCGTAACATTAGTAACAATG 59.935 40.000 0.00 0.00 40.93 2.82
104 105 1.276421 ACAAGAGAGCCAGCGTAACAT 59.724 47.619 0.00 0.00 0.00 2.71
131 132 4.778579 AGATTCTCCACCATTGATGACAG 58.221 43.478 0.00 0.00 0.00 3.51
135 136 4.135306 CCTGAGATTCTCCACCATTGATG 58.865 47.826 11.12 0.00 0.00 3.07
204 205 2.356667 CCCCCTGGGTTTGAGCTC 59.643 66.667 12.71 6.82 38.25 4.09
366 384 3.986116 AACGGGGGAGAGGAGGAGC 62.986 68.421 0.00 0.00 0.00 4.70
395 418 0.614697 TTCGTGGAGGATGCTCTGGA 60.615 55.000 14.40 6.29 0.00 3.86
396 419 0.250234 TTTCGTGGAGGATGCTCTGG 59.750 55.000 14.40 4.02 0.00 3.86
397 420 2.099141 TTTTCGTGGAGGATGCTCTG 57.901 50.000 14.40 4.91 0.00 3.35
398 421 2.224523 TGTTTTTCGTGGAGGATGCTCT 60.225 45.455 14.40 0.00 0.00 4.09
399 422 2.151202 TGTTTTTCGTGGAGGATGCTC 58.849 47.619 5.52 5.52 0.00 4.26
400 423 2.270352 TGTTTTTCGTGGAGGATGCT 57.730 45.000 0.00 0.00 0.00 3.79
401 424 4.083003 TGTTATGTTTTTCGTGGAGGATGC 60.083 41.667 0.00 0.00 0.00 3.91
402 425 5.621197 TGTTATGTTTTTCGTGGAGGATG 57.379 39.130 0.00 0.00 0.00 3.51
403 426 6.488683 TCTTTGTTATGTTTTTCGTGGAGGAT 59.511 34.615 0.00 0.00 0.00 3.24
432 455 2.978018 GCCCCTCGTTGGCTTTTCG 61.978 63.158 5.55 0.00 45.70 3.46
635 662 1.238625 TAAAAGCAACGAAGGGCGGG 61.239 55.000 0.00 0.00 46.49 6.13
636 663 0.109919 GTAAAAGCAACGAAGGGCGG 60.110 55.000 0.00 0.00 46.49 6.13
637 664 0.452122 CGTAAAAGCAACGAAGGGCG 60.452 55.000 0.00 0.00 42.90 6.13
638 665 0.728129 GCGTAAAAGCAACGAAGGGC 60.728 55.000 0.00 0.00 42.90 5.19
639 666 0.452122 CGCGTAAAAGCAACGAAGGG 60.452 55.000 0.00 0.00 42.90 3.95
640 667 0.452122 CCGCGTAAAAGCAACGAAGG 60.452 55.000 4.92 0.00 42.90 3.46
641 668 0.509499 TCCGCGTAAAAGCAACGAAG 59.491 50.000 4.92 0.00 42.90 3.79
642 669 0.509499 CTCCGCGTAAAAGCAACGAA 59.491 50.000 4.92 0.00 42.90 3.85
643 670 1.286354 CCTCCGCGTAAAAGCAACGA 61.286 55.000 4.92 0.00 42.90 3.85
644 671 1.131826 CCTCCGCGTAAAAGCAACG 59.868 57.895 4.92 0.00 43.12 4.10
645 672 0.442699 CTCCTCCGCGTAAAAGCAAC 59.557 55.000 4.92 0.00 36.85 4.17
760 787 4.455606 AGAATAAAGCTATGTGGTGGAGC 58.544 43.478 0.00 0.00 36.42 4.70
805 841 3.036959 GGAGGAGGAGGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
814 850 0.687757 CTGGAATGGACGGAGGAGGA 60.688 60.000 0.00 0.00 0.00 3.71
844 880 0.539438 CAGGGGAGGAGGATCGAGAG 60.539 65.000 0.00 0.00 34.37 3.20
896 938 2.230660 GGGAACTTTCAGGTGTCAAGG 58.769 52.381 0.00 0.00 0.00 3.61
