Multiple sequence alignment - TraesCS7A01G386400

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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 TraesCS7A01G386400 chr7A 100.000 2713 0 0 1 2713 562095807 562098519 0.000000e+00 5011.0
1 TraesCS7A01G386400 chr2D 93.790 934 45 3 1768 2701 648874341 648875261 0.000000e+00 1391.0
2 TraesCS7A01G386400 chr2D 83.843 229 32 4 1774 1997 103163913 103164141 2.120000e-51 213.0
3 TraesCS7A01G386400 chr2D 85.185 189 22 2 158 346 354805947 354806129 3.570000e-44 189.0
4 TraesCS7A01G386400 chr7B 88.877 935 89 9 855 1776 651389912 651390844 0.000000e+00 1136.0
5 TraesCS7A01G386400 chr7B 94.217 415 22 2 1363 1776 36571716 36571303 1.370000e-177 632.0
6 TraesCS7A01G386400 chr7B 82.353 731 91 16 128 854 651389158 651389854 3.870000e-168 601.0
7 TraesCS7A01G386400 chr7B 86.282 554 43 14 1771 2322 584642294 584641772 3.030000e-159 571.0
8 TraesCS7A01G386400 chr3B 93.226 620 28 3 2094 2713 733616153 733615548 0.000000e+00 900.0
9 TraesCS7A01G386400 chr3B 94.012 334 20 0 1768 2101 733617007 733616674 8.670000e-140 507.0
10 TraesCS7A01G386400 chr3B 80.423 378 39 11 1999 2359 766359168 766359527 3.470000e-64 255.0
11 TraesCS7A01G386400 chr4B 95.663 415 17 1 1363 1776 16696267 16695853 0.000000e+00 665.0
12 TraesCS7A01G386400 chr5D 95.181 415 19 1 1363 1776 437095329 437095743 0.000000e+00 654.0
13 TraesCS7A01G386400 chr5D 94.699 415 21 1 1363 1776 402715469 402715883 0.000000e+00 643.0
14 TraesCS7A01G386400 chr1B 95.181 415 19 1 1363 1776 542706946 542707360 0.000000e+00 654.0
15 TraesCS7A01G386400 chr1B 85.627 327 27 13 1998 2322 13906420 13906112 2.610000e-85 326.0
16 TraesCS7A01G386400 chr1B 87.600 250 14 9 1768 2015 13906839 13906605 9.570000e-70 274.0
17 TraesCS7A01G386400 chr1B 84.536 194 23 3 158 351 175663579 175663765 4.610000e-43 185.0
18 TraesCS7A01G386400 chr7D 95.388 412 16 3 1366 1776 377672643 377672234 0.000000e+00 652.0
19 TraesCS7A01G386400 chr7D 82.895 228 35 3 1774 1997 621146636 621146409 4.580000e-48 202.0
20 TraesCS7A01G386400 chr7D 84.737 190 21 4 158 346 553508543 553508361 1.660000e-42 183.0
21 TraesCS7A01G386400 chr3D 95.533 403 18 0 1366 1768 481886745 481886343 0.000000e+00 645.0
22 TraesCS7A01G386400 chr3D 87.253 557 37 16 1768 2322 424488767 424489291 2.990000e-169 604.0
23 TraesCS7A01G386400 chr3D 87.745 408 36 6 1381 1776 436913632 436913227 5.290000e-127 464.0
24 TraesCS7A01G386400 chr3D 82.157 510 74 8 939 1442 613780353 613780851 3.230000e-114 422.0
25 TraesCS7A01G386400 chr3D 87.698 252 28 3 1073 1322 436913892 436913642 9.500000e-75 291.0
26 TraesCS7A01G386400 chr3D 84.656 189 23 2 158 346 564623822 564624004 1.660000e-42 183.0
27 TraesCS7A01G386400 chr3D 95.283 106 3 1 752 857 436935095 436934992 1.670000e-37 167.0
28 TraesCS7A01G386400 chrUn 86.559 558 40 16 1768 2323 283592447 283592971 1.400000e-162 582.0
29 TraesCS7A01G386400 chr3A 82.226 557 92 6 900 1452 749470106 749470659 8.790000e-130 473.0
30 TraesCS7A01G386400 chr1D 82.456 228 36 3 1774 1997 267600742 267600969 2.130000e-46 196.0
31 TraesCS7A01G386400 chr1D 85.714 189 21 2 158 346 464631693 464631875 7.660000e-46 195.0
32 TraesCS7A01G386400 chr1D 85.185 189 22 2 158 346 371664937 371665119 3.570000e-44 189.0
33 TraesCS7A01G386400 chr6D 85.714 189 21 2 158 346 48155499 48155317 7.660000e-46 195.0
34 TraesCS7A01G386400 chr6D 85.714 189 21 2 158 346 289616404 289616586 7.660000e-46 195.0
35 TraesCS7A01G386400 chr4D 84.656 189 23 2 158 346 57032434 57032252 1.660000e-42 183.0
36 TraesCS7A01G386400 chr4A 79.851 134 23 2 2358 2490 402708329 402708199 8.000000e-16 95.3


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 TraesCS7A01G386400 chr7A 562095807 562098519 2712 False 5011.0 5011 100.0000 1 2713 1 chr7A.!!$F1 2712
1 TraesCS7A01G386400 chr2D 648874341 648875261 920 False 1391.0 1391 93.7900 1768 2701 1 chr2D.!!$F3 933
2 TraesCS7A01G386400 chr7B 651389158 651390844 1686 False 868.5 1136 85.6150 128 1776 2 chr7B.!!$F1 1648
3 TraesCS7A01G386400 chr7B 584641772 584642294 522 True 571.0 571 86.2820 1771 2322 1 chr7B.!!$R2 551
4 TraesCS7A01G386400 chr3B 733615548 733617007 1459 True 703.5 900 93.6190 1768 2713 2 chr3B.!!$R1 945
5 TraesCS7A01G386400 chr1B 13906112 13906839 727 True 300.0 326 86.6135 1768 2322 2 chr1B.!!$R1 554
6 TraesCS7A01G386400 chr3D 424488767 424489291 524 False 604.0 604 87.2530 1768 2322 1 chr3D.!!$F1 554
7 TraesCS7A01G386400 chr3D 436913227 436913892 665 True 377.5 464 87.7215 1073 1776 2 chr3D.!!$R3 703
8 TraesCS7A01G386400 chrUn 283592447 283592971 524 False 582.0 582 86.5590 1768 2323 1 chrUn.!!$F1 555
9 TraesCS7A01G386400 chr3A 749470106 749470659 553 False 473.0 473 82.2260 900 1452 1 chr3A.!!$F1 552

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
63 64 0.037790 GAAAGCTGTCGCCTCTCTGT 60.038 55.0 0.0 0.00 36.60 3.41 F
64 65 0.037790 AAAGCTGTCGCCTCTCTGTC 60.038 55.0 0.0 0.00 36.60 3.51 F
666 672 0.040067 CTTTGCAGTTGTTCCTCGCC 60.040 55.0 0.0 0.00 0.00 5.54 F
