Multiple sequence alignment - TraesCS1A01G179200

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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 TraesCS1A01G179200 chr1A 100.000 2321 0 0 1 2321 323894149 323896469 0.000000e+00 4287.0
1 TraesCS1A01G179200 chr1A 85.294 238 35 0 1000 1237 323961239 323961476 1.780000e-61 246.0
2 TraesCS1A01G179200 chr1A 98.718 78 1 0 1644 1721 323895714 323895791 3.110000e-29 139.0
3 TraesCS1A01G179200 chr1A 98.718 78 1 0 1566 1643 323895792 323895869 3.110000e-29 139.0
4 TraesCS1A01G179200 chr1D 88.681 910 62 26 129 1003 252566195 252567098 0.000000e+00 1072.0
5 TraesCS1A01G179200 chr1D 92.308 689 41 9 1642 2321 252569251 252569936 0.000000e+00 968.0
6 TraesCS1A01G179200 chr1D 90.000 340 16 2 1000 1339 252567152 252567473 7.670000e-115 424.0
7 TraesCS1A01G179200 chr1D 85.000 240 32 3 1000 1237 252596111 252596348 8.290000e-60 241.0
8 TraesCS1A01G179200 chr1D 93.182 88 6 0 1410 1497 270900916 270901003 1.870000e-26 130.0
9 TraesCS1A01G179200 chr1D 88.571 70 7 1 1339 1407 252568458 252568527 1.480000e-12 84.2
10 TraesCS1A01G179200 chr1B 87.313 938 49 28 127 1003 360513209 360512281 0.000000e+00 1009.0
11 TraesCS1A01G179200 chr1B 91.483 681 54 4 1642 2321 360467552 360466875 0.000000e+00 933.0
12 TraesCS1A01G179200 chr1B 90.196 357 13 2 1000 1356 360512227 360511893 1.640000e-121 446.0
13 TraesCS1A01G179200 chr1B 88.793 116 12 1 1 116 456994461 456994347 8.650000e-30 141.0
14 TraesCS1A01G179200 chr3D 94.382 89 5 0 1410 1498 104029090 104029002 1.120000e-28 137.0
15 TraesCS1A01G179200 chr6A 94.318 88 5 0 1410 1497 459514907 459514994 4.020000e-28 135.0
16 TraesCS1A01G179200 chr5A 94.318 88 5 0 1410 1497 577784104 577784191 4.020000e-28 135.0
17 TraesCS1A01G179200 chr6D 93.182 88 6 0 1410 1497 345490390 345490303 1.870000e-26 130.0
18 TraesCS1A01G179200 chr4A 92.308 91 7 0 1410 1500 175649101 175649011 1.870000e-26 130.0
19 TraesCS1A01G179200 chr3B 92.391 92 6 1 1410 1500 449887085 449886994 1.870000e-26 130.0
20 TraesCS1A01G179200 chr3A 91.489 94 6 2 1405 1497 622703027 622702935 6.730000e-26 128.0
21 TraesCS1A01G179200 chr2A 89.109 101 9 1 1410 1510 718971977 718971879 8.710000e-25 124.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G179200 chr1A 323894149 323896469 2320 False 1521.666667 4287 99.145333 1 2321 3 chr1A.!!$F2 2320
1 TraesCS1A01G179200 chr1D 252566195 252569936 3741 False 637.050000 1072 89.890000 129 2321 4 chr1D.!!$F3 2192
2 TraesCS1A01G179200 chr1B 360466875 360467552 677 True 933.000000 933 91.483000 1642 2321 1 chr1B.!!$R1 679
3 TraesCS1A01G179200 chr1B 360511893 360513209 1316 True 727.500000 1009 88.754500 127 1356 2 chr1B.!!$R3 1229

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
323 335 0.336392 TTCTGGCTCAGGCTCTCCTA 59.664 55.0 0.0 0.0 41.93 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 2585 0.110295 TTGGGTCACTGACATGTGGG 59.89 55.0 1.15 0.0 38.4 4.61 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
24 25 3.698765 GGTGGGCCCAAACTGATG 58.301 61.111 30.64 0.00 0.00 3.07
25 26 1.076549 GGTGGGCCCAAACTGATGA 59.923 57.895 30.64 0.00 0.00 2.92
26 27 0.541764 GGTGGGCCCAAACTGATGAA 60.542 55.000 30.64 0.00 0.00 2.57
27 28 1.337118 GTGGGCCCAAACTGATGAAA 58.663 50.000 30.64 0.00 0.00 2.69
28 29 1.901833 GTGGGCCCAAACTGATGAAAT 59.098 47.619 30.64 0.00 0.00 2.17
29 30 3.096092 GTGGGCCCAAACTGATGAAATA 58.904 45.455 30.64 0.00 0.00 1.40
30 31 3.096092 TGGGCCCAAACTGATGAAATAC 58.904 45.455 26.33 0.00 0.00 1.89
31 32 3.096092 GGGCCCAAACTGATGAAATACA 58.904 45.455 19.95 0.00 0.00 2.29
32 33 3.131046 GGGCCCAAACTGATGAAATACAG 59.869 47.826 19.95 0.00 39.65 2.74
34 35 4.380867 GGCCCAAACTGATGAAATACAGTG 60.381 45.833 0.00 0.00 44.94 3.66
35 36 4.380867 GCCCAAACTGATGAAATACAGTGG 60.381 45.833 0.00 0.00 44.94 4.00
36 37 4.380867 CCCAAACTGATGAAATACAGTGGC 60.381 45.833 0.00 0.00 44.94 5.01
37 38 4.460382 CCAAACTGATGAAATACAGTGGCT 59.540 41.667 0.00 0.00 44.94 4.75
38 39 5.396484 CAAACTGATGAAATACAGTGGCTG 58.604 41.667 0.00 0.00 44.94 4.85
39 40 4.558226 ACTGATGAAATACAGTGGCTGA 57.442 40.909 2.91 0.00 44.18 4.26
40 41 4.910195 ACTGATGAAATACAGTGGCTGAA 58.090 39.130 2.91 0.00 44.18 3.02
41 42 5.316167 ACTGATGAAATACAGTGGCTGAAA 58.684 37.500 2.91 0.00 44.18 2.69
42 43 5.948162 ACTGATGAAATACAGTGGCTGAAAT 59.052 36.000 2.91 0.00 44.18 2.17
43 44 6.127814 ACTGATGAAATACAGTGGCTGAAATG 60.128 38.462 2.91 0.00 44.18 2.32
44 45 5.945191 TGATGAAATACAGTGGCTGAAATGA 59.055 36.000 2.91 0.00 35.18 2.57
45 46 6.433716 TGATGAAATACAGTGGCTGAAATGAA 59.566 34.615 2.91 0.00 35.18 2.57
46 47 6.258230 TGAAATACAGTGGCTGAAATGAAG 57.742 37.500 2.91 0.00 35.18 3.02
47 48 6.003326 TGAAATACAGTGGCTGAAATGAAGA 58.997 36.000 2.91 0.00 35.18 2.87
48 49 6.489700 TGAAATACAGTGGCTGAAATGAAGAA 59.510 34.615 2.91 0.00 35.18 2.52
49 50 6.899393 AATACAGTGGCTGAAATGAAGAAA 57.101 33.333 2.91 0.00 35.18 2.52
50 51 6.899393 ATACAGTGGCTGAAATGAAGAAAA 57.101 33.333 2.91 0.00 35.18 2.29
51 52 4.936891 ACAGTGGCTGAAATGAAGAAAAC 58.063 39.130 2.91 0.00 35.18 2.43
52 53 4.402155 ACAGTGGCTGAAATGAAGAAAACA 59.598 37.500 2.91 0.00 35.18 2.83