901 943 1.228154 GCGGGGAACTTTCAGGTGT 60.228 57.895 0.00 0.00 0.00 4.16
1032 1077 0.108329 AGTTCTGATTACCGTGGCCG 60.108 55.000 0.00 0.00 0.00 6.13
1046 1091 7.238486 TGAAAATAGAAGAGCAGAGAGTTCT 57.762 36.000 0.00 0.00 39.76 3.01
1047 1092 8.491331 AATGAAAATAGAAGAGCAGAGAGTTC 57.509 34.615 0.00 0.00 0.00 3.01
1094 1157 5.509272 CGAAGTACGTAAAATCTACGAGCAA 59.491 40.000 10.98 0.00 42.94 3.91
1124 1187 3.591254 AAGGAGAACGACGGCTGCC 62.591 63.158 9.11 9.11 0.00 4.85
1125 1188 1.627550 GAAAGGAGAACGACGGCTGC 61.628 60.000 0.00 1.35 0.00 5.25
1153 1261 0.748450 AGGTTGAAACGACCTCACGA 59.252 50.000 4.99 0.00 44.04 4.35
1160 1268 8.433893 GTTCTCTAATCTAAAGGTTGAAACGAC 58.566 37.037 0.00 0.00 0.00 4.34
1171 1279 8.800031 GTTTACTCTGCGTTCTCTAATCTAAAG 58.200 37.037 0.00 0.00 0.00 1.85
1210 1318 6.373216 TCCTGCACCTATACATGTTGTTAAAC 59.627 38.462 2.30 0.00 36.78 2.01
1398 1507 5.415701 ACCGGCCTAATTGATATTGCATAAG 59.584 40.000 0.00 0.00 0.00 1.73
1411 1540 2.092429 ACATGATGTGACCGGCCTAATT 60.092 45.455 0.00 0.00 0.00 1.40
1468 1597 4.223255 TCCCACATTGATTGATTGCAACAT 59.777 37.500 0.00 0.00 36.72 2.71
1488 1617 4.541973 ATGTTGATTGAAAGGCTTTCCC 57.458 40.909 31.17 21.64 38.90 3.97
1594 1723 3.055819 TCAGGTTCAGTCACTATCTTGGC 60.056 47.826 0.00 0.00 0.00 4.52
1612 1742 0.254178 CAATCAGGGTCAGGGTCAGG 59.746 60.000 0.00 0.00 0.00 3.86
1613 1743 0.393537 GCAATCAGGGTCAGGGTCAG 60.394 60.000 0.00 0.00 0.00 3.51
1614 1744 1.685224 GCAATCAGGGTCAGGGTCA 59.315 57.895 0.00 0.00 0.00 4.02
1615 1745 1.450312 CGCAATCAGGGTCAGGGTC 60.450 63.158 0.00 0.00 0.00 4.46
1616 1746 2.671070 CGCAATCAGGGTCAGGGT 59.329 61.111 0.00 0.00 0.00 4.34
1617 1747 2.825836 GCGCAATCAGGGTCAGGG 60.826 66.667 0.30 0.00 0.00 4.45
1714 1845 1.677633 GGGTTGCTAACATGGCCGT 60.678 57.895 0.00 0.00 0.00 5.68
1799 1930 3.507162 TTGAGAAAAGGGCAGATGACA 57.493 42.857 0.00 0.00 0.00 3.58
1899 2031 1.176527 CTTGTTCGGCACCATGGAAT 58.823 50.000 21.47 0.00 0.00 3.01
1938 2070 6.674694 AGAATTTCAGTCACTATGTGATGC 57.325 37.500 3.65 0.00 44.63 3.91
2001 2133 2.093553 AGAACTTCCATGAGCAGCTCTC 60.094 50.000 23.15 9.66 42.23 3.20
2015 2147 7.100409 ACTATGGTCAGAAGCTTTAGAACTTC 58.900 38.462 15.40 0.00 42.13 3.01
2048 2184 3.425162 AATCCCTGTCAGGTGAAAGTC 57.575 47.619 17.85 0.00 31.93 3.01
2180 2316 3.204526 CCACTTCATGAAGCTGGATCTC 58.795 50.000 32.17 0.00 41.99 2.75
2267 2403 2.410687 CGAGCTCTCTTCTCCCGCA 61.411 63.158 12.85 0.00 0.00 5.69