1010 1075 0.252696 TACACTGCCATGGAGGAGGT 60.253 55.0 18.4 8.77 41.22 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 1122 0.036164 CAACATGACCCAACCGAGGA 59.964 55.000 0.00 0.00 0.00 3.71 R
1359 1434 0.400213 TGGCCCAGGTTTACACAGAG 59.600 55.000 0.00 0.00 0.00 3.35 R
1609 1694 1.149101 TGGATTATGGAAGGGCCTCC 58.851 55.000 6.46 10.93 37.63 4.30 R
2668 3489 1.829222 GCCCAGTAAGCCTGTAGTACA 59.171 52.381 2.36 2.36 39.74 2.90 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
20 21 3.133946 GGAGATCCCGTGCCTCTC 58.866 66.667 0.00 0.00 35.69 3.20
21 22 1.456705 GGAGATCCCGTGCCTCTCT 60.457 63.158 0.00 0.00 36.49 3.10
22 23 0.178987 GGAGATCCCGTGCCTCTCTA 60.179 60.000 0.00 0.00 36.49 2.43
23 24 0.955905 GAGATCCCGTGCCTCTCTAC 59.044 60.000 0.00 0.00 34.03 2.59
24 25 0.259065 AGATCCCGTGCCTCTCTACA 59.741 55.000 0.00 0.00 0.00 2.74
25 26 0.671251 GATCCCGTGCCTCTCTACAG 59.329 60.000 0.00 0.00 0.00 2.74
26 27 0.259065 ATCCCGTGCCTCTCTACAGA 59.741 55.000 0.00 0.00 0.00 3.41
27 28 0.259065 TCCCGTGCCTCTCTACAGAT 59.741 55.000 0.00 0.00 0.00 2.90
28 29 0.671251 CCCGTGCCTCTCTACAGATC 59.329 60.000 0.00 0.00 0.00 2.75
29 30 1.393603 CCGTGCCTCTCTACAGATCA 58.606 55.000 0.00 0.00 0.00 2.92
30 31 1.066303 CCGTGCCTCTCTACAGATCAC 59.934 57.143 0.00 0.00 32.61 3.06
31 32 2.020720 CGTGCCTCTCTACAGATCACT 58.979 52.381 0.00 0.00 33.25 3.41
32 33 2.032799 CGTGCCTCTCTACAGATCACTC 59.967 54.545 0.00 0.00 33.25 3.51
33 34 3.287222 GTGCCTCTCTACAGATCACTCT 58.713 50.000 0.00 0.00 32.93 3.24
34 35 3.315191 GTGCCTCTCTACAGATCACTCTC 59.685 52.174 0.00 0.00 32.93 3.20
35 36 3.201930 TGCCTCTCTACAGATCACTCTCT 59.798 47.826 0.00 0.00 0.00 3.10
36 37 3.815401 GCCTCTCTACAGATCACTCTCTC 59.185 52.174 0.00 0.00 0.00 3.20
37 38 4.444876 GCCTCTCTACAGATCACTCTCTCT 60.445 50.000 0.00 0.00 0.00 3.10
38 39 5.300752 CCTCTCTACAGATCACTCTCTCTC 58.699 50.000 0.00 0.00 0.00 3.20
39 40 5.290493 TCTCTACAGATCACTCTCTCTCC 57.710 47.826 0.00 0.00 0.00 3.71
40 41 4.968719 TCTCTACAGATCACTCTCTCTCCT 59.031 45.833 0.00 0.00 0.00 3.69
41 42 5.070446 TCTCTACAGATCACTCTCTCTCCTC 59.930 48.000 0.00 0.00 0.00 3.71
42 43 4.968719 TCTACAGATCACTCTCTCTCCTCT 59.031 45.833 0.00 0.00 0.00 3.69
43 44 4.156455 ACAGATCACTCTCTCTCCTCTC 57.844 50.000 0.00 0.00 0.00 3.20
44 45 3.133691 CAGATCACTCTCTCTCCTCTCG 58.866 54.545 0.00 0.00 0.00 4.04
45 46 3.038280 AGATCACTCTCTCTCCTCTCGA 58.962 50.000 0.00 0.00 0.00 4.04
46 47 3.454447 AGATCACTCTCTCTCCTCTCGAA 59.546 47.826 0.00 0.00 0.00 3.71
47 48 3.704800 TCACTCTCTCTCCTCTCGAAA 57.295 47.619 0.00 0.00 0.00 3.46
48 49 3.605634 TCACTCTCTCTCCTCTCGAAAG 58.394 50.000 0.00 0.00 0.00 2.62
49 50 2.097466 CACTCTCTCTCCTCTCGAAAGC 59.903 54.545 0.00 0.00 0.00 3.51
50 51 2.026262 ACTCTCTCTCCTCTCGAAAGCT 60.026 50.000 0.00 0.00 0.00 3.74
51 52 2.355756 CTCTCTCTCCTCTCGAAAGCTG 59.644 54.545 0.00 0.00 0.00 4.24
52 53 2.091541 CTCTCTCCTCTCGAAAGCTGT 58.908 52.381 0.00 0.00 0.00 4.40
53 54 2.088423 TCTCTCCTCTCGAAAGCTGTC 58.912 52.381 0.00 0.00 0.00 3.51
54 55 0.805614 TCTCCTCTCGAAAGCTGTCG 59.194 55.000 20.64 20.64 42.48 4.35
55 56 0.800300 CTCCTCTCGAAAGCTGTCGC 60.800 60.000 21.82 0.00 40.88 5.19
56 57 1.807573 CCTCTCGAAAGCTGTCGCC 60.808 63.158 21.82 0.00 40.88 5.54
57 58 1.214062 CTCTCGAAAGCTGTCGCCT 59.786 57.895 21.82 0.00 40.88 5.52
58 59 0.800300 CTCTCGAAAGCTGTCGCCTC 60.800 60.000 21.82 0.00 40.88 4.70
59 60 1.214062 CTCGAAAGCTGTCGCCTCT 59.786 57.895 21.82 0.00 40.88 3.69
60 61 0.800300 CTCGAAAGCTGTCGCCTCTC 60.800 60.000 21.82 0.00 40.88 3.20
61 62 1.214062 CGAAAGCTGTCGCCTCTCT 59.786 57.895 14.46 0.00 36.60 3.10
62 63 1.075425 CGAAAGCTGTCGCCTCTCTG 61.075 60.000 14.46 0.00 36.60 3.35
63 64 0.037790 GAAAGCTGTCGCCTCTCTGT 60.038 55.000 0.00 0.00 36.60 3.41
64 65 0.037790 AAAGCTGTCGCCTCTCTGTC 60.038 55.000 0.00 0.00 36.60 3.51
65 66 2.202544 GCTGTCGCCTCTCTGTCG 60.203 66.667 0.00 0.00 0.00 4.35
66 67 2.202544 CTGTCGCCTCTCTGTCGC 60.203 66.667 0.00 0.00 0.00 5.19
67 68 2.673341 TGTCGCCTCTCTGTCGCT 60.673 61.111 0.00 0.00 0.00 4.93
68 69 2.202544 GTCGCCTCTCTGTCGCTG 60.203 66.667 0.00 0.00 0.00 5.18
69 70 2.673341 TCGCCTCTCTGTCGCTGT 60.673 61.111 0.00 0.00 0.00 4.40
70 71 2.259818 CGCCTCTCTGTCGCTGTT 59.740 61.111 0.00 0.00 0.00 3.16
71 72 2.091112 CGCCTCTCTGTCGCTGTTG 61.091 63.158 0.00 0.00 0.00 3.33
72 73 1.739562 GCCTCTCTGTCGCTGTTGG 60.740 63.158 0.00 0.00 0.00 3.77
73 74 1.668294 CCTCTCTGTCGCTGTTGGT 59.332 57.895 0.00 0.00 0.00 3.67
74 75 0.668706 CCTCTCTGTCGCTGTTGGTG 60.669 60.000 0.00 0.00 0.00 4.17
75 76 1.287730 CTCTCTGTCGCTGTTGGTGC 61.288 60.000 0.00 0.00 0.00 5.01
76 77 1.301244 CTCTGTCGCTGTTGGTGCT 60.301 57.895 0.00 0.00 0.00 4.40
77 78 1.287730 CTCTGTCGCTGTTGGTGCTC 61.288 60.000 0.00 0.00 0.00 4.26
78 79 2.661537 TGTCGCTGTTGGTGCTCG 60.662 61.111 0.00 0.00 0.00 5.03
79 80 2.355837 GTCGCTGTTGGTGCTCGA 60.356 61.111 0.00 0.00 0.00 4.04
80 81 1.738099 GTCGCTGTTGGTGCTCGAT 60.738 57.895 0.00 0.00 0.00 3.59
81 82 1.737735 TCGCTGTTGGTGCTCGATG 60.738 57.895 0.00 0.00 0.00 3.84
82 83 1.737735 CGCTGTTGGTGCTCGATGA 60.738 57.895 0.00 0.00 0.00 2.92
83 84 1.291184 CGCTGTTGGTGCTCGATGAA 61.291 55.000 0.00 0.00 0.00 2.57