53 54 4.980434 CAGTGGCTGAAATGAAGAAAACAG 59.020 41.667 0.00 0.00 32.44 3.16
54 55 4.646492 AGTGGCTGAAATGAAGAAAACAGT 59.354 37.500 0.00 0.00 0.00 3.55
55 56 4.741676 GTGGCTGAAATGAAGAAAACAGTG 59.258 41.667 0.00 0.00 0.00 3.66
56 57 4.202141 TGGCTGAAATGAAGAAAACAGTGG 60.202 41.667 0.00 0.00 0.00 4.00
57 58 4.037923 GGCTGAAATGAAGAAAACAGTGGA 59.962 41.667 0.00 0.00 0.00 4.02
58 59 5.451798 GGCTGAAATGAAGAAAACAGTGGAA 60.452 40.000 0.00 0.00 0.00 3.53
59 60 6.218746 GCTGAAATGAAGAAAACAGTGGAAT 58.781 36.000 0.00 0.00 0.00 3.01
60 61 7.370383 GCTGAAATGAAGAAAACAGTGGAATA 58.630 34.615 0.00 0.00 0.00 1.75
61 62 7.327032 GCTGAAATGAAGAAAACAGTGGAATAC 59.673 37.037 0.00 0.00 0.00 1.89
62 63 8.231692 TGAAATGAAGAAAACAGTGGAATACA 57.768 30.769 0.00 0.00 0.00 2.29
63 64 8.690884 TGAAATGAAGAAAACAGTGGAATACAA 58.309 29.630 0.00 0.00 0.00 2.41
64 65 9.528018 GAAATGAAGAAAACAGTGGAATACAAA 57.472 29.630 0.00 0.00 0.00 2.83
65 66 9.533253 AAATGAAGAAAACAGTGGAATACAAAG 57.467 29.630 0.00 0.00 0.00 2.77
66 67 7.873719 TGAAGAAAACAGTGGAATACAAAGA 57.126 32.000 0.00 0.00 0.00 2.52
67 68 8.463930 TGAAGAAAACAGTGGAATACAAAGAT 57.536 30.769 0.00 0.00 0.00 2.40
68 69 9.567776 TGAAGAAAACAGTGGAATACAAAGATA 57.432 29.630 0.00 0.00 0.00 1.98
69 70 9.827411 GAAGAAAACAGTGGAATACAAAGATAC 57.173 33.333 0.00 0.00 0.00 2.24
70 71 8.918202 AGAAAACAGTGGAATACAAAGATACA 57.082 30.769 0.00 0.00 0.00 2.29
71 72 9.349713 AGAAAACAGTGGAATACAAAGATACAA 57.650 29.630 0.00 0.00 0.00 2.41
72 73 9.394477 GAAAACAGTGGAATACAAAGATACAAC 57.606 33.333 0.00 0.00 0.00 3.32
73 74 8.691661 AAACAGTGGAATACAAAGATACAACT 57.308 30.769 0.00 0.00 0.00 3.16
74 75 8.691661 AACAGTGGAATACAAAGATACAACTT 57.308 30.769 0.00 0.00 0.00 2.66
75 76 9.787435 AACAGTGGAATACAAAGATACAACTTA 57.213 29.630 0.00 0.00 0.00 2.24
76 77 9.436957 ACAGTGGAATACAAAGATACAACTTAG 57.563 33.333 0.00 0.00 0.00 2.18
77 78 9.436957 CAGTGGAATACAAAGATACAACTTAGT 57.563 33.333 0.00 0.00 0.00 2.24
85 86 8.904099 ACAAAGATACAACTTAGTACAGCTTT 57.096 30.769 0.00 0.00 0.00 3.51
86 87 9.338622 ACAAAGATACAACTTAGTACAGCTTTT 57.661 29.630 0.00 0.00 0.00 2.27
87 88 9.599322 CAAAGATACAACTTAGTACAGCTTTTG 57.401 33.333 0.00 0.00 0.00 2.44
88 89 9.555727 AAAGATACAACTTAGTACAGCTTTTGA 57.444 29.630 0.00 0.00 0.00 2.69
89 90 8.764524 AGATACAACTTAGTACAGCTTTTGAG 57.235 34.615 0.00 0.00 0.00 3.02
90 91 7.819900 AGATACAACTTAGTACAGCTTTTGAGG 59.180 37.037 0.00 0.00 0.00 3.86
91 92 5.681639 ACAACTTAGTACAGCTTTTGAGGT 58.318 37.500 0.00 0.00 0.00 3.85
92 93 5.527582 ACAACTTAGTACAGCTTTTGAGGTG 59.472 40.000 4.24 4.24 42.40 4.00
93 94 4.642429 ACTTAGTACAGCTTTTGAGGTGG 58.358 43.478 9.99 0.00 41.16 4.61
94 95 1.897560 AGTACAGCTTTTGAGGTGGC 58.102 50.000 9.99 3.31 41.16 5.01
95 96 1.142870 AGTACAGCTTTTGAGGTGGCA 59.857 47.619 9.99 0.00 41.16 4.92
96 97 1.537202 GTACAGCTTTTGAGGTGGCAG 59.463 52.381 9.99 0.00 41.16 4.85
97 98 0.825010 ACAGCTTTTGAGGTGGCAGG 60.825 55.000 9.99 0.00 41.16 4.85
98 99 0.538057 CAGCTTTTGAGGTGGCAGGA 60.538 55.000 0.00 0.00 34.04 3.86
99 100 0.538287 AGCTTTTGAGGTGGCAGGAC 60.538 55.000 0.00 0.00 0.00 3.85
100 101 0.538287 GCTTTTGAGGTGGCAGGACT 60.538 55.000 0.00 0.00 0.00 3.85
101 102 1.528129 CTTTTGAGGTGGCAGGACTC 58.472 55.000 6.79 6.79 0.00 3.36
102 103 1.072965 CTTTTGAGGTGGCAGGACTCT 59.927 52.381 12.99 0.00 32.58 3.24
103 104 2.024176 TTTGAGGTGGCAGGACTCTA 57.976 50.000 12.99 5.04 32.58 2.43
104 105 2.254152 TTGAGGTGGCAGGACTCTAT 57.746 50.000 12.99 0.00 32.58 1.98
105 106 2.254152 TGAGGTGGCAGGACTCTATT 57.746 50.000 12.99 0.00 32.58 1.73
106 107 1.833630 TGAGGTGGCAGGACTCTATTG 59.166 52.381 12.99 0.00 32.58 1.90
107 108 1.139853 GAGGTGGCAGGACTCTATTGG 59.860 57.143 6.54 0.00 0.00 3.16
108 109 0.464554 GGTGGCAGGACTCTATTGGC 60.465 60.000 0.00 0.00 37.84 4.52
109 110 0.543749 GTGGCAGGACTCTATTGGCT 59.456 55.000 0.00 0.00 38.14 4.75
110 111 0.543277 TGGCAGGACTCTATTGGCTG 59.457 55.000 0.00 0.00 38.14 4.85
111 112 0.543749 GGCAGGACTCTATTGGCTGT 59.456 55.000 0.00 0.00 34.85 4.40
112 113 1.661341 GCAGGACTCTATTGGCTGTG 58.339 55.000 0.00 0.00 0.00 3.66
113 114 1.065854 GCAGGACTCTATTGGCTGTGT 60.066 52.381 0.00 0.00 0.00 3.72
114 115 2.168521 GCAGGACTCTATTGGCTGTGTA 59.831 50.000 0.00 0.00 0.00 2.90
115 116 3.369471 GCAGGACTCTATTGGCTGTGTAA 60.369 47.826 0.00 0.00 0.00 2.41
116 117 4.832248 CAGGACTCTATTGGCTGTGTAAA 58.168 43.478 0.00 0.00 0.00 2.01
117 118 5.245531 CAGGACTCTATTGGCTGTGTAAAA 58.754 41.667 0.00 0.00 0.00 1.52
118 119 5.705441 CAGGACTCTATTGGCTGTGTAAAAA 59.295 40.000 0.00 0.00 0.00 1.94
119 120 5.940470 AGGACTCTATTGGCTGTGTAAAAAG 59.060 40.000 0.00 0.00 0.00 2.27
120 121 5.938125 GGACTCTATTGGCTGTGTAAAAAGA 59.062 40.000 0.00 0.00 0.00 2.52
121 122 6.092807 GGACTCTATTGGCTGTGTAAAAAGAG 59.907 42.308 0.00 0.00 35.27 2.85
122 123 5.940470 ACTCTATTGGCTGTGTAAAAAGAGG 59.060 40.000 0.00 0.00 33.80 3.69
123 124 5.876357 TCTATTGGCTGTGTAAAAAGAGGT 58.124 37.500 0.00 0.00 0.00 3.85
124 125 6.303839 TCTATTGGCTGTGTAAAAAGAGGTT 58.696 36.000 0.00 0.00 0.00 3.50
125 126 5.869649 ATTGGCTGTGTAAAAAGAGGTTT 57.130 34.783 0.00 0.00 0.00 3.27
299 311 3.010200 ACAATGGCAAGATTCCTCTCC 57.990 47.619 0.00 0.00 0.00 3.71