2307 2443 1.376609 GGTATCAGCACCTTTGGCCG 61.377 60.000 0.00 0.00 35.55 6.13
2388 2525 1.614996 TGTGGCGGTGAATTGAATGT 58.385 45.000 0.00 0.00 0.00 2.71
2402 2539 4.808558 TGAAGTGCTTGAATAAATGTGGC 58.191 39.130 0.00 0.00 0.00 5.01
2413 2550 8.946085 CAAAATAGGTTAGTATGAAGTGCTTGA 58.054 33.333 0.00 0.00 0.00 3.02
2426 2563 5.234329 CGATGATCGCACAAAATAGGTTAGT 59.766 40.000 0.41 0.00 31.14 2.24
2427 2564 5.462068 TCGATGATCGCACAAAATAGGTTAG 59.538 40.000 10.45 0.00 40.21 2.34
2430 2567 3.792401 TCGATGATCGCACAAAATAGGT 58.208 40.909 10.45 0.00 40.21 3.08
2432 2569 9.680946 CTATTTATCGATGATCGCACAAAATAG 57.319 33.333 21.60 21.60 40.21 1.73
2485 2626 1.210722 GTGGATCCTCCCTCTGGAAAC 59.789 57.143 14.23 0.00 41.17 2.78
2580 2721 5.008613 CAGGGTTACATTGGTGTATATGTGC 59.991 44.000 0.00 0.00 40.35 4.57
2591 2732 1.734163 GACGGACAGGGTTACATTGG 58.266 55.000 0.00 0.00 0.00 3.16
2593 2734 0.390735 GCGACGGACAGGGTTACATT 60.391 55.000 0.00 0.00 0.00 2.71
2596 2737 2.505557 CGCGACGGACAGGGTTAC 60.506 66.667 0.00 0.00 0.00 2.50
2612 2753 3.190874 GAGATAGTTGACCAGAAAGGCG 58.809 50.000 0.00 0.00 43.14 5.52
2624 2765 4.160736 TCACACTGTCACGAGATAGTTG 57.839 45.455 9.42 11.00 42.73 3.16
2627 2768 4.964555 CGTAATCACACTGTCACGAGATAG 59.035 45.833 5.11 5.11 38.78 2.08
2628 2769 4.201881 CCGTAATCACACTGTCACGAGATA 60.202 45.833 0.00 0.00 0.00 1.98
2633 2774 2.060326 ACCGTAATCACACTGTCACG 57.940 50.000 0.00 0.00 0.00 4.35
2634 2775 3.386486 TCAACCGTAATCACACTGTCAC 58.614 45.455 0.00 0.00 0.00 3.67
2636 2777 5.390567 GGAATTCAACCGTAATCACACTGTC 60.391 44.000 7.93 0.00 0.00 3.51
2637 2778 4.454504 GGAATTCAACCGTAATCACACTGT 59.545 41.667 7.93 0.00 0.00 3.55
2648 2791 2.489329 CTCTGCATTGGAATTCAACCGT 59.511 45.455 7.93 0.00 38.31 4.83
2797 2940 3.303495 CGACGAACAAAGGTATGTAGCTG 59.697 47.826 0.00 0.00 33.75 4.24
2837 2980 7.012044 GGTTTCTTTACACACTAGCTCTTTCAA 59.988 37.037 0.00 0.00 0.00 2.69
2861 3004 0.548031 CCCTGCAGGATGTACATGGT 59.452 55.000 34.91 0.00 39.31 3.55
2863 3006 1.487976 AGACCCTGCAGGATGTACATG 59.512 52.381 34.91 16.70 39.31 3.21
2957 3100 1.333619 GTGCAAGAAGAGCAACGGAAA 59.666 47.619 0.00 0.00 44.64 3.13
2978 3121 2.728817 GTCTCGCGGATAGGGTGG 59.271 66.667 6.13 0.00 0.00 4.61
3109 3257 4.153655 GGTGACGGTCACTTTCTATTTTCC 59.846 45.833 33.00 14.06 46.19 3.13
3126 3274 5.215160 CAAAGATGAAGAAAAAGGGTGACG 58.785 41.667 0.00 0.00 0.00 4.35
3142 3292 5.711976 AGGTGAACTGGGAAATACAAAGATG 59.288 40.000 0.00 0.00 0.00 2.90