84 85 0.874390 GCTGTTGGTGCTCGATGAAA 59.126 50.000 0.00 0.00 0.00 2.69
85 86 1.135859 GCTGTTGGTGCTCGATGAAAG 60.136 52.381 0.00 0.00 0.00 2.62
86 87 2.416747 CTGTTGGTGCTCGATGAAAGA 58.583 47.619 0.00 0.00 0.00 2.52
87 88 2.143122 TGTTGGTGCTCGATGAAAGAC 58.857 47.619 0.00 0.00 0.00 3.01
88 89 1.126846 GTTGGTGCTCGATGAAAGACG 59.873 52.381 0.00 0.00 0.00 4.18
89 90 0.601057 TGGTGCTCGATGAAAGACGA 59.399 50.000 0.00 0.00 37.03 4.20
95 96 1.103803 TCGATGAAAGACGAGGGAGG 58.896 55.000 0.00 0.00 34.49 4.30
96 97 0.528684 CGATGAAAGACGAGGGAGGC 60.529 60.000 0.00 0.00 0.00 4.70
97 98 0.827368 GATGAAAGACGAGGGAGGCT 59.173 55.000 0.00 0.00 0.00 4.58
98 99 0.827368 ATGAAAGACGAGGGAGGCTC 59.173 55.000 5.78 5.78 0.00 4.70
99 100 1.258445 TGAAAGACGAGGGAGGCTCC 61.258 60.000 25.80 25.80 35.23 4.70
100 101 0.973496 GAAAGACGAGGGAGGCTCCT 60.973 60.000 31.39 18.20 40.43 3.69
101 102 0.335361 AAAGACGAGGGAGGCTCCTA 59.665 55.000 31.39 0.00 37.25 2.94
102 103 0.558712 AAGACGAGGGAGGCTCCTAT 59.441 55.000 31.39 20.96 37.25 2.57
103 104 0.111639 AGACGAGGGAGGCTCCTATC 59.888 60.000 31.39 25.99 37.25 2.08
104 105 1.228306 ACGAGGGAGGCTCCTATCG 60.228 63.158 37.21 37.21 44.96 2.92
105 106 1.974343 CGAGGGAGGCTCCTATCGG 60.974 68.421 34.37 23.41 39.94 4.18
106 107 2.203714 AGGGAGGCTCCTATCGGC 60.204 66.667 31.39 14.75 36.57 5.54
107 108 3.686045 GGGAGGCTCCTATCGGCG 61.686 72.222 31.39 0.00 36.57 6.46
108 109 2.597805 GGAGGCTCCTATCGGCGA 60.598 66.667 26.44 13.87 32.53 5.54
109 110 1.979693 GGAGGCTCCTATCGGCGAT 60.980 63.158 26.95 26.95 32.53 4.58
110 111 1.536943 GGAGGCTCCTATCGGCGATT 61.537 60.000 28.93 7.81 32.53 3.34
111 112 0.109039 GAGGCTCCTATCGGCGATTC 60.109 60.000 28.93 13.54 0.00 2.52
112 113 1.079750 GGCTCCTATCGGCGATTCC 60.080 63.158 28.93 16.46 0.00 3.01
113 114 1.079750 GCTCCTATCGGCGATTCCC 60.080 63.158 28.93 8.64 0.00 3.97
114 115 1.536943 GCTCCTATCGGCGATTCCCT 61.537 60.000 28.93 6.42 0.00 4.20
115 116 0.244994 CTCCTATCGGCGATTCCCTG 59.755 60.000 28.93 11.90 0.00 4.45
116 117 0.469331 TCCTATCGGCGATTCCCTGT 60.469 55.000 28.93 4.73 0.00 4.00
117 118 0.319900 CCTATCGGCGATTCCCTGTG 60.320 60.000 28.93 9.30 0.00 3.66
118 119 0.319900 CTATCGGCGATTCCCTGTGG 60.320 60.000 28.93 0.00 0.00 4.17
119 120 1.046472 TATCGGCGATTCCCTGTGGT 61.046 55.000 28.93 2.20 0.00 4.16
120 121 2.311688 ATCGGCGATTCCCTGTGGTC 62.312 60.000 18.14 0.00 0.00 4.02
121 122 2.124695 GGCGATTCCCTGTGGTCC 60.125 66.667 0.00 0.00 0.00 4.46
122 123 2.670148 GGCGATTCCCTGTGGTCCT 61.670 63.158 0.00 0.00 0.00 3.85
123 124 1.153349 GCGATTCCCTGTGGTCCTC 60.153 63.158 0.00 0.00 0.00 3.71
124 125 1.141881 CGATTCCCTGTGGTCCTCG 59.858 63.158 0.00 0.00 0.00 4.63
125 126 1.320344 CGATTCCCTGTGGTCCTCGA 61.320 60.000 0.00 0.00 33.08 4.04
126 127 1.123928 GATTCCCTGTGGTCCTCGAT 58.876 55.000 0.00 0.00 0.00 3.59
145 146 3.541713 GCTCCTCCCGGCGATTCT 61.542 66.667 9.30 0.00 0.00 2.40
147 148 3.200887 CTCCTCCCGGCGATTCTCG 62.201 68.421 9.30 0.00 43.89 4.04
161 162 4.271816 CTCGATGGTCCTCGGCGG 62.272 72.222 7.21 0.00 39.13 6.13
190 191 1.666011 CGATACCCCATGGTCCTCG 59.334 63.158 11.73 9.64 43.06 4.63
191 192 0.826256 CGATACCCCATGGTCCTCGA 60.826 60.000 11.73 0.00 43.06 4.04
195 196 4.530857 CCCATGGTCCTCGACGGC 62.531 72.222 11.73 0.00 32.65 5.68
197 198 3.822192 CATGGTCCTCGACGGCGA 61.822 66.667 15.22 15.22 45.71 5.54
198 199 3.823330 ATGGTCCTCGACGGCGAC 61.823 66.667 10.67 6.59 42.51 5.19
225 226 0.258774 AGGCCAGTCCTCTCTCTCTC 59.741 60.000 5.01 0.00 43.20 3.20
245 246 2.093973 TCTCTCTCGCTCACCCAATTTC 60.094 50.000 0.00 0.00 0.00 2.17
249 250 1.000896 CGCTCACCCAATTTCCCCT 60.001 57.895 0.00 0.00 0.00 4.79
254 255 2.759560 CCCAATTTCCCCTGGCCG 60.760 66.667 0.00 0.00 0.00 6.13
275 276 2.231721 GGCGAGCTAGGATTAGGGTTAG 59.768 54.545 0.00 0.00 0.00 2.34
285 286 0.454600 TTAGGGTTAGCAGCTCGACG 59.545 55.000 0.00 0.00 0.00 5.12
323 324 2.992089 CAGGTGCTGCTATTACCCG 58.008 57.895 0.00 0.00 35.03 5.28
325 326 1.146263 GGTGCTGCTATTACCCGCT 59.854 57.895 0.00 0.00 0.00 5.52
327 328 0.462047 GTGCTGCTATTACCCGCTGT 60.462 55.000 0.00 0.00 0.00 4.40
354 358 2.430921 GTGCTCGTGCGCTGTAGT 60.431 61.111 15.29 0.00 45.43 2.73
355 359 2.126463 TGCTCGTGCGCTGTAGTC 60.126 61.111 9.73 0.56 43.34 2.59
356 360 3.241059 GCTCGTGCGCTGTAGTCG 61.241 66.667 9.73 4.25 0.00 4.18
368 372 2.621338 CTGTAGTCGCCATGTCATGTT 58.379 47.619 11.84 0.00 0.00 2.71
378 382 1.929806 ATGTCATGTTGCCGCTGCTG 61.930 55.000 0.70 0.00 38.71 4.41
379 383 2.281692 TCATGTTGCCGCTGCTGT 60.282 55.556 0.70 0.00 38.71 4.40
387 391 2.912624 GCCGCTGCTGTTTCTTGCT 61.913 57.895 0.00 0.00 33.53 3.91
389 393 1.509644 CCGCTGCTGTTTCTTGCTGA 61.510 55.000 0.00 0.00 0.00 4.26
407 411 2.389866 GATGCATGCCGCTTCTGCTC 62.390 60.000 16.68 0.00 43.06 4.26
415 419 4.742201 GCTTCTGCTCGTGGCCGA 62.742 66.667 0.00 0.00 41.73 5.54
430 434 0.457035 GCCGACCCGTACTGATGTTA 59.543 55.000 0.00 0.00 0.00 2.41
431 435 1.068127 GCCGACCCGTACTGATGTTAT 59.932 52.381 0.00 0.00 0.00 1.89
432 436 2.482490 GCCGACCCGTACTGATGTTATT 60.482 50.000 0.00 0.00 0.00 1.40