305 317 2.620108 GGCAAGATTCCTCTCCTGCTTT 60.620 50.000 0.00 0.00 36.12 3.51
323 335 0.336392 TTCTGGCTCAGGCTCTCCTA 59.664 55.000 0.00 0.00 41.93 2.94
476 488 3.427573 TCTTGGTTCGAGATCACCACTA 58.572 45.455 6.19 0.00 43.02 2.74
507 519 3.041940 CGCCAGAACCACACCGTC 61.042 66.667 0.00 0.00 0.00 4.79
508 520 2.426023 GCCAGAACCACACCGTCT 59.574 61.111 0.00 0.00 0.00 4.18
509 521 1.668151 GCCAGAACCACACCGTCTC 60.668 63.158 0.00 0.00 0.00 3.36
510 522 1.004918 CCAGAACCACACCGTCTCC 60.005 63.158 0.00 0.00 0.00 3.71
511 523 1.372997 CAGAACCACACCGTCTCCG 60.373 63.158 0.00 0.00 0.00 4.63
512 524 2.737376 GAACCACACCGTCTCCGC 60.737 66.667 0.00 0.00 0.00 5.54
513 525 4.309950 AACCACACCGTCTCCGCC 62.310 66.667 0.00 0.00 0.00 6.13
661 749 1.531739 TTTCACTTCCCCGCATTGCC 61.532 55.000 2.41 0.00 0.00 4.52
682 770 3.249320 CCATATTTCTCAGCATCACCACG 59.751 47.826 0.00 0.00 0.00 4.94
694 782 1.790755 TCACCACGTTGTATCTGCAC 58.209 50.000 0.00 0.00 0.00 4.57
719 813 9.659830 ACTTTACATGTTTTAAGCTAGTTTTCG 57.340 29.630 2.30 0.00 0.00 3.46
720 814 9.113876 CTTTACATGTTTTAAGCTAGTTTTCGG 57.886 33.333 2.30 0.00 0.00 4.30
772 866 4.408596 TCCTTTGCCCAGTGAGAAATTTTT 59.591 37.500 0.00 0.00 0.00 1.94
783 877 4.024048 GTGAGAAATTTTTCGAGCCAGTGA 60.024 41.667 4.44 0.00 41.92 3.41
908 1005 3.816920 CGTTGACGCGACAGCTCG 61.817 66.667 20.75 17.33 43.28 5.03
909 1006 2.428569 GTTGACGCGACAGCTCGA 60.429 61.111 15.93 0.00 43.06 4.04
910 1007 1.801913 GTTGACGCGACAGCTCGAT 60.802 57.895 15.93 0.00 43.06 3.59
911 1008 1.514228 TTGACGCGACAGCTCGATC 60.514 57.895 15.93 0.00 43.06 3.69
946 1043 2.149973 AAACTCAGGCCATGATTCCC 57.850 50.000 5.01 0.00 37.28 3.97
948 1045 0.982852 ACTCAGGCCATGATTCCCGA 60.983 55.000 5.01 0.00 37.28 5.14
994 1091 9.708092 ACTACTCCAAGTTTTCAGTATAAGTTC 57.292 33.333 0.00 0.00 0.00 3.01
997 1094 5.410439 TCCAAGTTTTCAGTATAAGTTCGGC 59.590 40.000 0.00 0.00 0.00 5.54
1073 1227 2.616330 CCACAAATGTGCCGTCGCT 61.616 57.895 8.03 0.00 44.34 4.93
1148 1302 2.180017 GCGTAGGAGTTCCGCGAA 59.820 61.111 8.23 0.00 42.08 4.70
1149 1303 1.444895 GCGTAGGAGTTCCGCGAAA 60.445 57.895 8.23 0.00 42.08 3.46
1241 1395 4.660938 GCCTCCACCACCACCACC 62.661 72.222 0.00 0.00 0.00 4.61
1242 1396 3.174987 CCTCCACCACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
1243 1397 2.113139 CTCCACCACCACCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
1244 1398 3.491598 CTCCACCACCACCACCACC 62.492 68.421 0.00 0.00 0.00 4.61
1245 1399 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1246 1400 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1247 1401 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1248 1402 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
1249 1403 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
1250 1404 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1251 1405 4.947147 CCACCACCACCACCACCG 62.947 72.222 0.00 0.00 0.00 4.94
1384 2526 1.066858 TGCGAAGACCTTGATCTGGAC 60.067 52.381 11.38 6.13 0.00 4.02
1386 2528 2.419297 GCGAAGACCTTGATCTGGACAT 60.419 50.000 11.38 0.02 0.00 3.06
1387 2529 3.193263 CGAAGACCTTGATCTGGACATG 58.807 50.000 11.38 0.00 0.00 3.21
1388 2530 3.368843 CGAAGACCTTGATCTGGACATGT 60.369 47.826 0.00 0.00 0.00 3.21
1389 2531 4.583871 GAAGACCTTGATCTGGACATGTT 58.416 43.478 0.00 0.00 0.00 2.71
1390 2532 5.624509 CGAAGACCTTGATCTGGACATGTTA 60.625 44.000 0.00 0.00 0.00 2.41
1391 2533 5.762179 AGACCTTGATCTGGACATGTTAA 57.238 39.130 0.00 0.00 0.00 2.01
1392 2534 6.319048 AGACCTTGATCTGGACATGTTAAT 57.681 37.500 0.00 0.00 0.00 1.40
1393 2535 6.352516 AGACCTTGATCTGGACATGTTAATC 58.647 40.000 0.00 2.05 0.00 1.75
1394 2536 6.157645 AGACCTTGATCTGGACATGTTAATCT 59.842 38.462 0.00 0.00 0.00 2.40
1395 2537 6.725364 ACCTTGATCTGGACATGTTAATCTT 58.275 36.000 0.00 0.00 0.00 2.40
1396 2538 6.600822 ACCTTGATCTGGACATGTTAATCTTG 59.399 38.462 0.00 0.00 0.00 3.02
1397 2539 6.039047 CCTTGATCTGGACATGTTAATCTTGG 59.961 42.308 0.00 4.56 0.00 3.61
1398 2540 6.312141 TGATCTGGACATGTTAATCTTGGA 57.688 37.500 0.00 0.00 0.00 3.53
1399 2541 6.115446 TGATCTGGACATGTTAATCTTGGAC 58.885 40.000 0.00 0.00 0.00 4.02
1400 2542 4.503910 TCTGGACATGTTAATCTTGGACG 58.496 43.478 0.00 0.00 0.00 4.79
1401 2543 4.221924 TCTGGACATGTTAATCTTGGACGA 59.778 41.667 0.00 0.00 0.00 4.20
1402 2544 5.097742 TGGACATGTTAATCTTGGACGAT 57.902 39.130 0.00 0.00 0.00 3.73
1403 2545 4.875536 TGGACATGTTAATCTTGGACGATG 59.124 41.667 0.00 0.00 0.00 3.84
1404 2546 4.260784 GGACATGTTAATCTTGGACGATGC 60.261 45.833 0.00 0.00 0.00 3.91
1405 2547 4.517285 ACATGTTAATCTTGGACGATGCT 58.483 39.130 0.00 0.00 0.00 3.79
1406 2548 4.943705 ACATGTTAATCTTGGACGATGCTT 59.056 37.500 0.00 0.00 0.00 3.91
1407 2549 5.065218 ACATGTTAATCTTGGACGATGCTTC 59.935 40.000 0.00 0.00 0.00 3.86
1416 2558 4.758692 CGATGCTTCGGTGCCTAT 57.241 55.556 13.82 0.00 41.74 2.57
1417 2559 2.229039 CGATGCTTCGGTGCCTATG 58.771 57.895 13.82 0.00 41.74 2.23
1418 2560 0.249447 CGATGCTTCGGTGCCTATGA 60.249 55.000 13.82 0.00 41.74 2.15
1419 2561 1.221414 GATGCTTCGGTGCCTATGAC 58.779 55.000 0.00 0.00 0.00 3.06
1420 2562 0.541392 ATGCTTCGGTGCCTATGACA 59.459 50.000 0.00 0.00 0.00 3.58