3143 3293 5.892348 AGGTGAACTGGGAAATACAAAGAT 58.108 37.500 0.00 0.00 0.00 2.40
3145 3295 5.772521 CAAGGTGAACTGGGAAATACAAAG 58.227 41.667 0.00 0.00 0.00 2.77
3146 3296 4.038642 GCAAGGTGAACTGGGAAATACAAA 59.961 41.667 0.00 0.00 0.00 2.83
3147 3297 3.572255 GCAAGGTGAACTGGGAAATACAA 59.428 43.478 0.00 0.00 0.00 2.41
3148 3298 3.153919 GCAAGGTGAACTGGGAAATACA 58.846 45.455 0.00 0.00 0.00 2.29
3149 3299 3.421844 AGCAAGGTGAACTGGGAAATAC 58.578 45.455 0.00 0.00 0.00 1.89
3150 3300 3.806949 AGCAAGGTGAACTGGGAAATA 57.193 42.857 0.00 0.00 0.00 1.40
3151 3301 2.683211 AGCAAGGTGAACTGGGAAAT 57.317 45.000 0.00 0.00 0.00 2.17
3192 3342 4.202419 TGGTGTAACTCCTTGTAGCACAAT 60.202 41.667 2.83 0.00 35.47 2.71
3208 3358 2.932855 TCACATTTCGGGTGGTGTAA 57.067 45.000 0.00 0.00 36.90 2.41
3275 3425 5.388944 CAAACATCAGTTCTAGCTCTTTGC 58.611 41.667 0.00 0.00 36.84 3.68
3350 3500 1.906574 TCTATCAAGCCCGTCCTGTTT 59.093 47.619 0.00 0.00 0.00 2.83
3440 3590 4.202461 ACCTCCATTTTCTCACAGCTACAA 60.202 41.667 0.00 0.00 0.00 2.41
3886 4036 5.494794 CGTTAACATTTGCAAAGATTACGCG 60.495 40.000 18.19 17.53 0.00 6.01
3950 4100 0.394565 ACAGACACAGGCCTCTTGTC 59.605 55.000 26.96 26.96 40.04 3.18
4117 4268 5.047660 GTGGCTGGGTTCTCATATCTAGTAG 60.048 48.000 0.00 0.00 0.00 2.57
4292 4474 1.027357 GTAGCCTGCAATCATGTGGG 58.973 55.000 0.00 0.00 0.00 4.61
4374 4556 2.159393 TCAGTCAGCACAAGTTGTTTGC 60.159 45.455 5.57 8.08 40.59 3.68
4417 4599 5.181748 AGCTCACAATTCAGATCAGGTAAC 58.818 41.667 0.00 0.00 0.00 2.50
4419 4601 5.426689 AAGCTCACAATTCAGATCAGGTA 57.573 39.130 0.00 0.00 0.00 3.08
4421 4603 4.458295 ACAAAGCTCACAATTCAGATCAGG 59.542 41.667 0.00 0.00 0.00 3.86
4434 4619 4.098416 GCCATTAATCGAACAAAGCTCAC 58.902 43.478 0.00 0.00 0.00 3.51
4466 4651 1.829222 TCTGGGCTTAGGTTTCGGTAG 59.171 52.381 0.00 0.00 0.00 3.18
4706 4891 3.865745 CAGTTCTGAATCCGTCACCATAC 59.134 47.826 0.00 0.00 31.13 2.39
4793 4978 5.570234 TTTCCTTGTGTTACACAGGAAAC 57.430 39.130 32.73 9.49 45.20 2.78
4850 5035 7.229308 ACATTCATCTCCTTATGTATGTGCAT 58.771 34.615 7.89 0.00 42.64 3.96
4885 5070 3.146847 GTCACTGAAATCCGAACCCTTT 58.853 45.455 0.00 0.00 0.00 3.11
4998 5183 9.057089 GCTGCTAGTTACATTGGTATTTCTTAT 57.943 33.333 0.00 0.00 0.00 1.73
5028 5213 8.766994 AAATACCTCAATACATTAGCATTGGT 57.233 30.769 0.00 0.00 33.77 3.67
5164 5351 6.151144 AGGATTCGAGGTTAATGGTTTTTCTG 59.849 38.462 0.00 0.00 0.00 3.02