433 437 3.243501 GCCGACCCGTACTGATGTTATTA 60.244 47.826 0.00 0.00 0.00 0.98
444 448 7.009815 CGTACTGATGTTATTATTGTTCGTGGT 59.990 37.037 0.00 0.00 0.00 4.16
450 454 2.279935 TTATTGTTCGTGGTTGGCCT 57.720 45.000 3.32 0.00 35.27 5.19
455 459 3.190738 TTCGTGGTTGGCCTCCCTG 62.191 63.158 3.32 2.26 35.27 4.45
463 467 1.640593 TTGGCCTCCCTGTGTGTTCA 61.641 55.000 3.32 0.00 0.00 3.18
466 470 1.589716 GCCTCCCTGTGTGTTCATGC 61.590 60.000 0.00 0.00 0.00 4.06
472 476 0.949397 CTGTGTGTTCATGCTGCTGT 59.051 50.000 0.00 0.00 0.00 4.40
474 478 2.549329 CTGTGTGTTCATGCTGCTGTTA 59.451 45.455 0.00 0.00 0.00 2.41
475 479 3.148412 TGTGTGTTCATGCTGCTGTTAT 58.852 40.909 0.00 0.00 0.00 1.89
479 483 5.569059 GTGTGTTCATGCTGCTGTTATTTAC 59.431 40.000 0.00 0.00 0.00 2.01
480 484 5.095490 GTGTTCATGCTGCTGTTATTTACC 58.905 41.667 0.00 0.00 0.00 2.85
481 485 4.157656 TGTTCATGCTGCTGTTATTTACCC 59.842 41.667 0.00 0.00 0.00 3.69
487 491 2.945668 CTGCTGTTATTTACCCTGCTCC 59.054 50.000 0.00 0.00 0.00 4.70
499 503 1.735920 CTGCTCCTGTGTCGTGCTC 60.736 63.158 0.00 0.00 0.00 4.26
502 506 1.730902 CTCCTGTGTCGTGCTCGTG 60.731 63.158 8.17 0.00 38.33 4.35
535 539 1.149101 AAGATAATGGGGCGATGGGT 58.851 50.000 0.00 0.00 0.00 4.51
629 635 3.726517 CGGGTTCAGCCTTGCGTG 61.727 66.667 0.00 0.00 37.43 5.34
638 644 3.953775 CCTTGCGTGGACCTGGGT 61.954 66.667 0.00 0.00 0.00 4.51
640 646 4.263572 TTGCGTGGACCTGGGTGG 62.264 66.667 0.00 0.00 42.93 4.61
643 649 4.033776 CGTGGACCTGGGTGGCAT 62.034 66.667 0.00 0.00 40.22 4.40
644 650 2.044946 GTGGACCTGGGTGGCATC 60.045 66.667 0.00 0.00 40.22 3.91
658 664 1.286880 GCATCGCCTTTGCAGTTGT 59.713 52.632 0.00 0.00 39.90 3.32
666 672 0.040067 CTTTGCAGTTGTTCCTCGCC 60.040 55.000 0.00 0.00 0.00 5.54
668 674 2.665185 GCAGTTGTTCCTCGCCGT 60.665 61.111 0.00 0.00 0.00 5.68
673 679 1.959226 TTGTTCCTCGCCGTTGAGC 60.959 57.895 0.00 0.00 34.56 4.26
695 701 5.399013 GCAGTTGTGCGTTATTTATTTCCT 58.601 37.500 0.00 0.00 40.71 3.36
699 705 4.980590 TGTGCGTTATTTATTTCCTGCTG 58.019 39.130 0.00 0.00 0.00 4.41
702 708 4.082517 TGCGTTATTTATTTCCTGCTGCAA 60.083 37.500 3.02 0.00 0.00 4.08
707 713 7.700234 CGTTATTTATTTCCTGCTGCAAACATA 59.300 33.333 3.02 0.00 0.00 2.29
708 714 8.807581 GTTATTTATTTCCTGCTGCAAACATAC 58.192 33.333 3.02 0.00 0.00 2.39
721 727 3.689161 GCAAACATACACATGCCTGACTA 59.311 43.478 0.00 0.00 35.39 2.59
724 730 6.038161 GCAAACATACACATGCCTGACTATTA 59.962 38.462 0.00 0.00 35.39 0.98
748 754 7.346751 ACCTGAAATGTGACACTTATTTGTT 57.653 32.000 7.20 0.00 0.00 2.83
749 755 7.202526 ACCTGAAATGTGACACTTATTTGTTG 58.797 34.615 7.20 0.00 0.00 3.33
750 756 7.068103 ACCTGAAATGTGACACTTATTTGTTGA 59.932 33.333 7.20 0.00 0.00 3.18
786 792 4.866486 GTCATGATTTGGGATTGCTTGTTC 59.134 41.667 0.00 0.00 0.00 3.18
806 812 6.053650 TGTTCAGAAGCTTCCATGATATCAG 58.946 40.000 22.81 3.67 0.00 2.90
807 813 5.224821 TCAGAAGCTTCCATGATATCAGG 57.775 43.478 22.81 11.09 0.00 3.86
827 833 5.705441 TCAGGTCCTTCACAATTCATGTTAC 59.295 40.000 0.00 0.00 41.46 2.50
832 838 8.184192 GGTCCTTCACAATTCATGTTACAATAG 58.816 37.037 0.00 0.00 41.46 1.73
833 839 8.730680 GTCCTTCACAATTCATGTTACAATAGT 58.269 33.333 0.00 0.00 41.46 2.12
866 929 9.722056 CTCAATAAGTTAGATATTGTGGTTTGC 57.278 33.333 6.26 0.00 40.20 3.68
910 973 8.352201 TCATCAGACTTTCAATTGGTTTGTTAG 58.648 33.333 5.42 0.00 36.65 2.34
921 984 5.890424 TTGGTTTGTTAGTTATAGCTGGC 57.110 39.130 0.00 0.00 0.00 4.85
933 996 6.462500 AGTTATAGCTGGCTGATGATTACTG 58.538 40.000 5.25 0.00 0.00 2.74
937 1000 2.223433 GCTGGCTGATGATTACTGCAAC 60.223 50.000 0.00 0.00 34.70 4.17
959 1022 2.095059 GCAGAGTTTGCGATGGAACAAT 60.095 45.455 0.00 0.00 43.25 2.71
982 1047 1.826054 CTCTCGGCCGACATCCTCT 60.826 63.158 27.28 0.00 0.00 3.69
994 1059 4.390264 CGACATCCTCTACAGATCCTACA 58.610 47.826 0.00 0.00 0.00 2.74
1010 1075 0.252696 TACACTGCCATGGAGGAGGT 60.253 55.000 18.40 8.77 41.22 3.85
1011 1076 1.077930 CACTGCCATGGAGGAGGTG 60.078 63.158 18.40 11.68 41.22 4.00
1023 1088 3.244561 TGGAGGAGGTGTTTCTGAATCAC 60.245 47.826 18.74 18.74 0.00 3.06
1035 1100 2.037121 TCTGAATCACGTGAGGAAGCAA 59.963 45.455 24.41 3.23 0.00 3.91
1057 1122 0.737715 GCTCGTCAAACCGCAGATCT 60.738 55.000 0.00 0.00 0.00 2.75
1065 1130 3.211288 CCGCAGATCTCCTCGGTT 58.789 61.111 15.69 0.00 37.33 4.44
1068 1133 1.144936 GCAGATCTCCTCGGTTGGG 59.855 63.158 0.00 0.00 0.00 4.12
1122 1193 3.197983 GGGTCCTCTACATAGCAAACACT 59.802 47.826 0.00 0.00 0.00 3.55
1264 1337 1.612513 CCAAATGACCCCCGGATCA 59.387 57.895 0.73 3.91 0.00 2.92
1275 1348 1.227102 CCGGATCATGGCCCTGAAA 59.773 57.895 15.14 0.00 0.00 2.69
1281 1354 2.079170 TCATGGCCCTGAAACACAAA 57.921 45.000 8.44 0.00 0.00 2.83
1325 1400 5.913137 ATTCAGGTATTTCATTTTGCCGA 57.087 34.783 0.00 0.00 0.00 5.54
1452 1528 3.155093 GCCAAGAGCATACCATTTGTG 57.845 47.619 0.00 0.00 42.97 3.33
1465 1541 2.548493 CCATTTGTGCAAAGTCCCAAGG 60.548 50.000 3.70 0.00 33.32 3.61
1510 1586 9.626045 TCTCACATAATAATTACTCGTGCTATG 57.374 33.333 0.00 0.00 0.00 2.23
1511 1587 9.411801 CTCACATAATAATTACTCGTGCTATGT 57.588 33.333 0.00 0.00 30.78 2.29
1577 1662 9.524496 ACCTACCTAAAAAGTTCGGAATTTAAT 57.476 29.630 0.00 0.00 0.00 1.40