1421 2563 0.541392 TGCTTCGGTGCCTATGACAT 59.459 50.000 0.00 0.00 0.00 3.06
1422 2564 0.940126 GCTTCGGTGCCTATGACATG 59.060 55.000 0.00 0.00 0.00 3.21
1423 2565 1.743772 GCTTCGGTGCCTATGACATGT 60.744 52.381 0.00 0.00 0.00 3.21
1424 2566 1.935873 CTTCGGTGCCTATGACATGTG 59.064 52.381 1.15 0.00 0.00 3.21
1425 2567 0.177836 TCGGTGCCTATGACATGTGG 59.822 55.000 1.15 0.00 0.00 4.17
1426 2568 0.177836 CGGTGCCTATGACATGTGGA 59.822 55.000 1.15 0.00 0.00 4.02
1427 2569 1.202687 CGGTGCCTATGACATGTGGAT 60.203 52.381 1.15 0.00 0.00 3.41
1428 2570 2.498167 GGTGCCTATGACATGTGGATC 58.502 52.381 1.15 0.00 0.00 3.36
1429 2571 2.498167 GTGCCTATGACATGTGGATCC 58.502 52.381 1.15 4.20 0.00 3.36
1430 2572 2.126057 TGCCTATGACATGTGGATCCA 58.874 47.619 11.44 11.44 0.00 3.41
1431 2573 2.509131 TGCCTATGACATGTGGATCCAA 59.491 45.455 18.20 7.57 0.00 3.53
1432 2574 2.880890 GCCTATGACATGTGGATCCAAC 59.119 50.000 18.20 11.54 0.00 3.77
1433 2575 3.685265 GCCTATGACATGTGGATCCAACA 60.685 47.826 18.20 16.96 0.00 3.33
1434 2576 4.132336 CCTATGACATGTGGATCCAACAG 58.868 47.826 18.20 11.42 0.00 3.16
1435 2577 2.495155 TGACATGTGGATCCAACAGG 57.505 50.000 18.20 19.55 0.00 4.00
1436 2578 1.704628 TGACATGTGGATCCAACAGGT 59.295 47.619 24.72 24.72 0.00 4.00
1437 2579 2.086869 GACATGTGGATCCAACAGGTG 58.913 52.381 27.59 19.87 0.00 4.00
1438 2580 1.704628 ACATGTGGATCCAACAGGTGA 59.295 47.619 24.20 4.37 0.00 4.02
1439 2581 2.086869 CATGTGGATCCAACAGGTGAC 58.913 52.381 18.20 1.41 0.00 3.67
1440 2582 1.434188 TGTGGATCCAACAGGTGACT 58.566 50.000 18.20 0.00 46.44 3.41
1452 2594 3.233355 GGTGACTGACCCACATGTC 57.767 57.895 0.00 0.00 39.10 3.06
1453 2595 0.396435 GGTGACTGACCCACATGTCA 59.604 55.000 0.00 0.00 42.75 3.58
1459 2601 0.396435 TGACCCACATGTCAGTGACC 59.604 55.000 20.43 3.06 40.22 4.02
1460 2602 0.321653 GACCCACATGTCAGTGACCC 60.322 60.000 20.43 0.00 42.05 4.46
1461 2603 1.059584 ACCCACATGTCAGTGACCCA 61.060 55.000 20.43 3.20 42.05 4.51
1462 2604 0.110295 CCCACATGTCAGTGACCCAA 59.890 55.000 20.43 2.34 42.05 4.12
1463 2605 1.478471 CCCACATGTCAGTGACCCAAA 60.478 52.381 20.43 1.95 42.05 3.28
1464 2606 1.881973 CCACATGTCAGTGACCCAAAG 59.118 52.381 20.43 8.14 42.05 2.77
1465 2607 1.881973 CACATGTCAGTGACCCAAAGG 59.118 52.381 20.43 6.15 42.05 3.11
1466 2608 0.883833 CATGTCAGTGACCCAAAGGC 59.116 55.000 20.43 0.00 36.11 4.35
1467 2609 0.478072 ATGTCAGTGACCCAAAGGCA 59.522 50.000 20.43 0.00 36.11 4.75
1468 2610 0.179020 TGTCAGTGACCCAAAGGCAG 60.179 55.000 20.43 0.00 36.11 4.85
1469 2611 0.890996 GTCAGTGACCCAAAGGCAGG 60.891 60.000 12.54 0.00 36.11 4.85
1470 2612 1.151450 CAGTGACCCAAAGGCAGGT 59.849 57.895 0.00 0.00 39.75 4.00
1471 2613 1.151450 AGTGACCCAAAGGCAGGTG 59.849 57.895 0.00 0.00 36.17 4.00
1472 2614 2.203480 TGACCCAAAGGCAGGTGC 60.203 61.111 0.00 0.00 36.17 5.01
1482 2624 4.095590 GCAGGTGCCTTTAAGCCA 57.904 55.556 0.00 0.00 34.31 4.75
1483 2625 1.586541 GCAGGTGCCTTTAAGCCAC 59.413 57.895 0.00 0.00 34.31 5.01
1484 2626 1.877576 GCAGGTGCCTTTAAGCCACC 61.878 60.000 16.25 16.25 35.46 4.61
1485 2627 1.303317 AGGTGCCTTTAAGCCACCG 60.303 57.895 17.64 0.00 38.31 4.94
1486 2628 1.302993 GGTGCCTTTAAGCCACCGA 60.303 57.895 9.37 0.00 0.00 4.69
1487 2629 0.891904 GGTGCCTTTAAGCCACCGAA 60.892 55.000 9.37 0.00 0.00 4.30
1488 2630 0.521735 GTGCCTTTAAGCCACCGAAG 59.478 55.000 0.00 0.00 0.00 3.79
1489 2631 1.241315 TGCCTTTAAGCCACCGAAGC 61.241 55.000 0.00 0.00 0.00 3.86
1490 2632 0.960861 GCCTTTAAGCCACCGAAGCT 60.961 55.000 0.00 0.00 44.19 3.74
1491 2633 0.804989 CCTTTAAGCCACCGAAGCTG 59.195 55.000 0.00 0.00 40.49 4.24
1492 2634 0.169009 CTTTAAGCCACCGAAGCTGC 59.831 55.000 0.00 0.00 40.49 5.25
1493 2635 1.573829 TTTAAGCCACCGAAGCTGCG 61.574 55.000 7.28 7.28 40.49 5.18
1494 2636 2.725203 TTAAGCCACCGAAGCTGCGT 62.725 55.000 14.34 0.00 40.49 5.24
1511 2653 2.414768 CGTCCGTTAATCTTTGACGC 57.585 50.000 0.00 0.00 41.71 5.19
1515 2657 3.617263 GTCCGTTAATCTTTGACGCATCT 59.383 43.478 0.00 0.00 35.60 2.90
1563 3383 9.739276 TCTGATTAAAGAAGGTTTGTCATGTAT 57.261 29.630 0.00 0.00 0.00 2.29
1572 3392 9.458374 AGAAGGTTTGTCATGTATTTAAAAACG 57.542 29.630 0.00 0.00 0.00 3.60
1573 3393 9.240159 GAAGGTTTGTCATGTATTTAAAAACGT 57.760 29.630 0.00 0.00 0.00 3.99
1574 3394 8.568732 AGGTTTGTCATGTATTTAAAAACGTG 57.431 30.769 0.00 0.00 34.57 4.49
1575 3395 8.192110 AGGTTTGTCATGTATTTAAAAACGTGT 58.808 29.630 0.00 0.00 34.81 4.49
1576 3396 8.809478 GGTTTGTCATGTATTTAAAAACGTGTT 58.191 29.630 0.00 0.00 34.81 3.32
1580 3400 9.999009 TGTCATGTATTTAAAAACGTGTTTACA 57.001 25.926 10.49 8.52 34.81 2.41
1605 3425 9.498307 CATGTTTACAATAAAAGTATTCGTCCC 57.502 33.333 0.00 0.00 0.00 4.46
1606 3426 8.618702 TGTTTACAATAAAAGTATTCGTCCCA 57.381 30.769 0.00 0.00 0.00 4.37
1607 3427 9.064706 TGTTTACAATAAAAGTATTCGTCCCAA 57.935 29.630 0.00 0.00 0.00 4.12
1612 3432 9.418045 ACAATAAAAGTATTCGTCCCAATTTTG 57.582 29.630 0.00 0.00 0.00 2.44
1629 3449 7.781763 CAATTTTGGACTAGCGTTCTTTAAG 57.218 36.000 0.00 0.00 0.00 1.85
1630 3450 7.360361 CAATTTTGGACTAGCGTTCTTTAAGT 58.640 34.615 0.00 0.00 0.00 2.24
1631 3451 6.930667 TTTTGGACTAGCGTTCTTTAAGTT 57.069 33.333 0.00 0.00 0.00 2.66