5194 5389 6.435292 AGGTTAGTGAAGCCTTCTTAAGAA 57.565 37.500 16.85 16.85 33.30 2.52
5236 5431 5.016173 ACTGGCTAAATAATGTGAAGGCAA 58.984 37.500 0.00 0.00 41.48 4.52
5296 5503 6.238566 CGTTTGCTCCTTATGAATGATGATGT 60.239 38.462 0.00 0.00 0.00 3.06
5303 5510 4.142622 TGCTTCGTTTGCTCCTTATGAATG 60.143 41.667 0.00 0.00 0.00 2.67
5304 5511 4.009675 TGCTTCGTTTGCTCCTTATGAAT 58.990 39.130 0.00 0.00 0.00 2.57
5305 5512 3.407698 TGCTTCGTTTGCTCCTTATGAA 58.592 40.909 0.00 0.00 0.00 2.57
5345 7759 1.609072 CGTCAACTGTGTCTCCTCTCA 59.391 52.381 0.00 0.00 0.00 3.27
5398 7815 2.827642 GCCCAGCATCAGTCCTGC 60.828 66.667 0.00 0.00 39.97 4.85
5412 7829 0.179468 TTATGTTGTAGAGGCCGCCC 59.821 55.000 5.55 0.00 0.00 6.13
5463 7880 4.510038 ACTCATGGTGAAGACAAAATGC 57.490 40.909 0.00 0.00 0.00 3.56
5491 7908 6.457799 GGTGGCCTTCTACATAAAAACATACG 60.458 42.308 3.32 0.00 0.00 3.06
5517 7934 3.282021 TGTTTCTTATCCTGCATGAGCC 58.718 45.455 0.00 0.00 41.13 4.70
5547 7964 5.527582 GCTGTTTATTACTGGACCGATTGAT 59.472 40.000 0.00 0.00 0.00 2.57
5554 7971 8.782339 TTACTTTAGCTGTTTATTACTGGACC 57.218 34.615 0.00 0.00 0.00 4.46
5585 8002 9.738832 GTACTTCTATCAGAGTATTGGAAGTTC 57.261 37.037 10.02 0.00 41.06 3.01
5595 8012 9.862149 TGGTGATTATGTACTTCTATCAGAGTA 57.138 33.333 0.00 0.00 0.00 2.59
5605 8022 5.822519 TCCTTGCATGGTGATTATGTACTTC 59.177 40.000 17.54 0.00 0.00 3.01
5625 8042 1.229209 TTCCTCCTGCCTCGTCCTT 60.229 57.895 0.00 0.00 0.00 3.36
5644 8061 6.912591 GGTCTGACATTGTAAAAGTGTTCAAG 59.087 38.462 10.38 0.00 0.00 3.02
5677 8094 2.498078 TCTGGTGTACCGATGTTGCATA 59.502 45.455 0.00 0.00 39.43 3.14
5678 8095 1.277842 TCTGGTGTACCGATGTTGCAT 59.722 47.619 0.00 0.00 39.43 3.96
5694 8111 9.092876 GATCTTCTCTTATGTTTAACTGTCTGG 57.907 37.037 0.00 0.00 0.00 3.86
5724 8141 6.892456 TCCTCTAGTGATAAACTGTCTGATGT 59.108 38.462 0.00 0.00 40.26 3.06
5773 8193 8.043113 TGATTTATGTTGCACTATCTTCTCTGT 58.957 33.333 0.00 0.00 0.00 3.41
5774 8194 8.429493 TGATTTATGTTGCACTATCTTCTCTG 57.571 34.615 0.00 0.00 0.00 3.35
5775 8195 9.107177 CTTGATTTATGTTGCACTATCTTCTCT 57.893 33.333 0.00 0.00 0.00 3.10
5799 8223 4.471386 TGTAGAAGGCCAAAGCTCTATCTT 59.529 41.667 5.01 0.00 39.73 2.40
5815 8239 7.011482 GCCTGTAATGTACCTCAATTGTAGAAG 59.989 40.741 5.13 0.00 0.00 2.85
5877 8301 3.006430 TGCAGTTAGTCTTGTCATTCGGA 59.994 43.478 0.00 0.00 0.00 4.55
5895 8319 5.984926 AGTGATTTTGGTTGTAACATTGCAG 59.015 36.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.