1603 1688 2.538141 CCCTTCTGGCCTGGTTCCA 61.538 63.158 10.07 0.00 0.00 3.53
1609 1694 1.140852 TCTGGCCTGGTTCCATATTCG 59.859 52.381 10.07 0.00 32.37 3.34
1610 1695 0.182537 TGGCCTGGTTCCATATTCGG 59.817 55.000 3.32 0.00 0.00 4.30
1625 1710 1.518367 TTCGGAGGCCCTTCCATAAT 58.482 50.000 11.40 0.00 37.05 1.28
1637 1722 5.129320 GCCCTTCCATAATCCAATTCTTTGT 59.871 40.000 0.00 0.00 0.00 2.83
1710 1797 9.224267 GTTATATTTGCATCAGATGGACTATGT 57.776 33.333 12.54 6.61 0.00 2.29
1719 1806 4.956075 TCAGATGGACTATGTGAGCACTTA 59.044 41.667 1.99 0.00 34.45 2.24
1721 1808 6.070824 TCAGATGGACTATGTGAGCACTTAAA 60.071 38.462 1.99 0.00 34.45 1.52
1760 1847 7.047891 GTGGATATAGTTCATTGTTCACCTCA 58.952 38.462 0.00 0.00 0.00 3.86
1776 1863 6.861065 TCACCTCAGAATGTAAGTTGTTTC 57.139 37.500 0.00 0.00 37.40 2.78
1783 1870 9.261180 CTCAGAATGTAAGTTGTTTCTTCTGTA 57.739 33.333 8.68 0.00 39.25 2.74
1882 1971 7.333672 GGTACAACCTCACGAGAGAATTATTTT 59.666 37.037 11.76 0.00 44.98 1.82
1919 2008 5.945784 ACACAGTTACATGTATGCCTTCAAT 59.054 36.000 6.36 0.00 0.00 2.57
1979 2068 0.827507 TGAGCTTGGCTTTCAACCCC 60.828 55.000 0.00 0.00 39.88 4.95
1980 2069 0.827507 GAGCTTGGCTTTCAACCCCA 60.828 55.000 0.00 0.00 39.88 4.96
2028 2319 6.721571 ATCAAGTCATACACCGTTTTAGTG 57.278 37.500 0.00 0.00 41.15 2.74
2111 2930 2.280797 GCTGTGTGGAGCGAACCA 60.281 61.111 0.00 0.00 37.63 3.67
2146 2965 0.994050 AGGGGTCCTTATGGCCCTTC 60.994 60.000 19.71 9.59 41.45 3.46
2305 3126 8.780846 TGCGGTTCTCTTAAATAGTTTGAATA 57.219 30.769 0.00 0.00 0.00 1.75
2323 3144 9.145865 GTTTGAATAATTTAGCATTTCGGGAAA 57.854 29.630 0.00 0.00 34.46 3.13
2324 3145 9.883142 TTTGAATAATTTAGCATTTCGGGAAAT 57.117 25.926 0.89 0.89 41.33 2.17
2325 3146 9.883142 TTGAATAATTTAGCATTTCGGGAAATT 57.117 25.926 3.97 0.00 38.84 1.82
2407 3228 6.195700 ACCGGGCTCTAGATTATGTACATAT 58.804 40.000 16.16 6.91 0.00 1.78
2458 3279 7.823745 TGGAGAAATATGGCTTTCCTATTTC 57.176 36.000 6.27 6.27 39.50 2.17
2471 3292 8.257306 GGCTTTCCTATTTCATTGTCCATTAAA 58.743 33.333 0.00 0.00 0.00 1.52
2554 3375 8.972127 TCTTATCTCCTGATGTGTATAATAGCC 58.028 37.037 0.00 0.00 34.32 3.93
2654 3475 6.449956 TGGGAGTTATAGAGGGACTTTATGT 58.550 40.000 0.00 0.00 41.55 2.29
2666 3487 3.063997 GGACTTTATGTCGCACATTCCTG 59.936 47.826 7.02 0.85 46.24 3.86
2668 3489 4.517285 ACTTTATGTCGCACATTCCTGAT 58.483 39.130 7.02 0.00 39.88 2.90
2684 3505 8.511934 ACATTCCTGATGTACTACAGGCTTACT 61.512 40.741 24.04 10.71 47.00 2.24
2701 3522 4.700213 GCTTACTGGGCTAAGAATGAACAA 59.300 41.667 0.00 0.00 0.00 2.83
2710 3531 7.391554 TGGGCTAAGAATGAACAATGCTATATC 59.608 37.037 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.178987 TAGAGAGGCACGGGATCTCC 60.179 60.000 14.65 0.00 40.29 3.71
4 5 0.955905 GTAGAGAGGCACGGGATCTC 59.044 60.000 11.31 11.31 39.83 2.75
5 6 0.259065 TGTAGAGAGGCACGGGATCT 59.741 55.000 0.00 0.00 0.00 2.75
6 7 0.671251 CTGTAGAGAGGCACGGGATC 59.329 60.000 0.00 0.00 0.00 3.36
7 8 0.259065 TCTGTAGAGAGGCACGGGAT 59.741 55.000 0.00 0.00 0.00 3.85
8 9 0.259065 ATCTGTAGAGAGGCACGGGA 59.741 55.000 0.00 0.00 0.00 5.14
9 10 0.671251 GATCTGTAGAGAGGCACGGG 59.329 60.000 0.00 0.00 0.00 5.28
10 11 1.066303 GTGATCTGTAGAGAGGCACGG 59.934 57.143 9.07 0.00 31.59 4.94
11 12 2.020720 AGTGATCTGTAGAGAGGCACG 58.979 52.381 15.46 0.00 40.13 5.34
12 13 3.287222 AGAGTGATCTGTAGAGAGGCAC 58.713 50.000 14.29 14.29 37.56 5.01
13 14 3.201930 AGAGAGTGATCTGTAGAGAGGCA 59.798 47.826 0.00 0.00 0.00 4.75
14 15 3.815401 GAGAGAGTGATCTGTAGAGAGGC 59.185 52.174 0.00 0.00 0.00 4.70
15 16 5.296151 AGAGAGAGTGATCTGTAGAGAGG 57.704 47.826 0.00 0.00 0.00 3.69
16 17 5.070981 AGGAGAGAGAGTGATCTGTAGAGAG 59.929 48.000 0.00 0.00 0.00 3.20
17 18 4.968719 AGGAGAGAGAGTGATCTGTAGAGA 59.031 45.833 0.00 0.00 0.00 3.10
18 19 5.070981 AGAGGAGAGAGAGTGATCTGTAGAG 59.929 48.000 0.00 0.00 0.00 2.43
19 20 4.968719 AGAGGAGAGAGAGTGATCTGTAGA 59.031 45.833 0.00 0.00 0.00 2.59
20 21 5.296151 AGAGGAGAGAGAGTGATCTGTAG 57.704 47.826 0.00 0.00 0.00 2.74
21 22 4.202212 CGAGAGGAGAGAGAGTGATCTGTA 60.202 50.000 0.00 0.00 0.00 2.74
22 23 3.432186 CGAGAGGAGAGAGAGTGATCTGT 60.432 52.174 0.00 0.00 0.00 3.41
23 24 3.133691 CGAGAGGAGAGAGAGTGATCTG 58.866 54.545 0.00 0.00 0.00 2.90
24 25 3.038280 TCGAGAGGAGAGAGAGTGATCT 58.962 50.000 0.00 0.00 0.00 2.75
25 26 3.469008 TCGAGAGGAGAGAGAGTGATC 57.531 52.381 0.00 0.00 0.00 2.92
26 27 3.924114 TTCGAGAGGAGAGAGAGTGAT 57.076 47.619 0.00 0.00 0.00 3.06
27 28 3.605634 CTTTCGAGAGGAGAGAGAGTGA 58.394 50.000 0.00 0.00 0.00 3.41
28 29 2.097466 GCTTTCGAGAGGAGAGAGAGTG 59.903 54.545 4.98 0.00 0.00 3.51
29 30 2.026262 AGCTTTCGAGAGGAGAGAGAGT 60.026 50.000 4.98 0.00 0.00 3.24
30 31 2.355756 CAGCTTTCGAGAGGAGAGAGAG 59.644 54.545 4.98 0.00 0.00 3.20
31 32 2.290641 ACAGCTTTCGAGAGGAGAGAGA 60.291 50.000 4.98 0.00 0.00 3.10
32 33 2.091541 ACAGCTTTCGAGAGGAGAGAG 58.908 52.381 4.98 0.00 0.00 3.20
33 34 2.088423 GACAGCTTTCGAGAGGAGAGA 58.912 52.381 4.98 0.00 0.00 3.10
34 35 1.202132 CGACAGCTTTCGAGAGGAGAG 60.202 57.143 17.19 0.00 41.78 3.20
35 36 0.805614 CGACAGCTTTCGAGAGGAGA 59.194 55.000 17.19 0.00 41.78 3.71