1632 3452 6.930667 TTTGGACTAGCGTTCTTTAAGTTT 57.069 33.333 0.00 0.00 0.00 2.66
1633 3453 8.436046 TTTTGGACTAGCGTTCTTTAAGTTTA 57.564 30.769 0.00 0.00 0.00 2.01
1634 3454 8.436046 TTTGGACTAGCGTTCTTTAAGTTTAA 57.564 30.769 0.00 0.00 0.00 1.52
1635 3455 7.647907 TGGACTAGCGTTCTTTAAGTTTAAG 57.352 36.000 0.00 0.00 0.00 1.85
1636 3456 7.436118 TGGACTAGCGTTCTTTAAGTTTAAGA 58.564 34.615 0.21 0.21 0.00 2.10
1637 3457 8.092687 TGGACTAGCGTTCTTTAAGTTTAAGAT 58.907 33.333 5.23 0.00 32.09 2.40
1638 3458 9.578439 GGACTAGCGTTCTTTAAGTTTAAGATA 57.422 33.333 5.23 0.00 32.09 1.98
1765 3586 7.455008 AGAGTATAGGGTGGTCATAATACAAGG 59.545 40.741 0.00 0.00 0.00 3.61
1796 3617 1.993956 TTGGTGGGTTGATGACAAGG 58.006 50.000 0.00 0.00 36.64 3.61
2007 3830 8.519799 TTTTGTCAAGTCTCTTTACAGGAAAT 57.480 30.769 0.00 0.00 0.00 2.17
2056 3886 3.436700 AAAAACTCTTTGCAAGGTCGG 57.563 42.857 8.56 3.39 0.00 4.79
2157 3987 2.289010 GGGTGAGCTGGAAACAAAATGG 60.289 50.000 0.00 0.00 42.06 3.16
2167 3997 6.179906 TGGAAACAAAATGGGCATTTTCTA 57.820 33.333 0.00 0.00 46.01 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.541764 TTCATCAGTTTGGGCCCACC 60.542 55.000 28.70 18.98 40.81 4.61
8 9 1.337118 TTTCATCAGTTTGGGCCCAC 58.663 50.000 28.70 15.32 0.00 4.61
9 10 2.323999 ATTTCATCAGTTTGGGCCCA 57.676 45.000 24.45 24.45 0.00 5.36
10 11 3.096092 TGTATTTCATCAGTTTGGGCCC 58.904 45.455 17.59 17.59 0.00 5.80
11 12 3.763897 ACTGTATTTCATCAGTTTGGGCC 59.236 43.478 0.00 0.00 41.33 5.80
12 13 4.380867 CCACTGTATTTCATCAGTTTGGGC 60.381 45.833 0.00 0.00 42.05 5.36
13 14 4.380867 GCCACTGTATTTCATCAGTTTGGG 60.381 45.833 0.00 0.00 42.05 4.12
14 15 4.460382 AGCCACTGTATTTCATCAGTTTGG 59.540 41.667 0.00 0.00 42.05 3.28
15 16 5.181811 TCAGCCACTGTATTTCATCAGTTTG 59.818 40.000 0.00 0.00 42.05 2.93
16 17 5.316167 TCAGCCACTGTATTTCATCAGTTT 58.684 37.500 0.00 0.00 42.05 2.66
17 18 4.910195 TCAGCCACTGTATTTCATCAGTT 58.090 39.130 0.00 0.00 42.05 3.16
18 19 4.558226 TCAGCCACTGTATTTCATCAGT 57.442 40.909 0.00 0.00 44.32 3.41
19 20 5.885230 TTTCAGCCACTGTATTTCATCAG 57.115 39.130 0.00 0.00 37.65 2.90
20 21 5.945191 TCATTTCAGCCACTGTATTTCATCA 59.055 36.000 0.00 0.00 32.61 3.07
21 22 6.441093 TCATTTCAGCCACTGTATTTCATC 57.559 37.500 0.00 0.00 32.61 2.92
22 23 6.660521 TCTTCATTTCAGCCACTGTATTTCAT 59.339 34.615 0.00 0.00 32.61 2.57
23 24 6.003326 TCTTCATTTCAGCCACTGTATTTCA 58.997 36.000 0.00 0.00 32.61 2.69
24 25 6.500684 TCTTCATTTCAGCCACTGTATTTC 57.499 37.500 0.00 0.00 32.61 2.17
25 26 6.899393 TTCTTCATTTCAGCCACTGTATTT 57.101 33.333 0.00 0.00 32.61 1.40
26 27 6.899393 TTTCTTCATTTCAGCCACTGTATT 57.101 33.333 0.00 0.00 32.61 1.89
27 28 6.265196 TGTTTTCTTCATTTCAGCCACTGTAT 59.735 34.615 0.00 0.00 32.61 2.29
28 29 5.592282 TGTTTTCTTCATTTCAGCCACTGTA 59.408 36.000 0.00 0.00 32.61 2.74
29 30 4.402155 TGTTTTCTTCATTTCAGCCACTGT 59.598 37.500 0.00 0.00 32.61 3.55
30 31 4.935702 TGTTTTCTTCATTTCAGCCACTG 58.064 39.130 0.00 0.00 0.00 3.66
31 32 4.646492 ACTGTTTTCTTCATTTCAGCCACT 59.354 37.500 0.00 0.00 0.00 4.00
32 33 4.741676 CACTGTTTTCTTCATTTCAGCCAC 59.258 41.667 0.00 0.00 0.00 5.01
33 34 4.202141 CCACTGTTTTCTTCATTTCAGCCA 60.202 41.667 0.00 0.00 0.00 4.75
34 35 4.037923 TCCACTGTTTTCTTCATTTCAGCC 59.962 41.667 0.00 0.00 0.00 4.85
35 36 5.186996 TCCACTGTTTTCTTCATTTCAGC 57.813 39.130 0.00 0.00 0.00 4.26
36 37 8.352201 TGTATTCCACTGTTTTCTTCATTTCAG 58.648 33.333 0.00 0.00 0.00 3.02
37 38 8.231692 TGTATTCCACTGTTTTCTTCATTTCA 57.768 30.769 0.00 0.00 0.00 2.69
38 39 9.528018 TTTGTATTCCACTGTTTTCTTCATTTC 57.472 29.630 0.00 0.00 0.00 2.17
39 40 9.533253 CTTTGTATTCCACTGTTTTCTTCATTT 57.467 29.630 0.00 0.00 0.00 2.32
40 41 8.912988 TCTTTGTATTCCACTGTTTTCTTCATT 58.087 29.630 0.00 0.00 0.00 2.57
41 42 8.463930 TCTTTGTATTCCACTGTTTTCTTCAT 57.536 30.769 0.00 0.00 0.00 2.57
42 43 7.873719 TCTTTGTATTCCACTGTTTTCTTCA 57.126 32.000 0.00 0.00 0.00 3.02
43 44 9.827411 GTATCTTTGTATTCCACTGTTTTCTTC 57.173 33.333 0.00 0.00 0.00 2.87
44 45 9.349713 TGTATCTTTGTATTCCACTGTTTTCTT 57.650 29.630 0.00 0.00 0.00 2.52
45 46 8.918202 TGTATCTTTGTATTCCACTGTTTTCT 57.082 30.769 0.00 0.00 0.00 2.52
46 47 9.394477 GTTGTATCTTTGTATTCCACTGTTTTC 57.606 33.333 0.00 0.00 0.00 2.29
47 48 9.131791 AGTTGTATCTTTGTATTCCACTGTTTT 57.868 29.630 0.00 0.00 0.00 2.43
48 49 8.691661 AGTTGTATCTTTGTATTCCACTGTTT 57.308 30.769 0.00 0.00 0.00 2.83
49 50 8.691661 AAGTTGTATCTTTGTATTCCACTGTT 57.308 30.769 0.00 0.00 0.00 3.16
50 51 9.436957 CTAAGTTGTATCTTTGTATTCCACTGT 57.563 33.333 0.00 0.00 0.00 3.55
51 52 9.436957 ACTAAGTTGTATCTTTGTATTCCACTG 57.563 33.333 0.00 0.00 33.32 3.66
59 60 9.991906 AAAGCTGTACTAAGTTGTATCTTTGTA 57.008 29.630 0.00 0.00 35.70 2.41
60 61 8.904099 AAAGCTGTACTAAGTTGTATCTTTGT 57.096 30.769 0.00 0.00 37.25 2.83
61 62 9.599322 CAAAAGCTGTACTAAGTTGTATCTTTG 57.401 33.333 0.00 0.00 0.00 2.77
62 63 9.555727 TCAAAAGCTGTACTAAGTTGTATCTTT 57.444 29.630 0.00 0.00 0.00 2.52
63 64 9.209175 CTCAAAAGCTGTACTAAGTTGTATCTT 57.791 33.333 0.00 0.00 0.00 2.40
64 65 7.819900 CCTCAAAAGCTGTACTAAGTTGTATCT 59.180 37.037 0.00 0.00 0.00 1.98
65 66 7.603024 ACCTCAAAAGCTGTACTAAGTTGTATC 59.397 37.037 0.00 0.00 0.00 2.24
66 67 7.387948 CACCTCAAAAGCTGTACTAAGTTGTAT 59.612 37.037 0.00 0.00 0.00 2.29
67 68 6.704493 CACCTCAAAAGCTGTACTAAGTTGTA 59.296 38.462 0.00 0.00 0.00 2.41
68 69 5.527582 CACCTCAAAAGCTGTACTAAGTTGT 59.472 40.000 0.00 0.00 0.00 3.32
69 70 5.049405 CCACCTCAAAAGCTGTACTAAGTTG 60.049 44.000 0.00 0.00 0.00 3.16
70 71 5.063880 CCACCTCAAAAGCTGTACTAAGTT 58.936 41.667 0.00 0.00 0.00 2.66
71 72 4.642429 CCACCTCAAAAGCTGTACTAAGT 58.358 43.478 0.00 0.00 0.00 2.24
72 73 3.437049 GCCACCTCAAAAGCTGTACTAAG 59.563 47.826 0.00 0.00 0.00 2.18
73 74 3.181449 TGCCACCTCAAAAGCTGTACTAA 60.181 43.478 0.00 0.00 0.00 2.24
74 75 2.370519 TGCCACCTCAAAAGCTGTACTA 59.629 45.455 0.00 0.00 0.00 1.82
75 76 1.142870 TGCCACCTCAAAAGCTGTACT 59.857 47.619 0.00 0.00 0.00 2.73
76 77 1.537202 CTGCCACCTCAAAAGCTGTAC 59.463 52.381 0.00 0.00 0.00 2.90
77 78 1.545428 CCTGCCACCTCAAAAGCTGTA 60.545 52.381 0.00 0.00 0.00 2.74
78 79 0.825010 CCTGCCACCTCAAAAGCTGT 60.825 55.000 0.00 0.00 0.00 4.40
79 80 0.538057 TCCTGCCACCTCAAAAGCTG 60.538 55.000 0.00 0.00 0.00 4.24
80 81 0.538287 GTCCTGCCACCTCAAAAGCT 60.538 55.000 0.00 0.00 0.00 3.74
81 82 0.538287 AGTCCTGCCACCTCAAAAGC 60.538 55.000 0.00 0.00 0.00 3.51
82 83 1.072965 AGAGTCCTGCCACCTCAAAAG 59.927 52.381 0.00 0.00 0.00 2.27
83 84 1.140312 AGAGTCCTGCCACCTCAAAA 58.860 50.000 0.00 0.00 0.00 2.44
84 85 2.024176 TAGAGTCCTGCCACCTCAAA 57.976 50.000 0.00 0.00 0.00 2.69
85 86 2.237143 CAATAGAGTCCTGCCACCTCAA 59.763 50.000 0.00 0.00 0.00 3.02
86 87 1.833630 CAATAGAGTCCTGCCACCTCA 59.166 52.381 0.00 0.00 0.00 3.86
87 88 1.139853 CCAATAGAGTCCTGCCACCTC 59.860 57.143 0.00 0.00 0.00 3.85
88 89 1.207791 CCAATAGAGTCCTGCCACCT 58.792 55.000 0.00 0.00 0.00 4.00
89 90 0.464554 GCCAATAGAGTCCTGCCACC 60.465 60.000 0.00 0.00 0.00 4.61
90 91 0.543749 AGCCAATAGAGTCCTGCCAC 59.456 55.000 0.00 0.00 0.00 5.01
91 92 0.543277 CAGCCAATAGAGTCCTGCCA 59.457 55.000 0.00 0.00 0.00 4.92
92 93 0.543749 ACAGCCAATAGAGTCCTGCC 59.456 55.000 0.00 0.00 0.00 4.85
93 94 1.065854 ACACAGCCAATAGAGTCCTGC 60.066 52.381 0.00 0.00 0.00 4.85
94 95 4.471904 TTACACAGCCAATAGAGTCCTG 57.528 45.455 0.00 0.00 0.00 3.86
95 96 5.499004 TTTTACACAGCCAATAGAGTCCT 57.501 39.130 0.00 0.00 0.00 3.85
96 97 5.938125 TCTTTTTACACAGCCAATAGAGTCC 59.062 40.000 0.00 0.00 0.00 3.85
97 98 6.092807 CCTCTTTTTACACAGCCAATAGAGTC 59.907 42.308 0.00 0.00 0.00 3.36
98 99 5.940470 CCTCTTTTTACACAGCCAATAGAGT 59.060 40.000 0.00 0.00 0.00 3.24
99 100 5.940470 ACCTCTTTTTACACAGCCAATAGAG 59.060 40.000 0.00 0.00 0.00 2.43
100 101 5.876357 ACCTCTTTTTACACAGCCAATAGA 58.124 37.500 0.00 0.00 0.00 1.98
101 102 6.575162 AACCTCTTTTTACACAGCCAATAG 57.425 37.500 0.00 0.00 0.00 1.73
102 103 6.737346 GCAAACCTCTTTTTACACAGCCAATA 60.737 38.462 0.00 0.00 0.00 1.90
103 104 5.600696 CAAACCTCTTTTTACACAGCCAAT 58.399 37.500 0.00 0.00 0.00 3.16
104 105 4.679372 GCAAACCTCTTTTTACACAGCCAA 60.679 41.667 0.00 0.00 0.00 4.52
105 106 3.181480 GCAAACCTCTTTTTACACAGCCA 60.181 43.478 0.00 0.00 0.00 4.75
106 107 3.381045 GCAAACCTCTTTTTACACAGCC 58.619 45.455 0.00 0.00 0.00 4.85
107 108 3.042887 CGCAAACCTCTTTTTACACAGC 58.957 45.455 0.00 0.00 0.00 4.40
108 109 3.550030 CCCGCAAACCTCTTTTTACACAG 60.550 47.826 0.00 0.00 0.00 3.66
109 110 2.359531 CCCGCAAACCTCTTTTTACACA 59.640 45.455 0.00 0.00 0.00 3.72
110 111 2.287970 CCCCGCAAACCTCTTTTTACAC 60.288 50.000 0.00 0.00 0.00 2.90
111 112 1.957877 CCCCGCAAACCTCTTTTTACA 59.042 47.619 0.00 0.00 0.00 2.41
112 113 1.336517 GCCCCGCAAACCTCTTTTTAC 60.337 52.381 0.00 0.00 0.00 2.01
113 114 0.963225 GCCCCGCAAACCTCTTTTTA 59.037 50.000 0.00 0.00 0.00 1.52
114 115 1.045911 TGCCCCGCAAACCTCTTTTT 61.046 50.000 0.00 0.00 34.76 1.94
115 116 1.456705 TGCCCCGCAAACCTCTTTT 60.457 52.632 0.00 0.00 34.76 2.27
116 117 2.197324 TGCCCCGCAAACCTCTTT 59.803 55.556 0.00 0.00 34.76 2.52
117 118 2.597510 GTGCCCCGCAAACCTCTT 60.598 61.111 0.00 0.00 41.47 2.85
118 119 3.210012 ATGTGCCCCGCAAACCTCT 62.210 57.895 0.00 0.00 41.47 3.69
119 120 2.676471 ATGTGCCCCGCAAACCTC 60.676 61.111 0.00 0.00 41.47 3.85
120 121 2.990967 CATGTGCCCCGCAAACCT 60.991 61.111 0.00 0.00 41.47 3.50
121 122 4.740431 GCATGTGCCCCGCAAACC 62.740 66.667 0.00 0.00 41.47 3.27
122 123 3.988525 TGCATGTGCCCCGCAAAC 61.989 61.111 2.07 0.00 41.47 2.93
123 124 3.988525 GTGCATGTGCCCCGCAAA 61.989 61.111 2.07 0.00 41.47 3.68
294 306 0.612229 TGAGCCAGAAAGCAGGAGAG 59.388 55.000 0.00 0.00 34.23 3.20
299 311 1.002379 AGCCTGAGCCAGAAAGCAG 60.002 57.895 4.00 0.00 41.25 4.24
305 317 0.336392 TTAGGAGAGCCTGAGCCAGA 59.664 55.000 4.00 0.00 46.45 3.86
323 335 3.259876 TGACCAACGTTGCTACTAGGATT 59.740 43.478 22.93 0.00 0.00 3.01
431 443 1.748122 CACTGATGCTGCTGGGGTC 60.748 63.158 0.00 0.00 0.00 4.46
661 749 3.873361 ACGTGGTGATGCTGAGAAATATG 59.127 43.478 0.00 0.00 0.00 1.78
682 770 9.672086 TTAAAACATGTAAAGTGCAGATACAAC 57.328 29.630 0.00 0.00 33.63 3.32
694 782 9.113876 CCGAAAACTAGCTTAAAACATGTAAAG 57.886 33.333 0.00 5.00 0.00 1.85
719 813 6.699575 AAATCCATAGTGTTACATTGCTCC 57.300 37.500 0.00 0.00 0.00 4.70
772 866 1.202770 TCGATATCCTCACTGGCTCGA 60.203 52.381 0.00 0.00 38.05 4.04
811 905 1.821936 CACTTGGGCAGGCAAACAA 59.178 52.632 0.00 0.00 0.00 2.83