36 37 0.800300 GCGACAGCTTTCGAGAGGAG 60.800 60.000 25.57 0.00 41.78 3.69
37 38 1.213013 GCGACAGCTTTCGAGAGGA 59.787 57.895 25.57 0.00 41.78 3.71
38 39 1.807573 GGCGACAGCTTTCGAGAGG 60.808 63.158 25.57 0.00 41.78 3.69
39 40 0.800300 GAGGCGACAGCTTTCGAGAG 60.800 60.000 25.57 0.00 41.78 3.20
40 41 1.213013 GAGGCGACAGCTTTCGAGA 59.787 57.895 25.57 0.00 41.78 4.04
41 42 0.800300 GAGAGGCGACAGCTTTCGAG 60.800 60.000 25.57 0.00 41.78 4.04
42 43 1.213013 GAGAGGCGACAGCTTTCGA 59.787 57.895 25.57 0.00 41.78 3.71
43 44 1.075425 CAGAGAGGCGACAGCTTTCG 61.075 60.000 17.76 17.76 44.37 3.46
44 45 0.037790 ACAGAGAGGCGACAGCTTTC 60.038 55.000 0.00 0.00 44.37 2.62
45 46 0.037790 GACAGAGAGGCGACAGCTTT 60.038 55.000 0.00 0.00 44.37 3.51
46 47 1.589113 GACAGAGAGGCGACAGCTT 59.411 57.895 0.00 0.00 44.37 3.74
47 48 3.283303 GACAGAGAGGCGACAGCT 58.717 61.111 0.00 0.00 44.37 4.24
54 55 1.739562 CCAACAGCGACAGAGAGGC 60.740 63.158 0.00 0.00 0.00 4.70
55 56 0.668706 CACCAACAGCGACAGAGAGG 60.669 60.000 0.00 0.00 0.00 3.69
56 57 1.287730 GCACCAACAGCGACAGAGAG 61.288 60.000 0.00 0.00 0.00 3.20
57 58 1.300931 GCACCAACAGCGACAGAGA 60.301 57.895 0.00 0.00 0.00 3.10
58 59 1.287730 GAGCACCAACAGCGACAGAG 61.288 60.000 0.00 0.00 37.01 3.35
59 60 1.300931 GAGCACCAACAGCGACAGA 60.301 57.895 0.00 0.00 37.01 3.41
60 61 2.661566 CGAGCACCAACAGCGACAG 61.662 63.158 0.00 0.00 37.01 3.51
61 62 2.434658 ATCGAGCACCAACAGCGACA 62.435 55.000 0.00 0.00 37.01 4.35
62 63 1.738099 ATCGAGCACCAACAGCGAC 60.738 57.895 0.00 0.00 37.01 5.19
63 64 1.737735 CATCGAGCACCAACAGCGA 60.738 57.895 0.00 0.00 37.01 4.93
64 65 1.291184 TTCATCGAGCACCAACAGCG 61.291 55.000 0.00 0.00 37.01 5.18
65 66 0.874390 TTTCATCGAGCACCAACAGC 59.126 50.000 0.00 0.00 0.00 4.40
66 67 2.158449 GTCTTTCATCGAGCACCAACAG 59.842 50.000 0.00 0.00 0.00 3.16
67 68 2.143122 GTCTTTCATCGAGCACCAACA 58.857 47.619 0.00 0.00 0.00 3.33
68 69 1.126846 CGTCTTTCATCGAGCACCAAC 59.873 52.381 0.00 0.00 0.00 3.77
69 70 1.000394 TCGTCTTTCATCGAGCACCAA 60.000 47.619 0.00 0.00 0.00 3.67
70 71 0.601057 TCGTCTTTCATCGAGCACCA 59.399 50.000 0.00 0.00 0.00 4.17
71 72 1.272781 CTCGTCTTTCATCGAGCACC 58.727 55.000 1.88 0.00 44.82 5.01
76 77 1.103803 CCTCCCTCGTCTTTCATCGA 58.896 55.000 0.00 0.00 34.88 3.59
77 78 0.528684 GCCTCCCTCGTCTTTCATCG 60.529 60.000 0.00 0.00 0.00 3.84
78 79 0.827368 AGCCTCCCTCGTCTTTCATC 59.173 55.000 0.00 0.00 0.00 2.92
79 80 0.827368 GAGCCTCCCTCGTCTTTCAT 59.173 55.000 0.00 0.00 0.00 2.57
80 81 1.258445 GGAGCCTCCCTCGTCTTTCA 61.258 60.000 0.00 0.00 41.71 2.69
81 82 0.973496 AGGAGCCTCCCTCGTCTTTC 60.973 60.000 7.26 0.00 41.71 2.62
82 83 0.335361 TAGGAGCCTCCCTCGTCTTT 59.665 55.000 7.26 0.00 41.71 2.52
83 84 0.558712 ATAGGAGCCTCCCTCGTCTT 59.441 55.000 7.26 0.00 41.71 3.01
84 85 0.111639 GATAGGAGCCTCCCTCGTCT 59.888 60.000 7.26 0.00 41.71 4.18
85 86 1.238625 CGATAGGAGCCTCCCTCGTC 61.239 65.000 19.84 8.19 41.71 4.20
86 87 1.228306 CGATAGGAGCCTCCCTCGT 60.228 63.158 19.84 0.90 41.71 4.18
87 88 3.674906 CGATAGGAGCCTCCCTCG 58.325 66.667 16.15 16.15 41.71 4.63
99 100 0.319900 CCACAGGGAATCGCCGATAG 60.320 60.000 0.00 0.00 37.63 2.08
100 101 1.046472 ACCACAGGGAATCGCCGATA 61.046 55.000 0.00 0.00 37.63 2.92
101 102 2.311688 GACCACAGGGAATCGCCGAT 62.312 60.000 0.00 0.00 37.63 4.18
102 103 3.000819 ACCACAGGGAATCGCCGA 61.001 61.111 0.00 0.00 37.63 5.54
103 104 2.511600 GACCACAGGGAATCGCCG 60.512 66.667 0.00 0.00 37.63 6.46
104 105 2.124695 GGACCACAGGGAATCGCC 60.125 66.667 0.00 0.00 38.05 5.54
105 106 1.153349 GAGGACCACAGGGAATCGC 60.153 63.158 0.00 0.00 38.05 4.58
106 107 1.141881 CGAGGACCACAGGGAATCG 59.858 63.158 0.00 0.00 38.05 3.34
107 108 1.123928 ATCGAGGACCACAGGGAATC 58.876 55.000 0.00 0.00 38.05 2.52
108 109 0.833287 CATCGAGGACCACAGGGAAT 59.167 55.000 0.00 0.00 38.05 3.01
109 110 1.264749 CCATCGAGGACCACAGGGAA 61.265 60.000 0.00 0.00 41.22 3.97
110 111 1.685765 CCATCGAGGACCACAGGGA 60.686 63.158 0.00 0.00 41.22 4.20
111 112 2.903357 CCATCGAGGACCACAGGG 59.097 66.667 0.00 0.00 41.22 4.45
112 113 2.187946 GCCATCGAGGACCACAGG 59.812 66.667 0.00 0.00 41.22 4.00
113 114 1.142748 GAGCCATCGAGGACCACAG 59.857 63.158 0.00 0.00 41.22 3.66
114 115 2.359169 GGAGCCATCGAGGACCACA 61.359 63.158 0.00 0.00 41.22 4.17
115 116 2.022240 GAGGAGCCATCGAGGACCAC 62.022 65.000 0.00 0.00 41.22 4.16
116 117 1.758514 GAGGAGCCATCGAGGACCA 60.759 63.158 0.00 0.00 41.22 4.02
117 118 2.503382 GGAGGAGCCATCGAGGACC 61.503 68.421 0.00 0.00 41.22 4.46
118 119 2.503382 GGGAGGAGCCATCGAGGAC 61.503 68.421 0.00 0.00 41.22 3.85
119 120 2.123251 GGGAGGAGCCATCGAGGA 60.123 66.667 0.00 0.00 41.22 3.71
120 121 3.610669 CGGGAGGAGCCATCGAGG 61.611 72.222 0.00 0.00 38.95 4.63
147 148 4.593864 GAGCCGCCGAGGACCATC 62.594 72.222 0.00 0.00 45.00 3.51
209 210 2.774234 AGAGAGAGAGAGAGAGGACTGG 59.226 54.545 0.00 0.00 0.00 4.00
213 214 1.412710 GCGAGAGAGAGAGAGAGAGGA 59.587 57.143 0.00 0.00 0.00 3.71
214 215 1.414181 AGCGAGAGAGAGAGAGAGAGG 59.586 57.143 0.00 0.00 0.00 3.69
215 216 2.101415 TGAGCGAGAGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
216 217 2.107366 TGAGCGAGAGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
217 218 2.205074 GTGAGCGAGAGAGAGAGAGAG 58.795 57.143 0.00 0.00 0.00 3.20
218 219 1.134521 GGTGAGCGAGAGAGAGAGAGA 60.135 57.143 0.00 0.00 0.00 3.10
219 220 1.299541 GGTGAGCGAGAGAGAGAGAG 58.700 60.000 0.00 0.00 0.00 3.20
225 226 2.275318 GAAATTGGGTGAGCGAGAGAG 58.725 52.381 0.00 0.00 0.00 3.20
254 255 1.049402 AACCCTAATCCTAGCTCGCC 58.951 55.000 0.00 0.00 0.00 5.54
265 266 1.067212 CGTCGAGCTGCTAACCCTAAT 59.933 52.381 0.15 0.00 0.00 1.73
285 286 4.722700 ACATGACAGGGTGGCGGC 62.723 66.667 0.00 0.00 0.00 6.53
295 296 2.333291 CAGCACCTGCAACATGACA 58.667 52.632 0.00 0.00 45.16 3.58
346 350 0.528466 ATGACATGGCGACTACAGCG 60.528 55.000 0.00 0.00 35.00 5.18
347 351 0.933097 CATGACATGGCGACTACAGC 59.067 55.000 7.60 0.00 0.00 4.40
348 352 2.299993 ACATGACATGGCGACTACAG 57.700 50.000 19.39 0.00 33.60 2.74
349 353 2.345876 CAACATGACATGGCGACTACA 58.654 47.619 19.39 0.00 33.60 2.74
350 354 1.062587 GCAACATGACATGGCGACTAC 59.937 52.381 19.39 0.00 33.60 2.73
351 355 1.368641 GCAACATGACATGGCGACTA 58.631 50.000 19.39 0.00 33.60 2.59
352 356 1.308069 GGCAACATGACATGGCGACT 61.308 55.000 19.39 0.00 32.19 4.18
353 357 1.137404 GGCAACATGACATGGCGAC 59.863 57.895 19.39 8.29 32.19 5.19
354 358 3.589579 GGCAACATGACATGGCGA 58.410 55.556 19.39 0.00 32.19 5.54
356 360 2.202650 GCGGCAACATGACATGGC 60.203 61.111 19.39 13.24 38.62 4.40
357 361 1.138036 CAGCGGCAACATGACATGG 59.862 57.895 19.39 4.01 33.60 3.66
358 362 1.515519 GCAGCGGCAACATGACATG 60.516 57.895 14.02 14.02 40.72 3.21
368 372 3.033184 CAAGAAACAGCAGCGGCA 58.967 55.556 12.44 0.00 44.61 5.69
398 402 4.742201 TCGGCCACGAGCAGAAGC 62.742 66.667 2.24 0.00 45.59 3.86
407 411 4.789075 CAGTACGGGTCGGCCACG 62.789 72.222 9.07 12.23 42.74 4.94
415 419 6.477688 CGAACAATAATAACATCAGTACGGGT 59.522 38.462 0.00 0.00 0.00 5.28
419 423 8.193250 ACCACGAACAATAATAACATCAGTAC 57.807 34.615 0.00 0.00 0.00 2.73
430 434 2.752903 GAGGCCAACCACGAACAATAAT 59.247 45.455 5.01 0.00 39.06 1.28
431 435 2.156098 GAGGCCAACCACGAACAATAA 58.844 47.619 5.01 0.00 39.06 1.40
432 436 1.612199 GGAGGCCAACCACGAACAATA 60.612 52.381 5.01 0.00 39.06 1.90
433 437 0.893727 GGAGGCCAACCACGAACAAT 60.894 55.000 5.01 0.00 39.06 2.71
444 448 1.150536 GAACACACAGGGAGGCCAA 59.849 57.895 5.01 0.00 0.00 4.52
450 454 0.890542 GCAGCATGAACACACAGGGA 60.891 55.000 0.00 0.00 39.69 4.20
455 459 3.837213 ATAACAGCAGCATGAACACAC 57.163 42.857 0.00 0.00 39.69 3.82
463 467 2.689983 GCAGGGTAAATAACAGCAGCAT 59.310 45.455 0.00 0.00 0.00 3.79
466 470 2.945668 GGAGCAGGGTAAATAACAGCAG 59.054 50.000 0.00 0.00 0.00 4.24
472 476 3.369052 CGACACAGGAGCAGGGTAAATAA 60.369 47.826 0.00 0.00 0.00 1.40
474 478 1.066143 CGACACAGGAGCAGGGTAAAT 60.066 52.381 0.00 0.00 0.00 1.40
475 479 0.320374 CGACACAGGAGCAGGGTAAA 59.680 55.000 0.00 0.00 0.00 2.01
479 483 2.047844 CACGACACAGGAGCAGGG 60.048 66.667 0.00 0.00 0.00 4.45
480 484 2.740055 GCACGACACAGGAGCAGG 60.740 66.667 0.00 0.00 0.00 4.85
481 485 1.735920 GAGCACGACACAGGAGCAG 60.736 63.158 0.00 0.00 0.00 4.24
502 506 0.729116 TATCTTTTCGCTGCAGCTGC 59.271 50.000 34.22 31.89 39.32 5.25
511 515 1.305201 TCGCCCCATTATCTTTTCGC 58.695 50.000 0.00 0.00 0.00 4.70
520 524 2.194597 GCACCCATCGCCCCATTA 59.805 61.111 0.00 0.00 0.00 1.90
584 589 3.254024 AAGTGGTGCCGGGTAGCAG 62.254 63.158 17.41 0.00 45.14 4.24
585 590 3.246112 AAGTGGTGCCGGGTAGCA 61.246 61.111 13.12 13.12 41.46 3.49
586 591 2.746277 CAAGTGGTGCCGGGTAGC 60.746 66.667 2.18 7.41 0.00 3.58
592 597 2.978010 GGTGTCCAAGTGGTGCCG 60.978 66.667 0.00 0.00 36.34 5.69
596 601 2.508928 CGGTGGTGTCCAAGTGGT 59.491 61.111 0.00 0.00 34.18 4.16
618 623 3.052082 CAGGTCCACGCAAGGCTG 61.052 66.667 0.00 0.00 46.39 4.85
640 646 0.318955 AACAACTGCAAAGGCGATGC 60.319 50.000 10.10 10.10 45.35 3.91
642 648 0.598065 GGAACAACTGCAAAGGCGAT 59.402 50.000 0.00 0.00 45.35 4.58
643 649 0.465460 AGGAACAACTGCAAAGGCGA 60.465 50.000 0.00 0.00 45.35 5.54
644 650 0.040067 GAGGAACAACTGCAAAGGCG 60.040 55.000 0.00 0.00 45.35 5.52
654 660 1.860078 CTCAACGGCGAGGAACAAC 59.140 57.895 16.62 0.00 0.00 3.32
655 661 1.959226 GCTCAACGGCGAGGAACAA 60.959 57.895 16.62 0.00 33.36 2.83
658 664 2.048222 CTGCTCAACGGCGAGGAA 60.048 61.111 16.62 0.00 32.50 3.36
666 672 0.579630 TAACGCACAACTGCTCAACG 59.420 50.000 0.00 0.00 41.77 4.10
668 674 3.980646 AAATAACGCACAACTGCTCAA 57.019 38.095 0.00 0.00 41.77 3.02
673 679 5.286082 GCAGGAAATAAATAACGCACAACTG 59.714 40.000 0.00 0.00 0.00 3.16
681 687 5.861251 TGTTTGCAGCAGGAAATAAATAACG 59.139 36.000 0.00 0.00 37.41 3.18
687 693 5.242615 TGTGTATGTTTGCAGCAGGAAATAA 59.757 36.000 0.00 0.00 37.41 1.40
689 695 3.573538 TGTGTATGTTTGCAGCAGGAAAT 59.426 39.130 0.00 0.00 37.41 2.17
695 701 1.067706 GGCATGTGTATGTTTGCAGCA 60.068 47.619 0.00 0.00 36.82 4.41
699 705 2.489329 AGTCAGGCATGTGTATGTTTGC 59.511 45.455 0.00 0.00 36.65 3.68
702 708 6.055588 GGTAATAGTCAGGCATGTGTATGTT 58.944 40.000 0.00 0.00 36.65 2.71
707 713 3.774766 TCAGGTAATAGTCAGGCATGTGT 59.225 43.478 0.00 0.00 0.00 3.72
708 714 4.406648 TCAGGTAATAGTCAGGCATGTG 57.593 45.455 0.00 0.00 0.00 3.21