812 906 2.795110 GCACTTGGGCAGGCAAACA 61.795 57.895 0.00 0.00 0.00 2.83
820 914 2.925706 TACTCGGGCACTTGGGCA 60.926 61.111 0.00 0.00 45.66 5.36
903 1000 2.168106 AGCTGTGAAAGATGATCGAGCT 59.832 45.455 0.90 0.00 33.04 4.09
908 1005 6.369890 TGAGTTTACAGCTGTGAAAGATGATC 59.630 38.462 29.57 16.79 45.58 2.92
909 1006 6.233434 TGAGTTTACAGCTGTGAAAGATGAT 58.767 36.000 29.57 9.42 45.58 2.45
910 1007 5.610398 TGAGTTTACAGCTGTGAAAGATGA 58.390 37.500 29.57 8.39 45.58 2.92
946 1043 3.951306 TGACTTGACTTGCATTTGTTCG 58.049 40.909 0.00 0.00 0.00 3.95
948 1045 5.329035 AGTTGACTTGACTTGCATTTGTT 57.671 34.783 0.00 0.00 0.00 2.83
994 1091 1.016130 AAGAACAGTCGCATCAGCCG 61.016 55.000 0.00 0.00 37.52 5.52
997 1094 2.159734 GCTTGAAGAACAGTCGCATCAG 60.160 50.000 0.00 0.00 0.00 2.90
1073 1227 1.366787 TCCTCCCCCATACACCAACTA 59.633 52.381 0.00 0.00 0.00 2.24
1148 1302 3.692406 GCCTGGGACGAGTCGGTT 61.692 66.667 18.30 0.00 0.00 4.44
1231 1385 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
1232 1386 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
1233 1387 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1234 1388 4.947147 CGGTGGTGGTGGTGGTGG 62.947 72.222 0.00 0.00 0.00 4.61
1244 1398 2.550699 ATATGGTGGTGGCGGTGGTG 62.551 60.000 0.00 0.00 0.00 4.17
1245 1399 2.265467 GATATGGTGGTGGCGGTGGT 62.265 60.000 0.00 0.00 0.00 4.16
1246 1400 1.525995 GATATGGTGGTGGCGGTGG 60.526 63.158 0.00 0.00 0.00 4.61
1247 1401 1.887242 CGATATGGTGGTGGCGGTG 60.887 63.158 0.00 0.00 0.00 4.94
1248 1402 2.504032 CGATATGGTGGTGGCGGT 59.496 61.111 0.00 0.00 0.00 5.68
1249 1403 2.972505 GCGATATGGTGGTGGCGG 60.973 66.667 0.00 0.00 0.00 6.13
1250 1404 2.972505 GGCGATATGGTGGTGGCG 60.973 66.667 0.00 0.00 0.00 5.69
1251 1405 1.453015 TTGGCGATATGGTGGTGGC 60.453 57.895 0.00 0.00 0.00 5.01
1305 1462 2.438800 AGATCTAGTGGCACGGTAGT 57.561 50.000 12.71 0.00 0.00 2.73
1353 2495 3.609853 AGGTCTTCGCAAATCATAAGCA 58.390 40.909 0.00 0.00 0.00 3.91
1384 2526 5.490139 AAGCATCGTCCAAGATTAACATG 57.510 39.130 0.00 0.00 0.00 3.21
1386 2528 3.616821 CGAAGCATCGTCCAAGATTAACA 59.383 43.478 2.58 0.00 44.06 2.41
1387 2529 4.183539 CGAAGCATCGTCCAAGATTAAC 57.816 45.455 2.58 0.00 44.06 2.01
1400 2542 1.221414 GTCATAGGCACCGAAGCATC 58.779 55.000 1.64 0.00 35.83 3.91
1401 2543 0.541392 TGTCATAGGCACCGAAGCAT 59.459 50.000 1.64 0.00 35.83 3.79
1402 2544 0.541392 ATGTCATAGGCACCGAAGCA 59.459 50.000 1.64 0.00 35.83 3.91
1403 2545 0.940126 CATGTCATAGGCACCGAAGC 59.060 55.000 0.00 0.00 0.00 3.86
1404 2546 1.935873 CACATGTCATAGGCACCGAAG 59.064 52.381 0.00 0.00 0.00 3.79
1405 2547 1.406751 CCACATGTCATAGGCACCGAA 60.407 52.381 0.00 0.00 0.00 4.30
1406 2548 0.177836 CCACATGTCATAGGCACCGA 59.822 55.000 0.00 0.00 0.00 4.69
1407 2549 0.177836 TCCACATGTCATAGGCACCG 59.822 55.000 0.00 0.00 0.00 4.94
1408 2550 2.498167 GATCCACATGTCATAGGCACC 58.502 52.381 0.00 0.00 0.00 5.01
1409 2551 2.158769 TGGATCCACATGTCATAGGCAC 60.159 50.000 11.44 0.00 0.00 5.01
1410 2552 2.126057 TGGATCCACATGTCATAGGCA 58.874 47.619 11.44 0.00 0.00 4.75
1411 2553 2.880890 GTTGGATCCACATGTCATAGGC 59.119 50.000 15.91 0.00 0.00 3.93
1412 2554 4.132336 CTGTTGGATCCACATGTCATAGG 58.868 47.826 15.91 0.00 0.00 2.57
1413 2555 4.132336 CCTGTTGGATCCACATGTCATAG 58.868 47.826 15.91 6.29 34.57 2.23
1414 2556 3.523157 ACCTGTTGGATCCACATGTCATA 59.477 43.478 15.91 0.00 37.04 2.15
1415 2557 2.309755 ACCTGTTGGATCCACATGTCAT 59.690 45.455 15.91 0.00 37.04 3.06
1416 2558 1.704628 ACCTGTTGGATCCACATGTCA 59.295 47.619 15.91 8.10 37.04 3.58
1417 2559 2.086869 CACCTGTTGGATCCACATGTC 58.913 52.381 15.91 3.66 37.04 3.06
1418 2560 1.704628 TCACCTGTTGGATCCACATGT 59.295 47.619 15.91 15.16 37.04 3.21
1419 2561 2.086869 GTCACCTGTTGGATCCACATG 58.913 52.381 15.91 14.55 37.04 3.21
1420 2562 1.988107 AGTCACCTGTTGGATCCACAT 59.012 47.619 15.91 0.00 37.04 3.21
1421 2563 1.072173 CAGTCACCTGTTGGATCCACA 59.928 52.381 15.91 14.69 37.04 4.17
1422 2564 1.347707 TCAGTCACCTGTTGGATCCAC 59.652 52.381 15.91 10.58 39.82 4.02
1423 2565 1.347707 GTCAGTCACCTGTTGGATCCA 59.652 52.381 11.44 11.44 39.82 3.41
1424 2566 1.339151 GGTCAGTCACCTGTTGGATCC 60.339 57.143 4.20 4.20 42.84 3.36
1425 2567 1.339151 GGGTCAGTCACCTGTTGGATC 60.339 57.143 0.00 0.00 45.95 3.36
1426 2568 0.693049 GGGTCAGTCACCTGTTGGAT 59.307 55.000 0.00 0.00 45.95 3.41
1427 2569 0.692756 TGGGTCAGTCACCTGTTGGA 60.693 55.000 0.00 0.00 45.95 3.53
1428 2570 0.535102 GTGGGTCAGTCACCTGTTGG 60.535 60.000 0.00 0.00 45.95 3.77
1429 2571 0.180171 TGTGGGTCAGTCACCTGTTG 59.820 55.000 0.00 0.00 45.95 3.33
1430 2572 1.140312 ATGTGGGTCAGTCACCTGTT 58.860 50.000 0.00 0.00 45.95 3.16
1431 2573 0.397941 CATGTGGGTCAGTCACCTGT 59.602 55.000 0.00 0.00 45.95 4.00
1432 2574 0.397941 ACATGTGGGTCAGTCACCTG 59.602 55.000 0.00 0.00 45.95 4.00
1433 2575 0.687354 GACATGTGGGTCAGTCACCT 59.313 55.000 1.15 0.00 45.95 4.00
1434 2576 0.396435 TGACATGTGGGTCAGTCACC 59.604 55.000 1.15 0.00 42.56 4.02
1440 2582 0.396435 GGTCACTGACATGTGGGTCA 59.604 55.000 1.15 0.00 45.06 4.02
1441 2583 0.321653 GGGTCACTGACATGTGGGTC 60.322 60.000 1.15 0.00 38.40 4.46
1442 2584 1.059584 TGGGTCACTGACATGTGGGT 61.060 55.000 1.15 0.00 38.40 4.51