721 727 9.077885 ACAAATAAGTGTCACATTTCAGGTAAT 57.922 29.630 5.62 0.00 0.00 1.89
724 730 6.959639 ACAAATAAGTGTCACATTTCAGGT 57.040 33.333 5.62 0.00 0.00 4.00
749 755 9.903682 CCCAAATCATGACATAAGTATTTCATC 57.096 33.333 0.00 0.00 32.43 2.92
750 756 9.645128 TCCCAAATCATGACATAAGTATTTCAT 57.355 29.630 0.00 0.00 34.41 2.57
786 792 4.970711 ACCTGATATCATGGAAGCTTCTG 58.029 43.478 25.05 16.66 0.00 3.02
806 812 5.957842 TGTAACATGAATTGTGAAGGACC 57.042 39.130 0.00 0.00 38.99 4.46
807 813 8.730680 ACTATTGTAACATGAATTGTGAAGGAC 58.269 33.333 0.00 0.00 38.99 3.85
910 973 5.121454 GCAGTAATCATCAGCCAGCTATAAC 59.879 44.000 0.00 0.00 0.00 1.89
964 1027 0.535328 TAGAGGATGTCGGCCGAGAG 60.535 60.000 31.97 0.00 0.00 3.20
982 1047 2.700371 CCATGGCAGTGTAGGATCTGTA 59.300 50.000 0.00 0.00 34.57 2.74
994 1059 1.136329 AACACCTCCTCCATGGCAGT 61.136 55.000 6.96 0.00 35.26 4.40
1010 1075 3.744238 TCCTCACGTGATTCAGAAACA 57.256 42.857 20.40 0.00 0.00 2.83
1011 1076 3.120511 GCTTCCTCACGTGATTCAGAAAC 60.121 47.826 20.40 11.17 0.00 2.78
1035 1100 2.031919 TGCGGTTTGACGAGCCAT 59.968 55.556 0.00 0.00 35.47 4.40
1057 1122 0.036164 CAACATGACCCAACCGAGGA 59.964 55.000 0.00 0.00 0.00 3.71
1065 1130 1.759445 CCAACCAAACAACATGACCCA 59.241 47.619 0.00 0.00 0.00 4.51
1068 1133 2.593346 TGCCAACCAAACAACATGAC 57.407 45.000 0.00 0.00 0.00 3.06
1122 1193 2.513753 GGGACAACACATGAATCACCA 58.486 47.619 0.00 0.00 0.00 4.17
1158 1230 1.463674 CCTTAATGTCTTTGGCGCCT 58.536 50.000 29.70 6.93 0.00 5.52
1194 1266 0.999406 GAAAGCTCGCGTTATGCTCA 59.001 50.000 5.77 0.00 43.27 4.26
1214 1286 2.174685 TAGCTCATCCCTTACAGCCA 57.825 50.000 0.00 0.00 31.81 4.75
1264 1337 2.086610 ACTTTGTGTTTCAGGGCCAT 57.913 45.000 6.18 0.00 0.00 4.40
1275 1348 4.501915 CCCTTCATGCATCAAACTTTGTGT 60.502 41.667 0.00 0.00 0.00 3.72
1281 1354 1.927487 TGCCCTTCATGCATCAAACT 58.073 45.000 0.00 0.00 32.85 2.66
1288 1361 2.960384 CCTGAATAATGCCCTTCATGCA 59.040 45.455 0.00 0.00 43.97 3.96
1356 1431 1.339151 GCCCAGGTTTACACAGAGGAG 60.339 57.143 0.00 0.00 0.00 3.69
1359 1434 0.400213 TGGCCCAGGTTTACACAGAG 59.600 55.000 0.00 0.00 0.00 3.35
1361 1436 0.609131 CCTGGCCCAGGTTTACACAG 60.609 60.000 22.48 0.00 45.82 3.66
1443 1519 1.786937 TGGGACTTTGCACAAATGGT 58.213 45.000 0.00 0.00 0.00 3.55
1452 1528 0.804989 CATCGACCTTGGGACTTTGC 59.195 55.000 0.00 0.00 0.00 3.68
1603 1688 1.747444 ATGGAAGGGCCTCCGAATAT 58.253 50.000 6.46 0.00 38.44 1.28
1609 1694 1.149101 TGGATTATGGAAGGGCCTCC 58.851 55.000 6.46 10.93 37.63 4.30
1610 1695 3.532641 ATTGGATTATGGAAGGGCCTC 57.467 47.619 6.46 0.00 37.63 4.70
1625 1710 2.158593 TGGTTCGGGACAAAGAATTGGA 60.159 45.455 0.00 0.00 41.01 3.53
1637 1722 1.912731 TCTTCAATGGATGGTTCGGGA 59.087 47.619 0.00 0.00 0.00 5.14
1695 1782 3.966006 AGTGCTCACATAGTCCATCTGAT 59.034 43.478 2.63 0.00 0.00 2.90
1710 1797 4.216257 GCTTCCTGATTGTTTAAGTGCTCA 59.784 41.667 0.00 0.00 0.00 4.26
1719 1806 3.228188 TCCACAGCTTCCTGATTGTTT 57.772 42.857 0.00 0.00 41.77 2.83
1721 1808 4.785346 ATATCCACAGCTTCCTGATTGT 57.215 40.909 0.00 0.00 41.77 2.71
1760 1847 9.220767 GGATACAGAAGAAACAACTTACATTCT 57.779 33.333 0.00 0.00 33.73 2.40
1783 1870 4.469945 TCTCATTTCCGGTTTCTAGTGGAT 59.530 41.667 0.00 0.00 0.00 3.41
1882 1971 5.889219 TGTAACTGTGTTCTACGTGTACAA 58.111 37.500 0.00 0.00 0.00 2.41
1943 2032 9.101655 GCCAAGCTCATTTATACATTTCAAAAT 57.898 29.630 0.00 0.00 0.00 1.82
2028 2319 9.383519 CAGGTATCCACAATTATACATATGGTC 57.616 37.037 7.80 0.00 31.47 4.02
2111 2930 2.993863 ACCCCTTGGTTTAGAGGAACAT 59.006 45.455 0.00 0.00 44.75 2.71
2230 3051 8.713971 TGGAGATATGAACCAAATACTATGTGT 58.286 33.333 0.00 0.00 0.00 3.72
2231 3052 9.730705 ATGGAGATATGAACCAAATACTATGTG 57.269 33.333 0.00 0.00 37.24 3.21
2263 3084 2.863740 CCGCAGCAGTTAATCGAACATA 59.136 45.455 0.00 0.00 40.86 2.29
2274 3095 2.543777 TTAAGAGAACCGCAGCAGTT 57.456 45.000 0.00 0.00 0.00 3.16
2325 3146 9.955102 ACAGATGTCGGATATACAACTACTATA 57.045 33.333 0.00 0.00 29.87 1.31
2326 3147 8.865420 ACAGATGTCGGATATACAACTACTAT 57.135 34.615 0.00 0.00 29.87 2.12
2327 3148 8.687292 AACAGATGTCGGATATACAACTACTA 57.313 34.615 0.00 0.00 29.87 1.82
2383 3204 3.840991 TGTACATAATCTAGAGCCCGGT 58.159 45.455 0.00 0.00 0.00 5.28
2480 3301 9.142515 CTTTGTTGCATTAATAGAAGCATTTCA 57.857 29.630 0.00 0.00 36.80 2.69
2518 3339 7.545965 CACATCAGGAGATAAGAAACTACGTTT 59.454 37.037 0.00 0.00 33.96 3.60
2519 3340 7.036220 CACATCAGGAGATAAGAAACTACGTT 58.964 38.462 0.00 0.00 31.88 3.99
2520 3341 6.153000 ACACATCAGGAGATAAGAAACTACGT 59.847 38.462 0.00 0.00 31.88 3.57
2521 3342 6.565234 ACACATCAGGAGATAAGAAACTACG 58.435 40.000 0.00 0.00 31.88 3.51
2531 3352 6.890268 ACGGCTATTATACACATCAGGAGATA 59.110 38.462 0.00 0.00 31.88 1.98
2599 3420 4.576463 GGGTTGAGTAATAACATCCTGCAG 59.424 45.833 6.78 6.78 0.00 4.41
2601 3422 4.335594 GTGGGTTGAGTAATAACATCCTGC 59.664 45.833 0.00 0.00 0.00 4.85
2666 3487 3.492829 GCCCAGTAAGCCTGTAGTACATC 60.493 52.174 2.82 0.00 39.74 3.06
2668 3489 1.829222 GCCCAGTAAGCCTGTAGTACA 59.171 52.381 2.36 2.36 39.74 2.90
2684 3505 3.700538 AGCATTGTTCATTCTTAGCCCA 58.299 40.909 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.