1443 2585 0.110295 TTGGGTCACTGACATGTGGG 59.890 55.000 1.15 0.00 38.40 4.61
1444 2586 1.881973 CTTTGGGTCACTGACATGTGG 59.118 52.381 1.15 0.00 38.40 4.17
1445 2587 1.881973 CCTTTGGGTCACTGACATGTG 59.118 52.381 1.15 0.00 39.15 3.21
1446 2588 1.819305 GCCTTTGGGTCACTGACATGT 60.819 52.381 11.34 0.00 33.68 3.21
1447 2589 0.883833 GCCTTTGGGTCACTGACATG 59.116 55.000 11.34 0.00 33.68 3.21
1448 2590 0.478072 TGCCTTTGGGTCACTGACAT 59.522 50.000 11.34 0.00 33.68 3.06
1449 2591 0.179020 CTGCCTTTGGGTCACTGACA 60.179 55.000 11.34 0.00 33.68 3.58
1450 2592 0.890996 CCTGCCTTTGGGTCACTGAC 60.891 60.000 0.00 0.00 34.45 3.51
1451 2593 1.352622 ACCTGCCTTTGGGTCACTGA 61.353 55.000 0.00 0.00 34.45 3.41
1452 2594 1.151450 ACCTGCCTTTGGGTCACTG 59.849 57.895 0.00 0.00 34.45 3.66
1453 2595 1.151450 CACCTGCCTTTGGGTCACT 59.849 57.895 0.00 0.00 32.95 3.41
1454 2596 2.564721 GCACCTGCCTTTGGGTCAC 61.565 63.158 0.00 0.00 32.95 3.67
1455 2597 2.203480 GCACCTGCCTTTGGGTCA 60.203 61.111 0.00 0.00 32.95 4.02
1465 2607 4.095590 TGGCTTAAAGGCACCTGC 57.904 55.556 0.61 0.00 46.47 4.85
1471 2613 0.960861 AGCTTCGGTGGCTTAAAGGC 60.961 55.000 0.00 0.00 41.77 4.35
1472 2614 0.804989 CAGCTTCGGTGGCTTAAAGG 59.195 55.000 0.00 0.00 38.03 3.11
1473 2615 0.169009 GCAGCTTCGGTGGCTTAAAG 59.831 55.000 0.00 0.00 38.03 1.85
1474 2616 1.573829 CGCAGCTTCGGTGGCTTAAA 61.574 55.000 0.00 0.00 38.03 1.52
1475 2617 2.032634 CGCAGCTTCGGTGGCTTAA 61.033 57.895 0.00 0.00 38.03 1.85
1476 2618 2.434185 CGCAGCTTCGGTGGCTTA 60.434 61.111 0.00 0.00 38.03 3.09
1477 2619 4.626081 ACGCAGCTTCGGTGGCTT 62.626 61.111 11.19 0.00 38.03 4.35
1482 2624 2.424705 TTAACGGACGCAGCTTCGGT 62.425 55.000 11.19 6.30 0.00 4.69
1483 2625 1.082117 ATTAACGGACGCAGCTTCGG 61.082 55.000 11.19 5.05 0.00 4.30
1484 2626 0.297820 GATTAACGGACGCAGCTTCG 59.702 55.000 3.63 3.63 0.00 3.79
1485 2627 1.641577 AGATTAACGGACGCAGCTTC 58.358 50.000 0.00 0.00 0.00 3.86
1486 2628 2.094762 AAGATTAACGGACGCAGCTT 57.905 45.000 0.00 0.00 0.00 3.74
1487 2629 1.732259 CAAAGATTAACGGACGCAGCT 59.268 47.619 0.00 0.00 0.00 4.24
1488 2630 1.730064 TCAAAGATTAACGGACGCAGC 59.270 47.619 0.00 0.00 0.00 5.25
1489 2631 2.222508 CGTCAAAGATTAACGGACGCAG 60.223 50.000 0.00 0.00 43.69 5.18
1490 2632 1.722464 CGTCAAAGATTAACGGACGCA 59.278 47.619 0.00 0.00 43.69 5.24
1491 2633 2.414768 CGTCAAAGATTAACGGACGC 57.585 50.000 0.00 0.00 43.69 5.19
1493 2635 3.617263 AGATGCGTCAAAGATTAACGGAC 59.383 43.478 8.99 0.00 39.51 4.79
1494 2636 3.857052 AGATGCGTCAAAGATTAACGGA 58.143 40.909 8.99 0.00 40.92 4.69
1495 2637 4.600012 AAGATGCGTCAAAGATTAACGG 57.400 40.909 8.99 0.00 36.92 4.44
1527 2669 9.588096 AACCTTCTTTAATCAGATAACAACCTT 57.412 29.630 0.00 0.00 0.00 3.50
1529 2671 9.626045 CAAACCTTCTTTAATCAGATAACAACC 57.374 33.333 0.00 0.00 0.00 3.77
1536 3356 8.641498 ACATGACAAACCTTCTTTAATCAGAT 57.359 30.769 0.00 0.00 0.00 2.90
1579 3399 9.498307 GGGACGAATACTTTTATTGTAAACATG 57.502 33.333 0.00 0.00 0.00 3.21
1580 3400 9.233649 TGGGACGAATACTTTTATTGTAAACAT 57.766 29.630 0.00 0.00 0.00 2.71
1581 3401 8.618702 TGGGACGAATACTTTTATTGTAAACA 57.381 30.769 0.00 0.00 0.00 2.83
1586 3406 9.418045 CAAAATTGGGACGAATACTTTTATTGT 57.582 29.630 0.00 0.00 0.00 2.71
1587 3407 8.868916 CCAAAATTGGGACGAATACTTTTATTG 58.131 33.333 4.18 0.00 44.70 1.90
1588 3408 8.996024 CCAAAATTGGGACGAATACTTTTATT 57.004 30.769 4.18 0.00 44.70 1.40
1605 3425 7.360361 ACTTAAAGAACGCTAGTCCAAAATTG 58.640 34.615 0.00 0.00 0.00 2.32
1606 3426 7.506328 ACTTAAAGAACGCTAGTCCAAAATT 57.494 32.000 0.00 0.00 0.00 1.82
1607 3427 7.506328 AACTTAAAGAACGCTAGTCCAAAAT 57.494 32.000 0.00 0.00 0.00 1.82
1608 3428 6.930667 AACTTAAAGAACGCTAGTCCAAAA 57.069 33.333 0.00 0.00 0.00 2.44
1609 3429 6.930667 AAACTTAAAGAACGCTAGTCCAAA 57.069 33.333 0.00 0.00 0.00 3.28
1610 3430 7.927629 TCTTAAACTTAAAGAACGCTAGTCCAA 59.072 33.333 0.00 0.00 0.00 3.53
1611 3431 7.436118 TCTTAAACTTAAAGAACGCTAGTCCA 58.564 34.615 0.00 0.00 0.00 4.02
1612 3432 7.880059 TCTTAAACTTAAAGAACGCTAGTCC 57.120 36.000 0.00 0.00 0.00 3.85
1744 3565 6.841781 AACCTTGTATTATGACCACCCTAT 57.158 37.500 0.00 0.00 0.00 2.57
1765 3586 4.126437 CAACCCACCAATCTTCCAAAAAC 58.874 43.478 0.00 0.00 0.00 2.43
1796 3617 6.940298 TGATATAGGGTAAGCAATTTAGGTGC 59.060 38.462 0.00 0.00 42.55 5.01
1883 3704 5.805728 ACTATTCCACAGATCCGAAAACTT 58.194 37.500 0.00 0.00 0.00 2.66
1889 3710 7.162761 TGTTTTAAACTATTCCACAGATCCGA 58.837 34.615 9.33 0.00 0.00 4.55
1958 3780 5.633830 ATTGTGAGTTGTCAACATCCATC 57.366 39.130 17.78 6.71 33.27 3.51
2141 3971 1.422531 TGCCCATTTTGTTTCCAGCT 58.577 45.000 0.00 0.00 0.00 4.24
2157 3987 3.575256 TCATCCATGCCATAGAAAATGCC 59.425 43.478 0.00 0.00 0.00 4.40
2167 3997 5.189342 TGGTTTATTGTTTCATCCATGCCAT 59.811 36.000 0.00 0.00 0.00 4.40
2206 4036 7.768120 ACTCTCAGACAAAATTAGCAATAGAGG 59.232 37.037 0.00 0.00 31.95 3.69
2211 4041 6.865205 GCAAACTCTCAGACAAAATTAGCAAT 59.135 34.615 0.00 0.00 0.00 3.56
2222 4052 4.454678 ACATTTCAGCAAACTCTCAGACA 58.545 39.130 0.00 0.00 0.00 3.41
2228 4058 8.451908 ACTAAAAGTACATTTCAGCAAACTCT 57.548 30.769 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.